 
REBASE version 901                                              endnotea.901
 
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    REBASE, The Restriction Enzyme Database   http://rebase.neb.com
    Copyright (c)  Dr. Richard J. Roberts, 2018.   All rights reserved.
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Rich Roberts                                                    Dec 28 2018
 
PMID- 9092657
VI  - 25
DP  - 1997
TI  - Profile of the DNA recognition site of the archaeal homing endonuclease I-DmoI.
PG  - 1523-1530
AB  - I-DmoI is a homing enzyme of the LAGLI-DADG type that recognizes up to 20 bp of DNA and is
      encoded by an archaeal intron of the hyperthermophilic archaeon Desulfurococcus mobilis.  A
      combined mutational and DNA footprinting approach was employed to investigate the specificity
      of the I-DmoI-substrate interaction.  The results indicate that the enzyme binds primarily to
      short base paired regions that border the sites of DNA cleavage and intron insertion.  The
      minimal substrate spans no more than 15 bp and while sequence degeneracy is tolerated in the
      DNA binding regions, the sequence and size of the cleavage region is highly conserved.  The
      enzyme has a slow turnover rate and cuts the coding strand with a slight preference over the
      non-coding strand.  Complex formation produces some distortion of the DNA double helix within
      the cleavage region.  The data are compatible with the two DNA-binding domains of I-DmoI
      bridging the minor groove, where cleavage occurs, and interacting within the major groove on
      either side, thereby stabilizing a distorted DNA double helix.  This may provide a general
      mode of DNA interaction at least for the LAGLIDADG-type homing enzymes.
AU  - Aagaard C
AU  - Awayez MJ
AU  - Garrett RA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1997 25: 1523-1530.

PMID- 8618886
VI  - 92
DP  - 1995
TI  - Intercellular mobility and homing of an archaeal rDNA intron confers a selective advantage over intron- cells of Sulfolobus acidocaldarius.
PG  - 12285-12289
AB  - Some intron-containing rRNA genes of archaea encode homing-type endonucleases, which
      facilitate intron insertion at homologous sites in intron- alleles. These archaeal rRNA genes,
      in contrast to their eukaryotic counterparts, are present in single copies per cell, which
      precludes intron homing within one cell. However, given the highly conserved nature of the
      sequences flanking the intron, homing may occur in intron- rRNA genes of other archaeal cells.
      To test whether this occurs, the intron-containing 23S rRNA gene of the archaeal
      hyperthermophile Desulfurococcus mobilis, carried on nonreplicating bacterial vectors, was
      electroporated into an intron- culture of Sulfolobus acidocaldarius. PCR experiments
      demonstrated that the intron underwent homing and spread through the culture. By using a
      double drug-resistant mutant of S. acidocaldarius, it was shown that spreading resulted partly
      from a selective advantage of intron+ cells and partly from intercellular mobility of the
      intron and homing.
AU  - Aagaard C
AU  - Dalgaard JZ
AU  - Garrett RA
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1995 92: 12285-12289.

PMID- 26494663
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequence of Staphylococcus aureus S54F9 Isolated from a Chronic Disseminated Porcine Lung Abscess and Used in Human Infection Models.
PG  - e01207-15
AB  - We obtained a draft genome sequence of Staphylococcus aureus strain S54F9, which  was isolated
      from a chronic disseminated porcine lung abscess and used in porcine infection models. Genes
      coding for a number of toxins, including enterotoxins and superantigen, were demonstrated in
      this strain.
AU  - Aalbaek B
AU  - Jensen LK
AU  - Jensen HE
AU  - Olsen JE
AU  - Christensen H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01207-15.

PMID- 10857753
VI  - 65
DP  - 2000
TI  - Isolation and initial characterization of a novel zinc finger gene, DNMT3L, on 21q22.3, related to the cytosine-5-methyltransferase 3 gene family.
PG  - 293-298
AB  - We have isolated the DNMT3L gene that is related to the cytosine-5-methyltransferase 3 (DNMT3)
      family. The gene is located on chromosome 21q22.3 between the AIRE and the KIAA0653 genes and
      spans approximately 16 kb of genomic sequence. The encoded protein of 387 amino acids has a
      cysteine-rich region containing a novel-type zinc finger domain that is conserved in DNMT3A
      and DNMT3B but also in ATRX, a member of the SNF2 protein family. The novel domain, called an
      ADD (ATRX, DNMT3, DNMT3L)-type zinc finger, contains two subparts: a C2C2 and an imperfect PHD
      zinc finger. Expression of the DNMT3L mRNA was not detectable by Northern blotting; however,
      RT-PCR amplification revealed that it is expressed at low levels in several tissues including
      testis, ovary, and thymus.
AU  - Aapola U
AU  - Kawasaki K
AU  - Scott HS
AU  - Ollila J
AU  - Vihinen M
AU  - Heino M
AU  - Shintani A
AU  - Kawasaki K
AU  - Minoshima S
AU  - Krohn K
AU  - Antonarakis SE
AU  - Shimizu N
AU  - Kudoh J
AU  - Peterson P
PT  - Journal Article
TA  - Genomics
JT  - Genomics
SO  - Genomics 2000 65: 293-298.

PMID- 12177302
VI  - 30
DP  - 2002
TI  - Imprinting regulator DNMT3L is a transcriptional repressor associated with histone deacetylase activity.
PG  - 3602-3608
AB  - DNMT3L is a regulator of imprint establishment of normally methylated maternal genomic
      sequences. DNMT3L shows high similarity to the de novo DNA methyltransferases, DNMT3A and
      DNMT3B, however, the amino acid residues needed for DNA cytosine methyltransferase activity
      have been lost from the DNMT3L protein sequence.  Apart from methyltransferase activity,
      Dnmt3a and Dnmt3b serve as transcriptional repressors associating with histone deacetylase
      (HDAC) activity. Here we show that DNMT3L can also repress transcription by binding directly
      to HDAC1 protein. We have identified the PHD-like zinc finger of the ATRX domain as a main
      repression motif of DNMT3L, through which DNMT3L recruits the HDAC activity needed for
      transcriptional silencing.  Furthermore, we show that DNMT3L protein contains an active
      nuclear localisation signal at amino acids 156-159.  These results describe DNMT3L as a
      co-repressor protein and suggest that a transcriptionally repressed chromatin organisation
      through HDAC activity is needed for establishment of genomic imprints.
AU  - Aapola U
AU  - Liiv I
AU  - Peterson P
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2002 30: 3602-3608.

PMID- 11306809
VI  - 92
DP  - 2001
TI  - Isolation and initial characterization of the mouse Dnmt3L gene.
PG  - 122-126
AB  - We have isolated and sequenced the mouse zinc finger gene, Dnmt3l (DNA
      cytosine-5-methyltransferase 3-like), on mouse chromosome 10, showing similarity to members of
      the DNMT3/Dnmt3 family. The Dnmt3l protein contains an ADD zinc finger, which Dnmt3l shares
      with other Dnmt3 family members and Atrx. RT-PCR analysis showed Dnmt3l expression in testis,
      thymus, ovary, and heart, as well as in 7-day, 15-day, and 17-day mouse embryos.
AU  - Aapola U
AU  - Lyle R
AU  - Krohn K
AU  - Antonarakis SE
AU  - Peterson P
PT  - Journal Article
TA  - Cytogenet. Cell Genet.
JT  - Cytogenet. Cell Genet.
SO  - Cytogenet. Cell Genet. 2001 92: 122-126.

PMID- 15015937
VI  - 380
DP  - 2004
TI  - Epigenetic modifications affect the Dnmt3L expression.
PG  - 705-713
AB  - Imprinted genes are expressed from a single allele due to differential methylation of maternal
      or paternal alleles during gametogenesis. Dnmt3L, a member of de novo methyltranferase Dnmt3
      protein family, is a regulator of maternal imprinting. In the present study, we have
      characterised the promoter region of the mouse Dnmt3L gene. Transient transfection assays
      performed with 5'-deletion promoter constructs indicated a minimal promoter area within 440
      bp upstream from the translational start. Longer promoter constructs showed decreased activity
      suggesting the presence of repressor elements within the upstream sequences. According to
      electrophoretic mobility shift assays and mutation analysis minimal promoter region contained
      four functional binding sites for the Sp1 family of transcription factors, Sp1 and Sp3. In
      vitro methylation of Dnmt3L promoter constructs decreased the transcriptional activity
      dramatically demonstrating downregulation by cytosine methylation. This was supported by the
      results from bisulfite sequencing and quantitative RT-PCR analysis of different mouse cell
      lines and tissues. In testis and ES cells showing strong Dnmt3L expression, all studied CpG
      sites were fully unmethylated whereas non-expressive cell-lines and tissues with lesser Dnmt3L
      expression showed complete or diverse CpG methylation levels. Treatment of Dnmt3L
      non-expressive cell lines with deacetylase inhibitor trichostatin A and methyltransferase
      inhibitor 5-aza-2'-deoxycytidine induced the expression of Dnmt3L mRNA. Furthermore, we show
      that repressional effect of longer promoter fragments was also relieved by these inhibitors,
      altogether indicating an epigenetic control for Dnmt3L gene regulation.
AU  - Aapola U
AU  - Maenpaa K
AU  - Kaipia A
AU  - Peterson P
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 2004 380: 705-713.

PMID- 27198014
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Pseudomonas fluorescens Strain ET76, Isolated from Rice  Rhizosphere in Northwestern Morocco.
PG  - e00356-16
AB  - Pseudomonas fluorescens ET76 was isolated from rice rhizosphere in northwestern Morocco. Its
      draft genome was estimated to be 6,681,652 bp with 5,789 coding
      sequences (CDSs). Genes encoding for type I to VI secretion systems, PvdQ,
      proteases, siderophores, hydrogen cyanide synthase, ACC-deaminase, among others,
      highlight its potential use in biological control of plant pathogens.
AU  - Aarab S
AU  - Arakrak A
AU  - Ollero FJ
AU  - Megias M
AU  - Gomes DF
AU  - Ribeiro RA
AU  - Hungria M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00356-16.

PMID- 8233776
VI  - 21
DP  - 1993
TI  - A deletion mutant of the type IC restriction endonuclease EcoR124I expressing a novel DNA specificity.
PG  - 4435-4443
AB  - We have developed a complementation assay which allows us to distinguish between mutations
      affecting subunit assembly and mutations affecting DNA binding in the DNA recognition subunit
      (HsdS) of the multimeric restriction endonuclease EcoR124I. A number of random point mutations
      were constructed to test the validity of this assay. Two of the mutants produced were found to
      be truncated polypeptides that were still capable of complementation with the EcoR124I Hsd
      subunits to give an active restriction enzyme of novel DNA specificity. The N-terminal
      variable domain (responsible for recognition of GAA from the EcoR124I recognition sequence
      GaannnnnnRTCG) and the spacer region (central conserved region) is intact in both of these
      mutants. One of these mutant genes (hsdS(del50)) has been cloned as an active Mtase.
      Purification of the Mtase proved to be difficult because the complex is weak. However, Mtase
      activity was obtained from a soluble cell extract, and this allowed us to determine the DNA
      recognition sequence of the Mtase to be GAAnnnnnnnTTC. This recognition sequence is an
      inverted repeat of the 5'-end of the EcoR124I recognition sequence. This suggests that the
      mutant Mtase is assembled from two inverted HsdS(D50) subunits, possibly held together by the
      HsdM subunits.
AU  - Abadjieva A
AU  - Patel J
AU  - Webb M
AU  - Zinkevich V
AU  - Firman K
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 4435-4443.

PMID- 
VI  - 0
DP  - 1993
TI  - The domain structure of the DNA specificity subunit of type I restriction endonucleases.  II.  Mutations affecting subunit assembly.
PG  - 189-196
AB  - Type I restriction endonucleases are complex multimeric enzymes comprising three subunits.
      HsdM and HsdS are sufficient to produce an active methylase and have the stoichiometry M2S.
      To produce an active endonuclease the HsdR subunit is also required along with the cofactors
      ATP, Mg2+ and S-adenosylmethionine.  The stoichiometry of the endonuclease is less well
      defined and may be influenced by the level of production of the individual subunits.
      Classically mutations within the hsdR gene of type I R-M systems produced an R- M+ phenotype,
      while those in the hsdM or the hsdS produced an R-M- phenotype.  However, recently we have
      described temperature-sensitive mutations within the hsdS and hsdM genes of EcoK that are
      altered in their restriction phenotype.  These mutations appear to affect the ability of the
      HsdS or HsdM subunits to interact with the HsdR subunit.  In this paper we describe a number
      of observations that suggest the assembly of these multi-subunit enzymes may be controlled by
      the concentration of the individual subunits.  This type of control is shown to be correct and
      it represents a novel method for genetic control of enzyme function, beyond that of the
      control of transcription and translation.  We also propose a testable model of how this
      control may function within type I R-M systems.
AU  - Abadjieva A
AU  - Patel J
AU  - Zinkevich V
AU  - Weiserova M
AU  - Firman K
PT  - Journal Article
TA  - DNA Transfer and Gene Expression in Microorganisms
JT  - DNA Transfer and Gene Expression in Microorganisms
SO  - DNA Transfer and Gene Expression in Microorganisms 1993 0: 189-196.

PMID- 12879741
VI  - 48
DP  - 2003
TI  - Characterization of an EcoR1241 restriction-modification enzyme produced from a deleted form of the DNA-binding subunit, which results in a novel DNA specificity.
PG  - 319-328
AB  - We purified and characterized both the methyltransferase and the endonuclease containing the
      HsdS delta 50 subunit (type I restriction
      endonucleases are composed of three subunits--HsdR required for
      restriction, HsdM required for methylation and HsdS responsible for DNA
      recognition) produced from the deletion mutation hsdS delta 50 of the type
      IC R-M system EcoR 124I; this mutant subunit lacks the C-terminal 163
      residues of HsdS and produces a novel DNA specificity. Analysis of the
      purified HsDs delta 50 subunit indicated that during purification it is
      subject to partial proteolysis resulting in removal of approximately 1 kDa
      of the polypeptide at the C-terminus. This proteolysis prevented the
      purification of further deletion mutants, which were determined as having
      a novel DNA specificity in vivo. After biochemical characterization of the
      mutant DNA methyltransferase (MTase) and restriction endonuclease we found
      only one difference comparing with the wild-type enzyme--a significantly
      higher binding affinity of the MTase for the two substrates of
      hemimethylated and fully methylated DNA. This indicates that MTase delta
      50 is less able to discriminate the methylation status of the DNA during
      its binding. However, the mutant MTase still preferred hemimethylated DNA
      as the substrate for methylation. We fused the hsdM and hsdS delta 50
      genes and showed that the HsdM-HsdS delta 50 fusion protein is capable of
      dimerization confirming the model for assembly of this deletion mutant.
AU  - Abadjieva A
AU  - Scarlett G
AU  - Janscak P
AU  - Dutta CF
AU  - Firman K
PT  - Journal Article
TA  - Folia Microbiol. (Praha)
JT  - Folia Microbiol. (Praha)
SO  - Folia Microbiol. (Praha) 2003 48: 319-328.

PMID- 8051705
VI  - 241
DP  - 1994
TI  - Deletions within the DNA recognition subunit of M.EcoR124I that identify a region involved in protein-protein interactions between HsdS and HsdM.
PG  - 35-43
AB  - The DNA recognition subunit (HsdS) of type I restriction endonucleases can be divided into
      domains by means of amino acid identity between subunits from the same family. It has been
      proposed that DNA-protein interactions occur within the variable domains of the subunit and
      that protein-protein interactions involve the conserved domains. We have constructed a number
      of deletion mutants of HsdS that have allowed us to investigate protein-protein interactions.
      Using a combination of a "competitive" complementation assay and the ability of HsdM to
      "solubilize" HsdS, we have defined a region within the central conserved domain of HsdS that
      is responsible for HsdS-HsdM interaction. Computer analysis of amino acid identity between the
      N-terminal half and the C-terminal half of HsdS identifies a region (repeated in both
      conserved domains), one copy of which overlaps the region we have identified as essential for
      HsdS-HsdM interactions, which may be responsible for such protein-protein interactions.
AU  - Abadjieva A
AU  - Webb M
AU  - Patel J
AU  - Zinkevich V
AU  - Firman K
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1994 241: 35-43.

PMID- 29437105
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Eight Staphylococcus aureus Strains Isolated during Foodborne Outbreaks.
PG  - e01557-17
AB  - We report here the draft genome sequences of eight Staphylococcus aureus strains  isolated
      during three large food poisoning outbreaks in the Russian Federation.
      The strains were collected from clinical specimens and various foodstuff samples.
AU  - Abaev I
AU  - Skryabin Y
AU  - Kislichkina A
AU  - Bogun A
AU  - Korobova O
AU  - Dyatlov I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01557-17.

PMID- 26941146
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Exfoliative Toxin A-Producing Staphylococcus aureus Strains B-7772 and B-7777 (CC8/ST2993) and B-7774 (CC15/ST2126), Isolated in a  Maternity Hospital in the Central Federal District of Russia.
PG  - e00064-16
AB  - Staphylococcus aureus clonal complex 8 (CC8) has not been associated with staphylococcal
      scalded-skin syndrome (SSSS) in newborns and exfoliative toxin
      genes. Here, we report the draft genome sequences of exfoliative toxin
      A-producing B-7772, B-7777 (both CC8), and B-7774 (CC15) strains associated with
      SSSS in newborns.
AU  - Abaev I
AU  - Skryabin Y
AU  - Kislichkina A
AU  - Bogun A
AU  - Korobova O
AU  - Mayskaya N
AU  - Shemyakin I
AU  - Dyatlov I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00064-16.

PMID- 22843574
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Ureibacillus thermosphaericus Strain Thermo-BF, Isolated from Ramsar Hot Springs in Iran.
PG  - 4431
AB  - Ureibacillus thermosphaericus strain Thermo-BF is an aerobic, thermophilic bacillus which has
      been characterized to biosynthesize gold nanoparticles. Here
      we present the draft genome sequence of Ureibacillus thermosphaericus strain
      Thermo-BF which consists of a 2,864,162-bp chromosome. This is the first report
      of a shotgun sequenced draft genome of a species in the Ureibacillus genus.
AU  - Abbasalizadeh S
AU  - Salehi JG
AU  - Motamedi JM
AU  - Azarbaijani R
AU  - Parsa YL
AU  - Ahmad RM
AU  - Mardi M
AU  - Salekdeh GH
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4431.

PMID- 23166229
VI  - 86
DP  - 2012
TI  - Complete Genome Sequence of Cronobacter sakazakii Bacteriophage vB_CsaM_GAP161.
PG  - 13806-13807
AB  - Cronobacter sakazakii is an opportunistic pathogen that causes infant meningitis
      and is often associated with milk-based infant formula. We have fully sequenced
      the genome of a newly isolated lytic C. sakazakii myovirus, vB_CsaM_GAP161,
      briefly named GAP161. It consists of 178,193 bp and has a G+C content of 44.5%. A
      total of 277 genes, including 275 open reading frames and two tRNA-encoding
      genes, were identified. This phage is closely related to coliphages RB16 and RB43
      and Klebsiella pneumoniae phage KP15.
AU  - Abbasifar R
AU  - Kropinski AM
AU  - Sabour PM
AU  - Ackermann HW
AU  - Lingohr EJ
AU  - Griffiths MW
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 2012 86: 13806-13807.

PMID- 22628511
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Mycobacterium phlei Type Strain RIVM601174.
PG  - 3284-3285
AB  - Mycobacterium phlei is a rapidly growing nontuberculous Mycobacterium species that is
      typically nonpathogenic, with few reported cases of human disease. Here
      we report the whole genome sequence of M. phlei type strain RIVM601174.
AU  - Abdallah AM
AU  - Rashid M
AU  - Adroub SA
AU  - Arnoux M
AU  - Ali S
AU  - van Soolingen D
AU  - Bitter W
AU  - Pain A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3284-3285.

PMID- 22628510
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Mycobacterium xenopi Type Strain RIVM700367.
PG  - 3282-3283
AB  - Mycobacterium xenopi is a slow-growing, thermophilic, water-related Mycobacterium species.
      Like other nontuberculous mycobacteria, M. xenopi more commonly infects
      humans with altered immune function, such as chronic obstructive pulmonary
      disease patients. It is considered clinically relevant in a significant
      proportion of the patients from whom it is isolated. We report here the whole
      genome sequence of M. xenopi type strain RIVM700367.
AU  - Abdallah AM
AU  - Rashid M
AU  - Adroub SA
AU  - Elabdalaoui H
AU  - Ali S
AU  - van Soolingen D
AU  - Bitter W
AU  - Pain A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3282-3283.

PMID- 26472828
VI  - 3
DP  - 2015
TI  - Genome Sequence of a Multidrug-Resistant Strain of Stenotrophomonas maltophilia with Carbapenem Resistance, Isolated from King Abdullah Medical City, Makkah, Saudi Arabia.
PG  - e01166-15
AB  - The emergence and spread of multidrug-resistant (MDR) bacteria have been regarded as major
      challenges among health care-associated infections worldwide. Here, we report the draft genome
      sequence of an MDR Stenotrophomonas maltophilia strain isolated in 2014 from King Abdulla
      Medical City, Makkah, Saudi Arabia.
AU  - Abdel-Haleem AM
AU  - Rchiad Z
AU  - Khan BK
AU  - Abdallah AM
AU  - Naeem R
AU  - Nikhat SS
AU  - Solovyev V
AU  - Ahmed A
AU  - Pain A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01166-15.

PMID- 28522700
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Two Carbapenemase-Producing Acinetobacter baumannii Clinical Strains Isolated from Albanian and Togolese Patients.
PG  - e00115-17
AB  - We report here the draft genome sequences of two multidrug-resistant Acinetobacter baumannii
      clinical strains, H31499 and H31506, which were isolated
      at the Lausanne University Hospital in 2015 from an Albanian and a Togolese
      patient, respectively.
AU  - Abdelbary MMH
AU  - Prod'hom G
AU  - Greub G
AU  - Senn L
AU  - Blanc DS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00115-17.

PMID- 29724851
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Multidrug-Resistant Plesiomonas shigelloides Strain MS-17-188.
PG  - e00387-18
AB  - Plesiomonas shigelloides is a Gram-negative bacterium isolated from diverse environments.
      Here, we describe the complete genome sequence of the
      multidrug-resistant P. shigelloides strain MS-17-188, isolated from a diseased
      catfish. Availability of this genome will be beneficial for characterizing the
      molecular mechanisms of antibiotic resistance in this strain.
AU  - Abdelhamed H
AU  - Ozdemir O
AU  - Tekedar HC
AU  - Arick MAII
AU  - Hsu CY
AU  - Karsi A
AU  - Lawrence ML
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00387-18.

PMID- 29853512
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Multidrug-Resistant Edwardsiella ictaluri Strain MS-17-156.
PG  - e00477-18
AB  - Edwardsiella ictaluri is a significant pathogen of cultured fish, particularly channel
      catfish. Here, we present the complete genome sequence of a
      multidrug-resistant E. ictaluri strain, MS-17-156, isolated from diseased channel
      catfish. The genome sequence of this multidrug-resistant strain is expected to
      help us understand the molecular mechanism of antibiotic resistance in this
      important pathogen.
AU  - Abdelhamed H
AU  - Tekedar HC
AU  - Ozdemir O
AU  - Hsu CY
AU  - Arick MAII
AU  - Karsi A
AU  - Lawrence ML
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00477-18.

PMID- 26988039
VI  - 4
DP  - 2016
TI  - Draft Whole-Genome Sequence of Urease-Producing Sporosarcina koreensis.
PG  - e00096-16
AB  - Urease-producing microbes are of significance due to their potential application  in biocement
      production. Sporosarcina koreensis Q1 is a urease-producing bacterium belonging to the phylum
      Firmicutes. Here, we present the draft whole-genome sequence of S. koreensis Q1, isolated from
      a barchan sand dune in Qatar.
AU  - Abdul-Majid S
AU  - Graw MF
AU  - Nguyen H
AU  - Hay AG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00096-16.

PMID- 28684582
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of a Multidrug-Resistant Sequence Type 231 Outbreak-Associated Clone of Klebsiella pneumoniae, KP41-2015, Producing OXA-232 Carbapenemase.
PG  - e00604-17
AB  - Carbapenem-resistant Klebsiella pneumoniae infection is a rising public health threat due to
      limited therapeutic options. Here, we report the genome sequence of a multidrug-resistant K.
      pneumoniae sequence type 231 (ST231) strain associated with an outbreak of infections in an
      intensive care unit that carries a unique complement of resistance determinants.
AU  - Abdul-Momin MHF
AU  - Liakopoulos A
AU  - Wareham DW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00604-17.

PMID- 
VI  - 64
DP  - 1999
TI  - PsiI, a novel restriction endonuclease recognizing the DNA sequence 5'-TTA^TAA-3'.
PG  - 574-576
AB  - PsiI, a novel restriction endonuclease produced by the bacterial strain Pseudomonas sp.
      SE-G49, has been isolated and characterized. The enzyme cleaves DNA in the middle of its
      palindromic recognition sequence 5'-TTA^TAA-3'.  Thus, PsiI belongs to a rare group of type
      II restriction endonucleases whose recognition sites consist of AT base pairs only.
AU  - Abdurashitov MA
AU  - Belichenko OA
AU  - Lebedeva NA
AU  - Degtyarev SK
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1999 64: 574-576.

PMID- 9171079
VI  - 25
DP  - 1997
TI  - BstAPI, an ApaBI isoschizomer, cleaves DNA at 5'-GCANNNN/NTGC-3'.
PG  - 2301-2302
AB  - Cleavage positions of BstAPI, a new restriction endonuclease (Enase) that recognizes
      palindromic interrupted DNA sequence, have been determined.  Recognition sequences and
      cleavage sites comparison shows that BstAPI shares similarity with a number of type II
      restriction enzymes.
AU  - Abdurashitov MA
AU  - Belichenko OA
AU  - Shevchenko AV
AU  - Dedkov VS
AU  - Degtyarev SK
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1997 25: 2301-2302.

PMID- 9026716
VI  - 30
DP  - 1996
TI  - N.BstSE - site-specific nuclease from Bacillus stearothermophilus SE-589 - restriction endonuclease production.
PG  - 1261-1267
AB  - A site-specific nickase recognizing and cleaving
      the DNA site 5'-GAGTCNNNN^N-3' was isolated from Bacillus
      stearothermophilus SE-589 and named N.BstSE. Its properties
      indicate probable relation with type II restriction
      endonucleases.
AU  - Abdurashitov MA
AU  - Belichenko OA
AU  - Shevchenko AV
AU  - Degtyarev SK
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1996 30: 1261-1267.

PMID- 7651817
VI  - 23
DP  - 1995
TI  - SimI, a new restriction endonuclease that recognizes non-palindromic sequence 5'-GGGTC-3'(-3/0).
PG  - 2571-2572
AB  - SimI, a type II restriction endonuclease, has been isolated from Staphylococcus intermedius 6H
      using heparin and hydroxyapatite chromatographic steps. The crude extract contained
      approximately 3000 U SimI per gram of cells. Three cleavage positions of SimI on pUC19 DNA
      (approximately 999, 1480 and 1768) have been mapped by double digests with enzymes, BglI,
      Acc1131I (isoschizomer of ScaI), SalI, PvuI, NruGI (isoschizomer of Eam11051) and Mly1131
      (isoschizomer of NarI). A homology search has revealed that the pentanucleotide sequence
      5'-GGGTC-3' was located at these positions. The recognition sequence has been confirmed by
      comparison of cleavage patterns generated with SimI on commonly used DNAS with computer
      predicted ones. The number of SimI sites that occur in lambda, T7, adenovirus-2, pBR322 and
      pUC19 DNA, are 40, 94, 73, 8 and 3, respectively. The cleavage points of the restriction
      endonuclease SimI have been determined by sequencing of alpha-32P-labelled HindIII-XbaI and
      XbaI-EcoRI fragments of the pMVPRL plasmid by the modified Maxam-Gilbert method. The results
      indicate the SimI cleaves the DNA sequence shown below: 5'-GG/GTC-3' 3'-CCCAG/-5'.
AU  - Abdurashitov MA
AU  - Belichenko OA
AU  - Shevchenko AV
AU  - Degtyarev SK
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1995 23: 2571-2572.

PMID- 9441298
VI  - 33
DP  - 1997
TI  - AccBSI: A new restriction endonuclease from Acinetobacter calcoaceticus BS.
PG  - 556-558
AB  - The recognition site of a new restriction endonuclease from Acinetobacter calcoaceticus BS was
      determined.  This is a nonpalindromic sequence 5'-GAGCGG-3' 3'-CTCGCC-5.  AccBSI
      restrictase cleaves DNA chains in the middle of the recognition sequence; therefore, ligation
      of its digestion fragments restored AccBSI recognition sites and generated palindromic
      sequences recognized by SacI and SacII restrictases.
AU  - Abdurashitov MA
AU  - Kileva EV
AU  - Myakisheva TV
AU  - Dedkov VS
AU  - Shevchenko AV
AU  - Degtyarev SK
PT  - Journal Article
TA  - Prikl. Biokhim. Mikrobiol.
JT  - Prikl. Biokhim. Mikrobiol.
SO  - Prikl. Biokhim. Mikrobiol. 1997 33: 556-558.

PMID- 8654990
VI  - 172
DP  - 1996
TI  - BstF5I, an unusual isoschizomer of FokI.
PG  - 49-51
AB  - BstF5, a new restriction endonuclease (Enase) from Bacillus stearothermophilus
      F5, has been discovered.  This enzyme recognizes 5'-GGATG-3' and cleaves DNA, generating a
      2-base 3' extension: 5'-GGATG NN/-3' / 3'-CCTAC/NN-5'.  BstF5I is an isoschizomer of FokI
      and seems to be evolutionarily close to other nonpalindromic-recognizing ENases from
      thermophilic bacilli.
AU  - Abdurashitov MA
AU  - Kileva EV
AU  - Shinkarenko NM
AU  - Shevchenko AV
AU  - Dedkov VS
AU  - Degtyarev SK
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1996 172: 49-51.

PMID- 10732344
VI  - 34
DP  - 2000
TI  - The second methyltransferase of the BstF5I restriction-modification system is homologous to the C-terminal domains of FokI and StsI methylases.
PG  - 87-94
AB  - Nucleotide sequence of DNA-methyltransferase gene M. BstF51-2 was determined. This
      enzyme is a part of the restriction-modification system of Bacillus stearothermophilus strain
      F. On bacterial chromosome, gene bstF51M2 is located behind methylase gene M.BStF51-1 and has
      the same orientation. Protein encoded by gene bstF1M-2 contains conservative regions specific
      for adenine DNA-methyltransferase of class D12. DNA-methylase M.BstF51-2 is homologous to
      C-terminal domains of DNA methylases Fok1 enzymes M.Fok1 and M.Sts1 modifying the second DNA
      strand in the recognition site and Sts1 possessing the same recognition sequence. It is shown
      that the restriction-modification system BstF51 contains a unique enzyme M.BstF51-1 modifying
      the upper strand of the recognized sequence and M.BstF51-2 homologous to C-terminal parts of
      enzymes modifying the second DNA strand in the recognition site.
AU  - Abdurashitov MA
AU  - Netesova NA
AU  - Golikova LN
AU  - Gutorov VV
AU  - Belavin PA
AU  - Degtyarev SK
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2000 34: 87-94.

PMID- 12942634
VI  - 37
DP  - 2003
TI  - The unique FauI restriction-modification system: Cloning and protein sequence comparisons.
PG  - 619-624
AB  - The nucleotide sequence was established for the full-length Flavobacterium aquatile operon
      coding for the FauI restriction-modification system. The
      operon is unusual in structure and has the gene order control protein
      gene-DNA methyltransferase A gene-restriction endonuclease gene-DNA
      methyltransferase B gene, other than in the known analogs. The genes are
      similarly oriented and overlap. On evidence of sequence analysis, both
      methyltransferases are C5 enzymes, the control protein is similar to that
      of other restriction-modification systems, and restriction endonuclease is
      low-homologous to other enzymes cleaving the DNA upper strand in position
      4 or 5 relative to the recognition site.
AU  - Abdurashitov MA
AU  - Okhapkina SS
AU  - Netesova NA
AU  - Golikova LN
AU  - Gonchar DA
AU  - Degtyarev SK
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2003 37: 619-624.

PMID- 
VI  - 6
DP  - 2007
TI  - Comparative analysis of human chromosomal DNA digestion with restriction endonucleases in vitro and in silico.
PG  - 29-36
AB  - Theoretical analysis of human chromosomal DNA cleavage at 15 nucleotide sequences, which are
      the recognition sites of various restriction endonucleases, has been carried out.
      Distribution diagrams of calculated DNA fragments have been constructed based on earlier
      proposed method of mammalian genomes digestion in silico.  A similar study of human Alu- and
      LINE1-repeats nucleotide sequences, which are present in informational databases, has been
      performed and corresponding diagrams of DNA fragments distribution have been plotted.
      Distribution diagrams of chromosomal DNA digestion, which results in formation of low
      molecular weight DNA fragments, correspond to those for Alu-repeats; whereas the digestion,
      which results in formation of large molecular weight DNA fragments - are similar to those for
      LINE-repeats.  All theoretical data have been compared to experimental patterns of human
      genomic DNA cleavages with respective restriction endonucleases and a good correspondence for
      the most of DNA diagrams has been observed.
AU  - Abdurashitov MA
AU  - Tomilov VN
AU  - Chernukhin VA
AU  - Gonchar DA
AU  - Degtyarev SK
PT  - Journal Article
TA  - Medical Genetics
JT  - Medical Genetics
SO  - Medical Genetics 2007 6: 29-36.

PMID- 29798910
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of the Feruloyl Esterase-Producing Strain Lactobacillus fermentum CRL1446, a Probiotic for Malnutrition.
PG  - e00225-18
AB  - We report here the draft genome sequence of Lactobacillus fermentum CRL1446 (2,148,781 bp,
      51.4% G+C content). This strain exhibits feruloyl esterase
      activity and important technological and probiotic properties. Because of its
      proven beneficial effects in vivo, it represents an interesting candidate for the
      development of functional foods or pharmabiotics for malnutrition.
AU  - Abeijon MMC
AU  - Saavedra L
AU  - Gauffin CMP
AU  - Hebert EM
AU  - Medina RB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00225-18.

PMID- 28982983
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of a New Firmicutes Species Isolated from Anaerobic Biomass Hydrolysis.
PG  - e00686-17
AB  - A new Firmicutes isolate, strain HV4-6-A5C, was obtained from the hydrolysis stage of a
      mesophilic and anaerobic two-stage lab-scale leach-bed system for
      biomethanation of fresh grass. It is assumed that the bacterial isolate
      contributes to plant biomass degradation. Here, we report a draft annotated
      genome sequence of this organism.
AU  - Abendroth C
AU  - Hahnke S
AU  - Codoner FM
AU  - Klocke M
AU  - Luschnig O
AU  - Porcar M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00686-17.

PMID- 21994931
VI  - 193
DP  - 2011
TI  - Genome Sequence of Desulfosporosinus sp. OT, an Acidophilic Sulfate-Reducing Bacterium from Copper Mining Waste in Norilsk, Northern  Siberia.
PG  - 6104-6105
AB  - We have sequenced the genome of Desulfosporosinus sp. OT, a Gram-positive, acidophilic
      sulfate-reducing Firmicute isolated from copper tailing
      sediment in the Norilsk mining-smelting area in Northern Siberia, Russia.
      This represents the first sequenced genome of a Desulfosporosinus species.
      The genome has a size of 5.7 Mb and encodes 6,222 putative proteins.
AU  - Abicht HK
AU  - Mancini S
AU  - Karnachuk OV
AU  - Solioz M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6104-6105.

PMID- 27834704
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence for the Type Strain Vulcanibacillus modesticaldus BR, a Strictly Anaerobic, Moderately Thermophilic, and Nitrate-Reducing Bacterium  Isolated from Deep-Sea Hydrothermal Vents of the Mid-Atlantic Ridge.
PG  - e01246-16
AB  - Vulcanibacillus modesticaldus BRT was isolated from calcite-rich, metalliferous core samples
      collected at the Rainbow deep-sea hydrothermal vent field on the
      Mid-Atlantic Ridge. Here, we report the 2.2-Mb draft genome sequence for this
      strain, consisting of 100 contigs with a G+C content of 33.6% and 2,227
      protein-coding sequences.
AU  - Abin CA
AU  - Hollibaugh JT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01246-16.

PMID- 27834702
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the Type Strain Desulfuribacillus alkaliarsenatis AHT28, an Obligately Anaerobic, Sulfidogenic Bacterium Isolated from Russian Soda Lake  Sediments.
PG  - e01244-16
AB  - Desulfuribacillus alkaliarsenatis AHT28T is an obligately anaerobic, sulfur- and
      arsenate-reducing haloalkaliphile that was isolated from Russian soda lake
      sediments. Here, we present the 3.1-Mb draft genome sequence for this strain,
      consisting of 36 contigs with a G+C content of 37.5% and 2,978 protein-coding
      sequences.
AU  - Abin CA
AU  - Hollibaugh JT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01244-16.

PMID- 26543104
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Bacillus Species from the Rhizosphere of the Desert Plant Rhazya stricta.
PG  - e00957-15
AB  - In order to better understand the ecology and diversity of microbes in the rhizosphere of
      desert plants, we undertook a survey of Bacillus species isolated
      from soil around Rhazya stricta plants from the area around Jeddah, in The
      Kingdom, Saudi Arabia. We have sequenced the genomes of 8 Bacillus isolates
      representing four different species.
AU  - Abo-Aba SE
AU  - Sabir JS
AU  - Baeshen MN
AU  - Sabir MJ
AU  - Mutwakil MH
AU  - Baeshen NA
AU  - D'Amore R
AU  - Hall N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00957-15.

PMID- 26139719
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Mycoplasma gallinaceum.
PG  - e00712-15
AB  - Mycoplasma gallinaceum strain B2096 8B was isolated from domestic chickens in South Africa.
      The 845,307-bp full genome was sequenced, assembled, and annotated.
AU  - Abolnik C
AU  - Beylefeld A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00712-15.

PMID- 26044427
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Mycobacterium tuberculosis Strain MT43, a Representative of the Manu2 Genotype.
PG  - e00579-15
AB  - We announce the draft genome sequence of Mycobacterium tuberculosis strain MT43,  isolated
      from a pulmonary form of tuberculosis in French Polynesia. Analyzing its
      4,145,007-bp, 65.17% G+C chromosome confirmed a fully antibiotic-susceptible
      Manu2 spoligotype.
AU  - Aboubaker OD
AU  - Phelippeau M
AU  - Musso D
AU  - Robert C
AU  - Michelle C
AU  - Croce O
AU  - Drancourt M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00579-15.

PMID- 26044426
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Mycobacterium tuberculosis Strain MT11, Which Represents a New Lineage.
PG  - e00573-15
AB  - We sequenced the genome of Mycobacterium tuberculosis strain MT11, which exhibits a specific
      16S rRNA gene mutation found in 6% of French Polynesian M.
      tuberculosis isolates. It comprises a 4,110,293-bp chromosome with 65.15% G+C
      content, and it encodes 3,949 proteins and contains 85 predicted RNA genes. The
      TbD1 region is absent in strain MT11 as in modern M. tuberculosis strains.
AU  - Aboubaker OD
AU  - Phelippeau M
AU  - Musso D
AU  - Robert C
AU  - Michelle C
AU  - Croce O
AU  - Drancourt M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00573-15.

PMID- 28209834
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Staphylococcus pseudintermedius Type Strain LMG 22219.
PG  - e01651-16
AB  - We report the first complete genome sequence of LMG 22219 (=ON 86T = CCUG 49543T), the
      Staphylococcus pseudintermedius type strain isolated from feline
      lung tissue. This sequence information will facilitate phylogenetic comparisons
      of staphylococcal species and other bacteria at the genome level.
AU  - Abouelkhair MA
AU  - Riley MC
AU  - Bemis DA
AU  - Kania SA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01651-16.

PMID- 29519848
VI  - 6
DP  - 2018
TI  - Complete Genome Sequences of Three Staphylococcus pseudintermedius Strains Isolated from Botswana.
PG  - e01599-17
AB  - We report here the first whole-genome sequences for 3 strains of Staphylococcus
      pseudintermedius (112N, 113N, and 114N) isolated in Africa. Samples of this
      opportunistic pathogen were collected from nasal swabs obtained from healthy
      carrier dogs in Botswana. The sequence information will facilitate spatial
      phylogenetic comparisons of staphylococcal species and other bacteria at the
      genome level.
AU  - Abouelkhair MA
AU  - Thompson R
AU  - Riley MC
AU  - Bemis DA
AU  - Kania SA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01599-17.

PMID- 27767038
VI  - 6
DP  - 2016
TI  - Isolation and plasmid characterization of carbapenemase (IMP-4) producing Salmonella enterica Typhimurium from cats.
PG  - 35527
AB  - Carbapenem-resistant Enterobacteriaceae (CRE) are a pressing public health issue
      due to limited therapeutic options to treat such infections. CREs have been
      predominantly isolated from humans and environmental samples and they are rarely
      reported among companion animals. In this study we report on the isolation and
      plasmid characterization of carbapenemase (IMP-4) producing Salmonella enterica
      Typhimurium from a companion animal. Carbapenemase-producing S. enterica
      Typhimurium carrying blaIMP-4 was identified from a systemically unwell (index)
      cat and three additional cats at an animal shelter. All isolates were identical
      and belonged to ST19. Genome sequencing revealed the acquisition of a
      multidrug-resistant IncHI2 plasmid (pIMP4-SEM1) that encoded resistance to nine
      antimicrobial classes including carbapenems and carried the
      blaIMP-4-qacG-aacA4-catB3 cassette array. The plasmid also encoded resistance to
      arsenic (MIC-150 mM). Comparative analysis revealed that the plasmid pIMP4-SEM1
      showed greatest similarity to two blaIMP-8 carrying IncHI2 plasmids from
      Enterobacter spp. isolated from humans in China. This is the first report of CRE
      carrying a blaIMP-4 gene causing a clinical infection in a companion animal, with
      presumed nosocomial spread. This study illustrates the broader community risk
      entailed in escalating CRE transmission within a zoonotic species such as
      Salmonella, and in a cycle that encompasses humans, animals and the environment.
AU  - Abraham S
AU  - O'Dea M
AU  - Trott DJ
AU  - Abraham RJ
AU  - Hughes D
AU  - Pang S
AU  - McKew G
AU  - Cheong EY
AU  - Merlino J
AU  - Saputra S
AU  - Malik R
AU  - Gottlieb T
PT  - Journal Article
TA  - Sci. Rep.
JT  - Sci. Rep.
SO  - Sci. Rep. 2016 6: 35527.

PMID- 26067953
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Pseudomonas psychrophila MTCC 12324, Isolated from the Arctic at 79 degrees N.
PG  - e00578-15
AB  - Pseudomonas psychrophila MTCC 12324 is a facultatively psychrophilic bacterium isolated from
      the Arctic fjord Ny-alesund in the Svalbard Archipelago. Here, we
      present a 5.2-Mb draft genome sequence of P. psychrophila MTCC 12324, reported
      for the first time, from the Arctic. This enables a study of the cold adaptation
      mechanisms to survive under the extreme cold conditions.
AU  - Abraham WP
AU  - Thomas S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00578-15.

PMID- 26494687
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Pasteurella multocida Isolate P1062, Isolated from Bovine Respiratory Disease.
PG  - e01254-15
AB  - Here, we report the draft genome of Pasteurella multocida isolate P1062 recovered from
      pneumonic bovine lung in the United States in 1959.
AU  - Abrahante JE
AU  - Hunter SS
AU  - Maheswaran SK
AU  - Hauglund MJ
AU  - Tatum FM
AU  - Briggs RE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01254-15.

PMID- 23405337
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences of Two Virulent Serotypes of Avian Pasteurella multocida.
PG  - e00058-12
AB  - Here we report the draft genome sequences of two virulent avian strains of Pasteurella
      multocida. Comparative analyses of these genomes were done with the
      published genome sequence of avirulent P. multocida strain Pm70.
AU  - Abrahante JE
AU  - Johnson TJ
AU  - Hunter SS
AU  - Maheswaran SK
AU  - Hauglund MJ
AU  - Bayles DO
AU  - Tatum FM
AU  - Briggs RE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00058-12.

PMID- 25103770
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Two Pasteurella multocida Strains Isolated from Buffaloes in India with Hemorrhagic Septicemia Disease.
PG  - e00798-14
AB  - Pasteurella multocida serotype B:2 is the causative agent of hemorrhagic septicemia in cattle
      and buffaloes in Asia. It is an acute fatal disease and is
      considered one of the most economically important diseases in this region of the
      world. We present here the draft genome sequences of strains 2213 and 3213 of P.
      multocida.
AU  - Abrahante JE
AU  - Veeregowda BM
AU  - Hogtapur SS
AU  - Briggs RE
AU  - Maheswaran SK
AU  - Sreevatsan S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00798-14.

PMID- 26358608
VI  - 3
DP  - 2015
TI  - Complete Genome Sequences of Three Neisseria gonorrhoeae Laboratory Reference Strains, Determined Using PacBio Single-Molecule Real-Time Technology.
PG  - e01052-15
AB  - Neisseria gonorrhoeae, the etiological agent that causes the sexually transmitted infection
      gonorrhea, is a significant public health concern due to the emergence  of antimicrobial
      resistance. We report the complete genome sequences of three reference isolates with varied
      antimicrobial susceptibility that will aid in elucidating the genetic mechanisms that confer
      resistance.
AU  - Abrams AJ
AU  - Trees DL
AU  - Nicholas RA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01052-15.

PMID- 21705590
VI  - 193
DP  - 2011
TI  - Annotated genome sequence of Lactobacillus pentosus MP-10, which has probiotic potential, from naturally fermented Alorena green table olives.
PG  - 4559-4560
AB  - Lactobacillus pentosus MP-10 was isolated from brines of naturally-fermented Alorena green
      table olives. MP-10 has potential probiotic traits: inhibition of human pathogenic bacteria,
      survival at low pH (1.5) and bile slat tolerance (3%). Here, we report for the first time the
      annotated genome sequence of Lb. pentosus.
AU  - Abriouel H
AU  - Benomar N
AU  - Perez PR
AU  - Canamero MM
AU  - Galvez A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4559-4560.

PMID- 27634988
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of a Potential Probiotic, Lactobacillus pentosus MP-10,  Isolated from Fermented Alorena Table Olives.
PG  - e00854-16
AB  - We report here a 3,698,214-bp complete genome sequence of a potential probiotic Lactobacillus
      pentosus strain, MP-10, isolated from brines of naturally fermented
      Alorena green table olives; it is considered the largest sequenced genome among
      lactobacilli to date. The annotated genome sequence revealed the presence of
      3,558 open reading frames (ORFs) and 87 structural RNAs.
AU  - Abriouel H
AU  - Perez MB
AU  - Casado MMC
AU  - Lavilla LL
AU  - Hidalgo PM
AU  - Caballero GN
AU  - Franz CM
AU  - Galvez A
AU  - Benomar N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00854-16.

PMID- 8251165
VI  - 15
DP  - 1993
TI  - Excess PCR primers inhibit DNA cleavage by some restriction endonucleases.
PG  - 630-632
AB  - For cloning DNA segments into expression vectors, restriction endonuclease recognition sites
      can be generated by polymerase chain reaction utilizing synthetic oligonucleotides as PCR
      primers that contain the relevant sites.  Following PCR amplification, there usually remains a
      10-fold to 100-fold molar excess of unused primers over the desired amplified product in the
      reaction mixture.  These excess oligonucleotides may inhibit the cleavage of amplified
      products by the restriction enzyme and thus interfere in the generation of DNA fragments with
      compatible termini for cloning into expression vectors.  We have investigated the effect of
      single-stranded oligonucleotides containing a restriction endonuclease recognition site on the
      digestion of linearized double-stranded DNA substrates (mimicking PCR product) by the
      respective restriction enzymes.  This information will be useful in deciding if the removal of
      excess oligonucleotide primers is necessary or not.
AU  - Abrol S
AU  - Chaudhary VK
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 1993 15: 630-632.

PMID- 
VI  - 280
DP  - 2013
TI  - Light dependent activity of restriction endonucleases.
PG  - 597
AB  - Sequence-specific endonucleases with extended recognition sites can cleave a unique site in
      complex genomes. Since the nucleases can show off-target cleavage activity, spatio-temporal
      control of their activity is necessary for the precise genome engineering.  It would be
      desirable to control the enzymatic activity by an external signal, e.g. by light.  Such
      photoregulation is based on the azobenzene 'photoswitch'.  Azobenzene isomerizes between the
      extended trans- and the cis-configuration by illumination with UV (trans-cis) or blue light
      (cis-trans) as well as by thermal relaxation (cis-trans).  We are developing the 'molecular
      gate's strategy based on the fact that most type II restriction endonucleases are homodimers.
      The DNA-binding center is located in the interface between the two subunits.  It is possible
      to modify the protein at the entrance of the DNA-binding site and block its activity.  To
      create the obstacle for DNA penetration to the active center we suggest to use the ability of
      oligonucleotides containing azobenzene insertion to form a duplex.  Azobenzene in
      trans-configuration stabilizes the duplex and cis-configuration causes destabilization.  Thus
      formation and dissociation of the duplex can be reversibly photo-regulated.  The strategy is
      illustrated for the type II RE SsoII.  To choose the optimal length of the duplex 10-mer and
      15-mer modified oligonucleotides were synthesized.  After attachment to the protein these
      oligonucleoties are supposed to form 10-mer DNA duplexes.  The initial rates of DNA cleavage
      at 37oC upon UV-illumination was two times higher than upon blue light illumination.  Our
      results demonstrate the possibility of changing the enzymatic activity upon illumination. This
      work was supported by the program 'International Research Training Groups' (grants RFBR-DFG
      11-04-91338 and GRK 1384).
AU  - Abrosimova L
AU  - Monakhova M
AU  - Schierling B
AU  - Volkov E
AU  - Romanova E
AU  - Wende W
AU  - Pingoud A
AU  - Kubareva E
AU  - Oretskaya T
PT  - Journal Article
TA  - FEBS J.
JT  - FEBS J.
SO  - FEBS J. 2013 280: 597.

PMID- 24376208
VI  - 65
DP  - 2013
TI  - Thermo-switchable Activity of the Restriction Endonuclease SsoII Achieved by Site-Directed Enzyme Modification.
PG  - 1012-1016
AB  - In this work, the possibility of constructing a thermo-switchable enzyme according to the
      molecular gate strategy is demonstrated. The approach is based on the covalent attachment of
      oligodeoxyribonucleotides to cysteine residues of an enzyme adjacent to its active center to
      form a temporal barrier for enzyme-substrate complex formation. The activity of the modified
      enzyme that had been studied herethe restriction endonuclease SsoII (R.SsoII)was diminished by
      a factor of 180 at 25 degrees C that alm st abolished the enzymatic activity when compared
      with the unmodified enzyme. However, heating of the modified enzyme to 45 degrees C resulted
      in a 30-fold increase of activity. The activity of unmodified R.SsoII also increased on
      heating from 25 to 45 degrees; however, the difference did not exceed a factor of 3-4. The
      changes in enzymatic activity observed were shown to be reversible for both the unmodified and
      the modified R.SsoII. Variation of the length and the sequence of the attached oligodeoxyribon
      ucleotides might allow greater modulation of the activity of DNA-protein conjugates.
AU  - Abrosimova LA
AU  - Monakhova MV
AU  - Migur AY
AU  - Wolfgang W
AU  - Pingoud A
AU  - Kubareva EA
AU  - Oretskaya TS
PT  - Journal Article
TA  - Life
JT  - Life
SO  - Life 2013 65: 1012-1016.

PMID- 22768363
VI  - 6
DP  - 2012
TI  - Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1(T)), reclassification in the genus Sphaerochaeta as  Sphaerochaeta coccoides comb. nov. and emendations of the family Spirochaetaceae   and the genus Sphaer.
PG  - 194-209
AB  - Spirochaeta coccoides Droge et al. 2006 is a member of the genus Spirochaeta Ehrenberg 1835,
      one of the oldest named genera within the Bacteria. S. coccoides
      is an obligately anaerobic, Gram-negative, non-motile, spherical bacterium that
      was isolated from the hindgut contents of the termite Neotermes castaneus. The
      species is of interest because it may play an important role in the digestion of
      breakdown products from cellulose and hemicellulose in the termite gut. Here we
      provide a taxonomic re-evaluation for strain SPN1(T), and based on physiological
      and genomic characteristics, we propose its reclassification as a novel species
      in the genus Sphaerochaeta, a recently published sister group of the Spirochaeta.
      The 2,227,296 bp long genome of strain SPN1(T) with its 1,866 protein-coding and
      58 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea
      project.
AU  - Abt B et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 6: 194-209.

PMID- 21304688
VI  - 3
DP  - 2010
TI  - Complete genome sequence of Cellulomonas flavigena type strain (134).
PG  - 15-25
AB  - Cellulomonas flavigena (Kellerman and McBeth 1912) Bergey et al. 1923 is the type species of
      the genus Cellulomonas of the actinobacterial family
      Cellulomonadaceae. Members of the genus Cellulomonas are of special interest for
      their ability to degrade cellulose and hemicellulose, particularly with regard to
      the use of biomass as an alternative energy source. Here we describe the features
      of this organism, together with the complete genome sequence, and annotation.
      This is the first complete genome sequence of a member of the genus Cellulomonas,
      and next to the human pathogen Tropheryma whipplei the second complete genome
      sequence within the actinobacterial family Cellulomonadaceae. The 4,123,179 bp
      long single replicon genome with its 3,735 protein-coding and 53 RNA genes is
      part of the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Abt B et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 3: 15-25.

PMID- 21475582
VI  - 4
DP  - 2011
TI  - Complete genome sequence of Leadbetterella byssophila type strain (4M15).
PG  - 2-12
AB  - Leadbetterella byssophila Weon et al. 2005 is the type species of the genus Leadbetterella of
      the family Cytophagaceae in the phylum Bacteroidetes. Members
      of the phylum Bacteroidetes are widely distributed in nature, especially in
      aquatic environments. They are of special interest for their ability to degrade
      complex biopolymers. L. byssophila occupies a rather isolated position in the
      tree of life and is characterized by its ability to hydrolyze starch and
      gelatine, but not agar, cellulose or chitin. Here we describe the features of
      this organism, together with the complete genome sequence, and annotation. L.
      byssophila is already the 16(th) member of the family Cytophagaceae whose genome
      has been sequenced. The 4,059,653 bp long single replicon genome with its 3,613
      protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria
      and Archaea project.
AU  - Abt B et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 4: 2-12.

PMID- 21475589
VI  - 4
DP  - 2011
TI  - Complete genome sequence of Cellulophaga algicola type strain (IC166).
PG  - 72-80
AB  - Cellulophaga algicola Bowman 2000 belongs to the family Flavobacteriaceae within  the phylum
      'Bacteroidetes' and was isolated from Melosira collected from the
      Eastern Antarctic coastal zone. The species is of interest because its members
      produce a wide range of extracellular enzymes capable of degrading proteins and
      polysaccharides with temperature optima of 20-30 degrees C. This is the first
      completed genome sequence of a member of the genus Cellulophaga. The 4,888,353 bp
      long genome with its 4,285 protein-coding and 62 RNA genes consists of one
      circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and
      Archaea project.
AU  - Abt B et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 4: 72-80.

PMID- 23961314
VI  - 8
DP  - 2013
TI  - Genome sequence of the thermophilic fresh-water bacterium Spirochaeta caldaria type strain (H1(T)), reclassification of Spirochaeta caldaria, Spirochaeta  stenostrepta, and Spirochaeta zuelzerae in the genus Treponema as Treponema  caldaria comb. nov., T.
PG  - 88-105
AB  - Spirochaeta caldaria Pohlschroeder et al. 1995 is an obligately anaerobic, spiral-shaped
      bacterium that is motile via periplasmic flagella. The type strain,
      H1(T), was isolated in 1990 from cyanobacterial mat samples collected at a
      freshwater hot spring in Oregon, USA, and is of interest because it enhances the
      degradation of cellulose when grown in co-culture with Clostridium thermocellum.
      Here we provide a taxonomic re-evaluation for S. caldaria based on phylogenetic
      analyses of 16S rRNA sequences and whole genomes, and propose the
      reclassification of S. caldaria and two other Spirochaeta species as members of
      the emended genus Treponema. Whereas genera such as Borrelia and Sphaerochaeta
      possess well-distinguished genomic features related to their divergent
      lifestyles, the physiological and functional genomic characteristics of
      Spirochaeta and Treponema appear to be intermixed and are of little taxonomic
      value. The 3,239,340 bp long genome of strain H1(T) with its 2,869 protein-coding
      and 59 RNA genes is a part of the G enomic E ncyclopedia of Bacteria and Archaea
      project.
AU  - Abt B et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 88-105.

PMID- 28408667
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Roseomonas mucosa Strain AU37, Isolated from a Peripheral Intravenous Catheter.
PG  - e00128-17
AB  - Roseomonas mucosa is an opportunistic pathogen that causes infections in humans and is often
      associated with vascular catheter-related bacteremia. Here, we
      report the draft genome sequence of Roseomonas mucosa strain AU37, isolated from
      a peripheral intravenous catheter tip.
AU  - Abu CM
AU  - Wailan AM
AU  - Sidjabat HE
AU  - Zhang L
AU  - Marsh N
AU  - Rickard CM
AU  - Davies MR
AU  - McMillan DJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00128-17.

PMID- 25593261
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Uncultivated Toluene-Degrading Desulfobulbaceae Bacterium Tol-SR, Obtained by Stable Isotope Probing Using [13C6]Toluene.
PG  - e01423-14
AB  - The draft genome of a member of the bacterial family Desulfobulbaceae (phylum
      Deltaproteobacteria) was assembled from the metagenome of a sulfidogenic
      [(13)C6]toluene-degrading enrichment culture. The 'Desulfobulbaceae bacterium Tol-SR' genome
      is distinguished from related, previously sequenced genomes by suites of genes associated with
      anaerobic toluene metabolism, including bss, bbs, and bam.
AU  - AbuLaban N
AU  - Tan B
AU  - Dao A
AU  - Foght J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01423-14.

PMID- 25593260
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Uncultivated Desulfosporosinus sp. Strain Tol-M, Obtained by Stable Isotope Probing Using [13C6]Toluene.
PG  - e01422-14
AB  - A draft Desulfosporosinus genome was assembled from the metagenome of a methanogenic
      [(13)C6]toluene-degrading community. The Desulfosporosinus sp. strain Tol-M genome is
      distinguished from that of previously published Desulfosporosinus strain by containing bss,
      bbs, and bam genes encoding enzymes for anaerobic biodegradation of monoaromatic hydrocarbons
      and lacking dsrAB genes for dissimilatory sulfate reduction.
AU  - AbuLaban N
AU  - Tan B
AU  - Dao A
AU  - Foght J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01422-14.

PMID- 16672469
VI  - 72
DP  - 2006
TI  - Environmental whole-genome amplification to access microbial populations in contaminated sediments.
PG  - 3291-3301
AB  - Low-biomass samples from nitrate and heavy metal contaminated soils yield DNA amounts that
      have limited use for direct, native analysis and
      screening. Multiple displacement amplification (MDA) using phi29 DNA
      polymerase was used to amplify whole genomes from environmental,
      contaminated, subsurface sediments. By first amplifying the genomic DNA
      (gDNA), biodiversity analysis and gDNA library construction of microbes
      found in contaminated soils were made possible. The MDA method was
      validated by analyzing amplified genome coverage from approximately five
      Escherichia coli cells, resulting in 99.2% genome coverage. The method was
      further validated by confirming overall representative species coverage
      and also an amplification bias when amplifying from a mix of eight known
      bacterial strains. We extracted DNA from samples with extremely low cell
      densities from a U.S. Department of Energy contaminated site. After
      amplification, small-subunit rRNA analysis revealed relatively even
      distribution of species across several major phyla. Clone libraries were
      constructed from the amplified gDNA, and a small subset of clones was used
      for shotgun sequencing. BLAST analysis of the library clone sequences
      showed that 64.9% of the sequences had significant similarities to known
      proteins, and "clusters of orthologous groups" (COG) analysis revealed
      that more than half of the sequences from each library contained sequence
      similarity to known proteins. The libraries can be readily screened for
      native genes or any target of interest. Whole-genome amplification of
      metagenomic DNA from very minute microbial sources, while introducing an
      amplification bias, will allow access to genomic information that was not
      previously accessible. The reported SSU rRNA sequences and library clone
      end sequences are listed with their respective GenBank accession numbers,
      DQ 404590 to DQ 404652, DQ 404654 to DQ 404938, and DX 385314 to DX
      389173.
AU  - Abulencia CB
AU  - Wyborski DL
AU  - Garcia JA
AU  - Podar M
AU  - Chen W
AU  - Chang SH
AU  - Chang HW
AU  - Watson D
AU  - Brodie EL
AU  - Hazen TC
AU  - Keller M
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2006 72: 3291-3301.

PMID- 15936894
VI  - 247
DP  - 2005
TI  - Type II restriction modification systems of Prevotella bryantii TC1-1 and Prevotella ruminicola 23 strains and their effect on the efficiency  of DNA introduction via electroporation.
PG  - 177-183
AB  - The restriction endonucleases PbrTI and Pru2I, isoschizomers of Sau3AI and HaeIII, were
      partially purified and characterized from anaerobic
      rumen bacteria Prevotella bryantii TCl-1 and Prevotella ruminicola 23,
      respectively. These are the first type II restriction endonucleases
      discovered in strains of the genus Prevotella, and they represent one
      of the barriers hindering gene transfer in these microorganisms.
      Heterologous DNA was protected against the action of PbrTI or Pru2I
      by incubation in a cell-free extract of the respective strain which
      contained 20 mM EDTA. This led to the development of a protocol
      enabling successful electrotransformation of the P. bryantii TCl-1
      strain with a pRH3 Bacteroides-Escherichia coli shuttle vector
      containing up to 7-kb long DNA inserts. Plasmid DNA isolated from the
      transformed strain facilitated the transfer with further increased
      efficiency and made possible the introduction of ligation reaction
      products directly to P. bryantii TCl-1 without passing them first
      through E. coli.
AU  - Accetto T
AU  - Peterka M
AU  - Avgustin G
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2005 247: 177-183.

PMID- 28983010
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Enterococcus canintestini 49, a Potential Probiotic That Produces Multiple Bacteriocins.
PG  - e01131-17
AB  - Enterococcus canintestini 49, isolated from dog feces, is active against Clostridium
      perfringens, vancomycin-resistant enterococci, and Listeria
      monocytogenes Its draft genome sequence reported herein contains a gene cluster
      encoding multiple bacteriocins and indicates the absence of genes for virulence
      factors. These characteristics signify the strain's potential for use as a
      probiotic.
AU  - Acedo JZ
AU  - Ibarra RC
AU  - Miyata ST
AU  - Blaine AH
AU  - McMullen LM
AU  - Vederas JC
AU  - van Belkum MJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01131-17.

PMID- 11886077
VI  - 38
DP  - 2001
TI  - An alternative approach for screening active Bam HI variants: Overexpression in T-7 RNA polymerase based system.
PG  - 303-308
AB  - The type II restriction endonuclease, BamHI, has been overexpressed in E. coli by cloning the
      BamHI gene in frame with an E. coli Ribosome
      Binding Site (RBS) under the T7 promoter of an E. coli expression
      vector pRSET A. The expression level of BamHI endonuclease using this
      construct was found to be higher than that reported of the
      overexpressing clone pAEK14. Our overexpressing clone, pAABRw in BL21
      cells in presence of BamHI methylase in pMAP6 following induction with
      IPTG yields about 9.2x10(6) units per gram wet cell paste. In vivo
      activity of the recombinant endonuclease could be confirmed by the SOS
      induction assay in JH139 cells even in the absence of T7 polymerase and
      cognate BamHI methylase because of leaky expression in E.coli. This
      provides an alternate way to screen the active endonuclease and its
      variants.
AU  - Acharya AS
AU  - Roy KB
PT  - Journal Article
TA  - Indian J. Biochem. Biophys.
JT  - Indian J. Biochem. Biophys.
SO  - Indian J. Biochem. Biophys. 2001 38: 303-308.

PMID- 11549269
VI  - 287
DP  - 2001
TI  - Reduced activity of BamHI variants C54I, C64W, and C54D/C64R is consistent with the substrate-assisted catalysis model.
PG  - 153-159
AB  - Three specific mutants, C54I, C54W, and a double-mutant C54D:C64R of restriction endonuclease
      BamHI, were generated and studied to investigate the role, if any, of the 54th and 64th
      cysteine residues in the catalysis of BamHI. The mutation was achieved using the megaprimer
      approach for PCR. The mutant genes were cloned and characterized by sequencing. The mutant and
      the wild-type proteins were expressed and purified and their kinetic parameters were
      determined using short synthetic oligonucleotides as substrates. All mutants had higher K(m)
      values than that of the wild-type enzyme suggesting a decrease in the affinity of the enzyme
      for its substrate. The mutant protein C54W showed significant changes in the CD spectra
      vis-a-vis wild-type enzyme and had the lowest K(m)/K(cat) value among the mutants indicative
      of changes in the secondary structure of the protein. The melting curves of the mutant
      proteins overlapped that of the wild-type enzyme. Analysis of the K(cat) values in the context
      of cocrystal structure suggests that the effect of Cys54 mutation is probably through the
      perturbation of the local structure whereas reduced activity of the double mutant is
      consistent with the substrate-assisted catalysis mechanism.
AU  - Acharya AS
AU  - Roy KB
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 2001 287: 153-159.

PMID- 29338683
VI  - 19
DP  - 2018
TI  - Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains.
PG  - 54
AB  - BACKGROUND: Without knowledge of their genomic sequences, it is impossible to
      make functional models of the bacteria that make up human and animal microbiota.
      Unfortunately, the vast majority of publicly available genomes are only working
      drafts, an incompleteness that causes numerous problems and constitutes a major
      obstacle to genotypic and phenotypic interpretation. In this work, we began with
      an example from the class Bacteroidia in the phylum Bacteroidetes, which is
      preponderant among human orodigestive microbiota. We successfully identify the
      genetic loci responsible for assembly breaks and misassemblies and demonstrate
      the importance and usefulness of long-read sequencing and curated reannotation.
      RESULTS: We showed that the fragmentation in Bacteroidia draft genomes assembled
      from massively parallel sequencing linearly correlates with genomic repeats of
      the same or greater size than the reads. We also demonstrated that some of these
      repeats, especially the long ones, correspond to misassembled loci in three
      reference Porphyromonas gingivalis genomes marked as circularized (thus complete
      or finished). We prove that even at modest coverage (30X), long-read resequencing
      together with PCR contiguity verification (rrn operons and an integrative and
      conjugative element or ICE) can be used to identify and correct the wrongly
      combined or assembled regions. Finally, although time-consuming and
      labor-intensive, consistent manual biocuration of three P. gingivalis strains
      allowed us to compare and correct the existing genomic annotations, resulting in
      a more accurate interpretation of the genomic differences among these strains.
      CONCLUSIONS: In this study, we demonstrate the usefulness and importance of
      long-read sequencing in verifying published genomes (even when complete) and
      generating assemblies for new bacterial strains/species with high genomic
      plasticity. We also show that when combined with biological validation processes
      and diligent biocurated annotation, this strategy helps reduce the propagation of
      errors in shared databases, thus limiting false conclusions based on incomplete
      or misleading information.
AU  - Acuna-Amador L
AU  - Primot A
AU  - Cadieu E
AU  - Roulet A
AU  - Barloy-Hubler F
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2018 19: 54.

PMID- 28232451
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Archangium sp. Strain Cb G35.
PG  - e01678-16
AB  - In an effort to explore myxobacterial natural product biosynthetic pathways, the  draft genome
      sequence of Archangium sp. strain Cb G35 has been obtained. Analysis
      of the genome using antiSMASH predicts 49 natural product biosynthetic pathways.
      This genome will contribute to the investigation of myxobacterial secondary
      metabolite biosynthetic pathways.
AU  - Adaikpoh BI
AU  - Dowd SE
AU  - Stevens DC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01678-16.

PMID- 27602183
VI  - 11
DP  - 2016
TI  - Complete genome sequences of the Serratia plymuthica strains 3Rp8 and 3Re4-18, two rhizosphere bacteria with antagonistic activity towards fungal phytopathogens  and plant growth promoting abilities.
PG  - 61
AB  - The Serratia plymuthica strains 3Rp8 and 3Re4-18 are motile, Gram-negative, non-sporulating
      bacteria. Strain 3Rp8 was isolated from the rhizosphere of
      Brassica napus L. and strain 3Re4-18 from the endorhiza of Solanum tuberosum L.
      Studies have shown in vitro activity against the soil-borne fungi Verticillium
      dahliae Kleb., Rhizoctonia solani Kuhn, and Sclerotinia sclerotiorum. Here, we
      announce and describe the complete genome sequence of S. plymuthica 3Rp8
      consisting of a single circular chromosome of 5.5 Mb that encodes 4954
      protein-coding and 108 RNA-only encoding genes and of S. plymuthica 3Re4-18
      consisting of a single circular chromosome of 5.4 Mb that encodes 4845
      protein-coding and 109 RNA-only encoding genes. The whole genome sequences and
      annotations are available in NCBI under the locus numbers CP012096 and CP012097,
      respectively. The genome analyses revealed genes putatively responsible for the
      promising plant growth promoting and biocontrol properties including predicting
      factors such as secretion systems, iron scavenging siderophores, chitinases,
      secreted proteases, glucanases and non-ribosomal peptide synthetases, as well as
      unique genomic islands.
AU  - Adam E
AU  - Muller H
AU  - Erlacher A
AU  - Berg G
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 61.

PMID- 25657286
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Pseudomonas simiae Strain 2-36, an In Vitro Antagonist of Rhizoctonia solani and Gaeumannomyces graminis.
PG  - e01534-14
AB  - Pseudomonas simiae 2-36, isolated from a field plot under long-term mineral fertilization,
      exhibited strong in vitro antagonistic activities against
      Rhizoctonia solani and Gaeumannomyces graminis. We report here the draft genome
      sequence of Pseudomonas simiae 2-36, consisting of 6.4 Mbp with a 60.25% G+C
      content and 5,790 predicted protein-coding sequences.
AU  - Adam Z
AU  - Chen Q
AU  - Xu R
AU  - Diange AE
AU  - Bromfield ES
AU  - Tambong JT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01534-14.

PMID- 24407636
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Pseudomonas sp. Strain 2-92, a Biological Control Strain Isolated from a Field Plot Under Long-Term Mineral Fertilization.
PG  - e01121-13
AB  - Pseudomonas sp. strain 2-92, isolated from a Canadian field plot under long-term  mineral
      fertilization, strongly inhibits the growth of Fusarium graminearum,
      Rhizoctonia solani, and Gaeumannomyces graminis. Here, we report the draft genome
      sequence of Pseudomonas sp. strain 2-92.
AU  - Adam Z
AU  - Tambong JT
AU  - Chen Q
AU  - Lewis CT
AU  - Levesque CA
AU  - Xu R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01121-13.

PMID- 24855311
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Pantoea ananatis Strain LMG 2665T, a Bacterial Pathogen  of Pineapple Fruitlets.
PG  - e00489-14
AB  - We report the draft genome sequence of Pantoea ananatis LMG 2665(T), the bacterial causal
      agent of pineapple fruitlet rot.
AU  - Adam Z
AU  - Tambong JT
AU  - Lewis CT
AU  - Levesque CA
AU  - Chen W
AU  - Bromfield ES
AU  - Khan IU
AU  - Xu R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00489-14.

PMID- 24558232
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Arcobacter cibarius Strain LMG21996T, Isolated from Broiler Carcasses.
PG  - e00034-14
AB  - 
AU  - Adam Z
AU  - Whiteduck-Leveillee K
AU  - Cloutier M
AU  - Chen W
AU  - Lewis CT
AU  - Levesque CA
AU  - Topp E
AU  - Lapen DR
AU  - Tambong JT
AU  - Talbot G
AU  - Khan IU
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00034-14.

PMID- 24699950
VI  - 2
DP  - 2014
TI  - Draft genome sequences of two arcobacter strains isolated from human feces.
PG  - e00113-14
AB  - Arcobacter species are members of the family Campylobacteraceae and are considered emerging
      enteropathogens and potential zoonotic agents. Here, we report the draft genome sequences of
      two Arcobacter strains isolated from human feces in an effort to provide further genetic
      resources for understanding the pathogenic dynamics and diversity of this important genus.
AU  - Adam Z
AU  - Whiteduck-Leveillee K
AU  - Cloutier M
AU  - Chen W
AU  - Lewis CT
AU  - Levesque CA
AU  - Topp E
AU  - Lapen DR
AU  - Tambong JT
AU  - Talbot G
AU  - Khan IU
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00113-14.

PMID- 24831143
VI  - 2
DP  - 2014
TI  - Draft genome sequences of three arcobacter strains of pig and dairy cattle manure origin.
PG  - e00377-14
AB  - The genus Arcobacter has been associated with human illness and fecal contamination by humans
      and animals. Here, we announce the draft genome sequences
      of three strains of Arcobacter species cultured from pig and dairy cattle manure
      tanks. This information will assist in the characterization of features related
      to host specificities and identify potential pathogenic health risks to humans
      and animals.
AU  - Adam Z
AU  - Whiteduck-Leveillee K
AU  - Cloutier M
AU  - Tambong JT
AU  - Chen W
AU  - Lewis CT
AU  - Levesque CA
AU  - Topp E
AU  - Lapen DR
AU  - Talbot G
AU  - Khan IU
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00377-14.

PMID- 14600243
VI  - 149
DP  - 2003
TI  - Tetra-amino-acid tandem repeats are involved in HsdS complementation in type IC restriction-modification systems.
PG  - 3311-3319
AB  - All known type I restriction and modification (R-M) systems of Escherichia coli and Salmonella
      enterica belong to one of four discrete families: type
      IA, IB, IC or ID. The classification of type I systems from a wide range
      of other genera is mainly based on complementation and molecular evidence
      derived from the comparison of the amino acid similarity of the
      corresponding subunits. This affiliation was seldom based on the strictest
      requirement for membership of a family, which depends on relatedness as
      demonstrated by complementation tests. This paper presents data indicating
      that the type I NgoAV R-M system from Neisseria gonorrhoeae, despite the
      very high identity of HsdM and HsdR subunits with members of the type IC
      family, does not show complementation with E. coli type IC R-M systems.
      Sequence analysis of the HsdS subunit of several different potential type
      IC R-M systems shows that the presence of different tetra-amino-acid
      sequence repeats, e.g. TAEL, LEAT, SEAL, TSEL, is characteristic for type
      IC R-M systems encoded by distantly related bacteria. The other regions of
      the HsdS subunits potentially responsible for subunit interaction are also
      different between a group of distantly related bacteria, but show high
      similarity within these bacteria. Complementation between the NgoAV R-M
      system and members of the EcoR124 R-M family can be restored by changing
      the tetra-amino-acid repeat within the HsdS subunit. The authors propose
      that the type IC family of R-M systems could consist of several
      complementation subgroups whose specificity would depend on differences in
      the conserved regions of the HsdS polypeptide.
AU  - Adamczyk-Poplawska M
AU  - Kondrzycka A
AU  - Urbanek K
AU  - Piekarowicz A
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2003 149: 3311-3319.

PMID- 19758331
VI  - 300
DP  - 2009
TI  - Characterization of the NgoAXP: phase-variable type III restriction-modification system in Neisseria gonorrhoeae.
PG  - 25-35
AB  - Methyltransferases associated with type III restriction-modification (RM) systems are
      phase-variably expressed in a variety of pathogenic
      bacteria. NgoAXP, the type III RM system encoded by Neisseria
      gonorrhoeae, was characterized in this study. The cloned resngoAXP and
      ngoAXPmod genes were expressed in Escherichia coli strains. The
      restriction and modification activities of NgoAXP were confirmed in
      vivo by the lambda phage restriction and modification test and in vitro
      by the methylation of DNA substrates in the presence of
      [methyl-3H]AdoMet. As in all known type III systems, the restriction
      activity needed the presence of both genes, while the presence of the
      ngoAXPmod gene was sufficient for DNA methylation. Following its
      overexpression, the DNA methyltransferase M.NgoAXP was purified to
      apparent homogeneity using metal affinity chromatography. The specific
      sequence recognized by this enzyme was determined as a nonpalindromic
      sequence: 5'-CCACC-3', in which the adenine residue is methylated. We
      observed that in E. coli cells, the expression of the restriction
      phenotype associated with NgoAXP switched randomly. This phase
      variation was associated with the change in the number of
      pentanucleotide repeats (5'-CCAAC/G-3') present at the 5'-end of the
      coding region of the ngoAXPmod gene.
AU  - Adamczyk-Poplawska M
AU  - Lower M
AU  - Piekarowicz A
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2009 300: 25-35.

PMID- 21984785
VI  - 193
DP  - 2011
TI  - Deletion of One Nucleotide within the Homonucleotide Tract Present in the hsdS Gene Alters the DNA Sequence Specificity of Type I  Restriction-Modification System NgoAV.
PG  - 6750-6759
AB  - As a result of a frameshift mutation, the hsdS locus of the NgoAV type IC restriction and
      modification (RM) system comprises two genes, hsdS(NgoAV1)
      and hsdS(NgoAV2). The specificity subunit, HsdS(NgoAV), the product of the
      hsdS(NgoAV1) gene, is a naturally truncated form of an archetypal
      specificity subunit (208 N-terminal amino acids instead of 410). The
      presence of a homonucleotide tract of seven guanines (poly[G]) at the 3'
      end of the hsdS(NgoAV1) gene makes the NgoAV system a strong candidate for
      phase variation, i.e., stochastic addition or reduction in the guanine
      number. We have constructed mutants with 6 guanines instead of 7 and
      demonstrated that the deletion of a single nucleotide within the 3' end of
      the hsdS(NgoAV1) gene restored the fusion between the hsdS(NgoAV1) and
      hsdS(NgoAV2) genes. We have demonstrated that such a contraction of the
      homonucleotide tract may occur in vivo: in a Neisseria gonorrhoeae
      population, a minor subpopulation of cells appeared to have only 6
      guanines at the 3' end of the hsdS(NgoAV1) gene. Escherichia coli cells
      carrying the fused gene and expressing the NgoAVDelta RM system were able
      to restrict lambda phage at a level comparable to that for the wild-type
      NgoAV system. NgoAV recognizes the quasipalindromic interrupted sequence
      5'-GCA(N(8))TGC-3' and methylates both strands. NgoAVDelta recognizes DNA
      sequences 5'-GCA(N(7))GTCA-3' and 5'-GCA(N(7))CTCA-3', although the latter
      sequence is methylated only on the complementary strand within the
      5'-CTCA-3' region of the second recognition target sequence.
AU  - Adamczyk-Poplawska M
AU  - Lower M
AU  - Piekarowicz A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6750-6759.

PMID- Not carried by PubMed...
VI  - 57
DP  - 1996
TI  - Preventing autorestriction: A functional analysis of the pvuIIM and pvuIIW gene products.
PG  - 108
AB  - Restriction-modification systems must be regulated to prevent lethal
      autorestriction of the bacterial DNA.  Little is known about this regulation.  This
      dissertation examines several ways in which the restriction is controlled.  To date, the
      PvuII restriction-modification system had been understood to contain three genes coding
      for a DNA methyltransferase, a restriction endonuclease and a protein required for
      endonuclease expression.  There is a fourth open reading frame (ORF) within and opposite
      to the methyltransferase gene.  This ORF is transcribed  and has also been found in the
      SmaI restriction-modification system.  The sequence of the PvuII ORF resembles that of
      the PvuII endonuclease dimer interface.  Cells carrying clones of the ORF along with the
      intact restriction modification systems had decreased ability to restrict.  The synthetic
      peptide corresponding to this ORF inhibited renaturation of urea-denatured endonuclease in
      a concentration-dependent manner.  The ORF, named pvuIIW may delay appearance of
      endonuclease activity by increasing the concentration needed for dimerization, giving the
      methyltransferase additional time to protect the bacterial DNA.  A kinetic anlaysis of PvuII
      methyltransferase is the first reported for an N4-methylcytosine methyltransferase.  It
      revealed an ordered Bi Bi mechanism, with the preferred order of substrate binding as
      DNA first followed by S-adenosyl-L-methionine (AdoMet).  The enzyme was found to
      have a kcat of 0.07s-1, KmAdoMet was 4.2 uM and the KmDNA was 0.58 uM.  When the
      methyltransferase was preincubated with [3H-CH3]-AdoMet, the expected burst of product
      formation resulted when DNA was added.  However, preincubation of the
      methyltransferase with DNA gave a 3-5 second lag in product formation after the addition
      of AdoMet.  This suggests that the enzyme forms a catalytically-incompetent, dead-end
      complex with DNA in the absence of AdoMet.  The methyltransferase was also found to
      bind two molecules of the substrate AdoMet, each with a distinct affinity.  A kinetic model
      was proposed to explain formation of the dead-end complex with DNA in the absence of
      AdoMet, as well as a role for the second bound molecule of AdoMet.
AU  - Adams GM
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1996 57: 108.

PMID- 9204874
VI  - 36
DP  - 1997
TI  - The PvuII DNA (cytosine-N4)-methyltransferase comprises two trypsin-defined domains, each of which binds a molecule of S-adenosyl-L-methionine.
PG  - 8284-8292
AB  - Earlier studies have shown that PvuII methyltransferase is monomeric and transfers a methyl
      group from S-adenosyl-L-methionine to cytosine, generating N4-methylcytosine in duplex
      5'-CAGCTG-3' DNA.  This study examines the interactions between PvuII methyltransferase and
      AdoMet.  Trypsin preferentially cleaved the protein into two large fragments, with initial
      cleavages after Arg183 and Lys186.  UV-mediated photochemical labeling with [3H-CH3]AdoMet,
      followed by trypsin digestion, revealed that both large fragments of the protein were labeled.
      Rapid gel filtration confirmed that each molecule of the intact enzyme bound two molecules of
      AdoMet (net Kd = 9.3 microM).  When PvuII methyltransferase was preincubated with a range of
      [3H-CH3}AdoMet concentrations, bursts of product formation resulted upon DNA addition.  These
      data indicate that PvuII methyltransferase is catalytically competent with one and with two
      bound molecules of AdoMet.  These results, together with those from earlier studies, suggest
      possible roles for the second molecule of AdoMet.
AU  - Adams GM
AU  - Blumenthal RM
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1997 36: 8284-8292.

PMID- 7607491
VI  - 157
DP  - 1995
TI  - Gene pvuIIW: a possible modulator of PvuII endonuclease subunit association.
PG  - 193-199
AB  - The PvuII restriction-modification system has been found to contain three genes which code for
      a DNA methyltransferase (MTase), a restriction endonuclease (ENase) and a small protein
      required for expression of the ENase-encoding gene.  In addition, there is a small open
      reading frame (ORF) within and opposite to the MTase-encoding gene.  The region containing
      this ORF is transcribed, and the ORF has an excellent Shine-Dalgarno sequence with an ATA
      start codon.  A closely related ORF is present in the SmaI system.  The 28-amino-acid (aa)
      predicted peptide from the PvuII ORF resembles a region of the PvuII ENase at the dimer
      interface.  We have cloned this ORF, giving it an ATG start codon and putting it under the
      control of an inducible promoter: induction leads to a slight but significant decrease in
      restriction of bacteriophage lambda.  We also have obtained the 28-aa synthetic peptide, and
      are exploring the possibility that it modulates ENase subunit association.  While this peptide
      has no detectible effect on dimeric PvuII ENase, it inhibits renaturation of urea-denatured
      ENase in a concentration-dependent manner.  The ORF may represent an additional safeguard
      during establishment of the PvuII restriction-modification system in a new host cell, helping
      to delay the appearance of active ENase dimers, while the MTase accumulates and protects the
      host chromosome.
AU  - Adams GM
AU  - Blumenthal RM
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 193-199.

PMID- 7720955
VI  - 9
DP  - 1995
TI  - What is the significance of the internal duplication in the PvuII DNA methyltransferase?
PG  - A1399
AB  - The DNA methyltransferases (MTases) from type II restriction-modification systems are
      suggested to have evolved via a gene duplication mechanism. The evidence for this varies in
      quality and, in most MTases, any duplication which may have occurred has been obscured by
      divergence. The MTase gene from the PvuII restriction-modification system was previously
      cloned, sequenced and overexpressed in this laboratory. It contains an unusually clear
      sequence duplication, consistent with earlier gene duplication. We have studied the
      proteolytic susceptibility of PvuII MTase, and its interaction with the substrate methyl donor
      S-adenosylmethionine (AdoMet), to investigate the possibility that this monomeric MTase is
      functionally symmetrical. We have found that trypsin preferentially cleaves in the predicted
      hinge region between the sequence repeats, and that both parts of the protein can be
      crosslinked by UV irradiation to [3H-CH3]AdoMet.
AU  - Adams GM
AU  - Blumenthal RM
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1995 9: A1399.

PMID- 9608051
VI  - 46
DP  - 1998
TI  - The Peperomia mitochondrial coxI group I intron: Timing of horizontal transfer and subsequent evolution of the intron.
PG  - 689-696
AB  - The Peperomia polybotrya coxI gene intron is the only currently reported group I intron in a
      vascular plant mitochondrial genome and it likely originated by horizontal transfer from a
      fungal donor.  We provide a clearer picture of the horizontal transfer and a portrayal of the
      evolution of the group I intron since it was gained by the Peperomia mitochondrial genome.
      The intron was transferred recently in terms of plant evolution, being restricted to the
      single genus Peperomia among the order Piperales.  Additional support is presented for the
      suggestion that a recombination/repair mechanism was used by the intron for integration into
      the Peperomia mitochondrial genome, as a perfect 1:1 correspondence exists between the
      intron's presence in a species and the presence of divergent nucleotide markers flanking the
      intron insertion site.  Sequencing of coxI introns from additional Peperomia species revealed
      that several mutations have occurred in the intron since the horizontal transfer, but sequence
      alterations have not caused frameshifts or created stop codons in the intronic open reading
      frame.  In addition, two coxI pseudogenes in Peperomia cubensis were discovered that lack a
      large region of coxI exon 2 and contain a truncated version of the group I intron that likely
      cannot be spliced out.
AU  - Adams KL
AU  - Clements MJ
AU  - Vaughn JC
PT  - Journal Article
TA  - J. Mol. Evol.
JT  - J. Mol. Evol.
SO  - J. Mol. Evol. 1998 46: 689-696.

PMID- 10731132
VI  - 287
DP  - 2000
TI  - The genome sequence of Drosophila melanogaster.
PG  - 2185-2195
AB  - The fly Drosophila melanogaster is one of the most intensively studied organisms in biology
      and serves as a model system for the investigation of many developmental and cellular
      processes common to higher eukaryotes, including humans. We have determined the nucleotide
      sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila
      genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based
      sequence and a high-quality bacterial artificial chromosome physical map. Efforts are under
      way to close the remaining gaps; however, the sequence is of sufficient accuracy and
      contiguity to be declared substantially complete and to support an initial analysis of genome
      structure and preliminary gene annotation and interpretation. The genome encodes approximately
      13,600 genes, somewhat fewer than the smaller Caenorhabditis elegans genome, but with
      comparable functional diversity.
AU  - Adams MD et al
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2000 287: 2185-2195.

PMID- 20530228
VI  - 54
DP  - 2010
TI  - Genomewide analysis of divergence of antibiotic resistance determinants in closely related isolates of Acinetobacter baumannii.
PG  - 3569-3577
AB  - Multidrug resistance has emerged as a significant concern with infections
      caused by Acinetobacter baumannii. Ample evidence supports the involvement
      of mobile genetic elements in the transfer of antibiotic resistance genes,
      but the extent of variability and the rate of genetic change associated
      with the acquisition of antibiotic resistance have not been studied in
      detail. Whole-genome sequence analysis of six closely related clinical
      isolates of A. baumannii, including four from the same hospital, revealed
      extensive divergence of the resistance genotype that correlated with
      observed differences in antimicrobial susceptibility. Resistance genes
      associated with insertion sequences, plasmids, and a chromosomal
      resistance gene island all showed variability. The highly dynamic
      resistance gene repertoire suggests rapid evolution of drug resistance.
AU  - Adams MD
AU  - Chan ER
AU  - Molyneaux ND
AU  - Bonomo RA
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2010 54: 3569-3577.

PMID- 18931120
VI  - 190
DP  - 2008
TI  - Comparative genome sequence analysis of multidrug-resistant Acinetobacter baumannii.
PG  - 8053-8064
AB  - The recent emergence of multidrug resistance (MDR) in Acinetobacter
      baumannii has raised concern in health care settings worldwide. In order
      to understand the repertoire of resistance determinants and their
      organization and origins, we compared the genome sequences of three MDR
      and three drug-susceptible A. baumannii isolates. The entire MDR phenotype
      can be explained by the acquisition of discrete resistance determinants
      distributed throughout the genome. A comparison of closely related MDR and
      drug-susceptible isolates suggests that drug efflux may be a less
      significant contributor to resistance to certain classes of antibiotics
      than inactivation enzymes are. A resistance island with a variable
      composition of resistance determinants interspersed with transposons,
      integrons, and other mobile genetic elements is a significant but not
      universal contributor to the MDR phenotype. Four hundred seventy-five
      genes are shared among all six clinical isolates but absent from the
      related environmental species Acinetobacter baylyi ADP1. These genes are
      enriched for transcription factors and transporters and suggest
      physiological features of A. baumannii that are related to adaptation for
      growth in association with humans.
AU  - Adams MD
AU  - Goglin K
AU  - Molyneaux N
AU  - Hujer KM
AU  - Lavender H
AU  - Jamison JJ
AU  - MacDonald IJ
AU  - Martin KM
AU  - Russo T
AU  - Campagnari AA
AU  - Hujer AM
AU  - Bonomo RA
AU  - Gill SR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2008 190: 8053-8064.

PMID- 7748164
VI  - 17
DP  - 1995
TI  - Eukaryotic DNA methyltransferases - structure and function.
PG  - 139-145
AB  - Methylation of DNA plays an important role in the control of gene expression in higher
      eukaryotes. This is largely achieved by the packaging of methylated DNA into chromatin
      structures that are inaccessible to transcription factors and other proteins. Methylation
      involves the addition of a methyl group to the 5-position of the cytosine base in DNA, a
      reaction catalysed by a DNA (cytosine-5) methyltransferase. This reaction occurs in nuclear
      replication foci where the chromatin structure is loosened for replication, thereby allowing
      access to methyltransferases. Partly as a result of their recognizing the presence of a
      methylcytosine on the parental strand following replication, these large enzymes are able to
      maintain the distribution of methyl groups along the DNA of somatic cells and, thereby,
      maintain tissue-specific patterns of gene expression.
AU  - Adams RLP
PT  - Journal Article
TA  - Bioessays
JT  - Bioessays
SO  - Bioessays 1995 17: 139-145.

PMID- 
VI  - 0
DP  - 1996
TI  - Plant methyltransferases and their targets in the plant genome.
PG  - 95-108
AB  - In addition to the methylation of cytosine in some CG dinucleotides, plant genomes contain
      5-methylcytosine (a cytosine with a methyl group in place of the hydrogen at position 5) in
      the trinucleotide sequence mCNG, where N is reportedly any of the four common DNA bases.
      5-Methylcytosine has also been found in nonsymmetrical sequences in transgenes, but there is
      no evidence in plants for the N-4 methylcytosine that is found in some prokaryotes.  We have
      shown that CG and CNG methylation are carried out by different methyltransferases, and one
      possible consequence of this is that the two reactions could be independently regulated.  This
      would allow the methylation of CG and CNG sequences to have unrelated functions in the plant
      cell, although to date there are no data to support this suggestion.
AU  - Adams RLP
AU  - Pradhan S
AU  - Johnson CA
AU  - Lindsay H
AU  - Shek EWL
AU  - Jenkins GI
AU  - Urwin NAR
PT  - Journal Article
TA  - Epigenetic Mechanisms of Gene Regulation
JT  - Epigenetic Mechanisms of Gene Regulation
SO  - Epigenetic Mechanisms of Gene Regulation 1996 0: 95-108.

PMID- 29954919
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Two Novel Cellulolytic Streptomyces Strains Isolated from South African Rhizosphere Soil.
PG  - e00632-18
AB  - We report here the draft genome sequences of two novel strains of Streptomyces (NWU339 and
      NWU49) isolated from South African rhizosphere soils. Both strains
      were found to possess strong cellulolytic activity and contain numerous putative
      cellulase genes. Both genomes possess benzoate degradation pathways, while NWU49
      contains the genomic potential for enediyne biosynthesis.
AU  - Adegboye MF
AU  - Lobb B
AU  - Babalola OO
AU  - Doxey AC
AU  - Ma K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00632-18.

PMID- 25278534
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Bacillus subtilis Strain D7XPN1, Isolated from Commercial Bioreactor-Degrading Food Waste.
PG  - e00989-14
AB  - The analysis of the 4.1-Mb draft genome sequence of a moderately thermophilic, heterotrophic,
      and facultatively anaerobic bacterium, Bacillus subtilis strain
      D7XPN1, identified genes for a range of enzymes with potential in the
      biodegradation of food waste, a property consistent with the ecological habitat
      of the isolate.
AU  - Adelskov J
AU  - Patel BK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00989-14.

PMID- 25635015
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Paenibacillus Strain P1XP2, a Polysaccharide-Degrading,  Thermophilic, Facultative Anaerobic Bacterium Isolated from a Commercial  Bioreactor Degrading Food Waste.
PG  - e01484-14
AB  - The analysis of the ~5.8-Mb draft genome sequence of a moderately thermophilic, heterotrophic,
      facultative anaerobic bacterium, Paenibacillus strain P1XP2,
      identified genes for enzymes with the potential for degrading complex food
      wastes, a property consistent with the ecological habitat of the isolate.
AU  - Adelskov J
AU  - Patel BK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01484-14.

PMID- 28209824
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Cellulosilyticum sp. I15G10I2, a Novel Bacterium Isolated from a Coal Seam Gas Water Treatment Pond.
PG  - e01616-16
AB  - Cellulosilyticum sp. strain I15G10I2 was isolated from a coal seam gas water treatment pond at
      the Spring Gully water treatment facility, Roma, Queensland,
      Australia. Analysis of the genome of 4,489,861 bp and G+C content of 35.23%
      revealed that strain I15G10I2 shared limited similarity to members of the genus
      Cellulosilyticum, family Lachnospiraceae.
AU  - Adelskov J
AU  - Patel BK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01616-16.

PMID- 28450520
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the 1,2-Dichloroethane-Utilizing Micrococcus sp. Strain  NDB3Y10, Isolated from an Australian Bore Well Producing Coal Seam Gas.
PG  - e00255-17
AB  - Micrococcus luteus strain NDB3Y10, which utilizes 1,2-dichloroethane as a carbon  source, was
      isolated from a bore well that produces coal seam gas. The draft
      genome size of the strain was 2.49 Mb with a G+C content of 72.97%. Genes
      involved in the metabolism of halogenated substrates, including halogenated
      hydrocarbons, were identified.
AU  - Adelskov J
AU  - Patel BKC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00255-17.

PMID- 28450517
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Microbacterium sp. TNHR37B Isolated from a Heated Aquifer Bore Well of the Great Artesian Basin, Australia.
PG  - e00251-17
AB  - Microbacterium sp. strain TNHR37B was isolated from a geothermal bore well sample (50 degrees
      C) collected from a region of coal seam gas extraction activities.
      The 3.5-Mb genome with a G+C content of 69.9% contained unique genes, and a low
      similarity value for average nucleotide identity using BLAST was observed with
      the available 73 Microbacterium sp. genomes.
AU  - Adelskov J
AU  - Patel BKC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00251-17.

PMID- 29954897
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Mycoplasma arginini Strain NGR_2017.
PG  - e00577-18
AB  - We present the draft genome of Mycoplasma arginini strain NGR_2017. This strain was recovered
      in Nigeria from cell culture in 2017. The assembly contains 620,555
      bp in 12 contigs. It contains 561 coding sequences, 34 RNAs (29 tRNAs, 4 rRNAs,
      and 1 transfer-messenger RNA [tmRNA]), and a >26-kb integrative and conjugative
      element.
AU  - Adeniji JA
AU  - Faleye TOC
AU  - Adewumi OM
AU  - Olayinka OA
AU  - Donbraye E
AU  - Oluremi B
AU  - George UE
AU  - Arowolo OA
AU  - Omoruyi EC
AU  - Ifeorah MI
AU  - Akande A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00577-18.

PMID- 26966509
VI  - 11
DP  - 2016
TI  - Draft genome sequence and overview of the purple non sulfur bacterium Rhodopseudomonas palustris 42OL.
PG  - 24
AB  - Rhodopseudomonas palustris strain 42OL was isolated in 1973 from a sugar refinery waste
      treatment pond. The strain has been prevalently used for hydrogen
      production processes using a wide variety of waste-derived substrates, and
      cultured both indoors and outdoors, either freely suspended or immobilized. R.
      palustris 42OL was suitable for many other applications and capable of growing in
      very different culturing conditions, revealing a wide metabolic versatility. The
      analysis of the genome sequence allowed to identify the metabolic pathways for
      hydrogen and poly-beta-hydroxy-butyrate production, and confirmed the ability of
      using a wide range of organic acids as substrates.
AU  - Adessi A
AU  - Spini G
AU  - Presta L
AU  - Mengoni A
AU  - Viti C
AU  - Giovannetti L
AU  - Fani R
AU  - De Philippis R
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 24.

PMID- 23538904
VI  - 1
DP  - 2013
TI  - Draft Whole-Genome Sequence of Bacillus sonorensis Strain L12, a Source of Nonribosomal Lipopeptides.
PG  - e0009713
AB  - The Bacillus sonorensis L12 draft genome sequence is approximately 4,647,754 bp in size with a
      G+C content of 45.2%. Over 86% of the genome contains
      protein-encoding genes, including several gene clusters for de novo biosynthesis
      of the nonribosomal lipopeptides iturin, bacitracin, and fengycin, which could
      mean that the strain exhibits antifungal effects.
AU  - Adimpong DB
AU  - Sorensen KI
AU  - Nielsen DS
AU  - Thorsen L
AU  - Rasmussen TB
AU  - Derkx PM
AU  - Jespersen L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0009713.

PMID- 23405362
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Paenibacillus sp. Strain ICGEB2008 (MTCC 5639) Isolated from the Gut of Helicoverpa armigera.
PG  - e00026-12
AB  - Paenibacillus sp. strain ICGEB2008 (MTCC 5639) is a Gram-positive cellulolytic bacterium,
      isolated from the gut of Helicoverpa armigera. Here, we report the draft genome sequence of
      Paenibacillus sp. ICGEB2008. The annotation of the ~5.7-Mb sequence indicated a cluster of
      genes related to the glycosyl hydrolase family and the butanediol biosynthesis pathway.
AU  - Adlakha N
AU  - Ritturaj KH
AU  - Rajagopal R
AU  - Yazdani SS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00026-12.

PMID- 4350384
VI  - 299
DP  - 1973
TI  - Studies of SV40 DNA: V. Conversion of circular to linear SV40 DNA by restriction endonuclease from Escherichia coli B.
PG  - 177-188
AB  - Restriction endonuclease preparations from Escherichia coli strains B, K(P1)
      and B(RTF2) have been found to cleave SV40 DNA.  Purified E. coli B restriction
      endonuclease converted covalently closed circular SV40 DNA to predominantly
      full length linear molecules with intact single strands; open circular
      molecules were intermediates in the reaction.  After denaturation and
      renaturation, the linear products formed circular duplexes with high
      efficiency, indicating that individual SV40 DNA molecules had been cleaved by
      the B enzyme at different sites.  Consistent with this conclusion was the
      finding that digestion of the linear product with restriction endonuclease from
      Hemophilus influenzae yielded DNA fragments indistinguishable
      electrophoretically from those found after digestion of circular SV40 DNA with
      the same enzyme.
AU  - Adler SP
AU  - Nathans D
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1973 299: 177-188.

PMID- 28082484
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Micromonospora sp. Strain WMMB235, a Marine Ascidian-Associated Bacterium.
PG  - e01369-16
AB  - Micromonospora sp. strain WMMB235 was isolated in 2011 off the coast of the Florida Keys, USA,
      from a marine ascidian as part of an ongoing drug discovery
      project. Analysis of the ~7.1-Mb genome provides insight into this strain's
      biosynthetic potential, means of regulation, and response to coculturing
      conditions.
AU  - Adnani N
AU  - Braun DR
AU  - McDonald BR
AU  - Chevrette MG
AU  - Currie CR
AU  - Bugni TS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01369-16.

PMID- 27979952
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Rhodococcus sp. Strain WMMA185, a Marine Sponge-Associated Bacterium.
PG  - e01406-16
AB  - The Rhodococcus strain WMMA185 was isolated from the marine sponge Chondrilla nucula as part
      of ongoing drug discovery efforts. Analysis of the 4.44-Mb genome
      provides information regarding interspecies interactions as pertains to
      regulation of secondary metabolism and natural product biosynthetic potentials.
AU  - Adnani N
AU  - Braun DR
AU  - McDonald BR
AU  - Chevrette MG
AU  - Currie CR
AU  - Bugni TS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01406-16.

PMID- 24723703
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Aromatic Hydrocarbon-Degrading Bacterium Sphingobium sp. Strain Ant17, Isolated from Antarctic Soil.
PG  - e00212-14
AB  - Here, we present the draft genome sequence of Sphingobium sp. strain Ant17, an aromatic
      hydrocarbon-degrading bacterium that was isolated from Antarctic oil-contaminated soil. An
      analysis of this genome can lead to insights into the mechanisms of xenobiotic degradation
      processes at low temperatures and potentially aid in bioremediation applications.
AU  - Adriaenssens EM
AU  - Guerrero LD
AU  - Makhalanyane TP
AU  - Aislabie JM
AU  - Cowan DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00212-14.

PMID- 20888795
VI  - 402
DP  - 2010
TI  - Categoric prediction of metal ion mechanisms in the active sites of 17 select type II restriction endonucleases.
PG  - 177-179
AB  - Recently determined crystal structures of type II restriction endonucleases have produced a
      plethora of information on the basis for
      target site sequence selectivity. The positioning and role of metal
      ions in DNA recognition sites might reflect important properties of
      protein-DNA interaction. Although acidic and basic groups in the active
      sites can be identified, and in some cases divalent-metal binding sites
      delineated, a convincing picture clarifying the way in which the
      attacking hydroxide ion is generated, and the leaving group stabilized,
      has not been elucidated for any of the enzymes. We have examined the
      interatomic distances between metal ions and proposed key catalytic
      residues in the binding sites of seventeen type II restriction
      endonucleases whose crystal structures are documented in literature.
      The summary and critical evaluation of structural assignments and
      predictions made earlier have been useful to group these enzymes. All
      the enzymes used for this study have been categorized on the basis of
      the number of metal ions identified in their crystal structures. Among
      17 experimentally characterized (not putative) type II REases, whose
      apparently full-length sequences are available in REBASE, we predict 8
      (47%) to follow the single metal ion mechanism, 5 to follow the two
      metal ion mechanism, 2, the three metal ion mechanism, 1, the four
      metal ion mechanism and 1 the six metal ion mechanism.
AU  - Advani S
AU  - Mishra P
AU  - Dubey S
AU  - Thakur S
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 2010 402: 177-179.

PMID- 11112410
VI  - 279
DP  - 2000
TI  - Properties and secondary structure analysis of BanI endonuclease: identification of putative active site.
PG  - 11-16
AB  - Biochemical properties of Type II restriction enzyme BanI were characterized. Kinetic
      parameters were evaluated and an enhancement of rate was observed when the recognition site
      was located in a more central position in the substrate, suggesting that BanI locates its
      recognition site by a sliding mechanism. As BanI has three cysteine residues in its primary
      sequence, the effect of thiol inhibitors on BanI activity was also studied. Partial inhibition
      was observed only at a very high concentration of the inhibitor indicating that cysteine
      residues are not directly involved in catalysis. The gel electrophoretic mobility shift assay
      demonstrated specific complex formation between BanI and the DNA substrate in the presence of
      poly dI-dC and Mg(2+). A secondary structure analysis and comparison with EcoRI and BamHI
      crystal structure revealed a putative active site similar to that seen in BamHI but different
      in the order in which the catalytic domain (central beta-sheet) and recognition domain
      (adjacent alpha-helix) were arranged in the protein.
AU  - Advani S
AU  - Roy KB
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 2000 279: 11-16.

PMID- 10694473
VI  - 269
DP  - 2000
TI  - BanI restriction endonuclease binds in the major groove of DNA: An inhibition kinetic study using substrates with mismatch basepairs.
PG  - 35-40
AB  - Structural information on BanI-DNA interaction was obtained from simple inhibition kinetic
      assays using altered substrates. Self-complementary 13-mer oligodeoxynucleotides with or
      without mismatch basepairs in the BanI recognition sequence (GGPyPuCC) were synthesized. UV
      melting curves and CD spectra indicated double-stranded B-DNA structure for all the oligomers.
      Among the seven oligomers with recognition sequences, GGTACC, GGTGCC, GGTATC, GGCACC, GGAGCC,
      GGTAAC, and GGATCC, only the first two were cleaved with BanI. Kinetics of BanI cleavage of
      the native substrate was inhibited competitively by all of the other oligomers except the one
      with sequence GGCACC. From inhibition kinetic analysis in presence of a fixed concentration of
      the inhibitor, apparent K(m) and K(I) were determined. The data were analyzed in the context
      of alterations made in the hydrogen bonding potential in the major and minor groove of DNA
      within the recognition sequence due to basepair mismatches. Such analyses led to the
      conclusion that BanI, like BamHI, binds in the major groove and the central thymines make
      important contact with the protein.
AU  - Advani S
AU  - Roy KB
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 2000 269: 35-40.

PMID- 17277419
VI  - 4
DP  - 2007
TI  - DNA deformation energy as an indirect recognition mechanism in protein-DNA interactions.
PG  - 117-125
AB  - Proteins that bind to specific locations in genomic DNA control many basic cellular functions.
      Proteins detect their binding sites using
      both direct and indirect recognition mechanisms. Deformation energy,
      which models the energy required to bend DNA from its native shape to
      its shape when bound to a protein, has been shown to be an indirect
      recognition mechanism for one particular protein, Integration Host
      Factor (IHF). This work extends the analysis of deformation to two
      other DNA-binding proteins, CRP and SRF, and two enclonucleases, I-Crel
      and I-Ppol. Known binding sites for all five proteins showed
      statistically significant differences in mean deformation energy as
      compared to random sequences. Binding sites for the three DNA-binding
      proteins and one of the enclonucleases had mean deformation energies
      lower than random sequences. Binding sites for I-Ppol had mean
      deformation energy higher than random sequences. Classifiers that were
      trained using the deformation energy at each base pair step showed good
      cross-validated accuracy when classifying unseen sequences as binders
      or nonbinders. These results support DNA deformation energy as an
      indirect recognition mechanism across a wider range of DNA-binding
      proteins. Deformation energy may also have a predictive capacity for
      the underlying catalytic mechanism of DNA-binding enzymes.
AU  - Aeling KA
AU  - Steffen NR
AU  - Johnson M
AU  - Hatfield GW
AU  - Lathrop RH
AU  - Senear DF
PT  - Journal Article
TA  - IEEE/ACM Trans. Comput. Biol. Bioinform.
JT  - IEEE/ACM Trans. Comput. Biol. Bioinform.
SO  - IEEE/ACM Trans. Comput. Biol. Bioinform. 2007 4: 117-125.

PMID- 18178154
VI  - 367
DP  - 2008
TI  - Activation of the Salmonella Typhimurium Mrr protein.
PG  - 435-439
AB  - The Mrr protein of Escherichia coli K12 is a cryptic type IV restriction endonuclease with
      specificity for methylated DNA. Recently
      it was discovered that endogenous activation of E. coli Mrr could be
      triggered by high pressure stress, resulting in the generation of
      double strand breaks in the host chromosome and concomitant induction
      of the SOS response. In this report we focused on Mrr activity of
      Salmonella Typhimurium LT2, and although we surprisingly found no
      evidence of high pressure induced activation, a large number of
      constitutively activated Mrr mutants could be isolated when the mrr
      gene was routinely cloned in an expression vector. Analysis of several
      spontaneous mutants revealed different single mutations that rendered
      the Mrr protein constitutively active. Moreover, a spontaneous S.
      Typhimurium mutant could be isolated that displayed an increased basal
      SOS induction because of a point mutation in the chromosomal mrr gene.
      Based on these findings the physiological role of Mrr in the cell is
      discussed.
AU  - Aertsen A
AU  - Mebrhatu MT
AU  - Michiels CW
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 2008 367: 435-439.

PMID- 16313623
VI  - 58
DP  - 2005
TI  - Mrr instigates the SOS response after high pressure stress in Escherichia coli.
PG  - 1381-1391
AB  - The bacterial SOS response is not only a vital reply to DNA damage but also constitutes an
      essential mechanism for the generation of genetic
      variability that in turn fuels adaptation and resistance development in
      bacterial populations. Despite the extensive depiction of the SOS regulon
      itself, its activation by stresses different from typical DNA damaging
      treatments remains poorly characterized. Recently, we reported the RecA-
      and LexA-dependent induction of the SOS response in Escherichia coli
      MG1655 after exposure to high hydrostatic pressure (HP, approximately 100
      MPa), a physical stress of which the cellular effects are not well known.
      We now found this HP mediated SOS response to depend on RecB and not on
      RecF, which is a strong indication for the involvement of double strand
      breaks. As the pressures used in this work are thermodynamically unable to
      break covalent bonds in DNA, we hypothesized the involvement of a cellular
      function or pathway in the formation of this lesion. A specialized
      screening allowed us to identify the cryptic type IV restriction
      endonuclease Mrr as the final effector of this pathway. The HP SOS
      response and its corresponding phenotypes could be entirely attributed to
      the HP triggered activation of Mrr restriction activity. Several
      spontaneously occurring alleles of mrr, incapable of triggering the
      HP-induced SOS response, were isolated and characterized. These results
      provide evidence for a specific pathway that transmits the perception of
      HP stress to induction of the SOS response and support a role for Mrr in
      bacterial stress physiology.
AU  - Aertsen A
AU  - Michiels CW
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2005 58: 1381-1391.

PMID- 28280011
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Agrococcusbaldri Strain Marseille-P2731.
PG  - e00015-17
AB  - Agrococcus baldri strain Marseille-P2731 was isolated from a Siberian permafrost  specimen
      dated around 10 million years. The 3,021,022-bp genome of strain
      Marseille-P2731, with a 71.82% G+C content, includes 2,844 protein-coding genes,
      72 toxin/antitoxin modules, nine bacteriocin-encoding genes, and 1,266 genes
      associated with mobilome.
AU  - Afouda P
AU  - Dubourg G
AU  - Labas N
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00015-17.

PMID- 16873267
VI  - 80
DP  - 2006
TI  - Virion-associated restriction endonucleases of Chloroviruses.
PG  - 8114-8123
AB  - Chloroviruses are large, double-stranded-DNA, plaque-forming viruses that infect certain
      eukaryotic chlorella-like green algae. The
      prototype of the genus is Paramecium bursaria chlorella virus 1
      (PBCV-1). Chlorovirus genomes contain various amounts of methylated
      nucleotides due to virus-encoded DNA methyltransferases (NITases);
      about 25% of the MTases are associated with companion DNA site-specific
      (restriction) endonucleases (REases). These enzymes constitute virally
      encoded restriction-modification (R/M) systems. Although several of the
      chlorovirus R/M systems are characterized, their biological functions
      are unknown. The PBCV-1 proteome reveals that two virus-encoded REases,
      but not their companion MTases, are virion associated, suggesting that
      viral REases might help degrade the host DNA early in infection. To
      test this hypothesis, host chromosomal DNA from PBCV-1-infected cells
      was examined by pulsed-field gel electrophoresis. Initiation of host
      chromosomal DNA degradation occurred within 5 min postinfection (p.i.).
      The DNA degradation was insensitive to protein synthesis inhibitors or
      UV inactivation of virus particles, consistent with the agent being a
      small protein associated with the virion. Nuclease activities,
      including those of the two predicted REases and an uncharacterized
      general nuclease(s), were detected in disrupted PBCV-1 particles. The
      general nuclease(s) degraded both host and viral DNAs in vitro,
      although the viral DNA was not degraded in vivo, suggesting
      differential intracellular trafficking of the virion-associated
      nucleases. Infection with chloroviruses lacking an R/M system(s)
      resulted in either delayed host chromosomal DNA degradation or no
      detectable host chromatin changes. These immediate-early events
      associated with chlorovirus infections may facilitate rapid switching
      of the host transcriptional apparatus to viral transcription, which
      begins within 5 to 10 min p.i.
AU  - Agarkova IV
AU  - Dunigan DD
AU  - Van Etten JL
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 2006 80: 8114-8123.

PMID- 29439038
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of a Polymyxin B-Resistant Sequence Type 195 Clinical Isolate of Acinetobacter baumannii from India.
PG  - e00031-18
AB  - Acinetobacter baumannii has emerged as a troublesome nosocomial pathogen worldwide. We report
      here the draft genome sequence of polymyxin B-resistant
      sequence type 195 (ST195) A. baumannii strain GU71, isolated from a tertiary care
      hospital in the city of Guwahati, Assam, India.
AU  - Agarwal B
AU  - Agarwala N
AU  - Saikia S
AU  - Sarkar S
AU  - Ahmed G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00031-18.

PMID- 23405347
VI  - 1
DP  - 2013
TI  - Genome Sequence of Rhizobium lupini HPC(L) Isolated from Saline Desert Soil, Kutch (Gujarat).
PG  - e00071-12
AB  - The Rhizobium lupini strain HPC(L) was isolated from saline desert soil. It grows on minimal
      media supplemented with CaCO(3) as a carbon source. It can also grow under both oligotrophic
      and heteroptrophic conditions. We report the annotated genome sequence of this strain in a
      5.27-Mb scaffold.
AU  - Agarwal L
AU  - Purohit HJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00071-12.

PMID- 10458746
VI  - 65
DP  - 1999
TI  - Construction of a multi RE module: Exploitation of mechanochemistry of restriction endonucleases.
PG  - 233-239
AB  - We describe the construction of a multi-immobilized restriction endonuclease module (Multi RE
      module). We demonstrate that the applied mechanical stress enables modulation of enzyme
      activity and modulation of recognition site selectivity (in oligonucleotides of approximately
      200 bp) of immobilized restriction endonucleases. The central module which consists of
      different strips of immobilized restriction endonucleases allows limited digestion of a large
      DNA sample in a controlled manner as a function of applied mechanical stress on strips. The
      stress-activity relationship and the effect of repeated cycles of stress and relaxation on the
      immobilized strips are presented here.
AU  - Agarwal PK
AU  - Bhattacharya SK
PT  - Journal Article
TA  - Biotechnol. Bioeng.
JT  - Biotechnol. Bioeng.
SO  - Biotechnol. Bioeng. 1999 65: 233-239.

PMID- Not included in PubMed...
VI  - 1
DP  - 1990
TI  - Crystallization of DNA binding proteins with oligodeoxynucleotides.
PG  - 83-90
AB  - In contrast to oligodeoxynucleotides, protein:DNA complexes crystallize from a broad range of
      precipitants and conditions, much as proteins by themselves.  There are, however, a number of
      factors that should be considered, at least in the early stages of cocrystallization attempts.
      These include the length and construction of the oligodeoxynucleotide itself, a pH near or
      below neutrality, a stoichiometric excess of DNA, and di- and polyvalent cations.  By far the
      more important of these factors are the length of the DNA fragment and the nature of the
      terminal nucleotides.  Unfortunately, experience suggests that, in general, the length and
      construction of the DNA fragment for optimal crystal growth cannot be predictd in advance.  A
      systematic search of cocrystallization conditions with different DNA fragments will normally
      be required.  It is important to avoid sequences that provide possible subsites within the
      fragment or at junctions between fragments related by translations.  Sample purity, especially
      that of the DNA, can also have important effects.  Detailed protocols for the purification of
      chemically synthesized fragments are suggested.  Finally, a set of conditions for initial
      cocrystallization trails with a new DNA binding protein is suggested.
AU  - Aggarwal AK
PT  - Journal Article
TA  - Methods
JT  - Methods
SO  - Methods 1990 1: 83-90.

PMID- 7773740
VI  - 5
DP  - 1995
TI  - Structure and function of restriction endonucleases.
PG  - 11-19
AB  - Structures of two restriction endonucleases, BamHI and PvuII, were reported in the past year.
      This doubles the number of restriction endonuclease structures now known from two to four, and
      enables a comparative analysis of their structures and modes of DNA recognition. Despite a
      lack of sequence homology between the enzymes, BamHI turns out to resemble EcoRI, and PvuII
      turns out to resemble EcoRV. The active-site regions are structurally similar in all four
      enzymes, but their mechanisms of cleavage may differ.
AU  - Aggarwal AK
PT  - Journal Article
TA  - Curr. Opin. Struct. Biol.
JT  - Curr. Opin. Struct. Biol.
SO  - Curr. Opin. Struct. Biol. 1995 5: 11-19.

PMID- 9519292
VI  - 8
DP  - 1998
TI  - Novel site-specific DNA endonucleases.
PG  - 19-25
AB  - Site-specific hydrolysis of DNA is common to many biological processes.  Three new structures,
      FokI, I-CreI and PI-SceI, were reported in the past year, providing the first view of type IIs
      endonucleases and homing endonucleases.  Together, they reveal an extraordinary set of new
      mechanisms by which endonucleases target the hydrolysis of specific DNA sequences.
AU  - Aggarwal AK
AU  - Wah DA
PT  - Journal Article
TA  - Curr. Opin. Struct. Biol.
JT  - Curr. Opin. Struct. Biol.
SO  - Curr. Opin. Struct. Biol. 1998 8: 19-25.

PMID- 25573941
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Two Drug-Resistant Isolates of Pseudomonas aeruginosa Obtained from Keratitis Patients in India.
PG  - e01404-14
AB  - We report here the draft genomes of two drug (fluoroquinolone)-resistant clinical isolates of
      Pseudomonas aeruginosa obtained from the corneal scrapings of
      keratitis patients from India. The two annotated genomes are 6.31 Mb and 6.41 Mb
      in size. These genomes are expected to facilitate the identification and
      understanding of the genes associated with acquired multidrug resistance.
AU  - Aggarwal RK
AU  - Dawar C
AU  - Das S
AU  - Sharma S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01404-14.

PMID- 26868394
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a Versatile Hydrocarbon-Degrading Bacterium, Rhodococcus pyridinivorans Strain KG-16, Collected from Oil Fields in India.
PG  - e01704-15
AB  - We describe here a 5.8-Mb draft genome sequence of Rhodococcus pyridinivorans strain KG-16,
      which was obtained from the soil samples collected from the
      oilfields of Krishna-Godavari basin in India. This genomic resource can provide
      insights into the pathways and mechanisms of hydrocarbon degradation and
      potentially aid in bioremediation applications.
AU  - Aggarwal RK
AU  - Dawar C
AU  - Phanindranath R
AU  - Mutnuri L
AU  - Dayal AM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01704-15.

PMID- 26649148
VI  - 10
DP  - 2015
TI  - Draft genome of Gemmata massiliana sp. nov, a water-borne Planctomycetes species  exhibiting two variants.
PG  - 120
AB  - Gemmata massiliana is a new Planctomycetes bacterium isolated from a hospital water network in
      France, using a new culture medium. It is an aerobic
      microorganism with optimal growth at pH 8, at 30 degrees C and salinity </= 1.25
      % NaCl. G. massiliana is resistant to beta-lactam antibiotics, due to lack of
      peptidoglycan in its cell wall.G. massiliana shares a 97 % 16S rRNA gene sequence
      similarity with the nearest species, Gemmata obscuriglobus; and 99 % similarity
      with unnamed soil isolates. Its 9,249,437-bp genome consists in one chromosome
      and no detectable plasmid and has a 64.07 % G + C content, 32.94 % of genes
      encoding for hypothetical proteins. The genome contains an incomplete 19.6-kb
      phage sequence, 26 CRISPRs, 3 CAS and 15 clusters of secondary metabolites. G.
      massiliana genome increases knowledge of a poorly known world of bacteria.
AU  - Aghnatios R
AU  - Cayrou C
AU  - Garibal M
AU  - Robert C
AU  - Azza S
AU  - Raoult D
AU  - Drancourt M
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 120.

PMID- 24551231
VI  - 9
DP  - 2014
TI  - Microevolution during an Anthrax Outbreak Leading to Clonal Heterogeneity and Penicillin Resistance.
PG  - E89112
AB  - Anthrax is a bacterial disease primarily affecting grazing animals but it can
      also cause severe disease in humans. We have used genomic epidemiology to study
      microevolution of the bacterium in a confined outbreak in cattle which involved
      emergence of an antibiotic-resistant phenotype. At the time of death, the animals
      contained a heterogeneous population of Single Nucleotide Variants (SNVs), some
      being clonal but most being subclonal. We found that independent isolates from
      the same carcass had similar levels of SNV differences as isolates from different
      animals. Furthermore the relative levels of subclonal populations were different
      in different locations in the same carcass. The heterogeneity appeared to be
      derived in part from heterogeneity in the infectious dose. The resistance
      phenotype was linked to clonal mutations in an anti-sigma factor gene and in one
      case was preceded by an acquisition of a hypermutator phenotype. In another
      animal, small subclonal populations were observed with counteracting mutations
      that had turned off the resistance genes. In summary, this study shows the
      importance of accounting for both acquired and inherited heterogeneity when doing
      high-resolution infection tracing and when estimating the risks associated with
      penicillin treatment.
AU  - Agren J
AU  - Finn M
AU  - Bengtsson B
AU  - Segerman B
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2014 9: E89112.

PMID- 12480112
VI  - 217
DP  - 2002
TI  - Establishment of uncharacterized plasmids in Escherichia coli by in vitro transposition.
PG  - 249-254
AB  - We present a simple approach that permits any circular plasmid, such as uncharacterized
      plasmids from diverse prokaryotes, to be established in
      Escherichia coli, thereby facilitating subsequent structural and
      functional studies. An in vitro transposition reaction is used to
      introduce a well-characterized replicon and selectable marker into
      purified plasmids, which are then used to transform E. coli. The
      approach was demonstrated using a small 3.4-kb archaeal plasmid and a
      large 60-kb uncharacterized plasmid from a Gram-negative bacterium.
      Replicon function in E coli was tested for each plasmid, and direct
      sequencing of the large plasmid revealed similarity to
      restriction-modification systems.
AU  - Agron PG
AU  - Sobecky P
AU  - Andersen GL
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2002 217: 249-254.

PMID- 21622739
VI  - 193
DP  - 2011
TI  - Genome sequence of Lactococcus garvieae 21881, isolated in a case of human septicemia.
PG  - 4033-4034
AB  - Lactococcus garvieae is a Gram-positive bacterium considered as an important opportunistic
      emerging human pathogen and also a well recognized
      fish pathogen. Here, we present the draft genome sequence of Lactococcus
      garvieae strain 21881 (2,164,557 bp, with a G+C content of 37.9%), which
      represents the first report of a genome sequence on Lactococcus garvieae.
AU  - Aguado-Urda M
AU  - Lopez-Campos GH
AU  - Blanco MM
AU  - Fernandez-Garayzabal JF
AU  - Cutuli MT
AU  - Aspiroz C
AU  - Lopez-Alonso V
AU  - Gibello A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4033-4034.

PMID- 21685280
VI  - 193
DP  - 2011
TI  - Genome Sequence of Lactococcus garvieae 8831, Isolated from Rainbow Trout Lactococcosis Outbreaks in Spain.
PG  - 4263-4264
AB  - Lactococcus garvieae is the etiological agent of lactococcosis, one of the most important
      disease threats to the sustainability of the rainbow trout
      farming industry. Here, we present the draft genome sequence of
      Lactococcus garvieae strain 8831, isolated from diseased rainbow trout,
      which is composed of 2,087,276 bp with a G+C content of 38%.
AU  - Aguado-Urda M
AU  - Lopez-Campos GH
AU  - Gibello A
AU  - Cutuli MT
AU  - Lopez-Alonso V
AU  - Fernandez-Garayzabal JF
AU  - Blanco MM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4263-4264.

PMID- 23950117
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Virulent Avibacterium paragallinarum Serotype A Strain JF4211 and Identification of Two Toxins.
PG  - e00592-13
AB  - Avibacterium paragallinarum is an important pathogen of chicken livestock causing infectious
      coryza. Here, we report the draft genome sequence of the virulent A.
      paragallinarum serotype A strain JF4211 (2.8 Mbp and G+C content of 41%) and the
      two toxin operons discovered from the annotation of the genome.
AU  - Aguilar-Bultet L
AU  - Calderon-Copete SP
AU  - Frey J
AU  - Falquet L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00592-13.

PMID- 11063128
VI  - 11
DP  - 2000
TI  - Expression of an alternative Dnmt1 isoform during muscle differentiation.
PG  - 551-559
AB  - The methylation pattern of genomic DNA undergoes dramatic changes during
      mammalian development, with extensive de novo methylation occurring during
      gametogenesis and after implantation. We identified an alternative Dnmt1
      transcript in skeletal muscle by Northern blot analysis and cloned the
      corresponding cDNA by rapid amplification of cDNA ends and reverse
      transcription-PCR. Using an in vitro skeletal muscle differentiation
      system, we show that this alternative Dnmt1 isoform is specifically
      expressed in differentiated myotubes, whereas the ubiquitously expressed
      isoform is down-regulated during myogenesis. Sequence analysis showed that
      this skeletal Dnmt1 isoform is identical to the one present in testis,
      which had been described as untranslatable. Here we present evidence that
      this alternative Dnmt1 transcript present in testis and skeletal muscle is
      translated despite the presence of several out-of-frame upstream ATGs and
      gives rise to a shorter Dnmt1 isoform, which could play an active role in
      the change of DNA methylation patterns during gametogenesis and
      myogenesis.
AU  - Aguirre-Arteta AM
AU  - Grunewald I
AU  - Cardoso MC
AU  - Leonhardt H
PT  - Journal Article
TA  - Cell Growth Differ.
JT  - Cell Growth Differ.
SO  - Cell Growth Differ. 2000 11: 551-559.

PMID- 28302773
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Citrobacter freundii Strain A47, Resistant to the Mycotoxin Deoxynivalenol.
PG  - e00019-17
AB  - Here, we present the draft genome sequence of Citrobacter freundii strain A47 with a length of
      4,878,242 bp, which contains 4,357 putative protein coding
      genes, including 270 unique genes. This work is expected to assist in obtaining
      novel gene(s) that code for deoxynivalenol (DON) de-epoxidation enzyme(s).
AU  - Ahad R
AU  - Zhou T
AU  - Lepp D
AU  - Pauls KP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00019-17.

PMID- 23912978
VI  - 47
DP  - 2013
TI  - Complete genome sequence of Cannes 8 virus, a new member of the proposed family 'Marseilleviridae'.
PG  - 550-555
AB  - Marseillevirus is a giant virus that was isolated in 2007 by culturing water
      collected from a cooling tower in Paris, France, on Acanthamoeba polyphaga. Since
      then, five other marseilleviruses have been detected in environmental or human
      samples. The genomes of two of the six marseilleviruses have been described in
      detail. We describe herein the genome of Cannes 8 virus, a new member of the
      proposed family "Marseilleviridae." Cannes 8 virus was isolated from water
      collected from a cooling tower in Cannes in southeastern France. Its genome is a
      circular double-stranded DNA molecule with 374,041 base pairs, larger than the
      Marseillevirus and Lausannevirus genomes. This genome harbors 484 open reading
      frames predicted to encode proteins with sizes ranging from 50 to 1,537 amino
      acids, among which 380 (79 %) and 272 (56 %) are bona fide orthologs of
      Marseillevirus and Lausannevirus proteins, respectively. In addition, 407 and 336
      predicted proteins have significant hits against Marseillevirus and Lausannevirus
      proteins, respectively, and 294 proteins are shared by all three
      marseilleviruses. The Cannes 8 virus genome has a high level of collinearity (for
      96 % of orthologs) with the Marseillevirus genome. About two-thirds of the Cannes
      8 virus gene repertoire is composed of family ORFans. The description and
      annotation of the genomes of new marseilleviruses that will undoubtedly be
      recovered from environmental or clinical samples will be helpful to increase our
      knowledge of the pan-genome of the family "Marseilleviridae."
AU  - Aherfi S
AU  - Pagnier I
AU  - Fournous G
AU  - Raoult D
AU  - La Scola B
AU  - Colson P
PT  - Journal Article
TA  - Virus Genes
JT  - Virus Genes
SO  - Virus Genes 2013 47: 550-555.

PMID- 21914901
VI  - 193
DP  - 2011
TI  - Genome Sequence of Pasteurella multocida subsp. gallicida Anand1_poultry.
PG  - 5604
AB  - We report the finished and annotated genome sequence of Pasteurella multocida gallicida strain
      Anand1_poultry, which was isolated from the
      liver of a diseased adult female chicken. The strain causes a disease
      called 'fowl cholera,' which is a contagious disease in birds. We compared
      it with the published genome sequence of Pasteurella multocida Pm70.
AU  - Ahir VB
AU  - Roy A
AU  - Jhala MK
AU  - Bhanderi BB
AU  - Mathakiya RA
AU  - Bhatt VD
AU  - Padiya KB
AU  - Jakhesara SJ
AU  - Koringa PG
AU  - Joshi CG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5604.

PMID- 19290543
VI  - 282
DP  - 2009
TI  - Insensitivity of chloroplast gene expression to DNA methylation.
PG  - 17-24
AB  - Presence and possible functions of DNA methylation in plastid genomes of higher plants have
      been highly controversial. While a number of
      studies presented evidence for the occurrence of both cytosine and
      adenine methylation in plastid genomes and proposed a role of cytosine
      methylation in the transcriptional regulation of plastid genes, several
      recent studies suggested that at least cytosine methylation may be
      absent from higher plant plastid genomes. To test if either adenine or
      cytosine methylation can play a regulatory role in plastid gene
      expression, we have introduced cyanobacterial genes for adenine and
      cytosine DNA methyltransferases (methylases) into the tobacco plastid
      genome by chloroplast transformation. Using DNA cleavage with
      methylation-sensitive and methylation-dependent restriction
      endonucleases, we show that the plastid genomes in the transplastomic
      plants are efficiently methylated. All transplastomic lines are
      phenotypically indistinguishable from wild-type plants and, moreover,
      show no alterations in plastid gene expression. Our data indicate that
      the expression of plastid genes is not sensitive to DNA methylation
      and, hence, suggest that DNA methylation is unlikely to be involved in
      the transcriptional regulation of plastid gene expression.
AU  - Ahlert D
AU  - Stegemann S
AU  - Kahlau S
AU  - Ruf S
AU  - Bock R
PT  - Journal Article
TA  - Mol. Genet. Genomics
JT  - Mol. Genet. Genomics
SO  - Mol. Genet. Genomics 2009 282: 17-24.

PMID- 28418097
VI  - 19
DP  - 2017
TI  - Genome and epigenome of a novel marine Thaumarchaeota strain suggest viral infection, phosphorothioation DNA modification and multiple restriction systems.
PG  - 2434-2452
AB  - Marine Thaumarchaeota are abundant ammonia-oxidizers but have few representative
      laboratory-cultured strains. We report the cultivation of Candidatus
      Nitrosomarinus catalina SPOT01, a novel strain that is less warm-temperature
      tolerant than other cultivated Thaumarchaeota. Using metagenomic recruitment,
      strain SPOT01 comprises a major portion of Thaumarchaeota (4-54%) in temperate
      Pacific waters. Its complete 1.36 Mbp genome possesses several distinguishing
      features: putative phosphorothioation (PT) DNA modification genes; a region
      containing probable viral genes; and putative urea utilization genes. The PT
      modification genes and an adjacent putative restriction enzyme (RE) operon likely
      form a restriction modification (RM) system for defence from foreign DNA. PacBio
      sequencing showed >98% methylation at two motifs, and inferred PT guanine
      modification of 19% of possible TGCA sites. Metagenomic recruitment also reveals
      the putative virus region and PT modification and RE genes are present in 18-26%,
      9-14% and <1.5% of natural populations at 150 m with >/=85% identity to strain
      SPOT01. The presence of multiple probable RM systems in a highly streamlined
      genome suggests a surprising importance for defence from foreign DNA for dilute
      populations that infrequently encounter viruses or other cells. This new strain
      provides new insights into the ecology, including viral interactions, of this
      important group of marine microbes.
AU  - Ahlgren NA
AU  - Chen Y
AU  - Needham DM
AU  - Parada AE
AU  - Sachdeva R
AU  - Trinh V
AU  - Chen T
AU  - Fuhrman JA
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2017 19: 2434-2452.

PMID- 25061741
VI  - 13
DP  - 2014
TI  - Comprehensive gene expression analysis of the DNA (cytosine-5) methyltransferase family in rice (Oryza sativa L.).
PG  - 5159-5172
AB  - Cytosine DNA methylation is a conserved epigenetic regulatory mechanism in both plants and
      animals. DNA methyltransferases (DNA MTases) not only initiate (de novo) but also maintain the
      process of DNA methylation. Here, we characterized the genome-wide expression profiles of 10
      cytosine DNA MTase genes belonging to 4 subfamilies, MET1, CMT, DNMT2, and DRM, in rice.
      Tissue-specific gene expression analysis showed that all family members varied widely in their
      expression and specificities and might be involved in some basic metabolic pathways.
      Similarly, the expression of all rice cytosine DNA MTase genes was not regulated by plant
      hormones except OsDRM1a and OsDRM1b, which were downregulated by jasmonic acid. The
      transcription level of 10 genes in rice shoots and roots was also measured under salt and
      osmotic stress. Meanwhile, quantitative polymerase chain reaction data of the japonica and
      indica rice cultivars revealed that there is large variation in the expression activities of
      all genes. The results provide a foundation to further explore the roles of DNA MTases and the
      epigenetic regulation of abiotic stress responses in rice.
AU  - Ahmad F
AU  - Huang X
AU  - Lan HX
AU  - Huma T
AU  - Bao YM
AU  - Huang J
AU  - Zhang HS
PT  - Journal Article
TA  - Gen. Mol. Res.
JT  - Gen. Mol. Res.
SO  - Gen. Mol. Res. 2014 13: 5159-5172.

PMID- 7607479
VI  - 157
DP  - 1995
TI  - DNA recognition by the EcoP15I and EcoPI modification methyltransferases.
PG  - 143-147
AB  - The DNA-binding properties of the EcoP15I DNA methyltransferase (M.EcoP15I; MTase) were
      studied using electrophoretic mobility shift assays.  We show by molecular size-exclusion
      chromatography and dimethyl suberimidate crosslinking that M.EcoP15I is a dimer in solution.
      While M.EcoP15I binds approximately three-fold more tightly to its recognition sequence,
      5'-CAGCAG-3', than to non-specific sequences in the presence of AdoMet or its analogs, the
      discrimination between specific and non-specific sequences significantly increases in the
      presence of ATP.  These results suggest for the first time a role for ATP in DNA recognition
      by type-III restriction-modification enzymes.  Furthermore, we show that although c2 EcoPI
      mutant MTases are defective in AdoMet binding, they are still able to bind DNA in a
      sequence-specific manner.
AU  - Ahmad I
AU  - Krishnamurthy V
AU  - Rao DN
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 143-147.

PMID- 29846668
VI  - 46
DP  - 2018
TI  - Single-site DNA cleavage by Type III restriction endonuclease requires a site-bound enzyme and a trans-acting enzyme that are ATPase-activated.
PG  - 6229-6237
AB  - Endonucleolytic cleavage of DNA by Type III restriction-modification (RM) enzymes requires
      long-range communication between at least two recognition sites in
      inverted orientation. This results in convergence of two nuclease domains, one
      each from the enzymes loaded at the recognition sites with one still bound to the
      site. The nucleases catalyze scission of the single-strands leading to
      double-strand DNA break. An obscure feature of the Type III RM enzymes EcoP1I and
      EcoP15I is their ability to cleave DNA having a single recognition site under
      certain conditions. Here we demonstrate that single-site cleavage is the result
      of cooperation between an enzyme bound to the recognition site in cis and one in
      trans. DNA cleavage is catalyzed by converging nucleases that are activated by
      hydrolysis-competent ATPase in presence of their respective DNA substrates.
      Furthermore, a single activated nuclease cannot nick a strand on its own, and
      requires the partner. Based on the commonalities in the features of single-site
      and two-site cleavage derived from this study, we propose that their mechanism is
      similar. Furthermore, the products of two-site cleavage can act as substrates and
      activators of single-site cleavage. The difference in the two modes lies in how
      the two cooperating enzymes converge, which in case of single-site cleavage
      appears to be via 3D diffusion.
AU  - Ahmad I
AU  - Kulkarni M
AU  - Gopinath A
AU  - Saikrishnan K
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2018 46: 6229-6237.

PMID- 8181759
VI  - 142
DP  - 1994
TI  - Photolabeling of the EcoP15 DNA methyltransferase with S-adenosyl-L-methionine.
PG  - 67-71
AB  - Radioactivity from S-adenosyl-L[methyl-3H]methionine ([methyl-3H]AdoMet) was bound to the
      EcoP15 DNA methyltransferase (M.EcoP15) following short-wave ultraviolet (UV) irradiation. The
      labeled protein was subjected to polyacrylamide-gel electrophoresis in the presence of sodium
      dodecyl sulfate (SDS-PAGE), and detected by fluorography and autoradiography. Labeling was
      found to be dependent on the concentration of AdoMet and time of UV irradiation. The
      photolabeling by [methyl-3H]AdoMet was specific and blocked by S-adenosyl-L-homocysteine
      (AdoHcy) and sinefungin which are known to function as competitive inhibitors. Limited
      digestion of the M.EcoP15-AdoMet adduct by Staphylococcus aureus protease V8 generated three
      peptides of approx. 50, 32 and 30 kDa. Interestingly, only the 30-kDa peptide fragment
      contained radioactivity, as detected by SDS-PAGE, followed by fluorography and
      autoradiography. Further, sequencing of a few amino acids at the N-terminus of these peptides
      showed that the 30-kDa fragment was the N-terminal portion of M.EcoP15. These results suggest
      that photolabeling is at the AdoMet-binding site and that the N-terminal half of M.EcoP15 may
      be involved in substrate binding.
AU  - Ahmad I
AU  - Rao DN
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1994 142: 67-71.

PMID- 8994802
VI  - 31
DP  - 1996
TI  - Chemistry and biology of DNA methyltransferases.
PG  - 361-380
AB  - Recognition of a specific DNA sequence by a protein is probably the best example of
      macromolecular interactions leading to various events.  It is a prerequisite to understanding
      the basis of protein-DNA interactions to obtain a better insight into fundamental processes
      such as transcription, replication, repair, and recombination.  DNA methyltransferases with
      varying sequence specificities provide an excellent model system for understanding the
      molecular mechanism of specific DNA recognition.  Sequence comparison of cloned genes, along
      with mutational analyses and recent crystallographic studies, have clearly defined the
      functions of various conserved motifs.  These enzymes access their target base in an elegant
      manner by flipping it out of the DNA double helix.  The drastic protein-induced DNA
      distortion, first reported for HhaI DNA methyltransferase, appears to be a common mechanism
      employed by vairous proteins that need to act on bases.  A remarkable feature of the catalytic
      mechanism of DNA (cytosine-5) methyltransferases is the ability of these enzymes to induce
      deamination of the target cytosine in the absence of S-adenosyl-L-methionine or its analogs.
      The enzyme-catalyzed deamination reaction is postulated to be the major cause of mutational
      hotspots at CpG islands responsible for various human genetic disorders.  Methylation of
      adenine residues in Escherichia coli is known to regulate various processes such as
      transcription, replication, repair, recombination, transposition, and phage packaging.
AU  - Ahmad I
AU  - Rao DN
PT  - Journal Article
TA  - Crit. Rev. Biochem. Mol. Biol.
JT  - Crit. Rev. Biochem. Mol. Biol.
SO  - Crit. Rev. Biochem. Mol. Biol. 1996 31: 361-380.

PMID- 7932697
VI  - 242
DP  - 1994
TI  - Interaction of EcoP15I DNA methyltransferase with oligonucleotides containing the asymmetric sequence 5'-CAGCAG-3'.
PG  - 378-388
AB  - EcoP15I DNA methyltransferase (Mtase) recognizes the asymmetric sequence CAGCAG and catalyzes
      the transfer of a methyl group from S-adenosyl-L-methionine to the second adenine residue. We
      have investigated the DNA binding properties of EcoP15I DNA Mtase using gel mobility shift
      assays. EcoP15I DNA Mtase binds approximately threefold more tightly to DNA containing its
      recognition sequence, CAGCAG, than to non-specific sequences in the absence or presence of
      cofactors. Interestingly, in the presence of ATP the discrimination between specific and
      non-specific sequences increases significantly. These results suggest for the first time a
      role for ATP in DNA recognition by type III restriction-modification enzymes. In addition, we
      have shown that bromodeoxyuridine-containing oligonucleotides form complexes with EcoP15I DNA
      Mtase that are cross-linked upon irradiation. More importantly, we have shown that the
      crosslink site is at the site of DNA binding, since it can be suppressed by an excess of
      unmodified oligonucleotide. EcoP15I DNA Mtase exhibited Michaelis-Menten kinetics with both
      unmodified and bromodeoxyuridine-substituted DNA, with a higher specificity constant for the
      latter. Furthermore, gel mobility shift assays showed that proteolyzed EcoP15I DNA Mtase
      formed a specific complex with DNA, which had similar mobility as the native protein-DNA
      complex. Taken together these results form the basis for a detailed structure-function
      analysis of EcoP15I DNA Mtase.
AU  - Ahmad I
AU  - Rao DN
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1994 242: 378-388.

PMID- 8656425
VI  - 259
DP  - 1996
TI  - Functional analysis of conserved motifs in EcoP15I DNA methyltransferase.
PG  - 229-240
AB  - EcoP15I DNA methyltransferase recognizes the sequence 5'-CAGCAG-3' and transfers a methyl
      group to N-6 of the second adenine residue in the recognition sequence.  All N-6 adenine
      methyltransferases contain two highly conserved sequences, FxGxG (motif 1), postulated to form
      part of the S-adenosyl-L-methionine binding site and (D/N/S)PP(Y/F) (motif IV) involved in
      catalysis.  We have altered the second glycine residue in motif I to arginine and serine, and
      substituted tyrosine in motif IV with tryptophan in EcoP15I DNA methyltransferase, using
      site-directed mutagenesis.  The mutant enzymes were overexpressed, purified and characterized
      by biochemical methods.  The mutations in motif I completely abolished AdoMet binding but left
      target DNA recognition unaltered.  Although the mutation in motif IV resulted in loss of
      enzyme activity, we observed enhanced crosslinking of S-adenosyl-L-methionine and DNA.  This
      implies that DNA and AdoMet binding sites are close to motif IV.  Taken together, these
      results reinforce the importance of motif I in AdoMet binding and motif IV in catalysis.
      Additionally, limited proteolysis and UV crosslinking experiments with EcoP15I DNA
      methyltransferase imply that DNA binds in a cleft formed by two domains in the protein.
      Methylation protection analysis provides evidence for the fact that EcoP15I DNA Mtase makes
      contacts in the major groove of its substrate DNA.  Interestingly, hypermethylation of the
      guanine residue next to the target adenine residue indicates that the protein probably flips
      out the target adenine residue.
AU  - Ahmad I
AU  - Rao DN
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1996 259: 229-240.

PMID- 28254988
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Salmonellaenterica Serovar Typhi IMR_TP298/15, a Strain  with Intermediate Susceptibility to Ciprofloxacin, Isolated from a Typhoid  Outbreak.
PG  - e01740-16
AB  - Salmonella enterica serovar Typhi with reduced susceptibility to ciprofloxacin is increasingly
      being reported globally. An outbreak caused by Salmonella Typhi with
      decreased ciprofloxacin susceptibility has not been reported before in Malaysia.
      We present here the annotated draft genome of a Salmonella Typhi strain involved
      in a typhoid outbreak.
AU  - Ahmad N
AU  - Hii SY
AU  - Hashim R
AU  - Issa R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01740-16.

PMID- 28254972
VI  - 5
DP  - 2017
TI  - First Draft Genome Sequences of Malaysian Clinical Isolates of Corynebacterium diphtheriae.
PG  - e01670-16
AB  - Corynebacterium diphtheriae has caused multiple isolated diphtheria cases in Malaysia over the
      years. Here, we report the first draft genome sequences of 15
      Malaysia C. diphtheriae clinical isolates collected from the years 1981 to 2016.
AU  - Ahmad N
AU  - Hii SY
AU  - Mohd KMK
AU  - Abd WMA
AU  - Hashim R
AU  - Tang SN
AU  - Liow YL
AU  - Hamzah H
AU  - Dahalan NA
AU  - Seradja V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01670-16.

PMID- 22609915
VI  - 194
DP  - 2012
TI  - Comparative Genomic Analyses of 17 Clinical Isolates of Gardnerella vaginalis Provide Evidence of Multiple Genetically Isolated Clades Consistent with  Subspeciation into Genovars.
PG  - 3922-3937
AB  - Gardnerella vaginalis is associated with a spectrum of clinical conditions, suggesting high
      degrees of genetic heterogeneity among stains. Seventeen G.
      vaginalis isolates were subjected to a battery of comparative genomic analyses to
      determine their level of relatedness. For each measure, the degree of difference
      among the G. vaginalis strains was the highest observed among 23 pathogenic
      bacterial species for which at least eight genomes are available. Genome sizes
      ranged from 1.491 to 1.716 Mb; GC contents ranged from 41.18% to 43.40%; and the
      core genome, consisting of only 746 genes, makes up only 51.6% of each strain's
      genome on average and accounts for only 27% of the species supragenome.
      Neighbor-grouping analyses, using both distributed gene possession data and core
      gene allelic data, each identified two major sets of strains, each of which is
      composed of two groups. Each of the four groups has its own characteristic genome
      size, GC ratio, and greatly expanded core gene content, making the genomic
      diversity of each group within the range for other bacterial species. To test
      whether these 4 groups corresponded to genetically isolated clades, we inferred
      the phylogeny of each distributed gene that was present in at least two strains
      and absent in at least two strains; this analysis identified frequent homologous
      recombination within groups but not between groups or sets. G. vaginalis appears
      to include four nonrecombining groups/clades of organisms with distinct gene
      pools and genomic properties, which may confer distinct ecological properties.
      Consequently, it may be appropriate to treat these four groups as separate
      species.
AU  - Ahmed A
AU  - Earl J
AU  - Retchless A
AU  - Hillier SL
AU  - Rabe LK
AU  - Cherpes TL
AU  - Powell E
AU  - Janto B
AU  - Eutsey R
AU  - Hiller NL
AU  - Boissy R
AU  - Dahlgren ME
AU  - Hall BG
AU  - Costerton JW
AU  - Post JC
AU  - Hu FZ
AU  - Ehrlich GD
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3922-3937.

PMID- 24558242
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Boron-Tolerant and Moderately Halotolerant Bacterium Gracilibacillus boraciitolerans JCM 21714T.
PG  - e00097-14
AB  - Gracilibacillus boraciitolerans JCM 21714(T) has been characterized as a highly boron-tolerant
      and moderately halotolerant bacterium. Here, we report the draft
      genome sequence of this strain. The genome sequence facilitates an understanding
      of the biochemical functions of boron and provides a base to identify the gene(s)
      involved in the boron tolerance mechanism of the strain.
AU  - Ahmed I
AU  - Oshima K
AU  - Suda W
AU  - Kitamura K
AU  - Iida T
AU  - Ohmori Y
AU  - Fujiwara T
AU  - Hattori M
AU  - Ohkuma M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00097-14.

PMID- 11932464
VI  - 148
DP  - 2002
TI  - Identification of genetic differences between two Campylobacter jejuni strains with different colonization potentials.
PG  - 1203-1212
AB  - The consumption of poultry meat contaminated with Campylobacter jejuni is considered to be a
      risk factor for human campylobacteriosis. The
      development of targeted strategies to control campylobacters in
      broilers would benefit from knowledge of those bacterial factors
      important in colonization of the avian gut. During preliminary studies
      it was noted that C. jejuni NCTC 11168 was a poorer colonizer of
      chickens than strain 81116. This poor colonization could not be fully
      restored by in vivo passage, suggesting that it was a genetically
      endowed property of strain 11168. As the genome sequence is available
      for this strain, the technique of subtractive hybridization was used to
      identify gene fragments of strain 81116 not present in strain 11168.
      After two screening cycles, 24 out of 42 clones were identified as
      having DNA inserts specific for strain 81116. Six of these 24 clones
      contained gene fragment inserts with similarities to
      restriction-modification enzymes found in other bacteria. Two inserts
      had similarity to arsenic-resistance genes, whereas four others had
      similarities to cytochrome c oxidase III, dTDP-glucose 4,6-dehydratase,
      gamma-glutamyl transpeptidase and an abortive phage-resistance protein.
      At least some of these genes may be involved with colonization. A
      further six inserts had weak similarities to hypothetical proteins or
      to proteins with assigned functions from strain 11168. The remaining
      six clones had gene-fragment inserts with no database matches.
      Southern-blot analysis confirmed that strain-dependent variation
      existed for each of these DNA inserts. These results indicate that
      subtractive hybridization can successfully identify genes that are
      absent from the only C. jejuni strain for which the genome sequence is
      currently available.
AU  - Ahmed IH
AU  - Manning G
AU  - Wassenaar TM
AU  - Cawthraw S
AU  - Newell DG
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2002 148: 1203-1212.

PMID- 17912347
VI  - 2
DP  - 2007
TI  - Molecular analysis of a leprosy immunotherapeutic bacillus provides insights into Mycobacterium evolution.
PG  - E968
AB  - BACKGROUND: Evolutionary dynamics plays a central role in facilitating the
      mechanisms of species divergence among pathogenic and saprophytic mycobacteria.
      The ability of mycobacteria to colonize hosts, to proliferate and to cause
      diseases has evolved due to its predisposition to various evolutionary forces
      acting over a period of time. Mycobacterium indicus pranii (MIP), a taxonomically
      unknown 'generalist' mycobacterium, acts as an immunotherapeutic against leprosy
      and is approved for use as a vaccine against it. The large-scale field trials of
      this MIP based leprosy vaccine coupled with its demonstrated immunomodulatory and
      adjuvant property has led to human clinical evaluations of MIP in interventions
      against HIV-AIDS, psoriasis and bladder cancer. MIP, commercially available as
      'Immuvac', is currently the focus of advanced phase III clinical trials for its
      antituberculosis efficacy. Thus a comprehensive analysis of MIP vis-a-vis
      evolutionary path, underpinning its immanent immunomodulating properties is of
      the highest desiderata. PRINCIPAL FINDINGS: Genome wide comparisons together with
      molecular phylogenetic analyses by fluorescent amplified fragment length
      polymorphism (FAFLP), enterobacterial repetitive intergenic consensus (ERIC)
      based genotyping and candidate orthologues sequencing revealed that MIP has been
      the predecessor of highly pathogenic Mycobacterium avium intracellulare complex
      (MAIC) that did not resort to parasitic adaptation by reductional gene evolution
      and therefore, preferred a free living life-style. Further analysis suggested a
      shared aquatic phase of MAIC bacilli with the early pathogenic forms of
      Mycobacterium, well before the latter diverged as 'specialists'.
      CONCLUSIONS/SIGNIFICANCE: This evolutionary paradigm possibly affirms to marshall
      our understanding about the acquisition and optimization of virulence in
      mycobacteria and determinants of boundaries therein.
AU  - Ahmed N
AU  - Saini V
AU  - Raghuvanshi S
AU  - Khurana JP
AU  - Tyagi AK
AU  - Tyagi AK
AU  - Hasnain SE
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2007 2: E968.

PMID- 23133618
VI  - 7
DP  - 2012
TI  - Genomic comparison of Escherichia coli O104:H4 isolates from 2009 and 2011 reveals plasmid, and prophage heterogeneity, including shiga toxin encoding phage  stx2.
PG  - e48228
AB  - In May of 2011, an enteroaggregative Escherichia coli O104:H4 strain that had acquired a Shiga
      toxin 2-converting phage caused a large outbreak of bloody
      diarrhea in Europe which was notable for its high prevalence of hemolytic uremic
      syndrome cases. Several studies have described the genomic inventory and
      phylogenies of strains associated with the outbreak and a collection of
      historical E. coli O104:H4 isolates using draft genome assemblies. We present the
      complete, closed genome sequences of an isolate from the 2011 outbreak
      (2011C-3493) and two isolates from cases of bloody diarrhea that occurred in the
      Republic of Georgia in 2009 (2009EL-2050 and 2009EL-2071). Comparative genome
      analysis indicates that, while the Georgian strains are the nearest neighbors to
      the 2011 outbreak isolates sequenced to date, structural and nucleotide-level
      differences are evident in the Stx2 phage genomes, the mer/tet antibiotic
      resistance island, and in the prophage and plasmid profiles of the strains,
      including a previously undescribed plasmid with homology to the pMT virulence
      plasmid of Yersinia pestis. In addition, multiphenotype analysis showed that
      2009EL-2071 possessed higher resistance to polymyxin and membrane-disrupting
      agents. Finally, we show evidence by electron microscopy of the presence of a
      common phage morphotype among the European and Georgian strains and a second
      phage morphotype among the Georgian strains. The presence of at least two stx2
      phage genotypes in host genetic backgrounds that may derive from a recent common
      ancestor of the 2011 outbreak isolates indicates that the emergence of stx2
      phage-containing E. coli O104:H4 strains probably occurred more than once, or
      that the current outbreak isolates may be the result of a recent transfer of a
      new stx2 phage element into a pre-existing stx2-positive genetic background.
AU  - Ahmed SA et al
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2012 7: e48228.

PMID- 28912332
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Acute Hepatopancreatic Necrosis Disease-Causing Vibrio campbellii LA16-V1, Isolated from Penaeus vannamei Cultured in a Latin  American Country.
PG  - e01011-17
AB  - We report here the complete genome sequence of Vibrio campbellii, isolated from Penaeus
      vannamei cultured in a Latin American country. The Tn3-like transposon
      and pirAB genes were encoded on the plasmid pLA16-2. These data support the
      geographical variations in the virulence plasmid found among acute
      hepatopancreatic necrosis disease (AHPND)-causing Vibrio isolates from Latin
      America and Asia.
AU  - Ahn YS
AU  - Piamsomboon P
AU  - Tang KFJ
AU  - Han JE
AU  - Kim JH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01011-17.

PMID- 28056767
VI  - 18
DP  - 2017
TI  - Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods.
PG  - 19
AB  - BACKGROUND: Whole genome sequencing (WGS) is increasingly used in diagnostics and
      surveillance of infectious diseases. A major application for WGS is to use the
      data for identifying outbreak clusters, and there is therefore a need for methods
      that can accurately and efficiently infer phylogenies from sequencing reads. In
      the present study we describe a new dataset that we have created for the purpose
      of benchmarking such WGS-based methods for epidemiological data, and also present
      an analysis where we use the data to compare the performance of some current
      methods. RESULTS: Our aim was to create a benchmark data set that mimics
      sequencing data of the sort that might be collected during an outbreak of an
      infectious disease. This was achieved by letting an E. coli hypermutator strain
      grow in the lab for 8 consecutive days, each day splitting the culture in two
      while also collecting samples for sequencing. The result is a data set consisting
      of 101 whole genome sequences with known phylogenetic relationship. Among the
      sequenced samples 51 correspond to internal nodes in the phylogeny because they
      are ancestral, while the remaining 50 correspond to leaves. We also used the
      newly created data set to compare three different online available methods that
      infer phylogenies from whole-genome sequencing reads: NDtree, CSI Phylogeny and
      REALPHY. One complication when comparing the output of these methods with the
      known phylogeny is that phylogenetic methods typically build trees where all
      observed sequences are placed as leafs, even though some of them are in fact
      ancestral. We therefore devised a method for post processing the inferred trees
      by collapsing short branches (thus relocating some leafs to internal nodes), and
      also present two new measures of tree similarity that takes into account the
      identity of both internal and leaf nodes. CONCLUSIONS: Based on this analysis we
      find that, among the investigated methods, CSI Phylogeny had the best
      performance, correctly identifying 73% of all branches in the tree and 71% of all
      clades. We have made all data from this experiment (raw sequencing reads,
      consensus whole-genome sequences, as well as descriptions of the known phylogeny
      in a variety of formats) publicly available, with the hope that other groups may
      find this data useful for benchmarking and exploring the performance of
      epidemiological methods. All data is freely available at:
      https://cge.cbs.dtu.dk/services/evolution_data.php .
AU  - Ahrenfeldt J
AU  - Skaarup C
AU  - Hasman H
AU  - Pedersen AG
AU  - Aarestrup FM
AU  - Lund O
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2017 18: 19.

PMID- Not carried by PubMed...
VI  - 110
DP  - 1991
TI  - Bacterial infection restriction endonucleases, genetic damage and cancer.
PG  - 179-187
AB  - Restriction endonucleases are known to cut naked DNA at specific sites by
      recognizing their palindromes.  Similarly, in vitro in human and mammalian
      cells, restriction endonucleases have been shown to cause nonrandom chromosome
      damage, in addition to inducing gene amplification and mutations.  Bacteria,
      which are the source of restriction endonucleases, have also been shown to be
      clastogenic in vivo in human and mammalian cells.  Furthermore, it has been
      demonstrated that the bacteria cause nonrandom chromosome damage.  Normally,
      bacteria are phagocytized and their contents degraded by the cellular enzymes.
      However, it is possible that for some reason (mutation or physiological) the
      restriction endonucleases may cause specific chromosome damage, gene mutation
      or gene amplification, which in turn may involve oncogene activation, leading
      to cancer.
AU  - Ahuja YR
PT  - Journal Article
TA  - Biol. Zentralbl.
JT  - Biol. Zentralbl.
SO  - Biol. Zentralbl. 1991 110: 179-187.

PMID- 7523873
VI  - 310
DP  - 1994
TI  - Are rogue cells an indicator of cancer risk due to the action of bacterial restriction endonucleases?
PG  - 103-112
AB  - Cytogenetic surveys in normal individuals have occasionally shown the occurrence of cells with
      multiple chromosome-type aberrations in some of the subjects.  These cells, which are rare,
      have been termed as rogue cells.  Rogue cells, which have been observed worldwide, have a
      mysterious nature.  It has been suggested that they may give rise to cancer.  Various
      mechanisms have been considered for the causation of the rogue-cell phenomenon in the past but
      none of them appears to be fully justified.  In this paper we propose their occurrence due to
      the action of bacterial restriction endonucleases.
AU  - Ahuja YR
AU  - Obe G
PT  - Journal Article
TA  - Mutat. Res.
JT  - Mutat. Res.
SO  - Mutat. Res. 1994 310: 103-112.

PMID- 26430052
VI  - 3
DP  - 2015
TI  - Complete Genome Sequences of Evolved Arsenate-Resistant Metallosphaera sedula Strains.
PG  - e01142-15
AB  - Metallosphaera sedula is a thermoacidophilic crenarchaeote with a 2.19-Mb genome. Here, we
      report the genome sequences of several evolved derivatives of M. sedula  generated through
      adaptive laboratory evolution for enhanced arsenate resistance.
AU  - Ai C
AU  - McCarthy S
AU  - Schackwitz W
AU  - Martin J
AU  - Lipzen A
AU  - Blum P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01142-15.

PMID- 24526632
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of an Anaerobic, Thermophilic Bacterium, Thermoanaerobacterium aotearoense SCUT27, Isolated from a Hot Spring in China.
PG  - e00041-14
AB  - Thermoanaerobacterium aotearoense SCUT27, isolated from a hot spring in China, is a strictly
      anaerobic, thermophilic bacterium capable of degrading xylan and
      converting both pentose and hexose to ethanol with high yields. Here, we report
      the draft genome sequence of SCUT27, which reveals insights into the mechanisms
      of carbon source coutilization and xylan degradation in this thermophilic
      microorganism.
AU  - Ai H
AU  - Zhang J
AU  - Yang M
AU  - Yu P
AU  - Li S
AU  - Zhu M
AU  - Dong H
AU  - Wang S
AU  - Wang J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00041-14.

PMID- 21478345
VI  - 193
DP  - 2011
TI  - Complete genome sequence of probiotic Lactobacillus casei BD-II.
PG  - 3160-3161
AB  - Lactobacillus casei BD-II, a patented probiotic strain (U.S. patent 7,270,994 B2), was
      isolated from homemade koumiss in China and has been
      implemented in the industrial production as starter cultures. Here we
      report the complete genome sequence of BD-II which shows high similarity
      with the well studied probiotic BL23.
AU  - Ai L
AU  - Chen C
AU  - Zhou F
AU  - Wang L
AU  - Zhang H
AU  - Chen W
AU  - Guo B
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3160-3161.

PMID- 21566825
VI  - 40
DP  - 2011
TI  - Artificial DNA cutters for DNA manipulation and genome engineering.
PG  - 5657-5668
AB  - This tutorial review provides recent developments in artificial cutters for site-selective
      scission of DNA with the focus on chemistry-based DNA cutters. They are useful tools for
      molecular biology and biotechnology, since their site-selectivity of scission is much higher
      than that of naturally occurring restriction enzymes and also their scission site is freely
      chosen. In order to prepare these cutters, a DNA-cutting molecule is combined with a
      sequence-recognizing molecule in a covalent or non-covalent way. At targeted sites in
      single-stranded and double-stranded DNAs, the scission occurs via either oxidative cleavage of
      nucleotides or hydrolysis of phosphodiester linkages. Among many successful examples, an
      artificial restriction DNA cutter, prepared from Ce(IV)/EDTA and pseudo-complementary peptide
      nucleic acid, hydrolyzed double-stranded DNA at the target site. The scission site and
      scission specificity are determined simply in terms of the Watson-Crick rule so that even the
      whole genome of human beings was selectively cut at one predetermined site. Consistently,
      homologous recombination in human cells was successfully promoted by this tool. For the
      purpose of comparison, protein-based DNA cutters (e.g., zinc finger nucleases) are also
      briefly described. The potential applications of these cutters and their future aspects are
      discussed.
AU  - Aiba Y
AU  - Sumaoka J
AU  - Komiyama M
PT  - Journal Article
TA  - Chem. Soc. Rev.
JT  - Chem. Soc. Rev.
SO  - Chem. Soc. Rev. 2011 40: 5657-5668.

PMID- 26380631
VI  - 10
DP  - 2015
TI  - Draft-genome sequence of Shewanella algae strain C6G3.
PG  - 43
AB  - Shewanella algae strain C6G3, isolated from the 2 uppermost centimeters of muddy  sediment of
      Arcachon Bay (SW Atlantic French coast, sampled in October 2007) has  the capability to use a
      large panel of terminal electron acceptors under anaerobic condition, such as nitrate, nitrite
      and metal-oxide, and presents a great metabolic versatility. Here, we present the
      non-contiguous draft-genome sequence of Shewanella algae C6G3, which consists of a 4,879,425
      bp. The chromosome contains 5792 predicted genes. In total, the genome consists of 24 rRNA
      genes, 86 tRNA genes and 5660 genes assigned as protein-coding genes.
AU  - Aigle A
AU  - Michotey V
AU  - Bonin P
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 43.

PMID- 22535936
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of the Serotype k Streptococcus mutans Strain LJ23.
PG  - 2754-2755
AB  - Streptococcus mutans is the major pathogen of dental caries and occasionally causes infective
      endocarditis. Here we report the complete genome sequence of
      serotype k S. mutans strain LJ23, which was recently isolated from the oral
      cavity of a Japanese patient.
AU  - Aikawa C
AU  - Furukawa N
AU  - Watanabe T
AU  - Minegishi K
AU  - Furukawa A
AU  - Eishi Y
AU  - Oshima K
AU  - Kurokawa K
AU  - Hattori M
AU  - Nakano K
AU  - Maruyama F
AU  - Nakagawa I
AU  - Ooshima T
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2754-2755.

PMID- 2843805
VI  - 16
DP  - 1988
TI  - Restriction endonuclease RsrI from Rhodobacter sphaeroides, an isoschizomer of EcoRI:  purification and properties.
PG  - 7901-7916
AB  - We have purified RsrI endonuclease (R.RsrI), an isoschizomer of EcoRI, from Rhodobacter
      sphaeroides strain 630. The enzyme is homogeneous as judged by polyacrylamide gel
      electrophoresis and size-exclusion high-performance liquid chromatography. RsrI endonuclease
      is a dimer over the concentration range of 0.05 to 1.4 mg/ml. The reduced and denatured
      molecular weight of the enzyme is 30,000 Da. R.RsrI, like R.EcoRI, catalyzes the cleavage of
      duplex DNA and oligodeoxyribonucleotides between the first two residues of the sequence
      GAATTC. R.RsrI exhibits a kM of 14 nM and a kcat of 6.5 min-1 when reacting with pBR322 DNA at
      25C. R.RsrI differs from R.EcoRI in its N-terminal amino acid sequence, susceptibility to
      inhibition by antibodies, sensitivity to N-ethylmaleimide, isoelectric point, state of
      aggregation at high concentrations, temperature lability, and conditions for optimal reaction.
      R.RsrI displays a reduction of specificity (star activity) under conditions that also relax
      the specificity of R.EcoRI.
AU  - Aiken C
AU  - Gumport RI
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1988 16: 7901-7916.

PMID- 2927145
VI  - 13D
DP  - 1989
TI  - Interaction of RsrI endonuclease, an isoschizomer of EcoRI, with oligodeoxyribonucleotides containing base analogues.
PG  - 79
AB  - We have initiated a systematic kinetic study of the RsrI endonuclease, an
      isoschizomer of EcoRI, using oligodeoxyribonucleotides containing base
      analogues as substrates.  Several of these substrates were provided by Dr. L.
      McLaughlin, Boston College, who tested them with EcoRI.  All of the base
      substitutions tested affect the interaction of both enzymes with DNA.  In
      general, the effects with RsrI are more pronounced than with EcoRI, as measured
      by the greater reduction in the specificity constant (kcat/Km) for a given
      substitution.  For two substrates, the RsrI-catalyzed reaction was very slow;
      less than one-tenth the rate of the corresponding EcoRI reaction.  The lower
      tolerance of RsrI for base analogues in its recognition sequence may reflect a
      difference in the mechanisms by which these two enzymes recognize the same DNA
      sequence and cut it at the same site.  We are presently determining whether
      RsrI kinks and unwinds DNA to the same extent that EcoRI does.
AU  - Aiken C
AU  - Gumport RI
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1989 13D: 79.

PMID- 3956763
VI  - 45
DP  - 1986
TI  - RsrI and EcoRI are two different restriction endonucleases that recognize the same DNA sequence.
PG  - 1914
AB  - In order to study the recognition of specific DNA sequences by proteins, we
      have isolated RsrI endonuclease from Rhodopseudomonas sphaeroides strain 630.
      The preparation is approximately 80% pure, with one major band which comigrates
      on SDS gels with EcoRI endonuclease (M=30,000+-2000).  RsrI cleaves the duplex
      octanucleotide pGGAATTCC to form pGG.  Plasmid and phage DNA digests confirm
      that RsrI and EcoRI cleave the same sequence.  However, the enzymes appear to
      be different.  Antiserum to EcoRI required 1000-fold increased concentrations
      to effectively inhibit RsrI activity.  In addition, amino acid sequence
      analysis of the first 40 amino acids of RsrI revealed little homology with
      EcoRI.  Furthermore, the R. sphaeroides genome shows little homology with the
      EcoRI gene when tested by Southern blotting and hybridization with washing at
      low stringency.  A corresponding RsrI methylase activity has been identified
      and separated from the endonuclease by chromatography on phosphocellulose.
      This activity catalyzes the transfer of methyl groups from AdoMet to DNA,
      rendering the DNA resistant to cleavage by both RsrI and EcoRI endonucleases.
      It will be of interest to compare the mechanisms by which these enzymes
      recognize their common DNA sequence.
AU  - Aiken C
AU  - Milarski-Brown K
AU  - Gumport RI
PT  - Journal Article
TA  - Fed. Proc.
JT  - Fed. Proc.
SO  - Fed. Proc. 1986 45: 1914.

PMID- Not carried by PubMed...
VI  - 52
DP  - 1991
TI  - Sequence-specific recognition of DNA by RsrI endonuclease of Rhodobacter sphaeroides, an isoschizomer of EcoRI.
PG  - 1399
AB  - In order to study the interaction of RsrI endonuclease with its DNA recognition sequence and
      to determine whether RsrI recognizes DNA using a mechanism similar to that of EcoRI, I have
      purified milligram amounts of the enzyme to near homogeneity from its natural source,
      Rhodobacter sphaeroides strain 630. The enzyme comigrates with EcoRI during SDS-PAGE, with a
      reduced and denatured molecular weight of 30,000+/- 2000 Da. RsrI endonuclease is a dimer at
      concentrations of 0.05 to 1.4 mg/ml. In contrast to EcoRI, no tetrameric form was observed.
      The isoelectric point of the endonuclease was determined to be 7.0-different than the value of
      6.3 reported for EcoRI. The temperature and salt-dependence of the catalytic activity of RsrI
      also differ from those of EcoRI. The reaction exhibits Michaelis-Menten kinetics, and values
      of 14 nM and 6.5 min-1 were determined for Km and kcat, respectively using plasmid pBR322 as a
      substrate. RsrI endonuclease, unlike EcoRI, is inactivated by preincubating the enzyme with 10
      mM N-ethylmaleimide. This suggests that RsrI but not EcoRI has an essential sulfhydryl. RsrI
      endonuclease cleaves noncanonical sequences in reactions containing 12.5 mM Tris-HCl, 2.5 mM
      MgCl2, and 26% ethylene glycol. RsrI binding bends DNA by approximately 50 degrees and unwinds
      the DNA helix by 25 +/- 5 degree - values similar to those reported for EcoRI endonuclease.
      RsrI binding protects 12 nucleotides from cleavage by hydroxyl radical and MPE-Fe(II)
      footprinting reagents. I have tested the RsrI endonuclease with a series of
      decadeoxyribonucleotides containing base analogues as substrates. The kinetics of RsrI
      cleavage are affected by each substitution, and the effects are generally more pronounced than
      with EcoRI, as shown by the greater reduction in the specificity constant kcat/Km for a given
      substitution. For several substrates, cleavage by RsrI was very slow - less than one-tenth the
      rate of the corresponding EcoRI reaction. This lower tolerance of the RsrI endonuclease for
      functional group changes in its recognition site may reflect differences in the mechanisms by
      which RsrI and EcoRI recognize and cleave DNA.
AU  - Aiken CR
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1991 52: 1399.

PMID- 1918025
VI  - 266
DP  - 1991
TI  - The specific binding, bending, and unwinding of DNA by RsrI endonuclease, an isoschizomer of EcoRI endonuclease.
PG  - 19063-19069
AB  - To determine whether RsrI endonuclease recognizes and cleaves the sequence
      GAATTC in duplex DNA similarly to its isoschizomer EcoRI we initiated a
      functional comparison of the two enzymes.  Equilibrium binding experiments
      showed that at 20C RsrI endonuclease binds to specific and nonspecific
      sequences in DNA with affinities similar to those of EcoRI.  At 0C the affinity
      of RsrI for its specific recognition sequence is reduced 7-fold whereas the
      affinity for noncanonical sequences remains relatively unchanged.  Unlike
      EcoRI, incubation of RsrI endonuclease with N-ethylmaleimide inactivates the
      enzyme; however, preincubation with DNA prevents the inactivation.  The
      N-ethylmaleimide-treated enzyme fails to bind DNA as assayed by gel mobility
      shift assays.  Comparison of the deduced amino acid sequences of RsrI and EcoRI
      endonucleases suggests that modification of Cys245 is responsible for the
      inactivation.  Fe(II).EDTA and methidiumpropyl-EDTA.Fe(II) footprinting results
      indicate that RsrI, like EcoRI, protects 12 base pairs from cleavage when bound
      to its specific recognition sequence in the absence of Mg2+.  RsrI bends DNA by
      approximately 50 degrees, as determined by measuring the relative
      electrophoretic mobilities of specific RsrI-DNA complexes with the binding site
      in the center or near the end of the DNA fragment.  This value is similar to
      that reported for EcoRI.  RsrI also unwinds the DNA helix by 25 degrees +/- 5
      degrees, a value close to that reported for EcoRI endonuclease.  Collectively,
      these results indicate that the overall structural changes induced in the DNA
      by the binding of RsrI and EcoRI endonucleases to DNA in the absence of Mg2+
      are similar.  In the accompanying paper (Aiken, C.R., McLaughlin, L.W., and
      Gumport, R.I. (1991) J. Biol. Chem. 266, 19070-19078) we present results of
      studies of RsrI endonuclease using oligonucleotide substrates containing base
      analogues which suggest differences in the ways the two enzymes cleave DNA.
AU  - Aiken CR
AU  - Fisher EW
AU  - Gumport RI
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1991 266: 19063-19069.

PMID- 1664027
VI  - 208
DP  - 1991
TI  - Base analogs in study of restriction enzyme-DNA interactions.
PG  - 433-457
AB  - Enzymologists have long sought to discern the topography of the active sites of enzymes by
      examining substrate analogs for their ability to serve as reactants. Such investigations aim
      to contribute to our understanding of the kinetic and chemical mechanisms as well as the
      stereochemistry and stereoselectivity of a reaction.
AU  - Aiken CR
AU  - Gumport RI
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1991 208: 433-457.

PMID- 1918026
VI  - 266
DP  - 1991
TI  - The highly homologous isoschizomers RsrI endonuclease and EcoRI endonuclease do not recognize their target sequence identically.
PG  - 19070-19078
AB  - Using a series of decadeoxyribonucleotides containing base analogues as
      substrates we measured the steady-state kinetic parameters for the reaction
      catalyzed by RsrI endonuclease and compared the results to those with its
      isoschizomer EcoRI.  The kinetics of RsrI cleavage are affected by each
      substitution, with the effects being generally more deleterious than with
      EcoRI, as shown by the greater reduction in the specificity constant kcat/Km.
      The magnitudes of the effects of several substitutions are consistent with the
      formation of direct enzyme-nucleobase contacts at the indicated positions.
      With substrates containing 2-amino-purine or 2,6-diaminopurine at the central
      adenine or uracil at the outermost thymine in the recognition sequence,
      cleavage by RsrI was very slow, less than one-tenth the rate of the
      corresponding EcoRI-catalyzed reaction.  The lower tolerance of RsrI
      endonuclease for functional group changes in its recognition site may reflect
      differences in the mechanisms of DNA recognition by the two enzymes.  Although
      RsrI and EcoRI endonucleases bind with similar affinities to specific and
      nonspecific DNA sequences and appear to introduce similar structural
      distortions in DNA upon binding, the use of substrate analogues reveals
      significant differences at the level of catalysis in the mechanisms by which
      these two endonucleases recognize the duplex sequence GAATTC.
AU  - Aiken CR
AU  - McLaughlin LW
AU  - Gumport RI
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1991 266: 19070-19078.

PMID- 26788428
VI  - 4
DP  - 2016
TI  - In planta comparative transcriptomics of host-adapted strains of Ralstonia solanacearum.
PG  - e1549
AB  - Background. Ralstonia solanacearum is an economically important plant pathogen
      with an unusually large host range. The Moko (banana) and NPB (not pathogenic to
      banana) strain groups are closely related but are adapted to distinct hosts.
      Previous comparative genomics studies uncovered very few differences that could
      account for the host range difference between these pathotypes. To better
      understand the basis of this host specificity, we used RNAseq to profile the
      transcriptomes of an R. solanacearum Moko strain and an NPB strain under in vitro
      and in planta conditions. Results. RNAs were sequenced from bacteria grown in
      rich and minimal media, and from bacteria extracted from mid-stage infected
      tomato, banana and melon plants. We computed differential expression between each
      pair of conditions to identify constitutive and host-specific gene expression
      differences between Moko and NPB. We found that type III secreted effectors were
      globally up-regulated upon plant cell contact in the NPB strain compared with the
      Moko strain. Genes encoding siderophore biosynthesis and nitrogen assimilation
      genes were highly up-regulated in the NPB strain during melon pathogenesis, while
      denitrification genes were up-regulated in the Moko strain during banana
      pathogenesis. The relatively lower expression of oxidases and the denitrification
      pathway during banana pathogenesis suggests that R. solanacearum experiences
      higher oxygen levels in banana pseudostems than in tomato or melon xylem.
      Conclusions. This study provides the first report of differential gene expression
      associated with host range variation. Despite minimal genomic divergence, the
      pathogenesis of Moko and NPB strains is characterized by striking differences in
      expression of virulence- and metabolism-related genes.
AU  - Ailloud F
AU  - Lowe TM
AU  - Robene I
AU  - Cruveiller S
AU  - Allen C
AU  - Prior P
PT  - Journal Article
TA  - PeerJ
JT  - PeerJ
SO  - PeerJ 2016 4: e1549.

PMID- 23377788
VI  - 97
DP  - 2013
TI  - Glycerol assimilation and production of 1,3-propanediol by Citrobacter amalonaticus Y19.
PG  - 5001-5011
AB  - Citrobacter amalonaticus Y19 (Y19) was isolated because of its ability for carbon
      monoxide-dependent hydrogen production (water-gas shift reaction). This paper
      reports the assimilation of glycerol and the production of 1,3-propanediol
      (1,3-PDO) by Y19. Genome sequencing revealed that Y19 contained the genes for the
      utilization of glycerol and 1,2-propanediol (pdu operon) along with those for the
      synthesis of coenzyme B(12) (cob operon). On the other hand, it did not possess
      the genes for the fermentative metabolism of glycerol of Klebsiella pneumoniae,
      which consists of both the oxidative (dhaD and dhaK) and reductive (dhaB and
      dhaT) pathways. In shake-flask cultivation under aerobic conditions, Y19 could
      grow well with glycerol as the sole carbon source and produced 1,3-PDO. The level
      of 1,3-PDO production was improved when vitamin B(12) was added to the culture
      medium under aerobic conditions. Under anaerobic conditions, cell growth and
      1,3-PDO production on glycerol was also possible, but only when an exogenous
      electron acceptor, such as nitrate or fumarate, was added. This is the first
      report of the glycerol metabolism and 1,3-PDO production by C. amalonaticus Y19.
AU  - Ainala SK
AU  - Ashok S
AU  - Ko Y
AU  - Park S
PT  - Journal Article
TA  - Appl. Microbiol. Biotechnol.
JT  - Appl. Microbiol. Biotechnol.
SO  - Appl. Microbiol. Biotechnol. 2013 97: 5001-5011.

PMID- 23723394
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Pseudomonas denitrificans ATCC 13867.
PG  - e00257-13
AB  - Pseudomonas denitrificans ATCC 13867, a Gram-negative facultative anaerobic bacterium, is
      known to produce vitamin B12 under aerobic conditions. This paper
      reports the annotated whole-genome sequence of the circular chromosome of this
      organism.
AU  - Ainala SK
AU  - Somasundar A
AU  - Park S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00257-13.

PMID- 24814781
VI  - 80
DP  - 2014
TI  - The Plasmid Complement of Lactococcus lactis UC509.9 Encodes Multiple Bacteriophage Resistance Systems.
PG  - 4341-4349
AB  - Lactococcus lactis subsp. cremoris strains are used globally for the production of fermented
      dairy products, particularly hard cheeses. Believed to be of plant origin, L. lactis strains
      that are used as starter cultures have undergone extensive adaptation to the dairy
      environment, partially through the acquisition of extrachromosomal DNA in the form of plasmids
      that specify technologically important phenotypic traits. Here, we present a detailed analysis
      of the eight plasmids of L. lactis UC509.9, an Irish dairy starter strain. Key industrial
      phenotypes were mapped, and genes that are typically associated with lactococcal plasmids were
      identified. Four distinct, plasmid-borne bacteriophage resistance systems were identified,
      including two abortive infection systems, AbiB and AbiD1, thereby supporting the observed
      phage resistance of L. lactis UC509.9. AbiB escape mutants were generated for phage sk1, which
      were found to carry mutations in orf6, which encodes the major capsid protein of this phage.
AU  - Ainsworth S
AU  - Mahony J
AU  - van Sinderen D
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2014 80: 4341-4349.

PMID- 23405300
VI  - 1
DP  - 2013
TI  - Complete Genome of Lactococcus lactis subsp. cremoris UC509.9, Host for a Model Lactococcal P335 Bacteriophage.
PG  - e00119-12
AB  - Here, we report the complete genome of Lactococcus lactis subsp. cremoris UC509.9, an Irish
      dairy starter. The circular chromosome of L. lactis UC509.9
      represents the smallest among those of the sequenced lactococcal strains, while
      its large complement of eight plasmids appears to be a reflection of its
      adaptation to the dairy environment.
AU  - Ainsworth S
AU  - Zomer A
AU  - de Jager V
AU  - Bottacini F
AU  - van Hijum SA
AU  - Mahony J
AU  - van Sinderen D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00119-12.

PMID- 12836358
VI  - 1
DP  - 2001
TI  - Kinetic dissection of the multistep process in L1.ltrB intron mobility.
PG  - 249-250
AB  - A kinetic characterization is presented for intron insertion into a target duplex DNA site
      during L1.ltrB intron mobility. This reaction is catalyzed by a ribonucleoprotein particle
      (RNP), consisting of a lariat form of group II intron RNA and the intron-encoded LtrA protein.
      In the first stage of intron mobility, the RNA component of the enzyme by itself inserts
      directly into the target ds DNA site, and thus, the RNP enzyme does not carry out turnover.
      Using single-turnover kinetics, we established an in vitro kinetic assay system and
      investigated mechanism of the intron RNA insertion process.
AU  - Aizawa Y
AU  - Xiang Q
AU  - Pyle AM
PT  - Journal Article
TA  - Nucleic Acids Res. Suppl.
JT  - Nucleic Acids Res. Suppl.
SO  - Nucleic Acids Res. Suppl. 2001 1: 249-250.

PMID- 26767091
VI  - 11
DP  - 2016
TI  - High quality permanent draft genome sequence of Phaseolibacter flectens ATCC 12775(T), a plant pathogen of French bean pods.
PG  - 4
AB  - Phaseolibacter flectens strain ATCC 12775(T) (Halpern et al., Int J Syst Evol Microbiol
      63:268-273, 2013) is a Gram-negative, rod shaped, motile, aerobic,
      chemoorganotroph bacterium. Ph. flectens is as a plant-pathogenic bacterium on
      pods of French bean and was first identified by Johnson (1956) as Pseudomonas
      flectens. After its phylogenetic position was reexamined, Pseudomonas flectens
      was transferred to the family Enterobacteriaceae as Phaseolibacter flectens gen.
      nov., comb. nov. Here we describe the features of this organism, together with
      the draft genome sequence and annotation. The DNA GC content is 44.34 mol%. The
      chromosome length is 2,748,442 bp. It encodes 2,437 proteins and 89 RNA genes.
      Ph. flectens genome is part of the Genomic Encyclopedia of Type Strains, Phase I:
      the one thousand microbial genomes study.
AU  - Aizenberg-Gershtein Y
AU  - Izhaki I
AU  - Lapidus A
AU  - Copeland A
AU  - Reddy T
AU  - Huntemann M
AU  - Pillay M
AU  - Markowitz V
AU  - Goker M
AU  - Woyke T
AU  - Klenk HP
AU  - Kyrpides NC
AU  - Halpern M
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 4.

PMID- 12397186
VI  - 99
DP  - 2002
TI  - Genome sequence of Streptococcus mutans UA159, a cariogenic dental pathogen.
PG  - 14434-14439
AB  - Streptococcus mutans is the leading cause of dental caries (tooth decay) worldwide and is
      considered to be the most cariogenic of all of the oral streptococci. The genome of S. mutans
      UA159, a serotype c strain, has been completely sequenced and is composed of 2,030,936 base
      pairs. It contains 1,963 ORFs, 63% of which have been assigned putative functions. The genome
      analysis provides further insight into how S. mutans has adapted to surviving the oral
      environment through resource acquisition, defense against host factors, and use of gene
      products that maintain its niche against microbial competitors. S. mutans metabolizes a wide
      variety of carbohydrates via nonoxidative pathways, and all of these pathways have been
      identified, along with the associated transport systems whose genes account for almost 15% of
      the genome. Virulence genes associated with extracellular adherent glucan production,
      adhesins, acid tolerance, proteases, and putative hemolysins have been identified. Strain
      UA159 is naturally competent and contains all of the genes essential for competence and quorum
      sensing. Mobile genetic elements in the form of IS elements and transposons are prominent in
      the genome and include a previously uncharacterized conjugative transposon and a composite
      transposon containing genes for the synthesis of antibiotics of the gramicidin/bacitracin
      family; however, no bacteriophage genomes are present.
AU  - Ajdic D
AU  - McShan WM
AU  - McLaughlin RE
AU  - Savic G
AU  - Chang J
AU  - Carson MB
AU  - Primeaux C
AU  - Tian R
AU  - Kenton S
AU  - Jia H
AU  - Lin S
AU  - Qian Y
AU  - Li S
AU  - Zhu H
AU  - Najar F
AU  - Lai H
AU  - White J
AU  - Roe BA
AU  - Jerretti JJ
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2002 99: 14434-14439.

PMID- 25700409
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequence of a Bordetella pertussis Brazilian Vaccine Strain.
PG  - e01570-14
AB  - Despite the reduction in incidence after vaccination, pertussis disease is still considered a
      public health problem worldwide, mainly due to recent and potential  new outbreaks. We report
      here the complete genome of the Bordetella pertussis Butantan strain used in the Brazilian
      National Immunization Program as a whole-cell pertussis antigen to compose vaccines such as
      DTwP (diphtheria, tetanus, and whole-cell pertussis).
AU  - Akamatsu MA
AU  - Nishiyama MY Jr
AU  - Morone M
AU  - Oliveira UC
AU  - Bezerra MF
AU  - Sakauchi MA
AU  - Raw I
AU  - Junqueira-de-Azevedo IL
AU  - Kitajima JP
AU  - Carvalho E
AU  - Ho PL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01570-14.

PMID- 10403769
VI  - 260
DP  - 1999
TI  - Conjugation of plasmid DNAs with lactose via diazocoupling enhances resistance to restriction enzymes and acquires binding affinity to galactose-specific lectin.
PG  - 323-328
AB  - Oligosaccharide-plasmid DNA conjugates were synthesized simply and effectively via the
      diazocoupling method.  Plasmids (pUC19, pTRI-beta-actin, and pEGFP-C1) were treated with an
      N-beta-lactoside-substituted diazonium salt to yield diazocoupling products with degree of
      substitutions of 2.5-3.1 mol% of overall nucleobases. The lactose-pUC19 conjugate was found to
      resist restriction enzymes more strongly than the nonconjugated plasmid DNA and to acquire a
      strong binding affinity to galactose-specific lectin RCA(120). The diazocoupling modification
      of pTRI-beta-actin plasmid DNA little influenced in vitro transcription with T7 RNA
      polymerase. When lactose-pEGFP-C1 conjugate was transfected to baby hamster kidney (BHK) cells
      by means of cationic lipids, transduced gene was expressed in BHK cells similarly with the
      nonconjugated pEGFP-C1. The modification of plasmid DNA with carbohydrate enhanced the
      resistance to restriction enzymes and developed a strong binding affinity to
      galactose-specific lectin.
AU  - Akasaka T
AU  - Matsuura K
AU  - Emi N
AU  - Kobayashi K
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1999 260: 323-328.

PMID- 1839740
VI  - 3
DP  - 1991
TI  - A new approach to establishing the set of phages for typing methicillin-resistant Staphylococcus aureus.
PG  - 275-278
AB  - A new approach to using experimental phages for typing methicillin-resistant S.
      aureus (MRSA) non-sensitive to the phages of International Basic Set (IBS) is
      described.  The collection includes phage 85, modified on a culture of MRSA,
      and 5 phages induced from MRSA strains isolated in clinics of Moscow in
      1975-76.  Firstly, the modified phage selects cultures according to the
      specific character of its restriction-modification system, then the induced
      phages differentiate the selected strains into 5 groups (1,2,3,4,5) based on
      the specificity of the prophages they contain.  Group 1 strains can further be
      differentiated into 5 subgroups (A,B,C,D,E) by additional phages.  Forty-one
      MRSA strains isolated in 1987-90 in various hospitals of Moscow showing no
      sensitivity to IBS phages, were lysed by the modified phage, 15 of them
      belonging to Group 2 and isolated in the traumatological hospital, 26 belonging
      to Group 1 and were circulating in the burn center.  Twenty-three strains of
      Group 1 appertain to subgroup 1B and were isolated over a 4-year period from
      the burned surface of patients and from the throat of a medical staff carrier.
AU  - Akatov AK
AU  - Zueva VS
AU  - Dmitrenko OA
PT  - Journal Article
TA  - J. Chemother.
JT  - J. Chemother.
SO  - J. Chemother. 1991 3: 275-278.

PMID- 28183768
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Cystobacter ferrugineus Strain Cbfe23.
PG  - e01601-16
AB  - In an effort to explore myxobacterial natural product biosynthetic pathways, the  draft genome
      sequence of Cystobacter ferrugineus strain Cbfe23 has been obtained.
      Analysis of the genome using antiSMASH suggests a multitude of unique natural
      product biosynthetic pathways. This genome will contribute to the investigation
      of secondary metabolism in other myxobacterial species.
AU  - Akbar S
AU  - Dowd SE
AU  - Stevens DC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01601-16.

PMID- 25883296
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Biofilm-Forming Stenotrophomonas maltophilia Strain  53.
PG  - e00312-15
AB  - A clinical strain of Stenotrophomonas maltophilia (designated strain 53) was obtained, and a
      whole-genome sequence was generated. The subsequent draft
      whole-genome sequence demonstrated the presence of a number of genes encoding for
      proteins involved in resistance to a number of antimicrobial therapies.
AU  - Akbar S
AU  - Rout SP
AU  - Humphreys PN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00312-15.

PMID- 26044421
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Pseudomonas aeruginosa Strain PS3 and Citrobacter freundii Strain SA79 Obtained from a Wound Dressing-Associated Biofilm.
PG  - e00561-15
AB  - Two isolates, one from the genus Pseudomonas and the second from Citrobacter, were isolated
      from a wound dressing-associated biofilm. Following whole-genome
      sequencing, the two isolates presented genes encoding for resistance to
      antibiotics and those involved in exopolysaccharide production.
AU  - Akbar S
AU  - Rout SP
AU  - Humphreys PN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00561-15.

PMID- 
VI  - 16
DP  - 1999
TI  - The conjugal plasmid pLL10236 encodes lactose fermentation ability, restriction/modification activity, bacteriocin production and immunity in Lactococcus lactis subsp. Lactis LL102.
PG  - 487-494
AB  - A 36 kb plasmid, designed as pLL 10236, was determined in Lactococcus lactis subsp. Lactis
      LL102.  This plasmid mediates lactose fermentation ability (Lac+), bacteriocin production
      (Bac+) and immunity (Imm+), and restriction/modification (R+M+) activity against bacteriophage
      O1120 in strain LL102.  The conjugal ability of pLL 10236 and expression of pLL 10236 encoding
      traits were determined by using a Lac-, Bac-, Imm- and (R-M-) recipient strain L. lactis
      subsp. Lactis P81-1.
AU  - Akcelik M
PT  - Journal Article
TA  - Food Microbiol.
JT  - Food Microbiol.
SO  - Food Microbiol. 1999 16: 487-494.

PMID- 
VI  - 35
DP  - 2000
TI  - Phage resistance in Lactococcus lactis subsp lactis strains isolated from traditional fermented milk products in Turkey.
PG  - 473-481
AB  - Lactococcus lactis subsp. lactis strains isolated from traditional fermented milk products in
      Turkey were used to determine their phage
      resistance against three different lactic phages. The following modes
      of action were examined: phage adsorption inhibition in five strains,
      abortive infection (heat sensitive phage resistance) in three strains,
      restriction/modification in four strains and blocking of phage DNA
      injection in one strain. The genetic nature of the phage resistance
      systems in these strains was determined by comparison of phage
      proliferation parameters, e.g. adsorption (%), EOP, burst size, latent
      period and production of major capsid protein, between wild-type
      strains and their plasmid-cured derivatives.
AU  - Akcelik M
AU  - Sanlibaba P
AU  - Tukel C
PT  - Journal Article
TA  - Int. J. Food Sci. Technol.
JT  - Int. J. Food Sci. Technol.
SO  - Int. J. Food Sci. Technol. 2000 35: 473-481.

PMID- 
VI  - 101
DP  - 2001
TI  - Partial DNA methylation in Listeria monocytogenes creates variable populations of cells with altered virulence.
PG  - 411
AB  - We have recently identified variable patterns of DNA methylation sites in the major virulence
      region of the food borne pathogen Listeria
      monocytogenes. The degree of partial methylation is specific to the
      particular isolate, but high level methylation was only found in
      serotype 4b strains, which are associated with outbreaks of
      listeriosis. The methylation is visualised as reproducible band
      patterns when DNA from a culture of cells is subjected to restriction
      digest and southern hybridisation using a prfA-hlyA gene probe.
      Controls were carried out to ensure that this partial restriction was
      due to specific methylation and not due to simple enzyme inhibition.
      Use of isoschizomers with differing methylation sensitivities allowed
      us to identify this as cytosine-specific methylation. The gene
      responsible for this methylation was cloned and found to have homology
      to other cytosine methyl-transferases. To create these reproducible
      patterns of partial DNA methylation, the methylation event must be
      controlled. To investigate this, single Listeria monocytogenes cells,
      which can only be methylated at one of the susceptible sites, were used
      to inoculate tubes of broth and allowed to grow to stationary phase.
      When the DNA was recovered from each of these cultures, all samples
      exhibited exactly the same mixed pattern of DNA methylation indicating
      that these patterns are not inherited, but rather methylation at this
      locus must occur in a controlled manner. Either activity of the
      methylase is directly modulated or architecture of the chromosomal DNA
      must control access of the methylase to susceptible sites. In invasion
      assays using Caco-2 cell lines, a correlation could be found between
      the degree of DNA methylation associated with an isolate and the
      invasiveness of that strain. This suggests that the methylation may
      have an influence on gene expression and that in these cultures with
      highly variable methylation patterns, some cells may be pre-primed to
      cause disease.
AU  - Akhtar M
AU  - Perehinec TM
AU  - Nazli A
AU  - Hill PJ
AU  - Rees CED
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 2001 101: 411.

PMID- 27389268
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Burkholderia sp. Strain CCA53, Isolated from Leaf Soil.
PG  - e00630-16
AB  - Burkholderia sp. strain CCA53 was isolated from leaf soil collected in Higashi-Hiroshima City
      in Hiroshima Prefecture, Japan. Here, we present a draft
      genome sequence of this strain, which consists of a total of 4 contigs containing
      6,647,893 bp, with a G+C content of 67.0% and comprising 9,329 predicted coding
      sequences.
AU  - Akita H
AU  - Kimura Z
AU  - Yusoff MZ
AU  - Nakashima N
AU  - Hoshino T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00630-16.

PMID- 27932657
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Pseudomonas sp. Strain CCA1, Isolated from Leaf Soil.
PG  - e01371-16
AB  - Pseudomonas sp. strain CCA1 was isolated from leaf soil collected in Higashi-Hiroshima City in
      Hiroshima Prefecture, Japan. Here, we present a draft
      genome sequence of this strain. The genome consists of 24 contigs for a total of
      6,993,992 bp, 8,917 predicted coding sequences, and a GC content of 67.2%.
AU  - Akita H
AU  - Kimura ZI
AU  - Hoshino T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01371-16.

PMID- 28935726
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Ureibacillus thermosphaericus A1, a Thermophilic Bacillus Isolated from Compost.
PG  - e00910-17
AB  - Ureibacillus thermosphaericus A1 was isolated from compost collected in Munakata  City,
      Fukuoka Prefecture, Japan. Here, we report the first complete genome
      sequence of U. thermosphaericus The complete genome of this strain consists of
      3,488,104 bp with a GC content of 36.3% and comprises 3,362 predicted coding
      sequences.
AU  - Akita H
AU  - Kimura ZI
AU  - Matsushika A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00910-17.

PMID- 27313297
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Microbacterium sp. Strain HM58-2, Which Hydrolyzes Acylhydrazides.
PG  - e00554-16
AB  - We report the draft genome sequence of Microbacterium sp. strain HM58-2, which produces
      hydrazidase, an enzyme hydrolyzing acylhydrazides. The estimated genome
      size is 3.9 Mb. Genome sequence information of this strain will help to identify
      an assimilating mechanism of nonnatural compounds in this strain and to develop
      ecological applications.
AU  - Akiyama T
AU  - Ishige T
AU  - Kanesaki Y
AU  - Ito S
AU  - Oinuma K
AU  - Takaya N
AU  - Sasaki Y
AU  - Yajima S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00554-16.

PMID- 20828392
VI  - 11
DP  - 2010
TI  - The genome of Geobacter bemidjiensis, exemplar for the subsurface clade of Geobacter species that predominate in Fe(III)-reducing subsurface environments.
PG  - 490
AB  - BACKGROUND: Geobacter species in a phylogenetic cluster known as
      subsurface clade 1 are often the predominant microorganisms in subsurface
      environments in which Fe(III) reduction is the primary electron-accepting
      process. Geobacter bemidjiensis, a member of this clade, was isolated from
      hydrocarbon-contaminated subsurface sediments in Bemidji, Minnesota, and
      is closely related to Geobacter species found to be abundant at other
      subsurface sites. This study examines whether there are significant
      differences in the metabolism and physiology of G. bemidjiensis compared
      to non-subsurface Geobacter species. RESULTS: Annotation of the genome
      sequence of G. bemidjiensis indicates several differences in metabolism
      compared to previously sequenced non-subsurface Geobacteraceae, which will
      be useful for in silico metabolic modeling of subsurface bioremediation
      processes involving Geobacter species. Pathways can now be predicted for
      the use of various carbon sources such as propionate by G. bemidjiensis.
      Additional metabolic capabilities such as carbon dioxide fixation and
      growth on glucose were predicted from the genome annotation. The presence
      of different dicarboxylic acid transporters and two oxaloacetate
      decarboxylases in G. bemidjiensis may explain its ability to grow by
      disproportionation of fumarate. Although benzoate is the only aromatic
      compound that G. bemidjiensis is known or predicted to utilize as an
      electron donor and carbon source, the genome suggests that this species
      may be able to detoxify other aromatic pollutants without degrading them.
      Furthermore, G. bemidjiensis is auxotrophic for 4-aminobenzoate, which
      makes it the first Geobacter species identified as having a vitamin
      requirement. Several features of the genome indicated that G. bemidjiensis
      has enhanced abilities to respire, detoxify and avoid oxygen. CONCLUSION:
      Overall, the genome sequence of G. bemidjiensis offers surprising insights
      into the metabolism and physiology of Geobacteraceae in subsurface
      environments, compared to non-subsurface Geobacter species, such as the
      ability to disproportionate fumarate, more efficient oxidation of
      propionate, enhanced responses to oxygen stress, and dependence on the
      environment for a vitamin requirement. Therefore, an understanding of the
      activity of Geobacter species in the subsurface is more likely to benefit
      from studies of subsurface isolates such as G. bemidjiensis than from the
      non-subsurface model species studied so far.
AU  - Aklujkar M
AU  - Young ND
AU  - Holmes D
AU  - Chavan M
AU  - Risso C
AU  - Kiss HE
AU  - Han CS
AU  - Land ML
AU  - Lovley DR
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2010 11: 490.

PMID- 11443086
VI  - 183
DP  - 2001
TI  - Genome size determination and coding capacity of Sodalis glossinidius, an enteric symbiont of Tsetse flies, as revealed by hybridization to Escherichia coli gene arrays.
PG  - 4517-4525
AB  - Recent molecular characterization of various microbial genomes has revealed differences in
      genome size and coding capacity between obligate symbionts and intracellular pathogens versus
      free-living organisms. Multiple symbiotic microorganisms have evolved with tsetse fly, the
      vector of African trypanosomes, over long evolutionary times. Although these symbionts are
      indispensable for tsetse fecundity, the biochemical and molecular basis of their functional
      significance is unknown. Here, we report on the genomic aspects of the secondary symbiont
      Sodalis glossinidius. The genome size of Sodalis is approximately 2 Mb. Its DNA is subject to
      extensive methylation and based on some of its conserved gene sequences has an A+T content of
      only 45%, compared to the typically AT-rich genomes of endosymbionts. Sodalis also harbors an
      extrachromosomal plasmid about 134 kb in size. We used a novel approach to gain insight into
      Sodalis genomic contents, i.e., hybridizing its DNA to macroarrays developed for Escherichia
      coli, a closely related enteric bacterium. In this analysis we detected 1,800 orthologous
      genes, corresponding to about 85% of the Sodalis genome. The Sodalis genome has apparently
      retained its genes for DNA replication, transcription, translation, transport, and the
      biosynthesis of amino acids, nucleic acids, vitamins, and cofactors. However, many genes
      involved in energy metabolism and carbon compound assimilation are apparently missing, which
      may indicate an adaptation to the energy sources available in the only nutrient of  the tsetse
      host, blood. We present gene arrays as a rapid tool for comparative genomics in the absence of
      whole genome sequence to advance our understanding of closely related bacteria.
AU  - Akman L
AU  - Rio RVM
AU  - Beard CB
AU  - Aksoy S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2001 183: 4517-4525.

PMID- 12219091
VI  - 32
DP  - 2002
TI  - Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia.
PG  - 402-407
AB  - Many insects that rely on a single food source throughout their developmental cycle harbor
      beneficial microbes that provide nutrients
      absent from their restricted diet. Tsetse flies, the vectors of African
      trypanosomes, feed exclusively on blood and rely on one such intracellular
      microbe for nutritional provisioning and fecundity. As a result of
      co-evolution with hosts over millions of years, these mutualists have lost
      the ability to survive outside the sheltered environment of their host
      insect cells. We present the complete annotated genome of Wigglesworthia
      glossinidia brevipalpis, which is composed of one chromosome of 697,724
      base pairs (bp) and one small plasmid, called pWig1, of 5,200 bp. Genes
      involved in the biosynthesis of vitamin metabolites, apparently essential
      for host nutrition and fecundity, have been retained. Unexpectedly, this
      obligate's genome bears hallmarks of both parasitic and free-living
      microbes, and the gene encoding the important regulatory protein DnaA is
      absent.
AU  - Akman L
AU  - Yamashita A
AU  - Watanabe H
AU  - Oshima K
AU  - Shiba T
AU  - Hattori M
AU  - Aksoy S
PT  - Journal Article
TA  - Nat. Genet.
JT  - Nat. Genet.
SO  - Nat. Genet. 2002 32: 402-407.

PMID- 9593295
VI  - 28
DP  - 1998
TI  - Analyses of the cag pathogenicity island of Helicobacter pylori.
PG  - 37-53
AB  - Most strains of Helicobacter pylori from patients with peptic ulcer disease or intestinal-type
      gastric cancer carry cagA, a gene that encodes
      an immunodominant protein of unknown function, whereas many of the strains
      from asymptomatically infected persons lack this gene. Recent studies
      showed that the cagA gene lies near the right end of a approximately 37kb
      DNA segment (a pathogenicity island, or PAI) that is unique to cagA+
      strains and that the cag PAI was split in half by a transposable element
      insertion in the reference strain NCTC11638. In complementary experiments
      reported here, we also found the same cag PAI, and sequenced a 39 kb
      cosmid clone containing the left 'cagII' half of this PAI. Encoded in
      cagII were four proteins each with homology to four components of
      multiprotein complexes of Bordetella pertussis ('Ptl'), Agrobacterium
      tumefaciens ('Vir'), and conjugative plasmids ('Tra') that help deliver
      pertussis toxin and T (tumour inducing) and plasmid DNA, respectively, to
      target eukaryotic or prokaryotic cells, and also homologues of eukaryotic
      proteins that are involved in cytoskeletal structure. To the left of cagII
      in this cosmid were genes for homologues of HsIU (heat-shock protein) and
      Era (essential GTPase); to the right of cagII were homologues of genes for
      a type I restriction endonuclease and ion transport functions. Deletion of
      the cag PAI had no effect on synthesis of the vacuolating cytotoxin, but
      this deletion and several cag insertion mutations blocked induction of
      synthesis of proinflammatory cytokine IL-8 in gastric epithelial cells.
      Comparisons among H. pylori strains indicated that cag PAI gene content
      and arrangement are rather well conserved. We also identified two genome
      rearrangements with end-points in the cag PAI. One, in reference strain
      NCTC11638, involved IS605, a recently described transposable element (as
      also found by others). Another rearrangement, in 3 of 10 strains tested
      (including type strain NCTC11637), separated the normally adjacent cagA
      and picA genes and did not involve IS605. Our results are discussed in
      terms of how cag-encoded proteins might help trigger the damaging
      inflammatory responses in the gastric epithelium and possible
      contributions of DNA rearrangements to genome evolution.
AU  - Akopyants NS
AU  - Clifton SW
AU  - Kersulyte D
AU  - Crabtree JE
AU  - Youree BE
AU  - Reece CA
AU  - Bukanov NO
AU  - Drazek ES
AU  - Roe BA
AU  - Berg DE
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1998 28: 37-53.

PMID- 9789049
VI  - 95
DP  - 1998
TI  - PCR-based subtractive hybridization and differences in gene content among strains of Helicobacter pylori.
PG  - 13108-13113
AB  - Genes that are characteristic of only certain strains of a bacterial species can be of great
      biologic interest.  Here we describe a PCR-based subtractive hybridization method for
      efficiently detecting such DNAs and apply it to the gastric pathogen Helicobacter pylori.
      Eighteen DNAs specific to a monkey-colonizing strain (J166) were obtained by subtractive
      hybridization against an unrelated strain whose genome has been fully sequenced (26695).
      Seven J166-specific clones had no DNA sequence match to the 26695 genome, and 11 other clones
      were mixed, with adjacent patches that did and did not match any sequences in 26695.  At the
      protein level, seven clones had homology to putative DNA restriction-modification enzymes, and
      two had homology to putative metabolic enzymes.  Nine others had no database match with
      proteins of assigned function.  PCR tests of 13 unrelated H. pylori strains by using primers
      specific for 12 subtracted clones and complementary Southern bot hybridizations indicated that
      these DNAs are highly polymorphic in the H. pylori population, with each strain yielding a
      different pattern of gene-specific PCR amplification.  The search for polymorphic DNAs, as
      described here, should help identify previously unknown virulence genes in pathogens and
      provide new insights into microbial genetic diversity and evolution.
AU  - Akopyants NS
AU  - Fradkov A
AU  - Diatchenko L
AU  - Hill JE
AU  - Siebert PD
AU  - Lukyanov SA
AU  - Sverdlov ED
AU  - Berg DE
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1998 95: 13108-13113.

PMID- 28057731
VI  - 9
DP  - 2017
TI  - Extremely low genomic diversity of Rickettsia japonica distributed in Japan.
PG  - 124-133
AB  - Rickettsiae are obligate intracellular bacteria that have small genomes as a
      result of reductive evolution. Many Rickettsia species of the spotted fever group
      (SFG) cause tick-borne diseases known as "spotted fevers." The life cycle of SFG
      rickettsiae is closely associated with that of the tick, which is generally
      thought to act as a bacterial vector and reservoir that maintains the bacterium
      through transstadial and transovarial transmission. Each SFG member is thought to
      have adapted to a specific tick species, thus restricting the bacterial
      distribution to a relatively limited geographic region. These unique features of
      SFG rickettsiae allow investigation of how the genomes of such biologically and
      ecologically specialized bacteria evolve after genome reduction and the types of
      population structures that are generated. Here, we performed a nationwide,
      high-resolution phylogenetic analysis of R. japonica, an etiological agent of
      Japanese spotted fever that is distributed in Japan and Korea. The comparison of
      complete or nearly complete sequences obtained from 31 R. japonica strains
      isolated from various sources in Japan over the past 30 years demonstrated an
      extremely low level of genomic diversity. In particular, only 34 single
      nucleotide polymorphisms were identified among the 27 strains of the major
      lineage containing all clinical isolates and tick isolates from the three tick
      species. Our data provide novel insights into the biology and genome evolution of
      R. japonica, including the possibilities of recent clonal expansion and a long
      generation time in nature due to the long dormant phase associated with tick life
      cycles.
AU  - Akter A et al
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2017 9: 124-133.

PMID- 
VI  - 38
DP  - 2004
TI  - New site-specific endonucleases F-TflI, F-TflII, and F-TflIV encoded by bacteriophage T5.
PG  - 530-537
AB  - Site-specific endonucleases F-TflI, F-TflII, and F-TflIV have been revealed, which belong to
      the H-N-H family and are encoded by ORFs
      located in the tRNA gene region of bacteriophage T5. It has been shown
      that endonuclease F-TflIV introduces a double-strand break in a 17-bp
      pseudopalindromic DNA sequence to yield 1-nt 3'-protruding ends. Unlike
      F-TflIV, F-TflI, and F-TflII introduce single-strand breaks in
      asymmetrical, highly degenerate sequences, each cleaving only one
      (template or coding) strand. Amino acid sequence analysis has revealed
      a high homology of the enzymes in the region of the H-N-H motif and in
      the putative C-terminal catalytic domain. The N-terminal region of
      F-TflIV proved to be homologous to the HTH domain of LuxR-related
      transcriptional regulators, which is responsible for DNA recognition
      and binding. The N-terminal regions of F-TflI and F-TflII contain a
      composite motif NUMOD4, which is characteristic of a putative
      recognition domain of some H-N-H endonucleases. A two-domain structure,
      with the N-terminal recognition and C-terminal catalytic domains, and
      evolutionary origin via recombination of the catalytic and recognition
      domain-coding regions are proposed for F-TflI, F-TflII, and F-TflIV.
AU  - Akulenko NV
AU  - Ivashina TV
AU  - Shaloiko LA
AU  - Shlyapnikov MG
AU  - Ksenzenko VN
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2004 38: 530-537.

PMID- Not carried by PubMed...
VI  - 14
DP  - 1988
TI  - New restriction endonuclease from the soil strain Bacillus megaterium 12.
PG  - 105-108
AB  - The soil strain Bacillus megaterium 12 carrying a restriction-modification
      system has been discovered.  A Type 2 restriction endonuclease has been
      partially purified.  Bme12I has been shown to be an isoschizomer of Sau3AI.
AU  - Akulinin GE
AU  - Getko GA
AU  - Repin VE
AU  - Degtyarev SK
PT  - Journal Article
TA  - Izv. Sib. Otd. Akad. Nauk SSSR
JT  - Izv. Sib. Otd. Akad. Nauk SSSR
SO  - Izv. Sib. Otd. Akad. Nauk SSSR 1988 14: 105-108.

PMID- 26847884
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Oceanobacillus picturae Heshi-B3, Isolated from Fermented Rice Bran in a Traditional Japanese Seafood Dish.
PG  - e01621-15
AB  - Oceanobacillus picturae strain Heshi-B3 was isolated from rice bran in a traditional fermented
      seafood dish named Heshiko, which was produced in Fukui
      Prefecture in Japan. Here, we report the draft genome sequence of O. picturae
      strain Heshi B-3.
AU  - Akuzawa S
AU  - Nagaoka J
AU  - Kanekatsu M
AU  - Kanesaki Y
AU  - Suzuki T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01621-15.

PMID- 27034503
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Paenibacillus amylolyticus Heshi-A3, Isolated from Fermented Rice Bran in a Japanese Fermented Seafood Dish.
PG  - e00218-16
AB  - Paenibacillus amylolyticusstrain Heshi-A3 was isolated in Fukui prefecture, Japan, from
      fermented rice bran in Heshiko, a traditional dish that is produced
      by aging salted mackerel with fresh rice bran at an ambient temperature for
      around 7 months to over one year. Here, we report the draft genome sequence
      ofPaenibacillus amylolyticusstrain Heshi-A3.
AU  - Akuzawa S
AU  - Nagaoka J
AU  - Kanekatsu M
AU  - Kubota E
AU  - Ohtake R
AU  - Suzuki T
AU  - Kanesaki Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00218-16.

PMID- 9532739
VI  - 160
DP  - 1998
TI  - BstB7SI (R/CCGGY), a thermostable isoschizomer of Cfr10I, from a strain of Bacillus stearothermophilus isolated from oil-contaminated soil in Kuwait.
PG  - 205-208
AB  - Isolates of thermophilic bacteria from desert soil in Kuwait, heavily
      contaminated with crude
      oil, have been screened for the presence of restriction endonuclease activity. One of the
      isolates (B7S),
      identified as Bacillus stearothermophilus, showed a high level of restriction endonuclease
      activity when a cell-
      free extract was incubated with lambda bacteriophage DNA at 65oC.  A type II restriction
      endonuclease
      (BstB7SI) has been partially purified from this isolate.  BstB7SI recognizes the six-base
      sequence RCCGGY
      (R=A or G; Y=T or C) and hydrolyses the phosphodiester bond in both strands of the
      DNA substrate
      between the first and second bases of the recognition sequence 5'-R/CCGGY-3' producing
      four-base 5'
      overhangs.  BstB7SI is therefore an isoschizomer of the mesophilic prototype restriction
      endonuclease
      Cfr10I.  BstB7SI has a pH optimum of 9.7, requires 10 mM MgCl2 and 75 mM NaCl for
      maximum activity,
      and retains full enzyme activity when incubated for 5 min at temperatures up to 70oC.
AU  - Al-Awadhi S
AU  - Welch SG
AU  - Smith KE
AU  - Williams RAD
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1998 160: 205-208.

PMID- 24604653
VI  - 2
DP  - 2014
TI  - Whole-Genome Sequencing and Annotation of a Clinical Isolate of Mycobacterium tuberculosis from Mumbai, India.
PG  - e00154-14
AB  - We report here the annotated genome sequence of a clinical isolate of Mycobacterium
      tuberculosis from Mumbai, India.
AU  - Al-Rashdi ASA
AU  - Jadhav BL
AU  - Deshpande T
AU  - Deshpande U
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00154-14.

PMID- 25359913
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Two Vibrionaceae Species, Vibrio ponticus C121 and Photobacterium aphoticum C119, Isolated as Coral Reef Microbiota.
PG  - e01095-14
AB  - Here, the draft genome sequences of two Vibrionaceae, Vibrio ponticus C121 and Photobacterium
      aphoticum C119, which were isolated from the coral reef vicinity
      in Okinawa, Japan, are reported. The genome provides further insight into the
      genomic plasticity, biocomplexity, and ecophysiology, including pathogenicity and
      evolution, of these genera.
AU  - Al-Saari N
AU  - Meirelles PM
AU  - Mino S
AU  - Suda W
AU  - Oshima K
AU  - Hattori M
AU  - Ohkuma M
AU  - Thompson FL
AU  - Gomez-Gil B
AU  - Sawabe T
AU  - Sawabe T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01095-14.

PMID- 28963208
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Bacillus subtilis AS2, a Heavy Crude Oil-Degrading and Biosurfactant-Producing Bacterium Isolated from a Soil Sample.
PG  - e00969-17
AB  - Here, we report the draft genome sequence of Bacillus subtilis AS2 that was isolated from
      heavy crude oil-contaminated soil samples from sludge pits of an
      Omani heavy-oil field. B. subtilis AS2 was able to biodegrade heavy crude oil and
      produce biosurfactant. In order to provide a better understanding of the
      biodegradation mechanism and biosynthesis of metabolites, the B. subtilis AS2
      genome was sequenced and compared to those of other B. subtilis strains.
AU  - Al-Sayegh A
AU  - Al-Wahaibi Y
AU  - Joshi S
AU  - Al-Bahry S
AU  - Elshafie A
AU  - Al-Bemani A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00969-17.

PMID- 22887656
VI  - 194
DP  - 2012
TI  - Whole-Genome Shotgun Sequence of the Sulfur-Oxidizing Chemoautotroph Pseudaminobacter salicylatoxidans KCT001.
PG  - 4743-4744
AB  - The facultatively sulfur-oxidizing chemolithoautotrophic alphaproteobacterium Pseudaminobacter
      salicylatoxidans KCT001 (MTCC 7265) belongs to the family
      Phyllobacteriaceae of the order Rhizobiales. Analysis of its genome offers
      valuable insight into the adaptive specializations and evolution of free-living
      soil bacteria that are phylogenetically closely related to symbiotic and invasive
      rhizobacteria.
AU  - Alam M
AU  - Roy C
AU  - Pyne P
AU  - Agarwal A
AU  - George A
AU  - Ghosh W
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4743-4744.

PMID- 
VI  - 10A
DP  - 2006
TI  - Characterization of the cytotoxic effect of a chimeric restriction enzyme, H1 degrees-FokI.
PG  - 147-159
AB  - Our primary goal was to create an efficient cytotoxic agent. To do this, we created a gene
      that expresses a chimeric hybrid of the linker
      histone, H1(0) and the nuclease domain of the type IIs restriction
      enzyme, FokI. The linkage of the FokI nuclease domain to a high
      affinity but low DNA-sequence-specificity binding protein is unique. It
      is highly cytotoxic. We demonstrate, by transiently transfecting 3T3
      mouse fibroblasts, that 63% of the cells taking up the chimeric gene
      are killed. The chimeric protein is localized to the nucleus. An
      extract of the protein produced in E. coli degrades DNA, indicating
      that it is nucleolytically active. The ultimate mechanism through which
      the chimeric protein produces cell death is likely through the
      induction of apoptosis.
AU  - Alam N
AU  - Sittman DB
PT  - Journal Article
TA  - Gene Ther. Mol. Biol.
JT  - Gene Ther. Mol. Biol.
SO  - Gene Ther. Mol. Biol. 2006 10A: 147-159.

PMID- 16348479
VI  - 57
DP  - 1991
TI  - Molecular characterization of three small isometric-headed bacteriophages which vary in their sensitivity to the lactococcal phage resistance plasmid pTR2030.
PG  - 1346-1353
AB  - Lactococcus lactis LMA12-4 is a pTR2030 transconjugant that has been used as an
      industrial starter culture because of its resistance to phages predominant in
      cheese plants.  Plasmid pTR2030 interferes with susceptible phages in this host
      strain via two mechanisms, restriction and modification (R/M) and abortive
      infection (Hsp).  After prolonged use of LMA12-4 transconjugants in the
      industry, two different bacteriophages, designated nck202.Phi 48 (Phi 48) and
      nck202.Phi 50 (Phi 50), were isolated which could produce plaques on LMA12-4
      containing pTR2030.  In this study, these two phages were characterized and
      compared with a third phage, nck202.Phi 31 (Phi 31), which is susceptible to
      both the R/M and Hsp activities encoded by pTR2030.  Phage Phi-48 was not
      susceptible to inhibition by Hsp, whereas Phi 50 was unaffected by either the
      R/M or Hsp mechanisms.  All three were small isometric-headed phages, but small
      differences were noted between the phages in the structural details of the tail
      base plate, susceptibility to chloroform treatment, and requirements for
      calcium infectivity.  The phage genomes were all between 29.9 and 31.9 kb in
      length.  Phages Phi 31 and Phi 48 harbored cohesive ends, whereas the phage Phi
      50 genome was circularly permuted, terminally redundant, and carried a putative
      packaging initiation site.  DNA-DNA hybridization experiments conducted between
      the phages revealed a common region in Phi 48 and Phi 50 that may correlate
      with the resistance of the two phages to the Hsp-abortive infection induced by
      pTR2030.  Phage Phi 50 also harbored DNA sequences that shared homology to
      pTR2030 in the region where R/M activities have been localized on the plasmid.
      Molecular characterization of the three phages localized regions within the
      genomes of the pTR2030-resistant phages that may be responsible for
      circumventing plasmid-encoded Hsp and R/M defense mechanisms in lactococci.
AU  - Alatossava T
AU  - Klaenhammer TR
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1991 57: 1346-1353.

PMID- 25908125
VI  - 3
DP  - 2015
TI  - Genome Sequence of Methanosarcina soligelidi SMA-21, Isolated from Siberian Permafrost-Affected Soil.
PG  - e00270-15
AB  - Here, we announce the genome sequence of Methanosarcina soligelidi SMA-21, an anaerobic
      methanogenic archaeon that was previously isolated from Siberian
      permafrost-affected soil. The sequencing of strain SMA-21 yielded a 4.06-Mb
      genome with 41.5% G+C content, containing a total of 2,647 open reading frames.
AU  - Alawi M
AU  - Shapiro N
AU  - Woyke T
AU  - Horn F
AU  - Bakermans C
AU  - Wagner D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00270-15.

PMID- 29177929
VI  - 31
DP  - 2017
TI  - Structure and dynamics of mesophilic variants from the homing endonuclease I-DmoI.
PG  - 1063-1072
AB  - I-DmoI, from the hyperthermophilic archaeon Desulfurococcus mobilis, belongs to the LAGLIDADG
      homing endonuclease protein family. Its members are highly specific
      enzymes capable of recognizing long DNA target sequences, thus providing
      potential tools for genome manipulation. Working towards this particular
      application, many efforts have been made to generate mesophilic variants of
      I-DmoI that function at lower temperatures than the wild-type. Here, we report a
      structural and computational analysis of two I-DmoI mesophilic mutants. Despite
      very limited structural variations between the crystal structures of these
      variants and the wild-type, a different dynamical behaviour near the cleavage
      sites is observed. In particular, both the dynamics of the water molecules and
      the protein perturbation effect on the cleavage site correlate well with the
      changes observed in the experimental enzymatic activity.
AU  - Alba J
AU  - Marcaida MJ
AU  - Prieto J
AU  - Montoya G
AU  - Molina R
AU  - D'Abramo M
PT  - Journal Article
TA  - J. Comput. Aided Mol. Des.
JT  - J. Comput. Aided Mol. Des.
SO  - J. Comput. Aided Mol. Des. 2017 31: 1063-1072.

PMID- 18813943
VI  - 218
DP  - 2008
TI  - Evolution of DNA-methylation machinery: DNA methyltransferases and methyl-DNA binding proteins in the amphioxus Branchiostoma floridae.
PG  - 691-701
AB  - DNA methylation is an epigenetic mark associated with gene regulation and cell memory,
      silencing of transposable elements, genomic
      imprinting, and repression of spurious transcription of duplicated
      sequences. These roles have varied widely during animal evolution and
      current functions depend on the specific methylation pattern of the
      species under consideration. The patterns of methylation are
      established, maintained, and translated into appropriate functional
      states by the DNA-methylation machinery, which includes three groups of
      methyltransferase enzymes, Dnmt1, Dnmt2 and Dnmt3, and five methyl-DNA
      binding proteins, Mbd1, Mbd2, Mbd3, Mbd4, and MeCP2. In this study, I
      have identified the members of the Dnmt and the Mbd gene families in
      the cephalochordate amphioxus (Branchiostoma floridae), the most basal
      extant chordate and one of the closest sister groups of vertebrates.
      Database searches, phylogenetic studies and protein domain analyses
      revealed the presence of the three major groups of Dnmt enzymes in the
      cephalochordate genome, whereas only two Mbd members, Mbd2/3 and Mbd4,
      were found. Analysis of the amphioxus methylation machinery suggested
      that the complexity and the structural organization of cephalochordate
      methyltransferases do not differ substantially from those of current
      vertebrate enzymes, while new Mbd proteins arose in vertebrates, which
      perhaps minimized certain collateral effects associated with the major
      genomic changes that occurred during the invertebrate-vertebrate
      transition.
AU  - Albalat R
PT  - Journal Article
TA  - Dev. Genes Evol.
JT  - Dev. Genes Evol.
SO  - Dev. Genes Evol. 2008 218: 691-701.

PMID- 27257193
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Bacillus subtilis ALBA01, a Strain with Antagonistic Activity against the Soilborne Fungal Pathogen of Onion Setophoma terrestris.
PG  - e00455-16
AB  - Bacillus subtilis is a nonpathogenic bacterium that lives in soil and has long been used as
      biological control agent in agriculture. Here, we report the genome
      sequence of a B. subtilis strain isolated from rhizosphere of onion that shows
      strong biological activity against the soilborne fungal pathogen Setophoma
      terrestris.
AU  - Albarracin OAG
AU  - Tobares RA
AU  - Ducasse DA
AU  - Smania AM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00455-16.

PMID- 25059872
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Multidrug-Resistant Clinical Isolate Dermabacter hominis 1368.
PG  - e00728-14
AB  - Dermabacter hominis is a common colonizer of the healthy human skin and is rarely detected as
      an opportunistic human pathogen. The genome sequence of the
      multidrug-resistant D. hominis strain 1368, isolated from blood cultures of a
      pyelonephritis patient, provides insights into the repertoire of antibiotic
      resistance genes.
AU  - Albersmeier A
AU  - Bomholt C
AU  - Glaub A
AU  - Ruckert C
AU  - Soriano F
AU  - Fernandez-Natal I
AU  - Tauch A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00728-14.

PMID- 29930064
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Bifidobacterium longum UMA026, Isolated from Holstein Dairy Cow Feces.
PG  - e00559-18
AB  - The draft genome sequence of an isolate identified as Bifidobacterium longum is communicated
      herein. This strain was isolated from the feces of a 1-week-old
      Holstein dairy cow. The draft genome of this Bifidobacterium longum isolate is
      2.39 Mb in length, with a G+C content of 60.1%.
AU  - Albert K
AU  - Sela DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00559-18.

PMID- 28663296
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Alloscardovia macacae UMA81211 and UMA81212, Isolated from the Feces of a Rhesus Macaque (Macaca mulatta).
PG  - e00581-17
AB  - Here, we provide the draft genome sequences of two isolates identified as Alloscardovia
      macacae These bacteria originated from the feces of a rhesus
      macaque. The draft genomes of both Alloscardovia macacae isolates are ~1.8 Mb in
      length, with a G+C content of 56.1%.
AU  - Albert K
AU  - Sela DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00581-17.

PMID- 29746549
VI  - 13
DP  - 2018
TI  - Circularly permuted variants of two CG-specific prokaryotic DNA methyltransferases.
PG  - e0197232
AB  - The highly similar prokaryotic DNA (cytosine-5) methyltransferases (C5-MTases) M.MpeI and
      M.SssI share the specificity of eukaryotic C5-MTases (5'-CG), and can
      be useful research tools in the study of eukaryotic DNA methylation and
      epigenetic regulation. In an effort to improve the stability and solubility of
      complementing fragments of the two MTases, genes encoding circularly permuted
      (CP) variants of M.MpeI and M.SssI were created, and cloned in a plasmid vector
      downstream of an arabinose-inducible promoter. MTase activity of the CP variants
      was tested by digestion of the plasmids with methylation-sensitive restriction
      enzymes. Eleven of the fourteen M.MpeI permutants and six of the seven M.SssI
      permutants had detectable MTase activity as indicated by the full or partial
      protection of the plasmid carrying the cpMTase gene. Permutants cp62M.MpeI and
      cp58M.SssI, in which the new N-termini are located between conserved motifs II
      and III, had by far the highest activity. The activity of cp62M.MpeI was
      comparable to the activity of wild-type M.MpeI. Based on the location of the
      split sites, the permutants possessing MTase activity can be classified in ten
      types. Although most permutation sites were designed to fall outside of conserved
      motifs, and the MTase activity of the permutants measured in cell extracts was in
      most cases substantially lower than that of the wild-type enzyme, the high
      proportion of circular permutation topologies compatible with MTase activity is
      remarkable, and is a new evidence for the structural plasticity of C5-MTases. A
      computer search of the REBASE database identified putative C5-MTases with CP
      arrangement. Interestingly, all natural circularly permuted C5-MTases appear to
      represent only one of the ten types of permutation topology created in this work.
AU  - Albert P
AU  - Varga B
AU  - Zsibrita N
AU  - Kiss A
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2018 13: e0197232.

PMID- 2915934
VI  - 17
DP  - 1989
TI  - Improved control of partial DNA restriction enzyme digest in agarose using limiting concentrations of Mg++.
PG  - 808
AB  - Partial digests of DNA for cloning experiments are usually performed using
      either the quantity of restriction enzyme or incubation time, or both, as
      controlling factors.  However, we have found that more precise and reproducible
      partial digests are obtained, when a limiting concentration of the required
      cofactor Mg++ is used.  This method is especially useful for partial digests of
      DNA contained in agarose.  In agarose, diffusion time of the much smaller Mg++
      ion is shorter than that of a restriction enzyme.  The result is a more
      homogenous digestion of the DNA throughout the agarose block.  Since the
      concentration of Mg++ in this procedure is usually only 10% or less of that
      normally used, the digestion is easily interrupted by excess EDTA.  We have
      successfully applied this partial digestion technique with EcoRI to obtain
      large human DNA fragments that have been used to construct artificial yeast
      chromosomes (YAC) of several hundred kb in length.
AU  - Albertsen HM
AU  - Le Paslier D
AU  - Abderrahim H
AU  - Dausset J
AU  - Cann H
AU  - Cohen D
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 808.

PMID- 23707974
VI  - 31
DP  - 2013
TI  - Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes.
PG  - 533-538
AB  - Reference genomes are required to understand the diverse roles of microorganisms in ecology,
      evolution, human and animal health, but most species remain uncultured. Here we present a
      sequence composition-independent approach to recover high-quality microbial genomes from
      deeply sequenced metagenomes. Multiple metagenomes of the same community, which differ in
      relative population abundances, were used to assemble 31 bacterial genomes, including rare
      (<1% relative abundance) species, from an activated sludge bioreactor. Twelve genomes were
      assembled into complete or near-complete chromosomes. Four belong to the candidate bacterial
      phylum TM7 and represent the most complete genomes for this phylum to date (relative
      abundances, 0.06-1.58%). Reanalysis of published metagenomes reveals that differential
      coverage binning facilitates recovery of more complete and higher fidelity genome bins than
      other currently used methods, which are primarily based on sequence composition. This approach
      will be an important addition to the standard metagenome toolbox and greatly improve access to
      genomes of uncultured microorganisms.
AU  - Albertsen M
AU  - Hugenholtz P
AU  - Skarshewski A
AU  - Nielsen KL
AU  - Tyson GW
AU  - Nielsen PH
PT  - Journal Article
TA  - Nat. Biotechnol.
JT  - Nat. Biotechnol.
SO  - Nat. Biotechnol. 2013 31: 533-538.

PMID- 21926159
VI  - 40
DP  - 2012
TI  - The Caulobacter crescentus DNA-(adenine-N6)-methyltransferase CcrM methylates DNA in a distributive manner.
PG  - 1708-1716
AB  - 
AU  - Albu RF
AU  - Jurkowski TP
AU  - Jeltsch A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: 1708-1716.

PMID- 22639453
VI  - 13
DP  - 2012
TI  - DNA Interaction of the CcrM DNA Methyltransferase: A Mutational and Modeling Study.
PG  - 1304-1311
AB  - Caulobacter crescentus CcrM is a DNA-(adenine N6)-methyltransferase that methylates adenine in
      the sequence GANTC with high specificity. To
      investigate its mechanism of DNA recognition, we used the crystal
      structure of a related methyltransferase (M1.MboII, which modifies
      GAAGA) as a starting point, and docked into it a DNA substrate to
      identify the protein regions that approach the DNA. After alignment of
      CcrM and M1.MboII, we identified four candidate regions in CcrM to
      contain residues involved in DNA recognition. We mutated 20 amino acid
      residues within these regions, purified the CcrM variants, and
      determined their DNA-binding and catalytic activity on a cognate GANTC
      substrate and on nine near-cognate substrates, each of which contained
      a single base-pair substitution in the recognition sequence.
      Altogether, we identified four residues in two of the regions,
      mutations of which resulted in a strong (>100-fold) reduction of
      methylation activity. Our data show that DNA recognition by CcrM is a
      cooperative process, because disruption of critical contacts led to
      loss of catalytic activity but not to a relaxation in specificity. In
      addition, we identified a change in the readout of the fifth base pair
      in the GANTC sequence with two other CcrM variants that showed smaller
      reductions in overall activity. Based on this and the sequence
      alignment of CcrM with other DNA methyltransferases of same or related
      recognition sequence, we propose roles for these two regions in DNA
      recognition by CcrM.
AU  - Albu RF
AU  - Zacharias M
AU  - Jurkowski TP
AU  - Jeltsch A
PT  - Journal Article
TA  - Chembiochem
JT  - Chembiochem
SO  - Chembiochem 2012 13: 1304-1311.

PMID- 28883150
VI  - 5
DP  - 2017
TI  - Genome Sequence of Ralstonia pseudosolanacearum Strains with Compatible and Incompatible Interactions with the Major Tomato Resistance Source Hawaii 7996.
PG  - e00982-17
AB  - We report here the complete genome sequences of two Ralstonia pseudosolanacearum  strains,
      isolated from the warm northeast region of Brazil. They display
      divergent (compatible versus incompatible) interactions with the resistant tomato
      line Hawaii 7996. Polymorphisms were detected in a subset of effector genes that
      might be associated with these contrasting phenotypes.
AU  - Albuquerque GMR
AU  - Souza EB
AU  - Silva AMF
AU  - Lopes CA
AU  - Boiteux LS
AU  - Fonseca MEN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00982-17.

PMID- 18408155
VI  - 105
DP  - 2008
TI  - The genome of Bacillus coahuilensis reveals adaptations essential for survival in the relic of an ancient marine environment.
PG  - 5803-5808
AB  - The Cuatro Cienegas Basin (CCB) in the central part of the Chihuahan desert (Coahuila, Mexico)
      hosts a wide diversity of microorganisms
      contained within springs thought to be geomorphological relics of an
      ancient sea. A major question remaining to be answered is whether bacteria
      from CCB are ancient marine bacteria that adapted to an oligotrophic
      system poor in NaCl, rich in sulfates, and with extremely low phosphorus
      levels (<0.3 muM). Here, we report the complete genome sequence of
      Bacillus coahuilensis, a sporulating bacterium isolated from the water
      column of a desiccation lagoon in CCB. At 3.35 Megabases this is the
      smallest genome sequenced to date of a Bacillus species and provides
      insights into the origin, evolution, and adaptation of B. coahuilensis to
      the CCB environment. We propose that the size and complexity of the B.
      coahuilensis genome reflects the adaptation of an ancient marine bacterium
      to a novel environment, providing support to a "marine isolation origin
      hypothesis" that is consistent with the geology of CCB. This genomic
      adaptation includes the acquisition through horizontal gene transfer of
      genes involved in phosphorous utilization efficiency and adaptation to
      high-light environments. The B. coahuilensis genome sequence also revealed
      important ecological features of the bacterial community in CCB and offers
      opportunities for a unique glimpse of a microbe-dominated world last seen
      in the Precambrian.
AU  - Alcaraz LD et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2008 105: 5803-5808.

PMID- 20504335
VI  - 11
DP  - 2010
TI  - Understanding the evolutionary relationships and major traits of Bacillus through comparative genomics.
PG  - 332
AB  - BACKGROUND: The presence of Bacillus in very diverse environments reflects
      the versatile metabolic capabilities of a widely distributed genus.
      Traditional phylogenetic analysis based on limited gene sampling is not
      adequate for resolving the genus evolutionary relationships. By
      distinguishing between core and pan-genome, we determined the evolutionary
      and functional relationships of known Bacillus. RESULTS: Our analysis is
      based upon twenty complete and draft Bacillus genomes, including a newly
      sequenced Bacillus isolate from an aquatic environment that we report for
      the first time here. Using a core genome, we were able to determine the
      phylogeny of known Bacilli, including aquatic strains whose position in
      the phylogenetic tree could not be unambiguously determined in the past.
      Using the pan-genome from the sequenced Bacillus, we identified functional
      differences, such as carbohydrate utilization and genes involved in signal
      transduction, which distinguished the taxonomic groups. We also assessed
      the genetic architecture of the defining traits of Bacillus, such as
      sporulation and competence, and showed that less than one third of the B.
      subtilis genes are conserved across other Bacilli. Most variation was
      shown to occur in genes that are needed to respond to environmental cues,
      suggesting that Bacilli have genetically specialized to allow for the
      occupation of diverse habitats and niches. CONCLUSIONS: The aquatic
      Bacilli are defined here for the first time as a group through the
      phylogenetic analysis of 814 genes that comprise the core genome. Our data
      distinguished between genomic components, especially core vs. pan-genome
      to provide insight into phylogeny and function that would otherwise be
      difficult to achieve. A phylogeny may mask the diversity of functions,
      which we tried to uncover in our approach. The diversity of sporulation
      and competence genes across the Bacilli was unexpected based on previous
      studies of the B. subtilis model alone. The challenge of uncovering the
      novelties and variations among genes of the non-subtilis groups still
      remains. This task will be best accomplished by directing efforts toward
      understanding phylogenetic groups with similar ecological niches.
AU  - Alcaraz LD
AU  - Moreno-Hagelsieb G
AU  - Eguiarte LE
AU  - Souza V
AU  - Herrera-Estrella L
AU  - Olmedo-Alvarez G
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2010 11: 332.

PMID- 21183675
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Algoriphagus sp. PR1, Bacterial Prey of a Colony-Forming Choanoflagellate.
PG  - 1485-1486
AB  - Bacteria are the primary food source of choanoflagellates, the closest known relatives of
      animals. Studying signaling interactions between the
      Gram-negative Bacteroidetes bacterium Algoriphagus sp. PR1 and its
      predator, the choanoflagellate Salpingoeca rosetta, provides a promising
      avenue for testing hypotheses regarding the involvement of bacteria in
      animal evolution. Here we announce the complete genome sequence of
      Algoriphagus sp. PR1 and initial findings from its annotation.
AU  - Alegado RA
AU  - Ferriera S
AU  - Nusbaum C
AU  - Young SK
AU  - Zeng Q
AU  - Imamovic A
AU  - Fairclough SR
AU  - King N
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 1485-1486.

PMID- 19027788
VI  - 61
DP  - 2009
TI  - Characterization of pRS5: A theta-type plasmid found in a strain of Pediococcus pentosaceus isolated from wine that can be used to generate cloning vectors for lactic acid bacteria.
PG  - 130-134
AB  - The nucleotide sequence of pRS5 (10153 bp) is reported. Through sequence analysis, 9 open
      reading frames (ORFs) were identified and the
      following features observed: a region likely involved in replication
      whose structural features indicate that pRS5 belongs to the pUCL287
      group of theta-type replicons, and hypothetical proteins putatively
      involved in plasmid copy number control, restriction-modification
      system, toxin-antitoxin system and a putative integrase. Shuttle
      vectors for Escherichia coli and lactic acid bacteria (LAB) as well as
      a small cloning vector for direct use in LAB were constructed using the
      replication region of pRS5. The ability of such vectors to accept and
      express other genes was assessed. All pRS5-derivatives were maintained
      at a high rate over 200 generations without selective pressure.
AU  - Alegre MT
AU  - Rodriguez MC
AU  - Mesas JM
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 2009 61: 130-134.

PMID- 30533888
VI  - 7
DP  - 2018
TI  - Draft Genome Sequence of a Streptomycete Isolated from Potato Common Scab Lesions in the State of Sinaloa, Mexico.
PG  - e00827-18
AB  - Streptomyces sp. strain V2 was isolated from potato scab lesions in the state of  Sinaloa,
      Mexico, and appears to be responsible for outbreaks in the area. The
      thaxtomin cluster was found in the approximately 10.2-Mb genome; this cluster is
      associated with potato common scab disease in other potato pathogens.
AU  - Alejo-Viderique A
AU  - Contreras-Castro L
AU  - Felix-Gastelum R
AU  - Maldonado LA
AU  - Quintana ET
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e00827-18.

PMID- 23950137
VI  - 1
DP  - 2013
TI  - Genome Sequence of the Probiotic Strain Lactobacillus rhamnosus (Formerly Lactobacillus casei) LOCK900.
PG  - e00640-13
AB  - Lactobacillus rhamnosus LOCK900 fulfills the criteria required for probiotic strains. In this
      study, we report a whole-genome sequence of this isolate and
      compare it with other L. rhamnosus complete genome sequences already published.
AU  - Aleksandrzak-Piekarczyk T
AU  - Koryszewska-Baginska A
AU  - Bardowski J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00640-13.

PMID- 24435874
VI  - 2
DP  - 2014
TI  - Genomic Sequencing of Two Coffee-Infecting Strains of Xylella fastidiosa Isolated from Brazil.
PG  - e01190-13
AB  - Here, we describe the draft genome sequences of two Xylella fastidiosa strains: Xf6c and Xf32,
      which have been obtained from infected coffee plants in Brazil,
      and are associated with the disease known as coffee leaf scorch (CLS).
AU  - Alencar VC
AU  - Barbosa D
AU  - Santos DS
AU  - Oliveira AC
AU  - de Oliveira RC
AU  - Nunes LR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01190-13.

PMID- 25838487
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Aneurinibacillus migulanus Strain Nagano.
PG  - e00232-15
AB  - Aneurinibacillus migulanus is characterized by inhibition of growth of a range of
      plant-pathogenic bacteria and fungi. Here, we report the high-quality draft
      genome sequences of A. migulanus Nagano.
AU  - Alenezi FN
AU  - Weitz HJ
AU  - Belbahri L
AU  - Ben Rebah H
AU  - Luptakova L
AU  - Jaspars M
AU  - Woodward S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00232-15.

PMID- 25838489
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Aneurinibacillus migulanus NCTC 7096.
PG  - e00234-15
AB  - Aneurinibacillus migulanus has biocontrol activities against fungal, fungus-like, and
      bacterial plant pathogens with different levels of efficacy depending on the
      target pathogens. Here, we report the high-quality draft genome sequence of A.
      migulanus NCTC 7096.
AU  - Alenezi FN
AU  - Weitz HJ
AU  - Belbahri L
AU  - Nidhal J
AU  - Luptakova L
AU  - Jaspars M
AU  - Woodward S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00234-15.

PMID- 359411
VI  - 14
DP  - 1978
TI  - R.M.EcoRI coding plasmids derived from recombinant R factor.
PG  - 1466-1469
AB  - Bacteriophages P1vir and Mu-1 have been used for transductional shortening of a recombinant R
      factor coding for R.M.EcoRI isolated by Yoshimori et al.  P1 shortening made possible the
      isolation of transmissive isogenic plasmids coding for R.M.EcoRI and differing in antibiotic
      resistance, as well as isolation of plasmids differing only in their R.M.EcoRI genes.  Mu-1
      mediated shortening favored the isolation of transmissive R plasmids having lost the
      resistance to chloramphenicol but having all other markers of the recombinant R factor intact.
      The data are interpreted in support of Yoshimori et al.'s supposition concerning the
      existence of R.M.EcoRI coding recombinant R factor of Escherichia coli.
AU  - Aleshkin GI
AU  - Skavronskaya AG
PT  - Journal Article
TA  - Genetika
JT  - Genetika
SO  - Genetika 1978 14: 1466-1469.

PMID- 3025697
VI  - 4
DP  - 1985
TI  - Plasmid recombination stimulated by restriction endonuclease EcoRI in vivo: formation of recombinant plasmids in recA+-cells of E. coli.
PG  - 15-21
AB  - The possible participation of restriction endonuclease EcoRI in recombination of compatible
      nonhomologous plasmids in E. coli cells has been studied.  To study the process, plasmids RP4
      and R245 have been transferred by conjugation into the recipient cells of E. coli harboring
      one of isogenic plasmids, pSA14 and pSA25, different for the genes coding restriction
      endonuclease EcoRI.  The genetic analysis of transconjugant phenotypes, coded by the plasmids,
      has permitted to register the recombinant plasmids after compatibility of parent plasmids in
      E. coli cells.  Recombination of plasmid RP4 with the plasmid pSA14, carrying EcoRI genes, has
      been registered in E. coli cells, producing the restriction endonuclease, while plasmid
      recombination has not been found in the cells harboring plasmid pSA25, isogenic for all genes,
      except for EcoRI genes, with plasmid pSA14.  Restriction endonuclease EcoRI is concluded to
      stimulate site specific recombination of nonhomologous compatible plasmids in vivo.
      EcoRI-mediated recombination of plasmid R245 with plasmid pSA14 is discussed.
AU  - Aleshkin GI
AU  - Strikhanov SN
AU  - Skavronskaya AG
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1985 4: 15-21.

PMID- 27198015
VI  - 4
DP  - 2016
TI  - The Draft Genome Sequence of Paenibacillus polymyxa Strain CCI-25 Encompasses High Potential for Secondary Metabolite Production.
PG  - e00366-16
AB  - We report here the draft genome sequence of Paenibacillus polymyxa strain CCI-25, which
      displays strong antifungal and antibacterial activities in vitro The genome
      encompasses nonribosomal peptide synthetases predicted to encode a tridecaptin,
      polymyxin, fusaricidin, an iturin-like synthetase, a lantibiotic similar to
      paenicidin A, as well as a type 1 polyketide synthase.
AU  - Aleti G
AU  - Antonielli L
AU  - Corretto E
AU  - Nikolic B
AU  - Sessitsch A
AU  - Brader G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00366-16.

PMID- 27469947
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the Mycobacterium tuberculosis Complex Pathogen M. mungi, Identified in a Banded Mongoose (Mungos mungo) in Northern Botswana.
PG  - e00471-16
AB  - Mycobacterium mungi, a Mycobacterium tuberculosis complex pathogen, has emerged in banded
      mongoose in northern Botswana and Northwest Zimbabwe. The pathogen is
      transmitted through infected secretions used in olfactory communication behavior
      (K. A. Alexander, C. E. Sanderson, M. H. Larsen, S. Robbe-Austerman, M. C.
      Williams, and M. V. Palmer, mBio 7(3):e00281-16, 2016,
      http://dx.doi.org/10.1128/mBio.00281-16). We announce here the draft genome
      sequence of this emerging pathogen.
AU  - Alexander KA
AU  - Larsen MH
AU  - Robbe-Austerman S
AU  - Stuber TP
AU  - Camp PM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00471-16.

PMID- 27563039
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Neisseria weaveri Strain NCTC13585.
PG  - e00815-16
AB  - Neisseria weaveri is a commensal organism of the canine oral cavity and an occasional
      opportunistic human pathogen which is associated with dog bite wounds.
      Here we report the first complete genomic sequence of the N. weaveri NCTC13585
      (CCUG30381) strain, which was originally isolated from a patient with a canine
      bite wound.
AU  - Alexander S
AU  - Fazal MA
AU  - Burnett E
AU  - Deheer-Graham A
AU  - Oliver K
AU  - Holroyd N
AU  - Parkhill J
AU  - Russell JE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00815-16.

PMID- 27660796
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Plesiomonas shigelloides Type Strain NCTC10360.
PG  - e01031-16
AB  - Plesiomonas shigelloides is a Gram-negative rod within the Enterobacteriaceae family. It is a
      gastrointestinal pathogen of increasing notoriety, often
      associated with diarrheal disease. P. shigelloides is waterborne, and infection
      is often linked to the consumption of seafood. Here, we describe the first
      complete genome for P. shigelloides type strain NCTC10360.
AU  - Alexander S
AU  - Fazal MA
AU  - Burnett E
AU  - Deheer-Graham A
AU  - Oliver K
AU  - Holroyd N
AU  - Parkhill J
AU  - Russell JE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01031-16.

PMID- 28163827
VI  - 12
DP  - 2017
TI  - The complete genome sequence of the yogurt isolate Streptococcus thermophilus ACA-DC 2.
PG  - 18
AB  - Streptococcus thermophilus ACA-DC 2 is a newly sequenced strain isolated from traditional
      Greek yogurt. Among the 14 fully sequenced strains of S. thermophilus
      currently deposited in the NCBI database, the ACA-DC 2 strain has the smallest
      chromosome, containing 1,731,838 bp. The annotation of its genome revealed the
      presence of 1,850 genes, including 1,556 protein-coding genes, 70 RNA genes and
      224 potential pseudogenes. A large number of pseudogenes were identified. This
      was also accompanied by the absence of pathogenic features suggesting evolution
      of strain ACA-DC 2 through genome decay processes, most probably due to
      adaptation to the milk ecosystem. Analysis revealed the existence of one complete
      lactose-galactose operon, several proteolytic enzymes, one exopolysaccharide
      cluster, stress response genes and four putative antimicrobial peptides.
      Interestingly, one CRISPR-cas system and one orphan CRISPR, both carrying only
      one spacer, were predicted indicating low activity or inactivation of the cas
      proteins. Nevertheless, four putative restriction-modification systems were
      determined that may compensate any deficiencies of the CRISPR-cas system.
      Furthermore, whole genome phylogeny indicated three distinct clades within S.
      thermophilus. Comparative analysis among selected strains representative for each
      clade, including strain ACA-DC 2, revealed a high degree of conservation at the
      genomic scale, but also strain specific regions. Unique genes and genomic islands
      of strain ACA-DC 2 contained a number of genes potentially acquired through
      horizontal gene transfer events, that could be related to important technological
      properties for dairy starters. Our study suggests genomic traits in strain ACA-DC
      2 compatible to the production of dairy fermented foods.
AU  - Alexandraki V
AU  - Kazou M
AU  - Blom J
AU  - Pot B
AU  - Tsakalidou E
AU  - Papadimitriou K
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 18.

PMID- 28839034
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of the Yogurt Isolate Lactobacillus delbrueckii subsp. bulgaricus ACA-DC 87.
PG  - e00868-17
AB  - Lactobacillus delbrueckii subsp. bulgaricus is widely used in the production of yogurt and
      cheese. In this study, we present the complete genome sequence of L.
      delbrueckii subsp. bulgaricus ACA-DC 87 isolated from traditional Greek yogurt.
      Whole-genome analysis may reveal desirable technological traits of the strain for
      dairy fermentations.
AU  - Alexandraki V
AU  - Kazou M
AU  - Pot B
AU  - Tsakalidou E
AU  - Papadimitriou K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00868-17.

PMID- 25953171
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Polyhydroxyalkanoate-Producing Bacterium Burkholderia sacchari LMG 19450 Isolated from Brazilian Sugarcane Plantation  Soil.
PG  - e00313-15
AB  - Burkholderia sacchari LMG 19450, isolated from the soil of a sugarcane plantation in Brazil,
      accumulates large amounts of polyhydroxyalkanoates from sucrose,
      xylose, other carbohydrates, and organic acids. We present the draft genome
      sequence of this industrially relevant bacterium, which is 7.2 Mb in size and has
      a G+C content of 64%.
AU  - Alexandrino PM
AU  - Mendonca TT
AU  - Guaman BLP
AU  - Cherix J
AU  - Lozano-Sakalauskas GC
AU  - Fujita A
AU  - Ramos FE
AU  - Long P
AU  - Padilla G
AU  - Taciro MK
AU  - Gomez JG
AU  - Silva LF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00313-15.

PMID- 1406385
VI  - 54
DP  - 1992
TI  - Methylococcus whittenburyi - producer of MwhI, new isoschizomer of HpaI.
PG  - 70-73
AB  - Type II specific restriction endonucleases (restrictases) draw so much interest not only
      because gene engineering is based on using them but also because they are convenient objects
      to solve the problem of nucleic acid-protein recognition. The list of these enzymes is being
      enlarged, though some of them are more preferable for practical use. HpaI (from Haemophilus
      parainfluenzae) is one such enzyme. A restriction endonuclease has been detected in
      Methylococcus whittenburyi recognizing the same nucleotide sequence as HpaI. The new
      isoschizomer was named MwhI according to the existing nomenclature. As M. whittenburyi (as
      compared to H. parainfluenze) grows on simple mineral medium, is not pathogenic, comprises a
      single enzyme, it might be promising for enzyme production.
AU  - Alexeyev MF
AU  - Gunkovskaya NV
AU  - Romanovskaya VA
AU  - Malashenko YR
PT  - Journal Article
TA  - Mikrobiol. Zh.
JT  - Mikrobiol. Zh.
SO  - Mikrobiol. Zh. 1992 54: 70-73.

PMID- 24831154
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Coprothermobacter proteolyticus DSM 5265.
PG  - e00470-14
AB  - Here we present the complete 1,424,912-bp genome sequence of Coprothermobacter proteolyticus
      DSM 5265, isolated from a thermophilic digester fermenting tannery
      wastes and cattle manure.
AU  - Alexiev A
AU  - Coil DA
AU  - Badger JH
AU  - Enticknap J
AU  - Ward N
AU  - Robb FT
AU  - Eisen JA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00470-14.

PMID- 27151785
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Klebsiella pneumoniae UCD-JA29 Isolated from a Patient with Sepsis.
PG  - e00234-16
AB  - Here, we present the 6,155,188-bp draft genome sequence of Klebsiella pneumoniae  UCD-JA29,
      isolated from blood cultures from a patient with sepsis at the
      University of California, Davis Medical Center in Sacramento, California, USA.
AU  - Alexiev A
AU  - Coil DA
AU  - Jospin G
AU  - Eisen JA
AU  - Adams JY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00234-16.

PMID- 26966219
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Cobetia sp. UCD-24C, Isolated from Roots and Leaves of the Seagrass Zostera marina.
PG  - e00116-16
AB  - Here, we present the 4,230,758-bp draft genome for Cobetia sp. UCD-24C. This strain was
      isolated from Zostera marina roots collected in Woods Hole,
      Massachusetts, USA.
AU  - Alexiev A
AU  - Krusor ML
AU  - Jospin G
AU  - Lang JM
AU  - Eisen JA
AU  - Coil DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00116-16.

PMID- 26893412
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Two Pseudoalteromonas Strains Isolated from Roots and Leaf Blades of the Seagrass Zostera marina.
PG  - e00010-16
AB  - Here, we present the draft genome sequences for Pseudoalteromonas sp. strain UCD-33C and
      Pseudoalteromonas lipolytica UCD-48B. Pseudoalteromonas sp. UCD-33C
      was isolated from Zostera marina roots and P. lipolytica UCD-48B from Z. marina
      leaf blades, both collected in Woods Hole, MA. These assemblies contain 4,479,285
      bp and 4,592,435 bp, respectively.
AU  - Alexiev A
AU  - Krusor ML
AU  - Jospin G
AU  - Lang JM
AU  - Eisen JA
AU  - Coil DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00010-16.

PMID- 28232453
VI  - 5
DP  - 2017
TI  - Genome Sequence of Dehalobacter sp. Strain TeCB1, Able To Respire Chlorinated Benzenes.
PG  - e01681-16
AB  - Dehalobacter sp. strain TeCB1 was isolated from groundwater contaminated with a mixture of
      organohalides and is able to respire 1,2,4,5-tetrachlorobenzene and
      1,2,4-trichlorobenzene. Here, we report its 3.13-Mb draft genome sequence.
AU  - Alfan-Guzman R
AU  - Ertan H
AU  - Manefield M
AU  - Lee M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01681-16.

PMID- 23155485
VI  - 2
DP  - 2012
TI  - A type III restriction-modification system in Mycoplasma mycoides subsp. capri.
PG  - 120115
AB  - the sequenced genome of Mycoplasma mycoides subsp. capri revealed the presence of a Type III
      restriction-modification system (MmyCI).  The methyltransferase (modification) subunit of
      MmyCI (M.MmyCI) was shown to recognize the sequence 5'-TGAG-3' and methylate the adenine.
      The coding region of the methyltransferase gene contains 12 consecutive AG dinucleotide
      repeats that result in a translational termination at a TAA codon immediately beyond the
      repeat region.  This strain does not have MmyCI activity.  A clone was found with 10 AG
      repeats such that the gene is in frame, and this strain has MmyCI activity, suggesting that
      the expression of the MmyCI methyltransferase may be phase variable.
AU  - Algire MA
AU  - Montague MG
AU  - Vashee S
AU  - Lartigue C
AU  - Merryman C
PT  - Journal Article
TA  - Open Biology
JT  - Open Biology
SO  - Open Biology 2012 2: 120115.

PMID- 27198017
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a Multidrug-Resistant Klebsiella pneumoniae Strain Isolated from King Abdullah Medical City, Makkah, Saudi Arabia.
PG  - e00375-16
AB  - Multidrug-resistant (MDR) Gram-negative infections represent a growing problem and a serious
      global threat. Carbapenem-resistant Klebsiella pneumoniae is
      perhaps cause the most difficult infection to treat and is associated with
      increased morbidity and mortality. Here, we report the draft genome sequence of
      an MDR K. pneumoniae strain isolated from Makkah, Saudi Arabia.
AU  - Algowaihi R
AU  - Ashgar S
AU  - Sirag B
AU  - Shalam S
AU  - Nassir A
AU  - Ahmed A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00375-16.

PMID- 28209830
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Pseudomonas aeruginosa FA-HZ1, an Efficient Dibenzofuran-Degrading Bacterium.
PG  - e01634-16
AB  - Pseudomonas sp. FA-HZ1, an efficient dibenzofuran-degrading bacterium, was isolated from
      landfill leachate. Here, we present the complete genome sequence of
      strain FA-HZ1, which contains only one circular chromosome. The complete genome
      sequence will be essential for revealing the molecular mechanisms of dibenzofuran
      degradation.
AU  - Ali F
AU  - Hu H
AU  - Xu P
AU  - Tang H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01634-16.

PMID- 27932661
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the Anaerobic Ammonium-Oxidizing Bacterium 'Candidatus Brocadia sp. 40'.
PG  - e01377-16
AB  - The anaerobic ammonium-oxidizing (anammox) bacterium 'Candidatus Brocadia sp. 40'
      demonstrated the fastest growth rate compared to others in this taxon. Here, we
      report the 2.93-Mb draft genome sequence of this bacterium, which has 2,565
      gene-coding regions, 41 tRNAs, and a single rrn operon.
AU  - Ali M
AU  - Haroon MF
AU  - Narita Y
AU  - Zhang L
AU  - Rangel SD
AU  - Okabe S
AU  - Saikaly PE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01377-16.

PMID- 29326227
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Lactobacillus fermentum NCDC 400, Isolated from a Traditional Indian Dairy Product.
PG  - e01492-17
AB  - We announce here the draft genome sequence of Lactobacillus fermentum NCDC 400, a potential
      probiotic strain isolated from a traditional Indian dairy product. The genome size of
      Lactobacillus fermentum NCDC 400 is 1.89 Mb, and the assembled sequence consists of 185
      contigs joined into 138 scaffolds.
AU  - Ali SA
AU  - Kumar S
AU  - Mohanty AK
AU  - Behare P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01492-17.

PMID- 26358590
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Dickeya sp. Isolates B16 (NIB Z 2098) and S1 (NIB Z 2099) Causing Soft Rot of Phalaenopsis Orchids.
PG  - e00973-15
AB  - The genus Dickeya contains bacteria causing soft rot of economically important crops and
      ornamental plants. Here, we report the draft genome sequences of two Dickeya sp. isolates from
      rotted leaves of Phalaenopsis orchids.
AU  - Alic S
AU  - Naglic T
AU  - Llop P
AU  - Toplak N
AU  - Koren S
AU  - Ravnikar M
AU  - Dreo T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00973-15.

PMID- 24675854
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Antarctic Polyextremophile Nesterenkonia sp. Strain  AN1.
PG  - e00197-14
AB  - Nesterenkonia sp. strain AN1 was isolated from Antarctic soil and is a polyextremophile, being
      tolerant of low temperatures, high salt concentrations,
      and high alkalinity. Here we report the draft genome sequence of this strain.
AU  - Aliyu H
AU  - De Maayer P
AU  - Rees J
AU  - Tuffin M
AU  - Cowan DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00197-14.

PMID- 28751382
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Anoxybacillus sp. Strain UARK-01, a New Thermophilic Lignin-Utilizing Bacterium Isolated from Soil in Arkansas, USA.
PG  - e00588-17
AB  - The draft genome of Anoxybacillus sp. strain UARK-01, a novel lignin-utilizing thermophilic
      soil bacterium, represents the first sequence of an Anoxybacillus
      isolate from the United States. The genome was sequenced using the Illumina MiSeq
      platform, de novo assembled using SeqMan NGen, and annotated at NCBI. The genome
      sequence revealed genes for laccase and lignocellulose degradation enzymes.
AU  - Alkahem ATH
AU  - Rhoads DD
AU  - Barabote RD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00588-17.

PMID- 26205859
VI  - 3
DP  - 2015
TI  - Genome Sequence of Geobacillus sp. Strain ZGt-1, an Antibacterial Peptide-Producing Bacterium from Hot Springs in Jordan.
PG  - e00799-15
AB  - This paper reports the draft genome sequence of the firmicute Geobacillus sp. strain ZGt-1, an
      antibacterial peptide producer isolated from the Zara hot spring
      in Jordan. This study is the first report on genomic data from a thermophilic
      bacterial strain isolated in Jordan.
AU  - Alkhalili RN
AU  - Hatti-Kaul R
AU  - Canback B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00799-15.

PMID- 29348348
VI  - 6
DP  - 2018
TI  - Whole-Genome Sequence of a Mycobacterium goodii Isolate from a Pediatric Patient  in South Africa.
PG  - e01478-17
AB  - We describe here the draft genome sequence of a Mycobacterium goodii isolate from a pediatric
      patient in Western Cape, South Africa. To our knowledge, this is the
      second reported genome of this rapidly growing nontuberculous mycobacterial
      species.
AU  - Allam M
AU  - Joseph L
AU  - Ismail F
AU  - Said H
AU  - Ismail NA
AU  - Ismail A
AU  - Mtshali S
AU  - Mnyameni F
AU  - Goussard P
AU  - Pekeur JC
AU  - Lourens A
AU  - Omar SV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01478-17.

PMID- 29930052
VI  - 6
DP  - 2018
TI  - Whole-Genome Sequences of Listeria monocytogenes Sequence Type 6 Isolates Associated with a Large Foodborne Outbreak in South Africa, 2017 to 2018.
PG  - e00538-18
AB  - We report whole-genome sequences for 10 Listeria monocytogenes sequence type 6 isolates
      associated with a large listeriosis outbreak in South Africa, which
      occurred over the period of 2017 to 2018. The possibility of listeriosis
      spreading beyond South Africa's borders as a result of exported contaminated food
      products prompted us to make the genome sequences publicly available.
AU  - Allam M
AU  - Tau N
AU  - Smouse SL
AU  - Mtshali PS
AU  - Mnyameni F
AU  - Khumalo ZTH
AU  - Ismail A
AU  - Govender N
AU  - Thomas J
AU  - Smith AM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00538-18.

PMID- 
VI  - 59
DP  - 1999
TI  - The dynamic origin of sequence discrimination by the EcoRI DNA methyltransferase.
PG  - 3407B
AB  - All living cells use DNA modifying enzymes to maintain or expand the information encoded
      within the genome.  These enzymes catalyze the chemical transformation of sterically occluded
      target DNA residues within a huge excess of nontarget DNA.  Enzyme-DNA complexes reveal
      striking distortions of DNA structure such as DNA bending and base flipping; yet, the
      mechanism whereby DNA distortion modulates sequence specificity is only now being elucidated.
      Intriguing mechanistic questions remain unresolved.  Do DNA modifying enzymes capture
      transient structural intermediates or actively induce the conformational changes required for
      DNA binding and catalysis?  Determination of the temporal correlation between the individual
      steps in the reaction pathway provides a means to discern the origin of sequence
      discrimination.  For the EcoRI DNA methyltransferase nearly absolute synchrony between DNA
      binding and base flipping transitions are revealed during both complex assembly and
      disassembly.  Because the rate of product formation under presteady-state conditions is
      determined not by the methylation reaction, but rather by the pre-catalytic isomerization of
      the complex, the base flipping transition is the selection gate whereby the commitment to
      catalysis is manifested.  Our characterization of a methyltransferase mutant which unlike the
      wild type methyltransferase displays no detectable DNA bending, shows that slowing the rate of
      an obligate pre-catalytic isomerization can result in enhanced discrimination for an
      induced-fit enzyme.  The recent extension of the experimental methodologies developed in this
      work to other base flipping enzymes is providing fundamental information concerning the
      integration of DNA distortion and enzyme specificity for other crucial enzymes that modify or
      repair the DNA.  Finally, the high signal to noise, solution-based nature, and millisecond
      timing resolution of this enabling technology is compatible with the rapid throughput
      screening of protein-DNA interactions.
AU  - Allan BW
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1999 59: 3407B.

PMID- 9442083
VI  - 273
DP  - 1998
TI  - Direct real time observation of base flipping by the EcoRI DNA methyltransferase.
PG  - 2368-2373
AB  - DNA methyltransferases are excellent prototypes for investigating DNA distortion and enzyme
      specificity because catalysis requires the extrahelical stabilization of the target base
      within the enzyme active site.  The energetics and kinetics of base flipping by the EcoRI DNA
      methyltransferase were investigated by two methods.  First, equilibrium dissociation constants
      (KD/DNA) were determined for the binding of the methyltransferase to DNA containing abasic
      sites or base analogs incorporated at the target base.  Consistent with a base flipping
      mechanism, tighter binding to oligonucleotides containing destabilized target base pairs was
      observed.  Second, total intensity stopped flow fluorescence measurements of DNA containing
      2-aminopurine allowed presteady-state real time observation of the base flipping transition.
      Following the rapid formation of an enzyme-DNA collision complex, a biphasic increase in total
      intensity was observed.  The fast phase dominated the total intensity increase with a rate
      nearly identical to k(methylation) determined by rapid chemical quench-flow techniques.  The
      restacking of the extrahelical base also revealed biphasic kinetics with the recovered
      amplitudes from these off-rate experiments matching very closely to those observed during the
      base unstacking process.  These results provide the first direct and continuous observation of
      base flipping and show that at least two distinct conformation transitions occurred at the
      flipped base subsequent to complex formation.  Furthermore, our results suggest that the
      commitment to catalysis during the methylation of the target site is not determined at the
      level of the chemistry step but rather is mediated by prior intramolecular isomerization
      within the enzyme-DNA complex.
AU  - Allan BW
AU  - Beechem JM
AU  - Lindstrom WM
AU  - Reich NO
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1998 273: 2368-2373.

PMID- 10383435
VI  - 274
DP  - 1999
TI  - DNA bending by EcoRI DNA methyltransferase accelerates base flipping but compromises specificity.
PG  - 19269-19275
AB  - EcoRI DNA methyltransferase was previously shown to bend its cognate DNA sequence by 52
      degrees and stabilize the target adenine in an extrahelical orientation. We describe the
      characterization of an EcoRI DNA methyltransferase mutant in which histidine 235 was
      selectively replaced with asparagine. Steady-state kinetic and thermodynamic parameters for
      the H235N mutant revealed only minor functional consequences: DNA binding affinity (KDDNA) was
      reduced 10-fold, and kcat was decreased 30%. However, in direct contrast to the wild type
      enzyme, DNA bending within the mutant enzyme-DNA complexes was not observed by scanning force
      microscopy. The bending-deficient mutant showed enhanced discrimination against the
      methylation at nontarget sequence DNA. This enhancement of enzyme discrimination was
      accompanied by a change in the rate-limiting catalytic step. No presteady-state burst of
      product formation was observed, indicating that the chemistry step (or prior event) had become
      rate-limiting for methylation. Direct observation of the base flipping transition showed that
      the lack of burst kinetics was entirely due to slower base flipping. The combined data show
      that DNA bending contributes to the correct assembly of the enzyme-DNA complex to accelerate
      base flipping and that slowing the rate of this precatalytic isomerization can enhance
      specificity.
AU  - Allan BW
AU  - Garcia R
AU  - Maegley K
AU  - Mort J
AU  - Wong D
AU  - Lindstrom W
AU  - Beechem JM
AU  - Reich NO
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1999 274: 19269-19275.

PMID- 8942637
VI  - 35
DP  - 1996
TI  - Targeted base stacking disruption by the EcoRI DNA methyltransferase.
PG  - 14757-14762
AB  - We describe a novel fluorescence-based assay for detecting DNA conformational alterations
      within enzyme--DNA complexes.  The target adenine for EcoRI DNA methyltransferase to the
      duplex binding site results in a 14-fold increase in fluorescence intensity with a 10 nm blue
      shift.  The fluorescence is ~50% of that observed with equimolar free nucleoside, consistent
      with extrahelical stabilization of the target base in the enzyme--DNA complex.  The shift in
      lambda/max further implies the base is placed into a low dielectric environment.  For
      adenine-specific DNA methyltransferases, a hydrophobic pocket composed of highly conserved
      amino acids lies proximal to the cofactor binding site.  Substitution of 2-aminopurine
      adjacent to the target base also results in detectable changes in fluorescence emission
      following complex formation with the methyltransferase.  Thus, other classes of enzymes
      hypothesized to utilize base flipping can be investigated by this method.
AU  - Allan BW
AU  - Reich NO
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1996 35: 14757-14762.

PMID- 
VI  - 74
DP  - 1998
TI  - Simultaneous real-time measurement of binding base-flipping, and dissociation base unflipping in EcoRI DNA methyltransferase.
PG  - A69
AB  - Many DNA binding proteins generate large changes in the conformation of DNA upon interaction.
      High signal-to-noise data of the exact correlation in-time between the binding event and DNA
      conformational change, would allow a much deeper understanding of this process.  In this
      study, "doubly-labeled" 2-color fluorescent DNA has been synthesized and utilized in
      stopped-flow fluorescence experiments, allowing the simultaneous measurement of DNA binding
      (via anisotropy changes of 5'-Rhodamine-X labeled 14mers; red-signal) and internal
      base-flipping (via changes in the fluorescence intensity of 2-aminopurine at the target
      methylation site; blue signal) (see figure for end-points; up arrow, down arrow indicates
      protein addition).  The binding-rate (kon = 1.6 x 10^7M-1 s-1) and base-flipping rates in
      EcoRI MTase were found to be almost absolutely correlated, whereas differences in off-rate and
      "unflipping" were detected.
AU  - Allan BW
AU  - Reich NO
AU  - Beechem JM
PT  - Journal Article
TA  - Biophys. J.
JT  - Biophys. J.
SO  - Biophys. J. 1998 74: A69.

PMID- 10220317
VI  - 38
DP  - 1999
TI  - Measurement of the absolute temporal coupling between DNA binding and base flipping.
PG  - 5308-5314
AB  - The absolute temporal couplings between DNA binding and base flipping were examined for the
      EcoRI DNA methyltransferase.  The binding event (monitored using rhodamine-x fluorescence
      anisotropy) was monophasic with a second-order on-rate of 1.1 x 10^7 M-1 s-1 <- kon <- 2.25 x
      10^7 M-1 s-1.  Base-flipping kinetics (monitored using 2-aminopurine fluorescence intensity)
      were essentially synchronous with the binding kinetics, with less than a 4 ms delay between
      enzyme binding and target base flipping.  The 4 ms delay translates into a base-flipping rate
      of at least 195 s-1, when the data are analyzed in terms of a sequential DNA binding and
      base-flipping reaction mechanism.  Synchrony of binding and base flipping was only observed
      during the first 80% of the reaction, and an additional 20% base-flipping signal occurred well
      after DNA binding was complete.  This additional 2AP fluorescence change, with an effective
      rate of 0.55 s-1, is an intramolecular isomerization reaction which greatly accelerates the
      dissociation of the enzyme from DNA.  The correlation between the dissociation of the
      enzyme-DNA complex and the restacking of the extrahelical base also revealed a very tight
      coupling of these two events.  Both dissociation and base restacking were found to be
      biphasic.  These data are consistent with the following mechanism.  The initial binding rate
      and base-flipping rates map very closely with previously determined pre-steady-state
      burst-rate kinetics for methyl transfer.  Hence, binding, flipping, and methylation appear to
      occur in nearly a single concerted step.  The bound complex then slowly isomerizes (0.1 s-1)
      to a distinct configuration that accelerates the product-release phase of the reaction.  The
      product-release enzyme configuration dissociates from DNA approximately 8 times faster than
      the initial bound complex (0.18 s-1 vs. 0.024 s-1).  When the enzyme dissociates from the DNA
      along the product-release pathway, the target base remains in an extrahelical conformation and
      restacks at a rate of only 0.6 s-1 .  This "multicolor" fluorescence kinetic approach directly
      measures the absolute temporal correlation between DNA binding and base flipping, with
      millisecond timing resolution.  The data reveal that even when the B-DNA structure is altered
      in a radical manner (e.g., via base flipping), enzymes can perform this operation in a highly
      efficient, if not completely concerted manner.
AU  - Allan BW
AU  - Reich NO
AU  - Beechem JM
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1999 38: 5308-5314.

PMID- 22260654
VI  - 13
DP  - 2012
TI  - High resolution clustering of Salmonella enterica serovar Montevideo strains using a next-generation sequencing approach.
PG  - 32
AB  - BACKGROUND: Next-Generation Sequencing (NGS) is increasingly being used as a
      molecular epidemiologic tool for discerning ancestry and traceback of the most
      complicated, difficult to resolve bacterial pathogens. Making a linkage between
      possible food sources and clinical isolates requires distinguishing the suspected
      pathogen from an environmental background and placing the variation observed into
      the wider context of variation occurring within a serovar and among other closely
      related foodborne pathogens. Equally important is the need to validate these high
      resolution molecular tools for use in molecular epidemiologic traceback. Such
      efforts include the examination of strain cluster stability as well as the
      cumulative genetic effects of sub-culturing on these clusters. Numerous isolates
      of S. Montevideo were shot-gun sequenced including diverse lineage
      representatives as well as numerous replicate clones to determine how much
      variability is due to bias, sequencing error, and or the culturing of isolates.
      All new draft genomes were compared to 34 S. Montevideo isolates previously
      published during an NGS-based molecular epidemiological case study. RESULTS:
      Intraserovar lineages of S. Montevideo differ by thousands of SNPs, that are only
      slightly less than the number of SNPs observed between S. Montevideo and other
      distinct serovars. Much less variability was discovered within an individual S.
      Montevideo clade implicated in a recent foodborne outbreak as well as among
      individual NGS replicates. These findings were similar to previous reports
      documenting homopolymeric and deletion error rates with the Roche 454 GS Titanium
      technology. In no case, however, did variability associated with sequencing
      methods or sample preparations create inconsistencies with our current
      phylogenetic results or the subsequent molecular epidemiological evidence gleaned
      from these data. CONCLUSIONS: Implementation of a validated pipeline for NGS data
      acquisition and analysis provides highly reproducible results that are stable and
      predictable for molecular epidemiological applications. When draft genomes are
      collected at 15x-20x coverage and passed through a quality filter as part of a
      data analysis pipeline, including sub-passaged replicates defined by a few SNPs,
      they can be accurately placed in a phylogenetic context. This reproducibility
      applies to all levels within and between serovars of Salmonella suggesting that
      investigators using these methods can have confidence in their conclusions.
AU  - Allard MW
AU  - Luo Y
AU  - Strain E
AU  - Li C
AU  - Keys CE
AU  - Son I
AU  - Stones R
AU  - Musser SM
AU  - Brown EW
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2012 13: 32.

PMID- 23383127
VI  - 8
DP  - 2013
TI  - On the evolutionary history, population genetics and diversity among isolates of Salmonella Enteritidis PFGE pattern JEGX01.0004.
PG  - E55254
AB  - Facile laboratory tools are needed to augment identification in contamination
      events to trace the contamination back to the source (traceback) of Salmonella
      enterica subsp. enterica serovar Enteritidis (S. Enteritidis). Understanding the
      evolution and diversity within and among outbreak strains is the first step
      towards this goal. To this end, we collected 106 new S. Enteriditis isolates
      within S. Enteriditis Pulsed-Field Gel Electrophoresis (PFGE) pattern JEGX01.0004
      and close relatives, and determined their genome sequences. Sources for these
      isolates spanned food, clinical and environmental farm sources collected during
      the 2010 S. Enteritidis shell egg outbreak in the United States along with
      closely related serovars, S. Dublin, S. Gallinarum biovar Pullorum and S.
      Gallinarum. Despite the highly homogeneous structure of this population, S.
      Enteritidis isolates examined in this study revealed thousands of SNP differences
      and numerous variable genes (n = 366). Twenty-one of these genes from the
      lineages leading to outbreak-associated samples had nonsynonymous (causing amino
      acid changes) changes and five genes are putatively involved in known Salmonella
      virulence pathways. While chromosome synteny and genome organization appeared to
      be stable among these isolates, genome size differences were observed due to
      variation in the presence or absence of several phages and plasmids, including
      phage RE-2010, phage P125109, plasmid pSEEE3072_19 (similar to pSENV), plasmid
      pOU1114 and two newly observed mobile plasmid elements pSEEE1729_15 and
      pSEEE0956_35. These differences produced modifications to the assembled bases for
      these draft genomes in the size range of approximately 4.6 to 4.8 mbp, with S.
      Dublin being larger ( approximately 4.9 mbp) and S. Gallinarum smaller (4.55 mbp)
      when compared to S. Enteritidis. Finally, we identified variable S. Enteritidis
      genes associated with virulence pathways that may be useful markers for the
      development of rapid surveillance and typing methods, potentially aiding in
      traceback efforts during future outbreaks involving S. Enteritidis PFGE pattern
      JEGX01.0004.
AU  - Allard MW
AU  - Luo Y
AU  - Strain E
AU  - Pettengill J
AU  - Timme R
AU  - Wang C
AU  - Li C
AU  - Keys CE
AU  - Zheng J
AU  - Stones R
AU  - Wilson MR
AU  - Musser SM
AU  - Brown EW
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2013 8: E55254.

PMID- 24699966
VI  - 2
DP  - 2014
TI  - Fully Assembled Genome Sequence for Salmonella enterica subsp. enterica Serovar Javiana CFSAN001992.
PG  - e00293-14
AB  - Volume 1, no. 2, e00081-13, 2013.  Page 1: The article byline should read as given above.
      Page 2: The following should be added to the Acknowledgments.  "Research reported in this
      publication was supported by the Small Business Innovation Research Program (NIGMS) of the
      National Institutes of Health under award number R44GM105125 to R.J.R.  The content is solely
      the responsibility of the authors and does not necessarily represent the official views of the
      National Institutes of Health."
AU  - Allard MW
AU  - Muruvanda T
AU  - Strain E
AU  - Timme R
AU  - Luo Y
AU  - Wang C
AU  - Keys CE
AU  - Payne J
AU  - Cooper T
AU  - Luong K
AU  - Song Y
AU  - Chin CS
AU  - Korlach J
AU  - Roberts RJ
AU  - Evans P
AU  - Musser SM
AU  - Brown EW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00293-14.

PMID- 23516208
VI  - 1
DP  - 2013
TI  - Fully Assembled Genome Sequence for Salmonella enterica subsp. enterica Serovar Javiana CFSAN001992.
PG  - e00081-13
AB  - We report a closed genome of Salmonella enterica subsp. enterica serovar Javiana  (S.
      Javiana). This serotype is a common food-borne pathogen and is often associated with fresh-cut
      produce. Complete (finished) genome assemblies will support pilot studies testing the utility
      of next-generation sequencing (NGS) technologies in public health laboratories.
AU  - Allard MW
AU  - Muruvanda T
AU  - Strain E
AU  - Timme R
AU  - Luo Y
AU  - Wang C
AU  - Keys CE
AU  - Payne J
AU  - Cooper T
AU  - Luong K
AU  - Song Y
AU  - Chin CS
AU  - Korlach J
AU  - Roberts RJ
AU  - Evans P
AU  - Musser SM
AU  - Brown EW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00081-13.

PMID- 17267615
VI  - 104
DP  - 2007
TI  - Genome dynamics in a natural archaeal population.
PG  - 1883-1888
AB  - Evolutionary processes that give rise to, and limit, diversification within
      strain populations can be deduced from the form and distribution of genomic
      heterogeneity. The extent of genomic change that distinguishes the acidophilic
      archaeon Ferroplasma acidarmanus fer1 from an environmental population of the
      same species from the same site, fer1(env), was determined by comparing the
      1.94-megabase (Mb) genome sequence of the isolate with that reconstructed from 8
      Mb of environmental sequence data. The fer1(env) composite sequence sampled
      approximately 92% of the isolate genome. Environmental sequence data were also
      analyzed to reveal genomic heterogeneity within the coexisting, coevolving
      fer1(env) population. Analyses revealed that transposase movement and the
      insertion and loss of blocks of novel genes of probable phage origin occur
      rapidly enough to give rise to heterogeneity in gene content within the local
      population. Because the environmental DNA was derived from many closely related
      individuals, it was possible to quantify gene sequence variability within the
      population. All but a few gene variants show evidence of strong purifying
      selection. Based on the small number of distinct sequence types and their
      distribution, we infer that the population is undergoing frequent genetic
      recombination, resulting in a mosaic genome pool that is shaped by selection. The
      larger genetic potential of the population relative to individuals within it and
      the combinatorial process that results in many closely related genome types may
      provide the basis for adaptation to environmental fluctuations.
AU  - Allen EE
AU  - Tyson GW
AU  - Whitaker RJ
AU  - Detter JC
AU  - Richardson PM
AU  - Banfield JF
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2007 104: 1883-1888.

PMID- 22887661
VI  - 194
DP  - 2012
TI  - Genome Sequence of Stenotrophomonas maltophilia PML168, Which Displays Baeyer-Villiger Monooxygenase Activity.
PG  - 4753-4754
AB  - Stenotrophomonas maltophilia PML168 was isolated from Wembury Beach on the English Coast from
      a rock pool following growth and selection on agar plates.
      Here we present the permanent draft genome sequence, which has allowed prediction
      of function for several genes encoding enzymes relevant to industrial
      biotechnology, including a novel flavoprotein monooxygenase.
AU  - Allen MJ
AU  - Tait K
AU  - Muhling M
AU  - Weynberg K
AU  - Bradley C
AU  - Trivedi U
AU  - Gharbi K
AU  - Nissimov J
AU  - Mavromatis K
AU  - Jensen CN
AU  - Grogan G
AU  - Ali ST
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4753-4754.

PMID- 25637842
VI  - 212
DP  - 2015
TI  - Identification of a gene in Mycoplasma hominis associated with preterm birth and microbial burden in intra-amniotic infection.
PG  - 779.e1-779.e13
AB  - OBJECTIVE: Microbial invasion of the amniotic cavity is associated with
      spontaneous preterm labor and adverse pregnancy outcome, and Mycoplasma hominis
      often is present. However, the pathogenic process by which M hominis invades the
      amniotic cavity and gestational tissues, often resulting in chorioamnionitis and
      preterm birth, remains unknown. We hypothesized that strains of M hominis vary
      genetically with regards to their potential to invade and colonize the amniotic
      cavity and placenta. STUDY DESIGN: We sequenced the entire genomes of 2 amniotic
      fluid isolates and a placental isolate of M hominis from pregnancies that
      resulted in preterm births and compared them with the previously sequenced genome
      of the type strain PG21. We identified genes that were specific to the amniotic
      fluid/placental isolates. We then determined the microbial burden and the
      presence of these genes in another set of subjects from whom samples of amniotic
      fluid had been collected and were positive for M hominis. RESULTS: We identified
      2 genes that encode surface-located membrane proteins (Lmp1 and Lmp-like) in the
      sequenced amniotic fluid/placental isolates that were truncated severely in PG21.
      We also identified, for the first time, a microbial gene of unknown function that
      is referred to in this study as gene of interest C that was associated
      significantly with bacterial burden in amniotic fluid and the risk of preterm
      delivery in patients with preterm labor. CONCLUSION: A gene in M hominis was
      identified that is associated significantly with colonization and/or infection of
      the upper reproductive tract during pregnancy and with preterm birth.
AU  - Allen-Daniels MJ
AU  - Serrano MG
AU  - Pflugner LP
AU  - Fettweis JM
AU  - Prestosa MA
AU  - Koparde VN
AU  - Brooks JP
AU  - Strauss JF III
AU  - Romero R
AU  - Chaiworapongsa T
AU  - Eschenbach DA
AU  - Buck GA
AU  - Jefferson KK
PT  - Journal Article
TA  - Am. J. Obstet. Gynecol.
JT  - Am. J. Obstet. Gynecol.
SO  - Am. J. Obstet. Gynecol. 2015 212: 779.e1-779.e13.

PMID- 4745657
VI  - 12
DP  - 1973
TI  - Fragments produced by cleavage of lambda deoxyribonucleic acid with the Hemophilus parainfluenzae restriction enzyme HpaII.
PG  - 3972-3977
AB  - One of the restricting enzymes extracted from Hemophilus parainfluenzae, HpaII,
      is shown to cleave lambda DNA at more than 50 sites.  The resulting DNA
      fragments have been prepared from a variety of deletion or
      deletion-substitution mutants of lambda, and analyzed by polyacrylamide gel
      electrophoresis.  The major DNA segments (larger than 0.3 Mdalton) produced by
      digestion of lambda DNA have been mapped and many of the cleavage sites in the
      immunity region, in the b2 region, and to the right of the immunity region have
      been identified.
AU  - Allet B
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1973 12: 3972-3977.

PMID- 4572006
VI  - 241
DP  - 1973
TI  - Mapping the DNA fragments produced by cleavage of lambda DNA with endonuclease RI.
PG  - 120-123
AB  - None
AU  - Allet B
AU  - Jeppesen PGN
AU  - Katagiri KJ
AU  - Delius H
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1973 241: 120-123.

PMID- 509525
VI  - 18
DP  - 1979
TI  - Structure analysis at the ends of the intervening DNA sequences in the chloroplast 23S ribosomal genes of C. reinhardii.
PG  - 55-60
AB  - All of the chloroplast 23S ribosomal genes of C. reinhardii are interrupted by a 0.87 kb
      sequence.  We have sequenced the DNA across the two ends of this intervening element.  In
      parallel, we have examined the nucleotide sequences in the corresponding part of the 23S
      ribosomal RNA.  This allowed us to locate precisely the boundaries between the coding (that
      is, transcribed into mature 23S rRNA) and the noncoding DNA.  The results show that the
      intervening sequence is flanked by two identical sets of 3 bp (5'-CGT) oriented as direct
      repeats.  In addition, a sequence of 5 bp (5'-CGTGA) lies exactly next to one end and is
      found very close (16 bp) to the other end, in the coding part of the gene.  These two sets are
      also oriented as direct repeats.  Finally, sequences near one end of the intervening element
      are found with a few alterations near the other end, but in an inverted orientation.  Possible
      interpretations of these results are discussed.
AU  - Allet B
AU  - Rochaix J-D
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1979 18: 55-60.

PMID- 8799111
VI  - 93
DP  - 1996
TI  - Direct atomic force microscope imaging of EcoRI endonuclease site specifically bound to plasmid DNA molecules.
PG  - 8826-8829
AB  - Direct imaging with the atomic force microscope has been used to identify specific nucleotide
      sequences in plasmid DNA molecules.  This was accomplished using EcoRI(Gln-111), a mutant of
      the restriction enzyme that has a 1000-fold greater binding affinity than the wild-type enzyme
      but with cleavage rate constants reduced by a factor of 10^4.  ScaI-linearized plasmids with
      single (pBS+) and double (pGEM-luc and pSV-beta-galactosidase) EcoRI recognition sites were
      imaged, and the bound enzyme was localized to a 50- to 100-nt resolution.  The high affinity
      for the EcoRI binding site exhibited by this mutant endonuclease, coupled with an observed low
      level of nonspecific binding, should prove valuable for physically mapping large DNA clones by
      direct atomic force microscope imaging.
AU  - Allison DP
AU  - Kerper PS
AU  - Doktycz MJ
AU  - Spain JA
AU  - Modrich P
AU  - Larimer FW
AU  - Thundat T
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1996 93: 8826-8829.

PMID- 11889106
VI  - 184
DP  - 2002
TI  - Complete genomic sequence of SfV, a serotype-converting temperate bacteriophage of Shigella flexneri.
PG  - 1974-1987
AB  - Bacteriophage SfV is a temperate serotype-converting phage of Shigella flexneri. SfV encodes
      the factors involved in type V O-antigen
      modification, and the serotype conversion and integration-excision
      modules of the phage have been isolated and characterized. We now
      report on the complete sequence of the SfV genome (37,074 bp). A total
      of 53 open reading frames were predicted from the nucleotide sequence,
      and analysis of tile corresponding proteins was used to construct a
      functional map. The general organization of the genes in the SfV genome
      is similar to that of bacteriophage X, and numerous features of the
      sequence are described. The superinfection immunity system of SfV
      includes a lambda-like repression system and a P4-like transcription
      termination mechanism. Sequence analysis also suggests that SfV encodes
      multiple DNA methylases, and experiments confirmed that orf-41 encodes
      a Dam methylase. Studies conducted to determine if the phage-encoded
      methylase confers host DNA methylation showed that the two S. flexneri
      strains analyzed encode their own Dam methylase. Restriction mapping
      and sequence analysis revealed that the phage genome has cos sites at
      the termini. The tail assembly and structural genes of SfV show
      homology to those of phage Mu and Mu-like prophages in the genome of
      Escherichia coli O157:H7 and Haemophilus influenzae. Significant
      homology (30% of the genome in total) between sections of the early,
      regulatory, and structural regions of the SfV genome and the e14 and
      KpLE1 prophages in the E. coli K-12 genome were noted, suggesting that
      these three phages have common evolutionary origins.
AU  - Allison GE
AU  - Angeles D
AU  - Tran-Dinh N
AU  - Verma NK
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2002 184: 1974-1987.

PMID- 
VI  - 8
DP  - 1998
TI  - Phage resistance mechanisms in lactic acid bacteria.
PG  - 207-226
AB  - Dairy fermentations involving Lactococcus lactis and more recently Streptococcus thermophilus,
      are commonly attacked by bacteriophages.  Efforts to protect these dairy starter cultures have
      resulted in a significant body of knowledge about the bacteriophages, their interactions with
      the host, and natural phage defense mechanisms that have evolved within bacteria operating
      under the most dynamic and devastating phage environment faced by industrial fermentations.
      This paper will overview this area and discuss the novel genetic approaches that are now being
      investigated in an effort to provide long term phage protection to dairy starter cultures hat
      are used extensively in the industry. A review.
AU  - Allison GE
AU  - Klaenhammer TR
PT  - Journal Article
TA  - Int. Dairy Journal
JT  - Int. Dairy Journal
SO  - Int. Dairy Journal 1998 8: 207-226.

PMID- 2838139
VI  - 4
DP  - 1988
TI  - Restriction site mapping is in separation theory.
PG  - 97-101
AB  - A computer algorithm for restriction-site mapping consists of a generator of
      partial maps and a consistency checker.  This paper examines consistency
      checking and argues that a method based on separation theory extracts the
      maximum amount of information from fragment lengths in digest data.  It results
      in the minimum number of false maps being generated.
AU  - Allison L
AU  - Yee CN
PT  - Journal Article
TA  - Comput. Appl. Biosci.
JT  - Comput. Appl. Biosci.
SO  - Comput. Appl. Biosci. 1988 4: 97-101.

PMID- 27609916
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of 15 Isolates of Listeria monocytogenes Serotype 1/2a, Subgroup ST204.
PG  - e00935-16
AB  - Listeria monocytogenes sequence type 204 (ST204) strains have been isolated from  a range of
      food, environmental, and clinical sources in Australia. This study
      describes the draft genome sequences of 15 isolates collected from meat and dairy
      associated sources.
AU  - Allnutt TR
AU  - Bradbury MI
AU  - Fanning S
AU  - Chandry PS
AU  - Fox EM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00935-16.

PMID- 29496831
VI  - 6
DP  - 2018
TI  - Closed Genome Sequence of Vibrio cholerae O1 El Tor Inaba Strain A1552.
PG  - e00098-18
AB  - Vibrio cholerae is a Gram-negative waterborne human pathogen and the causative agent of
      cholera. Here, we present the complete genome sequence of the seventh
      pandemic O1 biovar El Tor Inaba strain A1552 isolated in 1992. This clinical
      strain has served as an important model strain for studying cholera pathogenicity
      traits.
AU  - Allue-Guardia A
AU  - Echazarreta M
AU  - Koenig SSK
AU  - Klose KE
AU  - Eppinger M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00098-18.

PMID- 25700401
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Strain R13-38 from a Francisella tularensis Outbreak in Sweden.
PG  - e01517-14
AB  - We have whole-genome sequenced a Francisella tularensis subsp. holarctica (also known as type
      B) strain from an outbreak in Sweden in 2013, derived from a privately owned well for drinking
      water.
AU  - Alm E
AU  - Advani A
AU  - Brave A
AU  - Wahab T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01517-14.

PMID- 9923682
VI  - 397
DP  - 1999
TI  - Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori.
PG  - 176-180
AB  - Helicobacter pylori, one of the most common bacterial pathogens of humans, colonizes the
      gastric mucosa, where it appears to persist throughout the host's life unless the patient is
      treated.  Colonization induces chronic gastric inflammation which can progress to a variety of
      diseases, ranging in severity from superficial gastritis and peptic ulcer to gastric cancer
      and mucosal-associated lymphoma.  Strain-specific genetic diversity has been proposed to be
      involved in the organism's ability to cause different diseases or even be beneficial to the
      infected host and to participate in the lifelong chronicity of infection.  Here we compare the
      complete genomic sequences of two untreated H. pylori isolates.  This is, to our knowledge,
      the first such genomic comparison.  H. pylori was believed to exhibit a large degree of
      genomic and allelic diversity, but we find that the overall genomic organization, gene order
      and predicted proteomes (sets of proteins encoded by the genomes) of the two strains are quite
      similar.  Between 6 to 7% of the genes are specific to each strain, with almost half of these
      genes being clustered in a single hypervariable region. Full author list: Alm, R.A., Ling,
      L.-S.L., Moir, D.T., King, B.L., Brown, E.D., Doig, P.C., Smith, D.R., Noonan, B., Guild,
      B.C., deJonge, B.L., Carmel, G., Tummino, P.J., Caruso, A., Uria-Nickelsen, M., Mills, D.M.,
      Ives, C., Gibson, R., Merberg, D., Mills, S.
AU  - Alm RA
AU  - Ling L-SL
AU  - Moir DT
AU  - King BL
AU  - Brown ED
AU  - Doig PC
AU  - Smith DR
AU  - Noonan B
AU  - Guild BC
AU  - deJonge BL
AU  - Carmel G
AU  - Tummino PJ
AU  - Caruso A
AU  - Uria-Nickelsen M
AU  - Mills DM
AU  - Ives C
AU  - Gibson R
AU  - Merberg D
AU  - Mills S
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1999 397: 176-180.

PMID- 10682319
VI  - 77
DP  - 1999
TI  - Analysis of the genetic diversity of Helicobacter pylori: the tale of two genomes.
PG  - 834-846
AB  - Infection with Helicobacter pylori has been linked to numerous severe gastroduodenal diseases
      including peptic ulcer and gastric cancer. Several techniques have
      been used to measure the genetic heterogeneity of H. pylori at several different levels and to
      determine whether there is any correlation with severity of disease. The
      availability of two completed genome sequences from unrelated strains (J99 and 26,695) has
      allowed an analysis of the level of diversity from a large-scale yet detailed
      perspective. Although the two chromosomes are organized differently in a limited number of
      discrete regions, the genome size and gene order of these two "high-virulence"
      (cagA+ and vacA+) H. pylori isolates was found to be highly similar. The regions of
      organizational difference are associated with insertion sequences, DNA
      restriction/modification genes, repeat sequences, or a combination of the above. A significant
      level of variation at the nucleotide level is seen across the genome, providing an
      explanation for why the nucleotide-based typing techniques have such high discriminatory power
      among independent H. pylori isolates. This nucleotide variation together
      with the organizational rearrangements appears to have provided an over-estimation of the gene
      order diversity of H. pylori as assessed by pulse-field gel electrophoresis.
      Functional assignments are assigned to approximately only 60% of the gene products in each
      strain, with one-half of the remaining gene products of unknown function having
      homologues in other bacteria, while the remainder appear to be H. pylori-specific. Between 6%
      and 7% of the coding capacity of each strain are genes that are absent from the
      other strain, with almost one-half of these strain-specific genes located in a single
      hypervariable region called the plasticity zone. The majority of the strain-specific genes in
      each strain are also H. pylori-specific, with no homologues being identified in the public
      databases. Significantly, over one-half of the functionally assigned strain-specific
      genes in both H. pylori J99 and 26695 encode DNA restriction/modification enzymes. Analysis of
      the level of conservation between orthologues from the two strains indicates
      that the H. pylori specific genes have a lower level of conservation than those orthologues to
      which a putative function can be assigned. The plasticity zone represents one of
      several regions across each genome that is comprised of lower (G+C)% content DNA, some of
      which has been detected in self-replicating plasmids, suggesting that both
      horizontal transfer from other species and plasmid integration are responsible for the
      strain-specific diversity at this locus. These analyses have yielded results with
      important implications for understanding the genetic diversity of H. pylori and its associated
      diseases, and imply a need to reassess the respective roles of bacterial and host
      factors in H. pylori associated diseases.
AU  - Alm RA
AU  - Trust TJ
PT  - Journal Article
TA  - J. Mol. Med.
JT  - J. Mol. Med.
SO  - J. Mol. Med. 1999 77: 834-846.

PMID- 29371360
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of the Antimycin-Producing Bacterium Streptomyces sp. Strain SM8, Isolated from the Marine Sponge Haliclona simulans.
PG  - e01535-17
AB  - Streptomyces sp. strain SM8, isolated from Haliclona simulans, possesses antifungal and
      antibacterial activities and inhibits the calcineurin pathway in
      yeast. The draft genome sequence is 7,145,211 bp, containing 5,929 predicted
      coding sequences. Several secondary metabolite biosynthetic gene clusters are
      present, encoding known and novel metabolites, including antimycin.
AU  - Almeida EL
AU  - Margassery LM
AU  - Kennedy J
AU  - Dobson ADW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01535-17.

PMID- 29371359
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Pseudomonas putida CA-3, a Bacterium Capable of Styrene  Degradation and Medium-Chain-Length Polyhydroxyalkanoate Synthesis.
PG  - e01534-17
AB  - Pseudomonas putida strain CA-3 is an industrial bioreactor isolate capable of synthesizing
      biodegradable polyhydroxyalkanoate polymers via the metabolism of
      styrene and other unrelated carbon sources. The pathways involved are subject to
      regulation by global cellular processes. The draft genome sequence is 6,177,154
      bp long and contains 5,608 predicted coding sequences.
AU  - Almeida EL
AU  - Margassery LM
AU  - O'Leary N
AU  - Dobson ADW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01534-17.

PMID- 27660768
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of 40 Salmonella enterica Serovar Typhimurium Strains Isolated from Humans and Food in Brazil.
PG  - e00892-16
AB  - Salmonellosis is an important health problem worldwide and Salmonella enterica serovar
      Typhimurium is one of the most common isolated serovars. Here, we
      reported the draft genomes of 40 S Typhimurium strains isolated from humans and
      food in Brazil. These draft genomes will improve phylogenetic analysis and will
      help enhance our understanding of strains of this serovar isolated in Brazil.
AU  - Almeida F
AU  - Medeiros MI
AU  - Rodrigues DP
AU  - Payne J
AU  - Timme RE
AU  - Allard MW
AU  - Falcao JP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00892-16.

PMID- 19061402
VI  - 22
DP  - 2009
TI  - A draft genome sequence of Pseudomonas syringae pv. tomato T1 reveals a type III effector repertoire significantly divergent from that of Pseudomonas syringae pv. tomato DC3000.
PG  - 52-62
AB  - Diverse gene products including phytotoxins, pathogen-associated molecular
      patterns, and type III secreted effectors influence interactions between
      Pseudomonas syringae strains and plants, with additional yet
      uncharacterized factors likely contributing as well. Of particular
      interest are those interactions governing pathogen-host specificity.
      Comparative genomics of closely related pathogens with different host
      specificity represents an excellent approach for identification of genes
      contributing to host-range determination. A draft genome sequence of
      Pseudomonas syringae pv. tomato T1, which is pathogenic on tomato but
      nonpathogenic on Arabidopsis thaliana, was obtained for this purpose and
      compared with the genome of the closely related A. thaliana and tomato
      model pathogen P. syringae pv. tomato DC3000. Although the overall genetic
      content of each of the two genomes appears to be highly similar, the
      repertoire of effectors was found to diverge significantly. Several P.
      syringae pv. tomato T1 effectors absent from strain DC3000 were confirmed
      to be translocated into plants, with the well-studied effector AvrRpt2
      representing a likely candidate for host-range determination. However, the
      presence of avrRpt2 was not found sufficient to explain A. thaliana
      resistance to P. syringae pv. tomato T1, suggesting that other effectors
      and possibly type III secretion system-independent factors also play a
      role in this interaction.
AU  - Almeida NF
AU  - Yan S
AU  - Lindeberg M
AU  - Studholme DJ
AU  - Schneider DJ
AU  - Condon B
AU  - Liu H
AU  - Viana CJ
AU  - Warren A
AU  - Evans C
AU  - Kemen E
AU  - Maclean D
AU  - Angot A
AU  - Martin GB
AU  - Jones JD
AU  - Collmer A
AU  - Setubal JC
AU  - Vinatzer BA
PT  - Journal Article
TA  - Mol. Plant Microbe Interact.
JT  - Mol. Plant Microbe Interact.
SO  - Mol. Plant Microbe Interact. 2009 22: 52-62.

PMID- 27066196
VI  - 11
DP  - 2016
TI  - The genome anatomy of Corynebacterium pseudotuberculosis VD57 a highly virulent strain causing Caseous lymphadenitis.
PG  - 29
AB  - Corynebacterium pseudotuberculosis strain VD57 (Cp_VD57), a highly virulent, nonmotile,
      non-sporulating, and a mesophilic bacterium, was isolated from a
      goat's granulomatous lesion in the municipality of Juazeiro, Bahia State, Brazil.
      Here, we describe a set of features of the strain, together with the details of
      its complete genome sequence and annotation. The genome comprises of a 2.5 Mbp
      long, single circular genome with 2,101 protein-coding genes, 12 rRNA, 49 tRNA
      and 47 pseudogenes and a G + C content of 52.85 %. Genetic variation was detected
      in Cp_VD57 using C. pseudotuberculosis strain 1002 as reference, wherein small
      genomic insertions and deletions were identified. The comparative analysis of the
      genome sequence provides means to better understand the host pathogen
      interactions of this strain and can also help us to understand the molecular and
      genetic basis of virulence of this bacterium.
AU  - Almeida S et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 29.

PMID- 27609922
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of the Attenuated Corynebacterium pseudotuberculosis Strain T1.
PG  - e00947-16
AB  - We present here the genome sequence of the attenuated Corynebacterium pseudotuberculosis
      strain T1. The sequencing was performed with an Ion Torrent
      Personal Genome Machine platform. The genome is a circular chromosome of
      2,337,201 bp, with a G+C content of 52.85% and a total of 2,125 coding sequences
      (CDSs), 12 rRNAs, 49 tRNAs, and 24 pseudogenes.
AU  - Almeida S
AU  - Loureiro D
AU  - Portela RW
AU  - Mariano DC
AU  - Sousa TJ
AU  - Pereira FL
AU  - Dorella FA
AU  - Carvalho AF
AU  - Moura-Costa LF
AU  - Leal CA
AU  - Figueiredo HC
AU  - Meyer R
AU  - Azevedo V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00947-16.

PMID- 26769931
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a Novel Desulfobacteraceae Member from a Sulfate-Reducing Bioreactor Metagenome.
PG  - e01540-15
AB  - Sulfate-reducing bacteria are important players in the global sulfur cycle and of considerable
      commercial interest. The draft genome sequence of a sulfate-reducing
      bacterium of the family Desulfobacteraceae, assembled from a sulfate-reducing
      bioreactor metagenome, indicates that heavy-metal- and acid-resistance traits of
      this organism may be of importance for its application in acid mine drainage
      mitigation.
AU  - Almstrand R
AU  - Pinto AJ
AU  - Figueroa LA
AU  - Sharp JO
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01540-15.

PMID- 28546487
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Saccharomonospora sp. Strain LRS4.154, a Moderately Halophilic Actinobacterium with the Biotechnologically Relevant Polyketide  Synthase and Nonribosomal Peptide Synthetase Systems.
PG  - e00392-17
AB  - The draft genome sequence of Saccharomonospora sp. strain LRS4.154, a moderately  halophilic
      actinobacterium, has been determined. The genome has 4,860,108 bp, a
      G+C content of 71.0%, and 4,525 open reading frames (ORFs). The clusters of PKS
      and NRPS genes, responsible for the biosynthesis of a large number of
      biomolecules, were identified in the genome.
AU  - Alonso-Carmona S
AU  - Vera-Gargallo B
AU  - de la Haba RR
AU  - Ventosa A
AU  - Sandoval-Trujillo H
AU  - Ramirez-Duran N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00392-17.

PMID- 22815450
VI  - 194
DP  - 2012
TI  - Genome Sequence of Micromonospora lupini Lupac 08, Isolated from Root Nodules of  Lupinus angustifolius.
PG  - 4135
AB  - Micromonospora strains have been isolated from diverse niches, including soil, water, and
      marine sediments and root nodules of diverse symbiotic plants. In this
      work, we report the genome sequence of Micromonospora lupini Lupac 08 isolated
      from root nodules of the wild legume Lupinus angustifolious.
AU  - Alonso-Vega P
AU  - Normand P
AU  - Bacigalupe R
AU  - Pujic P
AU  - Lajus A
AU  - Vallenet D
AU  - Carro L
AU  - Coll P
AU  - Trujillo ME
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4135.

PMID- 28473391
VI  - 5
DP  - 2017
TI  - First Whole-Genome Sequences of Two Multidrug-Resistant Acinetobacter baumannii Strains Isolated from a Moroccan Hospital Floor.
PG  - e00298-17
AB  - This report describes the whole-genome shotgun sequences of two multidrug-resistant
      Acinetobacter baumannii strains, ABE8_07 and ABE12_M,
      isolated from a Moroccan hospital floor. These two genome sequences will initiate
      the study and characterization of the Acinetobacter baumannii genome in Morocco.
AU  - Alouane T
AU  - Uwingabiye J
AU  - Lemnouer A
AU  - Lahlou L
AU  - Laamarti M
AU  - Kartti S
AU  - Benhrif O
AU  - El Misbahi H
AU  - Frikh M
AU  - Benlahlou Y
AU  - Bssaibis F
AU  - El Abbassi S
AU  - Kabbage S
AU  - Maleb A
AU  - Elouennass M
AU  - Ibrahimi A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00298-17.

PMID- 19477083
VI  - 59
DP  - 2011
TI  - The effect of methylation on some biological parameters in Salmonella enterica serovar Typhimurium.
PG  - 192-198
AB  - Cell growth is tightly coupled to DNA replication and its methylation [Proc Nail Acad Sci US A
      93 (1996) 12206-12211]. In a culture medium,
      growing of Salmonella Typhimurium (S. Typhimurium) mutant cells
      (dam(-)) decreased (2.5 fold) relative to the wild type strain
      (dam(+)). In this study, we show that the reason for this growth
      deficiency is due to the DNA methylation. The absence of a Dam
      methyltransferase protein results in poor growth efficiency and
      disturbs the synchrony of replication initiation in vivo, as evaluated
      by flow cytometry. On the other hand, we show that lack of methylation
      could increase the DNA response to thermal stress (decreasing the DNA
      melting temperature, T-m), and the reason for this effect is due to the
      methylation status and not to the number of guanine and cytosine bases
      (G + C) in the duplex DNA. Our results show that methylation is an
      epigenetic factor that may play a key role in the cell growth, the
      synchrony of DNA replication [C R Biologies 330 (2007) 576-580] and the
      stress protection.
AU  - Aloui A
AU  - Tagourti J
AU  - El May A
AU  - Petit DJ
AU  - Landoulsi A
PT  - Journal Article
TA  - Pathol. Biol. (Paris)
JT  - Pathol. Biol. (Paris)
SO  - Pathol. Biol. (Paris) 2011 59: 192-198.

PMID- 8443331
VI  - 64
DP  - 1993
TI  - Restriction enzymes have altered cleavage rates at sites near certain sequences.
PG  - A280
AB  - Under appropriate environmental conditions, e.g. supercoiled DNA, 50-100 uM cobalt hexamine,
      the DNA sequence (CG)4 forms non-B or Z-type structures. Restriction enzymes, e.g. BglI,
      EcoRV, HaeIII, MboI, NotI, PstI, TaqI, cutting at sites up to circa 50 base pairs from
      inserted (CG)4 segments show enhanced cleavage rates (in the presence of cobalt hexamine)
      relative to cleavage rates for DNA fragments not containing the (CG)4. We have previously
      shown that the sequence TCTTG is a hot spot for the binding of the carcinogen
      N-acetoxy-N-acetyl-2-aminofluorene. Restriction enzymes cleaving near an inserted TCTTG
      segment have decreased reaction rates. Gel retardation binding studies and exonuclease
      footprinting studies suggest that the observed alterations in restriction enzyme reaction
      rates arise from changes in the binding of the restriction enzyme to DNA when either (CG)4 or
      TCTTG segments are present. These studies suggest that certain sequences can modulate DNA
      functions.
AU  - Aloyo MC
AU  - Campbell D
AU  - Combates NJ
AU  - Gonzalez J
AU  - Kwok Y
AU  - Sheardy RD
AU  - Winkle SA
PT  - Journal Article
TA  - Biophys. J.
JT  - Biophys. J.
SO  - Biophys. J. 1993 64: A280.

PMID- 12957947
VI  - 69
DP  - 2003
TI  - Characterization of a theta-type plasmid from Lactobacillus sakei: a potential basis for low-copy-number vectors in lactobacilli.
PG  - 5574-5584
AB  - The complete nucleotide sequence of the 13-kb plasmid pRV500, isolated from Lactobacillus
      sakei RV332, was determined. Sequence analysis enabled
      the identification of genes coding for a putative type I
      restriction-modification system, two genes coding for putative
      recombinases of the integrase family, and a region likely involved in
      replication. The structural features of this region, comprising a putative
      ori segment containing 11- and 22-bp repeats and a repA gene coding for a
      putative initiator protein, indicated that pRV500 belongs to the pUCL287
      subfamily of theta-type replicons. A 3.7-kb fragment encompassing this
      region was fused to an Escherichia coli replicon to produce the shuttle
      vector pRV566 and was observed to be functional in L. sakei for plasmid
      replication. The L. sakei replicon alone could not support replication in
      E. coli. Plasmid pRV500 and its derivative pRV566 were determined to be at
      very low copy numbers in L. sakei. pRV566 was maintained at a reasonable
      rate over 20 generations in several lactobacilli, such as Lactobacillus
      curvatus, Lactobacillus casei, and Lactobacillus plantarum, in addition to
      L. sakei, making it an interesting basis for developing vectors. Sequence
      relationships with other plasmids are described and discussed.
AU  - Alpert CA
AU  - Crutz-Le CAM
AU  - Malleret C
AU  - Zagorec M
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2003 69: 5574-5584.

PMID- 26112787
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Leptospira interrogans Serovar Bratislava, Strain PigK151.
PG  - e00678-15
AB  - Leptospira interrogans serovar Bratislava infection occurs in multiple domestic and wildlife
      species and is associated with poor reproductive performance in
      swine and horses. We present the complete genome assembly of strain PigK151
      comprising two chromosomes, CI (4.457 Mbp) and CII (358 kbp).
AU  - Alt DP
AU  - Wilson-Welder JH
AU  - Bayles DO
AU  - Cameron C
AU  - Adler B
AU  - Bulach DM
AU  - Seemann T
AU  - Lehane MJ
AU  - Haines LR
AU  - Darby AC
AU  - Hall N
AU  - Radford AD
AU  - Zuerner RL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00678-15.

PMID- 15671160
VI  - 102
DP  - 2005
TI  - Inaugural Article: From the Cover: Complete genome sequence of the probiotic lactic acid bacterium Lactobacillus acidophilus NCFM.
PG  - 3906-3912
AB  - Lactobacillus acidophilus NCFM is a probiotic bacterium that has been produced commercially
      since 1972. The complete genome is 1,993,564 nt and
      devoid of plasmids. The average GC content is 34.71% with 1,864 predicted
      ORFs, of which 72.5% were functionally classified. Nine phage-related
      integrases were predicted, but no complete prophages were found. However,
      three unique regions designated as potential autonomous units (PAUs) were
      identified. These units resemble a unique structure and bear
      characteristics of both plasmids and phages. Analysis of the three PAUs
      revealed the presence of two R/M systems and a prophage maintenance system
      killer protein. A spacers interspersed direct repeat locus containing 32
      nearly perfect 29-bp repeats was discovered and may provide a unique
      molecular signature for this organism. In silico analyses predicted 17
      transposase genes and a chromosomal locus for lactacin B, a class II
      bacteriocin. Several mucus- and fibronectin-binding proteins, implicated
      in adhesion to human intestinal cells, were also identified. Gene clusters
      for transport of a diverse group of carbohydrates, including
      fructooligosaccharides and raffinose, were present and often accompanied
      by transcriptional regulators of the lacI family. For protein degradation
      and peptide utilization, the organism encoded 20 putative peptidases,
      homologs for PrtP and PrtM, and two complete oligopeptide transport
      systems. Nine two-component regulatory systems were predicted, some
      associated with determinants implicated in bacteriocin production and acid
      tolerance. Collectively, these features within the genome sequence of L.
      acidophilus are likely to contribute to the organisms' gastric survival
      and promote interactions with the intestinal mucosa and microbiota.
AU  - Altermann E
AU  - Russell WM
AU  - Azcarate-Peril MA
AU  - Barrangou R
AU  - Buck BL
AU  - McAuliffe O
AU  - Souther N
AU  - Dobson A
AU  - Duong T
AU  - Callanan M
AU  - Lick S
AU  - Hamrick A
AU  - Cano R
AU  - Klaenhammer TR
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2005 102: 3906-3912.

PMID- 23144400
VI  - 194
DP  - 2012
TI  - Genome Sequence of Rhizobium grahamii CCGE502, a Broad-Host-Range Symbiont with Low Nodulation Competitiveness in Phaseolus vulgaris.
PG  - 6651-6652
AB  - Here we present the genome sequence of Rhizobium grahamii CCGE502. R. grahamii groups with
      other newly described broad-host-range species, which are not very
      efficient Phaseolus vulgaris symbionts, with a wide geographic distribution and
      which constitutes a novel Rhizobium clade.
AU  - Althabegoiti MJ
AU  - Lozano L
AU  - Torres-Tejerizo G
AU  - Ormeno-Orrillo E
AU  - Rogel MA
AU  - Gonzalez V
AU  - Martinez-Romero E
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6651-6652.

PMID- 28546485
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Magnesium-Dissolving Lactococcus garvieae A1, Isolated from Soil.
PG  - e00386-17
AB  - The probiotic bacterium Lactococcus garvieae A1, isolated from soil, is interesting for
      biomining applications. Here, we report the draft genome sequence
      and annotation of this strain, with a focus on metal transporter enzymes.
AU  - Altin G
AU  - Nikerel E
AU  - Sahin F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00386-17.

PMID- 9916318
VI  - 828
DP  - 1998
TI  - Purification of TaqI endonuclease from Thermus aquaticus.
PG  - 373-381
AB  - A purification procedure for the thermostable restriction enzyme TaqI was developed using
      high-performance ion-exchange liquid chromatography.  The effects of various operating
      conditions on the separation behavior of TaqI endonuclease from the cell extracts were
      investigated for optimization and scaling up.  The separation of the enzyme by HPLC was found
      to be strongly dependent on the sample volume, slope of linear gradient and order of the
      ion-exchange columns.  The final yield of the enzyme is also dependent to a great extent upon
      the number of fractionation steps employed to purify the enzyme.  In the present study, 4000 U
      TaqI endonuclease per mg. Protein was recovered from 2g Thermus aquaticus cells with a
      two-step purification protocol in one day.  The purification factor was 24.  Compared to other
      classical methods of purification reported in literature with 4,000 or 32,000 U enzyme from
      200 g of Thermus aquaticus cells, HPLC yielded 190,000 U enzyme from 200g cells using cation
      and anion HPLC  columns sequentially and thus resulted in a higher efficiency.
AU  - Altintas MM
AU  - Ozer N
AU  - Ulgen KO
PT  - Journal Article
TA  - J. Chromatogr. A
JT  - J. Chromatogr. A
SO  - J. Chromatogr. A 1998 828: 373-381.

PMID- 
VI  - 19
DP  - 1999
TI  - Growth of Thermus aquaticus and its TaqI endonuclease production.
PG  - 45-56
AB  - The culture behavior of Thermus aquaticus was characterized.  The response of the bacterium to
      various carbon (tryptone, glucose, glycerol) and nitrogen sources (yeast extract, NaNO3,
      (NH4)2SO4, leucine, thymine, thiamine, glutamic acid) was studied.  Amino acids did not
      support growth, but Castenholz salt medium supplemented with yeast extract and glucose or
      tryptone resulted in good growth and production.  A suitable medium composition giving the
      highest biomass concentration and enzyme yield was developed.  The simple medium containing
      TYE-NaCl resulted in the highest biomass concentration, whereas Castenholz mineral medium
      supplemented with tryptone and yeast extract gave the highest specific activity and enzyme
      yield.  The effect of inoculum age and size on growth was also investigated in order to
      improve the yield and process consistency.  The use of shake flasks inoculated with
      precultures at their early or late stationary phase resulted in the same biomass concentration
      (0.560+- 0.015 g/l) and similar maximum specific growth rates (0.258 +- 0.003 h-1).  Inoculum
      sizes between 1 and 2.5 percent were optimal for cell growth.  As the other papers on
      thermophilic microorganisms, including the T. aquaticus YT-1 strain, gave qualitative
      information on growth, the results presented here cannot be compared with others on a
      quantitative basis.  TaqI endonuclease was purified using a 5 step protocol including cell
      disruption, adsorption, precipitation, column chromatography and final dialysis.  The enriched
      fraction had a specific activity of 33,600 U TaqI endonuclease per mg protein.
AU  - Altintas MM
AU  - Ulgen KO
PT  - Journal Article
TA  - Acta Biotechnol.
JT  - Acta Biotechnol.
SO  - Acta Biotechnol. 1999 19: 45-56.

PMID- 30061376
VI  - 86
DP  - 2018
TI  - Genome plasticity of agr-defective Staphylococcus aureus during clinical infection.
PG  - e00331-18
AB  - Therapy for bacteremia caused by Staphylococcus aureus is often ineffective, even
      when treatment conditions are optimal according to experimental protocols.
      Adapted subclones, such as those bearing mutations that attenuate agr-mediated
      virulence activation, are associated with persistent infection and patient
      mortality. To identify additional alterations in agr-defective mutants, we
      sequenced and assembled the complete genomes of clone pairs from colonizing and
      infected sites of several patients in whom S. aureus demonstrated a within-host
      loss of agr function. We report that events associated with agr inactivation
      result in agr-defective blood and nares strain pairs that are enriched in
      mutations compared to pairs from wild-type controls. The random distribution of
      mutations between colonizing and infecting strains from the same patient, and
      between strains from different patients, suggests that much of the genetic
      complexity of agr-defective strains result from prolonged infection or
      therapy-induced stress. However, in one of the agr-defective infecting strains,
      multiple genetic changes resulted in increased virulence in a murine model of
      bloodstream infection, bypassing the mutation of agr and raising the possibility
      that some changes were selected. Expression profiling correlated the elevated
      virulence of this agr-defective mutant to restored expression of the
      agr-regulated ESAT6-like Type VII secretion system, a known virulence factor.
      Thus, additional mutations outside the agr locus can contribute to
      diversification and adaptation during infection by S. aureusagr mutants
      associated with poor patient outcome.
AU  - Altman DR et al
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2018 86: e00331-18.

PMID- 10831840
VI  - 249
DP  - 2000
TI  - Primary structure and expression of the Xiphophorus DNA-(cytosine-5)-methyltransferase XDNMT-1.
PG  - 75-82
AB  - Small aquarium fishes become increasingly important in the study of normal vertebrate
      development and disease. Differential DNA methylation might play a role in these processes. In
      the teleost Xiphophorus, a well-established animal model for melanoma formation,
      tumour-specific hypomethylation of the melanoma-inducing gene ONC-Xmrk has been observed. We
      have isolated a cDNA for the DNA-(cytosine-5)-methyltransferase XDNMT-1 from this organism,
      which encodes the first full-length protein from a fish species. Linkage analysis showed that
      Xdnmt-1 is different from the Xiphophorus tumour suppressor R, which is involved in the
      transcriptional repression of the ONC-Xmrk melanoma oncogene in healthy fish. As methylation
      has been implicated in the regulation of ONC-Xmrk expression, XDNMT-1 might play a role by
      acting up- or downstream of R. Expression analysis demonstrated that the Xdnmt-1 transcript is
      present in all adult tissues and cell lines tested. However, developing embryos show a
      spatially and temporally regulated expression pattern suggesting that the enzyme might play a
      role during development in fish.
AU  - Altschmied J
AU  - Volff J
AU  - Winkler C
AU  - Gutbrod H
AU  - Korting C
AU  - Pagany M
AU  - Schartl M
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 2000 249: 75-82.

PMID- 22965079
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Pseudomonas sp. Strain Ag1, Isolated from the Midgut of  the Malaria Mosquito Anopheles gambiae.
PG  - 5449
AB  - A Pseudomonas sp. bacterium was isolated from the midguts of Anopheles gambiae mosquitoes.
      Here we present the annotated Pseudomonas sp. draft genome sequence
      as a contribution to the efforts of characterization of the mosquito gut
      microbiome.
AU  - Alvarez C
AU  - Kukutla P
AU  - Jiang J
AU  - Yu W
AU  - Xu J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5449.

PMID- 8316078
VI  - 8
DP  - 1993
TI  - Complex transcription of an operon encoding the Sall restriction-modification system of Streptomyces albus G.
PG  - 243-252
AB  - High-resolution S1 nuclease mapping of mRNA synthesized in vivo, in vitro run-off
      transcription with RNA polymerase from Streptomyces lividans and gene fusions were used to
      analyse the transcriptional organization of the Sall restriction-modification system of
      Streptomyces albus G. The sallR and sallM genes that encode the restriction endonuclease and
      its cognate methyltransferase constitute an operon which is mainly transcribed from sal-pR1, a
      promoter located immediately upstream of sallR, with two possible minor promoters further
      upstream. Another promoter, sal-pM, is within the 3' end of the sallR coding region, and
      allows expression of the modification gene in the absence of sal-pR1. The sal-pM promoter
      might be involved in the establishment of modification prior to restriction endonuclease
      activity. Sequences upstream of the apparent transcriptional start sites for sal-pR1 and
      sal-pM show similarity with the -10 region of typical vegetatively expressed eubacterial
      promoters, but appropriately centered -35 regions are absent.
AU  - Alvarez MA
AU  - Chater KF
AU  - Rosario MR
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1993 8: 243-252.

PMID- 9003289
VI  - 253
DP  - 1996
TI  - Comparative analysis of expression of the SalI restriction-modification system in Escherichia coli and Streptomyces.
PG  - 74-80
AB  - The salIR and salIM genes encode the endonuclease and methyltransferase components of the SalI
      restriction-modification system from Streptomyces albus G.  Expression of the salI genes in
      Escherichia coli was investigated and major differences with Streptomyces were found.  In E.
      coli there is no detectable expression of the salIR gene due to inactivity of the sal-pR
      promoter region.  In the natural host of the system this region directs transcription of the
      salI genes as a bicistronic message.  In contrast to salIR, salIM is transcribed in the
      heterologous host from a promoter within the salI DNA.  Since sal-pR is not active, the gene
      cannot be expressed as part of the salI operon.  It is probably transcribed from sal-pM, a
      promoter internal to the operon which allows independent expression of the modification gene
      in Streptomyces.  Replacement of sal-pR by the strong pLac promoter allows expression of salIR
      in E. coli and enhances expression of salIM.  The resulting strain produces about 10 times
      more endonuclease than a Streptomyces clone containing the SalI system under the control of
      sal-pR.
AU  - Alvarez MA
AU  - Gomez A
AU  - Gomez P
AU  - Brooks JE
AU  - Rodicio MR
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1996 253: 74-80.

PMID- 7607497
VI  - 157
DP  - 1995
TI  - Expression of the SalI restriction-modification system of Streptomyces albus G in Escherichia coli.
PG  - 231-232
AB  - The salIR and salIM genes of Streptomyces albus G encode the restriction endonuclease (ENase)
      and DNA methyltransferase (MTase) of the SalI restriction-modification (R-M) system.  In S.
      albus G, the genes constitute an operon that is mainly transcribed from a promoter located
      upstream from SalIR, the first gene of the operon.  In addition, a second promoter, at the 3'
      end of SalIR, allows independent transcription of the MTase gene.  Expression of salIR and
      salIM in Escherichia coli was investigated.  The ENase gene was not expressed in the
      heterologous host, probably due to inactivity of the main promoter of the salI operon.  In
      contrast to salIR, salIM was functional in E. coli.  Preliminary S1 nuclease mapping
      experiments suggest that the alternative promoter of the MTase gene can initiate transcription
      in the heterologous, as well as in the homologous host.
AU  - Alvarez MA
AU  - Gomez A
AU  - Gomez P
AU  - Rodicio MR
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 231-232.

PMID- 26769935
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequence of a Beijing Extensively Drug-Resistant Mycobacterium tuberculosis Clinical Isolate from Buenaventura, Colombia.
PG  - e01549-15
AB  - Extensively drug-resistant Mycobacterium tuberculosis (XDR-TB) has been reported  to the WHO
      by 100 countries, including Colombia. An estimated 9.0% of people with
      multidrug-resistant TB have XDR-TB. We report the genome sequence of a Beijing
      XDR-TB clinical isolate from Buenaventura, Colombia. The genome sequence is
      composed of 4,298,162 bp with 4,359 genes.
AU  - Alvarez N
AU  - Haft D
AU  - Hurtado UA
AU  - Robledo J
AU  - Rouzaud F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01549-15.

PMID- 27313305
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequencing of a Haarlem Extensively Drug-Resistant Mycobacterium tuberculosis Clinical Isolate from Medellin, Colombia.
PG  - e00566-16
AB  - Colombia is one of the 105 countries that has reported at least one case of extensively
      drug-resistant tuberculosis (XDR-TB). The Mycobacterium tuberculosis
      Haarlem genotype is ubiquitous worldwide. Here, we report the high-quality draft
      genome sequence of a Colombian Haarlem XDR-TB clinical isolate composed of
      4,329,127 bp with 4,386 genes.
AU  - Alvarez N
AU  - Haft D
AU  - Hurtado UA
AU  - Robledo J
AU  - Rouzaud F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00566-16.

PMID- 27034498
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequencing of Two Latin American-Mediterranean Extensively Drug-Resistant Mycobacterium tuberculosis Clinical Isolates from Medellin,  Colombia.
PG  - e00192-16
AB  - Colombia, with a tuberculosis incidence of 33 cases per 100,000 population, is one of the
      countries that have reported extensively drug-resistant Mycobacterium
      tuberculosis (XDR-TB). We report the high-quality draft genome sequences of two
      Latin American-Mediterranean XDR-TB clinical isolates (TBR-152 and TBR-175),
      comprising 4,303,775 bp and 4,330,115 bp, respectively.
AU  - Alvarez N
AU  - Haft D
AU  - Hurtado UA
AU  - Robledo J
AU  - Rouzaud F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00192-16.

PMID- 26205868
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Biofilm-Hyperproducing Acinetobacter baumannii Clinical Strain MAR002.
PG  - e00824-15
AB  - We report the draft genome sequence of Acinetobacter baumannii strain MAR002, a
      biofilm-hyperproducing clinical strain isolated during the study CP/09/0033
      (GEIH/REIPI-Ab2010, Spain). The genome of A. baumannii MAR002 has an approximate
      length of 3,717,929 bp and 3,300 protein-coding sequences, with a C+G content of
      39.09%.
AU  - Alvarez-Fraga L
AU  - Lopez M
AU  - Merino M
AU  - Rumbo-Feal S
AU  - Tomas M
AU  - Bou G
AU  - Poza M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00824-15.

PMID- 29725499
VI  - 13
DP  - 2018
TI  - High quality draft genome sequences of Mycoplasma agassizii strains PS6(T) and 723 isolated from Gopherus tortoises with upper respiratory tract disease.
PG  - 12
AB  - Mycoplasma agassizii is one of the known causative agents of upper respiratory tract disease
      (URTD) in Mojave desert tortoises (Gopherus agassizii) and in
      gopher tortoises (Gopherus polyphemus). We sequenced the genomes of M. agassizii
      strains PS6(T) (ATCC 700616) and 723 (ATCC 700617) isolated from the upper
      respiratory tract of a Mojave desert tortoise and a gopher tortoise,
      respectively, both with signs of URTD. The PS6(T) genome assembly was organized
      in eight scaffolds, had a total length of 1,274,972 bp, a G + C content of
      28.43%, and contained 979 protein-coding genes, 13 pseudogenes and 35 RNA genes.
      The 723 genome assembly was organized in 40 scaffolds, had a total length of
      1,211,209 bp, a G + C content of 28.34%, and contained 955 protein-coding genes,
      seven pseudogenes, and 35 RNA genes. Both genomes exhibit a very similar
      organization and very similar numbers of genes in each functional category. Pairs
      of orthologous genes encode proteins that are 93.57% identical on average.
      Homology searches identified a putative cytadhesin. These genomes will enable
      studies that will help understand the molecular bases of pathogenicity of this
      and other Mycoplasma species.
AU  - Alvarez-Ponce D
AU  - Weitzman CL
AU  - Tillett RL
AU  - Sandmeier FC
AU  - Tracy CR
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2018 13: 12.

PMID- Not included in PubMed...
VI  - 372
DP  - 1991
TI  - The recognition of DNA by the EcoRV restriction endonuclease: Accuracy and cation dependence.
PG  - 627
AB  - In order to investigate the accuracy of the EcoRV restriction endonuclease we have synthesized
      20 single stranded oligodeoxynucleotides similarly as described for EcoRI recently. These can
      be hybridized to give a set of double stranded substrates comprising the canonical recognition
      sequence, the 9 sequences deviating from it by one base pair (star substrates) or the 18
      sequences with all possible mismatched base pairs within the recognition sequence (mismatch
      substrates).
AU  - Alves J
AU  - Kohler E
AU  - Selent U
AU  - Thielking V
AU  - Wolfes H
AU  - Pingoud A
PT  - Journal Article
TA  - Biol. Chem. Hoppe Seyler
JT  - Biol. Chem. Hoppe Seyler
SO  - Biol. Chem. Hoppe Seyler 1991 372: 627.

PMID- 6323183
VI  - 140
DP  - 1984
TI  - The influence of sequences adjacent to the recognition site on the cleavage of oligodeoxynucleotides by the EcoRI endonuclease.
PG  - 83-92
AB  - We have investigated the influence of the nucleotide sequence adjacent to the
      recognition site on the rate of cleavage of DNA by the restriction endonuclease
      EcoRI.  For this purpose two decadeoxynucleotides, d(G-G-G-A-A-T-T-C-t-T) (Ia)
      and d(A-A-G-A-A-t-T-C-C-C) (Ib) were synthesized.  The duplex Ia Ib is cleaved
      by EcoRI preferentially in the dA-rich strand (approximately 10 times over the
      dG-rich strand).  The individual nucleotides Ia and Ib are also cleaved by
      EcoRI, Ib at a higher rate than Ia and both at a lower rate than Ia Ib.  The
      temperature dependence of the reaction rate shows that only double-stranded
      oligodeoxynucleotides are substrates for the EcoRI endonuclease.  We have,
      furthermore, synthesized oligomers of d(G-G-A-A-T-T-C-C), which contain two,
      three and four EcoRI sites, respectively.  These oligodeoxynucleotides are
      preferentially cleaved at the sites next to the 5' end, where the recognition
      site is only flanked by one dG dC base pair, in contrast to the other sites
      which are flanked by three such pairs.  These data indicate that sequences
      adjacent to the recognition site influence the rate of cleavage: dA dT base
      pairs enhance and dG dC base pairs slow down the hydrolytic activity of the
      EcoRI endonuclease.
AU  - Alves J
AU  - Pingoud A
AU  - Haupt W
AU  - Langowski J
AU  - Peters F
AU  - Maass G
AU  - Wolff C
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1984 140: 83-92.

PMID- 6282584
VI  - 124
DP  - 1982
TI  - Two identical subunits of the EcoRI restriction endonuclease co-operate in the binding and cleavage of the palindromic substrate.
PG  - 139-142
AB  - The cleavage of radioactively labelled double-stranded d(G-G-A-A-T-T-C-C) was
      studied in single turnover experiments with substrate and enzyme both being in
      the micromolar range.  The reaction rate was found to increase with enzyme
      concentration until a ratio of one tetrameric enzyme to two double-stranded
      substrates was reached, further increase of the enzyme concentration then leads
      to a sharp decline of the reaction rate.  These findings are interpreted in the
      following manner.  (a) Two subunits of the EcoRI endonuclease co-operate in
      binding and possibly also in cleaving the palindromic substrate.  (b) The
      enzymatic action of the EcoRI endonuclease is inhibited by excess enzyme,
      possibly due to unspecific binding of the enzyme-substrate complex.  The
      self-inhibition of EcoRI endonuclease has also been observed with
      macromolecular substrates.
AU  - Alves J
AU  - Pingoud A
AU  - Langowski J
AU  - Urbanke C
AU  - Maass G
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1982 124: 139-142.

PMID- 2659077
VI  - 28
DP  - 1989
TI  - Changing the hydrogen-bonding potential in the DNA binding site of EcoRI by site-directed mutagenesis drastically reduces the enzymatic activity, not the preference of this restriction endonuclease for cleavage within the site GAATTC.
PG  - 2678-2684
AB  - According to the X-ray structure analysis of an EcoRI-oligodeoxynucleotide
      complex [McClarin et al. (1986) Science 234, 1526], sequence specificity is
      mediated by 12 hydrogen bonds, 6 from each of the two identical subunits of the
      dimeric enzyme to the recognition site -GAATTC-: Arg200 forms two hydrogen
      bonds with guanine, while Glu144 and Arg145 form four hydrogen bonds to
      adjacent adenine residues.  Changing the hydrogen-bonding potential at the
      recognition site without perturbing the rest of the interface should lead to
      the recognition of degenerate sequences [Rosenberg et al. (1987) in Protein
      Engineering (Oxender, D.L., & Fox, C.F., Eds.) pp 237-250, Liss, New York].  We
      have shown previously that replacing Glu144 by Gln and Arg145 by Lys affects
      the activity of the enzyme, not, however, its specificity [Wolfes et al. (1986)
      Nucleic Acids Res. 14, 9063].  We show now that mutation of Arg200 to Lys, the
      double mutation Glu144Arg145 to GlnLys, and the triple mutation
      Glu144Arg145Arg200 to GlnLysLys do not lead to a detectable degeneracy of the
      specificity of cleavage by EcoRI but significantly impair the catalytic
      activity of this enzyme.  A detailed analysis of the steady-state kinetics of
      cleavage of pUC8 DNA and a tridecadeoxynucleotide substrate demonstrates that
      the reduction in activity for all DNA binding site mutants investigated so far
      is mainly due to a decrease in Kcat, with the exception of the Arg200 to Lys
      mutant, which is only impaired in its Km.  This observation is confirmed by
      nitrocellulose filter experiments which show that this mutant has a lower
      affinity toward oligodeoxynucleotide substrates than the other DNA binding site
      mutants and a much lower affinity than wild-type EcoRI.  While these and
      previous data clearly demonstrate that Glu144, Arg145, and Arg200 are essential
      for efficient substrate binding and catalysis, their involvement in the
      specific recognition is more intricate than proposed on the basis of the X-ray
      structure analysis.  Our results also suggest that the specificity of EcoRI
      cannot easily be relaxed, and in particular not without affecting its activity.
AU  - Alves J
AU  - Ruter T
AU  - Geiger R
AU  - Fliess A
AU  - Maass G
AU  - Pingoud A
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1989 28: 2678-2684.

PMID- 7669777
VI  - 34
DP  - 1995
TI  - Accuracy of the EcoRV restriction endonuclease: binding and cleavage studies with oligodeoxynucleotide substrates containing degenerate recognition sequences.
PG  - 11191-11197
AB  - In order to investigate the accuracy of the EcoRV restriction endonuclease, we have
      synthesized a set of double-stranded oligodeoxynucleotides comprising the canonical
      recognition sequence, the 9 star sequences (i.e., sequences deviating by one base pair from
      the canonical sequence), and the 18 mismatch sequences (i.e. sequences deviating by one base
      from the canonical sequence).  For each individual single strand of all these 28 substrates we
      have measured the rate of phosphodiester bond cleavage under normal buffer conditions.
      Double-strand cleavage of star substrates is at least 5 orders of magnitude slower than
      cleavage of the canonical substrate.  In contrast, most of the mismatch substrates are
      accepted more readily.  In the absence of the essential cofactor Mg2+, EcoRV binds weakly but
      equally to the canonical and degenerate substrates (i.e., KDiss is in the micromolar range).
      However, the inactive catalytic site mutant D90A in the presence of Mg2+ binds the canonical
      substrate 1-2 orders of magnitude better than degenerate substrates.  Therefore, the EcoRV
      endonuclease needs the essential cofactor Mg2+ to create thermodynamic discrimination between
      degenerate and canonical sites.  But the main discrimination is kinetically controlled and
      takes place during cleavage.  While in the canonical substrate both single strands are cleaved
      with an equal velocity, in all other substrates one single strand is cleaved faster than the
      other one, resulting in a dissociation of the enzyme from the DNA between the two cuts.  In
      vivo this may lead to repair of the erroneous cleavage site by DNA ligases.  The order of
      single-strand nicking together with the division of base contacts on both subunits suggests
      that correct recognition by one subunit triggers cleavage by the other one.
AU  - Alves J
AU  - Selent U
AU  - Wolfes H
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1995 34: 11191-11197.

PMID- 1892579
VI  - 8
DP  - 1991
TI  - The recognition of DNA by the EcoRV restriction endonuclease:  accuracy and cation dependence.
PG  - a007
AB  - None
AU  - Alves J
AU  - Thielking V
AU  - Selent U
AU  - Kohler E
AU  - Wolfes H
AU  - Pingoud A
PT  - Journal Article
TA  - J. Biomol. Struct. Dyn.
JT  - J. Biomol. Struct. Dyn.
SO  - J. Biomol. Struct. Dyn. 1991 8: a007.

PMID- 2611219
VI  - 28
DP  - 1989
TI  - Fluorescence stopped-flow kinetics of the cleavage of synthetic oligodeoxynucleotides by the EcoRI restriction endonuclease.
PG  - 7879-7888
AB  - We have investigated in fluorescence stopped-flow and temperature-jump
      experiments the EcoRI-catalyzed cleavage of synthetic palindromic
      tridecadeoxynucleotides which contain the EcoRI site but differ in the flanking
      sequences.  The overall reaction can be resolved in several reactions which
      were analyzed by a nonlinear least-squares fitting procedure on the
      experimental data.  The result of this analysis is a minimal scheme that
      describes the overall reaction in terms of the rate constants of the individual
      reactions.  According to this scheme EcoRI and the tridecadeoxynucleotide
      substrates associate in the presence of Mg2+ in a nearly diffusion-controlled
      process.  This is followed by a reaction which is or includes the cleavage of
      the first phosphodiester bond.  There is no indication for a time-resolved
      conformational transition prior to catalysis.  After cleavage of the first
      strand, dissociation of the nicked double strand can occur, which then
      rearranges to the original palindromic double-stranded substrate and is bound
      again by the enzyme.  Alternatively, the nicked double strand can be cleaved in
      the second strand.  This reaction is followed by product release from the
      enzyme.  The magnitude of the individual rate constants depends on the
      substrate used; the differences explain the preference of EcoRI for substrates
      that contain AT as compared to GC base pairs next to the recognition site.
AU  - Alves J
AU  - Urbanke C
AU  - Fliess A
AU  - Maass G
AU  - Pingoud A
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1989 28: 7879-7888.

PMID- 
VI  - 14
DP  - 2004
TI  - Protein engineering of restriction enzymes.
PG  - 393-411
AB  - Restriction endonucleases are among the most accurate enzymes known.  Consequently, changing
      their very high sequence specificity is one of the scientific goals in studying these enzymes.
      This review focuses on protein engineering regarding Type II restriction enzymes.  They
      comprise the vast majority of the about 3600 entities listed in REBASE today, although the
      number of those studied in detail is far smaller.  First, we will discuss different approaches
      to changing the recognition of a given sequence starting with rational design using
      site-directed mutagenesis and progressing to random mutagenesis combined with in vivo
      selection.  Then, we will describe attempts to lengthen the recognition sequence by designing
      additional enzyme contacts to DNA.  As the dimeric nature of all restriction enzymes doubles
      the effect of each amino acid exchange, we will also discuss engineering of subunit
      composition.  Finally, we will speculate on possible future directions of protein engineering
      of restriction enzymes.
AU  - Alves J
AU  - Vennekohl P
PT  - Journal Article
TA  - Nucleic Acids Mol. Biol.
JT  - Nucleic Acids Mol. Biol.
SO  - Nucleic Acids Mol. Biol. 2004 14: 393-411.

PMID- 23345457
VI  - 5
DP  - 2013
TI  - Genome evolution and phylogenomic analysis of candidatus kinetoplastibacterium, the betaproteobacterial endosymbionts of strigomonas and angomonas.
PG  - 338-350
AB  - It has been long known that insect-infecting trypanosomatid flagellates from the genera
      Angomonas and Strigomonas harbor bacterial endosymbionts (Candidatus Kinetoplastibacterium or
      TPE [trypanosomatid proteobacterial endosymbiont]) that supplement the host metabolism. Based
      on previous analyses of other bacterial endosymbiont genomes from other lineages, a
      stereotypical path of genome evolution in such bacteria over the duration of their association
      with the eukaryotic host has been characterized. In this work, we sequence and analyze the
      genomes of five TPEs, perform their metabolic reconstruction, do an extensive phylogenomic
      analyses with all available Betaproteobacteria, and compare the TPEs with their nearest
      betaproteobacterial relatives. We also identify a number of housekeeping and central
      metabolism genes that seem to have undergone positive selection. Our genome structure analyses
      show total synteny among the five TPEs despite millions of years of divergence, and that this
      lineage follows the common path of genome evolution observed in other endosymbionts of diverse
      ancestries.
      As previously suggested by cell biology and biochemistry experiments, Ca.
      Kinetoplastibacterium spp. preferentially maintain those genes necessary for the biosynthesis
      of compounds needed by their hosts. We have also shown that metabolic and informational genes
      related to the cooperation with the host are overrepresented amongst genes shown to be under
      positive selection. Finally, our phylogenomic analysis shows that, while being in the
      Alcaligenaceae family of Betaproteobacteria, the closest relatives of these endosymbionts are
      not in the genus Bordetella as previously reported, but more likely in the Taylorella genus.
AU  - Alves JM
AU  - Serrano MG
AU  - Maia-da-Silva F
AU  - Voegtly LJ
AU  - Matveyev AV
AU  - Teixeira MM
AU  - Camargo EP
AU  - Buck GA
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2013 5: 338-350.

PMID- 26823595
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Corynebacterium pseudotuberculosis Strain PA01, Isolated from Sheep in Para, Brazil.
PG  - e01664-15
AB  - Corynebacterium pseudotuberculosis is the etiological agent of caseous lymphadenitis disease.
      In this work, we present the first complete genome
      sequence of Corynebacterium pseudotuberculosis strain PA01, isolated in northern
      Brazil from an infected sheep. The genome length is 2,337,920 bp, and 2,003
      coding sequences (CDS), 12 rRNAs, and 49 tRNAs were predicted.
AU  - Alves JT
AU  - Veras AA
AU  - Cavalcante AL
AU  - de Sa PH
AU  - Dias LM
AU  - Guimaraes LC
AU  - Morais E
AU  - Silva AG
AU  - Azevedo V
AU  - Ramos RT
AU  - Silva A
AU  - Carneiro AR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01664-15.

PMID- 
VI  - 63
DP  - 1998
TI  - Thermophilic strain Bacillus species AA contains several site-specific endonucleases.
PG  - 636-645
AB  - Thermophilic strain Bacillus species AA contains several site-specific endonucleases and three
      of them have been identified.  BspAAI recognizes the sequence 5'-C/TCGAG-3' and cleaves it
      after the first "C" forming 4-nucleotide 5'-ends and is an isoschizomer of XhoI.  BspAAII
      recognizes the sequence 5'-T/CTAGA-3' and cleaves it after the first "T" forming
      4-nucleotide 5'-ends and is an isoschizomer of XbaI.  BspAAIII recognizes the sequence
      5'-GGATCC-3' and is an isomer of BamHI.  The optimal temperature and pH values are 42-48 C
      and 7.0-8.0, respectively.
AU  - Alzhanov DT
AU  - Alzhanova DV
AU  - Zheleznaya LA
AU  - Matvienko NI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1998 63: 636-645.

PMID- 9526116
VI  - 63
DP  - 1998
TI  - Isolation and characterization of site-specific endonuclease Bsp123I from thermophilic strain Bacillus species 123.
PG  - 207-211
AB  - The preparation of site-specific endonuclease Bsp123I was isolated and purified from the
      thermophilic strain Bacillus species 123.  Endonuclease Bsp123I recognizes the sequence CGCG
      and cleaves it in the middle between nucleotides G and C, producing blunt ends.  Thus, Bsp123I
      is an isoschizomer of FnuDII.  The maximal activity of the enzyme is displayed at 42 C, pH
      8.0, 100mM NaCl, 10mM MgCl2.
AU  - Alzhanova DV
AU  - Alzhanov DT
AU  - Zheleznaya LA
AU  - Matvienko NI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1998 63: 207-211.

PMID- 27151794
VI  - 4
DP  - 2016
TI  - Genome Sequences of Salmonella enterica subsp. enterica Serovar Lubbock Strains Isolated from Liver Abscesses of Feedlot Cattle.
PG  - e00319-16
AB  - The genome sequencing of 13 Salmonella enterica subsp. enterica serovar Lubbock strains
      isolated from liver abscesses of feedlot cattle is reported here. The
      availability of these genomes will help to further understand the etiologic role
      of Salmonella strains in liver abscesses of cattle and will serve as references
      in microbial trace-back studies to improve food safety.
AU  - Amachawadi RG
AU  - Thomas M
AU  - Nagaraja TG
AU  - Scaria J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00319-16.

PMID- 26067964
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Escherichia coli O157:H7 Strains Rafaela_II (Clade 8) and 7.1_Anguil (Clade 6) from Cattle in Argentina.
PG  - e00617-15
AB  - Escherichia coli O157:H7 is a major etiologic agent of diseases in humans that cause diarrhea,
      hemorrhagic colitis, and hemolytic-uremic syndrome. Here, we
      report the draft genome sequences of two strains isolated from cattle that had
      high levels of Shiga toxin 2 and high lethality in mice.
AU  - Amadio AF
AU  - Amigo N
AU  - Puebla AF
AU  - Farber MD
AU  - Cataldi AA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00617-15.

PMID- 19654019
VI  - 62
DP  - 2009
TI  - Complete sequence of three plasmids from Bacillus thuringiensis INTA-FR7-4 environmental isolate and comparison with related plasmids from the Bacillus cereus group.
PG  - 172-182
AB  - Bacillus thuringiensis is an insect pathogen used worldwide as a
      bioinsecticide. It belongs to the Bacillus cereus sensu lato group as well
      as Bacillus anthracis and B. cereus. Plasmids from this group of organisms
      have been implicated in pathogenicity as they carry the genes responsible
      for different types of diseases that affect mammals and insects. Some
      plasmids, like pAW63 and pBT9727, encode a functional conjugation
      machinery allowing them to be transferred to a recipient cell. They also
      share extensive homology with the non-functional conjugation apparatus of
      pXO2 from B. anthracis. In this study we report the complete sequence of
      three plasmids from an environmental B. thuringiensis isolate from
      Argentina, obtained by a shotgun sequencing method. We obtained the
      complete nucleotide sequence of plasmids pFR12 (12,095bp), pFR12.5
      (12,459bp) and pFR55 (55,712bp) from B. thuringiensis INTA-FR7-4. pFR12
      and pFR12.5 were classified as cryptic as they do not code for any obvious
      functions besides replication and mobilization. Both small plasmids were
      classified as RCR plasmids due to similarities with the replicases they
      encode. Plasmid pFR55 showed a structural organization similar to that
      observed for plasmids pAW63, pBT9727 and pXO2. pFR55 also shares a tra
      region with these plasmids, containing genes related to T4SS and
      conjugation. A comparison between pFR55 and conjugative plasmids led to
      the postulation that pFR55 is a conjugative plasmid. Genes related to
      replication functions in pFR55 are different to those described for
      plasmids with known complete sequences. pFR55 is the first completely
      sequenced plasmid with a replication machinery related to that of ori44.
      The analysis of the complete sequence of plasmids from an environmental
      isolate of B. thuringiensis permitted the identification of a near
      complete conjugation apparatus in pFR55, resembling those of plasmids
      pAW63, pBT9727 and pXO2. The availability of this sequence is a step
      forward in the study of the molecular basis of the conjugative process in
      Gram positive bacteria, particularly due to the similarity with known
      conjugation systems. It is also a contribution to the expansion of the
      non-pathogenic B. cereus plasmid gene pool.
AU  - Amadio AF
AU  - Benintende GB
AU  - Zandomeni RO
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 2009 62: 172-182.

PMID- 29458677
VI  - 68
DP  - 2018
TI  - Methylomusa anaerophila gen. nov., sp. nov., an anaerobic methanol-utilizing bacterium isolated from a microbial fuel cell.
PG  - 1118-1122
AB  - Abacterial strain, designated MMFC1(T), was isolated from a methanol-fed
      microbial fuel cell that had been inoculated with sludge obtained from a
      wastewater-treatmentfacility in a chemical plant. The strain grows by fermenting
      methanol to produce acetate under anaerobic conditions, while homoacetogenic
      growth is not observed. MMFC1(T) also grows on pyruvate and lactate but not on
      sugars and other organic acids. Cells are curved rods and motile, have
      peritrichous flagella, and form endospores. The genome sequence of strain
      MMFC1(T) supports the physiological data. Phylogenetic analysis based on the 16S
      rRNA gene sequence shows that strain MMFC1(T) is affiliated with the family
      Sporomusaceae, while the closest relative is Sporomusa ovata with
      nucleotide-sequencesimilarity of 93.5 %. Major fatty acids are iso-C13 : 0 3-OH,
      C16 : 1omega9 and iso-C17 : 0. On the basis of its physiological, genomic and
      phylogenetic features, a novel genus and species are proposed to accommodate
      strain MMFC1(T), with the name Methylomusa anaerophila gen. nov., sp. nov. The
      type strain of Methylomusa anaerophila is MMFC1(T) (=JCM 31821(T) = KCTC
      15592(T)).
AU  - Amano N
AU  - Yamamuro A
AU  - Miyahara M
AU  - Kouzuma A
AU  - Abe T
AU  - Watanabe K
PT  - Journal Article
TA  - Int. J. Syst. Evol. Microbiol.
JT  - Int. J. Syst. Evol. Microbiol.
SO  - Int. J. Syst. Evol. Microbiol. 2018 68: 1118-1122.

PMID- 22535939
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Bacterioplanktonic, Mixotrophic Vibrio campbellii Strain PEL22A, Isolated in the Abrolhos Bank.
PG  - 2759-2760
AB  - Vibrio campbellii PEL22A was isolated from open ocean water in the Abrolhos Bank. The genome
      of PEL22A consists of 6,788,038 bp (the GC content is 45%). The number
      of coding sequences (CDS) is 6,359, as determined according to the Rapid
      Annotation using Subsystem Technology (RAST) server. The number of ribosomal
      genes is 80, of which 68 are tRNAs and 12 are rRNAs. V. campbellii PEL22A
      contains genes related to virulence and fitness, including a complete
      proteorhodopsin cluster, complete type II and III secretion systems, incomplete
      type I, IV, and VI secretion systems, a hemolysin, and CTXPhi.
AU  - Amaral GR
AU  - Silva BS
AU  - Santos EO
AU  - Dias GM
AU  - Lopes RM
AU  - Edwards RA
AU  - Thompson CC
AU  - Thompson FL
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2759-2760.

PMID- 22374947
VI  - 194
DP  - 2012
TI  - Genome Sequence of Weissella confusa LBAE C39-2, Isolated from a Wheat Sourdough.
PG  - 1608-1609
AB  - Weissella confusa is a rod-shaped heterofermentative lactic acid bacterium from the family of
      Leuconostocaceae. Here we report the draft genome sequence of the
      strain W. confusa LBAE C39-2 isolated from a traditional French wheat sourdough.
AU  - Amari M
AU  - Laguerre S
AU  - Vuillemin M
AU  - Robert H
AU  - Loux V
AU  - Klopp C
AU  - Morel S
AU  - Gabriel B
AU  - Remaud-Simeon M
AU  - Gabriel V
AU  - Moulis C
AU  - Fontagne-Faucher C
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1608-1609.

PMID- 22374950
VI  - 194
DP  - 2012
TI  - Whole-Genome Sequence of the Human Pathogen Legionella pneumophila Serogroup 12 Strain 570-CO-H.
PG  - 1613-1614
AB  - We present the genomic sequence of the human pathogen Legionella pneumophila serogroup 12
      strain 570-CO-H (ATCC 43290), a clinical isolate from the Colorado
      Department of Health, Denver, CO. This is the first example of a genome sequence
      of L. pneumophila from a serogroup other than serogroup 1. We highlight the
      similarities and differences relative to six genome sequences that have been
      reported for serogroup 1 strains.
AU  - Amaro F
AU  - Gilbert JA
AU  - Owens S
AU  - Trimble W
AU  - Shuman HA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1613-1614.

PMID- 24578273
VI  - 2
DP  - 2014
TI  - Insight into the Draft Genome Sequence of Human Isolate Lactobacillus rhamnosus LR231, a Bacterium with Probiotic Potential.
PG  - e00111-14
AB  - Lactobacillus rhamnosus strain LR231 was isolated from the feces of healthy human subjects. It
      is observed to be a potential probiotic strain, having a broad
      spectrum of antimicrobial activity against a wide range of human pathogens and
      food pathogens. Here, we provide the 2.59-Mb draft genome sequence of L.
      rhamnosus LR231.
AU  - Ambalam P
AU  - Pithva S
AU  - Kothari C
AU  - Kothari R
AU  - Parmar N
AU  - Nathani NM
AU  - Koringa PG
AU  - Joshi CG
AU  - Dave JM
AU  - Vyas BR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00111-14.

PMID- 25838494
VI  - 3
DP  - 2015
TI  - Genome Sequence of Bacillus mycoides B38V, a Growth-Promoting Bacterium of Sunflower.
PG  - e00245-15
AB  - Bacillus mycoides B38V is a bacterium isolated from the sunflower rhizosphere that is able to
      promote plant growth and N uptake. The genome of the isolate has
      approximately 5.80 Mb and presents sequence codifiers for plant growth-promoting
      characteristics, such as nitrate reduction and ammonification and
      iron-siderophore uptake.
AU  - Ambrosini A
AU  - Sant'Anna FH
AU  - de Souza R
AU  - Tadra-Sfeir M
AU  - Faoro H
AU  - Alvarenga SM
AU  - Pedrosa FO
AU  - Souza EM
AU  - Passaglia LM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00245-15.

PMID- 23405336
VI  - 1
DP  - 2013
TI  - Genome Sequence of the Sulfate-Reducing Bacterium Desulfotomaculum hydrothermale  Lam5(T).
PG  - e00114-12
AB  - Here, we report the draft genome sequence of Desulfotomaculum hydrothermale, a
      sulfate-reducing, spore-forming bacterium isolated from a Tunisian hot spring. The genome is
      composed of 2.7 Mb, with a G+C content of 49.48%, and it contains 2,643 protein-coding
      sequences.
AU  - Amin O
AU  - Fardeau ML
AU  - Valette O
AU  - Hirschler-Rea A
AU  - Barbe V
AU  - Medigue C
AU  - Vacherie B
AU  - Ollivier B
AU  - Bertin PN
AU  - Dolla A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00114-12.

PMID- 26494688
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Achromobacter sp. Strain DMS1, Capable of Degrading Polyaromatic Hydrocarbons Isolated from the Industrially Perturbed Environment of Amlakhadi Canal, India.
PG  - e01264-15
AB  - Here, we report the draft genome sequence of Achromobacter sp. strain DMS1, which is 4.9 Mbp
      and has 3,727 coding sequences (CDSs), and is capable of degrading xenobiotic compounds and
      harboring genes for aromatic hydrocarbon metabolism. Its genome will unravel the basic
      mechanism involved in bioremediation of anthropogens.
AU  - Amin S
AU  - Shah B
AU  - Jain K
AU  - Patel A
AU  - Patel N
AU  - Joshi CG
AU  - Madamwar D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01264-15.

PMID- 14507369
VI  - 50
DP  - 2003
TI  - Bacteriophage T4-encoded Stp can be replaced as activator of anticodon nuclease by a normal host cell metabolite.
PG  - 129-143
AB  - The bacterial tRNALys-specific anticodon nuclease is known as a phage T4 exclusion system. In
      the uninfected host cell anticodon nuclease is kept
      latent due to the association of its core protein PrrC with the DNA
      restriction-modification endonuclease EcoprrI. Stp, the T4-encoded peptide
      inhibitor of EcoprrI activates the latent enzyme. Previous in vitro work
      indicated that the activation by Stp is sensitive to DNase and requires
      added nucleotides. Biochemical and mutational data reported here suggest
      that Stp activates the latent holoenzyme when its EcoprrI component is
      tethered to a cognate DNA substrate. Moreover, the activation is driven by
      GTP hydrolysis, possibly mediated by the NTPase domain of PrrC. The data
      also reveal that Stp can be replaced as the activator of latent anticodon
      nuclease by certain pyrimidine nucleotides, the most potent of which is
      dTTP. The activation by dTTP likewise requires an EcoprrI DNA substrate
      and GTP hydrolysis but involves a different form of the latent
      holoenzyme/DNA complex. Moreover, whereas Stp relays its activating effect
      through EcoprrI, dTTP targets PrrC. The activation of the latent enzyme by
      a normal cell constituent hints that anticodon nuclease plays additional
      roles, other than warding off phage T4 infection.
AU  - Amitsur M
AU  - Benjamin S
AU  - Rosner R
AU  - Chapman-Shimshoni D
AU  - Meidler R
AU  - Blanga S
AU  - Kaufmann G
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2003 50: 129-143.

PMID- 1639077
VI  - 11
DP  - 1992
TI  - HSD restriction-modification proteins partake in latent anticodon nuclease.
PG  - 3129-3134
AB  - Phage T4-induced anticodon nuclease triggers cleavage-ligation of the host tRNALys. The enzyme
      is encoded in latent form by the optional Escherichia coli locus prr and is activated by the
      product of the phage stp gene. Anticodon nuclease latency is attributed to the masking of the
      core function prrC by flanking elements homologous with type I restriction -modification genes
      (prrA-hsdM and prrD-hadR). Activation of anticodon nuclease in extracts of uninfected prr+
      cells required synthetic Stp, ATP and GTP and appeared to depend on endogenous DNA. Stp could
      be substituted by a small, heat-stable E. coli factor, hinting that anticodon nuclease may be
      mobilized in cellular situations other thant T4 infection. Hsd antibodies recognized the
      anticodon nuclease holoenzyme but not the prrC-encoded core. Taken together, these data
      indicate that Hsd proteins partake in the latent ACNase complex where they mask the core
      factor PrrC. Presumable, this making interaction is disrupted by Stp in conjunction with Hsd
      ligands. The Hsd-PrrC interaction may signify coupling and mutal enhancement of two
      prokaryotic restriction systems operating at the DNA and tRNA levels.
AU  - Amitsur M
AU  - Morad I
AU  - Chapman-Shimshoni D
AU  - Kaufmann G
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1992 11: 3129-3134.

PMID- 27609924
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Leptospira interrogans Serovar Bataviae Strain LepIMR 22 Isolated from a Rodent in Johor, Malaysia.
PG  - e00956-16
AB  - Leptospira interrogans serovar Bataviae was recently identified as one of the persistent
      Leptospira serovars in Malaysia. Here, we report the draft genome
      sequence of the L. interrogans serovar Bataviae strain LepIMR 22 isolated from
      kidney of a rodent in Johor, Malaysia.
AU  - Amran F
AU  - Mohd KMK
AU  - Mohamad S
AU  - Mat RA
AU  - Ahmad N
AU  - Goris MG
AU  - Muhammad AH
AU  - Noor HNA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00956-16.

PMID- 24558244
VI  - 2
DP  - 2014
TI  - Genome Sequence of Enterococcus faecium Strain LCT-EF297, Which Has Specific Biochemical Features.
PG  - e00102-14
AB  - An Enterococcus faecium strain was sent into space on the Shenzhou-VIII craft. After space
      flight, the strain E. faecium LCT-EF297 was selected based on its
      metabolic properties.
AU  - An L
AU  - Li Y
AU  - Chen Z
AU  - Chang D
AU  - Zhang X
AU  - Guo Y
AU  - Wang J
AU  - Li T
AU  - Dai W
AU  - Liu C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00102-14.

PMID- 29371366
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Four Salmonella enterica subsp. enterica Serovar Enteritidis Strains Implicated in Infections of Avian and Human Hosts.
PG  - e01550-17
AB  - Salmonella enterica subsp. enterica serovar Enteritidis is a wide-host-range pathogen.
      Occasionally, it is involved in invasive infections, leading to a high
      mortality rate. Here, we present the draft genome sequences of four S Enteritidis
      strains obtained from human and avian hosts that had been involved in bacteremia,
      gastroenteritis, and primary infections.
AU  - An R
AU  - Lin P
AU  - Bougouffa S
AU  - Essack M
AU  - Boxrud D
AU  - Bajic VB
AU  - Vidovic S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01550-17.

PMID- 26337881
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Desulfocarbo indianensis SCBM, a New Genus of Sulfate-Reducing Bacteria, Isolated from Water Extracted from an Active Coalbed Methane Gas Well.
PG  - e00970-15
AB  - We used Illumina MiSeq technology to sequence the whole genome of Desulfocarbo indianensis
      SCBM, a new genus of sulfate-reducing bacteria isolated from a coal bed in Indiana, USA. This
      draft genome represents the first sequenced genome of the genus Desulfocarbo and the second
      known genome of the order Desulfarculales.
AU  - An TT
AU  - Picardal FW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00970-15.

PMID- 22843598
VI  - 194
DP  - 2012
TI  - Genome Sequence of Sphingobium indicum B90A, a Hexachlorocyclohexane-Degrading Bacterium.
PG  - 4471-4472
AB  - Sphingobium indicum B90A, an efficient degrader of hexachlorocyclohexane (HCH) isomers, was
      isolated in 1990 from sugarcane rhizosphere soil in Cuttack, India.
      Here we report the draft genome sequence of this bacterium, which has now become
      a model system for understanding the genetics, biochemistry, and physiology of
      HCH degradation.
AU  - Anand S
AU  - Sangwan N
AU  - Lata P
AU  - Kaur J
AU  - Dua A
AU  - Singh AK
AU  - Verma M
AU  - Kaur J
AU  - Khurana JP
AU  - Khurana P
AU  - Mathur S
AU  - Lal R
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4471-4472.

PMID- 24604638
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of a Brucella ceti ST26 Strain Isolated from a Striped Dolphin (Stenella coeruleoalba) on the Coast of Italy.
PG  - e00068-14
AB  - Brucella spp. are important pathogens affecting a wide range of terrestrial and aquatic
      animals. We report the complete and annotated genome sequence of Brucella
      ceti ST26 strain TE10759-12, isolated from a striped dolphin (Stenella
      coeruleoalba) stranded along the Italian shoreline in March of 2012.
AU  - Ancora M
AU  - Marcacci M
AU  - Orsini M
AU  - Zilli K
AU  - Di Giannatale E
AU  - Garofolo G
AU  - Camma C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00068-14.

PMID- 26534993
VI  - 112
DP  - 2015
TI  - Bacterial clade with the ribosomal RNA operon on a small plasmid rather than the chromosome.
PG  - 14343-14347
AB  - rRNA is essential for life because of its functional importance in protein synthesis. The rRNA
      (rrn) operon encoding 16S, 23S, and 5S rRNAs is
      located on the main chromosome in all bacteria documented to date and is frequently used as a
      marker of chromosomes. Here, our genome analysis of a plant-associated alphaproteobacterium,
      Aureimonas sp. AU20, indicates that this strain has its sole rrn operon on a small (9.4 kb),
      high-copy-number replicon. We designated this unusual replicon carrying the rrn operon on the
      background of an rrn-lacking chromosome (RLC) as the rrn-plasmid. Four of 12 strains close to
      AU20 also had this RLC/rrn-plasmid organization. Phylogenetic analysis showed that those
      strains having the RLC/rrn-plasmid organization represented one cladewithin the genus
      Aureimonas. Our finding introduces a previously unaddressed viewpoint into studies of
      genetics, genomics, and evolution in microbiology and biology in general.
AU  - Anda M
AU  - Ohtsubo Y
AU  - Okubo T
AU  - Sugawara M
AU  - Nagata Y
AU  - Tsuda M
AU  - Minamisawa K
AU  - Mitsui H
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2015 112: 14343-14347.

PMID- 23915186
VI  - 14
DP  - 2013
TI  - Comparison of the complete genome sequence of two closely related isolates of 'Candidatus Phytoplasma australiense' reveals genome plasticity.
PG  - 529
AB  - Background: 'Candidatus Phytoplasma australiense' is associated with at least nine diseases
      in Australia and New Zealand. The impact of this
      phytoplasma is considerable, both economically and environmentally. The
      genome of a NZ isolate was sequenced in an effort to understand its
      pathogenicity and ecology. Comparison with a closely related Australian
      isolate enabled us to examine mechanisms of genomic
      rearrangement.Results: The complete genome sequence of a strawberry
      lethal yellows (SLY) isolate of 'Candidatus Phytoplasma australiense'
      was determined. It is a circular genome of 959,779 base pairs with 1126
      predicted open reading frames. Despite being 80 kbp larger than another
      'Ca. Phytoplasma australiense' isolate PAa, the variation between
      housekeeping genes was generally less than 1% at a nucleotide level.
      The difference in size between the two isolates was largely due to the
      number and size of potential mobile units (PMUs), which contributed to
      some changes in gene order. Comparison of the genomes of the two
      isolates revealed that the highly conserved 5' UTR of a putative
      DNA-directed RNA polymerase seems to be associated with insertion and
      rearrangement events. Two types of PMUs have been identified on the
      basis of the order of three to four conserved genes, with both PMUs
      appearing to have been present in the last common ancestor of 'Ca.
      Phytoplasma asteris' and 'Ca. Phytoplasma australiense'. Comparison
      with other phytoplasma genomes showed that modification methylases
      were, in general, species-specific. A putative methylase (xorIIM) found
      in 'Ca. Phytoplasma australiense' appeared to have no analogue in any
      other firmicute, and we believe has been introduced by way of lateral
      gene transfer. A putative retrostransposon (ltrA) analogous to that
      found in OY-M was present in both isolates, although all examples in
      PAa appear to be fragments. Comparative analysis identified highly
      conserved 5' and 3' UTR regions of ltrA, which may indicate how the
      gene is excised and inserted.Conclusions: Comparison of two assembled
      'Ca. Phytoplasma australiense' genomes has shown they possess a high
      level of plasticity. This comparative analysis has yielded clues as to
      how rearrangements occur, and the identification of sets of genes that
      appear to be associated with these events.
AU  - Andersen MT
AU  - Liefting LW
AU  - Havukkala I
AU  - Beever RE
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2013 14: 529.

PMID- 24309736
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of the Epidemic and Highly Virulent CTX-M-15-Producing H30-Rx Subclone of Escherichia coli ST131.
PG  - e00988-13
AB  - We report the complete genome sequence, including five complete plasmid sequences, of
      Escherichia coli ST131 isolate JJ1886. The isolate was obtained in
      2007 in the United States from a patient with fatal urosepsis and belongs to the
      virulent, CTX-M-15-producing H30-Rx sublineage.
AU  - Andersen PS
AU  - Stegger M
AU  - Aziz M
AU  - Contente-Cuomo T
AU  - Gibbons HS
AU  - Keim P
AU  - Sokurenko EV
AU  - Johnson JR
AU  - Price LB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00988-13.

PMID- 8317710
VI  - 211
DP  - 1993
TI  - Construction of DNA libraries of A-T rich organisms using EcoRI star activity.
PG  - 325-327
AB  - Construction of genomic or expression libraries involves size fractionation of the DNA to be
      cloned by one of several methods. Methods of fractionation include mechanical shearing,
      digestion with DNAse, or digestion with restriction endonucleases that cleave frequently
      within a genome (i.e., Sau3AI). The latter method is most frequently used for practical
      reasons. Near-random cleavage is best obtained by partial digestion with an enzyme that most
      frequently cleaves a given genome. The frequency of cleavage of each restriction endonuclease
      within a given genome is dependent on the G + C content of each individual organism.
      Therefore, a restriction endonuclease with an A-T rich recognition sequence would be preferred
      when cloning DNA from organisms with A-T rich genomes. We describe the use of EcoRI star
      activity to generate near-random DNA, from A-T rich genomes, for cloning. Expression/genomic
      libraries for three A-T rich bacteria were easily and successfully constructed using this
      method.
AU  - Anderson B
AU  - McDonald G
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 1993 211: 325-327.

PMID- 12993208
VI  - 170
DP  - 1952
TI  - Variation in Vi-Phage II of Salmonella typhi.
PG  - 492-494
AB  - The recent description of phenotypic variation in bacteriophages by Luria and
      Bertani has prompted us to publish the results of experiments carried out in
      1947 which show analogous features.  The object of the work was primarily to
      investigate the possibility of tracing a specific Vi-phage type of Salmonella
      typhi in which "degraded" variants had arisen (see Craigie and Felix).  It was
      hoped also to gain more information about the mechanism of "degradation" of
      cultures and the processes concerned in the adaptation of Vi-phage II of
      Craigie and Yen to the specific Vi-types of S. typhi.  Degradation in a
      spsecific Vi-type can take all forms from the appeaerance of minor
      cross-reactions with heterologous phages, typical of partly degraded strains,
      to the full susceptibility to all adapted phages which characterizes Type A.
AU  - Anderson ES
AU  - Felix A
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1952 170: 492-494.

PMID- 4584174
VI  - 71
DP  - 1973
TI  - Bacteriophage restriction in Salmonella typhimurium by R factors and transfer factors.
PG  - 619
AB  - A total of 2716 R factors and transfer factors isolated from Escherichia coli
      and Salmonellas of human and animal origin were studied for their
      phage-restrictive effects in Salmonella typhimurium phage type 36.  All of 1402
      wild fi+ factors were non-restricting.  The F factor of E. coli K12 was unique
      among the F-like factors tested in that it inhibited lysis of type 36 by one
      typing phage.  In contrast, eleven distinct changes in the phage type of 36
      were produced by fi- I-like factors.  I-like plasmids can thus be subdivided by
      this method.  I-like R factors and transfer factors from human and animal
      enterobacteria were categorized by their phage-restrictive effects in type 36.
      Factors resembling delta in this respect predominated among fi- I-like factor
      from human E. coli and S. typhimurium and from porcine E. coli.  delta-like and
      ColI-like fi-factors were equally distributed in bovine S. typhimurium.
      ColI-like factors were commonest in bovine and avian E. coli.
AU  - Anderson ES
AU  - Threlfall EJ
AU  - Carr JM
AU  - Savoy LG
PT  - Journal Article
TA  - J. Hyg. (Lond)
JT  - J. Hyg. (Lond)
SO  - J. Hyg. (Lond) 1973 71: 619.

PMID- 24501647
VI  - 9
DP  - 2013
TI  - Genome sequence of Frateuria aurantia type strain (Kondo 67(T)), a xanthomonade isolated from Lilium auratium Lindl.
PG  - 83-92
AB  - Frateuria aurantia (ex Kondo and Ameyama 1958) Swings et al. 1980 is a member of  the
      bispecific genus Frateuria in the family Xanthomonadaceae, which is already
      heavily targeted for non-type strain genome sequencing. Strain Kondo 67(T) was
      initially (1958) identified as a member of 'Acetobacter aurantius', a name that
      was not considered for the approved list. Kondo 67(T) was therefore later
      designated as the type strain of the newly proposed acetogenic species Frateuria
      aurantia . The strain is of interest because of its triterpenoids (hopane
      family). F. aurantia Kondo 67(T) is the first member of the genus Frateura whose
      genome sequence has been deciphered, and here we describe the features of this
      organism, together with the complete genome sequence and annotation. The
      3,603,458-bp long chromosome with its 3,200 protein-coding and 88 RNA genes is a
      part of the G enomic E ncyclopedia of Bacteria and Archaea project.
AU  - Anderson I et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 9: 83-92.

PMID- 21304736
VI  - 3
DP  - 2010
TI  - Complete genome sequence of Methanothermus fervidus type strain (V24S).
PG  - 315-324
AB  - Methanothermus fervidus Stetter 1982 is the type strain of the genus
      Methanothermus. This hyperthermophilic genus is of a thought to be endemic in
      Icelandic hot springs. M. fervidus was not only the first characterized organism
      with a maximal growth temperature (97 degrees C) close to the boiling point of
      water, but also the first archaeon in which a detailed functional analysis of its
      histone protein was reported and the first one in which the function of
      2,3-cyclodiphosphoglycerate in thermoadaptation was characterized. Strain V24S(T)
      is of interest because of its very low substrate ranges, it grows only on H(2) +
      CO(2). This is the first completed genome sequence of the family
      Methanothermaceae. Here we describe the features of this organism, together with
      the complete genome sequence and annotation. The 1,243,342 bp long genome with
      its 1,311 protein-coding and 50 RNA genes is a part of the Genomic Encyclopedia
      of Bacteria and Archaea project.
AU  - Anderson I et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 3: 315-324.

PMID- 22180806
VI  - 5
DP  - 2011
TI  - Complete genome sequence of Staphylothermus hellenicus P8.
PG  - 12-20
AB  - Staphylothermus hellenicus belongs to the order Desulfurococcales within the archaeal phylum
      Crenarchaeota. Strain P8(T) is the type strain of the species and
      was isolated from a shallow hydrothermal vent system at Palaeochori Bay, Milos,
      Greece. It is a hyperthermophilic, anaerobic heterotroph. Here we describe the
      features of this organism together with the complete genome sequence and
      annotation. The 1,580,347 bp genome with its 1,668 protein-coding and 48 RNA
      genes was sequenced as part of a DOE Joint Genome Institute (JGI) Laboratory
      Sequencing Program (LSP) project.
AU  - Anderson I et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 5: 12-20.

PMID- 22180810
VI  - 5
DP  - 2011
TI  - Complete genome sequence of Ferroglobus placidus AEDII12DO.
PG  - 50-60
AB  - Ferroglobus placidus belongs to the order Archaeoglobales within the archaeal phylum
      Euryarchaeota. Strain AEDII12DO is the type strain of the species and was
      isolated from a shallow marine hydrothermal system at Vulcano, Italy. It is a
      hyperthermophilic, anaerobic chemolithoautotroph, but it can also use a variety
      of aromatic compounds as electron donors. Here we describe the features of this
      organism together with the complete genome sequence and annotation. The 2,196,266
      bp genome with its 2,567 protein-coding and 55 RNA genes was sequenced as part of
      a DOE Joint Genome Institute Laboratory Sequencing Program (LSP) project.
AU  - Anderson I et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 5: 50-60.

PMID- 21304660
VI  - 1
DP  - 2009
TI  - Complete genome sequence of Halorhabdus utahensis type strain (AX-2).
PG  - 218-225
AB  - Halorhabdus utahensis Waino et al. 2000 is the type species of the genus, which is of
      phylogenetic interest because of its location on one of the deepest
      branches within the very extensive euryarchaeal family Halobacteriaceae. H.
      utahensis is a free-living, motile, rod shaped to pleomorphic, Gram-negative
      archaeon, which was originally isolated from a sediment sample collected from the
      southern arm of Great Salt Lake, Utah, USA. When grown on appropriate media, H.
      utahensis can form polyhydroxybutyrate (PHB). Here we describe the features of
      this organism, together with the complete genome sequence, and annotation. This
      is the first complete genome sequence of the a member of halobacterial genus
      Halorhabdus, and the 3,116,795 bp long single replicon genome with its 3027
      protein-coding and 48 RNA genes is part of the Genomic Encyclopedia of Bacteria
      and Archaea project.
AU  - Anderson I et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2009 1: 218-225.

PMID- 23408178
VI  - 7
DP  - 2012
TI  - Genome sequence of the flexirubin-pigmented soil bacterium Niabella soli type strain (JS13-8(T)).
PG  - 210-220
AB  - Niabella soli Weon et al. 2008 is a member of the Chitinophagaceae, a family within the class
      Sphingobacteriia that is poorly characterized at the genome
      level, thus far. N. soli strain JS13-8(T) is of interest for its ability to
      produce a variety of glycosyl hydrolases. The genome of N. soli strain JS13-8(T)
      is only the second genome sequence of a type strain from the family
      Chitinophagaceae to be published, and the first one from the genus Niabella. Here
      we describe the features of this organism, together with the complete genome
      sequence and annotation. The 4,697,343 bp long chromosome with its 3,931
      protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia ofBacteria
      andArchaea project.
AU  - Anderson I et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 7: 210-220.

PMID- 23407703
VI  - 6
DP  - 2012
TI  - Complete genome sequence of the moderately thermophilic mineral-sulfide-oxidizing firmicute Sulfobacillus acidophilus type strain (NAL(T)).
PG  - 1-13
AB  - Sulfobacillus acidophilus Norris et al. 1996 is a member of the genus Sulfobacillus which
      comprises five species of the order Clostridiales.
      Sulfobacillus species are of interest for comparison to other sulfur and iron
      oxidizers and also have biomining applications. This is the first completed
      genome sequence of a type strain of the genus Sulfobacillus, and the second
      published genome of a member of the species S. acidophilus. The genome, which
      consists of one chromosome and one plasmid with a total size of 3,557,831 bp
      harbors 3,626 protein-coding and 69 RNA genes, and is a part of the
      GenomicEncyclopedia ofBacteria andArchaea project.
AU  - Anderson I et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 6: 1-13.

PMID- 22768361
VI  - 6
DP  - 2012
TI  - Genome sequence of the homoacetogenic bacterium Holophaga foetida type strain (TMBS4(T)).
PG  - 174-184
AB  - Holophaga foetida Liesack et al. 1995 is a member of the phylum Acidobacteria and is of
      interest for its ability to anaerobically degrade aromatic compounds and
      for its production of volatile sulfur compounds through a unique pathway. The
      genome of H. foetida strain TMBS4(T) is the first to be sequenced for a
      representative of the class Holophagae. Here we describe the features of this
      organism, together with the complete genome sequence (improved high quality
      draft), and annotation. The 4,127,237 bp long chromosome with its 3,615
      protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria
      and Archaea project.
AU  - Anderson I et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 6: 174-184.

PMID- 22768359
VI  - 6
DP  - 2012
TI  - Complete genome sequence of the thermophilic sulfate-reducing ocean bacterium Thermodesulfatator indicus type strain (CIR29812(T)).
PG  - 155-164
AB  - Thermodesulfatator indicus Moussard et al. 2004 is a member of the Thermodesulfobacteriaceae,
      a family in the phylum Thermodesulfobacteria that is
      currently poorly characterized at the genome level. Members of this phylum are of
      interest because they represent a distinct, deep-branching, Gram-negative
      lineage. T. indicus is an anaerobic, thermophilic, chemolithoautotrophic sulfate
      reducer isolated from a deep-sea hydrothermal vent. Here we describe the features
      of this organism, together with the complete genome sequence, and annotation. The
      2,322,224 bp long chromosome with its 2,233 protein-coding and 58 RNA genes is a
      part of the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Anderson I et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 6: 155-164.

PMID- 22675596
VI  - 6
DP  - 2012
TI  - Complete genome sequence of Halopiger xanaduensis type strain (SH-6T).
PG  - 31-42
AB  - Halopiger xanaduensis is the type species of the genus Halopiger and belongs to the
      euryarchaeal family Halobacteriaceae. H. xanaduensis strain SH-6, which is designated as the
      type strain, was isolated from the sediment of a salt lake in Inner Mongolia, Lake
      Shangmatala. Like other members of the family Halobacteriaceae, it is an extreme halophile
      requiring at least 2.5 M salt for growth. We report here the sequencing and annotation of the
      4,355,268 bp genome, which includes one chromosome and three plasmids. This genome is part of
      a Joint Genome Institute (JGI) Community Sequencing Program (CSP) project to sequence diverse
      haloarchaeal genomes.
AU  - Anderson I et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 6: 31-42.

PMID- 21886859
VI  - 4
DP  - 2011
TI  - Complete genome sequence of Nitratifractor salsuginis type strain (E9I37-1).
PG  - 322-330
AB  - Nitratifractor salsuginis Nakagawa et al. 2005 is the type species of the genus
      Nitratifractor, a member of the family Nautiliaceae. The species is of interest
      because of its high capacity for nitrate reduction via conversion to N(2) through
      respiration, which is a key compound in plant nutrition. The strain is also of
      interest because it represents the first mesophilic and facultatively anaerobic
      member of the Epsilonproteobacteria reported to grow on molecular hydrogen. This
      is the first completed genome sequence of a member of the genus Nitratifractor
      and the second sequence from the family Nautiliaceae. The 2,101,285 bp long
      genome with its 2,121 protein-coding and 54 RNA genes is a part of the Genomic
      Encyclopedia of Bacteria and Archaea project.
AU  - Anderson I et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 4: 322-330.

PMID- 21886865
VI  - 4
DP  - 2011
TI  - Complete genome sequence of the hyperthermophilic chemolithoautotroph Pyrolobus fumarii type strain (1A).
PG  - 381-392
AB  - Pyrolobus fumarii Blochl et al. 1997 is the type species of the genus Pyrolobus,  which
      belongs to the crenarchaeal family Pyrodictiaceae. The species is a
      facultatively microaerophilic non-motile crenarchaeon. It is of interest because
      of its isolated phylogenetic location in the tree of life and because it is a
      hyperthermophilic chemolithoautotroph known as the primary producer of organic
      matter at deep-sea hydrothermal vents. P. fumarii exhibits currently the highest
      optimal growth temperature of all life forms on earth (106 degrees C). This is
      the first completed genome sequence of a member of the genus Pyrolobus to be
      published and only the second genome sequence from a member of the family
      Pyrodictiaceae. Although Diversa Corporation announced the completion of
      sequencing of the P. fumarii genome on September 25, 2001, this sequence was
      never released to the public. The 1,843,267 bp long genome with its 1,986
      protein-coding and 52 RNA genes is a part of the Genomic Encyclopedia of Bacteria
      and Archaea project.
AU  - Anderson I et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 4: 381-392.

PMID- 21304656
VI  - 1
DP  - 2009
TI  - Complete genome sequence of Methanoculleus marisnigri Romesser et al. 1981 type strain JR1.
PG  - 189-196
AB  - Methanoculleus marisnigri Romesser et al. 1981 is a methanogen belonging to the order
      Methanomicrobiales within the archaeal phylum Euryarchaeota. The type
      strain, JR1, was isolated from anoxic sediments of the Black Sea. M. marisnigri
      is of phylogenetic interest because at the time the sequencing project began only
      one genome had previously been sequenced from the order Methanomicrobiales. We
      report here the complete genome sequence of M. marisnigri type strain JR1 and its
      annotation. This is part of a Joint Genome Institute 2006 Community Sequencing
      Program to sequence genomes of diverse Archaea.
AU  - Anderson IJ et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2009 1: 189-196.

PMID- 19341479
VI  - 10
DP  - 2009
TI  - The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota.
PG  - 145
AB  - BACKGROUND: Staphylothermus marinus is an anaerobic, sulfur-reducing peptide fermenter of the
      archaeal phylum Crenarchaeota. It is the third heterotrophic, obligate sulfur reducing
      crenarchaeote to be sequenced and provides an opportunity for comparative analysis of the
      three genomes. RESULTS: The 1.57 Mbp genome of the hyperthermophilic crenarchaeote
      Staphylothermus marinus has been completely sequenced. The main energy generating pathways
      likely involve 2-oxoacid:ferredoxin oxidoreductases and ADP-forming acetyl-CoA synthases. S.
      marinus possesses several enzymes not present in other crenarchaeotes including a sodium
      ion-translocating decarboxylase likely to be involved in amino acid degradation. S. marinus
      lacks sulfur-reducing enzymes present in the other two sulfur-reducing crenarchaeotes that
      have been sequenced -- Thermofilum pendens and Hyperthermus butylicus. Instead it has three
      operons similar to the mbh and mbx operons of Pyrococcus furiosus, which may play a role in
      sulfur reduction and/or hydrogen production. The two marine organisms, S. marinus and H.
      butylicus, possess more sodium-dependent transporters than T. pendens and use symporters for
      potassium uptake while T. pendens uses an ATP-dependent potassium transporter. T. pendens has
      adapted to a nutrient-rich environment while H. butylicus is adapted to a nutrient-poor
      environment, and S. marinus lies between these two extremes. CONCLUSION: The three
      heterotrophic sulfur-reducing crenarchaeotes have adapted to their habitats, terrestrial vs.
      marine, via their transporter content, and they have also adapted to environments with
      differing levels of nutrients. Despite the fact that they all use sulfur as an electron
      acceptor, they are likely to have different pathways for sulfur reduction.
AU  - Anderson IJ et al
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2009 10: 145.

PMID- 27617060
VI  - 11
DP  - 2016
TI  - Complete genome sequence of the Antarctic Halorubrum lacusprofundi type strain ACAM 34.
PG  - 70
AB  - Halorubrum lacusprofundi is an extreme halophile within the archaeal phylum Euryarchaeota. The
      type strain ACAM 34 was isolated from Deep Lake, Antarctica.
      H. lacusprofundi is of phylogenetic interest because it is distantly related to
      the haloarchaea that have previously been sequenced. It is also of interest
      because of its psychrotolerance. We report here the complete genome sequence of
      H. lacusprofundi type strain ACAM 34 and its annotation. This genome is part of a
      2006 Joint Genome Institute Community Sequencing Program project to sequence
      genomes of diverse Archaea.
AU  - Anderson IJ et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 70.

PMID- 21304657
VI  - 1
DP  - 2009
TI  - Complete genome sequence of Methanocorpusculum labreanum type strain Z.
PG  - 197-203
AB  - Methanocorpusculum labreanum is a methanogen belonging to the order Methanomicrobiales within
      the archaeal kingdom Euryarchaeota. The type strain Z
      was isolated from surface sediments of Tar Pit Lake in the La Brea Tar Pits in
      Los Angeles, California. M. labreanum is of phylogenetic interest because at the
      time the sequencing project began only one genome had previously been sequenced
      from the order Methanomicrobiales. We report here the complete genome sequence of
      M. labreanum type strain Z and its annotation. This is part of a 2006 Joint
      Genome Institute Community Sequencing Program project to sequence genomes of
      diverse Archaea.
AU  - Anderson IJ
AU  - Sieprawska-Lupa M
AU  - Goltsman E
AU  - Lapidus A
AU  - Copeland A
AU  - Glavina Del Rio T
AU  - Tice H
AU  - Dalin E
AU  - Barry K
AU  - Pitluck S
AU  - Hauser L
AU  - Land M
AU  - Lucas S
AU  - Richardson P
AU  - Whitman WB
AU  - Kyrpides NC
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2009 1: 197-203.

PMID- 21304655
VI  - 1
DP  - 2009
TI  - Complete genome sequence of Staphylothermus marinus Stetter and Fiala 1986 type strain F1.
PG  - 183-188
AB  - Staphylothermus marinus Fiala and Stetter 1986 belongs to the order Desulfurococcales within
      the archaeal phylum Crenarchaeota. S. marinus is a
      hyperthermophilic, sulfur-dependent, anaerobic heterotroph. Strain F1 was
      isolated from geothermally heated sediments at Vulcano, Italy, but S. marinus has
      also been isolated from a hydrothermal vent on the East Pacific Rise. We report
      the complete genome of S. marinus strain F1, the type strain of the species. This
      is the fifth reported complete genome sequence from the order Desulfurococcales.
AU  - Anderson IJ
AU  - Sun H
AU  - Lapidus A
AU  - Copeland A
AU  - Glavina Del Rio T
AU  - Tice H
AU  - Dalin E
AU  - Lucas S
AU  - Barry K
AU  - Land M
AU  - Richardson P
AU  - Huber H
AU  - Kyrpides NC
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2009 1: 183-188.

PMID- Not included in PubMed...
VI  - 3
DP  - 1993
TI  - Restriction endonucleases and modification methylases.
PG  - 24-30
AB  - Restriction endonucleases and modification methylases offer excellent systems for studying
      protein-DNA interactions. The past year has seen the experimental verification of some aspects
      of the catalytic mechanisms of both types of enzyme. The first structures of methylases were
      determined and a number of endonuclease structures should become available soon.
AU  - Anderson JE
PT  - Journal Article
TA  - Curr. Opin. Struct. Biol.
JT  - Curr. Opin. Struct. Biol.
SO  - Curr. Opin. Struct. Biol. 1993 3: 24-30.

PMID- 30087402
VI  - 8
DP  - 2018
TI  - Citrobacter freundii fitness during bloodstream infection.
PG  - 11792
AB  - Sepsis resulting from microbial colonization of the bloodstream is a serious
      health concern associated with high mortality rates. The objective of this study
      was to define the physiologic requirements of Citrobacter freundii in the
      bloodstream as a model for bacteremia caused by opportunistic Gram-negative
      pathogens. A genetic screen in a murine host identified 177 genes that
      contributed significantly to fitness, the majority of which were broadly
      classified as having metabolic or cellular maintenance functions. Among the
      pathways examined, the Tat protein secretion system conferred the single largest
      fitness contribution during competition infections and a putative Tat-secreted
      protein, SufI, was also identified as a fitness factor. Additional work was
      focused on identifying relevant metabolic pathways for bacteria in the
      bloodstream environment. Mutations that eliminated the use of glucose or mannitol
      as carbon sources in vitro resulted in loss of fitness in the murine model and
      similar results were obtained upon disruption of the cysteine biosynthetic
      pathway. Finally, the conservation of identified fitness factors was compared
      within a cohort of Citrobacter bloodstream isolates and between Citrobacter and
      Serratia marcescens, the results of which suggest the presence of conserved
      strategies for bacterial survival and replication in the bloodstream environment.
AU  - Anderson MT
AU  - Mitchell LA
AU  - Zhao L
AU  - Mobley HL
PT  - Journal Article
TA  - Sci. Rep.
JT  - Sci. Rep.
SO  - Sci. Rep. 2018 8: 11792.

PMID- 28536292
VI  - 8
DP  - 2017
TI  - Capsule Production and Glucose Metabolism Dictate Fitness during Serratia marcescens Bacteremia.
PG  - e00740-17
AB  - Serratia marcescens is an opportunistic pathogen that causes a range of human
      infections, including bacteremia, keratitis, wound infections, and urinary tract
      infections. Compared to other members of the Enterobacteriaceae family, the
      genetic factors that facilitate Serratia proliferation within the mammalian host
      are less well defined. An in vivo screen of transposon insertion mutants
      identified 212 S. marcescens fitness genes that contribute to bacterial survival
      in a murine model of bloodstream infection. Among those identified, 11 genes were
      located within an 18-gene cluster encoding predicted extracellular polysaccharide
      biosynthesis proteins. A mutation in the wzx gene contained within this locus
      conferred a loss of fitness in competition infections with the wild-type strain
      and a reduction in extracellular uronic acids correlating with capsule loss. A
      second gene, pgm, encoding a phosphoglucomutase exhibited similar
      capsule-deficient phenotypes, linking central glucose metabolism with capsule
      production and fitness of Serratia during mammalian infection. Further evidence
      of the importance of central metabolism was obtained with a pfkA glycolytic
      mutant that demonstrated reduced replication in human serum and during murine
      infection. An MgtB magnesium transporter homolog was also among the fitness
      factors identified, and an S. marcescens mgtB mutant exhibited decreased growth
      in defined medium containing low concentrations of magnesium and was outcompeted
      ~10-fold by wild-type bacteria in mice. Together, these newly identified genes
      provide a more complete understanding of the specific requirements for S.
      marcescens survival in the mammalian host and provide a framework for further
      investigation of the means by which S. marcescens causes opportunistic
      infections.IMPORTANCESerratia marcescens is a remarkably prolific organism that
      replicates in diverse environments, including as an opportunistic pathogen in
      human bacteremia. The genetic requirements for S. marcescens survival in the
      mammalian bloodstream were defined in this work by transposon insertion
      sequencing. In total, 212 genes that contribute to bacterial fitness were
      identified. When sorted via biological function, two of the major fitness
      categories identified herein were genes encoding capsule polysaccharide
      biogenesis functions and genes involved in glucose utilization. Further
      investigation determined that certain glucose metabolism fitness genes are also
      important for the generation of extracellular polysaccharides. Together, these
      results identify critical biological processes that allow S. marcescens to
      colonize the mammalian bloodstream.
AU  - Anderson MT
AU  - Mitchell LA
AU  - Zhao L
AU  - Mobley HLT
PT  - Journal Article
TA  - MBio
JT  - MBio
SO  - MBio 2017 8: e00740-17.

PMID- 9823893
VI  - 396
DP  - 1998
TI  - The genome sequence of Rickettsia prowazekii and the origin of mitochondria.
PG  - 133-140
AB  - We describe here the complete genome sequence (1,111,523 base pairs) of the obligate
      intracellular parasite Rickettsia prowazekii, the causative agent of epidemic typhus.  This
      genome contains 834 protein-coding genes.  The functional profiles of these genes show
      similarities to those of mitochondrial genes: no genes required for anaerobic glycolysis are
      found in either R. prowazekii or mitochondrial genomes, but a complete set of genes encoding
      components of the tricarboxylic acid cycle and the respiratory-chain complex is found in R.
      prowazekii.  In effect, ATP production in Rickettsia is the same as that in mitochondria.
      Many genes involved in the biosynthesis and regulation of biosynthesis of amino acids and
      nucleosides in free-living bacteria are absent from R. prowazekii and mitochondria.  Such
      genes seem to have been replaced by homologues in the nuclear (host) genome.  The R.
      prowazekii genome contains the highest proportion of non-coding DNA (24%) detected so far in a
      microbial genome.  Such non-coding sequences may be degraded remnants of 'neutralized' genes
      that await elimination from the genome.  Phylogenetic analyses indicate that R. prowazekii is
      more closely related to mitochondria than is any other microbe studied so far.
AU  - Andersson SGE
AU  - Zomorodipour A
AU  - Andersson JO
AU  - Sicheritz-Ponten T
AU  - Alsmark UCM
AU  - Podowski RM
AU  - Naslund AK
AU  - Eriksson A-S
AU  - Winkler HH
AU  - Kurland CG
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1998 396: 133-140.

PMID- Not carried by PubMed...
VI  - 61
DP  - 1985
TI  - Novel DNA enzymes:  specificity and application.
PG  - 239-255
AB  - None
AU  - Ando T
PT  - Journal Article
TA  - Reports Inst. Phys. Chem. Res.
JT  - Reports Inst. Phys. Chem. Res.
SO  - Reports Inst. Phys. Chem. Res. 1985 61: 239-255.

PMID- 12774765
VI  - 124
DP  - 2003
TI  - Presence of hrgA and hrgB (iceA2) differentially associated with Helicobacter pylori virulence.
PG  - A272-A273
AB  - In the hpyI and hpyIII loci of Helicobacter pylori, the restriction endonuclease-encoding gene
      of these Restriction-Modification (R-M)
      systems can be replaced by a specific non-related gene: hrgA can
      replace hpyIIIR, and hrgB (formerly called iceA2) can replace hpyIR.
      Thus, there are 2 genotypes for each locus, either bearing or lacking
      the R-gene. Although both hrgB and hrgA have been associated with H.
      pylori virulence, we now examined the correlation between the hpyI and
      hpyIII genotypes with pathogenicity in greater detail. 174 H. pylori
      strains were assessed for sensitivity to MboI (indicative of hpyIIIM
      activity) and NlaIII (for hpyIM) digestion. Presence of hpyIIIR or
      hrgA, of hpyIR (iceA1) or hrgB, and of cagA and vacA was determined by
      PCR and/or LIPA. The induction of IL-8 in co-cultured AGS cells was
      determined for representative strains. We assessed the correlation
      between genotypes, clinical features, and IL-8 induction. In all
      strains examined, hrgA was found to be mutually exclusive with hpyIIIR,
      and iceA1 with hrgB; the presence of hrgA and hrgB were independent.
      HpyIM and HpyIIIM activities were detected in 100% and 95%,
      respectively, of the strains studied. Among 132 Asian strains, the
      combination hpyIIIR/iceA1 is the most common genotype (52%) and
      hrgA/hrgB is least (4%) common, whereas in 42 Western strains
      hpyIIIR/hrgB (40%), and hrgA/hrgB (31%) are the most common. The 33
      strains with iceA1 induced significantly more IL-8 (median 1483 pg/ml,
      range 287-2898) (p = 0.03) than 30 strains with hrgB (median 955 pg/ml,
      range 151-2452), whereas there was no difference in relation to the
      hpyIII locus. In Asian strains from gastric cancer patients (n=43, all
      cagA positive and vacA s1), 41% were hrgA and 20% were hrgB. This is an
      overrepresentation of hrgA, but not of hrgB, compared with non-gastric
      cancer diseases. Although gastric cancer strains from Western countries
      were not available for analysis, in patients with duodenal or gastric
      ulcer, hrgA but not hrgB was overrepresented (71%) compared to
      non-ulcer dyspepsia (39%, p<0.05) isolates. Conclusion: In this study,
      hrgA presence correlates with H. pylori clinical outcome, whereas iceA1
      presence was associated with enhanced IL-8 induction.
AU  - Ando T
AU  - Aras R
AU  - Kusugami K
AU  - Peek RM
AU  - Blaser MJ
AU  - Wassenaar TM
PT  - Journal Article
TA  - Gastroenterology
JT  - Gastroenterology
SO  - Gastroenterology 2003 124: A272-A273.

PMID- 12486066
VI  - 185
DP  - 2003
TI  - Evolutionary history of hrgA, which replaces the restriction gene hpyIIIR in the hpyIII locus of Helicobacter pylori.
PG  - 295-301
AB  - A recently identified Helicobacter pylori gene, hrgA, was previously reported to be present in
      70 (33%) of 208 strains examined (T. Ando, T. M.
      Wassenaar, R. M. Peek, R. A. Aras, A. I. Tschumi, L.-J. Van Doorn, K.
      Kusugami, and M. J. Blaser, Cancer Res. 62:2385-2389, 2002). Sequence
      analysis of nine such strains indicated that in each strain hrgA replaced
      hpyIIIR, which encodes a restriction endonuclease and which, together with
      the gene for its cognate methyltransferase, constitutes the hpyIII locus.
      As a consequence of either the hrgA insertion or independent mutations,
      hpyIIIM function was lost in 11 (5%) of the 208 strains examined,
      rendering chromosomal DNA sensitive to MboI digestion. The evolutionary
      history of the locus containing either hpyIII or hrgA was reconstructed.
      By homologous recombination involving flanking sequences, hrgA and hpyIIIR
      can replace one another in the hpyIII locus, and there is simultaneous
      replacement of several flanking genes. These findings, combined with the
      hpyIM/iceA2 locus discovered previously, suggest that the two most
      strongly conserved methylase genes of H. pylori, hpyIIIM and hpyIM, are
      both preceded by alternative genes that compete for presence at their
      loci.
AU  - Ando T
AU  - Aras RA
AU  - Kusugami K
AU  - Blaser MJ
AU  - Wassenaar TM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2003 185: 295-301.

PMID- 
VI  - 0
DP  - 1982
TI  - Site-specific restriction endodeoxyribonucleases in Bacilli.
PG  - 66-70
AB  - Biochemical studies on the biological phenomena of restriction and modification
      of phages have resulted in the discovery of site-specific endonucleases (type
      II restriction endonucleases) that cleave double-stranded DNA at or near
      nucleotide sequences specific to each enzyme.  Site-specific endonucleases have
      been widely used as tools for research in molecular biology, particularly that
      on recombinant DNA.  During restriction and modification of phage Phi105C, we
      previously observed that Bacillus subtilis (including B. amyloliquefaciens) had
      site-specific restriction endonucleases BamNI and BamNx, which recognize  5'
      G^G A T C C 3' and 5' G^G A C C 3' 3' C C T A G^G 5'     3' C C T G^G5'
      respectively, and cut the phosphodiester bonds as indicated by arrows.  We
      have, since then, systematically screened strains of Bacilli for site-specific
      endonucleases.  In this paper, we describe related biochemical studies.
AU  - Ando T
AU  - Hayase E
AU  - Ikawa S
AU  - Shibata T
PT  - Journal Article
TA  - Microbiology-1982
JT  - Microbiology-1982
SO  - Microbiology-1982 1982 0: 66-70.

PMID- 
VI  - 25
DP  - 2010
TI  - Restriction-modification systems may be associated with Helicobacter pylori virulence.
PG  - S95-S98
AB  - Restriction-modification (R-M) systems are exclusive to unicellular organisms and ubiquitous
      in the bacterial world. Bacteria use R-M
      systems as a defense against invasion by foreign DNA. Analysis of the
      genome sequences of Helicobacter pylori strains 26 695 and J99
      identified an extraordinary number of genes with homology to R-M genes
      in other bacterial species. All H. pylori strains possess their own
      unique complement of active R-M systems. All of the methylases that
      have been studied so far were present in all major human population
      groupings, suggesting that their horizontal acquisition pre-dated the
      separation of these populations. The two most strongly conserved
      methylase genes of H. pylori, hpy IM and hpy IIIM, are both preceded by
      alternative genes that compete for presence at their loci, and
      furthermore these genes may be associated with H. pylori pathogenicity.
      Further study should investigate the roles of H. pylori R-M systems.
AU  - Ando T
AU  - Ishiguro K
AU  - Watanabe O
AU  - Miyake N
AU  - Kato T
AU  - Hibi S
AU  - Mimura S
AU  - Nakamura M
AU  - Miyahara R
AU  - Ohmiya N
AU  - Niwa Y
AU  - Goto H
PT  - Journal Article
TA  - J. Gastroenterol. Hepatol.
JT  - J. Gastroenterol. Hepatol.
SO  - J. Gastroenterol. Hepatol. 2010 25: S95-S98.

PMID- 11179242
VI  - 120
DP  - 2001
TI  - H. pylori strains with the novel gene MboX are correlated with gastric cancer in Asian patients.
PG  - A652
AB  - Background: H. pylori exhibits substantial genomic diversity that at least in part influences
      clinical outcome.  Type II restriction-modification (R-M) systems are highly diverse between
      strains, a characteristic unique for H. pylori.  HpyIII, a restriction enzyme found in H.
      pylori, is highly homologous to MboI, which recognizes GATC.  We sought to determine the
      variability of hpyIII R-M genotypes in H. pylori strains and whether differences are linked to
      geographic origin or clinical features.  Method: We examined 228 strains (US 50, South America
      12, Europe 15, Asia 147, Oceana 4), by assessing digestion of chromosomal DNA by MboI, and by
      performing PCR for hpyIII.  We assessed the correlation between hpyIII status, other
      genotypes, and clinical features among 182 strains (50 US, 85 Japan, 28 China, and 19 Korea).
      cagA, vacA, and iceA status were determined by PCR and LIPA.  Results: Eleven (5%) of 228
      strains tested were MboI-sensitive, and by PCR, 10 (91%) of these 11 did not have hpyIIIR.  In
      these 10 strains, we identified a novel gene (that we termed MboX) in the hpyIII position,
      followed by the cognate methylase, hpyIIIM.  MboX has substantial homology with C. jejuni
      Cj1602, but no function is known for either.  Strain 88-29 which is Mbo-I-sensitive, possesses
      hpyIII, but the upstream promoter is truncated.  We next examined the hpyIII locus in 217
      MboI-resistant strains, and found that 148 (68%) have hpyIIIR, and 69 (32%) have MboX.  In
      Western countries, MboX is more prevalent (55%) than in Asia (25%) (p<0.0001, c2).  In Asia,
      MboX is more prevalent among gastric cancer patients (18/43; 42%) than non-cancer patients
      (14/89; 16%) (p=0.001, c2).  Al 132 Asian strains tested were cagA+, but among US strains,
      MboX is more prevalent in those that are cagA+ (19/29; 63%) than cagA (7/20; 35%) (p=0.04,
      c2).  In vitro, MboX can be replaced by hpyIIIR, and vice versa, by homologous recombination.
      Conclusion: The hpyIII locus may contain either hpyIIIR or MboX, followed by hpyIIIM.  MboX is
      a novel strain-specific gene that is associated with gastric cancer among H. pylori isolates
      from Asian patients.  If this observation is confirmed, MboX may be used in the future to
      identify individuals of higher gastric cancer risk.
AU  - Ando T
AU  - Peek RM Jr
AU  - Kusugami K
AU  - Van Doorn L-J
AU  - Wassenaar T
AU  - Kim S-K
AU  - Blaser MJ
PT  - Journal Article
TA  - Gastroenterology
JT  - Gastroenterology
SO  - Gastroenterology 2001 120: A652.

PMID- 412233
VI  - 22
DP  - 1977
TI  - Host-controlled modification and restriction and the relating enzymes in Bacillus subtilis and other Bacillus strains.
PG  - 1012-1019
AB  - 
AU  - Ando T
AU  - Shibata T
PT  - Journal Article
TA  - Tanpakushitsu Kakusan Koso
JT  - Tanpakushitsu Kakusan Koso
SO  - Tanpakushitsu Kakusan Koso 1977 22: 1012-1019.

PMID- 3003813
VI  - 30
DP  - 1985
TI  - Restriction endonucleases.
PG  - 1429-1444
AB  - Review - in Japanese
AU  - Ando T
AU  - Shibata T
AU  - Kazami J
PT  - Journal Article
TA  - Tanpakushitsu Kakusan Koso
JT  - Tanpakushitsu Kakusan Koso
SO  - Tanpakushitsu Kakusan Koso 1985 30: 1429-1444.

PMID- 11956101
VI  - 62
DP  - 2002
TI  - A Helicobacter pylori restriction endonuclease-replacing gene, hrgA, is associated with gastric cancer in Asian strains.
PG  - 2385-2389
AB  - The sensitivity of Helicobacter pylori chromosomal DNA to MboI digestion was investigated in
      208 strains from several continents. Only
      11 (5%) of the strains were sensitive to MboI, and it was hypothesized that
      HpyIII, a type II restriction/modification enzyme with sequence
      homology to MboI, mediated the protection. This was confirmed by PCR
      analysis of the gene locus of hpyIII, normally composed of hpyIIIR and
      hpyIIIM. In all but one strain sensitive to MboI, no PCR product of
      hpyIIIR was obtained. In contrast, all strains yielded a product for
      hpyIIIM, independent of MboI phenotype. Further examination of the
      hpyIII locus in strains lacking a hpyIIIR PCR product identified a
      novel gene, hrgA, upstream of hpyIIIM. All 208 strains examined had
      either hpyIIIR or hrgA, but not both, upstream of hpyIIIM. Although
      hrgA has homology with a Campylobacter jejuni gene (Cj1602), its
      function is not known. In Western countries, hrgA was more prevalent
      (53%) than in Asia (25%; P<0.0001, chi2). In Asia, hrgA was more
      prevalent among gastric cancer patients (18 of 43; 42%) than among
      noncancer patients (16 of 95; 17%; P=0.001, chi2). All 143 Asian
      strains tested were cagA+, but among Western strains, hrgA was more
      prevalent in cagA+ strains (26 of 42; 62%) than in cagA- strains (9 of
      23; 39%; P=0.04, chi2). In coculture with epithelial cells, hpyIIIR and
      hrgA strains did not show any significant differences in interleukin-8
      induction and apoptosis. Although a direct function for hrgA in
      virulence could not be demonstrated, our data indicate that hrgA is a
      strain-specific gene that might be associated with gastric cancer among
      H. pylori isolates from Asian patients.
AU  - Ando T
AU  - Wassenaar TM
AU  - Peek RM Jr
AU  - Aras RA
AU  - Tschumi AI
AU  - van Doorn L-Jan
AU  - Kusugami K
AU  - Blaser MJ
PT  - Journal Article
TA  - Cancer Res.
JT  - Cancer Res.
SO  - Cancer Res. 2002 62: 2385-2389.

PMID- 11697346
VI  - 291S
DP  - 2001
TI  - hypX shares a genomic locus with the restriction endonuclease gene hpyIIIR in Helicobacter pylori.
PG  - 28
AB  - A novel gene, hypX, with potential predictive value to differentiate virulence amongst
      cagA-positive H. pylori strains has been identified.  This gene may replace hpyIIIR, a
      restriction endonuclease that, together with its methyltransferase, constitutes the hpyIII
      locus, which is homologous to the MboI R-M system.  hypX has substantial homology with Cj1602
      in C. jejuni, but the function for both is unknown.  From 208 strains examined, originating
      from several continents, hypX and hpyIIIR were found to be mutually exclusive in the hpyIII
      locus.  Of the 138 strains bearing hpyIIIR, which we designated Type I, 137 (99%) are Mbo-I
      resistant.  Of the 70 strains bearing hypX, or Type II, 14% are MboI-sensitive.  Type I and
      Type II strains were compared for linkage to geographic origin or clinical features.  In
      Western countries, hypX is more prevalent (53%) than in Asian (25%) (p is less than or equal
      to 0.001, c2).  In Asian, hypX is more prevalent among gastric cancer patients (18/43; 42%)
      than non-cancer patients (16/95; 17%) (p=0.001, X2).  All 143 Asian strains tested were cagA+
      strains (24/39; 62%) than in cagA- strains (9/22; 41%) (p=0.04, X2).  Although a direct
      function for phpX in virulence was not examined, we postulate that hypX is a strain-specific
      marker that might be associated with gastric cancer among H. pylori isolates from Asian
      patients.  Gene -specific assays for hypX may provide tools to identify individuals of higher
      gastric cancer risk in populations in which cagA-positive strains predominate.
AU  - Ando T
AU  - Wassenaar TM
AU  - Peek RM
AU  - Aras RA
AU  - Kusugami K
AU  - van Doom L
AU  - Blaser MJ
PT  - Journal Article
TA  - Int. J. Med. Microbiol.
JT  - Int. J. Med. Microbiol.
SO  - Int. J. Med. Microbiol. 2001 291S: 28.

PMID- 10972824
VI  - 37
DP  - 2000
TI  - Restriction-modification system differences in Helicobacter pylori are a barrier to interstrain plasmid transfer.
PG  - 1052-1065
AB  - Helicobacter pylori cells are naturally competent for the uptake of both plasmid and
      chromosomal DNA. However, we demonstrate that there are strong barriers to transformation of
      H. pylori strains by plasmids derived from unrelated strains. We sought to determine the
      molecular mechanisms underlying these barriers. Transformation efficiency was assessed using
      pHP1, an Escherichia coli-H. pylori shuttle vector conferring kanamycin resistance.
      Transformation of 33 H. pylori strains was attempted with pHP1 purified from either E. coli or
      H. pylori, and was successfully introduced into only 11 strains. Digestion of H. pylori
      chromosomes with different restriction endonucleases (REs) showed that DNA methylation
      patterns vary substantially among strains. The strain most easily transformed, JP26, was found
      to have extremely low endogenous RE activity and to lack a restriction-modification (R-M)
      system, homologous to MboI, which is highly conserved among H. pylori strains. When we
      introduced this system to JP26, pHP1 from MboI.M+ JP26, but not from wild-type JP26,
      transformed MboI R-M+ JP26 and heterologous MboI R-M+ wild-type H. pylori strains. Parallel
      studies with pHP1 from dam+ and dam- E. coli strains confirmed these findings. These data
      indicate that the endogenous REs of H. pylori strains represent a critical barrier to
      interstrain plasmid transfer among H. pylori.
AU  - Ando T
AU  - Xu Q
AU  - Torres M
AU  - Kusugami K
AU  - Israel DA
AU  - Blaser MJ
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2000 37: 1052-1065.

PMID- 1827657
VI  - 2
DP  - 1991
TI  - Kpn378I - a type II restriction endonuclease from Klebsiella pneumoniae.
PG  - 31-32
AB  - A strain of Klebsiella pneumoniae isolated from the air showed the presence of
      a type II restriction endonuclease. Selection for clones that would not form
      capsula resulted in the isolation of a non-pathogenic subclone. The yield of
      the highly purified enzyme is 40,000 units per g of cells. Judging from the
      fragmentation pattern of lambda phage DNA, the sequence specificity of
      R.Kpn378I is indistinguishable from that of SacII endonuclease. Optimal
      reaction conditions are: 50-70mM NaCl/KCl, 10 mM MgCl2, pH 7.5-8.5, 37C. Unlike
      SacII, Kpn378I is not inhibited by NaCl or KCl at concentrations up to 120mM.
AU  - Andreeva IS
AU  - Afinogenova GN
AU  - Lebedev IR
AU  - Nadolinnaya IG
AU  - Pustoshilova NM
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1991 2: 31-32.

PMID- 1649968
VI  - 0
DP  - 1991
TI  - Site specific restriction endonuclease Rme21I from Rhizobium meliloti.
PG  - 30-31
AB  - A new site specific restriction endonuclease Rme21I from Rhizobium meliloti has
      been shown to recognize the following nucleotide sequence 5'-ATCGAT-3' in the
      doublestranded DNA.  Thus, the enzyme is a true isoschizomer of the restriction
      endonucleases Bsu15I and ClaI.
AU  - Andreeva IS
AU  - Afinogenova GN
AU  - Lebedev LR
AU  - Pustoshilova NM
AU  - Gordienko NY
AU  - Maistrenko GG
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1991 0: 30-31.

PMID- 27274361
VI  - 11
DP  - 2016
TI  - Complete genome sequence of Leuconostoc gelidum subsp. gasicomitatum KG16-1, isolated from vacuum-packaged vegetable sausages.
PG  - 40
AB  - Leuconostoc gelidum subsp. gasicomitatum is a predominant lactic acid bacterium (LAB) in
      spoilage microbial communities of different kinds of modified-atmosphere
      packaged (MAP) food products. So far, only one genome sequence of a
      poultry-originating type strain of this bacterium (LMG 18811(T)) has been
      available. In the current study, we present the completely sequenced and
      functionally annotated genome of strain KG16-1 isolated from a vegetable-based
      product. In addition, six other vegetable-associated strains were sequenced to
      study possible 'niche' specificity suggested by recent multilocus sequence
      typing. The genome of strain KG16-1 consisted of one circular chromosome and
      three plasmids, which together contained 2,035 CDSs. The chromosome carried at
      least three prophage regions and one of the plasmids encoded a galactan
      degradation cluster, which might provide a survival advantage in plant-related
      environments. The genome comparison with LMG 18811(T) and six other vegetable
      strains suggests no major differences between the meat- and vegetable-associated
      strains that would explain their 'niche' specificity. Finally, the comparison
      with the genomes of other leuconostocs highlights the distribution of
      functionally interesting genes across the L. gelidum strains and the genus
      Leuconostoc.
AU  - Andreevskaya M
AU  - Hultman J
AU  - Johansson P
AU  - Laine P
AU  - Paulin L
AU  - Auvinen P
AU  - Bjorkroth J
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 40.

PMID- 20402814
VI  - 15
DP  - 2010
TI  - Type I Restriction-Modification Loci Reveal High Allelic Diversity in Clinical Helicobacter pylori Isolates.
PG  - 114-125
AB  - Background: A remarkable variety of restriction-modification (R-M) systems is
      found in Helicobacter pylori. Since they encompass a large portion of
      the strain-specific H. pylori genes and therefore contribute to genetic
      variability, they are suggested to have an impact on disease outcome.
      Type I R-M systems comprise three different subunits and are the most
      complex of the three types of R-M systems.
      Aims:
      We investigated the genetic diversity and distribution of type I
      R-M systems in clinical isolates of H. pylori.
      Material and methods:
      Sixty-one H. pylori isolates from a Swedish hospital based
      case-control study and 6 H. pylori isolates of a Swedish
      population-based study were analyzed using polymerase chain reaction
      for the presence of the three R-M systems' subunits. Representative
      gene variants were sequenced.
      Results:
      Although the hsdM and hsdR genes appeared conserved in our clinical
      H. pylori isolates, the sequences of the hsdS loci were highly
      variable. Despite their sequence diversity, the genes per se were
      present at high frequencies. We identified a number of novel allelic
      hsdS variants, which are distinct from corresponding hsdS loci in the
      sequenced H. pylori strains 26695, J99 and HPAG1. In analyses of paired
      H. pylori isolates, obtained from the same individuals with a 4-year
      interval, we observed genetic modifications of hsdS genes in patients
      with atrophic gastric mucosa.
      Discussion:
      We propose that the genetic variability of hsdS genes in a
      bacterial population will give rise to new specificities of these
      enzymes, which might lead to adaptation to an ever-changing gastric
      environment.
AU  - Andres S
AU  - Skoglund A
AU  - Nilsson C
AU  - Krabbe M
AU  - Bjorkholm B
AU  - Engstrand L
PT  - Journal Article
TA  - Helicobacter
JT  - Helicobacter
SO  - Helicobacter 2010 15: 114-125.

PMID- 21441523
VI  - 193
DP  - 2011
TI  - Genome sequence of high acetic acid resistant bacteria: Gluconacetobacter europaeus LMG 18890T, Gluconacetobacter europaeus LMG 18494 (references  strains), Gluconacetobacter europaeus 5P3 and Gluconacetobacter oboediens  174Bp2 (isolated from vinegar).
PG  - 2670-2671
AB  - Bacteria of the genus Gluconacetobacter are usually involved in the industrial production of
      vinegars with high acetic acid concentration. We
      describe here the genome sequence of three Gluconacetobacter europaeus
      strains, a very common bacterial species from industrial fermenters, as
      well as of a Gluconacetobacter oboediens strain.
AU  - Andres-Barrao C
AU  - Falquet L
AU  - Calderon-Copete SP
AU  - Descombes P
AU  - Ortega PR
AU  - Barja F
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 2670-2671.

PMID- 16887647
VI  - 4
DP  - 1998
TI  - FgoI, a type II restriction endonuclease from the thermoanaerobe Fervidobacterium gondwanense AB39T.
PG  - 227-232
AB  - Restriction endonuclease activity was detected in 11 out of 13 Fervidobacterium isolates,
      including F. islandicum H21T, F. gondwanense AB39T, and nine other Fervidobacterium-like
      strains isolated from the Great Artesian Basin of Australia.  The restriction endonuclease
      from F. gondwanense AB39T was partially purified and designated FgoI.  FgoI recognized a 4
      nucleotide sequence 5'-CTAG-3' and cleaved between nucleotides C and T to produce a 2 base
      5' overhang (5'C/TAG-3').  As predicted from the enzyme recognition and cleavage
      specificity, FgoI was found to cleave phage DNA 13 times, phiX174 three times, pBR322 five
      times, pUC18 four times, and pSK six times.  FgoI exhibited a broad temperature optimum range
      (between 60 to 70oC) and was active at pH 6.5 to 8.5, but not at pH 9.0.  Manganese could
      replace magnesium as a cofactor for activity, but not cobalt chloride, calcium chloride,
      cupric chloride, or zinc chloride.  The restriction endonuclease was completely inactivated by
      phenol/chloroform extraction and was heat inactivated at 80 C for 60 min or at 100 C for 15
      min.  FgoI has been identified as a heat stable isoschizomer of the Type II restriction
      endonucleases, MaeI and BfaI.
AU  - Andrews KT
AU  - Patel BKC
AU  - Clarke FM
PT  - Journal Article
TA  - Anaerobe
JT  - Anaerobe
SO  - Anaerobe 1998 4: 227-232.

PMID- 3023990
VI  - 0
DP  - 1986
TI  - Molecular mechanism of the protection of phage DNA from restriction endonuclease of Staphylococcus aureus cells.
PG  - 43-45
AB  - A representative of the group of virulent staphylococcal bacteriophages Sb-I is
      not limited by the systems of host specificity of DNA in reproduction in
      Staphylococcus aureus cells.  It was also shown that the DNA of this phage is
      not subjected to fragmentation by Sau3A and other restriction endonucleases
      specific for the GATC site.  By restriction analysis of cloned fragments of
      phage DNA in the plasmid pBR322, replicated in E. coli HB101, it was
      established that virus-specific protection is determined by the absence of a
      GATC site in the phage genome.  The evolutionary nature of the elimination of
      the recognition site in the DNA of virulent staphylophages as a method of
      protection from the main type of restriction of the phage DNA in S. aureus
      cells is discussed.
AU  - Andriashvili IA
AU  - Kvachadze LI
AU  - Vashakidze RP
AU  - Adamiya RS
AU  - Chanishvili TG
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1986 0: 43-45.

PMID- 29650575
VI  - 6
DP  - 2018
TI  - Genome Sequences of Five Mycobacterium bovis Strains Isolated from Farmed Animals and Wildlife in Canada.
PG  - e00258-18
AB  - Mycobacterium bovis is the causative agent of bovine tuberculosis, an infectious  disease that
      affects both animals and humans and thus presents a risk to public
      health and the livestock industry. Here, we report the genome sequences of five
      Mycobacterium bovis strains that represent major genotype clusters observed in
      farmed animals and wildlife in Canada.
AU  - Andrievskaia O
AU  - Duceppe MO
AU  - Lloyd D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00258-18.

PMID- 29976607
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Klebsiella pneumoniae Strain ICIS-278_PBV, Isolated from the Feces of a Healthy 59-Year-Old Man from Orenburg, Russia.
PG  - e00576-18
AB  - This report describes the draft genome sequence of Klebsiella pneumoniae strain ICIS-278_PBV,
      isolated from the feces of a healthy 59-year-old man from Orenburg,
      Russia. The size of the genome was 5,584,615 bp (57.2% G+C content). Annotation
      revealed 5,302 coding sequences, including 5,254 proteins, 23 rRNA genes, and 81
      tRNA genes.
AU  - Andryuschenko SV
AU  - Zdvizhkova IA
AU  - Perunova NB
AU  - Bukharin OV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00576-18.

PMID- 24309744
VI  - 1
DP  - 2013
TI  - Genome Sequence of Parvimonas micra Strain A293, Isolated from an Abdominal Abscess from a Patient in the United Kingdom.
PG  - e01025-13
AB  - Parvimonas micra is an important oral microbe that has the ability to grow and proliferate
      within oral biofilms and is involved in periodontal disease, leading
      to gingival bleeding, gingival recession, alveolar bone loss, and tooth mobility.
      However, occasionally these normally oral pathogens can cause infections at other
      sites in the body. We present the genome sequence of Parvimonas micra strain
      A293, a smooth Parvimonas micra strain isolated from an abdominal abscess from a
      patient at Barts Hospital, London, United Kingdom.
AU  - Ang MY
AU  - Dymock D
AU  - Tan JL
AU  - Thong MH
AU  - Tan QK
AU  - Wong GJ
AU  - Paterson IC
AU  - Choo SW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01025-13.

PMID- 24526626
VI  - 2
DP  - 2014
TI  - Genome Sequence of Fusobacterium nucleatum Strain W1481, a Possible New Subspecies Isolated from a Periodontal Pocket.
PG  - e00009-14
AB  - Fusobacterium nucleatum is a bacterial species commonly detected in dental plaque within the
      human oral cavity, with some strains associated with periodontal
      disease, one of the most common clinical bacterial infections in the human body.
      The exact mechanisms of its pathogenesis are still not completely understood. In
      this study, we present the genome sequence and annotation of F. nucleatum strain
      W1481, isolated from a periodontal pocket of a dental patient at the University
      of Bristol, United Kingdom, the 16S rRNA gene sequencing of which showed it to be
      markedly different from the five previously named subspecies.
AU  - Ang MY
AU  - Dymock D
AU  - Tan JL
AU  - Thong MH
AU  - Tan QK
AU  - Wong GJ
AU  - Paterson IC
AU  - Choo SW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00009-14.

PMID- 25780501
VI  - 9
DP  - 2014
TI  - Non-contiguous finished genome sequence and description of Clostridium saudii sp. nov.
PG  - 8
AB  - Clostridium saudii strain JCC(T) sp. nov. is the type strain of C. saudii sp. nov., a new
      species within the genus Clostridia. This strain, whose genome is
      described here, was isolated from a fecal sample collected from an obese
      24-year-old (body mass index 52 kg/m2) man living in Jeddah, Saudi Arabia. C.
      saudii is a Gram-positive, anaerobic bacillus. Here we describe the features of
      this organism, together with the complete genome sequence and annotation. The
      3,653,762 bp long genome contains 3,452 protein-coding and 53 RNA genes,
      including 4 rRNA genes.
AU  - Angelakis E
AU  - Bibi F
AU  - Ramasamy D
AU  - Azhar EI
AU  - Jiman-Fatani AA
AU  - Aboushoushah SM
AU  - Lagier JC
AU  - Robert C
AU  - Caputo A
AU  - Yasir M
AU  - Fournier PE
AU  - Raoult D
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 8.

PMID- 20935097
VI  - 192
DP  - 2010
TI  - Genome Sequence of the Polysaccharide-Degrading, Thermophilic Anaerobe Spirochaeta thermophila DSM 6192.
PG  - 6492-6493
AB  - Spirochaeta thermophila is a thermophilic, free-living anaerobe that is able to degrade
      various alpha- and beta-linked sugar polymers, including
      cellulose. We report here the complete genome sequence of S. thermophila
      DSM 6192, which is the first genome sequence of a thermophilic,
      free-living member of the Spirochaetes phylum. The genome data reveal a
      high density of genes encoding enzymes from more than 30 glycoside
      hydrolase families, a noncellulosomal enzyme system for (hemi)cellulose
      degradation, and indicate the presence of a novel carbohydrate-binding
      module.
AU  - Angelov A
AU  - Liebl S
AU  - Ballschmiter M
AU  - Bomeke M
AU  - Lehmann R
AU  - Liesegang H
AU  - Daniel R
AU  - Liebl W
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 6492-6493.

PMID- 
VI  - 0
DP  - 2011
TI  - Characterization of Plasmid pPO1 from the Hyperacidophile Picrophilus oshimae.
PG  - 723604
AB  - Picrophilus oshimae and Picrophilus torridus are free-living, moderately thermophilic and
      acidophilic organisms from the lineage of
      Euryarchaeota. With a pH optimum of growth at pH 0.7 and the ability to
      even withstand molar concentrations of sulphuric acid, these organisms
      represent the most extreme acidophiles known. So far, nothing is known
      about plasmid biology in these hyperacidophiles. Also, there are no
      genetic tools available for this genus. We have mobilized the 7.6 Kbp
      plasmid from P. oshimae in E. coli by introducing origin-containing
      transposons and described the plasmid in terms of its nucleotide
      sequence, copy number in the native host, mode of replication, and
      transcriptional start sites of the encoded ORFs. Plasmid pPO1 may
      encode a restriction/modification system in addition to its replication
      functions. The information gained from the pPO1 plasmid may prove
      useful in developing a cloning system for this group of extreme
      acidophiles.
AU  - Angelov A
AU  - Voss J
AU  - Liebl W
PT  - Journal Article
TA  - Archaea
JT  - Archaea
SO  - Archaea 2011 0: 723604.

PMID- 10518621
VI  - 27
DP  - 1999
TI  - Construction of a recombinant adenovirus for efficient delivery of the I-SceI yeast endonuclease to human cells and its application in the in vivo cleavage of chromosomes to expose new potential telomeres.
PG  - 4276-4281
AB  - We have constructed a replication-defective adenovirus vector encoding the yeast I- SceI
      endonuclease under the control of the murine cytomegalovirus immediate-early gene promoter
      (AdM SceI) for efficient delivery of this enzyme to mammalian cells.  We present evidence of
      AdM SceI-mediated I-Sce I protein expression and cleavage activity in replication-permissive
      293 cells, and of cleavage of chromosomes in vivo in both 293 cells and in non-permissive
      human cells. We have exploited this system for the generation of chromosomes capped by
      artificial telomeric sequences in cells with integrated plasmids containing telomeric DNA
      arrays adjacent to an I-SceI recognition site. The properties of the AdM SceI virus described
      here make it a useful tool for studying biological processes involving induction of DNA
      breaks, recombination and gene targeting in cells grown in culture and in vivo.
AU  - Anglana M
AU  - Bacchetti S
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1999 27: 4276-4281.

PMID- 8921892
VI  - 178
DP  - 1996
TI  - Isolation of cDNA clones encoding DNA methyltransferase of sea urchin P. lividus: expression during embryonic development.
PG  - 57-61
AB  - A full-length cDNA, encoding a DNA (cytosine-5)-methyltransferase has been assembled from a
      series of overlapping cDNA clones isolated from P. lividus sea urchin embryo cDNA libraries.
      The cDNA contains 103 bp 5'-UTR, 4839 bp open reading frame corresponding to a 1612 amino
      acids protein and 2240 bp 3'-UTR including a terminal 18-bp poly(A) tail.  Both the cDNA and
      the encoded protein are the longest so far reported for DNA Mtases.  The protein shows five
      distinct and sequential regions of identity with the other animal DNA Mtases, with values of
      identity from zero to 80%.  Northern blot analyses reveal a single RNA band of about 7.5 kb in
      length showing a highly regulated concentration pattern during development with peak value at
      the four blastomere stage.
AU  - Aniello F
AU  - Locascio A
AU  - Fucci L
AU  - Geraci G
AU  - Branno M
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1996 178: 57-61.

PMID- 12527191
VI  - 302
DP  - 2003
TI  - Structural organization of the sea urchin DNA (cytosine-5)-methyltransferase gene and characterization of five alternative spliced transcripts.
PG  - 1-9
AB  - Sea urchin DNA (cytosine-5)-methyltransferase (Dnmt1) that is responsible for maintenance of
      DNA methylation patterns clearly shares similarity with
      various Dnmt1s identified in vertebrates. In this study, we determined the
      structure of the sea urchin Dnmt1 gene by screening a genomic library of
      the sea urchin Paracentrotus lividus with the complementary DNA (cDNA) as
      probe. Analysis of the positive clones demonstrated that the Dnmt1 gene
      consists of 34 exons and 33 introns spanning a distance of 35 kb. All
      exon-intron junction sequences agree with the GT/AG consensus with the
      exception of the 3' acceptor site of intron 8 where CT replaces AG
      consensus.The differences in the total number of exons between sea urchin
      and mouse genes reside mainly in the N-terminal region of the protein
      (exons 5-7 of the sea urchin, exons 5-12 of the mouse) where there is very
      low similarity in the amino acid sequence.By reverse
      transcription-polymerase chain reaction using oligonucleotides spanning
      different regions of the cDNA we carried out a comprehensive analysis of
      alternative splicing of the Dnmt1 messenger RNA (mRNA) in sea urchin
      embryos at different stages of development. We demonstrated the presence
      of at least five alternative spliced mRNAs that are regulated during
      development and are translated in truncated or deleted proteins.
AU  - Aniello F
AU  - Villano G
AU  - Corrado M
AU  - Locascio A
AU  - Russo MT
AU  - D'Aniello SD
AU  - Francone M
AU  - Fucci L
AU  - Branno M
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 2003 302: 1-9.

PMID- 26786317
VI  - 44
DP  - 2016
TI  - Phase variation of a Type IIG restriction-modification enzyme alters site-specific methylation patterns and gene expression in Campylobacter jejuni  strain NCTC11168.
PG  - 4581-4594
AB  - Phase-variable restriction-modification systems are a feature of a diverse range  of bacterial
      species. Stochastic, reversible switches in expression of the
      methyltransferase produces variation in methylation of specific sequences.
      Phase-variable methylation by both Type I and Type III methyltransferases is
      associated with altered gene expression and phenotypic variation. One
      phase-variable gene of Campylobacter jejuni encodes a homologue of an unusual
      Type IIG restriction-modification system in which the endonuclease and
      methyltransferase are encoded by a single gene. Using both inhibition of
      restriction and PacBio-derived methylome analyses of mutants and phase-variants,
      the cj0031c allele in C. jejuni strain NCTC11168 was demonstrated to specifically
      methylate adenine in 5'CCCGA and 5'CCTGA sequences. Alterations in the levels of
      specific transcripts were detected using RNA-Seq in phase-variants and mutants of
      cj0031c but these changes did not correlate with observed differences in
      phenotypic behaviour. Alterations in restriction of phage growth were also
      associated with phase variation (PV) of cj0031c and correlated with presence of
      sites in the genomes of these phages. We conclude that PV of a Type IIG
      restriction-modification system causes changes in site-specific methylation
      patterns and gene expression patterns that may indirectly change adaptive traits.
AU  - Anjum A
AU  - Brathwaite KJ
AU  - Aidley J
AU  - Connerton PL
AU  - Cummings NJ
AU  - Parkhill J
AU  - Connerton I
AU  - Bayliss CD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2016 44: 4581-4594.

PMID- 25377705
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Sulfitobacter sp. CB2047, a Member of the Roseobacter Clade of Marine Bacteria, Isolated from an Emiliania huxleyi Bloom.
PG  - e01125-14
AB  - We announce the draft genome sequence of Sulfitobacter sp. strain CB2047, a marine bacterium
      of the Roseobacter clade, isolated from a phytoplankton bloom.
      The genome encodes pathways for the catabolism of aromatic compounds as well as
      transformations of carbon monoxide and sulfur species. The strain also encodes a
      prophage as well as the gene transfer agent (GTA), both of which are prevalent
      among members of the Rhodobacterales order.
AU  - Ankrah NY
AU  - Lane T
AU  - Budinoff CR
AU  - Hadden MK
AU  - Buchan A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01125-14.

PMID- 8764487
VI  - 140
DP  - 1996
TI  - Improved electro-transformation of highly DNA-restrictive corynebacteria with DNA extracted from starved Escherichia coli.
PG  - 247-251
AB  - Differences of up to 33,000-fold in electro-transformability of highly DNA restrictive
      corynebacteria are observed in the DNA of a shuttle plasmid extracted from Escherichia coli
      hosts propagated in different nutritional conditions.  Growth of the host in minimal medium
      increases plasmid transformability is reverted by supplementing with methionine, an obligate
      S-adenosyl-methionine (SAM) precursor.  This suggests that an E. coli nutritionally modulated
      SAM-dependent DNA-methyltransferase may be involved in this phenomenon.
AU  - Ankri S
AU  - Reyes O
AU  - Leblon G
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1996 140: 247-251.

PMID- 28982991
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Pseudomonas stutzeri Strain KMS 55, an Endophytic Diazotroph Isolated from Rice Roots.
PG  - e00972-17
AB  - Pseudomonas stutzeri strain KMS 55 (MTCC 12703) is an isolate from the root tissues of rice
      (Oryza sativa L.) that displays a high biological nitrogen
      fixation ability. Here, we report the complete genome sequence of this strain,
      which contains 4,637,820 bp, 4,289 protein-coding genes, 5,006 promoter
      sequences, 62 tRNAs, a single copy of 5S-16S-23S rRNA, and a genome average GC
      content of 51.18%. Analysis of the ~4.64-Mb genome sequence will give support to
      increased understanding of the genetic determinants of host range, endophytic
      colonization behavior, endophytic nitrogen fixation, and other plant-beneficial
      roles of Pseudomonas stutzeri.
AU  - Annapurna K
AU  - Govindasamy V
AU  - Sharma M
AU  - Rajrana Y
AU  - Swarnalakshmi K
AU  - Paul S
AU  - Ghosh A
AU  - Chikara SK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00972-17.

PMID- 26358588
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of a Bordetella pertussis Strain with the Virulence-Associated Allelic Variant ptxP3, Isolated in Italy.
PG  - e00944-15
AB  - Despite a universal immunization program, pertussis has persisted and resurged, and is of
      particular concern for infants in terms of morbidity and mortality. Here, we report the genome
      sequence of a Bordetella pertussis strain with the virulence-associated allelic variant ptxP3,
      isolated from a 45-day-old infant.
AU  - Anselmo A
AU  - Buttinelli G
AU  - Ciammaruconi A
AU  - Midulla F
AU  - Nicolai A
AU  - Fortunato A
AU  - Palozzi A
AU  - Fillo S
AU  - Lista F
AU  - Stefanelli P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00944-15.

PMID- 26272575
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Neisseria gonorrhoeae Sequence Type 1407, a Multidrug-Resistant Clinical Isolate.
PG  - e00903-15
AB  - Gonorrhea may become untreatable due to the spread of resistant or multidrug-resistant
      strains. Cefixime-resistant gonococci belonging to sequence
      type 1407 have been described worldwide. We report the genome sequence of
      Neisseria gonorrhoeae strain G2891, a multidrug-resistant isolate of sequence
      type 1407, collected in Italy in 2013.
AU  - Anselmo A
AU  - Ciammaruconi A
AU  - Carannante A
AU  - Neri A
AU  - Fazio C
AU  - Fortunato A
AU  - Palozzi AM
AU  - Vacca P
AU  - Fillo S
AU  - Lista F
AU  - Stefanelli P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00903-15.

PMID- 
VI  - 
DP  - 2011
TI  - Phylogenomic analysis of Escherichia coli methyltransferases and characterization of a novel subfamily of enzymes performing methyl transfer.
PG  - 1-271
AB  - Methyltransferases, which catalyze the transfer of a methyl group from the donor
      S-adenosyl-L-methionine to a substrate molecule, are an ancient superfamily of enzymes
      comprising significant sequence and structural diversity.  They are involved with nearly every
      conceivable biological process, having evolved to perform this same biochemical reaction on a
      wide variety of substrates including DNA, RNA, proteins, lipids, and small molecules.
      Identifying sequence-structure-function relationships within this superfamily presents
      considerable challenges, and this thesis comprises several computational and experimental
      projects directed towards that end.  We examined different types of prokaryotic
      methyltransferases by phylogenetic profiling and comparative genomic approaches, finding that
      those involved with translation exhibit relatively low rates of gene loss and horizontal
      exchange.  DNA methyltransferases, by contrast, undergo frequent horizontal exchange and are
      not vertically inherited for long periods of time.  We found the model organism Escherichia
      coli K-12 encodes a total of 48 known and 14 probable methyltransferases, and we mined the
      literature to identify methylation activities for which the enzyme responsible was unknown.
      Careful comparison of these two data sets enabled predictions of the activities of many of the
      uncharacterized methyltransferases. We validated one of these predictions by mass
      spectrometry, showing that the yliG gene product (renamed RimO) modifies a universally
      conserved aspartic acid residue in ribosomal protein S12.  This modification (-SCH3 addition)
      involves a radical-SAM mediated sulfur insertion as well as a methylation reaction.  RimO thus
      belongs to a unique methyltransferase subfamily called methylthiotransferases (MTTases), and
      we showed phylogenetically that MTTases comprise four subclades, of which RimO orthologs form
      one.  We predicted substrates for the two remaining uncharacterized subclades and validated
      one of these predictions, showing that YqeV of B. subtilis methylthiolates specific tRNA
      adenosine residues. Despite acting on different substrates (protein vs. tRNA), all found
      MTTase subclades share a surprisingly high degree of sequence similarity in the predicted
      substrate-binding region.  We used this similarity to computationally identify candidate
      residues involved with substrate specificity.  These proteins exhibit a novel protein fold
      compared to other methyltransferases, and we present preliminary biochemical results that shed
      light on the nature of the methylation reaction carried out by RimO.
AU  - Anton BP
PT  - Journal Article
TA  - Ph.D. Thesis, Boston University
JT  - Ph.D. Thesis, Boston University
SO  - Ph.D. Thesis, Boston University 2011 : 1-271.

PMID- 27034504
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of the Engineered Escherichia coli SHuffle Strains and Their Wild-Type Parents.
PG  - e00230-16
AB  - SHuffle strains are genetically engineeredEscherichia colistrains that are capable of
      oxidizing cysteines within proteins to form disulfide bonds. Here we
      present the complete genome of both the K-12 and B versions of SHuffle strains
      along with their parental ancestors. These strains have been of significant use
      to both the general scientific community and the biotech industry, interested in
      producing novel disulfide-bonded proteins that were hitherto unable to be
      expressed in standardE. coliexpression strains.
AU  - Anton BP
AU  - Fomenkov A
AU  - Raleigh EA
AU  - Berkmen M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00230-16.

PMID- 27556252
VI  - 11
DP  - 2016
TI  - Comparative Methylome Analysis of the Occasional Ruminant Respiratory Pathogen Bibersteinia trehalosi.
PG  - e0161499
AB  - We examined and compared both the methylomes and the modification-related gene content of four
      sequenced strains of Bibersteinia trehalosi isolated from the
      nasopharyngeal tracts of Nebraska cattle with symptoms of bovine respiratory
      disease complex. The methylation patterns and the encoded DNA methyltransferase
      (MTase) gene sets were different between each strain, with the only common
      pattern being that of Dam (GATC). Among the observed patterns were three novel
      motifs attributable to Type I restriction-modification systems. In some cases the
      differences in methylation patterns corresponded to the gain or loss of MTase
      genes, or to recombination at target recognition domains that resulted in changes
      of enzyme specificity. However, in other cases the differences could be
      attributed to differential expression of the same MTase gene across strains. The
      most obvious regulatory mechanism responsible for these differences was slipped
      strand mispairing within short sequence repeat regions. The combined action of
      these evolutionary forces allows for alteration of different parts of the
      methylome at different time scales. We hypothesize that pleiotropic
      transcriptional modulation resulting from the observed methylomic changes may be
      involved with the switch between the commensal and pathogenic states of this
      common member of ruminant microflora.
AU  - Anton BP
AU  - Harhay GP
AU  - Smith TP
AU  - Blom J
AU  - Roberts RJ
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2016 11: e0161499.

PMID- 9073062
VI  - 187
DP  - 1997
TI  - Cloning and characterization of the BglII restriction-modification system reveals a possible evolutionary footprint.
PG  - 19-27
AB  - BglII, a type II restriction-modification (R-M) system from Bacillus globigii, recognizes the
      sequence 5'-AGATCT-3'.  The system has been cloned into E. coli in multiple steps: first the
      methyltransferase (Mtase) gene, bglIIM, was cloned from B. globigii RUB561, a variant
      containing an inactivated endonuclease (Enase) gene (bglIIR).  Next the ENase protein (R.
      BglII) was purified to  homogeneity from RUB562, a strain expressing the complete R-M system.
      Oligonucleotide probes specific for the 5' end of the gene were then synthesized and used to
      locate bglIIR, and the gene was isolated and cloned in a subsequent step.  The nucleotide
      sequence of the system has been determined, and several interesting features have been found.
      The genes are tandemly arranged, with bglIIR preceding bglIIM.  The amino acid sequence of
      M.BglII is compared to those of other known MTases.  A third gene encoding a protein with
      sequence similarity to known C elements of other R-M sysems is found upstream of bglIIR.  This
      is the first instance of a C gene being associated with an R-M system where the R and M genes
      are collinear.  In addition, open reading frames (ORFs) resembling genes involved with DNA
      mobility are found in close association with BglII.  These may shed light on the evolution of
      the R-M system.
AU  - Anton BP
AU  - Heiter DF
AU  - Benner JS
AU  - Hess EJ
AU  - Greenough L
AU  - Moran LS
AU  - Slatko BE
AU  - Brooks JE
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1997 187: 19-27.

PMID- 26010885
VI  - 10
DP  - 2015
TI  - Complete Genome Sequence of ER2796, a DNA Methyltransferase-Deficient Strain of Escherichia coli K-12.
PG  - E0127446
AB  - We report the complete sequence of ER2796, a laboratory strain of Escherichia
      coli K-12 that is completely defective in DNA methylation. Because of its lack of
      any native methylation, it is extremely useful as a host into which heterologous
      DNA methyltransferase genes can be cloned and the recognition sequences of their
      products deduced by Pacific Biosciences Single-Molecule Real Time (SMRT)
      sequencing. The genome was itself sequenced from a long-insert library using the
      SMRT platform, resulting in a single closed contig devoid of methylated bases.
      Comparison with K-12 MG1655, the first E. coli K-12 strain to be sequenced, shows
      an essentially co-linear relationship with no major rearrangements despite many
      generations of laboratory manipulation. The comparison revealed a total of 41
      insertions and deletions, and 228 single base pair substitutions. In addition,
      the long-read approach facilitated the surprising discovery of four gene
      conversion events, three involving rRNA operons and one between two cryptic
      prophages. Such events thus contribute both to genomic homogenization and to
      bacteriophage diversification. As one of relatively few laboratory strains of E.
      coli to be sequenced, the genome also reveals the sequence changes underlying a
      number of classical mutant alleles including those affecting the various native
      DNA methylation systems.
AU  - Anton BP
AU  - Mongodin EF
AU  - Agrawal S
AU  - Fomenkov A
AU  - Byrd DR
AU  - Roberts RJ
AU  - Raleigh EA
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2015 10: E0127446.

PMID- 27834703
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of NEB 5-alpha, a Derivative of Escherichia coli K-12 DH5alpha.
PG  - e01245-16
AB  - Escherichia coli K-12 DH5alpha is one of the most popular and widely available laboratory
      strains, but, surprisingly, no complete genome sequence has been
      publicly available. Here, we report the complete, finished sequence of NEB
      5-alpha (DH5alpha fhuA2). It should serve as a useful reference for researchers
      working with DH5alpha.
AU  - Anton BP
AU  - Raleigh EA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01245-16.

PMID- 15317774
VI  - 186
DP  - 2004
TI  - Transposon-mediated linker insertion scanning mutagenesis of the Escherichia coli McrA endonuclease.
PG  - 5699-5707
AB  - McrA is one of three functions that restrict modified foreign DNA in Escherichia coli K-12,
      affecting both methylated and hydroxymethylated
      substrates. We present here the first systematic analysis of the
      functional organization of McrA by using the GPS-LS insertion scanning
      system. We collected in-frame insertions of five amino acids at 46
      independent locations and C-terminal truncations at 20 independent
      locations in the McrA protein. Each mutant was assayed for in vivo
      restriction of both methylated and hydroxymethylated bacteriophage
      (M.HpaII-modified lambda and T4gt, respectively) and for induction of the
      E. coli SOS response in the presence of M.HpaII methylation, indicative of
      DNA damage. Our findings suggest the presence of an N-terminal DNA-binding
      domain and a C-terminal catalytic nuclease domain connected by a linker
      region largely tolerant of amino acid insertions. DNA damage inflicted by
      a functional C-terminal domain is required for restriction of phage T4gt.
      Disruption of the N-terminal domain abolishes restriction of both
      substrates. Surprisingly, truncation mutations that spare the N-terminal
      domain do not mediate DNA damage, as measured by SOS induction, but
      nevertheless partially restrict M.HpaII-modified lambda in vivo. We
      suggest a common explanation for this "restriction without damage" and a
      similar observation seen in vivo with McrB, a component of another of the
      modified-DNA restriction functions. Briefly, we propose that unproductive
      site-specific binding of the protein to a vulnerable position in the
      lambda genome disrupts the phage development program at an early stage. We
      also identified a single mutant, carrying an insertion in the N-terminal
      domain, which could fully restrict lambda but did not restrict T4gt at
      all. This mutant may have a selective impairment in substrate recognition,
      distinguishing methylated from hydroxymethylated substrates. The study
      shows that the technically easy insertion scanning method can provide a
      rich source of functional information when coupled with effective
      phenotype tests.
AU  - Anton BP
AU  - Raleigh EA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2004 186: 5699-5707.

PMID- 12620628
VI  - 219
DP  - 2003
TI  - Characterization of a novel unique restriction-modification system from Yersinia enterocolitica O:8 1B.
PG  - 249-252
AB  - Genetic manipulations with enteropathogenic Yersinia enterocolitica O:8 are complicated by the
      presence of an efficient PstI-like YenI
      restriction-modification (R-M) system. We have characterized the YenI R-M
      system in Y. enterocolitica O:8, biotype 1B. A 5039 bp DNA fragment of the
      pSAK2 recombinant plasmid carrying the yenI locus was used to determine
      the nucleotide sequence. DNA sequence analysis identified a single 2481 bp
      open reading frame (ORF) that encodes an 826 amino acid large polypeptide
      having an apparent molecular mass of 93 kDa. The N-terminal part of the
      YenI ORF has 45 and 40% identity to PstI and BsuI methyltransferases
      (MTases), respectively; while the C-terminal part depicts 55 and 45%
      identity to endonucleases (ENases) of both isoschyzomeric enzymes. The
      yenI gene was cloned into pT7-5 plasmid and has been shown to encode a
      single polypeptide of expected molecular mass. A specific recognition
      sequence, typical to the type II R-M systems and single peptide
      organization, typical to type IV R-M systems, make YenI unique among known
      restriction-modification systems. We have constructed a truncated
      recombinant variant of YenI enzyme, which conserved only MTase activity,
      and that can be applied to YenI methylation of the DNA to be transformed
      into Y. enterocolitica O:8 biotype 1B strains.
AU  - Antonenko V
AU  - Pawlow V
AU  - Heesemann J
AU  - Rakin A
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2003 219: 249-252.

PMID- 15008812
VI  - 6
DP  - 2004
TI  - Strain-specific genomic regions of Ruminococcus flavefaciens FD-1 as revealed by combinatorial random-phase genome sequencing and suppressive subtractive hybridization.
PG  - 335-346
AB  - Two closely related strains of the Gram-positive, cellulolytic ruminal
      bacterium Ruminococcus flavefaciens were compared at the genomic level by
      suppressive subtractive hybridization. The two strains investigated in
      this study differ by 1.94% in their respective 16S rDNA genes. Three
      hundred and eighty-four PCR-amplified products were cloned and then
      screened for their strain identity by dot blot hybridization. Based on
      redundancy percentages of the clones sequenced, 9.5% of the genome of the
      R. flavefaciens FD-1 strain is not present in the JM1 strain. The majority
      of identities of individual cloned subtracted products (642 bp average
      length) bore no relation to deposited sequences in GenBank (42% of the
      subtracted library), whereas of those with putative assigned functions 7%
      are loosely associated with fibre-degradation, 6% with insertion elements,
      transposons and phage-like ORFs, 5% with cell membrane associated proteins
      and 3% with signal transduction. Subtracted sequences were then
      supplemented with the draft (2 x coverage) genome sequence of R.
      flavefaciens FD-1 to indicate potential regions of rearrangement within
      the genome, including a novel insertion sequence.
AU  - Antonopoulos DA
AU  - Nelson KE
AU  - Morrison M
AU  - White BA
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2004 6: 335-346.

PMID- 7311907
VI  - 50
DP  - 1981
TI  - [Methylcobalamin-dependent enzymatic methylation of DNA in a cell-free extract of Propionibacterium shermanii].
PG  - 631-635
AB  - The regulation of the functional activity of Propionibacterium shermanii cells by cobalamin is
      accompanied by an increase in the methylation of their DNA at the
      cytosine residue: the DNA from B12-deficient cells is undermethylated as compared
      with the DNA from control cells, i. e. cells synthesizing corrinoids. The results
      of in vitro experiments make it possible to correlate this phenomenon with the
      capability of DNA methylases from B12-deficient and control cells to function
      with different donors of methyl groups. Just as the enzymes methylating adenine
      and cytosine in B12-deficient cells, adenine DNA methylase from cells
      synthesizing corrinoids is active in vitro with S-adenosylmethionine. Cytosine
      DNA methylase from P. shermanii control cells is inactive with
      S-adenosylmethionine and transfers methyl groups only in the presence of
      cobalamins.
AU  - Antoshkina NV
AU  - Vorob'eva LI
AU  - Bur'ianov IaI
PT  - Journal Article
TA  - Mikrobiologiia
JT  - Mikrobiologiia
SO  - Mikrobiologiia 1981 50: 631-635.

PMID- 440158
VI  - 48
DP  - 1979
TI  - [Participation of methylcobalamin in the methylation of Propionibacterium shermanii DNA].
PG  - 217-221
AB  - Propionibacterium shermanii is characterized by a high content of 5-methylcytosine (5 MC). The
      level of 5-MC in B12-deficient cells of the culture
      is twice as low as in the control. The in vitro treatment of DNA isolated from
      the B12-deficient cells with methyl-cobalamin in the presence of the extract of
      control cells possessing the activity of DNA-methylase increases the content of
      5-MC to the control level. No additional methylation of DNA in vitro takes place
      in the absence of the methylase system and in the presence of other forms of
      corrynoids. The methylating activity is displayed either in the presence of
      methionine or without it. The inhibitor of methylcobalamin, i.e.
      diftorchlormethyl-cobalamin, blocks methylation of DNA. Small quantities of
      S-adenosylmethionine are necessary for the reaction of methylation.
AU  - Antoshkina NV
AU  - Vorob'eva LI
AU  - Iordan EP
PT  - Journal Article
TA  - Mikrobiologiia
JT  - Mikrobiologiia
SO  - Mikrobiologiia 1979 48: 217-221.

PMID- 21705588
VI  - 193
DP  - 2011
TI  - Genome sequence of Salinisphaera shabanensis, a gammaproteobacterium from the harsh, variable environment of the brine-seawater interface of the  Shaban Deep in the Red Sea.
PG  - 4555-4556
AB  - We present the genome of Salinisphaera shabanensis isolated from a brine-seawater interface
      and representing a new order within the
      Gammaproteobacteria. Adaptations to physicochemical and nutrient
      availability fluctuation include six genes encoding heavy metal
      translocating P-type ATPases, multiple genes involved in iron-uptake,
      siderophore production and poly-beta-hydroxybutyrate synthesis.
AU  - Antunes A
AU  - Alam I
AU  - Bajic VB
AU  - Stingl U
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4555-4556.

PMID- 21705593
VI  - 193
DP  - 2011
TI  - Genome sequence of Halorhabdus tiamatea, the first archaeon isolated from a deep-sea anoxic brine lake.
PG  - 4553-4554
AB  - We present the draft genome of Halorhabdus tiamatea, the first member of the Archaea ever
      isolated from a deep-sea anoxic brine. Genome comparison
      with H. utahensis, revealed some striking differences, including marked
      increase in genes associated with trans-membrane transport, and putative
      genes for a trehalose synthase and a lactate-dehydrogenase.
AU  - Antunes A
AU  - Alam I
AU  - Bajic VB
AU  - Stingl U
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4553-4554.

PMID- 21705599
VI  - 193
DP  - 2011
TI  - Genome sequence of Haloplasma contractile, an unusual contractile bacterium from a deep-sea anoxic brine lake.
PG  - 4551-4552
AB  - We present the draft genome of Haloplasma contractile, isolated from a deep-sea brine and
      representing a new order between Firmicutes and
      Mollicutes. Its complex morphology with contractile protrusions might be
      strongly influenced by the presence of seven MreB/Mbl homologs, which
      appear to be the highest copy number ever reported.
AU  - Antunes A
AU  - Alam I
AU  - El Dorry H
AU  - Siam R
AU  - Robertson A
AU  - Bajic VB
AU  - Stingl U
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4551-4552.

PMID- 27056225
VI  - 4
DP  - 2016
TI  - Genome Sequence of Bacillus anthracis Strain Stendal, Isolated from an Anthrax Outbreak in Cattle in Germany.
PG  - e00219-16
AB  - In July 2012, an anthrax outbreak occurred among cattle in northern Germany resulting in ten
      losses. Here, we report the draft genome sequence ofBacillus
      anthracisstrain Stendal, isolated from one of the diseased cows.
AU  - Antwerpen M
AU  - Elschner M
AU  - Gaede W
AU  - Schliephake A
AU  - Grass G
AU  - Tomaso H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00219-16.

PMID- 25301643
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Strain BF-4, a Lysinibacillus-Like Bacillus Isolated during an Anthrax Outbreak in Bavaria.
PG  - e00918-14
AB  - We report the draft genome sequence of Lysinibacillus sp. strain BF-4. Strain BF-4 has a
      notably small genome for a free-living bacillus, with a size of 2.63
      Mbp. In agreement with phenotypic observations, the genome lacks genes essential
      for endospore formation.
AU  - Antwerpen M
AU  - Georgi E
AU  - Zimmermann P
AU  - Hoermansdorfer S
AU  - Meyer H
AU  - Grass G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00918-14.

PMID- 23105087
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Bacillus anthracis BF-1, Isolated from Bavarian Cattle.
PG  - 6360-6361
AB  - Bacillus anthracis BF-1 was isolated from a cow in Bavaria (Germany) that had succumbed to
      anthrax. Here, we report the draft genome sequence of this strain,
      which belongs to the European B2 subclade of B. anthracis. The closest
      phylogenetic neighbor of strain BF-1 is a strain isolated from cattle in France.
AU  - Antwerpen M
AU  - Proenca DN
AU  - Ruckert C
AU  - Licht K
AU  - Kalinowski J
AU  - Hanczaruk M
AU  - Tiemann C
AU  - Grass G
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6360-6361.

PMID- 28280006
VI  - 5
DP  - 2017
TI  - Genome Sequence of Historical Bacillus anthracis Strain Tyrol 4675 Isolated from  a Bovine Anthrax Case in Austria.
PG  - e00002-17
AB  - In 1988, an outbreak of anthrax occurred among cattle in the Austrian state of Tyrol. Since
      then, Austria has been declared anthrax-free. Here, we report the
      draft genome sequence of one of these last outbreak strains, Bacillus anthracis
      Tyrol 4675, isolated from a diseased cow.
AU  - Antwerpen M
AU  - Wolfel R
AU  - Grass G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00002-17.

PMID- 23405342
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of a Francisella tularensis subsp. holarctica Strain from Germany Causing Lethal Infection in Common Marmosets.
PG  - e00135-12
AB  - Here, we describe the genome sequence of the Francisella tularensis subsp. holarctica strain
      F92, belonging to the Franco-Iberian subgroup. This strain
      represents the first-time isolate of this subgroup in Germany and was obtained
      from naturally infected marmosets.
AU  - Antwerpen MH
AU  - Schacht E
AU  - Kaysser P
AU  - Splettstoesser WD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00135-12.

PMID- 25331649
VI  - 15
DP  - 2014
TI  - The genomic landscape of the verrucomicrobial methanotroph Methylacidiphilum fumariolicum SolV.
PG  - 914
AB  - Background: Aerobic methanotrophs can grow in hostile volcanic environments and use methane as
      their sole source of energy. The discovery of three verrucomicrobial Methylacidiphilum strains
      has revealed diverse metabolic pathways used by these methanotrophs, including mechanisms
      through which methane is oxidized. The basis of a complete understanding of these processes
      and of how these bacteria evolved and are able to thrive in such extreme environments
      partially resides in the complete characterization of their genome and its
      architecture.Results: In this study, we present the complete genome sequence of
      Methylacidiphilum fumariolicum SolV, obtained using Pacific Biosciences single-molecule
      real-time (SMRT) sequencing technology. The genome assembles to a single 2.5 Mbp chromosome
      with an average GC content of 41.5%. The genome contains 2,741 annotated genes and 314
      functional subsystems including all key metabolic pathways that are associated with
      Methylacidiphilum strains, including the CBB pathway for CO2 fixation. However, it does not
      encode the serine cycle and ribulose monophosphate pathways for carbon fixation. Phylogenetic
      analysis of the particulate methane mono-oxygenase operon separates the Methylacidiphilum
      strains from other verrucomicrobial methanotrophs. RNA-Seq analysis of cell cultures growing
      in three different conditions revealed the deregulation of two out of three pmoCAB operons. In
      addition, genes involved in nitrogen fixation were upregulated in cell cultures growing in
      nitrogen fixing conditions, indicating the presence of active nitrogenase. Characterization of
      the global methylation state of M. fumariolicum SolV revealed methylation of adenines and
      cytosines mainly in the coding regions of the genome. Methylation of adenines was
      predominantly associated with 5'-(m6)ACN(4)GT-3' and 5'-CC(m6)AN(5)CTC-3'
      methyltransferase recognition motifs whereas methylated cytosines were not associated with any
      specific motif.Conclusions: Our findings provide novel insights into the global methylation
      state of verrucomicrobial methanotroph M. fumariolicum SolV. However, partial conservation of
      methyltransferases between M. fumariolicum SolV and M. infernorum V4 indicates potential
      differences in the global methylation state of Methylacidiphilum strains. Unravelling the M.
      fumariolicum SolV genome and its epigenetic regulation allow for robust characterization of
      biological processes that are involved in oxidizing methane. In turn, they offer a better
      understanding of the evolution, the underlying physiological and ecological properties of SolV
      and other Methylacidiphilum strains.
AU  - Anvar SY
AU  - Frank J
AU  - Pol A
AU  - Schmitz A
AU  - Kraaijeveld K
AU  - den Dunnen JT
AU  - Op den Camp HJ
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2014 15: 914.

PMID- 11522819
VI  - 29
DP  - 2001
TI  - Enzymatic properties of de novo-type mouse DNA (cytosine-5) methyltransferases.
PG  - 3506-3512
AB  - We have purified GST-fused recombinant mouse Dnmt3a and three isoforms of mouse Dnmt3b to near
      homogeneity. Dnmt3b3, an isoform of Dnmt3b, did not have DNA methylation activity.  Dnmt3a,
      Dnmt3b1 or Dnmt3b2 showed similar activity toward poly(dG-dC)-poly(dG-dC) for measuring de
      novo methylation activity, and toward poly(dI-dC)-poly(dI-dC) for measuring total activity.
      This indicates that the enzymes are de novo-type DNA methyltransferases. The enzyme activity
      was inhibited by NaCl or KCl at concentrations >100 mM. The kinetic parameter, K(m)(AdoMet),
      for Dnmt3a, Dnmt3b1 and Dnmt3b2 was 0.4, 1.2 and 0.9 microM when poly(dI-dC)-poly(dI-dC) was
      used, and 0.3, 1.2 and 0.8 microM when poly(dG-dC)-poly(dG-dC) was used, respectively. The
      K(m)(DNA) values for Dnmt3a, Dnmt3b1 and Dnmt3b2 were 2.7, 1.3 and 1.5 microM when
      poly(dI-dC)-poly(dI-dC) was used, and 3.5, 1.0 and 0.9 microM when poly(dG-dC)-poly(dG-dC) was
      used, respectively. For the methylation specificity, Dnmt3a significantly methylated CpG >>
      CpA. On the other hand, Dnmt3b1 methylated CpG > CpT >/= CpA. Immuno-purified Dnmt3a,
      Myc-tagged and overexpressed in HEK 293T cells, methylated CpG >> CpA > CpT. Neither Dnmt3a
      nor Dnmt3b1 methylated the first cytosine of CpC.
AU  - Aoki A
AU  - Suetake I
AU  - Miyagawa J
AU  - Fujio T
AU  - Chijiwa T
AU  - Sasaki H
AU  - Tajima S
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2001 29: 3506-3512.

PMID- 29311089
VI  - 62
DP  - 2018
TI  - Molecular Characterization of IMP-1-Producing Enterobacter cloacae Complex Isolates in Tokyo.
PG  - e02091-17
AB  - Although KPC enzymes are most common among carbapenemases produced by
      Enterobacter cloacae complex globally, the epidemiology varies from one country
      to another. While previous studies have suggested that IMP enzymes are most
      common in Japan, detailed analysis has been scarce thus far. Here, we carried out
      a molecular epidemiological study and plasmid analysis of IMP-1-producing E.
      cloacae complex isolates collected from three hospitals in central Tokyo using
      whole-genome sequencing. Seventy-one isolates were classified into several
      sequence types (STs), and 49 isolates were identified as Enterobacter hormaechei
      ST78. Isolates of ST78 were divided into three clades by core-genome single
      nucleotide polymorphism (SNP)-based phylogenetic analysis. Whereas isolates of
      clade 3 were isolated from only one hospital, isolates of clade 1 and 2 were
      identified from multiple hospitals. Ten of 12 clade 1 isolates and 1 of 4 clade 2
      isolates carried blaIMP-1 on IncHI2 plasmids, with high similarity of genetic
      structures. In addition, these plasmids shared backbone structures with IncHI2
      plasmids carrying blaIMP reported from other countries of the Asia-Pacific
      region. All isolates of clade 3 except one carried blaIMP-1 in In1426 on IncW
      plasmids. An isolate of clade 3, which lacked IncW plasmids, carried blaIMP-1 in
      In1426 on an IncFIB plasmid. These observations suggest that IMP-producing E.
      cloacae complex isolates with a diversity of host genomic backgrounds have spread
      in central Tokyo, and they indicate the possible contribution of IncHI2 plasmids
      toward this phenomenon.
AU  - Aoki K
AU  - Harada S
AU  - Yahara K
AU  - Ishii Y
AU  - Motooka D
AU  - Nakamura S
AU  - Akeda Y
AU  - Iida T
AU  - Tomono K
AU  - Iwata S
AU  - Moriya K
AU  - Tateda K
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2018 62: e02091-17.

PMID- 28546492
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Photobacterium damselae subsp. piscicida Strain OT-51443 Isolated from Yellowtail (Seriola quinqueradiata) in Japan.
PG  - e00404-17
AB  - Pseudotuberculosis caused by infection of Photobacterium damselae subsp. piscicida has caused
      serious economic damages to aquaculture farms worldwide.
      Here, the whole-genome sequence of P. damselae subsp. piscicida strain OT-51443,
      isolated in Japan, was determined and suggests that this genome consists of two
      chromosomes and five plasmids.
AU  - Aoki T
AU  - Teru Y
AU  - Morimoto N
AU  - Kono T
AU  - Sakai M
AU  - Takano T
AU  - Hawke JP
AU  - Fukuda Y
AU  - Takeyama H
AU  - Hikima JI
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00404-17.

PMID- 28619806
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Geobacter pelophilus Strain Dfr2, a Ferric Iron-Reducing Bacterium.
PG  - e00537-17
AB  - Here, we report a draft genome sequence of Geobacter pelophilus strain Dfr2, a ferric
      iron-reducing bacterium. This genome information will further our
      understanding of the mechanisms underlying electron transfer from microorganisms
      to ferric iron oxides.
AU  - Aoyagi T
AU  - Koike H
AU  - Morita T
AU  - Sato Y
AU  - Habe H
AU  - Hori T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00537-17.

PMID- Not carried by PubMed...
VI  - 6
DP  - 1990
TI  - Sensitivity to phages of Streptomyces coelicolor strains harbouring type II restriction endonucleases.
PG  - 71-75
AB  - The role of type II restriction endonucleases in phage development in two
      different strains of Streptomyces coelicolor has been analyzed.  Two of ten
      phages tested (PhiA4 and R4c1) presented a low efficiency of plating (e.o.p.)
      in the studied strains.  The isolation of host-range mutants of PhiA4 and R4c1,
      with improved e.o.p. and higher adsorption capability in these two bacterial
      strains, suggests that the presence of host endonucleases is not the main
      barrier for these phages, but rather adsorption inability.
AU  - Aparicio JF
AU  - Barbes C
AU  - Hardisson C
AU  - Sanchez J
PT  - Journal Article
TA  - Microbiol. Sem.
JT  - Microbiol. Sem.
SO  - Microbiol. Sem. 1990 6: 71-75.

PMID- 28522713
VI  - 5
DP  - 2017
TI  - Amylases and Their Importance during Glycan Degradation: Genome Sequence Release  of Salmonella Amylase Knockout Strains.
PG  - e00355-17
AB  - Amylases catalyze the cleavage of alpha-d-1,4 and alpha-d-1,6-glycosidic bonds in starch and
      related carbohydrates. Amylases are widely distributed in nature and
      are important in carbohydrate metabolism. This is the release of four single and
      two double deletions in Salmonella enterica serovar Typhimurium LT2 that are
      important for glycan degradation during infection.
AU  - Arabyan N
AU  - Huang BC
AU  - Weimer BC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00355-17.

PMID- 28596411
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Salmonella Lysozyme Gene Knockout Mutants.
PG  - e00519-17
AB  - Lysozyme enzymes hydrolyze the beta-1,4-glycosidic bond in oligosaccharides. These enzymes are
      part of a broad group of glucoside hydrolases that are poorly
      characterized; however, they are important for growth and are being recognized as
      emerging virulence factors. This is the release of four
      lysozyme-encoding-gene-deletion mutants in Salmonella enterica serovar
      Typhimurium LT2.
AU  - Arabyan N
AU  - Huang BC
AU  - Weimer BC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00519-17.

PMID- 28774970
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Salmonella enterica Serovar Typhimurium LT2 with Deleted Chitinases That Are Emerging Virulence Factors.
PG  - e00659-17
AB  - Chitinases are glycosyl hydrolases that catalyze the hydrolysis of the beta-1,4 linkages in
      complex carbohydrates and those that contain GlcNAc. These enzymes
      are considered emerging virulence factors during infection because the host
      glycan changes. This is the release of four single chitinase deletion mutants in
      Salmonella enterica serovar Typhimurium LT2.
AU  - Arabyan N
AU  - Huang BC
AU  - Weimer BC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00659-17.

PMID- 28495784
VI  - 5
DP  - 2017
TI  - Implication of Sialidases in Salmonella Infection: Genome Release of Sialidase Knockout Strains from Salmonella enterica Serovar Typhimurium LT2.
PG  - e00341-17
AB  - Sialidases, which are widely distributed in nature, cleave the alpha-ketosidic bond of
      terminal sialic acid residue. These emerging virulence factors degrade
      the host glycan. We report here the release of seven sialidase and one sialic
      acid transporter deletion in Salmonella enterica serovar Typhimurium strain LT2,
      which are important in cellular invasion during infection.
AU  - Arabyan N
AU  - Weis AM
AU  - Huang BC
AU  - Weimer BC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00341-17.

PMID- 26929790
VI  - 11
DP  - 2016
TI  - Draft genomic sequence of Nereida ignava CECT 5292(T), a marine bacterium of the  family Rhodobacteraceae.
PG  - 21
AB  - Nereida ignava strain 2SM4(T) (= CECT 5292(T) = DSM 16309(T) = CIP 108404(T) = CCUG 49433(T))
      is a marine bacterium belonging to the Roseobacter group of the
      family Rhodobacteraceae within the class Alphaproteobacteria. The strain was
      isolated from sea water surrounding cultivated oysters 2-3 miles off the
      Mediterranean coast near Valencia (Spain) and was phylogenetically related to
      uncultured clones of gall symbiont bacteria of some species of Prionitis alga.
      Here we describe the genome sequence and annotation of this organism, the type
      strain of the single species of this genus. The genome comprised 2,888,349 bp,
      2,872 protein-coding genes and 52 RNA genes. The annotation revealed the capacity
      to produce bacteriocins, vitamins and auxins. Besides, it contained sulfur
      cycling related genes.
AU  - Arahal DR
AU  - Pujalte MJ
AU  - Rodrigo-Torres L
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 21.

PMID- 25767236
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Vibrio renopiscarius Strains CECT 8603T and CECT 8604,  Two Marine Gammaproteobacteria Isolated from Cultured Gilthead Sea Bream (Sparus   aurata).
PG  - e00099-15
AB  - Vibrio renopiscarius DCR 1-4-2(T) (CECT 8603(T)) and DCR 1-4-12 (CECT 8604) were  isolated
      from healthy gilthead sea bream (Sparus aurata) from Mediterranean fish
      farms (Castellon, Spain). Their draft genome sequences (30 and 44 contigs,
      respectively) have 4.3 Mbp and a G+C content of 45.2 mol% and contain almost
      3,700 protein-encoding genes.
AU  - Arahal DR
AU  - Rodrigo-Torres L
AU  - Lucena T
AU  - Pujalte MJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00099-15.

PMID- 24855309
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Actibacterium mucosum KCTC 23349, a Marine Alphaproteobacterium with Complex Ionic Requirements Isolated from Mediterranean   Seawater at Malvarrosa Beach, Valencia, Spain.
PG  - e00486-14
AB  - Strain R46 (CECT 7668; KCTC 23349), a nomenclatural type of Actibacterium mucosum, was
      isolated from surface seawater collected at Malvarrosa Beach
      (Valencia, Spain) in July 2008. The draft genome sequence of strain R46
      (approximately 3.72 Mbp) contains 22 scaffolds and 3,619 protein-encoding genes, with a G+C
      content of 60.8 mol%.
AU  - Arahal DR
AU  - Shao Z
AU  - Lai Q
AU  - Pujalte MJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00486-14.

PMID- 20348262
VI  - 192
DP  - 2010
TI  - Complete genome sequence of the thermophilic, obligately chemolithoautotrophic hydrogen-oxidizing bacterium Hydrogenobacter  thermophilus TK-6.
PG  - 2651-2652
AB  - Hydrogenobacter thermophilus is a thermophilic, obligately chemolithoautotrophic and aerobic
      hydrogen-oxidizing bacterium. It is
      unique in its ability to fix carbon dioxide via the reductive
      tricarboxylic acid cycle under aerobic conditions. It utilizes molecular
      hydrogen, elemental sulfur, or thiosulfate as the sole energy source.
      Here, we report the complete genome sequence of H. thermophilus TK-6.
AU  - Arai H
AU  - Kanbe H
AU  - Ishii M
AU  - Igarashi Y
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 2651-2652.

PMID- 30533902
VI  - 7
DP  - 2018
TI  - Complete Genome Sequence of a Moderately Thermophilic Facultative Chemolithoautotrophic Hydrogen-Oxidizing Bacterium, Hydrogenophilus  thermoluteolus TH-1.
PG  - e00857-18
AB  - Hydrogenophilus spp., which are moderately thermophilic aerobic betaproteobacteria, are widely
      distributed in geothermal environments. They fix
      carbon dioxide via the Calvin-Benson-Bassham cycle and exhibit rapid autotrophic
      growth using hydrogen as an energy source. Here, we report the complete genome
      sequence of Hydrogenophilus thermoluteolus strain TH-1.
AU  - Arai H
AU  - Shomura Y
AU  - Higuchi Y
AU  - Ishii M
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e00857-18.

PMID- 856787
VI  - 130
DP  - 1977
TI  - New R plasmid-mediated restriction-modification system of deoxyribonucleic acid conferred by group E R plasmids.
PG  - 529-531
AB  - A new R plasmid-mediated restriction-modification system of deoxyribonucleic
      acid was identified.  This system is specific for group E plasmids which have
      been detected in unidentified marine Vibrio fish pathogens.
AU  - Arai T
AU  - Aoki T
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1977 130: 529-531.

PMID- 20524651
VI  - 114
DP  - 2010
TI  - Theoretical Study of the Catalytic Mechanism of DNA-(N4-Cytosine)-Methyltransferase from the Bacterium Proteus vulgaris.
PG  - 8467-8473
AB  - In this paper the reaction mechanism for methylation of cytosine at the exocyclic N4 position
      catalyzed by M.PvuII has been explored by means of hybrid quantum mechanics/molecular
      mechanics (QM/MM) methods.   A reaction model was prepared by placing a single cytosine base
      in the active site of the enzyme. In this model the exocyclic amino group of the base
      establishes hydrogen bond interactions with the hydroxyl oxygen atom of Ser53 and the carbonyl
      oxygen atom of Pro54. The reaction mechanism involves a direct methyl transfer from AdoMet to
      the N4 atom and a proton transfer from this atom to Ser53, which in turn transfers a proton to
      Asp96. Different timings for the proton transfers and methylation steps have been explored at
      the AM1/MM and B3LYP/MM levels including localization and characterization of stationary
      structures. At our best estimate the reaction proceeds by means of a simultaneous but
      asynchronous proton transfer from Ser53 to Asp96 and from N4 of cytosine to Ser53 followed by
      a direct methyl transfer from AdoMet to the exocyclic N4 of cytosine.
AU  - Aranda J
AU  - Roca M
AU  - Lopez-Canut V
AU  - Tunon I
PT  - Journal Article
TA  - J. Phys. Chem. B
JT  - J. Phys. Chem. B
SO  - J. Phys. Chem. B 2010 114: 8467-8473.

PMID- 22699309
VI  - 10
DP  - 2012
TI  - Substrate promiscuity in DNA methyltransferase M.PvuII. A mechanistic insight.
PG  - 5395-5400
AB  - M. PvuII is a DNA methyltransferase from the bacterium Proteus vulgaris that catalyzes
      methylation of cytosine at the N4 position. This enzyme
      also displays promiscuous activity catalyzing methylation of adenine at
      the N6 position. In this work we use QM/MM methods to investigate the
      reaction mechanism of this promiscuous activity. We found that N6
      methylation in M. PvuII takes place by means of a stepwise mechanism in
      which deprotonation of the exocyclic amino group is followed by the
      methyl transfer. Deprotonation involves two residues of the active
      site, Ser53 and Asp96, while methylation takes place directly from the
      AdoMet cofactor to the target nitrogen atom. The same reaction
      mechanism was described for cytosine methylation in the same enzyme,
      while the reversal timing, that is methylation followed by
      deprotonation, has been described in M. TaqI, an enzyme that catalyzes
      the N6-adenine DNA methylation from Thermus aquaticus. These
      mechanistic findings can be useful to understand the evolutionary paths
      followed by N-methyltransferases.
AU  - Aranda J
AU  - Roca M
AU  - Tunon I
PT  - Journal Article
TA  - Org. Biomol. Chem.
JT  - Org. Biomol. Chem.
SO  - Org. Biomol. Chem. 2012 10: 5395-5400.

PMID- 25347783
VI  - 136
DP  - 2014
TI  - Dynamics and Reactivity in Thermus aquaticus N6-Adenine Methyltransferase.
PG  - 16227-16239
AB  - M.TaqI is a DNA methyltransferase from Thermus aquaticus that catalyzes the transfer of a
      methyl group from S-adenosyl-L-methionine to the N6 position of an adenine, a process
      described only in prokaryotes. We have used full atomistic classical molecular dynamics
      simulations to explore the protein-SAM-DNA ternary complex where the target adenine is flipped
      out into the active site. Key protein DNA interactions established by the target adenine in
      the active site are described in detail. The relaxed structure was used for a combined quantum
      mechanics/molecular mechanics exploration of the reaction mechanism using the string method.
      According to our free energy calculations the reaction takes place through a stepwise
      mechanism where the methyl transfer precedes the abstraction of the proton from the exocyclic
      amino group. The methyl transfer is the rate-determining step, and the obtained free energy
      barrier is in good agreement with the value derived from the experimental rate constant. Two
      possible candidates to extract the leftover proton have been explored: a water molecule found
      in the active site and Asn105, a residue activated by the hydrogen bonds formed through the
      amide hydrogens. The barrier for the proton abstraction is smaller when Asn105 acts as a base.
      The reaction mechanisms can be different in other N6-DNA-methyltransferases, as determined
      from the exploration of the reaction mechanism in the Asn105Asp M.TaqI mutant.
AU  - Aranda J
AU  - Zinovjev K
AU  - Roca M
AU  - Tunon I
PT  - Journal Article
TA  - J. Am. Chem. Soc.
JT  - J. Am. Chem. Soc.
SO  - J. Am. Chem. Soc. 2014 136: 16227-16239.

PMID- 
VI  - 280
DP  - 2013
TI  - Molecular dynamics and QM/MM free energy profiles of cytosine C5-methyltransferase M.Hhai.
PG  - 105
AB  - The target of this work is the study of mechanism of the reaction catalyzed by M.Hhai, an
      enzyme that belongs to the restriction-modification system of the bacterium Haemophilus
      haemolyticus which catalyzes the methyl transfer from S-adenosil-L-metionine to C5 position of
      a cytosine base of DNA, working at the 5'-GCGC-3' sequence generating C5-methyl-cytosine.
      The X-Ray structure of the enzyme complexed with SAM and a DNA sequence was the starting point
      of our simulations.  We performed all calculations considering the whole enzymatic and DNA
      environment and the solvation effect by including the enzyme in a orthorhombic box of TIP3P
      water molecules of 88 x 87 x 99 A of side, including sodium counterions to neutralize the
      charge of the system.  Using the NAMD program we equilibrated the system by means of 10 ns of
      classical molecular dynamics with the AMBER force field, employing periodic boundary
      conditions, Ewald summations, a temperature of 300 K and a time step of 1 fs.  We then
      performed 100 ns MD simulaton in order to analyze the most important interactions formed
      between the enzyme and DNA, the interactions within the active site, how the unpaired base is
      stabilized and how the DNA helix accommodates the great perturbation that a flipped out base
      means for its structure.  To analyse the chemical reaction we performed 500 ps of quantum
      mechanics/molecular mechanics (QM/MM) MD simulation at 300 K using Dynamo program.  Quantum
      subsystem was treated using the AM1 semiempirical hamiltonian adding corrections at the
      M062x/6-311 + G level.  By means of the on-the-fly string method the minimum free energy path
      for each step of the reaction was obtained.  Then, the path collective variable was defined
      along these paths, to obtain the potential of mean force using umbrella sampling.
AU  - Aranda J
AU  - Zinovjev K
AU  - Swiderek K
AU  - Roca M
AU  - Tunon I
PT  - Journal Article
TA  - FEBS J.
JT  - FEBS J.
SO  - FEBS J. 2013 280: 105.

PMID- 11697346
VI  - 291S
DP  - 2001
TI  - Helicobacter pylori regulates hpyII restriction-modification function using gene deletion and horizontal reacquisition.
PG  - 95
AB  - Helicobacter pylori possess strain-specific complements of functional restriction-modification
      systems.  The large number of R-M's homologous to those in other bacterial species and their
      strain-specificity suggests that H. pylori may have horizontally acquired these genes.  A type
      IIs R-M system, HpyII, was active in 2 of the 6 H. pylori strains studied.  We now demonstrate
      that in most strains lacking HpyII.M function there is complete absence of the R-M system.
      Direct DNA repeats of 80-bp flanking the hpyII R-M system allow its deletion, resulting in an
      "empty-site" genotype.  We show that strains possessing this empty-site genotype and strains
      with a full but inactive hpyII R-M can reacquire the hpyII R-M cassette and functional
      activity through natural transformation by DNA from the parental R+M+ strain.  Identical
      isolates divergent for the presence of an active HpyII R-M pose different restriction barriers
      to transformation by foreign DNA.  That H. pylori can regulate HpyII R-M function through
      deletion or mutation, and subsequent horizontal reacquisition of the hpyII R-M cassette
      providing an example of a novel mechanism for R-M regulation, supports the hypothesis that H.
      pylori populations use mutation and transformation to regulate gene function.
AU  - Aras RA
PT  - Journal Article
TA  - Int. J. Med. Microbiol.
JT  - Int. J. Med. Microbiol.
SO  - Int. J. Med. Microbiol. 2001 291S: 95.

PMID- 
VI  - 100
DP  - 2000
TI  - Conservation of a type IIs restriction-modification system in Helicobacter pylori with homology to the MboII R-M system in Moraxella bovis.
PG  - 290-291
AB  - Bacteria use restriction and modification systems as a defense against invasion from foreign
      DNA.  Comparison of the genomes from Helicobacter pylori strains 26695 and J99 identified a
      number of strain-specific R-M systems.  Here we show the conservation of a type IIs R-M system
      among 18 H. pylori strains and its possible involvement in horizontal gene transfer.  Strain
      26695 has a potential type IIs R-M system that has homology to the Moraxella bovis MboII R-M
      system, which recognizes the non-palindromic sequence GAAGA.  PCR analysis of 17 other strains
      show that 10 contain a complete R-M system, 2 contain partial R-M systems and 5 contain no R-M
      system.  Sequence analysis of the 5' end of the restriction endonuclease subunit from 7
      different strains shows predominantly synonymous variations in codon usage; indicating the
      locus is under substantial selective pressure.  For all strains except J188, which has a
      nonfunctional RE subunit, presence of both methyltransferases (MTs) correlates with protection
      of genomic DNA from MboII digestion, implying that the MTs are responsible for modification of
      the sequence GAAGA.  G+C content and phylogenetic analysis indicates that the H. pylori type
      IIs R-M system may have been acquired through horizontal gene transfer.
AU  - Aras RA
AU  - Blaser MJ
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 2000 100: 290-291.

PMID- 
VI  - 102
DP  - 2002
TI  - Horizontal transfer of the Helicobacter pylori restriction-modification system, HpyII, by a conjugation-like mechanism.
PG  - 165-166
AB  - Helicobacter pylori, gram-negative, curved bacteria that colonize the human gastric mucosa,
      possess a large number of genes for
      restriction-modification (R-M) systems, and essentially every strain
      possesses a unique complement of functional and partial R-M systems.
      Nearly half of the H. pylori strains studied possess an active, type
      IIs R-M system, HpyII, with the recognition sequence GAAGA.
      Recombination between direct repeats that flank the R-M allows for its
      deletion whereas strains lacking hpyIIRM can acquire this cassette
      through natural transformation. We now asked whether strains lacking
      HpyII R-M activity can acquire an active 4.8 kb hpyIIRM cassette
      (containing a kanamycin resistance (aphA) marker) through a
      DNase-resistant mechanism. We found that hpyIIRM strains 6c and J166
      acquired an hpyIIRM cassette from strain 6a, through a DNase-resistant
      mechanism, if strains are isogenic (6a fwdarw 6c;
      frequency=3.5e-7+-4.0e-7), but not if strains are non-isogenic (6a
      fwdarw J166; frequency<1.8e-8). The frequency of conjugation-like
      transfer of a point mutation conferring streptomycin resistance was not
      significantly (p=0.47) different for isogenic
      (frequency=2.7e-6+-2.3e-6) and non-isogenic (frequency=1.6e-6+-4.8e-7)
      strains. A non-isogenic strain, J188, containing a full but inactive
      hpyIIRM reactivated its HpyII R-M through natural transformation
      (frequency=2.4e-7+-1.5e-7) but not through conjugation-like
      (frequency<6.6e-8), horizontal acquisition of a functional hpyIIRM.
      Strain J188 was transformed with the hpyIIRM cassette at a
      significantly (p<0.05) lower frequency then was the isogenic 6a strain
      (frequency=7.9e-6+-2.0e-6). These data indicate that a conjugation-like
      mechanism contributes to the transfer of large (4.8 kb) fragments of
      chromosomal DNA between H. pylori strains and that inactive or partial
      R-M systems may act as contingency genes that can be reactivated upon
      recombination with a functional allele. That functional R-M systems
      appear to restrict acquisition of chromosomal DNA suggests that there
      is a double-stranded DNA intermediate in the H. pylori uptake process.
AU  - Aras RA
AU  - Small AJ
AU  - Ando T
AU  - Blaser MJ
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 2002 102: 165-166.

PMID- 12490707
VI  - 30
DP  - 2002
TI  - Helicobacter pylori interstrain restriction-modification diversity prevents genome subversion by chromosomal DNA from competing strains.
PG  - 5391-5397
AB  - Helicobacter pylori, bacteria that colonize the human gastric mucosa, possess a large number
      of genes for restriction-modification (R-M) systems, and essentially, every strain possesses a
      unique complement of functional and partial R-M systems. Nearly half of the H.pylori strains
      studied possess an active type IIs R-M system, HpyII, with the recognition sequence GAAGA.
      Recombination between direct repeats that flank the R-M cassette allows for its deletion
      whereas strains lacking hpyIIRM can acquire this cassette through natural transformation. We
      asked whether strains lacking HpyII R-M activity can acquire an active hpyIIRM cassette
      [containing a 1.4 kb kanamycin resistance (aphA) marker], whether such acquisition is DNase
      sensitive or resistant and whether restriction barriers limit acquisition of chromosomal DNA.
      Our results indicate that natural transformation and conjugation-like mechanisms may
      contribute to the transfer of large (4.8 kb) insertions of chromosomal DNA between H.pylori
      strains, that inactive or partial R-M systems can be reactivated upon recombination with a
      functional allele, consistent with their being contingency genes, and that H.pylori R-M
      diversity limits acquisition of chromosomal DNA fragments of 1 kb.
AU  - Aras RA
AU  - Small AJ
AU  - Ando T
AU  - Blaser MJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2002 30: 5391-5397.

PMID- 11703661
VI  - 42
DP  - 2001
TI  - Regulation of the HpyII restriction-modification system of Helicobacter pylori by gene deletion and horizontal reconstitution.
PG  - 369-382
AB  - Helicobacter pylori, Gram-negative, curved bacteria colonizing the human stomach, possess
      strain-specific complements of functional
      restriction-modification (R-M) systems. Restriction-modification
      systems have been identified in most bacterial species studied and are
      believed to have evolved to protect the host genome from invasion by
      foreign DNA. The large number of R-Ms homologous to those in other
      bacterial species and their strain-specificity suggest that H. pylori
      may have horizontally acquired these genes. A type IIs
      restriction-modification system, hpyIIRM, was active in two out of the
      six H. pylori strains studied. We demonstrate now that in most strains
      lacking M.HpyII function, there is complete absence of the R-M system.
      Direct DNA repeats of 80 bp flanking the hpyIIRM system allow its
      deletion, resulting in an 'empty-site' genotype. We show that strains
      possessing this empty-site genotype and strains with a full but
      inactive hpyIIRM can reacquire the hpyIIRM cassette and functional
      activity through natural transformation by DNA from the parental R-M+
      strain. Identical isolates divergent for the presence of an active
      HpyII R-M pose different restriction barriers to transformation by
      foreign DNA. That H. pylori can lose HpyII R-M function through
      deletion or mutation, and can horizontally reacquire the hpyIIRM
      cassette, is, in composite, a novel mechanism for R-M regulation,
      supporting the general hypothesis that H. pylori populations use
      mutation and transformation to regulate gene function.
AU  - Aras RA
AU  - Takata T
AU  - Ando T
AU  - van der Ende A
AU  - Blaser MJ
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2001 42: 369-382.

PMID- 
VI  - 101
DP  - 2001
TI  - Helicobacter pylori variants from a single host that differ in the presence of the hpyII restriction-modification system.
PG  - 296
AB  - Helicobacter pylori are gram-negative, curved bacteria that reside in the human gastric
      mucosa. Sequencing of two independent H. pylori
      strains, 26695 and J99, identified an extraordinary number of
      restriction-modification (R-M) genes. Many are strain-specific, have
      deviant G+C content, and are associated with genomic rearrangements,
      suggesting their horizontal acquisition from other bacteria. Strain
      26695 possesses a type IIs R-M system, hpyII R-M, with homology to the
      Moraxella bovis MboII R-M system, recognizing the sequence GAAGA. Since
      genomic analysis identified 80-nucleotide direct repeats flanking the
      26695 R-M system that could permit deletion of intervening regions, we
      searched for isolates from a single host that differ in hpyII R-M
      status. The resistance of an isolate's DNA to MboII digestion was used
      to indicate the presence of the hpyII R-M system. From a Dutch patient,
      we found two isolates that differed. Using primers specific for
      different regions of the hpyII R-M, all expected PCR products were
      present for the resistant isolate (2a), but were absent for the
      sensitive isolate (2b). PCR using primers that flank the repeat
      sequences amplified a 3.5 kb PCR product in strain 2a (consistent with
      a full hpyII R-M system), and an "empty-site" (276bp) product in strain
      2b (consistent with deletion of the R-M system and one repeat);
      sequencing of the "empty-site" product confirmed the deletion. That the
      strains had identical RAPD and RFLP profiles and were otherwise
      identical in susceptibility to 13 other restriction enzymes indicate
      that they are clonal variants rather than different strains. Parallel
      results were found for paired isolates obtained from one of the
      patient's daughters. The isolation from a single host of clonal
      variants divergent in hpyII R-M status, coupled with the sequence data
      suggest deletion in vivo, findings consistent with the hypothesis of
      R-M system mobility within H. pylori.
AU  - Aras RA
AU  - Takata T
AU  - van der Ende A
AU  - Blaser MJ
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 2001 101: 296.

PMID- 27013052
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequence of Corynebacterium pseudotuberculosis 262 Biovar equi Isolated from Cow Milk.
PG  - e00176-16
AB  - We report the complete genome sequence ofCorynebacterium pseudotuberculosis262, isolated from
      a bovine host.C. pseudotuberculosisis an etiological agent of
      diseases with medical and veterinary relevance. The genome contains 2,325,749 bp,
      52.8% G+C content, 2,022 coding sequences (CDS), 50 pseudogenes, 48 tRNAs, and 12
      rRNAs.
AU  - Araujo CL
AU  - Dias LM
AU  - Veras AA
AU  - Alves JT
AU  - Cavalcante AL
AU  - Dowson CG
AU  - Azevedo V
AU  - Ramos RT
AU  - Silva A
AU  - Carneiro AR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00176-16.

PMID- 28336591
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Corynebacterium pseudotuberculosis Strain PA07 Biovar ovis, Isolated from a Sheep Udder in Amazonia.
PG  - e00040-17
AB  - In this work, we present the draft genome sequence of Corynebacterium pseudotuberculosis
      strain PA07 biovar ovis, isolated from a caseous secretion
      from a sheep udder in Para, Brazil. The genome contains 2,320,235 bp, 52.2% G+C
      content, 2,191 coding sequences (CDSs), five pseudogenes, 48 tRNAs, and three
      rRNAs.
AU  - Araujo FA
AU  - Marques JM
AU  - de Moura VA
AU  - Schneider MP
AU  - Andrade SS
AU  - Lima AC
AU  - Guimaraes LC
AU  - Folador AR
AU  - Silva A
AU  - Ramos RT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00040-17.

PMID- 11104769
VI  - 276
DP  - 2001
TI  - The dnmt1 target recognition domain resides in the n terminus.
PG  - 6930-6936
AB  - DNA-cytosine-5-methyltransferase 1 (DNMT1) is the enzyme believed to be responsible for
      maintaining the epigenetic information encoded by DNA methylation patterns. The target
      recognition domain of DNMT1, the domain responsible for recognizing hemimethylated CGs, is
      unknown. However, based on homology with bacterial cytosine DNA methyltransferases it has been
      postulated that the entire catalytic domain, including the target recognition domain, is
      localized to 500 amino acids at the C terminus of the protein. The N-terminal domain has been
      postulated to have a regulatory role, and it has been suggested that the mammalian DNMT1 is a
      fusion of a prokaryotic methyltransferase and a mammalian DNA-binding protein. Using a
      combination of in vitro translation of different DNMT1 deletion mutant peptides and a
      solid-state hemimethylated substrate, we show that the target recognition domain of DNMT1
      resides in the N terminus (amino acids 122-417) in proximity to the proliferating cell nuclear
      antigen binding site. Hemimethylated CGs were not recognized specifically by the postulated
      catalytic domain. We have previously shown that the hemimethylated substrates utilized here
      act as DNMT1 antagonists and inhibit DNA replication. Our results now indicate that the
      DNMT1-PCNA interaction can be disrupted by substrate binding to the DNMT1 N terminus. These
      results point toward new directions in our understanding of the structure-function of DNMT1.
AU  - Araujo FD
AU  - Croteau S
AU  - Slack AD
AU  - Milutinovic S
AU  - Bigey P
AU  - Price GB
AU  - Zannis-Hajopoulos M
AU  - Szyf M
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2001 276: 6930-6936.

PMID- 10092611
VI  - 274
DP  - 1999
TI  - Identification of initiation sites for DNA replication in the human dnmt1 (DNA-methyltransferase) locus.
PG  - 9335-9341
AB  - Vertebrates have developed multiple mechanisms to coordinate the replication of epigenetic and
      genetic information.  Dnmt1 encodes the maintenance enzyme DNA-methyltransferase, which is
      responsible for propagating the DNA methylation pattern and the epigenetic information that it
      encodes during replication.  Direct sequence analysis and bisulfite mapping of the 5' region
      of DNA-methyltransferase 1 have indicated the presence of many sequence elements associated
      with previously characterized origins of DNA replication.  This study tests the hypothesis
      that the dnmt1 region containing these elements is an origin of replication in human cells.
      First, we demonstrate that a vector containing this dnmt1 sequence is able to support
      autonomous replication when transfected into HeLa cells.  Second, using a gel retardation
      assay, we show that it contains a site for binding of origin-rich sequences binding activity,
      a recently purified replication protein.  Finally, using competitive polymerase chain
      reaction, we show that replication initiates in this region in vivo.  Based on these lines of
      evidence, we propose that initiation sites for DNA replication are located between the first
      intron and exon 7 of the human dnmt1 locus.
AU  - Araujo FD
AU  - Knox JD
AU  - Ramchandrani S
AU  - Pelletier R
AU  - Bigey P
AU  - Price G
AU  - Szyf M
AU  - Zannis-Hadjopoulos M
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1999 274: 9335-9341.

PMID- 10982859
VI  - 28
DP  - 2000
TI  - Holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories.
PG  - 3417-3432
AB  - Holliday junction resolvases (HJRs) are key enzymes of DNA recombination. A detailed computer
      analysis of the structural and evolutionary relationships of HJRs and related nucleases
      suggests that the HJR function has evolved independently from at least four distinct
      structural folds, namely RNase H, endonuclease, endonuclease VII-colicin E and RusA. The
      endonuclease fold, whose structural prototypes are the phage lambda exonuclease, the very
      short patch repair nuclease (Vsr) and type II restriction enzymes, is shown to encompass by
      far a greater diversity of nucleases than previously suspected. This fold unifies archaeal
      HJRs, repair nucleases such as RecB and Vsr, restriction enzymes and a variety of predicted
      nucleases whose specific activities remain to be determined. Within the RNase H fold a new
      family of predicted HJRs, which is nearly ubiquitous in bacteria, was discovered, in addition
      to the previously characterized RuvC family. The proteins of this family, typified by
      Escherichia coli YqgF, are likely to function as an alternative to RuvC in most bacteria, but
      could be the principal HJRs in low-GC Gram-positive bacteria and Aquifex. Endonuclease VII of
      phage T4 is shown to serve as a structural template for many nucleases, including McrA and
      other type II restriction enzymes. Together with colicin E7, endonuclease VII defines a
      distinct metal-dependent nuclease fold. As a result of this analysis, the principal HJRs are
      now known or confidently predicted for all bacteria and archaea whose genomes have been
      completely sequenced, with many species encoding multiple potential HJRs. Horizontal gene
      transfer, lineage-specific gene loss and gene family expansion, and non-orthologous gene
      displacement seem to have been major forces in the evolution of HJRs and related nucleases. A
      remarkable case of displacement is seen in the Lyme disease spirochete Borrelia burgdorferi,
      which does not possess any of the typical HJRs, but instead encodes, in its chromosome and
      each of the linear plasmids, members of the lambda exonuclease family predicted to function as
      HJRs. The diversity of HJRs and related nucleases in bacteria and archaea contrasts with their
      near absence in eukaryotes. The few detected eukaryotic representatives of the endonuclease
      fold and the RNase H fold have probably been acquired from bacteria via horizontal gene
      transfer. The identity of the principal HJR(s) involved in recombination in eukaryotes remains
      uncertain; this function could be performed by topoisomerase IB or by a novel, so far
      undetected, class of enzymes. Likely HJRs and related nucleases were identified in the genomes
      of numerous bacterial and eukaryotic DNA viruses. Gene flow between viral and cellular genomes
      has probably played a major role in the evolution of this class of enzymes. This analysis
      resulted in the prediction of numerous previously unnoticed nucleases, some of which are
      likely to be new restriction enzymes.
AU  - Aravind L
AU  - Makarova KS
AU  - Koonin EV
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2000 28: 3417-3432.

PMID- 
VI  - 0
DP  - 1971
TI  - Host-controlled variation.
PG  - 83-96
AB  - About twenty years ago a number of similar observations were made in work with various
      bacteriophage species.  They showed that the host range of a given phage preparation depended
      on the bacterial strain in which the phage had last propagated.  This effect was called
      host-controlled variation to distinguish its host-dependent and thus genetically unstable
      nature from persistent hereditary chcanges such as are found in host-range mutants.  Many
      examples now are known to reflect the phenomena described in this chapter:  strain-specific
      restriction and modification of DNA.
AU  - Arber W
PT  - Journal Article
TA  - Bacteriophage Lambda
JT  - Bacteriophage Lambda
SO  - Bacteriophage Lambda 1971 0: 83-96.

PMID- 
VI  - 5
DP  - 2004
TI  - Genetic Variation and Molecular Evolution.
PG  - 331-352
AB  - The comparison of DNA sequences of genes and entire genomes offers interesting insights into
      the possible evolutionary relatedness of genetic information of living organisms.  Together
      with a relatively rich database from experimental microbial genetics, conclusions can be drawn
      on the molecular mechanisms by which genetic variations are spontaneously generated.  A number
      of different specific mechanisms contribute to the overall mutagenesis.  These mechanisms are
      here grouped into three natural strategies of the spontaneous generation of genetic
      variations: local changes of DNA sequences, intragenomic rearrangement of DNA segments, and
      acquisition of foreign DNA by horizontal gene transfer.  These three strategies have different
      qualities with regard to their contributions to the evolutionary process.  As a general rule,
      none of the known mechanisms producing genetic variants is clearly directed.  Rather, the
      resulting alterations in the inherited genomes are more random.  In addition, usually only a
      minority of resulting variants provide a selective advantage.  Interestingly, in most of the
      molecular mechanisms involved, the products of so-called evolution genes are involved as
      generators of genetic variation and/or as modulators of the frequencies of genetic variation.
      Products of evolution genes work in tight collaboration with nongenetic factors such as
      structural flexibilities and chemical instabilities of molecules, chemical and physical
      mutagens, and random encounter.  All of these aspects contributing to the spontaneous
      generation of genetic variations together form the core of the theory of molecular evolution.
      This theory brings neo-Darwinism to the molecular level.  In view of the increasing evidence
      coming particularly from microbial genetics, knowledge of molecular evolution can be seen as a
      confirmation of Darwinism at the level of biologically active molecules, in particular,
      nucleic acids and proteins.  Philosophical and practical implications of this knowledge will
      be briefly discussed.
AU  - Arber W
PT  - Journal Article
TA  - Encyclopedia of Molecular Cell Biology and Molecular Medicine.
JT  - Encyclopedia of Molecular Cell Biology and Molecular Medicine.
SO  - Encyclopedia of Molecular Cell Biology and Molecular Medicine. 2004 5: 331-352.

PMID- 
VI  - 3
DP  - 2012
TI  - Restriction Enzymes: From Their Discovery to Their Applications.
PG  - 33-38
AB  - As a contribution to the history of science, the discovery and the functions of bacterial
      restriction endonucleases, as well as their
      applications in molecular genetic analysis and in biotechnological
      innovations, including genetic engineering, are described here from the
      personal viewpoint of the author.
AU  - Arber W
PT  - Journal Article
TA  - Biovalley Monographs
JT  - Biovalley Monographs
SO  - Biovalley Monographs 2012 3: 33-38.

PMID- 
VI  - 83
DP  - 2002
TI  - Roots, strategies and prospects of functional genomics - functional genomics, human genome, bioinformatic software and polymerase chain  reaction; a review.
PG  - 826-828
AB  - AUTHOR ABSTRACT - This essay traces,the historical development of classical and molecular
      genetics from their early roots to the actual
      research strategies and their prospects. Attention is also given to the
      risk evaluation of genetic engineering by comparing designed genetic
      alterations with the spontaneous genetic variation known to form the
      substrate for biological evolution. DERWENT ABSTRACT: Roots, strategies
      and prospects of functional genomics was discussed with respect to
      historical development of classical molecular genetics from their early
      roots to the actual research strategies and their prospects. Classical
      genetics has its roots in the 19th century, when Gregor Mendel carried
      out experiments with peas displaying phenotypically distinct traits
      which got inherited to the progeny. However, efficient methods to
      experimentally determine large extents of such sequences were still
      missing. In the 1950s and 1960s it also became clear that bacteria
      succeed by a number of different strategies to hold the frequency of
      acquisition of foreign genetic information low. One of these strategies
      is the widely encountered phenomenon of restriction and modification of
      DNA. Restriction-modification systems allow bacteria to specifically
      distinguish foreign DNA from the cell's own DNA. As a consequence,
      foreign DNA becomes cleaved into fragments upon its entry into the
      cell. In 1970 investigators succeeded in preparing recombinant DNA
      molecules in vitro and to get them replicated after their transfer into
      appropriate host cells. In these experiments plasmids and viral genomes
      served as gene vectors into which fragments of DNA, often prepared by
      restriction cleavage, were spliced. In 1990s, the gateway to the
      determination of the nucleotide sequences of entire genomes was thus
      open. More recently, the DNA sequences of several eukaryotic organisms
      were published, including the human genome of about three billion base
      pairs(3 pages)
AU  - Arber W
PT  - Journal Article
TA  - Curr. Sci.
JT  - Curr. Sci.
SO  - Curr. Sci. 2002 83: 826-828.

PMID- Not carried by PubMed...
VI  - B60
DP  - 1994
TI  - On the generation of genetic diversity in microorganisms.
PG  - 357-364
AB  - Bacterial genetics strongly influenced the development of molecular genetic strategies and
      techniques now available to study gene structure and functions of practically any living
      organisms.  It also revealed natural processes of horizontal gene transfer (transformation,
      conjugation, phage-mediated transduction) as well as systems (e.g. restriction-modification
      systems) to hold such gene transfer in tolerably low frequencies to ensure a certain degree of
      genetic stability.  Work with bacterial and bacteriophage systems has helped to unravel both
      homologous and non-homologous enzyme-mediated recombination processes at the molecular level.
      The acquired knowledge now helps to understand molecular processes contributing to the
      generation of genetic variation, especially DNA rearrangements resulting from transposition
      and from site-specific recombination which sometimes occurs at secondary crossing-over sites.
      Present knowledge on the genetic plasticity of haploid microorganisms offers insights into
      the molecular basis for the natural interplay between mutagenesis and selection.  This
      approach greatly profits from the short generation times and relatively small genome sizes of
      haploid microorganisms which allows one to investigate population genetic questions and to
      draw conclusions on the mechanisms of evolutionary processes.
AU  - Arber W
PT  - Journal Article
TA  - Proc. Indian Natn. Sci. Acad.
JT  - Proc. Indian Natn. Sci. Acad.
SO  - Proc. Indian Natn. Sci. Acad. 1994 B60: 357-364.

PMID- 4602489
VI  - 14
DP  - 1974
TI  - DNA Modification and Restriction.
PG  - 1-37
AB  - The reader of the scientific literature may have had his attention attracted
      recently to a growing number of highly interesting reports on research on DNA
      restriction endonucleases and DNA modification methylases.  A striking
      illustration is the November 1972 issue of the Proceedings of the National
      Academy of Sciences of the United States of America:  it contains seven papers
      on restriction endonucleases, and none of the 16 authors signed more than one
      of these papers.
AU  - Arber W
PT  - Journal Article
TA  - Prog. Nucleic Acid Res. Mol. Biol.
JT  - Prog. Nucleic Acid Res. Mol. Biol.
SO  - Prog. Nucleic Acid Res. Mol. Biol. 1974 14: 1-37.

PMID- 5318444
VI  - 19
DP  - 1965
TI  - Host-controlled modification of bacteriophage.
PG  - 365-378
AB  - Host-controlled modification of viruses is a general term applied to those
      cases in which passage through certain host strains imparts one or more new,
      nonheritable properties to the virus without altering its genetic information
      content.  The terms of host-induced modification, host-controlled variation, or
      host-induced variation are sometimes used as synonyms to designate the same
      phenomena.  However, we would like to recommend the use of "host-controlled
      modification," at least for the cases discussed in this paper, since control
      mechanisms are involved here rather than induction phenomena and since the term
      "variation" may erroneously suggest some change in the genetic message.
AU  - Arber W
PT  - Journal Article
TA  - Annu. Rev. Microbiol.
JT  - Annu. Rev. Microbiol.
SO  - Annu. Rev. Microbiol. 1965 19: 365-378.

PMID- Not included in PubMed...
VI  - 25
DP  - 1970
TI  - Strain-specific restriction and modification of DNA.
PG  - 99-100
AB  - Experimental investigation of the molecular mechanism of host-controlled
      modification of bacteriophages has led to the discovery of very interesting
      bacterial enzyme systems.  Each of these systems has a specific restriction
      enzyme (endonuclease) and a specific modification enzyme (DNA methylase).  Both
      enzymes appear to work with high affinity on the same position of DNA.  This
      point of affinity consists of a quite definite sequence of 6 to 9 DNA base
      pairs.  The recognition of the point of affinity by the enzymes is taken over
      by a gene product as the common factor for both enzyme activities.  The genetic
      basis of the activities, the enzymes themselves and the substrate can be
      experimentally investigated and offer the molecular biologist an interesting
      model of the specific interaction of enzymes with nucleic acids.  The
      biological significance of DNA restriction lies in an effective defence
      mechanism against infection with foreign genetic material.  For a detailed
      account of the present knownledge on this subject, the reader is referred to a
      review by Arber and Linn (Ann. Rev. Biochem. 38, 467[1969].
AU  - Arber W
PT  - Journal Article
TA  - Bull. Schweiz. Akad. Med. Wiss.
JT  - Bull. Schweiz. Akad. Med. Wiss.
SO  - Bull. Schweiz. Akad. Med. Wiss. 1970 25: 99-100.

PMID- Not included in PubMed...
VI  - 56
DP  - 1969
TI  - Host-controlled modification of DNA.
PG  - 155-160
AB  - None
AU  - Arber W
PT  - Journal Article
TA  - Naturwissenschaften
JT  - Naturwissenschaften
SO  - Naturwissenschaften 1969 56: 155-160.

PMID- 377489
VI  - 205
DP  - 1979
TI  - Promotion and limitation of genetic exchange.
PG  - 361-365
AB  - None
AU  - Arber W
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1979 205: 361-365.

PMID- 14013582
VI  - 25
DP  - 1962
TI  - Specificites biologiques de l'acide desoxyribonucleique.
PG  - 668-681
AB  - A new biological specificity of phage DNA molecules is described, which is
      distinct from the genetic specificity of DNA residing in the base sequence.
      Unlike the genetic specificity this newly discovered "host specificity" is not
      multiplied as DNA replicates, but is nevertheless shown to be fixed firmly to
      the DNA molecule and so to be transferred into progeny molecules jointly with
      the parental DNA material.  Production of DNA host specificity is governed both
      by the bacterial genome and by episomes which are present in the cell.  Host
      specificity apparently exists not only on phage DNA but as well on the DNA of
      the host itself.  It is thought to be the element changed in "host controlled
      modification" of phage and also the element recognized by restricting hosts
      which degrade nonadapted, infecting DNA.
AU  - Arber W
PT  - Journal Article
TA  - Pathol. Microbiol. (Basel)
JT  - Pathol. Microbiol. (Basel)
SO  - Pathol. Microbiol. (Basel) 1962 25: 668-681.

PMID- 14290343
VI  - 11
DP  - 1965
TI  - Host specificity of DNA produced by Escherichia coli V. The role of Methionine in the Production of Host Specificity.
PG  - 247-256
AB  - Bacteriophage lambda grown in auxotrophic met-, pro- or arg- strains of
      Escherichia coli K12 in the presence of the required amino acids show an
      efficiency of plating of approximately 1 on E. coli strains K12 and C.
      However, if met- cells are deprived of methionine during a portion of the
      latent period, the efficiency of plating of the progeny phage is lower on the
      host K12 than on strain C.  Similar results are obtained with met- auxotrophs
      of strains B and K12 (P1); deprivation of methionine during the latent period
      results in the production of phage with lower efficiency of plating on the host
      strain than on strain C.  Such an effect is not observed following a similar
      starvation for proline or arginine.  These results suggest that methionine is
      specifically required for the production of host specificity of DNA.
AU  - Arber W
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1965 11: 247-256.

PMID- Not carried by PubMed...
VI  - 18
DP  - 1968
TI  - Host-controlled restriction and modification of bacteriophage.
PG  - 295-314
AB  - Viral properties have frequently been reported to undergo non-heritable changes
      upon passage through certain host strains.  But very little was known about the
      molecular mechanisms forming the basis of such host-controlled modifications,
      when we started in 1960 to investigate one particular virus-host system.  This
      work, carried out with bacteriophage lambda and a few host strains all derived
      from Escherichia coli, soon revealed the existence of a highly specific
      recognition mechanism able to screen infecting and intracellular DNA molecules
      for absence or presence on these molecules of a host-specific stamp.  This has
      more recently been identified as nucleotide methylation.  It is the scope of my
      contribution to this symposium to lay out the crucial experiments and arguments
      that lead to the present understanding of this system, which may be interpreted
      as serving the cell as a defense mechanism against infection with foreign
      genetic material.
AU  - Arber W
PT  - Journal Article
TA  - Symp. Soc. Gen. Microbiol.
JT  - Symp. Soc. Gen. Microbiol.
SO  - Symp. Soc. Gen. Microbiol. 1968 18: 295-314.

PMID- 5338985
VI  - 20
DP  - 1966
TI  - Host specificity of DNA produced by Escherichia coli.   9. Host-controlled modification of bacteriophage fd.
PG  - 483-496
AB  - Host-controlled modification is shown to occur with four related male-specific
      bacteriophage strains containing single-stranded DNA: fd,f1,M13 and F12.  All
      four phages are restricted and modified in bacteria with B host specificity,
      the first three also in P1-lysogenic cells.  None of the phages is restricted
      in strains with K host specificity or carrying the episome RTF-2.  The
      bacterial characters rB mB which control the B host specificity of lambda DNA,
      are also responsible for restriction and modification of phage fd.  The
      apparent difference in K restriction, which is encountered by lambda, but not
      by fd, is thought to find its explanation in the small molecular size of fd
      DNA, on which K specificity sites might be lacking.  Indeed, restriction and
      modification act on the DNA of fd:  DNA from fd phages which infect restricting
      host cells is partially broken down to acid-soluble products.  On the other
      hand, one-cycle growth of fd.B on non-restricting and non-modifying Kr-m-
      bacteria yields, among a majority of progeny of fd.Kr-m- phage, some phage
      particles with parental B host specificity, and they also have parental DNA as
      shown by density labelling of the infecting phage.  The efficiency of such
      transfer of parental fd.B DNA was found to be 0.12 if measured after 18 minutes
      incubation of the infected cells.  The implication of this transfer on the
      mechanism of phage DNA replication is discussed.
AU  - Arber W
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1966 20: 483-496.

PMID- 14187905
VI  - 23
DP  - 1964
TI  - Host specificity of DNA produced by Escherichia coli.  III.  Effects on transduction mediated by lambda dg.
PG  - 173-182
AB  - Transducing phage lambda dg carrying bacterial gal markers shows the same
      effects of host-controlled modification as does normal lambda.  Phage grown on
      Escherichia coli K12 is restricted (not accepted) on E. coli B and K12(P1), and
      phage grown on B is restricted on K12 and K12(P1) independently of whether the
      gal markers of lambda dg originated from the K12 or B chromosome.  Transduction
      to a restricting host yields a very low proportion of gal+ transductants, which
      are mostly heterogenotes.  Superinfecting restricted lambda phage does not
      exert helper functions for lysogenization or reproduction of nonrestricted
      lambda dg particles.  In cells infected with restricted lambda dg and
      superinfected with nonrestricted lambda, a greatly increased transduction
      frequency is observed, probably due to marker rescue.  A small helper effect is
      observed in cells infected with restricted lambda dg and restricted lambda,
      presumably caused by help in lysogenization in those few cells which accept the
      infecting lambda dg.  For nonrestricting hosts it is known that ultraviolet
      irradiated lambda dg no longer transduces by lysogenization but by stable
      integration of the gal markers into the bacterial chromosome.  The same
      behavior is found for restricting recipients.  Here, the maximum number of
      stable transductants is not notably higher than the number of heterogenotic
      transductants obtained on the same bacteria infected with nonirradiated lambda
      dg.  This is in agreement with the notion that most of the restricted genomes
      are degraded after their injection.  Particles giving rise to stable
      transduction show a very low UV sensitivity.  The ease with which stable
      transduction occurs probably reflects the degree of homology between endo- and
      exogenotic gal regions.
AU  - Arber W
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1964 23: 173-182.

PMID- Not included in PubMed...
VI  - 2
DP  - 1977
TI  - What is the function of DNA restriction enzymes?
PG  - N176-N178
AB  - None
AU  - Arber W
PT  - Journal Article
TA  - Trends Biochem. Sci.
JT  - Trends Biochem. Sci.
SO  - Trends Biochem. Sci. 1977 2: N176-N178.

PMID- 4908450
VI  - 34
DP  - 1969
TI  - Origin and properties of type A host specificity in Escherichia coli.
PG  - 147
AB  - 
AU  - Arber W
PT  - Journal Article
TA  - Pathol. Microbiol. (Basel)
JT  - Pathol. Microbiol. (Basel)
SO  - Pathol. Microbiol. (Basel) 1969 34: 147.

PMID- 19041737
VI  - 72
DP  - 2009
TI  - Genetically encoded generators of genetic variants.
PG  - 836-837
AB  - Several specific molecular mechanisms contribute to the generation of genetic variants at low
      rates. Some of these mechanisms involve the action of specific gene products as variation
      generators. We discuss here known as well as still hypothetical ways by which natural reality
      may succeed to keep the rates of genetic variation at low levels that insure a relatively high
      genetic stability of the individual organisms.
AU  - Arber W
PT  - Journal Article
TA  - J. Proteomics
JT  - J. Proteomics
SO  - J. Proteomics 2009 72: 836-837.

PMID- 1909374
VI  - 33
DP  - 1991
TI  - Elements in microbial evolution.
PG  - 4-12
AB  - Spontaneous mutation, selection, and isolation are key elements in biological evolution.
      Molecular genetic approaches reveal a multitude of different mechanisms by which spontaneous
      mutants arise. Many of these mechanisms depend on enzymes, which often do not act fully at
      random on the DNA, although a large number of sites of action can be observed. Of particular
      interest in this respect are DNA rearrangement processes, e.g., by transposition and by
      site-specific recombination systems. The development of gene functions has thus to be seen as
      the result of both DNA rearrangement processes and sequence alterations brought about by
      nucleotide substitutions and small local deletions, insertions, and duplications. Prokaryotic
      microorganisms are particularly appropriate for studying the effects of spontaneous mutation
      and thus microbial evolution, as they have haploid genomes, so that genetic alterations become
      rapidly apparent phenotypically. In addition, bacteria and their viruses and plasmids have
      relatively small genomes and short generation times, which also facilitate research on
      evolutionary processes. Besides the strategy of development of gene functions in the vertical
      transmission of genomes from generation to generation, the acquisition of short DNA segments
      from other organisms appears to be an important strategy in microbial evolution. In this
      process of horizontal evolution natural vector DNA molecules are often involved. Because of
      acquisition barriers, the acquisition strategy works best for relatively small DNA segments,
      hence at the level of domains, single genes, or at most operons. Among the many enzymes and
      functional systems involved in vertical and horizontal microbial evolution, some may serve
      primarily for essential life functions in each individual and only secondarily contribute to
      evolution.Others, however, might serve primarily for evolution and thus exert their biological
      functions at the level of populations rather than at that of a single organism.
AU  - Arber W
PT  - Journal Article
TA  - J. Mol. Evol.
JT  - J. Mol. Evol.
SO  - J. Mol. Evol. 1991 33: 4-12.

PMID- 10640595
VI  - 24
DP  - 2000
TI  - Genetic variation: molecular mechanisms and impact on microbial evolution.
PG  - 1-7
AB  - On the basis of established knowledge of microbial genetics one can distinguish three major
      natural strategies in the spontaneous
      generation of genetic variations in bacteria. These strategies are: (1)
      small local changes in the nucleotide sequence of the genome, (2)
      intragenomic reshuffling of segments of genomic sequences and (3) the
      acquisition of DNA sequences from another organism. The three general
      strategies differ in the quality of their contribution to microbial
      evolution. Besides a number of non-genetic factors, various specific
      gene products are involved in the generation of genetic variation and
      in the modulation of the fequency of genetic variation. The underlying
      genes are called evolution genes. They act for the benefit of the
      biological evolution of populations as opposed to the action of
      housekeeping genes and accessory genes which are for the benefit of
      individuals. Examples of evolution genes acting as variation generators
      are found in the transposition of mobile genetic elements and in
      so-called site-specific recombination systems. DNA repair systems and
      restriction-modification systems are examples of modulators of the
      frequency of genetic variation. The involvement of bacterial viruses
      and of plasmids in DNA reshuffling and in horizontal gene transfer is a
      hint for their evolutionary functions. Evolution genes are thought to
      undergo biological evolution themselves, but natural selection for
      their functions is indirect, at the level of populations, and is called
      second-order selection. In spite of an involvement of gene products in
      the generation of genetic variations, evolution genes do not
      programmatically direct evolution towards a specific goal. Rather, a
      steady interplay between natural selection and mixed populations of
      genetic variants gives microbial evolution its direction.
AU  - Arber W
PT  - Journal Article
TA  - FEMS Microbiol. Rev.
JT  - FEMS Microbiol. Rev.
SO  - FEMS Microbiol. Rev. 2000 24: 1-7.

PMID- 13862047
VI  - 5
DP  - 1962
TI  - Host Specificity of DNA Producted by Escherichia Coli:  I. Host controlled modification of bacteriophage lambda.
PG  - 18-36
AB  - Lambda bacteriophage particles carry a "host specificity" determined by the
      bacterial strains on which they were produced.  Upon infection of a different
      bacterial host (1) the phage DNA may be either accepted or rejected on the
      basis of this specificity, (2) if accepted, the phage multiplies and progeny
      phage are produced.  Those progeny to which the parental phage DNA molecule is
      transferred, in either conserved or semi-conserved form, also receive the
      parental phage host specificity.  All progeny containing only newly synthesized
      DNA receive only the specificity of the new bacterial host.  It is concluded
      that host specificity is carried on the bacteriophage DNA.  Phage P1, present
      in a bacterial cell as either prophage or vegetative phage, imparts to lambda
      DNA multiplying in the same cell a host specificity over and above that
      determined by the host itself.  Such P1-induced specificity can be impressed
      equally well onto replicating and non-replicating lambda DNA.
AU  - Arber W
AU  - Dussoix D
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1962 5: 18-36.

PMID- 14062909
VI  - 21
DP  - 1963
TI  - On the host-controlled modification of bacteriophage lambda.
PG  - 30-35
AB  - Phage lambda.C, grown on Escherichia coli strain C, is restricted on E. coli
      strains K12, K12(P1) and B251, and its DNA is broken down after injection into
      these bacteria strains.  Phage lambda.K(P1)-that is, grown on K12 or K12(P1)-is
      accepted by C, but undergoes host controlled modification upon reproduction in
      C (Weigle and Bertani, 1953).  In a one-cycle growth of lambda.K(P1) on E. coli
      C, parental DNA and host specificity undergo linked transfer into the progeny.
      Thus, host specificity is a property of the DNA molecule, as was previously
      shown for phage lambda in another host system (Arber and Dussoix, 1962).  Host
      specificity is serially transferable, and the probability of transfer to the
      progeny is constant for any given DNA strand under given experimental
      conditions.
AU  - Arber W
AU  - Hattman S
AU  - Dussoix D
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1963 21: 30-35.

PMID- 4873409
VI  - 30
DP  - 1967
TI  - Mutational loss of B-specific restriction of the bacteriophage fd.
PG  - 946-952
AB  - Bacteriophage fd undergoes host-controlled restriction and modification in
      strains of E. coli B: non modified phage fd.O plates with a probability of only
      7 x 10-4 on B strains 2027.  Phage mutants u1 were isolated showing an
      efficiency of plating of 3 x 10-2 on B.  Starting from such intermediately
      restricted fd genomes, completely unrestricted double mutants, u1, u2 were
      found.  No notable changes in the physiological properties of the mutants were
      observed.  The stepwise loss of restriction is taken as an evidence that the fd
      DNA molecule carries two B-specific sites, which are most probably determined
      by a specific base sequence, in confirmation of findings made before upon
      methylation analysis of fd DNA.
AU  - Arber W
AU  - Kuhnlein U
PT  - Journal Article
TA  - Pathol. Microbiol. (Basel)
JT  - Pathol. Microbiol. (Basel)
SO  - Pathol. Microbiol. (Basel) 1967 30: 946-952.

PMID- Not carried by PubMed...
VI  - 8
DP  - 1970
TI  - Repair and modification of genetic material:  DNA modification and restriction.
PG  - 180
AB  - B-specific modification enzyme has been partly purified from extracts of
      Escherichia coli strain B.  This enzyme specifically methylates unmodified DNA
      and thereby renders the DNA resistant to cleavage by endonuclease R.B.
      S-adenosylmethionine is the methyl donor, and the product of the reaction is
      6-methylaminopurine.  These observations confirm older in vivo results on the
      chemical nature of strain-specific modification.  Quantitatively, each fully
      modified specificity site on the DNA contains two methylated bases, one on each
      strand.  At the genetic level, two independent systems of host specificity have
      been found to reside in strains of E. coli 15.  One of these systems, called A,
      has its genetic determinants located on the bacterial chromosome, linked to the
      thr region.  This observation suggests its relation to the K- and B-specificity
      types.  The genetic basis for the 15-specific and modification, on the other
      hand, resides on a plasmid which by a number of criteria is shown to be related
      to phage P1.  In particular, P1 and the plasmid in question seem to possess
      homologous replicators.  In vivo complementation data obtained with various
      restriction- and modification-deficient mutants measure the functional
      relatedness of the various host specificity systems.
AU  - Arber W
AU  - Kuhnlein U
PT  - Journal Article
TA  - Int. Congr. Biochem.
JT  - Int. Congr. Biochem.
SO  - Int. Congr. Biochem. 1970 8: 180.

PMID- 4897066
VI  - 38
DP  - 1969
TI  - DNA modification and restriction.
PG  - 467-500
AB  - In this review, we have subdivided the discussion on DNA modification and
      restriction into three convenient (if somewhat arbitrary) areas of study:  (a)
      the enzymatic activities in vivo and in vitro; (b) the substrate, with the
      characterization of "specificity sites" as particular regions on DNA molecules
      showing affinity for modification and restriction activities; and (c) the
      genetic determinants for the enzymatic activities.  Limitations of length
      necessitate the consideration of only those experimental observations which
      seem to us the most relevant for the understanding of the phenomena.
      Previously published reviews may fill some of the gaps that will appear, but
      for the remaining ones we must refer the reader to the original literature.  In
      particular, we regret the omission of studies made with bacterial strains other
      than E. coli, although many of these systems seem strongly related in their
      fundamental properties to those discussed here.  Finaly, the thoroughly
      explored restriction by E. coli of unglucosylated T-even phage must also be
      omitted.
AU  - Arber W
AU  - Linn S
PT  - Journal Article
TA  - Annu. Rev. Biochem.
JT  - Annu. Rev. Biochem.
SO  - Annu. Rev. Biochem. 1969 38: 467-500.

PMID- 14258067
VI  - 51
DP  - 1965
TI  - Host specificity of DNA produced by Escherichia coli.  VI.  Effects on bacterial conjugation.
PG  - 137-148
AB  - Bacterial host cells endow the DNA of bacteriophage lambda and that of the
      transducing phage lambda with host specificity (Arber and Dussoix 1962; Arber
      1964).  This label on the DNA plays an important role in phage infection.  In
      the absence of the required host specificity, the bacteria degrade the DNA of
      the infecting phage, which is then said to be restricted (Dussoix and Arber
      1962).  Preliminary evidence has been given by Arber and Dussoix (1961) and
      Arber (1962) that bacterial DNA is also subject to this same control mechanism.
      The enzymatic system endowing lambda DNA with host specificity would thus act
      on the host DNA as well, and the host specificity could play a role in the
      decision of whether DNA transferred in conjugation from male to female bacteria
      is accepted or rejected.  This last action can be checked by measuring the
      frequency of formation of recombinants, provided other factors antagonistic to
      genetic integration, such as nonhomology of the male and female DNA molecules,
      are also considered.  The present paper gives an account of experiments carried
      out to investigate restriction in bacterial conjugation involving Hfr, F+,
      F-gal+, F-lac+ and (RTF)+ donor strains.  Since our first experiments the
      results have been confirmed and extended by various other investigators (Boice
      and Luria 1963; Hoekstra and De Haan 1963; Glover, Schell, Symonds and Stacey
      1963; Pittard 1964; Boyer 1964).
AU  - Arber W
AU  - Morse ML
PT  - Journal Article
TA  - Genetics
JT  - Genetics
SO  - Genetics 1965 51: 137-148.

PMID- 4555674
VI  - 115
DP  - 1972
TI  - Host specificity of DNA produced by Escherichia coli.
PG  - 195-207
AB  - Bacteria with A-specific restriction plate unmodified phage lambda with an
      efficiency of 10-2.  One mutational event can produce restriction insensitive
      (sAo) mutants of lambda.  These differ from the original sA form of lambda by
      no other property than their response to A-host specificity.  Two-parental
      phage crosses involving sA and sAo, respectively, as non-selective marker
      allowed to map sA between genes cII and O.  These data indicate that sA is the
      only site on lambda DNA with affinity for A-specific restriction.  Lambda DNA
      is thus an interesting substrate in in vitro A-specific restriction and
      modification.  Using an assay based on the infectivity of lambda DNA on
      helper-infected bacteria, A-specific modification activity was found in
      partially purified sonicates of bacteria with A-host specificity.  In parallel
      to modification, 3H-methyl label from S-adenosylmethionine, the only cofactor
      required for modification, was transferred to unmodified lambda DNA.  No
      association of radioactivity was observed in control experiments with DNA from
      either modified lambda.A or from a lambda sAo mutant.  These data suggest that
      A-specific modification is brought about by DNA methylation and that the sAo
      mutation not only abolished the affinity for A-specific restriction, but also
      for A-specific modification.
AU  - Arber W
AU  - Rifat A
AU  - Wauters-Willems D
AU  - Kuhnlein U
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1972 115: 195-207.

PMID- Not carried by PubMed...
VI  - 5
DP  - 1966
TI  - Kinetics of reproduction of nucleic acids and their role in biosynthesis of proteins.
PG  - 5
AB  - Various filamentous, male specific phages containing single stranded DNA
      undergo host-controlled modification in E. coli B and in P1 lysogenic bacteria.
      The B-specific modification is directed by those gene regions of E. coli which
      also are responsible for host-controlled modification of DNA of the bacterial
      host itself, and of other phages such as lambda.  Study of restriction and
      modification with phage fd reveals:  (1) a correlation between restriction in
      phage reproduction and appearance of acid soluble breakdown products from the
      infecting DNA molecule; (2) a correlation between occurrence of modification
      and a distinct increase in the level of 6-methylaminopurine carried by the
      phage DNA.  E. coli K12 does not restrict phage fd, nor does fd-K show a higher
      level of methylated bases than fd grown on mutants of K12 which are deficient
      in providing bacterial DNA with K-specific modification.  Absence of K-specific
      sites on the small DNA molecule (about 4500 nucleotides) of phage fd could
      reasonably explain these facts.  Bacteria of strain K12 infected at very low
      multiplicity with 2H and 15N density labelled fdB liberate, among early progeny
      phage, particles which still have the parental B-specific modification and
      carry heavy, parental DNA molecules wrapped into light, new phage proteins.
      This finding, besides confirming that host specificity of phage fd is closely
      associated with the DNA molecule, demonstrates that single stranded DNA
      molecules of infecting fd phage have a fair chance to be transferred into phage
      progeny particles.
AU  - Arber W
AU  - Smith JD
PT  - Journal Article
TA  - Int. Congr. Microbiol.
JT  - Int. Congr. Microbiol.
SO  - Int. Congr. Microbiol. 1966 5: 5.

PMID- 4920152
VI  - 108
DP  - 1970
TI  - Host specificity of DNA produced by Escherichia coli. XII.  The two restriction and modification systems of strain 15T-.
PG  - 203-217
AB  - E. coli 15T- carries two distinct sets of DNA restriction and modification
      activities.  The genetic information for system A is contained in the bacterial
      chromosome and linked to the thr region.  This fact suggests host specificity A
      to be related to those of strains K and B.  The genes controlling system 15 are
      on a plasmid which is related to phage P1: it competes with P1 for stable
      inheritance in the carried state and it genetically recombines with P1.  This
      recombination may produce plasmid genomes with newly assorted characters.  One
      of them is an active, P1-like prophage with the 15-specific instead of the
      parental P1-specific restriction and modification characters.  Superinfection
      of 15T- with P1 may also result in curing of the bacteria from the restriction
      plasmid.  Both A- and 15-specific restrictions and modifications act on
      bacterial DNA, on the DNA of various sex factors and on the DNA of certain
      bacteriophages, e.g. of phage lambda.  Phage 82 DNA is sensitive only to
      15-specific restriction, but not to A-specific restriction.  Independently of
      the A- and 15-specific restrictions, the growth of phage lambdain E. coli 15T-
      encounters another limitation of yet unknown nature.  No such limitation is
      observed either with phage 82 or with mutants of lambda occurring at a
      frequency of about 10-5.
AU  - Arber W
AU  - Wauters-Willems D
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1970 108: 203-217.

PMID- Not included in PubMed...
VI  - 34
DP  - 1975
TI  - Strain-specific modification and restriction of DNA in bacteria.
PG  - 3-22
AB  - Within the last few years bacterial restriction endonucleases have become an
      important tool in genetic, structural and functional studies of DNA.  Many of
      these enzymes reproducibly cleave large double-stranded DNA molecules at sites
      determined by particular nucleotide sequences.  This yields unique populations
      of smaller fragments.  Since the site of cleavage is usually unique for each
      restriction endonclease, any genome can in principle be cleaved by application
      of one or several properly chosen enzyme preparations into DNA fragments of any
      desired length and containing any desired genetic message.  These possibilities
      have attracted widespread attention to the molecular mechanism of these
      enzymes, in particular their interaction with their DNA substrate.  Bacterial
      strains producing restriction endonucleases must necessarily have developed a
      mechanism to protect their own DNA from intracellular cleavage.  In those
      strains studied up to date, this protection is brought about by the enzymatic
      methylation of specific nucleotides and is generally known as strain-specific
      modification of DNA.  This modification related methylation which usually
      represents only a fraction of the methylated bases in DNA clearly defines one
      of the roles of DNA methylation, that is to protect the nucleic acid from
      specific endonucleolytic cleavage.  On the other hand, the biological role of
      strain-specific restriction of DNA is generally believed to reside in a
      primitive system of immunity of bacteria against invasion by foreign genetic
      material.  Bacterial strains not possessing any known restriction-modification
      system (R-M system) are perfectly viable.  Therefore, restriction appears to be
      a dispensable function.  Nevertheless, many naturally occurring bacterial
      strains do possess one or several independent R-M systems, which suggests that
      restriction is not absolutely worthless to bacteria.  A closer look at several
      R-M systems allows us to distinguish two general types of mechanisms.  These
      were tentatively called type I and type II by Boyer (1971).  It is the object
      of our contribution to this symposium to discuss the present state of knowledge
      concerning these two types of restriction and modification mechanisms, and we
      would like to do so by presenting selected examples rather than by strictly
      defining the types.  It is quite likely that future studies may reveal other
      mechanisms with distinctly different features.  Recently published reviews in
      this field were written by Boyer (1971), Meselson et al. (1972) and Arber
      (1974).  The nomenclature used follows the recommendations made by Arber and
      Linn (1969), Smith and Nathans (1973) and Arber (1974).
AU  - Arber W
AU  - Yuan R
AU  - Bickle TA
PT  - Journal Article
TA  - Post Synthetic Modification of Macromolecules.  Symposium at 9th FEBS Meeting, Budapest. 1974
JT  - Post Synthetic Modification of Macromolecules.  Symposium at 9th FEBS Meeting, Budapest. 1974
SO  - Post Synthetic Modification of Macromolecules.  Symposium at 9th FEBS Meeting, Budapest. 1974 1975 34: 3-22.

PMID- 27013035
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the Bacteriocin-Producing Strain Enterococcus faecium M3K31, Isolated from Griffon Vultures (Gyps fulvus subsp. fulvus).
PG  - e00055-16
AB  - Enterococcus faeciumM3K31 is a bacteriocinogenic lactic acid bacterium (LAB) isolated from
      griffon vulture (Gyps fulvussubsp.fulvus) feces. The draft genome
      sequence of this strain provides genetic data that support its biotechnological
      potential.
AU  - Arbulu S
AU  - Frantzen C
AU  - Lohans CT
AU  - Cintas LM
AU  - Herranz C
AU  - Holo H
AU  - Diep DB
AU  - Vederas JC
AU  - Hernandez PE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00055-16.

PMID- 27417838
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the Bacteriocinogenic Strain Enterococcus faecalis DBH18, Isolated from Mallard Ducks (Anas platyrhynchos).
PG  - e00663-16
AB  - Here, we report the draft genome sequence of Enterococcus faecalis DBH18, a bacteriocinogenic
      lactic acid bacterium (LAB) isolated from mallard ducks (Anas
      platyrhynchos). The assembly contains 2,836,724 bp, with a G+C content of 37.6%.
      The genome is predicted to contain 2,654 coding DNA sequences (CDSs) and 50 RNAs.
AU  - Arbulu S
AU  - Jimenez JJ
AU  - Borrero J
AU  - Sanchez J
AU  - Frantzen C
AU  - Herranz C
AU  - Nes IF
AU  - Cintas LM
AU  - Diep DB
AU  - Hernandez PE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00663-16.

PMID- 21208457
VI  - 12
DP  - 2011
TI  - The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli.
PG  - 9
AB  - biotechnology. E. coli W (ATCC 9637), one of four strains designated as safe for laboratory
      purposes, has not been sequenced. E. coli W is a fast-growing strain and is the only safe
      strain that can utilize sucrose as a carbon source.  Lifecycle analysis has demonstrated that
      sucrose from sugarcane is a preferred carbon source for industrial
      bioprocesses.  Results: We have sequenced and annotated the genome of E. coli W. The
      chromosome is 4,900,968 bp and encodes 4,764 ORFs. Two plasmids, pRK1 (102,536 bp) and pRK2
      (5,360 bp), are also present. W has unique features relative to other sequenced laboratory
      strains (K-12, B and Crooks): it has a larger genome and belongs to phylogroup B1 rather than
      A. W also grows on a much broader range of carbon sources than does K-12.
      A genome-scale reconstruction was developed and validated in order to interrogate metabolic
      properties.  Conclusions: The genome of W is more similar to commensal and pathogenic B1
      strains than phylogroup A strains, and therefore has greater utility for comparative analyses
      with these strains. W should therefore be the strain of choice, or 'type strain' for group
      B1 comparative analyses. The genome annotation and tools created here
      are expected to allow further utilization and development of E. coli W as an industrial
      organism for sucrose-based bioprocesses. Refinements in our E. coli metabolic reconstruction
      allow it to more accurately define E. coli metabolism relative to previous models.
AU  - Archer CT
AU  - Kim JF
AU  - Jeong H
AU  - Park JH
AU  - Vickers CE
AU  - Lee SY
AU  - Nielsen LK
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2011 12: 9.

PMID- Not carried by PubMed...
VI  - 71
DP  - 1971
TI  - Restriction and modification and the phage typing of true Corynebacteria.
PG  - 181
AB  - Corynebacterium ulcerans, strain 603, neither restricts nor modifies phages Z
      and Zv.  However, C. diphtheriae, strain C7, C. ovis, strain 21, and C.
      belfanti, strain 1030, each produces a distinct restricting endonuclease.
      These we have designated r1, r2, r3, respectively.  Each is in turn linked to a
      distinct host controlled modification which specifically and epigenetically
      renders the phage DNA immune to the action of restricting enzyme.  These are
      designated m1, m2 and m3.  Thus, whereas strain 603 is m0r0, nonrestricting
      nonmodifying, strain C7 is m1r1.  Stocks of Zv phage produced in C7 have the m1
      phenotype.  By preparing phage stocks of m0, m1, m2 and m3 phenotypes the
      discriminatory powers of these phages have been extended when used in
      conjunction with bar mutation and lysogenic immunity in a system of phage
      typing.  This system allows for distinguishing between each of 21 bacteria,
      some of which differ from one another by only one gene; some by one prophage.
      Since the host strains require methionine, certain comparisons between the
      basis for the modification in Zv and that reported for lambda can be made.
AU  - Arden SB
AU  - Barksdale L
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1971 71: 181.

PMID- 25780498
VI  - 9
DP  - 2014
TI  - Genome sequence of the dark pink pigmented Listia bainesii microsymbiont Methylobacterium sp. WSM2598.
PG  - 5
AB  - Strains of a pink-pigmented Methylobacterium sp. are effective nitrogen- (N2) fixing
      microsymbionts of species of the African crotalarioid genus Listia. Strain
      WSM2598 is an aerobic, motile, Gram-negative, non-spore-forming rod isolated in
      2002 from a Listia bainesii root nodule collected at Estcourt Research Station in
      South Africa. Here we describe the features of Methylobacterium sp. WSM2598,
      together with information and annotation of a high-quality draft genome sequence.
      The 7,669,765 bp draft genome is arranged in 5 scaffolds of 83 contigs, contains
      7,236 protein-coding genes and 18 RNA-only encoding genes. This rhizobial genome
      is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 G enomic E
      ncyclopedia for B acteria and A rchaea- R oot N odule B acteria (GEBA-RNB)
      project.
AU  - Ardley J
AU  - Tian R
AU  - Howieson J
AU  - Yates R
AU  - Brau L
AU  - Han J
AU  - Lobos E
AU  - Huntemann M
AU  - Chen A
AU  - Mavromatis K
AU  - Markowitz V
AU  - Ivanova N
AU  - Pati A
AU  - Goodwin L
AU  - Woyke T
AU  - Kyrpides N
AU  - Reeve W
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 5.

PMID- 26664655
VI  - 10
DP  - 2015
TI  - High-quality permanent draft genome sequence of Ensifer medicae strain WSM244, a  microsymbiont isolated from Medicago polymorpha growing in alkaline soil.
PG  - 126
AB  - Ensifer medicae WSM244 is an aerobic, motile, Gram-negative, non-spore-forming rod that can
      exist as a soil saprophyte or as a legume microsymbiont of Medicago
      species. WSM244 was isolated in 1979 from a nodule recovered from the roots of
      the annual Medicago polymorpha L. growing in alkaline soil (pH 8.0) in Tel Afer,
      Iraq. WSM244 is the only acid-sensitive E. medicae strain that has been sequenced
      to date. It is effective at fixing nitrogen with M. polymorpha L., as well as
      with more alkaline-adapted Medicago spp. such as M. littoralis Loisel., M.
      scutellata (L.) Mill., M. tornata (L.) Mill. and M. truncatula Gaertn. This
      strain is also effective with the perennial M. sativa L. Here we describe the
      features of E. medicae WSM244, together with genome sequence information and its
      annotation. The 6,650,282 bp high-quality permanent draft genome is arranged into
      91 scaffolds of 91 contigs containing 6,427 protein-coding genes and 68 RNA-only
      encoding genes, and is one of the rhizobial genomes sequenced as part of the DOE
      Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root
      Nodule Bacteria (GEBA-RNB) project proposal.
AU  - Ardley J
AU  - Tian R
AU  - O'Hara G
AU  - Seshadri R
AU  - Reddy TB
AU  - Pati A
AU  - Woyke T
AU  - Markowitz V
AU  - Ivanova N
AU  - Kyrpides N
AU  - Howieson J
AU  - Reeve W
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 126.

PMID- 27013037
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Streptococcus agalactiae Serotype Ia and III Isolates from Tilapia Farms in Thailand.
PG  - e00122-16
AB  - Streptococcus agalactiaeserotypes Ia and III were isolated from infected tilapia  in cage and
      pond culture farms in Thailand during 2012 to 2014, in which
      pathogenicity analysis demonstrated that serotype III showed higher virulence
      than serotype Ia. Here, we report the draft genome sequencing of piscineS.
      agalactiaeserotypes Ia and III.
AU  - Areechon N
AU  - Kannika K
AU  - Hirono I
AU  - Kondo H
AU  - Unajak S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00122-16.

PMID- 26383657
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the First Hypermucoviscous Klebsiella quasipneumoniae subsp. quasipneumoniae Isolate from a Bloodstream Infection.
PG  - e00952-15
AB  - Klebsiella quasipneumoniae is a recently described species, formerly identified as K.
      pneumoniae phylogroup KpII. Information on pathogenic and virulence potential of this species
      are lacking. We sequenced the genome of a hypermucoviscous K. quasipneumoniae clinical isolate
      showing a virulence genes content (allABCDRS, kfuABC, and mrkABCDFHIJ) peculiar to
      hypervirulent K. pneumoniae strains.
AU  - Arena F
AU  - Henrici DeAL
AU  - Pieralli F
AU  - Di Pilato V
AU  - Giani T
AU  - Torricelli F
AU  - D'Andrea MM
AU  - Rossolini GM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00952-15.

PMID- 25814608
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Kitasatospora griseola Strain MF730-N6, a Bafilomycin, Terpentecin, and Satosporin Producer.
PG  - e00208-15
AB  - We report here the draft genome sequence of Kitasatospora griseola strain MF730-N6, a known
      producer of bafilomycin, terpentecin, and satosporins. The
      current assembly comprises 8 contigs covering 7.97 Mb. Genome annotation revealed
      7,225 protein coding sequences, 100 tRNAs, 40 rRNA genes, and 23 secondary
      metabolite biosynthetic gene clusters.
AU  - Arens JC
AU  - Haltli B
AU  - Kerr RG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00208-15.

PMID- 9665841
VI  - 280
DP  - 1998
TI  - I-PpoI and I-CreI homing site sequence degeneracy determined by random mutagenesis and sequential in vitro enrichment.
PG  - 345-353
AB  - Plasmid libraries containing partially randomized cleavage sites for the eukaryotic homing
      endonucleases I-PpoI and I-CreI were constructed, and sites that could be cleaved by I-PpoI or
      I-CreI were selectively recovered by successive cycles of cleavage and gel separation followed
      by religation and growth in Escherichia coli.  Twenty-one different I-PpoI-sensitive homing
      sites, including the native homing site, were isolated.  These sites were identical at four
      nucleotide positions within the 15 bp homing site, had a restricted pattern of base
      substitutions at the remaining 11 positions and displayed a preference for purines flanking
      the top strand of the homing site sequence.  Twenty-one different I-CreI-sensitive homing
      sites, including the native site, were isolated.  Ten nucleotide positions were identical in
      homing site variants that were I-CreI-sensitive and required the addition of SDS for efficient
      cleavage product release.  Four of those ten positions were identical in homing sites that did
      not require SDS for product release.  There was a preference for pyrimidines flanking the top
      strand of the homing site sequence.  Three of the 24 I-CreI homing site nucleotide positions
      apparently lacked informational content, i.e. were permissive of cleavage when occupied by any
      nucleotide.  These results suggest that I-PpoI and I-CreI make a larger number of DNA-protein
      contacts across their homing site sequences, and that different subsets of these contacts may
      be sufficient to maintain a high degree of sequence-specific homing site recognition and
      cleavage.  The sequential enrichment protocol we used should be useful for defining the
      sequence degeneracy and informational content of other homing endonuclease target sites.
AU  - Argast GM
AU  - Stephens KM
AU  - Emond MJ
AU  - Monnat RJ Jr
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1998 280: 345-353.

PMID- 28444231
VI  - 9
DP  - 2017
TI  - Whole genome sequencing of 7 strains of Staphylococcus lugdunensis allows identification of mobile genetic elements.
PG  - 0
AB  - Coagulase negative staphylococci are normal inhabitant of the human skin flora
      that account for an increasing number of infections, particularly
      hospital-acquired infections. Staphylococcus lugdunensis has emerged as a most
      virulent species causing various infections with clinical characteristics close
      to what clinicians usually observe with Staphylococcus aureus and both bacteria
      share more than 70% of their genome. Virulence of S. aureus relies on a large
      repertoire of virulence factors, many of which are encoded on mobile genetic
      elements. S. lugdunensis also bears various putative virulence genes but only one
      complete genome with extensive analysis has been published with one prophage
      sequence (phiSL2) and a unique plasmid was previously described. In this study,
      we performed de novo sequencing, whole genome assembly and annotation of seven
      strains of S. lugdunensis from VISLISI clinical trial. We searched for the
      presence of virulence genes and mobile genetics elements using bioinformatics
      tools. We identified four new prophages, named phiSL2 to phiSL4, belonging to the
      Siphoviridae class and five plasmids, named pVISLISI_1 to pVISLISI_5. Three
      plasmids are homologous to known plasmids that include, amongst others, one S.
      aureus plasmid. The two other plasmids were not described previously. This study
      provides a new context for the study of S. lugdunensis virulence suggesting the
      occurrence of several genetic recombination' with other staphylococci.
AU  - Argemi X
AU  - Martin V
AU  - Loux V
AU  - Dahyot S
AU  - Lebeurre J
AU  - Guffroy A
AU  - Martin M
AU  - Velay A
AU  - Keller D
AU  - Riegel P
AU  - Hansmann Y
AU  - Paul N
AU  - Prevost G
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2017 9: 0.

PMID- 2988943
VI  - 4
DP  - 1985
TI  - Evidence for a repeating domain in type I restriction enzymes.
PG  - 1351-1355
AB  - The primary structures of the recognition subunit (hsdS) in type I restriction
      enzymes from three isolates of Escherichia coli were compared and aligned by
      use of amino acid physical properties.  A repeating domain was found in each of
      the subunits suggesting a pseudo-dimeric structure.  Secondary structure
      predictions delineated two helical regions in each domain which suggested that
      the recognition subunits may act in a fashion similar to that proposed for
      repressor and activator molecules; namely, interaction with double-stranded DNA
      through helices and in two successive major grooves on the same DNA side.  One
      helical motif could provide the specific recognition site and the other, the
      restriction site.
AU  - Argos P
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1985 4: 1351-1355.

PMID- 
VI  - 34
DP  - 2014
TI  - IDENTIFICATION AND DESIGN OF NEW C5-DNA METHYLTRANSFERASE INHIBITORS AND THEIR BIOLOGICAL ACTIVITY.
PG  - 5813-5814
AB  - DNA methylation is involved in the regulation of gene expression and plays an important role
      in normal developmental processes and disease.  In particular, the epigenetic landscape is
      altered in cancers where abnormal hypermethylation leads to silencing of certain genes such as
      tumor suppressor genes.  In mammals, DNA methyltransferases are the enzymes responsible for
      DNa methylation on the position 5 of cytidine in a CpG context.  Few direct enzyme inhibitors
      are known and those have several drawbacks.  In order to identify novel inhibitors, we
      developed three chemical strategies.  First a fluorescene High-Throughput Screening for the
      inhibition of the murine catalytic Dnmt3a/3L complex on the chemical library of the Museum
      Naturelle d'Historie Naturelle and found twelve hits with low micromolar activities.
      Interestingly, they showed little cytotoxicity.  Dichlone, a small halogenated naphthoquinone,
      classically used as pesticide and fungicide, showed the lowest Ec50 at 460 NM.  Two molecules
      including Dichlone, efficiently reactivated YFP gene expression in a stable HEK293 cell line
      by promoter demethylation.  Their efficacy was comparable to the DNMT inhibitor of reference
      5-azecytidine.  Second, based on molecular modeling studies of quinolone inhibitor SGI1027 in
      the crystal structure of M.HhaI C5 DNA methyltransferase, suggesting that the quinolone and
      the aminopyridimine are important for the interaction with the substrates and the protein, we
      synthesized twenty five new derivatives.
AU  - Arimondo PB
PT  - Journal Article
TA  - Anticancer Res.
JT  - Anticancer Res.
SO  - Anticancer Res. 2014 34: 5813-5814.

PMID- 25814610
VI  - 3
DP  - 2015
TI  - Draft Genome of the Multidrug-Resistant Acinetobacter baumannii Strain A155 Clinical Isolate.
PG  - e00212-15
AB  - Acinetobacter baumannii is a bacterial pathogen with serious implications on human health, due
      to increasing reports of multidrug-resistant strains isolated
      from patients. Total DNA from the multidrug-resistant A. baumannii strain A155
      clinical isolate was sequenced to greater than 65x coverage, providing
      high-quality contig assemblies.
AU  - Arivett BA
AU  - Fiester SE
AU  - Ream DC
AU  - Centron D
AU  - Ramirez MS
AU  - Tolmasky ME
AU  - Actis LA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00212-15.

PMID- 27516516
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Pseudomonas aeruginosa Isolates from Wounded Military Personnel.
PG  - e00829-16
AB  - Pseudomonas aeruginosa, a Gram-negative bacterium that causes severe hospital-acquired
      infections, is grouped as an ESKAPE (Enterococcus faecium,
      Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii,
      Pseudomonas aeruginosa, and Enterobacter species) pathogen because of its
      extensive drug resistance phenotypes and effects on human health worldwide. Five
      multidrug resistant P. aeruginosa strains isolated from wounded military
      personnel were sequenced and annotated in this work.
AU  - Arivett BA
AU  - Ream DC
AU  - Fiester SE
AU  - Kidane D
AU  - Actis LA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00829-16.

PMID- 27516515
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Escherichia coli Isolates from Wounded Military Personnel.
PG  - e00828-16
AB  - Members of the Escherichia coli bacterial family have been grouped as ESKAPE (Enterococcus
      faecium, Staphylococcus aureus, Klebsiella pneumoniae,
      Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species)
      pathogens because of their extensive drug resistance phenotypes and increasing
      threat to human health. The genomes of six extended-spectrum beta-lactamase
      (ESBL)-producing E. coli strains isolated from wounded military personnel were
      sequenced and annotated.
AU  - Arivett BA
AU  - Ream DC
AU  - Fiester SE
AU  - Kidane D
AU  - Actis LA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00828-16.

PMID- 27563036
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Acinetobacter baumannii Isolates from Wounded Military  Personnel.
PG  - e00773-16
AB  - Acinetobacter baumannii is a Gram-negative bacterium capable of causing hospital-acquired
      infections that has been grouped with Enterococcus faecium,
      Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii,
      Pseudomonas aeruginosa, and Enterobacter species as ESKAPE pathogens because of
      their extensive drug resistance phenotypes and increasing risk to human health.
      Twenty-four multidrug-resistant A. baumannii strains isolated from wounded
      military personnel were sequenced and annotated.
AU  - Arivett BA
AU  - Ream DC
AU  - Fiester SE
AU  - Kidane D
AU  - Actis LA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00773-16.

PMID- 25593250
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Klebsiella pneumoniae Clinical Type Strain ATCC 13883 and Three Multidrug-Resistant Clinical Isolates.
PG  - e01385-14
AB  - Klebsiella pneumoniae is a Gram-negative human pathogen capable of causing hospital-acquired
      infections with an increasing risk to human health. The total
      DNA from four clinically relevant strains was sequenced to >100x coverage,
      providing high-quality genome assemblies for K. pneumoniae strains ATCC 13883,
      KP4640, 101488, and 101712.
AU  - Arivett BA
AU  - Ream DC
AU  - Fiester SE
AU  - Mende K
AU  - Murray CK
AU  - Thompson MG
AU  - Kanduru S
AU  - Summers AM
AU  - Roth AL
AU  - Zurawski DV
AU  - Actis LA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01385-14.

PMID- 16223716
VI  - 280
DP  - 2005
TI  - Mva1269I: A monomeric type IIS restriction endonuclease from micrococcus varians with two EcoRI- and FokI-like catalytic domains.
PG  - 41584-41594
AB  - Type II restriction endonuclease Mva1269I recognizes an asymmetric DNa sequence 5'-GAATGCN*
      -3'/5' -NG* CATTC-3' and cuts top and bottom DNA strands at positions, indicated by the "*"
      symbol.  Most restriction endonucleases require dimerization to cleave both strands of DNA.
      We found that Mva1269I is a monomer both in solution and upon binding of cognate DNA.  Protein
      fold-recognition analysis revealed that Mva1269I comprises two "PD-(D/E)XK" domains.  The
      N-terminal domain is related to the 5'-GAATTC-3'-specific restriction endonuclease EcoRI,
      whereas the C-terminal one resembles the nonspecific nuclease domain is related to the
      5'-GAATTC-3'-specific restriction endonuclease EcoRI, whereas the C-terminal one resembles
      the nonspecific nuclease domain of restriction endonuclease FokI.  Inactivation of the
      C-terminal catalytic site transformed Mva1269I into a very active bottom strand-nicking
      enzyme, whereas mutants in the N-terminal domain nicked the top strand, but only at elevated
      enzyme concentrations.  We found that the cleavage of the bottom strand is a prerequisite for
      the cleavage of the top strand.  We suggest that Mva1269I evolved the ability to recognize and
      to cleave its asymmetrical target by a fusion of an EcoRI-like domain, which incises the
      bottom strand within the target, and a FokI-like domain that completes the cleavage within the
      nonspecific region outside the target sequence.  Our results have implications for the
      molecular evolution of restriction endonucleases, as well as for perspectives of engineering
      new restriction and nicking enzymes with asymmetric target sites.
AU  - Armalyte E
AU  - Bujnicki JM
AU  - Giedriene J
AU  - Gasiunas G
AU  - Kosinski J
AU  - Lubys A
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2005 280: 41584-41594.

PMID- 15459382
VI  - 306
DP  - 2004
TI  - The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism.
PG  - 79-86
AB  - Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are
      responsible for approximately 20% of global carbon
      fixation. We report the 34 million-base pair draft nuclear genome of the
      marine diatom Thalassiosira pseudonana and its 129 thousand-base pair
      plastid and 44 thousand-base pair mitochondrial genomes. Sequence and
      optical restriction mapping revealed 24 diploid nuclear chromosomes. We
      identified novel genes for silicic acid transport and formation of
      silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes
      for several types of polyunsaturated fatty acids, use of a range of
      nitrogenous compounds, and a complete urea cycle, all attributes that
      allow diatoms to prosper in aquatic environments.
AU  - Armbrust EV et al
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2004 306: 79-86.

PMID- 27895127
VI  - 85
DP  - 2017
TI  - The Pathogenic Potential of Proteus mirabilis is Enhanced by Other Uropathogens During Polymicrobial Urinary Tract Infection.
PG  - e00808-16
AB  - Urinary catheter use is prevalent in health care settings, and polymicrobial
      colonization by urease-positive organisms, such as Proteus mirabilis and
      Providencia stuartii, commonly occurs with long-term catheterization. We
      previously demonstrated that coinfection with P. mirabilis and P. stuartii
      increased overall urease activity in vitro and disease severity in a model of
      urinary tract infection (UTI). In this study, we expanded these findings to a
      murine model of catheter-associated UTI (CAUTI), delineated the contribution of
      enhanced urease activity to coinfection pathogenesis, and screened for enhanced
      urease activity with other common CAUTI pathogens. In the UTI model, coinfected
      mice exhibited higher urine pH values, urolithiasis, bacteremia, and more
      pronounced tissue damage and inflammation compared to single infections, despite
      having a similar bacterial burden within the urinary tract. The presence of P.
      stuartii, regardless of urease production by this organism, was sufficient to
      enhance P. mirabilis urease activity and increase disease severity, and enhanced
      urease activity was the predominant factor driving tissue damage and
      dissemination of both organisms to the bloodstream during coinfection. These
      findings were largely recapitulated in the CAUTI model. Other uropathogens also
      enhanced P. mirabilis urease activity in vitro, including recent clinical
      isolates of Escherichia coli, Enterococcus faecalis, Klebsiella pneumoniae, and
      Pseudomonas aeruginosa. We therefore conclude that the underlying mechanism of
      enhanced urease activity may represent a widespread target for limiting
      detrimental consequences of polymicrobial catheter colonization, particularly by
      P. mirabilis and other urease-positive bacteria.
AU  - Armbruster CE
AU  - Smith SN
AU  - Johnson AO
AU  - DeOrnellas V
AU  - Eaton KA
AU  - Yep A
AU  - Mody L
AU  - Wu W
AU  - Mobley HL
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2017 85: e00808-16.

PMID- 24009126
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences of Helicobacter pylori Strains HPARG63 and HPARG8G, Cultured from Patients with Chronic Gastritis and Gastric Ulcer Disease.
PG  - e00700-13
AB  - Helicobacter pylori colonizes the human gastric mucosa, leading to a spectrum of  gastric
      diseases in susceptible populations. Here we announce the draft genome
      sequences of strains HPARG8G and HPARG63. The data for both genome sequences
      provide insights regarding the diversity in gene content and rearrangement of the
      genomic islands commonly harbored by H. pylori.
AU  - Armitano RI
AU  - Zerbetto DePG
AU  - Matteo MJ
AU  - Revale S
AU  - Romero S
AU  - Traglia GM
AU  - Catalano M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00700-13.

PMID- 6278444
VI  - 10
DP  - 1982
TI  - Preferential site-dependent cleavage by restriction endonuclease PstI.
PG  - 993-1007
AB  - The four identical recognition sites for the restriction endonuclease PstI in
      purified plasmid pSM1 DNA I are cleaved at markedly different rates.  The order
      and relative frequencies of cleavage at these four PstI sites have been
      determined from the order of appearance of partial cleavage products and from
      an analysis of production of specific unit length linear molecules.  The same
      pattern of preferential cleavage is also found when linear, nicked circular, or
      relaxed closed circular forms of the same plasmid DNA are used as substrates
      for PstI.  Inspection of the nucleotide sequences immediately adjoining each of
      the PstI sites suggests that the presence of adjacent runs of G-C base pairs
      confers significant resistance to cleavage.
AU  - Armstrong K
AU  - Bauer WR
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1982 10: 993-1007.

PMID- 6306575
VI  - 11
DP  - 1983
TI  - Site-dependent cleavage of pBR322 DNA by restriction endonuclease HinfI.
PG  - 4109-4126
AB  - Cleavage of pBR322 DNA I by the restriction endonuclease HinfI is preferentially inhibited at
      specific HinfI cleavage sites.  These sites in pBR322 DNA I have been identified and ordered
      with respect to the frequency with which they are cleaved.  The HinfI site most resistant to
      cleavage in pBR322 DNA I is unique in that runs of G-C base pairs are immediately adjacent on
      both sides.  Two differently permuted linear (DNA III) species were produced by cleavage with
      two different restriction endonucleases, PstI and AvaI.  Only one of these linear molecules,
      that produced by PstI, exhibits the same preferential cleavage pattern as DNA I.  The second
      linear species, that arising from AvaI digestion, shows pronounced relative inhibition of
      cleavage at the HinfI sites nearest the ends of the molecule (100 and 120 base pairs away,
      respectively).  This result suggests that proximity to the termini of a linear DNA molecule
      might also influence preferential cleavage.  The possibility of formation of stem-loop
      structures does not appear to influence preferential cleavage by HinfI.
AU  - Armstrong KA
AU  - Bauer WR
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1983 11: 4109-4126.

PMID- 10873785
VI  - 272
DP  - 2000
TI  - SNDV, a novel virus of the extremely thermophilic and acidophilic archaeon Sulfolobus.
PG  - 409-416
AB  - We describe a novel virus, SNDV (Sulfolobus neozealandicus droplet-shaped virus), of the
      crenarchaeotal archaeon Sulfolobus, which was found in a carrier state in a Sulfolobus strain
      isolated from a field sample from New Zealand. SNDV particles are droplet-shaped and densely
      covered by thin tail fibers at their pointed ends. The virion consists of a core and a coat.
      The latter has the appearance of a beehive and has a surface that is either helically ribbed
      or a stack of hoops. The genome is cccDNA of 20 kb, which is modified by dam-like methylation.
      It is cleaved by only a few type II restriction enzymes e.g., DpnI but not MboI, demonstrating
      an N(6)-methylation of the adenine residue in GATC sequences. The DNA-modifying system
      differentiates between virus and host. We postulate a virus-encoded methylase that is active
      on hemimethylated DNA. The host range of SNDV is confined to few Sulfolobus strains from New
      Zealand.  The virus persists in an unstable carrier state rather than as a prophage. Due to
      its uniqueness we propose to assign it to a novel virus family termed Guttaviridae.
AU  - Arnold HP
AU  - Ziese U
AU  - Zillig W
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 2000 272: 409-416.

PMID- 28385840
VI  - 5
DP  - 2017
TI  - Genome Sequences of Potential Probiotic Lactobacillus rhamnosus Isolates from Human Infants.
PG  - e00107-17
AB  - Probiotics provide health benefits to their hosts, including modulation of host immune
      response, inhibition of colonization by pathogens, modulation of the gut
      microbiota, and epithelial barrier enhancement. Here, we present the draft genome
      sequences of two newly isolated Lactobacillus rhamnosus strains of probiotic
      potential from healthy human infants.
AU  - Arnold JW
AU  - Monteagudo-Mera A
AU  - Altermann E
AU  - Cadenas MB
AU  - Thompson AL
AU  - Azcarate-Peril MA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00107-17.

PMID- 26139712
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Pseudomonas aeruginosa Strain WS136, a Highly Cytotoxic  ExoS-Positive Wound Isolate Recovered from Pyoderma Gangrenosum.
PG  - e00680-15
AB  - Pseudomonas aeruginosa is an opportunistic pathogen that typically infects patients with a
      compromised immune defense. Here, we present the improved 6.5-Mb
      draft genome of strain WS136, an ExoS-positive and ExoU-negative highly cytotoxic
      chronic wound isolate recovered from pyoderma gangrenosum of a patient who
      received bone marrow transplantation.
AU  - Arnold M
AU  - Wibberg D
AU  - Blom J
AU  - Schatschneider S
AU  - Winkler A
AU  - Kutter Y
AU  - Ruckert C
AU  - Albersmeier A
AU  - Albaum S
AU  - Goesmann A
AU  - Zange S
AU  - Heesemann J
AU  - Puhler A
AU  - Hogardt M
AU  - Vorholter FJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00680-15.

PMID- 16310802
VI  - 355
DP  - 2005
TI  - Engineering of large numbers of highly specific homing endonucleases that induce recombination on novel DNA targets.
PG  - 443-458
AB  - The last decade has seen the emergence of a universal method for precise and efficient genome
      engineering. This method relies on the use of sequence-specific endonucleases such as homing
      endonucleases. The structures of several of these proteins are known, allowing for
      site-directed mutagenesis of residues essential for DNA binding. Here, we show that a
      semi-rational approach can be used to derive hundreds of novel proteins from I-CreI, a homing
      endonuclease from the LAGLIDADG family. These novel endonucleases display a wide range of
      cleavage patterns in yeast and mammalian cells that in most cases are highly specific and
      distinct from I-CreI. Second, rules for protein/DNA interaction can be inferred from
      statistical analysis. Third, novel endonucleases can be combined to create heterodimeric
      protein species, thereby greatly enhancing the number of potential targets. These results
      describe a straightforward approach for engineering novel endonucleases with tailored
      specificities, while preserving the activity and specificity of natural homing endonucleases,
      and thereby deliver new tools for genome engineering.
AU  - Arnould S
AU  - Chames P
AU  - Perez C
AU  - Lacroix E
AU  - Duclert A
AU  - Epinat JC
AU  - Stricher F
AU  - Petit AS
AU  - Patin A
AU  - Guillier S
AU  - Rolland S
AU  - Prieto J
AU  - Blanco FJ
AU  - Bravo J
AU  - Montoya G
AU  - Serrano L
AU  - Duchateau P
AU  - Paques F
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2005 355: 443-458.

PMID- 21047873
VI  - 24
DP  - 2011
TI  - The I-CreI meganuclease and its engineered derivatives: applications from cell modification to gene therapy.
PG  - 27-31
AB  - Meganucleases (MNs) are highly specific enzymes that can induce homologous recombination in
      different types of cells, including
      mammalian cells. Consequently, these enzymes are used as scaffolds for
      the development of custom gene-targeting tools for gene therapy or
      cell-line development. Over the past 15 years, the high resolution
      X-ray structures of several MNs from the LAGLIDADG family have improved
      our understanding of their protein-DNA interaction and mechanism of DNA
      cleavage. By developing and utilizing high-throughput screening methods
      to test a large number of variant-target combinations, we have been
      able to re-engineer scores of I-CreI derivatives into custom enzymes
      that target a specific DNA sequence of interest. Such customized MNs,
      along with wild-type ones, have allowed for exploring a large range of
      biotechnological applications, including protein-expression cell-line
      development, genetically modified plants and animals and therapeutic
      applications such as targeted gene therapy as well as a novel class of
      antivirals.
AU  - Arnould S
AU  - Delenda C
AU  - Grizot S
AU  - Desseaux C
AU  - Paques F
AU  - Silva GH
AU  - Smith J
PT  - Journal Article
TA  - Protein Eng. Des. Sel.
JT  - Protein Eng. Des. Sel.
SO  - Protein Eng. Des. Sel. 2011 24: 27-31.

PMID- 17561112
VI  - 371
DP  - 2007
TI  - Engineered I-Crel derivatives cleaving sequences from the human XPC gene can induce highly efficient gene correction in mammalian cells.
PG  - 49-65
AB  - Meganucleases are sequence-specific endonucleases which recognize large (> 12 bp) target sites
      in living cells and can stimulate homologous
      gene targeting by a 1000-fold factor at the cleaved locus. We have
      recently described a combinatorial approach to redesign the I-Crel
      meganuclease DNA-binding interface, in order to target chosen
      sequences. However, engineering was limited to the protein regions
      shown to directly interact with DNA in a base-specific manner. Here, we
      take advantage of I-Crel natural degeneracy, and of additional
      refinement steps to extend the number of sequences that can be
      efficiently cleaved. We searched the sequence of the human XPC gene,
      involved in the disease Xeroderma Pigmentosum (XP), for potential
      targets, and chose three sequences that differed from the I-Crel
      cleavage site over their entire length, including the central four
      base-pairs, whose role in the DNA/protein recognition and cleavage
      steps remains very elusive. Two out of these targets could be cleaved
      by engineered I-Crel derivatives, and we could improve the activity of
      weak novel meganucleases, to eventually match the activity of the
      parental I-Crel scaffold. The novel proteins maintain a narrow cleavage
      pattern for cognate targets, showing that the extensive redesign of the
      I-Crel protein was not made at the expense of its specificity. Finally,
      we used a chromosomal reporter system in CHO-K1 cells to compare the
      gene targeting frequencies induced by natural and engineered
      meganucleases. Tailored I-Crel derivatives cleaving sequences from the
      XPC gene were found to induce high levels of gene targeting, similar to
      the I-Crel scaffold or the I-SceI "gold standard". This is the first
      time an engineered homing endonuclease has been used to modify a
      chromosomal locus.
AU  - Arnould S
AU  - Perez C
AU  - Cabaniols J-P
AU  - Smith J
AU  - Gouble A
AU  - Grizot S
AU  - Epinat J-C
AU  - Duclert A
AU  - Duchateau P
AU  - Paques F
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2007 371: 49-65.

PMID- 6336742
VI  - 153
DP  - 1983
TI  - Phenotypic reversal in dam mutants of Escherichia coli K-12 by a recombinant plasmid containing the dam+ gene.
PG  - 562-565
AB  - A recombinant plasmid, pMQ3, carrying the dam gene of Escherichia coli K-12, was constructed
      and transformed into dam+ and dam- strains. Both dam- and dam+ strains containing pMQ3 showed
      a wild phenotype for all traits, including mutation rate, except for a 10-fold increase in DNA
      adenine methylase activity.
AU  - Arraj JA
AU  - Marinus MG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1983 153: 562-565.

PMID- Not included in PubMed...
VI  - 20
DP  - 1990
TI  - Expression of a DNA methylation (dam) gene in Escherichia coli K-12.
PG  - 133-136
AB  - Plasmid pMQ3, carrying the dam gene of Escherichia coli on a 6.1 Kb fragment, shows a tenfold
      increase in relative DNA adenine methylase activity, while plasmid pdam118, with a 1.14 Kb dam
      insert, shows only a twofold increase, although both plasmids were derived from plasmid
      pLC13-42. Since a copy number effect did not seem to be the cause of this difference, we have
      subcloned pMQ3 in order to determine whether the additional chromosomal DNA present in this
      plasmid is responsible for the enhancement of methylase activity. We show that the 346 base
      pairs upstream of dam contain sequences necessary for expression. DNA sequence analysis has
      revealed that in pdam 118 only the 118 bases 5' to the dam gene are present in other
      constructs and that the additional upstream material is pBR322 DNA. This shows that pdam118
      carries a DNA duplication.
AU  - Arraj JA
AU  - Wu T-H
AU  - Marinus MG
PT  - Journal Article
TA  - Curr. Microbiol.
JT  - Curr. Microbiol.
SO  - Curr. Microbiol. 1990 20: 133-136.

PMID- 415144
VI  - 118
DP  - 1978
TI  - A new restriction endonuclease from Streptomyces albus G.
PG  - 127-135
AB  - A restriction endonuclease, SalI, has been partially purified from Streptomyces
      albus G.  This enzyme cleaves adenovirus-2 DNA at three sites, bacteriophage
      lambda DNA at two sites, but does not cleave simian virus 40 DNA or PhiX174
      DNA.  It recognizes the sequence 5'-G^T-C-G-A-C-3' 3'-C-A-G-C-T-^G-5' and cuts
      at the siteds indicated by the arrows.  An endonuclease (XamI) with similar
      specificity has also been isolated from Xanthomonas amaranthicola.
AU  - Arrand JR
AU  - Myers PA
AU  - Roberts RJ
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1978 118: 127-135.

PMID- 20195515
VI  - 6
DP  - 2010
TI  - Structure, function, and evolution of the Thiomonas spp. genome.
PG  - e1000859
AB  - Bacteria of the Thiomonas genus are ubiquitous in extreme environments, such as arsenic-rich
      acid mine drainage (AMD).  The genome of one of these strains, Thiomonas sp. 3As, was
      sequenced, annotated, and examined, revealing specific adaptations allowing this bacterium to
      survive and grow in its highly toxic environment. In order to explore genomic diversity as
      well as genetic evolution in Thiomonas spp., a comparative genomic hybridization (CGH)
      approach was used on eight different strains of the Thiomonas genus, including five strains of
      the same species. Our results suggest that the Thiomonas genome has evolved through the gain
      or loss of genomic islands and that this evolution is influenced by the specific environmental
      conditions in which the strains live.
AU  - Arsene-Ploetze F et al
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2010 6: e1000859.

PMID- 22465332
VI  - 425
DP  - 2012
TI  - DNA extraction method with improved efficiency and specificity using DNA methyltransferase and 'click' chemistry.
PG  - 169-174
AB  - In an attempt to develop an alternative method to extract DNA from complex samples with much
      improved sensitivity and efficiency, here we
      report a proof-of-concept work for a new DNA extraction method using
      DNA methyltransferase (Mtase) and 'click' chemistry. According to our
      preliminary data, the method has improved the current methods by (i)
      employing a DNA-specific enzyme, TaqI DNA Mtase, for improved
      selectivity, and by (ii) capturing the DNA through covalent bond to the
      functionalized surface, enabling a broad range of treatments yielding
      the final sample DNA with minimal loss and higher purity such that it
      will be highly compatible with downstream analyses. By employing Mtase,
      a highly DNA specific and efficient enzyme, and click chemistry, we
      demonstrated that as little as 0.1 fg of lambda-DNA (close to copy
      number 1) was captured on silica (Si)-based beads by forming a covalent
      bond between an azide group on the surface and the propargyl moiety on
      the DNA. This method holds promise in versatile applications where
      extraction of minute amounts of DNA plays critical roles such as basic
      and applied molecular biology research, bioforensic and biosecurity
      sciences, and state-of-the-art detection methods.
AU  - Artyukhin AB
AU  - Woo YH
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 2012 425: 169-174.

PMID- 29674530
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of a Highly Resistant Streptococcus pneumoniae Serotype 15A Strain Isolated from Blood.
PG  - e00167-18
AB  - After the introduction of the pneumococcal conjugate vaccine in Malaysia in recent years, the
      emergence of nonvaccine serotypes is of concern, particularly
      the antibiotic-resistant strains, with an increase specifically in serotype 15A.
      Here, we report the draft genome sequence of Streptococcus pneumoniae strain
      SS40_16, isolated from the blood sample of a 19-month-old female in 2016. SS40_16
      is a multidrug-resistant strain with resistance to penicillin (MIC, >/=2
      microg/ml), tetracycline, and trimethoprim-sulfamethoxazole. The strain belongs
      to serotype 15A and sequence type 1591 (ST1591).
AU  - Arushothy R
AU  - Ahmad N
AU  - Amran F
AU  - Hashim R
AU  - Samsuddin N
AU  - Che ACR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00167-18.

PMID- 1301500
VI  - 11-1
DP  - 1992
TI  - Purification and characterization of DNA methyltransferase Sau6782 of Staphylococcus aureus.
PG  - 26-29
AB  - 
AU  - Arutyunyan EE
AU  - Gonchar NA
AU  - Gruber IM
AU  - Nikolskaya NI
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1992 11-1: 26-29.

PMID- 1651765
VI  - 56
DP  - 1991
TI  - Isoelectrofocusing of methylation and restriction enzymes of Staphylococcus aureus 6782.
PG  - 281-288
AB  - The behaviour of methylation and restriction enzymes of Staphylococcus aureus
      6782 during their isoelectrofocusing on ampholines was studied.  It was found
      that the R.Sau6782I enzyme is represented by two isoforms, RI and RII, with
      isoelectric points of 4.2 and 7.9, respectively.  Data from isoelectrofocusing
      analysis suggest that RI and RII are devoid of the relaxed specificity found in
      the original preparation.  It was shown that the relaxed specificity is also
      inherent in the isoschizomeric enzyme, R.Sau3AI.  Isoelectrofocusing of the
      original preparation of R.Sau3AI, as is the case for R.Sau6782I, allows the
      identification of two peaks, RI and RII, and the separation of each peak from
      the trace activity.  Multiple forms of DNA-methylase of the Sau6782I type are
      represented by four isoenzymes possessing acidic properties.  The method allows
      one to single out from the total methylase pool a modifying methylase with pI
      (3.9) that is close to that of R.Sau6782I and thus the enzyme cannot serve for
      correct separation of restriction and methylation enzymes of Sau6782I.
AU  - Arutyunyan EE
AU  - Gonchar NA
AU  - Levchenko IY
AU  - Gruber IM
AU  - Nikolskaya II
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1991 56: 281-288.

PMID- 3004036
VI  - 31
DP  - 1985
TI  - Restricting Endonuclease SAU 6782.
PG  - 127-132
AB  - Data are described on identification, isolation and purification of restricting
      endonuclease Sau 6782 as well as on estimation of the enzyme recognition site.
      Conditions were developed for growing of Staphylococcus aureus 6782 strain,
      which enabled to produce a maximal yield of the restricting activity containing
      minimal level of nucleases.  The procedure for isolation and purification of
      restrictase Sau 6782 involved affinity chromatography on Blue Sepharose and
      cation exchange chromatography on phosphocellulose PII.  The enzyme preparation
      obtained was free from impurities of unspecific nucleases.  The yield of the
      Sau 6782 restrictase constituted 1,0 un from 1 g of the culture cells.
      Restrictase Sau 6782 recognized the nucleotide sequence 5'...GATC...3' and was
      the isoshizomere of the Sau 3A enzyme.
AU  - Arutyunyan EE
AU  - Gruber IM
AU  - Polyachenko VM
AU  - Kvachadze LJ
AU  - Andriashvili IA
AU  - Chanishvili TG
AU  - Nikolskaya II
PT  - Journal Article
TA  - Vopr. Med. Khim.
JT  - Vopr. Med. Khim.
SO  - Vopr. Med. Khim. 1985 31: 127-132.

PMID- 2363265
VI  - 36
DP  - 1990
TI  - Isolation of methylases from Sau 6782 strain.
PG  - 75-79
AB  - A heterogenous profile of methylases was found in S. aureus 6782.  A procedure
      was developed for isolation of individual methylases from Sau 6782, free of Sau
      6782 restrictases and unspecific nucleases, by means of hydrophobic
      chromatography on phenyl-Sepharose.  Ion exchange, affinity chromatographies
      and gel filtration were also used for isolation of the Sau 6782 methylases.
      But this technique was of limited suitability for isolation of individual
      methylating enzymes of the Sau 6782 type because it did not allow the complete
      separation of these methylases from contaminating enzymes of DNA degradation.
      Effects of salts, glycerol and Triton X-100 on activity of total preparation of
      methylases Sau 6782 were studied.  Na+ and K+ chlorides, ammonium sulfate at
      concentrations 0.4 M and higher as well as Triton X-100 reversibly inhibited
      the methylase activity followed by complete reduction up to initial level after
      dialysis.  Glycerol at 60% concentration activated Sau 6782 methylases by 50%
      and stabilized the enzyme.
AU  - Arutyunyan EE
AU  - Gruber IM
AU  - Polyachenko VM
AU  - Nikolskaya II
AU  - Debov SS
PT  - Journal Article
TA  - Vopr. Med. Khim.
JT  - Vopr. Med. Khim.
SO  - Vopr. Med. Khim. 1990 36: 75-79.

PMID- 4216763
VI  - 133
DP  - 1974
TI  - Restriction and modification in Bacillus subtilis.  Induction of a modifying activity in Bacillus subtilis 168.
PG  - 175-177
AB  - Bacillus subtilis strain 5GR will restrict and modify phage SPO2 previously grown in strain
      168.  SPO2 grown in 168 pretreated with Mitomycin C is less restricted by 5GR.  Strain MB500
      is temperature inducible for the defective PBSX prophage.  SPO2 grown in MB500 at inducing
      temperature is less restricted by 5GR compared to phage grown in MB500 at non-inducing
      temperature.  It is suggested that strain 168 carries genetic determinants for modification of
      SPO2 DNA, and that those determinants may be associated with the defective phage PBSX.
AU  - Arwert F
AU  - Rutberg L
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1974 133: 175-177.

PMID- 25395629
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Bacillus megaterium Type Strain ATCC 14581.
PG  - e01124-14
AB  - Bacillus megaterium is a Gram-positive, rod-shaped, spore-forming bacterium of
      biotechnological importance. Here, we report a 5.7-Mbp draft genome sequence of
      B. megaterium ATCC 14581, which is the type strain of the species.
AU  - Arya G
AU  - Petronella N
AU  - Crosthwait J
AU  - Carrillo CD
AU  - Shwed PS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01124-14.

PMID- 28360165
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Lactobacillus fermentum MTCC 25067 (Formerly TDS030603), a Viscous Exopolysaccharide-Producing Strain Isolated from Indian  Fermented Milk.
PG  - e00091-17
AB  - Lactobacillus fermentum MTCC 25067 (formerly TDS030603) is capable of producing a highly
      viscous slime exopolysaccharide. We report here the complete genome
      sequence of the strain, which was deciphered by using PacBio single-molecule
      real-time sequencing technology.
AU  - Aryantini NP
AU  - Prajapati JB
AU  - Urashima T
AU  - Fukuda K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00091-17.

PMID- 25377716
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Cellulophaga lytica HI1 Using PacBio Single-Molecule  Real-Time Sequencing.
PG  - e01148-14
AB  - We report here the complete genome sequence of Cellulophaga lytica HI1 isolated from a
      seawater table located at the Kewalo Marine Laboratory (Honolulu, HI).
      This is the first complete de novo genome assembly of C. lytica HI1 using PacBio
      single-molecule real-time (SMRT) sequencing, which resulted in a single scaffold
      of 3.8 Mb.
AU  - Asahina AY
AU  - Hadfield MG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01148-14.

PMID- 25700414
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Pseudoalteromonas luteoviolacea HI1, Determined Using Roche 454 and PacBio Single-Molecule Real-Time Hybrid Sequencing.
PG  - e01590-14
AB  - We report here the 6.0-Mb draft genome assembly of Pseudoalteromonas luteoviolacea strain HI1
      using Roche 454 and PacBio single-molecule real-time hybrid-sequencing analysis. This strain
      is of biological importance since it has  the capacity to induce the settlement and
      metamorphosis of the serpulid polychaete Hydroides elegans and the coral Pocillopora
      damicornis.
AU  - Asahina AY
AU  - Hadfield MG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01590-14.

PMID- 29976610
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Lactobacillus paracasei EG9, a Strain Accelerating Free Amino Acid Production during Cheese Ripening.
PG  - e00627-18
AB  - Lactobacillus paracasei EG9 is a strain isolated from well-ripened cheese and accelerates free
      amino acid production during cheese ripening. Its complete
      genome sequence was determined using the PacBio RS II platform, revealing a
      single circular chromosome of 2,927,257 bp, a G+C content of 46.59%, and three
      plasmids.
AU  - Asahina Y
AU  - Shiroma A
AU  - Nakano K
AU  - Tamotsu H
AU  - Ashimine N
AU  - Shinzato M
AU  - Minami M
AU  - Shimoji M
AU  - Nakanishi T
AU  - Ohki S
AU  - Teruya K
AU  - Satou K
AU  - Kobayashi M
AU  - Hagi T
AU  - Moriya N
AU  - Suzuki C
AU  - Tajima A
AU  - Nomura M
AU  - Hirano T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00627-18.

PMID- 8391858
VI  - 26
DP  - 1993
TI  - Restriction endonuclease recognition and Southern hybridization of bromodeoxyuridine-substituted genomic DNA.
PG  - 271-280
AB  - Human glioma cell lines exposed to various concentrations of bromodeoxyuridine (BrdUrd) were
      studied to determine the effect of BrdUrd substitution on restriction endonuclease recognition
      and Southern hybridization of genomic DNA. BrdUrd substitution had no effect on the
      recognition of restriction endonucleases. When the exposure to BrdUrd was 2 h or less and the
      BrdUrd substitution rate was less than 40%, there was no difference in the density of
      hybridized bands after Southern hybridization using human non-recombinant complementary DNA as
      a probe. Hybridization was suppressed significantly by exposures longer than 24 h or BrdUrd
      substitution rates greater than 40%. These results suggest that the Brdurd substitution rate
      and the exposure time to BrdUrd influence the hybridization reaction by a DNA probe. Brief
      exposure (up to 2 h) to BrdUrd does not influence restriction endonuclease recognition or
      Southern hybridization of genomic DNA.
AU  - Asai A
AU  - Hirai H
AU  - Bodell WJ
AU  - Hoshino T
PT  - Journal Article
TA  - Cell Prolif.
JT  - Cell Prolif.
SO  - Cell Prolif. 1993 26: 271-280.

PMID- 28254967
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Five Shiga Toxin-Producing Escherichia coli Strains Isolated from Wild Deer in Japan.
PG  - e01455-16
AB  - Shiga toxin-producing Escherichia coli (STEC) is one of the major foodborne pathogens. Having
      observed the wide distribution of this pathogen in wild deer,
      we report here the draft genome sequence of five STEC strains isolated from wild
      deer (Cervus nippon yesoensis) in Hokkaido, Japan.
AU  - Asakura H
AU  - Ikeda T
AU  - Yamamoto S
AU  - Kabeya H
AU  - Sugiyama H
AU  - Takai S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01455-16.

PMID- 28619796
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Campylobacter jejuni CAM970 and C. coli CAM962, Associated with a Large Outbreak of Foodborne Illness in Fukuoka, Japan, in 2016.
PG  - e00508-17
AB  - Here, we report the draft genome sequences of Campylobacter jejuni CAM970 and C.  coli CAM962,
      which were associated with a large outbreak of foodborne illness
      originating from undercooked chicken sushi in Fukuoka, Japan, in May 2016. Their
      genome sizes were 1,690,901 and 1,704,736 bp, with 22 and 23 rRNAs, 9 and 9
      tRNAs, and 411x and 419x coverage for C. jejuni CAM970 and C. coli CAM962,
      respectively.
AU  - Asakura H
AU  - Takahashi N
AU  - Yamamoto S
AU  - Maruyama H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00508-17.

PMID- 28839036
VI  - 5
DP  - 2017
TI  - Genome Sequence of Clostridium botulinum Strain Adk2012 Associated with a Foodborne Botulinum Case in Tottori, Japan, in 2012.
PG  - e00872-17
AB  - We report here a draft genome sequence of Clostridium botulinum Adk2012 responsible for a
      foodborne botulism case that occurred in Tottori, Japan, in
      2012. Its genome size was 2,904,173 bp, with 46 rRNAs and 54 tRNAs, at a coverage
      of 14.5x.
AU  - Asakura H
AU  - Yamamoto S
AU  - Momose Y
AU  - Kato H
AU  - Iwaki M
AU  - Shibayama K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00872-17.

PMID- 19304752
VI  - 37
DP  - 2009
TI  - From damaged genome to cell surface: transcriptome changes during bacterial cell death triggered by loss of a restriction-modification gene  complex.
PG  - 3021-3031
AB  - Genetically programmed cell deaths play important roles in unicellular prokaryotes. In
      postsegregational killing, loss of a gene complex from a
      cell leads to its descendants' deaths. With type II
      restriction-modification gene complexes, such death is triggered by
      restriction endonuclease's attacks on under-methylated chromosomes. Here,
      we examined how the Escherichia coli transcriptome changes after loss of
      PaeR7I gene complex. At earlier time points, activation of SOS genes and
      sigma(E)-regulon was noticeable. With time, more SOS genes,
      stress-response genes (including sigma(S)-regulon, osmotic-, oxidative-
      and periplasmic-stress genes), biofilm-related genes, and many hitherto
      uncharacterized genes were induced, and genes for energy metabolism,
      motility and outer membrane biogenesis were repressed. As expected from
      the activation of sigma(E)-regulon, the death was accompanied by cell
      lysis and release of cellular proteins. Expression of several
      sigma(E)-regulon genes indeed led to cell lysis. We hypothesize that some
      signal was transduced, among multiple genes involved, from the damaged
      genome to the cell surface and led to its disintegration. These results
      are discussed in comparison with other forms of programmed deaths in
      bacteria and eukaryotes.
AU  - Asakura Y
AU  - Kobayashi I
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: 3021-3031.

PMID- 21785135
VI  - 39
DP  - 2011
TI  - Evolutionary genome engineering using a restriction-modification system.
PG  - 9034-9046
AB  - Modification of complex microbial cellular processes is often necessary to obtain organisms
      with particularly favorable characteristics, but such
      experiments can take many generations to achieve. In the present article,
      we accelerated the experimental evolution of Escherichia coli populations
      under selection for improved growth using one of the
      restriction-modification systems, which have shaped bacterial genomes.
      This resulted in faster evolutionary changes in both the genome and
      bacterial growth. Transcriptome/genome analysis at various stages enabled
      prompt identification of sequential genome rearrangements and dynamic
      gene-expression changes associated with growth improvement. The changes
      were related to cell-to-cell communication, the cell death program, as
      well as mass production and energy consumption. These observed changes
      imply that improvements in microorganism population growth can be achieved
      by inactivating the cellular mechanisms regulating fraction of active
      cells in a population. Some of the mutations were shown to have additive
      effects on growth. These results open the way for the application of
      evolutionary genome engineering to generate organisms with desirable
      properties.
AU  - Asakura Y
AU  - Kojima H
AU  - Kobayashi I
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2011 39: 9034-9046.

PMID- 10048488
VI  - 5
DP  - 1998
TI  - Structural analysis of Arabidopsis thaliana chromosome 5. VIII. Sequence features of the regions of 1,081,958 bp covered by seventeen physically assigned P1 and TAC clones.
PG  - 379-391
AB  - A total of 17 Pl and TAC clones each representing an assigned region of
      chromosome 5 were isolated from P1 and TAC genomic libraries of
      Arabidopsis thaliana Columbia, and their nucleotide sequences were
      determined. The length of the clones sequenced in this study summed up to
      1,081,958 bp. As we have previously reported the sequence of 9,072,622 bp
      by analysis of 125 P1 and TAC clones, the total length of the sequences of
      chromosome 5 determined so far is now 10,154,580 bp. The sequences were
      subjected to similarity search against protein and EST databases and
      analysis with computer programs for gene modeling. As a consequence, a
      total of 253 potential protein-coding genes with known or predicted
      functions were identified. The positions of exons, which do not show
      apparent similarity to known genes were also assigned using computer
      programs for exon prediction. The average density of the genes identified
      in this study was 1 gene per 4277 bp. Introns were observed in 74% of the
      potential protein genes, and the average number per gene and the average
      length of the introns were 4.3 and 168 bp, respectively. The sequence data
      and gene information are available on the World Wide Web database KAOS
      (Kazusa Arabidopsis data Opening Site) at http://www.kazusa.or.jp/arabi/.
AU  - Asamizu E
AU  - Sato S
AU  - Kaneko T
AU  - Nakamura Y
AU  - Kotani H
AU  - Miyajima N
AU  - Tabata S
PT  - Journal Article
TA  - DNA Res.
JT  - DNA Res.
SO  - DNA Res. 1998 5: 379-391.

PMID- 29225730
VI  - 12
DP  - 2017
TI  - Draft genome sequences of Bradyrhizobium shewense sp. nov. ERR11(T) and Bradyrhizobium yuanmingense CCBAU 10071(T).
PG  - 74
AB  - The type strain of the prospective 10.1601/nm.30737 sp. nov. ERR11(T), was isolated from a
      nodule of the leguminous tree Erythrina brucei native to
      Ethiopia. The type strain 10.1601/nm.1463
      10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+10071 (T), was isolated from the
      nodules of Lespedeza cuneata in Beijing, China. The genomes of ERR11(T) and
      10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+10071 (T) were sequenced by DOE-JGI
      and deposited at the DOE-JGI genome portal as well as at the European Nucleotide
      Archive. The genome of ERR11(T) is 9,163,226 bp in length and has 102 scaffolds,
      containing 8548 protein-coding and 86 RNA genes. The
      10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+10071 (T) genome is arranged in 108
      scaffolds and consists of 8,201,522 bp long and 7776 protein-coding and 85 RNA
      genes. Both genomes contain symbiotic genes, which are homologous to the genes
      found in the complete genome sequence of 10.1601/nm.24498
      10.1601/strainfinder?urlappend=%3Fid%3DUSDA+110 (T). The genes encoding for
      nodulation and nitrogen fixation in ERR11(T) showed high sequence similarity with
      homologous genes found in the draft genome of peanut-nodulating 10.1601/nm.27386
      10.1601/strainfinder?urlappend=%3Fid%3DLMG+26795 (T). The nodulation genes
      nolYA-nodD2D1YABCSUIJ-nolO-nodZ of ERR11(T) and
      10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+10071 (T) are organized in a similar
      way to the homologous genes identified in the genomes of
      10.1601/strainfinder?urlappend=%3Fid%3DUSDA+110 (T), 10.1601/nm.25806
      10.1601/strainfinder?urlappend=%3Fid%3DUSDA+4 and 10.1601/nm.1462
      10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+05525. The genomes harbor hupSLCFHK
      and hypBFDE genes that code the expression of hydrogenase, an enzyme that helps
      rhizobia to uptake hydrogen released by the N2-fixation process and genes
      encoding denitrification functions napEDABC and norCBQD for nitrate and nitric
      oxide reduction, respectively. The genome of ERR11(T) also contains nosRZDFYLX
      genes encoding nitrous oxide reductase. Based on multilocus sequence analysis of
      housekeeping genes, the novel species, which contains eight strains formed a
      unique group close to the 10.1601/nm.25806 branch. Genome Average Nucleotide
      Identity (ANI) calculated between the genome sequences of ERR11(T) and closely
      related sequences revealed that strains belonging to 10.1601/nm.25806 branch
      (10.1601/strainfinder?urlappend=%3Fid%3DUSDA+4 and
      10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+15615), were the closest strains to
      the strain ERR11(T) with 95.2% ANI. Type strain ERR11(T) showed the highest DDH
      predicted value with 10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+15615 (58.5%),
      followed by 10.1601/strainfinder?urlappend=%3Fid%3DUSDA+4 (53.1%). Nevertheless,
      the ANI and DDH values obtained between ERR11(T) and
      10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+15615 or
      10.1601/strainfinder?urlappend=%3Fid%3DUSDA+4 were below the cutoff values (ANI
      >/= 96.5%; DDH >/= 70%) for strains belonging to the same species, suggesting
      that ERR11(T) is a new species. Therefore, based on the phylogenetic analysis,
      ANI and DDH values, we formally propose the creation of 10.1601/nm.30737 sp. nov.
      with strain ERR11(T) (10.1601/strainfinder?urlappend=%3Fid%3DHAMBI+3532
      (T)=10.1601/strainfinder?urlappend=%3Fid%3DLMG+30162 (T)) as the type strain.
AU  - Aserse AA
AU  - Woyke T
AU  - Kyrpides NC
AU  - Whitman WB
AU  - Lindstrom K
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 74.

PMID- 28163823
VI  - 12
DP  - 2017
TI  - Draft genome sequence of type strain HBR26T and description of Rhizobium aethiopicum sp. nov.
PG  - 14
AB  - Rhizobium aethiopicum sp. nov. is a newly proposed species within the genus Rhizobium. This
      species includes six rhizobial strains; which were isolated from
      root nodules of the legume plant Phaseolus vulgaris growing in soils of Ethiopia.
      The species fixes nitrogen effectively in symbiosis with the host plant P.
      vulgaris, and is composed of aerobic, Gram-negative staining, rod-shaped
      bacteria. The genome of type strain HBR26T of R. aethiopicum sp. nov. was one of
      the rhizobial genomes sequenced as a part of the DOE JGI 2014 Genomic
      Encyclopedia project designed for soil and plant-associated and newly described
      type strains. The genome sequence is arranged in 62 scaffolds and consists of
      6,557,588 bp length, with a 61% G + C content and 6221 protein-coding and 86 RNAs
      genes. The genome of HBR26T contains repABC genes (plasmid replication genes)
      homologous to the genes found in five different Rhizobium etli CFN42T plasmids,
      suggesting that HBR26T may have five additional replicons other than the
      chromosome. In the genome of HBR26T, the nodulation genes nodB, nodC, nodS, nodI,
      nodJ and nodD are located in the same module, and organized in a similar way as
      nod genes found in the genome of other known common bean-nodulating rhizobial
      species. nodA gene is found in a different scaffold, but it is also very similar
      to nodA genes of other bean-nodulating rhizobial strains. Though HBR26T is
      distinct on the phylogenetic tree and based on ANI analysis (the highest value
      90.2% ANI with CFN42T) from other bean-nodulating species, these nod genes and
      most nitrogen-fixing genes found in the genome of HBR26T share high identity with
      the corresponding genes of known bean-nodulating rhizobial species (96-100%
      identity). This suggests that symbiotic genes might be shared between
      bean-nodulating rhizobia through horizontal gene transfer. R. aethiopicum sp.
      nov. was grouped into the genus Rhizobium but was distinct from all recognized
      species of that genus by phylogenetic analyses of combined sequences of the
      housekeeping genes recA and glnII. The closest reference type strains for HBR26T
      were R. etli CFN42T (94% similarity of the combined recA and glnII sequences) and
      Rhizobium bangladeshense BLR175T (93%). Genomic ANI calculation based on
      protein-coding genes also revealed that the closest reference strains were R.
      bangladeshense BLR175T and R. etli CFN42T with ANI values 91.8 and 90.2%,
      respectively. Nevertheless, the ANI values between HBR26T and BLR175T or CFN42T
      are far lower than the cutoff value of ANI (> = 96%) between strains in the same
      species, confirming that HBR26T belongs to a novel species. Thus, on the basis of
      phylogenetic, comparative genomic analyses and ANI results, we formally propose
      the creation of R. aethiopicum sp. nov. with strain HBR26T (=HAMBI 3550T=LMG
      29711T) as the type strain. The genome assembly and annotation data is deposited
      in the DOE JGI portal and also available at European Nucleotide Archive under
      accession numbers FMAJ01000001-FMAJ01000062.
AU  - Aserse AA
AU  - Woyke T
AU  - Kyrpides NC
AU  - Whitman WB
AU  - Lindstrom K
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 14.

PMID- 21516800
VI  - 47
DP  - 2011
TI  - Is the cytosine DNA methyltransferase gene MET1 regulated by DNA methylation in Arabidopsis thaliana plants?
PG  - 279-288
AB  - The methylation patterns of the MET1 gene in organs of Arabidopsis thaliana were studied by
      Southern blot hybridization of DNA samples
      hydrolyzed with differentially methylation-sensitive restriction
      endonucleases. A highly methylated on internal cytosine residue CCGG
      site was found 1.5 kb upstream of the gene, whereas CCGG sites located
      in more proximal parts of the 5'-flanking region and the gene itself
      are essentially unmethylated. This methylation pattern was observed in
      different organs of plants belonging to two different ecotypes as well
      as in different transgenic plant lines. The methylation level of a CCGG
      site in exon 3 (2.1 kb from the gene's 5'-end) occurred to be variable
      between different transgenic plant lines and two ecotypes studied.
      Transcription levels of the MET1 gene vary slightly in organs of
      wild-type plants without any obvious correlation with its methylation.
      The transgenic antisense MET1 constructs expressed in plant genome do
      affect both MET1 methylation and its transcription but again without
      any obvious correlation. The comparative investigation of transcription
      levels of different genes of cytosine DNA methyltransferase family MET
      (MET1, MET2a, MET2b, MET3) and their methylation patterns shows that
      there may exist some mechanisms defending the most actively transcribed
      gene MET1 of this family from methylation mediated silencing. In
      contrast to DRM2 gene we could not find any adenine methylated GATC
      sites in the MET1 gene.
AU  - Ashapkin VV
AU  - Kutueva LI
AU  - Vanyushin BF
PT  - Journal Article
TA  - Genetika
JT  - Genetika
SO  - Genetika 2011 47: 279-288.

PMID- 12482594
VI  - 532
DP  - 2002
TI  - The gene for domains rearranged methyltransferase (DRM2) in Arabidopsis thaliana plants is methylated at both cytosine and adenine residues.
PG  - 367-372
AB  - The methylation patterns of cytosine and adenine residues in the Arabidopsis thaliana gene for
      domains rearranged methyltransferase (DRM2) were studied in wild-type and several transgene
      plant lines containing antisense fragments of the cytosine DNA-methyltransferase gene METI
      under the control of copper-inducible promoters. It was shown that the promoter region of the
      DRM2 gene is mostly unmethylated at the internal cytosine residue in CCGG sites whereas the
      3'-end proximal part of the gene coding region is highly methylated. The DRM2 gene was found
      to be also methylated at adenine residues in some GATC sequences. Cytosine methylation in CCGG
      sites and adenine methylation in GATC sites in the DRM2 gene are variable between wild-type
      and different transgenic plants. The induction of antisense METI constructs with copper ions
      in transgene plants in most cases leads to further alterations in the DRM2 gene methylation
      patterns.
AU  - Ashapkin VV
AU  - Kutueva LI
AU  - Vanyushin BF
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 2002 532: 367-372.

PMID- 7684508
VI  - 302
DP  - 1993
TI  - Alteration of gene expression by restriction enzymes electroporated into plant cells.
PG  - 75-82
AB  - The alteration in the expression of a B-glucuronidase (GUS) reporter gene was used to monitor
      the effect of restriction endonuclease electroporated into the tobacco (Nicotiana tabacum L.)
      protoplasts. Restriction enzyme (RE) HindIII which does not have a recognition site within the
      gene cassette, had little effect on enzyme activity. In contrast restriction endonucleases
      HaeIII and Sau3AI which possess 8 and 16 recognition sites in the GUS cassette, were found to
      reduce the enzyme activity by 89% and 94% respectively when compared to control
      electroporations. Restriction-site mutation analysis (RSM) and Southern blot analysis
      indicated the enzymatic degradation of GUS coding sequence by the REs HaeIII and Sau3AI.
      Results of this study suggest that on electroporation, REs can enter into plant cells and
      alter the expression of the GUS gene. The alteration of gene expression is thus correlated
      with the digestion of GUS template DNA. Future applications of this technique could include
      addressing fundamental questions with regard to DNA repair, site-specific recombination,
      identifying mutations, insertional mutagenesis, enhancement of stable transformation and gene
      tagging in plants.
AU  - Ashraf M
AU  - Altschuler M
AU  - Galasinski S
AU  - Griffiths TD
PT  - Journal Article
TA  - Mutat. Res.
JT  - Mutat. Res.
SO  - Mutat. Res. 1993 302: 75-82.

PMID- 16738662
VI  - 441
DP  - 2006
TI  - Computational redesign of endonuclease DNA binding and cleavage specificity.
PG  - 656-659
AB  - The reprogramming of DNA-binding specificity is an important challenge for computational
      protein design that tests current understanding of
      protein - DNA recognition, and has considerable practical relevance for
      biotechnology and medicine(1-6). Here we describe the computational
      redesign of the cleavage specificity of the intron-encoded homing
      endonuclease I-MsoI(7) using a physically realistic atomic-level
      forcefield(8,9). Using an in silico screen, we identified single
      base-pair substitutions predicted to disrupt binding by the wild-type
      enzyme, and then optimized the identities and conformations of clusters
      of amino acids around each of these unfavourable substitutions using
      Monte Carlo sampling(10). A redesigned enzyme that was predicted to
      display altered target site specificity, while maintaining wild-type
      binding affinity, was experimentally characterized. The redesigned
      enzyme binds and cleaves the redesigned recognition site similar to
      10,000 times more effectively than does the wild-type enzyme, with a
      level of target discrimination comparable to the original endonuclease.
      Determination of the structure of the redesigned nuclease-recognition
      site complex by X-ray crystallography confirms the accuracy of the
      computationally predicted interface. These results suggest that
      computational protein design methods can have an important role in the
      creation of novel highly specific endonucleases for gene therapy and
      other applications.
AU  - Ashworth J
AU  - Havranek JJ
AU  - Duarte CM
AU  - Sussman D
AU  - Monnat RJ
AU  - Stoddard BL
AU  - Baker D
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2006 441: 656-659.

PMID- 20435674
VI  - 38
DP  - 2010
TI  - Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs.
PG  - 5601-5608
AB  - Site-specific homing endonucleases are capable of inducing gene conversion via homologous
      recombination. Reprogramming their cleavage specificities
      allows the targeting of specific biological sites for gene correction or
      conversion. We used computational protein design to alter the cleavage
      specificity of I-MsoI for three contiguous base pair substitutions,
      resulting in an endonuclease whose activity and specificity for its new
      site rival that of wild-type I-MsoI for the original site. Concerted
      design for all simultaneous substitutions was more successful than a
      modular approach against individual substitutions, highlighting the
      importance of context-dependent redesign and optimization of protein-DNA
      interactions. We then used computational design based on the crystal
      structure of the designed complex, which revealed significant
      unanticipated shifts in DNA conformation, to create an endonuclease that
      specifically cleaves a site with four contiguous base pair substitutions.
      Our results demonstrate that specificity switches for multiple concerted
      base pair substitutions can be computationally designed, and that
      iteration between design and structure determination provides a route to
      large scale reprogramming of specificity.
AU  - Ashworth J
AU  - Taylor GK
AU  - Havranek JJ
AU  - Quadri SA
AU  - Stoddard BL
AU  - Baker D
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2010 38: 5601-5608.

PMID- 26067974
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Gerbil-Adapted Carcinogenic Helicobacter pylori Strain 7.13.
PG  - e00641-15
AB  - We report here the draft genome sequence of Helicobacter pylori strain 7.13, a gerbil-adapted
      strain that causes gastric cancer in gerbils. Strain 7.13 is
      derived from clinical strain B128, isolated from a patient with a duodenal ulcer.
      This study reveals genes associated with the virulence of the strain.
AU  - Asim M
AU  - Chikara SK
AU  - Ghosh A
AU  - Vudathala S
AU  - Romero-Gallo J
AU  - Krishna US
AU  - Wilson KT
AU  - Israel DA
AU  - Peek RM Jr
AU  - Chaturvedi R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00641-15.

PMID- 27688323
VI  - 4
DP  - 2016
TI  - Genome Sequence of Klebsiella quasipneumoniae subsp. similipneumoniae MB373, an Effective Bioremediator.
PG  - e01068-16
AB  - Klebsiella quasipneumoniae subsp. similipneumoniae MB373 was isolated from effluent of the
      Hattar Industrial Estate, Haripur, Pakistan. K. quasipneumoniae
      subsp. similipneumoniae has few cultivated/characterized members so far.
      Whole-genome sequencing revealed its potential for metal and toxin resistance,
      which further elucidated various enzymatic processes for the degradation of
      xenobiotics, illuminating its bioremediation applications.
AU  - Aslam F
AU  - Yasmin A
AU  - Thomas T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01068-16.

PMID- 26251499
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Mycobacterium bohemicum Strain DSM 44277T.
PG  - e00878-15
AB  - The Mycobacterium bohemicum strain is a nontuberculosis species mainly responsible for
      pediatric cervical lymphadenitis. The draft genome of M.
      bohemicum DSM 44277(T) comprises 5,097,190 bp exhibiting a 68.64% G+C content,
      4,840 protein-coding genes, and 75 predicted RNA genes.
AU  - Asmar S
AU  - Phelippeau M
AU  - Robert C
AU  - Croce O
AU  - Drancourt M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00878-15.

PMID- 26543113
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Mycobacterium peregrinum Strain CSUR P2098.
PG  - e01274-15
AB  - Mycobacterium peregrinum is a nonpigmented rapid growing nontuberculosis species  belonging to
      the Mycobacterium fortuitum group. The draft genome of M. peregrinum
      type I CSUR P2098 comprises 7,109,836 bp exhibiting a 66.23% G+C content, 6,894
      protein-coding genes, and 100 predicted RNA genes. Its genome analysis suggests
      this species differs from Mycobacterium senegalense.
AU  - Asmar S
AU  - Rascovan N
AU  - Robert C
AU  - Drancourt M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01274-15.

PMID- 27516522
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Mycobacterium acapulcensis Strain CSURP1424.
PG  - e00836-16
AB  - Mycobacterium acapulcensis is a rapidly growing scotochromogenic acid-fast bacillus. The draft
      genome of M. acapulcensis CSURP1424 comprises 5,290,974 bp,
      exhibiting a 66.67% G+C content, 4,870 protein-coding genes, and 71 predicted RNA
      genes.
AU  - Asmar S
AU  - Rascovan N
AU  - Robert C
AU  - Drancourt M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00836-16.

PMID- 26586900
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Mycobacterium mucogenicum Strain CSUR P2099.
PG  - e01369-15
AB  - Mycobacterium mucogenicum is a rapid-growing, nontuberculosis Mycobacterium species. The draft
      genome of M. mucogenicum CSUR P2099 comprises 6,210,127 bp
      exhibiting a 67.2% G+C content, 6,003 protein-coding genes, and 91 predicted RNA
      genes.
AU  - Asmar S
AU  - Rascovan N
AU  - Robert C
AU  - Drancourt M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01369-15.

PMID- 26543131
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Mycobacterium neworleansense Strain ATCC 49404T.
PG  - e01314-15
AB  - Mycobacterium neworleansense is a rapid growing nontuberculosis species belonging to the
      Mycobacterium fortuitum complex. The draft genome of M. neworleansense
      ATCC 49404(T) comprises 6,287,317 bp exhibiting a 66.85% G+C content, 5,997
      protein-coding genes, and 89 predicted RNA genes.
AU  - Asmar S
AU  - Robert C
AU  - Croce O
AU  - Caputo A
AU  - Drancourt M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01314-15.

PMID- 23704185
VI  - 1
DP  - 2013
TI  - Complete Genome of a Methanosarcina mazei Strain Isolated from Sediment Samples from an Amazonian Flooded Area.
PG  - e00271-13
AB  - Methanosarcina mazei is a strictly anaerobic methanogen from the Methanosarcinales order,
      which is known for its broad catabolic range among
      methanogens and is widespread throughout diverse environments. The draft genome of the strain
      presented here was cultivated from sediment samples collected from the Tucurui hydroelectric
      power station reservoir.
AU  - Assis-das-Gracas D
AU  - Thiago-Juca-Ramos R
AU  - Vieira-Araujo AC
AU  - Zahlouth R
AU  - Ribeiro-Carneiro A
AU  - Souza-Lopes T
AU  - Azevedo-Barauna R
AU  - Azevedo V
AU  - Cruz-Schneider MP
AU  - Pellizari VH
AU  - Silva A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00271-13.

PMID- 29853502
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of the Novel Enterobacter cloacae Strain amazonensis, a Highly Heavy Metal-Resistant Bacterium from a Contaminated Stream in Amazonas,  Brazil.
PG  - e00450-18
AB  - Here, we report the draft genome of the Enterobacter cloacae strain amazonensis,  a bacterium
      highly resistant to mercury that was isolated from a metal- and
      sewage-contaminated stream in Amazonas, Brazil. The exploration of the 5.0-Mb
      genome revealed 104 genes encoding resistance to toxic compounds and heavy
      metals, highlighting the potential biotechnological applications of this strain.
AU  - Astolfi MCT
AU  - Carvalho EBS
AU  - de Barros AM
AU  - Pinto MV
AU  - de Lacerda LB
AU  - Nogueira VB
AU  - Lopes EF
AU  - Astolfi-Filho S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00450-18.

PMID- 27174283
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Staphylococcus aureus MCRF184, a Necrotizing Fasciitis-Causing Methicillin-Sensitive Sequence Type 45 Staphylococcus Strain.
PG  - e00374-16
AB  - We report here the complete genome sequence of a highly virulent methicillin-sensitive
      Staphylococcus aureus strain, MCRF184, belonging to
      sequence type 45. This staphylococcal strain was isolated from a surgical biopsy
      specimen from a patient with necrotizing fasciitis.
AU  - Aswani V
AU  - Mau B
AU  - Shukla SK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00374-16.

PMID- 26215614
VI  - 6
DP  - 2015
TI  - A biphasic epigenetic switch controls immunoevasion, virulence and niche adaptation in non-typeable Haemophilus influenzae.
PG  - 7828
AB  - Non-typeable Haemophilus influenzae contains an N(6)-adenine DNA-methyltransferase (ModA) that
      is subject to phase-variable expression (random
      ON/OFF switching). Five modA alleles, modA2, modA4, modA5, modA9 and modA10,
      account for over two-thirds of clinical otitis media isolates surveyed. Here, we
      use single molecule, real-time (SMRT) methylome analysis to identify the
      DNA-recognition motifs for all five of these modA alleles. Phase variation of
      these alleles regulates multiple proteins including vaccine candidates, and key
      virulence phenotypes such as antibiotic resistance (modA2, modA5, modA10),
      biofilm formation (modA2) and immunoevasion (modA4). Analyses of a modA2 strain
      in the chinchilla model of otitis media show a clear selection for ON switching
      of modA2 in the middle ear. Our results indicate that a biphasic epigenetic
      switch can control bacterial virulence, immunoevasion and niche adaptation in an
      animal model system.
AU  - Atack JM
AU  - Srikhanta YN
AU  - Fox KL
AU  - Jurcisek JA
AU  - Brockman KL
AU  - Clark TA
AU  - Boitano M
AU  - Power PM
AU  - Jen FE
AU  - McEwan AG
AU  - Grimmond SM
AU  - Smith AL
AU  - Barenkamp SJ
AU  - Korlach J
AU  - Bakaletz LO
AU  - Jennings MP
PT  - Journal Article
TA  - Nat. Commun.
JT  - Nat. Commun.
SO  - Nat. Commun. 2015 6: 7828.

PMID- 29452952
VI  - 26
DP  - 2018
TI  - Phasevarions of Bacterial Pathogens: Methylomics Sheds New Light on Old Enemies.
PG  - 715-726
AB  - A wide variety of bacterial pathogens express phase-variable DNA methyltransferases that
      control expression of multiple genes via epigenetic mechanisms. These randomly switching
      regulons - phasevarions - regulate genes involved in pathogenesis, host adaptation, and
      antibiotic resistance. Individual phase-variable genes can be identified in silico as they
      contain easily recognized features such as simple sequence repeats (SSRs) or inverted repeats
      (IRs) that mediate the random switching of expression. Conversely, phasevarion-controlled
      genes do not contain any easily identifiable features. The study of DNA methyltransferase
      specificity using Single-Molecule, Real-Time (SMRT) sequencing and methylome analysis has
      rapidly advanced the analysis of phasevarions by allowing methylomics to be combined with
      whole-transcriptome/proteome analysis to comprehensively characterize these systems in a
      number of important bacterial pathogens.
AU  - Atack JM
AU  - Tan A
AU  - Bakaletz LO
AU  - Jennings MP
AU  - Seib KL
PT  - Journal Article
TA  - Trends Microbiol.
JT  - Trends Microbiol.
SO  - Trends Microbiol. 2018 26: 715-726.

PMID- 30304532
VI  - 46
DP  - 2018
TI  - Streptococcus suis contains multiple phase-variable methyltransferases that show  a discrete lineage distribution.
PG  - 11466-11476
AB  - Streptococcus suis is a major pathogen of swine, responsible for a number of chronic and acute
      infections, and is also emerging as a major zoonotic pathogen, particularly in South-East
      Asia. Our study of a diverse population of S. suis shows that this organism contains both Type
      I and Type III phase-variable methyltransferases. In all previous examples, phase-variation of
      methyltransferases results in genome wide methylation differences, and results in differential
      regulation of multiple genes, a system known as the phasevarion (phase-variable regulon). We
      hypothesized that each variant in the Type I and Type III systems encoded a methyltransferase
      with a unique specificity, and could therefore control a distinct phasevarion, either by
      recombination-driven shuffling between different specificities (Type I) or by biphasic on-off
      switching via simple sequence repeats (Type III). Here, we present the identification of the
      target specificities for each Type III allelic variant from S. suis using single-molecule,
      real-time methylome analysis. We demonstrate phase-variation is occurring in both Type I and
      Type III methyltransferases, and show a distinct association between methyltransferase type
      and presence, and population clades. In addition, we show that the phase-variable Type I
      methyltransferase was likely acquired at the origin of a highly virulent zoonotic
      sub-population.
AU  - Atack JM
AU  - Weinert LA
AU  - Tucker AW
AU  - Husna AU
AU  - Wileman TM
AU  - Hadjirin NF
AU  - Hoa NT
AU  - Parkhill J
AU  - Maskell DJ
AU  - Blackall PJ
AU  - Jennings MP
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2018 46: 11466-11476.

PMID- 29554328
VI  - 46
DP  - 2018
TI  - A survey of Type III restriction-modification systems reveals numerous, novel epigenetic regulators controlling phase-variable regulons; phasevarions.
PG  - 3532-3542
AB  - Many bacteria utilize simple DNA sequence repeats as a mechanism to randomly switch genes on
      and off. This process is called phase variation. Several phase-variable N6-adenine
      DNA-methyltransferases from Type III restriction-modification systems have been reported in
      bacterial pathogens. Random switching of DNA methyltransferases changes the global DNA
      methylation pattern, leading to changes in gene expression. These epigenetic regulatory
      systems are called phasevarions - phase-variable regulons. The extent of these phase-variable
      genes in the bacterial kingdom is unknown. Here, we interrogated a database of
      restriction-modification systems, REBASE, by searching for all simple DNA sequence repeats in
      mod genes that encode Type III N6-adenine DNA-methyltransferases. We report that 17.4% of Type
      III mod genes (662/3805) contain simple sequence repeats. Of these, only one-fifth have been
      previously identified. The newly discovered examples are widely distributed and include many
      examples in opportunistic pathogens as well as in environmental species. In many cases,
      multiple phasevarions exist in one genome, with examples of up to 4 independent phasevarions
      in some species. We found several new types of phase-variable mod genes, including the first
      example of a phase-variable methyltransferase in pathogenic Escherichia coli. Phasevarions are
      a common epigenetic regulation contingency strategy used by both pathogenic and non-pathogenic
      bacteria.
AU  - Atack JM
AU  - Yang Y
AU  - Seib KL
AU  - Zhou Y
AU  - Jennings MP
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2018 46: 3532-3542.

PMID- 11452031
VI  - 29
DP  - 2001
TI  - Characterisation of the structure of ocr, the gene 0.3 protein of bacteriophage T7.
PG  - 3059-3068
AB  - The product of gene 0.3 of bacterlophage T7, ocr, is a potent inhibitor of type I DNA
      restriction and modification enzymes. We have used
      biophysical methods to examine the mass, stability, shape and surface
      charge distribution of ocr. Ocr is a dimeric protein with hydrodynamic
      behaviour equivalent to a prolate ellipsoid of axial ratio 4.3 +/-
      0.7:1 and mass of 27 kDa. The protein is resistant to denaturation but
      removal of the C-terminal region reduces stability substantially. Six
      amino acids, N4, D25, N43, D62, S68 and W94, are all located on the
      surface of the protein and N4 and S68 are also located at the interface
      between the two 116 amino acid monomers. Negatively charged amino acid
      side chains surround W94 but these side chains are not part of the
      highly acidic C-terminus after W94. Ocr is able to displace a short DNA
      duplex from the binding site of a type I enzyme with a dissociation
      constant of the order of 100 pM or better. These results suggest that
      ocr is of a suitable size and shape to effectively block the DNA
      binding site of a type I enzyme and has a large negatively charged
      patch on its surface. This charge distribution may be complementary to
      the charge distribution within the DNA binding site of type I DNA
      restriction and modification enzymes.
AU  - Atanasiu C
AU  - Byron O
AU  - McMiken H
AU  - Sturrock SS
AU  - Dryden DTF
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2001 29: 3059-3068.

PMID- 12235377
VI  - 30
DP  - 2002
TI  - Interaction of the ocr gene 0.3 protein of bacteriophage T7 with EcoKI restriction/modification enzyme.
PG  - 3936-3944
AB  - The ocr protein, the product of gene 0.3 of bacteriophage T7, is a structural mimic of the
      phosphate backbone of B-form DNA. In total it mimics 22 phosphate groups over 24 bp of DNA.
      This mimicry allows it to block DNA binding by type I DNA restriction enzymes and to inhibit
      these enzymes. We have determined that multiple ocr dimers can bind stoichiometrically to the
      archetypal type I enzyme, EcoKI. One dimer binds to the core methyltransferase and two to the
      complete bifunctional restriction and modification enzyme. Ocr can also bind to the component
      subunits of EcoKI. Binding affinity to the methyltransferase core is extremely strong with a
      large favourable enthalpy change and an unfavourable entropy change. This strong interaction
      prevents the dissociation of the methyltransferase which occurs upon dilution of the enzyme.
      This stabilisation arises because the interaction appears to involve virtually the entire
      surface area of ocr and leads to the enzyme completely wrapping around ocr.
AU  - Atanasiu C
AU  - Su T-J
AU  - Sturrock SS
AU  - Dryden DTF
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2002 30: 3936-3944.

PMID- 2243794
VI  - 18
DP  - 1990
TI  - Complete nucleotide sequence of the PvuII restriction enzyme gene from Proteus vulgaris.
PG  - 6434
AB  - None
AU  - Athanasiadis A
AU  - Gregoriu M
AU  - Thanos D
AU  - Kokkinidis M
AU  - Papamatheakis J
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 6434.

PMID- 1748988
VI  - 222
DP  - 1991
TI  - Purification, crystallization and preliminary X-ray diffraction studies of the PvuII endonuclease.
PG  - 451-453
AB  - The PvuII endonuclease (PvuIIR) is a restriction enzyme from a type II
      restriction-modification system of Proteus vulgaris coded on plasmid pPvu1.
      The protein recognizes the DNA sequence 5' CAG'CTG 3' and shows no sequence
      homology to other restriction enzymes.  This makes PvuIIR an interesting
      subject for structural determination.  A purification procedure was developed
      that yields milligram quantitites of the PvuIIR from plasmids expressed in the
      Escherichia coli strain HB101.  The protein was crystallized using ammonium
      sulphate as precipitant.  The crystals are orthorhombic, space group P2(1)2(1)2
      with cell dimensions: a=84.2 Angstrom, b=106.2 Angstrom, c=46.9 Angstrom.  The
      asymmetric unit contains one PvuIIR dimer.  Diffraction extends to 2.3
      Angstrom, so the crystals may permit structural determination at atomic
      resolution.
AU  - Athanasiadis A
AU  - Kokkinidis M
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1991 222: 451-453.

PMID- 15299919
VI  - 53
DP  - 1997
TI  - Purification, crystallization and preliminary x-ray analysis of the M.BseCI DNA methyltransferase from Bacillus stearothermophilus.
PG  - 477-479
AB  - The DNA methyltransferase M.BseCI from B. stearothermophilus methylates the N6 atom of the 3'
      adenine in the sequence 5'-ATCGAT-3'.  The 579-residue protein has been isolated and
      crystallized using seeding and microdialysis techniques.  The crystals are monoclinic, space
      group P21 with cell dimensions a=53.7, b=85.7, c=151.8A and b=95.1o, two molecules in the
      asymmetric unit and diffract to at least 2.5A resolution.
AU  - Athanasiadis A
AU  - Papanikolau Y
AU  - Rina M
AU  - Papadovasilaki M
AU  - Dauter Z
AU  - Petratos K
AU  - Bouriotis V
AU  - Kokkindis M
PT  - Journal Article
TA  - Acta Crystallogr. D Biol. Crystallogr.
JT  - Acta Crystallogr. D Biol. Crystallogr.
SO  - Acta Crystallogr. D Biol. Crystallogr. 1997 53: 477-479.

PMID- 7664066
VI  - 1
DP  - 1994
TI  - Crystal structure of PvuII endonuclease reveals extensive structural homologies to EcoRV.
PG  - 469-475
AB  - The crystal structure of the dimeric PvuII restriction endonuclease (R.PvuII) has been
      determined at a resolution of 2.4 angstroms. The protein has a mixed a/b architecture and
      consists of two subdomains. Despite a lack of sequence homology, extensive structural
      similarities exist between one R.PvuII subdomain and the DNA-binding subdomain of EcoRV
      endonuclease (R.EcoRV); the dimerization subdomains are unrelated. Within the similar domains,
      flexible segments of R.PvuII are topologically equivalent to the DNA-binding turns of R.EcoRV;
      potential catalytic residues can be deduced from the structural similarities to R.EcoRV.
      Conformational flexibility is important for the interaction with DNA. A possible
      classification of endonuclease structures on the basis of the positions of the scissile
      phosphates is discussed.
AU  - Athanasiadis A
AU  - Vlassi M
AU  - Kotsifaki D
AU  - Tucker PA
AU  - Wilson KS
AU  - Kokkinidis M
PT  - Journal Article
TA  - Nat. Struct. Biol.
JT  - Nat. Struct. Biol.
SO  - Nat. Struct. Biol. 1994 1: 469-475.

PMID- 26272574
VI  - 3
DP  - 2015
TI  - High-Quality Draft Genome Sequence of Francisella tularensis subsp. holarctica Strain OR96-0246.
PG  - e00898-15
AB  - The bacterial pathogen Francisella tularensis was recently renewed as a tier-one  select
      agent. F. tularensis subsp. tularensis (type A) and holarctica (type B)
      are of clinical relevance. Here, we report the complete genome of a virulent F.
      tularensis type B strain and describe its usefulness in comparative genomics.
AU  - Atkins LM
AU  - Holder ME
AU  - Ajami NJ
AU  - Metcalf GA
AU  - Weissenberger GM
AU  - Wang M
AU  - Vee V
AU  - Han Y
AU  - Muzny DM
AU  - Gibbs RA
AU  - Petrosino JF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00898-15.

PMID- 
VI  - 14
DP  - 2016
TI  - SMRT-seq reveals an epigenetic switch.
PG  - 546
AB  - Streptococcus pneumonia uses genetic diversification as a strategy to achieve phenotypic
      plasticity.  For example, DNA inversion of the hsdS genes of type I restriction-modification
      systems determines whether S. pneumonia forms opaque or transparent colonies, which have
      different colonization and virulence characteristics.  Zhang and colleagues now use
      single-molecule, real-time sequencing to show the allelic variation of hsdS that results from
      site-specific recombination forms part of an epigenetic switch.
AU  - Attar N
PT  - Journal Article
TA  - Nat. Rev. Microbiol.
JT  - Nat. Rev. Microbiol.
SO  - Nat. Rev. Microbiol. 2016 14: 546.

PMID- 25395643
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Bacillus alcalophilus AV1934, a Classic Alkaliphile Isolated from Human Feces in 1934.
PG  - e01175-14
AB  - Bacillus alcalophilus AV1934, isolated from human feces, was described in 1934 before
      microbiome studies and recent indications of novel potassium ion coupling
      to motility in this extremophile. Here, we report draft sequences that will
      facilitate an examination of whether that coupling is part of a larger cycle of
      potassium ion-coupled transporters.
AU  - Attie O
AU  - Jayaprakash A
AU  - Shah H
AU  - Paulsen IT
AU  - Morino M
AU  - Takahashi Y
AU  - Narumi I
AU  - Sachidanandam R
AU  - Satoh K
AU  - Ito M
AU  - Krulwich TA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01175-14.

PMID- 
VI  - 48
DP  - 2008
TI  - Analysis of the Methanobrevibacter ruminantium draft genome: understanding methanogen biology to inhibit their action in the rumen.
PG  - 83-88
AB  - Methane is produced in the foregut (rumen) of ruminants by methanogens, which act as terminal
      reducers of carbon in the rumen system. The
      multistep methanogenesis pathway is well elucidated, mainly from the
      study of non-rumen methanogens, but the adaptations that allow
      methanogens to grow and persist in the rumen are not well understood.
      The Pastoral Greenhouse Gas Research Consortium is sequencing the
      genome of Methanobrevibacter ruminantium, a prominent methanogen in New
      Zealand ruminants, as part of a project to mitigate greenhouse gases.
      The genome is similar to 3.0Mb in size with a guanine-cytosine (GC)
      content of 33.68%. All of the components of the methanogenesis pathway
      have been identified and comparison of these gene sequences with those
      from Methanothermobacter thermoautotrophicus and Methanosphaera
      stadtmanae indicates that methanogenesis gene organisation is conserved
      within the Methanobacteriales. The genome of M. ruminantium contains a
      prophage sequence (designated phi mru) with distinct functional modules
      encoding phage integration, DNA replication and packaging, capsid
      proteins and lysis functions. A low GC region found at the distal end
      of the phage sequence harbours a putative DNA restriction/modification
      system which might provide additional protection against foreign DNA.
      The genome also contains many large surface proteins with
      characteristics that indicate that they may mediate association with
      other rumen microbes. Approximately half of the genes identified within
      the genome have no known function. Determining the function of these
      new genes will assist in de. ning the role of M. ruminantium in methane
      formation in the rumen and help identify means to control methane
      emissions from ruminant animals.
AU  - Attwood GT
AU  - Kelly WJ
AU  - Altermann EH
AU  - Leahy SC
PT  - Journal Article
TA  - Aust. J. Exp. Agr.
JT  - Aust. J. Exp. Agr.
SO  - Aust. J. Exp. Agr. 2008 48: 83-88.

PMID- 21515811
VI  - 28
DP  - 2011
TI  - Diversification of Wolbachia endosymbiont in the Culex pipiens mosquito.
PG  - 2761-2772
AB  - The alpha-proteobacteria Wolbachia are among the most common intracellular bacteria and have
      recently emerged as important drivers of arthropod biology. Wolbachia commonly act as
      reproductive parasites in arthropods by inducing cytoplasmic incompatibility (CI), a type of
      conditional sterility between hosts harboring incompatible infections. In this study, we
      examined the evolutionary histories of Wolbachia infections, known as wPip, in the common
      house mosquito Culex pipiens, which exhibits the greatest variation in CI crossing patterns
      observed in any insect. We first investigated a panel of twenty wPip strains for their genetic
      diversity through a multi-locus scheme combining thirteen Wolbachia genes. Because Wolbachia
      depend primarily on maternal transmission for spreading within arthropod populations, we also
      studied the variability in the co-inherited Cx. pipiens mitochondria. In total, we identified
      fourteen wPip haplotypes, which all share a monophyletic origin and clearly cluster into five
      distinct wPip groups. The diversity of Cx. pipiens mitochondria was extremely reduced, which
      is likely a consequence of cytoplasmic hitchhiking driven by a unique and recent Wolbachia
      invasion. Phylogenetic evidence indicates that wPip infections and mitochondrial DNA have
      co-diverged through stable co-transmission within the cytoplasm and shows that a rapid
      diversification of wPip has occurred. The observed pattern demonstrates that a considerable
      degree of Wolbachia diversity can evolve within a single host species over short evolutionary
      periods. In addition, multiple signatures of recombination were found in most wPip genomic
      regions, leading us to conclude that the mosaic nature of wPip genomes may play a key role in
      their evolution.
AU  - Atyame CM
AU  - Delsuc F
AU  - Pasteur N
AU  - Weill M
AU  - Duron O
PT  - Journal Article
TA  - Mol. Biol. Evol.
JT  - Mol. Biol. Evol.
SO  - Mol. Biol. Evol. 2011 28: 2761-2772.

PMID- 21114563
VI  - 20
DP  - 2011
TI  - Multiple Wolbachia determinants control the evolution of cytoplasmic incompatibilities in Culex pipiens mosquito populations.
PG  - 286-298
AB  - Wolbachia are maternally inherited endosymbionts that can invade arthropod
      populations through manipulation of their reproduction. In mosquitoes,
      Wolbachia induce embryonic death, known as cytoplasmic incompatibility
      (CI), whenever infected males mate with females either uninfected or
      infected with an incompatible strain. Although genetic determinants of CI
      are unknown, a functional model involving the so-called mod and resc
      factors has been proposed. Natural populations of Culex pipiens mosquito
      display a complex CI relationship pattern associated with the highest
      Wolbachia (wPip) genetic polymorphism reported so far. We show here that
      C. pipiens populations from La Reunion, a geographically isolated island
      in the southwest of the Indian Ocean, are infected with genetically
      closely related wPip strains. Crossing experiments reveal that these
      Wolbachia are all mutually compatible. However, crosses with genetically
      more distant wPip strains indicate that Wolbachia strains from La Reunion
      belong to at least five distinct incompatibility groups (or crossing
      types). These incompatibility properties which are strictly independent
      from the nuclear background, formally establish that in C. pipiens, CI is
      controlled by several Wolbachia mod/resc factors.
AU  - Atyame CM
AU  - Duron O
AU  - Tortosa P
AU  - Pasteur N
AU  - Fort P
AU  - Weill M
PT  - Journal Article
TA  - Mol. Ecol.
JT  - Mol. Ecol.
SO  - Mol. Ecol. 2011 20: 286-298.

PMID- 9541562
VI  - 36
DP  - 1998
TI  - Evidence of a restriction/modification system in Lactobacillus delbrueckii subsp. lactis CNRZ 326.
PG  - 271-273
AB  - Lactobacillus delbrueckii subsp. lactis (Lb. lactis) CNRZ 326 is widely used in the
      propagation of Lb. delbrueckii bacteriophages.  In this study, evidence is presented that this
      strain possesses a restriction-modification system. The mitomycin C-induced temperate
      bacteriophage lb539 has a reduced efficiency of plaquing (EOP) on CNRZ 326 cells (EOP=10^-3),
      but after several passages on this strain, or on the indicator strain Lb. lactis LKT, the
      recovered phages (phages lb539.326 and lb539.LKT) have an EOP equal to 1.  Restrictive
      development on CNRZ 326 was also observed after phage lb539.326 was propagated on the strain
      Lb. lactis CRL 934.  The R/M system was also active against the virulent Lb. delbrueckii phage
      ll-h.  Plasmid DNA was not detected in CNRZ 326, which suggests that the R/M system described
      is chromosomally encoded.
AU  - Auad L
AU  - Peril MAA
AU  - de Ruiz Holgado AAP
AU  - Raya RR
PT  - Journal Article
TA  - Curr. Microbiol.
JT  - Curr. Microbiol.
SO  - Curr. Microbiol. 1998 36: 271-273.

PMID- 2146591
VI  - 18
DP  - 1990
TI  - Purification and characterization of an isoschizomer of SphI from Bacillus circulans.
PG  - 6152
AB  - None
AU  - Aubert E
AU  - Spurgeon S
AU  - Ray W
AU  - Davies J
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 6152.

PMID- 27516511
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Highly Rifampin-Resistant Propionibacterium namnetense NTS 31307302T Isolated from a Patient with a Bone Infection.
PG  - e00819-16
AB  - Propionibacterium namnetense was recently described as a potential bone pathogen, which is
      closely related to Propionibacterium acnes, a skin commensal
      microorganism. Here, we report the draft genome sequence of the highly
      rifampin-resistant strain NTS 31307302(T) isolated from a patient with a tibia
      infection.
AU  - Aubin GG
AU  - Kambarev S
AU  - Bemer P
AU  - Lawson PA
AU  - Corvec S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00819-16.

PMID- 28126936
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of an Erythromycin-Resistant Propionibacterium acnes Isolate Recovered from Folliculitis of the Scalp.
PG  - e01490-16
AB  - Propionibacterium acnes is now well-known and recognized for its implication in the
      pathogenesis of acne vulgaris. Here, we report the draft genome sequence of
      an erythromycin-resistant P. acnes strain isolated from a case of folliculitis of
      the scalp belonging to phylotype IA1 and sequence type 18 (ST18).
AU  - Aubin GG
AU  - Kambarev S
AU  - Guillouzouic A
AU  - Khammari A
AU  - Dreno B
AU  - Corvec S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01490-16.

PMID- 27979946
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Four Propionibacterium acnes Strains Isolated from Implant-Related Infections.
PG  - e01395-16
AB  - Propionibacterium acnes was previously described as a potential implant-related pathogen.
      Here, we report the draft genome sequence of four P. acnes strains,
      isolated from spine material, hip arthroplasty, and knee arthroplasty infections
      in France belonging to different sequence types (ST18, ST27, and ST36).
AU  - Aubin GG
AU  - Kambarev S
AU  - Guillouzouic A
AU  - Lepelletier D
AU  - Bemer P
AU  - Corvec S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01395-16.

PMID- 
VI  - 217
DP  - 1999
TI  - Exploring the N-terminal function of murine methyltransferase.
PG  - 453
AB  - The mammalian DNA methyltransferase methylates specific cytosine residues on the host genome.
      DNA methylation is essential for development, gene regulation, and aberrant DNA methylation
      leads to tumorgenesis.  We are using a highly homogeneous preparation of the murine DCMTase to
      gain basic insights into its function, and the design of novel anti-cancer strategies.
      DCMTase contains a large, poorly characterized N-terminal domain not found in bacterial
      enzymes that have similar functions.  This domain binds zinc with characteristics of a zinc
      finger.  We have probed the affect of zinc binding on numerous aspects of DCMTase functions.
      Methylation spreading, activation by adjacent 5-methylcytosine residues with single stranded
      DNA as a substrate, is one of these functions, and is of particular interest.  This activation
      may lead to the process of "methylation spreading" and our approach will determine if the zinc
      plays a role in this regulation of enzyme function.
AU  - Aubol BE
AU  - Reich NO
PT  - Journal Article
TA  - ACS Abstracts
JT  - ACS Abstracts
SO  - ACS Abstracts 1999 217: 453.

PMID- 14511672
VI  - 310
DP  - 2003
TI  - Murine DNA cytosine C5-methyltransferase: in vitro studies of de novo methylation spreading.
PG  - 209-214
AB  - The preference of murine DNA (cytosine-5)-methyltransferase (Dnmt1) for single stranded DNA
      substrates is increased up to 50-fold by the presence
      of a proximal 5-methyl cytosine (5(me)C). This modulation is
      distance-dependent and is due to an enhanced binding affinity and minor
      changes in catalytic efficiency. No modulation was observed with double
      stranded DNA. Modulation requires that the 5(me)C moiety be attached to
      the DNA strand containing the CpG methylation target. Our results support
      a model in which 5(me)C binding by the enzyme occurs to at least one site
      outside the region involved in CpG recognition. No modulation in response
      to 5(me)C is observed with the bacterial enzyme M.SssI, which lacks the
      large N-terminal regulatory domain found in Dnmt1. We suggest that this
      allosteric modulation involves the N-terminal domain of Dnmt1.
AU  - Aubol BE
AU  - Reich NO
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 2003 310: 209-214.

PMID- 27013036
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Turicibacter sp. Strain H121, Isolated from the Feces of a Contaminated Germ-Free Mouse.
PG  - e00114-16
AB  - Turicibacterbacteria are commonly detected in the gastrointestinal tracts and feces of humans
      and animals, but their phylogeny, ecological role, and pathogenic
      potential remain unclear. We present here the first complete genome sequence
      ofTuricibactersp. strain H121, which was isolated from the feces of a mouse line
      contaminated following germ-free derivation.
AU  - Auchtung TA
AU  - Holder ME
AU  - Gesell JR
AU  - Ajami NJ
AU  - Duarte RT
AU  - Itoh K
AU  - Caspi RR
AU  - Petrosino JF
AU  - Horai R
AU  - Zarate-Blades CR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00114-16.

PMID- 21745361
VI  - 11
DP  - 2011
TI  - The genome sequence of Brucella pinnipedialis B2/94 sheds light on the evolutionary history of the genus Brucella.
PG  - 200
AB  - ABSTRACT: BACKGROUND: Since the discovery of the Malta fever agent,
      Brucella melitensis, in the 19th century, six terrestrial
      mammal-associated Brucella species were recognized over the next century.
      More recently the number of novel Brucella species has increased and among
      them, isolation of species B. pinnipedialis and B. ceti from marine
      mammals raised many questions about their origin as well as on the
      evolutionary history of the whole genus. RESULTS: We report here on the
      first complete genome sequence of a Brucella strain isolated from marine
      mammals, Brucella pinnipedialis strain B2/94. A whole gene-based
      phylogenetic analysis shows that five main groups of host-associated
      Brucella species rapidly diverged from a likely free-living ancestor close
      to the recently isolated B. microti. However, this tree lacks the
      resolution required to resolve the order of divergence of those groups.
      Comparative analyses focusing on a) genome segments unshared between B.
      microti and B. pinnipedialis, b) gene deletion/fusion events and c)
      positions and numbers of Brucella specific IS711 elements in the available
      Brucella genomes provided enough information to propose a branching order
      for those five groups. CONCLUSIONS: In this study, it appears that the
      closest relatives of marine mammal Brucella sp. are B. ovis and Brucella
      sp. NVSL 07-0026 isolated from a baboon, followed by B. melitensis and B.
      abortus strains, and finally the group consisting of B. suis strains,
      including B. canis and the group consisting of the single B. neotomae
      species. We were not able, however, to resolve the order of divergence of
      the two latter groups.
AU  - Audic S
AU  - Lescot M
AU  - Claverie JM
AU  - Cloeckaert A
AU  - Zygmunt MS
PT  - Journal Article
TA  - BMC Evol. Biol.
JT  - BMC Evol. Biol.
SO  - BMC Evol. Biol. 2011 11: 200.

PMID- 19653890
VI  - 10
DP  - 2009
TI  - Brucella microti: the genome sequence of an emerging pathogen.
PG  - 352
AB  - ABSTRACT: BACKGROUND: Using a combination of pyrosequencing and
      conventional Sanger sequencing, the complete genome sequence of the
      recently described novel Brucella species, Brucella microti, was
      determined. B. microti is a member of the genus Brucella within the
      Alphaproteobacteria, which consists of medically important highly
      pathogenic facultative intracellular bacteria. In contrast to all other
      Brucella species, B. microti is a fast growing and biochemically very
      active microorganism with a phenotype more similar to that of
      Ochrobactrum, a facultative human pathogen. The atypical phenotype of B.
      microti prompted us to look for genomic differences compared to other
      Brucella species and to look for similarities with Ochrobactrum. RESULTS:
      The genome is composed of two circular chromosomes of 2,117,050 and
      1,220,319 base pairs. Unexpectedly, we found that the genome sequence of
      B. microti is almost identical to that of Brucella suis 1330 with an
      overall sequence identity of 99.84% in aligned regions. The most
      significant structural difference between the two genomes is a
      bacteriophage-related 11,742 base pairs insert only present in B. microti.
      However, this insert is unlikely to have any phenotypical consequence.
      Only four protein coding genes are shared between B. microti and
      Ochrobactrum anthropi but impaired in other sequenced Brucella. The most
      noticeable difference between B. microti and other Brucella species was
      found in the sequence of the 23S ribosomal RNA gene. This unusual
      variation could have pleiotropic effects and explain the fast growth of B.
      microti. CONCLUSIONS: Contrary to expectations from the phenotypic
      analysis, the genome sequence of B. microti is highly similar to that of
      known Brucella species, and is remotely related to the one of O. anthropi.
      How the few differences in gene content between B. microti and B. suis
      1330 could result in vastly different phenotypes remains to be elucidated.
      This unexpected finding will complicate the task of identifying virulence
      determinants in the Brucella genus. The genome sequence of B. microti will
      serve as a model for differential expression analysis and complementation
      studies. Our results also raise some concerns about the importance given
      to phenotypical traits in the definition of bacterial species.
AU  - Audic S
AU  - Lescot M
AU  - Claverie JM
AU  - Scholz HC
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2009 10: 352.

PMID- 30533893
VI  - 7
DP  - 2018
TI  - Draft Genome Sequences of Lactobacillus salivarius A3iob and Lactobacillus johnsonii CRL1647, Novel Potential Probiotic Strains for Honeybees (Apis  mellifera L.).
PG  - e00975-18
AB  - This report describes the draft genome sequences of Lactobacillus salivarius A3iob and
      Lactobacillus johnsonii CRL1647, probiotic strains isolated from the
      gut of honeybee Apis mellifera workers. The reads were generated by a
      whole-genome sequencing (WGS) strategy on an Illumina MiSeq sequencer and were
      assembled into contigs with total sizes of 2,054,490 and 2,137,413 bp for the
      A3iob and CRL1647 strains, respectively. The draft genome sequences of L.
      salivarius A3iob and L. johnsonii CRL1647 will be useful for further studies of
      the specific genetic features of these strains and for understanding the
      mechanisms of their probiotic properties.
AU  - Audisio MC
AU  - Albarracin L
AU  - Torres MJ
AU  - Saavedra L
AU  - Hebert EM
AU  - Villena J
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e00975-18.

PMID- 6319759
VI  - 49
DP  - 1984
TI  - Evidence that Escherichia coli virus T1 induces a DNA methyltransferase.
PG  - 588-590
AB  - DNA of Escherichia coli virus T1 is resistant to MboI cleavage and appears
      to be heavily methylated.  Analysis of methylation by the isoschizomeric restriction
      enzymes Sau3AI and DpnI revealed that recognition sites for E. coli DNA adenine
      methylase (dam methylase) are methylated.  The same methylation pattern was found for
      virus T1 DNA grown on an E. coli dam host, indicating a T1-specific DNA
      methyltransferase.
AU  - Auer B
AU  - Schweiger M
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1984 49: 588-590.

PMID- 28983004
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Enterohemorrhagic Escherichia coli O157:H7 Strain MC2 Isolated from Cattle in France.
PG  - e01097-17
AB  - Enterohemorrhagic Escherichia coli (EHEC) with serotype O157:H7 is a major foodborne pathogen.
      Here, we report the draft genome sequence of EHEC O157:H7
      strain MC2 isolated from cattle in France. The assembly contains 5,400,376 bp
      that encoded 5,914 predicted genes (5,805 protein-encoding genes and 109 RNA
      genes).
AU  - Auffret P
AU  - Segura A
AU  - Bertin Y
AU  - Klopp C
AU  - Bouchez O
AU  - Kerouredan M
AU  - Bibbal D
AU  - Brugere H
AU  - Forano E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01097-17.

PMID- 29650572
VI  - 6
DP  - 2018
TI  - Draft Whole-Genome Sequence of the Fluorene-Degrading Sphingobium sp. Strain LB126, Isolated from Polycyclic Aromatic Hydrocarbon-Contaminated Soil.
PG  - e00249-18
AB  - We report here the draft whole-genome sequence of a fluorene-degrading bacterium, Sphingobium
      sp. strain LB126. The genes involved in the upper biodegradation
      pathway of fluorene are located on a plasmid, and the lower pathway that
      generates tricarboxylic acid cycle intermediates is initiated by the
      meta-cleavage of protocatechuic acid that is chromosomally encoded.
AU  - Augelletti F
AU  - Tremblay J
AU  - Agathos SN
AU  - Stenuit B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00249-18.

PMID- 22374959
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of the Highly Hemolytic Strain Bacillus cereus F837/76.
PG  - 1630
AB  - Highly hemolytic strain Bacillus cereus F837/76 was isolated in 1976 from a contaminated
      prostate wound. The complete nucleotide sequence of this strain
      reported here counts nearly 36,500 single-nucleotide differences from the closest
      sequenced strain, Bacillus thuringiensis Al Hakam. F827/76 also contains a 10-kb
      plasmid that was not detected in the Al Hakam strain.
AU  - Auger S
AU  - Galleron N
AU  - Segurens B
AU  - Dossat C
AU  - Bolotin A
AU  - Wincker P
AU  - Sorokin A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1630.

PMID- 29563531
VI  - 8
DP  - 2018
TI  - Virulence factors of Moraxella catarrhalis outer membrane vesicles are major targets for cross-reactive antibodies and have adapted during evolution.
PG  - 4955
AB  - Moraxella catarrhalis is a common human respiratory tract pathogen. Its virulence
      factors associated with whole bacteria or outer membrane vesicles (OMVs) aid
      infection, colonization and may induce specific antibodies. To investigate
      pathogen-host interactions, we applied integrated bioinformatic and
      immunoproteomic (2D-electrophoresis, immunoblotting, LC-MS/MS) approaches. We
      showed that OMV proteins engaged exclusively in complement evasion and
      colonization strategies, but not those involved in iron transport and metabolism,
      are major targets for cross-reacting antibodies produced against phylogenetically
      divergent M. catarrhalis strains. The analysis of 31 complete genomes of M.
      catarrhalis and other Moraxella revealed that OMV protein-coding genes belong to
      64 orthologous groups, five of which are restricted to M. catarrhalis. This
      species showed a two-fold increase in the number of OMV protein-coding genes
      relative to its ancestors and animal-pathogenic Moraxella. The appearance of
      specific OMV factors and the increase in OMV-associated virulence proteins during
      M. catarrhalis evolution is an interesting example of pathogen adaptation to
      optimize colonization. This precisely targeted cross-reactive immunity against M.
      catarrhalis may be an important strategy of host defences to counteract this
      phenomenon. We demonstrate that cross-reactivity is closely associated with the
      anti-virulent antibody repertoire which we have linked with adaptation of this
      pathogen to the host.
AU  - Augustyniak D
AU  - Seredynski R
AU  - McClean S
AU  - Roszkowiak J
AU  - Roszniowski B
AU  - Smith DL
AU  - Drulis-Kawa Z
AU  - Mackiewicz P
PT  - Journal Article
TA  - Sci. Rep.
JT  - Sci. Rep.
SO  - Sci. Rep. 2018 8: 4955.

PMID- 27789629
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Two Drug-Resistant Mycobacterium tuberculosis Isolates  from Myanmar.
PG  - e00850-16
AB  - Multidrug-resistant tuberculosis (MDR-TB) and lately, extensively drug-resistant  TB (XDR-TB)
      are increasing global health concerns. Here, we present the genome
      sequences of two MDR-TB isolates from Myanmar, one of 27 countries with a high
      MDR-TB burden, and describe a number of mutations consistent with these being
      XDR-TB isolates.
AU  - Aung HL
AU  - Tun T
AU  - Permina E
AU  - Nyunt WW
AU  - Aung ST
AU  - Thinn KK
AU  - Crump JA
AU  - Cook GM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00850-16.

PMID- 28596405
VI  - 5
DP  - 2017
TI  - Genome Sequence of Paracoccus contaminans LMG 29738T, Isolated from a Water Microcosm.
PG  - e00487-17
AB  - We announce here the complete genome sequence of Paracoccus contaminans LMG 29738T, which we
      recently isolated from a contaminated water microcosm. The
      genome consists of a 2.94-Mb chromosome and a 94-kb plasmid. To our knowledge, we
      provide the first DNA methylation analysis of a Paracoccus species.
AU  - Aurass P
AU  - Karste S
AU  - Trost E
AU  - Glaeser SP
AU  - Kampfer P
AU  - Flieger A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00487-17.

PMID- 29724850
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Escherichia coli AS19, an Antibiotic-Sensitive Variant of E. coli Strain B REL606.
PG  - e00385-18
AB  - The chemically mutagenized Escherichia coli strain AS19 was isolated on the basis of its
      enhanced sensitivity to different antibiotics, in particular to
      actinomycin. The strain was later modified to study rRNA modifications that
      confer antibiotic resistance. Here, we present the genome sequence of the variant
      E. coli AS19-RrmA().
AU  - Avalos M
AU  - Boetzer M
AU  - Pirovano W
AU  - Arenas NE
AU  - Douthwaite S
AU  - van Wezel GP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00385-18.

PMID- 21515762
VI  - 193
DP  - 2011
TI  - Genomes of the two chronological isolates (Helicobacter pylori 2017 and 2018) of the West African Helicobacter pylori strain 908, obtained from a  single patient.
PG  - 3385-3386
AB  - The diverse clinical outcomes of colonization by Helicobacter pylori reflect need to
      understand genomic rearrangements enabling the bacterium
      to adapt to host niches and exhibit varied colonization/virulence
      potential. We describe genome sequences of the two serial isolates, H.
      pylori 2017 and 2018 (the chronological sub-clones of H. pylori 908),
      cultured in 2003 from corpus and antrum, respectively, of an African
      patient who suffered from recrudescent duodenal ulcer disease. The genome
      sequences when compared with the genome of parent strain, HP 908 (isolated
      from antrum of the same patient in 1994) revealed genomic alterations
      relevant in virulence optimization or host-specific adaptation.
AU  - Avasthi TS
AU  - Devi SH
AU  - Taylor TD
AU  - Kumar N
AU  - Baddam R
AU  - Kondo S
AU  - Suzuki Y
AU  - Lamouliatte H
AU  - Megraud F
AU  - Ahmed N
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3385-3386.

PMID- 21685291
VI  - 193
DP  - 2011
TI  - Genome of Multidrug-Resistant Uropathogenic Escherichia coli Strain NA114 from India.
PG  - 4272-4273
AB  - Uropathogenic Escherichia coli (UPEC) causes serious infections in people at risk and has a
      significant environmental prevalence due to
      contamination by human and animal excreta. In developing countries, UPEC
      assumes importance in certain dwellings because of poor community/personal
      hygiene and exposure to contaminated water or soil. We report the complete
      genome sequence of E. coli strain NA114 from India, a UPEC strain with a
      multidrug resistance phenotype and the capacity to produce
      extended-spectrum beta-lactamase. The genome sequence and comparative
      genomics emanating from it will be significant in under-standing the
      genetic makeup of diverse UPEC strains and in boosting the development of
      new diagnostics/vaccines.
AU  - Avasthi TS
AU  - Kumar N
AU  - Baddam R
AU  - Hussain A
AU  - Nandanwar N
AU  - Jadhav S
AU  - Ahmed N
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4272-4273.

PMID- 28000419
VI  - 19
DP  - 2017
TI  - Genomic and physiological analyses of 'Reinekea forsetii' reveal a versatile opportunistic lifestyle during spring algae blooms.
PG  - 1209-1221
AB  - Gammaproteobacterial Reinekea spp. were detected during North Sea spring algae
      blooms in the years 2009-2012, with relative abundances of up to 16% in the
      bacterioplankton. Here, we explore the ecophysiology of 'R. forsetii' strain
      Hel1_31_D35 that was isolated during the 2010 spring bloom using (i) its manually
      annotated, high-quality closed genome, (ii) re-analysis of in situ data from the
      2009-2012 blooms and (iii) physiological tests. High resolution analysis of 16S
      rRNA gene sequences suggested that 'R. forsetii' dominated Reinekea populations
      during these blooms. This was corroborated by retrieval of almost complete
      Hel1_31_D35 genomes from 2009 and 2010 bacterioplankton metagenomes. Strain
      Hel1_31_D35 can use numerous low-molecular weight substrates including diverse
      sugar monomers, and few but relevant algal polysaccharides such as mannan,
      alpha-glucans, and likely bacterial peptidoglycan. It oxidizes thiosulfate to
      sulfate, and ferments under anoxic conditions. The strain can attach to algae and
      thrives at low phosphate concentrations as they occur during blooms. Its genome
      encodes RTX toxin and secretion proteins, and in cultivation experiments
      Hel1_31_D35 crude cell extracts inhibited growth of a North Sea Polaribacter
      strain. Our data suggest that the combination of these traits make strain
      Hel1_31_D35 a versatile opportunist that is particularly competitive during
      spring phytoplankton blooms.
AU  - Avci B
AU  - Hahnke RL
AU  - Chafee M
AU  - Fischer T
AU  - Gruber-Vodicka H
AU  - Tegetmeyer HE
AU  - Harder J
AU  - Fuchs BM
AU  - Amann RI
AU  - Teeling H
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2017 19: 1209-1221.

PMID- 26586875
VI  - 3
DP  - 2015
TI  - Genome Sequence of Streptococcus phocae subsp. phocae Strain ATCC 51973T Isolated from a Harbor Seal (Phoca vitulina).
PG  - e01307-15
AB  - Streptococcus phocae subsp. phocae is a pathogen that affects different pinniped  and
      mammalian species. This announcement reports the genome sequence of the type
      strain ATCC 51973 isolated in Norway from clinical specimens of harbor seal
      (Phoca vitulina), revealing interesting genes related to possible virulence
      factors.
AU  - Avendano-Herrera R
AU  - Poblete-Morales M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01307-15.

PMID- 25502668
VI  - 2
DP  - 2014
TI  - Genome Sequence of Streptococcus phocae subsp. salmonis Strain C-4T, Isolated from Atlantic Salmon (Salmo salar).
PG  - e01269-14
AB  - Streptococcus phocae subsp. salmonis is a fish pathogen that has an important impact on the
      Chilean salmon industry. Here, we report the genome sequence of the
      type strain C-4(T) isolated from Atlantic salmon (Salmo salar), showing a number
      of interesting features and genes related to its possible virulence factors.
AU  - Avendano-Herrera R
AU  - Suarez R
AU  - Lazo E
AU  - Bravo D
AU  - Llegues KO
AU  - Romalde JL
AU  - Godoy MG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01269-14.

PMID- 25301658
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Paenibacillus sp. Strain MSt1 with Broad Antimicrobial Activity, Isolated from Malaysian Tropical Peat Swamp Soil.
PG  - e01024-14
AB  - We report the draft genome sequence of Paenibacillus sp. strain MSt1, which has broad-range
      antimicrobial activity, isolated from tropical peat swamp soil. Genes
      involved in antimicrobial biosynthesis are found to be present in this genome.
AU  - Aw YK
AU  - Ong KS
AU  - Yule CM
AU  - Gan HM
AU  - Lee SM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01024-14.

PMID- 22493200
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Naturally Plasmid-Free Lactobacillus plantarum Strain NC8  (CCUG 61730).
PG  - 2391-2392
AB  - Lactobacillus plantarum is a highly versatile lactic acid bacterium found in various
      ecological niches, such as fermented vegetable, meat, and dairy products
      and the gastrointestinal tract. We sequenced the genome of L. plantarum NC8, a
      naturally plasmid-free strain, which has been used as a model strain in many
      laboratories worldwide.
AU  - Axelsson L
AU  - Rud I
AU  - Naterstad K
AU  - Blom H
AU  - Renckens B
AU  - Boekhorst J
AU  - Kleerebezem M
AU  - van Hijum S
AU  - Siezen RJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2391-2392.

PMID- 28450500
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Streptomyces sp. Strain IB2014011-1, Isolated from Trichoptera sp. Larvae of Lake Baikal.
PG  - e00062-17
AB  - Unique ecosystems with specific environmental conditions have been proven to be a promising
      source for isolation of new actinobacterial strains. Ancient Lake
      Baikal is one of the greatest examples of an ecosystem with high species
      biodiversity and endemicity caused by long-lasting isolated evolution and stable
      environmental conditions. Herein we report the draft genome sequence of
      Streptomyces sp. strain IB2014011-1, which was isolated from insect Trichoptera
      sp. larvae collected at the bottom of Lake Baikal.
AU  - Axenov-Gribanov DV
AU  - Tokovenko BT
AU  - Rebets YV
AU  - Voytsekhovskaya IV
AU  - Shatilina ZM
AU  - Protasov ES
AU  - Luzhetskyy AN
AU  - Timofeyev MA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00062-17.

PMID- 25462918
VI  - 193
DP  - 2015
TI  - Dam methylation is required for efficient biofilm production in Salmonella enterica serovar Enteritidis.
PG  - 15-22
AB  - The ecological success of Salmonella enterica to survive in different environments is due, in
      part, to the ability to form biofilms, something which is especially important for food
      industry. The aim of the current study was to evaluate the involvement of Dam methylation in
      biofilm production in S. Enteritidis strains. The ability to generate biofilms was analyzed in
      wild type and dam mutant strains. In S. Enteritidis, the absence of Dam affected the capacity
      to develop pellicles at the air-liquid interface and reduced the ability to form biofilm on
      polystyrene surfaces.,Curli and cellulose production, determined by Congo red and calcofluor
      assays, were affected in dam mutant strains. Relative quantitative real-time PCR experiments
      showed that the expression of csgD and csgA genes is reduced in mutants lacking dam gene with
      respect to the wild type strains, whereas transcript levels of bcsA are not affected in the
      absence of Dam. To our knowledge, this is the first report on the participation of Dam
      methylation on biofilm production in Enteritidis or any other serovar of S. enterica. Results
      presented here suggest that changes in gene expression required for biofilm production are
      finely regulated by Dam methylation. Thus, Dam methylation could modulate csgD expression and
      upregulate the expression of factors related with biofilm production, including curli and
      cellulose. This study contributes to the understanding of biofilm regulation in Salmonella
      spp. and to the design of new strategies to prevent food contamination and humans and animals
      infections.
AU  - Aya-Castaneda MR
AU  - Sarnacki SH
AU  - Noto-Llana M
AU  - Lopez-Guerra AG
AU  - Giacomodonato MN
AU  - Cerquetti MC
PT  - Journal Article
TA  - Int. J. Food Microbiol.
JT  - Int. J. Food Microbiol.
SO  - Int. J. Food Microbiol. 2015 193: 15-22.

PMID- 28963206
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Lactobacillus salivarius L28 Isolated from Ground Beef.
PG  - e00955-17
AB  - In this report, we describe the draft genome sequence of a newly discovered probiotic strain,
      Lactobacillus salivarius L28. L. salivarius L28 demonstrates
      antagonistic effects against human foodborne pathogens, including Escherichia
      coli O157:H7, Salmonella spp., and Listeria monocytogenes, in coculture
      experiments and food matrices.
AU  - Ayala DI
AU  - Cook PW
AU  - Campos DL
AU  - Brashears MM
AU  - den Bakker H
AU  - Nightingale KK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00955-17.

PMID- 29622613
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Enterococcus faecium Strain J19, Isolated from Cabbage.
PG  - e00213-18
AB  - Herein, we report the draft genome sequence of a newly discovered probiotic strain,
      Enterococcus faecium J19, which was isolated from cabbage. Strain J19 has
      shown antagonistic effects against the human foodborne pathogen Listeria
      monocytogenes in coculture and in different food matrices.
AU  - Ayala DI
AU  - Cook PW
AU  - Campos DL
AU  - Franco JG
AU  - Brashears MM
AU  - den Bakker H
AU  - Nightingale KK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00213-18.

PMID- 28912308
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Epilithonimonas sp. FP211-J200, Isolated from an Outbreak Episode on a Rainbow Trout (Oncorhynchus mykiss) Farm.
PG  - e00819-17
AB  - Here, we report the draft genome sequence of Epilithonimonas sp. FP211-J200, isolated from
      rainbow trout head kidney cells. The size of the genome is
      4,110,772 bp, with a G+C content of 37.1%. The Epilithonimonas sp. FP211-J200
      genome has genes related to tetracycline and beta-lactam resistance. This is the
      first reported Epilithonimonas species genome isolated from a fish host.
AU  - Ayala M
AU  - Segovia C
AU  - Rojas R
AU  - Miranda C
AU  - Santander J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00819-17.

PMID- 28385859
VI  - 5
DP  - 2017
TI  - Genome Sequence of Mannheimia haemolytica Serotype 1 Strain 16041065 BH.
PG  - e01721-16
AB  - Here, we report the genome sequence of Mannheimia haemolytica serotype 1 strain 16041065 BH,
      which was recently isolated from a Midwestern calf that died due to
      Mannheimia haemolytica-induced pneumonia. This genome comprised a total of 2.7
      Mb, with an N50 of 122 kb, and maintained hemolytic activity when grown on blood
      heart infusion agar supplemented with 5% sheep's blood.
AU  - Ayalew S
AU  - Confer AW
AU  - Hansen RD
AU  - Couger MB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01721-16.

PMID- 28385858
VI  - 5
DP  - 2017
TI  - Genome Sequence of a Spontaneous Nonhemolytic Mutant of Mannheimia haemolytica 16041065 GH.
PG  - e01720-16
AB  - We report here the draft genome sequence of a spontaneous nonhemolytic mutant of  Mannheimia
      haemolytica 16041065 GH. This mutant arose during routine passage and
      was devoid of hemolytic activity on standard blood agars. This genome sequence
      had a total size of 2.7 Mb with an N50 of 117 kb.
AU  - Ayalew S
AU  - Confer AW
AU  - Hansen RD
AU  - Couger MB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01720-16.

PMID- 24831140
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Pseudomonas aeruginosa Strain RB, a Bacterium Capable of Synthesizing Cadmium Selenide Nanoparticles.
PG  - e00368-14
AB  - Pseudomonas aeruginosa strain RB is a bacterium capable of synthesizing cadmium selenide
      (CdSe) nanoparticles and was isolated from a soil sample. Here, we
      present the draft genome sequence of P. aeruginosa strain RB. To the best of our
      knowledge, this is the first report of a draft genome of a CdSe-synthesizing
      bacterium.
AU  - Ayano H
AU  - Kuroda M
AU  - Soda S
AU  - Ike M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00368-14.

PMID- 24435857
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Type Strain Sediminibacterium salmoneum NJ-44 and Sediminibacterium sp. Strain C3, a Novel Strain Isolated from Activated Sludge.
PG  - e01073-13
AB  - The genus Sediminibacterium comprises species present in diverse natural and engineered
      environments. Here, we report for the first time the genome sequences
      of the type strain Sediminibacterium salmoneum NJ-44 (NBRC 103935) and
      Sediminibacterium sp. strain C3 (BNM541), isolated from activated sludge, a
      valuable model for the study of substrate-dependent autoaggregation.
AU  - Ayarza JM
AU  - Figuerola EL
AU  - Erijman L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01073-13.

PMID- 23516234
VI  - 1
DP  - 2013
TI  - Complete Genome of Serratia sp. Strain FGI 94, a Strain Associated with Leaf-Cutter Ant Fungus Gardens.
PG  - e0023912
AB  - Serratia sp. strain FGI 94 was isolated from a fungus garden of the leaf-cutter ant Atta
      colombica. Analysis of its 4.86-Mbp chromosome will help advance our
      knowledge of symbiotic interactions and plant biomass degradation in this ancient
      ant-fungus mutualism.
AU  - Aylward FO et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0023912.

PMID- 23469353
VI  - 1
DP  - 2013
TI  - Complete Genome of Enterobacteriaceae Bacterium Strain FGI 57, a Strain Associated with Leaf-Cutter Ant Fungus Gardens.
PG  - e00238-12
AB  - The Enterobacteriaceae bacterium strain FGI 57 was isolated from a fungus garden  of the
      leaf-cutter ant Atta colombica. Analysis of its single 4.76-Mbp chromosome
      will shed light on community dynamics and plant biomass degradation in ant fungus
      gardens.
AU  - Aylward FO et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00238-12.

PMID- 16442652
VI  - 123
DP  - 2006
TI  - Hin4II, a new prototype restriction endonuclease from Haemophilus influenzae RFL4: Discovery, cloning and expression in Escherichia coli.
PG  - 288-296
AB  - The genes encoding restriction-modification system of unknown specificity Hin4II from
      Haemophilus influenzae RFL4 were cloned in
      Escherichia coli and sequenced. The Hin4II system comprises three
      tandemly arranged genes coding for m6A DNA methyltransferase, m5C DNA
      methyltransferase and restriction endonuclease, respectively.
      Restriction endonuclease was expressed in E. coli and purified to
      apparent homogeneity. The DNA recognition sequence and cleavage
      positions were determined. R.Hin4II recognizes the novel
      non-palindromic sequence 5'-CCTTC-3' and cleaves the DNA 6 and 5 nt
      downstream in the top and bottom strand, respectively. The new
      prototype restriction endonuclease Hin4II was classified as a potential
      candidate of HNH nuclease family after comparison against SMART
      database. An amino acid sequence motif 297H-X-14-N-X-8-H of Hin4II was
      proposed as forming a putative catalytic center.
AU  - Azarinskas A
AU  - Maneliene Z
AU  - Jakubauskas A
PT  - Journal Article
TA  - J. Biotechnol.
JT  - J. Biotechnol.
SO  - J. Biotechnol. 2006 123: 288-296.

PMID- 28280035
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of a Multidrug-Resistant Nosocomial Serratia marcescens Strain That Persisted in a Hospital in Kemerovo, Russian Federation.
PG  - e01764-16
AB  - Serratia marcescens is a frequent cause of health care-associated infections and  has led to
      multiple outbreaks. Here, we report the draft genome of a
      multidrug-resistant S. marcescens strain 189 which was isolated in 2012 as a
      predominant clone in a neonatal hospital in Kemerovo.
AU  - Azarov D
AU  - Goncharov A
AU  - Karaseva A
AU  - Brodina T
AU  - Lebedeva E
AU  - Taranenko I
AU  - Feting A
AU  - Bakaev M
AU  - Brusina E
AU  - Zueva L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01764-16.

PMID- 18539810
VI  - 74
DP  - 2008
TI  - Analysis of the genome sequence of Lactobacillus gasseri ATCC 33323 reveals the molecular basis of an autochthonous intestinal organism.
PG  - 4610-4625
AB  - This study presents the complete genome sequence of Lactobacillus gasseri ATCC 33323, a
      neotype strain of human origin and a native
      species found commonly in the gastrointestinal tracts of neonates and
      adults. The plasmid-free genome was 1,894,360 bp in size and predicted
      to encode 1,810 genes. The GC content was 35.3%, similar to the GC
      content of its closest relatives, L. johnsonii NCC 533 (34%) and L.
      acidophilus NCFM (34%). Two identical copies of the prophage LgaI
      (40,086 bp), of the Sfi11-like Siphoviridae phage family, were
      integrated tandomly in the chromosome. A number of unique features were
      identified in the genome of L. gasseri that were likely acquired by
      horizontal gene transfer and may contribute to the survival of this
      bacterium in its ecological niche. L. gasseri encodes two restriction
      and modification systems, which may limit bacteriophage infection. L.
      gasseri also encodes an operon for production of heteropolysaccharides
      of high complexity. A unique alternative sigma factor was present
      similar to that of B. caccae ATCC 43185, a bacterial species isolated
      from human feces. In addition, L. gasseri encoded the highest number of
      putative mucus-binding proteins (14) among lactobacilli sequenced to
      date. Selected phenotypic characteristics that were compared between
      ATCC 33323 and other human L. gasseri strains included carbohydrate
      fermentation patterns, growth and survival in bile,,oxalate
      degradation, and adhesion to intestinal epithelial cells, in vitro. The
      results from this study indicated high intraspecies variability from a
      genome encoding traits important for survival and retention in the
      gastrointestinal tract.
AU  - Azcarate-Peril MA
AU  - Altermann E
AU  - Goh YJ
AU  - Tallon R
AU  - Sanozky-Dawes RB
AU  - Pfeiler EA
AU  - O'Flaherty S
AU  - Buck BL
AU  - Dobson A
AU  - Duong T
AU  - Miller MJ
AU  - Barrangou R
AU  - Klaenhammer TR
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2008 74: 4610-4625.

PMID- 
VI  - 0
DP  - 1990
TI  - Restriction endonuclease in Clostridium acetobutylicum strain NI-4081.
PG  - 249-250
AB  - That a restriction-modification system may exist in Clostridium acetobutylicum
      strain NI-4081 was suggested by the observation that the efficiency of plasmid
      transformation was dependent upon the DNA source of the replicon, and by
      difficulties encountered in gene cloning experiments with DNA of heterologous
      Clostridia.  These findings led us to search for restriction endonuclease and
      methylase activities in strain NI-4081.
AU  - Azeddoug H
AU  - Hubert J
AU  - Reysset G
PT  - Journal Article
TA  - Clinical and Molecular Aspects of Anaerobes
JT  - Clinical and Molecular Aspects of Anaerobes
SO  - Clinical and Molecular Aspects of Anaerobes 1990 0: 249-250.

PMID- 2612893
VI  - 65
DP  - 1989
TI  - Characterization of a methyl-specific restriction system in Clostridium acetobutylicum strain N1-4081.
PG  - 323-326
AB  - A type II restriction endonuclease, named CacI, was detected in Clostridium acetobutylicum
      strain N1-4081. CacI cleaved the tetranucleotide sequence [5'-GATC-3']. The modification
      system consisted of the methylation of the adenine present in this sequence. CacI, an
      isoschizomer of MboI, is inactive on dam methylated substrates.
AU  - Azeddoug H
AU  - Hubert J
AU  - Reysset G
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1989 65: 323-326.

PMID- 2040424
VI  - 78
DP  - 1991
TI  - Recognition sequence of a new methyl-specific restriction system from Clostridium acetobutylicum strain ABKn8.
PG  - 153-156
AB  - A new type II restriction endonuclease, named CacII was detected in Clostridium
      acetobutylicum strain ABKn8.  CacII cleaved the hexanucleotide sequence
      [5'-GCN^NGC-3'] and generated blunt ends.  Up to now no isoschizomer of CacII
      has been described. Note that the name of this enzyme has been changed to
      Cac8I.
AU  - Azeddoug H
AU  - Reysset G
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1991 78: 153-156.

PMID- 1526445
VI  - 95
DP  - 1992
TI  - Characterization of restriction endonuclease BfrBI from Bacteroides fragilis strains BE3 and AIP 10006.
PG  - 133-136
AB  - A new type II restriction endonuclease, named BfrBI, was detected in two stains of Bacteroides
      fragilis, BE3 and AIP 10006 (NCTC 9343T). The enzyme BfrBI, an isoschizomer of NsiI and Ava
      III, recognized the hexanucleotide sequence [5'-ATG CAT-3'], with a cleavage site generating
      blunt ends.
AU  - Azeddoug H
AU  - Reysset G
AU  - Sebald M
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1992 95: 133-136.

PMID- 25745007
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Streptococcus equinus (Streptococcus bovis) HC5, a Lantibiotic Producer from the Bovine Rumen.
PG  - e00085-15
AB  - Streptococcus equinus (Streptococcus bovis) HC5 is a bacteriocinogenic lactic acid bacterium
      with simple growth requirements. The draft genome sequence of S.
      equinus HC5 consists of 1,846,241 bp, with a G+C content of 37.04%. In silico
      analysis indicated that S. equinus HC5 might be useful to control bacteria that
      are detrimental to livestock animals.
AU  - Azevedo AC
AU  - Bento CB
AU  - Ruiz JC
AU  - Queiroz MV
AU  - Mantovani HC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00085-15.

PMID- 29437107
VI  - 6
DP  - 2018
TI  - Complete Closed Genome Sequence of Nontoxigenic Invasive Corynebacterium diphtheriae bv. mitis Strain ISS 3319.
PG  - e01566-17
AB  - The genome sequence of the human pathogen Corynebacterium diphtheriae bv. mitis strain ISS
      3319 was determined and closed in this study. The genome is estimated to have 2,404,936 bp
      encoding 2,257 proteins. This strain also possesses a plasmid of 1,960 bp.
AU  - Azevedo-Antunes C
AU  - Richardson EJ
AU  - Quick J
AU  - Fuentes-Utrilla P
AU  - Isom GL
AU  - Goodall EC
AU  - Moller J
AU  - Hoskisson PA
AU  - Mattos-Guaraldi AL
AU  - Cunningham AF
AU  - Loman NJ
AU  - Sangal V
AU  - Burkovski A
AU  - Henderson IR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01566-17.

PMID- 30533905
VI  - 7
DP  - 2018
TI  - Draft Genome Sequence of the Pristinamycin-Producing Strain Streptomyces sp. SW4, Isolated from Soil in Nusa Kambangan, Indonesia.
PG  - e00912-18
AB  - Streptomyces sp. strain SW4 exhibited broad-spectrum antibacterial activity toward
      Gram-positive and Gram-negative pathogens. The 7.5-Mb draft genome
      sequence gives insight into the complete secondary metabolite production capacity
      and reveals genes putatively responsible for its antibacterial activity.
AU  - Aziz S
AU  - Mast Y
AU  - Wohlleben W
AU  - Gross H
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e00912-18.

PMID- Not carried by PubMed...
VI  - 4
DP  - 1988
TI  - Bacillus thuringiensis restrictase sensitive to dam-methylation.
PG  - 197-198
AB  - A new restriction enzyme from Bacillus thuringiensis is described. It is an isoschizomer of
      ClaI and is sensitive to dam methylation.
AU  - Azizbekyan RR
AU  - Rebentish BA
AU  - Netyksa EM
PT  - Journal Article
TA  - Biotekhnologiya
JT  - Biotekhnologiya
SO  - Biotekhnologiya 1988 4: 197-198.

PMID- 8394507
VI  - 1-2
DP  - 1992
TI  - Site-specific restriction endonuclease from Bacillus thuringiensis var. Kumantoenis.
PG  - 13-15
AB  - Site-specific restriction endonucleases are widely used in recombinant DNA technology for the
      construction of various molecular vectors. Possessing different specificity toward definite
      nucleotide sequences, they permit the construction of recombinant DNA molecules for their
      subsequent introduction into cells and yet, the presence of restriction-modification systems
      in the cells of the recipient bacteria limit the effectiveness of the introduction of foreign
      DNA. Recent investigations on site-specific restriction endonucleases have been conducted
      along two lines: the search for new restriction-modification systems and the search for
      recipients lacking restriction endonucleases. The entoropathogenic bacteria Bacillus
      thuringiensis, which produce a crystalline protein endotoxin, are finding wide use as
      ecologically safe biological insecticides. Earlier we detected restriction endonucleases of
      various specificity in the cells of strains of various B. thuringiensis serovariants. In the
      course of genetic manipulations with B. thuringiensis (H18) strain 4W1, we found that this
      strain limits the development of certain phages. In this work we studied the mechanism of the
      limitation of phage development and isolated two site-specific endonucleases from cells of the
      strain 4W1.
AU  - Azizbekyan RR
AU  - Rebentish BA
AU  - Netyksa EM
AU  - Bychkova MA
AU  - Bolotin AP
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1992 1-2: 13-15.

PMID- 6323119
VI  - 274
DP  - 1984
TI  - Site specific restriction endonuclease from a Bacillus thuringiensis strain.
PG  - 742-744
AB  - Site-specific restriction endonucleases are used in recombinant DNA methodology
      for the construction of recombinant DNAs and the creation of strains that
      produce biologically active compounds on the basis of them.  The second aspect
      of the use of restriction endonucleases is due to the possibility of their use
      for blocking the expression of foreign genetic information; in particular,
      restriction systems can be introduced into strains that produce biologically
      active compounds to increase their resistance to infection by bacteriophages.
AU  - Azizbekyan RR
AU  - Rebentish BA
AU  - Stepanova TV
AU  - Netyksa EM
AU  - Bychkova MA
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1984 274: 742-744.

PMID- 6091104
VI  - 81
DP  - 1984
TI  - Restriction endonucleases can be used to study B-Z junctions in supercoiled DNA.
PG  - 5714-5718
AB  - Plasmids containing (C-G)n inserts have been used to study the inhibition of cleavage by
      restriction endonucleases due to Z-DNA formation in negatively supercoiled plasmids.  The
      enzyme BssHII, which recognizes G-C-G-C-G-C, is strongly inhibited when the insert forms
      Z-DNA.  The BamHI recognition sequence (G-G-A-T-C-C) was placed in four different positions
      near the B-Z junction and the inhibition of BamHI cleavage was determined as a function of
      negative superhelical density.  Formation of Z-DNA in the (C-G)n insert inhibited cleavage by
      BamHI when its recognition sequence was located immediately adjacent to the insert or four
      base pairs away from it.  However, no inhibition was found when the BamHI recognition site was
      eight base pairs away.  These experiments help to define the limits of the structural
      perturbation associated with the B-Z junction.
AU  - Azorin F
AU  - Hahn R
AU  - Rich A
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1984 81: 5714-5718.

PMID- 19638423
VI  - 37
DP  - 2009
TI  - Whole-genome analyses reveal genetic instability of Acetobacter pasteurianus.
PG  - 5768-5783
AB  - Acetobacter species have been used for brewing traditional vinegar and are
      known to have genetic instability. To clarify the mutability, Acetobacter
      pasteurianus NBRC 3283, which forms a multi-phenotype cell complex, was
      subjected to genome DNA sequencing. The genome analysis revealed that
      there are more than 280 transposons and five genes with hyper-mutable
      tandem repeats as common features in the genome consisting of a 2.9-Mb
      chromosome and six plasmids. There were three single nucleotide mutations
      and five transposon insertions in 32 isolates from the cell complex. The
      A. pasteurianus hyper-mutability was applied for breeding a
      temperature-resistant strain grown at an unviable high-temperature (42
      degrees C). The genomic DNA sequence of a heritable mutant showing
      temperature resistance was analyzed by mutation mapping, illustrating that
      a 92-kb deletion and three single nucleotide mutations occurred in the
      genome during the adaptation. Alpha-proteobacteria including A.
      pasteurianus consists of many intracellular symbionts and parasites, and
      their genomes show increased evolution rates and intensive genome
      reduction. However, A. pasteurianus is assumed to be a free-living
      bacterium, it may have the potentiality to evolve to fit in natural niches
      of seasonal fruits and flowers with other organisms, such as yeasts and
      lactic acid bacteria.
AU  - Azuma Y
AU  - Hosoyama A
AU  - Matsutani M
AU  - Furuya N
AU  - Horikawa H
AU  - Harada T
AU  - Hirakawa H
AU  - Kuhara S
AU  - Matsushita K
AU  - Fujita N
AU  - Shirai M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: 5768-5783.

PMID- 28883136
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Comamonas testosteroni R2, Consisting of Aromatic Compound Degradation Genes for Phenol Hydroxylase.
PG  - e00875-17
AB  - Comamonas testosteroni strain R2 was isolated from a continuous culture enriched  by a low
      concentration of phenol-oxygenating activities with low Ks values (below
      1 muM). The draft genome sequence of C. testosteroni strain R2 reported here may
      contribute to determining the phenol degradation gene cluster.
AU  - Azwani F
AU  - Suzuki K
AU  - Honjyo M
AU  - Tashiro Y
AU  - Futamata H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00875-17.

PMID- 14500908
VI  - 100
DP  - 2003
TI  - Complete genome sequence and analysis of Wolinella succinogenes.
PG  - 11690-11695
AB  - To understand the origin and emergence of pathogenic bacteria, knowledge of the genetic
      inventory from their nonpathogenic relatives is a prerequisite.
      Therefore, the 2.11-megabase genome sequence of Wolinella succinogenes, which is
      closely related to the pathogenic bacteria Helicobacter pylori and Campylobacter
      jejuni, was determined. Despite being considered nonpathogenic to its bovine
      host, W. succinogenes holds an extensive repertoire of genes homologous to known
      bacterial virulence factors. Many of these genes have been acquired by lateral
      gene transfer, because part of the virulence plasmid pVir and an N-linked
      glycosylation gene cluster were found to be syntenic between C. jejuni and
      genomic islands of W. succinogenes. In contrast to other host-adapted bacteria,
      W. succinogenes does harbor the highest density of bacterial sensor kinases found
      in any bacterial genome to date, together with an elaborate signaling circuitry
      of the GGDEF family of proteins. Because the analysis of the W. succinogenes
      genome also revealed genes related to soil- and plant-associated bacteria such as
      the nif genes, W. succinogenes may represent a member of the epsilon
      proteobacteria with a life cycle outside its host.
AU  - Baar C
AU  - Eppinger M
AU  - Raddatz G
AU  - Simon J
AU  - Lanz C
AU  - Klimmek O
AU  - Nandakumar R
AU  - Gross R
AU  - Rosinus A
AU  - Keller H
AU  - Jagtap P
AU  - Linke B
AU  - Meyer F
AU  - Lederer H
AU  - Schuster SC
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2003 100: 11690-11695.

PMID- 30533918
VI  - 7
DP  - 2018
TI  - Draft Genome Sequence of Shewanella algidipiscicola H1, a Highly Chromate-Resistant Strain Isolated from Mediterranean Marine Sediments.
PG  - e00905-18
AB  - The ability of different Shewanella spp. to convert heavy metals and toxic substances into
      less toxic products by using them as electron acceptors has led
      to their use in environmental clean-up strategies. We present here the draft
      genome sequence of Shewanella algidipiscicola H1, a strain resistant to high
      concentrations of chromates.
AU  - Baaziz H
AU  - Lemaire ON
AU  - Jourlin-Castelli C
AU  - Iobbi-Nivol C
AU  - Mejean V
AU  - Alatou R
AU  - Fons M
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e00905-18.

PMID- 17951380
VI  - 190
DP  - 2008
TI  - Genome sequence of Staphylococcus aureus strain Newman and comparative analysis of staphylococcal genomes: polymorphism and evolution of two major pathogenicity    islands.
PG  - 300-310
AB  - Strains of Staphylococcus aureus, an important human pathogen, display up to 20%  variability
      in their genome sequence, and most sequence information is available
      for human clinical isolates that have not been subjected to genetic analysis of
      virulence attributes. S. aureus strain Newman, which was also isolated from a
      human infection, displays robust virulence properties in animal models of disease
      and has already been extensively analyzed for its molecular traits of
      staphylococcal pathogenesis. We report here the complete genome sequence of S.
      aureus Newman, which carries four integrated prophages, as well as two large
      pathogenicity islands. In agreement with the view that S. aureus Newman prophages
      contribute important properties to pathogenesis, fewer virulence factors are
      found outside of the prophages than for the highly virulent strain MW2. The
      absence of drug resistance genes reflects the general antibiotic-susceptible
      phenotype of S. aureus Newman. Phylogenetic analyses reveal clonal relationships
      between the staphylococcal strains Newman, COL, NCTC8325, and USA300 and a
      greater evolutionary distance to strains MRSA252, MW2, MSSA476, N315, Mu50, JH1,
      JH9, and RF122. However, polymorphism analysis of two large pathogenicity islands
      distributed among these strains shows that the two islands were acquired
      independently from the evolutionary pathway of the chromosomal backbones of
      staphylococcal genomes. Prophages and pathogenicity islands play central roles in
      S. aureus virulence and evolution.
AU  - Baba T
AU  - Bae T
AU  - Schneewind O
AU  - Takeuchi F
AU  - Hiramatsu K
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2008 190: 300-310.

PMID- 19074389
VI  - 191
DP  - 2009
TI  - Complete genome sequence of Macrococcus caseolyticus strain JSCS5402, reflecting the ancestral genome of the human-pathogenic staphylococci.
PG  - 1180-1190
AB  - We isolated the methicillin-resistant Macrococcus caseolyticus strain JCSC5402 from animal
      meat in a supermarket and determined its whole-genome
      nucleotide sequence. This is the first report on the genome analysis of a
      macrococcal species that is evolutionarily closely related to the human
      pathogens Staphylococcus aureus and Bacillus anthracis. The essential
      biological pathways of M. caseolyticus are similar to those of
      staphylococci. However, the species has a small chromosome (2.1 MB) and
      lacks many sugar and amino acid metabolism pathways and a plethora of
      virulence genes that are present in S. aureus. On the other hand, M.
      caseolyticus possesses a series of oxidative phosphorylation machineries
      that are closely related to those in the family Bacillaceae. We also
      discovered a probable primordial form of a Macrococcus methicillin
      resistance gene complex, mecIRAm, on one of the eight plasmids harbored by
      the M. caseolyticus strain. This is the first finding of a
      plasmid-encoding methicillin resistance gene. Macrococcus is considered to
      reflect the genome of ancestral bacteria before the speciation of
      staphylococcal species and may be closely associated with the origin of
      the methicillin resistance gene complex of the notorious human pathogen
      methicillin-resistant S. aureus.
AU  - Baba T
AU  - Kuwahara-Arai K
AU  - Uchiyama I
AU  - Takeuchi F
AU  - Ito T
AU  - Hiramatsu K
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2009 191: 1180-1190.

PMID- 12044378
VI  - 359
DP  - 2002
TI  - Genome and virulence determinants of high virulence community-acquired MRSA.
PG  - 1819-1827
AB  - BACKGROUND: A new type of meticillin-resistant Staphylococcus aureus (MRSA), designated
      community-acquired MRSA, is becoming increasingly
      noticeable in the community, some strains of which cause fatal infections
      in otherwise healthy individuals. By contrast with hospital-acquired MRSA,
      community-acquired MRSA is more susceptible to non beta-lactam antibiotics.
      We investigated the high virulence potential of certain strains of this
      bacterium. METHODS: We ascertained the whole genome sequence of MW2, a
      strain of community-acquired MRSA, by shotgun cloning and sequencing. MW2
      caused fatal septicaemia and septic arthritis in a 16-month-old girl in
      North Dakota, USA, in 1998. The genome of this strain was compared with
      those of hospital-acquired MRSA strains, including N315 and Mu50.
      FINDINGS: Meticillin resistance gene (mecA) in MW2 was carried by a novel
      allelic form (type IVa) of staphylococcal cassette chromosome mec
      (SCCmec), by contrast with type II in N315 and Mu50. Type IVa SCCmec did
      not carry any of the multiple antibiotic resistance genes reported in type
      II SCCmec. By contrast, 19 additional virulence genes were recorded in the
      MW2 genome. All but two of these virulence genes were noted in four of the
      seven genomic islands of MW2. INTERPRETATION: MW2 carried a range of
      virulence and resistance genes that was distinct from those displayed on
      the chromosomes of extant S aureus strains. Most genes were carried by
      specific allelic forms of genomic islands in the MW2 chromosome. The
      combination of allelic forms of genomic islands is the genetic basis that
      determines the pathogenicity of medically important phenotypes of S
      aureus, including those of community-acquired MRSA strains.
AU  - Baba T
AU  - Takeuchi F
AU  - Kuroda M
AU  - Yuzawa H
AU  - Aoki K
AU  - Oguchi A
AU  - Nagai Y
AU  - Iwama N
AU  - Asano K
AU  - Naimi T
AU  - Kuroda H
AU  - Cui L
AU  - Yamamoto K
AU  - Hiramatsu K
PT  - Journal Article
TA  - Lancet
JT  - Lancet
SO  - Lancet 2002 359: 1819-1827.

PMID- 28495783
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Streptococcus dysgalactiae subsp. equisimilis Strain C161L1 Isolated in Vellore, India.
PG  - e00336-17
AB  - Streptococcus dysgalactiae subsp. equisimilis belongs to the beta-hemolytic group C and G
      pyogenic group of streptococci. Here, we report the draft genome of the
      S. dysgalactiae subsp. equisimilis strain C161L1 from Vellore, a region in
      southern India with a high incidence rate of S. dysgalactiae subsp. equisimilis
      infection. This genome is 2.1 Mb long, with a 39.82% G+C content, and encodes
      2,022 genes.
AU  - Babbar A
AU  - Nitsche-Schmitz DP
AU  - Pieper DH
AU  - Barrantes I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00336-17.

PMID- 1648209
VI  - 19
DP  - 1991
TI  - SsbI, an isoschizomer of HindIII isolated from Streptomyces scabies.
PG  - 3457
AB  - SsbI is a restriction endonuclease identified in cell lysates of the soil
      bacterium Streptomyces scabies, isolate FL1.  SsbI was partially purified by
      DEAE-Sephadex chromatography to remove contaminating nuclease activity.  The
      partially purified SsbI fraction was used to determine the recognition sequence
      and the cleavage site for the endonuclease.
AU  - Babcock MJ
AU  - Schottel JL
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 3457.

PMID- 18762194
VI  - 383
DP  - 2008
TI  - DNA Distortion and Specificity in a Sequence-Specific Endonuclease.
PG  - 186-204
AB  - Five new structures of the Q138F HincII enzyme bound to a total of three different DNA
      sequences and three different metal ions (Ca(2+), Mg(2+),
      and Mn(2+)) are presented. While previous structures were produced from
      soaking Ca(2+) into preformed Q138F HincII/DNA crystals, the new
      structures are derived from cocrystallization with Ca(2+), Mg(2+), or
      Mn(2+). The Mn(2)(+)-bound structure provides the first view of a product
      complex of Q138F HincII with cleaved DNA. Binding studies and a crystal
      structure show how Ca(2+) allows trapping of a Q138F HincII complex with
      noncognate DNA in a catalytically incompetent conformation. Many Q138F
      HincII/DNA structures show asymmetry, despite the binding of a symmetric
      substrate by a symmetric enzyme. The various complexes are fit into a
      model describing the different conformations of the DNA-bound enzyme and
      show how DNA conformational energetics determine DNA-cleavage rates by the
      Q138F HincII enzyme.
AU  - Babic AC
AU  - Little EJ
AU  - Manohar VM
AU  - Bitinaite J
AU  - Horton NC
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2008 383: 186-204.

PMID- 17033890
VI  - 63
DP  - 2007
TI  - Maintenance DNA methyltransferase (Met1) and silencing of CpG-methylated foreign DNA in Volvox carteri.
PG  - 325-336
AB  - DNA methylation plays an important role in the gene-silencing network of higher eukaryotes. We
      have analyzed the 21.5-kb maintenance
      methyltransferase (M-MTase) gene, met1, of the multicellular green alga
      Volvox carteri. The met1 transcript was detected only during the period
      when DNA replication and cell division are taking place. It encodes a
      238 kDa protein containing eight C-terminal activity domains typical of
      M-MTases, plus upstream DNA-binding domains including the ProDom domain
      PD003757, which experimental analyses in animal systems have indicated
      is required for targeting the enzyme to DNA-replication foci. Several
      insertions of unknown function make Volvox Met1 the largest known
      member of the Met1/Dnmt1 family. Here we also show that several
      endogenous transposon families are CpG-methyated in Volvox, which we
      think causes them to be inactive. This view is supported by the
      observation that an in vitro CpG-methylated gene introduced into Volvox
      was maintained in the methylated and silent state over > 100
      generations. Thus, we believe that Met1 recognizes and perpetuates the
      in vitro methylation signal, and that the silencing machinery is then
      able to transduce such a methylation-only signal into a stable
      heterochromatic (and silent) state.
AU  - Babinger P
AU  - Volkl R
AU  - Cakstina I
AU  - Maftei A
AU  - Schmitt R
PT  - Journal Article
TA  - Plant Mol. Biol.
JT  - Plant Mol. Biol.
SO  - Plant Mol. Biol. 2007 63: 325-336.

PMID- 12665299
VI  - 1
DP  - 2002
TI  - Iodouracil-mediated photocrosslinking of DNA to EcoRII restriction endonuclease in catalytic conditions.
PG  - 636-640
AB  - We used a XeCl excimer laser with 50 ns pulses, a frequency of 0.3 Hz and a wavelength of 308
      nm in appropriate conditions for the photocrosslinking
      of EcoRII restriction endonuclease to a 14-mer DNA duplex, containing a
      5-iodo-2'-deoxyuridine residue (IdU). IdU replaced the thymidine residue
      within the EcoRII recognition sequence 5'-CCT/AGG. The binding of EcoRII
      endonuclease to the IdU-containing DNA duplex was analyzed by gel
      retardation assay in the presence of Ca2+ or Mg2+ ions. Photocrosslinking
      of EcoRII to the IdU-containing DNA duplex occurred in a pre-reactive
      complex formed in the presence of Ca2+ ions. Photocrosslinking yields as a
      function of time and UV-laser light intensity were studied.
AU  - Babkina OV
AU  - Chutko CA
AU  - Shashkov AA
AU  - Dzhidzhoev MS
AU  - Eritja R
AU  - Gromova ES
PT  - Journal Article
TA  - Photochem. Photobiolog.
JT  - Photochem. Photobiolog.
SO  - Photochem. Photobiolog. 2002 1: 636-640.

PMID- 11186006
VI  - 34
DP  - 2000
TI  - Recombinant components of the EcoRII restriction-modification system: Restriction endonuclease can interact with DNA-RNA duplexes.
PG  - 1065-1073
AB  - To obtain recombinant restriction endonuclease (R) and methylase (M) of the EcoRII
      restriction-modification system, bacterial strains
      overproducing their functional hexahistidine derivatives were
      constructed. Active full-length EcoRII was produced only in cells
      that also expressed M.EcoRII from a multicopy plasmid. Recombinant
      EcoRII bound with hybrid DNA-RNA duplexes.
AU  - Babkina OV
AU  - Evstafieva AG
AU  - Chichkova NV
AU  - Vartapetian AB
AU  - Muller S
AU  - Baskunov VB
AU  - Petrauskene OV
AU  - Kochetkov SN
AU  - Gromova ES
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2000 34: 1065-1073.

PMID- 9914964
VI  - 32
DP  - 1998
TI  - Restriction endonuclease EcoRII hydrolyzes one of the two DNA restriction sites forming the catalytic complex.
PG  - 793-796
AB  - Hydrolysis of 71-mer substrates containing two EcoRII recognition sites was considered in
      order to investigate the two-site mechanism of DNA recognition, which implies the presence in
      the catalytic complex of four internucleotide bonds cleavable by the enzyme.  It is shown that
      the enzyme hydrolyzes only two phosphodiester bonds in one enzyme-substrate complex.  To find
      out whether both bonds belong to one and the same or different recognition sites, scissile
      phosphodiester bonds in one of the recognition sites in the 71-mer duplexes were replaced with
      nonscissile pyrophosphate bonds alternatively or in both strands simultaneously.  This allowed
      one to preclude hydrolysis of the corresponding bonds.  It is shown that endonuclease EcoRII
      cleaves simultaneously two internucleotide phosphodiester bonds belonging to the same
      recognition site.
AU  - Babkina OV
AU  - Petrauskene OV
AU  - Gromova ES
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1998 32: 793-796.

PMID- 24285658
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of the Mesoplasma florum W37 Strain.
PG  - e00879-13
AB  - Mesoplasma florum is a small-genome fast-growing mollicute that is an attractive  model for
      systems and synthetic genomics studies. We report the complete
      825,824-bp genome sequence of a second representative of this species, M. florum
      strain W37, which contains 733 predicted open reading frames and 35 stable RNAs.
AU  - Baby V
AU  - Matteau D
AU  - Knight TF
AU  - Rodrigue S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00879-13.

PMID- 219202
VI  - 128
DP  - 1979
TI  - Methylation and cleavage sequences of the EcoP1 restriction-modification enzyme.
PG  - 143-163
AB  - EcoP1 is a restriction modification enzyme encoded by bacteriophage P1.  It
      requires ATP for cleavage and S-adenosyl methionine for methylation of DNA.  We
      have mapped the sites of both cleavage and methylation in simian virus 40 DNA
      and determined their sequences.  The enzyme methylates the sequence A-G-mA-C-C
      and cuts the DNA 25 to 27 base-pairs form the site of methylation in the 3'
      direction, with a two to four base-pair stagger between cuts.  Consistent with
      the fact that the methylation sequence is asymmetric, the enzyme methylates
      only one strand in vitro.  One variant of simian virus 40 has acquired an
      additional EcoP1 methylation and cleavage site by changing a A-G-A-A-C sequence
      to A-G-A-C-C.
AU  - Bachi B
AU  - Reiser J
AU  - Pirrotta V
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1979 128: 143-163.

PMID- 11427539
VI  - 276
DP  - 2001
TI  - Dnmt3a and Dnmt3b are transcriptional repressors that exhibit unique localization properties to heterochromatin.
PG  - 32282-32287
AB  - We demonstrate that the recently identified DNA methyltransferases, Dnmt3a and Dnmt3b, like
      DNMT1, repress transcription in a methylation-independent manner. Dnmt3a and Dnmt3b repress
      transcription primarily through a plant homeodomain-like motif that is shared with the ATRX
      protein but is not present in DNMT1. Unlike DNMT1, which localizes to replication foci during
      S-phase in murine embryonic fibroblasts, Dnmt3a co-localizes with heterochromatin protein 1
      alpha (HP1 alpha) and methyl-CpG binding proteins throughout the cell cycle to
      late-replicating pericentromeric heterochromatin. In contrast to Dnmt3a, Dnmt3b remained
      diffuse in the nucleus of embryonic fibroblasts at all cell cycle stages. However, Dnmt3a and
      Dnmt3b co-localize to these pericentromeric heterochromatin regions in murine embryonic stem
      cells. This finding is important to the fact that mutations in DNMT3B are found in the
      developmental syndrome, ICF (immunodeficiency, centromeric heterochromatin instability, and
      facial anomalies), which involves extensive loss of methylation from pericentromeric regions.
      The localization of Dnmt3a and Dnmt3b was unaffected in Dnmt1 null embryonic stem cells, which
      lose the majority of methylation at pericentromeric major satellite repeats, suggesting that
      these enzymes are not dependent upon preexisting methylation for their targeting. DNMT1 is
      then positioned to reestablish transcriptionally repressive chromatin as cells replicate,
      while Dnmt3a and Dnmt3b may help to establish such chromatin in late S-phase and maintain this
      repressive heterochromatin throughout the cell cycle in a developmentally and/or cell type
      manner.
AU  - Bachman KE
AU  - Rountree MR
AU  - Baylin SB
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2001 276: 32282-32287.

PMID- 6254852
VI  - 11
DP  - 1980
TI  - A cautionary note on the use of certain restriction endonucleases with methylated substrates.
PG  - 169-171
AB  - Methylation of adenine and cytosine residues in DNA isolated from common strains of
      Escherichia coli K-12 can render that DNA resistant to cleavage by certain restriction
      endonucleases at those sites at which the recognition sequence for such an endonuclease
      overlaps (but does not include) a sequence recognized by methylases specified by the dam or
      dcm gene.
AU  - Backman K
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1980 11: 169-171.

PMID- 28360177
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of 24 Lactococcus lactis Strains.
PG  - e01737-16
AB  - The lactic acid bacterium Lactococcus lactis is widely used for the production of fermented
      dairy products. Here, we present the draft genome sequences of 24 L.
      lactis strains isolated from different environments and geographic locations.
AU  - Backus L
AU  - Wels M
AU  - Boekhorst J
AU  - Dijkstra AR
AU  - Beerthuyzen M
AU  - Kelly WJ
AU  - Siezen RJ
AU  - van Hijum SA
AU  - Bachmann H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01737-16.

PMID- 11359795
VI  - 276
DP  - 2001
TI  - Recombinant Human DNA (Cytosine-5) Methyltransferase. III. Allosteric control, reaction order, and influence of plasmid topology and triplet repeat length on methylation of the Fragile X CGG.CCG sequence.
PG  - 18605-18613
AB  - Steady-state kinetic analyses revealed that the methylation reaction of the human DNA
      (cytosine-5) methyltransferase 1 (DNMT1) is repressed by the N-terminal domain comprising the
      first 501 amino acids, and that repression is relieved when methylated DNA binds to this
      region. DNMT1 lacking the first 501 amino acids retains its preference for hemimethylated DNA.
      The methylation reaction proceeds by a sequential mechanism, and either substrate
      (S-adenosyl-l-methionine and unmethylated DNA) may be the first to bind to the active site.
      However, initial binding of S-adenosyl-l-methionine is preferred. The binding affinities of
      DNA for both the regulatory and the catalytic sites increase in the presence of methylated CpG
      dinucleotides and vary considerably (more than one hundred times) according to DNA sequence.
      DNA topology strongly influences the reaction rates, which increased with increasing negative
      superhelical tension. These kinetic data are consistent with the role of DNMT1 in maintaining
      the methylation patterns throughout development and suggest that the enzyme may be involved in
      the etiology of fragile X, a syndrome characterized by de novo methylation of a greatly
      expanded CGG.CCG triplet repeat sequence.
AU  - Bacolla A
AU  - Pradhan S
AU  - Larson JE
AU  - Roberts RJ
AU  - Wells RD
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2001 276: 18605-18613.

PMID- 10551869
VI  - 274
DP  - 1999
TI  - Recombinant human DNA (cytosine-5) methyltransferase. II. Steady-state kinetics reveal allosteric activation by methylated DNA.
PG  - 33011-33019
AB  - Initial velocity determinations were conducted with human DNA (cytosine-5) methyltransferase
      (DNMT1) on unmethylated and hemimethylated DNA templates in order to assess the mechanism of
      the reaction. Initial velocity data with DNA and S-adenosylmethionine (AdoMet) as variable
      substrates and product inhibition studies with methylated DNA and S-adenosylhomocysteine
      (AdoHcy) were obtained and evaluated as double-reciprocal plots. These relationships were
      linear for plasmid DNA, exon-1 from the imprinted small nuclear ribonucleoprotein-associated
      polypeptide N, (CGG.CCG)(12), (m(5)CGG.CCG)(12), and (CGG.CCG)(73) but were not linear for
      (CGG.Cm(5)CG)(12). Inhibition by AdoHcy was apparently competitive versus AdoMet and
      uncompetitive/noncompetitive versus DNA at </=20 microM AdoMet. Addition of the product
      (methylated DNA) to unmethylated plasmid DNA increased V(max(app)) resulting in mixed
      stimulation and inhibition. Velocity equations indicated a two-step mechanism as follows:
      first, activation of DNMT1 by methylated DNA that bound to an allosteric site, and second, the
      addition of AdoMet and DNA to the catalytic site. The preference of DNMT1 for hemimethylated
      DNA may be the result of positive cooperativity of AdoMet binding mediated by allosteric
      activation by the methylated CG steps. We propose that this activation plays a role in vivo in
      the regulation of maintenance methylation.
AU  - Bacolla A
AU  - Pradhan S
AU  - Roberts RJ
AU  - Wells RD
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1999 274: 33011-33019.

PMID- 25744992
VI  - 3
DP  - 2015
TI  - Complete Genome of Geobacter pickeringii G13T, a Metal-Reducing Isolate from Sedimentary Kaolin Deposits.
PG  - e00038-15
AB  - We used PacBio sequencing to assemble the genome of the pristine freshwater isolate Geobacter
      pickeringii G13(T) into a single 3,618,700-bp circular
      chromosome polished to 99.999% accuracy (quality value [QV], 50). This isolate
      shares several features with other Geobacter spp., including genes for
      degradation of aromatics and an abundance of multiheme c-type cytochromes.
AU  - Badalamenti JP
AU  - Bond DR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00038-15.

PMID- 27081146
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Streptomyces albus SM254, a Potent Antagonist of Bat  White-Nose Syndrome Pathogen Pseudogymnoascus destructans.
PG  - e00290-16
AB  - We sequenced and annotated the complete 7,170,504-bp genome of a novel secondary
      metabolite-producingStreptomycesstrain,Streptomyces albusSM254, isolated from
      copper-rich subsurface fluids at ~220-m depth within the Soudan Iron Mine
      (Soudan, MN, USA).
AU  - Badalamenti JP
AU  - Erickson JD
AU  - Salomon CE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00290-16.

PMID- 26294635
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Achromobacter xylosoxidans MN001, a Cystic Fibrosis Airway Isolate.
PG  - e00947-15
AB  - The genome of Achromobacter xylosoxidans MN001, a strain isolated from sputum derived from an
      adult cystic fibrosis patient, was sequenced using combined
      single-molecule real-time and Illumina sequencing. Assembly of the complete
      genome resulted in a 5,876,039-bp chromosome, representing the smallest A.
      xylosoxidans genome sequenced to date.
AU  - Badalamenti JP
AU  - Hunter RC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00947-15.

PMID- 25767222
VI  - 3
DP  - 2015
TI  - Genomes of Geoalkalibacter ferrihydriticus Z-0531T and Geoalkalibacter subterraneus Red1T, Two Haloalkaliphilic Metal-Reducing Deltaproteobacteria.
PG  - e00039-15
AB  - We sequenced and annotated genomes of two haloalkaliphilic Deltaproteobacteria,
      Geoalkalibacter ferrihydriticus Z-0531(T) (DSM 17813) and Geoalkalibacter
      subterraneus Red1(T) (DSM 23483). During assembly, we discovered that the DSMZ
      stock culture of G. subterraneus was contaminated. We reisolated G. subterraneus
      in axenic culture and redeposited it in DSMZ and JCM.
AU  - Badalamenti JP
AU  - Krajmalnik-Brown R
AU  - Torres CI
AU  - Bond DR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00039-15.

PMID- 22689247
VI  - 194
DP  - 2012
TI  - Genetic Fine Structure of a Salmonella enterica Serovar Typhi Strain Associated with the 2005 Outbreak of Typhoid Fever in Kelantan, Malaysia.
PG  - 3565-3566
AB  - Among enteric pathogens, Salmonella enterica serovar Typhi is responsible for the largest
      number of food-borne outbreaks and fatalities. The ability of the
      pathogen to cause systemic infection for extended durations leads to a high cost
      of disease control. Chronic carriers play important roles in the evolution of
      Salmonella Typhi; therefore, identification and in-depth characterization of
      isolates from clinical cases and carriers, especially those from zones of
      endemicity where the pathogen has not been extensively studied, are necessary.
      Here, we describe the genome sequence of the highly virulent Salmonella Typhi
      strain BL196/05 isolated during the outbreak of typhoid in Kelantan, Malaysia, in
      2005. The whole-genome sequence and comparative genomics of this strain should
      enable us to understand the virulence mechanisms and evolutionary dynamics of
      this pathogen in Malaysia and elsewhere.
AU  - Baddam R
AU  - Kumar N
AU  - Thong KL
AU  - Ngoi ST
AU  - Teh CS
AU  - Yap KP
AU  - Chai LC
AU  - Avasthi TS
AU  - Ahmed N
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3565-3566.

PMID- 22933755
VI  - 194
DP  - 2012
TI  - Whole-Genome Sequences and Comparative Genomics of Salmonella enterica Serovar Typhi Isolates from Patients with Fatal and Nonfatal Typhoid Fever in Papua New  Guinea.
PG  - 5122-5123
AB  - Many of the developing countries of the Southeast Asian region are significantly  affected by
      endemic typhoid fever, possibly as a result of marginal living
      standards. It is an important public health problem in countries such as Papua
      New Guinea, which is geographically close to some of the foci of endemicity in
      Asia. The severity of the disease varies in different regions, and this may be
      attributable to genetic diversity among the native strains. Genome sequence data
      on strains from different countries are needed to clearly understand their
      genetic makeup and virulence potential. We describe the genomes of two Salmonella
      Typhi isolates from patients with fatal and nonfatal cases of typhoid fever in
      Papua New Guinea. We discuss in brief the underlying sequencing methodology,
      assembly, genome statistics, and important features of the two draft genomes,
      which form an essential step in our functional molecular infection epidemiology
      program centering on typhoid fever. The comparative genomics of these and other
      isolates would enable us to identify genetic rearrangements and mechanisms
      responsible for endemicity and the differential severity of pathogenic
      salmonellae in Papua New Guinea and elsewhere.
AU  - Baddam R
AU  - Thong KL
AU  - Avasthi TS
AU  - Shaik S
AU  - Yap KP
AU  - Teh CS
AU  - Chai LC
AU  - Kumar N
AU  - Ahmed N
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5122-5123.

PMID- 16980487
VI  - 188
DP  - 2006
TI  - Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter  crescentus.
PG  - 6841-6850
AB  - The dimorphic prosthecate bacteria (DPB) are alpha-proteobacteria that reproduce in an
      asymmetric manner rather than by binary fission and are of
      interest as simple models of development. Prior to this work, the only
      member of this group for which genome sequence was available was the model
      freshwater organism Caulobacter crescentus. Here we describe the genome
      sequence of Hyphomonas neptunium, a marine member of the DPB that differs
      from C. crescentus in that H. neptunium uses its stalk as a reproductive
      structure. Genome analysis indicates that this organism shares more genes
      with C. crescentus than it does with Silicibacter pomeroyi (a closer
      relative according to 16S rRNA phylogeny), that it relies upon a
      heterotrophic strategy utilizing a wide range of substrates, that its cell
      cycle is likely to be regulated in a similar manner to that of C.
      crescentus, and that the outer membrane complements of H. neptunium and C.
      crescentus are remarkably similar. H. neptunium swarmer cells are highly
      motile via a single polar flagellum. With the exception of cheY and cheR,
      genes required for chemotaxis were absent in the H. neptunium genome.
      Consistent with this observation, H. neptunium swarmer cells did not
      respond to any chemotactic stimuli that were tested, which suggests that
      H. neptunium motility is a random dispersal mechanism for swarmer cells
      rather than a stimulus-controlled navigation system for locating specific
      environments. In addition to providing insights into bacterial
      development, the H. neptunium genome will provide an important resource
      for the study of other interesting biological processes including
      chromosome segregation, polar growth, and cell aging.
AU  - Badger JH et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2006 188: 6841-6850.

PMID- 27516517
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Gulbenkiania indica Strain HT27T (DSM 17901T) Isolated from a Sulfur Spring in India.
PG  - e00830-16
AB  - Gulbenkiania indica strain HT27(T) was isolated from a sulfur spring. Here, we report the
      first representative draft genome sequence of a type strain of the
      genus Gulbenkiania The estimated genome is 2.8 Mb, with 2,713 protein-coding
      sequences.
AU  - Badhai J
AU  - Narayan KD
AU  - Whitman WB
AU  - Das SK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00830-16.

PMID- 27516514
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Chelatococcus sambhunathii Strain HT4T (DSM 18167T) Isolated from a Hot Spring in India.
PG  - e00825-16
AB  - The moderately thermophilic bacterium Chelatococcus sambhunathii strain HT4(T) was isolated
      from hot spring sediment. Based upon the draft genome sequence, the
      genome is 4.4 Mb and encodes 4,147 proteins.
AU  - Badhai J
AU  - Whitman WB
AU  - Das SK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00825-16.

PMID- 28450528
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Rhizobiumpusense Strain NRCPB10T (LMG 25623T) Isolated from Rhizosphere Soil of Chickpeas (Cicer arietinum L.) Grown in India.
PG  - e00282-17
AB  - Rhizobium pusense strain NRCPB10T was isolated from rhizosphere soil of chickpeas (Cicer
      arietinum L.). Based upon the draft genome sequence, the genome is 5.28 Mb
      and encodes 5,064 proteins.
AU  - Badhai J
AU  - Whitman WB
AU  - Das SK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00282-17.

PMID- 
VI  - 
DP  - 2005
TI  - Role of DNA adenine methylase in regulation of bacterial gene expression, virulence, and the elicitation of immune responses.
PG  - 1-149
AB  - The threat of emerging infectious diseases and bio-warfare agents has underscored the need for
      development of safe and effective anti-microbial therapies.  One viable approach to address
      this issue is through protective vaccination, which second to water sanitation, is the
      principal method for reduction of morbidity and mortality worldwide.  This dissertation
      describes the role of the DNA adenine methylase as a global regulator of bacterial virulence
      and the utility of Dam-based technology for the development of live-attenuated vaccines that
      elicit potent states of immunity against a variety of infectious agents.  Dam is a highly
      conserved enzyme found in many pathogens, and is involved in a variety of cellular processes
      including the regulation of bacterial virulence and elicitation of protective immune
      responses.  Work presented in this dissertation has further evaluated the role of Dam in
      regulation of several virulence factors in Salmonella typhimurium and Yersinia
      pseudotuberculosis.  Studies in Yersinia revealed that Dam overproduction alters the stringent
      regulation of many virulence factors, including a principal Yersinia immunogen, LcrV, and an
      actin cytotoxin, YopE.  Dysregulation of these virulence factors may be the mechanism by which
      dam mutants elicit protective immunity against Yersinia infections in vaccinated hosts.  In
      Salmonella, Dam regulates the expression of several virulence genes as well.  Moreover,
      expression of these genes was differentially affected by altered Dam levels in closely-related
      pathogenic and non-pathogenic strains of Salmonella.  These data suggest that differential
      gene regulation, rather than gross genomic differences contributes to the virulence
      disparities observed between these pathogenic and non-pathogenic isolates.  Finally, by
      expressing reovirus antigens in Salmonella, the possibility of using Dam-based vaccines as
      carriers of foreign antigens was investigated.  Effective live-attenuated carrier vaccines
      could be used to protect hosts from a variety of diseases for which no therapy is currently
      available.  Investigating the role of Dam in regulation of virulence factors in pathogens such
      as Salmonella and Yersinia will not only help decipher its role in regulation of virulence in
      other pathogens, but will also help design new vaccines that provide potent immunity against a
      wide range of infectious diseases that threaten the safety of public health worldwide.
AU  - Badie G
PT  - Journal Article
TA  - Ph.D. Thesis, Univ. of California, Santa Barbara
JT  - Ph.D. Thesis, Univ. of California, Santa Barbara
SO  - Ph.D. Thesis, Univ. of California, Santa Barbara 2005 : 1-149.

PMID- 15501808
VI  - 72
DP  - 2004
TI  - LcrV synthesis is altered by DNA adenine methylase overproduction in Yersinia pseudotuberculosis and is required to confer immunity in  vaccinated hosts.
PG  - 6707-6710
AB  - Yersinia pseudotuberculosis mutants that overproduce the DNA adenine methylase (Dam(OP)
      Yersinia) are attenuated, confer robust protective
      immune responses, and synthesize or secrete several Yersinia outer
      proteins (Yops) under conditions that are nonpermissive for synthesis
      and secretion in wild-type strains. To understand the molecular basis
      of immunity elicited by Dam(OP) Yersinia, we investigated the effects
      of Dam overproduction on the synthesis and localization of a principal
      Yersinia immunogen, LcrV, a low-calcium-responsive virulence factor
      involved in Yop synthesis, localization, and suppression of host
      inflammatory activities. Dam overproduction relaxed the stringent
      temperature and calcium regulation of LcrV synthesis. Moreover, the
      LcrV-dependent synthesis and localization of the actin cytotoxin, YopE,
      were shown to be relaxed in Dam(OP) cells, suggesting that the
      synthesis and localization of Yops can occur via both LcrV-dependent
      and -independent mechanisms. Last, the immunity conferred by Dam(OP)
      Yersinia was strictly dependent on the presence of LcrV, which may
      result from its role (i) as an immunogen, (ii) as an immunomodullator
      of host anti-inflammatory activities, or (iii) in the altered synthesis
      and localization of Yops that could contribute to immunogen repertoire
      expansion.
AU  - Badie G
AU  - Heithoff DM
AU  - Mahan MJ
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2004 72: 6707-6710.

PMID- 17172341
VI  - 189
DP  - 2007
TI  - Altered Levels of Salmonella DNA Adenine Methylase Are Associated with Defects in Gene Expression, Motility, Flagellar Synthesis, and Bile  Resistance in the Pathogenic Strain 14028 but Not in the Laboratory Strain  LT2.
PG  - 1556-1564
AB  - Comparative genomic analysis has revealed limited strain diversity between Salmonella
      pathogenic and nonpathogenic isolates. Thus, some of the
      relative virulence and host-immune response disparities may be credited to
      differential gene regulation rather than gross differences in genomic
      content. Here we show that altered levels of Salmonella DNA adenine
      methylase (Dam) resulted in acute defects in virulence-associated gene
      expression, motility, flagellin synthesis, and bile resistance in the
      Salmonella pathogenic strain 14028 but not in avirulent laboratory strain
      LT2. The defects in motility exhibited by 14028 in response to altered Dam
      levels was not dependent on the presence of the regulatory protein, RpoS.
      The transitioning between flagellar types (phase variation) was also
      differentially regulated in 14028 versus LT2 in response to dam levels,
      resulting in distinct differences in flagellin expression states. These
      data suggest that differential gene regulation may contribute to the
      relative virulence disparities observed between Salmonella serovars that
      are closely related at the DNA level.
AU  - Badie G
AU  - Heithoff DM
AU  - Sinsheimer RL
AU  - Mahan MJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2007 189: 1556-1564.

PMID- 29449395
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of the Bacillus pumilus Phage Leo2.
PG  - e00066-18
AB  - Bacillus spp. are ubiquitous Gram-positive microbes with many ecological and symbiotic
      interactions and can be pathogens. Phage Leo2 was found to infect a
      Bacillus pumilus strain isolated from soil. The sequence of phage Leo2 revealed
      74 genes; 31% of the genes have associated functions, and 67% of coding regions
      are unidentified open reading frames.
AU  - Badran S
AU  - Morales N
AU  - Schick P
AU  - Jacoby B
AU  - Villella W
AU  - Lorenz T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00066-18.

PMID- 28572313
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Blood Disease Bacterium A2 HR-MARDI, a Pathogen Causing  Banana Bacterial Wilt.
PG  - e00408-17
AB  - Blood disease bacterium A2 HR-MARDI was isolated from banana plants infected with banana blood
      disease and which were planted in Kuala Kangsar, Malaysia. Here, we
      report a draft genome sequence of blood disease bacterium A2 HR-MARDI, which
      could provide important information on the virulence mechanism of this pathogen.
AU  - Badrun R
AU  - Abu BN
AU  - Laboh R
AU  - Redzuan R
AU  - Bala JI
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00408-17.

PMID- 19412677
VI  - 13
DP  - 2009
TI  - Characterization of DNA polymerase from the hyperthermophilic archaeon Thermococcus marinus and its application to PCR.
PG  - 657-667
AB  - The family B DNA polymerase gene from the archaeon Thermococcus marinus (Tma) contains a long
      open reading frame of 3,939 bp that encodes 1,312
      amino acid residues. The gene is split by one intervening sequence that
      forms a continuous open reading frame with the two polymerase exteins. In
      this study, the Tma DNA polymerase gene both with (precursor form) and
      without (mature form) its intein was expressed in Escherichia coli,
      purified by heat treatment and HiTrap Heparin HP column chromatography and
      characterized. Primary sequence analysis of the mature Tma polymerase
      showed high sequence identity with DNA polymerases in the genus
      Thermococcus. The expressed precursor form was easily spliced during
      purification steps. The molecular mass of the purified Tma DNA polymerases
      is about 90 kDa, as estimated by SDS-PAGE. Both Tma DNA polymerases showed
      the same properties. PCR performed with this enzyme was found to be
      optimal in the presence of 50 mM Tris-HCl (pH 8.4), 40 mM KCl, 12.5 mM
      (NH(4))(2)SO(4,) 2 mM MgCl(2,) 0.05% Triton X-100 and 0.0075% BSA.
      Furthermore, long-range PCR and time-saving PCR were performed using
      various specific ratios of Taq and Tma DNA polymerases (Tma plus DNA
      polymerase).
AU  - Bae H
AU  - Kim KP
AU  - Lee JI
AU  - Song JG
AU  - Kil EJ
AU  - Kim JS
AU  - Kwon ST
PT  - Journal Article
TA  - Extremophiles
JT  - Extremophiles
SO  - Extremophiles 2009 13: 657-667.

PMID- 19634205
VI  - 297
DP  - 2009
TI  - Characterization of intein homing endonuclease encoded in the DNA polymerase gene of Thermococcus marinus.
PG  - 180-188
AB  - The DNA polymerase gene of Thermococcus marinus (Tma) contains an intein inserted at the pol-b
      site that possesses a 1611-bp ORF encoding
      a 537-amino acid residue. The LAGLIDADG motif, often found in
      site-specific DNA endonucleases, was detected within the amino acid
      sequence of the intein. The intein endonuclease, denoted as PI-Tma, was
      purified as a naturally spliced product from the expression of the
      complete DNA polymerase gene in Escherichia coli. PI-Tma cleaved
      intein-less DNA sequences, leaving four-base-long, 3'-hydroxyl
      overhangs with 5'-phosphate. Nonpalindromic recognition sequences 19 bp
      long were also identified using partially complementary oligonucleotide
      pair sequences inserted into the plasmid pET-22b(+). Cleavage by PI-Tma
      was optimal when present in 50 mM glycine-NaOH (pH 10.5), 150 mM KCl
      and 12 mM MgCl2 at 70 degrees C.
AU  - Bae H
AU  - Kim KP
AU  - Song JM
AU  - Kim JH
AU  - Yang JS
AU  - Kwon ST
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2009 297: 180-188.

PMID- Not carried by PubMed...
VI  - 31
DP  - 1993
TI  - Purification and characterization of a restriction endonuclease from Streptomyces exfoliatus.
PG  - 544-549
AB  - Thirty strains of Streptomyces sp. isolated from soil samples were screened for the presence
      of site-specific endonuclease.  One strain among them showed endonuclease activity to cleave
      lambda DNA.  This study describes the purification and characterization of a site-specific
      restriction endonuclease SexIII from Streptomyces exfoliatus.  The purification procedure
      includes streptomycin sulfate treatment, DEAE-cellulose, hydroxylapatite, phosphocellulose P11
      column chromatography.  This enzyme required high Mg2+ concentration (20-40 mM), and showed
      maximal activity at neutral pH(7-8) in the absence of NaCl.  The enzyme did not require salt
      for its activity and was inhibited by over 75 mM NaCl.  SexIII cut lambda DNA and plasmid
      pBluescript, recognized the hexanucleotide sequence 5'-CCGC/GG-3', and proved to be an
      isoschizomer of SacII.
AU  - Bae M
AU  - Par J-O
AU  - Hwang H-Y
AU  - Yim J
PT  - Journal Article
TA  - Korean J. Microbiol.
JT  - Korean J. Microbiol.
SO  - Korean J. Microbiol. 1993 31: 544-549.

PMID- Not carried by PubMed...
VI  - 32
DP  - 1994
TI  - Purification of restriction endonuclease, SdiI, from Steptomyces diastatochromogenes.
PG  - 297-300
AB  - About thirty bacterial strains of Actinomycetes, isolated from the soil, were examined for the
      presence of restriction endonuclease activity.  Streptomyces diastatochromogenes, which was
      identified previously, was found to contain restriction endonuclease activity.  The
      purification of this enzyme, SdiI, was carried out via streptomycin sulfate precipitation and
      ammonium sulfate fractionation followed by hydroxylapatite column chromatography.  Sephacryl
      S-200 HR column chromatography and a second hydroxylapatite column chromatography.
      SDS-polyacrylamide gel electrophoresis of the active protein (purified from various column
      chromatography) resulted in 35,000 Da protein.
AU  - Bae M
AU  - Song E-S
PT  - Journal Article
TA  - Korean J. Microbiol.
JT  - Korean J. Microbiol.
SO  - Korean J. Microbiol. 1994 32: 297-300.

PMID- Not carried by PubMed...
VI  - 32
DP  - 1994
TI  - Characterization of the restriction endonuclease, SdiI, from Streptomyces diastatochromogenes.
PG  - 301-305
AB  - In catalytic properties of the restriction endonuclease, SdiI, which was purified from
      Streptomyces diastatochromogenes, this enzyme was active over a wide pH range between 7.0 and
      12.5 and up to 60oC and 500 mM NaCl.  It was stable between 20oC and 60oC, and MgCl2 is
      essential for endonuclease activity.  The restriction map of lambda DNA which was obtained by
      double digestion with various enzymes suggested that SdiI was an isoschizomer of XhoI.  From
      the determination of the restriction site, based on DNA sequencing, the recognition and
      cleavage specificity of SdiI was concluded to be
      5'-C/TCGA G-3'
      3'-G AGCT/C-5'.
AU  - Bae M
AU  - Song E-S
AU  - Hwang H-Y
AU  - Yim J
PT  - Journal Article
TA  - Korean J. Microbiol.
JT  - Korean J. Microbiol.
SO  - Korean J. Microbiol. 1994 32: 301-305.

PMID- Not carried by PubMed...
VI  - 31
DP  - 1993
TI  - Numerical identification of Streptomyces sp. 58 producing restriction endonuclease SexIII, a novel isoschizomer of SacII.
PG  - 465-470
AB  - Numerical identification was carried out for an isolate of Streptomyces sp. 58 producing a new
      restriction endonuclease SexIII.  Fifty taxonomic unit characters were tested and the data
      were analyzed numerically using the TAXON program.  The isolate was identified to the major 5
      of Streptomyces.  Therefore, it was concluded that the isolate was identified to be a member
      of Streptomyces exfoliatus.
AU  - Bae M
AU  - Suh W-N
AU  - Park J-O
AU  - Kim HT
AU  - Lee K-J
PT  - Journal Article
TA  - Korean J. Microbiol.
JT  - Korean J. Microbiol.
SO  - Korean J. Microbiol. 1993 31: 465-470.

PMID- Not carried by PubMed...
VI  - 22
DP  - 1994
TI  - Numerical identification of a Streptomyces strain producing restriction endonuclease SdiI.
PG  - 126-133
AB  - Numerical identification was applied for Streptomyces sp. 264, an isolate producing a new
      restriction endonuclease SdiI. The restriction enzyme would appear to be an isoschizomer of
      XhoI. Fifty taxonomic unit characters were tested and the data obtained were analyzed
      numerically by using the TAXON program. The isolate was identified to be the major cluster 19
      of Streptomyces and best matched to S. diastatochromogenes. It was, therefore, concluded that
      the isolate was identified to be a member of Streptomyces diastatochromogenes.
AU  - Bae M
AU  - Suh W-N
AU  - Song E-S
AU  - Lee K-J
PT  - Journal Article
TA  - Korean J. Appl. Microbiol. Biotechnol.
JT  - Korean J. Appl. Microbiol. Biotechnol.
SO  - Korean J. Appl. Microbiol. Biotechnol. 1994 22: 126-133.

PMID- Not carried by PubMed...
VI  - 21
DP  - 1993
TI  - Numerical identification of a Streptomyces strain producing a thermotolerable restriction endonuclease SviI.
PG  - 299-305
AB  - Numerical identification was carried out for an isolate of Streptomyces D2-5 producing a new
      restriction endonuclease SviI. Fifty taxonomic unit characters were tested and the data were
      analyzed numerically using the TAXON program. The isolate was best matched to Streptomyces
      violochromogenes in the major cluster 18 of Streptomyces. Therefore, it was concluded that the
      isolate was identified to be a member of Streptomyces violochromogenes.
AU  - Bae M
AU  - Yun M-S
AU  - Kim H-T
AU  - Lee K-J
PT  - Journal Article
TA  - Korean J. Appl. Microbiol. Biotechnol.
JT  - Korean J. Appl. Microbiol. Biotechnol.
SO  - Korean J. Appl. Microbiol. Biotechnol. 1993 21: 299-305.

PMID- 30533895
VI  - 7
DP  - 2018
TI  - Draft Genome Sequence of Deinococcus koreensis SJW1-2(T), a Gamma Radiation-Resistant Bacterium Isolated from River Water.
PG  - e00894-18
AB  - Deinococcus koreensis SJW1-2(T) was isolated from river water and was observed to be highly
      resistant to gamma radiation. In this study, we report a draft genome
      sequence which revealed that SJW1-2(T) possesses genes involved in nucleotide
      excision repair. The primary genomic information will aid in elucidating the DNA
      repair mechanism during ionizing radiation.
AU  - Baek K
AU  - Chung EJ
AU  - Choi GG
AU  - Nam YH
AU  - Choi A
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e00894-18.

PMID- 28912310
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Prevotella copri Isolated from the Gut of a Healthy Indian Adult.
PG  - e00834-17
AB  - Prevotella copri, a Gram-negative anaerobic rod-shaped bacterium, is frequently associated
      with the human gastrointestinal tract and influences host physiology,
      immunity, and metabolic pathways. In the present study, we report the draft
      genome sequence of P. copri isolated from the gut of a healthy Indian adult.
AU  - Bag S
AU  - Ghosh TS
AU  - Das B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00834-17.

PMID- 29025929
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequence of Bifidobacterium longum Strain Indica, Isolated from the  Gut of a Healthy Indian Adult.
PG  - e01017-17
AB  - Bifidobacterium longum, a Gram-positive rod-shaped anaerobic bacterium, inhabits  the human
      gastrointestinal tract and contributes significantly to oligosaccharide
      production, amino acid metabolism, and protection against intestinal
      inflammation. Here, we report the whole-genome sequence of B. longum, which was
      isolated from the gastrointestinal tract of a healthy Indian adult.
AU  - Bag S
AU  - Ghosh TS
AU  - Das B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01017-17.

PMID- 29051237
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequence of a Megasphaera elsdenii Strain Isolated from the Gut of a Healthy Indian Adult Subject.
PG  - e01033-17
AB  - Megasphaera elsdenii has been previously reported in the gut of ruminating animals. Its role
      as an animal probiotic is being investigated, specifically from
      the perspective of enhancing animal productivity. Herein, we report the draft
      genome sequence of M. elsdenii strain indica isolated from the stool sample of a
      healthy Indian subject.
AU  - Bag S
AU  - Ghosh TS
AU  - Das B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01033-17.

PMID- 29146862
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Faecalibacterium prausnitzii Isolated from the Gut of a Healthy Indian Adult.
PG  - e01286-17
AB  - Faecalibacterium prausnitzii is the most abundant (~4%) member of the phylum Firmicutes found
      in the colon of healthy humans. It is a strict anaerobe and
      plays an important role in intestinal homeostasis. Here, we report the complete
      genome sequence of F. prausnitzii strain Indica.
AU  - Bag S
AU  - Ghosh TS
AU  - Das B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01286-17.

PMID- 29167267
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Collinsella aerofaciens Isolated from the Gut of a Healthy Indian Subject.
PG  - e01361-17
AB  - Collinsella aerofaciens, a rod-shaped nonmotile obligate anaerobe, is the most abundant
      actinobacterium in the gastrointestinal tract of healthy humans. An
      altered abundance of C. aerofaciens may be linked with several health disorders,
      including irritable bowel syndrome. In the present study, we report the complete
      genome sequence of C. aerofaciens strain indica.
AU  - Bag S
AU  - Ghosh TS
AU  - Das B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01361-17.

PMID- 29074663
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Arsenic-Resistant Microbacterium sp. Strain SZ1 Isolated from Arsenic-Bearing Gold Ores.
PG  - e01183-17
AB  - Microbacterium sp. strain SZ1 isolated from gold ores of a Malaysia gold mine was found to be
      highly resistant to arsenic. Here, we report the draft genome sequence of SZ1, which may
      provide further insights into understanding its arsenic resistance mechanism. In this draft
      genome, a complete set of ars operons and two additional scattered ars genes were encoded.
AU  - Bahari ZM
AU  - Ibrahim Z
AU  - Jaafar J
AU  - Shahir S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01183-17.

PMID- 
VI  - 
DP  - 2009
TI  - Biophysical characterization and biochemical direction of methyltransferase-DNA-interactions.
PG  - 1-192
AB  - 
AU  - Bahr M
PT  - Journal Article
TA  - Ph.D. Thesis, Germany
JT  - Ph.D. Thesis, Germany
SO  - Ph.D. Thesis, Germany 2009 : 1-192.

PMID- 29599158
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Pseudomonas gingeri Strain LMG 5327, the Causative Agent of Ginger Blotch in Agaricus bisporus.
PG  - e00196-18
AB  - The draft genome sequence of Pseudomonas gingeri LMG 5327 (NCPPB 3146), the causative agent of
      ginger blotch in Agaricus bisporus, is reported. Together with
      another mushroom pathogen, Pseudomonas agarici, it belongs to a distinct
      phylogenomic group.
AU  - Bahrami T
AU  - Zarvandi S
AU  - De Mot R
AU  - Gross H
AU  - Changi-Ashtiani M
AU  - Shahani T
AU  - Rokni-Zadeh H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00196-18.

PMID- 10921084
VI  - 28
DP  - 1997
TI  - Mammalian DNA methylase.
PG  - 67-69
AB  - 
AU  - Bai J
AU  - He Z
PT  - Journal Article
TA  - Shengli Kexue Jinzhan
JT  - Shengli Kexue Jinzhan
SO  - Shengli Kexue Jinzhan 1997 28: 67-69.

PMID- 26633631
VI  - 528
DP  - 2015
TI  - Functional overlap of the Arabidopsis leaf and root microbiota.
PG  - 364-369
AB  - Roots and leaves of healthy plants host taxonomically structured bacterial
      assemblies, and members of these communities contribute to plant growth and
      health. We established Arabidopsis leaf- and root-derived microbiota culture
      collections representing the majority of bacterial species that are reproducibly
      detectable by culture-independent community sequencing. We found an extensive
      taxonomic overlap between the leaf and root microbiota. Genome drafts of 400
      isolates revealed a large overlap of genome-encoded functional capabilities
      between leaf- and root-derived bacteria with few significant differences at the
      level of individual functional categories. Using defined bacterial communities
      and a gnotobiotic Arabidopsis plant system we show that the isolates form
      assemblies resembling natural microbiota on their cognate host organs, but are
      also capable of ectopic leaf or root colonization. While this raises the
      possibility of reciprocal relocation between root and leaf microbiota members,
      genome information and recolonization experiments also provide evidence for
      microbiota specialization to their respective niche.
AU  - Bai Y
AU  - Muller DB
AU  - Srinivas G
AU  - Garrido-Oter R
AU  - Potthoff E
AU  - Rott M
AU  - Dombrowski N
AU  - Munch PC
AU  - Spaepen S
AU  - Remus-Emsermann M
AU  - Huttel B
AU  - McHardy AC
AU  - Vorholt JA
AU  - Schulze-Lefert P
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2015 528: 364-369.

PMID- Not carried by PubMed...
VI  - 0
DP  - 1998
TI  - Purification and characterization of type II restriction endonuclease (HpyI) of Helicobacter pylori.
PG  - 120
AB  - This study describes the purification and characterization of type II restriction endonuclease
      of Helicobacter pylori, a Gram-negative spiral bacterium associated with type B gastritis,
      peptic ulcer, and gastric cancer in human.  Helicobacter pylori cytosol was subjected to
      polyethyleneimine treatment, salt precipitation, heparin-sepharose column chromatography, and
      fast protein liquid chromatography using Resource Q column and Mono Q column to purify the
      type II restriction endonuclease.  HpyI was characterized to recognize the sequence
      5'-GT(G/C)AC-3', yielding 5-base 5' protruding ends.  The restriction sequence was
      identical to that of Tsp45I.  The molecular weight of native protein was estimated to be 22
      kDa by size exclusion chromatography of FPLC.  The enzyme exhibited its maximal activity in
      the presence of 10-20 mM NaCl, but was inhibited completely in the presence of NaCl more than
      80 mM.  The enzyme showed its maximal activity in the presence of 1-10 mM MgCl2.  The optimal
      pH and temperature for enzyme activity was pH 9.0 and 37E, respectively.  MnCl2 could not
      substitute for MgCl2 in reaction mixture.  And addition of YA-mercaptoethanol and bovine serum
      albumin in reaction mixture led to loss of enzyme activity of HpyI.  HpyI was confirmed to
      digest genomic DNAs of enteric bacteria to less than 1 kb while it could not cut the genomic
      DNAs of Helicobacter pylori isolates.  Eighty HpyI restriction sites were found in the whole
      genome sequence of H. pylori reported by the Institute for Genomic Research, which are less
      than 2.5% of estimated numbers of HpyI restriction sites in the whole genome.  The pBR322 DNA
      that was treated with the crude extract of H. pylori cytosol in the presence of 0.3 mM
      S-adenosylmethionine was partially protected from HpyI restriction.  Therefore, the enzymatic
      activity in the crude extract is likely a DNA methyltransferase.  H. pylori DNA is supposed to
      be protected from HpyI restriction by the rareness of HpyI restriction sites and methylation
      of the site.  Taken together, HpyI might be the one of the barriers preventing the
      introduction of foreign DNAs into H. pylori.
AU  - Baik SC
AU  - Lee WK
AU  - Song JY
AU  - Choi YJ
AU  - Rye BD
AU  - Choi SH
AU  - Cho MJ
AU  - Rhee KH
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1998 0: 120.

PMID- 25395652
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Massilia sp. Strain BSC265, Isolated from Biological Soil Crust of Moab, Utah.
PG  - e01199-14
AB  - Massilia sp. BSC265 was isolated from a biological soil crust near Moab, Utah. The strain
      appears to be capable of chemotaxis and exopolysaccharide synthesis
      for biofilm adhesion. The BSC265 genome contains a complete dissimilatory nitrate
      reduction pathway as well as a TCA cycle, making it a facultative anaerobe.
AU  - Bailey AC
AU  - Kellom M
AU  - Poret-Peterson AT
AU  - Noonan K
AU  - Hartnett HE
AU  - Raymond J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01199-14.

PMID- 25395651
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Bacillus sp. Strain BSC154, Isolated from Biological Soil Crust of Moab, Utah.
PG  - e01198-14
AB  - Bacillus sp. BSC154 was isolated from a biological soil crust near Moab, Utah. The strain
      appears to be capable of chemotaxis and biofilm production. The BSC154
      genome contains iron siderophore production, nitrate reduction, mixed
      acid-butanediol fermentation, and assimilatory and dissimilatory sulfate
      metabolism pathways.
AU  - Bailey AC
AU  - Kellom M
AU  - Poret-Peterson AT
AU  - Noonan K
AU  - Hartnett HE
AU  - Raymond J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01198-14.

PMID- 25395650
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Microvirga sp. Strain BSC39, Isolated from Biological Soil Crust of Moab, Utah.
PG  - e01197-14
AB  - Microvirga sp. BSC39 was isolated from a biological soil crust near Moab, Utah. The strain
      appears to be capable of chemotaxis and exopolysaccharide synthesis
      for biofilm adhesion. The BSC39 genome contains iron siderophore uptake and
      hydrolysis enzymes; however, it lacks siderophore synthesis pathways, suggesting
      the uptake of siderophores produced by neighboring microbes.
AU  - Bailey AC
AU  - Kellom M
AU  - Poret-Peterson AT
AU  - Noonan K
AU  - Hartnett HE
AU  - Raymond J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01197-14.

PMID- 3040892
VI  - 132
DP  - 1986
TI  - Inhibition of restriction in Streptomyces clavuligerus by heat treatment.
PG  - 2945-2947
AB  - Inefficient transformation of Streptomyces clavuligerus protoplasts by DNA from
      the plasmid pIJ702, isolated from S. lividans, was attributed to restriction in
      view of the observation that efficient transformation was observed using
      modified pIJ702 (isolated from S. clavuligerus).  The restriction system could
      be partially inhibited by treating protoplasts at 45C prior to transformation.
      This treatment increased the transformation frequencies of pIJ702 DNA by
      100-fold and was used to introduce other plasmids into S. clavuligerus.
AU  - Bailey CR
AU  - Winstanley DJ
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1986 132: 2945-2947.

PMID- 29217792
VI  - 5
DP  - 2017
TI  - Genome Sequence of Listeria monocytogenes Strain F4244, a 4b Serotype.
PG  - e01324-17
AB  - Listeria monocytogenes is an opportunistic invasive foodborne pathogen. Here, we  performed
      whole-genome sequencing of L. monocytogenes strain F4244 (serotype 4b)
      using Illumina sequencing. The sequence showed 94.5% identity with strain F2365,
      serotype 4b, and 90.6% with EGD-e, serotype 1/2a.
AU  - Bailey TW
AU  - do Nascimento NC
AU  - Bhunia AK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01324-17.

PMID- 
VI  - 104
DP  - 2004
TI  - Setting the phage for evolution: The mechanism of host exclusion of bacteriophage T4 IPI.
PG  - 392
AB  - Interaction of bacteria and phages has led to the evolution of complex phage exclusion systems
      and cognate exclusion avoidance mechanisms.  Chief among these are restriction-modification
      system enzymes that attack the invading phage DNA and against which phages employ various
      strategies including DNA modification.  The T-even phages of the myoviridae utilize extended
      DNA modifications to host RMS's with base methylations, 100% hydroxymethylated-cytosine, and
      alpha-, beta-, and other-glucosylated HmC derivaties.  The injected DNA-bound T4 IPI protein
      (~350 molecules/DNA), nonessential in most hosts, has been shown to be necessary for
      productive T4 infection of the pathogenic E. coli K isolate CT596.  This host has now been
      shown to harbor a prophage that encodes the RMS genes gIBEGs (36.649 kb) and gIBEGd (26.854
      kb), with 65% and 48% identity to H. pylori sequences of unknown function that have been
      cloned and shown to be necessary and sufficient to restrict T4 DNA lacking IPI.
      GpIBEGs/gpIBEGd encode a novel Type IV RMS that, unlike previously discovered E. coli
      restriction systems, is able to digest the glucosylated-HmC T4 DNA, and is apparently
      physically blocked from its recognition sequence by the presence of IPI on the DNA.  Active
      tag derivatized forms of the two proteins have been purified to near homogeneity.  The
      proteins are  inactive separately, but together degrade in apparently non-sequence-specific
      manner glucosylated-HmC DNA substrates, with no activity against non-modified templates such
      as T4 C-DNA.  The activity is stimulated by 1-2mM GTP and this effect is inhibited by excess
      ATP.  It appears that this bacterial restriction system has evolved specifically to combat
      infections by T-even phages.  Pursuing this struggle, the T-evens have evolved a highly
      diverse and, in some cases, expanded family of capsid-targeted internal protein I (IPI) locus
      gene products that may specifically shield the diverse modifications of their HmC residues
      from IBEG family RMS's.
AU  - Bair CL
AU  - Black LW
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 2004 104: 392.

PMID- 17188297
VI  - 366
DP  - 2007
TI  - A Type IV Modification Dependent Restriction Nuclease that Targets Glucosylated Hydroxymethyl Cytosine Modified DNAs.
PG  - 768-778
AB  - The Escherichia coli CT596 prophage exclusion genes gmrS and gmrD were found to encode a novel
      type IV modification-dependent restriction
      nuclease that targets and digests glucosylated (glc)-hydroxymethylcytosine
      (HMC) DNAs. The protein products GmrS (36 kDa) and GmrD (27 kDa) were
      purified and found to be inactive separately, but together degraded
      several different glc-HMC modified DNAs (T4, T2 and T6). The GMR enzyme is
      able to degrade both alpha-glucosy-HMC T4 DNA and beta-glucosyl-HMC T4
      DNA, whereas no activity was observed against non-modified DNAs including
      unmodified T4 cytosine (C) DNA or non-glucosylated T4 HMC DNA. Enzyme
      activity requires NTP, favors UTP, is stimulated by calcium, and initially
      produces 4 kb DNA fragments that are further degraded to low molecular
      mass products. The enzyme is inhibited by the T4 phage internal protein I*
      (IPI*) to which it was found to bind. Overall activities of the purified
      GmrSD enzyme are in good agreement with the properties of the cloned gmr
      genes in vivo and suggest a restriction enzyme specific for sugar modified
      HMC DNAs. IPI* thus represents a third generation bacteriophage defense
      against restriction nucleases of the Gmr type.
AU  - Bair CL
AU  - Black LW
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2007 366: 768-778.

PMID- 17188711
VI  - 366
DP  - 2007
TI  - Exclusion of Glucosyl-Hydroxymethylcytosine DNA Containing Bacteriophages Is Overcome by the Injected Protein Inhibitor IPI*.
PG  - 779-789
AB  - The Escherichia coli isolate CT596 excludes infection by the Myoviridae T4 ip1(-) phage that
      lacks the encapsidated IPI* protein normally injected into the host with the phage DNA.
      Screening of a CT596 genomic library identified adjacent genes responsible for this exclusion,
      gmrS (942 bp) and gmrD (708 bp) that are encoded by a cryptic prophage DNA. The two genes are
      necessary and sufficient to confer upon a host the ability to exclude infection by T4 ip1(-)
      phage and other glucosyl-hydroxymethylcytosine (glc-HMC) Tevens lacking the ip1 gene, yet
      allow infection by phages with non-glucoslyated cytosine (C) DNA that lack the ip1 gene. A
      plasmid expressing the ip1 gene product, IPI*, allows growth of Tevens lacking ip1 on E. coli
      strains carrying the cloned gmrS/gmrD genes. Members of the Teven family carry a diverse and,
      in some cases, expanded set of ip1 locus genes. In vivo analysis suggests a family of gmr
      genes that specifically target sugar-HMC modified DNA have evolved to exclude Teven phages,
      and these exclusion genes have in turn been countered by a family of injected exclusion
      inhibitors that likely help determine the host range of different glc-HMC phages.
AU  - Bair CL
AU  - Rifat D
AU  - Black LW
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2007 366: 779-789.

PMID- 30533914
VI  - 7
DP  - 2018
TI  - Draft Genome Sequence of the Plant Growth-Promoting Rhizobacterium Pseudomonas protegens Strain BNJ-SS-45, Isolated from Rhizosphere Soil of Wheat (Triticum  aestivum).
PG  - e00926-18
AB  - Here, we present the draft genome sequence of Pseudomonas protegens strain BNJ-SS-45, which
      was isolated from wheat rhizosphere. The genome is assembled
      with 7,116,445 bp with a GC content of 63.34% consisting of 32 scaffolds. The
      genome is useful in prediction of secondary metabolites, particularly rhizoxin,
      pyoverdine, and bacteriocin.
AU  - Bajpai A
AU  - Shende KK
AU  - Meena N
AU  - Suravajhala P
AU  - Medicherla KM
AU  - Johri BN
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e00926-18.

PMID- 29682168
VI  - 13
DP  - 2018
TI  - Genome sequence of Planktotalea frisia type strain (SH6-1(T)), a representative of the Roseobacter group isolated from the North Sea during a phytoplankton  bloom.
PG  - 7
AB  - Planktotalea frisia SH6-1(T) Hahnke et al. (Int J Syst Evol Microbiol 62:1619-24, 2012) is a
      planktonic marine bacterium isolated during a phytoplankton bloom from
      the southern North Sea. It belongs to the Roseobacter group within the
      alphaproteobacterial family Rhodobacteraceae. Here we describe the draft genome
      sequence and annotation of the type strain SH6-1(T). The genome comprises
      4,106,736 bp and contains 4128 protein-coding and 38 RNA genes. The draft genome
      sequence provides evidence for at least three extrachromosomal elements, encodes
      genes for DMSP utilization, quorum sensing, photoheterotrophy and a type IV
      secretion system. This indicates not only adaptation to a free-living lifestyle
      of P. frisia but points also to interactions with prokaryotic or eukaryotic
      organisms.
AU  - Bakenhus I
AU  - Voget S
AU  - Poehlein A
AU  - Brinkhoff T
AU  - Daniel R
AU  - Simon M
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2018 13: 7.

PMID- 20421484
VI  - 107
DP  - 2010
TI  - Enigmatic, ultrasmall, uncultivated Archaea.
PG  - 8806-8811
AB  - Metagenomics has provided access to genomes of as yet uncultivated microorganisms
      in natural environments, yet there are gaps in our knowledge-particularly for
      Archaea-that occur at relatively low abundance and in extreme environments.
      Ultrasmall cells (<500 nm in diameter) from lineages without cultivated
      representatives that branch near the crenarchaeal/euryarchaeal divide have been
      detected in a variety of acidic ecosystems. We reconstructed composite,
      near-complete approximately 1-Mb genomes for three lineages, referred to as ARMAN
      (archaeal Richmond Mine acidophilic nanoorganisms), from environmental samples
      and a biofilm filtrate. Genes of two lineages are among the smallest yet
      described, enabling a 10% higher coding density than found genomes of the same
      size, and there are noncontiguous genes. No biological function could be inferred
      for up to 45% of genes and no more than 63% of the predicted proteins could be
      assigned to a revised set of archaeal clusters of orthologous groups. Some core
      metabolic genes are more common in Crenarchaeota than Euryarchaeota, up to 21% of
      genes have the highest sequence identity to bacterial genes, and 12 belong to
      clusters of orthologous groups that were previously exclusive to bacteria. A
      small subset of 3D cryo-electron tomographic reconstructions clearly show
      penetration of the ARMAN cell wall and cytoplasmic membranes by protuberances
      extended from cells of the archaeal order Thermoplasmatales. Interspecies
      interactions, the presence of a unique internal tubular organelle [Comolli, et
      al. (2009) ISME J 3:159-167], and many genes previously only affiliated with
      Crenarchaea or Bacteria indicate extensive unique physiology in organisms that
      branched close to the time that Cren- and Euryarchaeotal lineages diverged.
AU  - Baker BJ
AU  - Comolli LR
AU  - Dick GJ
AU  - Hauser LJ
AU  - Hyatt D
AU  - Dill BD
AU  - Land ML
AU  - Verberkmoes NC
AU  - Hettich RL
AU  - Banfield JF
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2010 107: 8806-8811.

PMID- 
VI  - 20
DP  - 2006
TI  - Proteins by design.
PG  - 26-32
AB  - Imagine having the power to create a brand new protein - biosensor for any small molecule,
      say, or a novel enzyme - on demand.  It's not pure fantasy.  Computational structural biology
      is poised to put this power into our hands.  Along with a team of research groups around the
      world, we have begun designing novel proteins and folds from scratch, computing amino acid
      sequences that will fold to create enzymatic activities never before seen in nature.  The
      possibilities are limited only by our imaginations: Picture an endonuclease designed to thwart
      malaria, molecular sensors for bioterror agents, or a vaccine that HIV is less likely to
      evolve around.  The mechanics of these engineering feats are closely related, perhaps not
      surprisingly, to their logical inverse: structure prediction.  Scientists have for years tried
      to develop methods for predicting a protein's structure simply from its amino acid sequence.
      Imagine that in the time it takes to sequence the genome of an organism, scientists could also
      characterize the structure of each of its proteins.  This would unveil biomolecular
      interactions, structural homologies, functional roles, and potential drug targets that might
      never be found from gene sequence alone.  Although there is still a long way to go, with
      improvements to algorithms and increases in computing power, exciting progress is being made
      in both prediction and design.
AU  - Baker D
PT  - Journal Article
TA  - The Scientist
JT  - The Scientist
SO  - The Scientist 2006 20: 26-32.

PMID- 3039984
VI  - 146
DP  - 1987
TI  - The influence of the dT.dG mispair on the activity of the human DNA (cytosine-5) methyltransferase.
PG  - 596-602
AB  - Synthetic oligodeoxynucleotides containing a dT-dG mispair at a centrally located d(pCG) dimer
      are methylated at a moderate rate by highly purified human DNA (cytosine-5) methyltransferase
      (E.C.2.1.1.37). The presence of a mispaired dT in one strand induced the enzyme to
      preferentially methylate the opposite strand.
AU  - Baker DJ
AU  - Hardy TA
AU  - Smith SS
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1987 146: 596-602.

PMID- 3248725
VI  - 74
DP  - 1988
TI  - Recognition of structural perturbations in DNA by human DNA(cytosine-5)methyltransferase.
PG  - 207-210
AB  - We have used oligodeoxynucleotides to study DNA methyltransferase activity on several types of
      DNA structure in which the cytosine is mispaired to test these predictions. These sequences,
      30 nt in length, containing either C-C or A-C mismatches have been studied in detail. In both
      cases mispaired cytosines are selectively enhanced as acceptors of DNA methylation. Our
      findings with the C-C mispair are illustrative. A kinetic comparison showed that a duplex
      containing a C-C mispair was methylated about seven-fold faster than a complementary
      unmethylated duplex of otherwise identical sequence. Autoradiographic analysis of the
      enzymatically methylated product showed that the methyl groups were applied to each of the
      cytosines in the mismatch with about equal efficiency. MspI (but not HpaII) was able to
      partially cleave the duplex structure containing the mismatch, suggesting that there is a
      dynamic equilibrium in solution between structures like those shown in Fig. 1. The d(pCCGG)
      recognition site is regenerated in structures (2) and (4).
AU  - Baker DJ
AU  - Kan JLC
AU  - Smith SS
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 207-210.

PMID- 8240363
VI  - 196
DP  - 1993
TI  - Transition state analogs as affinity labels for human DNA methyltransferases.
PG  - 864-871
AB  - A new class of affinity labels has been developed for human DNA (cytosine-5)
      methyltransferases. These oligodeoxynucleotides contain 5-fluorodeoxycytidine at a mispair
      within the recognition motif of the human enzyme. They were not effectively recognized by
      bacterial methyltransferases. They can be viewed as analogs of the intermediates transiently
      produced by methyltransferases during catalysis. Affinity labelling patterns suggest that both
      the structurally induced activity and the methyl-directed activity of the human enzymes
      operate by the same mechanism and reside on the same polypeptide chains.
AU  - Baker DJ
AU  - Laayoun A
AU  - Smith SS
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1993 196: 864-871.

PMID- 26021915
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of 24570, the Type Strain of Shigella flexneri.
PG  - e00393-15
AB  - Shigella flexneri is a diarrheal pathogen that causes a large disease burden worldwide. We
      sequenced the genome of the publicly available type strain (S.
      flexneri 2a strain 24570) of this bacterial species to increase its utility as a
      reference. We present genome assembly results and comparisons with other
      reference strains.
AU  - Baker KS
AU  - Parkhill J
AU  - Thomson NR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00393-15.

PMID- 2986391
VI  - 2
DP  - 1985
TI  - Obtaining the preparations of immobilized restrictases SalI and PvuII.
PG  - 32-34
AB  - Conditions for the immobilization of specific endonucleases SalI and PvuII on
      BrCN-activated Sepharose 4B have been selected.  Some physico-chemical
      properties of the preparations of immobilized restrictases SalI and PvuII have
      been characterized.  The specific and general activity values of the
      preparations thus obtained have been established.  The immobilized enzymes have
      been used for the multiple restriction of the DNA of phage lambda and the DNA
      of Neisseria meningitidis.
AU  - Bakh NL
AU  - Semina IE
PT  - Journal Article
TA  - Zh. Mikrobiol. Epidemiol. Immunobiol.
JT  - Zh. Mikrobiol. Epidemiol. Immunobiol.
SO  - Zh. Mikrobiol. Epidemiol. Immunobiol. 1985 2: 32-34.

PMID- 2992364
VI  - 30
DP  - 1985
TI  - Isolation and Purification of Restriction Endonuclease PmiI from Pseudomonas Mirabilis 1667.
PG  - 342-344
AB  - A new restriction endonuclease PmiI was detected in Proteus mirabilis 1667.
      The enzyme hydrolyzes DNA of the phage lambda into 10 electrophoretically
      separating fragments with molecular weights of 1.3-7.9 mD.  With the use of
      two-stage chromatography on sepharose and phosphocellulose it is possible to
      obtain restriction endonuclease PmiI free of the admixtures of ballast
      proteins, nonspecific nucleases and phosphatases.
AU  - Bakh NL
AU  - Tsvetkova NV
AU  - Semina IE
AU  - Tarasov AP
AU  - Mileikovskaya MM
AU  - Gruber IM
AU  - Polyachenko VM
AU  - Romanenko EE
PT  - Journal Article
TA  - Antibiot. Med. Biotekhnol.
JT  - Antibiot. Med. Biotekhnol.
SO  - Antibiot. Med. Biotekhnol. 1985 30: 342-344.

PMID- 16507575
VI  - 281
DP  - 2006
TI  - Nuclear import of Ho endonuclease utilizes two nuclear localization signals and four importins of the ribosomal import system.
PG  - 12218-12226
AB  - Activity of Ho, the yeast mating switch endonuclease, is restricted to a narrow time window of
      the cell cycle. Ho is unstable and despite
      being a nuclear protein is exported to the cytoplasm for proteasomal
      degradation. We report here the molecular basis for the highly
      efficient nuclear import of Ho and the relation between its short
      half-life and passage through the nucleus. The Ho nuclear import
      machinery is functionally redundant, being based on two bipartite
      nuclear localization signals, recognized by four importins of the
      ribosomal import system. Ho degradation is regulated by the DNA damage
      response and Ho retained in the cytoplasm is stabilized, implying that
      Ho acquires its crucial degradation signals in the nucleus. Ho arose by
      domestication of a fungal VMA1 intein. A comparison of the primary
      sequences of Ho and fungal VMA1 inteins shows that the Ho nuclear
      localization signals are highly conserved in all Ho proteins, but are
      absent from VMA1 inteins. Thus adoption of a highly efficient import
      strategy occurred very early in the evolution of Ho. This may have been
      a crucial factor in establishment of homothallism in yeast, and a key
      event in the rise of the Saccharomyces sensu stricto.
AU  - Bakhrat A
AU  - Baranes K
AU  - Krichevsky O
AU  - Rom I
AU  - Schlenstedt G
AU  - Pietrokovski S
AU  - Raveh D
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2006 281: 12218-12226.

PMID- 15020462
VI  - 166
DP  - 2004
TI  - Homology modeling and mutational analysis of Ho endonuclease of yeast.
PG  - 721-728
AB  - Ho endonuclease is a LAGLIDADG homing endonuclease that initiates mating-type interconversion
      in yeast. Ho is encoded by a free-standing
      gene but shows 50% primary sequence similarity to the intein
      (protein-intron encoded) PI-SceI. Ho is unique among LAGLIDADG
      endonucleases in having a 120-residue C-terminal putative zinc finger
      domain. The crystal structure of PI-SceI revealed a bipartite enzyme
      with a protein-splicing domain (Hint) and intervening endonuclease
      domain. We made a homology model for Ho on the basis of the PI-SceI
      structure and performed mutational analysis of putative critical
      residues, using a mating-type switch as a bioassay for activity and
      GFP-fusion proteins to detect nuclear localization. We found that
      residues of the N-terminal sequence of the Hint domain are important
      for Ho activity, in particular the DNA recognition region. C-terminal
      residues of the Hint domain are dispensable for Ho activity; however,
      the C-terminal putative zinc finger domain is essential. Mutational
      analysis indicated that residues in Ho that are conserved relative to
      catalytic, active-site residues in PI-SceI and other related homing
      endonucleases are essential for Ho activity. Our results indicate that
      in addition to the conserved catalytic residues, Hint domain residues
      and the zinc finger domain have evolved a critical role in Ho activity.
AU  - Bakhrat A
AU  - Jurica MS
AU  - Stoddard BL
AU  - Raveh D
PT  - Journal Article
TA  - Genetics
JT  - Genetics
SO  - Genetics 2004 166: 721-728.

PMID- 708697
VI  - 17
DP  - 1978
TI  - Rapid, single-step purification of restriction endonucleases on Cibacron blue F3GA-agarose.
PG  - 4136-4139
AB  - After sonication and high-speed centrifugation, crude extracts of B.
      amyloliquefaciens, P. alcalifaciens, X. holicola, and B. globiggi were absorbed
      on the dye Cibacron blue F3GA covalently cross-linked to agarose.  The
      restriction endonucleases BamHI, PalI, XhoI, and BglI together with BglII were
      isolated by elution of the dye column with linear gradients to 0.5 M NaCl.  The
      enzymes so purified were free of contaminating nucleic acids and other
      nucleases and were sufficiently concentrated for direct, specific DNA
      hydrolysis.
AU  - Baksi K
AU  - Rogerson DL
AU  - Rushizky GW
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1978 17: 4136-4139.

PMID- Not included in PubMed...
VI  - 37
DP  - 1978
TI  - Rapid purification of restriction endonucleases on Cibacron Blue F3GA.
PG  - 1414
AB  - At present, purification of Type II restriction nucleases involves, after cell
      breakage and high-speed centrifugation, at least two more steps: DNA removal
      and column chromatography of the enzyme(s).  We show that the high-speed
      supernatant may be directly adsorbed on Cibacron Blue F3GA covalently
      cross-linked to agarose (CB) and restriction enzymes eluted with linear
      gradients from 0-0.5 M NaCl.  Per gram of frozen cells, 700 or more units of
      Bgl (I and II), Xho (I and II) and PalI were so isolated, free of contaminating
      nuclease activity as judged by electrophoresis of lambda DNA digests on 1.4%
      agarose gels.  The oligonucleotide band patterns observed agreed with those
      reported by others for the purified enzymes.  While the content of restriction
      nuclease activity varied between different batches of frozen cells, the
      recovery of enzyme activity islated by CB chromatography is comparable to that
      obtained by other procedures.  The extent of purification (Lowry protein) was
      55-fold (PalI).  Purified AluI, BamHI, XhoI and HaeIII (the isoschizomer of
      PalI) (N.E. Biolabs) were similarly bound on and eluted by serum albumin at 5
      mg/ml or calf thymus nucleic acid at 125 microgram/ml.
AU  - Baksi K
AU  - Rushizky GW
PT  - Journal Article
TA  - Fed. Proc.
JT  - Fed. Proc.
SO  - Fed. Proc. 1978 37: 1414.

PMID- 231393
VI  - 99
DP  - 1979
TI  - Purification of the restriction endonuclease PalI.
PG  - 207-212
AB  - The restriction endonuclease PalI was purified from Providencia alcalifaciens 1650-fold with a
      yield of 33%.  The purified protein moved as a single band upon polyacrylamide gel
      electrophoresis.  When this was carried out in the presence of sodium dodecyl sulfate, a
      molecular weight of 31,000 was obtained for PalI.  Gel filtration through Sephacryl S200 gave
      molecular weights ranging from 44,000 to 53,000 when 58 to 1870 ng/ml enzyme were used,
      respectively.  Other properties of the enzyme are described.
AU  - Baksi K
AU  - Rushizky GW
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 1979 99: 207-212.

PMID- 28007859
VI  - 4
DP  - 2016
TI  - Novel Observations in 11 Heteroresistant Vancomycin-Intermediate Methicillin-Resistant Staphylococcus aureus Strains from South India.
PG  - e01425-16
AB  - We report here the draft genome sequences of 11 heteroresistant vancomycin-intermediate
      Staphylococcus aureus (hVISA) strains from bloodstream infection. All strains harbor mutations
      in vraSR, graSR, walKR, and/or tcaRAB and are often implicated as the frequently mutated
      candidate genes in hVISA phenotypes.
AU  - Bakthavatchalam YD
AU  - Veeraraghavan B
AU  - Peter JV
AU  - Rajinikanth J
AU  - Inbanathan FY
AU  - Devanga RNK
AU  - Rajamani SSK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01425-16.

PMID- 23558535
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Rhodococcus ruber Strain BKS 20-38.
PG  - e0013913
AB  - We report the 6.1-Mb genome sequence of Rhodococcus ruber strain BKS 20-38, isolated from the
      palm tree rhizosphere soil of Bhitarkanika National Park,
      Odhisha, India. The draft genome sequence of strain BKS 20-38 consists of
      6,126,900 bp, with a G+C content of 69.72%, 5,716 protein-coding genes, and 49
      RNAs.
AU  - Bala M
AU  - Kumar S
AU  - Raghava GP
AU  - Mayilraj S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0013913.

PMID- 23538906
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Rhodococcus qingshengii Strain BKS 20-40.
PG  - e0012813
AB  - We report the 5.8-Mb genome sequence of Rhodococcus qingshengii strain BKS 20-40, isolated
      from a palm tree rhizosphere soil sample from Bhitarkanika National
      Park, Odisha, India. The strain is capable of degrading cholesterol moiety. The
      draft genome of strain BKS 20-40 consists of 6,601,618 bp, with 62.4% G+C
      content.
AU  - Bala M
AU  - Kumar S
AU  - Raghava GP
AU  - Mayilraj S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0012813.

PMID- 22967207
VI  - 337
DP  - 2012
TI  - A novel gene, ardD, determines antirestriction activity of the non-conjugative transposon Tn5053 and is located antisense within the tniA gene.
PG  - 55-60
AB  - The mercury-resistance transposon Tn5053 inhibits restriction activity of the type I
      restriction-modification endonuclease EcoKI in
      Escherichia coli K12 cells. This is the first report of antirestriction
      activity of a non-conjugative transposon. The gene (ardD) coding for
      the antirestriction protein has been cloned. The ardD gene is located
      within the tniA gene, coding for transposase, on the complementary
      strand. The direction of transcription is opposite to transcription of
      the tniA gene.
AU  - Balabanov VP
AU  - Kotova VY
AU  - Kholodii GY
AU  - Mindlin SZ
AU  - Zavilgelsky GB
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2012 337: 55-60.

PMID- 22670523
VI  - 46
DP  - 2012
TI  - Comparative analysis of antirestriction activity of the ArdA and ArdB proteins encoded by genes of the R64 transmissible plasmid (IncI1).
PG  - 269-275
AB  - Antirestriction proteins ArdA and ArdB are specific inhibitors of type I
      restriction-modification enzymes. The ardA and yfeB (ardB) genes were cloned from the
      transmissible plasmid R64 in the pUC18 and pZE21 vectors. The R64 ArdA and ArdB proteins were
      shown to inhibit only restriction activity of the type I restriction-modification enzyme
      (EcoKI) in Escherichia coli K12 cells. In contrast to ArdA, ArdB inhibited EcoKI restriction
      activity only at a high intracellular concentration. Antirestriction activity of ArdB did not
      depend on the ClpXP protease. The yfeB (ardB) gene of the R64 plasmid is transcribed from a
      weak promoter located upstream of yfeA.
AU  - Balabanov VP
AU  - Pustovoit KS
AU  - Zavilgelsky GB
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2012 46: 269-275.

PMID- 28360163
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Staphylococcus aureus Strain Wood 46.
PG  - e00087-17
AB  - Here, we report the first complete genome sequence of the Staphylococcus aureus strain Wood
      46. Wood 46 has played an important role in understanding the
      virulence and pathogenesis of S. aureus infections. This report will assist
      efforts in vaccine development against methicillin-resistant S. aureus (MRSA)
      infections.
AU  - Balachandran M
AU  - Riley MC
AU  - Bemis DA
AU  - Kania SA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00087-17.

PMID- 22974320
VI  - 83
DP  - 2013
TI  - Integrating conjugative elements of the SXT/R391 family from fish-isolated Vibrios encode restriction-modification systems that confer resistance to bacteriophages.
PG  - 457-467
AB  - Integrating conjugative elements (ICEs) of the SXT/R391 family have been described in Vibrios,
      mainly Vibrio cholerae, and other bacteria
      as carriers of variable gene content conferring adaptive advantages
      upon their hosts, including antimicrobial resistance and motility
      regulation. However, our knowledge on their host range and ecological
      significance is still limited. Here, we report the identification and
      characterization of ICEVspPor3 and ICEValSpa1, two novel ICEs of the
      SXT/R391 family from fish-isolated Vibrio splendidus and Vibrio
      alginolyticus, respectively. We found that ICEVspPor3 carries
      tetracycline and HgCl2 resistance determinants and can be transferred
      by conjugation to Escherichia coli and to several species of marine
      bacteria including some of the major bacterial fish pathogens in marine
      aquaculture, whereas ICEValSpa1 lacks resistance genes. Interestingly,
      both ICEs harbor genes encoding distinct restrictionmodification (RM)
      systems. We demonstrate here that these RM systems, when expressed in
      E. coli, confer protection to infection by T1 bacteriophage and by
      environmental water bacteriophages. Our results provide evidences that
      the variable gene content of ICEs of the SXT/R391 family encodes
      fitness functions beyond those related to antimicrobial resistance and
      motility regulation and suggest that the host range of these elements
      in the marine environment might be broader than expected.
AU  - Balado M
AU  - Lemos ML
AU  - Osorio CR
PT  - Journal Article
TA  - FEMS Microbiol. Ecol.
JT  - FEMS Microbiol. Ecol.
SO  - FEMS Microbiol. Ecol. 2013 83: 457-467.

PMID- 26358595
VI  - 3
DP  - 2015
TI  - Genome Sequences of Two Multidrug-Resistant Acinetobacter baumannii Clinical Strains Isolated from Southern India.
PG  - e01010-15
AB  - Acinetobacter baumannii is an emerging nosocomial pathogen causing infections worldwide. In
      this study, we determined the genome sequences of two multidrug-resistant A. baumannii
      clinical strains isolated from a hospital in southern India. Genome analyses indicate that
      both the strains harbor numerous horizontally transferred genetic elements and antibiotic
      resistance cassettes.
AU  - Balaji V
AU  - Rajenderan S
AU  - Anandan S
AU  - Biswas I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01010-15.

PMID- 25814617
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequencing of a Vibrio cholerae El Tor Strain Isolated in the Imported Cholera Focus in Siberia.
PG  - e01550-14
AB  - The draft genome sequence of Vibrio cholerae O1 strain I-1263, isolated from a patient in the
      imported focus in Siberia, was determined. The established
      structural features of the mobile genetic elements indicate stage-by-stage
      formation of a highly pathogenic V. cholerae clone and promote understanding of
      the mechanisms of evolutionary pathogen transformations.
AU  - Balakhonov SV
AU  - Mironova LV
AU  - Basov EA
AU  - Gladkikh AS
AU  - Afanasev MV
AU  - Ganin VS
AU  - Urbanovich LY
AU  - Sidorova EA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01550-14.

PMID- 29025943
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Bacillus aryabhattai Strain PHB10, a Poly(3-Hydroxybutyrate)-Accumulating Bacterium Isolated from Domestic Sewerage.
PG  - e01072-17
AB  - Bacillus aryabhattai PHB10 is a poly(3-hydroxybutyrate) (PHB)-accumulating bacterium isolated
      from domestic sewerage. Here, we report the 4.19-Mb draft
      genome sequence, with 4,050 protein-coding genes and a G+C content of 37.5%. This
      sequence will be helpful in the study of the high-level PHB accumulation
      mechanism of the strain.
AU  - Balakrishna PA
AU  - Jaya KA
AU  - Thulasi K
AU  - Reghunathan D
AU  - Prasannakumar M
AU  - Kumarapillai H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01072-17.

PMID- 1338050
VI  - 11
DP  - 1992
TI  - Cleavage by restriction enzymes of DNA modified with the antitumour drug cis-diamminedichloroplatinum (II).
PG  - 579-588
AB  - The effect of binding of an antitumour drug cis-diamminedichloroplatinum (II)
      (cis-[Pt(NH3)2Cl2]) to DNA on cutting effectiveness of BamHI, EcoRI, and SalI restriction
      endonucleases was quantitatively determined. The platinum complex inhibits the cleavage of
      plasmid pHC624 DNA linearized by BglI restrictase. From the present results we conclude that
      the yield of restriction endonuclease cleavage is also lowered if the platinum complex is
      bound outside the recognition DNA sequence of these enzymes. We propose that the origin of
      platinum adducts on DNA outside the recognition sequence can decrease the yield of restriction
      enzyme cleavage via inducing a conformational perturbation in the DNA recognition sequence of
      these enzymes and also via inhibition of the linear diffusion of these enzymes on DNA.
AU  - Balcarova A
AU  - Mrazek J
AU  - Kleinwachter W
AU  - Brabec V
PT  - Journal Article
TA  - Gen. Physiol. Biophys.
JT  - Gen. Physiol. Biophys.
SO  - Gen. Physiol. Biophys. 1992 11: 579-588.

PMID- 3025691
VI  - 2
DP  - 1985
TI  - Expression of cloned gene for methyltransferase from Bacillus subtilis bacteriophage SPbetaB.
PG  - 26-28
AB  - Expression of the methyltransferase gene from Bacillus subtilis lysogenizing phage SPbetaB was
      studied by analyzing the sensitivity of the hybrid plasmid DNAs to restriction by the enzymes
      BspRI, HpaII and MspI.  This gene produces the methylase M.BsuPbetaBI with specificity for
      5'-GGCC.  The fragment carrying the SPbetaB derived gene also directs the synthesis in E.
      coli of a second methylase activity (M.BsuPbetaBII) with 5'-CCGG specificity.  Indirect
      evidence suggests that the two SPbetaB modification activities are encoded by the same gene.
AU  - Baldauf F
AU  - Kiss A
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1985 2: 26-28.

PMID- 17101654
VI  - 75
DP  - 2007
TI  - Identification of Helicobacter pylori genes that contribute to stomach colonization.
PG  - 1005-1016
AB  - Chronic infection of the human stomach by Helicobacter pylori leads to a variety of
      pathological sequelae, including peptic ulcer and gastric
      cancer, resulting in significant human morbidity and mortality. Several
      genes have been implicated in disease related to H. pylori infection,
      including the vacuolating cytotoxin and the cag pathogenicity island.
      Other factors important for the establishment and maintenance of infection
      include urease enzyme production, motility, iron uptake, and stress
      response. We utilized a C57BL/6 mouse infection model to query a
      collection of 2,400 transposon mutants in two different bacterial strain
      backgrounds for H. pylori genetic loci contributing to colonization of the
      stomach. Microarray-based tracking of transposon mutants allowed us to
      monitor the behavior of transposon insertions in 758 different gene loci.
      Of the loci measured, 223 (29%) had a predicted colonization defect. These
      included previously described H. pylori virulence genes, genes implicated
      in virulence in other pathogenic bacteria, and 81 hypothetical proteins.
      We have retested 10 previously uncharacterized candidate colonization gene
      loci by making independent null alleles and have confirmed their
      colonization phenotypes by using competition experiments and by
      determining the dose required for 50% infection. Of the genetic loci
      retested, 60% have strain-specific colonization defects, while 40% have
      phenotypes in both strain backgrounds for infection, highlighting the
      profound effect of H. pylori strain variation on the pathogenic potential
      of this organism.
AU  - Baldwin DN
AU  - Shepherd B
AU  - Kraemer P
AU  - Hall MK
AU  - Sycuro LK
AU  - Pinto-Santini DM
AU  - Salama NR
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2007 75: 1005-1016.

PMID- 10693139
VI  - 37
DP  - 2000
TI  - Manganese(II) as a probe for the mechanism and specificity of restriction endonucleases.
PG  - 345-364
AB  - A review of the role of metal ions in DNA cleavage by restriction enzymes and the experimental
      possibilities offered by substituting manganese for magnesium.
AU  - Baldwin GS
AU  - Gormley NA
AU  - Halford SE
PT  - Journal Article
TA  - Metal Ions in Biological Systems, Vol. 37: Manganese and its role in Biological Processes.
JT  - Metal Ions in Biological Systems, Vol. 37: Manganese and its role in Biological Processes.
SO  - Metal Ions in Biological Systems, Vol. 37: Manganese and its role in Biological Processes. 2000 37: 345-364.

PMID- 7821559
VI  - 22
DP  - 1994
TI  - Rapid reaction kinetics on the EcoRV restriction endonuclease.
PG  - 300S
AB  - The EcoRV restriction endonuclease cleaves DNA between the central TpA step of its 6 bp
      recognition sequence (GATATC) leaving blunt ends. It utilizes Mg2+ as its sole cofactor in the
      hydrolysis of the phosphodiester backbone. Previous studies have provided a wealth of
      information on the structure and function of the EcoRV restriction endonuclease. Perhaps the
      most surprising aspect of EcoRV's properties is that it binds all DNA sequences with equal
      affinity, yet it cleaves its target sequence with a 10^6 fold preference over the next best
      site. The very high degree of specificity exhibited by EcoRV is thus derived from catalysis,
      as opposed to sequence specific DNA binding. Nearly all of these previous studies were
      performed under steady state conditions, and have consequently provided little insight into
      the reaction pathway. We have used rapid reaction techniques under single turnover conditions
      to resolve intermediates in the reaction pathway with the aim of determining the mechanism of
      catalysis.
AU  - Baldwin GS
AU  - Halford SE
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 1994 22: 300S.

PMID- 8289281
VI  - 235
DP  - 1994
TI  - Ligand-induced conformational states of the cytosine-specific DNA methyltransferase M.HgaI-2.
PG  - 545-553
AB  - The interaction of one of the two DNA methyltransferases encoded by the HgaI restriction and
      modification system, M.HgaI-2, with substrates and substrate analogues is described. Circular
      dichroism spectroscopy has been used to demonstrate that addition of the methyl donor,
      S-adenosyl-L-methionine and the inhibitory substrate analogue sinefungin, both induce
      conformational transitions in the protein in the absence of DNA. Moreover, the addition of DNA
      is shown to enhance the apparent secondary structure of M.HgaI-2 whilst addition of sinefungin
      or S-adenosyl-L-methionine reduces apparent secondary structure. The circular dichroism
      spectrum of the abortive complex between the enzyme, DNA and sinefungin is dominated by the
      conformational properties of the binary complex of enzyme and sinefungin alone. Addition of a
      specific oligodeoxynucleotide duplex in which the target cytosine is replaced by a
      pyrimidinone, leads to a further ligand induced conformational transition as determined by
      electrophoretic analysis. The addition of sinefungin, or S-adenosyl-L-methionine, to M.HgaI-2
      bound to the reactive oligodeoxynucleotide duplex, leads to yet another conformational
      transition in the protein as determined by the differential susceptibility of ternary and
      binary complexes to proteolysis. These experiments identify at least six ligand-inducible
      conformational states of M.HgaI-2 and, in view of the sequence similarity amongst this class
      of enzymes, suggest that conformational flexibility is a general feature of C-5
      cytosine-specific DNA methyltransferases. Moreover, the substitution of the target cytosine by
      a pyrimidinone mimics the effect of 5-azacytosine incorporation into DNA.
AU  - Baldwin GS
AU  - Kelly SM
AU  - Price NC
AU  - Wilson GW
AU  - Connolly BA
AU  - Artymiuk PJ
AU  - Hornby DP
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1994 235: 545-553.

PMID- 10329128
VI  - 288
DP  - 1999
TI  - DNA cleavage by the EcoRV restriction endonuclease: Roles in divalent metal ions in specificity and catalysis.
PG  - 87-103
AB  - The roles of divalent metal ions in DNA cleavage by the EcoRV endonuclease were studied by
      using Co2+ or Mn2+ as substitutes for the natural cofactor Mg2+.  In steady-state experiments
      with a 12 bp oligonucleotide substrate, Co2+ yielded a similar turnover rate to that with
      Mg2+, but Mn2+ gave a slower rate.  Single turnovers of EcoRV on this substrate were analyzed
      by stopped-flow and quench-flow methods, to determine the rates for the formation of the
      ternary enzyme-DNA-metal complex, the hydrolysis of the phosphodiester bonds and the
      dissociation of the cleaved DNA.  With Co2+, all three steps had similar rates to those with
      Mg2+.  In contrast, Mn2+ gave a faster rate for phosphodiester hydrolysis than either Mg2+ or
      Co2+, but a slower rate for product dissociation, thus accounting for its low turnover rate.
      Single turnovers on plasmids also yielded faster rates for substrate hydrolysis with Mn2+
      compared to Mg2+ and Co2+.  Since Mn2+ gave the most rapid rates for the hydrolytic step,
      despite being less electronegative than Co2+, the function of the metal ion at the active site
      of EcoRV cannot be just the polarization of the scissile phosphate.  Moreover, the minimal
      scheme for the Co2+-catalysed reaction requires two metal ions for DNA cleavage.  The metal
      ions seem to be involved in the precise positioning of both the substrate and the water that
      acts as the attacking nucleophile and in activating that water molecule.  A model is presented
      to account for how two metal ions might fulfil these functions.
AU  - Baldwin GS
AU  - Sessions RB
AU  - Erskine SG
AU  - Halford SE
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1999 288: 87-103.

PMID- 7819266
VI  - 34
DP  - 1995
TI  - Rapid reaction analysis of the catalytic cycle of the EcoRV restriction endonuclease.
PG  - 705-714
AB  - We have used the intrinsic tryptophan fluorescence of the EcoRV restriction endonuclease to
      monitor changes in protein conformation during binding and cleavage of a duplex
      oligodeoxynucleotide substrate. Appropriate conditions for single-turnover reactions were
      first determined by steady-state kinetics. When single turnovers were monitored by
      stopped-flow fluorescence, the mixing together of EcoRV oligonucleotide and MgCl2 resulted in
      a rapid increase in tryptophan fluorescence followed by a slow decrease. Further analysis by
      order-of-mixing and quench experiments showed that the transient increase in fluorescence was
      due to a conformational change coupled to DNA binding, while the subsequent decay was
      concomitant with phosphodiester hydrolysis. The rate of the latter step varied with the
      concentration of Mg2+ ions, but another Mg2+-dependent transition was observed upon the
      addition of MgCl2 to a preformed enzyme--DNA complex. These results lead to a reaction scheme
      in which one Mg2+ binds to the active site prior to phosphodiester hydrolysis but a second
      Mg2+ is then needed to carry out the hydrolytic reaction. This scheme is correlated to the
      crystal structures of the EcoRV endonuclease and its complexes with DNA and Mg2+ ions.
AU  - Baldwin GS
AU  - Vipond IB
AU  - Halford SE
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1995 34: 705-714.

PMID- 375073
VI  - 59
DP  - 1979
TI  - Characterization of DNA adenine methylation mutants of Escherichia coli K12.
PG  - 157-165
AB  - The phenotypic traits of 7 independently isolated dam mutants of Escherichia coli have been
      examined. The mutant strains differ from the wildtype in the following respects: (1) decreased
      DNA adenine methylase activity in vivo and in vitro; (2) a 14--85-fold increase in spontaneous
      mutability; (3) decreased survival after ultraviolet irradiation; (4) a 10--21-fold increase
      in spontaneous induction of lambda phage from lysogens; (5) a 3--17-fold increase in the level
      of recombination; and (6) inviability of double mutants containing dam- and recB- or recC-.
      Unmethylated fd phage chromosomes are able to replicate normally in dam- mutants. A mutant
      strain in which the dcm gene is deleted is viable, showing that the dcm gene product is
      dispensible for growth.
AU  - Bale A
AU  - d'Alarcao M
AU  - Marinus MG
PT  - Journal Article
TA  - Mutat. Res.
JT  - Mutat. Res.
SO  - Mutat. Res. 1979 59: 157-165.

PMID- 8066089
VI  - 19
DP  - 1994
TI  - Expression, purification, and crystallization of restriction endonuclease PvuII with DNA containing its recognition site.
PG  - 77-79
AB  - We have overexpressed the type II restriction endonuclease PvuII (R.PvuII) in E. coli,
      prepared large amounts of the homogeneous enzyme, and crystallized it with an oligonucleotide
      carrying a PvuII recognition site. The cocrystals are orthorhombic space group P212121 with
      cell constants a = 95.8 A, b = 86.3 A, c = 48.5 A, and diffract X-rays to at least 2.7 A.
      There is a complex of two protein subunits and one oligonucleotide duplex in the asymmetric
      unit.
AU  - Balendiran K
AU  - Bonventre J
AU  - Knott R
AU  - Jack W
AU  - Benner J
AU  - Schildkraut I
AU  - Anderson JE
PT  - Journal Article
TA  - Proteins
JT  - Proteins
SO  - Proteins 1994 19: 77-79.

PMID- 2828032
VI  - 6
DP  - 1987
TI  - Construction and use of chimeric SPR/Phi3T DNA methyltransferases in the definition of sequence recognizing enzyme regions.
PG  - 3543-3549
AB  - Multispecific DNA methyltransferases (Mtases) of temperate Bacillus subtilis
      phages SPR and Phi3T methylate the internal cytosine of the sequence GGCC.
      They differ in their capacity to methylate additional sequences.  These are
      CCGG anad CC(A/T)GG in SPR and GCNGC in Phi3T.  Introducing unique restriction
      sites at equivalent locations within the two genes facilitated the construction
      of chimeric genes.  These expressed Mtase activity at a level comparable to
      that of the parental genes.  The methylation specificity of chimeric enzymes
      was correlated with the location of chimeric fusions.  This analysis, which
      also included the use of mutant genes, showed that domains involved in the
      recognition of target sequences unique to each enezyme [CCGG, CC(A/T)GG or
      GCNGC] are represented by the central non-conserved parts of the proteins,
      whilst recognition of the sequence (GGCC), which is a target for both enzymes,
      is determined by an adjacent conserved region.
AU  - Balganesh TS
AU  - Reiners L
AU  - Lauster R
AU  - Noyer-Weidner M
AU  - Wilke K
AU  - Trautner TA
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1987 6: 3543-3549.

PMID- 15520287
VI  - 14
DP  - 2004
TI  - Genome sequence of Haloarcula marismortui: A halophilic archaeon from the Dead Sea.
PG  - 2221-2234
AB  - We report the complete sequence of the 4,274,642-bp genome of Haloarcula marismortui, a
      halophilic archaeal isolate from the Dead Sea. The genome
      is organized into nine circular replicons of varying G+C compositions
      ranging from 54% to 62%. Comparison of the genome architectures of
      Halobacterium sp. NRC-1 and H. marismortui suggests a common ancestor for
      the two organisms and a genome of significantly reduced size in the
      former. Both of these halophilic archaea use the same strategy of high
      surface negative charge of folded proteins as means to circumvent the
      salting-out phenomenon in a hypersaline cytoplasm. A multitiered
      annotation approach, including primary sequence similarities, protein
      family signatures, structure prediction, and a protein function
      association network, has assigned putative functions for at least 58% of
      the 4242 predicted proteins, a far larger number than is usually achieved
      in most newly sequenced microorganisms. Among these assigned functions
      were genes encoding six opsins, 19 MCP and/or HAMP domain signal
      transducers, and an unusually large number of environmental response
      regulators-nearly five times as many as those encoded in Halobacterium sp.
      NRC-1-suggesting H. marismortui is significantly more physiologically
      capable of exploiting diverse environments. In comparing the physiologies
      of the two halophilic archaea, in addition to the expected extensive
      similarity, we discovered several differences in their metabolic
      strategies and physiological responses such as distinct pathways for
      arginine breakdown in each halophile. Finally, as expected from the larger
      genome, H. marismortui encodes many more functions and seems to have fewer
      nutritional requirements for survival than does Halobacterium sp. NRC-1.
AU  - Baliga NS
AU  - Bonneau R
AU  - Facciotti MT
AU  - Pan M
AU  - Glusman G
AU  - Deutsch EW
AU  - Shannon P
AU  - Chiu Y
AU  - Weng RS
AU  - Gan RR
AU  - Hung P
AU  - Date SV
AU  - Marcotte E
AU  - Hood L
AU  - Ng WV
PT  - Journal Article
TA  - Genome Res.
JT  - Genome Res.
SO  - Genome Res. 2004 14: 2221-2234.

PMID- 1459953
VI  - 174
DP  - 1992
TI  - Dramatic changes in Fis levels upon nutrient upshift in Escherichia coli.
PG  - 8043-8056
AB  - Fis is a small basic DNA-binding protein from Escherichia coli that was identified because of
      its role in site-specific DNA recombination
      reactions. Recent evidence indicates that Fis also participates in
      essential cell processes such as rRNA and tRNA transcription and
      chromosomal DNA replication. In this report, we show that Fis levels vary
      dramatically during the course of cell growth and in response to changing
      environmental conditions. When stationary-phase cells are subcultured into
      a rich medium, Fis levels increase from less than 100 to over 50,000
      copies per cell prior to the first cell division. As cells enter
      exponential growth, nascent synthesis is largely shut off, and
      intracellular Fis levels decrease as a function of cell division. Fis
      synthesis also transiently increases when exponentially growing cells are
      shifted to a richer medium. The magnitude of the peak of Fis synthesis
      appears to reflect the extent of the nutritional upshift. fis mRNA levels
      closely resemble the protein expression pattern, suggesting that
      regulation occurs largely at the transcriptional level. Two RNA
      polymerase-binding sites and at least six high-affinity Fis-binding sites
      are present in the fis promoter region. We show that expression of the fis
      operon is negatively regulated by Fis in vivo and that purified Fis can
      prevent stable complex formation by RNA polymerase at the fis promoter in
      vitro. However, autoregulation only partially accounts for the expression
      pattern of Fis. We suggest that the fluctuations in Fis levels may serve
      as an early signal of a nutritional upshift and may be important in the
      physiological roles Fis plays in the cell.
AU  - Ball CA
AU  - Osuna R
AU  - Ferguson KC
AU  - Johnson RC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1992 174: 8043-8056.

PMID- 19690367
VI  - 65
DP  - 2009
TI  - Structure of the restriction-modification controller protein C.Esp1396I.
PG  - 900-905
AB  - The controller protein of the Esp1396I restriction-modification (R-M) system binds
      differentially to three distinct operator sequences
      upstream of the methyltransferase (M) and endonuclease (R) genes to
      regulate the timing of gene expression. The crystal structure of a
      complex of the protein with two adjacent operator DNA sequences has
      been reported; however, the structure of the free protein has not yet
      been determined. Here, the crystal structure of the free protein is
      reported, with seven dimers in the asymmetric unit. Two of the 14
      monomers show an alternative conformation to the major conformer in
      which the side chains of residues 43-46 in the loop region flanking the
      DNA-recognition helix are displaced by up to 10 A. It is proposed that
      the adoption of these two conformational states may play a role in
      DNA-sequence promiscuity. The two alternative conformations are also
      found in the R35A mutant structure, which is otherwise identical to the
      native protein. Comparison of the free and bound protein structures
      shows a 1.4 A displacement of the recognition helices when the dimer is
      bound to its DNA target.
AU  - Ball N
AU  - Streeter SD
AU  - Kneale GG
AU  - McGeehan JE
PT  - Journal Article
TA  - Acta Crystallogr. D Biol. Crystallogr.
JT  - Acta Crystallogr. D Biol. Crystallogr.
SO  - Acta Crystallogr. D Biol. Crystallogr. 2009 65: 900-905.

PMID- 22941636
VI  - 40
DP  - 2012
TI  - The structural basis of differential DNA sequence recognition by restriction-modification controller proteins.
PG  - 10532-10542
AB  - Controller (C) proteins regulate the expression of restriction-modification (RM)  genes in a
      wide variety of RM systems. However, the RM system Esp1396I is of
      particular interest as the C protein regulates both the restriction endonuclease
      (R) gene and the methyltransferase (M) gene. The mechanism of this finely tuned
      genetic switch depends on differential binding affinities for the promoters
      controlling the R and M genes, which in turn depends on differential DNA sequence
      recognition and the ability to recognize dual symmetries. We report here the
      crystal structure of the C protein bound to the M promoter, and compare the
      binding affinities for each operator sequence by surface plasmon resonance.
      Comparison of the structure of the transcriptional repression complex at the M
      promoter with that of the transcriptional activation complex at the R promoter
      shows how subtle changes in protein-DNA interactions, underpinned by small
      conformational changes in the protein, can explain the molecular basis of
      differential regulation of gene expression.
AU  - Ball NJ
AU  - McGeehan JE
AU  - Streeter SD
AU  - Thresh SJ
AU  - Kneale GG
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: 10532-10542.

PMID- 8542276
VI  - 5
DP  - 1995
TI  - Exploring the bowels of DNA methylation.
PG  - 1013-1016
AB  - The role DNA methylation is thought to have in cancer has become increasingly complex.  In the
      late 1970s and early 1980s, it was shown that methylation of CpG sites in DNA can exert a
      negative influence on gene expression.  Treatment of fibroblastic 10T1/2 cells in culture with
      demethylating agents, such as 5-azacytidine, facilitated the emergence of novel muscle or
      brain-related cell types, presumably by removing methyl groups from developmentally important
      genes, allowing their expression.  One of the genes responsible for the myogenesis programme,
      MyoD, was subsequently found to be methylated in the original 10T1/2 cells, but became
      demethylated (and expressed) in their muscle progeny.  Relevance to cancer development was
      suggested by the observation that tumour cells tend to have hypomethylated DNA, and
      consequently begin to express genes that could confer a growth advantage.  Obligingly, some
      genes that are hypomethylated in cancers turned out to be oncogenes, completing a satisfying
      hypothetical loop.  This concept gained further support with the observation that carcinogenic
      alkylating agents can induce DNA hypomethylation, in addition to their known mutagenic
      effects, possibly by preventing cytosine methylation at sites adjacent to O6-alkylguanosine
      residues.  The conclusion to be drawn from these studies was that hypomethylation of tumour
      DNA would allow uncontrolled or aberrant oncogene expression, with obvious advantages for
      tumour cell growth.
AU  - Balmain A
PT  - Journal Article
TA  - Curr. Biol.
JT  - Curr. Biol.
SO  - Curr. Biol. 1995 5: 1013-1016.

PMID- 18952803
VI  - 191
DP  - 2009
TI  - The complete genome sequence of Helicobacter pylori strain G27.
PG  - 447-448
AB  - Helicobacter pylori is a gram-negative pathogen that colonizes the stomachs of over half the
      world's population and causes a spectrum of gastric diseases
      including gastritis, ulcers, and gastric carcinoma. The H. pylori species
      exhibits unusually high levels of genetic variation between strains. Here we
      announce the complete genome sequence of H. pylori strain G27, which has been
      used extensively in H. pylori research.
AU  - Baltrus DA
AU  - Amieva MR
AU  - Covacci A
AU  - Lowe TM
AU  - Merrell DS
AU  - Ottemann KM
AU  - Stein M
AU  - Salama NR
AU  - Guillemin K
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2009 191: 447-448.

PMID- 21799664
VI  - 7
DP  - 2011
TI  - Dynamic evolution of pathogenicity revealed by sequencing and comparative genomics of 19 Pseudomonas syringae isolates.
PG  - e1002132
AB  - Closely related pathogens may differ dramatically in host range, but the
      molecular, genetic, and evolutionary basis for these differences remains unclear.
      In many Gram- negative bacteria, including the phytopathogen Pseudomonas
      syringae, type III effectors (TTEs) are essential for pathogenicity, instrumental
      in structuring host range, and exhibit wide diversity between strains. To capture
      the dynamic nature of virulence gene repertoires across P. syringae, we screened
      11 diverse strains for novel TTE families and coupled this nearly saturating
      screen with the sequencing and assembly of 14 phylogenetically diverse isolates
      from a broad collection of diseased host plants. TTE repertoires vary
      dramatically in size and content across all P. syringae clades; surprisingly few
      TTEs are conserved and present in all strains. Those that are likely provide
      basal requirements for pathogenicity. We demonstrate that functional divergence
      within one conserved locus, hopM1, leads to dramatic differences in
      pathogenicity, and we demonstrate that phylogenetics-informed mutagenesis can be
      used to identify functionally critical residues of TTEs. The dynamism of the TTE
      repertoire is mirrored by diversity in pathways affecting the synthesis of
      secreted phytotoxins, highlighting the likely role of both types of virulence
      factors in determination of host range. We used these 14 draft genome sequences,
      plus five additional genome sequences previously reported, to identify the core
      genome for P. syringae and we compared this core to that of two closely related
      non-pathogenic pseudomonad species. These data revealed the recent acquisition of
      a 1 Mb megaplasmid by a sub-clade of cucumber pathogens. This megaplasmid encodes
      a type IV secretion system and a diverse set of unknown proteins, which
      dramatically increases both the genomic content of these strains and the
      pan-genome of the species.
AU  - Baltrus DA
AU  - Nishimura MT
AU  - Romanchuk A
AU  - Chang JH
AU  - Mukhtar MS
AU  - Cherkis K
AU  - Roach J
AU  - Grant SR
AU  - Jones CD
AU  - Dangl JL
PT  - Journal Article
TA  - PLoS Pathog.
JT  - PLoS Pathog.
SO  - PLoS Pathog. 2011 7: e1002132.

PMID- 24459267
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of a Phylogenetically Diverse Suite of Pseudomonas syringae Strains from Multiple Source Populations.
PG  - e01195-13
AB  - Here, we report the draft genome sequences for 7 phylogenetically diverse isolates of
      Pseudomonas syringae, obtained from numerous environmental sources
      and geographically proximate crop species. Overall, these sequences provide a
      wealth of information about the differences (or lack thereof) between isolates
      from disease outbreaks and those from other sources.
AU  - Baltrus DA
AU  - Yourstone S
AU  - Lind A
AU  - Guilbaud C
AU  - Sands DC
AU  - Jones CD
AU  - Morris CE
AU  - Dangl JL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01195-13.

PMID- 
VI  - 0
DP  - 1989
TI  - Transduction of plasmid DNA in Streptomyces spp.
PG  - 163-167
AB  - None
AU  - Baltz RH
AU  - McHenney MA
PT  - Journal Article
TA  - Genetics and Molecular Biology of Industrial Microorganisms
JT  - Genetics and Molecular Biology of Industrial Microorganisms
SO  - Genetics and Molecular Biology of Industrial Microorganisms 1989 0: 163-167.

PMID- 9482749
VI  - 17
DP  - 1998
TI  - Structural basis for MutH activation in E. coli mismatch repair and relationship of MutH to restriction endonucleases.
PG  - 1526-1534
AB  - MutS, MutL and MutH are the three essential proteins for initiation of methyl-directed DNA
      mismatch repair to correct mistakes made during DNA replication in Escherichia coli.  MutH
      cleaves a newly synthesized and unmethylated daughter strand 5' to the sequence d(GATC) in a
      hemi-methylated duplex.  Activation of MutH requires the recognition of a DNA mismatch by MutS
      and MutL.  We have crystallized MutH in two space groups and solved the structures at 1.7 and
      2.3 Angstrom resolution, respectively.  The active site of MutH is located at an interface
      between two subdomains that pivot relative to one another, as revealed by comparison of the
      crystal structures, and this presumably regulates the nuclease activity.  The relative motion
      of the two subdomains in MutH correlates with the position of a protruding C-terminal helix.
      This helix appears to act as a molecular lever through which MutS and MutL may communicate the
      detection of a DNA mismatch and activate MutH.  With sequence homology to Sau3AI and
      structural similarity to PvuII endonuclease, MutH is clearly related to these enzymes by
      divergent evolution, and this suggests that type II restriction endonucleases evolved from a
      common ancestor.
AU  - Ban C
AU  - Yang W
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1998 17: 1526-1534.

PMID- 26575107
VI  - 6
DP  - 2015
TI  - Characterization of unstable pEntYN10 from enterotoxigenic Escherichia coli (ETEC) O169:H41.
PG  - 735-744
AB  - Enterotoxigenic Escherichia coli (ETEC) serotype O169:H41 has been an extremely
      destructive epidemic ETEC type worldwide. The strain harbors a large unstable
      plasmid that is regarded as responsible for its virulence, although its etiology
      has remained unknown. To examine its genetic background specifically on the
      unstable retention and responsibility in the unique adherence to epithelial cells
      and enterotoxin production, the complete sequence of a plasmid, pEntYN10,
      purified from the serotype strain was determined. The length is 145,082 bp; its
      GC content is 46.15%. It contains 182 CDSs, which include 3 colonization factors
      (CFs), an enterotoxin, and large number of insertion sequences. The repertory of
      plasmid stability genes was extraordinarily scant. Uniquely, results showed that
      3 CFs, CS6, CS8 (CFA/III)-like, and K88 (F4)-like were encoded redundantly in the
      plasmid with unique variations among previously known subtypes. These three CFs
      preserved their respective gene structures similarly to those of other ETEC
      strains reported previously with unique sequence variations respectively. It is
      particularly interesting that the K88-like gene cluster of pEntYN10 had 2
      paralogous copies of faeG, which encodes the major component of fimbrial
      structure. It remains to be verified how the unique variations found in the CFs
      respectively affect the affinity to infected cells, host range, and virulence of
      the ETEC strain.
AU  - Ban E
AU  - Yoshida Y
AU  - Wakushima M
AU  - Wajima T
AU  - Hamabata T
AU  - Ichikawa N
AU  - Abe H
AU  - Horiguchi Y
AU  - Hara-Kudo Y
AU  - Kage-Nakadai E
AU  - Yamamoto T
AU  - Wada T
AU  - Nishikawa Y
PT  - Journal Article
TA  - Virulence
JT  - Virulence
SO  - Virulence 2015 6: 735-744.

PMID- 21841035
VI  - 77
DP  - 2011
TI  - Effects of DNA Methylation on Expression of Virulence Genes in Streptococcus mutans.
PG  - 7236-7242
AB  - Bacteria produce a variety of enzymes capable of methylating DNA. In many species, the
      majority of adenine methylation is accomplished by
      the DNA adenine methylase Dam. In Escherichia coli the Dam methylase
      plays roles in the initiation of replication, mismatch repair, and gene
      regulation. In a number of other bacterial species, mutation or
      overexpression of Dam leads to attenuation of virulence. Homologues of
      the dam gene exist in some members of the Firmicutes, including
      Streptococcus mutans, a dental pathogen. An S. mutans strain
      inactivated in the dam gene (SMU.504; here designated damA) was
      engineered, and phenotypes linked to cariogenicity were examined. A
      prominent observation was that the damA mutant produced greater amounts
      of glucan than the parental strain. Real-time PCR confirmed
      upregulation of gtfB. To determine whether other loci were affected by
      the damA mutation, a microarray analysis was carried out. Seventy genes
      were upregulated at least 2-fold in the damA mutant, and 33 genes were
      downregulated at least 2-fold. In addition to gtfB (upregulated
      2.6-fold; 1.7-fold when measured by real-time PCR), other upregulated
      virulence factors included gbpC (upregulated 2.1-fold) and loci
      predicted to encode bacteriocins (upregulated 2- to 7-fold). Various
      sugar transport operons were also upregulated, the most extreme being
      the cellobiose operon (upregulated nearly 40-fold). Expression of sacB,
      encoding fructosyltransferase, was downregulated 2.4-fold. The sequence
      5'-GATC-3' appeared to constitute the recognition sequence for
      methylation. These results provide evidence that DNA methylation in S.
      mutans has a global effect on gene expression, including that of genes
      associated with cariogenic potential.
AU  - Banas JA
AU  - Biswas S
AU  - Zhu M
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2011 77: 7236-7242.

PMID- 1870972
VI  - 19
DP  - 1991
TI  - Identification and sequence analysis of a methylase gene in Porphyromonas gingivalis.
PG  - 4189-4192
AB  - A gene from the periodontal organism Porphyromonas gingivalis has been identified as encoding
      a DNA methylase. The gene, referred to as pgiIM, has been sequenced and found to contain a
      reading frame of 864 basepairs. The putative amino acid sequence of the encoded methylase was
      288 amino acids, and shared 47% and 31% homology with the Streptococcus pneumoniae DpnII and
      E. coli Dam methylases, respectively. The activity and specificity of the PgiI methylase
      (M.PgiI) was confirmed by cloning the gene into a dam- strain of E. coli (JM110) and
      performing a restriction analysis on the isolated DNA with enzymes whose activities depended
      upon the methylation state of the DNA. The data indicated that M.PgiI, like DpnII and Dam,
      methylated the adenine residue within the sequence 5'-GATC-3'.
AU  - Banas JA
AU  - Ferretti JJ
AU  - Progulske-Fox A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 4189-4192.

PMID- Not carried by PubMed...
VI  - 91
DP  - 1991
TI  - Identification of a methylase gene in Porphyromonas gingivalis.
PG  - 174
AB  - Sequence analysis of a portion of the P. gingivalis genome revealed an open reading frame
      which encoded a protein whose putative amino acid sequence shared approximately fifty percent
      and thirty percent identity with the Streptococcus pneumoniae Dpn methylase and Escherichia
      coli Dam methylase, respectively. The P. gingivalis methylase was cloned into pUC18 and
      transformed into E. coli JM110 (dam). Plasmid DNA isolated from transformants could be cut
      with DpnI which only cuts at methylated 5'-GATC-3' sites, but not with NdeII which will not
      cut at methylated 5'-GATC-3' sites. The methylase was expressed in both orientations. These
      results suggest that the gene cloned from P. gingivalis specifies an adenine methylase that
      recognizes the sequence 5'-GATC-3'.
AU  - Banas JA
AU  - Ferretti JJ
AU  - Progulske-Fox A
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1991 91: 174.

PMID- 12051942
VI  - 319
DP  - 2002
TI  - Free energy and structural pathways of base flipping in a DNA GCGC containing sequence.
PG  - 141-160
AB  - Structural distortions of DNA are essential for its biological function due to the genetic
      information of DNA not being physically accessible in the duplex state. Base flipping is one
      of the simplest structural distortions of DNA and may represent an initial event in strand
      separation required to access the genetic code. Flipping is also utilized by DNA-modifying and
      repair enzymes to access specific bases. It is typically thought that base flipping (or
      base-pair opening) occurs via the major groove whereas minor groove flipping is only possible
      when mediated by DNA-binding proteins. Here, umbrella sampling with a novel center-of-mass
      pseudodihedral reaction coordinate was used to calculate the individual potentials of mean
      force (PMF) for flipping of the Watson-Crick (WC) paired C and G bases in the CCATGCGCTGAC DNA
      dodecamer. The novel reaction coordinate allowed explicit investigation of the complete
      flipping process via both the minor and major groove pathways. The minor and major groove
      barriers to flipping are similar for C base flipping while the major groove barrier is
      slightly lower for G base flipping. Minor groove flipping requires distortion of the WC
      partner while the flipping base pulls away from its partner during major groove flipping. The
      flipped states are represented by relatively flat free energy surfaces, with a small, local
      minimum observed for the flipped G base. Conserved patterns of phosphodiester backbone
      dihedral distortions during flipping indicate their essential role in the flipping process.
      During flipping, the target base tracks along the respective grooves, leading to
      hydrogen-bonding interactions with neighboring base-pairs. Such hydrogen-bonding interactions
      with the neighboring sequence suggest a novel mechanism of sequence dependence in DNA
      dynamics.
AU  - Banavali NK
AU  - MacKerell AD Jr
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2002 319: 141-160.

PMID- 2832536
VI  - 69
DP  - 1988
TI  - An analysis of restriction endonuclease sites in cyanophages infecting the heterocystous cyanobacteria Anabaena and Nostoc.
PG  - 739-743
AB  - An analysis of restriction endonuclease cleavage of DNA isolated from cyanophages that infect
      Anabaena and Nostoc species of cyanobacteria has provided evidence for counter-selection of
      restriction endonuclease sites. These include sites containing subsequences which are
      methylated by host (Anabaena PCC 7120) methylase(s) akin to the dam and dcm enzymes of
      Escherichia coli. Other sites which are counter-selected have no common sequence structure.
      The latter include those of the endogenous restriction endonucleases of the host, but other
      absent sequences are not attributable to isoschizomers of any known Anabaena or Nostoc
      restriction endonuclease. The cyanophages differ in their tolerance to DNA methylation.
      Isolates A-4L, AN-13 and AN-23 do not tolerate adenosine methylation in the GATC sequence
      whereas two cyanophages, A-1L and AN-10 (which are related) do tolerate dam-like methylation
      of this sequence. In addition, A-1L allows cytosine methylation at GGCC sequences, but AN-10
      has counter-selected these sequences and the remaining sites are not methylated. Analysis of
      native and cloned A-4L DNA suggests that counter-selection has occurred against all sequences
      which would be methylated by the host at either adenosine or cytosine nucleotides.
AU  - Bancroft I
AU  - Smith RJ
PT  - Journal Article
TA  - J. Gen. Virol.
JT  - J. Gen. Virol.
SO  - J. Gen. Virol. 1988 69: 739-743.

PMID- Not carried by PubMed...
VI  - 57
DP  - 1996
TI  - Study of cytosine to thymine mutations at the sites of dcm and M.HpaII methyltransferases.
PG  - 2535B-2536B
AB  - It has been proposed that sites of methylation are "hotspots" for C to T mutations in
      bacterial and human genomes.  I have developed a very sensitive genetic reversion assay that
      quantifies the frequency of C to T mutations at various methylation sites and the repair of
      resulting mismatches by DNA repair processes in Escherichia coli.  I have demonstrated that
      the presence of HpaII methyltransferase (Mtase) in E. coli causes a substantial increase in C
      to T mutations at CG sites.  This is similar to the known mutagenic effects of E. coli MTase
      Dcm within its own recognition sequence.  Using this genetic system, I have tested a homolog
      of an E. coli DNA repair gene in Haemophilus parainfluenzae for antimutagenic activity.
      Unexpectedly, the homology was found to have little effect on the reversion frequency.  Using
      this system, I have also shown that in vitro HpaII and SssI Mtases can convert cytosine to
      uracil.  These studies define 5-methylcytosine as an intrinsic mutagen and further elaborate
      the mutagenic potential of cytosine Mtases.  Multi-copy clones of E. coli DNA cytosine
      methyltransferases (C5 Mtases) Dcm and M.EcoRII cause ~50 fold increase in C to T mutations at
      their canonical site of methylation, 5'-CmeCAGG (meC is 5-methylcytosine).  I have observed
      that these plasmids also cause transition mutations at the second cytosine in the sequences
      CCGGG at ~10-fold lower frequency.  Similarly, M.HpaII was found to cause a significant
      increase in C to T mutations at a CCAG site -- in addition to causing mutations at its
      canonical site of methylation, CCGG.  Using a plasmid that substantially overprodces M.EcoRII,
      I have shown that in vivo methylation at CCSGG (S is C or G) and other non-canonical sites
      could be detected using a gel electrophoretic assay.  There is a direct correlation between
      the level of M.EcoRII activity in cells, the extent of methylation at non-canonical sites and
      frequency of mutations at these same sites.  Overproduction of M.EcoRII in cells also causes
      degradation of DNA and induction of the SOS response.  I have shown that in vitro, M.EcoRII
      methylates an oligonucleotide duplex containing a CCGGG site at a slow rate suggesting that
      overproduction of the enzyme is essential for significant amounts of such methylation to
      occur.  Together these results show that C5 Mtases occasionally methylate cellular DNA at
      non-canonical sites and suggest that in E. coli methylation-specific restriction systems and
      DNA mismatch correction systems may have evolved to accommodate this fact.  These results also
      suggest that mutational effects of cytosine methyltransferases may be much broader than
      previously imagined.
AU  - Bandaru B
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1996 57: 2535B-2536B.

PMID- 8631830
VI  - 271
DP  - 1996
TI  - Overproduction of DNA cytosine methyltransferases causes methylation and C-T mutations at non-canonical sites.
PG  - 7851-7859
AB  - Multicopy clones of Escherichia coli cytosine methyltransferases Dcm and EcoRII methylase (M.
      EcoRII) cause ~50-fold increase in C-T mutations at their canonical site of methylation.
      5'-CmeCAGG (meC is 5-methylcytosine).  These plasmids also cause transition mutations at the
      second cytosine in the sequences CCGGG at ~10-fold lower frequency.  Similarly, M.HpaII was
      found to cause a significant increase in C-T mutations at a CCAG site, in addition to causing
      mutations at its canonical site of methylation, CCGG.  Using a plasmid that substantially
      overproduces M.EcoRII, in vivo methylation at CCSGG (S is C or G) and other noncanonical sites
      could be detected using a gel electrophoretic assay.  There is a direct correlation between
      the level of M.EcoRII activity in cells, the extent of methylation at non-canonical sites and
      frequency of mutations at these same sites.  Overproduction of M.EcoRII in cells also causes
      degradation of DNA and induction of the SOS response.  In vitro, M. EcoRII methylates an
      oligonucleotide duplex containing a CCGGG site at a slow rate, suggesting that overproduction
      of the enzyme is essential for significant amounts of such methylation to occur.  Together
      these results show that cytosine methyltransferases occasionally methylate cellular DNA at
      non-canonical sites and suggest that in E. coli, methylation-specific restriction systems and
      sequence specificity of the DNA mismatch correction systems may have evolved to accommodate
      this fact.  These results also suggest that mutational effects of cytosine methyltransferases
      may be much broader than previously imagined.
AU  - Bandaru B
AU  - Gopal J
AU  - Bhagwat AS
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1996 271: 7851-7859.

PMID- 7751315
VI  - 177
DP  - 1995
TI  - HpaII methyltransferase is mutagenic in Escherichia coli.
PG  - 2950-2952
AB  - A genetic reversion assay to study C-to-T mutations within CG sites in DNA is described. It
      was used to demonstrate that the presence of HpaII methyltransferase (MTase) in Escherichia
      coli causes a substantial increase in C-to-T mutations at CG sites. This is similar to the
      known mutagenic effects of E. coli MTase Dcm within its own recognition sequence. With this
      genetic system, a homolog of an E. coli DNA repair gene in Haemophilus parainfluenzae was
      tested for antimutagenic activity. Unexpectedly, the homolog was found to have little effect
      on the reversion frequency. The system was also used to show that HpaII and SssI MTases can
      convert cytosine to uracil in vitro. These studies define 5-methylcytosine as an intrinsic
      mutagen and further elaborate the mutagenic potential of cytosine MTases.
AU  - Bandaru B
AU  - Wyszynski M
AU  - Bhagwat AS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1995 177: 2950-2952.

PMID- 2989534
VI  - 182
DP  - 1985
TI  - Inhibition of the type I restriction-modification enzymes EcoB and EcoK by the gene 0.3 protein of bacteriophage T7.
PG  - 567-578
AB  - The gene 0.3 protein of bacteriophage T7 is a potent inhibitor of the
      restriction-modification enzymes EcoB and EcoK, both in vivo and in vitro.  We have
      analyzed the ability of purified 0.3 protein to inhibit different steps in the reactions of
      EcoB
      and EcoK with DNA.  Most of our experiments were done with EcoK, but selected tests
      with EcoB indicate that the two enzymes are affected by 0.3 protein in the same way.
      Purified 0.3 protein binds tightly to free enzyme, apparently to one of the small subunits,
      and prevents it from binding to DNA.  If EcoK is allowed to form specific recognition
      complexes with unmodified DNA before 0.3 protein is added, relatively low levels of 0.3
      protein prevent the nuclease activity that would otherwise appear upon addition of ATP, but
      considerably higher levels are needed to prevent formation of filter-binding complexes or
      ATPase activity.  This, together with other results, suggests that the binding site for 0.3
      protein is protected in recognition complexes and in the early stages of the ATP-stimulated
      reactions, but that it becomes accessible again before cleavage of the DNA, perhaps after
      the translocation step.  If added after the nuclease reaction is substantially over, 0.3
      protein
      has little effect on ATPase activity, and indeed, the subunit having the binding site for 0.3
      protein apparently dissociates from the enzyme-DNA complex.  The methylase activity of
      EcoK on hemi-methylated recognition sites is strongly inhibited by 0.3 protein added at any
      stage of the reaction.
AU  - Bandyopadhyay PK
AU  - Studier FW
AU  - Hamilton DL
AU  - Yuan R
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1985 182: 567-578.

PMID- 8125341
VI  - 140
DP  - 1994
TI  - The DNA adenine methyltransferase-encoding gene (dam) of Vibrio cholerae.
PG  - 67-71
AB  - The DNA adenine methyltransferase (MTase)-encoding gene (dam) of Vibrio cholerae, an organism
      belonging to the family Vibrionaceae, has been cloned and the complete nucleotide (nt)
      sequence determined. V. cholerae dam encodes a 21.5-kDa protein and is directly involved in
      methyl-directed DNA mismatch repair. It can substitute for the Escherichia coli enzyme and can
      suppress the phenotypic traits associated with E. coli dam mutants. Overproduction of V.
      cholerae Dam MTase does not result in hypermutability in either V. cholerae or E. coli cells.
      Overproduction of V. cholerae Dam in a pUC plasmid, however, fails to suppress the
      2-aminopurine (2-AP0-sensitive phenotype of E. coli dam mutants. Homology between the nt and
      deduced amino acid (aa) sequences of the E. coli and V. cholerae dam genes is only 30-35%.
AU  - Bandyopadhyay R
AU  - Das J
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1994 140: 67-71.

PMID- 2688642
VI  - 165
DP  - 1989
TI  - A mutation in the dam gene of Vibrio cholerae: 2-aminopurine sensitivity with intact GATC methylase activity.
PG  - 561-567
AB  - Vibrio cholerae mutants sensitive to 2-aminopurine (2AP) but with DNA adenine methylase
      activity similar to parental cells have been isolated. The mutant strains were sensitive to
      ultraviolet light (UV), methyl methane sulphonate (MMS) and 9-aminoacridine. The spontaneous
      mutation frequency of the mutants were not significantly affected. Attempts to isolate dam V.
      cholerae cells by screening 2AP sensitive cells have not been successful. All of the mutant
      phenotypes could be suppressed by introducing the plasmid pRB103 carrying the dam gene of
      Escherichia coli into the mutant cells.
AU  - Bandyopadhyay R
AU  - Sengupta A
AU  - Das J
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1989 165: 561-567.

PMID- 28473384
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Pannonibacter indicus Strain HT23T (DSM 23407T), a Highly Arsenate-Tolerant Bacterium Isolated from a Hot Spring in India.
PG  - e00283-17
AB  - Pannonibacter indicus strain HT23T, a highly arsenate-tolerant bacterium, was isolated from a
      tropical hot spring. The estimated genome is 4.2 Mb with 3,818
      protein-coding sequences containing putative genes, some of which are involved in
      arsenate resistance.
AU  - Bandyopadhyay S
AU  - Whitman WB
AU  - Das SK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00283-17.

PMID- 28007848
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the Nonpathogenic, Thermotolerant, and Exopolysaccharide-Producing Bacillus anthracis Strain PFAB2 from Panifala Hot Water Spring in West Bengal, India.
PG  - e01346-16
AB  - Bacillus anthracis is the causative agent of fatal anthrax in both animals and humans. It is
      prevalently pathogenic. Here, we present a Bacillus anthracis PFAB2 strain from a relatively
      unexplored Panifala hot water spring in West Bengal, India. It is nonpathogenic,
      exopolysaccharide producing, and thermotolerant in nature.
AU  - Banerjee A
AU  - Halder U
AU  - Chaudhry V
AU  - Varshney RK
AU  - Mantri S
AU  - Bandopadhyay R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01346-16.

PMID- 21347417
VI  - 6
DP  - 2011
TI  - Functional analysis of an acid adaptive DNA adenine methyltransferase from Helicobacter pylori 26695.
PG  - e16810
AB  - HP0593 DNA-(N(6)-adenine)-methyltransferase (HP0593 MTase) is a member of a Type  III
      restriction-modification system in Helicobacter pylori strain 26695. HP0593
      MTase has been cloned, overexpressed and purified heterologously in Escherichia
      coli. The recognition sequence of the purified MTase was determined as
      5'-GCAG-3'and the site of methylation was found to be adenine. The activity of
      HP0593 MTase was found to be optimal at pH 5.5. This is a unique property in
      context of natural adaptation of H. pylori in its acidic niche. Dot-blot assay
      using antibodies that react specifically with DNA containing m6A modification
      confirmed that HP0593 MTase is an adenine-specific MTase. HP0593 MTase occurred
      as both monomer and dimer in solution as determined by gel-filtration
      chromatography and chemical-crosslinking studies. The nonlinear dependence of
      methylation activity on enzyme concentration indicated that more than one
      molecule of enzyme was required for its activity. Analysis of initial velocity
      with AdoMet as a substrate showed that two molecules of AdoMet bind to HP0593
      MTase, which is the first example in case of Type III MTases. Interestingly,
      metal ion cofactors such as Co(2+), Mn(2+), and also Mg(2+) stimulated the HP0593
      MTase activity. Preincubation and isotope partitioning analyses clearly indicated
      that HP0593 MTase-DNA complex is catalytically competent, and suggested that DNA
      binds to the MTase first followed by AdoMet. HP0593 MTase shows a distributive
      mechanism of methylation on DNA having more than one recognition site.
      Considering the occurrence of GCAG sequence in the potential promoter regions of
      physiologically important genes in H. pylori, our results provide impetus for
      exploring the role of this DNA MTase in the cellular processes of H. pylori.
AU  - Banerjee A
AU  - Rao DN
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2011 6: e16810.

PMID- 16549669
VI  - 152
DP  - 2006
TI  - An orphan DNA (cytosine-5-)-methyltransferase in Vibrio cholerae.
PG  - 1055-1062
AB  - 5-Methyl cytosine (m5C was detected in genomic DNA of the enteric pathogen Vibrio cholerae by
      HPLC analysis and immunoblotting with
      m5C-specific antibody. Although cleavage with the restriction
      endonuclease EcoRII revealed the absence of a Dcm homologue in V.
      cholerae, analysis of the genome sequence indicated the presence of a
      gene, designated in this study as vchM, which encodes a DNA
      (cytosine-5-)-methyltransferase (m5C-MTase) designated M.Vch. M.Vch is
      not associated with a restriction endonuclease or a mismatch very short
      patch repair (Vsr)-like endonuclease and is hence an 'orphan' or
      solitary MTase, although analysis of a phylogenetic tree indicated that
      related cytosine MTases are all components of restriction-modification
      systems. M.Vch recognizes and methylates the first 5' C in the
      degenerate sequence 5'-RCCGGY-3'. RT-PCR analysis suggested that vchM
      gene expression is increased during the stationary phase of growth.
      During stationary phase, the spontaneous mutation frequency in the V.
      cholerae wild-type strain was significantly higher than in the
      corresponding vchM mutant strain, suggesting that the presence of M.Vch
      and the absence of a very short patch (VSP) repair-like system imposes
      upon V. cholerae a mutator phenotype.
AU  - Banerjee S
AU  - Chowdhury R
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2006 152: 1055-1062.

PMID- 15610823
VI  - 139
DP  - 2005
TI  - Entamoeba histolytica DNA methyltransferase (Ehmeth) is a nuclear matrix protein that binds EhMRS2, a DNA that includes a scaffold/matrix  attachment region (S/MAR).
PG  - 91-97
AB  - The protozoan parasite Entamoeba histolytica express a cytosine-5 DNA methyltransferase
      (Ehmeth) that belongs to the DNMT2 protein family.
      The biological function of members of this DNMT2 family is unknown. In
      the present study, we have demonstrated that Ehmeth is a nuclear matrix
      protein. Indeed, we showed by south-western analysis and yeast
      one-hybrid system that Ehmeth binds to EhMRS2, a DNA element which
      contains the eukaryotic consensus scaffold/inatrix attachment regions
      (S/MAR) bipartite recognition sequences. S/MARs have been implicated in
      a variety of important functions, such as genome organization and gene
      expression. The methylation status of cytosine located within EhMRS2
      was analyzed by bisulfite genomic sequencing. We observed the presence
      of methylated cytosine within the 3'-end of EhMRS2. These data provide
      the first evidence that a member of the DNMT2 family interacts with a
      S/MAR containing DNA element.
AU  - Banerjee S
AU  - Fisher O
AU  - Lohia A
AU  - Ankri S
PT  - Journal Article
TA  - Mol. Biochem. Parasitol.
JT  - Mol. Biochem. Parasitol.
SO  - Mol. Biochem. Parasitol. 2005 139: 91-97.

PMID- 25635013
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Four Vibrio parahaemolyticus Isolates from Clinical Cases in Canada.
PG  - e01482-14
AB  - Vibrio parahaemolyticus is a leading cause of bacterial gastroenteritis following ingestion of
      contaminated seafood. This report presents the draft genome
      sequences of four clinical strains of V. parahaemolyticus isolated in Canada. All
      four strains lack traditional pathogenic markers and possess uniquely individual
      characteristics identified using other typing criteria.
AU  - Banerjee S
AU  - Petronella N
AU  - Chew LC
AU  - Farber J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01482-14.

PMID- 7748494
VI  - 14
DP  - 1995
TI  - Effect of mercury substitution of DNA on its susceptibility to cleavage by restriction endonucleases.
PG  - 445-450
AB  - Mercurated DNA was synthesized in vitro by substituting Hg-dCTP or Hg-dUMP for dCTP in one
      strand of M13mp8DNA in a DNA polymerase I reaction. Restriction enzymes, including SmaI, PstI,
      BamHI, HindIII, and HincII, were completely inactive when their recognition sites were fully
      substituted with Hg-dCMP, while Hg-dUMP containing DNA was hydrolyzed to some extent. Under
      conditions favoring star activities, or when DNA was substituted with a low level of
      mercury-nucleotide, DNA was cleaved by restriction enzymes. Susceptibility to degrading and
      synthesizing enzymes and insensitivity to restriction endonucleases of fully mercurated DNA
      makes mercuration an attractive molecular "tag" for in vitro manipulation and selective
      isolation of Hg-DNA.
AU  - Banfalvi G
AU  - Sarkar N
PT  - Journal Article
TA  - DNA Cell Biol.
JT  - DNA Cell Biol.
SO  - DNA Cell Biol. 1995 14: 445-450.

PMID- 29167246
VI  - 5
DP  - 2017
TI  - Complete 4.55-Megabase-Pair Genome of 'Candidatus Fluviicola riflensis,' Curated  from Short-Read Metagenomic Sequences.
PG  - e01299-17
AB  - We report the 4.55-Mbp genome of 'Candidatus Fluviicola riflensis' (Bacteroidetes) that was
      manually curated to completion from Illumina data. 'Ca
      Fluviicola riflensis' is a facultative anaerobe. Its ability to grow over a range
      of O2 levels may favor its proliferation in an aquifer adjacent to the Colorado
      River in the United States.
AU  - Banfield JF
AU  - Anantharaman K
AU  - Williams KH
AU  - Thomas BC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01299-17.

PMID- 29930043
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Bacillus subtilis Strain DKU_NT_02, Isolated from Traditional Korean Food Using Soybean (Chung-gook-jang) for High-Quality Poly-gamma-Glutamic Acid Activity.
PG  - e00525-18
AB  - The complete genome sequence of Bacillus subtilis strain DKU_NT_02, isolated from traditional
      Korean food using soybeans (chung-gook-jang), is presented here. This
      strain was chosen to help identify genetic factors with high-quality
      poly-gamma-glutamic acid (gammaPGA) activity.
AU  - Bang MS
AU  - Jeong HW
AU  - Lee YJ
AU  - Lee SJ
AU  - Lee SC
AU  - Shin JI
AU  - Oh CH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00525-18.

PMID- 28774991
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Bacillus subtilis Strain DKU_NT_01 Isolated from Traditional Korean Food Containing Soybean (Chung-gook-jang).
PG  - e00769-17
AB  - Here, we report the whole-genome sequence of Bacillus subtilis strain DKU_NT_01 isolated from
      traditional Korean food containing soybean (chung-gook-jang). The
      de novo genome of Bacillus subtilis strain DKU_NT_01 has one contig and G+C
      content of 55.4%, is 4,954,264 bp in length, and contains 5,011 coding sequences
      (CDSs).
AU  - Bang MS
AU  - Jeong HW
AU  - Lee YJ
AU  - Oh HY
AU  - Lee SJ
AU  - Shim MS
AU  - Shin JI
AU  - Oh CH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00769-17.

PMID- 30533916
VI  - 7
DP  - 2018
TI  - Draft Genome Sequence of Salmonella enterica subsp. enterica Serotype Typhimurium Sequence Type 313, Isolated from India.
PG  - e00990-18
AB  - Salmonella enterica subsp. enterica serotype Typhimurium sequence type 313 (ST313) is most
      commonly associated with invasive nontyphoidal Salmonella disease
      in Africa among patients with HIV infection and malignancy. Here, we report a
      draft genome sequence of S. Typhimurium ST313, isolated from an elderly
      immunosuppressed patient from India with non-Hodgkins lymphoma.
AU  - Bangera SR
AU  - Umakanth S
AU  - Mukhopadhyay AK
AU  - Leekitcharoenphon P
AU  - Chowdhury G
AU  - Hendriksen RS
AU  - Ballal M
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e00990-18.

PMID- 15272401
VI  - 190
DP  - 2004
TI  - Progress toward Characterization of the Group A Streptococcus Metagenome: Complete Genome Sequence of a Macrolide-Resistant Serotype M6 Strain.
PG  - 727-738
AB  - We describe the genome sequence of a macrolide-resistant strain (MGAS10394) of serotype M6
      group A Streptococcus (GAS). The genome is
      1,900,156 bp in length, and 8 prophage-like elements or remnants compose
      12.4% of the chromosome. A 8.3-kb prophage remnant encodes the SpeA4
      variant of streptococcal pyrogenic exotoxin A. The genome of strain
      MGAS10394 contains a chimeric genetic element composed of prophage genes
      and a transposon encoding the mefA gene conferring macrolide resistance.
      This chimeric element also has a gene encoding a novel surface-exposed
      protein (designated "R6 protein"), with an LPKTG cell-anchor motif located
      at the carboxyterminus. Surface expression of this protein was confirmed
      by flow cytometry. Humans with GAS pharyngitis caused by serotype M6
      strains had antibody against the R6 protein present in convalescent, but
      not acute, serum samples. Our studies add to the theme that GAS
      prophage-encoded extracellular proteins contribute to host-pathogen
      interactions in a strain-specific fashion.
AU  - Banks DJ
AU  - Porcella SF
AU  - Barbian KD
AU  - Beres SB
AU  - Philips LE
AU  - Voyich JM
AU  - DeLeo FR
AU  - Martin JM
AU  - Somerville GA
AU  - Musser JM
PT  - Journal Article
TA  - J. Infect. Dis.
JT  - J. Infect. Dis.
SO  - J. Infect. Dis. 2004 190: 727-738.

PMID- 14673771
VI  - 188
DP  - 2003
TI  - Structure and distribution of an unusual chimeric genetic element encoding macrolide resistance in phylogenetically diverse clones of group A Streptococcus.
PG  - 1899-1909
AB  - The resistance of group A Streptococcus (GAS) to macrolide antibiotics is now a worldwide
      problem. Preliminary sequencing of the genome of an
      erythromycin-resistant serotype M6 clone that was responsible for a
      pharyngitis outbreak in Pittsburgh, Pennsylvania, was conducted to
      determine the structure of the genetic element containing the mefA gene,
      which encodes a macrolide efflux protein. The mefA gene is associated with
      a 58.8-kb chimeric genetic element composed of a transposon inserted into
      a prophage. This element also encodes a putative extracellular protein
      with a cell-wall anchoring motif (LPKTG) located at the carboxyterminus.
      The mefA element was present in phylogenetically diverse GAS strains
      isolated throughout the United States. Culture supernatants, prepared
      after mitomycin C treatment, of a strain representing the outbreak clone
      contained mefA element DNA in a DNAse-resistant form. Together, these data
      provide new information about the molecular genetic basis of macrolide
      resistance and dissemination in GAS strains.
AU  - Banks DJ
AU  - Porcella SF
AU  - Barbian KD
AU  - Martin JM
AU  - Musser JM
PT  - Journal Article
TA  - J. Infect. Dis.
JT  - J. Infect. Dis.
SO  - J. Infect. Dis. 2003 188: 1899-1909.

PMID- 16788202
VI  - 188
DP  - 2006
TI  - Functional Identification of Conjugation and Replication Regions of the Tetracycline Resistance Plasmid pCW3 from Clostridium perfringens.
PG  - 4942-4951
AB  - Clostridium perfringens causes fatal human infections, such as gas
      gangrene, as well as gastrointestinal diseases in both humans and animals.
      Detailed molecular analysis of the tetracycline resistance plasmid pCW3
      from C. perfringens has shown that it represents the prototype of a unique
      family of conjugative antibiotic resistance and virulence plasmids. We
      have identified the pCW3 replication region by deletion and transposon
      mutagenesis and showed that the essential rep gene encoded a basic protein
      with no similarity to any known plasmid replication proteins. An 11-gene
      conjugation locus containing 5 genes that encoded putative proteins with
      similarity to proteins from the conjugative transposon Tn916 was
      identified, although the genes' genetic arrangements were different.
      Functional genetic studies demonstrated that two of the genes in this
      transfer clostridial plasmid (tcp) locus, tcpF and tcpH, were essential
      for the conjugative transfer of pCW3, and comparative analysis confirmed
      that the tcp locus was not confined to pCW3. The conjugation region was
      present on all known conjugative plasmids from C. perfringens, including
      an enterotoxin plasmid and other toxin plasmids. These results have
      significant implications for plasmid evolution, as they provide evidence
      that a nonreplicating Tn916-like element can evolve to become the
      conjugation locus of replicating plasmids that carry major virulence genes
      or antibiotic resistance determinants.
AU  - Bannam TL
AU  - Teng WL
AU  - Bulach D
AU  - Lyras D
AU  - Rood JI
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2006 188: 4942-4951.

PMID- 21954306
VI  - 2
DP  - 2011
TI  - Necrotic Enteritis-Derived Clostridium perfringens Strain with Three Closely Related Independently Conjugative Toxin and Antibiotic Resistance Plasmids.
PG  - e00190-11
AB  - The pathogenesis of avian necrotic enteritis involves NetB, a pore-forming
      toxin produced by virulent avian isolates of Clostridium perfringens type
      A. To determine the location and mobility of the netB structural gene, we
      examined a derivative of the tetracycline-resistant necrotic enteritis
      strain EHE-NE18, in which netB was insertionally inactivated by the
      chloramphenicol and thiamphenicol resistance gene catP. Both tetracycline
      and thiamphenicol resistance could be transferred either together or
      separately to a recipient strain in plate matings. The separate
      transconjugants could act as donors in subsequent matings, which
      demonstrated that the tetracycline resistance determinant and the netB
      gene were present on different conjugative elements. Large plasmids were
      isolated from the transconjugants and analyzed by high-throughput
      sequencing. Analysis of the resultant data indicated that there were
      actually three large conjugative plasmids present in the original strain,
      each with its own toxin or antibiotic resistance locus. Each plasmid
      contained a highly conserved 40-kb region that included plasmid
      replication and transfer regions that were closely related to the 47-kb
      conjugative tetracycline resistance plasmid pCW3 from C. perfringens. The
      plasmids were as follows: (i) a conjugative 49-kb tetracycline resistance
      plasmid that was very similar to pCW3, (ii) a conjugative 82-kb plasmid
      that contained the netB gene and other potential virulence genes, and
      (iii) a 70-kb plasmid that carried the cpb2 gene, which encodes a
      different pore-forming toxin, beta2 toxin. IMPORTANCE: The anaerobic
      bacterium Clostridium perfringens can cause an avian gastrointestinal
      disease known as necrotic enteritis. Disease pathogenesis is not well
      understood, although the plasmid-encoded pore-forming toxin NetB, is an
      important virulence factor. In this work, we have shown that the plasmid
      that carries the netB gene is conjugative and has a 40-kb region that is
      very similar to replication and transfer regions found within each of the
      sequenced conjugative plasmids from C. perfringens. We also showed that
      this strain contained two additional large plasmids that were also
      conjugative and carried a similar 40-kb region. One of these plasmids
      encoded beta2 toxin, and the other encoded tetracycline resistance. To our
      knowledge, this is the first report of a bacterial strain that carries
      three closely related but different independently conjugative plasmids.
      These results have significant implications for our understanding of the
      transmission of virulence and antibiotic resistance genes in pathogenic
      bacteria.
AU  - Bannam TL
AU  - Yan XX
AU  - Harrison PF
AU  - Seemann T
AU  - Keyburn AL
AU  - Stubenrauch C
AU  - Weeramantri LH
AU  - Cheung JK
AU  - McClane BA
AU  - Boyce JD
AU  - Moore RJ
AU  - Rood JI
PT  - Journal Article
TA  - MBio
JT  - MBio
SO  - MBio 2011 2: e00190-11.

PMID- 24482526
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of a Mycobacterium avium Complex Isolate from a Broadbill Bird.
PG  - e01268-13
AB  - We report the draft genome sequence of a Mycobacterium avium complex isolate. This isolate has
      an estimated genome size of 5.1 Mb with an average GC content of
      68.9% and is predicted to carry 4,497 protein-encoding genes and 317 pseudogenes.
AU  - Bannantine JP
AU  - Bayles DO
AU  - Robbe-Austerman S
AU  - Burrell AM
AU  - Stabel JR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01268-13.

PMID- 24503996
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Mycobacterium avium subsp. paratuberculosis, Isolated from Human Breast Milk.
PG  - e01252-13
AB  - Mycobacterium avium subsp. paratuberculosis is the etiologic agent of Johne's disease in
      ruminants and has also been associated with human Crohn's disease. We
      report the complete genome sequence of M. avium subsp. paratuberculosis, isolated
      from the breast milk of a Crohn's disease patient. This sequence has high
      identity with characterized strains recovered from cattle.
AU  - Bannantine JP
AU  - Li L
AU  - Mwangi M
AU  - Cote R
AU  - Raygoza GJA
AU  - Kapur V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01252-13.

PMID- 4920420
VI  - 61
DP  - 1970
TI  - Analysis of an R+ strain carrying two fi- sex factors.
PG  - 273-281
AB  - An Escherichia coli K12 strain, J5-3 (R313), was presumed to carry a fi-R factor, R313, which
      determined resistance to the drugs tetracycline, streptomycin and sulphonamide, and also
      determined a host specificity, hsII.  When this strain was used as a donor of drug resistance,
      separation of R factor-carried determinants was observed in ex-conjugants.  Resistance to Tc
      and hsII character were not separated, nor was resistance to Sm separated from resistance to
      Su, but separation of these two pairs of characters was observed.  Tetracycline-sensitive
      segregants, obtained by penicillin selection, were resistant to Sm and Su, but had lost the
      hsII character.  Similarly, segregants for selected sensitivity to Su were sensitive to Sm,
      but resistant to Tc and hsII+.  The same pattern of separation of characters was also observed
      when drug resistance was transduced with phage PI, with the additional finding that the Sm and
      Su resistant transductants lacked sex factor activity.  The resistance to Sm carried by these
      transductants could be mobilized by an fi-R factor, R143.  Explanations of this behavior are
      considered, including the possibility that the strain J5-3 (R313) had carried two fi-R
      factors.  This explanation would also require that the transduction of an R factor by phage PI
      is not always complete.
AU  - Bannister D
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1970 61: 273-281.

PMID- 4868172
VI  - 30
DP  - 1968
TI  - Restriction and modification of bacteriophages by R+ strains of Escherichia coli K12.
PG  - 735-738
AB  - None
AU  - Bannister D
AU  - Glover SW
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1968 30: 735-738.

PMID- 4922982
VI  - 61
DP  - 1970
TI  - The isolation and properties of non-restricting mutants of two different host specificities associated with drug resistance factors.
PG  - 63-71
AB  - Non-restricting (r-) mutants of two different host specificities carried by
      resistance transfer factors have been isolated.  As previously found with other
      host specificities, the non-restricting mutants were of two phenotypes:  those
      that retained the ability to modify DNA, and those which had lost the ability
      to modify DNA.  These mutants were tested for complementation with wild-type
      host specificities carried either on the Escherichia coli chromosome, on
      resistance transfer factors, or on the phage PI.  No complementation was
      observed and possible explanations for this finding are considered.
AU  - Bannister D
AU  - Glover SW
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1970 61: 63-71.

PMID- 21742891
VI  - 193
DP  - 2011
TI  - Complete genome sequence of Clostridium acetobutylicum DSM 1731, a solvent-producing strain with multireplicon genome architecture.
PG  - 5007-5008
AB  - Clostridium acetobutylicum is an important microorganism for solvent production. We report the
      complete genome sequence of C. acetobutylicum
      DSM 1731, a genome with multi-replicon architecture. Comparison with the
      sequenced type strain C. acetobutylicum ATCC 824, the genome of strain
      DSM1731 harbors a 1.7 kb insertion and a novel 11.1 kb plasmid, which
      might be acquired during evolution.
AU  - Bao G
AU  - Wang R
AU  - Zhu Y
AU  - Dong H
AU  - Mao S
AU  - Zhang Y
AU  - Chen Z
AU  - Li Y
AU  - Ma Y
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5007-5008.

PMID- 23405358
VI  - 1
DP  - 2013
TI  - Genome Sequence of Klebsiella oxytoca M5al, a Promising Strain for Nitrogen Fixation and Chemical Production.
PG  - e00074-12
AB  - Klebsiella oxytoca is an important microorganism for nitrogen fixation and chemical
      production. Here, we report an annotated draft genome of K. oxytoca
      strain M5al that contains 5,256 protein-coding genes and 95 structural RNAs,
      which provides a genetic basis for a better understanding of the physiology of
      this species.
AU  - Bao G
AU  - Zhang Y
AU  - Du C
AU  - Chen Z
AU  - Li Y
AU  - Cao Z
AU  - Ma Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00074-12.

PMID- 24928416
VI  - 14
DP  - 2014
TI  - Differential efficiency in exogenous DNA acquisition among closely related Salmonella strains: implications in bacterial speciation.
PG  - 157
AB  - BACKGROUND: Acquisition of exogenous genetic material is a key event in bacterial
      speciation. It seems reasonable to assume that recombination of the incoming DNA
      into genome would be more efficient with higher levels of relatedness between the
      DNA donor and recipient. If so, bacterial speciation would be a smooth process,
      leading to a continuous spectrum of genomic divergence of bacteria, which,
      however, is not the case as shown by recent findings. The goal of this study was
      todetermine if DNA transfer efficiency is correlated with the levels of sequence
      identity. RESULTS: To compare the relative efficiency of exogenous DNA
      acquisition among closely related bacteria, we carried out phage-mediated
      transduction and plasmid-mediated transformation in representative Salmonella
      strains with different levels of relatedness. We found that the efficiency was
      remarkably variable even among genetically almost identical bacteria. Although
      there was a general tendency that more closely related DNA donor-recipient pairs
      had higher transduction efficiency, transformation efficiency exhibited over a
      thousand times difference among the closely related Salmonella strains.
      CONCLUSION: DNA acquisition efficiency is greatly variable among bacteria that
      have as high as over 99% identical genetic background, suggesting that bacterial
      speciation involves highly complex processes affected not only by whether
      beneficial exogenous DNA may exist in the environment but also the "readiness" of
      the bacteria to accept it.
AU  - Bao HX
AU  - Tang L
AU  - Yu L
AU  - Wang XY
AU  - Li Y
AU  - Deng X
AU  - Li YG
AU  - Li A
AU  - Zhu DL
AU  - Johnston RN
AU  - Liu GR
AU  - Feng Y
AU  - Liu SL
PT  - Journal Article
TA  - BMC Microbiol.
JT  - BMC Microbiol.
SO  - BMC Microbiol. 2014 14: 157.

PMID- 25197451
VI  - 9
DP  - 2014
TI  - Genome sequence of the anaerobic bacterium Bacillus sp. strain ZYK, a selenite and nitrate reducer from paddy soil.
PG  - 646-654
AB  - Bacillus sp. strain ZYK, a member of the phylum Firmicutes, is of interest for its ability to
      reduce nitrate and selenite and for its resistance to arsenic
      under anaerobic conditions. Here we describe some key features of this organism,
      together with the complete genome sequence and annotation. The 3,575,797 bp long
      chromosome with its 3,454 protein-coding and 70 RNA genes, and the information
      gained from its sequence will be relevant to the elucidation of
      microbially-mediated transformations of nitrogen, selenium and arsenic in paddy
      soil.
AU  - Bao P
AU  - Su JQ
AU  - Hu ZY
AU  - Haggblom MM
AU  - Zhu YG
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 646-654.

PMID- 11997336
VI  - 12
DP  - 2002
TI  - A complete sequence of the T. tengcongensis genome.
PG  - 689-700
AB  - Thermoanaerobacter tengcongensis is a rod-shaped, gram-negative, anaerobic
      eubacterium that was isolated from a freshwater hot spring in Tengchong,
      China. Using a whole-genome-shotgun method, we sequenced its 2,689,445-bp
      genome from an isolate, MB4(T) (Genbank accession no. AE008691). The
      genome encodes 2588 predicted coding sequences (CDS). Among them, 1764
      (68.2%) are classified according to homology to other documented proteins,
      and the rest, 824 CDS (31.8%), are functionally unknown. One of the
      interesting features of the T. tengcongensis genome is that 86.7% of its
      genes are encoded on the leading strand of DNA replication. Based on
      protein sequence similarity, the T. tengcongensis genome is most similar
      to that of Bacillus halodurans, a mesophilic eubacterium, among all fully
      sequenced prokaryotic genomes up to date. Computational analysis on genes
      involved in basic metabolic pathways supports the experimental discovery
      that T. tengcongensis metabolizes sugars as principal energy and carbon
      source and utilizes thiosulfate and element sulfur, but not sulfate, as
      electron acceptors. T. tengcongensis, as a gram-negative rod by empirical
      definitions (such as staining), shares many genes that are characteristics
      of gram-positive bacteria whereas it is missing molecular components
      unique to gram-negative bacteria. A strong correlation between the G + C
      content of tDNA and rDNA genes and the optimal growth temperature is found
      among the sequenced thermophiles. It is concluded that thermophiles are a
      biologically and phylogenetically divergent group of prokaryotes that have
      converged to sustain extreme environmental conditions over evolutionary
      timescale. Full author list: Bao, Q., Tian, Y., Li, W., Xu, Z., Xuan, Z., Hu, S., Dong, W.,
      Yang, J., Chen, Y., Xue, Y., Xu, Y., Lai, X., Huang, L., Dong, X., Ma, Y., Ling, L., Tan, H.,
      Chen, R., Wang, J., Yu, J., Yang, H.
AU  - Bao Q
AU  - Tian Y
AU  - Li W
AU  - Xu Z
AU  - Xuan Z
AU  - Hu S
AU  - Dong W
AU  - Yang J
AU  - Chen Y
AU  - Xue Y
AU  - Xu Y
AU  - Lai X
AU  - Huang L
AU  - Dong X
AU  - Ma Y
AU  - Ling L
AU  - Tan H
AU  - Chen R
AU  - Wang J
AU  - Yu J
AU  - Yang H
PT  - Journal Article
TA  - Genome Res.
JT  - Genome Res.
SO  - Genome Res. 2002 12: 689-700.

PMID- 25792045
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Raoultella ornithinolytica Strain S12, a Lignin-Degrading Bacterium Isolated from Forest Soil.
PG  - e00104-15
AB  - We report the complete genome sequence of Raoultella ornithinolytica strain S12,  isolated
      from a soil sample collected from areas bordering rotten wood and wet
      soil on Mt. Zijin, Nanjing. The complete genome of this bacterium may contribute
      toward the discovery of efficient lignin-degrading pathways.
AU  - Bao W
AU  - Zhou Y
AU  - Jiang J
AU  - Xu Z
AU  - Hou L
AU  - Leung FC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00104-15.

PMID- 18164625
VI  - 58
DP  - 2008
TI  - Expression and purification of BmrI restriction endonuclease and its N-terminal cleavage domain variants.
PG  - 42-52
AB  - BmrI (ACTGGG N5/N4) is one of the few metal-independent restriction endonucleases (REases)
      found in bacteria. The BmrI
      restriction-modification system was cloned by the methylase selection
      method, inverse PCR, and PCR. BmrI REase shows significant amino acid
      sequence identity to BfiI and a putative endonuclease MspBNCORF3798 from
      the sequenced Mesorhizobium sp. BNC1 genome. The EDTA-resistant BmrI REase
      was successfully over-expressed in a pre-modified E. coli strain from
      pET21a or pBAC-expIQ vectors. The recombinant BmrI REase shows strong
      promiscuous activity (star activity) in NEB buffers 1, 4, and an EDTA
      buffer. Star activity was diminished in buffers with 100-150mM NaCl and
      10mM MgCl(2). His-tagged BmrI192, the N-terminal cleavage domain of BmrI,
      was expressed in E. coli and purified from inclusion bodies. The refolded
      BmrI192 protein possesses non-specific endonuclease activity. BmrI192
      variants with a single Ser to Cys substitution (S76C or S90C) and BmrI200
      (T200C) with a single Cys at the C-terminal end were also constructed and
      purified. BmrI200 digests both single-strand (ss) and double-strand (ds)
      DNA and the nuclease activity on ss DNA is at least 5-fold higher than
      that on ds DNA. The Cys-containing BmrI192 and BmrI200 nuclease variants
      may be useful for coupling to other DNA binding elements such as synthetic
      zinc fingers, thio-containing locked nucleic acids (LNA) or peptide
      nucleic acids (PNA).
AU  - Bao Y
AU  - Higgins L
AU  - Zhang P
AU  - Chan SH
AU  - Laget S
AU  - Sweeney S
AU  - Lunnen K
AU  - Xu SY
PT  - Journal Article
TA  - Protein Expr. Purif.
JT  - Protein Expr. Purif.
SO  - Protein Expr. Purif. 2008 58: 42-52.

PMID- 24831147
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Dyella jiangningensis Strain SBZ3-12, Isolated from the Surfaces of Weathered Rock.
PG  - e00416-14
AB  - Dyella jiangningensis strain SBZ3-12 can weather biotite and release Al and Fe from biotite
      under nutrient-poor conditions. Here, we report the first complete
      genome sequence of D. jiangningensis strain SBZ3-12, which may facilitate a
      better understanding of the molecular mechanism behind mineral weathering.
AU  - Bao Y
AU  - Kwok AH
AU  - He L
AU  - Jiang J
AU  - Huang Z
AU  - Leung FC
AU  - Sheng X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00416-14.

PMID- 25225265
VI  - 196
DP  - 2014
TI  - Unique Genomic Arrangements in an Invasive Serotype M23 strain of Streptococcus pyogenes Identify Genes that Induce Hypervirulence.
PG  - 4089-4102
AB  - The first genome sequence of a Group A Streptococcus pyogenes M23 (emm23)
      serotype (M23ND), isolated from an invasive human infection, has been completed.
      This opacity factor-negative (SOF-) strain is composed of a circular chromosome
      of 1,846,477 bp. Gene profiling showed that this strain contained six
      phage-encoded and 24 chromosomally-inherited well-known virulence factors, as
      well as 11 pseudogenes. The bacterium has acquired four large prophage elements,
      PhiM23ND.1-4, harboring genes encoding streptococcal superantigen (ssa),
      streptococcal pyrogenic exotoxins (spe) C, H, and I, and DNases spd1 and spd3,
      with phage integrase genes present at one flank of each phage insertion,
      suggesting that the phages were integrated by horizontal gene transfer.
      Comparative analyses revealed unique large-scale genomic rearrangements that
      differ from previously sequenced GAS strains. These rearrangements resulted in an
      imbalanced genomic architecture and translocations of chromosome-encoded
      virulence genes. The covS sensor in M23ND was identified as a pseudogene,
      resulting in attenuation of speB function and increased expression of the
      chromosomal virulence factors, mga, emm23, scpA, fibronectin-binding proteins
      (sfb1 and fbp54), streptolysin O (slo), hyaluronic acid capsule (hasA),
      streptokinase (ska), and a 2 DNases (spd and spd3), which were verified by PCR.
      These genes are responsible for facilitating host epithelial cell binding and
      and/or immune evasion, thus further contributing to the virulence of M23ND. In
      conclusion, strain M23ND has become highly pathogenic as the result of a
      combination of multiple genetic factors, particularly gene composition and
      mutations, prophage integrations, unique genomic rearrangements, and regulated
      expression of critical virulence factors.
AU  - Bao Y
AU  - Liang Z
AU  - Booyjzsen C
AU  - Mayfield JA
AU  - Li Y
AU  - Lee SW
AU  - Ploplis VA
AU  - Song H
AU  - Castellino FJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2014 196: 4089-4102.

PMID- 27044623
VI  - 198
DP  - 2016
TI  - Genomic Characterization of a Pattern D Streptococcus pyogenes emm53 Isolate Reveals a Genetic Rationale for Invasive Skin Tropicity.
PG  - 1712-1724
AB  - The genome of an invasive skin-tropic strain (AP53) of serotype M53 Group
      AStreptococcus pyogenes(GAS) is composed of a circular chromosome of 1,860,554
      bp, and encodes genetic markers for infection at skin locales,viz,emmgene-family
      Pattern D and FCT type-3. Through genome-scale comparisons of AP53 with other GAS
      genomes, we identified 596 candidate SNPs that reveal a potential genetic basis
      for skin tropism. The genome of AP53 differed by approximately 30 point mutations
      from a noninvasive Pattern D M53 strain (Alab49), four of which are located in
      virulence genes. One pseudogene, yielding an inactive sensor kinase (CovS-) of
      the two-component transcriptional regulator, CovRS, a major determinant for
      invasiveness, severely attenuated expression of the secreted cysteine protease,
      SpeB, and enhanced expression of the hyaluronic acid capsule, as compared to the
      isogenic noninvasive AP53/CovS+ The collagen-binding protein transcript,sclB,
      differed in the number of 5' -pentanucleotide repeats in the signal peptides of
      AP53 and Alab49 (9vs15), translating into different lengths of their signal
      peptides, which nonetheless maintained a full-length translatable coding frame.
      Further, the GAS AP53 acquired two phages that are absent in Alab49. One such
      phage (PhiAP53.2) contains the known virulence factor superantigen exotoxin gene
      tandem,speK-slaA Overall, we conclude that this bacterium has evolved in multiple
      ways, including mutational variations of regulatory genes, short tandem repeat
      polymorphisms, large-scale genomic alterations, and acquisition of phages, all of
      which may be involved in shaping the adaptation of GAS in specific infectious
      environments and contribute to its enhanced virulence. IMPORTANCE: Infectious
      strains ofS. pyogenes(GAS) are classified by their serotypes, relating to the
      surface M-protein, theemm-like subfamily pattern, and their tropicity toward
      nasopharynx and/or skin. It is generally agreed that M-proteins from Pattern D
      strains, which also directly bind human host plasminogen, are skin-tropic. We
      have sequenced and characterized the genome of an invasive Pattern D GAS strain
      (AP53) in comparison to a very similar strain (Alab49) that is noninvasive, and
      developed a genomic rationale as to possible reasons for the skin tropicity of
      these two strains and the greater invasiveness of AP53.
AU  - Bao YJ
AU  - Liang Z
AU  - Mayfield JA
AU  - Donahue DL
AU  - Carothers KE
AU  - Lee SW
AU  - Ploplis VA
AU  - Castellino FJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2016 198: 1712-1724.

PMID- 27587832
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Methylosinus sp. Strain 3S-1, an Isolate from Rice Root  in a Low-Nitrogen Paddy Field.
PG  - e00932-16
AB  - N2-fixing methanotrophs play an important role in the methane-nitrogen cycle in rice paddies.
      We report here the draft genome sequence of Methylosinus sp. strain
      3S-1 isolated from rice root in a paddy field without N fertilizer input.
AU  - Bao Z
AU  - Shinoda R
AU  - Minamisawa K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00932-16.

PMID- 29930076
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Bacillus velezensis LABIM40, an Effective Antagonist  of Fungal Plant Pathogens.
PG  - e00595-18
AB  - Bacillus velezensis strain LABIM40 holds high potential for biological control of plant
      pathogens. Its complete genome contains one chromosome of 3,972,310 bp with
      3,777 DNA coding sequences and displays 33 gene clusters potentially involved in
      the suppression of fungal pathogens.
AU  - Baptista JP
AU  - Sanches PP
AU  - Teixeira GM
AU  - Morey AT
AU  - Tavares ER
AU  - Yamada-Ogatta SF
AU  - da Rocha SPD
AU  - Hungria M
AU  - Ribeiro RA
AU  - Balbi-Pena MI
AU  - Chideroli RT
AU  - Pereira UP
AU  - de Oliveira AG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00595-18.

PMID- 
VI  - 4
DP  - 2018
TI  - Bacterial virulence against an oceanic bloom-forming phytoplankter is mediated by algal DMSP.
PG  - eaau5716
AB  - Emiliania huxleyi is a bloom-forming microalga that affects the global sulfur cycle by
      producing large amounts of
      dimethylsulfoniopropionate (DMSP) and its volatile metabolic product dimethyl sulfide.
      Top-down regulation of
      E. huxleyi blooms has been attributed to viruses and grazers; however, the possible
      involvement of algicidal bacteria
      in bloom demise has remained elusive. We demonstrate that a Roseobacter strain, Sulfitobacter
      D7, that we isolated
      from a North Atlantic E. huxleyi bloom, exhibited algicidal effects against E. huxleyi upon
      coculturing. Both the alga
      and the bacterium were found to co-occur during a natural E. huxleyi bloom, therefore
      establishing this host-pathogen
      system as an attractive, ecologically relevant model for studying algal-bacterial interactions
      in the
      oceans. During interaction, Sulfitobacter D7 consumed and metabolized algal DMSP to produce
      high amounts of
      methanethiol, an alternative product of DMSP catabolism. We revealed a unique strain-specific
      response, in which
      E. huxleyi strains that exuded higher amounts of DMSP were more susceptible to Sulfitobacter
      D7 infection. Intriguingly,
      exogenous application of DMSP enhanced bacterial virulence and induced susceptibility in an
      algal
      strain typically resistant to the bacterial pathogen. This enhanced virulence was highly
      specific to DMSP compared
      to addition of propionate and glycerol which had no effect on bacterial virulence. We propose
      a novel function for
      DMSP, in addition to its central role in mutualistic interactions among marine organisms, as a
      mediator of bacterial
      virulence that may regulate E. huxleyi blooms.
AU  - Barak-Gavish N
AU  - Frada MJ
AU  - Lee PA
AU  - DiTullio GR
AU  - Ku C
AU  - Malitsky S
AU  - Aharoni A
AU  - Green SJ
AU  - Kartvelishvily E
AU  - Sheyn U
AU  - Schatz D
AU  - Vardi A
PT  - Journal Article
TA  - Sci. Adv.
JT  - Sci. Adv.
SO  - Sci. Adv. 2018 4: eaau5716.

PMID- 23929477
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Streptomyces rapamycinicus Strain NRRL 5491, the Producer of the Immunosuppressant Rapamycin.
PG  - e00581-13
AB  - Streptomyces rapamycinicus strain NRRL 5491 produces the important drug rapamycin. It has a
      large genome of 12.7 Mb, of which over 3 Mb consists of 48
      secondary metabolite biosynthesis clusters.
AU  - Baranasic D
AU  - Gacesa R
AU  - Starcevic A
AU  - Zucko J
AU  - Blazic M
AU  - Horvat M
AU  - Gjuracic K
AU  - Fujs S
AU  - Hranueli D
AU  - Kosec G
AU  - Cullum J
AU  - Petkovic H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00581-13.

PMID- 25035320
VI  - 2
DP  - 2014
TI  - Genome Sequences of the Oxytetracycline Production Strain Streptomyces rimosus R6-500 and Two Mutants with Chromosomal Rearrangements.
PG  - e00517-14
AB  - The genome sequence of Streptomyces rimosus R6-500, an industrially improved strain which
      produces high titers of the important antibiotic oxytetracycline, is
      reported, as well as the genome sequences of two derivatives arising due to the
      genetic instability of the strain.
AU  - Baranasic D
AU  - Zucko J
AU  - Nair M
AU  - Pain A
AU  - Long PF
AU  - Hranueli D
AU  - Cullum J
AU  - Starcevic A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00517-14.

PMID- 29326221
VI  - 6
DP  - 2018
TI  - Genome Sequences of Acholeplasma laidlawii Strains with Increased Resistance to Tetracycline and Melittin.
PG  - e01446-17
AB  - Acholeplasma laidlawii is a well-suited model for studying the molecular basis for adapting
      mollicutes to environmental conditions. Here, we present the
      whole-genome sequences of two strains of A. laidlawii with increased resistance
      to tetracycline and melittin.
AU  - Baranova NB
AU  - Malygina TY
AU  - Medvedeva ES
AU  - Boulygina EA
AU  - Siniagina MN
AU  - Dramchini MA
AU  - Prottoy RA
AU  - Mouzykantov AA
AU  - Davydova MN
AU  - Chernova OA
AU  - Chernov VM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01446-17.

PMID- 2824288
VI  - 56
DP  - 1987
TI  - A genetic system for isolation and characterization of TaqI restriction endonuclease mutants.
PG  - 13-27
AB  - The gene encoding TaqI restriction endonuclease has been subcloned downstream
      from an inducible phoA promoter.  Certain strains of Escherichia coli remain
      viable when endonuclease is expressed, even in the absence of (protective)
      methylation.  Infecting lambda phage DNA is not restricted in vivo.  One E.
      coli strain, MM294, exhibited a temperature-sensitive phenotype when TaqI
      endonuclease was induced.  This allowed for design of an in vivo plate assay
      for identification of specially constructed two-codon insertion mutants in the
      endonuclease gene.  These mutants exhibited a wide range of in vitro
      activities, including wild-type activity, greater activity in low-salt buffer,
      and sequence-specific nicking activity.
AU  - Barany F
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1987 56: 13-27.

PMID- 2842230
VI  - 65
DP  - 1988
TI  - The TaqI star reaction:  strand preferences reveal hydrogen-bond donor and acceptor sites in canonical sequence recognition.
PG  - 149-165
AB  - TaqI endonuclease recognizes and cleaves its canonical sequence, TCGA, with complete fidelity
      under standard conditions. In the presence of some organic solvents, TaqI endonuclease
      introduced additional single-strand and double-strand cuts at sequences termed TaqI star
      sites. Using middle-labeled DNA, the relative rates of cleavage of each strand were
      simultaneously determined for several star sites. These star recognition sequences differed
      from the canonical sequence by a single base, and all potential star sites were either nicked
      or cleaved. Star sites within the middle labeled substrate represented ten of the twelve
      possible star sequences for each strand. For each group of identical star sites, one strand
      was consistently preferred for cleavage. Based on these preferences, a model for TaqI
      recognition of the TCGA sequence is proposed. According to this model, sequence discrimination
      is mediated by eight hydrogen bonds formed between TaqI and the cognate nucleotides within the
      major groove.
AU  - Barany F
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 65: 149-165.

PMID- 2915549
VI  - 13A
DP  - 1989
TI  - Isolation and characterization of TaqI restriction endonuclease mutants.
PG  - 82
AB  - The gene encoding the TaqI restriction endonuclease (recognition sequence T^CGA) has been
      subcloned downstream of an inducible phoA promoter, and overproduced to 30% of cellular
      proteins. E. coli cells remain viable at 37C when endonuclease is expressed, even in the
      absence of (protective) methylation. Analysis of wild type TaqI endonuclease star activity
      (cleavage at closely related sequences) revealed that for a particular star site, one strand
      of the DNA duplex was preferentially cleaved. Based on these preferences, a model is proposed
      that sequence specific discrimination is mediated by 8 hydrogen bonds formed by TaqI and
      specific base groups in the major groove. Using a strain that produces beta-galactosidase upon
      DNA damage, and a temperature dependent in vivo plate assay as screens, over two dozen
      two-codon insertion mutants have been isolated. These are being characterized with respect to
      in vitro canonical site activity, DNA binding using gel mobility shifts, and star site
      activity.
AU  - Barany F
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1989 13A: 82.

PMID- 3266861
VI  - 74
DP  - 1988
TI  - How TaqI endonuclease recognizes its cognate sequence.
PG  - 63-65
AB  - Meeting Abstract
AU  - Barany F
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 63-65.

PMID- 3470568
VI  - 11C
DP  - 1987
TI  - Two codon insertion mutagenesis of the TaqI restriction endonuclease.
PG  - 240
AB  - Recently, the thermophilic TaqI restriction endonuclease and corresponding
      methylase (recognition sequence TCGA) have been cloned.  The endonuclease gene
      has been subcloned under inducible control of an alkaline phosphatase promoter,
      in a small high copy plasmid.  Surprisingly, E. coli cells overproducing TaqI
      endonuclese are still viable at 37C, even in the absence of (protective)
      methylation.  Indeed, neither transforming DNA nor infecting lambda phage are
      restricted by cells harboring TaqI.  However, certain cells harboring this
      plasmid are barely viable at 42C, and this phenotype has been exploited as a
      plate assay for in vivo TaqI endonuclease activity.  Single stranded hexameric
      linkers were inserted into the endonuclease gene using biological selection,
      and the resultant two codon insertion mutants were assayed in vitro for TaqI
      endonuclease activity.  A wide range of enzymatic activity was observed, from
      wild type activity (3 mutants), slight temperature dependency (2 mutants),
      moderate activity (2 mutants), greater activity in low salt buffers (2
      mutants), nicking activity ( 1 mutant), to no activity (2 mutants, and 2 small
      in-1. Slatko, B., Movan, L., Jager, T., Benner, J., Simcox, T., & Wilson, G.
      Ms in preparation 1986.  2. Barany, F. (1985) Proc. Natl. Acad. Sci. USA
      82:4202-4206.
AU  - Barany F
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1987 11C: 240.

PMID- 2842231
VI  - 65
DP  - 1988
TI  - Overproduction, purification and crystallization of TaqI restriction endonuclease.
PG  - 167-177
AB  - Under phoA promoter control, TaqI endonuclease was overproduced to 5% of
      Escherichia coli cellular proteins.  This was achieved by fusing the
      endonuclease gene to the first four codons of the alkaline phosphatase signal
      sequence.  For maximal overproduction (30% of cellular proteins), a putative
      14-bp hairpin within the endonuclease coding sequence was replaced with
      degenerate codons  In addition, TaqI methylase was required to protect host
      DNA.  The endonuclease was purified in sufficient amounts for crystallization.
AU  - Barany F
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 65: 167-177.

PMID- 1339363
VI  - 112
DP  - 1992
TI  - Cloning and sequencing of genes encoding the TthHB8I restriction and modification enzymes: comparison with the isoschizomeric TaqI enzymes.
PG  - 3-12
AB  - Genes encoding the TthHB8I restriction and modification (R-M) system from
      Thermus thermophilus HB8 (recognition sequence T^CGA) were cloned in
      Escherichia coli.  The genes have the same transcriptional orientation, with
      the last 13 codons of the methyltransferase (MTase) overlapping the first 13
      codons of the endonuclease (ENase).  Nucleotide sequence analysis of the TthB8I
      ENase revealed a single chain of 263 amino acid (aa) residues that share a 77%
      identity with the corrected isoschizomeric TaqI ENase.  Likewise, the Tth MTase
      (428 aa) shares a 79% identity with the corrected sequence of the TaqI MTase.
      This high degree of aa conservation suggests a common origin between the Taq
      and Tth R-M systems.  However, codon usage and G + C content for the R-M genes
      differed markedly from that of other cloned Thermus genes.  This suggests that
      these R-M genes were only recently introduced into the genus Thermus.
AU  - Barany F
AU  - Danzitz M
AU  - Zebala J
AU  - Mayer A
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1992 112: 3-12.

PMID- 1551602
VI  - 112
DP  - 1992
TI  - The corrected nucleotide sequences of the TaqI restriction and modification enzymes reveal a thirteen-codon overlap.
PG  - 91-95
AB  - The nucleotide sequence of the genes encoding methyltransferase TaqI (M.TaqI)
      and restriction endonuclease TaqI (R.TaqI) with the recognition sequence, TCGA,
      were analyzed in clones isolated from independent libraries.  The genes,
      originally reported as 363 and 236 codons long [Slatko et al., Nucleic Acids
      Res. 15 (1987) 9781-9796] were determined as 421 and 263 codons long,
      respectively.  The C terminus of the taqIM gene overlaps the N terminus of the
      taqIR gene by 13 codons, as observed with the isoschizomeric TthHB8I
      restriction-modification system [Barany et al., Gene 112 (1992) 13-20].
      Removal of the overlapping codons did not interfere with in vivo M.TaqI
      activity.  We postulate the overlap plays a role in regulating taqIR
      expression.
AU  - Barany F
AU  - Slatko B
AU  - Danzitz M
AU  - Cowburn D
AU  - Schildkraut I
AU  - Wilson GG
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1992 112: 91-95.

PMID- 1551592
VI  - 112
DP  - 1992
TI  - Correlation between insertion mutant activities and amino acid sequence identities of the TaqI and TthHB8 restriction endonucleases.
PG  - 13-20
AB  - A two-codon insertion mutagenesis method has been generalized.  Over two dozen
      insertion mutants throughout the gene encoding TaqI restriction endonuclease
      were constructed and activity was characterized.  All mutants with activity
      either cleaved or nicked the canonical T^CGA recognition sequence.  Some
      insertion mutants created duplication of gene regions, termed Gemini proteins,
      which still retained activity.  The correlation between mutants with poor
      activity and the regions of shared amino identity between the isoschizomeric
      Taq I and TthHB8I suggests these regions are involved in DNA recognition and/or
      catalysis.
AU  - Barany F
AU  - Zebala J
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1992 112: 13-20.

PMID- 10712697
VI  - 35
DP  - 2000
TI  - The archaeal halophilic virus-encoded Dam-like methyltransferase M.Phi Ch1-I methylates adenine residues and complements dam mutants in the low salt environment of Escherichia coli.
PG  - 1168-1179
AB  - The genome of the archaeal virus phi Ch1, infecting Natrialba magadii (formerly
      Natronobacterium magadii), is composed of 58.5 kbp linear ds
      DNA. Virus particles contain several RNA species in sizes of 100-800
      nucleotides. A fraction of phi Ch1 genomes is modified within
      5'-GATC-3' and related sequences, as determined by various restriction
      enzyme digestion analyses. High performance liquid chromatography
      revealed a fifth base, in addition to the four nucleosides, which was
      identified as N-6-methyladenosine. Genetic analyses and subsequent
      sequencing led to the identification of a DNA (N-6-adenine)
      methyltransferase (mtase) gene. The protein product was designated
      M.phi Ch1-I. By the localization of the most conserved motifs (a DPPY
      motif occurring before FxGxG), the enzyme was placed within the
      beta-subgroup of the (N-6-adenine) methyltransferase class. The mtase
      gene of phi Ch1 was classified as a 'late' gene, as determined by
      measuring the kinetics of mRNA and protein expression in N. magadii
      during the lytic cycle of phi Ch1. After infection of cells, M.phi
      Ch1-I mRNA and protein could be detected in lower amounts than in the
      situation of virus induction from lysogenic cells. Consequently, only
      about 5% of the phi Ch1 progeny genomes after infection of N. magadii
      carry the M.phi Ch1-I methylation in contrast to 50% of virus genomes
      generated by induction of phi Ch1-lysogenic N. magadii cells.
      Heterologous expression of the mtase from a halophile with 3 M
      cytoplasmic salt concentration showed an unexpected feature: the
      protein was active in the low environment of Escherichia coli and was
      able to methylate DNA in vivo. Interestingly, it seemed to exhibit a
      higher sequence specificity in E. coli that resulted in adenine
      methylation exclusively in the sequence 5'-GATC-3'. Additionally,
      expression of M.phi Ch1-I in dam(-) E. coli cells led to a complete
      substitution of the function of M.Dam in DNA mismatch repair.
AU  - Baranyi U
AU  - Klein R
AU  - Lubitz W
AU  - Kruger DH
AU  - Witte A
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2000 35: 1168-1179.

PMID- 29097467
VI  - 5
DP  - 2017
TI  - Genome Sequences of 34 Shiga Toxin-Producing Escherichia coli Isolates from Swine and Other Sources.
PG  - e01214-17
AB  - Shiga toxin-producing Escherichia coli (STEC) bacteria are foodborne pathogens that can be
      carried by various animals. The swine STEC population is partially
      composed of host-specific strains that are often not well characterized. In this
      work, the genome sequences of a number of swine STEC strains are presented.
AU  - Baranzoni GM
AU  - Fratamico PM
AU  - Kim GH
AU  - Reichenberger ER
AU  - Funk JA
AU  - Manning SD
AU  - Bosilevac JM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01214-17.

PMID- 27469964
VI  - 4
DP  - 2016
TI  - Complete Genome Sequences of Escherichia coli O157:H7 Strains SRCC 1675 and 28RC, Which Vary in Acid Resistance.
PG  - e00743-16
AB  - The level of acid resistance among Escherichia coli O157:H7 strains varies, and strains with
      higher resistance to acid may have a lower infectious dose. The
      complete genome sequences belonging to two strains of Escherichia coli O157:H7
      with different levels of acid resistance are presented here.
AU  - Baranzoni GM
AU  - Fratamico PM
AU  - Reichenberger ER
AU  - Kim GH
AU  - Breidt F
AU  - Kay K
AU  - Oh DH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00743-16.

PMID- 27856912
VI  - 354
DP  - 2016
TI  - The DNA methyltransferase DNMT3C protects male germ cells from transposon activity.
PG  - 909-912
AB  - DNA methylation is prevalent in mammalian genomes and plays a central role in the epigenetic
      control of development. The mammalian DNA methylation machinery is
      thought to be composed of three DNA methyltransferase enzymes (DNMT1, DNMT3A, and
      DNMT3B) and one cofactor (DNMT3L). Here, we describe the discovery of Dnmt3C, a
      de novo DNA methyltransferase gene that evolved via a duplication of Dnmt3B in
      rodent genomes and was previously annotated as a pseudogene. We show that DNMT3C
      is the enzyme responsible for methylating the promoters of evolutionarily young
      retrotransposons in the male germ line and that this specialized activity is
      required for mouse fertility. DNMT3C reveals the plasticity of the mammalian DNA
      methylation system and expands the scope of the mechanisms involved in the
      epigenetic control of retrotransposons.
AU  - Barau J
AU  - Teissandier A
AU  - Zamudio N
AU  - Roy S
AU  - Nalesso V
AU  - Herault Y
AU  - Guillou F
AU  - Bourc'his D
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2016 354: 909-912.

PMID- 25395628
VI  - 2
DP  - 2014
TI  - Genome Sequence of Corynebacterium pseudotuberculosis MB20 bv. equi Isolated from a Pectoral Abscess of an Oldenburg Horse in California.
PG  - e00977-14
AB  - The genome of Corynebacterium pseudotuberculosis MB20 bv. equi was sequenced using the Ion
      Personal Genome Machine (PGM) platform, and showed a size of
      2,363,089 bp, with 2,365 coding sequences and a GC content of 52.1%. These
      results will serve as a basis for further studies on the pathogenicity of C.
      pseudotuberculosis bv. equi.
AU  - Barauna RA
AU  - Guimaraes LC
AU  - Veras AA
AU  - de Sa PH
AU  - Gracas DA
AU  - Pinheiro KC
AU  - Silva AS
AU  - Folador EL
AU  - Benevides LJ
AU  - Viana MV
AU  - Carneiro AR
AU  - Schneider MP
AU  - Spier SJ
AU  - Edman JM
AU  - Ramos RT
AU  - Azevedo V
AU  - Silva A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00977-14.

PMID- 28163825
VI  - 12
DP  - 2017
TI  - Genomic analysis of four strains of Corynebacterium pseudotuberculosis bv. Equi isolated from horses showing distinct signs of infection.
PG  - 16
AB  - The genomes of four strains (MB11, MB14, MB30, and MB66) of the species Corynebacterium
      pseudotuberculosis biovar equi were sequenced on the Ion Torrent
      PGM platform, completely assembled, and their gene content and structure were
      analyzed. The strains were isolated from horses with distinct signs of infection,
      including ulcerative lymphangitis, external abscesses on the chest, or internal
      abscesses on the liver, kidneys, and lungs. The average size of the genomes was
      2.3 Mbp, with 2169 (Strain MB11) to 2235 (Strain MB14) predicted coding sequences
      (CDSs). An optical map of the MB11 strain generated using the KpnI restriction
      enzyme showed that the approach used to assemble the genome was satisfactory,
      producing good alignment between the sequence observed in vitro and that obtained
      in silico. In the resulting Neighbor-Joining dendrogram, the C.
      pseudotuberculosis strains sequenced in this study were clustered into a single
      clade supported by a high bootstrap value. The structural analysis showed that
      the genomes of the MB11 and MB14 strains were very similar, while the MB30 and
      MB66 strains had several inverted regions. The observed genomic characteristics
      were similar to those described for other strains of the same species, despite
      the number of inversions found. These genomes will serve as a basis for
      determining the relationship between the genotype of the pathogen and the type of
      infection that it causes.
AU  - Barauna RA
AU  - Ramos RT
AU  - Veras AA
AU  - de Sa PH
AU  - Guimaraes LC
AU  - das Gracas DA
AU  - Carneiro AR
AU  - Edman JM
AU  - Spier SJ
AU  - Azevedo V
AU  - Silva A
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 16.

PMID- 28125655
VI  - 12
DP  - 2017
TI  - Assessing the Genotypic Differences between Strains of Corynebacterium pseudotuberculosis biovar equi through Comparative Genomics.
PG  - E0170676
AB  - Seven genomes of Corynebacterium pseudotuberculosis biovar equi were sequenced on
      the Ion Torrent PGM platform, generating high-quality scaffolds over 2.35 Mbp.
      This bacterium is the causative agent of disease known as "pigeon fever" which
      commonly affects horses worldwide. The pangenome of biovar equi was calculated
      and two phylogenomic approaches were used to identify clustering patterns within
      Corynebacterium genus. Furthermore, other comparative analyses were performed
      including the prediction of genomic islands and prophages, and SNP-based
      phylogeny. In the phylogenomic tree, C. pseudotuberculosis was divided into two
      distinct clades, one formed by nitrate non-reducing species (biovar ovis) and
      another formed by nitrate-reducing species (biovar equi). In the latter group,
      the strains isolated from California were more related to each other, while the
      strains CIP 52.97 and 1/06-A formed the outermost clade of the biovar equi. A
      total of 1,355 core genes were identified, corresponding to 42.5% of the
      pangenome. This pangenome has one of the smallest core genomes described in the
      literature, suggesting a high genetic variability of biovar equi of C.
      pseudotuberculosis. The analysis of the similarity between the resistance islands
      identified a higher proximity between the strains that caused more severe
      infectious conditions (infection in the internal organs). Pathogenicity islands
      were largely conserved between strains. Several genes that modulate the
      pathogenicity of C. pseudotuberculosis were described including peptidases,
      recombination enzymes, micoside synthesis enzymes, bacteriocins with
      antimicrobial activity and several others. Finally, no genotypic differences were
      observed between the strains that caused the three different types of infection
      (external abscess formation, infection with abscess formation in the internal
      organs, and ulcerative lymphangitis). Instead, it was noted that there is a
      higher phenetic correlation between strains isolated at California compared to
      the other strains. Additionally, high variability of resistance islands suggests
      gene acquisition through several events of horizontal gene transfer.
AU  - Barauna RA
AU  - Ramos RT
AU  - Veras AA
AU  - Pinheiro KC
AU  - Benevides LJ
AU  - Viana MV
AU  - Guimaraes LC
AU  - Edman JM
AU  - Spier SJ
AU  - Azevedo V
AU  - Silva A
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2017 12: E0170676.

PMID- 26659675
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Hydrocarbon-Degrading Bacterium Alcanivorax dieselolei KS-293 Isolated from Surface Seawater in the Eastern Mediterranean  Sea.
PG  - e01424-15
AB  - We report here the draft genome sequence of Alcanivorax dieselolei KS-293, a
      hydrocarbonoclastic bacterium isolated from the Mediterranean Sea, by supplying
      diesel oil as the sole carbon source. This strain contains multiple putative
      genes associated with hydrocarbon degradation pathways and that are highly
      similar to those described in A. dieselolei type strain B5.
AU  - Barbato M
AU  - Mapelli F
AU  - Chouaia B
AU  - Crotti E
AU  - Daffonchio D
AU  - Borin S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01424-15.

PMID- 24723724
VI  - 2
DP  - 2014
TI  - Genome Sequence of the Salmonella enterica subsp. enterica Serovar Namur Strain 05-2929, Lacking the Salmonella Atypical Fimbrial Operon.
PG  - e00299-14
AB  - This paper announces the genome sequence and annotation of Salmonella enterica subsp. enterica
      serovar Namur strain 05-2929. S. Namur is a new serovar (39:z4,z23:-) that was isolated from a
      patient with salmonellosis in 2005 in Namur, Belgium, and has been identified as lacking the
      Salmonella atypical fimbrial (saf) operon.
AU  - Barbau-Piednoir E
AU  - Bertrand S
AU  - Roosens NH
AU  - De Keersmaecker SC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00299-14.

PMID- 25858836
VI  - 3
DP  - 2015
TI  - Genome Sequence of EU-Unauthorized Genetically Modified Bacillus subtilis Strain  2014-3557 Overproducing Riboflavin, Isolated from a Vitamin B2 80% Feed Additive.
PG  - e00214-15
AB  - This paper announces the genome sequence and annotation of the genetically modified (GM)
      Bacillus subtilis strain 2014-3557 overproducing riboflavin
      (vitamin B2). This GM-strain is unauthorized in the European Union. Nevertheless,
      it has been isolated from a lot of vitamin B2 (riboflavin) 80% feed grade
      imported to Europe from China.
AU  - Barbau-Piednoir E
AU  - De Keersmaecker SC
AU  - Wuyts V
AU  - Gau C
AU  - Pirovano W
AU  - Costessi A
AU  - Philipp P
AU  - Roosens NH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00214-15.

PMID- 21868806
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Streptomyces cattleya NRRL 8057, a Producer of Antibiotics and Fluorometabolites.
PG  - 5055-5056
AB  - Streptomyces cattleya, a producer of the antibiotics thienamycin and cephamycin C, is one of
      the rare bacteria known to synthesize fluorinated
      metabolites. The genome consists of two linear replicons. The genes
      involved in fluorine metabolism and in the biosynthesis of the antibiotic
      thienamycin were mapped on both replicons.
AU  - Barbe V
AU  - Bouzon M
AU  - Mangenot S
AU  - Badet B
AU  - Poulain J
AU  - Segurens B
AU  - Vallenet D
AU  - Marliere P
AU  - Weissenbach J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5055-5056.

PMID- 15514110
VI  - 32
DP  - 2004
TI  - Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium.
PG  - 5766-5779
AB  - Acinetobacter sp. strain ADP1 is a nutritionally versatile soil bacterium closely related to
      representatives of the well-characterized Pseudomonas
      aeruginosa and Pseudomonas putida. Unlike these bacteria, the
      Acinetobacter ADP1 is highly competent for natural transformation which
      affords extraordinary convenience for genetic manipulation. The circular
      chromosome of the Acinetobacter ADP1, presented here, encodes 3325
      predicted coding sequences, of which 60% have been classified based on
      sequence similarity to other documented proteins. The close evolutionary
      proximity of Acinetobacter and Pseudomonas species, as judged by the
      sequences of their 16S RNA genes and by the highest level of bidirectional
      best hits, contrasts with the extensive divergence in the GC content of
      their DNA (40 versus 62%). The chromosomes also differ significantly in
      size, with the Acinetobacter ADP1 chromosome <60% of the length of the
      Pseudomonas counterparts. Genome analysis of the Acinetobacter ADP1
      revealed genes for metabolic pathways involved in utilization of a large
      variety of compounds. Almost all of these genes, with orthologs that are
      scattered in other species, are located in five major 'islands of
      catabolic diversity', now an apparent 'archipelago of catabolic
      diversity', within one-quarter of the overall genome. Acinetobacter ADP1
      displays many features of other aerobic soil bacteria with metabolism
      oriented toward the degradation of organic compounds found in their
      natural habitat. A distinguishing feature of this genome is the absence of
      a gene corresponding to pyruvate kinase, the enzyme that generally
      catalyzes the terminal step in conversion of carbohydrates to pyruvate for
      respiration by the citric acid cycle. This finding supports the view that
      the cycle itself is centrally geared to the catabolic capabilities of this
      exceptionally versatile organism.
AU  - Barbe V
AU  - Vallenet D
AU  - Fonknechten N
AU  - Kreimeyer A
AU  - Oztas S
AU  - Labarre L
AU  - Cruveiller S
AU  - Robert C
AU  - Duprat S
AU  - Wincker P
AU  - Ornston LN
AU  - Weissenbach J
AU  - Marliere P
AU  - Cohen GN
AU  - Medigue C
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2004 32: 5766-5779.

PMID- 21571998
VI  - 193
DP  - 2011
TI  - Complete genome sequence of Methanosaeta concilii, a specialist in aceticlastic methanogenesis.
PG  - 3668-3669
AB  - Complete genome sequence of Methanosaeta concilii, a specialist in Aceticlastic
      Methanogenesis.
      episome, has been determined and exhibits considerable differences in gene
      content from that of Methanosaeta thermophila.
AU  - Barber RD
AU  - Zhang L
AU  - Harnack M
AU  - Olson MV
AU  - Kaul R
AU  - Ingram-Smith C
AU  - Smith KS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3668-3669.

PMID- Not included in PubMed...
VI  - 55
DP  - 1988
TI  - DNA-methyltransferase activities in Streptomyces antibioticus.
PG  - 59-64
AB  - Several DNA methyltransferases have been detected in Streptomyces antibioticus ETHZ 7451.  One
      of these enzymes was purified and partially characterized from crude extracts of Streptomyces
      antibioticus ETHZ 7451.  This enzyme only methylates the adenine residues of DNA.  However,
      lambda and pBR322 DNAs were not protected in vitro with the methylase, indicating that the
      enzyme does not seem to form part of a restriction-modification system.  Remarkably, the
      efficiency of the enzyme is significantly higher on the DNA isolated from aerial mycelium than
      from substrate mycelium in S. antibioticus.
AU  - Barbes C
AU  - Hardisson C
AU  - Novella IS
AU  - Yebra MJ
AU  - Sanchez J
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1988 55: 59-64.

PMID- 2210336
VI  - 69
DP  - 1990
TI  - Effects of sinefungin and S-adenosylhomocysteine on DNA and protein methyltransferases from Streptomyces and other bacteria.
PG  - 239-244
AB  - Sinefungin is a naturally occurring nucleoside isolated from cultures of
      Streptomyces griseolus and S. incarnatus.  It is structurally related to
      S-adenosyl-methionine (SAM) and S-adenosyl-L-homocysteine (SAH).  Its effect
      and level of action on prokaryotes has not been studied with the same detail as
      with eukaryotic cells.  In this report we describe the effect of sinefungin and
      SAH on several Streptomyces methyltransferases (DNA and protein MTases) and on
      other bacterial DNA-MTases.  Protein MTases are resistant to sinefungin,
      whereas DNA-MTases are inhibited.  Adenine MTases however, seem more sensitive
      to this analogue than cytosine MTases.
AU  - Barbes C
AU  - Sanchez J
AU  - Yebra MJ
AU  - Robert-Gero M
AU  - Hardisson C
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1990 69: 239-244.

PMID- 6094478
VI  - 160
DP  - 1984
TI  - DNA adenine methylation of GATC sequences appeared recently in the Escherichia coli lineage.
PG  - 586-590
AB  - We have examined the presence of methylated adenine at GATC sequences (Dam phenotype) in the
      DNA of 23 eubacteria and 13 archaebacteria by using isoschizomer restriction enzymes. We have
      found a completely Dam+ phenotype in bacteria of nine genera related to the families
      Enterobacteriaceae, Parvobacteriaceae, and Vibrionaceae, and in the five cyanobacteria tested.
      We have found a partial Dam+ phenotype in the two archaebacteria Halobacterium saccharovorum
      and Methanobacterium sp. strain Ivanov. All of the other archaebacteria (three genera) and
      eubacteria (nine genera) tested were Dam-. Phylogenetic analysis, based on the evolutionary
      tree of Fox et al., indicates that dam methylation in the Escherichia coli lineage appeared
      recently in bacterial evolution and is restricted to a small range of closely related
      bacteria.
AU  - Barbeyron T
AU  - Kean K
AU  - Forterre P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1984 160: 586-590.

PMID- 20550456
VI  - 202
DP  - 2010
TI  - Methicillin-resistant coagulase-negative staphylococci in the community: high homology of SCCmec IVa between Staphylococcus epidermidis and major clones of methicillin-resistant Staphylococcus aureus.
PG  - 270-281
AB  - BACKGROUND: Data on community spread of methicillin-resistant
      coagulase-negative staphylococci (MR-CoNS) are scarce. We assessed their
      potential role as a reservoir of staphylococcal cassette chromosome mec
      (SCCmec) IVa, the leading SCCmec subtype in community-acquired
      methicillin-resistant Staphylococcus aureus (CA-MRSA). METHODS: Nasal
      carriage of MR-CoNS was prospectively investigated in 291 adults at
      hospital admission. MR-CoNS were characterized by SCCmec typing,
      long-range polymerase chain reaction (PCR) for SCCmec IV, and
      multiple-locus variable-number tandem repeat analysis (MLVA) for
      Staphylococcus epidermidis (MRSE) strains. Three SCCmec IVa elements were
      fully sequenced. RESULTS: The carriage rate of MR-CoNS was 19.2% (25.9%
      and 16.5% in patients with and patients without previous exposure to the
      health care system, respectively; P = .09). MR-CoNS strains (n = 83,
      including 58 MRSE strains with highly heterogeneous MLVA patterns) carried
      SCCmec type IVa (n = 9, all MRSE), other SCCmec IV subtypes (n = 9,
      including 7 MRSE), other SCCmec types (n = 15), and nontypeable SCCmec (n
      = 50). Long-range PCR indicated structural homology between SCCmec IV in
      MRSE and that in MRSA. Complete sequences of SCCmec IVa from 3 MRSE
      strains were highly homologous to those available for CA-MRSA, including
      major clones USA300 and USA400. CONCLUSIONS: MR-CoNS are probably
      disseminated in the community, notably in subjects without previous
      exposure to the health care system. MRSE, the most prevalent species, may
      act as a reservoir of SCCmec IVa for CA-MRSA.
AU  - Barbier F
AU  - Ruppe E
AU  - Hernandez D
AU  - Lebeaux D
AU  - Francois P
AU  - Felix B
AU  - Desprez A
AU  - Maiga A
AU  - Woerther PL
AU  - Gaillard K
AU  - Jeanrot C
AU  - Wolff M
AU  - Schrenzel J
AU  - Andremont A
AU  - Ruimy R
PT  - Journal Article
TA  - J. Infect. Dis.
JT  - J. Infect. Dis.
SO  - J. Infect. Dis. 2010 202: 270-281.

PMID- 22582381
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Flavobacterium indicum GPSTA100-9T, Isolated from Warm Spring Water.
PG  - 3024-3025
AB  - We report here the complete annotated genome sequence of Flavobacterium indicum CIP 109464(T)
      (= GPTSA100-9(T)), isolated from warm spring water in Assam, India.  The genome sequence of F.
      indicum revealed a number of interesting features and genes in relation to its environmental
      lifestyle.
AU  - Barbier P
AU  - Houel A
AU  - Loux V
AU  - Poulain J
AU  - Bernardet JF
AU  - Touchon M
AU  - Duchaud E
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3024-3025.

PMID- 27932646
VI  - 4
DP  - 2016
TI  - Genome Sequence of Airborne Acinetobacter sp. Strain 5-2Ac02 in the Hospital Environment, Close to the Species of Acinetobacter towneri.
PG  - e01343-16
AB  - Acinetobacter spp. are found in 53% of air colonization samples from the hospital environment.
      In this work, we sequenced all the genome of airborne Acinetobacter
      sp. strain 5-2Ac02. We found important features at the genomic level in regards
      to the rhizome. By phylogenetic analysis, A. towneri was the species most closely
      related to Acinetobacter sp. 5-2Ac02.
AU  - Barbosa BG
AU  - Fernandez-Garcia L
AU  - Gato E
AU  - Lopez M
AU  - Blasco L
AU  - Leao RS
AU  - Albano RM
AU  - Fernandez B
AU  - Cuenca FF
AU  - Pascual A
AU  - Bou G
AU  - Marques EA
AU  - Tomas M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01343-16.

PMID- 29025941
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of a Rare Pigmented Mycobacterium avium subsp. paratuberculosis Type C Strain.
PG  - e01066-17
AB  - Mycobacterium avium subsp. paratuberculosis is the causative agent of paratuberculosis. We
      report here the draft genome sequence of a rare pigmented M.
      avium subsp. paratuberculosis type C strain, comprising 58 contigs and having a
      genome size of 4,851,414 bp. The genome will assist in the execution of
      pigmentation and virulence studies on this mycobacterium.
AU  - Barbosa P
AU  - Leao C
AU  - Usie A
AU  - Amaro A
AU  - Botelho A
AU  - Pinto C
AU  - Inacio J
AU  - Stevenson K
AU  - Ramos AM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01066-17.

PMID- 27284141
VI  - 4
DP  - 2016
TI  - Chromosome and Plasmids of the Tick-Borne Relapsing Fever Agent Borrelia hermsii.
PG  - e00528-16
AB  - The zoonotic pathogen Borrelia hermsii bears its multiple paralogous genes for variable
      antigens on several linear plasmids. Application of combined long-read
      and short-read next-generation sequencing provided complete sequences for
      antigen-encoding plasmids as well as other linear and circular plasmids and the
      linear chromosome of the genome.
AU  - Barbour AG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00528-16.

PMID- 24526628
VI  - 2
DP  - 2014
TI  - Genome Sequence of Borrelia parkeri, an Agent of Enzootic Relapsing Fever in Western North America.
PG  - e00018-14
AB  - Borrelia parkeri is a relapsing fever agent that rarely causes human infection, unlike other
      North American species. B. parkeri strain HR1 was isolated from
      Ornithodoros parkeri ticks. The sequences of its linear chromosome and large
      plasmid were determined by next-generation sequencing. These confirmed its closer
      relatedness to Borrelia turicatae than to Borrelia hermsii.
AU  - Barbour AG
AU  - Campeau MS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00018-14.

PMID- 
VI  - 0
DP  - 1995
TI  - Barriers to recombination: restriction.
PG  - 31-58
AB  - The biological barrier provided by restriction is far from complete, and it can be quantified
      by determining the titre of unmodified phages on the restricting strain relative to the titre
      on a non-restricting strain.  For phage genomes with small numbers of targets, the barrier
      increases with target number, as witnessed by a decrease in the efficiency of plating (eop).
      Foreign DNA can be recognized and attacked by restriction endonucleases irrespective of its
      mode of entry into the cell and nature has many tricks for combating restriction.
      Nevertheless, a recipient strain with a restriction system is endowed with a potential barrier
      to the intrusion of large DNA molecules should these molecules include the relevant, but
      unmodified, target sequences.  Whether or not the cutting of larger DNA molecules into smaller
      ones is necessarily a barrier to genetic recombination is of critical concern, since DNA
      breaks can be substrates for recombination.  The restriction of foreign DNA is dependent on
      the donor bacterium lacking a modification system that protects its DNA against attack by a
      restriction system present within a recipient cell.  Any evaluation of the importance of
      restriction to the transfer of genetic information requires an awareness of the diversity of
      restriction specificities within a bacterial species.  This review considers what is known
      about the diversity of restriction systems within the Enterobacteriaceae, but most
      particularly within the best studied species, Escherichia coli.  In the absence of any truly
      systematic analyses, the focus will be primarily on screens for chromosomally encoded
      restriction and modification (R-M) systems.
AU  - Barcus VA
AU  - Murray NE
PT  - Journal Article
TA  - Population Genetics of Bacteria
JT  - Population Genetics of Bacteria
SO  - Population Genetics of Bacteria 1995 0: 31-58.

PMID- 7498762
VI  - 140
DP  - 1995
TI  - The diversity of alleles at the hsd locus in natural populations of Escherichia coli.
PG  - 1187-1197
AB  - In enteric bacteria three discrete families of type I restriction and modification systems
      (IA, IB and ID) are encoded by alleles of the serB-linked hsd locus.  Probes specific for each
      of the three families were used to monitor the distribution of related systems in 37 of the
      72 wild-type Escherichia coli strains comprising the ECOR collection.  All 25 members of group
      A in this collection were screened; 12 were probe-positive, nine have hsd genes in the IA
      family, two in the IB and one in the ID.  Twelve strains, representing all groups other than
      A, were screened; five were probe-positive, one has hsd genes in the IA family, one in the IB
      and three in the ID.  The type ID genes are the first representatives of this family in E.
      coli, the probe-negative strains could have alternative families of hsd genes.  The type IA
      and IB systems added at least five new specificities to the five already identified in natural
      isolates of E. coli.  The distribution of alleles is inconsistant with the dendrogram of the
      bacterial strains derived from other criteria.  This discrepancy and the dissimilar coding
      sequences of allelic hsd genes both imply lateral transfer of hsd genes.
AU  - Barcus VA
AU  - Titheradge AJB
AU  - Murray NE
PT  - Journal Article
TA  - Genetics
JT  - Genetics
SO  - Genetics 1995 140: 1187-1197.

PMID- 20796277
VI  - 8
DP  - 2010
TI  - A mixed community of actinomycetes produce multiple antibiotics for the fungus farming ant Acromyrmex octospinosus.
PG  - 109
AB  - BACKGROUND: Attine ants live in an intensely studied tripartite mutualism
      with the fungus Leucoagaricus gongylophorus, which provides food to the
      ants, and with antibiotic-producing actinomycete bacteria. One hypothesis
      suggests that bacteria from the genus Pseudonocardia are the sole,
      co-evolved mutualists of attine ants and are transmitted vertically by the
      queens. A recent study identified a Pseudonocardia-produced antifungal,
      named dentigerumycin, associated with the lower attine Apterostigma
      dentigerum consistent with the idea that co-evolved Pseudonocardia make
      novel antibiotics. An alternative possibility is that attine ants sample
      actinomycete bacteria from the soil, selecting and maintaining those
      species that make useful antibiotics. Consistent with this idea, a
      Streptomyces species associated with the higher attine Acromyrmex
      octospinosus was recently shown to produce the well-known antifungal
      candicidin. Candicidin production is widespread in environmental isolates
      of Streptomyces, so this could either be an environmental contaminant or
      evidence of recruitment of useful actinomycetes from the environment. It
      should be noted that the two possibilities for actinomycete acquisition
      are not necessarily mutually exclusive. RESULTS: In order to test these
      possibilities we isolated bacteria from a geographically distinct
      population of A. octospinosus and identified a candicidin-producing
      Streptomyces species, which suggests that they are common mutualists of
      attine ants, most probably recruited from the environment. We also
      identified a Pseudonocardia species in the same ant colony that produces
      an unusual polyene antifungal, providing evidence for co-evolution of
      Pseudonocardia with A. octospinosus. CONCLUSIONS: Our results show that a
      combination of co-evolution and environmental sampling results in the
      diversity of actinomycete symbionts and antibiotics associated with attine
      ants.
AU  - Barke J
AU  - Seipke RF
AU  - Gruschow S
AU  - Heavens D
AU  - Drou N
AU  - Bibb MJ
AU  - Goss RJ
AU  - Yu DW
AU  - Hutchings MI
PT  - Journal Article
TA  - BMC Biol.
JT  - BMC Biol.
SO  - BMC Biol. 2010 8: 109.

PMID- 6087291
VI  - 12
DP  - 1984
TI  - A second type II restriction endonuclease from Thermus aquaticus with an unusual sequence specificity.
PG  - 5567-5581
AB  - A type II restriction endonuclease activity free of TaqI was prepared from Thermus aquaticus
      YT.  The fraction contains two endonucleolytic components with apparently different
      specificities, however the major activity is sufficiently dominant to allow partial digestion
      analysis of the position of recognition sites.  A precise determination of the location of
      cleavage sites in pBR322 DNA and a computer-aided search for regions of homology in the
      vicinity of the cut sites indicate that this enzyme recognizes the nonpalindromic sequences
      GACCGA or CACCCA.  Other related sequences are not cleaved, in particular, GACCCA and CACCGA,
      indicating that the enzyme requires the identity of nucleotides in the first and fifth
      positions, a type of specificity that has not been previously reported.  The position of
      cleavage is located outside of the site and is represented as:
      5'-GACCGANNNNNNNNN^NN-3'
      3'-CTGGCTNNNNNNNNN^NN-5'.
AU  - Barker D
AU  - Hoff M
AU  - Oliphant A
AU  - White R
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1984 12: 5567-5581.

PMID- 21317334
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Mycoplasma haemofelis, a Hemotropic Mycoplasma.
PG  - 2060-2061
AB  - Here, we present the genome sequence of Mycoplasma haemofelis strain Langford 1, representing
      the first hemotropic mycoplasma (hemoplasma)
      species to be completely sequenced and annotated. Originally isolated from
      a cat with hemolytic anemia, this strain induces severe hemolytic anemia
      when inoculated into specific-pathogen-free-derived cats. The genome
      sequence has provided insights into the biology of this uncultivatable
      hemoplasma and has identified potential molecular mechanisms underlying
      its pathogenicity.
AU  - Barker EN
AU  - Helps CR
AU  - Peters IR
AU  - Darby AC
AU  - Radford AD
AU  - Tasker S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 2060-2061.

PMID- 8469984
VI  - 260
DP  - 1993
TI  - Methylation and imprinting: from host defense to gene regulation?
PG  - 309-310
AB  - 
AU  - Barlow DP
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1993 260: 309-310.

PMID- 17065187
VI  - 58
DP  - 2006
TI  - Diverse class 2 integrons in bacteria from beef cattle sources.
PG  - 1133-1138
AB  - OBJECTIVES: The purpose of this study was to determine the diversity of class 2 integrons in
      bacteria isolated from beef cattle sources. METHODS:
      The variable regions of a subset of 11 class 2 integron-containing
      bacteria were analysed by PCR and DNA sequencing for the presence of novel
      rearrangements. RESULTS: A total of six different class 2 integron arrays
      were identified and four of these were fully characterized. Three of the
      four arrays characterized have been previously described; however the
      remaining array is unlike previously described class 2 integrons. The
      novel class 2 integron was found in Providencia stuartii and contains an
      apparently functional class 2 integrase. Examination of the variable
      region of the P. stuartii integron identified nine open reading frames,
      mostly of unknown function, and represents the first report of a class 2
      integron without inserted antibiotic resistance gene cassettes.
      CONCLUSIONS: This study has identified a novel class 2 integron found in
      P. stuartii that contains an apparently functional naturally occurring
      class 2 integrase. Further investigation of this novel class 2 integron is
      required to determine the impact of a functional class 2 integrase upon
      the evolution of class 2 integrons.
AU  - Barlow RS
AU  - Gobius KS
PT  - Journal Article
TA  - J. Antimicrob. Chemother.
JT  - J. Antimicrob. Chemother.
SO  - J. Antimicrob. Chemother. 2006 58: 1133-1138.

PMID- 29954907
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Bifidobacterium Strains Isolated from Dietary Supplements and Cultured Food Products.
PG  - e00610-18
AB  - Here, we present the genome sequences of 23 Bifidobacterium isolates from several commercially
      available dietary supplements and cultured food products. Strains of
      this genus are natural inhabitants of the mammalian mouth, gastrointestinal
      tract, and vagina. Some species are considered beneficial to human health.
AU  - Barnaba TJ
AU  - Gangiredla J
AU  - Mammel MK
AU  - Lacher DW
AU  - Elkins CA
AU  - Lampel KA
AU  - Whitehouse CA
AU  - Tartera C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00610-18.

PMID- 28348835
VI  - 2
DP  - 2016
TI  - Whole genome analysis of Yersinia ruckeri isolated over 27 years in Australia and New Zealand reveals geographical endemism over multiple lineages and recent evolution under host selection.
PG  - E000095
AB  - Yersinia ruckeri is a salmonid pathogen with widespread distribution in
      cool-temperate waters including Australia and New Zealand, two isolated
      environments with recently developed salmonid farming industries. Phylogenetic
      comparison of 58 isolates from Australia, New Zealand, USA, Chile, Finland and
      China based on non-recombinant core genome SNPs revealed multiple deep-branching
      lineages, with a most recent common ancestor estimated at 18 500 years BP (12
      355-24 757 95% HPD) and evidence of Australasian endemism. Evolution within the
      Tasmanian Atlantic salmon serotype O1b lineage has been slow, with 63 SNPs
      describing the variance over 27 years. Isolates from the prevailing lineage are
      poorly/non-motile compared to a lineage pre-vaccination, introduced in 1997,
      which is highly motile but has not been isolated since from epizootics. A
      non-motile phenotype has arisen independently in Tasmania compared to Europe and
      USA through a frameshift in fliI, encoding the ATPase of the flagella cluster. We
      report for the first time lipopolysaccharide O-antigen serotype O2 isolates in
      Tasmania. This phenotype results from deletion of the O-antigen cluster and
      consequent loss of high-molecular-weight O-antigen. This phenomenon has occurred
      independently on three occasions on three continents (Australasia, North America
      and Asia) as O2 isolates from the USA, China and Tasmania share the O-antigen
      deletion but occupy distant lineages. Despite the European and North American
      origins of the Australasian salmonid stocks, the lineages of Y. ruckeri in
      Australia and New Zealand are distinct from those of the northern hemisphere,
      suggesting they are pre-existing ancient strains that have emerged and evolved
      with the introduction of susceptible hosts following European colonization.
AU  - Barnes AC
AU  - Delamare-Deboutteville J
AU  - Gudkovs N
AU  - Brosnahan C
AU  - Morrison R
AU  - Carson J
PT  - Journal Article
TA  - Microbial Genomics
JT  - Microbial Genomics
SO  - Microbial Genomics 2016 2: E000095.

PMID- 2983340
VI  - 82
DP  - 1985
TI  - Regulated expression of endonuclease EcoRI in Saccharomyces cerevisiae: Nuclear entry and biological consequences.
PG  - 1354-1358
AB  - In an investigation to determine how proteins are localized within the nucleus
      of a cell, we demonstrate that the restriction endonuclease EcoRI is able to
      enter and function within the nucleus of Saccharomyces cerevisiae when this
      prokaryotic protein is synthesized in vivo.  The EcoRI endonuclease was
      produced in yeast under the transcriptional control of a regulated yeast
      promoter by ligating a DNA fragment containing only coding sequences for the
      endonuclease to the promoter element of the yeast GAL1 gene (the structural
      gene for galactokinase, EC 2.7.1.6).  Yeast cells harboring a plasmid
      containing this promoter-gene fusion are able to grow under conditions that
      repress transcription from the Gal1 promoter.  However, under inducing
      conditions, these yeast cells are unable to grow.  Moreover, rad52 mutants,
      which are deficient in the repair of double-strand breaks, are more sensitive
      to the presence of the promoter-gene fusion plasmid than are wild-type cells.
      We demonstrate that the EcoRI endonuclease activity is present in lysates
      prepared from yeast transformants grown under conditions that induce
      transcription of GAL1, but this activity is not detectable in cells grown under
      conditions that repress transcription from the promoter.  Furthermore, analysis
      of yeast chromosomal DNA shows that the endonuclease enters the yeast nucleus
      and cleaves DNA specifically at EcoRI recognition sites.
AU  - Barnes G
AU  - Rine J
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1985 82: 1354-1358.

PMID- 25279840
VI  - 9
DP  - 2014
TI  - Selective Microbial Genomic DNA Isolation Using Restriction Endonucleases.
PG  - e109061
AB  - To improve the metagenomic analysis of complex microbiomes, we have repurposed restriction
      endonucleases as methyl specific DNA binding proteins. As an example, we use DpnI immobilized
      on magnetic beads. The ten minute extraction technique allows specific binding of genomes
      containing the DpnI G(m6) ATC motif common in the genomic DNA of many bacteria including
      gamma-proteobacteria. Using synthetic genome mixtures, we demonstrate 80% recovery of
      Escherichia coli genomic DNA even when only femtogram quantities are spiked into 10 mu g of
      human DNA background. Binding is very specific with less than 0.5% of human DNA bound. Next
      Generation Sequencing of input and enriched synthetic mixtures results in over 100-fold
      enrichment of target genomes relative to human and plant DNA. We also show comparable
      enrichment when sequencing complex microbiomes such as those from creek water and human
      saliva. The technique can be broadened to other restriction enzymes allowing for the selective
      enrichment of trace and unculturable organisms from complex microbiomes and the stratification
      of organisms according to restriction enzyme enrichment.
AU  - Barnes HE
AU  - Liu G
AU  - Weston CQ
AU  - King P
AU  - Pham LK
AU  - Waltz S
AU  - Helzer KT
AU  - Day L
AU  - Sphar D
AU  - Yamamoto RT
AU  - Forsyth RA
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2014 9: e109061.

PMID- 29051505
VI  - 7
DP  - 2017
TI  - Large-scale genomic analyses reveal the population structure and evolutionary trends of Streptococcus agalactiae strains in Brazilian fish farms.
PG  - 13538
AB  - Streptococcus agalactiae is a major pathogen and a hindrance on tilapia farming
      worldwide. The aims of this work were to analyze the genomic evolution of
      Brazilian strains of S. agalactiae and to establish spatial and temporal
      relations between strains isolated from different outbreaks of streptococcosis. A
      total of 39 strains were obtained from outbreaks and their whole genomes were
      sequenced and annotated for comparative analysis of multilocus sequence typing,
      genomic similarity and whole genome multilocus sequence typing (wgMLST). The
      Brazilian strains presented two sequence types, including a newly described ST,
      and a non-typeable lineage. The use of wgMLST could differentiate each strain in
      a single clone and was used to establish temporal and geographical correlations
      among strains. Bayesian phylogenomic analysis suggests that the studied Brazilian
      population was co-introduced in the country with their host, approximately 60
      years ago. Brazilian strains of S. agalactiae were shown to be heterogeneous in
      their genome sequences and were distributed in different regions of the country
      according to their genotype, which allowed the use of wgMLST analysis to track
      each outbreak event individually.
AU  - Barony GM
AU  - Tavares GC
AU  - Pereira FL
AU  - Carvalho AF
AU  - Dorella FA
AU  - Leal CAG
AU  - Figueiredo HCP
PT  - Journal Article
TA  - Sci. Rep.
JT  - Sci. Rep.
SO  - Sci. Rep. 2017 7: 13538.

PMID- 3202841
VI  - 255
DP  - 1988
TI  - A DNA-modification methylase from Bacillus stearothermophilus V.
PG  - 699-703
AB  - A type II modification methylase (M.BstVI) was partially purified from the
      thermophilic bacterium Bacillus stearothermophilus V.  The methylase catalyses
      the transfer of methyl groups from S-adenosyl-L-methionine to unmodified
      double-stranded DNA.  The product of methylation was identified by paper
      chromatography as N6-methyladenine.  Since M.BstVI protects DNA against
      cleavage by BstVI and XhoI restriction endonucleases, it follows that it
      methylates the adenine residue in the sequence 5'-C-T-C-G-A-G-3'.
AU  - Barra R
AU  - Chiong M
AU  - Gonzalez E
AU  - Vasquez C
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 1988 255: 699-703.

PMID- 23929481
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Strain SA_ST125_MupR of Methicillin-Resistant Staphylococcus aureus ST125, a Major Clone in Spain.
PG  - e00588-13
AB  - Here, we report the draft genome sequence of a methicillin-resistant Staphylococcus aureus
      (MRSA) strain with high-level mupirocin resistance
      (SA_ST125_MupR), isolated from a patient with recurrent bacteremia. This strain
      belonged to sequence type ST125, which was responsible for more than 50% of the
      health care-associated infections caused by MRSA in Spain.
AU  - Barrado L
AU  - Viedma E
AU  - Vindel A
AU  - Otero JR
AU  - Chaves F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00588-13.

PMID- 27151788
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the First Pathogenic Leptospira Isolates from Ecuador.
PG  - e00271-16
AB  - Pathogenic Leptospira spp. cause leptospirosis upon contact with mucosa through wounds or
      ingestion, leading to headaches, fever, jaundice, kidney or liver
      failure, or death in about 1.3 million people each year. Here, we present the
      draft genomes of one L. santarosai isolate and two L. interrogans isolates from
      Ecuador.
AU  - Barragan V
AU  - Sahl JW
AU  - Wiggins K
AU  - Chiriboga J
AU  - Salinas A
AU  - Cantos NE
AU  - Loor MN
AU  - Intriago BI
AU  - Morales M
AU  - Trueba G
AU  - Pearson T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00271-16.

PMID- 19376856
VI  - 191
DP  - 2009
TI  - Comparison of the complete genome sequences of Bifidobacterium animalis subsp. lactis DSM 10140 and Bl-04.
PG  - 4144-4151
AB  - Bifidobacteria are important members of the human gut flora, especially in infants.
      Comparative genomic analysis of two Bifidobacterium animalis
      subsp. lactis strains revealed evolution by internal deletion of
      consecutive spacer-repeat units within a novel clustered regularly
      interspaced short palindromic repeat locus, which represented the largest
      differential content between the two genomes. Additionally, 47 single
      nucleotide polymorphisms were identified, consisting primarily of
      nonsynonymous mutations, indicating positive selection and/or recent
      divergence. A particular nonsynonymous mutation in a putative glucose
      transporter was linked to a negative phenotypic effect on the ability of
      the variant to catabolize glucose, consistent with a modification in the
      predicted protein transmembrane topology. Comparative genome sequence
      analysis of three Bifidobacterium species provided a core genome set of
      1,117 orthologs complemented by a pan-genome of 2,445 genes. The genome
      sequences of the intestinal bacterium B. animalis subsp. lactis provide
      insights into rapid genome evolution and the genetic basis for adaptation
      to the human gut environment, notably with regard to catabolism of dietary
      carbohydrates, resistance to bile and acid, and interaction with the
      intestinal epithelium. The high degree of genome conservation observed
      between the two strains in terms of size, organization, and sequence is
      indicative of a genomically monomorphic subspecies and explains the
      inability to differentiate the strains by standard techniques such as
      pulsed-field gel electrophoresis.
AU  - Barrangou R
AU  - Briczinski EP
AU  - Traeger LL
AU  - Loquasto JR
AU  - Richards M
AU  - Horvath P
AU  - Coute-Monvoisin AC
AU  - Leyer G
AU  - Rendulic S
AU  - Steele JL
AU  - Broadbent JR
AU  - Oberg T
AU  - Dudley EG
AU  - Schuster S
AU  - Romero DA
AU  - Roberts RF
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2009 191: 4144-4151.

PMID- 25502457
VI  - 34
DP  - 2015
TI  - Bacteriophage exclusion, a new defense system.
PG  - 134-135
AB  - The ability to withstand viral predation is critical for survival of most microbes.
      Accordingly, a plethora of phage resistance
      systems has been identified in bacterial genomes (Labrie et al, 2010), including
      restriction-modification systems (R-M) (Tock
AU  - Barrangou R
AU  - van der Oost J
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 2015 34: 134-135.

PMID- 2667217
VI  - 5
DP  - 1989
TI  - The great GATC:  DNA methylation in E. coli.
PG  - 139-143
AB  - In Escherichia coli the methylation of the adenine in the sequence 5'-GATC-3' is catalysed
      by the dam gene product, a DNA adenine methylase. We review the proposed roles for this
      methylation, and the sequence it modifies, in mismatch repair, DNA-protein interaction, gene
      expression, the initiation of chromosome replication, chromosome segregation, chromosome
      structure and the occurrence of mutational hotspots.
AU  - Barras F
AU  - Marinus MG
PT  - Journal Article
TA  - Trends Genet.
JT  - Trends Genet.
SO  - Trends Genet. 1989 5: 139-143.

PMID- 22275099
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Probiotic Strain Pediococcus acidilactici MA18/5M.
PG  - 901
AB  - Pediococcus acidilactici MA18/5M is a commercially available probiotic that is widely used in
      swine, poultry, aquaculture feeds, and human
      dietary supplements. We prepared a genome sequence for this strain
      consisting of 2 scaffolds totaling 1,992,928 bases including gaps for a
      total of 3,346 bases and a G+C content of 42%.
AU  - Barreau G
AU  - Tompkins TA
AU  - de Carvalho VG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 901.

PMID- 22740677
VI  - 194
DP  - 2012
TI  - Draft Genome of Streptomyces tsukubaensis NRRL 18488, the Producer of the Clinically Important Immunosuppressant Tacrolimus (FK506).
PG  - 3756-3757
AB  - The macrocyclic polyketide tacrolimus (FK506) is a potent immunosuppressant that  prevents
      T-cell proliferation produced solely by Streptomyces species. We report
      here the first draft genome sequence of a true FK506 producer, Streptomyces
      tsukubaensis NRRL 18488, the first tacrolimus-producing strain that was isolated
      and that contains the full tacrolimus biosynthesis gene cluster.
AU  - Barreiro C et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3756-3757.

PMID- 25523783
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Principal Etiological Agent of Farmer's Lung Disease, Saccharopolyspora rectivirgula.
PG  - e01340-14
AB  - Saccharopolyspora rectivirgula is the main cause of farmer's lung disease. The development of
      recombinant antigens to standardize the serodiagnosis of the
      disease requires knowledge of the S. rectivirgula genome. We sequenced the genome
      of an environmental strain, S. rectivirgula DSM 43113. A total of 3,221 proteins
      were found to be encoded in a short 3.9-Mb genome.
AU  - Barrera C
AU  - Valot B
AU  - Rognon B
AU  - Zaugg C
AU  - Monod M
AU  - Millon L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01340-14.

PMID- 25278524
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Campylobacter fetus subsp. venerealis bv. venerealis Strain B6 and bv. intermedius Strain 642-21.
PG  - e00943-14
AB  - Campylobacter fetus subsp. venerealis is an important venereal pathogen. We sequenced the
      genomes of Campylobacter fetus subsp. venerealis bv. venerealis
      strain B6 and bv. intermedius strain 642-21. The genetic variability of these
      Australian strains will facilitate the study of mechanisms of geographical
      adaptation of these pathogens that impact livestock.
AU  - Barrero RA
AU  - Moolhuijzen P
AU  - Indjein L
AU  - Venus B
AU  - Keeble-Gagnere G
AU  - Power J
AU  - Bellgard MI
AU  - Lew-Tabor AE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00943-14.

PMID- 24285656
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences of Multidrug-Resistant Acinetobacter sp. Strains from Colombian Hospitals.
PG  - e00868-13
AB  - The draft genome sequences of the strains Acinetobacter baumannii 107m, Acinetobacter
      nosocomialis 28F, and Acinetobacter pittii 42F, isolated from
      Colombian hospitals, are reported here. These isolates are causative of
      nosocomial infections and are classified as multidrug resistant, as they showed
      resistance to four different antibiotic groups.
AU  - Barreto-Hernandez E
AU  - Falquet L
AU  - Reguero MT
AU  - Mantilla JR
AU  - Valenzuela EM
AU  - Gonzalez E
AU  - Cepeda A
AU  - Escalante A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00868-13.

PMID- 23045482
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Lantibiotic Bacteriocin Producer Streptococcus salivarius  Strain K12.
PG  - 5959-5960
AB  - Streptococcus salivarius is a prevalent commensal species of the oropharyngeal tract. S.
      salivarius strain K12 is an isolate from the saliva of a healthy child,
      used as an oral probiotic. Here, we report its genome sequence, i.e., the full
      sequence of the 190-kb megaplasmid pSsal-K12 and a high-quality draft 2.2-Gb
      chromosomal sequence.
AU  - Barretto C
AU  - Alvarez-Martin P
AU  - Foata F
AU  - Renault P
AU  - Berger B
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5959-5960.

PMID- 27856580
VI  - 4
DP  - 2016
TI  - Genome Sequence of Lactobacillus fermentum Strain NCC2970 (CNCM I-5068).
PG  - e01254-16
AB  - Lactobacillus fermentum NCC2970 (CNCM I-5068) is a lactic acid bacterium originating from the
      Nestle Culture Collection. Here, we disclose its full 1.9-Gb
      genome sequence comprising one chromosome with no plasmid.
AU  - Barretto C
AU  - Ngom-Bru C
AU  - Genevaz A
AU  - Fournier C
AU  - Moine D
AU  - Kassam M
AU  - Iltis A
AU  - Sagory-Zalkind P
AU  - Ciron PE
AU  - Faucherand G
AU  - Descombes P
AU  - Duboux S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01254-16.

PMID- 2467142
VI  - 13D
DP  - 1989
TI  - Site-directed mutagenesis of the EcoRV methylase for the study of the functional role of the conserved sequences in N6-adenine methylases.
PG  - 211
AB  - EcoRV methylase has been used as a model system to investigate the function of the conserved
      sequences in N6-adenine methylases. The EcoRV methylase gene was subcloned and the methylase
      protein was purified by multiple chromatographic steps. The highly conserved DPPY potein
      sequence in the EcoRV methylase was changed using site-directed oligonucleotide mutagenesis in
      both conservative and radical ways. We produced protein sequence changes at the D, the first P
      and the Y so that the predicted secondary and unknown tertiary structures of this region were
      not only gently perturbed but also disrupted. The EcoRV methylase with the first change (DPPY
      to EPPY) was subcloned back into a modified pUC19 vector. This change produced a methylase
      which unlike the wild-type enzyme does not fully methylate in vivo the genomic or vector DNA.
      We are examining the catalytic properties of the wild-type EcoRV methylase and some
      mutagenized methylase proteins. Also efforts will be made to determine whether SAM or DNA
      binding, if any, remains in mutant methylases.
AU  - Barshevsky T
AU  - Benner JS
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1989 13D: 211.

PMID- 3074018
VI  - 74
DP  - 1988
TI  - Cloning of the HhaI and HinPI restriction-modification systems.
PG  - 5-7
AB  - The genes for the HhaI (Roberts et al., 1976) and HinPI (Roberts, 1987)
      restriction-modification (R-M) systems have been cloned in pBR322.  The HhaI
      system was isolated on a 9-kb PstI fragment, and the HinPI system was isolated
      on two PstI fragments of 1.5 and 4.6 kb in length.  The clones were isolated by
      selecting for recombinant molecules that had protectively modified themselves.
      The HhaI and HinPI R-M systems recognize the same sequence, GCGC, but
      hybridization between the DNA fragments encoding them does not take place.
      Note:  this should be HinP1I.
AU  - Barsomian JM
AU  - Card CO
AU  - Wilson GG
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 5-7.

PMID- 
VI  - 
DP  - 1999
TI  - Genetic variation in Neisseria meningitidis.
PG  - 1-115
AB  - Neisseria meningitidis or meningococcus is a Gram-negative diplococcus that is a member of the
      family of the Neisseriaceae, belonging to the beta subdivision of the proteobacteria.  The
      genus Neisseria includes closely related species.  These diplococci are primarily commensals
      of the mucous membranes of mammals.  N. meningitidis and N. gonorrhoeae, are well-known
      pathogens of man, although various Neisseria species are opportunistic pathogens (e.g. N.
      flavescens and N. lactamica).  The meningococcus, usually carried in the nasopharynx and
      oroparynx of humans, is distinguished from other Neisseria species on the basis of its sugar
      metabolism.  The Neisseria are usually described as being immobile, though a recent report
      suggests that they may display "twitching motility".
AU  - Bart A
PT  - Journal Article
TA  - Ph.D. Thesis, Univ. Amsterdam, Netherlands
JT  - Ph.D. Thesis, Univ. Amsterdam, Netherlands
SO  - Ph.D. Thesis, Univ. Amsterdam, Netherlands 1999 : 1-115.

PMID- 10913691
VI  - 188
DP  - 2000
TI  - Representational difference analysis of Neisseria meningitidis identifies sequences that are specific for the hyper-virulent lineage III clone.
PG  - 111-114
AB  - Neisseria meningitidis may cause meningitis and septicemia.  Since the early 1980s, an
      increased incidence of meningococcal disease has been caused by the lineage III clone in many
      countries in Europe and in New Zealand.  We hypothesized that lineage III meningococci have
      specific DNA sequences, providing an opportunity to facilitate epidemiological studies by
      detecting lineage III isolates rapidly.  Applying representational difference analysis on one
      lineage III tester strain and two non-lineage III driver strains, we identified three lineage
      III-specific sequences, probably part of a single locus encoding a restriction modification
      system.  A PCR based on one of these sequences identified lineage III meningococcal isolates
      with a sensitivity of 100% and a specificity of 93%, which is superior to the serological
      identification of lineage III isolates.
AU  - Bart A
AU  - Dankert J
AU  - van der Ende A
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2000 188: 111-114.

PMID- 10096093
VI  - 31
DP  - 1999
TI  - Operator sequences for the regulatory proteins of restriction modification systems.
PG  - 1275-1281
AB  - For some type II restriction modification systems, it has been shown that transcription of the
      methylase gene and the restriction endonuclease gene is regulated by the control gene product.
      In these systems, C is located directly upstream of R, and in most systems M is located
      divergently from CR.  The control element is a short (~80 amino acids) protein containing a
      helix-turn-helix DNA-binding motif, distantly related to the well-known phage lambda cl
      regulator.
AU  - Bart A
AU  - Dankert J
AU  - van der Ende A
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1999 31: 1275-1281.

PMID- 
VI  - 101
DP  - 2001
TI  - The NmeSI restriction-modification system identified by representational difference analysis of a hypervirulent Neisseria  meningitidis strain.
PG  - 303
AB  - Neisseria meningitidis is a Gram-negative bacterium that may cause meningitis, sepsis or both.
      In the past two decades, an increase in the
      incidence of meningococcal disease in the Netherlands and various other
      countries has been observed. This increase is mainly due to the
      genotypically related lineage III meningococci. We hypothesize that a
      genetic trait is responsible for the observed clonal and hypervirulent
      phenotype of lineage III strains. Chromosomal DNA differences between
      lineage III strains and non-lineage III strains were identified using
      representational difference analysis. Thus, a 1.8 kb locus that is
      specific for lineage III meningococci was identified. The locus
      contains three open reading frames encoding the NmeSI restriction
      modification system. The methyltransferase gene was cloned and
      expressed in Escherichia coli. The site AGTACT was found to be
      N4-cytosine modified by the recombinant enzyme. Chromosomal DNA of
      lineage III strains was shown to be methylated at AGTACT sequences, in
      contrast to DNA of non-lineage III strains. In conclusion, lineage III
      strains differ from endemic strains by the presence of a specific
      restriction modification system, causing differential methylation of
      chromosomal DNA. The restriction modification system may contribute to
      the clonal and hypervirulent character of lineage III strains by
      influencing horizontal gene transfer and transcription.
AU  - Bart A
AU  - Pannekoek Y
AU  - Dankert J
AU  - van der Ende A
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 2001 101: 303.

PMID- 11179359
VI  - 69
DP  - 2001
TI  - NmeSI restriction-modification system identified by representational difference analysis of a hypervirulent Neisseria meningitidis strain.
PG  - 1816-1820
AB  - Neisseria meningitidis is a gram-negative bacterium that may cause meningitis, sepsis, or
      both. The increase in the incidence of
      meningococcal disease in various countries in the past 2 decades is
      mainly due the genotypically related lineage III meningococci. The
      chromosomal DNA differences between lineage III strains and non-lineage
      III strains were identified using representational difference analysis.
      Thus, a 1.8-kb locus that is specific for lineage III meningococci was
      identified. The locus contains three open reading frames encoding the
      NmeSI restriction-modification system. The methyltransferase gene was
      cloned and expressed in Escherichia coli. Site AGTACT was found to be
      modified by the enzyme. In conclusion, lineage III strains differ from
      endemic strains by the presence of a specific restriction-modification
      system. This restriction-modification system may contribute to the
      clonal and hypervirulent character of lineage III strains by
      influencing horizontal gene transfer and transcription.
AU  - Bart A
AU  - Pannekoek Y
AU  - Dankert J
AU  - van der Ende A
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2001 69: 1816-1820.

PMID- 16091626
VI  - 33
DP  - 2005
TI  - Direct detection of methylation in genomic DNA.
PG  - e124
AB  - The identification of methylated sites on bacterial genomic DNA would be a useful tool to
      study the major roles of DNA methylation in prokaryotes: distinction of
      self and nonself DNA, direction of post-replicative mismatch repair, control of
      DNA replication and cell cycle, and regulation of gene expression. Three types of
      methylated nucleobases are known: N6-methyladenine, 5-methylcytosine and
      N4-methylcytosine. The aim of this study was to develop a method to detect all
      three types of DNA methylation in complete genomic DNA. It was previously shown
      that N6-methyladenine and 5-methylcytosine in plasmid and viral DNA can be
      detected by intersequence trace comparison of methylated and unmethylated DNA. We
      extended this method to include N4-methylcytosine detection in both in vitro and
      in vivo methylated DNA. Furthermore, application of intersequence trace
      comparison was extended to bacterial genomic DNA. Finally, we present evidence
      that intrasequence comparison suffices to detect methylated sites in genomic DNA.
      In conclusion, we present a method to detect all three natural types of DNA
      methylation in bacterial genomic DNA. This provides the possibility to define the
      complete methylome of any prokaryote.
AU  - Bart A
AU  - van Passel MW
AU  - van Amsterdam K
AU  - van der Ende A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2005 33: e124.

PMID- 26607899
VI  - 3
DP  - 2015
TI  - Complete Genome Sequences of 11 Bordetella pertussis Strains Representing the Pandemic ptxP3 Lineage.
PG  - e01394-15
AB  - Pathogen adaptation has contributed to the resurgence of pertussis. To facilitate our
      understanding of this adaptation we report here 11 completely closed and
      annotated Bordetella pertussis genomes representing the pandemic ptxP3 lineage.
      Our analyses included six strains which do not produce the vaccine components
      pertactin and/or filamentous hemagglutinin.
AU  - Bart MJ
AU  - van der Heide HG
AU  - Zeddeman A
AU  - Heuvelman K
AU  - van Gent M
AU  - Mooi FR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01394-15.

PMID- 21070624
VI  - 11
DP  - 2010
TI  - Comparative genomics of prevaccination and modern Bordetella pertussis strains.
PG  - 627
AB  - BACKGROUND: Despite vaccination since the 1950s, pertussis has persisted and
      resurged. It remains a major cause of infant death worldwide and is the most
      prevalent vaccine-preventable disease in developed countries. The resurgence of
      pertussis has been associated with the expansion of Bordetella pertussis strains
      with a novel allele for the pertussis toxin (Ptx) promoter, ptxP3, which have
      replaced resident ptxP1 strains. Compared to ptxP1 strains, ptxP3 produce more
      Ptx resulting in increased virulence and immune suppression. To elucidate how B.
      pertussis has adapted to vaccination, we compared genome sequences of two ptxP3
      strains with four strains isolated before and after the introduction vaccination.
      RESULTS: The distribution of SNPs in regions involved in transcription and
      translation suggested that changes in gene regulation play an important role in
      adaptation. No evidence was found for acquisition of novel genes. Modern strains
      differed significantly from prevaccination strains, both phylogenetically and
      with respect to particular alleles. The ptxP3 strains were found to have diverged
      recently from modern ptxP1 strains. Differences between ptxP3 and modern ptxP1
      strains included SNPs in a number of pathogenicity-associated genes. Further,
      both gene inactivation and reactivation was observed in ptxP3 strains relative to
      modern ptxP1 strains. CONCLUSIONS: Our work suggests that B. pertussis adapted by
      successive accumulation of SNPs and by gene (in)activation. In particular changes
      in gene regulation may have played a role in adaptation.
AU  - Bart MJ
AU  - van Gent M
AU  - van der Heide HG
AU  - Boekhorst J
AU  - Hermans P
AU  - Parkhill J
AU  - Mooi FR
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2010 11: 627.

PMID- 25540342
VI  - 2
DP  - 2014
TI  - Complete Genome Sequences of Bordetella pertussis Isolates B1917 and B1920, Representing Two Predominant Global Lineages.
PG  - e01301-14
AB  - Bordetella pertussis is the causative agent of pertussis, a disease which has resurged despite
      vaccination. We report the complete, annotated genomes of
      isolates B1917 and B1920, representing two lineages predominating globally in the
      last 50 years. The B1917 lineage has been associated with the resurgence of
      pertussis in the 1990s.
AU  - Bart MJ
AU  - Zeddeman A
AU  - van der Heide HG
AU  - Heuvelman K
AU  - van Gent M
AU  - Mooi FR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01301-14.

PMID- 11353082
VI  - 29
DP  - 2001
TI  - Two Arabidopsis methylation-deficiency mutations confer only partial effects on a methylated endogenous gene family.
PG  - 2127-2134
AB  - In Arabidopsis a SWI2/SNF2 chromatin remodeling factor-related protein DDM1 and a cytosine
      methyltransferase MET1 are required for maintenance of genomic cytosine methylation. Mutations
      in either gene cause global demethylation. In this work we have assessed the effects of these
      mutations on the PAI tryptophan biosynthetic gene family, which consists of four densely
      methylated genes arranged as a tail-to-tail inverted repeat plus two unlinked singlet genes.
      The methylation mutations caused only partial demethylation of the PAI loci: ddm1 had a strong
      effect on the singlet genes but a weaker effect on the inverted repeat, whereas met1 had a
      stronger effect on the inverted repeat than on the singlet genes. The double ddm1 met1 mutant
      also displayed partial demethylation of the PAI genes, with a pattern similar to the ddm1
      single mutant. To determine the relationship between partial methylation and expression for
      the singlet PAI2 gene we constructed a novel reporter strain of Arabidopsis in which PAI2
      silencing could be monitored by a blue fluorescent plant phenotype diagnostic of tryptophan
      pathway defects. This reporter strain revealed that intermediate levels of methylation
      correlate with intermediate suppression of the fluorescent phenotype.
AU  - Bartee L
AU  - Bender J
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2001 29: 2127-2134.

PMID- 11459824
VI  - 15
DP  - 2001
TI  - Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene.
PG  - 1753-1758
AB  - Plants maintain cytosine methylation at CG and non-CG residues to control gene expression and
      genome stability. In a screen for Arabidopsis mutants that alter methylation and silencing of
      a densely methylated endogenous reporter gene, we recovered 11 loss-of-function alleles in the
      CMT3 chromomethylase gene. The cmt3 mutants displayed enhanced expression and reduced
      methylation of the reporter, particularly at non-CG cytosines. CNG methylation was also
      reduced at repetitive centromeric sequences. Thus, CMT3 is a key determinant for non-CG
      methylation. The lack of CMT homologs in animal genomes could account for the observation that
      in contrast to plants, animals maintain primarily CG methylation.
AU  - Bartee L
AU  - Malagnac F
AU  - Bender J
PT  - Journal Article
TA  - Genes Dev.
JT  - Genes Dev.
SO  - Genes Dev. 2001 15: 1753-1758.

PMID- 29773635
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of the Fish Pathogen Flavobacterium columnare Strain MS-FC-4.
PG  - e00429-18
AB  - Flavobacterium columnare MS-FC-4 is a highly virulent genetic group 1 (formerly genomovar I)
      strain isolated from rainbow trout (Oncorhynchus mykiss). The draft
      genome consists of three contigs totaling 3,449,277 bp with 2,811 predicted open
      reading frames. F. columnare MS-FC-4 is a model strain for functional genomic
      analyses.
AU  - Bartelme RP
AU  - Barbier P
AU  - Lipscomb RS
AU  - LaPatra SE
AU  - Newton RJ
AU  - Evenhuis JP
AU  - McBride MJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00429-18.

PMID- 27340080
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of the Fish Pathogen Flavobacterium columnare Strain C#2.
PG  - e00624-16
AB  - Flavobacterium columnare is a Gram-negative bacterial pathogen that causes columnaris disease
      of freshwater fish. Flavobacterium columnare strain C#2 was
      isolated from a diseased warm-water fish and is typed as genomovar II. The genome
      consists of a single 3.33-Mb circular chromosome with 2,689 predicted coding
      genes.
AU  - Bartelme RP
AU  - Newton RJ
AU  - Zhu Y
AU  - Li N
AU  - LaFrentz BR
AU  - McBride MJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00624-16.

PMID- 21283578
VI  - 6
DP  - 2011
TI  - An Unexpected Location of the Arginine Catabolic Mobile Element (ACME) in a USA300-Related MRSA StrainJ3 region.
PG  - e16193
AB  - In methicillin resistant Staphylococcus aureus (MRSA), the arginine catabolic mobile element
      (ACME) was initially described in USA300 (t008-ST8) where it is located downstream of the
      staphylococcal cassette chromosome mec (SCCmec). A common health-care associated MRSA in
      Copenhagen, Denmark (t024-ST8) is clonally related to USA300 and is frequently PCR
      positive for the ACME specific arcA-gene. This study is the first to describe an ACME element
      upstream of the SCCmec in MRSA. By traditional SCCmec typing schemes, the SCCmec of t024-ST8
      strain M1 carries SCCmec IVa, but full sequencing of the cassette revealed that the entire J3
      region had no homology to published SCCmec IVa. Within the J3 region of M1 was a 1705 bp
      sequence only similar to a sequence in S. haemolyticus strain JCSC1435 and 2941 bps with no
      homology found in GenBank. In addition to the usual direct repeats (DR) at each extremity of
      SCCmec, M1 had two new DR between the orfX gene and the J3 region of the SCCmec. The region
      between the orfX DR (DR1) and DR2 contained the ccrAB4 genes. An ACME II-like element was
      located between DR2 and DR3. The entire 26,468 bp sequence between DR1 and DR3 was highly
      similar to parts of the ACME composite island of S. epidermidis strain ATCC12228. Sequencing
      of an ACME negative t024-ST8 strain (M299) showed that DR1 and the sequence between DR1 and
      DR3 was missing. The finding of a mobile ACME II-like element inserted downstream of orfX and
      upstream of SCCmec indicates a novel recombination between staphylococcal species.
AU  - Bartels MD
AU  - Hansen LH
AU  - Boye K
AU  - Sorensen SJ
AU  - Westh H
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2011 6: e16193.

PMID- 25931602
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequencing of 10 Pseudomonas syringae Strains Representing Different Host Range Spectra.
PG  - e00379-15
AB  - Pseudomonas syringae is a ubiquitous bacterium that readily persists in environmental habitats
      as a saprophyte and also is responsible for numerous
      diseases of crops. Here, we report the whole-genome sequences of 10 strains
      isolated from both woody and herbaceous plants that will contribute to the
      elucidation of the determinants of their host ranges.
AU  - Bartoli C
AU  - Carrere S
AU  - Lamichhane JR
AU  - Varvaro L
AU  - Morris CE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00379-15.

PMID- Not carried by PubMed...
VI  - 195
DP  - 1988
TI  - Transition metal complexes in the design of synthetic restriction enzymes.
PG  - 44
AB  - Restriction endonucleases recognize specific double-stranded DNA sequences and
      cleave both strands to yield 5'phosphate and 3'hydroxyl termini.  Coordination
      complexes have now been designed which simulate specific binding and catalytic
      features of restriction endonucleases.  Based upon a matching of shapes and
      symmetries, phenanthroline derivatives of ruthenium complexes have been
      prepared which recognize a variety of distinct conformations along the strand.
      Transition metal complexes may be converted to novel DNA cleaving molecules by
      tethering of polyamine arms onto the DNA binding moiety.  These polyamine arms,
      directed to the sugar-phosphate backbone provide chelating centers for divalent
      metal ions such as Zn2+, Cd2+, and Pb2+, and upon activation with these metal
      ions, double-stranded hydrolytic cleavage of the phosphodiester linkages is
      observed.  Aspects of both binding specificity and reactivity of the metal
      complexes with DNA will be described.
AU  - Barton JK
PT  - Journal Article
TA  - ACS Abstracts
JT  - ACS Abstracts
SO  - ACS Abstracts 1988 195: 44.

PMID- 6282860
VI  - 257
DP  - 1982
TI  - The presence of zinc in the restriction enzyme EcoRI*.
PG  - 7911-7914
AB  - We have determined that the restriction endonuclease EcoRI contains 1.0 +- 0.1
      eq of zinc/monomeric enzyme.  DNA cleavage by EcoRI is inhibited by
      orthophenanthroline after preincubation of the enzyme with the chelating agent.
      A similar inhibition by the nonchelating meta-phenanthroline is not seen.  The
      sensitivity of the inhibition by the neutral ligand ortho-phenanthroline to
      preincubation is consistent with the tightly bound and inaccessible nature of
      the metal site.  Extensive dialysis against the ortho-phenanthroline inhibitor
      leads to the release of the bound metal with the concomitant loss of enzyme
      activity.  The tightly bound Zn2+ cation, then, appears to be necessary for
      enzyme function.  The finding of zinc in EcoRI further illustrates the ubiquity
      of Zn2+ to DNA-protein complexes.
AU  - Barton JK
AU  - Basile LA
AU  - Paranawithana SR
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1982 257: 7911-7914.

PMID- 3011080
VI  - 25
DP  - 1986
TI  - Restriction endonuclease EcoRI alters the Enantiomeric Preference of Chiral Metallointercalators for DNA:  an illustration of a protein-induced DNA conformational change.
PG  - 2205-2211
AB  - A conformational change in the DNA plasmid ColE1 appears to occur upon specific
      binding of the restriction endonuclese EcoRI.  Enzyme association alters the
      chiral discrimination found in binding metallointercalators to DNA sites.  The
      complexes tris(1,10-phenanthroline) ruthenium(II), Ru(phen) 32+, and
      tris(4,7-diphenyl-1,10-phenanthroline)cobalt(III), Co(DIP)33+, in general, bind
      stereoselectively to DNA helices, with enantiomers processing the D
      configuration bound preferentially by right-handed B-DNA.  In the presence of
      EcoRI, however, this enantioselectivity is altered.  The chiral intercalators,
      at micromolar concentrations, inhibit the reaction of EcoRI, but for each
      enantiomeric pair it is the K enantiomer, which binds only poorly to a B-DNA
      helix, that inhibits EcoRI preferentially.  Kinetic studies in the presence of
      K in the presence of K-Ru(DIP)32+ indicate that the enzyme inhibition occurs as
      a result of the K enantiomer binding to the enzyme-DNA complex as well as to
      the free enzyme.  Furthermore, photolytic strand cleavage experiments using
      Co(DIP)33+ indicate that the metal complex interacts directly at the
      protein-bound DNA site.  Increasing concentrations of bound EcoRI stimulate
      photoactivated cleavage of the DNA helix by K-Co(DIP)33+, until a protein
      concentration is reached where specific DNA recognition sites are saturated
      with enzyme.  Thus, although K-Co(DIP)33+ does not bind closely to the DNA in
      the absence of enzyme, specific binding of EcoRI appears to alter the DNA
      structure so as to permit the close association of the K isomer to the DNA
      helix.  Mapping experiments demonstrate that this association leads to
      photocleavage of DNA by the cobalt complex at or very close to the EcoRI
      recognition site.  This study provides evidence that in solution, under
      enzymatic conditions, a DNA-binding protein may distort the DNA helical
      structure and further illustrates how small molecular probes of DNA
      conformation might be used in examining the structure of protein-bound DNA
      sites.
AU  - Barton JK
AU  - Paranawithana SR
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1986 25: 2205-2211.

PMID- 2627557
VI  - 54
DP  - 1989
TI  - Isolation, purification and some properties of restrictase and methylase BstNI from Bacillus stearothermophilus.
PG  - 1894-1903
AB  - Restriction-methylation enzymes BstNI from Bacillus stearothermophilus were
      isolated and purified.  These enzymes are related to a new class of
      restriction-methylation enzymes of the second type, whose modifying component
      is N4-cytosine-DNA-methylase.  Both enzymes recognize the DNA sequence
      CC(A/T)GG.  Restrictase BstNI is a protein made up of one subunit with a
      molecular mass of 25 kDa.  The temperature optima for restrictase and methylase
      BstNI are around 60C.  Possible uses of BstNI restriction-methylation enzymes
      for the analysis of cytosine methylation in bacterial and higher plant DNA are
      discussed.
AU  - Baryshev MM
AU  - Buryanov YI
AU  - Kosykh VG
AU  - Bayev AA
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1989 54: 1894-1903.

PMID- 21525128
VI  - 39
DP  - 2011
TI  - Native homing endonucleases can target conserved genes in humans and in animal models.
PG  - 6646-6659
AB  - In recent years, both homing endonucleases (HEases) and zinc-finger nucleases (ZFNs) have been
      engineered and selected for the targeting of
      desired human loci for gene therapy. However, enzyme engineering is
      lengthy and expensive and the off-target effect of the manufactured
      endonucleases is difficult to predict. Moreover, enzymes selected to
      cleave a human DNA locus may not cleave the homologous locus in the
      genome of animal models because of sequence divergence, thus hampering
      attempts to assess the in vivo efficacy and safety of any engineered
      enzyme prior to its application in human trials. Here, we show that
      naturally occurring HEases can be found, that cleave desirable human
      targets. Some of these enzymes are also shown to cleave the homologous
      sequence in the genome of animal models. In addition, the distribution
      of off-target effects may be more predictable for native HEases. Based
      on our experimental observations, we present the HomeBase algorithm,
      database and web server that allow a high-throughput computational
      search and assignment of HEases for the targeting of specific loci in
      the human and other genomes. We validate experimentally the predicted
      target specificity of candidate fungal, bacterial and archaeal HEases
      using cell free, yeast and archaeal assays.
AU  - Barzel A
AU  - Privman E
AU  - Peeri M
AU  - Naor A
AU  - Shachar E
AU  - Burstein D
AU  - Lazary R
AU  - Gophna U
AU  - Pupko T
AU  - Kupiec M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2011 39: 6646-6659.

PMID- 4354078
VI  - 74
DP  - 1973
TI  - SV40 DNA:  Quantitative conversion of closed circular to open circular form by an ethidium bromide-restricted endonuclease.
PG  - 739-742
AB  - Closed circular molecules of SV40 DNA can be quantitatively converted to the
      open circular form by digestion with endonucleases in the presence of ethidium
      bromide.  Under these conditions almost no molecules were digested beyond the
      open circular form, whereas in the absence of the dye the DNA was completely
      fragmented.
AU  - Barzilai R
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1973 74: 739-742.

PMID- 23409268
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of a Clostridium botulinum Isolate from Water Used for Cooling at a Plant Producing Low-Acid Canned Foods.
PG  - e00200-12
AB  - Clostridium botulinum is a pathogen of concern for low-acid canned foods. Here we report draft
      genomes of a neurotoxin-producing C. botulinum strain isolated from
      water samples used for cooling low-acid canned foods at a canning facility. The
      genome sequence confirmed that this strain belonged to C. botulinum serotype B1,
      albeit with major differences, including thousands of unique single nucleotide
      polymorphisms (SNPs) compared to other genomes of the same serotype.
AU  - Basavanna U
AU  - Gonzalez-Escalona N
AU  - Timme R
AU  - Datta S
AU  - Schoen B
AU  - Brown EW
AU  - Zink D
AU  - Sharma SK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00200-12.

PMID- 28596388
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Two Staphylococcus aureus Strains Isolated in Succession from a Case of Bacteremia.
PG  - e00259-17
AB  - Staphylococcus aureus strains MEH1 and MEH7 were successively isolated from the blood of a
      patient with recurrent bacteremia. The submitted draft genomes of
      strains MEH1 and MEH7 are 2,914,972 and 2,911,704 bp, respectively.
AU  - Basco MDS
AU  - Revollo JR
AU  - McKinzie PB
AU  - Agnihothram S
AU  - Kothari A
AU  - Saccente M
AU  - Hart ME
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00259-17.

PMID- 22750883
VI  - 30
DP  - 2012
TI  - A hybrid approach for the automated finishing of bacterial genomes.
PG  - 701-707
AB  - Advances in DNA sequencing technology have improved our ability to characterize
      most genomic diversity. However, accurate resolution of large structural events
      is challenging because of the short read lengths of second-generation
      technologies. Third-generation sequencing technologies, which can yield longer
      multikilobase reads, have the potential to address limitations associated with
      genome assembly. Here we combine sequencing data from second- and
      third-generation DNA sequencing technologies to assemble the two-chromosome
      genome of a recent Haitian cholera outbreak strain into two nearly finished
      contigs at >99.9% accuracy. Complex regions with clinically relevant structure
      were completely resolved. In separate control assemblies on experimental and
      simulated data for the canonical N16961 cholera reference strain, we obtained 14
      scaffolds of greater than 1 kb for the experimental data and 8 scaffolds of
      greater than 1 kb for the simulated data, which allowed us to correct several
      errors in contigs assembled from the short-read data alone. This work provides a
      blueprint for the next generation of rapid microbial identification and
      full-genome assembly.
AU  - Bashir A et al
PT  - Journal Article
TA  - Nat. Biotechnol.
JT  - Nat. Biotechnol.
SO  - Nat. Biotechnol. 2012 30: 701-707.

PMID- 28301471
VI  - 12
DP  - 2017
TI  - Genomic confirmation of vancomycin-resistant Enterococcus transmission from deceased donor to liver transplant recipient.
PG  - e0170449
AB  - In a liver transplant recipient with vancomycin-resistant Enterococcus (VRE) surgical site and
      bloodstream infection, a combination of pulsed-field gel
      electrophoresis, multilocus sequence typing, and whole genome sequencing
      identified that donor and recipient VRE isolates were highly similar when
      compared to time-matched hospital isolates. Comparison of de novo assembled
      isolate genomes was highly suggestive of transplant transmission rather than
      hospital-acquired transmission and also identified subtle internal rearrangements
      between donor and recipient missed by other genomic approaches. Given the
      improved resolution, whole-genome assembly of pathogen genomes is likely to
      become an essential tool for investigation of potential organ transplant
      transmissions.
AU  - Bashir A
AU  - Attie O
AU  - Sullivan M
AU  - Sebra R
AU  - Singh KV
AU  - Altman D
AU  - Pak T
AU  - Dutta J
AU  - Chacko K
AU  - Webster E
AU  - Lewis M
AU  - Hamula C
AU  - Delli-Carpini KW
AU  - Murray BE
AU  - Kasarskis A
AU  - van Bakel H
AU  - Huprikar S
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2017 12: e0170449.

PMID- 24368767
VI  - 289
DP  - 2014
TI  - The UHRF1 Protein Stimulates the Activity and Specificity of the Maintenance DNA Methyltransferase DNMT1 by an Allosteric Mechanism.
PG  - 4106-4115
AB  - The ubiquitin-like, containing PHD and RING finger domains protein 1 (UHRF1) is essential for
      maintenance DNA methylation by DNA methyltransferase 1 (DNMT1). UHRF1 has been shown to
      recruit DNMT1 to replicated DNA by the ability of its SET and RING-associated (SRA) domain to
      bind to hemimethylated DNA. Here, we demonstrate that UHRF1 also increases the activity of
      DNMT1 by almost 5-fold. This stimulation is mediated by a direct interaction of both proteins
      through the SRA domain of UHRF1 and the replication focus targeting sequence domain of DNMT1,
      and it does not require DNA binding by the SRA domain. Disruption of the interaction between
      DNMT1 and UHRF1 by replacement of key residues in the replication focus targeting sequence
      domain led to a strong reduction of DNMT1 stimulation. Additionally, the interaction with
      UHRF1 increased the specificity of DNMT1 for methylation of hemimethylated CpG sites. These
      findings show that apart from the targeting of DNMT1 to the replicated DNA UHRF1 increases the
      activity and specificity of DNMT1, thus exerting a multifaceted influence on the maintenance
      of DNA methylation.
AU  - Bashtrykov P
AU  - Jankevicius G
AU  - Jurkowska RZ
AU  - Ragozin S
AU  - Jeltsch A
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2014 289: 4106-4115.

PMID- 22641038
VI  - 586
DP  - 2012
TI  - Mechanistic details of the DNA recognition by the Dnmt1 DNA methyltransferase.
PG  - 1821-1823
AB  - A recently solved Dnmt1-DNA crystal structure revealed several enzyme-DNA contacts and large
      structural rearrangements of the DNA at
      the target site, including the flipping of the non-target strand base
      of the base pair flanking the CpG site and formation of a non-canonical
      base pair between the non-target strand Gua and the flanking base pair.
      Here, we show that the contacts of the enzyme to the target base and
      the Gua:5mC base pair that are observed in the structure are very
      important for catalytic activity. The contacts to the non-target strand
      Gua are not important since its exchange by Ade stimulated activity.
      Except target base flipping, we could not find evidence that the DNA
      rearrangements have a functional role.
AU  - Bashtrykov P
AU  - Ragozin S
AU  - Jeltsch A
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 2012 586: 1821-1823.

PMID- 15654762
VI  - 44
DP  - 2005
TI  - Effects of benzo[a]pyrene-deoxyguanosine lesions on DNA methylation catalyzed by EcoRII DNA methyltransferase and on DNA cleavage effected  by EcoRII restriction endonuclease.
PG  - 1054-1066
AB  - DNA methylation is an important cellular mechanism for controlling gene expression. Whereas
      the mutagenic properties of many DNA adducts, e.g.,
      those arising from polycyclic aromatic hydrocarbons, have been widely
      studied, little is known about their influence on DNA methylation. We
      have constructed site-specifically modified 18-mer oligodeoxynucleotide
      duplexes containing a pair of stereoisomeric adducts derived from a
      benzo[a]pyrene-derived diol epoxide [(+)- and
      (-)-r7,t8-dihydroxy-t9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene, or
      B[a]PDE] bound to the exocyclic amino group of guanine. The adducts,
      either (+)- or (-)-trans-anti-B[a]P-N-2-dG (G*), positioned either at
      the 5'-side or the 3'-side deoxyguanosine residue in the recognition
      sequence of EcoRII restriction-modification enzymes (5'-...CCA/TGG...)
      were incorporated into 18-mer oligodeoxynucleotide duplexes. The
      effects of these lesions on complex formation and the catalytic
      activity of the EcoRII DNA methyltransferase (M.EcoRII) and EcoRII
      restriction endonuclease (R.EcoRII) were investigated. The M.EcoRII
      catalyzes the transfer of a methyl group to the C5 position of the
      3'-side cytosine of each strand of the recognition sequence, whereas
      R.EcoRII catalyzes cleavage of both strands. The binding of R.EcoRII to
      the oligodeoxynucleotide duplexes and the catalytic cleavage were
      completely abolished when G* was positioned at the 3'-side dG position
      (5'-...CCTGG*...). When G* was at the 5'-side dG position, binding was
      moderately diminished, but cleavage was completely blocked. In the case
      of M.EcoRII, binding is diminished by factors of 5-30 but the catalytic
      activity was either abolished or reduced 4-80-fold when the adducts
      were located at either position. Somewhat smaller effects were observed
      with hemimethylated oligodeoxynucleotide duplexes. These findings
      suggest that epigenetic effects, in addition to genotoxic effects, need
      to be considered in chemical carcinogenesis initiated by B[a]PDE, since
      the inhibition of methylation may allow the expression of genes that
      promote tumor development.
AU  - Baskunov VB
AU  - Subach FV
AU  - Kolbanovskiy A
AU  - Kolbanovskiy M
AU  - Eremin SA
AU  - Johnson F
AU  - Bonala R
AU  - Geacintov NE
AU  - Gromova ES
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2005 44: 1054-1066.

PMID- 6301172
VI  - 19
DP  - 1983
TI  - Restriction endonucleases as a possible factor in the evolution of DNA nucleotide composition.
PG  - 20-24
AB  - On the basis of a statistical analysis of the nucleotide and codogenic
      composition of the sites for restriction endonucleases of type II it was
      concluded that restriction endoncleases may perform an evolutionary function as
      catalysts of the site-specific accumulation of the bacterial pre-genome in
      parallel with a change in its nucleotide composition in the direction of its
      enrichment with AT pairs and the amino acid composition of the proteins in the
      direction of a decrease in the content of alanine, arginine, proline and
      glycine.
AU  - Basnakyan AG
AU  - Votrin II
PT  - Journal Article
TA  - Zh. Evol. Biokhim. Fiziol.
JT  - Zh. Evol. Biokhim. Fiziol.
SO  - Zh. Evol. Biokhim. Fiziol. 1983 19: 20-24.

PMID- 25573940
VI  - 3
DP  - 2015
TI  - Complete Genome Sequences of Citrobacter braakii Strains GTA-CB01 and GTA-CB04, Isolated from Ground Beef.
PG  - e01307-14
AB  - Citrobacter braakii is a Gram-negative bacterium belonging to the Enterobacteriaceae family.
      Here, we report 5.2- and 5.0-Mb genome assemblies for
      C. braakii strains GTA-CB01 and GTA-CB04, respectively.
AU  - Basra P
AU  - Koziol A
AU  - Wong A
AU  - Carrillo CD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01307-14.

PMID- 23950123
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Clostridium tyrobutyricum Strain UC7086, Isolated from Grana Padano Cheese with Late-Blowing Defect.
PG  - e00614-13
AB  - Clostridium tyrobutyricum is considered the main agent of late-blowing defect in  the
      production of hard cheese. Here, we described the draft genome sequences and
      annotation of C. tyrobutyricum strain UC7086, which was isolated from Grana
      Padano cheese with blowing defect, and C. tyrobutyricum DSM 2637 type strain in a
      comparative study.
AU  - Bassi D
AU  - Fontana C
AU  - Gazzola S
AU  - Pietta E
AU  - Puglisi E
AU  - Cappa F
AU  - Cocconcelli PS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00614-13.

PMID- 28104661
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Four Alkaliphilic Bacteria Belonging to the Anaerobacillus Genus.
PG  - e01493-16
AB  - The draft genomes of the alkaliphilic, anaerobic bacteria, Anaerobacillus arseniciselenatis,
      A. alkalidiazotrophicus, and A. alkalilacustris, and a novel
      closely related isolate of the Anaerobacillus genus are reported here. These
      assembled genomes will help identify, at the molecular level, the phenotypic
      differences between the species of this poorly characterized genus.
AU  - Bassil NM
AU  - Lloyd JR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01493-16.

PMID- 1563635
VI  - 113
DP  - 1992
TI  - Overproduction, purification and characterization of M.HinfI methyltransferase and its deletion mutant.
PG  - 83-88
AB  - We have used the polymerase chain reaction to alter transcriptional and translational signals
      surrounding the hinfIM gene [encoding M.HinfI methyltransferase (MTase)] so as to achieve
      overexpression in Escherichia coli. The PCR-generated hinfIM gene was subcloned in a
      high-expression vector under control of the hybrid trp-lac promoter. In addition, the positive
      retroregulator stem-loop sequence derived from the crystal protein-encoding gene of Bacillus
      thuringiensis was inserted downstream from hinfIM. Using a similar approach, we have also
      constructed overproducer clones of a deletion mutant of M.HinfI MTase that has 97 amino acids
      from the C terminus deleted. The plasmid from the mutant clones is fully protected from HinfI
      restriction endonuclease digestion. It appears that the functional properties (recognition and
      catalytic functions) are encoded within this mutant gene. The overproducer clones yield the
      wild type (wt) and the mutant enzymes to about 10% of total cellular protein upon induction
      with 1 mM IPTG. The wt M.HinfI and the mutant MTase were purified to near electrophoretic
      homogeneity by phosphocellulose, DEAE and gel chromatography. Their monomer sizes by
      SDS/polyacrylamide-gel electrophoresis are 43 kDa and 31 kDa, respectively, in good agreement
      with that predicted from the nucleotide sequence. DNA methylation experiments with purified
      enzymes using single-strand and double-strand M13mp18 DNA substrates indicate that while wt
      enzyme methylates both forms of DNA substrates, the mutant enzyme appears to preferentially
      methylate ss DNA substrate.
AU  - Bassing CH
AU  - Kim Y-G
AU  - Li L
AU  - Chandrasegaran S
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1992 113: 83-88.

PMID- 28935730
VI  - 5
DP  - 2017
TI  - Conservation and Recombination in the Genome Sequence of Haemophilus influenzae Type f WAPHL1.
PG  - e00929-17
AB  - We report here the second draft genome sequence of a bloodstream isolate of Haemophilus
      influenzae serotype f. Three discrete 3.1- to 7.8-kb sites contained
      80% of the variability in the genome, consistent with recombination in known
      virulence factors.
AU  - Bateman AC
AU  - Perez-Osorio AC
AU  - Li Z
AU  - Tran M
AU  - Greninger AL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00929-17.

PMID- 28935722
VI  - 5
DP  - 2017
TI  - Genome and Plasmid Sequences of Escherichia coli KV7, an Extended-Spectrum beta-Lactamase Isolate Derived from Feces of a Healthy Pig.
PG  - e00595-17
AB  - We present single-contig assemblies for Escherichia coli strain KV7 (serotype O27,
      phylogenetic group D) and its six plasmids, isolated from a healthy pig, as
      determined by PacBio RS II and Illumina MiSeq sequencing. The chromosome of
      4,997,475 bp and G+C content of 50.75% harbored 4,540 protein-encoding genes.
AU  - Bateman MD
AU  - de Vries SPW
AU  - Gupta S
AU  - Guardabassi L
AU  - Cavaco LM
AU  - Grant AJ
AU  - Holmes MA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00595-17.

PMID- 
VI  - 49
DP  - 2008
TI  - Discovery of XB05, a potent antiproliferative agent and novel non-nucleoside inhibitor of DNA methyltransferase 1.
PG  - 783
AB  - While investigating the biological properties of fluorine-containing organic molecules, we
      recently identified a novel small molecule, named XB05, which has tumor-selective
      antiproliferative activity. The molecule was submitted to the Developmental Therapeutics
      Program (DTP) at the National Cancer Institute (NCI) for testing in the 60 human tumor cell
      line screen. The results confirmed that XB05 has potent activity against a diverse range of
      cancer cell lines and also revealed an unusual activity profile, with a more than 1000-fold
      difference in GI50 values between the most and least sensitive lines. For example, colon,
      brain, renal, prostate and breast tumor cells were particularly sensitive to XB05, whereas
      other tumor types were substantially less responsive. The GI50 values for the sensitive cell
      lines were in the 10 - 100 nM range.
      We analyzed the DTP data using the on-line COMPARE program, which allows comparison of the
      activity profile with the 43,000 compounds in the public database and which has been validated
      as grouping together agents with similar mechanisms of action, irrespective of their
      structure. When we used XB05 as a COMPARE seed, we found a strong correlation (Pearson
      coefficient 0.82) with a compound known as halomon.
      Halomon is a marine-derived natural product, which has promising anticancer activity. However,
      its development has been severely limited because attempts to re-isolate it from its natural
      source or to develop an efficient synthesis have not enabled production of sufficient compound
      for testing. Halomon was recently reported to be an inhibitor of human DNA methyltransferase 1
      (DNMT1), the enzyme responsible for maintaining DNA methylation after each cell division.
      DNMT1 is considered an attractive target for epigenetic therapy of cancer because
      methylation-induced silencing of tumor suppressor genes occurs frequently in cancer cells.
      XB05 has now been tested in various cell-free and cell-based assays of DNA methylation. We
      find that it is a potent inhibitor of recombinant DNMT1 activity in vitro, with an IC50 of 10
      nM. Moreover, XB05 could reactivate expression of several silenced tumor suppressor genes in
      cancer cells at concentrations of 100 nM or less.
      In conclusion, XB05 is a novel agent with potent antiproliferative activity against cell lines
      derived from common cancers and a new type of DNMT1 inhibitor. XB05 is a mechanistic mimic of
      a natural product named halomon, but, in contrast to halomon, XB05 can be easily and
      inexpensively synthesized in large quantities. XB05 may also have substantial advantages over
      other existing DNMT inhibitors such as 5-azacytidine and decitabine. XB05 is more active than
      these agents in cell-free or cell-based DNMT assays and will likely be less toxic because it
      cannot be incorporated into DNA. Also, whereas 5-azacytidine and decitabine are rapidly
      degraded in aqueous solutions, XB05 appears to be completely stable.
AU  - Bates PJ
AU  - Hammond GB
AU  - Xu B
AU  - Aponte JC
AU  - Malik MT
AU  - Martin AN
AU  - Choi EW
AU  - Thomas SD
AU  - Casson LK
AU  - Trent JO
PT  - Journal Article
TA  - Proc. Amer. Assoc. Cancer Res.
JT  - Proc. Amer. Assoc. Cancer Res.
SO  - Proc. Amer. Assoc. Cancer Res. 2008 49: 783.

PMID- 11729187
VI  - 277
DP  - 2002
TI  - Many type IIs restriction endonucleases interact with two recognition sites before cleaving DNA.
PG  - 4024-4033
AB  - Type IIs restriction endonucleases recognize asymmetric DNA sequences and cleave both DNA
      strands at fixed positions, typically several base pairs away from the recognition site.
      These enzymes are generally monomers that transiently associate to form dimmers to cleave both
      strands.  Their reactions could involve bridging interactions between two copies of their
      recognition sequence.  To examine this possibility, several type IIs enzymes were tested
      against substrates with either one or two target sites.  Some of the enzymes cleaved the DNA
      with two target sites at the same rate as that with one site, but most cut their two-site
      substrate more rapidly than the one-site DNA.  In some cases, the two sites were cut
      sequentially, at rates that were equal to each other but that exceeded the rate on the
      one-site DNA.  In another case, the DNA with two sites was cleaved rapidly at one site, but
      the residual site was cleaved at a much slower rate.  In a further example, the two sites were
      cleaved concertedly to give directly the final products cut at both sites.  Many type IIs
      enzymes thus interact with two copies of their recognition sequence before cleaving DNA,
      although via several different mechanisms.
AU  - Bath AJ
AU  - Milsom SE
AU  - Gormley NA
AU  - Halford SE
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2002 277: 4024-4033.

PMID- 28007854
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Multitrait Plant Growth-Promoting Bacillus sp. Strain RZ2MS9.
PG  - e01402-16
AB  - Bacillus sp. strain RZ2MS9 is a multitrait soybean and maize growth-promoting bacterium
      isolated in Brazil from guarana's rhizosphere. Here, we present the draft genome sequence of
      RZ2MS9 and its genes involved in many features related to plant growth promotion.
AU  - Batista BD
AU  - Taniguti LM
AU  - Almeida JR
AU  - Azevedo JL
AU  - Quecine MC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01402-16.

PMID- 26988044
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Burkholderia ambifaria RZ2MS16, a Plant Growth-Promoting Rhizobacterium Isolated from Guarana, a Tropical Plant.
PG  - e00125-16
AB  - Burkholderia ambifaria strain RZ2MS16 was isolated from the rhizosphere of Amazon guarana in
      Brazil. This bacterium exhibits a remarkable capacity to promote the
      growth of corn and soybean. Here, we report the draft genome sequence of RZ2MS16
      and some genes related to multiple traits involved in plant growth promotion.
AU  - Batista BD
AU  - Taniguti LM
AU  - Monteiro-Vitorello CB
AU  - Azevedo JL
AU  - Quecine MC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00125-16.

PMID- 24558231
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Gallinarum Biovar Pullorum Strain FCAV198, a Brazilian Chicken Pathogen.
PG  - e00028-14
AB  - Salmonella enterica subsp. enterica serovar Gallinarum biovar Pullorum is a bird-restricted
      pathogen which causes pullorum disease. The strain FCAV198 was
      isolated from a pool of chicken ovaries in Brazil, and its genome may be helpful
      for studies involving molecular mechanisms related to pathogenesis and other
      related applications.
AU  - Batista DF
AU  - Freitas NOC
AU  - Leite LR
AU  - Varani AM
AU  - Araujo FM
AU  - Salim A
AU  - Almeida AM
AU  - Ribeiro SA
AU  - Oliveira GC
AU  - Barrow PA
AU  - Berchieri JA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00028-14.

PMID- 10427032
VI  - 65
DP  - 1999
TI  - Development of a system for genetic manipulation of Bartonella bacilliformis.
PG  - 3441-3448
AB  - Lack of a system for site-specific genetic manipulation has severely hindered studies on the
      molecular biology of all Bartonella species. We report the first site-specific mutagenesis and
      complementation for a Bartonella species. A highly transformable strain of B. bacilliformis,
      termed JB584, was isolated and found to exhibit a significant increase in transformation
      efficiency with the broad-host-range plasmid pBBR1MCS-2, relative to wild-type strains.
      Restriction analyses of genomic preparations with the methylation-sensitive restriction
      enzymes ClaI and StuI suggest that strain JB584 possesses a dcm methylase mutation that
      contributes to its enhanced transformability. A suicide plasmid, pUB1, which contains a
      polylinker, a pMB1 replicon, and a nptI kanamycin resistance cassette, was constructed. An
      internal 508-bp fragment of the B. bacilliformis flagellin gene (fla) was cloned into pUB1 to
      generate pUB508, a fla-targeting suicide vector. Introduction of pUB508 into JB584 by
      electroporation generated eight Kan(r) clones of B. bacilliformis.  Characterization of one of
      these strains, termed JB585, indicated that allelic exchange between pUB508 and fla had
      occurred. Analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis,
      immunoblotting, and electron microscopy showed that synthesis of flagellin encoded by fla and
      secretion/assembly of flagella were abolished.  Complementation of fla in trans was
      accomplished with a pBBR1MCS recombinant containing the entire wild-type fla gene (pBBRFLAG).
      These data conclusively show that inactivation of fla results in a bald, nonmotile phenotype
      and that pMB1 and REP replicons make suitable B. bacilliformis suicide and shuttle vectors,
      respectively. When used in conjunction with the highly transformable strain JB584, this system
      for site-specific genetic manipulation and complementation provides a new venue for studying
      the molecular biology of B. bacilliformis.
AU  - Battisti JM
AU  - Minnick MF
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1999 65: 3441-3448.

PMID- 21296963
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Yersinia enterocolitica subsp. palearctica Serogroup O:3.
PG  - 2067
AB  - We report here the first finished and annotated genome sequence of a representative of the
      most epidemiologically successful Yersinia group, Y.
      enterocolitica subsp. palearctica strain Y11, serotype O:3, biotype 4.
      This strain is a certified type strain of the German DSMZ collection (DSM
      no. 13030; Yersinia enterocolitica subsp. palearctica) that was isolated
      from the stool of a human patient (H. Neubauer, S. Aleksic, A. Hensel, E.
      J. Finke, and H. Meyer. Int. J. Med. Microbiol. 290:61-64, 2000).
AU  - Batzilla J
AU  - Hoper D
AU  - Antonenka U
AU  - Heesemann J
AU  - Rakin A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 2067.

PMID- 25607372
VI  - 520
DP  - 2015
TI  - Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation.
PG  - 243-247
AB  - DNA methylation is an epigenetic modification associated with transcriptional repression of
      promoters and is essential for mammalian development. Establishment
      of DNA methylation is mediated by the de novo DNA methyltransferases DNMT3A and
      DNMT3B, whereas DNMT1 ensures maintenance of methylation through replication.
      Absence of these enzymes is lethal, and somatic mutations in these genes have
      been associated with several human diseases. How genomic DNA methylation patterns
      are regulated remains poorly understood, as the mechanisms that guide recruitment
      and activity of DNMTs in vivo are largely unknown. To gain insights into this
      matter we determined genomic binding and site-specific activity of the mammalian
      de novo DNA methyltransferases DNMT3A and DNMT3B. We show that both enzymes
      localize to methylated, CpG-dense regions in mouse stem cells, yet are excluded
      from active promoters and enhancers. By specifically measuring sites of de novo
      methylation, we observe that enzymatic activity reflects binding. De novo
      methylation increases with CpG density, yet is excluded from nucleosomes.
      Notably, we observed selective binding of DNMT3B to the bodies of transcribed
      genes, which leads to their preferential methylation. This targeting to
      transcribed sequences requires SETD2-mediated methylation of lysine 36 on histone
      H3 and a functional PWWP domain of DNMT3B. Together these findings reveal how
      sequence and chromatin cues guide de novo methyltransferase activity to ensure
      methylome integrity.
AU  - Baubec T
AU  - Colombo DF
AU  - Wirbelauer C
AU  - Schmidt J
AU  - Burger L
AU  - Krebs AR
AU  - Akalin A
AU  - Schubeler D
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2015 520: 243-247.

PMID- 28803482
VI  - 7
DP  - 2017
TI  - Corynebacterium glutamicum chassis C1*: Building and testing a novel platform host for synthetic biology and industrial biotechnology.
PG  - 132-144
AB  - Targeted top-down strategies for genome reduction are considered to have a high
      potential for providing robust basic strains for synthetic biology and industrial
      biotechnology. Recently, we created a library of 26 genome-reduced strains of
      Corynebacterium glutamicum carrying broad deletions in single gene clusters and
      showing wild-type-like biological fitness. Here, we proceeded with combinatorial
      deletions of these irrelevant gene clusters in two parallel orders, and the
      resulting library of 28 strains was characterized under various environmental
      conditions. The final chassis strain C1* carries a genome reduction of 13.4% (412
      deleted genes) and shows wild-type-like growth behavior in defined medium with
      d-glucose as carbon and energy source. Moreover, C1* proves to be robust against
      several stresses (including oxygen limitation) and shows long-term growth
      stability under defined and complex medium conditions. In addition to providing a
      novel prokaryotic chassis strain, our results comprise a large strain library and
      a revised genome annotation list, which will be valuable sources for future
      systemic studies of C. glutamicum.
AU  - Baumgart M et al
PT  - Journal Article
TA  - ACS Synth. Biol.
JT  - ACS Synth. Biol.
SO  - ACS Synth. Biol. 2017 7: 132-144.

PMID- 23892752
VI  - 79
DP  - 2013
TI  - Construction of a prophage-free variant of Corynebacterium glutamicum ATCC 13032 - a platform strain for basic research and industrial biotechnology.
PG  - 6006-6015
AB  - The activity of bacteriophages and phage-related mobile elements is a major
      source for genome rearrangements and genetic instability of their bacterial
      hosts. The genome of the industrial amino acid producer Corynebacterium
      glutamicum ATCC 13032 contains three prophages (CGP1-3) of so far unknown
      functionality. Several phage genes are regularly expressed and the large prophage
      CGP3 ( approximately 190 kbp) has recently been shown to be induced under certain
      stress conditions. Here, we present the construction of MB001, a prophage-free
      variant of C. glutamicum ATCC 13032 with a 6 % reduced genome. This strain does
      not show any unfavorable properties during extensive phenotypic characterization
      under various standard and stress conditions. As expected, we observed an
      improved growth and fitness of MB001 under SOS-response inducing conditions that
      trigger CGP3 induction in the wild type strain. Further studies revealed that
      MB001 has a significantly increased transformation efficiency and produced about
      30 % more of the heterologous model protein eYFP, presumably as a consequence of
      an increased plasmid copy number. These effects were attributed to the loss of
      the restriction-modification system (cg1996-98) located within CGP3. The deletion
      of the prophages without any negative effect results in a novel platform strain
      for metabolic engineering and represents a useful step towards the construction
      of a C. glutamicum chassis genome of strain ATCC 13032 for biotechnological
      applications and synthetic biology.
AU  - Baumgart M
AU  - Unthan S
AU  - Ruckert C
AU  - Sivalingam J
AU  - Grunberger A
AU  - Kalinowski J
AU  - Bott M
AU  - Noack S
AU  - Frunzke J
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2013 79: 6006-6015.

PMID- 479170
VI  - 254
DP  - 1979
TI  - Use of short synthetic DNA duplexes as substrates for the restriction endonucleases HpaII and MnoI.
PG  - 8943-8950
AB  - In an attempt to determine whether cleavage by restriction enzymes is specified solely by the
      nucleotide sequence at the recognition site or whether additional factors (e.g. the size of
      the DNA or partial disruption of the DNA helix to form cruciform structures) are involved in
      recognition, two restriction enzymes, HpaII and MnoI, were tested for their ability to cleave
      synthetic DNA duplexes of limited size and well-defined sequence.  DNA duplexes ranging from 6
      to 13 base pairs in length were shown to be recognized with high efficiency by HpaII and were
      cleaved specifically within the HpaII recognition sequence.  5' d-C^C-G-G 3'  3' G-G-C^C-d
      5'.  HpaII was totally inactive against single-stranded DNA; therefore, both strands of the
      DNA duplex are necessary for cleavage to occur.  In two of the DNA duplexes, the recognition
      sequences were located at the end of a base paired region and were thus almost certainly
      present in the form of a linear duplex.  The fact that HpaII could cleave these duplexes
      suggests that the information for HpaII recognition resides in the nucleotide sequence alone.
      By incubation of these synthetic duplexes with restriction nuclease from MnoI we have shown
      that the cleavage site for MnoI is identical with that of HpaII.  Although HpaII and MnoI
      nucleases are isoschizomers, they do difer somewhat in their mode of action on the short
      synthetic DNA duplexes.  With the duplexes used as substrates, it was found that whereas the
      HpaII nuclease preferentially cleaved the pyrimidine-rich strand (3 to 4 times over the
      purine-rich strand), the MnoI nuclease cleaved both strands at an equal rate.
AU  - Baumstark BR
AU  - Roberts RJ
AU  - RajBhandary UL
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1979 254: 8943-8950.

PMID- 8347627
VI  - 32
DP  - 1993
TI  - Formation of a cleavasome: enhancer DNA-2 stabilizes an active conformation of NaeI dimer.
PG  - 8291-8298
AB  - Cleavage of DNA by NaeI-type restriction enzymes is stimulated by a DNA element with affinity
      for the activator site of the enzyme: a cleavage-enhancer DNA element. Measurements of the
      mobility of NaeI activity in comparison with protein standards on gel permeation columns and
      glycerol gradients demonstrated that NaeI, without enhancer, can form a 70,000 MW dimer. The
      dimer, however is inactive: it could not cleave the resistant NaeI site in M13mp18 DNA in the
      absence of enhancer. In cleavage assays, enhancer stimulated either DNA nicking or DNA
      cleavage, depending upon NaeI concentration, and reduced the NaeI concentration required for
      the transition from nicking to cleavage activity. A gel mobility-shift assay of the
      interaction of NaeI with enhancer showed the formation of two complexes. Results using
      different sized DNAs and different percentage acrylamide gels for gel mobility-shift analysis
      implied that the two complexes were caused by NaeI monomer and dimer structures rather than
      one and two DNA binding. Dimer formation increased with the affinity of enhancer for NaeI. UV
      cross-linking captured the NaeI-enhancer complex; electrophoretic analysis of the cross-linked
      products showed NaeI dimer bound to enhancer. These results imply a model for cleavage
      enhancement in which enhancer binding stabilizes an active NaeI dimer conformation
      (cleavasome) that cleaves both DNA strands before dissociating.
AU  - Baxter BK
AU  - Topal MD
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1993 32: 8291-8298.

PMID- 22684507
VI  - 40
DP  - 2012
TI  - Engineering domain fusion chimeras from I-OnuI family LAGLIDADG homing endonucleases.
PG  - 7985-8000
AB  - Although engineered LAGLIDADG homing endonucleases (LHEs) are finding increasing  applications
      in biotechnology, their generation remains a challenging,
      industrial-scale process. As new single-chain LAGLIDADG nuclease scaffolds are
      identified, however, an alternative paradigm is emerging: identification of an
      LHE scaffold whose native cleavage site is a close match to a desired target
      sequence, followed by small-scale engineering to modestly refine recognition
      specificity. The application of this paradigm could be accelerated if methods
      were available for fusing N- and C-terminal domains from newly identified LHEs
      into chimeric enzymes with hybrid cleavage sites. Here we have analyzed the
      structural requirements for fusion of domains extracted from six single-chain
      I-OnuI family LHEs, spanning 40-70% amino acid identity. Our analyses demonstrate
      that both the LAGLIDADG helical interface residues and the linker peptide
      composition have important effects on the stability and activity of chimeric
      enzymes. Using a simple domain fusion method in which linker peptide residues
      predicted to contact their respective domains are retained, and in which limited
      variation is introduced into the LAGLIDADG helix and nearby interface residues,
      catalytically active enzymes were recoverable for approximately 70% of domain
      chimeras. This method will be useful for creating large numbers of chimeric LHEs
      for genome engineering applications.
AU  - Baxter S
AU  - Lambert AR
AU  - Kuhar R
AU  - Jarjour J
AU  - Kulshina N
AU  - Parmeggiani F
AU  - Danaher P
AU  - Gano J
AU  - Baker D
AU  - Stoddard BL
AU  - Scharenberg AM
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: 7985-8000.

PMID- 22434884
VI  - 40
DP  - 2012
TI  - Phase variable genes of Campylobacter jejuni exhibit high mutation rates and specific mutational patterns but mutability is not the major determinant of  population structure during host colonization.
PG  - 5876-5889
AB  - Phase variation of surface structures occurs in diverse bacterial species due to  stochastic,
      high frequency, reversible mutations. Multiple genes of Campylobacter
      jejuni are subject to phase variable gene expression due to mutations in polyC/G
      tracts. A modal length of nine repeats was detected for polyC/G tracts within C.
      jejuni genomes. Switching rates for these tracts were measured using
      chromosomally-located reporter constructs and high rates were observed for cj1139
      (G8) and cj0031 (G9). Alteration of the cj1139 tract from G8 to G11 increased
      mutability 10-fold and changed the mutational pattern from predominantly
      insertions to mainly deletions. Using a multiplex PCR, major changes were
      detected in 'on/off' status for some phase variable genes during passage of C.
      jejuni in chickens. Utilization of observed switching rates in a stochastic,
      theoretical model of phase variation demonstrated links between mutability and
      genetic diversity but could not replicate observed population diversity. We
      propose that modal repeat numbers have evolved in C. jejuni genomes due to
      molecular drivers associated with the mutational patterns of these polyC/G
      repeats, rather than by selection for particular switching rates, and that
      factors other than mutational drift are responsible for generating genetic
      diversity during host colonization by this bacterial pathogen.
AU  - Bayliss CD
AU  - Bidmos FA
AU  - Anjum A
AU  - Manchev VT
AU  - Richards RL
AU  - Grossier JP
AU  - Wooldridge KG
AU  - Ketley JM
AU  - Barrow PA
AU  - Jones MA
AU  - Tretyakov MV
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: 5876-5889.

PMID- 16914439
VI  - 34
DP  - 2006
TI  - High allelic diversity in the methyltransferase gene of a phase variable type III restriction-modification system has implications for the fitness  of Haemophilus influenzae.
PG  - 4046-4059
AB  - Phase variable restriction-modification (R-M) systems are widespread in Eubacteria.
      Haemophilus influenzae encodes a phase variable homolog of
      Type III R-M systems. Sequence analysis of this system in 22 non-typeable
      H.influenzae isolates revealed a hypervariable region in the central
      portion of the mod gene whereas the res gene was conserved. Maximum
      likelihood (ML) analysis indicated that most sites outside this
      hypervariable region experienced strong negative selection but evidence of
      positive selection for a few sites in adjacent regions. A phylogenetic
      analysis of 61 Type III mod genes revealed clustering of these
      H.influenzae mod alleles with mod genes from pathogenic Neisseriae and,
      based on sequence analysis, horizontal transfer of the mod-res complex
      between these species. Neisserial mod alleles also contained a
      hypervariable region and all mod alleles exhibited variability in the
      repeat tract. We propose that this hypervariable region encodes the target
      recognition domain (TRD) of the Mod protein and that variability results
      in alterations to the recognition sequence of this R-M system. We argue
      that the high allelic diversity and phase variable nature of this R-M
      system have arisen due to selective pressures exerted by diversity in
      bacteriophage populations but also have implications for other fitness
      attributes of these bacterial species.
AU  - Bayliss CD
AU  - Callaghan MJ
AU  - Moxon ER
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2006 34: 4046-4059.

PMID- 16179392
VI  - 102
DP  - 2005
TI  - Rapid directional shift of mitochondrial DNA heteroplasmy in animal tissues by a mitochondrially targeted restriction endonuclease.
PG  - 14392-14397
AB  - Frequently, mtDNA with pathogenic mutations coexist with wild-type genomes (mtDNA
      heteroplasmy). Mitochondrial dysfunction and disease ensue only
      when the proportion of mutated mtDNAs is high, thus a reduction in this
      proportion should provide an effective therapy for these disorders. We
      developed a system to decrease specific mtDNA haplotypes by expressing a
      mitochondrially targeted restriction endonuclease, ApaLI, in cells of
      heteroplasmic mice. These mice have two mtDNA haplotypes, of which only
      one contains an ApaLI site. After transfection of cultured hepatocytes
      with mitochondrially targeted ApaLI, we found a rapid, directional, and
      complete shift in mtDNA heteroplasmy (2-6 h). We tested the efficacy of
      this approach in vivo, by using recombinant viral vectors expressing the
      mitochondrially targeted ApaLI. We observed a significant shift in mtDNA
      heteroplasmy in muscle and brain transduced with recombinant viruses. This
      strategy could prevent disease onset or reverse clinical symptoms in
      patients harboring certain heteroplasmic pathogenic mutations in mtDNA.
AU  - Bayona-Bafaluy MP
AU  - Blits B
AU  - Battersby BJ
AU  - Shoubridge EA
AU  - Moraes CT
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2005 102: 14392-14397.

PMID- 24926046
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Insecticidal Streptomyces sp. Strain PCS3-D2, Isolated from Mangrove Soil in Philippines.
PG  - e00448-14
AB  - A draft genome sequence of a Streptomyces sp. isolated from mangrove soil in Cebu,
      Philippines, is described here. This isolate produced compounds with
      contact insecticidal activity against important corn pests. The genome contains
      7,479,793 bp (in 27 scaffolds), 6,297 predicted genes, and 29 secondary
      metabolite biosynthetic gene clusters.
AU  - Bayot-Custodio AN
AU  - Alcantara EP
AU  - Zulaybar TO
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00448-14.

PMID- 12107144
VI  - 184
DP  - 2002
TI  - Genomic and Functional Analyses of SXT, an Integrating Antibiotic Resistance Gene Transfer Element Derived from Vibrio cholerae.
PG  - 4259-4269
AB  - SXT is representative of a family of conjugative-transposon-like mobile
      genetic elements that encode multiple antibiotic resistance genes. In
      recent years, SXT-related conjugative, self-transmissible integrating
      elements have become widespread in Asian Vibrio cholerae. We have
      determined the 100-kb DNA sequence of SXT. This element appears to be a
      chimera composed of transposon-associated antibiotic resistance genes
      linked to a variety of plasmid- and phage-related genes, as well as to
      many genes from unknown sources. We constructed a nearly comprehensive set
      of deletions through the use of the one-step chromosomal gene inactivation
      technique to identify SXT genes involved in conjugative transfer and
      chromosomal excision. SXT, unlike other conjugative transposons, utilizes
      a conjugation system related to that encoded by the F plasmid. More than
      half of the SXT genome, including the composite transposon-like structure
      that contains its antibiotic resistance genes, was not required for its
      mobility. Two SXT loci, designated setC and setD, whose predicted amino
      acid sequences were similar to those of the flagellar regulators FlhC and
      FlhD, were found to encode regulators that activate the transcription of
      genes required for SXT excision and transfer. Another locus, designated
      setR, whose gene product bears similarity to lambdoid phage CI repressors,
      also appears to regulate SXT gene expression.
AU  - Beaber JW
AU  - Hochhut B
AU  - Waldor MK
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2002 184: 4259-4269.

PMID- 28385855
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of a Canine Isolate of Methicillin-Resistant Staphylococcus haemolyticus.
PG  - e00146-17
AB  - Staphylococcus haemolyticus strain SW007 was isolated from a nasal swab taken from a healthy
      dog. The isolate is resistant to methicillin, mupirocin,
      macrolides, and sulfonamides. The SW007 draft genome is 2,325,410 bp and contains
      2,277 coding sequences, including 60 tRNAs and nine complete rRNA-coding regions.
AU  - Bean DC
AU  - Wigmore SM
AU  - Wareham DW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00146-17.

PMID- 28209829
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Staphylococcus cohnii subsp. urealyticus Isolated from a Healthy Dog.
PG  - e01628-16
AB  - Staphylococcus cohnii subsp. urealyticus strain SW120 was isolated from the ear swab of a
      healthy dog. The isolate is resistant to methicillin and fusidic acid.
      The SW120 draft genome is 2,805,064 bp and contains 2,667 coding sequences,
      including 58 tRNAs and nine complete rRNA coding regions.
AU  - Bean DC
AU  - Wigmore SM
AU  - Wareham DW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01628-16.

PMID- 28935742
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Three Coxiella burnetii Strains Isolated from Q Fever Patients.
PG  - e00986-17
AB  - In the current study, we determined the draft genome sequences of three Coxiella  burnetii
      human disease isolates. The Coxiella burnetii Turkey (RSA315) and Dyer
      (RSA345) strains were isolated from acute Q fever patients, while the Ko (Q229)
      strain was isolated from a Q fever endocarditis patient.
AU  - Beare PA
AU  - Jeffrey BM
AU  - Martens CA
AU  - Heinzen RA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00986-17.

PMID- 28963209
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of the Avirulent Coxiella burnetii Dugway 7D77-80 and Dugway 7E65-68 Strains Isolated from Rodents in Dugway, Utah.
PG  - e00984-17
AB  - Here, we present the draft genome sequences of the Coxiella burnetii Dugway 7D77-80 and Dugway
      7E65-68 strains, which were isolated from rodents in Dugway,
      UT, in the 1950s. The strains reside in a distinct genomic group of C. burnetii
      and are considered avirulent despite having the largest genomes of the Coxiella
      genus.
AU  - Beare PA
AU  - Jeffrey BM
AU  - Martens CA
AU  - Heinzen RA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00984-17.

PMID- 28963210
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Historical Strains of Coxiella burnetii Isolated from Cow's Milk and a Goat Placenta.
PG  - e00985-17
AB  - Here, we report draft genome sequences of historical strains of Coxiella burnetii derived from
      cow's milk and the placenta of a goat that had aborted. The
      California and Ohio milk strains display a different sequence type than do
      contemporary milk strains.
AU  - Beare PA
AU  - Jeffrey BM
AU  - Martens CA
AU  - Pearson T
AU  - Heinzen RA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00985-17.

PMID- 9401036
VI  - 179
DP  - 1997
TI  - Evidence of participation of McrBs in McrBC restriction in Escherichia coli K-12.
PG  - 7768-7775
AB  - The McrBC restriction system has the ability to restrict DNA containing
      5-hydroxymethylcytosine, N4-methylcytosine, and 5-methylcytosine at specific sequences.  The
      mcrB gene produces two gene products.  The complete mcrB open reading frame produces a 51-kDa
      protein (McrBL) and a 33-kDa protein (McrBS).  The smaller McrB polypeptide is produced from
      an in-frame, internal translational start site in the mcrB gene.  The McrBs is unknown,
      although there has been speculation that it plays some role in the modulation of McrBC
      restriction.  Studies of the function of McrBs have been challenging since it is produced in
      frame with McrBL.  In this study, we tested the effects of underproduction (via antisense RNA)
      and overproduction (via gene dosage) of mcrBC gene products on restriction levels of the
      mcrBC+ strain JM107.  Among the parameters monitoredwas the induction of SOS responses, which
      indicate DNA damage.  Evidence from this study suggests that McrBS is necessary for
      stabilization of the McrBC restriction complex in vivo.
AU  - Beary TP
AU  - Braymer HD
AU  - Achberger EC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1997 179: 7768-7775.

PMID- Not carried by PubMed...
VI  - 89
DP  - 1989
TI  - Characterization of genes involved in the McrB restriction system of Escherichia coli K12.
PG  - 180
AB  - The McrB system of E. coli K12 restricts DNA modified at the sequence 'GmC'.
      Two of the genes involved in the restriction of 5-methylcytosine
      (5mC)-containing DNA are mcrB and mcrC.  The nucleic acid sequences of these
      genes were used to predict open reading frames encoding peptides consistent
      with the 51-kilodalton (kDa) mcrB gene product and the 39-kDa mcrC gene
      product.  Based on the nucleotide sequence and the analysis of frameshift
      mutations within the mcrB gene, an internal, in phase translational start was
      identified specifying a peptide of 33 kDa.  It has been shown that the genetic
      components required for the restriction of DNA containing 5mC are different
      than those for the restriction of nonglucosylated hydroxymethylcytosine
      (hmC)-containing T4 phage DNA.  The possible involvement of the 33-kDa peptide
      in the control of the 5mC-specific and hmC-specific activities was examined.
      We found evidence for genetic elements downstream of the mcrC gene that
      influence the restriction of DNA containing modified cytosine residues.
AU  - Beary TP
AU  - Ross TK
AU  - Braymer HD
AU  - Achberger EC
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1989 89: 180.

PMID- 25667270
VI  - 83
DP  - 2015
TI  - Molecular analysis of the asymptomatic bacteriuria Escherichia coli strain VR50 reveals adaptation to the urinary tract by gene acquisition.
PG  - 1749-1764
AB  - Urinary tract infections (UTIs) are among the most common infectious diseases of
      humans, with Escherichia coli responsible for >80% of all cases. One extreme of
      UTI is asymptomatic bacteriuria (ABU), which occurs as an asymptomatic carrier
      state that resembles commensalism. To understand the evolution and molecular
      mechanisms that underpin ABU, the genome of the ABU E. coli strain VR50 was
      sequenced. Analysis of the complete genome indicated that it most resembles E.
      coli K-12, with the addition of a 94-kb genomic island (GI-VR50-pheV), eight
      prophages, and multiple plasmids. GI-VR50-pheV has a mosaic structure and
      contains genes encoding a number of UTI-associated virulence factors, namely, Afa
      (afimbrial adhesin), two autotransporter proteins (Ag43 and Sat), and aerobactin.
      We demonstrated that the presence of this island in VR50 confers its ability to
      colonize the murine bladder, as a VR50 mutant with GI-VR50-pheV deleted was
      attenuated in a mouse model of UTI in vivo. We established that Afa is the
      island-encoded factor responsible for this phenotype using two independent
      deletion (Afa operon and AfaE adhesin) mutants. E. coli VR50afa and VR50afaE
      displayed significantly decreased ability to adhere to human bladder epithelial
      cells. In the mouse model of UTI, VR50afa and VR50afaE displayed reduced bladder
      colonization compared to wild-type VR50, similar to the colonization level of the
      GI-VR50-pheV mutant. Our study suggests that E. coli VR50 is a commensal-like
      strain that has acquired fitness factors that facilitate colonization of the
      human bladder.
AU  - Beatson SA et al
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2015 83: 1749-1764.

PMID- 21183677
VI  - 193
DP  - 2010
TI  - Genome sequence of the emerging pathogen Aeromonas caviae.
PG  - 1286-1287
AB  - Aeromonas caviae is a Gram-negative, motile and rod-shaped facultative anaerobe that is
      increasingly being recognised as a cause of diarrhea in  children. Here we present the first
      genome sequence of an A. caviae strain  which was isolated as the sole pathogen from a child
      with profuse diarrhea.
AU  - Beatson SA
AU  - Das-Gracas-de-Luna M
AU  - Bachmann NL
AU  - Alikhanm NF
AU  - Hanksm KR
AU  - Sullivanm MJ
AU  - Weem BA
AU  - Freitas-Almeida AC
AU  - Dos Santos PA
AU  - de Melo JT
AU  - Squire DJ
AU  - Cunningham AF
AU  - Fitzgerald JR
AU  - Henderson IR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 193: 1286-1287.

PMID- 6288662
VI  - 152
DP  - 1982
TI  - Action of restriction endonucleases on transforming DNA of Haemophilus influenzae.
PG  - 332-337
AB  - Cleavage of DNA from Haemophilus influenzae with restriction endonucleases
      caused inactivation of transforming ability to an extent that depended on the
      genetic marker and the enzyme.  The rate of inactivation, but not the final
      level of survival, depended on the concentration of enzyme in the restriction
      digest.  In general, the greatest extent of inactivation of transforming
      activity was obtained with endonucleases that are known to produce the shortest
      fragments.  We electrophoresed restriction digests of H. influenzae DNA in
      agarose gels and assayed transforming activity of DNA extracted from gel
      slices.  In this way, we determined the lengths of restriction fragments that
      contain genetic markers of H. influenzae.  For the marker that we studied most
      thoroughly (nov), the shortest restriction fragment that possessed detectable
      transforming activity was a 0.9-kilobase pair fragment produced by endonuclease
      R - PstI.  The shortest marker-bearing restriction fragment that retained
      substantial transforming activity (50% of value for undigested DNA) was a
      2.1-kilobase pair EcoRI fragment bearing the kan marker.  Among marker-bearing
      restriction fragments 1 to 4 kilobase pairs in length, survival of transforming
      activity varied 10,000-fold.  We relate these observations to the recent
      finding by Sisco and Smith (Proc. Natl. Acad. Sci. USA 76: 972-976, 1979) that
      efficient entry of DNA into competent H. influenzae cells appears to require
      the presence of a recognition sequence that is scattered throughout the
      Haemophilus genome in many more copies than in unrelated genomes.
AU  - Beattie KL
AU  - Wakil AE
AU  - Driggers PH
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1982 152: 332-337.

PMID- 6286418
VI  - 18
DP  - 1982
TI  - BvuI: a site-specific endonuclease from Bacillus vulgatis.
PG  - 61-67
AB  - A site-specific endodeoxyribonuclease was partially purified from an extract of
      osmotically shocked spheroplasts of a Bacillus vulgatis strain; the enzyme has
      been designated BvuI and its activity was characterized.  The locations of
      BvuI-generated cleavages on bacteriophage lambda and M13 derivatives mp7, mp8
      and mp9, SV40 and pBR322 DNA molecules were determined.  BvuI was shown to
      recognize the DNA sequence	5'-G-Pu-G-C-Py-^C-3'	3'-C-^Py-C-G-Pu-G-5'and cleaves
      it at the positions indicated by arrows.  Two identical BvuI recognition sites
      separated by fourteen nucleotide pairs were shown to occur within the
      tetracycline resistance gene of pBR322; BvuI should be used for molecular
      cloning in that plasmid vector.
AU  - Beaty JS
AU  - Mclean-Bowen CA
AU  - Brown LR
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1982 18: 61-67.

PMID- 28855338
VI  - 114
DP  - 2017
TI  - Methylation-dependent DNA discrimination in natural transformation of Campylobacter jejuni.
PG  - E8053-E8061
AB  - Campylobacter jejuni, a leading cause of bacterial gastroenteritis, is naturally  competent.
      Like many competent organisms, C. jejuni restricts the DNA that can be
      used for transformation to minimize undesirable changes in the chromosome.
      Although C. jejuni can be transformed by C. jejuni-derived DNA, it is poorly
      transformed by the same DNA propagated in Escherichia coli or produced with PCR.
      Our work indicates that methylation plays an important role in marking DNA for
      transformation. We have identified a highly conserved DNA methyltransferase,
      which we term Campylobacter transformation system methyltransferase (ctsM), which
      methylates an overrepresented 6-bp sequence in the chromosome. DNA derived from a
      ctsM mutant transforms C. jejuni significantly less well than DNA derived from
      ctsM+ (parental) cells. The ctsM mutation itself does not affect transformation
      efficiency when parental DNA is used, suggesting that CtsM is important for
      marking transforming DNA, but not for transformation itself. The mutant has no
      growth defect, arguing against ongoing restriction of its own DNA. We further
      show that E. coli plasmid and PCR-derived DNA can efficiently transform C. jejuni
      when only a subset of the CtsM sites are methylated in vitro. A single
      methylation event 1 kb upstream of the DNA involved in homologous recombination
      is sufficient to transform C. jejuni, whereas otherwise identical unmethylated
      DNA is not. Methylation influences DNA uptake, with a slight effect also seen on
      DNA binding. This mechanism of DNA discrimination in C. jejuni is distinct from
      the DNA discrimination described in other competent bacteria.
AU  - Beauchamp JM
AU  - Leveque RM
AU  - Dawid S
AU  - DiRita VJ
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2017 114: E8053-E8061.

PMID- 26074426
VI  - 6
DP  - 2015
TI  - Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes.
PG  - 7438
AB  - Beyond its role in host defense, bacterial DNA methylation also plays important roles in the
      regulation of gene expression, virulence and antibiotic resistance.
      Bacterial cells in a clonal population can generate epigenetic heterogeneity to
      increase population-level phenotypic plasticity. Single molecule, real-time
      (SMRT) sequencing enables the detection of N6-methyladenine and
      N4-methylcytosine, two major types of DNA modifications comprising the bacterial
      methylome. However, existing SMRT sequencing-based methods for studying bacterial
      methylomes rely on a population-level consensus that lacks the single-cell
      resolution required to observe epigenetic heterogeneity. Here, we present SMALR
      (single-molecule modification analysis of long reads), a novel framework for
      single molecule-level detection and phasing of DNA methylation. Using seven
      bacterial strains, we show that SMALR yields significantly improved resolution
      and reveals distinct types of epigenetic heterogeneity. SMALR is a powerful new
      tool that enables de novo detection of epigenetic heterogeneity and empowers
      investigation of its functions in bacterial populations.
AU  - Beaulaurier J
AU  - Zhang XS
AU  - Zhu S
AU  - Sebra R
AU  - Rosenbluh C
AU  - Deikus G
AU  - Shen N
AU  - Munera D
AU  - Waldor MK
AU  - Chess A
AU  - Blaser MJ
AU  - Schadt EE
AU  - Fang G
PT  - Journal Article
TA  - Nat. Commun.
JT  - Nat. Commun.
SO  - Nat. Commun. 2015 6: 7438.

PMID- 29227468
VI  - 36
DP  - 2017
TI  - Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation.
PG  - 61-69
AB  - Shotgun metagenomics methods enable characterization of microbial communities in  human
      microbiome and environmental samples. Assembly of metagenome sequences does not output whole
      genomes, so computational binning methods have been developed to cluster sequences into genome
      'bins'. These methods exploit sequence composition, species abundance, or chromosome
      organization but cannot fully distinguish closely related species and strains. We present a
      binning method that incorporates bacterial DNA methylation signatures, which are detected
      using single-molecule real-time sequencing. Our method takes advantage of these endogenous
      epigenetic barcodes to resolve individual reads and assembled contigs into species- and
      strain-level bins. We validate our method using synthetic and real microbiome sequences. In
      addition to genome binning, we show that our method links plasmids and other mobile genetic
      elements to their host species in a real microbiome sample. Incorporation of DNA methylation
      information into shotgun metagenomics analyses will complement existing methods to enable more
      accurate sequence binning.
AU  - Beaulaurier J
AU  - Zhu S
AU  - Deikus G
AU  - Mogno I
AU  - Zhang XS
AU  - Davis-Richardson A
AU  - Canepa R
AU  - Triplett EW
AU  - Faith JJ
AU  - Sebra R
AU  - Schadt EE
AU  - Fang G
PT  - Journal Article
TA  - Nat. Biotechnol.
JT  - Nat. Biotechnol.
SO  - Nat. Biotechnol. 2017 36: 61-69.

PMID- 12015329
VI  - 277
DP  - 2002
TI  - An essential role for DNA methyltransferase DNMT3B in cancer cell survival.
PG  - 28176-28181
AB  - Abnormal methylation and associated silencing of tumor suppressor genes is a common feature of
      many types of cancers. The observation of persistent methylation in human cancer cells lacking
      the maintenance methyltransferase DNMT1 suggests the involvement of other DNA
      methyltransferases in gene silencing in cancer. To test this hypothesis, we have evaluated
      methylation and gene expression in cancer cells specifically depleted of DNMT3A or DNMT3B, de
      novo methyltransferases that are expressed in adult tissues. Here we have shown that depletion
      of DNMT3B, but not DNMT3A, induced apoptosis of human cancer cells but not normal cells.
      DNMT3B depletion reactivated methylation-silenced gene expression but did not induce global or
      juxtacentromeric satellite demethylation as did specific depletion of DNMT1. Furthermore, the
      effect of DNMT3B depletion was rescued by exogenous expression of either of the splice
      variants DNMT3B2 or DNMT3B3 but not DNMT1. These results indicate that DNMT3B has significant
      site selectivity that is distinct from DNMT1, regulates aberrant gene silencing, and is
      essential for cancer cell survival.
AU  - Beaulieu N
AU  - Morin S
AU  - Chute IC
AU  - Robert M-F
AU  - Nguyen H
AU  - MacLeod AR
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2002 277: 28176-28181.

PMID- 11551190
VI  - 40
DP  - 2001
TI  - How does a DNA interacting enzyme change its specificity during molecular evolution? A site-directed mutagenesis study at the DNA binding site of the DNA-(adenine-N(6))-methyltransferase EcoRV.
PG  - 10956-10965
AB  - The EcoRV DNA-(adenine-N6)-methyltransferase (MTase) recognizes GATATC sequences and modifies
      the first adenine residue within this site. Parts of its DNA interface show high sequence
      homology to DNA MTases of the dam family which recognize and modify GATC sequences. A
      phylogenetic analysis of M.EcoRV and dam-MTases suggests that EcoRV arose in evolution from a
      primordial dam-MTase in agreement with the finding that M.EcoRV also methylates GATC sites
      albeit at a strongly reduced rate. GATCTC sites that deviate in only one position from the
      EcoRV sequence are preferred over general dam sites. We have investigated by site-directed
      mutagenesis the function of 17 conserved and nonconserved residues within three loops flanking
      the DNA binding cleft of M.EcoRV. M.EcoRV contacts the GATATC sequence with two highly
      cooperative recognition modules. The contacts to the GAT-part of the recognition sequence are
      formed by residues conserved between dam MTases and M.EcoRV. Mutations at these positions lead
      to an increase in the discrimination between GATATC and GATC substrates. Our data show that
      the change in sequence specificity from dam (GATC) to EcoRV (GATATC) was accompanied by the
      generation of a second recognition module that contacts the second half of the target
      sequence. The new DNA contacts are formed by residues from all three loops that are not
      conserved between M.EcoRV and dam MTases. Mutagenesis at important residues within this module
      leads to variants that show a decreased ability to recognize the TC-part of the GATATC
      sequence.
AU  - Beck C
AU  - Cranz S
AU  - Solmaz M
AU  - Roth M
AU  - Jeltsch A
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2001 40: 10956-10965.

PMID- 12450373
VI  - 41
DP  - 2002
TI  - Probing the DNA interface of the EcoRV DNA-(adenine-N6)-methyltransferase by site-directed mutagenesis, fluorescence spectroscopy, and UV cross-linking.
PG  - 14103-14110
AB  - The EcoRV DNA-(adenine-N6)-methyltransferase recognizes GATATC sites and methylates the DNA as
      indicated. It is related to the large family of dam methyltransferases which modify GATC
      sites. We have studied the interaction of DNA with M.EcoRV and 12 M.EcoRV variants using
      oligonucleotides containing 2-aminopurine as a fluorescence probe in equilibrium and
      stopped-flow DNA binding studies and 5-iododeoxyuracil for UV cross-linking. M.EcoRV binds to
      DNA in a multistep binding reaction, including two different conformations of the specific
      enzyme-DNA complex, and induces a strong conformational change of the DNA at the fourth
      position of the recognition site. Mutations at residues forming contacts to the GAT part of
      the recognition site reduce the stability of both specific enzyme-DNA complexes. Two enzyme
      variants which fail to recognize the ATC part do not induce the deformation of the DNA which
      explains why they cannot interact properly with the recognition site. Other mutations at
      residues which interact with the ATC part selectively reduce the stability of the second
      enzyme-DNA complex. These results show that when approaching the DNA M.EcoRV first contacts
      the GAT part of the target site. Since the residues mediating these contacts are conserved
      among M.EcoRV and dam MTases, the kinetics of formation of the enzyme-DNA complex correspond
      to the evolutionary history of the protein. Whether the observation that evolutionarily
      conserved contacts are formed early during complex formation is a general rule for DNA
      interacting enzymes or proteins that change their specificity during evolution remains to be
      seen.
AU  - Beck C
AU  - Jeltsch A
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2002 41: 14103-14110.

PMID- 26430034
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Strict Anaerobe Clostridium homopropionicum LuHBu1 (DSM 5847).
PG  - e01112-15
AB  - Here, we report the draft genome sequence of Clostridium homopropionicum LuHBu1 (DSM 5847(T)),
      a strictly anaerobic bacterium, which performs propionate fermentation and is capable of
      growing with 2-, 3-, or 4-hydroxybutyrate as its sole substrate. The genome consists of a
      single chromosome of 3.65 Mb.
AU  - Beck MH
AU  - Poehlein A
AU  - Bengelsdorf FR
AU  - Schiel-Bengelsdorf B
AU  - Daniel R
AU  - Durre P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01112-15.

PMID- 27081124
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the Strict Anaerobe Clostridium neopropionicum X4 (DSM 3847T).
PG  - e00209-16
AB  - Here, we report the draft genome sequence ofClostridium neopropionicumX4 (DSM 3847(T)), a
      strictly anaerobic bacterium capable of fermenting ethanol and CO2to
      propionate, acetate, and propanol. The genome consists of a single chromosome
      (3.19 Mb).
AU  - Beck MH
AU  - Poehlein A
AU  - Bengelsdorf FR
AU  - Schiel-Bengelsdorf B
AU  - Daniel R
AU  - Durre P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00209-16.

PMID- 8139933
VI  - 22
DP  - 1994
TI  - Introduction of arbitrary sequences into genes by use of class IIs restriction enzymes.
PG  - 886-887
AB  - Introduction of additional nucleotides or modification of sequences at locations where no
      convenient restriction endonuclease recognition site is available can be rather difficult,
      especially if one has to conserve a particular reading frame and new cleavage sites cannot
      simply be generated by taking advantage of the degeneracy of the genetic code. Overlap
      extension can be very useful, however it has some limitations in fragment length and it can
      take some time to find optimal conditions for a particular reaction. Using inverse primers to
      amplify small plasmids followed by blunt-end ligation also has some restrictions (e.g.
      amplification of a longer DNA sequence than necessary; use of polymerases with proof-reading
      activity). We wanted to insert a DNA sequence coding for four histidine residues and an
      enterokinase cleavage site between the signal sequence and the mature sequence of human
      placental alkaline phosphatase for purification. We added the enterokinase recognition site in
      order to allow regeneration of the authentic N-terminus of the enzyme. Here we describe a
      convenient way to achieve this, using class IIs restriction endonucleases. Class IIs
      restriction endonucleases cut DNA several nucleotides away from their recognition site
      irrespective of the interventing sequence. This can be exploited to generate arbitrary sticky
      ends for in-frame fusion of DNA sequences, combining two PCR reactions with a simple cloning
      step.
AU  - Beck R
AU  - Burtscher H
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1994 22: 886-887.

PMID- 26159529
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of a CTX-M-15-Producing Klebsiella pneumoniae Outbreak Strain from Multilocus Sequence Type 514.
PG  - e00742-15
AB  - We report here the genome sequence of a multidrug-resistant Klebsiella pneumoniae strain,
      which caused an outbreak in a neonatal ward in 2011. The genome consists
      of a single chromosome (5,278 kb) and three plasmids (362 kb, 5 kb, and 4 kb).
AU  - Becker L
AU  - Bunk B
AU  - Eller C
AU  - Steglich M
AU  - Pfeifer Y
AU  - Werner G
AU  - Nubel U
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00742-15.

PMID- 2842760
VI  - 85
DP  - 1988
TI  - Ultraviolet footprinting accurately maps sequence-specific contacts and DNA kinking in the EcoRI endonuclease-DNA complex.
PG  - 6247-6251
AB  - The UV footprinting technique has been used to detect contacts between EcoRI
      endonuclease and its recognition sequence at single nucleotide resolution.
      Comparison of the UV-footprinting results to the published crystal structure of
      the EcoRI endonuclease-DNA complex allows us to determine how UV light detects
      protein-DNA contacts.  We find that kinking of the DNA helix in the complex
      greatly enhances the UV photoreactivity of DNA at the site of the kink.  In
      contrast to kinking, contacts between the endonuclease and the DNA bases
      inhibit the UV photoreactivity of DNA.  Similar analysis of a proteolytically
      modified endonuclease that exhibits the same sequence specificity as wild-type
      enzyme but that does not cleave DNA supports these conclusions.  Furthermore,
      detection of enhanced photoreactivity at the same kink in the modified
      enzyme-DNA complex allows us to conclude that the loss of cleavage activity by
      the modified endonuclease is not due to its failure to kink DNA.
AU  - Becker MM
AU  - Lesser D
AU  - Kurpiewski M
AU  - Baranger A
AU  - Jen-Jacobson L
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1988 85: 6247-6251.

PMID- 7642495
VI  - 177
DP  - 1995
TI  - Two genes involved in the phase-variable phi C31 resistance mechanism of Streptomyces coelicolor A3(2).
PG  - 4681-4689
AB  - The phage growth limitation (Pgl) system of Streptomyces coelicolor confers resistance to phi
      C31 and its homoimmune phages. The positions of the pgl genes
      within a 16-kb clone of S. coelicolor DNA were defined by subcloning, insertional
      inactivation, and deletion mapping. Nucleotide sequencing and functional analysis
      identified two genes, pglY and pglZ, required for the Pgl+ (phage-resistant)
      phenotype. pglY and pglZ, which may be translationally coupled, are predicted to
      encode proteins with M(r)S of 141,000 and 104,000, respectively. Neither protein
      shows significant similarity to other known proteins, but PglY has a putative
      ATP/GTP binding motif. The pglY and pglZ genes are cotranscribed from a single
      promoter which appears to be constitutive and is not induced by phage infection.
AU  - Bedford DJ
AU  - Laity C
AU  - Buttner MJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1995 177: 4681-4689.

PMID- 1369142
VI  - 38
DP  - 1992
TI  - Continuous production of restriction endonucleases: continuous two-stage cultivation with E. coli JM103; continuous cell disintegration and purification by affinity chromatography.
PG  - 220-225
AB  - The optimization of the production of recombinant DNA-derived proteins in Escherichia coli was
      investigated. We chose restriction endonucleases EcoRI and EcoRV from E. coli as model
      proteins, despite the observation that overproduction can result in a toxic effect to the
      cells. The enzymes were expressed as fusion proteins consisting of protein A from
      Staphylococcus aureus and the desired enzymes in order to facilitate purification. The
      expression of the fusion protein was induced by a temperature shift using the PR promoter of
      phage lambda regulated by the repressor plasmid pRK248cI. Data from batch fermentations
      provided the basis for planning a continuous two-stage fermentation. The EcoRI enzyme activity
      was investigated as a function of the induction time after cell disintegration and allowed an
      estimation of yield of the continuous culture. Plasmid instability, which was only observed
      under continuous conditions, could be prevented by adding tetracycline (resistance of the
      repressor plasmid) to the medium. We established a continuous cell disintegration system and
      purified the fusion protein semicontinuously by affinity chromatography. The biological
      activity of the fusion protein was the same as the native endonuclease so there was no need
      for cleavage of the fusion protein and the product could be used without further processing.
AU  - Beer HD
AU  - Maschke HE
AU  - Schugerl K
PT  - Journal Article
TA  - Appl. Microbiol. Biotechnol.
JT  - Appl. Microbiol. Biotechnol.
SO  - Appl. Microbiol. Biotechnol. 1992 38: 220-225.

PMID- 10325404
VI  - 12
DP  - 1999
TI  - Methanobacterium thermoformicicum thymine DNA mismatch glycosylase: conversion of an N-glycosylase to an AP lyase.
PG  - 333-340
AB  - The thymine DNA mismatch glycosylase from Methanobacterium thermoformicicum, a member of the
      endonuclease III family of repair proteins, excises the pyrimidine base from T-G and U-G
      mismatches. Unlike endonuclease III, it does not cleave the phosphodiester backbone by a
      beta-elimination reaction. This cleavage event has been attributed to a nucleophilic attack by
      the conserved Lys120 of endonuclease III on the aldehyde group at C1' of the deoxyribose and
      subsequent Schiff base formation. The inability of TDG to perform this beta-elimination event
      appears to be due to the presence of a tyrosine residue at the position equivalent to Lys120
      in endonuclease III. The purpose of this work was to investigate the requirements for AP lyase
      activity. We replaced Tyr126 in TDG with a lysine residue to determine if this replacement
      would yield an enzyme with an associated AP lyase activity capable of removing a mismatched
      pyrimidine. We observed that this replacement abolishes the glycosylase activity of TDG but
      does not affect substrate recognition. It does, however, convert the enzyme into an AP lyase.
      Chemical trapping assays show that this cleavage proceeds through a Schiff base intermediate
      and suggest that the amino acid at position 126 interacts with C1' on the deoxyribose sugar.
AU  - Begley TJ
AU  - Cunningham RP
PT  - Journal Article
TA  - Protein Eng.
JT  - Protein Eng.
SO  - Protein Eng. 1999 12: 333-340.

PMID- 12509271
VI  - 2
DP  - 2003
TI  - Kinetics and binding of the tymine-DNA mismatch glycosylase, Mig-Mth, with mismatch-containing DNA substrates.
PG  - 107-120
AB  - We have examined the removal of thymine residues from T-G mismatches in DNA by the thymine-DNA
      mismatch glycosylase from Methanobacterium thermoautrophicum (Mig-Mth), within the context of
      the base excision repair (BER) pathway, to investigate why this glycosylase has such low
      activity in vitro. Using single-turnover kinetics and steady-state kinetics, we calculated the
      catalytic and product dissociation rate constants for Mig-Mth, and determined that Mig-Mth is
      inhibited by product apyrimidinic (AP) sites in DNA. Electrophoretic mobility shift assays
      (EMSA) provide evidence that the specificity of product binding is dependent upon the base
      opposite the AP site. The binding of Mig-Mth to DNA containing the non-cleavable substrate
      analogue difluorotoluene (F) was also analyzed to determine the effect of the opposite base on
      Mig-Mth binding specificity for substrate-like duplex DNA. The results of these experiments
      support the idea that opposite strand interactions play roles in determining substrate
      specificity. Endonuclease IV, which cleaves AP sites in the next step of the BER pathway, was
      used to analyze the effect of product removal on the overall rate of thymine hydrolysis by
      Mig-Mth. Our results support the hypothesis that endonuclease IV increases the apparent
      activity of Mig-Mth significantly under steady-state conditions by preventing reassociation of
      enzyme to product.
AU  - Begley TJ
AU  - Haas BJ
AU  - Morales JC
AU  - Kool ET
AU  - Cunningham RP
PT  - Journal Article
TA  - DNA Repair
JT  - DNA Repair
SO  - DNA Repair 2003 2: 107-120.

PMID- 20139311
VI  - 76
DP  - 2010
TI  - Rickettsia felis infection in a common household insect pest, Liposcelis bostrychophila (Psocoptera: Liposcelidae).
PG  - 2280-2285
AB  - Many species of Rickettsia are well-known mammalian pathogens transmitted
      by blood-feeding arthropods. However, molecular surveys are continually
      uncovering novel Rickettsia species, often in unexpected hosts, including
      many arthropods that do not feed on blood. This study reports a systematic
      molecular characterization of a Rickettsia infecting the psocid Liposcelis
      bostrychophila (Psocoptera: Liposcelidae), a common and cosmopolitan
      household pest. Surprisingly, the psocid Rickettsia is shown to be
      Rickettsia felis, a human pathogen transmitted by fleas that causes
      serious morbidity and occasional mortality. The plasmid from the psocid R.
      felis was sequenced and was found to be virtually identical to the one in
      R. felis from fleas. As Liposcelis insects are often intimately associated
      with humans and other vertebrates, it is speculated that they acquired R.
      felis from fleas. Whether the R. felis in psocids causes disease in
      vertebrates is not known and warrants further study.
AU  - Behar A
AU  - McCormick LJ
AU  - Perlman SJ
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2010 76: 2280-2285.

PMID- 25573926
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Extremely Halophilic Bacterium Halomonas salina Strain CIFRI1, Isolated from the East Coast of India.
PG  - e01321-14
AB  - Halomonas salina strain CIFRI1 is an extremely salt-stress-tolerant bacterium isolated from
      the salt crystals of the east coast of India. Here we report the
      annotated 3.45-Mb draft genome sequence of strain CIFRI1 having 86 contigs with
      3,139 protein coding loci, including 62 RNA genes.
AU  - Behera BK
AU  - Das P
AU  - Maharana J
AU  - Paria P
AU  - Mandal SN
AU  - Meena DK
AU  - Sharma AP
AU  - Jayarajan R
AU  - Dixit V
AU  - Verma A
AU  - Vellarikkal SK
AU  - Scaria V
AU  - Sivasubbu S
AU  - Rao AR
AU  - Mohapatra T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01321-14.

PMID- 27028007
VI  - 11
DP  - 2016
TI  - The Identification of Novel Diagnostic Marker Genes for the Detection of Beer Spoiling Pediococcus damnosus Strains Using the BlAst Diagnostic Gene findEr.
PG  - E0152747
AB  - As the number of bacterial genomes increases dramatically, the demand for easy to
      use tools with transparent functionality and comprehensible output for applied
      comparative genomics grows as well. We present BlAst Diagnostic Gene findEr
      (BADGE), a tool for the rapid prediction of diagnostic marker genes (DMGs) for
      the differentiation of bacterial groups (e.g. pathogenic / nonpathogenic). DMG
      identification settings can be modified easily and installing and running BADGE
      does not require specific bioinformatics skills. During the BADGE run the user is
      informed step by step about the DMG finding process, thus making it easy to
      evaluate the impact of chosen settings and options. On the basis of an example
      with relevance for beer brewing, being one of the oldest biotechnological
      processes known, we show a straightforward procedure, from phenotyping, genome
      sequencing, assembly and annotation, up to a discriminant marker gene PCR assay,
      making comparative genomics a means to an end. The value and the functionality of
      BADGE were thoroughly examined, resulting in the successful identification and
      validation of an outstanding novel DMG (fabZ) for the discrimination of harmless
      and harmful contaminations of Pediococcus damnosus, which can be applied for
      spoilage risk determination in breweries. Concomitantly, we present and compare
      five complete P. damnosus genomes sequenced in this study, finding that the
      ability to produce the unwanted, spoilage associated off-flavor diacetyl is a
      plasmid encoded trait in this important beer spoiling species.
AU  - Behr J
AU  - Geissler AJ
AU  - Schmid J
AU  - Zehe A
AU  - Vogel RF
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2016 11: E0152747.

PMID- 3109889
VI  - 6
DP  - 1987
TI  - Organization of multispecific DNA methyltransferases encoded by temperate Bacillus subtilis phages.
PG  - 1137-1142
AB  - B. subtilis phage Rho11s codes for a multispecific DNA methyltransferase
      (Mtase) which methylates cytosine within the sequences GGCC and GAGCTC.  The
      Mtase gene of Rho11s was isolated and sequenced.  It has 1509 bp, corresponding
      to 503 amino acids (aa).  The enzyme's Mr of 57.2 kd predicted from the
      nucleotide sequence was verified by direct Mr determinations of the Mtase.  A
      comparison of the aa sequence of the Rho11s Mtase with those of related phages
      SPR and Phi3T, which differ in their methylation potential, revealed
      generalities in the building plan of such enzymes.  At least 70% of the aa of
      each enzyme are contained in two regions of 243 and 109 aa at the N and C
      termini respectively, which are highly conserved among the three enzymes.  In
      each enzyme, variable sequences separate the conserved regions.  Variability is
      generated through the single or multiple use of related and unrelated sequence
      motifs.  We propose that the recognition of those DNA target sequences, which
      are unique for each of the three enzymes, is determined by these variable
      regions.  Evolutionary relationships between the three enzymes are discussed.
AU  - Behrens B
AU  - Noyer-Weidner M
AU  - Pawlek B
AU  - Lauster R
AU  - Balganesh TS
AU  - Trautner TA
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1987 6: 1137-1142.

PMID- Not included in PubMed...
VI  - 189
DP  - 1983
TI  - Restriction and modification in Bacillus subtilis:  construction of hybrid lambda and SPP1 phages containing a DNA methyltransferase gene from B. subtilis phage SPR.
PG  - 10-16
AB  - The gene of B. subtilis phage SPR, specifying DNA methyltransferase activity
      was identified within a 3.1 Md EcoRI fragment of SPR DNA.  This fragment was
      cloned in E. coli using a lambda insertion vector.  A 1.25 Md PstI fragment
      with this gene was subsequently derived from the lambda/SPR hybrid phage and
      subcloned in B. subtilis using a new SPP1 vector, whose construction is
      described.
AU  - Behrens B
AU  - Pawlek B
AU  - Morelli G
AU  - Trautner TA
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1983 189: 10-16.

PMID- 22740658
VI  - 194
DP  - 2012
TI  - Genome Sequence of Helicobacter pylori hpEurope Strain N6.
PG  - 3725-3726
AB  - Helicobacter pylori colonizes about half of the world's population. It is a causative agent
      of stomach diseases, including malignant tumors. We report the
      genome sequence of strain N6, which is widely used in H. pylori research and
      appreciated for its large cell size and high transformation efficiency.
AU  - Behrens W
AU  - Bonig T
AU  - Suerbaum S
AU  - Josenhans C
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3725-3726.

PMID- 10988064
VI  - 289
DP  - 2000
TI  - Bacterial rhodopsin: evidence for a new type of phototrophy in the sea.
PG  - 1902-1906
AB  - Extremely halophilic archaea contain retinal-binding integral membrane
      proteins called bacteriorhodopsins that function as light-driven proton
      pumps. So far, bacteriorhodopsins capable of generating a chemiosmotic
      membrane potential in response to light have been demonstrated only in
      halophilic archaea. We describe here a type of rhodopsin derived from
      bacteria that was discovered through genomic analyses of naturally
      occuring marine bacterioplankton. The bacterial rhodopsin was encoded in
      the genome of an uncultivated gamma-proteobacterium and shared highest
      amino acid sequence similarity with archaeal rhodopsins. The protein was
      functionally expressed in Escherichia coli and bound retinal to form an
      active, light-driven proton pump. The new rhodopsin exhibited a
      photochemical reaction cycle with intermediates and kinetics
      characteristic of archaeal proton-pumping rhodopsins. Our results
      demonstrate that archaeal-like rhodopsins are broadly distributed among
      different taxa, including members of the domain Bacteria. Our data also
      indicate that a previously unsuspected mode of bacterially mediated
      light-driven energy generation may commonly occur in oceanic surface
      waters worldwide.
AU  - Beja O
AU  - Aravind L
AU  - Koonin EV
AU  - Suzuki MT
AU  - Hadd A
AU  - Nguyen LP
AU  - Jovanovich SB
AU  - Gates CM
AU  - Feldman RA
AU  - Spudich JL
AU  - Spudich EN
AU  - DeLong EF
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2000 289: 1902-1906.

PMID- 26430054
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of a Necrotoxigenic Escherichia coli Isolate.
PG  - e01152-15
AB  - Here, we present the draft genome sequence of a necrotoxigenic Escherichia coli strain
      isolated from a patient following a very rapidly evolving, lethal necrotizing fasciitis.
AU  - Bekal S
AU  - Lin A
AU  - Vincent A
AU  - Berry C
AU  - Gilmour M
AU  - Fournier E
AU  - Cote JC
AU  - Tremblay C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01152-15.

PMID- 29997583
VI  - 9
DP  - 2018
TI  - Integrative and Conjugative Elements (ICEs) in Pasteurellaceae Species and Their  Detection by Multiplex PCR.
PG  - 1329
AB  - Strains of the Pasteurellaceae bacteria Pasteurella multocida and Mannheimia haemolytica are
      major etiological agents of bovine respiratory disease (BRD).
      Treatment of BRD with antimicrobials is becoming more challenging due to the
      increasing occurrence of resistance in infecting strains. In Pasteurellaceae
      strains exhibiting resistance to multiple antimicrobials including
      aminoglycosides, beta-lactams, macrolides and sulfonamides, the resistance
      determinants are often chromosomally encoded within integrative and conjugative
      elements (ICEs). To gain a more comprehensive picture of ICE structures, we
      sequenced the genomes of six strains of P. multocida and four strains of M.
      haemolytica; all strains were independent isolates and eight of them were
      multiple-resistant. ICE sequences varied in size from 49 to 79 kb, and were
      comprised of an array of conserved genes within a core region and varieties of
      resistance genes within accessory regions. These latter regions mainly account
      for the variation in the overall ICE sizes. From the sequence data, we developed
      a multiplex PCR assay targeting four conserved core genes required for
      integration and maintenance of ICE structures. Application of this assay on 75
      isolates of P. multocida and M. haemolytica reveals how the presence and
      structures of ICEs are related to their antibiotic resistance phenotypes. The
      assay is also applicable to other members of the Pasteurellaceae family including
      Histophilus somni and indicates how clustering and dissemination of the
      resistance genes came about.
AU  - Beker M
AU  - Rose S
AU  - Lykkebo CA
AU  - Douthwaite S
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2018 9: 1329.

PMID- 25477406
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Streptomyces fradiae ATCC 19609, a Strain Highly Sensitive to Antibiotics.
PG  - e01247-14
AB  - We report here a sequence of the genome of the Streptomyces fradiae ATCC 19609 strain,
      initially isolated from the soil, which produces tylosin. S. fradiae is
      highly sensitive to different classes of antibiotics, compared to the
      sensitivities of other bacteria. We have identified 9 groups of genes directly or
      indirectly involved in the resistome formation.
AU  - Bekker OB
AU  - Klimina KM
AU  - Vatlin AA
AU  - Zakharevich NV
AU  - Kasianov AS
AU  - Danilenko VN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01247-14.

PMID- 2835759
VI  - 24
DP  - 1988
TI  - A simple technique for detection of restriction endonucleases in bacterial colonies.
PG  - 121-124
AB  - A simple technique is proposed for detection of bacterial restriction
      endonucleases.  Analysis is performed directly in the cells from colonies
      cultivated on Petri dishes.  The cells collected with an inoculation loop are
      treated with lysozyme and Triton X-100.  After centrifugation the supernatant
      is tested for endonuclease activity.  The technique enables up to 100 colonies
      to be tested in 3-4 hr.
AU  - Belavin PA
AU  - Dedkov VS
AU  - Degtyarev SK
PT  - Journal Article
TA  - Prikl. Biokhim. Mikrobiol.
JT  - Prikl. Biokhim. Mikrobiol.
SO  - Prikl. Biokhim. Mikrobiol. 1988 24: 121-124.

PMID- 2742622
VI  - 15
DP  - 1989
TI  - Substrate specificity of DNA methylase from Flavobacterium okeanokoites.
PG  - 417-418
AB  - The specificity of DNA methylase M.FokI towards oligonucleotides containing the
      sequence 5' GGATG was investigated, and N6-methyladenine in the GGATG chain was
      shown to be the only product of the modification.
AU  - Belavin PA
AU  - Gorbunov YA
AU  - Malygin EG
AU  - Rechkunova NI
AU  - Degtyarev SK
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1989 15: 417-418.

PMID- 26679577
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Aneurinibacillus migulanus E1, a Gramicidin S- and d-Phenylalanyl-l-Propyl Diketopiperazine-Deficient Mutant.
PG  - e01441-15
AB  - We report here the complete genome sequence of the Aneurinibacillus migulanus E1  mutant
      deficient in gramicidin S (GS) and d-phenylalanyl-l-propyl
      diketopiperazine (DKP) formation. The genome consists of a circular chromosome
      (6,301,904 bp, 43.20% G+C content) without any plasmid. The complete genome
      sequence enables further investigation of the biosynthetic mechanism and the
      biological function of gramicidin S.
AU  - Belbahri L
AU  - Alenezi FN
AU  - Luptakova L
AU  - Rateb ME
AU  - Woodward S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01441-15.

PMID- 26067955
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Burkholderia cepacia Strain LO6.
PG  - e00587-15
AB  - Burkholderia cepacia strain LO6 is a betaproteobacterium that was isolated from a cystic
      fibrosis patient. Here we report the 6.4 Mb draft genome sequence
      assembled into 2 contigs. This genome sequence will aid the transcriptomic
      profiling of this bacterium and help us to better understand the mechanisms
      specific to pulmonary infections.
AU  - Belcaid M
AU  - Kang Y
AU  - Tuanyok A
AU  - Hoang TT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00587-15.

PMID- 26413199
VI  - 10
DP  - 2015
TI  - Genome sequence of Anoxybacillus ayderensis AB04(T) isolated from the Ayder hot spring in Turkey.
PG  - 70
AB  - Species of Anoxybacillus are thermophiles and, therefore, their enzymes are suitable for many
      biotechnological applications. Anoxybacillus ayderensis AB04(T)
      (= NCIMB 13972(T) = NCCB 100050(T)) was isolated from the Ayder hot spring in
      Rize, Turkey, and is one of the earliest described Anoxybacillus type strains.
      The present work reports the cellular features of A. ayderensis AB04(T), together
      with a high-quality draft genome sequence and its annotation. The genome is
      2,832,347 bp long (74 contigs) and contains 2,895 protein-coding sequences and
      103 RNA genes including 14 rRNAs, 88 tRNAs, and 1 tmRNA. Based on the genome
      annotation of strain AB04(T), we identified genes encoding various glycoside
      hydrolases that are important for carbohydrate-related industries, which we
      compared with those of other, sequenced Anoxybacillus spp. Insights into
      under-explored industrially applicable enzymes and the possible applications of
      strain AB04(T) were also described.
AU  - Belduz AO
AU  - Canakci S
AU  - Chan KG
AU  - Kahar UM
AU  - Chan CS
AU  - Yaakop AS
AU  - Goh KM
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 70.

PMID- 11000275
VI  - 28
DP  - 2000
TI  - DNA methylation at the CfrBI site is involved in expression control in the CfrBI restriction-modification system.
PG  - 3817-3822
AB  - We have previously found that genes of the CfrBI restriction-modification (R-M) system from
      Citrobacter freundii are oriented divergently and that their promoter regions overlap. The
      overlapping promoters suggest regulation of gene expression at the transcriptional level. In
      this study the transcription regulation of CfrBI R-M genes was analyzed in vivo and in vitro
      in Escherichia coli. It was shown that in the presence of CfrBI methyltransferase (M.CfrBI),
      cell galactokinase activity decreases 10-fold when the galactokinase gene (galK) is under the
      control of the cfrBIM promoter and increases 20-fold when galK is under the control of the
      cfrBIR promoter. The CfrBI site, proven to be unique for the entire CrfBI R-M gene sequence,
      is located in the -35 cfrBIM promoter region and is in close vicinity of the -10 cfrBIR
      promoter region. A comparison of the cfrBIM and the cfrBIR promoter activities in the in vitro
      transcription system using methylated and unmethylated DNA fragments as templates demonstrated
      that the efficiency of CfrBI R-M gene transcription is regulated by enzymatic modification at
      the N-4-position of cytosine bases of the CfrBI site by M.CfrBI.  From the results of the in
      vivo and in vitro experiments we suggest a new model of gene expression regulation in type II
      R-M systems.
AU  - Beletskaya IV
AU  - Zakharova MV
AU  - Shlyapnikov MG
AU  - Semenova LM
AU  - Solonin AS
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2000 28: 3817-3822.

PMID- 8943036
VI  - 93
DP  - 1996
TI  - Transcription-induced mutations: increase in C to T mutations in the nontranscribed strand during transcription in Escherichia coli.
PG  - 13919-13924
AB  - Cytosines in single-stranded DNA deaminate to uracils at 140 times the rate for cytosines in
      double-stranded DNA.  If resulting uracils are not replaced with cytosine, C to T mutations
      occur.  These facts suggest that cellular processes such as transcription that create
      single-stranded DNA should promote C to T mutations.  We tested this hypothesis with the
      Escherichia coli tac promoter and found that induction of transcription causes ~4-fold
      increase in the frequency of C to U or 5-methylcytosine to T deaminations in the
      nontranscribed strand.  Excess mutations caused by C to U deaminations were reduced, but not
      eliminated, by uracil-DNA glycosylase.  Similarly, mutations caused by 5-methylcytosine to T
      deaminations were only partially reduced by the very short-patch repair process in E. coli.
      These effects are unlikely to be caused by differential repair of the two strands, and our
      results suggest that all actively transcribed genes in E. coli should acquire more C to T
      mutations in the nontranscribed strand.
AU  - Beletskii A
AU  - Bhagwat AS
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1996 93: 13919-13924.

PMID- 
VI  - 16
DP  - 2005
TI  - Back to Basics: Structure, function, evolution and application of homing endonucleases and inteins.
PG  - 1-10
AB  - "It is a profound and necessary truth that the deep things in science are not found because
      they are useful; they are found because it was possible to find them." (Robert Oppenheimer,
      1904-1967).  Oppenheimer's words resonate with this book's theme, which is how both applied
      and theoretical science can emanate from answers to basic questions - whether they are being
      asked to model organisms or in test tubes - about molecular structure and mechanism.  Thus,
      fundamental work on DNA, RNA and proteins, which encode or constitute homing endonucleases and
      inteins, is leading to refined theories of evolution in prokaryotes and eukaryotes on the one
      hand, and the development of laboratory tools and health-care reagents on the other.  Homing
      endonucleases and inteins, sometimes referred to as "protein introns", are linked at many
      levels.  First, homing endonucleases are frequently encoded by introns that self-splice at the
      RNA level, in analogy to inteins that self-splice at the protein level. Second, homing
      endonucleases similar to those encoded by introns are often found embedded within and
      co-translated with inteins.  Third, both types of intervening sequence are mobile elements,
      capable of movement from genome to genome.  Fourth, the endonuclease component of both introns
      and inteins imparts their mobility.  Fifth, each of these mobile intervening sequences is
      thought to have originated from invasion of the gene encoding the self-splicing element, the
      intron or intein, by an endonuclease gene, the primordial mobile element.  The final unifying
      theme is the exploitation of introns, inteins and homing endonucleases by chemists,
      geneticists, structural biologists and engineers, to generate reagents and tools that are
      useful in basic research, biotechnology and medicine. This chapter serves as an introduction
      to the volume entitled Homing Endonucleases and Inteins, which provides a wonderful
      illustration of the point that fundamental studies of structure and mechanism fuel
      evolutionary theory and technology development alike.
AU  - Belfort M
PT  - Journal Article
TA  - Nucleic Acids Mol. Biol.
JT  - Nucleic Acids Mol. Biol.
SO  - Nucleic Acids Mol. Biol. 2005 16: 1-10.

PMID- 14665667
VI  - 17
DP  - 2003
TI  - Two for the price of one: a bifunctional intron-encoded DNA endonuclease-RNA maturase.
PG  - 2860-2863
AB  - Homing endonucleases are enzymes that are typically encoded by intervening sequences of
      various kinds -- introns that splice at the RNA level, or inteins that splice at the protein
      level.  The endonucleases function primarily to mobilize these elements, which are often
      self-splicing, by facilitating their integration to new sites in DNA.  Because these sites are
      most often allelic intronless or inteinless sites, this form of mobility is termed homing, and
      the target sequences are termed homing sites.  Homing endonucleases sometimes do double duty,
      also functioning as maturases, which promote RNA splicing.  Maturases are usually intron
      specific, and act as cofactors that bind their intron-containing precursor RNA to facilitate
      splicing.  Nevertheless, catalysis required for splicing remains a property of the RNA.
AU  - Belfort M
PT  - Journal Article
TA  - Genes Dev.
JT  - Genes Dev.
SO  - Genes Dev. 2003 17: 2860-2863.

PMID- 24510256
VI  - 1123
DP  - 2014
TI  - Homing Endonucleases: From Genetic Anomalies to Programmable Genomic Clippers.
PG  - 1-26
AB  - Homing endonucleases are strong drivers of genetic exchange and horizontal transfer of both
      their own genes and their local genetic environment. The mechanisms that govern the function
      and evolution of these genetic oddities have been well documented over the past few decades at
      the genetic, biochemical, and structural levels. This wealth of information has led to the
      manipulation and reprogramming of the endonucleases and to their exploitation in genome
      editing for use as therapeutic agents, for insect vector control and in agriculture. In this
      chapter we summarize the molecular properties of homing endonucleases and discuss their
      strengths and weaknesses in genome editing as compared to other site-specific nucleases such
      as zinc finger endonucleases, TALEN, and CRISPR-derived endonucleases.
AU  - Belfort M
AU  - Bonocora RP
PT  - Journal Article
TA  - Methods Mol. Biol.
JT  - Methods Mol. Biol.
SO  - Methods Mol. Biol. 2014 1123: 1-26.

PMID- 
VI  - 20
DP  - 2003
TI  - A multicomponent, multifunctional intron endonuclease, I-TevI.
PG  - 834-835
AB  - I-TevI is a homing endonuclease that is encoded by and promotes the mobility of the td intron
      of phage T4.  This 28-kD protein is remarkable in that it is site specific, yet recognizes a
      target site of ~37 bp in a sequence-tolerant fashion.  The enzyme consists of two functionally
      distinct domains, an N-terminal catalytic domain connected by a 75-amino acid linker.  What
      has previously been defined as the DNA-binding domain has an extended structure consisting of
      three distinct modules which contact ~20 bp of the homing site: A Zn finger, an alpha-helix
      and a small helix-turn-helix subdomain.  It is now known that the zinc finger is not required
      for DNA binding or catalysis, but rather is a spring-like component of the linker that directs
      the catalytic domain to cleave the homing site at a fixed distance from the intron insertion
      site.  In contrast, the catalytic domain, which contains the conserved GIY-YIG motif
      characteristic of this family of homing endonucleases, is a compactly folded structure.  It is
      provocative that there are similarities in the three-dimensional arrangement of the
      catalytically important residues and the cation-binding site with those of I-PpoI, a member of
      this His-Cys-box family of homing endonucleases.  These results suggest the possibility of
      mechanistic relationships among these different families of enzymes, but whether this
      represents convergent or divergent evolution is not known.  Regardless, the picture that has
      built is one of a catalytic GIY-YIG cartridge that has become associated with modules that
      direct DNA binding and distance measurement.  Surprisingly, the DNA-binding domain has
      recently been shown to interact with regulatory sequences upstream of the I-TevI gene, such
      that I-TevI acts as a repressor of its own synthesis.  Thus, I-TevI is a multicomponent,
      multifunctional molecule that has evolved site-specific cleavage and autorepression functions
      to maximize the invasiveness and persistence of its host intron.
AU  - Belfort M
AU  - Edgell D
AU  - Shub D
AU  - Van Roey P
AU  - Derbyshire V
PT  - Journal Article
TA  - J. Biomol. Struct. Dyn.
JT  - J. Biomol. Struct. Dyn.
SO  - J. Biomol. Struct. Dyn. 2003 20: 834-835.

PMID- 8530436
VI  - 270
DP  - 1995
TI  - Mechanisms of intron mobility.
PG  - 30237-30240
AB  - Group I and group II introns, which splice via RNA-catalyzed pathways, can invade DNA
      sequences by virtue of proteins expressed from open reading frames (ORFs) contained within
      them.  These intron products are endonucleases in the case of group I introns and reverse
      transcriptases (RTs) with associated endonuclease activity in the case of the group II
      introns.  Two kinds of mobility reactions will be considered for each intron type: homing into
      cognate intronless alleles and transposition to non-allelic sites.
AU  - Belfort M
AU  - Perlman PS
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1995 270: 30237-30240.

PMID- 7608058
VI  - 177
DP  - 1995
TI  - Prokaryotic introns and inteins: a panoply of form and function.
PG  - 3897-3903
AB  - Following their initial discovery, introns and RNA splicing were considered, along with the
      nuclear envelope, as characteristics that distinguish eukaryotes from prokaryotes (the
      eubacteria, referred to simply as bacteria, and the archaebacteria, referred to as archaea).
      This dogma became shaky with the identification of putative introns in tRNA genes of archaea
      and finally crumbled with the discovery of self-splicing group I introns in the phages of
      purple bacteria, which was followed by the discovery of group I and group II introns in
      bacterial cells. Another breakthrough was the recent discovery of a nuclear pre-mRNA-like
      intron in a bacterial plasmid. The variety of intervening sequences (IVSs) that span the
      phylogenetic spectrum was further extended by the discovery of inteins, elements that can
      splice at the protein level, in eukaryotes, archaea, and bacteria. This minireview will
      illustrate that interrupted genes can no longer be considered the province of eukaryotes, but
      rather than many forms of IVSs are phylogenetically diverse, occurring also in bacterial and
      archaeal genomes.
AU  - Belfort M
AU  - Reaban ME
AU  - Coetzee T
AU  - Dalgaard JZ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1995 177: 3897-3903.

PMID- 9254693
VI  - 25
DP  - 1997
TI  - Homing endonucleases: keeping the house in order.
PG  - 3379-3388
AB  - Homing endonucleases are rare-cutting enzymes encoded by introns and inteins.  They have
      striking structural and functional properties that distinguish them from restriction enzymes.
      Nomenclature conventions analogous to those for restriction enzymes have been developed for
      the homing endonucleases.  Recent progress in understanding the structure and function of the
      four families of homing enzymes is reviewed.  Of particular interest are the first reported
      structures of homing endonucleases of the LAGLIDADG family.  The exploitation of the homing
      enzymes in genome analysis and recombination research is also summarized.  Finally, the
      evolution of homing endonucleases is considered, both at the structure-function level and in
      terms of their persistence in widely divergent biological systems.
AU  - Belfort M
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1997 25: 3379-3388.

PMID- 
VI  - 22
DP  - 2005
TI  - Modular assembly of a multi-functional homing endonuclease.
PG  - 809
AB  - Homing endonucleases are usually encoded within self-splicing introns or inteins, and are
      found in all three biological kingdoms.  The endonuclease genes and their host intron or
      intein are composite selfish genetic elements that spread between related genomes by a process
      called homing.  The homing pathway is initiated by the endonuclease binding to a sequence, the
      homing site, centered on the intron insertion site of intronless alleles.  The role of the
      homing endonuclease is limited to introduction of a double-strand break close to the intron
      IS.  I-TevI, a member of the GIY-YIG family of homing endonucleases, is a site-specific yet
      sequence tolerant enzyme.  It is remarkably extended molecule consisting of a well-folded
      catalytic domain connected to a series of sub-domains by extended regions.  These include a
      Zn-finger, a minor-goove binding helix and a helix-turn-helix subdomain.  The modular nature
      of the enzyme is pertinent to the evolution of homing endonucleases.  We have begun to assess
      the role of each subdomain in endonuclease function.  Most interestingly, we have found that
      the Zn-finger subdomain does not play a role in substrate DNA binding.  Rather it is required
      for positioning the catalytic domain at a set distance from the primary binding site for
      cleavage to occur.  The next challenge is trying to understand the nature of the linker that
      connects the catalytic and DNA-binding domains and how it interacts with the Zn-finger to
      mediate distance determination.  In addition, recent work has shown that the enzyme is
      bi-functional and can act as an auto-repressor.  It can bind to a site present in its promoter
      region that exhibits sequence similarity to its homing site, but does not cleave the DNA.  It
      is the very modular nature of the enzyme, with distinct sequence requirements for binding and
      cleavage, that facilitates its bifunctionality by binding in the absence of cleavage, leading
      to transcriptional repression.
AU  - Belfort M
AU  - Van Roey P
AU  - Derbyshire V
PT  - Journal Article
TA  - J. Biomol. Struct. Dyn.
JT  - J. Biomol. Struct. Dyn.
SO  - J. Biomol. Struct. Dyn. 2005 22: 809.

PMID- 28751398
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Enterococcus faecalis DD14, a Bacteriocinogenic Lactic Acid Bacterium with Anti-Clostridium Activity.
PG  - e00695-17
AB  - We report the draft genome sequence of Enterococcus faecalis DD14, a strain isolated from
      meconium of a healthy newborn at Roubaix Hospital (France). The
      strain displayed antagonism against a set of Gram-positive bacteria through
      concomitant production of lactic acid and bacteriocin. The genome has a size of
      2,893,365 bp and a 37.3% G+C ratio and is predicted to contain at least 2,755
      coding sequences and 62 RNAs.
AU  - Belguesmia Y
AU  - Leclere V
AU  - Duban M
AU  - Auclair E
AU  - Drider D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00695-17.

PMID- 8597074
VI  - 82
DP  - 1995
TI  - A microassay for measuring cytosine DNA methyltransferase activity during tumor progression.
PG  - 335-340
AB  - The cytosine DNA methyltransferase (MT) enzyme, which catalyzes DNA
      methylation at CpG sites, is overexpressed at the mRNA level during the progressive stages of
      colon cancer.  This paper describes the adaptation of a sensitive microassay for determining
      MT
      enzyme activity during tumor progression in human colon and murine lung.  MT activity was
      progressively elevated in mucosa from familial adenomatosis polyposis patients, mucosa
      adjacent
      to cancers, and in colonic adenocarcinomas when compared to colonic mucosa from control
      patients.  In addition, the activity of this enzyme was increased in alveolar type II but not
      Clara
      cells isolated from A/J mice following carcinogen exposure and continued to increase during
      tumor
      progression.  The use of a microassay for measuring MT activity indicates that changes in
      enzyme
      activity were in general agreement with previous findings of increased MT mRNA levels during
      colon cancer progression and also implicates the involvement of this pathway in lung cancer
      development.
AU  - Belinsky SA
AU  - Nikula KJ
AU  - Baylin SB
AU  - Issa J-P
PT  - Journal Article
TA  - Toxicol. Lett.
JT  - Toxicol. Lett.
SO  - Toxicol. Lett. 1995 82: 335-340.

PMID- 8633014
VI  - 93
DP  - 1996
TI  - Increased cytosine DNA-methyltransferase activity is target-cell-specific and an early event in lung cancer.
PG  - 4045-4050
AB  - The association between increased DNA-methyltransferase (DNA-MTase) activity
      and tumor development suggests a fundamental role for this enzyme in the initiation and
      progression of cancer.  A true functional role for DNA-MTase in the neoplastic process would
      be
      further substantiated if the target cells affected by the initiating carcinogen exhibit
      changes in
      enzyme activity.  This hypothesis was addressed by examining DNA-MTase activity in alveolar
      type II (target) and Clara (nontarget) cells from A/J and C3H mice that exhibit high and low
      susceptibility, respectively, for lung tumor formation.  Increased DNA-MTase activity was
      found
      only in the target alveolar type II cells of the susceptible A.J mouse and caused a marked
      increase
      in overall DNA methylation in these cells.  Both DNA-MTase and DNA methylation changes were
      detected 7 days after carcinogen exposure and, thus, were early events in neoplastic
      evolution.
      Increased gene expression was also detected by RNA in situ hybridization in hypertrophic
      alveolar
      type II cells of carcinogen-treated A/J mice, indicating that elevated levels of expression
      may be a
      biomarker for premalignancy.  Enzyme activity increased incrementally during lung cancer
      progression and coincided with increased expression of the DNA-MTase gene in hyperplasias,
      adenomas, and carcinomas.  Thus, these results indicate that early increases in DNA-MTase
      activity are strongly associated with neoplastic development and constitute a key step in
      carcinogenesis.  The detection of premalignant lung disease through increased DNA-MTase
      expression and the possibility of blocking the deleterious effects of this change with
      specific
      inhibitors will offer new intervention strategies for lung cancer.
AU  - Belinsky SA
AU  - Nikula KJ
AU  - Baylin SB
AU  - Issa J-PJ
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1996 93: 4045-4050.

PMID- 21511449
VI  - 167
DP  - 2012
TI  - Purification and characterization of SepII a new restriction endonuclease from Staphylococcus epidermidis.
PG  - 90-94
AB  - A Type II restriction enzyme SepII has been purified to apparent homogeneity from the
      gram-positive coccus,Staphylococcus epidermidis.
      The purification included an ammonium sulfate precipitation followed by
      Q-sepharose, heparin-sepharose and MonoQ column chromatography on an
      FPLC system. SDS-PAGE analysis showed a denatured molecular weight of
      29 kDa. The effects of temperature, pH, NaCl, Mn2+,Ca2+, and Mg2+ ion
      concentrations were studied to determine the optimal reaction
      conditions. The enzyme exhibits near maximal levels of activity between
      pH 8-10, at 10-20 mM MgCl2, 100-150 mM NaCl and 1 mM DTT. The results
      also show that in NEB Buffer 3 the enzyme is active over a broad
      temperature range from 0 to 70 degrees C, and in the absence of DNA,
      enzyme thermostability is observed up to 50 degrees C for 20 min, while
      most of the original activity is conserved in 50% glycerol for weeks at
      room temperature. Single and double digestion in presence of commercial
      restriction enzymes of known DNA substrates (lambda, pBR322, pET21,
      pTrcHisB, pPB67) showed that the purified SepII recognized and cleaved
      the same site as EcoRV. Genomic DNA modification status was also
      determined.
AU  - Belkebir A
AU  - Azeddoug H
PT  - Journal Article
TA  - Microbiol. Res.
JT  - Microbiol. Res.
SO  - Microbiol. Res. 2012 167: 90-94.

PMID- 23017231
VI  - 168
DP  - 2013
TI  - Metal ion dependence of DNA cleavage by SepMI and EhoI restriction endonucleases.
PG  - 99-105
AB  - Most of type II restriction endonucleases show an absolute requirement for divalent metal ions
      as cofactors for DNA cleavage. While Mg2+ is
      the natural cofactor other metal ions can substitute it and mediate the
      catalysis, however Ca2+ (alone) only supports DNA binding. To
      investigate the role of Mg2+ in DNA cleavage by restriction
      endonucleases, we have studied the Mg2+ and Mn2+ concentration
      dependence of DNA cleavage by SepMI and EhoI. Digestion reactions were
      carried out at different Mg2+ and Mn2+ concentrations at constant ionic
      strength. These enzymes showed different behavior regarding the ions
      requirement, SepMI reached near maximal level of activity between 10
      and 20 mM while no activity was detected in the presence of Mn2+ and in
      the presence of Ca2+ cleavage activity was significantly decreased.
      However, EhoI was more highly active in the presence of Mn2+ than in
      the presence of Mg2+ and can be activated by Ca2+. Our results propose
      the two-metal ion mechanism for EhoI and the one-metal ion mechanism
      for SepMI restriction endonuclease. The analysis of the kinetic
      parameters under steady state conditions showed that SepMI had a K-m
      value for pTrcHisB DNA of 6.15 nM and a V-max of 1.79 x 10(-2) nM
      min(-1), while EhoI had a K-m for pUC19 plasmid of 8.66 nM and a V-max
      of 2 x 10(-2) nM min(-1). (C) 2012 Elsevier GmbH. All rights reserved.
AU  - Belkebir A
AU  - Azeddoug H
PT  - Journal Article
TA  - Microbiol. Res.
JT  - Microbiol. Res.
SO  - Microbiol. Res. 2013 168: 99-105.

PMID- 29472323
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of the Facultative Methylotroph Methylobacterium extorquens TK 0001 Isolated from Soil in Poland.
PG  - e00018-18
AB  - Methylobacterium extorquens TK 0001 (DSM 1337, ATCC 43645) is an aerobic pink-pigmented
      facultative methylotrophic alphaproteobacterium isolated from soil
      in Poland. Here, we report the whole-genome sequence and annotation of this
      organism, which consists of a single 5.71-Mb chromosome.
AU  - Belkhelfa S
AU  - Labadie K
AU  - Cruaud C
AU  - Aury JM
AU  - Roche D
AU  - Bouzon M
AU  - Salanoubat M
AU  - Doring V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00018-18.

PMID- 11371527
VI  - 183
DP  - 2001
TI  - Very-Short-Patch Repair in Escherichia coli Requires the dam Adenine Methylase.
PG  - 3631-3635
AB  - Strains of Escherichia coli which lack the dam-encoded adenine methylase are mutators due to a
      reduction in the efficiency of postreplication mismatch repair. In this study, we show that
      Dam(-) strains are also defective in very-short-patch repair, the system which corrects T/G
      mismatches arising from the deamination of 5-methylcytosine. This defect is associated with
      decreased levels of Vsr, the endonuclease which initiates short-patch repair. We also show
      that production of the dcm-encoded cytosine methylase is unaffected in Dam(-) strains. Since
      the dcm and vsr genes are cotranscribed, the regulation of Vsr by Dam is probably
      posttranscriptional.
AU  - Bell DC
AU  - Cupples CG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2001 183: 3631-3635.

PMID- 15263089
VI  - 101
DP  - 2004
TI  - Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors.
PG  - 11105-11110
AB  - The bacterial family Enterobacteriaceae is notable for its well studied human pathogens,
      including Salmonella, Yersinia, Shigella, and Escherichia spp. However, it also contains
      several plant pathogens. We report the genome sequence of a plant pathogenic enterobacterium,
      Erwinia carotovora subsp. atroseptica (Eca) strain SCRI1043, the causative agent of soft rot
      and blackleg potato diseases. Approximately 33% of Eca genes are not shared with sequenced
      enterobacterial human pathogens, including some predicted to facilitate unexpected metabolic
      traits, such as nitrogen fixation and opine catabolism. This proportion of genes also contains
      an overrepresentation of pathogenicity determinants, including possible horizontally acquired
      gene clusters for putative type IV secretion and polyketide phytotoxin synthesis. To
      investigate whether these gene clusters play a role in the disease process, an arrayed set of
      insertional mutants was generated, and mutations were identified. Plant bioassays showed that
      these mutants were significantly reduced in virulence, demonstrating both the presence of
      novel pathogenicity determinants in Eca, and the impact of functional genomics in expanding
      our understanding of phytopathogenicity in the Enterobacteriaceae.
AU  - Bell KS et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2004 101: 11105-11110.

PMID- 2165250
VI  - 18
DP  - 1990
TI  - Intron mobility in phage T4 is dependent upon a distinctive class of endonucleases and independent of DNA sequences encoding the intron core: mechanistic and evolutionary implications.
PG  - 3763-3770
AB  - Although mobility of the phylogenetically widespread group I introns appears to be
      mechanistically similar, the phage T4 intron-encoded endonucleases that promote mobility of
      the td and sunY introns are different from their eukaryotic counterparts. Most notably, they
      cleave at a distance from the intron insertion sites. The td enzyme was shown to cleave 23-26
      nt 5' and the sunY endonuclease 13-15 nt 3' to the intron insertion site to generate 3-nt or
      2-nt 3'-OH extensions, respectively. The absolute coconversion of exon markers between the
      distant cleavage and insertion sites is consistent with the double-strand-break repair model
      for intron mobility. As a further critical test of the model we have demonstrated that the
      mobility event is independent of DNA sequences that encode the catalytic intron core
      structure. Thus, in derivatives in which the lacZ or kanR coding sequences replace the intron,
      these marker genes are efficiently inserted into intron-minus alleles when the cognate
      endonuclease is provided in trans. The process is therefore endonuclease-dependent, rather
      than dependent on the intron per se. These findings, which imply that the endonucleases rather
      than the introns themselves were the primordial mobile elements, are incorporated into a model
      for the evolution of mobile introns.
AU  - Bell-Pedersen D
AU  - Quirk S
AU  - Clyman J
AU  - Belfort M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 3763-3770.

PMID- 2555262
VI  - 82
DP  - 1989
TI  - A site-secific endonuclease and co-conversion of flanking exons associated with the mobile td intron of phage T4.
PG  - 119-126
AB  - The product of the td intron open reading frame (ORF) of phage T4 is required for
      high-frequency transfer of the intervening sequence from intron-plus (In+) to intron-minus
      (In-) alleles. In vivo studies have demonstrated that the td ORF product targets cleavage of
      td In- DNA, and that cleavage is correlated with intron inheritance [Quirk et al., Cell 56
      (1989) 455-465]. In the present study we show by in vitro synthesis of the td intron ORF
      product, that the protein possesses endonuclease activity and efficiently cleaves
      double-stranded DNA at or near the site of intron integration. In addition, we demonstrate
      that intron insertion is accompanied by co-conversion of the flanking exon sequences.
      Co-conversion of markers within 50 nt surrounding the site of intron insertion occurred at a
      high frequency (80-100%), and decreased at greater distance from the intervening sequence.
      Co-conversion may provide a mechanism for maintaining exon-intron RNA contacts required for
      accurate splicing of the relocated intron. Cleavage of target DNA by an intron endonuclease
      and co-conversion of flanking exon sequences are both features associated with mobile introns
      of eukaryotes, indicating a common mechanism for intron transfer in the eukaryotic kingdoms.
AU  - Bell-Pedersen D
AU  - Quirk SM
AU  - Aubrey M
AU  - Belfort M
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1989 82: 119-126.

PMID- 1881913
VI  - 88
DP  - 1991
TI  - I-TevI, the endonuclease encoded by the mobile td intron, recognizes binding and cleavage domains on its DNA target.
PG  - 7719-7723
AB  - Mobility of the phage T4 td intron depends on activity of an intron-encoded endonuclease
      (I-TevI), which cleaves a homologous intronless (delta-In) target gene. The double-strand
      break initiates a recombination event that leads to intron transfer. We found previously that
      I-TevI cleaves td-delta-IN target DNA 23-26 nucleotides upstream of the intron insertion site.
      DNase I-footprinting experiments and gel-shift assays indicate that I-TevI makes primary
      contacts around the intron insertion site. A synthetic DNA duplex spanning the insertion site
      but lacking the cleavage site was shown to bind I-TevI specifically, and when cloned, to
      direct cleavage into vector sequences. The behavior of the cloned duplex and that of deletion
      and insertion mutants support a primary role for sequences surrounding the insertion site in
      directing I-TevI binding, conferring cleavage ability, and determining cleavage polarity. On
      the other hand, sequences around the cleavage site were shown to influence cleavage efficiency
      and cut-site selection. The role of cleavage-site sequences in determining cleavage distance
      argues against a strict "ruler" mechanism for cleavage by I-TevI. The complex nature of the
      homing site recognized by this unusual type of endonuclease is considered in the context of
      intron spread.
AU  - Bell-Pedersen D
AU  - Quirk SM
AU  - Bryk M
AU  - Belfort M
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1991 88: 7719-7723.

PMID- 10388822
VI  - 152
DP  - 1999
TI  - I-SceI endonuclease, a new tool for studying DNA double-strand break repair mechanisms in Drosophila.
PG  - 1037-1044
AB  - As a step toward the development of a homologous recombination system in Drosophila, we have
      developed a methodology to target double-strand breaks (DSBs) to a specific position in the
      Drosophila genome. This method uses the mitochondrial endonuclease I-SceI that recognizes and
      cuts an 18-bp restriction site. We find that >6% of the progeny derived from males that carry
      a marker gene bordered by two I-SceI sites and that express I-SceI in their germ line lose the
      marker gene. Southern blot analysis and sequencing of the regions surrounding the I-SceI sites
      revealed that in the majority of the cases, the introduction of DSBs at the I-SceI sites
      resulted in the complete deletion of the marker gene; the other events were associated with
      partial deletion of the marker gene. We discuss a number of applications for this novel
      technique, in particular its use to study DSB repair mechanisms.
AU  - Bellaiche Y
AU  - Mogila V
AU  - Perrimon N
PT  - Journal Article
TA  - Genetics
JT  - Genetics
SO  - Genetics 1999 152: 1037-1044.

PMID- 19596810
VI  - 37
DP  - 2009
TI  - Differences between Ca2+ and Mg2+ in DNA binding and release by the SfiI restriction endonuclease: implications for DNA looping.
PG  - 5443-5453
AB  - Many enzymes acting on DNA require Mg(2+) ions not only for catalysis but also to bind DNA.
      Binding studies often employ Ca(2+) as a substitute for
      Mg(2+), to promote DNA binding whilst disallowing catalysis. The SfiI
      endonuclease requires divalent metal ions to bind DNA but, in contrast to
      many systems where Ca(2+) mimics Mg(2+), Ca(2+) causes SfiI to bind DNA
      almost irreversibly. Equilibrium binding by wild-type SfiI cannot be
      conducted with Mg(2+) present as the DNA is cleaved so, to study the
      effect of Mg(2+) on DNA binding, two catalytically-inactive mutants were
      constructed. The mutants bound DNA in the presence of either Ca(2+) or
      Mg(2+) but, unlike wild-type SfiI with Ca(2+), the binding was reversible.
      With both mutants, dissociation was slow with Ca(2+) but was in one case
      much faster with Mg(2+). Hence, Ca(2+) can affect DNA binding differently
      from Mg(2+). Moreover, SfiI is an archetypal system for DNA looping; on
      DNA with two recognition sites, it binds to both sites and loops out the
      intervening DNA. While the dynamics of looping cannot be measured with
      wild-type SfiI and Ca(2+), it becomes accessible with the mutant and
      Mg(2+).
AU  - Bellamy SR
AU  - Kovacheva YS
AU  - Zulkipli IH
AU  - Halford SE
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: 5443-5453.

PMID- 17870087
VI  - 373
DP  - 2007
TI  - A Switch in the Mechanism of Communication between the Two DNA-Binding Sites in the SfiI Restriction Endonuclease.
PG  - 1169-1183
AB  - While many Type II restriction enzymes are dimers with a single DNA-binding cleft between the
      subunits, SfiI is a tetramer of identical
      subunits. Two of its subunits (a dimeric unit) create one DNA-binding
      cleft, and the other two create a second cleft on the opposite side of the
      protein. The two clefts bind specific DNA cooperatively to give a complex
      of SfiI with two recognition sites. This complex is responsible for
      essentially all of the DNA-cleavage reactions by SfiI: virtually none is
      due to the complex with one site. The communication between the
      DNA-binding clefts was examined by disrupting one of the very few polar
      interactions in the otherwise hydrophobic interface between the dimeric
      units: a tyrosine hydroxyl was removed by mutation to phenylalanine. The
      mutant protein remained tetrameric in solution and could bind two DNA
      sites. But instead of being activated by binding two sites, like wild-type
      SfiI, it showed maximal activity when bound to a single site and had a
      lower activity when bound to two sites. This interaction across the dimer
      interface thus enforces in wild-type SfiI a cooperative transition between
      inactive and active states in both dimers, but without this interaction as
      in the mutant protein, a single dimer can undergo the transition to give a
      stable intermediate with one inactive dimer and one active dimer.
AU  - Bellamy SR
AU  - Milsom SE
AU  - Kovacheva YS
AU  - Sessions RB
AU  - Halford SE
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2007 373: 1169-1183.

PMID- 18848951
VI  - 384
DP  - 2008
TI  - Fidelity of DNA Sequence Recognition by the SfiI Restriction Endonuclease Is Determined by Communications between Its Two DNA-Binding Sites.
PG  - 557-563
AB  - The SfiI restriction endonuclease is a tetramer in which two subunits form a dimeric unit that
      contains one DNA binding cleft and the other two
      subunits contain a second cleft on the opposite side of the protein. Full
      activity requires both clefts to be filled with its recognition sequence:
      SfiI has low activity when bound to one site. The ability of SfiI to
      cleave non-cognate sites, one base pair different from the true site, was
      initially tested on substrates that lacked specific sites but which
      contained either one or multiple non-cognate sites. No cleavage of the DNA
      with one non-cognate site was detected, while a small fraction of the DNA
      with multiple sites was nicked. The alternative sequences were, however,
      cleaved in both strands, albeit at low levels, when the DNA also carried
      either a recognition site for SfiI or the termini generated by SfiI.
      Further tests employed a mutant of SfiI, altered at the dimer interface,
      which was known to be more active than wild-type SfiI when bound to a
      single site. This mutant similarly failed to cleave DNA with one
      non-cognate site, but cleaved the substrates with multiple non-cognate
      sites more readily than did the native enzyme. To cleave additional sites,
      SfiI thus needs to interact concurrently with either two non-cognate sites
      or one non-cognate and one cognate site (or the termini thereof), yet this
      arrangement is still restrained from cleaving the alternative site unless
      the communication pathway between the two DNA-binding clefts is disrupted.
AU  - Bellamy SR
AU  - Mina P
AU  - Retter SE
AU  - Halford SE
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2008 384: 557-563.

PMID- 15826661
VI  - 348
DP  - 2005
TI  - Cleavage of individual DNA strands by the different subunits of the heterodimeric restriction endonuclease BbvCI.
PG  - 641-653
AB  - BbvCI cleaves an asymmetric DNA sequence, 5'-CC^TCAGC-3'/5'-GC^TGAGG-3', as indicated.
      While many Type II
      restriction enzymes consist of identical subunits, BbvCI has two
      different subunits: R-1, which acts at GC^TGAGG; and R-2,
      which acts at CC^TCAGC. Some mutants of BbvCI with defects
      in one subunit either R1-R2+ or R1+R2-, cleave only one strand, that
      attacked by the native subunit. In analytical ultracentrifugation at
      various concentrations of protein, wild-type and mutant BbvCI enzymes
      aggregated extensively, but are R1R2 heterodimers at the concentrations
      used in DNA cleavage reactions. On a plasmid with one recognition site,
      wild-type BbvCI cleaved both strands before dissociating from the DNA,
      while the R1-R2+ and R1+R2- mutants acted almost exclusively on their
      specified strands, albeit at relatively slow rates. During the
      wild-type reaction, the DNA is cleaved initially in one strand, mainly
      that targeted by the R, subunit. The other strand is then cleaved
      slowly by R-2 before the enzyme dissociates from the DNA. Hence, the
      nicked form accumulates as a transient intermediate. This behaviour
      differs from that of many other restriction enzymes, which cut both
      strands at equal rates. However, the activities of the R-1(+) and
      R-2(+) subunits in the wild-type enzyme can differ from their
      activities in the R1+R2- and R1-R2+ mutants. Each active site in BbvCI
      therefore influences the other.
AU  - Bellamy SRW
AU  - Milsom SE
AU  - Scott DJ
AU  - Daniels LE
AU  - Wilson GG
AU  - Halford SE
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2005 348: 641-653.

PMID- 
VI  - 0
DP  - 1996
TI  - A phase-variable type III restriction-modification system in Neisseria gonorrhoeae.
PG  - 360-361
AB  - Neisseria gonorrhoeae possesses a number of type II restriction/modification systems but
      characteristically expresses fewer restriction enzyme activities than corresponding
      methyltransferases.  Methyltransferase specificities have been identified for S.NgoI
      (PuGCGCPy), S.NgoII (GGCC), S.NgoIII (CCGCGG), S.NgoIV (GCCGGC), S.NgoV (GGNNCC), S.NgoVI
      (GATC), S.NgoVII (GC[C/G]GC), S.NgoVIII (TCACC) of purified methyltransferase which recognizes
      the sequence GTAN5CTC (S.NgoIX).  Restriction enzymes have been detected which correspond to
      the sequences for NgoI, II, III, IV, and IX in various strains.  We have identified the genes
      encoding a type III restriction modification system present in all strains of N. gonorrhoeae
      tested.  Sequence analysis of the ngoX locus from strain MS11 indicate the predicted protein
      for the restriction enzyme (NgoX.R) is 59% identical to the restriction enzyme of the P1
      system.  The modification enzyme (NgoX.M) is predicted to be 38% identical to the modification
      enzyme of the P1 system. The postulated 5' region of the ngoX.M gene is unusual in that the
      predicted start codon is followed by a series of direct pentameric repeats reminiscent of the
      signal-peptide encoding region of neisserial opa genes, responsible for regulating expression
      of opa genes by "phase variation".  The ngoX.M gene of strain MS11 contains eight repeat
      elements (an out-of-frame configuration) while strain FA228 contains twelve repeat elements
      (an in-frame configuration).  Mutations constructed in Escherichia coli and returned to the
      gonococcal chromosome by allelic replacement indicate that the ngoX.M gene is expressed in
      strain FA228 but not in strain MS11 but the gene is phase-variable from both the on and off
      configurations.  Phase variation cannot be detected in the viable cell population in wild-type
      strains.  Purified heterodimeric NgoX enzyme is active against DNA purified from strains MS11
      mk (no expression of NgoX.M) and FA228 ngoX.M::lacZ but not strain FA228 (expresses NgoX.M).
AU  - Belland RJ
AU  - Morrison SG
AU  - Hogan D
PT  - Journal Article
TA  - Abs. Tenth Int. Conf. Pathogenegic Neisseria
JT  - Abs. Tenth Int. Conf. Pathogenegic Neisseria
SO  - Abs. Tenth Int. Conf. Pathogenegic Neisseria 1996 0: 360-361.

PMID- 1676386
VI  - 101
DP  - 1991
TI  - Classification of type-II restriction endonucleases and cloning of non-identical cohesive-end fragments without self-polymerization using nonpalindromic oligodeoxyribonucleotide adapters.
PG  - 67-74
AB  - Enzymatic partial filling-in of recessed 3'-end sequences, left after digestion
      of DNA by the restriction endonucleases (ENases) Sau3AI and SalI, with the
      Klenow fragment of E. coli DNA polymerase I allows the forced ligation of the
      resulting fragments; this technology is already used for subcloning and for
      genomic bank construction.  To simplify and generalize its utilization,
      class-II ENases have been arranged into 16 different families according to the
      composition of the 5'-protruding sequences present after cleavage.  Moreover,
      this system was extended to allow the joining of noncompatible ends by the use
      of nonpalindromic complementary oligodeoxyribonucleotides (NPCOs) containing
      two nucleotides protruding at each 5' end.  The use of these synthetic adapters
      maintains all the advantages of the initial gap-filling cloning technique: only
      one insert can be cloned per vector molecule and no self-ligation or
      -polymerization can occur with any of the DNA molecules involved.  Only 22 such
      oligodeoxyribonucleotides are needed to generate the 60 NPCO pairs necessary to
      ligate to each other any member of twelve ENase families when the regeneration
      of ENase recognition sites is not required.
AU  - Bellemare G
AU  - Potvin C
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1991 101: 67-74.

PMID- 16452431
VI  - 188
DP  - 2006
TI  - The genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium Thiobacillus denitrificans.
PG  - 1473-1488
AB  - The complete genome sequence of Thiobacillus denitrificans ATCC 25259 is the first to become
      available for an obligately chemolithoautotrophic,
      sulfur-compound-oxidizing, beta-proteobacterium. Analysis of the
      2,909,809-bp genome will facilitate our molecular and biochemical
      understanding of the unusual metabolic repertoire of this bacterium,
      including its ability to couple denitrification to sulfur-compound
      oxidation, to catalyze anaerobic, nitrate-dependent oxidation of Fe(II)
      and U(IV), and to oxidize mineral electron donors. Notable genomic
      features include (i) genes encoding c-type cytochromes totaling 1 to 2
      percent of the genome, which is a proportion greater than for almost all
      bacterial and archaeal species sequenced to date, (ii) genes encoding two
      [NiFe]hydrogenases, which is particularly significant because no
      information on hydrogenases has previously been reported for T.
      denitrificans and hydrogen oxidation appears to be critical for anaerobic
      U(IV) oxidation by this species, (iii) a diverse complement of more than
      50 genes associated with sulfur-compound oxidation (including sox genes,
      dsr genes, and genes associated with the AMP-dependent oxidation of
      sulfite to sulfate), some of which occur in multiple (up to eight) copies,
      (iv) a relatively large number of genes associated with inorganic ion
      transport and heavy metal resistance, and (v) a paucity of genes encoding
      organic-compound transporters, commensurate with obligate
      chemolithoautotrophy. Ultimately, the genome sequence of T. denitrificans
      will enable elucidation of the mechanisms of aerobic and anaerobic
      sulfur-compound oxidation by beta-proteobacteria and will help reveal the
      molecular basis of this organism's role in major biogeochemical cycles
      (i.e., those involving sulfur, nitrogen, and carbon) and groundwater
      restoration.
AU  - Beller HR
AU  - Chain PS
AU  - Letain TE
AU  - Chakicherla A
AU  - Larimer FW
AU  - Richardson PM
AU  - Coleman MA
AU  - Wood AP
AU  - Kelly DP
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2006 188: 1473-1488.

PMID- 19262690
VI  - 4
DP  - 2009
TI  - Genome sequence of the pathogenic intestinal spirochete brachyspira hyodysenteriae reveals adaptations to its lifestyle in the porcine large intestine.
PG  - E4641
AB  - Brachyspira hyodysenteriae is an anaerobic intestinal spirochete that
      colonizes the large intestine of pigs and causes swine dysentery, a
      disease of significant economic importance. The genome sequence of B.
      hyodysenteriae strain WA1 was determined, making it the first
      representative of the genus Brachyspira to be sequenced, and the
      seventeenth spirochete genome to be reported. The genome consisted of a
      circular 3,000,694 base pair (bp) chromosome, and a 35,940 bp circular
      plasmid that has not previously been described. The spirochete had 2,122
      protein-coding sequences. Of the predicted proteins, more had similarities
      to proteins of the enteric Escherichia coli and Clostridium species than
      they did to proteins of other spirochetes. Many of these genes were
      associated with transport and metabolism, and they may have been gradually
      acquired through horizontal gene transfer in the environment of the large
      intestine. A reconstruction of central metabolic pathways identified a
      complete set of coding sequences for glycolysis, gluconeogenesis, a
      non-oxidative pentose phosphate pathway, nucleotide metabolism,
      lipooligosaccharide biosynthesis, and a respiratory electron transport
      chain. A notable finding was the presence on the plasmid of the genes
      involved in rhamnose biosynthesis. Potential virulence genes included
      those for 15 proteases and six hemolysins. Other adaptations to an enteric
      lifestyle included the presence of large numbers of genes associated with
      chemotaxis and motility. B. hyodysenteriae has diverged from other
      spirochetes in the process of accommodating to its habitat in the porcine
      large intestine.
AU  - Bellgard MI
AU  - Wanchanthuek P
AU  - La T
AU  - Ryan K
AU  - Moolhuijzen P
AU  - Albertyn Z
AU  - Shaban B
AU  - Motro Y
AU  - Dunn DS
AU  - Schibeci D
AU  - Hunter A
AU  - Barrero R
AU  - Phillips ND
AU  - Hampson DJ
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2009 4: E4641.

PMID- 25953172
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Pseudomonas sp. Strain 10-1B, a Polycyclic Aromatic Hydrocarbon Degrader in Contaminated Soil.
PG  - e00325-15
AB  - Pseudomonas sp. strain 10-1B was isolated from artificially polluted soil after selective
      enrichment. Its draft genome consists of several predicted genes that
      are involved in the hydroxylation of the aromatic ring, which is the
      rate-limiting step in the biodegradation of polycyclic aromatic hydrocarbons.
AU  - Bello-Akinosho M
AU  - Adeleke R
AU  - Swanevelder D
AU  - Thantsha M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00325-15.

PMID- 2838133
VI  - 4
DP  - 1988
TI  - Construction of restriction maps.
PG  - 111-116
AB  - A computer program is described, which constructs maps of restriction
      endonuclease cleavage sites in linear or circular DNA molecules, given the
      fragment lengths in single and double digestions with two enzymes.  The
      algorithm is based upon a partition method and a very simple rule to chain
      fragments.  The program is written in Prolog II.
AU  - Bellon B
PT  - Journal Article
TA  - Comput. Appl. Biosci.
JT  - Comput. Appl. Biosci.
SO  - Comput. Appl. Biosci. 1988 4: 111-116.

PMID- 18096197
VI  - 373
DP  - 2008
TI  - Temperate bacteriophage Phi O18P from an Aeromonas media isolate: Characterization and complete genome sequence.
PG  - 25-29
AB  - group of 74 Aeromonas isolates from surface water of three ponds in Bielefeld, Germany was
      screened for prophage induction after UV
      irradiation. The phage Phi O18P was induced from the Aeromonas media
      isolate O18. Phi O18P belongs to the Myoviridae phage family. The
      complete nucleotide sequence of the double stranded DNA genome
      ofbacteriophage Phi O18P consists of 33,985 bp. The genome has 5'
      protruding cohesive ends of 16 bases. On the Phi O18P genome 46 open
      reading frames (orfs) were identified which are organized in the
      modules integration and regulation, replication, head, packaging, tail
      and lysis. Additionally the phage DNA includes a methylase gene.
      Comparison of the genome architecture with those of other
      bacteriophages revealed significant similarities to the P2 phage family
      and especially to the prophages of Aeromonas salmonicida and the Vibrio
      cholerae phage K139.
AU  - Bellstein F
AU  - Dreiseikelmann B
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 2008 373: 25-29.

PMID- 7708494
VI  - 23
DP  - 1995
TI  - A motif conserved among the type I restriction-modification enzymes and antirestriction proteins: a possible basis for mechanism of action of plasmid-encoded antirestriction functions.
PG  - 785-787
AB  - Antirestriction proteins Ard encoded by some self-transmissible plasmids specifically inhibit
      restriction by members of all three families of type I restriction-modification (R-M) systems
      in E. coli. Recently, we have identified the amino acid region, 'antirestriction' domain,
      that is conserved within different plasmid and phage T7-encoded antirestriction proteins and
      may be involved in interaction with the type I R-M systems. In this paper we demonstrate that
      this amino acid sequence shares considerable similarity with a well-known conserved sequence
      (the Argos repeat) found in the DNA sequence specificity (S) polypeptides of type I systems.
      We suggest that the presence of these similar motifs in restriction and antirestriction
      proteins may give a structural basis for their interaction and that the antirestriction action
      of Ard proteins may be a result of the competition between the 'antirestriction' domains of
      Ard proteins and the similar conserved domains of the S subunits that are believed to play a
      role in the subunit assembly of type I R-M systems.
AU  - Belogurov AA
AU  - Delver EP
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1995 23: 785-787.

PMID- 10686096
VI  - 296
DP  - 2000
TI  - Antirestriction protein Ard (Type C) encoded by IncW plasmid pSa has a high similarity to the "Protein Transport" domain of TraC1 primase of promiscuous plasmid RP4.
PG  - 969-977
AB  - The IncW plasmid pSa contains the gene ard encoding an antirestriction function that is
      specific for type I restriction and modification systems. The nucleotide
      sequence of ard was determined and an appropriate polypeptide of about 33 kDa was identified
      in Escherichia coli T7 expression system. Analysis of deduced amino acid
      sequence of Ard encoded by pSa revealed that this protein has no significant similarities with
      the known Ard proteins (ArdA and ArdB types) except the "antirestriction"
      motif (14 amino acid residues in length) conserved for all known Ard proteins. This finding
      suggests that pSa Ard may be classified as a new type of Ard proteins which we
      designated ArdC. The remarkable feature of ArdC is that it has a high degree of similarity
      (about 38 % identity) to the N-terminal region of RP4 TraC1 primase which
      includes about 300 amino acid residues and seems to be essential for binding to the
      single-stranded DNA and TraC1 protein transport to the recipient cells during the
      conjugal transfer of plasmid DNA. ArdC also binds to single-stranded DNA. In addition, this
      protein is able in vitro to protect the single-stranded but not double-stranded
      plasmid DNA against the activity of type II restriction endonuclease HhaI that cleaves both
      single and double-stranded DNA. We suggest that like TraC1, ArdC would be
      transported as a result of their interaction with the single-stranded DNA of transferred
      plasmid strand during conjugative passage through the cell envelope to the recipient
      bacterium. Such properties of ArdC protein might be useful to protect immediately the incoming
      single-stranded DNA from the host endonucleases.
AU  - Belogurov AA
AU  - Delver EP
AU  - Agafonova OV
AU  - Belogurova NG
AU  - Lee LY
AU  - Kado CI
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2000 296: 969-977.

PMID- 8393008
VI  - 175
DP  - 1993
TI  - Plasmid pKM101 encodes two nonhomologous antirestriction proteins (ArdA and ArdB) whose expression is controlled by homologous regulatory sequences.
PG  - 4843-4850
AB  - The Inc plasmid pKM101 (a derivative of R46) encodes the antirestriction protein ArdB
      (alleviation of restriction of DNA) in addition to another antirestriction protein, ArdA,
      described previously. The relevant gene, ardB was located in the leading region of pKM101,
      about 7 kb from oriT. The nucleotide sequence of ardB was determined, and an appropriate
      polypeptide was identified in maxicells of Escherichia coli. Like ArdA, ArdB efficiently
      inhibits restriction by members of the three known families of type I systems of E. coli and
      only slightly affects the type II enzymes, EcoRI. However, in contrast to ArdA, ArdB is
      ineffective against the modification activity of the type I (EcoK) system. Comparison of
      deduced amino acid sequences of ArdA and ArdB revealed only one small region of similarity
      (nine residues), suggesting that this region may be somehow involved in the interaction with
      the type I restriction systems. We also found that the expression of both ardA and ardB genes
      is controlled jointly by two pKM101-encoded proteins, ArdK and ArdR, with molecular weights of
      about 15,000 and 20,000 respectively. The finding that the sequences immediately upstream of
      ardA and ardB share about 94% identity over 218 bp suggests that their expression may be
      controlled by ArdK and ArdR at the transcriptional level. Deletion studies and promoter probe
      analysis of these sequences revealed the regions responsible for the action of ArdK and ArdR
      as regulatory proteins. We propose that both types of antirestriction proteins may play a
      pivotal role in overcoming the host restriction barrier by self-transmissible broad-host-range
      plasmids. It seems likely that the ardKR-dependent regulatory system serves in this case as a
      genetic switch that controls the expression of plasmid-encoded antirestriction functions
      during mating.
AU  - Belogurov AA
AU  - Delver EP
AU  - Rodzevich OV
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1993 175: 4843-4850.

PMID- 1321121
VI  - 174
DP  - 1992
TI  - IncN plasmid pKM101 and IncI1 Plasmid ColIb-P9 encode homologous antirestriction proteins in their leading regions.
PG  - 5079-5085
AB  - The IncN plasmid pKM101 (a derivative of R46), like the the IncI1 plasmid ColIb-P9, carries a
      gene (ardA, for alleviation of restriction of DNA) encoding an antirestriction function, ardA
      was located about 4 kb from the origin of transfer, in the region transferred early during
      bacterial conjugation. The nucleotide sequence of ardA was determined, and an appropriate
      polypeptide with the predicted molecular weight of about 19,500 was identified in maxicells of
      Escherichia coli. Comparison of the deduced amino acid sequences of the antirestriction
      proteins of the unrelated plasmids pKM101 and ColIb (ArdA and Ard, respectively) revealed that
      these proteins have about 60% identify. Like ColIb ard, pMK101 ArdA specifically inhibits both
      the restriction and modification activities of five type I systems of E. coli tested and does
      not influence type III (EcoPI) restriction or the 5-methylcytosine-specific restriction
      systems McrA and McrBC. However, in contrast to ColIb ard, pKM101 ArdA is effective against
      the type II enzyme EcoRI. The Ard proteins are believed to overcome the host restriction
      barrier during bacterial conjugation. We have also identified two other genes of pKM101, ardR
      and ardK, which seem to control ardA activity and ardA-medicated lethality, respectively. Our
      findings suggest that ardR may serve as a genetic switch that determines whether the ard-A
      encoded antirestriction function is induced during mating.
AU  - Belogurov AA
AU  - Delver EP
AU  - Rodzevich OV
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1992 174: 5079-5085.

PMID- 2833697
VI  - 12
DP  - 1987
TI  - Alleviation of type I restriction in Escherichia coli: Effect of 2-amino-purine and 5-bromouracil.
PG  - 34-40
AB  - 2-aminopurine and 5-bromouracil, strong mutagens of the base analog type, were found to induce
      efficiently the alleviation of type I restriction in Escherichia coli.  2-AP induced
      restriction alleviation occurs in recA, lexA and mut- mutants, but no additional relief of
      restriction is registered in dam- bacteria in the presence of sublethal 2-AP concentrations.
      2-AP specifically alleviates type I restriction in Escherichia coli (EcoA, EcoB, EcoD, and
      EcoK) and does not affect restriction system of types II (EcoRI) and III (EcoPI).  We suggest
      that 2-AP-induced mismatches and other replication errors may be signals inducing restriction
      alleviation in Escherichia coli.
AU  - Belogurov AA
AU  - Efimova EP
AU  - Delver EP
AU  - Zavilgelsky GB
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1987 12: 34-40.

PMID- 2828936
VI  - 9
DP  - 1987
TI  - Alleviation of I type restriction in E. coli: Effect of a dam mutation.
PG  - 10-16
AB  - The host-controlled EcoK-restriction of unmodified phages lambda.0 and T7 ocr, is 100-fold
      alleviated in dam- mutants of E. coli.  In addition the EcoK modification activity is
      considerably decreased in dam- strains.  Type I and III restriction (EcoB, EcoD, EcoK and
      EcoPI) were relieved in dam- mutants, but no alleviation of EcoRI restriction occurred in dam-
      strains.  We interpret the alleviation of the type I restriction in dam- mutants as a
      consequence of induction of the function, which interferes with the type I restriction
      systems.
AU  - Belogurov AA
AU  - Efimova EP
AU  - Delver EP
AU  - Zavilgelsky GB
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1987 9: 10-16.

PMID- 2989658
VI  - 198
DP  - 1985
TI  - The novel gene(s) ARD of plasmid pKM101: alleviation of EcoK restriction.
PG  - 509-513
AB  - The host-controlled K restriction of unmodified phage lambda was 10-100 fold
      alleviated in the wild-type strain E.coli K12, carrying plasmid pKM101 of
      incompability group N.  pKM101-mediated release of K restriction was also
      observed in lexA-, recA-, and recB- strains of E.coli K12.  By restriction
      mapping Tn5 insertions in pKM101, which reduced pKM101-mediated alleviation of
      restriction, were shown to be located within the BglIIB fragment approximately
      11kb anticlockwise from the RI site of pKM101.  We have termed the gene(s)
      promoting the alleviation of K restriction of phage lambda ard (alleviation of
      restriction of DNA).  It was shown (1) that ard function affected only the EcoK
      restriction system and not the EcoB, EcoRI, EcoRIII, or EcoPI systems, (2) ard
      gene(s) did not mediate EcoK type modification of lambda DNA and did not
      increase the modification activity of the EcoK system in a way similar to that
      observed with gene ral of bacteriophage lambda.
AU  - Belogurov AA
AU  - Yussifov TN
AU  - Kotova VU
AU  - Zavilgelsky GB
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1985 198: 509-513.

PMID- 6305613
VI  - 269
DP  - 1983
TI  - Effect of plasmid pKM101 on the K-specific restriction-modification of bacteriophage lambda DNA.
PG  - 738-741
AB  - 
AU  - Belogurov AA
AU  - Zavilgelskii GB
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1983 269: 738-741.

PMID- 379609
VI  - 13
DP  - 1979
TI  - The repair of the interstrand cross links in DNA: Role of restriction system K.
PG  - 160-168
AB  - The interstrand cross links formed in the DNA after psoralen plus light treatment of bacteria
      E. coli K12 and bacteriophage lambda are repaired by the restriction and modification system
      K.  Strain E. coli C, which does not have the restriction and modification system is 2 times
      more sensitive to psoralen plus light treatment, than the wild type E. coli K12.  But these
      strains are equally sensitive to inactivation by UV-light (254 nm).  By studying the
      sedimentation of bacterial DNA in alkaline sucrose it was found that cells of E. coli C are
      deficieint in filling of gaps, appearing in parental DNA after enzymatic excision of the arms
      of cross links.  In experiments with bacteriophage lambda (W-reactivation,
      prophage-reactivation), treated by psoralen plus light, it was shown that E. coli C and
      mutants of E. coli K12 rR-mR+/- are deficient in non-recombination lexA-dependent repair of
      cross links.  The function of restriction and recognition of restriction and modification
      system are essential for repair of cross links.  It is suggested that the restriction and
      modification system K acts either as a regulatory protein or as a protector of single-stranded
      regions of DNA against nuclease attack.
AU  - Belogurov AA
AU  - Zavilgelsky GB
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1979 13: 160-168.

PMID- 6265314
VI  - 17
DP  - 1981
TI  - Transformation and transduction of Bacillus subtilis strains possessing the BsuR system of restriction-modification by nonmodified and modified plasmid pUB110 DNA.
PG  - 794-800
AB  - Plasmid pUB110 DNA is restricted and modified during transformation of Bacillus subtilis cells
      possessing the BsuR system of restriction-modification.  Restriction has comparatively little
      influence on the frequency of plasmid transformation only reducing it 20 times.  The frequency
      of transduction of nonmodified plasmid DNA into modifying recipient cells, using phage Ar9 is
      also reduced a little.  The frequency of transduction of chromosomal markers is much more
      lowered under the same experimental conditions.
AU  - Belova TS
AU  - Surikov NN
AU  - Prozorov AA
PT  - Journal Article
TA  - Genetika
JT  - Genetika
SO  - Genetika 1981 17: 794-800.

PMID- 15212790
VI  - 236
DP  - 2004
TI  - A new vector, pGID052, for genetic transfer in Oenococcus oeni.
PG  - 53-60
AB  - Despite the large number of techniques available for the transformation of
      bacteria, several species are still resistant to the introduction of
      foreign DNA. Oenococcus oeni are among the organisms that are particularly
      refractory to transformation. However, conjugal experiments from
      Lactococcus lactis to O. oeni with a new plasmid, pGID052, were performed
      via mobilization with success. This plasmid, a derivative of pORI19,
      encompasses: (i) the oriT of pIP501, which permitted the transfer to O.
      oeni, (ii) the replication genes of a native Leuconostoc citreum plasmid.
      Frequencies of 10(-7) conjugants per recipient were found. The transfer
      did not affect the structure of this low-copy-number plasmid. Moreover,
      pGID052 seems segregationally stable and could be used in the future as an
      expression vector.
AU  - Beltramo C
AU  - Oraby M
AU  - Bourel G
AU  - Garmyn D
AU  - Guzzo J
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2004 236: 53-60.

PMID- 26464750
VI  - 10
DP  - 2015
TI  - Draft genome sequence of Mesotoga strain PhosAC3, a mesophilic member of the bacterial order Thermotogales, isolated from a digestor treating phosphogypsum in  Tunisia.
PG  - 12
AB  - Mesotoga strain PhosAc3 was the first mesophilic cultivated member of the order Thermotogales.
      This genus currently contain two described species, M. prima and
      M. infera. Strain PhosAc3, isolated from a Tunisian digestor treating
      phosphogypsum, is phylogenetically closely related to M. prima strain
      MesG1.Ag.4.2(T). Strain PhosAc3 has a genome of 3.1 Mb with a G+C content of
      45.2%. It contains 3,051 protein-coding genes of which 74.6% have their best
      reciprocal BLAST hit in the genome of the type species, strain MesG1.Ag.4.2(T).
      For this reason we propose to assign strain PhosAc3 as a novel ecotype of the
      Mesotoga prima species. However, in contrast with the M. prima type strain, (i)
      it does not ferment sugars but uses them only in the presence of elemental sulfur
      as terminal electron acceptor, (ii) it produces only acetate and CO2 from sugars,
      whereas strain MesG1.Ag.4.2(T) produces acetate, butyrate, isobutyrate,
      isovalerate, 2-methyl-butyrate and (iii) sulfides are also end products of the
      elemental sulfur reduction in theses growth conditions.
AU  - Ben Hania W
AU  - Fadhlaoui K
AU  - Brochier-Armanet C
AU  - Persillon C
AU  - Postec A
AU  - Hamdi M
AU  - Dolla A
AU  - Ollivier B
AU  - Fardeau ML
AU  - Le Mer J
AU  - Erauso G
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 12.

PMID- 26203324
VI  - 10
DP  - 2015
TI  - Complete genome sequence and description of Salinispira pacifica gen. nov., sp. nov., a novel spirochaete isolated form a hypersaline microbial mat.
PG  - 7
AB  - During a study of the anaerobic microbial community of a lithifying hypersaline microbial mat
      of Lake 21 on the Kiritimati atoll (Kiribati Republic, Central
      Pacific) strain L21-RPul-D2(T) was isolated. The closest phylogenetic neighbor
      was Spirochaeta africana Z-7692(T) that shared a 16S rRNA gene sequence identity
      value of 90% with the novel strain and thus was only distantly related. A
      comprehensive polyphasic study including determination of the complete genome
      sequence was initiated to characterize the novel isolate. Cells of strain
      L21-RPul-D2(T) had a size of 0.2 - 0.25 x 8-9 mum, were helical, motile, stained
      Gram-negative and produced an orange carotenoid-like pigment. Optimal conditions
      for growth were 35 degrees C, a salinity of 50 g/l NaCl and a pH around 7.0.
      Preferred substrates for growth were carbohydrates and a few carboxylic acids.
      The novel strain had an obligate fermentative metabolism and produced ethanol,
      acetate, lactate, hydrogen and carbon dioxide during growth on glucose. Strain
      L21-RPul-D2(T) was aerotolerant, but oxygen did not stimulate growth. Major
      cellular fatty acids were C14:0, iso-C15:0, C16:0 and C18:0. The major polar
      lipids were an unidentified aminolipid, phosphatidylglycerol, an unidentified
      phospholipid and two unidentified glycolipids. Whole-cell hydrolysates contained
      L-ornithine as diagnostic diamino acid of the cell wall peptidoglycan. The
      complete genome sequence was determined and annotated. The genome comprised one
      circular chromosome with a size of 3.78 Mbp that contained 3450 protein-coding
      genes and 50 RNA genes, including 2 operons of ribosomal RNA genes. The DNA G + C
      content was determined from the genome sequence as 51.9 mol%. There were no
      predicted genes encoding cytochromes or enzymes responsible for the biosynthesis
      of respiratory lipoquinones. Based on significant differences to the uncultured
      type species of the genus Spirochaeta, S. plicatilis, as well as to any other
      phylogenetically related cultured species it is suggested to place strain
      L21-RPul-D2(T) (=DSM 27196(T) = JCM 18663(T)) in a novel species and genus, for
      which the name Salinispira pacifica gen. nov., sp. nov. is proposed.
AU  - Ben Hania W
AU  - Joseph M
AU  - Schumann P
AU  - Bunk B
AU  - Fiebig A
AU  - Sproer C
AU  - Klenk HP
AU  - Fardeau ML
AU  - Spring S
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 7.

PMID- 21398539
VI  - 193
DP  - 2011
TI  - Complete genome sequence of the canine pathogen Staphylococcus pseudintermedius.
PG  - 2363-2364
AB  - We report the first whole genome sequence for a clinical isolate of Staphylococcus
      pseudintermedius (ED99), the major pathogen responsible for canine bacterial pyoderma. S.
      pseudintermedius contains numerous mobile genetic elements, and encodes an array of putative
      virulence factors including superantigenic, cytolytic and exfoliative toxins, and cell-wall
      associated surface proteins.
AU  - Ben Zakour NL
AU  - Bannoehr J
AU  - van den Broek AH
AU  - Thoday KL
AU  - Fitzgerald JR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 2363-2364.

PMID- 2453846
VI  - 16
DP  - 1988
TI  - Effect of cytosine methylation on the cleavage of oligonucleotide duplexes with restriction endonucleases HpaII and MspI.
PG  - 4160
AB  - the pattern of eucaryotic DNA methylation is commonly determined by restriction
      analysis with methylation-sensitive enzymes.  Due to the likely biological
      significance of hemimethylated CpG dinucleotides, we investigated the MspI and
      HpaII hydrolysis of synthetic 29-mer oligos (Fig. 1a), unmethylated,
      hemimethylated or fully-methylated at the internal C residue of their
      recognition site CCGG.  As shown in Fig. 1b, MspI cleaved all the four
      substrates, irrespective of their state of methylation.  HpaII failed to digest
      the symmetrically-methylated duplex (mC29/mC33), while the unmethylated duplex
      (C29/C33) was completely and efficiently digested.  Surprisingly, neither
      cleavage nor nicking of the unmethylated strand were observed with the
      hemimethylated substrates.  These results demonstrate that the use of HpaII in
      the search for regions of active, unmethylated chromatin would fail to identify
      hemimethylated CpG sites, recently shown to be involved in the process of
      transcriptional gene activation.
AU  - Ben-Hattar J
AU  - Jiricny J
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1988 16: 4160.

PMID- 7750734
VI  - 128
DP  - 1995
TI  - pUCL287 plasmid from Tetragenococcus halophila (Pediococcus halophilus) ATCC 33315 represents a new theta-type replicon family of lactic acid bacteria.
PG  - 167-175
AB  - A cryptic plasmid, pUCL287, was isolated from Tetragenococcus halophila
      (Pediococcus halophilus) ATCC 33315. It had a theta-type mechanism of
      replication in its natural host. Its minimal replicon, Rep287, was
      isolated on a 1.6-kb EcoRI fragment. The Rep287 host range included the
      genera Pediococcus, Enterococcus, Lactobacillus and Leuconostoc but not
      genus Lactococcus. Plasmids hybridizing to pUCL287 are rare among lactic
      acid bacteria. As assessed by hybridization, Rep287 is dissimilar to pAM
      beta 1, pIP501 and pUCL22, representatives of the most common theta-type
      replicon groups in Gram-positive bacteria. Therefore, pUCL287 appears to
      represent a new theta-type replicon family from lactic acid bacteria.
AU  - Benachour A
AU  - Frere J
AU  - Novel G
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1995 128: 167-175.

PMID- 25301652
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Streptococcus bovis Strains ATCC 33317 and JB1.
PG  - e01012-14
AB  - We report the draft genome sequences of Streptococcus bovis strain ATCC 33317 (CVM42251)
      isolated from cow dung and strain JB1 (CVM42252) isolated from a cow
      rumen in 1977. The strains were sequenced using the Genome Sequencer FLX 454
      system. The genome sizes are approximately 2 Mb and 2.2 Mb, respectively.
AU  - Benahmed FH
AU  - Gopinath GR
AU  - Harbottle H
AU  - Cotta MA
AU  - Luo Y
AU  - Henderson C
AU  - Teri P
AU  - Soppet D
AU  - Rasmussen M
AU  - Whitehead TR
AU  - Davidson M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01012-14.

PMID- 24459266
VI  - 2
DP  - 2014
TI  - Whole-Genome Sequencing of Salmonella enterica subsp. enterica Serovar Cubana Strains Isolated from Agricultural Sources.
PG  - e01184-13
AB  - We report the draft genomes of Salmonella enterica subsp. enterica serovar Cubana strain
      CVM42234, isolated from chick feed in 2012, and S. Cubana strain 76814,
      isolated from swine in 2004. The genome sizes are 4,975,046 and 4,936,251 bp,
      respectively.
AU  - Benahmed FH
AU  - Gopinath GR
AU  - Wang H
AU  - Jean-Gilles BJ
AU  - Grim C
AU  - Cheng CM
AU  - McClelland M
AU  - Ayers S
AU  - Abbott J
AU  - Desai P
AU  - Frye JG
AU  - Weinstock G
AU  - Hammack TS
AU  - Hanes DE
AU  - Rasmussen MA
AU  - Davidson MK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01184-13.

PMID- 27609912
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Clostridium septicum Strain CSUR P1044, Isolated from the Human Gut Microbiota.
PG  - e00922-16
AB  - Clostridium septicum is one of the first pathogenic anaerobes to be identified. Here, we
      announce the genome draft sequence of C. septicum strain CSUR P1044
      isolated from the gut of a healthy adult. Its chromosome genome consists of 3.2
      Mbp with a plasmid of 32 Kbp. C. septicum strain CSUR P1044 has a G+C content of
      27.5%, and is composed of 3,125 protein-coding genes together with 103 RNA genes,
      including 22 rRNA genes.
AU  - Benamar S
AU  - Cassir N
AU  - Caputo A
AU  - Cadoret F
AU  - La Scola B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00922-16.

PMID- 26798088
VI  - 4
DP  - 2016
TI  - Genome Sequence of a Clostridium neonatale Strain Isolated in a Canadian Neonatal Intensive Care Unit.
PG  - e01431-15
AB  - Clostridium neonatale is a Gram-positive endospore-forming obligate anaerobe first isolated
      from the feces of premature neonates during an intensive care unit
      outbreak of necrotizing enterocolitis (NEC) in a Canadian neonatal intensive care
      unit. Here, we announce the genome draft sequence of this bacterium. It is
      composed of 4,710,818 bp and contains 4,169 protein-coding genes and 80 RNA
      genes, including 11 rRNA genes.
AU  - Benamar S
AU  - Cassir N
AU  - La Scola B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01431-15.

PMID- 25540358
VI  - 2
DP  - 2014
TI  - Genome Sequence of Afipia felis Strain 76713, Isolated in Hospital Water Using an Amoeba Co-Culture Procedure.
PG  - e01367-14
AB  - Afipia felis is a Gram-negative alphaproteobacterium originally described as the  agent of
      cat-scratch disease (CSD). We sequenced the genome from a strain of A.
      felis, which was recovered from a hospital water sample using an amoebal
      co-culture procedure. It is composed of 3,989,646 bp, with a G+C content of
      61.27% and encodes 4,068 protein-coding genes and 53 RNA genes.
AU  - Benamar S
AU  - La Scola B
AU  - Croce O
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01367-14.

PMID- 2095920
VI  - 72
DP  - 1990
TI  - Characterization and comparison of virulent bacteriophages of Streptococcus thermophilus isolated from yogurt.
PG  - 855-862
AB  - Seven virulent bacteriophages of Streptococcus thermophilus were characterized at the
      molecular level and classified into 2 subgroups (A and B) by DNA/DNA hybridization experiments
      and analysis of their structural proteins. Two representatives of subgroups A and B were
      compared to 3 representatives of Neve's subgroups I, II and III (Neve et al, 1989) by
      Southern blot experiments. These isometric-headed phages possess a double-stranded DNA genome
      varying between 30-44 kilobase (kb) pairs. Subgroup A is composed of 3 phages (phi 57 as
      representative) with similar structural proteins as determined by sodium dodecyl
      sulfate-polyacrylamide gel (SDS-PAGE) electrophoresis (estimated molecular weight of 31,000
      and 27,500 for phage phi 57 and 32,000 and 27,000 for the 2 others). A common structural
      protein of 43,000 was found for phages of subgroup B. Phages phi 57(subgroup D) and a10/J9 or
      PO (Neve's subgroups I or II, respectively) belonged to the same subgroup as determined by
      DNA/DNA hybridization experiments. Partial DNA homology was detected among all the phages
      tested except for phage phi ST27 of AW Jarvis. Phage-host interactions were also investigated
      by cross-propagation of the 7 studied phages on different indicator strains. A complete lack
      of correlation existed between the DNA homology grouping of the phages and their host range.
      Various restriction-modification systems were detected in some of the Streptococcus
      thermophilus strains.
AU  - Benbadis L
AU  - Faelen M
AU  - Slos P
AU  - Fazel A
AU  - Mercenier A
PT  - Journal Article
TA  - Biochimie
JT  - Biochimie
SO  - Biochimie 1990 72: 855-862.

PMID- 1785940
VI  - 57
DP  - 1991
TI  - Purification, properties, and sequence specificity of SslI, a new type II restriction endonuclease from Streptococcus salivarius subsp. thermophilus.
PG  - 3677-3678
AB  - SslI, a type II restriction endonuclease, was purified from Streptococcus
      salivarius subsp. thermophilus strain BSN 45.  SslI is an isoschizomer of
      BstNI.  SslI activity was maximum at pH 8.8, 0 to 50 mM NaCl, 2 to 8 mM Mg2+,
      and 42C.  Activity against phage DNA in vitro was demonstrated.
AU  - Benbadis L
AU  - Garel JR
AU  - Hartley DL
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1991 57: 3677-3678.

PMID- 17921274
VI  - 73
DP  - 2007
TI  - Metagenomic characterization of Chesapeake Bay virioplankton.
PG  - 7629-7641
AB  - Viruses are ubiquitous and abundant throughout the biosphere. In marine systems,
      virus-mediated processes can have significant impacts on microbial diversity and on global
      biogeocehmical cycling. However, viral genetic diversity remains poorly characterized. To
      address this shortcoming, a metagenomic library was constructed from Chesapeake Bay
      virioplankton. The resulting sequences constitute the largest collection of long-read
      double-stranded DNA (dsDNA) viral metagenome data reported to date. BLAST homology comparisons
      showed that Chesapeake Bay virioplankton contained a high proportion of unknown (homologous
      only to environmental sequences) and novel (no significant homolog) sequences. This analysis
      suggests that dsDNA viruses are likely one of the largest reservoirs of unknown genetic
      diversity in the biosphere. The taxonomic origin of BLAST homologs to viral library sequences
      agreed well with reported abundances of cooccurring bacterial subphyla within the estuary and
      indicated that cyanophages were abundant. However, the low proportion of Siphophage homologs
      contradicts a previous assertion that this family comprises most bacteriophage diversity.
      Identification and analyses of cyanobacterial homologs of the psbA gene illustrated the value
      of metagenomic studies of virioplankton. The phylogeny of inferred PsbA protein sequences
      suggested that Chesapeake Bay cyanophage strains are endemic in that environment.  The ratio
      of psbA homologous sequences to total cyanophage sequences in the metagenome indicated that
      the psbA gene may be nearly universal in Chesapeake Bay cyanophage genomes. Furthermore, the
      low frequency ofpsbD homologs in the library supports the prediction that Chesapeake Bay
      cyanophage populations are dominated by Podoviridae.
AU  - Bench SR
AU  - Hanson TE
AU  - Williamson KE
AU  - Ghosh D
AU  - Radosovich M
AU  - Wang K
AU  - Wommack KE
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2007 73: 7629-7641.

PMID- 23995632
VI  - 195
DP  - 2013
TI  - Exploring the roles of DNA methylation in the metal-reducing bacterium Shewanella oneidensis MR-1.
PG  - 4966-4974
AB  - We performed whole genome analyses of DNA methylation in Shewanella oneidensis MR-1 to examine
      its possible role in regulating gene expression and other
      cellular processes. Single-Molecule Real Time (SMRT) sequencing revealed
      extensive methylation of adenine (N6mA) throughout the genome. These methylated
      bases were located in five sequence motifs, including three novel targets for
      Type I restriction/modification enzymes. The sequence motifs targeted by putative
      methyltranferases were determined via SMRT sequencing of gene knockout mutants.
      In addition, we found S. oneidensis MR-1 cultures grown under various culture
      conditions displayed different DNA methylation patterns. However, the small
      number of differentially methylated sites could not be directly linked to the
      much larger number of differentially expressed genes in these conditions,
      suggesting DNA methylation is not a major regulator of gene expression in S.
      oneidensis MR-1. The enrichment of methylated GATC motifs in the origin of
      replication indicate DNA methylation may regulate genome replication in a manner
      similar to that seen in Escherichia coli. Furthermore, comparative analyses
      suggest that many Gammaproteobacteria, including all members of the
      Shewanellaceae family, may also utilize DNA methylation to regulate genome
      replication.
AU  - Bendall ML
AU  - Luong K
AU  - Wetmore KM
AU  - Blow M
AU  - Korlach J
AU  - Deutschbauer A
AU  - Malmstrom RR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2013 195: 4966-4974.

PMID- 11511339
VI  - 106
DP  - 2001
TI  - A vicious cycle: RNA silencing and DNA methylation in plants.
PG  - 129-132
AB  - Several new studies have stimulated intense interest in understanding the mechanism and
      evolutionary significance of RNA silencing, the targeted degradation of RNA.  RNA silencing is
      typically triggered by double-stranded RNA (dsRNA).  The dsRNA trigger is diced into very
      small species of 21-25 nt (siRNAs), which then guide sequence-specific cleavage of other
      homologous RNAs, such as messenger RNAs.  Thus, both the trigger and target RNAs are
      ultimately destroyed.  This mechanism occurs in eukaryotic organisms as diverse as the
      laboratory plant Arabidopsis thaliana, nematode worms, and mice.  It is speculated that RNA
      silencing exists as a defense against invasive dsRNA species such as RNA viruses.  In fact,
      plants can recover from infection by RNA viruses via RNA silencing.  RNA silencing might also
      have a role in developmental regulation.  Furthermore, RNA silencing induced by injected dsRNA
      or dsRNA expressed from a transgene provides a powerful tool for reverse genetics in animals
      and plants.
AU  - Bender J
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 2001 106: 129-132.

PMID- 26586871
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of the Gut Commensal and Laboratory Strain Enterococcus faecium 64/3.
PG  - e01275-15
AB  - The genome sequence of the commensal and widely used laboratory strain
      Enterococcus faecium 64/3 was resolved by means of PacificBioscience and Illumina
      whole-genome sequencing. The genome comprises 2,575,333 bp with 2,382 coding
      sequences as assigned by NCBI.
AU  - Bender JK
AU  - Fiedler S
AU  - Klare I
AU  - Werner G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01275-15.

PMID- 23516225
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Microbacterium sp. Strain UCD-TDU (Phylum Actinobacteria).
PG  - e0012013
AB  - Here, we present the draft genome sequence of Microbacterium sp. strain UCD-TDU,  a member of
      the phylum Actinobacteria. The assembly contains 3,746,321 bp (in 8
      scaffolds). This strain was isolated from a residential toilet as part of an
      undergraduate student research project to sequence reference genomes of microbes
      from the built environment.
AU  - Bendiks ZA
AU  - Lang JM
AU  - Darling AE
AU  - Eisen JA
AU  - Coil DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0012013.

PMID- 25197503
VI  - 9
DP  - 2014
TI  - Non-contiguous finished genome sequence and description of Paucisalibacillus algeriensis sp. nov.
PG  - 1352-1365
AB  - Paucisalibacillus algeriensis strain EB02(T) is the type strain of Paucisalibacillus
      algeriensis sp. nov., a new species within the genus
      Paucisalibacillus. This strain, whose genome is described here, was isolated from
      soil sample from the hypersaline lake Ezzemoul Sabkha in northeastern Algeria.
      Paucisalibacillus algeriensis is a Gram-positive and strictly aerobic bacterium.
      Here we describe the features of this organism, together with the complete genome
      sequence and annotation. The 4,006,766 bp long genome (1 chromosome but no
      plasmid) exhibits a low G+C content of 36% and contains 3,956 protein-coding and
      82 RNA genes, including 9 rRNA genes.
AU  - Bendjama E
AU  - Loucif L
AU  - Diene SM
AU  - Michelle C
AU  - Gacemi-Kirane D
AU  - Rolain JM
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 1352-1365.

PMID- 25197482
VI  - 9
DP  - 2014
TI  - Non-contiguous finished genome sequence and description of Bacillus massilioalgeriensis sp. nov.
PG  - 1046-1061
AB  - Strain EB01(T) sp. nov. is the type strain of Bacillus massilioalgeriensis, a new species
      within the genus Bacillus. This strain, whose genome is described here,
      was isolated from sediment sample of the hypersaline lake Ezzemoul sabkha in
      northeastern Algeria. B. massilioalgeriensis is a facultative anaerobic
      Gram-positive bacillus. Here we describe the features of this organism, together
      with the complete genome sequence and annotation. The 5,269,577 bp long genome
      contains 5,098 protein-coding and 95 RNA genes, including 12 rRNA genes.
AU  - Bendjama E
AU  - Loucif L
AU  - Diene SM
AU  - Michelle C
AU  - Gacemi-Kirane D
AU  - Rolain JM
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 1046-1061.

PMID- 22038959
VI  - 193
DP  - 2011
TI  - Genome Sequence of the Diazotrophic Gram-Positive Rhizobacterium Paenibacillus riograndensis SBR5T.
PG  - 6391-6392
AB  - Paenibacillus riograndensis SBR5(T), a nitrogen-fixing Gram-positive rhizobacterium isolated
      from a wheat field in the south of Brazil, has a
      great potential for agricultural applications due to its plant growth
      promotion effects. Here we present the draft genome sequence of P.
      riograndensis SBR5(T). Its 7.37-Mb genome encodes determinants of the
      diazotrophic lifestyle and plant growth promotion, such as nitrogen
      fixation, antibiotic resistance, nitrate utilization, and iron uptake.
AU  - Beneduzi A
AU  - Campos S
AU  - Ambrosini A
AU  - de Souza R
AU  - Granada C
AU  - Costa P
AU  - Arruda L
AU  - Moreira F
AU  - Vargas LK
AU  - Weiss V
AU  - Tieppo E
AU  - Faoro H
AU  - de Souza EM
AU  - Pedrosa FO
AU  - Passaglia LM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6391-6392.

PMID- 18769471
VI  - 15
DP  - 2008
TI  - A mammalian microRNA cluster controls DNA methylation and telomere recombination via Rbl2-dependent regulation of DNA methyltransferases (vol 15, pg 268, 2008).
PG  - 998
AB  - Dicer initiates RNA interference by generating small RNAs involved in various silencing
      pathways.  Dicer participates in centromeric silencing, but its role in the epigenetic
      regulation of other chromatin domains has not been explored.  Here we show that Dicer1
      deficiency in Mus musculus leads to decreased DNA methylation, concomitant with increased
      telomere recombination and telomere elongation.  These DNA-methylation defects correlate with
      decreased expression of Dnmt1, Dnmt3a and Dnmt3b DNA methyltransferases, and methylation
      levels can be recoverd by their overexpression.  We identify the retinoblastoma-like 2 protein
      as responsible for decreased Dnmt expression in Dicer1-null cells, suggesting the existence of
      Dicer-dependent small RNAs that target Rbl2.  We identify the miR-290 cluster as being
      downregulated in Dicer1-deficient cells and show that it silences Rbl2, thereby controlling
      Dnmt expression.  These results identify a pathway by which miR-290 directly regulates
      Rbl2-dependent Dnmt expression, indirectly affecting telomere-length homeostasis.
AU  - Benetti R
AU  - Gonzalo S
AU  - Jaco I
AU  - Munoz P
AU  - Gonzalez S
AU  - Schoeftner S
AU  - Murchison E
AU  - Andl T
AU  - Chen T
AU  - Klatt P
AU  - Li E
AU  - Serrano M
AU  - Millar S
AU  - Hannon G
AU  - Blasco MA
PT  - Journal Article
TA  - Nat. Struct. Mol. Biol.
JT  - Nat. Struct. Mol. Biol.
SO  - Nat. Struct. Mol. Biol. 2008 15: 998.

PMID- 25767241
VI  - 3
DP  - 2015
TI  - Genome Sequence of Corynebacterium ulcerans Strain FRC11.
PG  - e00112-15
AB  - Here, we present the genome sequence of Corynebacterium ulcerans strain FRC11. The genome
      includes one circular chromosome of 2,442,826 bp (53.35% G+C content),
      and 2,210 genes were predicted, 2,146 of which are putative protein-coding genes,
      with 12 rRNAs and 51 tRNAs; 1 pseudogene was also identified.
AU  - Benevides LJ et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00112-15.

PMID- 26450730
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of the Acetogenic Bacterium Moorella thermoacetica DSM 2955T.
PG  - e01157-15
AB  - Here, we report the complete genome sequence of Moorella thermoacetica DSM 2955(T), an
      acetogenic bacterium, which uses the Wood-Ljungdahl pathway for reduction of H2 + CO2 or CO.
      The genome consists of a single circular chromosome  (2.62 Mb).
AU  - Bengelsdorf FR
AU  - Poehlein A
AU  - Esser C
AU  - Schiel-Bengelsdorf B
AU  - Daniel R
AU  - Durre P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01157-15.

PMID- 27908997
VI  - 4
DP  - 2016
TI  - Genome Sequence of the Acetogenic Bacterium Butyribacterium methylotrophicum DSM  3468T.
PG  - e01338-16
AB  - Butyribacterium methylotrophicum DSM 3468T is an acetogenic methylotrophic, anaerobic, carbon
      monoxide-oxidizing bacterium that produces acetate, butyrate,
      and butanol. The genome consists of a single chromosome (4.3 Mb) and harbors
      3,989 predicted protein-encoding genes.
AU  - Bengelsdorf FR
AU  - Poehlein A
AU  - Schiel-Bengelsdorf B
AU  - Daniel R
AU  - Durre P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01338-16.

PMID- 26634756
VI  - 3
DP  - 2015
TI  - Genome Sequence of the Acetogenic Bacterium Oxobacter pfennigii DSM 3222T.
PG  - e01408-15
AB  - Here, we report the draft genome sequence of Oxobacter pfennigii DSM 3222(T), an  anaerobic,
      acetogenic, carbon monoxide-oxidizing, and butyrate-producing
      bacterium. The genome consists of a chromosome with a size of 4.49 Mbp.
AU  - Bengelsdorf FR
AU  - Poehlein A
AU  - Schiel-Bengelsdorf B
AU  - Daniel R
AU  - Durre P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01408-15.

PMID- 
VI  - 5
DP  - 1995
TI  - Sequence context and DNA reactivity: Application to sequence-specific cleavage of DNA.
PG  - 1-55
AB  - Reactions between duplex DNA and ligands are largely dictated and mediated by the interplay of
      the structural, thermodynamic, and dynamic characteristics of DNA and the recognition
      mechanisms of reacting ligands.  Ligands that bind to DNA span a broad range of sizes from
      small cations to large proteins and assembled protein aggregates.  As might be expected, a
      wide variety of experimental strategies have been exploited to examine the sequence
      specificity, or lack thereof, exhibited by ligands that interact with DNA.  Sequence-dependent
      variations in local conformation and charge configuration along DNA are thought to be the
      principal means by which ligands discriminate between various DNA sequences.  In efforts to
      define the thermodynamic basis of such sequence-specific discrimination, a variety of
      parameters have been evaluated from studies of DNA alone and ligand/DNA complexes.
AU  - Benight AS
AU  - Gallo FJ
AU  - Paner TM
AU  - Bishop KD
AU  - Faldasz BD
AU  - Lane MJ
PT  - Journal Article
TA  - Adv. Biophys. Chem.
JT  - Adv. Biophys. Chem.
SO  - Adv. Biophys. Chem. 1995 5: 1-55.

PMID- 16279806
VI  - 48
DP  - 2005
TI  - Identification of borinic esters as inhibitors of bacterial cell growth and bacterial methyltransferases, CcrM and MenH.
PG  - 7468-7476
AB  - As bacteria continue to develop resistance toward current antibiotics, we find ourselves in a
      continual battle to identify new antibacterial agents and targets. We report herein a class of
      boron-containing compounds termed borinic esters that have broad spectrum antibacterial
      activity with minimum inhibitory concentrations (MIC) in the low microgram/mL range. These
      compounds were identified by screening for inhibitors against Caulobacter crescentus CcrM, an
      essential DNA methyltransferase from gram negative alpha-proteobacteria. In addition, we
      demonstrate that borinic esters inhibit menaquinone methyltransferase in gram positive
      bacteria using a new biochemical assay for MenH from Bacillus subtilis. Our data demonstrate
      the potential for further development of borinic esters as antibacterial agents as well as
      leads to explore more specific inhibitors against two essential bacterial enzymes.
AU  - Benkovic SJ
AU  - Baker SJ
AU  - Alley MRK
AU  - Woo YH
AU  - Zhang YK
AU  - Akama T
AU  - Mao WM
AU  - Baboval J
AU  - Rajagopalan PTR
AU  - Wall M
AU  - Kahng LS
AU  - Tavassoli A
AU  - Shapiro L
PT  - Journal Article
TA  - J. Med. Chem.
JT  - J. Med. Chem.
SO  - J. Med. Chem. 2005 48: 7468-7476.

PMID- 26798106
VI  - 4
DP  - 2016
TI  - Complete Genome Sequences of the Obligate Symbionts 'Candidatus Sulcia muelleri'  and 'Ca. Nasuia deltocephalinicola' from the Pestiferous Leafhopper Macrosteles  quadripunctulatus (Hemiptera: Cicadellidae).
PG  - e01604-15
AB  - Two bacterial symbionts of the European pest leafhopper, Macrosteles quadripunctulatus
      (Hemiptera: Cicadellidae), were fully sequenced. 'Candidatus
      Sulcia muelleri' and 'Ca. Nasuia deltocephalinicola' represent two of the
      smallest known bacterial genomes at 190 kb and 112 kb, respectively. Genome
      sequences are nearly identical to strains reported from the closely related host
      species, M. quadrilineatus.
AU  - Bennett GM
AU  - Abba S
AU  - Kube M
AU  - Marzachi C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01604-15.

PMID- 
VI  - 
DP  - 1987
TI  - Restriction enzymes with asymmetrical recognition sites.
PG  - 1-196
AB  - The class-II restriction endonucleases, CauI and CauII, recognize the DNA
      sequences, 5'-GG(A/T)CC-3' and 5'-CC(C/G)GG-3', respectively.  Both of these
      enzymes have been purified to homogeneity.  Molecular weight measurements
      indicate that the active form of the CauI enzyme is a dimer of identical
      protein subunits (of Mr 2 x 27500).  In contrast, CauII appears to be a
      heterologous dimer made up of different protein subunits (one of Mr 31500 and
      one of Mr 29000).  Kinetic studies using the replicative DNA (RFI) of phage
      PhiX174 as substrate, suggest that CauI and CauII cleave duplex DNA by a
      concerted mechanism, in which both strands of the DNA are cut within the
      lifetime of a single enzyme-DNA complex.  Each endonuclease shows the same
      activity towards its recognition site on both the supercoiled and relaxed forms
      of PhiX174 RFDNA.  This implies that the unwinding of the DNA plays no
      significant role in either the CauI or CauII cleavage reaction.  In standard
      reactions, CauI and CauII display high specificities towards their recognition
      sequences.  However, in the presence of dimethyl sulphoxide and at high pH,
      each enzyme cleaves DNA at sites that differ from its recognition sequence by
      one nucleotide.  The CauII enzyme cleaves DNA to generate fragments that have
      at their 5' termini, single nucleotide extensions of either 5'C or 5'G.
      Ligation of these fragments generates cytosine:cytosine in duplex DNA.
AU  - Bennett SP
PT  - Journal Article
TA  - Ph.D. Thesis, University of Bristol, UK
JT  - Ph.D. Thesis, University of Bristol, UK
SO  - Ph.D. Thesis, University of Bristol, UK 1987 : 1-196.

PMID- Not carried by PubMed...
VI  - 49
DP  - 1988
TI  - Restriction enzymes with asymmetrical recognition sites.
PG  - 722B
AB  - The class II restriction endonucleases, CauI and CauII, recognize the DNA
      sequences, 5'-GG(A/T)CC-3' and 5' -CC(C/G)GG-3', respectively.  Both of these
      enzymes have been purified to homogeneity.  Molecular weight measurements
      indicate that the active form of the CauI enzyme is a dimer of identical
      protein subunits (of Mr 2x27,500).  In contrast, CauII appears to be a
      heterologous dimer made up of different protein subunits (one of Mr 31,500 and
      one of Mr 29,000).  Kinetic studies using the replicative DNA (RFI) of phage
      PhiX174 as substrate, suggest that CauI and CauII cleave duplex DNA by a
      concerted mechanism, in which both strands of the DNA are cut within the
      lifetimes of a single enzyme-DNA complex.  Each endonuclease shows the same
      activity towards its recognition site on both the supercoiled and relaxed forms
      of PhiX174 RFDNA.  This implies that the unwinding of the DNA plays no
      significant role in either the CauI or CauII cleavage reaction.  In standard
      reactions, CauI and CauII display high specificities towards their recognition
      sequences.  However, in the presence of dimethyl sulphoxide and at high pH,
      each enzyme cleaves DNA at sites that differ from its recognition sequence by
      one nucleotide.  The CauII enzyme cleaves DNA to generate fragments of DNA that
      have at their 5' terminal, single nucleotide extensions of either 5' C or 5'G.
      Ligation of these fragments generates cytosine:cytosine in duplex DNA.
AU  - Bennett SP
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1988 49: 722B.

PMID- 
VI  - 
DP  - 1987
TI  - Mechanism and specificity of two restriction enzymes, CauI and CauII, that recognize asymmetrical DNA sequences.
PG  - 239-250
AB  - Type II restriction endonucleases are enzymes that recognize specific nucleotide sequences on
      duplex DNA and cleave both strands of the duplex at fixed locations relative to their
      recognition sites.  The only co-factor that they need is Mg2+, while type I and type III
      restriction enzymes also need ATP and S-adenosyl methionine for maximal activity.  Type I and
      type III enzymes also differ from type II by cleaving DNA at variable distances from their
      recognition sites.  Hence, the study of type II restriction enzymes was initially motivated by
      their unique applications in the analysis of DNA and in the construction of recombinant DNA
      molecules.  However, these enzymes also provide examples of DNA-protein interactions whose
      mechanisms are amenable to molecular analysis.
AU  - Bennett SP
AU  - Halford SE
PT  - Journal Article
TA  - DNA-ligand interactions: from drugs to proteins.
JT  - DNA-ligand interactions: from drugs to proteins.
SO  - DNA-ligand interactions: from drugs to proteins. 1987 : 239-250.

PMID- Not included in PubMed...
VI  - 14
DP  - 1986
TI  - Cytosine: cytosine formed in duplex DNA by the ligation of NciI- or CauII-cleaved DNA.
PG  - 259
AB  - The type II restriction endonucleases, CauII and its isoschizomer NciI, recognize the sequence
      5'-C-C/-G-G-G-3' 3'-G-G-C/-C-C-5' on duplex DNA and cleave each strand at the sites marked
      by arrows.  Hence these enzymes generate fragments of double-stranded DNA that have single
      nucleotide 5' extensions of either G or C.  The DNA ligase encoded by bacteriophage T4 can
      ligate DNA molecules that have either cohesive termini (due to single-strand extensions) or
      blunt ends.  The efficiency of blunt-end ligations is usually low but can be increased by
      adding polyethylene glycol to the reactions.
AU  - Bennett SP
AU  - Halford SE
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 1986 14: 259.

PMID- 2695290
VI  - 30
DP  - 1989
TI  - Recognition of DNA by Type II restriction enzymes.
PG  - 57-104
AB  - A review
AU  - Bennett SP
AU  - Halford SE
PT  - Journal Article
TA  - Curr. Top. Cell. Regul.
JT  - Curr. Top. Cell. Regul.
SO  - Curr. Top. Cell. Regul. 1989 30: 57-104.

PMID- 27348854
VI  - 18
DP  - 2016
TI  - Polysaccharide utilisation loci of Bacteroidetes from two contrasting open ocean sites in the North Atlantic.
PG  - 4456-4470
AB  - Marine Bacteroidetes have pronounced capabilities of degrading high molecular
      weight organic matter such as proteins and polysaccharides. Previously we
      reported on 76 Bacteroidetes-affiliated fosmids from the North Atlantic Ocean's
      boreal polar and oligotrophic subtropical provinces. Here, we report on the
      analysis of further 174 fosmids from the same libraries. The combined,
      re-assembled dataset (226 contigs; 8.8 Mbp) suggests that planktonic
      Bacteroidetes at the oligotrophic southern station use more peptides and
      bacterial and animal polysaccharides, whereas Bacteroidetes at the polar station
      (East-Greenland Current) use more algal and plant polysaccharides. The latter
      agrees with higher abundances of algae and terrigenous organic matter, including
      plant material, at the polar station. Results were corroborated by in-depth
      bioinformatic analysis of 14 polysaccharide utilisation loci from both stations,
      suggesting laminarin-specificity for four and specificity for sulfated xylans for
      two loci. In addition, one locus from the polar station supported use of
      non-sulfated xylans and mannans, possibly of plant origin. While peptides likely
      represent a prime source of carbon for Bacteroidetes in open oceans, our data
      suggest that as yet unstudied clades of these Bacteroidetes have a surprisingly
      broad capacity for polysaccharide degradation. In particular, laminarin-specific
      PULs seem widespread and thus must be regarded as globally important.
AU  - Bennke CM
AU  - Kruger K
AU  - Kappelmann L
AU  - Huang S
AU  - Gobet A
AU  - Schuler M
AU  - Barbe V
AU  - Fuchs BM
AU  - Michel G
AU  - Teeling H
AU  - Amann RI
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2016 18: 4456-4470.

PMID- 21952542
VI  - 193
DP  - 2011
TI  - Genome Sequence of Weissella thailandensis fsh4-2.
PG  - 5868
AB  - Weissella thailandensis fsh4-2 is a heterofermentative lactic acid bacterium isolated from the
      Korean fermented seafood condiment jeotkal.
      Here we report the draft genome sequence of W. thailandensis fsh4-2 (1,651
      genes, 1,436 encoding known proteins, 183 encoding unknown proteins, 32
      RNA genes), which consists of 50 large contigs of >100 bp.
AU  - Benomar N
AU  - Abriouel H
AU  - Lee H
AU  - Cho GS
AU  - Huch M
AU  - Pulido RP
AU  - Holzapfel WH
AU  - Galvez A
AU  - Franz CM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5868.

PMID- 16672428
VI  - 44
DP  - 2006
TI  - Presence of a novel DNA methylation enzyme in methicillin-resistant Staphylococcus aureus isolates associated with pig farming leads to  uninterpretable results in standard pulsed-field gel electrophoresis  analysis.
PG  - 1875-1876
AB  - Genomic DNA from methicillin-resistant Staphylococcus aureus isolates recovered from pigs and
      their caretakers proved resistant to SmaI
      digestion, leading to uninterpretable results in standard pulsed-field gel
      electrophoresis. This is the result of a yet unknown
      restriction/methylation system in the genus Staphylococcus with the
      recognition sequence CCNGG.
AU  - Bens CC
AU  - Voss A
AU  - Klaassen CH
PT  - Journal Article
TA  - J. Clin. Microbiol.
JT  - J. Clin. Microbiol.
SO  - J. Clin. Microbiol. 2006 44: 1875-1876.

PMID- 24962815
VI  - 93
DP  - 2014
TI  - Evolution of hypervirulence by a MRSA clone through acquisition of a transposable element.
PG  - 664-681
AB  - Staphylococcus aureus has evolved as a pathogen that causes a range of diseases
      in humans. There are two dominant modes of evolution thought to explain most of
      the virulence differences between strains. First, virulence genes may be acquired
      from other organisms. Second, mutations may cause changes in the regulation and
      expression of genes. Here we describe an evolutionary event in which
      transposition of an IS element has a direct impact on virulence gene regulation
      resulting in hypervirulence. Whole-genome analysis of a methicillin-resistant S.
      aureus (MRSA) strain USA500 revealed acquisition of a transposable element
      (IS256) that is absent from close relatives of this strain. Of the multiple
      copies of IS256 found in the USA500 genome, one was inserted in the promoter
      sequence of repressor of toxins (Rot), a master transcriptional regulator
      responsible for the expression of virulence factors in S. aureus. We show that
      insertion into the rot promoter by IS256 results in the derepression of cytotoxin
      expression and increased virulence. Taken together, this work provides new
      insight into evolutionary strategies by which S. aureus is able to modify its
      virulence properties and demonstrates a novel mechanism by which horizontal gene
      transfer directly impacts virulence through altering toxin regulation.
AU  - Benson MA
AU  - Ohneck EA
AU  - Ryan C
AU  - Alonzo F III
AU  - Smith H
AU  - Narechania A
AU  - Kolokotronis SO
AU  - Satola SW
AU  - Uhlemann AC
AU  - Sebra R
AU  - Deikus G
AU  - Shopsin B
AU  - Planet PJ
AU  - Torres VJ
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2014 93: 664-681.

PMID- 12000953
VI  - 417
DP  - 2002
TI  - Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2).
PG  - 141-147
AB  - Streptomyces coelicolor is a representative of the group of soil-dwelling, filamentous
      bacteria responsible for producing most natural antibiotics used in human and veterinary
      medicine.  Here we report the 8,667,507 base pair linear chromosome of this organism,
      containing the largest number of genes so far discovered in a bacterium.  The 7,825 predicted
      genes include more than 20 clusters coding for known or predicted secondary metabolites.  The
      genome contains an unprecedented proportion of regulatory genes, predominantly those likely to
      be involved in responses to external stimuli and stresses, and many duplicated gene sets that
      may represent 'tissue-specific' isoforms operating in different phases of colonial
      development, a unique situation for a bacterium.  An ancient synteny was revealed between the
      central 'core' of the chromosome and the whole chromosome of pathogens Mycobacterium
      tuberculosis and Corynebacterium diphtheriae.  The genome sequence will greatly increase our
      understanding of microbial life in the soil as well as aiding the generation of new drug
      candidates by genetic engineering.
AU  - Bentley SD et al
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2002 417: 141-147.

PMID- 12606174
VI  - 361
DP  - 2003
TI  - Sequencing and analysis of the genome of the Whipple's disease bacterium Tropheryma whipplei.
PG  - 637-644
AB  - BACKGROUND: Whipple's disease is a rare multisystem chronic infection, involving the
      intestinal tract as well as various other organs. The
      causative agent, Tropheryma whipplei, is a Gram-positive bacterium about
      which little is known. Our aim was to investigate the biology of this
      organism by generating and analysing the complete DNA sequence of its
      genome. METHODS: We isolated and propagated T whipplei strain TW08/27 from
      the cerebrospinal fluid of a patient diagnosed with Whipple's disease. We
      generated the complete sequence of the genome by the whole genome shotgun
      method, and analysed it with a combination of automatic and manual
      bioinformatic techniques. FINDINGS: Sequencing revealed a condensed 925938
      bp genome with a lack of key biosynthetic pathways and a reduced capacity
      for energy metabolism. A family of large surface proteins was identified,
      some associated with large amounts of non-coding repetitive DNA, and an
      unexpected degree of sequence variation. INTERPRETATION: The genome
      reduction and lack of metabolic capabilities point to a host-restricted
      lifestyle for the organism. The sequence variation indicates both known
      and novel mechanisms for the elaboration and variation of surface
      structures, and suggests that immune evasion and host interaction play an
      important part in the lifestyle of this persistent bacterial pathogen.
AU  - Bentley SD et al
PT  - Journal Article
TA  - Lancet
JT  - Lancet
SO  - Lancet 2003 361: 637-644.

PMID- 25414510
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Hoeflea sp. Strain BAL378, a Potential Producer of Bioactive Compounds.
PG  - e01213-14
AB  - Some phytoplankton-associated marine bacteria produce bioactive compounds. Members of the
      genus Hoeflea may be examples of such bacteria; however, data
      describing their metabolisms are scarce. Here, we report the draft genome
      sequence of Hoeflea sp. strain BAL378, a putative producer of bacteriocins,
      polyketides, and auxins, as demonstrated by genome mining.
AU  - Bentzon-Tilia M
AU  - Riemann L
AU  - Gram L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01213-14.

PMID- 5240030
VI  - 59
DP  - 1968
TI  - Restriction of infectious bacteriophage fd DNA's and an assay for in vitro host-controlled restriction and modification.
PG  - 1294-1299
AB  - Arber has shown that bacteriophage fd, which contains single-stranded circular
      DNA (Marvin and Schaller) is restricted by E. coli B and E. coli (P1)+.  This
      report presents detailed data on the restriction of both the infectious,
      single-stranded fd-phage DNA and the infectious, double-stranded fd-replicative
      form (RF) DNA.  It also describes an infectivity assay for in vitro
      host-controlled restriction and modification.  This assay has been used to find
      restriction enzymes in fractionated extracts of E. coli.
AU  - Benzinger R
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1968 59: 1294-1299.

PMID- 8019437
VI  - 32
DP  - 1994
TI  - Refolding of denatured restriction endonucleases with ribosomal preparations from Methanosarcina barkeri.
PG  - 315-323
AB  - Two restriction endonucleases, EcoRI and HindIII were denatured by guanidine HCl or by storing
      at room temperature (28oC) for several days. The activity of these enzymes could be restored
      by incubating with ribosomal preparations from an archaebacterium Methanosarcina barkeri.
      These results hint at a possible role of ribosomal preparations in folding polypeptides and
      could be useful in working with restriction enzymes in experiments on genetic engineering and
      molecular biology.
AU  - Bera AK
AU  - Das B
AU  - Chattopadhyay S
AU  - Dasgupta C
PT  - Journal Article
TA  - Biochem. Mol. Biol. Int.
JT  - Biochem. Mol. Biol. Int.
SO  - Biochem. Mol. Biol. Int. 1994 32: 315-323.

PMID- 26594306
VI  - 10
DP  - 2015
TI  - Complete genome sequence of type strain ARh 1, an obligately chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium isolated from a  Kenyan soda lake.
PG  - 105
AB  - Thioalkalivibrio paradoxus strain ARh 1T is a chemolithoautotrophic, non-motile,
      Gram-negative bacterium belonging to the Gammaproteobacteria that was isolated
      from samples of haloalkaline soda lakes. It derives energy from the oxidation of
      reduced sulfur compounds and is notable for its ability to grow on thiocyanate as
      its sole source of electrons, sulfur and nitrogen. The full genome consists of
      3,756,729 bp and comprises 3,500 protein-coding and 57 RNA-coding genes. This
      organism was sequenced as part of the community science program at the DOE Joint
      Genome Institute.
AU  - Berben T
AU  - Sorokin DY
AU  - Ivanova N
AU  - Pati A
AU  - Kyrpides N
AU  - Goodwin LA
AU  - Woyke T
AU  - Muyzer G
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 105.

PMID- 26512310
VI  - 10
DP  - 2015
TI  - Partial genome sequence of the haloalkaliphilic soda lake bacterium Thioalkalivibrio thiocyanoxidans ARh 2(T).
PG  - 85
AB  - Thioalkalivibrio thiocyanoxidans strain ARh 2(T) is a sulfur-oxidizing bacterium  isolated
      from haloalkaline soda lakes. It is a motile, Gram-negative member of
      the Gammaproteobacteria. Remarkable properties include the ability to grow on
      thiocyanate as the sole energy, sulfur and nitrogen source, and the capability of
      growth at salinities of up to 4.3 M total Na(+). This draft genome sequence
      consists of 61 scaffolds comprising 2,765,337 bp, and contains 2616
      protein-coding and 61 RNA-coding genes. This organism was sequenced as part of
      the Community Science Program of the DOE Joint Genome Institute.
AU  - Berben T
AU  - Sorokin DY
AU  - Ivanova N
AU  - Pati A
AU  - Kyrpides N
AU  - Goodwin LA
AU  - Woyke T
AU  - Muyzer G
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 85.

PMID- 26512309
VI  - 10
DP  - 2015
TI  - Partial genome sequence of Thioalkalivibrio thiocyanodenitrificans ARhD 1(T), a chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium capable of  complete denitrification.
PG  - 84
AB  - Thioalkalivibrio thiocyanodenitrificans strain ARhD 1(T) is a motile, Gram-negative bacterium
      isolated from soda lakes that belongs to the
      Gammaproteobacteria. It derives energy for growth and carbon fixation from the
      oxidation of sulfur compounds, most notably thiocyanate, and so is a
      chemolithoautotroph. It is capable of complete denitrification under anaerobic
      conditions. The draft genome sequence consists of 3,746,647 bp in 3 scaffolds,
      containing 3558 protein-coding and 121 RNA genes. T. thiocyanodenitrificans ARhD
      1(T) was sequenced as part of the DOE Joint Genome Institute Community Science
      Program.
AU  - Berben T
AU  - Sorokin DY
AU  - Ivanova N
AU  - Pati A
AU  - Kyrpides N
AU  - Goodwin LA
AU  - Woyke T
AU  - Muyzer G
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 84.

PMID- 9501183
VI  - 95
DP  - 1998
TI  - A cell cycle-regulated adenine DNA methyltransferase from Caulobacter crescentus processively methylates GANTC sites on hemimethylated DNA.
PG  - 2874-2879
AB  - The kinetic properties of an adenine DNA methyltransferase involved in cell cycle regulation
      of Caulobacter crescentus have been elucidated by using defined unmethylated or hemimethylated
      DNA substrates.  Catalytic efficiency is significantly enhanced with a DNAHM substrate.
      Biphasic kinetic behavior during methyl incorporation is observed when unmethylated or DNAHM
      substrates are used, indicating that a step after chemistry limits enzyme turnover and is most
      likely the release of enzyme from methylated DNA product.  The enzyme is thermally inactivated
      at 30oC within 20 min; this process substantially decreased in the presence of saturating
      concentrations of DNAHM, suggesting that the enzyme preferentially binds DNA before
      S-adenosylmethionine.  The activity of the enzyme shows an unusual sensitivity to salt levels,
      apparently dissociating more rapidly from methylated DNA product as the salt level is
      decreased.  The enzyme acts processively during methylation of specific DNA sequences,
      indicating a preferred order of product release in which S-adenosylhomocysteine is released
      from enzyme before fully methylated DNA.  The kinetic behavior and activity of the enzyme are
      consistent with the temporal constraints during the cell cycle-regulated methylation of newly
      replicated chromosomal DNA.
AU  - Berdis AJ
AU  - Lee I
AU  - Coward JK
AU  - Stephens C
AU  - Wright R
AU  - Shapiro L
AU  - Benkovic SJ
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1998 95: 2874-2879.

PMID- 26988043
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of 10 Bacillus subtilis Strains That Form Spores with High or Low Heat Resistance.
PG  - e00124-16
AB  - Here, we report the draft genome sequences of 10 isolates of Bacillus subtilis, a spore
      forming Gram-positive bacterium. The strains were selected from food
      products and produced spores with either high or low heat resistance.
AU  - Berendsen EM
AU  - Wells-Bennik MH
AU  - Krawczyk AO
AU  - de Jong A
AU  - van Heel A
AU  - Eijlander RT
AU  - Kuipers OP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00124-16.

PMID- 27151781
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Seven Thermophilic Spore-Forming Bacteria Isolated from Foods That Produce Highly Heat-Resistant Spores, Comprising Geobacillus spp.,  Caldibacillus debilis, and Anoxybacillus flavithermus.
PG  - e00105-16
AB  - Here, we report the draft genomes of five strains of Geobacillus spp., one Caldibacillus
      debilis strain, and one draft genome of Anoxybacillus flavithermus,
      all thermophilic spore-forming Gram-positive bacteria.
AU  - Berendsen EM
AU  - Wells-Bennik MH
AU  - Krawczyk AO
AU  - de Jong A
AU  - van Heel A
AU  - Holsappel S
AU  - Eijlander RT
AU  - Kuipers OP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00105-16.

PMID- 28007866
VI  - 4
DP  - 2016
TI  - Draft Whole-Genome Sequence of a Catalase-Negative Staphylococcus aureus subsp. aureus (Sequence Type 25) Strain Isolated from a Patient with Endocarditis and Septic Arthritis.
PG  - e01442-16
AB  - Staphylococcus aureus strains without catalase activity are rare, challenging to  identify
      with conventional biochemical methods, and, despite a supposed decreased pathogenicity, can
      still cause disease. The first whole-genome sequence of a catalase-negative S. aureus isolate
      causing severe recurrent invasive infection with two novel missense mutations in the katA gene
      is reported here.
AU  - Berenger B
AU  - Chen J
AU  - Bernier AM
AU  - Bernard K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01442-16.

PMID- 12761157
VI  - 71
DP  - 2003
TI  - Physical Map and Genome Sequencing Survey of Mycoplasma haemofelis (Haemobartonella felis).
PG  - 3657-3662
AB  - Mycoplasma haemofelis is an uncultivable red-cell pathogen of cats.
      Isolated M. haemofelis DNA was used to create a bacterial artificial
      chromosome library and physical map. Random sequencing of this material
      revealed 75 genes that had not been previously reported for M. haemofelis
      or any other hemotrophic mycoplasma.
AU  - Berent LM
AU  - Messick JB
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2003 71: 3657-3662.

PMID- 16636287
VI  - 103
DP  - 2006
TI  - Molecular genetic anatomy of inter- and intraserotype variation in the human bacterial pathogen group A Streptococcus.
PG  - 7059-7064
AB  - In recent years we have studied the relationship between strain genotypes and patient
      phenotypes in group A Streptococcus (GAS), a model human
      bacterial pathogen that causes extensive morbidity and mortality
      worldwide. We have concentrated our efforts on serotype M3 organisms
      because these strains are common causes of pharyngeal and invasive
      infections, produce unusually severe invasive infections, and can exhibit
      epidemic behavior. Our studies have been hindered by the lack of
      genome-scale phylogenies of multiple GAS strains and whole-genome
      sequences of multiple serotype M3 strains recovered from individuals with
      defined clinical phenotypes. To remove some of these impediments, we
      sequenced to closure the genome of four additional GAS strains and
      conducted comparative genomic resequencing of 12 contemporary serotype M3
      strains representing distinct genotypes and phenotypes. Serotype M3
      strains are a single phylogenetic lineage. Strains from asymptomatic
      throat carriers were significantly less virulent for mice than
      sterile-site isolates and evolved to a less virulent phenotype by multiple
      genetic pathways. Strain persistence or extinction between epidemics was
      strongly associated with presence or absence, respectively, of the
      prophage encoding streptococcal pyrogenic exotoxin A. A serotype M3 clone
      significantly underrepresented among necrotizing fasciitis cases has a
      unique frameshift mutation that truncates MtsR, a transcriptional
      regulator controlling expression of genes encoding iron-acquisition
      proteins. Expression microarray analysis of this clone confirmed
      significant alteration in expression of genes encoding iron metabolism
      proteins. Our analysis provided unprecedented detail about the molecular
      anatomy of bacterial strain genotype-patient phenotype relationships.
AU  - Beres SB
AU  - Richter EW
AU  - Nagiec MJ
AU  - Sumby P
AU  - Porcella SF
AU  - DeLeo FR
AU  - Musser JM
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2006 103: 7059-7064.

PMID- 18716664
VI  - 3
DP  - 2008
TI  - Genome sequence of a Lancefield group C Streptococcus zooepidemicus strain causing epidemic nephritis: new information about an old disease.
PG  - E3026
AB  - Outbreaks of disease attributable to human error or natural causes can provide
      unique opportunities to gain new information about host-pathogen interactions and
      new leads for pathogenesis research. Poststreptococcal glomerulonephritis (PSGN),
      a sequela of infection with pathogenic streptococci, is a common cause of
      preventable kidney disease worldwide. Although PSGN usually occurs after
      infection with group A streptococci, organisms of Lancefield group C and G also
      can be responsible. Despite decades of study, the molecular pathogenesis of PSGN
      is poorly understood. As a first step toward gaining new information about PSGN
      pathogenesis, we sequenced the genome of Streptococcus equi subsp. zooepidemicus
      strain MGCS10565, a group C organism that caused a very large and unusually
      severe epidemic of nephritis in Brazil. The genome is a circular chromosome of
      2,024,171 bp. The genome shares extensive gene content, including many virulence
      factors, with genetically related group A streptococci, but unexpectedly lacks
      prophages. The genome contains many apparently foreign genes interspersed around
      the chromosome, consistent with the presence of a full array of genes required
      for natural competence. An inordinately large family of genes encodes secreted
      extracellular collagen-like proteins with multiple integrin-binding motifs. The
      absence of a gene related to speB rules out the long-held belief that
      streptococcal pyrogenic exotoxin B or antibodies reacting with it singularly
      cause PSGN. Many proteins previously implicated in GAS PSGN, such as
      streptokinase, are either highly divergent in strain MGCS10565 or are not more
      closely related between these species than to orthologs present in other
      streptococci that do not commonly cause PSGN. Our analysis provides a comparative
      genomics framework for renewed appraisal of molecular events underlying APSGN
      pathogenesis.
AU  - Beres SB
AU  - Sesso R
AU  - Pinto SW
AU  - Hoe NP
AU  - Porcella SF
AU  - Deleo FR
AU  - Musser JM
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2008 3: E3026.

PMID- 12122206
VI  - 99
DP  - 2002
TI  - Genome sequence of a serotype M3 strain of group A Streptococcus: Phage-encoded toxins, the high-virulence phenotype, and clone emergence.
PG  - 10078-10083
AB  - Genome sequences are available for many bacterial strains, but there has been little progress
      in using these data to understand the molecular basis of pathogen emergence and differences in
      strain virulence. Serotype M3 strains of group A Streptococcus (GAS) are a common cause of
      severe invasive infections with unusually high rates of morbidity and mortality. To gain
      insight into the molecular basis of this high-virulence phenotype, we sequenced the genome of
      strain MGAS315, an organism isolated from a patient with streptococcal toxic shock syndrome.
      The genome is composed of 1,900,521 bp, and it shares approximately 1.7 Mb of related genetic
      material with genomes of serotype M1 and M18 strains. Phage-like elements account for the
      great majority of variation in gene content relative to the sequenced M1 and M18 strains.
      Recombination produces chimeric phages and strains with previously uncharacterized arrays of
      virulence factor genes. Strain MGAS315 has phage genes that encode proteins likely to
      contribute to pathogenesis, such as streptococcal pyrogenic exotoxin A (SpeA) and SpeK,
      streptococcal superantigen (SSA), and a previously uncharacterized phospholipase A(2)
      (designated Sla).  Infected humans had anti-SpeK, -SSA, and -Sla antibodies, indicating that
      these GAS proteins are made in vivo.  SpeK and SSA were pyrogenic and toxic for rabbits.
      Serotype M3 strains with the phage-encoded speK and sla genes increased dramatically in
      frequency late in the 20th century, commensurate with the rise in invasive disease caused by
      M3 organisms. Taken together, the results show that phage-mediated recombination has played a
      critical role in the emergence of a new, unusually virulent clone of serotype M3 GAS.
AU  - Beres SB
AU  - Sylva GL
AU  - Barbian KD
AU  - Lei B
AU  - Hoff JS
AU  - Mammarella ND
AU  - Liu M-Y
AU  - Smoot JC
AU  - Porcella SF
AU  - Parkins LD
AU  - Campbell DS
AU  - Smith TM
AU  - McCormick JK
AU  - Leung DYM
AU  - Schlievert PM
AU  - Musser JM
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2002 99: 10078-10083.

PMID- 9447657
VI  - 5
DP  - 1997
TI  - The Helicobacter pylori genome sequence: genetic factors for long life in the gastric mucosa.
PG  - 468-474
AB  - The complete DNA sequence of the chromosome of a strain of Helicobacter pylori was released in
      mid-1997 by The Institute for Genomic Research, a long-awaited and warmly welcomed event that
      should greatly stimulate research on this pathogen and benefit public health.  Infection by H,
      pylori occurs in more than half of all people worldwide and is a major cause of severe
      gastritis and peptic ulcer disease and an early risk factor for gastric cancer, although most
      infections are asymptomatic and some might even be beneficial.  H. pylori is Gram-negative,
      fastidious in its nutritional requirements and microaerophilic: it chronically infects human
      gastric epithelial cell surfaces and the overlying mucin layer.  Although some infections are
      cleared spontaneously after a brief acute phase, many last for years or decades, and it is
      these infections that are most often implicated in overt disease.
AU  - Berg DE
AU  - Hoffman PS
AU  - Appelmelk BJ
AU  - Kusters JG
PT  - Journal Article
TA  - Trends Microbiol.
JT  - Trends Microbiol.
SO  - Trends Microbiol. 1997 5: 468-474.

PMID- 19680555
VI  - 4
DP  - 2009
TI  - Diversity and strain specificity of plant cell wall degrading enzymes revealed by the draft genome of Ruminococcus flavefaciens FD-1.
PG  - E6650
AB  - BACKGROUND: Ruminococcus flavefaciens is a predominant cellulolytic rumen bacterium, which
      forms a multi-enzyme cellulosome complex that could play an integral role in the ability of
      this bacterium to degrade plant cell wall polysaccharides. Identifying the major enzyme types
      involved in plant cell wall degradation is essential for gaining a better understanding of the
      cellulolytic capabilities of this organism as well as highlighting potential enzymes for
      application in improvement of livestock nutrition and for conversion of cellulosic biomass to
      liquid fuels. METHODOLOGY/PRINCIPAL FINDINGS: The R. flavefaciens FD-1 genome was sequenced to
      29x-coverage, based on pulsed-field gel electrophoresis estimates (4.4 Mb), and assembled into
      119 contigs providing 4,576,399 bp of unique sequence. As much as 87.1% of the genome encodes
      ORFs, tRNA, rRNAs, or repeats. The GC content was calculated at 45%. A total of 4,339 ORFs was
      detected with an average gene length of 918 bp. The cellulosome model for R. flavefaciens was
      further refined by sequence analysis, with at least 225 dockerin-containing ORFs, including
      previously characterized cohesin-containing scaffoldin molecules. These dockerin-containing
      ORFs encode a variety of catalytic modules including glycoside hydrolases (GHs),
      polysaccharide lyases, and carbohydrate esterases. Additionally, 56 ORFs encode proteins that
      contain carbohydrate-binding modules (CBMs). Functional microarray analysis of the genome
      revealed that 56 of the cellulosome-associated ORFs were up-regulated, 14 were down-regulated,
      135 were unaffected, when R. flavefaciens FD-1 was grown on cellulose versus cellobiose. Three
      multi-modular xylanases (ORF01222, ORF03896, and ORF01315) exhibited the highest levels of
      up-regulation. CONCLUSIONS/SIGNIFICANCE: The genomic evidence indicates that R. flavefaciens
      FD-1 has the largest known number of fiber-degrading enzymes likely to be arranged in a
      cellulosome architecture. Functional analysis of the genome has revealed that the growth
      substrate drives expression of enzymes predicted to be involved in carbohydrate metabolism as
      well as expression and assembly of key cellulosomal enzyme components.
AU  - Berg-Miller ME
AU  - Antonopoulos DA
AU  - Rincon MT
AU  - Band M
AU  - Bari A
AU  - Akraiko T
AU  - Hernandez A
AU  - Thimmapuram J
AU  - Henrissat B
AU  - Coutinho PM
AU  - Borovok I
AU  - Jindou S
AU  - Lamed R
AU  - Flint HJ
AU  - Bayer EA
AU  - White BA
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2009 4: E6650.

PMID- 22004549
VI  - 14
DP  - 2012
TI  - Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome.
PG  - 207-227
AB  - Viruses are the most abundant biological entities on the planet and play an
      important role in balancing microbes within an ecosystem and facilitating
      horizontal gene transfer. Although bacteriophages are abundant in rumen
      environments, little is known about the types of viruses present or their
      interaction with the rumen microbiome. We undertook random pyrosequencing of
      virus-enriched metagenomes (viromes) isolated from bovine rumen fluid and
      analysed the resulting data using comparative metagenomics. A high level of
      diversity was observed with up to 28,000 different viral genotypes obtained from
      each environment. The majority (~78%) of sequences did not match any previously
      described virus. Prophages outnumbered lytic phages approximately 2:1 with the
      most abundant bacteriophage and prophage types being associated with members of
      the dominant rumen phyla (Firmicutes and Proteobacteria). Metabolic profiling
      based on SEED subsystems revealed an enrichment of sequences with putative
      functional roles in DNA and protein metabolism, but a surprisingly low proportion
      of sequences assigned to carbohydrate and amino acid metabolism. We expanded our
      analysis to include previously described metagenomic data and 14 reference
      genomes. Clustered regularly interspaced short palindromic repeats (CRISPR) were
      detected in most of the microbial genomes, suggesting previous interactions
      between viral and microbial communities.
AU  - Berg-Miller ME
AU  - Yeoman CJ
AU  - Chia N
AU  - Tringe SG
AU  - Angly FE
AU  - Edwards RA
AU  - Flint HJ
AU  - Lamed R
AU  - Bayer EA
AU  - White BA
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2012 14: 207-227.

PMID- 10866973
VI  - 79
DP  - 2000
TI  - Translocation-independent dimerization of the EcoKI endonuclease visualized by atomic force microscopy.
PG  - 479-484
AB  - Bacterial type I restriction/modification systems are capable of performing multiple actions
      in response to the methylation pattern on
      their DNA recognition sequences. The enzymes making up these systems
      serve to protect the bacterial cells against viral infection by binding
      to their recognition sequences on the invading DNA and degrading it
      after extensive ATP-driven translocation, DNA cleavage has been thought
      to occur as the result of a collision between two translocating enzyme
      complexes. Using atomic force microscopy (AFM), we show here that EcoKI
      dimerizes rapidly when bound to a plasmid containing two recognition
      sites for the enzyme. Dimerization proceeds in the absence of ATP and
      is also seen with an EcoKI mutant (K477R) that is unable to translocate
      DNA. Only monomers are seen when the enzyme complex binds to a plasmid
      containing a single recognition site. Based on our results, we propose
      that the binding of EcoKI to specific DNA target sequences is
      accompanied by a conformational change that leads rapidly to
      dimerization. This event is followed by ATP-dependent translocation and
      cleavage of the DNA.
AU  - Berge T
AU  - Ellis DJ
AU  - Dryden DTF
AU  - Edwardson JM
AU  - Henderson RM
PT  - Journal Article
TA  - Biophys. J.
JT  - Biophys. J.
SO  - Biophys. J. 2000 79: 479-484.

PMID- Not included in PubMed...
VI  - 11
DP  - 1990
TI  - Taxonomic significance of differences in DNA methylation within the Mycoplasma mycoides cluster' detected with restriction endonucleases MboI and DpnI.
PG  - 48-51
AB  - DNA from 22 strains belonging to the Mycoplasma mycoides cluster was tested for
      methylation of adenine in GATC sequences by its resistance or susceptibility to
      digestion by the restriction endonucleases MboI, which is inhibited by the
      methylation, or DpnI, which requires the methylation.  Strains of bovine
      serogroup 7, M. mycoides subsp. mycoides SC, and some M. mycoides subsp. capri
      strains plus M. capricolum strain Cal Kid lacked the methylation, whereas other
      strains of M. mycoides subsp. capri and of M. capricolum, plus the F38-like and
      M. mycoides subsp. mycoides LC strains, possessed it.  We conclude that this
      simple test could provide a valuable criterion in identifying these
      mycoplasmas.
AU  - Bergemann AD
AU  - Whitley JC
AU  - Finch LR
PT  - Journal Article
TA  - Lett. Appl. Microbiol.
JT  - Lett. Appl. Microbiol.
SO  - Lett. Appl. Microbiol. 1990 11: 48-51.

PMID- 23733457
VI  - 57
DP  - 2013
TI  - Characterization of a new blaOXA-48-carrying Plasmid in Enterobacteriaceae.
PG  - 4064-4067
AB  - In this work we characterized a new 160-kb blaOXA-48-harboring IncL/M-type
      plasmid, isolated from a Klebsiella pneumoniae strain from France. Moreover, we
      report the transfer of a 60-kb OXA-48 encoding plasmid from Klebsiella pneumoniae
      to other Enterobacteriaceae in two patients.
AU  - Berger S
AU  - Alauzet C
AU  - Aissa N
AU  - Henard S
AU  - Rabaud C
AU  - Bonnet R
AU  - Lozniewski A
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2013 57: 4064-4067.

PMID- 29146846
VI  - 5
DP  - 2017
TI  - High-Quality Draft Genome Sequence of 'Candidatus Methanoperedens sp.' Strain BLZ2, a Nitrate-Reducing Anaerobic Methane-Oxidizing Archaeon Enriched in an  Anoxic Bioreactor.
PG  - e01159-17
AB  - The high-quality draft genome of 'Candidatus Methanoperedens sp.' strain BLZ2, a
      nitrate-reducing archaeon anaerobically oxidizing methane, is presented. The
      genome was obtained from an enrichment culture and measures 3.74 Mb. It harbors
      two nitrate reductase gene clusters, an ammonium-forming nitrite reductase, and
      the complete reverse methanogenesis pathway. Methane that escapes to the
      atmosphere acts as a potent greenhouse gas. Global methane emissions are
      mitigated by methanotrophs, which oxidize methane to CO2 'Candidatus
      Methanoperedens spp.' are unique methanotrophic archaea that can perform
      nitrate-dependent anaerobic oxidation of methane. A high-quality draft genome
      sequence of only 85 contigs from this archaeon is presented here.
AU  - Berger S
AU  - Frank J
AU  - Dalcin MP
AU  - Jetten MSM
AU  - Welte CU
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01159-17.

PMID- 7856834
VI  - 222
DP  - 1994
TI  - Expanding the potential of restriction endonucleases: Use of hapaxoterministic enzymes.
PG  - 1-8
AB  - A new class of restriction endonucleases called hapoxoterministic enzymes, hapaxomers for
      short, has been defined. A hapaxomer cleaves DNA outside the recognition site or within an
      interrupted "palindrome" at bases which are not specified producing fragments with asymmetric,
      staggered ends. Such termini are unique; in the general case, the protrusions of a fragment
      obtained with the aid of a hapaxomer cannot self-hybridize, nor can the fragment be ligated to
      the vast majority of other fragments produced by the same enzyme. When the fragments generated
      by a hapaxoterministic enzyme are mixed, they can reassemble in only one configuration--that
      of the original structure from which they were derived. Hapaxomers, then, are characterized
      not by their recognition sites, which may be symmetric or asymmetric, but by their cleavage
      sites. The ability to reunite once-contiguous fragments efficiently means that hapaxomers
      cleaving DNA at many locations are virtually equivalent to restriction enzymes cutting at
      unique sites. These properties can be exploited for applications such as site-specific
      mutagenesis or the isolation of large intact DNA fragments.
AU  - Berger SL
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 1994 222: 1-8.

PMID- 11265302
VI  - 160
DP  - 2001
TI  - Gene modification with hapaxoterministic restriction enzymes.
PG  - 443-458
AB  - Subcloning can be extraordinarily easy or extremely difficult.  The simplest case requires
      cleavage of the desired fragment from the DNA in which it is located with one or two
      restriction enzymes, cleavage of the plasmid that will serve as the ultimate recipient with
      the same enzymes, and ligation of the fragment to the plasmid.  In a somewhat more complicated
      version of simple cloning, the investigator uses the polymerase chain reaction to amplify the
      DNA to be subcloned.  In this case, restriction sites can be incorporated into the primers
      used for PCR, generating products with the desired restriction sites located near the ends of
      the newly synthesized DNA.  After cleavage of those sites, the fragment is ready for insertion
      into an appropriately cut vector.  The major disadvantage of the method is the need for
      sequencing the amplified material, because even the best of the thermostable polymerases makes
      mistakes that might render the DNA useless for the anticipated application.
AU  - Berger SL
PT  - Journal Article
TA  - Methods Mol. Biol.
JT  - Methods Mol. Biol.
SO  - Methods Mol. Biol. 2001 160: 443-458.

PMID- 2201947
VI  - 18
DP  - 1990
TI  - The double role of methyl donor and allosteric effector of S-adenosyl-methionine for Dam methylase of E. coli.
PG  - 4369-4375
AB  - The turnover of DNA-adenine-methylase of E. coli strongly decreases when the temperature is
      lowered. This has allowed us to study the binding of Dam methylase on 14 bp DNA fragments at
      0C by gel retardation in the presence of Ado-Met, but without methylation taking place. The
      enzyme can bind nonspecific DNA with low affinity. Binding to the specific sequence occurs in
      the absence of S-adenosylmethionine (Ado-Met), but is activated by the presence of the methyl
      donor. The two competitive inhibitors of Ado-Met, sinefungin and S-adenosyl-homocysteine, can
      neither activate this binding to DNA by themselves, nor inhibit this activation by Ado-Met.
      This suggests that Ado-Met could bind to Dam methylase in two different environments. In one
      of them, it could play the role of an allosteric effector which would reinforce the affinity
      of the enzyme for the GATC site. The analogues can not compete for such binding. In the other
      environment Ado-Met would be in the catalytic site and could be exchanged by its analogues. We
      have also visualized conformational changes in Dam methylases induced by the simultaneous
      binding of Ado-Met and the specific target sequence of the enzyme, by an anomaly of migration
      and partial resistance to proteolytic treatment of the ternary complex Ado-Met/Dam
      methylase/GATC.
AU  - Bergerat A
AU  - Guschlbauer W
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 4369-4375.

PMID- 1862071
VI  - 88
DP  - 1991
TI  - Allosteric and catalytic binding of S-adenosylmethionine to Escherichia coli DNA adenine methyltransferase monitored by 3H NMR.
PG  - 6394-6397
AB  - Adenine methylation of GATC sequences in DNA is carried out by the DNA adenine
      methyltransferase with the methyl group source being the cofactor
      S-adenosylmethionine.  We report 3H NMR studies on the interaction of DNA
      adenine methyltransferase with S-adenosylmethionine and the reaction when the
      ternary complex is formed with an oligonucleotide containing a GATC site.  The
      methylation reaction was also studied in the presence of a competitive
      inhibitor and this showed two successive stages involved in the methylation and
      tw sites of binding for S-adenosylmethionine.
AU  - Bergerat A
AU  - Guschlbauer W
AU  - Fazakerley GV
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1991 88: 6394-6397.

PMID- 2645286
VI  - 264
DP  - 1989
TI  - Preferential site-specific hemimethylation of GATC sites in pBR322 DNA by dam methyltransferase from Escherichia coli.
PG  - 4064-4070
AB  - The methylation pattern of the 22 GATC sites of pBR322 (dam-) by Dam methyltransferase from
      Escherichia coli has been studied. Preferential hemimethylation took place at positions 3042
      and 349. It was found that these preferential methylations were the same in supercoiled
      circular and linear DNAs. The flanking regions of these preferentially methylated sites
      contain three GC pairs on one side and two AT pairs and one GC pair on the other. This
      preferential methylation was confirmed on a 126-base pair oligonucleotide containing two GATC
      sites with different flanking sequences. The next sites methylated were, in both cases, the
      first GATC site on the AT-rich side, although the orientation was different. The rapid
      methylation of a second and third neighboring GATC site on the same plasmid suggests a
      processive mechanism. The implications of the orientation of hemimethylation are discussed in
      the context of the recognition of a palindromic target site by a monomeric DNA-binding
      protein.
AU  - Bergerat A
AU  - Kriebardis A
AU  - Guschlbauer W
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1989 264: 4064-4070.

PMID- 8533472
VI  - 11
DP  - 1995
TI  - The sequence of a 44,420 bp fragment located on the left arm of chromosome XIV from Saccharomyces cerevisiae.
PG  - 967-974
AB  - We have determined the complete nucleotide sequence of a 44 420 bp DNA fragment from
      chromosome XIV of Saccharomyces cerevisiae. The sequence data revealed 23 open reading frames
      (ORFs) larger than 300 bp, covering 73.5% of the sequence. The ORFs N2418, N2428, N2441, N2474
      and N2480 correspond to previously sequenced S. cerevisiae genes coding respectively for the
      mitochondrial import protein Mas5, the nucleolar protein Nop2, the outer mitochondrial
      membrane porin Por1, the cytochrome c oxidase polypeptide VA precursor CoxA and the yeast
      protein tyrosine phosphatase Msg5. Translation products of three other ORFs N2406, N2411 and
      N2430 exhibit similarity to previously known S. cerevisiae proteins: the ribosomal protein
      YL9A, the protein Nca3 involved in the mitochondrial expression of subunits 6 and 8 of the ATP
      synthase and actin; in addition N2505 presents strong similarity to an ORF of chromosome IX.
      The predicted protein products of ORFs N2417 and N2403 present similarities with domains from
      proteins of other organisms: the Candida maltosa cycloheximide-resistance protein, the human
      interleukin enhancer-binding factor (ILF-2). The 12 remaining ORFs show no significant
      similarity to known proteins. In addition, we have detected a DNA region very similar to the
      yeast transposon Ty 1-15 of which insertion has disrupted a tRNA(Asp) gene.
AU  - Bergez P
AU  - Doignon F
AU  - Crouzet M
PT  - Journal Article
TA  - Yeast
JT  - Yeast
SO  - Yeast 1995 11: 967-974.

PMID- 19578403
VI  - 5
DP  - 2009
TI  - Run-off Replication of Host-Adaptability Genes is Associated with Gene Transfer Agents in the Genome of Mouse-Infecting Bartonella grahamii.
PG  - e1000546
AB  - The genus Bartonella comprises facultative intracellular bacteria adapted to mammals,
      including previously recognized and emerging human pathogens. We report the 2,341,328 bp
      genome sequence of Bartonella grahamii, one of the most prevalent Bartonella species in wild
      rodents. Comparative genomics revealed that rodent-associated Bartonella species have higher
      copy numbers of genes for putative host-adaptability factors than the related human-specific
      pathogens. Many of these gene clusters are located in a highly dynamic region of 461 kb. Using
      hybridization to a microarray designed for the B. grahamii genome, we observed a massive,
      putatively phage-derived run-off replication of this region. We also identified a novel gene
      transfer agent, which packages the bacterial genome, with an over-representation of the
      amplified DNA, in 14 kb pieces. This is the first observation associating the products of
      run-off replication with a gene transfer agent. Because of the high concentration of gene
      clusters for host-adaptation proteins in the amplified region, and since the genes encoding
      the gene transfer agent and the phage origin are well conserved in Bartonella, we hypothesize
      that these systems are driven by selection. We propose that the coupling of run-off
      replication with gene transfer agents promotes diversification and rapid spread of
      host-adaptability factors, facilitating host shifts in Bartonella.
AU  - Berglund EC
AU  - Frank AC
AU  - Calteau A
AU  - Vinnere PO
AU  - Granberg F
AU  - Eriksson AS
AU  - Naslund K
AU  - Holmberg M
AU  - Lindroos H
AU  - Andersson SG
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2009 5: e1000546.

PMID- 9628330
VI  - 379
DP  - 1998
TI  - DNA demethylation: Turning genes on.
PG  - 401-407
AB  - The regulation of eukaryotic gene expression is a complicated process involving the
      interaction of a large number of transacting factors with specific cis-regulatory elements.
      DNA methylation plays a role in this scheme by acting in cis to modulate protein-DNA
      interactions.  Several lines of evidence indicate that methylation serves to silence
      transcription, mainly through indirect mechanisms involving the assembly of repressive
      nucleoprotein complexes.  DNA demethylation is mostly an active enzymatic process, controlled
      by cis regulatory elements which provide binding sites for trans demethylation factors.  In
      the immune system DNA methylation plays multiple roles, such as regulating both gene
      expression and gene rearrangement.
AU  - Bergman Y
AU  - Mostoslavsky R
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1998 379: 401-407.

PMID- 25838492
VI  - 3
DP  - 2015
TI  - Genome Sequence of Kosakonia radicincitans Strain YD4, a Plant Growth-Promoting Rhizobacterium Isolated from Yerba Mate (Ilex paraguariensis St. Hill.).
PG  - e00239-15
AB  - Kosakonia radicincitans strain YD4 is a rhizospheric isolate from yerba mate (Ilex
      paraguariensis St. Hill.) with plant growth-promoting effects on this crop.
      Genes involved in different plant growth-promoting activities are present in this
      genome, suggesting its potential as a bioinoculant for yerba mate.
AU  - Bergottini VM
AU  - Filippidou S
AU  - Junier T
AU  - Johnson S
AU  - Chain PS
AU  - Otegui MB
AU  - Zapata PD
AU  - Junier P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00239-15.

PMID- 26634759
VI  - 3
DP  - 2015
TI  - Genome Sequence of Rapid Beer-Spoiling Isolate Lactobacillus brevis BSO 464.
PG  - e01411-15
AB  - The genome of brewery-isolate Lactobacillus brevis BSO 464 was sequenced and assembly produced
      a chromosome and eight plasmids. This bacterium tolerates
      dissolved CO2/pressure and can rapidly spoil packaged beer. This genome is useful
      for analyzing the genetics associated with beer spoilage by lactic acid bacteria.
AU  - Bergsveinson J
AU  - Pittet V
AU  - Ewen E
AU  - Baecker N
AU  - Ziola B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01411-15.

PMID- 28232423
VI  - 5
DP  - 2017
TI  - Genome Sequence of Megasphaera cerevisiae NSB1, a Bacterium Isolated from a Canning Line and Able To Grow in Beer with High Alcohol Content.
PG  - e01686-16
AB  - The genome sequence of the brewery isolate Megasphaera cerevisiae NSB1 was determined. Strain
      NSB1 tolerates 5% (vol/vol) alcohol, which is higher than
      previously reported for M. cerevisiae The NSB1 genome will help elucidate
      genetics required for alcohol tolerance and niche adaptation of this
      Gram-negative beer-spoilage bacterium.
AU  - Bergsveinson J
AU  - Thomson E
AU  - Jacoby D
AU  - Coady Y
AU  - Ziola B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01686-16.

PMID- 8567625
VI  - 271
DP  - 1996
TI  - Accurate scanning of the BssHII endonuclease in search for its DNA cleavage site.
PG  - 1837-1840
AB  - A facilitated diffusion mechanism has been proposed to account for the kinetic efficiency with
      which restriction endonucleases are able to locate DNA recognition sites.  Such a mechanism
      involves the initial formation of the DNA, with the subsequent diffusion of the protein along
      the DNA helix until either a recognition site is located or the protein dissociates into
      solution.  Protein translocation may be facilitated by either sliding along the DNA, hopping
      to nearby sites, or intersegment transfer over larger distances.  Previous analyses of the
      manner in which restriction enzymes cleave DNA substrates did rule out the latter mechanism.
      To discriminate between protein sliding or scanning and protein hopping, we designed a unique
      DNA template with three overlapping, mutually exclusive recognition sites for the BssHII
      endonuclease.  Analysis of the cleavage pattern demonstrated efficient usage of both external
      sites, whereas the centrally located site was not efficiently cleaved.  These results confirm
      that linear diffusion of the BssHII enzyme occurs by scanning along the DNA.  Furthermore, the
      scanning enzyme was found to stop and cleave at the first site encountered.  Thus, a sliding
      restriction endonuclease recognizes cleavage sites with high fidelity, without skipping of
      potential sites.
AU  - Berkhout B
AU  - van Wamel J
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1996 271: 1837-1840.

PMID- 372183
VI  - 254
DP  - 1979
TI  - The effects of substituted pyrimidines in DNAs on cleavage by sequence-specific endonucleases.
PG  - 2551-2560
AB  - The rates of cleavage of DNAs containing substituents at position 5 of thymine
      or cytosine have been measured for a variety of sequence-specific
      endonucleases, so as to determine which features in the DNA sequence are being
      probed.  Phage PhiE DNA fully substituted with 5-hydroxymethyluracil is cleaved
      more slowly by enzymes whose recognition sequences contain A-T base pairs than
      are DNAs containing thymine, but both types of DNA are cleaved at similar rates
      by enzymes recognizing sequences composed only of G-C base pairs.  Phage PBS2
      DNA with uracil completely substituted for thymine is cleaved slowly by several
      enzymes which recognize sequences containing A-T base pairs (endonucleases
      HpaI, HindII, and HindIII), while the rates of cleavage by other enzymes
      (endonucleases EcoRI and BamHI) are not affected.  Phage lambda- and P22 DNAs
      containing 5-bromouracil are cleaved more slowly by several enzymes
      (endonucleases HindIII, HpaI, BamHI) than are thymine-containing DNAs.  Enzymes
      that recognize sequence isomers with the composition G:C:2A:2T (endonucleases
      EcoRI, HpaI, HindIII) are not equally affected by substitution at position 5 of
      thymine, suggesting that they differ in their contacts with A-T base pairs.
      DNA containing glucosylated 5-hydroxymethylcytosine in place of cytosine is
      resistant to cleavage by all the endonucleases examined.
AU  - Berkner KL
AU  - Folk WR
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1979 254: 2551-2560.

PMID- 24833
VI  - 5
DP  - 1978
TI  - Overmethylation of DNAs by the EcoRI methylase.
PG  - 435-450
AB  - EcoRI methylase is able to catalyze methyl incorporation into DNA at sequences
      other than the canonical EcoRI site.  At high enzyme concentrations and over a
      wide range of pH and ionic strengths, EcoRI methylase modifies polyoma DNA
      (which contains one EcoRI site) at a number of sites.  This modification
      prevents EcoRI endonuclease activity, and thus is presumably at or near the
      EcoRI sequences (5')NAATTN.
AU  - Berkner KL
AU  - Folk WR
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1978 5: 435-450.

PMID- 863878
VI  - 252
DP  - 1977
TI  - EcoRI cleavage and methylation of DNAs containing modified pyrimidines in the recognition sequence.
PG  - 3185-3193
AB  - The effects of substituents at position 5 in the pyrimidine ring of a variety
      of phage DNAs upon EcoRI endonuclease and methylase activities have been
      examined.  The replacement of cytidine in DNA with glucosylated
      hydroxymethylcytidine confers resistance to cleavage by the EcoRI endonuclease.
      Substitution of thymidine in DNA by hydroxymethyluridine (a change in the
      methyl at position 5 of thymidine for a hydroxymethyl) lowers the maximal
      velocity of endonucleolytic cleavage 20-fold, but has no detectble effect upon
      the Km.  Substitution of thymidine in DNA by uridine (a change in the methyl at
      position 5 of thymidine for a hydrogen atom) has no effect upon either the
      maximal velocity or the Km.  The effect of these modifications upon EcoRI
      methylase activity was markedly different.  DNA containing glucosylated
      hydroxymethylcytidine is methylated as well as normal DNA.  DNA containing
      uridine or hydroxymethyluridine, in place of thymidine, is much more poorly
      methylated than normal DNA.  These different sensitivities of the EcoRI
      endonuclease and methylase to modifications in the pyrimidine rings of DNA
      suggest there are significant differences in the manner by which these enzymes
      recognize and bind to the canonical EcoRI sequence.
AU  - Berkner KL
AU  - Folk WR
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1977 252: 3185-3193.

PMID- 218943
VI  - 254
DP  - 1979
TI  - Quantitation of the various termini generated by Type II restriction endonucleases using the polynucleotide kinase exchange reaction.
PG  - 2561-2564
AB  - Parameters of the polynucleotide kinase-catalyzed exchange reaction between [gamma32P]ATP and
      5'-phosphoryl DNAs have been measured with the termini generated by the following
      endonucleases: EcoRI (Berkner, K.L. and Folk, W.R. (1977) J. Biol. Chem. 252:3176-3184),
      HpaII, BamHI, and HindIII (external termini); HindII and HpaI (blunt termini); HaeII and HhaI
      (internal termini). In every case, exchange is reproducible and proportional to the number of
      termini. However, in most cases, the exchange reaction does not proceed to the theoretical
      maximum. External termini and single-stranded DNAs are labeled more rapidly and to
      approximately 5-fold higher levels than blunt or internal termini. Concentrations of 100 to
      200 micromolar ADP and 12 micromolar ATP are optimal for labeling all types of termini with
      the exchange reaction.
AU  - Berkner KL
AU  - Folk WR
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1979 254: 2561-2564.

PMID- 6303160
VI  - 129
DP  - 1983
TI  - An assay for the rates of cleavage of specific sites in DNA by restriction endonucleases:  Its use to study the cleavage of phage lambda DNA by EcoRI and phage P22 DNA containing thymine or 5-bromouracil by HindIII.
PG  - 446-456
AB  - A method to measure the rates of cleavage of specific sites in DNAs by restriction
      endonucleases is described.  Partial digests are prepared by incubating DNAs with limiting
      amounts of endonuclease.  The termini generated by cleavage are labeled with 32P by the
      polynucleotide kinase-exchange reaction.  The labeled termini are then identified by
      completing the digestion with the same endonuclease and separating the products by gel
      electrophoresis. As the products of complete digestion of DNA are often easily separated and
      can be unequivocally identified, this procedure permits comparison of the rates of cleavage of
      specific sites in DNAs:  furthermore, because detection of the products of cleavage utilizes
      radioautography and does not depend upon their size, or amount, only small amounts of DNA need
      to be utilized.  This method has been used to examine the cleavage of phgae lambda DNA by
      EcoRI endonuclease, and to demonstrate that 5-bromouracil substitution in phage P22 DNA
      reduces the rate of cleavage of most sites by HindIII endonuclease approximately threefold and
      the rate of cleavage of one site approximately tenfold.
AU  - Berkner KL
AU  - Folk WR
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 1983 129: 446-456.

PMID- 24253042
VI  - 289
DP  - 2014
TI  - The DNA Methyltransferase Dnmt1 Directly Interacts with the SET and RING Finger-associated (SRA) Domain of the Multifunctional Protein Uhrf1 to Facilitate Accession of the Catalytic Center to Hemi-methylated DNA.
PG  - 379-386
AB  - Dnmt1 is responsible for the maintenance DNA methylation during replication to propagate
      methylation patterns to the next generation. The replication foci targeting sequence (RFTS),
      which plugs the catalytic pocket, is necessary for recruitment of Dnmt1 to the replication
      site. In the present study we found that the DNA methylation activity of Dnmt1 was DNA
      length-dependent and scarcely methylated 12-bp short hemi-methylated DNA. Contrarily, the
      RFTS-deleted Dnmt1 and Dnmt1 mutants that destroyed th hydrogen bonds between the RFTS and
      catalytic domain showed significant DNA methylation activity even toward 12-bp hemi-methylated
      DNA. The DNA methylation activity of the RFTS-deleted Dnmt1 toward 12-bp hemi-methylated DNA
      was strongly inhibited on the addition of RFTS, but to a lesser extent by Dnmt1 harboring the
      mutations that impair the hydrogen bond formation. The SRA domain of Uhrf1, which is a
      prerequisite factor for maintenance methylation and selectively binds to hemi-methylated DNA,
      stimulated  the DNA methylation activity of Dnmt1. The SRA to Dnmt1 concentration ratio was
      the determinant for the maximum stimulation. In addition, a mutant SRA, which had lost the DNA
      binding activity but was able to bind to Dnmt1, stimulated the DNA methylation activity of
      Dnmt1. The results indicate that the DNA methylation activity of Dnmt1 was stimulated on the
      direct interaction of the SRA and Dnmt1. The SRA facilitated acceptance of the 12-bp
      fluorocytosine-containing DNA by the catalytic center. We propose t hat the SRA removes the
      RFTS plug from the catalytic pocket to facilitate DNA acceptance by the catalytic center.
AU  - Berkyurek AC
AU  - Suetake I
AU  - Arita K
AU  - Takeshita K
AU  - Nakagawa A
AU  - Shirakawa M
AU  - Tajima S
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2014 289: 379-386.

PMID- 24812221
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Mycobacterium tuberculosis Clinical Strain G-12-005.
PG  - e00385-14
AB  - Infection caused by drug-resistant Mycobacterium tuberculosis is a growing concern, especially
      in eastern Europe. We report an annotated draft genome
      sequence of M. tuberculosis strain G-12-005 obtained from a patient in Georgia.
AU  - Berland JL
AU  - de Carvalho FM
AU  - de Almeida LG
AU  - Bablishvili N
AU  - Gauthier M
AU  - Paranhos-Baccala G
AU  - de Vasconcelos AT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00385-14.

PMID- Not included in PubMed...
VI  - 7
DP  - 1981
TI  - Synthesis of oligodeoxynucleotides containing the sequence GGTACC and their interaction with KpnI restriction endonuclease.
PG  - 1224-1232
AB  - It has been shown that in the phosphotriester synthesis of
      oligodeoxynucleotides the simultaneous use of a dimethoxytrityl and a levulinyl
      residue to protect the 5'-OH and 3'-OH, respectively, permits the growth of the
      oligonucleotide chain in both directions: 3' 5 5' and 5' 5 3'.  Using this
      approach, the oligodeoxynucleotides GGTACC, GGTACCGG, CCGGTACC, and CCGGTACCGG
      containing the recognition site for KpnI restriction endonuclease have been
      synthesized.  In a study of their interaction with this restrictase it has been
      found that for the normal functioning of the enzyme the GGTACC site in its
      substrate must be flanked in both chains from the 5'-end and in at least one
      chain from the 3'-end.
AU  - Berlin YA
AU  - Butkus VV
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1981 7: 1224-1232.

PMID- 25035326
VI  - 2
DP  - 2014
TI  - Whole-Genome Sequencing of an Isoniazid-Resistant Clinical Isolate of Mycobacterium tuberculosis Strain MtURU-002 from Uruguay.
PG  - e00655-14
AB  - The incidence of tuberculosis in Uruguay has been effectively reduced to <30 per  100,000
      population, although an increase in nonrisk populations in the last few
      years is evident. Here, we present the genome sequence of Mycobacterium
      tuberculosis strain MtURU-002 isolated from a patient showing bilateral pulmonary
      tuberculosis that was resistant to isoniazid.
AU  - Berna L
AU  - Iraola G
AU  - Greif G
AU  - Coitinho C
AU  - Rivas CM
AU  - Naya H
AU  - Robello C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00655-14.

PMID- 
VI  - 116
DP  - 1998
TI  - Isolation of a cDNA coding for DNA (cytosine-5)-methyltransferase (Accession No. AJ002140) from Lycopersicon esculentum.
PG  - 446
AB  - 
AU  - Bernacchia G
AU  - Para A
AU  - Pedrali-Noy G
AU  - Cella R
PT  - Journal Article
TA  - Plant Physiol.
JT  - Plant Physiol.
SO  - Plant Physiol. 1998 116: 446.

PMID- 9680985
VI  - 13
DP  - 1998
TI  - Carrot DNA-methyltransferase is encoded by two classes of genes with differing patterns of expression.
PG  - 317-329
AB  - In the present study, the isolation and characterization of two distinct cDNAs that code for
      carrot DNA (cytosine-5)-methyltransferase (DNA-METase) are reported.  The screening of a cDNA
      library with a carrot genomic DNA fragment, previously obtained by PCR using degenerate
      primers, has led to the isolation of clones that belong to two distinct classes of genes (Met1
      and Met2) which differ in sequence and size.  Met1-5 and Met2-21 derived amino acid sequences
      are more than 85% identical for most of the polypeptide and completely diverge at the
      N-terminus.  The larger size of the Met2-21 cDNA is due to the presence of nearly perfect
      fivefold repeat of a 171 bp sequence present only once in the Met1-5 cDNA.  Northern  and in
      situ hybridization analyses with young carrot plants and somatic embryos indicate that both
      genes are maximally expressed in proliferating cells (suspension cells, meri-stems and leaf
      primordia), but differ quantitatively and spatially in their mode of expression.  Polyclonal
      antibodies were raised in rabbit using fusion proteins corresponding to the regulatory and
      catalytic regions of the most highly expressed gene (Met1-5).  In nuclear carrot extracts,
      both antibodies were found to recognize a band of about 200 kDa along with some additional
      bands of lower size.  These results provide the first direct demonstration that DNA-METases of
      a higher eukaryote are encoded by a gene family.
AU  - Bernacchia G
AU  - Primo A
AU  - Giorgetti L
AU  - Pitto L
AU  - Cella R
PT  - Journal Article
TA  - Plant J.
JT  - Plant J.
SO  - Plant J. 1998 13: 317-329.

PMID- 26988047
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequence of Multidrug-Resistant Campylobacter coli Strain COL B1-266, Isolated from the Colombian Poultry Chain.
PG  - e00130-16
AB  - Campylobacter coli is considered one of the main causes of food-borne illness worldwide. We
      report here the whole-genome sequence of multidrug-resistant
      Campylobacter coli strain COL B1-266, isolated from the Colombian poultry chain.
      The genome sequences encode genes for a variety of antimicrobial resistance
      genes, including aminoglycosides, beta-lactams, lincosamides, fluoroquinolones,
      and tetracyclines.
AU  - Bernal JF
AU  - Donado-Godoy P
AU  - Arevalo A
AU  - Duarte C
AU  - Realpe ME
AU  - Diaz PL
AU  - Gomez Y
AU  - Rodriguez F
AU  - Agarwala R
AU  - Landsman D
AU  - Marino-Ramirez L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00130-16.

PMID- 26988048
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequences of Two Campylobacter coli Isolates from the Antimicrobial  Resistance Monitoring Program in Colombia.
PG  - e00131-16
AB  - Campylobacter coli, along with Campylobacter jejuni, is a major agent of gastroenteritis and
      acute enterocolitis in humans. We report the whole-genome
      sequences of two multidrug-resistance C. coli strains, isolated from the
      Colombian poultry chain. The isolates contain a variety of antimicrobial
      resistance genes for aminoglycosides, lincosamides, fluoroquinolones, and
      tetracycline.
AU  - Bernal JF
AU  - Donado-Godoy P
AU  - Valencia MF
AU  - Leon M
AU  - Gomez Y
AU  - Rodriguez F
AU  - Agarwala R
AU  - Landsman D
AU  - Marino-Ramirez L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00131-16.

PMID- Not carried by PubMed...
VI  - 0
DP  - 1986
TI  - Restriction endonuclease from Thermus ruber.
PG  - 204
AB  - Chromosomal DNA purified from some strains ascribed to the genus Thermus were
      digestable by restriction endonuclease TaqI, indicating that these strains do
      not possess the TaqI restriction-modification system.  These strains were
      tested for the possession of restriction enzymes with potentially novel sites
      of recognition and cleavage.  Thermus ruber BKMB-1258 has a restriction enzyme
      designated TruI, which was separated from other nucleases by phosphocellulose
      column chromatography.  From digestion patterns of DNA from bacteriophage
      lambda and phiX174 RF, and plasmids pBR322 and pAT153, the recognition sequence
      of TruI was identified as GG(A/T)CC, which is the same as for AvaII.  This was
      confirmed by TruI-AvaII double digests.
AU  - Bernal WM
AU  - Raven NDH
AU  - Williams RAD
PT  - Journal Article
TA  - Proceedings 14th Int. Congress Microbiol.
JT  - Proceedings 14th Int. Congress Microbiol.
SO  - Proceedings 14th Int. Congress Microbiol. 1986 0: 204.

PMID- 29760866
VI  - 13
DP  - 2018
TI  - Short genome report of cellulose-producing commensal Escherichia coli 1094.
PG  - 13
AB  - Bacterial surface colonization and biofilm formation often rely on the production of an
      extracellular polymeric matrix that mediates cell-cell and cell-surface
      contacts. In Escherichia coli and many Betaproteobacteria and Gammaproteobacteria
      cellulose is often the main component of the extracellular matrix. Here we report
      the complete genome sequence of the cellulose producing strain E. coli 1094 and
      compare it with five other closely related genomes within E. coli phylogenetic
      group A. We present a comparative analysis of the regions encoding genes
      responsible for cellulose biosynthesis and discuss the changes that could have
      led to the loss of this important adaptive advantage in several E. coli strains.
      Data deposition: The annotated genome sequence has been deposited at the European
      Nucleotide Archive under the accession number PRJEB21000.
AU  - Bernal-Bayard J
AU  - Gomez-Valero L
AU  - Wessel A
AU  - Khanna V
AU  - Bouchier C
AU  - Ghigo JM
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2018 13: 13.

PMID- Not carried by PubMed...
VI  - 89
DP  - 1989
TI  - Cloning and characterization of the SphI restriction-modification system from S. phaeochromogenes.
PG  - 206
AB  - SphI, a Type II restriction-modification system from the actinomycete
      Streptomyces phaeochromogenes, recognizes the sequence GCATGC.  The
      endonuclease cleaves at GCATG^C leaving a 3'four base overhang.  A 5.4kb insert
      carrying the methylase gene has been cloned into the PstI site of pBR322 and
      expressed in E. coli at a low level as evidenced by incomplete modification of
      chromosomal DNA and lack of modification of phage DNA in vivo.  The clone has
      no endonuclease activity.  The plasmid has been extensively mapped; deletion
      subcloning has been used to locate the methylase gene.  The entire 5.4kb
      methylase fragment has also been cloned into the Streptomyces promoter-probe
      plasmids, pIJ486 and pIJ487 and the low copy Streptomyces vector, pIJ922.
      Expression of the SphI methylase gene will be discussed.
AU  - Bernan V
AU  - Sznyter LA
AU  - Vaccaro CM
AU  - Jager-Quinton T
AU  - Wilson G
AU  - Brooks JE
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1989 89: 206.

PMID- 12686632
VI  - 149
DP  - 2003
TI  - DNA restriction is a barrier to natural transformation in Pseudomonas stutzeri JM300.
PG  - 895-901
AB  - Natural transformation is a mechanism for intra- and interspecific transfer of chromosomal DNA
      in Pseudomonas stutzeri. During this process a
      single strand derived from duplex DNA is transported into the cytoplasm
      and recombined with resident DNA. By electroporation, which introduces
      duplex DNA into cells, 100-fold lower transformation frequencies of P.
      stutzeri JM300 were observed with shuttle vector or broad-host-range
      plasmid DNA when the plasmids had replicated in Escherichia coli and not
      in P. stutzeri JM300. Moreover, the natural transformation with cloned
      chromosomal P. stutzeri JM300 DNA was reduced about 40-fold when the DNA
      had not been propagated in P. stutzeri JM300 but in E. coli. Restriction
      was also active during natural transformation by single-stranded DNA.
      Restriction during natural transformation and electroporation was
      abolished in mutants isolated from mutagenized JM300 cells after applying
      a multiple plasmid electroporation strategy for the enrichment of
      restriction-defective strains. The mutants had retained the ability for
      DNA modification. The P. stutzeri strain ATCC 17587 was found to have no
      restriction-modification system as seen in JM300. It is discussed whether
      restriction during natural transformation acts at presynaptic or
      postsynaptic stages of transforming DNA. Restriction as a barrier to
      transformation apparently contributes to sexual isolation and therefore
      may promote speciation in the highly diverse species P. stutzeri.
AU  - Berndt C
AU  - Meier P
AU  - Wackernagel W
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2003 149: 895-901.

PMID- 23407329
VI  - 6
DP  - 2012
TI  - Complete genome sequence of Pyrobaculum oguniense.
PG  - 336-345
AB  - Pyrobaculum oguniense TE7 is an aerobic hyperthermophilic crenarchaeon isolated from a hot
      spring in Japan. Here we describe its main chromosome of 2,436,033 bp,
      with three large-scale inversions and an extra-chromosomal element of 16,887 bp.
      We have annotated 2,800 protein-coding genes and 145 RNA genes in this genome,
      including nine H/ACA-like small RNA, 83 predicted C/D box small RNA, and 47
      transfer RNA genes. Comparative analyses with the closest known relative, the
      anaerobe Pyrobaculum arsenaticum from Italy, reveals unexpectedly high synteny
      and nucleotide identity between these two geographically distant species. Deep
      sequencing of a mixture of genomic DNA from multiple cells has illuminated some
      of the genome dynamics potentially shared with other species in this genus.
AU  - Bernick DL
AU  - Karplus K
AU  - Lui LM
AU  - Coker JK
AU  - Murphy JN
AU  - Chan PP
AU  - Cozen AE
AU  - Lowe TM
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 6: 336-345.

PMID- 27635007
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Microbacterium hominis LCDC-84-0209T Isolated from a Human Lung Aspirate and Microbacterium laevaniformans LCDC 91-0039 Isolated from   a Human Blood Culture.
PG  - e00989-16
AB  - Draft genomes for Microbacterium hominis 84-0209(T) and M. laevaniformans 91-0039 were
      studied. Genome sizes (bps, [G+C contents]) were 3,506,522 (70.96%) and
      2,999,965 (69.51%), respectively. Annotation revealed: (M. hominis) three rRNA
      sequences, 45 tRNA genes, and 3,218 coding sequences; (M. laevaniformans) three
      rRNA sequences, 49 tRNA genes, and 2,874 coding sequences.
AU  - Bernier AM
AU  - Bernard K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00989-16.

PMID- 26950329
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Trueperella bernardiae LCDC 89-0504T, Isolated from a Human Blood Culture.
PG  - e01634-15
AB  - We report here the draft genome sequence of Trueperella bernardiae LCDC 89-0504(T), an
      organism linked to mild to severe infections in humans and
      animals. The genome size is 2,028,874 bp, with a G+C content of 65.44%.
      Annotation of the genome revealed 5 rRNA sequences, 48 tRNA genes, and 1,762
      coding sequences.
AU  - Bernier AM
AU  - Bernard K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01634-15.

PMID- 27389276
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence for the Type Strain of Corynebacterium afermentans LCDC 88-0199T, Isolated from a Human Blood Culture.
PG  - e00661-16
AB  - A draft genome for Corynebacterium afermentans LCDC 88-0199(T) was investigated.  The size of
      the genome was 2,345,615 bp with an observed G+C content of 64.85%.
      Annotation revealed 2 rRNA sequences, 54 tRNA genes, and 2,164 coding sequences.
      Genome coverage was 85x and consisted of 24 contigs with an N50 of 187,988 bp.
AU  - Bernier AM
AU  - Bernard K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00661-16.

PMID- 28153894
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequences of Four Corynebacterium CDC Group F-1 Strains Isolated from Urine.
PG  - e01537-16
AB  - Three draft and one complete genome sequence from strains isolated from urine and consistent
      with Corynebacterium CDC group F-1 were assembled and studied. Genome
      sizes ranged between 2.3 and 2.44 Mb, with G+C content between 60.4% and 60.7%.
AU  - Bernier AM
AU  - Peters GA
AU  - Bernard K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01537-16.

PMID- Not included in PubMed...
VI  - 29
DP  - 1970
TI  - Altered P2 bacteriophage restriction in E. coli B.
PG  - 860
AB  - P2 phage grown on E. coli C (P2.C) grows very well in E. coli C but is highly
      restricted in E. coli B.  The plating efficiences of P2.C with E. coli C and E.
      coli B grown in nutrient broth are of the order of 1 and 10-7, respectively.
      This retriction can be altered by changing the growth conditions of E. coli B.
      Thus growth on salts-glucose medium gives a 100-fold increase in plating
      efficiency compared to cultures grown in enriched broth.  When E. coli B is
      grown in salts-glucose medium supplemented with amino acids, purines,
      pyrimidines, and vitamins, the higher P2.C plating efficiencies are found only
      with those cultures not supplemented with methionine.  Conditions which lead to
      the depletion of intracellular methionine or S-adenosylmethionine in the
      prototrophic E. coli B further increase the P2.C plating efficiencies.  Plating
      efficiency can also be raised by infection with T3 phage.  However, infection
      with T3 mutants unable to produce the T3-specific early enzyme which cleaves
      S-adenosylmethionine does not alter the plating efficiency.  These results
      suggest that S-adenosylmethionine is involved in the mechanism of restriction
      of P2 phage.
AU  - Bernstein RL
AU  - Dharmgrongartama B
AU  - Srinivasan PR
PT  - Journal Article
TA  - Fed. Proc.
JT  - Fed. Proc.
SO  - Fed. Proc. 1970 29: 860.

PMID- 19775431
VI  - 10
DP  - 2009
TI  - Complete genome sequence of the sugarcane nitrogen-fixing endophyte Gluconacetobacter diazotrophicus Pal5.
PG  - 450
AB  - BACKGROUND: Gluconacetobacter diazotrophicus Pal5 is an endophytic diazotrophic bacterium that
      lives in association with sugarcane plants. It has important
      biotechnological features such as nitrogen fixation, plant growth promotion,
      sugar metabolism pathways, secretion of organic acids, synthesis of auxin and the
      occurrence of bacteriocins. RESULTS: Gluconacetobacter diazotrophicus Pal5 is the
      third diazotrophic endophytic bacterium to be completely sequenced. Its genome is
      composed of a 3.9 Mb chromosome and 2 plasmids of 16.6 and 38.8 kb, respectively.
      We annotated 3,938 coding sequences which reveal several characteristics related
      to the endophytic lifestyle such as nitrogen fixation, plant growth promotion,
      sugar metabolism, transport systems, synthesis of auxin and the occurrence of
      bacteriocins. Genomic analysis identified a core component of 894 genes shared
      with phylogenetically related bacteria. Gene clusters for gum-like polysaccharide
      biosynthesis, tad pilus, quorum sensing, for modulation of plant growth by indole
      acetic acid and mechanisms involved in tolerance to acidic conditions were
      identified and may be related to the sugarcane endophytic and plant-growth
      promoting traits of G. diazotrophicus. An accessory component of at least 851
      genes distributed in genome islands was identified, and was most likely acquired
      by horizontal gene transfer. This portion of the genome has likely contributed to
      adaptation to the plant habitat. CONCLUSION: The genome data offer an important
      resource of information that can be used to manipulate plant/bacterium
      interactions with the aim of improving sugarcane crop production and other
      biotechnological applications.
AU  - Bertalan M et al
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2009 10: 450.

PMID- 29519838
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Lactobacillus helveticus Strain Lh 12 Isolated from Natural Whey Starter.
PG  - e00139-18
AB  - Lactobacillus helveticus is a lactic acid bacterium widely used in cheese-making  and for the
      production of bioactive peptides from milk proteins. Here, we
      describe the draft genome sequence and annotation of L. helveticus strain Lh 12
      isolated from natural whey starter used in the production of Grana Padano cheese.
AU  - Bertani G
AU  - Bassi D
AU  - Gatti M
AU  - Cocconcelli PS
AU  - Neviani E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00139-18.

PMID- 13034700
VI  - 65
DP  - 1953
TI  - Host controlled variation in bacterial viruses.
PG  - 113-121
AB  - Passage through new hosts or new tissues is a widely used method for altering
      the properties of viruses.  In some instances selection of spontaneous mutants
      has been demonstrated to be the mechanism causing the variation (Luria, 1945).
      Nonhereditary mechanisms sometimes have been postulated, but since no such case
      has been analyzed sufficiently, it is often assumed that selection of mutants
      is the only possible mechanism.  A detailed analysis of two cases of variation
      in two different bacterial viruses is reported in this paper.  In both these
      cases we are dealing with nonheritable alterations stemming directly from
      passage through a new host and not with mutations.  A somewhat similar case of
      host controlled variation involving other bacterial viruses has been reported
      recently by Luria and Human (1952).
AU  - Bertani G
AU  - Weigle JJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1953 65: 113-121.

PMID- 24201194
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Plant Pathogen Dickeya zeae DZ2Q, Isolated from Rice in Italy.
PG  - e00905-13
AB  - Dickeya zeae is an emerging rice (Oryza sativa) pathogen causing bacterial foot rot. Related
      pathogens affect maize (Zea mays) and potato (Solanum tuberosum) and
      a variety of important ornamental and floral plants. Here, we present the draft
      genome sequence of D. zeae DZ2Q, an isolate obtained from rice grown in Italy.
AU  - Bertani I
AU  - Passos-da-Silva D
AU  - Abbruscato P
AU  - Piffanelli P
AU  - Venturi V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00905-13.

PMID- 20531937
VI  - 5
DP  - 2010
TI  - The Waddlia Genome: A Window into Chlamydial Biology.
PG  - e10890
AB  - Growing evidence suggests that a novel member of the Chlamydiales order, Waddlia chondrophila,
      is a potential agent of miscarriage in humans and abortion in ruminants. Due to the lack of
      genetic tools to manipulate chlamydia, genomic analysis is proving to be the most incisive
      tool in stimulating investigations into the biology of these obligate intracellular
      bacteria. 454/Roche and Solexa/Illumina technologies were thus used to sequence and assemble
      de novo the full genome of the first representative of the Waddliaceae family, W.
      chondrophila. The bacteria possesses a 291169312bp chromosome and a 159593 bp low-copy number
      plasmid that might integrate into the bacterial chromosome. The Waddlia genome displays
      numerous repeated sequences indicating different genome dynamics from classical chlamydia
      which almost completely lack repetitive elements. Moreover, W. chondrophila exhibits many
      virulence factors also present in classical chlamydia, including a functional type III
      secretion system, but also a large complement of specific factors for resistance to host or
      environmental stresses. Large families of outer membrane proteins were identified indicating
      that these highly immunogenic proteins are not Chlamydiaceae specific and might have been
      present in their last common ancestor.  Enhanced metabolic capability for the synthesis of
      nucleotides, amino acids, lipids and other co-factors suggests that the common ancestor of the
      modern Chlamydiales may have been less dependent on their eukaryotic host. The fine-detailed
      analysis of biosynthetic pathways brings us closer to possibly developing a synthetic medium
      to grow W. chondrophila, a critical step in the development of genetic tools. As a whole, the
      availability of the W. chondrophila genome opens new possibilities in Chlamydiales research,
      providing new insights into the evolution of members of the order Chlamydiales and the biology
      of the Waddliaceae.
AU  - Bertelli C
AU  - Collyn F
AU  - Croxatto A
AU  - Ruckert C
AU  - Polkinghorne A
AU  - Kebbi-Beghdadi C
AU  - Goesmann A
AU  - Vaughan L
AU  - Greub G
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2010 5: e10890.

PMID- 25342672
VI  - 2
DP  - 2014
TI  - Criblamydia sequanensis Harbors a Megaplasmid Encoding Arsenite Resistance.
PG  - e00949-14
AB  - Criblamydia sequanensis is an amoeba-resisting bacterium recently isolated from the Seine
      River. This Chlamydia-related bacterium harbors a genome of
      approximately 3 Mbp and a megaplasmid of 89,525 bp. The plasmid encodes several
      efflux systems and an operon for arsenite resistance. This first genome sequence
      within the Criblamydiaceae family enlarges our view on the evolution and the
      ecology of this important bacterial clade largely understudied so far.
AU  - Bertelli C
AU  - Goesmann A
AU  - Greub G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00949-14.

PMID- Not carried by PubMed...
VI  - 84
DP  - 1984
TI  - An apparently restriction deficient mutant of Streptomyces achromogenes var streptozoticus can be transformed by plasmid pIJ350.
PG  - H74
AB  - We have isolated a mutant of S. achromogenes var streptozoticus (SAS) which
      differed from wild type in respect to digestion of chromosomal DNA by NaeI and
      susceptibility to phage infection.  While DNA of SAS was resistant to digestion
      by NaeI, the DNA of mutant AB301 was NaeI-sensitive.  We found that AB301 could
      be infected by 4 phages to which wild type SAS was resistant.  We were able to
      transform AB301 with plasmid pIJ350 (confirmed by mini-prepping transformants),
      although we had never successfully transformed wild type SAS with this or any
      other plasmid.  The DNA of pIJ 350 and phages PhiCC 53, PhiCC 55, and PhiCC 57
      was cut by NaeI, but that of phage PhiCC 26 was not.  We suggest that
      restriction by NaeI is one barrier to transformation in SAS and that loss of
      this barrier (and additional possible restriction barriers) contributed to the
      successful transformation of this previously recalcitrant species.
AU  - Bertinuson A
AU  - Illingworth CA
AU  - Otto CJ
AU  - Hornemann U
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1984 84: H74.

PMID- 24812214
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Stenotrophomonas maltophilia SeITE02, a Gammaproteobacterium Isolated from Selenite-Contaminated Mining Soil.
PG  - e00331-14
AB  - Stenotrophomonas maltophilia strain SeITE02 was isolated from the rhizosphere of  the
      selenium-hyperaccumulating legume Astragalus bisculcatus. In this report, we
      provide the 4.56-Mb draft genome sequence of S. maltophilia SeITE02, a
      gammaproteobacterium that can withstand high concentrations of selenite and
      reduce these to elemental selenium.
AU  - Bertolini C
AU  - van Aerle R
AU  - Lampis S
AU  - Moore KA
AU  - Paszkiewicz K
AU  - Butler CS
AU  - Vallini G
AU  - van der Giezen M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00331-14.

PMID- 15522920
VI  - 17
DP  - 2004
TI  - Covalent DNA display as a novel tool for directed evolution of proteins in vitro.
PG  - 699-707
AB  - We present a novel method for the directed evolution of polypeptides, which combines in vitro
      compartmentalization and covalent DNA display. A
      library of linear DNA fragments is co-packaged with an in vitro
      transcription/translation mixture in the compartments of a water-in-oil
      emulsion. Experimental conditions are adjusted so that, in most cases, one
      compartment contains one DNA molecule. The DNA fragments encode fusion
      proteins containing a DNA-methyltransferase (M.Hae III), which can form a
      covalent bond with a 5-fluorodeoxycytidine base at the extremity of the
      DNA fragment. The resulting library of DNA-protein fusions is extracted
      from the emulsion and DNA molecules displaying a protein with desired
      binding properties are selected from the pool of DNA-protein fusions by
      affinity panning on target antigens. We applied this methodology in model
      selection experiments, using specific ligands for the capture of peptides
      and globular proteins bound to DNA. We observed enrichment factors
      >1000-fold for selections performed in separate emulsions and up to
      150-fold for selections performed using mixtures of DNA molecules. M.Hae
      III could be fused to small globular proteins (such as calmodulin and
      fibronectin domains), which are ideally suited for the generation of
      combinatorial libraries and for the isolation of novel binding
      specificities.
AU  - Bertschinger J
AU  - Neri D
PT  - Journal Article
TA  - Protein Eng. Des. Sel.
JT  - Protein Eng. Des. Sel.
SO  - Protein Eng. Des. Sel. 2004 17: 699-707.

PMID- 28428298
VI  - 5
DP  - 2017
TI  - Genome Sequence of Staphylococcus saprophyticus DPC5671, a Strain Isolated from Cheddar Cheese.
PG  - e00193-17
AB  - The draft genome sequence of Staphylococcus saprophyticus DPC5671, isolated from  cheddar
      cheese, was determined. S. saprophyticus is a common Gram-positive
      bacterium detected on the surface of smear-ripened cheese and other fermented
      foods.
AU  - Bertuzzi AS
AU  - Guinane CM
AU  - Crispie F
AU  - Kilcawley KN
AU  - McSweeney PLH
AU  - Rea MC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00193-17.

PMID- 30179231
VI  - 5
DP  - 2018
TI  - Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments.
PG  - 180154
AB  - Prochlorococcus and Synechococcus are the dominant primary producers in marine
      ecosystems and perform a significant fraction of ocean carbon fixation. These
      cyanobacteria interact with a diverse microbial community that coexists with
      them. Comparative genomics of cultivated isolates has helped address questions
      regarding patterns of evolution and diversity among microbes, but the fraction
      that can be cultivated is miniscule compared to the diversity in the wild. To
      further probe the diversity of these groups and extend the utility of reference
      sequence databases, we report a data set of single cell genomes for 489
      Prochlorococcus, 50 Synechococcus, 9 extracellular virus particles, and 190
      additional microorganisms from a diverse range of bacterial, archaeal, and viral
      groups. Many of these uncultivated single cell genomes are derived from samples
      obtained on GEOTRACES cruises and at well-studied oceanographic stations, each
      with extensive suites of physical, chemical, and biological measurements. The
      genomic data reported here greatly increases the number of available
      Prochlorococcus genomes and will facilitate studies on evolutionary biology,
      microbial ecology, and biological oceanography.
AU  - Berube PM et al
PT  - Journal Article
TA  - Sci. Data
JT  - Sci. Data
SO  - Sci. Data 2018 5: 180154.

PMID- 28751406
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Pseudomonas syringae PDD-32b-74, a Model Strain for Ice-Nucleation Studies in the Atmosphere.
PG  - e00742-17
AB  - We report here the whole genome sequence of Pseudomonas syringae PDD-32b-74, a
      gammaproteobacterium isolated from cloud water. This microorganism is equipped
      with ice-nucleation protein and biosurfactant genes that could potentially be
      involved in physicochemical processes in the atmosphere and clouds.
AU  - Besaury L
AU  - Amato P
AU  - Sancelme M
AU  - Delort AM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00742-17.

PMID- 28663290
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Pseudomonas graminis PDD-13b-3, a Model Strain Isolated  from Cloud Water.
PG  - e00464-17
AB  - The whole genome of Pseudomonas graminis PDD-13b-3, a strain of bacteria isolated from cloud
      water, was sequenced. This showed that this microorganism is equipped
      with genes that could potentially be involved in its survival in the atmosphere
      and clouds: those for oxidative stress and carbon starvation responses, DNA
      repair, and iron uptake.
AU  - Besaury L
AU  - Amato P
AU  - Wirgot N
AU  - Sancelme M
AU  - Delort AM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00464-17.

PMID- 11520857
VI  - 2
DP  - 2001
TI  - Converting MlyI endonuclease into a nicking enzyme by changing its oligomerization state.
PG  - 782-786
AB  - N.Bst NBI is a nicking endonuclease that recognizes the sequence GAGTC and nicks one DNA
      strand specifically. The Type IIs endonuclease, Mly I, also recognizes GAGTC, but cleaves both
      DNA strands. Sequence comparisons revealed significant similarities between N.Bst NBI and Mly
      I. Previous studies showed that Mly I dimerizes in the presence of a cognate DNA, whereas
      N.Bst NBI remains a monomer. This suggests that dimerization may be required for
      double-stranded cleavage. To test this hypothesis, we used a multiple alignment to design
      mutations to disrupt the dimerization function of Mly I. When Tyr491 and Lys494 were both
      changed to alanine, the mutated endonuclease, N.Mly I, no longer formed a dimer and cleaved
      only one DNA strand specifically. Thus, we have shown that changing the oligomerization state
      of an enzyme changes its enzymatic function. This experiment also established a protocol that
      could be applied to other Type IIs endonucleases in order to generate more novel nicking
      endonucleases.
AU  - Besnier CE
AU  - Kong H
PT  - Journal Article
TA  - EMBO Rep.
JT  - EMBO Rep.
SO  - EMBO Rep. 2001 2: 782-786.

PMID- 21949075
VI  - 193
DP  - 2011
TI  - Whole Genome Association Study on Tissue Tropism Phenotypes in Group A Streptococcus.
PG  - 6651-6663
AB  - Group A Streptococcus (GAS) has a rich evolutionary history of horizontal transfer among its
      core genes. Yet, despite extensive genetic mixing, GAS strains have discrete ecological
      phenotypes. To further our understanding of the molecular basis for ecological phenotypes,
      comparative genomic hybridization of a set of 97 diverse strains to a GAS pan-genome
      microarray was undertaken, and the association of accessory genes with emm genotypes that
      define tissue tropisms for infection was determined. Of the 22 non-prophage, accessory gene
      regions (AGRs) identified, only three AGRs account for all statistically significant linkage
      disequilibrium among strains having the genotypic biomarkers for throat versus skin infection
      specialist. Networked evolution and population structure analysis of loci representing each of
      the AGRs reveals that most strains with the skin specialist and generalist biomarkers form
      discrete clusters, whereas strains with the throat specialist biomarker are highly diverse. To
      identify co-inherited and co-selected accessory genes, the strength of genetic associations
      was determined for all possible pair wise combinations of accessory genes among the 97 GAS
      strains. Accessory genes showing very strong associations provide the basis for an
      evolutionary model, which reveals that a major transition between many throat and skin
      specialist haplotypes correlates with the gain or loss of genes encoding fibronectin-binding
      proteins. This study employs a novel synthesis of tools to help delineate the major genetic
      changes associated with key adaptive shifts in an extensively recombined bacterial species.
AU  - Bessen DE
AU  - Kumar N
AU  - Hall GS
AU  - Riley DR
AU  - Luo F
AU  - Lizano S
AU  - Ford CN
AU  - McShan WM
AU  - Nguyen SV
AU  - Dunning-Hotopp JC
AU  - Tettelin H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6651-6663.

PMID- 3224759
VI  - 16
DP  - 1988
TI  - Structure of mammalian DNA methyltransferase as deduced from the inferred amino acid sequence and direct studies of the protein.
PG  - 944-947
AB  - DNA (cytosine-5)-methyltransferase establishes and maintains methylation patterns in the
      genome of higher eukaryotes.  This enzyme has been purified, and the cDNA which encodes it has
      been cloned and sequenced.  DNA MeTase appears to contain a large (1000 amino acid) N-terminal
      domain that contains potential metal-binding sites.  This domain appears to contain a series
      of five to seven structural units of Mr about 20,000, since post-translational processing in
      vivo or partial proteolysis of the purified protein in vitro leads to the production of a
      series of catalytically active species differing in Mr by units of 20,000.  The N-terminal
      domain is fused to a small (570 amino acid) C-terminal domain that is related to bacterial
      type II cytosine methyltransferases.  The relevance of these findings for the biological
      function of DNA MeTase is discussed.
AU  - Bestor T
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 1988 16: 944-947.

PMID- 3473446
VI  - 15
DP  - 1987
TI  - Supercoiling-dependent sequence specificity of mammalian DNA mthyltransferase.
PG  - 3835-3843
AB  - Negative supercoiling of substrate DNA dramatically alters the in vitro sequence specificity
      of mammalian DNA methyltransferase.  This result suggests in vivo site selection by DNA MeTase
      could be regulated by conformational information in the form of alternative secondary
      structures indicated in DNA by local supercoiling or by the binding of specific nuclear
      proteins.  DNA in the left-handed Z-form is shown not to be a substrate for mammalian DNA
      MeTase.  The sensitivity of DNA MeTase to DNA structure may also make it useful as a probe for
      sequences which undergo supercoiling-dependent structural transitions in vitro.
AU  - Bestor T
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1987 15: 3835-3843.

PMID- 3210246
VI  - 203
DP  - 1988
TI  - Cloning and sequencing of a cDNA encoding DNA methyltransferase of mouse cells.
PG  - 971-983
AB  - A cDNA encoding DNA (cytosine-5)-methyltransferase (DNA MTase) of mouse cells has been cloned
      and sequenced.  The nucleotide sequence contains an open reading frame sufficient to encode a
      polypeptide of 1573 amino acid residues, which is close to the apparent size of the largest
      species of DNA MTase found in mouse cells.  The carboxylterminal 570 amino acid residues of
      the inferred protein sequence shows striking similarities to bacterial type II DNA cytosine
      methyltransferases and appears to represent a catalytic methyltransferase domain.  The
      amino-terminal portion of the molecule may be involved in regulating the activity of the
      carboxyl-terminal methyltransferase domain, since antibodies directed against a peptide
      sequence located within this region inhibits transmethylase activity in vitro.  A 5200 base
      DNA MTase-specific mRNA was found to be expressed in all mouse cell types tested, and cell
      lines known to have different genomic methylation patterns were found to contain DNA MTase
      proteins of similar or identical sizes and de novo sequence specificities.  The implications
      of these findings for an understanding of the mechanisms involved in the establishment and
      maintenance of methylation patterns are discussed.
AU  - Bestor T
AU  - Laudano A
AU  - Mattaliano R
AU  - Ingram V
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1988 203: 971-983.

PMID- 
VI  - 0
DP  - 1996
TI  - DNA methyltransferases in mammalian development and genome defense.
PG  - 61-76
AB  - The mammalian genome is modified by the addition of about 3 x 10^7 methyl groups, all at the 5
      position of cytosine and most at 5'-CpG-3' dinucleotides.  Methylation patterns are
      transmitted by clonal inheritance and increase the information content of the genome;
      transcription is repressed when CpG sites within promoters are methylated.  Cytosine
      methylation is dangerous: 5-methylcytosine (m5C) is the major endogenous mutagen (deamination
      results in C-T transition mutations at CpG sites, which account for about one-third of all
      mutations in humans, and tumor suppressor genes are frequently inactivated by ectopic de novo
      methylation of promoter regions.  However, there must be benefits that yield a net selective
      advantage.  This is shown by the retention of cytosine methylation by virtually all organisms
      with genomes of more than 5 x 10^8 bp and by the fact that perturbations of methylation
      patterns are lethal to mouse embryos and to differentiated cells.  Severe developmental
      abnormalities are seen when m5C levels are reduced in Arabidopsis as the result of mutations
      at uncharacterized loci or by expression of a DNA methyltransferase antisense construct.
      Although methylation patterns clearly play an essential role in large-genome eukaryotes, the
      nature of that role is not understood.  It is argued here that an understanding of the
      regulation of de novo methylation will reveal the biological function of methylation patterns.
AU  - Bestor TH
PT  - Journal Article
TA  - Epigenetic Mechanisms of Gene Regulation
JT  - Epigenetic Mechanisms of Gene Regulation
SO  - Epigenetic Mechanisms of Gene Regulation 1996 0: 61-76.

PMID- 1628623
VI  - 11
DP  - 1992
TI  - Activation of mammalian DNA methyltransferase by cleavage of a Zn binding regulatory domain.
PG  - 2611-2617
AB  - Mammalian DNA (cytosine-5) methyltransferase contains a C-terminal domain that is closely
      related to bacterial cytosine-5 restriction methyltransferases. This methyltransferase domain
      is linked to a large N-terminal domain. It is shown here that the N-terminal domain contains a
      Zn binding site and that the N- and C-terminal domains can be separated by cleavage with
      trypsin or Staphylococcus aureus protease V8; the protease V8 cleavage site was determined by
      Edman degradation to lie 10 residues C-terminal of the run of alternating lysyl and glycyl
      residues which joins the two domains and six residues N-terminal of the first sequence motif
      conserved between the mammalian and bacterial cytosine methyltransferases. While the intact
      enzyme had little activity on unmethylated DNA substrates, cleavage between the domains caused
      a large stimulation of the initial velocity of methylation of unmethylated DNA without
      substantial change in the rate of methylation of hemimethylated DNA. These findings indicate
      that the N-terminal domain of DNA methyltransferase ensures the clonal propagation of
      methylation patterns through inhibition of the de novo activity of the C-terminal domain.
      Mammalian DNA methyltransferase is likely to have arisen via fusion of a prokaryotic-like
      restriction methyltransferase and an unrelated DNA binding protein. Stimulation of the de novo
      activity of DNA methyltransferase by proteolytic cleavage in vivo may contribute to the
      process of ectopic methylation observed in the DNA of aging animals, tumors and in lines of
      cultured cells.
AU  - Bestor TH
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1992 11: 2611-2617.

PMID- 1968655
VI  - 326
DP  - 1990
TI  - DNA methylation: evolution of a bacterial immune function into a regulator of gene expression and genome structure in higher eukaryotes.
PG  - 179-187
AB  - The amino acid sequence of mammalian DNA methyltransferase has been deduced from the
      nucleotide sequence of a cloned cDNA. It appears that the mammalian enzyme arose during
      evolution via fusion of a prokaryotic restriction methyltransferase gene and a second gene of
      unknown function. Mammalian DNA methyltransferase currently comprises an N-terminal domain of
      about 1000 amino acids that may have a regulatory role and a C-terminal 570 amino acid domain
      that retains similarities to bacterial restriction methyltransferases. The sequence
      similarities among mammalian and bacterial DNA cytosine methyltransferases suggest a common
      evolutionary origin. DNA methylation is uncommon among those eukaryotes having genomes of less
      than 108 base pairs, but nearly universal among large-genome eukaryotes. This and other
      considerations make it likely that sequence inactivation by DNA methylation has evolved to
      compensate for the expansion of the genome that has accompanied the development of higher
      plants and animals. As methylated sequences are usually propagated in the repressed,
      nuclease-insensitive state, it is likely that DNA methylation compartmentalizes the genome to
      facilitate gene regulation by reducing the total amount of DNA sequence that must be scanned
      by DNA-binding regulatory proteins. DNA methylation is involved in immune recognition in
      bacteria but appears to regulate the structure and expression of the genome in complex higher
      eukaryotes. I suggest that the DNA-methylating system of mammals was derived from that of
      bacteria by way of a hypothetical intermediate that carried out selective de novo methylation
      of exogenous DNA and propagated the methylated DNA in the repressed state within its own
      genome. During the evolution of complex plants and animals the inactivating effects of DNA
      methylation spread to extraneous cellular sequences, such as highly repetitive DNA and
      transposable elements, and later to tissue-specific genes. Modern large-genome eukaryotes have
      adapted a primitive prokaryotic immune system to enable them to manage a genome that has
      expanded more than 1000-fold as a result of accumulation of extraneous sequences and
      tissue-specific genes.
AU  - Bestor TH
PT  - Journal Article
TA  - Philos. Trans. R. Soc. Lond. B. Biol. Sci.
JT  - Philos. Trans. R. Soc. Lond. B. Biol. Sci.
SO  - Philos. Trans. R. Soc. Lond. B. Biol. Sci. 1990 326: 179-187.

PMID- 11005794
VI  - 9
DP  - 2000
TI  - The DNA methyltransferases of mammals.
PG  - 2395-2402
AB  - The biological significance of 5-methylcytosine was in doubt for many years, but is no longer,
      Through targeted mutagenesis in mice it has
      been learnt that every protein shown by biochemical tests to be
      involved in the establishment, maintenance or interpretation of genomic
      methylation patterns is encoded by an essential gene. A human genetic
      disorder (ICF syndrome) has recently been shown to be caused by
      mutations in the DNA methyltransferase 3B (DNMT3B) gene, A second human
      disorder (Rett syndrome) has been found to result from mutations in the
      MECP2 gene, which encodes a protein that binds to methylated DNA.
      Global genome demethylation caused by targeted mutations in the DNA
      methyltransferase-l (Dnmt1) gene has shown that cytosine methylation
      plays essential roles in X-inactivation, genomic imprinting and genome.
      stabilization. The majority of genomic 5-methylcytosine is now known to
      enforce the transcriptional silence of the enormous burden of
      transposons and retroviruses that have accumulated in the mammalian
      genome. It has also become clear that programmed changes in methylation
      patterns are less important in the regulation of mammalian development
      than was previously believed. Although a number of outstanding
      questions have yet to be answered (one of these questions involves the
      nature of the cues that designate sites for methylation at particular
      stages of gametogenesis and early development), studies of DNA
      methyltransferases are likely to provide further insights into the
      biological functions of genomic methylation patterns.
AU  - Bestor TH
PT  - Journal Article
TA  - Hum. Mol. Genet.
JT  - Hum. Mol. Genet.
SO  - Hum. Mol. Genet. 2000 9: 2395-2402.

PMID- 3248734
VI  - 74
DP  - 1988
TI  - Cloning of a mammalian DNA methyltransferase.
PG  - 9-12
AB  - Cloning and sequencing of cDNA clones has shown that mammalian DNA
      (cytosine-5)-methyltransferase comprises a 1000-amino acid (aa) N-terminal
      region of unknown function and a 570-aa C-terminal region that is clearly
      related to bacterial Type II cytosine restriction methyltransferases.  These
      findings indicate that the mammalian enzyme contains at least two structural
      domains and suggest a common evolutionary origin for mammalian and prokaryotic
      DNA (cytosine-5)-methyltransferases.
AU  - Bestor TH
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 9-12.

PMID- Not carried by PubMed...
VI  - 5
DP  - 1993
TI  - Methylation patterns in the vertebrate genome.
PG  - 57-60
AB  - The estimated amount of DNA in a mammalian cell is 6x109 base pairs, the equivalent of more
      than 2 m of linear DNA. Cells of some amphibians and vascular plants contain even larger
      amounts. However, only a small fraction of the genome is available for interaction with
      transcription factors that regulate gene expression, and the accessibility of specific
      sequences to these factors appears to be controlled in large part by methylation at the 5
      position of cytosine residues in 5'-CpG-3' dinucleotides. Most DNA in large-genome
      eukaryotes is methylated and inaccessible to the transcription apparatus, whereas promoter
      regions are normally unmethylated and accessible to regulatory factors. Methylation of
      promoter regions prevents transcription, as in the case of genes inactivated by genomic
      imprinting and those on the inactive X chromosome. Programmed changes in the methylation
      status of DNA may also be involved in the regulation of tissue-specific genes during
      development, although this hypothesis remains controversial. Another unsolved question concern
      the ways in which sex-and tissue-specific methylation patterns are established during
      gametogenesis and early development; this is an important issue for human health because
      certain human diseases are likely to involve defective establishment or maintenance of genomic
      methylation patterns.
AU  - Bestor TH
PT  - Journal Article
TA  - J. NIH Res.
JT  - J. NIH Res.
SO  - J. NIH Res. 1993 5: 57-60.

PMID- 6577443
VI  - 80
DP  - 1983
TI  - Two DNA methyltransferases from murine erythroleukemia cells: purification, sequence specificity, and mode of interaction with DNA.
PG  - 5559-5563
AB  - Dye-ligand chromatography on Cibacron blue F3GA-agarose has been used to resolve two species
      of DNA (cytosine-5-)-methyltransferase from nuclear
      extracts of uninduced Friend murine erythroleukemia cells. Each species
      has been highly purified; the activities in the first and second peaks
      were associated with polypeptides of Mr 150,000 and 175,000, respectively.
      Analysis of substrate specificity with synthetic DNAs and restriction
      fragments of phi X174 replicative form DNA and pBR322 DNA showed that
      neither enzyme had dependence on the sequence context of CpG
      dinucleotides; poly(dG-dC) had the greatest methyl-accepting activity of
      any unmethylated DNA substrate tested. De novo methylation by both enzymes
      was inefficient relative to methylation of hemimethylated sites.
      Methyl-accepting activity was strongly dependent on DNA chain length. This
      observation suggests that binding to DNA, followed by one-dimensional
      diffusion of enzyme along the DNA molecule, is important in the mechanism
      by which DNA methyltransferase locates its recognition sites.
AU  - Bestor TH
AU  - Ingram VM
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1983 80: 5559-5563.

PMID- 3857609
VI  - 82
DP  - 1985
TI  - Growth-dependent expression of multiple species of DNA methyltransferase in murine erythroleukemia cells.
PG  - 2674-2678
AB  - Friend murine erythroleukemia cells were found to contain three distinct species of DNA
      (cytosine-5-)-methyltransferase whose relative proportions were a characteristic function of
      the proliferative state of the cells.  Rapidly proliferating cells contained a Mr 190,000
      species of DNA MeTase, whereas cells in the late logarithmic/early plateau phase of cellular
      growth contained two species of Mr 150,000 and 175,000 (DNA MeTases I and II); stationary
      phase cells contained primarily DNA MeTase I.  The three species of DNA MeTase displayed
      structural similarities, as determined by analysis of partial proteolysis products, and have
      similar de novo sequence specificites in transmethylation reactions involving purified enzyme
      and prokaryotic DNA.  The different relative proportions of the enzymes in cells under
      different growth conditions suggest that the three species of DNA MeTase fulfill different
      roles in processes leading to the perpetuation of DNA methylation patterns.
AU  - Bestor TH
AU  - Ingram VM
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1985 82: 2674-2678.

PMID- 7917329
VI  - 6
DP  - 1994
TI  - DNA methyltransferases.
PG  - 380-389
AB  - Mammals have long been known to tag their DNA by the addition of methyl groups to cytosine
      residues. Only quite recently, however, has the functional significance of DNA methylation
      established a firm footing. Evidence now indicates that DNA methylation is essential for
      development, and is involved in both programmed and ectopic gene inactivation. Recent
      structural and mechanistic work on bacterial cytosine-5-methyltransferases has provided much
      insight into the function of the carboxy-terminal catalytic domain of eukaryotic
      cytosine-5-methyltransferases; evidence is emerging that the amino-terminal domain targets the
      enzyme to the replication machinery and may be involved in sensing the pre-existing
      methylation state of the DNA.
AU  - Bestor TH
AU  - Verdine GL
PT  - Journal Article
TA  - Curr. Opin. Cell Biol.
JT  - Curr. Opin. Cell Biol.
SO  - Curr. Opin. Cell Biol. 1994 6: 380-389.

PMID- 29982426
VI  - 10
DP  - 2018
TI  - Comparative Genomic Analysis of Two Chilean Renibacterium salmoninarum Isolates and the type strain ATCC 33209T.
PG  - 1816-1822
AB  - Renibacterium salmoninarum, a slow-growing facultative intracellular pathogen
      belonging to the high C + G content Actinobacteria phylum, is the causative agent
      of bacterial kidney disease, a progressive granulomatous infection affecting
      salmonids worldwide. This Gram-positive bacterium has existed in the Chilean
      salmonid industry for >30 years, but little or no information is available
      regarding the virulence mechanisms and genomic characteristics of Chilean
      isolates. In this study, the genomes of two Chilean isolates (H-2 and DJ2R) were
      sequenced, and a search was conducted for genes and proteins involved in
      virulence and pathogenicity, and we compare with the type strain ATCC 33209 T
      genome. The genome sizes of H-2 and DJ2R are 3,155,332 bp and 3,155,228 bp,
      respectively. They genomes presented six ribosomal RNA, 46 transcription RNA, and
      25 noncodingRNA, and both had the same 56.27% G + C content described for the
      type strain ATCC 33209 T. A total of 3,522 and 3,527 coding sequences were found
      for H-2 and DJ2R, respectively. Meanwhile, the ATCC 33209 T type strain had 3,519
      coding sequences. The in silico genome analysis revealed a genes related to
      tricarboxylic acid cycle, glycolysis, iron transport and others metabolic
      pathway. Also, the data indicated that R salmoninarum may have a variety of
      possible virulence-factor and antibiotic-resistance strategies. Interestingly,
      many of genes had high identities with Mycobacterium species, a known pathogenic
      Actinobacteria bacterium. In summary, this study provides the first insights into
      and initial steps towards understanding the molecular basis of antibiotic
      resistance, virulence mechanisms and host/environment adaptation in two Chilean
      R. salmoninarum isolates that contain proteins of which were similar to those of
      Mycobacterium. Furthermore, important information is presented that could
      facilitate the development of preventive and treatment measures against R.
      salmoninarum in Chile and worldwide.
AU  - Bethke J
AU  - Yanez AJ
AU  - Avendano-Herrera R
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2018 10: 1816-1822.

PMID- 776705
VI  - 35
DP  - 1976
TI  - A restriction endonuclease analysis of the bacterial plasmid controlling the ecoRI restriction and modification of DNA.
PG  - 2037-2043
AB  - Genetic analyses of DNA restriction and modification mechanisms have been encumbered by the
      inability to rigorously select for mutant phenotypes associated
      with these systems. The application of restriction endonucleases has now proved
      to be a successful approach to the genetic analyses of small genomes that are
      recalcitrant to the more standard genetic techniques. Restriction endonucleases
      EcoRI and HindIII were used to analyze the structure of the plasmid genome
      responsible for the EcoRI restriction endonuclease and modification methylase.
      This plasmid in the original clinical isolate of Escherichia coli appears to be
      identical to the ColE 1 plasmid except for a 1.95 kilobase pair segment which
      contains these genes. A preliminary restriction map of this plasmid is presented.
AU  - Betlach M
AU  - Hershfield V
AU  - Chow L
AU  - Brown W
AU  - Goodman H
AU  - Boyer HW
PT  - Journal Article
TA  - Fed. Proc.
JT  - Fed. Proc.
SO  - Fed. Proc. 1976 35: 2037-2043.

PMID- 17115055
VI  - 24
DP  - 2006
TI  - The genome and transcriptomes of the anti-tumor agent Clostridium novyi-NT.
PG  - 1573-1580
AB  - Bacteriolytic anti-cancer therapies employ attenuated bacterial strains that selectively
      proliferate within tumors. Clostridium novyi-NT spores
      represent one of the most promising of these agents, as they generate
      potent anti-tumor effects in experimental animals. We have determined the
      2.55-Mb genomic sequence of C. novyi-NT, identifying a new type of
      transposition and 139 genes that do not have homologs in other bacteria.
      The genomic sequence was used to facilitate the detection of transcripts
      expressed at various stages of the life cycle of this bacterium in vitro
      as well as in infections of tumors in vivo. Through this analysis, we
      found that C. novyi-NT spores contained mRNA and that the spore
      transcripts were distinct from those in vegetative forms of the bacterium.
AU  - Bettegowda C
AU  - Huang X
AU  - Lin J
AU  - Cheong I
AU  - Kohli M
AU  - Szabo SA
AU  - Zhang X
AU  - Diaz LA Jr
AU  - Velculescu VE
AU  - Parmigiani G
AU  - Kinzler KW
AU  - Vogelstein B
AU  - Zhou S
PT  - Journal Article
TA  - Nat. Biotechnol.
JT  - Nat. Biotechnol.
SO  - Nat. Biotechnol. 2006 24: 1573-1580.

PMID- 29348334
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Phenotypically Distinct Janthinobacterium sp. Isolates  Cultured from the Hudson Valley Watershed.
PG  - e01426-17
AB  - Investigation of the Hudson Valley watershed reveals many violacein-producing bacteria. These
      are of interest for their biotherapeutic potential in treating
      chytrid infections of amphibians. The draft whole-genome sequences for seven
      Janthinobacterium isolates with a variety of phenotypes are provided in this
      study.
AU  - Bettina AM
AU  - Doing G
AU  - O'Brien K
AU  - Perron GG
AU  - Jude BA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01426-17.

PMID- 26472846
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Planomicrobium glaciei UCD-HAM (Phylum Firmicutes).
PG  - e01209-15
AB  - Here, we present the draft genome of Planomicrobium glaciei, a member of the phylum
      Firmicutes, found at the University of California Davis. Paired-end, 300-bp reads were
      generated on an Illumina MiSeq. The assembly consists of 3,925,122 bp, contained in 109
      contigs, with a G+C content of 46.7%.
AU  - Betts MN
AU  - Jospin G
AU  - Eisen JA
AU  - Coil DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01209-15.

PMID- 12949880
VI  - 42
DP  - 2003
TI  - Polycyclic Aromatic DNA-base surrogates: High-affinity binding to an adenine-specific base-flipping DNA methyltransferase.
PG  - 3958-3960
AB  - DNA methylation is an important biological event that serves diverse cellular functions such
      as protection against endogenous restriction endonucleases, direction of DNA-mismatch repair,
      as well as regulation of gene expression and DNA replication.  DNA methylation is catalyzed by
      DNA methyltransferases (MTases), which bind to specific DNA sequences and transfer a methyl
      group from S-adenosyl-L-methionine to the exocyclic amino groups of adenine or cytosine or to
      C5 of cytosine.  Interestingly, methylation is commenced by flipping the target nucleotide
      completely out of the helix.  The energy cost for disrupting Watson-Crick hydrogen bonds and
      base-stacking interactions is mainly compensated by specific binding of the target bases
      within the active sites of the enzymes and by stabilizing the formed apparent abasic site.
      Three different mechanisms of abasic-site stabilization have been observed in crystal
      structures of DNA MTases complexed with DNA.  The cytosine-specific DNA MTases M.HhaI and
      M.HaeIII either only insert an amino acid side chain into the opened space or insert an amino
      acid side chain in addition to rearranging the base pairing.  This is in contrast to the
      adenine-specific DNA MTase M.TaqI.  In this case, the formed unpaired partner base is inserted
      into the opened space, resulting in interstrand stacking.
AU  - Beuck C
AU  - Singh I
AU  - Bhattacharya A
AU  - Hecker W
AU  - Parmar VS
AU  - Seitz O
AU  - Weinhold E
PT  - Journal Article
TA  - Angew. Chem. Int. Ed. Engl.
JT  - Angew. Chem. Int. Ed. Engl.
SO  - Angew. Chem. Int. Ed. Engl. 2003 42: 3958-3960.

PMID- 27445365
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of an Enterococcus thailandicus Strain Isolated from Bovine Feces.
PG  - e00576-16
AB  - Here, we report the first draft genome sequence of Enterococcus thailandicus isolated from the
      feces of feedlot cattle in Southern Alberta.
AU  - Beukers AG
AU  - Zaheer R
AU  - Goji N
AU  - Cook SR
AU  - Amoako KK
AU  - Chaves AV
AU  - Ward MP
AU  - McAllister TA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00576-16.

PMID- 25593253
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Pseudoalteromonas sp. Strain OCN003, Isolated from Kane'ohe Bay, O'ahu, Hawaii.
PG  - e01396-14
AB  - Pseudoalteromonas sp. strain OCN003 is a marine gammaproteobacterium that was isolated from a
      diseased colony of the common Hawaiian reef coral, Montipora capitata, found on a reef
      surrounding Moku o Lo'e in Kane'ohe Bay, Hawaii. Here, we report the complete genome of
      Pseudoalteromonas sp. strain OCN003.
AU  - Beurmann S
AU  - Videau P
AU  - Ushijima B
AU  - Smith AM
AU  - Aeby GS
AU  - Callahan SM
AU  - Belcaid M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01396-14.

PMID- 22811533
VI  - 86
DP  - 2012
TI  - Spread of a Distinct Stx2-Encoding Phage Prototype among Escherichia coli O104:H4 Strains from Outbreaks in Germany, Norway, and Georgia.
PG  - 10444-10455
AB  - Shiga toxin 2 (Stx2)-producing Escherichia coli (STEC) O104:H4 caused one of the
      world's largest outbreaks of hemorrhagic colitis and hemolytic uremic syndrome in
      Germany in 2011. These strains have evolved from enteroaggregative E. coli (EAEC)
      by the acquisition of the Stx2 genes and have been designated enteroaggregative
      hemorrhagic E. coli. Nucleotide sequencing has shown that the Stx2 gene is
      carried by prophages integrated into the chromosome of STEC O104:H4. We studied
      the properties of Stx2-encoding bacteriophages which are responsible for the
      emergence of this new type of E. coli pathogen. For this, we analyzed Stx
      bacteriophages from STEC O104:H4 strains from Germany (in 2001 and 2011), Norway
      (2006), and the Republic of Georgia (2009). Viable Stx2-encoding bacteriophages
      could be isolated from all STEC strains except for the Norwegian strain. The Stx2
      phages formed lysogens on E. coli K-12 by integration into the wrbA locus,
      resulting in Stx2 production. The nucleotide sequence of the Stx2 phage P13374 of
      a German STEC O104:H4 outbreak was determined. From the bioinformatic analyses of
      the prophage sequence of 60,894 bp, 79 open reading frames were inferred.
      Interestingly, the Stx2 phages from the German 2001 and 2011 outbreak strains
      were found to be identical and closely related to the Stx2 phages from the
      Georgian 2009 isolates. Major proteins of the virion particles were analyzed by
      mass spectrometry. Stx2 production in STEC O104:H4 strains was inducible by
      mitomycin C and was compared to Stx2 production of E. coli K-12 lysogens.
AU  - Beutin L
AU  - Hammerl JA
AU  - Strauch E
AU  - Reetz J
AU  - Dieckmann R
AU  - Kelner-Burgos Y
AU  - Martin A
AU  - Miko A
AU  - Strockbine NA
AU  - Lindstedt BA
AU  - Horn D
AU  - Monse H
AU  - Huettel B
AU  - Muller I
AU  - Stuber K
AU  - Reinhardt R
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 2012 86: 10444-10455.

PMID- 18515483
VI  - 74
DP  - 2008
TI  - Evaluation of major types of Shiga toxin 2E-producing Escherichia coli bacteria present in food, pigs, and the environment as potential pathogens for humans.
PG  - 4806-4816
AB  - Shiga toxin 2e (Stx2e)-producing strains from food (n = 36), slaughtered
      pigs (n = 25), the environment (n = 21), diseased pigs (n = 19), and
      humans (n = 9) were investigated for production of Stx2e by enzyme-linked
      immunosorbent assay, for virulence markers by PCR, and for their serotypes
      to evaluate their role as potential human pathogens. Stx2e production was
      low in 64% of all 110 strains. Stx2e production was inducible by mitomycin
      C but differed considerably between strains. Analysis by nucleotide
      sequencing and transcription of stx(2e) genes in high- and
      low-Stx2e-producing strains showed that toxin production correlated with
      transcription rates of stx(2e) genes. DNA sequences specific for the int,
      Q, dam, and S genes of the stx(2e) bacteriophage P27 were found in 109
      strains, indicating cryptic P27-like prophages, although 102 of these were
      not complete for all genes tested. Genes encoding intimin (eae),
      enterohemorrhagic Escherichia coli hemolysin (ehx), or other stx(1) or
      stx(2) variants were not found, whereas genes for heat-stable enterotoxins
      STI, STII, or EAST1 were present in 54.5% of the strains. Seven major
      serotypes that were associated with diseased pigs (O138:H14, O139:H1, and
      O141:H4) or with slaughter pigs, food, and the environment (O8:H4, O8:H9,
      O100:H30, and O101:H9) accounted for 60% of all Stx2e strains. The human
      Stx2e isolates did not belong to these major serotypes of Stx2e strains,
      and high production of Stx2e in human strains was not related to diarrheal
      disease. The results from this study and other studies do not point to
      Stx2e as a pathogenicity factor for diarrhea and hemolytic uremic syndrome
      in humans.
AU  - Beutin L
AU  - Kruger U
AU  - Krause G
AU  - Miko A
AU  - Martin A
AU  - Strauch E
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2008 74: 4806-4816.

PMID- 9461215
VI  - 391
DP  - 1998
TI  - Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana.
PG  - 485-488
AB  - The plant Arabidopsis thaliana has become an important model species for the study of many
      aspects of plant biology.  The relatively small size of the nuclear genome and the
      availability of extensive physical maps of the five chromosomes provide a feasible basis for
      initiating sequencing of the five chromosomes.  The YAC-based physical map of chromosome 4 was
      used to construct a sequence-ready map of cosmid and BAC clones covering a 1.9-megabase
      contiguous region, and the sequence of this region is reported here.  Analysis of the sequence
      revealed an average gene density of one gene every 4.8 kilobases, and 54% of the predicted
      genes had significant similarity to known genes.  Other interesting features were found, such
      as the sequence of a disease-resistance gene locus, the distribution of retroelements, the
      frequent occurrence of clustered gene families, and the sequence of several classes of genes
      not previously encountered in plants.
AU  - Bevan M et al
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1998 391: 485-488.

PMID- 10784050
VI  - 146
DP  - 2000
TI  - The homologous terminal sequence of the Streptomyces lividans chromosome and SLP2 plasmid.
PG  - 911-922
AB  - The chromosome of Streptomyces lividans shares 15.4 kb homology with one end of the linear
      plasmid SLP2, consisting of a 10.1 kb terminal sequence
      followed by the 5.3 kb transposable element Tn4811. The 10.1 kb terminal
      sequence was determined. The mean G+C content of this sequence is 67.9
      mol% with a striking G vs C bias in the last kb. The terminal 232 nt
      contained 10 palindromic sequences with potential to form complex
      secondary structures. One typical Streptomyces coding sequence (designated
      ORF1) of 2643 bp was predicted in the determined sequence. The amino acid
      sequence of the ORF1 product contained a DEAH helicase motif, and
      exhibited similarity to type I restriction enzyme HsdR subunits in the
      database, suggesting a possible role in replication of the telomeres.
      However, all the ORF1 sequences on the chromosome and SLP2 could be
      simultaneously knocked out by targeted recombination without affecting the
      viability of the cells and the linearity of the chromosome and SLP2. This
      ruled out ORF1 as an essential component in the maintenance of the linear
      chromosome and plasmids.
AU  - Bey SJ
AU  - Tsou MF
AU  - Huang CH
AU  - Yang CC
AU  - Chen CW
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2000 146: 911-922.

PMID- 26769930
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Actinobaculum massiliense Strain FC3.
PG  - e01537-15
AB  - Actinobaculum massiliense strain FC3 was isolated from the urine of a patient with acute
      cystitis. The 2.06-Mb genome of strain FC3 contains 17 toxin/antitoxin
      modules and 9 bacteriocin-encoding genes that may play a role in virulence. The
      genome also exhibits 693 genes acquired by lateral gene transfer.
AU  - Beye M
AU  - Bakour S
AU  - Labas N
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01537-15.

PMID- 29682169
VI  - 13
DP  - 2018
TI  - Draft genome sequence of Fermentimonas caenicola strain SIT8, isolated from the human gut.
PG  - 8
AB  - We report the properties of a draft genome sequence of the bacterium Fermentimonas caenicola
      strain SIT8 (= CSUR P1560). This strain, whose genome is
      described here, was isolated from the fecal flora of a healthy 28-month-old
      Senegalese boy. Strain SIT8 is a facultatively anaerobic Gram-negative bacillus.
      Here we describe the features of this organism, together with the complete genome
      sequence and annotation. The 2,824,451-bp long (1 chromosome but no plasmid)
      contains 2354 protein-coding and 46 RNA genes, including four rRNA genes.
AU  - Beye M
AU  - Bakour S
AU  - Traore SI
AU  - Rathored J
AU  - Labas N
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2018 13: 8.

PMID- 24501626
VI  - 8
DP  - 2013
TI  - Genome sequence of Phaeobacter caeruleus type strain (DSM 24564(T)), a surface-associated member of the marine Roseobacter clade.
PG  - 403-419
AB  - In 2009 Phaeobacter caeruleus was described as a novel species affiliated with the marine
      Roseobacter clade, which, in turn, belongs to the class
      Alphaproteobacteria. The genus Phaeobacter is well known for members that produce
      various secondary metabolites. Here we report of putative quorum sensing systems,
      based on the finding of six N-acyl-homoserine lactone synthetases, and show that
      the blue color of P. caeruleus is probably due to the production of the secondary
      metabolite indigoidine. Therefore, P. caeruleus might have inhibitory effects on
      other bacteria. In this study the genome of the type strain DSM 24564(T) was
      sequenced, annotated and characterized. The 5,344,419 bp long genome with its
      seven plasmids contains 5,227 protein-coding genes (3,904 with a predicted
      function) and 108 RNA genes.
AU  - Beyersmann PG
AU  - Chertkov O
AU  - Petersen J
AU  - Fiebig A
AU  - Chen A
AU  - Pati A
AU  - Ivanova N
AU  - Lapidus A
AU  - Goodwin LA
AU  - Chain P
AU  - Detter JC
AU  - Rohde M
AU  - Gronow S
AU  - Kyrpides NC
AU  - Woyke T
AU  - Simon M
AU  - Goker M
AU  - Klenk HP
AU  - Brinkhoff T
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 403-419.

PMID- 28232441
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Mycoplasma pullorum Isolated from Domestic Chickens.
PG  - e01647-16
AB  - The 1,007,172-bp complete genome of Mycoplasma pullorum strain B359_6, isolated from domestic
      chickens, has been sequenced, assembled, and annotated.
AU  - Beylefeld A
AU  - Abolnik C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01647-16.

PMID- 11279183
VI  - 276
DP  - 2001
TI  - Chemical probing shows that the intron-encoded endonuclease I-SceI distorts DNA through binding in monomeric form to its homing site.
PG  - 25243-25253
AB  - Despite its small size (27.6 kDa), the group I intron-encoded I-SceI endonuclease initiates
      intron homing by recognizing and specifically cleaving a large intronless DNA sequence. Here,
      we used gel shift assays and footprinting experiments to analyze the interaction between
      I-SceI and its target. I-SceI was found to bind to its substrate in monomeric form.
      Footprinting using DNase I, hydroxyl radical, phenanthroline copper complexes, UV/DH-MePyPs
      photosensitizer, and base-modifying reagents revealed the asymmetric nature of the interaction
      and provided a first glimpse into the architecture of the complex. The protein interacts in
      the minor and major grooves and distorts DNA at three distinct sites: one at the intron
      insertion site and the other two, respectively, downstream (-8, -9) and upstream (+9, +10)
      from this site. The protein appears to stabilize the DNA curved around it by bridging the
      minor groove on one face of the helix. The scissile phosphates would lie on the outside of the
      bend, facing in the same direction relative to the DNA helical axis, as expected for an
      endonuclease that generates 3' overhangs. An internally consistent model is proposed in which
      the protein would take advantage of the concerted flexibility of the DNA sequence to induce a
      synergistic binding/kinking process, resulting in the correct positioning of the enzyme active
      site.
AU  - Beylot B
AU  - Spassky A
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2001 276: 25243-25253.

PMID- 27617058
VI  - 11
DP  - 2016
TI  - Draft genome sequence of Thermoactinomyces sp. strain AS95 isolated from a Sebkha in Thamelaht, Algeria.
PG  - 68
AB  - The members of the genus Thermoactinomyces are known for their protein degradative capacities.
      Thermoactinomyces sp. strain AS95 is a Gram-positive
      filamentous bacterium, isolated from moderately saline water in the Thamelaht
      region of Algeria. This isolate is a thermophilic aerobic bacterium with the
      capacity to produce extracellular proteolytic enzymes. This strain exhibits up to
      99 % similarity with members of the genus Thermoactinomyces, based on 16S rRNA
      gene sequence similarity. Here we report on the phenotypic features of
      Thermoactinomyces sp. strain AS95 together with the draft genome sequence and its
      annotation. The genome of this strain is 2,558,690 bp in length (one chromosome,
      but no plasmid) with an average G + C content of 47.95 %, and contains 2550
      protein-coding and 60 RNA genes together with 64 ORFs annotated as proteases.
AU  - Bezuidt OK
AU  - Gomri MA
AU  - Pierneef R
AU  - Van Goethem MW
AU  - Kharroub K
AU  - Cowan DA
AU  - Makhalanyane TP
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 68.

PMID- 26679578
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Thermophilic Geobacillus sp. Strain Sah69, Isolated from Saharan Soil, Southeast Algeria.
PG  - e01447-15
AB  - Geobacillus spp. are potential sources of novel enzymes, such as those involved in the
      degradation of recalcitrant polymers. Here, we report a Geobacillus genome
      that may help reveal genomic differences between this strain and publicly
      available representatives of the same genus from diverse niches.
AU  - Bezuidt OK
AU  - Makhalanyane TP
AU  - Gomri MA
AU  - Kharroub K
AU  - Cowan DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01447-15.

PMID- 1336091
VI  - 216
DP  - 1992
TI  - Restriction enzymes: Properties and Use.
PG  - 199-224
AB  - Most experiments in molecular biology involve the use of restriction enzymes (REs) at some
      stage of the experiment. The ability of these enzymes to cut DNA at a specific sequence of
      bases has greatly stimulated the growth of recombinant DNA technology. The popularity of these
      enzymes is, in part, due to their wide commercial availability and the simplicity of their
      use. Over 1900 REs are known and of these 275 are available from companies based around the
      world. The purpose of this chapter is to list all commercially available enzymes, to describe
      their general properties, the basic procedures for their use, and ways of troubleshooting
      problems encountered in their use. Although the number of enzymes being discussed is large, a
      few simple rules apply to virtually all the enzymes. One of the aims of this chapter is to
      show that most enzymes can be used successfully without the help of pre-made kits, colorful
      charts, complex buffers, or specialized equipment. Some of this ground has been covered in
      previous reviews by Fuchs and Blakesley, Brooks, and Roberts and Macelis.
AU  - Bhagwat AS
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1992 216: 199-224.

PMID- 8682220
VI  - 10
DP  - 1996
TI  - Transcription is intrinsically mutagenic: Direct correlation between transcription and C to U or 5meC to T deaminations in the non-transcribed strand.
PG  - A962
AB  - Among mutations induced by external agents, more mutations occur in the
      non-transcribed than the transcribed strand.  This strand bias occurs because of preferential
      repair of the transcribed strand.  We have now shown that there is also a strand bias in the
      spontaneous process of hydrolytic deamination of cytosine and 5-methylcytosine (5meC)
      and it causes accumulation of C to T mutations in the non-transcribed strand.  To
      demonstrate this, we used a genetic reversion system involving a transcriptionally regulated
      kanamycin-resistance gene.  Induction of transcription increased the frequency of
      conversion of target C to T only when it was present in the non-transcribed strand.  We
      conclude that the mutations occur as a result of deamination of C or 5meC because
      mismatch correction processes that repair U:G and T:G mismatches partially suppress the
      mutations.  Further, methylation of target cytosine increases frequency of mutations -
      consistent with the higher rate of hydrolytic deamination of 5meC compared to C.  The
      non-transcribed strand suffers more deaminations probably because it is in single-stranded
      state during transcription, and deamination of cytosines in single-stranded DNA is ~1000
      times the rate in double-stranded DNA.  Because transcription requires separation of the
      two DNA strands, we suggest that similar strand bias in hydrolytic deamination of C and
      5meC must exist in all transcription events.
AU  - Bhagwat AS
AU  - Beletskii A
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1996 10: A962.

PMID- 1727392
VI  - 6
DP  - 1992
TI  - The mechanism of activation of EcoRII endonuclease.
PG  - A281
AB  - EcoRII is unusual among restriction enzymes in that it requires a high density
      of its sites [sequence- 5'-CC(A/T)GG-3'] in a DNA for efficient cleavage.
      Substrates such as phage T3 and T7 that contain only a few well separated sites
      for the enzyme are cut poorly, while DNAs that contain several sites for the
      enzyme are cut efficiently.  Interestingly, pBR322, pUC119 or short
      oligonucleotide duplexes containing a single site for the enzyme can activate
      the enzyme to cut poor substrates.  We are investigating the mechanism of this
      activation using short oligonucleotide duplexes.  We have shown that activator
      short duplexes are themselves cleaved poorly by the enzyme despite the fact
      that the enzyme binds to the duplexes efficiently.  Thus, binding of the enzyme
      to the substrate is not sufficient for cleavage.  As expected, pUC119 DNA can
      activate EcoRII to cut these duplexes.  We have also shown that the inefficient
      step in the reaction is not the release of the product after catalysis.
      Interestingly, the efficiency of cleavage of a duplex increases with its
      concentration in the reaction, ie. a duplex can act as its own activator.
      Further, at high concentrations, a duplex can activate the enzyme to cut
      another duplex.  Our results show that EcoRII endonuclease resembles
      recombinational enzymes such as gamma/delta resolvase and phage lambda Int
      protein in that it requires the simultaneous binding of two DNA molecules for
      catalysis.
AU  - Bhagwat AS
AU  - Gabbara S
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1992 6: A281.

PMID- 2104830
VI  - 265
DP  - 1990
TI  - Primary sequence of the EcoRII endonuclease and properties of its fusions with beta-galactosidase.
PG  - 767-773
AB  - The EcoRII endonuclease cleaves DNA containing the sequence CC(A/T)GG before the first
      cytosine. The methylation of the second cytosine in the sequence by either the EcoRII
      methylase or Dcm, a chromosomally coded protein in Escherichia coli, inhibits the cleavage.
      The gene for the EcoRII endonuclease was mapped by analysis of derivatives containing linker
      insertions, transposon insertions, and restriction fragment deletions. Surprisingly, plasmids
      carrying the wild-type endonuclease gene and the EcoRII methylase gene interrupted by
      transposon insertions appeared to be lethal to dcm+ strains of E. coli. We conclude that not
      all the EcoRII/Dcm recognition sites in the cellular DNA are methylated in dcm+ strains. The
      DNA sequence of a 1650-base pair fragment containing the endonuclease gene was determined. It
      revealed an open reading frame that could code for a 45.6-kDa protein. This predicted size is
      consistent with the known size of the endonuclease monomer (44 kDa). The endonuclease and
      methylase genes appear to be transcribed convergently from separate promoters. The reading
      frame of the endonuclease gene was confirmed at three points by generating random protein
      fusions between the endonuclease and beta-galactosidase, followed by an analysis of the
      sequence at the junctions. One of these fusions is missing 18 COOH-terminal amino acids of the
      endonuclease but still displays significant ability to restrict incoming phage in addition to
      beta-galactosidase activity. No striking similarity between the sequence of the endonuclease
      and any other protein in the PIR data base was found. The knowledge of the primary sequence of
      the endonuclease and the availability of the various constructs involving its gene should be
      helpful in the study of the interaction of the enzyme with its substrate DNA.
AU  - Bhagwat AS
AU  - Johnson B
AU  - Weule K
AU  - Roberts RJ
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1990 265: 767-773.

PMID- 1579457
VI  - 20
DP  - 1992
TI  - DNA mismatch correction by very short patch repair may have altered the abundance of oligonucleotides in the E. coli genome.
PG  - 1663-1668
AB  - A base mismatch correction process in E. coli K-12 called Very Short Patch (VSP) repair
      corrects T:G mismatches to C:G when found in certain sequence contexts. Two of the substrate
      mismatches (5'-CTWGG/3'-GGW'CC; W = A or T) occur in the context of cytosine methylation in
      DNA and reduce the mutagenic effects of 5-methylcytosine deamination to thymine. However, VSP
      repair is also known to repair T:G mismatches that are not expected to arise from
      5-methylcytosine deamination (example--CTAG/GGT-C). In these cases, if the original base pair
      were a T:A, VSP repair would cause a T to C transition. We have carried out Markov chain
      analysis of an E. coli sequence database to determine if repair at the latter class of sites
      has altered the abundance of the relevant tetranucleotides. The results are consistent with
      the prediction that VSP repair would tend to deplete the genome of the 'T' containing
      sequences (example--CTAG), while enriching it for the corresponding 'C' containing sequences
      (CCAG). Further, they provide an explanation for the known scarcity of CTAG containing
      restriction enzyme sites among the genomes of enteric bacteria and identify VSP repair as a
      force in shaping the sequence composition of bacterial genomes.
AU  - Bhagwat AS
AU  - McClelland M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 1663-1668.

PMID- 6946274
VI  - 182
DP  - 1981
TI  - Structure and properties of the region of homology between plasmids pMB1 and ColE1.
PG  - 505-507
AB  - Physical maps of the two independently isolated Escherichia coli plasmids, pMB1
      and Co1E1, were prepared with 13 restriction endonucleases and compared.  A 5.1
      kilobase continuous region covering 55% of pMB1 and 75% of Co1E1 was found to
      have similar, but non-identical, restriction maps.  The differences in the maps
      of this region probably arose by localized mutational events rather than by
      major sequence rearrangements.  The F-factor was found to mobilize pMB1
      efficiently for conjugal transfer.  A region on pMB1 required for its
      F-mediated transfer was mapped.  Results of our study combined with results of
      other investigators suggest that pMB1 and Co1E1 share functional properties
      such as colicin production, colicin immunity, mode of replication, and
      mobilization by the F-factor, and that the sequences required to code these
      functions are contained within the 5.1 kilobase homologous region.  A
      nomenclature for the genes encoding restriction and modification enzymes is
      proposed.
AU  - Bhagwat AS
AU  - Person S
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1981 182: 505-507.

PMID- 2435706
VI  - 169
DP  - 1987
TI  - Genetic analysis of the 5-azacytidine sensitivity of Escherichia coli K-12.
PG  - 1537-1546
AB  - DNA containing 5-azacytidine (5-azaC) has been shown to form stable detergent-resistent
      complexes with cytosine methylases. We reasoned that if 5-azaC treatment causes protein-DNA
      cross-links in vivo, then mutations in DNA repair and recombination genes may increase the
      sensitivity of a cell to 5-azaC. We found that although recA (defective) and lexA
      (induction-negative) mutants of Escherichia coli were very sensitive to the drug, mutations in
      uvrA and ung genes had little effect on cell lethality. The sensitivity of recA strains to
      5-azaC was dose dependent and was enhanced by the overproduction of a DNA cytosine methylase
      in the cell. Unexpectedly, a strain of E. coli carrying a recA mutation and a deletion of the
      DNA cystosine methylase gene (dcm) was found to be significantly sensitive to 5-azaC. Study of
      mutations in the pyrimidine salvage pathway of E. coli suggests that direct phosphorylation of
      5-azaC, rather than phosphorylation of its degradation products, is largely responsible for
      the lethal effects of the drug. The addition of uracil to the growth medium had little effect
      on cell lethality of recA mutants, but it partially reversed the inhibition of cell growth
      caused by 5-azaC. This reversal of the bacteriostatic effects of the drug could not be
      achieved by adding cytosine or orotic acid to the growth medium and required the presence of
      functional UMP-pyrophosphorylase (gene upp) in the cell.
AU  - Bhagwat AS
AU  - Roberts RJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1987 169: 1537-1546.

PMID- 3163070
VI  - 12A
DP  - 1988
TI  - The ability of DCM and EcoRII methylases to methylate CC(A/T)GG sequences is not sufficient for their participation in very short patch repair at the same sites.
PG  - 282
AB  - E. coli has the ability to correct mismatches such as -CTAGG- -CTTGG- -GGTCC- -GGACC- to
      restore CC(A/T)GG sites by a mechanism called very short patch (VSP) repair. It also codes for
      a DNA cytosine methylase, Dcm, that methylates the second cytosine within CC(A/T)GG sequence
      at its C5 position. Several mutations in dcm that lack the ability to methylate are defective
      in VSP repair as well, suggesting a role for dcm in VSP repair. We have isolated a deletion
      mutant of dcm that is active in methylation, but inactive in VSP repair. Another strain of E.
      coli carries the restriction-modification system EcoRII that includes a DNA methylase with the
      same sequence specificity as Dcm. The two enzymes methylate the same cytosine in the sequence
      at the identical position, but EcoRII methylase cannot complement dcm mutations defective in
      VSP repair. This is despite the fact that the two methylases share signficant sequence
      homology. It appears that the two methylases have evolved to perform separate functions in the
      cell.
AU  - Bhagwat AS
AU  - Sohail A
AU  - Lieb M
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1988 12A: 282.

PMID- Not included in PubMed...
VI  - 83
DP  - 1988
TI  - Methylation abilities of EcoRII and DCM methylases are not sufficient for their involvement in very short patch repair.
PG  - 173-178
AB  - Dcm, a methylase coded by a chromosomal gene in E. coli K-12, methylates the second cytosine
      in the sequence CC(A/T)GG. E. coli can repair mismatches in DNA such as -CTAGG- or -CTTGG-
      -GGTCC- -GGACC- in favor of the lower strand, creating CC(A/T)GG sites. This is called very
      short patch (VSP) repair. Mutation dcm6 destroys the ability of the cell to methylate DNA and
      to repair mismatches of the kind mentioned above. The methylase in the
      restriction-modification system EcoRII recognizes and methylates the same sequence as Dcm. We
      have found that the gene for the EcoRII methylase is closely related to dcm. Despite these
      similarities, EcoRII methylase cannot complement the dcm6 mutation for VSP repair. We have
      also studied the ability of certain deletion derivatives of the cloned dcm gene to complement
      the dcm6 mutation. At least two deletions complement the mutation for methylation but not for
      repair. A mutated methylase may lose a role in DNA repair without losing its methylating
      ability.
AU  - Bhagwat AS
AU  - Sohail A
AU  - Lieb M
PT  - Journal Article
TA  - UCLA Symp. Mol. Cell. Biol.
JT  - UCLA Symp. Mol. Cell. Biol.
SO  - UCLA Symp. Mol. Cell. Biol. 1988 83: 173-178.

PMID- 3011742
VI  - 166
DP  - 1986
TI  - Cloning and characterization of the dcm locus of Escherichia coli K-12.
PG  - 751-755
AB  - The dcm locus of Escherichia coli K-12 has been shown to code for a methylase that methylates
      the second cytosine within the sequence 5'-CC(A/T)GG-3'. This sequence is also recognized by
      the EcoRII restriction-modification system coded by the E. coli plasmid N3. The methylase
      within the EcoRII system methylates the same cytosine as the dcm protein. We have isolated,
      from a library of E. coli K-12 DNA, two overlapping clones that carry the dcm locus. We show
      that the two clones carry overlapping sequences that are present in a dcm+ strain, but are
      absent in a dcm deletion strain. We also show that the cloned gene codes for a methylase, that
      it complements mutations in the EcoRII methylase, and that it protects EcoRII recognition
      sites from cleavage by the EcoRII endonuclease. We found no phage restriction activity
      associated with the dcm clones.
AU  - Bhagwat AS
AU  - Sohail A
AU  - Roberts RJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1986 166: 751-755.

PMID- 23950119
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Lignocellulose-Degrading Thermophilic Bacterium Geobacillus sp. Strain WSUCF1.
PG  - e00595-13
AB  - Geobacillus sp. strain WSUCF1 is a thermophilic spore-forming member of the phylum Firmicutes,
      isolated from a soil sample collected from the compost
      facility. We report the draft genome sequence of this isolate with an estimated
      genome size of 3.4 Mb. The genome sequence of this isolate revealed several genes
      encoding glycoside hydrolases, making it a potential candidate for plant biomass
      degradation.
AU  - Bhalla A
AU  - Kainth AS
AU  - Sani RK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00595-13.

PMID- 29146843
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of Vibrio cholerae-Specific Bacteriophages 24 and X29.
PG  - e01013-17
AB  - The complete genomes of two Vibrio cholerae bacteriophages of potential interest  for cholera
      bacteriophage (phage) therapy were sequenced and annotated. The
      genome size of phage 24 is 44,395 bp encoding 71 putative proteins, and that of
      phage X29 is 41,569 bp encoding 68 putative proteins.
AU  - Bhandare SG
AU  - Warry A
AU  - Emes RD
AU  - Hooton SPT
AU  - Barrow PA
AU  - Atterbury RJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01013-17.

PMID- 25593258
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Halomonas hydrothermalis MTCC 5445, Isolated from the West Coast of India.
PG  - e01419-14
AB  - We announce here the draft genome sequence of Halomonas hydrothermalis MTCC 5445, a halophilic
      bacterium of the class Gammaproteobacteria. It was isolated from the
      sea coast of Aadri, Veraval, Gujarat, India. Its genome contains genes for
      polyhydroxybutyrate (PHB), a biodegradable polymer that can be used as a
      substitute for petroleum plastics.
AU  - Bharadwaj SvV
AU  - Shrivastav A
AU  - Dubey S
AU  - Ghosh T
AU  - Paliwal C
AU  - Maurya R
AU  - Mishra S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01419-14.

PMID- 27609929
VI  - 4
DP  - 2016
TI  - Complete Genome Sequences of Neisseria gonorrhoeae with Coresistance to First-Line Antimicrobials.
PG  - e00966-16
AB  - Neisseria gonorrhoeae strains with coresistance to the first-line antimicrobial treatments
      azithromycin and ceftriaxone are an emerging public health threat.
      Here, we present the complete genome sequences of three strains of N.
      gonorrhoeae, including one susceptible strain and two strains with coresistance
      to ceftriaxone and azithromycin.
AU  - Bharat A
AU  - Martin I
AU  - Demczuk W
AU  - Allen V
AU  - Haldane D
AU  - Hoang L
AU  - Mulvey MR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00966-16.

PMID- 15280231
VI  - 167
DP  - 2004
TI  - Genetic Transformation of Neurospora tetrasperma, Demonstration of Repeat-Induced Point Mutation (RIP) in Self-Crosses and a Screen for Recessive RIP-Defective Mutants.
PG  - 1155-1164
AB  - The pseudohomothallic fungus Neurospora tetrasperma is naturally resistant
      to the antibiotic hygromycin. We discovered that mutation of its erg-3
      (sterol C-14 reductase) gene confers a hygromycin-sensitive phenotype that
      can be used to select transformants on hygromycin medium by
      complementation with the N. crassa erg-3+ and bacterial hph genes.
      Cotransformation of hph with PCR-amplified DNA of other genes enabled us
      to construct strains duplicated for the amplified DNA. Using
      transformation we constructed self-fertile strains that were homoallelic
      for an ectopic erg-3+ transgene and a mutant erg-3 allele at the
      endogenous locus. Self-crosses of these strains yielded erg-3 mutant
      ascospores that produced colonies with the characteristic morphology on
      Vogel's sorbose agar described previously for erg-3 mutants of N. crassa.
      The mutants were generated by repeat-induced point mutation (RIP), a
      genome defense process that causes numerous G:C to A:T mutations in
      duplicated DNA sequences. Homozygosity for novel recessive RIP-deficient
      mutations was signaled by self-crosses of erg-3-duplication strains that
      fail to produce erg-3 mutant progeny. Using this assay we isolated a
      UV-induced mutant with a putative partial RIP defect. RIP-induced mutants
      were isolated in rid-1 and sad-1, which are essential genes, respectively,
      for RIP and another genome defense mechanism called meiotic silencing by
      unpaired DNA.
AU  - Bhat A
AU  - Tamuli R
AU  - Kasbekar DP
PT  - Journal Article
TA  - Genetics
JT  - Genetics
SO  - Genetics 2004 167: 1155-1164.

PMID- 9206831
VI  - 276
DP  - 1997
TI  - Dealing with database explosion: A cautionary note.
PG  - 1724-1725
AB  - Carol J. Bult et al. Report the first entire archaea genome sequence of Methanococcus
      jannashii (Mja).  Because the initial gene assignments were conservative, we anticipated that
      much interesting biological information would be missing.  We searched the database for
      additional open reading frames, and found 15 ORFs: four within intergenic regions (1 through
      M4, Table 1); five overlapping with previously identified ORFs but that read off in a
      different frame (M5 through M9, Table 1); and six that are extended or truncated as a result
      of potential frameshifts (M10 through M15, Table 2).  Although the potential frameshifts we
      describe might be bona fide, it cannot be ruled out that they represent actual sequencing
      artifacts.  Erroneous sequences in public databases are a substantial problem and have been
      estimated to be in the range of 0.37 to 2.9 errors per 1000 nucleotides, making data
      interpretation sometimes difficult.  This is especially true, for example, in studies that
      utilize protein and DNA sequence information to estimate evolutionary distances.  It is not
      known how the error rate in this study compares with error rates in the database, but a
      previous study suggests that error rates generally vary between 1 in 5000 to 1 in 10,000
      nucleotides.
AU  - Bhatia U
AU  - Robison K
AU  - Gilbert W
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1997 276: 1724-1725.

PMID- 25635017
VI  - 3
DP  - 2015
TI  - Genome Sequence of a Sulfate-Reducing Thermophilic Bacterium, Thermodesulfobacterium commune DSM 2178T (Phylum Thermodesulfobacteria).
PG  - e01490-14
AB  - Here, we present the complete genome sequence of Thermodesulfobacterium commune DSM 2178(T) of
      the phylum Thermodesulfobacteria.
AU  - Bhatnagar S
AU  - Badger JH
AU  - Madupu R
AU  - Khouri HM
AU  - O'Connor EM
AU  - Robb FT
AU  - Ward NL
AU  - Eisen JA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01490-14.

PMID- 25635016
VI  - 3
DP  - 2015
TI  - Genome Sequence of the Sulfate-Reducing Thermophilic Bacterium Thermodesulfovibrio yellowstonii Strain DSM 11347T (Phylum Nitrospirae).
PG  - e01489-14
AB  - Here, we present the complete 2,003,803-bp genome of a sulfate-reducing thermophilic
      bacterium, Thermodesulfovibrio yellowstonii strain DSM 11347(T).
AU  - Bhatnagar S
AU  - Badger JH
AU  - Madupu R
AU  - Khouri HM
AU  - O'Connor EM
AU  - Robb FT
AU  - Ward NL
AU  - Eisen JA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01489-14.

PMID- 
VI  - 74
DP  - 1998
TI  - The origin of adaptive mutations: Explaining the mutational spectra of Lac+ revertants of the Escherichia coli strain FC40.
PG  - 583-590
AB  - Reversion of lacI33-lacZ frameshift mutation to produce Lac+ colonies takes place by
      demonstrably different mechanisms in growing and starving cultures of strains (such as FC40)
      harboring this mutation.  The revertants appear to arise in starving cells only under
      conditions where they can immediately promote growth.  This is reminiscent of Lamarckism.
      Here we propose a mutagenic mechanism which is Darwinian inasmuch as it is blind to the
      adaptive fitness of the mutants but can explain the mutational spectra seen in C40 and certain
      other strains.  This mechanism can produce mutations only in the neighborhood of a
      methylatable cytosine.
AU  - Bhattacharjee SK
AU  - Mahajan SK
PT  - Journal Article
TA  - Curr. Sci.
JT  - Curr. Sci.
SO  - Curr. Sci. 1998 74: 583-590.

PMID- 26445627
VI  - 10
DP  - 2015
TI  - Complete genome sequence of the chromate-reducing bacterium Thermoanaerobacter thermohydrosulfuricus strain BSB-33.
PG  - 74
AB  - Thermoanaerobacter thermohydrosulfuricus BSB-33 is a thermophilic gram positive obligate
      anaerobe isolated from a hot spring in West Bengal, India. Unlike other
      T. thermohydrosulfuricus strains, BSB-33 is able to anaerobically reduce Fe(III)
      and Cr(VI) optimally at 60 degrees C. BSB-33 is the first Cr(VI) reducing T.
      thermohydrosulfuricus genome sequenced and of particular interest for
      bioremediation of environmental chromium contaminations. Here we discuss features
      of T. thermohydrosulfuricus BSB-33 and the unique genetic elements that may
      account for the peculiar metal reducing properties of this organism. The T.
      thermohydrosulfuricus BSB-33 genome comprises 2597606 bp encoding 2581 protein
      genes, 12 rRNA, 193 pseudogenes and has a G + C content of 34.20 %. Putative
      chromate reductases were identified by comparative analyses with other
      Thermoanaerobacter and chromate-reducing bacteria.
AU  - Bhattacharya P
AU  - Barnebey A
AU  - Zemla M
AU  - Goodwin L
AU  - Auer M
AU  - Yannone SM
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 74.

PMID- Not included in PubMed...
VI  - 17
DP  - 1995
TI  - Metabolic burden as reflected by maintenance coefficient of recombinant Escherichia coli overexpressing target gene.
PG  - 1155-1160
AB  - Metabolic burden as a consequence of the overexpression of a target gene in a recombinant
      strain of E. coli 1727 has been analyzed with respect to the maintenance energy coefficient
      (m).  The values of 'm' for the host, uninduced recombinant and IPTG induced recombinant
      were determined to be 0.12, 0.17 and 0.32 g.g-1.h-1 respectively.  Transient plasmid
      instability and a nearly 33% fall in maximum specific growth rate were observed under
      conditions of enhanced requirements for maintenance energy.
AU  - Bhattacharya S
AU  - Dubey AK
PT  - Journal Article
TA  - Biotechnol. Lett.
JT  - Biotechnol. Lett.
SO  - Biotechnol. Lett. 1995 17: 1155-1160.

PMID- 
VI  - 4
DP  - 2000
TI  - Amino acid residues involved in catalysis and DNA binding by cytosine DNA methyltransferase MspI.
PG  - 109-120
AB  - Chemical modifications of chosen amino acid residues: arginine, histidine, cysteine, glycine
      and tryptophan have been attempted to investigate their role in catalysis and DNA binding by
      MspI DNA methyltransferase (M.MspI).  The catalytic inactivation following modifications of
      two arginine and three histidine moieties was a consequence of loss of DNA binding property of
      the methyltransferase.  Modification of a single cysteine residue completely abolished the
      ability of M.MspI to transfer a methyl group but there was no loss of DNA binding activity.
      While tryptophan had no apparent functional role, glycine was critical for AdoMet binding and
      target base methylation by the M.MspI.
AU  - Bhattacharya SK
AU  - Dubey AK
PT  - Journal Article
TA  - J. Biochem. Mol. Biol. Biophys.
JT  - J. Biochem. Mol. Biol. Biophys.
SO  - J. Biochem. Mol. Biol. Biophys. 2000 4: 109-120.

PMID- 12027887
VI  - 269
DP  - 2002
TI  - The N-terminus of m5C-DNA methyltransferase MspI is involved in its topoisomerase activity.
PG  - 2491-2497
AB  - DNA cytosine methyltransferase MspI (M.MspI) must require a different type of interaction of
      protein with DNA from other bacterial DNA
      cytosine methyltransferases (m5C-MTases) to evoke the topoisomerase
      activity that it possesses in addition to DNA-methylation ability. This
      may require a different structural organization in the solution phase
      from the reported consensus structural arrangement for m5C-MTases.
      Limited proteolysis of M.MspI, however, generates two peptide
      fragments, a large one (p26) and a small one (p18), consistent with
      reported m5C-MTase structures. Examination of the amino-acid sequence
      of M.MspI revealed similarity to human topoisomerase I at the
      N-terminus. Alignment of the amino-acid sequence of M.MspI also
      uncovered similarity (residues 245-287) to the active site of human DNA
      ligase I. To evaluate the role of the N-terminus of M.MspI,
      2-hydroxy-5-nitrobenzyl bromide (HNBB) was used to truncate M.MspI
      between residues 34 and 35. The purified HNBB-truncated protein has a
      molecular mass of approximately 45 kDa, retains DNA binding and
      methyltransferase activity, but does not possess topoisomerase
      activity. These findings were substantiated using a purified
      recombinant MspI protein with the N-terminal 34 amino acids deleted.
      Changing the N-terminal residues Trp34 and Tyr74 to alanine results in
      abolition of the topoisomerase I activity while the methyltransferase
      activity remains intact.
AU  - Bhattacharya SK
AU  - Dubey AK
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 2002 269: 2491-2497.

PMID- 12385973
VI  - 6
DP  - 2002
TI  - Transient DNA binding by a proteolytic peptide from m5C-DNA methyltransferase MspI.
PG  - 357-364
AB  - A peptide fragment (p26) generated as a result of limited tryptic proteolysis of
      methyltransferase MspI retains transient but non-specific DNA binding capability. The
      transient DNA binding by p26 was characterized with respect to physicochemical factors.
      Limited proteolysis was performed to probe gross structural deviation from the reported
      two-domain organization for m5C-MTases, in light of topoisomerase activity shown by MspI,
      resulted in two peptide fragments; a large fragment p26 and a small fragment p18, consistent
      with the other reported m5C-MTase structures. The purified large peptide fragment p26, spans
      between 6 and 251 in the amino acid sequence of M.MspI. The peptide p26 does not bind
      S-adenosylmethionine, although in the intact protein the AdoMet binding region can be mapped
      to a region in the protein that is present in this peptide. Such transient DNA binding has not
      been reported for other protolytic product of any other m5C-DNA methyltransferase.
AU  - Bhattacharya SK
AU  - Dubey AK
PT  - Journal Article
TA  - J. Biochem. Mol. Biol. Biophys.
JT  - J. Biochem. Mol. Biol. Biophys.
SO  - J. Biochem. Mol. Biol. Biophys. 2002 6: 357-364.

PMID- Not included in PubMed...
VI  - 20
DP  - 1997
TI  - Effects of dissolved oxygen and oxygen mass transfer on overexpression of target gene in recombinant E. coli.
PG  - 355-360
AB  - Overexpression of target gene (MspI methylase) in recombinant Escherichia coli has been
      studied in response to dissolved oxygen mass transfer.  The rate of target gene expression
      attained its maximum value (2.67 U mg^-1p^-1h^-1) when the culture was induced with 1 mM
      isopropyl-beta-D-thiogalactopyranoside (IPTG) in the mid-exponential phase of growth.  The
      maximum value of 6.7 x 10^2 U mg^-1p^-1 for the target gene expression was attained in about 3
      h of postinduction cultivation.  An oxygen-sufficient condition (0.22 mmoles l^-1) was
      necessary to obtain optimal expression and cell productivity.  Expression of the target gene
      upon induction was accompanied by an increase in oxygen uptake rate (OUR) of the cells and
      decrease in dissolved oxygen (DO) concentration in the cultivation broth.  Volumetric oxygen
      transfer coefficient (Kla) of 61 h^-1 was optimum for cell productivity of uninduced culture
      while that for the induced culture was 84 h^-1 which was optimum for foreign protein synthesis
      also.
AU  - Bhattacharya SK
AU  - Dubey AK
PT  - Journal Article
TA  - Enzyme Microb. Technol.
JT  - Enzyme Microb. Technol.
SO  - Enzyme Microb. Technol. 1997 20: 355-360.

PMID- 9104039
VI  - 13
DP  - 1997
TI  - High-level expression of a heterologous gene in Escherichia coli in response to carbon-nitrogen source and C/N ration in a batch bioreactor.
PG  - 151-155
AB  - Overexpression of the target gene in a recombinant strain of Escherichia coli has been
      analyzed in view of changes in the carbon-nitrogen source and as a function of C/N ratio.  The
      rate of target gene expression varied over a range of 200%, and the yield coefficient for the
      target gene product changed over 400% with change in carbon source at 10 gL^-1 in M9 medium.
      With variation in nitrogen, source, however, only marginal changes (10-15%) occurred in these
      parameters of overexpression.  Higher concentration, for example 2.5 g L^-1, of any nitrogen
      source adversely affected heterologous expression as rate of target gene expression declined
      in the range 35%-50% and the yield coefficient of foreign protein decreased between 45% and
      60%.  A C/N ratio of 15 was found to be optimum for both parameters for overexpression and
      host specific parameters such as specific growth rate and observed yield coefficient for
      cellular growth.  An analysis with respect to temperature and pH revealed that host and
      expression parameters were quite susceptible to changes in these factors.
AU  - Bhattacharya SK
AU  - Dubey AK
PT  - Journal Article
TA  - Biotechnol. Prog.
JT  - Biotechnol. Prog.
SO  - Biotechnol. Prog. 1997 13: 151-155.

PMID- 10329670
VI  - 274
DP  - 1999
TI  - Kinetic mechanism of cytosine DNA methyltransferase MspI.
PG  - 14743-14749
AB  - A kinetic analysis of MspI DNA methyltransferase (M.MspI) is presented. The enzyme catalyzes
      methylation of lambda-DNA, a 50-kilobase pair linear molecule with multiple M.MspI-specific
      sites, with a specificity constant (kcat/KM) of 0.9 x 10^8 M-1 s-1. But the values of the
      specificity constants for the smaller DNA substrates (121 and 1459 base pairs (bp)) with
      single methylation target or with multiple targets (sonicated lambda-DNA) were less by an
      order of magnitude. Product inhibition of the M.MspI-catalyzed methylation reaction by
      methylated DNA is competitive with respect to DNA and noncompetitive with respect to
      S-adenosylmethionine (AdoMet). The S-adenosylhomocysteine inhibition of the methylation
      reaction is competitive with respect to AdoMet and uncompetitive with respect to DNA. The
      presteady state kinetic analysis showed a burst of product formation when AdoMet was added to
      the enzyme preincubated with the substrate DNA. The burst is followed by a constant rate of
      product formation (0.06 mol per mol of enzyme s-1) which is similar to catalytic constants
      (kcat = approximately 0.056 s-1) measured under steady state conditions. The isotope exchange
      in chasing the labeled methyltransferase-DNA complex with unlabeled DNA and AdoMet leads to a
      reduced burst as compared with the one involving chase with labeled DNA and AdoMet. The enzyme
      is capable of exchanging tritium at C-5 of target cytosine in the substrate DNA in the absence
      of cofactor AdoMet. The kinetic data are consistent with an ordered Bi Bi mechanism for the
      M.MspI-catalyzed DNA methylation where DNA binds first.
AU  - Bhattacharya SK
AU  - Dubey AK
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1999 274: 14743-14749.

PMID- Not included in PubMed...
VI  - 20
DP  - 1994
TI  - Preparation and properties of restriction endonuclease SphI coupled to a nylon fabric filter.
PG  - 141-146
AB  - A procedure has been devised for covalent coupling of SphI, a type II restriction endonuclease
      (EC 3.1.2.1.4) from Streptomyces phaeochromogenes, to a nylon-fabric filter.  Immobilized SphI
      preparations were characterized with respect to operational parameters, re-usability and
      stability during storage.  It is shown that immobilization of SphI on nylon filter discs did
      not affect the enzymic behavior of the enzyme, but did enhance its thermal stability.  The
      rates of inactivation of free and bound SphI at 45oC were determined to be 5.0 h-1 and 3.0 h-1
      respectively.  The membrane-bound preparations could be stored for over 2 months at 4oC
      without significant loss of activity, compared with free enzyme, which had lost most of its
      activity during this period.  The insolubilized R. SphI could be used up to three times.
AU  - Bhattacharya SK
AU  - Dubey AK
PT  - Journal Article
TA  - Biotechnol. Appl. Biochem.
JT  - Biotechnol. Appl. Biochem.
SO  - Biotechnol. Appl. Biochem. 1994 20: 141-146.

PMID- Not included in PubMed...
VI  - 18
DP  - 1996
TI  - Expression parameters for target gene cloned in Escherichia coli in response to phosphate supply.
PG  - 1145-1148
AB  - A recombinant strain of E. coli 1727 overexpressed a target gene at enhanced levels when
      supplied with an excess of inorganic phosphate.  The rate of target gene expression, the yield
      coefficient for the target gene product and the plasmid copy number increased significantly:
      50%, 100% and 40% respectively at 125 mM excess phosphate.  This was, however, accompanied by
      a 26% decrease in the specific growth rate and 30% in the cellular growth yield coefficient.
AU  - Bhattacharya SK
AU  - Dubey AK
PT  - Journal Article
TA  - Biotechnol. Lett.
JT  - Biotechnol. Lett.
SO  - Biotechnol. Lett. 1996 18: 1145-1148.

PMID- 10050851
VI  - 397
DP  - 1999
TI  - A mammalian protein with specific demethylase activity for mCpG DNA.
PG  - 579-583
AB  - DNA-methylation patterns are important for regulating genome functions, and are determined by
      the enzymatic processes of methylation and demethylation.  The demethylating enzyme has now
      been identified; a mammalian complementary DNA encodes a methyl-CpG-binding domain, bears a
      demethylase activity that transforms methylated cytosine bases to cytosine, and demethylates a
      plasmid when the cDNA is translated or transiently transfected into human embryonal kidney
      cells in vitro.  The discovery of this DNA demethylase should provide a basis for the
      molecular and developmental analysis of the role of DNA methylation and demethylation.
AU  - Bhattacharya SK
AU  - Ramchandani S
AU  - Cervoni N
AU  - Szyf M
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1999 397: 579-583.

PMID- 25744997
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Exopolysaccharide-Producing Cyanobacterium Aphanocapsa montana BDHKU 210001.
PG  - e00057-15
AB  - We report for the first time the draft genome sequence of Aphanocapsa montana BDHKU 210001, a
      halotolerant cyanobacterium isolated from India. This is a marine
      exopolysaccharide (EPS)-producing cyanobacterium. The genome of this species is
      assembled into 11.50 million bases, with 296 scaffolds carrying approximately
      7,296 protein-coding genes.
AU  - Bhattacharyya S
AU  - Chandrababunaidu MM
AU  - Sen D
AU  - Panda A
AU  - Ghorai A
AU  - Bhan S
AU  - Sanghi N
AU  - Tripathy S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00057-15.

PMID- 6256238
VI  - 8
DP  - 1980
TI  - Cation-dependence of the restriction endodeoxyribonuclease EcoRI.
PG  - 634
AB  - The restriction endodeoxyribonucleases and DNA methylases provide excellent examples for the
      enzymologist of highly specific protein-nucleic acid interactions.  The endodeoxyribonuclease
      EcoRI is comparatively easy to prepare, and is therefore among the best studied of these
      restriction enzymes.  It is unusual (although not unique) in that its recognition sequence
      depends on the exact assay conditions.  At low pH and high ionic strength the enzyme
      recognizes the DNA sequence.
AU  - Bhave N
AU  - Woodhead JL
AU  - Malcolm ADB
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 1980 8: 634.

PMID- 16740122
VI  - 387
DP  - 2006
TI  - Functional analysis of amino acid residues at the dimerisation interface of Kpnl DNA methyltransferase.
PG  - 515-523
AB  - KpnI DNA-(N-6-adenine) methyltransferase (M.Kpnl) recognises the sequence 5'-GGTACC-3' and
      transfers the methyl group from
      S-adenosyl-L-methionine (AdoMet) to the N6 position of the adenine
      residue in each strand. Earlier studies have shown that M.Kpnl exists
      as a dimer in solution, unlike most other MTases. To address the
      importance of dimerisation for enzyme function, a three-dimensional
      model of M.Kpnl was obtained based on protein fold-recognition
      analysis, using the crystal structures of M.Rsrl and M.MbollA as
      templates. Residues l146, l161 and Y167, the side chains of which are
      present in the putative dimerisation interface-in the model, were
      targeted for site-directed mutagenesis. Methylation and in vitro
      restriction assays showed that the mutant MTases are catalytically
      inactive. Mutation at the l146 position resulted in complete disruption
      of the dimer. The replacement of l146 led to drastically reduced DNA
      and cofactor binding. Substitution of l161 resulted in weakening of the
      interaction between monomers, leading to both monomeric and dimeric
      species. Steady-state fluorescence measurements showed that the
      wild-type KpnI MTase induces structural distortion in bound DNA, while
      the mutant MTases do not. The results establish that monomeric MTase is
      catalytically inactive and that dimerisation is an essential event for
      M.Kpnl to catalyse the methyl transfer reaction.
AU  - Bheemanaik S
AU  - Bujnicki JM
AU  - Nagaraja V
AU  - Rao DN
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 2006 387: 515-523.

PMID- 12506109
VI  - 278
DP  - 2003
TI  - Kinetic and catalytic properties of dimeric KpnI DNA methyltransferase.
PG  - 7863-7874
AB  - KpnI DNA-(N(6)-adenine)-methyltransferase (KpnI MTase) is a member of a
      restriction-modification (R-M) system in Klebsiella pneumoniae and
      recognizes the sequence 5'-GGTACC-3'. It modifies the recognition sequence
      by transferring the methyl group from S-adenosyl-l-methionine (AdoMet) to
      the N(6) position of adenine residue. KpnI MTase occurs as a dimer in
      solution as shown by gel filtration and chemical cross-linking analysis.
      The nonlinear dependence of methylation activity on enzyme concentration
      indicates that the functionally active form of the enzyme is also a dimer.
      Product inhibition studies with KpnI MTase showed that
      S-adenosyl-l-homocysteine is a competitive inhibitor with respect to
      AdoMet and noncompetitive inhibitor with respect to DNA. The methylated
      DNA showed noncompetitive inhibition with respect to both DNA and AdoMet.
      A reduction in the rate of methylation was observed at high concentrations
      of duplex DNA. The kinetic analysis where AdoMet binds first followed by
      DNA, supports an ordered bi bi mechanism. After methyl transfer,
      methylated DNA dissociates followed by S-adenosyl-l-homocysteine.
      Isotope-partitioning analysis showed that KpnI MTase-AdoMet complex is
      catalytically active.
AU  - Bheemanaik S
AU  - Chandrashekaran S
AU  - Nagaraja V
AU  - Rao DN
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2003 278: 7863-7874.

PMID- 
VI  - 399
DP  - 2006
TI  - Structure, function and mechanism of exocyclic DNA methyltransferases (vol 399, pg 177, 2006).
PG  - 543
AB  - In Table 2, the Kd(DNA) values for the enzyme M.EcoRI were incorrect.  The correct table
      appears here.
AU  - Bheemanaik S
AU  - Reddy YVR
AU  - Rao DN
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 2006 399: 543.

PMID- 16987108
VI  - 399
DP  - 2006
TI  - Structure, function and mechanism of exocyclic DNA methyltransferases.
PG  - 177-190
AB  - DNA MTases (methyltransferases) catalyse the transfer of methyl groups to DNA from AdoMet
      (S-adenosyl-L-methionine) producing AdoHcy
      (S-adenosyl-L-homocysteine) and methylated DNA. The C-5 and N-4
      positions of cytosine and N-6 position of adenine are the target sites
      for methylation. All three methylation patterns are found in
      prokaryotes, whereas cytosine at the C-5 position is the only
      methylation reaction that is known to occur in eukaryotes. In general,
      MTases are two-domain proteins comprising one large and one small
      domain with the DNA-binding cleft located at the domain interface. The
      striking feature of all, the structurally characterized DNA MTases is
      that they share a common core structure referred to as an
      'AdoMet-dependent MTase fold'. DNA methylation has been reported to be
      essential for bacterial virulence, and it has been suggested that DNA
      adenine MTases (Dams) could be potential targets for both vaccines and
      antimicrobials. Drugs that block Dam could slow down bacterial growth
      and therefore drug-design initiatives could result in a whole new
      generation of antibiotics. The transfer of larger chemical entities in
      A MTase-catalysed reaction has been reported and this represents an
      interesting challenge for bio-organic chemists. In general, amino
      MTases could therefore be used as delivery systems for fluorescent or
      other reporter groups on to DNA. This is one of the potential
      applications of DNA MTases towards developing non-radioactive DNA
      probes and these could have interesting applications in molecular
      biology. Being nucleotide-sequence-specific, DNA MTases provide
      excellent model systems for studies on protein-DNA interactions. The
      focus of this review is on the chemistry, enzymology and structural
      aspects of exocyclic amino MTases.
AU  - Bheemanaik S
AU  - Reddy YVR
AU  - Rao DN
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 2006 399: 177-190.

PMID- 21048863
VI  - 2010
DP  - 2010
TI  - Kinetics of methylation by EcoP1I DNA methyltransferase.
PG  - 302731
AB  - EcoP1I DNA MTase (M.EcoP1I), an N6-adenine MTase from bacteriophage P1, is a part of the
      EcoP1I restriction-modification
      (R-M) system which belongs to the Type III R-M system. It recognizes the sequence
      5'-AGACC-3' and methylates the internal adenine. M.EcoP1I requires Mg2+ for the transfer of
      methyl groups to DNA. M.EcoP1I is shown to exist as dimer in solution, and even at high salt
      concentrations (0.5M) the dimeric M.EcoP1I does not dissociate into monomers suggesting a
      strong interaction
      between the monomer subunits. Preincubation and isotope partitioning studies with M.EcoP1I
      indicate a kinetic mechanism where the duplex DNA binds first followed by AdoMet.
      Interestingly, M.EcoP1I methylates DNA substrates in the presence of Mn2+ and Ca2+ other than
      Mg2+ with varying affinities. Amino acid analysis and methylation assays in the presence of
      metal ions suggest that M.EcoP1I has indeed two metal ion-binding sites [358ID(x)n . . .
      ExK401 and 600DxDxD604 motif]. EcoP1I DNA MTase catalyzes the transfer of methyl groups using
      a distributive mode of methylation on DNA containing more than one recognition site. A
      chemical modification of EcoP1I DNA MTase using N-ethylmaleimide resulted in an irreversible
      inactivation of enzyme activity suggesting the possible role of cysteine residues in
      catalysis.
AU  - Bheemanaik S
AU  - Sistla S
AU  - Krishnamurthy V
AU  - Sampath A
AU  - Desirazu NR
PT  - Journal Article
TA  - Enzyme Res.
JT  - Enzyme Res.
SO  - Enzyme Res. 2010 2010: 302731.

PMID- 27151803
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequence of Vibrio alginolyticus Isolated from the Mucus of the Coral Fungia danai in the Andaman Sea, India.
PG  - e00339-16
AB  - Vibrio alginolyticus, a halophilic Gram-negative bacterium, which is found in temperate marine
      and estuarine environments, is known to cause infections in
      humans and other organisms. We sequenced the genome of
      sulfamethoxazole-trimthoprim-positive V. alginolyticus strain 4-19 isolated from
      the mucus of the coral Fungia danai in the Andaman Sea, India.
AU  - Bhotra T
AU  - Singh DV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00339-16.

PMID- 25540344
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Lactobacillus casei Lbs2.
PG  - e01326-14
AB  - We report here a 3.2-Mb draft assembled genome of Lactobacillus casei Lbs2. The bacterium
      shows probiotic and immunomodulatory activities. The genome assembly
      and annotation will help to identify molecules and pathways responsible for
      interaction between the host immune system and the microbe.
AU  - Bhowmick S
AU  - Malar M
AU  - Das A
AU  - Kumar-Thakur B
AU  - Saha P
AU  - Das S
AU  - Rashmi HM
AU  - Batish VK
AU  - Grover S
AU  - Tripathy S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01326-14.

PMID- 8817492
VI  - 18
DP  - 1995
TI  - Mechanism of antigenic variation in Mycoplasma pulmonis: interwoven, site-specific DNA inversions.
PG  - 703-714
AB  - The chromosome of the murine pathogen Mycoplasma pulmonis undergoes rearrangements at a high
      frequency.  We show that some of these rearrangements regulate the phase-variable expression
      of a cluster of genes (the vsa locus) that encode the variable V-1 surface antigens.  Only one
      vsa gene is associated with an expression site; the other vsa genes are transcriptionally
      silent.  The silent genes lack the 5' end region (promoter and ribosome-binding site) that is
      present in the expressed gene, and DNA rearrangements regulate gene expression by reassorting
      the 5' end region from an expressed gene with the 3' end region from a previously silent
      gene.  All vsa rearrangements identified so far are site-specific DNA inversions that occur
      between copies of a specific 34bp sequence that is conserved in each vsa gene.  Interestingly,
      DNA inversions within the vsa locus apparently occur in concert with inversion of the hsd1
      element, which regulates restriction and modification activity in M. pulmonis.
AU  - Bhugra B
AU  - Voelker LL
AU  - Zou N
AU  - Yu H
AU  - Dybvig K
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1995 18: 703-714.

PMID- 22123761
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Seawater Bacterium Glaciecola nitratireducens FR1064T.
PG  - 7006-7007
AB  - Glaciecola nitratireducens strain FR1064(T) was isolated from seawater and described as a new
      species by Baik et al. in 2006. The genome size is
      about 1.01 to 1.26 Mb smaller than two reported Glaciecola genomes,
      indicating the gain or loss of large genome segments in the evolution of
      Glaciecola strains.
AU  - Bian F
AU  - Qin QL
AU  - Xie BB
AU  - Shu YL
AU  - Zhang XY
AU  - Yu Y
AU  - Chen B
AU  - Chen XL
AU  - Zhou BC
AU  - Zhang YZ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 7006-7007.

PMID- 22275105
VI  - 194
DP  - 2012
TI  - Genome sequences of six pseudoalteromonas strains isolated from arctic sea ice.
PG  - 908-909
AB  - Yu et al. (Polar Biol. 32:1539-1547, 2009) isolated 199 Pseudoalteromonas strains from Arctic
      sea ice. We sequenced the genomes of six of these
      strains, which are affiliated to different Pseudoalteromonas species based
      on 16S rRNA gene sequences, facilitating the study of physiology and
      adaptation of Arctic sea ice Pseudoalteromonas strains.
AU  - Bian F
AU  - Xie BB
AU  - Qin QL
AU  - Shu YL
AU  - Zhang XY
AU  - Yu Y
AU  - Chen B
AU  - Chen XL
AU  - Zhou BC
AU  - Zhang YZ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 908-909.

PMID- 21602384
VI  - 77
DP  - 2011
TI  - Disruption of a Type II Endonuclease (TDE0911) Enables Treponema denticola ATCC 35405 To Accept an Unmethylated Shuttle Vector.
PG  - 4573-4578
AB  - The oral spirochete Treponema denticola is associated with human periodontal disease. T.
      denticola ATCC 35405 and ATCC 33520 are two
      routinely used laboratory strains. Compared to T. denticola ATCC 33520,
      ATCC 35405 is more virulent but less accessible to genetic
      manipulations. For instance, the shuttle vectors of ATCC 33520 cannot
      be transformed into strain ATCC 35405. The lack of a shuttle vector has
      been a barrier to study the biology and virulence of T. denticola ATCC
      35405. In this report, we hypothesize that T. denticola ATCC 35405 may
      have a unique DNA restriction-modification (R-M) system that prevents
      it from accepting the shuttle vectors of ATCC 33520 (e. g., the shuttle
      plasmid pBFC). To test this hypothesis, DNA restriction digestion, PCR,
      and Southern blot analyses were conducted to identify the differences
      between the R-M systems of these two strains. DNA restriction digestion
      analysis of these strains showed that only the cell extract from ATCC
      35405 was able to digest pBFC. Consistently, PCR and Southern blot
      analyses revealed that the genome of T. denticola ATCC 35405 encodes
      three type II endonucleases that are absent in ATCC 33520. Among these
      three endonucleases, TDE0911 was predicted to cleave unmethylated
      double-stranded DNA and to be most likely responsible for the cleavage
      of unmethylated pBFC. In agreement with this prediction, the mutant of
      TDE0911 failed to cleave unmethylated pBFC plasmid, and it could accept
      the unmethylated shuttle vector. The study described here provides us
      with a new tool and strategy to genetically manipulate T. denticola, in
      particular ATCC 35405, and other strains that may carry similar
      endonucleases.
AU  - Bian J
AU  - Li C
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2011 77: 4573-4578.

PMID- 16126220
VI  - 352
DP  - 2005
TI  - The type I restriction endonuclease EcoR124I, couples ATP hydrolysis to bidirectional DNA translocation.
PG  - 837-859
AB  - Type I restriction endonuclease holoenzymes contain methylase (M), restriction (R) and
      specificity (S) subunits, present in an M-2:R-2:S-1
      stoichiometry. These enzymes bind to specific DNA sequences and
      translocate dsDNA in an ATP-dependent manner toward the holoenzyme
      anchored at the recognition sequence. Once translocation is impeded,
      DNA restriction, which functions to protect the host cell from invading
      DNA, takes place. Translocation and DNA cleavage are afforded by the
      two diametrically opposed R-subunits. To gain insight into the
      mechanism of translocation, a detailed characterization of the ATPase
      activity of EcoR124I was done. Results show that following recognition
      sequence binding, ATP hydrolysis-coupled, bidirectional DNA
      translocation by EcoR124I ensues, with the R-subunits transiently
      disengaging, on average, every 515 bp. Macroscopic processivity of
      2031( 184) bp is maintained, as the R-subunits remain in close
      proximity to the DNA through association with the methyltransferase.
      Transient uncoupling of ATP hydrolysis from translocation results in
      3.1( 0.4) ATP molecules being hydrolyzed per base-pair translocated
      per R-subunit. This is the first clear demonstration of the coupling of
      ATP hydrolysis to dsDNA translocation, albeit inefficient. Once
      translocation is impeded on supercoiled DNA, the DNA is cleaved. DNA
      cleavage inactivates the EcoR124I holoenzyme partially and reversibly,
      which explains the stoichiometric behaviour of type I restriction
      enzymes. Inactivated holoenzyme remains bound to the DNA at the
      recognition sequence and immediately releases the nascent ends. The
      release of nascent ends was demonstrated using a novel,
      fluorescence-based, real-time assay that takes advantage of the ability
      of the Escherichia coli RecBCD enzyme to unwind restricted dsDNA. The
      resulting unwinding of EcoR124I-restricted DNA by RecBCD reveals
      coordination between the restriction-modification and recombination
      systems that functions to destroy invading DNA efficiently. In
      addition, we demonstrate the displacement of EcoR124I following DNA
      cleavage by the translocating RecBCD enzyme, resulting in the
      restoration of catalytic function to EcoR124I.
AU  - Bianco PR
AU  - Hurley EM
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2005 352: 837-859.

PMID- 19336412
VI  - 37
DP  - 2009
TI  - Type I restriction endonucleases are true catalytic enzymes.
PG  - 3377-3390
AB  - Type I restriction endonucleases are intriguing, multifunctional complexes that restrict DNA
      randomly, at sites distant from the target sequence.
      Restriction at distant sites is facilitated by ATP hydrolysis-dependent,
      translocation of double-stranded DNA towards the stationary enzyme bound
      at the recognition sequence. Following restriction, the enzymes are
      thought to remain associated with the DNA at the target site, hydrolyzing
      copious amounts of ATP. As a result, for the past 35 years type I
      restriction endonucleases could only be loosely classified as enzymes
      since they functioned stoichiometrically relative to DNA. To further
      understand enzyme mechanism, a detailed analysis of DNA cleavage by the
      EcoR124I holoenzyme was done. We demonstrate for the first time that type
      I restriction endonucleases are not stoichiometric but are instead
      catalytic with respect to DNA. Further, the mechanism involves formation
      of a dimer of holoenzymes, with each monomer bound to a target sequence
      and, following cleavage, each dissociates in an intact form to bind and
      restrict subsequent DNA molecules. Therefore, type I restriction
      endonucleases, like their type II counterparts, are true enzymes. The
      conclusion that type I restriction enzymes are catalytic relative to DNA
      has important implications for the in vivo function of these previously
      enigmatic enzymes.
AU  - Bianco PR
AU  - Xu C
AU  - Chi M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: 3377-3390.

PMID- 27979930
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of 40 Pseudomonas aeruginosa Clinical Strains Isolated from the Sputum of a Single Cystic Fibrosis Patient Over an 8-Year Period.
PG  - e01205-16
AB  - We report draft genome sequences of 40 Pseudomonas aeruginosa strains, isolated from the
      sputum of a single cystic fibrosis patient over eight years. Analyses
      indicated a correlation between multidrug-resistant phenotypes and population
      structure. Our data provide new insights into the mechanisms leading to
      acquisition of antibiotic resistance in P. aeruginosa.
AU  - Bianconi I
AU  - D'Arcangelo S
AU  - Benedet M
AU  - Bailey KE
AU  - Esposito A
AU  - Piffer E
AU  - Mariotto A
AU  - Baldo E
AU  - Dinnella G
AU  - Gualdi P
AU  - Schinella M
AU  - Donati C
AU  - Jousson O
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01205-16.

PMID- 4902072
VI  - 39
DP  - 1969
TI  - Host-controlled restriction and modification of filamentous I- and F-specific bacteriophages.
PG  - 605-607
AB  - In the study of strain-specific DNA restriction and modification, the DNA
      molecules of small bacteriophages have proved very useful, particularly those
      possessing only one sitie of affinity for the enzymes of a given restriction
      and modification system.  The male specific phage fd and other small phages
      closely related to fd undergo host-controlled modification in E. coli B, and
      some are also modified in P1-lysogenic strains.  However, they are not
      restricted in E. coli K12 or in strains carrying two other specificity systems,
      as shown here, probably because their DNA lacks the appropriate specificity
      sites.  With the aim of finding small phages restricted by host specificity
      systems to which fd does not respond, we have screened other filamentous
      bacteriophages for their responses to these sytems, including the two
      I-specific phages If1 and If2 and two additional F-specific phages, Ec9 and HR.
AU  - Bickle T
AU  - Arber W
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1969 39: 605-607.

PMID- 
VI  - 0
DP  - 1993
TI  - The ATP-dependent restriction enzymes.
PG  - 89-109
AB  - *

        I. Introduction

      

       II. Type I restriction enzymes

              A. Occurrences

              B. Structural genes

              C. Family relationships among type I restriction enzymes

                  1. DNA and protein sequence homologies within families

                  2. DNA and protein sequence homologies between families

              D. Evolution of DNA sequence specificity in type I enzymes

                  1. By homologous recombination

                  2. By unequal crossing over

                  3. By transposition

              E. Enzyme structure and mechanisms

                  1. Enzyme structures

                  2. Enzyme mechanisms

      

      III. Type III restriction enzymes

              A. Occurrence

              B. Genetics

              C. Enzyme mechanism

              D. DNA cleavage

      

       IV. Concluding remarks

      

AU  - Bickle TA
PT  - Journal Article
TA  - Nucleases
JT  - Nucleases
SO  - Nucleases 1993 0: 89-109.

PMID- 
VI  - 0
DP  - 1982
TI  - The ATP-dependent restriction endonucleases.
PG  - 85-108
AB  - None
AU  - Bickle TA
PT  - Journal Article
TA  - Nucleases
JT  - Nucleases
SO  - Nucleases 1982 0: 85-108.

PMID- 
VI  - 1
DP  - 1987
TI  - DNA restriction and modification systems.
PG  - 692-696
AB  - The phenomenon of DNA restriction and modification was discovered in
      Escherichia coli more than three decades ago by Bertani and Weigle in the
      course of experiments with the phages P2 and lambda.  They found that phages
      grown on E. coli K-12 plated with equal efficiency on strains K-12 and C, but
      the converse was not true:  phage grown on E. coli C plated with high
      efficiency on E. coli C but poorly on E. coli K-12.  Moreover, a single cycle
      of growth in E. coli C was sufficient to remove the ability to grow well in E.
      coli K-12.  The molecular explanation for this Lamarckian effect came from a
      series of experiments conducted in Arber's laboratory in the 1960s.  The DNA of
      phage grown in E. coli C is degraded by a DNA sequence-specific endonuclese
      present in E. coli K-12.  When the phage are grown in E. coli K-12, the DNA is
      protected from the endonuclease because a DNA methylase present in E. coli K-12
      and absent from E. coli C methylates the sequences recognized by the
      endonuclease, rendering them resistant to digestion.  Arber coined the term
      host-controlled restriction and modification of DNA to describe this
      phenomenon.  The endonuclease involved is a restriction endonuclease, and the
      methylase is a modification methylase.  The primary function of the
      modification methylase is to protect the cell's own genome from restriction.
      Restriction and modification systems (R-M systems) are common throughout the
      procaryotic world, and this chapter will focus on those systems that have been
      found in E. coli, Salmonella typhimurium, and their close relatives.  Several
      comprehensive reviews on restriction and modification have been published
      recently.  These reviews should be consulted for details of the enzymology of
      R-M systems and for references to the early literature.
AU  - Bickle TA
PT  - Journal Article
TA  - Escherichia coli and Salmonella typhimurium: Cellular and molecular biology.
JT  - Escherichia coli and Salmonella typhimurium: Cellular and molecular biology.
SO  - Escherichia coli and Salmonella typhimurium: Cellular and molecular biology. 1987 1: 692-696.

PMID- 14651606
VI  - 51
DP  - 2004
TI  - Restricting restriction.
PG  - 3-5
AB  - Systems biology is a new, fashionable and well-funded discipline, which to quote from a recent
      review aims to 'examine the structure and dynamics of cellular and organismal function, raher
      than the characteristics of isolated parts of a cell or organism . . . '.  Systems biology
      will do this by profiting from the vast amounts of biological information that are available
      in the genomics era and make extensive use of computer modelling.  But: 'many breakthroughs
      in experimental devices, advanced software and analytical methods are required before the
      achievements of system biology can live up to their much-touted potential'.  This edition of
      Molecular Microbiology contains a paper that is the product of traditional experimental
      biology but which could serve as a test case for systems biology.  The paper shows how
      bacteria integrate such disparate subsystems as DNA restriction, homologous recombination and
      regulated proteolysis to protect their chromosomes from degradation.  When systems biology can
      predict this level of choreography, it will be a mature discipline.
AU  - Bickle TA
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2004 51: 3-5.

PMID- 6249679
VI  - 8
DP  - 1980
TI  - Adenosine triphosphate-requiring restriction enzymes.
PG  - 396-397
AB  - None
AU  - Bickle TA
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 1980 8: 396-397.

PMID- 15335992
VI  - 2
DP  - 1992
TI  - Phage introns on the hop: an alternative view.
PG  - 150-151
AB  - The nuclease encoded by a rare bacteriophage intron is very similar to one class of bacterial
      restriction enzyme, and may provide clues as to the co-evolution of host and phage.
AU  - Bickle TA
PT  - Journal Article
TA  - Curr. Biol.
JT  - Curr. Biol.
SO  - Curr. Biol. 1992 2: 150-151.

PMID- 356045
VI  - 75
DP  - 1978
TI  - ATP-induced conformational changes in the restriction endonuclease from Escherichia coli K-12.
PG  - 3099-3103
AB  - ATP induces a conformational change in the Escherichia coli K-12 restriction
      enzyme that allows it to discriminate between unmodified and modified DNA
      recognition sequences.  This conformational change does not require ATP
      hydrolysis.  However, ATP hydrolysis is a requirement for DNA cleavage.
AU  - Bickle TA
AU  - Brack C
AU  - Yuan R
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1978 75: 3099-3103.

PMID- 6248427
VI  - 9
DP  - 1980
TI  - The DNA sequence recognised by BglI.
PG  - 205-212
AB  - The restriction enzyme BglI recognizes the DNA sequence: 5'-GCCNNNN^NGGC-3'
      3'-CGGN^NNNNCCG-5' and cleaves it in the position shown by the arrows to leave
      3' single-stranded protrusions three bases long.
AU  - Bickle TA
AU  - Ineichen K
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1980 9: 205-212.

PMID- 8336674
VI  - 57
DP  - 1993
TI  - Biology of DNA Restriction.
PG  - 434-450
AB  - *

      Introduction

      Type I R-M Systems

      Type I Systems Form Families of Related Enzymes

      Structure of hsd Genes

      Evolution of DNA Sequence Recognition by Recombination between hsdS Genes

      Mutations Affecting Modification Activity

      Type II R-M Systems

      Evolutionary Aspects

      Control of Expression of Type II RM Genes

      Cytosine Can Be Methylated on Either C-5 or N4: Consequences for Mutagenesis

      Type II Restriction Endonuclease That Require Two Recognition Sites for Cleavage

      What is the Function of Type IIS Enzymes?

      Type III R-M Systems

      Genetics of Type III Systems

      DNA Recognition by Type III Enzymes:

         Different Sequence Requirements for Restriction and Modification

      Sty LTI System

      Restriction Systems Specific and Modified DNA

      DpnI and DpnII

      Rediscovery of Methyl-Directed Restriction in E. coli

      McrBC

      McrA

      Mrr

      Phage Antirestriction

      Recent Developments

      "Nature Red in Tooth and Claw": The case of Phage T4

      Concluding Remarks

      Acknowledgments

      References

      

AU  - Bickle TA
AU  - Kruger DH
PT  - Journal Article
TA  - Microbiol. Rev.
JT  - Microbiol. Rev.
SO  - Microbiol. Rev. 1993 57: 434-450.

PMID- 909783
VI  - 4
DP  - 1977
TI  - A simple, general procedure for purifying restriction endonucleases.
PG  - 2561-2572
AB  - A simple, general method for purifying restriction endonucleases is described.
      The method employs precipitation of nucleic acids from crude extracts with
      polyethyleneimine followed by affinity chromatography on columns of heparin
      covalently linked to agarose.  Most of the sixteen enzymes tested could be
      purified to a degree sufficient for DNA sequencing work by this method
      sometimes supplemented by at most one step of ion exchange chromatography.
AU  - Bickle TA
AU  - Pirrotta V
AU  - Imber R
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1977 4: 2561-2572.

PMID- 6246333
VI  - 65
DP  - 1980
TI  - Purification and properties of the BglI and II endonucleases.
PG  - 132-138
AB  - The presence of two distinct restriction endonucleases in Bacillus globigii,
      BglI and II, was first reported by Wilson and Young.
AU  - Bickle TA
AU  - Pirrotta V
AU  - Imber R
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1980 65: 132-138.

PMID- Not carried by PubMed...
VI  - B510
DP  - 1983
TI  - Methods for purification of restriction enzymes.
PG  - 1-8
AB  - None
AU  - Bickle TA
AU  - Streiff M
PT  - Journal Article
TA  - Nucleic Acid Biochem.
JT  - Nucleic Acid Biochem.
SO  - Nucleic Acid Biochem. 1983 B510: 1-8.

PMID- 25197485
VI  - 9
DP  - 2014
TI  - The complete genome sequence of Clostridium indolis DSM 755(T.).
PG  - 1089-1104
AB  - Clostridium indolis DSM 755(T) is a bacterium commonly found in soils and the feces of birds
      and mammals. Despite its prevalence, little is known about the
      ecology or physiology of this species. However, close relatives, C.
      saccharolyticum and C. hathewayi, have demonstrated interesting metabolic
      potentials related to plant degradation and human health. The genome of C.
      indolis DSM 755(T) reveals an abundance of genes in functional groups associated
      with the transport and utilization of carbohydrates, as well as citrate, lactate,
      and aromatics. Ecologically relevant gene clusters related to nitrogen fixation
      and a unique type of bacterial microcompartment, the CoAT BMC, are also detected.
      Our genome analysis suggests hypotheses to be tested in future culture based work
      to better understand the physiology of this poorly described species.
AU  - Biddle AS et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 1089-1104.

PMID- 17686983
VI  - 104
DP  - 2007
TI  - Fossil genes and microbes in the oldest ice on earth.
PG  - 13455-13460
AB  - Although the vast majority of ice that formed on the Antarctic continent over the past 34
      million years has been lost to the oceans, pockets of
      ancient ice persist in the Dry Valleys of the Transantarctic Mountains.
      Here we report on the potential metabolic activity of microbes and the
      state of community DNA in ice derived from Mullins and upper Beacon
      Valleys. The minimum age of the former is 100 ka, whereas that of the
      latter is approximately 8 Ma, making it the oldest known ice on Earth. In
      both samples, radiolabeled substrates were incorporated into
      macromolecules, and microbes grew in nutrient-enriched meltwaters, but
      metabolic activity and cell viability were critically compromised with
      age. Although a 16S rDNA-based community reconstruction suggested
      relatively low bacterial sequence diversity in both ice samples,
      metagenomic analyses of community DNA revealed many diverse orthologs to
      extant metabolic genes. Analyses of five ice samples, spanning the last 8
      million years in this region, demonstrated an exponential decline in the
      average community DNA size with a half-life of approximately 1.1 million
      years, thereby constraining the geological preservation of microbes in icy
      environments and the possible exchange of genetic material to the oceans.
AU  - Bidle KD
AU  - Lee S
AU  - Marchant DR
AU  - Falkowski PG
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2007 104: 13455-13460.

PMID- 
VI  - 45
DP  - 2001
TI  - Characterization of pEC156, a ColE1-type plasmid from Escherichia coli E1585-68 that carries genes of the EcoVIII restriction-modification system.
PG  - 161
AB  - Type II restriction-modification systems are common in prokaryotes.  It is believed that they
      evolved to protect these organisms against viral invasion.  Genes encoding R-M systems are
      often present on natural plasmids which may facilitate the spread of these systems among
      bacteria by horizontal gene transfer.  It has been shown that the genes coding for R-M systems
      can increase the stability of the plasmids which carry them.  Bacterial strains isolated from
      clinical specimens are especially abundant in plasmids.  Some of them possess Hsd (host
      specificity for DNA) plasmids carrying R-M systems.  The strain of E. coli E1585-68 used in
      our study was isolated from a patient in England in 1973, and since then it has often been
      used as a reference strain for the E. coli O156 serotype.  Later it was discovered that this
      strain possesses a natural plasmid (pEC156), carrying genes for the EcoVIII R-M system, a
      HindIII isoschizomer.  The complete 4312-bp sequence of the plasmid pEC156 has been
      determined.  The plasmid, numbering 20 copies per cell, has been sequenced on both strands and
      the sequence has been deposited in GenBank (Accession No. AF158026).  The pEC156 plasmid
      carries genes encoding the EcoVIII R-M system - an isoschizomer of HindIII from Haemophilus
      influenzae.  Nucleotide sequence analysis of pEC156 suggests that this plasmid possesses a
      ColE1 replicon.  It consists of an origin of replication and two untranslated genes encoding
      RNAI and RNAII, both involved in the regulation of plasmid DNA replication.  The replication
      region also contains a gene, encoding a 64-amino-acid Rom-like (RNA one modulator) peptide,
      which presumably is involved in the negative regulation of plasmid pEC156 replication by
      stabilizing the NRAI-RNAII complex.  The DNA sequence homologous to the rom region of ColE1
      plasmids was also identified.  The stable maintenance of ColE1 plasmids in bacteria depends on
      the existence of cis-acting cer locus, which ensures that at cell division each daughter cell
      receives at least one copy of the plasmid.  Computational analysis of pEC156 nucleotide
      sequence revealed the presence of a DNA region that has high homology to the cer locus of
      ColE1 plasmid.  The replication of all ColE1-type plasmids is dependent on the activity of E.
      coli DNA polymerase I.  It was shown that pEC156 derivatives carrying antibiotic resistance
      genes failed to replicate in an E. coli polA12(ts) mutant at 43oC.  It was also shown that the
      pEC156 plasmid copy number increase after treating bacteria with chloramphenicol and decrease
      in E. coli pcnB80 mutant.  The pEC156 plasmid carries the genes encoding the EcoVIII R-M
      system belonging to type II family.  This system consists of two separate enzymes: an
      endonuclease and cognate methyltransferase.  The first of them is the EcoVIII endonuclease
      which recognizes specific nucleotide sequence and is capable of cleaving two strands of DNA at
      the recognition site, between two adenine residues in the recognition site:
      A'A/AGCT-3'/3'TTCGA/A.  the second component is the methyltransferase, which protects
      bacterial DNA against cleavage by cognate endonuclease.  Both proteins have been purified and
      characterized.
AU  - Biedrzycka I
AU  - Sektas M
AU  - Kaczorowski T
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 2001 45: 161.

PMID- 15782221
VI  - 2
DP  - 2005
TI  - Quantification of random genomic mutations.
PG  - 285-290
AB  - Cancer cells contain numerous clonal mutations. It has been theorized that malignant cells
      sustain an elevated mutation rate and, as a consequence, harbor yet larger numbers of random
      point mutations. Testing this hypothesis has been precluded by lack of an assay to measure
      random mutations-that is, mutations that occur in only one or a few cells of a population. We
      have established a method that has permitted us to detect and identify rare random mutations
      in human cells, at a frequency of 1 per 10(8) base pairs. The assay is based on gene capture,
      by hybridization with a uracil-containing probe, followed by magnetic separation. Mutations
      that render the mutational target sequence non-cleavable by a restriction enzyme are
      quantified by dilution to single molecules and real-time quantitative PCR amplification. The
      assay can be extended to quantify mutation in any DNA-based organism, at different sites in
      the genome, in introns and exons, in unselected and selected genes, and in proliferating and
      quiescent cells.
AU  - Bielas JH
AU  - Loeb LA
PT  - Journal Article
TA  - Nat. Methods
JT  - Nat. Methods
SO  - Nat. Methods 2005 2: 285-290.

PMID- 11936104
VI  - 372
DP  - 2002
TI  - Determination of the turnover number of the restriction endonuclease EcoRI using evanescent wave technology.
PG  - 308-313
AB  - Binding and catalytic activity of the type II restriction endonuclease EcoRI on immobilized
      DNA has been observed in real time using three different evanescent wave biosensors and two
      different immobilization techniques.  The method gives direct access to the turnover number
      (kcat) without the necessity for the determination of any concentration or activity.  The
      combination of different evanescent wave techniques gives access to the catalytic mechanism
      and allows the determination of the rate limiting step.
AU  - Bier FF
AU  - Kleinjung F
AU  - Schmidt PM
AU  - Scheller FW
PT  - Journal Article
TA  - Anal. Bioanal. Chem.
JT  - Anal. Bioanal. Chem.
SO  - Anal. Bioanal. Chem. 2002 372: 308-313.

PMID- 9988694
VI  - 274
DP  - 1999
TI  - Modified oligonucleotides as bona fide antagonists of proteins interacting with DNA.
PG  - 4594-4606
AB  - The study of the biological role of DNA methyltransferase has been impeded by the lack of
      direct and specific inhibitors.  This report describes the design of potent DNA based
      antagonists of DNA MeTase and their utilization to define the interactions of DNA MeTase with
      its substrate and to study its biological role.  We demonstrate that the size, secondary
      structure, hemimethylation, and phosphorothioate modification strongly affect the antagonists
      interaction with DNA MeTase whereas base substitutions do not have a significant effect.  To
      study whether DNA MeTase is critical for cellular transformation, human lung non-small
      carcinoma cells were treated with the DNA MeTase antagonists.  Ex vivo, hairpin inhibitors of
      DNA MeTase are localized to the cell nucleus in lung cancer cells.  They inhibit DNA MeTase,
      cell growth, and anchorage independent growth (an indicator of tumorigenesis in cell culture)
      in a dose-dependent manner.  The inhibitors developed in this study are the first documented
      example of direct inhibitors of DNA MeTase in living cells and of modified oligonucleotides as
      bona fide antagonists of critical cellular proteins.
AU  - Bigey P
AU  - Knox JD
AU  - Croteau S
AU  - Bhattacharya SK
AU  - Theberge J
AU  - Szyf M
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1999 274: 4594-4606.

PMID- 10721735
VI  - 242
DP  - 2000
TI  - Transcriptional regulation of the human DNA methyltransferase (dnmt1) gene.
PG  - 407-418
AB  - DNA methylation is an important component of the epigenetic control of genome functions.
      Understanding the regulation of the DNA Methyltransferase (dnmt1) gene expression is critical
      for comprehending how DNA methylation is coordinated with other critical biological
      processes. In this paper, we investigate the transcriptional regulatory
      region of the human dnmt1 gene using a combination of RACE, RNase
      protection analysis and CAT assays. We identified one major and three
      minor transcription initiation sites in vivo (P1-P4), which are
      regulated by independent enhancers and promoter sequences. The minimal
      promoter elements of P1, P2 and P4 are mapped within 256 bp upstream of
      their respective transcription initiation sites. P1 is nested within a
      CC-rich area, similar to other housekeeping genes, whereas P2-P4 are
      found in CG-poor areas. Three c-Jun-dependent enhancers are located
      downstream to P1 and upstream to P2-P4, thus providing a molecular
      explanation for the responsiveness of dnmt1 to oncogenic signals that
      are mediated by the Ras-c-Jun oncogenic signaling pathway.
AU  - Bigey P
AU  - Ramchandani S
AU  - Theberge J
AU  - Araujo FD
AU  - Szyf M
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 2000 242: 407-418.

PMID- 4578426
VI  - 244
DP  - 1973
TI  - Recognition sequence of a restriction enzyme.
PG  - 7-10
AB  - Restriction endonuclease EcoRII makes about twenty double-stranded breaks per
      molecule of lambda h80 DNA.  The 5'- terminal sequences are pC-C-A-G-G and
      pC-C-T-G-G.  These are complementary and rotationally symmetrical, showing how
      the enzyme may produce DNA fragments with short cohesive ends.
AU  - Bigger CH
AU  - Murray K
AU  - Murray NE
PT  - Journal Article
TA  - Nature New Biol.
JT  - Nature New Biol.
SO  - Nature New Biol. 1973 244: 7-10.

PMID- 14752001
VI  - 20
DP  - 2004
TI  - In silico analysis of complete bacterial genomes: PCR, AFLP-PCR and endonuclease restriction.
PG  - 798-799
AB  - We have developed a website, www.in-silico.com, which runs a software program that performs
      three basic tasks in completely sequenced bacterial genomes by in silico analysis: PCR
      amplification, amplified fragment length polymorphism (AFLP-PCR) and endonuclease restriction.
      For PCR, after selection of the genome and introduction of primers, fragment size, DNA
      sequence and corresponding open reading frame (ORF) identity of the resulting PCR product is
      computed. Plasmids of sequenced species may be included in the analysis. Theoretical AFLP-PCR
      analyzes similar parameters, and includes a suggestion tool providing a list of commercial
      restriction enzyme pairs yielding up to 50 amplicons in the selected genome. Endonuclease
      restriction analysis of complete genomes and plasmids calculates the number of restriction
      sites for endonucleases in a given genome. If the number of fragments is 50 or fewer, pulsed
      field gel electrophoresis image and restriction maps are illustrated. Other tools that have
      been included in this site are ORF search by name and DNA to protein translation as well as
      restriction digestion of user-defined DNA sequences. AVAILABILITY: This is a new molecular
      biology resource freely available over the Internet at http://www.in-silico.com
AU  - Bikandi J
AU  - San MR
AU  - Rementeria A
AU  - Garaizar J
PT  - Journal Article
TA  - Bioinformatics
JT  - Bioinformatics
SO  - Bioinformatics 2004 20: 798-799.

PMID- 10593932
VI  - 274
DP  - 1999
TI  - Reactions of type II restriction endonucleases with 8-base pair recognition sites.
PG  - 36379-36386
AB  - Type II restriction endonucleases usually recognize 4-6-base pair (bp) sites on DNA and cleave
      each site in a separate reaction.  A few type II endonucleases have 8-bp recognition sites,
      but these seem unsuited for restriction, since their sites are rare on most DNA. Moreover,
      only one endonuclease that recognizes a target containing 8 bp has been examined to date, and
      this enzyme, SfiI, needs two copies of this site for its DNA cleavage reaction. In this study,
      several endonucleases with 8-bp sites were tested on plasmids that have either one or two
      copies of the relevant sequence to determine if they also need two sites. SgfI, SrfI, FseI,
      PacI, PmeI, Sse8781I, and SdaI all acted through equal and independent reactions at each site.
      AscI cleaved the DNA with one site at the same rate as that with two sites but acted
      processively on the latter. In contrast, SgrAI showed a marked preference for the plasmid with
      two sites and cleaved both sites on this DNA in a concerted manner, like SfiI. Endonucleases
      that require two copies of an 8-bp sequence may be widespread in nature, where, despite this
      seemingly inappropriate requirement, they may function in DNA restriction.
AU  - Bilcock DT
AU  - Daniels LE
AU  - Bath AJ
AU  - Halford SE
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1999 274: 36379-36386.

PMID- 10096090
VI  - 31
DP  - 1999
TI  - DNA restriction dependent on two recognition sites: activities of the SfiI restriction-modification system in Escherichia coli.
PG  - 1243-1254
AB  - In contrast to many type II restriction enzymes, dimeric proteins that cleave DNA at
      individual recognition sites 4-6 bp long, the SfiI endonuclease is a tetrameric protein that
      binds to two copies of an elongated sequence before cutting the DNA at both sites.  The mode
      of action of the SfiI endonuclease thus seems more appropriate for DNA rearrangements than for
      restriction. To elucidate its biological function, strains of Escherichia coli expressing the
      SfiI restriction-modification system were transformed with plasmids carrying SfiI sites. The
      SfiI system often failed to restrict the survival of a plasmid with one SfiI site, but
      plasmids with two or more sites were restricted efficiently.  Plasmids containing methylated
      SfiI sites were not restricted.  No rearrangements of the plasmids carrying SfiI sites were
      detected among the transformants.  Hence, provided the target DNA contains at least two
      recognition sites, SfiI displays all of the hallmarks of a restriction-modification system as
      opposed to a recombination system in E. coli cells.,  The properties of the system in vivo
      match those of the enzyme in vitro.  For both restriction in vivo and DNA cleavage in vitro,
      SfiI operates best with two recognition sites on the same DNA.
AU  - Bilcock DT
AU  - Halford SE
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1999 31: 1243-1254.

PMID- 26316635
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Alteromonas macleodii Strain MIT1002, Isolated from an Enrichment Culture of the Marine Cyanobacterium Prochlorococcus.
PG  - e00967-15
AB  - Alteromonas spp. are heterotrophic gammaproteobacteria commonly found in marine environments.
      We present here the draft genome sequence of Alteromonas macleodii  MIT1002, which was
      isolated from an enrichment culture of the marine cyanobacterium Prochlorococcus NATL2A. This
      genome contains a mixture of features previously seen only within either the 'surface' or
      'deep' Alteromonas ecotype.
AU  - Biller SJ
AU  - Coe A
AU  - Martin-Cuadrado AB
AU  - Chisholm SW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00967-15.

PMID- 26594307
VI  - 10
DP  - 2015
TI  - Genome sequence and description of the anaerobic lignin-degrading bacterium sp. nov.
PG  - 106
AB  - Tolumonas lignolytica BRL6-1T sp. nov. is the type strain of T. lignolytica sp. nov., a
      proposed novel species of the Tolumonas genus. This strain was isolated
      from tropical rainforest soils based on its ability to utilize lignin as a sole
      carbon source. Cells of Tolumonas lignolytica BRL6-1T are mesophilic, non-spore
      forming, Gram-negative rods that are oxidase and catalase negative. The genome
      for this isolate was sequenced and returned in seven unique contigs totaling
      3.6Mbp, enabling the characterization of several putative pathways for lignin
      breakdown. Particularly, we found an extracellular peroxidase involved in lignin
      depolymerization, as well as several enzymes involved in beta-aryl ether bond
      cleavage, which is the most abundant linkage between lignin monomers. We also
      found genes for enzymes involved in ferulic acid metabolism, which is a common
      product of lignin breakdown. By characterizing pathways and enzymes employed in
      the bacterial breakdown of lignin in anaerobic environments, this work should
      assist in the efficient engineering of biofuel production from lignocellulosic
      material.
AU  - Billings AF
AU  - Fortney JL
AU  - Hazen TC
AU  - Simmons B
AU  - Davenport KW
AU  - Goodwin L
AU  - Ivanova N
AU  - Kyrpides NC
AU  - Mavromatis K
AU  - Woyke T
AU  - DeAngelis KM
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 106.

PMID- 10024571
VI  - 67
DP  - 1999
TI  - Complete nucleotide sequence of the 27-kilobase virulence related locus (vrl) of Dichelobacter nodosus: evidence for extrachromosomal origin.
PG  - 1277-1286
AB  - The vrl locus is preferentially associated with virulent isolates
      of the ovine footrot pathogen, Dichelobacter nodosus. The complete
      nucleotide sequence of this 27.1-kb region has now been determined. The
      data reveal that the locus has a G+C content much higher than the rest
      of the D. nodosus chromosome and contains 22 open reading frames (ORFs)
      encoding products including a putative adenine-specific methylase, two
      potential DEAH ATP-dependent helicases, and two products with sequence
      similarity to a bacteriophage resistance system. These ORFs are all in
      the same orientation, and most are either overlapping or separated by
      only a few nucleotides, suggesting that they comprise an operon and are
      translationally coupled. Expression vector studies have led to the
      identification of proteins that correspond to many of these ORFs. These
      data, in combination with evidence of insertion of vrl into the 3' end
      of an ssrA gene, are consistent with the hypothesis that the vrl locus
      was derived from the insertion of a bacteriophage or plasmid into the
      D. nodosus genome.
AU  - Billington SJ
AU  - Huggins AS
AU  - Johanesen PA
AU  - Crellin PK
AU  - Cheung JK
AU  - Katz ME
AU  - Wright CL
AU  - Haring V
AU  - Rood JI
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 1999 67: 1277-1286.

PMID- 16966401
VI  - 50
DP  - 2006
TI  - Multiple genetic elements carry the tetracycline resistance gene, tet(W) in the animal pathogen, Arcanobacterium pyogenes.
PG  - 3580-3587
AB  - The tet(W) gene is associated with tetracycline resistance in a wide range
      of bacterial species, including obligately anaerobic rumen bacteria and
      isolates from the human gut and oral mucosa. However, little is known
      about how this gene is disseminated and the types of genetic elements it
      is carried on. We examined tetracycline-resistant isolates of the animal
      commensal and opportunistic pathogen Arcanobacterium pyogenes, all of
      which carried tet(W), and identified three genetic elements designated
      ATE-1, ATE-2, and ATE-3. These elements were found in 25%, 35%, and 60% of
      tetracycline-resistant isolates, respectively, with some strains carrying
      both ATE-2 and ATE-3. ATE-1 shows characteristics of a mobilizable
      transposon, and the tet(W) genes from strains carrying this element can be
      transferred at low frequencies between A. pyogenes strains. ATE-2 has
      characteristics of a simple transposon, carrying only the resistance gene
      and a transposase, while in ATE-3, the tet(W) gene is associated with a
      streptomycin resistance gene that is 100% identical at the DNA level with
      the aadE gene from the Campylobacter jejuni plasmid pCG8245. Both ATE-2
      and ATE-3 show evidence of being carried on larger genetic elements, but
      conjugation to other strains was not observed under the conditions tested.
      ATE-1 was preferentially associated with A. pyogenes strains of bovine
      origin, while ATE-2 and ATE-3 elements were primarily found in porcine
      isolates, suggesting that these elements may circulate in different
      environments. In addition, four alleles of the tet(W) gene, primarily
      associated with different elements, were detected among A. pyogenes
      isolates.
AU  - Billington SJ
AU  - Jost BH
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2006 50: 3580-3587.

PMID- 9066112
VI  - 148
DP  - 1997
TI  - Utilization of alkaline phosphatase fusions to identify secreted proteins, including potential efflux proteins and virulence factors from Helicobacter pylori.
PG  - 63-68
AB  - The targeted genomic strategy of random fusions to a partial gene encoding
      a signal sequence-deficient fragment of bacterial alkaline phosphatase was
      utilized to screen for secreted proteins in Helicobacter pylori. The
      rationale for targeting extracytoplasmic proteins was based on the
      hypothesis that most virulence factors and vaccine candidates are secreted
      or exported proteins. In addition, extracytosolic proteins represent good
      potential targets for drug intervention since they are in general more
      accessible to drugs than are cytoplasmically localized proteins. The
      application of this strategy to H. pylori allowed the identification of
      putative virulence factors and novel targets for drug intervention
      including four putative antibiotic efflux genes. The strategy used here is
      rapid and technically simple, relatively inexpensive, adaptable to a wide
      variety of microbes and genetic systems, and selects for expressed and
      accessible proteins.
AU  - Bina JE
AU  - Nano F
AU  - Hancock REW
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1997 148: 63-68.

PMID- 
VI  - 17
DP  - 2007
TI  - Characterization of spontaneous phage-resistant variants of Streptococcus thermophilus by randomly amplified polymorphic DNA analysis and identification of phage-resistance mechanisms.
PG  - 1115-1122
AB  - A total of 100 spontaneous phage-resistant mutants isolated from nine commercial Streptococcus
      thermophilus strains were characterized
      preliminarily by randomly amplified polymorphic DNA (RAPD) and the
      nature of their phage-resistance mechanisms was investigated. Only for
      mutants isolated from one strain, free phages were detected in their
      culture supernatants when these were titrated on the sensitive strain,
      suggesting that the mutants could have acquired the resistance
      phenotype by integrating the phage in their genomes (lysogeny).
      Adsorption interference was observed in the derivatives isolated from
      two strains. For mutants isolated from two other strains.
      restriction-modification (R-M) type systems were detected. In one of
      these cases, R-M was probably combined with another intracellular
      anti-phage system. In most cases, the molecular profiles (RAPD
      fingerprints) obtained with four arbitrary primers showed a high
      similarity among parent strains and their respective phage-resistant
      mutants. Some of these mutants were identified as potentially improved
      strains for industrial use.
AU  - Binetti AG
AU  - Suarez VB
AU  - Tailliez P
AU  - Reinheimer JA
PT  - Journal Article
TA  - Int. Dairy Journal
JT  - Int. Dairy Journal
SO  - Int. Dairy Journal 2007 17: 1115-1122.

PMID- 346412
VI  - 6
DP  - 1978
TI  - Restriction endonucleases and modification methylases in bacteria.
PG  - 315-324
AB  - There are three mechanisms by which foreign DNA may enter a prokaryotic organism: conjugation
      between Gram-negative bacteria, uptake of exogenous DNA (transformation) and infection by
      viral (bacteriophage) nucleic acid.  The interaction between a bacteriophage and its host
      bacterial cell has been extensively investigated.  A bacterium can restrict phage infection
      through its ability to degrade the infectious DNA on entry into the cell.  This is achieved by
      site-specific deoxyriboendonucleases, called restriction endonucleases, that cleave DNA into a
      limited, but defined, number of fragments, which are then susceptible to exonuclease attack.
      The bacterium can prevent cleavage of its chromosomal DNA by site-specific methylation of the
      nucleotide bases, for which another activity, the DNA-modification methylase, is responsible.
      The modification methylase can also modify bacteriophage DNA on entry into the cell, thus
      making the modified phage DNA resistant to the action of the restriction endonuclease.
      Although the modification methylase protects the host bacterial chromosome, it can also afford
      protection to the invading phage DNA; as a result, phages grown in a given bacterial strain
      are insensitive to restriction by that strain. A review.
AU  - Bingham AHA
AU  - Atkinson T
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 1978 6: 315-324.

PMID- 724493
VI  - 5
DP  - 1978
TI  - A specific endonuclease from Bacillus caldolyticus.
PG  - 3457-3467
AB  - The purification and characterization of a new restriction endonuclease, BclI,
      from the extreme thermophile Bacillus caldolyticus is reported.  This enzyme
      recognizes the sequence 5'-T^-G-A-T-C-A-3' 3'-A-C-T-A-G^-T-5' and cleaves at
      the positions indicated by the arrows.
AU  - Bingham AHA
AU  - Atkinson T
AU  - Sciaky D
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1978 5: 3457-3467.

PMID- 6286421
VI  - 18
DP  - 1982
TI  - Isolation of two restriction endonucleases from Chloroflexus aurantiacus (CauI, CauII).
PG  - 87-91
AB  - The purification and characterization of two restriction endonucleases from the
      photosynthetic gliding bacterium Chloroflexus aurantiacus are described.
AU  - Bingham AHA
AU  - Darbyshire J
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1982 18: 87-91.

PMID- 324801
VI  - 76
DP  - 1977
TI  - The purification of restriction endonuclease EcoRI by precipitation involving polyethyleneimine.
PG  - 250-256
AB  - The restriction endonuclease EcoRI from an Escherichia coli containing the
      plasmid pMB 1,3 or 4 is widely used in the analysis and manipulation of DNA
      molecules.  The enzyme has been used in the physical mapping of viral genomes
      and mitochondrial DNA, the preliminary analysis of DNA molecules and since
      cleavage with EcoRI yields cohesive terminii, in the in vitro construction of
      recombinant DNA molecules.  Homogeneous enzyme preparations are not essential
      for the in vitro analysis and manipulation of DNA molecules; a preparation
      completely free of contaminating non-specific nucleases is adequate for most
      experiments.  There are several published procedures for the puruification of
      EcoRI, however they all suffer from two major disadvantages, the large number
      of steps involved in the preparation of exonuclease-free material and the poor
      yields of the enzyme finally obtained.  The use of polyethyleneimine (PEI) for
      the removal of nucleic acids from microbial extracts was demonstrated by
      Atkinson and Jack, and it was found that if this procedure was carried out
      under conditions of low ionic strength with an extract of E. coli RY13 the
      EcoRI activity precipitated with the PEI-DNA complex.  This paper describes a
      rapid, two step method for the purification of exonuclease-free EcoRI
      restriction endonuclease in high yield, based on elution of the enzyme from a
      PEI precipitated DNA-enzyme complex.  The preparation of other restriction
      endonucleases using a similar technique is also discussed.
AU  - Bingham AHA
AU  - Sharman AF
AU  - Atkinson T
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1977 76: 250-256.

PMID- 25767223
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of a Metronidazole-Resistant Helicobacter pylori Strain.
PG  - e00051-15
AB  - We report here the complete genome sequence of a metronidazole-resistant Helicobacter pylori
      strain (MET(r)). The MET(r) strain was obtained under
      exposure of H. pylori 26695 on agar plates with low metronidazole concentrations.
      The genome data provide insight into the genomic changes of H. pylori under
      selection by metronidazole in vitro.
AU  - Binh TT
AU  - Suzuki R
AU  - Kwon DH
AU  - Yamaoka Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00051-15.

PMID- 24233587
VI  - 1
DP  - 2013
TI  - Complete Genome Sequences of Helicobacter pylori Clarithromycin-Resistant Strains.
PG  - e00912-13
AB  - We report the complete genome sequences of two Helicobacter pylori clarithromycin-resistant
      strains. Clarithromycin (CLR)-resistant strains were
      obtained under the exposure of H. pylori strain 26695 on agar plates with low
      clarithromycin concentrations. The genome data provide insights into the genomic
      changes of H. pylori under selection by clarithromycin in vitro.
AU  - Binh TT
AU  - Suzuki R
AU  - Shiota S
AU  - Kwon DH
AU  - Yamaoka Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00912-13.

PMID- 22675586
VI  - 5
DP  - 2011
TI  - Complete genome sequence of Desulfurispirillum indicum stain S5.
PG  - 371-378
AB  - Desulfurispirillum indicum strain S5T is a strictly anaerobic bacterium isolated from river
      se-diment in Chennai, India. D. indicum belongs to the deep branching phylum of
      Chrysioge-netes, which currently only includes three other cultured species. Strain S5T is the
      type strain of the species and it is capable of growth using selenate, selenite, arsenate,
      nitrate or nitrite as terminal electron acceptors. The 2,928,377 bp genome encodes 2,619
      proteins and 49 RNA genes, and the information gained from its sequence will be relevant to
      the elucidation of mi-crobially-mediated transformations of arsenic and selenium, in addition
      to deepening our knowledge of the underrepresented phylum of Chrysiogenetes.
AU  - Bini E et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 5: 371-378.

PMID- 7523114
VI  - 13
DP  - 1994
TI  - Self-splicing group I intron in cyanobacterial initiator methionine tRNA: evidence for lateral transfer of introns in bacteria.
PG  - 4629-4635
AB  - A group I self-splicing intron has been found in the anticodon loop of
      tRNA(fMet) genes in three cyanobacterial genera: Dermocarpa, Scytonema and
      Synechocystis; it is absent in nine others. The Synechocystis intron is
      also interrupted by an open reading frame (ORF) of 150 codons. Of these
      three bacteria, only Scytonema also contains the group I intron that has
      previously been reported in tRNA(Leu) (UAA) genes in both cyanobacteria
      and chloroplasts. The presence of an ORF in the tRNA(fMet) intron, the
      sporadic distribution of the intron among cyanobacteria and the lack of
      correlation between relatedness of the intron sequences and the bacteria
      in which they reside, are all consistent with recent introduction of this
      intron by lateral transfer.
AU  - Biniszkiewicz D
AU  - Cesnaviciene E
AU  - Shub DA
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1994 13: 4629-4635.

PMID- 29903822
VI  - 6
DP  - 2018
TI  - Genome Sequence of a Canadian Vibrio parahaemolyticus Isolate with Unique Mobilizing Capacity.
PG  - e00520-18
AB  - Vibrio parahaemolyticus is a clinically significant marine bacterium implicated in
      gastroenteritis among consumers of raw or undercooked seafood. This report
      presents the whole-genome sequence of a unique strain of V. parahaemolyticus
      isolated from oysters harvested in Canada.
AU  - Bioteau A
AU  - Huguet K
AU  - Burrus V
AU  - Banerjee S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00520-18.

PMID- 9174957
VI  - 9
DP  - 1996
TI  - Oriented immobilization of restriction endonuclease EcoRI.
PG  - 683-690
AB  - Two activated matrices have been developed to determine whether immobilization chemistry can
      be used to orient proteins on a support.  Restriction endonuclease EcoRI from Escherichia coli
      RY13 (E.C.3.1.23.13) was used as a model in these studies.  Thiol-activated Sephadex G-10 was
      used to couple the EcoRI endonuclease through its free sulfhydryl, while amino-activated
      Sephadex G-10 was used to couple it randomly through its free carboxyl groups.  To determine
      whether the enzyme was immobilized randomly or specifically, both lower and higher molecular
      weight substrates were used.  The polymerase chain reaction amplified multiple cloning site
      region of pBluescript KS obtained using T3 and T7 primers was considered as the small
      substrate.  The plasmid Sp64 containing firefly luciferase gene was the large substrate.
      Immobilized EcoRI preparations were characterized with respect to repeated usage and storage
      stability.  The EcoRI immobilized on thiopropyl-Sepharose 4B could be stored for over 14 days
      at 4oC without observable loss of activity.  In an independent experiment the same gel was
      used thrice repeatedly without any discernible loss of activity.
AU  - Bircakova M
AU  - Truksa M
AU  - Scouten WH
PT  - Journal Article
TA  - J. Mol. Recognit.
JT  - J. Mol. Recognit.
SO  - J. Mol. Recognit. 1996 9: 683-690.

PMID- 1377983
VI  - 70
DP  - 1992
TI  - The essentials of DNA methylation.
PG  - 5-8
AB  - An obstacle to progress in understanding eukaryotic DNA methylation has been the lack of a
      good genetic system - the most favorable eukaryotes for genetic analysis (yeasts,
      Caenorhabditis, Drosophila) have no detectable methylation in their genomes. Not only has this
      hampered progress, but the clear evidence for life without methylation that these organisms
      provide has raised questions about the relevance of the whole phenomenon. The current status
      of methylation is reviewed.
AU  - Bird A
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1992 70: 5-8.

PMID- 10636791
VI  - 286
DP  - 1999
TI  - DNA methylation de novo.
PG  - 2287-2288
AB  - In an ideal world, biological processes would be understood at the molecular level by first
      identifying all the participating components and then by deducing their roles in the system
      through experiment.  In reality, knowledge of each component is hard-won, and the temptation
      to assume that the key players are those that are currently known, ever-present.  Fortunately,
      as human cDNA sequencing approaches saturation, candidate components in mammalian systems are
      becoming easier to find.  One beneficiary is the field of DNA methylation in which researchers
      study the shutting down of gene expression through the addition of methyl groups to cytosine
      bases in the DNA.  Few players are more important in this arena than DNA methyltransferases,
      the enzymes responsible for methylating DNA.  Thanks to DNA sequence databases, a clutch of
      new Dnmts as well as proteins that bind methylated C bases have recently been uncovered.
      Three recent papers make clear that several of these newly recognized Dnmts are capable of de
      novo DNA methylation (that is, addition of methyl groups to DNA that has not been methylated
      before).  The new work demonstrates the crucial importance of an appropriately methylated
      genome for successful embryonic development.
AU  - Bird A
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1999 286: 2287-2288.

PMID- 2981636
VI  - 40
DP  - 1985
TI  - A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA.
PG  - 91-99
AB  - About 1% of the mouse genome is cleaved by HpaII to give a discrete fraction on
      gels.  The nonmethylated fraction is present in all tested tissues, including
      sperm, and contains HpaII sites at about 15 times their frequency in bulk DNA.
      About 80% of the fraction is composed of sequences that occur once or a few
      times per genome; the remainder is largely rDNA.  Unlike bulk DNA, the fraction
      is not deficient in CpG, and this may be directly due to the lack of
      methylation.  Genomic mapping of three nonribosomal fragments showed that they
      are part of islands of DNA within which nonmethylated HpaII and HhaI sites are
      highly concentrated.  We estimate about 30,000 islands per haploid genome and
      discuss evidence that many may be associated with genes.
AU  - Bird A
AU  - Taggart M
AU  - Frommer M
AU  - Miller OJ
AU  - Macleod D
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1985 40: 91-99.

PMID- 7732579
VI  - 11
DP  - 1995
TI  - Gene number, noise reduction and biological complexity.
PG  - 94-100
AB  - Preliminary estimates suggest that gene number, and hence biological complexity, increased
      suddenly at two periods of macroevolutionary change (the origin of eukaryotes and the origin
      of vertebrates), but otherwise remained relatively constant. As the genome is in constant
      flux, what normally constrains the number of different genes that an organism can retain?
      Here, I suggest that an important limitation on gene number is the efficiency of mechanisms
      that reduce transcriptional background noise. The appearance of both eukaryotes and
      vertebrates coincided with novel mechanisms of noise reduction.
AU  - Bird AP
PT  - Journal Article
TA  - Trends Genet.
JT  - Trends Genet.
SO  - Trends Genet. 1995 11: 94-100.

PMID- 487434
VI  - 17
DP  - 1979
TI  - Methylated and unmethylated DNA compartments in the sea urchin genome.
PG  - 889-901
AB  - Sea urchin (Echinus esculentus) DNA has been separated into high and low molecular weight
      fractions by digestion with the mCpG-sensitive restriction endonucleases HpaII, HhaI and AvaI.
      The separation was due to differences in methylation at the recognition sequences for these
      enzymes because an mCpG-insensitive isoschizomer of HpaII (MspI digested HpaII-resistant DNA
      to low molecular weight, showing that many HapII sites were in fact present in this fraction;
      and because 3H-methyl methionine administered to embryos was incorporated into the high
      molecular weight HpaII-, HhaI- and AvaI-resistant fraction, but not significantly into the low
      molecular weight fraction. The fraction resistant to HpaII, HhaI and AvaI amounted to about
      401f the total DNA. It consisted of long sequence tracts between 15 and well over 50 kb in
      length, in which many sites for each of these enzymes were methylated consecutively. The
      remaining 600f the genome, (m-), was not significantly methylated. Methylated and unmethylated
      fractions were considered to be subfractions of the genome because enriched unique sequences
      from one fraction cross-reassociated poorly with the other fraction and specific sequences
      were found in either (m+) or (m-) but not in both (see below). Similar (m+) and (m-)
      compartments were found in embryos, germ cells and adult somatic tissues. Furthermore, we
      found no evidence for changes in the sequence composition of (m+) or (m-) between sperm,
      embryo or intestine DNAs, although low levels of exchange would not have been detected. Using
      cloned Echinus histone DNA, heterologous 5S DNA and ribosomal DNA probes, we have found that
      each of these gene families belongs to the unmethylated DNA compartment in all the tissues
      examined. In particular, there was no detectable methylation of histone DNA either in early
      embryos, which are thought to be actively transcribing the bulk of histone genes, or in sperm
      and gastrulae, in which most histone genes are not being transcribed. In contrast to these
      gene families, sequences complementary to an internally repetitious Echinus DNA clone were
      found primarily in the methylated DNA compartment. nt.
AU  - Bird AP
AU  - Taggart MH
AU  - Smith BA
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1979 17: 889-901.

PMID- 10589672
VI  - 99
DP  - 1999
TI  - Methylation-induced repression - belts, braces, and chromatin.
PG  - 451-454
AB  - DNA methylation is essential for development in the mouse and plays an important role in
      inactivation of the X-chromosome and genomic imprinting.  It may also contribute to
      immobilization of mammalian transposons, suppression of transcriptional noise, and the control
      of tissue-specific gene expression, but decisive evidence on these points is lacking.  The
      theme that is common to all these phenomena is transcriptional repression.  Work on animals,
      plants, and fungi now leaves little doubt that gene silencing is a major biological
      consequence of DNA methylation.
AU  - Bird AP
AU  - Wolffe AP
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1999 99: 451-454.

PMID- 23599294
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences of Two Bulgarian Bacillus anthracis Strains.
PG  - e00152-13
AB  - Bacillus anthracis strains previously isolated from Bulgaria form a unique subcluster within
      the A1.a cluster that is typical for isolates from southeastern
      Europe. Here, we report the draft genome sequences of two Bulgarian B. anthracis
      strains belonging to the A branch (A.Br.)008/009 canonical single nucleotide
      polymorphism (SNP) group of the major A branch.
AU  - Birdsell DN
AU  - Antwerpen M
AU  - Keim P
AU  - Hanczaruk M
AU  - Foster JT
AU  - Sahl JW
AU  - Wagner DM
AU  - Grass G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00152-13.

PMID- 29270248
VI  - 12
DP  - 2017
TI  - Complete genome sequence analysis of Archaeoglobus fulgidus strain 7324 (DSM 8774), a hyperthermophilic archaeal sulfate reducer from a North Sea oil field.
PG  - 79
AB  - Archaeoglobus fulgidus is the type species of genus Archaeoglobus Stetter 1998, a
      hyperthermophilic sulfate reducing group within the Archaeoglobi class of the
      euryarchaeota phylum. Members of this genus grow heterotrophically or
      chemolithoautotrophically with sulfate or thiosulfate as electron acceptors.
      Except for A. fulgidus strain 7324 and the candidate species 'Archaeoglobus
      lithotrophicus', which both originate from deep oil-fields, the other members of
      this genus have been recovered from marine hydrothermal systems. Here we describe
      the features of the A. fulgidus strain 7324 genome as compared to the A. fulgidus
      VC16 type strain. The 2.3 Mbp genome sequence of strain 7324 shares about 93.5%
      sequence identity with that of strain VC16(T) but is about 138 Kbp longer, which
      is mostly due to two large 'insertions' carrying one extra cdc6 (cell-cycle
      control protein 6) gene, extra CRISPR elements and mobile genetic elements, a
      high-GC ncRNA gene (hgcC) and a large number of hypothetical gene functions. A
      comparison with four other Archaeoglobus spp. genomes identified 1001 core
      Archaeoglobus genes and more than 2900 pan-genome orthologous genes.
AU  - Birkeland NK
AU  - Schonheit P
AU  - Poghosyan L
AU  - Fiebig A
AU  - Klenk HP
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 79.

PMID- 15113406
VI  - 5
DP  - 2004
TI  - Frequent occurrence of recognition site-like sequences in the restriction endonucleases.
PG  - 30
AB  - BACKGROUND: There are two different theories about the development of the genetic code. Woese
      suggested that it was developed in connection with the
      amino acid repertoire, while Crick argued that any connection between
      codons and amino acids is only the result of an "accident". This question
      is fundamental to understand the nature of specific protein-nucleic acid
      interactions. RESULTS: The nature of specific protein-nucleic acid
      interaction between restriction endonucleases (RE) and their recognition
      sequences (RS) was studied by bioinformatics methods. It was found that
      the frequency of 5-6 residue long RS-like oligonucleotides is unexpectedly
      high in the nucleic acid sequence of the corresponding RE (p < 0.05 and p
      < 0.001 respectively, n = 7). There is an extensive conservation of these
      RS-like sequences in RE isoschizomers. A review of the seven available
      crystallographic studies showed that the amino acids coded by codons that
      are subsets of recognition sequences were often closely located to the RS
      itself and they were in many cases directly adjacent to the codon-like
      triplets in the RS.  Fifty-five examples of this codon-amino acid
      co-localization are found and analyzed, which represents 41.5% of total
      132 amino acids which are localized within 8 angstroms distance to the C1' atoms
      in the DNA. The average distance between the closest atoms in the codons
      and amino acids is 5.5 +/- 0.2 A (mean +/- S.E.M, n = 55), while the
      distance between the nitrogen and oxygen atoms of the co-localized
      molecules is significantly shorter, (3.4 +/- 0.2 A, p < 0.001, n = 15),
      when positively charged amino acids are involved. This is indicating that
      an interaction between the nucleic- and amino acids might occur.
      CONCLUSION: We interpret these results in favor of Woese and suggest that
      the genetic code is "rational" and there is a stereospecific relationship
      between the codes and the amino acids.
AU  - Biro JC
AU  - Biro JM
PT  - Journal Article
TA  - BMC Bioinformatics
JT  - BMC Bioinformatics
SO  - BMC Bioinformatics 2004 5: 30.

PMID- 3029689
VI  - 15
DP  - 1987
TI  - Cleavage of single stranded oligonucleotides by EcoRI restriction endonuclease.
PG  - 709-716
AB  - The 31mer 5'-TCA ACG CTA GAA TTC GGA TCC ATC GCT TGG T, the complementary 33mer
      5'-CCA AGC GAT GGA TCC GAA TTC TAG CGT TGA GAT, the 40 mer 5'-GGC CAG GAT GGT
      GAA GAA TTC GAT CCG GTA CGT AGC TAA G, and the complementary 42mer 5'-TAC TTA
      GCT ACG TAC CGG ATC GAA TTC TTC ACC ATC CTG GCC were synthesized and their
      reactivity towards EcoRI was studied.  It was found that the 31mer and the
      40mer were cleaved at a comparable rate to the 31mer-33mer hybrid and the
      40mer-42mer hybrid, respectively.  The rate of cleavage of the 33mer and the
      42mer was an order of magnitude lower.  To rule out possible intermolecular
      duplex formation, the 33mer was immobilized on cellulose by ligation and
      labelled with a 32P-dCTP using Klenow fragment of E. coli DNA polymerase.
      EcoRI cleaved this immobilized oligomer into specific fragments.
AU  - Bischofberger N
AU  - Ng PG
AU  - Webb TR
AU  - Matteucci MD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1987 15: 709-716.

PMID- 26159522
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of a Natural Root Isolate, Bacillus subtilis UD1022, a Potential Plant Growth-Promoting Biocontrol Agent.
PG  - e00696-15
AB  - Bacillus subtilis, which belongs to the phylum Firmicutes, is the most widely studied
      Gram-positive model organism. It is found in a wide variety of
      environments and is particularly abundant in soils and in the gastrointestinal
      tracts of ruminants and humans. Here, we present the complete genome sequence of
      the newly described B. subtilis strain UD1022. The UD1022 genome consists of a
      4.025-Mbp chromosome, and other major findings from our analysis will provide
      insights into the genomic basis of it being a plant growth-promoting
      rhizobacterium (PGPR) with biocontrol potential.
AU  - Bishnoi U
AU  - Polson SW
AU  - Sherrier DJ
AU  - Bais HP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00696-15.

PMID- 374743
VI  - 128
DP  - 1979
TI  - A DNA sequence cleaved by restriction endonuclease R.EcoRI in only one strand.
PG  - 545-559
AB  - Restriction endonuclease EcoRI cuts both strands of the DNA sequence GAATTC
      generating two separate frayed ends (Hedgpeth et al., 1972).  Here it is shown
      that under standard digestion conditions, the enzyme also attacks the sequence
      GAATTA, but cuts only one strand.  The resulting nick is an efficient
      initiation point for DNA synthesis by Escherichia coli DNA polymerase I,
      allowing the selective labelling of one strand of the DNA duplex.  In buffers
      of low molarity and high pH (8.5), EcoRI cleaves sequences with the form NAATTN
      (Polisky et al., 1975).  Thus it seems that under both sets of conditions the
      enzyme recognizes the four-base-pair core sequence AATT, and that its ability
      to cleave different adjacent phosphodiester bonds varies with pH and ionic
      strength.
AU  - Bishop JO
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1979 128: 545-559.

PMID- 25342692
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Enteritidis Strain SEJ.
PG  - e01084-14
AB  - Salmonella enterica constitutes a group of enteric pathogens with a broad host range,
      including humans, reptiles, and birds. S. enterica subsp. enterica is a
      common cause of inflammatory diarrhea in humans. We present the draft genome of
      S. enterica subsp. enterica serovar Enteritidis strain SEJ, including a 59-kbp
      plasmid.
AU  - Bishop-Lilly KA
AU  - Frey KG
AU  - Daligault HE
AU  - Davenport KW
AU  - Bruce DC
AU  - Chain PS
AU  - Coyne SR
AU  - Chertkov O
AU  - Freitas T
AU  - Jaissle J
AU  - Koroleva GI
AU  - Ladner JT
AU  - Minogue TD
AU  - Palacios GF
AU  - Redden CL
AU  - Xu Y
AU  - Johnson SL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01084-14.

PMID- 25212618
VI  - 2
DP  - 2014
TI  - Genome sequencing of 15 clinical Vibrio isolates, including 13 non-o1/non-o139 serogroup strains.
PG  - e00893-14
AB  - We present draft genome sequences of 15 clinical Vibrio isolates of various serogroups. These
      are valuable data for use in studying Vibrio cholerae genetic
      diversity, epidemic potential, and strain attribution.
AU  - Bishop-Lilly KA
AU  - Johnson SL
AU  - Verratti K
AU  - Luu T
AU  - Khiani A
AU  - Awosika J
AU  - Mokashi VP
AU  - Chain PS
AU  - Sozhamannan S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00893-14.

PMID- 17148461
VI  - 282
DP  - 2007
TI  - A mutation in the Mod subunit of EcoP15I restriction enzyme converts the DNA methyltransferase to a site-specific endonuclease.
PG  - 3520-3530
AB  - A closer inspection of the amino acid sequence of EcoP15I DNA methyltransferase revealed a
      region of similarity to the PDXn(D/E)XK
      catalytic site of type II restriction endonucleases, except for methionine
      in EcoP15I DNA methyltransferase instead of proline. Substitution of
      methionine at position 357 by proline converts EcoP15I DNA
      methyltransferase to a site-specific endonuclease. EcoP15I-M357P DNA
      methyltransferase specifically binds to the recognition sequence
      5'-CAGCAG-3' and cleaves DNA asymmetrically EcoP151-M357P.DNA
      methyltransferase specifically binds to the recognition sequence
      5'-CAGCAG-3' and cleaves DNA asymmetrically, 5'-CAGCAG(N)(10)-3', as
      indicated by the arrows, in presence of magnesium ions.
AU  - Bist P
AU  - Madhusoodanan UK
AU  - Rao DN
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2007 282: 3520-3530.

PMID- 12917398
VI  - 278
DP  - 2003
TI  - Identification and mutational analysis of Mg2+ binding site in EcoP15I DNA methyltransferase: involvement in target base eversion.
PG  - 41837-41848
AB  - EcoP15I DNA methyltransferase catalyzes the transfer of the methyl group of
      S-adenosyl-l-methionine to the N6 position of the second adenine within
      the double-stranded DNA sequence 5'-CAGCAG-3'. To achieve catalysis, the
      enzyme requires a magnesium ion. Binding of magnesium to the enzyme
      induces significant conformational changes as monitored by circular
      dichroism spectroscopy. EcoP15I DNA methyltransferase was rapidly
      inactivated by micromolar concentrations of ferrous sulfate in the
      presence of ascorbate at pH 8.0. The inactivated enzyme was cleaved into
      two fragments with molecular masses of 36 and 35 kDa. Using this affinity
      cleavage assay, we have located the magnesium binding-like motif to amino
      acids 355-377 of EcoP15I DNA methyltransferase. Sequence homology
      comparisons between EcoP15I DNA methyltransferase and other restriction
      endonucleases allowed us to identify a PD(X)n(D/E)XK-like sequence as the
      putative magnesium ion binding site. Point mutations generated in this
      region were analyzed for their role in methyltransferase activity, metal
      coordination, and substrate binding. Although the mutant
      methyltransferases bind DNA and S-adenosyl-l-methionine as well as the
      wild-type enzyme does, they are inactive primarily because of their
      inability to flip the target base. Collectively, these data are consistent
      with the fact that acidic amino acid residues of the region 355-377 in
      EcoP15I DNA methyltransferase are important for the critical positioning
      of magnesium ions for catalysis. This is the first example of
      metal-dependent function of a DNA methyltransferase. These findings
      provide impetus for exploring the role(s) of metal ions in the structure
      and function of DNA methyltransferases.
AU  - Bist P
AU  - Rao DN
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2003 278: 41837-41848.

PMID- 11419939
VI  - 310
DP  - 2001
TI  - S-adenosyl-L-methionine is required for DNA cleavage by type III restriction enzymes.
PG  - 93-109
AB  - The requirement of S-adenosyl-L-methionine (AdoMet) in the cleavage reaction carried out by
      type III restriction-modification enzymes has
      been investigated. We show that DNA restriction by EcoPI restriction
      enzyme does not take place in the absence of exogenously added AdoMet.
      Interestingly, the closely related EcoP15I enzyme has endogenously
      bound AdoMet and therefore does not require the addition of the
      cofactor for DNA cleavage. By employing a variety of AdoMet analogs,
      which differ structurally from AdoMet, this study demonstrates that the
      carboxyl group and any substitution at the epsilon carbon of methionine
      is absolutely essential for DNA cleavage. Such analogs could bring
      about the necessary conformational change(s) in the enzyme, which make
      the enzyme proficient in DNA cleavage. Our studies, which include
      native polyacrylamide gel electrophoresis, molecular size exclusion
      chromatography, UV, fluorescence and circular dichroism spectroscopy,
      clearly demonstrate that the holoenzyme and apoenzyme forms of EcoP15I
      restriction enzyme have different conformations. Furthermore, the Res
      and Mod subunits of the EcoP15I restriction enzyme can be separated by
      gel filtration chromatography in the presence of 2 M NaCl.
      Reconstitution experiments, which involve mixing of the isolated
      subunits, result in an apoenzyme form, which is restriction proficient
      in the presence of AdoMet. However, mixing the Res subunit with Mod
      subunit deficient in AdoMet binding does not result in a functional
      restriction enzyme. These observations are consistent with the fact
      that AdoMet is required for DNA cleavage. In vivo complementation of
      the defective mod allele with a wild-type mod allele showed that an
      active restriction enzyme could be formed. Furthermore, we show that
      while the purified c2-134 mutant restriction enzyme is unable to cleave
      DNA, the c2-440 mutant enzyme is able to cleave DNA albeit poorly.
      Taken together, these results suggest that AdoMet binding causes
      conformational changes in the restriction enzyme and is necessary to
      bring about DNA cleavage.
AU  - Bist P
AU  - Sistla S
AU  - Krishnamurthy V
AU  - Acharya A
AU  - Chandrakala B
AU  - Rao DN
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2001 310: 93-109.

PMID- 29326212
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Thermoanaerobacterium sp. Strain RBIITD, a Butyrate-  and Butanol-Producing Thermophile.
PG  - e01411-17
AB  - Thermoanaerobacterium sp. strain RBIITD was isolated from contaminated rich growth medium at
      55 degrees C in an anaerobic chamber. It primarily produces
      butyrate as a fermentation product from plant biomass-derived sugars. The
      whole-genome sequence of the strain is 3.4 Mbp, with 3,444 genes and 32.48% GC
      content.
AU  - Biswas R
AU  - Huntemann M
AU  - Clum A
AU  - Pillay M
AU  - Palaniappan K
AU  - Varghese N
AU  - Mikhailova N
AU  - Stamatis D
AU  - Reddy TBK
AU  - Daum C
AU  - Shapiro N
AU  - Ivanova N
AU  - Kyrpides NC
AU  - Woyke T
AU  - Guss AM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01411-17.

PMID- 26227599
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Five Clinical Methicillin-Resistant Staphylococcus aureus Isolates and a Methicillin-Resistant Staphylococcus epidermidis Isolate.
PG  - e00836-15
AB  - We report the complete draft genome sequences of five individually isolated strains of
      methicillin-resistant Staphylococcus aureus (MRSA) and a
      Staphylococcus epidermidis strain. These clinically important isolates have
      staphylococcal cassette chromosome mec type A, while Panton-Valentine leukocidin
      (PVL) toxin coding genes were present in MRSA isolates only.
AU  - Biswas RK
AU  - Kock MM
AU  - Adelowotan T
AU  - Strasheim W
AU  - Mahomed TG
AU  - Salawu A
AU  - Ehlers MM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00836-15.

PMID- 27811096
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Lactobacillus rhamnosus Strain LRB.
PG  - e01208-16
AB  - Lactobacillus rhamnosus is a Gram-positive facultative heterofermentative lactic  acid
      bacterium. It is often isolated from the gastrointestinal tract, mouth,
      vagina, and fermented dairy products. We have isolated the L. rhamnosus strain
      LRB from a healthy baby tooth that had naturally fallen out. Here, we report the
      annotated whole-genome sequence of LRB.
AU  - Biswas S
AU  - Biswas I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01208-16.

PMID- 22887682
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Streptococcus mutans GS-5, a Serotype c Strain.
PG  - 4787-4788
AB  - Streptococcus mutans, a principal causative agent of dental caries, is considered to be the
      most cariogenic among all oral streptococci. Of the four S. mutans
      serotypes (c, e, f, and k), serotype c strains predominate in the oral cavity.
      Here, we present the complete genome sequence of S. mutans GS-5, a serotype c
      strain originally isolated from human carious lesions, which is extensively used
      as a laboratory strain worldwide.
AU  - Biswas S
AU  - Biswas I
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4787-4788.

PMID- 1923776
VI  - 19
DP  - 1991
TI  - Esp3I - a novel type IIs restriction endonuclease from Hafnia alvei that recognizes the sequence 5'-CGTCTC(N)1/5-3' .
PG  - 5076
AB  - A new type IIs restriction endonuclease, Esp3I, has been isolated from Hafnia
      alvei RFL3*.  Esp3I recognizes the non-palindromic sequence 5'-CGTCTC-3' and
      cleaves DNA one nucleotide to the right from the noted recognition strand.
AU  - Bitinaite J
AU  - Grigaite R
AU  - Maneliene Z
AU  - Butkus V
AU  - Janulaitis A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 5076.

PMID- 1408816
VI  - 20
DP  - 1992
TI  - Alw26I, Eco31I and Esp3I - type IIs methyltransferases modifying cytosine and adenine in complementary strands of the target DNA.
PG  - 4981-4985
AB  - *The specificity of three DNA methyltransferases M.Alw261, M.Eco31I and M.Esp3I,

      isolated from Acinetobacter lwoffi RFL26, Escherichia coli RFL31 and Hafnia

      alvei RFL3+, respectively, was determined. All the enzymes methylate both

      strands of asymmetric recognition sites yielding m5C in the top-strand and

      m6A in the bottom-strand, as below: 

      

         5'-GTm5CTC      5'-GGTm5CTC     5'-CGTm5CTC 

         3'-Cm6AGAG      3'-CCm6AGAG     3'-GCm6AGAG

         (M.Alw26I)      (M.Eco31I)      (M.Esp3I)

      are the first members of type IIs methyltransferases that modify different

      types of nucleotides in the recognition sequence.

      

AU  - Bitinaite J
AU  - Maneliene Z
AU  - Menkevicius S
AU  - Klimasauskas S
AU  - Butkus V
AU  - Janulaitis A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 4981-4985.

PMID- 12172806
VI  - 267
DP  - 2002
TI  - Evolutionary relationship of Alw261, Eco31I and Esp3I, restriction endonucleases that recognise overlapping sequences.
PG  - 664-672
AB  - Type II restriction endonucleases (ENases) have served as models for understanding the
      enzyme-based site-specific cleavage of DNA. Using the
      knowledge gained from the available crystal structures, a number of
      attempts have been made to alter the specificity of ENases by
      mutagenesis. The negative results of these experiments argue that the
      three-dimensional structure of DNA-ENase complexes does not provide
      enough information to enable us to understand the interactions between
      DNA and ENases in detail. This conclusion calls for alternative
      approaches to the study of structure-function relationships related to
      the specificity of ENases. Comparative analysis of ENases that manifest
      divergent substrate specificities, but at the same time are
      evolutionarily related to each other, may be helpful in this respect.
      The success of such studies depends to a great extent on the
      availability of related ENases that recognise partially overlapping
      nucleotide sequences (e.g. sets of enzymes that bind to recognition
      sites of increasing length). In this study we report the cloning and
      sequence analysis of genes for three Type I IS restriction-modification
      (RM) systems. The genes encoding the ENases Alw26I, Eco31I and Esp3I
      (whose recognition sequences are 5'-GTCTC-3', 5'-GGTCTC-3' and
      5'-CGTCTC-3'. respectively) and their accompanying methyltransferases
      (MTases) have been cloned and the deduced amino acid sequences of their
      products have been compared. In pairwise comparisons, the degree of
      sequence identity between Alw261, Eco31I and Esp3I ENases is higher
      than that observed hitherto among ENases that recognise partially
      overlapping nucleotide sequences. The sequences of Alw26I, Eco31I and
      Esp3I also reveal identical mosaic patterns of sequence conservation,
      which supports the idea that they are evolutionarily related and
      suggests that they should show a high level of structural similarity.
      Thus these ENases represent very attractive models for the study of the
      molecular basis of variation in the specific recognition of DNA
      targets. The corresponding MTases are represented by proteins of
      unusual structural and functional organisation. Both M.Alw26I and
      M.Esp3I are represented by a single bifunctional protein, which is
      composed of an m6A-MTase domain fused to aN m5C-MTase domain. In
      contrast, two separate genes encode the m6A-MTase and m5C-MTase in
      the Eco31I RM system. Among the known bacterial m5C-MTases, the m5C-MTases of M.Alw26I,
      M.Eco31I and M.Esp3I represent unique examples of
      the circular permutation of their putative target recognition domains
      together with the conserved motifs IX and X.
AU  - Bitinaite J
AU  - Mitkaite G
AU  - Dauksaite V
AU  - Jakubauskas A
AU  - Timinskas A
AU  - Vaisvila R
AU  - Lubys A
AU  - Janulaitis A
PT  - Journal Article
TA  - Mol. Genet. Genomics
JT  - Mol. Genet. Genomics
SO  - Mol. Genet. Genomics 2002 267: 664-672.

PMID- 11818524
VI  - 99
DP  - 2002
TI  - Self-generated DNA termini relax the specificity of SgrAI restriction endonuclease.
PG  - 1164-1169
AB  - The primary target of SgrAI restriction endonuclease is a multiple sequence of the form
      5'-Cpu^CCGGPyG. Previous work had indicated that SgrAI must bind two recognition sites
      simultaneously for catalysis [Bilcock, D. T., Daniels, L. E., Bath, A. J. & Halford, S. E.
      (1999) J. Biol. Chem. 274, 36379-36386]. In the present study, SgrAI is shown to cleave not
      only its canonical sequences, but also the sequences 5'-CPuCCGGPy(A,T,C) and 5'-CPuCCGGGG,
      both referred to as secondary sequences. On plasmid pSK7, SgrAI cleaves secondary sites
      26-fold slower than the canonical site. However, the same plasmid, but without the canonical
      site, is cleaved 200-fold slower. We show that DNA termini generated by cleaving the canonical
      site for SgrAI assist in the cleavage of secondary sites. The SgrAI-termini in cis with
      respect to secondary site are markedly preferred over those in trans. The SgrAI-termini
      provided in a form of oligonucleotide duplex are also shown to stimulate canonical site
      cleavage. At a 40-fold molar excess of the SgrAI-termini over substrate, the SgrAI specificity
      is shown to improve by two orders of magnitude, because of concurrent 10-fold increase in the
      cleavage of canonical site and 50-fold decrease in the cleavage of secondary sites. The
      unconventional reaction pathway by which SgrAI utilizes the self-generated DNA termini to
      cleave its DNA targets has not been observed hitherto among type II restriction endonucleases.
      Based on our work and previous reports, a pathway of DNA binding and cleavage by the SgrAI
      restriction endonuclease is proposed.
AU  - Bitinaite J
AU  - Schildkraut I
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2002 99: 1164-1169.

PMID- 9724744
VI  - 95
DP  - 1998
TI  - FokI dimerization is required for DNA cleavage.
PG  - 10570-10575
AB  - FokI is a type IIs restriction endonuclease comprised of a DNA recognition domain and a
      catalytic domain.  The structural similarity of the FokI catalytic domain to the type II
      restriction endonuclease BamHI monomer suggested that the FokI catalytic domains may dimerize.
      In addition, the FokI structure, presented in an accompanying paper in this issue of
      Proceedings, reveals a dimerization interface between catalytic domains.  We provide evidence
      here that FokI catalytic domain must dimerize for DNA cleavage to occur.  First, we show that
      the rate of DNA cleavage catalyzed by various concentrations of FokI are not directly
      proportional to the protein concentration, suggesting a cooperative effect for DNA cleavage.
      Second, we constructed a FokI variant, FokN13Y, which is unable to bind the FokI recognition
      sequence but when mixed with wild-type FokI increases the rate of DNA cleavage.  Additionally,
      the FokI catalytic domain that lacks the DNA binding domain was shown to increase the rate of
      wild-type FokI cleavage of DNA.  We also constructed an FokI variant, FokD483A, R487A, which
      should be defective for dimerization because the altered residues reside at the putative
      dimerization interface.  Consistent with the FokI dimerization model, the variant FokD483A,
      R487A revealed greatly impaired DNA cleavage.  Based on our work and previous reports, we
      discuss a pathway of DNA binding, dimerization, and cleavage by FokI endonuclease.
AU  - Bitinaite J
AU  - Wah DA
AU  - Aggarwal AK
AU  - Schildkraut I
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1998 95: 10570-10575.

PMID- 2984047
VI  - 182
DP  - 1985
TI  - Characterization of restriction-modification enzymes Cfr13I from Citrobacter freundii RFL13.
PG  - 509-513
AB  - This communication describes some properties of R.Cfr13I and M.Cfr13I, isolated from
      Citrobacter freundii RFL13. R.Cfr13I restriction enzyme recognizes the 5'-G^GNCC sequence and
      cleaves, as indicated by the arrow. M.Cfr13I methylase modifies the internal cytosine
      producing m5C (5'-GGNm5CC). R.Cfr13I is sensitive not only to this type of substrate
      modification but also to hemimethylation in overlapping sites by M.Cfr10I (internal cytosine
      of R.Cfr13I recognition is methylated) and M.HpaII (external cytosine is methylated). From
      these results the sensitivity of R.Cfr13I to methylation by dcm methylase of E.coli in
      overlapping sites is deduced.
AU  - Bitinaite JB
AU  - Klimasauskas SJ
AU  - Butkus VV
AU  - Janulaitis A
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1985 182: 509-513.

PMID- 26380635
VI  - 10
DP  - 2015
TI  - Non contiguous-finished genome sequence and description of Bacillus jeddahensis sp. nov.
PG  - 47
AB  - Strain JCE(T) was isolated from the fecal sample of a 24-year-old obese man living in Jeddah,
      Saudi Arabia. It is an aerobic, Gram-positive, rod-shaped bacterium. This strain exhibits a
      16S rRNA nucleotide sequence similarity of 97.5 % with Bacillus niacini, the phylogenetically
      closest species with standing nomenclature. Moreover, the strain JCE(T) presents many
      phenotypic differences, when it is compared to other Bacillus species, and shows a low
      MALDI-TOF Mass Spectrometry score that does not allow any identification. Thus, it is likely
      that this strain represents a new species. Here we describe the features of this  organism,
      together with the complete genome sequence and annotation. The 4,762,944 bp long genome (1
      chromosome but no plasmid) contains 4,654 protein-coding and 98 RNAs genes, including 92 tRNA
      genes. The strain JCE(T) differs from most of the other closely Bacillus species by more than
      1 % in G + C content. In addition, digital DNA-DNA hybridization values for the genome of the
      strain JCE(T) against the closest Bacillus genomes range between 19.5 to 28.1, that confirming
      again its new species status. On the basis of these polyphasic data made of phenotypic and
      genomic analyses, we propose the creation of Bacillus jeddahensis sp. nov. that contains the
      strain JCE(T).
AU  - Bittar F
AU  - Bibi F
AU  - Ramasamy D
AU  - Lagier JC
AU  - Azhar EI
AU  - Jiman-Fatani AA
AU  - Al-Ghamdi AK
AU  - Nguyen TT
AU  - Yasir M
AU  - Fournier PE
AU  - Raoult D
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 47.

PMID- 24578271
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Pedobacter sp. Strain V48, Isolated from a Coastal Sand  Dune in the Netherlands.
PG  - e00094-14
AB  - Pedobacter sp. strain V48 participates in an interaction with Pseudomonas fluorescens which
      elicits interaction-induced phenotypes. We report the draft
      genome sequence of Pedobacter sp. V48, consisting of 6.46 Mbp. The sequence will
      contribute to improved understanding of the genus and facilitate genomic analysis
      of the model interspecies interaction with P. fluorescens.
AU  - Bitzer AS
AU  - Garbeva P
AU  - Silby MW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00094-14.

PMID- 25197453
VI  - 9
DP  - 2014
TI  - High quality draft genome sequence of Streptomyces sp. strain AW19M42 isolated from a sea squirt in Northern Norway.
PG  - 676-686
AB  - Here we report the 8 Mb high quality draft genome of Streptomyces sp. strain AW19M42, together
      with specific properties of the organism and the generation,
      annotation and analysis of its genome sequence. The genome encodes 7,727 putative
      open reading frames, of which 6,400 could be assigned with COG categories. Also,
      62 tRNA genes and 8 rRNA operons were identified. The genome harbors several gene
      clusters involved in the production of secondary metabolites. Functional
      screening of the isolate was positive for several enzymatic activities, and some
      candidate genes coding for those activities are listed in this report. We find
      that this isolate shows biotechnological potential and is an interesting target
      for bioprospecting.
AU  - Bjerga GE
AU  - Hjerde E
AU  - De Santi C
AU  - Williamson AK
AU  - Smalas AO
AU  - Willassen NP
AU  - Altermark B
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 676-686.

PMID- 12105196
VI  - 277
DP  - 2002
TI  - Colonization of germ-free transgenic mice with genotyped Helicobacter pylori strains from a case-control study of gastric cancer reveals a  correlation between host responses and HsdS components of type I  restriction-modification systems.
PG  - 34191-34197
AB  - Helicobacter pylori infects the stomachs of half of all humans. It has a relatively benign
      relationship with most hosts but produces severe
      pathology, including gastric cancer, in others. Identifying the relative
      contributions of host, microbial, and environmental factors to the outcome
      of infection has been challenging. Here we describe one approach for
      identifying microbial genes that affect the magnitude of host responses to
      infection. Single colony purified H. pylori isolates were obtained from 25
      cases and 71 controls in a Swedish case-control study of gastric cancer.
      Strains were first phenotyped based on their ability to produce adhesins
      that recognize two classes of human gastric epithelial receptors. Thirteen
      binding strains and two non-binding controls were then subjected to whole
      genome genotyping using H. pylori DNA microarrays. A cohort of "variable"
      genes was identified based on a microarray-determined call of "absent" in
      at least one member of the strain panel. Each strain was subsequently
      introduced into two types of germ-free transgenic mice, each programmed to
      express a different host factor postulated to pose increased risk for
      development of severe pathology. Expression of biomarkers of host defense
      was quantitated 4 weeks after inoculation, and the magnitude of the
      response correlated with bacterial genotype. The proportion of genes
      encoding HsdS homologs (specificity subunit of heterooligomeric type I
      restriction-modification systems) was significantly higher in the pool of
      18 variable genes whose presence directly correlated with a robust host
      response than their proportion in the remaining 352 members of the
      variable gene pool. This suggests that the functions of these HsdS
      homologs may include control of expression of microbial determinants that
      affect the extent of gastric responses to this potentially virulent
      pathogen.
AU  - Bjorkholm BM
AU  - Guruge JL
AU  - Oh JD
AU  - Syder AJ
AU  - Salama N
AU  - Guillemin K
AU  - Falkow S
AU  - Nilsson C
AU  - Falk PG
AU  - Engstrand L
AU  - Gordon JI
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2002 277: 34191-34197.

PMID- 27635011
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Histamine-Producing Morganella psychrotolerans Strains.
PG  - e01001-16
AB  - Histamine-producing bacteria are responsible for scombrotoxin (histamine) fish poisoning, a
      leading cause of fish poisoning in the United States. We report here
      the first draft genomes of three histamine-producing Morganella psychrotolerans
      strains, isolated from tuna and mahi-mahi.
AU  - Bjornsdottir-Butler K
AU  - Leon MS
AU  - Benner RA Jr
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01001-16.

PMID- 25931609
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Histamine-Producing Photobacterium kishitanii and Photobacterium angustum, Isolated from Albacore (Thunnus alalunga) and Yellowfin   (Thunnus albacares) Tuna.
PG  - e00400-15
AB  - Histamine-producing bacteria are responsible for scombrotoxin (histamine) fish poisoning, a
      leading cause of fish poisoning in the United States. We report here
      the draft genome sequences of four histamine-producing (HP) Photobacterium
      kishitanii strains and nine HP Photobacterium angustum strains isolated from
      tuna.
AU  - Bjornsdottir-Butler K
AU  - McCarthy SA
AU  - Dunlap PV
AU  - Timme RE
AU  - Benner RA Jr
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00400-15.

PMID- 27660786
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Histamine- and Non-Histamine-Producing Photobacterium Strains.
PG  - e01008-16
AB  - Histamine-producing bacteria (HPBs) have recently been identified from the marine environment.
      The identification and characterization of HPBs is important to
      developing effective mitigation strategies for scombrotoxin fish poisoning. We
      report here the draft genomes of seven histamine-producing and two
      non-histamine-producing marine Photobacterium strains.
AU  - Bjornsdottir-Butler K
AU  - Sanchez LM
AU  - Dunlap PV
AU  - Benner RA Jr
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01008-16.

PMID- 16677300
VI  - 60
DP  - 2006
TI  - Control of the endonuclease activity of type I restriction-modification systems is required to maintain chromosome integrity following  homologous recombination.
PG  - 883-893
AB  - A type I restriction-modification enzyme will bind to an unmethylated target sequence in DNA
      and, while still bound to the target,
      translocate DNA through the protein complex in both directions. DNA
      breakage occurs when two translocating complexes collide. However, if
      type I restriction-modification systems bind to unmodified target
      sequences within the resident bacterial chromosome, as opposed to
      incoming 'foreign' DNA, their activity is curtailed; a process known as
      restriction alleviation (RA). We have identified two genes in
      Escherichia coli, rnhA and recG, mutations in which lead to the
      alleviation of restriction. Induction of RA in response to these
      mutations is consistent with the production of unmodified target
      sequences following DNA synthesis associated with both homologous
      recombination and R-loop formation. This implies that a normal function
      of RA is to protect the bacterial chromosome when recombination
      generates unmodified products. For EcoKI, our experiments demonstrate
      the contribution of two pathways that serve to protect unmodified DNA
      in the bacterial chromosome: the primary pathway in which ClpXP
      degrades the restriction endonucleas and a mechanism dependent on the
      lar gene within Rac, a resident, defective prophage of E. coli K-12.
      Previously, the potential of the second pathway has only been
      demonstrated when expression of lar has been elevated. Our data
      identify the effect of lar from the repressed prophage.
AU  - Blakely GW
AU  - Murray NE
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2006 60: 883-893.

PMID- 2851535
VI  - 5
DP  - 1987
TI  - Restriction endonuclease:  cleavage, ligation, and sensitivity.
PG  - 51-102
AB  - Restriction endonucleases are important tools for the molecular biologist.
      These enzymes are routinely used to subdivide DNA molecules in a very specific,
      predictable fashion, allowing one to isolate certain regions for study.  DNA
      sequencing, cloning, mapping, hybridization, and genome characterization are
      some of the more common procedures incorporating restriction endonuclease
      treated DNA.  The characteristics of the restriction endonucleases and their
      reactions have been reviewed.  A comprehensive listing of the enzymes and the
      diversity of microbiological sources appears in this volume.  Informative
      tables on some characteristics of restriction endonucleases have appeared
      elsewhere.  Tabulated in this chapter are a number of facts frequently used
      when planning experiments that utilize restriction endonucleases.  The final
      table summarizes a number of general characteristics of the enzyme which should
      be valuable when designing complex strategies or trouble-shooting unexpected
      results.
AU  - Blakesley RW
PT  - Journal Article
TA  - Gene Amplif. Anal.
JT  - Gene Amplif. Anal.
SO  - Gene Amplif. Anal. 1987 5: 51-102.

PMID- 6101043
VI  - 1
DP  - 1981
TI  - Restriction endonuclease: specificities, diversities and computer analysis.
PG  - 1-43
AB  - I. Introduction II. Table I: DNA cleavage frequency for restriction
      endonucleases with known recognition sequences III. Table II: DNA cleavage
      frequency for restriction endonucleases with undetermined recognition sequences
      IV. Table III: Microorganisms as sources for restriction endonucleases V. Table
      IV: Reaction conditions for certain restriction endonucleases VI. Table V:
      Restriction endonuclease cross reference: Tables I-IV, references VII. Table
      VI: Restriction endonuclease site combinations for ligation.
AU  - Blakesley RW
PT  - Journal Article
TA  - Gene Amplif. Anal.
JT  - Gene Amplif. Anal.
SO  - Gene Amplif. Anal. 1981 1: 1-43.

PMID- 71298
VI  - 252
DP  - 1977
TI  - Duplex regions in "single-stranded" PhiX174 DNA are cleaved by a restriction endonuclease from Haemophilus aegyptius.
PG  - 7300-7306
AB  - DNA from bacteriophage PhiX174 is cleaved by several DNA restriction
      endonucleases.  We wish to determine whether or not the recognition sites are
      within duplex regions in this single-stranded DNA.  We report here the
      influence of two perturbants of duplex DNA structure, temperature and
      actinomycin, on the cleavage of PhiX174 (single-stranded, circular) DNA and its
      double-stranded, replicative form (RF DNA) by the restriction endonuclease,
      HaeIII.  The conditions for optimal rates of cleavage for the (+)-strand and RF
      DNA's by HaeIII were virtually identical (25 mM Tris/HCl, pH 7.5; 5 mM MgCl2;
      30 mM NaCl).  At 37C, RF DNA was cleaved 16 times faster than (+)-strand DNA.
      When the initial rates of reaction for both DNA's were measured as a function
      of temperature of incubation, the maximum rates occurred at 72C and 47C for the
      RF and (+)-strand DNA's, respectively.  At 10-15C above the respective maxima,
      the rates fell to zero.  Near the temperature optima, a preferential
      disappearance of certain fragments with temperature occurred with (+)-strand,
      but not with RF DNA.  These results indicate that the HaeIII restriction sites
      in PhiX174 (+)-strand DNA are located in several different, noncontiguous,
      duplex regions with different sequence-dependent tM values.  The rate of
      cleavage of each DNA was also inhibited by actinomycin; 50% inhibition occurred
      at a molar ratio (actinomycin/nucleotide) of 1.2 for RF and 0.04 for (+)-strand
      DNA.  Netropson, which, like actinomycin binds only to duplex DNA, inhibited
      the cleavage of both DNA's.  The restriction endonuclease HhaI, gave results
      similar to those found for HaeIII.  RF DNA was cleaved once by the restriction
      endonuclease, PstI; (+)-strand DNA was not cleaved.  This result for (+)-strand
      would be expected if intramolecular base-pairing were required for cleavage.
      RF and (+)-strand DNA's were also cleaved by MboI and HinfI.  Neither DNA was
      cleaved by BamHI, SmaI, or SalI.  These results indicate that certain DNA
      restriction endonucleases cleave "single-stranded" viral DNA's at duplex
      regions.
AU  - Blakesley RW
AU  - Dodgson JB
AU  - Nes IF
AU  - Wells RD
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1977 252: 7300-7306.

PMID- 809717
VI  - 257
DP  - 1975
TI  - Single-stranded DNA from PhiX174 and M13 is cleaved by certain restriction endonucleases.
PG  - 421-422
AB  - During a systematic survey of the substrate specificities of a variety of
      restriction endonucleases, it was discovered that the Haemophilus aegyptius
      restriction endonuclease III (HaeIII) specifically cleaved 'single-stranded'
      DNA from PhiX174 and M13.  Since these DNAs are not doubled-stranded and
      restriction enzymes recognize duplex DNA with twofold sequence symmetry, this
      result was unexpected.  This finding is significant with regard to the
      conformation of single-stranded viral DNA as well as the biochemical mechanism
      and physiological role of restriction enzymes.
AU  - Blakesley RW
AU  - Wells RD
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1975 257: 421-422.

PMID- 25183669
VI  - 28
DP  - 2014
TI  - ModM DNA methyltransferase methylome analysis reveals a potential role for Moraxella catarrhalis phasevarions in otitis media.
PG  - 5197-5207
AB  - Moraxella catarrhalis is a significant cause of otitis media and exacerbations of
      chronic obstructive pulmonary disease. Here, we characterize a phase-variable DNA
      methyltransferase (ModM), which contains 5'-CAAC-3' repeats in its open reading
      frame that mediate high-frequency mutation resulting in reversible on/off
      switching of ModM expression. Three modM alleles have been identified (modM1-3),
      with modM2 being the most commonly found allele. Using single-molecule, real-time
      (SMRT) genome sequencing and methylome analysis, we have determined that the
      ModM2 methylation target is 5'-GARm6AC-3', and 100% of these sites are methylated
      in the genome of the M. catarrhalis 25239 ModM2 on strain. Proteomic analysis of
      ModM2 on and off variants revealed that ModM2 regulates expression of multiple
      genes that have potential roles in colonization, infection, and protection
      against host defenses. Investigation of the distribution of modM alleles in a
      panel of M. catarrhalis strains, isolated from the nasopharynx of healthy
      children or middle ear effusions from patients with otitis media, revealed a
      statistically significant association of modM3 with otitis media isolates. The
      modulation of gene expression via the ModM phase-variable regulon (phasevarion),
      and the significant association of the modM3 allele with otitis media, suggests a
      key role for ModM phasevarions in the pathogenesis of this organism.-Blakeway, L.
      V., Power, P. M., Jen, F. E.-C., Worboys, S. R., Boitano, M., Clark, T. A.,
      Korlach, J., Bakaletz, L. O., Jennings, M. P., Peak, I. R., Seib, K. L. ModM DNA
      methyltransferase methylome analysis reveals a potential role for Moraxella
      catarrhalis phasevarions in otitis media.
AU  - Blakeway LV
AU  - Power PM
AU  - Jen FE
AU  - Worboys SR
AU  - Boitano M
AU  - Clark TA
AU  - Korlach J
AU  - Bakaletz LO
AU  - Jennings MP
AU  - Peak IR
AU  - Seib KL
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 2014 28: 5197-5207.

PMID- 9044253
VI  - 23
DP  - 1997
TI  - Identification and analysis of genes from Streptomyces pristinaespiralis encoding enzymes involved in the biosynthesis of the 4-dimethylamino-L-phenylalanine precursor of pristinamycin I.
PG  - 191-202
AB  - Four pap genes (papA, papB, papC, papM) were found by sequencing near to snbA, a Streptomyces
      pristinaespiralis gene which was previously shown to encode one of the pristinamycin I (PI)
      synthetases. Analysis of the homologies observed from the deduced amino acid sequences
      suggested that these four genes could be involved in the biosynthesis of the PI precursor
      4-dimethylamino-L-phenylalanine (DMPAPA). This was first verified when disruption of papA in
      S. pristinaespiralis led to a PI- phenotype, which was reversed by the addition of DMPAPA into
      the culture medium. Further confirmation was obtained when papM was overexpressed in
      Escherichia coli and the corresponding protein purified to homogeneity. It catalysed the two
      successive N-methylation steps of 4-amino-L-phenylalanine leading to DMPAPA via
      4-methylamino-L-phenylalanine. These results allowed us to assign a function to each of the
      four pap genes and to propose a biosynthetic pathway for DMPAPA.
AU  - Blanc V
AU  - Gil P
AU  - Bamas-Jacques N
AU  - Lorenzon S
AU  - Zagorec M
AU  - Schleuniger J
AU  - Bisch D
AU  - Blanche F
AU  - Debussche L
AU  - Crouzet J
AU  - Thibaut D
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1997 23: 191-202.

PMID- Not carried by PubMed...
VI  - 2
DP  - 1995
TI  - Activity of restriction enzymes in a PCR mix.
PG  - 14
AB  - By cutting PCR products with restriction enzymes, the resulting DNA fragments can be cloned
      directionally into vector DNA.  Alternatively, researchers can use this cleavage procedure to
      verify that the DNA of interest has been successfully amplified or even to show a Restriction
      Fragment Length Polymorphism (RFLP) in the amplified fragments.  For maximum convenience, the
      restriction enzyme digest would be performed directly in the PCR mix, without prior
      purification of the amplified fragment.  To investigate which restriction enzymes show
      sufficient activity to be used directly in the PCR mix, we performed an activity test with 50
      selected restriction enzymes.
AU  - Blanck A
AU  - Gluck B
AU  - Wartbichler R
AU  - Bender S
AU  - Poll M
AU  - Brandl A
PT  - Journal Article
TA  - Biochemica
JT  - Biochemica
SO  - Biochemica 1995 2: 14.

PMID- 30284644
VI  - 31
DP  - 2018
TI  - Chromosomal Sil system contributes to silver resistance in E. coli ATCC 8739.
PG  - 1101-1114
AB  - The rise of antibiotic resistance in pathogenic bacteria is endangering the efficacy of
      antibiotics, which consequently results in greater use of silver as a biocide. Chromosomal
      mapping of the Cus system or plasmid encoded Sil system and their relationship with silver
      resistance was studied for several gram-negative bacteria. However, only few reports
      investigated silver detoxification mediated by the Sil system integrated in Escherichia coli
      chromosome. Accordingly, this work aimed to study the Sil system in E. coli ATCC 8739 and to
      produce evidence for its role in silver resistance development. Silver resistance was induced
      in E. coli ATCC 8739 by stepwise passage in culture media containing increasing concentrations
      of AgNO3. The published genome of E. coli ATCC 8739 contains a region showing strong homology
      to the Sil system genes. The role of this region in E. coli ATCC 8739 was assessed by
      monitoring the expression of silC upon silver stress, which resulted in a 350-fold increased
      expression. De novo sequencing of the whole genome of a silver resistant strain derived from
      E. coli ATCC 8739 revealed mutations in ORFs putative for SilR and CusR. The silver resistant
      strain (E. coli AgNO3R) showed constitutive expression of silC which posed a cost of fitness
      resulting in retarded growth. Furthermore, E. coli AgNO3R exhibited cross-resistance to
      ciprofloxacin and a slightly increased tolerance to ampicillin. This study demonstrates that
      E. coli is able to develop resistance to silver, which may pose a threat towards an effective
      use of silver compounds as antiseptics.
AU  - Blanco-Massani M
AU  - Klumpp J
AU  - Widmer M
AU  - Lehmann RP
AU  - Schuppler M
PT  - Journal Article
TA  - Biometals
JT  - Biometals
SO  - Biometals 2018 31: 1101-1114.

PMID- 16790566
VI  - 34
DP  - 2006
TI  - PrrC-anticodon nuclease: functional organization of a prototypical bacterial restriction RNase.
PG  - 3209-3219
AB  - The tRNA(Lys) anticodon nuclease PrrC is associated in latent form with the type Ic DNA
      restriction endonuclease EcoprrI and activated by a phage
      T4-encoded inhibitor of EcoprrI. The activation also requires the
      hydrolysis of GTP and presence of dTTP and is inhibited by ATP. The
      N-proximal NTPase domain of PrrC has been implicated in relaying the
      activating signal to a C-proximal anticodon nuclease site by interacting
      with the requisite nucleotide cofactors [Amitsur et al. (2003) Mol.
      Microbiol., 50, 129-143]. Means described here to bypass PrrC's
      self-limiting translation and thermal instability allowed purifying an
      active mutant form of the protein, demonstrating its oligomeric structure
      and confirming its anticipated interactions with the nucleotide cofactors
      of the activation reaction. Mutagenesis and chemical rescue data shown
      implicate the C-proximal Arg320, Glu324 and, possibly, His356 in anticodon
      nuclease catalysis. This triad exists in all the known PrrC homologs but
      only some of them feature residues needed for tRNA(Lys) recognition by the
      Escherichia coli prototype. The differential conservation and consistent
      genetic linkage of the PrrC proteins with EcoprrI homologs portray them as
      a family of restriction RNases of diverse substrate specificities that are
      mobilized when an associated DNA restriction nuclease is compromised.
AU  - Blanga-Kanfi S
AU  - Amitsur M
AU  - Azem A
AU  - Kaufmann G
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2006 34: 3209-3219.

PMID- 3194200
VI  - 16
DP  - 1988
TI  - An oligodeoxynucleotide affinity column for the isolation of sequence specific DNA binding proteins.
PG  - 10283-10299
AB  - A nucleic acid affinity matrix containing a short oligodeoxynucleotide ligand
      has been prepared as an example of a material which can be used for the rapid
      and effective isolation of sequence specific DNA binding proteins.  Two
      complementary oligodeoxynucleotides have been employed, one of which contains a
      small 5'-spacer arm with a terminal thiol group.  Using this terminal thiol
      group, the ligand can be covalently coupled to Tresyl-activated Sepharose 4B or
      Epoxy-activated Sepharose 6B via a thioether linkage.  This approach allows the
      specific attachment of the nucleic acid ligand via its 5'-terminus to the
      insoluble matrix.  The double stranded affinity material was obtained by
      annealing of the complementary DNA fragment.  As an example, we have used an
      eicosomer affinity column containing the sequence d(GAATTC) for the isolation
      of the EcoRI restriction endonuclease.  Using a single column, the enzyme could
      be isolated by eluting the column with a single step or multistep gradient of
      increasing salt concentration.  The enzyme was purified to 75%-85% homogeneity
      with yields of 0.1 mg to 0.2 mg from 0.5 g of cell paste.
AU  - Blanks R
AU  - McLaughlin LW
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1988 16: 10283-10299.

PMID- 28912312
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Corynebacterium kefirresidentii SB, Isolated from Kefir.
PG  - e00877-17
AB  - The genus Corynebacterium includes Gram-positive species with a high G+C content. We report
      here a novel species, Corynebacterium kefirresidentii SB, isolated from
      kefir grains collected in Germany. Its draft genome sequence was remarkably
      dissimilar (average nucleotide identity, 76.54%) to those of other
      Corynebacterium spp., confirming that this is a unique novel species.
AU  - Blasche S
AU  - Kim Y
AU  - Patil KR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00877-17.

PMID- 27056211
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a Vancomycin-Resistant and Vancomycin-Dependent Enterococcus faecium Isolate.
PG  - e00059-16
AB  - Vancomycin-resistant enterococci have emerged as major nosocomial pathogens worldwide. While
      antimicrobial pressure promotes nosocomial colonization with
      these enterococci, prolonged exposure to vancomycin may foster the transition
      from vancomycin resistance to vancomycin dependence. Here, we report the draft
      genome sequence of a vancomycin-dependentEnterococcus faeciumisolate showing
      partial teicoplanin dependence.
AU  - Blaschitz M
AU  - Lepuschitz S
AU  - Wagner L
AU  - Allerberger F
AU  - Indra A
AU  - Ruppitsch W
AU  - Huhulescu S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00059-16.

PMID- 29326210
VI  - 6
DP  - 2018
TI  - Complete Genome Sequencing of Acinetobacter sp. Strain LoGeW2-3, Isolated from the Pellet of a White Stork, Reveals a Novel Class D Beta-Lactamase Gene.
PG  - e01405-17
AB  - Whole-genome sequencing of Acinetobacter sp. strain LoGeW2-3, isolated from the pellet of a
      white stork (Ciconia ciconia), reveals the presence of a plasmid of
      179,399 bp encoding a CRISPR-Cas (clustered regularly interspaced short
      palindromic repeats and associated genes) system of the I-F type, and the
      chromosomally encoded novel class D beta-lactamase OXA-568.
AU  - Blaschke U
AU  - Skiebe E
AU  - Kaatz M
AU  - Higgins PG
AU  - Pfeifer Y
AU  - Wilharm G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01405-17.

PMID- 28126932
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Acinetobacter sp. Strain NCu2D-2 Isolated from a Mouse.
PG  - e01415-16
AB  - Whole-genome sequencing of Acinetobacter sp. strain NCu2D-2, isolated from the trachea of a
      mouse, revealed the presence of a plasmid of 309,964 bp with little
      overall similarity to known plasmids and enriched in insertion sequences (ISs)
      closely related to IS elements known from the nosocomial pathogen Acinetobacter
      baumannii.
AU  - Blaschke U
AU  - Wilharm G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01415-16.

PMID- 
VI  - 13
DP  - 1998
TI  - Interaction between organophosphorus compounds and DNA assayed by the restriction endonuclease EcoRI.
PG  - 61-67
AB  - Restriction endonucleases due to the nature of their action may provide information on the
      location or the sequence specificity of a compound that binds to DNA.  On the other hand, the
      action of the enzymes may be disturbed by compounds that have an ability to methylate DNA
      bases.  The latter feature can be considered as a simple method for primary selection of
      potentially genotoxic compounds.  In the present work we investigated the action of
      restriction endonuclease EcoRI on DNA which had been incubated with some organophosphorus
      agents.  PUC19 plasmid DNA at a concentration of 78 microgram/ml was incubated for 72 h with
      organophosphorus insecticides parathion, methylparathion and their main metabolites: paraoxon
      and methylparaoxon, respectively, at a concentration of 300 microM.  After incubation
      non-bound insecticides were removed and DNA was subjected to 1 h incubation with the
      restriction endonuclease EcoRI and electrophoresed in 0.8% agarose gel.  The organophosphorus
      compound methylparaoxon evoked unwinding of supercoiled DNA and the action of EcoRI on the DNA
      was disturbed that was displayed in changes in restriction pattern.
AU  - Blasiak J
AU  - Kowalik J
PT  - Journal Article
TA  - Acta Univ. Lodz. Folia Biochim. Biophys.
JT  - Acta Univ. Lodz. Folia Biochim. Biophys.
SO  - Acta Univ. Lodz. Folia Biochim. Biophys. 1998 13: 61-67.

PMID- 
VI  - 120
DP  - 1998
TI  - Distorting duplex DNA by dimethylenesulfone substitution: A new class of "transition state analog" inhibitors for restriction enzymes.
PG  - 2674-2675
AB  - After they bind (but before they cleave) duplex DNA, some restriction enzymes (such as EcoRV
      and EcoRI) distort the duplex.  The distorted duplex is not, of course, in its ground-state
      conformation; it requires "binding energy" to bend DNA.  Thus, an analogue of DNA that
      generates this distortion in the unbound state (without altering other features of the
      substrate that are recognized by the enzyme) should bind to these restriction enzymes with a
      higher affinity than the DNA substrate itself.  This is, of course, the principle underlying
      transition-state analogues generally, which approximate in structure the "distorted"
      transition state (or a distorted high-energy intermediate) for an enzymatic reaction.
AU  - Blattler MO
AU  - Wenz C
AU  - Pingoud A
AU  - Benner SA
PT  - Journal Article
TA  - J. Am. Chem. Soc.
JT  - J. Am. Chem. Soc.
SO  - J. Am. Chem. Soc. 1998 120: 2674-2675.

PMID- 9278503
VI  - 277
DP  - 1997
TI  - The complete genome sequence of Escherichia coli K-12.
PG  - 1453-1462
AB  - The 4,639,221-base pair sequence of Escherichia coli K-12 is presented. Of 4288 protein-coding
      genes annotated, 38 percent have no attributed function.  Comparison with five other sequenced
      microbes reveals ubiquitous as well as narrowly distributed gene families; many families of
      similar genes within E. coli are also evident.  The largest family of paralogous proteins
      contains 80 ABC transporters.  The genome as a whole is strikingly organized with respect to
      the local direction of replication; guanines, oligonucleotides possibly related to replication
      and recombination, and most genes are so oriented.  The genome also contains insertion
      sequence elements, phage remnants, and many other patches of unusual composition indicating
      genome plasticity through horizontal transfer.
AU  - Blattner FR
AU  - Plunkett G III
AU  - Bloch CA
AU  - Perna NT
AU  - Burland V
AU  - Riley M
AU  - Collado-Vides J
AU  - Glasner JD
AU  - Rode CK
AU  - Mayhew GF
AU  - Gregor J
AU  - Davis NW
AU  - Kirkpatrick HA
AU  - Goeden MA
AU  - Rose DJ
AU  - Mau B
AU  - Shao Y
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1997 277: 1453-1462.

PMID- 25502678
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Mannitol-Producing Strain Lactobacillus mucosae CRL573.
PG  - e01292-14
AB  - Lactobacillus mucosae CRL573, isolated from child fecal samples, efficiently converts fructose
      and/or sucrose into the low-calorie sugar mannitol when
      cultured in modified MRS medium at pH 5.0. Also, the strain is capable of
      producing bacteriocin. The draft genome sequence of this strain with potential
      industrial applications is presented here.
AU  - Bleckwedel J
AU  - Teran LC
AU  - Bonacina J
AU  - Saavedra L
AU  - Mozzi F
AU  - Raya RR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01292-14.

PMID- 22408246
VI  - 194
DP  - 2012
TI  - The Complete Genome of Bacillus amyloliquefaciens subsp. plantarum CAU B946 Contains a Gene Cluster for Nonribosomal Synthesis of Iturin A.
PG  - 1845-1846
AB  - The genome of the rhizobacterium Bacillus amyloliquefaciens subsp. plantarum CAU  B946 was
      4.02 Mb in size and harbored 3,823 genes (coding sequences [CDS]). Nine
      giant gene clusters were dedicated to nonribosomal synthesis of antimicrobial
      compounds. Remarkably, strain CAU B946 possessed a gene cluster involved in
      synthesis of iturin A.
AU  - Blom J
AU  - Rueckert C
AU  - Niu B
AU  - Wang Q
AU  - Borriss R
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1845-1846.

PMID- 26251482
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Burkholderia contaminans, a Burkholderia cepacia Complex Species That Is Increasingly Recovered from Cystic Fibrosis Patients.
PG  - e00766-15
AB  - Burkholderia contaminans belongs to the Burkholderia cepacia complex (BCC), a group of
      bacteria that are ubiquitous in the environment and capable of infecting
      the immunocompromised and people with cystic fibrosis. We report here draft
      genome sequences for the B. contaminans type strain LMG 23361 and an Argentinian
      cystic fibrosis sputum isolate.
AU  - Bloodworth RA
AU  - Selin C
AU  - Lopez DeVMA
AU  - Drevinek P
AU  - Galanternik L
AU  - Degrossi J
AU  - Cardona ST
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00766-15.

PMID- 23868131
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences of Two Yersinia pseudotuberculosis ST43 (O:1b) Strains, B-7194 and B-7195.
PG  - e00510-13
AB  - We report the first draft genome sequences of two Yersinia pseudotuberculosis sequence type 43
      (ST43) (O:1b) strains, B-7194 and B-7195, isolated in Russia.
      The total lengths of the assemblies are 4,427,121 bp and 4,608,472 bp, and 3,819
      and 4,018 coding sequences, respectively, were predicted within the genomes.
AU  - Blouin Y
AU  - Platonov ME
AU  - Pourcel C
AU  - Evseeva VV
AU  - Afanas'ev MV
AU  - Balakhonov SV
AU  - Anisimov AP
AU  - Vergnaud G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00510-13.

PMID- 27634990
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the Bactrocera oleae Symbiont 'Candidatus Erwinia dacicola'.
PG  - e00896-16
AB  - 'Candidatus Erwinia dacicola' is a Gammaproteobacterium that forms a symbiotic association
      with the agricultural pest Bactrocera oleae Here, we present a 2.1-Mb
      draft hybrid genome assembly for 'Ca. Erwinia dacicola' generated from
      single-cell and metagenomic data.
AU  - Blow F
AU  - Gioti A
AU  - Starns D
AU  - Ben-Yosef M
AU  - Pasternak Z
AU  - Jurkevitch E
AU  - Vontas J
AU  - Darby AC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00896-16.

PMID- 27660769
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Stenotrophomonas maltophilia SBo1 Isolated from Bactrocera oleae.
PG  - e00905-16
AB  - Bacteria of the genus Stenotrophomonas are ubiquitous in the environment and are  increasingly
      associated with insects. Stenotrophomonas maltophilia SBo1 was
      cultured from the gut of Bactrocera oleae The draft genome sequence presented
      here will inform future investigations into the nature of the interaction between
      insects and their microbiota.
AU  - Blow F
AU  - Vontas J
AU  - Darby AC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00905-16.

PMID- 28473371
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Chryseobacterium Strain CBo1 Isolated from Bactrocera oleae.
PG  - e00177-17
AB  - Bacteria of the genus Chryseobacterium have previously been identified as mutualists of plants
      and insects. Chryseobacterium strain CBo1 was cultured from
      the gut of the agricultural pest Bactrocera oleae and its whole genome sequenced.
      This genomic resource will aid investigations into the transition of microbes
      between plant and invertebrate hosts.
AU  - Blow F
AU  - Vontas J
AU  - Darby AC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00177-17.

PMID- 26870957
VI  - 12
DP  - 2016
TI  - The Epigenomic Landscape of Prokaryotes.
PG  - e1005854
AB  - DNA methylation acts in concert with restriction enzymes to protect the integrity of
      prokaryotic genomes. Studies in a limited number of organisms suggest that
      methylation also contributes to prokaryotic genome regulation, but the prevalence
      and properties of such non-restriction-associated methylation systems remain
      poorly understood. Here, we used single molecule, real-time sequencing to map DNA
      modifications including m6A, m4C, and m5C across the genomes of 230 diverse
      bacterial and archaeal species. We observed DNA methylation in nearly all (93%)
      organisms examined, and identified a total of 834 distinct reproducibly
      methylated motifs. This data enabled annotation of the DNA binding specificities
      of 620 DNA Methyltransferases (MTases), doubling known specificities for
      previously hard to study Type I, IIG and III MTases, and revealing their
      extraordinary diversity. Strikingly, 48% of organisms harbor active Type II
      MTases with no apparent cognate restriction enzyme. These active 'orphan' MTases
      are present in diverse bacterial and archaeal phyla and show motif specificities
      and methylation patterns consistent with functions in gene regulation and DNA
      replication. Our results reveal the pervasive presence of DNA methylation
      throughout the prokaryotic kingdoms, as well as the diversity of sequence
      specificities and potential functions of DNA methylation systems.
AU  - Blow MJ et al
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2016 12: e1005854.

PMID- 7836656
VI  - 29
DP  - 1994
TI  - PCR directed preparation and single step purification of highly active histidine-tagged restriction endonuclease HgiBI (GGWCC).
PG  - 113-121
AB  - The polymerase-chain-reaction technique is used to produce fusion proteins via deletion of any
      intervening piece of DNA. Here a stretch of six histidine codons is fused to the 3'-terminus
      of any defined gene using a standard plasmid vector or a derivative thereof. The advantage
      over existing methods is that no other amino acids besides the six histidines are added to the
      protein terminus and only one oligonucleotide needs to be synthesized as special primer. Genes
      of interest must only be cloned in the correct orientation into a universal multilinker. Using
      just one specific primer derived from the 3'-terminus of the gene and one standard primer
      derived from the six histidine codons the fusion is performed by amplifying the entire vector
      system as described for inverse PCR. As an example, we report on the modification and
      purification of the restriction endonuclease HgiBI (GGWCC). Enzymatically active protein was
      obtained in a single step purification under nondenaturing conditions with a purity greater
      than 95% according to polyacrylamide gel electrophoresis.
AU  - Blum E
AU  - Horst G
AU  - Kroger M
PT  - Journal Article
TA  - J. Biochem. Biophys. Methods
JT  - J. Biochem. Biophys. Methods
SO  - J. Biochem. Biophys. Methods 1994 29: 113-121.

PMID- 7607468
VI  - 157
DP  - 1995
TI  - PCR-directed preparation and single-step purification of highly active histidine-tagged restriction endonuclease HgiBI (GGWCC).
PG  - 107-108
AB  - The polymerase chain reaction was used to produce His6 fusion proteins via deletion of an
      intervening piece of DNA.  The generally applicable method was performed using a standard
      primer with the advantage that the fusion does not produce additional amino acids.  In a
      single-step purification highly purified, enzymatically active restriction endonuclease was
      obtained.
AU  - Blum E
AU  - Horst G
AU  - Kroger M
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 107-108.

PMID- 22740662
VI  - 194
DP  - 2012
TI  - Genome Analysis of Bovine-Mastitis-Associated Escherichia coli O32:H37 Strain P4.
PG  - 3732
AB  - Escherichia coli is a major pathogen of bovine intramammary infections. Here we report the
      first draft of the genome sequence of the E. coli O32:H37 P4 strain,
      which is widely used in experimental bovine mastitis studies.
AU  - Blum S
AU  - Sela N
AU  - Heller ED
AU  - Sela S
AU  - Leitner G
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3732.

PMID- 3333367
VI  - 5
DP  - 1987
TI  - The PvuII restriction-modification system:  cloning, characterization and use in revealing in E. coli barrier to certain methylases or methylated DNAs.
PG  - 227-245
AB  - The physiology of the type II restriction-modification systems (RMS2s) is not
      yet understood in detail.  Relatively few RMS2s have actually been demonstrated
      to carry out the role for which they were named:  restriction of DNA entry into
      the cell through selective endonuclease action.  On the other hand, there are
      numerous examples of DNA methylases, biochemically identical to RMS2 enzymes
      but apparently lacking a cognate endonuclease activity, for which no role has
      yet been discovered.  Our limited knowledge in this area has hindered attempts
      to understand why the genes for certain RMS2s have been difficult to clone and
      express.  Several basic questions remain to be answered regarding the
      regulation of and sequence recognition by RMS2 enzymes.  Also, does the
      methylase of a newly introduced RMS2 have to fully protect the DNA of its new
      host before the endonuclease gene is expressed, or can the cell repair a
      significant amount of endonucleolytic damage?  And what are the effects of a
      foreign DNA methylase on the cell?  We have cloned and characterized the genes
      for the PvuII RMS2 from Proteus vulgaris and, in the course of studies designed
      to examine their regulation, found that the majority of E. coli strains tested
      are poorly transformed by these genes.  We found that this effect is due to the
      PvuII methylase, not to the endonuclease, and that DNAs methyolated by the
      PvuII methylase also transform most tested strains poorly.  Others have found
      this effect with several other DNA methylases, and it has raised new questions
      about gene cloning procedures and about E. coli physiology.
AU  - Blumenthal RM
PT  - Journal Article
TA  - Gene Amplif. Anal.
JT  - Gene Amplif. Anal.
SO  - Gene Amplif. Anal. 1987 5: 227-245.

PMID- Not included in PubMed...
VI  - 4
DP  - 1986
TI  - E. coli can restrict methylated DNA and may skew genomic libraries.
PG  - 302-305
AB  - None
AU  - Blumenthal RM
PT  - Journal Article
TA  - Trends Biotechnol.
JT  - Trends Biotechnol.
SO  - Trends Biotechnol. 1986 4: 302-305.

PMID- Not carried by PubMed...
VI  - 11
DP  - 1989
TI  - Cloning and restriction of methylated DNA in Escherichia coli.
PG  - 41-46
AB  - A review of mcr systems.
AU  - Blumenthal RM
PT  - Journal Article
TA  - BRL Focus
JT  - BRL Focus
SO  - BRL Focus 1989 11: 41-46.

PMID- 11175890
VI  - 8
DP  - 2001
TI  - A Taq attack displaces bases.
PG  - 101-103
AB  - The cocrystal structure of TaqI DNA methyltransferase in complex with its specific DNA
      substrate adds to the growing list of structurally confirmed DNA base-flipping enzymes, and
      provides a basis for the general mechanism of AdoMet-dependent DNA N-methylation.
AU  - Blumenthal RM
AU  - Cheng X
PT  - Journal Article
TA  - Nat. Struct. Biol.
JT  - Nat. Struct. Biol.
SO  - Nat. Struct. Biol. 2001 8: 101-103.

PMID- 2854810
VI  - 74
DP  - 1988
TI  - Isolation of mutants in a DNA methyltransferase through mcr-B-mediated restriction.
PG  - 271-273
AB  - A procedure has been developed that permits the positive selection of mutants
      in a DNA methyltransferase (MTase) gene.  The stringency of this selection can
      be varied so as to yield null mutants only, or a mixture of null and partially
      defective mutants.  The procedure was developed with the PvuII MTase gene
      (pvuIIM), which was subcloned into a bacteriophage Lambda vector.  Growth of
      this lambda pvuIIM construct on an mcrB+ host selected for non-methylating
      mutants, and the stringency of selection was proportional to the number of
      consecutive lytic cycles.  Many cytosine MTases have been found to generate
      substrates for mcrB-mediated restriction, and this procedure should be
      applicable to a number of cytosine MTase genes.
AU  - Blumenthal RM
AU  - Cotterman MM
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 271-273.

PMID- 2997113
VI  - 164
DP  - 1985
TI  - Cloning of a restriction-modification system from Proteus vulgaris and its use in analyzing a methylase-sensitive phenotype in Escherichia coli.
PG  - 501-509
AB  - A 4.84 kilobasepair plasmid was isolated from Proteus vulgaris (ATCC 13315) and
      cloned into the plasmid vector pBR322.  Plasmid pBR322 contains substrate sites
      for the restriction endonucleases PvuI and PvuII.  The recombinant plasmids
      were resistant to in vitro cleavage by PvuII but not PvuI endonuclease and were
      found to cause production of PvuII endonuclease or methylase activity or both
      in Escherichia coli strain HB101.  The approximate endonuclease and methylase
      gene boundaries were determined through subcloning, Bal31 resection,
      insertional inactivation, DNA-dependent translation, and partial DNA
      sequencing.  The two genes are adjacent and appear to be divergently
      transcribed.  Most E. coli strains tested were poorly transformed by the
      recombinant plasmids, and this was shown by subcloning and insertional
      inactivation to be due to the dPvuII methylase gene.  At a low freqency, stable
      methylase-producing transformants of a "methylase-sensitive" strain were
      obtained, and efficiently-transformed cell mutants were isolated from them.
AU  - Blumenthal RM
AU  - Gregory SA
AU  - Cooperider JS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1985 164: 501-509.

PMID- Not carried by PubMed...
VI  - 99
DP  - 1999
TI  - C.PvuII, an unusual transcriptional activator conserved among restriction-modification systems.
PG  - 354
AB  - The pvuII restriction-modification system is a type II system, which means that its
      restriction endonuclease and modification methyltransferase are independently active proteins.
      Because the PvuII genes are carried on a plasmid their expression must be regulated such that
      movement into a new host cell is initially followed by expression of the methyltransferase
      gene alone, so that the new host's DNA is protected before endonuclease activity appears.
      Previous studies have identified a regulatory gene (pvuIIC) between the divergently-oriented
      genes for the restriction endonuclease (pvuIIM), with pvuIIC in the same orientation as and
      partially overlapping pvuIIR.  The product of pvuIIC, C.PvuII, was found to act in trans and
      to be required for expression of pvuIIR.  We have demonstrated that premature expression of
      pvuIIC prevents establishment of the PvuII genes, consistent with the model that requiring
      C.PvuII for pvuIIR expression provides a timing delay essential for protection of the new
      host's DNA.  We find that the opposing pvuIIC and pvuIIM transcripts overlap by over 60
      nucleotides at their 5' ends, raising the possibility that their hybridization might play a
      regulatory role.  We furthermore characterize the action of C.PvuII, demonstrating that it is
      a sequence-specific DNA-binding protein that binds the DNA just upstream of the pvuIIC
      promoter and stimulates transcription of both pvuIIC and pvuIIR into a polycistronic mRNA. The
      location of CoPvuII binding immediately adjacent to the pvuIIC transcriptional stating points
      is highly unusual among transcriptional activators.  Another surprise is that we found no
      evidence for a pvuIIR-specific promoter, leaving open the question of whether the endonuclease
      gene is actually expressed (if at low levels) as early in establishment as the
      methyltransferase gene.  We are exploring the role of predicted hairpins in the mRNA just
      upstream of pvuIIR, one of which would obstruct the Shine-Dalgarno sequence and might be used
      to delay the appearance of endonuclease activity.
AU  - Blumenthal RM
AU  - Vijesurier RM
AU  - Carlock L
AU  - Dunbar JC
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1999 99: 354.

PMID- 21216991
VI  - 193
DP  - 2011
TI  - Complete Genome Sequences for the Anaerobic, Extremely Thermophilic Plant Biomass-Degrading Bacteria Caldicellulosiruptor hydrothermalis,  Caldicellulosiruptor kristjanssonii, Caldicellulosiruptor kronotskyensis,  Caldicellulosiruptor owensensis, and Cal.
PG  - 1483-1484
AB  - The genus Caldicellulosiruptor contains the most thermophilic, plant biomass-degrading
      bacteria isolated to date. Previously, genome sequences
      from three cellulolytic members of this genus were reported (C.
      saccharolyticus, C. bescii, and C. obsidiansis). To further explore the
      physiological and biochemical basis for polysaccharide degradation within
      this genus, five additional genomes were sequenced: C. hydrothermalis, C.
      kristjanssonii, C. kronotskyensis, C. lactoaceticus, and C. owensensis.
      Taken together, the seven completed and one draft-phase
      Caldicellulosiruptor genomes suggest that, while central metabolism is
      highly conserved, significant differences in glycoside hydrolase
      inventories and numbers of carbohydrate transporters exist, a finding
      which likely relates to variability observed in plant biomass degradation
      capacity.
AU  - Blumer-Schuette SE et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 1483-1484.

PMID- 2830135
VI  - 228
DP  - 1988
TI  - Enzymatic sequence-specific spin labeling of a DNA fragment containing the recognition sequence of EcoRI endonuclease.
PG  - 33-36
AB  - Deoxyuridine analogs spin labeled in position 5 have been enzymatically
      incorporated sequence specifically into an oligodeoxyribonucleotide to form a
      spin-labeled 26-mer.  The 26-mer contains the EcoRI-binding site and two labels
      which are located symmetrically close to the binding site.  The labels are
      separated from one another far beyond the Heisenberg spin-exchange distance.
      The local base motion as determined by ESR spectroscopy is of the order of 4 ns
      in the oligonucleotide duplex.  This is the same value as reported earlier for
      local T motions in polynucleotide duplexes, thereby providing direct
      experimental evidence that the ESR line shape of spin levels covalently
      attached to nucleic acids depends primarily on the local dynamics of the
      nucleic acid building blocks.
AU  - Bobst AM
AU  - Pauly GT
AU  - Keyes RS
AU  - Bobst EV
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1988 228: 33-36.

PMID- 19400638
VI  - 48
DP  - 2010
TI  - Xanthomonas AvrBs3 family-type III effectors: discovery and function.
PG  - 419-436
AB  - Xanthomonads are bacterial plant pathogens that cause diseases on many plant species,
      including important crops. Key to pathogenicity of most Xanthomonas
      pathovars is a Hrp-type III secretion (T3S) system that translocates effector
      proteins into plant cells. Within the eukaryotic cell, the effectors are thought
      to perform a variety of tasks to support bacterial virulence, proliferation, and
      dissemination. We are only beginning to understand the host targets of different
      effectors. The largest effector family found in Xanthomonas spp. is the
      AvrBs3/PthA or TAL (transcription activator-like) family. TAL effectors act as
      transcriptional activators in the plant cell nucleus. Specificity of TAL
      effectors is determined by a novel modular DNA-binding domain. Here, we describe
      the discovery of TAL effectors and their structure, activity, and host targets.
AU  - Boch J
AU  - Bonas U
PT  - Journal Article
TA  - Annu. Rev. Phytopathol.
JT  - Annu. Rev. Phytopathol.
SO  - Annu. Rev. Phytopathol. 2010 48: 419-436.

PMID- 22681538
VI  - 113
DP  - 2012
TI  - Bacteriophage adenine methyltransferase: a life cycle regulator? Modelled using Vibrio harveyi myovirus like.
PG  - 1001-1013
AB  - The adenine methyltransferase (DAM) gene methylates GATC sequences that have been demonstrated
      in various bacteria to be a powerful gene
      regulator functioning as an epigenetic switch, particularly with
      virulence gene regulation. However, overproduction of DAM can lead to
      mutations, giving rise to variability that may be important for
      adaptation to environmental change. While most bacterial hosts carry a
      DAM gene, not all bacteriophage carry this gene. Currently, there is no
      literature regarding the role DAM plays in life cycle regulation of
      bacteriophage. Vibriocampbellii strain 642 carries the bacteriophage
      Vibrioharveyi myovirus like (VHML) that has been proven to increase
      virulence. The complete genome sequence of VHML bacteriophage revealed
      a putative adenine methyltransferase gene. Using VHML, a new model of
      phage life cycle regulation, where DAM plays a central role between the
      lysogenic and lytic states, will be hypothesized. In short, DAM
      methylates the rha antirepressor gene and once methylation is removed,
      homologous CI repressor protein becomes repressed and non-functional
      leading to the switching to the lytic cycle. Greater understanding of
      life cycle regulation at the genetic level can, in the future, lead to
      the genesis of chimeric bacteriophage with greater control over their
      life cycle for their safe use as probiotics within the aquaculture
      industry.
AU  - Bochow S
AU  - Elliman J
AU  - Owens L
PT  - Journal Article
TA  - J. Appl. Microbiol.
JT  - J. Appl. Microbiol.
SO  - J. Appl. Microbiol. 2012 113: 1001-1013.

PMID- 27276422
VI  - 24
DP  - 2016
TI  - Indirect DNA Sequence Readout by LAGLIDADG Homing Endonucleases.
PG  - 839-840
AB  - In this issue of Structure, Lambert et al. (2016) describe extensive structural and functional
      work on meganucleases, the group of homing endonucleases most
      commonly adapted to genome engineering applications. The data are of interest to
      structural biologists, evolutionary biologists, protein designers, and genome
      engineers.
AU  - Bochtler M
PT  - Journal Article
TA  - Structure
JT  - Structure
SO  - Structure 2016 24: 839-840.

PMID- 16628220
VI  - 25
DP  - 2006
TI  - Nucleotide flips determine the specificity of the Ecl18kI restriction endonuclease.
PG  - 2219-2229
AB  - Restricion endonuclease Ecl18kI is specific for the sequence /CCNGG and cleaves it before the
      outer C to generate 5 nt 5'-overhangs. It has been suggested that Ecl18kI is evolutionarily
      related to NgoMIV, a 6-bp cutter that cleaves the sequence G/CCGGC and leaves 4 nt
      5'-overhangs. Here, we report the crystal structure of the Ecl18kI-DNA complex at 1.7 A
      resolution and compare it with the known structure of the NgoMIV-DNA complex. We find that
      Ecl18kI flips both central nucleotides within the CCNGG sequence and buries the extruded bases
      in pockets within the protein. Nucleotide flipping disrupts Watson-Crick base pairing, induces
      a kink in the DNA and shifts the DNA register by 1 bp, making the distances between scissile
      phosphates in the Ecl18kI and NgoMIV cocrystal structures nearly identical. Therefore, the two
      enzymes can use a conserved DNA recognition module, yet recognize different sequences, and
      form superimposable dimers, yet generate different cleavage patterns. Hence, Ecl18kI is the
      first example of a restriction endonuclease that flips nucleotides to achieve specificity for
      its recognition site.
AU  - Bochtler M
AU  - Szczepanowski RH
AU  - Tamulaitis G
AU  - Grazulis S
AU  - Czapinska H
AU  - Manakova E
AU  - Siksnys V
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 2006 25: 2219-2229.

PMID- 2020540
VI  - 19
DP  - 1991
TI  - Cloning and characterization of the MboII restriction-modification system.
PG  - 1007-1013
AB  - The two genes encoding the class IIS restriction-modification system MboII from
      Moraxella bovis were cloned separately in two compatible plasmids and expressed
      in E. coli RR1DeltaM15.  The nucleotide sequences of the MboII endonuclease
      (R.MboII) and methylase (M.MboII) genes were determined and the putative start
      codon of R.MboII was confirmed by amino acid sequence analysis.  The mboIIR
      gene specifies a protein of 110 amino acids (MW:48,617) while the mboIIM gene
      codes for a putative 260-residue polypeptide (MW:30,077).  Both genes are
      aligned in the same orientation.  The coding region of the methylase gene ends
      11 bp upstream of the start codon of the restrictase gene.  Comparing the amino
      acid sequence of M.MboII with sequences of other N6 adenine methyltransferases
      reveals a significant homology to M.RsrI, M.HinfI and M.DpnA.  Furthermore,
      M.MboII shows homology to the N4-cytosine methyltransferase BamHI.
AU  - Bocklage H
AU  - Heeger K
AU  - Muller-Hill B
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 1007-1013.

PMID- 24558246
VI  - 2
DP  - 2014
TI  - Whole-Genome Sequence of Ralstonia solanacearum P673, a Strain Capable of Infecting Tomato Plants at Low Temperatures.
PG  - e00106-14
AB  - Ralstonia solanacearum is the causal agent of bacterial wilt, one of the most destructive
      bacterial plant diseases. We present the whole-genome sequence of the
      strain P673 (phylotype IIB, sequevar 4). This strain is capable of producing
      disease in tomato plants at low temperatures. P673 has 311 unique genes.
AU  - Bocsanczy AM
AU  - Huguet-Tapia JC
AU  - Norman DJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00106-14.

PMID- 20033072
VI  - 4
DP  - 2010
TI  - Comparative community genomics in the Dead Sea: an increasingly extreme environment.
PG  - 399-407
AB  - Owing to the extreme salinity ( approximately 10 times saltier than the
      oceans), near toxic magnesium levels (approximately 2.0 M Mg(2+)), the
      dominance of divalent cations, acidic pH (6.0) and high-absorbed radiation
      flux rates, the Dead Sea represents a unique and harsh ecosystem. Measures
      of microbial presence (microscopy, pigments and lipids) indicate that
      during rare bloom events after exceptionally rainy seasons, the microbial
      communities can reach high densities. However, most of the time, when the
      Dead Sea level is declining and halite is precipitating from the water
      column, it is difficult to reliably measure the presence of microorganisms
      and their activities. Although a number of halophilic Archaea have been
      previously isolated from the Dead Sea, polar lipid analyses of biomass
      collected during Dead Sea blooms suggested that these isolates were not
      the major components of the microbial community of these blooms. In this
      study, in an effort to characterize the perennial microbial community of
      the Dead Sea and compare it with bloom assemblages, we performed
      metagenomic analyses of concentrated biomass from hundreds of liters of
      brine and of microbial material from the last massive Dead Sea bloom. The
      difference between the two conditions was reflected in community
      composition and diversity, in which the bloom was different and less
      diverse from the residual brine population. The distributional patterns of
      microbial genes suggested Dead Sea community trends in mono- and divalent
      cation metabolisms as well as in transposable elements. This may indicate
      possible mechanisms and pathways enabling these microbes to survive in
      such a harsh environment.
AU  - Bodaker I
AU  - Sharon I
AU  - Suzuki MT
AU  - Feingersch R
AU  - Shmoish M
AU  - Andreishcheva E
AU  - Sogin ML
AU  - Rosenberg M
AU  - Maguire ME
AU  - Belkin S
AU  - Oren A
AU  - Beja O
PT  - Journal Article
TA  - ISME J.
JT  - ISME J.
SO  - ISME J. 2010 4: 399-407.

PMID- 22123758
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of the Aerobic Marine Methanotroph Methylomonas methanica MC09.
PG  - 7001-7002
AB  - Methylomonas methanica MC09 is a mesophilic, halotolerant, aerobic, methanotrophic member of
      the Gammaproteobacteria, isolated from coastal
      seawater. Here we present the complete genome sequence of this strain, the
      first available from an aerobic marine methanotroph.
AU  - Boden R et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 7001-7002.

PMID- 21478352
VI  - 193
DP  - 2011
TI  - Draft genome sequence of the chemolithoheterotrophic halophilic methylotroph Methylophaga thiooxydans DMS010.
PG  - 3154-3155
AB  - Methylophaga thiooxydans is a mesophilic, obligately halophilic bacterium that is capable of
      methylotrophic growth on a range of one-carbon
      compounds as well as chemolithoheterotrophic growth at the expense of
      thiosulfate. Here we present the draft genome sequence of Methylophaga
      thiooxydans DMS010 (DSM 22068(T), VKM B2586(T)), the type strain of the
      species, which has allowed prediction of the genes involved in one-carbon
      metabolism, nitrogen metabolism and other aspects of central metabolism.
AU  - Boden R
AU  - Ferriera S
AU  - Johnson J
AU  - Kelly DP
AU  - Murrell JC
AU  - Schafer H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3154-3155.

PMID- 27708749
VI  - 11
DP  - 2016
TI  - Permanent draft genome of Thermithiobaclillus tepidarius DSM 3134T, a moderately  thermophilic, obligately chemolithoautotrophic member of the Acidithiobacillia.
PG  - 74
AB  - Thermithiobacillus tepidarius DSM 3134T was originally isolated (1983) from the waters of a
      sulfidic spring entering the Roman Baths (Temple of Sulis-Minerva) at
      Bath, United Kingdom and is an obligate chemolithoautotroph growing at the
      expense of reduced sulfur species. This strain has a genome size of 2,958,498 bp.
      Here we report the genome sequence, annotation and characteristics. The genome
      comprises 2,902 protein coding and 66 RNA coding genes. Genes responsible for the
      transaldolase variant of the Calvin-Benson-Bassham cycle were identified along
      with a biosynthetic horseshoe in lieu of Krebs' cycle sensu stricto. Terminal
      oxidases were identified, viz. cytochrome c oxidase (cbb3, EC 1.9.3.1) and
      ubiquinol oxidase (bd, EC 1.10.3.10). Metalloresistance genes involved in
      pathways of arsenic and cadmium resistance were found. Evidence of horizontal
      gene transfer accounting for 5.9 % of the protein-coding genes was found,
      including transfer from Thiobacillus spp. and Methylococcus capsulatus Bath,
      isolated from the same spring. A sox gene cluster was found, similar in structure
      to those from other Acidithiobacillia - by comparison with Thiobacillus thioparus
      and Paracoccus denitrificans, an additional gene between soxA and soxB was found,
      annotated as a DUF302-family protein of unknown function. As the Kelly-Friedrich
      pathway of thiosulfate oxidation (encoded by sox) is not used in
      Thermithiobacillus spp., the role of the operon (if any) in this species remains
      unknown. We speculate that DUF302 and sox genes may have a role in periplasmic
      trithionate oxidation.
AU  - Boden R
AU  - Hutt LP
AU  - Huntemann M
AU  - Clum A
AU  - Pillay M
AU  - Palaniappan K
AU  - Varghese N
AU  - Mikhailova N
AU  - Stamatis D
AU  - Reddy T
AU  - Ngan CY
AU  - Daum C
AU  - Shapiro N
AU  - Markowitz V
AU  - Ivanova N
AU  - Woyke T
AU  - Kyrpides N
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 74.

PMID- 28057750
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequences and Classification of Streptococcus agalactiae Strains Isolated from Laboratory-Reared Long-Evans Rats (Rattus norvegicus).
PG  - e01435-16
AB  - In collaboration with the CDC's Streptococcus Laboratory, we report here the whole-genome
      sequences of seven Streptococcus agalactiae bacteria isolated from laboratory-reared
      Long-Evans rats. Four of the S. agalactiae isolates were associated with morbidity accompanied
      by endocarditis, metritis, and fatal septicemia, providing an opportunity for comparative
      genomic analysis of this opportunistic pathogen.
AU  - Bodi-Winn C
AU  - Dzink-Fox J
AU  - Feng Y
AU  - Shen Z
AU  - Bakthavatchalu V
AU  - Fox JG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01435-16.

PMID- 27540065
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Stenotrophomonas maltophilia Strains Sm32COP, Sm41DVV,  Sm46PAILV, SmF3, SmF22, SmSOFb1, and SmCVFa1, Isolated from Different Manures in   France.
PG  - e00841-16
AB  - Stenotrophomonas maltophilia is a major opportunistic human pathogen responsible  for
      nosocomial infections. Here, we report the draft genome sequences of Sm32COP,
      Sm41DVV, Sm46PAILV, SmF3, SmF22, SmSOFb1, and SmCVFa1, isolated from different
      manures in France, which provide insights into the genetic determinism of
      intrinsic or acquired antibiotic resistance in this species.
AU  - Bodilis J
AU  - Youenou B
AU  - Briolay J
AU  - Brothier E
AU  - Favre-Bonte S
AU  - Nazaret S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00841-16.

PMID- 6317689
VI  - 258
DP  - 1983
TI  - Effect of nucleotide analogs on the cleavage of DNA by the restriction enzymes AluI, DdeI, HinfI, RsaI, and TaqI.
PG  - 15206-15213
AB  - The cleavage of specific DNA sequences by the restriction endonucleases AluI,
      DdeI, HinfI, RsaI, and TaqI has been studied by monitoring the effect of
      various nucleotide modifications on the rate of DNA digestion.  Bacteriophage
      fd DNA was completely substituted in one strand with a single nucleotide
      analog, using an in vitro primed DNA synthesis reaction on a single-stranded
      viral DNA template.  Twelve deoxynucleotide analogs were incorporated into
      these DNA substrates:  2-aminopurine, 2,6-diaminopurine, deoxytubercidin,
      deoxyuridine, 5-bromodeoxyuridine, 5-allylamine deoxyuridine, 5-biotinyl
      deoxyuridine, deoxypseudouridine, deoxyinosine, 8-azadeoxyguanosine,
      5-iododeoxycytidine, and 5-bromodeoxycytidine.  The restriction enzymes tested
      varied considerably in their ability to digest hemi-substituted DNAs containing
      these modified nucleotides.  Structural alterations in the base pairs
      immediately adjacent to the phosphodiester bonds cleaved by the enzyme reduced
      the rate of enzyme activity most dramatically, and in most cases more than a
      single determinant on each base pair altered activity.  Interactions with
      nucleotides outside the recognition site seem to have little importance in the
      binding or catalytic activity of these enzymes.
AU  - Bodnar JW
AU  - Zempsky W
AU  - Warder D
AU  - Bergson C
AU  - Ward DC
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1983 258: 15206-15213.

PMID- 18203750
VI  - 36
DP  - 2008
TI  - Transcription regulation of the type II restriction-modification system AhdI.
PG  - 1429-1442
AB  - The Restriction-modification system AhdI contains two convergent transcription units, one with
      genes encoding methyltransferase subunits M and S and another with genes encoding the
      controller (C) protein and the restriction endonuclease (R). We show that AhdI transcription
      is controlled by two independent regulatory loops that are well-optimized to ensure successful
      establishment in a naive bacterial host. Transcription from the strong MS promoter is
      attenuated by methylation of an AhdI site overlapping the -10 element of the promoter.
      Transcription from the weak CR promoter is regulated by the C protein interaction with two
      DNA-binding sites. The interaction with the promoter-distal high-affinity site activates
      transcription, while interaction with the weaker promoter-proximal site represses it. Because
      of high levels of cooperativity, both C protein-binding sites are always occupied in the
      absence of RNA polymerase, raising a question how activated transcription is achieved. We
      develop a mathematical model that is in quantitative agreement with the experiment and
      indicates that RNA polymerase outcompetes C protein from the promoter-proximal-binding site.
      Such an unusual mechanism leads to a very inefficient activation of the R gene transcription,
      which presumably helps control the level of the endonuclease in the cell.
AU  - Bogdanova E
AU  - Djordjevic M
AU  - Papapanagiotou I
AU  - Heyduk T
AU  - Kneale G
AU  - Severinov K
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2008 36: 1429-1442.

PMID- 19336410
VI  - 37
DP  - 2009
TI  - Transcription regulation of restriction-modification system Esp1396I.
PG  - 3354-3366
AB  - The convergently transcribed restriction (R) and methylase (M) genes of the
      Restriction-Modification system Esp1396I are tightly regulated by a
      controller (C) protein that forms part of the CR operon. We have mapped
      the transcriptional start sites from each promoter and examined the
      regulatory role of C.Esp1396I in vivo and in vitro. C-protein binding at
      the CR and M promoters was analyzed by DNA footprinting and a range of
      biophysical techniques. The distal and proximal C-protein binding sites at
      the CR promoter are responsible for activation and repression,
      respectively. In contrast, a C-protein dimer binds to a single site at the
      M-promoter to repress the gene, with an affinity much greater than for the
      CR promoter. Thus, during establishment of the system in a naive host, the
      activity of the M promoter is turned off early, preventing excessive
      synthesis of methylase. Mutational analysis of promoter binding sites
      reveals that the tetranucleotide inverted repeats long believed to be
      important for C-protein binding to DNA are less significant than
      previously thought. Instead, symmetry-related elements outside of these
      repeats appear to be critical for the interaction and are discussed in
      terms of the recent crystal structure of C.Esp139I bound to the CR
      promoter.
AU  - Bogdanova E
AU  - Zakharova M
AU  - Streeter S
AU  - Taylor J
AU  - Heyduk T
AU  - Kneale G
AU  - Severinov K
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: 3354-3366.

PMID- 21784931
VI  - 193
DP  - 2011
TI  - Two New Complete Genome Sequences Offer Insight into Host and Tissue Specificity of Plant Pathogenic Xanthomonas spp.
PG  - 5450-5464
AB  - Xanthomonas is a large genus of bacteria that collectively cause disease on more than 300
      plant species. The broad host range of the genus
      contrasts with stringent host and tissue specificity for individual
      species and pathovars. Whole-genome sequences of Xanthomonas campestris
      pv. raphani strain 756C and X. oryzae pv. oryzicola strain BLS256,
      pathogens that infect the mesophyll tissue of the leading models for plant
      biology, Arabidopsis thaliana and rice, respectively, were determined and
      provided insight into the genetic determinants of host and tissue
      specificity. Comparisons were made with genomes of closely related strains
      that infect the vascular tissue of the same hosts and across a larger
      collection of complete Xanthomonas genomes. The results suggest a model in
      which complex sets of adaptations at the level of gene content account for
      host specificity and subtler adaptations at the level of amino acid or
      noncoding regulatory nucleotide sequence determine tissue specificity.
AU  - Bogdanove AJ et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5450-5464.

PMID- 29718463
VI  - 46
DP  - 2018
TI  - Engineering altered protein-DNA recognition specificity.
PG  - 4845-4871
AB  - Protein engineering is used to generate novel protein folds and assemblages, to impart new
      properties and functions onto existing proteins, and to enhance our
      understanding of principles that govern protein structure. While such approaches
      can be employed to reprogram protein-protein interactions, modifying protein-DNA
      interactions is more difficult. This may be related to the structural features of
      protein-DNA interfaces, which display more charged groups, directional hydrogen
      bonds, ordered solvent molecules and counterions than comparable protein
      interfaces. Nevertheless, progress has been made in the redesign of protein-DNA
      specificity, much of it driven by the development of engineered enzymes for
      genome modification. Here, we summarize the creation of novel DNA specificities
      for zinc finger proteins, meganucleases, TAL effectors, recombinases and
      restriction endonucleases. The ease of re-engineering each system is related both
      to the modularity of the protein and the extent to which the proteins have
      evolved to be capable of readily modifying their recognition specificities in
      response to natural selection. The development of engineered DNA binding proteins
      that display an ideal combination of activity, specificity, deliverability, and
      outcomes is not a fully solved problem, however each of the current platforms
      offers unique advantages, offset by behaviors and properties requiring further
      study and development.
AU  - Bogdanove AJ
AU  - Bohm A
AU  - Miller JC
AU  - Morgan RD
AU  - Stoddard BL
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2018 46: 4845-4871.

PMID- 322977
VI  - 233
DP  - 1977
TI  - DNA modification in vitro by E. coli C and E. coli MRE 600 DNA-cytosine-methyltransferases: increased resistance of bacteriophage lambda DNA to the RII restriction system.
PG  - 498-501
AB  - 
AU  - Bogdarina IG
AU  - Burianov II
AU  - Baev AA
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1977 233: 498-501.

PMID- 380660
VI  - 44
DP  - 1979
TI  - Isolation and properties of DNA-cytosine-methyltransferase EcoRII and E. coli K12.
PG  - 440-452
AB  - The methods of isolation and partial purification of two DNA-cytosine-methylases EcoRII and E.
      coli K12 are described.  After chromatography on phosphocellulose the enzymes were purified
      100-fold, the yield being 30%.  Further purification of the enzymes was performed by
      sedimentation in a sucrose concentration gradient.  Both enzymes have native molecular weights
      of 50,000; DC-methylase from E. coli K12 may simultaneously occur in the forms with molecular
      weights of 70,000, 90,000 and 110,000.  Both DC-methylases modify identical nucleotide
      sequences of DNA, have equal numbers of methylation sites in phage lambda DNA and provide in
      vitro a complete protection of phage lambda DNA against restriction endonuclease EcoRII.
      DC-methylases E. coli K12 and EcoRII differ in their chromatographic behavior on
      phosphocellulose and capacity to form complexes with the cell DNA-adenine-methylase.
AU  - Bogdarina IG
AU  - Buryanov YI
AU  - Bayev AA
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1979 44: 440-452.

PMID- 375062
VI  - 13
DP  - 1979
TI  - Isolation and properties of DNA-cytosine-methyl-transferase from Escherichia coli C.
PG  - 281-291
AB  - The method of isolation and partial purification of DNA-cytosine-methyltransferase from E.
      coli C is described.  The enzyme underwent approximately 100-fold purification.  The obtained
      preparation of DC-methylase can be additionally considerably purified by sedimentation in
      sucrose gradient.  Native molecular weight of DC-methylase from E. coli C is 70,000.  The
      activity of the enzyme does not depend on Mg2+ ions.  The DC-methylase from E. coli C provides
      DNA of lambda phage in vitro with full resistance against restriction endonuclease EcoRII.  In
      DNA methylated by DC-methylase the modified cytosine, mainly in C-MC and C-MC-T sequences,
      corresponds to the pyrimidine sequences of specific site EcoRII.  DNA of lambda.B phage
      contains approximately 80 sites for modification by DC-methylase E. coli C.  The results
      obtained point to the same specificity in vitro of DNA-cytosine-methylase E. coli C and
      DNA-methylase EcoRII.
AU  - Bogdarina IG
AU  - Buryanov YI
AU  - Bayev AA
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1979 13: 281-291.

PMID- 3022116
VI  - 55
DP  - 1986
TI  - A technique for the detection of new strains producing enzymes involved in DNA modification and restriction - isoschizomers and isomethylomers of the known restrictases and methylases.
PG  - 699-700
AB  - The paper describes a technique for the detection of new strains producing enzymes which
      mediate DNA modification and restriction, and isoschizomers and isomethylomers of the known
      restriction endonucleases and methylases.  Three Bacillus subtilis strains whose DNA carries a
      BamHI modification have been found.  Two of these strains exert the restrictase activity with
      an R.BamHI specificity.
AU  - Bogdarina IG
AU  - Nadirova IM
AU  - Buryanov YI
PT  - Journal Article
TA  - Mikrobiologiia
JT  - Mikrobiologiia
SO  - Mikrobiologiia 1986 55: 699-700.

PMID- 6581040
VI  - 273
DP  - 1983
TI  - Methylation of DNA of phages T3 and T7 by various types of DNA-adenine methylases and inhibition of the EcoK methylase by the ocR+ protein.
PG  - 234-237
AB  - In recent years interest in the study of the role of site-specific DNA methylation in cells of
      prokaryotes, eukaryotes, and their viruses in the regulation of gene activity has increased
      substantially. It is known that the manifestation of the activity of the ocR+ gene of
      bacteriophages T3 and T7 in infected Escherichia coli cells suppresses the restriction and
      modification of the virus DNA by Type I enzymes, and, moreover, the methylation of
      bacteriophage T3 DNA does not occur at all, as a result of breakdown of the intracellular
      S-adenosyl-L-methionine by SAMase (S-adenosyl-L-methionine hydrolase), which is also coded by
      the gene 0.3 of phage T3. In view of this it is of interest to study the methylation of DNA of
      phages T3 and T7 by DNA-adenine methylases EcoK and EcoDam in vivo and to determine the
      influence of the ocR gene on the activity of these enzymes. For this purpose we determined the
      number of CH3 groups incorporated into the phage genome by various DNA methylases in vitro to
      determine the number of recognition sites in their DNA that are not methylated in vivo.
AU  - Bogdarina IG
AU  - Reuter M
AU  - Kruger DH
AU  - Buryanov YI
AU  - Baev AAA
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1983 273: 234-237.

PMID- 789109
VI  - 68
DP  - 1976
TI  - DNA-cytosine methylation in E. coli MRE 600 cells.
PG  - 177-180
AB  - Two DNA-cytosine methyltransferases (Dcm I and II) modifying cytosine in different nucleotide
      sequences have been isolated from E. coli MRE 600 cells. Physiological role of these
      methylases is still unknown but it is possible that one of them is connected with the DNA
      modification and restriction system. This supposition is supported by the fact that the main
      targets in DNA fro Dcm II are the pyrimidine sequences C-m5C and C-m5C-T (m5C:
      5-methylcytosine) identical to pyrimidine fragments in DNA sequences, which are methylated by
      DNA methylase of resistance factor RII. The work presents the data on in vivo methylation of
      cytosine in E. coli MRE 600 DNA and we describe a new method for separate determination of Dcm
      I and Dcm II action in the cell. Structural peculiarities of nucleotide sequences recognized
      by two enzymes constitute the basis of this method. More that 90% of cytosine modified by Dcm
      I appears in the sequence Pu-m5C-C-Pu and about 30% of cytosine methylated by Dcm II is
      detected in the sequence Pu-C-m5C-Pu. So, separate determination of Dcm I and Dcm II activity
      in the cell is based on quantitative estimation of 5-methylcytosine content at 5'- and
      3'-termini of Pu-C-C-Pu- sequences of E. coli MRE 600 DNA.
AU  - Bogdarina IG
AU  - Vagabova LM
AU  - Buryanov YI
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1976 68: 177-180.

PMID- 28153906
VI  - 5
DP  - 2017
TI  - The Genome Sequence of an Oxytetracycline-Resistant Isolate of the Fish Pathogen  Piscirickettsia salmonis Harbors a Multidrug Resistance Plasmid.
PG  - e01571-16
AB  - The amount of antibiotics needed to counteract frequent piscirickettsiosis outbreaks is a
      major concern for the Chilean salmon industry. Resistance to
      antibiotics may contribute to this issue. To understand the genetics underlying
      Piscirickettsia salmonis-resistant phenotypes, the genome of AY3800B, an
      oxytetracycline-resistant isolate bearing a multidrug resistance plasmid, is
      presented here.
AU  - Bohle H
AU  - Henriquez P
AU  - Grothusen H
AU  - Navas E
AU  - Bustamante F
AU  - Bustos P
AU  - Mancilla M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01571-16.

PMID- 25523762
VI  - 2
DP  - 2014
TI  - Comparative Genome Analysis of Two Isolates of the Fish Pathogen Piscirickettsia  salmonis from Different Hosts Reveals Major Differences in Virulence-Associated  Secretion Systems.
PG  - e01219-14
AB  - Outbreaks caused by Piscirickettsia salmonis are one of the major threats to the
      sustainability of the Chilean salmon industry. We report here the annotated draft
      genomes of two P. salmonis isolates recovered from different salmonid species. A
      comparative analysis showed that the number of virulence-associated secretion
      systems constitutes a main genomic difference.
AU  - Bohle H
AU  - Henriquez P
AU  - Grothusen H
AU  - Navas E
AU  - Sandoval A
AU  - Bustamante F
AU  - Bustos P
AU  - Mancilla M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01219-14.

PMID- 26294623
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Bacillus cytotoxicus CVUAS 2833, a Very Close Relative to Type Strain NVH 391-98 Isolated from a Different Location.
PG  - e00901-15
AB  - We report the draft genome sequence of Bacillus cytotoxicus CVUAS 2833, isolated  from potato
      puree in Germany (2007), which is-despite its clearly different
      source-very similar to the type strain B. cytotoxicus NVH 391-98 isolated in
      France (average nucleotide identity, 99.5%).
AU  - Bohm ME
AU  - Huptas C
AU  - Krey VM
AU  - Scherer S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00901-15.

PMID- 26067980
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Bordetella pertussis D420.
PG  - e00657-15
AB  - Bordetella pertussis is the causative agent of whooping cough, a highly contagious, acute
      respiratory illness that has seen resurgence despite the use of
      vaccines. We present the complete genome sequence of a clinical strain of B.
      pertussis, D420, which is representative of a currently circulating clade of this
      pathogen.
AU  - Boinett CJ
AU  - Harris SR
AU  - Langridge GC
AU  - Trainor EA
AU  - Merkel TJ
AU  - Parkhill J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00657-15.

PMID- 20093192
VI  - 47
DP  - 2010
TI  - Sexual mating of Botrytis cinerea illustrates PRP8 intein HEG activity.
PG  - 392-398
AB  - Strains of Botrytis cinerea are polymorphic for the presence of an intein in the Prp8 gene
      (intein +/-). The intein encodes a homing endonuclease
      (HEG). During meiosis in an intein +/- heterozygote, the homing
      endonuclease initiates intein 'homing' by inducing gene conversion. In
      such meioses, the homing endonuclease triggers gene conversion of the
      intein together with its flanking sequences into the empty allele. The
      efficiency of gene conversion of the intein was found to be 100%. The
      extent of flanking sequence affected by the gene conversion varied in
      different meioses. A survey of the inteins and flanking sequences of a
      group B. cinerea isolates indicates that there are two distinct variants
      of the intein both of which have active HEGs. The survey also suggests
      that the intein has been actively homing during the evolution of the
      species and that the PRP8 intein may have entered the species by
      horizontal transfer.
AU  - Bokor AA
AU  - van Kan JA
AU  - Poulter RT
PT  - Journal Article
TA  - Fungal. Genet. Biol.
JT  - Fungal. Genet. Biol.
SO  - Fungal. Genet. Biol. 2010 47: 392-398.

PMID- 
VI  - 
DP  - 2007
TI  - Identification and characterization of interactions between de novo DNA methyltransferase 3b and thymine-DNA glycosylase.
PG  - 1-141
AB  - The majority of methylation found in the vertebrate genome occurs at carbon 5 of the cytosine
      pyrimidine ring within CpG dinucleotides.  DNA methylation patterns are established during
      early embryogenesis by the de novo methyltransferases, Dnmt3a and Dnmt3b.  These patterns play
      a large role in genetic commitment and cellular differentiation via the heritable repression
      of certain developmental programs.  An important in vivo function of Dnmt3b is methylation of
      the centromeric and pericentromeric satellite repeats, regions of heterochromatin that are
      rich in methylated CpG sites.  Methylation of these repeats contributes to the higher-order
      heterochromatin structure that is essential to maintain genomic stability, repression of
      aberrant mitotic recombination and assurance of proper chromosome segregation.  Mutations that
      ablate Dnmt3b activity, exemplified by those found in the autosomal recessive genetic
      disorder, ICF syndrome, lead to hypomethylation of the pericentromeric satellite repeats
      resulting in chromatin decondensationa nd enhanced chromosomal rearrangements.  A significant
      source of endogenous DNa damage is the spontaneous hydrolytic deamination of cytosine and
      5-methylcytosine to uracil and thymidine, thereby generating U.G and T.C mismatches,
      respectively.  If these promutagenic lesions are not repaired, C - T transition mutations
      occur during replication.  Mechanisms to repair such damage have evolved in the form of
      mismatch-specific DNA glycosylases.  G/T mismatch-specific thymine-DNA glycosylase initiates
      post-replicative base excision repair at G.G and U.G mismatches ultimately leading to
      reformation of the original C.G base pair.  Tdg was isolated as a positive protein interactor
      with Dnmt3b in a yeast two-hybrid screen.  Subsequently, interaction between the endogenous
      proteins was demonstrated.  It was determined that Dnmt3b and Tdg are targeted to genomic
      regions of heterochromatin.  the regions/domains of Dnmt3b that mediate the interaction with
      Tdg were determined to be regions that have been previously identified as necessary for
      targeting Dnmt3b to pericentromeric heterochromatin.  A t.G mismatch repair assay utilizing ES
      cells nullizygous for different DNA methyltransferases was developed to study the effect of
      DNA methyltransferases on base excision repair.  Results of these experiments suggest that DNA
      methyltransferases potentiate T.G mismatch repair.  During this course of investigation, it
      was determined that a putative RNA component is essential for proper T.G mismatch repair.
AU  - Boland MJ
PT  - Journal Article
TA  - Ph.D. Thesis, University of Nebraska, USA
JT  - Ph.D. Thesis, University of Nebraska, USA
SO  - Ph.D. Thesis, University of Nebraska, USA 2007 : 1-141.

PMID- 
VI  - 0
DP  - 2009
TI  - Mammalian DNA methyltransferases Catalytic mechanism, structure, and functions.
PG  - 37-65
AB  - 5-Methylcytosine was first detected in mammalian DNA 60 years ago and within six years, it was
      demonstrated that the only dinucleotide with significant 5mC content was 5mC,G.  It took
      almost another decade to determine that cytosine residues were enzymatically methylated after
      incorporation into DNA, establishing the basis for epigenetic modulation of gene expression.
      The first demonstrations that inhibition of DNA methylation could induce differentiation of
      cultured cells were published in the late 1970s.  Since then, it has become increasingly clear
      that DNA methylation plays a number of important roles in cellular homeostasis and regulation
      of normal mammalian development.  Methylation of DNA promotes genomic stability through
      repression of mitotic recombination and transposition, assuring proper chromatid segregation
      and maintenance of higher-order heterochromatin structure.  Genomic methylation patterns also
      play a crucial role during embryogenesis, leading to temporal transcriptional repression of
      critical developmental programs during cellular differentiation through its ability to
      regulate chromatin structure.  Additionally, DNA methylation is integral to the processes of
      genomic imprinting and gene dosage compensation in females through inactivation of one X
      chromosome.  A variety of tumors exhibit aberrant DNA methylation patterns.  The most common
      change is an early global loss or reduction in DNA methylation, that is hypomethylation.  This
      is followed by localized promoter hypermethylation of tumor-suppressor genes.
AU  - Boland MJ
AU  - Christman JK
PT  - Journal Article
TA  - Nutrients and Epigenetics
JT  - Nutrients and Epigenetics
SO  - Nutrients and Epigenetics 2009 0: 37-65.

PMID- 
VI  - 46
DP  - 2005
TI  - A novel interaction between thymine DNA-glycosylase and the de novo methyltransferase, Dnmt3b.
PG  - 645
AB  - DNA methylation patterns are established shortly before gastrulation by the de novo
      methyltransferases, Dnmt3a and Dnmt3b.  The majority of methylation found in the vertebrate
      genome occurs at carbon 5 of cytosine (m5C) within CpG dinucleotides.  These patterns are
      thought to set the stage for genetic commitment and cellular differentiation.  Aberrant DNA
      methylation has been implicated in cancer and certain genetic diseases.  An important in vivo
      function of Dnmt3b is methylation of the pericentric heterochromatin major satellite repeats.
      DNA methylation of these repeats contributes to the higher-order chromatin structure necessary
      for genome stability and proper sister chromatid segregation during mitosis.  Mutations that
      ablate Dnmt3b activity such as those found in the rare recessive genetic disorder, ICF
      syndrome lead to hypomethylation of the pericentric satellite repeats.  This results in
      chromatin decondensation and enhanced chromosomal rearrangements.  Analogous chromosomal
      abnormalities have been observed in breast carcinoma, ovarian epithelial carcinoma, and
      pediatric Wilms tumors although they have not been directly attributed to Dnmt3b malfunction.
      Dnmt3b is composed of multiple domains, suggesting it can form interactions with many
      proteins.  In order to further elucidate how de novo methylation is regulated, we initiated a
      search for proteins that interact with Dnmt3b.  Using Dnmt3b as bait in a yeast two-hybrid
      screen of a murine embryonic cDNA library, we isolated thymine DNA-glycosylase (Tdg) as a
      positive protein interactor.  This interaction has been confirmed by coimmunoprecipitation. We
      show that both the catalytic domain and the PWWP domain of Dnmt3b are able to interact with
      Tdg.  In addition, we demonstrate an in vivo nuclear interaction between Tdg and Dnmt3b in HEK
      293T cells using confocal microscopy.  The interaction between Dnmt3b and Tdg is enhanced in
      mitotic cells and can be induced by arresting cells in mitosis with the cell cycle inhibitors
      vinblastine and demecolcine.  Spontaneous hydrolytic deamination of C or m5C residues within a
      CpG dinucleotide results in U:G or T:G mismatches, respectively.  Mechanisms to repair such
      damage have evolved in the form of mismatch-specific DNA glycosylases.  Tdg initiates the base
      excision repair of T:G and U:G mismatches leading to reformation of a C:G base pair.  The
      evidence presented here supports the hypothesis that the association of Dnmt3b and Tdg
      promotes genomic stability and reduces the incidence of pericentromeric heterochromatin
      rearrangement through repair of T:G and/or U:G mismatches followed by or simultaneous with
      methylation of the repaired product, thereby restoring the original methylation status at that
      locus.  Supported by NIH R21-CA91315 to JKC.
      Note: Our subsequent studies of endogenous interactions between Dnmt3b and Tdg in murine P19
      cells did not confirm the enhancement of interaction between these enzymes during mitosis.
      This suggests that the result reported above may be the result of an elevated,
      non-physiological level of exogenously expressed Dnmt3b and Tdg.
AU  - Boland MJ
AU  - Christman JK
PT  - Journal Article
TA  - Proc. Amer. Assoc. Cancer Res.
JT  - Proc. Amer. Assoc. Cancer Res.
SO  - Proc. Amer. Assoc. Cancer Res. 2005 46: 645.

PMID- 18452947
VI  - 379
DP  - 2008
TI  - Characterization of Dnmt3b:Thymine-DNA Glycosylase Interaction and Stimulation of Thymine Glycosylase-Mediated Repair by DNA  Methyltransferase(s) and RNA.
PG  - 492-504
AB  - Methylation of cytosine residues in CpG dinucleotides plays an important role in epigenetic
      regulation of gene expression and chromatin
      structure/stability in higher eukaryotes. DNA methylation patterns are
      established and maintained at CpG dinucleotides by DNA methyltransferases
      (Dnmt1, Dnmt3a, and Dnmt3b). In mammals and many other eukaryotes, the CpG
      dinucleotide is underrepresented in the genome. This loss is postulated to
      be the result of unrepaired deamination of cytosine and 5-methylcytosine
      to uracil and thymine, respectively. Two thymine glycosylases are believed
      to reduce the impact of 5-methylcytosine deamination. G/T
      mismatch-specific thymine-DNA glycosylase (Tdg) and methyl-CpG binding
      domain protein 4 can both excise uracil or thymine at U.G and T.G
      mismatches to initiate base excision repair. Here, we report the
      characterization of interactions between Dnmt3b and both Tdg and
      methyl-CpG binding domain protein 4. Our results demonstrate (1) that both
      Tdg and Dnmt3b are colocalized to heterochromatin and (2) reduction of T.G
      mismatch repair efficiency upon loss of DNA methyltransferase expression,
      as well as a requirement for an RNA component for correct T.G mismatch
      repair.
AU  - Boland MJ
AU  - Christman JK
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2008 379: 492-504.

PMID- 14633971
VI  - 17
DP  - 2003
TI  - Structural and biochemical analyses of DNA and RNA binding by a bifunctional homing endonuclease and group I intron splicing factor.
PG  - 2875-2888
AB  - We determined the crystal structure of a bifunctional group I intron splicing factor and
      homing endonuclease, termed the I-AniI maturase, in
      complex with its DNA target at 2.6 A resolution. The structure
      demonstrates the remarkable structural conservation of the beta-sheet
      DNA-binding motif between highly divergent enzyme subfamilies. DNA
      recognition by I-AniI was further studied using nucleoside deletion and
      DMS modification interference analyses. Correlation of these results with
      the crystal structure provides information on the relative importance of
      individual nucleotide contacts for DNA recognition. Alignment and modeling
      of two homologous maturases reveals conserved basic surface residues,
      distant from the DNA-binding surface, that might be involved in RNA
      binding. A point mutation that introduces a single negative charge in this
      region uncouples the maturase and endonuclease functions of the protein,
      inhibiting RNA binding and splicing while maintaining DNA binding and
      cleavage.
AU  - Bolduc JM
AU  - Spiegel PC
AU  - Chatterjee P
AU  - Brady KL
AU  - Downing ME
AU  - Caprara MG
AU  - Waring RB
AU  - Stoddard BL
PT  - Journal Article
TA  - Genes Dev.
JT  - Genes Dev.
SO  - Genes Dev. 2003 17: 2875-2888.

PMID- 16820047
VI  - 7
DP  - 2006
TI  - The genome of the square archaeon Haloquadratum walsbyi: life at the limits of water activity.
PG  - 169
AB  - ABSTRACT: BACKGROUND: The square halophilic archaeon Haloquadratum walsbyi dominates
      NaCl-saturated and MgCl2 enriched aquatic ecosystems, which
      imposes a serious desiccation stress, caused by the extremely low water
      activity. The genome sequence was analyzed and physiological and physical
      experiments were carried out in order to reveal how H. walsbyi has
      specialized into its narrow and hostile ecological niche and found ways to
      cope with the desiccation stress. RESULTS: A rich repertoire of proteins
      involved in phosphate metabolism, phototrophic growth and extracellular
      protective polymers, including the largest archaeal protein (9159 amino
      acids), a homolog to eukaryotic mucins, are amongst the most outstanding
      features. A relatively low GC content (47.9%), 15-20% less than in other
      halophilic archaea, and one of the lowest coding densities (76.5%) known
      for prokaryotes might be an indication for the specialization in its
      unique environment CONCLUSIONS: Although no direct genetic indication was
      found that can explain how this peculiar organism retains its square
      shape, the genome revealed several unique adaptive traits that allow this
      organism to thrive in its specific and extreme niche.
AU  - Bolhuis HH
AU  - Palm PP
AU  - Wende AA
AU  - Falb MM
AU  - Rampp MM
AU  - Rodriguez-Valera FF
AU  - Pfeiffer FF
AU  - Oesterhelt DD
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2006 7: 169.

PMID- 7476854
VI  - 248
DP  - 1995
TI  - Tagging pathogenicity genes in Ustilago maydis by restriction enzyme-mediated integration (REMI).
PG  - 547-552
AB  - In the maize pathogenic fungus Ustilago maydis integration of transforming DNA at homologous
      or heterologous sites is often accompanied by duplications of the DNA.  We show that it is
      possible to generate single-copy integration events with high efficiency by restriction
      enzyme-mediated integration (REMI).  In about 50% of cases, a plasmid that contains a single
      BamHI site is integrated at chromosomal BamHI sites, if BamHI is added to the transformation
      mixtures.  In the other cases it appears that integration events have also occurred
      preferentially at BamHI sites, but without restoration of the recognition sites.  Using REMI
      we have generated approximately 1000 insertion mutants.  Pathogenicity tests demonstrated that
      about 1-2% of these mutants were unable to induce symptoms when tested in planta.  For two of
      the mutants we have shown that the phenotype is linked to the insertion event.
AU  - Bolker M
AU  - Bohnert HU
AU  - Braun KH
AU  - Gorl J
AU  - Kahmann R
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1995 248: 547-552.

PMID- 24019993
VI  - 7
DP  - 2013
TI  - Complete genome sequence of Nitrosomonas sp. Is79, an ammonia oxidizing bacterium adapted to low ammonium concentrations.
PG  - 469-482
AB  - Nitrosomonas sp. Is79 is a chemolithoautotrophic ammonia-oxidizing bacterium that belongs to
      the family Nitrosomonadaceae within the phylum Proteobacteria. Ammonia
      oxidation is the first step of nitrification, an important process in the global
      nitrogen cycle ultimately resulting in the production of nitrate. Nitrosomonas
      sp. Is79 is an ammonia oxidizer of high interest because it is adapted to low
      ammonium and can be found in freshwater environments around the world. The
      3,783,444-bp chromosome with a total of 3,553 protein coding genes and 44 RNA
      genes was sequenced by the DOE-Joint Genome Institute Program CSP 2006.
AU  - Bollmann A et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 7: 469-482.

PMID- 26383661
VI  - 3
DP  - 2015
TI  - Genome Sequences of the Race 1 and Race 4 Xanthomonas campestris pv. campestris Strains CFBP 1869 and CFBP 5817.
PG  - e01023-15
AB  - Xanthomonas campestris pv. campestris is the causal agent of black rot on Brassicaceae. The
      draft genome sequences of strains CFBP 1869 and CFBP 5817 have  been determined and are the
      first ones corresponding to race 1 and race 4 strains, which have a predominant agronomic and
      economic impact on cabbage cultures worldwide.
AU  - Bolot S
AU  - Cerutti A
AU  - Carrere S
AU  - Arlat M
AU  - Fischer-Le SM
AU  - Portier P
AU  - Poussier S
AU  - Jacques MA
AU  - Noel LD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01023-15.

PMID- 23405315
VI  - 1
DP  - 2013
TI  - Genome Sequence of Xanthomonas campestris pv. campestris Strain Xca5.
PG  - e00032-12
AB  - An annotated high-quality draft genome sequence for Xanthomonas campestris pv. campestris race
      1 strain Xca5 (originally described as X. campestris pv.
      armoraciae), the causal agent of black rot on Brassicaceae plants, has been
      determined. This genome sequence is a valuable resource for comparative genomics
      within the campestris pathovar.
AU  - Bolot S
AU  - Guy E
AU  - Carrere S
AU  - Barbe V
AU  - Arlat M
AU  - Noel LD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00032-12.

PMID- 23990580
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Xanthomonas cassavae Type Strain CFBP 4642.
PG  - e00679-13
AB  - We report the draft genome sequence of the Xanthomonas cassavae type strain CFBP  4642, the
      causal agent of bacterial necrosis on cassava plants. These data will
      allow the comparison of this nonvascular pathogen with the vascular pathogen
      Xanthomonas axonopodis pv. manihotis, both infecting the same host, which will
      facilitate the development of diagnostic tools.
AU  - Bolot S
AU  - Munoz BA
AU  - Cunnac S
AU  - Ortiz E
AU  - Szurek B
AU  - Noel LD
AU  - Arlat M
AU  - Jacques MA
AU  - Gagnevin L
AU  - Portier P
AU  - Fischer-Le SM
AU  - Carrere S
AU  - Koebnik R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00679-13.

PMID- 23846270
VI  - 1
DP  - 2013
TI  - Genome Sequences of Three Atypical Xanthomonas campestris pv. campestris Strains, CN14, CN15, and CN16.
PG  - e00465-13
AB  - Xanthomonas campestris pv. campestris is the causal agent of black rot on Brassicaceae. The
      draft genome sequences of three strains (CN14, CN15, and CN16)
      that are highly aggressive on Arabidopsis have been determined. These genome
      sequences present an unexpected genomic diversity in X. campestris pv.
      campestris, which will be valuable for comparative analyses.
AU  - Bolot S
AU  - Roux B
AU  - Carrere S
AU  - Jiang BL
AU  - Tang JL
AU  - Arlat M
AU  - Noel LD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00465-13.

PMID- 25035333
VI  - 2
DP  - 2014
TI  - Genome Sequence of 'Candidatus Arthromitus' sp. Strain SFB-Mouse-NL, a Commensal  Bacterium with a Key Role in Postnatal Maturation of Gut Immune Functions.
PG  - e00705-14
AB  - 'Candidatus Arthromitus' sp. strain SFB-mouse-NL (SFB, segmented filamentous bacteria) is a
      commensal bacterium necessary for inducing the postnatal
      maturation of homeostatic innate and adaptive immune responses in the mouse gut.
      Here, we report the genome sequence of this bacterium, which sets it apart from
      earlier sequenced mouse SFB isolates.
AU  - Bolotin A
AU  - de Wouters T
AU  - Schnupf P
AU  - Bouchier C
AU  - Loux V
AU  - Rhimi M
AU  - Jamet A
AU  - Dervyn R
AU  - Boudebbouze S
AU  - Blottiere HM
AU  - Sorokin A
AU  - Snel J
AU  - Cerf-Bensussan N
AU  - Gaboriau-Routhiau V
AU  - van de Guchte M
AU  - Maguin E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00705-14.

PMID- 22328746
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Lactococcus lactis subsp. cremoris A76.
PG  - 1241-1242
AB  - We report the complete genome sequence of Lactococcus lactis subsp. cremoris A76, a dairy
      strain isolated from a cheese production outfit. Genome analysis detected
      two contiguous islands fitting to the L. lactis subsp. lactis rather than to the
      L. lactis subsp. cremoris lineage. This indicates the existence of genetic
      exchange between the diverse subspecies, presumably related to the technological
      process.
AU  - Bolotin A
AU  - Quinquis B
AU  - Ehrlich SD
AU  - Sorokin A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1241-1242.

PMID- 11337471
VI  - 11
DP  - 2001
TI  - The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403.
PG  - 731-753
AB  - Lactococcus lactis is a nonpathogenic AT-rich gram-positive bacterium closely related to the
      genus Streptococcus and is the most commonly used cheese starter. It is also the
      best-characterized lactic acid bacterium. We sequenced the genome of the laboratory strain
      IL1403, using a novel two-step strategy that comprises diagnostic sequencing of the entire
      genome and a shotgun polishing step. The genome contains 2,365,589 base pairs and encodes 2310
      proteins, including 293 protein-coding genes belonging to six prophages and 43 insertion
      sequence (IS) elements. Nonrandom distribution of IS elements indicates that the chromosome of
      the sequenced strain may be a product of recent recombination between two closely related
      genomes. A complete set of late competence genes is present, indicating the ability of L.
      lactis to undergo DNA transformation. Genomic sequence revealed new possibilities for
      fermentation pathways and for aerobic respiration. It also indicated a horizontal transfer of
      genetic information from Lactococcus to gram-negative enteric bacteria of
      Salmonella-Escherichia group.
AU  - Bolotin A
AU  - Wincker P
AU  - Mauger S
AU  - Jaillon O
AU  - Malarme K
AU  - Weissenbach J
AU  - Ehrlich SD
AU  - Sorokin A
PT  - Journal Article
TA  - Genome Res.
JT  - Genome Res.
SO  - Genome Res. 2001 11: 731-753.

PMID- 12193633
VI  - 184
DP  - 2002
TI  - R391: a Conjugative Integrating Mosaic Comprised of Phage, Plasmid, and Transposon Elements.
PG  - 5158-5169
AB  - The conjugative, chromosomally integrating element R391 is the archetype
      of the IncJ class of mobile genetic elements. Originally found in a South
      African Providencia rettgeri strain, R391 carries antibiotic and mercury
      resistance traits, as well as genes involved in mutagenic DNA repair.
      While initially described as a plasmid, R391 has subsequently been shown
      to be integrated into the bacterial chromosome, employing a phage-like
      integration mechanism closely related to that of the SXT element from
      Vibrio cholerae O139. Analysis of the complete 89-kb nucleotide sequence
      of R391 has revealed a mosaic structure consisting of elements originating
      in bacteriophages and plasmids and of transposable elements. A total of 96
      open reading frames were identified; of these, 30 could not be assigned a
      function. Sequence similarity suggests a relationship of large sections of
      R391 to sequences from Salmonella, in particular those corresponding to
      the putative conjugative transfer proteins, which are related to the
      IncHI1 plasmid R27. A composite transposon carrying the kanamycin
      resistance gene and a novel insertion element were identified. Challenging
      the previous assumption that IncJ elements are plasmids, no plasmid
      replicon was identified on R391, suggesting that they cannot replicate
      autonomously.
AU  - Boltner D
AU  - MacMahon C
AU  - Pembroke JT
AU  - Strike P
AU  - Osborn AM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2002 184: 5158-5169.

PMID- 2587236
VI  - 17
DP  - 1989
TI  - Asp700I, a novel isoschizomer of XmnI from Achromobacter species 700 recognizing 5'-GAANN/NNTTC-3'.
PG  - 8879
AB  - None
AU  - Bolton BJ
AU  - Comer M
AU  - Kessler C
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 8879.

PMID- 2587281
VI  - 17
DP  - 1989
TI  - AspHI, a novel isoschizomer of HgiAI from Achromobacter species H recognizing 5'-GWGCW/C-3'.
PG  - 9500
AB  - None
AU  - Bolton BJ
AU  - Holtke H-J
AU  - Schmitz GG
AU  - Jarsch M
AU  - Kessler C
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 9500.

PMID- Not carried by PubMed...
VI  - 330
DP  - 1988
TI  - Screening for novel type II restriction endonucleases.
PG  - 376
AB  - Site specific endonucleases have become indispensable tools for recombinant DNA
      techniques.  Although to date the recognition sequences for 115 different class
      II restriction endonucleases have been reported, additional enzymes with novel
      specificities are required for the analysis and manipulation of DNA.  We have
      examined a wide variety of bacteria for the presence of class II restriction
      endonucleases.  Our aim was to find novel specific activities, to purity and
      characterize the enzymes and to determine the specificities in respect to their
      recognition sequence and cleavage position.  Hewre we give an overview on the
      occurance of class II enzymes in various microorganisms tested and describe a
      new class IIS enzyme discovered in Kluyvera species 632.
AU  - Bolton BJ
AU  - Kaluza K
AU  - Herz MJ
AU  - Berger G
AU  - Kessler C
AU  - Schmitz G
PT  - Journal Article
TA  - Fresenius Z. Anal. Chem.
JT  - Fresenius Z. Anal. Chem.
SO  - Fresenius Z. Anal. Chem. 1988 330: 376.

PMID- Not included in PubMed...
VI  - 182
DP  - 1985
TI  - Asp718 from a non-pathogenic species of the genus Achromobacter: a KpnI isoschizomer generating DNA-fragments with 5'-protruding ends.
PG  - 130-134
AB  - A new type II restriction endonuclease Asp718 has been isolated from the
      non-pathogenic species of Achromobacter 718.  This novel enzyme, an
      isoschizomer of KpnI, recognizes and cleaves specifically within the nucleotide
      sequence:5'-G^GTAC-C-3'3'-C-CATG^G-5'In contrast to KpnI, Asp718 generates
      fragments with 5'-protruding single-stranded ends.  These 5'-terminal
      extensions of the Asp718 fragments may be efficiently labeled with T4
      polynucleotide kinase, whereas the recessed 3'-ends are suitable substrates for
      the terminal labeling reaction applying Klenow enzyme.  The presence of only
      one restriction activity in this Achromobacter strain facilitates the
      preparation of Asp718 free of other contaminating site-specific nucleases which
      could interfere with the in vitro digestion of DNA.
AU  - Bolton BJ
AU  - Nesch G
AU  - Comer MJ
AU  - Wolf W
AU  - Kessler C
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1985 182: 130-134.

PMID- 2326178
VI  - 18
DP  - 1990
TI  - EclXI, a novel isoschizomer of XmaIII from Enterobacter cloacae 590 recognizing 5'-C/GGCCG-3' .
PG  - 381
AB  - None
AU  - Bolton BJ
AU  - Reischl U
AU  - Holtke H-J
AU  - Schmitz GG
AU  - Jarsch M
AU  - Kessler C
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 381.

PMID- 2843429
VI  - 66
DP  - 1988
TI  - Ksp632I: a novel class IIS restriction endonuclease from Kluyvera species 632 with the asymmetric hexanucleotide recognition sequence: 5'-CTCTTCN^-3' 3'-GAGAAGNNNN^-5' .
PG  - 31-43
AB  - A new class-IIS restriction endonuclease, Ksp632I, with novel sequence
      specificity has been discovered in a non-pathogenic species of Kluyvera.  The
      presence of only a single site-specific activity in this Kluyvera sp. strain
      632 enables Ksp632I to be isolated in highly purified form free of
      contaminating nucleases.  Ksp632I recognition sites and cleavage positions were
      deduced using experimental and computer-assisted mapping and sequencing.  The
      cleavage specificity corresponds to the sequence 5'-CTCTTCN^NNN-N-3'
      3'-GAGAAGN-NNN^N-5' The enzyme recognizes an asymmetric hexanucleotide sequence
      and cleaves in the presence of Mg2+ ions specific phosphodiester bonds in both
      DNA strands, 1 and 4 nucleotides distal to the recognition sequence.  The
      staggered cuts generate 5'-protruding ends with single-stranded
      5'-phosphorylated trinucleotides.  Several slow cleavage sites for Ksp632I were
      observed on lambda cI857 Sam7 DNA.  Ksp632I may complement other class-IIS
      enzymes in the universal restriction approach and may serve as a tool for
      generating defined unidirectional deletions or insertions.
AU  - Bolton BJ
AU  - Schmitz GG
AU  - Jarsch M
AU  - Comer MJ
AU  - Kessler C
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 66: 31-43.

PMID- 2587269
VI  - 17
DP  - 1989
TI  - KspI, a novel isoschizomer of SacII from Kluyvera species recognizing 5'-CCGC/GG-3'.
PG  - 9476
AB  - None
AU  - Bolton BJ
AU  - Schmitz GG
AU  - Jarsch M
AU  - Kessler C
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 9476.

PMID- 2162524
VI  - 18
DP  - 1990
TI  - AspI, a novel isoschizomer of Tht111l from Achromobacter species 699 recognizing 5'-GACN/NNGTC-3'.
PG  - 3422
AB  - None
AU  - Bolton BJ
AU  - Schmitz GG
AU  - Jarsch M
AU  - Kessler C
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 3422.

PMID- 24092791
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Aeromonas veronii Hm21, a Symbiotic Isolate from the Medicinal Leech Digestive Tract.
PG  - e00800-13
AB  - Aeromonas veronii strain Hm21 was isolated from the digestive tract of the medicinal leech
      Hirudo verbana and has been used to identify genes that are
      important for host colonization. This species is also a symbiont in the gut of
      zebrafish and is a pathogen of mammals and fish. We present here a 4.68-Mbp draft
      genome sequence for Hm21.
AU  - Bomar L
AU  - Stephens WZ
AU  - Nelson MC
AU  - Velle K
AU  - Guillemin K
AU  - Graf J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00800-13.

PMID- 24092787
VI  - 1
DP  - 2013
TI  - Whole-Genome Sequence of the Clinical Strain Corynebacterium argentoratense DSM 44202, Isolated from a Human Throat Specimen.
PG  - e00793-13
AB  - Corynebacterium argentoratense is part of the human skin microbiota and is occasionally
      detected in the upper respiratory tract of patients suffering from
      tonsillitis. The complete DNA sequence of the type strain DSM 44202 comprises
      2,031,902 bp, yielding the smallest genome sequenced thus far for a
      corynebacterium associated with humans.
AU  - Bomholt C
AU  - Glaub A
AU  - Gravermann K
AU  - Albersmeier A
AU  - Brinkrolf K
AU  - Ruckert C
AU  - Tauch A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00793-13.

PMID- 24855298
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Nonstarter Bacteriocin-Producing Strain Enterococcus mundtii CRL35.
PG  - e00444-14
AB  - Enterococcus mundtii CRL35 is a bacteriocinogenic strain isolated from an artisanal cheese of
      northwestern Argentina. Here we report its draft genome
      sequence, consisting of 82 contigs. In silico genomic analysis of
      biotechnological properties was performed to determine the potential of this
      microorganism to be used in a food model system.
AU  - Bonacina J
AU  - Saavedra L
AU  - Suarez NE
AU  - Sesma F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00444-14.

PMID- 8889548
VI  - 6
DP  - 1996
TI  - Normalization and subtraction: two approaches to facilitate gene discovery.
PG  - 791-806
AB  - Large-scale sequencing of cDNAs randomly picked from libraries has proven
      to be a very powerful approach to discover (putatively) expressed
      sequences that, in turn, once mapped, may greatly expedite the process
      involved in the identification and cloning of human disease genes.
      However, the integrity of the data and the pace at which novel sequences
      can be identified depends to a great extent on the cDNA libraries that are
      used. Because altogether, in a typical cell, the mRNAs of the prevalent
      and intermediate frequency classes comprise as much as 50-65% of the total
      mRNA mass, but represent no more than 1000-2000 different mRNAs, redundant
      identification of mRNAs of these two frequency classes is destined to
      become overwhelming relatively early in any such random gene discovery
      programs, thus seriously compromising their cost-effectiveness. With the
      goal of facilitating such efforts, previously we developed a method to
      construct directionally cloned normalized cDNA libraries and applied it to
      generate infant brain (INIB) and fetal liver/spleen (INFLS) libraries,
      from which a total of 45,192 and 86,088 expressed sequence tags,
      respectively, have been derived. While improving the representation of the
      longest cDNAs in our libraries, we developed three additional methods to
      normalize cDNA libraries and generated over 35 libraries, most of which
      have been contributed to our integrated Molecular Analysis of Genomes and
      Their Expression (IMAGE) Consortium and thus distributed widely and used
      for sequencing and mapping. In an attempt to facilitate the process of
      gene discovery further, we have also developed a subtractive hybridization
      approach designed specifically to eliminate (or reduce significantly the
      representation of) large pools of arrayed and (mostly) sequenced clones
      from normalized libraries yet to be (or just partly) surveyed. Here we
      present a detailed description and a comparative analysis of four methods
      that we developed and used to generate normalize cDNA libraries from human
      (15), mouse (3), rat (2), as well as the parasite Schistosoma mansoni (1).
      In addition, we describe the construction and preliminary characterization
      of a subtracted liver/spleen library (INFLS-SI) that resulted from the
      elimination (or reduction of representation) of -5000 INFLS-IMAGE clones
      from the INFLS library.
AU  - Bonaldo MF
AU  - Lennon G
AU  - Soares MB
PT  - Journal Article
TA  - Genome Res.
JT  - Genome Res.
SO  - Genome Res. 1996 6: 791-806.

PMID- 2108897
VI  - 66
DP  - 1990
TI  - Interspecies electro-transformation in Corynebacteria.
PG  - 263-270
AB  - Plasmid DNA was efficiently electro-transformed into intact cells of nine Corynebacteria
      strains belonging to Brevibacterium lactofermentum, Brevibacterium flavum, Corynebacterium
      glutamicum and Corynebacterium melassecola.  Relationships were explored between
      transformation efficiency and parameters such as electric field strength and pulse length, DNA
      concentration, physiological state and concentration of the cells.  In optimal conditions,
      more than 10^7 transformants per microgram of DNA could be obtained.  Electrotransformation
      with plasmid DNA isolated from different sources indicates that DNA modification may play a
      role in transformation efficiency.
AU  - Bonamy C
AU  - Guyonvarch A
AU  - Ryes O
AU  - David F
AU  - Leblon G
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1990 66: 263-270.

PMID- 10753866
VI  - 275
DP  - 2000
TI  - Characterization of the human DNA methyltransferase splice variant dnmt1b.
PG  - 10754-10760
AB  - Tissue- and gene-specific patterns of cytosine-DNA methylation are characteristic features of
      vertebrate genomes. The generation and proper maintenance of DNA methylation patterns are
      essential for embryonic development, as demonstrated by the lethal phenotypes of mice with
      either a targeted disruption of Dnmt1, the gene responsible for the maintenance of DNA
      methylation, or targeted disruption of Dnmt3a or Dnmt3b, the genes involved in generation of
      newly formed methylation patterns. Recently, a novel mRNA, Dnmt1b, resulting from alternative
      splicing of Dnmt1 was identified (Hsu, D. W., Lin, M. J., Lee, T. L., Wen, S. C., Chen, X.,
      and Shen, C. K., (1999) Proc. Natl. Acad. Sci. U. S. A. 96, 9751-9756). The abundance of
      Dnmt1b mRNA was estimated by semiquantitative reverse transcription polymerase chain reaction
      and was suggested to encode a major C-5 DNA methyltransferase isoform. Here we report
      characterization of this novel DNA methyltransferase transcript, Dnmt1b, and its protein
      product in human cell lines and in freshly isolated human peripheral blood mononuclear cells.
      The abundance of Dnmt1b transcript, as determined by quantitative RNase protection analysis,
      was determined to range from 6% to 25% of Dnmt1 in human cells. Second generation antisense
      inhibitors targeted to the 5'- and 3'-ends of Dnmt1 inhibited the accumulation of both Dnmt1
      and Dnmt1b in cells. Dnmt1b protein purified from a baculovirus expression system was
      demonstrated to be a functional DNA methyltransferase, and to have Michaelis constants for
      both DNA and S-adenosyl-L-methionine similar to baculovirus-expressed Dnmt1. However,
      antibodies raised against Dnmt1b epitopes demonstrated that Dnmt1b protein was present at
      approximately 2-5% of the level of Dnmt1 and therefore represents only a minor DNA
      methyltransferase isoform in human cells.
AU  - Bonfils C
AU  - Beaulieu N
AU  - Chan E
AU  - Cotton-Montpetit J
AU  - MacLeod AR
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2000 275: 10754-10760.

PMID- 6254986
VI  - 255
DP  - 1980
TI  - Assembly of the mitochondrial membrane system.
PG  - 11927-11941
AB  - The oxi3 locus of yeast mitochondrial DNA has been sequenced in Saccharomyces cerevisiae
      D273-10B. The sequence was obtained from the mitochondrial genomes of a series of cytoplasmic
      "petite" mutants selected for the retention of genetic markers in the oxi3 locus. The oxi3
      locus has been ascertained to code for Subunit 1 of cytochrome oxidase. The Subunit 1 gene is
      9,979 nucleotides long, consisting of seven to eight exons that account for only 16% of the
      gene sequence. The coding sequences have been identified on the basis of protein sequence
      homology with Subunit 1 of human cytochrome oxidase. The yeast Subunit 1 is 510 amino acid
      residues long and has a molecular weight of 56,000. In addition to the exon sequences, the
      Subunit I gene contains six to seven introns. The first four introns have long reading frames
      that are continuous with the exon coding sequences. These reading frames are potentially
      capable for coding for basic proteins with molecular weights ranging from 30,000 to 80,000.
      The first two introns of the gene have a sequence homology of 50%, while the reading frame of
      the fourth intron is 70% homologous with an intron of the apocytochrome b gene. At least five
      stable transcripts have been found by Northern blot hybridizations with single-stranded DNA
      probes containing either exon or intron sequences. A 1.9-kilobase transcript hybridizes only
      with probes from the exon regions of the gene. This RNA species has been tentatively
      identified as the fully processed messenger of Subunit 1. Other transcripts are detected with
      intron probes. Three transcripts with sizes of 2.5, 2.4, and 0.85 kilobases appear to be
      stable excision products from the first, second, and fifth introns.
AU  - Bonitz SG
AU  - Coruzzi G
AU  - Thalenfeld BE
AU  - Tzagoloff A
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1980 255: 11927-11941.

PMID- 2269876
VI  - 136
DP  - 1990
TI  - Transfer of plasmid DNA to Brevibacterium lactofermentum by electrotransformation.
PG  - 2107-2112
AB  - The Escherichia coli-Brevibacterium lactofermentum shuttle vector pBLA was introduced into
      intact cells of B. lactofermentum by electrotransformation.  Several parameters of this
      procedure such as voltage and cell concentration were analysed.  Optimal conditions gave an
      efficiency of 10^6 transformants per microgram of DNA.  Two recalcitrant strains could be
      electrotransformed when an ampicillin pretreatment step was used.  Electrotransformation
      experiments using DNAse or different structural forms of plasmid DNA showed that the
      electrotransformation process is quite different from natural transformation involving
      competence development.  Restriction-modification-proficient B. lactofermentum could be
      efficiently electrotransformed with pBLA DNA isolated from E. coli.  This
      restriction-modification system therefore seems to be overcome by electrotransformation.  Thus
      electrotransformation may efficiently replace the protoplast bacterial transformation method.
AU  - Bonnassie S
AU  - Burini J-F
AU  - Oreglia J
AU  - Trautwetter A
AU  - Patte J-C
AU  - Sicard AM
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1990 136: 2107-2112.

PMID- 2283029
VI  - 72
DP  - 1990
TI  - Isolation and characterization of a restriction and modification deficient mutant of Brevibacterium lactofermentum.
PG  - 143-146
AB  - In order to facilitate genetic engineering in amino-acid producing bacteria we
      have isolated two restriction-deficient Brevibacterium lactofermentum strains.
      They have been selected for their ability to obtain a high yield of plaques
      from CL31 phage which was grown on Corynebacterium lilium.  These mutant
      strains do not restrict either phage DNA by transfection or DNA from the
      shuttle vector pBLA extracted from Escherichia coli by protoplast
      transformation.  These mutants have also lost modification activity.  We also
      report the presence of a restriction modification system in C. lilium ATCC
      15990.
AU  - Bonnassie S
AU  - Oreglia J
AU  - Trautwetter A
AU  - Sicard AM
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1990 72: 143-146.

PMID- 18544605
VI  - 36
DP  - 2008
TI  - Sliding and jumping of single EcoRV restriction enzymes on non-cognate DNA.
PG  - 4118-4127
AB  - The restriction endonuclease EcoRV can rapidly locate a short recognition site within long
      non-cognate DNA using 'facilitated diffusion'. This
      process has long been attributed to a sliding mechanism, in which the
      enzyme first binds to the DNA via nonspecific interaction and then moves
      along the DNA by 1D diffusion. Recent studies, however, provided evidence
      that 3D translocations (hopping/jumping) also help EcoRV to locate its
      target site. Here we report the first direct observation of sliding and
      jumping of individual EcoRV molecules along nonspecific DNA. Using
      fluorescence microscopy, we could distinguish between a slow 1D diffusion
      of the enzyme and a fast translocation mechanism that was demonstrated to
      stem from 3D jumps. Salt effects on both sliding and jumping were
      investigated, and we developed numerical simulations to account for both
      the jump frequency and the jump length distribution. We deduced from our
      study the 1D diffusion coefficient of EcoRV, and we estimated the number
      of jumps occurring during an interaction event with nonspecific DNA. Our
      results substantiate that sliding alternates with hopping/jumping during
      the facilitated diffusion of EcoRV and, furthermore, set up a framework
      for the investigation of target site location by other DNA-binding
      proteins.
AU  - Bonnet I
AU  - Biebricher A
AU  - Porte PL
AU  - Loverdo C
AU  - Benichou O
AU  - Voituriez R
AU  - Escude C
AU  - Wende W
AU  - Pingoud A
AU  - Desbiolles P
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2008 36: 4118-4127.

PMID- 26586886
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Serratia rubidaea CIP 103234T Reference Strain, a Human-Opportunistic Pathogen.
PG  - e01340-15
AB  - We provide here the first genome sequence of a Serratia rubidaea isolate, a
      human-opportunistic pathogen. This reference sequence will permit a comparison of
      this species with others of the Serratia genus.
AU  - Bonnin RA
AU  - Girlich D
AU  - Imanci D
AU  - Dortet L
AU  - Naas T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01340-15.

PMID- 23114767
VI  - 57
DP  - 2013
TI  - Comparative genomics of IncL/M-type plasmids; evolution by acquisition of resistance genes and insertion sequences.
PG  - 674-676
AB  - IncL/M-type plasmids R446b and R471a were originally isolated from Morganella
      morganii (formerly Proteus morganii) as the first members of the IncL/M group of
      multidrug resistance (MDR) plasmids (6, 7)....
AU  - Bonnin RA
AU  - Nordmann P
AU  - Carattoli A
AU  - Poirel L
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2013 57: 674-676.

PMID- 22511964
VI  - 7
DP  - 2012
TI  - Characterization of an IncFII Plasmid Encoding NDM-1 from Escherichia coli ST131.
PG  - E34752
AB  - BACKGROUND: The current spread of the gene encoding the metallo-ss-lactamase
      NDM-1 in Enterobacteriaceae is linked to a variety of surrounding genetic
      structures and plasmid scaffolds. METHODOLOGY: The whole sequence of plasmid
      pGUE-NDM carrying the bla(NDM-1) gene was determined by high-density
      pyrosequencing and a genomic comparative analysis with other bla(NDM-1)-negative
      IncFII was performed. PRINCIPAL FINDINGS: Plasmid pGUE-NDM replicating in
      Escherichia coli confers resistance to many antibiotic molecules including
      beta-lactams, aminoglycosides, trimethoprim, and sulfonamides. It is 87,022 bp
      in-size and carries the two beta-lactamase genes bla(NDM-1) and bla(OXA-1),
      together with three aminoglycoside resistance genes aacA4, aadA2, and aacC2.
      Comparative analysis of the multidrug resistance locus contained a module
      encompassing the bla(NDM-1) gene that is actually conserved among different
      structures identified in other enterobacterial isolates. This module was
      constituted by the bla(NDM-1) gene, a fragment of insertion sequence ISAba125 and
      a bleomycin resistance encoding gene. SIGNIFICANCE: This is the first
      characterized bla(NDM-1)-carrying IncFII-type plasmid. Such association between
      the bla(NDM-1) gene and an IncFII-type plasmid backbone is extremely worrisome
      considering that this plasmid type is known to spread efficiently, as examplified
      with the worldwide dissemination of bla(CTX-M-15)-borne IncFII plasmids.
AU  - Bonnin RA
AU  - Poirel L
AU  - Carattoli A
AU  - Nordmann P
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2012 7: E34752.

PMID- 23354281
VI  - 68
DP  - 2013
TI  - Complete sequence of broad-host-range plasmid pNOR-2000 harbouring the metallo-beta-lactamase gene blaVIM-2 from Pseudomonas aeruginosa.
PG  - 1060-1065
AB  - OBJECTIVES: Metallo-beta-lactamases (MBLs) are increasingly reported not only in
      Enterobacteriaceae but also in Pseudomonas spp. These enzymes hydrolyse all
      beta-lactams, including carbapenems, and are not inhibited by beta-lactamase
      inhibitors. The aim of this study was to fully characterize a plasmid bearing the
      bla(VIM-2) MBL gene identified in a Pseudomonas aeruginosa isolate. METHODS: This
      plasmid was fully sequenced by high-density pyrosequencing and annotated using
      the GenDB version 2.0 annotation tool. The evaluation of the broad-host-range
      replication of the pNOR-2000 replication initiation gene was assessed using
      electro-transformation and conjugation assays and the distribution of this
      replicase gene was evaluated using an international collection of VIM-producing
      Pseudomonas spp. RESULTS: Analysis of the 21 880 bp sequence of pNOR-2000
      revealed a truncated and non-functional transfer operon, in addition to novel
      genes encoding a serine protease and toxin/antitoxin addiction systems. This
      broad-host-range plasmid shares high gene synteny with part of the mobile genomic
      island pKLC102 identified in P. aeruginosa strain C. CONCLUSIONS: We report here
      the complete nucleotide sequence of plasmid pNOR-2000 from a P. aeruginosa
      clinical isolate harbouring the integron-located MBL gene bla(VIM-2).
AU  - Bonnin RA
AU  - Poirel L
AU  - Nordmann P
AU  - Eikmeyer FG
AU  - Wibberg D
AU  - Puhler A
AU  - Schluter A
PT  - Journal Article
TA  - J. Antimicrob. Chemother.
JT  - J. Antimicrob. Chemother.
SO  - J. Antimicrob. Chemother. 2013 68: 1060-1065.

PMID- 21962489
VI  - 160
DP  - 2012
TI  - Using the fluorescence decay of 2-aminopurine to investigate conformational change in the recognition sequence of the EcoRV DNA-(adenine-N6)-methyltransferase on enzyme binding.
PG  - 28-34
AB  - The EcoRV DNA methyltransferase methylates the first adenine in the GATATC recognition
      sequence. It is presumed that methylation proceeds
      by a nucleotide flipping mechanism but no crystal structure is
      available to confirm this. A popular solution-phase assay for
      nucleotide flipping employs the fluorescent adenine analogue,
      2-aminopurine (2AP), substituted at the methylation target site; a
      substantial increase in fluorescence intensity on enzyme binding
      indicates flipping. However, this appeared to fail for M.EcoRV, since
      2AP substituted for the non-target adenine in the recognition sequence
      showed a much greater intensity increase than 2AP at the target site.
      This anomaly is resolved by recording the fluorescence decay of 2AP
      which shows that the target 2AP is indeed flipped by the enzyme, but
      its fluorescence is quenched by interaction with aromatic residues in
      the catalytic site, whereas bending of the duplex at the non-target
      site alleviates inter-base quenching and exposes the 2AP to solvent.
AU  - Bonnist EYM
AU  - Liebert K
AU  - Dryden DTF
AU  - Jeltsch A
AU  - Jones AC
PT  - Journal Article
TA  - Biophys. Chem.
JT  - Biophys. Chem.
SO  - Biophys. Chem. 2012 160: 28-34.

PMID- 24510259
VI  - 1123
DP  - 2014
TI  - Mapping Homing Endonuclease Cleavage Sites Using In Vitro Generated Protein.
PG  - 55-67
AB  - Mapping the precise position of endonucleolytic cleavage sites is a fundamental experimental
      technique used to describe the function of a homing endonuclease. However, these proteins are
      often recalcitrant to cloning and over-expression in biological systems because of toxicity
      induced by spurious DNA cleavage events. In this chapter we outline the steps to successfully
      express a homing endonuclease in vitro and use this product in nucleotide-resolution cleavage
      assays.
AU  - Bonocora RP
AU  - Belfort M
PT  - Journal Article
TA  - Methods Mol. Biol.
JT  - Methods Mol. Biol.
SO  - Methods Mol. Biol. 2014 1123: 55-67.

PMID- 15547290
VI  - 186
DP  - 2004
TI  - A self-splicing group I intron in DNA polymerase genes of T7-like bacteriophages.
PG  - 8153-8155
AB  - Group I introns are inserted into genes of a wide variety of bacteriophages of gram-positive
      bacteria. However, among the phages of
      enteric and other gram-negative proteobacteria, introns have been
      encountered only in phage T4 and several of its close relatives. Here we
      report the insertion of a self-splicing group I intron in the coding
      sequence of the DNA polymerase genes of PhiI and W31, phages that are
      closely related to T7. The introns belong to subgroup IA2 and both contain
      an open reading frame, inserted into structural element P6a, encoding a
      protein belonging to the HNH family of homing endonucleases. The introns
      splice efficiently in vivo and self-splice in vitro under mild conditions
      of ionic strength and temperature. We conclude that there is no barrier
      for maintenance of group I introns in phages of proteobacteria.
AU  - Bonocora RP
AU  - Shub DA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2004 186: 8153-8155.

PMID- 19200727
VI  - 19
DP  - 2009
TI  - A likely pathway for formation of mobile group I introns.
PG  - 223-228
AB  - Mobile group I introns are RNA splicing elements that have been invaded by endonuclease genes.
      These endonucleases facilitate intron mobility by a
      unidirectional, duplicative gene-conversion process known as homing [1].
      Survival of the invading endonuclease depends upon its ability to promote
      intron mobility. Therefore, the endonuclease must either quickly change
      its cleavage specificity to match the site of intron insertion, or it must
      already be preadapted to cleave this sequence. Here we show that the group
      I intron in the DNA polymerase gene of T7-like bacteriophage PhiI is
      mobile, dependent upon its intronic HNH homing endonuclease gene, I-TslI.
      We also show that gene 5.3 of phage T3, located adjacent to its intronless
      DNA polymerase gene, is a homologous homing endonuclease gene whose
      protein product initiates efficient spread of gene 5.3 into empty sites in
      related phages. Both of these endonucleases cleave intronless DNA
      polymerase genes at identical positions. This shared feature between an
      intronic and free-standing endonuclease is unprecedented. Based on this
      evidence, we propose that introns and their homing endonucleases evolve
      separately to target the same highly conserved sequences, uniting
      afterwards to create a composite mobile element.
AU  - Bonocora RP
AU  - Shub DA
PT  - Journal Article
TA  - Curr. Biol.
JT  - Curr. Biol.
SO  - Curr. Biol. 2009 19: 223-228.

PMID- 11251845
VI  - 39
DP  - 2001
TI  - A novel group I intron-encoded endonuclease specific for the anticodon region of tRNA(fMet) genes.
PG  - 1299-1306
AB  - Open reading frames (ORFs) are frequently inserted into group I self-splicing introns. These
      ORFs encode either maturases that are
      required for splicing of the intron or DNA endonucleases that promote
      intron mobility. A self-splicing intron in the tRNA(fMet) gene of
      Synechocystis PCC 6803, which has been proposed to have moved laterally
      within the cyanobacteria, contains an ORF that is unrelated to known
      intron-encoded endonucleases or maturases. Here, using an in vitro
      transcription-translation system, we show that this intronic ORF
      encodes a double-strand DNA endonuclease, I-Ssp6803I. I-Ssp6803I
      cleaves each strand of the intronless tRNA(fMet) gene adjacent to the
      anticodon triplet leaving 3 bp 3' extensions and has no activity at
      intron-exon boundaries. Using an in vitro cleavage assay and scanning
      deletion mutants of the intronless target site, the minimal recognition
      site was determined to be a partially palindromic 20 bp region
      encompassing the entire anticodon stem and loop of the tRNA(fMet) gene.
      I-Ssp6803I represents a novel intron-encoded DNA endonuclease and is
      the first example of a chromosomally encoded group I intron
      endonuclease in bacteria.
AU  - Bonocora RP
AU  - Shub DA
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2001 39: 1299-1306.

PMID- 28798163
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Multiple Frackibacter Strains Isolated from Hydraulically Fractured Shale Environments.
PG  - e00608-17
AB  - The genomes of three novel Frackibacter strains (WG11, WG12, and WG13) were sequenced. These
      strains were isolated from hypersaline fluid collected from a
      hydraulically fractured natural gas well. These genomes provide information on
      the mechanisms necessary for growth in these environments and offer insight into
      interactions with other community members.
AU  - Booker AE
AU  - Johnston MD
AU  - Daly RA
AU  - Wrighton KC
AU  - Wilkins MJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00608-17.

PMID- 11875430
VI  - 20
DP  - 2002
TI  - An electrical probe of protein-DNA interactions on DNA-modified surfaces.
PG  - 282-286
AB  - DNA charge transport chemistry is found to provide a sensitive method for probing
      protein-dependent changes in DNA structure and enzymatic reactions. Here we describe the
      development of an electrochemical assay of protein binding to DNA-modified electrodes based
      upon the detection of associated perturbations in DNA base stacking. Gold electrode surfaces
      that were modified with loosely packed DNA duplexes, covalently crosslinked to a redox-active
      intercalator and containing the binding site of the test protein, were constructed. Charge
      transport through DNA as a function of protein binding was then assayed. Substantial
      attenuation in current is seen in the presence of the base-flipping enzymes HhaI methylase and
      uracil DNA glycosylase, as well as with TATA-binding protein. When restriction endonuclease
      PvuII (R.PvuII) binds to its methylated target, little base-stacking perturbation occurs and
      little diminution in current flow is observed. Importantly, the kinetics of restriction by
      R.PvuII of its nonmethylated target is also easily monitored electrochemically. This approach
      should be generally applicable to assaying protein--DNA interactions and reactions on
      surfaces.
AU  - Boon EM
AU  - Salas JE
AU  - Barton JK
PT  - Journal Article
TA  - Nat. Biotechnol.
JT  - Nat. Biotechnol.
SO  - Nat. Biotechnol. 2002 20: 282-286.

PMID- 25197459
VI  - 9
DP  - 2014
TI  - Draft genome sequences and description of Lactobacillus rhamnosus strains L31, L34, and L35.
PG  - 744-754
AB  - Lactobacillus rhamnosus is a facultative, lactic acid bacterium in the phylum Firmicutes.
      Lactobacillus spp. are generally considered beneficial, and specific
      strains of L. rhamnosus are validated probiotics. We describe the draft genomes
      of three L. rhamnosus strains (L31, L34, and L35) isolated from the feces of Thai
      breastfed infants, which exhibit anti-inflammatory properties in vitro. The three
      genomes range between 2.8 - 2.9 Mb, and contain approximately 2,700 protein
      coding genes.
AU  - Boonma P
AU  - Spinler JK
AU  - Qin X
AU  - Jittaprasatsin C
AU  - Muzny DM
AU  - Doddapaneni H
AU  - Gibbs R
AU  - Petrosino J
AU  - Tumwasorn S
AU  - Versalovic J
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 744-754.

PMID- 24233591
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Geobacillus thermoleovorans Strain B23.
PG  - e00944-13
AB  - Here, we report the draft genome sequence of Geobacillus thermoleovorans strain B23, which was
      isolated from a deep subterranean petroleum reservoir in Japan. An
      array of genes related to unique long-chain alkane degradation pathways in G.
      thermoleovorans B23 has been identified by whole-genome analyses of this strain.
AU  - Boonmak C
AU  - Takahasi Y
AU  - Morikawa M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00944-13.

PMID- 
VI  - 134
DP  - 2014
TI  - Inhibition of restriction endonucleases by biofunctionalized silver nanoparticles: An in vitro study.
PG  - 24-26
AB  - Ecofriendly synthesis of metal nanoparticles and their unique properties hold promise for
      innovative therapeutic applications. In the present study, rapid, novel, low cost method for
      synthesis of silver nanoparticles (AgNPs) using aqueous leaves extract of medicinal plant
      Euphorbia heterophylla (E. heterophylla) is reported. AgNPs synthesized by plant extract
      exhibited absorption peak at 422 nm in UV-vis spectroscopy. Transmission electron microscopy
      micrographs revealed presence of AgNPs with average size of 13 nm with grain and triangular
      shapes. Fourier Transform Infrared Spectroscopy analysis revealed role of leaves metabolites
      as reducing and capping agent in synthesis of AgNPs. X ray diffraction pattern and selected
      area electron diffraction study confirmed crystalline nature of AgNPs. Inhibition of DNA
      cutting activity of restriction endonucleases (EcoRI, HindIII and BamHI) by biofunctionalized
      AgNPs in agarose gel electrophoresis is first time reported in the present study. This
      potential of AgNPs can be useful for enhancing effectiveness of phage therapy by acting as
      synergistic cocktail with bacteriophages to kill bacteria via inhibition of their restriction
      endonucleases.
AU  - Borase HP
AU  - Patil CD
AU  - Salunkhe RB
AU  - Suryawanshi RK
AU  - Salunke BK
AU  - Patil SV
PT  - Journal Article
TA  - Mater. Lett.
JT  - Mater. Lett.
SO  - Mater. Lett. 2014 134: 24-26.

PMID- 785220
VI  - 146
DP  - 1976
TI  - The construction in vitro of transducing derivatives of phage lambda.
PG  - 199-207
AB  - Methods are described for the construction of plaque-forming, transducing
      derivatives of phage lambda, using appropriate receptor genomes and fragments
      of DNA generated by the restriction enzymes endo R.EcoRI and endo R.HindIII.
      The general properties of the transducing derivatives are described and
      discussed.  Plaque-forming phages carrying the E. coli trp, his, cysB, thyA,
      supD, supE, supF, hsd, tna and lig genes have been isolated.
AU  - Borck K
AU  - Beggs JD
AU  - Brammar WJ
AU  - Hopkins AS
AU  - Murray NE
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1976 146: 199-207.

PMID- Not included in PubMed...
VI  - 35
DP  - 1966
TI  - The methylation of nucleic acids.
PG  - 275-298
AB  - The evidence for the methylation of nucleic acids at the macromolecular level
      has been presented in several review articles and, therefore, will not be
      repeated here.  The biochemistry of the phenomenon will be emphasized in this
      article and the biological implications in a companion article in which all
      alterations of macromolecules effected by enzymes will be reviewed.
AU  - Borek E
AU  - Srinivasan PR
PT  - Journal Article
TA  - Annu. Rev. Biochem.
JT  - Annu. Rev. Biochem.
SO  - Annu. Rev. Biochem. 1966 35: 275-298.

PMID- 2454631
VI  - 14
DP  - 1988
TI  - Synthetic oligodeoxynucleotides in studying MspI restriction endonuclease.
PG  - 333-339
AB  - Interaction of MspI restriction endonuclease with a series of
      oligodeoxynucleotides varying in stability of secondary structure and in
      location of the restriction site, has been studied.  It is shown that a
      functionally active MspI site must be double-stranded and flanked from both
      sides.  Separate MspI cleavage of dodecanucleotides dCGACCCGGGATC and
      dGATCCCGGGTCG is inhibited by the reaction products as well as by
      non-homological hexanucleotides dGGTACC and dGGATCC (but not by dCGGCGC).
      Polyethylene glycol in low concentrations (1-3%) promotes and in higher
      concentrations (7-14%) inhibits the cleavage.  A scheme of MspI functioning is
      suggested including the enzyme's step-by-step recognition of the restriction
      site and its nonspecific interaction with flanking segments of DNA, which leads
      to formation of the productive complex.
AU  - Boreskov YG
AU  - Titeeva GR
AU  - Berlin YA
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1988 14: 333-339.

PMID- 23671703
VI  - 8
DP  - 2013
TI  - Fidelity Index Determination of DNA Methyltransferases.
PG  - e63866
AB  - DNA methylation is the most frequent form of epigenetic modification in the cell, which
      involves gene regulation in eukaryotes and protection
      against restriction enzymes in prokaryotes. Even though many
      methyltransferases exclusively modify their cognate sites, there have
      been reports of those that exhibit promiscuity. Previous experimental
      approaches used to characterize these methyltransferases do not provide
      the exact concentration at which off-target methylation occurs. Here,
      we present the first reported fidelity index (FI) for a number of DNA
      methyltransferases. We define the FI as the ratio of the highest amount
      of methyltransferase that exhibits no star activity (off-target
      effects) to the lowest amount that exhibits complete modification of
      the cognate site. Of the methyltransferases assayed, M. MspI and M.
      AluI exhibited the highest fidelity of >= 250 and >= 500, respectively,
      and do not show star activity even at very high concentrations. In
      contrast, M. HaeIII, M.EcoKDam and M. BamHI have the lowest fidelity of
      4, 4 and 2, respectively, and exhibit star activity at concentrations
      close to complete methylation of the cognate site. The fidelity indexes
      provide vital information on the usage of methyltransferases and are
      especially important in applications where site specific methylation is
      required.
AU  - Borgaro JG
AU  - Benner N
AU  - Zhu ZY
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2013 8: e63866.

PMID- 23482393
VI  - 41
DP  - 2013
TI  - Characterization of the 5-hydroxymethylcytosine-specific DNA restriction endonucleases.
PG  - 4198-4206
AB  - In T4 bacteriophage, 5-hydroxymethylcytosine (5hmC) is incorporated into DNA during
      replication. In response, bacteria may have developed
      modification-dependent type IV restriction enzymes to defend the cell from
      T4-like infection. PvuRts1I was the first identified restriction enzyme to
      exhibit specificity toward hmC over 5-methylcytosine (5mC) and cytosine. By using
      PvuRts1I as the original member, we identified and characterized a number of
      homologous proteins. Most enzymes exhibited similar cutting properties to
      PvuRts1I, creating a double-stranded cleavage on the 3' side of the modified
      cytosine. In addition, for efficient cutting, the enzymes require two cytosines
      21-22-nt apart and on opposite strands where one cytosine must be modified.
      Interestingly, the specificity determination unveiled a new layer of complexity
      where the enzymes not only have specificity for 5-beta-glucosylated hmC
      (5betaghmC) but also 5-alpha-glucosylated hmC (5alphaghmC). In some cases, the
      enzymes are inhibited by 5betaghmC, whereas in others they are inhibited by
      5alphaghmC. These observations indicate that the position of the sugar ring
      relative to the base is a determining factor in the substrate specificity of the
      PvuRts1I homologues. Lastly, we envision that the unique properties of select
      PvuRts1I homologues will permit their use as an additive or alternative tool to
      map the hydroxymethylome.
AU  - Borgaro JG
AU  - Zhu Z
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2013 41: 4198-4206.

PMID- 1666962
VI  - 4
DP  - 1991
TI  - Chromium Bound to DNA alters cleavage by restriction endonucleases.
PG  - 638-641
AB  - None
AU  - Borges KM
AU  - Wetterhahn KE
PT  - Journal Article
TA  - Chem. Res. Toxicol.
JT  - Chem. Res. Toxicol.
SO  - Chem. Res. Toxicol. 1991 4: 638-641.

PMID- 7476192
VI  - 16
DP  - 1995
TI  - Exploring the Mycoplasma capricolum genome: a minimal cell reveals its physiology.
PG  - 955-967
AB  - We report on the analysis of 214kb of the parasitic eubacterium Mycoplasma capricolum
      sequenced by genomic walking techniques. The 287 putative proteins detected to date represent
      about half of the estimated total number of 500 predicted for this organism. A large fraction
      of these (75%) can be assigned a likely function as a result of similarity searches. Several
      important features of the functional organization of this small genome are already apparent.
      Among these are (i) the expected relatively large number of enzymes involved in metabolic
      transport and activation, for efficient use of host cell nutrients; (ii) the presence of
      anabolic enzymes; (iii) the unexpected diversity of enzymes involved in DNA replication and
      repair; and (iv) a sizeable number of orthologues (82 so far) in Escherichia coli. This survey
      is beginning to provide a detailed view of how M. capricolum manages to maintain essential
      cellular processes with a genome much smaller than that of its bacterial relatives.
AU  - Bork P
AU  - Ouzounis C
AU  - Casari G
AU  - Schneider R
AU  - Sander C
AU  - Dolan M
AU  - Gilbert W
AU  - Gillevet PM
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1995 16: 955-967.

PMID- 20111862
VI  - 86
DP  - 2010
TI  - Genotypic diversity in Oenococcus oeni by high-density microarray comparative genome hybridization and whole genome sequencing.
PG  - 681-691
AB  - Many bacteria display substantial intra-specific genomic diversity that
      produces significant phenotypic variation between strains of the same
      species. Understanding the genetic basis of these strain-specific
      phenotypes is especially important for industrial microorganisms where
      these characters match individual strains to specific industrial
      processes. Oenococcus oeni, a bacterium used during winemaking, is one
      such industrial species where large numbers of strains show significant
      differences in commercially important industrial phenotypes. To ascertain
      the basis of these phenotypic differences, the genomic content of ten wine
      strains of O. oeni were mapped by array-based comparative genome
      hybridization (aCGH). These strains comprised a genomically diverse group
      in which large sections of the reference genome were often absent from
      individual strains. To place the aCGH results in context, whole genome
      sequence was obtained for one of these strains and compared with two
      previously sequenced, unrelated strains. While the three strains shared a
      core group of conserved ORFs, up to 10% of the coding potential of any one
      strain was specific to that isolate. The genome of O. oeni is therefore
      likely to be much larger than that present in any single strain and it is
      these strain-specific regions that are likely to be responsible for
      differences in industrial phenotypes.
AU  - Borneman AR
AU  - Bartowsky EJ
AU  - McCarthy J
AU  - Chambers PJ
PT  - Journal Article
TA  - Appl. Microbiol. Biotechnol.
JT  - Appl. Microbiol. Biotechnol.
SO  - Appl. Microbiol. Biotechnol. 2010 86: 681-691.

PMID- 2498058
VI  - 304
DP  - 1989
TI  - PaeD253 restriction-modification system determined by pBS253 biodegradation plasmid of Pseudomonas aeruginosa.
PG  - 1472-1474
AB  - None
AU  - Boronin AM
AU  - Kochetkov VV
AU  - Kulakov LA
AU  - Tusupbekova GA
AU  - Alieva RM
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1989 304: 1472-1474.

PMID- 19923434
VI  - 106
DP  - 2009
TI  - Identification of a region of the DNMT1 methyltransferase that regulates the maintenance of genomic imprints.
PG  - 20806-20811
AB  - Reprogramming of DNA methylation patterns during mammalian preimplantation development
      involves the concurrent maintenance of
      methylation on differentially methylated domains (DMDs) of imprinted
      genes and a marked reduction of global (non-DMD) genomic methylation.
      In the developing mammalian embryo, one allele of a DMD is
      unmethylated, and the opposite parental allele is methylated, having
      inherited this methylation from the parental gamete. The maintenance of
      DMDs is important for monoallelic imprinted gene expression and normal
      development of the embryo. Because the DNMT1 cytosine methyltransferase
      governs maintenance methylation in mammals, rearrangements of non-DMD,
      but not DMD methylation in preimplantation embryos suggest that the
      preimplantation DNMT1-dependent maintenance mechanism specifically
      targets DMD sequences. We explored this possibility using an engineered
      mouse ES cell line to screen for mutant DNMT1 proteins that protect
      against the loss of DMD and/or global (non-DMD) methylation in the
      absence of the wild-type endogenous DNMT1 methyltransferase. We
      identified DNMT1 mutants that were defective in maintenance of
      either-DMD and/or non-DMD methylation. Among these, one mutant
      maintained non-DMD methylation but not imprinted DMD methylation and
      another mutant maintained just DMD methylation. The mutated amino acids
      of these mutants reside in a mammal-specific, disordered region near
      the amino terminus of DNMT1. These findings suggest that DNMT1
      participates in epigenetic reprogramming through its ability to
      distinguish different categories of methylated sequences.
AU  - Borowczyk E
AU  - Mohan KN
AU  - D'Aiuto L
AU  - Cirio MC
AU  - Chaillet JR
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2009 106: 20806-20811.

PMID- 29700156
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of a VIM-1-Producing Salmonella enterica subsp. enterica Serovar Infantis Isolate Derived from Minced Pork Meat.
PG  - e00327-18
AB  - Carbapenems are considered last-resort antibiotics used to treat human infections caused by
      multidrug-resistant bacteria. In 2011, VIM-1 carbapenemase-producing
      Salmonella enterica subsp. enterica serovar Infantis strains were isolated from
      livestock for the first time in Germany. Here, we announce the complete genome
      sequence of the first German blaVIM-1-harboring Salmonella Infantis isolate
      (15-SA01028) originating from food.
AU  - Borowiak M
AU  - Fischer J
AU  - Baumann B
AU  - Hammerl JA
AU  - Szabo I
AU  - Malorny B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00327-18.

PMID- 28912328
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Paratyphi B Sequence Type 28 Harboring mcr-1.
PG  - e00991-17
AB  - In 2015, plasmid-mediated colistin resistance was reported to be caused by a mobilized
      phosphoethanolamine transferase gene (mcr-1) in Enterobacteriaceae
      Here, we announce the complete genome sequence of the earliest
      d-tartrate-fermenting Salmonella enterica subsp. enterica serovar Paratyphi B
      isolate harboring mcr-1 from the collection of the German National Reference
      Laboratory for Salmonella.
AU  - Borowiak M
AU  - Hammerl JA
AU  - Fischer J
AU  - Szabo I
AU  - Malorny B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00991-17.

PMID- 28572311
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Mycobacterium kansasii Clinical Strains.
PG  - e00406-17
AB  - Mycobacterium kansasii is a nontuberculous mycobacterial (NTM) pathogen, frequently isolated
      from clinical samples and responsible for a large part of NTM
      infections in the human population. Here, we report the draft genome sequences of
      12 M. kansasii strains isolated from clinical and host-associated sources from
      the Netherlands, Germany, and Poland.
AU  - Borowka P
AU  - Lach J
AU  - Bakula Z
AU  - van Ingen J
AU  - Safianowska A
AU  - Brzostek A
AU  - Dziadek J
AU  - Strapagiel D
AU  - Jagielski T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00406-17.

PMID- 23846268
VI  - 1
DP  - 2013
TI  - Genome Sequence of 'Candidatus Methanomassiliicoccus intestinalis' Issoire-Mx1, a Third Thermoplasmatales-Related Methanogenic Archaeon from Human Feces.
PG  - e00453-13
AB  - 'Candidatus Methanomassiliicoccus intestinalis' Issoire-Mx1 is a methanogenic archaeon found
      in the human gut and is a representative of the novel order of
      methanogens related to Thermoplasmatales. Its complete genome sequence is
      presented here.
AU  - Borrel G
AU  - Harris HM
AU  - Parisot N
AU  - Gaci N
AU  - Tottey W
AU  - Mihajlovski A
AU  - Deane J
AU  - Gribaldo S
AU  - Bardot O
AU  - Peyretaillade E
AU  - Peyret P
AU  - O'Toole PW
AU  - Brugere JF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00453-13.

PMID- 23209209
VI  - 194
DP  - 2012
TI  - Genome Sequence of 'Candidatus Methanomethylophilus alvus' Mx1201, a Methanogenic Archaeon from the Human Gut Belonging to a Seventh Order of Methanogens.
PG  - 6944-6945
AB  - We report the draft genome sequence of 'Candidatus Methanomethylophilus alvus' Mx1201, a
      methanogen present in the human gut. It was enriched from human feces
      under anaerobic conditions with methanol as the substrate. Its circular genome,
      of around 1.7 Mb, contains genes needed for methylotrophic methanogenesis from
      methanol and tri-, di-, and monomethylamine.
AU  - Borrel G
AU  - Harris HM
AU  - Tottey W
AU  - Mihajlovski A
AU  - Parisot N
AU  - Peyretaillade E
AU  - Peyret P
AU  - Gribaldo S
AU  - O'Toole PW
AU  - Brugere JF
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6944-6945.

PMID- 16932843
VI  - 11
DP  - 2007
TI  - Genome and proteome characterization of the psychrophilic Flavobacterium bacteriophage 11b.
PG  - 95-104
AB  - Virion DNA of bacteriophage 11b (phi 11b), which infects a psychrophilic Flavobacterium
      isolate from Arctic sea-ice, was
      determined to consist of 36,012 bp. With 30.6% its GC content
      corresponds to that of host-genus species and is the lowest of all
      phages of Gram-negative bacteria sequenced so far. Similarities of
      several of 65 predicted ORFs, genome organization and phylogeny suggest
      an affiliation to 'mesophilic' nonmarine siphoviruses, e.g. to
      bacteriophages SPP1 and HK97. Early genes presumably encode an
      essential recombination factor (ERF), a single strand binding (SSB)
      protein, an endonuclease, and a DNA methylase. The late gene segment is
      likely to contain a terminase, portal, minor head, protease and a major
      capsid gene. Five ORFs exhibited similarities to Bacteroidetes species
      and seem to reflect the host specificity of the phage. Among
      PAGE-separated virion proteins that were identified by MALDI-ToF mass
      spectrometry are the portal, the major capsid, and a putative conserved
      tail protein. The phi 11b genome is the first to be described of a
      cultivated virus infecting a psychrophilic host as well as a
      Bacteroidetes bacterium.
AU  - Borriss M
AU  - Lombardot T
AU  - Glockner FO
AU  - Becher D
AU  - Albrecht D
AU  - Schweder T
PT  - Journal Article
TA  - Extremophiles
JT  - Extremophiles
SO  - Extremophiles 2007 11: 95-104.

PMID- 20817842
VI  - 61
DP  - 2011
TI  - Relationship of Bacillus amyloliquefaciens clades associated with strains DSM7T and FZB42: a proposal for Bacillus amyloliquefaciens subsp. amyloliquefaciens subsp. nov. and plantarum subsp. nov. based on their discriminating complete genome sequences.
PG  - 1786-1801
AB  - The whole genome sequenced rhizobacterium FZB42 (Chen et al., 2007) and other plant-associated
      Bacillus strains either designated as Bacillus amyloliquefaciens or Bacillus subtilis are used
      commercially to promote growth and health of crop plants. Previous investigations revealed
      that the strains represent an own ecotype related to B. amyloliquefaciens, however its exact
      taxonomic position remains elusive (Reva et al., 2004). Here we have demonstrated ability to
      colonize Arabidopsis roots for a group of Bacillus strains, closely related to FZB42.
      According to their phenotypic traits the strains were similar to Bacillus amyloliquefaciens
      DSM 7T, but differed considerably in DNA sequences of the genes encoding 16S rRNA, gyrase
      subunit A (gyrA), and histidine kinase (cheA) from the type strain. Phylogenetic analysis
      performed with partial 16S rRNA, gyrA, and cheA sequences revealed that plant-associated
      Bacillus strains including FZB42 form a lineage, which can be discriminated from the cluster
      of strains closely related to B. amyloliquefaciens DSM 7T. DNA-DNA hybridization (DDH)
      performed with genomic DNAs from DSM 7T and FZB42 yielded 63.7 to 71.2 % homology. As
      complementary approach, we used several genomic methods, as direct whole genome comparison,
      digital DDH, and microarray-based comparative genomic hybridization (M-CGH). Plant-associated
      strains were discriminated from DSM 7T and B. subtilis type strain by their different
      potential to synthesize non-ribosomally lipopeptides and polyketides. According to the
      differences found in marker gene sequences and the whole genomes, we propose the two B.
      amyloliquefaciens subspecies, 'plantarum' for their plant-associated, and
      'amyloliquefaciens', for their non-plant associated representatives. This is in line with
      results of DDH, MCGH, and the MALDI TOF mass spectrometry of cellular components which are
      justifying that both ecovars represent two different subspecies.
AU  - Borriss R
AU  - Chen X
AU  - Rueckert C
AU  - Blom J
AU  - Becker A
AU  - Baumgarth B
AU  - Fan B
AU  - Pukall R
AU  - Schumann P
AU  - Sproer C
AU  - Junge H
AU  - Vater J
AU  - Puhler A
AU  - Klenk HP
PT  - Journal Article
TA  - Int. J. Syst. Evol. Microbiol.
JT  - Int. J. Syst. Evol. Microbiol.
SO  - Int. J. Syst. Evol. Microbiol. 2011 61: 1786-1801.

PMID- 25860249
VI  - 10
DP  - 2015
TI  - Comparative genomic analysis identifies divergent genomic features of pathogenic Enterococcus cecorum including a type IC CRISPR-Cas system, a capsule locus, an epa-like locus, and putative host tissue binding proteins.
PG  - E0121294
AB  - Enterococcus cecorum (EC) is the dominant enteric commensal of adult chickens and
      contributes to the gut consortia of many avian and mammalian species. While EC
      infection is an uncommon zoonosis, like other enterococcal species it can cause
      life-threating nosocomial infection in people. In contrast to other enterococci
      which are considered opportunistic pathogens, emerging pathogenic strains of EC
      cause outbreaks of musculoskeletal disease in broiler chickens. Typical morbidity
      and mortality is comparable to other important infectious diseases of poultry. In
      molecular epidemiologic studies, pathogenic EC strains were found to be
      genetically clonal. These findings suggested acquisition of specific virulence
      determinants by pathogenic EC. To identify divergent genomic features and
      acquired virulence determinants in pathogenic EC; comparative genomic analysis
      was performed on genomes of 3 pathogenic and 3 commensal strains of EC.
      Pathogenic isolates had smaller genomes with a higher GC content, and they
      demonstrated large regions of synteny compared to commensal isolates. A molecular
      phylogenetic analysis demonstrated sequence divergence in pathogenic EC genomes.
      At a threshold of 98% identity, 414 predicted proteins were identified that were
      highly conserved in pathogenic EC but not in commensal EC. Among these, divergent
      CRISPR-cas defense loci were observed. In commensal EC, the type IIA arrangement
      typical for enterococci was present; however, pathogenic EC had a type IC locus,
      which is novel in enterococci but commonly observed in streptococci. Potential
      mediators of virulence identified in this analysis included a polysaccharide
      capsular locus similar to that recently described for E. faecium, an epa-like
      locus, and cell wall associated proteins which may bind host extracellular
      matrix. This analysis identified specific genomic regions, coding sequences, and
      predicted proteins which may be related to the divergent evolution and increased
      virulence of emerging pathogenic strains of EC.
AU  - Borst LB
AU  - Suyemoto MM
AU  - Scholl EH
AU  - Fuller FJ
AU  - Barnes HJ
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2015 10: E0121294.

PMID- 27789644
VI  - 4
DP  - 2016
TI  - Genome Sequence of the Multiple-Protease-Producing Strain Geobacillus thermoleovorans N7, a Thermophilic Bacterium Isolated from Paniphala Hot Spring,   West Bengal, India.
PG  - e01202-16
AB  - Here, we present the draft genome sequence of Geobacillus thermoleovorans strain  N7 (MCC
      3175), isolated from Paniphala Hot Spring, West Bengal, India, which
      contains genes that encode several industrially and medically important
      thermostable enzymes like neutral protease, xylose isomerase, rhamnogalacturonan
      acetylesterase, nitrate and nitrite reductase, l-asparaginase, glutaminase, and
      RNase P.
AU  - Bose S
AU  - Mukherjee T
AU  - Sen U
AU  - Roy C
AU  - Rameez MJ
AU  - Ghosh W
AU  - Mukhopadhyay SK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01202-16.

PMID- 28095778
VI  - 18
DP  - 2017
TI  - The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights.
PG  - 93
AB  - BACKGROUND: Pseudoalteromonas is a genus of ubiquitous marine bacteria used as model organisms
      to study the biological mechanisms involved in the adaptation to
      cold conditions. A remarkable feature shared by these bacteria is their ability
      to produce secondary metabolites with a strong antimicrobial and antitumor
      activity. Despite their biotechnological relevance, representatives of this genus
      are still lacking (with few exceptions) an extensive genomic characterization,
      including features involved in the evolution of secondary metabolites production.
      Indeed, biotechnological applications would greatly benefit from such analysis.
      RESULTS: Here, we analyzed the genomes of 38 strains belonging to different
      Pseudoalteromonas species and isolated from diverse ecological niches, including
      extreme ones (i.e. Antarctica). These sequences were used to reconstruct the
      largest Pseudoalteromonas pangenome computed so far, including also the two main
      groups of Pseudoalteromonas strains (pigmented and not pigmented strains). The
      downstream analyses were conducted to describe the genomic diversity, both at
      genus and group levels. This allowed highlighting a remarkable genomic
      heterogeneity, even for closely related strains. We drafted all the main
      evolutionary steps that led to the current structure and gene content of
      Pseudoalteromonas representatives. These, most likely, included an extensive
      genome reduction and a strong contribution of Horizontal Gene Transfer (HGT),
      which affected biotechnologically relevant gene sets and occurred in a
      strain-specific fashion. Furthermore, this study also identified the genomic
      determinants related to some of the most interesting features of the
      Pseudoalteromonas representatives, such as the production of secondary
      metabolites, the adaptation to cold temperatures and the resistance to abiotic
      compounds. CONCLUSIONS: This study poses the bases for a comprehensive
      understanding of the evolutionary trajectories followed in time by this peculiar
      bacterial genus and for a focused exploitation of their biotechnological
      potential.
AU  - Bosi E
AU  - Fondi M
AU  - Orlandini V
AU  - Perrin E
AU  - Maida I
AU  - de Pascale D
AU  - Tutino ML
AU  - Parrilli E
AU  - Lo GA
AU  - Filloux A
AU  - Fani R
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2017 18: 93.

PMID- 27559429
VI  - 11
DP  - 2016
TI  - Complete genome sequence of thermophilic Bacillus smithii type strain DSM 4216(T).
PG  - 52
AB  - Bacillus smithii is a facultatively anaerobic, thermophilic bacterium able to use a variety of
      sugars that can be derived from lignocellulosic feedstocks. Being
      genetically accessible, it is a potential new host for biotechnological
      production of green chemicals from renewable resources. We determined the
      complete genomic sequence of the B. smithii type strain DSM 4216(T), which
      consists of a 3,368,778 bp chromosome (GenBank accession number CP012024.1) and a
      12,514 bp plasmid (GenBank accession number CP012025.1), together encoding 3880
      genes. Genome annotation via RAST was complemented by a protein domain analysis.
      Some unique features of B. smithii central metabolism in comparison to related
      organisms included the lack of a standard acetate production pathway with no
      apparent pyruvate formate lyase, phosphotransacetylase, and acetate kinase genes,
      while acetate was the second fermentation product.
AU  - Bosma EF
AU  - Koehorst JJ
AU  - van Hijum SA
AU  - Renckens B
AU  - Vriesendorp B
AU  - van de Weijer AH
AU  - Schaap PJ
AU  - de Vos WM
AU  - van der Oost J
AU  - van Kranenburg R
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 52.

PMID- 26823596
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of MIDG2331, a Genetically Tractable Serovar 8 Clinical  Isolate of Actinobacillus pleuropneumoniae.
PG  - e01667-15
AB  - We report here the complete annotated genome sequence of a clinical serovar 8 isolate
      Actinobacillus pleuropneumoniae MIDG2331. Unlike the serovar 8 reference
      strain 405, MIDG2331 is amenable to genetic manipulation via natural
      transformation as well as conjugation, making it ideal for studies of gene
      function.
AU  - Bosse JT
AU  - Chaudhuri RR
AU  - Li Y
AU  - Leanse LG
AU  - Fernandez CR
AU  - Coupland P
AU  - Holden MT
AU  - Bazzolli DM
AU  - Maskell DJ
AU  - Tucker AW
AU  - Wren BW
AU  - Rycroft AN
AU  - Langford PR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01667-15.

PMID- 27152133
VI  - 11
DP  - 2016
TI  - Complete genome sequence of an agr-dysfunctional variant of the ST239 lineage of  the methicillin-resistant Staphylococcus aureus strain GV69 from Brazil.
PG  - 34
AB  - Staphylococcus aureus is a versatile Gram-positive coccus frequently found colonizing the skin
      and nasal membranes of humans. The acquisition of the
      staphylococcal cassette chromosome mec was a major milestone in the evolutionary
      path of methicillin-resistant S. aureus. This genetic element carries the mecA
      gene, the main determinant of methicillin resistance. MRSA is involved in a
      plethora of opportunistic infectious diseases. The accessory gene regulator is
      the major S. aureus quorum sensing system, playing an important role in
      staphylococcal virulence, including the development of biofilms. We report the
      complete genome sequence (NCBI BioProject ID: PRJNA264181) of the
      methicillin-resistant S. aureus strain GV69 (= CMVRS P4521), a variant of the
      ST239 lineage that presents with a natural attenuation of agr-RNAIII
      transcription and a moderate accumulation of biofilm.
AU  - Botelho AM
AU  - Costa MO
AU  - Beltrame CO
AU  - Ferreira FA
AU  - Cortes MF
AU  - Bandeira PT
AU  - Lima NC
AU  - Souza RC
AU  - Almeida LG
AU  - Vasconcelos AT
AU  - Nicolas MF
AU  - Figueiredo AM
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 34.

PMID- 29954884
VI  - 6
DP  - 2018
TI  - Whole-Genome Sequence of Salmonella enterica subsp. enterica Serovar Typhimurium  Strain WG49 and Escherichia coli Strain WG5 Used in South Africa for Phage Detection in Water Samples.
PG  - e00372-18
AB  - Salmonella enterica subsp. enterica serovar Typhimurium WG49 is widely used for enumeration of
      F-specific RNA (F-RNA) coliphages in water. Escherichia coli WG5
      is broadly used for the detection and enumeration of somatic coliphages in water
      samples. We report here the genome sequences of these bacterial strains used in
      South Africa under ISO methods 10705-1 and 10705-2.
AU  - Bothma L
AU  - Gonzalez-Ibeas D
AU  - Mienie C
AU  - Bezuidenhout CC
AU  - Adeleke R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00372-18.

PMID- 22038957
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Bifidobacterium animalis subsp. lactis BLC1.
PG  - 6387-6388
AB  - Bifidobacterium animalis subsp. lactis BLC1 is a probiotic bacterium that is widely exploited
      by food industries as the active ingredient of various
      functional foods. Here we report the complete genome sequence of B.
      animalis subsp. lactis BLC1, which is expected to provide insights into
      the biology of this health-promoting microorganism and improve our
      understanding of its phylogenetic relatedness with other members of the B.
      animalis subsp. lactis taxon.
AU  - Bottacini F
AU  - Dal Bello F
AU  - Turroni F
AU  - Milani C
AU  - Duranti S
AU  - Foroni E
AU  - Viappiani A
AU  - Strati F
AU  - Mora D
AU  - van Sinderen D
AU  - Ventura M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6387-6388.

PMID- 23028506
VI  - 7
DP  - 2012
TI  - Bifidobacterium asteroides PRL2011 Genome Analysis Reveals Clues for Colonization of the Insect Gut.
PG  - E44229
AB  - Bifidobacteria are known as anaerobic/microaerophilic and fermentative
      microorganisms, which commonly inhabit the gastrointestinal tract of various
      animals and insects. Analysis of the 2,167,301 bp genome of Bifidobacterium
      asteroides PRL2011, a strain isolated from the hindgut of Apis mellifera var.
      ligustica, commonly known as the honey bee, revealed its predicted capability for
      respiratory metabolism. Conservation of the latter gene clusters in various B.
      asteroides strains enforces the notion that respiration is a common metabolic
      feature of this ancient bifidobacterial species, which has been lost in currently
      known mammal-derived Bifidobacterium species. In fact, phylogenomic based
      analyses suggested an ancient origin of B. asteroides and indicates it as an
      ancestor of the genus Bifidobacterium. Furthermore, the B. asteroides PRL2011
      genome encodes various enzymes for coping with toxic products that arise as a
      result of oxygen-mediated respiration.
AU  - Bottacini F
AU  - Milani C
AU  - Turroni F
AU  - Sanchez B
AU  - Foroni E
AU  - Duranti S
AU  - Serafini F
AU  - Viappiani A
AU  - Strati F
AU  - Ferrarini A
AU  - Delledonne M
AU  - Henrissat B
AU  - Coutinho P
AU  - Fitzgerald GF
AU  - Margolles A
AU  - van Sinderen D
AU  - Ventura M
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2012 7: E44229.

PMID- 29294107
VI  - 46
DP  - 2018
TI  - Comparative genome and methylome analysis reveals restriction/modification system diversity in the gut commensal Bifidobacterium breve.
PG  - 1860-1877
AB  - Bifidobacterium breve represents one of the most abundant bifidobacterial species in the
      gastro-intestinal tract of breast-fed infants, where their presence is
      believed to exert beneficial effects. In the present study whole genome
      sequencing, employing the PacBio Single Molecule, Real-Time (SMRT) sequencing
      platform, combined with comparative genome analysis allowed the most extensive
      genetic investigation of this taxon. Our findings demonstrate that genes encoding
      Restriction/Modification (R/M) systems constitute a substantial part of the B.
      breve variable gene content (or variome). Using the methylome data generated by
      SMRT sequencing, combined with targeted Illumina bisulfite sequencing (BS-seq)
      and comparative genome analysis, we were able to detect methylation recognition
      motifs and assign these to identified B. breve R/M systems, where in several
      cases such assignments were confirmed by restriction analysis. Furthermore, we
      show that R/M systems typically impose a very significant barrier to genetic
      accessibility of B. breve strains, and that cloning of a
      methyltransferase-encoding gene may overcome such a barrier, thus allowing future
      functional investigations of members of this species.
AU  - Bottacini F
AU  - Morrissey R
AU  - Roberts RJ
AU  - James K
AU  - van Breen J
AU  - Egan M
AU  - Lambert J
AU  - van Limpt K
AU  - Knol J
AU  - Motherway MO
AU  - van Sinderen D
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2018 46: 1860-1877.

PMID- 25326305
VI  - 81
DP  - 2014
TI  - Discovery of a conjugative megaplasmid in Bifidobacterium breve.
PG  - 166-176
AB  - Bifidobacterium breve is a common and sometimes very abundant inhabitant of the human gut.
      Genome sequencing of B. breve JCM 7017 revealed the presence of an extrachromosomal element,
      designated pMP7017 consisting of more than 190 kb, thus representing the first reported
      bifidobacterial megaplasmid. In silico characterization of this element revealed several
      genomic features supporting a stable establishment of the megaplasmid in its host, illustrated
      by predicted CRISPR-Cas functions that are known to protect the host against intrusion of
      foreign DNA. Interestingly, pMP7017 is also predicted to encode a conjugative DNA transfer
      apparatus and consistent with this notion we demonstrate conjugal transfer of pMP7017 to
      representative strains of B. breve and B. longum subsp.
      longum. We furthermore demonstrate the presence of a megaplasmid with homology to
      pMP7017 in three B. longum subsp. longum strains.
AU  - Bottacini F
AU  - O'Connell-Motherway M
AU  - Casey E
AU  - McDonnell B
AU  - Mahony J
AU  - Ventura M
AU  - van Sinderen D
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2014 81: 166-176.

PMID- 24581150
VI  - 15
DP  - 2014
TI  - Comparative genomics of the Bifidobacterium breve taxon.
PG  - 170
AB  - BACKGROUND: Bifidobacteria are commonly found as part of the microbiota of the
      gastrointestinal tract (GIT) of a broad range of hosts, where their presence is
      positively correlated with the host's health status. In this study, we assessed
      the genomes of thirteen representatives of Bifidobacterium breve, which is not
      only a frequently encountered component of the (adult and infant) human gut
      microbiota, but can also be isolated from human milk and vagina. RESULTS: In
      silico analysis of genome sequences from thirteen B. breve strains isolated from
      different environments (infant and adult faeces, human milk, human vagina) shows
      that the genetic variability of this species principally consists of hypothetical
      genes and mobile elements, but, interestingly, also genes correlated with the
      adaptation to host environment and gut colonization. These latter genes specify
      the biosynthetic machinery for sortase-dependent pili and exopolysaccharide
      production, as well as genes that provide protection against invasion of foreign
      DNA (i.e. CRISPR loci and restriction/modification systems), and genes that
      encode enzymes responsible for carbohydrate fermentation. Gene-trait matching
      analysis showed clear correlations between known metabolic capabilities and
      characterized genes, and it also allowed the identification of a gene cluster
      involved in the utilization of the alcohol-sugar sorbitol. CONCLUSIONS: Genome
      analysis of thirteen representatives of the B. breve species revealed that the
      deduced pan-genome exhibits an essentially close trend. For this reason our
      analyses suggest that this number of B. breve representatives is sufficient to
      fully describe the pan-genome of this species. Comparative genomics also
      facilitated the genetic explanation for differential carbon source utilization
      phenotypes previously observed in different strains of B. breve.
AU  - Bottacini F
AU  - O'Connell-Motherway M
AU  - Kuczynski J
AU  - O'Connell KJ
AU  - Serafini F
AU  - Duranti S
AU  - Milani C
AU  - Turroni F
AU  - Lugli GA
AU  - Zomer A
AU  - Zhurina D
AU  - Riedel C
AU  - Ventura M
AU  - van Sinderen D
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2014 15: 170.

PMID- 28522724
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Staphylococcus epidermidis Clinical Strain GOI1153754-03-14 Isolated from an Infected Knee Prosthesis.
PG  - e00378-17
AB  - We announce the draft genome sequence of Staphylococcus epidermidis clinical strain
      GOI1153754-03-14, isolated from an infected orthopedic prosthesis. The
      reported genomic sequence will provide valuable information concerning the
      mechanisms of the biofilm formation on metallic implants.
AU  - Bottagisio M
AU  - Soggiu A
AU  - Lovati AB
AU  - Toscano M
AU  - Piras C
AU  - Romano CL
AU  - Bonizzi L
AU  - Roncada P
AU  - Drago L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00378-17.

PMID- 2996986
VI  - 37
DP  - 1985
TI  - High-level production of the EcoRI endonuclease under the control of the pL promoter of bacteriophage lambda.
PG  - 229-239
AB  - Escherichia coli strains overproducing the EcoRI restriction endonuclease have
      been constructed, using lambda pL promoter expression vectors.  In a first step
      we constructed endRI::lacZ gene fusions by fusing the N-terminal part of the
      endRI gene with a lacZ gene fragment, whereafter the hybrid gene was positioned
      randomly under the control of the pL promoter to optimize the level of
      expression.  These plasmids direct the synthesis of large amounts of fusion
      protein approaching 30% of the total cellular protein content.  In most cases
      the overproduced protein forms enzymatically inactive intracellular aggregates.
      The position of the promoter in front of the hybrid gene had little effect on
      the level of expression, except in fusions directly affecting the
      ribosome-binding site (RBS).  In a second step, several of these promoter-gene
      configurations were used to reconstruct the intact endRI gene in appropriate
      hosts producing EcoRI methylase and cI-coded repressor.  The levels of EcoRI
      endonuclease overproduction were similar to that obtained for the corresponding
      fusion protein, despite the fourfold difference in protein size.  Intracellular
      precipitation was also observed with the overproduced EcoRI endonuclease.
AU  - Botterman J
AU  - Zabeau M
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1985 37: 229-239.

PMID- 2421674
VI  - 93
DP  - 1985
TI  - High-level production of the restriction endonucleases EcoRI and EcoRV in Escherichia coli.
PG  - S38
AB  - Type II restriction and modification systems constitute an attractive system for analysis of
      sequence-specific DNA-protein interaction.  These systems comprise a site-specific
      endonuclease, which recognizes short target sequences in DNA at which they produce double
      stranded cleavages, and a companion methylase, which specifically modifies this target
      sequence to protect the host's DNA against degradation by the endonuclease.  However, the
      limited available quantitites and elaborate purification procedures of these proteins hinder
      biochemical and crystallographic studies.  The EcoRI and EcoRV restriction and modification
      system have been cloned and characterized.  The development of a versatile plasmid expression
      vector system based on the strong pL and pR promoters which are negatively regulated by the cI
      repressor of phage lambda, made it possible to construct strains overproducing the enzymes.
      The expression can be experimentally controlled in strains producing a temperature-sensitive
      repressor (cIts), which is readily switched off and on at respectively low (28C) and high
      temperatures (42C).  Since restriction endonucleases are potentially lethal to the cell, a
      strategy was developed in which the expression of the EcoRI endonuclease (endRI) was first
      optimized in an inactive form: an endRI-lacZ hybrid gene was randomly positioned downstream
      from the pL promoter.  Optimal promoter-gene configurations were used to reconstruct the
      intact gene under pL promoter control in appropriate hosts producing EcoRI methylase and cI
      repressor.  Production levels of the EcoRI endonuclease reached 30% total cellular protein
      content upon temperature induction, yielding after purification 5mg/g cells pure active
      enzyme. Similar optimization of the expression of the EcoRV endonuclease yielded only moderate
      levels of synthesis (2-5% total cellular protein content), which was nonetheless useful for
      purification (1mg/g cells).  Further improvements of the ribosome binding site gave better
      production.  Moreover, deletion of a putative regulatory signal downstream of the gene led to
      increased levels of enzyme synthesis and indicated a possible mechanism for regulation of
      prokaryotic gene expression, in which protein synthesis is modulated at the level of
      translation initiation. (1) J. Botterman and M. Zabeau, Gene, in press. (2) J. Botterman, D.
      DeBuyser, J. Spriet, M. Zabeau and G. Vansteenkiste, Biotechnology and Bioengineering, in
      press. (3) L. Bougueleret, M. Tenchini, J. Botterman and M. Zabeau, Nucl. Acids Res., in
      press. (4) J. Botterman, E. DeAlmeida, L. Bougueleret and M. Zabeau, UCLA Symposia on
      Molecular and Cellular Biology 1985.
AU  - Botterman J
AU  - Zabeau M
PT  - Journal Article
TA  - Arch. Int. Physiol. Biochim.
JT  - Arch. Int. Physiol. Biochim.
SO  - Arch. Int. Physiol. Biochim. 1985 93: S38.

PMID- 29371369
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Mycobacterium sp. Strain 3519A.
PG  - e01565-17
AB  - Mycobacterium sp. strain 3519A is a nontuberculous mycobacterium isolated from sputum from a
      Cambodian patient with a pulmonary infection. We report here the
      first complete 7.3-Mbp-long genome sequence of Mycobacterium sp. 3519A with
      66.35% GC content, encoding 7,029 protein-coding genes, 50 tRNAs, and 5 rRNA
      genes.
AU  - Bouam A
AU  - Levasseur A
AU  - Bonnet M
AU  - Borand L
AU  - Van Goethem C
AU  - Drancourt M
AU  - Godreuil S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01565-17.

PMID- 29449406
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Mycobacterium sp. Strain 4858.
PG  - e01604-17
AB  - Mycobacterium sp. strain 4858 is a nontuberculous mycobacterium isolated from sputum in a
      Cambodian patient with a pulmonary infection. We report the first
      complete 5.6-Mbp-long genome sequence of Mycobacterium strain 4858, with 68.24%
      GC content, carrying 5,255 protein-coding genes, 47 tRNAs, and 3 rRNA genes.
AU  - Bouam A
AU  - Levasseur A
AU  - Bonnet M
AU  - Borand L
AU  - Van Goethem C
AU  - Drancourt M
AU  - Godreuil S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01604-17.

PMID- 29674548
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Mycobacterium porcinum CSURP1564.
PG  - e00291-18
AB  - Mycobacterium porcinum is a rapidly growing environmental mycobacterium responsible for
      opportunistic infections. The 7,025,616-bp draft genome of M.
      porcinum strain CSURP1564 exhibits a 66.71% G+C content, 6,687 protein-coding
      genes, and 65 predicted RNA genes. In silico DNA-DNA hybridization confirms its
      assignment to the Mycobacterium fortuitum complex.
AU  - Bouam A
AU  - Levasseur A
AU  - Drancourt M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00291-18.

PMID- 29348332
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Mycobacterium setense CSUR47.
PG  - e01415-17
AB  - Mycobacterium setense CSUR47 is a rapidly growing Mycobacterium species strain isolated from
      pus collected from a left maxillary sinus in Marseille, France.
      Here, we report the complete 6,278,097-bp genome sequence of M. setense CSUR47,
      which exhibits a 66.40% GC content and encodes 5,863 protein-coding genes, 48
      tRNAs, and 9 rRNAs.
AU  - Bouam A
AU  - Levasseur A
AU  - Drancourt M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01415-17.

PMID- 28473389
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Mycobacterium boenickei CIP 107829.
PG  - e00292-17
AB  - Mycobacterium boenickei is a rapidly growing mycobacterium isolated for the first time from a
      leg wound in the United States. Its 6,506,908-bp draft genome
      exhibits a 66.77% G+C content, 6,279 protein-coding genes, and 59 predicted RNA
      genes. In silico DNA-DNA hybridization confirms its assignment to the
      Mycobacterium fortuitum complex.
AU  - Bouam A
AU  - Robert C
AU  - Croce O
AU  - Levasseur A
AU  - Drancourt M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00292-17.

PMID- 28385843
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Mycobacterium colombiense.
PG  - e00119-17
AB  - Mycobacterium colombiense is a rapidly growing mycobacterium initially isolated from the blood
      of an HIV-positive patient in Colombia. Its 5,854,893-bp draft
      genome exhibits a G+C content of 67.64%, 5,233 protein-coding genes, and 54
      predicted RNA genes.
AU  - Bouam A
AU  - Robert C
AU  - Levasseur A
AU  - Drancourt M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00119-17.

PMID- 23105046
VI  - 194
DP  - 2012
TI  - Genome Sequence of Staphylococcus aureus Newbould 305, a Strain Associated with Mild Bovine Mastitis.
PG  - 6292-6293
AB  - Staphylococcus aureus is a major etiological agent of mastitis in ruminants. We report here
      the genome sequence of bovine strain Newbould 305, isolated in the
      1950s in a case of bovine mastitis and now used as a model strain able to
      reproducibly induce chronic mastitis in cows.
AU  - Bouchard D
AU  - Peton V
AU  - Almeida S
AU  - Le Marechal C
AU  - Miyoshi A
AU  - Azevedo V
AU  - Berkova N
AU  - Rault L
AU  - Francois P
AU  - Schrenzel J
AU  - Even S
AU  - Hernandez D
AU  - Le Loir Y
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6292-6293.

PMID- 4616721
VI  - 366
DP  - 1974
TI  - Isolation and in vitro restriction of unmethylated DNA from Escherichia coli K.
PG  - 135-142
AB  - A previous report (Bouche, J.P.C. (1973) J. Bacteriol. 115, 752-761) has
      presented evidence that a part of the DNA synthesized in a methionine starved
      dnaB mutant after return to the permissive temperature is completely or almost
      completely unmethylated.  We describe here the isolation of this DNA, and
      either its methylation in vitro by Escherichia coli K methylases, or its
      restriction by endonucleases K and RI from E. coli, and dII from Haemophilus
      influenzae.  These experiments show that this DNA not only lacks methylation
      due to the general (non-modifying) methylases, but also due to the K
      modifiction methylase.  Furthermore, the levels of restriction of this DNA were
      found to be equivalent to those of an E. coli K DNA deficient only in
      modification.  We conclude that there is no significant overlap in vitro
      between the sequence specificities of major non-modifying methylases and of the
      endonucleases tested.
AU  - Bouche JPC
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1974 366: 135-142.

PMID- 11467810
VI  - 84
DP  - 2001
TI  - DNA sequence analysis of three Lactococcus lactis plasmids encoding phage resistance mechanisms.
PG  - 1610-1620
AB  - The three Lactococcus lactis plasmids pSRQ700, pSRQ800, and pSRQ900 encode the previously
      described anti-phage resistance mechanisms
      LlaDCHI, AbiK, and AbiQ, respectively. Since these plasmids are likely
      to be introduced into industrial Lactococcus lactis strains used to
      manufacture commercial fermented dairy products, their complete DNA
      sequences were determined and analyzed. The plasmids pSRQ700 (7784 bp),
      pSRQ800 (7858 bp), and pSRQ900 (10,836 bp) showed a similar genetic
      organization including a common lactococcal theta-type replicon. A
      second replication module showing features of the pMV158 family of
      rolling circle replicons was also found on pSRQ700. The theta
      replication regions of the three plasmids were associated with two
      additional coding regions, one of which encodes for HsdS, the
      specificity subunit of the type I restriction/modification system. When
      introduced into L. lactis IL1403, the HsdS of pSRQ800 and pSRQ900
      conferred a weak resistance against phage P008 (936 species). These
      results indicated that both HsdS subunits can complement the
      chromosomally encoded type I restriction/modification system in IL1403.
      The genes involved in the phage resistance systems LlaDCHI, AbiK, and
      AbiQ were found in close proximity to and downstream of the replication
      modules. In pSRQ800 and pSRQ900, transfer origins and putative tyrosine
      recombinases were found upstream of the theta replicons. Genes encoding
      recombination proteins were also found on pSRQ700. Finally, open
      reading frames associated with bacteriocin production were found on
      pSRQ900, but no anti-lactococcal activity was detected. Based on our
      current knowledge, these three plasmids are safe and suitable for
      food-grade applications.
AU  - Boucher I
AU  - Emond E
AU  - Parrot M
AU  - Moineau S
PT  - Journal Article
TA  - J. Dairy Sci.
JT  - J. Dairy Sci.
SO  - J. Dairy Sci. 2001 84: 1610-1620.

PMID- 16417647
VI  - 6
DP  - 2006
TI  - Recovery and evolutionary analysis of complete integron gene cassette arrays from Vibrio.
PG  - 3
AB  - ABSTRACT: BACKGROUND: Integrons are genetic elements capable of the
      acquisition, rearrangement and expression of genes contained in gene
      cassettes. Gene cassettes generally consist of a promoterless gene
      associated with a recombination site known as a 59-base element (59-be).
      Multiple insertion events can lead to the assembly of large
      integron-associated cassette arrays. The most striking examples are found
      in Vibrio, where such cassette arrays are widespread and can range from 30
      kb to 150 kb. Besides those found in completely sequenced genomes, no such
      array has yet been recovered in its entirety. We describe an approach to
      systematically isolate, sequence and annotate large integron gene cassette
      arrays from bacterial strains. RESULTS: The complete Vibrio sp. DAT722
      integron cassette array was determined through the streamlined approach
      described here. To place it in an evolutionary context, we compare the
      DAT722 array to known vibrio arrays and performed phylogenetic analyses
      for all of its components (integrase, 59-be sites, gene cassette encoded
      genes). It differs extensively in terms of genomic context as well as gene
      cassette content and organization. The phylogenetic tree of the 59-be
      sites collectively found in the Vibrio gene cassette pool suggests
      frequent transfer of cassettes within and between Vibrio species, with
      slower transfer rates between more phylogenetically distant relatives. We
      also identify multiple cases where non-integron chromosomal genes seem to
      have been assembled into gene cassettes and others where cassettes have
      been inserted into chromosomal locations outside integrons. CONCLUSIONS:
      Our systematic approach greatly facilitates the isolation and annotation
      of large integrons gene cassette arrays. Comparative analysis of the
      Vibrio sp. DAT722 integron obtained through this approach to those found
      in other vibrios confirms the role of this genetic element in promoting
      lateral gene transfer and suggests a high rate of gene gain/loss relative
      to most other loci on vibrio chromosomes. We identify a relation between
      the phylogenetic distance separating two species and the rate at which
      they exchange gene cassettes, interactions between the non-mobile portion
      of bacterial genomes and the vibrio gene cassette pool as well as
      intragenomic translocation events of integrons in vibrios.
AU  - Boucher Y
AU  - Nesbo CL
AU  - Joss MJ
AU  - Robinson A
AU  - Mabbutt BC
AU  - Gillings MR
AU  - Doolittle WF
AU  - Stokes HW
PT  - Journal Article
TA  - BMC Evol. Biol.
JT  - BMC Evol. Biol.
SO  - BMC Evol. Biol. 2006 6: 3.

PMID- 6328432
VI  - 12
DP  - 1984
TI  - Characterization of the genes coding for the EcoRV restriction and modification system of Escherichia coli.
PG  - 3659-3677
AB  - A plasmid encoding the recently described Eco RV restriction and modification system has been
      isolated and characterized.  This plasmid, pLB1, is 6.2 kb long and carries only the EcoRV
      genes.  A subclone of 3 kb has been inserted in pBR322.  The relative positions of the
      endonuclease and the methylase genes were determined by the construction of a set of
      overlapping deletions generated by Bal31 resection.  The DNA sequence of a 2.2 kb fragment
      containing the two genes was determined.  The two genes are transcribed divergently from a 310
      bp region and the assignment of the coding region has been confirmed by direct aminoacid
      sequence analysis.  Possible mechanisms of the regulation of the endonuclease gene expression
      at the translational level are proposed and discussed.
AU  - Bougueleret L
AU  - Schwarzstein M
AU  - Tsugita A
AU  - Zabeau M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1984 12: 3659-3677.

PMID- 2989776
VI  - 13
DP  - 1985
TI  - Overproduction of the EcoRV endonuclease and methylase.
PG  - 3823-3839
AB  - Strains overproducing the EcoRV endonuclease and methylase have been obtained by inserting
      each of the two genes in expression vectors containing the lambda PL promoter.  The methylase
      is overproduced to a level reaching 5-10% of the total cellular proteins, which represents a
      50-100 fold increase.  A 30 fold overproduction of endonuclease was achieved by randomly
      positioning the EcoRV gene downstream of the lambda PL promoter.  The situation in the
      endonuclease overproducing clone resembles that encountered in maxi-cells.  The strains
      described here allowed a quick purification of both enzymes in sufficient amounts for
      crystallisation attempts.
AU  - Bougueleret L
AU  - Tenchini ML
AU  - Botterman J
AU  - Zabeau M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1985 13: 3823-3839.

PMID- 22904045
VI  - 78
DP  - 2012
TI  - Virioplankton community structure in Tunisian solar salterns.
PG  - 7429-7437
AB  - The microbial community inhabiting Sfax solar salterns on the east coast of
      Tunisia has been studied by means of different molecular and culture-dependent
      tools that have unveiled the presence of novel microbial groups as well as a
      community structure different from that of other coastal hypersaline
      environments. We have focused on the study of the viral assemblages of these
      salterns and their changes along the salinity gradient and over time. Viruses
      from three ponds (C4, M1, and TS) encompassing salinities from moderately
      hypersaline to saturated (around 14, 19, and 35%, respectively) were sampled in
      May and October 2009 and analyzed by transmission electron microscopy (TEM) and
      pulsed-field gel electrophoresis (PFGE). Additionally, for all three October
      samples and the May TS sample, viral metagenomic DNA was cloned in fosmids, end
      sequenced, and analyzed. Viral concentration, as well as virus-to-cell ratios,
      increased along the salinity gradient, with around 10(10) virus-like particles
      (VLPs)/ml in close-to-saturation ponds, which represents the highest viral
      concentration reported so far for aquatic systems. Four distinct morphologies
      could be observed with TEM (spherical, tailed, spindled, and filamentous) but
      with various proportions in the different samples. Metagenomic analyses indicated
      that every pond harbored a distinct viral assemblage whose G+C content could be
      roughly correlated with that of the active part of the microbial community that
      may have constituted the putative hosts. As previously reported for hypersaline
      metaviromes, most sequences did not have matches in the databases, although some
      were conserved among the Sfax metaviromes. BLASTx, BLASTp, and dinucleotide
      frequency analyses indicated that (i) factors additional to salinity could be
      structuring viral communities and (ii) every metavirome had unique gene contents
      and dinucleotide frequencies. Comparison with hypersaline metaviromes available
      in the databases indicated that the viral assemblages present in
      close-to-saturation environments located thousands of kilometers apart presented
      some common traits among them in spite of their differences regarding the
      putative hosts. A small core metavirome for close-to-saturation systems was found
      that contained 7 sequences of around 100 nucleotides (nt) whose function was not
      hinted at by in silico search results, although it most likely represents
      properties essential for hyperhalophilic viruses.
AU  - Boujelben I
AU  - Yarza P
AU  - Almansa C
AU  - Villamor J
AU  - Maalej S
AU  - Anton J
AU  - Santos F
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2012 78: 7429-7437.

PMID- 26586898
VI  - 3
DP  - 2015
TI  - Genome Sequences of Three Strains of the Pseudomonas aeruginosa PA7 Clade.
PG  - e01366-15
AB  - Draft genome sequences of three P. aeruginosa strains from the PA7 clade are presented here.
      Their lengths are 6.36 (EML528), 6.44 (EML545), and 6.33 Mb
      (EML548). Comparisons with the PA7 genome showed 5,113 conserved coding sequences
      (CDSs), and significant numbers of strain-specific CDSs. Their analysis will
      improve our understanding of this highly divergent clade.
AU  - Boukerb AM
AU  - Marti R
AU  - Cournoyer B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01366-15.

PMID- 1909786
VI  - 19
DP  - 1991
TI  - The restriction enzyme AlwNI is blocked by overlapping methylation.
PG  - 4774
AB  - Most strains of E. coli contain two sequence specific methylases, Dam and Dcm. The adenine
      residue of the sequence GATC is methylated at the N6 position by the Dam methylase whereas the
      Dcm methylase recognizes the sequences CC(A/T)GG methylating the internal cytosine at the C5
      position. The commercially available restriction enzyme AlwNI (New England Biolabs) has a
      recognition sequence CAGNNN^CTG and is a useful enzyme for creating deletions. One site
      AGCCCCTGgcaa is a potential dcm site and AlwNI cleavage at this site is blocked by dcm
      methylation.
AU  - Bourbonniere M
AU  - Nalbantoglu J
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 4774.

PMID- 15318244
VI  - 431
DP  - 2004
TI  - Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L.
PG  - 96-99
AB  - Mammalian genomes employ heritable cytosine methylation in the long-term silencing of
      retrotransposons and genes subject to genomic imprinting and X chromosome inactivation. Little
      is known of the mechanisms that direct cytosine methylation to specific sequences. Here we
      show that DNA methyltransferase 3-like (Dnmt3L (ref. 1)) is expressed in testes during a brief
      perinatal period in the non-dividing precursors of spermatogonial stem cells at a stage where
      retrotransposons undergo de novo methylation. Deletion of the Dnmt3L gene prevented the de
      novo methylation of both long-terminal-repeat (LTR) and non-LTR retrotransposons, which were
      transcribed at high levels in spermatogonia and spermatocytes. Loss of Dnmt3L from early germ
      cells also caused meiotic failure in spermatocytes, which do not express Dnmt3L. Whereas
      dispersed repeated sequences were demethylated in mutant germ cells, tandem repeats in
      pericentric regions were methylated normally. This result indicates that the Dnmt3L protein
      might have a function in the de novo methylation of dispersed repeated sequences in a
      premeiotic genome scanning process that occurs in male germ cells at about the time of birth.
AU  - Bourchis D
AU  - Bestor TH
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2004 431: 96-99.

PMID- 11719692
VI  - 294
DP  - 2001
TI  - Dnmt3L and the establishment of maternal genomic imprints.
PG  - 2536-2539
AB  - Complementary sets of genes are epigenetically silenced in male
      and female gametes in a process termed genomic imprinting. The Dnmt3L gene
      is expressed during gametogenesis at stages where genomic imprints are
      established. Targeted disruption of Dnmt3L caused azoospermia in homozygous
      males, and heterozygous progeny of homozygous females died before
      midgestation. Bisulfite genomic sequencing of DNA from oocytes and embryos
      showed that removal of Dnmt3L prevented methylation of sequences that are
      normally maternally methylated. The defect was specific to imprinted
      regions, and global genome methylation levels were not affected. Lack of
      maternal methylation imprints in heterozygous embryos derived from
      homozygous mutant oocytes caused biallelic expression of genes that are
      normally expressed only from the allele of paternal origin. The key
      catalytic motifs characteristic of DNA cytosine methyltransferases have
      been lost from Dnmt3L, and the protein is more likely to act as a regulator
      of imprint establishment than as a DNA methyltransferase.
AU  - Bourchis D
AU  - Xu G-L
AU  - Lin C-S
AU  - Bollman B
AU  - Bestor TH
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2001 294: 2536-2539.

PMID- 28369499
VI  - 45
DP  - 2017
TI  - High pressure activation of the Mrr restriction endonuclease in Escherichia coli  involves tetramer dissociation.
PG  - 5323-5332
AB  - A sub-lethal hydrostatic pressure (HP) shock of approximately 100 MPa elicits a RecA-dependent
      DNA damage (SOS) response in Escherichia coli K-12, despite the
      fact that pressure cannot compromise the covalent integrity of DNA. Prior screens
      for HP resistance identified Mrr (Methylated adenine Recognition and
      Restriction), a Type IV restriction endonuclease (REase), as instigator for this
      enigmatic HP-induced SOS response. Type IV REases tend to target modified DNA
      sites, and E. coli Mrr activity was previously shown to be elicited by expression
      of the foreign M.HhaII Type II methytransferase (MTase), as well. Here we
      measured the concentration and stoichiometry of a functional GFP-Mrr fusion
      protein using in vivo fluorescence fluctuation microscopy. Our results
      demonstrate that Mrr is a tetramer in unstressed cells, but shifts to a dimer
      after HP shock or co-expression with M.HhaII. Based on the differences in
      reversibility of tetramer dissociation observed for wild-type GFP-Mrr and a
      catalytic mutant upon HP shock compared to M.HhaII expression, we propose a model
      by which (i) HP triggers Mrr activity by directly pushing inactive Mrr tetramers
      to dissociate into active Mrr dimers, while (ii) M.HhaII triggers Mrr activity by
      creating high affinity target sites on the chromosome, which pull the equilibrium
      from inactive tetrameric Mrr toward active dimer.
AU  - Bourges AC
AU  - Torres MOE
AU  - Ghosh A
AU  - Tadesse WM
AU  - Declerck N
AU  - Aertsen A
AU  - Royer CA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2017 45: 5323-5332.

PMID- 18611278
VI  - 9
DP  - 2008
TI  - Large scale variation in Enterococcus faecalis illustrated by the genome analysis of strain OG1RF.
PG  - R110
AB  - BACKGROUND: Enterococcus faecalis has emerged as a major hospital
      pathogen. To explore its diversity, we sequenced E. faecalis strain OG1RF,
      which is commonly used for molecular manipulation and virulence studies.
      RESULTS: The 2,739,625 base pair chromosome of OG1RF was found to contain
      approximately 232 kilobases unique to this strain compared to V583, the
      only publicly available sequenced strain. Almost no mobile genetic
      elements were found in OG1RF. The 64 areas of divergence were classified
      into three categories. First, OG1RF carries 39 unique regions, including 2
      CRISPR loci and a new WxL locus. Second, we found nine replacements where
      a sequence specific to V583 was substituted by a sequence specific to
      OG1RF. For example, the iol operon of OG1RF replaces a possible prophage
      and the vanB transposon in V583. Finally, we found 16 regions that were
      present in V583 but missing from OG1RF, including the proposed
      pathogenicity island, several probable prophages, and the cpsCDEFGHIJK
      capsular polysaccharide operon. OG1RF was more rapidly but less frequently
      lethal than V583 in the mouse peritonitis model and considerably
      outcompeted V583 in a murine model of urinary tract infections.
      CONCLUSION: E. faecalis OG1RF carries a number of unique loci compared to
      V583, but the almost complete lack of mobile genetic elements demonstrates
      that this is not a defining feature of the species. Additionally, OG1RF's
      effects in experimental models suggest that mediators of virulence may be
      diverse between different E. faecalis strains and that virulence is not
      dependent on the presence of mobile genetic elements.
AU  - Bourgogne A et al
PT  - Journal Article
TA  - Genome Biology
JT  - Genome Biology
SO  - Genome Biology 2008 9: R110.

PMID- 3032016
VI  - 160
DP  - 1987
TI  - High-performance liquid chromatography for the purification of restriction endonucleases, application to BanII, SacI, and SphI.
PG  - 127-134
AB  - Conventional fractionation methods are time consuming, thus they prolong the
      time required to process low-stability restriction enzymes.  We now report a
      rapid and effective two-step chromatographic method that affords high purity
      endonucleases in a short time.  Accordingly, an inexpensive chromatographic
      adsorbent such as phosphocellulose or dyed agarose in the first step is coupled
      to a high-performance ion exchanger, namely, MonoQ, in the second step.  The
      purification schemes reported here are now in routine use to prepare
      high-purity BanII, SacI, and SphI as judged by the "overdigestion" and
      "cut-ligate-recut" stringent quality tests.
AU  - Bouriotis V
AU  - Zafeiropoulos A
AU  - Clonis YD
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 1987 160: 127-134.

PMID- 12595133
VI  - 84
DP  - 2002
TI  - Complex restriction enzymes: NTP-driven molecular motors.
PG  - 1047-1059
AB  - Survival is assuredly the prime directive for all living organisms either as individuals or as
      a species. One of the main challenges encountered by bacterial populations is the danger of
      bacteriophage attacks, since infection of a single bacterium may rapidly propagate, decimating
      the entire population. In order to protect themselves against this acute threat, bacteria have
      developed an array of defence mechanisms, which range from preventing the infection itself via
      interference with bacteriophage adsorption to the cell surface and prevention of phage DNA
      injection, to degradation of the injected phage DNA. This last defence mechanism is catalysed
      by the bacterial restriction-modification (R-M) systems, and in particular, by nucleoside
      5'-triphosphate (NTP)-dependent restriction enzymes, e.g. type I and type III R-M systems or
      the modification-dependent endonucleases. Type I and type III restriction systems have dual
      properties. They may either act as methylases and protect the host's own DNA against
      restriction by methylating specific residues, or they catalyse ATP-dependent endonuclease
      activity so that invading foreign DNA lacking the host-specific methylation is degraded. These
      defence mechanism systems are further complemented by the presence of methylation-dependent,
      GTP-dependent endonucleases that restricts specifically methylated DNA. Although all three
      types of endonucleases are structurally very different, they share a common functional
      mechanism. They recognise and bind to specific DNA sequences but do not cleave DNA within
      those target sites. They belong to the general class of DNA motor proteins, which use the free
      energy associated with nucleoside 5'-triphosphate hydrolysis to translocate DNA so that the
      subsequent DNA cleavage event occurs at a distance from the endonuclease recognition site.
      Moreover, DNA cleavage appears to be a random process triggered upon stalling of the DNA
      translocation process and requiring dimerisation of the bound endonucleases for a concerted
      break of both DNA strands. In this review, we present a detailed description and analysis of
      the functional mechanism of the three known NTP-dependent restriction systems: type I and type
      III restriction-modification enzymes, as well as the methylation-dependent McrBC endonuclease.
AU  - Bourniquel AA
AU  - Bickle TA
PT  - Journal Article
TA  - Biochimie
JT  - Biochimie
SO  - Biochimie 2002 84: 1047-1059.

PMID- 11982337
VI  - 47
DP  - 2002
TI  - DNA sequence and functional analysis of Lactobacillus delbrueckii subsp. lactis plasmids pN42 and pJBL2.
PG  - 153-157
AB  - The plasmids pN42 and pJBL2 were isolated from the Lactobacillus delbrueckii subsp. lactis
      strains NCC88 and JCL414. DNA sequence determination and bioinformatic analysis revealed a
      strikingly conserved genetic organization containing five major, highly conserved open reading
      frames (ORFs). Transformation studies indicated that ORF2 (consisting of a primase fused to a
      replicative DNA helicase), ori, and ORF3 constitute the minimal requirements for replication
      of pN42 in the heterologous host Lactococcus lactis. The ORF1's are predicted to encode type
      I restriction-modification (R-M) system HsdS subunits with different specificities on either
      plasmid, suggesting that these plasmids may be involved in host defense by expanding their
      host R-M system repertoire. These plasmids constitute the basis for the construction of novel
      L. delbrueckii vectors.
AU  - Bourniquel AA
AU  - Casey MG
AU  - Mollet B
AU  - Pridmore RD
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 2002 47: 153-157.

PMID- 
VI  - 102
DP  - 2002
TI  - Type I restriction-modification systems from Lactobacillus delbrueckii subsp. lactis.
PG  - 238
AB  - Background: Lactobacillus delbrueckii subsp. lactis is a lactic acid bacterium used worldwide
      for the production of Swiss-type hard cheeses.
      Whereas other dairy starters, e.g. Lactococcus lactis or Streptococcus
      thermophilus, are highly susceptible to bacteriophage infections, very
      few phages are known to target L. delbrueckii ssp. suggesting these
      bacteria possess a very active and reliable/versatile endogenous
      defense mechanism. Type I restriction-modification (R-M) systems are
      acknowledged defense mechanisms that depend on the generation of novel
      specificities for adaptability. Methods: Type I R-M hsd (host
      specificity for DNA) gene clusters were isolated from two strains of L.
      delbrueckii subsp. lactis, sequenced and characterized. In vivo
      transcription of the identified genes was verified by Northern
      blotting. The hsdR (restriction), hsdM (modification) and hsdS
      (specificity of DNA binding) genes were cloned into expression vectors
      for overexpression in Escherichia coli. The expressed proteins were
      purified, tested for activity and their recognition sites determined.
      Results: Both L. delbrueckii subsp. lactis strains examined possess
      type I R-M systems. The two hsd clusters (apprx8 kb) share a similar
      genetic organization consisting of: (i) the hsdR, hsdM and hsdS genes
      coding for a type I restriction enzyme, (ii) a second hsdS gene with a
      truncated 5'-end, and (iii) a gene similar to phage integrases. The
      HsdR and HsdM snbunits on both strains are highly conserved (98%
      identity), whereas the hsds genes code for subunits with different
      specificities i.e. the two type I restriction enzymes have different
      recognition sites. Conclusion: Until recently, research on type I R-M
      systems focused on the enterobacteriaceae group in which hsd genes are
      but slightly conserved in-between strains. In the gram-positive
      bacterium L. delbrueckii subsp. lactis type I R-M genes are
      well-conserved, genetic variability being limited to the DNA binding
      domains of hsdS determining enzyme specificity. The presence of
      truncated hsdS and integrases genes in the hsd clusters suggests that
      novel specificities might be generated by domain shuffling.
AU  - Bourniquel AA
AU  - Mollet B
AU  - Bickle TA
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 2002 102: 238.

PMID- 6778900
VI  - 47
DP  - 1980
TI  - Multiple modification/restriction systems in lactic streptococci and their significance in defining a phage-typing system.
PG  - 401-409
AB  - The reactions between 6 strains of mesophilic lactic steptococci and their respective phages
      were studied quantitatively. Of 30 nonhomologous reactions, the bacteria were fully sensitive
      in 4 and restricted the phages in 23. A mathematical model was developed that was used to
      identify at least 4 and probably 5 modification restriction (M/R) systems of which up to 3
      were found in the same strain. The model was based on 24 measued values and correctly
      predicted the values of 5 others. One of the 3 negative reactions was shown to be due to a
      restriction beyond the limit of detection, a second was due to lysogeny or lack of adsorption,
      but was shown to have the predicted value when the homologous phage was modified on the host
      of the challenging phage. In the last reaction a measurable restriction was predicted, but
      could not be proven by means of a modified phage. These results suggest M/R to be one of the
      main defenses of the lactic streptococci against their phages. They explaim why host range is
      not a useful criterion in the classification of phages and suggest a rational approach to the
      definition of a starter rotation.
AU  - Boussemaer JP
AU  - Schrauwen PP
AU  - Sourrouille JL
AU  - Guy P
PT  - Journal Article
TA  - J. Dairy Res.
JT  - J. Dairy Res.
SO  - J. Dairy Res. 1980 47: 401-409.

PMID- Not carried by PubMed...
VI  - 13
DP  - 1997
TI  - Cell death in bacterial populations: caused or programmed?  Accepted or deliberate?
PG  - 73-80
AB  - In bacterial cells, plasmids are stabilized by numerous different mechanisms.  Here we
      describe three different ways which mediate plasmid maintenance by selectively killing plasmid
      free cells.  In the first system, plasmid genes encode a stable toxic protein (or the stable
      corresponding mRNA) and an unstable antidote (or a small unstable antisense RNA which inhibits
      the translation of the messenger).  The expression of the lethality is regulated
      post-translationally (e.g. ccd system from plasmid F in Escherichia coli) or
      post-transcriptionally (e.g. hok system from plasmid R1 in E. coli).  In the second system
      (e.g. rm genes of Pseudomonas aeruginosa R7) plasmid genes encode a stable type II restriction
      enzyme and the unstable cognate methylase which offers protection from endonucleolytic attack
      by the restriction enzyme.  The third system is composed of a complex operon (e.g. MccB17
      system in E. coli) whose genes encode the synthesis and maturation of a cytotoxic protein and
      for a polypeptide which confers resistance or immunity to the killer cell by an unknown
      mechanism.  The plasmid-free cells are killed by the cytotoxic protein excreted by bacteria
      carrying the plasmid.  The set of two or more genes carried by a plasmid responsible for the
      lethal consequences of plasmid loss can be viewed as an addiction module or a selfish symbiote
      according to Yarmolinsky and Naito, respectively; the loss of these genomic units lead the
      cells to an unavoidable death.
AU  - Boutibonnes P
PT  - Journal Article
TA  - Med. Sci. (Paris)
JT  - Med. Sci. (Paris)
SO  - Med. Sci. (Paris) 1997 13: 73-80.

PMID- 27303739
VI  - 1
DP  - 2016
TI  - Genome Structural Diversity among 31 Bordetella pertussis Isolates from Two Recent U.S. Whooping Cough Statewide Epidemics.
PG  - e00036-16
AB  - During 2010 and 2012, California and Vermont, respectively, experienced statewide epidemics of
      pertussis with differences seen in the demographic affected, case clinical presentation, and
      molecular epidemiology of the circulating strains. To overcome limitations of the current
      molecular typing methods for pertussis, we utilized whole-genome sequencing to gain a broader
      understanding of how current circulating strains are causing large epidemics. Through the use
      of combined next-generation sequencing technologies, this study compared de novo,
      single-contig genome assemblies from 31 out of 33 Bordetella pertussis isolates collected
      during two separate pertussis statewide epidemics and 2 resequenced vaccine strains. Final
      genome architecture assemblies were verified with whole-genome optical mapping. Sixteen
      distinct genome rearrangement profiles were observed in epidemic isolate genomes, all of which
      were distinct from the genome structures of the two resequenced vaccine strains. These
      rearrangements appear to be mediated by repetitive sequence elements, such as high-copy-number
      mobile genetic elements and rRNA operons. Additionally, novel and previously identified single
      nucleotide polymorphisms were detected in 10 virulence-related genes in the epidemic isolates.
      Whole-genome variation analysis identified state-specific variants, and coding regions bearing
      nonsynonymous mutations were classified into functional annotated orthologous groups.
      Comprehensive studies on whole genomes are needed to understand the resurgence of pertussis
      and develop novel tools to better characterize the molecular epidemiology of evolving B.
      pertussis populations. IMPORTANCE Pertussis, or whooping cough, is the most poorly controlled
      vaccine-preventable bacterial disease in the United States, which has experienced a resurgence
      for more than a decade. Once viewed as a monomorphic pathogen, B. pertussis strains
      circulating during epidemics exhibit diversity visible on a genome structural level,
      previously undetectable by traditional sequence analysis using short-read technologies. For
      the first time, we combine short- and long-read sequencing platforms with restriction optical
      mapping for single-contig, de novo assembly of 31 isolates to investigate two geographically
      and temporally independent U.S. pertussis epidemics. These complete genomes reshape our
      understanding of B. pertussis evolution and strengthen molecular epidemiology toward one day
      understanding the resurgence of pertussis.
AU  - Bowden KE
AU  - Weigand MR
AU  - Peng Y
AU  - Cassiday PK
AU  - Sammons S
AU  - Knipe K
AU  - Rowe LA
AU  - Loparev V
AU  - Sheth M
AU  - Weening K
AU  - Tondella ML
AU  - Williams MM
PT  - Journal Article
TA  - mSphere
JT  - mSphere
SO  - mSphere 2016 1: e00036-16.

PMID- 14580211
VI  - 42
DP  - 2003
TI  - Investigation of restriction enzyme cofactor requirements: A relationship between metal ion properties and sequence specificity.
PG  - 12643-12653
AB  - Restriction enzymes are important model systems for understanding the mechanistic
      contributions of metal ions to nuclease activity. These
      systems are unique in that they combine distinct functions which have been
      shown to depend on metal ions: high-affinity DNA binding,
      sequence-specific recognition of DNA, and Mg(II)-dependent phosphodiester
      cleavage. While Ca(II) and Mn(II) are commonly used to promote DNA binding
      and cleavage, respectively, the metal ion properties that are critical to
      the support of these functions are not clear. To address this question, we
      assessed the abilities of a series of metal ions to promote DNA binding,
      sequence specificity, and cleavage in the representative PvuII
      endonuclease. Among the metal ions tested [Ca(II), Sr(II), Ba(II),
      Eu(III), Tb(III), Cd(II), Mn(II), Co(II), and Zn(II)], only Mn(II) and
      Co(II) were similar enough to Mg(II) to support detectable cleavage
      activity. Interestingly, cofactor requirements for the support of DNA
      binding are much more permissive; the survey of DNA binding cofactors
      indicated that Cd(II) and the heavier and larger alkaline earth metal ions
      Sr(II) and Ba(II) were effective cofactors, stimulating DNA binding
      affinity 20-200-fold. Impressively, the trivalent lanthanides Tb(III) and
      Eu(III) promoted DNA binding as efficiently as Ca(II), corresponding to an
      increase in affinity over 1000-fold higher than that observed under
      metal-free conditions. The trend for DNA binding affinity supported by
      these ions suggests that ionic radius and charge are not critical to the
      promotion of DNA binding. To examine the role of metal ions in sequence
      discrimination, we determined specificity factors
      [K(a)(specific)/K(a)(nonspecific)] in the presence of Cd(II), Ba(II), and
      Tb(III). Most interestingly, all of these ions compromised sequence
      specificity to some degree compared to Ca(II), by either increased
      affinity for a noncognate sequence, decreased affinity for the cognate
      sequence, or both. These results suggest that while amino acid-base
      contacts are important for specificity, the properties of metal ion
      cofactors at the catalytic site are also critical for sequence
      discrimination. This insight is invaluable to our efforts to understand
      and subsequently design sequence-specific nucleases.
AU  - Bowen LM
AU  - Dupureur CM
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2003 42: 12643-12653.

PMID- 15568821
VI  - 43
DP  - 2004
TI  - Lanthanide spectroscopic studies of the dinuclear and Mg(II)-dependent PvuII restriction endonuclease.
PG  - 15286-15295
AB  - Type II restriction enzymes are homodimeric systems that bind four to eight base pair
      palindromic recognition sequences of DNA and catalyze
      metal ion-dependent phosphodiester cleavage. While Mg(II) is required
      for cleavage in these enzymes, in some systems Ca(II) promotes avid
      substrate binding and sequence discrimination. These properties make
      them useful model systems for understanding the roles of alkaline earth
      metal ions in nucleic acid processing. We have previously shown that
      two Ca(II) ions stimulate DNA binding by Pvull endonuclease and that
      the trivalent lanthanide ions Tb(III) and Eu(III) support subnanomolar
      DNA binding in this system. Here we capitalize on this behavior,
      employing a unique combination of luminescence spectroscopy and DNA
      binding assays to characterize Ln(III) binding behavior by this enzyme.
      Upon excitation of tyrosine residues, the emissions of both Tb(III) and
      Eu(III) are enhanced severalfold. This enhancement is reduced by the
      addition of a large excess of Ca(II), indicating that these ions bind
      in the active site. Poor enhancements and affinities in the presence of
      the active site variant E68A indicate that Glu68 is an important
      Ln(III) ligand, similar to that observed with Ca(II), Mg(II), and
      Mn(II). At low micromolar Eu(III) concentrations in the presence of
      enzyme (10-20 muM), Eu(III) excitation F-7(0) --> D-5(0) spectra yield
      one dominant peak at 579.2 nm. A second, smaller peak at 579.4 nm is
      apparent at high Eu(III) concentrations (150 muM). Titration data for
      both Tb(III) and Eu(III) fit well to a two-site model featuring a
      strong site (K-d = 1-3 muM) and a much weaker site (K-d approximate to
      100-200 muM). Experiments with the E68A variant indicate that the Glu68
      side chain is not required for the binding of this second Ln(III)
      equivalent; however, the dramatic increase in DNA binding affinity
      around 100 muM Ln(III) for the wild-type enzyme and metal-enhanced
      substrate affinity for E68A are consistent with functional relevance
      for this weaker site. This discrimination of sites should make it
      possible to use lanthanide substitution and lanthanide spectroscopy to
      probe individual metal ion binding sites, thus adding an important tool
      to the study of restriction enzyme structure and function.
AU  - Bowen LM
AU  - Muller G
AU  - Riehl JP
AU  - Dupureur CM
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2004 43: 15286-15295.

PMID- 30165537
VI  - 46
DP  - 2018
TI  - A model for the evolution of prokaryotic DNA restriction-modification systems based upon the structural malleability of Type I restriction-modification  enzymes.
PG  - 9067-9080
AB  - Restriction Modification (RM) systems prevent the invasion of foreign genetic material into
      bacterial cells by restriction and protect the host's genetic
      material by methylation. They are therefore important in maintaining the
      integrity of the host genome. RM systems are currently classified into four types
      (I to IV) on the basis of differences in composition, target recognition,
      cofactors and the manner in which they cleave DNA. Comparing the structures of
      the different types, similarities can be observed suggesting an evolutionary link
      between these different types. This work describes the 'deconstruction' of a
      large Type I RM enzyme into forms structurally similar to smaller Type II RM
      enzymes in an effort to elucidate the pathway taken by Nature to form these
      different RM enzymes. Based upon the ability to engineer new enzymes from the
      Type I 'scaffold', an evolutionary pathway and the evolutionary pressures
      required to move along the pathway from Type I RM systems to Type II RM systems
      are proposed. Experiments to test the evolutionary model are discussed.
AU  - Bower EKM
AU  - Cooper LP
AU  - Roberts GA
AU  - White JH
AU  - Luyten Y
AU  - Morgan RD
AU  - Dryden DTF
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2018 46: 9067-9080.

PMID- 27587822
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the Psychrophilic Gliding Species Gelidibacter algens ACAM 536.
PG  - e00908-16
AB  - A draft genome sequence was obtained from the type strain of Gelidibacter algens  (ACAM 536).
      This species was isolated from sea-ice diatom assemblages collected
      from Ellis Fjord, Eastern Antarctica. The genome of ACAM 536 is a single circular
      chromosome with an estimated size of 4.50 Mbp.
AU  - Bowman JP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00908-16.

PMID- 28912321
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Plant Pathogen Streptomyces sp. Strain 11-1-2.
PG  - e00968-17
AB  - Streptomyces sp. strain 11-1-2 is a Gram-positive filamentous bacterium that was  isolated
      from a common scab lesion on a potato tuber. The strain is highly
      pathogenic to plants but does not produce the virulence-associated Streptomyces
      phytotoxin thaxtomin A. Here, we report the draft genome sequence of Streptomyces
      sp. 11-1-2.
AU  - Bown L
AU  - Bignell DRD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00968-17.

PMID- 9649620
VI  - 26
DP  - 1998
TI  - Novel site-specific DNA modification in Streptomyces: analysis of preferred intragenic modification sites present in a 5.7 kb amplified DNA sequence.
PG  - 3364-3371
AB  - Both Streptomyces lividans and Streptomyces avermitilis encode similar systems of
      post-replicative DNA modification which act site-specifically on closely opposed
      guanines on either strand. The modifications can be detected since they react in
      vitro with an oxidative derivative of Tris, resulting in strand cleavage.
      Previous analysis of the preferred modification site of plasmid pIJ101 indicated
      that extensive amounts of flanking sequence, including direct and inverted repeat
      structures, are required to direct modification in vivo within a central 6 bp
      palindrome. We have now examined the preferred modification sites of a
      chromosomal element, the 5.7 kb amplified DNA sequence (ADS5.7) found in certain
      S. lividans mutants. In contrast to the pIJ101 site, each of the ADS5. 7sites is
      intragenic and modified with a 10-fold reduced frequency. However, similar
      extents of flanking sequence are required for authentic double-strand
      modification; deletion mutants exhibited different modification profiles,
      including displaced double-stranded or single-stranded modi-fication. Comparison
      of different modification sites reveals conservation of the central core
      sequence, but no significant similarities between flanking sequences. Enhanced
      modification was detected in a cloned region of the ADS5.7, suggesting that local
      DNA topology, probably influenced by both DNA supercoiling and the nature of
      flanking sequences, can influence the modifying activity.
AU  - Boybek A
AU  - Ray TD
AU  - Evans MC
AU  - Dyson PJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1998 26: 3364-3371.

PMID- 3016643
VI  - 14
DP  - 1986
TI  - Isolation and computer-aided characterization of MmeI, a Type II restriction endonuclease from Methylophilus methylotrophus.
PG  - 5255-5274
AB  - A Type II restriction endonuclease, MmeI, has been purified from the obligate
      methylotroph, Methylophilus methylotrophus.  The enzyme was shown to have the
      non-palindromic recognition sequence 5' - T C C Pu A C (N) 20- 3' 3' - A G G Py
      T G (N) 18 - 5' and to cleave (as indicated) on the 3' side, generating a two
      nucleotide 3' projection.  Determination of the recognition sequence was
      achieved using two new computer programs; RECOG, which predicts recognition
      sequences from the pattern of restriction fragments obtained from DNAs of known
      sequence, and GELSIM, which generates graphical simulations of DNA band
      patterns obtained by gel electrophoresis of restriction digests of sequenced
      DNA molecules.
AU  - Boyd AC
AU  - Charles IG
AU  - Keyte JW
AU  - Brammar WJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1986 14: 5255-5274.

PMID- 30312401
VI  - 0
DP  - 2018
TI  - Results from the Canadian Nosocomial Infection Surveillance Program for detection of carbapenemase-producing Acinetobacter spp. in Canadian hospitals, 2010-16.
PG  - 0
AB  - Objectives: Globally there is an increased prevalence of carbapenem-resistant
      Acinetobacter spp. (CRAs) and carbapenemase-producing Acinetobacter spp. (CPAs)
      in the hospital setting. This increase prompted the Canadian Nosocomial Infection
      Surveillance Program (CNISP) to conduct surveillance of CRA colonizations and
      infections identified from patients in CNISP-participating hospitals between 2010
      and 2016. Methods: Participating acute care facilities across Canada submitted
      CRAs from 1 January 2010 to 31 December 2016. Patient data were collected from
      medical records using a standardized questionnaire. WGS was conducted on all CRAs
      and data underwent single nucleotide variant analysis, resistance gene detection
      and MLST. Results: The 7 year incidence rate of CRA was 0.02 per 10 000 patient
      days and 0.015 per 1000 admissions, with no significant increase observed over
      the surveillance period (P > 0.73). Ninety-four CRA isolates were collected from
      58 hospitals, of which 93 (98.9%) were CPA. Carbapenemase OXA-235 group (48.4%)
      was the most common due to two separate clusters, followed by the OXA-23 group
      (41.9%). Patients with a travel history were associated with 38.8% of CRA cases.
      The all-cause 30 day mortality rate for infected cases was 24.4 per 100 CRA
      cases. Colistin was the most active antimicrobial agent (95.8% susceptibility).
      Conclusions: CRA remains uncommon in Canadian hospitals and the incidence did not
      increase from 2010 to 2016. Almost half of the cases were from two clusters
      harbouring OXA-235-group enzymes. Previous medical treatment during travel
      outside of Canada was common.
AU  - Boyd DA
AU  - Mataseje LF
AU  - Pelude L
AU  - Mitchell R
AU  - Bryce E
AU  - Roscoe D
AU  - Embree J
AU  - Katz K
AU  - Kibsey P
AU  - Lavallee C
AU  - Simor AE
AU  - Taylor G
AU  - Turgeon N
AU  - Langley JM
AU  - Amaratunga K
AU  - Mulvey MR
PT  - Journal Article
TA  - J. Antimicrob. Chemother.
JT  - J. Antimicrob. Chemother.
SO  - J. Antimicrob. Chemother. 2018 0: 0.

PMID- 2203541
VI  - 62
DP  - 1990
TI  - The role of dam methyltransferase in the control of DNA replication in E. coli.
PG  - 981-989
AB  - The timing and control of initiation of DNA replication in E. coli was studied under
      conditions where the cellular level of dam methyltransferase was controlled by a
      temperature-inducible promoter. Flow cytometry was used to demonstrate that the synchrony of
      initiation at the several origins within each cell was critically dependent on the level of
      dam methyltransferase. Initiations were shown to be synchronous only in a narrow temperature
      range. The data are explained by a model where a newly replicated and therefore hemimethylated
      oriC is inert for reinitiation. Such a model may be applicable to eukaryotic cells, where
      classes of origins are initiated in synchrony and only once per cell cycle.
AU  - Boye E
AU  - Lobner-Olesen A
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1990 62: 981-989.

PMID- 1537808
VI  - 174
DP  - 1992
TI  - Quantitation of Dam methyltransferase in Escherichia coli.
PG  - 1682-1685
AB  - An antiserum against Escherichia coli Dam methyltransferase has been developed in rabbits and
      employed to detect and quantitate the enzyme in immunoblots. A wild-type, rapidly growing E.
      coli cell (doubling time = 30 min) was found to contain about 130 molecules of Dam
      methyltransferase.
AU  - Boye E
AU  - Marinus MG
AU  - Lobner-Olesen A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1992 174: 1682-1685.

PMID- 14240953
VI  - 88
DP  - 1964
TI  - Genetic control of restriction and modification in Escherichia coli.
PG  - 1652-1660
AB  - Bacterial crosses with K-12 strains of Escherichia coli as Hfr donors (Hfr
      Hayes, Hfr Cavalli, and Hfr P4X-6) and B/r strains of E. coli as F- recipients
      were found to differ from crosses between K-12 Hfr donors and K-12 F-
      recipients in two ways:  (i) recombinants (leu,pro, lac, and gal) did not
      appear at discrete time intervals but did appear simultaneously 30 min after
      matings were initiated, and (ii) the linkage of unselected markers to selected
      markers was reduced.  Integration of a genetic region linked to the threonine
      locus of K-12 into the B/r genome resulted in a hybrid which no longer gave
      anomalous results in conjugation experiments.  A similar region of the B strain
      was introduced into the K-12 strain, which then behaved as a typical B F-
      recipient.  These observations are interpreted as the manifestation of
      host-controlled modification and restriction on the E. coli chromosome.  This
      was verified by experiments on the restriction and modification of the
      bacteriophage lambda, F-lac, F-gal, and sex-factor, F1.  It was found that the
      genetic region that controlled the mating responses of the K-12 and B/r strains
      also controlled the modification and restriction properties of these two
      strains.  The genes responsible for the restricting and modifying properties of
      the K-12 and B strains of E. coli were found to be allelic, linked to each
      other, and linked to the threonine locus.
AU  - Boyer H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1964 88: 1652-1660.

PMID- 4944861
VI  - 46
DP  - 1971
TI  - The in vitro restriction of the replicative form of W.T. and mutant fd phage DNA.
PG  - 703-710
AB  - Tritium- and 32P-labeled replicative form DNA of wild-type and restriction-site
      mutants of the male specific phage fd were used as substrates for purified
      Escherichia coli B restriction endonuclease and the products of the reaction
      were analyzed by zonal centrifugation.  The products of the
      endonuclease-treated unmodified wild-type RF DNA were found to be two fragments
      about one-third and two-thirds the size of the genome.  The product of the
      endonuclease-treated unmodified RF DNA of mutants partially resistant to in
      vivo restriction was a single linear molecule.  The unmodified RF of phage
      mutants totally resistant to in vivo restriction was undegraded by the E. coli
      B restriction endonuclease.  These observations confirm the hypothesis of Arber
      and Kuhnlein (1967) that the wild-type phage genome has two sites (each of
      which consists of a limited sequence of base pairs), sensitive to the E. coli B
      restriction endonuclease and mutational alteration of one or both sites results
      in mutants either partially or completely resistant to E. coli B restriction.
      All of the seven independently altered sites were found to be insensitive to
      both steps of the restriction endonuclease attack; i.e., no single strand
      phosphodiester bond cleavages were detected.  However, by using nitrocellulose
      membrane filters to measure the interaction of the B restriction endonuclease
      with fd RF DNA, we found that one of the mutant RF formed measurable amounts of
      enzyme-substrate complexes.  In one other case no measurable complexes were
      formed between the endonuclease and a mutant restriction site.  This suggests
      that the restriction endonuclease relies on the proper sequence of base pairs
      for recognition (formation of enzyme-substrate complex) and for the enzymatic
      cleavage of phosphodiester bonds.
AU  - Boyer H
AU  - Scibienski E
AU  - Slocum H
AU  - Roulland-Dussoix D
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1971 46: 703-710.

PMID- 4949033
VI  - 25
DP  - 1971
TI  - DNA restriction and modification mechanisms in bacteria.
PG  - 153-176
AB  - The restriction and modification of DNA as currently understood was first
      recognized as a unique biological mechanism because of the effect it has on the
      ability of a bacteriophage to propagate on related bacterial strains.  Similar
      observations were made prior to these reports, but they were never clearly
      defined or pursued on an experimental basis.  The restriction and modification
      of phage lambda by several host specificities found in E. coli has been
      extensively exploited and has led to the general concept that two enzymes, an
      endonuclease and a methylase, are responsible for the restriction and
      modification of DNA.  The restriction endonuclease makes a double-strand
      scission at a specific sequence of base pairs if it is unmodified, and the
      modification methylase modifies this sequence of base pairs to render it
      insensitive to the restriction endonuclease.  This mechanism (hs) appears to be
      quite general in bacteria, but it should be pointed out that some restriction
      and modification systems (e.g., the restriction and modification of T-even
      phages, 87) could have a different molecular basis.  The plan of this review is
      to treat the restriction and modification of DNA as a general bacterial
      mechanism.  Emphasis will be placed on the two types of hs mechanisms
      associated with E. coli, and two models of protein-polynucleotide interaction
      are presented to account for the two types of restriction and modification
      mechanisms.
AU  - Boyer HW
PT  - Journal Article
TA  - Annu. Rev. Microbiol.
JT  - Annu. Rev. Microbiol.
SO  - Annu. Rev. Microbiol. 1971 25: 153-176.

PMID- 4599005
VI  - 33
DP  - 1974
TI  - Restriction and modification of DNA: enzymes and substrates.
PG  - 1125-1127
AB  - A great deal of interest in the restriction and modification of DNA has been
      generated in the past few years and a symposium devoted to some aspects of this
      biological mechanism was part of the 1973 Federation Meeting.
AU  - Boyer HW
PT  - Journal Article
TA  - Fed. Proc.
JT  - Fed. Proc.
SO  - Fed. Proc. 1974 33: 1125-1127.

PMID- 4124385
VI  - 244
DP  - 1973
TI  - DNA substrate site for the EcoRII restriction endonuclease and modification methylase.
PG  - 40-43
AB  - The same nucleotide sequence in double stranded DNA restricted in double
      stranded DNA restricted by the EcoRII restriction endonuclease is methylated by
      the EcoRII modification methylase.  The EcoRII endonucleolytic cleavages
      generate DNA fragments with cohesive termini.
AU  - Boyer HW
AU  - Chow LT
AU  - Dugaiczyk A
AU  - Hedgpeth J
AU  - Goodman HM
PT  - Journal Article
TA  - Nature New Biol.
JT  - Nature New Biol.
SO  - Nature New Biol. 1973 244: 40-43.

PMID- 
VI  - 34
DP  - 1975
TI  - The methylation of DNA as the biochemical basis of host controlled modification of DNA in bacteria.
PG  - 23-37
AB  - In 1962 the work of Arber and Dussoix (Arber and Dussoix, 1962; Dussoix and
      Arber, 1962) provided the conceptual framework for the study of the enzymatic
      basis of the host controlled modification and restriction of bacteriophage
      lambda.  Restriction and modification of phage lambda had received scant
      attention until this time, probably because of its peripheral role to the ideas
      occupying the attention of most molecular biologists of the time.  It had been
      a long established fact that when a bacterial virus had been propagated on one
      bacterial host, it would have a low efficiency of plating after infection of a
      related host strain (for reviews see Arber and Linn, 1969; Boyer, 1971;
      Meselson et al., 1972).  However, after one round of replication on the new
      host, the few virus particles which were propagated would be modified in some
      way to have the capacity to subsequently plate on that strain with a high
      efficiency of plating (see Table 1).
AU  - Boyer HW
AU  - Greene PJ
AU  - Meagher RB
AU  - Betlach MC
AU  - Russel D
AU  - Goodman HM
PT  - Journal Article
TA  - FEBS J.
JT  - FEBS J.
SO  - FEBS J. 1975 34: 23-37.

PMID- 4896022
VI  - 41
DP  - 1969
TI  - A complementation analysis of the restriction and modification of DNA in Escherichia coli.
PG  - 459-472
AB  - A complementation analysis of host-controlled modification and restriction of
      DNA by Escherichia coli has been carried out by examining the restriction and
      modification phenotypes of partial, permanent diploids containing various
      arrangements of wild type and mutant restriction and modification alleles.
      Intercistronic complementation was observed between three classes of
      restriction and modification mutants of E. coli B, indicating that at least
      three cistrons (the ram cistrons) are involved in the genetic control of the
      restriction and modification of DNA.  Mutations in one cistron (ramA) result in
      a loss of restriction activity but not in modification activity (r-m+).
      Mutations in a second cistron (ramC) result in a loss of restriction and
      modification activities (r-m-).  Mutations in  third cistron result in a loss
      of modification activity and appear to be lethal unless accompanied by a
      mutation in the ramA or ramC cistrons.  A fourth class of mutations, which are
      linked to the other ram cistrons and are expressed phenotypically as r-m-
      mutants, are trans dominant to the wild-type ram alleles.  It is not known if
      this latter class of mutants represents a fourth cistron of the ram locus.
      Complementation was observed between E. coli K12 and B ramA and ramC mutations
      and the host specificity of the restored restriction activity was dependent on
      an intact ramC cistron.  However, complementation was not detected between the
      P1 and K12 or P1 and B ram alleles.  A general model for the genetic control of
      the restriction and modification properties of E. coli strains and their
      episomes is presented.
AU  - Boyer HW
AU  - Roulland-Dussoix D
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1969 41: 459-472.

PMID- 20007369
VI  - 106
DP  - 2009
TI  - Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms.
PG  - 21848-21853
AB  - Giant viruses such as Mimivirus isolated from amoeba found in aquatic habitats show biological
      sophistication comparable to that of simple cellular life forms and seem to evolve by similar
      mechanisms, including extensive gene duplication and horizontal gene transfer (HGT), possibly
      in part through a viral parasite, the virophage. We report here the isolation of "Marseille"
      virus, a previously uncharacterized giant virus of amoeba. The virions of Marseillevirus
      encompass a 368-kb genome, a minimum of 49 proteins, and some messenger RNAs. Phylogenetic
      analysis of core genes indicates that Marseillevirus is the prototype of a family of
      nucleocytoplasmic large DNA viruses (NCLDV) of eukaryotes. The genome repertoire of the virus
      is composed of typical NCLDV core genes and genes apparently obtained from eukaryotic hosts
      and their parasites or symbionts, both bacterial and viral. We propose that amoebae are
      "melting pots" of microbial evolution where diverse forms emerge, including giant viruses with
      complex gene repertoires of various origins.
AU  - Boyer M
AU  - Yutin N
AU  - Pagnier I
AU  - Barrassi L
AU  - Fournous G
AU  - Espinosa L
AU  - Robert C
AU  - Azza S
AU  - Sun S
AU  - Rossmann MG
AU  - Suzan-Monti M
AU  - La Scola B
AU  - Koonin EV
AU  - Raoult D
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2009 106: 21848-21853.

PMID- 22207740
VI  - 194
DP  - 2012
TI  - Complete Genome Sequences of Three Pseudomonas aeruginosa Isolates with Phenotypes of Polymyxin B Adaptation and Inducible Resistance.
PG  - 529-530
AB  - Clinical 'superbug' isolates of Pseudomonas aeruginosa were previously observed to be
      resistant to several antibiotics, including polymyxin B,
      and/or to have a distinct, reproducible adaptive polymyxin resistance
      phenotype, identified by observing 'skipped' wells (appearance of extra
      turbid wells) during broth microdilution testing. Here we report the
      complete assembled draft genome sequences of three such polymyxin
      resistant P. aeruginosa strains (9BR, 19BR, and 213BR).
AU  - Boyle B
AU  - Fernandez L
AU  - Laroche J
AU  - Kukavica-Ibrulj I
AU  - Mendes CM
AU  - Hancock RW
AU  - Levesque RC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 529-530.

PMID- 23105076
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Swine Pathogen Streptococcus suis Serotype 2 Strain S735.
PG  - 6343-6344
AB  - Streptococcus suis is a major swine pathogen responsible for significant, worldwide economic
      losses in the swine industry, in addition to being an emerging
      zoonotic agent. Strains of serotype 2 are the most commonly associated with
      infections causing meningitis, endocarditis, and septicemia. Here we present the
      genome sequence of S. suis serotype 2 strain S735.
AU  - Boyle B
AU  - Vaillancourt K
AU  - Bonifait L
AU  - Charette SJ
AU  - Gottschalk M
AU  - Grenier D
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6343-6344.

PMID- 8568865
VI  - 255
DP  - 1996
TI  - Crystal structure of Citrobacter freundii restriction endonuclease Cfr10I at 2.15 A resolution.
PG  - 176-186
AB  - The X-ray crystal structure of Citrobacter freundii restriction endonuclease Cfr10I has been
      determined at a resolution of 2.15 Angstroms by multiple isomorphous replacement methods and
      refined to an R-factor of 19.64%.  The structure of Cfr10I represents the first structure of a
      restriction endonuclease recognizing a degenerate nucleotide sequence.  Structural comparison
      of Cfr10I with previously solved structures of other restriction enzymes suggests that
      recognition of specific sequence occurs through contacts in the major and the minor grooves of
      DNA.  The arrangement of the putative active site residues shows some striking differences
      from previously described restriction endonucleases and supports a two-metal-ion mechanism of
      catalysis.
AU  - Bozic D
AU  - Grazulis S
AU  - Siksnys V
AU  - Huber R
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1996 255: 176-186.

PMID- 25593266
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Robinsoniella peoriensis Strain WTD, Isolated from the Fecal Material of a Wood Turtle.
PG  - e01444-14
AB  - Here, we report the draft genome of Robinsoniella peoriensis strain WTD, which was isolated
      from the fecal material of a wood turtle. The genome size was
      7,391,415 bp with 41.1 mol% G+C.
AU  - Braasch JL
AU  - Lapin CN
AU  - Dowd SE
AU  - McLaughlin RW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01444-14.

PMID- 8365404
VI  - 216
DP  - 1993
TI  - Restriction-enzyme cleavage of DNA modified by platinum (II) complexes.
PG  - 183-187
AB  - The effect of binding of cis-diamminedichloroplatinum(II), its trans isomer and
      diethylenetriaminechloroplatinum(II) chloride to DNA on the splicing effectiveness of BamHI,
      EcoRI and SalI restriction endonucleases has been determined by means of gel electrophoresis.
      All three platinum complexes inhibit the cleavage of linearized plasmid DNA. In addition, the
      three platinum complexes bound to DNA constitute a barrier across which the linear diffusion
      of EcoRI on DNA is difficult. We interpret these findings to mean that the splicing
      effectiveness of restriction enzymes is influenced by bifunctional and monofunctional DNA
      adducts of platinum via both steric interference and DNA conformational distortions. Whereas
      the platinum adducts in the restriction sites or in their very closed proximity inhibit the
      cleavage, the lesions occurring a greater distance from the restriction site can slow down the
      process of the localization of recognition sequences.
AU  - Brabec V
AU  - Balcarova Z
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1993 216: 183-187.

PMID- 138746
VI  - 108
DP  - 1976
TI  - Mapping of recognition sites for the restriction endonuclease from Escherichia coli K12 on bacteriophage PM2 DNA.
PG  - 583-593
AB  - Two different methods have been used to locate the recognition sites for the
      restriction endonuclease from Escherichia coli K12 on the genome of
      bacteriophage PM2.  The first method employs purified fragments of PM2 DNA
      produced by digestion with HindIII.  The fragments are tested for their ability
      to support the ATPase activity of the enzyme or, alternatively, to inhibit it
      in the presence of intact substrate DNA.  In this way, recognition sites were
      assigned to the HindIII fragments 2, 6 and 7.  An independent approach involved
      the study of complexes between the enzyme and either the HindIII fragments or
      linear DNA produced by cleavage of PM2 DNA at the unique site for HpaII.
      Electron microscopic analysis of such preparations allowed mapping of the three
      recognition sites to 40, 60 and 62 map units from the HpaII cleavage site.
AU  - Brack C
AU  - Eberle H
AU  - Bickle TA
AU  - Yuan R
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1976 108: 583-593.

PMID- 22374960
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Clostridium sporogenes PA 3679, the Common Nontoxigenic  Surrogate for Proteolytic Clostridium botulinum.
PG  - 1631-1632
AB  - Clostridium sporogenes PA 3679 is widely used as a nontoxigenic surrogate for proteolytic
      strains of Clostridium botulinum in the derivation and validation of
      thermal processes in food. Here we report the draft assembly and annotation of
      the C. sporogenes PA 3679 genome. Preliminary analysis demonstrates a high degree
      of relatedness between C. sporogenes PA 3679 and sequenced strains of proteolytic
      C. botulinum.
AU  - Bradbury M
AU  - Greenfield P
AU  - Midgley D
AU  - Li D
AU  - Tran-Dinh N
AU  - Vriesekoop F
AU  - Brown JL
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1631-1632.

PMID- 30110167
VI  - 81
DP  - 2018
TI  - Complete Genome of Micromonospora sp. Strain B006 Reveals Biosynthetic Potential of a Lake Michigan Actinomycete.
PG  - 2057-2068
AB  - Actinomycete bacteria isolated from freshwater environments are an unexplored
      source of natural products. Here we report the complete genome of the Great
      Lakes-derived Micromonospora sp. strain B006, revealing its potential for natural
      product biosynthesis. The 7-megabase pair chromosome of strain B006 was sequenced
      using Illumina and Oxford Nanopore technologies followed by Sanger sequencing to
      close remaining gaps. All identified biosynthetic gene clusters (BGCs) were
      manually curated. Five known BGCs were identified encoding desferrioxamine,
      alkyl- O-dihydrogeranylmethoxyhydroquinone, a spore pigment, sioxanthin, and
      diazepinomicin, which is currently in phase II clinical trials to treat
      Phelan-McDermid syndrome and co-morbid epilepsy. We report here that strain B006
      is indeed a producer of diazepinomicin and at yields higher than previously
      reported. Moreover, 11 of the 16 identified BGCs are orphan, eight of which were
      transcriptionally active under the culture condition tested. Orphan BGCs include
      an enediyne polyketide synthase and an uncharacteristically large, 36-module
      polyketide synthase-nonribosomal peptide synthetase BGC. We developed a genetics
      system for Micromonospora sp. B006 that will contribute to deorphaning BGCs in
      the future. This study is one of the few attempts to report the biosynthetic
      capacity of a freshwater-derived actinomycete and highlights this resource as a
      potential reservoir for new natural products.
AU  - Braesel J
AU  - Crnkovic CM
AU  - Kunstman KJ
AU  - Green SJ
AU  - Maienschein-Cline M
AU  - Orjala J
AU  - Murphy BT
AU  - Eustaquio AS
PT  - Journal Article
TA  - J. Nat. Prod.
JT  - J. Nat. Prod.
SO  - J. Nat. Prod. 2018 81: 2057-2068.

PMID- 1086799
VI  - 70
DP  - 1976
TI  - The use of antibiotics actinomycin D and distamycin A for mapping of phage lambda HindIII fragments.
PG  - 91-95
AB  - The antibiotics distamycin A and actinomycin D interact with double-stranded
      DNA forming noncovalently bound complexes.  This interaction is rather
      selective: distamycin forms complexes preferentially with d(A/T) rich regions
      whereas actinomycin binds d(G/C) rich regions of DNA.  This property has
      offered a possibility to use these antibiotics for effective and highly
      selective protection of the cleavage sites recognized by restriction
      endonucleases.  The recognition site of endo R. HindIII 5'AAGCTT 3'TTCGAA may
      be protected by both actinomycin D and distamycin A as long as it contains TT
      and GC sequences favourable for interaction of distamycin and actinomycin with
      template DNA.  It has been demonstrated that different EcoRI recognition sites
      on lambda DNA may be effectively blocked by different antibiotic concentrations
      due to the peculiarities of the environment of different recognition sites.  In
      the present paper it is shown that certain endo R. HindIII sites of phage
      lambda DNA may be effectively protected with actinomycin whereas some other
      sites are protected with distamycin.  This allows us to obtain a set of larger
      overlapping fragments of DNA (hereafter we shall term them as distamycin and
      actinomycin protected fragments) and to establish the location of all HindIII
      fragments on the physical map of phage lambda DNA.  The data reported here and
      earlier lead to a conclusion that the antibiotics may be useful for DNA mapping
      and for obtaining new vector molecules.
AU  - Braga EA
AU  - Nosikov VV
AU  - Polyanovsky OL
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1976 70: 91-95.

PMID- 1204484
VI  - 225
DP  - 1975
TI  - Limitation of the action of restriction endonucleases by antibiotics bound to DNA.
PG  - 707-710
AB  - The effect of the antibiotics distamycin A and actinomycin D on the splitting
      of DNA by restriction endonucleases was studied.  Electrophoresis showed that
      antibiotics binding with DNA can compete with the corresponding enzymes.  Their
      selectivity was determined by the nucleotide sequence of the recognition
      section for the enzyme and also the immediate neighbourhood of these DNA
      sections.  With EcoRI and phage lambda DNA it was shown that distamycin A
      limited the number of sections split by restriction endonuclease.
AU  - Braga EA
AU  - Nosikov VV
AU  - Tanyashin VI
AU  - Zhuze AL
AU  - Polyanovskii OL
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1975 225: 707-710.

PMID- 23474435
VI  - 138
DP  - 2013
TI  - Comparative analysis of genes encoding key steroid core oxidation enzymes in fast-growing Mycobacterium spp. strains.
PG  - 41-53
AB  - A comparative genome analysis of Mycobacterium spp. VKM Ac-1815D, 1816D and 1817D
      strains used for efficient production of key steroid intermediates
      (androst-4-ene-3,17-dione, AD, androsta-1,4-diene-3,17-dione, ADD, 9alpha-hydroxy
      androst-4-ene-3,17-dione, 9-OH-AD) from phytosterol has been carried out by deep
      sequencing. The assembled contig sequences were analyzed for the presence
      putative genes of steroid catabolism pathways. Since
      3-ketosteroid-9alpha-hydroxylases (KSH) and 3-ketosteroid-Delta(1)-dehydrogenase
      (Delta(1) KSTD) play key role in steroid core oxidation, special attention was
      paid to the genes encoding these enzymes. At least three genes of Delta(1) KSTD
      (kstD), five genes of KSH subunit A (kshA), and one gene of KSH subunit B of
      3-ketosteroid-9alpha-hydroxylases (kshB) have been found in Mycobacterium sp. VKM
      Ac-1817D. Strains of Mycobacterium spp. VKM Ac-1815D and 1816D were found to
      possess at least one kstD, one kshB and two kshA genes. The assembled genome
      sequence of Mycobacterium sp. VKM Ac-1817D differs from those of 1815D and 1816D
      strains, whereas these last two are nearly identical, differing by 13 single
      nucleotide substitutions (SNPs). One of these SNPs is located in the coding
      region of a kstD gene and corresponds to an amino acid substitution Lys (135) in
      1816D for Ser (135) in 1815D. The findings may be useful for targeted genetic
      engineering of the biocatalysts for biotechnological application.
AU  - Bragin EY
AU  - Shtratnikova VY
AU  - Dovbnya DV
AU  - Schelkunov MI
AU  - Pekov YA
AU  - Malakho SG
AU  - Egorova OV
AU  - Ivashina TV
AU  - Sokolov SL
AU  - Ashapkin VV
AU  - Donova MV
PT  - Journal Article
TA  - J. Steroid Biochem. Mol. Biol.
JT  - J. Steroid Biochem. Mol. Biol.
SO  - J. Steroid Biochem. Mol. Biol. 2013 138: 41-53.

PMID- 3035193
VI  - 193
DP  - 1987
TI  - Sequences that adopt non-B-DNA conformation in form V DNA as probed by enzymic methylation.
PG  - 201-211
AB  - pBR322 form V DNA is a highly torsionally strained molecule with a linking
      number of zero.  We have used sequence-specific DNA methylases as probes for
      B-DNA in this molecule, exploiting the inability of methylases to methylate
      single-stranded DNA and Z-DNA, both of which are known to occur in form V DNA.
      Some sequences in form V DNA were shown to be totally in the B-form, others
      were totally in an altered, unmethylatable conformation, while still other
      sites appeared to exist partly in altered and partly in normal B-conformation.
      Some potential Z-forming sequences (alternating pyrimidine/purine) of less than
      seven base-pairs were not in the Z conformation in form V DNA, whereas others
      did adopt an altered structure, indicating a modulating influence of flanking
      sequences.  Furthermore, regions of imperfect alternating pyrimidine/purine
      structure were sometimes capable of adopting an altered structure.  In
      addition, some regions of altered structure had no apparent Z-forming
      sequences, nor were they in polypurine stretches, which have also been proposed
      to form left-handed DNA.  These non-B-DNA conformations may represent novel
      left-handed helical structures or sequences that become single stranded under
      torsional strain.  Long regions of either altered (unmethylatable) DNA or B-DNA
      were not always observed.  In fact, one region showed three transitions between
      B-like DNA and altered structure within 26 base-pairs.
AU  - Brahmachari SK
AU  - Shouche YS
AU  - Cantor CR
AU  - McClelland M
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1987 193: 201-211.

PMID- 15375138
VI  - 186
DP  - 2004
TI  - Complete Genomic Sequence of Bacteriophage B3, a Mu-Like Phage of Pseudomonas aeruginosa.
PG  - 6560-6574
AB  - Bacteriophage B3 is a transposable phage of Pseudomonas aeruginosa. In
      this report, we present the complete DNA sequence and annotation of the B3
      genome. DNA sequence analysis revealed that the B3 genome is 38,439 bp
      long with a G+C content of 63.3%. The genome contains 59 proposed open
      reading frames (ORFs) organized into at least three operons. Of these
      ORFs, the predicted proteins from 41 ORFs (68%) display significant
      similarity to other phage or bacterial proteins. Many of the predicted B3
      proteins are homologous to those encoded by the early genes and head genes
      of Mu and Mu-like prophages found in sequenced bacterial genomes. Only two
      of the predicted B3 tail proteins are homologous to other
      well-characterized phage tail proteins; however, several Mu-like prophages
      and transposable phage D3112 encode approximately 10 highly similar
      proteins in their predicted tail gene regions. Comparison of the B3
      genomic organization with that of Mu revealed evidence of multiple genetic
      rearrangements, the most notable being the inversion of the proposed B3
      immunity/early gene region, the loss of Mu-like tail genes, and an extreme
      leftward shift of the B3 DNA modification gene cluster. These differences
      illustrate and support the widely held view that tailed phages are genetic
      mosaics arising by the exchange of functional modules within a diverse
      genetic pool.
AU  - Braid MD
AU  - Silhavy JL
AU  - Kitts CL
AU  - Cano RJ
AU  - Howe MM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2004 186: 6560-6574.

PMID- 27570304
VI  - 56
DP  - 2016
TI  - Identification of DNA Methyltransferase Genes in Human Pathogenic Bacteria by Comparative Genomics.
PG  - 134-141
AB  - DNA methylation plays an important role in gene expression and virulence in some  pathogenic
      bacteria. In this report, we describe DNA methyltransferases (MTases)
      present in human pathogenic bacteria and compared them with related species,
      which are not pathogenic or less pathogenic, based in comparative genomics. We
      performed a search in the KEGG database of the KEGG database orthology groups
      associated with adenine and cytosine DNA MTase activities (EC: 2.1.1.37, EC:
      2.1.1.113 and EC: 2.1.1.72) in 37 human pathogenic species and 18 non/less
      pathogenic relatives and performed comparisons of the number of these MTases
      sequences according to their genome size, the DNA MTase type and with their
      non-less pathogenic relatives. We observed that Helicobacter pylori and Neisseria
      spp. presented the highest number of MTases while ten different species did not
      present a predicted DNA MTase. We also detected a significant increase of adenine
      MTases over cytosine MTases (2.19 vs. 1.06, respectively, p < 0.001). Adenine
      MTases were the only MTases associated with restriction modification systems and
      DNA MTases associated with type I restriction modification systems were more
      numerous than those associated with type III restriction modification systems
      (0.84 vs. 0.17, p < 0.001); additionally, there was no correlation with the
      genome size and the total number of DNA MTases, indicating that the number of DNA
      MTases is related to the particular evolution and lifestyle of specific species,
      regulating the expression of virulence genes in some pathogenic bacteria.
AU  - Brambila-Tapia AJ
AU  - Poot-Hernandez AC
AU  - Perez-Rueda E
AU  - Rodriguez-Vazquez K
PT  - Journal Article
TA  - Indian J. Microbiol.
JT  - Indian J. Microbiol.
SO  - Indian J. Microbiol. 2016 56: 134-141.

PMID- 21304750
VI  - 3
DP  - 2010
TI  - Complete genome sequence of Methanoplanus petrolearius type strain (SEBR 4847).
PG  - 203-211
AB  - Methanoplanus petrolearius Ollivier et al. 1998 is the type strain of the genus Methanoplanus.
      The strain was originally isolated from an offshore oil field from
      the Gulf of Guinea. Members of the genus Methanoplanus are of interest because
      they play an important role in the carbon cycle and also because of their
      significant contribution to the global warming by methane emission in the
      atmosphere. Like other archaea of the family Methanomicrobiales, the members of
      the genus Methanoplanus are able to use CO(2) and H(2) as a source of carbon and
      energy; acetate is required for growth and probably also serves as carbon source.
      Here we describe the features of this organism, together with the complete genome
      sequence and annotation. This is the first complete genome sequence of a member
      of the family Methanomicrobiaceae and the sixth complete genome sequence from the
      order Methanomicrobiales. The 2,843,290 bp long genome with its 2,824
      protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria
      and Archaea project.
AU  - Brambilla E et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 3: 203-211.

PMID- 4615175
VI  - 90
DP  - 1974
TI  - Restriction of lambda trp bacteriophages by Escherichia coli K.
PG  - 633-647
AB  - trp-transducing derivatives of phage lambda have been used to study Escherichia
      coli K specific restriction in vivo.  The expression of the trp genes from
      unmodified phages during infection of a rec+, restricting host is eliminated by
      restriction.  In a K-restricting recB,C host, where degradation of restricted
      phage DNA is prevented, expression of the trp genes is little affected by the
      presence of a single unmodified, K-restriction recognition site, even when that
      site is within the trpE gene.  RI restriction, in contrast to K restriction,
      prevents trp gene expression in a recB,C host when the restriction target is
      between the trp genes and the relevant promoter.  The presence of two
      K-restriction recognition sites in a lambda trp phage can have a marked effect
      on trp gene expression.  This effect can be interpreted as the result of
      preferential breakage between the two restriction recognition sites.  We
      conclude that K restriction does not break susceptible DNA at, or even
      preferentially near, a restriction recognition sequence.
AU  - Brammar WJ
AU  - Murray NE
AU  - Winton S
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1974 90: 633-647.

PMID- 23314785
VI  - 4
DP  - 2013
TI  - Tough nuts to crack Site-directed mutagenesis of bifidobacteria remains a challenge.
PG  - 197-202
AB  - Most members of the genus Bifidobacterium are commensals of the human gastrointestinal tract
      and some strains were shown to exert beneficial effects on their host. Based on these effects
      and due to their status as GRAS (generally recognized as safe) microorganisms, specific
      strains of bifidobacteria are marketed as probiotics. Despite their important role in food and
      dairy industries, the mechanisms responsible for the probiotic effects of bifidobacteria are
      mostly unknown. Over the last decade, the genomes of a large number of bifidobacteria have
      been sequenced and analyzed. This has yielded a number of genes and their products that are
      speculated to contribute to the probiotic effects of bifidobacteria. The gold standard to
      demonstrate a role for specific genes is the analysis of mutants. At present, only a small
      number of mutants of bifidobacteria have been generated by targeted mutagenesis. This is owed
      to the genetic inaccessibility of most strains and a lack of appropriate molecular tools.
      Successful generation of mutants of bifidobacteria was achieved by various methods including
      classical suicide vector strategies, increase of transformation efficiencies by methylation of
      plasmids and the use of temperature-sensitive vectors. In this commentary, we will describe
      the methods successfully used for mutagenesis of bifidobacteria and discuss their advantages
      and limitations.
AU  - Brancaccio VF
AU  - Zhurina DS
AU  - Riedel CU
PT  - Journal Article
TA  - Bioengineered
JT  - Bioengineered
SO  - Bioengineered 2013 4: 197-202.

PMID- 27716345
VI  - 15
DP  - 2016
TI  - Dissection of exopolysaccharide biosynthesis in Kozakia baliensis.
PG  - 170
AB  - BACKGROUND: Acetic acid bacteria (AAB) are well known producers of commercially
      used exopolysaccharides, such as cellulose and levan. Kozakia (K.) baliensis is a
      relatively new member of AAB, which produces ultra-high molecular weight levan
      from sucrose. Throughout cultivation of two K. baliensis strains (DSM 14400, NBRC
      16680) on sucrose-deficient media, we found that both strains still produce high
      amounts of mucous, water-soluble substances from mannitol and glycerol as (main)
      carbon sources. This indicated that both Kozakia strains additionally produce new
      classes of so far not characterized EPS. RESULTS: By whole genome sequencing of
      both strains, circularized genomes could be established and typical EPS forming
      clusters were identified. As expected, complete ORFs coding for levansucrases
      could be detected in both Kozakia strains. In K. baliensis DSM 14400 plasmid
      encoded cellulose synthase genes and fragments of truncated levansucrase operons
      could be assigned in contrast to K. baliensis NBRC 16680. Additionally, both K.
      baliensis strains harbor identical gum-like clusters, which are related to the
      well characterized gum cluster coding for xanthan synthesis in Xanthomanas
      campestris and show highest similarity with gum-like heteropolysaccharide (HePS)
      clusters from other acetic acid bacteria such as Gluconacetobacter diazotrophicus
      and Komagataeibacter xylinus. A mutant strain of K. baliensis NBRC 16680 lacking
      EPS production on sucrose-deficient media exhibited a transposon insertion in
      front of the gumD gene of its gum-like cluster in contrast to the wildtype
      strain, which indicated the essential role of gumD and of the associated gum
      genes for production of these new EPS. The EPS secreted by K. baliensis are
      composed of glucose, galactose and mannose, respectively, which is in agreement
      with the predicted sugar monomer composition derived from in silico genome
      analysis of the respective gum-like clusters. CONCLUSIONS: By comparative sugar
      monomer and genome analysis, the polymeric substances secreted by K. baliensis
      can be considered as unique HePS. Via genome sequencing of K. baliensis DSM 14400
      + NBRC 16680 we got first insights into the biosynthesis of these novel HePS,
      which is related to xanthan and acetan biosynthesis. Consequently, the present
      study provides the basis for establishment of K. baliensis strains as novel
      microbial cell factories for biotechnologically relevant, unique polysaccharides.
AU  - Brandt JU
AU  - Jakob F
AU  - Behr J
AU  - Geissler AJ
AU  - Vogel RF
PT  - Journal Article
TA  - Microb. Cell Fact.
JT  - Microb. Cell Fact.
SO  - Microb. Cell Fact. 2016 15: 170.

PMID- 28428295
VI  - 5
DP  - 2017
TI  - Multiple Genome Sequences of Heteropolysaccharide-Forming Acetic Acid Bacteria.
PG  - e00185-17
AB  - We report here the complete genome sequences of the acetic acid bacteria (AAB) Acetobacter
      aceti TMW 2.1153, A. persici TMW 2.1084, and Neoasaia chiangmaiensis
      NBRC 101099, which secrete biotechnologically relevant heteropolysaccharides
      (HePSs) into their environments. Upon genome sequencing of these AAB strains, the
      corresponding HePS biosynthesis pathways were identified.
AU  - Brandt JU
AU  - Jakob F
AU  - Geissler AJ
AU  - Behr J
AU  - Vogel RF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00185-17.

PMID- 27834714
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Mycobacterium bovis Strain D-10-02315 Isolated from Wild Boar.
PG  - e01268-16
AB  - Mycobacterium bovis is the etiologic agent of bovine tuberculosis, a chronic infectious
      disease, affecting livestock, wild animals, and sometimes humans. We
      report the draft genome sequence of a Mycobacterium bovis strain isolated from
      wild boar of spoligotype SB0120 (or BCG-like) also present in wildlife-livestock
      multi-host systems.
AU  - Branger M
AU  - Hauer A
AU  - Michelet L
AU  - Karoui C
AU  - Cochard T
AU  - De Cruz K
AU  - Henault S
AU  - Boschiroli ML
AU  - Biet F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01268-16.

PMID- 28684564
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Three Mycobacterium bovis Strains Identified in Cattle  and Wildlife in France.
PG  - e00410-17
AB  - Mycobacterium bovis is the etiologic agent of bovine tuberculosis, a chronic infectious
      disease affecting livestock, wild animals, and sometimes humans. We
      report here three draft genome sequences of Mycobacterium bovis strains of
      spoligotypes SB0821 and SB0134, isolated from wildlife but circulating in
      wildlife-livestock multihost systems, and SB0121, circulating exclusively in
      cattle.
AU  - Branger M
AU  - Hauer A
AU  - Michelet L
AU  - Karoui C
AU  - Cochard T
AU  - De Cruz K
AU  - Henault S
AU  - Boschiroli ML
AU  - Biet F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00410-17.

PMID- 
VI  - 61
DP  - 2001
TI  - Development and characterization of DNA methyltransferase inhibitors.
PG  - 5291-B
AB  - Enzymatic methylation of carbon 5 of cytosine bases is an epigenetic modification that is
      implicated in the silencing of tumor suppressor genes in various forms of cancer.  As a
      potential therapeutic approach for the treatment of such tumors, the goal of this project was
      to develop direct, mechanism-based inhibitors of mammalian DNA (cytosine-C5)-methyltransferase
      (DNMT1), which is the enzyme responsible for the maintenance of established methylation
      patterns in the genome.  The inhibition of the bacterial DNA (Cytosine-C5)-methyltransferase,
      HhaI methyltransferase (M.HhaI), was initially examined because of the large volume of
      structural information reported for this enzyme and because of the high degree of homology
      between catalytic domains of M.HhaI and DNMT1.  The oligodeoxyribonucleotide (ODN) inhibitor
      containing an abasic site in the target position (normally occupied by cytosine) was the most
      potent inhibitor of M.HhaI in comparison to a variety of other ODN inhibitors containing other
      modified target bases.  In addition to this potent inhibition, correlations were found between
      binding of M.HhaI to the most potent ODN inhibitors and the ability of these ODNs to induce a
      major M.HhaI conformational change.  Analysis of the catalytic efficiency of purified,
      recombinant DNMTI (rD-NMT1) with a variety of substrates revealed the preference of rDNMT1 for
      single-stranded substrates that formed stem-loop structures containing DNMT1 recognition
      sites.  These ODNs were substituted with various potential inhibitory target bases and were
      tested for the ability to inhibit rDNMT1 activity.  Of the inhibitors tested, ODNs containing
      abasic target sites were again found to be the most potent inhibitors and were also found to
      induce a dramatic conformational change of DNMT1.  In conclusion, the results show that ODNs
      containing an abasic target site are potent inhibitors of DNMT1 activity, which may be
      effective in vivo inhibitors of DNMT1 and potential therapeutic agents for treatment of
      cancer.
AU  - Brank AS
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 2001 61: 5291-B.

PMID- 12368098
VI  - 323
DP  - 2002
TI  - Inhibition of HhaI DNA (cytosine-C5) methyltransferase by oligodeoxyribonucleotides containing 5-Aza-2'-deoxycytidine: Examination of the intertwined roles of co-factor, target, transition state structure and enzyme conformation.
PG  - 53-67
AB  - The presence of 5-azacytosine (ZCyt) residues in DNA leads to potent inhibition of DNA
      (cytosine-C5) methyltranferases (C5-MTases) in vivo and in vitro. Enzymatic methylation of
      cytosine in mammalian DNA is an epigenetic modification that can alter gene activity and
      chromosomal stability, influencing both differentiation and tumorigenesis. Thus, it is
      important to understand the critical mechanistic determinants of ZCyt's inhibitory action.
      Although several DNA C5-MTases have been reported to undergo essentially irreversible binding
      to ZCyt in DNA, there is little agreement as to the role of AdoMet and/or methyl transfer in
      stabilizing enzyme interactions with ZCyt. Our results demonstrate that formation of stable
      complexes between HhaI methyltransferase (M.HhaI) and oligodeoxyribonucleotides containing
      ZCyt at the target position for methylation (ZCyt-ODNs) occurs in both the absence and
      presence of co-factors, AdoMet and AdoHcy. Both binary and ternary complexes survive SDS-PAGE
      under reducing conditions and take on a compact conformation that increases their
      electrophoretic mobility in comparison to free M.HhaI. Since methyl transfer can occur only in
      the presence of AdoMet, these results suggest (1) that the inhibitory capacity of ZCyt in DNA
      is based on its ability to induce a stable, tightly closed conformation of M.HhaI that
      prevents DNA and co-factor release and (2) that methylation of ZCyt in DNA is not required for
      inhibition of M.HhaI.
AU  - Brank AS
AU  - Eritja R
AU  - Garcia R
AU  - Marquez V
AU  - Christman J
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2002 323: 53-67.

PMID- 12071696
VI  - 25
DP  - 2002
TI  - Optimization of baculovirus-mediated expression and purification of  hexahistidine-tagged murine DNA (cytosine-C5)-methyltransferase-1 in   Spodoptera frugiperda 9 cells.
PG  - 31-40
AB  - Enzymatic DNA methylation of carbon 5 of cytosines is an epigenetic  modification that plays a
      role in regulating gene expression,
      differentiation, and tumorigenesis. DNA (cytosine-C5)-methyltransferase-1
      is the enzyme responsible for maintaining established methylation patterns
      during replication in mammalian cells. It is composed of a large (approximately 1100 amino
      acids (a.a.)) amino-terminal region containing many putative
      regulatory domains and a smaller (approximately 500 a.a.) carboxy-terminal
      region containing conserved, catalytic domains. In this study, murine DNA
      (cytosine C5)-methyltransferase-1, fused to an amino-terminal
      hexahistidine tag, was expressed by infecting Spodoptera frugiperda cells
      for 46 h with a recombinant baculovirus carrying the DNA
      (cytosine-C5)-methyltransferase-1 cDNA. A total of 3 X 10^8 infected S.
      frugiperda cells yielded approximately 1 mg of full-length,
      hexahistidine-tagged DNA (cytosine-C5)-methyltransferase-1, which was
      purified approximately 450-fold from RNase-treated S. frugiperda cell extracts
      by nickel affinity chromatography. The characterization of
      hexahistidine-tagged DNA (cytosine-C5)-methyltransferase-1 through DNA
      methylation and inhibitor-binding assays indicated that the purified
      enzyme had at least a 30-fold higher catalytic efficiency with
      hemimethylated double-stranded oligodeoxyribonucleotide substrates than
      unmethylated substrates and was most active with small
      oligodeoxyribonucleotide substrates with a capacity for forming stem-loop
      structures. The expression and purification procedures reported here
      differ significantly from the original reports of baculovirus-mediated
      hexahistidine-tagged DNA (cytosine-C5)-methyltransferase-1 expression and
      purification by nickel affinity chromatography and provide a consistent
      yield of active enzyme.
AU  - Brank AS
AU  - Van Bemmel DM
AU  - Christman JK
PT  - Journal Article
TA  - Protein Expr. Purif.
JT  - Protein Expr. Purif.
SO  - Protein Expr. Purif. 2002 25: 31-40.

PMID- 21296964
VI  - 193
DP  - 2011
TI  - Genome of a European Fresh-Vegetable Food Safety Outbreak Strain of Salmonella enterica subsp. enterica Serovar Weltevreden.
PG  - 2066
AB  - The genome of Salmonella enterica subsp. enterica serovar Weltevreden strain 2007-60-3289-1
      was sequenced. The genome sequence of this
      fresh-vegetable isolate from Scandinavia will be useful for the
      elucidation of plant host factors in comparison to other serovars of S.
      enterica subsp. enterica.
AU  - Brankatschk K
AU  - Blom J
AU  - Goesmann A
AU  - Smits TH
AU  - Duffy B
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 2066.

PMID- 7607529
VI  - 157
DP  - 1995
TI  - A transposon-like sequence adjacent to the AccI restriction-modification operon.
PG  - 69-72
AB  - We have cloned and sequenced the accIRM genes from Weeksella zoohelcum (the original
      identification of this strain as Acinetobacter calcoaceticus was incorrect).  Our sequence
      differs in the coding regions from a previously published sequence by the addition of three
      nucleotides near the 3' end of the DNA methyltransferase-encoding gene (accIM).  We have
      sequenced approx. 3 kb beyond this operon.  Two genes were found, convergently transcribed
      with the R-M operon.  The first of these genes encodes a protein which shows significant
      similarity to the recombinases of the phage integrase family.  The W. zoohelcum recombinase
      may function as a transposon resolvase, as in Tn4430.  The recombinase-encoding gene is
      followed by a putative transposase (Tnp), which is in turn followed by a terminator which is
      predicted to be Rho-dependent for the recombinase-Tnp operon and Rho-independent for the
      convergent R-M operon.  Since the G+C content of the two operons is notably different, it is
      possible that the terminator is at the extremity of the mobile element and serves to protect
      it from incoming transcription.
AU  - Brassard S
AU  - Paquet H
AU  - Roy PH
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 69-72.

PMID- 24265498
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Universal Bacteriophage Host Strain Campylobacter jejuni subsp. jejuni PT14.
PG  - e00969-13
AB  - Campylobacter jejuni strain PT14 is a clinical isolate previously used to propagate
      bacteriophages in the United Kingdom phage typing scheme. The strain
      has proven useful in the isolation of Campylobacter bacteriophages from several
      sources, and it functions as a model host in phage therapy experiments with
      poultry and poultry meat.
AU  - Brathwaite KJ
AU  - Siringan P
AU  - Moreton J
AU  - Wilson R
AU  - Connerton IF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00969-13.

PMID- 29650587
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Actinobacterial Strain Kineosporia sp. R_H_3, a Neutrophilic Iron-Depositing Bacterium.
PG  - e00335-18
AB  - The draft genome sequence of a neutrophilic iron-depositing actinobacterial strain,
      Kineosporia sp. R_H_3, is reported here. Detailed analysis of the genome
      can elucidate the role of specific cytochromes for Fe oxidation and how this
      organism might receive energy from Fe oxidation. To date, this is the second
      publicly available genome sequence of a Kineosporia strain.
AU  - Braun B
AU  - Kunzel S
AU  - Schroder J
AU  - Szewzyk U
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00335-18.

PMID- 28839033
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Strain R_RK_3, an Iron-Depositing Isolate of the Genus Rhodomicrobium, Isolated from a Dewatering Well of an Opencast Mine.
PG  - e00864-17
AB  - Rhodomicrobium sp. strain R_RK_3 is an iron-depositing bacterium from which we report the
      draft genome. This strain was isolated from ochrous depositions of a
      mining well pump in Germany. The Illumina NextSeq technique was used to sequence
      the genome of the strain.
AU  - Braun B
AU  - Kunzel S
AU  - Schroder J
AU  - Szewzyk U
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00864-17.

PMID- 28798175
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Gram-Positive Neutrophilic Iron-Precipitating Kineosporia sp. Strain A_224.
PG  - e00763-17
AB  - We report here the draft genome sequence of the neutrophilic iron-precipitating Kineosporia
      sp. strain A_224. Analysis of the predicted genes may improve our
      knowledge of its role in ochrous formations in natural and technical water
      systems. This is the first public genome sequence of a Kineosporia aurantiaca
      strain.
AU  - Braun B
AU  - Kunzel S
AU  - Szewzyk U
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00763-17.

PMID- 29650584
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Strain B 225, an Iron-Depositing Isolate of the Genus Novosphingobium.
PG  - e00325-18
AB  - Here, we report the draft genome sequence of Novosphingobium sp. strain B 225, an
      iron-depositing bacterium isolated from a phenazone-amended naturally grown
      biofilm. This biofilm was grown in the Unteres Odertal National Park, Germany.
      Illumina NextSeq sequencing was used to determine the genome of the strain.
AU  - Braun B
AU  - Kunzel S
AU  - Szewzyk U
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00325-18.

PMID- 28818902
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Ideonella sp. Strain A 288, Isolated from an Iron-Precipitating Biofilm.
PG  - e00803-17
AB  - Here, we report the draft genome sequence of the betaproteobacterium Ideonella sp. strain
      A_228. This isolate, obtained from a bog iron ore-containing
      floodplain area in Germany, provides valuable information about the genetic
      diversity of neutrophilic iron-depositing bacteria. The Illumina NextSeq
      technique was used to sequence the draft genome sequence of the strain.
AU  - Braun B
AU  - Kunzel S
AU  - Szewzyk U
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00803-17.

PMID- 27587815
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of 'Candidatus Viadribacter manganicus' Isolated from a  German Floodplain Area.
PG  - e00897-16
AB  - Iron- and manganese-depositing bacteria occur in many soils and all water systems, and their
      biogenic depositions of ochre in technical systems may cause
      severe clogging problems and monetary losses. 'Candidatus Viadribacter
      manganicus' is a small coccoid, iron- and manganese-depositing bacterium isolated
      from the Lower Oder Valley National Park, Germany.
AU  - Braun B
AU  - Szewzyk U
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00897-16.

PMID- 29437114
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Dietzia sp. Strain WMMA184, a Marine Coral-Associated Bacterium.
PG  - e01582-17
AB  - Dietzia sp. strain WMMA184 was isolated from the marine coral Montastraea faveolata as part of
      ongoing drug discovery efforts. Analysis of the 4.16-Mb
      genome provides information regarding interspecies interactions as it pertains to
      the regulation of secondary metabolism and natural product biosynthesis
      potential.
AU  - Braun DR
AU  - Chevrette MG
AU  - Acharya D
AU  - Currie CR
AU  - Rajski SR
AU  - Ritchie KB
AU  - Bugni TS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01582-17.

PMID- 29472337
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Micromonospora sp. Strain WMMA1996, a Marine Sponge-Associated Bacterium.
PG  - e00077-18
AB  - Micromonospora sp. strain WMMA1996 was isolated in 2013 off the coast of the Florida Keys,
      United States, from a marine sponge as part of bacterial
      coculture-based drug discovery initiatives. Analysis of the approximately 6.44-Mb
      genome reveals this microbe's potential role in the discovery of new drugs.
AU  - Braun DR
AU  - Chevrette MG
AU  - Acharya DD
AU  - Currie CR
AU  - Rajski SR
AU  - Bugni TS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00077-18.

PMID- 
VI  - 28
DP  - 2010
TI  - Structural study of the inhibition of DNA (cytosine-5) methyltransferases by original non-nucleoside inhibitors.
PG  - 20-22
AB  - 
AU  - Braun J
PT  - Journal Article
TA  - Chim. Nouv.
JT  - Chim. Nouv.
SO  - Chim. Nouv. 2010 28: 20-22.

PMID- 28126949
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Flavobacterium johnsoniae CI04, an Isolate from the Soybean Rhizosphere.
PG  - e01535-16
AB  - Flavobacterium johnsoniae CI04 was coisolated with Bacillus cereus from a root of a
      field-grown soybean plant in Arlington, WI, and selected as a model for
      studying commensalism between members of the Cytophaga-Flavobacterium-Bacteroides
      group and B. cereus Here we report the draft genome sequence of F. johnsoniae
      CI04 obtained by Illumina sequencing.
AU  - Bravo JI
AU  - Lozano GL
AU  - Handelsman J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01535-16.

PMID- 29348359
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of the Type Strain of Macrococcus canis.
PG  - e01507-17
AB  - The first complete genome sequence of the recently described Macrococcus canis species has
      been determined for the strain KM45013(T) (=DSM 101690(T) = CCOS 969(T) = CCUG 68920(T) = CCM
      8748(T)). The strain was isolated from a dog with rhinitis and contains a putative
      gamma-hemolysin and a mecB-carrying staphylococcal cassette chromosome mec element
      (SCCmecKM45013).
AU  - Brawand SG
AU  - Rychener L
AU  - Schwendener S
AU  - Pantucek R
AU  - Perreten V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01507-17.

PMID- Not carried by PubMed...
VI  - 96
DP  - 1996
TI  - The dam methyltransferase of a Salmonella typhimurium insertion mutant.
PG  - 500
AB  - A Salmonella typhimurium temperature-sensitive (ts) mutant was obtained after
      transposition mutagenesis with a miniTn10dTc element.  This mutant replicated well at 28oC but
      showed impaired growth at 37oC on LB agar.  Microscopic analysis revealed that the mutant
      produced filaments when cultured at 37oC.  Sequences flanking the insertion site were cloned
      by a
      "jumping PCR" technique.  Sequencing data demonstrated that the miniTn10d Tc was inserted at
      position 804 of the dam gene.  The Dam protein, coded by dam, methylates adenines in 5'-
      GATC-3' sequences.  The miniTn10d Tc insertion created a stop codon truncating the
      translation
      of the Dam last 10 amino acids.  The insertion site GGCTCTGTA was duplicated due to the
      transposition.  DNA digestion with MboI, DpnI and Sau3AI showed that the mutant genomic DNA
      contained methylated and unmethylated GATC sites.  The S. typhimurium wt dam gene showed
      82% and 92% homology in their nucleotide and deduced amino acid sequences, respectively, with
      the E. coli dam gene.  Mutant transformation with pTP166, which overproduces E. coli Dam,
      complemented the mutant phenotype.  We also constructed a recombinant plasmid (pDeldam)
      which mimics the deletion produced by the miniTn10d Tc insertion.  The pDeldam was used to
      transform an E. coli dam mutant.  The transformants showed a ts phenotype identical to that of
      the
      S. typhimurium insertion mutant.  We conclude that deletion of the last 10 amino acids from
      protein Dam diminished the methylase activity and conferred a ts phenotype.
AU  - Brawer R
AU  - Batista FD
AU  - Burrone O
AU  - Sordelli DO
AU  - Cerquetti MC
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1996 96: 500.

PMID- 9575240
VI  - 169
DP  - 1998
TI  - A temperature-sensitive DNA adenine methyltransferase mutant of Salmonella typhimurium.
PG  - 530-533
AB  - A temperature-sensitive mutant of Salmonella typhimurium was isolated earlier after transposon
      mutagenesis with Tn10dTet.  The mutant D220 grows well at 28 C but has a lower growth rate and
      forms filaments at 37 C.  Transposon-flanking fragments of mutant D220 DNA were cloned and
      sequenced.  The transposon was inserted in the dam gene between positions 803 and 804
      (assigned allele number: dam-231::Tn10dTet) and resulted in a predicted ten-amino-acid-shorter
      Dam protein.  The insertion created a stop codon that led to a truncated Dam protein with a
      temperature-sensitive phenotype.  The insertion dam-231::Tn10dTet resulted in a dam "leaky"
      phenotype since methylated and unmethylated adenines in GATC sequences were present.  In
      addition, the dam-231::Tn10dTet insertion rendered dam mutants temperature-sensitive for
      growth depending upon the genetic background of the S. typhimurium strain.  The wild-type dam
      gene of S. typhimurium exhibited 82% identity with the Escherichia coli dam gene.
AU  - Brawer R
AU  - Batista FD
AU  - Burrone OR
AU  - Sordelli DO
AU  - Cerquetti MC
PT  - Journal Article
TA  - Arch. Microbiol.
JT  - Arch. Microbiol.
SO  - Arch. Microbiol. 1998 169: 530-533.

PMID- 24285667
VI  - 1
DP  - 2013
TI  - Genome Sequences of Five B1 Subcluster Mycobacteriophages.
PG  - e00968-13
AB  - Mycobacteriophages infect members of the Mycobacterium genus in the phylum Actinobacteria and
      exhibit remarkable diversity. Genome analysis groups the
      thousands of known mycobacteriophages into clusters, of which the B1 subcluster
      is currently the third most populous. We report the complete genome sequences of
      five additional members of the B1 subcluster.
AU  - Breakwell DP
AU  - Barrus EZ
AU  - Benedict AB
AU  - Brighton AK
AU  - Fisher JN
AU  - Gardner AV
AU  - Kartchner BJ
AU  - Ladle KC
AU  - Lunt BL
AU  - Merrill BD
AU  - Morrell JD
AU  - Burnett SH
AU  - Grose JH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00968-13.

PMID- 21398545
VI  - 193
DP  - 2011
TI  - Complete genome sequence of the commensal Enterococcus faecalis 62 isolated from a healthy Norwegian infant.
PG  - 2377-2378
AB  - The genome of Enterococcus faecalis 62, a commensal isolate from a healthy Norwegian infant,
      revealed multiple adaptive traits to the gastro intestinal tract (GIT) environment and the
      milk containing diet of a breast fed infant. Adaptation to a commensal existence was
      emphasized by lactose and other carbohydrate metabolism genes within genomic islands
      accompanied by the absence of virulence traits.
AU  - Brede DA
AU  - Snipen LG
AU  - Ussery DW
AU  - Nederbragt AJ
AU  - Nes IF
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 2377-2378.

PMID- 25197454
VI  - 9
DP  - 2014
TI  - Genome sequence and emended description of Leisingera nanhaiensis strain DSM 24252(T) isolated from marine sediment.
PG  - 687-703
AB  - Leisingera nanhaiensis DSM 24252(T) is a Gram-negative, motile, rod-shaped marine
      Alphaproteobacterium, isolated from sandy marine sediments. Here we present the
      non-contiguous genome sequence and annotation together with a summary of the
      organism's phenotypic features. The 4,948,550 bp long genome with its 4,832
      protein-coding and 64 RNA genes consists of one chromosome and six
      extrachromosomal elements with lengths of 236 kb, 92 kb, 61 kb, 58 kb, 56 kb, and
      35 kb, respectively. The analysis of the genome showed that DSM 24252(T)
      possesses all genes necessary for dissimilatory nitrite reduction, and the strain
      was shown to be facultatively anaerobic, a deviation from the original
      description that calls for an emendation of the species. Also present in the
      genome are genes coding for a putative prophage, for gene-transfer agents and for
      the utilization of methylated amines. Phylogenetic analysis and intergenomic
      distances indicate that L. nanhaiensis might not belong to the genus Leisingera.
AU  - Breider S et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 687-703.

PMID- 18541415
VI  - 159
DP  - 2008
TI  - Viral diversity and dynamics in an infant gut.
PG  - 367-373
AB  - Metagenomic sequencing of DNA viruses from the feces of a healthy week-old
      infant revealed a viral community with extremely low diversity. The
      identifiable sequences were dominated by phages, which likely influence
      the diversity and abundance of co-occurring microbes. The most abundant
      fecal viral sequences did not originate from breast milk or formula,
      suggesting a non-dietary initial source of viruses. Certain sequences were
      stable in the infant's gut over the first 3 months of life, but microarray
      experiments demonstrated that the overall viral community composition
      changed dramatically between 1 and 2 weeks of age.
AU  - Breitbart M
AU  - Haynes M
AU  - Kelley S
AU  - Angly F
AU  - Edwards RA
AU  - Felts B
AU  - Mahaffy JM
AU  - Mueller J
AU  - Nulton J
AU  - Rayhawk S
AU  - Rodriguez-Brito B
AU  - Salamon P
AU  - Rohwer F
PT  - Journal Article
TA  - Res. Microbiol.
JT  - Res. Microbiol.
SO  - Res. Microbiol. 2008 159: 367-373.

PMID- 14526037
VI  - 185
DP  - 2003
TI  - Metagenomic analyses of an uncultured viral community from human feces.
PG  - 6220-6223
AB  - Here we present the first metagenomic analyses of an uncultured viral community from human
      feces, using partial shotgun sequencing. Most of the
      sequences were unrelated to anything previously reported. The recognizable
      viruses were mostly siphophages, and the community contained an estimated
      1,200 viral genotypes.
AU  - Breitbart M
AU  - Hewson I
AU  - Felts B
AU  - Mahaffy JM
AU  - Nulton J
AU  - Salamon P
AU  - Rohwer F
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2003 185: 6220-6223.

PMID- 12384570
VI  - 99
DP  - 2002
TI  - Genomic analysis of uncultured marine viral communities.
PG  - 14250-14255
AB  - Viruses are the most common biological entities in the oceans by an order of magnitude.
      However, very little is known about their diversity. Here we report a genomic analysis of two
      uncultured marine viral communities. Over 65% of the sequences were not significantly similar
      to previously reported sequences, suggesting that much of the diversity is previously
      uncharacterized. The most common significant hits among the known sequences were to viruses.
      The viral hits included sequences from all of the major families of dsDNA tailed phages, as
      well as some algal viruses. Several independent mathematical models based on the observed
      number of contigs predicted that the most abundant viral genome comprised 2-3% of the total
      population in both communities, which was estimated to contain between 374 and 7,114 viral
      types. Overall, diversity of the viral communities was extremely high. The results also showed
      that it would be possible to sequence the entire genome of an uncultured marine viral
      community.
AU  - Breitbart M
AU  - Salamon P
AU  - Andresen B
AU  - Mahaffy JM
AU  - Segall AM
AU  - Mead D
AU  - Azam F
AU  - Rohwer F
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2002 99: 14250-14255.

PMID- 1437572
VI  - 20
DP  - 1992
TI  - VDE endonuclease cleaves Saccharomyces cerevisiae genomic DNA at a single site: physical mapping of the VMA1 gene.
PG  - 5484
AB  - A DNA endonuclease, VDE, is derived from the VMA1 gene product of the yeast Saccharomyces
      cerevisiae and is related to other nucleases involved in nucleic acid rearrangements. Analysis
      of two cleavages sites showed that VDE recognizes an extended sequence,
      5'=TATSYATGYYGGGTGY^GGRG-AARKMGKKAAWGAAAWG-3', and leaves a staggered double-strand break
      with 4-bp 3'-hydroxyl overhangs. Cleavage of one site in the VMA1(delta)vde allele
      (previously deleted for the segment encoding VDE) during meiosis of a heterozygous diploid
      initiates a gene conversion event that transforms the mutant allele into a full-length VMA1
      gene. Here VDE cleavage of this same site in vitro was used to physically map the VMA1 locus.
AU  - Bremer MCD
AU  - Gimble FS
AU  - Thorner J
AU  - Smith CL
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 5484.

PMID- 10205183
VI  - 18
DP  - 1999
TI  - Binding of SeqA protein to DNA requires interaction between two or more complexes bound to separate hemimethylated GATC sequences.
PG  - 2304-2310
AB  - The SeqA protein binds to the post-replicative forms of the origins of replication of the
      Escherichia coli chromosome (oriC) and the P1 plasmid (P1oriR) at hemimethylated GATC adenine
      methylation sites.  It appears to regulate replication by preventing premature reinitiation.
      However, SeqA binding is not exclusive to replication origins: different fragments with
      hemimethylated GATC sites can bind SeqA in vitro when certain rules apply.  Most notably, more
      than one such site must be present on a bound fragment.  The protein appears to recognize
      individual hemimethylated sites, but must undergo an obligate cooperative interaction with a
      nearby found protein for stable binding.  SeqA contacts both DNA strands in a discrete patch
      at each hemimethylated GATC sequence.  All four GATC bases are contacted and are essential for
      binding.  Although the recognized sequence is symmetrical, the footprint on the methylated
      strand is always broader, suggesting that the bound protein is positioned asymmetrically with
      its orientation dictated by the position of the unique methyl group.  Studies of alternative
      spacings and relative orientations of adjacent sites suggest that each site may be recognized
      by a symmetrical dimer with an induced asymmetry in one of the subunits similar to that seen
      with certain type II restriction endonucleases.
AU  - Brendler T
AU  - Austin S
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1999 18: 2304-2310.

PMID- 4080551
VI  - 13
DP  - 1985
TI  - T4 RNA ligase catalyzed synthesis of base analogue-containing oligodeoxyribonucleotides and a characterization of their thermal stabilities.
PG  - 8665-8684
AB  - Self-complementary oligodeoxyribonucleotides containing the base analogues
      2-aminopurine, 2,6-diaminopurine, N6-methyladenine, uracil, and 5-bromouracil
      were synthesized by a general method that allows incorporation of the analogues
      at specific positions.  The method uses chemically synthesized partial
      sequences but circumvents the need for protected base analogues by
      incorporating their unprotected 3',5'-bisphosphate derivatives enzymatically.
      T4 RNA ligase was used to add the analogues to the oligodeoxyribonucleotides
      with yields from 54 to greater than 95 percent.  Oligodeoxyribonucleotides were
      joined to the oligodeoxyribonucleotides containing the analogues at their
      3'-termini in yields from 22 to 81 percent.  The high yields obtained in these
      joinings suggest that RNA ligase should be of general use for the specific
      incorporation of other deoxyribonucleoside analogues into
      oligodeoxyribonucleotides.  The oligodeoxyribonucleotides containing the base
      analogues were characterized by their mobilities during HPLC, nucleoside
      compositions, sequences, and thermal stabilities.
AU  - Brennan CA
AU  - Gumport RI
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1985 13: 8665-8684.

PMID- 3011781
VI  - 261
DP  - 1986
TI  - The effects of base analogue substitutions on the methylation by the EcoRI modification methylase of octadeoxyribonucleotides containing modified EcoRI recognition sequences.
PG  - 7279-7286
AB  - We have examined the DNA-protein interactions involved in the recognition of a
      specific hexameric sequence, GAATTC, by the EcoRI modification methylase by
      using derivatives of an oligodeoxyribonucleotide that contain a variety of base
      analogues.  The base analogues 2-aminopurine, 5-bromocytosine, 5-bromouracil,
      2,6-diaminopurine, hypoxanthine, 5-methylcytosine, N6-methyladenine, and uracil
      were incorporated as single substitutions into the octadeoxyribonucleotide
      d(pG-G-A-A-T-T-C-C).  The effects of the substitutions on the ability of the
      enzyme to methylate the modified substrates were monitored by determining the
      steady state kinetic values of the reaction in the presence of the cosubstrate,
      S-adenosylmethionine.  The substitutions resulted in effects ranging from
      complete inactivity to enhanced reactivity.  The enzyme exhibited
      Michaelis-Menten kinetics with those analogues that were active, whereas the
      octanucleotides containing hypoxanthine at the guanine site, N6-methyladenine
      at the first or 2-aminopurine at the second adenine site, or uracil at the
      second thymine site were completely inactive.  The results are discussed in
      terms of the possible interactions between the methylase and its recognition
      sequence.  In addition, the interactions are compared to those of the EcoRI
      restriction endonuclease, which has been similarly tested with the same
      analogue oligonucleotides.  The results of that study are reported in an
      accompanying paper.  Although both enzymes recognize the same sequence, they do
      so in different ways.
AU  - Brennan CA
AU  - Van Cleve MD
AU  - Gumport RI
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1986 261: 7279-7286.

PMID- 3011780
VI  - 261
DP  - 1986
TI  - The effects of base analogue substitutions on the cleavage by the EcoRI restriction endonuclease of octadeoxyribonucleotides containing modified EcoRI recognition sequences.
PG  - 7270-7278
AB  - It has been proposed that recognition of specific DNA sequences by proteins is
      accomplished by hydrogen bond formation between the protein and particular
      groups that are accessible in the major and minor grooves of the DNA.  We have
      examined the DNA-protein interactions involved in the recognition of the
      hexameric DNA sequence, GAATTC, by the EcoRI restriction endonuclease by using
      derivatives of an oligodeoxyribonucleotide that contain a variety of base
      analogues.  The base analogues hypoxanthine, 2-aminopurine, 2,6-diaminopurine,
      N6-methyladenine, 5-bromouracil, uracil, 5-bromocytosine, and 5-methylcytosine
      were incorporated as single substitutions into the octadeoxyribonucleotide
      d(pG-G-A-A-T-T-C-C).  The effects of the substitutions on the interactions
      between the EcoRI endonuclease and its recognition sequence were monitored by
      determining the steady state kinetic values of the hydrolysis reaction.  The
      substitutions resulted in effects that varied from complete inactivity to
      enhanced reactivity.  The enzyme exhibited Michaelis-Menten kinetics with those
      substrates that were reactive, whereas octanucleotide analoguues containing
      N6-methyladenine at either adenine position, uracil at the second thymine
      position, of 5-bromocytosine or 5-methylcytosine at the cytosine position were
      unreactive.  The results are discussed in terms of possible effects on the
      interactions between the enzyme and its recognition site during the reaction.
      An accompanying paper presents the results of a similar study using these
      oligonucleotides with the EcoRI modification methylase.
AU  - Brennan CA
AU  - Van Cleve MD
AU  - Gumport RI
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1986 261: 7270-7278.

PMID- 28883151
VI  - 5
DP  - 2017
TI  - Genome Sequence of Oceanimonas doudoroffii ATCC 27123T.
PG  - e00996-17
AB  - Oceanimonas doudoroffii ATCC 27123T is an obligately aerobic Gram-negative rod of the class
      Gammaproteobacteria It was first isolated from surface seawater off the
      coast of Oahu, HI, USA, in 1972. The predicted genome size is 3,832,938 bp (G+C
      content, 60.03%), which contains 3,524 predicted coding sequences.
AU  - Brennan MA
AU  - Trachtenberg AM
AU  - McClelland WD
AU  - MacLea KS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00996-17.

PMID- 8622983
VI  - 93
DP  - 1996
TI  - Stimulation of intrachromosomal homologous recombination in human cells by electroporation with site-specific endonucleases.
PG  - 3608-3612
AB  - In somatic mammalian cells, homologous recombination is a rare event.  To study
      the effects of chromosomal breaks on frequency of homologous recombination, site-specific
      endonucleases were introduced into human cells by electroporation.  Cell lines with a partial
      duplication within the HPRT (hypoxanthine phosphoribosyltransferase) gene were created through
      gene targeting.  Homologous, intrachromosomal recombination between the repeated regions of
      the gene can reconstruct a functioning, wild-type gene.  Treatment of thse cells with the
      restriction
      endonuclease XbaI, which has a recognition site within the repeated region of HPRT homology,
      increased the frequency of homologous recombination by more than 10-fold.  Recombination
      frequency was similarly increased by treatment with the rare-cutting yeast endonuclease
      PI-SceI
      when a cleavage site was placed within the repeated region of HPRT.  In contrast, four
      restriction
      enzymes that cut at positions either outside of the repeated regions or between them produced
      no
      change in recombination frequency.  The results suggest that homologous recombination between
      intrachromosomal repeats can be specificially initiated by a double-strand break occurring
      within
      regions of homology, consistent with the predictions of a double-strand-break-repair model.
AU  - Brenneman M
AU  - Gimble FS
AU  - Wilson JH
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1996 93: 3608-3612.

PMID- 16570845
VI  - 301
DP  - 2006
TI  - DNA methyltransferases: Facts, clues, mysteries.
PG  - 45-66
AB  - DNA methylation plays a pivotal role during development in mammals and is central to
      transcriptional silencing. The DNA methyltransferases
      (DNMTs) are responsible for the generation of genomic methylation
      patterns leading to gene silencing, but the underlying molecular basis
      remains largely shrouded in mystery. Here we review our current
      understanding of the mechanisms by which DNMTs repress transcription
      and how they are targeted to preferred DNA sequences. Emerging evidence
      points to an essential and intricate web of interactions between DNMTs
      and the chromatin environment in which they function. The recent
      identification of novel transcription factors recruiting the DNMTs may
      open new avenues of research into the origin of DNA methylation
      patterns. Thanks to these emerging clues, researchers have begun to
      lift the veil on the multi-faceted DNMTs, but there remains fascinating
      work ahead for whoever wants to fully understand DNMTs and their role
      in the mammalian cell.
AU  - Brenner C
AU  - Fuks F
PT  - Journal Article
TA  - Curr. Top. Microbiol. Immunol.
JT  - Curr. Top. Microbiol. Immunol.
SO  - Curr. Top. Microbiol. Immunol. 2006 301: 45-66.

PMID- 23908292
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Bacillus cereus Strain F, Isolated from Ancient Permafrost.
PG  - e00561-13
AB  - Bacillus cereus strain F was isolated and cultured from a sample of permafrost, aged
      presumably about 3 million years, on the Mammoth Mountain (62 degrees 56'N,
      133 degrees 59'E). These genome data provide the basis to investigate Bacillus
      cereus F, identified as a long-term survivor of the extremely cold and close
      environment.
AU  - Brenner EV
AU  - Brouchkov AV
AU  - Kurilshikov AM
AU  - Griva GI
AU  - Kashuba E
AU  - Kashuba VI
AU  - Melefors O
AU  - Repin VE
AU  - Melnikov VP
AU  - Vlassov VV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00561-13.

PMID- Not carried by PubMed...
VI  - 94
DP  - 1994
TI  - Cloning of the Type II methyltransferase from chlorobenzoate degrader Pseudomonas putida P111.
PG  - 459
AB  - Pseudomonas putida P111 is able to utilize a broad range of mono-, di-, and trichlorinated
      benzoates for growth. Phenotypical varient of this strain, designated P111B, was isolated to
      enable the cloning of the gene complex specifying degradation of ortho-chlorinated benzoates
      which was found on the indigenous plasmid pPB111. However, the cloning of this gene(s) was
      hampered by the presence of the Type II restriction and modification (R-M) system, designed
      PpuI, detected on the same plasmid. The R-M system has the same specificity as the R-M system
      EcoRI, e.g. the restriction endonuclease and the methylase both recognize the sequence
      G/AATTC. The gene for the methyltransferase PpuI was cloned into a broad host range cosmid
      pLAFR3, in selection step including the transformation of DNA isolated from all recombinant
      clones, and predigested thoroughly with EcoRI restriction endonuclease. Thus, only the DNA
      from recombinants protected by the methyltransferase PpuI was not linearized and was able to
      transform the recipient strain E. coli HB101. The region containing the gene for the
      methyltransferase PpuI was further subcloned and reintroduced into the cosmid pLAFR3. The
      isoschizomer enzymes recognizing the sequence G/AATTC were found in two reports on conjugative
      plasmids (EcoRI, RrsII), therefore the comparison of their sequences may be an important
      evolutionary development.
AU  - Brenner V
AU  - Focht DD
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1994 94: 459.

PMID- 2183182
VI  - 18
DP  - 1990
TI  - Cloning and nucleotide sequence of the gene encoding the EcaI DNA methyltransferase.
PG  - 355-359
AB  - The gene coding for the GGTNACC specific EcaI DNA methyltransferase (M.EcaI)
      has been cloned in E. coli from Enterobacter cloacae and its nucleotide
      sequence has been determined.  The ecaIM gene codes for a protein of 452 amino
      acids (Mr:51,111).  It was determined that M.EcaI is an adenine
      methyltransferase.  M.EcaI shows limited amino acid sequence similarity to
      other adenine methyltransferases.  A clone that expresses EcaI
      methyltransferase at high level was constructed.
AU  - Brenner V
AU  - Venetianer P
AU  - Kiss A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 355-359.

PMID- 11470352
VI  - 201
DP  - 2001
TI  - First evidence for a restriction-modification system in Leptospira sp.
PG  - 139-143
AB  - The LE1 leptophage exhibited a host range restricted to the saprophytic Leptospira hiflexa
      [Saint Girons et al., Res. Microbiol. 141 (1990)
      1131-1133] and mainly to the Patoc 1 strain (hereafter called PFRA)
      kept in the Paris, France collection. Results of titration of LEI
      lysates indicated the presence of a host-controlled modification and
      restriction system within PUSA (Patoc 1 strain maintained in the
      Morgantown, WV, USA collection) that was absent in PFRA. Because
      genomic DNA of PITAL (Patoc 1 strain maintained in Trieste, Italy)
      appeared smeared in pulsed field gel electrophoresis (PFGE), this
      strain is likely to contain nucleases that are activated upon DNA
      isolation. Moreover, comparative Nod digestions of PUSA and PFRA DNAs,
      as visualized by PFGE, indicated that PUSA belonged to a different
      serovar than PFRA. Finally, 16S ribosomal sequence analysis indicated
      that PUSA belonged to the saprophytic Leptospira meyeri species, while
      PITAL and PFRA appertained to L. biflexa. The evolutionary significance
      and the importance of the restriction and modification enzymes or
      non-specific nucleases within strains for genetic experiments are
      discussed.
AU  - Brenot A
AU  - Werts C
AU  - Ottone C
AU  - Sertour N
AU  - Charon NW
AU  - Postic D
AU  - Baranton G
AU  - Saint GI
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2001 201: 139-143.

PMID- 2162784
VI  - 264
DP  - 1990
TI  - McrI:  a novel class-II restriction endonuclease from Micrococcus cryophilus recognizing 5'-CGRY/CG-3'.
PG  - 218-222
AB  - A new class-II restriction endonuclease, McrI, with a novel sequence
      specificity as isolated from the Gram-positive eubacterium Micrococcus
      cryophilus.  McrI recognizes the palindromic hexanucleotide sequence
      5'-CGRY^CG-3'
      3'-GC^YRGC-5'.  The novel enzyme in the presence of Mg2+-ions cleaves
      specifically both strands as indicated by the arrows.  The staggered cuts
      generate 3'-protruding ends with single-stranded 5'-RY-3' dinucleotide
      extensions.  The McrI recognition sequence was deduced from mapping data on
      DNAs of bacteriophages PhiX174 RF and M13mp18 RF characterized by one and four
      cleavage sites, respectively.  The cut positions within both strands of the
      recognition sequence were determined in sequencing experiments by analyzing
      hydrolysis of phosphodiester bonds within a polylinker region of M13mp18 RF DNA
      containing an additional McrI recognition site including treatment with T4 DNA
      polymerase.  The novel enzyme may be a useful tool for cloning experiments by
      completion of the enzymes EclXI (5'-C/GGCCG-3'), NotI (5'-GC/GGCCGC-3'), PvuI
      (5'-CGAT/CG-3') as well as EaeI (5'-Y/GGCCR-3') and XhoII (5'-Y/GATCR-3')
      characterized by partly identical sequence specificities.
AU  - Brensing-Kuppers J
AU  - Reischl U
AU  - Schmitz GS
AU  - Kaluza K
AU  - Jarsch M
AU  - Kessler C
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1990 264: 218-222.

PMID- 9241245
VI  - 25
DP  - 1997
TI  - DNA duplexes with reactive dialdehyde groups as novel reagents for cross-linking to restriction-modification enzymes.
PG  - 3302-3309
AB  - To create new, effective reagents for affinity modification of restriction-modification
      enzymes, a regio-selective method for reactive dialdehyde group incorporation into
      oligonucleotides, based on insertion of a 1-beta-D-galactopyranosylthymine residue, has been
      developed.  We synthesized DNA duplex analogs of the substrates of the EcoRII and MvaI R-M
      enzymes that contained a galactose or periodate-oxidized galactose residue as single
      substituents either in the center of the EcoRII (MvaI) recognition site or in the flanking
      nucleotide sequence.  The dependence of binding, cleavage and methylation of these substrate
      analogs on the modified sugar location in the duplex was determined.  Cross-linking of the
      reagents to the enzymes under different conditions was examined.  M.EcoRII covalent attachment
      to periodate-oxidized substrate analogs proceeded in a specific way and to a large extent
      depended on the location of the reactive dialdehyde group in the substrate.  The yield of
      covalent attachment to a DNA duplex with a dialdehyde group in the flanking sequence with
      EcoRII or MvaI methylases was 9-20% and did not exceed 4% for R.EcoRII.
AU  - Brevnov MG
AU  - Gritsenko OM
AU  - Mikhailov SN
AU  - Efimtseva EV
AU  - Ermolinsky BS
AU  - Van Aeroschot A
AU  - Herdewijn P
AU  - Repyk AV
AU  - Gromova ES
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1997 25: 3302-3309.

PMID- 7607480
VI  - 157
DP  - 1995
TI  - Interaction of the MvaI and SsoII methyltransferases with DNAs altered at the central base pair of the recognition sequence.
PG  - 149-152
AB  - The interaction of the MvaI and SsoII DNA methyltransferases (MTases; M.MvaI and M.SsoII,
      respectively) with a set of synthetic DNA duplexes, containing an M.MvaI and an M.SsoII
      recognition site (CCWGG), was investigated.  In these DNA duplexes dA or dT of the recognition
      site was replaced by nucleoside analogs with modified sugar moieties and heterocyclic bases
      (2'-deoxy-2'-fluorouridine (flU), 1-(b-D-2'-deoxy-threo-pentofuranosyl) thymine (xT),
      1-(b-D-3'-deoxy-threo-pentofuranosyl)uracil (tU)), or by 1,3-propanediol (Prd).  A new
      approach for monitoring methylation of each strand of DNA duplexes by MTases was developed.
      It allowed the determination of the influence of the modification in one DNA strand on the
      methylation of the other.  In most cases, for both M.MvaI and M.SsoII, sugar analog-containing
      duplexes showed inhibition of methylation of only the modified strand.  Prd-containing DNA
      duplexes were not substrates for M.MvaI.  M.SsoII did not methylate DNA duplexes in which the
      dT residue was replaced by Prd.
AU  - Brevnov MG
AU  - Kubareva EA
AU  - Romanova EA
AU  - Volkov EM
AU  - Karyagina AS
AU  - Nikolskaya II
AU  - Gromova ES
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 149-152.

PMID- 8592499
VI  - 29
DP  - 1995
TI  - Influence of a single modification of the DNA sugar-phosphate backbone on the functioning of restriction endonucleases EcoRII, MvaI, and BstNI.
PG  - 1294-1300
AB  - Oligonucleotide duplexes containing modified nucleoside residues
      1-(2'-deoxy-betaD-threo-pentofuranosyl)thymine (xT) or
      1-(3'-deoxy-betaD-threo-pentofuranosyl)uracil (tU) in the center of the recognition site for
      EcoRII, MvaI, and BstNI (CCWGG) were constructed and examined in respect of their
      physicochemical and substrate properties.  The restriction endonucleases proved to differ in
      their sensitivity to the resulting conformational distortions.  For the first time with
      EcoRII, the xT-containing analog turned out to be a much better substrate and, moreover, an
      activator of the enzyme.
AU  - Brevnov MG
AU  - Kubareva EA
AU  - Volkov EM
AU  - Romanova EA
AU  - Oretskaya TS
AU  - Gromova ES
AU  - Shabarova ZA
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1995 29: 1294-1300.

PMID- 28860254
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Mesorhizobium ciceri bv. biserrulae WSM1497, an Efficient Nitrogen-Fixing Microsymbiont of the Forage Legume Biserrula pelecinus.
PG  - e00902-17
AB  - We report here the complete genome sequence of Mesorhizobium ciceri bv. biserrulae strain
      WSM1497, the efficient nitrogen-fixing microsymbiont and
      commercial inoculant in Australia of the forage legume Biserrula pelecinus The
      genome consists of 7.2 Mb distributed across a single chromosome (6.67 Mb) and a
      single plasmid (0.53 Mb).
AU  - Brewer RJM
AU  - Haskett TL
AU  - Ramsay JP
AU  - O'Hara GW
AU  - Terpolilli JJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00902-17.

PMID- 16787973
VI  - 22
DP  - 2006
TI  - DomainSieve: a protein domain-based screen that led to the identification of dam-associated genes with potential link to DNA maintenance.
PG  - 1935-1941
AB  - Motivation: The Dam methyltransferase (DamMT) activity, broadly distributed in association
      with restriction endonucleases, as part of
      the restriction-modification defense systems, has evolved to become
      intimately associated with essential biological functions in a few
      organisms. In Escherichia coli, DamMT is involved in multiple aspects
      of DNA maintenance, replication initiation, daughter chromosome
      segregation, DNA mismatch repair, gene expression control, etc.
      The participation of DamMT in such a diverse set of functions
      required that other genes adapted, or emerged through evolution, in
      response to the DamMT-induced modification of the genomic environment.
      One example is SeqA, a protein that senses the methylation status of
      the origin of replication of the chromosome to control the timing of
      replication initiation.
      Interestingly, seqA is only present in a few DamMT-specifying
      proteobacteria. This observation led us to hypothesize that other
      genes, specifying related functions, might also be found in these
      organisms. To test this hypothesis, we implemented a large-scale
      comparative genomic screen meant to identify genes specifying DNA
      methylation sensing domains, probably involved in DNA maintenance
      functions.
      Results: We carried out a phylogenetic analysis of DamMT,
      identifying two contrasting behaviors of the protein. Based on this
      phylogeny, we defined precisely a set of genomes, in which the protein
      activity is likely to be involved in DNA maintenance functions, the
      'resident' dam genomes. We defined a second set of genomes, in which
      DamMT is not resident. We developed a new tool, 'DomainSieve', in
      order to screen these two sets for protein domains that are strictly
      associated with 'resident' dam genomes.
      This approach was rewarding and generated a list of genes, among
      which some, at least, specify activities with clear linkage to
      DamMT-dependent DNA methylation and DNA maintenance.
AU  - Brezellec P
AU  - Hoebeke M
AU  - Hiet MS
AU  - Pasek S
AU  - Ferat JL
PT  - Journal Article
TA  - Bioinformatics
JT  - Bioinformatics
SO  - Bioinformatics 2006 22: 1935-1941.

PMID- 9653552
VI  - 5
DP  - 1998
TI  - Inhibiting the dimeric restriction endonuclease EcoRI using interfacial helical peptides.
PG  - 339-343
AB  - Many enzymes are active only in a dimeric form, including a variety of type II restriction
      endonucleases.  Disruption of subunit interactions is therefore a potential method for
      multimeric enzyme inhibition.  EcoRI is a homodimeric restriction endonuclease, the dimeric
      interface of which consists of a four-helix bundle.  We set out to design helical peptides to
      interact with this interface and block dimer formation, thus rendering EcoRI inactive.  Here
      we describe two synthetic, helical peptides based on the interfacial region of EcoRI.  Both
      peptides inhibit the enzyme, but the peptide derived from the alpha4 helix of EcoRI had both a
      higher helical content and better efficacy than a variant peptide, alpha4(Leu), that has three
      lle-Leu mutations (IC50 values of 27 microM and 90 microM, and helical contents of 29% and
      10%, respectively).  Size-exclusion chromatography confirmed that the alpha4 peptide disrupted
      dimerization of EcoRI, and circular dichroism indicated that EcoRI remained folded upon
      binding to alpha4.  Inhibition with alpha4 and alpha4(Leu) was shown to be specific for EcoRI,
      as the dimeric restriction enzyme PvuII was not affected by the peptides.
AU  - Brickner M
AU  - Chmielewski J
PT  - Journal Article
TA  - Chem. Biol.
JT  - Chem. Biol.
SO  - Chem. Biol. 1998 5: 339-343.

PMID- 22636780
VI  - 194
DP  - 2012
TI  - Genome Sequencing of a Genetically Tractable Pyrococcus furiosus Strain Reveals a Highly Dynamic Genome.
PG  - 4097-4106
AB  - The model archaeon Pyrococcus furiosus grows optimally near 100 degrees C on carbohydrates and
      peptides. Its genome sequence (NCBI) was determined 12 years
      ago. A genetically tractable strain, COM1, was very recently reported, and here
      we describe its genome sequence. Of 1,909,827 bp in size, it is 1,571 bp longer
      (0.1%) than the reference NCBI sequence. The COM1 genome contains numerous
      chromosomal rearrangements, deletions, and single base changes. COM1 also has 45
      full or partial insertion sequences (ISs) compared to 35 in the reference NCBI
      strain, and these have resulted in the direct deletion or insertional
      inactivation of 13 genes. Another seven genes were affected by chromosomal
      deletions and are predicted to be nonfunctional. In addition, the amino acid
      sequences of another 102 of the 2,134 predicted gene products are different in
      COM1. These changes potentially impact various cellular functions, including
      carbohydrate, peptide, and nucleotide metabolism; DNA repair; CRISPR-associated
      defense; transcriptional regulation; membrane transport; and growth at 72 degrees
      C. For example, the IS-mediated inactivation of riboflavin synthase in COM1
      resulted in a riboflavin requirement for growth. Nevertheless, COM1 grew on
      cellobiose, malto-oligosaccharides, and peptides in complex and minimal media at
      98 and 72 degrees C to the same extent as did both its parent strain and a new
      culture collection strain (DSMZ 3638). This was in spite of COM1 lacking several
      metabolic enzymes, including nonphosphorylating glyceraldehyde-3-phosphate
      dehydrogenase and beta-glucosidase. The P. furiosus genome is therefore of high
      plasticity, and the availability of the COM1 sequence will be critical for the
      future studies of this model hyperthermophile.
AU  - Bridger SL
AU  - Lancaster WA
AU  - Poole FLII
AU  - Schut GJ
AU  - Adams MW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4097-4106.

PMID- 21685277
VI  - 193
DP  - 2011
TI  - Genome Sequence of Listeria monocytogenes Scott A, a Clinical Isolate from a Food-Borne Listeriosis Outbreak.
PG  - 4284-4285
AB  - Listeria monocytogenes is an opportunistic food-borne pathogen and the causative agent of
      listeriosis in animals and humans. We present the
      genome sequence of Listeria monocytogenes Scott A, a widely distributed
      and frequently used serovar 4b clinical isolate from the 1983 listeriosis
      outbreak in Massachusetts.
AU  - Briers Y
AU  - Klumpp J
AU  - Schuppler M
AU  - Loessner MJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4284-4285.

PMID- 
VI  - 0
DP  - 1995
TI  - Characterization of a restriction endonuclease from Pasteurella haemolytica serotype A1 and construction of a gene-replacement Aroa mutant.
PG  - 221-222
AB  - A new restriction endonuclease, PhaI, was isolated from P. haemolytica
      serotype
      1, strain NADC D60, obtained from pneumonic bovine lung.  PhaI recognizes the 5 base
      non-
      palindromic sequences 5'-GCATC-3' and 5'-GATGC-3'.  Cleavage occurs 5 bases 3'
      from the
      former recognition site and 9 bases 5' from the latter.  A gene encoding for a
      methyltransferase
      which protects against PhaI cleavage was cloned from P. haemolytica into E. coli.
      Whereas
      unmethylated plasmid DNA containing a P. haemolytica origin of replication was unable to
      transform P. haemolytica when introduced by electroporation, the same plasmid DNA
      obtained
      from E. coli which contained cloned PhaI methyltransferase could do so.  The aroA gene of
      P.
      haemolytica serotype A1 was cloned and sequenced.  A P. haemolytica ampicillin-
      resistance
      fragment was cloned into the unique NdeI site of aroA.  A hybrid plasmid was constructed
      by
      joining the aroA replacement plasmid with the 4.2 kb P. haemolytica plasmid which
      encodes
      streptomycin resistance.  Following PhaI methylation, the hybrid plasmid was introduced
      into P.
      haemolytica by electroporation.  Allelic exchange between the replacement plasmid and
      chromosome of P. haemolytica gave rise to an ampicillin-resistant mutant which was
      unable to
      grow on medium deficient in tryptophan.  Although transformation efficiency with
      methylated
      hybrid plasmid was <10^3/ug, the hybrid was capable of unstable replication in P.
      haemolytica, so
      this system may be suitable for construction of additional gene-replacement mutants.
AU  - Briggs RE
AU  - Tatum FM
PT  - Journal Article
TA  - Haemophilus, Actinobacillus and Pasteurella
JT  - Haemophilus, Actinobacillus and Pasteurella
SO  - Haemophilus, Actinobacillus and Pasteurella 1995 0: 221-222.

PMID- 16269758
VI  - 71
DP  - 2005
TI  - Generation and molecular characterization of new temperature-sensitive plasmids intended for genetic engineering of Pasteurellaceae.
PG  - 7187-7195
AB  - Temperature-sensitive (TS) plasmids were generated through chemical mutagenesis of a
      derivative of the streptomycin resistance parent plasmid pD70, isolated from Mannheimia
      hemolytica serotype 1. Three TS plasmids which failed to replicate at or above 42 degrees C in
      M. hemolytica but which were fully functional below 31 degrees C were selected for further
      analysis. Two of the TS plasmids were shown by sequencing to possess unique single-base-pair
      mutations. The third TS plasmid contained a unique base pair substitution and a second
      mutation that had been previously identified. These mutations were clustered within a 200-bp
      region of the presumed plasmid origin of replication. Site-directed single-nucleotide
      substitutions were introduced into the wild-type pD70 origin of replication to confirm that
      mutations identified by sequencing had conferred thermoregulated replication. Deletion
      analysis on the wild-type pD70 plasmid replicon revealed that approximately 720 bp are
      necessary for plasmid maintenance. Replication of the TS plasmids was thermoregulated in
      Pasteurella multocida and Haemophilus somnus as well. To consistently transform H. somnus with
      TS plasmid, in vitro DNA methylation with commercially available HhaI methyltransferase was
      necessary to protect against the organism's restriction enzyme HsoI (recognition sequence
      5'-GCGC-3') characterized herein.
AU  - Briggs RE
AU  - Tatum FM
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2005 71: 7187-7195.

PMID- 8031094
VI  - 60
DP  - 1994
TI  - Characterization of a restriction endonuclease, PhaI, from Pasteurella haemolytica Serotype A1 and protection of heterologous DNA by a cloned PhaI methyltransferase gene.
PG  - 2006-2010
AB  - Pasteurella haemolytica is the leading cause of economic loss to the beef cattle industry in
      the United States and an important etiologic agent worldwide. Study of P. haemolytica is
      hindered by researchers' inability to genetically manipulate the organism. A new restriction
      endonuclease, PhaI, an isoschizomer of SfaNI (R.J. Roberts, Methods Enzymol. 65:19-36, 1980),
      was isolated from P. haemolytica serotype I, strain NADC-D60, obtained from pneumonic bovine
      lung, PhaI recognizes the 5-base nonpalindromic sequences 5'-GCATC-3' and 5'-GATGC-3'.
      Cleavage occurs 5 bases 3' from the former recognition site and 9 bases 5' from the latter
      recognition site. A gene encoding a methyltransferase which protects against PhaI cleavage was
      cloned from P. haemolytica NADC-D60 into Escherichia coli. Whereas unmethylated plasmid DNA
      containing a P. haemolytica origin of replication was unable to transform P. haemolytica when
      introduced by electroporation, the same plasmid DNA obtained from E. coli which contained a
      cloned PhaI methyltransferase gene could do so. The data indicate that PhaI is an effective
      barrier to the introduction and establishment of exogenous DNA in P. haemolytica.
AU  - Briggs RE
AU  - Tatum FM
AU  - Casey TA
AU  - Frank GH
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1994 60: 2006-2010.

PMID- Not carried by PubMed...
VI  - 94
DP  - 1994
TI  - Characterization of a restriction endonuclease, PhaI, from Pasteurella haemolytica serotype A1 and protection of heterologous DNA by cloned PhaI methyltransferase.
PG  - 132
AB  - Pasteurella haemolytica is the leading cause of economic loss to the beef cattle industry in
      the US, and an important etiologic agent worldwide. Study of P. haemolytica is hindered by
      researchers' inability to genetically manipulate the organism. A new restriction
      endonuclease, PhaI, an isoschizomer of SfaNI, was isolated from Pasteurella haemolytica
      serotype 1, strain NADC-D60, obtained from pneumonic bovine lung. PhaI recognizes the 5 base
      non-palindromic sequences 5'-GCATC-3' and 5'-GATGC-3'. Cleavage occurs 5 bases 3' from
      the former recognition site and 9 bases 5' from the latter recognition site. A gene encoding
      for a methyltransferase which protects against PhaI cleavage was cloned from P. haemolytica
      NADC-D60 into E. coli. Whereas unmethylated plasmid DNA containing a P. haemolytica origin of
      replication was unable to transform P. haemolytica when introduced by electroporation, the
      same plasmid DNA obtained from E. coli which contained cloned PhaI methyltransferase could do
      so. The data indicate that PhaI is an effective barrier to the introduction and establishment
      of exogenous DNA in P. haemolytica.
AU  - Briggs RE
AU  - Tatum FM
AU  - Casey TA
AU  - Frank GH
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1994 94: 132.

PMID- 28751386
VI  - 5
DP  - 2017
TI  - Genome Sequence of the Dichloromethane-Degrading Bacterium Hyphomicrobium sp. Strain GJ21.
PG  - e00622-17
AB  - The genome sequence of Hyphomicrobium sp. strain GJ21, isolated in the Netherlands from
      samples of environments contaminated with halogenated pollutants
      and capable of using dichloromethane as its sole carbon and energy source, was
      determined.
AU  - Bringel F et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00622-17.

PMID- 16926437
VI  - 74
DP  - 2006
TI  - Nucleotide Sequence Analysis of the Enteropathogenic Escherichia coli Adherence Factor Plasmid pMAR7.
PG  - 5408-5413
AB  - The complete nucleotide sequence was determined for pMAR7, an
      enteropathogenic Escherichia coli (EPEC) adherence factor (EAF) plasmid
      that contains genes encoding a type IV attachment pilus (Bfp) and the
      global virulence regulator per. Prototypic EAF plasmid pMAR7 is
      self-transmissible, unlike the smaller EAF plasmid pB171, which has no
      genes encoding conjugative functions. The tra locus, a highly conserved
      33-kb segment found in pMAR7, is similar to the tra (conjugation) region
      of the F plasmid. ISEc13 copies flanking the pMAR7 tra region could
      potentially mobilize or delete the tra genes. Hybridization of 134 EPEC
      strains showed that a complete tra region is present only in strains of
      the EPEC1 clonal group. This study confirms EPEC's potential for
      dissemination of virulence attributes by horizontal transfer of the EAF
      plasmid.
AU  - Brinkley C
AU  - Burland V
AU  - Keller R
AU  - Rose DJ
AU  - Boutin AT
AU  - Klink SA
AU  - Blattner FR
AU  - Kaper JB
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2006 74: 5408-5413.

PMID- 2055475
VI  - 100
DP  - 1991
TI  - The cleavage site of restriction endonuclease MnlI.
PG  - 267-268
AB  - The cleavage site generated by restriction endonuclease MnlI has the structure:
      5'-CCTC(N)7-3'
      3'-GGAG(N)6-5'  with one-nucleotide 3' overhang.
AU  - Brinkley P
AU  - Bautista DS
AU  - Graham FL
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1991 100: 267-268.

PMID- 23045487
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Turicella otitidis ATCC 51513, Isolated from Middle Ear  Fluid from a Child with Otitis Media.
PG  - 5968-5969
AB  - Turicella otitidis is an unusual corynebacterium with a controversial role in otitis media in
      children. Metabolic capabilities deduced from the draft genome
      indicate its adaptation to habitats on the human skin and in the intestine. The
      lack of candidate virulence factors implies that T. otitidis has a low pathogenic
      potential.
AU  - Brinkrolf K
AU  - Schneider J
AU  - Knecht M
AU  - Ruckert C
AU  - Tauch A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5968-5969.

PMID- 26251491
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Bacillus megaterium Siphophage Stahl.
PG  - e00857-15
AB  - Stahl is a siphophage active against Bacillus megaterium, a Gram-positive bacterium often used
      as a model system in research and as a protein production
      strain in industrial applications. Here, we present the complete annotated genome
      of phage Stahl and describe its major features.
AU  - Brizendine AM
AU  - Rousseau S
AU  - Hernandez AC
AU  - Kuty EGF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00857-15.

PMID- 16295655
VI  - 50
DP  - 2005
TI  - The use of bacteriophages in eliminating polyresistant strains of Staphylococcus aureus and Streptococcus agalactiae.
PG  - 187-194
AB  - Temperate bacteriophages were induced in and released from isolates of Staphylococcus aureus
      and Streptococcus agalactiae using mitomycin C. Various specific indicator cultures were
      tested for providing clear plaques after phage infection. Specific lytic mixture of
      bacteriophages was prepared using the induced, modified and laboratory variants of phages.
      Under laboratory conditions, the mixture eliminated all isolates from the tested collection of
      microorganisms. The restriction barrier of some bacterial isolates to bacteriophage infection
      was overcome either by UV irradiation or in vitro modification of bacteriophage DNA with
      specific methyltransferases. Conjugative R plasmids, capable of replication in G(+) and G(-)
      bacteria, were detected and isolated from S. aureus and S. agalactiae antibiotic-resistant
      strains.
AU  - Brnakova Z
AU  - Farkasovska J
AU  - Godany A
PT  - Journal Article
TA  - Folia Microbiol. (Praha)
JT  - Folia Microbiol. (Praha)
SO  - Folia Microbiol. (Praha) 2005 50: 187-194.

PMID- 23969047
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence for Lactobacillus helveticus CNRZ 32, an Industrial Cheese Starter and Cheese Flavor Adjunct.
PG  - e00590-13
AB  - Lactobacillus helveticus is a lactic acid bacterium widely used in the manufacture of cheese
      and for production of bioactive peptides from milk
      proteins. We present the complete genome sequence for L. helveticus CNRZ 32, a
      strain particularly recognized for its ability to reduce bitterness and
      accelerate flavor development in cheese.
AU  - Broadbent JR
AU  - Hughes JE
AU  - Welker DL
AU  - Tompkins TA
AU  - Steele JL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00590-13.

PMID- 23035691
VI  - 13
DP  - 2012
TI  - Analysis of the Lactobacillus casei supragenome and its influence in species evolution and lifestyle adaptation.
PG  - 533
AB  - BACKGROUND: The broad ecological distribution of L. casei makes it an insightful
      subject for research on genome evolution and lifestyle adaptation. To explore
      evolutionary mechanisms that determine genomic diversity of L. casei, we
      performed comparative analysis of 17 L. casei genomes representing strains
      collected from dairy, plant, and human sources. RESULTS: Differences in L. casei
      genome inventory revealed an open pan-genome comprised of 1,715 core and 4,220
      accessory genes. Extrapolation of pan-genome data indicates L. casei has a
      supragenome approximately 3.2 times larger than the average genome of individual
      strains. Evidence suggests horizontal gene transfer from other bacterial species,
      particularly lactobacilli, has been important in adaptation of L. casei to new
      habitats and lifestyles, but evolution of dairy niche specialists also appears to
      involve gene decay. CONCLUSIONS: Genome diversity in L. casei has evolved through
      gene acquisition and decay. Acquisition of foreign genomic islands likely confers
      a fitness benefit in specific habitats, notably plant-associated niches. Loss of
      unnecessary ancestral traits in strains collected from bacterial-ripened cheeses
      supports the hypothesis that gene decay contributes to enhanced fitness in that
      niche. This study gives the first evidence for a L. casei supragenome and
      provides valuable insights into mechanisms for genome evolution and lifestyle
      adaptation of this ecologically flexible and industrially important lactic acid
      bacterium. Additionally, our data confirm the Distributed Genome Hypothesis
      extends to non-pathogenic, ecologically flexible species like L. casei.
AU  - Broadbent JR
AU  - Neeno-Eckwall EC
AU  - Stahl B
AU  - Tandee K
AU  - Cai H
AU  - Morovic W
AU  - Horvath P
AU  - Heidenreich J
AU  - Perna NT
AU  - Barrangou R
AU  - Steele JL
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2012 13: 533.

PMID- 17400740
VI  - 189
DP  - 2007
TI  - YhdJ, a Nonessential CcrM-Like DNA Methyltransferase of Escherichia coli and Salmonella enterica.
PG  - 4325-4327
AB  - The Caulobacter crescentus DNA adenine methyltransferase CcrM and its homologs in the
      alpha-Proteobacteria are essential for viability. CcrM is
      34% identical to the yhdJ gene products of Escherichia coli and Salmonella
      enterica. This study provides evidence that the E. coli yhdJ gene encodes
      a DNA adenine methyltransferase. In contrast to an earlier report,
      however, we show that yhdJ is not an essential gene in either E. coli or
      S. enterica.
AU  - Broadbent SE
AU  - Balbontin R
AU  - Casadesus J
AU  - Marinus MG
AU  - van der Woude M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2007 189: 4325-4327.

PMID- 23723407
VI  - 1
DP  - 2013
TI  - Whole-Genome Draft Sequences of Three Multidrug-Resistant Klebsiella pneumoniae Strains Available from the American Type Culture Collection.
PG  - e00312-13
AB  - Infection with multidrug-resistant Klebsiella pneumoniae is a significant problem worldwide,
      requiring a better understanding of how various strains are able to
      defeat current antibiotic therapies and cause disease. Here, we report the draft
      genome sequences of three K. pneumoniae strains harboring the SHV-18, KPC-2, or
      NDM-1 beta-lactamases.
AU  - Broberg CA
AU  - Palacios M
AU  - Miller VL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00312-13.

PMID- 25291761
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Klebsiella pneumoniae Strain ATCC 43816 KPPR1, a Rifampin-Resistant Mutant Commonly Used in Animal, Genetic, and Molecular Biology  Studies.
PG  - e00924-14
AB  - Klebsiella pneumoniae is an urgent public health threat due to the spread of
      carbapenem-resistant strains causing serious, and frequently fatal, infections.
      To facilitate genetic, molecular, and immunological studies of this pathogen, we
      report the complete chromosomal sequence of a genetically tractable, prototypical
      strain used in animal models.
AU  - Broberg CA
AU  - Wu W
AU  - Cavalcoli JD
AU  - Miller VL
AU  - Bachman MA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00924-14.

PMID- 
VI  - 30
DP  - 2007
TI  - Restriction-modification systems in Mycoplasma spp.
PG  - 236-244
AB  - Restriction and Modification (R-M) systems are present in all Mycoplasma species sequenced so
      far. The presence of these genes poses
      barriers to gene transfer and could protect the cell against phage
      infections. The number and types of R-M genes between different
      Mycoplasma species are variable, which is characteristic of a
      polymorphism. The majority of the CDSs code for Type III R-M systems
      and particularly for methyltransferase enzymes, which suggests that
      functions other than the protection against the invasion of
      heterologous DNA may exist. A possible function of these enzymes could
      be the protection against the invasion of other but similar R-M
      systems. In Mycoplasma hyopneumoniae strain J, three of the putative
      methyltransferase genes were clustered in a region forming a genomic
      island. Many R-M CDSs were mapped in the vicinity of transposable
      elements suggesting an association between these genes and reinforcing
      the idea of R-M systems as mobile selfish DNA. Also, many R-M genes
      present repeats within their coding sequences, indicating that their
      expression is under the control of phase variation mechanisms.
      Altogether, these data suggest that R-M systems are a remarkable
      characteristic of Mycoplasma species and are probably involved in the
      adaptation of these bacteria to different environmental conditions.
AU  - Brocchi M
AU  - de Vasconcelos ATR
AU  - Zaha A
PT  - Journal Article
TA  - Genet. Mol. Biol.
JT  - Genet. Mol. Biol.
SO  - Genet. Mol. Biol. 2007 30: 236-244.

PMID- 4453003
VI  - 88
DP  - 1974
TI  - Nucleotide sequences at the sites of action of the deoxyribonucleic acid modification enzyme of bacteriophage P1.
PG  - 437-443
AB  - Labelled oligonucleotides have been fractionated from DNAase digests of phage
      lambda DNA that had been methylated with the phage P1 modification enzyme and
      S-[methyl-14C]adenosyl-L-methionine.  The longest sequences established are the
      tetranucleotides pG-A*-T-C and pA*-T-C-T, which, together with the other
      sequences determined, particularly pA*-G-A, show that the modification enzyme,
      M.EcoP1, methylates adenine residues within defined sequences and suggest that
      the oligonucleotide sequence recognized by this enzyme is the hexanucleotide
      pA-G-A-T-C-T.  The duplex formed by base-pairing this hexanucleotide with its
      complementary sequence resembles the recognition sequence for several
      restriction enzymes in being bisected by an axis of 2-fold rotational symmetry.
AU  - Brockes JP
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1974 88: 437-443.

PMID- 4584025
VI  - 133
DP  - 1973
TI  - The deoxyribonucleic acid-modification enzyme of bacteriophage P1. Subunit structure.
PG  - 629-633
AB  - The bacteriophage P1 modification enzyme was purified 1400-fold from induced
      lysogens of a thermoinducible mutant of bacteriophage P1.  The most purified
      fraction, when analysed by polyacrylamide-gel electropohoresis in sodium
      dodecyl sulphate, showed two principal stained bands.  The two bands
      co-sedimented in a glycerol gradient with the modification activity, at a rate
      which, when compared with the rate of sedimentation of marker proteins,
      corresponds to a sedimentation coefficient in water of 6S.  The mobilities of
      the bands on sodium dodecyl sulphate-polyacrylamide-gel electrophoresis
      corresponded to polypeptides of molecular weight 70000 and 45000 and they were
      present in equimolar amounts.  It was concluded that the 6S species of the
      enzyme is a dimer of unlike subunits.
AU  - Brockes JP
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 1973 133: 629-633.

PMID- 5073742
VI  - 127
DP  - 1972
TI  - The deoxyribonucleic acid modification enzyme of bacteriophage P1: Purification and properties.
PG  - 1-10
AB  - The bacteriophage P1 modification enzyme, assayed by the specific methylation
      of unmodified bacteriophage 82 DNA, has been purified 500-fold from a
      bacteriophage P1 lysogen of Escherichia coli.  The enzyme catalyses the
      incorporation of approximately 20-24 methyl groups per bacteriophage 82 DNA
      molecule.  The sole product of methylation is 6-methylaminopurine.  Methylation
      of unmodified bacteriophage DNA confers protection against a challenge by
      purified bacteriophage P1 restriction enzyme.  The pH optimum is 6.0-6.25: the
      apparent Km for S-adenosyl-L-methionine is 5 microM.
AU  - Brockes JP
AU  - Brown PR
AU  - Murray K
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 1972 127: 1-10.

PMID- 18281701
VI  - 36
DP  - 2008
TI  - Phage T4 SegB protein is a homing endonuclease required for the preferred inheritance of T4 tRNA gene region occurring in co-infection with a related phage.
PG  - 2094-2105
AB  - Homing endonucleases initiate nonreciprocal transfer of DNA segments containing their own
      genes and the flanking sequences by cleaving the
      recipient DNA. Bacteriophage T4 segB gene, which is located in a
      cluster of tRNA genes, encodes a protein of unknown function,
      homologous to homing endonucleases of the GIY-YIG family. We
      demonstrate that SegB protein is a site-specific endonuclease, which
      produces mostly 3 2-nt protruding ends at its DNA cleavage site.
      Analysis of SegB cleavage sites suggests that SegB recognizes a 27-bp
      sequence. It contains 11-bp conserved sequence, which corresponds to a
      conserved motif of tRNA TC stem-loop, whereas the remainder of the
      recognition site is rather degenerate. T4-related phages T2L, RB1 and
      RB3 contain tRNA gene regions that are homologous to that of phage T4
      but lack segB gene and several tRNA genes. In co-infections of phages
      T4 and T2L, segB gene is inherited with nearly 100 of efficiency. The
      preferred inheritance depends absolutely on the segB gene integrity and
      is accompanied by the loss of the T2L tRNA gene region markers. We
      suggest that SegB is a homing endonuclease that functions to ensure
      spreading of its own gene and the surrounding tRNA genes among
      T4-related phages.
AU  - Brok-Volchanskaya VS
AU  - Kadyrov FA
AU  - Sivogrivov DE
AU  - Kolosov PM
AU  - Sokolov AS
AU  - Shlyapnikov MG
AU  - Kryukov VM
AU  - Granovsky IE
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2008 36: 2094-2105.

PMID- 23785449
VI  - 8
DP  - 2013
TI  - Plasmidome-Analysis of ESBL-Producing Escherichia coli Using Conventional Typing and High-Throughput Sequencing.
PG  - E65793
AB  - Infections caused by Extended spectrum beta-lactamase (ESBL)-producing E. coli
      are an emerging global problem, threatening the effectiveness of the extensively
      used beta-lactam antibiotics. ESBL dissemination is facilitated by plasmids,
      transposons, and other mobile elements. We have characterized the plasmid content
      of ESBL-producing E. coli from human urinary tract infections. Ten diverse
      isolates were selected; they had unrelated pulsed-field gel electrophoresis
      (PFGE) types (<90% similarity), were from geographically dispersed locations and
      had diverging antibiotic resistance profiles. Three isolates belonged to the
      globally disseminated sequence type ST131. ESBL-genes of the CTX-M-1 and CTX-M-9
      phylogroups were identified in all ten isolates. The plasmid content (plasmidome)
      of each strain was analyzed using a combination of molecular methods and
      high-throughput sequencing. Hidden Markov Model-based analysis of unassembled
      sequencing reads was used to analyze the genetic diversity of the plasmid samples
      and to detect resistance genes. Each isolate contained between two and eight
      distinct plasmids, and at least 22 large plasmids were identified overall. The
      plasmids were variants of pUTI89, pKF3-70, pEK499, pKF3-140, pKF3-70, p1ESCUM,
      pEK204, pHK17a, p083CORR, R64, pLF82, pSFO157, and R721. In addition, small
      cryptic high copy-number plasmids were frequent, containing one to seven open
      reading frames per plasmid. Three clustered groups of such small cryptic plasmids
      could be distinguished based on sequence similarity. Extrachromosomal prophages
      were found in three isolates. Two of them resembled the E. coli P1 phage and one
      was previously unknown. The present study confirms plasmid multiplicity in
      multi-resistant E. coli. We conclude that high-throughput sequencing successfully
      provides information on the extrachromosomal gene content and can be used to
      generate a genetic fingerprint of possible use in epidemiology. This could be a
      valuable tool for tracing plasmids in outbreaks.
AU  - Brolund A
AU  - Franzen O
AU  - Melefors O
AU  - Tegmark-Wisell K
AU  - Sandegren L
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2013 8: E65793.

PMID- 6950932
VI  - 150
DP  - 1982
TI  - Sequence specificity of DNA adenine methylase in the protozoan Tetrahymena thermophila.
PG  - 993-996
AB  - The sequence specificity of the Tetrahymena DNA-adenine methylase was determined by
      nearest-neighbor analyses of in vivo and in vitro methylated DNA.  In vivo all four common
      bases were found to the 5' side of N6-methyladenine, but only thymidine was 3'.  Homologous
      DNA already methylated in vivo and heterologous Micrococcus luteus DNA were methylated in
      vitro by a partially purified DNA-adenine methylase activity isolated from Terrahymena
      macronuclei.  The in vitro-methylated sequence differed from the in vivo sequence in that both
      thymidine and cytosine were 3' nearest neighbors of N6-methyladenine.
AU  - Bromberg S
AU  - Pratt K
AU  - Hattman S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1982 150: 993-996.

PMID- 28869059
VI  - 40
DP  - 2017
TI  - Soybeans inoculated with root zone soils of Canadian native legumes harbour diverse and novel Bradyrhizobium spp. that possess agricultural potential.
PG  - 440-447
AB  - An assessment was made of the evolutionary relationships of soybean nodulating
      bacteria associated with legumes native to eastern Canada to identify potential
      new sources of soybean inoculant strains. Short season soybeans were used to
      selectively trap bacteria from root zone soils of four native legume species.
      Screening of more than 800 bacterial isolates from soybean root nodules by
      analysis of recA gene sequences followed by analyses of selected genotypes using
      six core and two symbiosis (nodC and nifH) gene sequences permitted
      identification of diverse taxa that included eight novel and four named
      Bradyrhizobium species as well as lineages attributed to the genera Afipia and
      Tardiphaga. Plant tests showed that symbionts related to four named species as
      well as a novel Bradyrhizobium lineage were highly efficient with regard to
      nitrogen fixation on soybeans relative to an inoculant strain. A new symbiovar
      (sv. septentrionalis) is proposed based on a group of four novel Bradyrhizobium
      spp. that possess distinctive nodC and nifH gene sequences and symbiotic
      characteristics. Evidence is provided for horizontal transfer of sv.
      septentrionalis symbiosis genes between novel Bradyrhizobium spp., a process that
      rendered recipient bacteria ineffective on soybeans. Diverse lineages of
      non-symbiotic and symbiotic Bradyrhizobium spp. co-occured within monophyletic
      clusters in a phylogenetic tree of concatenated core genes, suggesting that loss
      and/or gain of symbiosis genes has occurred in the evolutionary history of the
      bacterial genus. Our data suggest that symbiont populations associated with
      legumes native to eastern Canada harbour elite strains of Bradyrhizobium for
      soybean inoculation.
AU  - Bromfield ESP
AU  - Cloutier S
AU  - Tambong JT
AU  - Tran-Thi TV
PT  - Journal Article
TA  - Syst. Appl. Microbiol.
JT  - Syst. Appl. Microbiol.
SO  - Syst. Appl. Microbiol. 2017 40: 440-447.

PMID- 26950330
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Lactobacillus plantarum SF2A35B.
PG  - e01638-15
AB  - The lactic acid bacterium Lactobacillus plantarum is intensively studied as a model probiotic
      species. Here, we present the draft genome sequence of the
      exopolysaccharide-producing strain SF2A35B.
AU  - Bron PA
AU  - Lee IC
AU  - Backus L
AU  - van Hijum SA
AU  - Wels M
AU  - Kleerebezem M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01638-15.

PMID- 6246332
VI  - 65
DP  - 1980
TI  - Purification and properties of the Bsu endonuclease.
PG  - 112-132
AB  - For various reasons Bacillus subtilis is an attractive organism to study
      restriction and modification.  It is easy to grow and to manipulate, has a
      fairly detailed genetic map, and, most important, possesses a simple
      transformation/transfection system.  This enables the introduction of
      biologically active DNA into cells of defined R-M background, and the analysis
      of its fate.  In addition, the effects of in vitro treatments of biologically
      active DNA with restriction and modification enzymes can conveniently be
      studied by means of transformation and transfection.  Restriction and
      modification in B. subtilis were demonstrated some years ago.  A site-specific
      type II restriction endonuclease, Bsu, has been purified and characterized from
      B. subtilis strain R.  The enzyme cleaves susceptible DNAs in the middle of the
      tetranucleotide sequence 5'GGCC3'.  Resistance to Bsu is conferred to DNA by
      the modification methylase from the same strain, which methylates the internal
      C residues of the recognition sequence.  We will describe the purification and
      properties of Bsu.
AU  - Bron S
AU  - Horz W
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1980 65: 112-132.

PMID- 2830465
VI  - 211
DP  - 1988
TI  - Restriction and modification in Bacillus subtilis Marburg 168:  Target sites and effects on plasmid transformation.
PG  - 186-189
AB  - The effects of the restriction system of Bacillus subtilis strain M on plasmid
      transformation were studied.  Plasmid pHV1401 DNA prepared from B. subtilis
      transformed the restriction-proficient M strain 100 times more efficiently than
      the DNA prepared from Escherichia coli, while the two DNA preparations
      transformed restriction-deficient derivatives of that strain with similar
      efficiencies.  This indicates that transformation with pHV1401 is sensitive to
      the M restriction system.  pHV1401 contains three CTCGAG (XhoI sites).
      Successive removal of these abolished the effect of restriction.  This
      indicates that the XhoI sites are the targets for the M restriction system.
AU  - Bron S
AU  - Janniere L
AU  - Ehrlich SD
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1988 211: 186-189.

PMID- 6256602
VI  - 179
DP  - 1980
TI  - Restriction and modification in B. subtilis:  the role of homology between donor and recipient DNA in transformation and transfection.
PG  - 111-117
AB  - Non-modified DNAs from phages SPO2 and Phi105, and prophage DNAs extracted from
      lysogens carrying these phages, were used to transfect isogenic r-m- B.
      subtilis recipients which were either non-lysogenic, or had been lysogenized
      with a homologous or a non-homologous phage.  Restriction of transfecting phage
      and prophage DNA occurred in non-lysogenic recipients and in recipients
      lysogenic for a non-homologous phage.  No effect of restriction was observed
      when phage or prophage DNA was used to transfect recipients carrying a
      homologous prophage.  This is analogous to the absence of restriction in
      transformation and indicates that in B. subtilis the distinction between
      transforming and transfecting DNA is not made at the initial stages of DNA
      uptake and processing, but rather at later stages, where recognition of
      homologous regions in donor and recipient DNA plays an important role.
AU  - Bron S
AU  - Luxen E
AU  - Trautner TA
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1980 179: 111-117.

PMID- 6406685
VI  - 46
DP  - 1983
TI  - Resistance of bacteriophage H1 to restriction and modification by Bacillus subtilis R.
PG  - 703-708
AB  - H1, a 5-hydroxymethyluracil (HMU)-containing Bacillus subtilis bacteriophage,
      was neither restricted nor modified upon infection of B. subtilis R cells.  In
      vitro, H1 DNA was not restricted by BsuR under standard conditions (200 mM
      salt), although the expected frequency of -GGCC- cleavage sites was
      approximately 250.  However, four specific sites were cleaved under nonstandard
      conditions (low salt or high pH) or in the presence of organic solvents, like
      dimethyl sulfoxide and glycerol.  After the substitution of thymine for HMU by
      DNA cloning in B. subtilis, a BsuR cleavage site was restricted and modified
      under standard conditions.  No additional sites were detected after
      shotgun-cloning of about 11% of the chromosome.  The nucleotide sequence of a
      cleavage site was found to be
      5'..C-A-Hmu-A-A-C-Hmu-Hmu-Hmu-G-G-C-C-Hmu-A-G-..3', which shows the presence of
      a bona fide BsuR (GGCC) recognition sequence, flanked by (Hmu-A)-rich
      sequences.  The results suggested that the resistance of H1 to restriction and
      modification by B. subtilis R was due to (i) a strong bias against the
      GGCC-recognition sequence and (ii) protection of the four remaining GGCC sites
      as a consequence of HMU-A base pairs flanking the sites.
AU  - Bron S
AU  - Luxen E
AU  - Venema G
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1983 46: 703-708.

PMID- 6283159
VI  - 42
DP  - 1982
TI  - Restriction and modification in Bacillus subtilis: Effects on transfection under marker rescue conditions.
PG  - 357-364
AB  - The role of homology between donor and recipient DNAs in the protection of transfecting DNA
      against restriction by competent Bacillus subtilis R cells was studied under marker rescue
      conditions with modified helper phage.  By comparing restriction under conditions of
      preinfection marker rescue and superinfection marker rescue, the significance of DNA homology
      during the initial stages of DNA processing by competent cells could be studied.  The results
      showed that in both preinfection and superinfection, complete protection against restriction
      of transfectants produced via rescue by the modified homologous helper chromosome occurred.
      Even up to 90 min after entry, DNA entering the helper-mediated pathway of transfection was
      not affected by restriction.  The significance of these findings is discussed in the general
      context of the role of DNA homology between donor and recipient on the fate of donor DNA in
      competent B. subtilis, in particular in relation to the effects on restriction.
AU  - Bron S
AU  - Luxen E
AU  - Venema G
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1982 42: 357-364.

PMID- 6436649
VI  - 195
DP  - 1984
TI  - Restriction of hemimethylated DNA by the Bacillus subtilis R system.
PG  - 370-373
AB  - The effects of restriction by the BsuR system on hemimethylated SPP1 DNA were investigated.
      In vitro, single-stranded nicks were introduced in the nonmodified strand of the
      hemimethylated DNA at the same sites as recognized in nonmodified homoduplex DNA.
      Transfection with BsuR-treated hemimethylated DNA was severely reduced.  In vivo, transfection
      with hemimethylated DNA was also severely reduced in competent B. subtilis R cells.  In
      contrast, transfection of protoplasts of the R strain with this DNA was not affected.  The
      apparent restriction by competent cells was attributed to the special mode of processing of
      transfecting DNA.
AU  - Bron S
AU  - Luxen E
AU  - Venema G
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1984 195: 370-373.

PMID- 6256601
VI  - 179
DP  - 1980
TI  - Restriction and modification in B. subtilis:  Effects on transformation and transfection with native and single-stranded DNA.
PG  - 103-110
AB  - The effects of restriction in vivo by competent B. subtilis R cells and in
      vitro by purified endonuclease BsuR on transformation and transfection with
      native and denatured DNA were investigated.  The results show that
      transformation by either native, or denatured DNA is not affected by
      restriction, whereas transfection both with native and denatured SPP1 DNA is
      severely restricted.  In contrast to the results obtained in vivo, the
      biological activity of native and denatured transforming DNA is destroyed by
      BsuR in vitro, as is the transfecting activity of native and denatured SPP1
      DNA.  The sensitivity of denatured DNA, either with mixtures of the
      complementary strands or with separated single strands alone, is significantly
      lower than that of native DNA.  The results are discussed in the context of
      possible mechanisms underlying the different responses of transforming and
      transfecting DNA to in vivo restriction by B. subtilis R cells.
AU  - Bron S
AU  - Luxen E
AU  - Venema G
AU  - Trautner T
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1980 179: 103-110.

PMID- 814403
VI  - 143
DP  - 1975
TI  - Restriction and modification in B. subtilis: Nucleotide sequence recognized by restriction endonuclease R.BsuR from strain R.
PG  - 25-33
AB  - Restriction endonuclease R from Bacillus subtilis strain R cleaves nonmodified
      SPP1 DNA in approximately 80, and lambda DNA in about 200 different sites.  DNA
      digests with this endonuclease and with endonuclease HaeIII from Haemophilus
      aegyptius show identical fragmentation patterns on gel electrophoresis,
      indicating that the two enzymes recognize the same nucleotide sequence.  The
      polynucleotide kinase reaction was used in conjunction with two-dimensional
      ionophoretic nucleotide mapping methods to identify the 5'-nucleotide sequences
      at the sites of cleavage by the B. subtilis restriction endonuclease.  The
      results show that the recognition sequence is 5' N-G-G^C-C-N- 3' 3'
      N-C-C^G-G-N- 5' where arrows indicate the point of strand scission.  Each of
      the four possible nucleotides can occur in the positions flanking the
      recognition site.
AU  - Bron S
AU  - Murray K
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1975 143: 25-33.

PMID- 2856
VI  - 143
DP  - 1975
TI  - Restriction and Modification in B. subtilis:  Purification and General Properties of a Restriction Endonuclease from Strain R.
PG  - 13-23
AB  - All Bacillus subtilis R-type strains showing the phenomena of restriction and
      modification contain an endonuclease that inactiviates in vitro the biological
      activity of a variety of DNAs lacking R-specific modification, such as
      transfecting SPP1, SPO2 and Phi-105 DNA, and transforming B. subtilis 168-type
      DNA.  The corresponding DNAs carrying R-specific modification are resistant to
      the enzyme.  The enzyme has been purified approximately 400-fold and is
      essentially free from contaminating double strand-directed unspecific exo- or
      endonuclease activity.  Only Mg2+ is required as cofactor.  The substrate DNAs
      are cleaved at specific sites.  The double-stranded fragments produced from
      SPP1 DNA (molecular weight 2.5 x 107) have an average molecular weight of about
      300,000.
AU  - Bron S
AU  - Murray K
AU  - Trautner TA
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1975 143: 13-23.

PMID- 27056213
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Campylobacter jejuni Bf, an Atypical Strain Able To Grow under Aerobiosis.
PG  - e00120-16
AB  - In this study, we describe the draft genome sequence of aCampylobacter jejuniclinical isolate
      issued from a French patient suffering from severe
      campylobacteriosis. This atypical strain is characterized by an unusual
      resistance to oxygen and the ability to grow under an aerobic atmosphere, a
      characteristic as-of-yet unique to this species.
AU  - Bronnec V
AU  - Haddad N
AU  - Cruveiller S
AU  - Hernould M
AU  - Tresse O
AU  - Zagorec M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00120-16.

PMID- 4580736
VI  - 55
DP  - 1973
TI  - Location of the DNA-adenine methylase gene on the genetic map of phage T2.
PG  - 285-288
AB  - The location of the gene controlling DNA-adenine methylase activity is reported to be in the
      region between genes 49 and rI on the T2 genetic map. A new nomenclature is proposed to
      describe the various phage types affected by mutations in the methylase gene.
AU  - Brooks J
AU  - Hattman S
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1973 55: 285-288.

PMID- Not carried by PubMed...
VI  - 75
DP  - 1975
TI  - In vitro methylation of phage lambda.
PG  - 225
AB  - Phage T2 produces an adenine-specific DNA methylase. Certain mutants (designated damh) produce
      an altered enzyme which methylates various forms of T2 DNA to higher extents than does the
      wild-type (dam+) enzyme. The higher methylation by damh protects nonglucosylated T2 DNA
      against P1-restriction. We have studied in vitro methylation of phage lambda DNA by the dam+
      and damh enzymes (using both crude extracts and highly purified enzyme preparations). DNA from
      lambda grown in Escherichia coli strain K (=lambda.K DNA) is methylated to a two-fold greater
      extent by the damh enzyme; ca.150 and ca.300 MeAde residues per lambda DNA are produced by
      dam+ and damh, respectively (the same stoichiometry is observed with lambda.K(P1)DNA).
      Following methylation by dam+ enzyme there is no change in the ability of lambda.K DNA to
      transfect spheroplasts derived from E. coli K or K(P1); the relative transfecting titer
      remains ca.10000 fold higher on K than K(P1). In contrast, methylation by the damh enzyme
      resulted in a 1000 to 10000 fold increase in transfection ability on K(P1) spheroplasts; the
      transfection efficiency on K(P1) was 20 to 40% that observed on K (under similar conditions
      lambda.K(P1) DNA transfected both spheroplast preparations equally well). Thus, the damh
      methylase recognizes more sites on lambda DNA than the dam+ enzyme; the additional methylation
      protects against P1-restriction.
AU  - Brooks J
AU  - Masurekar M
AU  - Hattman S
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1975 75: 225.

PMID- 
VI  - 
DP  - 1977
TI  - A comparative study of the wild type and mutant forms of phage T2 DNA-adenine methylase.
PG  - 1-188
AB  - Bacteriophage T2 produces an adenine-specific DNA methylase.  Certain mutants (designated
      damh) produce an altered enzyme which methylates T2 DNA to a higher extent than does the wild
      type (dam+) enzyme.  The higher methylation by the damh enzyme protects nonglucosylated phage
      against P1 restriction.  The position of the T2 dam gene on the phage genetic map was
      determined by a series of three-factor crosses.  The gene was located between the 49 and rI
      loci on the map.  The kinetics of enzyme production were also studied: under the conditions
      used, overproduction of methylase activity could not be achieved by blocking DNA synthesis.
AU  - Brooks JE
PT  - Journal Article
TA  - Ph.D. Thesis, University of Rochester
JT  - Ph.D. Thesis, University of Rochester
SO  - Ph.D. Thesis, University of Rochester 1977 : 1-188.

PMID- 2821353
VI  - 152
DP  - 1987
TI  - Properties and uses of restriction endonucleases.
PG  - 113-129
AB  - This chapter focuses on the properties and uses of restriction endonucleases.
      The large battery of endonucleases now commercially available will first be
      described in terms of nomenclature and properties.  The next section will cover
      basic methods for their use in mapping and genetic engineering experiments, and
      a final section will focus on the more detailed aspects of selecting
      endonucleases for generating ends compatible with subsequent steps of
      construction.
AU  - Brooks JE
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1987 152: 113-129.

PMID- 2537955
VI  - 17
DP  - 1989
TI  - Cloning the BamHI restriction modification system.
PG  - 979-997
AB  - BamHI, a Type II restriction modification system from Bacillus amyloliquefaciens H recognizes
      the sequence GGATCC. The methylase and endonuclease genes have been cloned into E. coli in
      separate steps; the clone is able to restrict unmodified phage. Although within the clone the
      methylase and endonuclease genes are present on the same pACYC184 vector, the system can be
      maintained in E. coli only with an additional copy of the methylase gene present on a separate
      vector. The initial selection for BamHI methylase activity also yielded a second BamHI
      methylase gene which is not homologous in DNA sequence and hybridizes to different genomic
      restriction fragments than does the endonuclease-linked methylase gene. Finally, the
      interaction of the BamHI system with the E. coli Dam and the Mcr A and B functions, have been
      studied and are reported here.
AU  - Brooks JE
AU  - Benner JS
AU  - Heiter DF
AU  - Silber KR
AU  - Sznyter LA
AU  - Jager-Quinton T
AU  - Moran LS
AU  - Slatko BE
AU  - Wilson GG
AU  - Nwankwo DO
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 979-997.

PMID- 3248715
VI  - 74
DP  - 1988
TI  - Cloning and characterization of the BamHI restriction modification system.
PG  - 13
AB  - Meeting Abstract
AU  - Brooks JE
AU  - Benner JS
AU  - Silber KR
AU  - Heiter DF
AU  - Sznyter LA
AU  - Jager-Quinton T
AU  - Wilson GG
AU  - Moran LS
AU  - Slatko BE
AU  - Nwankwo DO
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 13.

PMID- 6300769
VI  - 11
DP  - 1983
TI  - The isolation and characterization of the Escherichia coli DNA adenine methylase (dam) gene.
PG  - 837-851
AB  - The E. coli dam (DNA adenine methylase) enzyme is known to methylate the sequence GATC. A
      general method for cloning sequence-specific DNA methylase genes was used to isolate the dam
      gene on a 1.14 kb fragment, inserted in the plasmid vector pBR322. Subsequent restriction
      mapping and subcloning experiments established a set of approximate boundaries of the gene.
      The nucleotide sequence of the dam gene was determined, and analysis of that sequence revealed
      a unique open reading frame which corresponded in length to that necessary to code for a
      protein the size of dam. Amino acid composition derived from this sequence corresponds closely
      to the amino acid composition of the purified dam protein. Enzymatic and DNA:DNA hybridization
      methods were used to investigate the possible presence of dam genes in a variety of
      prokaryotic organisms.
AU  - Brooks JE
AU  - Blumenthal RM
AU  - Gingeras TR
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1983 11: 837-851.

PMID- 370403
VI  - 126
DP  - 1978
TI  - In vitro methylation of bacteriophage lambda DNA by wild type (dam+) mutant (damh) forms of the phage T2 DNA adenine methylase.
PG  - 381-394
AB  - The wild-type (dam+) and mutant (damh) forms of the bacteriophage T2 DNA adenine methylase
      have been partially purified; these enzymes methylate the sequence, 5'...G-A-Py...3'
      (Hattman et al., 1978a). However, in vitro methylation studies using phage lambda DNA revealed
      the following: (1) T2 dam+ and damh enzymes differ in their ability to methylate lambda DNA;
      under identical reaction conditions the T2 damh enzyme methylated lambda DNA to a higher level
      than did the dam+ enzyme. However, the respective methylation sites are equally distributed on
      the l and r strands. (2) Methylation with T2 damh, but not T2 dam+ protected lambda against P1
      restriction. This was demonstrated by transfection of Escherichia coli (P1) spheroplasts and
      by cleavage with R.EcoP1. (3) T2 dam+ and damh were similarly capable of methylating G-A-T-C
      sequences on lambda DNA; e.g. k-dam3 DNA (contains no N6-methyladenine) methylated with either
      enzyme was made resistant to cleavage by R.DpnII. In contrast, only the T2 damh modified DNA
      was resistant to further methylation by M.EcoP1 (which methylates the sequence
      5'...A-G-A-C-Py...3'; Hattman et al., 1978b). (4) lambda.dam3 DNA was partially methylated
      to the same level with T2 dam+ or T2 damh; the two enzymes producted different patterns of
      G-A-C versus G-A-T methylation. We propose that the T2 dam+ enzyme methylates G-A-C sequences
      less efficiently than the T2 damh methylase; this property does not entirely account for the
      large difference in methylation levels produced by the two enzymes.
AU  - Brooks JE
AU  - Hattman S
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1978 126: 381-394.

PMID- 1901989
VI  - 19
DP  - 1991
TI  - Characterization of the cloned BamHI restriction modification system:  its nucleotide sequence, properties of the methylase, and expression in heterologous hosts.
PG  - 841-850
AB  - The BamHI restriction modification system was previously cloned into E. coli and maintained
      with an extra copy of the methylase gene on a high copy vector (Brooks et al, (1989) Nucl.
      Acids Res. 17, 979-997). The nucleotide sequence of a 3014 bp region containing the
      endonuclease (R) and methylase (M) genes has now been determined. The sequence predicts a
      methylase protein of 423 amino acids, Mr 49,527, and an endonuclease protein of 213 amino
      acids, Mr 24,570. Between the two genes is a small open reading frame capable of encoding a
      102 amino acid protein, Mr 13,351. The M.BamHI enzyme has been purified from a high expression
      clone, its amino terminal sequence determined, and the nature of its substrate modification
      studied. The BamHI methylase modifies the internal C within its recognition sequence at the N4
      position. Comparisons of the deduced amino acid sequence of M.BamHI have been made with those
      available for other DNA methylases: among them, several contain five distinct regions, 12 to
      22 amino acids in length, of pronounced sequence similarity. Finally, stability and expression
      of the BamHI system in both E. coli and B. subtilis have been studied. The results suggest R
      and M expression are carefully regulated in a natural host like B. subtilis.
AU  - Brooks JE
AU  - Nathan PD
AU  - Landry D
AU  - Sznyter LA
AU  - Waite-Rees P
AU  - Ives CL
AU  - Moran LS
AU  - Slatko BE
AU  - Benner JS
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 841-850.

PMID- Not carried by PubMed...
VI  - 87
DP  - 1987
TI  - Cloning of the BamHI restriction-modification system.
PG  - 154
AB  - BamHI, a TypeII restriction-modification system from Bacillus
      amyloliquefaciens, recognizes the sequence GGATCC.  The system has been cloned
      into E. coli in two steps.  First the methylase gene was cloned into pBR322 and
      a derivative expressing higher levels was constructed using a pUC vector.  The
      endonuclease gene was then located using Southern blot analyses; HindIII
      fragments large enough to contain the endonuclease gene were cloned into
      pACYC184, introduced into a host containing the methylase gene and screened for
      endonuclease activity.  Both genes are stably maintained in E. coli on separate
      but compatible plasmids.
AU  - Brooks JE
AU  - Nwankwo D
AU  - Sznyter L
AU  - Jager T
AU  - Wilson G
AU  - Heiter D
AU  - Slatko B
AU  - Benner J
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1987 87: 154.

PMID- 6278441
VI  - 10
DP  - 1982
TI  - Modification profiles of bacterial genomes.
PG  - 913-934
AB  - DNAs were prepared from twenty-six bacterial species and digested with a
      variety of restriction endonucleases to determine what modifications the DNAs
      carry.  Several general conclusions could be made: 1) First, in no instance was
      the DNA of a restriction enzyme strain cleaved by its own restriction enzyme.
      2) The specificity of the DNA modification was the same as that of its
      restriction counterpart; there were no cases of the DNAs being modified against
      a less specific class of restriction enzymes. 3) In most (but not all) cases,
      the resistance of a bacterium's DNA to its own restriction enzyme could be
      generalized to include resistance to all other restriction enzymes with the
      same specificity (isoschizomers).  4) DNA modified within the central tetramer
      of a recognition sequence is usually protected against cleavage by all related
      hexameric enzymes possessing that central tetramer.  Only three families of DNA
      presented in this study disobey this rule.  5) Finally, a significant number of
      cases emerge where bacterial DNA carries a modification but no corresponding
      restriction endonuclease activity.
AU  - Brooks JE
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1982 10: 913-934.

PMID- 2381222
VI  - 14A
DP  - 1990
TI  - Cloning and characterization of the SphI restriction modification system from Streptomyces phaeochromogenes.
PG  - 106
AB  - SphI, a Type II restriction modification from Streptomyces phaeochromogenes,
      recognizes the sequence GCATGC.  The endonuclease cleaves at GCATG^C to
      generate a 3' four base overhang.  A 5.4 kb PstI fragment from the S.
      phaeochromogenes genome has been cloned into pBR322 and shown to express the
      SphI methylase at low level in E. coli.  Clones carrying the fragment have no
      endonuclease activity.  Extensive mapping and subcloning have been used to
      determine the position and orientation of the m gene.  The nucleotide sequence
      of the region is now being determined.  The entire 5.4 kb fragment and also
      various restriction fragments have been transferred into S. lividans on pIJ486,
      pIJ487 and also the low copy vector pIJ922.  Their expression in Streptomyces
      will be discussed.
AU  - Brooks JE
AU  - Sznyter L
AU  - Vaccaro C
AU  - Arnaud M
AU  - Jager-Quinton T
AU  - Wilson G
AU  - Moran L
AU  - Slatko B
AU  - Bernan V
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1990 14A: 106.

PMID- 22965106
VI  - 194
DP  - 2012
TI  - Whole-Genome Shotgun Sequence of Rhodococcus Species Strain JVH1.
PG  - 5492-5493
AB  - Here we present a whole-genome shotgun sequence of Rhodococcus species strain JVH1, an
      organism capable of degrading a variety of organosulfur compounds. In
      particular, JVH1 is able to selectively cleave carbon-sulfur bonds within alkyl
      chains. A large number of oxygenases were identified, consistent with other
      members of the genus.
AU  - Brooks SL
AU  - Van Hamme JD
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5492-5493.

PMID- 22461557
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of the Nontoxigenic Clostridium difficile Strain CD37.
PG  - 2125-2126
AB  - Here we report the draft genome sequence of Clostridium difficile strain CD37, the first
      nontoxigenic strain sequenced. Every sequenced strain of Clostridium
      difficile has been shown to contain multiple different mobile genetic elements.
      The draft genome sequence of strain CD37 reveals the presence of two putative
      conjugative transposons.
AU  - Brouwer MS
AU  - Allan E
AU  - Mullany P
AU  - Roberts AP
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2125-2126.

PMID- 26966220
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Acinetobacter bereziniae HPC229, a Carbapenem-Resistant  Clinical Strain from Argentina Harboring blaNDM-1.
PG  - e00117-16
AB  - We report here the draft genome sequence of an NDM-1-producing Acinetobacter bereziniae
      clinical strain, HPC229. This strain harbors both plasmid and
      chromosomal resistance determinants toward different beta-lactams and
      aminoglycosides as well as several types of multidrug efflux pumps, most likely
      representing an adaptation strategy for survival under different environments.
AU  - Brovedan M
AU  - Marchiaro PM
AU  - Moran-Barrio J
AU  - Revale S
AU  - Cameranesi M
AU  - Brambilla L
AU  - Viale AM
AU  - Limansky AS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00117-16.

PMID- 24096417
VI  - 79
DP  - 2013
TI  - Diverse broad-host-range plasmids from freshwater carry few accessory genes.
PG  - 7684-7695
AB  - Broad-host-range self-transferable plasmids are known to facilitate bacterial
      adaptation by spreading genes between phylogenetically distinct hosts. These
      plasmids typically have a conserved backbone region and a variable accessory
      region that encodes host-beneficial traits. We do not know, however, how well
      plasmids that do not encode accessory functions can survive in nature. The goal
      of this study was to characterize the backbone and accessory gene content of
      plasmids that were captured from freshwater sources without selecting for a
      particular phenotype or cultivating their host. To do this, triparental matings
      were used such that the only required phenotype was the plasmid's ability to
      mobilize a nonconjugative plasmid. Based on complete genome sequences of 10
      plasmids, only 5 carried identifiable accessory gene regions, and none carried
      antibiotic resistance genes. The plasmids belong to four known incompatibility
      groups (IncN, IncP-1, IncU, and IncW) and two potentially new groups. Eight of
      the plasmids were shown to have a broad host range, being able to transfer into
      alpha-, beta-, and gammaproteobacteria. Because of the absence of antibiotic
      resistance genes, we resampled one of the sites and compared the proportion of
      captured plasmids that conferred antibiotic resistance to their hosts with the
      proportion of such plasmids captured from the effluent of a local wastewater
      treatment plant. Few of the captured plasmids from either site encoded antibiotic
      resistance. A high diversity of plasmids that encode no or unknown accessory
      functions is thus readily found in freshwater habitats. The question remains how
      the plasmids persist in these microbial communities.
AU  - Brown CJ
AU  - Sen D
AU  - Yano H
AU  - Bauer ML
AU  - Rogers LM
AU  - Van der Auwera GA
AU  - Top EM
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2013 79: 7684-7695.

PMID- 26083755
VI  - 523
DP  - 2015
TI  - rRNA introns, odd ribosomes, and small enigmatic genomes across a large radiation of phyla.
PG  - 208
AB  - Aprominent feature of the bacterial domain is a radiation of major
      lineages that are defined as candidate phyla because they lack isolated
      representatives. Bacteria from these phyla occur in diverse
      environments1 and are thought to mediate carbon and hydrogen
      cycles2. Genomic analyses of a few representatives suggested that
      metabolic limitations have prevented their cultivation2-6. Here we
      reconstructed 8 complete and 789 draft genomes from bacteria
      representing.35 phyla and documented features that consistently
      distinguish these organisms from other bacteria. We infer that this
      group, which may comprise .15% of the bacterial domain, has
      shared evolutionary history, and describe it as the candidate phyla
      radiation (CPR). All CPR genomes are small and most lack numerous
      biosynthetic pathways. Owing to divergent 16S ribosomal
      RNA (rRNA) gene sequences, 50-100% of organisms sampled
      from specific phyla would evade detection in typical cultivationindependent
      surveys. CPR organisms often have self-splicing
      introns and proteins encoded within their rRNA genes, a feature
      rarely reported in bacteria. Furthermore, they have unusual ribosome
      compositions. All are missing a ribosomal protein often
      absent in symbionts, and specific lineages are missing ribosomal
      proteins and biogenesis factors considered universal in bacteria.
      This implies different ribosome structures and biogenesis mechanisms,
      and underlines unusual biology across a large part of the
      bacterial domain.
AU  - Brown CT
AU  - Hug LA
AU  - Thomas BC
AU  - Sharon I
AU  - Castelle CJ
AU  - Singh A
AU  - Wilkins MJ
AU  - Williams KH
AU  - Banfield JF
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2015 523: 208.

PMID- 22815452
VI  - 194
DP  - 2012
TI  - Genome Annotation of Five Mycoplasma canis Strains.
PG  - 4138-4139
AB  - To understand its potential to cause invasive disease, the genome of Mycoplasma canis strain
      PG14(T) from a dog's throat was compared to those of isolates from
      the genital tract or brain of dogs. The average nucleotide identity between
      strain pairs is 98%, and their genome annotations are similar.
AU  - Brown DR
AU  - May M
AU  - Michaels DL
AU  - Barbet AF
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4138-4139.

PMID- 206873
VI  - 5
DP  - 1978
TI  - Cae I: an endonuclease isolated from the African green monkey with properties indicating site-specific cleavage of homologous and heterologous mammalian DNA.
PG  - 1093-1107
AB  - Component a DNA is a highly repetitive sequence that comprises nearly a quarter of the African
      green monkey (Ceropithecus aethiops) genome.  A previous microbial restriction enzyme analysis
      showed that the repeat structure of component a DNA is based upon a nonomeric unit of 176  - 4
      base-pairs.  An endonuclease, provisionally termed CaeI, has been isolated from African green
      monkey teste that cleaves component a DNA into multimeric segments based upon the same repeat
      periodicity as that revealed by microbial restriction enzymes. The primary sites of CaeI
      cleavage in the component a sequence appear to be 120 +- 6 base-pairs distant from the HindIII
      sites and 73 +- 6 base-pairs distant from the EcoRI* sites.  CaeI has been partially
      characterized with special reference to the effects of ATP and S-adenosylmethionine on the
      cleavage of component a DNA.  CaeI may be a member of a class of similar site-specific
      nucleases present in mammalian cells. CaeI also cleave mouse satellite DNA into a multimeric
      series of discrete segments: the periodicty of this series is shorter than that revealed by
      EcoRII restriction analysis of mouse satellite DNA.
AU  - Brown FL
AU  - Musich PR
AU  - Maio J
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1978 5: 1093-1107.

PMID- 25614575
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Rhodovulum sp. Strain NI22, a Naphthalene-Degrading Marine Bacterium.
PG  - e01475-14
AB  - Rhodovulum sp. strain NI22 is a hydrocarbon-degrading member of the genus Rhodovulum. The
      draft genome of Rhodovulum sp. NI22 is 3.8 Mb in size, with 3,756
      coding sequences and 64.4% G+C content. The catechol and gentisate pathways for
      naphthalene degradation are predicted to be present in Rhodovulum sp. NI22.
AU  - Brown LM
AU  - Gunasekera TS
AU  - Bowen LL
AU  - Ruiz ON
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01475-14.

PMID- 29217799
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Pseudomonas stutzeri Strain 19, an Isolate Capable of Efficient Degradation of Aromatic Hydrocarbons.
PG  - e01373-17
AB  - Pseudomonas stutzeri strain 19 is a Gram-negative bacterium capable of degrading  aromatic
      hydrocarbons. The draft genome of P. stutzeri 19 is estimated to be 5.1
      Mb, containing 4,652 protein-coding genes and a G+C content of 63.3%. Multiple
      genes responsible for the degradation of aromatics are present in this strain.
AU  - Brown LM
AU  - Gunasekera TS
AU  - Ruiz ON
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01373-17.

PMID- 28126947
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Nocardioides luteus Strain BAFB, an Alkane-Degrading Bacterium Isolated from JP-7-Polluted Soil.
PG  - e01529-16
AB  - Nocardioides luteus strain BAFB is a Gram-positive bacterium that efficiently degrades C8 to
      C11 alkanes aerobically. The draft genome of N. luteus BAFB is
      5.76 Mb in size, with 5,358 coding sequences and 69.9% G+C content. The genes
      responsible for alkane degradation are present in this strain.
AU  - Brown LM
AU  - Gunasekera TS
AU  - Ruiz ON
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01529-16.

PMID- 25377703
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Pseudomonas aeruginosa ATCC 33988, a Bacterium Highly Adapted to Fuel-Polluted Environments.
PG  - e01113-14
AB  - Pseudomonas aeruginosa ATCC 33988 is highly adapted to grow in jet and diesel fuel, with a
      defined regulation of adaptive genes and metabolization of
      n-alkanes. The draft genome of strain ATCC 33988 is 6.4 Mb in size, with 5,975
      coding sequences and 66.3% G+C content, and it is highly similar to that of the
      clinical strain P. aeruginosa PAO1.
AU  - Brown LM
AU  - Gunasekera TS
AU  - Ruiz ON
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01113-14.

PMID- 27340079
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Gordonia sihwensis Strain 9, a Branched Alkane-Degrading Bacterium.
PG  - e00622-16
AB  - Gordonia sihwensis strain 9 is a Gram-positive bacterium capable of efficient aerobic
      degradation of branched and normal alkanes. The draft genome of G.
      sihwensis S9 is 4.16 Mb in size, with 3,686 coding sequences and 68.1% G+C
      content. Alkane monooxygenase and P-450 cytochrome genes required for alkane
      degradation are predicted in G. sihwensis S9.
AU  - Brown LM
AU  - Gunasekera TS
AU  - Striebich RC
AU  - Ruiz ON
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00622-16.

PMID- 6249681
VI  - 8
DP  - 1980
TI  - Sequence determination of restriction-endonuclease recognition sites.
PG  - 398-399
AB  - Restriction endonucleases are widely used in the study of the physical structure of DNA
      molecules, and in the genetic manipulation of DNA molecules in vitro.  They also provided
      interesting and useful model systems for the study of protein-DNA interactions.  A knowledge
      of the DNA sequence that is recognized by a restriction endonuclease, and of the structure of
      the termini of the DNA fragments, is essential to the prediction of the uses to which the
      enzyme may be put.
AU  - Brown NL
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 1980 8: 398-399.

PMID- 6251231
VI  - 140
DP  - 1980
TI  - The specific non-symmetrical sequence recognized by restriction endonuclease MboII.
PG  - 143-148
AB  - The restriction endonuclease MboII, isolated from Moraxella bovis (ATCC 10900),
      cleaves bacteriophage PhiX174am3 replicative form I DNA into ten fragments.
      The physical map of these fragments has been aligned with the sequence of
      PhiX174 DNA.  There is no sequence with 2-fold rotational symmetry common to
      the region of all ten cleavage sites.  However, the non-symmetrical sequence
      5'-G-A-A-G-A-3' 3'-C-T-T-C-T-5' occurs near to each cleavage site.  Precise
      mapping of the cleavages in both DNA strands at several sites places the cuts
      eight nucleotides to the right of the upper sequence and seven nucleotides to
      the right of the lower sequence.
AU  - Brown NL
AU  - Hutchison CA III
AU  - Smith M
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1980 140: 143-148.

PMID- 6247247
VI  - 9
DP  - 1980
TI  - HgiAI: A restriction endonuclease from Herpetosiphon giganteus HP1023.
PG  - 49-68
AB  - A new class II restriction endonuclease, HgiAI has been partially purified from
      Herpetosiphon giganteus HP1023.  The enzyme activity has been characterized and
      shown to recognize the family of related hexanucleotide sequences 5'-G
      (A/T)-G-C-(A/T)^C-3' 3'-C^(A/T)-C-G-(A/T)-G-5' where the second and fifth
      nucleotide pairs are A:T pairs in either orientation.  Cleavage occurs as
      shown, to give DNA fragments with 3'-terminal tetranucleotide extensions.  The
      recognition sites of the enzymes SacI and SStI (GAGCT^C) form a subset of the
      recognition site of HgiAI.  One of the four possible tetranucleotide
      3'-extenions (cohesive ends), generated by HgiAI is identical with those
      generated by SacI and SstI, another is identical with that of PstI.  HgiAI
      should be useful for molecular cloning.
AU  - Brown NL
AU  - McClelland M
AU  - Whitehead PR
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1980 9: 49-68.

PMID- 6246360
VI  - 65
DP  - 1980
TI  - A general method for defining restriction enzyme cleavage and recognition sites.
PG  - 391-404
AB  - Class II restriction endonucleases cleave double-stranded DNA into specific
      fragments.  These enzymes are powerful tools for the dissection of DNA, and
      they are essential for the construction of recombinant DNA molecules and for
      DNA sequence determination.
AU  - Brown NL
AU  - Smith M
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1980 65: 391-404.

PMID- 955064
VI  - 65
DP  - 1976
TI  - The mapping and sequence determination of the single site in PhiX174am3 replicative form DNA cleaved by restriction endonuclease PstI.
PG  - 284-287
AB  - A large number of restriction endonucleases have now been isolated from
      prokaryotes.  We have tested some of these enzymes on the covalently-closed
      replicative form (RFI) of PhiX174am3 DNA.  The restriction endonuclease from
      Providencia stuarti 164 (PstI) was found to convert RFI DNA to a linear form of
      apparent unit length. In this paper we describe the mapping of the single PstI
      site in PhiX174am3 RFI DNA and the determination of the sequence cleaved.  This
      is the symmetrical hexanucleotide sequence: 5'-C-T-G-C-A-^G-3'
      3'-G-^A-C-G-T-C-5' The methods used to determine the sequence recognised by
      PstI and the site of cleavage within that sequence are novel, and should be of
      general use.
AU  - Brown NL
AU  - Smith M
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1976 65: 284-287.

PMID- 269384
VI  - 74
DP  - 1977
TI  - Cleavage specificity of the restriction endonuclease isolated from Haemophilus gallinarum (HgaI).
PG  - 3213-3216
AB  - The nucleotide sequences in the replicative form (duplex) of PhiX174 DNA around
      six sites cut by HgaI, a restriction endonuclease from Haemophilus gallinarum,
      have been compared.  The enzyme produces a staggered cleavage resulting in a
      pentanucleotide 5'-terminal extension.  The sequences within and immediately
      surrounding the pentanucleotide cleavage site have no obvious relationship.
      However, the sequence 5'-G-A-C-G-C-3' 3'-C-T-G-C-G-5' occurs five nucleotide
      pairs to the left of the cut in the upper strand and 10 nucleotide pairs to the
      left of the cut in the lower strand and, therefore, is believed to constitute
      the recognition in which recognition and cleavage sites lack 2-fold rotational
      symmetry.  The method used to define the cleavage site is of general
      applicability.
AU  - Brown NL
AU  - Smith M
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1977 74: 3213-3216.

PMID- 9632832
VI  - 14
DP  - 1998
TI  - Frame: detection of genomic sequencing errors.
PG  - 367-371
AB  - Motivation: The underlying error rate for genomic sequencing sometimes results in the
      introduction of artificial frameshifts and in-frame stop codons into putative protein encoding
      genes.  Severe errors are then introduced into the inferred transcripts through
      mis-translation or premature termination.  Results: We describe a system for screening
      segments of DNA for frameshift and in-frame stop errors in coding regions.  The method is
      based on homology matching using blastx to compare all six reading frames of the query
      nucleotide sequence against selected protein sequence databases.  Fragments of protein
      matching neighboring regions of the query DNA are united and extended laterally to define
      candidate open reading frames, within which, frameshifts and stops are identified.  Suitable
      targets include prokaryotic or other intron-free genomic sequence and complementary DNA's.
      As an example of its use, we report here two frameshifted ORFs that deviate from the original
      TIGR sequence annotations for the recently released Helicobacter pylori genome.  Availability:
      The tool is accessible via the URL http://www.sander.ebi.ac.uk/frame/.  Contact:
      brown@ebi.ac.uk.
AU  - Brown NP
AU  - Sander C
AU  - Bork P
PT  - Journal Article
TA  - Bioinformatics
JT  - Bioinformatics
SO  - Bioinformatics 1998 14: 367-371.

PMID- 21357488
VI  - 193
DP  - 2011
TI  - Genome Sequence of the Mercury-Methylating Strain Desulfovibrio desulfuricans ND132.
PG  - 2078-2079
AB  - Desulfovibrio desulfuricans strain ND132 is an anaerobic sulfate-reducing bacterium (SRB)
      capable of producing methylmercury (MeHg), a potent human
      neurotoxin. The mechanism of methylation by this and other organisms is
      unknown. We present the 3.8-Mb genome sequence to provide further insight
      into microbial mercury methylation.
AU  - Brown SD et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 2078-2079.

PMID- 21602336
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of the Haloalkaliphilic, Hydrogen-Producing bacterium Halanaerobium hydrogenoformans.
PG  - 3682-3683
AB  - Halanaerobium hydrogenoformans is an alkaliphilic bacterium capable of biohydrogen production
      at pH 11 and 7% (w/v) salt. We present the 2.6 Mb
      genome sequence to provide insights into its physiology and potential for
      bioenergy applications.
AU  - Brown SD
AU  - Begemann MB
AU  - Mormile MR
AU  - Wall JD
AU  - Han CS
AU  - Goodwin LA
AU  - Pitluck S
AU  - Land ML
AU  - Hauser LJ
AU  - Elias DA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3682-3683.

PMID- 23950126
VI  - 1
DP  - 2013
TI  - Draft genome sequences for three mercury-methylating, sulfate-reducing bacteria.
PG  - e00618-13
AB  - The genetic basis for bacterial mercury methylation has been described recently.  For insights
      into the physiology of mercury-methylating bacteria, we present
      genome sequences for Desulfococcus multivorans strain DSM 2059, Desulfovibrio
      alkalitolerans strain DSM 16529, and Desulfovibrio species strain X2.
AU  - Brown SD
AU  - Hurt RA Jr
AU  - Gilmour CC
AU  - Elias DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00618-13.

PMID- 26251500
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Escherichia coli NCM3722.
PG  - e00879-15
AB  - Escherichia coli NCM3722 is a prototrophic K-12 strain with robust physiologic phenotypes. We
      report the complete 4,678,045-bp chromosome and 67,545-bp F-like
      plasmid of this unique model organism.
AU  - Brown SD
AU  - Jun S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00879-15.

PMID- 22493196
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Rhizobium sp. Strain PDO1-076, a Bacterium Isolated from Populus deltoides.
PG  - 2383-2384
AB  - Rhizobium sp. strain PDO1-076 is a plant-associated bacterium isolated from Populus deltoides,
      and its draft genome sequence is reported.
AU  - Brown SD
AU  - Klingeman DM
AU  - Lu TY
AU  - Johnson CM
AU  - Utturkar SM
AU  - Land ML
AU  - Schadt CW
AU  - Doktycz MJ
AU  - Pelletier DA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2383-2384.

PMID- 22628515
VI  - 194
DP  - 2012
TI  - Draft Genome Sequences for Clostridium thermocellum Wild-Type Strain YS and Derived Cellulose Adhesion-Defective Mutant Strain AD2.
PG  - 3290-3291
AB  - Clostridium thermocellum wild-type strain YS is an anaerobic, thermophilic, cellulolytic
      bacterium capable of directly converting cellulosic substrates into
      ethanol. Strain YS and a derived cellulose adhesion-defective mutant strain, AD2,
      played pivotal roles in describing the original cellulosome concept. We present
      their draft genome sequences.
AU  - Brown SD
AU  - Lamed R
AU  - Morag E
AU  - Borovok I
AU  - Shoham Y
AU  - Klingeman DM
AU  - Johnson CM
AU  - Yang Z
AU  - Land ML
AU  - Utturkar SM
AU  - Keller M
AU  - Bayer EA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3290-3291.

PMID- 22628508
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence for Microbacterium laevaniformans Strain OR221, a Bacterium Tolerant to Metals, Nitrate, and Low pH.
PG  - 3279-3280
AB  - Microbacterium laevaniformans strain OR221 was isolated from subsurface sediments obtained
      from the Field Research Center (FRC) in Oak Ridge, TN. It was
      characterized as a bacterium tolerant to heavy metals, such as uranium, nickel,
      cobalt, and cadmium, as well as nitrate and low pH. We present its draft genome
      sequence.
AU  - Brown SD
AU  - Palumbo AV
AU  - Panikov N
AU  - Ariyawansa T
AU  - Klingeman DM
AU  - Johnson CM
AU  - Land ML
AU  - Utturkar SM
AU  - Epstein SS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3279-3280.

PMID- 22933770
VI  - 194
DP  - 2012
TI  - Draft Genome Sequences for Two Metal-Reducing Pelosinus fermentans Strains Isolated from a Cr(VI)-Contaminated Site and for Type Strain R7.
PG  - 5147-5148
AB  - Pelosinus fermentans 16S rRNA gene sequences have been reported from diverse geographical
      sites since the recent isolation of the type strain. We present the
      genome sequence of the P. fermentans type strain R7 (DSM 17108) and genome
      sequences for two new strains with different abilities to reduce iron, chromate,
      and uranium.
AU  - Brown SD
AU  - Podar M
AU  - Klingeman DM
AU  - Johnson CM
AU  - Yang ZK
AU  - Utturkar SM
AU  - Land ML
AU  - Mosher JJ
AU  - Hurt RA Jr
AU  - Phelps TJ
AU  - Palumbo AV
AU  - Arkin AP
AU  - Hazen TC
AU  - Elias DA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5147-5148.

PMID- 23580709
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence for Desulfovibrio africanus Strain PCS.
PG  - e00144-13
AB  - Desulfovibrio africanus strain PCS is an anaerobic sulfate-reducing bacterium (SRB) isolated
      from sediment from Paleta Creek, San Diego, CA. Strain PCS is
      capable of reducing metals such as Fe(III) and Cr(VI), has a cell cycle, and is
      predicted to produce methylmercury. We present the D. africanus PCS genome
      sequence.
AU  - Brown SD
AU  - Utturkar SM
AU  - Arkin AP
AU  - Deutschbauer AM
AU  - Elias DA
AU  - Hazen TC
AU  - Chakraborty R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00144-13.

PMID- 23045501
VI  - 194
DP  - 2012
TI  - Twenty-One Genome Sequences from Pseudomonas Species and 19 Genome Sequences from Diverse Bacteria Isolated from the Rhizosphere and Endosphere of Populus  deltoides.
PG  - 5991-5993
AB  - To aid in the investigation of the Populus deltoides microbiome, we generated draft genome
      sequences for 21 Pseudomonas strains and 19 other diverse bacteria
      isolated from Populus deltoides roots. Genome sequences for isolates similar to
      Acidovorax, Bradyrhizobium, Brevibacillus, Caulobacter, Chryseobacterium,
      Flavobacterium, Herbaspirillum, Novosphingobium, Pantoea, Phyllobacterium,
      Polaromonas, Rhizobium, Sphingobium, and Variovorax were generated.
AU  - Brown SD
AU  - Utturkar SM
AU  - Klingeman DM
AU  - Johnson CM
AU  - Martin SL
AU  - Land ML
AU  - Lu TY
AU  - Schadt CW
AU  - Doktycz MJ
AU  - Pelletier DA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5991-5993.

PMID- 25189589
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Pelosinus sp. Strain UFO1 Assembled Using Single-Molecule Real-Time DNA Sequencing Technology.
PG  - e00881-14
AB  - Pelosinus species can reduce metals such as Fe(III), U(VI), and Cr(VI) and have been isolated
      from diverse geographical regions. Five draft genome sequences have
      been published. We report the complete genome sequence for Pelosinus sp. strain
      UFO1 using only PacBio DNA sequence data and without manual finishing.
AU  - Brown SD
AU  - Utturkar SM
AU  - Magnuson TS
AU  - Ray AE
AU  - Poole FL
AU  - Lancaster WA
AU  - Thorgersen MP
AU  - Adams MW
AU  - Elias DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00881-14.

PMID- 21642452
VI  - 193
DP  - 2011
TI  - Genome Sequence of the Mercury-Methylating and Pleomorphic Desulfovibrio africanus strain Walvis Bay.
PG  - 4037-4038
AB  - Desulfovibrio africanus strain Walvis Bay is an anaerobic sulfate-reducing bacterium (SRB)
      capable of producing methylmercury (MeHg), a potent human
      neurotoxin. The mechanism of methylation by this and other organisms is
      unknown. We present the 4.2 Mb genome sequence to provide further insight
      into microbial mercury methylation and sulfate-reducing bacteria.
AU  - Brown SD
AU  - Wall JD
AU  - Kucken AM
AU  - Gilmour CC
AU  - Podar M
AU  - Brandt CC
AU  - Teshima H
AU  - Detter JC
AU  - Han CS
AU  - Land ML
AU  - Lucas S
AU  - Han J
AU  - Pennacchio L
AU  - Nolan M
AU  - Pitluck S
AU  - Woyke T
AU  - Goodwin L
AU  - Palumbo AV
AU  - Elias DA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4037-4038.

PMID- Not carried by PubMed...
VI  - 2
DP  - 1991
TI  - Restriction and modification.
PG  - 260-284
AB  - *

      1. Restriction endonucleases. Almost 1500 restriction endonucleases are now known and over 150

      are commercially-available. Complete lists plus details of restriction sites and reaction

      conditions have been published.

      

      2. Site-specific methylases. At the last count 117 site-specific methylases had been

      characterized. A full list including recognition sequences and other relevant information is

      available.

      

      3. Restriction fragment patterns. Restriction fragments are frequently used as size markers

      for agarose and polyacrylamide gel electrophoresis. Figures 1-6 are restriction endonuclease

      digests that have been computer-generated assuming that all digests are run in 1.4% agarose.

      The scale on the left is in base-pairs.

      

AU  - Brown TA
PT  - Journal Article
TA  - Essential Molecular Biology
JT  - Essential Molecular Biology
SO  - Essential Molecular Biology 1991 2: 260-284.

PMID- 4216020
VI  - 71
DP  - 1974
TI  - Restriction endonuclease cleavage maps of animal mitochondrial DNAs.
PG  - 4617-4621
AB  - The restriction endonuclease, HindIII, gives rise to three fragments in each of
      the three mitochondrial DNAs isolated from the established mammalian cell lines
      LA9 (mouse), HeLa (human), and BSC-1 (African green monkey).  The restriction
      endonuclease, EcoRI gives rise to three fragments in mitochondrial DNA from
      HeLa and to two in DNAs form LA9 and BSC-1.  The sizes and the orders of the
      fragments in the respective genomes have been determined with data obtained
      from the electron microscope.  The origin and the direction of replication have
      been designated in each of the cleavage maps.  Polyacrylamide gel
      electrophoretic analyses demonstrated that additional fragments not detectable
      in the electron microscope and larger than 50 nucleotide pairs were not
      present.
AU  - Brown WM
AU  - Vinograd J
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1974 71: 4617-4621.

PMID- 29674551
VI  - 6
DP  - 2018
TI  - Draft Whole-Genome Sequences of Three Diarrheagenic Escherichia coli Strains Isolated from Farmed Deer in New Zealand.
PG  - e00300-18
AB  - Escherichia coli bacteria commonly colonize the gastrointestinal tracts of farmed ruminants.
      Cattle are a well-recognized reservoir of zoonotic E. coli; we report
      here, however, the draft genome sequences of three diarrheagenic E. coli strains
      isolated from farmed red deer (Cervus elaphus) in the Manawatu region of New
      Zealand.
AU  - Browne AS
AU  - Biggs PJ
AU  - Elliott A
AU  - Jaros P
AU  - French NP
AU  - Midwinter AC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00300-18.

PMID- 15840710
VI  - 102
DP  - 2005
TI  - Danna and Nathans: Restriction enzymes and the boon to modern molecular biology.
PG  - 5909
AB  - In 1971, a paper published in PNAS helped jump-start the era of modern molecular biology and
      biotechnology, eventually giving rise to many of the genetic advances that seem so commonplace
      today.  The article, written by Academy member Daniel Nathans and his then graduate student,
      Kathleen Danna, exposed the marvelous utility of restriction enzymes.  In the accompanying
      Perspective highlighting this classic work of scientific literature, Rich Roberts provides a
      historial account of the scientific discoveries leading up to the PNAS paper and the
      unparalleled scientific advances made after its publication.
AU  - Brownlee C
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2005 102: 5909.

PMID- 25414496
VI  - 2
DP  - 2014
TI  - Exploring the Genome of a Butyric Acid Producer, Clostridium butyricum INCQS635.
PG  - e01169-14
AB  - The draft genome sequence of Clostridium butyricum INCQS635 was obtained by means of ion
      sequencing. The genome provides further insight into the genetic
      repertoire involved with metabolic pathways related to the fermentation of
      different compounds and organic solvents synthesis (i.e., butyric acid) with
      biofuel applications.
AU  - Bruce T
AU  - Leite FG
AU  - Tschoeke DA
AU  - Miranda M
AU  - Pereira N Jr
AU  - Valle R
AU  - Thompson CC
AU  - Thompson FL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01169-14.

PMID- 17464242
VI  - 13
DP  - 2007
TI  - DNA methyltransferase inhibitors for cancer therapy.
PG  - 17-22
AB  - Aberrant DNA methylation patterns, including hypermethylation of tumor suppressor genes, have
      been described in many human cancers. These epigenetic mutations can be reversed by DNA
      methyltransferase inhibitors, which provide novel opportunities for cancer therapy. Clinical
      concepts for epigenetic therapies are currently being developed by using azanucleosides for
      the treatment of leukemias and other tumors. These trials will greatly benefit from the
      inclusion of molecular markers for monitoring epigenetic changes in patients and for
      maximizing biologic responses. In addition, novel inhibitors need to be developed that result
      in a direct and specific inhibition of DNA methyltransferase activity. Several recent
      developments indicate that rational design of small molecule DNA methyltransferase inhibitors
      is feasible and that this approach can result in the establishment of novel drug candidates.
      The use of novel DNA methyltransferase inhibitors in clinical trials that allow monitoring of
      drug-induced DNA methylation changes should provide the foundation for improved epigenetic
      cancer therapies.
AU  - Brueckner B
AU  - Kuck D
AU  - Lyko F
PT  - Journal Article
TA  - Cancer J.
JT  - Cancer J.
SO  - Cancer J. 2007 13: 17-22.

PMID- 27313293
VI  - 4
DP  - 2016
TI  - Genome Sequences of Four Strains of Mycobacterium avium subsp. hominissuis, Isolated from Swine and Humans, Differing in Virulence in a Murine Intranasal  Infection Model.
PG  - e00533-16
AB  - This paper announces the genome sequences of four strains of Mycobacterium avium  subsp.
      hominissuis, isolated from cases of lymphadenopathy in swine and humans,
      differing in virulence in a murine intranasal infection model.
AU  - Bruffaerts N
AU  - Vluggen C
AU  - Duytschaever L
AU  - Mathys V
AU  - Saegerman C
AU  - Chapeira O
AU  - Huygen K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00533-16.

PMID- 12552129
VI  - 100
DP  - 2003
TI  - The genome sequence of Clostridium tetani, the causative agent of tetanus disease.
PG  - 1316-1321
AB  - Tetanus disease is one of the most dramatic and globally prevalent diseases of humans and
      vertebrate animals, and has been reported for over
      24 centuries. The manifestation of the disease, spastic paralysis, is
      caused by the second most poisonous substance known, the tetanus toxin,
      with a human lethal dose of approximately 1 ng/kg. Fortunately, this
      disease is successfully controlled through immunization with tetanus
      toxoid; nevertheless, according to the World Health Organization, an
      estimated 400,000 cases still occur each year, mainly of neonatal tetanus.
      The causative agent of tetanus disease is Clostridium tetani, an anaerobic
      spore-forming bacterium, whose natural habitat is soil, dust, and
      intestinal tracts of various animals. Here we report the complete genome
      sequence of toxigenic C. tetani E88, a variant of strain Massachusetts.
      The genome consists of a 2,799,250-bp chromosome encoding 2,372 ORFs. The
      tetanus toxin and a collagenase are encoded on a 74,082-bp plasmid,
      containing 61 ORFs. Additional virulence-related factors could be
      identified, such as an array of surface-layer and adhesion proteins (35
      ORFs), some of them unique to C. tetani. Comparative genomics with the
      genomes of Clostridium perfringens, the causative agent of gas gangrene,
      and Clostridium acetobutylicum, a nonpathogenic solvent producer, revealed
      a remarkable capacity of C. tetani: The organism can rely on an extensive
      sodium ion bioenergetics. Additional candidate genes involved in the
      establishment and maintenance of a pathogenic lifestyle of C. tetani are
      presented.
AU  - Bruggemann H
AU  - Baumer S
AU  - Fricke WF
AU  - Wiezer A
AU  - Liesegang H
AU  - Decker I
AU  - Herzberg C
AU  - Martinez-Arias R
AU  - Merkl R
AU  - Henne A
AU  - Gottschalk G
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2003 100: 1316-1321.

PMID- 15286373
VI  - 305
DP  - 2004
TI  - The Complete Genome Sequence of Propionibacterium Acnes, a Commensal of Human Skin.
PG  - 671-673
AB  - Propionibacterium acnes is a major inhabitant of adult human skin, where it resides within
      sebaceous follicles, usually as a harmless commensal although it has been implicated in acne
      vulgaris formation. The entire genome sequence of this Gram positive bacterium encodes 2333
      putative genes and revealed numerous gene products involved in degrading host molecules,
      including sialidases, neuraminidases, endoglycoceramidases, lipases, and pore forming factors.
      Surface associated and other immunogenic factors have been identified, which might be involved
      in triggering acne inflammation and other P. acnes associated diseases.
AU  - Bruggemann H
AU  - Henne A
AU  - Hoster F
AU  - Liesegang H
AU  - Wiezer A
AU  - Strittmatter A
AU  - Hujer S
AU  - Durre P
AU  - Gottschalk G
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2004 305: 671-673.

PMID- 26500717
VI  - 10
DP  - 2015
TI  - Complete genome sequences of Geobacillus sp. Y412MC52, a xylan-degrading strain isolated from obsidian hot spring in Yellowstone National Park.
PG  - 81
AB  - Geobacillus sp. Y412MC52 was isolated from Obsidian Hot Spring, Yellowstone National Park,
      Montana, USA under permit from the National Park Service. The
      genome was sequenced, assembled, and annotated by the DOE Joint Genome Institute
      and deposited at the NCBI in December 2011 (CP002835). Based on 16S rRNA genes
      and average nucleotide identity, Geobacillus sp. Y412MC52 and the related
      Geobacillus sp. Y412MC61 appear to be members of a new species of Geobacillus.
      The genome of Geobacillus sp. Y412MC52 consists of one circular chromosome of
      3,628,883 bp, an average G + C content of 52 % and one circular plasmid of 45,057
      bp and an average G + C content of 45 %. Y412MC52 possesses arabinan,
      arabinoglucuronoxylan, and aromatic acid degradation clusters for degradation of
      hemicellulose from biomass. Transport and utilization clusters are also present
      for other carbohydrates including starch, cellobiose, and alpha- and
      beta-galactooligosaccharides.
AU  - Brumm P
AU  - Land ML
AU  - Hauser LJ
AU  - Jeffries CD
AU  - Chang YJ
AU  - Mead DA
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 81.

PMID- 27123157
VI  - 11
DP  - 2016
TI  - Complete genome sequences of Geobacillus sp. WCH70, a thermophilic strain isolated from wood compost.
PG  - 33
AB  - Geobacillus sp. WCH70 was one of several thermophilic organisms isolated from hot composts in
      the Middleton, WI area. Comparison of 16 S rRNA sequences showed the
      strain may be a new species, and is most closely related to G. galactosidasius
      and G. toebii. The genome was sequenced, assembled, and annotated by the DOE
      Joint Genome Institute and deposited at the NCBI in December 2009 (CP001638). The
      genome of Geobacillus species WCH70 consists of one circular chromosome of
      3,893,306 bp with an average G + C content of 43 %, and two circular plasmids of
      33,899 and 10,287 bp with an average G + C content of 40 %. Among sequenced
      organisms, Geobacillus sp. WCH70 shares highest Average Nucleotide Identity (86
      %) with G. thermoglucosidasius strains, as well as similar genome organization.
      Geobacillus sp. WCH70 appears to be a highly adaptable organism, with an
      exceptionally high 125 annotated transposons in the genome. The organism also
      possesses four predicted restriction-modification systems not found in other
      Geobacillus species.
AU  - Brumm PJ
AU  - Land ML
AU  - Mead DA
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 33.

PMID- 26442136
VI  - 10
DP  - 2015
TI  - Complete genome sequence of Geobacillus thermoglucosidasius C56-YS93, a novel biomass degrader isolated from obsidian hot spring in Yellowstone National Park.
PG  - 73
AB  - Geobacillus thermoglucosidasius C56-YS93 was one of several thermophilic organisms isolated
      from Obsidian Hot Spring, Yellowstone National Park, Montana,
      USA under permit from the National Park Service. Comparison of 16 S rRNA
      sequences confirmed the classification of the strain as a G. thermoglucosidasius
      species. The genome was sequenced, assembled, and annotated by the DOE Joint
      Genome Institute and deposited at the NCBI in December 2011 (CP002835). The
      genome of G. thermoglucosidasius C56-YS93 consists of one circular chromosome of
      3,893,306 bp and two circular plasmids of 80,849 and 19,638 bp and an average G +
      C content of 43.93 %. G. thermoglucosidasius C56-YS93 possesses a xylan
      degradation cluster not found in the other G. thermoglucosidasius sequenced
      strains. This cluster appears to be related to the xylan degradation cluster
      found in G. stearothermophilus. G. thermoglucosidasius C56-YS93 possesses two
      plasmids not found in the other two strains. One plasmid contains a novel gene
      cluster coding for proteins involved in proline degradation and metabolism, the
      other contains a collection of mostly hypothetical proteins.
AU  - Brumm PJ
AU  - Land ML
AU  - Mead DA
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 73.

PMID- 26465632
VI  - 10
DP  - 2015
TI  - Complete Genome Sequence of Thermus aquaticus Y51MC23.
PG  - e0138674
AB  - Thermus aquaticus Y51MC23 was isolated from a boiling spring in the Lower Geyser  Basin of
      Yellowstone National Park. Remarkably, this T. aquaticus strain is able
      to grow anaerobically and produces multiple morphological forms. Y51MC23 is a
      Gram-negative, rod-shaped organism that grows well between 50 degrees C and 80
      degrees C with maximum growth rate at 65 degrees C to 70 degrees C. Growth
      studies suggest that Y51MC23 primarily scavenges protein from the environment,
      supported by the high number of secreted and intracellular proteases and
      peptidases as well as transporter systems for amino acids and peptides. The
      genome was assembled de novo using a 350 bp fragment library (paired end
      sequencing) and an 8 kb long span mate pair library. A closed and finished genome
      was obtained consisting of a single chromosome of 2.15 Mb and four plasmids of
      11, 14, 70, and 79 kb. Unlike other Thermus species, functions usually found on
      megaplasmids were identified on the chromosome. The Y51MC23 genome contains two
      full and two partial prophage as well as numerous CRISPR loci. The high identity
      and synteny between Y51MC23 prophage 2 and that of Thermus sp. 2.9 is
      interesting, given the 8,800 km separation of the two hot springs from which they
      were isolated. The anaerobic lifestyle of Y51MC23 is complex, with multiple
      morphologies present in cultures. The use of fluorescence microscopy reveals new
      details about these unusual morphological features, including the presence of
      multiple types of large and small spheres, often forming a confluent layer of
      spheres. Many of the spheres appear to be formed not from cell envelope or outer
      membrane components as previously believed, but from a remodeled peptidoglycan
      cell wall. These complex morphological forms may serve multiple functions in the
      survival of the organism, including food and nucleic acid storage as well as
      colony attachment and organization.
AU  - Brumm PJ
AU  - Monsma S
AU  - Keough B
AU  - Jasinovica S
AU  - Ferguson E
AU  - Schoenfeld T
AU  - Lodes M
AU  - Mead DA
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2015 10: e0138674.

PMID- 26634764
VI  - 3
DP  - 2015
TI  - Draft Whole-Genome Sequence of Serratia marcescens Strain RM66262, Isolated from  a Patient with a Urinary Tract Infection.
PG  - e01423-15
AB  - Serratia marcescens strains are ubiquitous bacteria isolated from environmental niches and
      also constitute emergent nosocomial opportunistic pathogens. Here, we
      report on the draft genome sequence of S. marcescens strain RM66262, which was
      isolated from a patient with urinary tract infection in the Bacteriology Service
      of the Rosario National University, Rosario, Argentina.
AU  - Bruna RE
AU  - Revale S
AU  - Garcia VE
AU  - Mariscotti JF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01423-15.

PMID- 16887390
VI  - 296
DP  - 2006
TI  - Complete sequence of the large virulence plasmid pSFO157 of the sorbitol-fermenting enterohemorrhagic Escherichia coli O157:H(-) strain 3072/96.
PG  - 467-474
AB  - The large virulence plasmid pSFO157 of sorbitol-fermenting E. coli
      O157:H(-) strain 3072/96 has a size of 121,239bp and contains 96 open
      reading frames >50bp. It is therefore 29,162bp larger (ca. 32%) than
      plasmid pO157 of E. coli O157:H7 strain EDL933. Major differences between
      the plasmids are the absence of katP, espP, and toxB in pSFO157 and,
      instead of these, the presence of the sfp fimbriae gene cluster and a
      large part of an F-plasmid transfer region, the latter accounting for most
      of the additional DNA. The differences in the order of the genes and their
      composition, as well as the presence of a number of replication-associated
      genes and mobile genetic elements suggests that the large E. coli O157
      virulence plasmids have a complex evolutionary origin.
AU  - Brunder W
AU  - Karch H
AU  - Schmidt H
PT  - Journal Article
TA  - Int. J. Med. Microbiol.
JT  - Int. J. Med. Microbiol.
SO  - Int. J. Med. Microbiol. 2006 296: 467-474.

PMID- 23144395
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of the Naphthalene-Degrading Bacterium Pseudomonas stutzeri AN10 (CCUG 29243).
PG  - 6642-6643
AB  - Pseudomonas stutzeri AN10 (CCUG 29243) can be considered a model strain for aerobic
      naphthalene degradation. We report the complete genome sequence of this
      bacterium. Its 4.71-Mb chromosome provides insights into other biodegradative
      capabilities of strain AN10 (i.e., benzoate catabolism) and suggests a high
      number of horizontal gene transfer events.
AU  - Brunet-Galmes I
AU  - Busquets A
AU  - Pena A
AU  - Gomila M
AU  - Nogales B
AU  - Garcia-Valdes E
AU  - Lalucat J
AU  - Bennasar A
AU  - Bosch R
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6642-6643.

PMID- 29930047
VI  - 6
DP  - 2018
TI  - Genome Sequence of a Staphylococcus epidermidis Strain (GTH12) Associated with Candida albicans SC5314 Cultured under Hypoxia at 37 degrees C in Glycerol for 12 Weeks.
PG  - e00533-18
AB  - Polymicrobial infections with mixed-species biofilms are important health problems because of
      increased antimicrobial resistance and worse patient outcomes
      than with monomicrobial infections. Here, we present the whole-genome sequence of
      Staphylococcus epidermidis strain GTH12, which was cocultured with the yeast
      Candida albicans SC5314 (generating C. albicans strain SC5314 GTH12), thus
      providing genomic information on polymicrobial infections.
AU  - Bruno DDCF
AU  - Bartelli TF
AU  - Briones MRS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00533-18.

PMID- 23950130
VI  - 1
DP  - 2013
TI  - Genome Sequence of the Autotrophic Acetogen Clostridium autoethanogenum JA1-1 Strain DSM 10061, a Producer of Ethanol from Carbon Monoxide.
PG  - e00628-13
AB  - Clostridium autoethanogenum is an anaerobic, autotrophic acetogen that is capable of
      converting CO and CO2 into ethanol and acetate. Here we report the draft
      genome sequence of C. autoethanogenum JA1-1 strain DSM 10061 (4.5 Mbp; G+C
      content, 37.5%) and the findings obtained from annotation of the genome sequence.
AU  - Bruno-Barcena JM
AU  - Chinn MS
AU  - Grunden AM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00628-13.

PMID- 25342695
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Geobacillus icigianus Strain G1w1T Isolated from Hot Springs in the Valley of Geysers, Kamchatka (Russian Federation).
PG  - e01098-14
AB  - The Geobacillus icigianus G1w1(T) strain was isolated from sludge samples of unnamed vaporing
      hydrothermal (97 degrees capital ES, Cyrillic) outlets situated
      in a geyser in the Troinoy region (Valley of Geysers, Kronotsky Nature Reserve,
      Kamchatka, Russian Federation; 54 degrees 25'51.40'N, 160 degrees 7'41.40'E).
      The sequenced and annotated genome is 3,457,810 bp and encodes 3,342 genes.
AU  - Bryanskaya AV
AU  - Rozanov AS
AU  - Logacheva MD
AU  - Kotenko AV
AU  - Peltek SE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01098-14.

PMID- 17656724
VI  - 317
DP  - 2007
TI  - Candidatus Chloracidobacterium thermophilum: an aerobic phototrophic Acidobacterium.
PG  - 523-526
AB  - Only five bacterial phyla with members capable of chlorophyll (Chl)-based
      phototrophy are presently known. Metagenomic data from the phototrophic
      microbial mats of alkaline siliceous hot springs in Yellowstone National
      Park revealed the existence of a distinctive bacteriochlorophyll
      (BChl)-synthesizing, phototrophic bacterium. A highly enriched culture of
      this bacterium grew photoheterotrophically, synthesized BChls a and c
      under oxic conditions, and had chlorosomes and type 1 reaction centers.
      "Candidatus Chloracidobacterium thermophilum" is a BChl-producing member
      of the poorly characterized phylum Acidobacteria.
AU  - Bryant DA
AU  - Costas AM
AU  - Maresca JA
AU  - Chew AG
AU  - Klatt CG
AU  - Bateson MM
AU  - Tallon LJ
AU  - Hostetler J
AU  - Nelson WC
AU  - Heidelberg JF
AU  - Ward DM
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2007 317: 523-526.

PMID- 7707369
VI  - 247
DP  - 1995
TI  - Selection of a remote cleavage site by I-TevI, the td intron-encoded endonuclease.
PG  - 197-210
AB  - I-TevI, a double-strand DNA endonuclease involved in the mobility of the td intron of phage
      T4, is highly unusual in that it binds and cleaves intronless td alleles (td homing sites) in
      a site-specific but sequence-tolerant manner. The endonuclease binds to sequences flanking the
      intron insertion site and near the remote cleavage site, located 23 and 25 nucleotides away on
      the top and bottom strands, respectively. Mapping studies indicate that I-TevI has both
      sequence and distance sensors that function during cut-site selection. Although I-TevI
      cleavage of many insertion and deletion variants of the homing site is impaired, double-strand
      breaks are generated at positions that collectively span two turns of the helix, indicating
      that the interaction is extraordinarily flexible. However, the endonuclease does exhibit
      spacing preferences between its binding domains, and sequence preferences near the cleavage
      site, with the G:C pair at -23 implicated as a cleavage determinant. Furthermore, I-TevI
      appears to function through interactions across the minor groove at the cleavage site, as it
      does at the intron insertion site, and to be capable of cleaving sequentially, first on the
      bottom and then on the top strand. These properties of I-TevI are incorporated in a model
      wherein the endonuclease effects distant cleavage via a flexible hinge.
AU  - Bryk M
AU  - Belisle M
AU  - Mueller JE
AU  - Belfort M
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1995 247: 197-210.

PMID- 8491202
VI  - 12
DP  - 1993
TI  - The td intron endonuclease I-TevI makes extensive sequence-tolerant contacts across the minor groove of its DNA target.
PG  - 2141-2149
AB  - I-TevI, a double-strand DNA endonuclease encoded by the mobile td intron of phage T4, has
      specificity for the intronless td allele. Genetic and physical studies indicate that the
      enzyme makes extensive contact with its DNA substrate over at least three helical turns and
      around the circumference of the helix. Remarkably, no single nucleotide within a 48 bp region
      encompassing this interaction domain is essential for cleavage. Although two subdomains (DI
      and DII) contain preferred sequences, a third domain (DIII), a primary region of contact with
      the enzyme, displays much lower sequence preference. While DII and DIII suffice for
      recognition and binding of I-TevI, all three domains are important for formation of a
      cleavage-competent complex. Mutational, footprinting and interference studies indicate
      predominant interactions of I-TevI across the minor groove and phosphate backbone of the DNA.
      Contacts appear not to be at the single nucleotide level; rather redundant interactions and/or
      structural recognition are implied. These unusual properties provide a basis for understanding
      how I-TevI recognizes T-even phage DNA, which is heavily modified in the major groove. These
      recognition characteristics may increase the range of natural substrates available to the
      endonuclease, thereby extending the invasive potential of the mobile intron.
AU  - Bryk M
AU  - Quirk SM
AU  - Mueller JE
AU  - Loizos N
AU  - Lawrence C
AU  - Belfort M
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1993 12: 2141-2149.

PMID- 6283092
VI  - 154
DP  - 1982
TI  - Steps in the reaction mechanism of the Haemophilus influenzae Rf restriction endonuclease.
PG  - 615-627
AB  - HinfIII is a restriction modification enzyme isolated from Haemophilus
      influenzae strain Rf. It requires ATP for cleavage and S-adenosyl-L-methionine
      for methylation of DNA.  S-Adenosyl-L-methionine acts as an allosteric effector
      in the endonuclease reaction.  The enzyme forms a complex with unmodified DNA
      in the absence of ATP and S-adenosyl-L-methionine.  This complex is sensitive
      to inhibition by heparin.  S-Adenosyl-L-methionine is required for the
      formation of a complex that is insensitive to such inhibition.  ATP acts as an
      allosteric effector of HinfIII, and induces DNA cleavage followed probably by
      the release of the enzyme from the DNA.
AU  - Brzezinski R
AU  - Piekarowicz A
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1982 154: 615-627.

PMID- 16912116
VI  - 103
DP  - 2006
TI  - How to become a uropathogen: Comparative genomic analysis of extraintestinal pathogenic Escherichia coli strains.
PG  - 12879-12884
AB  - Uropathogenic Escherichia coli (UPEC) strain 536 (O6:K15:H31) is one of the model organisms of
      extraintestinal pathogenic E. coli (ExPEC). To
      analyze this strain's genetic basis of urovirulence, we sequenced the
      entire genome and compared the data with the genome sequence of UPEC
      strain CFT073 (O6:K2:H1) and to the available genomes of nonpathogenic E.
      coli strain MG1655 (K-12) and enterohemorrhagic E. coli. The genome of
      strain 536 is approximately 292 kb smaller than that of strain CFT073.
      Genomic differences between both UPEC are mainly restricted to large
      pathogenicity islands, parts of which are unique to strain 536 or CFT073.
      Genome comparison underlines that repeated insertions and deletions in
      certain parts of the genome contribute to genome evolution. Furthermore,
      427 and 432 genes are only present in strain 536 or in both UPEC,
      respectively. The majority of the latter genes is encoded within smaller
      horizontally acquired DNA regions scattered all over the genome. Several
      of these genes are involved in increasing the pathogens' fitness and
      adaptability. Analysis of virulence-associated traits expressed in the two
      UPEC O6 strains, together with genome comparison, demonstrate the marked
      genetic and phenotypic variability among UPEC. The ability to accumulate
      and express a variety of virulence-associated genes distinguishes ExPEC
      from many commensals and forms the basis for the individual virulence
      potential of ExPEC. Accordingly, instead of a common virulence mechanism,
      different ways exist among ExPEC to cause disease.
AU  - Brzuszkiewicz E
AU  - Bruggemann H
AU  - Liesegang H
AU  - Emmerth M
AU  - Olschlager T
AU  - Nagy G
AU  - Albermann K
AU  - Wagner C
AU  - Buchrieser C
AU  - Emody L
AU  - Gottschalk G
AU  - Hacker J
AU  - Dobrindt U
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2006 103: 12879-12884.

PMID- 23932911
VI  - 303
DP  - 2013
TI  - Legionella oakridgensis ATCC 33761 genome sequence and phenotypic characterization reveals its replication capacity in amoebae.
PG  - 514-528
AB  - Legionella oakridgensis is able to cause Legionnaires' disease, but is less
      virulent compared to L. pneumophila strains and very rarely associated with human
      disease. L. oakridgensis is the only species of the family legionellae which is
      able to grow on media without additional cysteine. In contrast to earlier
      publications, we found that L. oakridgensis is able to multiply in amoebae. We
      sequenced the genome of L. oakridgensis type strain OR-10 (ATCC 33761). The
      genome is smaller than the other yet sequenced Legionella genomes and has a
      higher G+C-content of 40.9%. L. oakridgensis lacks a flagellum and it also lacks
      all genes of the flagellar regulon except of the alternative sigma-28 factor FliA
      and the anti-sigma-28 factor FlgM. Genes encoding structural components of type
      I, type II, type IV Lvh and type IV Dot/Icm, Sec- and Tat-secretion systems could
      be identified. Only a limited set of Dot/Icm effector proteins have been
      recognized within the genome sequence of L. oakridgensis. Like in L. pneumophila
      strains, various proteins with eukaryotic motifs and eukaryote-like proteins were
      detected. We could demonstrate that the Dot/Icm system is essential for
      intracellular replication of L. oakridgensis. Furthermore, we identified new
      putative virulence factors of Legionella.
AU  - Brzuszkiewicz E
AU  - Schulz T
AU  - Rydzewski K
AU  - Daniel R
AU  - Gillmaier N
AU  - Dittmann C
AU  - Holland G
AU  - Schunder E
AU  - Lautner M
AU  - Eisenreich W
AU  - Luck C
AU  - Heuner K
PT  - Journal Article
TA  - Int. J. Med. Microbiol.
JT  - Int. J. Med. Microbiol.
SO  - Int. J. Med. Microbiol. 2013 303: 514-528.

PMID- 22843577
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of the B12-Producing Shimwellia blattae Strain DSM 4481, Isolated from a Cockroach.
PG  - 4436
AB  - Here we announce the complete genome sequence of the coenzyme B(12)-producing enteric
      bacterium Shimwellia blattae (formerly Escherichia blattae). The genome
      consists of a single chromosome (4,158,636 bp). The genome size is smaller than
      that of most other enteric bacteria. Genome comparison revealed significant
      differences from the Escherichia coli genome.
AU  - Brzuszkiewicz E
AU  - Waschkowitz T
AU  - Wiezer A
AU  - Daniel R
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4436.

PMID- 10230396
VI  - 3
DP  - 1999
TI  - Hypermutation in pathogenic bacteria: frequent phase variation in meningococci is a phenotypic trait of a specialized mutator biotype.
PG  - 435-445
AB  - Expression of serogroup B meningococcal capsular polysaccharide undergoes frequent phase
      variation involving reversible frameshift mutations within a homopolymeric repeat in the siaD
      gene. A high rate of phase variation is the consequence of a biochemical defect in
      methyl-directed mismatch repair. The mutator phenotype is associated to the absence of DNA
      adenine methyltransferase (Dam) activity in all pathogenic isolates and in 50% of commensal
      strains. Analysis of the meningococcal dam gene region revealed that in all Dam- strains a
      gene encoding a putative restriction endonuclease (drg) that cleaves only the methylated DNA
      sequence 5'-GmeATC-3' replaced the dam gene. Insertional inactivation of the dam and/or drg
      genes indicated that high rates of phase variation and hypermutator phenotype are caused by
      absence of a functional dam gene.
AU  - Bucci C
AU  - Lavitola A
AU  - Salvatore P
AU  - Del Giudice L
AU  - Massardo DR
AU  - Bruni CB
AU  - Alifano P
PT  - Journal Article
TA  - Mol. Cell
JT  - Mol. Cell
SO  - Mol. Cell 1999 3: 435-445.

PMID- 27979943
VI  - 4
DP  - 2016
TI  - High-Quality Draft Genome Sequence of the Actinobacterium Nocardia terpenica IFM  0406, Producer of the Immunosuppressant Brasilicardins, Using Illumina and PacBio  Technologies.
PG  - e01391-16
AB  - The bacterium Nocardia terpenica IFM 0406 is known as the producer of the immunosuppressant
      brasilicardin A. Here, we report the completely sequenced
      genome of strain IFM 0406, which facilitates the heterologous expression of the
      brasilicardin biosynthetic gene cluster but also unveils the intriguing
      biosynthetic capacity of the strain to produce secondary metabolites.
AU  - Buchmann A
AU  - Eitel M
AU  - Koch P
AU  - Schwarz PN
AU  - Stegmann E
AU  - Wohlleben W
AU  - Wolanski M
AU  - Krawiec M
AU  - Zakrzewska-Czerwinska J
AU  - Mendez C
AU  - Botas A
AU  - Nunez LE
AU  - Moris F
AU  - Cortes J
AU  - Gross H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01391-16.

PMID- 11115111
VI  - 38
DP  - 2000
TI  - The virulence plasmid pWR100 and the repertoire of proteins secreted by the type III secretion apparatus of Shigella flexneri.
PG  - 760-771
AB  - Bacteria of Shigella spp. are the causative agents of shigellosis. The
      virulence traits of these pathogens include their ability to enter into
      epithelial cells and induce apoptosis in macrophages. Expression of these
      functions requires the Mxi-Spa type III secretion apparatus and the
      secreted IpaA-D proteins, all of which are encoded by a virulence plasmid.
      In wild-type strains, the activity of the secretion apparatus is tightly
      regulated and induced upon contact of bacteria with epithelial cells. To
      investigate the repertoire of proteins secreted by Shigella flexneri in
      conditions of active secretion, we determined the N-terminal sequence of
      14 proteins that are secreted by a mutant in which secretion was
      deregulated. Sequencing of the virulence plasmid pWR100 of the S. flexneri
      strain M90T (serotype 5) has allowed us to identify the genes encoding
      these secreted proteins and suggests that approximately 25 proteins are
      secreted by the type III secretion apparatus. Analysis of the G+C content
      and the relative positions of genes and open reading frames carried by the
      plasmid, together with information concerning the localization and
      function of encoded proteins, suggests that pWR100 contains blocks of
      genes of various origins, some of which were initially carried by four
      different plasmids.
AU  - Buchrieser C
AU  - Glaser P
AU  - Rusniok C
AU  - Nedjari H
AU  - D'Hauteville H
AU  - Kunst F
AU  - Sansonetti P
AU  - Parsot C
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2000 38: 760-771.

PMID- 24501651
VI  - 9
DP  - 2013
TI  - Complete genome sequence of the marine methyl-halide oxidizing Leisingera methylohalidivorans type strain (DSM 14336(T)), a representative of the  Roseobacter clade.
PG  - 128-141
AB  - Leisingera methylohalidivorans Schaefer et al. 2002 emend. Vandecandelaere et al. 2008 is the
      type species of the genus Leisingera. The genus belongs to the
      Roseobacter clade (Rhodobacteraceae, Alphaproteobacteria), a widely distributed
      lineage in marine environments. Leisingera and particularly L.
      methylohalidivorans strain MB2(T) is of special interest due to its
      methylotrophy. Here we describe the complete genome sequence and annotation of
      this bacterium together with previously unreported aspects of its phenotype. The
      4,650,996 bp long genome with its 4,515 protein-coding and 81 RNA genes consists
      of three replicons, a single chromosome and two extrachromosomal elements with
      sizes of 221 kb and 285 kb.
AU  - Buddruhs N
AU  - Chertkov O
AU  - Petersen J
AU  - Fiebig A
AU  - Chen A
AU  - Pati A
AU  - Ivanova N
AU  - Lapidus A
AU  - Goodwin LA
AU  - Chain P
AU  - Detter JC
AU  - Gronow S
AU  - Kyrpides NC
AU  - Woyke T
AU  - Goker M
AU  - Brinkhoff T
AU  - Klenk HP
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 9: 128-141.

PMID- 29192088
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Bacillus altitudinis P-10, a Potential Bioprotectant  against Xanthomonas oryzae pv. oryzae, Isolated from Rice Rhizosphere in Java,  Indonesia.
PG  - e01388-17
AB  - Bacillus altitudinis P-10 was isolated from the rhizosphere of rice grown in an organic rice
      field and provides strong antagonism against the bacterial blight
      caused by Xanthomonas oryzae pv. oryzae in rice. Herein, we provide the complete
      genome sequence and a possible explanation of the antibiotic function of the P-10
      strain.
AU  - Budiharjo A
AU  - Jeong H
AU  - Wulandari D
AU  - Lee S
AU  - Ryu CM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01388-17.

PMID- 3021244
VI  - 51
DP  - 1986
TI  - Cleavage of DNA adsorbed on the surface of phospholipid membranes by Type II restriction endonucleases.
PG  - 1496-1498
AB  - The hydrolysis of phage lambda DNA by restriction endonucleases of type II in the presence of
      model membranes from egg phosphatidylcholine was studied.  It was shown that the degree of
      hydrolysis of DNA by the enzymes BspI, PstI, and BamHI under these conditions is sharply
      reduced.  This is not associated with irreversible inactivation of the enzymes in their
      interaction with the membrane.  The most probable explanation for the inhibition of DNA
      hydrolysis in the presence of phospholipid vesicles is a change in the substrate properties of
      the DNA as a result of its adsorption on the surface of the phospholipid membrane with the
      participation of Mg2+ ions.
AU  - Budker VG
AU  - Degtyarev SK
AU  - Sokolov AV
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1986 51: 1496-1498.

PMID- 21368196
VI  - 108
DP  - 2011
TI  - Neisseria meningitidis is structured in clades associated with restriction modification systems that modulate homologous recombination.
PG  - 4494-4499
AB  - Molecular data on a limited number of chromosomal loci have shown that the population of
      Neisseria meningitidis (Nm), a deadly human pathogen, is
      structured in distinct lineages. Given that the Nm population undergoes
      substantial recombination, the mechanisms resulting in the evolution of
      these lineages, their persistence in time, and the implications for the
      pathogenicity of the bacterium are not yet completely understood. Based on
      whole-genome sequencing, we show that Nm is structured in phylogenetic
      clades. Through acquisition of specific genes and through insertions and
      rearrangements, each clade has acquired and remodeled specific genomic
      tracts, with the potential to impact on the commensal and virulence
      behavior of Nm. Despite this clear evidence of a structured population, we
      confirm high rates of detectable recombination throughout the whole Nm
      chromosome. However, gene conversion events were found to be longer within
      clades than between clades, suggesting a DNA cleavage mechanism associated
      with the phylogeny of the species. We identify 22 restriction modification
      systems, probably acquired by horizontal gene transfer from outside of the
      species/genus, whose distribution in the different strains coincides with
      the phylogenetic clade structure. We provide evidence that these
      clade-associated restriction modification systems generate a differential
      barrier to DNA exchange consistent with the observed population structure.
      These findings have general implications for the emergence of lineage
      structure and virulence in recombining bacterial populations, and they
      could provide an evolutionary framework for the population biology of a
      number of other bacterial species that show contradictory population
      structure and dynamics.
AU  - Budroni S
AU  - Siena E
AU  - Dunning HJC
AU  - Seib KL
AU  - Serruto D
AU  - Nofroni C
AU  - Comanducci M
AU  - Riley DR
AU  - Daugherty SC
AU  - Angiuoli SV
AU  - Covacci A
AU  - Pizza M
AU  - Rappuoli R
AU  - Moxon ER
AU  - Tettelin H
AU  - Medini D
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2011 108: 4494-4499.

PMID- 12928499
VI  - 100
DP  - 2003
TI  - The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000.
PG  - 10181-10186
AB  - We report the complete genome sequence of the model bacterial pathogen Pseudomonas syringae
      pathovar tomato DC3000 (DC3000), which is pathogenic
      on tomato and Arabidopsis thaliana. The DC3000 genome (6.5 megabases)
      contains a circular chromosome and two plasmids, which collectively encode
      5,763 ORFs. We identified 298 established and putative virulence genes,
      including several clusters of genes encoding 31 confirmed and 19 predicted
      type III secretion system effector proteins. Many of the virulence genes
      were members of paralogous families and also were proximal to mobile
      elements, which collectively comprise 7% of the DC3000 genome. The
      bacterium possesses a large repertoire of transporters for the acquisition
      of nutrients, particularly sugars, as well as genes implicated in
      attachment to plant surfaces. Over 12% of the genes are dedicated to
      regulation, which may reflect the need for rapid adaptation to the diverse
      environments encountered during epiphytic growth and pathogenesis.
      Comparative analyses confirmed a high degree of similarity with two
      sequenced pseudomonads, Pseudomonas putida and Pseudomonas aeruginosa, yet
      revealed 1,159 genes unique to DC3000, of which 811 lack a known function.
AU  - Buell CR et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2003 100: 10181-10186.

PMID- 10356279
VI  - 15
DP  - 1999
TI  - DSC confirmation that vitrification is not necessary for stabilization of the restriction enzyme EcoRI dried with saccharides.
PG  - 577-579
AB  - The glass transition temperature (Tg) of preparations of the restriction enzyme EcoRI,
      vacuum-dried in the presence of sucrose, trehalose, or raffinose, was determined using
      differential scanning calorimetry.  Tg values were well below those expected for low-moisture
      sucrose, trehalose, or raffinose, and this was attributed to the presence of glycerol (a
      plasticizer), which was a main component of the restriction enzyme preparation.  This was
      verified by determining the glass transition temperature of glycerol, which was found to be
      (onset value) -77 C.  Present results confirmed that vitrification (i.e., glass formation) was
      not necessary for enzyme protection in present low-moisture saccharide systems.  As shown in
      previous work, the enzyme EcoRI was very stable when stored at 37/45 C in spite of the fact
      that sugar matrices were completely rubbery, as unequivocally demonstrated in the present
      work.
AU  - Buera MP
AU  - Rossi S
AU  - Moreno S
AU  - Chirife J
PT  - Journal Article
TA  - Biotechnol. Prog.
JT  - Biotechnol. Prog.
SO  - Biotechnol. Prog. 1999 15: 577-579.

PMID- 25883279
VI  - 3
DP  - 2015
TI  - Two Draft Genome Sequences of a New Serovar of Salmonella enterica, Serovar Lubbock.
PG  - e00215-15
AB  - Salmonella enterica is principally a foodborne pathogen that shows considerable serovar
      diversity. In this report, we present two draft genome sequences of
      Salmonella enterica subsp. enterica serovar Lubbock, a novel serovar.
AU  - Bugarel M
AU  - den Bakker HC
AU  - Nightingale KK
AU  - Brichta-Harhay DM
AU  - Edrington TS
AU  - Loneragan GH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00215-15.

PMID- 10205294
VI  - 64
DP  - 1999
TI  - Possibilities of the method of step-by-step complication of ligand structure in studies of protein-nucleic acid interactions: mechanisms of functioning of some replication, repair, topoisomerization, and restriction enzymes.
PG  - 291-305
AB  - X-Ray structure analysis is one of the most informative methods for investigation of enzymes.
      However, it does not provide quantitative estimation of the relative efficiency of formation
      of contacts revealed by this method, and when interpreting the data this does not allow taking
      into account the relative contribution of some specific and nonspecific interactions to the
      total affinity of nucleic acids (NA) to enzymes. This often results in unjustified
      overestimation of the role of specific enzyme--NA contacts in affinity and specificity of
      enzyme action. In recent years we have developed new approaches to analysis of the mechanisms
      of protein--nucleic acid interactions allowing quantitative estimation of the relative
      contribution of virtually every nucleotide unit (including individual structural elements) to
      the total affinity of enzymes to long DNA and RNA molecules. It is shown that the interaction
      between enzymes and NA on the molecular level can be successfully analyzed by the methods of
      synthesis and analysis, that is, step-by-step simplification or complication of the structure
      of a long NA-ligand. This approach allows the demonstration that complex formation including
      formation of contacts between enzymes and specific NA units can provide neither high affinity
      of the enzymes to NA nor the specificity of their action. Using a number of
      sequence-independent replication and repair enzymes specifically recognizing a modified unit
      in DNA and also some sequence-dependent topoisomerization and restriction enzymes as examples,
      it was shown that virtually all nucleotide units within the DNA binding cleft interact with
      the enzyme, and high affinity mainly (up to 5-7 of 7-10 orders of magnitude) is provided by
      many weak additive interactions between these enzymes and various structural elements of the
      individual NA nucleotide units. At the same time, the relative contribution of specific
      interactions to the total affinity of NA is rather small and does not exceed 1-2 orders of
      magnitude. Specificity of enzyme action is provided by the stages of the enzyme-dependent NA
      adaptation to the optimal conformation and directly of catalysis: kcat increases by 3-7 orders
      of magnitude when changing from nonspecific to specific NA. In the present work we summarized
      our experience in studies of enzymes by the method of step-by-step complication of the ligand
      structure and performed a detailed analysis of the features of this approach and its
      possibilities for the study of protein--nucleic acid interactions on the molecular level.
AU  - Bugreev DV
AU  - Nevinsky GA
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1999 64: 291-305.

PMID- 27856590
VI  - 4
DP  - 2016
TI  - Complete Genome Sequences for Three Chromosomes of the Burkholderia stabilis Type Strain (ATCC BAA-67).
PG  - e01294-16
AB  - We report here the complete annotated genome sequence of the Burkholderia stabilis type strain
      ATCC BAA-67. There were three circular chromosomes with a
      combined size of 8,527,947 bp and G+C composition of 66.4%. These characteristics
      closely resemble the genomes of other sequenced members of the Burkholderia
      cepacia complex.
AU  - Bugrysheva JV
AU  - Cherney B
AU  - Sue D
AU  - Conley AB
AU  - Rowe LA
AU  - Knipe KM
AU  - Frace MA
AU  - Loparev VN
AU  - Avila JR
AU  - Anderson K
AU  - Hodge DR
AU  - Pillai SP
AU  - Weigel LM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01294-16.

PMID- 26634765
VI  - 3
DP  - 2015
TI  - Finished Annotated Genome Sequence of Burkholderia pseudomallei Strain Bp1651, a  Multidrug-Resistant Clinical Isolate.
PG  - e01427-15
AB  - Burkholderia pseudomallei strain Bp1651, a human isolate, is resistant to all clinically
      relevant antibiotics. We report here on the finished genome sequence
      assembly and annotation of the two chromosomes of this strain. This genome
      sequence may assist in understanding the mechanisms of antimicrobial resistance
      for this pathogenic species.
AU  - Bugrysheva JV
AU  - Sue D
AU  - Hakovirta J
AU  - Loparev VN
AU  - Knipe K
AU  - Sammons SA
AU  - Ranganathan-Ganakammal S
AU  - Changayil S
AU  - Srinivasamoorthy G
AU  - Weil MR
AU  - Tatusov RL
AU  - Gee JE
AU  - Elrod MG
AU  - Hoffmaster AR
AU  - Weigel LM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01427-15.

PMID- 6092231
VI  - 29
DP  - 1984
TI  - Restriction and modification in Bacillus subtilis: nucleotide sequence, functional organization and product of the DNA methyltransferase gene of bacteriophage SPR.
PG  - 51-61
AB  - Bacillus subtilis phage SPR codes for a DNA methyltransferase (Mtase) which
      methylates the 5' cytosine in the sequence GGCC and both cytosies in the
      sequence CCGG.  A 2126-bp fragment of SPR DNA containing the Mtase gene has
      been sequenced.  This fragment has only one significant open reading frame of
      1347 bp, which corresponds to the Mtase gene.  Within the sequence the Mtase
      promoter has been defined by S1 mapping.  The size of the SPR Mtase predicted
      from the deduced amino acid composition is 49.9 kDal.  This is in agreement
      with both the Mr of the purified enzyme and with that of the SPR Mtase gene
      product identified here by minicell technique.  Base changes leading to mutants
      affected in Mtase activity were localized within the Mtase gene.
AU  - Buhk H-J
AU  - Behrens B
AU  - Tailor R
AU  - Wilke K
AU  - Prada JJ
AU  - Gunthert U
AU  - Noyer-Weidner M
AU  - Jentsch S
AU  - Trautner TA
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1984 29: 51-61.

PMID- 357430
VI  - 253
DP  - 1978
TI  - Characterization of a restriction enzyme from Escherichia coli K carrying a mutation in the modification subunit.
PG  - 6756-6760
AB  - The restriction enzyme from a restriction and modification-deficient strain of
      Escherichia coli K mutated in the modification gene (hsdM) has been purified
      using an in vitro complementation assay with a mutant restriction enzyme from a
      strain lacking only restriction.  The restriction enzyme from the hsdM mutant
      lacks all of the activities that are associated with the wild type enzyme:
      binding of unmodified DNA to filters, cleavage, or methylation of unmodified
      DNA and ATP hydrolysis.  It is shown that the enzyme from this hsdM mutant
      cannot bind S-adenosylmethionine, an allosteric effector in the restriction
      reaction.  In the absence of enzyme activation by S-adenosylmethionine, no
      binding to unmodified DNA takes place.  A comparison with other mutant
      restriction enzymes allows us to outline the biochemical role of the subunits
      of the E. coli K restriction endonuclease.
AU  - Buhler R
AU  - Yuan R
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1978 253: 6756-6760.

PMID- 26450724
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Lactobacillus johnsonii Strain 16, Isolated from Mice.
PG  - e01141-15
AB  - Here, we report the genome sequence of Lactobacillus johnsonii, a member of the gut
      lactobacilli. This draft genome of L. johnsonii strain 16 isolated from C57BL/6J mice enables
      the identification of bacterial genes responsible for host-specific gut persistence.
AU  - Buhnik-Rosenblau K
AU  - Danin-Poleg Y
AU  - Elgavish S
AU  - Kashi Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01141-15.

PMID- 26458527
VI  - 36
DP  - 2015
TI  - A full genomic characterization of the development of a stable Small Colony Variant cell-type by a clinical Staphylococcus aureus strain.
PG  - 345-355
AB  - A key to persistent and recurrent Staphylococcus aureus infections is its ability to adapt to
      diverse and toxic conditions. This ability includes a switch into a
      biofilm or to the quasi-dormant Small Colony Variant (SCV). The development and
      molecular attributes of SCVs have been difficult to study due to their rapid
      reversion to their parental cell-type. We recently described the unique induction
      of a matrix-embedded and stable SCV cell-type in a clinical S. aureus strain
      (WCH-SK2) by growing the cells with limiting conditions for a prolonged
      timeframe. Here we further study their characteristics. They possessed an
      increased viability in the presence of antibiotics compared to their non-SCV
      form. Their stability implied that there had been genetic changes; we therefore
      determined both the genome sequence of WCH-SK2 and its stable SCV form at a
      single base resolution, employing Single Molecular Real-Time (SMRT) sequencing
      that enabled the methylome to also be determined. The genetic features of WCH-SK2
      have been identified; the SCCmec type, the pathogenicity and genetic islands and
      virulence factors. The genetic changes that had occurred in the stable SCV form
      were identified; most notably being in MgrA, a global regulator, and RsbU, a
      phosphoserine phosphatase within the regulatory pathway of the sigma factor SigB.
      There was a shift in the methylomes of the non-SCV and stable SCV forms. We have
      also shown a similar induction of this cell-type in other S. aureus strains and
      performed a genetic comparison to these and other S. aureus genomes. We
      additionally map RNAseq data to the WCH-SK2 genome in a transcriptomic analysis
      of the parental, SCV and stable SCV cells. The results from this study represent
      the unique identification of a suite of epigenetic, genetic and transcriptional
      factors that are implicated in the switch in S. aureus to its persistent SCV
      form.
AU  - Bui LMG
AU  - Kidd SP
PT  - Journal Article
TA  - Infect. Genet. Evol.
JT  - Infect. Genet. Evol.
SO  - Infect. Genet. Evol. 2015 36: 345-355.

PMID- 28522714
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Fish Strain Edwardsiella tarda NCIMB 2034.
PG  - e00359-17
AB  - Edwardsiella tarda is an important pathogen for fish. The strain NCIMB 2034, obtained from the
      National Collection of Industrial Food and Marine Bacteria, was
      isolated from unknown diseased fish in the United States. The draft genome
      sequence has 3.79 Mb with a G+C content of 57.1% and >3,340 protein-coding genes.
AU  - Bujan N
AU  - Lasa A
AU  - E-Toranzo A
AU  - Magarinos B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00359-17.

PMID- 28209828
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Edwardsiellapiscicida Strain ACC35.1 Isolated from Diseased Turbot (Scophthalmus maximus) in Europe.
PG  - e01626-16
AB  - Edwardsiella piscicida is a bacterial fish pathogen with a high degree of virulence. The
      strain ACC35.1 was isolated from diseased turbot in Europe. The
      draft genome sequence comprises 3.84 Mb with a G+C content of 59.8% and >3,450
      protein-coding genes.
AU  - Bujan N
AU  - Toranzo AE
AU  - Magarinos B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01626-16.

PMID- 
VI  - 14
DP  - 2004
TI  - Molecular phylogenetics of restriction endonucleaseses.
PG  - 63-93
AB  - 1. Discovery and classification of restriction enzymes.  The phenomenon of restriction and
      modification was first discovered in the early 1950s.  It was observed that certain strains of
      bacteria inhibited (restricted) the growth of bacteriophages previously propagated on a
      different strain.  In the early 1960s, it was found that the restriction is due to the
      enzymatic cleavage of the phage DNA by sequence-specific endonucleases (REases), which are
      sensitive to covalent modification of bases in the target sequence.  Some of the REases
      produced discrete DNA fragments upon cleavage.  This property proved very useful for analyzing
      and rearranging DNA, which soon prompted the rapid development of genetic engineering
      techniques as well as the search for more REases with novel recognition sequences.  It was in
      the mid-1970s when cloning of R-M enzymes themselves began.  It was found that most of
      restriction enzymes are genetically linked with modification enzymes of cognate specificity,
      forming R-M systems, but a few solitary enzymes were also characterized.
AU  - Bujnicki JM
PT  - Journal Article
TA  - Nucleic Acids Mol. Biol.
JT  - Nucleic Acids Mol. Biol.
SO  - Nucleic Acids Mol. Biol. 2004 14: 63-93.

PMID- 10654258
VI  - 50
DP  - 2000
TI  - Phylogeny of the restriction endonuclease-like superfamily inferred from comparison of protein structures.
PG  - 39-44
AB  - To date all attempts to derive a phyletic relationship among restriction endonucleases
      (ENases) from multiple sequence alignments have been limited by extreme divergence of these
      enzymes.  Based on the approach of Johnson et al. (1990), I report for the first time the
      evolutionary tree of the ENase-like protein superfamily inferred from quantitative comparison
      of atomic coordinates of structurally characterized enzymes. The results presented are in
      harmony with previous comparisons obtained by crystallographic analyses. It is shown that
      lambda-exonuclease initially diverged from the common ancestor and then two "endonucleolytic"
      families branched out, separating "blunt end cutters" from "5' four-base overhand cutters."
      These data may contribute to a better understanding of ENases and encourage the use of
      structure-based methods for inference of phylogenetic relationship among extremely divergent
      proteins. In addition, the comparison of three-dimensional structures of ENase-like domains
      provides a platform for further clustering analyses of sequence similarities among different
      branches of this large protein family, rational choice of homology modeling templates, and
      targets for protein engineering.
AU  - Bujnicki JM
PT  - Journal Article
TA  - J. Mol. Evol.
JT  - J. Mol. Evol.
SO  - J. Mol. Evol. 2000 50: 39-44.

PMID- 11930990
VI  - 50
DP  - 2001
TI  - A model of structure and action of Sau3AI restriction endonuclease that comprises two MutH-like endonuclease domains within a single polypeptide.
PG  - 219-231
AB  - Sau3AI is a type II endonuclease that cleaves GATC sequences, producing sticky ends with
      4-nucleotide 5'-overhangs.  Its activity is inhibited by cytosine C5-methylation within the
      target sequence.  In the N-terminus, Sau3AI exhibits sequence similarity to the GATC-specific
      single-strand nicking endonuclease MutH implicated in mismatch repair.  Sequence analysis of
      Sau3AI and its homologs reveals that Sau3AI possesses an additional MutH-like domain in the
      C-terminus.  Structure prediction suggests that the C-terminal domain lacks the endonuclease
      active site but retains all putative DNA-binding elements.  As an illustration of these
      findings, a model of quaternary structure of Sau3AI complexed with the target DNA is
      presented.  These predictions have implications for evolution, structure and function of
      bacterial DNA repair enzymes and restriction endonucleases.
AU  - Bujnicki JM
PT  - Journal Article
TA  - Acta Microbiol. Pol.
JT  - Acta Microbiol. Pol.
SO  - Acta Microbiol. Pol. 2001 50: 219-231.

PMID- 11479932
VI  - 1
DP  - 1999
TI  - Comparison of protein structures reveals monophyletic origin of AdoMet-dependent methyltransferase family and mechanistic convergence rather than recent differentiation of N4-cytosine and N6-adenine DNA methylation.
PG  - 175-182
AB  - Phylogenetic analysis of the S-adenosyl-L-methionine-dependent methyltransferases was
      performed based on similarity of positions of main chain alpha-carbon atoms in published
      structures of members of this superfamily.  The evolutionary tree was inferred and the problem
      of mono/polyphyletic origin of DNA methyltransferases from the Rossmann-fold enzymes was
      solved, bridging two seemingly antithetical hypotheses.  The comparison of protein structures
      provides evidence for an evolutionary link between widely diverged subfamilies of RNA and DNA
      N6-adenine methyltransferases and argues against the close homology of N6-adenine and
      N4-cytosine methyltransferases, apparent from biochemical data and comparison of fragments of
      sequences.  Such evolutionary analysis of methyltransferases has never been published yet in
      the literature and will guide further phylogenetical studies based on both sequence and
      structure comparison.
AU  - Bujnicki JM
PT  - Journal Article
TA  - In Silico Biology
JT  - In Silico Biology
SO  - In Silico Biology 1999 1: 175-182.

PMID- 11914127
VI  - 2
DP  - 2002
TI  - Sequence permutations in the molecular evolution of DNA methyltransferases.
PG  - 3
AB  - BACKGROUND: DNA methyltransferases (MTases), unlike MTases acting on other substrates, exhibit
      sequence permutation. Based on the sequential order of the cofactor-binding subdomain, the
      catalytic subdomain, and the target recognition domain (TRD), several classes of permutants
      have been proposed. The majority of known DNA MTases fall into the alpha, beta, and gamma
      classes. There is only one member of the zeta class known and no members of the delta and
      epsilon classes have been identified to date. Two mechanisms of permutation have been
      proposed: one involving gene duplication and in-frame fusion, and the other involving inter-
      and intragenic shuffling of gene segments. RESULTS: Two novel cases of sequence permutation in
      DNA MTases implicated in restriction-modification systems have been identified, which suggest
      that members of the delta and zeta classes (M.MwoI and M.TvoORF1413P, respectively) evolved
      from beta-class MTases. This is the first identification of the delta-class MTase and the
      second known zeta-class MTase (the first zeta-class member among DNA:m4C and m6A-MTases).
      CONCLUSIONS: Fragmentation of a DNA MTase gene may result from attack of nucleases, for
      instance when the RM system invades a new cell. Its reassembly into a functional form, the
      order of motifs notwithstanding, may be strongly selected for, if the cognate ENase gene
      remains active and poses a threat to the host's chromosome. The "cut-and-paste" mechanism is
      proposed for beta-delta permutation, which is non-circular and involves relocation of one
      segment of a gene. The circular beta-zeta permutation may be explained both by gene
      duplication or shuffling of gene fragments. These two mechanisms are not mutually exclusive
      and probably both played a role in the evolution of permuted DNA MTases.
AU  - Bujnicki JM
PT  - Journal Article
TA  - BMC Evol. Biol.
JT  - BMC Evol. Biol.
SO  - BMC Evol. Biol. 2002 2: 3.

PMID- 14529527
VI  - 4
DP  - 2003
TI  - Crystallographic and bioinformatic studies on restriction endonucleases: Inference of evolutionary relationships in the 'midnight zone' of homology.
PG  - 327-337
AB  - Type II restriction endonucleases (ENases) cleave DNA with remarkable sequence specificity.
      Their discovery in 1970 and studies on molecular
      genetics and biochemistry carried out over the past four decades laid
      foundations for recombinant DNA techniques. Today, restriction enzymes are
      indispensable tools in molecular biology and molecular medicine and a
      paradigm for proteins that specifically interact with DNA as well as a
      challenging target for protein engineering. The
      sequence-structure-function relationships for these proteins are therefore
      of central interest in biotechnology. However, among numerous ENase
      sequences, only a few exhibit statistically significant similarity in
      pairwise comparisons, which was initially interpreted as evidence for the
      lack of common origin. Nevertheless, X-ray crystallographic studies of
      seemingly dissimilar type II ENases demonstrated that they share a common
      structural core and metal-binding/catalytic site, arguing for extreme
      divergence rather than independent evolution. A similar nuclease domain
      has been also identified in various enzymes implicated in DNA repair and
      recombination. Ironically, following the series of crystallographic
      studies suggesting homology of all type II ENases, bioinformatic studies
      provided evidence that some restriction enzymes are in fact diverged
      members of unrelated nuclease superfamilies: Nuc, HNH and GIY-YIG. Hence,
      the restriction enzymes as a whole, represent a group of functionally
      similar proteins, which evolved on multiple occasions and subsequently
      diverged into the "midnight zone" of homology, where common origins within
      particular groups can be inferred only from structure-guided comparisons.
      The structure-guided approaches used for this purpose include:
      identification of functionally important residues using superposition of
      atomic coordinates, alignment of sequence profiles enhanced by secondary
      structures, fold recognition, and homology modeling. This review covers
      recent results of comparative analyses of restriction enzymes from the
      four currently known superfamilies of nucleases with distinct folds, using
      crystallographic and bioinformatic methods, with the emphasis on
      theoretical predictions and their experimental validation by site-directed
      mutagenesis and biochemical analyses of the mutants.
AU  - Bujnicki JM
PT  - Journal Article
TA  - Curr. Protein Pept. Sci.
JT  - Curr. Protein Pept. Sci.
SO  - Curr. Protein Pept. Sci. 2003 4: 327-337.

PMID- 10828365
VI  - 27
DP  - 2000
TI  - Homology modelling of the DNA 5mC methyltransferase M.BssHII. Is permutation of functional subdomains common to all subfamilies of DNA methyltransferases?
PG  - 195-204
AB  - This work presents a full tertiary model of the M.BssHII methyltransferase (MTase) complexed
      with substrate DNA and cofactor
      S-adenosyl-L-methionine, built by homology modelling based on
      previously solved complete structures of DNA MTases M.HaeIII and
      M.HhaI. M.BssHII and the template proteins show high sequence
      similarity, which indicates that they are evolutionary related.
      However, they are topologically different: M.BssHII is a circularly
      permuted variant of template MTases (Xu et al. Nucleic Acids Res.
      1997,25:3991). The model developed in this work will be a good starting
      point and valuable help in designing mutagenesis experiments to better
      understand the biological function of methyltransferases and the
      process of domain swapping.
AU  - Bujnicki JM
PT  - Journal Article
TA  - Int. J. Biol. Macromol.
JT  - Int. J. Biol. Macromol.
SO  - Int. J. Biol. Macromol. 2000 27: 195-204.

PMID- 11996004
VI  - 48
DP  - 2001
TI  - Understanding the evolution of restriction-modification systems: Clues from sequence and structure comparisons.
PG  - 935-967
AB  - Restriction-modification (RM) systems comprise two opposing enzymatic activities: a
      restriction endonuclease, that targets specific DNA
      sequences and performs endonucleolytic cleavage, and a modification
      methyltransferase that renders these sequences resistant to cleavage.
      Studies on molecular genetics and biochemistry of RM systems have been
      carried out over the past four decades, laying foundations for modern
      molecular biology and providing important models for mechanisms of
      highly specific protein-DNA interactions. Although the number of known,
      relevant sequences 3D structures of RM proteins is growing steadily, we
      do not fully understand their functional diversities from an
      evolutionary perspective and we are not yet able to engineer new
      sequence specificities based on rational approaches. Recent findings on
      the evolution of RM systems and on their structures and mechanisms of
      action have led to a picture in which conserved modules with defined
      function are shared between different RM proteins and other enzymes
      involved in nucleic acid biochemistry. On the other hand, it has been
      realized that some of the modules have been replaced in the evolution
      by unrelated domains exerting similar function. The aim of this review
      is to give a survey on the recent progress in the field of structural
      phylogeny of RM enzymes with special emphasis on studies of
      sequence-structure-function relationships and emerging potential
      applications in biotechnology.
AU  - Bujnicki JM
PT  - Journal Article
TA  - Acta Biochim. Pol.
JT  - Acta Biochim. Pol.
SO  - Acta Biochim. Pol. 2001 48: 935-967.

PMID- 15121902
VI  - 32
DP  - 2004
TI  - Sequence-structure-function studies of tRNA:m5C methyltransferase Trm4p and its relationship to DNA:m5C and RNA:m5U methyltransferases.
PG  - 2453-2463
AB  - Three types of methyltransferases (MTases) generate 5-methylpyrimidine in nucleic acids,
      forming m5U in RNA, m5C in RNA and m5C in DNA. The DNA:m5C
      MTases have been extensively studied by crystallographic, biophysical,
      biochemical and computational methods. On the other hand, the
      sequence-structure-function relationships of RNA:m5C MTases remain
      obscure, as do the potential evolutionary relationships between the three
      types of 5-methylpyrimidine-generating enzymes. Sequence analyses and
      homology modeling of the yeast tRNA:m5C MTase Trm4p (also called Ncl1p)
      provided a structural and evolutionary platform for identification of
      catalytic residues and modeling of the architecture of the RNA:m5C MTase
      active site. The analysis led to the identification of two invariant
      residues that are important for Trm4p activity in addition to the
      conserved Cys residues in motif IV and motif VI that were previously found
      to be critical. The newly identified residues include a Lys residue in
      motif I and an Asp in motif IV. A conserved Gln found in motif X was found
      to be dispensable for MTase activity. Locations of essential residues in
      the model of Trm4p are in very good agreement with the X-ray structure of
      an RNA:m5C MTase homolog PH1374. Theoretical and experimental analyses
      revealed that RNA:m5C MTases share a number of features with either
      RNA:m5U MTases or DNA:m5C MTases, which suggested a tentative phylogenetic
      model of relationships between these three classes of 5-methylpyrimidine
      MTases. We infer that RNA:m5C MTases evolved from RNA:m5U MTases by
      acquiring an additional Cys residue in motif IV, which was adapted to
      function as the nucleophilic catalyst only later in DNA:m5C MTases,
      accompanied by loss of the original Cys from motif VI, transfer of a
      conserved carboxylate from motif IV to motif VI and sequence permutation.
AU  - Bujnicki JM
AU  - Feder M
AU  - Ayres CL
AU  - Redman KL
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2004 32: 2453-2463.

PMID- 12355263
VI  - 55
DP  - 2002
TI  - Structure prediction and phylogenetic analysis of a functionally diverse family of proteins homologous to the MT-A70 subunit of the  human mRNA:m6A methyltransferase.
PG  - 431-444
AB  - MT-A70 is the S-adenosylmethionine-binding subunit of human mRNA:m6A methyltransferase
      (MTase), an enzyme that sequence-specifically
      methylates adenines in pre-mRNAs. The physiological importance yet
      limited understanding of MT-A70 and its apparent lack of similarity to
      other known RNA MTases combined to make this protein an attractive
      target for bioinformatic analysis. The sequence of MT-A70 was subjected
      to extensive in silico analysis to identify orthologous and paralogous
      polypeptides. This analysis revealed that the MT-A70 family comprises
      four subfamilies with varying degrees of interrelatedness. One
      subfamily is a small group of bacterial DNA:m6A MTases. The other three
      subfamilies are paralogous eukaryotic lineages, two of which have not
      been associated with MTase activity but include proteins having
      substantial regulatory effects. Multiple sequence alignments and
      structure prediction for members of all four subfamilies indicated a
      high probability that a consensus MTase fold domain is present.
      Significantly, this consensus fold shows the permuted topology
      characteristic of the beta class of MTases, which to date has only been
      known to include DNA MTases.
AU  - Bujnicki JM
AU  - Feder M
AU  - Radlinska M
AU  - Blumenthal RM
PT  - Journal Article
TA  - J. Mol. Evol.
JT  - J. Mol. Evol.
SO  - J. Mol. Evol. 2002 55: 431-444.

PMID- 10467693
VI  - 48
DP  - 1999
TI  - Molecular phylogenetics of DNA 5mC-methyltransferases.
PG  - 19-30
AB  - We have identified a total of 88 members of the DNA-(cytosine-5) methyltransferase (5mC MTase)
      family whose sequences have been deposited in the databases. The results of a comparison of
      these sequences is presented in the form of an alignment-based phylogenetic tree and sequence
      logos for 10 conserved motifs. Phylogenetic analysis showed that members of the family
      aggregate into subfamilies which are usually consistent with their target specificity.
      However, it was also shown that similar target specificity does not necessarily imply close
      homology of the catalytic domain of MTases, which strongly supports the hypothesis that target
      recognition evolved independently of catalytic properties. This analysis also indicate that
      the 5mC MTase was present in the cenancestor (last common ancestor) of eubacteria,
      archaebacteria, and eukaryotes. The phylogeny of the 5mC MTases catalytic domain provides the
      basis for establishing the patterns of evolutionary change that characterize this family of
      proteins with conserved structural core and variable and mobile modules not directly involved
      in formation of the active site.
AU  - Bujnicki JM
AU  - Radlinska M
PT  - Journal Article
TA  - Acta Microbiol. Pol.
JT  - Acta Microbiol. Pol.
SO  - Acta Microbiol. Pol. 1999 48: 19-30.

PMID- 10536161
VI  - 27
DP  - 1999
TI  - Molecular evolution of DNA-(cytosine-N4) methyltransferases: evidence for their polyphyletic origin.
PG  - 4501-4509
AB  - DNA N4-cytosine methyltransferases (N4mC MTases) are a family of S -adenosyl-L-methionine
      (AdoMet)-dependent MTases. Members of this family were previously found to share nine
      conserved sequence motifs, but the evolutionary basis of these similarities has never been
      studied in detail. We performed phylogenetic analysis of 37 known and potential new family
      members from the multiple sequence alignment using distance matrix, parsimony and maximum
      likelihood approaches to infer the evolutionary relationship among the N4mC MTases and
      classify them into groups of orthologs. All the treeing algorithms employed as well as results
      of exhaustive sequence database searching support a scenario, in which the majority of N4mC
      MTases, except for M.BalI and M.BamHI, arose by divergence from a common ancestor.
      Interestingly, MTases M.BalI and M.BamHI apparently originated from N6-adenine MTases and
      represent the most recent addendum to the N4mC MTase family. In addition to the previously
      reported nine sequence motifs, two more conserved sequence patches were detected. Phylogenetic
      analysis also provided the evidence for massive horizontal transfer of MTase genes, presumably
      with the whole restriction-modification systems, between Bacteria and Archaea.
AU  - Bujnicki JM
AU  - Radlinska M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1999 27: 4501-4509.

PMID- 11720310
VI  - 50
DP  - 2001
TI  - Cloning and characterization of M.LmoA118I, a novel DNA:m4C methyltransferase from the Listeria  monocytogenes Phage A118, a close homolog of M.NgoMXV.
PG  - 155-160
AB  - A homolog of M.NgoMXV DNA:M4C methyltransferase has been identified among the open reading
      frames deduced from the genomic sequence of Listeria monocytogenes phage A118.  The gene
      coding for this putative protein has been cloned in Escherichia coli and its enzymatic
      activity in vivo in this host have been analyzed.  Remarkably, although M.NgoMXV and
      M.LmoA118I exhibit high sequence similarity (58% identical and 19% conservatively substituted
      residues), their target preferences differ: both proteins exhibit "relaxed" sequence
      specificity, but while M.LmoA118I more efficiently methylates GGCC sites, it seems to target
      only a subset of CCWGG sites methylated by M.NgoMXV.
AU  - Bujnicki JM
AU  - Radlinska M
PT  - Journal Article
TA  - Acta Microbiol. Pol.
JT  - Acta Microbiol. Pol.
SO  - Acta Microbiol. Pol. 2001 50: 155-160.

PMID- 10690633
VI  - 48
DP  - 1999
TI  - Is the HemK family of putative S-adenosylmethionine-dependent methyltransferases a "missing" zeta subfamily of adenine methyltransferases?  A hypothesis.
PG  - 247-249
AB  - Previous comparative studies revealed close similarity among various groups of
      S-adenosyl-L-methionine-dependent methyltransferases, indicating their common evolutionary
      origin.  We present evidence for a remarkable similarity between the sequence and predicted
      structure of HemK (a widespread family of putative proteins encoded in genomes from bacteria
      to humans) and the catalytic domain of the gamma-subfamily of adenine-specific DNA MTases
      (N6mA MTases).  We predict the structure and function of the putative catalytic domain of HemK
      proteins and speculate that the target-recognizing function may be conferred by the N-terminal
      variable region.
AU  - Bujnicki JM
AU  - Radlinska M
PT  - Journal Article
TA  - Life
JT  - Life
SO  - Life 1999 48: 247-249.

PMID- 10972843
VI  - 37
DP  - 2000
TI  - Atomic model of the 5-methylcytosine-specific restriction enzyme McrA reveals an atypical zinc finger and structural similarity to beta beta alpha-Me endonucleases.
PG  - 1280-1281
AB  - Using a novel FFAS algorithm for supersensitive sequence comparison and fold recognition, we
      have identified a domain in the 5-methylcytosine-specific restriction enzyme (ENase) McrA from
      Escherichia coli that is common to the beta beta alpha-Me superfamily of nucleases.  We
      carried out extensive threading of the McrA sequence onto the known protein structures and
      detected a high compatibility with conformation assumed by the DNase domain of colicins E7 and
      E9, although it displays no significant similarity to the sequences of these proteins.  The
      model presented reveals that McrA shares a putative zinc finger with homologous group II
      intron maturases and the more remotely related coliphage T4 endonuclease VII, despite the fact
      that this structure is absent from colicins.  This is the first robust structure prediction of
      an ENase ever performed.  It strongly suggests that ENases do not all share the same
      three-dimensional fold and, as a functional class of proteins, they should be regarded as
      products of convergent evolution.
AU  - Bujnicki JM
AU  - Radlinska M
AU  - Rychlewski L
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2000 37: 1280-1281.

PMID- 11996005
VI  - 48
DP  - 2001
TI  - Cloning of the Haemophilus influenzae Dam methyltransferase and analysis of its relationship to the Dam methyltransferase encoded by the HP1 phage.
PG  - 969-983
AB  - In this paper we report cloning and experimental characterization of the DNA adenine
      methyltransferase (dam) gene from Haemophilus
      influenzae and comparison of its product with the Dam protein from the
      lysogenic phage of H. influenzae, HP1. Molecular modeling of M.HinDam
      and M.HP1Dam was carried out, providing a framework for a comparative
      analysis of these enzymes and their close homologs in the structural
      context. Both proteins share the common fold and essential
      cofactor-binding and catalytic residues despite overall divergence.
      However, subtle but significant differences in the cofactor-binding
      pocket have been identified. Moreover, while M.HinDam seems to contact
      its target DNA sequence using a number of loops, most of them are
      missing from M.HP1Dam. Analysis of both MTases suggests that their
      catalytic activity was derived from a common ancestor, but similar
      sequence specificities arose by convergence.
AU  - Bujnicki JM
AU  - Radlinska M
AU  - Zaleski P
AU  - Piekarowicz A
PT  - Journal Article
TA  - Acta Biochim. Pol.
JT  - Acta Biochim. Pol.
SO  - Acta Biochim. Pol. 2001 48: 969-983.

PMID- 11739889
VI  - 14
DP  - 2001
TI  - Three-dimensional modeling of the I-TevI homing endonuclease catalytic domain, a GIY-YIG superfamily member, using NMR restraints and Monte Carlo dynamics.
PG  - 717-721
AB  - Using a recent version of the SICHO algorithm for in silico protein folding, we made a blind
      prediction of the tertiary structure of the N-terminal, independently folded, catalytic domain
      (CD) of the I-TevI homing endonuclease, a representative of the GIY-YIG superfamily of homing
      endonucleases. The secondary structure of the I-TevI CD has been determined using NMR
      spectroscopy, but computational sequence analysis failed to detect any protein of known
      tertiary structure related to the GIY-YIG nucleases (Kowalski et al., Nucleic Acids Res.,
      1999, 27, 2115-2125). To provide further insight into the structure-function relationships of
      all GIY-YIG superfamily members, including the recently described subfamily of type II
      restriction enzymes (Bujnicki et al., Trends Biochem. Sci., 2000, 26, 9-11), we incorporated
      the experimentally determined and predicted secondary and tertiary restraints in a reduced
      (side chain only) protein model, which was minimized by Monte Carlo dynamics and simulated
      annealing. The subsequently elaborated full atomic model of the I-TevI CD allows the available
      experimental data to be put into a structural context and suggests that the GIY-YIG domain may
      dimerize in order to bring together the conserved residues of the active site.
AU  - Bujnicki JM
AU  - Rotkiewicz P
AU  - Kolinski A
AU  - Rychlewski L
PT  - Journal Article
TA  - Protein Eng.
JT  - Protein Eng.
SO  - Protein Eng. 2001 14: 717-721.

PMID- 11324759
VI  - 22
DP  - 2001
TI  - The herpesvirus alkaline exonuclease belongs to the restriction endonuclease PD-(D/E)XK superfamily: Insight from molecular modeling and phylogenetic analysis.
PG  - 219-230
AB  - The PD-(D/E)XK superfamily of deoxyribonucleases (Enases) comprises restriction endonucleases,
      exonucleases and nicking enzymes, which share a common fold and the architecture of the active
      site.  Their extreme divergence generally hampers identification of novel members based solely
      on sequence comparisons.  Here we report a remote similarity between the phage lambda
      exonuclease (lambda-exo), branching out early in the evolutionary history of Enases, with the
      family of alkaline exonucleases encoded by various viruses infecting higher Eukaryota.  The
      predicted structural compatibility and the conservation of the functionally important residues
      between AE and Enases strongly suggest a distant evolutionary relationship between these
      proteins.  According to the results of extensive sequence database mining, sequence/structure
      threading and molecular modeling it is plausible that the AE proteins with lambda-exo and some
      other putative phage-encoded exonucleases form a distinct subfamily of PD-(D/E)XK Enases.  The
      phylogenetic history of this subfamily is inferred using sequence alignment and distance
      matrix methods.
AU  - Bujnicki JM
AU  - Rychlewski L
PT  - Journal Article
TA  - Virus Genes
JT  - Virus Genes
SO  - Virus Genes 2001 22: 219-230.

PMID- 11313145
VI  - 267
DP  - 2001
TI  - Identification of a PD-(D/E)XK-like domain with a novel configuration of the endonuclease active site in the methyl-directed restriction enzyme Mrr and its homologs.
PG  - 183-191
AB  - The Escherichia coli K-12 restriction enzyme Mrr recognizes and cleaves N6-methyladenine- and
      5-methylcytosine-containing DNA. Its amino acid sequence has been subjected to structure
      prediction and comparison with other sequences from publicly available sources. The results
      obtained suggest that Mrr and related putative endonucleases possess a cleavage domain typical
      for all the so far structurally characterized type II restriction enzymes, however with an
      unusual glutamine residue at the central position of the (D/E)-(D/E)XK hallmark of the active
      site. The 'missing' acidic side chain was instead found anchored in a different, unusual
      position, suggesting that Mrr represents a third topological variant of the endonuclease
      active site in addition to the two alternatives determined previously (Skirgaila et al., 1998.
      J. Mol. Biol. 279, 473-481). One of the newly identified putative endonucleases from the Mrr
      family is composed of two diverged cleavage domains, which possess both the 'typical' D-EXK
      and the 'Mrr-like' D-QXK variants of the active site. Among the Mrr homologs there are also
      proteins from yeast, in which restriction phenotype has not been observed, suggesting that the
      free-standing Eukaryotic PD-(D/E)XK superfamily members might be implicated in other cellular
      processes involving enzymatic DNA cleavage.
AU  - Bujnicki JM
AU  - Rychlewski L
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 2001 267: 183-191.

PMID- 11344334
VI  - 10
DP  - 2001
TI  - Unusual evolutionary history of the tRNA splicing endonuclease EndA: Relationship to the LAGLIDADG and PD-(D/E)XK deoxyribonucleases.
PG  - 656-660
AB  - The tRNA splicing endoribonuclease EndA from Methanococcus jannaschii is a homotetramer formed
      via heterologous interaction between the two pairs of homodimers. Each monomer consists of two
      alpha/beta domains, the N-terminal domain (NTD) and the C-terminal domain (CTD) containing the
      RNase A-like active site. Comparison of the EndA coordinates with the publicly available
      protein structure database revealed the similarity of both domains to site-specific
      deoxyribonucleases: the NTD to the LAGLIDADG family and the CTD to the PD-(D/E)XK family.
      Superposition of the NTD on the catalytic domain of LAGLIDADG homing endonucleases allowed a
      suggestion to be made about which amino acid residues of the tRNA splicing nuclease might
      participate in formation of a presumptive cryptic deoxyribonuclease active site. On the other
      hand, the CTD and PD-(D/E)XK endonucleases, represented by restriction enzymes and a phage
      lambda exonuclease, were shown to share extensive similarities of the structural framework, to
      which entirely different active sites might be attached in two alternative locations. These
      findings suggest that EndA evolved from a fusion protein with at least two distinct
      endonuclease activities: the ribonuclease, which made it an essential "antitoxin" for the
      cells whose RNA genes were interrupted by introns, and the deoxyribonuclease, which provided
      the means for homing-like mobility. The residues of the noncatalytic CTDs from the positions
      corresponding to the catalytic side chains in PD-(D/E)XK deoxyribonucleases map to the surface
      at the opposite side to the tRNA binding site, for which no function has been implicated. Many
      restriction enzymes from the PD-(D/E)XK superfamily might have the potential to maintain an
      additional active or binding site at the face opposite the deoxyribonuclease active site, a
      property that can be utilized in protein engineering.
AU  - Bujnicki JM
AU  - Rychlewski L
PT  - Journal Article
TA  - Protein Sci.
JT  - Protein Sci.
SO  - Protein Sci. 2001 10: 656-660.

PMID- 11165501
VI  - 26
DP  - 2001
TI  - Polyphyletic evolution of type II restriction enzymes revisited: two independent sources of second-hand folds revealed.
PG  - 9-11
AB  - Using algorithms for protein sequence analysis we predict that some of the canonical type II
      and type IIS restriction enzymes have an active site with a substantially different
      architecture and fold from the "typical" PD-(D/E)xK superfamily.  These results suggest that
      they are related to nucleases from the HNH and GIY-YIG superfamilies.
AU  - Bujnicki JM
AU  - Rychlewski L
AU  - Radlinska M
PT  - Journal Article
TA  - Trends Biochem. Sci.
JT  - Trends Biochem. Sci.
SO  - Trends Biochem. Sci. 2001 26: 9-11.

PMID- 16973745
VI  - 103
DP  - 2006
TI  - Genome reduction in Leptospira borgpetersenii reflects limited transmission potential.
PG  - 14560-14565
AB  - Leptospirosis is one of the most common zoonotic diseases in the world, resulting in high
      morbidity and mortality in humans and affecting global
      livestock production. Most infections are caused by either Leptospira
      borgpetersenii or Leptospira interrogans, bacteria that vary in their
      distribution in nature and rely on different modes of transmission. We
      report the complete genomic sequences of two strains of L. borgpetersenii
      serovar Hardjo that have distinct phenotypes and virulence. These two
      strains have nearly identical genetic content, with subtle frameshift and
      point mutations being a common form of genetic variation. Starkly limited
      regions of synteny are shared between the large chromosomes of L.
      borgpetersenii and L. interrogans, probably the result of frequent
      recombination events between insertion sequences. The L. borgpetersenii
      genome is approximately 700 kb smaller and has a lower coding density than
      L. interrogans, indicating it is decaying through a process of insertion
      sequence-mediated genome reduction. Loss of gene function is not random
      but is centered on impairment of environmental sensing and metabolite
      transport and utilization. These features distinguish L. borgpetersenii
      from L. interrogans, a species with minimal genetic decay and that
      survives extended passage in aquatic environments encountering a mammalian
      host. We conclude that L. borgpetersenii is evolving toward dependence on
      a strict host-to-host transmission cycle.
AU  - Bulach DM
AU  - Zuerner RL
AU  - Wilson P
AU  - Seemann T
AU  - McGrath A
AU  - Cullen PA
AU  - Davis J
AU  - Johnson M
AU  - Kuczek E
AU  - Alt DP
AU  - Peterson-Burch B
AU  - Coppel RL
AU  - Rood JI
AU  - Davies JK
AU  - Adler B
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2006 103: 14560-14565.

PMID- 
VI  - 279
DP  - 2012
TI  - Dam methylase accessibility as an instrument for analysis of mammalian chromatin structure.
PG  - 493
AB  - The study of regulatory mechanisms operating at the level of the chromatin fiber is one of the
      rapidly developing fields of modern molecular biology.  Changes in chromatin condensation
      state is one of the main regulatory mechanisms of cell functions, such as transcription,
      replication, DNA repair, and other processes. The lack of information on dynamic behavior of
      extended chromatin regions leads to a gap in our understanding of mechanisms of coordinated
      expression regulation of gene ensembles.  Chromatin structure analysis is in many cases based
      on the accessibility of chromatin DNA to modifying agents.  The main benefits are granted by
      in vivo detecting agents such as Dam methylase, for example.  For a 140 kb human genome locus,
      an analysis of the distribution of Dam methylase accessible sites, DNase I sensitive and
      resistant regions, and acetylated histone H3 molecules was performed and compared with
      transcriptional activity of the genes within the locus.  It was demonstrated that promoter
      regions of all highly and moderately transcribed genes are highly accessible to methylation by
      Dam methylase.  In contrast, promoters of non-transcribed genes showed a very low extent of
      Dam methylation.  Some highly Dam methylase accessible regions are present in the intergenic
      regions of the locus suggesting that the latter contain either unidentified non-coding
      transcripts or extended regulatory elements like locus control regions.
AU  - Bulanenkova S
AU  - Kotova E
AU  - Snezhkov E
AU  - Akopov S
AU  - Nikolaev L
AU  - Sverdlov E
PT  - Journal Article
TA  - FEBS J.
JT  - FEBS J.
SO  - FEBS J. 2012 279: 493.

PMID- 25035321
VI  - 2
DP  - 2014
TI  - Curtobacterium sp. Genome Sequencing Underlines Plant Growth Promotion-Related Traits.
PG  - e00592-14
AB  - Endophytic bacteria are microorganisms residing in plant tissues without causing  disease
      symptoms. Here, we provide the high-quality genome sequence of
      Curtobacterium sp. strain S6, isolated from grapevine plant. The genome assembly
      contains 2,759,404 bp in 13 contigs and 2,456 predicted genes.
AU  - Bulgari D
AU  - Minio A
AU  - Casati P
AU  - Quaglino F
AU  - Delledonne M
AU  - Bianco PA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00592-14.

PMID- 1104586
VI  - 124
DP  - 1975
TI  - Deoxyribonucleic acid modification by intermediate-type modification mutants of Escherichia coli K-12 and B.
PG  - 1395-1402
AB  - The modification of bacteriophages grown on r-m+- restriction and modification
      mutants of Escherichia coli K-12 or B appears to be related to the number of
      restriction-specific sites in the viral genome.  Bacteriophage fd and its
      mutant U1 fd, which carry two and one B-specific sites, respectively, are not
      modified in vivo by rB-mB+- mutant strains.  In vitro treatment of fd RF.B+-
      deoxyribonucleic acid (DNA) or U1 fd RF.B+- DNA by endo R.EcoB results in
      cleavage of the substrate DNA.  Lambda bacteriophge, after growth in r-m+-
      mutant host strains (k.K+- or k.B+-), is partially protected from in vivo
      degradation by wild-type homospecific strains.  Its efficiency of plating on
      these strains is approximately 10-2.  However, a hybrid Phi80-lambda phage
      which carries only one K-specific site (skk-1) is not modified by rK-mK+-
      strains.  Labeled DNAs from k.B+- and k.K+- phages were used as substrates for
      endo R.Eco B and endo R.Eco K nucleases.  Zonal centrifugation analysis of the
      products of the reactions indicate that rK-mK+- mutants do not protect lambda
      DNA from in vitro degradation by endo R.EcoK.  In contrast, rB-mB+- mutants
      appear to partially protect lambda DNA from attack by endo R.Eco B.
AU  - Bulkacz J
AU  - Roulland-Dussoix D
AU  - Boyer HW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1975 124: 1395-1402.

PMID- 17640084
VI  - 24
DP  - 2007
TI  - Expression and of murine DNA methyltransferases Dnmt1 and Dnmt3a in the yeast Saccharomyces cerevisiae.
PG  - 871-882
AB  - Murine DNA methyltransferases Dnmt1 and Dnmt3a were expressed in the yeast Saccharomyces
      cerevisiae. Adjustment to yeast preferences of the
      nucleotide sequences upstream and downstream of the translation
      initiation sites of both cDNAs was needed to obtain significant levels
      of the methyltransferases. Both proteins were correctly localized to
      the nucleus and their presence had no measurable influence on the
      functioning of yeast cells. Both Dnmt1 and Dnmt3a expressed in yeast
      cells were enzymatically active in vitro, and in vivo in the genomic
      DNA of the transgenic S. cerevisiae ca. 0.06% and 0.4%, respectively,
      of cytosines became methylated. This level of DNA methylation is about
      100- to 10-fold less than that observed in mammalian cells. The
      constructed system may be used to investigate the in vivo specificity
      of individual mammalian DNA methyltransferases and to search for
      additional factors needed to allow more efficient in vivo methylation
      of chromatincontained DNA and to study their mechanism of action.
AU  - Bulkowska U
AU  - Ishikawa T
AU  - Kurlandzka A
AU  - Trzcinska-Danielewicz J
AU  - Derlacz R
AU  - Fronk J
PT  - Journal Article
TA  - Yeast
JT  - Yeast
SO  - Yeast 2007 24: 871-882.

PMID- 20006993
VI  - 398
DP  - 2010
TI  - A tale of tails: Sialidase is key to success in a model of phage therapy against K1-capsulated Escherichia coli.
PG  - 79-86
AB  - Prior studies treating mice infected with Escherichia coli O18:K1:H7 observed that phages
      requiring the K1 capsule for infection (K1-dep) were superior to capsule-independent (K1-ind)
      phages. We show that three K1-ind phages all have low fitness when grown on cells in serum
      whereas fitnesses of four K1-dep phages were high. The difference is serum-specific, as
      fitnesses in broth overlapped. Sialidase activity was associated with all K1-dep virions
      tested but no K1-ind virions, a phenotype supported by sequence analyses. Adding endosialidase
      to cells infected with K1-ind phage increased fitness in serum by enhancing productive
      infection after adsorption. We propose that virion sialidase activity is the primary
      determinant of high fitness on cells grown in serum, and thus in a mammalian host. Although
      the benefit of sialidase is specific to K1-capsulated bacteria, this study may provide a
      scientific rationale for selecting phages for therapeutic use in many systemic infections.
AU  - Bull JJ
AU  - Vimr ER
AU  - Molineux IJ
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 2010 398: 79-86.

PMID- 8493118
VI  - 21
DP  - 1993
TI  - Sensitivity of HincII to CpG methylation.
PG  - 2021
AB  - Restriction fragment length polymorphism (RFLP) analysis in human genetics can be confounded
      by the sensitivity of restriction enzymes to cytosine methylation that occurs at many
      cytosine-guanine (CpG) dinucleotides. Previous reports provided conflicting information on the
      sensitivity of HincII to C methylation (1-3). We identified alleles at a chromosome 4p16 locus
      that were inherited in a non-Mendelian manner due to inhibition of HincII cleavage by CpG
      methylation. We confirmed that cleavage by HincII, whose recognition sequence is
      5'GTPyPuAC3', is inhibited by the presence of 5-methyl-cytosine at the terminal base of its
      recognition site.
AU  - Bull LN
AU  - Hewitt JE
AU  - Cox DR
AU  - Myers RM
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 2021.

PMID- Not carried by PubMed...
VI  - 94
DP  - 1994
TI  - Cloning of the SA system for the restriction and modification of DNA from Salmonella typhimurium into phage lambda.
PG  - 224
AB  - The Salmonella typhimurium SA system of genes for the restriction and modification of DNA (R-M
      system), the first such system recognized in this organism, has been cloned. Selection for the
      SA genes has been difficult since all SA E. coli/Salmonella hybrids derived years ago failed
      to express either SA restriction or modification when tested at this time. However, such a
      hybrid between E. coli and Salmonella typhi, designated LB4019, was found still to express SA
      restriction and modification. Several libraries consisting of partial SauIIIA digests of
      genomic S. typhimurium DNA ligated to phageEMBL4 and amplified on the non-restriction,
      non-modifying strain of E. coli NM477, were plated out on a lawn of LB4019. All plaques which
      were produced on LB4019 were picked, plated out on NM477 and the efficiencies of plating (eop)
      on LB4019 determined. From one library, a number of plaques plated out at eop of 1. In
      addition, plaques that gave significantly higher eop than unmodified phageEMBL on LB4019 (1 x
      10-3) were isolated. The phages fell into four groups relative to their eop on LB4019. Group 1
      clones consistently plated with an eop of 1.0, group 2 an eop of about 0.5, group 3 an eop of
      about 0.2 and group 4 an eop of about 0.02. The cloning of these apparently partially
      SA-modified clones in addition to the completely SA-modified clones was unexpected and is
      unique to this system. Restriction analysis indicates that the sizes of the fragments cloned
      in the four groups are similar. A molecular and genetic analysis of representative clones is
      in progress.
AU  - Bullas LR
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1994 94: 224.

PMID- 1102934
VI  - 139
DP  - 1975
TI  - DNA restriction and modification systems in Salmonella.  III.  SP, a Salmonella potsdam system allelic to the SB system in Salmonella typhimurium.
PG  - 177-188
AB  - By screening 42 Salmonella strains with P3, a temperate bacteriophage with an
      unusally wide host range, five new DNA restriction and modification systems
      (R-M systems) were identified in five different serotypes in Kauffmann-White
      group C.  One of these systems, SP, in a Pl-sensitive strain of S. potsdam, was
      analyzed genetically by Pl transduction methods in which SP was transferred
      into S. typhimurium and E. coli/S. typhimurium hybrids.  It was found that the
      genes of the SP system were allelic and functionally homologous to the genes of
      the SB system of S. typhimurium.
AU  - Bullas LR
AU  - Colson C
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1975 139: 177-188.

PMID- 6243623
VI  - 141
DP  - 1980
TI  - Deoxyribonucleic acid restriction and modification systems in Salmonella:  chromosomally located systems of different serotypes.
PG  - 275-292
AB  - With the use of four different phages, Salmonella strains representing 85 different serotypes
      were examined to determine their restriction-modification phenotype.  They fell into one of
      three groups on this basis:  group 1, those which lacked the common LT system; group 2, those
      in which only the LT system could be recognized; and group 3, those which possessed the LT
      system and at least one other system shown with some serotypes to be closely linked to serB.
      The specificity of the serB-linked restricted-modification system was unique for each
      serotype, but different strains of the same serotype expressed the same specificity.  Two of
      the systems were shown to behave in genetic crosses as functional alleles of the S.
      typhimurium SB system.  It is possible that these serB-linked restriction-modification systems
      constitute a large multiallelic series of genes extending throughout the Salmonella genus and
      Escherichia coli.  We suggest that the division of the Salmonella into the three
      restriction-modification groups may be significant in defining a biological grouping of the
      different serotypes within the genus which may ultimately be useful in describing the
      Salmonella species.  From the genetic relatedness between the genes of some of the Salmonella
      restriction-modification systems with those of the E. coli systems, we deduce that the
      restriction endonucleases produced by the Salmonella serB-linked systems are of type I.
      Determination of the nucleotide sequences of the recognition sites of the restriction
      endonucleases of selected Salmonella systems should further our understanding of specificity
      with these enzymes.
AU  - Bullas LR
AU  - Colson C
AU  - Neufeld B
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1980 141: 275-292.

PMID- 784901
VI  - 95
DP  - 1976
TI  - DNA restriction and modification systems in Salmonella. SQ, a new system derived by recombination between the SB system of Salmonella typhimurium and the SP system of Salmonella potsdam.
PG  - 166-172
AB  - As a result of PI-mediated cotransduction with serB from Salmonella potsdam to
      the Escherichia coli/Salmonella typhimurium hybrid 4617, one recombinant,
      L4004, was isolated which had a restriction-modification (R-M) system different
      from the SB and SP systems of its parents, and was designated SQ.  The genes of
      complementation experiments to be functionally related to those of the K system
      of E. coli.  Evidence that the SQ system in L4004 arose as the result of a
      recombination event within the hsdS genes of SB and SP is discussed.
AU  - Bullas LR
AU  - Colson C
AU  - van Pel A
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1976 95: 166-172.

PMID- Not carried by PubMed...
VI  - 96
DP  - 1996
TI  - Cryptic genes for the restriction and modification of DNA in Salmonella typhi and Salmonella gallinarum.
PG  - 258
AB  - Salmonella typhi and Salmonella gallinarum fail to express the StyLTI and StyII
      genes for the restriction and modification of DNA which are expressed by other Salmonella
      serotypes.  S. typhi transformed by either pRUCL531 with the S. typhimurium StyLTI restriction
      and modification genes or pXC1 with the StyLTIII modification gene, has a reduced ability to
      propagate within human Mac6 macrophage-like cells.  In P1 transductions from S. typhi to an E.
      coli/Salmonella StyLTIII+ recipient, the "lack of expression" of StyLTIII is co-transduced
      with
      serB to 17% of recombinants.  These observations prompted us to investigate whether S. typhi
      and
      S. gallinarum might possess cryptic StyLTI or StyLTIII systems of genes.  We isolated a 1.8kb
      DNA sequence which included the end of the modification gene and the beginning of the
      restriction
      gene of StyLTI, and a 2.6 kb sequence which included parts of the StyLTIII modification and
      specificity genes, and used them as probes in Southern hybridizations to genomic DNA of S.
      typhi
      and S. gallinarum.  The DNA of both serotypes hybridized strongly to both probes.  Thus, S.
      typhi and S. gallinarum both possess cryptic StyLTI and StyLTIII R-M genes.  Since pRUCL531-
      and pXC1-transformed S. typhi have reduced growth parameters in Mac6, it is likely that the S.
      typhi cryptic R-M genes are concerned with the ability of this serotype to propagate within
      human
      macrophages.
AU  - Bullas LR
AU  - Harding G
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1996 96: 258.

PMID- Not carried by PubMed...
VI  - 69
DP  - 1969
TI  - Host-induced modification of Salmonella potsdam bacteriophage P3 by growth in E. coli.
PG  - 157
AB  - The temperate Salmonella potsdam bacteriophage P3 lyses E. coli K and E. coli C
      with high efficiency.  Growth of P3 in either E. coli K (producing phage P3.K)
      or E. coli C (phage P3-C) modified the phage so that its original Salmonella
      host is now insensitive, but the phage retains the ability to grow on either
      strain of E. coli.  P3, therefore, propagated on S. potsdam (phage P3.S) has an
      unrestricted host range, while P3.K and P3.C are restricted.  Rare P3.K and
      P3.C phages (10-6) will grow on the original Salmonella host producing
      unrestricted phages identical to P3.S.  E. coli is readily lysogenized by P3.S,
      in which it is also inducible by UV light.  Phages grown either on Salmonella
      or E. coli appear to be serologically identical, although comparison of the
      rates of neutralization suggest that slight structural changes of the phage
      particle may have occurred in E. coli, rendering P3.K and P3.C more susceptible
      than P3.S to neutralization by antiserum produced against P3.S.  These and
      other results indicate that a host-induced modification of the Salmonella phage
      P3.S occurs by growth in E. coli K or E. coli C.  Similar results have been
      obtained for the related Salmonella phage P9a.
AU  - Bullas LR
AU  - Nutter RL
PT  - Journal Article
TA  - Bacteriol. Proc.
JT  - Bacteriol. Proc.
SO  - Bacteriol. Proc. 1969 69: 157.

PMID- Not carried by PubMed...
VI  - 87
DP  - 1987
TI  - Evidence of additional families of TypeI hsd genes concerned with the restriction and modification of DNA in Salmonella.
PG  - 154
AB  - Hybridization and complementation experiments have shown that serB-linked genes
      for the restriction and modification of DNA in E. coli and Salmonella comprise
      at least two "families".  A third "family" consists of genes on a plasmid.  We
      have prepared DNA probes from the cloned genes of the two chromosomal
      families--hsdSB and hsdSP from the first family and hsdA from the second
      family.  In addition we prepared a probe from the hsdSEN genes (from S.
      enteritidis) which we had earlier cloned in phage lambda and subcloned into
      pUC18 and whose family relationship was unknown.  With each of these probes
      radioactively labelled with 32P and Southern gel transfer, we have performed a
      series of hybridization experiments with the DNA from six E. coli/Salmonella
      hybrids possessing the serB-linked hsd genes from a Salmonella serotype.
      Neither of the two probes from the first family nor the A probe of the second
      family hybridized with the DNA from any of the hybrids.  The SEN probe
      hybridized with DNA from only two of the six hybrids.  Thus additional families
      of the Type1 hsd genes must exist in Salmonella.
AU  - Bullas LR
AU  - Rajadas PT
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1987 87: 154.

PMID- 6352690
VI  - 156
DP  - 1983
TI  - Salmonella typhimurium LT2 strains which are r- m+ for all three chromosomally located systems of DNA restriction and modification.
PG  - 471-474
AB  - We describe the derivation of two strains of Salmonella typhimurium LT2 which are r- m+ for
      all three of the known chromosomal genes for the restriction and modification of DNA, hsdLT,
      hsdSA, and hsdSB; the strains were designated LB5000 and LB5010.  LB5000 is a smooth
      derivative sensitive to phage P22; LB5010 is a galE strain sensitive to phage P1.
AU  - Bullas LR
AU  - Ryu J-I
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1983 156: 471-474.

PMID- 8688087
VI  - 273
DP  - 1996
TI  - Complete genome sequence of the Methanogenic archaeon, Methanococcus jannaschii.
PG  - 1058-1073
AB  - The complete 1.66-megabase pair genome sequence of an autotrophic archaeon, Methanococcus
      jannaschii, and its 58- and 16-kilobase pair extrachromosomal elements have been determined by
      whole-genome random sequencing.  A total of 1738 predicted protein coding genes were
      identified; however, only a minority of those (38 percent) could be assigned a putative
      cellular role with high confidence.  Although the majority of genes related to energy
      production, cell division, and metabolism in M. jannaschii are most similar to those found in
      Bacteria, most of the genes involved in transcription, translation, and replication in M.
      jannaschii are more similar to those found in Eukaryotes.
AU  - Bult CJ et al
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1996 273: 1058-1073.

PMID- 6271275
VI  - 1
DP  - 1981
TI  - The use of the restriction endonuclease DdeI for mapping related DNAs.
PG  - 223-228
AB  - Restriction endonuclease mapping of BK virus strain GS using DdeI has allowed
      us to correct and extend the previously published map.
AU  - Buluwela L
AU  - Malcolm ADB
AU  - Coleman DV
AU  - Gardner SD
PT  - Journal Article
TA  - Biosci. Rep.
JT  - Biosci. Rep.
SO  - Biosci. Rep. 1981 1: 223-228.

PMID- 10385322
VI  - 17
DP  - 1999
TI  - Quantifying DNA-protein interactions by double-stranded DNA arrays.
PG  - 573-577
AB  - We have created double-stranded oligonucleotide arrays to perform highly parallel
      investigations of DNA-protein interactions.  Arrays of single-stranded DNA oligonucleotides,
      synthesized by a combination of photolithography and solid-state chemistry, have been used for
      a variety of applications, including large-scale mRNA expression monitoring, genotyping, and
      sequence-variation analysis. We converted a single-stranded to a double-stranded array by
      synthesizing a constant sequence at every position on an array and then annealing and
      enzymatically extending a complementary primer. The efficiency of second-strand synthesis was
      demonstrated by incorporation of fluorescently labeled dNTPs (2'-deoxyribonucleoside
      5'-triphosphates) and by terminal transferase addition of a fluorescently labeled ddNTP. The
      accuracy of second-strand synthesis was demonstrated by digestion of the arrayed
      double-stranded DNA (dsDNA) on the array with sequence-specific restriction enzymes. We showed
      dam methylation of dsDNA arrays by digestion with DpnI, which cleaves when its recognition
      site is methylated. This digestion demonstrated that the dsDNA arrays can be further
      biochemically modified and that the DNA is accessible for interaction with DNA-binding
      proteins. This dsDNA array approach could be extended to explore the spectrum of
      sequence-specific protein binding sites in genomes.
AU  - Bulyk ML
AU  - Gentalen E
AU  - Lockhart DJ
AU  - Church GM
PT  - Journal Article
TA  - Nat. Biotechnol.
JT  - Nat. Biotechnol.
SO  - Nat. Biotechnol. 1999 17: 573-577.

PMID- 24903877
VI  - 2
DP  - 2014
TI  - Genome Sequences of Seven Mycoplasma hyosynoviae Strains Isolated from the Joint  Tissue of Infected Swine (Sus scrofa).
PG  - e00552-14
AB  - Mycoplasma hyosynoviae is a Gram-negative bacterium that can cause debilitating arthritis in
      swine. Currently, there are no M. hyosynoviae genome sequences in
      the GenBank database, which makes it impossible to understand its pathogenesis,
      nutrition, or colonization characteristics, or to devise an effective strategy
      for its control. Here, we report the genome sequences of seven strains of M.
      hyosynoviae. Within each genome, several virulence factors were identified that
      may prove important in the pathogenesis of M. hyosynoviae-mediated arthritis and
      serve as potential virulence markers that may be critical in vaccine development.
AU  - Bumgardner E
AU  - Bey RF
AU  - Kittichotirat W
AU  - Bumgarner RE
AU  - Lawrence PK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00552-14.

PMID- 6091689
VI  - 9
DP  - 1983
TI  - BbvII:  A new site-specific endonuclease from Bacillus brevis 80.
PG  - 1578-1580
AB  - BbvII, a new site-specific endonuclease, has been isolated from Bacillus brevis
      80 by gel-filtration and chromatography on heparin-Sepharose.  The endonuclease
      recognizes a non-symmetrical sequence 5'-GTGTTC-3'/3'-CAGAAG-5' in
      double-stranded DNA and cleaves DNA in both strands outside the recognition
      sequence.
AU  - Bunina ZF
AU  - Kramarov VM
AU  - Mazanov AL
AU  - Pachkunov DM
AU  - Smolianinov VV
AU  - Matvienko NN
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1983 9: 1578-1580.

PMID- Not included in PubMed...
VI  - 10
DP  - 1984
TI  - XphI - A new sequence-specific endonuclease from Xanthomonas phaseoli.
PG  - 1333-1335
AB  - A sequence-specific endonuclease XphI was purified by chromatography on
      Ultrogel AcA-44 and phosphocellulose.  The final preparation is free of
      admixtures of non-specific nucleases.  It is demonstrated that endonuclease
      XphI recognized 5'-CTGCAG-3' sequence like endonuclease PstI.  According to gel
      filtration data, the molecular mass of endonuclease is 47000+2000.  DNA
      methylated by methylases which block its hydrolysis by endonuclease PstI, is
      also resistant to the cleavage by endonuclease XphI.
AU  - Bunina ZF
AU  - Kramarov VM
AU  - Smolyaninov VV
AU  - Tolstova LA
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1984 10: 1333-1335.

PMID- Not carried by PubMed...
VI  - 4
DP  - 1988
TI  - Dynamics of site-specific endonuclease accumulation in Caryophanon latum L. cells.
PG  - 621-623
AB  - None
AU  - Bunina ZF
AU  - Smolyaninov VV
PT  - Journal Article
TA  - Biotekhnologiya
JT  - Biotekhnologiya
SO  - Biotekhnologiya 1988 4: 621-623.

PMID- 12626704
VI  - 31
DP  - 2003
TI  - Crystal structure of the Escherichia coli dcm very-short-patch DNA repair endonuclease bound to its reaction product-site in a DNA superhelix.
PG  - 1633-1639
AB  - Very-short-patch repair (Vsr) enzymes occur in a variety of bacteria, where they initiate
      nucleotide excision repair of G:T mismatches arising
      by deamination of 5-methyl-cytosines in specific regulatory sequences. We
      have now determined the structure of the archetypal dcm-Vsr endonuclease
      from Escherichia coli bound to the cleaved authentic
      hemi-deaminated/hemi-methylated dcm sequence 5'-C-OH-3'
      5'-p-T-p-A-p-G-p-G-3'/3'-G-p-G-p-T-p(Me5)C-p-C formed by self-assembly of
      a 12mer oligonucleotide into a continuous nicked DNA superhelix. The
      structure reveals the presence of a Hoogsteen base pair within the
      deaminated recognition sequence and the substantial distortions of the DNA
      that accompany Vsr binding to product sites.
AU  - Bunting KA
AU  - Roe SM
AU  - Headley A
AU  - Brown T
AU  - Savva R
AU  - Pearl LH
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2003 31: 1633-1639.

PMID- 27932654
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Antarctic Methanogen Enriched from Dry Valley Permafrost.
PG  - e01362-16
AB  - A genomic reconstruction belonging to the genus Methanosarcina was assembled from metagenomic
      data from a methane-producing enrichment of Antarctic permafrost.
      This is the first methanogen genome reported from permafrost of the Dry Valleys
      and can help shed light on future climate-affected methane dynamics.
AU  - Buongiorno J
AU  - Bird JT
AU  - Krivushin K
AU  - Oshurkova V
AU  - Shcherbakova V
AU  - Rivkina EM
AU  - Lloyd KG
AU  - Vishnivetskaya TA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01362-16.

PMID- 25540336
VI  - 2
DP  - 2014
TI  - Whole-Genome Sequencing Identifies an Atypical Listeria monocytogenes Strain Isolated from Pet Foods.
PG  - e01243-14
AB  - Four Listeria isolates, including an atypical strain, were isolated from various  pet foods
      and sequenced. We report here the draft genome sequences of these
      isolates and a comparative genomic analysis with a closely related human clinical
      isolate. An analysis of the atypical strain identified a frameshift mutation in
      the prfA gene.
AU  - Burall LS
AU  - Grim C
AU  - Gopinath G
AU  - Laksanalamai P
AU  - Datta AR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01243-14.

PMID- 1691886
VI  - 176
DP  - 1990
TI  - 5-Azacytidine-resistant mutants of Chlorella Virus IL-3A.
PG  - 311-315
AB  - Many dsDNA-containing viruses which infect the unicellular, eukaryotic
      Chlorella-like green alga strain NC64A encode for DNA methyltransferases and
      DNA site-specific (restriction) endonucleases.  We have hypothesized that these
      endonucleases help degrade host DNA permitting deoxynucleotides to recycle into
      virus DNA.  This hypothesis was tested by isolating deletion mutants of
      Chlorella virus IL-3A lacking functional genes for the cytosine
      methyltransferase M.CviJI and the cognate site-specific endonuclease CviJI.
      The growth and burst sizes of the mutants and parent virus were identical.
      Also host nuclear and chloroplast DNAs disappeared from infected cells at the
      same rates.  Thus M.CviJI and CviJI activities are not required for IL-3A
      replication and CviJI activity is not essential for host DNA degradation.
AU  - Burbank DE
AU  - Shields SL
AU  - Schuster AM
AU  - Van Etten JL
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1990 176: 311-315.

PMID- 6279877
VI  - 153
DP  - 1981
TI  - Complexes formed between the restriction endonuclease EcoK and heteroduplex DNA.
PG  - 425-440
AB  - The complexes between the Escherichia coli K restriction endonuclease and
      heteroduplex DNA (one strand methylated and one unmethylated) have been
      characterized and shown to have different properties from those formed with
      unmodified DNA.  The nature of the heteroduplex complex appears to commit the
      enzyme to its methylase mode.
AU  - Burckhardt J
AU  - Weisemann J
AU  - Hamilton DL
AU  - Yuan R
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1981 153: 425-440.

PMID- 6260781
VI  - 256
DP  - 1981
TI  - Characterization of the DNA methylase activity of the restriction enzyme from Escherichia coli K.
PG  - 4024-4032
AB  - The restriction endonuclease from Escherichia coli K is a multifunctional
      protein which efficiently methylates heteroduplex DNA (one strand modified and
      one strand unmodified) in the presence of S-adenosylmethionine (AdoMet), ATP,
      and Mg2+.  The methylase activity is catalytic, and seems to modify different
      heteroduplex host specificity sites for E. coli K with equal efficiency.
AU  - Burckhardt J
AU  - Weisemann J
AU  - Yuan R
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1981 256: 4024-4032.

PMID- 23819038
VI  - 5
DP  - 2013
TI  - Peculiarities of the Regulation of Gene Expression in the Ecl18kI RestrictionModification System.
PG  - 70-80
AB  - Transcription regulation in bacterial restriction-modification (R-M) systems is an important
      process, which provides coordinated expression levels of tandem enzymes, DNA methyltransferase
      (MTase) and restriction endonuclease (RE) protecting cells against penetration of alien DNA.
      The present study focuses on (cytosine-5)-DNA methyltransferase Ecl18kI (M. Ecl18kI), which is
      almost identical to DNA methyltransferase SsoII (M. SsoII) in terms of its structure and
      properties. Each of these enzymes inhibits expression of the intrinsic gene and activates
      expression of the corresponding RE gene via binding to the regulatory site in the promoter
      region of these genes. In the present work, complex formation of M. Ecl18kI and RNA polymerase
      from Escherichia.oli with the promoter regions of the MTase and RE genes is studied. The
      mechanism of regulation of gene expression in the Ecl18kI R-M system is thoroughly
      investigated. M. Ecl18kI and RNA polymerase are shown to compete for binding to the promoter
      region. However, no direct contacts between M. Ecl18kI and RNA polymerase are detected. The
      properties of M. Ecl18kI and M. SsoII mutants are studied. Amino acid substitutions in the
      N-terminal region of M. Ecl18kI, which performs the regulatory function, are shown to
      influence not only M. Ecl18kI capability to interact with the regulatory site and to act as a
      transcription factor, but also its ability to bind and methylate the substrate DNA. The loss
      of methylation activity does not prevent MTase from performing its regulatory function and
      even increases its affinity to the regulatory site. However, the presence of the domain
      responsible for methylation in the M. Ecl18kI molecule is necessary for M. Ecl18kI to perform
      its regulatory function.
AU  - Burenina OY
AU  - Fedotova EA
AU  - Ryazanova AY
AU  - Protsenko AS
AU  - Zakharova MV
AU  - Karyagina AS
AU  - Solonin AS
AU  - Oretskaya TS
AU  - Kubareva EA
PT  - Journal Article
TA  - Acta Naturae
JT  - Acta Naturae
SO  - Acta Naturae 2013 5: 70-80.

PMID- 6304467
VI  - 189
DP  - 1983
TI  - Restriction endonuclease BglI as a tool for in vitro reconstruction and recombination of plasmid and bacteriophage genomes.
PG  - 269-274
AB  - The restriction endonuclease BglI produces different individual fragment ends from different
      cut sites.  This property has allowed us to reconstruct efficiently several commonly used
      plasmid and bacteriophage genomes and a number of recombinant plasmids containing up to seven
      BglI restriction sites from their constituent BglI fragments.  It is demonstrated that in
      vitro reconstitution from BglI fragments can be used to create, in a simple way, recombinant
      DNA molecules by recombining in vitro BglI fragments from different mutated or otherwise
      related genomes.  Further applications of the method are discussed.
AU  - Burger KJ
AU  - Schinzel R
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1983 189: 269-274.

PMID- 16983344
VI  - 26
DP  - 2007
TI  - Viral oncoproteins target the DNA methyltransferases.
PG  - 1650-1655
AB  - Small DNA tumour viruses have evolved a number of mechanisms to drive nondividing cells into S
      phase. Virally encoded oncoproteins such as
      adenovirus E1A and human papillomavirus (HPV) E7 can bind an array of
      cellular proteins to override proliferation arrest. The DNA
      methyltransferase Dnmt1 is the major mammalian enzyme responsible for
      maintaining CpG methylation patterns in the cell following replication.
      One of the hallmarks of tumour cells is disrupted DNA methylation
      patterns, highlighting the importance of the proper regulation of DNA
      methyltransferases in normal cell proliferation. Here, we show that
      adenovirus 5 E1A and HPV-16 E7 associate in vitro and in vivo with the
      DNA methyltransferase Dnmt1. Consistent with this interaction, we find
      that E1A and E7 can purify DNA methyltransferase activity from nuclear
      extracts. These associations are direct and mediated by the extreme
      N-terminus of E1A and the CR3 zinc-finger domain of E7. Furthermore, we
      find that a point mutant at leucine 20 of E1A, a residue known to be
      critical for its transformation functions, is unable to bind Dnmt1 and
      DNA methyltransferase activity. Finally, both E1A and E7 can stimulate
      the methyltransferase activity of Dnmt1 in vitro. Our results provide
      the first indication that viral oncoproteins bind and regulate Dnmt1
      enzymatic activity. These observations open up the possibility that
      this association may be used to control cellular proliferation pathways
      and suggest a new mechanism by which small DNA tumour viruses can steer
      cells through the cell cycle.
AU  - Burgers WA
AU  - Blanchon L
AU  - Pradhan S
AU  - de Launoit Y
AU  - Kouzarides T
AU  - Fuks F
PT  - Journal Article
TA  - Oncogene
JT  - Oncogene
SO  - Oncogene 2007 26: 1650-1655.

PMID- 26472822
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Three Strains of Geobacillus stearothermophilus Isolated from a Milk Powder Manufacturing Plant.
PG  - e00939-15
AB  - Three strains of Geobacillus stearothermophilus (designated A1, P3, and D1) were  isolated
      from a New Zealand milk powder manufacturing plant. Here, we describe their draft genome
      sequences. This information provided the first genomic insights into the nature of G.
      stearothermophilus strains present in the milk powder manufacturing environment.
AU  - Burgess SA
AU  - Cox MP
AU  - Flint SH
AU  - Lindsay D
AU  - Biggs PJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00939-15.

PMID- 25745004
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of the Urethral Catheter Isolate Myroides sp. A21.
PG  - e00068-15
AB  - Myroides sp. A21, isolated from a urethral catheterized patient without symptoms  of a urinary
      tract infection in Germany, proved to be extensively drug resistant.
      Here, we report the 4.16-Mb complete genome sequence of strain A21, carrying
      unusual pathogenicity islands and explaining the features of multidrug
      resistance.
AU  - Burghartz M
AU  - Bunk B
AU  - Sproer C
AU  - Voget S
AU  - Daniel R
AU  - Overmann J
AU  - Jahn M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00068-15.

PMID- 24503991
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Polyextremophilic Halorubrum sp. Strain AJ67, Isolated from Hyperarsenic Lakes in the Argentinian Puna.
PG  - e01096-13
AB  - Halorubrum sp. strain AJ67, an extreme halophilic UV-resistant archaeon, was isolated from
      Laguna Antofalla in the Argentinian Puna. The draft genome sequence
      suggests the presence of potent enzyme candidates that are essential for survival
      under multiple environmental extreme conditions, such as high UV radiation,
      elevated salinity, and the presence of critical arsenic concentrations.
AU  - Burguener GF
AU  - Maldonado MJ
AU  - Revale S
AU  - Fernandez DoPD
AU  - Rascovan N
AU  - Vazquez M
AU  - Farias ME
AU  - Marti MA
AU  - Turjanski AG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01096-13.

PMID- 1387206
VI  - 20
DP  - 1992
TI  - Evidence for a previously undetected CpG methyl-directed restriction system in E.coli.
PG  - 4368
AB  - 
AU  - Burkhart JG
AU  - Burkhart BA
AU  - Sampson K
AU  - Malling HV
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 4368.

PMID- 
VI  - 81
DP  - 2002
TI  - Function of the porphyromonas gingivalis DNA adenine methylase in the expression of virulence.
PG  - A-497
AB  - Objectives: DNA adenine methylases (dam) modify specific sequences of DNA and thus regulate
      the expression of certain genes in many species of bacteria.  Therefore, the dam gene is a
      prime target for the development of broad-spectrum antibiotics and vaccines.  Our lab has
      previously identified pgiM, a Porphyromonas gingivalis 381 (P. gingivalis) dam gene that
      restores wild-type function to an Escherichia coli dam- mutant.  Recently, it was shown that
      the dam gene of Salmonella typhimurium (S. typhimurium) regulates the expression of virulence
      genes activated by the global regulator, PhoP.  dam-, avirulent strains of S. typhimurium
      showed complete restoration of virulence when complemented with the S. typhimurium dam gene.
      We hypothesized that pgiM may play a similar role in the regulation of virulence in P.
      gingivalis.  Methods: To test this theory, we constructed the dam complementation plasmid,
      pDC1. pDC1 is a derivative of pWKS30, a modified version of pBluescriptIIks, and contains a
      1.1 kb region of P. gingivalis DNA harboring pgiM.  Subsequently, we transformed the non-polar
      dam- mutant S. typhimurium MT2188D232 with pDC1.  Transformed cells were plated onto Luria
      Bertani agar plates containing 50 ug/ml of ampicillin.  Analysis of plasmid preps performed on
      five of the resulting clones confirmed the presence of pDC1.  Next, the complemented S.
      typhimurium mutant clones were plated onto Luria Bertani agar plates containing 0.6 mg/ml of
      2-aminopurine.  In addition, we used a 5' truncated form of pgiM in a single crossover
      through homologous recombination, to construct a P. gingivalis dam- mutant.  Results: The
      complemented clones grew on 2-aminopurine, indicating a restoration of the dam gene adenine
      methylase in P. gingivalis irulence.  Conclusion: This data demonstrates that the P. ginivalis
      dam gene can functionally complement the S. typhimurium dam gene.
AU  - Burks JN
AU  - Wujick CT
AU  - Marshall LM
AU  - Kozarov EV
AU  - Progulske-Fox A
PT  - Journal Article
TA  - J. Dent. Res.
JT  - J. Dent. Res.
SO  - J. Dent. Res. 2002 81: A-497.

PMID- 7610040
VI  - 23
DP  - 1995
TI  - Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes.
PG  - 2105-2119
AB  - The 338.5 kb of the Escherichia coli genome described here together with previously described
      segments bring the total of contiguous finished sequence of this genome to >1 Mb.  Of 319 open
      reading frames found in this 338.5 kb segment, 147 (46%) are potential new genes.  The
      positions of several genes which had been previously located here by mapping or partial
      sequencing have been confirmed.  Several ORFs have functions suggested by similarities to
      other characterized genes but cannot be assigned with certainty.  Fifteen of the ORFs of
      unknown function had been previously sequenced.  Eight transfer RNAs are encoded in the region
      and there are two grey holes in which no features were found.  The attachment site for phage
      P4 and three insertion sequences were located.  The region was also analyzed for chi sites,
      bend sites, REP elements and other repeats.  A computer search identified potential promoters
      and tentative transcription units were assigned.  The occurrence of the rare tetramer CTAG was
      analyzed in 1.6 Mb of contiguous E. coli sequence.  Hypotheses addressing the rarity and
      distribution of CTAG are discussed.
AU  - Burland V
AU  - Plunkett G III
AU  - Sofia HJ
AU  - Daniels DL
AU  - Blattner FR
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1995 23: 2105-2119.

PMID- 9722640
VI  - 26
DP  - 1998
TI  - The complete DNA sequence and analysis of the large virulence plasmid of Escherichia coli O157:H7.
PG  - 4196-4204
AB  - The complete DNA sequence of pO157, the large virulence plasmid of EHEC strain O157:H7 EDL
      933, is presented.  The 92 kb F-like plasmid is composed of segments of putative virulence
      genes in a framework of replication and maintenance regions, with seven insertion sequence
      elements, located mostly at the boundaries of the virulence segments.  One hundred open
      reading frames were identified, of which 19 were previously sequenced potential virulence
      genes.  Forty-two ORFs were sufficiently similar to known proteins for suggested functions to
      be assigned, and 22 had no convincing similarity with any known proteins.  Of the newly
      identified genes, an unusually large ORF of 3169 amino acids has a putative cytotoxin active
      site shared with the large clostridial toxin (LCT) family and proteins such as ToxA and B of
      Clostridium difficile.  A conserved motif was detected that links the large ORF and the LCT
      proteins with the OCH1 family of glycosyltransferases.  In the complete sequence, the mosaic
      form can be observed at the levels of base composition, codon usage and gene organization.
      Insights were obtained from patterns of DNA composition as well as the pathogenic and
      'housekeeping' gene segments.  Evolutionary trees built from shared plasmid maintenance
      genes show that even these genes have heterogeneous origins.
AU  - Burland V
AU  - Shao Y
AU  - Perna NT
AU  - Plunkett G
AU  - Sofia HJ
AU  - Blattner FR
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1998 26: 4196-4204.

PMID- 22461544
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Halophilic Archaeon Halococcus hamelinensis.
PG  - 2100-2101
AB  - Halococcus hamelinensis was isolated from hypersaline stromatolites in Shark Bay, Australia.
      Here we report the genome sequence (3,133,046 bp) of H. hamelinensis,
      which provides insights into the ecology, evolution, and adaptation of this novel
      microorganism.
AU  - Burns BP
AU  - Gudhka RK
AU  - Neilan BA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2100-2101.

PMID- 11282600
VI  - 67
DP  - 2001
TI  - Characterization of a novel type II restriction-modification system, Sth368I, encoded by the integrative element ICESt1 of Streptococcus thermophilus CNRZ368.
PG  - 1522-1528
AB  - A novel type II restriction and modification (R-M) system, Sth368I, which confers resistance
      to ST84, was found in Streptococcus thermophilus CNRZ368 but not in the very closely related
      strain A054. Partial sequencing of the integrative conjugative element ICESt1, carried by S.
      thermophilus CNRZ368 but not by A054, revealed a divergent cluster of two genes, sth368IR and
      sth368IM. The protein sequence encoded by sth368IR is related to the type II endonucleases
      R.LlaKR2I and R.Sau3AI, which recognize and cleave the sequence 5'-GATC-3'. The protein
      sequence encoded by sth368IM is very similar to numerous type II 5-methylcytosine
      methyltransferases, including M.LlaKR2I and M.Sau3AI. Cell extracts of CNRZ368 but not A054
      were found to cleave at the GATC site. Furthermore, the C residue of the sequence 5'-GATC-3'
      was found to be methylated in CNRZ368 but not in A054. Cloning and integration of a copy of
      sth368IR and sth368IM in the A054 chromosome confers on this strain phenotypes similar to
      those of CNRZ368, i.e., phage resistance, endonuclease activity of cell extracts, and
      methylation of the sequence 5'-GATC-3'. Disruption of sth368IR removes resistance and
      restriction activity. We conclude that ICESt1 encodes an R-M system, Sth368I, which recognizes
      the sequence 5'-GATC-3' and is related to the Sau3AI and LlaKR2I restriction systems.
AU  - Burrus V
AU  - Bontemps C
AU  - Decaris B
AU  - Guedon G
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2001 67: 1522-1528.

PMID- 16598018
VI  - 72
DP  - 2006
TI  - SXT-Related Integrating Conjugative Element in New World Vibrio cholerae.
PG  - 3054-3057
AB  - SXT-related integrating conjugative elements (ICEs) became prevalent in
      Asian Vibrio cholerae populations after V. cholerae O139 emerged. Here, we
      describe an SXT-related ICE, ICEVchMex1, in a Mexican environmental V.
      cholerae isolate. Identification of ICEVchMex1 represents the first
      description of an SXT-related ICE in the Western Hemisphere. The
      significant differences between the SXT and ICEVchMex1 genomes suggest
      that these ICEs have evolved independently.
AU  - Burrus V
AU  - Quezada-Calvillo R
AU  - Marrero J
AU  - Waldor MK
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2006 72: 3054-3057.

PMID- 26752266
VI  - 48
DP  - 2016
TI  - Genomic analysis of 38 Legionella species identifies large and diverse effector repertoires.
PG  - 167-175
AB  - Infection by the human pathogen Legionella pneumophila relies on the translocation of
      approximately 300 virulence proteins, termed effectors, which
      manipulate host cell processes. However, almost no information exists regarding
      effectors in other Legionella pathogens. Here we sequenced, assembled and
      characterized the genomes of 38 Legionella species and predicted their effector
      repertoires using a previously validated machine learning approach. This analysis
      identified 5,885 predicted effectors. The effector repertoires of different
      Legionella species were found to be largely non-overlapping, and only seven core
      effectors were shared by all species studied. Species-specific effectors had
      atypically low GC content, suggesting exogenous acquisition, possibly from the
      natural protozoan hosts of these species. Furthermore, we detected numerous new
      conserved effector domains and discovered new domain combinations, which allowed
      the inference of as yet undescribed effector functions. The effector collection
      and network of domain architectures described here can serve as a roadmap for
      future studies of effector function and evolution.
AU  - Burstein D
AU  - Amaro F
AU  - Zusman T
AU  - Lifshitz Z
AU  - Cohen O
AU  - Gilbert JA
AU  - Pupko T
AU  - Shuman HA
AU  - Segal G
PT  - Journal Article
TA  - Nat. Genet.
JT  - Nat. Genet.
SO  - Nat. Genet. 2016 48: 167-175.

PMID- 15531154
VI  - 14
DP  - 2004
TI  - Homing endonuclease genes: the rise and fall and rise again of a selfish element.
PG  - 609-615
AB  - Homing endonuclease genes (HEGs) are selfish genetic elements that spread by first cleaving
      chromosomes that do not contain them and then getting copied across to the broken chromosome
      as a byproduct of the repair process. The success of this strategy will depend on the
      opportunities for homing - in other words, the frequency with which HEG(+) and HEG(-)
      chromosomes come into contact - which varies widely among host taxa. HEGs are also unusual in
      that the selection pressure for endonuclease function disappears if they become fixed in a
      population, which makes them susceptible to degeneration and imposes a need for regular
      horizontal transmission between species. HEGs will be selected to reduce the harm done to the
      host organism, and this is expected to influence the evolution of their sequence specificity
      and maturase functions. HEGs may also be domesticated by their hosts, and are currently being
      put to human uses.
AU  - Burt A
AU  - Koufopanou V
PT  - Journal Article
TA  - Curr. Opin. Genet. Dev.
JT  - Curr. Opin. Genet. Dev.
SO  - Curr. Opin. Genet. Dev. 2004 14: 609-615.

PMID- 25723923
VI  - 22
DP  - 2015
TI  - Radiation damage to nucleoprotein complexes in macromolecular crystallography.
PG  - 213-224
AB  - Significant progress has been made in macromolecular crystallography over recent  years in
      both the understanding and mitigation of X-ray induced radiation damage
      when collecting diffraction data from crystalline proteins. In contrast, despite
      the large field that is productively engaged in the study of radiation chemistry
      of nucleic acids, particularly of DNA, there are currently very few X-ray
      crystallographic studies on radiation damage mechanisms in nucleic acids.
      Quantitative comparison of damage to protein and DNA crystals separately is
      challenging, but many of the issues are circumvented by studying pre-formed
      biological nucleoprotein complexes where direct comparison of each component can
      be made under the same controlled conditions. Here a model protein-DNA complex
      C.Esp1396I is employed to investigate specific damage mechanisms for protein and
      DNA in a biologically relevant complex over a large dose range (2.07-44.63 MGy).
      In order to allow a quantitative analysis of radiation damage sites from a
      complex series of macromolecular diffraction data, a computational method has
      been developed that is generally applicable to the field. Typical specific damage
      was observed for both the protein on particular amino acids and for the DNA on,
      for example, the cleavage of base-sugar N1-C and sugar-phosphate C-O bonds.
      Strikingly the DNA component was determined to be far more resistant to specific
      damage than the protein for the investigated dose range. At low doses the protein
      was observed to be susceptible to radiation damage while the DNA was far more
      resistant, damage only being observed at significantly higher doses.
AU  - Bury C
AU  - Garman EF
AU  - Ginn HM
AU  - Ravelli RB
AU  - Carmichael I
AU  - Kneale G
AU  - McGeehan JE
PT  - Journal Article
TA  - J. Synchrotron. Radiat.
JT  - J. Synchrotron. Radiat.
SO  - J. Synchrotron. Radiat. 2015 22: 213-224.

PMID- 15707929
VI  - 338
DP  - 2005
TI  - The use of prokaryotic DNA methyltransferases as experimental and analytical tools in modern biology.
PG  - 1-11
AB  - Prokaryotic DNA methyltransferases (MTases) are used as experimental and research tools in
      molecular biology and molecular genetics due to
      their ability to recognize and transfer methyl groups to target bases
      in specific DNA sequences. As a practical tool, prokaryotic DNA MTases
      can be used in recombinant DNA technology for in vitro alteration and
      enhancing of cleavage specificity of restriction endonucleases. The
      ability of prokaryotic DNA MTases to methylate cytosine residues in
      specific sequences, which are also methylated in eukaryotic DNA, makes
      it possible to use them as analytical reagent for determination of the
      site-specific level of methylation in eukaryotic DNA. In vivo DNA
      methylation by prokaryotic DNA MTases is used in different techniques
      for probing chromatin structure and protein-DNA interactions.
      Additional prospects are opened by development of the methods of DNA
      methylation targeted to predetermined DNA sequences by fusion of DNA
      MTases to DNA binding proteins. This review will discuss the
      application of prokaryotic DNA MTases of Type II in the methods and
      approaches mentioned above.
AU  - Buryanov Y
AU  - Shevchuk T
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 2005 338: 1-11.

PMID- 2467142
VI  - 13D
DP  - 1989
TI  - The purification and characterization of BstNI modification methylase.
PG  - 211
AB  - We have isolated and purified the BstNI modification methylase (M.BstNI) from
      Bacillus stearothermophilus.  This enzyme catalyses the transfer of methyl
      groups from AdoMet to CC(A/T)GG DNA sequences yielding N4-methylcytosine.  This
      modification renders the DNA resistant to cleavage by both BstNI and EcoRII
      restriction endonucleases.  At the same time M.BstNI is able to modify the DNA
      previously methylated by EcoRII methylase while the DNA methylated by M.BstNI
      is resistant to EcoRII methylation.  This property of two methylases can be
      used for analysis of the 5-methylcytosine presence in plant DNA in the
      CC(A/T)GG sequence.  We have partially purified M.BstNI by DEAE-cellulose,
      phosphocellulose and hydroxylapatite column chromatography.  The enzyme has a
      molecular weight of 60 kD as determined by gel-filtration and
      SDS-polyacrylamide gel electrophoresis.  E. coli clones were isolated from
      libraries of B. stearothermophilus DNA fragments in pUC19 by selecting for
      self-modified molecules that were resistant to BstNI endonuclease digestion.
AU  - Buryanov YI
AU  - Baryshev MM
AU  - Kosykh VG
AU  - Bayev AA
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1989 13D: 211.

PMID- 348497
VI  - 88
DP  - 1978
TI  - Site specificity and chromatographic properties of E. coli K12 and EcoRII DNA-cytosine methylases.
PG  - 251-254
AB  - It has been shown that DNA methylation in vitro by DNA-cytosine methylase from E. coli K12
      provides phage lambda DNA with complete resistance against EcoRII restriction endonuclease.
      E. coli C DNA-cytosine methylase and E. coli MRE 600 DNA-cytosine methylase II also provide
      lambda DNA with resistance against RII restriction in transfection experiments.  It is likely
      that all these DNA-cytosine methylases can display the same or overlapping site specificity as
      EcoRII DNA methylase.  For E. coli MRE 600 DNA-cytosine methylase II and E. coli C
      DNA-cytosine methylation in vivo the major targets in DNA are the dinucleotide C-m5C and
      trinucleotide C-m5C-T (m5C:5-methylcytosine).  These pyrimidine fragments of DNA are identical
      to pyrimidine sequences of the DNA site modified by EcoRII DNA methylase:
      5'...C-m5C-A-G-G...3'  3'...G-G-T-m5C-C...5' However, the pattern of DNA modification in
      vitro by E. coli K12 DNA-cytosine methylase and RII DNA methylase and the only major target
      sequences C-m5C-T for these two enzymes do not correspond to the in vivo methylation pattern
      of E. coli K12 DNA and to the mode of RII DNA methylase action.  The aim of this communication
      is the additional analysis of DNA sequences methylated in vitro by RII and E. coli K12
      DNA-cytosine methylases.  The results reported here show that E. coli K12 DNA-cytosine
      methylase and RII DNA methylase display the same site specificity which is identical to that
      of E. coli C and E. coli MRE 600 DNA-cytosine methylases.  Our data on chromatographic
      behavior of RII DNA methylase on phosphocellulose differ from those in (1).
AU  - Buryanov YI
AU  - Bogdarina IG
AU  - Bayev AA
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1978 88: 251-254.

PMID- 795622
VI  - 230
DP  - 1976
TI  - DNA-cytosine methylation in Escherichia coli MRE 600 cells.
PG  - 976-978
AB  - 
AU  - Buryanov YI
AU  - Bogdarina IG
AU  - Vagabova LM
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1976 230: 976-978.

PMID- 338273
VI  - 237
DP  - 1977
TI  - Isolation of DNA-cytosine methyltransferases from E. coli B (RII), E. coli K12 and E. coli K12 (RII).  Analysis of nucleotide sequences anlayzed in vitro.
PG  - 465-468
AB  - 
AU  - Buryanov YI
AU  - Bogdarina IT
AU  - Baev AA
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1977 237: 465-468.

PMID- 6357295
VI  - 48
DP  - 1983
TI  - On the ability of E. coli DNA methylases to modify denatured DNA's.
PG  - 1752-1754
AB  - Adenine and cytosine DNA methylases from different strains of E. coli are able to methylate
      denaturated and single-stranded DNA's.
AU  - Buryanov YI
AU  - Kholodkov OA
AU  - Bogdarina IG
AU  - Neserenko VF
AU  - Zakharchenko VN
AU  - Chernov AP
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1983 48: 1752-1754.

PMID- 773618
VI  - 227
DP  - 1976
TI  - Specificity of different fractions of DNA-cytosine-methylase from Escherichia coli MRE 600.
PG  - 228-231
AB  - 
AU  - Buryanov YI
AU  - Nesterenko VF
AU  - Dyacheniko GP
AU  - Korunskii OF
AU  - Skryabin GK
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1976 227: 228-231.

PMID- 7011757
VI  - 257
DP  - 1981
TI  - Different molecular structure of DNA methylases EcoRII and Eco MRE600 dcmII.
PG  - 495-497
AB  - The cells of most strains of Escherichia coli contain DNA methylases that exhibit site
      specificity of the methylase EcoRII. DNA methylases of the EcoRII type provide the host
      chromosome with complete protection against the restriction endonuclease EcoRII and the
      rapidly amplified DNAs of phages and plasmids with partial protection against this
      endonuclease. In contrast to the plasmid nature of the enzymes of modification and restriction
      of EcoRII, DNA methylases of the EcoRII type are determined by a chromosomal gene of E. coli,
      and there is no corresponding restriction endonuclease in E. coli cells.
AU  - Buryanov YI
AU  - Nesterenko VF
AU  - Kosykh VG
AU  - Baev AA
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1981 257: 495-497.

PMID- 773620
VI  - 227
DP  - 1976
TI  - The presence of two DNA-cytosine methylases in cells of Escherichia coli MRE600.
PG  - 1472-1475
AB  - None
AU  - Buryanov YI
AU  - Nesterenko VF
AU  - Vagabova LM
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1976 227: 1472-1475.

PMID- 16097936
VI  - 70
DP  - 2005
TI  - DNA methyltransferases and structural-functional specificity of eukaryotic DNA modification.
PG  - 730-742
AB  - Properties of the main families of mammalian, plant, and fungal DNA methyltransferases are
      considered. Structural-functional specificity of
      eukaryotic genome sequences methylated by DNA methyltransferases is
      characterized. The total methylation of cytosine in DNA sequences is
      described, as well as its relation with RNA interference. Mechanisms of
      regulation of expression and modulation of DNA methyltransferase
      activity in the eukaryotic cell are discussed.
AU  - Buryanov YI
AU  - Shevchuk TV
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2005 70: 730-742.

PMID- 7607509
VI  - 157
DP  - 1995
TI  - Effect of the M.EcoRII methyltransferase-encoding gene on the phenotype of Nicotiana tabacum transgenic cells.
PG  - 283-287
AB  - The EcoRII DNA methyltransferase (M.EcoRII; MTase) modifies a cytosine in the DNA sequence
      CCWGG which contains a CNG methylation motif characteristic of plant DNA.  The gene (ecoRIIM)
      encoding this MTase has been cloned into the T-DNA of the wild-type Agrobacterium Ti-plasmid
      pTiC58 downstream from the plant expression nopaline synthase-encoding gene promoter.
      Nicotiana tabacum cells have been transformed with Agrobacterium tumefaciens harboring this
      recombinant Ti-plasmid.  The primary transformed tabacco tissue line has given rise to novel
      stable lines which are morphologically distinctive.  Southern hybridization analysis of all
      transformed tissue lines has shown the presence, in each of them, of ecoRIIM.  The tissue
      studied differed in morphology in callus culture, dependence on phytohormones and the ability
      to synthesize nopaline.
AU  - Buryanov YI
AU  - Zakharchenko NS
AU  - Shevchuk TV
AU  - Bogdarina IG
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 283-287.

PMID- 7028433
VI  - 259
DP  - 1981
TI  - Isolation, purification and properties of adenine DNA methylase Eco dam.
PG  - 1492-1495
AB  - 
AU  - Buryanov YI
AU  - Zakharenko VN
AU  - Baev AA
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1981 259: 1492-1495.

PMID- 3074020
VI  - 74
DP  - 1988
TI  - Interaction of the Eco Dam methyltransferase with synthetic oligodeoxyribonucleotides.
PG  - 67-69
AB  - Meeting Abstract
AU  - Buryanov YI
AU  - Zinovev VV
AU  - Gorbunov YA
AU  - Tuzikov FV
AU  - Rechkunova NI
AU  - Malygin EG
AU  - Bayev AA
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 67-69.

PMID- 6368265
VI  - 168
DP  - 1984
TI  - Does the DNA methylase Eco dam pair nucleotide sequences to form site-specific duplexes?
PG  - 166-168
AB  - The Eco dam methylase is active on denatured DNA and single-stranded synthetic
      oligonucleotides containing GATC sites.  The results suggest that on interaction with
      single-stranded oligonucleotides the Eco dam methylase is able to form a duplex structure
      within the GATC site, and that this duplex site is a substrate for enzyme.
AU  - Buryanov YI
AU  - Zinoviev VV
AU  - Vienozhinskis MT
AU  - Malygin EG
AU  - Nesterenko VF
AU  - Popov SG
AU  - Gorbunov YA
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1984 168: 166-168.

PMID- 29773616
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Riemerella anatipestifer Isolate 17CS0503.
PG  - e00274-18
AB  - Riemerella anatipestifer is a Gram-negative bacterium belonging to the family
      Flavobacteriaceae It is primarily associated with acute septicemia in younger
      birds. The R. anatipestifer isolate 17CS0503 described here was isolated from a
      Peking duck (Anas platyrhynchos domesticus) in Hannover, Germany, in 1999.
AU  - Busch A
AU  - Ryll M
AU  - Immel A
AU  - Kornell S
AU  - Krause-Kyora B
AU  - Tomaso H
AU  - Hotzel H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00274-18.

PMID- 28336603
VI  - 5
DP  - 2017
TI  - High-Quality Draft Genome Sequence of Francisella tularensis subsp. holarctica Strain 08T0073 Isolated from a Wild European Hare.
PG  - e01577-16
AB  - Here, we report a high-quality draft genome sequence of Francisella tularensis subsp.
      holarctica strain 08T0073, isolated from the cadaver of a wild European
      hare (Lepus europaeus) found near Helmstedt, Lower Saxony, Germany, in 2007. In
      Germany, infected hares are a major source of tularemia in humans.
AU  - Busch A
AU  - Thomas P
AU  - Myrtennas K
AU  - Forsman M
AU  - Braune S
AU  - Runge M
AU  - Tomaso H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01577-16.

PMID- 29496832
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Streptomyces lavendulae subsp. lavendulae CCM 3239 (Formerly 'Streptomyces aureofaciens CCM 3239'), a Producer of the Angucycline-Type Antibiotic Auricin.
PG  - e00103-18
AB  - Streptomyces lavendulae subsp. lavendulae CCM 3239 produces the angucycline antibiotic auricin
      and was thought to be the type strain of Streptomyces
      aureofaciens We report the complete genome sequence of this strain, which
      consists of a linear chromosome and the linear plasmid pSA3239, and demonstrate
      it to be S. lavendulae subsp. lavendulae.
AU  - Busche T
AU  - Novakova R
AU  - Al'Dilaimi A
AU  - Homerova D
AU  - Feckova L
AU  - Rezuchova B
AU  - Mingyar E
AU  - Csolleiova D
AU  - Bekeova C
AU  - Winkler A
AU  - Sevcikova B
AU  - Kalinowski J
AU  - Kormanec J
AU  - Ruckert C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00103-18.

PMID- 24179119
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Pseudomonas azotifigens Strain DSM 17556T (6H33bT), a Nitrogen Fixer Strain Isolated from a Compost Pile.
PG  - e00893-13
AB  - Pseudomonas azotifigens strain 6H33b(T) is a nitrogen fixer isolated from a hyperthermal
      compost pile in 2005 by Hatayama and collaborators. Here we report
      the draft genome, which has an estimated size of 5.0 Mb, exhibits an average G+C
      content of 66.73%, and is predicted to encode 4,536 protein-coding genes and 100
      RNA genes.
AU  - Busquets A et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00893-13.

PMID- 22965097
VI  - 194
DP  - 2012
TI  - Genome Sequence of Pseudomonas stutzeri Strain JM300 (DSM 10701), a Soil Isolate  and Model Organism for Natural Transformation.
PG  - 5477-5478
AB  - Pseudomonas stutzeri strain JM300 (DSM 10701) is a denitrifying soil isolate and  a model
      organism for natural transformation in bacteria. Here we report the first
      complete genome sequence of JM300, the reference strain of genomovar 8 for the
      species.
AU  - Busquets A
AU  - Pena A
AU  - Gomila M
AU  - Bosch R
AU  - Nogales B
AU  - Garcia-Valdes E
AU  - Lalucat J
AU  - Bennasar A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5477-5478.

PMID- 23929478
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Pseudomonas stutzeri Strain B1SMN1, a Nitrogen-Fixing and Naphthalene-Degrading Strain Isolated from Wastewater.
PG  - e00584-13
AB  - Pseudomonas stutzeri strain B1SMN1 is a naphthalene-degrading and simultaneously
      nitrogen-fixing strain isolated from a wastewater sample taken at a lagooning
      treatment plant in Menorca (Balearic Islands, Spain). Here we report the draft
      genome sequence of P. stutzeri B1SMN1. It is composed of a chromosome of an
      estimated size of 5.2 Mb and two plasmids of 44,324 bp and 56,118 bp.
AU  - Busquets A
AU  - Pena A
AU  - Gomila M
AU  - Mayol J
AU  - Bosch R
AU  - Nogales B
AU  - Garcia-Valdes E
AU  - Bennasar A
AU  - Lalucat J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00584-13.

PMID- 6190135
VI  - 11
DP  - 1983
TI  - The sequence GGCmCGG is resistant to MspI cleavage.
PG  - 3559-3569
AB  - MspI essentially fails to cut the sequence GGCmCGG at enzyme concentrations
      which give total digestion of CCGG, CmCGG and GGCCGG sites.  This result
      explains why certain sites in mammalian DNA are resistant to both MspI and HhaI
      and shows that this results from an idiosyncracy of MspI rather than a novel
      form of DNA methylation at this site in mammalian cells.
AU  - Busslinger M
AU  - deBoer E
AU  - Wright S
AU  - Grosveld FG
AU  - Flavell RA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1983 11: 3559-3569.

PMID- 28302777
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of Three Rhizobium gallicum Symbionts Associated with Common Bean (Phaseolus vulgaris).
PG  - e00030-17
AB  - The whole-genome sequences of three strains of Rhizobium gallicum reported here support the
      concept that the distinct nodulation host ranges displayed by the
      symbiovars gallicum and phaseoli can be largely explained by different symbiotic
      plasmids.
AU  - Bustos P
AU  - Santamaria RI
AU  - Perez-Carrascal OM
AU  - Acosta JL
AU  - Lozano L
AU  - Juarez S
AU  - Martinez-Flores I
AU  - Martinez-Romero E
AU  - Cevallos MA
AU  - Romero D
AU  - Davila G
AU  - Vinuesa P
AU  - Miranda F
AU  - Ormeno E
AU  - Gonzalez V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00030-17.

PMID- 3000450
VI  - 826
DP  - 1985
TI  - A new restriction endonuclease Eco31I recognizing a non-palindromic sequence.
PG  - 208-212
AB  - A restriction endonuclease with a novel site-specificity has been isolated from the
      Escherichia coli strain RFL31.  The nucleotide sequences around a single Eco311 cut on pBR322
      DNA and two cuts of lambda DNA have been compared.  A common 5'GAGACC/3'CTCTGG sequence
      occurs near each cleavage site.  Precise mapping of the cleavages in both DNA strands places
      the cuts five nucleotides to the left of the upper sequence and one nucleotide to the left of
      the lower sequence.  This enabled us to deduce the following recognition and cleavage
      specificity of Eco31I:
      5' GGTCTCN/
      3' CCAGAGN NNNN/.
AU  - Butkus V
AU  - Bitinaite J
AU  - Kersulyte D
AU  - Janulaitis A
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1985 826: 208-212.

PMID- 3004510
VI  - 11
DP  - 1985
TI  - Determination of substrate specificity of restriction endonuclease Eco78I.
PG  - 1572-1573
AB  - The recognition sequence and cleavage point of restriction endonuclease Eco78I
      have been determined at 5'-GGCG^CC-.  There are several known enzymes
      recognizing the same sequence, although the prototype NarI and isoschizomers
      NdaI and NunII cleave the substrate to produce 5'-protruding ends, whereas
      cleavage with isoschizomer BbeI results in 3'-protruding ends.  Therefore,
      restrictase Eco78I, generating flush ends, may be regarded as an enzyme with
      new specificity among the restriction endonucleases recognizing the
      5'-GGCGCC-sequence.
AU  - Butkus V
AU  - Kazlauskiene R
AU  - Gilvonauskaite R
AU  - Petrusyte M
AU  - Janulaitis A
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1985 11: 1572-1573.

PMID- 2994011
VI  - 13
DP  - 1985
TI  - Investigation of restriction-modification enzymes from M. varians RFL19 with a new type of specificity toward modification of substrate.
PG  - 5727-5746
AB  - The characterization of MvaI restriction-modification enzymes, isolated from Micrococcus
      varians RFL19, is reported. Both enzymes recognize the 5'CC^(A/T)GG nucleotide sequence. The
      endonuclease cleaves the sequence at the position indicated by the arrow, whereas the
      methylase modifies the internal cytosine, yielding N4-methylcytosine. This type of
      modification protects the substrate from R.MvaI cleavage. 5-methylcytosine in the same
      position of the recognition sequence does not protect the substrate from R.MvaI cleavage.
      R.MvaI proved to be the first example of a restriction endonuclease differentiating the
      position of the methyl group in the heterocyclic ring of cytosine, located in the same site of
      the recognition sequence. M.MvaI modifies DNA dcm+ in vitro yielding N4, 5-dimethylcytosine.
      N4-methylcytosine cannot be differentiated from cytosine using the Maxam-Gilbert DNA
      sequencing procedure.
AU  - Butkus V
AU  - Klimasauskas S
AU  - Kersulyte D
AU  - Vaitkevicius D
AU  - Lebionka A
AU  - Janulaitis A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1985 13: 5727-5746.

PMID- 
VI  - 6
DP  - 1987
TI  - The effects of N4- and C5-methylation of cytosine on DNA physical properties and restriction endonuclease action.
PG  - 119-127
AB  - Not long ago a new type of methylase, generating N4-methylcytosine (4mC) in DNA
      was isolated in our laboratory from Bacillus centrosporus (Janulaitis et al.,
      1983).  At present a number of the 4mC type methylases are isolated (Janulaitis
      et al., 1984; Butkus et al., 1985,1987) and a wide spread of N4-methylcytosine
      in DNA of thermophilic and mesophilic bacteria is well documented (Ehrlich et
      al., 1985,1987).  Since the two methylated cytosine bases occurred in native
      DNA, a comparison of the effects of N4- and C5-methylation on DNA
      physico-chemical properties and enzyme action seems to be of great interest.
AU  - Butkus V
AU  - Klimasauskas S
AU  - Petrauskiene L
AU  - Maneliene Z
PT  - Journal Article
TA  - Metabolism and Enzymology of Nucleic Acids
JT  - Metabolism and Enzymology of Nucleic Acids
SO  - Metabolism and Enzymology of Nucleic Acids 1987 6: 119-127.

PMID- 3671089
VI  - 15
DP  - 1987
TI  - Synthesis and physical characterization of DNA fragments containing N4-methylcytosine and 5-methylcytosine.
PG  - 8467-8478
AB  - The synthesis of N4-methyl-2'-deoxycytidine and its fully protected
      mononucleotide, suitable for the oligonucleotide synthesis by phosphotriester
      method is described.  A set of octanucleotides -d(CGCGCGCG), d(CG5mCGCGCG),
      d(CG4mCGCGCG) and dodecanucleotides -d(GGACCCGGGTCC), d(GGA5mCCCGGGTCC),
      d(GGA4mCCCGGGTCC) has been synthesized in a solution.  Physical
      characterization of the oligonucleotide duplexes by means of UV and CD
      spectrometry provides the evidence that 4mC similarly to 5mC favours the B-->Z
      transition, although both of these methylated cytosines inhibit the B-->A
      conformational change.  N4-Methylcytosine in contrast to 5-methylcytosine
      reduces the DNA double helix thermal stability.
AU  - Butkus V
AU  - Klimasauskas S
AU  - Petrauskiene L
AU  - Maneliene Z
AU  - Janulaitis A
AU  - Minchenkova LE
AU  - Schyolkina AK
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1987 15: 8467-8478.

PMID- 3040102
VI  - 909
DP  - 1987
TI  - Interaction of AluI, Cfr6I and PvuII restriction-modification enzymes with substrates containing either N4-methylcytosine or 5-methylcytosine.
PG  - 201-207
AB  - The cleavage specificity of R.Cfr6I, an isoschizomer of PvuII restriction
      endonuclease was determined to be 5'CAG^CTG and the methylation specificity of
      Cfr6I and PvuII methylases, 5'CAG4mCTG.  Thus, M.Cfr6I and M.PvuII are new
      additions to the list of methylases with N4-methylcytosine specificity.
      Neither of the above RM enzymes acts on the substrates containing either
      N4-methylcytosine or 5-methylcytosine in a cognate methylation position.
AU  - Butkus V
AU  - Klimasauskas S
AU  - Petrauskiene L
AU  - Maneliene Z
AU  - Lebionka A
AU  - Janulaitis A
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1987 909: 201-207.

PMID- 
VI  - 7
DP  - 1988
TI  - The effects of N4- and C5-methylation of cytosine on DNA physical properties and restriction endonuclease action.
PG  - 73-78
AB  - Not long ago a new type of methylase, generating N4-methylcytosine (4mC) in DNA
      was isolated in our laboratory from Bacillus centrosporus (Janulaitis et al.,
      1983).  At present a number of the 4mC type methylases are isolated (Janulaitis
      et al., 1984; Butkus et al., 1985; 1987) and the widespread occurrence of
      N4-methylcytosine in DNA of thermophilic and mesophilic bacteria is documented
      (Ehrlich et al., 1985, 1987).  Since the two methylated cytosine bases occur in
      native DNA, a comparison of the effects of N4- and C5-methylation on DNA
      physico-chemical properties and enzyme action seems to be of great interest.
AU  - Butkus V
AU  - Klimasauskas S
AU  - Petrauskiene L
AU  - Maneliene Z
AU  - Minchenkova LE
AU  - Schyolkina AK
AU  - Janulaitis A
PT  - Journal Article
TA  - Metabolism and Enzymology of Nucleic Acids
JT  - Metabolism and Enzymology of Nucleic Acids
SO  - Metabolism and Enzymology of Nucleic Acids 1988 7: 73-78.

PMID- 2821492
VI  - 15
DP  - 1987
TI  - Cleavage of methylated CCCGGG sequences containing either N4-methylcytosine or 5-methylcytosine with MspI, HpaII, SmaI, XmaI and Cfr9I restriction endonucleases.
PG  - 7091-7102
AB  - The cleavage specificity of R.Cfr9I was determined to be C/CCGGG whereas the
      methylation specificity of M.Cfr9I was C4mCCGGG.  The action of MspI, HpaII,
      SmaI, XmaI and Cfr9I restriction endonucleases on an unmethylated parent
      d(GGACCCGGGTCC) dodecanucleotide duplex and a set of oligonucleotide duplexes,
      containing all possible substitutions of either 4mC or 5mC for C in the CCCGGG
      sequence, was investigated.  It was found that 4mC methylation, in contrast to
      5mC, renders the CCCGGG site resistant to practically all the investigated
      endonucleases.  The cleavage of methylated substrates with restriction
      endonucleases is discussed.
AU  - Butkus V
AU  - Petrauskiene L
AU  - Maneliene Z
AU  - Klimasauskas S
AU  - Laucys V
AU  - Janulaitis A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1987 15: 7091-7102.

PMID- 2994519
VI  - 148
DP  - 1985
TI  - Analysis of products of DNA modification by methylases:  A procedure for the determination of 5- and N4-methylcytosines in DNA.
PG  - 194-198
AB  - Although many different methods are used for the identification of methylated heterocyclic
      bases in DNA not all of them possess the ability to discriminate N4-methylcytosine (m4C) and
      5-methylcytosine (m5C).  Therefore, some of the methods need additional reexamination.  This
      paper reinvestigates some chromatographic systems (thin-layer chromatography, paper
      chromatography, electrophoresis) most widely used in the analysis of minor bases occuring in
      nucleic acids according to their ability to separate m4C and m5C.  A simple procedure for the
      preparation of the sample and a chromatographic system for its analysis was developed.  The
      recommended chromatographic systems may be used for the simultaneous separation of not only
      m4C and m5C but also both methylated cytosines together with N6-methyladenine and
      7-methylguanine.
AU  - Butkus VV
AU  - Klimasauskas SJ
AU  - Janulaitis A
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 1985 148: 194-198.

PMID- 2996560
VI  - 11
DP  - 1985
TI  - Determination of substrate specificity of Eco47I and Eco52I restriction endonucleases.
PG  - 987-988
AB  - Cleavage sites for Eco47I and Eco52I restriction endonucleases, which are
      isoschizomers of AvaII and XmaIII, respectively, have been structurally
      elucidated.
AU  - Butkus VV
AU  - Petrusyte MP
AU  - Janulaitis A
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1985 11: 987-988.

PMID- 1653220
VI  - 173
DP  - 1991
TI  - High-frequency mobilization of broad-host-range plasmids into Neisseria gonorrhoeae requires methylation in the donor.
PG  - 5793-5799
AB  - Antibiotic resistance in Neisseria gonorrhoeae has been associated with the
      acquisition of R plasmids from heterologous organisms.  The broad-host-range
      plasmids of incompatibility groups P (IncP) and Q (IncQ) have played a role in
      this genetic exchange in nature.  We have utilized derivatives of RSF1010
      (IncQ) and RP1 (IncP) to demonstrate that the plethora of restriction barriers
      associated with the gonococci markedly reduces mobilization of plasmids from
      Escherichia coli into strains F62 and PGH 3-2.  Partially purified restriction
      endonucleases from these gonococcal strains can digest RSF1010 in vitro.
      Protection of RSF1010-km from digestion by gonococcal enzymes purified from
      strain F62 is observed when the plasmid is isolated from E. coli containing a
      coresident plasmid, pCAL7.  Plasmid pCAL7 produces a 5'-mCG-3' cytosine
      methylase (M.SssI).  The M.SssI methylase only partially protects RSF1010-km
      from digestion by restriction enzymes from strain PGH 3-2.  Total protection of
      RSF1010-km from PGH 3-2 restriction requires both pCAL7 and a second coresident
      plasmid, pFnuDI, which produces a 5'-GGmCC-3' cytosine methylase.  When both
      F62 and PGH 3-2 are utilized as recipients in heterospecific matings with E.
      coli, mobilization of RSF1010 from strains containing the appropriate
      methylases into the gonococci occurs at frequencies 4 orders of magnitude
      higher than from strains without the methylases.  Thus, protection of RSF1010
      from gonococcal restriction enzymes in vitro correlates with an increase in the
      conjugal frequency.  These data indicate that restriction is a major barrier
      against efficient conjugal transfer between N. gonorrhoeae and heterologous
      hosts.
AU  - Butler CA
AU  - Gotschlich EC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1991 173: 5793-5799.

PMID- 11443105
VI  - 183
DP  - 2001
TI  - Transcriptional analysis and regulation of expression of the ScrFI restriction-modification system of Lactococcus lactis subsp. cremoris UC503.
PG  - 4668-4673
AB  - ScrFI is a type II restriction-modification system from Lactococcus lactis which recognizes
      the nucleotide sequence 5'-CC^NGG-3', cleaving at the point indicated by the arrow, and it
      comprises an endonuclease gene that is flanked on either side by genes encoding two
      5-methylcytosine methylases. An open reading frame (orfX) of unknown function is located
      immediately upstream of these genes. In this study Northern analysis was performed, and it
      revealed that orfX, scrFIBM, and scrFIR are cotranscribed as a single polygenic mRNA molecule,
      while scrFIAM is transcribed independently. 5' extension analysis indicated that the start
      site for the scrFIAM promoter was a thymine located 4 bp downstream of the -10 motif. The
      transcriptional start site for the orfX promoter was also found to be a thymine which is more
      atypically located 24 bp downstream of the -10 motif proximal to the start codon. A
      helix-turn-helix motif was identified at the N-terminal end of one of the methylases
      (M.ScrFIA). In order to determine if this motif played a role in regulation of the ScrFI
      locus, M.ScrFIA was purified. It was then employed in gel retardation assays using fragments
      containing the two promoters found on the ScrFI operon, one located upstream of orfX and the
      other located just upstream of scrFIAM. M.ScrFIA was found to bind to the promoter region
      upstream of the gene encoding it, indicating that it may have a regulatory role. In further
      studies the two putative promoters were introduced into a vector (pAK80) upstream of a
      promoterless lacZ gene, and cloned fragments of the ScrFI locus were introduced in trans with
      each of these promoter constructs to investigate the effect on promoter activity. These
      results implicated M.ScrFIA in regulation of both promoters on the ScrFI locus.
AU  - Butler D
AU  - Fitzgerald GF
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2001 183: 4668-4673.

PMID- 23555547
VI  - 8
DP  - 2013
TI  - Pseudomonas syringae pv. actinidiae from Recent Outbreaks of Kiwifruit Bacterial Canker Belong to Different Clones that Originated in China.
PG  - e57464
AB  - A recently emerged plant disease, bacterial canker of kiwifruit (Actinidia deliciosa and A.
      chinensis), is caused by Pseudomonas syringae pv. actinidiae (PSA).  The disease was first
      reported in China nad Japan in the 1980s.  A severe breakout of PSA began in Italy in 2008 and
      has spread to other European countries.  PSA was found in both New Zealand and Chile in 2010.
      To study the evolution of the pathogen and analyse the transmission of PSA between countries,
      genomes of strands from China and Japan (where the genus Actinidia is endemic)m Italy, New
      Zealand and Chile were sequenced.  The genomes of PSA strains are very similar.  However, all
      strains from New Zealand share several single nucleotide polymorphisms (SNPs) that distinguish
      them from all other PSA strains.  Similarly, all the PSA strains from the 2008 Italian
      outbreak form a distinct clonal group and those from Chile form a third group.  In addition to
      the rare SNPs present in the core genones, there is abundant genetic diversity in a genomic
      island that is part of the accessory genome.  The island from several Chinese strains is
      almost identical to the island present in the New Zealand strains. The island from a different
      Chinese strain is identical to the island prsent in the strains from the recent Italian
      outbreak.  The Chilean strains of PSA carry a third variant of this island.  These genome
      islands are integrative conjugative elements (ICEs).  Sequencing of these ICEs provides
      evidence of three recent horizontal transmissions of ICE from other strains of Pseudomonas
      syringae to PSA.  The analyses of the core genome SNPs and the ICEs, combined with disease
      history, all support the hypothesis of an independent Chinese origin for both the Italian and
      the New Zealand outbreaks and suggest the Chilean strains also originate from China.
AU  - Butler MI
AU  - Stockwell PA
AU  - Black MA
AU  - Day RC
AU  - Lamont IL
AU  - Poulter RTM
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2013 8: e57464.

PMID- 28619805
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of Two Human Oral Microbiome Commensals, Streptococcus  salivarius ATCC 25975 and S. salivarius ATCC 27945.
PG  - e00536-17
AB  - Streptococcus salivarius strains are significant contributors to the human oral microbiome.
      Some possess unique fimbriae that give them the ability to
      coaggregate and colonize particular oral structures. We present here the complete
      genomes of Streptococcus salivarius Lancefield K-/K+ strains ATCC 25975 and ATCC
      27945, which can and cannot, respectively, produce fimbriae.
AU  - Butler RRIII
AU  - Soomer-James JTA
AU  - Frenette M
AU  - Pombert JF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00536-17.

PMID- 26868401
VI  - 4
DP  - 2016
TI  - Complete Genome Sequences of Two Interactive Moderate Thermophiles, Paenibacillus napthalenovorans 32O-Y and Paenibacillus sp. 32O-W.
PG  - e01717-15
AB  - Microorganisms with the capability to desulfurize petroleum are in high demand with escalating
      restrictions currently placed on fuel purity. Thermophilic
      desulfurizers are particularly valuable in high-temperature industrial
      applications. We report the whole-genome sequences of Paenibacillus
      napthalenovorans 32O-Y and Paenibacillus sp. 32O-W, which can and cannot,
      respectively, metabolize dibenzothiophene.
AU  - Butler RRIII
AU  - Wang J
AU  - Stark BC
AU  - Pombert JF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01717-15.

PMID- 21571999
VI  - 193
DP  - 2011
TI  - Genome sequence of a novel species, Propionibacterium humerusii.
PG  - 3678
AB  - As part of a larger project to sequence multiple clinical isolates of Propionibacterium acnes,
      we have produced a draft genome sequence of a
      novel Propionibacterium species that is closely related to, yet distinct
      (by sequence) from P. acnes. We have tentatively named this new species
      Propionibacterium humerusii.
AU  - Butler-Wu SM
AU  - Sengupta DJ
AU  - Kittichotirat W
AU  - Matsen FA
AU  - Bumgarner RE
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3678.

PMID- 24510100
VI  - 42
DP  - 2014
TI  - Type III restriction endonucleases are heterotrimeric: comprising one helicase-nuclease subunit and a dimeric methyltransferase that binds only one  specific DNA.
PG  - 5139-5150
AB  - Fundamental aspects of the biochemistry of Type III restriction endonucleases remain
      unresolved despite being characterized by numerous research groups in the
      past decades. One such feature is the subunit stoichiometry of these
      hetero-oligomeric enzyme complexes, which has important implications for the
      reaction mechanism. In this study, we present a series of results obtained by
      native mass spectrometry and size exclusion chromatography with multi-angle light
      scattering consistent with a 1:2 ratio of Res to Mod subunits in the EcoP15I,
      EcoPI and PstII complexes as the main holoenzyme species and a 1:1 stoichiometry
      of specific DNA (sDNA) binding by EcoP15I and EcoPI. Our data are also consistent
      with a model where ATP hydrolysis activated by recognition site binding leads to
      release of the enzyme from the site, dissociation from the substrate via a free
      DNA end and cleavage of the DNA. These results are discussed critically in the
      light of the published literature, aiming to resolve controversies and discuss
      consequences in terms of the reaction mechanism.
AU  - Butterer A
AU  - Pernstich C
AU  - Smith RM
AU  - Sobott F
AU  - Szczelkun MD
AU  - Toth J
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2014 42: 5139-5150.

PMID- 22535943
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of the Anaerobic Perchlorate-Reducing Bacterium Azospira suillum Strain PS.
PG  - 2767-2768
AB  - Azospira suillum strain PS (formally Dechlorosoma suillum strain PS) is a metabolically
      versatile betaproteobacterium first identified for its ability to
      grow by dissimilatory reduction of perchlorate and chlorate [denoted
      (per)chlorate]. Together with Dechloromonas species, these two genera represent
      the dominant (per)chlorate-reducing bacteria in mesophilic freshwater
      environments. In addition to (per)chlorate reduction, A. suillum is capable of
      the anaerobic oxidation of humic substances and is the first anaerobic
      nitrate-dependent Fe(II) oxidizer outside the Diaphorobacter and Acidovorax
      genera for which there is a completed genome sequence.
AU  - Byrne-Bailey KG
AU  - Coates JD
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2767-2768.

PMID- 20023012
VI  - 192
DP  - 2009
TI  - Completed genome sequence of the anaerobic iron oxidizing bacterium Acidovorax ebreus strain TPSY.
PG  - 1475-1476
AB  - Acidovorax ebreus strain TPSY is the first anaerobic nitrate-dependent Fe(II) oxidizer for
      which there is a completed genome sequence. Preliminary protein annotation revealed an
      organism optimized for survival in a complex environmental system. Here, we briefly report the
      completed and annotated genome sequence of strain TPSY.
AU  - Byrne-Bailey KG
AU  - Weber KA
AU  - Chair AH
AU  - Bose S
AU  - Knox T
AU  - Spanbauer TL
AU  - Chertkov O
AU  - Coates JD
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2009 192: 1475-1476.

PMID- 22493205
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of the Anaerobic, Nitrate-Dependent, Fe(II)-Oxidizing Bacterium Pseudogulbenkiania ferrooxidans Strain 2002.
PG  - 2400-2401
AB  - Pseudogulbenkiania ferrooxidans strain 2002 was isolated as a lithoautotrophic,
      Fe(II)-oxidizing, nitrate-reducing bacterium. Phylogenetically, it is in a clade
      within the family Neisseriaceae in the order Nessieriales of the class
      Betaproteobacteria. It is anticipated that comparative genomic analysis of this
      strain with other nitrate-dependent, Fe(II)-oxidizing bacteria will aid in the
      elucidation of the genetics and biochemistry underlying this critically important
      geochemical metabolism.
AU  - Byrne-Bailey KG
AU  - Weber KA
AU  - Coates JD
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2400-2401.

PMID- 20525829
VI  - 192
DP  - 2010
TI  - Complete genome sequence of the electricity-producing Thermincola potens strain JR.
PG  - 4078-4079
AB  - Thermincola potens strain JR is one of the first Gram-positive dissimilatory metal reducing
      bacteria (DMRB) for which there is a draft
      genome sequence. Consistent with the physiology of this organism,
      preliminary annotation revealed an abundance of multi-heme c-type
      cytochromes that are putatively associated with the periplasm and cell
      surface in a Gram-positive bacterium. Here we report the draft genome
      sequence of strain JR.
AU  - Byrne-Bailey KG
AU  - Wrighton KC
AU  - Melnyk RA
AU  - Agbo P
AU  - Hazen TC
AU  - Coates JD
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 4078-4079.

PMID- 2517016
VI  - 7
DP  - 1989
TI  - A general method to optimize the amount of enzyme in restriction and DNA modification reactions using the beta galactosidase blue-white plaques assay.
PG  - 132-135
AB  - We propose a simple and economical method for assaying the activity of
      restriction and other modifying enzymes.  The method involves assaying the use
      of the blue and white colored phenotypes of bacterial colonies obtained by
      digesting the polylinker sequence of M13 bacteriophage vectors followed by
      transformation in appropriate strains on X-gal/IPTG plates.  In conjunction
      with restriction enzymes and DNA ligases, the method can evaluate polymerase
      activity and can be applied to test 3'-5' exonuclease activities such as that
      of T4 DNA polymerase, without having to use expensive radioisotopes.  We
      describe its application in the assessment of restriction enzymes, DNA ligase
      and DNA polymerase activities.
AU  - Cab-Barrera EL
AU  - Barrera-Saldana HA
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 1989 7: 132-135.

PMID- 23704178
VI  - 1
DP  - 2013
TI  - Genome Sequence of Xanthomonas arboricola pv. Corylina, Isolated from Turkish Filbert in Colorado.
PG  - e00246-13
AB  - Previously, we reported the isolation of a bacterium producing leaf spots in Turkish filbert.
      Here, we present the draft genome assembly of the bacterium identified as Xanthomonas
      arboricola pv. corylina. To our knowledge, this is the first published genome of this pathovar
      of X. arboricola.
AU  - Caballero JI
AU  - Zerillo MM
AU  - Snelling J
AU  - Boucher C
AU  - Tisserat N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00246-13.

PMID- 25125654
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Haloalkaliphilic Exiguobacterium sp. Strain AB2 from Manleluag Ophiolitic Spring, Philippines.
PG  - e00840-14
AB  - Exiguobacterium sp. AB2 is a haloalkaliphilic bacterium isolated from a hyperalkaline spring
      in Manleluag, Pangasinan, Philippines. Sequencing of
      bacterial DNA assembled a 2.85 MB draft genome. Analysis suggests the presence of
      genes for tolerance to stresses such as elevated pH and salt concentrations and
      toxic metals.
AU  - Cabria GL
AU  - Argayosa VB
AU  - Lazaro JE
AU  - Argayosa AM
AU  - Arcilla CA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00840-14.

PMID- 23469360
VI  - 1
DP  - 2013
TI  - Whole-Genome Sequencing and Comparative Analysis of Yersinia pestis, the Causative Agent of a Plague Outbreak in Northern Peru.
PG  - e00249-12
AB  - The plague is a zoonotic disease caused by the bacterium . Here, we report the complete genome
      sequence of the strain INS, which was isolated from swollen lymph
      gland aspirate (bubo aspirate) of an infected patient from a pneumonic outbreak
      in 2010 in northern Peru.
AU  - Caceres O
AU  - Montenegro J
AU  - Padilla C
AU  - Tarazona D
AU  - Bailon H
AU  - Garcia P
AU  - Cespedes M
AU  - Valencia P
AU  - Guio H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00249-12.

PMID- 26543115
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Methanosphaerula palustris E1-9CT, a Hydrogenotrophic Methanogen Isolated from a Minerotrophic Fen Peatland.
PG  - e01280-15
AB  - Here, we report the complete genome sequence (2.92 Mb) of Methanosphaerula palustris E1-9C(T),
      a methanogen isolated from a minerotrophic fen. This is the
      first genome report of the Methanosphaerula genus, within the Methanoregulaceae
      family, in the Methanomicrobiales order. E1-9C(T) relatives are found in a wide
      range of ecological and geographical settings.
AU  - Cadillo-Quiroz H
AU  - Browne P
AU  - Kyrpides N
AU  - Woyke T
AU  - Goodwin L
AU  - Detter C
AU  - Yavitt JB
AU  - Zinder SH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01280-15.

PMID- 22363207
VI  - 10
DP  - 2012
TI  - Patterns of gene flow define species of thermophilic archaea.
PG  - E1001265
AB  - Despite a growing appreciation of their vast diversity in nature, mechanisms of
      speciation are poorly understood in Bacteria and Archaea. Here we use
      high-throughput genome sequencing to identify ongoing speciation in the
      thermoacidophilic Archaeon Sulfolobus islandicus. Patterns of homologous gene
      flow among genomes of 12 strains from a single hot spring in Kamchatka, Russia,
      demonstrate higher levels of gene flow within than between two persistent,
      coexisting groups, demonstrating that these microorganisms fit the biological
      species concept. Furthermore, rates of gene flow between two species are
      decreasing over time in a manner consistent with incipient speciation. Unlike
      other microorganisms investigated, we do not observe a relationship between
      genetic divergence and frequency of recombination along a chromosome, or other
      physical mechanisms that would reduce gene flow between lineages. Each species
      has its own genetic island encoding unique physiological functions and a unique
      growth phenotype that may be indicative of ecological specialization. Genetic
      differentiation between these coexisting groups occurs in large genomic
      "continents," indicating the topology of genomic divergence during speciation is
      not uniform and is not associated with a single locus under strong diversifying
      selection. These data support a model where species do not require physical
      barriers to gene flow but are maintained by ecological differentiation.
AU  - Cadillo-Quiroz H
AU  - Didelot X
AU  - Held NL
AU  - Herrera A
AU  - Darling A
AU  - Reno ML
AU  - Krause DJ
AU  - Whitaker RJ
PT  - Journal Article
TA  - PLoS Biology
JT  - PLoS Biology
SO  - PLoS Biology 2012 10: E1001265.

PMID- 29622615
VI  - 6
DP  - 2018
TI  - Genome Sequence of the Proteorhodopsin-Containing Bacterium Flavobacterium sp. Strain TH167, Isolated from Cyanobacterial Aggregates in a Eutrophic Lake.
PG  - e00217-18
AB  - Flavobacterium is the most abundant group of bacteria within the cyanobacterial aggregates in
      Lake Taihu, China. Here, we present the genome sequence and
      annotation of Flavobacterium sp. strain TH167. Genome analysis revealed the
      presence of a proteorhodopsin-encoding sequence, together with its
      retinal-producing pathway, indicating a putative photoheterotrophic lifestyle
      that generates energy from light.
AU  - Cai H
AU  - Chen F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00217-18.

PMID- 29213356
VI  - 12
DP  - 2017
TI  - High-quality draft genome sequence of Aquidulcibacter paucihalophilus TH1-2(T) isolated from cyanobacterial aggregates in a eutrophic lake.
PG  - 69
AB  - Aquidulcibacter paucihalophilus TH1-2(T) is a member of the family Caulobacteraceae within
      Alphaproteobacteria isolated from cyanobacterial
      aggregates in a eutrophic lake. The draft genome comprises 3,711,627 bp and 3489
      predicted protein-coding genes. The genome of strain TH1-2(T) has 270 genes
      encoding peptidases. And metallo and serine peptidases were found most
      frequently. A high number of genes encoding carbohydrate active enzymes (141
      CAZymes) also present in strain TH1-2(T) genome. Among CAZymes, 47 glycoside
      hydrolase families, 37 glycosyl transferase families, 38 carbohydrate esterases
      families, nine auxiliary activities families, seven carbohydrate-binding modules
      families, and three polysaccharide lyases families were identified. Accordingly,
      strain TH1-2(T) has a high number of transporters (91), the dominated ones are
      ATP-binding cassette transporters (61) and TonB-dependent transporters (28).
      Major TBDTs are Group I, which consisted of transporters for various types of
      dissolved organic matter. These genome features indicate adaption to
      cyanobacterial aggregates microenvironments.
AU  - Cai H
AU  - Zeng Y
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 69.

PMID- 25197498
VI  - 9
DP  - 2014
TI  - Non-contiguous finished genome sequence and description of Sulfurimonas hongkongensis sp. nov., a strictly anaerobic denitrifying, hydrogen- and  sulfur-oxidizing chemolithoautotroph isolated from marine sediment.
PG  - 1302-1310
AB  - Here, we report a type strain AST-10 representing a novel species Sulfurimonas hongkongensis
      within Epsilonproteobacteria, which is involved in marine
      sedimentary sulfur oxidation and denitrification. Strain AST-10(T) (= DSM
      22096(T) = JCM 18418(T)) was isolated from the coastal sediment at the Kai Tak
      Approach Channel connected to Victoria Harbour in Hong Kong. It grew
      chemolithoautotrophically using thiosulfate, sulfide or hydrogen as the sole
      electron donor and nitrate as the electron acceptor under anoxic conditions. It
      was rod-shaped and grew at 15-35 degrees C (optimum at 30 degrees C), pH 6.5-8.5
      (optimum at 7.0-7.5), and 10-60 g L(-1) NaCl (optimum at 30 g L(-1)). Genome
      sequencing and annotation of strain AST-10(T) showed a 2,302,023 bp genome size,
      with 34.9% GC content, 2,290 protein-coding genes, and 42 RNA genes, including 3
      rRNA genes.
AU  - Cai L
AU  - Shao MF
AU  - Zhang T
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 1302-1310.

PMID- 22040376
VI  - 10
DP  - 2011
TI  - Comparative genomics study of polyhydroxyalkanoates (PHA) and ectoine relevant genes from Halomonas sp. TD01 revealed extensive horizontal gene transfer events and co-evolutionary relationships.
PG  - 88
AB  - BACKGROUND: Halophilic bacteria have shown their significance in industrial
      production of polyhydroxyalkanoates (PHA) and are gaining more attention for
      genetic engineering modification. Yet, little information on the genomics and PHA
      related genes from halophilic bacteria have been disclosed so far. RESULTS: The
      draft genome of moderately halophilic bacterium, Halomonas sp. TD01, a strain of
      great potential for industrial production of short-chain-length
      polyhydroxyalkanoates (PHA), was analyzed through computational methods to reveal
      the osmoregulation mechanism and the evolutionary relationship of the enzymes
      relevant to PHA and ectoine syntheses. Genes involved in the metabolism of PHA
      and osmolytes were annotated and studied in silico. Although PHA synthase,
      depolymerase, regulator/repressor and phasin were all involved in PHA metabolic
      pathways, they demonstrated different horizontal gene transfer (HGT) events
      between the genomes of different strains. In contrast, co-occurrence of ectoine
      genes in the same genome was more frequently observed, and ectoine genes were
      more likely under coincidental horizontal gene transfer than PHA related genes.
      In addition, the adjacent organization of the homologues of PHA synthase phaC1
      and PHA granule binding protein phaP was conserved in the strain TD01, which was
      also observed in some halophiles and non-halophiles exclusively from
      gamma-proteobacteria. In contrast to haloarchaea, the proteome of Halomonas sp.
      TD01 did not show obvious inclination towards acidity relative to non-halophilic
      Escherichia coli MG1655, which signified that Halomonas sp. TD01 preferred the
      accumulation of organic osmolytes to ions in order to balance the intracellular
      osmotic pressure with the environment. CONCLUSIONS: The accessibility of genome
      information would facilitate research on the genetic engineering of halophilic
      bacteria including Halomonas sp. TD01.
AU  - Cai L
AU  - Tan D
AU  - Aibaidula G
AU  - Dong XR
AU  - Chen JC
AU  - Tian WD
AU  - Chen GQ
PT  - Journal Article
TA  - Microb. Cell Fact.
JT  - Microb. Cell Fact.
SO  - Microb. Cell Fact. 2011 10: 88.

PMID- 22887677
VI  - 194
DP  - 2012
TI  - Genome of Bacillus macauensis ZFHKF-1, a Long-Chain-Forming Bacterium.
PG  - 4780
AB  - Here, we report the draft genome sequence of Bacillus macauensis ZFHKF-1, a novel long-chain
      bacterium previously isolated and identified by us (Zhang T, Fan XJ,
      Hanada S, Kamagata Y, Fang HHP, J. Syst. Evol. Microbiol. 56:349-353, 2006). The
      genome provides basic genetic information to understand this particular species
      and explore the potential mechanism of long-chain formation. The type strain is
      ZFHKF-1 (= JCM 13285 = DSM 17262).
AU  - Cai L
AU  - Zhang T
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4780.

PMID- 29625286
VI  - 260
DP  - 2018
TI  - Complete genome sequence provides insights into the biodrying-related microbial function of Bacillus thermoamylovorans isolated from sewage sludge biodrying material.
PG  - 141-149
AB  - To enable the development of microbial agents and identify suitable candidate
      used for biodrying, the existence and function of Bacillus thermoamylovorans
      during sewage sludge biodrying merits investigation. This study isolated a strain
      of B. thermoamylovorans during sludge biodrying, submitted it for complete genome
      sequencing and analyzed its potential microbial functions. After biodrying, the
      moisture content of the biodrying material decreased from 66.33% to 50.18%, and
      B. thermoamylovorans was the ecologically dominant Bacillus, with the primary
      annotations associated with amino acid transport and metabolism (9.53%) and
      carbohydrate transport and metabolism (8.14%). It contains 96
      carbohydrate-active- enzyme-encoding gene counts, mainly distributed in glycoside
      hydrolases (33.3%) and glycosyl transferases (27.1%). The virulence factors are
      mainly associated with biosynthesis of capsule and polysaccharide capsule. This
      work indicates that among the biodrying microorganisms, B. thermoamylovorans has
      good potential for degrading recalcitrant and readily degradable components, thus
      being a potential microbial agent used to improve biodrying.
AU  - Cai L
AU  - Zheng SW
AU  - Shen YJ
AU  - Zheng GD
AU  - Liu HT
AU  - Wu ZY
PT  - Journal Article
TA  - Bioresource Technology
JT  - Bioresource Technology
SO  - Bioresource Technology 2018 260: 141-149.

PMID- 21725023
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Amycolicicoccus subflavus DQS3-9A1T, an actinomycete isolated from crude oil-polluted soil.
PG  - 4538-4539
AB  - Amycolicicoccus subflavus DQS3-9A1(T) , isolated from crude oil polluted soil in the Daqing
      Oilfield in China , is a type strain of a newly
      published novel species in the novel genus Amycolicicoccus. Here we report
      the complete genome of DQS3-9A1(T) and genes associated with oil-polluted
      environment.
AU  - Cai M
AU  - Chen WM
AU  - Nie Y
AU  - Chi CQ
AU  - Wang YN
AU  - Tang YQ
AU  - Li GY
AU  - Wu XL
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4538-4539.

PMID- 29097477
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Exiguobacterium sp. Strain N4-1P, a Psychrophilic Bioemulsifier Producer Isolated from a Cold Marine Environment in North Atlantic   Canada.
PG  - e01248-17
AB  - Here, we present the complete genome sequence of Exiguobacterium sp. strain N4-1P, a
      psychrophilic bacterium that produces bioemulsifier, isolated for the
      first time from petroleum hydrocarbon-contaminated sediment samples from
      shoreline Newfoundland, Canada. Many strains of the genus Exiguobacterium are
      extremophiles and have properties of biotechnological interest.
AU  - Cai Q
AU  - Ye X
AU  - Chen B
AU  - Zhang B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01248-17.

PMID- 29545295
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Two Dickeya dianthicola Isolates from Potato.
PG  - e00115-18
AB  - Here, we report two annotated draft genome sequences of Dickeya dianthicola isolates from
      potatoes collected in Delaware and West Virginia. The genomes of
      strains DE440 and WV516 show 99% similarity to each other and 96% and 95%
      similarity to the European strains IPO 980 and RNS04.9, respectively.
AU  - Cai W
AU  - Srivastava SK
AU  - Stulberg MJ
AU  - Nakhla MK
AU  - Rascoe J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00115-18.

PMID- 29930061
VI  - 6
DP  - 2018
TI  - Draft Whole-Genome Sequence of 'Candidatus Liberibacter asiaticus' Strain TX1712  from Citrus in Texas.
PG  - e00554-18
AB  - The draft genome sequence of 'Candidatus Liberibacter asiaticus' strain TX1712, obtained
      from a Texas citrus tree, is reported here. Strain TX1712 has a draft
      genome size of 1,203,333 bp, a G+C content of 36.4%, 1,230 predicted open reading
      frames, and 41 RNAs and comprises 97.4% of the psy62 reference genome.
AU  - Cai W
AU  - Yan Z
AU  - Rascoe J
AU  - Stulberg MJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00554-18.

PMID- 27688342
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of the Endophytic Biocontrol Strain Bacillus velezensis  CC09.
PG  - e01048-16
AB  - Bacillus velezensis is a heterotypic synonym of B. methylotrophicus, B. amyloliquefaciens
      subsp. plantarum, and Bacillus oryzicola, and has been used to
      control plant fungal diseases. In order to fully understand the genetic basis of
      antimicrobial capacities, we did a complete genome sequencing of the endophytic
      B. velezensis strain CC09. Genes tightly associated with biocontrol ability,
      including nonribosomal peptide synthetases, polyketide synthetases, iron
      acquisition, colonization, and volatile organic compound synthesis were
      identified in the genome.
AU  - Cai X
AU  - Kang X
AU  - Xi H
AU  - Liu C
AU  - Xue Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01048-16.

PMID- 23405327
VI  - 1
DP  - 2013
TI  - Complete Chromosome Sequence of Carnobacterium maltaromaticum LMA 28.
PG  - e00115-12
AB  - Within the lactic acid bacterium genus Carnobacterium, Carnobacterium maltaromaticum is one of
      the most frequently isolated species from natural
      environments and food. It potentially plays a major role in food product
      biopreservation. We report here on the 3.649-Mb chromosome sequence of C.
      maltaromaticum LMA 28, which was isolated from ripened soft cheese.
AU  - Cailliez-Grimal C
AU  - Chaillou S
AU  - Anba-Mondoloni J
AU  - Loux V
AU  - Afzal MI
AU  - Rahman A
AU  - Kergourlay G
AU  - Champomier-Verges MC
AU  - Zagorec M
AU  - Dalgaard P
AU  - Leisner JJ
AU  - Prevost H
AU  - Revol-Junelles AM
AU  - Borges F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00115-12.

PMID- 
VI  - 103
DP  - 2001
TI  - Inactivation of the EcoKI restriction in UV-irradiated Escherichia coli: The role of RecBCD enzyme.
PG  - 157-161
AB  - Background and Purpose: UV-induced restriction alleviation (UV-induced RA) has been known for
      a long time, but the mechanism underlying this
      phenomenon is not known. UV-induced RA depends on the induction of the
      SOS response and on the functional recBCD genes. The experiments
      described in this study attempt to clarify the role of the RecBCD
      enzyme in UV-induced RA
      Materials and Methods: Restriction alleviation (RA) is expressed as
      the efficiency of plating unmodified lambda virC.0 on UV-irradiated
      bacteria relative to the phage titer on E. coli C00r(k)(-)m(k)(-),
      lacking the EcoKI restriction-modification system.
      Results and Conclusions: Alleviation of EcoKI restriction following
      induction of the SOS response and its dependence on RecBDC enzyme after
      UV irradiation (UV induced RA) was further characterized. We examined
      the efficiency of plating unmodified lambda (RA) in bacteria with
      modified activities of RecBCD enzyme, i.e. in a recD mutant, in
      bacteria producing the truncated RecB(1.929) polypeptide instead of
      wild-type RecB and in a Gam(+)- producing strain in which the RecBCD
      enzyme interacts with the Gam protein of phage lambda It follows from
      the results presented here that the helicase activity of the RecBCD
      enzyme is involved in UV-induced RA.
AU  - Cajo GC
AU  - Brcic-Kostic K
AU  - Ivancic I
AU  - Trgovcevic Z
AU  - Salaj-Smic E
PT  - Journal Article
TA  - Periodicum Biologorum
JT  - Periodicum Biologorum
SO  - Periodicum Biologorum 2001 103: 157-161.

PMID- 17439637
VI  - 270
DP  - 2007
TI  - Phosphorylation of type IA restriction-modification complex enzyme EcoKI on the HsdR subunit.
PG  - 171-177
AB  - Phosphorylation of Type I restriction-modification (R-M) enzymes EcoKI, EcoAI, and EcoR124I -
      representatives of IA, IB, and IC families,
      respectively - was analysed in vivo by immunoblotting of endogenous
      phosphoproteins isolated from Escherichia coli strains harbouring the
      corresponding hsd genes, and in vitro by a phosphorylation assay using
      protein kinase present in subcellular fractions of E. coli. From all
      three R-M enzymes, the HsdR subunit of EcoKI system was the only
      subunit that was phosphorylated. Further, evidence is presented that
      HsdR is phosphorylated in vivo only when coproduced with HsdM and HsdS
      subunits - as part of assembled EcoKI restriction endonuclease, while
      the individually produced HsdR subunit is not phosphorylated. In vitro
      phosphorylation of the HsdR subunit of purified EcoKI endonuclease
      occurs on Thr, and is strictly dependent on the addition of a catalytic
      amount of cytoplasmic fraction isolated from E. coli. So far this is
      the first case of phosphorylation of a Type I R-M enzyme reported.
AU  - Cajthamlova K
AU  - Sisakova E
AU  - Weiser J
AU  - Weiserova M
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2007 270: 171-177.

PMID- 8995288
VI  - 272
DP  - 1997
TI  - DNA distortion and base flipping by the EcoRV DNA methyltransferase.
PG  - 490-496
AB  - The EcoRV DNA methyltransferase introduces a CH3 group at the 6-amino position of the first dA
      in the duplex sequence d(GATATC).  It has previously been reported that the methylase contacts
      the four phosphates (pNpNpGpA) at, and preceding, the 5'-end of the recognition sequence as
      well as the single dG in this sequence.  To study the possible role of the dA and T bases
      within the ATAT sequence, interference studies have been carried out using
      diethylpyrocarbonate and osmium tetroxide.  The methylase bound very strongly to
      hemimethylated oligonucleotides modified at the second AT, of the ATAT sequence, in the
      unmethylated strand of the duplex.  This probably arises because these modifications
      facilitate DNA distortion that follows the binding of the nucleic acid to the protein.
      Oligonucleotides containing modified bases at both the target dA base and its complementary T
      were used to determine whether this dA methylase flips out its target base in a similar manner
      to that observed for dC DNA methylases.  In binary EcoRV methylase-DNA complexes, analogues
      that weakened the base pair caused an increase in affinity between the protein and the nucleic
      acid.  In contrast, in ternary EcoRV methylase-DNA-sinefungin (an analogue of the natural
      co-factor, S-adenosyl-L-methionine (AdoMet)) complexes, only small differences in affinity
      were observed between the normal dA-T base pair and the analogues.  These results are almost
      identical to those seen with DNA dC methylases and support a base-flipping mechanism for DNA
      dA methylases.
AU  - Cal S
AU  - Connolly BA
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1997 272: 490-496.

PMID- 8557624
VI  - 271
DP  - 1996
TI  - The EcoRV modification methylase causes considerable bending of DNA upon binding to its recognition sequence GATATC.
PG  - 1008-1015
AB  - The EcoRV methyltransferase modifies DNA by the introduction of a methyl group at the 6-NH2
      position of the first deoxyadenosine in GATATC sequences.  The enzyme forms a stable and
      specific complex with GATATC sequences in the presence of a nonreactive analogue, such as
      sinefungin, of its natural cofactor S-adenosyl-L-methionine.  Using circular permutation band
      mobility shift analysis (in which the distance between the GATATC sequence and the end of the
      DNA is varied) of protein-DNA-cofactor complexes we have shown the methylase induces a bend of
      just over 60o in the bound DNA.  This was confirmed by phasing analysis, in which the spacing
      between the GATATC site and a poly(dA) tract is varied through a helical turn, which showed
      that the orientation of the induced curve was toward the major groove.  There was no
      significant difference in the bend angle measured using unmethylated GATATC sequences and
      hemimethylated sequences which contain G6-MeATATC in one strand only.  These are the natural
      substrates for the enzyme.  The EcoRV endonuclease, a very well characterized protein, served
      as a positive control.  DNA bending by this protein has been previously determined both by
      crystallographic and solution methods.  The two proteins bend DNA toward the major groove but
      the bend angle produced by the methylase, slightly greater than 60o, is a little larger than
      that observed with the endonuclease, which is approximately 44o.
AU  - Cal S
AU  - Connolly BA
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1996 271: 1008-1015.

PMID- 
VI  - 22
DP  - 2012
TI  - Imprinting: DNA Methyltransferases Illuminate Reprogramming.
PG  - R929-R931
AB  - 
AU  - Calarco JP
AU  - Martienssen RA
PT  - Journal Article
TA  - Curr. Biol.
JT  - Curr. Biol.
SO  - Curr. Biol. 2012 22: R929-R931.

PMID- 26472837
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Kocuria palustris MU14/1.
PG  - e01195-15
AB  - Presented here is the first completely assembled genome sequence of Kocuria palustris, an
      actinobacterial species with broad ecological distribution. The single, circular chromosome of
      K. palustris MU14/1 comprises 2,854,447 bp, has a  G+C content of 70.5%, and contains a
      deduced gene set of 2,521 coding sequences.
AU  - Calcutt MJ
AU  - Foecking MF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01195-15.

PMID- 21994925
VI  - 193
DP  - 2011
TI  - Genome Sequence of Mycoplasma putrefaciens Type Strain KS1.
PG  - 6094
AB  - Mycoplasma putrefaciens is a causative agent of contagious agalactia in goats. Reported herein
      is the complete genome sequence of the M.
      putrefaciens type strain KS1.
AU  - Calcutt MJ
AU  - Foecking MF
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6094.

PMID- 24558249
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Mycoplasma bovoculi Strain M165/69T (ATCC 29104).
PG  - e00115-14
AB  - Bovine ocular infections compromise animal health and result in significant economic losses.
      Mycoplasma bovoculi is an etiological agent of conjunctivitis.
      Presented here is the 760,240-bp complete genome sequence of the M. bovoculi type
      strain M165/69(T). An analysis of the deduced proteome provides insights into the
      adherence and antigenic variation mechanisms of the strain.
AU  - Calcutt MJ
AU  - Foecking MF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00115-14.

PMID- 26159538
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Mycoplasma hominis Strain Sprott (ATCC 33131), Isolated from a Patient with Nongonococcal Urethritis.
PG  - e00771-15
AB  - Presented here is the complete and annotated genome sequence of Mycoplasma hominis Sprott
      (ATCC 33131). The chromosome comprises 695,214 bp, which is
      approximately 30 kb larger than the syntenic genome of M. hominis PG21(T).
      Tetracycline resistance of strain Sprott is most probably conferred by the tetM
      determinant, harbored on a mosaic transposon-like structure.
AU  - Calcutt MJ
AU  - Foecking MF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00771-15.

PMID- 25720686
VI  - 3
DP  - 2015
TI  - Analysis of the Complete Mycoplasma hominis LBD-4 Genome Sequence Reveals Strain-Variable Prophage Insertion and Distinctive Repeat-Containing Surface Protein Arrangements.
PG  - e01582-14
AB  - The complete genome sequence of Mycoplasma hominis LBD-4 has been determined and the gene
      content ascribed. The 715,165-bp chromosome contains 620 genes, including 14 carried by a
      strain-variable prophage genome related to Mycoplasma fermentans MFV-1 and Mycoplasma
      arthritidis MAV-1. Comparative analysis with the  genome of M. hominis PG21(T) reveals
      distinctive arrangements of repeat-containing surface proteins.
AU  - Calcutt MJ
AU  - Foecking MF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01582-14.

PMID- 24994797
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of the Bovine Mastitis Pathogen Mycoplasma californicum  Strain ST-6T (ATCC 33461T).
PG  - e00648-14
AB  - Mycoplasma californicum is one of several mycoplasmal species associated with bovine mastitis.
      The complete genome sequence of 793,841 bp has been determined
      and annotated for the M. californicum ST-6 type strain, providing a resource for
      the identification of surface antigens and putative pathoadaptive features.
AU  - Calcutt MJ
AU  - Foecking MF
AU  - Fox LK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00648-14.

PMID- 25189590
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Bovine Mastitis Isolate Staphylococcus agnetis CBMRN 20813338.
PG  - e00883-14
AB  - Presented here is a draft genome sequence for Staphylococcus agnetis CBMRN 20813338, isolated
      from a lactating dairy cow with subclinical mastitis. The
      genome is approximately 2,416 kb and has 35.79% G+C content. Analysis of the
      deduced open reading frame (ORF) set identified candidate virulence attributes in
      addition to potential molecular targets for species identification.
AU  - Calcutt MJ
AU  - Foecking MF
AU  - Fry PR
AU  - Hsieh HY
AU  - Perry J
AU  - Stewart GC
AU  - Scholl DT
AU  - Messier S
AU  - Middleton JR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00883-14.

PMID- 25767245
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Mycoplasma flocculare Strain Ms42T (ATCC 27399T).
PG  - e00124-15
AB  - Mycoplasma flocculare is a commensal or low-virulence pathogen of swine. The complete
      778,866-bp genome sequence of M. flocculare strain Ms42(T) has been
      determined, enabling further comparison to genomes of the closely related
      pathogen Mycoplasma hyopneumoniae. The absence of the p97 and glpD genes may
      contribute to the attenuated virulence of M. flocculare.
AU  - Calcutt MJ
AU  - Foecking MF
AU  - Heidari MB
AU  - McIntosh MA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00124-15.

PMID- 25700402
VI  - 3
DP  - 2015
TI  - Sequence Analysis of Staphylococcus hyicus ATCC 11249T, an Etiological Agent of Exudative Epidermitis in Swine, Reveals a Type VII Secretion System Locus and a Novel 116-Kilobase Genomic Island Harboring Toxin-Encoding Genes.
PG  - e01525-14
AB  - Staphylococcus hyicus is the primary etiological agent of exudative epidermitis in swine.
      Analysis of the complete genome sequence of the type strain revealed a  locus encoding a type
      VII secretion system and a large chromosomal island harboring the genes encoding exfoliative
      toxin ExhA and an EDIN toxin homolog.
AU  - Calcutt MJ
AU  - Foecking MF
AU  - Hsieh HY
AU  - Adkins PR
AU  - Stewart GC
AU  - Middleton JR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01525-14.

PMID- 24336375
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Staphylococcus simulans UMC-CNS-990, Isolated from a Case of Chronic Bovine Mastitis.
PG  - e01037-13
AB  - Coagulase-negative staphylococci are frequently isolated from cases of subclinical bovine
      mastitis. Reported here is a draft genome sequence of
      Staphylococcus simulans UMC-CNS-990, an isolate recovered from a chronic
      intramammary infection of a Holstein cow. Unexpectedly, a cluster of genes
      encoding gas vesicle proteins was found within the 2,755-kb genome.
AU  - Calcutt MJ
AU  - Foecking MF
AU  - Hsieh HY
AU  - Perry J
AU  - Stewart GC
AU  - Middleton JR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01037-13.

PMID- 24136848
VI  - 1
DP  - 2013
TI  - Genome Sequence Analysis of Staphylococcus equorum Bovine Mastitis Isolate UMC-CNS-924.
PG  - e00840-13
AB  - Intramammary infections in dairy cattle are frequently caused by staphylococci, resulting in
      mastitis and associated economic losses. A draft genome sequence was
      determined for Staphylococcus equorum UMC-CNS-924, isolated from the milk of a
      Holstein cow, to better understand the genetic basis of its pathogenesis and
      adaptation to the bovine mammary gland.
AU  - Calcutt MJ
AU  - Foecking MF
AU  - Hsieh HY
AU  - Perry J
AU  - Stewart GC
AU  - Middleton JR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00840-13.

PMID- 24970830
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Moraxella bovoculi Strain 237T (ATCC BAA-1259T) Isolated from a Calf with Infectious Bovine Keratoconjunctivitis.
PG  - e00612-14
AB  - Moraxella bovoculi is a recently identified species, recovered from the bovine eye, which is
      under investigation as an etiological agent of infectious bovine
      keratoconjunctivitis. A draft genome sequence of the Moraxella bovoculi type
      strain 237(T) has been determined to identify features that may be important
      during host colonization.
AU  - Calcutt MJ
AU  - Foecking MF
AU  - Martin NT
AU  - Mhlanga-Mutangadura T
AU  - Reilly TJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00612-14.

PMID- 25237027
VI  - 2
DP  - 2014
TI  - Genome Sequence of Actinobacillus suis Type Strain ATCC 33415T.
PG  - e00926-14
AB  - The assembled and annotated genome of Actinobacillus suis ATCC 33415(T) is reported here. The
      2,501,598-bp genome encodes 2,246 open reading frames (ORFs)
      with strain variable incursion of an integrative conjugative element into a tRNA
      locus. Comparative analysis of the deduced gene set should inform our
      understanding of pathogenesis, genomic plasticity, and serotype variation.
AU  - Calcutt MJ
AU  - Foecking MF
AU  - Mhlanga-Mutangadura T
AU  - Reilly TJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00926-14.

PMID- 24786958
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Fusobacterium necrophorum subsp. funduliforme Bovine Liver Abscess Isolate B35.
PG  - e00412-14
AB  - Fusobacterium necrophorum is a Gram-negative anaerobic bacterium that causes foot rot and
      liver abscesses in cattle. F. necrophorum subsp. necrophorum and the less
      virulent organism F. necrophorum subsp. funduliforme are recognized. We present
      here a draft genome sequence of the bovine liver abscess isolate F. necrophorum
      subsp. funduliforme strain B35, which affords a genomic perspective of virulence
      and bovine adaptation.
AU  - Calcutt MJ
AU  - Foecking MF
AU  - Nagaraja TG
AU  - Stewart GC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00412-14.

PMID- 22408248
VI  - 194
DP  - 2012
TI  - Genome Sequence of Mycoplasma hyorhinis Strain GDL-1.
PG  - 1848
AB  - Mycoplasma hyorhinis impacts swine health and production in many countries, either as a
      primary pathogen or as a component of a polymicrobial infection.
      Isolates of this species are also common contaminants of tissue culture lines.
      The genome sequence of the cell culture isolate M. hyorhinis GDL-1 is presented
      herein.
AU  - Calcutt MJ
AU  - Foecking MF
AU  - Rosales RS
AU  - Ellis RJ
AU  - Nicholas RA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1848.

PMID- 25908137
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Mycoplasma yeatsii Strain GM274B (ATCC 43094).
PG  - e00328-15
AB  - Mycoplasma yeatsii is a goat mycoplasma species that, although an obligate parasite,
      accommodates this lifestyle as an inapparent commensalist.
      High-frequency transformation has also been reported for this species. The
      complete 895,051-bp genome sequence of strain GM274B has been determined,
      enabling an analysis of the features of this potential cloning host.
AU  - Calcutt MJ
AU  - Kent BN
AU  - Foecking MF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00328-15.

PMID- 26383655
VI  - 3
DP  - 2015
TI  - Genome Sequence Analysis of Mycoplasma sp. HU2014, Isolated from Tissue Culture.
PG  - e01086-15
AB  - The draft genome sequence of a novel Mycoplasma strain, designated Mycoplasma sp. HU2014, has
      been determined. The genome comprises 1,084,927 nucleotides and was obtained from a
      mycoplasma-infected culture of chicken DT40 cells. Phylogenetic analysis places this taxon in
      a group comprising the closely related species Mycoplasma yeatsii and Mycoplasma cottewii.
AU  - Calcutt MJ
AU  - Szikriszt B
AU  - Poti A
AU  - Molnar J
AU  - Gervai JZ
AU  - Tusnady GE
AU  - Foecking MF
AU  - Szuts D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01086-15.

PMID- 28798184
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence and Annotation of the Staphylococcus aureus Strain HG001.
PG  - e00783-17
AB  - Staphylococcus aureus is an opportunistic Gram-positive pathogen responsible for  a wide range
      of infections from minor skin abscesses to life-threatening
      diseases. Here, we report the draft genome assembly and current annotation of the
      HG001 strain, a derivative of the RN1 (NCT8325) strain with restored rbsU (a
      positive activator of SigB).
AU  - Caldelari I
AU  - Chane-Woon-Ming B
AU  - Noirot C
AU  - Moreau K
AU  - Romby P
AU  - Gaspin C
AU  - Marzi S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00783-17.

PMID- 25679537
VI  - 28
DP  - 2015
TI  - Comparative Genomic Analysis of Pseudomonas chlororaphis PCL1606 Reveals New Insight into Antifungal Compounds Involved in Biocontrol.
PG  - 249-260
AB  - Pseudomonas chlororaphis PCL1606 is a rhizobacterium that has biocontrol activity
      against many soilborne phytopathogenic fungi. The whole genome sequence of this
      strain was obtained using the Illumina Hiseq 2000 sequencing platform and was
      assembled using SOAP denovo software. The resulting 6.66-Mb complete sequence of
      the PCL1606 genome was further analyzed. A comparative genomic analysis using 10
      plant-associated strains within the fluorescent Pseudomonas group, including the
      complete genome of P. chlororaphis PCL1606, revealed a diverse spectrum of traits
      involved in multitrophic interactions with plants and microbes as well as
      biological control. Phylogenetic analysis of these strains using eight
      housekeeping genes clearly placed strain PCL1606 into the P. chlororaphis group.
      The genome sequence of P. chlororaphis PCL1606 revealed the presence of sequences
      that were homologous to biosynthetic genes for the antifungal compounds 2-hexyl,
      5-propyl resorcinol (HPR), hydrogen cyanide, and pyrrolnitrin; this is the first
      report of pyrrolnitrin encoding genes in this P. chlororaphis strain. Single-,
      double-, and triple-insertional mutants in the biosynthetic genes of each
      antifungal compound were used to test their roles in the production of these
      antifungal compounds and in antagonism and biocontrol of two fungal pathogens.
      The results confirmed the function of HPR in the antagonistic phenotype and in
      the biocontrol activity of P. chlororaphis PCL1606.
AU  - Calderon CE
AU  - Ramos C
AU  - de Vicente A
AU  - Cazorla FM
PT  - Journal Article
TA  - Mol. Plant Microbe Interact.
JT  - Mol. Plant Microbe Interact.
SO  - Mol. Plant Microbe Interact. 2015 28: 249-260.

PMID- 29724847
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Six Lactobacillus pentosus Strains Isolated from Brines of Traditionally Fermented Spanish-Style Green Table Olives.
PG  - e00379-18
AB  - Here, we report the genome sequences of six Lactobacillus pentosus strains isolated from
      traditional noninoculated Spanish-style green table olive brines.
      The total genome sizes varied between 3.77 and 4.039 Mbp. These genome sequences
      will assist in revealing the genes responsible for both technological and
      probiotic properties of these strains.
AU  - Calero-Delgado B
AU  - Martin-Platero AM
AU  - Perez-Pulido AJ
AU  - Benitez-Cabello A
AU  - Casimiro-Soriguer CS
AU  - Martinez-Bueno M
AU  - Arroyo-Lopez FN
AU  - Rodriguez-Gomez F
AU  - Bautista-Gallego J
AU  - Garrido-Fernandez A
AU  - Jimenez-Diaz R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00379-18.

PMID- 26044435
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Aliivibrio fischeri Strain 5LC, a Bacterium Retrieved from Gilthead Sea Bream (Sparus aurata) Larvae Reared in Aquaculture.
PG  - e00593-15
AB  - To shed light on the putative host-mediated lifestyle of the quintessential marine symbiont
      Aliivibrio fischeri, and on the symbiosis versus potentially
      pathogenic features of bacteria associated with farmed fish, we report the draft
      genome sequence of A. fischeri strain 5LC, a bacterium retrieved from gilthead
      sea bream (Sparus aurata) larvae.
AU  - Califano G
AU  - Franco T
AU  - Goncalves AC
AU  - Castanho S
AU  - Soares F
AU  - Ribeiro L
AU  - Mata L
AU  - Costa R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00593-15.

PMID- 16038930
VI  - 351
DP  - 2005
TI  - Crystal structure of a putative type I restriction-modification S subunit from Mycoplasma genitalium.
PG  - 749-762
AB  - The crystal structure of the eubacteria Mycoplasma genitalium ORF MG438 peptide, determined by
      multiple anomalous dispersion and refined at
      poly 2.3 angstrom resolution, reveals the organization of S subunits
      from the Type I restriction and modification system. The structure
      consists of two globular domains, with about 150 residues each,
      separated by a pair of 40 residue long antiparallel alpha-helices. The
      globular domains correspond to the variable target recognition domains
      (TRDs), as previously defined for S subunits on sequence analysis,
      while the two helices correspond to the central (CRI) and C-terminal
      (CR2) conserved regions, respectively. The structure of the MG438
      subunit presents an overall cyclic topology with an intramolecular
      2-fold axis that superimposes the N and the C-half parts, each half
      containing a globular domain and a conserved helix. TRDs are found to
      be structurally related with the small domain of the Type II N6-adenine
      DNA MTase TaqI. These relationships together with the structural
      peculiarities of MG438, in particular the presence of the
      intramolecular quasi-symmetry, allow the proposal of a model for S
      subunits recognition of their DNA targets in agreement with previous
      experimental results. In the crystal, two subunits of MG438 related by
      a crystallographic 2-fold axis present a large contact area mainly
      involving the symmetric interactions of a cluster of exposed
      hydrophobic residues. Comparison with the recently reported structure
      of an S subunit from the archaea Methanococcus jannaschii highlights
      the structural features preserved despite a sequence identity below
      20%, but also reveals important differences in the globular domains and
      in their disposition with respect to the conserved regions.
AU  - Calisto RM
AU  - Pich OQ
AU  - Pinol J
AU  - Fita I
AU  - Querol E
AU  - Carpena X
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2005 351: 749-762.

PMID- 27082731
VI  - 14
DP  - 2016
TI  - Structure of Type IIL Restriction-Modification Enzyme MmeI in Complex with DNA Has Implications for Engineering New Specificities.
PG  - e1002442
AB  - The creation of restriction enzymes with programmable DNA-binding and -cleavage specificities
      has long been a goal of modern biology. The recently discovered
      Type IIL MmeI family of restriction-and-modification (RM) enzymes that possess a
      shared target recognition domain provides a framework for engineering such new
      specificities. However, a lack of structural information on Type IIL enzymes has
      limited the repertoire that can be rationally engineered. We report here a
      crystal structure of MmeI in complex with its DNA substrate and an
      S-adenosylmethionine analog (Sinefungin). The structure uncovers for the first
      time the interactions that underlie MmeI-DNA recognition and methylation
      (5'-TCCRAC-3'; R = purine) and provides a molecular basis for changing
      specificity at four of the six base pairs of the recognition sequence
      (5'-TCCRAC-3'). Surprisingly, the enzyme is resilient to specificity changes at
      the first position of the recognition sequence (5'-TCCRAC-3'). Collectively, the
      structure provides a basis for engineering further derivatives of MmeI and
      delineates which base pairs of the recognition sequence are more amenable to
      alterations than others.
AU  - Callahan SJ
AU  - Luyten YA
AU  - Gupta YK
AU  - Wilson GG
AU  - Roberts RJ
AU  - Morgan RD
AU  - Aggarwal AK
PT  - Journal Article
TA  - PLoS Biology
JT  - PLoS Biology
SO  - PLoS Biology 2016 14: e1002442.

PMID- 22102043
VI  - 67
DP  - 2011
TI  - Crystallization and preliminary crystallographic analysis of the type IIL restriction enzyme MmeI in complex with DNA.
PG  - 1262-1265
AB  - Type IIL restriction enzymes have rejuvenated the search for user-specified DNA binding and
      cutting. By aligning and contrasting the
      highly comparable amino-acid sequences yet diverse recognition
      specificities across the family of enzymes, amino acids involved in DNA
      binding have been identified and mutated to produce alternative binding
      specificities. To date, the specificity of MmeI (a type IIL restriction
      enzyme) has successfully been altered at positions 3, 4 and 6 of the
      asymmetric TCCRAC (where R is a purine) DNA-recognition sequence. To
      further understand the structural basis of MmeI DNA-binding
      specificity, the enzyme has been crystallized in complex with its DNA
      substrate. The crystal belonged to space group P1, with unit-cell
      parameters a = 61.73, b = 94.96, c = 161.24 angstrom, alpha = 72.79,
      beta = 89.12, gamma = 71.68 degrees, and diffracted to 2.6 angstrom
      resolution when exposed to synchrotron radiation. The structure
      promises to reveal the basis of MmeI DNA-binding specificity and will
      complement efforts to create enzymes with novel specificities.
AU  - Callahan SJ
AU  - Morgan RD
AU  - Jain R
AU  - Townson SA
AU  - Wilson GG
AU  - Roberts RJ
AU  - Aggarwal AK
PT  - Journal Article
TA  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
JT  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
SO  - Acta Crystallogr. F Struct. Biol. Cryst. Commun. 2011 67: 1262-1265.

PMID- 17993529
VI  - 190
DP  - 2008
TI  - Genome sequence of Lactobacillus helveticus: an organism distinguished by selective gene loss and IS element expansion.
PG  - 727-735
AB  - Mobile genetic elements are major contributing factors to the generation of genetic diversity
      in prokaryotic organisms. For example insertion
      sequence (IS) elements have been shown to specifically contribute to niche
      adaptation by promoting a variety of genetic rearrangements. The complete
      genome sequence of the cheese culture Lactobacillus helveticus DPC 4571
      was determined and revealed significant conservation when compared to
      three non-dairy gut lactobacilli. Despite originating from significantly
      different environments, 65-75% of genes were conserved between the
      commensal and dairy lactobacilli which allowed key niche-specific gene
      sets to be described. However, the primary distinguishing feature was two
      hundred and thirteen IS elements in the DPC 4571 genome, ten times more
      than the other lactobacilli. Moreover, genome alignments revealed an
      unprecedented level of genome stability between these four Lactobacillus
      species considering the number of IS elements in the L. helveticus genome.
      Comparative analysis also indicated that the IS elements were not the
      primary agents of niche adaptation for the L. helveticus genome. A clear
      bias towards the loss of genes reported to be important for gut
      colonization was observed for the cheese culture but there was no clear
      evidence of IS-associated gene deletion and decay for the majority of
      genes lost. Furthermore, an extraordinary level of sequence diversity
      exists between copies of certain IS elements in the DPC 4571 genome
      indicating they may represent an ancient component of the L. helveticus
      genome. These data suggests a special unobtrusive relationship between the
      DPC 4571 genome and its mobile DNA complement.
AU  - Callanan M
AU  - Kaleta P
AU  - O'Callaghan J
AU  - O'Sullivan O
AU  - Jordan K
AU  - McAuliffe O
AU  - Sangrador-Vegas A
AU  - Slattery L
AU  - Fitzgerald GF
AU  - Beresford T
AU  - Ross RP
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2008 190: 727-735.

PMID- Not included in PubMed...
VI  - 178
DP  - 1984
TI  - A new sequence specific endonuclease EspI, of cyanobacterial origin.
PG  - 69-72
AB  - The isolation of a new sequence-specific endonuclease from a unicellular
      cyanobacterium is described.  This enzyme specifically cleaves the nucleotide
      sequence GC^TNAGC.
AU  - Calleja F
AU  - Dekker BMM
AU  - Coursin T
AU  - de Waard A
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1984 178: 69-72.

PMID- 2997722
VI  - 13
DP  - 1985
TI  - A new endonuclease recognizing the deoxynucleotide sequence C^CNNGG from the cyanobacterium Synechocystis 6701.
PG  - 6745-6751
AB  - A new sequence-specific endonuclease from the cyanobacterium Synechocystis
      species PCC 6701 has been purified and characterized.  This enzyme, SecI, is
      unique in recognizing the nucleotide sequence: 5' -C^C N N G G-3'3' -G G N N
      C^C-5'	and cleaves it at the position indicated by the ^ symbol.  Two other
      restriction endonucleases, SecII and SecIII, found in this organism are
      isoschizomers of MspI and MstII, respectively.
AU  - Calleja F
AU  - Tandeau de Marsac N
AU  - Coursin T
AU  - van Ormondt H
AU  - de Waard A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1985 13: 6745-6751.

PMID- 17418232
VI  - 369
DP  - 2007
TI  - Shape and Subunit Organisation of the DNA Methyltransferase M.AhdI by Small-angle Neutron Scattering.
PG  - 177-185
AB  - Type I restriction-modification (R-M) systems encode multisubunit/multidomain enzymes. Two
      genes (M and S) are required to form
      the methyltransferase (MTase) that methylates a specific base within the
      recognition sequence and protects DNA from cleavage by the endonuclease.
      The DNA methyltransferase M.AhdI is a 170 kDa tetramer with the
      stoichiometry M(2)S(2) and has properties typical of a type I MTase. The
      M.AhdI enzyme has been prepared with deuterated S subunits, to allow
      contrast variation using small-angle neutron scattering (SANS) methods.
      The SANS data were collected in a number of (1)H:(2)H solvent contrasts to
      allow matching of one or other of the subunits in the multisubunit enzyme.
      The radius of gyration (R(g)) and maximum dimensions (D(max)) of the M
      subunits in situ in the multisubunit enzyme (50 A and 190 A, respectively)
      are close of those of the entire MTase (51 A and 190 A). In contrast, the
      S subunits in situ have experimentally determined values of R(g)=35 A and
      D(max)=110 A, indicating their more central location in the enzyme. Ab
      initio reconstruction methods yield a low-resolution structural model of
      the shape and subunit organization of M.AhdI, in which the Z-shaped
      structure of the S subunit dimer can be discerned. In contrast, the M
      subunits form a much more elongated and extended structure. The core of
      the MTase comprises the two S subunits and the globular regions of the two
      M subunits, with the extended portion of the M subunits most probably
      forming highly mobile regions at the outer extremities, which collapse
      around the DNA when the MTase binds.
AU  - Callow P
AU  - Sukhodub A
AU  - Taylor JE
AU  - Kneale GG
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2007 369: 177-185.

PMID- 
VI  - 385-386
DP  - 2006
TI  - Preliminary neutron scattering studies of the Type I restriction-modification enzyme M.Ahdl.
PG  - 853-855
AB  - Type I restriction-modification (R-M) systems encode multisubunit/multidomain enzymes. Two
      genes (M and S) are required to
      form the 160kDa methyltransferase that methylates a specific base
      within the recognition sequence and protects DNA from cleavage by the
      endonuclease. Small angle neutron scattering (SANS) revealed an
      unusually large structural change in the EcoR124l methyltransferase
      following DNA binding; this involves a major repositioning of the
      subunits of the enzyme, resulting in a 60 angstrom reduction in the
      dimensions of the enzyme on forming a complex with DNA. The related
      methyltransferase M.Ahdl, with stoichiometry M2S2 has been prepared in
      two protonated/deuterated states (S and M subunits protonated, S
      deuterated and M protonated) for which SANS data have been collected in
      a number of H:D solvent contrasts. The contrast match point of the
      selectively deuterated enzyme confirms the successful reconstitution of
      the enzyme with deuterated S subunits. Ab initio shape determination
      using this contrast matched data is in progress to determine the
      subunit organization of M.Ahdl and the large change in structure that
      occurs on DNA binding.
AU  - Callow P
AU  - Timmins P
AU  - Kneale G
PT  - Journal Article
TA  - Phys. Rev., B Condens. Matter
JT  - Phys. Rev., B Condens. Matter
SO  - Phys. Rev., B Condens. Matter 2006 385-386: 853-855.

PMID- 12897023
VI  - 185
DP  - 2003
TI  - Regulated expression of the Escherichia coli dam gene.
PG  - 5012-5014
AB  - Regulated expression of the Escherichia coli dam gene has been achieved with the araBAD
      promoter lacking a ribosome binding site. Cultures of dam
      mutants containing plasmid pMQ430 show no detectable methylation in the
      absence of arabinose and complete methylation in its presence. Dam
      methyltransferase is a substrate for the Lon protease.
AU  - Calmann MA
AU  - Marinus MG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2003 185: 5012-5014.

PMID- 26089426
VI  - 3
DP  - 2015
TI  - Complete Genome Sequencing of a Multidrug-Resistant and Human-Invasive Salmonella enterica Serovar Typhimurium Strain of the Emerging Sequence Type 213 Genotype.
PG  - e00663-15
AB  - Salmonella enterica subsp. enterica serovar Typhimurium strain YU39 was isolated  in 2005 in
      the state of Yucatan, Mexico, from a human systemic infection. The
      YU39 strain is representative of the multidrug-resistant emergent sequence type
      213 (ST213) genotype. The YU39 complete genome is composed of a chromosome and
      seven plasmids.
AU  - Calva E
AU  - Silva C
AU  - Zaidi MB
AU  - Sanchez-Flores A
AU  - Estrada K
AU  - Silva GG
AU  - Soto-Jimenez LM
AU  - Wiesner M
AU  - Fernandez-Mora M
AU  - Edwards RA
AU  - Vinuesa P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00663-15.

PMID- 7607530
VI  - 157
DP  - 1995
TI  - Characterization of pPvu1, the autonomous plasmid from Proteus vulgaris that carries the genes of the PvuII restriction-modification system.
PG  - 73-79
AB  - Plasmid pPvu1 from Proteus vulgaris carries the genes of the PvuII restriction-modification
      system.  This report focuses on physical and functional features of the 4.84-kb plasmid, which
      shows a composite genetic architecture.  Plasmid pPvu1 has a replication origin and an
      incompatibility locus that each function in Escherichia coli, and an apparent cer
      recombination site.  The replication origin includes a possible RNAI gene, and the
      incompatibility locus closely resembles a rom gene.  These loci show substantial sequence
      similarity to corresponding loci from the E. coli plasmids P15A, ColEI and pSC101, and closely
      flank the PvuII genes.  The close association between a recombinational locus and the PvuII
      genes has implications for their mobility.
AU  - Calvin-Koons MD
AU  - Blumenthal RM
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 73-79.

PMID- 26067951
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Clinical Daptomycin-Nonsusceptible Methicillin-Resistant Staphylococcus aureus Strain APS211 and Its  Daptomycin-Susceptible Progenitor APS210.
PG  - e00568-15
AB  - To assess the genetic factors contributing to daptomycin resistance in Staphylococcus aureus,
      the draft genome of a clinically derived
      daptomycin-nonsusceptible isolate APS211 was generated and compared to the draft
      sequence of its susceptible progenitor strain APS210. Four genetic differences
      were identified including a previously described mutation within the mprF gene.
AU  - Cameron DR
AU  - Jiang JH
AU  - Abbott IJ
AU  - Spelman DW
AU  - Peleg AY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00568-15.

PMID- 26441910
VI  - 6
DP  - 2015
TI  - Insights on virulence from the complete genome of Staphylococcus capitis.
PG  - 980
AB  - Staphylococcus capitis is an opportunistic pathogen of the coagulase negative
      staphylococci (CoNS). Functional genomic studies of S. capitis have thus far been
      limited by a lack of available complete genome sequences. Here, we determined the
      closed S. capitis genome and methylome using Single Molecule Real Time (SMRT)
      sequencing. The strain, AYP1020, harbors a single circular chromosome of 2.44 Mb
      encoding 2304 predicted proteins, which is the smallest of all complete
      staphylococcal genomes sequenced to date. AYP1020 harbors two large mobile
      genetic elements; a plasmid designated pAYP1020 (59.6 Kb) and a prophage,
      PhiAYP1020 (48.5 Kb). Methylome analysis identified significant adenine
      methylation across the genome involving two distinct methylation motifs (1972
      putative 6-methyladenine (m6A) residues identified). Putative adenine
      methyltransferases were also identified. Comparative analysis of AYP1020 and the
      closely related CoNS, S. epidermidis RP62a, revealed a host of virulence factors
      that likely contribute to S. capitis pathogenicity, most notably genes important
      for biofilm formation and a suite of phenol soluble modulins (PSMs); the
      expression/production of these factors were corroborated by functional assays.
      The complete S. capitis genome will aid future studies on the evolution and
      pathogenesis of the coagulase negative staphylococci.
AU  - Cameron DR
AU  - Jiang JH
AU  - Hassan KA
AU  - Elbourne LD
AU  - Tuck KL
AU  - Paulsen IT
AU  - Peleg AY
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2015 6: 980.

PMID- 28546496
VI  - 5
DP  - 2017
TI  - Genome Sequence of Brevibacillus laterosporus UNISS 18, a Pathogen of Mosquitoes  and Flies.
PG  - e00419-17
AB  - The entomopathogenic properties of Brevibacillus laterosporus UNISS 18 against insects are
      well documented. Here, we report the whole-genome sequence of this
      strain, which revealed the presence of several insecticide action-related genes.
      The deriving genetic information will help to elucidate the mechanisms underlying
      strain specificity and virulence against diverse target pests.
AU  - Camiolo S
AU  - Porceddu A
AU  - Ruiu L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00419-17.

PMID- 19197347
VI  - 5
DP  - 2009
TI  - Adaptations to submarine hydrothermal environments exemplified by the genome of Nautilia profundicola.
PG  - e1000362
AB  - Submarine hydrothermal vents are model systems for the Archaean Earth environment, and some
      sites maintain conditions that may have favored the
      formation and evolution of cellular life. Vents are typified by rapid
      fluctuations in temperature and redox potential that impose a strong
      selective pressure on resident microbial communities. Nautilia
      profundicola strain Am-H is a moderately thermophilic, deeply-branching
      Epsilonproteobacterium found free-living at hydrothermal vents and is a
      member of the microbial mass on the dorsal surface of vent polychaete,
      Alvinella pompejana. Analysis of the 1.7-Mbp genome of N. profundicola
      uncovered adaptations to the vent environment--some unique and some shared
      with other Epsilonproteobacterial genomes. The major findings included:
      (1) a diverse suite of hydrogenases coupled to a relatively simple
      electron transport chain, (2) numerous stress response systems, (3) a
      novel predicted nitrate assimilation pathway with hydroxylamine as a key
      intermediate, and (4) a gene (rgy) encoding the hallmark protein for
      hyperthermophilic growth, reverse gyrase. Additional experiments indicated
      that expression of rgy in strain Am-H was induced over 100-fold with a 20
      degrees C increase above the optimal growth temperature of this bacterium
      and that closely related rgy genes are present and expressed in bacterial
      communities residing in geographically distinct thermophilic environments.
      N. profundicola, therefore, is a model Epsilonproteobacterium that
      contains all the genes necessary for life in the extreme conditions widely
      believed to reflect those in the Archaean biosphere--anaerobic, sulfur,
      H2- and CO2-rich, with fluctuating redox potentials and temperatures. In
      addition, reverse gyrase appears to be an important and common adaptation
      for mesophiles and moderate thermophiles that inhabit ecological niches
      characterized by rapid and frequent temperature fluctuations and, as such,
      can no longer be considered a unique feature of hyperthermophiles.
AU  - Campbell BJ
AU  - Smith JL
AU  - Hanson TE
AU  - Klotz MG
AU  - Stein LY
AU  - Lee CK
AU  - Wu D
AU  - Robinson JM
AU  - Khouri HM
AU  - Eisen JA
AU  - Cary SC
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2009 5: e1000362.

PMID- 26358600
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Three Antibiotic-Resistant Leuconostoc mesenteroides Strains of Dairy Origin.
PG  - e01018-15
AB  - Leuconostoc mesenteroides is a lactic acid bacterium (LAB) commonly associated with fermented
      foods. Here, we report the genome sequence of three selected dairy strains, showing atypical
      antibiotic resistances (AR). Genome analysis provided a better understanding of the genetic
      bases of AR in Leuconostoc and its potential  transferability among foodborne bacteria.
AU  - Campedelli I
AU  - Florez AB
AU  - Salvetti E
AU  - Delgado S
AU  - Orru L
AU  - Cattivelli L
AU  - Alegria A
AU  - Felis GE
AU  - Torriani S
AU  - Mayo B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01018-15.

PMID- 17302821
VI  - 63
DP  - 2007
TI  - Increased adherence and actin pedestal formation by dam-deficient enterohaemorrhagic Escherichia coli O157 : H7.
PG  - 1468-1481
AB  - Enterohaemorrhagic Escherichia coli (EHEC) are highly infectious pathogens capable of causing
      severe diarrhoeal illnesses. As a critical
      step during their colonization, EHEC adhere intimately to intestinal
      epithelial cells and generate F-actin 'pedestal' structures that
      elevate them above surrounding cell surfaces. Intimate adhesion and
      pedestal formation result from delivery of the EHEC type III secretion
      system (TTSS) effector proteins Tir and EspF(U) into the host cell and
      expression of the bacterial outer membrane adhesin, intimin. To
      investigate a role for DNA methylation during the regulation of
      adhesion and pedestal formation in EHEC, we deleted the dam (DNA
      adenine methyltransferase) gene from EHEC O157:H7 and demonstrate that
      this mutation results in increased interactions with cultured host
      cells. EHEC Delta dam exhibits dramatically elevated levels of
      adherence and pedestal formation when compared with wild-type EHEC, and
      expresses significantly higher protein levels of intimin, Tir and
      EspF(U). Analyses of GFP fusions, Northern blotting, reverse
      transcription polymerase chain reaction, and microarray experiments
      indicate that the abundance of Tir in the dam mutant is not due to
      increased transcription levels, raising the possibility that Dam
      methylation can indirectly control protein expression by a
      post-transcriptional mechanism. In contrast to other dam-deficient
      pathogens, EHEC Delta dam is capable of robust intestinal colonization
      of experimentally infected animals.
AU  - Campellone KG
AU  - Roe AJ
AU  - Lobner-Olesen A
AU  - Murphy KC
AU  - Magoun L
AU  - Brady MJ
AU  - Donohue-Rolfe A
AU  - Tzipori S
AU  - Gally DL
AU  - Leong JM
AU  - Marinus MG
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2007 63: 1468-1481.

PMID- 2838136
VI  - 4
DP  - 1988
TI  - Modification of DNA ends and detection of restriction enzyme recognition sequences in their ligated junctions.
PG  - 215-216
AB  - A program has been developed for the modelling of modifications in DNA ends,
      for the construction of ligated junctions, and for the analysis in these
      junctions of new restriction enzyme recognition sequences.  This program allows
      the analysis of restriction enzyme specificities in ligated junctions of
      cohesive or blunt DNA ends.  Cohesive ends are considered in their natural
      configuration or after modification by possible blunt-ending procedures.  The
      program also allows the modelling of partial filling-in for 5'-single-stranded
      ends.   This program has proven useful for the design of sequences with new
      restriction sites or to predict or confirm the sequences of junctions created
      by the ligation of modified ends.
AU  - Campione-Piccardo J
AU  - Moro R
PT  - Journal Article
TA  - Comput. Appl. Biosci.
JT  - Comput. Appl. Biosci.
SO  - Comput. Appl. Biosci. 1988 4: 215-216.

PMID- 28705959
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of 256 Salmonella enterica subsp. enterica Serovar Enteritidis Strains Isolated from Humans, Food, Chickens, and Farm Environments  in Brazil.
PG  - e00399-17
AB  - Salmonella enterica subsp. enterica serovar Enteritidis emerged in the late 1980s as the most
      isolated Salmonella serovar worldwide. Here, we report the draft
      genomes of 256 S Enteritidis strains isolated from humans, food, chickens, and
      farm environments in Brazil. These draft genomes will help enhance our
      understanding of this serovar in Brazil.
AU  - Campioni F
AU  - Cao G
AU  - Kastanis G
AU  - Sanchez LM
AU  - Bergamini AMM
AU  - Rodrigues DDP
AU  - Allard MW
AU  - Falcao JP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00399-17.

PMID- 29903808
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of 112 Salmonella enterica Serovar Dublin Strains Isolated from Humans and Animals in Brazil.
PG  - e00405-18
AB  - Salmonella enterica serovar Dublin is a strongly adapted serovar that causes enteritis and/or
      systemic disease in cattle and results in high rates of
      mortality. Here, we report the draft genome sequences of 112 S. Dublin strains
      isolated from humans and animals in Brazil. These draft genome sequences will
      help enhance our understanding of this serovar in Brazil.
AU  - Campioni F
AU  - Vilela FP
AU  - Cao G
AU  - Kastanis G
AU  - Miller D
AU  - Sanchez LM
AU  - Tiba-Casas MR
AU  - Fernandes SA
AU  - Rodrigues DDP
AU  - Costa RG
AU  - Allard MW
AU  - Falcao JP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00405-18.

PMID- 29853516
VI  - 6
DP  - 2018
TI  - Genome Sequence of a New Siphoviridae Phage Found in a Brazilian Bacillus thuringiensis Serovar israelensis Strain.
PG  - e01606-17
AB  - During the fermentation process, Bacillus thuringiensis (Bt) phages can result in bacterial
      death and decreased yield. In this work, we describe the genome of a
      new phage related to the Siphoviridae viral family from a Brazilian strain of Bt
      which showed high nucleotide sequence identity to the genomes of phages phi4l1
      and BtCS33.
AU  - Campos FS
AU  - Santos GR
AU  - Nascimento VL
AU  - Correia RFT
AU  - Cangussu ASR
AU  - Hoffmann K
AU  - Oliveira EE
AU  - Ribeiro BM
AU  - Aguiar RWS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01606-17.

PMID- 25395645
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Mercury-Resistant Bacterium Acinetobacter idrijaensis Strain MII, Isolated from a Mine-Impacted Area, Idrija, Slovenia.
PG  - e01177-14
AB  - We report here the first draft assembly for the genome of Acinetobacter idrijaensis strain
      MII, isolated from the Idrija mercury mine area (Slovenia).
      This strain shows a strikingly high tolerance to mercury, and the genome sequence
      shows genes involved in the mechanisms for heavy metal tolerance pathways and
      multidrug efflux pumps.
AU  - Campos-Guillen J
AU  - Caballero PJ
AU  - Cruz MJA
AU  - Molina VC
AU  - Salas RLM
AU  - Limpens GC
AU  - Garcia SI
AU  - Hernandez RMR
AU  - Soto AG
AU  - Cruz HA
AU  - Saldana GC
AU  - Romero GS
AU  - Pastrana MX
AU  - Alvarez HE
AU  - Gosar M
AU  - Dizdarevic T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01177-14.

PMID- 16672452
VI  - 72
DP  - 2006
TI  - Isolation and Sequencing of a Temperate Transducing Phage for Pasteurella multocida.
PG  - 3154-3160
AB  - A temperate bacteriophage (F108) has been isolated through mitomycin C
      induction of a Pasteurella multocida serogroup A strain. F108 has a
      typical morphology of the family Myoviridae, presenting a hexagonal head
      and a long contractile tail. F108 is able to infect all P. multocida
      serogroup A strains tested but not those belonging to other serotypes.
      Bacteriophage F108, the first P. multocida phage sequenced so far,
      presents a 30,505-bp double-stranded DNA genome with cohesive ends
      (CTTCCTCCCC cos site). The F108 genome shows the highest homology with
      those of Haemophilus influenzae HP1 and HP2 phages. Furthermore, an F108
      prophage attachment site in the P. multocida chromosome has been
      established to be inside a gene encoding tRNA(Leu). By using several
      chromosomal markers that are spread along the P. multocida chromosome, it has been
      demonstrated that F108 is able to perform generalized transduction. This fact, together with
      the absence of pathogenic genes in the F108 genome, makes this bacteriophage a valuable tool
      for P.multocida genetic manipulation.
AU  - Campoy S
AU  - Aranda J
AU  - Alvarez G
AU  - Barbe J
AU  - Llagostera M
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2006 72: 3154-3160.

PMID- 12427949
VI  - 148
DP  - 2002
TI  - A new regulatory DNA motif of the gamma subclass proteobacteria: identification of the LexA protein binding site of the plant pathogen  Xylella fastidiiosa.
PG  - 3583-3597
AB  - Escherichia coli LexA protein is the repressor of a gene network whose members are directly
      involved in the repair of damaged DNA and in the
      survival of bacterial cells until DNA lesions have been eliminated. The
      lexA gene is widely present in bacteria, although the sequences of only
      three LexA-binding sites are known: Gram-positive, alpha Proteobacteria
      and some members of gamma Proteobacteria represented by E. coli. Taking
      advantage of the fact that the genome sequence of the plant-pathogenic
      bacterium Xylella fastidiosa has been determined, its lexA gene has
      been cloned and overexpressed in E. coli to purify its product. After
      demonstration that X. fastidiosa lexA and recA genes are
      co-transcribed, gel mobility shift assays and directed mutagenesis
      experiments using the promoter of the lexA-recA transcriptional unit
      demonstrated that the X. fastidiosa LexA protein specifically binds the
      imperfect palindrome TTAGN(6)TACTA. This is the first LexA binding
      sequence identified in the gamma Proteobacteria differing from the E.
      coli-like LexA box. Although a computational search has revealed the
      presence of TTAGN(6)TACTA-like motifs upstream of X. fastidiosa genes
      other than lxA, X. fastidiosa LexA only binds the promoter of one of
      them, XF2313, encoding a putative DNA-modification methylase. Moreover,
      X. fastidiosa LexA protein does not bind any of the other genes whose
      homologues are regulated by the LexA repressor in E. coli (uvrA, uvrB,
      ssb, ruvAB, ftsK, dinG, recN and ybfE). RTPCR quantitative analysis has
      also demonstrated that lexA-recA and XF2313 genes, as well as the X.
      fastidiosa genes which are homologues to those of E. coli belonging to
      the LexA regulon, with the exception of ssb, are DNA damage-inducible
      in X. fastidiosa.
AU  - Campoy S
AU  - Mazon G
AU  - de Henestrosa ARF
AU  - Llagostera M
AU  - Monteiro PB
AU  - Barbe J
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2002 148: 3583-3597.

PMID- 12368430
VI  - 148
DP  - 2002
TI  - Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv.
PG  - 2967-2973
AB  - Original genome annotations need to be regularly updated if the information they contain is to
      remain accurate and relevant. Here the
      complete re-annotation of the genome sequence of Mycobacterium
      tuberculosis strain H37Rv is presented almost 4 years after the first
      submission. Eighty-two new protein-coding sequences (CDS) have been
      included and 22 of these have a predicted function. The majority were
      identified by manual or automated re-analysis of the genome and most of
      them were shorter than the 100 codon cut-off used in the initial genome
      analysis. The functional classification of 643 CDS has been changed based
      principally on recent sequence comparisons and new experimental data from
      the literature. More than 300 gene names and over 1000 targeted citations
      have been added and the lengths of 60 genes have been modified. Presently,
      it is possible to assign a function to 2058 proteins (52% of the 3995
      proteins predicted) and only 376 putative proteins share no homology with
      known proteins and thus could be unique to M. tuberculosis.
AU  - Camus JC
AU  - Pryor MJ
AU  - Medigue C
AU  - Cole ST
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2002 148: 2967-2973.

PMID- 24699964
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Mycobacterium bovis Strain AN5, Used for Production of Purified Protein Derivative.
PG  - e00277-14
AB  - Mycobacterium bovis strain AN5 has been used to produce purified protein derivative (PPD) for
      the intradermal test for bovine tuberculosis since it was introduced in 1948. This work
      reports the draft genome sequence of M. bovis AN5, which is used for the production of bovine
      PPD in Brazil, as well as comparisons to other strains of M. bovis and Mycobacterium
      tuberculosis.
AU  - Canevari CAB
AU  - Nishibe C
AU  - Moura A
AU  - de Alencar AP
AU  - de Azevedo IM
AU  - Hodon MA
AU  - Mota PM
AU  - Sales EB
AU  - Fonseca JAA
AU  - Almeida NF
AU  - Araujo FR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00277-14.

PMID- Not carried by PubMed...
VI  - 0
DP  - 1981
TI  - Restriction and modification in B. subtilis:  effects on plasmid transformation.
PG  - 179-187
AB  - In previous communications in this series we have demonstrated that bacterial
      transformation is resistent to restriction, whereas transfection is susceptible
      to restriction.  To explain this difference in the behaviour of the two kinds
      of DNA we have postulated that both transforming and transfecting DNA are first
      converted to single stranded DNA molecules in the course of DNA processing.
      Such single stranded transforming DNA would then hybridize to modified host DNA
      of complementary polarity to form donor/recipient complex.  This
      donor/recipient complex represents DNA heterozygous with respect to
      methylation.  It would be highly reactive to become totally modified and hence
      resistant to restriction.  In transfection, DNA/DNA hybridization would be
      between complementary strands of opposite polarity derived from different
      transfecting phage DNA molecules.  These molecules would be double stranded,
      nonmodified in the pairing regions and would hence be substrates for the
      restriction enzyme.  Major support for this interpretation came from
      experiments in which we had demonstrated that transfection of lysogenic cells
      with homologus phage DNA was insensitive to restriction.  This result pointed
      to the important role played by homology between donor and recipient DNA in the
      establishment of DNA taken up by restricting cells.
AU  - Canosi U
AU  - Luder G
AU  - Trautner TA
AU  - Bron S
PT  - Journal Article
TA  - Transformation 1980:  Proceedings of the Fifth European Meeting on Bacterial Transformation and Transfection
JT  - Transformation 1980:  Proceedings of the Fifth European Meeting on Bacterial Transformation and Transfection
SO  - Transformation 1980:  Proceedings of the Fifth European Meeting on Bacterial Transformation and Transfection 1981 0: 179-187.

PMID- 11334887
VI  - 495
DP  - 2001
TI  - Evolution and function of the Neisserial dam-replacing gene.
PG  - 178-183
AB  - Phase variation through slippage-like mechanisms involving homopolymeric tracts depends in
      part on the absence of Dam-methylase in
      several pathogenic isolates of Neisseria meningitidis, In Dam-defective
      strains drg (dam-replacing gene), flanked by pseudo-transposable small
      repeated elements (SREs), replaced dam. We demonstrate that drg encodes
      a restriction endonuclease (NmeBII) that cleaves 5'-GmeATC-3'. drg is
      also present in 50% of Neisseria lactamica strains, but in most of them
      it is inactive because of the absence of an SRE-providing, promoter.
      This is associated with the presence of GATmeC suggesting an
      alternative restriction-modification system (RM) specific for
      5'-GATC-3', similar to Sau3AI-RM of Staphylococcus aureus 3A.
      Lactococcus lactis KR2 and Listeria monocytogenes.
AU  - Cantalupo G
AU  - Bucci C
AU  - Salvatore P
AU  - Pagliarulo C
AU  - Roberti V
AU  - Lavitola A
AU  - Bruni CB
AU  - Alifano P
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 2001 495: 178-183.

PMID- 24899568
VI  - 5
DP  - 2014
TI  - Genomic mapping of phosphorothioates reveals partial modification of short consensus sequences.
PG  - 3951
AB  - Bacterial phosphorothioate (PT) DNA modifications are incorporated by Dnd proteins A-E and
      often function with DndF-H as a restriction-modification (R-M) system, as in Escherichia coli
      B7A. However, bacteria such as Vibrio cyclitrophicus FF75 lack dndF-H, which points to other
      PT functions. Here we report two novel, orthogonal technologies to map PTs across the genomes
      of B7A and FF75 with > 90% agreement: single molecule, real-time sequencing and deep
      sequencing of iodine-induced cleavage at PT (ICDS). In B7A, we detect PT on both strands of
      G(ps)AAC/G(ps)TTC motifs, but with only 12% of 40,701 possible sites modified. In contrast, PT
      in FF75 occurs as a single-strand modification at C(ps)CA, again with only 14% of 160,541
      sites modified. Single-molecule analysis indicates that modification could be partial at any
      particular genomic site even with active restriction by DndF-H, with direct interaction of
      modification proteins with GAAC/GTTC sites demonstrated with oligonucleotides. These results
      point to highly unusual target selection by PT-modification proteins and rule out known R-M
      mechanisms.
AU  - Cao B
AU  - Chen C
AU  - DeMott MS
AU  - Cheng Q
AU  - Clark TA
AU  - Xiong X
AU  - Zheng X
AU  - Butty V
AU  - Levine SS
AU  - Yuan G
AU  - Boitano M
AU  - Khai L
AU  - Song Yi
AU  - Zhou X
AU  - Deng Z
AU  - Turner SW
AU  - Korlach J
AU  - You D
AU  - Wang L
AU  - Chen S
AU  - Dedon PC
PT  - Journal Article
TA  - Nat. Commun.
JT  - Nat. Commun.
SO  - Nat. Commun. 2014 5: 3951.

PMID- 21622753
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Pusillimonas sp. T7-7, a cold-tolerate diesel oil-degrading bacterium isolated from the Bohai Sea in China.
PG  - 4021-4022
AB  - Pusillimonas sp. T7-7 is a diesel oil-degrading cold-tolerate bacterium isolated from the
      benthal mud of petroleum-contaminated site in Bohai Sea,
      China. We present here the complete genome sequence of T7-7. Genome
      analysis revealed many features of typical marine bacteria including the
      absence of intact sugar metabolic pathways, the presence of glyoxylate and
      gluconeogenesis pathways, and the abilities for nitrate assimilation and
      denitrification, as well as sulfate reduction and sulfite oxidation.
      Presence of novel genes for the degradation of diesel oils was suggested.
AU  - Cao B
AU  - Ma T
AU  - Ren Y
AU  - Ren Y
AU  - Li G
AU  - Li P
AU  - Guo X
AU  - Ding P
AU  - Feng L
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4021-4022.

PMID- 25040300
VI  - 93
DP  - 2014
TI  - Pathological phenotypes and in vivo DNA cleavage by unrestrained activity of a phosphorothioate- based restriction system in Salmonella.
PG  - 776-785
AB  - Prokaryotes protect their genomes from foreign DNA with a diversity of defence mechanisms,
      including a widespread restriction-modification (R-M) system involving phosphorothioate (PT)
      modification of the DNA backbone. Unlike classical R-M systems, highly partial PT modification
      of consensus motifs in bacterial genomes suggests an unusual mechanism of PT-dependent
      restriction. In Salmonella enterica, PT modification is mediated by four genes dptB-E, while
      restriction involves additional three genes dptF-H. Here, we performed a series of studies to
      characterize the PT-dependent restriction, and found that it presented several features
      distinct with traditional R-M systems. The presence of restriction genes in a PT-deficient
      mutant was not lethal, but instead resulted in several pathological phenotypes. Subsequent
      transcriptional profiling revealed the expression of > 600 genes was affected by restriction
      enzymes in cells lacking PT, including induction of bacteriophage, SOS response and DNA
      repair-related genes. These transcriptional responses are consistent with the observation that
      restriction enzymes caused extensive DNA cleavage in the absence of PT modifications in vivo.
      However, overexpression of restriction genes was lethal to the host in spite of the presence
      PT modifications. These results point to an unusual mechanism of PT-dependent DNA cleavage by
      restriction enzymes in the face of partial PT modification.
AU  - Cao Bo
AU  - Cheng Q
AU  - Gu C
AU  - Yao F
AU  - DeMott MS
AU  - Zheng X
AU  - Deng Z
AU  - Dedon PC
AU  - You D
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2014 93: 776-785.

PMID- 
VI  - 
DP  - 2002
TI  - Cosolute effects as probes of the role of water in DNA binding and catalysis by three restriction endonucleases.
PG  - 283
AB  - Site-specific protein-DNA interactions play important roles in many cellular processes and are
      regulated by many factors, including the amount and type of cytoplasmic solutes.  In this work
      I use restriction endonucleases EcoRI, BamHI and EcoRV endonucleases as models to probe the
      role of water in formation of protein-DNA complexes and to understand how osmolytes
      (cosolutes) promote protein-DNA association.  We observe that many cosolutes facilitate
      specific binding of protein to DNA; however the extent of the effect depends on the
      physico-chemical properties of the cosolute.  Our data show conclusively that cosolute effects
      are best understood from the perspective of 'preferential interaction' rather than those of
      'osmotic stress' or 'excluded volume effects.  Because we find that triethylene glycol is
      nearly completely excluded from the macromolecular surfaces, we use the dependence of the
      equilibrium association of protein and DNA on TEG concentration to estimate that 430, 350 and
      450 molecules of H2O are released upon formation of specific EcoRI, BamHI and EcoRV complexes,
      respectively.  The flanking sequence surrounding the specific site affects binding free energy
      but does not affect water stoichiometry.  We show that binding to nonspecific sites involves
      little water release whereas binding to miscognate sites (one incorrect base pair) entails
      intermediate water release.  Thus a massive amount of water release is a thermodynamic
      signature for the formation of the specific complex.  In addition, the experimental
      determination of water release permits us to establish for the first time that the hydrophobic
      effect can provide as much as -80 Kcal/mol, more than half of the driving force for specific
      binding.  There is no dependence on cosolute concentration for cleavage of specific sites.
      This implies that there is no additional release of water in achieving the specific transition
      state complex; thus the specific recognition complex closely resembles the transition-state
      complex.  By contrast, cosolutes enhance the cleavage of miscognate sites; we infer that the
      rearrangements required of the adaptive miscognate complex to achieve the transition state are
      accompanied by further release of water.
AU  - Cao D
PT  - Journal Article
TA  - Ph.D. Thesis, University of Pittsburgh
JT  - Ph.D. Thesis, University of Pittsburgh
SO  - Ph.D. Thesis, University of Pittsburgh 2002 : 283.

PMID- 25149677
VI  - 550
DP  - 2014
TI  - Genome-wide identification of cytosine-5 DNA methyltransferases and demethylases in Solanum lycopersicum.
PG  - 230-237
AB  - Recent studies have reported that decreased level of DNA cytosine methylation in the global
      genome was closely related to the initiation of tomato (Solanum lycopersicum) fruit ripening.
      However, genome-scale analysis of cytosine-5 DNA methyltransferases (C5-MTases) and
      demethylases in tomato has not been engaged. In this study, 7 C5-MTases and 3 demethylases
      were identified in tomato genome, which probably contributed to DNA cytosine methylation level
      in tomato. The 7 C5-MTases were categorized into 4 subgroups, and the 3 demethylases were
      classified into 2 subgroups based on phylogenetic analyses. Comprehensive analysis of their
      structure and genomic localization was also performed in this paper. According to online
      RNA-seq data, 4 S. lycopersicum C5-MTase (SlC5-MTase) genes (SlMET, SlDRM1L1, SlDRM5, SlMET3L)
      were expressed higher than others, and one DNA demethylase gene (SlDML) was significantly
      changed during tomato fruit development and ripening. Furthermore, all these five gene
      expressions at breaker (BK) stage changed with 1-methylcyclopropene (1-MCP) treatment,
      indicating that they were regulated by ethylene directly or indirectly in tomato fruit. In
      addition, subcellular localization analysis indicated that SlDRM1L1 and SlDRM5 located in the
      nucleus might have responsibility for RNA-directed DNA methylation (RdDM). Collectively, this
      paper provided a framework for gene discovery and functional characterization of C5-MTases and
      DNA demethylases in other Solanaceae species.
AU  - Cao D
AU  - Ju Z
AU  - Gao C
AU  - Mei X
AU  - Fu D
AU  - Zhu H
AU  - Luo Y
AU  - Zhu B
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 2014 550: 230-237.

PMID- 25720681
VI  - 3
DP  - 2015
TI  - Complete Sequences of Six IncA/C Plasmids of Multidrug-Resistant Salmonella enterica subsp. enterica Serotype Newport.
PG  - e00027-15
AB  - Multidrug-resistant (MDR) Salmonella enterica subsp. enterica serotype Newport has been a
      long-standing public health concern in the United States. We present the complete sequences of
      six IncA/C plasmids from animal-derived MDR S. Newport  ranging from 80.1 to 158.5 kb. They
      shared a genetic backbone with S. Newport IncA/C plasmids pSN254 and pAM04528.
AU  - Cao G
AU  - Allard MW
AU  - Hoffmann M
AU  - Monday SR
AU  - Muruvanda T
AU  - Luo Y
AU  - Payne J
AU  - Rump L
AU  - Meng K
AU  - Zhao S
AU  - McDermott PF
AU  - Brown EW
AU  - Meng J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00027-15.

PMID- 23682138
VI  - 1
DP  - 2013
TI  - Genome Sequences of Two Emerging Non-O157 Shiga Toxin-Producing Escherichia coli  Strains.
PG  - e00200-13
AB  - Shiga toxin-producing Escherichia coli (STEC) causes severe illness in humans, including
      hemorrhagic colitis and hemolytic uremic syndrome. A parallel
      evolutionary model was proposed in which E. coli strains of distinct phylogenies
      independently integrate Shiga toxin-encoding genes and evolve into STEC. We
      report the draft genomes of two emerging non-O157 STEC strains.
AU  - Cao G
AU  - Ju W
AU  - Rump L
AU  - Zhao S
AU  - Zou L
AU  - Wang C
AU  - Strain E
AU  - Luo Y
AU  - Timme R
AU  - Allard M
AU  - Brown E
AU  - Meng J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00200-13.

PMID- 24356842
VI  - 1
DP  - 2013
TI  - Draft genome sequence of pseudomonas strain p818, isolated from glyphosate-polluted soil.
PG  - e01079-13
AB  - Pseudomonas strain P818 was isolated from glyphosate-polluted soil in China. This bacterium
      presents a capacity for high glyphosate tolerance. We present the draft
      genome sequence of the strain Pseudomonas P818. The genes involved in the
      glyphosate tolerance were identified. This genomic information will facilitate
      the study of glyphosate tolerance mechanisms.
AU  - Cao G
AU  - Liu Y
AU  - Liu G
AU  - Wang J
AU  - Wang G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01079-13.

PMID- 25720683
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequences of 12 Clinical Strains of Listeria monocytogenes.
PG  - e01203-14
AB  - Listeria monocytogenes is a foodborne pathogen of global concern due to the high mortality
      rate among immunocompromised patients. Whole-genome sequences of 12 strains of L.
      monocytogenes from humans were reported. The availability of these  genomes should provide
      useful information on the evolutionary history and genetic diversity of L. monocytogenes.
AU  - Cao G
AU  - Zhang J
AU  - Xu X
AU  - Jin H
AU  - Yang X
AU  - Pan H
AU  - Allard M
AU  - Brown E
AU  - Meng J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01203-14.

PMID- 22933769
VI  - 194
DP  - 2012
TI  - Draft Genome Sequences of Eight Salmonella enterica Serotype Newport Strains from Diverse Hosts and Locations.
PG  - 5146
AB  - Salmonellosis is a major contributor to the global public health burden. Salmonella enterica
      serotype Newport has ranked among three Salmonella serotypes
      most commonly associated with food-borne outbreaks in the United States. It was
      thought to be polyphyletic and composed of independent lineages. Here we report
      draft genomes of eight strains of S. Newport from diverse hosts and locations.
AU  - Cao G
AU  - Zhao S
AU  - Strain E
AU  - Luo Y
AU  - Timme R
AU  - Wang C
AU  - Brown E
AU  - Meng J
AU  - Allard M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5146.

PMID- 27660792
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Streptomyces clavuligerus F613-1, an Industrial Producer of Clavulanic Acid.
PG  - e01020-16
AB  - Streptomyces clavuligerus strain F613-1 is an industrial strain with high-yield clavulanic
      acid production. In this study, the complete genome sequence of S.
      clavuligerus strain F613-1 was determined, including one linear chromosome and
      one linear plasmid, carrying numerous sets of genes involving in the biosynthesis
      of clavulanic acid.
AU  - Cao G
AU  - Zhong C
AU  - Zong G
AU  - Fu J
AU  - Liu Z
AU  - Zhang G
AU  - Qin R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01020-16.

PMID- 24526634
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Toxic Bloom-Forming Cyanobacterium Aphanizomenon flos-aquae NIES-81.
PG  - e00044-14
AB  - Aphanizomenon flos-aquae is a toxic filamentous cyanobacterium that causes water  blooms in
      freshwaters across the globe. We present the draft genome sequence of
      the A. flos-aquae strain NIES-81, which was determined by 454 pyrosequencing
      technology. The draft genome is ~5.7 Mb, containing 5,802 predicted
      protein-coding genes and 58 RNA genes, with a G+C content of 38.5%.
AU  - Cao H
AU  - Shimura Y
AU  - Masanobu K
AU  - Yin Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00044-14.

PMID- 27056223
VI  - 4
DP  - 2016
TI  - Genome Sequence of the Piezophilic, Mesophilic Sulfate-Reducing Bacterium Desulfovibrio indicus J2T.
PG  - e00214-16
AB  - The complete genome sequence ofDesulfovibrio indicusJ2(T), a member of the
      familyDesulfovibrionaceae, consists of 3,966,573-bp in one contig and encodes
      3,461 predicted genes, 5 noncoding RNAs, 3 rRNAs operons, and 52 tRNA-encoding
      genes. The genome is consistent with a heterotrophic, anaerobic lifestyle
      including the sulfate reduction pathway.
AU  - Cao J
AU  - Maignien L
AU  - Shao Z
AU  - Alain K
AU  - Jebbar M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00214-16.

PMID- 10387053
VI  - 38
DP  - 1999
TI  - Binding kinetics and footprinting of TaqI endonuclease: Effects of metal cofactors on sequence-specific interactions.
PG  - 8080-8087
AB  - Restriction endonucleases achieve sequence-specific recognition and strand cleavage through
      the interplay of base, phosphate backbone, and metal cofactor interactions. In this study, we
      investigate the binding kinetics of TaqI endonuclease using the wild-type enzyme and a binding
      proficient, catalysis deficient mutant TaqI-D137A both in the absence of a metal cofactor and
      in the presence of Mg2+ or Ca2+. As demonstrated by gel mobility shift analyses, TaqI
      endonuclease requires a metal cofactor for achieving high-affinity specific binding to its
      cognate sequence, TCGA. In the absence of a metal cofactor, the enzyme binds all DNA sequences
      (TaqI cognate site, star site, and nonspecific site) with essentially equal affinity, thereby
      exhibiting little discrimination. The dissociation constant of the cognate sequence in the
      presence of Mg2+ at 60 degrees C is 0.26 nM, a value comparable to our previously reported Km
      of 0.5 nM measured under steady-state conditions. The TaqI-TCGA-Mg2+ complex is stable, with a
      half-life of 21 min at 60 degrees C. The boundary of the protein-DNA interface is approximated
      to be about 18 bp as determined by DNase I footprinting. Data from this study support the
      notion that a metal cofactor plays a critical role for achieving sequence-specific
      discrimination in a subset of nucleases, including TaqI, EcoRV, and others.
AU  - Cao W
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1999 38: 8080-8087.

PMID- 9830053
VI  - 273
DP  - 1998
TI  - Identification of TaqI endonuclease active site residues by Fe2+-mediated oxidative cleavage.
PG  - 33002-33010
AB  - Metal cofactors (Mg2+ and Mn2+) modulate both specific DNA binding and strand cleavage in the
      TaqI endonuclease.  This work attempts to establish the structural basis of TaqI-DNA-metal2+
      interactions using an affinity cleavage technique.  The protein was cleaved by localized
      hydroxyl radicals generated by oxidizing Fe2+ within the metal binding sites.  Cleavage
      fragments were separated by SDS-polyacrylamide gel electrophoresis, and cleavage sites were
      determined using micropeptide sequencing.  Eleven amino acid residues in the vicinity of
      cleavage sites were selected for site-directed mutagenesis.  The negative charge at Asp137 is
      essential for DNA cleavage but not required for sequence specific binding.  Mutations at
      Asp142 abolish both specific binding and catalysis, except for D142E, which converts TaqI into
      a completely Mn2+-dependent endonuclease.  The positive charge at Lys158 appears to be
      important for both specific binding and catalysis.  Mutations at other sites affect binding
      and/or catalysis to different degrees, except Trp113 and Glu135, which appear to be
      nonessential for the TaqI enzyme activity.  The critical residues for TaqI function are
      distinct from the PDX14-20(E/D)XK catalytic motif elucidated from other endonucleases.
AU  - Cao W
AU  - Barany F
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1998 273: 33002-33010.

PMID- 11257528
VI  - 1546
DP  - 2001
TI  - Exploring the catalytic center of TaqI endonuclease: rescuing catalytic activity by double mutations and Mn(2+).
PG  - 253-260
AB  - TaqI is a metal-dependent endonuclease that recognizes T^CGA, with the arrow
      indicating the cleavage site. Mutations at K158 render the enzyme inactive and mutations at
      K157 significantly reduce DNA cleavage activity (W. Cao and F. Barany (1998) J. Biol. Chem.
      273, 33002-33010). Aspartate, glutamate, and histidine substitutions were made at K158 in the
      wild-type and K157S mutant TaqI endonuclease to understand the functional organization of the
      active site. None of the mutants was active with Mg(2+), but the DNA cleavage activities were
      partly rescued by Mn(2+) for K157S-K158E and K157S-K158H mutants. The rescuing effects were
      observed with Mn(2+) but not with other divalent cations. K157S-K158E required higher Mn(2+)
      concentrations than the wild-type enzyme for DNA cleavage activity, suggesting that a Mn(2+)
      ion is weakly bound at the 158 position. The need to neutralize K157 to recover the catalytic
      activity of K158E and K158H indicates that K158 and K157 may interact functionally. In analogy
      with EcoRV, Ca(2+) stimulated Mn(2+)-mediated cleavage for the wild-type TaqI, suggesting the
      existence of at least two metal ions at the catalytic center. A catalytic mechanism involving
      two metal ions and the K157-K158 pair is proposed for TaqI endonuclease.
AU  - Cao W
AU  - Lu J
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 2001 1546: 253-260.

PMID- 9332368
VI  - 197
DP  - 1997
TI  - Nucleotide sequences and gene organization of TaqI endonuclease isoschizomers from Thermus sp. SM32 and Thermus filiformis Tok6AI.
PG  - 205-214
AB  - Eight TaqI isoschizomer genes, two from Yellowstone National Park, one from Japan, two from
      New Zealand, two from Portugal, and one from the Azores (1000 miles west of Portugal), were
      PCR-amplified and sequenced.  Sequence alignment of isoschizomers isolated from close
      geographical locations shows identical or almost identical protein sequences, while
      isoschizomers from distant sites demonstrate considerable diversity, ranging from 54 to 75% in
      amino acid identity.  Accordingly, these isoschizomers were arranged into four geographical
      groups, i.e., USA as represented by Thermus aquaticus YT1, Japan by Thermus thermophilus HB8,
      New Zealand by thermus filiformis Tok5AI, Portugal by Thermus sp. SM32.  The complete ORFs of
      two new representative genes, tfiTok6AII and tsp32IR, were obtained by bubble PCR.  Unlike
      M.TaqI-R.TaqI and M.TthHB81-R.TthHB8I which exhibit an unusual 13-codon overlap, the methylase
      and endonuclease genes are each separated by 15 nucleotides in the TfiTok6AII and Tsp32IR
      restriction-modification systems.  Phylogenetic analysis suggests that initially TfiTok6AII
      diverged from a common ancestor, then Tsp32IR branched out, and finally TaqI and TthHB8I
      diverged from each other during evolution.
AU  - Cao W
AU  - Lu J
AU  - Barany F
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1997 197: 205-214.

PMID- 9657984
VI  - 333
DP  - 1998
TI  - Cloning and thermostability of TaqI endonuclease isoschizomers from Thermus species SM32 and Thermus filiformis Tok6A1.
PG  - 425-431
AB  - Two TaqI endonuclease (hereafter referred to as TaqI) isoschizomer genes, tsp32IR from Thermus
      species SM32 of Azores and tfiTok6A1I from T. filiformis Tok6A1 of New Zealand, were cloned in
      Escherichia coli.  The overexpressed enzymes were partly purified and their thermostability
      was determined.  In the medium-salt buffer, Tsp32IR, TfiTok6A1I and one previously cloned TaqI
      isoschizomer (TthHB8I) were more thermostable than TaqI.  Tsp32IR remained partly active up to
      90 C in the low-salt buffer.  Six amino acid residues that are identical in the three high
      thermostability isoschizomers (Tsp32IR, TfiTok6A1I and TthHB8I) but differ in TaqI might
      provide added rigidity for thermostabilization.  These include four proline residues located
      in or near loop regions, and one alanine and one arginine located at helix regions in the
      predicted TaqI endonuclease secondary structure.  The possible role of these residues in
      thermostabilization was evaluated by mutagenizing the TaqI enzyme.  Mutants generated at these
      six positions were less thermostable than wild-type TaqI.  The results suggest that the
      surrounding sequence or structural context might be as important as the mutation itself.
AU  - Cao W
AU  - Lu J
AU  - Welch SG
AU  - Williams RAD
AU  - Barany F
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 1998 333: 425-431.

PMID- 7857938
VI  - 34
DP  - 1995
TI  - Stringent and relaxed specificities of TaqI endonuclease: interactions with metal cofactors and DNA sequences.
PG  - 2276-2283
AB  - We have studied the roles of metal cofactors Mg2+ and Mn2+ in modulating substrate
      specificities during the enzymatic cycle of TaqI endonuclease using steady state and
      single-turnover kinetics. In the presence of Mg2+, stringent discrimination of TaqI against
      single base-pair changes (star sites) is manifested by the loss of tight, specific binding in
      the early stage of the enzymatic cycle. In the presence of Mn2+, relaxed specificity for a
      star site sequence is attributed to formation of three distinct classes of the ternary
      complexes: the highly activated TaqI-cognate-Mn2+ complex; the partially activated
      TaqI-star-Mn2+-complex; and the ground state, inactive TaqI-nonspecific-Mn2+ complex. In
      addition to a high affinity for a TaqI-DNA complex, Mn2+ also binds to TaqI in a
      DNA-independent fashion. This may facilitate enzyme activation, which could account for the
      observed relaxation in substrate specificity. Thus, the TaqI-DNA-Mn2+ could be formed by
      either of two pathways: TaqI binding to DNA followed by the binding of Mn2+ or TaqI first
      binding to Mn2+ followed by the addition of DNA. The inactive, nonspecific TaqI-star-Mg2+
      complex virtually prohibits transition state interactions, but a TaqI-star-Mn2+ complex
      attains a measurable single-turnover rate. In the late stages of the enzymatic cycle, high
      affinity of Mn2+ to a TaqI-DNA complex and to the TaqI enzyme may also account for a slower
      rate of product release.
AU  - Cao W
AU  - Mayer AN
AU  - Barany F
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1995 34: 2276-2283.

PMID- 28860252
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequences of Brucella melitensis Strain QY1, Isolated from Sheep in  Gansu, China.
PG  - e00896-17
AB  - The facultative intracellular Gram-negative bacterium Brucella melitensis causes  brucellosis
      in domestic and wild mammals, and it is a dominant pathogen
      responsible for human disease. This study reports the whole-genome sequencing of
      B. melitensis strain QY1, isolated from sheep suffering from abortion and
      arthritis in 2015 in Gansu, China.
AU  - Cao X
AU  - Li Z
AU  - Lou Z
AU  - Fu B
AU  - Liu Y
AU  - Shang Y
AU  - Jing Z
AU  - Zhou J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00896-17.

PMID- 29326214
VI  - 6
DP  - 2018
TI  - Whole-Genome Sequences of Brucella melitensis Strain QH61, Isolated from Yak in Qinghai, China.
PG  - e01422-17
AB  - The facultative intracellular Gram-negative bacterium Brucella melitensis causes  brucellosis
      in domestic and wild mammals. Brucella melitensis QH61 was isolated
      from a yak suffering from abortion in 2015 in Qinghai, China. Here, we report the
      whole-genome sequence of B. melitensis strain QH61.
AU  - Cao X
AU  - Li Z
AU  - Lou Z
AU  - Fu B
AU  - Liu Y
AU  - Shang Y
AU  - Zhou J
AU  - Jing Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01422-17.

PMID- 10781108
VI  - 97
DP  - 2000
TI  - Conserved plant genes with similarity to mammalian de novo DNA methyltransferases.
PG  - 4979-4984
AB  - DNA methylation plays a critical role in controlling states of gene activity in most
      eukaryotic organisms, and it is essential for proper growth and development. Patterns of
      methylation are established by de novo methyltransferases and maintained by maintenance
      methyltransferase activities. The Dnmt3 family of de novo DNA methyltransferases has recently
      been characterized in animals. Here we describe DNA methyltransferase genes from both
      Arabidopsis and maize that show a high level of sequence similarity to Dnmt3, suggesting that
      they encode plant de novo methyltransferases. Relative to all known eukaryotic
      methyltransferases, these plant proteins contain a novel arrangement of the motifs required
      for DNA methyltransferase catalytic activity. The N termini of these methyltransferases
      contain a series of ubiquitin-associated (UBA) domains. UBA domains are found in several
      ubiquitin pathway proteins and in DNA repair enzymes such as Rad23, and they may be involved
      in ubiquitin binding. The presence of UBA domains provides a possible link between DNA
      methylation and ubiquitin/proteasome pathways.
AU  - Cao X
AU  - Springer NM
AU  - Muszynski MG
AU  - Phillips RL
AU  - Kaeppler S
AU  - Jacobsen SE
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2000 97: 4979-4984.

PMID- 14680640
VI  - 13
DP  - 2003
TI  - Role of the DRM and CMT3 Methyltransferases in RNA-directed DNA methylation.
PG  - 2212-2217
AB  - RNA interference is a conserved process in which double-stranded RNA is processed into 21-25
      nucleotide siRNAs that trigger posttranscriptional
      gene silencing. In addition, plants display a phenomenon termed
      RNA-directed DNA methylation (RdDM) in which DNA with sequence identity to
      silenced RNA is de novo methylated at its cytosine residues. This
      methylation is not only at canonical CpG sites but also at cytosines in
      CpNpG and asymmetric sequence contexts. In this report, we study the role
      of the DRM and CMT3 DNA methyltransferase genes in the initiation and
      maintenance of RdDM. Neither drm nor cmt3 mutants affected the maintenance
      of preestablished RNA-directed CpG methylation. However, drm mutants
      showed a nearly complete loss of asymmetric methylation and a partial loss
      of CpNpG methylation. The remaining asymmetric and CpNpG methylation was
      dependent on the activity of CMT3, showing that DRM and CMT3 act
      redundantly to maintain non-CpG methylation. These DNA methyltransferases
      appear to act downstream of siRNAs, since drm1 drm2 cmt3 triple mutants
      show a lack of non-CpG methylation but elevated levels of siRNAs. Finally,
      we demonstrate that DRM activity is required for the initial establishment
      of RdDM in all sequence contexts including CpG, CpNpG, and asymmetric
      sites.
AU  - Cao XF
AU  - Aufsatz W
AU  - Zilberman D
AU  - Mette MF
AU  - Huang MS
AU  - Matzke M
AU  - Jacobsen SE
PT  - Journal Article
TA  - Curr. Biol.
JT  - Curr. Biol.
SO  - Curr. Biol. 2003 13: 2212-2217.

PMID- 12121623
VI  - 12
DP  - 2002
TI  - Role of the Arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing.
PG  - 1138-1144
AB  - Proper DNA methylation patterning requires the complementary processes of de novo methylation
      (the initial methylation of unmethylated DNA
      sequences) and maintenance methylation (the faithful replication of
      preexisting methylation). Arabidopsis has two types of
      methyltransferases with demonstrated maintenance activity: MET1, which
      maintains CpG methylation [1-3] and is homologous to mammalian DNMT1,
      and CHROMOMETHYLASE 3 (CMT3), which maintains CpNpG (N = A, T, C, or G)
      methylation [3,4] and is unique to the plant kingdom. Here we describe
      loss-of-function mutations in the Arabidopsis DOMAINS REARRANGED
      METHYLASE (DRM) genes [5] and provide evidence that they encode de novo
      methyltransferases. drm1 drm2 double mutants retained preexisting CpG
      methylation at the endogenous FWA locus but blocked de novo CpG
      methylation that is normally associated with FWA transgene silencing.
      Furthermore, drm1 drm2 double mutants blocked de novo CpNpG and
      asymmetric methylation and gene silencing of the endogenous SUPERMAN
      (SUP) gene, which is normally triggered by an inverted SUP repeat.
      However, drm1 drm2 double mutants did not show reactivation of
      previously established SUPERMAN epigenetic silenced alleles. Thus, drm
      mutants prevent the establishment but not the maintenance of gene
      silencing at FWA and SUP, suggesting that the DRMs encode the major de
      novo methylation enzymes affecting these genes.
AU  - Cao XF
AU  - Jacobsen SE
PT  - Journal Article
TA  - Curr. Biol.
JT  - Curr. Biol.
SO  - Curr. Biol. 2002 12: 1138-1144.

PMID- 12151602
VI  - 99
DP  - 2002
TI  - Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes.
PG  - 16491-16498
AB  - Many plant, animal, and fungal genomes contain cytosine DNA methylation in asymmetric sequence
      contexts (CpHpH, H = A, T, C). Although the enzymes responsible for this methylation are
      unknown, it has been assumed that asymmetric methylation is maintained by the persistent
      activity of de novo methyltransferases (enzymes capable of methylating previously unmodified
      DNA). We recently reported that the domains rearranged methylase (DRM) genes are required for
      de novo DNA methylation in Arabidopsis thaliana because drm1 drm2 double mutants lack the de
      novo methylation normally associated with transgene silencing. In this study, we have used
      bisulfite sequencing and Southern blot analysis to examine the role of the DRM loci in the
      maintenance of asymmetric methylation. At some loci, drm1 drm2 double mutants eliminated all
      asymmetric methylation. However, at the SUPERMAN locus, asymmetric methylation was only
      completely abolished in drm1 drm2 chromomethylase 3 (cmt3) triple mutant plants. drm1 drm2
      double mutants also showed a strong reduction of CpNpG (n = A, T, C, or G) methylation at some
      loci, but not at others. The drm1 drm2 cmt3 triple mutant plants did not affect CpG
      methylation at any locus tested, suggesting that the primary CpG methylases are encoded by the
      MET1 class of genes. Although neither the drm1 drm2 double mutants nor the cmt3 single mutants
      show morphological defects, drm1 drm2 cmt3 triple mutant plants show pleiotropic effects on
      plant development. Our results suggest that the DRM and CMT3 genes act in a partially
      redundant and locus-specific manner to control asymmetric and CpNpG methylation.
AU  - Cao XF
AU  - Jacobsen SE
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2002 99: 16491-16498.

PMID- 23558531
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Wohlfahrtiimonas chitiniclastica Strain SH04, Isolated from Chrysomya megacephala Collected from Pudong International Airport  in China.
PG  - e0011913
AB  - Wohlfahrtiimonas chitiniclastica bacilli that live in the larvae of a parasitic fly were
      recently isolated and are speculated to be the cause of fulminant
      sepsis. Here we report and analyze the complete genome sequence of
      Wohlfahrtiimonas chitiniclastica strain SH04. No complete genome sequence of a
      Wohlfahrtiimonas chitiniclastica isolate has been documented previously.
AU  - Cao XM
AU  - Chen T
AU  - Xu LZ
AU  - Yao LS
AU  - Qi J
AU  - Zhang XL
AU  - Yan QL
AU  - Deng YH
AU  - Guo TY
AU  - Wang J
AU  - Hu KX
AU  - Xu BL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0011913.

PMID- 23990586
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Human-Pathogenic Bacterium Vibrio alginolyticus E0666.
PG  - e00686-13
AB  - Vibrio alginolyticus is a Gram-negative halophilic bacterium with worldwide distribution. In
      this work, we report the draft genome sequence of a V.
      alginolyticus strain (E0666) isolated from Epinephelus coioides ascites in the
      Shantou city of Guangdong Province, China.
AU  - Cao Y
AU  - Liu XF
AU  - Zhang HL
AU  - Chen YJ
AU  - Hu CJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00686-13.

PMID- 23661471
VI  - 1
DP  - 2013
TI  - Genome Sequencing of Ralstonia solanacearum FQY_4, Isolated from a Bacterial Wilt Nursery Used for Breeding Crop Resistance.
PG  - e00125-13
AB  - Ralstonia solanacearum strain FQY_4 was isolated from a bacterial wilt nursery, which is used
      for breeding crops for Ralstonia resistance in China. Here, we
      report the complete genome sequence of FQY_4 and its comparison with other
      published R. solanacearum genomes, especially with the strains GMI1000 and Y45 in
      the same group.
AU  - Cao Y
AU  - Tian B
AU  - Liu Y
AU  - Cai L
AU  - Wang H
AU  - Lu N
AU  - Wang M
AU  - Shang S
AU  - Luo Z
AU  - Shi J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00125-13.

PMID- 3248716
VI  - 74
DP  - 1988
TI  - Maintenance of methylation patterns in Tetrahymena thermophila.
PG  - 103-104
AB  - Historically, the maintenance of methylation paterns in differentiated cells has been
      attributed to the action of a methyltransferase that functions after DNA replication and whose
      target is palindromic, hemimethylated sites. This maintenance methyltransferase is thought to
      methylate the daughter strand of newly replicated DNA, thus retaining the pattern of the
      parent through successive divisions. We have begun a molecular anlaysis of the maintenance of
      methylation patterns during somatic proliferation in the ciliated protozoan Tetrahymena
      thermophila. The data we have accumulated indicate that this process is more complex than a
      semiconservative copying model.
AU  - Capowski EE
AU  - Wells JM
AU  - Karrer KM
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 103-104.

PMID- 25342687
VI  - 2
DP  - 2014
TI  - Genome Sequences of Five Oenococcus oeni Strains Isolated from Nero Di Troia Wine from the Same Terroir in Apulia, Southern Italy.
PG  - e01077-14
AB  - Oenococcus oeni is the principal lactic acid bacterium responsible for malolactic fermentation
      in wine. Here, we announce the genome sequences of five O. oeni
      strains isolated from Nero di Troia wine undergoing spontaneous malolactic
      fermentation, and we report, for the first time, several genome sequences of
      strains isolated from the same terroir.
AU  - Capozzi V
AU  - Russo P
AU  - Lamontanara A
AU  - Orru L
AU  - Cattivelli L
AU  - Spano G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01077-14.

PMID- 24158549
VI  - 1
DP  - 2013
TI  - Genome Sequence of Rhodococcus sp. Strain BCP1, a Biodegrader of Alkanes and Chlorinated Compounds.
PG  - e00657-13
AB  - Rhodococcus sp. strain BCP1 cometabolizes chlorinated compounds and mineralizes a broad range
      of alkanes, as it is highly tolerant to them. The high-quality draft
      genome sequence of Rhodococcus sp. strain BCP1, consisting of 6,231,823 bp, with
      a G+C content of 70.4%, 5,902 protein-coding genes, and 58 RNA genes, is
      presented here.
AU  - Cappelletti M
AU  - Di Gennaro P
AU  - D'Ursi P
AU  - Orro A
AU  - Mezzelani A
AU  - Landini M
AU  - Fedi S
AU  - Frascari D
AU  - Presentato A
AU  - Zannoni D
AU  - Milanesi L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00657-13.

PMID- 26798092
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Two Multidrug-Resistant Extended-Spectrum-beta-Lactamase-Producing Klebsiella pneumoniae Strains Causing   Bloodstream Infections.
PG  - e01533-15
AB  - Multidrug-resistant (MDR) Klebsiella pneumoniae has become a major contributor to nosocomial
      bloodstream infections. Here, we report the draft genome sequences of
      two MDR extended-spectrum-beta-lactamase-producing strains causing bloodstream
      infections. These sequenced genomes display a wide-spectrum virulence arsenal and
      will help us understand the genomic basis of K. pneumoniae virulence.
AU  - Carasso E
AU  - Salmon-Divon M
AU  - Carmeli Y
AU  - Banin E
AU  - Navon-Venezia S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01533-15.

PMID- 22123704
VI  - 56
DP  - 2012
TI  - Evolution of IncA/C blaCMY-2-Carrying Plasmids by Acquisition of the blaNDM-1 Carbapenemase Gene.
PG  - 783-786
AB  - The bla(NDM-1) gene has been reported to be often located on broad-host-range
      plasmids of the IncA/C type in clinical but also environmental bacteria recovered
      from the New Delhi, India, area. IncA/C-type plasmids are the main vehicles for
      the spread of the cephalosporinase gene bla(CMY-2), frequently identified in the
      United States, Canada, and Europe. In this study, we completed the sequence of
      IncA/C plasmid pNDM-KN carrying the bla(NDM-1) gene, recovered from a Klebsiella
      pneumoniae isolate from Kenya. This sequence was compared with those of three
      IncA/C-type reference plasmids from Escherichia coli, Yersinia ruckeri, and
      Photobacterium damselae. Comparative analysis showed that the bla(NDM-1) gene was
      located on a widely diffused plasmid scaffold known to be responsible for the
      spread of bla(CMY-2)-like genes and consequently for resistance to broad-spectrum
      cephalosporins. Considering that IncA/C plasmids possess a broad host range, this
      scaffold might support a large-scale diffusion of the bla(NDM-1) gene among
      Gram-negative rods.
AU  - Carattoli A
AU  - Villa L
AU  - Poirel L
AU  - Bonnin RA
AU  - Nordmann P
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2012 56: 783-786.

PMID- Not carried by PubMed...
VI  - 7
DP  - 1990
TI  - Cloning and characterization of the PvuII restriction-modification system in Proteus vulgaris.  Purification of recombinant restrictase.
PG  - 167-175
AB  - The PvuII restriction-modification system (RMS) from P. vulgaris was cloned and
      expressed restrictase and methylase were studied in different E. coli strains.
      Only the E. coli strain HB101 (mcrB-) was efficiently transformed by plasmids
      carrying the RMSII PvuII.  A new procedure for the purification of recombinant
      PvuII restrictase was applied, using ion exchange chromatography.  The methods
      described in this paper allow the obtention of high amounts of PvuII
      restrictase free of contaminants.
AU  - Carballeira N
AU  - Jorge Y
AU  - Guerra M
AU  - Madrazo JJ
AU  - Lleonart R
AU  - Silva A
AU  - Garcia O
AU  - De La Fuente J
AU  - Herrera L
PT  - Journal Article
TA  - Biotecnol. Apl.
JT  - Biotecnol. Apl.
SO  - Biotecnol. Apl. 1990 7: 167-175.

PMID- 27908998
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequencing Applied to the Molecular Epidemiology of Shiga Toxin-Producing Escherichia coli O157:H7 in Argentina.
PG  - e01341-16
AB  - Shiga toxin-producing Escherichia coli strains are worldwide associated with sporadic human
      infections and outbreaks. In this work, we report the availability
      of high-quality draft whole-genome sequences for 19 O157:H7 strains isolated in
      Argentina.
AU  - Carbonari CC
AU  - Fittipaldi N
AU  - Teatero S
AU  - Athey TB
AU  - Pianciola L
AU  - Masana M
AU  - Melano RG
AU  - Rivas M
AU  - Chinen I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01341-16.

PMID- 7788720
VI  - 27
DP  - 1995
TI  - A group-I intron in the mitochondrial small subunit ribosomal RNA gene of Sclerotinia sclerotiorum.
PG  - 166-176
AB  - A 1,380-bp intervening sequence within the mitochondrial small subunit
      ribosomal RNA (mt SSU rRNA) gene of the fungus Sclerotinia sclerotiorum
      has been sequenced and identified as a group-I intron. This is the first
      report of an intron in the mt SSU rRNA gene. The intron shows close
      similarity in secondary structure to the subgroup-IC2 introns from
      Podospora (ND3i1, ND5i2, and COIi5) and Neurospora (ND5i1). The intron has
      an open reading frame (ORF) that encodes a putative protein of 420 amino
      acids which contains two copies of the LAGLI-DADG motif. The ORF belongs
      to a family of ORFs identified in Podospora (ND3i1, ND4Li1, ND4Li2, ND5i2,
      and COIi5) and Neurospora (ND5i1). The putative 420-aa polypeptide is also
      similar to a site-specific endonuclease in the chloroplast large subunit
      ribosomal RNA (LSU rRNA) gene of the green alga Chlamydomonas eugametos.
      In each clone of S. sclerotiorum examined, including several clones which
      were sampled over a 3-year period from geographically separated sites, all
      isolates either had the intron or lacked the intron within the mt SSU rRNA
      gene. Screening by means of Southern hybridization and PCR amplification
      detected the intron in the mt SSU rRNA genes of S. minor, S. trifoliorum
      and Sclerotium cepivorum, but not in other members of the Sclerotiniaceae,
      such as Botrytis anamorphs of Botryotinia spp., or in other ascomycetous
      and basidiomycetous fungi.
AU  - Carbone I
AU  - Anderson JB
AU  - Kohn LM
PT  - Journal Article
TA  - Curr. Genet.
JT  - Curr. Genet.
SO  - Curr. Genet. 1995 27: 166-176.

PMID- 2183189
VI  - 18
DP  - 1990
TI  - Cloning and characterization of the HpaII methylase gene.
PG  - 1377-1383
AB  - The HpaII restriction-modification system from Haemophilus parainfluenzae
      recognizes the DNA sequence CCGG.  The gene for the HpaII methylase has been
      cloned into E. coli and its nucleotide sequence has been determined.  The DNA
      of the clones is fully protected against cleavage by the HpaII restriction
      enzyme in vitro, indicating that the methylase gene is active in E. coli.  The
      clones were isolated in an McrA- strain of E. coli; attempts to isolate them in
      an McrA+ strain were unsuccessful.  The clones do not express detectable HpaII
      restriction endonuclease activity, suggesting that either the endonuclease gene
      is not expressed well in E. coli, or that it is not present in its entirety in
      any of the clones that we have isolated.  The derived amino acid sequence of
      the HpaII methylase shows overall similarity to other cytosine methylases.  It
      bears a particularly close resemblance to the sequences of the HhaI, BsuFI and
      MspI methylases.  When compared with three other methylases that recognize
      CCGG, the variable region of the HpaII methylase, which is believed to be
      responsible for sequence specific recognition, shows some similarity to the
      corresponding regions of the BsuFI and MspI methylases, but is rather
      dissimilar to that of the SPR methylase.
AU  - Card CO
AU  - Wilson GG
AU  - Weule K
AU  - Hasapes J
AU  - Kiss A
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 1377-1383.

PMID- 25377718
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Iron-Oxidizing Acidophile Leptospirillum ferriphilum Type Strain DSM 14647.
PG  - e01153-14
AB  - The genomic features of the Leptospirillum ferriphilum type strain DSM 14647 are  described
      here. An analysis of the predicted genes enriches our knowledge of the
      molecular basis of iron oxidation, improves our understanding of its role in
      industrial bioleaching, and suggests how it is adapted to live at extremely low
      pH.
AU  - Cardenas JP
AU  - Lazcano M
AU  - Ossandon FJ
AU  - Corbett M
AU  - Holmes DS
AU  - Watkin E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01153-14.

PMID- 26294616
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Pseudomonas sp. Strain LFM046, a Producer of Medium-Chain-Length Polyhydroxyalkanoate.
PG  - e00966-15
AB  - Pseudomonas sp. LFM046 is a medium-chain-length polyhydroxyalkanoate (PHAMCL) producer capable
      of using various carbon sources (carbohydrates, organic acids,
      and vegetable oils) and was first isolated from sugarcane cultivation soil in
      Brazil. The genome sequence was found to be 5.97 Mb long with a G+C content of
      66%.
AU  - Cardinali-Rezende J
AU  - Alexandrino PM
AU  - Nahat RA
AU  - Sant'Ana DP
AU  - Silva LF
AU  - Gomez JG
AU  - Taciro MK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00966-15.

PMID- 26798101
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Halomonas sp. HG01, a Polyhydroxyalkanoate-Accumulating  Strain Isolated from Peru.
PG  - e01598-15
AB  - Halomonas sp. strain HG01, isolated from a salt mine in Peru, is a halophilic aerobic
      heterotrophic bacterium accumulating poly-3-hydroxybutyrate and
      poly(3-hydroxybutyrate-co-3-hydroxyvalerate) from different carbon sources. Here,
      we report the draft genome sequence of this isolate, which was found to be
      3,665,487 bp long, with a G+C content of 68%.
AU  - Cardinali-Rezende J
AU  - Nahat RA
AU  - Guzman MCW
AU  - Carreno FCR
AU  - Silva LF
AU  - Taciro MK
AU  - Gomez JG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01598-15.

PMID- 10508852
VI  - 147
DP  - 1999
TI  - DNA methyltransferase is actively retained in the cytoplasm during early development.
PG  - 25-32
AB  - The overall DNA methylation level sharply decreases from the zygote to the blastocyst stage
      despite the presence of high levels of DNA methyltransferase (Dnmt1). Surprisingly, the enzyme
      is localized in the cytoplasm of early embryos despite the presence of several functional
      nuclear localization signals. We mapped a region in the NH(2)-terminal, regulatory domain of
      Dnmt1 that is necessary and sufficient for cytoplasmic retention during early development.
      Altogether, our results suggest that Dnmt1 is actively retained in the cytoplasm, which
      prevents binding to its DNA substrate in the nucleus and thereby contributes to the erasure of
      gamete-specific epigenetic information during early mammalian development.
AU  - Cardoso MC
AU  - Leonhardt H
PT  - Journal Article
TA  - J. Cell Biol.
JT  - J. Cell Biol.
SO  - J. Cell Biol. 1999 147: 25-32.

PMID- 27908996
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Aeromonas caviae CH129, a Marine-Derived Bacterium Isolated from the Coast of Sao Paulo State, Brazil.
PG  - e01336-16
AB  - We report here the draft genome sequence of Aeromonas caviae CH129, a marine-derived bacterium
      isolated from the coast of Sao Paulo state, Brazil.
      Genomic analysis revealed genes encoding enzymes involved in binding, transport,
      and chitin metabolism and different virulence-associated factors.
AU  - Cardozo FA
AU  - Alfonso VNC
AU  - Zimpel CK
AU  - Pessoa A
AU  - Rivera IN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01336-16.

PMID- 27856589
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Marine-Derived Aeromonas caviae CHZ306, a Potential Chitinase Producer Strain.
PG  - e01293-16
AB  - We report here a draft genome sequence of Aeromonas caviae CHZ306, a marine-derived bacterium
      with the ability to hydrolyze chitin and express high
      levels of chitinases. The assembly resulted in 65 scaffolds with approximately
      4.78 Mb. Genomic analysis revealed different genes encoding chitin-degrading
      enzymes that can be used for chitin derivative production.
AU  - Cardozo FA
AU  - Zimpel CK
AU  - Guimaraes AM
AU  - Pessoa A
AU  - Rivera IN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01293-16.

PMID- 6317200
VI  - 35
DP  - 1983
TI  - An mRNA maturase is encoded by the first intron of the mitochondrial gene for the subunit I of cytochrome oxidase in S. cerevisiae.
PG  - 733-742
AB  - We have localized ten oxi3- mutations in the first, ai1, intron of the coxI gene.  All are
      splicing deficient, being unable to excise the intron.  Complementation experiments disclose
      several domains in the intron ai1: the 5'-proximal and 3'-proximal domains harbor
      cis-dominant mutations, while trans-recessive ones are located in the intron's open reading
      frame.  Comprehensive analyses of allele-specific polypeptides accumulating in mutants show
      that they result from the translation of the intron's ORF;  We conclude that a specific mRNA
      maturase involved in splicing of oxidase mRNA is encoded by the intron ai1 in a manner similar
      to the cytochrome b mRNA maturase.
AU  - Carignani G
AU  - Groudinsky O
AU  - Frezza D
AU  - Schiavon E
AU  - Bergantino E
AU  - Slonimski PP
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1983 35: 733-742.

PMID- 27103727
VI  - 4
DP  - 2016
TI  - Complete Genome Sequences of Aerococcus christensenii CCUG 28831T, Aerococcus sanguinicola CCUG 43001T, Aerococcus urinae CCUG 36881T, Aerococcus urinaeequi  CCUG 28094T, Aerococcus urinaehominis CCUG 42038 BT, and Aerococcus viridans CCUG  4311T.
PG  - e00302-16
AB  - Strains belonging to the genus ITALIC! Aerococcusare causative agents of human and animal
      infections, including urogenital infections, bacteremia/septicemia,
      and infective endocarditis. This study reports the first fully closed and
      complete genome sequences of six type strains belonging to the genus ITALIC!
      Aerococcususing a combination of Illumina HiSeq and PacBio sequencing
      technologies.
AU  - Carkaci D
AU  - Dargis R
AU  - Nielsen XC
AU  - Skovgaard O
AU  - Fuursted K
AU  - Christensen JJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00302-16.

PMID- 29074652
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of the Temperate Klebsiella pneumoniae Phage KPP5665-2.
PG  - e01118-17
AB  - We describe here the genome sequence of the novel temperate Klebsiella pneumoniae phage
      KPP5665-2 isolated from a Klebsiella pneumoniae strain recovered from milk
      in Germany in 2016. The phage exhibited a narrow host range and a siphoviridal
      morphology. KPP5665-2-related prophage sequences were detected in whole-genome
      sequencing (WGS) data of various Klebsiella species isolates.
AU  - Carl G
AU  - Jackel C
AU  - Grutzke J
AU  - Hertwig S
AU  - Grobbel M
AU  - Malorny B
AU  - Rau J
AU  - Kasbohrer A
AU  - Hammerl JA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01118-17.

PMID- 20363791
VI  - 76
DP  - 2010
TI  - Partial chromosome sequence of Spiroplasma citri reveals extensive viral invasion and important gene decay.
PG  - 3420-3426
AB  - The assembly of 20,000 sequencing reads obtained from shotgun and chromosome-specific
      libraries of the Spiroplasma citri genome yielded 77
      chromosomal contigs totaling 1,674 kbp (92%) of the 1,820-kbp chromosome.
      The largest chromosomal contigs were positioned on the physical and
      genetic maps constructed from pulsed-field gel electrophoresis and
      Southern blot hybridizations. Thirty-eight contigs were annotated,
      resulting in 1,908 predicted coding sequences (CDS) representing an
      overall coding density of only 74%. Cellular processes, cell metabolism,
      and structural-element CDS account for 29% of the coding capacity, CDS of
      external origin such as viruses and mobile elements account for 24% of the
      coding capacity, and CDS of unknown function account for 47% of the coding
      capacity. Among these, 21% of the CDS group into 63 paralog families. The
      organization of these paralogs into conserved blocks suggests that they
      represent potential mobile units. Phage-related sequences were
      particularly abundant and include plectrovirus SpV1 and SVGII3 and
      lambda-like SpV2 sequences. Sixty-nine copies of transposases belonging to
      four insertion sequence (IS) families (IS30, IS481, IS3, and ISNCY) were
      detected. Similarity analyses showed that 21% of chromosomal CDS were
      truncated compared to their bacterial orthologs. Transmembrane domains,
      including signal peptides, were predicted for 599 CDS, of which 58 were
      putative lipoproteins. S. citri has a Sec-dependent protein export
      pathway. Eighty-four CDS were assigned to transport, such as
      phosphoenolpyruvate phosphotransferase systems (PTS), the ATP binding
      cassette (ABC), and other transporters. Besides glycolytic and ATP
      synthesis pathways, it is noteworthy that S. citri possesses a nearly
      complete pathway for the biosynthesis of a terpenoid.
AU  - Carle P
AU  - Saillard C
AU  - Carrere N
AU  - Carrere S
AU  - Duret S
AU  - Eveillard S
AU  - Gaurivaud P
AU  - Gourgues G
AU  - Gouzy J
AU  - Salar P
AU  - Verdin E
AU  - Breton M
AU  - Blanchard A
AU  - Laigret F
AU  - Bove JM
AU  - Renaudin J
AU  - Foissac X
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2010 76: 3420-3426.

PMID- 24723723
VI  - 2
DP  - 2014
TI  - Genome Sequence of Burkholderia cenocepacia H111, a Cystic Fibrosis Airway Isolate.
PG  - e00298-14
AB  - The Burkholderia cepacia complex (BCC) is a group of related bacterial species that are
      commonly isolated from environmental samples. Members of the BCC can cause respiratory
      infections in cystic fibrosis patients and immunocompromised individuals. We report here the
      genome sequence of Burkholderia cenocepacia H111, a well-studied model strain of the BCC.
AU  - Carlier A
AU  - Agnoli K
AU  - Pessi G
AU  - Suppiger A
AU  - Jenul C
AU  - Schmid N
AU  - Tummler B
AU  - Pinto-Carbo M
AU  - Eberl L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00298-14.

PMID- 9515694
VI  - 27
DP  - 1998
TI  - Endonuclease II of coliphage T4: a recombinase disguised as a restriction endonuclease?
PG  - 671-676
AB  - Endo ll shares with restriction endonucleases the property of cleaving foreign DNA while
      leaving the endonuclease-encoding genome intact, ensuring the survival of one DNA species in
      the cell.  In addition, in vivo Endo ll cleaves a specific DNA sequence and cleavage is
      context dependent.  These context effects extend over at least 1000 bp, largely limiting
      cleavage to once within this distance.  Like homing endonucleases, in vivo Endo ll recognizes
      a long, asymmetric and degenerate consensus sequence which has two distinct parts.
      Recognition of one part of the consensus sequence involves base-specific bonds, and
      recognition of the other involves sequence-dependent helical structure.  Endo ll fulfils an
      obvious short-term survival role in ensuring the dominance of phase DNA in an infected cell,
      but may also have a long-term evolutionary role, producing gene-size fragments of foreign DNA
      to be enrolled in the phage genetic repertoire.
AU  - Carlson K
AU  - Kosturko LD
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1998 27: 671-676.

PMID- 8386173
VI  - 268
DP  - 1993
TI  - DNA determinants of restriction.
PG  - 8908-8918
AB  - Endonuclease II of coliphage T4 is necessary for the in vivo restriction of plasmid DNA in
      phage-infected cells. Double-stranded restriction cleavage at 12 sites in pBR322 commenced
      before 10-min postinfection with T4 at 37C and proceeded more slowly in the presence of
      competing phage DNA than in its absence, utilizing the same sites in both cases; in a 200-base
      pair segment of the plasmid, single stranded nicks also were frequent. The plasmid sites were
      cleaved with a speed that varied with the site, yielding frequencies of cleavage at different
      sites varying between 10 and 90%, at 50-min postinfection. All sites contained good matches to
      a consensus, 5'-GRCCGCNTYGC-3', most frequently cleaved around the variable central base
      pair, generating fragments with blunt ends or 1-2-base 5' overhangs. Using the frequency of
      cleavage to determine a weighted consensus, a larger sequence, 5'-CGRCCGCNTTGSYNGC-3' was
      identified. Thus, DNA sequence elements 3' to the cut site appear important for rapid
      cleavage. Several models describing the sequence-dependent structure of DNA suggest structural
      anomalies around the cleavage sites. The endonuclease II restriction system is most similar to
      type II systems, although it differs from known type II systems in several respects.
AU  - Carlson K
AU  - Krabbe M
AU  - Nystrom AC
AU  - Kosturko LD
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1993 268: 8908-8918.

PMID- 
VI  - 
DP  - 1994
TI  - Restriction and Modification.
PG  - 369-381
AB  - A host-parasite interaction is an intricate balance of mutual attack and defense.  Several
      nucleases and other proteins encoded by Escherichia coli and T4 are involved in restriction
      and modification, processes in which an organism causes degradation of "foreign" DNA while
      modifying its own DNA to provide "immunity" to the restriction endonuclease(s).  Restriction
      endonucleases encoded by the host (E. coli, EcoK or EcoB, Mcr {Rgl}, and Mrr) and its prophage
      symbiont phage P1 (EcoP1) may restrict infecting phage DNA; in addition, E. coli exonuclease V
      (ExoV; the RecBCD enzyme) and possibly endonuclease I may degrade phage DNA as it enters the
      cell.  Phage-encoded nucleases, on the other hand, with endonuclease II (EndoII) as a crucial
      participant, cause the restriction cleavage and ultimate breakdown of host DNA and other
      cytosine-containing DNA in the cell.  The reutilization of host-derived nucleotides via a
      "nucleotide scavenge pathway" permits the production of about 20 phage equivalents of phage
      DNA per host genome scavenged.  Scavenging host DNA breakdown products this way undoubtedly is
      evolutionarily advantageous to the phage when nutrients are limited.
AU  - Carlson K
AU  - Raleigh EA
AU  - Hattman S
PT  - Journal Article
TA  - Molecular Biology of Bacteriophage T4
JT  - Molecular Biology of Bacteriophage T4
SO  - Molecular Biology of Bacteriophage T4 1994 : 369-381.

PMID- 6887350
VI  - 48
DP  - 1983
TI  - In vivo cleavage of cytosine-containing bacteriophage T4 DNA to genetically distinct, discretely sized fragments.
PG  - 18-30
AB  - Mutants of bacteriophage T4D that are defective in genes 42 (dCMP hydroxymethylase), 46 (DNA
      exonuclease), and 56 (dCTPase) produce limited amounts of phage DNA in Escherichia coli B. In
      this DNA, glucosylated 5-hydroxymethylcytosine is completely replaced by cytosine. We found
      that this DNA rapidly becomes fragmented in vivo to at least 16 discrete bands as visualized
      on agarose gels subjected to electrophoresis. The sizes of the fragments ranged from more than
      20 to less than 2 kilobase pairs. When DNAs from two of these bands were radioactively labeled
      in vitro by nick translation and hybridized to XbaI restriction fragments of
      cytosine-containing T4 DNA, evidence was obtained that the two bands are genetically distinct,
      i.e., they contain DNA from different parts of the T4 genome. Mutational inactivation of T4
      endonuclease II (gene denA) prevented the fragmentation. Three different mutations in T4
      endonuclease IV (gene denB) caused the same minor changes in the pattern of fragments. We
      conclude that T4 endonuclease II is required, and endonuclease IV is involved to a minor
      extent, in the in vivo production of these cytosine-containing T4 DNA fragments. We view these
      DNA fragments as "restriction fragments" since they represent degradation products of DNA
      "foreign" to T4, they are of discrete size, and they are genetically distinct. Thus, this
      report may represent the first, direct in vivo demonstration of discretely sized genetically
      distinct DNA restriction fragments.
AU  - Carlson K
AU  - Wiberg JS
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1983 48: 18-30.

PMID- 1340468
VI  - 6
DP  - 1992
TI  - Properties and localization of DNA methyltransferase in preimplantation mouse embryos: implications for genomic imprinting.
PG  - 2536-2541
AB  - Preimplantation mouse embryos contain very high levels of DNA methyltransferase activity. We
      show here that the form of DNA methyltransferase (DNA MTase) in early embryos differs from the
      form found in other cells and tissues by a slightly higher mobility on gel electrophoresis.
      Levels of DNA MTase were found to be very high throughout preimplantation development even
      though levels of 5-methylcytosine (m5C)in nuclear DNA are known to undergo a substantial
      decline in the same period. Confocal laser scanning microscopy of mouse embryos stained with
      DNA MTase-specific antibodies showed striking developmentally regulated changes in the
      distribution of DNA MTase. From the oocyte stage to the four-cell-stage, most DNA MTase was
      concentrated in peripheral cytoplasm, and nuclei did not contain detectable DNA MTase. In
      four-and eight-cell embryos, DNA MTase was seen in cytoplasmic granules; and in eight-cell
      embryos, DNA MTase was also present in large amounts in nuclei. Nuclei of blastocysts stained
      only faintly, whereas the cytoplasmic granules remained prominent. Paradoxically, DNA MTase
      was found to be at its highest levels in nuclei at a developmental stage where levels of m5C
      in DNA are decreasing most rapidly. Changes in methylation patterns in preimplanation embryos
      are therefore proposed to be under the control of unidentified regulatory factors rather than
      DNA MTase itself; these regulatory factors could be members of the group that contains the
      products of the Ssm-1 and Imp-1 genes, which are involved in the regulation of genomic
      imprinting.
AU  - Carlson LL
AU  - Page AW
AU  - Bestor TH
PT  - Journal Article
TA  - Genes Dev.
JT  - Genes Dev.
SO  - Genes Dev. 1992 6: 2536-2541.

PMID- 23144424
VI  - 194
DP  - 2012
TI  - Genome Sequence of Exiguobacterium antarcticum B7, Isolated from a Biofilm in Ginger Lake, King George Island, Antarctica.
PG  - 6689-6690
AB  - Exiguobacterium antarcticum is a psychotropic bacterium isolated for the first time from
      microbial mats of Lake Fryxell in Antarctica. Many organisms of the
      genus Exiguobacterium are extremophiles and have properties of biotechnological
      interest, e.g., the capacity to adapt to cold, which make this genus a target for
      discovering new enzymes, such as lipases and proteases, in addition to improving
      our understanding of the mechanisms of adaptation and survival at low
      temperatures. This study presents the genome of E. antarcticum B7, isolated from
      a biofilm sample of Ginger Lake on King George Island, Antarctic peninsula.
AU  - Carneiro AR et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6689-6690.

PMID- 24265499
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Serratia fonticola LMG 7882T Isolated from Freshwater.
PG  - e00971-13
AB  - Serratia fonticola is a Gram-negative bacterium with a wide distribution in aquatic
      environments. On some occasions, it has also been regarded as a
      significant human pathogen. In this work, we report the first draft genome
      sequence of an S. fonticola strain (LMG 7882T), which was isolated from
      freshwater.
AU  - Carneiro AR
AU  - Juca RRT
AU  - Barauna RA
AU  - de Sa PH
AU  - Marinho AD
AU  - Barbosa S
AU  - Pereira A
AU  - Alves A
AU  - Egas C
AU  - Correia A
AU  - Henriques I
AU  - Silva A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00971-13.

PMID- 28546489
VI  - 5
DP  - 2017
TI  - Genome Sequence of a Marine Spirillum, Oceanospirillum multiglobuliferum ATCC 33336T, Isolated from Japan.
PG  - e00396-17
AB  - Oceanospirillum multiglobuliferum ATCC 33336T is a motile gammaproteobacterium with bipolar
      tufted flagella, noted for its low salt tolerance compared to other
      marine spirilla. This strain was originally isolated from the putrid infusions of
      Crassostrea gigas near Hiroshima, Japan. This paper presents a draft genome
      sequence for O. multiglobuliferum ATCC 33336T.
AU  - Carney JG
AU  - Trachtenberg AM
AU  - Rheaume BA
AU  - Linnane JD
AU  - Pitts NL
AU  - Mykles DL
AU  - MacLea KS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00396-17.

PMID- 18070957
VI  - 52
DP  - 2008
TI  - New genetic element carrying the erythromycin resistance determinant erm (TR) in Streptococcus pneumoniae.
PG  - 619-625
AB  - erm(A) subclass erm(TR), a common macrolide resistance determinant in Streptococcus pyogenes
      but quite rare in Streptococcus pneumoniae, was
      found in a clinical S. pneumoniae isolate (AP200) from Italy. In this
      isolate, erm(TR) was found included in a genetic element approximately
      56 kb in size that did not appear to be conjugative but could be
      transferred by transformation. An erm (TR)-containing DNA fragment of
      approximately 10 kb was sequenced and 12 open reading frames (ORFs)
      were identified. Upstream of erm(TR), a regulatory protein of the TOR
      family and the two components of an efflux pump of the ABC type were
      found. Downstream of erm(TR), there were ORFs homologous to a
      spectinomycin phosphotransferase, transposases, and a relaxase. Since
      the genomic sequence of S. pyogenes MGAS10750 carrying erm(TR) became
      available, comparison between the erm (TR) -containing genetic elements
      in AP200 and in MGAS10750 was performed. The region flanking erm(TR) in
      MGAS10750 showed identity with AP200 for 10 ORFs out of 12. PCR mapping
      using primers designed on the sequence of MGAS10750 confirmed that
      AP200 carries a genetic element similar to that of MGAS10750. In AP200
      the genetic element was inserted inside an ORF homologous to spr0790 of
      S. pneumoniae R6, coding for a type I restriction modification system.
      Homologies between the insertion sites in AP200 and MGAS10750 consisted
      of eight conserved nucleotides, of which three were duplicated, likely
      representing target site duplication. The structure of the erm
      (TR)-carrying genetic element shows characteristics of a
      transposon/prophage remnant chimera. In AP200 this genetic element was
      designated Tn1806.
AU  - Carnilli R
AU  - Del Grosso M
AU  - Lannelli F
AU  - Pantostil A
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2008 52: 619-625.

PMID- 22328742
VI  - 194
DP  - 2012
TI  - Genome Sequencing of Five Shewanella baltica Strains Recovered from the Oxic-Anoxic Interface of the Baltic Sea.
PG  - 1236
AB  - Here we describe five Shewanella baltica genomes recovered from the same sample,  as well as
      12 years apart from the same sampling station. These genomes expand
      the collection of previously sequenced S. baltica strains and represent a
      valuable resource for assessing the role of environmental settings on genome
      adaptation.
AU  - Caro-Quintero A
AU  - Auchtung J
AU  - Deng J
AU  - Brettar I
AU  - Hofle M
AU  - Tiedje JM
AU  - Konstantinidis KT
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1236.

PMID- 8794746
VI  - 35
DP  - 1996
TI  - Different effects of histone H1 on de novo DNA methylation in vitro depend on both the DNA base composition and the DNA methyltransferase.
PG  - 11660-11667
AB  - We have characterized the inhibition exerted by histone H1 on the activity of human placenta
      DNA (cytosine-5-)-methyltransferase.  Our experiments demonstrate that the extent of
      inhibition depends on the DNA base composition, AT-rich substrates being more severely
      affected than GC-rich substrates and CpG-rich islands.  With bacterial SssI methylase, the
      effect is completely reversed since its activity on AT-rich substrates undergoes a 4-5-fold
      stimulation upon the addition of H1.  Poly(L-lysine) mimicks H1 effects, suggesting an
      essential role of lysine residues in both the inhibitory and stimulatory effects of H1.  By
      comparison of the different behaviors of the two enzymes, the inhibitory effect over the
      eukaryotic enzyme might be accounted for by hypothesizing a competition between minor
      groove-binding motifs (SPKK-like) present in placenta methylase as well as in histone H1.
AU  - Carotti D
AU  - Funiciello S
AU  - Lavia P
AU  - Caiafa P
AU  - Strom R
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1996 35: 11660-11667.

PMID- 9454602
VI  - 37
DP  - 1998
TI  - Influence of pre-existing methylation on the de novo activity of eukaryotic DNA methyltransferase.
PG  - 1101-1108
AB  - Aberrant de novo methylation of CpG island DNA sequences has been observed in cultured cell
      lines or upon malignant transformation but the mechanisms underlying this phenomenon are
      poorly understood.  Using eukaryotic DNA (cytosine-5)-methyltransferase (of both human and
      murine origin), we have studied the in vitro methylation pattern of three CpG islands.  Such
      sequences are intrinsically poor substrates of the enzyme, yet are efficiently methylated when
      a small amount of 5-methylcytosine is randomly introduced by the M.SssI prokaryotic DNA
      (cytosine-5)-methyltransferase prior to in vitro methylation by the eukaryotic enzyme.  A
      stimulation was also found with several other double-stranded DNA substrates, either natural
      or of synthetic origin, such as poly(dG-dC).poly(dG-dC).  An A+T-rich plasmid, pHbbeta1S,
      showed an initial stimulation, followed by a severe inhibition of the activity of DNA
      (cytosine-5)-methyltransferase.  Methylation of poly(dI-dC).poly(dI-dC) was instead inhibited
      by pre-existing 5-methylcytosines.  The extent of stimulation observed with
      poly(dG-dC).poly(dG-dC) depends on both the number and the distribution of the
      5-methylcytosine residues, which probably must not be too closely spaced for the stimulatory
      effect to be exerted.  The activity of the M.SssI prokaryotic DNA methyltransferase was not
      stimulated, but was inhibited by pre-methylation on either poly(dG-dC).poly(dG-dC) or
      poly(dI-dC).poly(dI-dC).  The prokaryotic and eukaryotic DNA methyltransferases also differed
      in sensitivity to poly(dG-m5dC).poly(dG-m5dC), which is highly inhibitory for eukaryotic
      enzymes and almost ineffective on prokaryotic enzymes.
AU  - Carotti D
AU  - Funiciello S
AU  - Palitti F
AU  - Strom R
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1998 37: 1101-1108.

PMID- 16893959
VI  - 34
DP  - 2006
TI  - Sequence-dependent enhancement of hydrolytic deamination of cytosines in DNA by the restriction enzyme PspGI.
PG  - 3762-3770
AB  - Hydrolytic deamination of cytosines in DNA creates uracil and, if unrepaired, these lesions
      result in C to T mutations. We have suggested
      previously that a possible way in which cells may prevent or reduce this
      chemical reaction is through the binding of proteins to DNA. We use a
      genetic reversion assay to show that a restriction enzyme, PspGI, protects
      cytosines within its cognate site, 5'-CCWGG (W is A or T), against
      deamination under conditions where no DNA cleavage can occur. It decreases
      the rate of cytosine deamination to uracil by 7-fold. However, the same
      protein dramatically increases the rate of deaminations within the site
      5'-CCSGG (S is C or G) by approximately 15-fold. Furthermore, a similar
      increase in cytosine deaminations is also seen with a catalytically
      inactive mutant of the enzyme showing that endonucleolytic ability of the
      protein is dispensable for its mutagenic action. The sequences of the
      mutants generated in the presence of PspGI show that only one of the
      cytosines in CCSGG is predominantly converted to thymine. Our results are
      consistent with PspGI 'sensitizing' the cytosine in the central base pair
      in CCSGG for deamination. Remarkably, PspGI sensitizes this base for
      damage despite its inability to form stable complexes at CCSGG sites.
      These results can be explained if the enzyme has a transient interaction
      with this sequence during which it flips the central cytosine out of the
      helix. This prediction was validated by modeling the structure of
      PspGI-DNA complex based on the structure of the related enzyme Ecl18kI
      which is known to cause base-flipping.
AU  - Carpenter M
AU  - Divvela P
AU  - Pingoud V
AU  - Bujnicki J
AU  - Bhagwat AS
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2006 34: 3762-3770.

PMID- 
VI  - 
DP  - 2008
TI  - Studies of base flipping by the Pyrococcus species GI-H restriction-modification system.
PG  - 
AB  - Water is the single most DNA damaging agent that cells regularly encounter.  Water induces DNA
      damage by a variety of mechanisms including depurination, depyrimidination, and deamination.
      Figure 1 shows some of the most frequently observed types of DNA damage.  Depurination and
      depyrimidination occur when a water molecular attacks at the C1' of deoxyribose kicking the
      DNA base off in an Sn2 type substitution.  Depurination occurs at a very high rate, inducing
      an estimated 18,000 abasic sites per cell, per day in a typical human cell.  Depyrimidination
      occurs about 300 fold less frequently than depurination.  Repair of abasic sites in
      Escherichia coli is similar to Base Excision Repair except that the abasic site is caused by
      hydrolytic attack of water and not by a DNA glycosylase.
AU  - Carpenter MA
PT  - Journal Article
TA  - Ph.D. Thesis, Wayne State Univ., Detroit, MI, USA
JT  - Ph.D. Thesis, Wayne State Univ., Detroit, MI, USA
SO  - Ph.D. Thesis, Wayne State Univ., Detroit, MI, USA 2008 : .

PMID- 18718929
VI  - 36
DP  - 2008
TI  - DNA base flipping by both members of the PspGI restriction-modification system.
PG  - 5417-5425
AB  - The PspGI restriction-modification system recognizes the sequence CCWGG. R.PspGI cuts DNA
      before the first C in the cognate sequence and M.PspGI is
      thought to methylate N4 of one of the cytosines in the sequence. M.PspGI
      enhances fluorescence of 2-aminopurine in DNA if it replaces the second C
      in the sequence, while R.PspGI enhances fluorescence when the fluorophore
      replaces adenine in the central base pair. This strongly suggests that the
      methyltransferase flips the second C in the recognition sequence, while
      the endonuclease flips both bases in the central base pair out of the
      duplex. M.PspGI is the first N4-cytosine MTase for which biochemical
      evidence for base flipping has been presented. It is also the first type
      IIP methyltransferase whose catalytic activity is strongly stimulated by
      divalent metal ions. However, divalent metal ions are not required for its
      base-flipping activity. In contrast, these ions are required for both base
      flipping and catalysis by the endonuclease. The two enzymes have similar
      temperature profiles for base flipping and optimal flipping occurs at
      temperatures substantially below the growth temperature of the source
      organism for PspGI and for the catalytic activity of endonuclease. We
      discuss the implications of these results for DNA binding by these enzymes
      and their evolutionary origin.
AU  - Carpenter MA
AU  - Bhagwat AS
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2008 36: 5417-5425.

PMID- 
VI  - 0
DP  - 2018
TI  - A strain of an emerging Indian pathotype of Xanthomonas oryzae pv. oryzae defeats the rice bacterial blight resistance gene xa13 without inducing a clade III SWEET gene and is nearly identical to a recent Thai isolate.
PG  - 0
AB  - The rice bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo) injects transcription
      activator-like
      effectors (TALEs) that bind and activate host susceptibility (S) genes important for disease.
      Clade III
      SWEET genes are major S genes for bacterial blight. The resistance genes xa5, which reduces
      TALE
      activity generally, and xa13, a SWEET11 allele not recognized by the cognate TALE, have been
      effectively
      deployed. However, strains that defeat both resistance genes individually were recently
      reported in India
      and Thailand. To gain insight into the mechanism(s), we completely sequenced the genome of one
      such
      strain from each country and examined the encoded TALEs. Strikingly, the two strains are
      clones, sharing
      nearly identical TALE repertoires, including a TALE known to activate SWEET11 strongly enough
      to be
      effective even when diminished by xa5. We next investigated SWEET gene induction by the Indian
      strain.
      The Indian strain induced no clade III SWEET in plants harbouring xa13, indicating a pathogen
      adaptation
      that relieves dependence on these genes for susceptibility. The findings open a door to
      mechanistic
      understanding of the role SWEET genes play in susceptibility and illustrate the importance of
      complete
      genome sequence-based monitoring of Xoo populations in developing varieties with effective
      disease
      resistance.
      Key
AU  - Carpenter S
AU  - Mishra P
AU  - Ghoshal C
AU  - Dash P
AU  - Wang L
AU  - Midha S
AU  - Laha GS
AU  - Lore J
AU  - Kositratana W
AU  - Singh N
AU  - Singh K
AU  - Patil P
AU  - Oliva R
AU  - Patarapuwadol S
AU  - Bogdanove AJ
AU  - Rai R
PT  - Journal Article
TA  - bioRxiv
JT  - bioRxiv
SO  - bioRxiv 2018 0: 0.

PMID- 24567731
VI  - 5
DP  - 2014
TI  - Development of pVCR94DeltaX from Vibrio cholerae, a prototype for studying multidrug resistant IncA/C conjugative plasmids.
PG  - 44
AB  - Antibiotic resistance has grown steadily in Vibrio cholerae over the last few
      decades to become a major threat in countries affected by cholera. Multi-drug
      resistance (MDR) spreads among clinical and environmental V. cholerae strains by
      lateral gene transfer often mediated by integrative and conjugative elements
      (ICEs) of the SXT/R391 family. However, in a few reported but seemingly isolated
      cases, MDR in V. cholerae was shown to be associated with other
      self-transmissible genetic elements such as conjugative plasmids. IncA/C
      conjugative plasmids are often found associated with MDR in isolates of
      Enterobacteriaceae. To date, IncA/C plasmids have not been commonly found in V.
      cholerae or other species of Vibrio. Here we present a detailed analysis of
      pVCR94DeltaX derived from pVCR94, a novel IncA/C conjugative plasmid identified
      in a V. cholerae clinical strain isolated during the 1994 Rwandan cholera
      outbreak. pVCR94 was found to confer resistance to sulfamethoxazole,
      trimethoprim, ampicillin, streptomycin, tetracycline, and chloramphenicol and to
      transfer at very high frequency. Sequence analysis revealed its mosaic nature as
      well as high similarity of the core genes responsible for transfer and
      maintenance with other IncA/C plasmids and ICEs of the SXT/R391 family. Although
      IncA/C plasmids are considered a major threat in antibiotics resistance, their
      basic biology has received little attention, mostly because of the difficulty to
      genetically manipulate these MDR conferring elements. Therefore, we developed a
      convenient derivative from pVCR94, pVCR94Delta X, a 120.5-kb conjugative plasmid
      which only codes for sulfamethoxazole resistance. Using pVCR94Delta X, we
      identified the origin of transfer (oriT) and discovered an essential gene for
      transfer, both located within the shared backbone, allowing for an annotation
      update of all IncA/C plasmids. pVCR94Delta X may be a useful model that will
      provide new insights on the basic biology of IncA/C conjugative plasmids.
AU  - Carraro N
AU  - Sauve M
AU  - Matteau D
AU  - Lauzon G
AU  - Rodrigue S
AU  - Burrus V
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2014 5: 44.

PMID- 28963198
VI  - 5
DP  - 2017
TI  - First Draft Genome Sequence of a Clinical Strain of Nocardia cerradoensis.
PG  - e00551-17
AB  - This paper reports the first draft genome sequence for a strain of Nocardia cerradoensis
      obtained from an immunocompetent patient with a knee infection. The
      8.2-Mb genome has 8,329 coding sequences, including intrinsic resistance genes,
      biosynthetic gene clusters for polyketide synthase and nonribosomal peptide
      synthase, virulence genes, and prophages.
AU  - Carrasco G
AU  - Monzon S
AU  - Jimenez P
AU  - Cuesta I
AU  - Bartolome-Alvarez J
AU  - Valdezate S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00551-17.

PMID- 3301526
VI  - 116
DP  - 1987
TI  - Spontaneous mutations occur near dam recognition sites in a dam- Escherichia coli host.
PG  - 343-347
AB  - The mismatch repair system of Escherichia coli K12 removes mispaired bases from DNA. Mismatch
      repair can occur on either strand of DNA if it lacks N6-methyladenines within
      5'-GATC-3'sequences. In hemimethylated heteroduplexes, repair occurs preferentially on the
      unmethylated strand. If both strands are fully methylated, repair is inhibited. Mutant (dam-)
      strains of E. coli defective in the adenine methylase that recognizes 5'-GATC-3' sequences
      (Dam), and therefore defective in mismatch repair, show increased spontaneous mutation rates
      compared to otherwise isogenic dam+ hosts. We have isolated and characterized 91 independent
      mutations that arise as a consequence of the Dam- defect in a plasmid-borne phage P22
      repressor gene, mnt. The majority of these mutations are A:T----G:C transitions that occur
      within six base pairs of the two 5'-GATC-3' sequences in the mnt gene. In contrast, the
      spectrum of mnt- mutations in a dam+ host is comprised of a majority of insertions of IS
      elements and deletions that do not cluster near Dam recognition sites. These results show that
      Dam-directed post-replicative mismatch repair plays a significant role in the rectification of
      potential transition mutations in vivo, and suggest that sequences associated with Dam
      recognition sites are particularly prone to replication or repair errors.
AU  - Carraway M
AU  - Youderian P
AU  - Marinus MG
PT  - Journal Article
TA  - Genetics
JT  - Genetics
SO  - Genetics 1987 116: 343-347.

PMID- 21214923
VI  - 8
DP  - 2011
TI  - Comparative genomic analysis of bacteriophages specific to the channel catfish pathogen Edwardsiella ictaluri.
PG  - 6
AB  - BACKGROUND: The bacterial pathogen Edwardsiella ictaluri is a primary
      cause of mortality in channel catfish raised commercially in aquaculture
      farms. Additional treatment and diagnostic regimes are needed for this
      enteric pathogen, motivating the discovery and characterization of
      bacteriophages specific to E. ictaluri. RESULTS: The genomes of three
      Edwardsiella ictaluri-specific bacteriophages isolated from geographically
      distant aquaculture ponds, at different times, were sequenced and
      analyzed. The genomes for phages eiAU, eiDWF, and eiMSLS are 42.80 kbp,
      42.12 kbp, and 42.69 kbp, respectively, and are greater than 95% identical
      to each other at the nucleotide level. Nucleotide differences were mostly
      observed in non-coding regions and in structural proteins, with
      significant variability in the sequences of putative tail fiber proteins.
      The genome organization of these phages exhibit a pattern shared by other
      Siphoviridae. CONCLUSIONS: These E. ictaluri-specific phage genomes reveal
      considerable conservation of genomic architecture and sequence identity,
      even with considerable temporal and spatial divergence in their isolation.
      Their genomic homogeneity is similarly observed among E. ictaluri
      bacterial isolates. The genomic analysis of these phages supports the
      conclusion that these are virulent phages, lacking the capacity for
      lysogeny or expression of virulence genes. This study contributes to our
      knowledge of phage genomic diversity and facilitates studies on the
      diagnostic and therapeutic applications of these phages.
AU  - Carrias A
AU  - Welch TJ
AU  - Waldbieser GC
AU  - Mead DA
AU  - Terhune JS
AU  - Liles MR
PT  - Journal Article
TA  - Virol. J.
JT  - Virol. J.
SO  - Virol. J. 2011 8: 6.

PMID- 12519752
VI  - 278
DP  - 2003
TI  - Amino Acid Substitutions at Position 43 of NaeI Endonuclease - Evidence for Changes in NaeI Structure.
PG  - 9733-9739
AB  - NaeI endonuclease contains a 10-amino acid region with sequence similarity to the active site
      KXDG motif of DNA ligase except for leucine (Leu-43) in
      NaeI ((43)LXDG(46)). Changing Leu-43 to lysine abolishes the NaeI
      endonuclease activity and replaces it with topoisomerase and recombinase
      activities. Here we report the results of substituting Leu-43 with
      alanine, arginine, asparagine, glutamate, and histidine. Quantitating
      specific activities and DNA binding values for the mutant proteins
      determined the range of amino acids at position 43 that alter NaeI
      mechanism. Substituting alanine, asparagine, glutamate, and histidine for
      Leu-43 maintained endonuclease activity, but at a lower level. On the
      other hand, substituting positively charged arginine, like lysine at
      position 43, converted NaeI to a topoisomerase with no observable
      double-strand cleavage activity. The specific activities of NaeI-43K and
      NaeI-43R and their relative sensitivities to salt, the
      topoisomerase-inhibiting drug
      N-[4-(9-acridinylamino)-3-methoxyphenyl]methane-sulfonamide (amsacrine)
      and single-stranded DNA showed that the two activities are similar. The
      effect of placing a positive charge at position 43 on NaeI structure was
      determined by measuring (for NaeI and NaeI-43K) relative susceptibilities
      to proteolysis, UV, circular dichroism spectra, and temperature melting
      transitions. The results provide evidence that a positive charge at
      position 43 induces dramatic changes in NaeI structure that affect both
      the Endo and Topo domains of NaeI. The identification of four putative DNA
      ligase motifs in NaeI leads us to speculate that structural changes that
      superimpose these motifs on the ligase structure may account for the
      changes in activity.
AU  - Carrick KL
AU  - Topal MD
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2003 278: 9733-9739.

PMID- 28254980
VI  - 5
DP  - 2017
TI  - Transcriptome Sequence of the Bloodstream Form of Trypanoplasma borreli, a Hematozoic Parasite of Fish Transmitted by Leeches.
PG  - e01712-16
AB  - Here, we report a transcriptome sequence of Trypanoplasma borreli isolated from its natural
      host, the common carp, Cyprinus carpio The transcriptome allows an
      analysis of abundant cell surface proteins and acts as a comparator for
      understanding the evolution and pathogenicity of other Kinetoplastida, including
      several that infect humans.
AU  - Carrington M
AU  - Doro E
AU  - Forlenza M
AU  - Wiegertjes GF
AU  - Kelly S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01712-16.

PMID- 29899517
VI  - 12
DP  - 2018
TI  - Involvement of Burkholderiaceae and sulfurous volatiles in disease-suppressive soils.
PG  - 23072321
AB  - Disease-suppressive soils are ecosystems in which plants suffer less from root
      infections due to the activities of specific microbial consortia. The
      characteristics of soils suppressive to specific fungal root pathogens are
      comparable to those of adaptive immunity in animals, as reported by Raaijmakers
      and Mazzola (Science 352:1392-3, 2016), but the mechanisms and microbial species
      involved in the soil suppressiveness are largely unknown. Previous taxonomic and
      metatranscriptome analyses of a soil suppressive to the fungal root pathogen
      Rhizoctonia solani revealed that members of the Burkholderiaceae family were more
      abundant and more active in suppressive than in non-suppressive soils. Here,
      isolation, phylogeny, and soil bioassays revealed a significant
      disease-suppressive activity for representative isolates of Burkholderia
      pyrrocinia, Paraburkholderia caledonica, P. graminis, P. hospita, and P.
      terricola. In vitro antifungal activity was only observed for P. graminis.
      Comparative genomics and metabolite profiling further showed that the antifungal
      activity of P. graminis PHS1 was associated with the production of sulfurous
      volatile compounds encoded by genes not found in the other four genera.
      Site-directed mutagenesis of two of these genes, encoding a dimethyl sulfoxide
      reductase and a cysteine desulfurase, resulted in a loss of antifungal activity
      both in vitro and in situ. These results indicate that specific members of the
      Burkholderiaceae family contribute to soil suppressiveness via the production of
      sulfurous volatile compounds.
AU  - Carrion VJ
AU  - Cordovez V
AU  - Tyc O
AU  - Etalo DW
AU  - de Bruijn I
AU  - de Jager VC
AU  - Medema MH
AU  - Eberl L
AU  - Raaijmakers JM
PT  - Journal Article
TA  - ISME J.
JT  - ISME J.
SO  - ISME J. 2018 12: 23072321.

PMID- 23846279
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Strain CBD-635, a Methicillin-Resistant Staphylococcus aureus USA100 Isolate.
PG  - e00491-13
AB  - We present the draft genome sequence of methicillin-resistant Staphylococcus aureus strain
      CBD-635, from the USA100 lineage. This is a sepsis isolate obtained
      from Tampa General Hospital. This strain is spa type t003 and multilocus sequence
      typing (MLST) type ST5, and it has been used by our group in the study of novel
      antimicrobial chemotherapeutics.
AU  - Carroll RK
AU  - Burda WN
AU  - Roberts JC
AU  - Peak KK
AU  - Cannons AC
AU  - Shaw LN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00491-13.

PMID- 24201195
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Clinical Isolate Acinetobacter nosocomialis Strain M2.
PG  - e00906-13
AB  - We report the 3.78-Mbp high-quality draft assembly of the genome from a clinical  isolate of
      Acinetobacter nosocomialis called strain M2 (previously known as
      Acinetobacter baumannii strain M2).
AU  - Carruthers MD
AU  - Harding CM
AU  - Baker BD
AU  - Bonomo RA
AU  - Hujer KM
AU  - Rather PN
AU  - Munson RS Jr
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00906-13.

PMID- 21378191
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of proteolytic Clostridium botulinum type A5 (B3') Strain H04402 065.
PG  - 2351-2352
AB  - H04402 065 is one of a very small group of strains of proteolytic Clostridium botulinum that
      form type A5 neurotoxin. Here, we report the complete 3.9 Mb genome sequence and annotation of
      strain H04402 065, which was isolated from a botulism patient in the UK in 2004.
AU  - Carter AT
AU  - Pearson BM
AU  - Crossman LC
AU  - Drou N
AU  - Heavens D
AU  - Baker D
AU  - Febrer M
AU  - Caccamo M
AU  - Grant KA
AU  - Peck MW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 2351-2352.

PMID- 6255438
VI  - 8
DP  - 1980
TI  - A comparison of DNA cleavage by the restriction enzymes SalPI and PstI.
PG  - 4943-4954
AB  - Methods for obtaining highly active, exonuclease-free, stable preparations of
      the Streptomyces albus P restriction enzyme SalPI are described.  SalPI and its
      isoschizomer PstI (from the taxonomically distant Providencia stuartii 164)
      both cleave their recognition sequence (5'-CTGCAG-3') to generate fragments
      terminating in tetranucleotide 3' extensions whose sequence is 5'-TGCA-3'.
      Bacteriophage R4G2 DNA, protected against SalPI cleavage by pregrowth on S.
      albus P, is also protected against PstI cleavage; and total DNA of both S.
      albus P and P. stuartii 164 is resistant to cleavage by both enzymes.
AU  - Carter JA
AU  - Chater KF
AU  - Bruton CJ
AU  - Brown NL
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1980 8: 4943-4954.

PMID- 17936302
VI  - 374
DP  - 2007
TI  - Strand-specific Contacts and Divalent Metal Ion Regulate Double-strand Break Formation by the GIY-YIG Homing Endonuclease I-BmoI.
PG  - 306-321
AB  - GIY-YIG homing endonucleases are modular enzymes consisting of a well-defined N-terminal
      catalytic domain connected to a variable
      C-terminal DNA-binding domain. Previous studies have revealed that the
      role of the DNA-binding domain is to recognize and bind intronless DNA
      substrate, positioning the N-terminal catalytic domain such that it is
      poised to generate a staggered double-strand break by an unknown
      mechanism. Interactions of the N-terminal catalytic domain with intronless
      substrate are therefore a critical step in the reaction pathway but have
      been difficult to define. Here, we have taken advantage of the reduced
      activity of I-BmoI, an isoschizomer of the well-studied bacteriophage T4
      homing endonuclease I-TevI, to examine double-strand break formation by
      I-BmoI. We present evidence demonstrating that I-BmoI generates a
      double-strand break by two sequential but chemically independent nicking
      reactions where divalent metal ion is a limiting factor in top-strand
      nicking. We also show by in-gel footprinting that contacts by the I-BmoI
      catalytic domain induce significant minor groove DNA distortions that
      occur independently of bottom-strand nicking. Bottom-strand contacts are
      critical for accurate top-strand nicking, whereas top-strand contacts have
      little influence on the accuracy of bottom-strand nicking. We discuss our
      results in the context of current models of GIY-YIG endonuclease function,
      with emphasis on the role of divalent metal ion and strand-specific
      contacts in regulating the activity of a single active site to generate a
      staggered double-strand break.
AU  - Carter JM
AU  - Friedrich NC
AU  - Kleinstiver B
AU  - Edgell DR
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2007 374: 306-321.

PMID- 28232440
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Enterotoxigenic Bacillus cereus Strains Obtained from Powdered Infant Formula.
PG  - e01644-16
AB  - We introduce the draft genome sequences of five enterotoxigenic Bacillus cereus strains: Bc
      12, Bc 67, Bc 111, Bc 112, and Bc 113, which were obtained from
      powdered infant formula. The genome sizes of the strains ranged from 5.5 to 5.8
      Mb, and the G+C contents were ~35.2%.
AU  - Carter L
AU  - Chase HR
AU  - Choi H
AU  - Jun S
AU  - Park J
AU  - Jeong S
AU  - Kim M
AU  - Han K
AU  - Lee C
AU  - Jeong H
AU  - Finkelstein S
AU  - Negrete F
AU  - Cinar HN
AU  - Tall BD
AU  - Gopinath GR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01644-16.

PMID- 29674560
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of a Natural Escherichia coli O145:H11 Isolate That Belongs to Phylogroup A.
PG  - e00349-18
AB  - Escherichia coli O145:H11 strain RM14721 was originally isolated from wildlife feces near a
      leafy greens-growing region in Yuma, AZ. This strain was initially
      positive for stx1; however, in subsequent cultures, stx1 was not detected by PCR.
      Here, we report the complete genome sequence and annotation of RM14721.
AU  - Carter MQ
AU  - Pham A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00349-18.

PMID- 29748413
VI  - 6
DP  - 2018
TI  - Complete Genome Sequences of Two Atypical Enteropathogenic Escherichia coli O145  Environmental Strains.
PG  - e00418-18
AB  - Escherichia coli O145 strains RM14715 and RM14723 were isolated from wildlife feces near a
      leafy greens-growing region in Yuma, Arizona. Both strains carry a
      distinct genotype compared with the E. coli O145 strains isolated from Salinas
      Valley, California. Here we report complete genome sequences and annotations of
      RM14715 and RM14723.
AU  - Carter MQ
AU  - Pham A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00418-18.

PMID- 28912313
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of a Shiga Toxin-Producing Enterobacter cloacae Clinical Isolate.
PG  - e00883-17
AB  - Enterobacter cloacae strain M12X01451 was isolated from a patient with mild diarrhea. This
      strain produces a novel subtype of Shiga toxin 1, Stx1e. The
      Stx1e-converting prophage in strain M12X01451 is stable and can infect other
      bacteria following induction. Here we report the complete genome sequence and
      annotation of strain M12X01451.
AU  - Carter MQ
AU  - Pham A
AU  - Huynh S
AU  - He X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00883-17.

PMID- 12808133
VI  - 100
DP  - 2003
TI  - Targeted cytosine methylation for in vivo detection of protein-DNA interactions.
PG  - 7743-7748
AB  - We report a technique, named targeted gene methylation (TAGM), for identifying in vivo
      protein-binding sites in chromatin. M.CviPI, a
      cytosine-5 DNA methyltransferase recognizing GC sites, is fused to a
      DNA-binding factor enabling simultaneous detection of targeted
      methylation, factor footprints, and chromatin structural changes by
      bisulfite genomic sequencing. Using TAGM with the yeast transactivator
      Pho4, methylation enrichments of up to 34- fold occur proximal to native
      Pho4-binding sites. Additionally, significant selective targeting of
      methylation is observed several hundred nucleotides away, suggesting the
      detection of long-range interactions due to higher-order chromatin
      structure. In contrast, at an extragenic locus lacking Pho4-binding sites,
      methylation levels are at the detection limit at early times after Pho4
      transactivation. Notably, substantial amounts of methylation are targeted
      by Pho4-M.CviPI under repressive conditions when most of the
      transactivator is excluded from the nucleus. Thus, TAGM enables rapid
      detection of DNA-protein interactions even at low occupancies and has
      potential for identifying factor targets at the genome-wide level.
      Extension of TAGM from yeast to vertebrates, which use methylation to
      initiate and propagate repressed chromatin, could also provide a valuable
      strategy for heritable inactivation of gene expression.
AU  - Carvin CD
AU  - Dhasarathy A
AU  - Friesenhahn LB
AU  - Jessen WJ
AU  - Kladde MP
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2003 100: 7743-7748.

PMID- 14602907
VI  - 31
DP  - 2003
TI  - Site-selective in vivo targeting of cytosine-5 DNA methylation by zinc-finger proteins.
PG  - 6493-6501
AB  - Cytosine-5 DNA methylation is a critical signal defining heritable epigenetic states of
      transcription. As aberrant methylation patterns often
      accompany disease states, the ability to target cytosine methylation to
      preselected regions could prove valuable in re-establishing proper gene
      regulation. We employ the strategy of targeted gene methylation in yeast,
      which has a naturally unmethylated genome, selectively directing de novo
      DNA methylation via the fusion of C5 DNA methyltransferases to
      heterologous DNA-binding proteins. The zinc-finger proteins Zif268 and
      Zip53 can target DNA methylation by M.CviPI or M.SssI 5-52 nt from single
      zinc-factor binding sites. Modification at specific GC (M.CviPI) or CG
      (M.SssI) sites is enhanced as much as 20-fold compared with strains
      expressing either the free enzyme or a fusion protein with the zinc-finger
      protein moiety unable to bind to DNA. Interestingly, methylation is also
      selectively targeted as far as 353 nt from the zinc-finger protein binding
      sites, possibly indicative of looping, nucleosomes or higher-order
      chromatin structure. These data demonstrate that methylation can be
      targeted in vivo to a potentially broad range of sequences using
      specifically engineered zinc-finger proteins. Further more, the selective
      targeting of methylation by zinc-finger proteins demonstrates that binding
      of distinct classes of factors can be monitored in living cells.
AU  - Carvin CD
AU  - Parr RD
AU  - Kladde MP
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2003 31: 6493-6501.

PMID- 16959970
VI  - 70
DP  - 2006
TI  - Epigenetic gene regulation in the bacterial world.
PG  - 830-856
AB  - Like many eukaryotes, bacteria make widespread use of postreplicative DNA methylation for the
      epigenetic control of DNA-protein interactions. Unlike eukaryotes, however, bacteria use DNA
      adenine methylation (rather than DNA cytosine methylation) as an epigenetic signal. DNA
      adenine methylation plays roles in the virulence of diverse pathogens of humans and livestock
      animals, including pathogenic Escherichia coh, Salmonella, Vibrio, Yersinia, Haemophilus, and
      Brucella. In Alphaproteobactetia, methylation of adenine at GANTC sites by the CcrM methylase
      regulates the cell cycle and couples gene transcription to DNA replication. In
      Gammaproteobacteria, adenine methylation at GATC sites by the Dam methylase provides signals
      for DNA replication, chromosome segregation, mismatch repair, packaging of bacteriophage
      genomes, transposase activity, and regulation of gene expression. Transcriptional repression
      by Dam methylation appears to be more common than transcriptional activation. Certain
      promoters are active only during the hemimethylation interval that follows DNA replication;
      repression is restored when the newly synthesized DNA strand is methylated In the E. coli
      genome, however, methylation of specific GATC sites can be blocked by cognate DNA binding
      proteins. Blockage of GATC methylation beyond cell division permits transmission of DNA
      methylation patterns to daughter cells and can give rise to distinct epigenetic states, each
      propagated by a positive feedback loop. Switching between alternative DNA methylation patterns
      can split clonal bacterial populations into epigenetic lineages in a manner reminiscent of
      eukaryotic cell differentiation. Inheritance of self-propagating DNA methylation patterns
      governs phase variation in the E. coli pap operon, the agn43 gene, and other loci encoding
      virulence-related cell surface functions.
AU  - Casadesus J
AU  - Low D
PT  - Journal Article
TA  - Microbiol. Mol. Biol. Rev.
JT  - Microbiol. Mol. Biol. Rev.
SO  - Microbiol. Mol. Biol. Rev. 2006 70: 830-856.

PMID- 
VI  - 
DP  - 1996
TI  - Methylation-related epigenetic signals in bacterial DNA.
PG  - 141-153
AB  - The term "epigenetic signals"  may seem extraneous to the life-style of bacteria, because the
      classic concept of epigenetics has been applied to the changes in gene expression that govern
      differentiation and development.  However, because differentiation is often associated with
      changes in DNA or chromatin structure, DNA modification has provided an attractive model for
      the study of epigenetic regulation.
AU  - Casadesus J
AU  - Torreblanca J
PT  - Journal Article
TA  - Epigenetic Mechanisms of Gene Regulation
JT  - Epigenetic Mechanisms of Gene Regulation
SO  - Epigenetic Mechanisms of Gene Regulation 1996 : 141-153.

PMID- 29449382
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Escherichia coli ML35.
PG  - e00034-18
AB  - We report here the complete genome sequence of Escherichia coli strain ML35. We assembled
      PacBio reads into a single closed contig with 169x mean coverage and
      then polished this contig using Illumina MiSeq reads, yielding a 4,918,774-bp
      sequence with 50.8% GC content.
AU  - Casale A
AU  - Clark S
AU  - Grasso M
AU  - Kryschuk M
AU  - Ritzer L
AU  - Trudeau M
AU  - Williams LE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00034-18.

PMID- 27908991
VI  - 4
DP  - 2016
TI  - Genome Sequence of the Fish Pathogen Yersinia ruckeri Strain 150, Isolated from Diseased Rainbow Trout.
PG  - e01331-16
AB  - We present here the draft genome of a pathogenic Yersinia ruckeri strain, isolated from
      rainbow trout (Oncorhynchus mykiss) affected by enteric redmouth
      disease. The chromosome has 3,826,775 bp, a GC content of 46.88%, and is
      predicted to contain 3,538 coding sequences. The data will be useful for
      comparative pathogenicity studies.
AU  - Cascales D
AU  - Guijarro JA
AU  - Reimundo P
AU  - Garcia-Torrico AI
AU  - Mendez J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01331-16.

PMID- 3549710
VI  - 262
DP  - 1987
TI  - Cloning, sequencing, in vivo promoter mapping, and expression in Escherichia coli of the gene for the HhaI methyltransferase.
PG  - 4770-4777
AB  - A 1476-base pair DNA fragment from Haemophilus haemolyticus containing the HhaI
      methyltransferase gene was isolated from a cell library and cloned into pBR322.
      The nucleotide sequence of this fragment was determined.  The structural gene
      is 981 nucleotides in length coding for a protein of 327 amino acids (Mr
      37,000).  The translational start signal (ATG) is preceded by the putative
      ribosome-binding site (TAAG).  Recombinant plasmids containing the
      1476-basepair fragment are completely methylated when isolated from Escherichia
      coli, as judged by their insusceptibility to the HhaI restriction endonuclease.
      However, the presence of an active HhaI methylase gene in certain E. coli
      stsrains results in a very poor yield of transformants and/or in
      vivo-originated deletions due to the Rgl functions of these hosts.  The in vivo
      transcription and initiation sites have been identified by S1 protection and
      primer-extension experiments using specific probes with total RNA prepared from
      E. coli cells (HB101 or RR1) which tolerate the expression of MHhaI.
AU  - Caserta M
AU  - Zacharias W
AU  - Nwankwo D
AU  - Wilson GG
AU  - Wells RD
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1987 262: 4770-4777.

PMID- 26067969
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Listeria monocytogenes Strain DPC6895, a Serotype 1/2b Isolate from Bovine Raw Milk.
PG  - e00629-15
AB  - Listeria monocytogenes is a foodborne pathogen and is the causative agent of listeriosis among
      humans and animals. The draft genome sequence of L.
      monocytogenes DPC6895, a serotype 1/2b strain isolated from the raw milk of a cow
      with subclinical bovine mastitis, is reported.
AU  - Casey A
AU  - McAuliffe O
AU  - Coffey A
AU  - Hunt K
AU  - Fanning S
AU  - Fox E
AU  - Jordan K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00629-15.

PMID- 27257200
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Listeria monocytogenes Serotype 4b Strains 944 and 2993 and Serotype 1/2c Strains 198 and 2932.
PG  - e00482-16
AB  - Listeria monocytogenes is a foodborne pathogen and the causative agent of listeriosis among
      humans and animals. The draft genome sequences of L.
      monocytogenes serotype 4b strains 944 and 2993 and serotype 1/2c strains 198 and
      2932 are reported here.
AU  - Casey A
AU  - McAuliffe O
AU  - Fox EM
AU  - Leong D
AU  - Gahan CG
AU  - Jordan K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00482-16.

PMID- 6300439
VI  - 45
DP  - 1983
TI  - Additional restriction endonuclease cleavage sites on the bacteriophage P22 genome.
PG  - 864-867
AB  - We present complete restriction endonuclease cleavage site maps of the
      bacteriophage P22 chromosome for 16 enzymes with six base recognition
      sequences, thereby positioning 116 new sites on the chromosome.  Twenty-four
      such restriction maps for P22 DNA, containing 162 sites, have now been
      completed, and three enzymes were found that did not cut P22 DNA.  Our results
      are consistent with the ideas that ClaI does not cleave the methylated
      recognition sequence ATCGMeAT or MeATCGAT and StuI does not cleave the
      methylated recognition sequence AGGCMeCT.
AU  - Casjens S
AU  - Hayden M
AU  - Jackson E
AU  - Deans R
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1983 45: 864-867.

PMID- 10672174
VI  - 35
DP  - 2000
TI  - A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochete Borrelia burgdorferi.
PG  - 490-516
AB  - We have determined that Borrelia burgdorferi strain B31 MI carries 21
      extrachromosomal DNA elements, the largest number known for any bacterium.
      Among these are 12 linear and nine circular plasmids, whose sequences
      total 610 694 bp. We report here the nucleotide sequence of three linear
      and seven circular plasmids (comprising 290 546 bp) in this infectious
      isolate. This completes the genome sequencing project for this organism;
      its genome size is 1 521 419 bp (plus about 2000 bp of undetermined
      telomeric sequences). Analysis of the sequence implies that there has been
      extensive and sometimes rather recent DNA rearrangement among a number of
      the linear plasmids. Many of these events appear to have been mediated by
      recombinational processes that formed duplications. These many regions of
      similarity are reflected in the fact that most plasmid genes are members
      of one of the genome's 161 paralogous gene families; 107 of these gene
      families, which vary in size from two to 41 members, contain at least one
      plasmid gene. These rearrangements appear to have contributed to a
      surprisingly large number of apparently non-functional pseudogenes, a very
      unusual feature for a prokaryotic genome. The presence of these damaged
      genes suggests that some of the plasmids may be in a period of rapid
      evolution. The sequence predicts 535 plasmid genes >/=300 bp in length
      that may be intact and 167 apparently mutationally damaged and/or
      unexpressed genes (pseudogenes). The large majority, over 90%, of genes on
      these plasmids have no convincing similarity to genes outside Borrelia,
      suggesting that they perform specialized functions.
AU  - Casjens S
AU  - Palmer N
AU  - van Vugt R
AU  - Huang WM
AU  - Stevenson B
AU  - Rosa P
AU  - Lathigra R
AU  - Sutton G
AU  - Peterson J
AU  - Dodson RJ
AU  - Haft D
AU  - Hickey E
AU  - Gwinn M
AU  - White O
AU  - Fraser CM
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2000 35: 490-516.

PMID- 15136040
VI  - 339
DP  - 2004
TI  - The chromosome of Shigella flexneri bacteriophage Sf6: complete nucleotide sequence, genetic mosaicism, and DNA packaging.
PG  - 379-394
AB  - Shigella flexneri temperate bacteriophage Sf6 is of interest in part because its
      prophageexpresses the oac gene that alters the antigenic
      properties of the surface O-antigen polysaccharide of its host bacterium.
      We have determined the complete sequence of its 39,044 bp genome. The
      sequence shows that Sf6 is a member of the canonical lambdoid phage group,
      and like other phages of this type has a highly mosaic genome. It has
      chromosomal regions that encode proteins >80% identical with at least 15
      different previously characterized lambdoid phages and prophages, but 43%
      of the genome, including the virion assembly genes, is homologous to the
      genome of one phage, HK620. An analysis of the nucleotide differences
      between Sf6 and HK620 indicates that even these similar regions are highly
      mosaic. This mosaicism suggests ways in which the virion structural
      proteins might interact with each other. The Sf6 early operons are
      arranged like a typical lambdoid phage, with "boundary sequences" often
      found between functional modules in the "metabolic" genome domain. By
      virtue of high degree of similarity in the encoding genes and their DNA
      target sites, we predict that the integrase, early transcription
      anti-terminator, CI and Cro repressors, and CII protein of Sf6 have DNA
      binding specificities very similar to the homologous proteins encoded byphages HK620, lambda,
      434 and P22, respectively. The late operon contains
      two tRNA genes. The Sf6 terminase genes are unusual. Analysis of in vivo
      initiation of the DNA packaging series showed that the Sf6 apparatus that
      recognizes DNA for packaging appears to cleave DNA for initiation of
      packaging series at many sites within a large region of about 1800 bp that
      includes a possible pac site. This is unlike previously characterized
      phage packaging mechanisms.
AU  - Casjens S
AU  - Winn-Stapley DA
AU  - Gilcrease EB
AU  - Morona R
AU  - Kuhlewein C
AU  - Chua JE
AU  - Manning PA
AU  - Inwood W
AU  - Clark AJ
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2004 339: 379-394.

PMID- 21217002
VI  - 193
DP  - 2011
TI  - Whole Genome Sequence of an Unusual Borrelia burgdorferi Sensu Lato Isolate.
PG  - 1489-1490
AB  - Human Lyme disease is caused by a number of related Borrelia burgdorferi sensu lato species.
      We report here the complete genome sequence of
      Borrelia sp. isolate SV1 from Finland. This isolate is to date the closest
      known relative of B. burgdorferi sensu stricto, but it is sufficiently
      genetically distinct from that species that it and its close relatives
      warrant its candidacy for new-species status. We suggest that this isolate
      should be named 'Borrelia finlandensis.'
AU  - Casjens SR
AU  - Fraser-Liggett CM
AU  - Mongodin EF
AU  - Qiu WG
AU  - Dunn JJ
AU  - Luft BJ
AU  - Schutzer SE
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 1489-1490.

PMID- 14996813
VI  - 186
DP  - 2004
TI  - The pKO2 Linear Plasmid Prophage of Klebsiella oxytoca.
PG  - 1818-1832
AB  - Temperate bacteriophages with plasmid prophages are uncommon in nature, and of these only
      phages N15 and PY54 are known to have a linear plasmid prophage with closed hairpin telomeres.
      We report here the complete nucleotide sequence of the 51,601-bp Klebsiella oxytoca linear
      plasmid pKO2, and we demonstrate experimentally that it is also a prophage. We call this
      bacteriophage phiKO2. An analysis of the 64 predicted phiKO2 genes indicate that it is a
      fairly close relative of phage N15; they share a mosaic relationship that is typical of
      different members of double-stranded DNA tailed-phage groups. Although the head, tail shaft,
      and lysis genes are not recognizably homologous between these phages, other genes such as the
      plasmid partitioning, replicase, prophage repressor, and protelomerase genes (and their
      putative targets) are so similar that we predict that they must have nearly identical DNA
      binding specificities. The phiKO2 virion is unusual in that its phage lambda-like tails have
      an exceptionally long (3,433 amino acids) central tip tail fiber protein. The phiKO2 genome
      also carries putative homologues of bacterial dinI and umuD genes, both of which are involved
      in the host SOS response. We show that these divergently transcribed genes are regulated by
      LexA protein binding to a single target site that overlaps both promoters.
AU  - Casjens SR
AU  - Gilcrease EB
AU  - Huang WM
AU  - Bunny KL
AU  - Pedulla ML
AU  - Ford ME
AU  - Houtz JM
AU  - Hatfull GF
AU  - Hendrix RW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2004 186: 1818-1832.

PMID- 22123755
VI  - 193
DP  - 2011
TI  - Whole-Genome Sequences of Two Borrelia afzelii and Two Borrelia garinii Lyme Disease Agent Isolates.
PG  - 6995-6996
AB  - Human Lyme disease is commonly caused by several species of spirochetes in the Borrelia genus.
      In Eurasia these species are largely Borrelia afzelii,
      B. garinii, B. burgdorferi, and B. bavariensis sp. nov. Whole-genome
      sequencing is an excellent tool for investigating and understanding the
      influence of bacterial diversity on the pathogenesis and etiology of Lyme
      disease. We report here the whole-genome sequences of four isolates from
      two of the Borrelia species that cause human Lyme disease, B. afzelii
      isolates ACA-1 and PKo and B. garinii isolates PBr and Far04.
AU  - Casjens SR
AU  - Mongodin EF
AU  - Qiu WG
AU  - Dunn JJ
AU  - Luft BJ
AU  - Fraser-Liggett CM
AU  - Schutzer SE
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6995-6996.

PMID- 23469333
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Anoxybacillus flavithermus TNO-09.006, a Thermophilic Sporeformer Associated with a Dairy-Processing Environment.
PG  - e00010-13
AB  - Spores of thermophilic spore-forming bacteria are a common cause of contamination in dairy
      products. We isolated the thermophilic strain TNO-09.006 from a
      milk-processing plant, and we report the complete genome of this isolate
      consisting of a single chromosome of 2.65 Mb.
AU  - Caspers MP
AU  - Boekhorst J
AU  - Abee T
AU  - Siezen RJ
AU  - Kort R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00010-13.

PMID- 27516503
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Four Thermophilic Spore Formers Isolated from a Dairy-Processing Environment.
PG  - e00757-16
AB  - Spores of thermophilic spore-forming bacteria are a common cause of contamination in dairy
      products. Here, we report draft genome sequences of four thermophilic
      strains from a milk-processing plant or standard milk, namely, a Geobacillus
      thermoglucosidans isolate (TNO-09.023), Geobacillus stearothermophilus
      TNO-09.027, and two Anoxybacillus flavithermus isolates (TNO-09.014 and
      TNO-09.016).
AU  - Caspers MP
AU  - Boekhorst J
AU  - de Jong A
AU  - Kort R
AU  - Nierop GM
AU  - Abee T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00757-16.

PMID- 30249703
VI  - 200
DP  - 2018
TI  - DNA Methylation by Restriction Modification Systems Affects the Global Transcriptome Profile in Borrelia burgdorferi.
PG  - e00395-18
AB  - Prokaryote restriction modification (RM) systems serve to protect bacteria from potentially
      detrimental foreign DNA. Recent evidence suggests that DNA
      methylation by the methyltransferase (MTase) components of RM systems can also
      have effects on transcriptome profiles. The type strain of the causative agent of
      Lyme disease, Borrelia burgdorferi B31, possesses two RM systems with
      N6-methyladenosine (m6A) MTase activity, which are encoded by the bbe02 gene
      located on linear plasmid lp25 and bbq67 on lp56. The specific recognition and/or
      methylation sequences had not been identified for either of these B. burgdorferi
      MTases, and it was not previously known whether these RM systems influence
      transcript levels. In the current study, single-molecule real-time sequencing was
      utilized to map genome-wide m6A sites and to identify consensus modified motifs
      in wild-type B. burgdorferi as well as MTase mutants lacking either the bbe02
      gene alone or both bbe02 and bbq67 genes. Four novel conserved m6A motifs were
      identified and were fully attributable to the presence of specific MTases.
      Whole-genome transcriptome changes were observed in conjunction with the loss of
      MTase enzymes, indicating that DNA methylation by the RM systems has effects on
      gene expression. Genes with altered transcription in MTase mutants include those
      involved in vertebrate host colonization (e.g., rpoS regulon) and acquisition
      by/transmission from the tick vector (e.g., rrp1 and pdeB). The results of this
      study provide a comprehensive view of the DNA methylation pattern in B.
      burgdorferi, and the accompanying gene expression profiles add to the emerging
      body of research on RM systems and gene regulation in bacteria.IMPORTANCE Lyme
      disease is the most prevalent vector-borne disease in North America and is
      classified by the Centers for Disease Control and Prevention (CDC) as an emerging
      infectious disease with an expanding geographical area of occurrence. Previous
      studies have shown that the causative bacterium, Borrelia burgdorferi, methylates
      its genome using restriction modification systems that enable the distinction
      from foreign DNA. Although much research has focused on the regulation of gene
      expression in B. burgdorferi, the effect of DNA methylation on gene regulation
      has not been evaluated. The current study characterizes the patterns of DNA
      methylation by restriction modification systems in B. burgdorferi and evaluates
      the resulting effects on gene regulation in this important pathogen.
AU  - Casselli T
AU  - Tourand Y
AU  - Scheidegger A
AU  - Arnold WK
AU  - Proulx A
AU  - Stevenson B
AU  - Brissette CA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2018 200: e00395-18.

PMID- 25197464
VI  - 9
DP  - 2014
TI  - Non-contiguous finished genome sequence and description of Bacteroides neonati sp. nov., a new species of anaerobic bacterium.
PG  - 794-806
AB  - Bacteroides neonati strain MS4(T), is the type strain of Bacteroides neonati sp.  nov., a new
      species within the genus Bacteroides. This strain, whose genome is
      described here, was isolated from a premature neonate stool sample. B. neonati
      strain MS4(T) is an obligate anaerobic Gram-negative bacillus. Here we describe
      the features of this organism, together with the complete genome sequence and
      annotation. The 5.03 Mbp long genome exhibits a G+C content of 43.53% and
      contains 4,415 protein-coding and 91 RNA genes, including 9 rRNA genes.
AU  - Cassir N
AU  - Croce O
AU  - Pagnier I
AU  - Benamar S
AU  - Couderc C
AU  - Robert C
AU  - Raoult D
AU  - La Scola B
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 794-806.

PMID- 
VI  - 6
DP  - 2011
TI  - Identification of restriction endonucleases sensitive to 5-cytosine methylation at non-CpG sites, including expanded (CAG)n/(CTG)n repeats.
PG  - 417-421
AB  - Most epigenetic studies assess methylation of 5'-CpG-3' sites but recent evidence indicates
      that non-CpG cytosine methylation occurs at
      high levels in humans and other species. This is most prevalent at
      5'-CHG-3', where H = A, C or T, and it preferentially occurs at
      5'-CpA-3' and 5'-CpT-3' sites. With the goal of facilitating the
      detection of non-CpG methylation, the restriction endonucleases ApeKI,
      BbvI, EcoP15I, Fnu4HI, MwoI and TseI were assessed for their
      sensitivity to 5-methylcytosine at GpCpA, GpCpT, GpCpC or GpCpG sites,
      where methylation is catalyzed by the DNA 5-cytosine 5'-GpC-3'
      methyltransferase M.CviPI. We tested a variety of sequences including
      various plasmid-based sites, a cloned disease-associated (CAG)83 center
      dot(CTG)83 repeat and in vitro synthesized tracts of only (CAG)500
      center dot(CTG) 500 or (CAG)800 center dot(CTG)800. The repeat tracts
      are enriched for the preferred CpA and CpT motifs. We found that none
      of the tested enzymes can cleave their recognition sequences when they
      are 5'-GpC-3' methylated. A genomic site known to convert its non-CpG
      methylation levels upon C2C12 differentiation was confirmed through the
      use of these enzymes. These enzymes can be useful in rapidly and easily
      determining the most common non-CpG methylation status in various
      sequence contexts, as well as at expansions of (CAG) n.(CTG) n repeat
      tracts associated with diseases like myotonic dystrophy and Huntington
      disease.
AU  - Castel AL
AU  - Nakamori M
AU  - Thornton CA
AU  - Pearson CE
PT  - Journal Article
TA  - EPIGENETICS
JT  - EPIGENETICS
SO  - EPIGENETICS 2011 6: 417-421.

PMID- 20033464
VI  - 16
DP  - 2010
TI  - Homology modeling and molecular dynamics simulations of HgiDII methyltransferase in complex with DNA and S-adenosyl-methionine: Catalytic mechanism and interactions with DNA.
PG  - 1213-1222
AB  - M.HgiDII is a methyltransferase (MTase) from Herpetosiphon giganteus that recognizes the
      sequence GTCGAC. This enzyme belongs to a group of
      MTases that share a high degree of amino acid similarity, albeit none
      of them has been thoroughly characterized. To study the catalytic
      mechanism of M.HgiDII and its interactions with DNA, we performed
      molecular dynamics simulations with a homology model of M.HgiDII
      complexed with DNA and S-adenosyl-methionine. Our results indicate that
      M.HgiDII may not rely only on Glu119 to activate the cytosine ring,
      which is an early step in the catalysis of cytosine methylation;
      apparently, Arg160 and Arg162 may also participate in the activation by
      interacting with cytosine O2. Another residue from the catalytic site,
      Val118, also played a relevant role in the catalysis of M.HgiDII.
      Val118 interacted with the target cytosine and kept water molecules
      from accessing the region of the catalytic pocket where Cys79 interacts
      with cytosine, thus preventing water-mediated disruption of
      interactions in the catalytic site. Specific recognition of DNA was
      mediated mainly by amino acids of the target recognition domain,
      although some amino acids (loop 80-88) of the catalytic domain may also
      contribute to DNA recognition. These interactions involved direct
      contacts between M.HgiDII and DNA, as well as indirect contacts through
      water bridges. Additionally, analysis of sequence alignments with
      closely related MTases helped us to identify a motif in the TRD of
      M.HgiDII that may be relevant to specific DNA recognition.
AU  - Castelan-Vega JA
AU  - Jimenez-Alberto A
AU  - Ribas-Aparicio RM
PT  - Journal Article
TA  - J. Mol. Model.
JT  - J. Mol. Model.
SO  - J. Mol. Model. 2010 16: 1213-1222.

PMID- 18345608
VI  - 51
DP  - 2008
TI  - Constrained analogues of procaine as novel small molecule inhibitors of DNA methyltransferase-1.
PG  - 2321-2325
AB  - Constrained analogues of procaine were synthesized, and their inhibiting activity against
      DNMT1 was tested. Among them, the most
      potent compound, derivative 3b, was also able to induce a recognizable
      demethylation of chromosomal satellite repeats in HL60 human myeloid
      leukemia cells and thus represents a lead compound for the development
      of a novel class of non-nucleoside DNMT1 inhibitors.
AU  - Castellano S
AU  - Kuck D
AU  - Sala M
AU  - Novellino E
AU  - Lyko F
AU  - Sbardella G
PT  - Journal Article
TA  - J. Med. Chem.
JT  - J. Med. Chem.
SO  - J. Med. Chem. 2008 51: 2321-2325.

PMID- 28280020
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of 18 Salmonella enterica subsp. enterica Serovar Oranienburg Strains Isolated from Rivers in Northwestern Mexico.
PG  - e01585-16
AB  - Salmonella enterica subsp. enterica serovar Oranienburg is recognized as a foodborne pathogen
      widely distributed in the environment. Here, we report 18
      draft genomes of S Oranienburg strains isolated from rivers in the northwestern
      region of Mexico.
AU  - Casteneda-Ruelas GM
AU  - Carreon-Gaxiola C
AU  - Castelan-Sanchez HG
AU  - Acatzi-Silva A
AU  - Romero-Martinez S
AU  - Garcia-Molina A
AU  - Jimenez-Edeza M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01585-16.

PMID- 29439037
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of the Siderophore-Degrading Soil Bacterium Mesorhizobium loti Strain LU.
PG  - e00029-18
AB  - Here, we present the draft genome of Mesorhizobium loti strain LU, a soil bacterium capable of
      degrading the trihydroxamate siderophore deferrioxamine B to
      its constituent monohydroxamic acids. Genome size was 6,399,828 bp, with a GC
      content of 61.5%. This draft genome consists of 35 scaffolds, with an N50 of
      389,921 bp.
AU  - Castignetti D
AU  - Polley N
AU  - Putonti C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00029-18.

PMID- 
VI  - 23
DP  - 2009
TI  - The role of GATC flanking sequences in the methylation efficiency of Escherichia coli DNA adenine methyltransferase.
PG  - 482.3
AB  - Escherichia coli DNA adenine methyltransferase (Dam) methylates the adenine in GATC sequences.
      The enzyme plays a crucial role in the
      timing of DNA replication, gene regulation, and mismatch repair. Many
      genes that Dam regulates are involved in pathogenesis. Previous in
      vitro studies showed that certain GATC sites were preferentially
      methylated depending upon the GATC flanking sequences. Sites rich in
      A/T base pairs tend to be less preferred than those rich in G/C. Poorly
      preferred GATC sites as determined by in vitro studies are also
      undermethylated in vivo. The lack of methylation at these sites is
      often important for the expression of pathogenic genes. Our goal is to
      determine if GATC flanking sequences affect Dam methylation efficiency
      at certain sites in vivo. We hypothesize that the same trend will hold
      true in vivo and G/C rich flanking sequences will be preferred.
      dam-minus cells were transformed with a plasmid containing the dam gene
      under control of the arabinose promoter. After growth at low
      concentrations of Dam we isolated the plasmid and observed the
      methylation levels of GATC sites. We found that a GATC with G/C rich
      flanking sequences was preferentially methylated compared to a
      consecutive GATC with A/T rich flanking sequences. Our studies will
      help in understanding how Dam is able to discriminate between GATC
      sites in vivo which is important for its various roles, particularly
      gene regulation.
AU  - Castillo A
AU  - Peterson S
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 2009 23: 482.3.

PMID- 26139724
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Vibrio alginolyticus Strains V1 and V2, Opportunistic Marine Pathogens.
PG  - e00729-15
AB  - We announce the draft genome sequences of Vibrio alginolyticus strains V1 and V2, isolated
      from juvenile Sparus aurata and Dentex dentex, respectively, during
      outbreaks of vibriosis. The genome sequences are 5,257,950 bp with a G+C content
      of 44.5% for V. alginolyticus V1 and 5,068,299 bp with a G+C content of 44.8% for
      strain V2. These genomes provide further insights into the putative virulence
      factors, prophage carriage, and evolution of this opportunistic marine pathogen.
AU  - Castillo D
AU  - D'Alvise P
AU  - Kalatzis PG
AU  - Kokkari C
AU  - Middelboe M
AU  - Gram L
AU  - Liu S
AU  - Katharios P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00729-15.

PMID- 26383670
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of the Fish Pathogen Vibrio harveyi Strains VH2 and VH5.
PG  - e01062-15
AB  - Vibrio harveyi is an important marine pathogen that is responsible for vibriosis  outbreaks in
      cultured fish and invertebrates worldwide. Here, we announce the draft genome sequences of V.
      harveyi strains VH2 and VH5, isolated from farmed juvenile Seriola dumerili during outbreaks
      of vibriosis in Crete, Greece.
AU  - Castillo D
AU  - D'Alvise P
AU  - Middelboe M
AU  - Gram L
AU  - Liu S
AU  - Kalatzis PG
AU  - Kokkari C
AU  - Katharios P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01062-15.

PMID- 29930054
VI  - 6
DP  - 2018
TI  - Genome Sequences of Shewanella baltica and Shewanella morhuae Strains Isolated from the Gastrointestinal Tract of Freshwater Fish.
PG  - e00541-18
AB  - We present here the genome sequences of Shewanella baltica strain CW2 and Shewanella morhuae
      strain CW7, isolated from the gastrointestinal tract of
      Salvelinus namaycush (lean lake trout) and Coregonus clupeaformis (whitefish),
      respectively. These genome sequences provide insights into the niche adaptation
      of these specific species in freshwater systems.
AU  - Castillo D
AU  - Gram L
AU  - Dailey FE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00541-18.

PMID- 29674546
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Shewanella sp. WE21, a Rare Isolate with Multiple Novel Large Genomic Islands.
PG  - e00277-18
AB  - We present here the whole-genome sequence of Shewanella sp. WE21, an unusual omega-3 fatty
      acid-producing bacterium isolated from the gastrointestinal tract
      of the freshwater fish Sander vitreus (walleye). This genome contains a number of
      unique, large genomic islands with genes not present in other Shewanella
      bacteria.
AU  - Castillo D
AU  - Gram L
AU  - Dailey FE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00277-18.

PMID- 26139725
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Vibrio parahaemolyticus VH3, Isolated from an Aquaculture Environment in Greece.
PG  - e00731-15
AB  - Vibrio parahaemolyticus is an important foodborne pathogen responsible for gastroenteritis
      outbreaks globally. It has also been identified as an important
      pathogen in aquatic organisms. Here, we report a draft genome sequence of V.
      parahaemolyticus, strain VH3, isolated from farmed juvenile greater amberjack,
      Seriola dumerili, in Greece.
AU  - Castillo D
AU  - Jun JW
AU  - D'Alvise P
AU  - Middelboe M
AU  - Gram L
AU  - Liu S
AU  - Katharios P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00731-15.

PMID- 29519824
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Six Vibrio diazotrophicus Strains Isolated from Deep Subsurface Sediments of the Baltic Sea.
PG  - e00081-18
AB  - We present here the draft genome sequences of six Vibrio diazotrophicus strains,  which were
      isolated from deep subseafloor sediments of the Baltic Sea. The
      genomic sequences contained several virulence and antibiotic resistance genes.
      These genome sequences provide insights into the genetic composition and
      evolution of the genus Vibrio in marine environments.
AU  - Castillo D
AU  - Vandieken V
AU  - Engelen B
AU  - Engelhardt T
AU  - Middelboe M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00081-18.

PMID- 27231372
VI  - 4
DP  - 2016
TI  - Genome Sequence of the Acetogenic Bacterium Moorella mulderi DSM 14980T.
PG  - e00444-16
AB  - Here, we report the draft genome sequence of Moorella mulderi DSM 14980(T), a thermophilic
      acetogenic bacterium, which is able to grow autotrophically on H2
      plus CO2 using the Wood-Ljungdahl pathway. The genome consists of a circular
      chromosome (2.99 Mb).
AU  - Castillo VGA
AU  - Poehlein A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00444-16.

PMID- 28912309
VI  - 5
DP  - 2017
TI  - First Whole-Genome Shotgun Sequence of a Promising Cellulase Secretor, Trichoderma koningiopsis Strain POS7.
PG  - e00823-17
AB  - Trichoderma koningiopsis strain POS7 produces significantly large amounts of cellulase enzymes
      in solid-state fermentation. The Illumina-based sequence
      analysis reveals an approximate genome size of 36.6 Mbp, with a G+C content of
      48.82% for T. koningiopsis POS7. Based on ab initio prediction, 12,661 coding
      genes were annotated.
AU  - Castrillo ML
AU  - Bich GA
AU  - Modenutti C
AU  - Turjanski A
AU  - Zapata PD
AU  - Villalba LL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00823-17.

PMID- 29255572
VI  - 12
DP  - 2017
TI  - Draft genome sequence of the type strain of the sulfur-oxidizing acidophile, Acidithiobacillus albertensis (DSM 14366).
PG  - 77
AB  - Acidithiobacillus albertensis is an extremely acidophilic, mesophilic, obligatory autotrophic
      sulfur-oxidizer, with potential importance in the bioleaching of
      sulfidic metal ores, first described in the 1980s. Here we present the draft
      genome sequence of Acidithiobacillus albertensis DSM 14366(T), thereby both
      filling a long-standing gap in the genomics of the acidithiobacilli, and
      providing further insight into the understanding of the biology of the non
      iron-oxidizing members of the Acidithiobacillus genus. The assembled genome is
      3,1 Mb, and contains 47 tRNAs, tmRNA gene and 2 rRNA operons, along with 3149
      protein-coding predicted genes. The Whole Genome Shotgun project was deposited in
      DDBJ/EMBL/GenBank under the accession MOAD00000000.
AU  - Castro M
AU  - Moya-Beltran A
AU  - Covarrubias PC
AU  - Gonzalez M
AU  - Cardenas JP
AU  - Issotta F
AU  - Nunez H
AU  - Acuna LG
AU  - Encina G
AU  - Holmes DS
AU  - Johnson DB
AU  - Quatrini R
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 77.

PMID- 27856592
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Microcystis aeruginosa CACIAM 03, a Cyanobacterium Isolated from an Amazonian Freshwater Environment.
PG  - e01299-16
AB  - Given its toxigenic potential, Microcystis aeruginosa is an important bloom-forming
      cyanobacterium. Here, we present a draft genome and annotation of
      the strain CACIAM 03, which was isolated from an Amazonian freshwater
      environment.
AU  - Castro WO
AU  - Lima AR
AU  - Moraes PH
AU  - Siqueira AS
AU  - Aguiar DC
AU  - Barauna AR
AU  - Martins LC
AU  - Fuzii HT
AU  - de Lima CP
AU  - Vianez-Junior JL
AU  - Nunes MR
AU  - Dall'Agnol LT
AU  - Goncalves EC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01299-16.

PMID- 25125649
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Haloferax sp. Strain ATB1, Isolated from a Semi-Arid Region in the Brazilian Caatinga.
PG  - e00812-14
AB  - Organisms in the Haloferax genus are extreme halophiles that grow in environments with pH
      values between 4 and 12, and temperatures between 0 degrees C and 60
      degrees C. In the present study, a draft of the first Haloferax sp. strain ATB1
      genome isolated from the region of Cariri (in Paraiba State, Brazil) is
      presented.
AU  - Castro WO
AU  - Torres-Ballesteros AM
AU  - Nakayama CR
AU  - Melo IS
AU  - Pellizari VH
AU  - Silva A
AU  - Ramos RT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00812-14.

PMID- 27340065
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of a Multidrug-Resistant Acinetobacter baumannii Isolate Obtained from a Mexican Hospital (Sequence Type 422).
PG  - e00583-16
AB  - Acinetobacter baumannii has emerged as a dangerous nosocomial pathogen, particularly for
      severely ill patients in intensive care units and patients with
      hematologic malignancies. Here, we present the complete genome sequence of a
      multidrug-resistant A. baumannii isolate, recovered from a Mexican hospital and
      classified as sequence type 422 according to the multilocus sequence typing
      Pasteur scheme.
AU  - Castro-Jaimes S
AU  - Salgado-Camargo AD
AU  - Grana-Miraglia L
AU  - Lozano L
AU  - Bocanegra-Ibarias P
AU  - Volkow-Fernandez P
AU  - Silva-Sanchez J
AU  - Castillo-Ramirez S
AU  - Cevallos MA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00583-16.

PMID- 28522725
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Five Enterococcus Species Isolated from the Gut of Patients with Suspected Clostridium difficile Infection.
PG  - e00379-17
AB  - We present draft genome sequences of five Enterococcus species from patients suspected of
      Clostridium difficile infection. Genome completeness was confirmed
      by presence of bacterial orthologs (97%). Gene searches using Hidden-Markov
      models revealed that the isolates harbor between seven and 11 genes involved in
      antibiotic resistance to tetracyclines, beta-lactams, and vancomycin.
AU  - Castro-Nallar E
AU  - Valenzuela SL
AU  - Baquedano S
AU  - Sanchez C
AU  - Fernandez F
AU  - Trombert AN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00379-17.

PMID- 18983124
VI  - 8
DP  - 2008
TI  - Control of Steric Hindrance on Restriction Enzyme Reactions with Surface-Bound DNA Nanostructures.
PG  - 4140-4145
AB  - To understand better enzyme/DNA interactions and to design innovative detectors based on DNA
      nanoarrays, we need to study the effect of
      nanometric confinement on the biochemical activity of the DNA
      molecules. We focus on the study of the restriction enzyme reactions
      (Dpnll within DNA nanostructures on flat gold films by atomic force
      microscopy (AFM). Typically we work with a few patches of DNA self
      assembled monolayers (SAMs) that are hundred nm in size and are
      lithographically fabricated within alkylthiol SAMs by AFM nanografting.
      We start by nanografting a few patches of a single-stranded DNA (ssDNA)
      molecule of 44 base pairs (bps) with a 4 bps recognition sequence
      (specific for Dpnll in the middle. Afterwards, reaction-ready DNA
      nanopatches are obtained by hybridization with a complementary 44bps
      ssDNA sequence. The enzymatic reactions were carried out over
      nanopatches with different density. By carrying out AFM height
      measurements, we are able to show that the capability of the Dpnll
      enzyme to reach and react at the recognition site is easily varied by
      controlling the DNA packing in the nanostructures. We have found strong
      evidence that inside our ordered DNA nanostructures the enzyme (that
      works as a dimer) can operate down to the limit in which the space
      between adjacent DNA molecules is equal to the size of the DNA/enzyme
      complex. Similar experiments were carried out with a DNA sequence
      without the recognition site, clearly finding that in that case the
      enzymatic reaction did not lead to digestion of the molecules. These
      findings suggest that it is possible to tune the efficiency of an
      enzymatic reaction on a surface by controlling the steric hindrance
      inside the DNA nanopatches without vary any further physical or
      chemical variable. These findings are opening the door to novel
      applications in both the fields of biosensing and fundamental
      biophysics.
AU  - Castronovo M
AU  - Radovic S
AU  - Grunwald C
AU  - Casalis L
AU  - Morgante M
AU  - Scoles G
PT  - Journal Article
TA  - Nano Lett.
JT  - Nano Lett.
SO  - Nano Lett. 2008 8: 4140-4145.

PMID- 3442330
VI  - 167
DP  - 1987
TI  - Determination of 5-methylcytosine by acid hydrolysis of DNA with hydrofluoric acid.
PG  - 347-351
AB  - Quantitation of 5-methylcytosine in DNA after acid hydrolysis has been
      inaccurate because deamination of cytosine and 5-methylcytosine occurs during
      the hydrolysis procedure.  There is little information in the literature
      regarding the use of hydrofluoric acid (HF) for DNA hydrolysis and we have
      therefore undertaken a systematic study of this process.  The
      deoxyribonucleotides of cytosine and 5-methylcytosine were shown not to undergo
      detectable levels of deaminatiton during prolonged periods (up to 24 h) at 80C
      in 48% HF.  Kinetic studies show that the release of purine and pyrimidine
      bases was complete by 4 h under these conditons.  Analysis of the
      5-methylcytosine content of DNA from various tissues gave levels that were very
      close to the values reported in the literature.  This method is ideally suited
      for the determination of the overall cytosine methylation levels in DNA.
AU  - Catania J
AU  - Keenan BC
AU  - Margison GP
AU  - Fairweather DS
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 1987 167: 347-351.

PMID- 2943635
VI  - 47
DP  - 1986
TI  - A restriction and modification model for the initiation and control of recombination in Neurospora.
PG  - 157-165
AB  - It is hypothesized that the products of Neurospora rec+ genes mask
      recombinators such as cog by modifying DNA and that unmodified recombinators
      act as recognition sites for an endonuclease with scission properties like
      those of the type I restriction enzymes found in E. coli.  These cut the DNA in
      both strands at some variable distance from a recognition site.  Repair of a
      two strand gap initiated in this way would require DNA synthesis using the
      information contained in the homologous DNA duplex, leading to gene conversion.
      Crossing over could follow from resolution of two Holliday structures formed
      during gap repair.  The hypothesis explains the polarity in the frequency of
      conversion events across genetic loci, the observation that chromosomes
      carrying recombinators are more often converted than is the homologue, and how
      recombinators can initiate conversion at a distance, as suggested by the
      pattern of conversion events in the his-3 locus in crosses heterozygous for the
      translocation TM429.
AU  - Catcheside DEA
PT  - Journal Article
TA  - Genet. Res.
JT  - Genet. Res.
SO  - Genet. Res. 1986 47: 157-165.

PMID- Not carried by PubMed...
VI  - 0
DP  - 1976
TI  - Restriction and modification in Thermophilic bacilli.
PG  - 358-366
AB  - Over the past several years we have been engaged in an effort to develop transformation in B.
      stearothermophilus.  Until recently these studies have met with little success.  During this
      time, however, a transfection system was established.  This system requires a 'helper phage'
      which may facilitate adsorption and/or uptake of the bacteriophage DNA from the environment.
      While studying the uptake and expression of infectious phage DNA, we observed that the
      efficiency of transfection varied as much as 1,000-fold depending upon the strain in which the
      phage were propagated.  These results suggested the presence of a restriction and modification
      system.  This hypothesis was verified when we identified, by efficiency of plating (EOP)
      studies, classical restriction and modification systems in these strains.  In this
      communication, we describe preliminary studies on the restriction and modification systems in
      B. stearothermophilus.
AU  - Catterall JF
AU  - Lees ND
AU  - Welker NE
PT  - Journal Article
TA  - Microbiology-1976
JT  - Microbiology-1976
SO  - Microbiology-1976 1976 0: 358-366.

PMID- 6246337
VI  - 65
DP  - 1980
TI  - Purification and Properties of the Bst1503 Endonuclease.
PG  - 167-170
AB  - Site-specific endonucleases have become invaluable to the study of the
      structure and function of DNA from both prokaryotic and eukaryotic organisms.
      Some enzymes of this class, the restriction endonucleases, have been shown to
      have a specific in vivo  function acting to protect bacterial cells from
      infection.  An associated enzyme, a modification methylase, must be present in
      cells producing a restriction enzyme to protect cellular DNA from digestion.
      It has recently been shown that restriction enzymes may be capable of promoting
      site-specific recombination in vivo.  The obligate thermophile Bacillus
      stearothermophilus  exhibited typical host-specific restriction and
      modification during infection by thermophilic bacteriophages.  A restriction
      endonuclease (endo R.Bst15035) was purified from B. stearothermophilus strain
      1503-4R.6  The purified Bst1503 retains its thermostability and is optimally
      active at temperatures near the optimal growth temperature of the organism.
      The enzyme is stable to long incubation at 65C in the absence of substrate and
      forms limit digests after similar incubations in the presence of DNA.  Bst1503
      is also stable to long term storage at 5C.
AU  - Catterall JF
AU  - Welker NE
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1980 65: 167-170.

PMID- Not carried by PubMed...
VI  - 37
DP  - 1974
TI  - Reduced efficiency of transfection in Bacillus stearothermophilus with modified phage DNA.
PG  - 9-10
AB  - The infection of B. stearothermophilus, strain 4S with the thermophilic phage
      TP-IC or TP-84 DNA requires the presence of helper phage TP-12.  The mechanism
      by which the helper phage initiates transfection is unknown.
AU  - Catterall JF
AU  - Welker NE
PT  - Journal Article
TA  - Mol. Genetics Bulletin
JT  - Mol. Genetics Bulletin
SO  - Mol. Genetics Bulletin 1974 37: 9-10.

PMID- 14105
VI  - 129
DP  - 1977
TI  - Isolation and properties of a thermostable restriction endonuclease (Endo R.Bst1503) .
PG  - 1110-1120
AB  - A restriction endonuclease was isolated from Bacillus stearothermophilus
      1503-4R (Bst1503) and purified to homogeneity.  The enzyme required Mg2+ ion as
      a cofactor.  Bst1503 exhibited maximal activity between pH 7.5 and 8.0 between
      60 and 65C, and with about 0.2mM Mg2+.  Bst1503 was not inactivated after
      exposure at 55 or 65C for up to 10h.  After 2h of incubation at 70C.  Bst1503
      was inactivated by 65%.  Bst1503 was rapidly inactivated at 75C.  A single
      protein-staining band having a molecular weight of 46,000 was obseved when
      Bst1503 was analyzed by sodium dodecyl sufate-polyacrylamide gel
      electrophoresis.  The enzyme was found to exist in two active forms, the
      predominating form with an S value of 8.3 (180,000) and the second form with an
      S value of 5.4 (96,000).  No conversion between the 8.3S and 5.4S forms was
      observed after storage.  Bst1503 recognized six sites in TP-1C deoxyribonucleic
      acid (DNA), one site in pSC101 and simian virus 40 DNAs, and three sites in
      kvir DNA.  Bst1503 and BamHI were determined to be isoschizomers.  The effect
      of temperatures on the activity and stability of BamHI was determined.
AU  - Catterall JF
AU  - Welker NE
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1977 129: 1110-1120.

PMID- 18276642
VI  - 36
DP  - 2008
TI  - Dynamics and consequences of DNA looping by the FokI restriction endonuclease.
PG  - 2073-2081
AB  - Genetic events often require proteins to be activated by interacting with two DNA sites,
      trapping the intervening DNA in a loop. While much is known about looping equilibria, only a
      few studies have examined DNA-looping dynamics experimentally. The restriction enzymes that
      cut DNA after interacting with two recognition sites, such as FokI, can be used to exemplify
      looping reactions. The reaction pathway for FokI on a supercoiled DNA with two sites was
      dissected by fast kinetics to reveal, in turn: the initial binding of a protein monomer to
      each site; the protein-protein association to form the dimer, trapping the loop; the
      subsequent phosphodiester hydrolysis step. The DNA motion that juxtaposes the sites ought on
      the basis of Brownian dynamics to take approximately 2 ms, but loop capture by FokI took 230
      ms. Hence, DNA looping by FokI is rate limited by protein association rather than DNA
      dynamics. The FokI endonuclease also illustrated activation by looping: it cut looped DNA 400
      times faster than unlooped DNA.
AU  - Catto LE
AU  - Bellamy SR
AU  - Retter SE
AU  - Halford SE
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2008 36: 2073-2081.

PMID- 16556912
VI  - 34
DP  - 2006
TI  - Protein assembly and DNA looping by the FokI restriction endonuclease.
PG  - 1711
AB  - The FokI restriction endonuclease recognizes an asymmetric DNA sequence and cuts both strands
      at fixed positions upstream of the site. The sequence is contacted by a single monomer of the
      protein, but the monomer has only one catalytic centre and forms a dimer to cut both strands.
      FokI is also known to cleave DNA with two copies of its site more rapidly than DNA with one
      copy. To discover how FokI acts at a single site and how it acts at two sites, its reactions
      were examined on a series of plasmids with either one recognition site or with two sites
      separated by varied distances, sometimes in the presence of a DNA-binding defective mutant of
      FokI. These experiments showed that, to cleave DNA with one site, the monomer bound to that
      site associates via a weak protein-protein interaction with a second monomer that remains
      detached from the recognition sequence. Nevertheless, the second monomer catalyses
      phosphodiester bond hydrolysis at the same rate as the DNA-bound monomer. On DNA with two
      sites, two monomers of FokI interact strongly, as a result of being tethered to the same
      molecule of DNA, and sequester the intervening DNA in a loop.
AU  - Catto LE
AU  - Ganguly S
AU  - Milsom SE
AU  - Welsh AJ
AU  - Halford SE
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2006 34: 1711.

PMID- 21839172
VI  - 176
DP  - 2011
TI  - Molecular dynamics simulations of human DNA methyltransferase 3B with selective inhibitor nanaomycin A.
PG  - 185-191
AB  - DNA methyltransferases (DNMTs) are involved in epigenetic regulation of the genome and are
      promising targets for therapeutic intervention in
      cancer and other diseases. Until now, very limited information is
      available concerning the molecular dynamics of DNMTs. The natural
      product nanaomycin A is the first selective inhibitor of DNMT3B that
      induce genomic demethylation. Herein we report long (>100 ns) molecular
      dynamics simulations for human DNMT3B bound to nanaomycin A with and
      without the presence of the cofactor S-adenosyl-L-methionine (SAM). We
      concluded that SAM favors the binding of nanaomycin A to DNMT3B. Key
      interactions of nanaomycin A with DNMT3B involve long lasting
      interactions with Arg731, Arg733, Arg832, and the catalytic Cys651.
      Results further support the previous hypothesis that nanaomycin A has
      key interactions with amino acid residues involved in the mechanism of
      methylation. This work represents one of the first molecular dynamics
      studies of DNMT3B. Results of this work shed light on the structure and
      binding recognition process of a key epigenetic enzyme with a small
      molecule inhibitor.
AU  - Caulfield T
AU  - Medina-Franco JL
PT  - Journal Article
TA  - J. Struct. Biol.
JT  - J. Struct. Biol.
SO  - J. Struct. Biol. 2011 176: 185-191.

PMID- 24356838
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Arsenite-Oxidizing Strain Aliihoeflea sp. 2WW, Isolated from Arsenic-Contaminated Groundwater.
PG  - e01072-13
AB  - Here, we report the draft genome sequence of the arsenite-oxidizing bacterium Aliihoeflea sp.
      strain 2WW, which consists of a 4.15-Mb chromosome and contains
      different genes that are involved in arsenic transformations.
AU  - Cavalca L
AU  - Corsini A
AU  - Andreoni V
AU  - Muyzer G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01072-13.

PMID- 26607893
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Corynebacterium pseudotuberculosis Strain E19, Isolated from a Horse in Chile.
PG  - e01385-15
AB  - Corynebacterium pseudotuberculosis is related to several diseases infecting horses and small
      ruminants, causing economic losses to agribusiness. Here, we
      present the genome sequence of C. pseudotuberculosis strain E19. The genome
      includes one circular chromosome 2,367,956 bp (52.1% G+C content), with 2,112
      genes predicted, 12 rRNAs, and 48 tRNAs.
AU  - Cavalcante AL
AU  - Dias LM
AU  - Alves JT
AU  - Veras AA
AU  - Guimaraes LC
AU  - Rocha FS
AU  - Gala-Garcia A
AU  - Retamal P
AU  - Ramos RT
AU  - Azevedo V
AU  - Silva A
AU  - Carneiro AR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01385-15.

PMID- 27660787
VI  - 4
DP  - 2016
TI  - Complete Genome Sequences of 17 Rapidly Growing Nontuberculous Mycobacterial Strains.
PG  - e01009-16
AB  - We report the complete genome sequences of 17 rapidly growing nontuberculous mycobacterial
      (NTM) strains, including 16 Mycobacterium abscessus complex strains
      and one M. immunogenum strain. These sequences add value to studies of the
      genetic diversity of rapidly growing NTM strains recovered from human specimens.
AU  - Caverly LJ
AU  - Spilker T
AU  - LiPuma JJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01009-16.

PMID- 27284156
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Mycobacterium abscessus subsp. bolletii.
PG  - e00543-16
AB  - We report the complete genome sequence of a Mycobacterium abscessus subsp. bolletii isolate
      recovered from a sputum culture from an individual with cystic
      fibrosis. This sequence is the first completed whole-genome sequence of M.
      abscessus subsp. bolletii and adds value to studies of M. abscessus complex
      genomics.
AU  - Caverly LJ
AU  - Spilker T
AU  - LiPuma JJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00543-16.

PMID- 3470568
VI  - 11C
DP  - 1987
TI  - Anions affect the in vitro function of endonuclease EcoRI.
PG  - 204
AB  - Environmental variables dictate the stability and function of protein-DNA
      interactions in vitro.  For instance, increasing the in vitro K+ concentration
      drastically affects both the rate and extent of the formation of EcoRI-DNA
      complexes (1).  Here we show the critical importance of anionic solution
      components in determining the functional activity of EcoRI.  K+ and glutamate
      are the predominant intracellular ionic species in E. coli and the in vivo
      concentrations of these ions can accumulate to greater than 0.9 and 0.25 M,
      respectively, as part of the osmotic adaptability of the organism.  Comparison
      of the extent of DNA cutting by EcoRI as a function of KCl or KGlu
      concentration in vitro indicates the rate of cleavage is not only highly
      sensitive to the K+ concentration but also to the types and concentrations of
      anions present.  Interestingly, substitution of glu- increases the rate of DNA
      dramatically in solutions of high K+ content.  Since Cl- is not a primary anion
      in E. coli, the results in KGlu are more likely to reflect the physiological
      function of the enzyme.  Our studies indicate that anions drastically affect
      the stability and function of protein-DNA interactions.  Kinetic studies
      therefore provide insight into the determinants of complex formation not
      obtainable from structural studies alone.
AU  - Cayley S
AU  - Record MT
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1987 11C: 204.

PMID- 20174605
VI  - 6
DP  - 2010
TI  - Analysis of the Legionella longbeachae genome and transcriptome uncovers unique strategies to cause Legionnaires' disease.
PG  - e1000851
AB  - Legionella pneumophila and L. longbeachae are two species of a large genus of bacteria that
      are ubiquitous in nature. L. pneumophila is mainly found
      in natural and artificial water circuits while L. longbeachae is mainly
      present in soil. Under the appropriate conditions both species are human
      pathogens, capable of causing a severe form of pneumonia termed
      Legionnaires' disease. Here we report the sequencing and analysis of four
      L. longbeachae genomes, one complete genome sequence of L. longbeachae
      strain NSW150 serogroup (Sg) 1, and three draft genome sequences another
      belonging to Sg1 and two to Sg2. The genome organization and gene content
      of the four L. longbeachae genomes are highly conserved, indicating strong
      pressure for niche adaptation. Analysis and comparison of L. longbeachae
      strain NSW150 with L. pneumophila revealed common but also unexpected
      features specific to this pathogen. The interaction with host cells shows
      distinct features from L. pneumophila, as L. longbeachae possesses a
      unique repertoire of putative Dot/Icm type IV secretion system substrates,
      eukaryotic-like and eukaryotic domain proteins, and encodes additional
      secretion systems. However, analysis of the ability of a dotA mutant of L.
      longbeachae NSW150 to replicate in the Acanthamoeba castellanii and in a
      mouse lung infection model showed that the Dot/Icm type IV secretion
      system is also essential for the virulence of L. longbeachae. In contrast
      to L. pneumophila, L. longbeachae does not encode flagella, thereby
      providing a possible explanation for differences in mouse susceptibility
      to infection between the two pathogens. Furthermore, transcriptome
      analysis revealed that L. longbeachae has a less pronounced biphasic life
      cycle as compared to L. pneumophila, and genome analysis and electron
      microscopy suggested that L. longbeachae is encapsulated. These
      species-specific differences may account for the different environmental
      niches and disease epidemiology of these two Legionella species.
AU  - Cazalet C
AU  - Gomez-Valero L
AU  - Rusniok C
AU  - Lomma M
AU  - Dervins-Ravault D
AU  - Newton HJ
AU  - Sansom FM
AU  - Jarraud S
AU  - Zidane N
AU  - Ma L
AU  - Bouchier C
AU  - Etienne J
AU  - Hartland EL
AU  - Buchrieser C
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2010 6: e1000851.

PMID- 15467720
VI  - 36
DP  - 2004
TI  - Evidence in the Legionella pneumophila genome for exploitation of host cell functions and high genome plasticity.
PG  - 1165-1173
AB  - Legionella pneumophila, the causative agent of Legionnaires' disease, replicates as an
      intracellular parasite of amoebae and persists in the
      environment as a free-living microbe. Here we have analyzed the complete
      genome sequences of L. pneumophila Paris (3,503,610 bp, 3,077 genes), an
      endemic strain that is predominant in France, and Lens (3,345,687 bp,
      2,932 genes), an epidemic strain responsible for a major outbreak of
      disease in France. The L. pneumophila genomes show marked plasticity, with
      three different plasmids and with about 13% of the sequence differing
      between the two strains. Only strain Paris contains a type V secretion
      system, and its Lvh type IV secretion system is encoded by a 36-kb region
      that is either carried on a multicopy plasmid or integrated into the
      chromosome. Genetic mobility may enhance the versatility of L.
      pneumophila. Numerous genes encode eukaryotic-like proteins or motifs that
      are predicted to modulate host cell functions to the pathogen's advantage.
      The genome thus reflects the history and lifestyle of L. pneumophila, a
      human pathogen of macrophages that coevolved with fresh-water amoebae.
AU  - Cazalet C
AU  - Rusniok C
AU  - Bruggemann H
AU  - Zidane N
AU  - Magnier A
AU  - Ma L
AU  - Tichit M
AU  - Jarraud S
AU  - Bouchier C
AU  - Vandenesch F
AU  - Kunst F
AU  - Etienne J
AU  - Glaser P
AU  - Buchrieser C
PT  - Journal Article
TA  - Nat. Genet.
JT  - Nat. Genet.
SO  - Nat. Genet. 2004 36: 1165-1173.

PMID- 28705974
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Klebsiella michiganensis 3T412C, Harboring an Arsenic Resistance Genomic Island, Isolated from Mine Tailings in Peru.
PG  - e00611-17
AB  - An arsenic resistance genomic island in the bacterium Klebsiella michiganensis 3T412C was
      isolated from mine tailings from Peru. This genomic island confers
      adaptation to extreme environments with high concentrations of arsenic. Isolate
      3T412C contained a complete set of genes involved in resistance to arsenic. This
      operon is surrounded by putative genes for resistance to other heavy metals.
AU  - Ccorahua-Santo R
AU  - Cervantes M
AU  - Duran Y
AU  - Aguirre M
AU  - Marin C
AU  - Ramirez P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00611-17.

PMID- 21633996
VI  - 12
DP  - 2011
TI  - C5-DNA Methyltransferase Inhibitors: From Screening to Effects on Zebrafish Embryo Development.
PG  - 1337-1345
AB  - DNA methylation is involved in the regulation of gene expression and plays an important role
      in normal developmental processes and diseases,
      such as cancer. DNA methyltransferases are the enzymes responsible for
      DNA methylation on the position 5 of cytidine in a CpG context. In
      order to identify and characterize novel inhibitors of these enzymes,
      we developed a fluorescence-based throughput screening by using a short
      DNA duplex immobilized on 96-well plates. We have screened 114 flavones
      and flavanones for the inhibition of the murine catalytic Dnmt3a/3L
      complex and found 36 hits with IC50 values in the lower micromolar and
      high nanomolar ranges. The assay, together with inhibition tests on two
      other methyltransferases, structure-activity relationships and docking
      studies, gave insights on the mechanism of inhibition. Finally, two
      derivatives effected zebrafish embryo development, and induced a global
      demethylation of the genome, at doses lower than the control drug,
      5-azacytidine.
AU  - Ceccaldi A
AU  - Rajavelu A
AU  - Champion C
AU  - Rampon C
AU  - Jurkowska R
AU  - Jankevicius G
AU  - Senamaud-Beaufort C
AU  - Ponger L
AU  - Gagey N
AU  - Ali HD
AU  - Tost J
AU  - Vriz S
AU  - Ros S
AU  - Dauzonne D
AU  - Jeltsch A
AU  - Guianvarc'h D
AU  - Arimondo PB
PT  - Journal Article
TA  - Chembiochem
JT  - Chembiochem
SO  - Chembiochem 2011 12: 1337-1345.

PMID- 23294304
VI  - 8
DP  - 2013
TI  - Identification of Novel Inhibitors of DNA Methylation by Screening of a Chemical Library.
PG  - 543-548
AB  - In order to discover new inhibitors of the DNA methyltransferase 3A/3L complex, we used a
      medium-throughput nonradioactive screen on a random
      collection of 1120 small organic compounds. After a primary hit
      detection against DNA methylation activity of the murine Dnmt3A/3L
      catalytic complex, we further evaluated the EC50 of the 12 most potent
      hits as well as their cytotoxicity on DU145 prostate cancer cultured
      cells. Interestingly, most of the inhibitors showed low micromolar
      activities and little cytotoxicity. Dichlone, a small halogenated
      naphthoquinone, classically used as pesticide and fungicide, showed the
      lowest EC50 at 460 nM. We briefly assessed the selectivity of a subset
      of our new inhibitors against hDNMT1 and bacterial Dnmts, including M.
      SssI and EcoDam, and the protein lysine methyltransferase PKMT G9a and
      the mode of inhibition. Globally, the tested molecules showed a clear
      preference for the DNA methyltransferases, but poor selectivity among
      them. Two molecules including Dichlone efficiently reactivated YFP gene
      expression in a stable HEK293 cell line by promoter demethylation.
      Their efficacy was comparable to the DNMT inhibitor of reference
      5-azacytidine.
AU  - Ceccaldi A
AU  - Rajavelu A
AU  - Ragozin S
AU  - Senamaud-Beaufort C
AU  - Bashtrykov P
AU  - Testa N
AU  - Dali-Ali H
AU  - Maulay-Bailly C
AU  - Amand S
AU  - Guianvarc'h D
AU  - Jeltsch A
AU  - Arimondo PB
PT  - Journal Article
TA  - ACS Chem. Biol.
JT  - ACS Chem. Biol.
SO  - ACS Chem. Biol. 2013 8: 543-548.

PMID- 24066026
VI  - 8
DP  - 2013
TI  - Functional metagenomics reveals novel pathways of prebiotic breakdown by human gut bacteria.
PG  - e72766
AB  - The human intestine hosts a complex bacterial community that plays a major role in nutrition
      and in maintaining human health. A functional metagenomic approach was used to explore the
      prebiotic breakdown potential of human gut bacteria, including non-cultivated ones. Two
      metagenomic libraries, constructed from ileum mucosa and fecal microbiota, were screened for
      hydrolytic activities on the prebiotic carbohydrates inulin, fructo-oligosaccharides,
      xylo-oligosaccharides, galacto-oligosaccharides and lactulose. The DNA inserts of 17 clones,
      selected from the 167 hits that were identified, were pyrosequenced in-depth, yielding in
      total 407, 420 bp of metagenomic DNA. From these sequences, we discovered novel prebiotic
      degradation pathways containing carbohydrate transporters and hydrolysing enzymes, for which
      we provided the first experimental proof of function. Twenty of these proteins are encoded by
      genes that are also present in the gut metagenome of at least 100 subjects, whatever are their
      ages or their geographical origin. The sequence taxonomic assignment indicated that still
      unknown bacteria, for which neither culture conditions nor genome sequence are available,
      possess the enzymatic machinery to hydrolyse the prebiotic carbohydrates tested. The results
      expand the vision on how prebiotics are metabolized along the intestine, and open new
      perspectives for the design of functional foods.
AU  - Cecchini D
AU  - Laville E
AU  - Laguerre S
AU  - Robe P
AU  - Leclerc M
AU  - Dore J
AU  - Henrissat B
AU  - Remaud-Simeon M
AU  - Monsan P
AU  - Potocki-Veronese G
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2013 8: e72766.

PMID- Not carried by PubMed...
VI  - 7
DP  - 1988
TI  - The influence of modifications on the cleavage of oligonucleotide duplexes by EcoRII and MvaI endonucleases.
PG  - 585-588
AB  - To study the interaction of the restriction endonucleases MvaI and EcoRII with DNA we have
      synthesized some modified oligonucleotides. The results of hydrolysis demonstrate that both
      enzymes cleave their substrate by different mechanisms.
AU  - Cech D
AU  - Pein C-D
PT  - Journal Article
TA  - Nucleosides and Nucleotides
JT  - Nucleosides and Nucleotides
SO  - Nucleosides and Nucleotides 1988 7: 585-588.

PMID- 223125
VI  - 6
DP  - 1979
TI  - Direct detection of methylated cytosine in DNA by use of the restriction enzyme MspI.
PG  - 2125-2132
AB  - The extent of methylation of the internal C in the sequence CCGG in DNA from
      various eukaryotic sources has been determined using the restriction enzyme
      MspI known to be specific for this sequence.  The methylation of the CCGG
      sequence is reflected in the restriction pattern obtained by DNA treated with
      MspI and its isoschizomer HpaII and analyzed by gel electrophoresis.  A direct
      method for detection of 5-methylcytosine in the sequence CCGG has been deviced.
      DNA fragments obtained with MspI were radioactively labeled at their 5' ends
      and subsequently degraded to the corresponding 5'-deoxyribonucleoside
      monophosphates.  5 methylcytidylic acid has been found in most of the 5' ends
      of MspI fragments of calf thymus DNA (about 90%) indicating heavy methylation
      of the sequence CCGG in calf thymus DNA.  The results also reveal a symmetric
      methylation of both strands at this sequence in calf thymus DNA.  In contrast,
      the CCGG sequence in other eukaryotic DNAs from organisms like Neurospora,
      Drosophila and Herpes virus proved to be undermethylated at this sequence.
AU  - Cedar H
AU  - Solage A
AU  - Glaser G
AU  - Razin A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1979 6: 2125-2132.

PMID- 10050847
VI  - 397
DP  - 1999
TI  - The amazing demethylase.
PG  - 568-569
AB  - DNA methylation is important for mediating repression of gene expression during mammalian
      development.  But although much is known about how methyl groups are added to DNA, little has
      been done to work out how they are taken off.  In an exciting article on page 579 of this
      issue, Bhattacharya et al. report that they have cloned a hitherto unknown gene which codes
      for a protein with a remarkable property - it can catalyse demethylation by directly removing
      methyl groups from 5-methyl-cytosine residues in DNA.
AU  - Cedar H
AU  - Verdine GL
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1999 397: 568-569.

PMID- 27013046
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of an Endophytic Actinoplanes Species, Encoding Uncommon trans-Acyltransferase Polyketide Synthases.
PG  - e00164-16
AB  - Actinoplanesis an endophytic actinobacterium isolated from the medicinal plantAmphipterygium
      adstringens The strain draft genome sequence reveals a gene
      cluster involved in the biosynthesis of a hybridtrans-acyltransferase (AT)
      polyketide, an unconventional bioactive metabolite never reported before in the
      genusActinoplanes.
AU  - Centeno-Leija S
AU  - Vinuesa P
AU  - Rodriguez-Pena K
AU  - Trenado-Uribe M
AU  - Cardenas-Conejo Y
AU  - Serrano-Posada H
AU  - Rodriguez-Sanoja R
AU  - Sanchez S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00164-16.

PMID- 25744995
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequence of Listeria monocytogenes Serovar 4b Strain IZSAM_Lm_hs2008, Isolated from a Human Infection in Italy.
PG  - e00053-15
AB  - Listeria monocytogenes is one of the most important foodborne pathogens. In this  report, we
      present the complete and annotated genome of L. monocytogenes sequence
      type 06 (ST06) serovar 4b strain IZSAM_Lm_hs2008, isolated from an adult
      immunocompetent patient who developed the disease and died.
AU  - Centorame P
AU  - Acciari VA
AU  - Orsini M
AU  - Torresi M
AU  - Iannetti L
AU  - Angius A
AU  - Di Giammartino D
AU  - Prencipe VA
AU  - Migliorati G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00053-15.

PMID- 27811089
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a Hospital-Associated Clone of Klebsiella pneumoniae ST340/CC258 Coproducing RmtG and KPC-2 Isolated from a Pediatric Patient.
PG  - e01130-16
AB  - We report here the draft genome sequence of a Klebsiella pneumoniae strain 1194/11, belonging
      to the hospital-associated sequence type 340 (ST340; clonal
      complex CC258), isolated from a catheter tip culture from a pediatric patient.
      The multidrug-resistant strain coproduced the 16S rRNA methyltransferase rRNA
      RmtG and beta-lactamases KPC-2 and CTX-M-15.
AU  - Cerdeira L
AU  - Fernandes MR
AU  - Francisco GR
AU  - Bueno MF
AU  - Ienne S
AU  - Souza TA
AU  - de Oliveira GD
AU  - Lincopan N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01130-16.

PMID- 22123771
VI  - 193
DP  - 2011
TI  - Complete genome sequence of Corynebacterium pseudotuberculosis strain CIP 52.97, isolated from a horse in Kenya.
PG  - 7025-7026
AB  - In this work, we report the whole-genome sequence of Corynebacterium
      pseudotuberculosis bv. equi strain CIP 52.97 (Collection Institut Pasteur),
      isolated in 1952 from a case of ulcerative lymphangitis in a Kenyan horse, which
      has evidently caused significant losses to agribusiness. Therefore, obtaining
      this genome will allow the detection of important targets for postgenomic
      studies, with the aim of minimizing problems caused by this microorganism.
AU  - Cerdeira LT et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 7025-7026.

PMID- 22038974
VI  - 193
DP  - 2011
TI  - Whole-Genome Sequence of Corynebacterium pseudotuberculosis PAT10 Strain Isolated from Sheep in Patagonia, Argentina.
PG  - 6420-6421
AB  - In this work, we report the complete genome sequence of a Corynebacterium pseudotuberculosis
      PAT10 isolate, collected from a lung abscess in an
      Argentine sheep in Patagonia, whose pathogen also required an
      investigation of its pathogenesis. Thus, the analysis of the genome
      sequence offers a means to better understanding of the molecular and
      genetic basis of virulence of this bacterium.
AU  - Cerdeira LT et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6420-6421.

PMID- 14602910
VI  - 31
DP  - 2003
TI  - The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129.
PG  - 6516-6523
AB  - Corynebacterium diphtheriae is a Gram-positive, non-spore forming, non-motile, pleomorphic rod
      belonging to the genus Corynebacterium and the
      actinomycete group of organisms. The organism produces a potent
      bacteriophage-encoded protein exotoxin, diphtheria toxin (DT), which
      causes the symptoms of diphtheria. This potentially fatal infectious
      disease is controlled in many developed countries by an effective
      immunisation programme. However, the disease has made a dramatic return in
      recent years, in particular within the Eastern European region. The
      largest, and still on-going, outbreak since the advent of mass
      immunisation started within Russia and the newly independent states of the
      former Soviet Union in the 1990s. We have sequenced the genome of a UK
      clinical isolate (biotype gravis strain NCTC13129), representative of the
      clone responsible for this outbreak. The genome consists of a single
      circular chromosome of 2 488 635 bp, with no plasmids. It provides
      evidence that recent acquisition of pathogenicity factors goes beyond the
      toxin itself, and includes iron-uptake systems, adhesins and fimbrial
      proteins. This is in contrast to Corynebacterium's nearest sequenced
      pathogenic relative, Mycobacterium tuberculosis, where there is little
      evidence of recent horizontal DNA acquisition. The genome itself shows an
      unusually extreme large-scale compositional bias, being noticeably higher
      in G+C near the origin than at the terminus.
AU  - Cerdeno-Tarraga AM et al
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2003 31: 6516-6523.

PMID- 15746427
VI  - 307
DP  - 2005
TI  - Extensive DNA inversions in the B. fragilis genome control variable gene expression.
PG  - 1463-1465
AB  - The obligately anaerobic bacterium Bacteroides fragilis, an opportunistic pathogen and
      inhabitant of the normal human colonic microbiota, exhibits
      considerable within-strain phase and antigenic variation of surface
      components. The complete genome sequence has revealed an unusual breadth
      (in number and in effect) of DNA inversion events that potentially control
      expression of many different components, including surface and secreted
      components, regulatory molecules, and restriction-modification proteins.
      Invertible promoters of two different types (12 group 1 and 11 group 2)
      were identified. One group has inversion crossover (fix) sites similar to
      the hix sites of Salmonella typhimurium. There are also four independent
      intergenic shufflons that potentially alter the expression and function of
      varied genes. The composition of the 10 different polysaccharide
      biosynthesis gene clusters identified (7 with associated invertible
      promoters) suggests a mechanism of synthesis similar to the O-antigen
      capsules of Escherichia coli.
AU  - Cerdeno-Tarraga AM et al
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2005 307: 1463-1465.

PMID- 21493687
VI  - 39
DP  - 2011
TI  - Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting.
PG  - E82
AB  - TALENs are important new tools for genome engineering. Fusions of transcription
      activator-like (TAL) effectors of plant pathogenic Xanthomonas spp. to the FokI
      nuclease, TALENs bind and cleave DNA in pairs. Binding specificity is determined
      by customizable arrays of polymorphic amino acid repeats in the TAL effectors. We
      present a method and reagents for efficiently assembling TALEN constructs with
      custom repeat arrays. We also describe design guidelines based on naturally
      occurring TAL effectors and their binding sites. Using software that applies
      these guidelines, in nine genes from plants, animals and protists, we found
      candidate cleavage sites on average every 35 bp. Each of 15 sites selected from
      this set was cleaved in a yeast-based assay with TALEN pairs constructed with our
      reagents. We used two of the TALEN pairs to mutate HPRT1 in human cells and ADH1
      in Arabidopsis thaliana protoplasts. Our reagents include a plasmid construct for
      making custom TAL effectors and one for TAL effector fusions to additional
      proteins of interest. Using the former, we constructed de novo a functional
      analog of AvrHah1 of Xanthomonas gardneri. The complete plasmid set is available
      through the non-profit repository AddGene and a web-based version of our software
      is freely accessible online.
AU  - Cermak T
AU  - Doyle EL
AU  - Christian M
AU  - Wang L
AU  - Zhang Y
AU  - Schmidt C
AU  - Baller JA
AU  - Somia NV
AU  - Bogdanove AJ
AU  - Voytas DF
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2011 39: E82.

PMID- Not carried by PubMed...
VI  - 97
DP  - 1997
TI  - Location of aroB and dam genes in the Salmonella typhimurium chromosome.
PG  - 318
AB  - Enterobacteria possess a functional dam methylase.  The dam gene of Escherichia coli in min 74
      is part of an operon that includes at least 3 other genes, aroK, aroB and urf74.3, and the
      distance between aroB and dam is less than 2 Kbp.  The dam gene of Salmonella typhimurium has
      been positioned on the chromosomal map in homology to E. coli.  We have recently isolated an
      insertional dam::Tn10dTc mutant of S. typhimurium.  Cotransduction frequencies of aroB and
      dam::Tn10tDc found in S. typhimurium (40%) do not agree with a map distance of 2 Kbp between
      these two genes, oligonucleotides matching E. coli aroB (ECaroB), S. typhimurium aroB
      (STaroB), E. coli dam (Ecdam) and S. typhimurium dam (Stdam) sequences were synthesized and
      tested as opposing PCR primers in the amplification of S. typhimurium and E. coli DNA.  ECaroB
      and Ecdam oligonucleotide primers produced a band of the expected size (1.6 Kbp) in the
      amplification of E. coli DNA.  A band of similar size was obtained using ECaroB and STdam as
      primers in the amplification of E. coli DNA.  No specific PCR product was yielded when STaroB
      and STdam were tested as primers in the amplification of S. typhimurium DNA.  These results
      support the hypothesis that there are differences between E. coli and S. typhimurium in this
      region of the chromosome.
AU  - Cerquetti MC
AU  - Brawer R
AU  - Gherardi MM
AU  - Sordelli DO
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1997 97: 318.

PMID- Not carried by PubMed...
VI  - 96
DP  - 1996
TI  - Map position of the dam gene in Salmonella typhimurium.
PG  - 491
AB  - Escherichia coli and Salmonella typhimurium DNA is methylated in the adenine
      residue in the sequence 5'-GATC-3'.  The DNA adenine methylase (dam) gene of E. coli is
      located
      at 74 min in a multicistronic operon containing aroK and aroB among other genes.  The S.
      typhimurium dam gene has not been mapped yet, although a gene order similar to that of E. coli
      (cys-G-dam-aroB) has been suggested.  The recently isolated dam::Tn10dTc mutant of S.
      typhimurium enabled us to locate the dam gene more precisely.  Transductional crosses were
      carried out using bacteriophage P22 lysates.  Double mutants of S. typhimurium DM6
      [csG::Tn5(Kan)-aroB] and DM53 (aroB-dam::Tn10dTc) were constructed in order to perform
      three-factor crosses.  Strain DM6 was transduced with a lysate grown on the dam::Tn10dTC
      mutant and a total of 129 tetracycline resistant (TetR) transductants were analyzed.  More
      than half
      (51%) of the TetR transductants maintained the cys- aro- phenotype, 42% were cys+ aro+, 5%
      were cys+ aro- and 2% were cys+ aro+.  DM53 was transduced with phage propagated on S.
      typhimurium ompR::Tn5.  Kanamycin resistant transductants were screened for sensitivity to 2
      aminopurine (2AP) and aro+ phenotype.  Eighty-three percent of the 72 KanR transductants were
      aro- and resistant to 2AP, 13% were aro- and sensitive to 2AP, and 3% were sensitive to 2 AP
      and
      aro-.  Our data support the order: cysG-aroB-dam-ompR on the S. typhimurium genetic map.
AU  - Cerquetti MC
AU  - Brawer R
AU  - Gherardi MM
AU  - Sordelli DO
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1996 96: 491.

PMID- 29449381
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Pseudomonas sp. Strain NC02, Isolated from Soil.
PG  - e00033-18
AB  - We report here the complete genome sequence of Pseudomonas sp. strain NC02, isolated from soil
      in eastern Massachusetts. We assembled PacBio reads into a
      single closed contig with 132x mean coverage and then polished this contig using
      Illumina MiSeq reads, yielding a 6,890,566-bp sequence with 61.1% GC content.
AU  - Cerra J
AU  - Donohue H
AU  - Kral A
AU  - Oser M
AU  - Rostkowski L
AU  - Zappia L
AU  - Williams LE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00033-18.

PMID- 2687877
VI  - 86
DP  - 1989
TI  - DpnA, a methylase for single-strand DNA in the DpnII restriction system, and its biological function.
PG  - 9223-9227
AB  - The two DNA-adenine methylases encoded by the DpnII restriction gene cassette
      were purified, and their activities were compared on various DNA substrates.
      DpnA was able to methylate single-strand DNA and double-strand DNA, whereas
      DpnM methylated only double-strand DNA.  Although both enzymes act at
      5'-GATC-3' in DNA, DpnA can also methylate sequences altered in the guanine
      position, but at a lower rate.  A deletion mutation in the dpnA gene was
      constructed and transferred to the chromosome.  Transmission by way of the
      transformation pathway of methylated and unmethylated plasmids to dpnA mutant
      and wild-type recipients was examined.  The mutant cells restricted
      unmethylated donor plasmid establishment much more strongly than did wild-type
      cells.  In the wild type, the single strands of donor plasmid DNA that enter by
      the transformation pathway are apparently methylated by DpnA prior to
      conversion of the plasmid to a double-strand form, in which the plasmid would
      be susceptible to the DpnII endonuclease.  The biological function of DpnA may,
      therefore, be the enhancement of plasmid transfer to DpnII-containing strains
      of Streptococcus pneumoniae.
AU  - Cerritelli S
AU  - Springhorn SS
AU  - Lacks SA
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1989 86: 9223-9227.

PMID- 2547974
VI  - 207
DP  - 1989
TI  - Crystallization of the DpnM methylase from the DpnII restriction system of Streptococcus pneumoniae.
PG  - 841-842
AB  - Three proteins, two DNA methylases and an endonuclease, from the DpnII
      restriction system of Streptococcus pneumoniae recognize the DNA sequence 5'
      GATC 3' but have very different amino acid sequences, which make them
      interesting subjects for structural determination.  A purification procedure
      was developed that conveniently yields milligram amounts of the DpnM methylase.
      The DpnM protein tends to precipitate at reduced ionic strength, and this
      property was exploited to yield well-formed bipyramidal crystals.  By X-ray
      diffraction, the crystals of DpnM were found to be orthorhombic, with cell
      dimensions a=56.9 angstrom, b=68.2 angstrom, c=84.5 angstrom; systematic
      absences identify the space group as P2/1 2/1 2/1.  Diffraction extends beyond
      3 angstrom, so the crystals may allow structural determination at atomic
      resolution.
AU  - Cerritelli S
AU  - White SW
AU  - Lacks SA
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1989 207: 841-842.

PMID- 2323503
VI  - 4
DP  - 1990
TI  - Two DNA methylases in the DpnII restriction system of Streptococcus pneumoniae.
PG  - A2295
AB  - The DpnII cassette contains three genes, dpnM, dpnA and dpnB, that encode,
      respectively, two DNA methylases, DpnM and DpnA, and the DpnII endonuclease.
      The two DNA-adenine methyltransferases were purified and characterized.  DpnM
      methylates only double-strand DNA at 5'-GATC-3'.  It is the major DNA
      methylating activity in S. pneumoniae and is homologous to the Dam methylase of
      Escherichia coli.  We have obtained crystals of DpnM methylase suitable for
      diffraction analysis.  At present we are in the process of determining the
      crystal structure using the multiwavelength anomalous dispersion procedure.
      DpnA, the other methylase in the DpnII restriction system, methylates
      single-strand and double-strand DNA, although it is more active in methylating
      DNA in single-strand form.  A deletion mutant in the dpnA gene was constructed
      and introduced into the chromosome.  The mutant cells have reduced ability to
      establish unmethylated donor plasmid, as compared to wild-type cells.  The role
      of DpnA may be to methylate the single strands of donor plasmid DNA that enter
      the cell by the transformation pathway, thereby protecting the subsequent
      reconstructed plasmid from DpnII endonuclease cleavage.  The biological
      function of DpnA, therefore, may be the enhancement of plasmid transfer to
      DpnII-containing strains of S. pneumoniae.
AU  - Cerritelli S
AU  - White SW
AU  - Springhorn SS
AU  - Lacks SA
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1990 4: A2295.

PMID- 25738257
VI  - 5
DP  - 2015
TI  - Mechanisms of High Temperature Resistance of Synechocystis sp. PCC 6803: An Impact of Histidine Kinase 34.
PG  - 676-699
AB  - Synechocystis sp. PCC 6803 is a widely used model cyanobacterium for studying
      responses and acclimation to different abiotic stresses. Changes in
      transcriptome, proteome, lipidome, and photosynthesis in response to short term
      heat stress are well studied in this organism, and histidine kinase 34 (Hik34) is
      shown to play an important role in mediating such response. Corresponding data on
      long term responses, however, are fragmentary and vary depending on parameters of
      experiments and methods of data collection, and thus are hard to compare. In
      order to elucidate how the early stress responses help cells to sustain long-term
      heat stress, as well as the role of Hik34 in prolonged acclimation, we examined
      the resistance to long-term heat stress of wild-type and DeltaHik34 mutant of
      Synechocystis. In this work, we were able to precisely control the long term
      experimental conditions by cultivating Synechocystis in automated
      photobioreactors, measuring selected physiological parameters within a time range
      of minutes. In addition, morphological and ultrastructural changes in cells were
      analyzed and western blotting of individual proteins was used to study the heat
      stress-affected protein expression. We have shown that the majority of wild type
      cell population was able to recover after 24 h of cultivation at 44 degrees C. In
      contrast, while DeltaHik34 mutant cells were resistant to heat stress within its
      first hours, they could not recover after 24 h long high temperature treatment.
      We demonstrated that the early induction of HspA expression and maintenance of
      high amount of other HSPs throughout the heat incubation is critical for
      successful adaptation to long-term stress. In addition, it appears that histidine
      kinase Hik34 is an essential component for the long term high temperature
      resistance.
AU  - Cerveny J
AU  - Sinetova MA
AU  - Zavrel T
AU  - Los DA
PT  - Journal Article
TA  - Life
JT  - Life
SO  - Life 2015 5: 676-699.

PMID- 10085064
VI  - 274
DP  - 1999
TI  - DNA demethylase is a processive enzyme.
PG  - 8363-8366
AB  - DNA methylation patterns are generated during development by a sequence of methylation and
      demethylation events.  We have recently demonstrated that mammals bear a bona fide demethylase
      enzyme that removes methyl groups from methylated cytosines.  A general genome wide
      demethylation occurs early in development and in differentiating cell lines.  This manuscript
      tests the hypothesis that the demethylase enzyme is a processive enzyme.  Using bisulfite
      mapping, this report demonstrates that demethylase is a processive enzyme and that the
      rate-limiting step in demethylation is the initiation of demethylation.  Initiation of
      demethylation is determined by the properties of the sequence.  Once initiated, demethylation
      progresses processively.  We suggest that these data provide a molecular explanation for
      global hypomethylation.
AU  - Cervoni N
AU  - Bhattacharya S
AU  - Szyf M
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1999 274: 8363-8366.

PMID- 11524416
VI  - 276
DP  - 2001
TI  - Demethylase activity is directed by histone acetylation.
PG  - 40778-40787
AB  - Mammalian genomes are compartmentalized into dense inactive chromatin that is hypermethylated
      and active open chromatin that is hypomethylated. It is generally accepted that this bimodal
      pattern of methylation is established during development and is then faithfully inherited
      through subsequent cell divisions by a maintenance DNA methyltransferase (DNMT1). The pattern
      of methylation is believed to direct local histone acetylation states. In contrast to this
      well accepted consensus, we show here using a transient transfection model that an active
      demethylase is involved in shaping patterns of methylation in somatic cells.  Demethylase
      activity is directed by the state of histone acetylation, and therefore, the resulting
      methylation pattern is determined by local histone acetylation states contrary to the accepted
      model. Our data support a new model suggesting that the pattern of methylation is maintained
      by a dynamic balance of methylation and demethylation activities and the local state of
      histone acetylation. This provides a simple mechanism for explaining why active genes are not
      methylated.
AU  - Cervoni N
AU  - Szyf M
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2001 276: 40778-40787.

PMID- 12527784
VI  - 31
DP  - 2003
TI  - Esp1396I restriction-modification system: Structural organization and mode of regulation.
PG  - 743-749
AB  - Esp1396I restriction-modification (RM) system recognizes an interrupted palindromic DNA
      sequence 5'-CCA(N)(5)TGG-3'. The Esp1396I RM system was
      found to reside on pEsp1396, a 5.6 kb plasmid naturally occurring in
      Enterobacter sp. strain RFL1396. The nucleotide sequence of the entire
      5622 bp pEsp1396 plasmid was determined on both strands. Identified genes
      for DNA methyltransferase (esp1396IM) and restriction endonuclease
      (esp1396IR) are transcribed convergently. The restriction endonuclease
      gene is preceded by the small ORF (esp1396IC) that possesses a strong
      helix-turn-helix motif and resembles regulatory proteins found in PvuII,
      BamHI and few other RM systems. Gene regulation studies revealed that
      C.Esp1396I acts as both a repressor of methylase expression and an
      activator of regulatory protein and restriction endonuclease expression.
      Our data indicate that C protein from Esp1396I RM system activates the
      expression of the Enase gene, which is co-transcribed from the promoter of
      regulatory gene, by the mechanism of coupled translation.
AU  - Cesnaviciene E
AU  - Mitkaite G
AU  - Stankevicius K
AU  - Janulaitis A
AU  - Lubys A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2003 31: 743-749.

PMID- 11718555
VI  - 314
DP  - 2001
TI  - Characterization of AloI, a Restriction-modification System of a New Type.
PG  - 205-216
AB  - We report the properties of the new AloI restriction and modification enzyme from
      Acinetobacter lwoffi Ks 4-8 that recognizes the DNA target 5' GGA(N)(6)GTTC3' (complementary
      strand 5' GAAC(N)(6)TCC3'), and the nucleotide sequence of the gene encoding this enzyme.
      AloI is a bifunctional large polypeptide (deduced M(r) 143 kDa) revealing both DNA
      endonuclease and methyltransferase activities. Depending on reaction cofactors, AloI cleaves
      double-stranded DNA on both strands, seven bases on the 5' side, and 12-13 bases on the 3'
      side of its recognition sequence, and modifies adenine residues in both DNA strands in the
      target sequence yielding N6-methyladenine. For cleavage activity AloI maintains an absolute
      requirement for Mg(2+) and does not depend on or is stimulated by either ATP or
      S-adenosyl-l-methionine. Modification function requires the presence of
      S-adenosyl-l-methionine and is stimulated by metal ions (Ca(2+)). The C-terminal and central
      parts of the protein were found to be homologous to certain specificity (HsdS) and
      modification (HsdM) subunits of type I R-M systems, respectively. The N-terminal part of the
      protein possesses the putative endonucleolytic motif DX(n)EXK of restriction endonucleases.
      The deduced amino acid sequence of AloI shares significant homology with polypeptides encoding
      HaeIV and CjeI restriction-modification proteins at the N-terminal and central, but not at the
      C-terminal domains. The organization of AloI implies that its evolution involved fusion of an
      endonuclease and the two subunits, HsdM and HsdS, of type I restriction enzymes. According to
      the structure and function properties AloI may be regarded as one more representative of a
      newly emerging group of HaeIV-like restriction endonucleases. Discovery of these enzymes opens
      new opportunities for constructing restriction endonucleases with a new specificity.
AU  - Cesnaviciene EE
AU  - Petrusyte MM
AU  - Kazlauskiene RR
AU  - Maneliene Z
AU  - Timinskas A
AU  - Lubys A
AU  - Janulaitis A
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2001 314: 205-216.

PMID- 26380637
VI  - 10
DP  - 2015
TI  - Genome sequence of the haloarchaeon Haloterrigena jeotgali type strain A29(T) isolated from salt-fermented food.
PG  - 49
AB  - Haloterrigena jeotgali is a halophilic archaeon within the family Natrialbaceae that was
      isolated from shrimp jeotgal, a traditional Korean salt-fermented food.  A29(T) is the type
      strain of H. jeotgali, and is a Gram-negative staining, non-motile, rod-shaped archaeon that
      grows in 10 %-30 % (w/v) NaCl. We present the annotated H. jeotgali A29(T) genome sequence
      along with a summary of its features. The 4,131,621 bp genome with a GC content of 64.9 %
      comprises 4,215 protein-coding genes and 127 RNA genes. The sequence can provide useful
      information on genetic mechanisms that enable haloarchaea to endure a hypersaline environment.
AU  - Cha IT
AU  - Lee MH
AU  - Kim BY
AU  - Cho YJ
AU  - Kim DW
AU  - Yim KJ
AU  - Song HS
AU  - Seo MJ
AU  - Rhee JK
AU  - Choi JS
AU  - Choi HJ
AU  - Yoon C
AU  - Roh SW
AU  - Nam YD
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 49.

PMID- 
VI  - 80
DP  - 2001
TI  - Characterization of a restriction endonuclease isolated from Bacillus subtilis F2.
PG  - 282A
AB  - The usefulness of restriction systems with their high substrate specificities for ds-DNA, and
      the processing of the free or packaged DNA during uptake into Bacillus subtilis cells made us
      study the restriction enzyme activity of one of our laboratory isolate, Bacillus subtilis F2
      which has been used for the propagation of the newly isolated PAK phage. During the life cycle
      of PAK phage in Bacillus subtilis F2 host, it has been noticed that DNA of the phage gets
      fragmented in vivo, therefore, it becomes important to explore the endonuclease activity in
      this strain.  A cell bound enzyme was isolated from Bacillus subtilis F2, and was
      characterized in a crude extract of the bacterial cell pellet.  The enzyme was shown to have
      endonuclease activity on bacteriophage lambda DNA and other DNA as well.  Interestingly,
      lambda DNA seems to have very few cut sites.  Another important characteristic of this enzyme
      is it has an optimum pH shifted toward alkaline range, which is 8.5, among 182 known
      restriction enzymes.  The optimum temperature was found to be 40 C.  It seems to work at high
      salt concentration.  Lysates extracted at pH 6 and 6.5 have shown endonuclease activity with a
      new profile of lambda DNA fragmentation of lysate extracted at pH 7.5.  Hence BsuF2 is a type
      II restriction enzyme it seems to have high potential to be used as a genetic tool in
      molecular biology.
AU  - Chaboki KM
PT  - Journal Article
TA  - Biophys. J.
JT  - Biophys. J.
SO  - Biophys. J. 2001 80: 282A.

PMID- 28751381
VI  - 5
DP  - 2017
TI  - Genome Sequence of Zymomonas mobilis subsp. mobilis NRRL B-1960.
PG  - e00562-17
AB  - Zymomonas mobilis subsp. mobilis is an efficient ethanol producer with application for
      industrial production of biofuel. To supplement existing Z.
      mobilis genomic resources and to facilitate genomic research, we used Oxford
      Nanopore and Illumina sequencing to assemble the complete genome of the beer
      spoilage isolate Z. mobilis subsp. mobilis strain NRRL B-1960.
AU  - Chacon-Vargas K
AU  - Chirino AA
AU  - Davis MM
AU  - Debler SA
AU  - Haimer WR
AU  - Wilbur JJ
AU  - Mo X
AU  - Worthing BW
AU  - Wainblat EG
AU  - Zhao S
AU  - Gibbons JG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00562-17.

PMID- 27445382
VI  - 4
DP  - 2016
TI  - Genome Sequence of Streptomyces sp. Strain RTd22, an Endophyte of the Mexican Sunflower.
PG  - e00693-16
AB  - We report here the complete genome sequence of Streptomyces sp. strain RTd22, an  endophytic
      actinobacterium that was isolated from the roots of the Mexican
      sunflower Tithonia diversifolia The bacterium's 11.1-Mb linear chromosome is
      predicted to encode a large number of unknown natural products.
AU  - Chagas FO
AU  - Ruzzini AC
AU  - Bacha LV
AU  - Samborskyy M
AU  - Conti R
AU  - Pessotti RC
AU  - de Oliveira LG
AU  - Clardy J
AU  - Pupo MT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00693-16.

PMID- 19766657
VI  - 395
DP  - 2010
TI  - Changing the DNA Recognition Specificity of the EcoDam DNA-(Adenine-N6)-Methyltransferase by Directed Evolution.
PG  - 79-88
AB  - EcoDam is an adenine-N6 DNA methyltransferase that methylates the GATC sites in the
      Escherichia coli genome. We have changed the target
      specificity of EcoDam from GATC to GATT by directed evolution, combining
      different random mutagenesis methods with restriction protection at GATT
      sites for selection and screening. By co-evolution of an enzyme library
      and a substrate library, we identified GATT as the best non-GATC site and
      discover a double mutation, R124S/P134S, as the first step to increase
      enzyme activity at GATT sites. After four generations of mutagenesis and
      selection, we obtained enzyme variants with new specificity for GATT.
      While the wild-type EcoDam shows no detectable activity at GATT sites in
      E. coli cells, some variants prefer methylation at GATT over GATC sites by
      about 10-fold in cells. In vitro DNA methylation kinetics carried out
      under single-turnover conditions using a hemimethylated GATC and a GATT
      oligonucleotide substrate confirmed that the evolved proteins prefer
      methylation of GATT sites to a similar degree. They show up to 1600-fold
      change in specificity in vitro and methylate the new GATT target site with
      20% of the rate of GATC methylation by the wild-type enzyme, indicating
      good activity. We conclude that the new methyltransferases are fully
      functional in vivo and in vitro but show a new target-site specificity.
AU  - Chahar S
AU  - Elsawy H
AU  - Ragozin S
AU  - Jeltsch A
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2010 395: 79-88.

PMID- 23144426
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of High-Melanin-Yielding Aeromonas media Strain WS.
PG  - 6693-6694
AB  - We sequenced the genome of the high-melanin-yielding Aeromonas media strain WS and then
      analyzed genes potentially involved in melanin formation. The 4.2-Mb
      draft genome carries multiple genes responsible for pyomelanin synthesis and
      other candidate genes identified in our separate study, which have no homolog in
      other strains of Aeromonas species.
AU  - Chai B
AU  - Wang H
AU  - Chen X
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6693-6694.

PMID- 
VI  - SI
DP  - 2007
TI  - The somatic form of the mouse Dnmt1 maintenance methyltransferase is expressed throughout preimplantation development.
PG  - 90
AB  - The inheritance of gametic epigenetic modifications of DNA is essential to the process of
      genomic imprinting, which in turn is essential for normal mammalian development. Patterns of
      CpG dinucleotide methylation on imprinted genes appear during gametogenesis due to the action
      of de novo cytosine methyltransferase activity. Although the inheritance of these methylation
      patterns during post-implantation development is due to the potent maintenance
      methyltransferase activity of the somatic form of the Dnmt1 cytosine methyltransferase
      (Dnmt1s), the molecular mechanism for maintaining imprinted methylation patterns during
      preimplantation development remains largely unknown. The goal of this study was to determine
      if Dnmt1s is a possible candidate enzyme for this mechanism by determining if Dnmt1s is
      expressed in wild-type preimplantation embryos. For these studies we used the UPT82 rabbit
      polyclonal antibody, which recognizes epitopes specific to Dnmt1s protein, but does not detect
      the shorter, oocyte-specific Dnmt1o protein.  Improved, sensitive techniques of Dnmt1s
      immunodetection with UPT82 were used. On immunoblots of extracts from 100 staged oocytes or
      staged embryos, UPT82 detects Dnmt1s in fully-grown oocyte (GV and MII stages), and in embryos
      at the 1-cell, 2-cell, 4-cell, 8-cell, morula and blastocyst stages. Using immunostaining and
      confocal microscopy, we showed that Dnmt1s is present in the cytoplasm at all stages, and in
      the nuclei of all stages except the 1-cell, pronuclear-stage embryos. Dnmt1s also failed to
      appear in the maternal and paternal pronuclei even in pronuclear-stage embryos derived from
      mouse strains that overexpress Dnmt1s in oocytes, and show greatly increased cytoplasmic
      Dnmt1s staining. Because DNA replication is very likely to have been completed at the time of
      pronuclear membrane breakdown, these observations indicate that DNA replicated at the first
      embryonic cell cycle is probably not exposed to Dnmt1s until well after the replication event.
      Using crosses between wild-type mice and mice carrying the Dnmt1V allele, which express only
      the Dnmt1o form of Dnmt1, we showed that Dnmt1s protein expressed in 1-cell and 2-cell embryos
      is derived from the oocyte, whereas Dnmt1s expressed afterwards is synthesized de novo during
      embryogenesis.  These findings indicate that Dnmt1s is expressed in all diploidnuclear stages
      of mouse preimplantation embryos, and suggest therefore that Dnmt1s is a strong candidate for
      the maintenance methyltransferase activity required for the inheritance of methylation
      imprints in the early mouse embryo.
AU  - Chaillet R
AU  - Cirio C
AU  - Navara C
PT  - Journal Article
TA  - Biol. Reprod.
JT  - Biol. Reprod.
SO  - Biol. Reprod. 2007 SI: 90.

PMID- 12700255
VI  - 185
DP  - 2003
TI  - Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea.
PG  - 2759-2773
AB  - Nitrosomonas europaea (ATCC 19718) is a gram-negative obligate chemolithoautotroph that can
      derive all its energy and reductant for
      growth from the oxidation of ammonia to nitrite. Nitrosomonas europaea
      participates in the biogeochemical N cycle in the process of
      nitrification. Its genome consists of a single circular chromosome of
      2,812,094 bp. The GC skew analysis indicates that the genome is divided
      into two unequal replichores. Genes are distributed evenly around the
      genome, with approximately 47% transcribed from one strand and
      approximately 53% transcribed from the complementary strand. A total of
      2,460 protein-encoding genes emerged from the modeling effort, averaging
      1,011 bp in length, with intergenic regions averaging 117 bp. Genes
      necessary for the catabolism of ammonia, energy and reductant generation,
      biosynthesis, and CO(2) and NH(3) assimilation were identified. In
      contrast, genes for catabolism of organic compounds are limited. Genes
      encoding transporters for inorganic ions were plentiful, whereas genes
      encoding transporters for organic molecules were scant. Complex repetitive
      elements constitute ca. 5% of the genome. Among these are 85 predicted
      insertion sequence elements in eight different families. The strategy of
      N. europaea to accumulate Fe from the environment involves several classes
      of Fe receptors with more than 20 genes devoted to these receptors.
      However, genes for the synthesis of only one siderophore, citrate, were
      identified in the genome. This genome has provided new insights into the
      growth and metabolism of ammonia-oxidizing bacteria.
AU  - Chain P
AU  - Lamerdin J
AU  - Larimer F
AU  - Regala W
AU  - Lao V
AU  - Land M
AU  - Hauser L
AU  - Hooper A
AU  - Klotz M
AU  - Norton J
AU  - Sayavedra-Soto L
AU  - Arciero D
AU  - Hommes N
AU  - Whittaker M
AU  - Arp D
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2003 185: 2759-2773.

PMID- 17030797
VI  - 103
DP  - 2006
TI  - Inaugural Article: Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility.
PG  - 15280-15287
AB  - Burkholderia xenovorans LB400 (LB400), a well studied, effective polychlorinated
      biphenyl-degrader, has one of the two largest known
      bacterial genomes and is the first nonpathogenic Burkholderia isolate
      sequenced. From an evolutionary perspective, we find significant
      differences in functional specialization between the three replicons of
      LB400, as well as a more relaxed selective pressure for genes located on
      the two smaller vs. the largest replicon. High genomic plasticity,
      diversity, and specialization within the Burkholderia genus are
      exemplified by the conservation of only 44% of the genes between LB400 and
      Burkholderia cepacia complex strain 383. Even among four B. xenovorans
      strains, genome size varies from 7.4 to 9.73 Mbp. The latter is largely
      explained by our findings that >20% of the LB400 sequence was recently
      acquired by means of lateral gene transfer. Although a range of genetic
      factors associated with in vivo survival and intercellular interactions
      are present, these genetic factors are likely related to niche breadth
      rather than determinants of pathogenicity. The presence of at least eleven
      "central aromatic" and twenty "peripheral aromatic" pathways in LB400,
      among the highest in any sequenced bacterial genome, supports this
      hypothesis. Finally, in addition to the experimentally observed redundancy
      in benzoate degradation and formaldehyde oxidation pathways, the fact that
      17.6% of proteins have a better LB400 paralog than an ortholog in a
      different genome highlights the importance of gene duplication and
      repeated acquirement, which, coupled with their divergence, raises
      questions regarding the role of paralogs and potential functional
      redundancies in large-genome microbes.
AU  - Chain PS et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2006 103: 15280-15287.

PMID- 16299333
VI  - 73
DP  - 2005
TI  - Whole-genome analyses of speciation events in pathogenic Brucellae.
PG  - 8353-8361
AB  - Despite their high DNA identity and a proposal to group classical Brucella species as biovars
      of Brucella melitensis, the commonly recognized Brucella species can be distinguished by
      distinct biochemical and fatty acid characters, as well as by a marked host range (e.g.,
      Brucella suis for swine, B. melitensis for sheep and goats, and Brucella abortus for cattle).
      Here we present the genome of B. abortus 2308, the virulent prototype biovar 1 strain, and its
      comparison to the two other human pathogenic Brucella species and to B. abortus field isolate
      9-941. The global distribution of pseudogenes, deletions, and insertions supports previous
      indications that B. abortus and B. melitensis share a common ancestor that diverged from B.
      suis. With the exception of a dozen genes, the genetic complements of both B. abortus strains
      are identical, whereas the three species differ in gene content and pseudogenes. The pattern
      of species-specific gene inactivations affecting transcriptional regulators and outer membrane
      proteins suggests that these inactivations may play an important role in the establishment of
      host specificity and may have been a primary driver of speciation in the genus Brucella.
      Despite being nonmotile, the brucellae contain flagellum gene clusters and display
      species-specific flagellar gene inactivations, which lead to the putative generation of
      different versions of flagellum-derived structures and may contribute to differences in host
      specificity and virulence. Metabolic changes such as the lack of complete metabolic pathways
      for the synthesis of numerous compounds (e.g., glycogen, biotin, NAD, and choline) are
      consistent with adaptation of brucellae to an intracellular life-style.
AU  - Chain PS
AU  - Comerci DJ
AU  - Tolmasky ME
AU  - Larimer FW
AU  - Malfatti SA
AU  - Vergez LM
AU  - Aguero F
AU  - Land ML
AU  - Ugalde RA
AU  - Garcia E
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2005 73: 8353-8361.

PMID- 16740952
VI  - 188
DP  - 2006
TI  - Complete Genome Sequence of Yersinia pestis Strains Antiqua and Nepal516: Evidence of Gene Reduction in an Emerging Pathogen.
PG  - 4453-4463
AB  - Yersinia pestis, the causative agent of bubonic and pneumonic plagues, has undergone detailed
      study at the molecular level. To further investigate
      the genomic diversity among this group and to help characterize lineages
      of the plague organism that have no sequenced members, we present here the
      genomes of two isolates of the "classical" antiqua biovar, strains Antiqua
      and Nepal516. The genomes of Antiqua and Nepal516 are 4.7 Mb and 4.5 Mb
      and encode 4,138 and 3,956 open reading frames, respectively. Though both
      strains belong to one of the three classical biovars, they represent
      separate lineages defined by recent phylogenetic studies. We compare all
      five currently sequenced Y. pestis genomes and the corresponding features
      in Yersinia pseudotuberculosis. There are strain-specific rearrangements,
      insertions, deletions, single nucleotide polymorphisms, and a unique
      distribution of insertion sequences. We found 453 single nucleotide
      polymorphisms in protein-coding regions, which were used to assess the
      evolutionary relationships of these Y. pestis strains. Gene reduction
      analysis revealed that the gene deletion processes are under selective
      pressure, and many of the inactivations are probably related to the
      organism's interaction with its host environment. The results presented
      here clearly demonstrate the differences between the two biovar antiqua
      lineages and support the notion that grouping Y. pestis strains based
      strictly on the classical definition of biovars (predicated upon two
      biochemical assays) does not accurately reflect the phylogenetic
      relationships within this species. A comparison of four virulent Y. pestis
      strains with the human-avirulent strain 91001 provides further insight
      into the genetic basis of virulence to humans.
AU  - Chain PS
AU  - Hu P
AU  - Malfatti SA
AU  - Radnedge L
AU  - Larimer F
AU  - Vergez LM
AU  - Worsham P
AU  - Chu MC
AU  - Andersen GL
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2006 188: 4453-4463.

PMID- 21685287
VI  - 193
DP  - 2011
TI  - Genome of Ochrobactrum anthropi ATCC 49188T, a Versatile Opportunistic Pathogen and Symbiont of Several Eukaryotic Hosts.
PG  - 4274-4275
AB  - Ochrobactrum anthropi is a common soil alphaproteobacterium that colonizes a wide spectrum of
      organisms and is being increasingly recognized as an
      opportunistic human pathogen. Potentially life-threatening infections,
      such as endocarditis, are included in the list of reported O. anthropi
      infections. These reports, together with the scant number of studies and
      the organism's phylogenetic proximity to the highly pathogenic brucellae,
      make O. anthropi an attractive model of bacterial pathogenicity. Here we
      report the genome sequence of the type strain O. anthropi ATCC 49188,
      which revealed the presence of two chromosomes and four plasmids.
AU  - Chain PS
AU  - Lang DM
AU  - Comerci DJ
AU  - Malfatti SA
AU  - Vergez LM
AU  - Shin M
AU  - Ugalde RA
AU  - Garcia E
AU  - Tolmasky ME
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4274-4275.

PMID- 15358858
VI  - 101
DP  - 2004
TI  - Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis.
PG  - 13826-13831
AB  - Yersinia pestis, the causative agent of plague, is a highly uniform clone that diverged
      recently from the enteric pathogen Yersinia pseudotuberculosis. Despite their close genetic
      relationship, they differ radically in their pathogenicity and transmission. Here, we report
      the complete genomic sequence of Y. pseudotuberculosis IP32953 and its use for detailed genome
      comparisons with available Y. pestis sequences. Analyses of identified differences across a
      panel of Yersinia isolates from around the world reveal 32 Y. pestis chromosomal genes that,
      together with the two Y. pestis-specific plasmids, to our knowledge, represent the only new
      genetic material in Y. pestis acquired since the the divergence from Y. pseudotuberculosis. In
      contrast, 149 other pseudogenes (doubling the previous estimate) and 317 genes absent from Y.
      pestis were detected, indicating that as many as 13% of Y. pseudotuberculosis genes no longer
      function in Y. pestis. Extensive insertion sequence-mediated genome rearrangements and
      reductive evolution through massive gene loss, resulting in elimination and modification of
      preexisting gene expression pathways, appear to be more important than acquisition of genes in
      the evolution of Y. pestis. These results provide a sobering example of how a highly virulent
      epidemic clone can suddenly emerge from a less virulent, closely related progenitor.
AU  - Chain PSG et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2004 101: 13826-13831.

PMID- 27445366
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Nocardia jinanensis, an Opportunistic Bacterial Pathogen That Causes Cellulitis.
PG  - e00593-16
AB  - The draft genome sequence of Nocardia jinanensis, an opportunistic pathogen that  can cause
      skin infections, reveals genes that may contribute to the lifestyle and
      pathogenicity of N. jinanensis The genome also reveals the biosynthetic capacity
      of N. jinanensis in producing mycolic acids, siderophores, and other polyketide
      and nonribosomal peptide-derived secondary metabolites.
AU  - Chakrabortti A
AU  - Li J
AU  - Liang ZX
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00593-16.

PMID- 28194258
VI  - 12
DP  - 2017
TI  - Complete genome sequence of Pseudomonas stutzeri strain RCH2 isolated from a Hexavalent Chromium [Cr(VI)] contaminated site.
PG  - 23
AB  - Hexavalent Chromium [Cr(VI)] is a widespread contaminant found in soil, sediment, and ground
      water in several DOE sites, including Hanford 100 H area. In order to
      stimulate microbially mediated reduction of Cr(VI) at this site, a poly-lactate
      hydrogen release compound was injected into the chromium contaminated aquifer.
      Targeted enrichment of dominant nitrate-reducing bacteria post injection resulted
      in the isolation of Pseudomonas stutzeri strain RCH2. P. stutzeri strain RCH2 was
      isolated using acetate as the electron donor and is a complete denitrifier.
      Experiments with anaerobic washed cell suspension of strain RCH2 revealed it
      could reduce Cr(VI) and Fe(III). The genome of strain RCH2 was sequenced using a
      combination of Illumina and 454 sequencing technologies and contained a circular
      chromosome of 4.6 Mb and three plasmids. Global genome comparisons of strain RCH2
      with six other fully sequenced P. stutzeri strains revealed most genomic regions
      are conserved, however strain RCH2 has an additional 244 genes, some of which are
      involved in chemotaxis, Flp pilus biogenesis and pyruvate/2-oxogluturate complex
      formation.
AU  - Chakraborty R
AU  - Woo H
AU  - Dehal P
AU  - Walker R
AU  - Zemla M
AU  - Auer M
AU  - Goodwin LA
AU  - Kazakov A
AU  - Novichkov P
AU  - Arkin AP
AU  - Hazen TC
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 23.

PMID- 23991253
VI  - 8
DP  - 2013
TI  - Complete genome sequence of Halorhodospira halophila SL1.
PG  - 206-214
AB  - Halorhodospira halophila is among the most halophilic organisms known. It is an obligately
      photosynthetic and anaerobic purple sulfur bacterium that exhibits
      autotrophic growth up to saturated NaCl concentrations. The type strain H.
      halophila SL1 was isolated from a hypersaline lake in Oregon. Here we report the
      determination of its entire genome in a single contig. This is the first genome
      of a phototrophic extreme halophile. The genome consists of 2,678,452 bp,
      encoding 2,493 predicted genes as determined by automated genome annotation. Of
      the 2,407 predicted proteins, 1,905 were assigned to a putative function. Future
      detailed analysis of this genome promises to yield insights into the halophilic
      adaptations of this organism, its ability for photoautotrophic growth under
      extreme conditions, and its characteristic sulfur metabolism.
AU  - Challacombe JF et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 206-214.

PMID- 17172329
VI  - 189
DP  - 2007
TI  - Complete Genome Sequence of Haemophilus somnus (Histophilus somni) Strain 129Pt and Comparison to Haemophilus ducreyi 35000HP and Haemophilus  influenzae Rd.
PG  - 1890-1898
AB  - Haemophilus somnus can be either a commensal of bovine mucosal surfaces or an opportunistic
      pathogen. Pathogenic strains of H. somnus are a
      significant cause of systemic disease in cattle. We report the genome
      sequence of H. somnus 129Pt, a nonpathogenic commensal preputial isolate,
      and the results of a genome-wide comparative analysis of H. somnus 129Pt,
      Haemophilus influenzae Rd, and Haemophilus ducreyi 35000HP. We found
      unique genes in H. somnus 129Pt involved in lipooligosaccharide
      biosynthesis, carbohydrate uptake and metabolism, cation transport, amino
      acid metabolism, ubiquinone and menaquinone biosynthesis, cell surface
      adhesion, biosynthesis of cofactors, energy metabolism, and electron
      transport. There were also many genes in common among the three organisms.
      Our comparative analyses of H. somnus 129Pt, H. influenzae Rd, and H.
      ducreyi 35000HP revealed similarities and differences in the numbers and
      compositions of genes involved in metabolism, host colonization, and
      persistence. These results lay a foundation for research on the host
      specificities and niche preferences of these organisms. Future comparisons
      between H. somnus 129Pt and virulent strains will aid in the development
      of protective strategies and vaccines to protect cattle against H. somnus
      disease.
AU  - Challacombe JF
AU  - Duncan AJ
AU  - Brettin TS
AU  - Bruce D
AU  - Chertkov O
AU  - Detter JC
AU  - Han CS
AU  - Misra M
AU  - Richardson P
AU  - Tapia R
AU  - Thayer N
AU  - Xie G
AU  - Inzana TJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2007 189: 1890-1898.

PMID- 27881415
VI  - 83
DP  - 2017
TI  - Whole genome relationships among Francisella bacteria of diverse origin define new species and provide specific regions for detection.
PG  - e02589-16
AB  - Francisella tularensis is a highly virulent zoonotic pathogen that causes
      tularemia and, because of weaponization efforts in past world wars, is considered
      a tier 1 biothreat agent. Detection and surveillance of F. tularensis may be
      confounded by the presence of uncharacterized, closely related organisms. Through
      DNA-based diagnostics and environmental surveys, novel clinical and environmental
      Francisella isolates have been obtained in recent years. Here we present 7 new
      Francisella genomes and a comparison of their characteristics to each other and
      to 24 publicly available genomes as well as a comparative analysis of 16S rRNA
      and sdhA genes from over 90 Francisella strains. Delineation of new species in
      bacteria is challenging, especially when isolates having very close genomic
      characteristics exhibit different physiological features-for example, when some
      are virulent pathogens in humans and animals while others are nonpathogenic or
      are opportunistic pathogens. Species resolution within Francisella varies with
      analyses of single genes, multiple gene or protein sets, or whole-genome
      comparisons of nucleic acid and amino acid sequences. Analyses focusing on single
      genes (16S rRNA, sdhA), multiple gene sets (virulence genes, lipopolysaccharide
      [LPS] biosynthesis genes, pathogenicity island), and whole-genome comparisons
      (nucleotide and protein) gave congruent results, but with different levels of
      discrimination confidence. We designate four new species within the genus;
      Francisella opportunistica sp. nov. (MA06-7296), Francisella salina sp. nov.
      (TX07-7308), Francisella uliginis sp. nov. (TX07-7310), and Francisella
      frigiditurris sp. nov. (CA97-1460). This study provides a robust comparative
      framework to discern species and virulence features of newly detected Francisella
      bacteria. IMPORTANCE: DNA-based detection and sequencing methods have identified
      thousands of new bacteria in the human body and the environment. In most cases,
      there are no cultured isolates that correspond to these sequences. While
      DNA-based approaches are highly sensitive, accurately assigning species is
      difficult without known near relatives for comparison. This ambiguity poses
      challenges for clinical cases, disease epidemics, and environmental surveillance,
      for which response times must be short. Many new Francisella isolates have been
      identified globally. However, their species designations and potential for
      causing human disease remain ambiguous. Through detailed genome comparisons, we
      identified features that differentiate F. tularensis from clinical and
      environmental Francisella isolates and provide a knowledge base for future
      comparison of Francisella organisms identified in clinical samples or
      environmental surveys.
AU  - Challacombe JF
AU  - Petersen JM
AU  - Gallegos-Graves V
AU  - Hodge D
AU  - Pillai S
AU  - Kuske CR
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2017 83: e02589-16.

PMID- 11353084
VI  - 29
DP  - 2001
TI  - The complete genome sequence of the murine respiratory pathogen  Mycoplasma pulmonis.
PG  - 2145-2153
AB  - Mycoplasma pulmonis is a wall-less eubacterium belonging to the Mollicutes (trivial name,
      mycoplasmas) and responsible for murine respiratory
      diseases. The genome of strain UAB CTIP is composed of a single circular 963 879 bp chromosome
      with a G + C content of 26.6 mol%, i.e. the lowest
      reported among bacteria, Ureaplasma urealyticum apart. This genome contains 782 putative
      coding sequences (CDSs) covering 91.4% of its length
      and a function could be assigned to 486 CDSs whilst 92 matched the gene sequences of
      hypothetical proteins, leaving 204 CDSs without significant
      database match. The genome contains a single set of rRNA genes and only 29 tRNAs genes. The
      replication origin oriC was localized by sequence
      analysis and by using the G + C skew method. Sequence polymorphisms within stretches of
      repeated nucleotides generate phase-variable protein
      antigens whilst a recombinase gene is likely to catalyse the site-specific DNA inversions in
      major M. pulmonis surface antigens. Furthermore, a
      hemolysin, secreted nucleases and a glycoprotease are predicted virulence factors.
      Surprisingly, several of the genes previously reported to be
      essential for a self-replicating minimal cell are missing in the M. pulmonis genome although
      this one is larger than the other mycoplasma genomes fully
      sequenced until now.
AU  - Chambaud I
AU  - Heilig R
AU  - Ferris S
AU  - Barbe V
AU  - Samson D
AU  - Galisson F
AU  - Moszer I
AU  - Dybvig K
AU  - Wroblewski H
AU  - Viari A
AU  - Rocha EPC
AU  - Blanchard A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2001 29: 2145-2153.

PMID- 16306233
VI  - 33
DP  - 2005
TI  - In vivo selection of engineered homing endonucleases using double-strand break induced homologous recombination.
PG  - e178
AB  - Homing endonucleases, endonucleases capable of recognizing long DNA sequences, have been shown
      to be a tool of choice for precise and efficient genome engineering. Consequently, the
      possibility to engineer novel endonucleases with tailored specificities is under strong
      investigation. In this report, we present a simple and efficient method to select
      meganucleases from libraries of variants, based on their cleavage properties. The method has
      the advantage of directly selecting for the ability to induce double-strand break induced
      homologous recombination in a eukaryotic environment. Model selections demonstrated high
      levels of enrichments. Moreover, this method compared favorably with phage display for
      enrichment of active mutants from a mutant library. This approach makes possible the
      exploration of large sequence spaces and thereby represents a valuable tool for genome
      engineering.
AU  - Chames P
AU  - Epinat JC
AU  - Guillier S
AU  - Patin A
AU  - Lacroix E
AU  - Paques F
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2005 33: e178.

PMID- 20808780
VI  - 5
DP  - 2010
TI  - Mechanistic Insights on the Inhibition of C5 DNA Methyltransferases by Zebularine.
PG  - e12388
AB  - In mammals DNA methylation occurs at position 5 of cytosine in a CpG context and regulates
      gene expression. It plays an important role in
      diseases and inhibitors of DNA methyltransferases (DNMTs)-the enzymes
      responsible for DNA methylation-are used in clinics for cancer therapy.
      The most potent inhibitors are 5-azacytidine and 5-azadeoxycytidine.
      Zebularine (1-(beta-D-ribofuranosyl)-2(1H)-pyrimidinone) is another
      cytidine analog described as a potent inhibitor that acts by forming a
      covalent complex with DNMT when incorporated into DNA. Here we bring
      additional experiments to explain its mechanism of action. First, we
      observe an increase in the DNA binding when zebularine is incorporated
      into the DNA, compared to deoxycytidine and 5-fluorodeoxycytidine,
      together with a strong decrease in the dissociation rate. Second, we
      show by denaturing gel analysis that the intermediate covalent complex
      between the enzyme and the DNA is reversible, differing thus from
      5-fluorodeoxycytidine. Third, no methylation reaction occurs when
      zebularine is present in the DNA. We confirm that zebularine exerts its
      demethylation activity by stabilizing the binding of DNMTs to DNA,
      hindering the methylation and decreasing the dissociation, thereby
      trapping the enzyme and preventing turnover even at other sites.
AU  - Champion C
AU  - Guianvarc'h D
AU  - Senamaud-Beaufort C
AU  - Jurkowska RZ
AU  - Jeltsch A
AU  - Ponger L
AU  - Arimondo PB
AU  - Guieysse-Peugeot AL
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2010 5: e12388.

PMID- 19478886
VI  - 5
DP  - 2009
TI  - Comparative Genomic Characterization of Francisella tularensis Strains Belonging to Low and High Virulence Subspecies.
PG  - e1000459
AB  - Tularemia is a geographically widespread, severely debilitating, and occasionally lethal
      disease in humans. It is caused by infection by a
      gram-negative bacterium, Francisella tularensis. In order to better
      understand its potency as an etiological agent as well as its potential
      as a biological weapon, we have completed draft assemblies and report
      the first complete genomic characterization of five strains belonging
      to the following different Francisella subspecies (subsp.): the F.
      tularensis subsp. tularensis FSC033, F. tularensis subsp. holarctica
      FSC257 and FSC022, and F. tularensis subsp. novicida GA99-3548 and
      GA99-3549 strains. Here, we report the sequencing of these strains and
      comparative genomic analysis with recently available public Francisella
      sequences, including the rare F. tularensis subsp. mediasiatica FSC147
      strain isolate from the Central Asian Region. We report evidence for
      the occurrence of large-scale rearrangement events in strains of the
      holarctica subspecies, supporting previous proposals that further
      phylogenetic subdivisions of the Type B clade are likely. We also find
      a significant enrichment of disrupted or absent ORFs proximal to
      predicted breakpoints in the FSC022 strain, including a genetic
      component of the Type I restriction-modification defense system. Many
      of the pseudogenes identified are also disrupted in the closely related
      rarely human pathogenic F. tularensis subsp. mediasiatica FSC147
      strain, including modulator of drug activity B (mdaB) (FTT0961), which
      encodes a known NADPH quinone reductase involved in oxidative stress
      resistance. We have also identified genes exhibiting sequence
      similarity to effectors of the Type III (T3SS) and components of the
      Type IV secretion systems (T4SS). One of the genes, msrA2 (FTT1797c),
      is disrupted in F. tularensis subsp. mediasiatica and has recently been
      shown to mediate bacterial pathogen survival in host organisms. Our
      findings suggest that in addition to the duplication of the Francisella
      Pathogenicity Island, and acquisition of individual loci, adaptation by
      gene loss in the more recently emerged tularensis, holarctica, and
      mediasiatica subspecies occurred and was distinct from evolutionary
      events that differentiated these subspecies, and the novicida
      subspecies, from a common ancestor. Our findings are applicable to
      future studies focused on variations in Francisella subspecies
      pathogenesis, and of broader interest to studies of genomic
      pathoadaptation in bacteria.
AU  - Champion MD et al
PT  - Journal Article
TA  - PLoS Pathog.
JT  - PLoS Pathog.
SO  - PLoS Pathog. 2009 5: e1000459.

PMID- 22965102
VI  - 194
DP  - 2012
TI  - Genome Sequence of Citrobacter sp. Strain A1, a Dye-Degrading Bacterium.
PG  - 5485-5486
AB  - Citrobacter sp. strain A1, isolated from a sewage oxidation pond, is a facultative aerobe and
      mesophilic dye-degrading bacterium. This organism degrades
      azo dyes efficiently via azo reduction and desulfonation, followed by the
      successive biotransformation of dye intermediates under an aerobic environment.
      Here we report the draft genome sequence of Citrobacter sp. A1.
AU  - Chan GF
AU  - Gan HM
AU  - Rashid NA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5485-5486.

PMID- 23012290
VI  - 194
DP  - 2012
TI  - Genome Sequence of Enterococcus sp. Strain C1, an Azo Dye Decolorizer.
PG  - 5716-5717
AB  - Enterococcus sp. strain C1 is a facultative anaerobe which was coisolated with Citrobacter sp.
      strain A1 from a sewage oxidation pond. Strain C1 could degrade
      azo dyes very efficiently via azo reduction and desulfonation in a
      microaerophilic environment. Here the draft genome sequence of Enterococcus sp.
      C1 is reported.
AU  - Chan GF
AU  - Gan HM
AU  - Rashid NA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5716-5717.

PMID- 24420881
VI  - 10
DP  - 1994
TI  - Isolation and characterization of restriction endonuclease EclHKI from an Enterobacter cloacae strain.
PG  - 30-32
AB  - An Enterobacter cloacae strain, producing restriction enzyme EclHKI, was isolated from a
      decaying potato. The enzyme is an isoschizomer of Eam1105I, which recognizes and cleaves
      GACNNN^NNGTC. EclHKI was produced at high activity (40000 U/g wet cells) and was purified from
      contaminants which interfere with restriction digestion by passing the cell lysate through
      DEAE-Sephacel and heparin columns. Activity was optimal at 37oC in a medium salt buffer.
AU  - Chan H-Y
AU  - Chan Y-C
AU  - Kam K-M
AU  - Shaw P-C
PT  - Journal Article
TA  - World J. Microbiol. Biotechnol.
JT  - World J. Microbiol. Biotechnol.
SO  - World J. Microbiol. Biotechnol. 1994 10: 30-32.

PMID- 22207751
VI  - 194
DP  - 2012
TI  - Whole-Genome Sequence of the Emerging Pathogen Mycobacterium abscessus Strain 47J26.
PG  - 549
AB  - Mycobacterium abscessus is a rapidly growing environmental mycobacterium commonly found in
      soil and water which is often also associated with
      infections in humans, particularly of the lung. We report herein the draft
      genome sequence of M. abscessus strain 47J26.
AU  - Chan J
AU  - Halachev M
AU  - Yates E
AU  - Smith G
AU  - Pallen M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 549.

PMID- 25814592
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Lysinibacillus sp. Strain A1, Isolated from Malaysian Tropical Soil.
PG  - e00095-15
AB  - In this work, we describe the genome of Lysinibacillus sp. strain A1, which was isolated from
      tropical soil. Analysis of its genome sequence shows the presence
      of a gene encoding for a putative peptidase responsible for nitrogen compounds.
AU  - Chan KG
AU  - Chen JW
AU  - Chang CY
AU  - Yin WF
AU  - Chan XY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00095-15.

PMID- 25745000
VI  - 3
DP  - 2015
TI  - Whole-Genome Analysis of Quorum-Sensing Burkholderia sp. Strain A9.
PG  - e00063-15
AB  - Burkholderia spp. rely on N-acyl homoserine lactone as quorum-sensing signal molecules which
      coordinate their phenotype at the population level. In this work,
      we present the whole genome of Burkholderia sp. strain A9, which enables the
      discovery of its N-acyl homoserine lactone synthase gene.
AU  - Chan KG
AU  - Chen JW
AU  - Tee KK
AU  - Chang CY
AU  - Yin WF
AU  - Chan XY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00063-15.

PMID- 25745006
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Aeromonas caviae Strain L12, a Quorum-Sensing Strain Isolated from a Freshwater Lake in Malaysia.
PG  - e00079-15
AB  - Here, we present the draft genome sequence of Aeromonas caviae strain L12, which  shows
      quorum-sensing activity. The availability of this genome sequence is
      important to the research of the quorum-sensing regulatory system in this
      isolate.
AU  - Chan KG
AU  - Chin PS
AU  - Tee KK
AU  - Chang CY
AU  - Yin WF
AU  - Sheng KY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00079-15.

PMID- 26659682
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequence of Stenotrophomonas maltophilia ZBG7B Reveals Its Biotechnological Potential.
PG  - e01442-15
AB  - Stenotrophomonas maltophilia ZBG7B was isolated from vineyard soil of Zellenberg, France.
      Here, we present the draft genome sequence of this bacterial strain,
      which has facilitated the prediction of function for several genes encoding
      biotechnologically important enzymes, such as xylosidase, xylanase, laccase, and
      chitinase.
AU  - Chan KG
AU  - Chong TM
AU  - Adrian TG
AU  - Kher HL
AU  - Hong KW
AU  - Grandclement C
AU  - Faure D
AU  - Yin WF
AU  - Dessaux Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01442-15.

PMID- 25792063
VI  - 3
DP  - 2015
TI  - Analysis of Pectate Lyase Genes in Dickeya chrysanthemi Strain L11, Isolated from a Recreational Lake in Malaysia: a Draft Genome Sequence Perspective.
PG  - e00145-15
AB  - Dickeya chrysanthemi is well known as a plant pathogen that caused major blackleg in the
      European potato industry in the 1990s. D. chrysanthemi strain L11 was
      discovered in a recreational lake in Malaysia. Here, we present its draft genome
      sequence.
AU  - Chan KG
AU  - Kher HL
AU  - Chang CY
AU  - Yin WF
AU  - Tan KH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00145-15.

PMID- 26021924
VI  - 3
DP  - 2015
TI  - Genome Anatomy of Streptococcus parasanguinis Strain C1A, Isolated from a Patient with Acute Exacerbation of Chronic Obstructive Pulmonary Disease, Reveals Unusual  Genomic Features.
PG  - e00541-15
AB  - Streptococcus parasanguinis causes invasive diseases. However, the mechanism by which it
      causes disease remains unclear. Here, we describe the complete genome
      sequence of S. parasanguinis C1A, isolated from a patient diagnosed with an acute
      exacerbation of chronic obstructive pulmonary disease. Several genes that might
      be associated with pathogenesis are also described.
AU  - Chan KG
AU  - Ng KT
AU  - Pang YK
AU  - Chong TM
AU  - Kamarulzaman A
AU  - Yin WF
AU  - Tee KK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00541-15.

PMID- 26404582
VI  - 3
DP  - 2015
TI  - Draft Genome Perspective of Staphylococcus saprophyticus Strain SU8, an N-Acyl Homoserine Lactone-Degrading Bacterium.
PG  - e01097-15
AB  - Staphylococcus saprophyticus strain SU8 was isolated from a pristine water source in Malaysia
      and it exhibited degradation of N-hexanoylhomoserine lactone. Here we report the draft genome
      sequence of S. saprophyticus strain SU8 to further understand its quorum quenching abilities.
AU  - Chan KG
AU  - Sulaiman J
AU  - Yong DA
AU  - Tee KK
AU  - Yin WF
AU  - Priya K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01097-15.

PMID- 25523782
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Cedecea neteri Strain SSMD04, a Bacterium Isolated from Pickled Mackerel Sashimi.
PG  - e01339-14
AB  - We report here the complete genome sequence of C. neteri SSMD04, a strain isolated from
      pickled mackerel sashimi, sequenced by third-generation sequencing
      technology. To the best of our knowledge, this is the first documentation that
      reports the complete genome of Cedecea neteri.
AU  - Chan KG
AU  - Tan KH
AU  - Yin WF
AU  - Tan JY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01339-14.

PMID- 25676763
VI  - 3
DP  - 2015
TI  - Genomic Insights of Pectobacterium carotovorum Strain M022 Quorum-Sensing Activity through Whole-Genome Sequencing.
PG  - e01554-14
AB  - Pectobacterium carotovorum is known to cause serious damage to various major crops worldwide.
      Here, we report the draft genome of Pectobacterium carotovorum
      strain M022, a freshwater isolate from a Malaysian waterfall, which has been
      reported as a plant pathogen and is able to communicate with N-acylhomoserine
      lactone-mediated quorum sensing.
AU  - Chan KG
AU  - Tan WS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01554-14.

PMID- 28748024
VI  - 12
DP  - 2017
TI  - Insights into Cedecea neteri strain M006 through complete genome sequence, a rare bacterium from aquatic environment.
PG  - 40
AB  - Cedecea neteri M006 is a rare bacterium typically found as an environmental isolate from the
      tropical rainforest Sungai Tua waterfall (Gombak, Selangor,
      Malaysia). It is a Gram-reaction-negative, facultative anaerobic, bacillus. Here,
      we explore the features of Cedecea neteri M006, together with its genome sequence
      and annotation. The genome comprised 4,965,436 bp with 4447 protein-coding genes
      and 103 RNA genes.
AU  - Chan KG
AU  - Tan WS
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 40.

PMID- 25767237
VI  - 3
DP  - 2015
TI  - Genome Sequence Analysis Reveals Evidence of Quorum-Sensing Genes Present in Aeromonas hydrophila Strain M062, Isolated from Freshwater.
PG  - e00100-15
AB  - Aeromonas hydrophila has emerged worldwide as a human pathogen. Here, we report the draft
      whole-genome sequence of a freshwater isolate from Malaysia, A.
      hydrophila strain M062, and its N-acylhomoserine lactone genes are also reported
      here.
AU  - Chan KG
AU  - Tan WS
AU  - Chang CY
AU  - Yin WF
AU  - Mumahad YNY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00100-15.

PMID- 25502672
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Pluralibacter gergoviae FB2, an N-Acyl Homoserine Lactone-Degrading Strain Isolated from Packed Fish Paste.
PG  - e01276-14
AB  - Pluralibacter gergoviae FB2, a bacterial strain isolated from packed food, has been found to
      exhibit quorum-quenching properties. Hence, we report the first,
      complete genome of P. gergoviae sequenced using the Pacific Biosciences
      single-molecule, real-time (SMRT) platform.
AU  - Chan KG
AU  - Tee KK
AU  - Yin WF
AU  - Tan JY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01276-14.

PMID- 24744329
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Quorum-Sensing and Quorum-Quenching Pseudomonas aeruginosa Strain MW3a.
PG  - e00258-14
AB  - Pseudomonas aeruginosa has a broad range of habitation, from aquatic environments to human
      lungs. The coexistence of quorum-sensing and quorum-quenching activities occurs in P.
      aeruginosa strain MW3a. In this work, we present the draft genome sequence of P. aeruginosa
      MW3a, an interesting bacterium isolated from a marine environment.
AU  - Chan KG
AU  - Wong CS
AU  - Yin WF
AU  - Chan XY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00258-14.

PMID- 24812228
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Pandoraea pnomenusa 3kgm, a Quorum-Sensing Strain Isolated from a Former Landfill Site.
PG  - e00427-14
AB  - Pandoraea pnomenusa strain 3kgm has been identified as a quorum-sensing strain isolated from
      soil. Here, we report the complete genome sequence of P. pnomenusa
      strain 3kgm by using the Pacific Biosciences single-molecule real-time (PacBio RS
      SMRT) sequencer high-resolution technology.
AU  - Chan KG
AU  - Yin WF
AU  - Goh SY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00427-14.

PMID- 24699957
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Pseudomonas aeruginosa Strain YL84, a Quorum-Sensing  Strain Isolated from Compost.
PG  - e00246-14
AB  - Here, we report the complete genome sequence of Pseudomonas aeruginosa strain YL84, which was
      isolated from compost. This strain was found to be a chitinase-producing quorum-sensing
      bacterium.
AU  - Chan KG
AU  - Yin WF
AU  - Lim YL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00246-14.

PMID- 26021935
VI  - 3
DP  - 2015
TI  - Pandoraea sp. Strain E26: Discovery of Its Quorum-Sensing Properties via Whole-Genome Sequence Analysis.
PG  - e00565-15
AB  - We report the draft genome sequence of Pandoraea sp. strain E26 isolated from a former
      landfill site, sequenced by the Illumina MiSeq platform. This genome
      sequence will be useful to further understand the quorum-sensing system of this
      isolate.
AU  - Chan KG
AU  - Yin WF
AU  - Tee KK
AU  - Chang CY
AU  - Priya K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00565-15.

PMID- 26941152
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequencing Analysis of Chromobacterium piscinae Strain ND17, a Quorum-Sensing Bacterium.
PG  - e00081-16
AB  - Here, we report the draft genome sequence of Chromobacterium piscinae strain ND17. This
      bacterium was isolated from a fresh water sample in Malaysia and
      exhibits quorum-sensing activity. This first draft genome of C. piscinae strain
      ND17 will pave the way to future studies of the quorum-sensing properties of this
      isolate.
AU  - Chan KG
AU  - Yunos NY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00081-16.

PMID- 21923906
VI  - 12
DP  - 2011
TI  - Updated genome assembly and annotation of Paenibacillus larvae, the agent of American foulbrood disease of honey bees.
PG  - 450
AB  - BACKGROUND: As scientists continue to pursue various 'omics-based research, there
      is a need for high quality data for the most fundamental 'omics of all: genomics.
      The bacterium Paenibacillus larvae is the causative agent of the honey bee
      disease American foulbrood. If untreated, it can lead to the demise of an entire
      hive; the highly social nature of bees also leads to easy disease spread, between
      both individuals and colonies. Biologists have studied this organism since the
      early 1900s, and a century later, the molecular mechanism of infection remains
      elusive. Transcriptomics and proteomics, because of their ability to analyze
      multiple genes and proteins in a high-throughput manner, may be very helpful to
      its study. However, the power of these methodologies is severely limited without
      a complete genome; we undertake to address that deficiency here. RESULTS: We used
      the Illumina GAIIx platform and conventional Sanger sequencing to generate a
      182-fold sequence coverage of the P. larvae genome, and assembled the data using
      ABySS into a total of 388 contigs spanning 4.5 Mbp. Comparative genomics analysis
      against fully-sequenced soil bacteria P. JDR2 and P. vortex showed that regions
      of poor conservation may contain putative virulence factors. We used GLIMMER to
      predict 3568 gene models, and named them based on homology revealed by BLAST
      searches; proteases, hemolytic factors, toxins, and antibiotic resistance enzymes
      were identified in this way. Finally, mass spectrometry was used to provide
      experimental evidence that at least 35% of the genes are expressed at the protein
      level. CONCLUSIONS: This update on the genome of P. larvae and annotation
      represents an immense advancement from what we had previously known about this
      species. We provide here a reliable resource that can be used to elucidate the
      mechanism of infection, and by extension, more effective methods to control and
      cure this widespread honey bee disease.
AU  - Chan QW
AU  - Cornman RS
AU  - Birol I
AU  - Liao NY
AU  - Chan SK
AU  - Docking TR
AU  - Jackman SD
AU  - Taylor GA
AU  - Jones SJ
AU  - de Graaf DC
AU  - Evans JD
AU  - Foster LJ
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2011 12: 450.

PMID- 15570069
VI  - 32
DP  - 2004
TI  - Cloning of CviPII nicking and modification system from chlorella virus Nys-1 and application of Nt.CviPII in random DNA amplification.
PG  - 6187-6199
AB  - The cloning and expression of the CviPII DNA nicking and modification system encoded by
      chlorella virus NYs-1 is described. The system consists of a co-linear MTase encoding gene
      (cviPIIM) and a nicking endonuclease encoding gene (cviPIINt) separated by 12 nt. M.CviPII
      possesses eight conserved amino acid motifs (I to VIII) typical of C5 MTases, but, like
      another chlorella virus MTase M.CviJI, lacks conserved motifs IX and X. In addition to
      modification of the first cytosine in CCD (D = A, G or T) sequences, M.CviPII modifies both
      the first two cytosines in CCAA and CCCG sites as well. Nt.CviPII has significant amino acid
      sequence similarity to Type II restriction endonuclease CviJI that recognizes an overlapping
      sequence (RG^CY). Nt.CviPII was expressed in Escherichia coli with or without a His-tag in a
      host pre-modified by M.CviPII. Recombinant Nt.CviPII recognizes the DNA sequence CCD and
      cleaves the phosphodiester bond 5' of the first cytosine while the other strand of DNA at
      this site is not affected. Nt.CviPII displays site preferences with CCR (R = A or G) sites
      preferred over CCT sites. Nt.CviPII is active from 16 to 65 degrees C with a temperature
      optimum of 30-45 degrees C. Nt.CviPII can be used to generate single-stranded DNAs (ssDNAs)
      for isothermal strand-displacement amplification. Nt.CviPII was used in combination with Bst
      DNA polymerase I large fragment to rapidly amplify anonymous DNA from genomic DNA or from a
      single bacterial colony.
AU  - Chan S-H
AU  - Zhu Z
AU  - Van Etten JL
AU  - Xu S-Y
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2004 32: 6187-6199.

PMID- 17855396
VI  - 35
DP  - 2007
TI  - Catalytic domain of restriction endonuclease BmrI as a cleavage module for engineering endonucleases with novel substrate specificities.
PG  - 6238-6248
AB  - Creating endonucleases with novel sequence specificities provides more possibilities to
      manipulate DNA. We have created a chimeric endonuclease
      (CH-endonuclease) consisting of the DNA cleavage domain of BmrI
      restriction endonuclease and C.BclI, a controller protein of the BclI
      restriction-modification system. The purified chimeric endonuclease,
      BmrI198-C.BclI, cleaves DNA at specific sites in the vicinity of the
      recognition sequence of C.BclI. Double-strand (ds) breaks were observed at
      two sites: 8 bp upstream and 18 bp within the C-box sequence. Using DNA
      substrates with deletions of C-box sequence, we show that the chimeric
      endonuclease requires the 5' half of the C box only for specific cleavage.
      A schematic model is proposed for the mode of protein-DNA binding and DNA
      cleavage. The present study demonstrates that the BmrI cleavage domain can
      be used to create combinatorial endonucleases that cleave DNA at specific
      sequences dictated by the DNA-binding partner. The resulting endonucleases
      will be useful in vitro and in vivo to create ds breaks at specific sites
      and generate deletions.
AU  - Chan SH
AU  - Bao Y
AU  - Ciszak E
AU  - Laget S
AU  - Xu SY
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2007 35: 6238-6248.

PMID- 20140205
VI  - 5
DP  - 2010
TI  - Cofactor Requirement of HpyAV Restriction Endonuclease.
PG  - e9071
AB  - Background: Helicobacter pylori is the etiologic agent of common gastritis and a risk factor
      for gastric cancer. It is also one of the richest sources of Type II restriction-modification
      (R-M) systems in microorganisms. Principal/Findings: We have cloned, expressed and purified a
      new restriction endonuclease HpyAV from H. pylori strain 26695. We determined the HpyAV DNA
      recognition sequence and cleavage site as CCTTC 6/5. In addition, we found that HpyAV has a
      unique metal ion requirement: its cleavage activity is higher with transition metal ions than
      in Mg++. The special metal ion requirement of HpyAV can be attributed to the presence of a HNH
      catalytic site similar to ColE9 nuclease instead of the canonical PD-X-D/EXK catalytic site
      found in many other REases. Site-directed mutagenesis was carried out to verify the catalytic
      residues of HpyAV. Mutation of the conserved metal-binding Asn311 and His320 to alanine
      eliminated cleavage activity. HpyAV variant H295A displayed approximately 1% of wt activity.
      Conclusions/Significance: Some HNH-type endonucleases have unique metal ion cofactor
      requirement for optimal activities. Homology modeling and site-directed mutagenesis confirmed
      that HpyAV is a member of the HNH nuclease family. The identification of catalytic residues in
      HpyAV paved the way for further engineering of the metal binding site. A survey of sequenced
      microbial genomes uncovered 10 putative R-M systems that show high sequence similarity to the
      HpyAV system, suggesting lateral transfer of a prototypic HpyAV-like R-M system among these
      microorganisms.
AU  - Chan SH
AU  - Opitz L
AU  - Higgins L
AU  - O'loane D
AU  - Xu S-Y
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2010 5: e9071.

PMID- 20805246
VI  - 39
DP  - 2011
TI  - Natural and engineered nicking endonucleases--from cleavage mechanism to engineering of strand-specificity.
PG  - 1-18
AB  - Restriction endonucleases (REases) are highly specific DNA scissors that have facilitated the
      development of modern molecular biology. Intensive studies of double strand (ds) cleavage
      activity of Type IIP REases, which recognize 4-8 bp palindromic sequences, have revealed a
      variety of mechanisms of molecular recognition and catalysis. Less well-studied are REases
      which cleave only one of the strands of dsDNA, creating a nick instead of a ds break.
      Naturally occurring nicking endonucleases (NEases) range from frequent cutters such as
      Nt.CviPII (;CCD; ; denotes the cleavage site) to rare-cutting homing endonucleases (HEases)
      such as I-HmuI. In addition to these bona fida NEases, individual subunits of some
      heterodimeric Type IIS REases have recently been shown to be natural NEases. The discovery and
      characterization of more REases that recognize asymmetric sequences, particularly Types IIS
      and IIA REases, has revealed recognition and cleavage mechanisms drastically different from
      the canonical Type IIP mechanisms, and has allowed researchers to engineer highly
      strand-specific NEases. Monomeric LAGLIDADG HEases use two separate catalytic sites for
      cleavage. Exploitation of this characteristic has also resulted in useful nicking HEases. This
      review aims at providing an overview of the cleavage mechanisms of Types IIS and IIA REases
      and LAGLIDADG HEases, the engineering of their nicking variants, and the applications of
      NEases and nicking HEases.
AU  - Chan SH
AU  - Stoddard BL
AU  - Xu SY
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2011 39: 1-18.

PMID- 16737828
VI  - 49
DP  - 2006
TI  - Cloning of Nt.CviQII nicking endonuclease and its cognate methyltransferase: M.CviQII methylates AG sequences.
PG  - 138-150
AB  - Chlorella virus NY-2A has a large, highly methylated dsDNA genome (45% of the cytosines are
      5-methylcytosine and 37% of the adenines are
      N-6-methyladenine). Here, we report the cloning, expression, and
      characterization of the NY-2A-encoded CviQII nicking-modification (N-M)
      system. The nicking endonuclease, Nt.CviQII, recognizes R down arrow AG
      (R = A or G, down arrow indicating cleavage site) sequences and cleaves
      the phosphodiester bond 5' to the adenosine. Because of the difficulty
      in cloning and expressing the wild-type Nt.CviQII, C-terminal
      truncation mutants were generated and full-length Nt.CviQII was
      reconstructed by intein-mediated peptide ligation. The truncation
      mutants and the reconstructed full-length Nt.CviQII have the same
      recognition and cleavage specificity as the native enzyme. Full-length
      and truncated Nt.CviQII produced by a cell-free
      transcription/translation system have similar reaction rates. The
      methyltransferase, M.CviQII, was also cloned and expressed. It modifies
      the adenine in AG doublets of DNA in vitro and in vivo in Escherichia
      coli. To our knowledge, M.CviQII is the first adenine methyltransferase
      that recognizes a dinucleotide. Therefore, M.CviQII may be a useful
      reagent for blocking endonuclease cleavage when restriction sites
      overlap with AG sequences.
AU  - Chan SH
AU  - Zhu ZY
AU  - Dunigan DD
AU  - Van Etten JL
AU  - Xu SY
PT  - Journal Article
TA  - Protein Expr. Purif.
JT  - Protein Expr. Purif.
SO  - Protein Expr. Purif. 2006 49: 138-150.

PMID- 14988555
VI  - 303
DP  - 2004
TI  - RNA silencing genes control de novo DNA methylation.
PG  - 1336
AB  - Cytosine DNA methylation silences harmful DNAs such as transposons and retroviruses.
      Maintenance DNA methyltransferases propagate pre-existing DNA methylation in the CG sequence
      context by methylating hemi-methylated sites after DNA replication.  Much less is understood
      about how invasive DNAs are initially recognized and how de novo DNA methyltransferases of the
      DNMT3 family (DRM1 and DRM2 in the plant Arabidopsis thaliana) are directed to unmethylated
      loci to initiate gene silencing.
AU  - Chan SW-L
AU  - Zilberman D
AU  - Xie Z
AU  - Johansen LK
AU  - Carrington JC
AU  - Jacobsen SE
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2004 303: 1336.

PMID- 23788535
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Bacillus atrophaeus UCMB-5137, a Plant Growth-Promoting  Rhizobacterium.
PG  - e00233-13
AB  - Bacillus atrophaeus UCMB-5137 shows an extraordinary activity in root colonization and plant
      and crop protection. Its draft genome sequence comprises
      21 contigs of 4.11 Mb, harboring 4,167 coding sequences (CDS). The genome carries
      several genes encoding antimicrobial lipopeptides and polyketides. Multiple
      horizontally acquired genes of possible importance for plant colonization were
      also found.
AU  - Chan WY
AU  - Dietel K
AU  - Lapa SV
AU  - Avdeeva LV
AU  - Borriss R
AU  - Reva ON
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00233-13.

PMID- 28360153
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequence and Fosfomycin Resistance of Bacillus sp. Strain G3(2015) Isolated from Seawater off the Coast of Malaysia.
PG  - e00067-17
AB  - Bacillus sp. is a Gram-positive bacterium that is commonly found in seawater. In  this study,
      the genome of marine Bacillus sp. strain G3(2015) was sequenced using
      MiSeq. The fosfomycin resistant gene fosB was identified upon bacterial genome
      annotation.
AU  - Chan XY
AU  - Chen JW
AU  - Adrian TG
AU  - Hong KW
AU  - Chang CY
AU  - Yin WF
AU  - Chan KG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00067-17.

PMID- 23105081
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of an Aeromonas sp. Strain 159 Clinical Isolate That Shows  Quorum-Sensing Activity.
PG  - 6350
AB  - Aeromonas is a pathogenic organism that is often found to infect humans. Here we  report the
      draft genome of a clinical isolate in Malaysia, Aeromonas sp. strain
      159, which shows N-acylhomoserine lactone production. In the draft genome of
      strain 159, luxI and luxR homologue genes were found to be located at contig 47,
      and these genes are believed to be important for the quorum-sensing system
      present in this pathogen.
AU  - Chan XY
AU  - Chua KH
AU  - Puthucheary SD
AU  - Yin WF
AU  - Chan KG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6350.

PMID- 25540357
VI  - 2
DP  - 2014
TI  - Whole-Genome Analysis of Aeromonas hydrophila Strain 187, Exhibiting Quorum-Sensing Activity.
PG  - e01360-14
AB  - Aeromonas hydrophila is a quorum-sensing (QS) bacterium that causes diarrhea in humans upon
      infection. Here, we report the genome of pathogenic Aeromonas
      hydrophila strain 187, which possesses a QS gene responsible for signaling
      molecule N-acyl homoserine lactone (AHL) synthesis and has been found to be
      located at contig 36.
AU  - Chan XY
AU  - Chua KH
AU  - Yin WF
AU  - Puthucheary SD
AU  - Chan KG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01360-14.

PMID- 25540346
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence for Treponema sp. OMZ 838 (ATCC 700772, DSM 16789), Isolated from a Necrotizing Ulcerative Gingivitis Lesion.
PG  - e01333-14
AB  - The oral treponeme bacterium Treponema sp. OMZ 838 was originally isolated from a human
      necrotizing ulcerative gingivitis (NUG) lesion. Its taxonomic status
      remains uncertain. The complete genome sequence length was determined to be
      2,708,067 bp, with a G+C content of 44.58%, and 2,236 predicted coding DNA
      sequences (CDS).
AU  - Chan Y
AU  - Ma AP
AU  - Lacap-Bugler DC
AU  - Huo YB
AU  - Keung LW
AU  - Leung FC
AU  - Watt RM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01333-14.

PMID- 24040217
VI  - 8
DP  - 2013
TI  - The Design and In Vivo Evaluation of Engineered I-OnuI-Based Enzymes for HEG Gene Drive.
PG  - e74254
AB  - The homing endonuclease gene (HEG) drive system, a promising genetic approach for controlling
      arthropod populations, utilises engineered nucleases to spread deleterious mutations that
      inactivate individual genes throughout a target population. Previous work with a naturally
      occurring LAGLIDADG homing endonuclease (I-SceI) demonstrated its feasibility in both
      Drosophila and Anopheles. Here we report on the next stage of this strategy: the redesign of
      HEGs with customized specificity in order to drive
AU  - Chan Y-S
AU  - Takeuchi R
AU  - Jarjour J
AU  - Huen DS
AU  - Stoddard BL
AU  - Russell S
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2013 8: e74254.

PMID- 26389736
VI  - 11
DP  - 2015
TI  - Translocation-coupled DNA cleavage by the Type ISP restriction-modification enzymes.
PG  - 870-877
AB  - Production of endonucleolytic double-strand DNA breaks requires separate strand cleavage
      events. Although catalytic mechanisms for simple, dimeric endonucleases
      are known, there are many complex nuclease machines that are poorly understood.
      Here we studied the single polypeptide Type ISP restriction-modification (RM)
      enzymes, which cleave random DNA between distant target sites when two enzymes
      collide after convergent ATP-driven translocation. We report the 2.7-A resolution
      X-ray crystal structure of a Type ISP enzyme-DNA complex, revealing that both the
      helicase-like ATPase and nuclease are located upstream of the direction of
      translocation, an observation inconsistent with simple nuclease-domain
      dimerization. Using single-molecule and biochemical techniques, we demonstrate
      that each ATPase remodels its DNA-protein complex and translocates along DNA
      without looping it, leading to a collision complex in which the nuclease domains
      are distal. Sequencing of the products of single cleavage events suggests a
      previously undescribed endonuclease model, where multiple, stochastic
      strand-nicking events combine to produce DNA scission.
AU  - Chand MK
AU  - Nirwan N
AU  - Diffin FM
AU  - van Aelst K
AU  - Kulkarni M
AU  - Pernstich C
AU  - Szczelkun MD
AU  - Saikrishnan K
PT  - Journal Article
TA  - Nat. Chem. Biol.
JT  - Nat. Chem. Biol.
SO  - Nat. Chem. Biol. 2015 11: 870-877.

PMID- 26966212
VI  - 4
DP  - 2016
TI  - Genome Sequencing of Serinicoccus chungangensis Strain CD08_5 Isolated from Duodenal Mucosa of a Celiac Disease Patient.
PG  - e00043-16
AB  - For the first time, we report here the 3.5-Mb genome of Serinicoccus chungangensis strain
      CD08_5, isolated from duodenal mucosa from a celiac disease
      (CD) patient. The specific annotations obtained revealed genes associated with
      virulence, disease, and defense, which predict its probable role in the
      pathogenesis of CD.
AU  - Chander AM
AU  - Kaur G
AU  - Nair RG
AU  - Dhawan DK
AU  - Kochhar R
AU  - Mayilraj S
AU  - Bhadada SK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00043-16.

PMID- 29074657
VI  - 5
DP  - 2017
TI  - Genome Sequence of Kocuria polaris Strain CD08_4, an Isolate from the Duodenal Mucosa of a Celiac Disease Patient.
PG  - e01158-17
AB  - We report here the 3.8-Mb genome sequence of Kocuria polaris strain CD08_4, an isolate from
      the duodenal mucosa of a celiac disease patient. The genome consists
      of specific virulence determinant genes, antibiotic resistance genes, genes for
      coping with oxidative stress, and genes responsible for iron acquisition and
      metabolism, suggestive of its pathogenic attributes.
AU  - Chander AM
AU  - Kumari M
AU  - Kochhar R
AU  - Dhawan DK
AU  - Bhadada SK
AU  - Mayilraj S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01158-17.

PMID- 27125478
VI  - 4
DP  - 2016
TI  - Genome Sequence of Kocuria palustris Strain CD07_3 Isolated from the Duodenal Mucosa of a Celiac Disease Patient.
PG  - e00210-16
AB  - We report here the 2.8-Mb genome of Kocuria palustris strain CD07_3 isolated from the duodenal
      mucosa of a celiac disease (CD) patient. The genome of the bacterium
      consists of specific virulence factor genes and antibiotic resistance genes that
      depict its pathogenic potential.
AU  - Chander AM
AU  - Nair RG
AU  - Kaur G
AU  - Kochhar R
AU  - Mayilraj S
AU  - Dhawan DK
AU  - Bhadada SK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00210-16.

PMID- 25745003
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Filamentous Marine Cyanobacterium Lyngbya confervoides Strain BDU141951.
PG  - e00066-15
AB  - Lyngbya confervoides strain BDU141951 is a fast-growing, unicellular, marine, nonheterocystous
      cyanobacterium forming long unbranched filaments inside sheaths.
      Here, we report the draft genome assembly of Lyngbya confervoides BDU141951 for
      the first time. The genome size is 8,799,693 bp and has 6,093 putative
      protein-coding genes assembled into 298 scaffolds.
AU  - Chandrababunaidu MM
AU  - Sen D
AU  - Tripathy S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00066-15.

PMID- 25700407
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Tolypothrix boutellei Strain VB521301.
PG  - e00001-15
AB  - We report here the draft genome sequence of the filamentous nitrogen-fixing cyanobacterium
      Tolypothrix boutellei strain VB521301. The organism is lipid rich  and hydrophobic and
      produces polyunsaturated fatty acids which can be harnessed for industrial purpose. The draft
      genome sequence assembled into 11,572,263 bp with 70 scaffolds and 7,777 protein coding genes.
AU  - Chandrababunaidu MM
AU  - Singh D
AU  - Sen D
AU  - Bhan S
AU  - Das S
AU  - Gupta A
AU  - Adhikary SP
AU  - Tripathy S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00001-15.

PMID- 26506267
VI  - 428
DP  - 2016
TI  - Origins of Programmable Nucleases for Genome Engineering.
PG  - 963-989
AB  - Genome engineering with programmable nucleases depends on cellular responses to a targeted
      double-strand break (DSB). The first truly targetable reagents were the
      zinc finger nucleases (ZFNs) showing that arbitrary DNA sequences could be
      addressed for cleavage by protein engineering, ushering in the breakthrough in
      genome manipulation. ZFNs resulted from basic research on zinc finger proteins
      and the FokI restriction enzyme (which revealed a bipartite structure with a
      separable DNA-binding domain and a non-specific cleavage domain). Studies on the
      mechanism of cleavage by 3-finger ZFNs established that the preferred substrates
      were paired binding sites, which doubled the size of the target sequence
      recognition from 9 to 18bp, long enough to specify a unique genomic locus in
      plant and mammalian cells. Soon afterwards, a ZFN-induced DSB was shown to
      stimulate homologous recombination in cells. Transcription activator-like
      effector nucleases (TALENs) that are based on bacterial TALEs fused to the FokI
      cleavage domain expanded this capability. The fact that ZFNs and TALENs have been
      used for genome modification of more than 40 different organisms and cell types
      attests to the success of protein engineering. The most recent technology
      platform for delivering a targeted DSB to cellular genomes is that of the
      RNA-guided nucleases, which are based on the naturally occurring Type II
      prokaryotic CRISPR-Cas9 system. Unlike ZFNs and TALENs that use protein motifs
      for DNA sequence recognition, CRISPR-Cas9 depends on RNA-DNA recognition. The
      advantages of the CRISPR-Cas9 system-the ease of RNA design for new targets and
      the dependence on a single, constant Cas9 protein-have led to its wide adoption
      by research laboratories around the world. These technology platforms have
      equipped scientists with an unprecedented ability to modify cells and organisms
      almost at will, with wide-ranging implications across biology and medicine.
      However, these nucleases have also been shown to cut at off-target sites with
      mutagenic consequences. Therefore, issues such as efficacy, specificity and
      delivery are likely to drive selection of reagents for particular purposes. Human
      therapeutic applications of these technologies will ultimately depend on risk
      versus benefit analysis and informed consent.
AU  - Chandrasegaran S
AU  - Carroll D
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2016 428: 963-989.

PMID- 3063606
VI  - 70
DP  - 1988
TI  - Cloning and sequencing the HinfI restriction and modification genes.
PG  - 387-392
AB  - The HinfI restriction and modification genes were cloned on a 3.9-kb PstI
      fragment inserted into the PstI site of plasmid pBR322.  Both genes are
      confined to an internal 2.3-kb BclI-AvaI subfragment.  This subfragment was
      sequenced.  Two large open reading frames (ORF's) are present.  ORF1 codes for
      the methylase [predicted 359 amino acids (aa)] and ORF2 codes for the
      endonuclease (predicted 252 or 272 aa).
AU  - Chandrasegaran S
AU  - Lunnen KD
AU  - Smith HO
AU  - Wilson GG
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 70: 387-392.

PMID- 
VI  - 1
DP  - 1988
TI  - Amino acid sequence homologies among twenty-five restriction endonucleases and methylases.
PG  - 149-156
AB  - The amino acid sequences of 17 DNA methylases were compared. They show extensive homologies
      that tend to cluster in distinct groups sharing similar DNA recognition sequences. Altogether
      they fall into 5 groups: (I) M.Dam(GATC), M.DpnII(GATC), M.T4(GATC), and M.EcoRV(GATATC) show
      extensive homology (28% to 34%). (II) M.HinfI(GANTC) and M.HhaII(GANTC) are 18.8% homologous
      in 128 amino acids of their amino-terminal regions. (III) M.TaqI(TCGA), M.CviBIII(TCGA),
      M.PaeR7I(CTCGAG) and M.PstI(CTGCAG) show regions of homology ranging from 103 to 128 residues
      in length with amino acid sequence identities of 22% to 28%. (IV) M.BspRI(GGCC),
      M.BsuRI(GGCC), M.SPR(GGCC, CCGG, CC(A/T)GG), M.EcoRII(CC(A/T)GG), M.Phi3T(GGCC,GCNGC) and
      M.HhaI(GCGC) show extensive homologies ranging from 22% to 66% in regions ranging from 25% to
      100% of their lengths. (V)M.EcoRI is not homologous to any of the above. All the 11 DNA
      adenine methylases contain a conserved DPPY or NPPY sequence within the homologous segments.
      This motif is probably involved in adenine recognition and AdoMet binding at the position of
      methylation. Three short regions of high homology were identified in the 6 cytosine
      methylases, namely the PC, ENVK, and RER homologies. The PC motif is believed to be involved
      in the catalytic mechanism of the cytosine methylases. Eight restriction enzyme sequences were
      also compared. No clearly significant homologies were observed. The restriction enzymes did
      not show homology to the methylases.
AU  - Chandrasegaran S
AU  - Smith HO
PT  - Journal Article
TA  - Structure and Expression. From Proteins to Ribosomes.
JT  - Structure and Expression. From Proteins to Ribosomes.
SO  - Structure and Expression. From Proteins to Ribosomes. 1988 1: 149-156.

PMID- 2835764
VI  - 1
DP  - 1986
TI  - Preliminary x-ray diffraction analysis of HhaII endonuclease-DNA cocrystals.
PG  - 263-266
AB  - HhaII restriction endonuclease purified from an overproducing recombinant E.
      coli clone has been cocrystallized with a heptanucleotide duplex,
      d-GGAGTCC:GGACTCC.  The cocrystals are monoclonic and belong to the space group
      C2.  The unit cell dimensions are a = 199.0+/-1.0 angstrom, b = 100.0+/-0.5
      angstrom, c = 80.3+/-0.4 angstrom, and b = 101.0+/-1.0o.  There appear to be
      two dimers per asymmetric unit and the crystals diffract to 4-angstrom
      resolution.
AU  - Chandrasegaran S
AU  - Smith HO
AU  - Amzel ML
AU  - Ysern X
PT  - Journal Article
TA  - Proteins
JT  - Proteins
SO  - Proteins 1986 1: 263-266.

PMID- 10494832
VI  - 380
DP  - 1999
TI  - Chimeric restriction enzymes: What is next?
PG  - 841-848
AB  - Chimeric restriction enzymes are a novel class of engineered nucleases in which the
      non-specific DNA cleavage domain of Fokl (a type IIS restriction endonuclease) is fused to
      other DNA-binding motifs. The latter include the three common eukaryotic DNA-binding motifs,
      namely the helix-turn-helix motif, the zinc finger motif and the basic helix-loop-helix
      protein containing a leucine zipper motif. Such chimeric nucleases have been shown to make
      specific cuts in vitro very close to the expected recognition sequences. The most important
      chimeric nucleases are those based on zinc finger DNA-binding proteins because of their
      modular structure. Recently, one such chimeric nuclease, Zif-QQR-F(N) was shown to find and
      cleave its target in vivo. This was tested by microinjection of DNA substrates and the enzyme
      into frog oocytes (Carroll et al., 1999). The injected enzyme made site-specific double-strand
      breaks in the targets even after assembly of the DNA into chromatin. In addition, this
      cleavage activated the target molecules for efficient homologous recombination. Since the
      recognition specificity of zinc fingers can be manipulated experimentally, chimeric nucleases
      could be engineered so as to target a specific site within a genome. The availability of such
      engineered chimeric restriction enzymes should make it feasible to do genome engineering, also
      commonly referred to as gene therapy.
AU  - Chandrasegaran S
AU  - Smith J
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1999 380: 841-848.

PMID- 3248721
VI  - 74
DP  - 1988
TI  - Overproduction and purification of the M.HhaII methyltransferase from Haemophilus haemolyticus.
PG  - 15-21
AB  - The HhaII methyltransferase gene from Haemophilus haemolyticus was subcloned in
      an expression vector under control of the hybrid trp-lac promoter.  Induction
      with isopropyl-Beta-D-thiogalactopyranoside results in overproduction of the
      methyltransferase to about 3% of total cellular protein.  The methyltransferase
      was purified to near electrophoretic homogeneity by phosphocellulose, DEAE, and
      gel chromatography.  Its monomer Mr by sodium dodecyl sulfate-polyacrylamide
      gel electrophoresis is 25 kDa, in good agreement with that predicted from the
      nucleotide sequence.  Crystals of the methyltransferase were obtained in the
      presence of a two-fold molar excess of the duplex oligodeoxynucleotide
      substrate 5'd-GGACTCC/CCTGAGG.
AU  - Chandrasegaran S
AU  - Wu LP
AU  - Valda E
AU  - Smith HO
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 15-21.

PMID- 8604336
VI  - 24
DP  - 1996
TI  - Restriction enzyme HincII is sensitive to methylation of cytosine that occurs 5' to the recognition sequence.
PG  - 1045-1046
AB  - In this paper we demonstrate that the HincII restriction endonuclease, in addition to being
      sensitive to methylation of the 3' A and C residues, is also sensitive to methylation of a
      cytosine immediately 5' to the recognition sequence.  Having encountered this property in
      one of the sites in the mouse c-fos gene, we confirmed the sensitivity of HincII to the 5'
      cytosine methylation in in vitro methylated pUC12, pBR322 and pfos-1 plasmids.
AU  - Chandrasekhar K
AU  - Raman R
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1996 24: 1045-1046.

PMID- 
VI  - 3
DP  - 1999
TI  - Purification and characterization of restriction endonuclease BasI from Bacillus species.
PG  - 225-229
AB  - After screening a variety of bacteria from soil for the DNA cleavage activity, a type II
      restriction endonuclease, BasI was isolated and characterized from a Bacillus species.  Using
      the purified enzyme the recognition sequence was determined.  The enzyme functions efficiently
      at low ionic strength, narrow pH range and at the optimum temperature of 30oC.
AU  - Chandrashekaran S
AU  - Babu P
AU  - Nagaraja V
PT  - Journal Article
TA  - J. Biochem. Mol. Biol. Biophys.
JT  - J. Biochem. Mol. Biol. Biophys.
SO  - J. Biochem. Mol. Biol. Biophys. 1999 3: 225-229.

PMID- 
VI  - 24
DP  - 1999
TI  - Characterization of DNA binding activities of over-expressed KpnI restriction endonuclease and modification methylase.
PG  - 269-277
AB  - The genes encoding the KpnI restriction endonuclease and methyltransferase from Klebsiella
      pneumoniae have been cloned and expressed in Escherichia coli using a two plasmid strategy.
      The gene for KpnI methylase with its promoter was cloned and expressed in pACYC184.  Even
      though the methylase clone is in a low copy number plasmid pACMK, high level expression of
      methylase is achieved.  A hyper-expressing clone of KpnI endonuclease, pETRK was engineered by
      cloning the R gene into the T7 expression system.  This strategy resulted in over-expression
      of KpnI endonuclease to about 15-30% of cellular protein.  Both the enzymes were purified
      using a single chromatographic step to apparent homogeneity.  The yield of purified
      endonuclease and methylase from one liter of culture was approximately 30 and 6 mg
      respectively.  Electrophoretic mobility shift assays show that both the enzymes are capable of
      binding to specific recognition sequence in the absence of any cofactors.  The complexes of
      KpnI methyl transferase and endonuclease with their cognate site exhibit distinctive behavior
      with respect to ionic requirement.
AU  - Chandrashekaran S
AU  - Babu P
AU  - Nagaraja V
PT  - Journal Article
TA  - J. Biosci.
JT  - J. Biosci.
SO  - J. Biosci. 1999 24: 269-277.

PMID- 15192117
VI  - 32
DP  - 2004
TI  - KpnI restriction endonuclease and methyltransferase exhibit contrasting mode of sequence recognition.
PG  - 3148-3155
AB  - The molecular basis of the interaction of KpnI restriction endonuclease (REase) and the
      corresponding methyltransferase (MTase) at their cognate recognition sequence is investigated
      using a range of footprinting techniques. DNase I protection analysis with the REase reveals
      the protection of a 14-18 bp region encompassing the hexanucleotide recognition sequence. The
      MTase, in contrast, protects a larger region. KpnI REase contacts two adjacent guanine
      residues and the single adenine residue in both the strands within the recognition sequence
      5'-GGTACC-3', inferred by dimethylsulfate (DMS) protection, interference and missing
      nucleotide interference analysis. In contrast, KpnI MTase does not show elaborate
      base-specific contacts. Ethylation interference analysis also showed the differential
      interaction of REase and MTase with phosphate groups of three adjacent bases on both strands
      within the recognition sequence. The single thymine residue within the sequence is hyper-
      reactive to the permanganate oxidation, consistent with MTase-induced base flipping. The REase
      on the other hand does not show any major DNA distortion. The results demonstrate that the
      differences in the molecular interaction pattern of the two proteins at the same recognition
      sequence reflect the contrasting chemistry of DNA cleavage and methylation catalyzed by these
      two dissimilar enzymes, working in combination as constituents of a cellular defense strategy.
AU  - Chandrashekaran S
AU  - Manjunatha UH
AU  - Nagaraja V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2004 32: 3148-3155.

PMID- 15375161
VI  - 279
DP  - 2004
TI  - Ca2+-mediated site-specific DNA cleavage and suppression of promiscuous activity of KpnI restriction endonuclease.
PG  - 49736-49740
AB  - The characteristic feature of type II restriction endonucleases (REases) is their exquisite
      sequence specificity and obligate Mg2+
      requirement for catalysis. Efficient cleavage of DNA only in the
      presence of Ca2+ ions, comparable with that of Mg2+, is previously not
      described. Most intriguingly, KpnI REase exhibits Ca2+-dependent
      specific DNA cleavage. Moreover, the enzyme is highly promiscuous in
      its cleavage pattern on plasmid DNAs in the presence of Mn2+ or Mg2+,
      with the complete suppression of promiscuous activity in the presence
      of Ca2+. KpnI methyltransferase does not exhibit promiscuous activity
      unlike its cognate REase. The REase binds to oligonucleotides
      containing canonical and mapped noncanonical sites with comparable
      affinities. However, the extent of cleavage is varied depending on the
      metal ion and the sequence. The ability of the enzyme to be promiscuous
      or specific may reflect an evolutionary design. Based on the results,
      we suggest that the enzyme KpnI represents an REase evolving to attain
      higher sequence specificity from an ancient nonspecific nuclease.
AU  - Chandrashekaran S
AU  - Saravanan M
AU  - Radha DR
AU  - Nagaraja V
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2004 279: 49736-49740.

PMID- 
VI  - 77
DP  - 1999
TI  - Identification and characterization of a type II restriction endonuclease, StrI from Streptomyces thermodiastaticus.
PG  - 273-276
AB  - A new type II restriction endonuclease, StrI has been identified from Streptomyces
      thermodiastaticus.  The enzyme has been purified using three column chromatography steps.  The
      enzyme recognizes a hexanucleotide sequence and cleaves DNA 5'-C/TCGAG-3' as indicated.  The
      optimum temperature, pH, and cation requirements for the enzyme activity were determined.
AU  - Chandrashekaran S
AU  - Shankar AB
AU  - Babu P
AU  - Paul BD
AU  - Nagaraja V
PT  - Journal Article
TA  - Curr. Sci.
JT  - Curr. Sci.
SO  - Curr. Sci. 1999 77: 273-276.

PMID- 9628359
VI  - 379
DP  - 1998
TI  - Design of a novel regulatory circuit for expression of restriction endonucleases.
PG  - 579-582
AB  - We have developed a new strategy with a very tight control for the expression of cloned genes.
      The system employed here is the T7 promoter-based expression system in which transcription
      activator protein C of bacteriophage Mu (Mu C) has been cloned to serve as a repressor in the
      regulatory circuit.  The system also includes pLysE, which encodes T7 lysozyme, an inhibitor
      of T7 RNA polymerase.  This ensures tight regulation of cloned genes in the uninduced state.
      Upon induction, the expressed Mu C protein binds to its cognate site thereby repressing lys
      transcription driven by the tet promoter.  In order to evaluate the tight control achieved in
      the system, and to check leaky expression, if any, we have cloned the gene for the SmaI
      restriction endonuclease without its cognate methylase.  For this purpose, a dicistronic unit
      was constructed by cloning the smaIR gene downstream of the Mu C gene.  SmaI expression was
      observed only in the induced cell extracts, demonstrating a tight control.  The system could
      be used to express the genes of other cloned restriction enzymes and has the potential for
      general applications.
AU  - Chandrashekharan S
AU  - Paul BD
AU  - Nagaraja V
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1998 379: 579-582.

PMID- 23405294
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences and Annotation of Enterococcus faecium Strain LCT-EF20.
PG  - e00083-12
AB  - The space environment is reported to cause biological alterations in microorganisms, such as
      growth, drug resistance, and virulence. Here, we present the model of Enterococcus faecium to
      investigate the effects of space conditions on the microbe and on the whole-genome sequences
      of the strain LCT-EF20 after being exposed to space flight.
AU  - Chang D
AU  - Zhu Y
AU  - Chen J
AU  - Fang X
AU  - Li T
AU  - Wang J
AU  - Guo Y
AU  - Su L
AU  - Xu G
AU  - Wang Y
AU  - Chen Z
AU  - Liu C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00083-12.

PMID- 23409254
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences of the Enterococcus faecium Strain LCT-EF258.
PG  - e00147-12
AB  - The space environment has been shown to affect microbes by altering various features,
      including morphology, growth rate, metabolism, virulence, drug
      resistance, and gene expression and mutation. Here we present the draft genome
      sequence of the Enterococcus faecium strain LCT-EF258, derived from the E.
      faecium strain CGMCC 1.1736, which was exposed to 17-day space flight.
AU  - Chang D
AU  - Zhu Y
AU  - Fang X
AU  - Li T
AU  - Wang J
AU  - Guo Y
AU  - Su L
AU  - Liu Y
AU  - Jiang X
AU  - Wang L
AU  - Guo N
AU  - Liu C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00147-12.

PMID- 22689242
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Enterococcus faecium Strain LCT-EF90.
PG  - 3556-3557
AB  - Enterococcus faecium is an opportunistic human pathogen, found widely in the human
      gastrointestinal tract, and can also be isolated from a variety of plants,
      animals, insects, and other environmental sources. Here, we present the fine
      draft genome sequence of E. faecium LCT-EF90.
AU  - Chang D
AU  - Zhu Y
AU  - Zou Y
AU  - Fang X
AU  - Li T
AU  - Wang J
AU  - Guo Y
AU  - Su L
AU  - Xia J
AU  - Yang R
AU  - Fang C
AU  - Liu C
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3556-3557.

PMID- 25573930
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Bordetella trematum Strain HR18.
PG  - e01357-14
AB  - The genus Bordetella is reportedly a human or animal pathogen and environmental microbe. We
      report the draft genome sequence of Bordetella trematum strain HR18,
      which was isolated from the rumen of Korean native cattle (Hanwoo; Bos taurus
      coreanae). It is the first genome sequence of a Bordetella sp. isolated from the
      rumen of cattle.
AU  - Chang DH
AU  - Jin TE
AU  - Rhee MS
AU  - Jeong H
AU  - Kim S
AU  - Kim BC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01357-14.

PMID- 25573931
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Acinetobacter sp. HR7, Isolated from Hanwoo, Korean Native Cattle.
PG  - e01358-14
AB  - Acinetobacter species have been reported as opportunistic pathogens. Here, we report the draft
      genome sequence of Acinetobacter sp. HR7 isolated from the rumen
      of cannulated Korean native cattle (Hanwoo; Bos taurus coreanae).
AU  - Chang DH
AU  - Rhee MS
AU  - Jeong H
AU  - Kim S
AU  - Kim BC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01358-14.

PMID- 22933753
VI  - 194
DP  - 2012
TI  - Genome Sequence of n-Alkane-Degrading Hydrocarboniphaga effusa Strain AP103T (ATCC BAA-332T).
PG  - 5120
AB  - Hydrocarboniphaga effusa strain AP103(T) (ATCC BAA-332(T)) is a member of the
      Gammaproteobacteria utilizing n-alkanes as the sole source of carbon and energy.
      Here we report the draft genome sequence of AP103(T), which consists of 5,193,926
      bp with a G + C content of 65.18%.
AU  - Chang HK
AU  - Zylstra GJ
AU  - Chae JC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5120.

PMID- 337302
VI  - 74
DP  - 1977
TI  - In vivo site-specific genetic recombination promoted by the EcoRI restriction endonuclease.
PG  - 4811-4815
AB  - Site-specific genetic recombination promoted in vivo by the EcoRI endonuclease
      has been demonstrated by using constructed hybrid plasmids in which the
      chloramphenicol resistance gene was inactivated by insertion of DNA fragments
      at an EcoRI site within the gene.  Such recombination can involve either the
      joining of intracellularly generated cohesive termini of the same DNA fragment
      or intermolecular ligation of different DNA fragments.  DNA cleavage and
      ligation in vivo are precise: recombinant DNA molecules show functional
      continuity of the gene sequence cleaved by the enzyme and regeneration of
      nucleotide recognition sites for both the EcoRI endonuclease and the EcoRI DNA
      methylase.  In other experiments, EcoRI-generated fragments of eukaryotic DNA
      that had not been modified by the Escherichia coli K methylase were shown to be
      taken up by bacterial cells and to undergo intracellular ligation to segments
      of bacterial plasmid DNA.
AU  - Chang S
AU  - Cohen SN
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1977 74: 4811-4815.

PMID- 28770030
VI  - 12
DP  - 2017
TI  - The complete genome sequence of the cold adapted crude-oil degrader: Pedobacter steynii DX4.
PG  - 45
AB  - Pedobacter steynii DX4 was isolated from the soil of Tibetan Plateau and it can use crude oil
      as sole carbon and energy source at 15 degrees C. The genome of
      Pedobacter steynii DX4 has been sequenced and served as basis for analysis its
      metabolic mechanism. It is the first genome of crude oil degrading strain in
      Pedobacter genus. The 6.58 Mb genome has an average G + C content of 41.31% and
      encodes 5464 genes. In addition, annotation revealed that Pedobacter steynii DX4
      has cold shock proteins, abundant response regulators for cell motility, and
      enzymes involved in energy conversion and fatty acid metabolism. The genomic
      characteristics could provide information for further study of oil-degrading
      microbes for recovery of crude oil polluted environment.
AU  - Chang S
AU  - Zhang G
AU  - Chen X
AU  - Long H
AU  - Wang Y
AU  - Chen T
AU  - Liu G
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 45.

PMID- 26607900
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of a 16SrII-A Subgroup Phytoplasma Associated with Purple Coneflower (Echinacea purpurea) Witches' Broom Disease in Taiwan.
PG  - e01398-15
AB  - The bacterial genus 'Candidatus Phytoplasma' contains a group of insect-transmitted plant
      pathogens in the class Mollicutes. Here, we report a
      draft genome assembly and annotation of strain NCHU2014, which belongs to the
      16SrII-A subgroup within this genus and is associated with purple coneflower
      witches' broom disease in Taiwan.
AU  - Chang SH
AU  - Cho ST
AU  - Chen CL
AU  - Yang JY
AU  - Kuo CH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01398-15.

PMID- 25977427
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequence of Aquamicrobium sp. Strain SK-2, a Polychlorinated Biphenyl-Utilizing Bacterium Isolated from Sewage Sludge.
PG  - e00439-15
AB  - Here, we report the whole-genome sequence of Aquamicrobium sp. strain SK-2, a bacterium which
      can use 2,2',4,4',5,5'-hexachlorobiphenyl as the sole carbon
      source for its growth. An approximately 9.23-Mb genome sequence of SK-2 will
      greatly facilitate research efforts regarding the study of the polychlorinated
      biphenyl (PCB) degradation mechanism.
AU  - Chang YC
AU  - Sawada K
AU  - Kim ES
AU  - Jung K
AU  - Kikuchi S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00439-15.

PMID- 22180814
VI  - 5
DP  - 2011
TI  - Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21).
PG  - 97-111
AB  - Ktedonobacter racemifer corrig. Cavaletti et al. 2007 is the type species of the  genus
      Ktedonobacter, which in turn is the type genus of the family
      Ktedonobacteraceae, the type family of the order Ktedonobacterales within the
      class Ktedonobacteria in the phylum 'Chloroflexi'. Although K. racemifer shares
      some morphological features with the actinobacteria, it is of special interest
      because it was the first cultivated representative of a deep branching
      unclassified lineage of otherwise uncultivated environmental phylotypes
      tentatively located within the phylum 'Chloroflexi'. The aerobic, filamentous,
      non-motile, spore-forming Gram-positive heterotroph was isolated from soil in
      Italy. The 13,661,586 bp long non-contiguous finished genome consists of ten
      contigs and is the first reported genome sequence from a member of the class
      Ktedonobacteria. With its 11,453 protein-coding and 87 RNA genes, it is the
      largest prokaryotic genome reported so far. It comprises a large number of
      over-represented COGs, particularly genes associated with transposons, causing
      the genetic redundancy within the genome being considerably larger than expected
      by chance. This work is a part of the Genomic Encyclopedia of Bacteria and
      Archaea project.
AU  - Chang YJ et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 5: 97-111.

PMID- 21304687
VI  - 3
DP  - 2010
TI  - Complete genome sequence of Acidaminococcus fermentans type strain (VR4).
PG  - 1-14
AB  - Acidaminococcus fermentans (Rogosa 1969) is the type species of the genus Acidaminococcus, and
      is of phylogenetic interest because of its isolated
      placement in a genomically little characterized region of the Firmicutes. A.
      fermentans is known for its habitation of the gastrointestinal tract and its
      ability to oxidize trans-aconitate. Its anaerobic fermentation of glutamate has
      been intensively studied and will now be complemented by the genomic basis. The
      strain described in this report is a nonsporulating, nonmotile, Gram-negative
      coccus, originally isolated from a pig alimentary tract. Here we describe the
      features of this organism, together with the complete genome sequence, and
      annotation. This is the first complete genome sequence of a member of the family
      Acidaminococcaceae, and the 2,329,769 bp long genome with its 2,101
      protein-coding and 81 RNA genes is part of the Genomic Encyclopedia of Bacteria
      and Archaea project.
AU  - Chang YJ et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 3: 1-14.

PMID- 12427957
VI  - 148
DP  - 2002
TI  - Identification of strain-specific genes located outside the plasticity zone in nine clinical isolates of Helicobacter pylori.
PG  - 3671-3680
AB  - Helicobacter pylori is a Gram-negative bacterium that is associated with
      the development of peptic ulcers and gastric carcinoma in humans. This
      species appears to be one of the most genetically variable bacteria
      described to date. The overall level of heterogeneity within strains of
      this organism was determined by comparing the genome sequences of two
      reference strains, J99 and 26695. The aim of this study was to measure the
      genetic diversity within strains of H. pylori by looking for
      strain-specific genes in nine H. pylori strains isolated from patients
      suffering from chronic gastritis (n=3), duodenal ulcers (n=3) or gastric
      cancer (n=3). Seven loci that contained strain-specific genes in strains
      J99 and 26695 were studied. These regions were subsequently amplified from
      most of the clinical isolates studied and their sequences were determined.
      ORFs were predicted from the sequence data and were compared to sequences
      within the databases. The results showed that the genes flanking the ORFs
      specific to either strain J99 or strain 26695 were also present in a
      similar configuration in the genomes of the nine clinical isolates.
      Moreover, in most regions, ORFs homologous to those found in the
      corresponding loci in the two reference strains were detected. However, in
      10 regions, genes similar to those located at another locus in the genome
      of J99 or 26695 were found. Finally, six strain-specific genes were
      identified in three regions of three of the H. pylori strains isolated
      from patients with duodenal ulcers (n=2) and gastric cancer (n=1). Of
      these six genes, five were putative genes and one was an orthologue of a
      gene encoding a transposase in Thermotoga maritima. However, no
      association with disease was found for these genes.
AU  - Chanto G
AU  - Occhialini A
AU  - Gras N
AU  - Alm RA
AU  - Megraud F
AU  - Marais A
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2002 148: 3671-3680.

PMID- 28729271
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequence of Acinetobacter pittii HUMV-6483 Isolated from Human Urine.
PG  - e00658-17
AB  - Acinetobacter pittii strain HUMV-6483 was obtained from urine from an adult patient. We report
      here its complete genome assembly using PacBio single-molecule
      real-time sequencing, which resulted in a chromosome with 4.07 Mb and a circular
      contig of 112 kb. About 3,953 protein-coding genes are predicted from this
      assembly.
AU  - Chapartegui-Gonzalez I
AU  - Lazaro-Diez M
AU  - Redondo-Salvo S
AU  - Alted-Perez L
AU  - Ocejo-Vinyals JG
AU  - Navas J
AU  - Ramos-Vivas J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00658-17.

PMID- 28883133
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Iridescent Marine Bacterium Cellulophaga lytica CECT 8139.
PG  - e00811-17
AB  - Some species of the genus Cellulophaga have been reported as having biotechnological interests
      and noteworthy physiological properties. We report
      here the draft genome sequence of Cellulophaga lytica CECT 8139, a bacterium that
      produces an intensely iridescent colony biofilm on agar surfaces.
AU  - Chapelais-Baron M
AU  - Goubet I
AU  - Duchaud E
AU  - Rosenfeld E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00811-17.

PMID- 24604645
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Coprobacter fastidiosus NSB1T.
PG  - e00122-14
AB  - Coprobacter fastidiosus is a Gram-negative obligate anaerobic bacterium belonging to the
      phylum Bacteroidetes. In this work, we report the draft genome sequence of
      C. fastidiosus strain NSB1(T) isolated from human infant feces.
AU  - Chaplin AV
AU  - Efimov BA
AU  - Khokhlova EV
AU  - Kafarskaia LI
AU  - Tupikin AE
AU  - Kabilov MR
AU  - Shkoporov AN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00122-14.

PMID- 26272572
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Lactobacillus fermentum NB-22.
PG  - e00896-15
AB  - We announce here a draft genome sequence of Lactobacillus fermentum NB-22, a strain isolated
      from human vaginal microbiota. The assembled sequence consists of
      190 contigs, joined into 137 scaffolds, and the total size is 2.01 Mb.
AU  - Chaplin AV
AU  - Shkoporov AN
AU  - Efimov BA
AU  - Pikina AP
AU  - Borisova OY
AU  - Gladko IA
AU  - Postnikova EA
AU  - Lordkipanidze AE
AU  - Kafarskaia LI
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00896-15.

PMID- 20228792
VI  - 464
DP  - 2010
TI  - The dynamic genome of Hydra.
PG  - 592-596
AB  - The freshwater cnidarian Hydra was first described in 1702 and has been the object of study
      for 300 years. Experimental studies of Hydra between 1736 and 1744 culminated in the discovery
      of asexual reproduction of an animal by budding, the first description of regeneration in an
      animal, and successful transplantation of tissue between animals. Today, Hydra is an important
      model for studies of axial patterning, stem cell biology and regeneration. Here we report the
      genome of Hydra magnipapillata and compare it to the genomes of the anthozoan Nematostella
      vectensis and other animals. The Hydra genome has been shaped by bursts of transposable
      element expansion, horizontal gene transfer, trans-splicing, and simplification of gene
      structure and gene content that parallel simplification of the Hydra life cycle. We also
      report the sequence of the genome of a novel bacterium stably associated with H.
      magnipapillata. Comparisons of the Hydra genome to the genomes of other animals shed light on
      the evolution of epithelia, contractile tissues, developmentally regulated transcription
      factors, the Spemann-Mangold organizer, pluripotency genes and the neuromuscular junction.
AU  - Chapman JA et al
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2010 464: 592-596.

PMID- 22247525
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of the Virulent Strain 01-B526 of the Fish Pathogen Aeromonas salmonicida.
PG  - 722-723
AB  - Aeromonas salmonicida is an important fish pathogen, mainly of salmonids. This bacterium
      causes a disease named furunculosis, which is particularly
      detrimental for the aquaculture industry. Here, we present the draft
      genome sequence of A. salmonicida 01-B526, a strain isolated from a brook
      trout that is more virulent than A. salmonicida reference strain A449, for
      which a genome sequence is available.
AU  - Charette SJ
AU  - Brochu F
AU  - Boyle B
AU  - Filion G
AU  - Tanaka KH
AU  - Derome N
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 722-723.

PMID- 23072412
VI  - 8
DP  - 2013
TI  - Selective enrichment of environmental DNA libraries for genes encoding nonribosomal peptides and polyketides by phosphopantetheine transferase-dependent complementation of siderophore biosynthesis.
PG  - 138-143
AB  - The cloning of DNA directly from environmental samples provides a means to
      functionally access biosynthetic gene clusters present in the genomes of the
      large fraction of bacteria that remains recalcitrant to growth in the laboratory.
      Herein, we demonstrate a method by which complementation of phosphopantetheine
      transferase deletion mutants can be used to restore siderophore biosynthesis and
      to therefore selectively enrich eDNA libraries for nonribosomal peptide
      synthetase (NRPS) and polyketide synthase (PKS) gene sequences to unprecedented
      levels. The common use of NRPS/PKS-derived siderophores across bacterial taxa
      makes this method generalizable and should allow for the facile selective
      enrichment of NRPS/PKS-containing biosynthetic gene clusters from large
      environmental DNA libraries using a wide variety of phylogenetically diverse
      bacterial hosts.
AU  - Charlop-Powers Z
AU  - Banik JJ
AU  - Owen JG
AU  - Craig JW
AU  - Brady SF
PT  - Journal Article
TA  - ACS Chem. Biol.
JT  - ACS Chem. Biol.
SO  - ACS Chem. Biol. 2013 8: 138-143.

PMID- 28774978
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Cronobacter sakazakii GP1999, Sequence Type 145, an Epiphytic Isolate Obtained from the Tomato's Rhizoplane/Rhizosphere Continuum.
PG  - e00723-17
AB  - We present here the draft genome of Cronobacter sakazakii GP1999, a sequence type 145 strain
      isolated from the rhizosphere of tomato plants. Assembly and
      annotation of the genome resulted in a genome of 4,504,670 bp in size, with 4,148
      coding sequences, and a GC content of 56.8%.
AU  - Chase HR
AU  - Eberl L
AU  - Stephan R
AU  - Jeong H
AU  - Lee C
AU  - Finkelstein S
AU  - Negrete F
AU  - Gangiredla J
AU  - Patel I
AU  - Tall BD
AU  - Gopinath GR
AU  - Lehner A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00723-17.

PMID- 27834695
VI  - 4
DP  - 2016
TI  - Genome Sequences of Malonate-Positive Cronobacter sakazakii Serogroup O:2, Sequence Type 64 Strains CDC 1121-73 and GK1025, Isolated from Human Bronchial  Wash and a Powdered Infant Formula Manufacturing Plant.
PG  - e01072-16
AB  - We introduce draft genome sequences of strains CDC1121-73 (human bronchial wash isolate) and
      GK1025 (powdered infant formula manufacturing facility isolate),
      which are both malonate-positive Cronobacter sakazakii serogroup O:2, sequence
      type 64. Assemblies for these strains have sizes of 4,442,307 and 4,599,266 bp
      and % G+C contents of 56.9 and 56.7, respectively.
AU  - Chase HR
AU  - Gopinath GR
AU  - Gangiredla J
AU  - Patel IR
AU  - Kothary MH
AU  - Carter L
AU  - Sathyamoorthy V
AU  - Lee B
AU  - Park E
AU  - Yoo YJ
AU  - Chung TJ
AU  - Choi H
AU  - Jun S
AU  - Park J
AU  - Jeong S
AU  - Kim M
AU  - Reich F
AU  - Klein G
AU  - Tall BD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01072-16.

PMID- 28082501
VI  - 5
DP  - 2017
TI  - Genome Sequence of Porphyromonas gingivalis Strain 381.
PG  - e01467-16
AB  - Porphyromonas gingivalis is associated with both oral and systemic diseases. Strain-specific
      P. gingivalis invasion phenotypes do not reliably predict disease
      presentation during in vivo studies. Here, we present the genome sequence of 381,
      a common laboratory strain, with a single contig of 2,378,872 bp and a G+C
      content of 48.36%.
AU  - Chastain-Gross RP
AU  - Xie G
AU  - Belanger M
AU  - Kumar D
AU  - Whitlock JA
AU  - Liu L
AU  - Raines SM
AU  - Farmerie WG
AU  - Daligault HE
AU  - Han CS
AU  - Brettin TS
AU  - Progulske-Fox A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01467-16.

PMID- 
VI  - 0
DP  - 1979
TI  - Some Recent Developments in Streptomyces Genetics.
PG  - 123-133
AB  - This review will be concerned with "nonchromosomal" genetics.  The omission of
      normal chromosomal genetics does not reflect a decline in its importance, but
      rather the absence of major advances since previous reviews, with the important
      exception of the development of protoplast fusion, which is dealt with by D.A.
      Hopwood elsewhere in this volume.  My approach is to consider what is known
      about the occurrence and genetic determination of "nonessential" (and therefore
      possibly plasmid-specified) functions in streptomycetes, and then to discuss
      aspects of plasmids and temperate phages relevant to the development of
      potential "recombinant DNA" systems in streptomycetes.
AU  - Chater KF
PT  - Journal Article
TA  - Genetics of Industrial Microorganisms
JT  - Genetics of Industrial Microorganisms
SO  - Genetics of Industrial Microorganisms 1979 0: 123-133.

PMID- 
VI  - 0
DP  - 1978
TI  - Restriction in Streptomyces.
PG  - 303-311
AB  - Restriction has been the subject of authoritative recent reviews, and I will
      give only a short introduction to it before pointing out its interest for the
      Streptomyces geneticist.  Many bacteria possess restriction enzymes, which are
      endodeoxy-ribonucleases that recognize specific short nucleotide sequences in
      double-stranded DNA and cleave both strands.  The cleavage sites may, like the
      recognition site, be specific (class II enzymes) or non-specific (class I
      enzymes).  The only co-factor required for class II enzymes is Mg++, whereas
      class I enzymes usually require ATP, Mg++ and S-adenosyl methionine.
      Restriction enzymes are obligatorily accompanied by so-called modifying enzymes
      that protect the cell's own DNA from endonucleolytic cleavage, by specific
      recognition and modification of the same sites as are recognized by the
      restriction enzyme.  Different species or even different wild-type isolates of
      the same species usually have restriction-modification (R-M) systems with
      different specificities.  Consequently DNA transferred from one species or
      strain to another, for example in phage infection or bacterial mating, will
      often be unprotected against endonucleolytic breakdown on entering the new host
      and may thus be inactivated.  In the case of a phage, a lower efficiency of
      plating (e.o.p.) restriction is observed on the second host.  However, incoming
      foreign DNA is also subject to host-specific modification, and if this is
      achieved before restriction, that DNA molecule is safe from endonucleolytic
      cleavage and retains its biological activity.  In the case of phage DNA the
      normal infective cycle ensues, detectable by plaque formation.  The recognition
      sites of type II enzymes are invariably palindromic, showing 2-fold rotational
      symmetry.  Moreover, cleavage been due to restriction or perhaps to
      inefficiency of pair formation between the species.  The e.o.p. of the
      temperate phage VP5 was therefore tested on the two strains and was shown to be
      independent of the previous host used for its propagation.  Either an R-M
      system was absent or, if it existed, VP5 was not susceptible to it.  It
      therefore seems that an R-M system which has recently been identified in S.
      albus G, and which will be described later, is the only one yet identified in
      Streptomycetes.
AU  - Chater KF
PT  - Journal Article
TA  - Nocardia and Streptomyces. Proceedings of the International Symposium on Nocardia and Streptomyces. Warsaw Oct 4-8 1978
JT  - Nocardia and Streptomyces. Proceedings of the International Symposium on Nocardia and Streptomyces. Warsaw Oct 4-8 1978
SO  - Nocardia and Streptomyces. Proceedings of the International Symposium on Nocardia and Streptomyces. Warsaw Oct 4-8 1978 1978 0: 303-311.

PMID- Not carried by PubMed...
VI  - 9
DP  - 1986
TI  - Streptomyces Phages and Their Applications to Streptomyces Genetics.
PG  - 119-158
AB  - Interest in Streptomyces phages was first caused by the occasional infestation
      of early antibiotic fermentation cultures.  The economic loss caused by lysed
      fermentation cultures was occasionally significant so that even today there is
      sometimes opposition to the import of Streptomyces phages into laboratories
      attached to production plants.  However, it is now clear that laboratory
      varieties of Streptomyces phages can be contained in the laboratory and turned
      to good account.  Many industrial laboratories are beginning to exploit them.
      This chapter is an account of recent developments in the study of Streptomyces
      phages and their use in genetic manipulation.  Its starting point is a fairly
      comprehensive review written several years ago (Lomovskaya et al., 1980);
      information given in detail there will be only briefly summarized here.  The
      most conspicuous advances since that time have been in, or have resulted from,
      the use of Streptomyces phages as DNA cloning vectors.  Techniques for
      isolating, assaying, and propagating Streptomyces phages from soil and from
      lysogens differ only in minor detail (related to the host's mycelial growth
      habit) from those used for eubacterial phages, which they resemble closely in
      structure and biology (Lomovskaya et al., 1980).  This resemblance is not
      surprising, since the gross molecular biology of streptomycetes is similar to
      that of other gram-positive bacteria.  Of course, there are interesting
      differences between streptomycetes and other bacteria (e.g., in morphology,
      antibiotic production, and high G + C content in DNA), and it is mainly as
      agents to help our understanding of the genetic basis of these phenomena that
      Streptomyces phages have come to be important topics of research.  Streptomyces
      phages are not the only tools available for such a purpose.  Some species of
      Streptomyces, notably S. coelicolor A3(2), have good chromosomal genetics
      (Hopwood, 1967; Hopwood et al., 1973; Hopwood and Chater, 1974; Hopwood and
      Merrick, 1977; Rhodes, this volume).  Highly efficient generalized
      recombination through protoplast fusion (Hopwood et al., 1977; Baltz, 1978) is
      broadly applicable to Streptomyces.  Transformation for chromosomal markers by
      liposome-entrapped DNA (Makins and Holt, 1981) has been reported for these
      gram-positive bacteria.  Moreover, an almost extravagant range of plasmid DNA
      cloning vectors for Streptomyces has come into use (reviewed by Chater et al.,
      1982a; Hopwood and Chater, 1982; Chater, 1983; Bib et al., 1983; Hopwood et
      al., this volume).  Streptomyces genetics has been the subject of two recent
      reviews (Chater and Hopwood, 1984; Hopwood and Chater, 1984).	This chapter will
      be almost wholly concerned with temperate phages (reflecting the bias in
      published data), and in particular with UC31, which is the most studied
      Streptomyces phage.
AU  - Chater KF
PT  - Journal Article
TA  - The Bacteria
JT  - The Bacteria
SO  - The Bacteria 1986 9: 119-158.

PMID- Not carried by PubMed...
VI  - 21
DP  - 1980
TI  - Actinophage DNA.
PG  - 65-74
AB  - Actinophage DNA is considered largely in relation to its possible uses in
      genetic engineering.  The G + C contents (determined by density) varied from 55
      to 69%.  The no. of target sites for various restriction enzymes bore some
      relation to base composition, high G + C content correlating with high
      frequencies of SalGI sites and very low frequencies of sites for EcoRI,
      HindIII, and HpaI.  Sites for BamHI and SalPI were absent from most actinophage
      DNA tested regardless of its base composition.  A transfection procedure was
      characterized, in which plaques could be visualised in soft agar overlays to
      which had been added actinophage DNA and protoplasts previously mixed in the
      presence of polyethylene glycol.  The procedure was effective with DNA of VP5,
      UC32, R4, U448, and S14 and protoplasts of Streptomyces coelicolor A3(2) or S.
      lividans 66.  	Deletion mutants of several phages (detected by virtue of their
      resistance to chelating agents) were obtained both spontaneously and after
      transfection of protoplasts with phage DNA pretreated with EcoRI and DNA
      ligase.  One deletion mutant of phage R4 lacked the single EcoRI target site,
      which is therefore dispensable and available as a DNA cloning site.  The
      occurrence of chelating-agent-resistant deletion mutants of some actinophages
      suggested that packaging of their DNA involved staggered, site-specific cutting
      of concatameric DNA.  This was corroborated by evidence that UC31, SH10, and
      probably R4 DNA molecules possess cohesive ends.
AU  - Chater KF
PT  - Journal Article
TA  - Dev. Ind. Microbiol.
JT  - Dev. Ind. Microbiol.
SO  - Dev. Ind. Microbiol. 1980 21: 65-74.

PMID- 896480
VI  - 4
DP  - 1977
TI  - A site-specific endodeoxyribonuclease from Streptomyces albus CMI 52766 sharing site-specificity with Providencia stuartii endonuclease PstI.
PG  - 1989-1998
AB  - A class II site-specific endodeoxyribonuclease (SalPI) was identified in
      cell-free extracts of Streptomyces albus CMI 52766 after high speed
      centrifugation and fractionation through BioGel A0.5M.  SalPI cleaves lambda
      DNA into at least 18 fragments.  Five cleavage sites were located in the linear
      lambda map by the use of double and triple restriction enzyme digests involving
      EcoRI, HindIII, SalGI and another new Streptomyces enzyme, SacI.  The results
      were indistinguishable from those previously obtained for a Providencia
      stuartii enzyme, PstI, by Smith, Blattner & Davies (Nucl. Acids Res. 1976 3:
      343).  SalPI and PstI were shown by a double digest test to have the same site
      specificity.  None of 34 phages tested was obviously restricted by S. albus CMI
      52766, and correspondingly DNA from two of them was not cleaved in vitro by
      SalPI.  DNA from a Streptomyces phage that does not form plaques on S. albus
      CMI 52766, and plasmid SCP2 DNA from S. coelicolor A3(2), were both cleaved.
AU  - Chater KF
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1977 4: 1989-1998.

PMID- Not included in PubMed...
VI  - 115
DP  - 1979
TI  - A New, Wide Host-range, Temperate Bacteriophage (R4) of Streptomyces and its Interaction with some Restriction-Modification Systems.
PG  - 431-442
AB  - A new temperate phage, R4, of Streptomyces was isolated from soil on a restriction-deficient
      mutant of S. albus G.  In its morphology, adsorption properties and growth kinetics R4
      resembled other temperate phages of Streptomyces though its requirements for Ca2+ and Mg2+
      were higher than usual. It was unable to form plaques above 34.5 C.  R4-mediated transduction
      was not detected.  Unlike other Streptomyces temperate phages, R4 had a wide host-range, which
      correlated better with the absence of detectable class II restriction enzymes than with
      conventional taxonomic divisions.  Many of the sensitive strains [but not, apparently, S.
      coelicolor A3(2)] could be lysogenized. With the wild-type R4, plaques were obtained on S.
      albus G only after growth on a restriction-deficient, modification-proficient mutant, and then
      only at a very low efficiency of plating.  All of these plaques were of a mutant type (R4G)
      which (unlike the parental R4 phage) showed conventional patterns of restriction-modification
      in the S. albus G (SalGI) and S. albus P (SalPI) systems.  R4G mutants, but not R4, were
      sensitive to a restriction-modification system present in two S. rimosus strains (2251 and
      NRRL 2234).  DNA from SalGI-unmodified (but not from modified) R4 or R4G was cleaved by SalGI
      into more than 30 fragments (mean size 1.35 kilobases; summed molecular weight (30.02x10^6).
      R4 DNA was cleaved at one site by EcoRI, at one site by SalPI (0 PstI), and not at all by
      HindIII or BamHI.
AU  - Chater KF
AU  - Carter AT
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1979 115: 431-442.

PMID- Not included in PubMed...
VI  - 109
DP  - 1978
TI  - Restriction of a bacteriophage in Streptomyces albus P (CMI 52766) by Endonuclease SalPI.
PG  - 181-185
AB  - Restriction has been hard to show in streptomycetes.  For example, in
      Streptomyces coelicolor A3(2) (a strain sensitive to many actinophages),
      restriction could be demonstrated only in a hybrid strain (S. coelicolor A3(2)
      X S. griseus kr.15) which possessed phage receptors from S. griseus kr.15 and a
      restriction system from S. coelicolor A3(2) (Lomovskaya et al., 1977). This
      paper reports the restriction and modification by S. albus P of a wide
      host-range temperate Streptomyces phage, R4, and it is shown that the agent of
      restriction is the endonuclease SalPI.
AU  - Chater KF
AU  - Carter AT
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1978 109: 181-185.

PMID- 977549
VI  - 128
DP  - 1976
TI  - Restriction of a bacteriophage of Streptomyces albus G involving endonuclease SalI.
PG  - 644-650
AB  - The bacteriophage Pa16, isolated from soil on Streptomyces albus G, was
      restricted when transferred from an alternative host back to S. albus G.
      Extracted unmodified Pa16 deoxyribonucleic acid was cleaved at a single site by
      a cell-free extract of S. albus G.  Fractions cleaving Pa16 deoxyribonucleic
      acid contained the endonuclease SalI first described by J. Arrand, P. Myers,
      and R.J. Roberts (unpublished data).  A mutant of S. albus G was isolated which
      was defective in both restriction and modification of Pa16.  This mutant lacked
      SalI activity.  It is concluded that SalI is the agent of restriction of Pa16
      by S. albus G.
AU  - Chater KF
AU  - Wilde LC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1976 128: 644-650.

PMID- 6246193
VI  - 116
DP  - 1980
TI  - Streptomyces albus G Mutants Defective in the SalGI Restriction-Modification System.
PG  - 323-334
AB  - Streptomyces albus G mutants (at least 12 of which were independent) defective
      in SalGI-mediated restriction (R-) were isolated after mutagenesis.  Some of
      them lacked detectable SalGI activity in cell-free extracts.  Some were also
      partially or completely defective in SalGI-associated modification (M-).  Loss
      of restriction rendered S. albus G sensitive to many phages to which it was
      normally totally resistant.  DNA from one such phage had many SalGI target
      sites (means, one site per 1.35 kilobases).  A mutant was isolated which was
      heat-sensitive for growth, apparently because it was restriction-proficient but
      temperature-sensitive for modification.  At a rather high frequency, this
      mutant generated spontaneous heat-tolerant derivatives which were nearly all
      R-.  Such R- mutants were always M- rather than being temperature-sensitive for
      modification.  In a limited genetic analysis, the determinants of restriction
      and modification did not recombine with each other, and since there was no
      reassortment of these phenotypes among the parental output of crosses it
      appeared that the determinants were located close together on the chromosome.
AU  - Chater KF
AU  - Wilde LC
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1980 116: 323-334.

PMID- 23814111
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Ammonia-Producing Acinetobacter sp. Strain MCC2139 from  Dairy Effluent.
PG  - e00410-13
AB  - We report the draft genome sequence of an ammonia-producing, esculin-hydrolyzing,
      catalase-positive, gram-negative bacterium, Acinetobacter sp. strain MCC2139.
      This bacterium, isolated from dairy sludge and with optimum growth at 37 degrees
      C, has a genome size of 2,967,280 bp with a G+C content of 42.3%.
AU  - Chatterjee D
AU  - Thakur AR
AU  - Raychaudhuri S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00410-13.

PMID- 1754388
VI  - 19
DP  - 1991
TI  - Genetic organization of the KpnI restriction-modification system.
PG  - 6505-6509
AB  - The KpnI restriction-modification (KpnI RM) system was previously cloned and
      expressed in E. coli.  The nucleotide sequences of the KpnI endonuclease
      (R.KpnI) and methylase (M.KpnI) genes have now been determined.  The sequence
      of the amino acid residues predicted from the endonuclease gene DNA sequence
      and the sequence of the first 12 NH2-terminal amino acids determined from the
      purified endonuclease protein were identical.  The KpnIR gene specifies a
      protein of 218 amino acids (MW:25,115), while the KpnIM gene coes for a protein
      of 417 amino acids (MW:47,582).  The two genes transcribe divergently with an
      intergenenic region of 167 nucleotides containing the putative promoter regions
      for both genes.  No protein sequence similarity was detected between R.KpnI and
      M.KpnI.  Comparison of the amino acid sequence of M.KpnI with sequences of
      various methylases revealed a significant homology to N6-adenine methylases, a
      partial homology to N4-cytosine methylases, and no homology to C5-methylases.
AU  - Chatterjee DK
AU  - Hammond AW
AU  - Blakesley RW
AU  - Adams SM
AU  - Gerard GF
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 6505-6509.

PMID- 12758073
VI  - 329
DP  - 2003
TI  - Functionally distinct nucleic acid binding sites for a group I intron encoded RNA maturase/DNA homing endonuclease.
PG  - 239-251
AB  - A large number of group I introns encode a family of homologous proteins that either promote
      intron splicing (maturases) or are site-specific DNA
      endonucleases that function in intron mobility (a process called
      "homing"). Genetic studies have shown that some of these proteins have
      both activities, yet how a single protein carries out both functions
      remains obscure. The similarity between respective DNA-binding sites and
      the RNA structure near the 5' and 3' splice sites has fueled speculation
      that such proteins may use analogous interactions to perform both
      functions. The Aspergillus nidulans mitochondrial COB group I intron
      encodes a bi-functional protein, I-AniI, that has both RNA maturase and
      site-specific DNA endonuclease activities in vitro. Here, we show that
      I-AniI shows distinctive features of the endonuclease family to which it
      belongs, including highly specific, tight binding and sequential DNA
      strand cleavage. Competition experiments demonstrate that I-AniI binds the
      COB intron RNA even in saturating concentrations of its DNA target site
      substrate, suggesting that the protein has a separate binding site for
      RNA. In addition, we provide evidence that two different DNA-binding site
      mutants of I-AniI have little effect on the protein's RNA maturation
      activity. Since RNA splicing is likely a secondary adaptation of the
      protein, these observations support a model in which homing endonucleases
      may have developed maturase function by utilizing a hitherto
      "non-functional" protein surface.
AU  - Chatterjee P
AU  - Brady KL
AU  - Solem A
AU  - Ho Y
AU  - Caprara MG
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2003 329: 239-251.

PMID- 
VI  - 28
DP  - 2000
TI  - Identification of an unusual restriction-modification system in bacteriophage MB78.
PG  - A171
AB  - A restriction-modification system has been identified in bacteriophage MB78, a virulent phage
      of Salmonella typhimurium isolated in this laboratory.  Genomic fragment of MB78 carrying the
      corresponding genes has been cloned in both orientations in pUC19.  The clones carrying the
      genes in the same orientation as that of the lacZ are mostly unstable.  However, those cloned
      in opposite orientation are stable.  Viability of transformants is strain-, orientation- and
      medium-dependent.  To clone the genes for restriction and modification enzymes separately, the
      genomic fragment containing the restriction-modification system was subcloned using AccI and
      SmaI enzymes.  One set of subclones contained active methylase gene, while the others
      contained an active endonuclease gene as well as truncated (inactive) methylase gene.  The
      former are stable and normal looking while the latter are unstable and looked distressed.
      Both the genes have been sequenced.  The methylase and restriction genes (only 228 and 333 bp
      respectively) are unusually small in comparison to respective bacterial genes.
AU  - Chaturvedi D
AU  - Chakravorty M
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 2000 28: A171.

PMID- 12670493
VI  - 303
DP  - 2003
TI  - Restriction-modification system in bacteriophage MB78.
PG  - 884-890
AB  - Restriction-modification system is present in bacteria to protect the cells against phage
      infection. Interestingly, the bacteriophage MB78, a
      virulent phage of Salmonella typhimurium possesses
      restriction-modification system. Permissive host transformed with plasmid
      having the genomic fragment of MB78 carrying the putative
      restriction-modification genes severely restrict the growth of the phage
      9NA. Growth of phage MB78 is also restricted to some extent. However, the
      temperate phage P22 is not restricted at all. Cloning of the the putative
      restriction-modification genes has been done in both orientations in
      different vectors. The clones carrying the genes in the same orientation
      as that of the lacZ in pUC19 are mostly unstable. However, those are
      stable when cloned in opposite orientation. Viability of the transformants
      is strain-, orientation-, and medium-dependent. The two genes have also
      been cloned individually/separately. Hosts carrying only the modification
      gene do not restrict growth of phages while the hosts carrying only the
      restriction gene do. The former produces stable transformants while the
      latter produces very unstable transformants which were viable only upto 36
      h or so. The colonies carrying modification gene were normal looking while
      those carrying the restriction gene were tiny, flat, and looked distressed
      resembling very much the clones carrying bacterial
      restriction-modification system. Amplification of the genes and subsequent
      cloning in expression vector will be carried out for characterization of
      the enzymes.
AU  - Chaturvedi D
AU  - Chakravorty M
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 2003 303: 884-890.

PMID- 29148967
VI  - 23
DP  - 2017
TI  - Group B Streptococcus Infections Caused by Improper Sourcing and Handling of Fish for Raw Consumption, Singapore, 2015-2016.
PG  - 1982-1990
AB  - We assessed microbial safety and quality of raw fish sold in Singapore during 2015-2016 to
      complement epidemiologic findings for an outbreak of infection with group B Streptococcus
      serotype III sequence type (ST) 283 associated with raw fish consumption. Fish-associated
      group B Streptococcus ST283 strains included strains nearly identical (0-2 single-nucleotide
      polymorphisms) with the human outbreak strain, as well as strains in another distinct ST283
      clade (57-71 single-nucleotide polymorphisms). Our investigations highlight the risk for
      contamination of freshwater fish (which are handled and distributed separately from saltwater
      fish sold as sashimi) and the need for improved hygienic handling of all fish for raw
      consumption. These results have led to updated policy and guidelines regarding the sale of
      ready-to-eat raw fish dishes in Singapore.
AU  - Chau ML et al
PT  - Journal Article
TA  - Emerg. Infect. Dis.
JT  - Emerg. Infect. Dis.
SO  - Emerg. Infect. Dis. 2017 23: 1982-1990.

PMID- 26564050
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Intermediate Rough Vaccine Strain Brucella abortus S19Deltaper Mutant.
PG  - e01336-15
AB  - Here, we report the genome sequence of the intermediate rough vaccine strain mutant, Brucella
      abortus S19Deltaper. The length of the draft genome was
      3,271,238 bp, with 57.2% G+C content. A total of 3,204 protein-coding genes and
      56 RNA genes were predicted.
AU  - Chaudhuri P
AU  - Goswami TTK
AU  - Lalsiamthara J
AU  - Kaur G
AU  - Vishnu US
AU  - Sankarasubramanian J
AU  - Gunasekaran P
AU  - Rajendhran J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01336-15.

PMID- 20098708
VI  - 5
DP  - 2010
TI  - Complete genome sequence and comparative metabolic profiling of the prototypical enteroaggregative Escherichia coli strain 042.
PG  - e8801
AB  - BACKGROUND: Escherichia coli can experience a multifaceted life, in some cases acting as a
      commensal while in other cases causing intestinal and/or
      extraintestinal disease. Several studies suggest enteroaggregative E. coli
      are the predominant cause of E. coli-mediated diarrhea in the developed
      world and are second only to Campylobacter sp. as a cause of
      bacterial-mediated diarrhea. Furthermore, enteroaggregative E. coli are a
      predominant cause of persistent diarrhea in the developing world where
      infection has been associated with malnourishment and growth retardation.
      METHODS: In this study we determined the complete genomic sequence of E.
      coli 042, the prototypical member of the enteroaggregative E. coli, which
      has been shown to cause disease in volunteer studies. We performed genomic
      and phylogenetic comparisons with other E. coli strains revealing
      previously uncharacterised virulence factors including a variety of
      secreted proteins and a capsular polysaccharide biosynthetic locus. In
      addition, by using Biolog Phenotype Microarrays we have provided a full
      metabolic profiling of E. coli 042 and the non-pathogenic lab strain E.
      coli K-12. We have highlighted the genetic basis for many of the metabolic
      differences between E. coli 042 and E. coli K-12. CONCLUSION: This study
      provides a genetic context for the vast amount of experimental and
      epidemiological data published thus far and provides a template for future
      diagnostic and intervention strategies.
AU  - Chaudhuri RR et al
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2010 5: e8801.

PMID- 27540077
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of an Industrially Important Bacillus sp. from Mandarmani Coastal Waters in Midnapur District, West Bengal, India.
PG  - e00867-16
AB  - Reported here is the draft genome sequence of an amylase-, protease-, DNase-, oxidase-,
      gelatinase-, and catalase-producing, Gram-positive diplobacillus (Bacillus sp. SM1 strain
      MCC2138), which was isolated from marine coastal waters and has the ability to degum raw silk
      fabric as well as Ramie fiber. The genome comprises 1.76 Mb with a GC content of 34.5%.
AU  - Chaudhuri SR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00867-16.

PMID- 24092793
VI  - 1
DP  - 2013
TI  - Whole-genome sequences of five oyster-associated bacteria show potential for crude oil hydrocarbon degradation.
PG  - e00802-13
AB  - Draft genome sequences of oyster-associated Pseudomonas stutzeri strain MF28, P.  alcaligenes
      strain OT69, P. aeruginosa strain WC55, Stenotrophomonas maltophilia
      strain MF89, and Microbacterium maritypicum strain MF109 are reported.
      Genome-wide surveys of these isolates suggest that the oyster microbiome, which
      remains largely understudied, has a strong potential to degrade crude oil.
AU  - Chauhan A
AU  - Green S
AU  - Pathak A
AU  - Thomas J
AU  - Venkatramanan R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00802-13.

PMID- 21742869
VI  - 193
DP  - 2011
TI  - Draft Genome Sequence of the Polycyclic Aromatic Hydrocarbon-Degrading, Genetically Engineered Bioluminescent Bioreporter Pseudomonas fluorescens  HK44.
PG  - 5009
AB  - Pseudomonas fluorescens strain HK44 (DSM 6700) is a genetically engineered lux-based
      bioluminescent bioreporter. Here we report the draft genome
      sequence of strain HK44. Annotation of  approximately 6.1 Mb sequence
      indicates that 30% of the traits are unique and distributed over 5 genomic
      islands, a prophage and two plasmids.
AU  - Chauhan A
AU  - Layton AC
AU  - Williams D
AU  - Smartt AE
AU  - Ripp S
AU  - Karpinets TV
AU  - Brown SD
AU  - Sayler GS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5009.

PMID- 28774987
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Deinococcus indicus DR1, a Novel Strain Isolated from a  Freshwater Wetland.
PG  - e00754-17
AB  - Deinococcus indicus strain DR1, a red-pigmented, arsenic- and radiation-resistant bacterium,
      was isolated from a water sample of the Dadri wetland, Uttar Pradesh,
      India. Here, we report a draft genome sequence of this strain, which may provide
      useful information regarding the genes and pathways involved in heavy-metal
      bioremediation.
AU  - Chauhan D
AU  - Srivastava PA
AU  - Yennamalli RM
AU  - Priyadarshini R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00754-17.

PMID- 27789633
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Brucella abortus SKN 13 Isolated from Placenta of Aborted Cattle in Gujarat, India.
PG  - e01123-16
AB  - Brucella abortus is generally known to cause brucellosis in cattle and buffalo. Here, we
      report the draft genome sequence of Brucella abortus SKN 13, isolated
      from aborted cattle placenta in the area of Gujarat, India, providing precious
      resources for comparative genomic analyses of Brucella field strains.
AU  - Chauhan HC
AU  - Patel BK
AU  - Chandel BS
AU  - Patel KB
AU  - Patel AC
AU  - Shrimali MD
AU  - Patel SS
AU  - Bhagat AG
AU  - Rajgor M
AU  - Patel MA
AU  - Patel M
AU  - Kala J
AU  - Patel B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01123-16.

PMID- 1659493
VI  - 37
DP  - 1991
TI  - Genetic transformation of Chainia and heat attenuation of its restriction system.
PG  - 713-715
AB  - A PEG-mediated transformation system for Chainia (NCL 82-5-1) was developed
      using a broad host range Streptomyces vector, pIJ702.  Protoplasts prepared
      from Chainia (NCL 81-5-1) were regenerated with 5% efficiency.  Transformation
      of the protoplasts with pIJ702 gave 10-20 transformants/microgram DNA.  The low
      efficiency of transformation is attributed to a restriction system in Chainia;
      this could be inhibited by treating the protoplasts at 42C for 10 min just
      before transformation.  The yield of transformants increased 100-fold when
      pIJ702 was modified by passage in Chainia.  Because the plasmid replicon was
      functional in Chainia and the modified plasmid was stably maintained, the
      transformation system should be useful for self-cloning in Chainia NCL 82-5-1
      of the many commercially important enzymes this strain is known to produce.
AU  - Chauthaiwale VM
AU  - Vyas PR
AU  - Deshpande VV
PT  - Journal Article
TA  - Can. J. Microbiol.
JT  - Can. J. Microbiol.
SO  - Can. J. Microbiol. 1991 37: 713-715.

PMID- 20959640
VI  - 18
DP  - 2011
TI  - Identification of the De Novo DNA Methyltransferase, DNMT3A2, as a Novel Regulator of Germ Cell Development.
PG  - 172A
AB  - The methylation of DNA is mediated by a family of DNA methyltransferases which play a role in
      the establishment and/or maintenance of DNA methylation patterns.  Previously, it was shown
      that the targeted disruption of both active isoforms of the de novo methyltransferase, Dnmt3a,
      in germ cells by conditional mouse knockout technology resulted in aberrant gametogenesis.
      The aim of this study was to evaluate the expression and function of DNMT3A in human fetal
      gonads and human embryonic stem cell (hESC)-derived germ cell differentiation.  In addition,
      the role of Dnmt3a in mouse primordial germ cells isolated from fetal gonads throughout
      development and in mouse embryonic germ cells, the pluripotent cells that PGCs form in vitro,
      was also investigated.
AU  - Chavez SL
AU  - Pera RAR
PT  - Journal Article
TA  - Reprod. Sci.
JT  - Reprod. Sci.
SO  - Reprod. Sci. 2011 18: 172A.

PMID- 24926049
VI  - 2
DP  - 2014
TI  - Genome Sequence of SCB34, a Sequence Type 131 Multidrug-Resistant Escherichia coli Isolate Causing Neonatal Early-Onset Sepsis.
PG  - e00514-14
AB  - SCB34 is a sequence type 131, highly invasive, multidrug-resistant Escherichia coli isolate
      that produced neonatal bacteremia. Whole-genome sequencing was
      performed using a 250-bp library on the Illumina MiSeq platform; 5,910,264 reads
      were assembled de novo using the A5 assembly pipeline. The total contig length
      was 5,227,742 bp; the RAST server was used for annotation.
AU  - Chavez-Bueno S
AU  - Day MW
AU  - Toby IT
AU  - Akins DR
AU  - Dyer DW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00514-14.

PMID- 23618715
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Biocontrol Bacterium Brevibacillus brevis Strain FJAT-0809-GLX.
PG  - e00160-13
AB  - Brevibacillus brevis strain FJAT-0809-GLX had significant inhibition on many plant and animal
      pathogens. The draft genome sequence of B. brevis FJAT-0809-GLX
      is 6 Mb in size and consists of 5,677 genes (protein-coding sequences [CDS]),
      with an average length of 933 bp and a G+C content of 47.30%. Compared with the
      published B. brevis strain NBRC 100599, 618 specific genes were identified in the
      strain FJAT-0809-GLX.
AU  - Che J
AU  - Liu B
AU  - Lin Y
AU  - Tang W
AU  - Tang J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00160-13.

PMID- 24051316
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Antarctic Bacterium Psychrobacter sp. Strain G.
PG  - e00725-13
AB  - Here, we report the complete genome sequence of Psychrobacter sp. strain G, isolated from King
      George Island, Antarctica, which can produce lipolytic enzymes
      at low temperatures. The genomics information of this strain will facilitate the
      study of the physiology, cold adaptation properties, and evolution of this genus.
AU  - Che S
AU  - Song L
AU  - Song W
AU  - Yang M
AU  - Liu G
AU  - Lin X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00725-13.

PMID- 28034853
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Biosafety Level 2 Opportunistic Pathogens Isolated from the Environmental Surfaces of the International Space Station.
PG  - e01263-16
AB  - The draft genome sequences of 20 biosafety level 2 (BSL-2) opportunistic pathogens isolated
      from the environmental surfaces of the International Space
      Station (ISS) were presented. These genomic sequences will help in understanding
      the influence of microgravity on the pathogenicity and virulence of these strains
      when compared with Earth strains.
AU  - Checinska SA
AU  - Singh NK
AU  - Allen JE
AU  - Thissen J
AU  - Jaing C
AU  - Venkateswaran K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01263-16.

PMID- 21507354
VI  - 101
DP  - 2011
TI  - The DNMT3 Family of Mammalian De Novo DNA Methyltransferases.
PG  - 255-285
AB  - The deposition of DNA methylation at promoters of transposons, X-linked genes, imprinted
      genes, and other lineage-specific genes is clearly
      associated with long-term transcriptional silencing. Thus, DNA
      methylation represents a key layer of epigenetic information in mammals
      that is required for embryonic development, germline differentiation,
      and, as shown more recently, for the function and maturation of
      neuronal tissues. The DNMT3A, DNMT3B, and DNMT3L proteins are primarily
      responsible for the establishment of genomic DNA methylation patterns
      and, as such, play an important role in human developmental,
      reproductive, and mental health. Progress in our understanding of this
      important protein family has been rapid in recent years and has been
      accompanied by stunning developments in the analysis of the human DNA
      methylome in multiple cell types. This review focuses on recent
      developments in the characterization of the DNMT3 family of DNA
      methyltransferases at the biochemical, structural, and functional
      levels. Interconnections between the DNA-based and histone-based layers
      of epigenetic information are particularly highlighted, as it is now
      clear that de now methylation occurs chiefly in the context of
      nucleosomal templates.
AU  - Chedin F
PT  - Journal Article
TA  - Prog. Mol. Biol. Transl. Sci.
JT  - Prog. Mol. Biol. Transl. Sci.
SO  - Prog. Mol. Biol. Transl. Sci. 2011 101: 255-285.

PMID- 12481029
VI  - 99
DP  - 2002
TI  - The DNA methyltransferase-like protein DNMT3L stimulates de novo methylation by Dnmt3a.
PG  - 16916-16921
AB  - Dnmt3L is required for the establishment of maternal methylation imprints at imprinting
      centers (ICs). Dnmt3L, however, lacks the conserved
      catalytic domain common to DNA methyltransferases. In an attempt to define
      its function, we coexpressed DNMT3L with each of the two known de novo
      methyltransferases, Dnmt3a and DNMT3B, in human cells and monitored de
      novo methylation by using replicating minichromosomes carrying various ICs
      as targets. Coexpression of DNMT3L with DNMT3B led to little or no change
      in target methylation. However, coexpression of DNMT3L with Dnmt3a
      resulted in a striking stimulation of de novo methylation by Dnmt3a.
      Stimulation was observed at maternally methylated ICs such as small
      nuclear ribonucleoprotein polypeptide N (SNRPN), Snrpn, and Igf2rAir, as
      well as at various nonimprinted sequences present on the episomes.
      Stimulation of Dnmt3a by DNMT3L was also observed at endogenous sequences
      in the genome. Therefore, DNMT3L acts as a general stimulatory factor for
      de novo methylation by Dnmt3a. The implications of these findings for the
      function of DNMT3L and Dnmt3a in DNA methylation and genomic imprinting
      are discussed.
AU  - Chedin F
AU  - Lieber MR
AU  - Hsieh CL
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2002 99: 16916-16921.

PMID- 28302774
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Streptococcus pyogenes emm14 JS95, a Necrotizing Fasciitis Strain Isolated in Israel.
PG  - e00025-17
AB  - Here, we report the complete genome sequence of the Streptococcus pyogenes emm14  strain JS95,
      isolated from a patient with necrotizing fasciitis. The
      streptococcal invasion locus (sil), the first quorum-sensing system characterized
      in S. pyogenes, was identified in this strain.
AU  - Chee JL
AU  - Ravins M
AU  - Hanski E
AU  - Chen SL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00025-17.

PMID- 22675597
VI  - 6
DP  - 2012
TI  - Draft genome sequence of Arthrospira platensis C1 (PCC9438).
PG  - 43-53
AB  - Arthrospira platensis is a cyanobacterium that is extensively cultivated outdoors on a large
      commercial scale for consumption as a food for humans and animals. It can be grown in
      monoculture under highly alkaline conditions, making it attractive for industrial production.
      Here we describe the complete genome sequence of A. platensis C1 strain and its annotation.
      The A. platensis C1 genome contains 6,089,210 bp including 6,108 protein-coding genes and 45
      RNA genes, and no plasmids. The genome information has been used for further comparative
      analysis, particularly of metabolic pathways, photosynthetic efficiency and barriers to gene
      transfer.
AU  - Cheevadhanarak S et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 6: 43-53.

PMID- 28729275
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequences of 14 Strains of Bradyrhizobium canariense and 1 Strain of Bradyrhizobium japonicum Isolated from Lupinus spp. in Algeria.
PG  - e00676-17
AB  - We report here the whole-genome sequences of 14 strains of Bradyrhizobium canariense, isolated
      from root nodules of Lupinus microanthus and Lupinus
      angustifolius, and 1 strain of Bradyrhizobium japonicum isolated from root
      nodules from Lupinus angustifolius in Algeria. These sequences add to the known
      diversity of this agronomically important genus.
AU  - Chekireb D
AU  - Crovadore J
AU  - Brachmann A
AU  - Chablais R
AU  - Cochard B
AU  - Lefort F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00676-17.

PMID- 29449389
VI  - 6
DP  - 2018
TI  - Draft Reference Genome Sequence of Corynebacterium mastitidis 16-1433, Isolated from a Mouse.
PG  - e00050-18
AB  - We report here a nearly complete draft genome sequence for a Corynebacterium mastitidis
      isolate from a mouse. The total read coverage is 198x, and the genome
      size is 2,264,319 bp with a 69.04% GC content. This genome complements the only
      other genome available for C. mastitidis, which was obtained from a sheep.
AU  - Cheleuitte-Nieves C
AU  - Gulvik CA
AU  - Humrighouse BW
AU  - Bell ME
AU  - Villarma A
AU  - Westblade LF
AU  - Lipman NS
AU  - Fischetti VA
AU  - McQuiston JR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00050-18.

PMID- 7739896
VI  - 23
DP  - 1995
TI  - Tyrosine 27 of the specificity polypeptide of EcoKI can be UV crosslinked to a bromodeoxyuridine-substituted DNA target sequence.
PG  - 1177-1183
AB  - The specificity (S) subunit of the restriction enzyme EcoKI imparts specificity for the
      sequence AAC(N6)GTGC. Substitution of thymine with bromodeoxyuridine in a 25 bp DNA duplex
      containing this sequence stimulated UV light-induced covalent cross-linking to the S subunit.
      Crosslinking occurred only at the residue complementary to the first adenine in the AAC
      sequence, demonstrating a close contact between the major groove at this sequence and the S
      subunit. Peptide sequencing of a proteolytically-digested, crosslinked complex identified
      tyrosine 27 in the S subunit as the site of crosslinking. This is consistent with the role of
      the N-terminal domain of the S subunit in recognizing the AAC sequence. Tyrosine 27 is
      conserved in the S subunits of the three type I enzymes that share the sequence AA in the
      trinucleotide component of their target sequence. This suggests that tyrosine 27 may make a
      similar DNA contact in these other enzymes.
AU  - Chen A
AU  - Powell LM
AU  - Dryden DTF
AU  - Murray NE
AU  - Brown T
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1995 23: 1177-1183.

PMID- 24501654
VI  - 9
DP  - 2013
TI  - Draft genome sequence of Rhodococcus rhodochrous strain ATCC 17895.
PG  - 175-184
AB  - Rhodococcus rhodochrous ATCC 17895 possesses an array of mono- and dioxygenases,  as well as
      hydratases, which makes it an interesting organism for biocatalysis.
      R. rhodochrous is a Gram-positive aerobic bacterium with a rod-like morphology.
      Here we describe the features of this organism, together with the complete genome
      sequence and annotation. The 6,869,887 bp long genome contains 6,609
      protein-coding genes and 53 RNA genes. Based on small subunit rRNA analysis, the
      strain is more likely to be a strain of Rhodococcus erythropolis rather than
      Rhodococcus rhodochrous.
AU  - Chen BS
AU  - Otten LG
AU  - Resch V
AU  - Muyzer G
AU  - Hanefeld U
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 9: 175-184.

PMID- 24589714
VI  - 9
DP  - 2014
TI  - The de novo DNA methyltransferase DNMT3A in development and cancer.
PG  - 669-677
AB  - DNA methylation, one of the best-characterized epigenetic modifications, plays essential roles
      in development, aging and diseases. The de novo DNA methyltransferase DNMT3A is responsible
      for the establishment of de novo genomic DNA methylation patterns and, as such, involved in
      normal development as well as in many diseases including cancer. In recent years, our
      understanding of this important protein has made significant progress, which was facilitated
      by stunning development in the analysis of the DNA methylome of multiple organs and cell
      types. In this review, recent developments in the characterization of DNMT3A were discussed
      with special emphasis on the roles of DNMT3A in development and cancer.
AU  - Chen Bi-F
AU  - Chan W-Yee
PT  - Journal Article
TA  - EPIGENETICS
JT  - EPIGENETICS
SO  - EPIGENETICS 2014 9: 669-677.

PMID- 17375201
VI  - 2
DP  - 2007
TI  - A Glimpse of Streptococcal Toxic Shock Syndrome from Comparative Genomics of S. suis 2 Chinese Isolates.
PG  - e315
AB  - BACKGROUND: Streptococcus suis serotype 2 (SS2) is an important zoonotic pathogen, causing
      more than 200 cases of severe human infection worldwide,
      with the hallmarks of meningitis, septicemia, arthritis, etc. Very
      recently, SS2 has been recognized as an etiological agent for
      streptococcal toxic shock syndrome (STSS), which was originally associated
      with Streptococcus pyogenes (GAS) in Streptococci. However, the molecular
      mechanisms underlying STSS are poorly understood. METHODS AND FINDINGS: To
      elucidate the genetic determinants of STSS caused by SS2, whole genome
      sequencing of 3 different Chinese SS2 strains was undertaken. Comparative
      genomics accompanied by several lines of experiments, including
      experimental animal infection, PCR assay, and expression analysis, were
      utilized to further dissect a candidate pathogenicity island (PAI). Here
      we show, for the first time, a novel molecular insight into Chinese
      isolates of highly invasive SS2, which caused two large-scale human STSS
      outbreaks in China. A candidate PAI of approximately 89 kb in length,
      which is designated 89K and specific for Chinese SS2 virulent isolates,
      was investigated at the genomic level. It shares the universal properties
      of PAIs such as distinct GC content, consistent with its pivotal role in
      STSS and high virulence. CONCLUSIONS: To our knowledge, this is the first
      PAI candidate from S. suis worldwide. Our finding thus sheds light on STSS
      triggered by SS2 at the genomic level, facilitates further understanding
      of its pathogenesis and points to directions of development on some
      effective strategies to combat highly pathogenic SS2 infections.
AU  - Chen C et al
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2007 2: e315.

PMID- 21515769
VI  - 193
DP  - 2011
TI  - Complete genome sequence of the probiotic bacterium Lactobacillus casei LC2W.
PG  - 3419-3420
AB  - Lactobacillus casei LC2W, a patented probiotic strain (EP 164209630B1), is isolated from
      Chinese traditional dairy products and has been implemented
      in the industrial production as starter cultures. Here we present the
      complete genome sequence of LC2W and the identification of a gene cluster
      implicated in the biosynthesis of exopolysaccharides.
AU  - Chen C
AU  - Ai L
AU  - Zhou F
AU  - Wang L
AU  - Zhang H
AU  - Chen W
AU  - Guo B
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3419-3420.

PMID- 22408240
VI  - 194
DP  - 2012
TI  - Genome Sequence of a Serotype b Non-JP2 Aggregatibacter actinomycetemcomitans Strain, ANH9381, from a Periodontally Healthy Individual.
PG  - 1837
AB  - Gram-negative Aggregatibacter actinomycetemcomitans can be distinguished (based on the
      promoter structure of the leukotoxin operon) into JP2 and non-JP2
      genotypes, with the former found to be more pathogenic than the latter. Here we
      report the first complete genome sequence of a serotype b non-JP2 strain of A.
      actinomycetemcomitans.
AU  - Chen C
AU  - Kittichotirat W
AU  - Chen W
AU  - Downey JS
AU  - Bumgarner R
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1837.

PMID- 20348265
VI  - 192
DP  - 2010
TI  - Genome sequence of naturally competent Aggregatibacter actinomycetemcomitans serotype a strain D7S-1.
PG  - 2643-2644
AB  - The major clonal lineages of the Gram-negative periodontal pathogen Aggregatibacter
      actinomycetemcomitans include serotype a, b, and c
      strains. Here, we report the draft genome sequence of a naturally
      competent serotype a strain, D7S-1, isolated from a patient with
      aggressive periodontitis.
AU  - Chen C
AU  - Kittichotirat W
AU  - Chen W
AU  - Downey JS
AU  - Si Y
AU  - Bumgarner R
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 2643-2644.

PMID- 19820097
VI  - 191
DP  - 2009
TI  - Genome sequence of Aggregatibacter actinomycetemcomitans serotype c strain D11S-1.
PG  - 7378-7379
AB  - Aggregatibacter actinomycetemcomitans is a major etiological agent of periodontitis. Here we
      report the complete genome sequence of a serotype c strain D11S-1, which was recovered from
      the subgingival plaque of a patient diagnosed with generalized aggressive periodontitis.
AU  - Chen C
AU  - Kittichotirat W
AU  - Si Y
AU  - Bumgarner R
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2009 191: 7378-7379.

PMID- 28450519
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Exiguobacterium sp. HVEsp1, a Thermophilic Bacterium Isolated from a Deep-Sea Hydrothermal Vent in the Okinawa Trough.
PG  - e00253-17
AB  - We report here the draft genome sequence of Exiguobacterium sp. HVEsp1, a thermophilic
      bacterium isolated from a deep-sea hydrothermal vent. The estimated
      genome size of this strain is 2,838,499 bp with a G+C content of 48.2%. The
      genome sequence data provide valuable information that will facilitate studies on
      the adaptation mechanisms of bacteria living in deep-sea hydrothermal vents.
AU  - Chen C
AU  - Sun L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00253-17.

PMID- 28400512
VI  - 114
DP  - 2017
TI  - Convergence of DNA methylation and phosphorothioation epigenetics in bacterial genomes.
PG  - 4501-4506
AB  - Explosive growth in the study of microbial epigenetics has revealed a diversity of chemical
      structures and biological functions of DNA modifications in restriction-modification (R-M) and
      basic genetic processes. Here, we describe the discovery of shared consensus sequences for two
      seemingly unrelated DNA modification systems, 6mA methylation and phosphorothioation (PT), in
      which sulfur replaces a nonbridging oxygen in the DNA backbone. Mass spectrometric analysis of
      DNA from Escherichia coli B7A and Salmonella enterica serovar Cerro 87, strains possessing
      PT-based R-M genes, revealed d(GPS6mA) dinucleotides in the GPS6mAAC consensus representing
      approximately 5% of the 1,100 to 1,300 PT-modified d(GPSA) motifs per genome, with 6mA arising
      from a yet-to-be-identified methyltransferase. To further explore PT and 6mA in another
      consensus sequence, GPS6mATC, we engineered a strain of E. coli HST04 to express Dnd genes
      from Hahella chejuensis KCTC2396 (PT in GPSATC) and Dam methyltransferase from E. coli DH10B
      (6mA in G6mATC). Based on this model, in vitro studies revealed reduced Dam activity in
      GPSATC-containing oligonucleotides whereas single-molecule real-time sequencing of HST04 DNA
      revealed 6mA in all 2,058 GPSATC sites (5% of 37,698 total GATC sites). This model system also
      revealed temperature-sensitive restriction by DndFGH in KCTC2396 and B7A, which was exploited
      to discover that 6mA can substitute for PT to confer resistance to restriction by the DndFGH
      system. These results point to complex but unappreciated interactions between DNA modification
      systems and raise the possibility of coevolution of interacting systems to facilitate the
      function of each.
AU  - Chen C
AU  - Wang L
AU  - Chen S
AU  - Wu X
AU  - Gu M
AU  - Chen X
AU  - Jiang S
AU  - Wang Y
AU  - Deng Z
AU  - Dedon PC
AU  - Chen S
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2017 114: 4501-4506.

PMID- 2820056
VI  - 237
DP  - 1987
TI  - Chemical Conversion of a DNA-binding protein into a site-specific nuclease.
PG  - 1197-1201
AB  - The tryptophan gene (trp) repressor of Escherichia coli has been converted into
      a site-specific nuclease by covalently attaching it to the
      1,10-phenanthroline-copper complex.  In its cuprous form, the coordination
      complex with hydrogen peroxide as a coreactant cleaves DNA by oxidatively
      attacking the deoxyribose moiety.  The chemistry for the attachment of
      1,10-phenanthroline to the trp repressor involves modification of lysyl
      residues with iminothiolane followed by alkylation of the resulting sulfhydryl
      groups with 5-iodoacetamido-1,10-phenanthroline.  The modified trp repressor
      cleaves the operators of aroH and trpEDCBA upon the addition of cupric ion and
      thiol in a reaction dependent on the corepressor L-tryptophan.  Scission was
      restricted to the binding site for the repressor, defined by deoxyribonuclease
      I footprinting.  Since DNA-binding proteins have recognition sequences
      approximately 20 base pairs long, the nucleolytic activities derived from them
      could be used to isolate long DNA fragments for sequencing or chromosomal
      mapping.
AU  - Chen C-HB
AU  - Sigman DS
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1987 237: 1197-1201.

PMID- 8764481
VI  - 140
DP  - 1996
TI  - Factors involved in the transformation of previously non-transformable Clostridium perfringens type B.
PG  - 185-191
AB  - The pre-shock incubation of cells plus DNA and the methylation state of plasmid DNA were found
      to play a role in the electroporation-based transformation of Clostridium perfringens 3626B.
      Following pre-shock incubation, the highest number of C. perfringens 3626B transformants was
      obtained when plasmid pGK201 was both dam+ dcm+ modified, while no transformants were obtained
      when pGK201 was not methylated or only dcm methylated.  This is consistent with the
      observation that plasmid pGK201 was protected against digestion by C. perfringens 3626B
      cell-associated nucleases for up to 3 min when methylated by both methylases.  C. perfringens
      3626B was successfully transformed only within a narrow cell recovery rate window.  The ermAM
      gene associated with pGK201 and pAK102 was found to integrate into the chromosome of C.
      perfringens strains 13A and 3626B.
AU  - Chen C-K
AU  - Boucle CM
AU  - Blaschek HP
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1996 140: 185-191.

PMID- 21257765
VI  - 193
DP  - 2011
TI  - Draft Genome Sequence of a Dominant Multidrug-resistant Neisseria gonorrhoeae strain TCDC-NG08107 from Sexual Network at High Risk of  Acquiring Human Immunodeficiency Virus and Syphilis.
PG  - 1788-1789
AB  - Neisseria gonorrhoeae infection is the second major cause of sexually transmitted diseases
      worldwide. Development of resistance to multiple classes of antimicrobials in N. gonorrhoeae
      has compromised treatment and disease control. Herein, we report the availability of the draft
      genome sequence of a multidrug-resistant N. gonorrhoeae isolate, TCDC-NG08107, which spread in
      groups of men who have sex with men (MSM) in Taiwan.
AU  - Chen CC
AU  - Hsia KC
AU  - Huang CT
AU  - Wong WW
AU  - Yen MY
AU  - Li LH
AU  - Lin KY
AU  - Chen KW
AU  - Li SY
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 1788-1789.

PMID- 21398540
VI  - 193
DP  - 2011
TI  - Genome Sequence of a Dominant Multidrug-resistant Acinetobacter baumannii strain TCDC-AB0715.
PG  - 2361-2362
AB  - Acinetobacter baumannii has emerged as a significant nosocomial pathogen worldwide. The
      increasing trend of carbapenem and fluoroquinolone resistance in A. baumannii severely limits
      the usage of therapeutic antimicrobial agents. Here, we report the genome sequence of a
      multidrug-resistant A. baumannii strain TCDC-AB0715 harboring both blaOXA-23 and blaOXA-66.
AU  - Chen CC
AU  - Lin YC
AU  - Sheng WH
AU  - Chen YC
AU  - Chang SC
AU  - Hsia KC
AU  - Liao MH
AU  - Li SY
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 2361-2362.

PMID- 23393137
VI  - 288
DP  - 2013
TI  - DNA 5-Methylcytosine Demethylation Activities of the Mammalian DNA Methyltransferases.
PG  - 9084-9091
AB  - Methylation at the 5-position of DNA cytosine on the vertebrate genomes is accomplished by the
      combined catalytic actions of three DNA
      methyltransferases (DNMTs), the de novo enzymes DNMT3A and DNMT3B and
      the maintenance enzyme DNMT1. Although several metabolic routes have
      been suggested for demethylation of the vertebrate DNA, whether active
      DNA demethylase(s) exist has remained elusive. Surprisingly, we have
      found that the mammalian DNMTs, and likely the vertebrates DNMTs in
      general, can also act as Ca2+ ion- and redox state-dependent active DNA
      demethylases. This finding suggests new directions for reinvestigation
      of the structures and functions of these DNMTs, in particular their
      roles in Ca2+ ion-dependent biological processes, including the
      genome-wide/local DNA demethylation during early embryogenesis, cell
      differentiation, neuronal activity-regulated gene expression, and
      carcinogenesis.
AU  - Chen CC
AU  - Wang KY
AU  - Shen CKJ
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2013 288: 9084-9091.

PMID- 22898819
VI  - 287
DP  - 2012
TI  - The Mammalian de Novo DNA Methyltransferases DNMT3A and DNMT3B Are Also DNA 5-Hydroxymethylcytosine Dehydroxymethylases.
PG  - 33116-33121
AB  - For cytosine (C) demethylation of vertebrate DNA, it is known that the TET proteins could
      convert 5-methyl C (5-mC) to 5-hydroxymethyl C
      (5-hmC). However, DNA dehydroxymethylase(s), or enzymes able to
      directly convert 5-hmC to C, have been elusive. We present in vitro
      evidence that the mammalian de novo DNA methyltransferases DNMT3A and
      DNMT3B, but not the maintenance enzyme DNMT1, are also redox-dependent
      DNA dehydroxymethylases. Significantly, intactness of the C methylation
      catalytic sites of these de novo enzymes is also required for their
      5-hmC dehydroxymethylation activity. That DNMT3A and DNMT3B function
      bidirectionally both as DNA methyltransferases and as
      dehydroxymethylases raises intriguing and new questions regarding the
      structural and functional aspects of these enzymes and their regulatory
      roles in the dynamic modifications of the vertebrate genomes during
      development, carcinogenesis, and gene regulation.
AU  - Chen CC
AU  - Wang KY
AU  - Shen CKJ
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2012 287: 33116-33121.

PMID- 24039691
VI  - 8
DP  - 2013
TI  - Characterization and Comparison of 2 Distinct Epidemic Community-Associated Methicillin-Resistant Staphylococcus aureus Clones of ST59 Lineage.
PG  - E63210
AB  - Sequence type (ST) 59 is an epidemic lineage of community-associated (CA)
      methicillin-resistant Staphylococcus aureus (MRSA) isolates. Taiwanese CA-MRSA
      isolates belong to ST59 and can be grouped into 2 distinct clones, a virulent
      Taiwan clone and a commensal Asian-Pacific clone. The Taiwan clone carries the
      Panton-Valentine leukocidin (PVL) genes and the staphylococcal chromosomal
      cassette mec (SCCmec) VT, and is frequently isolated from patients with severe
      disease. The Asian-Pacific clone is PVL-negative, carries SCCmec IV, and a
      frequent colonizer of healthy children. Isolates of both clones were
      characterized by their ability to adhere to respiratory A549 cells, cytotoxicity
      to human neutrophils, and nasal colonization of a murine and murine sepsis
      models. Genome variation was determined by polymerase chain reaction of selected
      virulence factors and by multi-strain whole genome microarray. Additionally, the
      expression of selected factors was compared between the 2 clones. The Taiwan
      clone showed a much higher cytotoxicity to the human neutrophils and caused more
      severe septic infections with a high mortality rate in the murine model. The
      clones were indistinguishable in their adhesion to A549 cells and persistence of
      murine nasal colonization. The microarray data revealed that the Taiwan clone had
      lost the o3-prophage that integrates into the beta-hemolysin gene and includes
      staphylokinase- and enterotoxin P-encoding genes, but had retained the genes for
      human immune evasion, scn and chps. Production of the virulence factors did not
      differ significantly in the 2 clonal groups, although more alpha-toxin was
      expressed in Taiwan clone isolates from pneumonia patients. In conclusion, the
      Taiwan CA-MRSA clone was distinguished by enhanced virulence in both humans and
      an animal infection model. The evolutionary acquisition of PVL, the higher
      expression of alpha-toxin, and possibly the loss of a large portion of the
      beta-hemolysin-converting prophage likely contribute to its higher pathogenic
      potential than the Asian-Pacific clone.
AU  - Chen CJ
AU  - Unger C
AU  - Hoffmann W
AU  - Lindsay JA
AU  - Huang YC
AU  - Gotz F
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2013 8: E63210.

PMID- 25144712
VI  - 9
DP  - 2014
TI  - Closely Related NDM-1-Encoding Plasmids from Escherichia coli and Klebsiella pneumoniae in Taiwan.
PG  - E104899
AB  - OBJECTIVE: Two plasmids carrying blaNDM-1 isolated from carbapenem-resistant
      Klebsiella pneumoniae (CR-KP) and carbapenem-resistant Escherichia coli (CR-EC)
      were sequenced. CR-KP and CR-EC were isolated from two Taiwanese patients without
      travel histories. METHODS: Complete sequencing of the plasmids (pLK75 and pLK78)
      was conducted using a shotgun approach. Annotation of the contigs was performed
      using the RAST Server, followed by manual inspection and correction. RESULTS:
      These similar plasmids were obtained from two patients with overlapping stays at
      the same hospital. The pLK75 and pLK78 plasmids were 56,489-bp and 56,072-bp in
      length, respectively. Plasmid annotation revealed a common backbone similar to
      the IncN plasmid pR46. The regions flanking the blaNDM-1 genes in these plasmids
      were very similar to plasmid pNDM-HU01 in Japan, which contains a complex class 1
      integron located next to an ISCR1 element. The ISCR1 element has been suggested
      to provide a powerful mechanism for mobilising antibiotic resistance genes.
      CONCLUSION: Two indigenous NDM-1-producing Enterobacteriaceae cases were
      identified for the first time in Taiwan, highlighting the alarming introduction
      of NDM-1-producing Enterobacteriaceae in this region.
AU  - Chen CJ
AU  - Wu TL
AU  - Lu PL
AU  - Chen YT
AU  - Fung CP
AU  - Chuang YC
AU  - Lin JC
AU  - Siu LK
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2014 9: E104899.

PMID- 14656965
VI  - 13
DP  - 2003
TI  - Comparative genome analysis of Vibrio vulnificus, a marine pathogen.
PG  - 2577-2587
AB  - The halophile Vibrio vulnificus is an etiologic agent of human mortality from seafood-borne
      infections. We applied whole-genome sequencing and
      comparative analysis to investigate the evolution of this pathogen. The
      genome of biotype 1 strain, V. vulnificus YJ016, was sequenced and
      includes two chromosomes of estimated 3377 kbp and 1857 kbp in size, and a
      plasmid of 48,508 bp. A super-integron (SI) was identified, and the SI
      region spans 139 kbp and contains 188 gene cassettes. In contrast to
      non-SI sequences, the captured gene cassettes are unique for any given
      Vibrio species and are highly variable among V. vulnificus strains.
      Multiple rearrangements were found when comparing the 5.3-Mbp V.
      vulnificus YJ016 genome and the 4.0-Mbp V. cholerae El Tor N16961 genome.
      The organization of gene clusters of capsular polysaccharide, iron
      metabolism, and RTX toxin showed distinct genetic features of V.
      vulnificus and V. cholerae. The content of the V. vulnificus genome
      contained gene duplications and evidence of horizontal transfer, allowing
      for genetic diversity and function in the marine environment. The genomic
      information obtained in this study can be applied to monitoring vibrio
      infections and identifying virulence genes in V. vulnificus.
AU  - Chen CY
AU  - Wu KM
AU  - Chang YC
AU  - Chang CH
AU  - Tsai HC
AU  - Liao TL
AU  - Liu YM
AU  - Chen HJ
AU  - Shen AB
AU  - Li JC
AU  - Su TL
AU  - Shao CP
AU  - Lee CT
AU  - Hor LI
AU  - Tsai SF
PT  - Journal Article
TA  - Genome Res.
JT  - Genome Res.
SO  - Genome Res. 2003 13: 2577-2587.

PMID- 
VI  - 15
DP  - 1997
TI  - Chemical modification of restriction endonuclease Bsp63I and its substrate.
PG  - 91-94
AB  - This paper reports on a study of the chemical modification of Bsp63I and its substrate by
      using group modification reagents.  The results show that the sulfhydryl group and the lysine
      residue are possibly the necessary group in the active center of Bsp63I.  The base sequence of
      d(GC), which is in the recognition sequence of Bsp63I, plays an important role in the
      catalysis of Bsp63I.
AU  - Chen D
PT  - Journal Article
TA  - Hunan Jiaoyu Xueyuan Xuebao
JT  - Hunan Jiaoyu Xueyuan Xuebao
SO  - Hunan Jiaoyu Xueyuan Xuebao 1997 15: 91-94.

PMID- 28385834
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Ralstonia solanacearum FJAT-1458, a Potential Biocontrol Agent for Tomato Wilt.
PG  - e00070-17
AB  - An avirulent strain of Ralstonia solanacearum FJAT-1458 was isolated from a living tomato.
      Here, we report the complete R. solanacearum FJAT-1458 genome
      sequence of 6,059,899 bp and 5,241 genes. This bacterial strain is a potential
      candidate as a biocontrol agent in the form of a plant vaccine for bacterial
      wilt.
AU  - Chen D
AU  - Liu B
AU  - Zhu Y
AU  - Wang J
AU  - Chen Z
AU  - Che J
AU  - Zheng X
AU  - Chen X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00070-17.

PMID- 28912315
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Ralstonia solanacearum FJAT-91, a High-Virulence Pathogen of Tomato Wilt.
PG  - e00900-17
AB  - Ralstonia solanacearum FJAT-91, which displays higher virulence toward plants belonging to the
      family Solanaceae, was isolated from a wilted tomato plant
      vessel in Fujian province, southeast China. Here, we report the complete genome
      sequence of R. solanacearum FJAT-91 using long-read single-molecule PacBio
      sequencing technology. The genome comprises a 3,873,214-bp circular chromosome
      and a 2,000,873-bp circular megaplasmid with an overall G+C content of 66.85%.
AU  - Chen D
AU  - Liu B
AU  - Zhu Y
AU  - Zhang H
AU  - Chen Z
AU  - Zheng X
AU  - Xiao R
AU  - Chen Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00900-17.

PMID- 1945846
VI  - 19
DP  - 1991
TI  - The inhibition of restriction endonuclease PvuII cleavage activity by methylation outside its recognition sequence.
PG  - 5703-5705
AB  - The recombinant plasmid pGEM4Z-ras DNA which was methylated on dam and dcm sites outside the
      PvuII recognition sequence was digested with restriction endonuclease PvuII, and one of the
      three PvuII sites was about 16-fold less efficient to cleave than either of the other two. On
      the contrary, the three PvuII sites were cleaved at about the same rate on the unmethylated
      DNA molecule. The results show that the cleavage inhibition of the methylated DNA on the
      certain PvuII site was caused by methylation outside the PvuII recognition sequence. Maybe an
      adjacent methylated dam site *A was responsible for the less efficient cleavage. This
      observation suggests that methylation outside the recognition sequence may be considered a new
      factor in the kinetic experiment of restriction endonuclease.
AU  - Chen D
AU  - Liu Q
AU  - Chen X
AU  - Zhao X
AU  - Chen Y
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 5703-5705.

PMID- 
VI  - 43
DP  - 1998
TI  - Molecular mechanism of the inhibitory effect of methylation outside the recognition sequence of restriction endonuclease PvuII on its cleavage activity.
PG  - 47-53
AB  - In 1991, we found that methylation outside the PvuII recognition sequence could partially
      inhibit its cleavage activity.  To clarify the molecular mechanism, three plasmids with
      different methylation states were constructed.  Then, together with the original one, four
      plasmids were digested with different amounts of PvuII.  Results show that methylation on both
      sites results in 90% inhibition; moving the methylated site one base further away decreases
      the inhibitory effect to about 30%; with the adjacent dam methylation site eliminated, the
      inhibitory effect disappears.  The data suggest that the inhibition of cleavage activity
      caused by outside methylation is not "all or none", and the degree of inhibition is dependent
      on the position and the number of methylated bases.
AU  - Chen D
AU  - Sun M
AU  - Liu Y
AU  - Shi G
AU  - Chen Y
PT  - Journal Article
TA  - Chinese Sci. Bull.
JT  - Chinese Sci. Bull.
SO  - Chinese Sci. Bull. 1998 43: 47-53.

PMID- 26380644
VI  - 10
DP  - 2015
TI  - High quality draft genomic sequence of Arenimonas donghaensis DSM 18148(T).
PG  - 59
AB  - Arenimonas donghaensis is the type species of genus Arenimonas which belongs to family
      Xanthomonadaceae within Gammaproteobacteria. In this study, a total of five type strains of
      Arenimonas were sequenced. The draft genomic information of  A. donghaensis DSM 18148(T) is
      described and compared with other four genomes of  Arenimonas. The genome size of A.
      donghaensis DSM 18148(T) is 2,977,056 bp distributed in 51 contigs, containing 2685
      protein-coding genes and 49 RNA genes.
AU  - Chen F
AU  - Wang H
AU  - Cao Y
AU  - Li X
AU  - Wang G
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 59.

PMID- 21245035
VI  - 39
DP  - 2011
TI  - Recognition of an expanded genetic alphabet by type-II restriction endonucleases and their application to analyze polymerase fidelity.
PG  - 3949-3961
AB  - To explore the possibility of using restriction enzymes in a synthetic biology based on
      artificially expanded genetic information systems
      (AEGIS), 24 type-II restriction endonucleases (REases) were challenged to
      digest DNA duplexes containing recognition sites where individual Cs and
      Gs were replaced by the AEGIS nucleotides Z and P [respectively,
      6-amino-5-nitro-3-(1'-beta-d-2'-deoxyribofuranosyl)-2(1H)-pyridone and
      2-amino-8-(1'-beta-d-2'-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4
      (8H)-one]. These AEGIS nucleotides implement complementary hydrogen bond
      donor-donor-acceptor and acceptor-acceptor-donor patterns. Results allowed
      us to classify type-II REases into five groups based on their performance,
      and to infer some specifics of their interactions with functional groups
      in the major and minor grooves of the target DNA. For three enzymes among
      these 24 where crystal structures are available (BcnI, EcoO109I and NotI),
      these interactions were modeled. Further, we applied a type-II REase to
      quantitate the fidelity polymerases challenged to maintain in a DNA duplex
      C:G, T:A and Z:P pairs through repetitive PCR cycles. This work thus adds
      tools that are able to manipulate this expanded genetic alphabet in vitro,
      provides some structural insights into the working of restriction enzymes,
      and offers some preliminary data needed to take the next step in synthetic
      biology to use an artificial genetic system inside of living bacterial
      cells.
AU  - Chen F
AU  - Yang Z
AU  - Yan M
AU  - Alvarado JB
AU  - Wang G
AU  - Benner SA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2011 39: 3949-3961.

PMID- 24309740
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Staphylococcus aureus Z172, a Vancomycin-Intermediate and Daptomycin-Nonsusceptible Methicillin-Resistant Strain Isolated in Taiwan.
PG  - e01011-13
AB  - We report the complete genome sequence of Z172, a representative strain of sequence type
      239-staphylococcal cassette chromosome mec type III (ST239-SCCmec
      type III) hospital-associated methicillin-resistant Staphylococcus aureus in
      Taiwan. Strain Z172 also exhibits a vancomycin-intermediate and
      daptomycin-nonsusceptible phenotype.
AU  - Chen FJ
AU  - Lauderdale TL
AU  - Wang LS
AU  - Huang IW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01011-13.

PMID- 28912314
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Dehalobacterium formicoaceticum Strain DMC, a Strictly Anaerobic Dichloromethane-Degrading Bacterium.
PG  - e00897-17
AB  - Dehalobacterium formicoaceticum utilizes dichloromethane as the sole energy source in defined
      anoxic bicarbonate-buffered mineral salt medium. The products
      are formate, acetate, inorganic chloride, and biomass. The bacterium's genome was
      sequenced using PacBio, assembled, and annotated. The complete genome consists of
      one 3.77-Mb circular chromosome harboring 3,935 predicted protein-encoding genes.
AU  - Chen G
AU  - Murdoch RW
AU  - Mack EE
AU  - Seger ES
AU  - Loffler FE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00897-17.

PMID- 3017522
VI  - 32
DP  - 1986
TI  - Restriction endonuclease activities in the legionellae.
PG  - 591-593
AB  - Studies of the restriction-modification system of bacteria led to the discovery
      of a number of endonucleases which recognize and cleave specific DNA base
      sequences.  These recognition sequences often consist of short palindromes and,
      in a number of instances, several different enzymes have been found with the
      same site specificity (isochizomers).  Because of their specificity,
      restriction endonucleases have been useful for the construction of recombinant
      DNA molecules and for DNA sequencing.  This system for detecting and destroying
      "foreign" DNA is found in such taxonomically diverse organisms as
      Acinetobacter, Nocardia, Nostoc, and Thermoplasma.  It is, therefore, not
      surprising to find restriction endonucleases in new groups of organisms as they
      are studied.  Because of differences in the recipient ability of several
      legionellae (Chen et al. 1984), we examined these strains for the presence of
      these enzymes.  We now report that several different restriction activities are
      present in various legionellae strains.
AU  - Chen GCC
AU  - Brown A
AU  - Lema MW
PT  - Journal Article
TA  - Can. J. Microbiol.
JT  - Can. J. Microbiol.
SO  - Can. J. Microbiol. 1986 32: 591-593.

PMID- 26203326
VI  - 10
DP  - 2015
TI  - Draft genome sequences for the obligate bacterial predators Bacteriovorax spp. of four phylogenetic clusters.
PG  - 11
AB  - Bacteriovorax is the halophilic genus of the obligate bacterial predators, Bdellovibrio and
      like organisms. The predators are known for their unique
      biphasic life style in which they search for and attack their prey in the free
      living phase; penetrate, grow, multiply and lyse the prey in the intraperiplasmic
      phase. Bacteriovorax isolates representing four phylogenetic clusters were
      selected for genomic sequencing. Only one type strain genome has been published
      so far from the genus Bacteriovorax. We report the genomes from non-type strains
      isolated from aquatic environments. Here we describe and compare the genomic
      features of the four strains, together with the classification and annotation.
AU  - Chen H
AU  - Brinkac LM
AU  - Mishra P
AU  - Li N
AU  - Lymperopoulou DS
AU  - Dickerson TL
AU  - Gordon-Bradley N
AU  - Williams HN
AU  - Badger JH
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 11.

PMID- 22923396
VI  - 78
DP  - 2012
TI  - Genomic and Transcriptomic Studies of an RDX (Hexahydro-1,3,5-Trinitro-1,3,5-Triazine)-Degrading Actinobacterium.
PG  - 7798-7800
AB  - Whole genome sequencing, transcriptomic analyses and metabolic reconstruction were used to
      investigate Gordonia sp. KTR9s ability to catabolize a range of compounds including explosives
      and steroids. Aspects of this mycolic acid-containing actinobacteriums catabolic potential
      were experimentally verified and compared with those of rhodococci and mycobacteria.
AU  - Chen H-P
AU  - Zhu S-H
AU  - Casabon I
AU  - Hallam SJ
AU  - Crocker FH
AU  - Mohn WW
AU  - Indest KJ
AU  - Eltis LD
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2012 78: 7798-7800.

PMID- 27313298
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequencing Analysis of Methicillin-Resistant Staphylococcus simulans Causing Surgical Site Infection.
PG  - e00555-16
AB  - Staphylococcus simulans is a normal part of the microbiota in humans and animals  and is
      rarely associated with human invasive infections. We present here the
      genome sequence of S. simulans CJ16, which caused the first case of surgical site
      infection. Adhesion proteins, including fibronectin-binding protein (FnbA),
      elastin-binding protein (EbpS), and cell wall-anchored protein (SasA, SasF, and
      SasH), were detected in the genome, which might promote the survival of S.
      simulans on human skin and pathogenesis of infections.
AU  - Chen J
AU  - Fang Q
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00555-16.

PMID- 2356119
VI  - 18
DP  - 1990
TI  - Heparin inhibits EcoRI endonuclease cleavage of DNA at certain EcoRI sites.
PG  - 3255
AB  - Studies presented here demonstrate that heparin inhibits EcoRI endonuclease
      cleavage of DNA whereas related proteoglycans show no effect.  The inhibition
      occurs at particular EcoRI sites that are near or overlap with palindromic
      sequences in the murine lambda5 and Lyt-2 genes.  Endogenous heparin from
      peritoneal mast cells co-isolates with DNA and inhibits digestion of peritoneal
      cell DNA at the inhibitable sites.  Digestion of spleen DNA is inhibited at the
      same sites when commerical heparin is added prior to digestion.  In both cases,
      the inhibition is abolished by pre-treating the DNA with heparinase.  Thus,
      potential artifacts in restriction fragment length analyses could occur with
      DNA isolated either from cells that are naturally rich in heparin or from cells
      to which heparin has been added, e.g., as an anticoagulant.
AU  - Chen J
AU  - Herzenberg LA
AU  - Herzenberg LA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 3255.

PMID- 24115539
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Xylella fastidiosa subsp. multiplex Strain Griffin-1 from Quercus rubra in Georgia.
PG  - e00756-13
AB  - The draft genome sequence of Xylella fastidiosa subsp. multiplex strain Griffin-1, isolated
      from a red oak tree (Quercus rubra) in Georgia, is reported
      here. The bacterium has a genome size of 2,387,314 bp, with a G+C content of
      51.7%. The Griffin-1 strain genome contains 2,903 predicted open reading frames
      and 50 RNA genes.
AU  - Chen J
AU  - Huang H
AU  - Chang CJ
AU  - Stenger DC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00756-13.

PMID- 29519826
VI  - 6
DP  - 2018
TI  - Whole-Genome Sequence of Phage-Resistant Strain Escherichia coli DH5alpha.
PG  - e00097-18
AB  - The genomes of many strains of Escherichia coli have been sequenced, as this organism is a
      classic model bacterium. Here, we report the genome sequence of
      Escherichia coli DH5alpha, which is resistant to a T4 bacteriophage (CCTCC AB
      2015375), while its other homologous E. coli strains, such as E. coli BL21,
      DH10B, and MG1655, are not resistant to phage invasions. Thus, understanding of
      the genome of the DH5alpha strain, along with comparative analysis of its genome
      sequence along with other sequences of E. coli strains, may help to reveal the
      bacteriophage resistance mechanism of E. coli.
AU  - Chen J
AU  - Li Y
AU  - Zhang K
AU  - Wang H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00097-18.

PMID- 27013039
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Alteromonas stellipolaris LMG 21856, a Budding Brown  Pigment-Producing Oligotrophic Bacterium Isolated from the Southern Ocean.
PG  - e00137-16
AB  - Here, we report the complete genome sequence ofAlteromonas stellipolarisLMG 21856, which was
      isolated from seawater collected from the Southern Ocean.A.
      stellipolarisLMG 21856 is a budding, psychrotrophic, brown pigment-producing, and
      oligotrophic bacterium.The complete genome of this bacterium contains 4,686,200
      bp, with a G+C content of 43.6%.
AU  - Chen J
AU  - Wang X
AU  - Zhu S
AU  - Chen Y
AU  - Yang J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00137-16.

PMID- 27103713
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Xylella fastidiosa subsp. fastidiosa Strain Stag's Leap.
PG  - e00240-16
AB  - ITALIC! Xylella fastidiosasubsp. ITALIC! fastidiosacauses Pierce's disease of grapevine.
      Presented here is the draft genome sequence of the Stag's Leap strain,
      previously used in pathogenicity/virulence assays to evaluate grapevine germplasm
      bearing Pierce's disease resistance and a phenotypic assessment of knockout
      mutants to determine gene function.
AU  - Chen J
AU  - Wu F
AU  - Zheng Z
AU  - Deng X
AU  - Burbank LP
AU  - Stenger DC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00240-16.

PMID- 21742872
VI  - 193
DP  - 2011
TI  - Genome sequence of a non-pathogenic Listeria monocytogenes serovar 4a strain M7.
PG  - 5019-5020
AB  - This report presents the complete and annotated genome sequence of a naturally non-pathogenic
      Listeria monocytogenes serovar 4a strain M7, isolated from cow's milk in Zhejiang province,
      China.
AU  - Chen J
AU  - Xia Y
AU  - Cheng C
AU  - Fang C
AU  - Shan Y
AU  - Jin G
AU  - Fang W
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5019-5020.

PMID- 20601474
VI  - 192
DP  - 2010
TI  - Two whole genome sequences of Xylella fastidiosa (strains M12 and M23) causing almond leaf scorch disease in California.
PG  - 4534
AB  - Xylella fastidiosa is a Gram negative plant pathogenic bacterium causing many economically
      important diseases including almond leaf scorch disease
      (ALSD) in California. Genome information greatly facilitates research in
      this nutritionally fastidious organism. Here we report the complete genome
      sequences of two ALSD strains, M12 and M23 of this bacterium.
AU  - Chen J
AU  - Xie G
AU  - Han S
AU  - Civerolo EL
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 4534.

PMID- 20576424
VI  - 26
DP  - 2010
TI  - A strategy for development of electrochemical DNA biosensor based on site-specific DNA cleavage of restriction endonuclease.
PG  - 144-148
AB  - A new strategy for development of electrochemical DNA biosensor based on site-specific DNA
      cleavage of restriction endonuclease and using
      quantum dots as reporter was reported in this paper The biosensor was
      fabricated by immobilizing a capture hairpin probe, thiolated single
      strand DNA labeled with biotin group, on a gold electrode BfuCl
      nuclease, which is able to specifically cleave only double strand DNA
      but not single strand DNA, was used to reduce background current and
      Improve the sensitivity We demonstrated that the capture hairpin probe
      can be cleaved by BfuCl nuclease in the absence of target DNA, but
      cannot be cleaved in the presence of target DNA. The difference before
      and after enzymatic cleavage was then monitored by electrochemical
      method after the quantum dots were dissolved from the hybrids Our
      results suggested that the usage of BfuCl nuclease obviously Improved
      the sensitivity and selectivity of the biosensor. We successfully
      applied this method to the sequence-selective discrimination between
      perfectly matched and mismatched target DNA including a single-base
      mismatched target DNA, and detected as low as 3 3 x 10(-14) M of
      complementary target DNA Furthermore, our above strategy was also
      verified with fluorescent method by designing a fluorescent molecular
      beacon (MB), which combined the capture hairpin probe and a pair of
      fluorophore (TAMRA) and quencher (DABCYL) The fluorescent results are
      consistent with that of electroanalysis, further indicating that the
      proposed new strategy indeed works as we expected.
AU  - Chen JH
AU  - Zhang J
AU  - Yang HH
AU  - Fu FF
AU  - Chen GN
PT  - Journal Article
TA  - Biosensors and Bioelectronics
JT  - Biosensors and Bioelectronics
SO  - Biosensors and Bioelectronics 2010 26: 144-148.

PMID- 23105069
VI  - 194
DP  - 2012
TI  - Genome Sequence of Dyella japonica Strain A8, a Quorum-Quenching Bacterium That Degrades N-Acylhomoserine Lactones, Isolated from Malaysian Tropical Soil.
PG  - 6331
AB  - Dyella japonica strain A8 is a Malaysian tropical soil bacterial strain which shows
      N-acylhomoserine lactone-degrading activity. Here, we present its draft
      genome sequence. A putative quorum-quenching gene was identified based on the
      genome sequence analysis of strain A8. To the best of our knowledge, this is the
      first genome announcement of a member from the genus of Dyella, and this is also
      the first work that reports the quorum-quenching activity of Dyella japonica.
AU  - Chen JW
AU  - Chan KG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6331.

PMID- 23144419
VI  - 194
DP  - 2012
TI  - Genome Sequence of Roseomonas sp. Strain B5, a Quorum-Quenching N-Acylhomoserine  Lactone-Degrading Bacterium Isolated from Malaysian Tropical Soil.
PG  - 6681-6682
AB  - Roseomonas sp. strain B5 was isolated from Malaysian tropical soil that showed
      N-acylhomoserine lactone degradation. This is the first genome announcement of a
      member from the genus of Roseomonas and the first report on the quorum-quenching
      activity of Roseomonas spp.
AU  - Chen JW
AU  - Gan HM
AU  - Yin WF
AU  - Chan KG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6681-6682.

PMID- 24368349
VI  - 1844
DP  - 2014
TI  - ArdA proteins from different mobile genetic elements can bind to the EcoKI Type I DNA methyltransferase of E. coli K12.
PG  - 505-511
AB  - Anti-restriction and anti-modification (anti-RM) is the ability to prevent cleavage by DNA
      restriction-modification (RM) systems of foreign DNA entering a new bacterial host. The
      evolutionary consequence of anti-RM is the enhanced dissemination of mobile genetic elements.
      Homologues of ArdA anti-RM proteins are encoded by genes present in many mobile genetic
      elements such as conjugative plasmids and transposons within bacterial genomes. The ArdA
      proteins cause anti-RM by mimicking the DNA structure bound by Type I RM enzymes. We have
      investigated ArdA proteins from the genomes of Enterococcus faecalis V583, Staphylococcus
      aureus Mu50 and Bacteroides fragilis NCTC 9343, and compared them to the ArdA protein
      expressed by the conjugative transposon Tn916. We find that despite having very different
      structural stability and secondary structure content, they can all bind to the EcoKI
      methyltransferase, a core component of the EcoKI Type I RM system. This finding indicates that
      the less structured ArdA proteins become fully folded upon binding. The ability of ArdA from
      diverse mobile elements to inhibit Type I RM systems from other bacteria suggests that they
      are an advantage for transfer not only between closely-related bacteria but also between more
      distantly related bacterial species.
AU  - Chen K
AU  - Reuter M
AU  - Sanghvi B
AU  - Roberts GA
AU  - Cooper LP
AU  - Tilling M
AU  - Blakely GW
AU  - Dryden DTF
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 2014 1844: 505-511.

PMID- 20599730
VI  - 398
DP  - 2010
TI  - Fusion of GFP to the M.EcoKI DNA methyltransferase produces a new probe of Type I DNA restriction and modification enzymes.
PG  - 254-259
AB  - We describe the fusion of enhanced green fluorescent protein to the C-terminus of the HsdS DNA
      sequence-specificity subunit of the Type I
      DNA modification methyltransferase M.EcoKI. The fusion expresses well
      in vivo and assembles with the two HsdM modification subunits. The
      fusion protein functions as a sequence-specific DNA methyltransferase
      protecting DNA against digestion by the EcoKI restriction endonuclease.
      The purified enzyme shows Forster resonance energy transfer to
      fluorescently-labelled DNA duplexes containing the target sequence and
      to fluorescently-labelled ocr protein, a DNA mimic that binds to the
      M.EcoKI enzyme. Distances determined from the energy transfer
      experiments corroborate the structural model of M.EcoKI.
AU  - Chen K
AU  - Roberts GA
AU  - Stephanou AS
AU  - Cooper LP
AU  - White JH
AU  - Dryden DTF
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 2010 398: 254-259.

PMID- 27193539
VI  - 915
DP  - 2016
TI  - The Type I Restriction Enzymes as Barriers to Horizontal Gene Transfer: Determination of the DNA Target Sequences Recognised by Livestock-Associated  Methicillin-Resistant Staphylococcus aureus Clonal Complexes 133/ST771 and 398.
PG  - 81-97
AB  - The Type I DNA restriction-modification (RM) systems of Staphylococcus aureus are known to act
      as a significant barrier to horizontal gene transfer between S.
      aureus strains belonging to different clonal complexes. The livestock-associated
      clonal complexes CC133/771 and CC398 contain Type I RM systems not found in human
      MRSA strains as yet but at some point transfer will occur. When this does take
      place, horizontal gene transfer of resistance will happen more easily between
      these strains. The reservoir of antibiotic resistance, virulence and
      host-adaptation genes present in livestock-associated MRSA will then potentially
      contribute to the development of newly evolving MRSA clones. The target sites
      recognised by the Type I RM systems of CC133/771 and CC398 were identified as
      CAG(N)5RTGA and ACC(N)5RTGA, respectively. Assuming that these enzymes recognise
      the methylation state of adenine, the underlined A and T bases indicate the
      unique positions of methylation. Target methylation points for enzymes from CC1
      were also identified. The methylation points for CC1-1 are CCAY(N)5TTAA and those
      for CC1-2 are CCAY(N)6 TGT with the underline indicating the adenine methylation
      site thus clearing up the ambiguity noted previously (Roberts et al. 2013,
      Nucleic Acids Res 41:7472-7484) for the half sites containing two adenine bases.
AU  - Chen K
AU  - Stephanou AS
AU  - Roberts GA
AU  - White JH
AU  - Cooper LP
AU  - Houston PJ
AU  - Lindsay JA
AU  - Dryden DT
PT  - Journal Article
TA  - Adv. Exp. Med. Biol.
JT  - Adv. Exp. Med. Biol.
SO  - Adv. Exp. Med. Biol. 2016 915: 81-97.

PMID- 15995215
VI  - 187
DP  - 2005
TI  - The genome of Sulfolobus acidocaldarius, a model organism of the Crenarchaeota.
PG  - 4992-4999
AB  - Sulfolobus acidocaldarius is an aerobic thermoacidophilic crenarchaeon which grows optimally
      at 80 degrees C and pH 2 in terrestrial solfataric springs.  Here, we describe the genome
      sequence of strain DSM639, which has been used for many seminal studies on archaeal and
      crenarchaeal biology.  The circular genome carries 2,225,959 bp (37% G+C) with 2,292 predicted
      protein-encoding genes.  Many of the smaller genes were identified for the first time on the
      basis of comparison of three Sulfolobus genome sequences.  Of the protein-coding genes, 305
      are exclusive to S.  acidocaldarius and 866 are specific to the Sulfolobus genus.  Moreover,
      82 genes for untranslated RNAs were identified and annotated.  Owing to the probable absence
      of active autonomous and nonautonomous mobile elements, the genome stability and organization
      of S.  acidocaldarius differ radically from those of Sulfolobus solfataricus and Sulfolobus
      tokodaii.  The S.  acidocaldarius genome contains an integrated, and probably encaptured,
      pARN-type conjugative plasmid which may facilitate intercellular chromosomal gene exchange in
      S.  acidocaldarius.  Moreover, it contains genes for a characteristic restriction modification
      system, a UV damage excision repair system, thermopsin, and an aromatic ring dioxygenase, all
      of which are absent from genomes of other Sulfolobus species.  However, it lacks genes for
      some of their sugar transporters, consistent with it growing on a more limited range of carbon
      sources.  These results, together with the many newly identified protein-coding genes for
      Sulfolobus, are incorporated into a public Sulfolobus database which can be accessed at
      http://dac.molbio.ku.dk/dbs/Sulfolobus.
AU  - Chen L
AU  - Brugger K
AU  - Skovgaard M
AU  - Redder P
AU  - She Q
AU  - Torarinsson E
AU  - Greve B
AU  - Awayez M
AU  - Zibat A
AU  - Klenk H-P
AU  - Garrett RA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2005 187: 4992-4999.

PMID- 26089425
VI  - 3
DP  - 2015
TI  - Genome Sequence of a Klebsiella pneumoniae Sequence Type 258 Isolate with Prophage-Encoded K. pneumoniae Carbapenemase.
PG  - e00659-15
AB  - We present the draft genome sequence of a Klebsiella pneumoniae carbapenemase (KPC)-producing
      sequence type 258 (ST258) K. pneumoniae strain, ST258_FL.
      Uniquely, strain ST258_FL harbors two copies of the blaKPC gene on the
      chromosome, one of which is integrated into a prophage.
AU  - Chen L
AU  - Chavda KD
AU  - DeLeo FR
AU  - Bryant KA
AU  - Jacobs MR
AU  - Bonomo RA
AU  - Kreiswirth BN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00659-15.

PMID- 23114770
VI  - 57
DP  - 2013
TI  - Complete nucleotide sequence of blaKPC-4 and blaKPC-5 harboring IncN and IncX plasmids from Klebsiella pneumoniae strains isolated in New Jersey.
PG  - 269-276
AB  - Klebsiella pneumoniae carbapenemase (KPC) producing Enterobacteriaceae have
      emerged as major nosocomial pathogens. bla(KPC), commonly located on Tn4401, is
      found in Gram-negative bacterial strains, with the two most common variants,
      bla(KPC-2) and bla(KPC-3), identified in plasmids with diverse genetic
      backgrounds. In this study, we examined bla(KPC-4) and bla(KPC-5) bearing
      plasmids recovered from two K. pneumoniae strains, isolated from a single New
      Jersey hospital in 2005 and 2006, respectively. IncN plasmid pBK31551 is 84kb in
      length, and harbors bla(KPC-4), bla(TEM-1), qnrB2, aac (3)-Ib, aph(3')-I, qacF,
      qacEDelta1, sul and dfrA14, which confer resistance to ss-lactams, quinolones,
      aminoglycosides, quaternary ammonium compounds and co-trimoxazole. The conserved
      regions within pBK31551 are similar to that of other IncN plasmids. Surprisingly,
      analysis of the Tn4401 sequence revealed a large IS110 and Tn6901carrying element
      (8.3kb) inserted into the istA gene, encoding glyoxalase/bleomycin resistance,
      alcohol dehydrogenase and S-formylglutathione hydrolase. Plasmid pBK31567 is 47kb
      in length, and harbors bla(KPC-5), dfrA5, qacEDelta1 and sul1. pBK31567 belongs
      to a novel IncX subgroup (IncX5), and possesses a highly syntenic plasmid
      backbone like other IncX plasmids; however, sequence similarity at the nucleotide
      level is divergent. The bla(KPC-5) gene is carried on a Tn4401 element, and
      differs from the genetic environment of bla(KPC-5) described in Pseudomonas
      aeruginosa strain P28 from Puerto Rico. This study underscores the genetic
      diversity of multidrug resistant plasmids involved in the spread of bla(KPC)
      genes, and highlights the mobility and plasticity of Tn4401. Comparative genomic
      analysis provides new insights into the evolution and dissemination of KPC
      plasmids belonging to different incompatibility groups.
AU  - Chen L
AU  - Chavda KD
AU  - Fraimow HS
AU  - Mediavilla JR
AU  - Melano RG
AU  - Jacobs MR
AU  - Bonomo RA
AU  - Kreiswirth BN
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2013 57: 269-276.

PMID- 24492370
VI  - 58
DP  - 2014
TI  - Molecular Survey of the Dissemination of Two blaKPC-Harboring IncFIA Plasmids in New Jersey and New York Hospitals.
PG  - 2289-2294
AB  - Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae strains have
      spread worldwide and become a major threat in health care facilities.
      Transmission of blaKPC, the plasmid-borne KPC gene, can be mediated by clonal
      spread and horizontal transfer. Here, we report the complete nucleotide sequences
      of two novel blaKPC-3-harboring IncFIA plasmids, pBK30661 and pBK30683. pBK30661
      is 74 kb in length, with a mosaic plasmid structure; it exhibits homologies to
      several other plasmids but lacks the plasmid transfer operon (tra) and the origin
      of transfer (oriT) that are required for plasmid transfer. pBK30683 is a
      conjugative plasmid with a cointegrated plasmid structure, comprising a 72-kb
      element that highly resembles pBK30661 (>99.9% nucleotide identities) and an
      extra 68-kb element that harbors tra and oriT. A PCR scheme was designed to
      detect the distribution of blaKPC-harboring IncFIA (pBK30661-like and
      pBK30683-like) plasmids in a collection of clinical Enterobacteriaceae isolates
      from 10 hospitals in New Jersey and New York. KPC-harboring IncFIA plasmids were
      found in 20% of 491 K. pneumoniae isolates, and all carried blaKPC-3.
      pBK30661-like plasmids were identified mainly in the epidemic sequence type 258
      (ST258) K. pneumoniae clone, while pBK30683-like plasmids were widely distributed
      in ST258 and other K. pneumoniae sequence types and among non-K. pneumoniae
      Enterobacteriaceae species. This suggests that both clonal spread and horizontal
      plasmid transfer contributed to the dissemination of blaKPC-harboring IncFIA
      plasmids in our area. Further studies are needed to understand the distribution
      of this plasmid group in other health care regions and to decipher the origins of
      pBK30661-like and pBK30683-like plasmids.
AU  - Chen L
AU  - Chavda KD
AU  - Melano RG
AU  - Hong T
AU  - Rojtman AD
AU  - Jacobs MR
AU  - Bonomo RA
AU  - Kreiswirth BN
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2014 58: 2289-2294.

PMID- 24614371
VI  - 58
DP  - 2014
TI  - Comparative Genomic Analysis of KPC-Encoding pKpQIL-Like Plasmids and Their Distribution in New Jersey and New York Hospitals.
PG  - 2871-2877
AB  - The global spread of Klebsiella pneumoniae carbapenemase (KPC) is predominately
      associated with K. pneumoniae strains genotyped as sequence type 258 (ST258). The
      first ST258-associated plasmid, pKpQIL, was described in Israel in 2006, but its
      history in the northeastern United States remains unknown. Six pKpQIL-like
      plasmids from four K. pneumoniae isolates (three ST258 and one ST234), one
      Escherichia coli isolate, and one Enterobacter aerogenes isolate, collected from
      2003 to 2010 in New York (NY) and New Jersey (NJ) hospitals, were completely
      sequenced. The sequences and overall sizes of the six plasmids are highly similar
      to those of pKpQIL; the major difference is that five of six NJ/NY strains harbor
      blaKPC-2, while pKpQIL contains blaKPC-3. Moreover, a 26.7-kb fragment was
      inverted in pKpQIL-234 (from ST234 K. pneumoniae), while a 14.5-kb region was
      deleted in pKpQIL-Ec (from ST131 E. coli). PCR screening of 284 other clinical K.
      pneumoniae isolates identified 101 (35.6%) harboring pKpQIL-like plasmids from 9
      of 10 surveyed hospitals, demonstrating the wide dissemination of pKpQIL in this
      region of endemicity. Among the positive isolates, 87.1% were typed as ST258 and
      88.1% carried blaKPC-2. The finding of pKpQIL-like plasmid in this study from
      strains that predate the initial report of KPC in Israel provides evidence that
      pKpQIL may have originated in the United States. Our findings demonstrate that
      pKpQIL plasmids are both spreading clonally in ST258 strains and spreading
      horizontally to different sequence types and species, further highlighting the
      clinical and public health concerns associated with carbapenem resistance.
AU  - Chen L
AU  - Chavda KD
AU  - Melano RG
AU  - Jacobs MR
AU  - Koll B
AU  - Hong T
AU  - Rojtman AD
AU  - Levi MH
AU  - Bonomo RA
AU  - Kreiswirth BN
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2014 58: 2871-2877.

PMID- 24395232
VI  - 58
DP  - 2014
TI  - Complete sequence of a KPC-producing IncN multidrug-resistant plasmid from an epidemic Escherichia coli ST131 strain in China.
PG  - 2422-2425
AB  - We report the nucleotide sequence of a novel blaKPC-2-harboring IncNplasmid,
      pECN580, from a multidrug-resistant Escherichia coli ST131 isolate recovered from
      Beijing, China. pECN580 harbors multiple antimicrobial resistance genes,
      including blaKPC-2, blaCTX-M-3, blaTEM-1, aac(6')-Ib-cr, qnrS1, arr-3 and dfrA14
      that confer beta-lactam, aminoglycoside, quinolone, rifampin and trimethoprim
      resistance. The emergence of blaKPC-2-harboring multidrug-resistant plasmid in
      epidemic E. coli ST131 clone poses a significant potential threat for both
      community and hospital settings.
AU  - Chen L
AU  - Hu H
AU  - Chavda KD
AU  - Zhao S
AU  - Liu R
AU  - Liang H
AU  - Zhang W
AU  - Wang X
AU  - Jacobs MR
AU  - Bonomo RA
AU  - Kreiswirth BN
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2014 58: 2422-2425.

PMID- 23830457
VI  - 53
DP  - 2013
TI  - Transposition of IS elements induced by electroporation of suicide plasmid in Acidithiobacillus caldus.
PG  - 165-169
AB  - Transposition insertional mutagenesis of the insertion sequences (IS elements) was discovered
      for the first time in Acidithiobacillus caldus
      (A. caldus), when A. caldus MTH-04 hsdM (type I
      restriction-modification system M-subunit) mutant was constructed by
      electroporation of a suicide plasmid. The IS element, specifically
      inserting into hsdM gene, was analyzed, identified, and named ISAtc2.
      The transposition frequency of ISAtc2 was ranged from 4% to 7%, and no
      reverse mutation occurred in the mutants after 50 generations of
      proliferation without selective pressure. These results revealed that
      transposition of IS elements on A. caldus chromosome could regulate the
      gene expression and metabolic pathways by gene inactivation, gene loss
      and gene acquisition. Therefore, the transposition of IS elements in A.
      caldus may be an important and unique regulation mechanism for
      adaptation to the living condition.
AU  - Chen L
AU  - Lin J
AU  - Liu X
AU  - Pang X
AU  - Lin H
AU  - Lin J
PT  - Journal Article
TA  - Enzyme Microb. Technol.
JT  - Enzyme Microb. Technol.
SO  - Enzyme Microb. Technol. 2013 53: 165-169.

PMID- 1932026
VI  - 30
DP  - 1991
TI  - Direct identification of the active-site nucleophile in a DNA (Cytosine-5)-methyltransferase.
PG  - 11018-11025
AB  - The overproduction, purification, and determination of the active-site catalytic nucleophile
      of the DNA (cytosine-5)-methyltransferase (DCMtase) enzyme, M.HaeIII are reported. Incubation
      of purified M.HaeIII with an oligodeoxynucleotide specifically modified with the
      mechanism-based inhibitor 5-fluoro-2'-deoxycytidine [Osterman, D.G., et al. (1988)
      Biochemistry 27,5204-5210], in the presence of the cofactor S-adenosyl-L-methionine (AdoMet),
      resulted in the formation of a covalent DNA-M.HaeIII complex, which was purified to
      homogeneity. Characterization of the intact complex showed it to consist of one molecule of
      the FdC-containing duplex oligonucleotide, one molecule of M.HaeIII, and one methyl group
      derived from AdoMet. Exhaustive proteolysis, reduction, and alkylation fof the DNA-M.HaeIII
      complex led to the isolation of two DNA-bound peptides-one each from treatment with Pronase or
      trypsin-which were subjected to peptide sequencing in order to identify the DNA attachment
      site. Both peptides were derived from the region of M.HaeIII containing a Pro-Cys sequence
      that is conserved in all known DCMtases. At the position of this conserved Cys residue
      (Cys71), in the sequence of each peptide, was found an unidentified amino acid residue; all
      other amino acid residues were in accord with the known sequence. It it thus concluded that
      Cys71 of M.HaeIII forms a covalent bond to DNA during catalytic methyl transfer. This finding
      represents a direct experimental verification for the hypothesis that the conserved Cys
      residue of DCMtases is the catalytic nucleophile [Wu, J.C., & Santi, D.V. (1987) J. Biol.
      Chem. 262,4778-4786]. Furthermore, the present studies provide ready access to large
      quantities of a homogeneous, covalent protein-DNA complex that is trapped at an intermediate
      state in catalysis.
AU  - Chen L
AU  - MacMillan AM
AU  - Chang W
AU  - Ezaz-Nikpay K
AU  - Lane WS
AU  - Verdine GL
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1991 30: 11018-11025.

PMID- Not included in PubMed...
VI  - 115
DP  - 1993
TI  - Mutational separation of DNA binding from catalysis in a DNA cytosine methyltransferase.
PG  - 5318-5319
AB  - Despite the substantial progress made toward understanding sequence-specific recognition of
      DNA by regulatory proteins, the details of catalysis by DNA-modifying proteins remain poorly
      understood. The inherently transient nature of catalytic protein-DNA complexes presents
      problems for their characterization by X-ray crystallography or NMR spectroscopy. Catalytic
      DNA-binding proteins thus present the challenge of discovering how to stall or subvert the
      catalytic process so as to obtain a stable macromolecular complex. In this communication we
      report the use of site-direced mutagenesis to separate catalysis from DNA binding in a DNA
      (cytosine-5)-methyltransferase (DC-Mtase) enzyme.
AU  - Chen L
AU  - MacMillan AM
AU  - Verdine GL
PT  - Journal Article
TA  - J. Am. Chem. Soc.
JT  - J. Am. Chem. Soc.
SO  - J. Am. Chem. Soc. 1993 115: 5318-5319.

PMID- 19726600
VI  - 47
DP  - 2009
TI  - Multiplex real-time PCR for rapid Staphylococcal cassette chromosome mec typing.
PG  - 3692-3706
AB  - Rapid identification and typing of methicillin (meticillin)-resistant
      Staphylococcus aureus (MRSA) is important for understanding the molecular
      epidemiology and evolution of MRSA and offers many advantages for
      controlling transmission in both health care and community settings. We
      developed a rapid molecular beacon real-time PCR (MB-PCR) assay for
      staphylococcal cassette chromosome mec (SCCmec) typing. The design of this
      system is based on the established definition of SCCmec types, namely, the
      combination of the mec class complex with the ccr allotype. The assay
      consists of two multiplex panels, the combination of which results in two
      targets (mec class, ccr) for each SCCmec type. MB-PCR panel I targets
      mecA, ccrB2, mecI, and the DeltamecR1-IS1272 junction (mec class B); it
      can definitively identify SCCmec types II and IV. MB-PCR panel II detects
      ccrC, ccrB1, ccrB3, ccrB4, and the DeltamecR1-IS431 junction (mec class
      C2) and is therefore capable of identifying SCCmec types I, III, V, and VI
      in combination with panel I. The method can also detect the recently
      described novel SCCmec type VIII (ccrAB4 with mec class A). Our assay
      demonstrated 100% concordance when applied to 162 MRSA strains previously
      characterized by traditional SCCmec typing schemes. Four geographically
      and temporally diverse S. aureus collections were also successfully
      classified by our assay, along with 1,683 clinical isolates comprising
      both hospital- and community-associated MRSA and methicillin-susceptible
      S. aureus strains. As many as 96 isolates can be classified easily within
      3 to 4 h, including DNA isolation, PCR cycling, and analysis. The assay is
      rapid, robust, sensitive, and cost-effective, allowing for high-throughput
      SCCmec typing of MRSA isolates.
AU  - Chen L
AU  - Mediavilla JR
AU  - Oliveira DC
AU  - Willey BM
AU  - de Lencastre H
AU  - Kreiswirth BN
PT  - Journal Article
TA  - J. Clin. Microbiol.
JT  - J. Clin. Microbiol.
SO  - J. Clin. Microbiol. 2009 47: 3692-3706.

PMID- 20479198
VI  - 54
DP  - 2010
TI  - Identification of a novel transposon (Tn6072) and a truncated staphylococcal cassette chromosome mec element in methicillin-resistant Staphylococcus aureus ST239.
PG  - 3347-3354
AB  - A novel composite transposon (Tn6072) resembling staphylococcal cassette
      chromosome mercury (SCCHg) was identified in a collection of sequence type
      (ST) 239 methicillin (meticillin)-resistant Staphylococcus aureus (MRSA)
      isolates from Romanian hospitals. Tn6072 is homologous to the 5' region of
      SCCHg found in staphylococcal cassette chromosome mec (SCCmec) type III
      prototype strain 85/2082 but lacks the characteristic mer operon. SCCHg
      has previously been reported to integrate downstream of orfX, at the same
      chromosomal location as SCCmec. Tn6072, by contrast, is demarcated by two
      IS431 elements, flanked by 8-bp direct repeats, and inserted upstream of
      the origin of replication, within an open reading frame homologous to
      SAR2700 of S. aureus strain MRSA252. Analysis of a geographically and
      temporally diverse collection of 111 strains from the ST239 clonal group
      uncovered 11 additional strains harboring Tn6072, demonstrating a
      lineage-specific insertion pattern. Complete sequence analysis of the
      SCCmec regions of two representative Romanian strains (BK16704, BK16691)
      revealed two additional novel structures derived from a type III SCCmec
      background. BK16704 possesses an SCCmec 3A.1.4 structure, with an IS256
      insertion downstream of the right chromosomal junction. In contrast, the
      SCCmec element of BK16691 is truncated downstream of the mec gene complex,
      with a 24-kb deletion encompassing the right chromosomal junction and an
      inverted downstream IS256 element. This structure, tentatively named
      "psiSCCmec16691," confers methicillin resistance but lacks most of the
      J1/J2 region, including the ccr gene complex. Taken together, these
      findings provide evidence for the continuing evolution of SCC elements, as
      well as the ST239 clonal group.
AU  - Chen L
AU  - Mediavilla JR
AU  - Smyth DS
AU  - Chavda KD
AU  - Ionescu R
AU  - Roberts RB
AU  - Robinson DA
AU  - Kreiswirth BN
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2010 54: 3347-3354.

PMID- 12904568
VI  - 149
DP  - 2003
TI  - Alteration of DNA adenine methylase (Dam) activity in Pasteurella multocida causes increased spontaneous mutation frequency and attenuation in mice.
PG  - 2283-2290
AB  - Pasteurella multocida is one of the primary bacterial pathogens associated with bovine
      respiratory disease (BRD) complex. Relatively few virulence
      factors of P. multocida have been characterized, and there is a need for
      improved vaccines for prevention of BRD. In other Gram-negative species,
      DNA adenine methylase (Dam) regulates the expression of virulence genes,
      and appropriate expression of Dam is required for virulence. In this
      study, the authors cloned and sequenced the P. multocida A1 dam gene and
      demonstrated that it is able to restore Dam function in an Escherichia
      coli dam mutant. When P. multocida dam was placed under the control of a
      constitutively expressed promoter on a plasmid, it caused an increased
      spontaneous mutation rate in P. multocida. In addition, the
      plasmid-mediated alteration of Dam production in P. multocida caused it to
      be highly attenuated in mice. These findings indicate that appropriate
      expression of Dam is required for virulence of P. multocida, which is
      believed to be the first report that Dam is required for virulence of a
      species in the Pasteurellaceae. Therefore, Dam may function as a virulence
      gene regulator in the Pasteurellaceae, similar to previously reported
      findings from other Gram-negative species.
AU  - Chen L
AU  - Paulsen DB
AU  - Scruggs DW
AU  - Banes MM
AU  - Reeks BY
AU  - Lawrence ML
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2003 149: 2283-2290.

PMID- 21925811
VI  - 155
DP  - 2012
TI  - Electrotransformation of Haemophilus parasuis with in vitro modified DNA based on a novel shuttle vector.
PG  - 310-316
AB  - The objective of the present study was to establish a valid transformation method of
      Haemophilus parasuis, the causative agent of
      Glasser's disease in pigs, using a novel H. parasuis-Escherichia coli
      shuttle vector. A 4.2 kb endogenous plasmid pYC93 was extracted from an
      H. parasuis field isolate and completely sequenced. Analysis of pYC93
      revealed a region approximately 800 bp showing high homology with the
      defined replication origin oriV of pLS88, a native plasmid identified
      in Haemophilus ducreyi. Based on the origin region of pYC93, E. coli
      cloning vector pBluescript SK(+) and the Tn903 derived kanamycin
      cassette, a shuttle vector pSHK4 was constructed by overlapping PCR
      strategy. When electroporation of the 15 H. parasuis serovar reference
      strains and one clinical isolate SH0165 with pSHK4 was performed, only
      one of these strains yielded transformants with an efficiency of 8.5 x
      10(2) CFUhlg of DNA. Transformation efficiency was notably increased
      (1.3 x 10(5) CFU/mu g of DNA) with vector DNA reisolated from the
      homologous transformants. This demonstrated that
      restriction-modification systems were involved in the barrier to
      transformation of H. parasuis. By utilizing an in vitro DNA
      modification method with cell-free extracts of the host H. parasuis
      strains, 15 out of 16 strains were transformable. The novel shuttle
      vector pSHK4 and the established electrotransformation method
      constitute useful tools for the genetic manipulation of H. parasuis to
      gain a better understanding of the pathogen.
AU  - Chen L
AU  - Wu D
AU  - Cai X
AU  - Guo F
AU  - Blackall PJ
AU  - Xu X
AU  - Chen H
PT  - Journal Article
TA  - Vet. Microbiol.
JT  - Vet. Microbiol.
SO  - Vet. Microbiol. 2012 155: 310-316.

PMID- 25237021
VI  - 2
DP  - 2014
TI  - Whole-Genome Sequences of Two Clinical Isolates of Extensively Drug-Resistant Mycobacterium tuberculosis from Zunyi, China.
PG  - e00910-14
AB  - Before 2013, 92 countries reported extensively drug-resistant Mycobacterium tuberculosis cases
      to the WHO. Here, we announce the genome sequences of two
      clinical isolates of extensively drug-resistant tuberculosis (XDR-TB) from Zunyi,
      China. The genome sequences are composed of 4,411,507 bp and 4,411,515 bp with
      2,210 and 2,071 variants, respectively, when compared to the H37Rv genome.
AU  - Chen L
AU  - Zhang DT
AU  - Zhang J
AU  - Su YA
AU  - Zhang H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00910-14.

PMID- Not carried by PubMed...
VI  - 42
DP  - 1996
TI  - The synthesis of nine kinds of oligodeoxynucleotide containing the recognition sequence for PstI and their interaction with enzyme.
PG  - 499-506
AB  - In this paper, nine kinds of oligodeoxynucleotide containing the recognition sequence of
      restriction endonuclease PstI have been synthesized by a solid phase phosphite-triester method
      or a combination of chemical and enzymatic methods.  The results of their enzymatic hydrolysis
      show that the existence of uridine in the recognition sequence of PstI has little influence on
      the cleavage of this strand, but reduces the cleavage rate of its complementary strand; PstI
      cleaves its substrate through  single strand cleavage in two steps.  The minimum PstI
      substrate is an eight to twelve long oligodeoxynucleotide containing its recognition sequence,
      and there is a requirement to the base pair numbers on both sides of PstI recognition
      sequence. The two cytidines in the recognition sequence of PstI don't play the same role in
      enzymatic hydrolysis.
AU  - Chen L
AU  - Zou G
AU  - Cao X
AU  - Rufan Z
PT  - Journal Article
TA  - J. Wuhan Univ.
JT  - J. Wuhan Univ.
SO  - J. Wuhan Univ. 1996 42: 499-506.

PMID- 23950120
VI  - 1
DP  - 2013
TI  - Genome Sequence of Klebsiella oxytoca SA2, an Endophytic Nitrogen-Fixing Bacterium Isolated from the Pioneer Grass Psammochloa villosa.
PG  - e00601-13
AB  - Klebsiella oxytoca strain SA2 is an endophytic nitrogen-fixing bacterium isolated from the
      pioneer grass Psammochloa villosa, which grows in the moving sand dunes
      of Ordos Plateau, China. The SA2 genome sequence provides the genetic background
      for understanding its endophytic lifestyle and survival in association with grass
      in nitrogen-poor environments.
AU  - Chen M
AU  - Lin L
AU  - Zhang Y
AU  - Sun L
AU  - An Q
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00601-13.

PMID- 29439045
VI  - 6
DP  - 2018
TI  - Draft Whole-Genome Sequences of Zhihengliuella halotolerans La12 and Microbacterium kitamiense Sa12, Strains with Cellulase Activity, Isolated from  the Qinghai-Tibetan Plateau.
PG  - e01531-17
AB  - We report the complete genome sequences of cellulolytic strains Zhihengliuella halotolerans
      La12 and Microbacterium kitamiense Sa12, which were isolated from
      soil samples collected from the Qinghai-Tibetan Plateau in Western China. The
      final assemblies of La12 and Sa12 comprise 3,712,694 bp, with over 111 contigs,
      and 3,830,439 bp, with over 39 contigs, respectively.
AU  - Chen M
AU  - Qin N
AU  - Pei W
AU  - Li Q
AU  - Yang Q
AU  - Chen Y
AU  - Huang D
AU  - Xiang Y
AU  - Lin L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01531-17.

PMID- 21994926
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of the Type Strain Pseudomonas stutzeri CGMCC 1.1803.
PG  - 6095
AB  - Here we report the complete genome sequence of Pseudomonas stutzeri strain CGMCC 1.1803
      (equivalent to ATCC 17588), the type strain of P. stutzeri,
      which encodes 4,138 open reading frames on a 4,547,930-bp circular
      chromosome. The CGMCC 1.1803 genome contains genes involved in
      denitrification, benzoate/catechol degradation, chemotaxis, and other
      functions.
AU  - Chen M
AU  - Yan Y
AU  - Zhang W
AU  - Lu W
AU  - Wang J
AU  - Ping S
AU  - Lin M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6095.

PMID- 25197499
VI  - 9
DP  - 2014
TI  - Complete genome sequence of Kosakonia sacchari type strain SP1(T.).
PG  - 1311-1318
AB  - Kosakonia sacchari sp. nov. is a new species within the new genus Kosakonia, which was
      included in the genus Enterobacter. K sacchari is a nitrogen-fixing
      bacterium named for its association with sugarcane (Saccharum officinarum L.). K
      sacchari bacteria are Gram-negative, aerobic, non-spore-forming, motile rods.
      Strain SP1(T) (=CGMCC1.12102(T)=LMG 26783(T)) is the type strain of the K
      sacchari sp. nov and is able to colonize and fix N2 in association with sugarcane
      plants, thus promoting plant growth. Here we summarize the features of strain
      SP1(T) and describe its complete genome sequence. The genome contains a single
      chromosome and no plasmids, 4,902,024 nucleotides with 53.7% GC content, 4,460
      protein-coding genes and 105 RNA genes including 22 rRNA genes, 82 tRNA genes,
      and 1 ncRNA gene.
AU  - Chen M
AU  - Zhu B
AU  - Lin L
AU  - Yang L
AU  - Li Y
AU  - An Q
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 1311-1318.

PMID- 29472346
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of an Extracellular Protease-Producing Bacterium, Stenotrophomonas bentonitica VV6, Isolated from Arctic Seawater.
PG  - e01610-17
AB  - The draft genome sequence of the extracellular protease-producing bacterium Stenotrophomonas
      bentonitica VV6, isolated from Arctic seawater, was established.
      The genome size was approximately 4.365 Mb, with a G+C content of 66.54%, and it
      contains 3,871 predicted protein-coding sequences (CDSs) and 60 tRNAs.
AU  - Chen MX
AU  - Li HY
AU  - Ye XS
AU  - He XY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01610-17.

PMID- 27836852
VI  - 83
DP  - 2017
TI  - Comparative Genomics Reveals the Diversity of Restriction-Modification Systems and DNA Methylation Sites in Listeria monocytogenes.
PG  - e02091-16
AB  - Listeria monocytogenes is a bacterial pathogen that is found in a wide variety of
      anthropogenic and natural environments. Genome sequencing technologies are
      rapidly becoming a powerful tool in facilitating our understanding of how
      genotype, classification phenotypes, and virulence phenotypes interact to predict
      the health risks of individual bacterial isolates. Currently, 57 closed L.
      monocytogenes genomes are publicly available, representing three of the four
      phylogenetic lineages, and they suggest that L. monocytogenes has high genomic
      synteny. This study contributes an additional 15 closed L. monocytogenes genomes
      that were used to determine the associations between the genome and methylome
      with host invasion magnitude. In contrast to previous findings, large chromosomal
      inversions and rearrangements were detected in five isolates at the chromosome
      terminus and within rRNA genes, including a previously undescribed inversion
      within rRNA-encoding regions. Each isolate's epigenome contained highly diverse
      methyltransferase recognition sites, even within the same serotype and
      methylation pattern. Eleven strains contained a single chromosomally encoded
      methyltransferase, one strain contained two methylation systems (one system on a
      plasmid), and three strains exhibited no methylation, despite the occurrence of
      methyltransferase genes. In three isolates a new, unknown DNA modification was
      observed in addition to diverse methylation patterns, accompanied by a novel
      methylation system. Neither chromosome rearrangement nor strain-specific patterns
      of epigenome modification observed within virulence genes were correlated with
      serotype designation, clonal complex, or in vitro infectivity. These data suggest
      that genome diversity is larger than previously considered in L. monocytogenes
      and that as more genomes are sequenced, additional structure and methylation
      novelty will be observed in this organism. IMPORTANCE: Listeria monocytogenes is
      the causative agent of listeriosis, a disease which manifests as gastroenteritis,
      meningoencephalitis, and abortion. Among Salmonella, Escherichia coli,
      Campylobacter, and Listeria-causing the most prevalent foodborne
      illnesses-infection by L. monocytogenes carries the highest mortality rate. The
      ability of L. monocytogenes to regulate its response to various harsh
      environments enables its persistence and transmission. Small-scale comparisons of
      L. monocytogenes focusing solely on genome contents reveal a highly syntenic
      genome yet fail to address the observed diversity in phenotypic regulation. This
      study provides a large-scale comparison of 302 L. monocytogenes isolates,
      revealing the importance of the epigenome and restriction-modification systems as
      major determinants of L. monocytogenes phylogenetic grouping and subsequent
      phenotypic expression. Further examination of virulence genes of select outbreak
      strains reveals an unprecedented diversity in methylation statuses despite high
      degrees of genome conservation.
AU  - Chen P
AU  - den Bakker HC
AU  - Korlach J
AU  - Kong N
AU  - Storey DB
AU  - Paxinos EE
AU  - Ashby M
AU  - Clark T
AU  - Luong K
AU  - Wiedmann M
AU  - Weimer BC
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2017 83: e02091-16.

PMID- 24725482
VI  - 22
DP  - 2014
TI  - Exploring bacterial epigenomics in the next-generation sequencing era: a new approach for an emerging frontier.
PG  - 292-300
AB  - Epigenetics has an important role for the success of foodborne pathogen persistence in diverse
      host niches. Substantial challenges exist in determining DNA methylation to situation-specific
      phenotypic traits. DNA modification, mediated by restriction-modification systems, functions
      as an immune response against antagonistic external DNA, and bacteriophage-acquired
      methyltransferases (MTase) and orphan MTases - those lacking the cognate restriction
      endonuclease - facilitate evolution of new phenotypes via gene expression modulation via DNA
      and RNA modifications, including methylation and phosphorothioation. Recent establishment of
      large-scale genome sequencing projects will result in a significant increase in genome
      availability that will lead to new demands for data analysis including new predictive
      bioinformatics approaches that can be verified with traditional scientific rigor. Sequencing
      technologies that detect modification coupled with mass spectrometry to discover new adducts
      is a powerful tactic to study bacterial epigenetics, which is poised to make novel and
      far-reaching discoveries that link biological significance and the bacterial epigenome.
AU  - Chen P
AU  - Jeannotte R
AU  - Weimer BC
PT  - Journal Article
TA  - Trends Microbiol.
JT  - Trends Microbiol.
SO  - Trends Microbiol. 2014 22: 292-300.

PMID- 28183778
VI  - 5
DP  - 2017
TI  - 100K Pathogen Genome Project: 306 Listeria Draft Genome Sequences for Food Safety and Public Health.
PG  - e00967-16
AB  - Listeria monocytogenes is a food-associated bacterium that is responsible for food-related
      illnesses worldwide. This is the initial public release of 306 L.
      monocytogenes genome sequences as part of the 100K Pathogen Genome Project. These
      isolates represent global genomic diversity in L. monocytogenes.
AU  - Chen P
AU  - Kong N
AU  - Huang B
AU  - Thao K
AU  - Ng W
AU  - Storey DB
AU  - Arabyan N
AU  - Foutouhi A
AU  - Foutouhi S
AU  - Weimer BC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00967-16.

PMID- 17196173
VI  - 353
DP  - 2007
TI  - Differential dependence on DNA ligase of type II restriction enzymes: A practical way toward ligase-free DNA automaton.
PG  - 733-737
AB  - DNA computing study is a new paradigm in computer science and biological computing fields. As
      one of DNA computing approaches, DNA automaton is
      composed of the hardware, input DNA molecule and state transition
      molecules. By now restriction enzymes are key hardware for DNA computing
      automaton. It has been found that DNA computing efficiency may be
      independent on DNA ligases when type IIS restriction enzymes like FokI are
      used as hardware. In this study, we compared FokI with four other distinct
      enzymes HgaI, BsmFI, BbsI, and BseMII, and found their differential
      independence on T4 DNA ligase when performing automaton reactions. Since
      DNA automaton is a potential powerful tool to tackle gene relationship in
      genomic network scale, the feasible ligase-free DNA automaton may set an
      initial base to develop functional DNA automata for various DNA technology
      development and implications in genetics study in the near future.
AU  - Chen P
AU  - Li J
AU  - Zhao J
AU  - He L
AU  - Zhang Z
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 2007 353: 733-737.

PMID- 24526629
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Bacillus subtilis Type Strain B7-S, Which Converts Ferulic Acid to Vanillin.
PG  - e00025-14
AB  - The Bacillus subtilis type strain B7-S was obtained through induction with ferulic acid. Here,
      we present the draft genome of strain B7-S, which contains
      5,313,924 bp, with a G+C content of 35.8%, 5,135 protein-coding genes, and 40
      tRNA-encoding genes.
AU  - Chen P
AU  - Li S
AU  - Yan L
AU  - Wang N
AU  - Yan X
AU  - Li H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00025-14.

PMID- 29437098
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of a New Halophilic Archaeon, Haloarcula taiwanensis, Isolated from a Solar Saltern in Southern Taiwan.
PG  - e01529-17
AB  - We report here the completion of the genome sequence of a new species of haloarchaea,
      Haloarcula taiwanensis, isolated in southern Taiwan. The
      3,721,706-bp genome consisted of chromosome I (2,966,258 bp, 63.6% GC content),
      chromosome II (525,233 bp, 59.6% GC content), plasmid pNYT1 (129,893 bp, 55.3% GC
      content), and plasmid pNYT2 (100,322 bp, 55.7% GC content).
AU  - Chen PC
AU  - Chen TW
AU  - Han YA
AU  - Ng WV
AU  - Yang CS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01529-17.

PMID- 18849429
VI  - 190
DP  - 2008
TI  - In Vitro CpG Methylation Increases the Transformation Efficiency of Borrelia burgdorferi Strains Harboring the Endogenous Linear Plasmid lp56.
PG  - 7885-7891
AB  - Borrelia burgdorferi is the causative agent of Lyme disease, the most common vector-borne
      illness in the Northern hemisphere.
      Low-passage-number infectious strains of B. burgdorferi exhibit
      extremely low transformation efficiencies-so low, in fact, as to hinder
      the genetic study of putative virulence factors. Two putative
      restriction-modification (R-M) systems, BBE02 contained on linear
      plasmid 25 ( lp25) and BBQ67 contained on lp56, have been postulated to
      contribute to this poor transformability. Restriction barriers posed by
      other bacteria have been overcome by the in vitro methylation of DNA
      prior to transformation. To test whether a methylation-sensitive
      restriction system contributes to poor B. burgdorferi transformability,
      shuttle plasmids were treated with the CpG methylase M. SssI prior to
      the electroporation of a variety of strains harboring different
      putative R-M systems. We found that for B. burgdorferi strains that
      harbor lp56, in vitro methylation increased transformation by at least
      1 order of magnitude. These results suggest that in vitro CpG
      methylation protects exogenous DNA from degradation by an
      lp56-contained R-M system, presumably BBQ67. The utility of in vitro
      methylation for the genetic manipulation of B. burgdorferi was
      exemplified by the ease of plasmid complementation of a B. burgdorferi
      B31 A3 BBK32 kanamycin-resistant ( B31 A3 BBK32:: Kan(r)) mutant,
      deficient in the expression of the fibronectin- and glycosaminoglycan (
      GAG)-binding adhesin BBK32. Consistent with the observation that
      several surface proteins may promote GAG binding, the B. burgdorferi
      B31 A3 BBK32:: Kanr mutant demonstrated no defect in the ability to
      bind purified GAGs or GAGs expressed on the surfaces of cultured cells.
AU  - Chen Q
AU  - Fischer JR
AU  - Benoit VM
AU  - Dufour NP
AU  - Youderian P
AU  - Leong JM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2008 190: 7885-7891.

PMID- 24928877
VI  - 80
DP  - 2014
TI  - Novel three-component Rieske non-heme iron oxygenase system catalyzing the N-dealkylation of chloroacetanilide herbicides in sphingomonads DC-6 and DC-2.
PG  - 5078-5085
AB  - Sphingomonads DC-6 and DC-2 degrade the chloroacetanilide herbicides alachlor,
      acetochlor, and butachlor via N-dealkylation. In this study, we report a
      three-component Rieske non-heme iron oxygenase (RHO) system catalyzing the
      N-dealkylation of these herbicides. The oxygenase component gene cndA is located
      in a transposable element that is highly conserved in the two strains. CndA
      shares 24 to 42% amino acid sequence identities with the oxygenase components of
      some RHOs that catalyze N- or O-demethylation. Two putative [2Fe-2S] ferredoxin
      genes and one glutathione reductase (GR)-type reductase gene were retrieved from
      the genome of each strain. These genes were not located in the immediate vicinity
      of cndA. The four ferredoxins share 64 to 72% amino acid sequence identities to
      the ferredoxin component of dicamba O-demethylase (DMO), and the two reductases
      share 62 to 65% amino acid sequence identities to the reductase component of DMO.
      cndA, the four ferredoxin genes, and the two reductases genes were expressed in
      Escherichia coli, and the recombinant proteins were purified using Ni-affinity
      chromatography. The individual components or the components in pairs displayed no
      activity; the enzyme mixture showed N-dealkylase activities toward alachlor,
      acetochlor, and butachlor only when CndA-His6 was combined with one of the four
      ferredoxins and one of the two reductases, suggesting that the enzyme consists of
      three components, a homo-oligomer oxygenase, a [2Fe-2S] ferredoxin, and a GR-type
      reductase, and CndA has a low specificity for the electron transport component
      (ETC). The N-dealkylase utilizes NADH, but not NADPH, as the electron donor.
AU  - Chen Q
AU  - Wang CH
AU  - Deng SK
AU  - Wu YD
AU  - Li Y
AU  - Yao L
AU  - Jiang JD
AU  - Yan X
AU  - He J
AU  - Li SP
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2014 80: 5078-5085.

PMID- 29798924
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Carbapenem-Resistant Klebsiella pneumoniae XPY20 Collected from a Bloodstream Infection Patient.
PG  - e00443-18
AB  - Bloodstream infections caused by carbapenem-resistant Klebsiella pneumoniae (CRKP) strains
      have been a severe problem with high clinical costs and high
      mortality rates. The blaKPC-2-producing CRKP strain XPY20 was collected from the
      blood of a patient. The genome characteristics and antimicrobial resistance
      mechanisms were determined using next-generation sequencing.
AU  - Chen Q
AU  - Zhou JW
AU  - Wu SH
AU  - Meng XH
AU  - Yu DJ
AU  - Wang XJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00443-18.

PMID- 26564040
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Bacillus tequilensis Strain FJAT-14262a.
PG  - e01317-15
AB  - Bacillus tequilensis FJAT-14262a is a Gram-positive rod-shaped bacterium. Here, we report the
      4,038,551-bp genome sequence of B. tequilensis FJAT-14262a, which
      will provide useful information for genomic taxonomy and phylogenomics of
      Bacillus.
AU  - Chen QQ
AU  - Liu B
AU  - Liu GH
AU  - Wang JP
AU  - Che JM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01317-15.

PMID- 29880589
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Lactobacillus reuteri WHH1689, Isolated from Traditional Chinese Highland Barley Wine.
PG  - e00425-18
AB  - Here, we report the complete genome sequence of Lactobacillus reuteri WHH1689, which was
      isolated from traditional Chinese highland barley wine in the Tibetan
      Plateau of China. The genome consists of a circular chromosome (2.04 Mb).
AU  - Chen S
AU  - Chen L
AU  - Chen L
AU  - Ren X
AU  - Ge H
AU  - Kang G
AU  - Sun S
AU  - Chen Z
AU  - Sun Y
AU  - Li Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00425-18.

PMID- 28495779
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Mycoplasma bovis Strain 08M.
PG  - e00324-17
AB  - Mycoplasma bovis is a major bacterial pathogen that can cause respiratory disease, mastitis,
      and arthritis in cattle. We report here the complete and
      annotated genome sequence of M. bovis strain 08M, isolated from a calf lung with
      pneumonia in China.
AU  - Chen S
AU  - Hao H
AU  - Zhao P
AU  - Gao P
AU  - He Y
AU  - Ji W
AU  - Wang Z
AU  - Lu Z
AU  - Liu Y
AU  - Chu Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00324-17.

PMID- 28932346
VI  - 12
DP  - 2017
TI  - Insights from the draft genome into the pathogenicity of a clinical isolate of Elizabethkingia meningoseptica Em3.
PG  - 56
AB  - Elizabethkingia meningoseptica is an emerging, healthcare-associated pathogen causing a high
      mortality rate in immunocompromised patients. We report the draft
      genome sequence of E. meningoseptica Em3, isolated from sputum from a patient
      with multiple underlying diseases. The genome has a length of 4,037,922 bp, a
      GC-content 36.4%, and 3673 predicted protein-coding sequences. Average nucleotide
      identity analysis (>95%) assigned the bacterium to the species E. meningoseptica.
      Genome analysis showed presence of the curli formation and assembly operon and a
      gene encoding hemagglutinins, indicating ability to form biofilm. In vitro
      biofilm assays demonstrated that E. meningoseptica Em3 formed more biofilm than
      E. anophelis Ag1 and E. miricola Emi3, both lacking the curli operon. A gene
      encoding thiol-activated cholesterol-dependent cytolysin in E. meningoseptica Em3
      (potentially involved in lysing host immune cells) was also absent in E.
      anophelis Ag1 and E. miricola Emi3. Strain Em3 showed alpha-hemolysin activity on
      blood agar medium, congruent with presence of hemolysin and cytolysin genes.
      Furthermore, presence of heme uptake and utilization genes demonstrated
      adaptations for bloodstream infections. Strain Em3 contained 12 genes conferring
      resistance to beta-lactams, including beta-lactamases class A, class B, and
      metallo-beta-lactamases. Results of comparative genomic analysis here provide
      insights into the evolution of E. meningoseptica Em3 as a pathogen.
AU  - Chen S
AU  - Soehnlen M
AU  - Downes FP
AU  - Walker ED
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 56.

PMID- 27789634
VI  - 4
DP  - 2016
TI  - Genome Sequence of Elizabethkingia meningoseptica EM1, Isolated from a Patient with a Bloodstream Infection.
PG  - e01137-16
AB  - Elizabethkingia meningoseptica EM1 was isolated from a whole-blood sample from a  female
      patient. The draft genome sequence of Em1 contains 4,038,467 bp, with a
      G+C content of 36.37%. A preliminary genome analysis showed that Em1 contains
      genes conferring resistance to beta-lactams. The bacterium has hemolysin genes
      and a set of genes involved in heme uptake and heme utilization, showing its
      potential to cause bloodstream infections. A clustered regularly interspaced
      short palindromic repeat (CRISPR)/CRISPR-associated protein (CRISPR/Cas) system
      was identified. Average nucleotide identity (ANI) analysis assigned the bacterium
      to the species E. meningoseptica (ANI, >95%). The annotated genome sequence
      provides the genetic basis for revealing its role as a pathogen in humans.
AU  - Chen S
AU  - Soehnlen M
AU  - Walker ED
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01137-16.

PMID- 29217787
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Haloparvum sedimenti Strain DYS4, the Type Species of the Genus Haloparvum, Isolated from a Salt Mine.
PG  - e00770-17
AB  - Here is the genome sequence of Haloparvum sedimenti DYS4, the type species of the genus
      Haloparvum, isolated from a salt mine. The DNA G+C content of this genome
      was 68.27 mol%. The scaffold N50 was 96,635 bp. The completely sequenced and
      annotated genome is 3,243,052 bp and contains 3,313 genes.
AU  - Chen S
AU  - Wang C
AU  - Li H
AU  - Shen Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00770-17.

PMID- 23144373
VI  - 194
DP  - 2012
TI  - Genome Sequence of Halorubrum sp. Strain T3, an Extremely Halophilic Archaeon Harboring a Virus-Like Element.
PG  - 6608-6609
AB  - Halorubrum sp. strain T3, harboring a virus-like element, was isolated from a sample collected
      from a solar saltern in Yunnan, China. Several strains of
      Halorubrum pleomorphic viruses were reported in this genus recently; however, the
      virus-host interaction in haloarchaea remains unclear. To explore this issue,
      here we present the genome sequence of Halorubrum sp. strain T3 (3,168,011 bp,
      68.48% G+C content).
AU  - Chen S
AU  - Wang C
AU  - Zhao Z
AU  - Yang ZL
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6608-6609.

PMID- 27103730
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Methanoculleus sediminis S3FaT, a Hydrogenotrophic Methanogen Isolated from a Submarine Mud Volcano in Taiwan.
PG  - e00308-16
AB  - Here, we announce the genome sequence of ITALIC! Methanoculleus sediminisS3Fa(T)(DSM
      29354(T)), a strict anaerobic methanoarchaeon, which was
      isolated from sediments near the submarine mud volcano MV4 located offshore in
      southwestern Taiwan. The 2.49-Mb genome consists of 2,459 predicted genes, 3
      rRNAs, 48 tRNAs, and 1 ncRNA. The sequence of this novel strain may provide more
      information for species delineation and the roles that this strain plays in the
      unique marine mud volcano habitat.
AU  - Chen SC
AU  - Chen MF
AU  - Weng CY
AU  - Lai MC
AU  - Wu SY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00308-16.

PMID- 16585510
VI  - 103
DP  - 2006
TI  - Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: A comparative genomics approach.
PG  - 5977-5982
AB  - Escherichia coli is a model laboratory bacterium, a species that is widely distributed in the
      environment, as well as a mutualist and pathogen in its human hosts. As such, E. coli
      represents an attractive organism to study how environment impacts microbial genome structure
      and function. Uropathogenic E. coli (UPEC) must adapt to life in several microbial communities
      in the human body, and has a complex life cycle in the bladder when it causes acute or
      recurrent urinary tract infection (UTI). Several studies designed to identify virulence
      factors have focused on genes that are uniquely represented in UPEC strains, whereas the role
      of genes that are common to all E. coli has received much less attention. Here we describe the
      complete 5,065,741-bp genome sequence of a UPEC strain recovered from a patient with an acute
      bladder infection and compare it with six other finished E. coli genome sequences. We searched
      3,470 ortholog sets for genes that are under positive selection only in UPEC strains. Our
      maximum likelihood-based analysis yielded 29 genes involved in various aspects of cell surface
      structure, DNA metabolism, nutrient acquisition, and UTI. These results were validated by
      resequencing a subset of the 29 genes in a panel of 50 urinary, periurethral, and rectal E.
      coli isolates from patients with UTI. These studies outline a computational approach that may
      be broadly applicable for studying strain-specific adaptation and pathogenesis in other
      bacteria.
AU  - Chen SL
AU  - Hung CS
AU  - Xu J
AU  - Reigstad CS
AU  - Magrini V
AU  - Sabo A
AU  - Blasiar D
AU  - Bieri T
AU  - Meyer RR
AU  - Ozersky P
AU  - Armstrong JR
AU  - Fulton RS
AU  - Latreille JP
AU  - Spieth J
AU  - Hooton TM
AU  - Mardis ER
AU  - Hultgren SJ
AU  - Gordon JI
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2006 103: 5977-5982.

PMID- 12897020
VI  - 185
DP  - 2003
TI  - Identification of long intergenic repeat sequences associated with DNA methylation sites in Caulobacter crescentus and other alpha-proteobacteria.
PG  - 4997-5002
AB  - A systematic search for motifs associated with CcrM DNA methylation sites revealed four long
      (>100-bp) motifs (CIR sequences) present in up to 21
      copies in Caulobacter crescentus. The CIR1 and CIR2 motifs exhibit a
      conserved inverted repeat organization, with a CcrM site in the center of
      one of the repeats.
AU  - Chen SL
AU  - Shapiro L
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2003 185: 4997-5002.

PMID- 23658245
VI  - 5
DP  - 2013
TI  - Genomic Diversity and Fitness of E. coli Strains Recovered from the Intestinal and Urinary Tracts of Women with Recurrent Urinary Tract Infection.
PG  - 184RA60
AB  - Urinary tract infections (UTIs) are common in women, and recurrence is a major
      clinical problem. Most UTIs are caused by uropathogenic Escherichia coli (UPEC).
      UPEC are generally thought to migrate from the gut to the bladder to cause UTI.
      UPEC form specialized intracellular bacterial communities in the bladder
      urothelium as part of a pathogenic mechanism to establish a foothold during acute
      stages of infection. Evolutionarily, such a specific adaptation to the bladder
      environment would be predicted to result in decreased fitness in other habitats,
      such as the gut. To examine this prediction, we characterized 45 E. coli strains
      isolated from the feces and urine of four otherwise healthy women with recurrent
      UTI. Multilocus sequence typing and whole genome sequencing revealed that two
      patients maintained a clonal population in both these body habitats throughout
      their recurrent UTIs, whereas the other two exhibited a wholesale shift in the
      dominant UPEC strain colonizing both sites. In vivo competition studies in mouse
      models, using isolates taken from one of the patients with a wholesale population
      shift, revealed that the strain that dominated her last UTI episode had increased
      fitness in both the gut and the bladder relative to the strain that dominated in
      preceding episodes. Increased fitness correlated with differences in the strains'
      gene repertoires and carbohydrate and amino acid utilization profiles. Thus, UPEC
      appear capable of persisting in both the gut and urinary tract without a fitness
      trade-off, emphasizing the need to widen our consideration of potential
      reservoirs for strains causing recurrent UTI.
AU  - Chen SL
AU  - Wu M
AU  - Henderson JP
AU  - Hooton TM
AU  - Hibbing ME
AU  - Hultgren SJ
AU  - Gordon JI
PT  - Journal Article
TA  - Sci. Transl. Med.
JT  - Sci. Transl. Med.
SO  - Sci. Transl. Med. 2013 5: 184RA60.

PMID- 15094296
VI  - 60
DP  - 2004
TI  - Structure and function of eukaryotic DNA methyltransferases.
PG  - 55-89
AB  - DNA methylation is a common epigenetic modification found in eukaryotic organisms ranging from
      fungi to mammals. Over the past 15 years, a number
      of eukaryotic DNA methyltransferases have been identified from various
      model organisms. These enzymes exhibit distinct biochemical properties and
      biological functions, partly due to their structural differences. The
      highly variable N-terminal extensions of these enzymes harbor various
      evolutionarily conserved domains and motifs, some of which have been shown
      to be involved in functional specializations. DNA methylation has
      divergent functions in different organisms, consistent with the notion
      that it is a dynamically evolving mechanism that can be adapted to fulfill
      various functions. Genetic studies using model organisms have provided
      evidence suggesting the progressive integration of DNA methylation into
      eukaryotic developmental programs during evolution.
AU  - Chen T
AU  - Li E
PT  - Journal Article
TA  - Curr. Top. Dev. Biol.
JT  - Curr. Top. Dev. Biol.
SO  - Curr. Top. Dev. Biol. 2004 60: 55-89.

PMID- 12897133
VI  - 23
DP  - 2003
TI  - Establishment and maintenance of genomic methylation patterns in mouse embryonic stem cells by Dnmt3a and Dnmt3b.
PG  - 5594-5605
AB  - We have previously shown that the DNA methyltransferases Dnmt3a and Dnmt3b carry out de novo
      methylation of the mouse genome during early
      postimplantation development and of maternally imprinted genes in the
      oocyte. In the present study, we demonstrate that Dnmt3a and Dnmt3b are
      also essential for the stable inheritance, or "maintenance," of DNA
      methylation patterns. Inactivation of both Dnmt3a and Dnmt3b in embryonic
      stem (ES) cells results in progressive loss of methylation in various
      repeats and single-copy genes. Interestingly, introduction of the Dnmt3a,
      Dnmt3a2, and Dnmt3b1 isoforms back into highly demethylated mutant ES
      cells restores genomic methylation patterns; these isoforms appear to have
      both common and distinct DNA targets, but they all fail to restore the
      maternal methylation imprints. In contrast, overexpression of Dnmt1 and
      Dnmt3b3 failed to restore DNA methylation patterns due to their inability
      to catalyze de novo methylation in vivo. We also show that
      hypermethylation of genomic DNA by Dnmt3a and Dnmt3b is necessary for ES
      cells to form teratomas in nude mice. These results indicate that genomic
      methylation patterns are determined partly through differential expression
      of different Dnmt3a and Dnmt3b isoforms.
AU  - Chen T
AU  - Ueda Y
AU  - Dodge JE
AU  - Wang Z
AU  - Li E
PT  - Journal Article
TA  - Mol. Cell. Biol.
JT  - Mol. Cell. Biol.
SO  - Mol. Cell. Biol. 2003 23: 5594-5605.

PMID- 12138111
VI  - 277
DP  - 2002
TI  - A novel Dnmt3a isoform produced from an alternative promoter localizes to euchromatin and its expression correlates with active de novo methylation.
PG  - 38746-38754
AB  - Previous studies have shown that the Dnmt3b gene encodes multiple variants via alternative
      splicing. However, only one form of Dnmt3a has been identified so far. We now report the
      discovery of a small form of Dnmt3a, termed Dnmt3a2, from both human and mouse. The transcript
      encoding Dnmt3a2 is initiated from a downstream intronic promoter. As a result, the Dnmt3a2
      protein lacks the N-terminal 223 (human) or 219 (mouse) amino acid residues of the full length
      Dnmt3a. Recombinant Dnmt3a2 protein displayed similar cytosine methyltransferase activity as
      Dnmt3a in vitro. However, Dnmt3a and Dnmt3a2 exhibited strikingly different subcellular
      localization patterns. Unlike Dnmt3a, which was concentrated on heterochromatin, Dnmt3a2
      displayed a localization pattern suggestive of euchromatin association. Dnmt3a2 is the
      predominant form in embryonic stem cells and embryonal carcinoma cells and can also be
      detected from testis, ovary, thymus, and spleen, whereas Dnmt3a is expressed at low levels
      ubiquitously. Comparison of human embryonal carcinoma cell lines with breast/ovarian cancer
      cell lines indicates that DNMT3A2 expression correlates with high de novo methylation
      activity. These findings suggest that Dnmt3a and Dnmt3a2 may have distinct DNA targets and
      different functions in development.
AU  - Chen T
AU  - Ueda Y
AU  - Xie S
AU  - Li E
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2002 277: 38746-38754.

PMID- 23144389
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Brevibacillus brevis Strain X23, a Biocontrol Agent against Bacterial Wilt.
PG  - 6634-6635
AB  - Brevibacillus brevis X23 is an appropriate biocontrol agent against bacterial wilt caused by
      Ralstonia solanacearum. We report herein the draft genome sequence
      (6,566,879 bp) and a circular plasmid (6,600 bp) of B. brevis X23, data which may
      be helpful for mining the antagonistic activity against R. solanacearum.
AU  - Chen W
AU  - Wang Y
AU  - Li D
AU  - Li L
AU  - Xiao Q
AU  - Zhou Q
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6634-6635.

PMID- 26404606
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Bifidobacterium actinocoloniiforme Type Strain DSM 22766T, Isolated from Bumblebee Digestive Tracts.
PG  - e01084-15
AB  - Bifidobacteria are one of the most important beneficial bacteria in the gut of mammals and
      insects. We sequenced the genome of B. actinocoloniiforme DSM 22766,  which was isolated from
      the digestive tracts of bumblebees. The genome contains 1,548 protein-coding genes, 49 RNAs
      and two CRISPR repeats.
AU  - Chen X
AU  - E Z
AU  - Gu D
AU  - Lv L
AU  - Li Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01084-15.

PMID- 
VI  - 29
DP  - 2009
TI  - Plant DNA methyltransferase.
PG  - 534-538
AB  - The addition of a methyl group to the carbon 5 of cytosine residues is the most common
      modification of DNA in higher plants.  Plant DNA methyltransferases can be divided into three
      classes based on their linear domain arrangement: DNA methyltransferase,
      chromomethyltransferase and domains-rearranged methyltrnasferase.  MET and CMT are responsible
      for the maintenance of methylation, and the latter has been found only in plants presently;
      DRM appears to be the principal de novo methyltransferase.  In this article, the structure,
      function and evolutionary aspects of the main plant DNA methyltransferases are analyzed in
      detail.
AU  - Chen X
AU  - Wang Z-C
PT  - Journal Article
TA  - Shengming De Huaxue
JT  - Shengming De Huaxue
SO  - Shengming De Huaxue 2009 29: 534-538.

PMID- 23868127
VI  - 1
DP  - 2013
TI  - Genome Sequence of Streptomyces violaceusniger Strain SPC6, a Halotolerant Streptomycete That Exhibits Rapid Growth and Development.
PG  - e00494-13
AB  - Streptomyces violaceusniger strain SPC6 is a halotolerant streptomycete isolated  from the
      Linze desert in China. The strain has a very high growth rate and a
      short life cycle for a streptomycete. For surface-grown cultures, the period from
      spore germination to formation of colonies with mature spore chains is only 2
      days at 37 degrees C. Additionally, the strain is remarkably resistant to
      osmotic, heat, and UV stress compared with other streptomycetes. Analysis of the
      draft genome sequence indicates that the strain has the smallest reported genome
      (6.4 Mb) of any streptomycete. The availability of this genome sequence allows us
      to investigate the genetic basis of adaptation for growth in an extremely arid
      environment.
AU  - Chen X
AU  - Zhang B
AU  - Zhang W
AU  - Wu X
AU  - Zhang M
AU  - Chen T
AU  - Liu G
AU  - Dyson P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00494-13.

PMID- 17704766
VI  - 25
DP  - 2007
TI  - Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42.
PG  - 1007-1014
AB  - Bacillus amyloliquefaciens FZB42 is a Gram-positive, plant-associated bacterium, which
      stimulates plant growth and produces secondary metabolites that suppress soil-borne plant
      pathogens. Its 3,918-kb genome, containing an estimated 3,693 protein-coding sequences, lacks
      extended phage insertions, which occur ubiquitously in the closely related Bacillus subtilis
      168 genome. The B. amyloliquefaciens FZB42 genome reveals an unexpected potential to produce
      secondary metabolites, including the polyketides bacillaene and difficidin. More than 8.5% of
      the genome is devoted to synthesizing antibiotics and siderophores by pathways not involving
      ribosomes. Besides five gene clusters, known from B. subtilis to mediate nonribosomal
      synthesis of secondary metabolites, we identified four giant gene clusters absent in B.
      subtilis 168. The pks2 gene cluster encodes the components to synthesize the macrolactin core
      skeleton.
AU  - Chen XH et al
PT  - Journal Article
TA  - Nat. Biotechnol.
JT  - Nat. Biotechnol.
SO  - Nat. Biotechnol. 2007 25: 1007-1014.

PMID- 26734118
VI  - 11
DP  - 2016
TI  - The complete genome sequence and analysis of a plasmid-bearing myxobacterial strain Myxococcus fulvus 124B02 (M 206081).
PG  - 1
AB  - Myxobacteria, phylogenetically located in the delta division of the Proteobacteria, are well
      known for characterized social behaviors and large
      genomes of more than 9 Mb in size. Myxococcus fulvus is a typical species of the
      genus Myxococcus in the family Myxococcaceae. M. fulvus 124B02, originally
      isolated from a soil sample collected in Northeast China, is the one and only
      presently known myxobacterial strain that harbors an endogenous autonomously
      replicating plasmid, named pMF1. The endogenous plasmid is of importance for
      understanding the genome evolution of myxobacteria, as well as for the
      development of genetic engineering tools in myxobacteria. Here we describe the
      complete genome sequence of this organism. M. fulvus 124B02 consists of a
      circular chromosome with a total length of 11,048,835 bp and a circular plasmid
      of 18,634 bp. Comparative genomic analyses suggest that pMF1 has a longstanding
      sustention within myxobacteria, and probably contributes to the genome expansion
      of myxobacteria.
AU  - Chen XJ
AU  - Han K
AU  - Feng J
AU  - Zhuo L
AU  - Li YJ
AU  - Li YZ
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 1.

PMID- 23977354
VI  - 8
DP  - 2013
TI  - Complete Genome Sequence of a Panton-Valentine Leukocidin-Negative Community-Associated Methicillin-Resistant Staphylococcus aureus Strain of Sequence type 72 from Korea.
PG  - E72803
AB  - In the past decade, community-associated (CA-) infections with
      methicillin-resistant Staphylococcus aureus (MRSA) have emerged throughout the
      world. Different CA-MRSA strains dominate in different geographical locations.
      Many CA-MRSA lineages contain genes coding for the Panton-Valentine leukocidin.
      However, the role of this leukotoxin in CA-MRSA pathogenesis is still
      controversial. The genome sequences of two key PVL-positive CA-MRSA strains
      (USA300, USA400) have been reported, but we lack information on the more recently
      found PVL-negative CA-MRSA strains. One such strain is the PVL-negative ST72, the
      main cause of CA-MRSA infections in Korea. Here, we report the entire genome
      sequence of CA-MRSA ST72 and analyze its gene content with a focus on virulence
      factors. Our results show that this strain does not have considerable differences
      in virulence factor content compared to other CA-MRSA strains (USA300, USA400),
      indicating that other toxins do not substitute for the lack of PVL in ST72. This
      finding is in accordance with the notion that differential expression of
      widespread virulence determinants, rather than the acquisition of additional
      virulence factors on mobile genetic elements, such as PVL, is responsible for the
      increased virulence of CA- compared to hospital-associated MRSA.
AU  - Chen Y
AU  - Chatterjee SS
AU  - Porcella SF
AU  - Yu YS
AU  - Otto M
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2013 8: E72803.

PMID- 29301880
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of USA100 Methicillin-Resistant Staphylococcus aureus Strain 209.
PG  - e01399-17
AB  - USA100 strains are significant contributors to the overall burden of health care-associated
      methicillin-resistant Staphylococcus aureus (MRSA) infections.
      Strain 209 is a representative MRSA isolate that serves as a model organism for
      agr type II studies and USA100 virulence assessments. We present a draft genome
      sequence of this strain.
AU  - Chen Y
AU  - Crosby HA
AU  - Oosthuysen WFII
AU  - Diekema DJ
AU  - Kelley ST
AU  - Horswill AR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01399-17.

PMID- 
VI  - 194
DP  - 2011
TI  - Draft genome sequence of an Acinetobacter genomic species 3 strain harboring a blaNDM-1 gene.
PG  - 204-205
AB  - Here we report the draft genome sequence of one Acinetobacter genomic species 3 strain, D499,
      which harbors the blaNDM-1 gene.  The total length of the assembled genome is 4,103,824 bp,
      and 3,896 coding sequences (CDSs) were predicted within the genome.  A previously unreported
      blaNDM-1-bearing plasmid was identified in this strain.
AU  - Chen Y
AU  - Cui Y
AU  - Pu F
AU  - Jiang G
AU  - Zhao X
AU  - Yuan Y
AU  - Zhao W
AU  - Li D
AU  - Liu H
AU  - Li Y
AU  - Liang T
AU  - Xu L
AU  - Wang Y
AU  - Song Q
AU  - Yang J
AU  - Liang L
AU  - Yang R
AU  - Han L
AU  - Song Y
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 194: 204-205.

PMID- 21914900
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Alicyclobacillus acidocaldarius Strain Tc-4-1.
PG  - 5602-5603
AB  - Alicyclobacillus acidocaldarius strain Tc-4-1 was initially isolated from a hot spring in
      Tengchong, China. This organism is both thermophilic and
      acidophilic. It can produce heat- and acid-stable enzymes, such as amylase
      and esterase, which may be important in industry. Here we report the whole
      genome sequence of the strain.
AU  - Chen Y
AU  - He Y
AU  - Zhang B
AU  - Yang J
AU  - Li W
AU  - Dong Z
AU  - Hu S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5602-5603.

PMID- 11198925
VI  - 10
DP  - 2000
TI  - In vivo expression of single-stranded DNA in mammalian cells with DNA enzyme sequences targeted to C-raf.
PG  - 415-422
AB  - The use of antisense oligodeoxynucleotides (AS-ODN) remains a viable method to downregulate
      selected gene function.  However, limitations to the antisense approach remain, such as (1)
      difficulties in delivery of the
      As-ODN into target tissues, (2) instability of As-ODN in vivo, (3) uncertainties about the
      precise mode of action, and (4) toxic effects in animal and human studies.  To circumvent some
      of these difficulties, we designed a vector set that directs the in vivo production of
      single-stranded DNA (ssDNA) of a desired target sequence with limited extraneous vector
      nucleotide sequences.  One plasmid was designed to express Moloney murine leukemia virus
      (MoMuLV) reverse transcriptase (RT).  Another expression plasmid contains the MoMuLV primer
      binding site at the 3' end of its RNA transcript so that an ssDNA would be synthesized by RT
      when both plasmids are cotransfected into cells.  To test this expression system, we
      constructed a plasmid set, pssXA/pssXB that produces ssRNA-cleaving DNA 10-23 enzyme (Santoro,
      S.W. and Joyce, G.F. (1977) Proc. Natl. Acad. Sci. USA 37, 13330-13342).  The DNA enzyme
      sequence was placed between two oligonucleotide arms that are complementary and able to
      specifically target C-raf kinase mRNA.  These plasmids were transfected into the A549 lung
      carcinoma cell line.  Reduced C-raf mRNA levels by up to 34%-36%, as determined by Northern
      blot analysis, were observed in the transfected cells.  Our results demonstrate the
      feasibility of using this novel ssDNA expression system to generate any sequence of interest
      in vivo for antisense, RNA-cleavage DNA enzyme, or triplex-forming strategies.
AU  - Chen Y
AU  - Ji YJ
AU  - Roxby R
AU  - Conrad C
PT  - Journal Article
TA  - Antisense Nucleic Acid Drug Dev.
JT  - Antisense Nucleic Acid Drug Dev.
SO  - Antisense Nucleic Acid Drug Dev. 2000 10: 415-422.

PMID- 23959310
VI  - 57
DP  - 2013
TI  - Whole Genome Sequencing of a Gentamicin-Resistant Campylobacter coli isolated from United States Retail Meats Reveals Novel Plasmid Mediated Aminoglycoside Resistance Genes.
PG  - 5398-5405
AB  - Aminoglycoside resistance in Campylobacter has been routinely monitored in the
      United States in clinical isolates since 1996 and in retail meats since 2002.
      Gentamicin resistance first appeared in a single human isolate of Campylobacter
      coli in 2000 and a single chicken meat isolate in 2007, after which it increased
      rapidly to account for 11.3% human isolates and 12.5% of retail isolates in 2010.
      Pulsed-field gel electrophoresis analysis indicated that gentamicin resistant C.
      coli isolates from retail meat were clonal. We sequenced the genomes of two
      strains in this clone using a next generation sequencing technique in order to
      investigate the genetic basis for the resistance. The gaps of one strain were
      closed using optical mapping and Sanger sequencing, and it is the first completed
      genome of C. coli. The two genomes are highly similar to each other. A
      self-transmissible plasmid carrying multiple antibiotics resistance genes was
      revealed within both genomes, encoding genes resistant to gentamicin, kanamycin,
      streptomycin, streptothricin, and tetracycline. Bioinformatics analysis and
      experimental results showed that gentamicin resistance was due to a
      phosphotransferase gene aph(2')-Ig not described previously. The phylogenetic
      relationship of this newly emerged clone to other Campylobacter sp. was
      determined by whole genome single nucleotide polymorphisms (SNPs) and showed that
      it clustered with the other poultry isolates and was separated from isolates from
      livestock.
AU  - Chen Y
AU  - Mukherjee S
AU  - Hoffmann M
AU  - Kotewicz ML
AU  - Young S
AU  - Abbott J
AU  - Luo Y
AU  - Davidson MK
AU  - Allard M
AU  - McDermott P
AU  - Zhao S
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2013 57: 5398-5405.

PMID- 21645368
VI  - 12
DP  - 2011
TI  - Comparative Genomic Analysis of Vibrio parahaemolyticus: Serotype Conversion and Virulence.
PG  - 294
AB  - BACKGROUND: Vibrio parahaemolyticus is a common cause of foodborne
      disease. Beginning in 1996, a more virulent strain having serotype O3:K6
      caused major outbreaks in India and other parts of the world, resulting in
      the emergence of a pandemic. Other serovariants of this strain emerged
      during its dissemination and together with the original O3:K6 were termed
      strains of the pandemic clone. Two genomes, one of this virulent strain
      and one pre-pandemic strain have been sequenced. We sequenced four
      additional genomes of V. parahaemolyticus in this study that were isolated
      from different geographical regions and time points. Comparative genomic
      analyses of six strains of V. parahaemolyticus isolated from Asia and Peru
      were performed in order to advance knowledge concerning the evolution of
      V. parahaemolyticus; specifically, the genetic changes contributing to
      serotype conversion and virulence. Two pre-pandemic strains and three
      pandemic strains, isolated from different geographical regions, were
      serotype O3:K6 and either toxin profiles (tdh+, trh-) or (tdh-, trh+). The
      sixth pandemic strain sequenced in this study was serotype O4:K68.
      RESULTS: Genomic analyses revealed that the trh+ and tdh+ strains had
      different types of pathogenicity islands and mobile elements as well as
      major structural differences between the tdh pathogenicity islands of the
      pre-pandemic and pandemic strains. In addition, the results of single
      nucleotide polymorphism (SNP) analysis showed that 94% of the SNPs between
      O3:K6 and O4:K68 pandemic isolates were within a 141 kb region surrounding
      the O- and K-antigen-encoding gene clusters. The "core" genes of V.
      parahaemolyticus were also compared to those of V. cholerae and V.
      vulnificus, in order to delineate differences between these three
      pathogenic species. Approximately one-half (49-59%) of each species' core
      genes were conserved in all three species, and 14-24% of the core genes
      were species-specific and in different functional categories. CONCLUSIONS:
      Our data support the idea that the pandemic strains are closely related
      and that recent South American outbreaks of foodborne disease caused by V.
      parahaemolyticus are closely linked to outbreaks in India. Serotype
      conversion from O3:K6 to O4:K68 was likely due to a recombination event
      involving a region much larger than the O-antigen- and K-antigen-encoding
      gene clusters. Major differences between pathogenicity islands and mobile
      elements are also likely driving the evolution of V. parahaemolyticus. In
      addition, our analyses categorized genes that may be useful in
      differentiating pathogenic Vibrios at the species level.
AU  - Chen Y
AU  - Stine OC
AU  - Badger JH
AU  - Gil AI
AU  - Nair GB
AU  - Nishibuchi M
AU  - Fouts DE
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2011 12: 294.

PMID- 21551300
VI  - 193
DP  - 2011
TI  - Genome sequences of Listeria monocytogenes strains J1816 and J1-220 associated with human outbreaks.
PG  - 3424-3425
AB  - Listeria monocytogenes has caused numerous human outbreaks. Here we report draft genomes of L.
      monocytogenes J1816 and J1-220, which belongs to the
      epidemic clone II and epidemic clone IV, respectively. Whole genome
      sequence analysis of these strains provides a tool for studying the
      short-term evolution of these epidemic clones.
AU  - Chen Y
AU  - Strain EA
AU  - Allard M
AU  - Brown EW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3424-3425.

PMID- 21952538
VI  - 193
DP  - 2011
TI  - Genome Sequence of Cronobacter sakazakii E899, a Strain Associated with Human Illness.
PG  - 5861
AB  - Cronobacter has caused numerous illnesses in neonates, infants, and children. Here we report
      the draft genome of Cronobacter sakazakii E899.
      Whole-genome sequence analysis of Cronobacter strains provides a tool for
      understanding the genomic regions specific to each individual species.
AU  - Chen Y
AU  - Strain EA
AU  - Allard M
AU  - Brown EW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5861.

PMID- 25465224
VI  - 7
DP  - 2015
TI  - A restriction enzyme-powered autonomous DNA walking machine: its application for a highly sensitive electrochemiluminescence assay of DNA.
PG  - 981-986
AB  - The construction of a restriction enzyme (Nt. AlwI)-powered DNA walking machine and its
      application for highly sensitive detection of DNA are described. DNA nanostructure tracks
      containing four overhang sequences with electrochemiluminescence (ECL) labels and
      complementary to the walker (target DNA) are self-assembled on the sensing electrode. The
      walker hybridizes with the complementary sequences on the tracks and forms specific
      recognition sites for Nt. AlwI, which cleaves the overhang sequences, releases the ECL labels
      and enables directional movement of the walker along the tracks. The formation of the
      nanostructure tracks and the Nt. AlwI-assisted cleavage of the overhang sequences in the
      presence of the walker are verified by using polyacrylamide gel electrophoresis analysis and
      cyclic voltammetry. The successive movement of the walker on the nanostructure tracks leads to
      continuous removal of massive ECL labels from the sensing electrode, which results in a
      significantly amplified suppression of the ECL emission for highly sensitive detection of
      sequence-specific DNA down to 0.19 pM. Results show that this DNA walking machine can also
      offer single-base mismatch discrimination capability. The successful application of the DNA
      walking machine for sequence-specific DNA detection can thus offer new opportunities for
      molecular machines in biosensing applications.
AU  - Chen Y
AU  - Xiang Y
AU  - Yuan R
AU  - Chai Y
PT  - Journal Article
TA  - Nanoscale
JT  - Nanoscale
SO  - Nanoscale 2015 7: 981-986.

PMID- 
VI  - 7
DP  - 2017
TI  - Revealing the Saline Adaptation Strategies of the Halophilic Bacterium Halomonas beimenensis through High-throughput Omics and Transposon Mutagenesis Approaches.
PG  - 0
AB  - Studies on the halotolerance of bacteria are attractive to the fermentation industry. However,
      a lack of sufficient genomic information has precluded an investigation of the halotolerance
      of Halomonas beimenensis. Here, we describe the molecular mechanisms of saline adaptation in
      H. beimenensis based on high-throughput omics and Tn5 transposon mutagenesis. The H.
      beimenensis genome is 4.05 Mbp and contains 3,807 genes, which were sequenced using short and
      long reads obtained via deep sequencing. Sixteen Tn5 mutants with a loss of halotolerance were
      identified. Orthologs of the
      mutated genes, such as nqrA, trkA, atpC, nadA, and gdhB, have significant biological functions
      in sodium efflux, potassium uptake, hydrogen ion transport for energy conversion, and
      compatible solute synthesis, which are known to control halotolerance. Other genes, such as
      spoT, prkA, mtnN, rsbV, lon, smpB, rfbC, rfbP, tatB, acrR1, and lacA, function in cellular
      signaling, quorum sensing, transcription/translation, and cell motility also shown critical
      functions for promoting a halotolerance. In addition, KCl application increased halotolerance
      and potassium-dependent cell motility in a high-salinity environment. Our results demonstrated
      that a combination of omics and mutagenesis could be used to facilitate the mechanistic
      exploitation of saline adaptation in H. beimenensis, which can be applied for
      biotechnological purposes.
AU  - Chen YH
AU  - Lin SS
AU  - Shyu YT
PT  - Journal Article
TA  - Sci. Rep.
JT  - Sci. Rep.
SO  - Sci. Rep. 2017 7: 0.

PMID- 25931599
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequence of an Epidemic Strain of Burkholderia pseudomallei vgh07 in Taiwan.
PG  - e00345-15
AB  - Here, we report the complete genome sequence of B. pseudomallei vgh07. This is an epidemic
      strain that was isolated from a melioidosis patient with
      arthro-osteomyelitis in Taiwan.
AU  - Chen YS
AU  - Lin HH
AU  - Hsueh PT
AU  - Liu PJ
AU  - Ni WF
AU  - Chung WC
AU  - Lin CP
AU  - Chen YL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00345-15.

PMID- 17526756
VI  - 51
DP  - 2007
TI  - Sequencing and comparative genomic analysis of pK29, a 269-kilobase conjugative plasmid encoding CMY-8 and CTX-M-3 beta-lactamases in  Klebsiella pneumoniae.
PG  - 3004-3007
AB  - A 269-kilobase conjugative plasmid, pK29, from a Klebsiella pneumoniae strain was sequenced.
      The plasmid harbors multiple antimicrobial
      resistance genes, including those encoding CMY-8 AmpC-type and CTX-M-3
      extended-spectrum beta-lactamases in the common backbone of IncHI2
      plasmids. Mechanisms for dissemination of the resistance genes are
      highlighted in comparative genomic analyses.
AU  - Chen YT
AU  - Lauderdale TL
AU  - Liao TL
AU  - Shiau YR
AU  - Shu HY
AU  - Wu KM
AU  - Yan JJ
AU  - Su IJ
AU  - Tsai SF
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2007 51: 3004-3007.

PMID- 19075060
VI  - 53
DP  - 2009
TI  - Mobilization of qnrB2 and ISCR1 in plasmids.
PG  - 1235-1237
AB  - The DNA sequences of two IncHI2 plasmids, pEC-IMP and pEC-IMPQ, from
      metallo-beta-lactamase-producing Enterobacter cloacae clinical isolates
      were determined. The two conjugative plasmids are almost identical, but
      pEC-IMPQ carries an additional segment containing an orf513 (ISCR1), a
      truncated 3' conserved sequence, and a qnrB2. Comparative analyses provide
      support for the proposed ISCR1-mediated gene mobilization.
AU  - Chen YT
AU  - Liao TL
AU  - Liu YM
AU  - Lauderdale TL
AU  - Yan JJ
AU  - Tsai SF
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2009 53: 1235-1237.

PMID- 24123430
VI  - 69
DP  - 2014
TI  - KPC-2-encoding plasmids from Escherichia coli and Klebsiella pneumoniae in Taiwan.
PG  - 628-631
AB  - OBJECTIVES: Two plasmids carrying blaKPC-2 isolated from carbapenem-resistant
      Escherichia coli (CR-EC) and carbapenem-resistant Klebsiella pneumoniae (CR-KP),
      respectively, were completely sequenced. The CR-KP strain was selected from an
      outbreak in 2012, and the CR-EC strain was the first blaKPC-2-carrying E. coli
      identified in the same carbapenem resistance monitoring programme in Taiwan.
      METHODS: Antimicrobial susceptibility tests, multilocus sequence typing (MLST)
      and the conjugal transfer of plasmids were performed. Complete sequencing of the
      plasmids was performed using a shotgun approach. RESULTS: The CR-EC and CR-KP
      strains in this study were determined to be ST410 and ST11, respectively, by
      MLST. From CR-EC, we identified a 145 kb conjugative plasmid that carries
      blaKPC-2, blaCMY-2, blaCTX-M-3 and blaTEM-1. The plasmid is a chimera composed of
      three regions related to IncI, IncN and RepFIC replicons. From CR-KP, we
      identified an 86.5 kb plasmid, pKPC-LK30, which carries blaKPC-2 and blaSHV-11.
      The plasmid is very similar to two blaKPC-2-carrying IncFIIK plasmids, but lacks
      one of the replication origins and cannot conjugate. CONCLUSIONS: The differences
      in cross-species transferability of the two plasmids can be explained by genetic
      differences between their backbones and could have resulted in the confined
      blaKPC-2-carrying CR-KP outbreak in Taiwan. Plasmid pKPC-LKEc is the first
      blaKPC-2-carrying plasmid identified from CR-EC in Taiwan. With relatively high
      transferability it should be closely monitored.
AU  - Chen YT
AU  - Lin JC
AU  - Fung CP
AU  - Lu PL
AU  - Chuang YC
AU  - Wu TL
AU  - Siu LK
PT  - Journal Article
TA  - J. Antimicrob. Chemother.
JT  - J. Antimicrob. Chemother.
SO  - J. Antimicrob. Chemother. 2014 69: 628-631.

PMID- 23282187
VI  - 13
DP  - 2012
TI  - Whole-genome sequencing and identification of Morganella morganii KT pathogenicity-related genes.
PG  - S4
AB  - BACKGROUND: The opportunistic enterobacterium, Morganella morganii, which can cause
      bacteraemia, is the ninth most prevalent cause of clinical infections in patients at Changhua
      Christian Hospital, Taiwan. The KT strain of M. morganii was isolated during postoperative
      care of a cancer patient with a gallbladder stone who developed sepsis caused by bacteraemia.
      M. morganii is sometimes encountered in nosocomial settings and has been causally linked to
      catheter-associated bacteriuria, complex infections of the urinary and/or hepatobiliary
      tracts, wound infection, and septicaemia. M. morganii infection is associated with a high
      mortality rate, although most patients respond well to appropriate antibiotic therapy. To
      obtain insights into the genome biology of M. morganii and the mechanisms underlying its
      pathogenicity, we used Illumina technology to sequence the genome of the KT strain and
      compared its sequence with the genome sequences of related bacteria. RESULTS: The 3,826,919-bp
      sequence contained in 58 contigs has a GC content of 51.15% and includes 3,565 protein-coding
      sequences, 72 tRNA genes, and 10 rRNA genes. The pathogenicity-related genes encode
      determinants of drug resistance, fimbrial adhesins, an IgA protease, haemolysins, ureases, and
      insecticidal and apoptotic toxins as well as proteins found in flagellae, the iron acquisition
      system, a type-3 secretion system (T3SS), and several two-component systems. Comparison with
      14 genome sequences from other members of Enterobacteriaceae revealed different degrees of
      similarity to several systems found in M. morganii. The most striking similarities were found
      in the IS4 family of transposases, insecticidal toxins, T3SS components, and proteins required
      for ethanolamine use (eut operon) and cobalamin (vitamin B12) biosynthesis. The eut operon and
      the gene cluster for cobalamin biosynthesis are not present in the other Proteeae genomes
      analysed. Moreover, organisation of the 19 genes of the eut operon differs from that found in
      the other non-Proteeae enterobacterial genomes. CONCLUSIONS: This is the first genome sequence
      of M. morganii, which is a clinically relevant pathogen. Comparative genome analysis revealed
      several pathogenicity-related genes and novel genes not found in the genomes of other members
      of Proteeae. Thus, the genome sequence of M. morganii provides important information
      concerning virulence and determinants of fitness in this pathogen.
AU  - Chen YT
AU  - Peng HL
AU  - Shia WC
AU  - Hsu FR
AU  - Ken CF
AU  - Tsao YM
AU  - Chen CH
AU  - Liu CE
AU  - Hsieh MF
AU  - Chen HC
AU  - Tang CY
AU  - Ku TH
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2012 13: S4.

PMID- 16940067
VI  - 50
DP  - 2006
TI  - Complete Nucleotide Sequence of pK245, a 98-Kilobase Plasmid Conferring Quinolone Resistance and Extended-Spectrum-beta-Lactamase Activity in a Clinical Klebsiella pneumoniae Isolate.
PG  - 3861-3866
AB  - A plasmid containing the qnrS quinolone resistance determinant and the
      gene encoding the SHV-2 beta-lactamase has been discovered from a clinical
      Klebsiella pneumoniae strain isolated in Taiwan. The complete 98-kb
      sequence of this plasmid, designated pK245, was determined by using a
      whole-genome shotgun approach. Transfer of pK245 conferred low-level
      resistance to fluoroquinolones in electroporant Escherichia coli epi300.
      The sequence of the immediate region surrounding qnrS in pK245 is nearly
      identical (>99% identity) to those of pAH0376 from Shigella flexneri and
      pINF5 from Salmonella enterica serovar Infantis, the two other
      qnrS-carrying plasmids reported to date, indicating a potential common
      origin. Other genes conferring resistance to aminoglycosides (aacC2, strA,
      and strB), chloramphenicol (catA2), sulfonamides (sul2), tetracycline
      (tetD), and trimethoprim (dfrA14) were also detected in pK245. The dfrA14
      gene is carried on a class I integron. Several features of this plasmid,
      including three separate regions containing putative replicons, a
      partitioning-control system, and a type II restriction modification
      system, suggest that it may be able to replicate and adapt in a variety of
      hosts. Although no critical conjugative genes were detected, multiple
      insertion sequence elements were found scattered throughout pK245, and
      these may facilitate the dissemination of the antimicrobial resistance
      determinants. We conclude that pK245 is a chimera which acquired its
      multiple antimicrobial resistance determinants horizontally from different
      sources. The identification of pK245 plasmid expands the repertoire of the
      coexistence of quinolone and extended-spectrum-beta-lactam resistance
      determinants in plasmids carried by various species of the family
      Enterobacteriaceae in different countries.
AU  - Chen YT
AU  - Shu HY
AU  - Li LH
AU  - Liao TL
AU  - Wu KM
AU  - Shiau YR
AU  - Yan JJ
AU  - Su IJ
AU  - Tsai SF
AU  - Lauderdale TL
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2006 50: 3861-3866.

PMID- 11088571
VI  - 62
DP  - 2000
TI  - Spontaneous base flipping in DNA and its possible role in methyltransferase binding.
PG  - 1133-1137
AB  - Recent crystallographic studies showed that HhaI and other methyltransferases flip their
      target DNA base completely out of a DNA helix.  This base flipping is also a key feature in a
      number of other enzyme-catalyzed processes involving DNA.  The mechanism of base flipping by
      these enzymes remains elusive.  Based on a full atomic level description of bond rotational
      motions we have studied the energetics of flipping a base in a B-DNA duplex in the absence of
      the enzyme.  We have also investigated the effect of the restraints from enzyme-distorted DNA
      backbone on the movement of a flipped base in several methyltransferase bound DNA crystal
      structures.  Our study on crystal B-DNA helices showed that a base could be flipped at an
      energy cost close to the enthalpy observed for base pair opening in premelting thermal
      fluctuations.  This suggests that spontaneous base flipping in DNA due to thermal fluctuation
      may be achieved.  Analysis of several crystal HhaI and HaeIII methyltransferase DNA duplex
      structures showed that the enzyme induced DNA backbone distortion severely restricts the
      movement of the flipped base, which indicates that during base flipping the backbone needs to
      adopt a substantially different conformation than that observed in the x-ray (enzyme-bound)
      structures.  Our results suggest the possible role of thermally induced transient base opening
      in facilitating recognition and binding of methyltransferases and other enzymes.
AU  - Chen YZ
AU  - Mohan V
AU  - Griffey RH
PT  - Journal Article
TA  - Phys. Rev. E
JT  - Phys. Rev. E
SO  - Phys. Rev. E 2000 62: 1133-1137.

PMID- 22887667
VI  - 194
DP  - 2012
TI  - Genome Sequence of Enterococcus faecium Clinical Isolate LCT-EF128.
PG  - 4765
AB  - Enterococcus faecium, an opportunistic human pathogen that inhabits the gastrointestinal
      tracts of most mammals, has emerged as an important
      opportunistic nosocomial pathogen and is a prominent cause of multiresistant
      nosocomial infections. Here, we report the draft genome sequence of strain
      LCT-EF128, isolated from clinical specimens.
AU  - Chen Z
AU  - Chang D
AU  - Zou Y
AU  - Su L
AU  - Zhu Y
AU  - Fang X
AU  - Wang J
AU  - Guo Y
AU  - Zhao J
AU  - Li D
AU  - Fang C
AU  - Yang R
AU  - Liu C
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4765.

PMID- 24143877
VI  - 44
DP  - 2013
TI  - Genome architecture changes and major gene variations of Andrias davidianus ranavirus (ADRV).
PG  - 101
AB  - Ranaviruses are emerging pathogens that have led to global impact and public
      concern. As a rarely endangered species and the largest amphibian in the world,
      the Chinese giant salamander, Andrias davidianus, has recently undergone
      outbreaks of epidemic diseases with high mortality. In this study, we isolated
      and identified a novel ranavirus from the Chinese giant salamanders that
      exhibited systemic hemorrhage and swelling syndrome with high death rate in China
      during May 2011 to August 2012. The isolate, designated Andrias davidianus
      ranavirus (ADRV), not only could induce cytopathic effects in different fish cell
      lines and yield high viral titers, but also caused severely hemorrhagic lesions
      and resulted in 100% mortality in experimental infections of salamanders. The
      complete genome of ADRV was sequenced and compared with other sequenced amphibian
      ranaviruses. Gene content and phylogenetic analyses revealed that ADRV should
      belong to an amphibian subgroup in genus Ranavirus, and is more closely related
      to frog ranaviruses than to other salamander ranaviruses. Homologous gene
      comparisons show that ADRV contains 99%, 97%, 94%, 93% and 85% homologues in RGV,
      FV3, CMTV, TFV and ATV genomes respectively. In addition, several variable major
      genes, such as duplicate US22 family-like genes, viral eukaryotic translation
      initiation factor 2 alpha gene and novel 75L gene with both motifs of nuclear
      localization signal (NLS) and nuclear export signal (NES), were predicted to
      contribute to pathogen virulence and host susceptibility. These findings confirm
      the etiologic role of ADRV in epidemic diseases of Chinese giant salamanders, and
      broaden our understanding of evolutionary emergence of ranaviruses.
AU  - Chen Z
AU  - Gui J
AU  - Gao X
AU  - Pei C
AU  - Hong Y
AU  - Zhang Q
PT  - Journal Article
TA  - Vet. Res.
JT  - Vet. Res.
SO  - Vet. Res. 2013 44: 101.

PMID- 2839359
VI  - 234
DP  - 1988
TI  - Isolation and characterization of restriction endonuclease BstYI from Bacillus stearothermophilus Y406.
PG  - 169-171
AB  - BstYI, an isoschizomer of XhoII and MflI, has been purified from Bacillus
      stearothermophilus Y406.  This enzyme recognized 5' Pu^GATCPy 3' in DNA and
      cleaved between Pu and G in this sequence.  BstYI can be easily isolated and
      purified by heparin-agarose column chromatography in a high yield (8000 units
      BstYI can be obtained per g wet wt of cells).
AU  - Chen Z
AU  - Kong H
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1988 234: 169-171.

PMID- Not carried by PubMed...
VI  - 28
DP  - 1989
TI  - Isolation and characterization of restriction endonucleases BstFI and BstSI from Bacillus stearothermophilus.
PG  - 363-366
AB  - Two type II restriction endonucleases, BstFI and BstSI, have been isolated from
      Bacillus stearothermophilus FH58 and Bacillus stearothermophilus S183.  The
      recognition sequence and cleavage site of BstFI is A/AGCTT; and C/PyCGPuG in
      BstSI.  Therefore, BstFI is the isoschizomer of HindIII and BstSI is the
      isoschizomer of AvaI.  These two enzymes can be easily purified with
      heparin-agarose.  10,000 units of BstFI and 24,000 units of BstSI can be
      purified per gram wet cell of FH58 or S183, respectively.  They have different
      thermostability.  BstFI and BatSI are stable under incubation at 45C for as
      long as 6 hours.  After 1 h incubation at 50C the relative activity of BstFI
      was reduced by 50%, whereas the relative activity of BstSI was reduced only by
      10% after 1 h incubation at 70C.
AU  - Chen Z
AU  - Kong H
AU  - Wang L
PT  - Journal Article
TA  - J. Fudan Univ. (Natural Sci.)
JT  - J. Fudan Univ. (Natural Sci.)
SO  - J. Fudan Univ. (Natural Sci.) 1989 28: 363-366.

PMID- 25502677
VI  - 2
DP  - 2014
TI  - Whole-Genome Sequence of Marine Bacterium Phaeodactylibacter xiamenensis Strain KD52, Isolated from the Phycosphere of Microalga Phacodactylum tricornutum.
PG  - e01289-14
AB  - Phaeodactylibacter xiamenensis KD52 is a novel bacterium isolated from a culture  of the alga
      Phaeodactylum tricornutum in Xiamen, Fujian Province, China. Here, we
      present the first draft genome sequence of this strain, which will provide an
      opportunity to further understand the functional genes related to signing for
      nutrition from the host algae and the molecular mechanisms underlying its
      beneficial properties.
AU  - Chen Z
AU  - Lei X
AU  - Li Y
AU  - Zhang J
AU  - Zhang H
AU  - Yang L
AU  - Zheng W
AU  - Xu H
AU  - Zheng T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01289-14.

PMID- 24604642
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Enterococcus faecium Strain LCT-EF301, Which Shows Changes in Biochemical Metabolism following Space Flight.
PG  - e00103-14
AB  - An Enterococcus faecium strain was sent into space on the Shenzhou-VIII mission.  After the
      space flight, the strain E. faecium LCT-EF301 was isolated and
      sequenced based on the changes to its metabolic properties.
AU  - Chen Z
AU  - Li Y
AU  - Chang D
AU  - An L
AU  - Guo Y
AU  - Wang J
AU  - Li T
AU  - Wang Y
AU  - Zhang X
AU  - Dai W
AU  - Liu C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00103-14.

PMID- 29301898
VI  - 6
DP  - 2018
TI  - Complete Genome Sequences of Two Multidrug-Resistant Mycobacterium tuberculosis Strains Isolated in Guiyang, China.
PG  - e01257-17
AB  - We identified the genome sequences of two Mycobacterium tuberculosis isolates. They were
      resistant to rifampin and isoniazid, as determined by the agar
      proportion method, but were susceptible to isoniazid, as determined by the DNA
      array method. The genome sequences showed that a katG deletion led to the false
      diagnosis of isoniazid resistance by DNA array.
AU  - Chen Z
AU  - Ou W
AU  - Fan X
AU  - Cui G
AU  - Wang Q
AU  - Li Q
AU  - Sun R
AU  - Wu X
AU  - Qin W
AU  - Wang Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01257-17.

PMID- 19176595
VI  - 22
DP  - 2009
TI  - Directed evolution of homing endonuclease I-SceI with altered sequence specificity.
PG  - 249-256
AB  - Homing endonucleases recognize specific long DNA sequences and catalyze double-stranded breaks
      that significantly stimulate homologous
      recombination, representing an attractive tool for genome targeting and
      editing. We previously described a two-plasmid selection system that
      couples enzymatic DNA cleavage with the survival of host cells, and
      enables directed evolution of homing endonucleases with altered cleavage
      sequence specificity. Using this selection system, we successfully evolved
      mutant I-SceI homing endonucleases with greatly increased cleavage
      activity towards a new target DNA sequence that differs from the wild-type
      cleavage sequence by 4 bp. The most highly evolved mutant showed a
      survival rate approximately 100-fold higher than that of wild-type I-SceI
      enzyme. The degree of selectivity displayed by a mutant isolated from one
      round of saturation mutagenesis for the new target sequence is comparable
      to that of wild-type I-SceI for the natural sequence. These results
      highlight the ability and efficiency of our selection system for
      engineering homing endonucleases with novel DNA cleavage specificities.
      The mutant identified from this study can potentially be used in vivo for
      targeting the new cleavage sequence within genomic DNA.
AU  - Chen Z
AU  - Wen F
AU  - Sun N
AU  - Zhao H
PT  - Journal Article
TA  - Protein Eng. Des. Sel.
JT  - Protein Eng. Des. Sel.
SO  - Protein Eng. Des. Sel. 2009 22: 249-256.

PMID- 23405363
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences of Two Clinical Isolates of Lactobacillus rhamnosus from Initial Stages of Dental Pulp Infection.
PG  - e00073-12
AB  - Here we report the draft genomic sequences of two clinical isolates of Lactobacillus rhamnosus
      from infected dental pulps representing the initial stages of infection of pulp tissue. Based
      on 454 FLX+ pyrosequencing, the two clinical isolates infecting vital pulp had a genome length
      of 2.9 Mbp with distinct genomic signatures.
AU  - Chen Z
AU  - Wilkins MR
AU  - Hunter N
AU  - Nadkarni MA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00073-12.

PMID- 3512533
VI  - 165
DP  - 1986
TI  - Genetic analysis of Bacillus stearothermophilus by protoplast fusion.
PG  - 994-1001
AB  - Efficient and reliable protoplasting, regeneration, and fusion techniques were
      established for the prototrophic strain Bacillus stearothermophilus NUB36.
      Auxotrophic mutants were isolated, and protoplast fusion was used to construct
      isogenic mutant strains and for chromosomal mapping.  Markers were mapped using
      two-, three-, and four-factor crosses.  The order of the markers was
      hom-1-thr-1-his-1-(gly-1 or gly-2)-pur-1-pur-2.  These markers may be analogous
      to hom, thrA, hisA, glyC, and purA markers on the Bacillus subtilis chromosome.
      No analogous pur-1 marker has been reported in B. subtilis.  The relative
      order of three of the markers (hom-1-thr-1-gly-1) was independently confirmed.
AU  - Chen Z
AU  - Wojcik SF
AU  - Welker NE
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1986 165: 994-1001.

PMID- Not carried by PubMed...
VI  - 28
DP  - 1989
TI  - Restriction and modification in a gram-negative thermophilic bacterium and isolation of restriction endonuclease TspAI.
PG  - 96-101
AB  - A restriction endonuclease TspAI had been isolated from the gram-negative and
      flagellate thermophilic bacterium FD230.  TspAI functions upon phage p228 in
      terms of restriction and modification.  By cleaving lambda DNA, pBR322DNA and
      Phi X174 RFDNA-Hae III fragment, it had been identified as a restriction
      endonuclease possessing the same recognition sequence as that of EcoRII, i.e.
      the cleavage site is CCA/TGG.  TspAI could be easily isolated and purified.
      The enzyme was active over a temperature range of 30-80C.  Moreover, it was
      stable at 60C for as long as 30 minutes.
AU  - Chen Z
AU  - Yang R
AU  - Chen B
AU  - Li R
PT  - Journal Article
TA  - J. Fudan Univ. (Natural Sci.)
JT  - J. Fudan Univ. (Natural Sci.)
SO  - J. Fudan Univ. (Natural Sci.) 1989 28: 96-101.

PMID- 16214805
VI  - 33
DP  - 2005
TI  - A highly sensitive selection method for directed evolution of homing endonucleases.
PG  - e154
AB  - Homing endonucleases are enzymes that catalyze DNA sequence specific double-strand breaks and
      can significantly stimulate homologous recombination at these breaks. These enzymes have great
      potential for applications such as gene correction in gene therapy or gene alteration in
      systems biology and metabolic engineering. However, homing endonucleases have a limited
      natural repertoire of target sequences, which severely hamper their applications. Here we
      report the development of a highly sensitive selection method for the directed evolution of
      homing endonucleases that couples enzymatic DNA cleavage with the survival of host cells.
      Using I-SceI as a model homing endonuclease, we have demonstrated that cells with wild-type
      I-SceI showed a high cell survival rate of 80-100% in the presence of the original I-SceI
      recognition site, whereas cells without I-SceI showed a survival rate <0.003%. This system
      should also be readily applicable for directed evolution of other DNA cleavage enzymes.
AU  - Chen Z
AU  - Zhao H
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2005 33: e154.

PMID- 
VI  - 83
DP  - 2005
TI  - Self-association of human de novo DNA methyltransferases, DNMT3A and DNMT3B.
PG  - 566
AB  - Proper control of cytosine methylation patterns is critical for mammalian development.  Two de
      novo DNA methyltransferases, Dnmt3a and Dnmt3b, are required for the establishment of DNA
      methylation patterns in germ cells and early embryos.  The mechanism by which DNMT3A and
      DNMT3B carry out de novo methylation remains largely unknown.  Here, using the yeast
      two-hybrid system and co-immunoprecipitation analysis, we demonstrate that human DNMT3A and
      DNMT3B are capable of self-association.  Deletion analysis revealed that the C-terminal
      catalytic domain is responsible for self-interaction.  Since most mutations causing
      immunodeficiency, centromeric instability, and facial anomalies syndrome occur in the
      catalytic domain of DNMT3B, we investigated whether these mutations can affect the ability of
      DNMT3B to self-interact.  Two DNMT3B ICF mutants (H814R and D817G) show reduced ability to
      interact with themselves in the yeast two-hybrid system.  In addition, DNMT3A interacts with
      DNMT3B through their C-terminal catalytic domains.  Self-association of the catalytic domain
      may play a role in regulating activity and function of DNMT3 methyltransferases.
AU  - Chen Z-X
AU  - Riggs AD
PT  - Journal Article
TA  - Biochem. Cell Biol.
JT  - Biochem. Cell Biol.
SO  - Biochem. Cell Biol. 2005 83: 566.

PMID- Not carried by PubMed...
VI  - 39
DP  - 1994
TI  - Identification of a new type-II restriction enzyme BsrGI from Bacillus stearothermophilus GR75.
PG  - 526-528
AB  - A new type II restriction endonuclease, BsrGI, has been isolated from Bacillus
      stearothermophilus GR75. BsrGI cleaves T7 DNA at 13 sites, Lambda DNA at 5 sites and M13mp19
      DNA at one site, but does not cleave pBR322 DNA and pUC19 DNA. The position of restriction
      site of BsrGI on M13mp19 DNA was mapped to position 1000 using double digests with restriction
      enzymes AvaII and BsrFI. The recognition sequence and cleavage site of BsrGI on M13mp19 DNA
      was determined directly by using the dideoxynucleotide chain-termination method with a
      synthetic counter-clockwise primer (1190-1175) downstream of the BsrGI restriction site.
      Sequencing data show that the recognition sequence and cleavage site of BsrGI is
      5'...T/GTACA...3'. Thus this enzyme recognizes the palindromic sequence 5'TGTACA3' and
      cleaves between 5'T and G, generating 5'-protruding single-strand ends 5'GTAC3'.
AU  - Chen ZF
AU  - Pan XS
PT  - Journal Article
TA  - Chinese Sci. Bull.
JT  - Chinese Sci. Bull.
SO  - Chinese Sci. Bull. 1994 39: 526-528.

PMID- 15861382
VI  - 95
DP  - 2005
TI  - Physical and functional interactions between the human DNMT3L protein and members of the de novo methyltransferase family.
PG  - 902-917
AB  - The de novo methyltransferase-like protein, DNMT3L, is required for methylation of imprinted
      genes in germ cells. Although enzymatically
      inactive, human DNMT3L was shown to act as a general stimulatory factor
      for de novo methylation by murine Dnmt3a. Several isoforms of DNMT3A
      and DNMT3B with development-stage and tissue-specific expression
      patterns have been described in mouse and human, thus bringing into
      question the identity of the physiological partner(s) for stimulation
      by DNMT3L. Here, we used an episome-based in vivo methyltransferase
      assay to systematically analyze five isoforms of human DNMT3A and
      DNMT3B for activity and stimulation by human DNMT3L. Our results show
      that human DNMT3A, DNMT3A2, DNMT3B1, and DNMT3B2 are catalytically
      competent, while DNMT3B3 is inactive in our assay. We also report that
      the activity of all four active isoforms is significantly increased
      upon co-expression with DNMT3L, albeit to varying extents. This is the
      first comprehensive description of the in vivo activities of the poorly
      characterized human DNMT3A and DNMT3B isoforms and of their functional
      interactions with DNMT3L. To further elucidate the mechanism by which
      DNMT3L stimulates DNA methylation, we have mapped in detail the domains
      that mediate interaction of human DNMT3L with human DNMT3A and DNMT3B.
      Our results show that the C-terminus of DNMT3L is the only region
      required for interaction with DNMT3A and DNMT3B and that interaction
      takes place through the C-terminal catalytic domain of DNMT3A and
      DNMT3B. The implications of these findings for the regulation of de
      novo methyltransferases and genomic imprinting are discussed.
AU  - Chen ZX
AU  - Mann JR
AU  - Hsieh CL
AU  - Riggs AD
AU  - Chedin F
PT  - Journal Article
TA  - J. Cell. Biochem.
JT  - J. Cell. Biochem.
SO  - J. Cell. Biochem. 2005 95: 902-917.

PMID- 24136846
VI  - 1
DP  - 2013
TI  - Genome Sequences of Salmonella enterica Serotype Typhimurium Blood Clinical Isolate ST4848/06 and Stool Isolate ST1489/06.
PG  - e00823-13
AB  - Salmonella enterica serotype Typhimurium human blood strains isolated from outside Africa are
      rarely sequenced. Here, we report the draft genome sequences
      of two S. Typhimurium clinical strains isolated in the same year, one from blood
      and another from stool, in order to gain insights into the genetic basis leading
      to invasive diseases.
AU  - Cheng CK
AU  - Au CH
AU  - Li L
AU  - Nong W
AU  - Law PT
AU  - Cheung WM
AU  - Ling JM
AU  - Kwan HS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00823-13.

PMID- Not carried by PubMed...
VI  - 12
DP  - 1996
TI  - Quantitive study on the inhibitive effect of methylation outside the recognition sequence of restriction endonuclease PvuII on its cleavage activity.
PG  - 36-41
AB  - The recombinant plasmid pSV2gpt-SV40 ori-antisense-ras (P1) was constructed. Using this
      plasmid as a model, it was confirmed that the DNA methylation outside the recognition sequence
      could inhibit the activity of restriction endonuclease PvuII.  Quantitive observation showed
      that the activity of the PvuII was reduced by 70 percent due to the DNA methylation outside
      the recognition sequence.
AU  - Cheng D-F
AU  - Liu Q
AU  - Zhao X-L
AU  - Dong Y-S
AU  - Li Q
PT  - Journal Article
TA  - Shengwu Huazue Zazhi
JT  - Shengwu Huazue Zazhi
SO  - Shengwu Huazue Zazhi 1996 12: 36-41.

PMID- 24501633
VI  - 8
DP  - 2013
TI  - Draft Genome Sequence of Amphibacillus jilinensis Y1(T), a Facultatively Anaerobic, Alkaliphilic and Halotolerant Bacterium.
PG  - 491-499
AB  - The genus Amphibacillus was established in 1990, and seven additional species were described
      in the past two decades. Amphibacillus jilinensis Y1(T) is a
      facultatively anaerobic and alkaliphilic bacterium isolated from a soda lake in
      China. Here we describe the structural and genetic features of the draft genome
      about the type strain Y1(T) (3,831,075 bp, with a G+C content of 37.27%). This is
      the first genome report of the Amphibacillus genus.
AU  - Cheng H
AU  - Fang MX
AU  - Jiang XW
AU  - Wu M
AU  - Zhu XF
AU  - Zheng G
AU  - Yang ZJ
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 491-499.

PMID- 28265340
VI  - 12
DP  - 2017
TI  - High quality draft genome sequence of an extremely halophilic archaeon Natrinema  altunense strain AJ2T.
PG  - 25
AB  - Natrinema altunense strain AJ2T, a halophilic archaeal strain, was isolated from  a
      high-altitude (3884 m) salt lake in Xinjiang, China. This strain requires at
      least 1.7 M NaCl to grow and can grow anaerobically in the presence of nitrate.
      To understand the genetics underlying its extreme phenotype, we de novo assembled
      the entire genome sequence of AJ2T (=CGMCC 1.3731T=JCM 12890T). We assembled
      3,774,135 bp of a total of 4.4 Mb genome in only 20 contigs and noted its high GC
      content (64.6%). Subsequently we predicted the gene content and generated genome
      annotation to identify the relationship between the epigenetic characteristics
      and genomic features. The genome sequence contains 52 tRNA genes, 3 rRNA genes
      and 4,462 protein-coding genes, 3792 assigned as functional or hypothetical
      proteins in nr database. This Whole Genome Shotgun project was deposited in
      DDBJ/EMBL/GenBank under the accession JNCS00000000. We performed a Bayesian
      (Maximum-Likelihood) phylogenetic analysis using 16S rRNA sequence and obtained
      its relationship to other strains in the Natrinema and Haloterrigena genera. We
      also confirmed the ANI value between every two species of Natrinema and
      Haloterrigena genera. In conclusion, our analysis furthered our understanding of
      the extreme-environment adapted strain AJ2T by characterizing its genome
      structure, gene content and phylogenetic placement. Our detailed case study will
      contribute to our overall understanding of why Natrinema strains can survive in
      such a high-altitude salt lake.
AU  - Cheng H
AU  - Huo YY
AU  - Hu J
AU  - Xu XW
AU  - Wu M
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 25.

PMID- 26847882
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Altererythrobacter marensis DSM 21428T, Isolated from Seawater.
PG  - e01607-15
AB  - Altererythrobacter marensis DSM 21428(T) was isolated from seawater collected around Mara
      Island, South Korea. The genomic characteristics of this strain
      support its potential for alkane-related compound degradation. A. marensis DSM
      21428(T) has potential applications in bioremediation projects concerning
      offshore petroleum spill prevention and response.
AU  - Cheng H
AU  - Wu YH
AU  - Huo YY
AU  - Wang CS
AU  - Xu XW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01607-15.

PMID- 25960197
VI  - 6
DP  - 2015
TI  - Molecular mechanism for USP7-mediated DNMT1 stabilization by acetylation.
PG  - 7023
AB  - DNMT1 is an important epigenetic regulator that plays a key role in the maintenance of DNA
      methylation. Here we determined the crystal structure of DNMT1
      in complex with USP7 at 2.9 A resolution. The interaction between the two
      proteins is primarily mediated by an acidic pocket in USP7 and Lysine residues
      within DNMT1's KG linker. This intermolecular interaction is required for
      USP7-mediated stabilization of DNMT1. Acetylation of the KG linker Lysine
      residues impair DNMT1-USP7 interaction and promote the degradation of DNMT1.
      Treatment with HDAC inhibitors results in an increase in acetylated DNMT1 and
      decreased total DNMT1 protein. This negative correlation is observed in
      differentiated neuronal cells and pancreatic cancer cells. Our studies reveal
      that USP7-mediated stabilization of DNMT1 is regulated by acetylation and provide
      a structural basis for the design of inhibitors, targeting the DNMT1-USP7
      interaction surface for therapeutic applications.
AU  - Cheng J
AU  - Yang H
AU  - Fang J
AU  - Ma L
AU  - Gong R
AU  - Wang P
AU  - Li Z
AU  - Xu Y
PT  - Journal Article
TA  - Nat. Commun.
JT  - Nat. Commun.
SO  - Nat. Commun. 2015 6: 7023.

PMID- 6088551
VI  - 259
DP  - 1984
TI  - Isolation of gram quantities of EcoRI restriction and modification enzymes from an overproducing strain.
PG  - 11571-11575
AB  - Structural genes for EcoRI restriction endonuclease and modification methylase
      have been inserted into the plasmid vector pKC3 (Shimatake, H., and Rosenberg,
      M. (1981) Nature (Lond.) 292, 128-132 downstream from the bacteriophage
      lambdapL promoter.  Upon induction of pL expression in strains producing a
      thermolabile lambda cI857 repressor, synthesis of EcoRI polypeptides is
      enhanced to the extent that after 4 h they represent several per cent of the
      total cell protein.  Purification of activities overproduced in this manner
      yields preparations of endonuclease and methylase which appear identical to
      those obtained from conventional sources, with overall yields corresponding to
      0.5 to 0.9 g of each enzyme/kg of cell paste.
AU  - Cheng S-C
AU  - Kim R
AU  - King K
AU  - Kim S-H
AU  - Modrich P
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1984 259: 11571-11575.

PMID- 6302074
VI  - 154
DP  - 1983
TI  - Positive-selection cloning vehicle useful for overproduction of hybrid proteins.
PG  - 1005-1008
AB  - Plasmid pSCC31 contains the EcoRI endonuclease gene downstream from lambda pL.
      It does not yield transformants upon introduction into Escherichia coli unless
      the structural integrity of the endonuclease is destroyed.  This makes it
      useful as a positive-selection cloning vehicle which can be employed for
      regulated overproduction of hybrid proteins.
AU  - Cheng S-C
AU  - Modrich P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1983 154: 1005-1008.

PMID- 24831136
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Bacillus bombysepticus, a Pathogen Leading to Bombyx  mori Black Chest Septicemia.
PG  - e00312-14
AB  - Bacillus bombysepticus is a Gram-positive spore-forming bacterium. Here, we announce the first
      complete genome sequence of this organism isolated from the
      cadavers of silkworm larvae that had been sick. The genome contains a single
      circular chromosome and a circular plasmid. Analyses of the B. bombysepticus
      genome will provide insights into its pathomechanisms and biology.
AU  - Cheng T
AU  - Lin P
AU  - Jin S
AU  - Wu Y
AU  - Fu B
AU  - Long R
AU  - Liu D
AU  - Guo Y
AU  - Peng L
AU  - Xia Q
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00312-14.

PMID- 29439033
VI  - 6
DP  - 2018
TI  - Genome Sequence of Serratia marcescens subsp. sakuensis Strain K27, a Marine Bacterium Isolated from Sponge (Haliclona amboinensis).
PG  - e00022-18
AB  - Serratia marcescens subsp. sakuensis strain K27 was isolated from sponge (Haliclona
      amboinensis). The genome of this strain consists of 5,325,727 bp, with
      5,140 open reading frames (ORFs), 3 rRNAs, and 67 tRNAs. It contains genes for
      the production of amylases, lipases, and proteases. Gene clusters for the
      biosynthesis of nonribosomal peptides and thiopeptide were also identified.
AU  - Cheng TH
AU  - Saidin J
AU  - Danish-Daniel M
AU  - Gan HM
AU  - Mat IMN
AU  - Abu BMF
AU  - Ismail N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00022-18.

PMID- 23516183
VI  - 1
DP  - 2013
TI  - Complete Genome of the Solvent-Tolerant Staphylococcus warneri Strain SG1.
PG  - e0003813
AB  - Staphylococcus warneri is a Gram-positive bacterium commonly found in human skin  flora. The
      genome of a laboratory S. warneri isolate, strain SG1, was sequenced
      to explore its mechanism of solvent tolerance and its potential as a chassis for
      biofuel production.
AU  - Cheng VW
AU  - Zhang G
AU  - Oyedotun KS
AU  - Ridgway D
AU  - Ellison MJ
AU  - Weiner JH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0003813.

PMID- 28302787
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Endophytic Herbaspirillum sp. Strain WT00C, a Tea Plant  Growth-Promoting Bacterium.
PG  - e01719-16
AB  - Endophytic Herbaspirillum sp. strain WT00C was isolated from tea plant (Camellia  sinensis
      L.). Here, we report the 6.08 Mb draft genome sequence of this strain,
      providing bioinformation about its agronomic benefits and capability to reduce
      selenate/selenite into red elemental selenium.
AU  - Cheng W
AU  - Zhan G
AU  - Liu W
AU  - Zhu R
AU  - Yu X
AU  - Li Y
AU  - Li Y
AU  - Wu W
AU  - Wang X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01719-16.

PMID- 7663118
VI  - 24
DP  - 1995
TI  - Structure and function of DNA methyltransferases.
PG  - 293-318
AB  - Perspectives and Overview
      DNA Methylation
      Types of DNA methylation
      C5-cytosine methyltransferases
      Catalytic mechanism
      HhaI methyltransferase
      Crystal Structure of a C5-cytosine Methyltransferase
      General protein topology: a two-domain structure
      Induced fit in Protein-DNA interactions
      Catalytic domain
      DNA-Recognition domain
      Summary and Discussion
      The Catalytic Domain is a Structural Framework for the SAM-dependent Methyltransferases
      TaqI methyltransferase
      Catechol O-methyltransferase
      Common catalytic-domain structure
      N6-adenine and N4-cytosine methylation
      Summary
AU  - Cheng X
PT  - Journal Article
TA  - Annu. Rev. Biophys. Biomol. Struct.
JT  - Annu. Rev. Biophys. Biomol. Struct.
SO  - Annu. Rev. Biophys. Biomol. Struct. 1995 24: 293-318.

PMID- 7773746
VI  - 5
DP  - 1995
TI  - DNA modification by methyltransferases.
PG  - 4-10
AB  - Enzymatic methylation of DNA plays important roles in both prokaryotes and eukaryotes.
      Structural study of the HhaI DNA methyltransferase has provided considerable insight into the
      chemistry of C5-cytosine methylation. The DNA-protein complex reveals a substrate cytosine
      flipped out of the double helix during the reaction, and a novel two-loop DNA-binding motif
      used for both sequence recognition and flipping the base. Structural comparison of HhaI
      C5-cytosine methyltransferase, TaqI N6-adenine methyltransferase, and catechol
      O-methyltransferase reveals a common catalytic domain structure, which might be universal
      among S-adenosyl-L-methionine (SAM)-dependent methyltransferases.
AU  - Cheng X
PT  - Journal Article
TA  - Curr. Opin. Struct. Biol.
JT  - Curr. Opin. Struct. Biol.
SO  - Curr. Opin. Struct. Biol. 1995 5: 4-10.

PMID- 8076590
VI  - 13
DP  - 1994
TI  - Structure of PvuII endonuclease with cognate DNA.
PG  - 3927-3935
AB  - We have determined the structure of PvuII endonuclease complexed with cognate DNA by X-ray
      crystallography. The DNA substrate is bound with a single homodimeric protein, each subunit of
      which reveals three structural regions. The catalytic region strongly resembles structures of
      other restriction endonucleases, even though these regions have dissimilar primary sequences.
      Comparison of the active site with those of EcoRV and EcoRI endonucleases reveals a conserved
      triplet sequence close to the reactive phosphodiester group and a conserved acidic pair that
      may represent the ligands for the catalytic cofactor Mg2+. The DNA duplex is not significantly
      bent and maintains a B-DNA-like conformation. The subunit interface region of the homodimeric
      protein consists of a pseudo-three-helix bundle. Direct contacts between the protein and the
      base pairs of the PvuII recognition site occur exclusively in the major groove through two
      antiparallel beta strands from the sequence recognition region of the protein. Water-mediated
      contacts are made in the minor grooves to central bases of the site. If restriction enzymes do
      share a common ancestor, as has been proposed, their catalytic regions have been very strongly
      conserved, while their subunit interfaces and DNA sequence recognition regions have undergone
      remarkable structural variation.
AU  - Cheng X
AU  - Balendiran K
AU  - Schildkraut I
AU  - Anderson JE
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1994 13: 3927-3935.

PMID- 7607478
VI  - 157
DP  - 1995
TI  - Crystal stucture of the PvuII restriction endonuclease.
PG  - 139-140
AB  - Crystal structures have now been determined for the R.PvuII restriction endonuclease as a
      protein-DNA complex and in apo-form.  The structures indicate how the interaction with DNA
      might proceed.
AU  - Cheng X
AU  - Balendiran K
AU  - Schildkraut I
AU  - Anderson JE
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 139-140.

PMID- 8805547
VI  - 4
DP  - 1996
TI  - Finding a basis for flipping bases.
PG  - 639-645
AB  - Rotation of a DNA nucleotide out of the double helix and into a protein binding pocket ('base
      flipping') was first observed in the structure of a DNA methyltransferase.  There is now
      evidence that a variety of proteins use base flipping in their interactions with DNA.  Though
      the mechanism for base flipping is still unclear, we propose a three-step pathway: recognizing
      the target site and increasing the interstrand phosphate-phosphate distance nearby, initiating
      base flipping by protein invasion of the DNA, and trapping the flipped DNA structure.
AU  - Cheng X
AU  - Blumenthal RM
PT  - Journal Article
TA  - Structure
JT  - Structure
SO  - Structure 1996 4: 639-645.

PMID- 18334209
VI  - 16
DP  - 2008
TI  - Mammalian DNA methyltransferases: A structural perspective.
PG  - 341-350
AB  - The methylation of mammalian DNA, primarily at CpG dinucleotides, has long been recognized to
      play a major role in controlling gene expression, among other functions.  Given their
      importance, it is surprising how many basic questions remain to be answered about the proteins
      responsible for this methylation and for coordination with the parallel chromatin-marking
      system that operates at the level of histone modification.  This article reviews recent
      studies on, and discusses the resulting biochemical and structural insights into, the DNA
      nucleotide methyltransferase (Dnmt) proteins 1, 3a, 3a2, 3b, and 3L.
AU  - Cheng X
AU  - Blumenthal RM
PT  - Journal Article
TA  - Structure
JT  - Structure
SO  - Structure 2008 16: 341-350.

PMID- 7956046
VI  - 58
DP  - 1993
TI  - Crystal structure of the HhaI DNA methyltransferase.
PG  - 331-338
AB  - Structures of M.HhaI with AdoMet and M.HhaI, DNA and AdoHcy are described.
AU  - Cheng X
AU  - Kumar S
AU  - Klimasauskas S
AU  - Roberts RJ
PT  - Journal Article
TA  - Cold Spring Harb. Symp. Quant. Biol.
JT  - Cold Spring Harb. Symp. Quant. Biol.
SO  - Cold Spring Harb. Symp. Quant. Biol. 1993 58: 331-338.

PMID- 8343957
VI  - 74
DP  - 1993
TI  - Crystal structure of the HhaI DNA methyltransferase complexed with S-adenosyl-L-methionine.
PG  - 299-307
AB  - The first three-dimensional structure of a DNA methyltranferase is presented. The crystal
      structure of the DNA (cytosine-5)-methyltransferase, M.HhaI (recognition sequence: GCGC),
      complexed with S-adenosyl-L-methionine has been determined and refined at 2.5 A resolution.
      The core of the structure is dominated by sequence motifs conserved among all DNA
      (cytosine-5)-methyltransferases, and these are responsible for cofactor binding and
      methyltransferase function.
AU  - Cheng X
AU  - Kumar S
AU  - Posfai J
AU  - Pflugrath JW
AU  - Roberts RJ
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1993 74: 299-307.

PMID- Not included in PubMed...
VI  - SA49
DP  - 1993
TI  - Crystal structure of HhaI DNA methyltransferase complexed with S-adenosyl-L-methionine.
PG  - 61
AB  - DNA methyltransferases are found in organisms ranging from bacteria to mammals. The DNA
      methyltransferase from the bacterium Haemophilus haemolyticus catalyzes the transfer of a
      methyl group from S-adenosyl-L-methionine (AdoMet) to C-5 of the internal cytosine in the DNA
      sequence GCGC. The three dimensional structure of the M.HhaI-AdoMet complex has been
      determined and refined at a resolution of 2.5 A. The structure is the first to be solved for
      any DNA methyltransferase as well as being the first for any methyltransferase that utilizes
      the ubiquitous methyl donor AdoMet. Due to the conserved nature of
      (cytosine-5)-methyltransferases, the information obtained from this structure can be
      generalized to the entire family, including the mammalian CpG methyltransferase.
AU  - Cheng X
AU  - Kumar S
AU  - Sha M
AU  - Roberts RJ
PT  - Journal Article
TA  - Acta Crystallogr. A
JT  - Acta Crystallogr. A
SO  - Acta Crystallogr. A 1993 SA49: 61.

PMID- 11557810
VI  - 29
DP  - 2001
TI  - AdoMet-dependent methylation, DNA methyltransferases and base flipping.
PG  - 3784-3795
AB  - Twenty AdoMet-dependent methyltransferases (MTases) have been characterized structurally by
      X-ray crystallography and NMR. These include seven DNA MTases, five RNA MTases, four protein
      MTases and four small molecule MTases acting on the carbon, oxygen or nitrogen atoms of their
      substrates. The MTases share a common core structure of a mixed seven-stranded beta-sheet
      (6|7^5|4|1|2^3|) referred to as an 'AdoMet-dependent MTase fold', with the exception
      of a protein arginine MTase which contains a compact consensus fold lacking the antiparallel
      hairpin strands (6|7^). The consensus fold is useful to identify
      hypothetical MTases during structural proteomics efforts on unannotated proteins. The same
      core structure works for very different classes of MTase including those that act on
      substrates differing in size from small molecules (catechol or glycine) to macromolecules
      (DNA, RNA and protein). DNA MTases use a 'base flipping' mechanism to deliver a specific
      base within a DNA molecule into a typically concave catalytic pocket. Base flipping involves
      rotation of backbone bonds in double-stranded DNA to expose an out-of-stack nucleotide, which
      can then be a substrate for an enzyme-catalyzed chemical reaction. The phenomenon is fully
      established for DNA MTases and for DNA base excision repair enzymes, and is likely to prove
      general for enzymes that require access to unpaired, mismatched or damaged nucleotides within
      base-paired regions in DNA and RNA. Several newly discovered MTase families in eukaryotes (DNA
      5mC MTases and protein arginine and lysine MTases) offer new challenges in the MTase field.
AU  - Cheng X
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2001 29: 3784-3795.

PMID- 
VI  - 13
DP  - 2003
TI  - Structural and functional analysis of methyltransferases.
PG  - 408
AB  - Our work involves structural characterization of AdoMet-dependent methyltransferases (MTases),
      including enzymes that covalently modify DNA and histones, a process that controls many
      cellular processes by affecting gene expression.  The DNA MTase structure comprises a
      seven-stranded beta sheet, flanked by alpha helices to form a doubly wound open aba sandwich,
      and is
      henceforth referred to as the Class 1 MTase structure.  Many of the known Class I MTases act
      on DNA to regulate gene expression, to repair mutations or to protect against bacterial
      restriction enzymes.  Initially, it was a mystery as to how MTases acted on nucleotides that
      are held inside the DNA duplex by base pairing and stacking -- seemingly inaccessible to the
      active site of an enzyme.  In a process termed 'base flipping', the enzyme simply rotates
      the target DNA on its flanking phosphodiester bonds such that the base projects into the
      catalytic pocket.  Protein arginine MTases (PRMTs) have broad substrates including histones H3
      and H4.  PRMT1 is the predominant PRMT in mammalian cells, accounting for 85% of cellular PRMT
      activity and is essential for early postimplantation development.  The structure of PRMT1
      forms a ring-like dimer, essential for AdoMet binding and enzymatic activity.  The AdoMet
      binding domain is a compact version of the Class I MTase fold.  A recently discovered class of
      these enzymes is the histone lysine MTase family, whose catalytic activity lies within a
      conserved domain, the SET domain.  Using entirely different structural scaffolding, the
      SET-domain MTases bind to a kinked AdoMet molecule on the opposite side of a narrow channel
      from the target nitrogen of the lysine substrate.  The C-terminal tail of the SET domain forms
      a pseudo knot and provides an integral part of the hydrophobic active-site pocket, including
      tyrosine residues implicated in the catalytic mechanism.  On the other hand, not all histone
      lysine MTases contain the SET domain; the yeast Dot1p histone H3-Lys79 MTase belongs to Class
      1 MTases.
AU  - Cheng XD
AU  - Collins RC
AU  - Jia D
AU  - Khan SI
AU  - Horton JR
AU  - Qiu C
AU  - Sawada K
AU  - Yang Z
AU  - Zhang X
PT  - Journal Article
TA  - Cell Res.
JT  - Cell Res.
SO  - Cell Res. 2003 13: 408.

PMID- 27881545
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of the Probiotic Strain Lactobacillus salivarius LPM01.
PG  - e01319-16
AB  - Lactobacillus salivarius LPM01 (DSM 22150) is a probiotic strain able to improve  health
      status in immunocompromised people. Here, we report its complete genome
      sequence deciphered by PacBio single-molecule real-time (SMRT) technology.
      Analysis of the sequence may provide insights into its functional activity and
      safety assessment.
AU  - Chenoll E
AU  - Codoner FM
AU  - Martinez-Blanch JF
AU  - Acevedo-Pierart M
AU  - Ormeno ML
AU  - Ramon D
AU  - Genoves S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01319-16.

PMID- 27103719
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Lactobacillus rhamnosus Strain BPL5 (CECT 8800), a Probiotic for Treatment of Bacterial Vaginosis.
PG  - e00292-16
AB  - ITALIC! Lactobacillus rhamnosusBPL5 (CECT 8800), is a probiotic strain suitable for the
      treatment of bacterial vaginosis. Here, we report its complete genome
      sequence deciphered by PacBio single-molecule real-time (SMRT) technology.
      Analysis of the sequence may provide insight into its functional activity.
AU  - Chenoll E
AU  - Codoner FM
AU  - Martinez-Blanch JF
AU  - Ramon D
AU  - Genoves S
AU  - Menabrito M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00292-16.

PMID- 24675853
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Bifidobacterium animalis subsp. lactis Strain CECT 8145, Able To Improve Metabolic Syndrome In Vivo.
PG  - e00183-14
AB  - Bifidobacterium animalis subsp. lactis strain CECT 8145 is able to reduce body fat content and
      improve metabolic syndrome biomarkers. Here, we report the draft
      genome sequence of this strain, which may provide insights into its safety status
      and functional role.
AU  - Chenoll E
AU  - Codoner FM
AU  - Silva A
AU  - Martinez-Blanch JF
AU  - Martorell P
AU  - Ramon D
AU  - Genoves S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00183-14.

PMID- 25838473
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Bifidobacterium longum subsp. infantis Strain CECT 7210, a Probiotic Strain Active against Rotavirus Infections.
PG  - e00105-15
AB  - Bifidobacterium longum subsp. infantis CECT 7210 is a probiotic strain able to inhibit
      rotavirus in vitro and protect against viral infection in both cell
      cultures and mice. Here, we report its complete genome sequence, as deciphered by
      PacBio single-molecule real-time (SMRT) technology. An analysis of the sequence
      may provide insights into its functional activity.
AU  - Chenoll E
AU  - Rivero M
AU  - Codoner FM
AU  - Martinez-Blanch JF
AU  - Ramon D
AU  - Genoves S
AU  - Moreno MJA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00105-15.

PMID- 21888552
VI  - 30
DP  - 2011
TI  - Mechanism of CpG DNA Methyltransferases M.SssI and Dnmt3a Studied by DNA Containing 2-Aminopurine.
PG  - 619-631
AB  - Murine DNA methyltransferases Dnmt3a-CD and M.SssI from Spiroplasma methylate cytosines at CpG
      sites.  The role of 6-oxo groups of guanines in DNA methylation by these enzymes has been
      studied using DNA substrates, which contained 2-aminopurine at different positions.  Removal
      of the 6-oxo group of the guanine located adjacent to the target cytosine in the CpG site
      dramatically reduces the stability of the methyltransferase-DNA complexes and leads to a
      significant decrease in the methylation.  Apparently, 06 of this guanine is involvd in the
      recognition of CpG sites by the enzymes.  Cooperative binding of Dnmt3a-CD to
      2-aminopurine-containing DNA and the formation of nonproductive enzyme-substrate complexes
      were observed.
AU  - Cherepanova NA
AU  - Minero AS
AU  - Rakhimova AR
AU  - Gromova ES
PT  - Journal Article
TA  - Nucleosides Nucleotides Nucleic Acids
JT  - Nucleosides Nucleotides Nucleic Acids
SO  - Nucleosides Nucleotides Nucleic Acids 2011 30: 619-631.

PMID- 
VI  - 75
DP  - 2010
TI  - Inhibition of murine DNA methyltransferase Dnmt3a by DNA duplexes containing pyrimidine-2(1H)-one.
PG  - 1244-1256
AB  - Here we studied the inhibition of the catalytic domain of Dnmt3a methyltransferase (Dnmt3a-CD)
      by DNA duplexes containing the mechanism-based inhibitor pyrimidine-2(1H)-one (P) instead of
      the target cytosine. It has been shown that conjugates of Dnmt3a-CD with P-DNA (DNA containing
      pyrimidine-2(1H)-one) are not stable to heating at 65A degrees C in 0.1% SDS. The yield of
      covalent intermediate increases in the presence of the regulatory factor Dnmt3L. The
      importance of the DNA minor groove for covalent intermediate formation during the methylation
      reaction catalyzed by Dnmt3a-CD has been revealed. P-DNA was shown to inhibit Dnmt3a-CD; the
      IC50 is 830 nM. The competitive mechanism of inhibition of Dnmt3a-CD by P-DNA has been
      elucidated. It is suggested that therapeutic effect of zebularine could be achieved by
      inhibition of not only Dnmt1 but also Dnmt3a.
AU  - Cherepanova NA
AU  - Zhuze AL
AU  - Gromova ES
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2010 75: 1244-1256.

PMID- 29437088
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Monaibacterium marinum C7(T), Isolated from Seawater from the Menai Straits, Wales, United Kingdom.
PG  - e01444-17
AB  - Here, we report the draft genome sequence of Monaibacterium marinum C7(T), a strain that
      represents a new member of the Roseobacter clade of the family
      Rhodobacteraceae (Alphaproteobacteria). The genome size of Monaibacterium marinum
      C7(T) is 3.7 Mb (3,734,267 bp), with a G+C content of 58.86%.
AU  - Chernikova TN
AU  - Kyrpides N
AU  - Bargiela R
AU  - Woyke T
AU  - Shapiro N
AU  - Whitman WB
AU  - Golyshin PN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01444-17.

PMID- 3031490
VI  - 1
DP  - 1987
TI  - Some peculiarities of the antirestriction mechanism of bacteriophage T5.
PG  - 14-19
AB  - Data are cited on the peculiarities of the unique antirestriction mechanism (ARM) of
      bacteriophage T5.  Phage T5 is not confined by the restriction systems of the second type,
      EcoRI, EcoRII, and EcoRV, although its ARM does not inactivate the restriction endonucleases
      of these systems.  There is no modification of phage T5 DNA at the EcoRII, EcoRI, and EcoRV
      sites in vivo; consequently, the protection of T5 DNA from the action of restriction
      endonucleases is not based on its modification by the ARM.  The ARM of phage T5 protects only
      its own DNA from restriction and does not protect foreign DNA (from phage lambda).  Four
      recognition sites for restriction endonuclease EcoRV have been mapped in T5 DNA and two sites
      for restriction endonuclease EcoRII and three sites for restriction endonuclease HpaI in FST.
      It was shown that in FST of phage T5 there are two zones with boundaries in the region of 5%
      of the length of T5 DNA.  Introduction of recognition sites for restriction endonucleases by
      mutagenesis into the terminal zone of FST leads to a confinement of the mutant T5 phage by the
      corresponding restriction system, whereas the presence of sites in the second zone of FST does
      not lead to confinement of the phage.  It is suggested that the action of (ARM) of phage T5 is
      based on prevention by the antirestriction protein of contact of the T5 DNA with the enzymes
      of the host restriction systems.
AU  - Chernov AP
AU  - Kaliman AV
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1987 1: 14-19.

PMID- 9011232
VI  - 61
DP  - 1996
TI  - Two site-specific endonucleases from thermophilic strain Bacillus species OV.
PG  - 1837-1847
AB  - Two site-specific endonucleases, BspOVI and BspOVII, were isolated from the thermophilic
      strain Bacillus species OV.  The highest activity of both the enzymes was observed at 48 C and
      did not depend on the presence of S-adenosyl-L-methionine and ATP.  BspOVI recognizes the
      sequence 5'-GACNNN/NNGTC-3' 3'-CTGNN/NNNCAG-5' and cleaves it as shown by the arrows.
      Consequently, it is an isoschizomer of Eam1105I and belongs to subclass IIN of endonucleases.
      BspOVI has an increased stability during storage.  The enzyme can be used to create T-vectors
      for direct cloning of PCR products.  BspOVII recognizes and cleaves the sequence
      5'-AT/CGAT-3' 3'-TAGC/TA-5' and, consequently, it is an isoschizomer of ClaI,.  BspOVII is
      blocked by methylation of adenine inside the recognition site.
AU  - Chernov AV
AU  - Lepikhov KA
AU  - Zheleznaya LA
AU  - Matvienko NI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1996 61: 1837-1847.

PMID- 7873679
VI  - 59
DP  - 1994
TI  - A new site-specific endonuclease-methylase from the thermophilic strain of Bacillus species LU11.
PG  - 1714-1729
AB  - A new site-specific endonuclease, BspLU11III, was isolated and purified to homogeneity from
      the thermophilic strain Bacillus species LU11. The enzyme recognizes the 5'-GGGAC-3'
      sequence on double-stranded DNA and cleaves it at two places, 10 and 11 nucleotides from the
      3'-end of the 5'-GGGAC-3' sequence and 14 and 15 nucleotides from the recognized site along
      the complementary strand. In solution the enzyme is a monomer with molecular mass of about 93
      kD. In the presence of S-adenosylmethionine the enzyme has methylase activity. The adenine
      residue in the recognition site is methylated on one of the DNA strands. The restriction
      activity of BspLU11III does not depend on ATP, but is stimulated by 80 microM
      S-adenosyl-methionine. Mg2+ is required for restriction activity. Star activity is observed in
      the presence of sodium chloride. BspLU11III is not a member of the three main classes of
      endonucleases, but has properties similar to type IV site-specific endonucleases.
AU  - Chernov AV
AU  - Matvienko NN
AU  - Zheleznaya LA
AU  - Matvienko NI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1994 59: 1714-1729.

PMID- 7739899
VI  - 23
DP  - 1995
TI  - BspLUII III, a bifunctional restriction and modification enzyme from a thermohilic strain Bacillus species LUII.
PG  - 1213-1214
AB  - BspLU11III, an isomer of FinI and BsmFI, was found to cleave DNA at two points 10, 11 and 14,
      15 bp in the different strands away from the recognition site, and in the presence of SAM it
      exhibits the adenine specific methyltransferase activity.
AU  - Chernov AV
AU  - Matvienko NN
AU  - Zheleznaya LA
AU  - Matvienko NI
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1995 23: 1213-1214.

PMID- 9461345
VI  - 378
DP  - 1997
TI  - Masc2, a C5-DNA-methyltransferase from Ascobolus immersus with similarity to methyltransferases of higher organisms.
PG  - 1467-1473
AB  - The filamentous fungus Ascobolus immersus represents a eukaryotic model organism to study
      genetic phenomena linked to DNA methylation.  Following our previous characterization of a
      gene, masc1 from A. immersus, encoding the 'de novo' C5-DNA-methyltransferase, we report
      here the identification of a second MTase gene, masc2.  The deduced peptide sequence of Masc2
      is similar to previously identified eukaryotic MTases and distinct from Masc1 by having a
      large N-terminal domain in addition to the ubiquitous C-terminal catalytic domain.  Following
      cloning of the gene, Masc2 was overexpressed and purified.  Masc2 shows MTase activity with
      double stranded DNAs.  Structural and biochemical properties of Masc2 suggest that it may
      function as a 'maintenance' MTase.  With this finding, A. immersus represents so far the
      only eukaryotic organism in which two possibly synergistically operating MTases have been
      identified.
AU  - Chernov AV
AU  - Vollmayr P
AU  - Walter J
AU  - Trautner TA
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1997 378: 1467-1473.

PMID- 7578583
VI  - 60
DP  - 1995
TI  - Site-specific endonuclease BspKT8 from the Thermophile strain Bacillus species KT8.
PG  - 1318-1325
AB  - A site-specific endonuclease recognizing the sequence 5'-AAGCTT-3' was isolated and purified
      to homogeneity from the thermophilic strain Bacillus species KT8.  The enzyme, BspKT8, has
      molecular mass 34kD and is a monomeric protein in solution.  The activity of BspKT8 does not
      depend on ATP and is not stimulated by S-adenosyl-L-methionine.  The enzyme has the highest
      activity in the wide temperature range from 37 to 48oC.  DNA is cleaved as indicated by the
      arrows 5'-A/AGCT T-3' 3'-T TCGA/A-5' hence, the enzyme is a class II restriction
      endonuclease and an isoschizomer of HindIII.
AU  - Chernov AV
AU  - Zheleznaya LA
AU  - Matvienko NI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1995 60: 1318-1325.

PMID- 27099792
VI  - 8
DP  - 2016
TI  - Cloning and characterization of the novel site-specific, methyl-dependent endonuclease EmlI that recognizse and digests 5mC methylated sequence 5'-G(5mC)/NG(5mC)-3'.
PG  - 117-125
AB  - 
AU  - Chernuhin VA
AU  - Gonchar DA
AU  - Abdurashidov MA
AU  - Belichenko OA
AU  - Dedkov VS
AU  - Mihnenkova NA
AU  - Lomakovskaja EN
AU  - Udal'cova SG
AU  - Degterev SH
PT  - Journal Article
TA  - Acta Naturae
JT  - Acta Naturae
SO  - Acta Naturae 2016 8: 117-125.

PMID- 
VI  - 3
DP  - 2007
TI  - New Restriction Endonuclease AluBI from Arthrobacter luteus B - AluI Isoshizomer, nonsensitive to Presence of 5-methylcytosine in the Recognition Sequence AGCT.
PG  - 21-27
AB  - A new restriction endonuclease AluBI has been discovered and characterized. AluBI is an
      isoshizomer of well known restriction endonuclease AluI, which recognizes DNA sequence AGCT.
      Unlike AluI, enzyme AluBI is able to cleave DNA when recognition sequence contains
      5-methylcytosines. AluBI also cleaves recognition sequence with two methylated cytosines, one
      modified at N4 and other at C5 positions. However, new enzyme doesn't cleave DNA with two
      N4-methylcytosines in the recognition site.
AU  - Chernukhin VA
AU  - Boltengagen AA
AU  - Tarasova GV
AU  - Dedkov VS
AU  - Degtyarev SK
PT  - Journal Article
TA  - Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol.
JT  - Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol.
SO  - Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol. 2007 3: 21-27.

PMID- 
VI  - 3
DP  - 2007
TI  - A novel site-specific endonuclease GluI recognizes methylated DNA sequence 5'-G(5mC)^NG(5mC)-3'/3'-(5mC)GN^(5mC)G.
PG  - 13-17
AB  - A novel site-specific endonuclease GluI from the bacterial strain GL24 has been isolated and
      characterized. The enzyme recognizes methylated DNA sequence
      5'-G(5mC)^NG(5mC)-3'/3'-(5mC)GN^(5mC)G-5' and cleaves it as it is shown by arrow. Due to
      its ability to cleave only modified DNA GluI may be useful for genetic engineering experiments
      as well as for determination of DNA methylation status in eucaryotes.
AU  - Chernukhin VA
AU  - Chmuzh EV
AU  - Tomilova YE
AU  - Nayakshina TN
AU  - Gonchar DA
AU  - Dedkov VS
AU  - Degtyarev SK
PT  - Journal Article
TA  - Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol.
JT  - Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol.
SO  - Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol. 2007 3: 13-17.

PMID- 14606938
VI  - 68
DP  - 2003
TI  - M.BstF5I-2 and M.BstF5I-4 DNA methyltransferases from BstF5I restriction-modification system of Bacillus stearothermophilus F5.
PG  - 967-975
AB  - The BstF5I restriction-modification system from Bacillus stearothermophilus F5 includes four
      site-specific DNA methyltransferases,
      thus differing from all known restriction-modification systems. Here we
      demonstrated for the first time that one bacterial cell can possess two
      pairs of methylases with identical substrate specificities (methylases
      BstF5I-1 and BstF5I-3 recognize GGATG, whereas methylases BstF5I-2 and
      BstF5I-4 recognize CATCC) that modify adenine residues on both DNA
      strands. Different chromatographic methods provide homogenous preparations
      of methylases BstF5I-2 and BstF5I-4. We estimated the principal kinetic
      parameters of the reaction of transfer of methyl group from the donor
      S-adenosyl-L-methionine to the recognition site 5;-CATCC-3; catalyzed by
      BstF5I-2 and BstF5I-4 DNA [N6-adenine]-methyltransferases from the BstF5I
      restriction-modification system.
AU  - Chernukhin VA
AU  - Golikova LN
AU  - Gonchar DA
AU  - Abdurashitov MA
AU  - Kashirina YG
AU  - Netesova NA
AU  - Degtyarev SK
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 2003 68: 967-975.

PMID- 
VI  - 28
DP  - 2016
TI  - Cloning and characterization of a new site specific methyl-directed endonuclease ElmI recognizing and cleaving C5-methylated DNA sequence 5'-G(5mC)^NG(5mC)-3'.
PG  - 42-51
AB  - As a result of the search of amino acid sequences homologous to MD-endonuclease BisI a
      putative open reading frames of MD-endonucleases have been identified in Enterobacteria
      genomes. A highly conserved DNA primary structure of these open reading frames in different
      genera of Enterobacteria (Escherichia, Klebsiella and Cronobacter) has allowed creating the
      primers for PCR screening, which was carried out on Enterobacteria DNA collected from natural
      sources.  The DNA fragment about 440 bp in length was amplified by use the genomic DNA of a
      wild E.coli LM N17 strain as a template and was inserted into the pMTL22 vector. The resulting
      endonuclease activity was detected in E.coli ER 2267 strain being transformed with obtained
      construction. A new enzyme named ElmI was purified by chromatographic techniques from
      recombinant strain biomass.  It was found this enzyme like BisI specifically cleaved
      methylated DNA sequence 5'-GCNGC-3' before the central nucleotide N in the case of the
      presence of two 5-methylcytosines within it. However, unlike BisI, ElmI more efficiently
      cleaves this sequence if more than two cytosine residues are methylated.
AU  - Chernukhin VA
AU  - Gonchar DA
AU  - Abdurashitov MA
AU  - Belichenko OA
AU  - Dedkov VS
AU  - Mikhnenkova NA
AU  - Lomakovskaya EN
AU  - Udalyeva SG
AU  - Degtyarev SK
PT  - Journal Article
TA  - Acta Naturae
JT  - Acta Naturae
SO  - Acta Naturae 2016 28: 42-51.

PMID- 
VI  - 70
DP  - 2005
TI  - Isolation and characterization of biochemical properties of DNA methyltransferase FauIA modifying the second cytosine in the  nonpalindromic sequence 5 '-CCCGC-3 '.
PG  - 829-837
AB  - A gene encoding DNA methyltransferase (methylase) FauIA of the restriction-modification system
      FauI from Flavobaclerium aquatile (recognizing sequence 5'-CCCGC-3') was cloned in pJW
      vector. The latter was used for transformation of E. coli RRI cells followed by subsequent
      thermoinduction and biomass elaboration. Highly purified DNA methyltransferase FauIA
      preparation was obtained using chromatography on different sorbents. The molecular mass of the
      isolated enzyme of about 39 kD corresponds to its theoretical value. The enzyme was
      characterized by temperature and pH optima of 33 degrees C and pH 7.5, respectively.
      Methylation of a synthetic oligonucleotide by FauIA methylase followed by its cleavage with
      various restrictases and analysis of the resultant restriction fragments revealed that FauIA
      methylase modified the second cytosine residue in the sequence 5'-CCCGC-3'. Kinetic analysis
      revealed Km and catalytic constant values of 0.16 mu M and 0.05 min(-1), respectively.
AU  - Chernukhin VA
AU  - Kashirina YG
AU  - Sukhanova KS
AU  - Abdurashitov MA
AU  - Gonchar DA
AU  - Degtyarev SK
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 2005 70: 829-837.

PMID- 
VI  - 2
DP  - 2006
TI  - New Eight Bases Cutter AbsI from Arthrobacter species Recognizes Palindromic DNA Sequence 5'-CC^TCGAGG-3'.
PG  - 29-34
AB  - Bacterial strain Arthrobacter species7M06 producing site-specific endonuclease AbsI has been
      discovered. AbsI recognizes palindromic octanucleotide DNA sequence 5'-CC^TCGAGG-3' and
      hydrolyzes it after second cytosine, producing 5'- sticky ends, which are compatible with
      sticky ends after DNA cleavage by restriction endonucleases XhoI (5'-C^TCGAG-3'), PspXI
      (5'-VC^TCGAGB-3') and SalI (5'-G^TCGAC-3'). Among all known rare-cutting site-specific
      endonucleases AbsI is the only enzyme which has no recognition sequences in standard
      substrates Lambda and T7 DNAs and Adenovirus type 2 DNA.
AU  - Chernukhin VA
AU  - Kashirina YG
AU  - Tomilova JE
AU  - Gonchar DA
AU  - Dedkov VS
AU  - Mikhnenkova NA
AU  - Degtyarev SK
PT  - Journal Article
TA  - Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol.
JT  - Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol.
SO  - Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol. 2006 2: 29-34.

PMID- 
VI  - 8
DP  - 2012
TI  - A new methyl-directed site-specific DNA endonuclease MteI cleaves nine nucleotides sequence 5-G(5mC)G(5mC)^NG(5mC)GC-3/3-CG(5mC)GN^(5mC)G(5mC)G-5.
PG  - 16-26
AB  - We have discovered and purified a new methyl-directed site-specific DNA endonuclease MteI from
      bacterial strain Microbacterium testaceum 17B. The enzyme recognizes methylated DNA sequence
      and doesnt cleave unmethylated DNA. MteI is a first methyl-directed site-specific DNA
      endonuclease recognizing a prolonged DNA sequence and its activity depends on a number of
      5-methycytosines and their positions in the recognition site. MteI cleaves DNA sequence
      5-G(5mC)G(5mC)NG(5mC)GC-3/3-CG(5mC)GN(5mC)G(5mC)G-5 as indicated by arrows and this
      nonanucleotide is a minimal recognition site. The enzyme activity is significantly higher if
      5-GC-3 dinucleotides in this site are replaced by 5-G(5mC)-3 dinucleotides and additional
      5-G(5mC)-3 dinucleotides are present at 5-ends in both DNA strands. Due to an ability to
      cleave only prolonged methylated DNA sequences MteI may find a practical application in the
      molecular biology and epigenetics studies.
AU  - Chernukhin VA
AU  - Kileva EV
AU  - Sokolova VA
AU  - Gonchar DA
AU  - Golikova LN
AU  - Dedkov VS
AU  - Mikhnenkova NA
AU  - Degtyarev SK
PT  - Journal Article
TA  - Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol.
JT  - Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol.
SO  - Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol. 2012 8: 16-26.

PMID- 20331425
VI  - 75
DP  - 2010
TI  - Substrate Specificity and Biochemical Properties of M3.BstF5I DNA Methyltransferase from the BstF5I Restriction-Modification System.
PG  - 63-71
AB  - Optimal conditions for DNA methylation by the M3.BstF5I enzyme from Bacillus
      stearothermophilus and kinetic parameters of lambda phage DNA
      modification and that of a number of oligonucleotide substrates are
      established. Comparison of M1.BstF5I and M3.BstF5I kinetic parameters
      revealed that with similar temperature optima and affinity for DNA,
      M3.BstF5I has nearly fourfold lower turnover number (0.24 min(-1)) and
      modifies the hemimethylated recognition site with lower efficiency
      under optimal conditions than the unmethylated one. In contrast to
      another three methylases of the BstF5I restriction-modification system,
      the M3. BstF5I enzyme is able to optionally modify the noncanonical
      5'-GGATC-3' DNA sequence with a rate more than one order of magnitude
      lower than the methylation rate of the canonical 5'-GGATG-3'
      recognition site.
AU  - Chernukhin VA
AU  - Kuznetsov VV
AU  - Gonchar DA
AU  - Kashirina YG
AU  - Netesova NA
AU  - Degtyarev SK
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2010 75: 63-71.

PMID- 
VI  - 0
DP  - 2006
TI  - A novel restriction endonuclease GlaI recognizes the methylated sequence 5'-G(5mC)^GC-3'.
PG  - 26-30
AB  - A novel restriction endonuclease GlaI from soil bacterium strain GL29 has been isolated and
      characterized. The enzyme recognizes the methylated DNA sequence 5'-G(m5C)^GC-3' and cleaves
      it as indicated by the arrow. Due to its ability to only cleave modified DNA, GlaI can find a
      practical application in genetic engineering experiments as well as in determination of
      eukaryotic DNA methylation status.
AU  - Chernukhin VA
AU  - Nayakshina TN
AU  - Abdurashitov MA
AU  - Tomilova YE
AU  - Mezentseva NV
AU  - Dedkov VS
AU  - Mikhnenkova NA
AU  - Gonchar DA
AU  - Degtyarev SK
PT  - Journal Article
TA  - Biotekhnologiya
JT  - Biotekhnologiya
SO  - Biotekhnologiya 2006 0: 26-30.

PMID- 
VI  - 7
DP  - 2011
TI  - A new site-specific methyl-directed DNA endonuclease PkrI recognizes and cuts methylated DNA sequence 5'-GCN^GC-3'/3'-CG^NCG-5' carrying at least three 5-methylcytosines.
PG  - 35-42
AB  - Type II restriction endonucleases are the most known and well studied enzymes among all
      site-specific DNA endonucleases.  As a rule restriction endonuclease and corresponding
      DNA-methyltransferase form restriction-modification system.  RE cleaves foreign DNA at a short
      recognition site, whereas a cognate MTase modifies the same sequence in a host DNA protecting
      it against digestion with RE.  Methyl-directed site-specific endonucleases hydrolyze only
      methylated DNA and their biochemical properties are similar to the restriction endonucleases
      ones.  Recently discovered at SibEnzyme site-specific 5-methylcytosine directed DNA
      endonucleases recognize and cleave different methylated DNA sequences, require only mg2+ ions
      as a cofactor and completely hydrolyze DNA.  Three MD endonucleases BlsI, BisI and GluI
      recognize different variants of methylated 5'-GCNGC-3' sequence and cleave DNA before or
      after N.  In the present work we describe a substrate specificity of new methyl-directed
      DNA-endonuclease PkrI, which recognizes methylated DNA sequence 5'-GCN^GC-3'/3'-CG(down
      arrow)NCG-5' carrying at lest three 5-methylcytosies and cleaves it as indicated by arrows.
AU  - Chernukhin VA
AU  - Nayakshina TN
AU  - Gonchar DA
AU  - Tomilova JE
AU  - Tarasova MV
AU  - Dedkov VS
AU  - Mikhenenkova NA
AU  - Degtyarev SK
PT  - Journal Article
TA  - Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol.
JT  - Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol.
SO  - Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol. 2011 7: 35-42.

PMID- 
VI  - 43
DP  - 2009
TI  - Purification and properties of recombinant DNA methyltransferase M2.BstSE of the BstSEI nickase-modification system.
PG  - 8-15
AB  - The operon for the Bacillus stearothermophilus SE-589 nickase-modification system (NM.BstSEI,
      recognition site 5'-GAGTC-3')
      includes two DNA methyltransferase (M.) genes, bstSEIM1 and bstSEIM2.
      The gene encoding M2.BstSEI was cloned in pJW and expressed in
      Escherichia coli cells. M2.BstSEI was purified by chromatography and
      displayed maximal activity at 55A degrees C and pH 7.5. The enzyme
      modified adenine in the nickase recognition site 5'-GAGTC-3' and was
      specific for 5'-GASTC-3' substrates. The kinetic parameters of the
      methylation reaction were determined. The catalytic constant was 2.2
      min(-1), and the Michaelis constant was 9.8 nM on T7 DNA and 5.8 mu M
      on SAM.
AU  - Chernukhin VA
AU  - Seggewiss J
AU  - Kashirina YG
AU  - Gonchar DA
AU  - Degtyarev SK
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2009 43: 8-15.

PMID- 
VI  - 3
DP  - 2007
TI  - Site-specific endonuclease BlsI recognizes DNA sequence 5'-G(5mC)N^GC-3' and cleaves it producing 3' sticky ends.
PG  - 28-33
AB  - A bacterial strain Bacillus simplex 23, a producer of a site-specific endonuclease BlsI has
      been discovered. BlsI recognizes the methylated DNA sequence 5'-G(5mC)NGC-3', like the
      earlier described site-specific endonuclease BisI (recognition site 5'-G(5mC)^NGC-3'), but
      differs in positions of DNA cleavage producing 3'-protruding ends. Due to its ability to
      cleave only methylated DNA, enzyme BlsI can find an application in gene engineering works as
      well as in determining the methylation status of eucaryotic DNA.
AU  - Chernukhin VA
AU  - Tomilova JE
AU  - Chmuzh EV
AU  - Sokolova OO
AU  - Dedkov VS
AU  - Degtyarev SK
PT  - Journal Article
TA  - Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol.
JT  - Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol.
SO  - Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol. 2007 3: 28-33.

PMID- Not carried by PubMed...
VI  - 3A
DP  - 1994
TI  - Site-selective targeting of duplex DNA with methyltransferase and biotinylated synthetic reagents.
PG  - 449-450
AB  - Site-selective interaction of some ligands with duplex DNA may provide
      the tools for developing gene-targeted drugs and for mapping of DNA and genomes.  In
      this study we have examined the interaction of methyltransferase and biotinylated both
      deoxyoligonucleotides and peptide nucleic acid (PNA) with duplex DNA.  It was shown
      that the target sequence can be EM detected via specific complex formation either with the
      enzyme per se or streptavidin as an EM marker.  These approaches allow the study  of the
      site-selective interaction of these ligands with DNA and introduce novel types of sequences
      for mapping of DNA and genomes.
AU  - Cherny DI
AU  - Kurakin AV
PT  - Journal Article
TA  - Electron Microsc.
JT  - Electron Microsc.
SO  - Electron Microsc. 1994 3A: 449-450.

PMID- 30275280
VI  - 200
DP  - 2018
TI  - Methylation-Induced Hypermutation in Natural Populations of Bacteria.
PG  - e00371-18
AB  - Methylation of DNA at the C5 position of cytosine occurs in diverse organisms. This
      modification can increase the rate of C->T transitions at the methylated
      position. In E. coli and related enteric bacteria, the inner C residues of the
      sequence CCWGG (W=A or T) are methylated by the Dcm enzyme. These sites are
      hotspots of mutation during rapid growth in the laboratory, but not in non
      dividing cells, in which repair by the Vsr protein is effective. It has been
      suggested that hypermutation at these sites is a laboratory artifact and does not
      occur in nature. Many other methyltransferases, with a variety of specificities,
      can be found in bacteria, usually associated with restriction enzymes and
      confined to a subset of the population. Their methylation targets are also
      possible sites of hypermutation. Here I show, using whole genome sequence data
      for thousands of isolates, that there is indeed considerable hypermutation at Dcm
      sites in natural populations: their transition rate is approximately eight times
      the average. I also demonstrate hypermutability of targets of restriction
      associated methyltransferases in several distantly related bacteria, ranging from
      a factor of 12 increase in transition rate to a factor of 58. In addition, I
      demonstrate how patterns of hypermutability inferred from massive sequence data
      can be used to determine previously unknown methylation patterns and
      methyltransferase specificities.IMPORTANCE A common type of DNA modification,
      addition of a methyl group to cytosine (C) at carbon atom C5, can greatly
      increase the rate of mutation of the C to a T. In mammals, methylation of CG
      sequences increases the rate of CG->TG mutations. It is unknown whether cytosine
      C5 methylation increases mutation rate in bacteria under natural conditions. I
      show that sites methylated by the Dcm enzyme exhibit an eight fold increase in
      mutation rate in natural bacterial populations. I also show that modifications at
      other sites in various bacteria also increase the mutation rate, in some cases by
      a factor of forty or more. Finally, I demonstrate how this phenomenon can be used
      to infer sequence specificities of methylation enzymes.
AU  - Cherry JL
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2018 200: e00371-18.

PMID- 22180815
VI  - 5
DP  - 2011
TI  - Complete genome sequence of Tolumonas auensis type strain (TA 4).
PG  - 112-120
AB  - Tolumonas auensis Fischer-Romero et al. 1996 is currently the only validly named  species of
      the genus Tolumonas in the family Aeromonadaceae. The strain is of
      interest because of its ability to produce toluene from phenylalanine and other
      phenyl precursors, as well as phenol from tyrosine. This is of interest because
      toluene is normally considered to be a tracer of anthropogenic pollution in
      lakes, but T. auensis represents a biogenic source of toluene. Other than
      Aeromonas hydrophila subsp. hydrophila, T. auensis strain TA 4(T) is the only
      other member in the family Aeromonadaceae with a completely sequenced type-strain
      genome. The 3,471,292 bp chromosome with a total of 3,288 protein-coding and 116
      RNA genes was sequenced as part of the DOE Joint Genome Institute Program JBEI
      2008.
AU  - Chertkov O et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 5: 112-120.

PMID- 21304712
VI  - 2
DP  - 2010
TI  - Complete genome sequence of Aminobacterium colombiense type strain (ALA-1).
PG  - 280-289
AB  - Aminobacterium colombiense Baena et al. 1999 is the type species of the genus Aminobacterium.
      This genus is of large interest because of its isolated
      phylogenetic location in the family Synergistaceae, its strictly anaerobic
      lifestyle, and its ability to grow by fermentation of a limited range of amino
      acids but not carbohydrates. Here we describe the features of this organism,
      together with the complete genome sequence and annotation. This is the second
      completed genome sequence of a member of the family Synergistaceae and the first
      genome sequence of a member of the genus Aminobacterium. The 1,980,592 bp long
      genome with its 1,914 protein-coding and 56 RNA genes is part of the Genomic
      Encyclopedia of Bacteria and Archaea project.
AU  - Chertkov O et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 2: 280-289.

PMID- 21475583
VI  - 4
DP  - 2011
TI  - Complete genome sequence of Thermomonospora curvata type strain (B9).
PG  - 13-22
AB  - Thermomonospora curvata Henssen 1957 is the type species of the genus Thermomonospora. This
      genus is of interest because members of this clade are
      sources of new antibiotics, enzymes, and products with pharmacological activity.
      In addition, members of this genus participate in the active degradation of
      cellulose. This is the first complete genome sequence of a member of the family
      Thermomonosporaceae. Here we describe the features of this organism, together
      with the complete genome sequence and annotation. The 5,639,016 bp long genome
      with its 4,985 protein-coding and 76 RNA genes is a part of the Genomic
      Encyclopedia of Bacteria and Archaea project.
AU  - Chertkov O et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 4: 13-22.

PMID- 21705585
VI  - 5
DP  - 2011
TI  - Complete genome sequence of Hirschia baltica type strain (IFAM 1418T).
PG  - 287-297
AB  - The family Hyphomonadaceae within the Alphaproteobacteria is largely comprised of bacte-ria
      isolated from marine environments with striking morphologies and an unusual mode of cell
      growth. Here, we report the complete genome sequence Hirschia baltica, which is only the
      second a member of the Hyphomonadaceae with a published genome sequence. H. bal-tica is of
      special interest because it has a dimorphic life cycle and is a stalked, budding bacte-rium.
      The 3,455,622 bp long chromosome and 84,492 bp plasmid with a total of 3,222 pro-tein-coding
      and 44 RNA genes were sequenced as part of the DOE Joint Genome Institute Program CSP 2008.
AU  - Chertkov O et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 5: 287-297.

PMID- 21914878
VI  - 193
DP  - 2011
TI  - Genome Sequence of the Probiotic Strain Bifidobacterium animalis subsp. lactis CNCM I-2494.
PG  - 5560-5561
AB  - Bifidobacterium animalis subsp. lactis CNCM I-2494 is part of a commercialized fermented dairy
      product with documented health benefits
      revealed by multiple randomized placebo-controlled clinical trials. Here
      we report the complete genome sequence of this strain, which has a
      circular genome of 1,943,113 bp with 1,660 open reading frames and 4
      ribosomal operons.
AU  - Chervaux C
AU  - Grimaldi C
AU  - Bolotin A
AU  - Quinquis B
AU  - Legrain-Raspaud S
AU  - van Hylckama VJE
AU  - Denariaz G
AU  - Smokvina T
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5560-5561.

PMID- 
VI  - 16
DP  - 2005
TI  - The LAGLIDADG homing endonuclease family.
PG  - 33-47
AB  - The LAGLIDADG protein family includes the first identified and biochemically characterized
      intron-encoded proteins, as described in this volume by Dujon.  It has been variously termed
      the "DOD", "Dodecapeptide', "dodecamer", and "decapeptide" endonuclease family, based on the
      conservation of a ten-residue sequence motif.  The LAGLIDADG endonucleases are the most
      diverse of the homing endonuclease families.  Their host range includes the genomes of plant
      and algal chloroplasts, fungal and protozoan mitochondria, bacteria and Archaea.  One reason
      for the wide phylogenetic distribution of LAGLIDADG genes appears to be their remarkable
      ability to invade unrelated types of intervening sequences, including group I introns,
      archaeal introns and inteins.  Descendents of LAGLIDADG homing endonucleases also include the
      yeast HO mating type switch endonuclease, which is encoded by an independent reading frame
      rather than within an intron, but does carry remnants of an inactive intein domain, and
      maturases that assist in RNA splicing.
AU  - Chevalier B
AU  - Monnat RJ Jr
AU  - Stoddard BL
PT  - Journal Article
TA  - Nucleic Acids Mol. Biol.
JT  - Nucleic Acids Mol. Biol.
SO  - Nucleic Acids Mol. Biol. 2005 16: 33-47.

PMID- 15518550
VI  - 43
DP  - 2004
TI  - Metal-dependent DNA cleavage mechanism of the I-CreI LAGLIDADG homing endonuclease.
PG  - 14015-14026
AB  - The LAGLIDADG homing endonucleases include free-standing homodimers, pseudosymmetric monomers,
      and related enzyme domains embedded within
      inteins. DNA-bound structures of homodimeric I-CreI and monomeric
      I-SceI indicate that three catalytic divalent metal ions are
      distributed across a pair of overlapping active sites, with one shared
      metal participating in both strand cleavage reactions. These structures
      differ in the precise position and binding interactions of the metals.
      We have studied the metal dependence for the I-CreI homodimer using
      site-directed mutagenesis of active site residues and assays of binding
      affinity and cleavage activity. We have also reassessed the binding of
      a nonactivating metal ion (calcium) in the wild-type enzyme-substrate
      complex, and determined the DNA-bound structure of two inactive enzyme
      mutants. The conclusion of these studies is that the catalytic
      mechanism of symmetric LAGLIDADG homing, endonucleases, and probably
      many of their monomeric cousins, involves a canonical two-metal
      mechanism in each of two active sites, which are chemically and
      structurally tethered to one another by a shared metal ion. Failure to
      occupy the shared metal site, as observed in the presence of calcium or
      when the metal-binding side chain from the LAGLIDADG motif (Asp 20) is
      mutated to asparagines, prevents cleavage by the enzyme.
AU  - Chevalier B
AU  - Sussman D
AU  - Otis C
AU  - Noel AJ
AU  - Turmel M
AU  - Lemieux C
AU  - Stephens K
AU  - Monnat RJ
AU  - Stoddard BL
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2004 43: 14015-14026.

PMID- 12758074
VI  - 329
DP  - 2003
TI  - Flexible DNA target site recognition by divergent homing endonuclease isoschizomers I-CreI and I-MsoI.
PG  - 253-269
AB  - Homing endonucleases are highly specific catalysts of DNA strand breaks that induce the
      transposition of mobile intervening sequences containing
      the endonuclease open reading frame. These enzymes recognize long DNA
      targets while tolerating individual sequence polymorphisms within those
      sites. Sequences of the homing endonucleases themselves diversify to a
      great extent after founding intron invasion events, generating highly
      divergent enzymes that recognize similar target sequences. Here, we
      visualize the mechanism of flexible DNA recognition and the pattern of
      structural divergence displayed by two homing endonuclease isoschizomers.
      We determined structures of I-CreI bound to two DNA target sites that
      differ at eight of 22 base-pairs, and the structure of an isoschizomer,
      I-MsoI, bound to a nearly identical DNA target site. This study
      illustrates several principles governing promiscuous base-pair recognition
      by DNA-binding proteins, and demonstrates that the isoschizomers display
      strikingly different protein/DNA contacts. The structures allow us to
      determine the information content at individual positions in the binding
      site as a function of the distribution of direct and water-mediated
      contacts to nucleotide bases, and provide an evolutionary snapshot of
      endonucleases at an early stage of divergence in their target specificity.
AU  - Chevalier B
AU  - Turmel M
AU  - Lemieux C
AU  - Monnat RJ
AU  - Stoddard BL
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2003 329: 253-269.

PMID- 12419232
VI  - 10
DP  - 2002
TI  - Design, activity, and structure of a highly specific artificial endonuclease.
PG  - 895-905
AB  - We have generated an artificial highly specific endonuclease by fusing domains of homing
      endonucleases I-Dmol and I-Crel and creating a new 1400
      Angstrom(2) protein interface between these domains. Protein engineering
      was accomplished by combining computational redesign and an in vivo
      protein-folding screen. The resulting enzyme, E-Drel (Engineered
      I-Dmol/I-Crel), binds a long chimeric DNA target site with nanomolar
      affinity, cleaving it precisely at a rate equivalent to its natural
      parents. The structure of an E-Drel/DNA complex demonstrates the accuracy
      of the protein interface redesign algorithm and reveals how catalytic
      function is maintained during the creation of the new endonuclease. These
      results indicate that it may be possible to generate novel highly specific
      DNA binding proteins from homing endonucleases.
AU  - Chevalier BS
AU  - Kortemme T
AU  - Chadsey MS
AU  - Baker D
AU  - Monnat RJ
AU  - Stoddard BL
PT  - Journal Article
TA  - Mol. Cell
JT  - Mol. Cell
SO  - Mol. Cell 2002 10: 895-905.

PMID- 11276249
VI  - 8
DP  - 2001
TI  - The homing endonuclease I-CreI uses three metals, one of which is shared between the two active sites.
PG  - 312-316
AB  - Homing endonucleases, like restriction enzymes, cleave double-stranded DNA at specific target
      sites. The cleavage mechanism(s) utilized by
      LAGLIDADG endonucleases have been difficult to elucidate; their active
      sites are divergent, and only one low resolution cocrystal structure
      has been determined, Here we report two high resolution structures of
      the dimeric I-CreI homing endonuclease bound to DNA: a substrate
      complex with calcium and a product complex with magnesium, The bound
      metals in both complexes are verified by manganese anomalous difference
      maps, The active sites are positioned close together to facilitate
      cleavage across the DNA minor groove; each contains one metal ion
      bound between a conserved aspartate (Asp 20) and a single scissile
      phosphate. A third metal ion bridges the two active sites. This
      divalent cation is bound between aspartate residues from the active
      site of each subunit and is in simultaneous contact with the scissile
      phosphates of both DNA strands. A metal-bound water molecule acts as
      the nucleophile and is part of an extensive network of ordered water
      molecules that are positioned by enzyme side chains; These structures
      illustrate a unique variant of a two-metal endonuclease mechanism is
      employed by the highly divergent LAGLIDADG enzyme family.
AU  - Chevalier BS
AU  - Monnat RJ Jr
AU  - Stoddard BL
PT  - Journal Article
TA  - Nat. Struct. Biol.
JT  - Nat. Struct. Biol.
SO  - Nat. Struct. Biol. 2001 8: 312-316.

PMID- 11557808
VI  - 29
DP  - 2001
TI  - Homing endonucleases: structural and functional insight into the catalysts of intron/intein mobility.
PG  - 3757-3774
AB  - Homing endonucleases confer mobility to their host intervening sequence, either an intron or
      intein, by catalyzing a highly specific double-strand break in a cognate allele lacking the
      intervening sequence. These proteins are characterized by their ability to bind long DNA
      target sites (14-40 bp) and their tolerance of minor sequence changes in these sites. A wealth
      of biochemical and structural data has been generated for these enzymes over the past few
      years. Herein we review our current understanding of homing endonucleases, including their
      diversity and evolution, DNA-binding and catalytic mechanisms, and attempts to engineer them
      to bind novel DNA substrates.
AU  - Chevalier BS
AU  - Stoddard BL
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2001 29: 3757-3774.

PMID- Not carried by PubMed...
VI  - 19
DP  - 1995
TI  - Isolation and purification of EcoRI restriction endonuclease.
PG  - 132-135
AB  - EcoRI restriction endonuclease was isolated from Escherichia coli RY13 and K121100.  The
      purification process involved treatment with ammonium sulfate, polyethyleneimine and
      phosphocellulose chromatography.  By this method a highly purified EcoRI restriction
      endonuclease can be prepared.  The enzyme recognizes unique sites on DNA, with the minimal
      recognition site being a hexanucleotide sequence characterized by 2-fold symmetry.  Thus, the
      EcoRI enzyme is one of the simplest sequence-specific DNA enzymes known and is well suited to
      a study of DNA sequence recognition by proteins.
AU  - Chi M-G
PT  - Journal Article
TA  - Junshi Yixue Kexueyuan Yuankan
JT  - Junshi Yixue Kexueyuan Yuankan
SO  - Junshi Yixue Kexueyuan Yuankan 1995 19: 132-135.

PMID- 24723720
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Six Listeria monocytogenes Strains Isolated from Dairy  Products from a Processing Plant in Southern Italy.
PG  - e00282-14
AB  - Here we announce the draft genome sequences of 6 Listeria monocytogenes strains from ricotta
      cheese produced in a dairy processing plant located in southern Italy and potentially involved
      in a multistate outbreak of listeriosis in the United States.
AU  - Chiara M
AU  - D'Erchia AM
AU  - Manzari C
AU  - Minotto A
AU  - Montagna C
AU  - Addante N
AU  - Santagada G
AU  - Latorre L
AU  - Pesole G
AU  - Horner DS
AU  - Parisi A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00282-14.

PMID- 29192085
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Vibrio splendidus DSM 19640.
PG  - e01368-17
AB  - Here, we present the draft genome sequence of Vibrio splendidus type strain DSM 19640. V.
      splendidus is an abundant species among coastal vibrioplankton. The
      assembly resulted in a 5,729,362-bp draft genome with 5,032 protein-coding
      sequences, 6 rRNAs, and 117 tRNAs.
AU  - Chibani CM
AU  - Poehlein A
AU  - Roth O
AU  - Liesegang H
AU  - Wendling CC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01368-17.

PMID- 29292131
VI  - 268
DP  - 2017
TI  - Complete genome sequence of Tsukamurella sp. MH1, a wide-chain length alkane-degrading actinomycete.
PG  - 1-5
AB  - Tsukamurella sp. strain MH1, capable to use a wide range of n-alkanes as the only
      carbon source, was isolated from petroleum-contaminated soil (Pitesti, Romania)
      and its complete genome was sequenced. The 4,922,396bp genome contains only one
      circular chromosome with a G+C content of 71.12%, much higher than the type
      strains of this genus (68.4%). Based on the 16S rRNA genes sequence similarity,
      strain MH1 was taxonomically identified as Tsukamurella carboxydivorans. Genome
      analyses revealed that strain MH1 is harboring only one gene encoding for the
      alkB-like hydroxylase, arranged in a complete alkane monooxygenase operon. This
      is the first complete genome of the specie T. carboxydivorans, which will provide
      insights into the potential of Tsukamurella sp. MH1 and related strains for
      bioremediation of petroleum hydrocarbons-contaminated sites and into the
      environmental role of these bacteria.
AU  - Chiciudean I
AU  - Nie Y
AU  - Tanase AM
AU  - Stoica I
AU  - Wu XL
PT  - Journal Article
TA  - J. Biotechnol.
JT  - J. Biotechnol.
SO  - J. Biotechnol. 2017 268: 1-5.

PMID- 
VI  - 
DP  - 1991
TI  - Cloning and genetic analysis of restriction and modification systems from Neisseria gonorrhoeae.
PG  - 1-126
AB  - Endonucleases with the specificities of S.NgoI and S.NgoIII were isolated from Neisseria
      gonorrhoeae MS11; but the remaining endonucleases with the specificities of S.NgoII, S.NgoIV,
      S.NgoV, S.NgoVI, S.NgoVIII, and S.NgoIX were not produced at detectable levels in MS11. The
      genes encoding the RM NgoMI (recognition sequence GCCGGC), the RM NgoMII (TCACC), and the RM
      NgoMIII (CCGCGG) from gonococcus MS11 were cloned in E. coli. The gene encoding the M.NgoBIII
      (GGNNCC) from gonococcus MUG116 was also cloned. The cloned endonuclease R.NgoMI was purified
      by column chromatography and the cutting site determined to be G/CCGGC. The base methylated in
      the sequence GCCGGC by the M.NgoMI in vivo was determined to be the the first C in the
      sequence GCCGGC. Plasmids encoding M.NgoMI, M.NgoMIII, and M.NgoBIII were restricted when
      these plasmids were used to transform MM294 (mcr+), due to the action of the mcr gene products
      on the methylated DNA. Plasmids encoding for M.NgoMII were not restricted because the mcr gene
      products do not recognize S.NgoMII specificity. The DNA sequence of the NgoMI
      restriction/methylation system was determined and two open reading frames were identified. The
      molecular weight of the purified endonuclease was determined to be 33,000 Dal, and was in good
      agreement with the size predicted from the DNA sequence (31,759 Dal). M.NgoMI contains the
      four conserved domains found in cytosine-specific DNA methylases, however the size and spacing
      between these domains are significantly different from that in the conserved domains in other
      cytosine-specific DNA methylases. Two restriction/modification mutants MUG700 and MUG701 were
      derived from MS11. Mutant MUG700 was RM NgoII negative, while mutant MUG701 was RM NgoMI
      negative, as determined by appropriate endonuclease digestion and Southern hybridizations. The
      RM NgoII and RM NgoMI systems seem involved in regulating the biosynthesis of LOS in N.
      gonorrhoeae. The RM NgoMI system also seems involved in regulating the stability of colony
      morphology. Finally, endonuclease R.NgoII was able to mediate host restriction in N.
      gonorrhoeae, while endonuclease R.NgoMI was not, even though both endonucleases were not
      produced at detectable levels in the strain MS11. [ The enzyme called NgoMI in this abstract
      has been renamed NgoMIV, Jan/1998. ] [ The enzyme called NgoMII in this abstract has been
      renamed NgoMVIII, Jan/1998. ]
AU  - Chien HR
PT  - Journal Article
TA  - Ph.D. Thesis, University of Maryland, USA
JT  - Ph.D. Thesis, University of Maryland, USA
SO  - Ph.D. Thesis, University of Maryland, USA 1991 : 1-126.

PMID- 15448271
VI  - 305
DP  - 2004
TI  - The genomic sequence of the accidental pathogen Legionella pneumophila.
PG  - 1966-1968
AB  - We present the genomic sequence of Legionella pneumophila, the bacterial agent of
      Legionnaires' disease, a potentially fatal pneumonia acquired from aerosolized contaminated
      fresh water. The genome includes a 45-kilobase pair element that can exist in chromosomal and
      episomal forms, selective expansions of important gene families, genes for unexpected
      metabolic pathways, and previously unknown candidate virulence determinants. We highlight the
      genes that may account for Legionella's ability to survive in protozoa, mammalian
      macrophages, and inhospitable environmental niches and that may define new therapeutic
      targets.
AU  - Chien M et al
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2004 305: 1966-1968.

PMID- Not carried by PubMed...
VI  - 88
DP  - 1988
TI  - Cloning and characterization of a restriction and modification system from Neisseria gonorrhoeae strain MS11.
PG  - 213
AB  - A type II restriction and modification (R/M) system from Neisseria gonorrhoeae MS11 was cloned
      and expressed in Escherichia coli HB101.  R/M clones were constructed by the partial digestion
      of DNA from MS11 with MboI and HpaII and its insertion into the BamHI and ClaI site of the
      cloning vector pHSS7.  The R/M clone, pCBB49, was identified by its resistance to cleavage
      with NaeI, a restriction enzyme that has 1 site in the cloning vector.  The R/M genes were
      encoded by a 2.5 kb fragment in plasmid pCBB49.1, a deletion derivative of pCBB49.  The
      restriction (NgoMI) and modification (M.NgoMI) enzymes were purified from HB101 (pCBB49.1) by
      column chromatography.  The recognition sequence for NgoMI was GCCGGC.  When plasmid pCBB49.1
      was introduced into HB101 (pFT180), the single NgoMI site of pFT180 was now resistant to
      cleavage by NaeI.  When pCBB49.1 was used to transform E. coli strains ER1563 (mcrB+) and
      ER1562 (mcrB), a two log difference in transformation frequencies was obtained due to the
      action of the mcrB gene product on the methylated DNA.
      [ The enzyme called NgoMI in this abstract has been renamed NgoMIV, Jan/1998. ]
AU  - Chien RH
AU  - Stein DC
AU  - Seifert HS
AU  - Floyd K
AU  - So M
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1988 88: 213.

PMID- 12393207
VI  - 215
DP  - 2002
TI  - BanAI a new isoschizomer of the type II restriction endonuclease HaeIII discovered in a Bacillus anthracis isolate from Amazon Basin.
PG  - 97-101
AB  - Bacillus anthracis was isolated and identified from a bacterial collection of samples from the
      Amazon river bank.  Type II restriction endonuclease activity was detected in this prokaryote,
      the enzyme was purified, the molecular mass of the native protein estimated by gel filtration,
      and optima pH, temperature and salt requirements were determined.  Quality control assays
      showed complete absence of 'non-specific nucleases'.  Restriction cleavage analysis and DNA
      sequencing of restriction fragments allowed unequivocal demonstration of 5'-GG/CC-3' as the
      recognition sequence.  This enzyme was named BanAI and is therefore an isoschizomer of the
      prototype restriction endonuclease HaeIII.  This is the first report of a type II restriction
      endonuclease identified, purified from a natural isolate of B. anthracis.
AU  - Chies JM
AU  - de O-Dias AC
AU  - Maia HMM
AU  - Astolfi-Filho S
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2002 215: 97-101.

PMID- 
VI  - 37
DP  - 2006
TI  - Isolation and characterization of Bliai, an isoschizomer of CLAI from Bacillus licheniformis.
PG  - 551-555
AB  - The restriction endonuclease BliAI, an isoschizomer of ClaI, which recognizes the sequence
      5'-AT down arrow CGAT-3', was purified from a
      natural isolate identified as Bacillus licheniformis. The restriction
      endonuclease was isolated from cell extracts using single-step
      purification by phosphocellulose column chromatography. The restriction
      endonuclease is active at 37 degrees C and over a wide range of pH and
      salt concentration. The molecular weight of the purified restriction
      enzyme is consistent with a value of 39 kDa.
AU  - Chies JM
AU  - Dias ACDO
AU  - Maia HMM
AU  - Braga LPDS
AU  - Astolfi-Filho S
PT  - Journal Article
TA  - Braz. J. Microbiol.
JT  - Braz. J. Microbiol.
SO  - Braz. J. Microbiol. 2006 37: 551-555.

PMID- 
VI  - 243
DP  - 2012
TI  - Expression and purification of Ltr-II: A homing endonuclease for gene targeting.
PG  - 475
AB  - Homing endonucleases are microbial enzymes that selectively form double-stranded breaks in DNA
      and drive gene conversion events via homologous recombination.  One type of homing
      endonuclease conaining the LADLIDADG catalytic motif recognizes long DNA sequences wqith high
      specificity and has successfully been used for targeting genes involved in both medicine
      (genetic diseases) and biotechnology.  LtrII is an intron-encoded LAGLIDADG homing
      endonuclease from the fungus Leptogaphium truncatum.  The results of the overexpression and
      purificaiton of LtrII will be shown.  In addition, initial kinetic results of LtrII with its
      target DNA sequence will be presented.
AU  - Chik J
AU  - Robins L
AU  - Stoddard B
PT  - Journal Article
TA  - ACS Abstracts
JT  - ACS Abstracts
SO  - ACS Abstracts 2012 243: 475.

PMID- 2434942
VI  - 23
DP  - 1987
TI  - Purification of restriction endonucleases using aqueous two-phase systems.
PG  - 84-92
AB  - A simple procedure was developed for testing and purification of restriction
      endonucleases MspI, PstI, BamHI, PvuI, PvuII that includes biomass destruction,
      fractionation of cell-free extracts in the aqueous two-phase (polyethylene
      glycol-dextran) system and chromatography of phosphocellulose.  Optimal
      conditions for the fractionation of MspI, PstI, BamHI, PvuII, EcoRI, EcoRII,
      BspRI, AluI were chosen.  For separation of PvuI and PvuII gel filtration
      through Biogel A-0.5 m was additionally introduced.
AU  - Chikaev NA
AU  - Baklanov MM
AU  - Ryazankin IA
AU  - Nechaev YS
PT  - Journal Article
TA  - Prikl. Biokhim. Mikrobiol.
JT  - Prikl. Biokhim. Mikrobiol.
SO  - Prikl. Biokhim. Mikrobiol. 1987 23: 84-92.

PMID- 7496527
VI  - 141
DP  - 1995
TI  - Distribution of the ardA family of antirestriction genes on conjugative plasmids.
PG  - 2157-2164
AB  - The ardA gene of I1 plasmid ColIb-P9 was previously shown to alleviate DNA restriction by type
      I enzymes and to promote conjugative transmission of the unmodified plasmid to a restricting
      host. To clarify the ecological role of ardA, its distribution was determined on plasmids from
      23 incompatibility groups using hybridization to the coding sequence as an assay. Hybridizing
      sequences, shown by nucleotide sequencing to have at least 60% identity with ardA, were
      detected on plasmids belonging to the I complex (IncB, I1 and K), the F complex (IncFV) and
      the IncN group. The ardA homologues were found to specify an antirestriction phenotype which
      was enhanced by genetic depression of the plasmid transfer system. ardA loci map in plasmid
      leading regions but show no consistent association with a particular type of
      origin-of-transfer or a leading region gene of the ssb (single-stranded DNA-binding protein),
      psiB (plasmid SOS inhibition) and hok (host killing) families. It may be significant that
      ardA+ plasmids are authentic enterobacterial plasmids and that type I restriction systems are
      associated historically with members of the Enterobacteriaceae.
AU  - Chilley PM
AU  - Wilkins BM
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 1995 141: 2157-2164.

PMID- 15475385
VI  - 32
DP  - 2004
TI  - KpnBI is the prototype of a new family (IE) of bacterial type I restriction-modification system.
PG  - e138
AB  - KpnBI is a restriction-modification (R-M) system recognized in the GM236 strain of Klebsiella
      pneumoniae. Here, the KpnBI modification genes were
      cloned into a plasmid using a modification expression screening method.
      The modification genes that consist of both hsdM (2631 bp) and hsdS (1344
      bp) genes were identified on an 8.2 kb EcoRI chromosomal fragment. These
      two genes overlap by one base and share the same promoter located upstream
      of the hsdM gene. Using recently developed plasmid R-M tests and a
      computer program RM Search, the DNA recognition sequence for the KpnBI
      enzymes was identified as a new 8 nt sequence containing one degenerate
      base with a 6 nt spacer, CAAANNNNNNRTCA. From Dam methylation and HindIII
      sensitivity tests, the methylation loci were predicted to be the
      italicized third adenine in the 5' specific region and the adenine
      opposite the italicized thymine in the 3' specific region. Combined with
      previous sequence data for hsdR, we concluded that the KpnBI system is a
      typical type I R-M system. The deduced amino acid sequences of the three
      subunits of the KpnBI system show only limited homologies (25 to 33%
      identity) at best, to the four previously categorized type I families (IA,
      IB, IC, and ID). Furthermore, their identity scores to other
      uncharacterized putative genome type I sequences were 53% at maximum.
      Therefore, we propose that KpnBI is the prototype of a new 'type IE'
      family.
AU  - Chin V
AU  - Valinluck V
AU  - Magaki S
AU  - Ryu J
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2004 32: e138.

PMID- 
VI  - 101
DP  - 2001
TI  - The KpnBI restriction-modification (R-M) system of Klebsiella pneumoniae strain GM236 is a prototype of a new family of type I R-M  systems.
PG  - 404-405
AB  - From genetic evidence, the KpnBI R-M system in Klebsiella pneumoniae strain GM236 was assumed
      to be either a type I or type III R-M system.
      The restriction subunit (hsdR) was previously cloned and sequenced.
      However, it did not show any close homology to the preexisting R-M
      systems. In this project the modification genes of the KpnBI system
      were cloned into a plasmid, pMECA, using a modification expression
      screening method. The modification genes were identified on an 8.2 kb
      EcoRI chromosomal fragment. The complete 8.2 kb fragment was sequenced
      and two open reading frames (ORF) were identified. The first ORF is
      2,631 bp in length and identified as the hsdM gene based on sequence
      homologies. Similarily, the second ORF, which was 1,344 bp in length
      and overlapped 1 base with the hsdM gene, was identified as the hsdS
      gene. The presence of both hsdM and hsdS genes is a unique
      characteristic of type I R-M systems. Therefore, the KpnBI system was
      concluded to be a type I system. Phage and plasmid modification tests
      as well as complementation tests with the HsdR subunit indicate that
      the modification genes are expressed in both Klebsiella and E. coli
      strains. Since the deduced amino acid sequences of all three subunits
      of the KpnBI did not show sufficient (more than 40%) homologies with
      any of the four categorized type I families (IA, IB, IC, and ID) we
      concluded that KpnBI represents a new type I family. This family was
      subsequently labeled type IE. The DNA recognition sequence of KpnBI
      system has also been elucidated using a plasmid transformation method
      currently developed in our laboratory. A further analysis of the inter-
      and intra-family protein sequence comparisons of the subunits of type I
      enzymes has allowed us to develop a criteria for grouping all the type
      I systems into more than 20 new type I families in addition to the 4
      existing families.
AU  - Chin VR
AU  - Valinluck V
AU  - Ryu J
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 2001 101: 404-405.

PMID- 
VI  - 75
DP  - 2000
TI  - Evolution of sequence recognition by restriction-modification enzymes: Selective pressure for specificity decrease.
PG  - 381
AB  - Several type II restriction-modification (RM) gene complexes kill host bacterial cells that
      have lost them, through attack on their chromosomal recognition sites.  Two RM gene complexes
      recognizing the same sequence cannot simultaneously enjoy such stabilization through
      post-segregational host killing, because one will defend chromosomal sites from attack by the
      other.  We analyzed intra-host competition between two RM gene complexes when the recognition
      sequence of one is included in that of the other.  When the EcoRII gene complex, recognizing
      5'CCWGG (W = A, T) is lost from the host, the SsoII gene complex, which recognizes 5'CCNGG
      (N = A, T, G, C) will prevent host death by protecting CCWGG sites on the chromosome.
      However, when the SsoII (CCNGG) gene complex is lost, the EcoRII (CCWGG) gene complex will be
      unable to prevent host death through attack by SsoII on 5'CCSGG (S = C, G) sites.  These
      predictions were verified in our experiments in which we analyzed plasmid maintenance, cell
      growth, cell shape and chromosomal DNA.  Our results demonstrate the presence of selective
      pressure for decrease in the specificity of recognition sequence of RM systems in the absence
      of invading DNA.
AU  - Chinen A
AU  - Naito Y
AU  - Handa N
AU  - Kobayashi I
PT  - Journal Article
TA  - Genes Genet. Syst.
JT  - Genes Genet. Syst.
SO  - Genes Genet. Syst. 2000 75: 381.

PMID- 11070049
VI  - 17
DP  - 2000
TI  - Evolution of sequence recognition by restriction-modification enzymes: selective pressure for specificity decrease.
PG  - 1610-1619
AB  - Several type II restriction-modification (RM) gene complexes kill host bacterial cells that
      have lost them, through attack on the chromosomal recognition sites of these cells. Two RM
      gene complexes recognizing the same sequence cannot simultaneously enjoy such stabilization
      through post-segregational host killing, because one will defend chromosomal sites from attack
      by the other. In the present work, we analyzed intrahost competition between two RM gene
      complexes when the recognition sequence of one was included in that of the other. When the
      EcoRII gene complex, recognizing 5'-CCWGG (W = A, T), is lost from the host, the SsoII gene
      complex, which recognizes 5'-CCNGG (N = A, T, G, C), will prevent host death by protecting
      CCWGG sites on the chromosome. However, when the SsoII (CCNGG) gene complex is lost, the
      EcoRII (CCWGG) gene complex will be unable to prevent host death through attack by SsoII on
      5'-CCSGG (S = C, G) sites. These predictions were verified in our experiments, in which we
      analyzed plasmid maintenance, cell growth, cell shape, and chromosomal DNA. Our results
      demonstrate the presence of selective pressure for decrease in the specificity of recognition
      sequence of RM systems in the absence of invading DNA.
AU  - Chinen A
AU  - Naito Y
AU  - Handa N
AU  - Kobayashi I
PT  - Journal Article
TA  - Mol. Biol. Evol.
JT  - Mol. Biol. Evol.
SO  - Mol. Biol. Evol. 2000 17: 1610-1619.

PMID- 
VI  - 11
DP  - 2000
TI  - Association of putative restriction modification genes with large genome polymorphisms suggested from comparison of Pyrococcus horikoshii and Pyrococcus abyssi genome sequences.
PG  - 339-340
AB  - Restriction-modification (RM) gene complexes encode two enzymatic functions, restriction and
      modification.  A restriction enzyme will recognize a specific sequence in DNA and cut the DNA
      unless it is methylated by a cognate modification enzyme.  RM systems will defend bacterial
      cells by attacking incoming foreign DNA.  It is widely held that bacteria have evolved RM
      systems and maintain them in order to protect their genome from invasion by foreign DNA such
      as bacteriophages and plasmids. We earlier reported that carrying a type II RM gene complex
      can increase the stability of a plasmid because cells that have lost the plasmid die.  From
      this and other observations, it was proposed that the relative frequency of RM gene complexes
      has increased through this post-segregational killing, in competitive exclusion, as well as
      through direct attack on invading DNA.
AU  - Chinen A
AU  - Uchiyama I
AU  - Kobayashi I
PT  - Journal Article
TA  - Genome Informatics
JT  - Genome Informatics
SO  - Genome Informatics 2000 11: 339-340.

PMID- 11163968
VI  - 259
DP  - 2000
TI  - Comparison between Pyrococcus horikoshii and Pyrococcus abyssi genome sequences reveals linkage of restriction-modification genes with large genome polymorphisms.
PG  - 109-121
AB  - Recent work suggests that restriction-modification gene complexes are mobile genetic elements
      that insert themselves into the genome and cause various genome rearrangements. In the present
      work, the complete genome sequences of Pyrococcus horikoshii and Pyrococcus abyssi, two
      species in a genus of hyperthermophilic archaeon (archaebacterium), were compared to detect
      large genome polymorphisms linked with restriction-modification gene homologs. Sequence
      alignments, GC content analysis, and codon usage analysis demonstrated the diversity of these
      homologs and revealed a possible case of relatively recent acquisition (horizontal transfer).
      In two cases out of the six large polymorphisms identified, there was insertion of a DNA
      segment with a modification gene homolog, accompanied by target deletion (simple
      substitution).  In two other cases, homologous DNA segments carrying a modification gene
      homolog were present at different locations in the two genomes (transposition). In both cases,
      substitution (insertion/deletion) in one of the two loci was accompanied by inversion of the
      adjacent chromosomal segment. In the fifth case, substitution by a DNA segment carrying type I
      restriction, modification, and specificity gene homologs was likewise accompanied by adjacent
      inversion. In the last case, two homologous DNA segments, were found at different loci in the
      two genomes (transposition), but only one of them had insertion of a modification homolog and
      an unknown ORF.  The possible relationship of these polymorphisms to attack by restriction
      enzymes on the chromosome will be discussed.
AU  - Chinen A
AU  - Uchiyama I
AU  - Kobayashi I
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 2000 259: 109-121.

PMID- 6891357
VI  - 18
DP  - 1982
TI  - [Genetic characteristics of a new phage resistance trait in Streptomyces coelicolor A3(2)].
PG  - 1945-1952
AB  - Phage resistance was investigated in the system of Streptomyces coelicolor A3(2) and phi C31
      actinophage. Resistance of A3(2) strain to phi C31 was
      shown to involve a novel mechanism responsible for the arrest of phage
      intracellular growth in the whole cell population. The phage resistance
      character designated Pgl+ (for 'phage growth limiting') is determined by a
      gene located on the A3(2) chromosome. The gene (pgl) controls phage
      'modification' which results in an inability of phage to lyse lysogenize
      Pgl+ host. Instability of the Pgl+ character was revealed. Pgl+ strains
      segregate Pgl variants at a high frequency, the majority of Pgl strains
      reverting to the initial Pgl+ phenotype with the same high frequency.
      Reversible Pgl+ in equilibrium Pgl transitions are a common feature of
      A3(2) cell population.
AU  - Chinenova TA
AU  - Mkrtumian NM
AU  - Lomovskaia ND
PT  - Journal Article
TA  - Genetika
JT  - Genetika
SO  - Genetika 1982 18: 1945-1952.

PMID- 20022807
VI  - 300
DP  - 2010
TI  - Identification of prophage gene z2389 in Escherichia coli EDL933 encoding a DNA cytosine methyltransferase for full protection of Notl sites.
PG  - 296-303
AB  - Pulsed-field gel electrophoresis (PFGE) analysis revealed that the genomes of some pathogenic
      Escherichia coli O157:H7 strains, including
      EDL933, were resistant to Noti digestion. An amino acid sequence
      comparison suggested that the z2389 gene carried on prophage CP-933R in
      strain EDL933 is likely to encode a C-5-cytosine methyltransferase. The
      z2389-equivalent gene was found in the Notl-resistant strains tested,
      but it was not detected in the Notl-susceptible strains. PFGE analysis
      of the wild-type EDL933 strain and of a z2389 null mutant revealed that
      z2389 was associated with full genome protection against Notl digestion
      and partial protection against Eagl digestion. In vitro methylation
      experiments with purified recombinant protein demonstrated that Z2389
      is capable of methylating Notl and Eagl sites. Sequencing of
      bisulfite-treated DNA indicated that the methylation occurred at the
      first cytosine residue of the Notl recognition sequence, whereas Eagl
      sites remained unmethylated or were methylated at the first cytosine
      residue. Thus, z2389 encodes a DNA cytosine methyltransferase that
      confers full protection to Notl sites.
AU  - Chiou CS
AU  - Li HY
AU  - Tung SK
AU  - Chen CY
AU  - Teng CH
AU  - Shu JC
AU  - Tseng JT
AU  - Hsu CY
AU  - Chen CC
PT  - Journal Article
TA  - Int. J. Med. Microbiol.
JT  - Int. J. Med. Microbiol.
SO  - Int. J. Med. Microbiol. 2010 300: 296-303.

PMID- 26769925
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Lactobacillus farciminis NBRC 111452, Isolated from Koso, a Japanese Sugar-Vegetable Fermented Beverage.
PG  - e01514-15
AB  - Here, we report the draft genome sequence of the Lactobacillus farciminis strain  NBRC 111452,
      isolated from koso, a Japanese sugar-vegetable fermented beverage.
      This genome information is of potential use in studies of Lactobacillus
      farciminis as a probiotic.
AU  - Chiou TY
AU  - Oshima K
AU  - Suda W
AU  - Hattori M
AU  - Takahashi T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01514-15.

PMID- 29650588
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Janthinobacterium sp. Strain ROICE36, a Putative Secondary Metabolite-Synthesizing Bacterium Isolated from Antarctic Snow.
PG  - e01553-17
AB  - The draft genome assembly of Janthinobacterium sp. strain ROICE36 has 207 contigs, with a
      total genome size of 5,977,006 bp and a G+C content of 62%.
      Preliminary genome analysis identified 5,363 protein-coding genes and a total of
      7 secondary metabolic gene clusters (encoding bacteriocins, nonribosomal
      peptide-synthetase [NRPS], terpene, hserlactone, and other ketide synthases).
AU  - Chiriac C
AU  - Baricz A
AU  - Coman C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01553-17.

PMID- Not included in PubMed...
VI  - 37
DP  - 1978
TI  - Purification of restriction endonucleases including the isolation of a novel activity using affinity chromatography.
PG  - 1415
AB  - We wish to report a new method for purifying EndoRs based on affinity
      fractionation.  To date purification of restriction endonucleases have been
      modifications of few early methods which are often tedious and time consuming.
      We have investigated the use of affinity matrices such as covalently bound
      pyran and Cibacron Blue F3Ga sepharose.  Pyran is a divinyl ether copolymer of
      maleic anhydride which in carboxylic acid solution hydrolyzes to the negatively
      charged polycarboxylic acid that simulates the negatively charged
      phosphodiester bond.  Cibacron Blue F3Ga is a derivative of a sulfonated
      polyaromatic dye and is widely used as a nonspecific affinity matrix.  Both
      matrices have high capacity, rapid development time and yield enzyme free from
      interfering activities.  Using these matrices we have purified several reported
      EndoRs such as BamHI, HinfI, PstI and XbaI.  We have also isolated a new Endo3
      from a clinical isolate H. influenzae Georgetown, which contains two major
      activities: HindGUI which we have temporarily assigned to be an isoschizomer of
      HhaI and HinGUII with the following fragmentation properties: PhiX174, 10;
      SV40, 12-14; lambda >50; and Adeno 2 >50.
AU  - Chirikjian JG
AU  - George A
AU  - Smith LA
PT  - Journal Article
TA  - Fed. Proc.
JT  - Fed. Proc.
SO  - Fed. Proc. 1978 37: 1415.

PMID- 6765645
VI  - 1
DP  - 1981
TI  - Sequence-specific endonucleases: General properties and specific characteristics.
PG  - 73-99
AB  - I. Introduction II. Sequence-specific endonucleases as reagents in molecular biology. III.
      Matrix bound sequence-specific endonucleases IV. General methods for determining
      sequence-specific endonuclease activity. V. Strategies for elucidating the recognition of DNA
      by sequence-specific endonucleases VI. Catalytic diversities among isoschizomers VII. Effect
      of hydrophobic reagents on sequence recognition and catalysis of sequence-specific
      endonucleases VIII. Conclusions
AU  - Chirikjian JG
AU  - George J
PT  - Journal Article
TA  - Gene Amplif. Anal.
JT  - Gene Amplif. Anal.
SO  - Gene Amplif. Anal. 1981 1: 73-99.

PMID- 17416667
VI  - 189
DP  - 2007
TI  - Genome of Methylobacillus flagellatus, Molecular Basis for Obligate Methylotrophy, and Polyphyletic Origin of Methylotrophy.
PG  - 4020-4027
AB  - Along with methane, methanol and methylated amines represent important biogenic atmospheric
      constituents; thus, not only methanotrophs but also
      nonmethanotrophic methylotrophs play a significant role in global carbon
      cycling. The complete genome of a model obligate methanol and methylamine
      utilizer, Methylobacillus flagellatus (strain KT) was sequenced. The
      genome is represented by a single circular chromosome of approximately 3
      Mbp, potentially encoding a total of 2,766 proteins. Based on genome
      analysis as well as the results from previous genetic and mutational
      analyses, methylotrophy is enabled by methanol and methylamine
      dehydrogenases and their specific electron transport chain components, the
      tetrahydromethanopterin-linked formaldehyde oxidation pathway and the
      assimilatory and dissimilatory ribulose monophosphate cycles, and by a
      formate dehydrogenase. Some of the methylotrophy genes are present in more
      than one (identical or nonidentical) copy. The obligate dependence on
      single-carbon compounds appears to be due to the incomplete tricarboxylic
      acid cycle, as no genes potentially encoding alpha-ketoglutarate, malate,
      or succinate dehydrogenases are identifiable. The genome of M. flagellatus
      was compared in terms of methylotrophy functions to the previously
      sequenced genomes of three methylotrophs, Methylobacterium extorquens (an
      alphaproteobacterium, 7 Mbp), Methylibium petroleiphilum (a
      betaproteobacterium, 4 Mbp), and Methylococcus capsulatus (a
      gammaproteobacterium, 3.3 Mbp). Strikingly, metabolically and/or
      phylogenetically, the methylotrophy functions in M. flagellatus were more
      similar to those in M. capsulatus and M. extorquens than to the ones in
      the more closely related M. petroleiphilum species, providing the first
      genomic evidence for the polyphyletic origin of methylotrophy in
      Betaproteobacteria.
AU  - Chistoserdova L
AU  - Lapidus A
AU  - Han C
AU  - Goodwin L
AU  - Saunders L
AU  - Brettin T
AU  - Tapia R
AU  - Gilna P
AU  - Lucas S
AU  - Richardson PM
AU  - Lidstrom ME
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2007 189: 4020-4027.

PMID- 15781495
VI  - 33
DP  - 2005
TI  - The genome sequence of Salmonella enterica serovar Choleraesuis, a highly invasive and resistant zoonotic pathogen.
PG  - 1690-1698
AB  - Salmonella enterica serovar Choleraesuis (S.Choleraesuis), a highly invasive serovar among
      non-typhoidal Salmonella, usually causes sepsis or
      extra-intestinal focal infections in humans. S.Choleraesuis infections
      have now become particularly difficult to treat because of the emergence
      of resistance to multiple antimicrobial agents. The 4.7 Mb genome sequence
      of a multidrug-resistant S.Choleraesuis strain SC-B67 was determined.
      Genome wide comparison of three sequenced Salmonella genomes revealed that
      more deletion events occurred in S.Choleraesuis SC-B67 and S.Typhi CT18
      relative to S.Typhimurium LT2. S.Choleraesuis has 151 pseudogenes, which,
      among the three Salmonella genomes, include the highest percentage of
      pseudogenes arising from the genes involved in bacterial chemotaxis
      signal-transduction pathways. Mutations in these genes may increase smooth
      swimming of the bacteria, potentially allowing more effective interactions
      with and invasion of host cells to occur. A key regulatory gene of
      TetR/AcrR family, acrR, was inactivated through the introduction of an
      internal stop codon resulting in overexpression of AcrAB that appears to
      be associated with ciprofloxacin resistance. While lateral gene transfer
      providing basic functions to allow niche expansion in the host and
      environment is maintained during the evolution of different serovars of
      Salmonella, genes providing little overall selective benefit may be lost
      rapidly. Our findings suggest that the formation of pseudogenes may
      provide a simple evolutionary pathway that complements gene acquisition to
      enhance virulence and antimicrobial resistance in S.Choleraesuis.
AU  - Chiu CH
AU  - Tang P
AU  - Chu C
AU  - Hu S
AU  - Bao Q
AU  - Yu J
AU  - Chou YY
AU  - Wang HS
AU  - Lee YS
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2005 33: 1690-1698.

PMID- 23661478
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Lactobacillus pobuzihii E100301T.
PG  - e00185-13
AB  - Lactobacillus pobuzihii E100301(T) is a novel Lactobacillus species previously isolated from
      pobuzihi (fermented cummingcordia) in Taiwan. Phylogenetically,
      this strain is closest to Lactobacillus acidipiscis, but its phenotypic
      characteristics can be clearly distinguished from those of L. acidipiscis. We
      present the draft genome sequence of strain L. pobuzihii E100301(T).
AU  - Chiu CM
AU  - Chang CH
AU  - Pan SF
AU  - Wu HC
AU  - Li SW
AU  - Chang CH
AU  - Lee YS
AU  - Chiang CM
AU  - Chen YS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00185-13.

PMID- 29167259
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequencing of Lactobacillus salivarius Strains BCRC 14759 and BCRC 12574.
PG  - e01336-17
AB  - Lactobacillus salivarius BCRC 14759 has been identified as a high-exopolysaccharide-producing
      strain with potential as a probiotic or
      fermented dairy product. Here, we report the genome sequences of L. salivarius
      BCRC 14759 and the comparable strain BCRC 12574, isolated from human saliva. The
      PacBio RSII sequencing platform was used to obtain high-quality assemblies for
      characterization of this probiotic candidate.
AU  - Chiu SH
AU  - Chen CC
AU  - Wang LT
AU  - Huang L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01336-17.

PMID- Not included in PubMed...
VI  - 52
DP  - 1988
TI  - Site specific deoxyribonuclease produced by a marine bacterium, Flavobacterium I 16-04.
PG  - 2107-2109
AB  - Since the discovery of HindII, more than 120 kinds of site-specific
      endodeoxyribonucleases (restriction enzymes) have been isolated from some 600
      species of bacteria and reported.  All of them have been obtained from
      terrestrial bacteria except FokI isolated from a marine bacterium,
      Flavobacterium okeanokoites.  Furthermore, the marine bacteria have not been as
      extensively studied as the terrestrial bacteria.  Under these circumstances, we
      have been attempting to survey site-specific endonucleases in the marine
      bacteria of the laboratory collection of the Ocean Research Institute,
      University of Tokyo.
AU  - Chiura H
AU  - Noro Y
AU  - Kanayama S
AU  - Ueda Y
AU  - Simidu U
AU  - Takagi J
PT  - Journal Article
TA  - Agric. Biol. Chem.
JT  - Agric. Biol. Chem.
SO  - Agric. Biol. Chem. 1988 52: 2107-2109.

PMID- 1579507
VI  - 20
DP  - 1992
TI  - Purification and characterization of AspMDI, an isoschizomer of Sau3AI, from a marine bacterium, Alcaligenes sp MD1.
PG  - 1996
AB  - A new type II restriction endonuclease, Asp MD1, was isolated from a pigmented marine
      bacterium Alcaligenes species MD1 which was collected from the open sea around Taiwan Island.
AU  - Chiura HX
AU  - Kamiyama T
AU  - Hirano H
AU  - Futagami M
AU  - Watahiki M
AU  - Kobayashi K
AU  - Simidu U
AU  - Takagi J
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 1996.

PMID- 23611633
VI  - 17
DP  - 2013
TI  - Genotyping of virulence-associated genes from biopsy specimens show high genetic diversity of Helicobacter pylori strains infecting patients in Venezuela.
PG  - e750-6
AB  - Background: Helicobacter pylori is a major cause of chronic gastritis and an established risk
      factor for gastric adenocarcinoma. This bacterium also exhibits an extraordinarily high
      genetic diversity.
      Methods: The genetic diversity of H. pylori strains from Venezuelan patients with chronic
      gastritis was evaluated by PCR-typing of vacA, cagA, iceA, and babA2 virulence-associated
      genes using DNA extracted directly from biopsies. The nucleotide sequence and prevalence of
      size variants of iceA1, iceA2, and babA2 PCR products were introduced in this analysis.
      Results: The frequency of vacA s1 was associated (p < 0.01) with moderate/severe grades of
      atrophic
      gastritis. The cagA, iceA1, iceA2, and babA2 genotypes were found in 70.6%, 66.4%, 33.6%, and
      92.3% of strains, respectively. The frequency of iceA2 and its subtype iceA2_D were higher (p
      < 0.015) in cases with moderate/severe granulocytic inflammation. The most prevalent combined
      genotypes were vacA
      s1m1/cagA/iceA1/babA2 (26.3%), vacA s2m2/iceA1/babA2 (19.5%), and vacA s1m1/cagA/iceA2/babA2
      (18.8%). Sequence analysis of iceA1, iceA2, and babA2 PCR-amplified fragments allowed us to
      define allelic variants and to increase the number of genotypes detected (from 19 to 62). A
      phylogenetic tree made with iceA1 sequences showed that the H. pylori strains analyzed here
      were grouped with those of Western origin.
      Conclusions: Our results show that patients from the western region of Venezuela have an
      elevated prevalence of infection with H. pylori strains carrying known virulence genotypes
      with high genetic diversity. This highlights the importance of identifying gene variants for
      an early detection of virulent genotypes.
AU  - Chiurillo MA
AU  - Moran Y
AU  - Canas M
AU  - Valderrama E
AU  - Granda N
AU  - Sayegh M
AU  - Ramirez JL
PT  - Journal Article
TA  - Int. J. Infect. Dis.
JT  - Int. J. Infect. Dis.
SO  - Int. J. Infect. Dis. 2013 17: e750-6.

PMID- 18845759
VI  - 322
DP  - 2008
TI  - Environmental genomics reveals a single-species ecosystem deep within Earth.
PG  - 275-278
AB  - DNA from low-biodiversity fracture water collected at 2.8-kilometer depth in a South African
      gold mine was sequenced and assembled into a single,
      complete genome. This bacterium, Candidatus Desulforudis audaxviator,
      composes >99.9% of the microorganisms inhabiting the fluid phase of this
      particular fracture. Its genome indicates a motile, sporulating,
      sulfate-reducing, chemoautotrophic thermophile that can fix its own
      nitrogen and carbon by using machinery shared with archaea. Candidatus
      Desulforudis audaxviator is capable of an independent life-style well
      suited to long-term isolation from the photosphere deep within Earth's
      crust and offers an example of a natural ecosystem that appears to have
      its biological component entirely encoded within a single genome.
AU  - Chivian D et al
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2008 322: 275-278.

PMID- 19995931
VI  - 54
DP  - 2010
TI  - Recombination between ccrC genes in a type V (5C2 and 5) staphylococcal cassette chromosome mec (SCCmec) of Staphylococcus aureus ST398 leads to conversion from methicillin resistance to methicillin susceptibility in vivo.
PG  - 783-791
AB  - Various types of the staphylococcal cassette chromosome mec (SCCmec) are known to confer
      methicillin resistance on the human pathogen Staphylococcus aureus. Such cassettes are not
      always stably maintained.  The present studies were aimed at identifying the mechanism
      underlying the in vivo conversion of methicillin-resistant S. aureus (MRSA) to
      methicillin-susceptible S. aureus (MSSA) derivatives as encountered in two patients suffering
      from pneumonia and an umbilicus infection, respectively. All MRSA and MSSA isolates identified
      belong to multilocus sequence type (MLST) 398, have spa type t034, and are Panton-Valentine
      leukocidin positive. Sequencing of 27,616 nucleotides from the chromosomal SCCmec insertion
      site in orfX to the hsdR gene for a restriction enzyme revealed a type V (5C2&5) SCCmec.
      Sequence comparisons show that parts of the cassette are highly similar to sequences within
      SCCmec elements from coagulase-negative staphylococci, indicating a possible common origin.
      The cassette investigated contains ccrC-carrying units on either side of its class C2b mec
      gene complex. In vivo loss of the mec gene complex was caused by recombination between the
      recombinase genes ccrC1 allele 8 and ccrC1 allele 10. In vitro, the SCCmec was very stable,
      and low-frequency MRSA-to-MSSA conversion was only observed when MRSA isolates were cultivated
      at 41 degrees C for prolonged periods of time. In this case also, loss of the mec complex was
      due to ccrC gene recombination. Interestingly, the MRSA and MSSA isolates studied displayed no
      detectable differences in competitive growth and virulence, suggesting that the presence of
      the intact type V (5C2&5) SCCmec has no negative bearing on staphylococcal fitness under the
      conditions used.
AU  - Chlebowicz MA
AU  - Nganou K
AU  - Kozytska S
AU  - Arends JP
AU  - Engelmann S
AU  - Grundmann H
AU  - Ohlsen K
AU  - van Dijl JM
AU  - Buist G
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2010 54: 783-791.

PMID- 8467964
VI  - 7
DP  - 1993
TI  - Determination of restriction enzyme digestion completeness under low target concentration.
PG  - A1304
AB  - A method for the determination of restriction enzyme digestion efficiency under low target
      concentration is described. Target DNA was serially diluted from 10 to the eleventh power
      molecules to 1 molecule. The DNA was digested with one unit of enzyme for one hour at 37C. The
      digestion was stopped by heating the reaction at 65C for 10 minutes. PCR was performed on the
      restriction digests to assay for completeness. Three primers were used: 2 forward primers and
      1 reverse primer. When both forward primers are used in conjunction with the reverse primer in
      PCR, products of 523 and 170 base pairs are observed. The restriction site of interest lies
      between the two forward primers. If the enzyme is active at low target concentration, only the
      170 base pair fragment is detected. Results have indicated that this technique is sensitive to
      detect completeness of a restriction enzyme digestion at low target DNA concentration. This
      protocol can be applicable for testing any restriction enzyme.
AU  - Chmelo R
AU  - Foltz L
AU  - Eadie JS
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1993 7: A1304.

PMID- 15667656
VI  - 5
DP  - 2005
TI  - A homology model of restriction endonuclease SfiI in complex with DNA.
PG  - 2
AB  - BACKGROUND: Restriction enzymes (REases) are commercial reagents commonly used in recombinant
      DNA technologies. They are attractive models for studying protein-DNA interactions and
      valuable targets for protein engineering. They are, however, extremely divergent: the amino
      acid sequence of a typical REase usually shows no detectable similarities to any other
      proteins, with rare exceptions of other REases that recognize identical or very similar
      sequences. From structural analyses and bioinformatics studies it has been learned that some
      REases belong to at least four unrelated and structurally distinct superfamilies of nucleases,
      PD-DxK, PLD, HNH, and GIY-YIG. Hence, they are extremely hard targets for structure prediction
      and homology-based inference of sequence-function relationships and the great majority of
      REases remain structurally and evolutionarily unclassified. RESULTS: SfiI is a REase which
      recognizes the interrupted palindromic sequence 5'GGCCNNNN--NGGCC3' and generates 3 nt long
      3' overhangs upon cleavage. SfiI is an archetypal Type IIF enzyme, which functions as a
      tetramer and cleaves two copies of the recognition site in a concerted manner. Its sequence
      shows no similarity to other proteins and nothing is known about the localization of its
      active site or residues important for oligomerization. Using the threading approach for
      protein fold-recognition, we identified a remote relationship between SfiI and BglI, a dimeric
      Type IIP restriction enzyme from the PD-DxK superfamily of nucleases, which recognizes the
      5'GCCNNNN--NGGC3' sequence and whose structure in complex with the substrate DNA is
      available. We constructed a homology model of SfiI in complex with its target sequence and
      used it to predict residues important for dimerization, tetramerization, DNA binding and
      catalysis. CONCLUSIONS: The bioinformatics analysis suggest that SfiI, a Type IIF enzyme, is
      more closely related to BglI, an "orthodox" Type IIP restriction enzyme, than to any other
      REase, including other Type IIF REases with known structures, such as NgoMIV. NgoMIV and BglI
      belong to two different, very remotely related branches of the PD-DxK superfamily: the
      alpha-class (EcoRI-like), and the beta-class (EcoRV-like), respectively. Thus, our analysis
      provides evidence that the ability to tetramerize and cut the two DNA sequences in a concerted
      manner was developed independently at least two times in the evolution of the PD-DxK
      superfamily of REases. The model of SfiI will also serve as a convenient platform for further
      experimental analyses.
AU  - Chmiel AA
AU  - Bujnicki JM
AU  - Skowronek KJ
PT  - Journal Article
TA  - BMC Struct. Biol.
JT  - BMC Struct. Biol.
SO  - BMC Struct. Biol. 2005 5: 2.

PMID- 15849215
VI  - 18
DP  - 2005
TI  - A theoretical model of restriction endonuclease NlaIV in complex with DNA, predicted by fold recognition and validated by site-directed  mutagenesis and circular dichroism spectroscopy.
PG  - 181-189
AB  - Restriction enzymes (REases) are commercial reagents commonly used in DNA manipulations and
      mapping. They are regarded as very attractive
      models for studying protein-DNA interactions and valuable targets for
      protein engineering. Their amino acid sequences usually show no
      similarities to other proteins, with rare exceptions of other REases
      that recognize identical or very similar sequences. Hence, they are
      extremely hard targets for structure prediction and modeling. NlaIV is
      a Type II REase, which recognizes the interrupted palindromic sequence
      GGNNCC (where N indicates any base) and cleaves it in the middle,
      leaving blunt ends. NlaIV shows no sequence similarity to other
      proteins and virtually nothing is known about its
      sequence-structure-function relationships. Using protein fold
      recognition, we identified a remote relationship between NlaIV and
      EcoRV, an extensively studied REase, which recognizes the GATATC
      sequence and whose crystal structure has been determined. Using the
      'FRankenstein's monster' approach we constructed a comparative model of
      NlaIV based on the EcoRV template and used it to predict the catalytic
      and DNA-binding residues. The model was validated by site-directed
      mutagenesis and analysis of the activity of the mutants in vivo and in
      vitro as well as structural characterization of the wild-type enzyme
      and two mutants by circular dichroism spectroscopy. The structural
      model of the NlaIV-DNA complex suggests regions of the protein sequence
      that may interact with the 'non-specific' bases of the target and thus
      it provides insight into the evolution of sequence specificity in
      restriction enzymes and may help engineer REases with novel
      specificities. Before this analysis was carried out, neither the
      three-dimensional fold of NlaIV, its evolutionary relationships or its
      catalytic or DNA-binding residues were known. Hence our analysis may be
      regarded as a paradigm for studies aiming at reducing 'white spaces' on
      the evolutionary landscape of sequence-function relationships by
      combining bioinformatics with simple experimental assays.
AU  - Chmiel AA
AU  - Radlinska M
AU  - Pawlak SD
AU  - Krowarsch D
AU  - Bujnicki JM
AU  - Skowronek KJ
PT  - Journal Article
TA  - Protein Eng. Des. Sel.
JT  - Protein Eng. Des. Sel.
SO  - Protein Eng. Des. Sel. 2005 18: 181-189.

PMID- 
VI  - 3
DP  - 2005
TI  - A Novel Restriction endonuclease BisI from Bacillus subtilis T30, recognizes a methylated DNA sequence 5'- G(m5C)^NGC-3'.
PG  - 22-26
AB  - Bacillus subtilis strain T30, producing a novel restriction endonuclease Bis I, has been
      isolated and characterized. The enzyme recognizes methylated DNA sequence 5'- G(m5C)^NGC-3'
      and cleaves it as shown by the arrow. Due to cleavage of only modified DNAs Bis I may find a
      practical application in genetic engineering experiments as well as in determination of
      eukaryotic DNA methylation status.
AU  - Chmuzh EV
AU  - Kashirina JG
AU  - Tomilova JE
AU  - Mezentseva NV
AU  - Dedkov VS
AU  - Gonchar DA
AU  - Abdurashitov MA
AU  - Degtyarev SK
PT  - Journal Article
TA  - Biotekhnologiya
JT  - Biotekhnologiya
SO  - Biotekhnologiya 2005 3: 22-26.

PMID- 17380889
VI  - 41
DP  - 2007
TI  - The Fsp4HI restriction-modification system: Gene cloning, comparison of protein structures, and biochemical properties of recombinant DNA methyltransferase M.Fsp4HI.
PG  - 43-50
AB  - Genes coding for the Flavobacterium sp. 4H restriction-modification (RM) system, which
      recognizes the sequence 5'-GCNGC-3', were cloned in Escherichia coli ER2267 and sequenced.
      The Fsp4HI RM system includes two genes: one for DNA methyltransferase (M.) and the other for
      restriction endonuclease (R.), immediately following the former in the same direction. The
      genes partly overlap. According to the deduced amino acid sequences, M.Fsp4HI belongs to C5
      DNA methyltransferases, whereas R.Fsp4HI is only slightly similar to some restriction enzymes
      recognizing similar sequences. M.Fsp4HI was purified by column chromatography. The optimal
      conditions for the enzyme are 30 degrees C and pH 7.5. M.Fsp4HI modifies the first cytosine in
      5'-GCNGC-3'.
AU  - Chmuzh EV
AU  - Kashirina YG
AU  - Tomilova YE
AU  - Chernukhin VA
AU  - Okhapkina SS
AU  - Gonchar DA
AU  - Dedkov VS
AU  - Abdurashitov MA
AU  - Degtyarev SK
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2007 41: 43-50.

PMID- 24158551
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Novel Peptoniphilus sp. Strain ChDC B134, Isolated from a Human Periapical Abscess Lesion.
PG  - e00822-13
AB  - The genus Peptoniphilus comprises butyrate-producing, nonsaccharolytic species that use
      peptone and amino acids as major energy sources. The novel Peptoniphilus
      sp. strain ChDC B134 (=KCOM 1628) was isolated from a human periapical abscess
      lesion. Here, we report the draft genome sequence of the strain.
AU  - Cho E
AU  - Park SN
AU  - Kim HK
AU  - Kim DS
AU  - Jung J
AU  - Baek JH
AU  - Lim YK
AU  - Jo E
AU  - Choi MH
AU  - Chang YH
AU  - Shin Y
AU  - Paek J
AU  - Shin JH
AU  - Kim J
AU  - Choi SH
AU  - Park HS
AU  - Kim H
AU  - Kook JK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00822-13.

PMID- 
VI  - 31
DP  - 2001
TI  - Characterization of type II restriction endonucleases (Hpy51-I) from Helicobacter pylori strain 51.
PG  - 207-215
AB  - This study describes the purification and characterization of a type II restriction
      endonuclease of Helicobacter pylori in order to understand the DNA restriction and
      modification of H. pylori.  H. pylori cell extract was subjected to polyethyleneimine
      treatment, salt precipitation, heparine-sepharose column chromatography, and fast protein
      liquid chromatography using Resource Q column and Mono Q column to purify the type II
      restriction endonuclease.  Hpy51-I was characterized to recognize the sequence
      5'-GT(G/C)AC-3', yielding 5-base 5' protruding ends.  The restriction sequence was
      identical to that of Tsp45I.  The enzyme exhibited its maximal activity in the presence of
      10~20 mM NaCl, but was inhibited completely in the presence of more than 80 mM NaCl.  The
      enzyme showed its maximal activity in the presence of 1~10 mM MCl2.  The optimal pH and
      temperature for enzyme activity was pH 9.0 and 37oC, respectively.  MnCl2 could not substitute
      for MgCl2 in reaction mixture.  Addition of beta-mercaptoethanol and bovine serum albumin in
      the reaction mixture led to loss of enzyme activity of Hpy51-I.  The whole cell extract of H.
      pylori strain 51 was confirmed to carry the enzyme activity for methylation of
      Hpy51-I-recognised sequence.  Hpy51-I digested genomic DNAs of enteric bacteria to less than I
      kb while it could not cut the genomic DNAs of H. pylori isolates.  In this study, the type II
      restriction enzyme (Hpy51-I) of H. pylori was identified and its biochemical properties
      characterized, demonstrating that Hpy51-I might be one of the barriers for preventing the
      introduction of foreign DNAs into H. pylori.
AU  - Cho M-J
AU  - Park J-U
AU  - Jeon BS
AU  - Pack J-W
AU  - Byun EY
AU  - Lee S-K
AU  - Park Y-H
AU  - Song J-H
AU  - Lee W-K
AU  - Baik S-C
AU  - Choi Y-J
AU  - Jung S-A
AU  - Choe M-Y
AU  - Choi S-H
AU  - Ko G-H
AU  - Youn H-S
AU  - Rhee K-H
PT  - Journal Article
TA  - J. Bact. Virol.
JT  - J. Bact. Virol.
SO  - J. Bact. Virol. 2001 31: 207-215.

PMID- 17483455
VI  - 104
DP  - 2007
TI  - The Orientia tsutsugamushi genome reveals massive proliferation of conjugative type IV secretion system and host-cell interaction genes.
PG  - 7981-7986
AB  - Scrub typhus is caused by the obligate intracellular rickettsia Orientia tsutsugamushi
      (previously called Rickettsia tsutsugamushi). The bacterium
      is maternally inherited in trombicuid mites and transmitted to humans by
      feeding larvae. We report here the 2,127,051-bp genome of the Boryong
      strain, which represents the most highly repeated bacterial genome
      sequenced to date. The repeat density of the scrub typhus pathogen is
      200-fold higher than that of its close relative Rickettsia prowazekii, the
      agent of epidemic typhus. A total of 359 tra genes for components of
      conjugative type IV secretion systems were identified at 79 sites in the
      genome. Associated with these are >200 genes for signaling and host-cell
      interaction proteins, such as histidine kinases, ankyrin-repeat proteins,
      and tetratrico peptide-repeat proteins. Additionally, the O. tsutsugamushi
      genome contains >400 transposases, 60 phage integrases, and 70 reverse
      transcriptases. Deletions and rearrangements have yielded unique gene
      combinations as well as frequent pseudogenization in the tra clusters. A
      comparative analysis of the tra clusters within the genome and across
      strains indicates sequence homogenization by gene conversion, whereas
      complexity, diversity, and pseudogenization are acquired by duplications,
      deletions, and transposon integrations into the amplified segments. The
      results suggest intragenomic duplications or multiple integrations of a
      massively proliferating conjugative transfer system. Diversifying
      selection on host-cell interaction genes along with repeated population
      bottlenecks may drive rare genome variants to fixation, thereby
      short-circuiting selection for low complexity in bacterial genomes.
AU  - Cho NH
AU  - Kim HR
AU  - Lee JH
AU  - Kim SY
AU  - Kim J
AU  - Cha S
AU  - Kim SY
AU  - Darby AC
AU  - Fuxelius HH
AU  - Yin J
AU  - Kim JH
AU  - Kim J
AU  - Lee SJ
AU  - Koh YS
AU  - Jang WJ
AU  - Park KH
AU  - Andersson SG
AU  - Choi MS
AU  - Kim IS
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2007 104: 7981-7986.

PMID- Not included in PubMed...
VI  - 1
DP  - 1990
TI  - DNA sequence-dependent cleavage sites of restriction endonuclease HphI.
PG  - 81-86
AB  - A class IIS restriction endonuclease HphI has been known to make a staggered
      cut always at the 8th base pair downstream of its recognition sequence
      5'GGTGA3', producing one-base 3' protruding ends, regardless of the DNA
      sequence around the cleavage site.  Since the cleavage sites of HphI are
      separate from its recognition sites, the effects of mutations around a cleavage
      site have been studied using a phage SP6 promoter-containing plasmid pSP64
      which has an HphI cleavage site near the transcription initiation site.  The
      exact cutting site of the lower strand was determined to be after the 8th
      nucleotide downstream of the recognition site, indicating a staggered cut at
      the 9th base pair downstream.  In addition, the same cutting site in the
      mutants carrying a few base pair deletions around the cleavage site is shown to
      be shifted.  These variations were not affected by any changes in reaction
      conditions.  These results suggest that the HphI cleavage site shifts depending
      on the DNA sequence, which might affect the DNA helical structure.
AU  - Cho S-H
AU  - Kang C
PT  - Journal Article
TA  - Mol. Cells
JT  - Mol. Cells
SO  - Mol. Cells 1990 1: 81-86.

PMID- 29439035
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Burkholderia sp. Strain WAC0059, a Bacterium Isolated from the Medicinal Fungus Antrodia cinnamomea.
PG  - e00027-18
AB  - Burkholderia sp. strain WAC0059 was isolated from a fruiting body of the medicinal fungus
      Antrodia cinnamomea collected in Taiwan. Here, we report the
      draft genome sequence of this bacterium to facilitate the investigation of its
      biology.
AU  - Cho ST
AU  - Chen CL
AU  - Yang Y
AU  - Wang TF
AU  - Kuo CH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00027-18.

PMID- 29674541
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Agrobacterium tumefaciens 1D1609.
PG  - e00253-18
AB  - Agrobacterium tumefaciens 1D1609 is a highly virulent strain isolated from a crown gall tumor
      of alfalfa (Medicago sativa L.). Compared to other
      well-characterized A. tumefaciens strains, such as C58 and Ach5, 1D1609 has a
      distinctive host range. Here, we report its complete genome sequence to
      facilitate future studies.
AU  - Cho ST
AU  - Haryono M
AU  - Chang HH
AU  - Santos MNM
AU  - Lai EM
AU  - Kuo CH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00253-18.

PMID- 21742893
VI  - 193
DP  - 2011
TI  - Genome Sequence of Lactobacillus salivarius GJ-24, a probiotic strain isolated from healthy adult intestine.
PG  - 5021-5022
AB  - The draft genome sequence of Lactobacillus salivarius GJ-24 isolated from the feces of healthy
      adults was determined. The properties including milk
      fermentation activity and bacteriocin production suggest its potential
      uses as a probiotic lactic acid bacterium and start culture for dairy
      products.
AU  - Cho YJ
AU  - Choi JK
AU  - Kim JH
AU  - Lim YS
AU  - Ham JS
AU  - Kang DK
AU  - Chun J
AU  - Paik HD
AU  - Kim GB
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5021-5022.

PMID- 29146847
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of a Psychrotolerant Denitrifying Bacterium, Janthinobacterium svalbardensis PAMC 27463.
PG  - e01178-17
AB  - We report here the complete genome sequence of Janthinobacterium svalbardensis PAMC 27463
      isolated from a freshwater lake on Barton Peninsula on King George
      Island, Antarctica. The genome consists of a chromosome with 6,274,078 bp which
      contains 5,585 genes, including 121 RNA genes.
AU  - Cho YJ
AU  - Jung YJ
AU  - Hong SG
AU  - Kim OS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01178-17.

PMID- 16040000
VI  - 334
DP  - 2005
TI  - Protein fragment complementation in M.HhaI DNA methyltransferase.
PG  - 1233-1240
AB  - The 5mC DNA methyltransferase M.HhaI can be split into two individually inactive N- and
      C-terminal fragments that together can form an active
      enzyme in vivo capable of efficiently methylating DNA. This active
      fragment pair was identified by creating libraries of M.HhaI gene
      fragment pairs and then selecting for the pairs that code for an active
      5mC methyltransferase. The site of bisection for successful protein
      fragment complementation in M.HhaI was in the variable region near the
      target recognition domain between motif VIII and TRD. This same region
      is the location of bifurcation in the naturally split 5mC
      methyltransferase M.AquI, the location for circular permutation in
      M.BssHII, and the location for previously engineered split versions of
      M.BspRI.
AU  - Choe W
AU  - Chandrasegaran S
AU  - Ostermeier M
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 2005 334: 1233-1240.

PMID- 26566423
VI  - 10
DP  - 2015
TI  - High-quality draft genome sequence of Gracilimonas tropica CL-CB462(T) (DSM 19535(T)), isolated from a Synechococcus culture.
PG  - 98
AB  - Gracilimonas tropica Choi et al. 2009 is a member of order Sphingobacteriales, class
      Sphingobacteriia. Three species of the genus Gracilimonas have been
      isolated from marine seawater or a salt mine and showed extremely halotolerant
      and mesophilic features, although close relatives are extremely halophilic or
      thermophilic. The type strain of the type species of Gracilimonas, G. tropica
      DSM19535(T), was isolated from a Synechococcus culture which was established from
      the tropical sea-surface water of the Pacific Ocean. The genome of the strain
      DSM19535(T) was sequenced through the Genomic Encyclopedia of Type Strains, Phase
      I: the one thousand microbial genomes project. Here, we describe the genomic
      features of the strain. The 3,831,242 bp long draft genome consists of 48 contigs
      with 3373 protein-coding and 53 RNA genes. The strain seems to adapt to phosphate
      limitation and requires amino acids from external environment. In addition,
      genomic analyses and pasteurization experiment suggested that G. tropica
      DSM19535(T) did not form spore.
AU  - Choi DH
AU  - Ahn C
AU  - Jang GI
AU  - Lapidus A
AU  - Han J
AU  - Reddy TB
AU  - Huntemann M
AU  - Pati A
AU  - Ivanova N
AU  - Markowitz V
AU  - Rohde M
AU  - Tindall B
AU  - Goker M
AU  - Woyke T
AU  - Klenk HP
AU  - Kyrpides NC
AU  - Cho BC
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 98.

PMID- 29093768
VI  - 12
DP  - 2017
TI  - Draft genome sequence of Marinobacterium rhizophilum CL-YJ9T (DSM 18822T), isolated from the rhizosphere of the coastal tidal-flat plant Suaeda japonica.
PG  - 65
AB  - The genus Marinobacterium belongs to the family Alteromonadaceae within the class
      Gammaproteobacteria and was reported in 1997. Currently the genus Marinobacterium
      contains 16 species. Marinobacterium rhizophilum CL-YJ9T was isolated from
      sediment associated with the roots of a plant growing in a tidal flat of
      Youngjong Island, Korea. The genome of the strain CL-YJ9T was sequenced through
      the Genomic Encyclopedia of Type Strains, Phase I: KMG project. Here we report
      the main features of the draft genome of the strain. The 5,364,574 bp long draft
      genome consists of 58 scaffolds with 4762 protein-coding and 91 RNA genes. Based
      on the genomic analyses, the strain seems to adapt to osmotic changes by
      intracellular production as well as extracellular uptake of compatible solutes,
      such as ectoine and betaine. In addition, the strain has a number of genes to
      defense against oxygen stresses such as reactive oxygen species and hypoxia.
AU  - Choi DH
AU  - Jang GI
AU  - Lapidus A
AU  - Copeland A
AU  - Reddy TBK
AU  - Mukherjee S
AU  - Huntemann M
AU  - Varghese N
AU  - Ivanova N
AU  - Pillay M
AU  - Tindall BJ
AU  - Goker M
AU  - Woyke T
AU  - Klenk HP
AU  - Kyrpides NC
AU  - Cho BC
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 65.

PMID- 26594308
VI  - 10
DP  - 2015
TI  - Complete genome sequence of US6-1.
PG  - 107
AB  - Novosphingobium pentaromativorans US6-1T is a species in the family Sphingomonadaceae.
      According to the phylogenetic analysis based on 16S rRNA gene
      sequence of the N. pentaromativorans US6-1T and nine genome-sequenced strains in
      the genus Novosphingobium, the similarity ranged from 93.9 to 99.9 % and the
      highest similarity was found with Novosphingobium sp. PP1Y (99.9 %), whereas the
      ANI value based on genomes ranged from 70.9 to 93 % and the highest value was 93
      %. This microorganism was isolated from muddy coastal bay sediments where the
      environment is heavily polluted by polycyclic aromatic hydrocarbons (PAHs). It
      was previously shown to be capable of degrading multiple PAHs, including
      benzo[a]pyrene. To further understand the PAH biodegradation pathways the
      previous draft genome of this microorganism was revised to obtain a complete
      genome using Illumina MiSeq and PacBio platform. The genome of strain US6-1T
      consists of 5,457,578 bp, which includes the 3,979,506 bp chromosome and five
      megaplasmids. It comprises 5110 protein-coding genes and 82 RNA genes. Here, we
      provide an analysis of the complete genome sequence which enables the
      identification of new characteristics of this strain.
AU  - Choi DH
AU  - Kwon YM
AU  - Kwon KK
AU  - Kim SJ
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 107.

PMID- 24501656
VI  - 9
DP  - 2013
TI  - Draft genome sequence of Rubidibacter lacunae strain KORDI 51-2(T), a cyanobacterium isolated from seawater of Chuuk lagoon.
PG  - 197-204
AB  - A photoautotrophic cyanobacterium, Rubidibacter lacunae was reported in 2008 for  the first
      time. The type strain, KORDI 51-2(T), was isolated from seawater of
      Chuuk lagoon located in a tropical area. Although it belonged to a clade
      exclusively comprised of extremely halotolerant strains by phylogenetic analyses,
      R. lacunae is known to be incapable of growth at high salt concentration over
      10%. Here we report the main features of the genome of R. lacunae strain KORDI
      51-2(T). The genome of R. lacunae contains a gene cluster for phosphonate
      utilization encoding three transporters, one regulator and eight C-P lyase
      subunits.
AU  - Choi DH
AU  - Ryu JY
AU  - Kwon KK
AU  - Lee JH
AU  - Kim C
AU  - Lee CM
AU  - Noh JH
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 9: 197-204.

PMID- 22535937
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Mycobacterium abscessus subsp. bolletii BDT.
PG  - 2756-2757
AB  - Mycobacterium abscessus subsp. bolletii is an increasing cause of human pulmonary disease and
      infections of the skin and soft tissues. Consistent reports of human infections indicate that
      M. bolletii is a highly pathogenic, emerging species of rapidly growing mycobacteria (RGM).
      Here we report the first whole-genome sequence of M. abscessus subsp. bolletii BD(T).
AU  - Choi G-E
AU  - Cho YJ
AU  - Koh WJ
AU  - Chun J
AU  - Cho SN
AU  - Shin SJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2756-2757.

PMID- 24201192
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Beta-Hemolytic Streptococcus iniae KCTC 11634.
PG  - e00897-13
AB  - Streptococcus iniae is a beta-hemolytic, Gram-positive coccus, which affects a broad range of
      freshwater and marine fish species, causing substantial economic
      losses in the aquaculture industry worldwide. Thus, it is very important to
      derive a complete genome sequence of the bacterium to aid in the development of
      vaccines and methods for preventing fish streptococcosis and zoonotic infections
      in humans. Here, we present the draft genome sequence of S. iniae KCTC 11634
      (1,955,615 bp, with a G+C content of 36.6%), which contains 1,868 putative coding
      sequences.
AU  - Choi HS
AU  - Kwon MG
AU  - Kim MS
AU  - Park MA
AU  - Kim DW
AU  - Park JY
AU  - Kim JS
AU  - Na YJ
AU  - Kim MY
AU  - Kim DS
AU  - Chae SH
AU  - Seo JS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00897-13.

PMID- 29025950
VI  - 5
DP  - 2017
TI  - High-Quality Draft Genome Sequence of Burkholderia contaminans CH-1, a Gram-Negative Bacterium That Metabolizes 2-Azahypoxanthine, a Plant  Growth-Regulating Compound.
PG  - e01148-17
AB  - Burkholderia contaminans strain CH-1 converts 2-azahypoxnathine to 2-aza-8-oxohypoxanthine,
      plant growth-regulating compounds, by oxidation. We
      report here the high-quality draft genome sequence of B. contaminans CH-1. The
      genome contains 8,065 protein-coding sequences, including several genes possibly
      involved in metabolizing 2-azahypoxanthine.
AU  - Choi JH
AU  - Sugiura H
AU  - Moriuchi R
AU  - Kawagishi H
AU  - Dohra H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01148-17.

PMID- Not carried by PubMed...
VI  - 15
DP  - 1987
TI  - A new restriction endonuclease from Clostridium thermocellum.
PG  - 352-355
AB  - The isolation and characterization of the Type II restriction endonuclease from Clostridium
      thermocellum ATCC 27405 is described. This enzyme (CthI endonuclease) is an isoschizomer of
      BclI endonuclease recognizing 5'-TGATCA-3'. CthI endonuclease requires Mg2+ ion for its
      activity and is maximally active at pH 7.5 to 10.5 in the presence of 0 to 10mM NaCl. CthI
      endonuclease is heat stable and has an optimum temperature of 60C. The activity of CthI enzyme
      is sensitive to dam methylation.
AU  - Choi KD
AU  - Kim K
AU  - Yoo OJ
PT  - Journal Article
TA  - Sanop Misaengmul Hakhoe Chi
JT  - Sanop Misaengmul Hakhoe Chi
SO  - Sanop Misaengmul Hakhoe Chi 1987 15: 352-355.

PMID- Not carried by PubMed...
VI  - 23
DP  - 1990
TI  - A new restriction endonuclease, CthII, from Clostridium thermocellum ATCC 27405.
PG  - 418-421
AB  - A new restriction enzyme has been isolated by DEAE-cellulose and phosphocellulose columns from
      a thermophilic anaerobic bacterium, Clostridium thermocellum ATCC 27405. Following CthI, the
      second peak of sequence specific endonuclease activity was eluted from the phosphocellulose
      column. The enzyme was designated as CthII. The recognition sequence of CthII was determined
      to be the dcm sequence, 5'-CC^(A/T) GG-3' and the cleavage site was indicated by the arrow.
      CthII endonuclease requires Mg2+ ion for its activity and is maximally active at a pH range
      from 8.0 to 9.0. CthII endonuclease is heat stable and has an optimum reaction temperature of
      55C. Like BstNI and ZanI this enzyme was able to cleave dcm-methylated DNA.
AU  - Choi KD
AU  - Yoo OJ
PT  - Journal Article
TA  - Korean Biochem. J.
JT  - Korean Biochem. J.
SO  - Korean Biochem. J. 1990 23: 418-421.

PMID- 22207741
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of the Rice Pathogen Pantoea ananatis Strain PA13.
PG  - 531
AB  - Pantoea ananatis is the causative agent of sheath and grain rot in rice. Here, we present the
      complete genome sequence of P. ananatis strain PA13,
      originally isolated from a diseased rice grain.
AU  - Choi O
AU  - Lim JY
AU  - Seo YS
AU  - Hwang I
AU  - Kim J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 531.

PMID- Not carried by PubMed...
VI  - 54
DP  - 1994
TI  - Restriction-modification systems and genetic variability of Xanthomonas oryzae pv.
PG  - 5462B-5463B
AB  - The XorII methyltransferase gene (xorIIM) and very short patch repair endonuclease gene

      (xorii.vsr) were cloned from Xanthomonas oryzae pv. oryzae, the rice bacterial leaf blight

      pathogen. XorIIM encodes a polypeptide of 47 KD and was identified as a monospecific m5

      cytosine methyltransferase gene. The xorii.vsr encodes a polypeptide of 19.7 KD and the gene

      is similar in sequence and size to the E. coli vsr gene of the DNA cytosine methylase system

      (Dcm). A population of X. oryzae pv. oryzae strains from major rice growing countries in Asia

      was evaluated for the presence or absence of the XorI and XorII restriction-modification (R-M)

      systems. Four clonal populations with the phenotype XorI+II+, XorI-II+, XorI+II-, XorI-II+,

      and XorI-II- were distributed in Asia. The XorII R-M system was predominantly found in

      southeast Asia, whereas the XorI modification system was most prevalent in northeast Asia. DNA

      polymorphisms were observed between strains in genomic sequences containing the XorII R-M

      genes; however, most Philippine strains and all the Indonesian and Korean strains had

      identical patterns. Based on the geographic distribution of both systems and the genome

      organization around the XorII system, I propose that the XorI system originated in northeast

      Asia and moved to southeast Asia, while the XorII system originated in southeast Asia. The

      existence of several phenotypes in some parts of Asia indicate that after movement of the

      systems the populations remained clonal.

      

      A marker-exchange mutant in which the avirulence gene locus avrXa7 was insertionally

      inactivated was significantly reduced in aggressiveness to susceptible rice cultivars.

      Aggressiveness was restored by complementation with a plasmid bearing the avrXa7 gene. Thus,

      avrXa7 codes for not only resistance-gene-specific avirulence function, but also for

      pathogenicity functions.

      

AU  - Choi S-H
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1994 54: 5462B-5463B.

PMID- 25125651
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of an Atypical Strain of Streptococcus pneumoniae Isolated  from a Respiratory Infection.
PG  - e00822-14
AB  - Next-generation sequencing was used to investigate an unknown clinical respiratory infection.
      This new strain of Streptococcus pneumoniae, ASVL_JC_0001,
      was isolated from a clinical specimen from a patient with bronchitis and
      pulmonary inflammation. The draft genome sequence, obtained with an Illumina
      MiSeq sequencing system, consists of 83 large contigs, a total of 2,092,532 bp
      long, and has a GC content of 40.3%.
AU  - Choi SC
AU  - Parker J
AU  - Richards VP
AU  - Ross K
AU  - Jilly B
AU  - Chen J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00822-14.

PMID- 20841325
VI  - 39
DP  - 2011
TI  - Identification of preferential target sites for human DNA methyltransferases.
PG  - 104-118
AB  - DNA methyltransferases (DNMTs) play an important role in establishing and maintaining DNA
      methylation. Aberrant expression of DNMTs and their
      isoforms has been found in many types of cancer, and their contribution to
      aberrant DNA methylation has been proposed. Here, we generated HEK 293T
      cells stably transfected with each of 13 different DNMTs (DNMT1, two
      DNMT3A isoforms, nine DNMT3B isoforms and DNMT3L) and assessed the DNA
      methylation changes induced by each DNMT. We obtained DNA methylation
      profiles of DNA repetitive elements and 1505 CpG sites from 808
      cancer-related genes. We found that DNMTs have specific and overlapping
      target sites and their DNA methylation target profiles are a reflection of
      the DNMT domains. By examining H3K4me3 and H3K27me3 modifications in the
      808 gene promoter regions using promoter ChIP-on-chip analysis, we found
      that specific de novo DNA methylation target sites of DNMT3A1 are
      associated with H3K4me3 modification that are transcriptionally active,
      whereas the specific target sites of DNMT3B1 are associated with H3K27me3
      modification that are transcriptionally inactive. Our data suggest that
      different DNMT domains are responsible for targeting DNA methylation to
      specific regions of the genome, and this targeting might be associated
      with histone modifications.
AU  - Choi SH
AU  - Heo K
AU  - Byun HM
AU  - An W
AU  - Lu W
AU  - Yang AS
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2011 39: 104-118.

PMID- 28684572
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Lactobacillus rhamnosus BFE5264, Isolated from Maasai Traditional Fermented Milk.
PG  - e00563-17
AB  - Here, we report the complete genome of Lactobacillus rhamnosus BFE5264, which was sequenced
      with the Pacific Biosciences RSII platform. The genome size is 3.01 Mb
      and includes 3,077 annotated coding sequences, including genes associated with
      the promotion of intestinal epithelial homeostasis through specific signaling
      pathways.
AU  - Choi SH
AU  - Ji Y
AU  - Park S
AU  - Mathara J
AU  - Holzapfel W
AU  - Kang J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00563-17.

PMID- 8078464
VI  - 244
DP  - 1994
TI  - Identification of the XorII methyltransferase gene and a vsr homolog from Xanthomonas oryzae pv. oryzae.
PG  - 383-390
AB  - The gene encoding the XorII methyltransferase (M.XorII) was cloned from Xanthomonas oryzae pv.
      oryzae and characterized in Escherichia coli. The M.XorII activity was localized to a 3.1 kb
      BamHI-BstXI fragment, which contained two open reading frames (ORFs) of 1272 nucleotides (424
      amino acids) and 408 nucleotides (136 amino acids). Ten polypeptide domains conserved in other
      M5 cytosine methyltransferases (MTases) were identified in the deduced amino acid sequence of
      the 1272 ORF. E. coli Mrr+ strains were transformed poorly by plasmids containing the XorII
      MTase gene, indicating the presence of at least one MeCG in the recognition sequence for
      M.XorII (CGATCG). The 408 nucleotide ORF was 36% identical at the amino acid level to
      sequences of the E. coli dcm-vsr gene, which is required for very short patch repair. X.
      oryzae pv. oryzae genomic DNA that is resistant to digestion by PvuI and XorII hybridizes with
      a 7.0 kb fragment containing the XorII MTase gene and vsr homolog, whereas DNA from strains
      that lack M.XorII activity do not hybridize with the fragment.
AU  - Choi SH
AU  - Leach JE
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1994 244: 383-390.

PMID- 9572933
VI  - 64
DP  - 1998
TI  - Distribution of Xanthomonas oryzae pv. oryzae DNA modification systems in Asia.
PG  - 1663-1668
AB  - The presence or absence of two DNA modification systems, XorI and XorII, in 195 strains of
      Xanthomonas oryzae pv. oryzae collected from different major rice-growing countries of Asia
      was assessed.  All four possible phenotypes (XorI+ XorII+, XorI+ XorII-, XorI- XorII+ and Xor-
      XorII-) were detected in the population at a ratio of approximately 1:2:2:2.  The XorI+ XorII+
      and XorI- XorII+ phenotypes were observed predominantly in strains from southeast Asia
      (Philippines, Malaysia, and Indonesia), whereas strains with the phenotypes XorI- XorII- and
      XorI+ XorII- were distributed in south Asia (India and Nepal) and northeast Asia (China, Korea
      and Japan), respectively.  Based on the prevalence and geographic distribution of the XorI and
      XorII systems, we suggest that the XorI modification system originated in northeast Asia and
      was later introduced to southeast Asia, while the XorII system originated in southeast Asia
      and moved to northeast Asia and south Asia.  Genomic DNA from all tested strains of X. oryzae
      pv. Oryzae that were resistant to digestion by endonuclease XorII or its isoschizomer PvuI
      also hybridized with a 7.0-kb clone that contained the XorII modification system, whereas
      strains that were digested by XorII or PvuI lacked DNA that hybridized with the clone.  Size
      polymorphisms were observed in fragments that hybridized with the 7.0-kb clone.  However, a
      single hybridization pattern generally was found in XorII+ strains within a country,
      indicating clonal maintenance of the XorII methyltransferase gene locus.  The locus was
      monomorphic for X. oryzae pv. Oryzae strains from the Philippines and all strains from
      Indonesia and Korea.
AU  - Choi SH
AU  - Vera Cruz CM
AU  - Leach JE
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1998 64: 1663-1668.

PMID- 25359911
VI  - 2
DP  - 2014
TI  - Genome Sequence of Bacillus amyloliquefaciens GB03, an Active Ingredient of the First Commercial Biological Control Product.
PG  - e01092-14
AB  - Bacillus amyloliquefaciens GB03 has been used as a representative commercialized  strain of
      the bacilli for biological control against a broad spectrum of plant
      pathogens and as a bio-fertilizer to promote growth and yield of field crops for
      more than two decades. Herein, we present the genome sequence and a brief
      analysis of strain GB03.
AU  - Choi SK
AU  - Jeong H
AU  - Kloepper JW
AU  - Ryu CM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01092-14.

PMID- Not carried by PubMed...
VI  - 24
DP  - 1986
TI  - Inhibition of SmaI, AvaI, NaeI and XmaI endonuclease activities by the methylation of DNA with HpaII methylase.
PG  - 86-90
AB  - The DNA methylated by HpaII methylase was not cleaved by SmaI, AvaI and NaeI
      endonucleases.  This experimental data could be interpreted as strong evidence
      that SmaI, AvaI and NaeI methylases which yet to be isolated would methylate on
      the inmost cytosine nucleotide within their hexameric recognition sequences.
      The facts that SmaI, AvaI and NaeI endonucleases cannot cleave the DNA
      methylated by HpaII methylase are the valuable informations for protecting DNAs
      upon cleavage reactions by SmaI, AvaI and NaeI endonucleases especially for
      cDNA insertion experiments into vector DNAs using SmaI, AvaI and NaeI
      oligonucleotide linkers.  In the case of XmaI endonuclease, partially cleaved
      DNA fragments were observed although the reaction rate was greatly decreased.
      This result implies that the methylation site of XmaI methylase which is yet to
      be isolated would not be the same as that of HpaII methylase in XmaI sequence.
AU  - Choi WS
AU  - Kang SC
AU  - Seo JS
AU  - Yoo OJ
PT  - Journal Article
TA  - Korean J. Microbiol.
JT  - Korean J. Microbiol.
SO  - Korean J. Microbiol. 1986 24: 86-90.

PMID- 23747700
VI  - 79
DP  - 2013
TI  - Identification and characterization of a novel flagellum-dependent Salmonella-infecting bacteriophage, iEPS5.
PG  - 4829-4837
AB  - A novel flagellatropic phage of Salmonella enterica serovar Typhimurium called
      iEPS5 was isolated and characterized. iEPS5 has an icosahedral head and a long
      non-contractile tail with a tail fiber. Genome sequencing revealed a
      double-stranded DNA of 59,254 bp having 73 open reading frames (ORFs). To
      identify the receptor for iEPS5, Tn5 transposon insertion mutants of S.
      Typhimurium SL1344 that were resistant to the phage were isolated. All of the
      phage-resistant mutants were found to have mutations in genes involved in
      flagellar formation, suggesting that the flagellum is the adsorption target of
      this phage. Analysis of phage infection using the DeltamotA mutant, which is
      flagellated but non-motile, demonstrated the requirement of flagellar rotation
      for iEPS5 infection. Further analysis of phage infection using the DeltacheY
      mutant revealed that iEPS5 could infect host bacteria only when the flagellum is
      rotating counterclockwise (CCW). These results suggested that the CCW-rotating
      flagellar filament is essential for phage adsorption and required for successful
      infection by iEPS5. In contrast to the well-studied flagellatropic phage Chi,
      iEPS5 cannot infect the DeltafliK mutant that makes a polyhook without a
      flagellar filament, suggesting that these two flagellatropic phages utilize
      different infection mechanisms. Here, we present evidences that iEPS5 may inject
      its DNA into the flagellar filament for infection by assessing DNA transfer from
      SYBR-gold-labeled iEPS5 to the host bacteria.
AU  - Choi Y
AU  - Shin H
AU  - Lee JH
AU  - Ryu S
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2013 79: 4829-4837.

PMID- Not carried by PubMed...
VI  - 32
DP  - 1994
TI  - Characterization of restriction endonuclease EagBI from Enterobacter agglomerans CBNU45.
PG  - 91-95
AB  - EagBI is a type II restriction endonuclease from Enterobacter agglomerans strain CBNU45
      isolated from soil.  EagBI was partially purified by DEAE-cellulose, phosphocellulose P11 and
      hydroxylapatite column chromatography.  EagBI recognizes and cleaves the sequence
      5'-CGAT/CG-3' and generates 2-base 3'-protruding cohesive ends.  The optimal reaction
      conditions of EagBI are 10mM Tris-HCl (pH 7.8), 6-10mM MgCl2 at 37oC.  The enzyme is maximally
      active in the absence of NaCl, able to cleave both dam- and dam+ DNAs and sensitive to heat
      treatment (at 65oC for 10 min).  Therefore, although EagBI is an isoschizomer of PvuI, it is
      more useful than PvuI in respect of the NaCl requirement and heat-stability.
AU  - Choi Y-J
AU  - Kim S-J
AU  - Hwang H-Y
AU  - Yim J
AU  - Kim J-C
PT  - Journal Article
TA  - Korean J. Microbiol.
JT  - Korean J. Microbiol.
SO  - Korean J. Microbiol. 1994 32: 91-95.

PMID- 22328757
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Marinobacterium stanieri S30, a Strain Isolated from a Coastal Lagoon in Chuuk State in Micronesia.
PG  - 1260
AB  - In this study, we isolated xylan-degrading bacteria from a coastal lagoon of Micronesia and
      identified the bacteria as Marinobacterium stanieri S30. GSFLX 454
      pyrosequencing and sequence analysis of the M. stanieri S30 genome generated
      4,007 predicted open reading frames (ORFs) that could be candidate genes for
      producing enzymes with different catalytic functions.
AU  - Choi YU
AU  - Kwon YK
AU  - Ye BR
AU  - Hyun JH
AU  - Heo SJ
AU  - Affan A
AU  - Yoon KT
AU  - Park HS
AU  - Oh C
AU  - Kang DH
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1260.

PMID- 2829119
VI  - 16
DP  - 1988
TI  - DNA containing the base analogue 2-aminoadenine:  preparation, use as hybridization probes and cleavage by restriction endonucleases.
PG  - 305-317
AB  - The base analogue 2-aminoadenine (2,6-diaminopurine,D) has been introduced at
      selected positions into synthetic oligodeoxyribonucleotides and DNA by the
      combined use of chemical and enzymatic methods.  2-aminoadenine substitution
      for adenine introduces changes in the minor groove of DNA and creates an
      additional hydrogen bond in the Watson-Crick base pair with thymine.
      Oligonucleotide hybridization probes containing 2-aminoadenine showed increased
      selectivity and hybridization strength during DNA-DNA hybridization to phage or
      genomic target DNA.  Properties of the base analogue with respect to DNA
      modifying enzymes were examined.  2-aminoadenine was used to probe minor groove
      determinants during the treatment of DNA by 12 restriction endonucleases.
      Inhibition of cleavage was found for several restriction enzymes.
AU  - Chollet A
AU  - Kawashima E
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1988 16: 305-317.

PMID- 8703028
VI  - 271
DP  - 1996
TI  - Protein splicing involving the Saccharomyces cerevisiae VMA intein.
PG  - 22159-22168
AB  - Protein splicing involves the excision of an internal protein segment, the intein, from a
      precursor protein and the concomitant ligation of the flanking N- and C-terminal regions.  It
      occurs in mesophilic bacteria, yeast, and thermophilic archaea.  The ability to control
      protein splicing of a thermophilic intein by temperature and pH in a foreign protein context
      facilitated the study of the mechanism of protein splicing in thermophiles.  On the other
      hand, no direct studies have been done on the mechanism of protein splicing in mesophiles.  We
      examined the splicing of a chimeric protein containing the intein of the vacuolar ATPase
      subunit (VMA) of Saccharomyces cerevisiae that involves cysteines rather than serines at the
      reaction center.  The steps in the splicing process were deduced by analyzing intermediates
      and side products that accumulate as a result of amino acid substitutions and were found to be
      analogous to those occurring in thermophiles.  Moreover, appropriate amino acid replacements
      allowed us to develop the first mesophilic in vitro protein splicing system as well as
      strategies for modulating the rate of protein splicing and for converting the splicing
      reaction to an efficient protein cleavage reaction at either splice junction.
AU  - Chong S
AU  - Shao Y
AU  - Paulus H
AU  - Benner J
AU  - Perler FB
AU  - Xu M-Q
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1996 271: 22159-22168.

PMID- 23144375
VI  - 194
DP  - 2012
TI  - Insights from the Genome Sequence of Quorum-Quenching Staphylococcus sp. Strain AL1, Isolated from Traditional Chinese Soy Sauce Brine Fermentation.
PG  - 6611-6612
AB  - We report the draft genome sequence of Staphylococcus sp. strain AL1, which degrades
      quorum-sensing molecules (namely, N-acyl homoserine lactones). To the
      best of our knowledge, this is the first documentation that reports the whole
      genome sequence and quorum-quenching activity of Staphylococcus sp. strain AL1.
AU  - Chong TM
AU  - Tung HJ
AU  - Yin WF
AU  - Chan KG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6611-6612.

PMID- 23105092
VI  - 194
DP  - 2012
TI  - Heavy-Metal Resistance of a France Vineyard Soil Bacterium, Pseudomonas mendocina Strain S5.2, Revealed by Whole-Genome Sequencing.
PG  - 6366
AB  - Here we present the draft genome of Pseudomonas mendocina strain S5.2, possessing tolerance to
      a high concentration of copper. In addition to being copper
      resistant, the genome of P. mendocina strain S5.2 contains a number of
      heavy-metal-resistant genes known to confer resistance to multiple heavy-metal
      ions.
AU  - Chong TM
AU  - Yin WF
AU  - Mondy S
AU  - Grandclement C
AU  - Dessaux Y
AU  - Chan KG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6366.

PMID- 23405341
VI  - 1
DP  - 2013
TI  - Whole-Genome Shotgun Sequencing of Mycobacterium abscessus M156, an Emerging Clinical Pathogen in Malaysia.
PG  - e00063-12
AB  - Mycobacterium abscessus is an emerging clinical pathogen commonly associated with
      non-tuberculous mycobacterial infections. We report herein the draft genome of M. abscessus
      strain M156.
AU  - Choo SW
AU  - Wong YL
AU  - Beh CY
AU  - Lokanathan N
AU  - Leong ML
AU  - Ong CS
AU  - Ng KP
AU  - Ngeow YF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00063-12.

PMID- 23012295
VI  - 194
DP  - 2012
TI  - Analysis of the Genome of Mycobacterium abscessus Strain M94 Reveals an Uncommon  Cluster of tRNAs.
PG  - 5724
AB  - Mycobacterium abscessus is a species of rapidly growing nontuberculous mycobacteria that is
      frequently associated with opportunistic infections in
      humans. Here, we report the annotated genome sequence of M. abscessus strain M94,
      which showed an unusual cluster of tRNAs.
AU  - Choo SW
AU  - Wong YL
AU  - Leong ML
AU  - Heydari H
AU  - Ong CS
AU  - Ng KP
AU  - Ngeow YF
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5724.

PMID- 22887675
VI  - 194
DP  - 2012
TI  - Annotated Genome Sequence of Mycobacterium massiliense Strain M154, Belonging to  the Recently Created Taxon Mycobacterium abscessus subsp. bolletii comb. nov.
PG  - 4778
AB  - Mycobacterium massiliense has recently been proposed as a member of Mycobacterium abscessus
      subsp. bolletii comb. nov. Strain M154, a clinical isolate from the
      bronchoalveolar lavage fluid of a Malaysian patient presenting with lower
      respiratory tract infection, was subjected to shotgun DNA sequencing with the
      Illumina sequencing technology to obtain whole-genome sequence data for
      comparison with other genetically related strains within the M. abscessus species
      complex.
AU  - Choo SW
AU  - Wong YL
AU  - Tan JL
AU  - Ong CS
AU  - Wong GJ
AU  - Ng KP
AU  - Ngeow YF
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4778.

PMID- 22628507
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Mycobacterium abscessus Strain M93.
PG  - 3278
AB  - Mycobacterium abscessus is a rapid-growing species of nontuberculous mycobacteria that is
      frequently associated with opportunistic infections in humans. We report
      herein the draft genome sequence of M. abscessus strain M93.
AU  - Choo SW
AU  - Wong YL
AU  - Yusoff AM
AU  - Leong ML
AU  - Wong GJ
AU  - Ong CS
AU  - Ng KP
AU  - Ngeow YF
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3278.

PMID- 22933758
VI  - 194
DP  - 2012
TI  - Genome Analysis of Mycobacterium massiliense Strain M172, Which Contains a Putative Mycobacteriophage.
PG  - 5128
AB  - The genome of Mycobacterium massiliense M172, isolated from a human sputum sample, was
      sequenced using Illumina GA IIX technology and found to contain
      5,204,460 bp, including putative genes for virulence and antibiotic resistance as
      well as a 92-kb genomic region most likely to correspond to a mycobacteriophage.
AU  - Choo SW
AU  - Yusoff AM
AU  - Wong YL
AU  - Wee WY
AU  - Ong CS
AU  - Ng KP
AU  - Ngeow YF
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5128.

PMID- 9546213
VI  - 5
DP  - 1998
TI  - Recognition of DNA methylation by zinc fingers.
PG  - 264-265
AB  - Zinc fingers are small DNA-binding motifs that occur in a large family of eukaryotic
      transcription factors.  The DNA-binding specificity of zinc fingers can be altered by protein
      engineering, for instance using phage display, to create novel protein domains which recognize
      predetermined sequences.  It has been proposed that tailored DNA-binding domains of this type
      can be incorporated into proteins such as restriction enzymes and transcription factors, in
      order to target particular DNA sequences or genes.  The zinc finger domains studied so far -
      whether naturally occurring, designed or selected - can bind specifically to various DNA sites
      containing the four major DNA bases: A, G, C and T.
AU  - Choo Y
PT  - Journal Article
TA  - Nat. Struct. Biol.
JT  - Nat. Struct. Biol.
SO  - Nat. Struct. Biol. 1998 5: 264-265.

PMID- 10981627
VI  - 10
DP  - 2000
TI  - Advances in zinc finger engineering.
PG  - 411-416
AB  - Recently developments have been made in engineering sequence-specific zinc finger DNA-binding
      proteins.  Advances in this area will soon make it routine to target proteins to specific DNA
      sequences associated with any given gene.  The primary interest is in the regulation of gene
      expression using customized transcription factors.  However, modular catalytic domains are
      also being developed in order to engineer chimeric proteins with customized restriction
      enzyme, methylase and integrase activity.
AU  - Choo Y
AU  - Isalan M
PT  - Journal Article
TA  - Curr. Opin. Struct. Biol.
JT  - Curr. Opin. Struct. Biol.
SO  - Curr. Opin. Struct. Biol. 2000 10: 411-416.

PMID- 6087394
VI  - 11
DP  - 1984
TI  - Two plasmid-determined restriction and modification systems in Streptococcus lactis.
PG  - 260-263
AB  - Two restriction and modification systems were found in Streptococcus lactis
      strain IL594 which was found to contain 9 plasmids designated pIL1 to pIL9.  On
      the basis of protoplast-induced curing experiments, we showed that a
      restriction and modification system was related to the presence of pIL6 or
      pIL7.  The pIL-6-determined restriction and modification system was related to
      the presence of pIL6 or pIL7.  The pIL-6-determined restriction and
      modification system was confirmed by cotransfer of the plasmid and of the
      restriction and modification system to a plasmid-free, nonrestricting
      derivative of S. lactis IL594.
AU  - Chopin A
AU  - Chopin M-C
AU  - Moillo-Batt A
AU  - Langella P
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 1984 11: 260-263.

PMID- 23041083
VI  - 511
DP  - 2012
TI  - Sequence of Leptospira santarosai serovar Shermani genome and prediction of virulence-associated genes.
PG  - 364-370
AB  - Leptospirosis, a widespread zoonosis, is a re-emerging infectious disease caused
      by pathogenic Leptospira species. In Taiwan, Leptospira santarosai serovar
      Shermani is the most frequently isolated serovar, causing both renal and systemic
      infections. This study aimed to generate a L. santarosai serovar Shermani genome
      sequence and categorize its hypothetical genes, particularly those associated
      with virulence. The genome sequence consists of 3,936,333 nucleotides and 4033
      predicted genes. Additionally, 2244 coding sequences could be placed into
      clusters of orthologous groups and the number of genes involving cell
      wall/membrane/envelope biogenesis and defense mechanisms was higher than that of
      other Leptospira spp. Comparative genetic analysis based on BLASTX data revealed
      that about 73% and 68.8% of all coding sequences have matches to pathogenic L.
      interrogans and L. borgpetersenii, respectively, and about 57.6% to saprophyte L.
      biflexa. Among the hypothetical proteins, 421 have a transmembrane region, 172
      have a signal peptide and 17 possess a lipoprotein signature. According to PFAM
      prediction, 32 hypothetical proteins have properties of toxins and surface
      proteins mediated bacterial attachment, suggesting they may have roles associated
      with virulence. The availability of the genome sequence of L. santarosai serovar
      Shermani and the bioinformatics re-annotation of leptospiral hypothetical
      proteins will facilitate further functional genomic studies to elucidate the
      pathogenesis of leptospirosis and develop leptospiral vaccines.
AU  - Chou LF
AU  - Chen YT
AU  - Lu CW
AU  - Ko YC
AU  - Tang CY
AU  - Pan MJ
AU  - Tian YC
AU  - Chiu CH
AU  - Hung CC
AU  - Yang CW
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 2012 511: 364-370.

PMID- 22535935
VI  - 194
DP  - 2012
TI  - Genome Sequence of Blastococcus saxobsidens DD2, a Stone-Inhabiting Bacterium.
PG  - 2752-2753
AB  - Members of the genus Blastococcus have been isolated from sandstone monuments, as well as from
      sea, soil, plant, and snow samples. We report here the genome
      sequence of a member of this genus, Blastococcus saxobsidens strain DD2, isolated
      from below the surface of a Sardinian wall calcarenite stone sample.
AU  - Chouaia B
AU  - Crotti E
AU  - Brusetti L
AU  - Daffonchio D
AU  - Essoussi I
AU  - Nouioui I
AU  - Sbissi I
AU  - Ghodhbane-Gtari F
AU  - Gtari M
AU  - Vacherie B
AU  - Barbe V
AU  - Medigue C
AU  - Gury J
AU  - Pujic P
AU  - Normand P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2752-2753.

PMID- 9353914
VI  - 143
DP  - 1997
TI  - Low-resolution sequencing of Rhodobacter sphaeroides 2.4.1T: chromosome II is a true chromosome.
PG  - 3085-3099
AB  - The photosynthetic bacterium Rhodobacter sphaeroides 2.4.1T has two chromosomes, CI
      (approximately 3.0 Mb) and CII (approximately 0.9 Mb). In this study a low-redundancy
      sequencing strategy was adopted to analyse 23 out of 47 cosmids from an ordered CII library.
      The sum of the lengths of these 23 cosmid inserts was approximately 495 kb, which comprised
      approximately 417 kb of unique DNA. A total of 1145 sequencing runs was carried out, with each
      run generating 559 +/- 268 bases of sequence to give approximately 640 kb of total sequence.
      After editing, approximately 2.8% bases per run were estimated to be ambiguous. After the
      removal of vector and Escherichia coli sequences, the remaining approximately 565 kb of R.
      sphaeroides sequences were assembled, generating approximately 291 kb of unique sequences.
      BLASTX analysis of these unique sequences suggested that approximately 131 kb (45% of the
      unique sequence) had matches to either known genes, or database ORFs of hypothetical or
      unknown function (dORFs). A total of 144 strong matches to the database was found; 101 of
      these matches represented genes encoding a wide variety of functions, e.g. amino acid
      biosynthesis, photosynthesis, nutrient transport, and various regulatory functions. Two rRNA
      operons (rrnB and rrnC) and five tRNAs were also identified. The remaining 160 kb of DNA
      sequence which did not yield database matches was then analysed using CODONPREFERENCE from the
      GCG package. This analysis suggested that 122 kb (42% of the total unique DNA sequence) could
      encode putative ORFs (pORFs), with the remaining 38 kb (13%) possibly representing non-coding
      intergenic DNA. From the data so far obtained, CII does not appear to be specialized for
      encoding any particular metabolic function, physiological state or growth condition. These
      data suggest that CII contains genes which are functionally as diverse as those found on any
      other bacterial chromosome and also contains sequences (pORFs), which may prove to be unique
      to this organism.
AU  - Choudhary M
AU  - Mackenzie C
AU  - Nereng K
AU  - Sodergren E
AU  - Weinstock GM
AU  - Kaplan S
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 1997 143: 3085-3099.

PMID- 17172323
VI  - 189
DP  - 2007
TI  - Genome Analyses of Three Strains of Rhodobacter sphaeroides: Evidence of Rapid Evolution of Chromosome II.
PG  - 1914-1921
AB  - Three strains of Rhodobacter sphaeroides of diverse origin have been under investigation in
      our laboratory for their genome complexities, including
      the presence of multiple chromosomes and the distribution of essential
      genes within their genomes. The genome of R. sphaeroides 2.4.1 has been
      completely sequenced and fully annotated, and now two additional strains
      (ATCC 17019 and ATCC 17025) of R. sphaeroides have been sequenced. Thus,
      genome comparisons have become a useful approach in determining the
      evolutionary relationships among different strains of R. sphaeroides. In
      this study, the concatenated chromosomal sequences from the three strains
      of R. sphaeroides were aligned, using Mauve, to examine the extent of
      shared DNA regions and the degree of relatedness among their
      chromosome-specific DNA sequences. In addition, the exact intra- and
      interchromosomal DNA duplications were analyzed using Mummer. Genome
      analyses employing these two independent approaches revealed that strain
      ATCC 17025 diverged considerably from the other two strains, 2.4.1 and
      ATCC 17029, and that the two latter strains are more closely related to
      one another. Results further demonstrated that chromosome II
      (CII)-specific DNA sequences of R. sphaeroides have rapidly evolved, while
      CI-specific DNA sequences have remained highly conserved. Aside from the
      size variation of CII of R. sphaeroides, variation in sequence lengths of
      the CII-shared DNA regions and their high sequence divergence among
      strains of R. sphaeroides suggest the involvement of CII in the evolution
      of strain-specific genomic rearrangements, perhaps requiring strains to
      adapt in specialized niches.
AU  - Choudhary M
AU  - Zanhua X
AU  - Fu YX
AU  - Kaplan S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2007 189: 1914-1921.

PMID- 
VI  - 36
DP  - 1999
TI  - Characterization of new type II restriction endonucleases from bacteria.
PG  - 165-171
AB  - The aim of the present study was to search the available microflora of Pakistan for new type
      II restriction endonucleases.  Twelve bacterial strains from the American Type Culture
      Collection and CAMB Culture Collection were screened for the presence of new type II
      restriction endonucleases.  Two strains, Arthrobacter picolinophilus (ATCC 27854) and
      Pseudomonas aeruginosa Q2 (CAMB 2637) yielded the endonucleases.  The type II restriction
      enzymes isolated and characterized from these strains are designated as ApiI and PaeQI.  These
      enzymes were purified by a combination of gel filtration, ion exchange and affinity
      chromatography.  The DNA sequences recognized by the two enzymes were determined by analysis
      of the fragment patterns generated on different substrate DNAs, Lambda, T7, pUC19, pBR322,
      PhiX174RFI.  The cleavage sites within the recognition sequences were also established by
      primed synthesis.  The newly discovered enzymes ApiI and PaeQI recognize and cleave 4-6
      nucleotide long DNA sequences 5'-CTGCAG-3', 5'-CCGCGG-3', respectively.
AU  - Choudhry S
PT  - Journal Article
TA  - Proc. Pakistan Acad. Sci.
JT  - Proc. Pakistan Acad. Sci.
SO  - Proc. Pakistan Acad. Sci. 1999 36: 165-171.

PMID- 24482504
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Pseudoalteromonas sp. Strain NW 4327 (MTCC 11073, DSM 25418), a Pathogen of the Great Barrier Reef Sponge Rhopaloeides odorabile.
PG  - e00001-14
AB  - To date, only one marine sponge pathogen (Pseudoalteromonas sp. strain NW 4327) has fulfilled
      Koch's postulates. We report the 4.48-Mbp draft genome sequence of
      this strain, which is pathogenic to the Great Barrier Reef sponge Rhopaloeides
      odorabile. The sequence provides valuable information on sponge-pathogen
      interactions, including the mode of transmission and associated virulence
      factors.
AU  - Choudhury JD
AU  - Pramanik A
AU  - Webster NS
AU  - Llewellyn LE
AU  - Gachhui R
AU  - Mukherjee J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00001-14.

PMID- 12854964
VI  - 21
DP  - 2003
TI  - Pentamidine-induced Alteration in Restriction Endonuclease Cleavage of Plasmid DNA.
PG  - 127-134
AB  - We have used restriction enzymes and DNaseI as probes to determine the specificity of
      pentamidine binding to plasmid DNA. Cleavage of plasmid
      pAZ130 by EcoRI, EcoRV and ApaI is inhibited by pentamidine, cleavage by
      XbaI, NotI and AvaI is unaffected, while cleavage by XhoI, which
      recognizes the same sequence as AvaI, is stimulated. DNaseI footprinting
      of DNA containing these restriction sites revealed that pentamidine
      protection is not strictly limited to AT-rich regions. We suggest that
      perturbation of the DNA micro- environment by pentamidine binding is
      responsible for its effect on nucleases.
AU  - Choudhury K
AU  - Leibowitz MJ
PT  - Journal Article
TA  - J. Biomol. Struct. Dyn.
JT  - J. Biomol. Struct. Dyn.
SO  - J. Biomol. Struct. Dyn. 2003 21: 127-134.

PMID- 7891691
VI  - 15
DP  - 1995
TI  - Induction of homologous recombination in mammalian chromosomes by using the I-SceI system of Saccharomyces cerevisiae.
PG  - 1968-1973
AB  - The mitochondrial intron-encoded endonuclease I-SceI of Saccharomyces cerevisiae has an 18-bp
      recognition sequence and, therefore, has a very low probability of cutting DNA, even within
      large genomes.  We demonstrate that double-strand breaks can be initiated by the I-SceI
      endonuclease at a predetermined location in the mouse genome and that the breaks can be
      repaired with a donor molecule homologous with regions flanking the breaks.  This induced
      homologous recombination is approximately 2 orders of magnitude more frequent than spontaneous
      homologous recombination and at least 10 times more frequent than random integration near an
      active promoter.  As a consequence of induced homologous recombination, a heterologous novel
      sequence can be inserted at the site of the break.  This recombination can occur at a variety
      of chromosomal targets in differentiated and multipotential cells.  These results demonstrate
      homologous recombination involving chromosomal DNA by the double-strand break repair mechanism
      in mammals and show the usefulness of very rare cutter endonucleases, such as I-SceI, for
      designing genome rearrangements.
AU  - Choulika A
AU  - Perrin A
AU  - Dujon B
AU  - Nicolas J-F
PT  - Journal Article
TA  - Mol. Cell. Biol.
JT  - Mol. Cell. Biol.
SO  - Mol. Cell. Biol. 1995 15: 1968-1973.

PMID- 7882137
VI  - 317
DP  - 1994
TI  - The yeast I-SceI meganuclease induces site-directed chromosomal recombination in mammalian cells.
PG  - 1013-1019
AB  - Double-strand breaks in genomic DNA stimulate recombination.  Until now it was not possible to
      induce in vivo site-directed double-strand breaks in a mammalian chromosomal target.  In this
      article we describe the use of I-SceI meganuclease, a very rare cutter yeast endonuclease, to
      induce site-directed double-strand breaks mediated recombination.  The results demonstrate the
      potential of the I-SceI system for chromosome manipulation in mammalian cells.
AU  - Choulika A
AU  - Perrin A
AU  - Dujon B
AU  - Nicolas J-F
PT  - Journal Article
TA  - C.R. Acad. Sci. III
JT  - C.R. Acad. Sci. III
SO  - C.R. Acad. Sci. III 1994 317: 1013-1019.

PMID- 21304665
VI  - 1
DP  - 2009
TI  - Complete genome sequence of Thermanaerovibrio acidaminovorans type strain (Su883).
PG  - 254-261
AB  - Thermanaerovibrio acidaminovorans (Guangsheng et al. 1997) Baena et al. 1999 is the type
      species of the genus Thermanaerovibrio and is of phylogenetic interest
      because of the very isolated location of the novel phylum Synergistetes. T.
      acidaminovorans Su883(T) is a Gram-negative, motile, non-spore-forming bacterium
      isolated from an anaerobic reactor of a sugar refinery in The Netherlands. Here
      we describe the features of this organism, together with the complete genome
      sequence, and annotation. This is the first completed genome sequence from a
      member of the phylum Synergistetes. The 1,848,474 bp long single replicon genome
      with its 1765 protein-coding and 60 RNA genes is part of the Genomic Encyclopedia
      of Bacteria and Archaea project.
AU  - Chovatia M et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2009 1: 254-261.

PMID- 29650567
VI  - 6
DP  - 2018
TI  - Genome Sequence of a Multidrug-Resistant Candida haemulonii Isolate from a Patient with Chronic Leg Ulcers in Israel.
PG  - e00176-18
AB  - Candida haemulonii is an emerging multidrug-resistant yeast that can cause invasive
      candidiasis. Here, we report the first genome sequence of C. haemulonii
      (isolate B11899) generated using PacBio sequencing technology. The estimated
      genome size was 13.3 Mb, with a GC content of 45.19%.
AU  - Chow NA
AU  - Gade L
AU  - Batra D
AU  - Rowe LA
AU  - Juieng P
AU  - Ben-Ami R
AU  - Loparev VN
AU  - Litvintseva AP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00176-18.

PMID- 22675593
VI  - 6
DP  - 2012
TI  - Complete genome sequence of Paenibacillus sp. strain JDR-2.
PG  - 1-10
AB  - Paenibacillus sp. strain JDR-2, an aggressively xylanolytic bacterium isolated from sweetgum
      (Liquidambar styraciflua) wood, is able to efficiently depolymerize, assimilate and metabolize
      4-O-methylglucuronoxylan, the predominant structural component of hardwood hemicelluloses. A
      basis for this capability was first supported by the identification of genes and
      characterization of encoded enzymes and has been further defined by the sequencing and
      annotation of the complete genome, which we describe. In addition to genes implicated in the
      utilization of a-1,4-xylan, genes have also been identified for the utilization of other
      hemicellulosic polysaccharides. The genome of Paenibacillus sp. JDR-2 contains 7,184,930 bp in
      a single replicon with 6,288 protein-coding and 122 RNA genes. Uniquely prominent are 874
      genes encoding proteins involved in carbohydrate transport and metabolism. The prevalence and
      organization of these genes support a metabolic potential for bioprocessing of hemicellulose
      fractions derived from lignocellulosic resources.
AU  - Chow V et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 6: 1-10.

PMID- 21551292
VI  - 193
DP  - 2011
TI  - Genome sequence of Vibrio rotiferianus strain DAT722.
PG  - 3381-3382
AB  - Vibrio rotiferianus is a marine pathogen capable of causing disease in various aquatic
      organisms. We announce the genome sequence of V.
      rotiferianus DAT722, which has a large chromosomal integron containing 116
      gene cassettes and is a model organism for studying the role of this
      system in vibrio evolution.
AU  - Chowdhury PR
AU  - Boucher Y
AU  - Hassan KA
AU  - Paulsen IT
AU  - Stokes HW
AU  - Labbate M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3381-3382.

PMID- 21518841
VI  - 55
DP  - 2011
TI  - Dissemination of multiple drug resistance genes by class 1 integrons in Klebsiella pneumoniae isolates from four countries: a comparative study.
PG  - 3140-3149
AB  - A comparative genetic analysis of 42 clinical Klebsiella pneumoniae isolates, resistant to two
      or more antibiotics belonging to the broad-spectrum beta-lactam group, sourced from Sydney,
      Australia, and three South American countries is presented. The study focuses on the genetic
      contexts of class 1 integrons, mobilizable genetic elements best known for their role in the
      rapid evolution of antibiotic resistance among Gram-negative pathogens. It was found that the
      class 1 integrons in this cohort were located in a number of different genetic contexts with
      clear regional differences. In Sydney, IS26-associated Tn21-like transposons on IncL/M
      plasmids contribute greatly to the dispersal of integron-associated multiple-drug-resistant
      (MDR) loci. In contrast, in the South American countries, Tn1696-like transposons on an IncA/C
      plasmid(s) appeared to be disseminating a characteristic MDR region. A range of mobile genetic
      elements is clearly being recruited by clinically important mobile class 1 integrons, and
      these elements appear to be becoming more common with time. This in turn is driving the
      evolution of complex and laterally mobile MDR units and may further complicate antibiotic
      therapy.
AU  - Chowdhury PR
AU  - Ingold A
AU  - Vanegas N
AU  - Martinez E
AU  - Merlino J
AU  - Merkier AK
AU  - Castro M
AU  - Rocha GG
AU  - Borthagaray G
AU  - Centron D
AU  - Toledo HB
AU  - Marquez CM
AU  - Stokes HW
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2011 55: 3140-3149.

PMID- Not included in PubMed...
VI  - 2
DP  - 1984
TI  - DNA modification methylases:  New uses in the manipulation of DNA.
PG  - 218-221
AB  - None
AU  - Christ C
AU  - Nelson M
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 1984 2: 218-221.

PMID- 10601013
VI  - 18
DP  - 1999
TI  - The monomeric homing endonuclease PI-SceI has two catalytic centres for cleavage of the two strands of its DNA substrate.
PG  - 6908-6916
AB  - The monomeric homing endonuclease PI-SceI cleaves the two strands of its DNA substrate in a
      concerted manner, which raises the question of whether this enzyme harbours one or two
      catalytic centres. If PI-SceI has only one catalytic centre, one would expect that
      cross-linking enzyme and substrate should prevent reorientation of the enzyme required to
      perform the second cut after having made the first cut: PI-SceI, however, when cross-linked to
      its substrate, is able to cleave both DNA strands. If PI-SceI has two catalytic centres, one
      would expect that it should be possible to inactivate one catalytic centre by mutation and
      obtain a variant with preference for a substrate nicked in one strand; such variants have been
      found. The structural homology between the catalytic domain of PI-SceI having a pseudo 2-fold
      symmetry, and I-CreI, a homodimeric homing endonuclease, suggests that in PI-SceI active site
      I, which attacks the top strand, comprises Asp218, Asp229 and Lys403, while Asp326, Thr341 and
      Lys301 make up active site II, which cleaves the bottom strand. Cleavage experiments with
      modified oligodeoxynucleotides and metal ion mapping experiments demonstrate that PI-SceI
      interacts differently with the two strands at the cleavage position, supporting a model of two
      catalytic centres.
AU  - Christ F
AU  - Schoettler S
AU  - Wende W
AU  - Steuer S
AU  - Pingoud A
AU  - Pingoud V
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1999 18: 6908-6916.

PMID- 10891273
VI  - 300
DP  - 2000
TI  - A model for the PI-SceIxDNA complex based on multiple base and phosphate backbone-specific photocross-links.
PG  - 867-875
AB  - We have synthesized different oligodeoxynucleotides carrying, in single positions of the >36
      bp recognition site of PI-SceI, photoreactive base analogues (5-iododeoxypyrimidines) or
      phosphate modifications (p-azidophenacylphosphorothioates) and used them in photocross-linking
      experiments with PI-SceI to probe the protein-DNA interface of the specific complex between
      the homing endonuclease PI-SceI and its DNA substrate. One base-specific and several
      backbone-specific cross-links were analyzed in detail: the cross-linking positions were
      identified by Edman degradation of isolated cross-linked peptide x oligodeoxynucleotide
      adducts
      and confirmed by site-directed mutagenesis. Based on these results and the crystal structure
      of PI-SceI, a model for the structure of the PI-SceI x DNA complex is proposed.
AU  - Christ F
AU  - Steuer S
AU  - Thole H
AU  - Wende W
AU  - Pingoud A
AU  - Pingoud V
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2000 300: 867-875.

PMID- 29798930
VI  - 6
DP  - 2018
TI  - High-Quality Draft Genome Sequence of Sphaerisporangium cinnabarinum ATCC 31213.
PG  - e00456-18
AB  - A high-quality draft genome sequence of Sphaerisporangium cinnabarinum ATCC 31213 is presented
      here. This bacterium produces several important bioactive compounds
      and may also produce functional amyloids. This is the first sequenced genome from
      the genus Sphaerisporangium, and it will be essential in determining the nature
      of the potential amyloid protein.
AU  - Christensen LFB
AU  - Otzen D
AU  - Dueholm MS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00456-18.

PMID- 14702296
VI  - 186
DP  - 2004
TI  - The methyltransferase from the LlaDII restriction-modification system influences the level of expression of its own gene.
PG  - 287-295
AB  - The type II restriction-modification (R-M) system LlaDII isolated from Lactococcus lactis
      contains two tandemly arranged genes, llaDIIR and llaDIIM, encoding a restriction endonuclease
      (REase) and a methyltransferase (MTase), respectively. Interestingly, two LlaDII recognition
      sites are present in the llaDIIM promoter region, suggesting that they may influence the
      activity of the promoter through methylation status. In this study, separate promoters for
      llaDIIR and llaDIIM were identified, and the regulation of the two genes at the
      transcriptional level was investigated. DNA fragments containing the putative promoters were
      cloned in a promoter probe vector and tested for activity in the presence and absence of the
      active MTase. The level of expression of the MTase was 5- to 10-fold higher than the level of
      expression of the REase. The results also showed that the presence of M.LlaDII reduced the in
      vivo expression of the llaDIIM promoter (P(llaDIIM)) up to 1,000-fold, whereas the activity of
      the llaDIIR promoter (P(llaDIIR)) was not affected. Based on site-specific mutations it was
      shown that both of the LlaDII recognition sites within P(llaDIIM) are required to obtain
      complete repression of transcriptional activity. No regulation was found for llaDIIR, which
      appears to be constitutively expressed.
AU  - Christensen LL
AU  - Josephsen J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2004 186: 287-295.

PMID- 7638194
VI  - 92
DP  - 1995
TI  - 5-methyl-2'-deoxycytidine in single-stranded DNA can act in cis to signal de novo DNA methylation.
PG  - 7347-7351
AB  - Methylation of cytosine residues in DNA plays an important role in regulating gene expression
      during vertebrate embryonic development.  Conversely, disruption of normal patterns of
      methylation is common in tumors and occurs early in progression of some human cancers.  In
      vertebrates, it appears that the same DNA methyltransferase maintains preexisting patterns of
      methylation during DNA replication and carries out de novo methylation to create new
      methylation patterns.  There are several indications that inherent signals in DNA structure
      can act in vivo to initiate or block de novo methylation in adjacent DNA regions.  To identify
      sequences capable of enhancing de novo methylation of DNA in vitro, we designed a series of
      oligodeoxyribonucleotide substrates with substrate cytosine residues in different sequence
      contexts.  We obtained evidence that some 5-methylcytosine residues in these single-stranded
      DNAs can stimulate de novo methylation of adjacent sites by murine DNA 5-cytosine
      methyltransferase as effectively as 5-methylcytosine residues in double-stranded DNA stimulate
      maintenance methylation.  This suggests that double-stranded DNA may not be the primary
      natural substrate for de novo methylation and that looped single-stranded structures formed
      during the normal course of DNA replication or repair serve as "nucleation" sites for de novo
      methylation of adjacent DNA regions.
AU  - Christman JK
AU  - Sheikhnejad G
AU  - Marasco CJ
AU  - Sufrin JR
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1995 92: 7347-7351.

PMID- 24675849
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of a New Homofermentative, Lactic Acid-Producing Enterococcus faecalis Isolate, CBRD01.
PG  - e00147-14
AB  - We report here the draft genome sequence of the novel homofermentative Enterococcus faecalis
      isolate CBRD01, which is capable of high lactic acid
      productivity and yields, with minimal nutritional requirements. The genome is 2.8
      Mbp, with 37% G+C, and contains genes for two lactate dehydrogenase (LDH) enzymes
      found in related organisms.
AU  - Christopher LP
AU  - Kapatral V
AU  - Vaisvil B
AU  - Emel G
AU  - Deveaux LC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00147-14.

PMID- 1762916
VI  - 19
DP  - 1991
TI  - Purification and substrate specificity of a T4 phage intron-encoded endonuclease.
PG  - 6863-6869
AB  - The T4 phage td intron-encoded endonuclease (I-Tev I) cleaves the intron-deleted
      td gene (td-delta-I) 23 nucleotides upstream of the intron insertion site on the noncoding
      strand and
      25 nucleotides upstream of this site on the coding strand, to generate a 2-base hydroxyl
      overhang
      in the 3' end of each DNA strand.  I-Tev I-157, a truncated form in which slightly more than
      one
      third (88 residues) of the endonuclease is deleted, was purified to homogeneity and shown to
      possess endonuclease activity similar to that of I-Tev I, the full-length enzyme (245
      residues).  The
      minimal length of the td-delta-I gene that was cleaved by I-Tev I and I-Tev I-157 has been
      determined to be exactly 39 basepairs, from -27 (upstream in exon1) to +12 (downstream in
      exon2) relative to the intron insertion site.  Similar to the full-length endonuclease, I-Tev
      I-157 cuts
      the intronless thymidylate synthase genes from such diverse organisms as Escherichia coli,
      Lactobacillus casei and the human.  The position and nature of the in vitro endonucleolytic
      cut in
      these genes are homologous to those in td-delta-I.  Point mutational analysis of the
      td-delta-I
      substrate based on the deduced consensus nucleotide sequence has revealed a very low degree of
      specificity on either side of the cleavage site, for both the full-length and truncated I-Tev
      I.
AU  - Chu FK
AU  - Maley F
AU  - Wang A-M
AU  - Pedersen-Lane J
AU  - Maley G
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 6863-6869.

PMID- 2159153
VI  - 87
DP  - 1990
TI  - Characterization of the restriction site of a prokaryotic intron-encoded endonuclease.
PG  - 3574-3578
AB  - The 1016-base-pair (bp) intron in the T4 bacteriophage thymidylate
      synthase gene (td) contains a 735-bp open reading frame that encodes a protein product
      with endonucleolytic activity.  The endonuclease shows specificity for the intronless form
      of the td gene.  Highly purified endonuclease cleaves the DNA of the intronless form of the
      td gene in vitro at 24 bp upstream of the exon 1-exon 2 junction, generating a 2-base
      staggered cut with 3'-hydroxyl overhangs.  Although the endonuclease cleaves in exon 1, it
      requires some exon 2 sequence for recognition.  The maximum recognition sequence lies in
      an 87-bp stretch, from 52 bp upstream to 35 bp downstream of the cleavage site, ending at
      11 bp into exon 2.  The td intron endonuclease appears involved in the conversion of the
      intronless form of td to intron-containing td gene in the T-even phages.  A role for intron
      mobility is discussed.
AU  - Chu FK
AU  - Maley G
AU  - Pedersen-Lane J
AU  - Wang A-M
AU  - Maley F
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1990 87: 3574-3578.

PMID- 6328492
VI  - 81
DP  - 1984
TI  - Intervening sequence in the thymidylate synthase gene of bacteriophage T4.
PG  - 3049-3053
AB  - The continuous sequence of 2.3 kilobases in a 3-kilobase DNA fragment encoding the structural
      gene for coliphage T4 thymidylate synthase (5,10-methylenetetrahydrofolate:dUMP
      C-methyltranferase, EC 2.1.1.45) was determined by using the M13 dideoxy chain-termination
      method. From the coding information within this gene and that provided by sequence analysis of
      selected CNBr peptides from the protein product, the primary structure of T4 thymidylate
      synthase was determined. The most significant finding of these studies is the presence of a
      1017-base-pair interruption two-thirds of the way through the nucleotide sequence of the
      structural gene. The 5'- and 3'-terminal ends of this intron are demarcated by an apparent
      stop and start codon, respectively. The corresponding methionine preceding the second coding
      region of the synthase is not incorporated into the final protein product. Structural evidence
      confirming the presence of the intervening sequence in the phage genome was obtained by
      restriction and hybridization analysis. Support for the presence of the intron was also
      obtained at the functional level by enzyme expression studies using selected td gene
      fragments. This work also confirms the findings of Purohit and Mathews, which reveal that the
      termination codon for the dihydrofolate reductase gene and the triplet intitiating thymidylate
      synthase overlap by a four-base stretch, A-T-G-A. The implications of this unusual gene
      arrangement are discussed.
AU  - Chu FK
AU  - Maley GF
AU  - Maley F
AU  - Belfort M
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1984 81: 3049-3053.

PMID- 3698096
VI  - 45
DP  - 1986
TI  - Characterization of the intron in the phage T4 thymidylate synthase gene and evidence for its self-excision from the primary transcript.
PG  - 157-166
AB  - The td gene contains a 735 bp open reading frame within its 1017 bp intron. A 12 nucleotide
      stretch may form a stable secondary structure with the putative Shine-Dalgarno sequence of the
      intron open reading frame and thus impair its translation. SP6 RNA polymerase transcripts of
      the td gene synthesized in vitro at 40oC encompass a 2.7 kb primary transcript, a 1.7 kb mRNA,
      and a 1 kb intron RNA. The excised intron RNA consisted of linear and cyclized forms. RNAase H
      studies and resistance of the cyclized intron to linearization by HeLa cell debranching enzyme
      suggest it to be circular. Self-splicing of isolated td primary transcript occurred only
      marginally at 28oC, but increased progressively to 50oC, and required the presence of both
      Mg++ and a guanosine cofactor. An internal guide sequence is evident which may align the 5'
      splice site with the 3' end, presumably for precise exon ligation.
AU  - Chu FK
AU  - Maley GF
AU  - West DK
AU  - Belfort M
AU  - Maley F
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1986 45: 157-166.

PMID- 21994928
VI  - 193
DP  - 2011
TI  - Genome Sequence of Mycoplasma capricolum subsp. capripneumoniae Strain M1601.
PG  - 6098-6099
AB  - Mycoplasma capricolum subsp. capripneumoniae is the causative agent of contagious caprine
      pleuropneumonia, a devastating disease of goats listed
      by the World Organization for Animal Health. Here we report the first
      complete genome sequence of this organism (strain M1601, a clinically
      isolated strain from China).
AU  - Chu Y
AU  - Gao P
AU  - Zhao P
AU  - He Y
AU  - Liao N
AU  - Jackman S
AU  - Zhao Y
AU  - Birol I
AU  - Duan X
AU  - Lu Z
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6098-6099.

PMID- 20729356
VI  - 192
DP  - 2010
TI  - Complete genome sequence of Staphylococcus aureus strain JKD6159, a unique Australian clone of ST93-IV community methicillin-resistant Staphylococcus  aureus.
PG  - 5556-5557
AB  - Community methicillin-resistant Staphylococcus aureus (cMRSA) is an emerging issue that has
      resulted in multiple worldwide epidemics. We
      report the first complete genome sequence of an ST93-MRSA-IV clinical
      isolate that caused severe invasive infection and a familial outbreak of
      skin infection. This isolate is a representative of the most common
      Australian clone of cMRSA that is more distantly related to the previously
      sequenced genomes of S. aureus.
AU  - Chua K
AU  - Seemann T
AU  - Harrison PF
AU  - Davies JK
AU  - Coutts SJ
AU  - Chen H
AU  - Haring V
AU  - Moore R
AU  - Howden BP
AU  - Stinear TP
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 5556-5557.

PMID- 24526641
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Two Cellulolytic Paenibacillus sp. Strains, MAEPY1 and  MAEPY2, from Malaysian Landfill Leachate.
PG  - e00065-14
AB  - We report the draft genome sequences of two Paenibacillus species with cellulose-degrading
      abilities isolated from landfill leachate. An array of genes
      putatively involved in cellulose degradation have been identified in both genome
      sequences, which can benefit various biotechnological industries.
AU  - Chua P
AU  - Yoo HS
AU  - Gan HM
AU  - Lee SM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00065-14.

PMID- 27979953
VI  - 4
DP  - 2016
TI  - Genome Sequence of 'Anthococcus,' a Novel Genus of the Family Streptococcaceae Isolated from Flowers.
PG  - e01410-16
AB  - Here, we report the draft whole-genome sequence of 'Anthococcus,' a novel genus of the
      family Streptococcaceae isolated from fresh flowers of a durian (Durio
      zibethinus) tree. The draft genome of Anthococcus sp. strain DF1 contains
      2,157,756 bp, with a G+C content of 33.0%.
AU  - Chuah LO
AU  - Yap KP
AU  - Thong KL
AU  - Liong MT
AU  - Ahmad R
AU  - Shamila-Syuhada AK
AU  - Rusul G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01410-16.

PMID- 8632476
VI  - 257
DP  - 1996
TI  - Characterisation of independent DNA and multiple Zn-binding domains at the N terminus of human DNA-(cytosine-5) methyltransferase: Modulating the property of a DNA-binding domain by contiguous Zn-binding motifs.
PG  - 935-948
AB  - We report here a detailed mapping and characterisation of a DNA-binding domain
      at the N terminus of human DNA-(cytosine-5) methyltransferase.  A small region, B1 (codon 202
      to 369), was first identified by its Zn- and gross DNA-binding properties.  Further
      fine-mapping
      using deletion and point mutation analysis shows that the DNA- and Zn-binding domains involve
      separate peptide motifs, KRRKTTPKEPTEKK (codons 202 to 215) for a bipartite DNA-binding
      oligopeptide (DB1) and Cx2CX13HX2D(X)23EX2EX13CX3H (codons 232 to 297) for possibly
      two contiguous Zn-binding domains (Azn), which can function independently.  However, B1
      (containing DB1 and AZn) differs from DB1 because it does not bind to a 30 base-pair duplex.
      Interestingly, H3 codons 202 to 974, which encloses B1 and B2 (containing the Zn-binding
      CX2CX2CX4CX2CX2C motif from codon 533 to 550) binds preferentially to 0.8 kb duplexes,
      compared with 0.4 and 0.6 kb duplexes.  As the homologous murine B1, which targets the murine
      methylase to replication foci, also binds to DNA and Zn, it is possible that the N terminus of
      mammalian methylase may be involved in sensing the appropriate length of newly synthesized
      DNA before methylation by its C terminus.  This may enable a time delay for the transient
      existence of hemi-methylation sites for their unknown biological functions in mammals.
AU  - Chuang LS-H
AU  - Ng H-H
AU  - Chia J-N
AU  - Li BFL
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1996 257: 935-948.

PMID- 9302295
VI  - 277
DP  - 1997
TI  - Human DNA-(cytosine-5) methyltransferase-PCNA complex as a target for p21WAF1.
PG  - 1996-2000
AB  - DNA-(cytosine-5) methyltransferase (MCMT) methylates newly replicated mammalian DNA, but the
      factors regulating this activity are unknown.  Here, MCMT is shown to bind proliferating cell
      nuclear antigen, an auxiliary factor for DNA replication and repair.  Binding of PCNA requires
      amino acids 163 to 174 of MCMT, occurs in intact cells at foci of newly replicated DNA, and
      does not alter MCMT activity.  A peptide derived from the cell cycle regulator p21WAF1 can
      disrupt the MCMT-PCNA interaction, which suggests that p21WAF1 may regulate methylation by
      blocking access of MCMT to PCNA.  MCMT and p21WAF1 may be linked in a regulatory pathway,
      because the extents of their expression are inversely related in both SV40-transformed and
      nontransformed cells.
AU  - Chuang LSH
AU  - Ian H-I
AU  - Koh TW
AU  - Ng H-H
AU  - Xu G
AU  - Li BFL
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1997 277: 1996-2000.

PMID- 11912126
VI  - 62
DP  - 2002
TI  - Selective depletion of human DNA-methyltransferase DNMT1 proteins by sulfonate-derived methylating agents.
PG  - 1592-1597
AB  - 5-Methylcytosine residues in the DNA (DNA methylation) are formed from the transfer of the
      methyl group from S-adenosylmethionine to the C-5
      position of cytosine by the DNA-(cytosine-5) methyltransferases
      (DNMTs). Although regional hypermethylation and global hypomethylation
      of the genome are commonly observed in neoplastic cells, how these
      aberrant methylation patterns occur remains unestablished. We report
      here that sulfonate-derived methylating agents, unlike
      N-methylnitrosourea or iodomethane, are potent in depleting DNMT1
      proteins in human cells, in addition to their DNA-damaging properties.
      Their effects on cellular DNMT1 are time and dosage dependent but
      independent of cell type. Unlike gamma-irradiation, these agents
      apparently do not activate the p53/p21(WAF1) DNA damage response
      pathway to deplete the DNMT1 proteins because cells with wild-type,
      mutated, or inactivated p53 behave similarly. However, cell cycle
      analysis and protease assay studies strongly suggest that
      methylmethanesulfonate may activate a cellular protease to degrade
      DNMT1. These results explain why reported observations on the effect of
      alkylating agents on DNMT1 activities in human cells vary significantly
      and provide a crucial link to understand the mechanism behind genomic
      hypomethylation.
AU  - Chuang LSH
AU  - Tan EHH
AU  - Oh HK
AU  - Li BFL
PT  - Journal Article
TA  - Cancer Res.
JT  - Cancer Res.
SO  - Cancer Res. 2002 62: 1592-1597.

PMID- 28408690
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Tetragenococcus muriaticus Strains 3MR10-3 and PMC-11-5 Isolated from Thai Fish Sauce during Natural Fermentation.
PG  - e00198-17
AB  - Tetragenococcus muriaticus strains 3MR10-3 and PMC-11-5 are homofermentative halophilic lactic
      acid bacteria isolated from Thai fish sauce during natural
      fermentation. Their draft genomes were sequenced. Our interest in these organisms
      is related to their impact on fish sauce flavor and their high osmotolerance.
AU  - Chuea-Nongthon C
AU  - Rodtong S
AU  - Yongsawatdigul J
AU  - Steele JL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00198-17.

PMID- 22988113
VI  - 109
DP  - 2012
TI  - Strain-dependent diversity in the Pseudomonas aeruginosa quorum-sensing regulon.
PG  - E2823-E2831
AB  - Quorum sensing allows bacteria to sense and respond to changes in population
      density. Acyl-homoserine lactones serve as quorum-sensing signals for many
      Proteobacteria, and acyl-homoserine lactone signaling is known to control
      cooperative activities. Quorum-controlled activities vary from one species to
      another. Quorum-sensing controls a constellation of genes in the opportunistic
      pathogen Pseudomonas aeruginosa, which thrives in a number of habitats ranging
      from soil and water to animal hosts. We hypothesized that there would be
      significant variation in quorum-sensing regulons among strains of P. aeruginosa
      isolated from different habitats and that differences in the quorum-sensing
      regulons might reveal insights about the ecology of P. aeruginosa. As a test of
      our hypothesis we used RNA-seq to identify quorum-controlled genes in seven P.
      aeruginosa isolates of diverse origins. Although our approach certainly overlooks
      some quorum-sensing-regulated genes we found a shared set of genes, i.e., a core
      quorum-controlled gene set, and we identified distinct, strain-variable sets of
      quorum-controlled genes, i.e., accessory genes. Some quorum-controlled genes in
      some strains were not present in the genomes of other strains. We detected a
      correlation between traits encoded by some genes in the strain-variable subsets
      of the quorum regulons and the ecology of the isolates. These findings indicate a
      role for quorum sensing in extension of the range of habitats in which a species
      can thrive. This study also provides a framework for understanding the molecular
      mechanisms by which quorum-sensing systems operate, the evolutionary pressures by
      which they are maintained, and their importance in disparate ecological contexts.
AU  - Chugani S
AU  - Kim BS
AU  - Phattarasukol S
AU  - Brittnacher MJ
AU  - Choi SH
AU  - Harwood CS
AU  - Greenberg EP
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2012 109: E2823-E2831.

PMID- 17442645
VI  - 1774
DP  - 2007
TI  - An EcoRI-RsrI chimeric restriction endonuclease retains parental sequence specificity.
PG  - 583-594
AB  - To test their structural and functional similarity, hybrids were constructed between EcoRI and
      RsrI, two restriction endonucleases recognizing the same DNA sequence and sharing 50% amino
      acid sequence identity. One of the chimeric proteins (EERE), in which the EcoRI segment
      His147-Ala206 was replaced with the corresponding RsrI segment, showed EcoRI/RsrI-specific
      endonuclease activity. EERE purified from inclusion bodies was found to have approximately
      100-fold weaker activity but higher specific DNA binding affinity, than EcoRI. Increased
      binding is consistent with results of molecular dynamics simulations, which indicate that the
      number of hydrogen bonds formed with the recognition sequence increased in the chimera as
      compared to EcoRI. The success of obtaining an EcoRI-RsrI hybrid endonuclease, which differs
      from EcoRI by 22 RsrI-specific amino acid substitutions and still preserves canonical cleavage
      specificity, is a sign of structural and functional similarity shared by the parental enzymes.
      This conclusion is also supported by computational studies, which indicate that construction
      of the EERE chimera did not induce substantial changes in the structure of EcoRI.
      Surprisingly, the chimeric endonuclease was more toxic to cells not protected by EcoRI
      methyltransferase, than the parental EcoRI mutant. Molecular modelling revealed structural
      alterations, which are likely to impede coupling between substrate recognition and cleavage
      and suggest a possible explanation for the toxic phenotype.
AU  - Chuluunbaatar T
AU  - Ivanenko-Johnston T
AU  - Fuxreiter M
AU  - Meleshko R
AU  - Rasko T
AU  - Simon I
AU  - Heitman J
AU  - Kiss A
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 2007 1774: 583-594.

PMID- 28725337
VI  - 12
DP  - 2017
TI  - Complete genome sequence of Leuconostoc suionicum DSM 20241T provides insights into its functional and metabolic features.
PG  - 38
AB  - The genome of Leuconostoc suionicum DSM 20241T (=ATCC 9135T = LMG 8159T = NCIMB 6992T) was
      completely sequenced and its fermentative metabolic pathways were
      reconstructed to investigate the fermentative properties and metabolites of
      strain DSM 20241T during fermentation. The genome of L. suionicum DSM 20241T
      consists of a circular chromosome (2026.8 Kb) and a circular plasmid (21.9 Kb)
      with 37.58% G + C content, encoding 997 proteins, 12 rRNAs, and 72 tRNAs.
      Analysis of the metabolic pathways of L. suionicum DSM 20241T revealed that
      strain DSM 20241T performs heterolactic acid fermentation and can metabolize
      diverse organic compounds including glucose, fructose, galactose, cellobiose,
      mannose, sucrose, trehalose, arbutin, salcin, xylose, arabinose and ribose.
AU  - Chun BH
AU  - Lee SH
AU  - Jeon HH
AU  - Kim DW
AU  - Jeon CO
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 38.

PMID- 22815438
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Bacillus anthracis H9401, an Isolate from a Korean Patient with Anthrax.
PG  - 4116-4117
AB  - Bacillus anthracis H9401 (NCCP 12889) is an isolate from a Korean patient with
      gastrointestinal anthrax. The whole genome of H9401 was sequenced. It is a
      circular chromosome containing 5,480 open reading frames (ORFs) and two plasmids,
      pXO1 containing 202 ORFs and pXO2 containing 110 ORFs. H9401 shows high
      pathogenicity and genome sequence similarity to Ames Ancestor.
AU  - Chun JH
AU  - Hong KJ
AU  - Cha SH
AU  - Cho MH
AU  - Lee KJ
AU  - Jeong DH
AU  - Yoo CK
AU  - Rhie GE
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4116-4117.

PMID- 23658781
VI  - 8
DP  - 2013
TI  - Construction of a stable replicating shuttle vector for Caldicellulosiruptor species: use for extending genetic methodologies to other members of this genus.
PG  - e62881
AB  - The recalcitrance of plant biomass is the most important barrier to its economic  conversion
      by microbes to products of interest. Thermophiles have special
      advantages for biomass conversion and members of the genus Caldicellulosiruptor
      are the most thermophilic cellulolytic microbes known. In this study, we report
      the construction of a replicating shuttle vector for Caldicellulosiruptor species
      based on pBAS2, the smaller of two native C. bescii plasmids. The entire plasmid
      was cloned into an E. coli cloning vector containing a pSC101 origin of
      replication and an apramycin resistance cassette for selection in E. coli. The
      wild-type C. bescii pyrF locus was cloned under the transcriptional control of
      the regulatory region of the ribosomal protein S30EA (Cbes2105), and the
      resulting vector was transformed into a new spontaneous deletion mutant in the
      pyrFA locus of C. bescii that allowed complementation with the pyrF gene alone.
      Plasmid DNA was methylated in vitro with a recently described cognate
      methyltransferase, M.CbeI, and transformants were selected for uracil
      prototrophy. The plasmid was stably maintained in low copy with selection but
      rapidly lost without selection. There was no evidence of DNA rearrangement during
      transformation and replication in C. bescii. A similar approach was used to
      screen for transformability of other members of this genus using M.CbeI to
      overcome restriction as a barrier and was successful for transformation of C.
      hydrothermalis, an attractive species for many applications. Plasmids containing
      a carbohydrate binding domain (CBM) and linker region from the C. bescii celA
      gene were maintained with selection and were structurally stable through
      transformation and replication in C. bescii and E. coli.
AU  - Chung D
AU  - Cha M
AU  - Farkas J
AU  - Westpheling J
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2013 8: e62881.

PMID- 22928042
VI  - 7
DP  - 2012
TI  - Methylation by a Unique alpha-class N4-Cytosine Methyltransferase Is Required for DNA Transformation of Caldicellulosiruptor bescii DSM6725.
PG  - e43844
AB  - Thermophilic microorganisms capable of using complex substrates offer special advantages for
      the conversion of lignocellulosic biomass to
      biofuels and bioproducts. Members of the Gram-positive bacterial genus
      Caldicellulosiruptor are anaerobic thermophiles with optimum growth
      temperatures between 65 degrees C and 78 degrees C and are the most
      thermophilic cellulolytic organisms known. In fact, they efficiently
      use biomass non-pretreated as their sole carbon source and in
      successive rounds of application digest 70% of total switchgrass
      substrate. The ability to genetically manipulate these organisms is a
      prerequisite to engineering them for use in conversion of these complex
      substrates to products of interest as well as identifying gene products
      critical for their ability to utilize non-pretreated biomass. Here, we
      report the first example of DNA transformation of a member of this
      genus, C. bescii. We show that restriction of DNA is a major barrier to
      transformation (in this case apparently absolute) and that methylation
      with an endogenous unique alpha-class N4-Cytosine methyltransferase is
      required for transformation of DNA isolated from E. coli. The use of
      modified DNA leads to the development of an efficient and reproducible
      method for DNA transformation and the combined frequencies of
      transformation and recombination allow marker replacement between
      non-replicating plasmids and chromosomal genes providing the basis for
      rapid and efficient methods of genetic manipulation.
AU  - Chung D
AU  - Farkas J
AU  - Huddleston JR
AU  - Olivar E
AU  - Westpheling J
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2012 7: e43844.

PMID- 21604181
VI  - 38
DP  - 2011
TI  - Identification and characterization of CbeI, a novel thermostable restriction enzyme from Caldicellulosiruptor bescii DSM 6725 and a member of a new subfamily of HaeIII-like enzymes.
PG  - 1867-1877
AB  - Potent HaeIII-like DNA restriction activity was detected in cell-free extracts of
      Caldicellulosiruptor bescii DSM 6725 using plasmid DNA
      isolated from Escherichia coli as substrate. Incubation of the plasmid
      DNA in vitro with HaeIII methyltransferase protected it from cleavage
      by HaeIII nuclease as well as cell-free extracts of C. bescii. The gene
      encoding the putative restriction enzyme was cloned and expressed in E.
      coli with a His-tag at the C-terminus. The purified protein was 38 kDa
      as predicted by the 981-bp nucleic acid sequence, was optimally active
      at temperatures between 75 degrees C and 85 degrees C, and was stable
      for more than 1 week when stored at 35 degrees C. The cleavage sequence
      was determined to be 50-GG/CC-30, indicating that CbeI is an
      isoschizomer of HaeIII. A search of the C. bescii genome sequence
      revealed the presence of both a HaeIII-like restriction endonuclease
      (Athe 2438) and DNA methyltransferase (Athe 2437). Preliminary analysis
      of other Caldicellulosiruptor species suggested that this
      restriction/modification activity is widespread in this genus. A
      phylogenetic analysis based on sequence alignment and conserved motif
      searches identified features of CbeI distinct from other members of
      this group and classified CbeI as a member of a novel subfamily of
      HaeIII-like enzymes.
AU  - Chung DH
AU  - Huddleston JR
AU  - Farkas J
AU  - Westpheling J
PT  - Journal Article
TA  - J. Ind. Microbiol. Biotechnol.
JT  - J. Ind. Microbiol. Biotechnol.
SO  - J. Ind. Microbiol. Biotechnol. 2011 38: 1867-1877.

PMID- 
VI  - 6
DP  - 2013
TI  - Overcoming restriction as a barrier to DNA transformation in Caldicellulosiruptor species results in efficient marker replacement.
PG  - 16187
AB  - Background: Thermophilic microorganisms have special advantages for the conversion of plant
      biomass to fuels and chemicals. Members of the genus Caldicellulosiruptor are the most
      thermophilic cellulolytic bacteria known. They have the ability to grow on a variety of
      non-pretreated biomass substrates at or near similar to 80 degrees C and hold promise for
      converting biomass to bioproducts in a single step. As for all such relatively uncharacterized
      organisms with desirable traits, the ability to genetically manipulate them is a prerequisite
      for making them useful. Metabolic engineering of pathways for product synthesis is relatively
      simple compared to engineering the ability to utilize non-pretreated biomass. Results: Here we
      report the construction of a deletion of cbeI (Cbes2438), which encodes a restriction
      endonuclease that is as a major barrier to DNA transformation of C. bescii. This is the first
      example of a targeted chromosomal deletion generated by homologous recombination in this genus
      and the resulting mutant, JWCB018 (Delta pyrFA Delta cbeI), is readily transformed by DNA
      isolated from E. coli without in vitro methylation. PCR amplification and sequencing suggested
      that this deletion left the adjacent methyltransferase (Cbes2437) intact. This was confirmed
      by the fact that DNA isolated from JWCB018 was protected from digestion by CbeI and HaeIII.
      Plasmid DNA isolated from C. hydrothermalis transformants were readily transformed into C.
      bescii. Digestion analysis of chromosomal DNA isolated from seven Caldicellulosiruptor species
      by using nine different restriction endonucleases was also performed to identify the
      functional restriction-modification activities in this genus. Conclusion: Deletion of the cbeI
      gene removes a substantial barrier to routine DNA transformation and chromosomal modification
      of C. bescii. This will facilitate the functional analyses of genes as well as metabolic
      engineering for the production of biofuels and bioproducts from biomass. An analysis of
      restriction-modification activities in members of this genus suggests a way forward to
      eliminating restriction as a barrier to DNA transformation and efficient genetic manipulation
      of this important group of hyperthermophiles.
AU  - Chung DW
AU  - Farkas J
AU  - Westpheling J
PT  - Journal Article
TA  - Biotechnol. Biofuels.
JT  - Biotechnol. Biofuels.
SO  - Biotechnol. Biofuels. 2013 6: 16187.

PMID- 29700134
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Paucibacter aquatile CR182(T), a Strain with Antimicrobial Activity Isolated from Freshwater of Nakdong River in South Korea.
PG  - e00194-18
AB  - This report details a draft genome sequence of Paucibacter aquatile CR182(T), isolated from
      river water, which contains 5,523,543 bp, has a G+C content of
      66.3%, and harbors 4,544 protein-coding genes in 4 contigs. These genome data
      provide insights into the genetic basis of this strain's antibacterial activity
      and adaptive mechanisms.
AU  - Chung EJ
AU  - Choi GG
AU  - Nam YH
AU  - Choi A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00194-18.

PMID- 18586945
VI  - 190
DP  - 2008
TI  - The Complete Genome Sequence of Neisseria gonorrhoeae NCCP11945.
PG  - 6035-6036
AB  - Neisseria gonorrhoeae is an obligate human pathogen that is the etiological agent of
      gonorrhea. We explored variations in genes of a
      multidrug-resistant N. gonorrhoeae Korean patient isolate in an effort to
      understand the prevalence, antibiotic resistance, and importance of
      horizontal gene transfer within this important, naturally competent
      organism. Here we report the complete annotated genome sequence of N.
      gonorrhoeae strain NCCP11945.
AU  - Chung GT
AU  - Yoo JS
AU  - Oh HB
AU  - Lee YS
AU  - Cha SH
AU  - Kim SJ
AU  - Yoo CK
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2008 190: 6035-6036.

PMID- 29122864
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of Mycobacteriophages Clautastrophe, Kingsolomon, Krypton555, and Nicholas.
PG  - e01129-17
AB  - We report here the complete genome sequences of four subcluster L3 mycobacteriophages newly
      isolated from soil samples, using Mycobacterium
      smegmatis mc(2)155 as the host. Comparative genomic analyses with four previously
      described subcluster L3 phages reveal strong nucleotide similarity and gene
      conservation, with several large insertions/deletions near their right genome
      ends.
AU  - Chung HM et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01129-17.

PMID- 27325916
VI  - 8
DP  - 2016
TI  - Complete genome sequence of Vibrio vulnificus FORC_017 isolated from a patient with a hemorrhagic rash after consuming raw dotted gizzard shad.
PG  - 22
AB  - BACKGROUND: Vibrio vulnificus, a resident in the human gut, is frequently found
      in seafood, causing food-borne illnesses including gastroenteritis and severe
      septicemia. While V. vulnificus has been known to be one of the major food-borne
      pathogens, pathogenicity and virulence factors are not fully understood yet. To
      extend our understanding of the pathogenesis of V. vulnificus at the genomic
      level, the genome of V. vulnificus FORC_017 isolated from a female patient
      experiencing a hemorrhagic rash was completely sequenced and analyzed. RESULTS:
      Three discontinuous contigs were generated from a hybrid assembly using Illumina
      MiSeq and PacBio platforms, revealing that the genome of the FORC_017 consists of
      two circular chromosomes and a plasmid. Chromosome I consists of 3,253,417-bp (GC
      content 46.49 %) containing 2943 predicted open reading frames (ORFs) and
      chromosome II of 1,905,745-bp (GC content 46.90 %) containing 1638 ORFs. The
      plasmid pFORC17 consists of 70,069-bp (GC content 43.77 %) containing 84 ORFs.
      The average nucleotide identity (ANI) value of the FORC_017 and CMCP6 strains was
      98.53, suggesting that they are closely related. CONCLUSIONS:
      Pathogenesis-associated genes including vvhA, rtx gene cluster, and various
      hemolysin genes were present in FORC_017. In addition, three complete secretion
      systems (Type I, II and VI) as well as iron uptake-related genes for virulence of
      the FORC_017 were detected, suggesting that this strain is pathogenic. Further
      comparative genome analysis revealed that FORC_017 and CMCP6 share major toxin
      genes including vvhA and rtx for pathogenesis activities. The genome information
      of the FORC_017 provides novel insights into pathogenicity and virulence factors
      of V. vulnificus.
AU  - Chung HY
AU  - Kim YT
AU  - Kim S
AU  - Na EJ
AU  - Ku HJ
AU  - Lee KH
AU  - Heo ST
AU  - Ryu S
AU  - Kim H
AU  - Choi SH
AU  - Lee JH
PT  - Journal Article
TA  - Gut Pathog.
JT  - Gut Pathog.
SO  - Gut Pathog. 2016 8: 22.

PMID- 27728961
VI  - 26
DP  - 2016
TI  - Genome Sequence of Bacillus cereus FORC_021, a Food-Borne Pathogen Isolated from a Knife at a Sashimi Restaurant.
PG  - 2030-2035
AB  - Bacillus cereus causes food-borne illness through contaminated foods; therefore,
      its pathogenicity and genome sequences have been analyzed in several studies. We
      sequenced and analyzed B. cereus strain FORC_021 isolated from a sashimi
      restaurant. The genome sequence consists of 5,373,294 bp with 35.36% GC contents,
      5,350 predicted CDSs, 42 rRNA genes, and 107 tRNA genes. Based on in silico
      DNA-DNA hybridization values, B. cereus ATCC 14579T was closest to FORC_021 among
      the complete genome-sequenced strains. Three major enterotoxins were detected in
      FORC_021. Comparative genomic analysis of FORC_021 with ATCC 14579T revealed that
      FORC_021 harbored an additional genomic region encoding virulence factors, such
      as putative ADP-ribosylating toxin, spore germination protein, internalin, and
      sortase. Furthermore, in vitro cytotoxicity testing showed that FORC_021
      exhibited a high level of cytotoxicity toward INT-407 human epithelial cells.
      This genomic information of FORC_021 will help us to understand its pathogenesis
      and assist in managing food contamination.
AU  - Chung HY
AU  - Lee KH
AU  - Ryu S
AU  - Yoon H
AU  - Lee JH
AU  - Kim HB
AU  - Kim H
AU  - Jeong HG
AU  - Choi SH
AU  - Kim BS
PT  - Journal Article
TA  - J. Microbiol. Biotechnol.
JT  - J. Microbiol. Biotechnol.
SO  - J. Microbiol. Biotechnol. 2016 26: 2030-2035.

PMID- 29449385
VI  - 6
DP  - 2018
TI  - Complete Genome Sequences of Enterobacter cancerogenus CR-Eb1 and Enterococcus sp. Strain CR-Ec1, Isolated from the Larval Gut of the Greater Wax Moth, Galleria  mellonella.
PG  - e00044-18
AB  - Enterobacter cancerogenus CR-Eb1 and Enterococcus sp. CR-Ec1 were isolated from the larval gut
      of Galleria mellonella, the greater wax moth. Here, we report the
      completed and annotated genome sequences of insect gut-dwelling bacteria.
AU  - Chung JH
AU  - Jeong H
AU  - Ryu CM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00044-18.

PMID- 23558532
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Serratia marcescens WW4.
PG  - e0012613
AB  - Serratia marcescens WW4 is a biofilm-forming bacterium isolated from paper machine aggregates.
      Under conditions of phosphate limitation, this bacterium
      exhibits intergeneric inhibition of Pseudomonas aeruginosa. Here, the complete
      genome sequence of S. marcescens WW4, which consists of one circular chromosome
      (5,241,455 bp) and one plasmid (pSmWW4; 3,248 bp), was determined.
AU  - Chung WC
AU  - Chen LL
AU  - Lo WS
AU  - Kuo PA
AU  - Tu J
AU  - Kuo CH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0012613.

PMID- 27738034
VI  - 4
DP  - 2016
TI  - Genome Sequence of Mycoplasma hyorhinis Isolated from Cell Cultures.
PG  - e01119-16
AB  - Mycoplasmas are major contaminants of mammalian cell cultures. Here, the complete genome
      sequence of Mycoplasma hyorhinis recovered from Madin-Darby bovine kidney
      (MDBK) cells is reported.
AU  - Cibulski SP
AU  - Siqueira FM
AU  - Teixeira TF
AU  - Mayer FQ
AU  - Almeida LG
AU  - Roehe PM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01119-16.

PMID- 25635023
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Pseudomonas fluorescens Strains PA4C2 and PA3G8 and Pseudomonas putida PA14H7, Three Biocontrol Bacteria against Dickeya  Phytopathogens.
PG  - e01503-14
AB  - Pseudomonas fluorescens strains PA4C2 and PA3G8 and Pseudomonas putida strain PA14H7 were
      isolated from potato rhizosphere and show an ability to inhibit the
      growth of Dickeya phytopathogens. Here, we report their draft genome sequences,
      which provide a basis for understanding the molecular mechanisms involved in
      antibiosis against Dickeya.
AU  - Cigna J
AU  - Raoul-des-Essarts Y
AU  - Mondy S
AU  - Helias V
AU  - Beury-Cirou A
AU  - Faure D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01503-14.

PMID- 28126929
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Semiconstitutive Red, Dry, and Rough Biofilm-Forming Commensal and Uropathogenic Escherichia coli Isolates.
PG  - e01249-16
AB  - Strains of Escherichia coli exhibit diverse biofilm formation capabilities. E. coli K-12
      expresses the red, dry, and rough (rdar) morphotype below 30 degrees C,
      whereas clinical isolates frequently display the rdar morphotype
      semiconstitutively. We sequenced the genomes of eight E. coli strains to
      subsequently investigate the molecular basis of semiconstitutive rdar morphotype
      expression.
AU  - Cimdins A
AU  - Luthje P
AU  - Li F
AU  - Ahmad I
AU  - Brauner A
AU  - Romling U
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01249-16.

PMID- 16672467
VI  - 72
DP  - 2006
TI  - Stolbur phytoplasma genome survey achieved using a suppression subtractive hybridization approach with high specificity.
PG  - 3274-3283
AB  - Phytoplasmas are unculturable bacterial plant pathogens transmitted by phloem-feeding
      hemipteran insects. DNA of phytoplasmas is difficult to
      purify because of their exclusive phloem location and low abundance in
      plants. To overcome this constraint, suppression subtractive hybridization
      (SSH) was modified and used to selectively amplify DNA of the stolbur
      phytoplasma infecting a periwinkle plant. Plasmid libraries were
      constructed, and the origins of the DNA inserts were verified by
      hybridization and PCR screenings. After a single round of SSH, there was
      still a significant level of contamination with plant DNA (around 50%).
      However, the modified SSH, which included a second round of subtraction
      (double SSH), resulted in an increased phytoplasma DNA purity (97%).
      Results validated double SSH as an efficient way to produce a genome
      survey for microbial agents unavailable in culture. Assembly of 266 insert
      sequences revealed 181 phytoplasma genetic loci which were annotated.
      Comparative analysis of 113 kbp indicated that among 217 protein coding
      sequences, 83% were homologous to "Candidatus Phytoplasma asteris" (OY-M
      strain) genes, with hits widely distributed along the chromosome. Most of
      the stolbur-specific SSH sequences were orphan genes, with the exception
      of two partial coding sequences encoding proteins homologous to a
      mycoplasma surface protein and riboflavin kinase.
AU  - Cimerman A
AU  - Arnaud G
AU  - Foissac X
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2006 72: 3274-3283.

PMID- 25008981
VI  - 68
DP  - 2014
TI  - PsasM2I, a Type II Restriction-Modification System in Pseudomonas savastanoi pv. savastanoi: Differential Distribution of Carrier Strains in the Environment and the Evolutionary History of Homologous RM Systems in the Pseudomonas syringae Complex.
PG  - 842-858
AB  - A type II restriction-modification system was
      found in a native plasmid of Pseudomonas savastanoi pv.
      savastanoi MLLI2. Functional analysis of the methyltransferase
      showed that the enzyme acts by protecting the DNA sequence
      CTGCAG from cleavage. Restriction endonuclease
      expression in recombinant Escherichia coli cells resulted in
      mutations in the REase sequence or transposition of insertion
      sequence 1A in the coding sequence, preventing lethal gene
      expression. Population screening detected homologous RM
      systems in other P. savastanoi strains and in the Pseudomonas
      syringae complex. An epidemiological survey carried out by
      sampling olive and oleander knots in two Italian regions
      showed an uneven diffusion of carrier strains, whose presence
      could be related to a selective advantage in maintaining the RM
      system in particular environments or subpopulations. Moreover,
      carrier strains can coexist in the same orchards, plants,
      and knot tissues with non-carriers, revealing unexpected genetic
      variability on a very small spatial scale. Phylogenetic analysis
      of the RM system and housekeeping gene sequences in the
      P. syringae complex demonstrated the ancient acquisition of the
      RM systems. However, the evolutionary history of the gene
      complex also showed the involvement of horizontal gene transfer
      between related strains and recombination events.
AU  - Cinelli T
AU  - Moscetti I
AU  - Matchi G
PT  - Journal Article
TA  - Microb. Ecol.
JT  - Microb. Ecol.
SO  - Microb. Ecol. 2014 68: 842-858.

PMID- 23868125
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Hydrogen- and Ethanol-Producing Anaerobic Alkalithermophilic Bacterium Caloramator celer.
PG  - e00471-13
AB  - Caloramator celer strain JW/YL-NZ35 is a Gram-positive thermophilic, alkalitolerant, and
      strictly anaerobic bacterium capable of producing hydrogen
      and ethanol under extreme conditions. The draft genome sequence presented here
      will provide valuable information to further explore the physiology of this
      species and its potential for biofuel production.
AU  - Ciranna A
AU  - Larjo A
AU  - Kivisto A
AU  - Santala V
AU  - Roos C
AU  - Karp M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00471-13.

PMID- 2536753
VI  - 264
DP  - 1989
TI  - Three additional operators, Op21, Op68, and Op88, of bacteriophage P1.
PG  - 3611-3617
AB  - The repressor of bacteriophage P1, encoded by the c1 gene, is responsible for maintaining the
      P1 prophage in the lysogenic state.  Previously, 11 c1 repressor binding sites or operators
      scattered over the whole genome of P1 have been found.  From sequence analysis an asymmetric,
      17-base pair consensus sequence, ATTGCTCTAATAAATTT, was derived.  Using a synthetic
      15-base-long oligodeoxyribonucleotide as operator probe, we have identified three additional
      operators.  We have mapped the operators at the positions 21, 68, and 88 of the P1 genome and
      determined their sequence.  These operators are controlled by c1 because corresponding P1 DNA
      fragments (I) require c1 repressor in vivo in order to be clonable in multicopy plasmids, (ii)
      exhibit a c1-repressible promoter activity, (iii) are retarded by c1 repressor protein during
      electrophoresis, and (iv) contain the 17-base pair consensus sequence with one mismatch base
      each.  Furthermore, we suggest that expression of the DNA adenine methylase (dam) encoded by
      P1 is controlled via Op68.
AU  - Citron M
AU  - Velleman M
AU  - Schuster H
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1989 264: 3611-3617.

PMID- 16617113
VI  - 103
DP  - 2006
TI  - Multireplicon genome architecture of Lactobacillus salivarius.
PG  - 6718-6723
AB  - Lactobacillus salivarius subsp. salivarius strain UCC118 is a bacteriocin-producing strain
      with probiotic characteristics. The 2.13-Mb
      genome was shown by sequencing to comprise a 1.83 Mb chromosome, a 242-kb
      megaplasmid (pMP118), and two smaller plasmids. Megaplasmids previously
      have not been characterized in lactic acid bacteria or intestinal
      lactobacilli. Annotation of the genome sequence indicated an intermediate
      level of auxotrophy compared with other sequenced lactobacilli. No
      single-copy essential genes were located on the megaplasmid. However,
      contingency amino acid metabolism genes and carbohydrate utilization
      genes, including two genes for completion of the pentose phosphate
      pathway, were megaplasmid encoded. The megaplasmid also harbored genes for
      the Abp118 bacteriocin, a bile salt hydrolase, a presumptive conjugation
      locus, and other genes potentially relevant for probiotic properties. Two
      subspecies of L. salivarius are recognized, salivarius and salicinius, and
      we detected megaplasmids in both subspecies by pulsed-field gel
      electrophoresis of sizes ranging from 100 kb to 380 kb. The discovery of
      megaplasmids of widely varying size in L. salivarius suggests a possible
      mechanism for genome expansion or contraction to adapt to different
      environments.
AU  - Claesson MJ
AU  - Li Y
AU  - Leahy S
AU  - Canchaya C
AU  - van Pijkeren JP
AU  - Cerdeno-Tarraga AM
AU  - Parkhill J
AU  - Flynn S
AU  - O'sullivan GC
AU  - Collins JK
AU  - Higgins D
AU  - Shanahan F
AU  - Fitzgerald GF
AU  - van Sinderen D
AU  - O'toole PW
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2006 103: 6718-6723.

PMID- 22493206
VI  - 194
DP  - 2012
TI  - Draft Genome Sequences of Helicobacter pylori Strains 17874 and P79.
PG  - 2402
AB  - Helicobacter pylori is a human pathogen that colonizes the human gastric mucosa,  causing
      gastritis, duodenal and gastric ulcers, and gastric carcinoma. Here we
      announce the draft genomes of H. pylori strain 17874, commonly used for studying
      motility, and P79, a strain for which plasmid vectors have been developed.
AU  - Clancy CD
AU  - Forde BM
AU  - Moore SA
AU  - O'Toole PW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2402.

PMID- 35516
VI  - 137
DP  - 1979
TI  - NgoII, a restriction endonuclease from Neisseria gonorrhoeae.
PG  - 1299-1307
AB  - EndoR.NgoII, a class II restriction endonuclease isolated from Neisseria gonorrhoeae, was
      purified to electrophoretic homogeneity.  We were able to separate it from another restriction
      endonuclease of N. gonorrhoeae, NgoI, by phosphocellulose chromatography.  NgoII is an
      isoschizomer of HaeIII, a restriction endonuclease of Haemophilus aegyptius, and was found to
      recognize the deoxyribonucleic acid nucleotide base sequence GGCC.  NgoII was able to digest
      phage lambda deoxyribonucleic acid over a wide pH range, with optimal activity at pH 8.5.  The
      enzyme has an absolute requirement for Mg2+; maximal enzyme activity was observed at 1 mM
      Mg2+.  The active enzyme has a molecular weight of 65,000 and appears to be composed of six
      subunits of identical molecular weight (11,000).  No methylase activity could be detected in
      the purified enzyme preparation.
      [ The enzyme called NgoI in this abstract has been renamed NgoCI, Jan/1998. ]
      [ The enzyme called NgoII in this abstract has been renamed NgoCII, Jan/1998. ]
AU  - Clanton DJ
AU  - Riggsby WS
AU  - Miller RV
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1979 137: 1299-1307.

PMID- 97270
VI  - 135
DP  - 1978
TI  - Identification of a new sequence-specific endonuclease NgoII, from Neisseria gonorrhoeae.
PG  - 270-273
AB  - A class II restriction endonuclease which recognizes the same nucleotide
      sequence as EndoR-HaeIII has been found in four of seven isolates of Neisseria
      gonorrhoeae.
AU  - Clanton DJ
AU  - Woodward JM
AU  - Miller RV
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1978 135: 270-273.

PMID- 24756024
VI  - 9
DP  - 2014
TI  - DNA Sequence Heterogeneity of Campylobacter jejuni CJIE4 Prophages and Expression of Prophage Genes.
PG  - E95349
AB  - Campylobacter jejuni carry temperate bacteriophages that can affect the biology
      or virulence of the host bacterium. Known effects include genomic rearrangements
      and resistance to DNA transformation. C. jejuni prophage CJIE1 shows sequence
      variability and variability in the content of morons. Homologs of the CJIE1
      prophage enhance both adherence and invasion to cells in culture and increase the
      expression of a specific subset of bacterial genes. Other C. jejuni temperate
      phages have so far not been well characterized. In this study we describe
      investigations into the DNA sequence variability and protein expression in a
      second prophage, CJIE4. CJIE4 sequences were obtained de novo from DNA sequencing
      of five C. jejuni isolates, as well as from whole genome sequences submitted to
      GenBank by other research groups. These CJIE4 DNA sequences were heterogenous,
      with several different insertions/deletions (indels) in different parts of the
      prophage genome. Two variants of a 3-4 kb region inserted within CJIE4 had
      different gene content that distinguished two major conserved CJIE4 prophage
      families. Additional indels were detected throughout the prophage. Detection of
      proteins in the five isolates characterized in our laboratory in isobaric Tags
      for Relative and Absolute Quantitation (iTRAQ) experiments indicated that
      prophage proteins within each of the two large indel variants were expressed
      during growth of the bacteria on Mueller Hinton agar plates. These proteins
      included the extracellular DNase associated with resistance to DNA transformation
      and prophage repressor proteins. Other proteins associated with known or
      suspected roles in prophage biology were also expressed from CJIE4, including
      capsid protein, the phage integrase, and MazF, a type II toxin-antitoxin system
      protein. Together with the results previously obtained for the CJIE1 prophage
      these results demonstrate that sequence variability and expression of moron genes
      are both general properties of temperate bacteriophages in C. jejuni.
AU  - Clark CG
AU  - Chong PM
AU  - McCorrister SJ
AU  - Mabon P
AU  - Walker M
AU  - Westmacott GR
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2014 9: E95349.

PMID- 18366706
VI  - 8
DP  - 2008
TI  - Sequence variability of Campylobacter temperate bacteriophages.
PG  - 49
AB  - Background: Prophages integrated within the chromosomes of Campylobacter jejuni isolates have
      been demonstrated very recently. Prior work with Campylobacter temperate bacteriophages, as
      well as evidence from prophages in other enteric bacteria, suggests these prophages might have
      a
      role in the biology and virulence of the organism. However, very little is known about the
      genetic variability of Campylobacter prophages which, if present, could lead to differential
      phenotypes in isolates carrying the phages versus those that do not. As a first step in the
      characterization of C. jejuni prophages, we investigated the distribution of prophage DNA
      within a C. jejuni population assessed the DNA and protein sequence variability within a
      subset of the putative prophages found.
      Results: Southern blotting of C. jejuni DNA using probes from genes within the three putative
      prophages of the C. jejuni sequenced strain RM 1221 demonstrated the presence of at least one
      prophage gene in a large proportion (27/35) of isolates tested. Of these, 15 were positive for
      5 or
      more of the 7 Campylobacter Mu-like phage 1 (CMLP 1, also designated Campylobacter jejuni
      integrated element 1, or CJIE 1) genes tested. Twelve of these putative prophages were chosen
      for further analysis. DNA sequencing of a 9,000 to 11,000 nucleotide region of each prophage
      demonstrated a close homology with CMLP 1 in both gene order and nucleotide sequence.
      Structural and sequence variability, including short insertions, deletions, and allele
      replacements, were found within the prophage genomes, some of which would alter the protein
      products of the ORFs involved. No insertions of novel genes were detected within the sequenced
      regions. The 12
      prophages and RM 1221 had a % G+C very similar to C. jejuni sequenced strains, as well as
      promoter regions characteristic of C. jejuni. None of the putative prophages were successfully
      induced and propagated, so it is not known if they were functional or if they represented
      remnant
      prophage DNA in the bacterial chromosomes.
      Conclusion: These putative prophages form a family of phages with conserved sequences, and
      appear to be adapted to Campylobacter. There was evidence for recombination among groups of
      prophages, suggesting that the prophages had a mosaic structure. In many of these properties,
      the Mu-like CMLP 1 homologs characterized in this study resemble temperate bacteriophages of
      enteric bacteria that are responsible for contributions to virulence and host adaptation.
AU  - Clark CG
AU  - Ng L-K
PT  - Journal Article
TA  - BMC Microbiol.
JT  - BMC Microbiol.
SO  - BMC Microbiol. 2008 8: 49.

PMID- 10997268
VI  - 29
DP  - 2000
TI  - Extended stability of restriction enzymes at ambient temperatures.
PG  - 536
AB  - The stability of restriction enzymes as supplied by manufacturers without any modification has
      been examined. No reduction in activity
      was observed for three enzymes (HindIII, EcoRI and Tsp5091) held at
      ambient temperature or 4 degrees C for the period of study (12 months),
      while activity was observed for up to 12 weeks after storage at 37
      degrees C, which was considerably better than following desiccation
      with trehalose, a recognized preservation technique. A larger trial of
      23 different restriction enzymes held at room temperature for one week
      showed that all enzymes retained significant activity. As a practical
      demonstration of the usefulness of this finding, enzymes were posted to
      Africa by conventional mail (cost $1 US) and shown to retain activity
      upon arrival after three weeks in transit (compared to a cost of $1000
      US by cold-chain transportation). Supplying enzymes to third-world
      markets should now be possible by removing the necessity for cold-chain
      transport. After arrival, enzymes can simply be stored in a standard
      domestic refrigerator.
AU  - Clark J
AU  - Harrison JC
AU  - Mdegela RH
AU  - March JB
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 2000 29: 536.

PMID- 12963055
VI  - 321
DP  - 2003
TI  - Methods for the design and analysis of oligodeoxynucleotide-based DNA (cytosine-5) methyltransferase inhibitors.
PG  - 50-64
AB  - Several second-generation inhibitors of DNA (cytosine-5) methyltransferases based on studies
      of modified synthetic
      oligodeoxynucleoides have been described. As an aid to studies of these
      inhibitors, we present an electronic structure-based algorithm that can be
      used as a method for predicting the nature of the expected inhibition by
      any noncytosine nucleotide target. Targeting by the major human enzyme
      (hDnmt1) is governed by the presence of a three-nucleotide motif. In
      hemimethylated DNA, this motif consists of a 5-methylcytosine targeting
      signal that causes the enzyme to probe the opposite strand for a normally
      paired guanosine or inosine residue and attempt to methylate the residue
      5' to that site. As a demonstration of the method, we apply these rules to
      the design and characterization of a novel oligodeoxynucleotide inhibitor
      of hDnmt1. This inhibitor takes advantage of the three-nucleotide
      recognition motif characteristic of hDnmt1 and shows that the enzyme is
      inhibited in vitro by non-CG methylation which targets the enzyme to
      normally basepaired but unproductive nucleotides such as dG, dA, and dT.
      Kinetic analysis at constant S-adenosyl-L-methionine concentration shows
      that representative inhibitory oligodeoxynucleotides are best viewed as
      weakly productive components of systems containing two DNA substrates.
      This model suggests that the most effective inhibitors are those with very
      low apparent Vmax and very low Km values. Oligodeoxynucleotides containing
      mispaired and unproductive targets such as dG, dA, dT, and dU are also
      inhibitory as secondary substrates for the human enzyme. Biologically,
      fail-safe mechanisms identified by the ab initio approach appear to be
      active in preventing potentially mutagenic deamination of dihydrocytosine
      and enzymatic methylation of dU.
AU  - Clark J
AU  - Shevchuk T
AU  - Kho MR
AU  - Smith SS
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 2003 321: 50-64.

PMID- 
VI  - 47
DP  - 2007
TI  - Missense Mutation of hsdR-Encoded Type I Restriction Enzyme Implicated in Transfer of Vancomycin-Resistance from Enterococcus to Staphylococcus aureus.
PG  - 83-84
AB  - Background:  Seven vanA-mediated vancomycin-resistant S. aureus (VRSA) cases have been
      reported. To prevent VRSA, it is important to understand the microbiological characteristics
      that allow for transfer of vanA from vancomycin-resistant Enterococcus (VRE) to S. aureus.
      Previously it was reported that S. aureus strain RN4220 readily acquires foreign DNA as a
      result of a missense mutation within the hsdR gene of the Type I restriction-modification
      system. Therefore we investigated the possibility that this mutation may have contributed to
      the transfer of vanA from Enterococcus to S. aureus.
      Methods:  The hsdR gene was amplified using primers, previously described by Waldron and
      Lindsay (2006. J. Bacteriol.), and both strands of this PCR product were sequenced using
      eleven additional primers.  The resulting sequences were compared to those of S. aureus
      8325-4, the parent strain of RN4220, and the S. aureus COL strain.
      Results:  The hsdR sequences of a VRSA isolate from each case were analyzed. For VRSA 1, 2, 5,
      and 6 no mutation was identified that changes the amino acid sequence. For VRSA 4, a base
      substitution was identified that resulted in a I to F amino acid change at position 774 and
      for VRSA 7, a base substitution resulted in a T to P amino acid change at position 362. For
      VRSA 3 a single-base deletion C, at base position 1382 (codon 461) created a frameshift and a
      premature stop codon at base position 1405. These changes would result in a truncation of the
      restriction enzyme from 930 amino acids to 469 amino acids. This truncation (50% of the
      protein) is less extensive than that reported for S. aureus RN4220 (21%).  Eight other S.
      aureus isolates (1 VRSA and 7 vancomycin-susceptible SA) from the same patient were
      characterized. These isolates were recovered from multiple body sites on different days, but
      were closely related by pulsed-field gel electrophoresis typing.  All 9 S. aureus isolates had
      the same hsdR gene mutation.
      Conclusions:  Three of the seven VRSA isolates has a mutation in the hsdR gene that resulted
      in a protein change. The amino acid substitutions identified in VRSA 4 and 7 have not been
      reported in another S. aureus and the significance of these changes is unknown. The missense
      mutation identified in VRSA 3 and related S. aureus isolates from the same patient likely
      results in a loss of function of the Type I restriction enzyme and may allow this strain to
      more readily acquire foreign DNA than strains with a functional restriction enzyme.
AU  - Clark NC
AU  - Zhu W
AU  - Patel JB
PT  - Journal Article
TA  - Abstr. InterSci. Conf. Antimicrob. Agents Chemother.
JT  - Abstr. InterSci. Conf. Antimicrob. Agents Chemother.
SO  - Abstr. InterSci. Conf. Antimicrob. Agents Chemother. 2007 47: 83-84.

PMID- 8065911
VI  - 22
DP  - 1994
TI  - High sensitivity mapping of methylated cytosines.
PG  - 2990-2997
AB  - An understanding of DNA methylation and its potential role in gene control during development,
      aging and cancer has been hampered by a lack of sensitive methods which can resolve exact
      methylation patterns from only small quantities of DNA. We have now developed a genomic
      sequencing technique which is capable of detecting every methylated cytosine on both strands
      of any target sequence, using DNA isolated from fewer than 100 cells. In this method, sodium
      bisulphite is used to convert cytosine residues to uracil residues in single-stranded DNA,
      under conditions whereby 5-methylcytosine remains non-reactive. The converted DNA is amplified
      with specific primers and sequenced. All the cytosine residues remaining in the sequence
      represent previously methylated cytosines in the genome. The work described has defined
      procedures that maximise the efficiency of denaturation, bisulphite conversion and
      amplification, to permit methylation mapping of single genes from small amounts of genomic
      DNA, readily available from germ cells and early developmental stages.
AU  - Clark SJ
AU  - Harrison J
AU  - Paul CL
AU  - Frommer M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1994 22: 2990-2997.

PMID- 23339471
VI  - 11
DP  - 2013
TI  - Enhanced 5-methylcytosine detection in single-molecule, real-time sequencing via  Tet1 oxidation.
PG  - 4
AB  - ABSTRACT: BACKGROUND: DNA methylation serves as an important epigenetic mark in both
      eukaryotic and prokaryotic organisms. In eukaryotes, the most common
      epigenetic mark is 5-methylcytosine, whereas prokaryotes can have
      6-methyladenine, 4-methylcytosine, or 5-methylcytosine. Single-molecule,
      real-time sequencing is capable of directly detecting all three types of modified
      bases. However, the kinetic signature of 5-methylcytosine is subtle, which
      presents a challenge for detection. We investigated whether conversion of
      5-methylcytosine to 5-carboxylcytosine using the enzyme Tet1 would enhance the
      kinetic signature, thereby improving detection. RESULTS: We characterized the
      kinetic signatures of various cytosine modifications, demonstrating that
      5-carboxylcytosine has a larger impact on the local polymerase rate than
      5-methylcytosine. Using Tet1-mediated conversion, we show improved detection of
      5-methylcytosine using in vitro methylated templates and apply the method to the
      characterization of 5-methylcytosine sites in the genomes of Escherichia coli
      MG1655 and Bacillus halodurans C-125. CONCLUSIONS: We have developed a method for
      the enhancement of directly detecting 5-methylcytosine during single-molecule,
      real-time sequencing. Using Tet1 to convert 5-methylcytosine to
      5-carboxylcytosine improves the detection rate of this important epigenetic
      marker, thereby complementing the set of readily detectable microbial base
      modifications, and enhancing the ability to interrogate eukaryotic epigenetic
      markers.
AU  - Clark TA
AU  - Lu X
AU  - Luong K
AU  - Dai Q
AU  - Boitano M
AU  - Turner SW
AU  - He C
AU  - Korlach J
PT  - Journal Article
TA  - BMC Biol.
JT  - BMC Biol.
SO  - BMC Biol. 2013 11: 4.

PMID- 22156058
VI  - 40
DP  - 2012
TI  - Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing.
PG  - e29
AB  - DNA methylation is the most common form of DNA modification in prokaryotic and eukaryotic
      genomes. We have applied the method of single-molecule, real-time (SMRT(R)) DNA sequencing
      that is capable of direct detection of modified bases at single-nucleotide resolution to
      characterize the specificity of several bacterial DNA methyltransferases (MTases). In addition
      to previously described SMRT sequencing of N6-methyladenine and 5-methylcytosine, we show that
      N4-methylcytosine also has a specific kinetic signature and is therefore identifiable using
      this approach. We demonstrate for all three prokaryotic methylation types that SMRT sequencing
      confirms the identity and position of the methylated base in cases where the MTase specificity
      was previously established by other methods. We then applied the method to determine the
      sequence context and methylated base identity for three MTases with unknown specificities. In
      addition, we also find evidence of unanticipated MTase promiscuity with some enzymes
      apparently also modifying sequences that are related, but not identical, to the cognate site.
AU  - Clark TA
AU  - Murray IA
AU  - Morgan RD
AU  - Kislyuk AO
AU  - Spittle KE
AU  - Boitano M
AU  - Fomenkov A
AU  - Roberts RJ
AU  - Korlach J
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: e29.

PMID- 25644009
VI  - 83
DP  - 2015
TI  - Comparative Genome Sequencing of Rickettsia rickettsii Strains Differing in Virulence.
PG  - 1568-1576
AB  - Rickettsia rickettsii is an obligate intracellular pathogen that is the causative agent of
      Rocky Mountain spotted fever. Strains of R. rickettsii differ dramatically in virulence. In a
      Guinea pig model of infection, the severity of disease as assessed by fever response varies
      from the most virulent, Sheila Smith, to Iowa which causes no fever. To identify potential
      determinants of virulence in R. rickettsii, the genomes of two additional strains were
      sequenced for comparison to known sequences (CGS). R. rickettsii Morgan and R strains were
      compared to the avirulent R. rickettsii Iowa and virulent R. rickettsii Sheila Smith. The
      Montana strains Sheila Smith and R  were found to be highly similar while the Eastern strains
      Iowa and Morgan were most similar to each other. A major surface antigen, rOmpA, is severely
      truncated in the Iowa strain. The region of ompA containing 13 tandem repeats was sequenced
      revealing only 7 shared SNP's (4 nonsynonymous) for R and Morgan strains compared to Sheila
      Smith with an additional 17 SNPs identified in Morgan. Another major surface antigen and
      autotransporter, rOmpB, exhibits a defect in processing in the Iowa strain such that the beta
      fragment is not cleaved. Sequence analysis of ompB reveals identical sequences between Iowa
      and Morgan strains and R identical to Sheila Smith. The number of SNPs and
      insertions/deletions between sequences of the two Montana strains and the two Eastern strains
      is low, thus narrowing the field of possible virulence factors.
AU  - Clark TR
AU  - Noriea NF
AU  - Bublitz DC
AU  - Ellison DW
AU  - Martens C
AU  - Lutter EI
AU  - Hackstadt T
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2015 83: 1568-1576.

PMID- 426781
VI  - 177
DP  - 1979
TI  - Purification, properties and specificity of the restriction endonuclease from Bacillus stearothermophilus.
PG  - 49-62
AB  - The restriction endonuclease BstI was purified from 70kg of Bacillus stearothermophilus.  The
      final product is at least 97% pure as judged by sodium dodecyl sulphate/polyacrylamide-gel
      electrophoresis; this major protein species co-migrates with the enzyme activity on native
      polyacrylamide-gel electrophoresis and isoelectric focusing.  Pure restriction endonuclease
      BstI has a subunit mol. wt. of 26000 and is probably a loosely associated dimer. The enzyme
      shows maximum activity at pH values between 7 and 9.5, and in the presence of 0.5-2mM-Mg2+.
      NaCl inhibits the restriction enzymeactivity. Restriction endonuclease BstI cleaves DNA in a
      position identical with that cleaved by endonuclease BamHI (for Bacillus amyloliquefaciens),
      i.e.:
      5'-G/-G-A-T-C-C-3'
      3'-C-C-T-A-G/-G-5'.
      In the presence of high concentrations of enzyme, DNA cleavage occurs at secondary sites.
      This side-specificity is enhanced by the addition of glycerol.  Preliminary studies indicate
      that these sites are of the type:
      5'-/G-A-T-C-3'
      3'-C-T-A-G/-5'.
AU  - Clarke CM
AU  - Hartley BS
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 1979 177: 49-62.

PMID- 21705601
VI  - 193
DP  - 2011
TI  - Complete genome sequence of the Crohn's disease-associated adherent-invasive Escherichia coli strain HM605.
PG  - 4540
AB  - Adherent-invasive Escherchia coli strains are increasingly being associated with intestinal
      pathologies. Here we present the genome
      sequence of E. coli HM605, a strain isolated from colonic biopsies of a
      patient with Crohn's disease.
AU  - Clarke DJ
AU  - Chaudhuri RR
AU  - Martin HM
AU  - Campbell BJ
AU  - Rhodes JM
AU  - Constantinidou C
AU  - Pallen MJ
AU  - Loman NJ
AU  - Cunningham AF
AU  - Browning DF
AU  - Henderson IR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4540.

PMID- 7972014
VI  - 91
DP  - 1994
TI  - A proposed mechanism for the self-splicing of proteins.
PG  - 11084-11088
AB  - Intervening protein sequences, called inteins, are intronlike elements that
      are removed posttranslationally, apparently by self-splicing.  The conserved and essential
      residues of precursor proteins consist of an asparagine as the last residue of the intein and
      a
      hydroxyl- or thiol-containing residue immediately following both splice junctions.
      Evidence for a branched intermediate has been reported; however, the chemical nature of
      the branched structure is unclear.  I propose a mechanism that includes the formation of a
      branched structure, provides an explanation for the reversal of branch formation observed
      at high pH, and accounts for each of the essential amino acids.  The branched structure is
      formed by nucleophilic attack of the asparagine side chain on the N-terminal splice
      junction.  The nature of this branched structure is a distinguishing feature of the model and
      can be experimentally tested.
AU  - Clarke ND
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1994 91: 11084-11088.

PMID- 
VI  - 
DP  - 2001
TI  - S-Adenosylmethionine-dependent methyltransferases.
PG  - 63-78
AB  - Mammalian S-adenosylmethionine-dependent methyltransferases each catalyze a reaction, giving
      rise to two products - S-adenosylhomocysteine and one of a variety of methylated biomolecules
      including nucleic acids, proteins, lipids, and small molecules.  S-adenosylhomocysteine is
      subsequently broken down to adenosine and homocysteine by S-adenosylhomocysteine hydrolase.
      The homocysteine formed can be either remethylated to methionine or converted to cysteine via
      cystathionine.  As such, these methyltransferases are bifunctional; they make up an essential
      part of the conduit for the conversion of methionine to cysteine in addition to generating
      methylated products.
AU  - Clarke S
AU  - Banfield K
PT  - Journal Article
TA  - Homocysteine in Health and Disease
JT  - Homocysteine in Health and Disease
SO  - Homocysteine in Health and Disease 2001 : 63-78.

PMID- 10671450
VI  - 182
DP  - 2000
TI  - Differential distribution of novel restriction-modification systems in clonal lineages of Neisseria meningitidis.
PG  - 1296-1303
AB  - Using representational difference analysis, we isolated novel meningococcal
      restriction-modification (R-M) systems. NmeBI, which is a homologue of the R-M system HgaI of
      Pasteurella volantium, was present in meningococci of the ET-5 complex and of lineage III.
      NmeAI was found in serogroup A, ET-37 complex, and cluster A4 meningococci. NmeDI was harbored
      by meningococci of the ET-37 complex and of cluster A4, but not by serogroup A meningococci.
      Two of the R-M systems, NmeBI and NmeDI, were located at homologous positions between the
      phenylalanyl-tRNA synthetase genes pheS and pheT, which appeared to be a preferential target
      for the insertion of foreign DNA in meningococci. The distribution of the three R-M systems
      was tested with 103 meningococcal strains comprising 49 sequence types. The vast majority of
      the strains had either NmeBI, NmeAI, or both NmeAI and NmeDI. Using cocultivation experiments,
      we could demonstrate that NmeBI, which was present in ET-5 complex meningococci, was
      responsible for a partial restriction of DNA transfer from meningococci of the ET-37 complex
      to meningococci of the ET-5 complex.
AU  - Claus H
AU  - Friedrich A
AU  - Frosch M
AU  - Vogel U
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2000 182: 1296-1303.

PMID- 11274117
VI  - 183
DP  - 2001
TI  - Genetic isolation of meningococci of the electrophoretic type 37 complex.
PG  - 2570-2575
AB  - Neisseria meningitidis (the meningococcus) is a naturally competent bacterial species in which
      intra- and interspecific horizontal gene transfer is a major source of genetic diversity. In
      strains of the electrophoretic type 37 (ET-37) complex and of the A4 cluster, we identified
      genomic DNA coding for a novel restriction-modification system and for the tail of a
      previously unidentified prophage. Furthermore, a novel 7.2-kb DNA segment restricted to clones
      of the ET-37 complex and the A4 cluster was isolated and shown to occur both as a plasmid
      (pJS-B) and as a chromosomal integration. Neither the genomic loci nor pJS-B was present in
      ET-5 complex, lineage 3, or serogroup A meningococci. The differential distribution of the DNA
      segments described herein, as well as of opcA, porB, nmeAI, nmeBI, and nmeDI described
      previously, supports the concept of genetic isolation of hypervirulent lineages responsible
      for most cases of serogroup C disease worldwide.
AU  - Claus H
AU  - Stoevesandt J
AU  - Frosch M
AU  - Vogel U
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2001 183: 2570-2575.

PMID- 25767228
VI  - 3
DP  - 2015
TI  - Two Complete and One Draft Genome Sequence of Nonproteolytic Clostridium botulinum Type E Strains NCTC 8266, NCTC 8550, and NCTC 11219.
PG  - e00083-15
AB  - Group II (gII) nonproteolytic Clostridium botulinum strains are a major cause of  foodborne
      botulism outbreaks. Here, we report two complete genome sequences of
      gII type E strains NCTC 8266 and NCTC 8550 and one draft genome sequence of type
      E NCTC 11219.
AU  - Clauwers C
AU  - Briers Y
AU  - Lavigne R
AU  - Michiels CW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00083-15.

PMID- 6285980
VI  - 697
DP  - 1982
TI  - Restriction enzyme cleavage of ultraviolet-damaged DNA.
PG  - 255-258
AB  - SV40 and pBR322 DNAs damaged by ultraviolet light were cleaved abnormally by
      several restriction enzymes because of damage to pyrimidines in the recognition
      sequences.  The use of a tandemly duplicated plasmid provided a particularly
      sensitive target molecule for detecting pyrimidine dimers and other possible
      photoproducts.  The relative efficiency with which cleavage was blocked
      (HindIII>TaqI>BamI>SalI>>HhaI, HaeIII) corresponds approximately to the
      relative frequency of pyrimidine dimer formation in the recognition sequences,
      but at a slightly higher frequency in potential sites for the non-cyclobutane
      T-C product.  The pyrimidine dimers appear to have a range of influence that
      extends 1 to 3 basepairs along the DNA molecule.  These effects provide clues
      to the way DNA damage from mutagens and carcinogens can interfere with specific
      enzyme-DNA interactions.
AU  - Cleaver JE
AU  - Samson L
AU  - Thomas GH
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1982 697: 255-258.

PMID- 181534
VI  - 30
DP  - 1976
TI  - Analysis of Herpesvirus DNA Substructure by means of Restriction Endonucleases.
PG  - 243-256
AB  - The mol. wt. and molar ratios of the HindIII and HpaI fragments of HSV-1 DNA
      and the EcoRI fragments of HSV-2 DNA have been determined.  Results obtained
      suggest that DNA isolated from both HSV-1 and HSV-2 consists of molecules with
      four different sequence arrangements which are present in similar amounts.  Our
      explanation of the cleavage patterns of these four genome arrangements with the
      different restriction enzymes is presented.  Some of the possible implications
      of these four genome arrangements for genetic recombination are discussed.
AU  - Clements JB
AU  - Cortini R
AU  - Wilkie NM
PT  - Journal Article
TA  - J. Gen. Virol.
JT  - J. Gen. Virol.
SO  - J. Gen. Virol. 1976 30: 243-256.

PMID- 24831138
VI  - 2
DP  - 2014
TI  - Genome Sequence of Serratia plymuthica V4.
PG  - e00340-14
AB  - Serratia spp. are gammaproteobacteria and members of the family Enterobacteriaceae. Here, we
      announce the genome sequence of Serratia plymuthica
      strain V4, which produces the siderophore serratiochelin and antimicrobial
      compounds.
AU  - Cleto S
AU  - Van der Auwera G
AU  - Almeida C
AU  - Vieira MJ
AU  - Vlamakis H
AU  - Kolter R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00340-14.

PMID- 22740665
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Providencia stuartii Clinical Isolate MRSN 2154.
PG  - 3736-3737
AB  - Here we present the complete genome sequence of Providencia stuartii MRSN 2154, isolated from
      an Afghan national. P. stuartii is a Gram-negative bacillus capable
      of causing infections in a wide variety of human tissues. Because Providencia
      readily acquires plasmids bearing drug resistance loci, it is of growing clinical
      significance.
AU  - Clifford RJ
AU  - Hang J
AU  - Riley MC
AU  - Onmus-Leone F
AU  - Kuschner RA
AU  - Lesho EP
AU  - Waterman PE
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3736-3737.

PMID- 21304635
VI  - 1
DP  - 2009
TI  - Complete genome sequence of Acidimicrobium ferrooxidans type strain (ICP).
PG  - 38-45
AB  - Acidimicrobium ferrooxidans (Clark and Norris 1996) is the sole and type species  of the
      genus, which until recently was the only genus within the actinobacterial
      family Acidimicrobiaceae and in the order Acidomicrobiales. Rapid oxidation of
      iron pyrite during autotrophic growth in the absence of an enhanced CO(2)
      concentration is characteristic for A. ferrooxidans. Here we describe the
      features of this organism, together with the complete genome sequence, and
      annotation. This is the first complete genome sequence of the order
      Acidomicrobiales, and the 2,158,157 bp long single replicon genome with its 2038
      protein coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria
      and Archaea project.
AU  - Clum A et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2009 1: 38-45.

PMID- 21304671
VI  - 1
DP  - 2009
TI  - Complete genome sequence of Pirellula staleyi type strain (ATCC 27377).
PG  - 308-316
AB  - Pirellula staleyi Schlesner and Hirsch 1987 is the type species of the genus Pirellula of the
      family Planctomycetaceae. Members of this pear- or
      teardrop-shaped bacterium show a clearly visible pointed attachment pole and can
      be distinguished from other Planctomycetes by a lack of true stalks. Strains
      closely related to the species have been isolated from fresh and brackish water,
      as well as from hypersaline lakes. Here we describe the features of this
      organism, together with the complete genome sequence and annotation. This is the
      first completed genome sequence of the order Planctomyces and only the second
      sequence from the phylum Planctobacteria/Planctomycetes. The 6,196,199 bp long
      genome with its 4773 protein-coding and 49 RNA genes is a part of the Genomic
      Encyclopedia of Bacteria and Archaea project.
AU  - Clum A et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2009 1: 308-316.

PMID- Not carried by PubMed...
VI  - 61
DP  - 1995
TI  - Some microbes have splicing proteins.
PG  - 344-347
AB  - The recent discovery of microbial genes whose products are spliced at the protein level,
      instead of at the mRNA level, adds an unexpected dimension of complexity to the ways in which
      genetic information flows from DNA to protein. These amazing protein elements, discovered
      about 5 years ago and now called inteins, typically catalyze both protein and DNA
      rearrangements.
AU  - Clyman J
PT  - Journal Article
TA  - ASM News
JT  - ASM News
SO  - ASM News 1995 61: 344-347.

PMID- 1321069
VI  - 6
DP  - 1992
TI  - Trans and cis requirements for intron mobility in a prokaryotic system.
PG  - 1269-1279
AB  - Intron mobility requires cleavage of an intronless allele by an intron-encoded endonuclease,
      followed by transfer of the intron into the cleaved recipient.  The mobile phage introns
      provide an opportunity to identify accessory functions involved in the intron inheritance
      process.  To test for trans and cis requirements of mobility in Escherichia coli, we have
      exploited the td intron of phage T4 in both phage T4 and lambda genetic backgrounds.  Mobility
      depends on host or phage recombinase functions, RecA or UvsX, respectively.  The process also
      requires a phage-encoded 5'-->3' exonuclease activity and associated annealing function that
      can be provided by phage lambda.  Finally, host-encoded 3'-->5' exonuclease activities are
      also implicated in intron inheritance.  We demonstrated further that restriction enzymes could
      substitute for the intron-encoded endonuclease, indicating that the endonuclease does not have
      an essential role in recombination.  Neither the precise position nor the nature of the
      double-strand break was critical to intron transfer.  These features provide insight into the
      recombination pathway and are factors impacting on the spread of introns throughout natural
      populations.
AU  - Clyman J
AU  - Belfort M
PT  - Journal Article
TA  - Genes Dev.
JT  - Genes Dev.
SO  - Genes Dev. 1992 6: 1269-1279.

PMID- 1332544
VI  - 205
DP  - 1992
TI  - Inhibition of restriction endonucleases by common clinical anticoagulants.
PG  - 368-369
AB  - Anticoagulated peripheral blood and bone marrow provide an accessible source of DNA for
      molecular studies. Successful results in such investigations often depend on full activity of
      labile restriction enzymes. Though occasional studies have shown heparin to be inhibitory, an
      often overlooked cause of enzyme inactivity is the effect of the anticoagulant used in sample
      collection. No systematic study regarding the effect of anticoagulants on restriction enzymes
      or techniques to remove anticoagulant contamination has been reported. The sensitivites of 18
      commonly used restriction endonucleases to sodium heparin, citric acid-sodium citrate-dextrose
      (ACD), and ethylenediaminetetraacetic acid (EDTA) and various methods of decontamination are
      presented.
AU  - Coad JE
AU  - Lander TA
AU  - Litz CE
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 1992 205: 368-369.

PMID- 28408691
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequence of Staphylococcus hominis Strain J31 Isolated from Healthy  Human Skin.
PG  - e01548-16
AB  - We report here the first whole-genome sequence of a skin-associated strain of Staphylococcus
      hominis determined using the PacBio long-read sequencing platform.
      S. hominis is a major commensal of the skin microflora. This genome sequence adds
      to our understanding of this species and will aid studies of gene traffic between
      staphylococci.
AU  - Coates-Brown R
AU  - Horsburgh MJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01548-16.

PMID- Not included in PubMed...
VI  - 37
DP  - 1987
TI  - Characterization of a restriction endonuclease from Ureaplasma urealyticum 960 and differences in deoxyribonucleic acid modification of human ureaplasmas.
PG  - 451-453
AB  - Uur960I, a restriction endonuclease from Ureaplasma urealyticum 960T, cleaved
      at the sequence 5'-GC/NGC-3' and is thus an isoschizomer of Fnu4HI.  Fnu4HI
      cleaved deoxyribonucleic acid from human ureaplasma serovars I,III, and VI but
      not II, IV, V, VII, VIII (strain 960), and IX.  This grouping of serovars,
      indicative of their deoxyribonucleic acid modification, matches that previously
      reported by others using different criteria.
AU  - Cocks BG
AU  - Finch LR
PT  - Journal Article
TA  - Int. J. Syst. Bacteriol.
JT  - Int. J. Syst. Bacteriol.
SO  - Int. J. Syst. Bacteriol. 1987 37: 451-453.

PMID- 6301822
VI  - 132
DP  - 1983
TI  - Physical map of Phage 2 C DNA: Evidence for the existence of large redundant ends.
PG  - 69-75
AB  - The chromosome of the Bacillus subtilis phage 2C, a linear molecule of double-stranded DNA of
      about 10^8 Da, in which thymine is completely replaced by hydroxymethyluracil, was cleaved by
      different endonucleases. In some cases restriction segments were much fewer than expected,
      suggesting a possible interference of the unusual base with the recognition mechanism of
      endonucleases. The physical map of 2C DNA was established by use of SalI and HaeIII
      restriction endonucleases, which yielded a limited number of fragments. The expected number of
      fragments was 240 for HaeIII and 23 for SalI; in reality, five segments were observed upon
      cleavage with HaeIII and four with SalI. The terminal fragments of the genome were first
      identified; the other fragments were ordered by hybridization and molecular weight
      determination of restriction fragments obtained by cleavage with the two endonucleases. In
      addition, hybridization of restriction fragments showed the presence of homologous regions at
      the ends of the 2C genome. The structure of these direct repetitive sequences was analyzed by
      cleavage with HaeIII and hybridization with EcoRI restriction fragments. Their size (9.2 MDa)
      was found to be about 1/11 of that of the whole chromosome.
AU  - Coene M
AU  - Hoet P
AU  - Cocito C
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1983 132: 69-75.

PMID- Not included in PubMed...
VI  - 43
DP  - 1969
TI  - Restriction without modification of phage 34/13 in a strain of Proteus mirabilis.
PG  - 356
AB  - Phage 34/13 prepared on its host strain Proteus mirabilis 13at does not form
      plaques on P. mirabilis strain N6 when serial dilutions are spotted on a lawn
      of the organism.  Low dilutions show areas of clearing due to bacterial lysis
      but no phage capable of forming plaques on N6 is obtained from these zones.
      Phage 34/13 adsorbs to an extent of 99% on strain N6 within 15 min.  With the
      use of 32P-labelled phage 34/13 DNA it is shown that within 15 min. of
      adsorption to N6, 57% of the label is in the medium in the form of acid-soluble
      nucleotides.  This figure is reduced to 11% when the phage adsorbs to its
      normal host 13at and 0.9% when the phage is mixed with a strain of P. mirabilis
      to which it does not adsorb.  This indicates that the DNA of phage 34/13 is
      restricted by strain N6.  The phage DNA which escapes restriction is not
      modified as no plaques are formed.  Phenotypically strain N6 behaves as if its
      genotype is r+m-.  It may be argued that r+m- strains should degrade their own
      DNA and be nonviable.  Strains of this genotype have never been isolated after
      mutagen treatment of wild strains.  Many bacteria which restrict foreign DNA
      owe this property to a prophage.  Strain N6 carries a prophage which on UV
      induction produces a defective phage which manifests itself as a bacteriocin
      which kills strains of P. mirabilis, and this plasmid may contribute to the
      restrictive process.  This has not been proved.  Attempts to isolate mutants of
      phage 34/13 which escape restriction have been unsuccessful.  Fruitless
      attempts have also been made to isolate r-m- or r-m+ mutants of strain N6 which
      would allow plaque formation by the phage.
AU  - Coetzee JN
AU  - Smit JA
PT  - Journal Article
TA  - S. Afr. Med. J.
JT  - S. Afr. Med. J.
SO  - S. Afr. Med. J. 1969 43: 356.

PMID- 12369198
VI  - 82
DP  - 2002
TI  - Bacteriophage-resistance systems in dairy starter strains: molecular analysis to application.
PG  - 303-321
AB  - Starter inhibition by bacteriophage infection in dairy fermentations can limit the usage of
      specific bacterial strains used in the
      manufacture of Cheddar, Mozzarella and other cheeses and can result in
      substantial economic losses. A variety of practical measures to
      alleviate the problem of phage infection have been adopted over the
      years but has invariably resulted in a very limited number of strains
      which can withstand intensive usage in industry. The application of
      genetic techniques to improve the phage-resistance of starter cultures
      for dairy fermentations has been intensively studied for the last 20
      years to a point where this approach now has significant potential to
      alleviate the problem. This paper highlights the recent findings and
      developments that have been described in the literature that will have
      an impact on improvement of the phage-resistance of starter cultures.
AU  - Coffey A
AU  - Ross RP
PT  - Journal Article
TA  - Antonie Van Leeuwenhoek
JT  - Antonie Van Leeuwenhoek
SO  - Antonie Van Leeuwenhoek 2002 82: 303-321.

PMID- 
VI  - 40
DP  - 2001
TI  - Traditional and molecular approaches to improving bacteriophage resistance of Cheddar and Mozzarella cheese starters.
PG  - 239-270
AB  - Infection by bacteriophage (bacterial viruses) during dairy fermentations remains a major
      cause of starter culture failure in
      Cheddar and Mozzarella manufacture, often resulting in substantial
      economic losses. A variety of practical measures to alleviate the
      problem of phage infection have been adopted over the years. The
      application of genetic techniques to improve the phage resistance of
      starter cultures for dairy fermentations is currently being explored
      and this approach has significant potential to alleviate the problem.
      This review highlights the significant developments that have been made
      in understanding the interaction between dairy starter cultures and
      bacteriophage in industry. It also describes the exploitation of
      molecular methodology to genetically defend these bacteria from the
      ever-present threat of bacteriophage and the scientific advances, which
      formed the basis for these achievements. Attention is also given to the
      development of food-grade approaches to improve genetic traits of
      industrial starter strains in the context of phage resistance.
AU  - Coffey A
AU  - Stokes D
AU  - Fitzgerald GF
AU  - Ross RP
PT  - Journal Article
TA  - Irish J. Agr. Food Res.
JT  - Irish J. Agr. Food Res.
SO  - Irish J. Agr. Food Res. 2001 40: 239-270.

PMID- 25395625
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of vB_EcoM_112, a T-Even-Type Bacteriophage Specific for Escherichia coli O157:H7.
PG  - e00393-14
AB  - Bacteriophage vB_EcoM_112 (formerly e11/2) is an Escherichia coli phage with specificity for
      the O157:H7 serotype. The vB_EcoM_112 genome sequence shares high
      degrees of similarity with the phage T4 genome sequence.
AU  - Coffey B
AU  - Ross RP
AU  - O'Flynn G
AU  - O'Sullivan O
AU  - Casey A
AU  - Callanan M
AU  - Coffey A
AU  - McAuliffe O
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00393-14.

PMID- 19419959
VI  - 284
DP  - 2009
TI  - Escherichia coli DNA Adenine Methyltransferase THE STRUCTURAL BASIS OF PROCESSIVE CATALYSIS AND INDIRECT READ-OUT.
PG  - 18390-18400
AB  - We have investigated the structural basis of processive GATC methylation by the Escherichia
      coli DNA adenine methyltransferase,
      which is critical in chromosome replication and mismatch repair. We
      determined the contribution of the orthologically conserved phosphate
      interactions involving residues Arg(95), Asn(126), Asn(132), Arg(116),
      and Lys(139), which directly contact the DNA outside the cognate
      recognition site (GATC) to processive catalysis, and that of residue
      Arg(137), which is not conserved and contacts the DNA backbone within
      the GATC sequence. Alanine substitutions at the conserved positions
      have large impacts on processivity yet do not impact k(cat)/K-m(DNA) or
      DNA affinity (K-D(DNA)). However, these mutants cause large preferences
      for GATC sites varying in flanking sequences when considering the
      pre-steady state efficiency constant k(chem)/K-D(DNA). These changes
      occur mainly at the level of the methylation rate constant, which
      results in the observed decreases in processive catalysis. Thus,
      processivity and catalytic efficiency (k(cat)/K-m(DNA)) are uncoupled
      in these mutants. These results reveal that the binding energy involved
      in DNA recognition contributes to the assembly of the active site
      rather than tight binding. Furthermore, the conserved residues
      (Arg(95), Asn(126), Asn(132), and Arg(116)) repress the modulation of
      the response of the enzyme to flanking sequence effects. Processivity
      impacted mutants do not show substrate-induced dimerization as is
      observed for the wild type enzyme. This study describes the structural
      means by which an enzyme that does not completely enclose its substrate
      has evolved to achieve processive catalysis, and how interactions with
      DNA flanking the recognition site alter this processivity.
AU  - Coffin SR
AU  - Reich NO
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2009 284: 18390-18400.

PMID- 18502761
VI  - 283
DP  - 2008
TI  - Modulation of Escherichia coli DNA methyltransferase activity by biologically derived GATC-flanking sequences.
PG  - 20106-20116
AB  - Escherichia coli DNA adenine methyltransferase (EcoDam) methylates the N-6 position of the
      adenine in the sequence 5'-GATC-3' and plays vital
      roles in gene regulation, mismatch repair, and DNA replication. It
      remains unclear how the small number of critical GATC sites involved in
      the regulation of replication and gene expression are differentially
      methylated, whereas the similar to 20,000 GATCs important for mismatch
      repair and dispersed throughout the genome are extensively methylated.
      Our prior work, limited to the pap regulon, showed that methylation
      efficiency is controlled by sequences immediately flanking the GATC
      sites. We extend these studies to include GATC sites involved in
      diverse gene regulatory and DNA replication pathways as well as sites
      previously shown to undergo differential in vivo methylation but whose
      function remains to be assigned. EcoDam shows no change in affinity
      with variations in flanking sequences derived from these sources, but
      methylation kinetics varied 12-fold. A-tracts immediately adjacent to
      the GATC site contribute significantly to these differences in
      methylation kinetics. Interestingly, only when the poly(A) is located
      5' of the GATC are the changes in methylation kinetics revealed.
      Preferential methylation is obscured when two GATC sites are positioned
      on the same DNA molecule, unless both sites are surrounded by large
      amounts of nonspecific DNA. Thus, facilitated diffusion and sequences
      immediately flanking target sites contribute to higher order
      specificity for EcoDam; we suggest that the diverse biological roles of
      the enzyme are in part regulated by these two factors, which may be
      important for other enzymes that sequence-specifically modify DNA.
AU  - Coffin SR
AU  - Reich NO
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2008 283: 20106-20116.

PMID- 19580332
VI  - 48
DP  - 2009
TI  - Escherichia coli DNA Adenine Methyltransferase: Intrasite Processivity and Substrate-Induced Dimerization and Activation.
PG  - 7399-7410
AB  - Methylation of GATC sites in Escherichia coli by DNA adenine methyltransferase (EcoDam) is
      essential for proper DNA replication
      timing, gene regulation, and mismatch repair. The low cellular
      concentration of EcoDam and the high number of GATC sites in the genome
      (similar to 20000) Support the reliance on methylation
      efficiency-enhancing strategies such as extensive intersite
      processivity. Here, we present evidence that EcoDam has evolved other
      unique mechanisms of activation not commonly observed with
      restriction-modification methyltransferases, EcoDam dimerizes oil
      short, synthetic DNA, resulting in enhanced catalysis; however,
      dimerization is not observed on large genomic DNA where the potential
      for intersite processive methylation precludes any
      dimerization-dependent activation. An activated form of the enzyme is
      apparent on large genomic DNA and can also be achieved with high
      concentrations of short, synthetic substrates. We suggest that this
      activation is inherent on polymeric DNA where either multiple GATC
      sites are available for methylation or the partitioning of the enzyme
      onto nonspecific DNA is favored. Unlike other restriction-modification
      methyltransferases, EcoDam carries out intrasite processive catalysis
      whereby the enzyme-DNA complex methylates both strands of an
      unmethylated GATC site prior to dissociation From the DNA. This occurs
      with short 21 bp oligonucleotides and is highly dependent upon salt
      concentrations. Kinetic modeling which invokes enzyme activation by
      both dimerization and excess substrate provides mechanistic insights
      into key regulatory checkpoints for an enzyme involved in multiple,
      diverse biological pathways.
AU  - Coffin SR
AU  - Reich NO
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2009 48: 7399-7410.

PMID- 6754713
VI  - 257
DP  - 1982
TI  - Demonstration of specific high affinity binding sites in plasmid DNA by photoaffinity labeling with an ethidium analog.
PG  - 13205-13207
AB  - We have used photoaffinity labeling of pBR322 DNA with
      8-azido-3-amino-5ethyl-6-phenylphenanthridinium chloride to demonstrate high affinity ethidium
      binding sites. Plasmid equilibrated with as little as 1 drug/DNA molecule was photoactivated,
      freed of uncomplexed drug by ethanol precipitation, and subjected to restriction analysis.
      There was highly specific, rather than random blockage of HhaI sites (d(GCGC))at low drug
      concentrations. Furthermore, the same 7 new digestion fragments were generated at drug to
      nucleotide ratios ranging from 1:100 to 1:8000. All the new DNA fragments had chain lengths
      greater than the largest HhaI fragment (393 base pairs). At higher ligand concentrations
      closely approximating those needed for equilibrium binding studies, detection of the high
      affinity sites was greatly masked. Drug binding to HhaI restriction fragments which had been
      prepared prior to the action of drug did not induce new bands. Furthermore, the larger DNA
      fragments from drug labeled plasmid were resistant to HhaI digestion over a wide range of
      enzyme concentrations. These findings suggest that ligand binding can be highly selective even
      between sites which have the same tetranucleotide sequence. Therefore, selective drug binding
      must be dictated not only by local base sequence preference, but also by other long range
      parameters.
AU  - Coffman GL
AU  - Gaubatz JW
AU  - Yielding KL
AU  - Yielding LW
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1982 257: 13205-13207.

PMID- 15602611
VI  - 3
DP  - 2005
TI  - Determinants of cofactor binding to DNA methyltransferases: insights from a systematic series of structural variants of  S-adenosylhomocysteine.
PG  - 152-161
AB  - S-Adenosylmethionine (AdoMet) is a commonly used cofactor, second only to ATP in the variety
      of reactions in which it participates. It is the
      methyl donor in the majority of methyl transfer reactions, including
      methylation of DNA, RNA, proteins and small molecules. Almost all
      structurally characterised methyltransferases share a conserved
      AdoMet-dependent methyltransferase fold, in which AdoMet is bound in
      the same orientation. Although potential interactions between the
      cofactor and methyltransferases have been inferred from crystal
      structures, there has not been a systematic study of the contributions
      of each functional group to binding. To explore the binding interaction
      we synthesised a series of seven analogues of the methyltransferase
      inhibitor S-adenosylhomocysteine (AdoHcy), each containing a single
      modi cation, and tested them for the ability to inhibit methylation by
      HhaI and HaeIII DNA methyltransferase. Comparison of the K-i values
      highlights the structural determinants for cofactor binding, and
      indicates which nucleoside and amino acid functional groups contribute
      significantly to AdoMet binding. An understanding of the binding of
      AdoHyc to methyltransferases will greatly assist the design of AdoMet
      inhibitors.
AU  - Cohen HM
AU  - Griffiths AD
AU  - Tawfik DS
AU  - Loakes D
PT  - Journal Article
TA  - Org. Biomol. Chem.
JT  - Org. Biomol. Chem.
SO  - Org. Biomol. Chem. 2005 3: 152-161.

PMID- 14985532
VI  - 17
DP  - 2004
TI  - Altering the sequence specificity of HaeIII methyltransferase by directed evolution using in vitro compartmentalization.
PG  - 3-11
AB  - Engineering the specificity of DNA-modifying enzymes has proven extremely challenging, as
      sequence recognition by these enzymes is poorly understood.  Here we used directed evolution
      to generate a variant of HaeIII methyltransferase that efficiently methylates a novel target
      site.  M.HaeIII methylates the internal cytosine of the canonical sequence GGCC, but there is
      promiscuous methylation of a variety of non-canonical sites, notably AGCC, at a reduced rate.
      Using in vitro compartmentalization, libraries of M.HaeIII genes were selected for the ability
      to efficiently methylate AGCC.  A two-step mutagenesis strategy, involving initial
      randomization of DNA-contracting residues followed by randomization of the loop that lies
      behind these residues, yielded a mutant with a 670-fold improvement in catalytic efficiency
      (kcat/KmDNA) using AGCC and a preference for AGCC over GGCC.  The mutant methylates three
      sites efficiently (AGCC, CGCC and GGCC).  Indeed, it methylates CGCC slightly more efficiently
      than AGCC.  However, the mutant discriminates against other non-canonical sites, including
      TGCC, as effectively as the wild-type enzyme.  This study provides a rate example of a
      laboratory-evolved enzyme whose catalytic efficiency surpasses that of the wild-type enzyme
      with the principal substrate.
AU  - Cohen HM
AU  - Tawfik DS
AU  - Griffiths AD
PT  - Journal Article
TA  - Protein Eng. Des. Sel.
JT  - Protein Eng. Des. Sel.
SO  - Protein Eng. Des. Sel. 2004 17: 3-11.

PMID- 12202773
VI  - 30
DP  - 2002
TI  - Promiscuous methylation of non-canonical DNA sites by HaeIII methyltransferase.
PG  - 3880-3885
AB  - The cytosine C5 methyltransferase M.HaeIII recognises and methylates the central cytosine of
      its canonical site GGCC. Here we report that M.HaeIII can also, with lower efficiency,
      methylate cytosines located in a wide range of non-canonical sequences. Using bisulphite
      sequencing we mapped the methyl-cytosine residues in DNA methylated in vitro and in vivo by
      M.HaeIII. Methyl-cytosine residues were observed in multiple sequence contexts, most commonly,
      but not exclusively, at star sites (sites differing by a single base from the canonical
      sequence). The most frequently used star sites had changes at positions 1 and 4, but there is
      little or no methylation at star sites changed at position 2. The rate of methylation of
      non-canonical sites can be quite significant: a DNA substrate lacking a canonical site was
      methylated by M.HaeIII in vitro at a rate only an order of magnitude slower than an otherwise
      identical substrate containing the canonical site. In vivo methylation of non-canonical sites
      may therefore be significant and may have provided the starting point for the evolution of
      restriction-modification systems with novel sequence specificities.
AU  - Cohen HM
AU  - Tawfik DS
AU  - Griffiths AD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2002 30: 3880-3885.

PMID- 26089422
VI  - 3
DP  - 2015
TI  - Genome Sequence of the Alkaline-Tolerant Cellulomonas sp. Strain FA1.
PG  - e00646-15
AB  - We present the genome of the cellulose-degrading Cellulomonas sp. strain FA1 isolated from an
      actively serpentinizing highly alkaline spring. Knowledge of
      this genome will enable studies into the molecular basis of plant material
      degradation in alkaline environments and inform the development of lignocellulose
      bioprocessing procedures for biofuel production.
AU  - Cohen MF
AU  - Hu P
AU  - Nguyen MV
AU  - Kamennaya N
AU  - Brown N
AU  - Woyke T
AU  - Kyrpides N
AU  - Holman HY
AU  - Torok T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00646-15.

PMID- 26998690
VI  - 48
DP  - 2016
TI  - A role for the bacterial GATC methylome in antibiotic stress survival.
PG  - 581-586
AB  - Antibiotic resistance is an increasingly serious public health threat. Understanding pathways
      allowing bacteria to survive antibiotic stress may unveil
      new therapeutic targets. We explore the role of the bacterial epigenome in
      antibiotic stress survival using classical genetic tools and single-molecule
      real-time sequencing to characterize genomic methylation kinetics. We find that
      Escherichia coli survival under antibiotic pressure is severely compromised
      without adenine methylation at GATC sites. Although the adenine methylome remains
      stable during drug stress, without GATC methylation, methyl-dependent mismatch
      repair (MMR) is deleterious and, fueled by the drug-induced error-prone
      polymerase Pol IV, overwhelms cells with toxic DNA breaks. In multiple E. coli
      strains, including pathogenic and drug-resistant clinical isolates, DNA adenine
      methyltransferase deficiency potentiates antibiotics from the beta-lactam and
      quinolone classes. This work indicates that the GATC methylome provides
      structural support for bacterial survival during antibiotic stress and suggests
      targeting bacterial DNA methylation as a viable approach to enhancing antibiotic
      activity.
AU  - Cohen NR
AU  - Ross CA
AU  - Jain S
AU  - Shapiro RS
AU  - Gutierrez A
AU  - Belenky P
AU  - Li H
AU  - Collins JJ
PT  - Journal Article
TA  - Nat. Genet.
JT  - Nat. Genet.
SO  - Nat. Genet. 2016 48: 581-586.

PMID- 24526646
VI  - 2
DP  - 2014
TI  - Whole-Genome Sequencing of the Nonproteolytic Bacillus anthracis V770-NP1-R Strain Reveals Multiple Mutations in Peptidase Loci.
PG  - e00075-14
AB  - We report the draft whole-genome sequence of the nonproteolytic Bacillus anthracis V770-NP1-R
      strain. Compared to those of other B. anthracis strains, the
      genome exhibits unique mutations in multiple targets potentially affecting
      proteolytic functions. One of these mutations is a deletion that disrupts the
      NprR quorum-sensing regulator of the NprA protease.
AU  - Cohen-Gihon I
AU  - Israeli O
AU  - Beth-Din A
AU  - Levy H
AU  - Cohen O
AU  - Shafferman A
AU  - Zvi A
AU  - Chitlaru T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00075-14.

PMID- 21690366
VI  - 108
DP  - 2011
TI  - The MspJI family of modification-dependent restriction endonucleases for epigenetic studies.
PG  - 11040-11045
AB  - MspJI is a novel modification-dependent restriction endonuclease that cleaves at a fixed
      distance away from the modification site. Here, we
      present the biochemical characterization of several MspJI homologs,
      including FspEI, LpnPI, AspBHI, RlaI, and SgrTI. All of the enzymes
      specifically recognize cytosine C5 modification (methylation or
      hydroxymethylation) in DNA and cleave at a constant distance
      (N-12/N-16) away from the modified cytosine. Each displays its own
      sequence context preference, favoring different nucleotides flanking
      the modified cytosine. By cleaving on both sides of fully modified CpG
      sites, they allow the extraction of 32-base long fragments around the
      modified sites from the genomic DNA. These enzymes provide powerful
      tools for direct interrogation of the epigenome. For example, we show
      that RlaI, an enzyme that prefers (m)CWG but not (m)CpG sites,
      generates digestion patterns that differ between plant and mammalian
      genomic DNA, highlighting the difference between their epigenomic
      patterns. In addition, we demonstrate that deep sequencing of the
      digested DNA fragments generated from these enzymes provides a feasible
      method to map the modified sites in the genome. Altogether, the MspJI
      family of enzymes represent appealing tools of choice for method
      development in DNA epigenetic studies.
AU  - Cohen-Karni D
AU  - Xu D
AU  - Apone L
AU  - Fomenkov A
AU  - Sun ZY
AU  - Davis PJ
AU  - Kinney SRM
AU  - Yamada-Mabuchi M
AU  - Xu SY
AU  - Davis T
AU  - Pradhan S
AU  - Roberts RJ
AU  - Zheng Y
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2011 108: 11040-11045.

PMID- 25858832
VI  - 3
DP  - 2015
TI  - Draft genome sequences of 26 porphyromonas strains isolated from the canine oral  microbiome.
PG  - e00187-15
AB  - We present the draft genome sequences for 26 strains of Porphyromonas (P. canoris, P. gulae,
      P. cangingavalis, P. macacae, and 7 unidentified) and an
      unidentified member of the Porphyromonadaceae family. All of these strains were
      isolated from the canine oral cavity, from dogs with and without early
      periodontal disease.
AU  - Coil DA
AU  - Alexiev A
AU  - Wallis C
AU  - O'Flynn C
AU  - Deusch O
AU  - Davis I
AU  - Horsfall A
AU  - Kirkwood N
AU  - Jospin G
AU  - Eisen JA
AU  - Harris S
AU  - Darling AE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00187-15.

PMID- 24558247
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of the Extreme Thermophile Dictyoglomus thermophilum H-6-12.
PG  - e00109-14
AB  - Here, we present the complete genome of the extreme thermophile, Dictyoglomus thermophilum
      H-6-12 (phylum Dictyoglomi), which consists of 1,959,987 bp.
AU  - Coil DA
AU  - Badger JH
AU  - Forberger HC
AU  - Riggs F
AU  - Madupu R
AU  - Fedorova N
AU  - Ward N
AU  - Robb FT
AU  - Eisen JA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00109-14.

PMID- 26586895
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Bacillus safensis JPL-MERTA-8-2, Isolated from a Mars-Bound Spacecraft.
PG  - e01360-15
AB  - Here, we present the draft genome of Bacillus safensis JPL-MERTA-8-2, a strain found in a
      spacecraft assembly cleanroom before launch of the Mars Exploration
      Rovers. The assembly contains 3,671,133 bp in 14 contigs.
AU  - Coil DA
AU  - Benardini JN
AU  - Eisen JA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01360-15.

PMID- 23661474
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Kocuria sp. Strain UCD-OTCP (Phylum Actinobacteria).
PG  - e00172-13
AB  - Here, we present the draft genome of Kocuria sp. strain UCD-OTCP, a member of the phylum
      Actinobacteria, isolated from a restaurant chair cushion. The assembly
      contains 3,791,485 bp (G+C content of 73%) and is contained in 68 scaffolds.
AU  - Coil DA
AU  - Doctor JI
AU  - Lang JM
AU  - Darling AE
AU  - Eisen JA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00172-13.

PMID- 26586867
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Porphyrobacter mercurialis (sp. nov.) Strain Coronado.
PG  - e00856-15
AB  - Here, we present the draft genome of Porphyrobacter mercurialis strain Coronado,  the proposed
      type strain for this species. The assembly contains 3,482,341 bp in
      10 contigs.
AU  - Coil DA
AU  - Eisen JA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00856-15.

PMID- 26798108
VI  - 4
DP  - 2016
TI  - Additional Draft Genome Sequences of Escherichia coli Strains Isolated from Septic Patients.
PG  - e01614-15
AB  - We present the draft genome sequences of eight uropathogenic strains of Escherichia coli
      isolated from blood cultures collected from patients with
      sepsis, an extension of previous sequencing work from the same cohort.
AU  - Coil DA
AU  - Jospin G
AU  - Eisen JA
AU  - Adams JY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01614-15.

PMID- 24233593
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Arsenate-Respiring Bacterium Chrysiogenes arsenatis  Strain DSM 11915.
PG  - e00953-13
AB  - Here we present the draft genome sequence of Chrysiogenes arsenatis strain DSM 11915, only the
      second genome sequence from the phylum Chrysiogenetes. This
      strictly anaerobic organism was isolated from arsenic-contaminated gold mine
      wastewater and respires arsenate or nitrate instead of oxygen. The assembly
      contains 2,824,977 bp in 22 scaffolds.
AU  - Coil DA
AU  - Lo JR
AU  - Chen R
AU  - Ward N
AU  - Robb FT
AU  - Eisen JA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00953-13.

PMID- 25125647
VI  - 2
DP  - 2014
TI  - Whole-Genome Sequence of a Multidrug-Resistant Mycobacterium tuberculosis Beijing Sequence Type 10 Isolate from an Outbreak in Thailand.
PG  - e00803-14
AB  - Infections with the Beijing family of Mycobacterium tuberculosis occur worldwide  and are
      endemic in Asian countries. We present the draft genome sequence of
      DS6701, a multidrug-resistant M. tuberculosis Beijing strain of sequence type 10.
      The isolate is a representative of strains isolated from a multidrug-resistant
      tuberculosis outbreak in Thailand.
AU  - Coker OO
AU  - Regmi SM
AU  - Suriyaphol P
AU  - Chininmanu K
AU  - Prammananan T
AU  - Chaiprasert A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00803-14.

PMID- 24385571
VI  - 2
DP  - 2014
TI  - Genome Sequence of the Boron-Tolerant and -Requiring Bacterium Bacillus boroniphilus.
PG  - e00935-13
AB  - Bacillus boroniphilus is a highly boron-tolerant bacterium that also requires this element for
      its growth. The complete genome sequence of B. boroniphilus was
      determined by a combination of shotgun sequencing and paired-end sequencing using
      454 pyrosequencing technology. A total of 84,872,624 reads from shotgun
      sequencing and a total of 194,092,510 reads from paired-end sequencing were
      assembled using Newbler 2.3. The estimated size of the draft genome is 5.2 Mb.
AU  - Col B
AU  - Ozkeserli Z
AU  - Kumar D
AU  - Ozdag H
AU  - Alakoc YD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00935-13.

PMID- 1369408
VI  - 10
DP  - 1992
TI  - Extraordinary stability of enzymes dried in trehalose: simplified molecular biology.
PG  - 1007-1011
AB  - We show that extremely fragile biomolecules such as DNA restriction and modifying enzymes can
      be dried in vitro in the presence of trehalose with no loss of activity, even after prolonged
      storage. A remarkable and unexpected property of the dried enzyme preparations is their
      ability to withstand prolonged exposure to temperatures as high as +70oC. This stability is
      unique to trehalose and is not found with other sugars irrespective of their physical or
      chemical properties. The immediate significance of these observations is the ability to
      convert enzymes used in molecular biology into stable reagents. The indefinite stability and
      high temperature tolerance of these dried enzymes should permit the design of convenient
      formats that may be of particular significance in the automation of genome mapping and
      sequencing projects. The stabilization of a wide range of biomolecules by trehalose also has
      practical implications for a number of areas ranging from basic science, through health care
      and agriculture, to bio-electronics.
AU  - Colaco C
AU  - Sen S
AU  - Thangavelu M
AU  - Pinder S
AU  - Roser B
PT  - Journal Article
TA  - Biotechnology
JT  - Biotechnology
SO  - Biotechnology 1992 10: 1007-1011.

PMID- 9520400
VI  - 95
DP  - 1998
TI  - The domain organization of NaeI endonuclease: Separation of binding and catalysis.
PG  - 3531-3536
AB  - NaeI is a remarkable type II restriction endonuclease.  It must bind two recognition sequences
      to cleave DNA, forms a covalent protein-DNA intermediate, and is only 1 aa change away from
      topoisomerase and recombinase activity.  The latter activities apparently derive from
      reactivation of a cryptic DNA ligase active site.  Here, we demonstrate that NaeI has two
      protease-resistant domains, involving approximately the N-terminal and C-terminal halves of
      the protein, linked by a protease-accessible region of 30 aa.  The domains were purified by
      cloning.  The C-terminal domain was shown by gel mobility-shift assay to have approximately
      8-fold lower DNA-binding ability than intact NaeI.  Analytical ultracentrifugation showed this
      domain to be a monomer in solution.  The N-terminal domain, which contains the catalytic
      region defined by random mutagenesis, do not bind DNA and was a mixture of different-sized
      complexes in solution implying that it mediates self-association.  DNA greatly inhibited
      proteolysis of the linker region.  The results identify the DNA-binding domain, imply that DNA
      cleavage and recognition are independent and separable, and lead us to speculate about a
      cleft-like structure for NaeI.
AU  - Colandene JD
AU  - Topal MD
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1998 95: 3531-3536.

PMID- 11076509
VI  - 2000
DP  - 2000
TI  - Evidence for mutations that break communication between the Endo and Topo domains in NaeI endonuclease/topoisomerase.
PG  - 13703-13707
AB  - NaeI is a type IIe endonuclease that interacts with two DNA recognition sequences to cleave
      DNA. One DNA sequence serves as a substrate and the other serves to activate cleavage. NaeI is
      divided into two domains whose structures parallel the two functionalities recognized in NaeI,
      endonuclease and topoisomerase. In this study, we report evidence for mutations that break
      interdomain functional communication in a NaeI-DNA complex. Deletion of the initial 124 amino
      acids of the N-terminal domain of NaeI converted NaeI to a monomer, consistent with
      self-association being mediated by the Endo domain.  Deletions within a small region of the
      C-terminal DNA binding domain of NaeI (amino acids 182-192) altered the recognition by NaeI of
      sequences flanking the NaeI recognition sequence. Substituting Ala for Arg182 within this
      region had no apparent effect on DNA binding but greatly reduced the extent of DNA cleavage
      even though it is not part of the catalytic Endo domain. Substituting Ala for Ile185 reduced
      the extent of DNA binding about 1000-fold. Substituting Ala for Lys189 altered flanking
      sequence recognition.  Residues 182-192 are away from the Endo domain responsible for cleavage
      and also face away from the modeled DNA binding faces of the apoprotein crystal structure. We
      propose that residues 182-192 are part of a web that mediates the flow of information between
      the NaeI Endo and Topo domains.
AU  - Colandene JD
AU  - Topal MD
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2000 2000: 13703-13707.

PMID- 2014176
VI  - 19
DP  - 1991
TI  - Cytosine methylated DNA synthesized by Taq polymerase used to assay methylation sensitivity of restriction endonuclease HinfI.
PG  - 391-394
AB  - We have studied the resistance of cytosine methylated DNA to digestion by the
      restriction endonuclease HinfI, using a simple PCR procedure to synthesize DNA
      of known sequence in which every cytosine is methylated at the 5 position.  We
      find that HinfI cannot digest cytosine methylated DNA at the concentrations
      normally used in restriction digests.  Complete digestion is possible using a
      vast excess of enzyme; under these conditions, the rate of HinfI digestion for
      cytosine methylated DNA is at least 1440-fold slower than for unmethylated DNA.
      The presence of an additional methylated cytosine at the degenerate position
      internal to the recognition sequence does not appear to increase the resistance
      to HinfI digestion.  We also tested HhaII, an isoschizomer of HinfI, and found
      that it is completely inactive on cytosine methylated DNA.  The procedure we
      have used should be of general applicability in determination of the
      methylation sensitivities of other restriction enzymes, as well as studies of
      the effects of methylation on gene expression in direct DNA transfer
      experiments.
AU  - Colasanti J
AU  - Sundaresan V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 391-394.

PMID- 29122883
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequencing of Lactobacillus Species from Two Commercial Probiotic Products.
PG  - e01279-17
AB  - Eight Lactobacillus strains, each intrinsically resistant to an antibiotic, were  isolated
      from two commercial probiotic products. Whole-genome sequencing
      identified two efflux transporters, a multidrug and extrusion protein (MATE)
      efflux transporter, and LmrCD, which may contribute to their intrinsic antibiotic
      resistance and may therefore facilitate their survival in the intestinal
      microbiota following antibiotic therapy.
AU  - Colavecchio A
AU  - Leo V
AU  - Zaccheo S
AU  - Jeukens J
AU  - Emond-Rheault JG
AU  - Hamel J
AU  - Kukavica-Ibrulj I
AU  - Levesque RC
AU  - Goodridge L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01279-17.

PMID- 11234002
VI  - 409
DP  - 2001
TI  - Massive gene decay in the leprosy bacillus.
PG  - 1007-1011
AB  - Leprosy, a chronic human neurological disease, results from infection with the obligate
      intracellular pathogen Mycobacterium leprae, a close relative of the tubercle bacillus.
      Mycobacterium leprae has the longest doubling time of all known bacteria and has thwarted
      every effort at culture in the laboratory.  Comparing the 3.27-megabase genome sequence of an
      armadillo-derived Indian isolate of the leprosy bacillus with that of Mycobacterium
      tuberculosis (4.41 Mb) provides clear explanations for these properties and reveals an extreme
      case of reductive evolution.  Less than half of the genome contains functional genes but
      pseudogenes, with intact counterparts in M. tuberculosis, abound.  Genome downsizing and the
      current mosaic arrangement appear to have resulted from extensive recombination events between
      dispersed repetitive sequences.  Gene deletion and decay have eliminated many important
      metabolic activities including siderophore production, part of the oxidative and most of the
      microaerophilic and anaerobic respiratory chains, and numerous catabolic systems and their
      regulatory circuits.
AU  - Cole ST et al
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2001 409: 1007-1011.

PMID- 9634230
VI  - 393
DP  - 1998
TI  - Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence.
PG  - 537-544
AB  - Countless millions of people have died from tuberculosis, a chronic infectious disease caused
      by the tubercle bacillus.  The complete genome sequence of the best-characterized strain of
      Mycobacterium tuberculosis, H37Rv, has been determined and analysed in order to improve our
      understanding of the biology of this slow-growing pathogen and to help the conception of new
      prophylactic and therapeutic interventions.  The genome comprises 4,411,529 base pairs,
      contains around 4,000 genes, and has a very high guanine + cytosine content that is reflected
      in the biased amino-acid content of the proteins. M. tuberculosis differs radically from other
      bacteria in that a very large portion of its coding capacity is devoted to the production of
      enzymes involved in lipogenesis and lipolysis, and to two new families of glycine-rich
      proteins with a repetitive structure that may represent a source of antigenic variation.
AU  - Cole ST et al
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1998 393: 537-544.

PMID- 16556843
VI  - 311
DP  - 2006
TI  - Genomic islands and the ecology and evolution of Prochlorococcus.
PG  - 1768-1770
AB  - Prochlorococcus ecotypes are a useful system for exploring the origin and function of
      diversity among closely related microbes. The genetic
      variability between phenotypically distinct strains that differ by less
      that 1% in 16S ribosomal RNA sequences occurs mostly in genomic islands.
      Island genes appear to have been acquired in part by phage-mediated
      lateral gene transfer, and some are differentially expressed under light
      and nutrient stress. Furthermore, genome fragments directly recovered from
      ocean ecosystems indicate that these islands are variable among
      cooccurring Prochlorococcus cells. Genomic islands in this free-living
      photoautotroph share features with pathogenicity islands of parasitic
      bacteria, suggesting a general mechanism for niche differentiation in
      microbial species.
AU  - Coleman ML
AU  - Sullivan MB
AU  - Martiny AC
AU  - Steglich C
AU  - Barry K
AU  - Delong EF
AU  - Chisholm SW
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2006 311: 1768-1770.

PMID- 21551312
VI  - 193
DP  - 2011
TI  - Genome sequence of the ethene- and vinyl chloride-oxidizing actinomycete Nocardioides sp. strain JS614.
PG  - 3399-3400
AB  - Nocardioides sp. strain JS614 grows on ethene and vinyl chloride (VC) as sole carbon and
      energy sources, and is of interest for bioremediation and
      biocatalysis. Sequencing the complete genome of JS614 provides insight
      into the genetic basis of alkene oxidation, supports ongoing research into
      the physiology and biochemistry of growth on ethene and VC, and provides
      biomarkers to facilitate detection of VC/ethene-oxidizers in the
      environment. This is the first genome sequence from the genus
      Nocardioides, and the first genome of a VC/ethene-oxidizing bacterium.
AU  - Coleman NV et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3399-3400.

PMID- 3004738
VI  - 44
DP  - 1986
TI  - Universal code equivalent of a yeast mitochondrial intron reading frame is expressed into E. coli as a specific double strand endonuclease.
PG  - 521-533
AB  - The intron of the mitochondrial 21S rRNA gene of Saccharomyces cerevisiae (r1 intron)
      possesses a 235 codon long internal open reading frame (r1 ORF) whose translation product
      determines the duplicative transposition of that intron during crosses between intron-plus
      strains (omega+) and intron-minus ones (omega-). Using site-directed mutagenesis, we have
      constructed a universal code equivalent of the r1 ORF that, under appropriate promoter
      control, allows the overexpression in E. coli of a protein identical to the mitochondrial
      intron encoded "transposase". This protein exhibits a double strand endonuclease activity
      specific for the omega site. This finding demonstrates, for the first time, the enzymatic
      activity of an intron encoded protein whose function is to promote the spreading of that
      intron by generating double strand breaks at a specific sequence within a gene.
AU  - Colleaux L
AU  - d'Auriol L
AU  - Betermier M
AU  - Cottarel G
AU  - Jacquier A
AU  - Galibert F
AU  - Dujon B
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1986 44: 521-533.

PMID- 2842757
VI  - 85
DP  - 1988
TI  - Recognition and cleavage site of the intron-encoded omega transposase.
PG  - 6022-6026
AB  - The optional group I intron of the mitochondrial 21S rRNA gene of Saccharomyces cerevisiae
      contains a 235-codon-long open reading frame the translation product of which (the omega
      transposase) catalyzes the formation of a double-strand break within the intron-minus (omega-)
      copies of the same gene. Purified omega transposase generates in vitro a 4-base-pair staggered
      cut with 3' hydroxyl overhangs at the extact position where the intron eventually inserts in
      the gene. Using randomly mutagenized synthetic olitonucleotides, single-base mutants were
      produced at 21 positions around the cleavage site. Experiments with these oligonucleotides
      show that the recognition site extends over an 18-base pair-long sequence within which minimal
      sequence degeneracy is tolerated. The intron-encoded omega transposase is, therefore, one of
      the most specific restriction endonucleases known to date.
AU  - Colleaux L
AU  - D'Auriol L
AU  - Galibert F
AU  - Dujon B
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1988 85: 6022-6026.

PMID- 1701210
VI  - 223
DP  - 1990
TI  - The apocytochrome b gene of Chlamydomonas smithii contains a mobile intron related to both Saccharomyces and Neurospora introns.
PG  - 288-296
AB  - The mitochondrial DNA of the two interfertile algal species Chlamydomonas smithii and
      Chlamydomonas reinhardtii are co-linear with the exception of ca. 1 kb insertion (the alpha
      insert) present in C. smithii DNA only. In vegetative diploids resulting from interspecific
      crosses, mitochondrial genomes are transmitted biparentally except for the alpha insert which
      is transmitted to all C. reinhardtii molecules in a manner reminiscent of the intron-mediated
      conversion event that occurs at the omega locus in yeast mitochondria, under the action of the
      I-SceI endonuclease. Here we report that the alpha insert corresponds to a typical group I
      intron of 1075 bp, inserted within the gene for apocytochrome b and containing a 237 codon
      open reading frame (ORF). We also report the complete sequence of the apocytochrome b gene of
      C. smithii. Comparison with the sequence of the same gene in C. reinhardtii reveals the
      precise intron insertion site. These data, together with the previous genetic data provide the
      first example of intron mobility in mitochondria of the plant kingdom. The product of the
      intronic ORF shows 36% amino acid identity with the I-SceI endonuclease whereas the intron
      ribozyme shows a 60% identity at the nucleotide level with the Neurospora crassa cob 1 intron.
      The possibility of a recent horizontal transfer of introns between fungi and algae is
      discussed.
AU  - Colleaux L
AU  - Michel-Wolwertz M-R
AU  - Matagne RF
AU  - Dujon B
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1990 223: 288-296.

PMID- Not included in PubMed...
VI  - 113
DP  - 1991
TI  - Sequence-specific bifunctional DNA ligands based on triple-helix-forming oligonucleotides inhibit restriction enzyme cleavage under physiological conditions.
PG  - 1457-1458
AB  - Intermolecular triplex formation has been demonstrated to inhibit DNA-protein
      interactions by the observation that selective binding of a third strand of DNA
      at the recognition site of restriction/modification enzymes prevents cleavage
      or methylation of the duplex.  Triplex formation has the potential to precisely
      modulate gene expression if targeted at protein binding sites involved in the
      regulation of a specific gene.  Intermolecular triplex formation occurs by
      binding of a homopyrimidine oligonucleotide to the major grrove of a
      homopurine-homopyrimidine stretch of DNA, parallel to the purine strand.
      Sequence specificity results from Hoogsteen pairing between thymine and
      protonated cytosine in the third pyrimidine strand and the Watson-Crick A.T and
      G.C pairs of the duplex, respectively.
AU  - Collier DA
AU  - Thuong NT
AU  - Helene C
PT  - Journal Article
TA  - J. Am. Chem. Soc.
JT  - J. Am. Chem. Soc.
SO  - J. Am. Chem. Soc. 1991 113: 1457-1458.

PMID- Not carried by PubMed...
VI  - 56
DP  - 1995
TI  - Regulation of intracellular S-adenosyl-L-methionine as a strategy for cloning restriction endonucleases.
PG  - 73B
AB  - Available strategies to clone restriction endonucleases (REs) are dependent on selection of
      the cognate DNA methyltransferase (Mtase), which are closely linked to the REs.  These
      strategies are indirect and less successful at cloning REs.  Therefore, a novel RE cloning
      strategy was conceived, proposed and developed.  This novel strategy is based on modulating
      the intracellular S-adenosyl-L-methionine (AdoMet) levels.  DNA Mtases require the methyl
      cofactor AdoMet to effect DNA methylation.  By reducing the intracellular AdoMet levels, the
      DNA Mtase is unable to effect DNA methylation.  Restriction endonucleases are present only
      with their cognate DNA methyltransferases to protect the host chromosomal DNA from degradation
      by its own expressed RE genes.  Under reduced levels of AdoMet the DNA Mtase is rendered
      ineffective and the RE will degrade the chromosomal DNA.  To reduce the intracellular AdoMet
      concentrations, several strategies were considered and bacteriophage T3
      S-adenosyl-L-methionine hydrolase (SAMase) was found to be useful for the development of this
      system.  To tightly control the expression of SAMase a novel expression system based on the
      TN10 tetracycline regulation, inducible with heated chlortetracycline, was developed.  The
      effect of SAMase in this system was first optimized by using a cloned M.BamHII (BamHII Mtase)
      to develop conditions to prevent methylation of this plasmid.  This in vivo reduction in DNA
      methylation provides opportunities for cellular studies involved with DNA methylation.  Since
      REs generate double stranded DNA breaks when the DNA is unprotected by the cognate DNA Mtase,
      a system was developed to monitor and assay for these breaks.  A chromosomal
      dinD1::beta-galactosidase promotor gene fusion, induced by double stranded DNA breaks, was P1
      transduced into an appropriate E. coli host.  The tetracycline regulon controlled SAMase was
      supplied on plasmid pACYC184 and the compatible (colE1 replicon) RM.EcoRI plasmid pRI13 was
      also present.  Inducing the expression of SAMase caused the dinD1 promotor to express the
      fused beta-galactosidase, suggesting that the cell was experiencing DNA double strand breaks
      due to the active RE, since the DNA Mtase was affected by reduction of the level of AdoMet.
      This data suggests that this novel cloning strategy is feasible.
AU  - Collier GB
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1995 56: 73B.

PMID- 8467964
VI  - 7
DP  - 1993
TI  - Development of a novel screening system for cloning restriction endonucleases.
PG  - A1303
AB  - We have developed a novel screening system for the cloning of prokaryotic restriction
      endonucleases. This system differs from existing strategies, since it is a screen for the
      restriction endonuclease. Present restriction endonuclease cloning strategies are dependent on
      screening or selecting for the cognate methyltransferase. The cognate methyltransferase
      appears to be necessary to prevent cellular death due to enzymatic cleavage of the host
      chromosomal DNA. This cloning strategy is dependent on modulating the intracellular levels of
      S-adenosyl-L-methionine, the biological methyl donor used by DNA methyltransferases. In the
      presence of a functional restriction endonuclease structural gene and limiting levels of
      S-adenosyl-L-methionine the chromosomal DNA is not methylated but is cleaved, causing cellular
      death or the induction of the SOS response. The methodology of modulating
      S-adenosyl-L-methionine has further application to other cellular phenomena.
AU  - Collier GB
AU  - Mattson TL
AU  - Connaughton JF
AU  - Kalloss WD
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1993 7: A1303.

PMID- 17942674
VI  - 104
DP  - 2007
TI  - A DNA methylation ratchet governs progression through a bacterial cell cycle.
PG  - 17111-17116
AB  - The Caulobacter cell cycle is driven by a cascade of transient regulators, starting with the
      expression of DnaA in G(1) and ending with the
      expression of the essential CcrM DNA methyltransferase at the completion
      of DNA replication. The timing of DnaA accumulation was found to be
      regulated by the methylation state of the dnaA promoter, which in turn
      depends on the chromosomal position of dnaA near the origin of replication
      and restriction of CcrM synthesis to the end of the cell cycle. The dnaA
      gene is preferentially transcribed from a fully methylated promoter. DnaA
      initiates DNA replication and activates the transcription of the next
      cell-cycle regulator, GcrA. With the passage of the replication fork, the
      dnaA promoter becomes hemimethylated, and DnaA accumulation drops. GcrA
      then activates the transcription of the next cell-cycle regulator, CtrA,
      once the replication fork passes through the ctrA P1 promoter, generating
      two hemimethylated copies of ctrA. The ctrA gene is preferentially
      transcribed from a hemimethylated promoter. CtrA then activates the
      transcription of ccrM, to bring the newly replicated chromosome to the
      fully methylated state, promoting dnaA transcription and the start of a
      new cell cycle. We show that the cell-cycle timing of CcrM is critical for
      Caulobacter fitness. The sequential changes in the chromosomal methylation
      state serve to couple the progression of DNA replication to cell-cycle
      events regulated by the master transcriptional regulatory cascade, thus
      providing a ratchet mechanism for robust cell-cycle control.
AU  - Collier J
AU  - McAdams HH
AU  - Shapiro L
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2007 104: 17111-17116.

PMID- 27789643
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of One Marine and One Clinical Vibrio parahaemolyticus Strain, Both Isolated in Sweden.
PG  - e01196-16
AB  - Vibrio parahaemolyticus is the leading bacterial pathogen associated with seafood consumption.
      Here, we report the draft genome sequences of one marine and one
      clinical strain, both isolated in Sweden. These sequences will inform future
      comparative analysis of V. parahaemolyticus in northern Europe.
AU  - Collin B
AU  - Pinnell LJ
AU  - Tallman JJ
AU  - Turner JW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01196-16.

PMID- 26272556
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of 'Candidatus Hepatoplasma crinochetorum' Ps, a Bacterial  Symbiont in the Hepatopancreas of the Terrestrial Isopod Porcellio scaber.
PG  - e00674-15
AB  - 'Candidatus Hepatoplasma crinochetorum' Ps is an extracellular symbiont residing  in the
      hepatopancreas of the terrestrial isopod Porcellio scaber. Its genome is
      highly similar to that of the close relative 'Ca. Hepatoplasma crinochetorum' Av
      from Armadillidium vulgare. However, instead of a clustered regularly interspaced
      short palindromic repeat (CRISPR)-Cas system, it encodes a type I restriction
      modification system.
AU  - Collingro A
AU  - Kostanjsek R
AU  - Toenshoff ER
AU  - Schulz F
AU  - Schuster L
AU  - Domann D
AU  - Horn M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00674-15.

PMID- 21690563
VI  - 28
DP  - 2011
TI  - Unity in variety -- the pan-genome of the Chlamydiae.
PG  - 3253-3270
AB  - Chlamydiae are evolutionarily well-separated bacteria that live exclusively within eukaryotic
      host cells.  They include important human pathogens such as Chlamydia trachomatis as well as
      symbionts of protozoa.  As these bacteria are experimentally challenging and genetically
      intractable, our knowledge about them is still limited.  In this study, we obtained the genome
      sequences of Simkania negevensis Z, Waddlia chondrophila 2032/99 and Parachlamydia
      acanthamoebae UV-7.  This enabled us to perform the first comprehensive comparative and
      phylogenomic analysis of representative members of four major families of the Chlamydiae,
      including the Chlamydiaceae.  We identifid a surprisingly large core gene set present in all
      genomes and a high number of diverse accessory genes in those Chlamydiae that do not primarily
      infect humans or animals, including a chemosensory system in P. acanthamoebae and a type IV
      secretion system.  In S. negevensis, the type IV secretion system is encoded on a large
      conjugative plasmid (pSn, 132 kb).  Phylogenetic analyses suggested that a plasmid similar to
      the S. negevensis plasmid was originally acquired by the lst common ancestor of all four
      families and that it was subsequently reduced, integrated into the chromosome, or lost during
      diversification, ultimately giving rise to the extant virulence-associated plasmid of
      pathogenic chlamydiae.  Other virulence factors, including a type III secretion system, are
      conserved among the Chlamydiae to variable degrees, and together with differences in the
      composition of the cell wall, reflect adaptation to different host cells including convergent
      evolution among the four chlamydial families.  Phylogenomic analysis focusing on chlamydial
      proteins with homology to plant proteins provided evidence for the aquisition of 53 chlamydial
      genes by a plant progenitor, lending further support for the hypothesis of an early
      interaction between a chlamydial ancestor and the primary photosynthetic eukaryote.
AU  - Collingro A
AU  - Tischler P
AU  - Weinmaier T
AU  - Penz T
AU  - Heinz E
AU  - Brunham RC
AU  - Read TD
AU  - Bavoil PM
AU  - Sachse K
AU  - Kahane S
AU  - Friedman MG
AU  - Rattei T
AU  - Myers GSA
AU  - Horn M
PT  - Journal Article
TA  - Mol. Biol. Evol.
JT  - Mol. Biol. Evol.
SO  - Mol. Biol. Evol. 2011 28: 3253-3270.

PMID- 21551313
VI  - 193
DP  - 2011
TI  - Draft genome of Phaeobacter gallaeciensis ANG1, a dominant member of the accessory nidamental gland of Euprymna scolopes.
PG  - 3397-3398
AB  - Phaeobacter gallaeciensis strain ANG1 represents the dominant member of the bacterial
      consortium within the reproductive accessory nidamental
      gland (ANG) of the squid Euprymna scolopes. We present a 4.59Mb assembly
      of its genome, which may provide clues as to how it benefits its host.
AU  - Collins AJ
AU  - Nyholm SV
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3397-3398.

PMID- 27257212
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Methylobacterium sp. Strain ARG-1 Isolated from the White-Rot Fungus Armillaria gallica.
PG  - e00398-16
AB  - Methylobacterium sp. strain ARG-1 was isolated from a cell culture of hyphal tips of the
      white-rot fungus Armillaria gallica We describe here the sequencing,
      assembly, and annotation of its genome, confirming the presence of genes involved
      in methylotrophy. This is the first genome announcement of a strain of
      Methylobacterium associated with A. gallica.
AU  - Collins C
AU  - Kowalski C
AU  - Zebrowski J
AU  - Tulchinskaya Y
AU  - Tai AK
AU  - James-Pederson M
AU  - Hirst R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00398-16.

PMID- 13312225
VI  - 2
DP  - 1956
TI  - Host-controlled variations in bacteriophages active against lactic Streptococci.
PG  - 261-271
AB  - Certain bacteriophages were very active against some strains of Streptococcus
      cremoris, and restricted in activity against others.  Drastic changes in
      activity were observed after one growth cycle.  The results of adsorption of a
      restricted bacteriophage was either no detected consequence, bacterial death,
      or bacterial death followed by bacteriophage reproduction.  The occurrence of
      each of the last two possibilities was found to be influenced by the
      multiplicity of infection.  Bacteriophage reproduction within the fruitful
      cells of a restrictive host produced progeny that were fully active on the
      cells of that host.  Alteration of the bacteriophgaes appeared limited to
      changes in virulence for particular hosts, the alterations not being
      accompanied by changes in adsorbability or changes in heat resistance.  Both
      the strain of infecting bacteriophage and the particular host were important
      factors in determining the specific virulence of the progeny.
AU  - Collins EB
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1956 2: 261-271.

PMID- 6248088
VI  - 30
DP  - 1980
TI  - Restriction endonucleases or the site-specific DNA endonucleases.
PG  - 541-547
AB  - Our present view of the site-specific endonucleases, which appear to be
      ubiquituous in the prokaryote kingdom, is probably heavily distorted by our
      search for tools for recombinant DNA technology.  Only those enzymes having
      recognition sequences in the range of three to seven specific bases have been
      isolated.  Of course the usefulness of these enzymes in the analysis of complex
      genomes, the rise of "reverse genetics", and the immediate breakthroughs in the
      area of gene expression in eukaryotes, particularly the understanding of tumour
      virus RNA processing and gene rearrangements in the expression of
      immunoglobulin genes has dominated the consciousness of the molecular and
      cell-biologists during the last five years.  There is great diversity of
      staggering, symmetry, asymmetry and degeneration in the recognition sequences
      found.  Taking into account also the genetic data on site-specific
      recombination and/or DNA degradation suggests that our present collection of
      endonucleases may only represent a narrow spectrum of specificities on an
      open-ended scale of complexity.  The enzymes themselves provide a rich pool to
      be exploited by the biophysicist and the biochemist to probe the subtleties of
      DNA-protein interaction.
AU  - Collins J
AU  - Mayer H
PT  - Journal Article
TA  - Arzneimittelforschung
JT  - Arzneimittelforschung
SO  - Arzneimittelforschung 1980 30: 541-547.

PMID- 17631616
VI  - 35
DP  - 2007
TI  - REPK: an analytical web server to select restriction endonucleases for terminal restriction fragment length polymorphism analysis.
PG  - W58-W62
AB  - Terminal restriction fragment length polymorphism (T-RFLP) analysis is a widespread technique
      for rapidly fingerprinting microbial communities.
      Users of T-RFLP frequently overlook the resolving power of well-chosen
      restriction endonucleases and often fail to report how they chose their
      enzymes. REPK (Restriction Endonuclease Picker) assists in the rational
      choice of restriction endonucleases for T-RFLP by finding sets of four
      restriction endonucleases that together uniquely differentiate
      user-designated sequence groups. With REPK, users can provide their own
      sequences (of any gene, not just 16S rRNA), specify the taxonomic rank of
      interest and choose from a number of filtering options to further narrow
      down the enzyme selection. Bug tracking is provided, and the source code
      is open and accessible under the GNU Public License v.2, at
      http://code.google.com/p/repk. The web server is available without access
      restrictions at http://rocaplab.ocean.washington.edu/tools/repk.
AU  - Collins RE
AU  - Rocap G
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2007 35: W58-W62.

PMID- 15271940
VI  - 72
DP  - 2004
TI  - YAPI, a new Yersinia pseudotuberculosis pathogenicity island.
PG  - 4784-4790
AB  - Pathogenicity islands (PAIs) are chromosomal clusters of pathogen-specific virulence genes
      often found at tRNA loci. In the
      Yersinia pseudotuberculosis 32777 chromosome, we characterized a 98-kb
      segment that has all of the characteristic features of a PAI, including
      insertion in a (phenylalanine) tRNA gene, the presence of a
      bacteriophage-like integrase-encoding gene, and direct repeats at the
      integration sites. The G+C content of the segment ranges from 31 to
      60%, reflecting a genetic mosaic: this is consistent with the notion
      that the sequences were horizontally acquired. The PAI, termed YAPI
      (for Yersinia adhesion pathogenicity island), carries 95 open reading
      frames and includes (i) the previously described pil operon, encoding a
      type IV pilus that contributes to pathogenicity (F. Collyn et al.,
      Infect. Immun. 70:6196-6205, 2002); (ii) a block of genes potentially
      involved in general metabolism; (iii) a gene cluster for a
      restriction-modification system; and (iv) a large number of mobile
      genetic elements. Furthermore, the PAI can excise itself from the
      chromosome at low frequency and in a precise manner, and deletion does
      not result in a significant decrease of bacterial virulence compared to
      inactivation of the fimbrial gene cluster alone. The prevalence and
      size of the PAI vary from one Y. pseudotuberculosis strain to another,
      and it can be found integrated into either of the two phe tRNA loci
      present on the species' chromosome. YAPI was not detected in the genome
      of the genetically closely related species Y. pestis, whereas a
      homologous PAI is harbored by the Y. enterocolitica chromosome.
AU  - Collyn F
AU  - Billault A
AU  - Mullet C
AU  - Simonet M
AU  - Marceau M
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2004 72: 4784-4790.

PMID- 4557386
VI  - 70
DP  - 1972
TI  - Expression of the Escherichia coli K, B and Phage P1 DNA host specificities in Salmonella typhimurium.
PG  - 123-128
AB  - The Escherichia coli K,B and phage P1 host specificity genes (hsp) were
      introduced into Salmonella typhimurium by means of E. coli Hfr x S. typhimurium
      F- crosses.  The three systems were found to govern modification and
      restriction of phages P22 and L.  The restriction coefficients were comparable
      to that of lambda for the PI system and were lower (about 100) for the K and B
      systems.  Phage grown on hspK+ and hspB+ recombinants was restricted by S.
      typhimurium independently of the restriction governed by the LT system.  This
      observation suggested that S. typhimurium possesses a previously undetected hsp
      locus allelic to those of E. coli K and B.
AU  - Colson AM
AU  - Colson C
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1972 70: 123-128.

PMID- 4902398
VI  - 58
DP  - 1969
TI  - Host-controlled restriction mutants of Salmonella typhimurium.
PG  - 57-64
AB  - Forty-eight independent restriction-deficient mutations of Salmonella typhimurium LT2 were
      isolated by using selective and non-selective methods.  With phage P22 it was shown that some
      mutations affected the restriction capacity only, while others affected both restriction and
      modification.  The host-restriction of S. typhimurium decreased the recovery of F-lac+
      infected cells and decreased the yield of recombinants in bacterial mating and in phage
      P22-mediated transduction.
AU  - Colson AM
AU  - Colson C
AU  - Van Pel A
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1969 58: 57-64.

PMID- Not included in PubMed...
VI  - 41
DP  - 1978
TI  - Genetics of R-M systems in Salmonella.
PG  - 123
AB  - Salmonella typhimurium LT2 and LT7 have three R-M systems coded by chromosomal genes.  Mutants
      with r-m+ and r-m- phenotypes have been isolated for each of them.  All three were first
      detected in Escherichia coli-S. typhimurium hybrids.  System LT was detected when phage P22
      from lac+ hybrids between E. coli Hfr and S. typhimurium LT7 mut (with a mutator gene) was
      plated on wild-type S. typhimurium.  All mutations affecting system LT are closely linked and
      situated between proA and proC.  System LT is present in the many Salmonella serotypes tested,
      with the exception of S. typhi.  System SA was first observed using hybrids with the hsdK
      genes of E. coli: phage L. (closely related to P22) from such hybrids underwent restriction in
      wild-type S. typhimurium, independently of the presence of system LT.  hsdSA is situated
      between pyrB and serB and was first thought to be the Salmonella allele of hsdK and hsdB in E.
      coli.  System SA was found in all S. typhimurium strains tested, but not in other Salmonella
      serotypes.
AU  - Colson C
PT  - Journal Article
TA  - Heredity
JT  - Heredity
SO  - Heredity 1978 41: 123.

PMID- 4947313
VI  - 69
DP  - 1971
TI  - A new Salmonella typhimurium DNA host specificity.
PG  - 345-351
AB  - The genetic properties of a new (hspS) host specificity of Salmonella
      typhimurium were investigated using bacteriophage L.  Phage L is a better
      substrate for S-specific restriction than phage P22.  Mutants deficient in
      S-restriction only were found at the same frequency as mutants deficient in
      both restriction and modification.  Crosses between S. typhimurium Hfr and S.
      typhimurium F- or between Escherichia coli and S. typhimurium showed that the S
      system has the same chromosomal location as the K system of E. coli.  The S
      system was introduced in E. coli and found to be effective on phage lambda.
AU  - Colson C
AU  - Colson AM
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1971 69: 345-351.

PMID- 4922671
VI  - 60
DP  - 1970
TI  - Chromosomal location of host specificity in Salmonella typhimurium.
PG  - 265-271
AB  - The chromosomal location of the genes for host specificity in Salmonella
      typhimurium has been investigated by F-mediated conjugation using host
      specificity mutants isolated previously.  It was found that the sites of
      mutations leading to two distinct phenotypes r-LTm+LT and r-LTm-LT, are closely
      linked to each other and are located near the marker proC.
AU  - Colson C
AU  - Colson AM
AU  - van Pel A
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1970 60: 265-271.

PMID- 5327803
VI  - 52
DP  - 1965
TI  - The location of the genes for host-controlled modification and restriction in Escherichia coli K-12.
PG  - 1043-1050
AB  - Recent experiments have clarified certain aspects of the processes of
      modification and restriction by which certain systems of host-controlled
      modification (HCM) operate in Escherichia coli (Arber 1962; Arber and Dussoix
      1962; Dussoix and Arber 1962; Glover, Schell, Symonds and Stacey 1963).  The
      two aspects of HCM have one thing in common:  they both involve the recognition
      of a particular base sequence in DNA.  However, basically they are very
      different, modification resulting in the addition of certain groups to DNA,
      while restriction leaves unmodified DNA in a condition in which it is open to
      attack by DNase.  This apparent dissimilarity in the processes of restriction
      and modification suggests that they are under independent genetic control.  One
      method of learning more about the genetic control of HCM in this system is to
      analyze it genetically.
AU  - Colson C
AU  - Glover SW
AU  - Symonds N
AU  - Stacey KA
PT  - Journal Article
TA  - Genetics
JT  - Genetics
SO  - Genetics 1965 52: 1043-1050.

PMID- 4601252
VI  - 129
DP  - 1974
TI  - DNA restriction and modification systems in Salmonella.  I.  SA and SB, two Salmonella typhimurium systems determined by genes with a chromosomal location comparable to that of the Escherichia coli hsd genes.
PG  - 325-337
AB  - Haploid hybrids between Salmonella typhimurium Hfr and Escherichia coli F-
      exercise two additive types of restriction and modification (SA and SB) on
      phage lambda.  System SA had been detected previously in S. typhimurium with
      phage L.  Independent mutants in the SA and SB systems were isolated.  P22- and
      P1-mediated transductions in S. typhimurium and in hybrids established that the
      genes governing these systems are independent but linked and situated
      counter-clockwise of ser B on the map, in the order:  pyrB-hsdSA-hsdSB-serB.
AU  - Colson C
AU  - van Pel A
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1974 129: 325-337.

PMID- 
VI  - 0
DP  - 1994
TI  - Homologous recombination, DNA repair and mycobacterial recA genes.
PG  - 217-226
AB  - Bacterial responses to DNA damage are highly conserved.  One system, the
      SOS response, involves the coordinately induced expression of over 20 genes through a
      common regulatory mechanism.  The RecA protein, found in most bacteria, plays a central
      role in the regulation of the SOS response.  In addition to its regulatory function, this
      protein also mediates genetic recombination and DNA repair.  Virtually nothing is known
      about these systems in mycobacteria.  However, since some mycobacteria are intracellular
      pathogens and many of the mechanisms involved in macrophage killing of such pathogens
      require the production of DNA-damaging agents such as peroxide and nitric oxide, DNA
      repair mechanisms are likely to be particularly important for mycobacterial survival.  In
      addition, homologous genetic recombination, a process mediated by RecA, is an important
      technique for the genetic manipulation of bacteria and could play an important role in our
      understanding of gene function.  In this chapter we discuss the mechanisms involved in
      homologous recombination and DNA repair, what is known about these systems in
      mycobacteria, and recent information on the unusual structure of the recA gene in the
      pathogenic mycobacteria.
AU  - Colston MJ
AU  - Davis EO
PT  - Journal Article
TA  - Tuberculosis: Pathogenesis, Protection, and Control
JT  - Tuberculosis: Pathogenesis, Protection, and Control
SO  - Tuberculosis: Pathogenesis, Protection, and Control 1994 0: 217-226.

PMID- 29773633
VI  - 6
DP  - 2018
TI  - Complete Genome Sequences of Two Bioluminescent Vibrio campbellii Strains Isolated from Biofouling Communities in the Bay of Bengal.
PG  - e00422-18
AB  - Vibrio campbellii is a pathogen of aquatic animals and has been proposed as a bacterial
      partner in the formation of bioluminescent milky seas. We present here
      the complete genome sequences assembled from Illumina and Oxford Nanopore data
      for two bioluminescent Vibrio campbellii strains (BoB-53 and BoB-90) isolated
      from biofouled moorings in the Bay of Bengal.
AU  - Colston SM
AU  - Ellis GA
AU  - Kim S
AU  - Wijesekera HW
AU  - Leary DH
AU  - Lin B
AU  - Kirkup BC
AU  - Hervey WJ IV
AU  - Vora GJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00422-18.

PMID- 29650571
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Aeromonas cavernicola sp. nov. DSM 24474(T), Isolated from a Cavern Brook in the Moravia Region of the Czech Republic.
PG  - e00227-18
AB  - Species of the Aeromonas genus can be found in numerous environmental milieus, including
      various water sources, and some species cause disease in animals. We
      present here the draft genome sequence for Aeromonas cavernicola DSM 24474(T), a
      novel species isolated from a freshwater brook within a cavern in the Czech
      Republic.
AU  - Colston SM
AU  - Navarro A
AU  - Martinez-Murcia AJ
AU  - Graf J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00227-18.

PMID- 29650570
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Aeromonas lusitana sp. nov. Strain DSM 24905(T), Isolated from a Hot Spring in Vila-Real, Portugal.
PG  - e00226-18
AB  - Aeromonas lusitana sp. nov. is an isolate derived from a study aimed at characterizing
      Aeromonas spp. from water sources used for recreation and
      agricultural purposes and assessing the implications these organisms have for
      human and animal health. We present here the 4.52-Mbp draft genome sequence of
      this novel species.
AU  - Colston SM
AU  - Navarro A
AU  - Martinez-Murcia AJ
AU  - Graf J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00226-18.

PMID- 14871304
VI  - 37
DP  - 2004
TI  - Efficient discovery of DNA polymorphisms in natural populations by Ecotilling.
PG  - 778-786
AB  - We have adapted the mutation detection technology used in Targeting Induced Local Lesions in
      Genomes (TILLING) to the discovery of polymorphisms in natural populations.  The genomic DNA
      of a queried individual is mixed with a references DNA and used to amplify a target 1-kbp
      region of DNA with asymmetrically labeled fluorescent primers.  Afer heating and annealing,
      heteroduplexes are nicked at mismatched sites by the endonuclease CEL I and cut strands are
      visualized using Li-cor gel analyzers.  Putative polymorphisms detected in one fluorescence
      channel can be verified by appearance of the opposite cut strand in the other channel.  We
      demonstrated the efficiency of this technology, called Ecotilling, by the discovery in 150+
      individuals of 55 haplotypes in five genes, ranging from sequences differing by a single
      nucleotide polymorphism to those representing complex haplotypes in five genes, ranging from
      sequences differing by a single nucleotide polymorphism to those representing complex
      haplotypes.  The discovered polymorphisms were confirmed by sequencing and included base-pair
      changes, small insertions and deletions, and variation in microsatellite repeat number.
      Ecotilling allows the rapid detection of variation in many individuals and is cost effective
      because only one individual for each haplotype needs to be sequenced.  The technology is
      applicable to any organism including those that are heterozygous and polyploid.
AU  - Comai L
AU  - Young K
AU  - Till BJ
AU  - Reynolds S
AU  - Greene EA
AU  - Codomo CA
AU  - Enns L
AU  - Johnson JE
AU  - Burtner C
AU  - Odden A
AU  - Henikoff S
PT  - Journal Article
TA  - Plant J.
JT  - Plant J.
SO  - Plant J. 2004 37: 778-786.

PMID- 23405316
VI  - 1
DP  - 2013
TI  - Draft Genome of Klebsiella pneumoniae Sequence Type 512, a Multidrug-Resistant Strain Isolated during a Recent KPC Outbreak in Italy.
PG  - e00035-12
AB  - Here, we present the draft genome sequence of Klebsiella pneumoniae subsp. pneumoniae sequence
      type 512 (ST512) isolated during a KPC-producer outbreak. This strain is resistant to
      beta-lactams, cephalosporins, fluoroquinolones, aminoglycosides, macrolides, tetracyclines,
      and carbapenems but susceptible to colistin. The ST512-K30BO genome is composed of 289 contigs
      for 5,392,844 bp with 56.9% G+C content.
AU  - Comandatore F
AU  - Gaibani P
AU  - Ambretti S
AU  - Landini MP
AU  - Daffonchio D
AU  - Marone P
AU  - Sambri V
AU  - Bandi C
AU  - Sassera D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00035-12.

PMID- 23405348
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences of Two Multidrug Resistant Klebsiella pneumoniae ST258 Isolates Resistant to Colistin.
PG  - e00113-12
AB  - Sequence type 258 (ST258) is the most widespread multidrug resistant (MDR) Klebsiella
      pneumoniae strain worldwide. Here, we report the draft genome sequences of two
      colistin-resistant MDR K. pneumoniae ST258 clinical strains isolated from hospital patients in
      Italy. These strains are resistant to beta-lactams, cephalosporins, fluoroquinolones,
      aminoglycosides, macrolides, tetracyclines, carbapenems, and colistin.
AU  - Comandatore F
AU  - Sassera D
AU  - Ambretti S
AU  - Landini MP
AU  - Daffonchio D
AU  - Marone P
AU  - Sambri V
AU  - Bandi C
AU  - Gaibani P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00113-12.

PMID- 16218579
VI  - 127
DP  - 2005
TI  - Methyltransferase-directed DNA strand scission.
PG  - 14136-14137
AB  - The study of prokaryotic DNA methyltransferases (MTases) has provided significant insight into
      eukaryotic MTases and the important role that methylation plays in mammalian biology.  The
      prokaryotic enzymes M.TaqI, M.EcoRI, and M.HhaI are all capable of using 5'-aziridine
      adenylate 1 in place of (S)-adenosyl-L-methionine in MTase-dependent DNA alkylation reactions.
      By virtue of the C8 azide, 1 is significant because it is capable of converting these DNA
      MTases into azidonucleoside transferases.  Not suprising, DNA modified with 1 is capable of
      undergoing very efficient Staudinger ligation with biotinylated triarylphosphines.
AU  - Comstock LR
AU  - Rajski SR
PT  - Journal Article
TA  - J. Am. Chem. Soc.
JT  - J. Am. Chem. Soc.
SO  - J. Am. Chem. Soc. 2005 127: 14136-14137.

PMID- 15778434
VI  - 33
DP  - 2005
TI  - Conversion of DNA methyltransferases into azidonucleosidyl transferases via synthetic cofactors.
PG  - 1644-1652
AB  - Aziridine-based cofactor mimics have been synthesized and are shown to undergo
      methyltransferase-dependent DNA alkylation. Notably, each cofactor
      mimic possesses an azide functionality, to which can be attached an
      assortment of unnatural groups following methyltransferase-dependent DNA
      delivery. DNA duplexes modified with these cofactor mimics are capable of
      undergoing the Staudinger ligation with phosphines tethered to biological
      functionalities following enzymatic modification. This methodology
      provides a new tool by which to selectively modify DNA in a
      methyltransferase-dependent way. The conversion of biological
      methyltransferases into azidonucleosidyl transferases demonstrated here
      also holds tremendous promise as a means of identifying, as yet, unknown
      substrates of methylation.
AU  - Comstock LR
AU  - Rajski SR
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2005 33: 1644-1652.

PMID- 26067959
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Stenotrophomonas maltophilia Strain UV74 Reveals Extensive Variability within Its Genomic Group.
PG  - e00611-15
AB  - We report the draft genome sequence of Stenotrophomonas maltophilia UV74, isolated from a
      vascular ulcer. This draft genome sequence shall contribute to
      the understanding of the evolution and pathogenicity of this species,
      particularly regarding isolates of clinical origin.
AU  - Conchillo-Sole O
AU  - Yero D
AU  - Coves X
AU  - Huedo P
AU  - Martinez-Servat S
AU  - Daura X
AU  - Gibert I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00611-15.

PMID- 11802735
VI  - 41
DP  - 2002
TI  - Dissecting the metal ion dependence of DNA binding by PvuII endonuclease.
PG  - 1335-1342
AB  - Divalent cations can provide an effective means of modulating the behavior of nucleic acid
      binding proteins. As a result, there is strong interest in understanding the role of metal
      ions in the function of both nucleic acid binding proteins and their enzymes. We have applied
      complementary fluorescence spectroscopic and nitrocellulose filter binding assays to
      quantitate the role of metal ions in mediating DNA binding and sequence specificity by the
      representative PvuII endonuclease. At pH 7.5 in the presence of the catalytically
      nonsupportive Ca(II), this enzyme binds the PvuII target sequence with a K(d) of 50 pM. Under
      strict metal-free conditions, the enzyme exhibits a K(d) of only 300 nM for the cognate
      sequence, an affinity which is weak relative to those measured for other systems in the
      absence of metal ions. This represents a 6000-fold increase in PvuII affinity for cognate DNA
      upon the addition of Ca(II). The pH dependences of both metal ion-dependent and metal
      ion-independent DNA binding are remarkably shallow throughout the physiological range; other
      characterized restriction enzymes exhibit more pronounced pH dependences of DNA binding even
      in the absence of metal ions. Similar measurements with noncognate sequences indicate that
      divalent metal ions are not important to nonspecific DNA binding; K(d) values are
      approximately 200 nM throughout the physiological pH range, a behavior shared with other
      endonucleases. While some of these results extend somewhat the range of expected behavior for
      restriction enzymes, these results indicate that PvuII endonuclease shares with other
      characterized systems a mechanism by which cognate affinity and sequence discrimination are
      most effectively achieved in the presence of divalent metal ions.
AU  - Conlan LH
AU  - Dupureur CM
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2002 41: 1335-1342.

PMID- 10572643
VI  - 27
DP  - 1999
TI  - Modulating restriction endonuclease activities and specificities using neutral detergents.
PG  - 955-960
AB  - It is well known that type II restriction enzyme activities and specificities can be modulated
      by altering solution conditions. The addition of co-solvents such as dimethyl sulfoxide
      (DMSO), alcohols and polyols can promote star activity, which is the cleavage of non-cognate
      sequences. While neutral detergents are often used to control protein aggregation, little is
      known about the effect of neutral detergents on restriction enzyme activities and
      specificities. We report here that BamHI, BglI, BglII, EcoRI, EcoRV, HindIII, MluI, PvuII,
      SalI and XhoI restriction endonucleases are remarkably tolerant of high concentrations of
      neutral detergents, Triton X-100, CHAPS and octyl glucoside. In most cases, lambda DNA
      cleavage rates were comparable to those observed in the absence of detergent. Indeed, the
      specific activities of SalI and XhoI were appreciably increased in the presence of Triton
      X-100. For all enzymes active in the presence of detergents, sequence specificity toward
      lambda DNA was not compromised. Assays of star cleavage of pUC18 by EcoRI, PvuII and BamHI
      endonucleases in equimolar concentrations of Triton X-100 and sucrose revealed reduced star
      activity in the detergent relative to the sucrose co-solvent. Interestingly, under star
      activity-promoting
      conditions, PvuII endonuclease displayed greater fidelity in Triton X-100 than in conventional
      buffer. Taken altogether, these results suggest that in some cases, neutral detergents can be
      used to manipulate restriction endonuclease reaction rates and specificities.
AU  - Conlan LH
AU  - Jose TJ
AU  - Thornton KC
AU  - Dupureur CM
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 1999 27: 955-960.

PMID- 
VI  - 
DP  - 2002
TI  - The influence of divalent metal ions on DNA binding and cleavage by the restriction enzyme PvuII endonuclease.
PG  - 143
AB  - Divalent metal ions can play an important role in the interactions beween nucleic acids and
      proteins.  Here, PvuII endonuclease is developed as a model system to study DNA binding and
      catalysis as a function of divalent metal ions.  A novel approach of equilibrium binding and
      kinetics of binding and cleavage is used to understand the influence of divalent metal ions on
      DNA recognition and catalysis.  In the presence of calcium, a divalent metal ion that does not
      support catalysis, the  interaction between the specific recognition site and PvuII
      endonuclease has a Kd of 53 +/- 10 pM (pH 7.5, 100 mM NaCl, 10 MM CaCl2).  A 6000 fold
      reduction in the dissociation constant is seen when metal ions are absent.  Specific DNA
      binding interactions exhibit an unusual shallow pH dependence.  Most protein-DNA interactions
      have a more pronounced pH effect.  Nonspecific DNA binding is independent of divalent metal
      ions; exhibiting a Kd near 200 nM (pH 7.5, 100 mM NaCl). Kinetic methods were developed to
      understand how many metal ions are involved with both DNA binding and catalysis.  This work
      presents the first comprehensive kinetic study of a restriction enzyme to show that more than
      one metal ion influences both the DNA cleavage and association rate constants.  Using Ca(II)
      to prevent turnover, the enzyme-DNA association rate constant is metal ion concentration
      dependent, exhibiting a 100 fold increase from metal-free experiments to those done in the
      presence of 10 mM Ca(II).  The association rate constant exhibited cooperative binding of at
      least four metal ions per PvuII endonuclease dimer.  The dissociation rate constant showed a
      shallow Ca(II) concentration dependence.  This provides new evidence that the metal ion
      influence on the DNA dissociation constant is due to alterations in the association rate
      constant.  Hill analysis of the cleavage rate constant as a function of Mg(II) concentration,
      indicates that at least three metal ions per endonuclease dimer are involved in DNA
      hydrolysis.  Combining the knowledge gained from equilibrium and kinetic studies provides
      unique insights on how metal ions influence DNA binding and catalysis for restriction enzymes.
AU  - Conlan LM
PT  - Journal Article
TA  - Ph.D. Thesis, Texas A and M Univ., College Station, TX, USA
JT  - Ph.D. Thesis, Texas A and M Univ., College Station, TX, USA
SO  - Ph.D. Thesis, Texas A and M Univ., College Station, TX, USA 2002 : 143.

PMID- 25232178
VI  - 6
DP  - 2014
TI  - Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae.
PG  - 254ra126
AB  - Public health officials have raised concerns that plasmid transfer between Enterobacteriaceae
      species may spread resistance to carbapenems, an antibiotic
      class of last resort, thereby rendering common health care-associated infections
      nearly impossible to treat. To determine the diversity of carbapenemase-encoding
      plasmids and assess their mobility among bacterial species, we performed
      comprehensive surveillance and genomic sequencing of carbapenem-resistant
      Enterobacteriaceae in the National Institutes of Health (NIH) Clinical Center
      patient population and hospital environment. We isolated a repertoire of
      carbapenemase-encoding Enterobacteriaceae, including multiple strains of
      Klebsiella pneumoniae, Klebsiella oxytoca, Escherichia coli, Enterobacter
      cloacae, Citrobacter freundii, and Pantoea species. Long-read genome sequencing
      with full end-to-end assembly revealed that these organisms carry the carbapenem
      resistance genes on a wide array of plasmids. K. pneumoniae and E. cloacae
      isolated simultaneously from a single patient harbored two different
      carbapenemase-encoding plasmids, indicating that plasmid transfer between
      organisms was unlikely within this patient. We did, however, find evidence of
      horizontal transfer of carbapenemase-encoding plasmids between K. pneumoniae, E.
      cloacae, and C. freundii in the hospital environment. Our data, including full
      plasmid identification, challenge assumptions about horizontal gene transfer
      events within patients and identify possible connections between patients and the
      hospital environment. In addition, we identified a new carbapenemase-encoding
      plasmid of potentially high clinical impact carried by K. pneumoniae, E. coli, E.
      cloacae, and Pantoea species, in unrelated patients and in the hospital
      environment.
AU  - Conlan S et al
PT  - Journal Article
TA  - Sci. Transl. Med.
JT  - Sci. Transl. Med.
SO  - Sci. Transl. Med. 2014 6: 254ra126.

PMID- 25540345
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of a Klebsiella pneumoniae Isolate with Chromosomally Encoded Carbapenem Resistance and Colibactin Synthesis Loci.
PG  - e01332-14
AB  - Klebsiella pneumoniae is an important nosocomial pathogen, and multidrug-resistant strains
      have become a worldwide concern. Here, we report the
      complete genome of a K. pneumoniae isolate with chromosomally integrated blaKPC
      genes and a colibactin synthesis locus.
AU  - Conlan S
AU  - Deming C
AU  - Tsai YC
AU  - Lau AF
AU  - Dekker JP
AU  - Korlach J
AU  - Segre JA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01332-14.

PMID- 27417839
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of a Klebsiella pneumoniae Strain Carrying blaNDM-1 on a Multidrug Resistance Plasmid.
PG  - e00664-16
AB  - Here, we report the genome sequence of a blaNDM-1-positive Klebsiella pneumoniae  AATZP
      isolate cultured from a perirectal surveillance swab collected upon
      admission of a patient to the NIH Clinical Center in 2014. Genome sequencing of
      this isolate revealed three plasmids, including one carrying the blaNDM-1 gene
      encoding resistance to carbapenems.
AU  - Conlan S
AU  - Lau AF
AU  - Palmore TN
AU  - Frank KM
AU  - Segre JA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00664-16.

PMID- 16269786
VI  - 71
DP  - 2005
TI  - Rhodopseudomonas palustris regulons detected by cross-species analysis of alphaproteobacterial genomes.
PG  - 7442-7452
AB  - Rhodopseudomonas palustris, an alpha-proteobacterium, carries out three of the chemical
      reactions that support life on this planet: the conversion of sunlight to chemical-potential
      energy; the absorption of carbon dioxide, which it converts to cellular material; and the
      fixation of atmospheric nitrogen into ammonia. Insight into the transcription-regulatory
      network that coordinates these processes is fundamental to understanding the biology of this
      versatile bacterium. With this goal in mind, we predicted regulatory signals genomewide, using
      a two-step phylogenetic-footprinting and clustering process that we had developed previously.
      In the first step, 4,963 putative transcription factor binding sites, upstream of 2,044 genes
      and operons, were identified using cross-species Gibbs sampling. Bayesian motif clustering was
      then employed to group the cross-species motifs into regulons. We have identified 101 putative
      regulons in R. palustris, including 8 that are of particular interest: a photosynthetic
      regulon, a flagellar regulon, an organic hydroperoxide resistance regulon, the LexA regulon,
      and four regulons related to nitrogen metabolism (FixK2, NnrR, NtrC, and sigma54). In some
      cases, clustering allowed us to assign functions to proteins that previously had been
      annotated with only putative functions; we have identified RPA0828 as the organic
      hydroperoxide resistance regulator and RPA1026 as a cell cycle methylase. In addition to
      predicting regulons, we identified a novel inverted repeat that likely forms a highly
      conserved stem-loop and that occurs downstream of over 100 genes.
AU  - Conlan S
AU  - Lawrence C
AU  - McCue LA
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2005 71: 7442-7452.

PMID- 2374727
VI  - 18
DP  - 1990
TI  - The complete sequence of the Bacillus amyloliquefaciens proviral H2, BamHI methylase gene.
PG  - 4002
AB  - None
AU  - Connaughton JF
AU  - Kaloss WD
AU  - Vanek PG
AU  - Nardone GA
AU  - Chirikjian JG
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 4002.

PMID- 3192615
VI  - 107
DP  - 1988
TI  - Cloning of the BamHI methyl transferase gene from Bacillus amyloliquefaciens.
PG  - 535a
AB  - We wish to report the initial characterization of a recombinant clone containing the BamHI
      methylase gene.  Genomic chromosomal DNA purified from Bacillus amyloliquefaciens was
      partially cleaved with HindIII, fractionated by size, and cloned into pSP64.  Plasmid DNA from
      this library was challenged with BamHI endonuclease and transformed into E. coli HB101.  A
      recombinant plasmid pBamM6.5 and a subclone pBamM2.5 were shown to contain the BamHI methylase
      gene based on three independent observations.  Both plasmids were found to be resistent to
      BamHI endonuclease cleavage, and chromosomal DNA isolated from E. coli HB101 cells harboring
      either of the plasmids pBamM6.5 or pBamM2.5 were resistant to cleavage by BamHI endonuclease.
      In addition, DNA isolated from lambda phage passaged through E. coli HB101 containing either
      plasmid were also resistant to BamHI cleavage.  Expression of the BamHI methylase gene is
      dependent on orientation in pSP64.  In these clones preliminary evidence indicates that
      methylase gene expression may be under the direction of the plasmid encoded LacZ promoter.
AU  - Connaughton JF
AU  - Vanek PG
AU  - Chirikjian JG
PT  - Journal Article
TA  - J. Cell Biol.
JT  - J. Cell Biol.
SO  - J. Cell Biol. 1988 107: 535a.

PMID- 3063644
VI  - 5
DP  - 1988
TI  - Cloning of the BamHI methyltransferase gene from Bacillus amyloliquefaciens.
PG  - 116-124
AB  - We wish to report the initial characterization of a recombinant clone
      containing the BamHI methylase gene.  Genomic chromosomal DNA purified from
      Bacillus amyloliquefaciens was partially cleaved with HindIII, fractionated by
      size, and cloned into pSP64.  Plasmid DNA from this library was challenged with
      BamHI endonuclease and transformed into Escherichia coli HB101.  A recombinant
      plasmid pBamM6.5 and a subclone pBamM2.5 were shown to contain the BamHI
      methylase gene based on three independent observations.  Both plasmids were
      found to be resistant to BamHI endonuclease cleavage, and chromosomal DNA
      isolated from E. coli HB101 cells harboring either of the plasmids pBamM6.5 or
      pBamM2.5 was resistant to cleavage by BamHI endonuclease.  In addition, DNA
      isolated from lambda phage passaged through E. coli HB101 containing either
      plasmid was also resistant to BamHI cleavage.  Expression of the BamHI
      methylase gene is dependent on orientation in pSP64.  In these clones
      preliminary evidence indicates that methylase gene expresion may be under the
      direction of the plasmid encoded LacZ promoter.
AU  - Connaughton JF
AU  - Vanek PG
AU  - Lee-Lin S-Q
AU  - Chirikjian JG
PT  - Journal Article
TA  - Gene Anal. Tech.
JT  - Gene Anal. Tech.
SO  - Gene Anal. Tech. 1988 5: 116-124.

PMID- 8004210
VI  - 30
DP  - 1994
TI  - Assay of restriction endonucleases using oligonucleotides.
PG  - 371-383
AB  - Type II restriction endonucleases cleave double-stranded DNA at sequence-specific sites
      typically 4-6 bp in length. Although large DNA molecules (viral DNA, plasmid DNA, and
      chromosomal DNA) are the physiological substrates for these enzymes, activity is often shown
      with small synthetic oligodeoxynucleotides providing that the recognition sequence is present.
      The use of oligodeoxynucleotide substrates often allows information to be obtained concerning
      the mechanism by which the particular endonuclease recognizes its cognate site so specifically
      and discriminates accurately against all other sequences. Excellent examples include a very
      thorough study with the EcoRI endonuclease that revealed the energetic bases of its
      specificity and experiments with the EcoRV endonuclease using oligodeoxynucleotides containing
      modified bases that demonstrated several direct contacts between enzyme and substrate. Central
      to all these experiments are methods for the assay of the activity a particular restriction
      endonuclease shows toward an oligonucleotide substrate.
AU  - Connolly BA
PT  - Journal Article
TA  - Methods Mol. Biol.
JT  - Methods Mol. Biol.
SO  - Methods Mol. Biol. 1994 30: 371-383.

PMID- 6088516
VI  - 259
DP  - 1984
TI  - The Stereochemical Course of the Restriction Endonuclease EcoRI-catalyzed reaction.
PG  - 10760-10763
AB  - The restriction endonuclease EcoRI hydrolyzes the Rp diastereomer of
      d(pGGsAATTCC), an analogue of d(pGGAATTCC) containing a chiral phosphorothioate
      group at the cleavage site between the deoxyguanosine and the deoxyadenosine
      residues (Connolly, B.A., Potter, B.V.L., Eckstein, F., Pingoud, A. and
      Grotjahn, L. (1984) Biochemistry 23: 3343-3453).  Performing the reaction in
      H2[18]O leads to d(pGG) and the hexanucleotide d([[18]O, S]pAATTCC) which has
      an [18]O-containing phosphorothioate group at the 5' terminus.  Further
      hydrolysis of this hexamer with nuclease P1 yields deoxyadenosine
      5'-O-[18]O)phosphorothioate which can be stereospecifically phosphorylated with
      adenylate kinase and pyruvate kinase to give Sp-[18]O deoxyadenosine
      5'-O-(1-thiotriphosphate).  31P NMR spectroscopy shows the oxygen-18 in this
      compound to be in a bridging position between the alpha- and beta-phosphorus
      atoms.  Thus, the hydrolysis reaction catalyzed by EcoRI proceeds with
      inversion of configuration at phosphorus.  This result is compatible with a
      direct enzyme-catalyzed nucleophilic attack of H2O at phosphorus without
      involvement of a covalent enzyme intermediate.
AU  - Connolly BA
AU  - Eckstein F
AU  - Pingoud A
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1984 259: 10760-10763.

PMID- 6087894
VI  - 23
DP  - 1984
TI  - Synthesis and characterization of an octanucleotide containing the EcoRI recognition sequence with a phosphorothioate group at the cleavage site.
PG  - 3443-3453
AB  - The synthesis and characterization of an octanucleotide, d(GGsAATTCC),
      containing the recognition sequence of the EcoRI restriction endonuclease with
      a phosphorothioate internucleotidic linkage at the cleavage site are described.
      Two approaches for the synthesis of the Rp and Sp diastereomers of this
      octamer by the phosphite method are presented.  The first consists of the
      addition of the sulfur instead of H2O to the phosphite at the appropriate
      position during chain elongation.  This method results in a mixture of
      diastereomers that can be separated by high-performance liquid chromatography
      after 5'-terminal phosphorylation.  The second uses the presynthesized and
      diastereomerically pure dinucleoside phosphorothioate d[Gp(S)A] for the
      addition to the growing oligonucleotide chain as a block.  The products are
      characterized by digestion with nuclease P1, fast atom bombardment mass
      spectrometry, 31P NMR spectroscopy, and conversion to d(GGAATTCC) by
      desulfurization with iodine.  Only the Rp diastereomers of d(GGsAATTCC) and its
      5'-phosphorylated derivative are cleaved by EcoRI endonuclease.  The rate of
      hydrolysis is slower than that of the unmodified octamer.  The phosphorothioate
      octamer will be useful for the determination of the stereochemical course of
      the EcoRI-catalyzed reaction.
AU  - Connolly BA
AU  - Potter BVL
AU  - Eckstein F
AU  - Pingoud A
AU  - Grotjahn L
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1984 23: 3443-3453.

PMID- 1408827
VI  - 20
DP  - 1992
TI  - Modified DNA fragments activate NaeI cleavage of refractory DNA sites.
PG  - 5127-5130
AB  - Endonuclease NaeI cleaves DNA using a two-site mechanism. The DNA-binding sites are
      nonidentical: they recognize different families of flanking sequences. A unique NaeI site that
      is resistant to cleavage resides in M13 double-stranded DNA. NaeI can be activated to cleave
      this site by small DNA fragments containing one or more NaeI sites. These activators are not
      practical for genetic engineering because unphosphorylated activators that are consumed during
      the cleavage of substrate give ends that may interfere with subsequent ligations. We show that
      a DNA fragment containing phosphorothioate linkages at the NaeI scissile bonds (S-activator)
      is not cleaved by NaeI, even though this S-activator binds to the substrate site. The
      S-activator activates NaeI to cleave M13 DNA under conditions that completely exhaust
      unsubstituted activator. These results demonstrate that activation is not coupled to cleavage
      of activator, that NaeI reverts to its inactive state soon after dissociation of the EA
      complex, and that S-activator makes for a nondepletable activator during prolonged
      incubations.
AU  - Conrad M
AU  - Topal MD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 5127-5130.

PMID- 2602372
VI  - 86
DP  - 1989
TI  - DNA and spermidine provide a switch mechanism to regulate the activity of restriction enzyme NaeI.
PG  - 9707-9711
AB  - Sequence-specific DNA-protein interactions are basic to DNA function.  To
      better understand these interactions, we studied the effect of position on
      cleavage of DNA by the type II restriction enzyme (EC 3.1.21.4) NaeI.  We
      discovered two classes of NaeI restriction sites: sites susceptible and sites
      resistant to cleavage.  Kinetic analysis showed that NaeI was activated by DNA
      containing cleavable NaeI sites to rapidly cleave resistant NaeI sites by a
      noncompetitive mechanism with a Km for substrate DNA of about 2 nM and a KA for
      activating DNA of about 6 nM; activation increased catalysis but not substrate
      binding.  Deletion mutagenesis in vitro showed that sequences flanking the NaeI
      recognition site were responsible for the differences between activating and
      nonactivating NaeI sites.  The polyamine spermidine had a dramatic effect on
      the interaction of NaeI with DNA; in the presence of 1 mM spermidine, resistant
      sites were cleaved rapidly and cleavable DNA inhibited cleavage.  The direct
      regulation of enzymatic activity by DNA sequences in trans, and the modulation
      of this regulation by a polyamine that is sensitive to the cell cycle, provides
      a regulatory switch mechanism.  The implications of this switch for biological
      control functions are discussed.
AU  - Conrad M
AU  - Topal MD
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1989 86: 9707-9711.

PMID- 28839041
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Vitreoscilla filiformis (ATCC 15551), Used as a Cosmetic Ingredient.
PG  - e00913-17
AB  - We report the first complete genome sequence of a Vitreoscilla filiformis strain  (ATCC 15551)
      that is used in the cosmetic industry as Vitreoscilla ferment. The
      assembled genome consisted of one chromosome and two plasmids. These data will
      provide valuable information and important insights into the physiology of this
      filamentous organism.
AU  - Contreras S
AU  - Sagory-Zalkind P
AU  - Blanquart H
AU  - Iltis A
AU  - Morand S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00913-17.

PMID- 29798922
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Two Marine Plantactinospora spp. from the Gulf of California.
PG  - e00436-18
AB  - Plantactinospora sp. strains BB1 and BC1 were isolated in 2009 from sediment samples of the
      Gulf of California from among almost 300 actinobacteria. Genome
      mining of their approximately 8.5-Mb sequences showed the bioprospecting
      potential of these rare actinomycetes, providing an insight to their ecological
      and biotechnological importance.
AU  - Contreras-Castro L
AU  - Maldonado LA
AU  - Quintana ET
AU  - Raggi L
AU  - Sanchez-Flores A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00436-18.

PMID- 29954899
VI  - 6
DP  - 2018
TI  - Genome Sequence of Acetomicrobium hydrogeniformans OS1.
PG  - e00581-18
AB  - Acetomicrobium hydrogeniformans, an obligate anaerobe of the phylum Synergistetes, was
      isolated from oil production water. It has the unusual ability
      to produce almost 4 molecules H2/molecule glucose. The draft genome of A.
      hydrogeniformans OS1 (DSM 22491(T)) is 2,123,925 bp, with 2,068 coding sequences
      and 60 RNA genes.
AU  - Cook LE
AU  - Gang SS
AU  - Ihlan A
AU  - Maune M
AU  - Tanner RS
AU  - McInerney MJ
AU  - Weinstock G
AU  - Lobos EA
AU  - Gunsalus RP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00581-18.

PMID- 12882313
VI  - 25
DP  - 2003
TI  - Methylated DNA labels for marking objects.
PG  - 89-94
AB  - We recently described a method for digitally labelling objects with DNA. Here we show that,
      using DNA methyltransferases to create polymorphic DNA
      templates, it is possible to significantly increase the number of labels
      that can be generated by this method. Nine double-stranded DNA templates
      of different length were methylated with either M.HaeIII or M.AluI
      methyltransferase, or both. Different mixtures of methylated and
      unmethylated versions of this template set were used to 'invisibly' label
      paper. The mixtures were eluted from the paper and the methylated status
      of the templates in each mixture successfully determined, and the labels
      read, by digestion with the complementary restriction endonuclease,
      followed by a polymerase chain reaction and agarose gel electrophoresis.
      One methylated DNA label was read after it had been left on paper for two
      months.
AU  - Cook LJ
AU  - Cox JPL
PT  - Journal Article
TA  - Biotechnol. Lett.
JT  - Biotechnol. Lett.
SO  - Biotechnol. Lett. 2003 25: 89-94.

PMID- Not carried by PubMed...
VI  - 34
DP  - 1995
TI  - Photochemically initiated protein splicing.
PG  - 1629-1630
AB  - Protein splicing is a post-translational rearrangement process in which an
      internal polypeptide segment (intein) is excised from a primary translation product, with
      concomitant ligation of the flanking polypeptides (exteins).  This process results in the
      production of two protein products from a single precursor polypeptide: the intein (often a
      homing endonuclease thought to initiate lateral transmission of the intein coding sequence)
      and the ligated exteins.
AU  - Cook SN
AU  - Jack WE
AU  - Xiong X
AU  - Danley LE
AU  - Ellman JA
AU  - Schultz PG
AU  - Noren CJ
PT  - Journal Article
TA  - Angew. Chem. Int. Ed. Engl.
JT  - Angew. Chem. Int. Ed. Engl.
SO  - Angew. Chem. Int. Ed. Engl. 1995 34: 1629-1630.

PMID- 24501637
VI  - 8
DP  - 2013
TI  - Draft genome sequence of Francisella tularensis subsp. holarctica BD11-00177.
PG  - 539-547
AB  - Francisella tularensis is a facultative intracellular bacterium in the class
      Gammaproteobacteria. This strain is of interest because it is the etiologic agent
      of tularemia and a highly virulent category A biothreat agent. Here we describe
      the draft genome sequence and annotation of Francisella tularensis subsp.
      holarctica BD11-00177, isolated from the first case of indigenous tularemia
      detected in The Netherlands since 1953. Whole genome DNA sequence analysis
      assigned this isolate to the genomic group B.FTNF002-00, which previously has
      been exclusively reported from Spain, France, Italy, Switzerland and Germany.
      Automatic annotation of the 1,813,372 bp draft genome revealed 2,103
      protein-coding and 46 RNA genes.
AU  - Coolen JP
AU  - Sjodin A
AU  - Maraha B
AU  - Hajer GF
AU  - Forsman M
AU  - Verspui E
AU  - Frenay HM
AU  - Notermans DW
AU  - de Vries MC
AU  - Reubsaet FA
AU  - Paauw A
AU  - Roeselers G
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 539-547.

PMID- 2362829
VI  - 18
DP  - 1990
TI  - The restriction enzyme EheI (GGC/GCC) is sensitive to CpG methylation.
PG  - 3667
AB  - None
AU  - Cooney CA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 3667.

PMID- 3221398
VI  - 204
DP  - 1988
TI  - Methylation is co-ordinated on the putative replication origins of Physarum ribosomal DNA.
PG  - 889-901
AB  - In Physarum polycephalum, the ribosomal DNA is found as 60,000 base-pair palindromes. Each
      rDNA has four symmetrically arranged replication origins flanked by ribosomal RNA genes. A
      particular sequence, the putative replication origin, is repeated at the approximate position
      of each origin and nowhere else in the molecule. On a typical rDNA molecule, only one origin
      is active per replication cycle. We show that both the level and co-ordination of methylation
      result in asymmetrically methylated rDNA molecules that are particularly hypomethylated at one
      of their four putative replication origins. This pattern of methylation on a typical rDNA
      molecule is consistent with a model where hypomethylation is a determinant of origin activity.
AU  - Cooney CA
AU  - Eykholt RL
AU  - Bradbury EM
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1988 204: 889-901.

PMID- 27103707
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Salmonella enterica subsp. enterica Serovar Berta ATCC  8392 and a Nalidixic Acid-Resistant Isolate of This Strain.
PG  - e00186-16
AB  - ITALIC! Salmonella entericasubspecies ITALIC! entericaserovar Berta has been isolated in
      multiple animal species and has been implicated in human disease.
      Here, we report a 4.7-Mbp draft genome sequence of ITALIC! S. entericaserovar
      Berta (ATCC strain 8392) and a nalidixic acid-resistant isolate derived from this
      strain.
AU  - Cooper A
AU  - Koziol AG
AU  - Carrillo CD
AU  - Lambert D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00186-16.

PMID- 26472847
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Mishmarhaemek Isolated from Bovine Feces.
PG  - e01210-15
AB  - Salmonella enterica subsp. enterica serovar Mishmarhaemek is a Gram-negative,
      non-spore-forming, rod-shaped bacterium implicated in human clinical disease. Here, we report
      a 4.8-Mbp draft genome sequence of a nalidixic acid-resistant isolate of S. serovar
      Mishmarhaemek.
AU  - Cooper A
AU  - Lambert D
AU  - Koziol AG
AU  - Seyer K
AU  - Carrillo CD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01210-15.

PMID- 8508780
VI  - 12
DP  - 1993
TI  - Protein splicing of the yeast TFP1 intervening protein sequence: a model for self-excision.
PG  - 2575-2583
AB  - Protein splicing is the protein analogue of RNA splicing in which the
      central portion (spacer) of a protein precursor is excised and the amino- and carboxy-
      terminal portions of the precursor reconnected.  The yeast Tfp1 protein undergoes a rapid
      protein splicing reaction to yield a spliced 69 kDa polypeptide and an excised 50 kDa spacer
      protein.  We have demonstrated that the 69 kDa species arises by reformation of a bona fide
      peptide bond.  Deletion analyses indicate that only sequences in the central spacer protein of
      the Tfp1 precursor are critical for the protein splicing reaction.  A fusion protein in which
      only the Tfp1 spacer domain was inserted into an unrelated protein also underwent efficient
      splicing, demonstrating that all of the information required for protein splicing resides
      within the spacer domain.  Alteration of Tfp1p splice junction residues blocked or
      kinetically impaired protein splicing.  A protein splicing model is presented in which
      asparagine rearrangement initiates the self-excision of the spacer protein from the Tfp1
      precursor.  The Tfp1 spacer protein belongs to a new class of intervening sequences that
      are excised at the protein rather than the RNA level.
AU  - Cooper AA
AU  - Chen Y-J
AU  - Lindorfer MA
AU  - Stevens TH
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1993 12: 2575-2583.

PMID- 7482702
VI  - 20
DP  - 1995
TI  - Protein splicing: self-splicing of genetically mobile elements at the protein level.
PG  - 351-356
AB  - Protein splicing is a newly discovered process that is the protein equivalent
      of RNA splicing.  Protein splicing proceeds through a branched protein intermediate, and
      in vitro studies indicate that the reaction is autocatalytic.  The excised 'intein' proteins
      are
      site-specific DNA endonucleases that catalyze genetic mobility of their DNA coding
      sequence by an 'intein homing' mechanism.
AU  - Cooper AA
AU  - Stevens TH
PT  - Journal Article
TA  - Trends Biochem. Sci.
JT  - Trends Biochem. Sci.
SO  - Trends Biochem. Sci. 1995 20: 351-356.

PMID- 8274142
VI  - 15
DP  - 1993
TI  - Protein splicing: Excision of intervening sequences at the protein level.
PG  - 667-674
AB  - Protein splicing is an extraordinary post-translational reaction that removes
      an intact central "spacer" domain (Sp) from precursor proteins (N-Sp-C) while splicing
      together the N- and C-domains of the precursor, via a peptide bond, to produce a new
      protein (N-C).  All of the available data on protein splicing fit a model in which these
      intervening sequences excise at the protein level via a self-splicing mechanism.  Several
      proteins have recently been discovered that undergo protein splicing, and in two such
      cases, the excised spacer protein is an endonuclease.  Such endonucleases are capable of
      conferring genetic mobility upon the intervening sequences that encodes them.  These
      intervening sequences define a new family of mobile genetic elements that are translated yet
      remain phenotypically silent by excising at the protein rather than the RNA level.
AU  - Cooper AA
AU  - Stevens TH
PT  - Journal Article
TA  - Bioessays
JT  - Bioessays
SO  - Bioessays 1993 15: 667-674.

PMID- 16622047
VI  - 152
DP  - 2006
TI  - The phylogeny of Staphylococcus aureus - which genes make the best intra-species markers?
PG  - 1297-1305
AB  - The ability to make informed decisions on the suitability of alternative marker loci is
      central for population and epidemiological investigations.
      This issue was addressed using Staphylococcus aureus as a model population
      by generating nucleotide sequence data from 33 gene fragments in a
      representative sample of 30 strains. Supplementing the data with
      pre-existing multilocus sequence typing data, an intra-species tree based
      on approximately 17.8 kb of sequence was reconstructed and the goodness of
      fit of each individual gene tree was computed. No strong association was
      noted between gene function per se and phylogenetic reliability, but it is
      suggested that candidate loci should possess at least the average degree
      of nucleotide diversity for all genes in the genome. In the case of S.
      aureus this threshold is >1 % mean pairwise diversity.
AU  - Cooper JE
AU  - Feil EJ
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2006 152: 1297-1305.

PMID- 21217004
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Campylobacter jejuni Strain S3.
PG  - 1491-1492
AB  - Campylobacter jejuni is one of the leading causes of bacterial gastroenteritis in the world;
      however, there is only one complete genome
      sequence of a poultry strain to date. Here we report the complete genome
      sequence and annotation of the second poultry strain, C. jejuni strain S3.
      This strain has been shown to be nonmotile, to be a poor invader in vitro,
      and to be a poor colonizer of poultry after minimal in vitro passage.
AU  - Cooper KK
AU  - Cooper MA
AU  - Zuccolo A
AU  - Law B
AU  - Joens LA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 1491-1492.

PMID- 24410921
VI  - 15
DP  - 2014
TI  - Comparative genomics of enterohemorrhagic Escherichia coli O145:H28 demonstrates  a common evolutionary lineage with Escherichia coli O157:H7.
PG  - 17
AB  - BACKGROUND: Although serotype O157:H7 is the predominant enterohemorrhagic Escherichia coli
      (EHEC), outbreaks of non-O157 EHEC that cause severe foodborne
      illness, including hemolytic uremic syndrome have increased worldwide. In fact,
      non-O157 serotypes are now estimated to cause over half of all the Shiga
      toxin-producing Escherichia coli (STEC) cases, and outbreaks of non-O157 EHEC
      infections are frequently associated with serotypes O26, O45, O103, O111, O121,
      and O145. Currently, there are no complete genomes for O145 in public databases.
      RESULTS: We determined the complete genome sequences of two O145 strains
      (EcO145), one linked to a US lettuce-associated outbreak (RM13514) and one to a
      Belgium ice-cream-associated outbreak (RM13516). Both strains contain one
      chromosome and two large plasmids, with genome sizes of 5,737,294 bp for RM13514
      and 5,559,008 bp for RM13516. Comparative analysis of the two EcO145 genomes
      revealed a large core (5,173 genes) and a considerable amount of strain-specific
      genes. Additionally, the two EcO145 genomes display distinct chromosomal
      architecture, virulence gene profile, phylogenetic origin of Stx2a prophage, and
      methylation profile (methylome). Comparative analysis of EcO145 genomes to other
      completely sequenced STEC and other E. coli and Shigella genomes revealed that,
      unlike any other known non-O157 EHEC strain, EcO145 ascended from a common
      lineage with EcO157/EcO55. This evolutionary relationship was further supported
      by the pangenome analysis of the 10 EHEC str ains. Of the 4,192 EHEC core genes,
      EcO145 shares more genes with EcO157 than with the any other non-O157 EHEC
      strains. CONCLUSIONS: Our data provide evidence that EcO145 and EcO157 evolved
      from a common lineage, but ultimately each serotype evolves via a
      lineage-independent nature to EHEC by acquisition of the core set of EHEC
      virulence factors, including the genes encoding Shiga toxin and the large
      virulence plasmid. The large variation between the two EcO145 genomes suggests a
      distinctive evolutionary path between the two outbreak strains. The distinct
      methylome between the two EcO145 strains is likely due to the presence of a
      BsuBI/PstI methyltransferase gene cassette in the Stx2a prophage of the strain
      RM13514, suggesting a role of horizontal gene transfer-mediated epigenetic
      alteration in the evolution of individual EHEC strains.
AU  - Cooper KK
AU  - Mandrell RE
AU  - Louie JW
AU  - Korlach J
AU  - Clark TA
AU  - Parker CT
AU  - Huynh S
AU  - Chain PS
AU  - Ahmed S
AU  - Carter MQ
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2014 15: 17.

PMID- 24855308
VI  - 2
DP  - 2014
TI  - Complete Genome Sequences of Two Escherichia coli O145:H28 Outbreak Strains of Food Origin.
PG  - e00482-14
AB  - Escherichia coli O145:H28 strain RM12581 was isolated from bagged romaine lettuce during a
      2010 U.S. lettuce-associated outbreak. E. coli O145:H28 strain RM12761
      was isolated from ice cream during a 2007 ice cream-associated outbreak in
      Belgium. Here we report the complete genome sequences and annotation of both
      strains.
AU  - Cooper KK
AU  - Mandrell RE
AU  - Louie JW
AU  - Korlach J
AU  - Clark TA
AU  - Parker CT
AU  - Huynh S
AU  - Chain PS
AU  - Ahmed S
AU  - Carter MQ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00482-14.

PMID- 8120883
VI  - 236
DP  - 1994
TI  - The domains of a type I DNA methyltransferase: interactions and role in recognition of DNA methylation.
PG  - 1011-1021
AB  - The DNA methyltransferases of type I restriction-modification systems are trimeric enzymes
      composed of one DNA specificity (S) subunit and two modification (M) subunits. The S subunit
      contains two large regions, each of which recognizes one part of the split, asymmetrical DNA
      target sequence. Each M subunit contains an amino acid motif for binding the methyl group
      donor and cofactor, S-adenosyl methionine. The EcoKI methyltransferase has a strong preference
      for methylating a hemimethylated DNA target rather than an unmodified target. We have used
      partial proteolytic digestion of EcoKI methyltransferase to generate polypeptide domains that
      we have identified by amino acid sequencing. The S subunit was cut into two large, folded
      domains each containing one DNA binding region. Binding of DNA partially protected the S
      subunit from digestion. The M subunit was also cut into two large domains joined together by a
      short flexible loop, and a C-terminal tail region. The short loop contained part of the
      S-adenosyl methionine binding motif, and cofactor binding protected the loop and the two large
      domains from proteolysis. The C-terminal domain of M remained associated with the N-terminal
      domain of the S subunit even after the rest of the protein had been digested. The conformation
      of the tail region of the M subunit was sensitive to the methylation state of DNA in ternary
      complexes also containing S-adenosyl methionine, and could differentiate between unmethylated
      and hemimethylated DNA substrates.
AU  - Cooper LP
AU  - Dryden DTF
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1994 236: 1011-1021.

PMID- 28180279
VI  - 45
DP  - 2017
TI  - DNA target recognition domains in the Type I restriction and modification systems of Staphylococcus aureus.
PG  - 3395-3406
AB  - Staphylococcus aureus displays a clonal population structure in which horizontal  gene
      transfer between different lineages is extremely rare. This is due, in part,
      to the presence of a Type I DNA restriction-modification (RM) system given the
      generic name of Sau1, which maintains different patterns of methylation on
      specific target sequences on the genomes of different lineages. We have
      determined the target sequences recognized by the Sau1 Type I RM systems present
      in a wide range of the most prevalent S. aureus lineages and assigned the
      sequences recognized to particular target recognition domains within the RM
      enzymes. We used a range of biochemical assays on purified enzymes and single
      molecule real-time sequencing on genomic DNA to determine these target sequences
      and their patterns of methylation. Knowledge of the main target sequences for
      Sau1 will facilitate the synthesis of new vectors for transformation of the most
      prevalent lineages of this 'untransformable' bacterium.
AU  - Cooper LP
AU  - Roberts GA
AU  - White JH
AU  - Luyten YA
AU  - Bower EKM
AU  - Morgan RD
AU  - Roberts RJ
AU  - Lindsay JA
AU  - Dryden DTF
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2017 45: 3395-3406.

PMID- 11058151
VI  - 97
DP  - 2000
TI  - Postsegregational killing does not increase plasmid stability but acts to mediate the exclusion of competing plasmids.
PG  - 12643-12648
AB  - Postsegregational killing (PSK) systems consist of a tightly linked toxin-antitoxin pair.
      Antitoxin must be continually produced to prevent
      the longer lived toxin from killing the cell. PSK systems on plasmids
      are widely believed to benefit the plasmid by ensuring its stable
      vertical inheritance. However, experimental tests of this "stability"
      hypothesis were not consistent with its predictions. We suggest an
      alternative hypothesis to explain the evolution of PSK: that PSK
      systems have been selected through benefiting host plasmids in
      environments where plasmids must compete during horizontal
      reproduction. In this "competition" hypothesis, success of PSK
      systems is a consequence of plasmid-plasmid competition, rather than
      from an adaptive plasmid-host relationship. In support of this
      hypothesis, a plasmid-encoded parDE PSK system mediated the exclusion
      of an isogenic Delta parDE plasmid. An understanding of how PSK systems
      influence plasmid success may provide insight into the evolution of
      other determinants (e.g., antibiotic resistance and virulence) also
      rendering a cell potentially dependent on an otherwise dispensable
      plasmid.
AU  - Cooper TF
AU  - Heinemann JA
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2000 97: 12643-12648.

PMID- 21304634
VI  - 1
DP  - 2009
TI  - Complete genome sequence of Desulfomicrobium baculatum type strain (X).
PG  - 29-37
AB  - Desulfomicrobium baculatum is the type species of the genus Desulfomicrobium, which is the
      type genus of the family Desulfomicrobiaceae. It is of phylogenetic
      interest because of the isolated location of the family Desulfomicrobiaceae
      within the order Desulfovibrionales. D. baculatum strain X(T) is a Gram-negative,
      motile, sulfate-reducing bacterium isolated from water-saturated manganese
      carbonate ore. It is strictly anaerobic and does not require NaCl for growth,
      although NaCl concentrations up to 6% (w/v) are tolerated. The metabolism is
      respiratory or fermentative. In the presence of sulfate, pyruvate and lactate are
      incompletely oxidized to acetate and CO(2). Here we describe the features of this
      organism, together with the complete genome sequence and annotation. This is the
      first completed genome sequence of a member of the deltaproteobacterial family
      Desulfomicrobiaceae, and this 3,942,657 bp long single replicon genome with its
      3494 protein-coding and 72 RNA genes is part of the Genomic Encyclopedia of
      Bacteria and Archaea project.
AU  - Copeland A et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2009 1: 29-37.

PMID- 21304647
VI  - 1
DP  - 2009
TI  - Complete genome sequence of Catenulispora acidiphila type strain (ID 139908).
PG  - 119-125
AB  - Catenulispora acidiphila Busti et al. 2006 is the type species of the genus Catenulispora, and
      is of interest because of the rather isolated phylogenetic
      location it occupies within the scarcely explored suborder Catenulisporineae of
      the order Actinomycetales. C. acidiphilia is known for its acidophilic, aerobic
      lifestyle, but can also grow scantly under anaerobic conditions. Under regular
      conditions, C. acidiphilia grows in long filaments of relatively short aerial
      hyphae with marked septation. It is a free living, non motile, Gram-positive
      bacterium isolated from a forest soil sample taken from a wooded area in
      Gerenzano, Italy. Here we describe the features of this organism, together with
      the complete genome sequence and annotation. This is the first complete genome
      sequence of the actinobacterial family Catenulisporaceae, and the 10,467,782 bp
      long single replicon genome with its 9056 protein-coding and 69 RNA genes is a
      part of the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Copeland A et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2009 1: 119-125.

PMID- 21304653
VI  - 1
DP  - 2009
TI  - Complete genome sequence of Atopobium parvulum type strain (IPP 1246).
PG  - 166-173
AB  - Atopobium parvulum (Weinberg et al. 1937) Collins and Wallbanks 1993 comb. nov. is the type
      strain of the species and belongs to the genomically yet unstudied
      Atopobium/Olsenella branch of the family Coriobacteriaceae. The species A.
      parvulum is of interest because its members are frequently isolated from the
      human oral cavity and are found to be associated with halitosis (oral malodor)
      but not with periodontitis. Here we describe the features of this organism,
      together with the complete genome sequence, and annotation. This is the first
      complete genome sequence of the genus Atopobium, and the 1,543,805 bp long single
      replicon genome with its 1369 protein-coding and 49 RNA genes is part of the
      Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Copeland A et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2009 1: 166-173.

PMID- 22768367
VI  - 6
DP  - 2012
TI  - Complete genome sequence of the orange-red pigmented, radioresistant Deinococcus  proteolyticus type strain (MRP(T)).
PG  - 240-250
AB  - Deinococcus proteolyticus (ex Kobatake et al. 1973) Brook and Murray 1981 is one  of currently
      47 species in the genus Deinococcus within the family
      Deinococcaceae. Strain MRP(T) was isolated from feces of Lama glama and possesses
      extreme radiation resistance, a trait is shares with various other species of the
      genus Deinococcus, with D. proteolyticus being resistant up to 1.5 Mrad of gamma
      radiation. Strain MRP(T) is of further interest for its carotenoid pigment. The
      genome presented here is only the fifth completed genome sequence of a member of
      the genus Deinococcus (and the forth type strain) to be published, and will
      hopefully contribute to a better understanding of how members of this genus
      adapted to high gamma- or UV ionizing-radiation. Here we describe the features of
      this organism, together with the complete genome sequence and annotation. The
      2,886,836 bp long genome with its four large plasmids of lengths 97 kbp, 132 kbp,
      196 kbp and 315 kbp harbors 2,741 protein-coding and 58 RNA genes and is a part
      of the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Copeland A et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 6: 240-250.

PMID- 22768358
VI  - 6
DP  - 2012
TI  - Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4(T)).
PG  - 145-154
AB  - Runella slithyformis Larkin and Williams 1978 is the type species of the genus Runella, which
      belongs to the Cytophagaceae, a family that was only recently
      classified to the order Cytophagales in the class Cytophagia. The species is of
      interest because it is able to grow at temperatures as low as 4 degrees C. This
      is the first completed genome sequence of a member of the genus Runella and the
      sixth sequence from the family Cytophagaceae. The 6,919,729 bp long genome
      consists of a 6.6 Mbp circular genome and five circular plasmids of 38.8 to 107.0
      kbp length, harboring a total of 5,974 protein-coding and 51 RNA genes and is a
      part of the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Copeland A et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 6: 145-154.

PMID- 22675595
VI  - 6
DP  - 2012
TI  - Complete genome sequence of the aerobic, heterotrophy Marinithermus hydrothermalis type strain (T1T) from a deep-sea hydrothermal vent chimney.
PG  - 21-30
AB  - Marinithermus hydrothermalis Sako et al. 2003 is the type species of the monotypic genus
      Marinithermus. M. hydrothermalis T1T was the first isolate within the phylum
      "Thermus-Deinococcus" to exhibit optimal growth under a salinity equivalent to that of sea
      water and to have an absolute requirement for NaCl for growth. M. hydrothermalis T1T is of
      interest because it may provide a new insight into the ecological significance of the aerobic,
      thermophilic decomposers in the circulation of organic compounds in deep-sea hydrothermal vent
      ecosystems. This is the first completed genome sequence of a member of the genus Marinithermus
      and the seventh sequence from the family Thermaceae. Here we describe the features of this
      organism, together with the complete genome sequence and annotation. The 2,269,167 bp long
      genome with its 2,251 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of
      Bacteria and Archaea project.
AU  - Copeland A et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 6: 21-30.

PMID- 22675587
VI  - 5
DP  - 2011
TI  - Complete genome sequence of the halophilic and highly halotolerant Chromohalobacter salexigens type strain (1H11T).
PG  - 379-388
AB  - Chromohalobacter salexigens is one of nine currently known species of the genus
      Chromoha-lobacter in the family Halomonadaceae. It is the most halotolerant of the so-called
      'mod-erately halophilic bacteria' currently known and, due to its strong euryhaline
      phenotype, it is an established model organism for prokaryotic osmoadaptation. C. salexigens
      strain 1H11T and Halomonas elongata are the first and the second members of the family
      Halomonada-ceae with a completely sequenced genome. The 3,696,649 bp long chromosome with a
      total of 3,319 protein-coding and 93 RNA genes was sequenced as part of the DOE Joint Genome
      Institute Program DOEM 2004.
AU  - Copeland A et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 5: 379-388.

PMID- 5338815
VI  - 54
DP  - 1966
TI  - Restriction in matings of Escherichia coli strain K-12 with strain B.
PG  - 441-452
AB  - Restriction in Escherichia coli limits the acceptance of genetic elements such
      as bacteriophage, sex-factor, and donated bacterial chromosomes.  As reported
      in this paper, restriction of K-12 genetic material by strain B is greatest
      early in the mating and later becomes constant.  Unlike restriction in B/r, no
      delay in the appearance of a proximal marker is found.  Also, the linkage
      between markers is not reduced by a constant amount, but is dependent upon the
      distance between the markers.  Restriction in strain B is responsible for only
      part of the reduction in the inheritance of genetic markers from K-12, whereas
      in strain B/r restriction accounts for the entire effect.
AU  - Copeland JC
AU  - Bryson V
PT  - Journal Article
TA  - Genetics
JT  - Genetics
SO  - Genetics 1966 54: 441-452.

PMID- 29519844
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Four Parasaccharibacter apium Strains Isolated from Honey Bees.
PG  - e00165-18
AB  - Parasaccharibacter apium displays multiple ecological strategies in its honey bee host. We
      sequenced the genomes of four strains found in larvae and the adult gut
      in order to better understand its ecology and relationship to other
      Acetobacteraceae The P. apium genome consists of 2,009,892 bp and 1,830
      protein-coding genes.
AU  - Corby-Harris V
AU  - Anderson KE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00165-18.

PMID- 
VI  - 
DP  - 2005
TI  - Homing endonuclease I-CreII: A novel dual-motif enzyme that catalyzes group I intron homing.
PG  - 1-148
AB  - I-CreII is a homing endonuclease from the Cr.psbA intron of Chlamydomonas reinhardtii.  It
      cleaves the exon 4-exon 5 junction of psbA DNA, thereby inducing a recombination event
      referred to as intron homing.  Homing endonucleases are classified into four main groups based
      on the presence of a catalytic domain unique to each group.  I-CreII is novel in that it
      appears to contain two catalytic domains, an H-N-H and a GIY-YIG.  The role of the puative
      GIY-YIG motif has been questioned, however, because I-CmoeI, a related protein, behaves like
      an H-N-H endonuclease.  Recently, Kim et al. (2005) showed that DNA cleavage by I-CreII leaves
      2-nt 3' OH overhands, which is a feature unique to GIY-YIG enzymes.  Thus, in order to
      resolve this question, I have performed new biochemical and kinetic analyses of wild-type and
      mutant proteins that have had a conserved residue in one of the motifs substituted with
      alanine.  The results indicate that not only does I-CreII have a functional GIY-YIG motif, but
      the data point to it as the catalytic domain.  From this new perspective, this is also the
      first quantitative study of a GIY-YIG endonuclease.  These data also provide the first direct
      evidence that an H-N-H motif can function primarily in DNA binding rather than catalysis- a
      finding that has implications for transcription factors from lower plants and protists that
      appear to have this motif.
AU  - Corina LE
PT  - Journal Article
TA  - Ph.D. Thesis, Southwestern Medical Center, Univ. of Texas, USA
JT  - Ph.D. Thesis, Southwestern Medical Center, Univ. of Texas, USA
SO  - Ph.D. Thesis, Southwestern Medical Center, Univ. of Texas, USA 2005 : 1-148.

PMID- 19651876
VI  - 37
DP  - 2009
TI  - Biochemical and mutagenic analysis of I-CreII reveals distinct but important roles for both the H-N-H and GIY-YIG motifs.
PG  - 5810-5821
AB  - Homing endonucleases typically contain one of four conserved catalytic motifs, and other
      elements that confer tight DNA binding. I-CreII, which
      catalyzes homing of the Cr.psbA4 intron, is unusual in containing two
      potential catalytic motifs, H-N-H and GIY-YIG. Previously, we showed that
      cleavage by I-CreII leaves ends (2-nt 3' overhangs) that are
      characteristic of GIY-YIG endonucleases, yet it has a relaxed metal
      requirement like H-N-H enzymes. Here we show that I-CreII can bind DNA
      without an added metal ion, and that it binds as a monomer, akin to
      GIY-YIG enzymes. Moreover, cleavage of supercoiled DNA, and estimates of
      strand-specific cleavage rates, suggest that I-CreII uses a sequential
      cleavage mechanism. Alanine substitution of a number of residues in the
      GIY-YIG motif, however, did not block cleavage activity, although DNA
      binding was substantially reduced in several variants. Substitution of
      conserved histidines in the H-N-H motif resulted in variants that did not
      promote DNA cleavage, but retained high-affinity DNA binding-thus
      identifying it as the catalytic motif. Unlike the non-specific H-N-H
      colicins, however; substitution of the conserved asparagine substantially
      reduced DNA binding (though not the ability to promote cleavage). These
      results indicate that, in I-CreII, two catalytic motifs have evolved to
      play important roles in specific DNA binding. The data also indicate that
      only the H-N-H motif has retained catalytic ability.
AU  - Corina LE
AU  - Qiu W
AU  - Desai A
AU  - Herrin DL
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: 5810-5821.

PMID- 28729281
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Campylobacter concisus ATCC 33237T and Draft Genome Sequences for an Additional Eight Well-Characterized C. concisus Strains.
PG  - e00711-17
AB  - We report the complete genome sequence of the Campylobacter concisus type strain  ATCC 33237
      and the draft genome sequences of eight additional well-characterized
      C. concisus strains. C. concisus has been shown to be a genetically heterogeneous
      species, and these nine genomes provide valuable information regarding the
      diversity within this taxon.
AU  - Cornelius AJ
AU  - Miller WG
AU  - Lastovica AJ
AU  - On SLW
AU  - French NP
AU  - Vandenberg O
AU  - Biggs PJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00711-17.

PMID- 29622611
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Megaplasmid-Bearing Streptomyces sp. Strains BF-3 and 4F, Isolated from the Great Salt Plains of Oklahoma.
PG  - e00208-18
AB  - Draft genome sequences of megaplasmid-bearing Streptomyces sp. strains BF-3 and 4F, isolated
      from the Great Salt Plains of Oklahoma, showed genome sizes of
      7,950,134 and 7,550,992 bp, respectively. Both genomes revealed the presence of
      genes involved in osmoregulation and stress response, potentially helping their
      survival in such an extreme environment.
AU  - Cornell CR
AU  - Marasini D
AU  - Fakhr MK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00208-18.

PMID- 27540049
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Bacillus thuringiensis Bacteriophage Smudge.
PG  - e00572-16
AB  - Smudge, a bacteriophage enriched from soil using Bacillus thuringiensis DSM-350 as the host,
      had its complete genome sequenced. Smudge is a myovirus with a
      genome consisting of 292 genes and was identified as belonging to the C1 cluster
      of Bacillus phages.
AU  - Cornell JL
AU  - Breslin E
AU  - Schuhmacher Z
AU  - Himelright M
AU  - Berluti C
AU  - Boyd C
AU  - Carson R
AU  - Del Gallo E
AU  - Giessler C
AU  - Gilliam B
AU  - Heatherly C
AU  - Nevin J
AU  - Nguyen B
AU  - Nguyen J
AU  - Parada J
AU  - Sutterfield B
AU  - Tukruni M
AU  - Temple L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00572-16.

PMID- 2582368
VI  - 13
DP  - 1985
TI  - Nomenclature for incompletely specified bases in nucleic acid sequences: recommendations 1984.
PG  - 3021-3030
AB  - With the introduction of methods of rapid nucleic acid sequence determination, synthesis of
      mixed oligonucleotide probes and computer-assisted analysis of nucleic acid sequences, the use
      of a single symbol to designate a variety of possible nucleotides at a single position has
      become widespread over the last few years. Whereas the use of, for example, the symbols R and
      Y to designate purine (A or G) and pyrimidine (C or T) ribonucleotides respectively is
      generally accepted, no agreed symbols exist for the other possible combinations. Indeed, a
      plethora of diverse systems have proliferated in the last few years. It is striking that, in
      one extreme case, the combination (C or G) has been represented by at least five different
      symbols. A standardized set of symbols is thus required to prevent confusion.
AU  - Cornish-Bowden A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1985 13: 3021-3030.

PMID- 28074120
VI  - 12
DP  - 2017
TI  - Complete genome sequence of the heavy metal resistant bacterium Agromyces aureus  AR33T and comparison with related Actinobacteria.
PG  - 2
AB  - Agromyces aureus AR33T is a Gram-positive, rod-shaped and motile bacterium belonging to the
      Microbacteriaceae family in the phylum Actinobacteria that was
      isolated from a former zinc/lead mining and processing site in Austria. In this
      study, the whole genome was sequenced and assembled combining sequences obtained
      from Illumina MiSeq and Sanger sequencing. The assembly resulted in the complete
      genome sequence which is 4,373,124 bp long and has a GC content of 70.1%.
      Furthermore, we performed a comparative genomic analysis with other related
      organisms: 6 Agromyces spp., 4 Microbacteriaceae spp. and 2 other members of the
      class Actinobacteria.
AU  - Corretto E
AU  - Antonielli L
AU  - Sessitsch A
AU  - Compant S
AU  - Hofer C
AU  - Puschenreiter M
AU  - Brader G
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 2.

PMID- 25977426
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of 10 Microbacterium spp., with Emphasis on Heavy Metal-Contaminated Environments.
PG  - e00432-15
AB  - Microbacterium spp. isolated from heavy metal (HM)-contaminated environments (soil and plants)
      can play a role in mobilization processes and in the
      phytoextraction of HM. Here, we report the whole-genome sequences and annotation
      of 10 Microbacterium spp. isolated from both HM-contaminated and -noncontaminated
      compartments.
AU  - Corretto E
AU  - Antonielli L
AU  - Sessitsch A
AU  - Kidd P
AU  - Weyens N
AU  - Brader G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00432-15.

PMID- 27313292
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a Copper-Resistant Marine Bacterium, Pantoea agglomerans Strain LMAE-2, a Bacterial Strain with Potential Use in Bioremediation.
PG  - e00525-16
AB  - Pantoea agglomerans LMAE-2 was isolated from seabed sediment moderately contaminated with
      Cu(2+) Here, we report its draft genome sequence, which has a
      size of 4.98 Mb. The presence of cop genes related with copper homeostasis in its
      genome may explain the resistance and strengthen its potential for use as
      bioremediation agent.
AU  - Corsini G
AU  - Valdes N
AU  - Pradel P
AU  - Tello M
AU  - Cottet L
AU  - Muino L
AU  - Karahanian E
AU  - Castillo A
AU  - Gonzalez AR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00525-16.

PMID- 23990587
VI  - 1
DP  - 2013
TI  - Whole-Genome Sequences of Two Staphylococcus aureus ST398 Strains of Human Origin, S94 and S100.
PG  - e00691-13
AB  - Sequence type 398 (ST398) Staphylococcus aureus was originally associated with animal
      infection. We announce the complete genome sequences of two ST398
      methicillin-susceptible S. aureus strains of human origin, S94 and S100. The
      genome sequences assist in the characterization of interesting ST398 features
      related to host specificities.
AU  - Corvaglia AR
AU  - Francois P
AU  - Bertrand X
AU  - Quentin R
AU  - Hernandez D
AU  - van der Mee-Marquet N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00691-13.

PMID- 20547849
VI  - 107
DP  - 2010
TI  - A type III-like restriction endonuclease functions as a major barrier to horizontal gene transfer in clinical Staphylococcus aureus strains.
PG  - 11954-11958
AB  - Staphylococcus aureus is an versatile pathogen that can cause life-threatening infections.
      Depending on the clinical setting, up to 50% of S. aureus infections are caused by
      methicillin-resistant strains (MRSA) that in most cases are resistant to many other
      antibiotics, making treatment difficult. The emergence of community-acquired MRSA drastically
      changed the picture by increasing the risk of MRSA infections. Horizontal transfer of genes
      encoding for antibiotic resistance or virulence factors is a major concern of
      multidrug-resistant S. aureus infections and epidemiology. We identified and characterized a
      type III-like restriction system present in clinical S. aureus strains that prevents
      transformation with DNA from other bacterial species. Interestingly, our analysis revealed
      that some clinical MRSA strains are deficient in this restriction system, and thus are
      hypersusceptible to the horizontal transfer of DNA from other species, such as Escherichia
      coli, and could easily acquire a vancomycin-resistance gene from enterococci. Inactivation of
      this restriction system dramatically increases the transformation efficiency of clinical S.
      aureus strains, opening the field of molecular genetic manipulation of these strains using DNA
      of exogenous origin.
AU  - Corvaglia AR
AU  - Francois P
AU  - Hernandez D
AU  - Perron K
AU  - Linder P
AU  - Schrenzel J
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2010 107: 11954-11958.

PMID- 26543126
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequence of Leptospira interrogans Serovar Hardjo Subtype Hardjoprajitno Strain Norma, Isolated from Cattle in a Leptospirosis Outbreak in   Brazil.
PG  - e01302-15
AB  - Leptospirosis is caused by pathogenic bacteria of the genus Leptospira spp. This  neglected
      re-emergent disease has global distribution and relevance in veterinary
      production. Here, we report the whole-genome sequence and annotation of
      Leptospira interrogans serovar Hardjo subtype Hardjoprajitno strain Norma,
      isolated from cattle in a livestock leptospirosis outbreak in Brazil.
AU  - Cosate MR
AU  - Soares SC
AU  - Mendes TA
AU  - Raittz RT
AU  - Moreira EC
AU  - Leite R
AU  - Fernandes GR
AU  - Haddad JP
AU  - Ortega JM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01302-15.

PMID- 28428300
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Enterococcus casseliflavus PAVET15 Obtained from the Oviduct Infection of the Cattle Tick (Rhipicephalus microplus) in Jiutepec, Morelos, Mexico.
PG  - e00196-17
AB  - Enterococcus spp. are Gram-positive lactic acid-producing bacteria found in the intestinal
      tracts of animals, like mammals, birds, and arthropods. Enterococcus
      spp. may cause oportunistic infections in vertebrate and invertebrate hosts. We
      report here the draft genome sequence of Enterococcus casseliflavus PAVET15
      containing 3,722,480 bp, with 80 contigs, an N50 of 179,476 bp, and 41.93% G+C
      content.
AU  - Cossio-Bayugar R
AU  - Miranda-Miranda E
AU  - Arreguin-Perez CA
AU  - Lozano L
AU  - Perez-de-la-Rosa D
AU  - Rocha-Martinez MK
AU  - Bravo-Diaz MA
AU  - Sachman-Ruiz B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00196-17.

PMID- 2395641
VI  - 18
DP  - 1990
TI  - Molecular recognition in the minor groove of the DNA helix. Studies on the synthesis of oligonucleotides and polynucleotides containing 3-deaza-2'-deoxyadenosine. Interaction of the oligonucleotides with the restriction endonuclease EcoRV.
PG  - 4771-4778
AB  - An improved procedure for the preparation of 3-deaza-2'-deoxyadenosine (d3CA)
      is described which is suitable for the synthesis of gram quantities of this
      analogue.  Using phosphoramidite chemistry d3CA has been incorporated into the
      EcoRV restriction endonuclease recognition sequence present in the
      self-complementary dodecamer d(GACGATATCGTC).  The modified oligonucleotides
      have been thoroughly characterised by nucleoside composition analysis, circular
      dichroism and thermal melting studies.  Studies with EcoRV show that
      incorporation of d3CA into either the central or outer dA-dT base-pair results
      in a substantial reduction in the rate of cleavage.  The two-step conversion of
      d3CA to 3-deaza-2'-deoxyadenosine-5'-O-triphosphate (d3CATP) via the
      5'-O-tosylate is also described.  d3CATP is not a substrate in the
      poly[d(AT)].poly[d(AT)] primed polymerisation for either E. coli DNA polymerase
      I or Micrococcus luteus DNA polymerase.  In a more detailed kinetic analysis
      d3CATP was shown to be a competitive inhibitor of E. coli DNA polymerase I with
      respect to dATP.
AU  - Cosstick R
AU  - Li X
AU  - Tuli DK
AU  - Williams DM
AU  - Connolly BA
AU  - Newman PC
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 4771-4778.

PMID- 28628615
VI  - 13
DP  - 2017
TI  - Flipping chromosomes in deep-sea archaea.
PG  - e1006847
AB  - One of the major mechanisms driving the evolution of all organisms is genomic rearrangement.
      In hyperthermophilic Archaea of the order Thermococcales, large
      chromosomal inversions occur so frequently that even closely related genomes are
      difficult to align. Clearly not resulting from the native homologous
      recombination machinery, the causative agent of these inversions has remained
      elusive. We present a model in which genomic inversions are catalyzed by the
      integrase enzyme encoded by a family of mobile genetic elements. We characterized
      the integrase from Thermococcus nautili plasmid pTN3 and showed that besides
      canonical site-specific reactions, it catalyzes low sequence specificity
      recombination reactions with the same outcome as homologous recombination events
      on DNA segments as short as 104bp both in vitro and in vivo, in contrast to other
      known tyrosine recombinases. Through serial culturing, we showed that the
      integrase-mediated divergence of T. nautili strains occurs at an astonishing
      rate, with at least four large-scale genomic inversions appearing within 60
      generations. Our results and the ubiquitous distribution of pTN3-like integrated
      elements suggest that a major mechanism of evolution of an entire order of
      Archaea results from the activity of a selfish mobile genetic element.
AU  - Cossu M
AU  - Badel C
AU  - Catchpole R
AU  - Gadelle D
AU  - Marguet E
AU  - Barbe V
AU  - Forterre P
AU  - Oberto J
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2017 13: e1006847.

PMID- 23929475
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of a Variant of the Methicillin-Resistant Staphylococcus aureus ST239 Lineage, Strain BMB9393, Displaying Superior Ability To Accumulate  ica-Independent Biofilm.
PG  - e00576-13
AB  - Biofilm is considered an important virulence factor in nosocomial infections. Herein, we
      report the complete genome sequence of a variant of
      methicillin-resistant Staphylococcus aureus, strain BMB9393, which is highly
      disseminated in Brazil. This strain belongs to the lineage ST239 and displays
      increased ability to accumulate ica-independent biofilm and to invade human
      epithelial cells.
AU  - Costa MO
AU  - Beltrame CO
AU  - Ferreira FA
AU  - Botelho AM
AU  - Lima NC
AU  - Souza RC
AU  - de Almeida LG
AU  - Vasconcelos AT
AU  - Nicolas MF
AU  - Figueiredo AM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00576-13.

PMID- 1389146
VI  - 13
DP  - 1992
TI  - The Efficiency of Restriction Endonuclease Digests Determined by PCR.
PG  - 190
AB  - Amplification of DNA by PCR should be stopped by a double-strand break in the template
      molecule. However, in the course of experiments designed to utilize restriction endonucleases
      (RE) to eliminate PCR amplification, we observed that extensive digestion rarely resulted in
      lack of a PCR product. We excluded one possible explanation for this obervation: "jumping" PCR
      where a 5' overhang will give rise to first-round products with short end homologies that may
      hybridize. Polymerization on this substrate would result in a complete template molecule.
      However, this will not occur for a 3' overhang or blunt end, yet we obtained similar
      amplification with DNA cut to give any type of end.
AU  - Costa ND
AU  - Thacker J
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 1992 13: 190.

PMID- 25883272
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Micrococcus sp. Strain MS-AsIII-49, an Arsenate-Reducing Isolate from Tropical Metal-Rich Sediment.
PG  - e00122-15
AB  - Micrococcus sp. strain MS-AsIII-49, which was isolated from a tropical metal-polluted stream
      sediment in Brazil, has the ability to reduce AsV to AsIII.
      Analysis of its draft genome revealed 186 contigs with a total size of 2,440,924
      bp encoding several metal resistance genes.
AU  - Costa PS
AU  - Tschoeke DA
AU  - Silva BS
AU  - Thompson F
AU  - Reis MP
AU  - Chartone-Souza E
AU  - Nascimento AM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00122-15.

PMID- 28559294
VI  - 199
DP  - 2017
TI  - Bypassing the restriction system to improve transformation of Staphylococcus epidermidis.
PG  - e00271-17
AB  - Staphylococcus epidermidis is the leading cause of infections on indwelling medical devices
      worldwide. Intrinsic antibiotic resistance and vigorous biofilm
      production have rendered these infections difficult to treat and, in some cases,
      require the removal of the offending medical prostheses. With the exception of
      two widely-passaged isolates RP62A and 1457, the pathogenesis of infections
      caused by clinical S. epidermidis strains is poorly understood due to the strong
      genetic barrier that precludes efficient transformation of foreign DNA into
      clinical isolates. The difficulty in transforming clinical S. epidermidis
      isolates is primarily due to the type I and IV restriction modification systems
      which act as genetic barriers. Here, we showed that efficient plasmid
      transformation of clinical S. epidermidis isolates from clonal complexes 2, 10
      and 89 could be realized by employing a plasmid artificial modification (PAM) in
      E. coli DC10B containing a Deltadcm mutation. This transformative technique
      should facilitate our ability to genetically modify clinical isolates of S.
      epidermidis and hence improve our understanding of its pathogenesis in human
      infections.ImportanceStaphylococcus epidermidis is a source of considerable
      morbidity worldwide. The underlying mechanisms contributing to the commensal and
      pathogenic lifestyles of S. epidermidis are poorly understood. Genetic
      manipulations of clinically relevant strains of S. epidermidis are largely
      prohibited due to the presence of a strong restriction barrier. With the
      introductions of the tools presented here, genetic manipulation has now become
      possible with clinically relevant S. epidermidis isolates, thus improving our
      understanding of S. epidermidis as a pathogen.
AU  - Costa SK
AU  - Donegan NP
AU  - Corvaglia AR
AU  - Francois P
AU  - Cheung AL
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2017 199: e00271-17.

PMID- 28428301
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequence of Corynebacterium pseudotuberculosis PA04, Isolated from the Lymph Node of a Sheep in the Amazon, Brazil.
PG  - e00202-17
AB  - This study reports the complete genome sequence of Corynebacterium pseudotuberculosis strain
      PA04, isolated from a sheep in the Amazon, Brazil. This
      bacterium is the etiological agent of caseous lymphadenitis. This genome contains
      2,338,093 bp, 52.2% G+C content, and a total of 2,104 coding sequences (CDSs), 41
      pseudogenes, 12 rRNAs, and 49 tRNAs.
AU  - Costa WLO
AU  - Alves JTC
AU  - Dias LM
AU  - Araujo CLA
AU  - Morais E
AU  - Silva AGM
AU  - Andrade SS
AU  - Ramos RTJ
AU  - Silva A
AU  - Folador ARC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00202-17.

PMID- 28630471
VI  - 7
DP  - 2017
TI  - Candidatus Mycoplasma girerdii replicates, diversifies, and co-occurs with Trichomonas vaginalis in the oral cavity of a premature infant.
PG  - 3764
AB  - Genital mycoplasmas, which can be vertically transmitted, have been implicated in
      preterm birth, neonatal infections, and chronic lung disease of prematurity. Our
      prior work uncovered 16S rRNA genes belonging to a novel, as-yet-uncultivated
      mycoplasma (lineage 'Mnola') in the oral cavity of a premature neonate. Here, we
      characterize the organism's associated community, growth status, metabolic
      potential, and population diversity. Sequencing of genomic DNA from the infant's
      saliva yielded 1.44 Gbp of high-quality, non-human read data, from which we
      recovered three essentially complete (including 'Mnola') and three partial draft
      genomes (including Trichomonas vaginalis). The completed 629,409-bp 'Mnola'
      genome (Candidatus Mycoplasma girerdii str. UC-B3) was distinct at the strain
      level from its closest relative, vaginally-derived Ca. M. girerdii str. VCU-M1,
      which is also associated with T. vaginalis. Replication rate measurements
      indicated growth of str. UC-B3 within the infant. Genes encoding
      surface-associated proteins and restriction-modification systems were especially
      diverse within and between strains. In UC-B3, the population genetic
      underpinnings of phase variable expression were evident in vivo. Unique among
      mycoplasmas, Ca. M. girerdii encodes pyruvate-ferredoxin oxidoreductase and may
      be sensitive to metronidazole. This study reveals a metabolically unique
      mycoplasma colonizing a premature neonate, and establishes the value of
      genome-resolved metagenomics in tracking phase variation.
AU  - Costello EK
AU  - Sun CL
AU  - Carlisle EM
AU  - Morowitz MJ
AU  - Banfield JF
AU  - Relman DA
PT  - Journal Article
TA  - Sci. Rep.
JT  - Sci. Rep.
SO  - Sci. Rep. 2017 7: 3764.

PMID- 8335261
VI  - 129
DP  - 1993
TI  - The single group-I intron in the chloroplast rrnL gene of Chlamydomonas humicola encodes a site-specific DNA endonuclease (I-ChuI).
PG  - 69-76
AB  - The single group-I intron (ChLSU-1) in the chloroplast (cp) large subunit rRNA-encoding gene
      (rrnL) of the green alga Chlamydomonas humicola is located at a position at which no introns
      have previously been characterized in other systems. In the present study, the nucleotide (nt)
      sequence of this 1118-bp intron was found to contain an internal open reading frame (ORF) that
      potentially encodes a basic protein of 218 amino acid residues. The putative C. humicola
      protein features two copies of the LAGLI-DADG motif and is part of the family of
      intron-encoded proteins comprising the endonucleases (ENases). I-SceI, I-SceI, I-SceIV and
      I-CsmI. Expression of the ChLSU.1 intron ORF in vitro in the presence of a 260-bp DNA fragment
      containing the exon 1-2 junction of an intronless version of the C. humicol rrnL resulted in
      specific cleavage of the DNA fragment very close to the intron insertion site. This novel
      intron-encoded ENase, designated I-ChuI, was also shown to generate a staggered cut with 4-nt
      (CTCG) 3'-OH overhangs 2 bp downstream from the intron insertion site.
AU  - Cote V
AU  - Mercier JP
AU  - Lemieux C
AU  - Turmel M
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1993 129: 69-76.

PMID- Not included in PubMed...
VI  - 43
DP  - 1997
TI  - Acetobacter strains contain DNA modified at GAATTC and GANTC.
PG  - 456-460
AB  - Total DNAs from nine strains of Acetobacter xylinum, two strains of Acetobacter aceti, and one
      Acetobacter pasteurianus strain were examined for the extent of digestion by various
      restriction endonucleases.  The majority of the endonucleases cleaved the total DNAs with a
      frequency expected from the number of sites present in DNA sequences deposited in the GenBank
      database.  However, the restriction enzyme digestions identified two different genomic DNA
      modifications in Acetobacter.  One sequence-specific modification protected total DNAs from
      seven of the A. xylinum strains against cleavage by EcoRI (GAATTC).  Digestion of total DNAs
      from A. xylinum ATCC 10245 (DNA not cut by EcoRI) and the closely related A. xylinum NRCC
      17005 (DNA cut by EcoRI) with Tsp509I (AATT) revealed differences in restriction frequencies
      adenine within GAATTC.  Another sequence-specific modification rendered total DNAs from all
      the 12 strains recalcitrant to digestion by HinfI.  The latter modification indicated that
      species of the genus Actobacter contain a solitary DNA methyltransferase that probably
      methylates adenine in GANTC.
AU  - Coucheron DH
PT  - Journal Article
TA  - Can. J. Microbiol.
JT  - Can. J. Microbiol.
SO  - Can. J. Microbiol. 1997 43: 456-460.

PMID- 26679586
VI  - 3
DP  - 2015
TI  - Draft Genome of the Arthrobacter sp. Strain Edens01.
PG  - e01475-15
AB  - We report the draft genome sequence of Arthrobacter sp. strain Edens01, isolated  from a leaf
      surface of a Rosa hybrid plant as part of the Howard Hughes Medical
      Institute-funded Student Initiated Microbial Discovery (SIMD) project. The genome
      has a total size of 3,639,179 bp and contig N50 of 454,897 bp.
AU  - Couger MB
AU  - Hanafy RA
AU  - Edens C
AU  - Budd C
AU  - French DP
AU  - Hoff WD
AU  - Elshahed MS
AU  - Youssef NH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01475-15.

PMID- 26659686
VI  - 3
DP  - 2015
TI  - The Draft Genome Sequence of Xanthomonas sp. Strain Mitacek01 Expands the Pangenome of a Genus of Plant Pathogens.
PG  - e01450-15
AB  - We report the draft genome sequence of Xanthomonas sp. strain Mitacek01, isolated from an
      indoor environment vending machine surface with frequent human use in
      Stillwater, Oklahoma, USA, as part of the Student-Initiated Microbial Discovery
      project. The genome has a total size of 3,617,426 bp and a contig N50 of
      1,906,967 bp.
AU  - Couger MB
AU  - Hanafy RA
AU  - Mitacek RM
AU  - Budd C
AU  - French DP
AU  - Hoff WD
AU  - Elshahed MS
AU  - Youssef NH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01450-15.

PMID- 26383650
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Environmental Isolate Chryseobacterium sp. Hurlbut01.
PG  - e01071-15
AB  - We report here the draft genome sequence of the environmental isolate Chryseobacterium sp.
      Hurlbut01, isolated from a light switch surface in Stillwater, OK, as part of the
      Student-Initiated Microbial Discovery (SIMD) project. The genome has a size of 3,899,838 bp
      and a contig N50 of 321 kb.
AU  - Couger MB
AU  - Hurlbut A
AU  - Murphy CL
AU  - Budd C
AU  - French DP
AU  - Hoff WD
AU  - Elshahed MS
AU  - Youssef NH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01071-15.

PMID- 26823574
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Five Pseudomonas aeruginosa Clinical Strains Isolated from Sputum Samples from Cystic Fibrosis Patients.
PG  - e01528-15
AB  - We report here the draft genome sequences of five Pseudomonas aeruginosa isolates obtained
      from sputum samples from two cystic fibrosis patients with chronic
      colonization. These closely related strains harbor 225 to 493 genes absent from
      the P. aeruginosa POA1 genome and contain 178 to 179 virulence factors and 29 to
      31 antibiotic resistance genes.
AU  - Couger MB
AU  - Wright A
AU  - Lutter EI
AU  - Youssef N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01528-15.

PMID- Not included in PubMed...
VI  - 17
DP  - 1987
TI  - Bacteriophage P1 encodes its own dam methylase.
PG  - 81
AB  - The packaging of P1 DNA during its life cycle has been shown to be dependent upon the
      methylation of the adenine residue in the sequence 5'-GATC-3' of the phage packaging site
      (pac).  In vitro studies have shown that unmethylated P1 DNA is not cut at the pac site, and
      the DNA is not packaged into the viral heads.  In an E. coli dam- host, which is unable to
      methylate 5'-GATC-3', P1 phage production lags about 20 min behind that in a dam+ host. This
      delayed production of phage is probably due to a need to synthesize a P1 dam analog before the
      pac site can be cleaved.  To study this process we have begun to characterize the P1 dam gene.
      A 13.5-kb region of P1 DNA was cloned into a lambda vector, and the hybrid was shown to encode
      a dam methylase based on its ability to methylate pBR322 DNA upon infection of an E. coli dam-
      host containing that plasmid.  The P1 dam gene borders the junction of P1 EcoRI fragments 3
      and 8.  This region of the P1 genome is currently being subcloned in order to localize the
      gene.  Following localization the gene will be mutagenized in an effort to further elucidate
      the role of the dam methylase in the P1 life cycle.
AU  - Coulby J
AU  - Sternberg N
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 1987 17: 81.

PMID- 3248723
VI  - 74
DP  - 1988
TI  - Characterization of the phage P1 dam gene.
PG  - 191
AB  - Meeting Abstract
AU  - Coulby JN
AU  - Sternberg NL
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 191.

PMID- 26251488
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Enterobacter cloacae UW5, a Rhizobacterium Capable of High Levels of Indole-3-Acetic Acid Production.
PG  - e00843-15
AB  - We report the complete genome sequence of Enterobacter cloacae UW5, an indole-3-acetic
      acid-producing rhizobacterium originally isolated from the
      rhizosphere of grass. The 4.9-Mbp genome has a G+C content of 54% and contains
      4,496 protein-coding sequences.
AU  - Coulson TJ
AU  - Patten CL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00843-15.

PMID- 23227987
VI  - 53
DP  - 2012
TI  - Direct sequencing of small genomes on the Pacific Biosciences RS without library  preparation.
PG  - 365-372
AB  - We have developed a sequencing method on the Pacific Biosciences RS sequencer (the PacBio) for
      small DNA molecules that avoids the need for a standard library
      preparation. To date this approach has been applied toward sequencing
      single-stranded and double-stranded viral genomes, bacterial plasmids, plasmid
      vector models for DNA-modification analysis, and linear DNA fragments covering an
      entire bacterial genome. Using direct sequencing it is possible to generate
      sequence data from as little as 1 ng of DNA, offering a significant advantage
      over current protocols which typically require 400-500 ng of sheared DNA for the
      library preparation.
AU  - Coupland P
AU  - Chandra T
AU  - Quail M
AU  - Reik W
AU  - Swerdlow H
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 2012 53: 365-372.

PMID- 24356832
VI  - 1
DP  - 2013
TI  - Genome Sequence of Strain MOLA814, a Proteorhodopsin-Containing Representative of the Betaproteobacteria Common in the Ocean.
PG  - e01062-13
AB  - Strain MOLA814 is a marine betaproteobacterium that was isolated from seawater in the Beaufort
      Sea. Here, we present its genome sequence and annotation. Genome
      analysis revealed the presence of a proteorhodopsin-encoding sequence together
      with its retinal-producing pathway, indicating that this strain might generate
      energy by using light.
AU  - Courties A
AU  - Riedel T
AU  - Jarek M
AU  - Intertaglia L
AU  - Lebaron P
AU  - Suzuki MT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01062-13.

PMID- 29242226
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Hyperthermophilic Archaeon Thermococcus sp. EXT12c, Isolated from the East Pacific Rise 9 degrees N.
PG  - e01385-17
AB  - We report the genome sequence of Thermococcus sp. EXT12c isolated from a deep-sea hydrothermal
      vent at the East Pacific Rise 9 degrees N. Microbes in the genus
      Thermococcus are able to grow anaerobically at high temperature, around neutral
      pH, and some of them under high hydrostatic pressure.
AU  - Courtine D
AU  - Alain K
AU  - Georges M
AU  - Bienvenu N
AU  - Morrison HG
AU  - Eren AM
AU  - Maignien L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01385-17.

PMID- 23969061
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Lactobacillus pasteurii CRBIP 24.76T.
PG  - e00660-13
AB  - We report the draft genome sequence of the type strain Lactobacillus pasteurii CRBIP 24.76,
      which is closely related to L. gigeriorum CRBIP 24.85(T), isolated
      from a chicken crop. The total length of the 29 contigs is about 1.9 Mb, with a
      G+C content of 40% and 1,946 coding sequences.
AU  - Cousin S
AU  - Clermont D
AU  - Creno S
AU  - Ma L
AU  - Loux V
AU  - Bizet C
AU  - Bouchier C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00660-13.

PMID- 23969062
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Lactobacillus hominis Strain CRBIP 24.179T, Isolated from Human Intestine.
PG  - e00662-13
AB  - We report the draft genome sequence of the strain Lactobacillus hominis CRBIP 24.179(T),
      isolated from a human clinical sample. The total length of the 28
      contigs is about 1.9 Mb, with a G+C content of 37% and 1,983 coding sequences.
AU  - Cousin S
AU  - Creno S
AU  - Ma L
AU  - Clermont D
AU  - Loux V
AU  - Bizet C
AU  - Bouchier C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00662-13.

PMID- 23969063
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences of Lactobacillus equicursoris CIP 110162T and Lactobacillus sp. Strain CRBIP 24.137, Isolated from Thoroughbred Racehorse Feces  and Human Urine, Respectively.
PG  - e00663-13
AB  - We report the draft genome sequences of strain Lactobacillus equicursoris CIP 110162(T),
      isolated from racehorse breed feces, and Lactobacillus sp. strain
      CRBIP 24.137, isolated from human urine; the two strains are closely related. The
      total lengths of the 116 and 62 scaffolds are about 2.157 and 2.358 Mb, with G+C
      contents of 46 and 45% and 2,279 and 2,342 coding sequences (CDSs), respectively.
AU  - Cousin S
AU  - Loux V
AU  - Ma L
AU  - Creno S
AU  - Clermont D
AU  - Bizet C
AU  - Bouchier C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00663-13.

PMID- 23045490
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Lactobacillus gigeriorum CRBIP 24.85T, Isolated from a Chicken Crop.
PG  - 5973
AB  - We report the draft genome of the strain Lactobacillus gigeriorum CRBIP 24.85(T), isolated
      from a chicken crop. The total length of the 60 scaffolds is about 1.9
      Mb, with a GC content of 38% and 2,062 protein-coding sequences (CDS).
AU  - Cousin S
AU  - Ma L
AU  - Creno S
AU  - Clermont D
AU  - Loux V
AU  - Bizet C
AU  - Bouchier C
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5973.

PMID- 10801134
VI  - 404
DP  - 2000
TI  - Retrotransposition of a bacterial group II intron.
PG  - 1018-1021
AB  - Self-splicing group II introns may be the evolutionary progenitors of eukaryotic spliceosomal
      introns, but the route by which they invade new chromosomal sites is unknown. To address the
      mechanism by which group II introns are disseminated, we have studied the bacterial L1.LtrB
      intron from Lactococcus lactis. The protein product of this intron, LtrA, possesses maturase,
      reverse transcriptase and endonuclease enzymatic activities. Together with the intron, LtrA
      forms a ribonucleoprotein (RNP) complex which mediates a process known as retrohoming. In
      retrohoming, the intron reverse splices into a cognate intronless DNA site. Integration of a
      DNA copy of the intron is recombinase independent but requires all three activities of LtrA.
      Here we report the first experimental demonstration of a group II intron invading ectopic
      chromosomal sites, which occurs by a distinct retrotransposition mechanism. This
      retrotransposition process is endonuclease-independent and recombinase-dependent, and is
      likely to involve reverse splicing of the intron RNA into cellular RNA targets. These
      retrotranspositions suggest a mechanism by which splicesomal introns may have become widely
      dispersed.
AU  - Cousineau B
AU  - Lawrence S
AU  - Smith D
AU  - Belfort M
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2000 404: 1018-1021.

PMID- 9727488
VI  - 94
DP  - 1998
TI  - Retrohoming of a bacterial group II intron: Mobility via complete reverse splicing, independent of homologous DNA recombination.
PG  - 451-462
AB  - The mobile group II intron of Lactococcus lactis, Ll.LtrB, provides the opportunity to analyze
      the homing pathway in genetically tractable bacterial systems.  Here, we show that Ll.LtrB
      mobility occurs by an RNA-based retrohoming mechanism in both Escherichia coli and L. lactis.
      Surprisingly, retrohoming occurs efficiently in the absence of RecA function, with a relaxed
      requirement for flanking exon homology and without coconversion of exon markers.  These
      results lead to a model for bacterial retrohoming in which the intron integrates into
      recipient DNA by complete reverse splicing and serves as the template for cDNA synthesis.  The
      retrohoming reaction is completed in unprecedented fashion by a DNA repair event that is
      independent of homologous recombination between the alleles.  Thus, Ll.LtrB has many features
      of retrotransposons, with practical and evolutionary implications.
AU  - Cousineau B
AU  - Smith D
AU  - Lawrence-Cavanagh S
AU  - Mueller JE
AU  - Yang J
AU  - Mills D
AU  - Manias D
AU  - Dunny G
AU  - Lambowitz AM
AU  - Belfort M
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1998 94: 451-462.

PMID- 23558537
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Rice Endophyte Burkholderia kururiensis M130.
PG  - e0022512
AB  - Burkholderia kururiensis M130 is one of the few characterized rice endophytes and was isolated
      from surface-sterilized rice roots. This bacterium shows strong growth-promoting effects,
      being able to increase rice yields. Here we present its draft genome sequence, which contains
      important traits for endophytic life and plant growth promotion.
AU  - Coutinho BG
AU  - Passos-da-Silva D
AU  - Previato JO
AU  - Mendonca-Previato L
AU  - Venturi V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0022512.

PMID- 29622605
VI  - 6
DP  - 2018
TI  - Complete Genome Sequences of Two Methicillin-Resistant Staphylococcus haemolyticus Isolates of Multilocus Sequence Type 25, First Detected by Shotgun  Metagenomics.
PG  - e00036-18
AB  - The emergence of nosocomial infections by multidrug-resistant Staphylococcus haemolyticus
      isolates has been reported in several European countries. Here, we
      report the first two complete genome sequences of S. haemolyticus sequence type
      25 (ST25) isolates 83131A and 83131B. Both isolates were isolated from the same
      clinical sample and were first identified through shotgun metagenomics.
AU  - Couto N
AU  - Chlebowicz MA
AU  - Raangs EC
AU  - Friedrich AW
AU  - Rossen JW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00036-18.

PMID- 29472906
VI  - 9
DP  - 2018
TI  - The DNA Methylome of the Hyperthermoacidophilic Crenarchaeon Sulfolobus acidocaldarius.
PG  - 137
AB  - DNA methylation is the most common epigenetic modification observed in the genomic DNA (gDNA)
      of prokaryotes and eukaryotes. Methylated nucleobases,
      N(6)-methyl-adenine (m6A), N(4)-methyl-cytosine (m4C), and 5-methyl-cytosine
      (m5C), detected on gDNA represent the discrimination mark between self and
      non-self DNA when they are part of restriction-modification systems in
      prokaryotes (Bacteria and Archaea). In addition, m5C in Eukaryotes and m6A in
      Bacteria play an important role in the regulation of key cellular processes.
      Although archaeal genomes present modified bases as in the two other domains of
      life, the significance of DNA methylations as regulatory mechanisms remains
      largely uncharacterized in Archaea. Here, we began by investigating the DNA
      methylome of Sulfolobus acidocaldarius. The strategy behind this initial study
      entailed the use of combined digestion assays, dot blots, and genome
      resequencing, which utilizes specific restriction enzymes, antibodies
      specifically raised against m6A and m5C and single-molecule real-time (SMRT)
      sequencing, respectively, to identify DNA methylations occurring in exponentially
      growing cells. The previously identified restriction-modification system,
      specific of S. acidocaldarius, was confirmed by digestion assay and SMRT
      sequencing while, the presence of m6A was revealed by dot blot and identified on
      the characteristic Dam motif by SMRT sequencing. No m5C was detected by dot blot
      under the conditions tested. Furthermore, by comparing the distribution of both
      detected methylations along the genome and, by analyzing DNA methylation profiles
      in synchronized cells, we investigated in which cellular pathways, in particular
      the cell cycle, this m6A methylation could be a key player. The analysis of
      sequencing data rejected a role for m6A methylation in another defense system and
      also raised new questions about a potential involvement of this modification in
      the regulation of other biological functions in S. acidocaldarius.
AU  - Couturier M
AU  - Lindas AC
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2018 9: 137.

PMID- 
VI  - 
DP  - 1988
TI  - New family of Type I restriction and modification systems.
PG  - 1-128
AB  - The chromosomally encoded type I restriction and modification system of Escherichia coli 15T,
      EcoA, behaves physiologically as a type I system, and in genetic crosses the hsdA genes behave
      as alleles of the hsd K genes of the archetypal type I system of E. coli K-12.  However,
      molecular experiments failed to demonstrate relatedness between the A and K systems.  Genes
      (hsdE) related to hsdA on the basis of DNA homology confer a new specificity to a natural
      isolate, E. coli A58.  The genes encoding EcoA and EcoE have an organization which mimics that
      of EcoK: there are three genes in the same order as those encoding EcoK, of which one, hsdS,
      confers the specificity.  The polypeptides of EcoA, EcoE, and CfrA (a new A-like system) show
      structural homology, demonstrated by immunological cross-reactivity.  The evidence presented
      indicates that EcoA and EcoE represent an alternative family of type I restriction and
      modification enzymes.  The recognition sequence of EcoE, 5'-GAG(N7)ATGC-3', is typical of
      type I systems.  Furthermore, heteroduplex analyses and nucleotide sequencing have indicated
      that the specificity genes of the A-like family show two large regions of variable sequence,
      interspersed and flanked by conserved sequences which include a repeated sequence.  Such an
      organization is similar to that of the K family specificity genes.  The hsdS genes of EcoA and
      EcoE show extensive homology throughout the proximal regions: both recognize the trinucleotide
      GAG.  In general no obvious similarity was detected between the primary sequences of the
      specificity polypeptides of the two families, with one remarkable exception: the proximal
      variable domain of the SB specificity polypeptide shows 44% identity to the proximal regions
      of the specificity subunits of both EcoA and EcoE.  Significantly, the StySB enzyme also
      recognizes the trinucleotide GAG.
AU  - Cowan GM
PT  - Journal Article
TA  - Ph.D. Thesis, University of Edinburgh, Edinburgh, Scotland
JT  - Ph.D. Thesis, University of Edinburgh, Edinburgh, Scotland
SO  - Ph.D. Thesis, University of Edinburgh, Edinburgh, Scotland 1988 : 1-128.

PMID- Not carried by PubMed...
VI  - 50
DP  - 1989
TI  - A new family of type I restriction and modification systems.
PG  - 441
AB  - The chromosomally encoded type I restriction and modification system of Escherichia coli 15T-,
      EcoA, behaves physiologically as a type I system, and in genetic crosses the hsd A genes
      behave as alleles of the hsd K genes of the archetypal type I system of E. coli K-12. However,
      molecular experiments failed to demonstrate relatedness between the A and K systems. Genes
      (hsd E) related to hsd A on the basis of DNA homology confer a new specificity to a natural
      isolate, E. coli A58. The genes encoding EcoA and EcoE have an organization which mimics that
      of EcoK: there are three genes in the same order as those encoding EcoK, of which one, hsdS,
      confers the specificity. The polypeptides of EcoA, EcoE, and CfrA (a new A-like system) show
      structural homology, demonstrated by immunological cross-reactivity. The evidence presented
      indicates that EcoA and EcoE represent an alternative family of type I restriction and
      modification enzyme. The recognition sequence of EcoE, 5'-GAG(N7)ATGC-3', is typical of type
      I systems. Furthermore, heteroduplex analyses and nucleotide sequencing have indicated that
      the specificity genes of the A-like family show two large regions of variable sequence,
      interspersed and flanked by conserved sequences which include a repeated sequence. Such an
      organization is similar to that of the K family specificity genes. The hsdS genes of EcoA and
      EcoE show extensive homology throughout the proximal regions: both recognize the trinucleotide
      GAG. In general no obvious similarity was detected between the primary sequences of the
      specificity polypeptides of the two families, with one remarkable exception the proximal
      variable domain of the SB specificity polypeptide shows 44% identity to the proximal regions
      of the specificity subunits of both EcoA and EcoE. Significantly, the StySB enzyme also
      recognizes the trinucleotide GAG.
AU  - Cowan GM
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1989 50: 441.

PMID- 3074012
VI  - 74
DP  - 1988
TI  - Defining domains in type-I restriction and modification enzymes.
PG  - 239-241
AB  - Meeting Abstract
AU  - Cowan GM
AU  - Daniel AS
AU  - Gann AAF
AU  - Kelleher JE
AU  - Murray NE
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 239-241.

PMID- 2642743
VI  - 56
DP  - 1989
TI  - Conservation of complex DNA recognition domains between families of restriction enzymes.
PG  - 103-109
AB  - One polypeptide, designated S, confers sequence-specificity to the multisubunit
      type I restriction enzymes.  Two families of such enzymes, K and A, include
      members that recognize diverse, bipartite, target sequences.  The S
      polypeptides of the K family, while having areas of near identity, also contain
      two extensive regions of variable sequence.  We now show that one of these,
      comprising the N-terminal 150 amino acids, specifies recognition of one
      component of the bipartite target sequence.  We have determined the sequence
      recognized by EcoE, a member of the A family.  This sequence, 5'GAG(N7)ATGC,
      has the trinucleotide GAG in common with EcoA and with StySB of the K family.
      We determined the nucleotide sequences of the S genes of EcoA and EcoE, and
      compared their predicted amino acid sequences with each other and with those of
      the five members of the K family.  There is no general sequence similarity
      between families, but the domain of the S polypeptide of StySB, which specifies
      GAG, shows nearly 50 per cent identity with the amino variable region of the S
      polypeptides of EcoA and EcoE.  A complex domain that recognizes and directs
      methylation of GAG is therefore common to enzymes of generally dissimilar amino
      acid sequence.
AU  - Cowan GM
AU  - Gann AAF
AU  - Murray NE
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1989 56: 103-109.

PMID- 
VI  - 14
DP  - 2004
TI  - Role of metal ions in promoting DNA binding and cleavage by restriction endonucleases.
PG  - 339-360
AB  - While three major classes of restriction endonucleases have been identified (Types I, II, and
      III), Type II are the most straightforward inasmuch as they require divalent magnesium as an
      essential cofactor but have no need for ATP.  A complete classification of Type II restriction
      nucleases has been presented elsewhere and the family is noted for the remarkable specificity
      and simplicity of its function.  These enzymes cleave both strands of double-strand DNA either
      at or near a recognition sequence that tends to be palindromic.  Consequently most restriction
      endonucleases are dimeric and recognize symmetric DNA sequences.  While showing many
      functional similarities in DNA recognition and catalytic cleavage, restriction endonucleases
      also display low sequence homology, and diversity in mechanisms of recognizing DNA target
      sequences and the positioning of metal cofactors.  Such diversity results in subtle variations
      in both protein binding locations and potential functional roles for essential metal cofactors
      that are only now coming under investigation.
AU  - Cowan JA
PT  - Journal Article
TA  - Nucleic Acids Mol. Biol.
JT  - Nucleic Acids Mol. Biol.
SO  - Nucleic Acids Mol. Biol. 2004 14: 339-360.

PMID- 29897968
VI  - 14
DP  - 2018
TI  - Evolution via recombination: Cell-to-cell contact facilitates larger recombination events in Streptococcus pneumoniae.
PG  - e1007410
AB  - Homologous recombination in the genetic transformation model organism Streptococcus pneumoniae
      is thought to be important in the adaptation and
      evolution of this pathogen. While competent pneumococci are able to scavenge DNA
      added to laboratory cultures, large-scale transfers of multiple kb are rare under
      these conditions. We used whole genome sequencing (WGS) to map transfers in
      recombinants arising from contact of competent cells with non-competent 'target'
      cells, using strains with known genomes, distinguished by a total of ~16,000
      SNPs. Experiments designed to explore the effect of environment on large scale
      recombination events used saturating purified donor DNA, short-term cell
      assemblages on Millipore filters, and mature biofilm mixed cultures. WGS of 22
      recombinants for each environment mapped all SNPs that were identical between the
      recombinant and the donor but not the recipient. The mean recombination event
      size was found to be significantly larger in cell-to-cell contact cultures (4051
      bp in filter assemblage and 3938 bp in biofilm co-culture versus 1815 bp with
      saturating DNA). Up to 5.8% of the genome was transferred, through 20
      recombination events, to a single recipient, with the largest single event
      incorporating 29,971 bp. We also found that some recombination events are
      clustered, that these clusters are more likely to occur in cell-to-cell contact
      environments, and that they cause significantly increased linkage of genes as far
      apart as 60,000 bp. We conclude that pneumococcal evolution through homologous
      recombination is more likely to occur on a larger scale in environments that
      permit cell-to-cell contact.
AU  - Cowley LA
AU  - Petersen FC
AU  - Junges R
AU  - Jimenez MJD
AU  - Morrison DA
AU  - Hanage WP
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2018 14: e1007410.

PMID- 6086574
VI  - 159
DP  - 1984
TI  - Restriction of bacteriophage plaque formation in Streptomyces spp.
PG  - 499-504
AB  - Several Streptomyces species that produce restriction endonucleases were
      characterized for their ability to propagate 10 different broad host range
      bacteriophages.  Each species displayed a different pattern of plaque
      formation.  A restrictionless mutant of S. albus G allowed plaque formation by
      all 10 phages, whereas the wildtype strain showed plaques with only 2 phages.
      DNA isolated from three of the phages was analyzed for the presence of
      restriction sites for Streptomyces species-encoded enzymes, and a very strong
      correlation was established between the failure to form plaques on Streptomyces
      species that produced particular restriction enzymes and the presence of the
      corresponding restriction sites in the phage DNA.  Also, the phages that lacked
      restriction sites in their DNA generally formed plaques on the corresponding
      restriction endonuclease-producing hosts at high efficiency.  The DNAs from the
      three phages analyzed also generally contained either many or no restriction
      sites for the Streptomyces species-produced enzymes, suggesting a strong
      evolutionary trend to either eliminate all or tolerate many restriction sites.
      The data indicate that restriction plays a major role in host range
      determination for Streptomyces phages.  Analysis of bacteriophage host ranges
      of many other uncharacterized Streptomyces hosts has identified four relatively
      nonrestricting hosts, at least two of which may be suitable hosts for gene
      cloning.  The data also suggest that several restriction systems remain to be
      identified in the genus Streptomyces.
AU  - Cox KL
AU  - Baltz RH
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1984 159: 499-504.

PMID- Not carried by PubMed...
VI  - 28
DP  - 1987
TI  - Acrolein, a metabolite of cyclophosphamide, alters DNA methylase activity in a non-competitive fashion by reacting with -SH groups of the enzyme.
PG  - 86
AB  - Cyclophosphamide induces urinary bladder cancer both in humans and rats. Acrolein, an active
      metabolite of cyclophosphamide, may be responsible for the bladder cancer induced by
      cyclophosphamide.  Experiments are in progress to determine the carcinogenicity of acrolein in
      rat bladder.  Studies have also been initiated to examine the biochemical lesions induced
      following exposure of urothelial cells to acrolein.  In vitro studies on the effect of
      acrolein on DNA methylase, a -SH containing enzyme (R. Cox, Cancer Res., 40:61, 1980), were
      initiated to determine if acrolein might alter the DNA methylation pattern. Acrolein was shown
      to react with the -SH group of cytochrome P450, resulting in inactivation (A.J. Marinello et
      al., Cancer Res., 44:4615, 1984).  DNA methylase was isolated from the liver and urothelium of
      rats and assayed as previously described (R. Cox, Biochem. Int., 5:787, 1982).  Acrolein
      inhibited DNA methylase activity by 50% and 92% at final concentrations of 10 and 100 microM
      acrolein.  Kinetic studies demonstrated non-competitive inhibition wiuth a Ki of 6.7 microM.
      The inhibition of DNA methylase by 20 microM acrolein was restored to 85% of its original
      activity when 100 microM dithiothreitol was added.  As the enzyme concentration was increased,
      the inhibition of DNA methylase by 20 microM acrolein was decreased, whereas increased amounts
      of DNA had no effect.  These data suggest that acrolein is a very good inhibitor of DNA
      methylase, in a non-competitive fashion, by reacting with the -SH groups of the protein.
AU  - Cox R
AU  - Goorha S
AU  - Irving C
PT  - Journal Article
TA  - Proc. Amer. Assoc. Cancer Res.
JT  - Proc. Amer. Assoc. Cancer Res.
SO  - Proc. Amer. Assoc. Cancer Res. 1987 28: 86.

PMID- 3345585
VI  - 9
DP  - 1988
TI  - Inhibition of DNA methylase activity by acrolein.
PG  - 463-465
AB  - Acrolein, a reactive metabolite of cyclophosphamide, may be responsible for bladder cancer
      induced by cyclophosphamide.  DNA methylase was isolated from the liver and urothelium of rats
      by high salt extraction of purified nuclei.  Acrolein at 10 microM inhibited liver and bladder
      DNA methylase activity by 30-50%.  Kinetic studies with the liver enzyme showed a competitive
      type of inhibition with a Ki of 6.7 microM.  Both dithiothreitol and glutathione afforded
      protection to the enzyme when added to the assay.  At near equimolar concentrations of
      glutathione to acrolein, the methylase retained 80-90% activity.  An increase in DNA had no
      effect on the inhibition by acrolein, whereas increased amounts of protein protected against
      acrolein inhibition, suggesting that acrolein reacted with the DNA methylase protein.  On the
      other hand, DNA that had been reacted with acrolein was unable to serve as a substrate for DNA
      methylase.  As the DNA adducts increased the methylation of the DNA decreased.  Thus, acrolein
      has the ability to react with DNA and the DNA methylase protein, either of which results in
      inhibition of DNA methylation.
AU  - Cox R
AU  - Goorha S
AU  - Irving CC
PT  - Journal Article
TA  - Carcinogenesis
JT  - Carcinogenesis
SO  - Carcinogenesis 1988 9: 463-465.

PMID- 24939888
VI  - 5
DP  - 2014
TI  - Evidence of Extensive DNA Transfer between Bacteroidales Species within the Human Gut.
PG  - e01305-14
AB  - The genome sequences of intestinal Bacteroidales strains reveal evidence of extensive
      horizontal gene transfer. In vitro studies of Bacteroides and other bacteria have addressed
      mechanisms of conjugative transfer and some phenotypic outcomes of these DNA acquisitions in
      the recipient, such as the acquisition of antibiotic resistance. However, few studies have
      addressed the horizontal transfer of genetic elements between bacterial species coresident in
      natural microbial communities, especially microbial ecosystems of humans. Here, we examine the
      genomes of Bacteroidales species from two human adults to identify genetic elements that were
      likely transferred among these Bacteroidales while they were coresident in the intestine.
      Using seven coresident Bacteroidales species from one individual and eight from another, we
      identified five large chromosomal regions, each present in a minimum of three of the
      coresident strains at near 100% DNA identity. These five regions are not found in any other
      sequenced Bacteroidetes genome at this level of identity and are likely all integrative
      conjugative elements (ICEs). Such highly similar and unique regions occur in only 0.4% of
      phylogenetically representative mock communities, providing strong evidence that these five
      regions were transferred between coresident strains in these subjects. In addition to the
      requisite proteins necessary for transfer, these elements encode proteins predicted to
      increase fitness, including orphan DNA methylases that may alter gene expression, fimbriae
      synthesis proteins that may facilitate attachment and the utilization of new substrates,
      putative secreted antimicrobial molecules, and a predicted type VI secretion system (T6SS),
      which may confer a competitive ecological advantage to these strains in their complex
      microbial ecosystem.IMPORTANCE By analyzing Bacteroidales strains coresident in the gut
      microbiota of two human adults, we provide strong evidence for extensive interspecies and
      interfamily transfer of integrative conjug!
      ative el
      ements within the intestinal microbiota of individual humans. In the recipient strain, we show
      that the conjugative elements themselves can be modified by the transposition of insertion
      sequences and retroelements from the recipient's genome, with subsequent transfer of these
      modified elements to other members of the microbiota. These data suggest that the genomes of
      our gut bacteria are substantially modified by other, coresident members of the ecosystem,
      resulting in highly personalized Bacteroidales strains likely unique to that individual. The
      genetic content of these ICEs suggests that their transfer from successful adapted members of
      an ecosystem confers beneficial properties to the recipient, increasing its fitness and
      allowing it to better compete within its particular personalized gut microbial ecosystem.
AU  - Coyne MJ
AU  - Zitomersky NL
AU  - McGuire AM
AU  - Earl AM
AU  - Comstock LE
PT  - Journal Article
TA  - MBio
JT  - MBio
SO  - MBio 2014 5: e01305-14.

PMID- 20081001
VI  - 76
DP  - 2010
TI  - Expanding Small-Molecule Functional Metagenomics through Parallel Screening of Broad-Host-Range Cosmid Environmental DNA Libraries in Diverse Proteobacteria.
PG  - 1633-1641
AB  - The small-molecule biosynthetic diversity encoded within the genomes of
      uncultured bacteria is an attractive target for the discovery of natural
      products using functional metagenomics. Phenotypes commonly associated
      with the production of small molecules, such as antibiosis, altered
      pigmentation, or altered colony morphology, are easily identified from
      screens of arrayed metagenomic library clones. However, functional
      metagenomic screening methods are limited by their intrinsic dependence on
      a heterologous expression host. Toward the goal of increasing the
      small-molecule biosynthetic diversity found in functional metagenomic
      studies, we report the phenotypic screening of broad-host-range
      environmental DNA libraries in six different proteobacteria: Agrobacterium
      tumefaciens, Burkholderia graminis, Caulobacter vibrioides, Escherichia
      coli, Pseudomonas putida, and Ralstonia metallidurans. Clone-specific
      small molecules found in culture broth extracts from pigmented and
      antibacterially active clones, as well as the genetic elements responsible
      for the biosynthesis of these metabolites, are described. The host strains
      used in this investigation provided access to unique sets of clones
      showing minimal overlap, thus demonstrating the potential advantage
      conferred on functional metagenomics through the use of multiple diverse
      host species.
AU  - Craig JW
AU  - Chang FY
AU  - Kim JH
AU  - Obiajulu SC
AU  - Brady SF
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2010 76: 1633-1641.

PMID- 6377015
VI  - 194
DP  - 1984
TI  - Induction of damage inducible (SOS) repair in dam mutants of Escherichia coli exposed to 2-aminopurine.
PG  - 539-540
AB  - 2-Aminopurine induces damage inducible (SOS) repair in an Escherichia coli dam-4 strain but
      not in a dam-4 mutS456 derivative or in dam+ bacteria.
AU  - Craig RJ
AU  - Arraj JA
AU  - Marinus MG
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1984 194: 539-540.

PMID- 17660745
VI  - 26
DP  - 2007
TI  - DNA looping and translocation provide an optimal cleavage mechanism for the type III restriction enzymes.
PG  - 3815-3825
AB  - EcoP15I is a type III restriction enzyme that requires two recognition sites in a defined
      orientation separated by up to 3.5 kbp to efficiently
      cleave DNA. The mechanism through which site-bound EcoP15I enzymes
      communicate between the two sites is unclear. Here, we use atomic force
      microscopy to study EcoP15I-DNA pre-cleavage complexes. From the number
      and size distribution of loops formed, we conclude that the loops observed
      do not result from translocation, but are instead formed by a contact
      between site-bound EcoP15I and a nonspecific region of DNA. This
      conclusion is confirmed by a theoretical polymer model. It is further
      shown that translocation must play some role, because when translocation
      is blocked by a Lac repressor protein, DNA cleavage is similarly blocked.
      On the basis of these results, we present a model for restriction by type
      III restriction enzymes and highlight the similarities between this and
      other classes of restriction enzymes.
AU  - Crampton N
AU  - Roes S
AU  - Dryden DT
AU  - Rao DN
AU  - Edwardson JM
AU  - Henderson RM
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 2007 26: 3815-3825.

PMID- 17646654
VI  - 104
DP  - 2007
TI  - Fast-scan atomic force microscopy reveals that the type III restriction enzyme EcoP15I is capable of DNA translocation and looping.
PG  - 12755-12760
AB  - Many DNA-modifying enzymes act in a manner that requires communication between two
      noncontiguous DNA sites.  These sites can be brought into contact either by a
      diffusion-mediated chance interaction between enzymes bound at the two sites, or by active
      translocation of the intervening DNA by a site-bound enzyme.  EcoP15I, a type III restriction
      enzyme, needs to interact with two recognition sites separated by up to 3,500 bp before it can
      cleave DNA.  Here, we have studied the behavior of EcoP15I, using a novel fast-scan atomic
      force microscope, which uses a miniaturized cantilever and scan stage to reduce the mechanical
      response time of the cantilever and to prevent the onset of resonant motion at high scan
      speeds.  With this instrument, we were able to achieve scan rates of up to 10 frames per s
      under fluid.  The improved time resolution allowed us to image EcoP15I in real time at scan
      rates of 1-3 frames per s.  EcoP15I translocated DNA in an ATP-dependent manner, at a rate of
      79 +/- 33 bp/s.  The accumulation of supercoiling, as a consequence of movemennt of EcoP15I
      along the DNA, could also be observed.  EcoP15I bound to its recognition site was also seen to
      make nonspecific contacts with other DNA sites, thus forming DNA loops and reducing the
      distance between the two recognition sites.  On the basis of our results, we conclude that
      EcoP15I uses two distinct mechanisms to communicate between two recognition sites: diffusive
      DNA loop formation and ATPase-driven translocation of the intervening DNA contour.
AU  - Crampton N
AU  - Yokokawa M
AU  - Dryden DTF
AU  - Edwardson J
AU  - Michael R
AU  - Desirazu N
AU  - Takeyasu K
AU  - Yoshimura SH
AU  - Henderson RM
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2007 104: 12755-12760.

PMID- 
VI  - 28
DP  - 2000
TI  - Molecular enzymology of the adenine-N6 DNA methyltransferase M.EcoRV: Site-directed mutagenesis analysis of DNA sequence and target base recognition.
PG  - A309
AB  - Methylation of DNA is important in many organisms and essential in mammals.  Nucleobases can
      be methylated at adenine-N6, cytosine-N4 or cytosine-C6 atoms by specific DNA
      methyltransferases.  The M.EcoRV DNA-(adenine-N6)-methyltransferase specifically transfers a
      methyl group from AdoMet to the first adenine within GATATC sequences.  Here, we have
      investigated the target base and DNA sequence recognition by M.EcoRV using site-directed
      mutagenesis.  We show that variants of M.EcoRV in which active site residues are exchanged
      (K16R, Y196W) show a >100 fold altered target base specificity and prefer methylation of
      cytosine residues over adenine residues.  M.EcoRV is closely related to the dam DNA
      methyltransferase which modifies adenine residues within GATC and M.EcoRV also accepts this
      sequence.  To investigate DNA recognition by M.EcoRV, several amino acid residues in putative
      DNA interacting regions were exchanged, i.e. in the variable domain of the enzyme as well as
      at the N-terminus.  The mutants were analyzed with respect to their ability to modify GATATC,
      GATC and GATCTC sequences in order to find out, which part of the recognition sequence is
      contacted by the corresponding amino acid residue.  Our data show that some of the variants
      display an increased specificity N136A, C140A, Lys141, Lys142 and Arg145 are important for DNA
      binding of the enzyme, and that the N-terminal part of the M.EcoRV protein is not only
      involved in AdoMet binding but also in DNA recognition.
AU  - Cranz S
AU  - Beck C
AU  - Roth M
AU  - Jeltsch A
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 2000 28: A309.

PMID- 18478107
VI  - 3
DP  - 2008
TI  - Genome sequence of Brucella abortus vaccine strain S19 compared to virulent strains yields candidate virulence genes.
PG  - e2193
AB  - The Brucella abortus strain S19, a spontaneously attenuated strain, has been used as a vaccine
      strain in vaccination of cattle against brucellosis
      for six decades. Despite many studies, the physiological and molecular
      mechanisms causing the attenuation are not known. We have applied
      pyrosequencing technology together with conventional sequencing to rapidly
      and comprehensively determine the complete genome sequence of the
      attenuated Brucella abortus vaccine strain S19. The main goal of this
      study is to identify candidate virulence genes by systematic comparative
      analysis of the attenuated strain with the published genome sequences of
      two virulent and closely related strains of B. abortus, 9-941 and 2308.
      The two S19 chromosomes are 2,122,487 and 1,161,449 bp in length. A total
      of 3062 genes were identified and annotated. Pairwise and reciprocal
      genome comparisons resulted in a total of 263 genes that were
      non-identical between the S19 genome and any of the two virulent strains.
      Amongst these, 45 genes were consistently different between the attenuated
      strain and the two virulent strains but were identical amongst the
      virulent strains, which included only two of the 236 genes that have been
      implicated as virulence factors in literature. The functional analyses of
      the differences have revealed a total of 24 genes that may be associated
      with the loss of virulence in S19. Of particular relevance are four genes
      with more than 60 bp consistent difference in S19 compared to both the
      virulent strains, which, in the virulent strains, encode an outer membrane
      protein and three proteins involved in erythritol uptake or metabolism.
AU  - Crasta OR
AU  - Folkerts O
AU  - Fei Z
AU  - Mane SP
AU  - Evans C
AU  - Martino-Catt S
AU  - Bricker B
AU  - Yu G
AU  - Du L
AU  - Sobral BW
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2008 3: e2193.

PMID- 7343642
VI  - 127
DP  - 1981
TI  - Evidence for plasmid-mediated restriction-modification in Mycobacterium avium intracellulare.
PG  - 333-338
AB  - Mycobacterium avium intracellular strain LR25 carries three plasmids with
      molecular weights of 11.2, 18.3 and 107 x 10(6) as determined by electron
      microscopy.  A number of phages propagated on Mycobacterium smegmatis ATCC 607
      were tested for their ability to infect strain LR25.  Phage JF2 gave an
      efficiency of plating of 10-4 on strain LR25, but phage JF2 propagated on
      strain LR25 infected strain LR25 and M. smegmatis with equal high efficiency.
      This indicated the presence of a restriction-modification (R-M) system in
      strain LR25 that was not present in M. smegmatis.  Strain LR25 was grown in the
      presence of acriflavine to eliminate the plasmids and tested for sensitivity to
      phage JF2.  One of forty colonies was found to be R-M-deficient.  This strain,
      designated strain LR163, lacks the three plasmids present in strain LR25.  The
      results indicate that the R-M system is plasmid-coded.  Strain LR163 was
      sensitive to several phages to which strain LR25 was resistant and for which we
      were unable to isolate modified phage.  This suggests that some plasmid-coded
      function in addition to restriction is involved.  An R-M system was also
      demonstrated in M. avium intracellulare strain LR131 using phage JF1.  This
      strain does not carry plasmids.
AU  - Crawford JT
AU  - Cave MD
AU  - Bates JH
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1981 127: 333-338.

PMID- 27979956
VI  - 4
DP  - 2016
TI  - Genome Sequences of Multidrug-Resistant, Colistin-Susceptible and -Resistant Klebsiella pneumoniae Clinical Isolates from Pakistan.
PG  - e01419-16
AB  - The emergence and spread of colistin resistance among multidrug-resistant (MDR) Klebsiella
      pneumoniae represent a critical threat to global health. Here, we
      report the complete genome sequences of 10 MDR, colistin-susceptible and
      -resistant K. pneumoniae clinical isolates obtained in Pakistan between 2010 and
      2013.
AU  - Crawford MA et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01419-16.

PMID- 6260587
VI  - 12
DP  - 1980
TI  - DNA modification induced during infection of Bacillus subtilis by phage Phi3T.
PG  - 17-24
AB  - The DNA of the Bacillus subtilis temperate phage Phi3T is not susceptible to
      cleavage by the restriction endonuclease HaeIII, although it is cut by many
      other restriction enzymes.  The host DNA from uninfected cells is cut by
      HaeIII.  We show that Phi3T DNA propagated in a
      restriction-modification-defective Escherichia coli cell can be digested by
      HaeIII.  Thus, Phi3T DNA does contain the nucleotide recognition sequence of
      HaeIII.  We suggest that this phage induces the modification of its own DNA.
      In support of this mechanism we show that extracts prepared from Phi3T-infected
      cells contain an activity which in the presence of S-adenosyl-L-methionine
      (SAM) can modify lambda DNA against cleavage by HaeIII.  The same in
      vitro-modified DNA is still susceptible to cleavage by other restriction
      endonucleases.
AU  - Cregg JM
AU  - Nguyen AH
AU  - Ito J
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1980 12: 17-24.

PMID- 96586
VI  - 85
DP  - 1978
TI  - EcoRI cleavage of DNA from Bacillus subtilis phage SPO1.
PG  - 601-605
AB  - The hydroxymethyluracil-containing DNA of B. subtilis phage SPO1 is cleaved only with low
      efficiency by restriction nuclease EcoRI.  The efficiency is greatly increased by EcoRI*
      conditions, but even under these conditions, the efficiency is less than with
      thymine-containing DNA.  In contrast with their effect on thymine-containing DNA, EcoRI*
      conditions do not appear to increase the number of sites on the SPO1 genome at which cleavage
      takes place.  We describe the fragments produced by a (nearly) limit digest of SPO1 DNA with
      EcoRI and assign most of the known SPO1 cistrons to specific fragments.
AU  - Cregg JM
AU  - Stewart CR
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1978 85: 601-605.

PMID- 23516191
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Pseudoalteromonas luteoviolacea Strain B (ATCC 29581).
PG  - e0004813
AB  - We report the 4.049-Mbp high-quality draft assembly of the Pseudoalteromonas luteoviolacea
      strain B (ATCC 29581) genome. This marine species is known to
      biosynthesize several antimicrobial compounds, including the purple pigment
      violacein. Whole-genome sequencing and genome mining will complement experimental
      studies aimed at elucidating novel biosynthetic pathways capable of producing
      pharmaceutically relevant molecules. Based upon 16S rRNA phylogenetic analysis,
      we propose that strain ATCC 29581 be classified as a distinct phylogenetic
      species of the genus Pseudoalteromonas.
AU  - Cress BF
AU  - Erkert KA
AU  - Barquera B
AU  - Koffas MA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0004813.

PMID- 23516192
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Escherichia coli Strain ATCC 23506 (Serovar O10:K5:H4).
PG  - e0004913
AB  - We report the 5.101-Mbp high-quality draft assembly of the Escherichia coli strain ATCC 23506
      (serovar O10:K5:H4, also known as NCDC Bi 8337-41) genome. This
      uropathogenic strain, commonly referred to as E. coli K5, produces N-acetyl
      heparosan, a glycosaminoglycan-like capsular polysaccharide and precursor to the
      anticoagulant pharmaceutical heparin. Metabolic reconstruction of this genome
      will enable the prediction of gene deletions and overexpressions that lead to
      increased heparosan production.
AU  - Cress BF
AU  - Greene ZR
AU  - Linhardt RJ
AU  - Koffas MA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0004913.

PMID- 23516189
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Escherichia coli Strain ATCC 23502 (Serovar O5:K4:H4).
PG  - e0004613
AB  - We report the 4.682-Mbp high-quality draft assembly of the Escherichia coli strain ATCC 23502
      (serovar O5:K4:H4, also known as NCDC U1-41) genome. This
      uropathogenic strain, commonly referred to as E. coli K4, produces a
      glycosaminoglycan-like capsular polysaccharide with a backbone similar in
      structure to unsulfated chondroitin, a precursor to the nutraceutically and
      potentially pharmaceutically valuable compound chondroitin sulfate. Metabolic
      reconstruction of this genome will enable prediction of genetic engineering
      strategies leading to increased chondroitin production.
AU  - Cress BF
AU  - Greene ZR
AU  - Linhardt RJ
AU  - Koffas MA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0004613.

PMID- 23516190
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Escherichia coli Strain Nissle 1917 (Serovar O6:K5:H1).
PG  - e0004713
AB  - We announce the availability of the 5.023-Mbp high-quality draft assembly of the  Escherichia
      coli strain Nissle 1917 (serovar O6:K5:H1) genome. Short genomic
      segments from this important probiotic strain have been available in public
      databases, but the full genome sequence has remained inaccessible. Thus,
      high-coverage, whole genome sequencing of E. coli Nissle 1917 is presented
      herein. Reannotation and metabolic reconstruction will enable comparative
      genomics analysis and model-guided predictions of genetic manipulations leading
      to increased production of the K5 capsular polysaccharide known as N-acetyl
      heparosan, a precursor to the anticoagulant pharmaceutical heparin.
AU  - Cress BF
AU  - Linhardt RJ
AU  - Koffas MA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0004713.

PMID- 29622616
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of the Fish Pathogen Flavobacterium columnare Genomovar III Strain PH-97028 (=CIP 109753).
PG  - e00222-18
AB  - Flavobacterium columnare strain PH-97028 (=CIP 109753) is a genomovar III reference strain
      that was isolated from a diseased Ayu fish in Japan. We report
      here the analysis of the first available genomovar III sequence of this species
      to aid in identification, epidemiological tracking, and virulence studies.
AU  - Criscuolo A
AU  - Chesneau O
AU  - Clermont D
AU  - Bizet C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00222-18.

PMID- 24625865
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Campylobacter coli Strain IPSID-1 Isolated from a Patient with Immunoproliferative Small Intestinal Disease.
PG  - e00079-14
AB  - The genome sequence and annotation of Campylobacter coli strain IPSID-1 are reported here.
      This bacterial isolate is the first to be cultured from a patient
      with immunoproliferative small intestinal disease (IPSID). The draft genome
      sequence is 1.683 Mb long, comprises 64 contigs, and has 31.26% G+C content.
AU  - Criscuolo A
AU  - de la Blanchardiere A
AU  - Coeuret S
AU  - Passet V
AU  - Saguet-Rysanek V
AU  - Vergnaud M
AU  - Verdon R
AU  - Leclercq A
AU  - Lecuit M
AU  - Brisse S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00079-14.

PMID- 25502663
VI  - 2
DP  - 2014
TI  - Genome Sequence of Bacillus simplex Strain P558, Isolated from a Human Fecal Sample.
PG  - e01241-14
AB  - Bacillus simplex strain P558 was isolated from a fecal sample of a 25-year-old Saudi male. We
      sequenced the 5.98-Mb genome of the strain and compared it to that
      of B. simplex strain 1NLA3E.
AU  - Croce O
AU  - Hugon P
AU  - Lagier JC
AU  - Bibi F
AU  - Robert C
AU  - Azhar EI
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01241-14.

PMID- 24812218
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Mycobacterium vulneris DSM 45247T.
PG  - e00370-14
AB  - We report the draft genome sequence of Mycobacterium vulneris DSM 45247(T) strain, an
      emerging, opportunistic pathogen of the Mycobacterium avium complex.
      The genome described here is composed of 6,981,439 bp (with a G+C content of
      67.14%) and has 6,653 protein-coding genes and 84 predicted RNA genes.
AU  - Croce O
AU  - Robert C
AU  - Raoult D
AU  - Drancourt M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00370-14.

PMID- 24786954
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Mycobacterium mageritense DSM 44476T.
PG  - e00354-14
AB  - We report the draft genome sequence of Mycobacterium mageritense strain DSM 44476(T) (CIP
      104973), a nontuberculosis species responsible for various
      infections. The genome described here is composed of 7,966,608 bp, with a G+C
      content of 66.95%, and contains 7,675 protein-coding genes and 120 predicted RNA
      genes.
AU  - Croce O
AU  - Robert C
AU  - Raoult D
AU  - Drancourt M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00354-14.

PMID- 24744338
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Mycobacterium asiaticum Strain DSM 44297.
PG  - e00320-14
AB  - We report the draft genome sequence of Mycobacterium asiaticum strain DSM 44297,  a tropical
      mycobacterium seldom responsible for human infection. The genome of M. asiaticum has a size of
      5,935,986 bp, with a 66.03% G+C content, encoding 5,591 proteins and 81 RNAs.
AU  - Croce O
AU  - Robert C
AU  - Raoult D
AU  - Drancourt M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00320-14.

PMID- 24744336
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Mycobacterium austroafricanum DSM 44191.
PG  - e00317-14
AB  - We announce the draft genome sequence of Mycobacterium austroafricanum DSM 44191(T) (=
      E9789-SA12441(T)), a non-tuberculosis species responsible for opportunistic infection. The
      genome described here has a size of 6,772,357 bp with a G+C content of 66.79% and contains
      6,419 protein-coding genes and 112 RNA genes.
AU  - Croce O
AU  - Robert C
AU  - Raoult D
AU  - Drancourt M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00317-14.

PMID- 24723727
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Mycobacterium cosmeticum DSM 44829.
PG  - e00315-14
AB  - We announce the draft genome sequence of Mycobacterium cosmeticum strain DSM 44829, a
      nontuberculous species responsible for opportunistic infection. The genome described here is
      composed of 6,462,090 bp, with a G+C content of 68.24%. It contains 6,281 protein-coding genes
      and 75 predicted RNA genes.
AU  - Croce O
AU  - Robert C
AU  - Raoult D
AU  - Drancourt M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00315-14.

PMID- 24874688
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Mycobacterium farcinogenes NCTC 10955.
PG  - e00523-14
AB  - We report the draft genome sequence of Mycobacterium farcinogenes NCTC 10955 (=DSM 43637(T)),
      a nontuberculosis species responsible for bovine farcy. The
      strain described here is composed of 6,139,893 bp, with a G+C content of 65.73%,
      and contains 5,816 protein-coding genes and 76 RNA genes.
AU  - Croce O
AU  - Robert C
AU  - Raoult D
AU  - Drancourt M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00523-14.

PMID- 28798166
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Three beta-Lactam-Catabolizing Soil Proteobacteria.<jour_book>Genome Announc.
PG  - e00653-17
AB  - Most antibiotics are derived from the soil, but their catabolism there, which is  necessary to
      close the antibiotic carbon cycle, remains uncharacterized. We
      report the first draft genome sequences of soil Proteobacteria identified for
      subsisting solely on beta-lactams as their carbon sources. The genomes encode
      multiple beta-lactamases, although their antibiotic catabolic pathways remain
      enigmatic.
AU  - Crofts TS
AU  - Wang B
AU  - Spivak A
AU  - Gianoulis TA
AU  - Forsberg KJ
AU  - Gibson MK
AU  - Johnsky LA
AU  - Broomall SM
AU  - Rosenzweig CN
AU  - Skowronski EW
AU  - Gibbons HS
AU  - Sommer MOA
AU  - Dantas G
PT  - Journal Article
TA  - 
JT  - 
SO  -  2017 5: e00653-17.

PMID- 29122877
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Three Terrestrial Isoprene-Degrading Rhodococcus Strains.
PG  - e01256-17
AB  - Isoprene is produced in abundance by plants and constitutes a carbon source for microbes. The
      genomes of three isoprene degraders isolated from tree leaves or
      soil from the campus of the University of East Anglia were sequenced. These
      high-GC-content isolates are actinobacteria belonging to the genus Rhodococcus.
AU  - Crombie AT
AU  - Emery H
AU  - McGenity TJ
AU  - Murrell JC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01256-17.

PMID- 24265489
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of the Sesbania Symbiont and Rice Growth-Promoting Endophyte Rhizobium sp. Strain IRBG74.
PG  - e00934-13
AB  - Rhizobium sp. strain IRBG74 is the first known nitrogen-fixing symbiont in the
      Agrobacterium/Rhizobium clade that nodulates the aquatic legume Sesbania sp. and
      is also a growth-promoting endophyte of wetland rice. Here, we present the
      sequence of the IRBG74 genome, which is composed of a circular chromosome, a
      linear chromosome, and a symbiotic plasmid, pIRBG74a.
AU  - Crook MB
AU  - Mitra S
AU  - Ane JM
AU  - Sadowsky MJ
AU  - Gyaneshwar P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00934-13.

PMID- 29700161
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Burkholderia cepacia ATCC 17759, a Polyhydroxybutyrate-Co-Valerate Copolymer-Producing Bacterium.
PG  - e00348-18
AB  - Burkholderia cepacia ATCC 17759, isolated from forest soils in Trinidad, accumulates large
      amounts of polyhydroxyalkanoate copolymers when grown on
      xylose, mannose, arabinose, other carbohydrates, and organic acid cosubstrates.
      This 8.72-Mb draft genome sequence of B. cepacia ATCC 17759 will provide better
      insight into this organism's utility in lignocellulose bioconversion.
AU  - Crooks C
AU  - Palmer JM
AU  - Lindner DL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00348-18.

PMID- 6143811
VI  - 36
DP  - 1984
TI  - Inhibition of bacterial DNA cytosine-5-methyltransferase by S-adenosyl-L-homocysteine and some related compounds.
PG  - 85-89
AB  - S-Adenosyl-L-homocysteine and five related compounds have been evaluated as inhibitors of a
      DNA cytosine-5-methyltransferase. DNA methylation was assayed in cell extracts from E. coli
      strain J6-2 dcm+, proficient in DNA cytosine-5-methyltransferase activity, containing
      substrate DNA isolated from E. coli strain J6-2 dcm-, a strain deficient in DNA
      cytosine-5-methyltransferase. S-Adenosyl-L-homocysteine and its 7-deaza analogue,
      S-tubercidinylhomocysteine, were competitive inhibitors of DNA cytosine-5-methyltransferase
      with Ki's of 14.2 and 17.6 microM, respectively, in the above enzyme assay.
AU  - Crooks PA
AU  - Tribe MJ
AU  - Pinney RJ
PT  - Journal Article
TA  - J. Pharm. Pharmacol.
JT  - J. Pharm. Pharmacol.
SO  - J. Pharm. Pharmacol. 1984 36: 85-89.

PMID- 29535201
VI  - 9
DP  - 2018
TI  - Insights into the Evolution of Host Association through the Isolation and Characterization of a Novel Human Periodontal Pathobiont, Desulfobulbus oralis.
PG  - e02061-17
AB  - The human oral microbiota encompasses representatives of many bacterial lineages  that have
      not yet been cultured. Here we describe the isolation and
      characterization of previously uncultured Desulfobulbus oralis, the first
      human-associated representative of its genus. As mammalian-associated microbes
      rarely have free-living close relatives, D. oralis provides opportunities to
      study how bacteria adapt and evolve within a host. This sulfate-reducing
      deltaproteobacterium has adapted to the human oral subgingival niche by
      curtailing its physiological repertoire, losing some biosynthetic abilities and
      metabolic independence, and by dramatically reducing environmental sensing and
      signaling capabilities. The genes that enable free-living Desulfobulbus to
      synthesize the potent neurotoxin methylmercury were also lost by D. oralis, a
      notably positive outcome of host association. However, horizontal gene
      acquisitions from other members of the microbiota provided novel mechanisms of
      interaction with the human host, including toxins like leukotoxin and hemolysins.
      Proteomic and transcriptomic analysis revealed that most of those factors are
      actively expressed, including in the subgingival environment, and some are
      secreted. Similar to other known oral pathobionts, D. oralis can trigger a
      proinflammatory response in oral epithelial cells, suggesting a direct role in
      the development of periodontal disease.IMPORTANCE Animal-associated microbiota
      likely assembled as a result of numerous independent colonization events by
      free-living microbes followed by coevolution with their host and other microbes.
      Through specific adaptation to various body sites and physiological niches,
      microbes have a wide range of contributions, from beneficial to disease causing.
      Desulfobulbus oralis provides insights into genomic and physiological
      transformations associated with transition from an open environment to a
      host-dependent lifestyle and the emergence of pathogenicity. Through a
      multifaceted mechanism triggering a proinflammatory response, D. oralis is a
      novel periodontal pathobiont. Even though culture-independent approaches can
      provide insights into the potential role of the human microbiome 'dark matter,'
      cultivation and experimental characterization remain important to studying the
      roles of individual organisms in health and disease.
AU  - Cross KL
AU  - Chirania P
AU  - Xiong W
AU  - Beall CJ
AU  - Elkins JG
AU  - Giannone RJ
AU  - Griffen AL
AU  - Guss AM
AU  - Hettich RL
AU  - Joshi SS
AU  - Mokrzan EM
AU  - Martin RK
AU  - Zhulin IB
AU  - Leys EJ
AU  - Podar M
PT  - Journal Article
TA  - MBio
JT  - MBio
SO  - MBio 2018 9: e02061-17.

PMID- 9207790
VI  - 16
DP  - 1997
TI  - A component of the transcriptional repressor MeCP1 shares a motif with DNA methyltransferase and HRX proteins.
PG  - 256-259
AB  - Methylation of cytosines within the sequence CpG is essential for mouse development and has
      been linked to transcriptional suppression in vertebrate systems.  Methyl-CpG binding proteins
      (MeCPs) 1 and 2 bind preferentially to methylated DNA and can inhibit transcription.  The gene
      for MeCP2 has been cloned and a methyl-CpG binding domain within it has been defined.  A
      search of DNA sequence databases with the MBD sequence identified a human cDNA with potential
      to encode an MBD-like region.  Sequencing of the complete cDNA revealed that the open reading
      frame also encodes two cysteine-rich domains that are found in animal DNA methyltransferases
      and in the mammalian HRX protein (also known as MLL and ALL-1).  HRX is related to Drosophila
      trithorax.  The protein, known as Protein Containing MBD (PCM1), was expressed in bacteria and
      shown to bind specifically to methylated DNA.  PCM1 also repressed transcription in vitro in a
      methylation-dependent manner.  A polyclonal antibody raised against the protein was able to
      'supershift' the native MeCP1 complex from HeLa cells, indicating that PCM1 is a component
      of mammalian MeCP1.
AU  - Cross SH
AU  - Meehan RR
AU  - Nan X
AU  - Bird A
PT  - Journal Article
TA  - Nat. Genet.
JT  - Nat. Genet.
SO  - Nat. Genet. 1997 16: 256-259.

PMID- 20802035
VI  - 192
DP  - 2010
TI  - A Commensal Gone Bad: Complete Genome Sequence of the Prototypical Enterotoxigenic Escherichia coli Strain H10407.
PG  - 5822-5831
AB  - In most cases, Escherichia coli exists as a harmless commensal organism, but it may on
      occasion cause intestinal and/or extraintestinal disease.
      Enterotoxigenic E. coli (ETEC) is the predominant cause of E.
      coli-mediated diarrhea in the developing world and is responsible for a
      significant portion of pediatric deaths. In this study, we determined the
      complete genomic sequence of E. coli H10407, a prototypical strain of
      enterotoxigenic E. coli, which reproducibly elicits diarrhea in human
      volunteer studies. We performed genomic and phylogenetic comparisons with
      other E. coli strains, revealing that the chromosome is closely related to
      that of the nonpathogenic commensal strain E. coli HS and to those of the
      laboratory strains E. coli K-12 and C. Furthermore, these analyses
      demonstrated that there were no chromosomally encoded factors unique to
      any sequenced ETEC strains. Comparison of the E. coli H10407 plasmids with
      those from several ETEC strains revealed that the plasmids had a mosaic
      structure but that several loci were conserved among ETEC strains. This
      study provides a genetic context for the vast amount of experimental and
      epidemiological data that have been published.
AU  - Crossman LC et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 5822-5831.

PMID- 18419807
VI  - 9
DP  - 2008
TI  - The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug  resistance determinants.
PG  - R74
AB  - ABSTRACT: BACKGROUND: Stenotrophomonas maltophilia is a nosocomial opportunistic pathogen of
      the Xanthomonadaceae. The organism has been
      isolated from both clinical and soil environments in addition to the
      sputum of cystic fibrosis patients and the immunocompromised. Whilst
      relatively distant phylogenetically, the closest sequenced relatives of S.
      maltophilia are the plant pathogenic xanthomonads. RESULTS: The genome of
      the bacteremia-associated isolate S. maltophilia K279a is 4,851,126 bp and
      of high G+C content. The sequence reveals an organism with a remarkable
      capacity for drug and heavy metal resistance. In addition to a number of
      genes conferring resistance to antimicrobial drugs of different classes
      via alternative mechanisms, nine resistance-nodulation-division (RND)-type
      putative antimicrobial efflux systems are present. Functional genomic
      analysis confirms a role in drug resistance for several of the novel RND
      efflux pumps. S. maltophilia possesses potentially mobile regions of DNA
      and encodes a number of pili and fimbriae likely to be involved in
      adhesion and biofilm formation that may also contribute to increased
      antimicrobial drug resistance. CONCLUSION: The panoply of antimicrobial
      drug resistance genes and mobile genetic elements found suggests that the
      organism can act as a reservoir of antimicrobial drug resistance
      determinants in a clinical environment, which is an issue of considerable
      concern.
AU  - Crossman LC et al
PT  - Journal Article
TA  - Genome Biol.
JT  - Genome Biol.
SO  - Genome Biol. 2008 9: R74.

PMID- 24130509
VI  - 9
DP  - 2013
TI  - Dominant Role of Nucleotide Substitution in the Diversification of Serotype 3 Pneumococci over Decades and during a Single Infection.
PG  - e1003868-100386
AB  - Streptococcus pneumoniae of serotype 3 possess a mucoid capsule and cause disease associated
      with high mortality rates
      relative to other pneumococci. Phylogenetic analysis of a complete reference genome and 81
      draft sequences from clonal
      complex 180, the predominant serotype 3 clone in much of the world, found most sampled
      isolates belonged to a clade
      affected by few diversifying recombinations. However, other isolates indicate significant
      genetic variation has accumulated
      over the clonal complex's entire history. Two closely related genomes, one from the blood and
      another from the
      cerebrospinal fluid, were obtained from a patient with meningitis. The pair differed in their
      behaviour in a mouse model of
      disease and in their susceptibility to antimicrobials, with at least some of these changes
      attributable to a mutation that upregulated
      the patAB efflux pump. This indicates clinically important phenotypic variation can accumulate
      rapidly through
      small alterations to the genotype.
AU  - Croucher NJ et al
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2013 9: e1003868-100386.

PMID- 25407023
VI  - 5
DP  - 2014
TI  - Diversification of bacterial genome content through distinct mechanisms over different timescales.
PG  - 5471
AB  - Bacterial populations often consist of multiple co-circulating lineages. Determining how such
      population structures arise requires understanding what drives bacterial diversification.
      Using 616 systematically sampled genomes, we show that Streptococcus pneumoniae lineages are
      typically characterized by combinations of infrequently transferred stable genomic islands:
      those moving primarily through transformation, along with integrative and conjugative elements
      and phage-related chromosomal islands. The only lineage containing extensive unique sequence
      corresponds to a set of atypical unencapsulated isolates that may represent a distinct
      species. However, prophage content is highly variable even within lineages, suggesting
      frequent horizontal transmission that would necessitate rapidly diversifying antiphage
      mechanisms to prevent these viruses sweeping through populations. Correspondingly, two loci
      encoding Type I restriction-modification systems able to change their specificity over short
      timescales through intragenomic recombination are ubiquitous across the collection. Hence
      short-term pneumococcal variation is characterized by movement of phage and intragenomic
      rearrangements, with the slower transfer of stable loci distinguishing lineages.
AU  - Croucher NJ
AU  - Coupland PG
AU  - Stevenson AE
AU  - Callendrello A
AU  - Bentley SD
AU  - Hanage WP
PT  - Journal Article
TA  - Nat. Commun.
JT  - Nat. Commun.
SO  - Nat. Commun. 2014 5: 5471.

PMID- 19114491
VI  - 191
DP  - 2009
TI  - Role of conjugative elements in the evolution of the multidrug-resistant pandemic clone Streptococcus pneumoniaeSpain23F ST81.
PG  - 1480-1489
AB  - Streptococcus pneumoniae is a human commensal and pathogen able to cause a variety of diseases
      that annually result in over a million deaths worldwide. The
      S. pneumoniae(Spain23F) sequence type 81 lineage was among the first recognized
      pandemic clones and was responsible for almost 40% of penicillin-resistant
      pneumococcal infections in the United States in the late 1990s. Analysis of the
      chromosome sequence of a representative strain, and comparison with other
      available genomes, indicates roles for integrative and conjugative elements in
      the evolution of pneumococci and, more particularly, the emergence of the
      multidrug-resistant Spain 23F ST81 lineage. A number of recently acquired loci
      within the chromosome appear to encode proteins involved in the production of, or
      immunity to, antimicrobial compounds, which may contribute to the proficiency of
      this strain at nasopharyngeal colonization. However, further sequencing of other
      pandemic clones will be required to establish whether there are any general
      attributes shared by these strains that are responsible for their international
      success.
AU  - Croucher NJ
AU  - Walker D
AU  - Romero P
AU  - Lennard N
AU  - Paterson GK
AU  - Bason NC
AU  - Mitchell AM
AU  - Quail MA
AU  - Andrew PW
AU  - Parkhill J
AU  - Bentley SD
AU  - Mitchell TJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2009 191: 1480-1489.

PMID- 22727669
VI  - 22
DP  - 2012
TI  - Cleavage and protection of locked nucleic acid-modified DNA by restriction endonucleases.
PG  - 4836-4838
AB  - Locked nucleic acid (LNA) is one of the most prominent nucleic acid analogues reported so far.
      We herein for the first time report cleavage
      by restriction endonuclease of LNA-modified DNA oligonucleotides. The
      experiments revealed that RsaI is an efficient enzyme capable of
      recognizing and cleaving LNA-modified DNA oligonucleotides.
      Furthermore, introduction of LNA nucleotides protects against cleavage
      by the restriction endonucleases PvuII, PstI, SacI, KpnI and EcoRI.
AU  - Crouzier L
AU  - Dubois C
AU  - Wengel J
AU  - Veedu RN
PT  - Journal Article
TA  - Bioorg. Med. Chem. Lett.
JT  - Bioorg. Med. Chem. Lett.
SO  - Bioorg. Med. Chem. Lett. 2012 22: 4836-4838.

PMID- 27469945
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequence of Enteractinococcus helveticum sp. nov. Strain UASWS1574 Isolated from Industrial Used Waters.
PG  - e00756-16
AB  - We report here the whole-genome shotgun sequences of the strain UASWS1574 of the  undescribed
      Enteractinococcus helveticum sp. nov., isolated from used water. This
      is the first genome registered for the whole genus.
AU  - Crovadore J
AU  - Calmin G
AU  - Chablais R
AU  - Cochard B
AU  - Lefort F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00756-16.

PMID- 27795260
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequence of Pseudomonas graminis Strain UASWS1507, a Potential Biological Control Agent and Biofertilizer Isolated in Switzerland.
PG  - e01096-16
AB  - We report here the whole-genome shotgun sequence of the strain UASWS1507 of the species
      Pseudomonas graminis, isolated in Switzerland from an apple tree. This is
      the first genome registered for this species, which is considered as a potential
      and valuable resource of biological control agents and biofertilizers for
      agriculture.
AU  - Crovadore J
AU  - Calmin G
AU  - Chablais R
AU  - Cochard B
AU  - Schulz T
AU  - Lefort F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01096-16.

PMID- 27795259
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequence of Bradyrhizobium elkanii Strain UASWS1016, a Potential Symbiotic Biofertilizer for Agriculture.
PG  - e01095-16
AB  - Bradyrhizobium elkanii UASWS1016 has been isolated from a wet oxidation sewage plant in Italy.
      Fully equipped for ammonia assimilation, heavy metal resistances,
      and aromatic compounds degradation, it carries a large type IV secretion system,
      specific of plant-associated microbes. Deprived of toxins, it could be considered
      for agricultural and environmental uses.
AU  - Crovadore J
AU  - Calmin G
AU  - Chablais R
AU  - Cochard B
AU  - Schulz T
AU  - Lefort F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01095-16.

PMID- 26450728
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequence of Pseudomonas putida Strain UASWS0946, a Highly Ammonia-Tolerant Nitrifying Bacterium Isolated from Sewage Sludge Aerobic Granules.
PG  - e01153-15
AB  - We report here the genome of Pseudomonas putida strain UASWS0946, a highly ammonia-tolerant
      nitrifying strain isolated from sewage sludge aerobic granules,  which displays adequate
      genetic equipment for soil depollution, sludge treatment, and biological fertilization in
      agriculture.
AU  - Crovadore J
AU  - Calmin G
AU  - Cochard B
AU  - Chablais R
AU  - Grizard D
AU  - Berthon JY
AU  - Lefort F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01153-15.

PMID- 26966217
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequence of Bradyrhizobium elkanii Strain UASWS1015, a Highly Ammonia-Tolerant Nitrifying Bacterium.
PG  - e00111-16
AB  - Bradyrhizobium elkanii UASWS1015 was isolated from a sewage plant in Switzerland. Its genome
      indicates that it is fully equipped for ammonia assimilation and
      aromatic compound degradation, and it displays a large type IV secretion system,
      which characterizes plant-associated microbes. Totally deprived of toxins, it
      could be considered for agricultural and environmental uses.
AU  - Crovadore J
AU  - Calmin G
AU  - Cochard B
AU  - Chablais R
AU  - Lefort F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00111-16.

PMID- 26112789
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequences of 15 Strains of Staphylococcus aureus subsp. aureus Isolated from Foodstuff and Human Clinical Samples.
PG  - e00684-15
AB  - The whole-genome sequences of 15 strains of Staphylococcus aureus (10 strains isolated from
      foodstuff samples in Switzerland and five from human clinical
      samples) were obtained by Illumina sequencing. Most strains fit within the known
      diversity for the species, but one (SA-120) possessed a higher G+C content and a
      higher number of genes than usual.
AU  - Crovadore J
AU  - Calmin G
AU  - Tonacini J
AU  - Chablais R
AU  - Baumgartner A
AU  - Schnyder B
AU  - Hodille E
AU  - Lefort F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00684-15.

PMID- 27284145
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequences of Seven Strains of Bacillus cereus Isolated from Foodstuff or Poisoning Incidents.
PG  - e00435-16
AB  - We present here the whole shotgun genome sequences of seven strains of Bacillus cereus
      isolated from foodstuff samples or food poisoning incidents.
AU  - Crovadore J
AU  - Calmin G
AU  - Tonacini J
AU  - Chablais R
AU  - Schnyder B
AU  - Messelhausser U
AU  - Lefort F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00435-16.

PMID- 27738050
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequence of Mesorhizobium hungaricum sp. nov. Strain UASWS1009, a Potential Resource for Agricultural and Environmental Uses.
PG  - e01158-16
AB  - We report here the whole-genome shotgun sequences of the strain UASWS1009 of the  species
      Mesorhizobium hungaricum sp. nov., which are different from any other
      known Mesorhizobium species. This is the first genome registered for this new
      species, which could be considered as a potential resource for agriculture and
      environmental uses.
AU  - Crovadore J
AU  - Cochard B
AU  - Calmin G
AU  - Chablais R
AU  - Schulz T
AU  - Lefort F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01158-16.

PMID- 27738044
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequence of Pseudomonas xanthomarina Strain UASWS0955, a Potential Biological Agent for Agricultural and Environmental Uses.
PG  - e01136-16
AB  - We report here the whole-genome shotgun sequence of the strain UASWS0955 of the species
      Pseudomonas xanthomarina, isolated from sewage sludge. This genome was
      obtained with an Illumina MiniSeq and is the second genome registered for this
      species, which is considered as a promising resource for agriculture and
      bioremediation of contaminated soils.
AU  - Crovadore J
AU  - Cochard B
AU  - Calmin G
AU  - Chablais R
AU  - Schulz T
AU  - Lefort F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01136-16.

PMID- 28473374
VI  - 5
DP  - 2017
TI  - Metagenome-Assembled Genome Sequence of Rhodopseudomonas palustris Strain ELI 1980, Commercialized as a Biostimulant.
PG  - e00221-17
AB  - We report here the draft genome sequence of strain ELI 1980 of Rhodopseudomonas palustris,
      commercialized as a biostimulant for agriculture. The genome was
      reconstructed from the metagenome of a commercial product containing this strain
      as its major component.
AU  - Crovadore J
AU  - Xu S
AU  - Chablais R
AU  - Cochard B
AU  - Lukito D
AU  - Calmin G
AU  - Lefort F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00221-17.

PMID- 28360175
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Pelagic Photoferrotroph Chlorobium phaeoferrooxidans.
PG  - e01584-16
AB  - Here, we report the draft genome sequence of Chlorobium phaeoferrooxidans, a photoferrotrophic
      member of the genus Chlorobium in the phylum Chlorobi This
      genome sequence provides insight into the metabolic capacity that underpins
      photoferrotrophy within low-light-adapted pelagic Chlorobi.
AU  - Crowe SA
AU  - Hahn AS
AU  - Morgan-Lang C
AU  - Thompson KJ
AU  - Simister RL
AU  - Lliros M
AU  - Hirst M
AU  - Hallam SJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01584-16.

PMID- 23908281
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Lactobacillus plantarum Strain 16, a Broad-Spectrum Antifungal-Producing Lactic Acid Bacterium.
PG  - e00533-13
AB  - Lactobacillus plantarum strain 16 restricts the growth of various food spoilage fungi and has
      the potential to be used as a biopreservative to improve the shelf
      life of foods. The complete genome sequence contains 3,044,678 bp with a G+C
      content of 44.74% and harbors the largest plasmid complement reported for this
      species to date.
AU  - Crowley S
AU  - Bottacini F
AU  - Mahony J
AU  - van Sinderen D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00533-13.

PMID- 6086403
VI  - 173
DP  - 1984
TI  - An Sau3AI restriction endonuclease isoschizomer from Bacillus cereus.
PG  - 99-102
AB  - The isolation and characterization of a restriction endonuclease from Bacillus
      cereus 10C 243 are described.  The enzyme recognizes the palindromic sequence
      5'-G(met-A,A)TC-3' as determined by PEI chromatography of pancreatic DNase,
      snake venom phosphodiesterase digestion products of labelled fragments,
      analysis of restriction digests from normal and N6-methyladenine-free DNA and
      direct sequence analysis of cloned fragments.  The staggered cleavage products
      with 5'-terminal pGATC extensions are efficiently labelled with polynucleotide
      kinase and are easily cloned into BamHI sites.  The enzyme, denoted Bce243, is
      thus an isoschizomer of SauAI.  Its use and potential advantages in
      substituting Sau3AI are discussed.
AU  - Cruz AK
AU  - Kidane G
AU  - Pires MQ
AU  - Rabinovitch L
AU  - Guaycurus TV
AU  - Morel CM
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1984 173: 99-102.

PMID- 2638923
VI  - 22
DP  - 1989
TI  - Restriction endonucleases from microorganisms isolated in Brazil: an isoschizomer of HaeIII from a thermophilic Bacillus sp.
PG  - 1321-1328
AB  - The isolation and characterization of a restriction endonuclease from a
      thermophilic strain of Bacillus is described.  The enzyme recognizes the
      palindromic sequence 5' GGCC 3' as determined by PEI-cellulose chromatography
      of pancreatic DNAse and snake venom phosphodiesterase digestion products of
      labelled DNA fragments, analysis of restriction digests and direct sequence
      analysis.  The enzyme, denominated BspBR, is an isoschizomer of HaeIII and
      BspRI.
AU  - Cruz AK
AU  - Pires MQ
AU  - Lima VG
AU  - Morel CM
PT  - Journal Article
TA  - Braz. J. Med. Biol. Res.
JT  - Braz. J. Med. Biol. Res.
SO  - Braz. J. Med. Biol. Res. 1989 22: 1321-1328.

PMID- 23709624
VI  - 5
DP  - 2013
TI  - The genome sequence of Streptomyces lividans 66 reveals a novel tRNA-dependent peptide biosynthetic system within a metal-related genomic island.
PG  - 1165-1175
AB  - The complete genome sequence of the original isolate of the model actinomycete
      Streptomyces lividans 66, also referred to as 1326, was deciphered after a
      combination of next-generation sequencing platforms and a hybrid assembly
      pipeline. Comparative analysis of the genomes of S. lividans 66 and closely
      related strains, including S. coelicolor M145 and S. lividans TK24, was used to
      identify strain-specific genes. The genetic diversity identified included a large
      genomic island with a mosaic structure, present in S. lividans 66 but not in the
      strain TK24. Sequence analyses showed that this genomic island has an anomalous
      (G + C) content, suggesting recent acquisition and that it is rich in
      metal-related genes. Sequences previously linked to a mobile conjugative element,
      termed plasmid SLP3 and defined here as a 94 kb region, could also be identified
      within this locus. Transcriptional analysis of the response of S. lividans 66 to
      copper was used to corroborate a role of this large genomic island, including two
      SLP3-borne "cryptic" peptide biosynthetic gene clusters, in metal homeostasis.
      Notably, one of these predicted biosynthetic systems includes an unprecedented
      nonribosomal peptide synthetase--tRNA-dependent transferase biosynthetic hybrid
      organization. This observation implies the recruitment of members of the
      leucyl/phenylalanyl-tRNA-protein transferase family to catalyze peptide bond
      formation within the biosynthesis of natural products. Thus, the genome sequence
      of S. lividans 66 not only explains long-standing genetic and phenotypic
      differences but also opens the door for further in-depth comparative genomic
      analyses of model Streptomyces strains, as well as for the discovery of novel
      natural products following genome-mining approaches.
AU  - Cruz-Morales P
AU  - Vijgenboom E
AU  - Iruegas-Bocardo F
AU  - Girard G
AU  - Yanez-Guerra LA
AU  - Ramos-Aboites HE
AU  - Pernodet JL
AU  - Anne J
AU  - van Wezel GP
AU  - Barona-Gomez F
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2013 5: 1165-1175.

PMID- 22328759
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of an Efficient Antibiotic-Producing Industrial Strain of Saccharomonospora azurea, SZMC 14600.
PG  - 1263
AB  - Although certain rare actinomycetes have been recognized as prolific sources of bioactive
      natural products, their potential for producing biologically active
      metabolites still remains unexplored. With the aim of gaining global insights
      into the genetic background and the metabolic capability of Saccharomonospora
      azurea SZMC 14600, whole-genome sequencing was performed.
AU  - Csepregi K
AU  - Valasek A
AU  - Penzes A
AU  - Toth Z
AU  - Kiss EI
AU  - Kerepesi I
AU  - Horvath B
AU  - Nagy I
AU  - Fekete C
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1263.

PMID- 22461549
VI  - 194
DP  - 2012
TI  - De Novo Genome Project of Cupriavidus basilensis OR16.
PG  - 2109-2110
AB  - Here we report on the complete genome sequence of Cupriavidus basilensis OR16 NCAIM BO2487.
      The genome of strain OR16 contains 7,534 putative coding sequences,
      including a large set of xenobiotics-degrading genes and a unique glucose
      dehydrogenase gene that is absent from other Cupriavidus genomes.
AU  - Cserhati M
AU  - Kriszt B
AU  - Szoboszlay S
AU  - Toth A
AU  - Szabo I
AU  - Tancsics A
AU  - Nagy I
AU  - Horvath B
AU  - Nagy I
AU  - Kukolya J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2109-2110.

PMID- 2839272
VI  - 3
DP  - 1987
TI  - A computer algorithm to determine the recognition site of restriction enzymes.
PG  - 245-246
AB  - A new algorithm is proposed to determine the type-II restriction endonucleases'
      recognition site knowing the digested DNA sequence and fragment lengths in an
      actual case.  The algorithm is implemented for the Commodore 64 microcomputer.
AU  - Csirik J
AU  - Magyar J
AU  - Polner G
PT  - Journal Article
TA  - Comput. Appl. Biosci.
JT  - Comput. Appl. Biosci.
SO  - Comput. Appl. Biosci. 1987 3: 245-246.

PMID- 18043634
VI  - 1
DP  - 2007
TI  - Genomic plasticity in prokaryotes: the case of the square haloarchaeon.
PG  - 235-245
AB  - The variability in genome content among closely related strains of
      prokaryotes has been one of the most remarkable discoveries of genomics.
      One way to approach the description of this so-called pan-genome is to
      compare one reference strain genome with metagenomic sequences from the
      environment. We have applied this approach to one extreme aquatic habitat,
      saturated brines in a solar saltern. The genome of Haloquadratum walsbyi
      strain DSM 16790 was compared to an environmental metagenome obtained from
      the exact site of its isolation. This approach revealed that some regions
      of the strain genome were scarcely represented in the metagenome. Here we
      have analyzed these genomic islands (GI) in the genome of DSM 16790 and
      compared them with the complete sequence of some fosmids from the
      environmental library. Two of the islands, GI 2 and GI 4, overlapped with
      two large guanine and cytosine (GC)-rich regions that showed evidence of
      high variability through mobile elements. GI 3 seemed to be a phage or
      phage-remnant acquired by the reference genome, but not present in most
      environmental lineages. Most differential gene content was related to
      small molecule transport and detection, probably reflecting adaptation to
      different pools of organic nutrients. GI 1 did not possess traces of
      mobile elements and had normal GC content. This island contained the main
      cluster of cell envelope glycoproteins and the variability found was
      different from the other GIs. Rather than containing different genes it
      consisted of homologs with low similarity. This variation might reflect a
      phage evasion strategy.
AU  - Cuadros-Orellana S
AU  - Martin-Cuadrado AB
AU  - Legault B
AU  - D'Auria G
AU  - Zhaxybayeva O
AU  - Papke RT
AU  - Rodriguez-Valera F
PT  - Journal Article
TA  - ISME J.
JT  - ISME J.
SO  - ISME J. 2007 1: 235-245.

PMID- Not carried by PubMed...
VI  - 75
DP  - 1996
TI  - Overexpression of E. coli EcoRI modification system enzymes.
PG  - 8-10
AB  - Escherichia coli RI (EcoRI) DNA restriction and modification enzymes are reponsible for host
      specificity of E. coli.  The restriction endonuclease enzyme recognizes a hexanucleotide
      repeat (5'-GAATTC-3') and cleaves double-stranded DNA in a staggered fashion between the
      guanine and first adenine residues.  The methyltransferase enzyme, or methylase, adds a methyl
      group to the second adenine, nearest the axis of symmetry, leaving the site resistant to
      endonuclease cleavage.  The endonuclease and methylase are two independent proteins which are
      coded for by distinct genes, and will be referred to collectively as the EcoRI modification
      system.
AU  - Cuculich PS
PT  - Journal Article
TA  - The Nucleus
JT  - The Nucleus
SO  - The Nucleus 1996 75: 8-10.

PMID- 8975604
VI  - 62
DP  - 1996
TI  - Characterization of a restriction-modification system of the thermotolerant methylotroph Bacillus methanolicus.
PG  - 1107-1111
AB  - We report the isolation of a restriction endonuclease, BmeTI, an isoschizomer of BclI, that
      recognizes the DNA sequence 5' TGATCA 3'.  We also report that BmeTI sites are modified to
      TGm6ATCA.  These findings provide the basis for devising strategies to prevent BmeTI
      restriction of any DNA introduced into Bacillus methanolicus.
AU  - Cue D
AU  - Hong L
AU  - Hanson RS
AU  - Flickinger MC
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1996 62: 1107-1111.

PMID- Not carried by PubMed...
VI  - 95
DP  - 1995
TI  - Characterization of a Bacillus methanolicus restriction/modification system.
PG  - 525
AB  - A restriction endonuclease (BmeI) has been isolated from the thermotolerant, methylotrophic
      bacterium Bacillus methanolicus.  BmeI is an isoschizomer of BclI, both enzymes cutting within
      the sequence, TGATCA.  The same restriction patterns are evident when phage DNA or
      HindIII-digested phage DNA are incubated with either BmeI or BclI or when phage DNA is
      digested with both BmeI and BclI.  Destruction of the BclI restriction site present in the
      integrational plasmid, pDQ500, resulted in a plasmid pDQ503, that is resistant to cleavage by
      both BmeI and BclI.  The modification specificity of the cognate BmeI methyltransferase was
      determined by Southern blotting of B. methanolicus chromosomal DNA that had been digested with
      PstI and either BclI, DpnI, MboI or Sau3AI and using the cloned B. methanolicus, lysC gene as
      the probe.  The results indicated that the single BmeI restriction site within lysC is
      modified to: TGm6ATCA.  We have successfully transformed B. methanolicus with several plasmid
      and integrational vectors (including pDQ503).  Our results suggest that B. methanolicus
      possesses a single, dominant restriction system or, that if a second restriction system
      exists, that the second restriction endonuclease is an infrequent cutter.
AU  - Cue D
AU  - Lam H
AU  - Hanson RS
AU  - Flickinger M
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1995 95: 525.

PMID- 24435873
VI  - 2
DP  - 2014
TI  - Genome Sequence of Martelella sp. Strain AD-3, a Moderately Halophilic Polycyclic Aromatic Hydrocarbon-Degrading Bacterium.
PG  - e01189-13
AB  - Martelella sp. strain AD-3, enriched from a petroleum-contaminated site with high salinity,
      can efficiently degrade polycyclic aromatic hydrocarbons. Here, we
      report the 4.75-Mb genome sequence of strain AD-3 with its genetic feature of
      helping to remediate environmental organic pollutants.
AU  - Cui C
AU  - Li P
AU  - Liu G
AU  - Tang H
AU  - Lin K
AU  - Luo Q
AU  - Liu S
AU  - Xu P
AU  - Liu Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01189-13.

PMID- 22450138
VI  - 89
DP  - 2012
TI  - Targeted gene engineering in Clostridium cellulolyticum H10 without methylation.
PG  - 201-208
AB  - Genetic engineering of Clostridium cellulolyticum has been developed slowly compared with that
      of other clostridial species, and one of the
      major reasons might be the restriction and modification (RM) system
      which degrades foreign DNA. Here, a putative Mspl endonuclease gene,
      ccel2866, was inactivated by a ClosTron-based gene disruption method.
      The resulting C cellulolyticum mutant H10 Delta mspl lost the Mspl
      endonuclease activity and can accept unmethylated DNA efficiently.
      Following that, an oxygen-independent green fluorescence protein gene
      was introduced into H10 Delta mspl without methylation, generating a
      convenient reporter system to evaluate the expression of heterologous
      protein in C. cellulolyticum by green fluorescence. To further
      demonstrate the efficiency of the H10 Delta mspl, double mutants H10
      Delta mspl Delta ldh and H10 Delta mspl Delta ack were constructed by
      disrupting lactate dehydrogenase gene ccel2485 and acetate kinase gene
      ccel2136 in H10 Delta mspl, respectively, without DNA methylation, and
      the stability of the double mutation was confirmed after the 100th
      generation. The mutant H10 Delta mspl constructed here can be used as a
      platform for further targeted gene manipulation conveniently and
      efficiently. It will greatly facilitate the metabolic engineering of C.
      cellulolyticum aiming at faster cellulose degradation and higher
      biofuel production at the molecular level.
AU  - Cui G-Z
AU  - Hong W
AU  - Zhang J
AU  - Li W-L
AU  - Feng Y
AU  - Liu Y-J
AU  - Cui Q
PT  - Journal Article
TA  - J. Microbiol. Methods
JT  - J. Microbiol. Methods
SO  - J. Microbiol. Methods 2012 89: 201-208.

PMID- 17569624
VI  - 12
DP  - 2007
TI  - Mobile group II intron targeting: applications in prokaryotes and perspectives in eukaryotes.
PG  - 4972-4985
AB  - Mobile group II introns are ribozymes and use a novel mechanism--target DNA-primed reverse
      transcription--to proliferate in DNA. Group II introns are a unique mobile element for their
      high sequence-specific, yet readily flexible target site recognition. Both the intron RNA and
      the intron-encoded protein (IEP) are involved in target site recognition, and the specificity
      is determined primarily by base pairing between the intron RNA and DNA target. Therefore, the
      intron RNA can be modified according to the desired target sequence for specific gene
      disruption. Group II intron knockout technology is mature in bacteria and is currently being
      developed in eukaryotes. This technology has great potential to revolutionize fields such as
      functional genomics, gene therapy, and cell line engineering.
AU  - Cui XX
AU  - Davis G
PT  - Journal Article
TA  - Front. Biosci.
JT  - Front. Biosci.
SO  - Front. Biosci. 2007 12: 4972-4985.

PMID- 27315164
VI  - 20
DP  - 2016
TI  - Expression and functional analysis of two NhaD type antiporters from the halotolerant and alkaliphilic Halomonas sp. Y2.
PG  - 631-639
AB  - Na(+)/H(+) antiporters play important roles in ion and pH homeostasis. In this
      study, two NhaD homologues that effectively catalyze Na(+)/H(+) antiporter were
      identified from Halomonas sp. Y2, a halotolerant and alkaliphilic strain isolated
      from sodium enriched black liquor. They exhibited high sequence identity of 72 %
      and similar binding affinities for Na(+) and Li(+) translocation, while having
      different pH profiles. Ha-NhaD1 was active at pH 6.0 and most active at pH
      8.0-8.5, whereas Ha-NhaD2 lacked activity at pH 6.0 but exhibited maximum
      activity at pH 9.5 or higher. Based on multiple alignments, 11 partially
      conserved residues were selected and corresponding mutants were generated for
      Ha-NhaD1. As expected, replacement of most of the hydrophobic residues abolished
      the cation exchange activities. Three serine residues at positions 200, 282 and
      353 in Ha-NhaD1 were replaceable by alanines with partial retention of activity.
      The S353A mutant exhibited significantly reduced binding affinity for Na(+) and
      Li(+), while S282 mutant exhibited an alkaline shift of about 1.5 pH units, as
      compared to the wild type Ha-NhaD1. Serine at position 282 was predicted to be
      located in transmembrane segment VIII and was found to be important in regulating
      pH sensitivity in concert with flanking residues.
AU  - Cui Y
AU  - Cheng B
AU  - Meng Y
AU  - Li C
AU  - Yin H
AU  - Xu P
AU  - Yang C
PT  - Journal Article
TA  - Extremophiles
JT  - Extremophiles
SO  - Extremophiles 2016 20: 631-639.

PMID- 23723401
VI  - 1
DP  - 2013
TI  - Genome Sequence of the Polycyclic Aromatic Hydrocarbon-Degrading Bacterium Strain Marinobacter nanhaiticus D15-8WT.
PG  - e00301-13
AB  - Marinobacter nanhaiticus strain D15-8W(T) was isolated from a phenanthrene-degrading
      consortium, enriched from sediment of the South China Sea.
      Here, we present the draft genome of strain D15-8W(T), which contains 5,358,309
      bp with a G+C content of 58.53% and contains 4,829 protein-coding genes and 47
      tRNA genes.
AU  - Cui Z
AU  - Gao W
AU  - Li Q
AU  - Xu G
AU  - Zheng L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00301-13.

PMID- 23908283
VI  - 1
DP  - 2013
TI  - Genome Sequence of the Pyrene- and Fluoranthene-Degrading Bacterium Cycloclasticus sp. Strain PY97M.
PG  - e00536-13
AB  - Cycloclasticus sp. strain PY97M was isolated from a phenanthrene-degrading consortium,
      enriched from Yellow Sea sediment of China. Here, we present the
      draft genome sequence of strain PY97M, which contains 2,359,509 bp with a G+C
      content of 41.92% and contains 2, 264 protein-coding genes and 40 tRNAs.
AU  - Cui Z
AU  - Xu G
AU  - Li Q
AU  - Gao W
AU  - Zheng L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00536-13.

PMID- 21183674
VI  - 193
DP  - 2010
TI  - Draft genome sequence of Turicibacter sanguinis PC909 isolated from human faeces.
PG  - 1288-1289
AB  - While the microbiota resident in the human gut is now known to provide a range of functions
      relevant to host health many of the microbial members of the community have not yet been
      cultured or are represented by a limited number of isolates. We describe here the draft genome
      sequence of Turicibacter sanguinis PC909, isolated from a pooled healthy human faecal sample
      as part of the Australian Human Gut Microbiome Project.
AU  - Cuiv PO
AU  - Klaassens ES
AU  - Durkin AS
AU  - Harkins DM
AU  - Foster L
AU  - McCorrison J
AU  - Torralba M
AU  - Nelson KE
AU  - Morrison M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 193: 1288-1289.

PMID- 
VI  - 104
DP  - 2004
TI  - Genetic and biochemical studies of the transformation barriers present in Shewanella oneidensis MR-1.
PG  - 320
AB  - Shewanella oneidensis is able to enzymatically reduce and precipitate a variety of heavy
      metals and is widely investigated for bioremediation of metals and radionuclides.  The
      availability of the complete genome sequence and its ability to grow both aerobically and
      anaerobically makes S. oneidensis MR-1 an extremely useful model system.  However, genetic
      studies of this organism have been slowed by the lack of an efficient transformation system.
      We are utilizing several approaches to investigate the genetic factors influencing
      transformation and to improve the transformation efficiency.  Utilizing a pUC-type plasmid
      isolated from MR-1, we were able to test various competent cell preparation methods,
      electrical parameters, and selection strategies to develop a method that improves
      electroporation efficiencies from less than 105 cfu/ug to almost 108/ug.  However, even these
      improved conditions yielded less than 103/ug when transforming MR-1 with the same plasmid
      isolated from E. coli.  This 100,000-fold reduction in efficiency with unmodified plasmid
      indicates a very active restriction-modification system in MR-1.  Analysis of the genome
      sequence indicates the presence of a dam methylase locus, three type II, and two Type I
      methylases on the chromosome and a Type II methylase on a 160 kb megaplasmid.  The use of a
      Type I restriction inhibitor did not improve transformation, indicating an active Type II
      system.  The Type II system borne on the megaplasmid has high homology to the ClaI restriction
      system, but no effect was observed with either in vivo modification using an E. coli strain
      expressing ClaI methylase (pHS17; NEB) or with in vitro modification of the test plasmid with
      M.TaqI (blocks ClaI cleavage).  One of the chromosomal Type II methylases is located within a
      lambda-like prophage, but is lacking the corresponding restriction subunit.  We are currently
      constructing MR-1 knockout mutants of the restriction subunits from the remaining two loci, as
      well as attempting to modify plasmid DNA in E. coli by co-expression of the corresponding
      Shewanella methylases, in hopes of overcoming the transformation barrier present in S.
      oneidensis.
AU  - Culley DE
AU  - Shi L
AU  - Reed S
AU  - Romme M
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 2004 104: 320.

PMID- 20093380
VI  - 59
DP  - 2010
TI  - A novel IS26 structure surrounds blaCTX-M genes in different plasmids from German clinical Escherichia coli isolates.
PG  - 580-587
AB  - This report focuses on the molecular characterization of 22
      extended-spectrum beta-lactamase-producing Escherichia coli isolates
      collected in a German university hospital during a period of 9 months in
      2006. Relationship analysis of clinical isolates was done via PFGE,
      multilocus sequence typing, plasmid profiling and additionally PCR for
      bla(ESBL) detection and determination of phylogroups. After conjugal
      transfer, plasmid isolation and subsequent PCR for bla(ESBL) detection and
      determination of incompatibility groups were performed. Using one-primer
      walking, up to 3600 bp upstream and downstream of different bla(CTX-M)
      genes could be sequenced. beta-Lactamases found were TEM-1 (n=14), SHV-5
      (n=1) and a wide variety of CTX-M types (n=21), i.e. CTX-M-15 (n=12),
      CTX-M-1 (n=4), CTX-M-14 (n=2), CTX-M-9 (n=1), CTX-M-3 (n=1) and one new
      type, CTX-M-65 (n=1). In 18 isolates, bla(ESBL) genes were located on
      conjugative plasmids of sizes between 40 and 180 kbp belonging to
      incompatibility groups FII (n=9), N (n=5) and I1 (n=4). bla(CTX-M) was
      found to be associated with the common elements ISEcp1, IS26 and IS903-D,
      but with unusual spacer sequences for ISEcp1 in two isolates. These
      insertion sequences, connected to bla(CTX-M) as well as other genes, were
      located between two IS26 elements in a configuration that has not yet been
      described. The results reveal the emergence of bla(ESBL), predominantly
      bla(CTX-M), located on different plasmids harboured by genotypically
      different E. coli strains. The identical gene arrangement in the
      bla(CTX-M) neighbourhood in plasmids of different incompatibility groups
      indicates a main role of IS26 in distribution of mobile resistance
      elements between different plasmids.
AU  - Cullik A
AU  - Pfeifer Y
AU  - Prager R
AU  - von Baum H
AU  - Witte W
PT  - Journal Article
TA  - J. Med. Microbiol.
JT  - J. Med. Microbiol.
SO  - J. Med. Microbiol. 2010 59: 580-587.

PMID- 2357736
VI  - 17
DP  - 1990
TI  - The complete DNA sequence of the mitochondrial genome of Podospora anserina.
PG  - 375-402
AB  - The complete 94,192 bp sequence of the mitochondrial genome from race s of
      Podospora anserina is presented (1 kb = 10(3) base pairs). Three regions
      unique to race A are also presented bringing the size of this genome to
      100,314 bp. Race s contains 31 group I introns (33 in race A) and 2 group
      II introns (3 in race A). Analysis shows that the group I introns can be
      categorized according to families both with regard to secondary structure
      and their open reading frames. All identified genes are transcribed from
      the same strand. Except for the lack of ATPase 9, the Podospora genome
      contains the same genes as its fungal counterparts, N. crassa and A.
      nidulans. About 20% of the genome has not yet been identified. DNA
      sequence studies of several excision-amplification plasmids demonstrate a
      common feature to be the presence of short repeated sequences at both
      termini with a prevalence of GGCGCAAGCTC.
AU  - Cummings DJ
AU  - McNally KL
AU  - Domenico JM
AU  - Matsuura ET
PT  - Journal Article
TA  - Curr. Genet.
JT  - Curr. Genet.
SO  - Curr. Genet. 1990 17: 375-402.

PMID- Not included in PubMed...
VI  - 21
DP  - 1992
TI  - Cloning the pea DNA methylase cDNA.
PG  - 7s
AB  - Both eukaryotic and prokaryotic cytosine methylases catalyse the transfer of a methyl group
      from S-adenosyl methionine to the 5-position of the cytosine ring in DNA. The cDNA coding for
      mouse and human methylase have been previously cloned. Comparison of the encoded proteins with
      prokaryotic type II cytosine methylase sequences shows that the carboxy terminal one-third of
      the eukaryotic enzymes shares significant homology with the prokaryotic enzymes. The
      arrangement of several sequence motifs has been preserved in the eukaryotic proteins. This
      includes a short amino acid sequence containing a pro-cys dipeptide which has been proved to
      the the catalytic center of at least one bacterial type II methylase.
AU  - Cummings M
AU  - Adams RLP
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 1992 21: 7s.

PMID- 23990578
VI  - 1
DP  - 2013
TI  - High-Quality Draft Genome Sequences of Two Xanthomonas citri pv. malvacearum Strains.
PG  - e00674-13
AB  - We report high-quality draft genome sequences of two strains (race 18 and 20) of  Xanthomonas
      citri pv. malvacearum, the causal agent of bacterial blight of
      cotton. Comparative genomics will help to decipher mechanisms provoking disease
      and triggering defense responses and to develop new molecular tools for
      epidemiological surveillance.
AU  - Cunnac S
AU  - Bolot S
AU  - Forero SN
AU  - Ortiz E
AU  - Szurek B
AU  - Noel LD
AU  - Arlat M
AU  - Jacques MA
AU  - Gagnevin L
AU  - Carrere S
AU  - Nicole M
AU  - Koebnik R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00674-13.

PMID- Not included in PubMed...
VI  - 5
DP  - 1981
TI  - Survey of phytopathogenic pseudomonads for a restriction and modification system active on the double-stranded ribonucleic acid phage Phi-6.
PG  - 247-249
AB  - A total of 380 pseudomonad strains from 39 nomenspecies and 41 strains from 7 other bacterial
      genera were screened for a double-stranded ribonucleic acid modification and restriction
      system using the double-stranded ribonucleic acid modification and restriction system using
      the double-stranded ribonucleic acid bacteriophage Phi-6.  Of these 421 strains, 8 showed the
      low plating efficiency (10^-5 to 10^-7) characteristic of such a system.  However, the phage
      propagated in 7 of the 8 were host-range mutants; the remaining strain showed some
      characteristics of a host-modification system but the results were equivocal.
AU  - Cuppels DA
AU  - Van Etten JL
AU  - Lambrecht P
AU  - Vidaver AK
PT  - Journal Article
TA  - Curr. Microbiol.
JT  - Curr. Microbiol.
SO  - Curr. Microbiol. 1981 5: 247-249.

PMID- 8548830
VI  - 84
DP  - 1996
TI  - Retrohoming: cDNA-mediated mobility.
PG  - 9-12
AB  - Last year was a vintage year for mobile group II introns.  In 1995 we moved from phenomenology
      to mechanistic insight, from enigmatic observations to a coherent appreciation of process.
      The finding that nucleated our understanding of the group II intron mobility event was the
      appearance of an extraordinary double-strand break in the target DNA: a break that provides an
      initiation site for reverse transcriptase, which mediates group II intron mobility; a break in
      which the excised intron RNA is covalently attached to one of the DNA ends; a break that is
      made by the protein and RNA products of the intron itself, with the RNA believed to be the
      catalyst responsible for one of the DNA strand cleavages.  In this minireview, we piece
      together the puzzle by describing the formation of this remarkable double-strand break, its
      role in group II intron mobility, and the evolutionary implications of the process.  Group II
      introns are catalytic RNAs that, like spliceosomal introns, splice via a lariat intermediate.
      The nuclear pre-mRNA introns are thought to be descended from the group II introns, which are
      found in both pro- and eukaryotes.  The functional domains of the self-splicing group II
      introns are suspected to have evolved to act in trans under the guise of the snRNAs.  The
      mobile group II introns are also phylogenetically linked to retroelements, which may provide
      clues as to how the group II introns have become disseminated.  The mobility of group II
      introns therefore engenders great evolutionary and mechanistic interest.
AU  - Curcio MJ
AU  - Belfort M
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1996 84: 9-12.

PMID- 27881542
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Four Alteromonas macleodii Strains Isolated from Copper Coupons and Grown Long-Term at Elevated Copper Levels.
PG  - e01311-16
AB  - Alteromonas macleodii is a marine bacterium involved in the early stages of biofouling on ship
      hulls treated with copper as an antifouling agent. We report
      here the draft genome sequences of an A. macleodii strain isolated from copper
      coupons and three laboratory mutants grown long-term at elevated copper levels.
AU  - Cusick KD
AU  - Dale JR
AU  - Little BJ
AU  - Biffinger JC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01311-16.

PMID- 17029241
VI  - 65
DP  - 2006
TI  - Identification of a new subfamily of HNH nucleases and experimental characterization of a representative member, HphI restriction endonuclease.
PG  - 867-876
AB  - The restriction endonuclease (REase) R. HphI is a Type IIS enzyme that recognizes the
      asymmetric target DNA sequence 5'-GGTGA-3' and in the
      presence of Mg2+ hydrolyzes phosphodiester bonds in both strands of the
      DNA at a distance of 8 nucleotides towards the 3' side of the target,
      producing a 1 nucleotide T-staggered cut in an unspecified sequence at
      this position. REases are typically ORFans that exhibit little
      similarity to each other and to any proteins in the database. However,
      bioinformatics analyses revealed that R.HphI is a member of a
      relatively big sequence family with a conserved C-terminal domain and a
      variable N-terminal domain. We predict that the C-terminal domains of
      proteins from this family correspond to the nuclease domain of the HNH
      superfamily rather than to the most common PD(D/E)XK superfamily of
      nucleases. We constructed a three-dimensional model of the R.HphI
      catalytic domain and validated our predictions by sitedirected
      mutagenesis and studies of DNA-binding and catalytic activities of the
      mutant proteins. We also analyzed the genomic neighborhood of R.HphI
      homologs and found that putative nucleases accompanied by a DNA
      methyltransferase (i.e. predicted REases) do not form a single group on
      a phylogenetic tree, but are dispersed among free-standing putative
      nucleases. This suggests that nucleases from the HNH superfamily were
      independently recruited to become REases in the context of RM systems
      multiple times in the evolution and that members of the HNH superfamily
      may be much more frequent among the so far unassigned REase sequences
      than previously thought.
AU  - Cymerman IA
AU  - Obarska A
AU  - Skowronek KJ
AU  - Lubys A
AU  - Bujnicki JM
PT  - Journal Article
TA  - Proteins
JT  - Proteins
SO  - Proteins 2006 65: 867-876.

PMID- 23209245
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of the Biocontrol Strain Serratia plymuthica A30, Isolated  from Rotting Potato Tuber Tissue.
PG  - 6999-7000
AB  - Serratia plymuthica A30 is a Gram-negative bacterium expressing antagonistic activity toward
      blackleg- and soft rot-causing Dickeya sp. biovar 3 ('Dickeya
      solani'). Here, we present the draft genome sequence of strain A30, which has
      been isolated from rotten potato tuber tissue.
AU  - Czajkowski R
AU  - van der Wolf JM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6999-7000.

PMID- 1662657
VI  - 109
DP  - 1991
TI  - Expression in mammalian cells of a cloned gene encoding murine DNA methyltransferase.
PG  - 259-263
AB  - Mammalian DNA cytosine-5-methyltransferase (MTase, EC 2.1.1.37) is an essential
      component for establishing and maintaining cell-type specific methylation
      patterns in the genome.  The cDNA for the murine enzyme was previously cloned
      in segments.  We have reconstructed the entire gene, encoding a protein of 1517
      amino acids, from a set of overlapping cDNA clones.  We report the assembly of
      two expression constructs in bacterial/mammalian shuttle vectors.
      Transcription in the first construct (pEMT) is driven by the cytomegalovirus
      enhancer/promoter and encodes a fusion protein with 15 additional aa at the N
      terminus, while the second construct (pJMT) is driven by the simian virus 40
      early promoter/enhancer upstream from the natural ATG codon.
      Immunofluorescence microscopy and immunoblot analysis have shown that both
      constructs direct the synthesis of MTase in COS-1 cells.  Enzyme activity in
      whole-cell lysates of transfected COS-1 cells transfected with pEMT and pJMT
      are on average tenfold and fivefold higher than in controls, respectively.  The
      specific activities of the recombinant and endogenous mouse-cell enzyme are
      similar.  These expression constructs will be of use in studies of DNA
      methylation in mammals.
AU  - Czank A
AU  - Hauselmann R
AU  - Page AW
AU  - Leonhardt H
AU  - Bestor TH
AU  - Schafner W
AU  - Hergersberg M
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1991 109: 259-263.

PMID- 30107581
VI  - 46
DP  - 2018
TI  - Activity and structure of EcoKMcrA.
PG  - 9829-9841
AB  - Escherichia coli McrA (EcoKMcrA) acts as a methylcytosine and hydroxymethylcytosine dependent
      restriction endonuclease. We present a
      biochemical characterization of EcoKMcrA that includes the first demonstration of
      its endonuclease activity, small angle X-ray scattering (SAXS) data, and a
      crystal structure of the enzyme in the absence of DNA. Our data indicate that
      EcoKMcrA dimerizes via the anticipated C-terminal HNH domains, which together
      form a single DNA binding site. The N-terminal domains are not homologous to SRA
      domains, do not interact with each other, and have separate DNA binding sites.
      Electrophoretic mobility shift assay (EMSA) and footprinting experiments suggest
      that the N-terminal domains can sense the presence and sequence context of
      modified cytosines. Pyrrolocytosine fluorescence data indicate no base flipping.
      In vitro, EcoKMcrA DNA endonuclease activity requires Mn2+ ions, is not strictly
      methyl dependent, and is not observed when active site variants of the enzyme are
      used. In cells, EcoKMcrA specifically restricts DNA that is modified in the
      correct sequence context. This activity is impaired by mutations of the nuclease
      active site, unless the enzyme is highly overexpressed.
AU  - Czapinska H
AU  - Kowalska M
AU  - Zagorskaite E
AU  - Manakova E
AU  - Slyvka A
AU  - Xu SY
AU  - Siksnys V
AU  - Sasnauskas G
AU  - Bochtler M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2018 46: 9829-9841.

PMID- 19720513
VI  - 165
DP  - 2010
TI  - Survey of genome organization and gene content of Corynebacterium pseudotuberculosis.
PG  - 312-320
AB  - Corynebacterium pseudotuberculosis is an intracellular pathogen that
      causes Caseous lymphadenitis (CLA) disease in sheep and goats. The
      widespread occurrence and the economic importance of this pathogen have
      prompted investigation of its pathogenesis. We used a genomic library of
      C. pseudotuberculosis to generate 1440 genomic survey sequences (GSSs);
      these were analyzed in silico with bioinformatics tools, using public
      databases for comparative analyses. We employed non-redundant unique
      sequences as a query for BLAST searches against the genome, the translated
      genome and the proteome of four other Corynebacterium species that have
      been completely sequenced. We were able to characterize approximately 8%
      of the genome of C. pseudotuberculosis, including previously undescribed
      functional group genes, based on the COG database; the GSSs classification
      into categories gave 13% information storage and processing, 14% cellular
      processes and 23% metabolism. We found a close relation between C.
      pseudotuberculosis and C. diphtheriae conserved-gene synteny in
      Corynebacteria species.
AU  - D'Afonseca V
AU  - Prosdocimi F
AU  - Dorella FA
AU  - Pacheco LG
AU  - Moraes PM
AU  - Pena I
AU  - Ortega JM
AU  - Teixeira S
AU  - Oliveira SC
AU  - Coser EM
AU  - Oliveira LM
AU  - Correa-de-Oliveira G
AU  - Meyer R
AU  - Miyoshi A
AU  - Azevedo V
PT  - Journal Article
TA  - Microbiol. Res.
JT  - Microbiol. Res.
SO  - Microbiol. Res. 2010 165: 312-320.

PMID- 28126933
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Plant Growth-Promoting Rhizobacterium Pseudomonas fluorescens Strain CREA-C16 Isolated from Pea (Pisum sativum L.) Rhizosphere.
PG  - e01456-16
AB  - Herein, we report the draft genome sequence of Pseudomonas fluorescens strain CREA-C16, a
      plant growth-promoting rhizobacterium that was isolated from the
      rhizosphere of Pisum sativum L. plants. The genome sequence is ~6 Mb in size,
      with a G+C content of 60.1%, and includes 4,457 candidate protein-encoding genes.
AU  - D'Agostino N
AU  - Sorrentino R
AU  - Scotti R
AU  - Salzano M
AU  - Aurilia V
AU  - Zaccardelli M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01456-16.

PMID- 26868393
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Proteus mirabilis NO-051/03, Representative of a Multidrug-Resistant Clone Spreading in Europe and Expressing the CMY-16 AmpC-Type  beta-Lactamase.
PG  - e01702-15
AB  - Proteus mirabilis NO-051/03, representative of a multidrug-resistant clone expressing the
      CMY-16 AmpC-type beta-lactamase and circulating in Europe since
      2003, was sequenced by a MiSeq platform using a paired-end approach. The genome
      was assembled in 100 scaffolds with a total length of 4,197,318 bp. Analysis of
      the draft genome sequence revealed the presence of several acquired resistance
      determinants to beta-lactams, aminoglycosides, phenicols, tetracyclines,
      trimethoprim, and sulfonamides, of one plasmid replicon, and of a type I-E
      clustered regularly interspaced short palindromic repeat (CRISPR)-associated
      protein (Cas) adaptive immune system.
AU  - D'Andrea MM
AU  - Giani T
AU  - Henrici DeAL
AU  - Ciacci N
AU  - Gniadkowski M
AU  - Miriagou V
AU  - Torricelli F
AU  - Rossolini GM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01702-15.

PMID- 27635010
VI  - 4
DP  - 2016
TI  - Permanent Draft Genome Sequence of Frankia sp. Strain BR, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina equisetifolia.
PG  - e01000-16
AB  - Frankia sp. strain BR is a member of Frankia lineage Ic and is able to reinfect plants of the
      Casuarinaceae family. Here, we report a 5.2-Mbp draft genome
      sequence with a G+C content of 70.0% and 4,777 candidate protein-encoding genes.
AU  - D'Angelo T
AU  - Oshone R
AU  - Abebe-Akele F
AU  - Simpson S
AU  - Morris K
AU  - Thomas WK
AU  - Tisa LS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01000-16.

PMID- 27389275
VI  - 4
DP  - 2016
TI  - Permanent Draft Genome Sequence for Frankia sp. Strain EI5c, a Single-Spore Isolate of a Nitrogen-Fixing Actinobacterium, Isolated from the Root Nodules of  Elaeagnus angustifolia.
PG  - e00660-16
AB  - Frankia sp. strain EI5c is a member of Frankia lineage III, which is able to reinfect plants
      of the Eleagnaceae, Rhamnaceae, Myricaceae, and Gymnostoma, as
      well as the genus Alnus Here, we report the 6.6-Mbp draft genome sequence of
      Frankia sp. strain EI5c with a G+C content of 72.14 % and 5,458 candidate
      protein-encoding genes.
AU  - D'Angelo T
AU  - Oshone R
AU  - Abebe-Akele F
AU  - Simpson S
AU  - Morris K
AU  - Thomas WK
AU  - Tisa LS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00660-16.

PMID- 2982799
VI  - 260
DP  - 1985
TI  - Purification and crystallization of the EcoRV restriction endonuclease.
PG  - 1987-1990
AB  - The type II restriction endonuclease EcoRV purified from a genetically
      engineered, overproducing strain has been crystallized.  Four crystal forms all
      obtained by precipitation with polyethylene glycol 4000 have been
      characterized.  Two of these are suitable for high resolution structure
      analysis.  Both are orthorhombic, have space group P2/12/1/2/1 and have similar
      unit cell dimensions of a = 58.2 angstrom, b = 71.7 angstrom, c = 130.6
      angstrom (form A) and a = 59.9 angstrom, b = 74.5 angstrom, c= 121.8 angstrom
      (form B).  They diffract to about 2 angstrom resolution and appear to have one
      dimer of 2 x 29,000 daltons in the asymmetric unit.
AU  - D'Arcy A
AU  - Brown RS
AU  - Zabeau M
AU  - van Resandt RW
AU  - Winkler FK
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1985 260: 1987-1990.

PMID- 21685292
VI  - 193
DP  - 2011
TI  - De Novo Sequencing and Assembly of the Whole Genome of Novosphingobium sp. Strain PP1Y.
PG  - 4296
AB  - Novosphingobium sp. strain PP1Y is a marine bacterium specifically adapted to use fuels as an
      energy source. We sequenced and assembled its entire
      genome using the Roche 454 genome sequencer system, which led to the
      identification of two plasmids and one megaplasmid, besides a 3.9-Mb
      circular chromosome.
AU  - D'Argenio V
AU  - Petrillo M
AU  - Cantiello P
AU  - Naso B
AU  - Cozzuto L
AU  - Notomista E
AU  - Paolella G
AU  - Di Donato A
AU  - Salvatore F
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4296.

PMID- 24762933
VI  - 2
DP  - 2014
TI  - Genome Sequence of Lactobacillus plantarum 19L3, a Strain Proposed as a Starter Culture for Slovenska Bryndza Ovine Cheese.
PG  - e00292-14
AB  - The genome sequence of Lactobacillus plantarum isolated from ovine cheese is presented here.
      This bacterium is proposed as a starter strain, named 19L3, for Slovenska bryndza cheese, a
      traditional Slovak cheese fulfilling European Food Safety Authority (EFSA) requirements.
AU  - D'Auria G
AU  - Dzunkova M
AU  - Moya A
AU  - Tomaska M
AU  - Kolosta M
AU  - Kmet V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00292-14.

PMID- 22123762
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Acidaminococcus intestini RYC-MR95, a Gram-Negative Bacterium from the Phylum Firmicutes.
PG  - 7008-7009
AB  - Acidaminococcus intestini belongs to the family Acidaminococcaceae, order Selenomonadales,
      class Negativicutes, phylum Firmicutes. Negativicutes
      show the double-membrane system of Gram-negative bacteria, although their
      chromosomal backbone is closely related to that of Gram-positive bacteria
      of the phylum Firmicutes. The complete genome of a clinical A. intestini
      strain is here presented.
AU  - D'Auria G
AU  - Galan JC
AU  - Rodriguez-Alcayna M
AU  - Moya A
AU  - Baquero F
AU  - Latorre A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 7008-7009.

PMID- 27125480
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Mycobacterium brumae ATCC 51384.
PG  - e00237-16
AB  - Here, we report the draft genome sequence of Mycobacterium brumae type strain ATCC 51384. This
      is the first draft genome sequence of M. brumae, a
      nonpathogenic, rapidly growing, nonchromogenic mycobacterium, with
      immunotherapeutic capacities.
AU  - D'Auria G
AU  - Torrents E
AU  - Luquin M
AU  - Comas I
AU  - Julian E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00237-16.

PMID- 27365360
VI  - 4
DP  - 2016
TI  - Genome Sequence of the Historical Clinical Isolate Burkholderia pseudomallei PHLS 6.
PG  - e00649-16
AB  - Here, we present the draft genome sequence of Burkholderia pseudomallei PHLS 6, a virulent
      clinical strain isolated from a melioidosis patient in Bangladesh in 1960. The draft genome
      consists of 39 contigs and is 7,322,181 bp long.
AU  - D'haeseleer P
AU  - Johnson SL
AU  - Davenport KW
AU  - Chain PS
AU  - Schoeniger J
AU  - Ray D
AU  - Sinha A
AU  - Williams KP
AU  - Pena J
AU  - Branda SS
AU  - El-Etr S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00649-16.

PMID- 
VI  - 20
DP  - 2004
TI  - Characterization of BflI - a thermostable, Co++-requiring isoschizomer of BsiYI from Anoxybacillus flavithermus.
PG  - 593-598
AB  - A thermophile, isolated from geothermal areas in the northern Himalayan region of India, was
      identified by partial 16S rDNA sequence (GenBank
      accession # AF482430) analysis as Anoxybacillus flavithermus. The
      isolate produced BflI (REBASE # 4910), a Type II restriction
      endonuclease, which recognized the sequence 5'-CCNNNN-N/NNGG-3' and was
      the isoschizomer of BsiYI. The enzyme was purified to homogeneity by
      passing through Cibacron Blue F3GA agarose, DEAE-cellulose,
      heparin-agarose and MonoQ FPLC. The purified enzyme (MW 36 kDa) worked
      best at 60 C in Promega's buffer C and preferentially required
      Co++(0.4 mM) as cofactor followed by Mg++ (10 mM) and Mn++ (1 mM). The
      enzyme showed high specific activity and worked in the presence of high
      concentrations of beta-mercaptoethanol (200 mM), Triton-X-100 (25%),
      urea (30%), formamide (6%) and guanidine (40 mM) and showed no star
      activity in the presence of 40% glycerol. In the absence of any
      stabilizing agent, BflI retained t(1/2) for at least 96 h at 37
      degreesC, 6 h at 60 C and 6 months at 4 C. N-terminal
      sequencing showed that its first 10 amino acid residues were
      DFHEDKTIAR.
AU  - D'Souza DR
AU  - Morgan RD
AU  - Parashar V
AU  - Capalash N
AU  - Sharma P
PT  - Journal Article
TA  - World J. Microbiol. Biotechnol.
JT  - World J. Microbiol. Biotechnol.
SO  - World J. Microbiol. Biotechnol. 2004 20: 593-598.

PMID- 29301901
VI  - 6
DP  - 2018
TI  - Two Draft Genome Sequences of Chromobacterium violaceum Isolates from the Rio Negro.
PG  - e01348-17
AB  - The draft genome sequences of two Chromobacterium violaceum strains isolated from the Rio
      Negro are reported here. These bacteria carry most genetic systems
      associated with the production of bioactive compounds, but unlike other C.
      violaceum strains, they lack a dedicated operon for arsenic resistance.
AU  - da Gama AM
AU  - de Almeida LG
AU  - Yamane T
AU  - Spira B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01348-17.

PMID- 27231360
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequence of Rummeliibacillus stabekisii Strain PP9 Isolated from Antarctic Soil.
PG  - e00416-16
AB  - The whole genome of Rummeliibacillus stabekisii PP9, isolated from a soil sample  from
      Antarctica, consists of a circular chromosome of 3,412,092 bp and a circular
      plasmid of 8,647 bp, with 3,244 protein-coding genes, 12 copies of the 16S-23S-5S
      rRNA operon, 101 tRNA genes, and 6 noncoding RNAs (ncRNAs).
AU  - da Mota FF
AU  - Vollu RE
AU  - Jurelevicius D
AU  - Seldin L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00416-16.

PMID- 24009118
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Streptococcus equi subsp. zooepidemicus Strain S31A1, Isolated from Equine Infectious Endometritis.
PG  - e00683-13
AB  - We present the draft genome sequence of Streptococcus equi subsp. zooepidemicus S31A1, a
      strain isolated from equine infectious endometritis in Denmark.
      Comparative analyses of this genome were done with four published reference
      genomes: S. zooepidemicus strains MGCS10565, ATCC 35246, and H70 and S. equi
      subsp. equi strain 4047.
AU  - da Piedade I
AU  - Skive B
AU  - Christensen H
AU  - Bojesen AM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00683-13.

PMID- 12024217
VI  - 417
DP  - 2002
TI  - Comparison of the genomes of two Xanthomonas pathogens with differing host specificities.
PG  - 459-463
AB  - The genus Xanthomonas is a diverse and economically important group of bacterial
      phytopathogens, belonging to the gamma-subdivision of the Proteobacteria. Xanthomonas
      axonopodis pv. citri (Xac) causes citrus canker, which affects most commercial citrus
      cultivars, resulting in significant losses worldwide. Symptoms include canker lesions, leading
      to abscission of fruit and leaves and general tree decline. Xanthomonas campestris pv.
      campestris (Xcc) causes black rot, which affects crucifers such as Brassica and Arabidopsis.
      Symptoms include marginal leaf chlorosis and darkening of vascular tissue, accompanied by
      extensive wilting and necrosis. Xanthomonas campestris pv. campestris is grown commercially to
      produce the exopolysaccharide xanthan gum, which is used as a viscosifying and stabilizing
      agent in many industries. Here we report and compare the complete genome sequences of Xac and
      Xcc. Their distinct disease phenotypes and host ranges belie a high degree of similarity at
      the genomic level. More than 80% of genes are shared, and gene order is conserved along most
      of their respective chromosomes. We identified several groups of strain-specific genes, and on
      the basis of these groups we propose mechanisms that may explain the differing host
      specificities and pathogenic processes.
AU  - da Silva ACR et al
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2002 417: 459-463.

PMID- 27198027
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Limnobacter sp. Strain CACIAM 66H1, a Heterotrophic Bacterium Associated with Cyanobacteria.
PG  - e00399-16
AB  - Ecological interactions between cyanobacteria and heterotrophic prokaryotes are poorly known.
      To improve the genomic studies of heterotrophic
      bacterium-cyanobacterium associations, the draft genome sequence (3.2 Mbp) of
      Limnobacter sp. strain CACIAM 66H1, found in a nonaxenic culture of Synechococcus
      sp. (cyanobacteria), is presented here.
AU  - da Silva FD
AU  - Lima AR
AU  - Moraes PH
AU  - Siqueira AS
AU  - Dall'Agnol LT
AU  - Barauna AR
AU  - Martins LC
AU  - Oliveira KG
AU  - de Lima CP
AU  - Nunes MR
AU  - Vianez-Junior JL
AU  - Goncalves EC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00399-16.

PMID- 26227593
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Shiga Toxin-Producing Escherichia coli Strain D92/09.
PG  - e00805-15
AB  - Escherichia coli is suspected to be involved with Crohn's disease. Adherence and  invasion to
      epithelial cells are properties commonly observed in these bacteria.
      Here, we present a draft genome sequence of E. coli D92/09, a multidrug-resistant
      strain, which besides showing these properties produces Shiga cytotoxin-1 and
      possibly other toxins.
AU  - Da Silva SAC
AU  - Rodrigues J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00805-15.

PMID- 30344888
VI  - 13
DP  - 2018
TI  - Insights into the draft genome sequence of bioactives-producing Bacillus thuringiensis DNG9 isolated from Algerian soil-oil slough.
PG  - 25
AB  - Bacillus thuringiensis is widely used as a bioinsecticide due to its ability to form
      parasporal crystals containing proteinaceous toxins. It is a member of the
      Bacillus cereus sensu lato, a group with low genetic diversity but produces
      several promising antimicrobial compounds. B. thuringiensis DNG9, isolated from
      an oil-contaminated slough in Algeria, has strong antibacterial, antifungal and
      biosurfactant properties. Here, we report the 6.06 Mbp draft genome sequence of
      B. thuringiensis DNG9. The genome encodes several gene inventories for the
      biosynthesis of bioactive compounds such as zwittermycin A, petrobactin,
      insecticidal toxins, polyhydroxyalkanoates and multiple bacteriocins. We expect
      the genome information of strain DNG9 will provide another model system to study
      pathogenicity against insect pests, plant diseases, and antimicrobial compound
      mining and comparative phylogenesis among the Bacillus cereus sensu lato group.
AU  - Daas MS
AU  - Rosana ARR
AU  - Acedo JZ
AU  - Douzane M
AU  - Nateche F
AU  - Kebbouche-Gana S
AU  - Vederas JC
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2018 13: 25.

PMID- 29599156
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Bacillus paralicheniformis F47, Isolated from an Algerian Salty Lake.
PG  - e00190-18
AB  - Bacillus paralicheniformis F47 was isolated from a salty lake in Ain Baida-Ouargla, southern
      Algeria. The genome contains genes for the production of
      several bioactive secondary metabolites, including the siderophore bacillibactin,
      the lipopeptides fengycin, surfactin, and lichenysin, the antibiotics bacitracin
      and kanosamine, and a putative circular bacteriocin.
AU  - Daas MS
AU  - Rosana ARR
AU  - Acedo JZ
AU  - Douzane M
AU  - Nateche F
AU  - Kebbouche-Gana S
AU  - Vederas JC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00190-18.

PMID- 28522726
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Bacillus cereus E41 and Bacillus anthracis F34 Isolated from Algerian Salt Lakes.
PG  - e00383-17
AB  - Two strains of Bacillus, B. cereus E41 and B. anthracis F34, were isolated from a salt lake in
      Ain M'lila-Oum El Bouaghi, eastern Algeria, and Ain Baida-Ouargla,
      southern Algeria, respectively. Their genomes display genes for the production of
      several bioactive secondary metabolites, including polyhydroxyalkanoate, iron
      siderophores, lipopeptides, and bacteriocins.
AU  - Daas MS
AU  - Rosana ARR
AU  - Acedo JZ
AU  - Nateche F
AU  - Kebbouche-Gana S
AU  - Vederas JC
AU  - Case RJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00383-17.

PMID- 
VI  - 53
DP  - 2013
TI  - Epigenomic Signatures in Basal Metazoans: DNA Methyltransferase in Pleurobrachia bachei.
PG  - E273
AB  - DNA methylation is an epigenetic modification crucial to cell differentiation and development.
      In the majority of bilaterians 5-methylcytosine DNA methylation occurs at CpG sites and
      islands controlling gene transcription.  Contrary to Drosophila and C. elegans that have lost
      this machinery, possibly due to their compact genome sizes and short life cycle, here we show
      that the phylum Ctenophora has conserved methylation machinery.  Using the data from the
      recently sequenced genome of Pleurobrachia bachei we cloned DNA 5-cytosine methyltransferase
      (DNMT) and characterized its expression in major developmental stages and adult ctenophores.
      Distinctive mRNA expression in the digestive system, (stomach, pharynx and mouth), tentacles
      and unique patterns in between ciliated comb rows in adult Pleurobrachia collectively suggest
      that DNMT mRNA expression levels are both cell-specific and noticeable in areas of high
      proliferation.  Next using colorimetric ELISA assay for methylated DNA we directly showed that
      DNA methylation does occur in the Pleurobrachia genome, although it was significantly lower
      than in the molluscan (Aplysia) and mammalian (Ratus) nervous tissues. Combined, our data
      suggest that the small genome of the ctenophore Pleurobrachia bachei has functional DNA
      methylation machinery, possibly involved in epigenetic control of somatic cell divisions and
      regulation of mRNA expression at zones of proliferation.
AU  - Dabe EC
AU  - Kohn AB
AU  - Bobkova Y
AU  - Kocot K
AU  - Citarella M
AU  - Bostwick CJ
AU  - Winters GC
AU  - Swalla BJ
AU  - Moroz LL
PT  - Journal Article
TA  - Integr. Comp. Biol.
JT  - Integr. Comp. Biol.
SO  - Integr. Comp. Biol. 2013 53: E273.

PMID- 22467209
VI  - 40
DP  - 2012
TI  - Chromosomal context and epigenetic mechanisms control the efficacy of genome editing by rare-cutting designer endonucleases.
PG  - 6367-6379
AB  - The ability to specifically engineer the genome of living cells at precise locations using
      rare-cutting designer endonucleases has broad
      implications for biotechnology and medicine, particularly for
      functional genomics, transgenics and gene therapy. However, the
      potential impact of chromosomal context and epigenetics on designer
      endonuclease-mediated genome editing is poorly understood. To address
      this question, we conducted a comprehensive analysis on the efficacy of
      37 endonucleases derived from the quintessential I-CreI meganuclease
      that were specifically designed to cleave 39 different genomic targets.
      The analysis revealed that the efficiency of targeted mutagenesis at a
      given chromosomal locus is predictive of that of homologous gene
      targeting. Consequently, a strong genome-wide correlation was apparent
      between the efficiency of targeted mutagenesis (0.1% to similar to 6%)
      with that of homologous gene targeting (0.1% to similar to 15%). In
      contrast, the efficiency of targeted mutagenesis or homologous gene
      targeting at a given chromosomal locus does not correlate with the
      activity of individual endonucleases on transiently transfected
      substrates. Finally, we demonstrate that chromatin accessibility
      modulates the efficacy of rare-cutting endonucleases, accounting for
      strong position effects. Thus, chromosomal context and epigenetic
      mechanisms may play a major role in the efficiency rare-cutting
      endonuclease-induced genome engineering.
AU  - Daboussi F et al
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: 6367-6379.

PMID- 24604646
VI  - 2
DP  - 2014
TI  - Genome Sequence of Mycoplasma hyorhinis Strain DBS 1050.
PG  - e00127-14
AB  - Mycoplasma hyorhinis is known as one of the most prevalent contaminants of mammalian cell and
      tissue cultures worldwide. Here, we present the complete
      genome sequence of the fastidious M. hyorhinis strain DBS 1050.
AU  - Dabrazhynetskaya A
AU  - Soika V
AU  - Volokhov D
AU  - Simonyan V
AU  - Chizhikov V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00127-14.

PMID- 24051324
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Methicillin-Resistant Staphylococcus aureus Strain SA16, Representative of an Endemic Clone from a Brazilian Hospital.
PG  - e00754-13
AB  - Here we report the draft genome sequence of a bloodstream isolate of methicillin-resistant
      Staphylococcus aureus strain SA16. Strain SA16 is a
      sequence type 5 (ST5)-staphylococcal cassette chromosome mec type II (SCCmec II)
      clone and was the most prevalent isolate at a Brazilian hospital during the
      second half of 2009.
AU  - Dabul AN
AU  - Kos VN
AU  - Gilmore MS
AU  - Camargo IL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00754-13.

PMID- 20807202
VI  - 78
DP  - 2010
TI  - Integrating conjugative elements of the SXT/R391 family trigger the excision and drive the mobilization of a new class of Vibrio genomic islands.
PG  - 576-588
AB  - In vibrios and enterobacteria lateral gene transfer is often facilitated by
      integrating conjugative elements (ICEs) of the SXT/R391 family. SXT/R391 ICEs
      integrate by site-specific recombination into prfC and transfer by conjugation, a
      process that is initiated at a specific locus called the origin of transfer
      (oriT(SXT) ). We identified genomic islands (GIs) harbouring a sequence that
      shares >63% identity with oriT(SXT) in three species of Vibrio. Unlike SXT/R391
      ICEs, these GIs are integrated into a gene coding for a putative stress-induced
      protein and do not appear to carry any gene coding for a conjugative machinery or
      for mobilization proteins. Our results show that SXT/R391 ICEs trigger the
      excision and mediate the conjugative transfer in trans of the three Vibrio GIs at
      high frequency. GIs' excision is independent of the ICE-encoded recombinase and
      is controlled by the ICE-encoded transcriptional activator SetCD, which is
      expressed during the host SOS response. Both mobI and traI, two ICE-borne genes
      involved in oriT recognition, are essential for GIs' transfer. We also found that
      SXT/R391 ICEs mobilize in trans over 1 Mb of chromosomal DNA located 5' of the
      GIs' integration site. Together these results support a novel mechanism of
      mobilization of GIs by ICEs of the SXT/R391 family.
AU  - Daccord A
AU  - Ceccarelli D
AU  - Burrus V
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2010 78: 576-588.

PMID- 29491853
VI  - 9
DP  - 2018
TI  - Cultivation and Genomic Analysis of 'Candidatus Nitrosocaldus islandicus,' an Obligately Thermophilic, Ammonia-Oxidizing Thaumarchaeon from a Hot Spring Biofilm in Graendalur Valley, Iceland.
PG  - 193
AB  - Ammonia-oxidizing archaea (AOA) within the phylum Thaumarchaeota are the only known aerobic
      ammonia oxidizers in geothermal environments. Although molecular
      data indicate the presence of phylogenetically diverse AOA from the Nitrosocaldus
      clade, group 1.1b and group 1.1a Thaumarchaeota in terrestrial high-temperature
      habitats, only one enrichment culture of an AOA thriving above 50 degrees C has
      been reported and functionally analyzed. In this study, we physiologically and
      genomically characterized a newly discovered thaumarchaeon from the
      deep-branching Nitrosocaldaceae family of which we have obtained a high (
      approximately 85%) enrichment from biofilm of an Icelandic hot spring (73 degrees
      C). This AOA, which we provisionally refer to as 'Candidatus Nitrosocaldus
      islandicus,' is an obligately thermophilic, aerobic chemolithoautotrophic ammonia
      oxidizer, which stoichiometrically converts ammonia to nitrite at temperatures
      between 50 and 70 degrees C. 'Ca. N. islandicus' encodes the expected repertoire
      of enzymes proposed to be required for archaeal ammonia oxidation, but
      unexpectedly lacks a nirK gene and also possesses no identifiable other enzyme
      for nitric oxide (NO) generation. Nevertheless, ammonia oxidation by this AOA
      appears to be NO-dependent as 'Ca. N. islandicus' is, like all other tested AOA,
      inhibited by the addition of an NO scavenger. Furthermore, comparative genomics
      revealed that 'Ca. N. islandicus' has the potential for aromatic amino acid
      fermentation as its genome encodes an indolepyruvate oxidoreductase (iorAB) as
      well as a type 3b hydrogenase, which are not present in any other sequenced AOA.
      A further surprising genomic feature of this thermophilic ammonia oxidizer is the
      absence of DNA polymerase D genes - one of the predominant replicative DNA
      polymerases in all other ammonia-oxidizing Thaumarchaeota. Collectively, our
      findings suggest that metabolic versatility and DNA replication might differ
      substantially between obligately thermophilic and other AOA.
AU  - Daebeler A
AU  - Herbold CW
AU  - Vierheilig J
AU  - Sedlacek CJ
AU  - Pjevac P
AU  - Albertsen M
AU  - Kirkegaard RH
AU  - de la Torre JR
AU  - Daims H
AU  - Wagner M
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2018 9: 193.

PMID- 10586498
VI  - 63
DP  - 1999
TI  - Site-directed mutagenesis of restriction endonuclease HindIII.
PG  - 1703-1707
AB  - Site-directed mutagenesis by inverse PCR was done on the HindIII gene.  Target residues to be
      mutated were chosen according to (i) the fact that a mutant obtained by sodium nitrite
      treatment showed almost no HindIII activity, where Asp-123 was replaced with Asn, and (ii) the
      model proposed by Stahl et al.  Seven kinds of mutants were obtained by PCR, and their
      enzymatic and biochemical properties were examined.  Three mutants, P50S, D108L, and D123N,
      showed fairly low HindIII activity.  On the other hand, the other four, P84Q, E85K, V106E, and
      K125N, retained the activity.  In particular, E86K showed higher activity than the wild type
      enzyme.  This fact was confirmed when activities of the purified wild type and E86K enzymes
      were assayed.  These results coincided fairly well with data using E. coli strains that carry
      the respective mutant plasmids, on their resistance to phage T7 and on growth rate.  We
      conclude that the PE motif at residues 50 and 51, and DXK motif at residues 108-110, are
      responsible for the enzymic reaction of HindIII.
AU  - Dahai T
AU  - Ando S
AU  - Takasaki Y
AU  - Tadano J
PT  - Journal Article
TA  - Biosci. Biotechnol. Biochem.
JT  - Biosci. Biotechnol. Biochem.
SO  - Biosci. Biotechnol. Biochem. 1999 63: 1703-1707.

PMID- 22916025
VI  - 8
DP  - 2012
TI  - Simple Methods for Generating and Detecting Locus-Specific Mutations Induced with TALENs in the Zebrafish Genome.
PG  - E1002861
AB  - The zebrafish is a powerful experimental system for uncovering gene function in
      vertebrate organisms. Nevertheless, studies in the zebrafish have been limited by
      the approaches available for eliminating gene function. Here we present simple
      and efficient methods for inducing, detecting, and recovering mutations at
      virtually any locus in the zebrafish. Briefly, double-strand DNA breaks are
      induced at a locus of interest by synthetic nucleases, called TALENs. Subsequent
      host repair of the DNA lesions leads to the generation of insertion and deletion
      mutations at the targeted locus. To detect the induced DNA sequence alterations
      at targeted loci, genomes are examined using High Resolution Melt Analysis, an
      efficient and sensitive method for detecting the presence of newly arising
      sequence polymorphisms. As the DNA binding specificity of a TALEN is determined
      by a custom designed array of DNA recognition modules, each of which interacts
      with a single target nucleotide, TALENs with very high target sequence
      specificities can be easily generated. Using freely accessible reagents and
      Web-based software, and a very simple cloning strategy, a TALEN that uniquely
      recognizes a specific pre-determined locus in the zebrafish genome can be
      generated within days. Here we develop and test the activity of four TALENs
      directed at different target genes. Using the experimental approach described
      here, every embryo injected with RNA encoding a TALEN will acquire targeted
      mutations. Multiple independently arising mutations are produced in each growing
      embryo, and up to 50% of the host genomes may acquire a targeted mutation. Upon
      reaching adulthood, approximately 90% of these animals transmit targeted
      mutations to their progeny. Results presented here indicate the TALENs are highly
      sequence-specific and produce minimal off-target effects. In all, it takes about
      two weeks to create a target-specific TALEN and generate growing embryos that
      harbor an array of germ line mutations at a pre-specified locus.
AU  - Dahlem TJ
AU  - Hoshijima K
AU  - Jurynec MJ
AU  - Gunther D
AU  - Starker CG
AU  - Locke AS
AU  - Weis AM
AU  - Voytas DF
AU  - Grunwald DJ
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2012 8: E1002861.

PMID- 28336587
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Propionibacterium avidum Strain UCD-PD2 Isolated from a  Feline Anal Sac.
PG  - e00034-17
AB  - Here, we present the draft genome sequence of Propionibacterium (Cutibacterium) avidum strain
      UCD-PD2. The assembly contains 2,667,287 bp in 51 contigs. The
      strain was isolated from anal sac secretion samples collected from a feral
      domestic cat (Felis catus) as part of a larger project to study the microbiology
      of cats.
AU  - Dahms PA
AU  - Martin AL
AU  - Ganz HH
AU  - Eisen JA
AU  - Coil DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00034-17.

PMID- 20828376
VI  - 10
DP  - 2010
TI  - Suppression subtractive hybridization identifies an autotransporter adhesin gene  of E. coli IMT5155 specifically associated with avian pathogenic Escherichia coli  (APEC).
PG  - 236
AB  - BACKGROUND: Extraintestinal pathogenic E. coli (ExPEC) represent a phylogenetically diverse
      group of bacteria which are implicated in a large range
      of infections in humans and animals. Although subgroups of different ExPEC
      pathotypes, including uropathogenic, newborn meningitis causing, and avian
      pathogenic E. coli (APEC) share a number of virulence features, there still might
      be factors specifically contributing to the pathogenesis of a certain subset of
      strains or a distinct pathotype. Thus, we made use of suppression subtractive
      hybridization and compared APEC strain IMT5155 (O2:K1:H5; sequence type complex
      95) with human uropathogenic E. coli strain CFT073 (O6:K2:H5; sequence type
      complex 73) to identify factors which may complete the currently existing model
      of APEC pathogenicity and further elucidate the position of this avian pathotype
      within the whole ExPEC group. RESULTS: Twenty-eight different genomic loci were
      identified, which are present in IMT5155 but not in CFT073. One of these loci
      contained a gene encoding a putative autotransporter adhesin. The open reading
      frame of the gene spans a 3,498 bp region leading to a putative 124-kDa adhesive
      protein. A specific antibody was raised against this protein and expression of
      the adhesin was shown under laboratory conditions. Adherence and adherence
      inhibition assays demonstrated a role for the corresponding protein in adhesion
      to DF-1 chicken fibroblasts. Sequence analyses revealed that the flanking regions
      of the chromosomally located gene contained sequences of mobile genetic elements,
      indicating a probable spread among different strains by horizontal gene transfer.
      In accordance with this hypothesis, the adhesin was found to be present not only
      in different phylogenetic groups of extraintestinal pathogenic but also of
      commensal E. coli strains, yielding a significant association with strains of
      avian origin. CONCLUSIONS: We identified a chromosomally located autotransporter
      gene in a highly virulent APEC strain which confers increased adherence of a
      non-fimbriated E. coli K-12 strain to a chicken fibroblast cell line. Even though
      flanked by mobile genetic elements and three different genetic regions upstream
      of the gene, most probably indicating horizontal gene transfer events, the
      adhesin gene was significantly linked with strains of avian origin. Due to the
      nucleotide sequence similarity of 98% to a recently published adhesin-related
      gene, located on plasmid pAPEC-O1-ColBM, the name aatA (APEC autotransporter
      adhesin A) was adopted from that study.Our data substantiate that AatA might not
      only be of relevance in APEC pathogenicity but also in facilitating their
      reservoir life style in the chicken intestine, which might pave the way for
      future intestinal preventive strategies.
AU  - Dai J
AU  - Wang S
AU  - Guerlebeck D
AU  - Laturnus C
AU  - Guenther S
AU  - Shi Z
AU  - Lu C
AU  - Ewers C
PT  - Journal Article
TA  - BMC Microbiol.
JT  - BMC Microbiol.
SO  - BMC Microbiol. 2010 10: 236.

PMID- 27445368
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Highly Virulent Haemophilus parasuis Serotype 11 Strain SC1401.
PG  - e00628-16
AB  - Haemophilus parasuis, a normal Gram-negative bacterium, may cause Glasser's disease and
      pneumonia in pigs. This study aims to identify the genes related to
      natural competence of the serotype 11 strain SC1401, which frequently shows
      competence and high pathogenicity. SC1401 shows many differences from strains
      without natural competence within the molecular basis. We performed complete
      genome sequencing together with restriction modification system analysis to lay
      the foundation for later study.
AU  - Dai K
AU  - Jin J
AU  - Wen Y
AU  - Wen X
AU  - He L
AU  - Cao S
AU  - Huang X
AU  - Wu R
AU  - Zhao Q
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00628-16.

PMID- 18424209
VI  - 30
DP  - 2008
TI  - A Three-Dimensional Model of a Group II Intron RNA and Its Interaction with the Intron-Encoded Reverse Transcriptase.
PG  - 472-485
AB  - Group II introns are self-splicing ribozymes believed to be the ancestors of spliceosomal
      introns. Many group II introns encode reverse
      transcriptases that promote both RNA splicing and intron mobility to new
      genomic sites. Here we used a circular permutation and crosslinking method
      to establish 16 intramolecular distance relationships within the mobile
      Lactococcus lactis Ll.LtrB-DeltaORF intron. Using these new constraints
      together with 13 established tertiary interactions and eight published
      crosslinks, we modeled a complete three-dimensional structure of the
      intron. We also used the circular permutation strategy to map RNA-protein
      interaction sites through fluorescence quenching and crosslinking assays.
      Our model provides a comprehensive structural framework for understanding
      the function of group II ribozymes, their natural structural variations,
      and the mechanisms by which the intron-encoded protein promotes RNA
      splicing and intron mobility. The model also suggests an arrangement of
      active site elements that may be conserved in the spliceosome.
AU  - Dai L
AU  - Chai D
AU  - Gu SQ
AU  - Gabel J
AU  - Noskov SY
AU  - Blocker FJ
AU  - Lambowitz AM
AU  - Zimmerly S
PT  - Journal Article
TA  - Mol. Cell
JT  - Mol. Cell
SO  - Mol. Cell 2008 30: 472-485.

PMID- 16796672
VI  - 60
DP  - 2006
TI  - Antigenic variation by Borrelia hermsii occurs through recombination between extragenic repetitive elements on linear plasmids.
PG  - 1329-1343
AB  - The relapsing fever agent Borrelia hermsii undergoes multiphasic antigenic variation through
      gene conversion of a unique expression site on a linear plasmid by an archived variable
      antigen gene. To further characterize this mechanism we assessed the repertoire and
      organization of archived variable antigen genes by sequencing approximately 85% of plasmids
      bearing these genes. Most archived genes shared with the expressed gene a less than or equal
      62 nucleotide (nt) region, the upstream homology sequence (UHS), that surrounded the start
      codon. The 59 archived variable antigen genes were arrayed in clusters with 13 repetitive, 214
      nt long downstream homology sequence (DHS) elements distributed among them. A fourteenth DHS
      element was downstream of the expression locus. Informative nucleotide polymorphisms in UHS
      regions and DHS elements were applied to the analysis of the expression site of relapse
      serotypes from 60 infected mice in a prospective study. For most recombinations, the upstream
      crossover occurred in the UHS's second half, and the downstream crossover was in the DHS's
      second half. Usually the closest archival DHS element was used, but occasionally a more
      distant DHS was employed. The downstream extragenic crossover site in B. hermsii contrasts
      with the downstream extragenic crossover site for antigenic variation in African trypanosomes.
AU  - Dai Q
AU  - Restrepo BI
AU  - Porcella SF
AU  - Raffel SJ
AU  - Schwan TG
AU  - Barbour AG
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2006 60: 1329-1343.

PMID- 27811093
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the Bacterium Comamonas aquatica CJG.
PG  - e01186-16
AB  - A Gram-negative bacterial strain, Comamonas aquatica CJG, absorbs low-density lipoprotein but
      not high-density lipoprotein in serum. Here, we report its draft
      genomic sequence of 3,764,434 bp, containing total 3,425 genes, 27% of which
      encode proteins for metabolism and energy conversion, and it is 30% identical to
      the genome of Comamonas testosteroni.
AU  - Dai W
AU  - Zhu Y
AU  - Wang X
AU  - Sakenova N
AU  - Yang Z
AU  - Wang H
AU  - Li G
AU  - He J
AU  - Huang D
AU  - Cai Y
AU  - Guo W
AU  - Wang Q
AU  - Feng T
AU  - Fan Q
AU  - Zheng T
AU  - Han A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01186-16.

PMID- 15946751
VI  - 1729
DP  - 2005
TI  - Isolation and expression analysis of genes encoding DNA methyltransferase in wheat (Triticum aestivum L.).
PG  - 118-125
AB  - DNA methylation of cytosine residues, catalyzed by DNA methyltransferases, is suggested to
      play important roles in regulating
      gene expression and plant development. In this study, we isolated four
      wheat cDNA fragments and one cDNA with open reading frame encoding
      putative DNA methyltransferase and designated TaMET1, TaMET2a, TaMET2b,
      TaCMT, TaMET3, respectively. BLASTX searches and phylogenetic analysis
      suggested that five cDNAs belonged to four classes (Dnmt1, Dnmt2, CMT
      and Dnmt3) of DNA methyltransferase genes. TaMET2a encoded a protein of
      376 aa and contained eight of ten conserved motifs characteristic of
      DNA methyltransferase. Genomic sequence of TaMET2a was obtained and
      found to contain ten introns and eleven exons. The expression analysis
      of the five genes revealed that they were expressed in developing seed,
      during germination and various vegetative tissues, but in quite
      different abundance. It was interesting to note that TaMET1 and TaMET3
      mRNAs were clearly detected in dry seeds. Moreover, the differential
      expression patterns of five genes were observed between wheat hybrid
      and its parents in leaf, stem and root of jointing stage, some were
      up-regulated while some others were down-regulated in the hybrid. We
      concluded that multiple wheat DNA methyltransferase genes were present
      and might play important roles in wheat growth and development.
AU  - Dai Y
AU  - Ni ZF
AU  - Dai J
AU  - Zhao T
AU  - Sun QX
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 2005 1729: 118-125.

PMID- 23872576
VI  - 79
DP  - 2013
TI  - Variation of the Virus-Related Elements within Syntenic Genomes of the Hyperthermophilic Archaeon Aeropyrum.
PG  - 5891-5898
AB  - The increasing number of genome sequences of archaea and bacteria show their
      adaptation to different environmental conditions at the genomic level. Aeropyrum
      spp. are aerobic and hyperthermophilic archaea. Aeropyrum camini was isolated
      from a deep-sea hydrothermal vent, and Aeropyrum pernix was isolated from a
      coastal solfataric vent. To investigate the adaptation strategy in each habitat,
      we compared the genomes of the two species. Shared genome features were a small
      genome size, a high GC content, and a large portion of orthologous genes (86 to
      88%). The genomes also showed high synteny. These shared features may have been
      derived from the small number of mobile genetic elements and the lack of a RecBCD
      system, a recombinational enzyme complex. In addition, the specialized physiology
      (aerobic and hyperthermophilic) of Aeropyrum spp. may also contribute to the
      entire-genome similarity. Despite having stable genomes, interference of synteny
      occurred with two proviruses, A. pernix spindle-shaped virus 1 (APSV1) and A.
      pernix ovoid virus 1 (APOV1), and clustered regularly interspaced short
      palindromic repeat (CRISPR) elements. Spacer sequences derived from the A. camini
      CRISPR showed significant matches with protospacers of the two proviruses
      infecting A. pernix, indicating that A. camini interacted with viruses closely
      related to APSV1 and APOV1. Furthermore, a significant fraction of the
      nonorthologous genes (41 to 45%) were proviral genes or ORFans probably
      originating from viruses. Although the genomes of A. camini and A. pernix were
      conserved, we observed nonsynteny that was attributed primarily to virus-related
      elements. Our findings indicated that the genomic diversification of Aeropyrum
      spp. is substantially caused by viruses.
AU  - Daifuku T
AU  - Yoshida T
AU  - Kitamura T
AU  - Kawaichi S
AU  - Inoue T
AU  - Nomura K
AU  - Yoshida Y
AU  - Kuno S
AU  - Sako Y
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2013 79: 5891-5898.

PMID- 3956763
VI  - 45
DP  - 1986
TI  - Restriction at mismatched sites in DNA.
PG  - 1783
AB  - Restriction endonucleases were tested for their ability to catalyze the
      cleavage of mismatch-containing recognition sites in DNA.  These mismatched
      base pairs were T-G, U-G or A-C in covalently closed, circular DNA molecules
      prepared by in vitro extension of chemically synthesized oligonucleotide
      primers annealed to an M13-derived viral DNA.  None of the tested restriction
      enzymes was able to completely cleave the mismatch-containing recognition sites
      of these heteroduplexes at a normal rate.  However, three of them, SmaI, SalI,
      SstI, partially digested certain T-G or U-G-substituted recognition sites under
      standard digestion conditions.  In these digests, there was an accumulation of
      DNA singly nicked at the mismatched recognition site.  The ability of SmaI and
      SstI to partially cleave at a mismatch was shown to depend on the nature and
      position of the mismatch within the corresponding recognition site.  In
      contrast to such partial cleavage, little or no digestion was obtained with
      AccI, HincII, HindIII, and KpnI at their corresponding tested
      mismatch-containing recognition sites.  Therefore, a transition-type
      substitution of only one strand of a recognition site can inhibit restriction
      endonuclease-catalyzed digestion at that site.
AU  - Daigle K
AU  - Shenoy S
AU  - Ehrlich K
AU  - Gehrke C
AU  - Ehrlich M
PT  - Journal Article
TA  - Fed. Proc.
JT  - Fed. Proc.
SO  - Fed. Proc. 1986 45: 1783.

PMID- 11071943
VI  - 28
DP  - 2000
TI  - Hjc resolvase is a distantly related member of the type II restriction endonuclease family.
PG  - 4540-4543
AB  - Hjc resolvase is an archaeal enzyme involved in homologous DNA recombination at the Holliday
      junction intermediate. However, the structure and the catalytic mechanism of the enzyme have
      not yet been identified.  We performed database searching using the amino acid sequence of the
      enzyme from Pyrococcus furiosus as a query. We detected 59 amino acid sequences showing weak
      but significant sequence similarity to the Hjc resolvase. The detected sequences included
      DpnII, HaeII and Vsr endonuclease, which belong to the type II restriction endonuclease
      family. In addition, a highly conserved region was identified from a multiple alignment of the
      detected sequences, which was similar to an active site of the type II restriction
      endonucleases. We substituted three conserved amino acid residues in the highly conserved
      region of the Hjc resolvase with Ala residues. The amino acid replacements inactivated the
      enzyme. The experimental study, together with the results of the database searching, suggests
      that the Hjc resolvase is a distantly related member of the type II restriction endonuclease
      family. In addition, the results of our database searches suggested that the members of the
      RecB domain superfamily are evolutionarily related to the type II restriction endonuclease
      family.
AU  - Daiyasu H
AU  - Komori K
AU  - Sakae S
AU  - Ishino Y
AU  - Toh H
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2000 28: 4540-4543.

PMID- 9720028
VI  - 144
DP  - 1998
TI  - Identification and sequencing of the groE operon and flanking genes of Lawsonia intracellularis: use in phylogeny.
PG  - 2073-2084
AB  - Proliferative enteropathy (PE) is a complex of diseases of commercial importance to the pig
      industry. The obligate intracellular bacterium Lawsonia intracellularis is consistently
      associated with PE and pure cultures of this bacterium have been used to reproduce PE in pigs.
      In this study L. intracellularis bacteria were purified directly from PE-affected tissue. DNA
      extracted from purified bacteria was used to construct a partial genomic library which was
      screened using sera from L. intracellularis-immunized rabbits. Two seroreactive recombinant
      clones were identified, one of which expressed proteins of 10 and 60 kDa. The sequence of the
      insert from this clone, pISI-2, revealed ORFs with sequence similarity to the groES/EL operon
      of Escherichia coli, the 505 ribosomal proteins L21 and L27 of E. coli, a GTP-binding protein
      of Bacillus subtilis and a possible protoporphyrinogen oxidase, HemK, of E. coli. Primers
      designed from unique sequences from the pISI-2 insert amplified DNA from infected, but not
      non-infected, porcine ilea; the amplicon sequence obtained from tissue-cultured L.
      intracellularis was identical to the corresponding sequence in pISI-2, confirming the origin
      of the clone. The sequence of L. intracellularis GroEL and other GroEL sequences in the
      databases were used to construct a partial phylogenetic tree. Analysis of the GroEL sequence
      relationship suggested that L. intracellularis is not significantly related to other organisms
      whose GroEL sequences are held in the databases and supports previous data from 16S sequence
      analyses suggesting that L. intracellularis is a member of a novel group of enteric pathogens.
AU  - Dale CJH
AU  - Moses EK
AU  - Ong CC
AU  - Morrow CJ
AU  - Reed MB
AU  - Hasse D
AU  - Strugnell RA
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 1998 144: 2073-2084.

PMID- 7974743
VI  - 10
DP  - 1994
TI  - Mobile introns and inteins: friend or foe?
PG  - 306-307
AB  - Since the discovery of introns, one question that has puzzled the scientific community has
      been whether these genetic elements are of functional importance to their host organism. One
      theory is that introns are selfish DNA elements whose mobility allows them to overcome
      selection against them. This theory seems especially plausible in the case of mobile group I
      introns, which encode site-specific DNA endonucleases and can invade genomes in a
      site-specific manner via a double-stranded break repair (DSBR) mechanism. Interestingly, it
      has recently been discovered that this mechanism also accounts for the mobility of archael
      introns and inteins, introns that are spliced at the level of the protein, several of which
      have been found in prokaryotic genomes. The discovery that this mechanism of mobility is not
      unique to group I introns and that this family of genetic elements is not limited to the
      genomes of bacteriophages and eurkaryotic nuclear and organelles revives the question of
      whether encoding these 'parasitic' DNA elements confers a selective advantage on the host
      genome.
AU  - Dalgaard JZ
PT  - Journal Article
TA  - Trends Genet.
JT  - Trends Genet.
SO  - Trends Genet. 1994 10: 306-307.

PMID- 1427083
VI  - 121
DP  - 1992
TI  - Protein-coding introns from the 23S rRNA-encoding gene form stable circles in the hyperthermophilic archaeon Pyrobaculum organotrophum.
PG  - 103-110
AB  - Two archaeal introns have been discovered in the single-copy 23S rRNA-encoding gene of the
      hyperthermophile, Pyrobaculum organotrophum.  After excision from rRNA transcripts, both
      introns circularize and are stably retained in the cell.  Putative proteins encoded by the
      introns and covering most of the intron sequence share a decapeptide motif with proteins
      encoded by another archaeal intron and by group I introns.
AU  - Dalgaard JZ
AU  - Garrett RA
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1992 121: 103-110.

PMID- 8390663
VI  - 90
DP  - 1993
TI  - A site-specific endonuclease encoded by a typical archaeal intron.
PG  - 5414-5417
AB  - The protein encoded by the archaeal intron in the 23S rRNA gene of the hyperthermophile
      Desulfurococcus mobilis is a double-strand DNase, that like group I intron homing
      endonucleases, is capable of cleaving an intronless allele of the gene. This enzyme, I-Dmo I,
      is unusual among the intron endonucleases in that it is thermostable and is expressed only
      from linear and cyclized intron species and not from the precursor RNA. However, in analogy to
      its eukaryotic counterparts, but unlike the bacteriophage enzymes, I-Dmo I makes a staggered
      double-strand cut that generates 4-nt 3' extensions. Additionally, although the archaeal and
      group I introns have entirely different structural properties and splicing pathways, I-DmoI
      shares sequence similarity, in the form of the LAGLIDADG motif, with group I intron
      endonucleases of eukaryotes. These observations support the independent evolutionary origin of
      endonucleases and intron core elements and are consistent with the invasive potential of
      endonuclease genes.
AU  - Dalgaard JZ
AU  - Garrett RA
AU  - Belfort M
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1993 90: 5414-5417.

PMID- 7961849
VI  - 269
DP  - 1994
TI  - Purification and characterization of two forms of I-DmoI, a thermophilic site-specific endonuclease encoded by an archaeal intron.
PG  - 28885-28892
AB  - The archaeal intron in the 23 S rRNA gene of the hyperthermophile Desulfurococcus mobilis has
      previously been shown to encode a site-specific DNA endonuclease that contains the LAGLIDADG
      motif. The enzyme, I-DmoI, has been shown to be active in two forms when expressed in vitro,
      from RNAs representing either the linear (I-DmoIl) or circular (I-DmoIc) intron. In this study
      we have overexpressed I-DmoIl and I-DmoIc and purified the enzymes from Escherichia coli. The
      optimal conditions for the enzymatic activity in vitro were determined, and the enzyme was
      used to delimit the recognition boundary on its DNA substrate (14-20 nucleotides), an
      intronless 23 S rRNA gene. Despite belonging to the archaeal kingdom, and being the product of
      a hyperthermophile, I-DmoI shares many properties with LAGLIDADG intron and intein
      endonucleases in other kingdoms. These results support the view that these phylogenetically
      diverse enzymes, which function to mobilize the DNA sequences that encode them, share a common
      ancestry.
AU  - Dalgaard JZ
AU  - Garrett RA
AU  - Belfort M
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1994 269: 28885-28892.

PMID- 9358175
VI  - 25
DP  - 1997
TI  - Statistical modeling and analysis of the LAGLIDADG family of site-specific endonucleases and identification of an intein that encodes a site-specific endonuclease of the HNH family.
PG  - 4626-4638
AB  - The LAGLIDADG and HNH families of site-specific DNA endonucleases encoded by viruses,
      bacteriophages as well as archaeal, eucaryotic nuclear and organellar genomes are
      characterized by the sequence motifs 'LAGLIDADG' and 'HNH', respectively.  These
      endonucleases have been shown to occur in different environments: LAGLIDADG endonucleases are
      found in inteins, archaeal and group I introns and as free standing open reading frames; HNH
      endonucleases occur in group I and group II introns and as ORFs.  Here, statistical models
      (hidden Markov models, HMMs) that encompass both the conserved motifs and more variable
      regions of these families have been created and employed to characterize known and potential
      new family members.  A number of new, putative LAGLIDADG and HNH endonucleases have been
      identified including an intein-encoded HNH sequence.  Analysis of an HMM-generated multiple
      alignment of 130 LAGLIDADG family members and the three-dimensional structure of the I-CreI
      endonuclease has enabled definition of the core elements of the repeated domain (~90 residues)
      that is present in this family of proteins.  A conserved negatively charged residue is
      proposed to be involved in catalysis.  Phylogenetic analysis of the two families indicates a
      lack of exchange of endonucleases between different mobile elements (environments) and between
      hosts from different phylogenetic kingdoms.  However, there does appear to have been
      considerable exchange of endonuclease domains amongst elements of the same type. Such events
      are suggested to be important for the formation of elements of new specificity.
AU  - Dalgaard JZ
AU  - Klar AJ
AU  - Moser MJ
AU  - Holley WR
AU  - Chatterjee A
AU  - Mian IS
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1997 25: 4626-4638.

PMID- 10089530
VI  - 54
DP  - 1998
TI  - Crystallization and preliminary crystallographic analysis of the archaeal intron-encoded endonuclease I-DmoI.
PG  - 1435-1436
AB  - Two forms of the archaeal intron-encoded site-specific endonuclease I-DmoI, namely I-DmoIc and
      I-DmoIl, have been purified and crystallized. Crystals of I-DmoIc are rod-shaped and diffract
      to 3.0 A resolution, but further analysis was hampered by twinning. Crystals of I-DmoIl, which
      is a six-amino-acid C-terminal truncation of I-DmoIc, are plate shaped and belong to space
      group C2 with cell parameters a = 93.72, b = 37.03, c = 55.56 A, beta = 113.4 degrees, with
      one molecule per asymmetric unit (Vm = 2.01 A3 Da-1). The crystals diffract to at least 2.3 A
      resolution. A complete native data set has been measured and structure determination is
      on-going.
AU  - Dalgaard JZ
AU  - Silva GH
AU  - Belfort M
AU  - Van Roey P
PT  - Journal Article
TA  - Acta Crystallogr. D Biol. Crystallogr.
JT  - Acta Crystallogr. D Biol. Crystallogr.
SO  - Acta Crystallogr. D Biol. Crystallogr. 1998 54: 1435-1436.

PMID- 16408089
VI  - 2
DP  - 2006
TI  - Direct transfer of extended groups from synthetic cofactors by DNA methyltransferases.
PG  - 31-32
AB  - S-Adenosyl-L-methionine is the major methyl donor for biological methylation reactions
      catalyzed by methyltransferases.  We report the first chemical synthesis of AdoMet analogs
      with extended carbon chains replacing the methyl group and their evaluation as cofactors for
      all three classes of DNA methyltransferases.  Extended groups containing a double or triple
      bond in the b position to the sulfonium center were transferred onto DNA in a catalytic and
      sequence-specific manner, demonstrating a high utility of such synthetic cofactors for
      targeted functionalization of biopolymers.
AU  - Dalhoff C
AU  - Lukinavicius G
AU  - Klimasauskas S
AU  - Weinhold E
PT  - Journal Article
TA  - Nat. Chem. Biol.
JT  - Nat. Chem. Biol.
SO  - Nat. Chem. Biol. 2006 2: 31-32.

PMID- 17487172
VI  - 1
DP  - 2006
TI  - Synthesis of S-adenosyl-L-methionine analogs and their use for sequence-specific transalkylation of DNA by methyltransferases.
PG  - 1879-1886
AB  - Here we describe a one-step synthetic procedure for the preparation of S-adenosyl-L-methionine
      analogs with extended carbon chains replacing the methyl group.  These AdoMet analogs function
      as efficient cofactors for DNA methyltransferases, and we provide a protocol for
      sequence-specific transfer of extended side chains from these AdoMet analogs to DNA by DNA
      MTases.  Direct chemoselective allylation or propargylation of S-adenosyl-L-homocysteine at
      sulfur is achieved under the acidic conditions needed to protect other nucleophilic positions
      in AdoHcy.  The unsaturated bonds in b position to the sulfonium center of the resulting
      AdoMet analogs are designed to stabilize the transition state formed upon DNA MTase-catalyzed
      nucleophilic attack at the carbon next to the sulfonium center and lead to efficient transfer
      of the extended side chains to DNA.  Using these protocols, sequence-specific functionalized
      DNA can be obtained within one to two weeks.
AU  - Dalhoff C
AU  - Lukinavicius G
AU  - Klimasauskas S
AU  - Weinhold E
PT  - Journal Article
TA  - Nat. Protoc.
JT  - Nat. Protoc.
SO  - Nat. Protoc. 2006 1: 1879-1886.

PMID- 23504020
VI  - 195
DP  - 2013
TI  - Characterization of Undermethylated Sites in Vibrio cholerae.
PG  - 2389-2399
AB  - The activities of DNA methyltransferases are important for a variety of cellular  functions in
      bacteria. In this study, we developed a modified high-throughput
      technique called methyl homopolymer tail mediated sequencing (methyl HTM-seq) to
      identify the undermethylated sites in the Vibrio cholerae genome for the two DNA
      methyltransferases, Dam, an adenine methyltransferase, and VchM, a cytosine
      methyltransferase, during growth in rich medium in vitro. Many of the
      undermethylated sites occurred in intergenic regions, and for most of these
      sites, we identified the transcription factors responsible for undermethylation.
      This confirmed the presence of previously hypothesized DNA-protein interactions
      for these transcription factors and provided insight into the biological state of
      these cells during growth in vitro. DNA adenine methylation has previously been
      shown to mediate heritable epigenetic switches in gene regulation. However, none
      of the undermethylated Dam sites tested showed evidence of regulation by this
      mechanism. This study is the first to identify undermethylated adenines and
      cytosines genomewide in a bacterium using second-generation sequencing
      technology.
AU  - Dalia AB
AU  - Lazinski DW
AU  - Camilli A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2013 195: 2389-2399.

PMID- 21886862
VI  - 4
DP  - 2011
TI  - Complete genome sequence of Haliscomenobacter hydrossis type strain (O).
PG  - 352-360
AB  - Haliscomenobacter hydrossis van Veen et al. 1973 is the type species of the genus
      Haliscomenobacter, which belongs to order 'Sphingobacteriales'. The species is of
      interest because of its isolated phylogenetic location in the tree of life,
      especially the so far genomically uncharted part of it, and because the organism
      grows in a thin, hardly visible hyaline sheath. Members of the species were
      isolated from fresh water of lakes and from ditch water. The genome of H.
      hydrossis is the first completed genome sequence reported from a member of the
      family 'Saprospiraceae'. The 8,771,651 bp long genome with its three plasmids of
      92 kbp, 144 kbp and 164 kbp length contains 6,848 protein-coding and 60 RNA
      genes, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Daligault H et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 4: 352-360.

PMID- 25359907
VI  - 2
DP  - 2014
TI  - Genome Assembly of Shigella flexneri ATCC 12022, a Quality Control Reference Strain.
PG  - e01052-14
AB  - Shigella flexneri causes shigellosis, severe and potentially life-threatening diarrhea, and
      accounts for 18% of shigellosis cases in the United States. Here,
      we present the 4.51-Mbp genome assembly of S. flexneri ATCC 12022, a quality
      control and reference strain, in 10 scaffolds.
AU  - Daligault HE et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01052-14.

PMID- 25301645
VI  - 2
DP  - 2014
TI  - Twenty Whole-Genome Bacillus sp. Assemblies.
PG  - e00958-14
AB  - Bacilli are genetically and physiologically diverse, ranging from innocuous to highly
      pathogenic. Here, we present annotated genome assemblies for 20 strains
      belonging to Bacillus anthracis, B. atrophaeus, B. cereus, B. licheniformis, B.
      macerans, B. megaterium, B. mycoides, and B. subtilis.
AU  - Daligault HE et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00958-14.

PMID- 25278527
VI  - 2
DP  - 2014
TI  - Genome Assembly of Methicillin-Resistant Quality Control Strain Staphylococcus aureus CDC73-57501 (ATCC 29247).
PG  - e00961-14
AB  - Staphylococcus aureus is a major cause of bacterial infections in the United States, with high
      percentages of serious infections resistant to a variety of
      beta-lactam antibiotics. Here, we present the scaffolded genome assembly into 16
      contigs of S. aureus CDC73-57501 (ATCC 29247), a methicillin-resistant quality
      control strain.
AU  - Daligault HE et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00961-14.

PMID- 26744368
VI  - 4
DP  - 2016
TI  - Draft Genomes for Eight Burkholderia mallei Isolates from Turkey.
PG  - e01234-15
AB  - Burkholderia mallei, the etiologic agent of glanders, is a Gram-negative, nonmotile,
      facultative intracellular pathogen. Although glanders has been
      eradicated from many parts of the world, the threat of B. mallei being used as a
      weapon is very real. Here we present draft genome assemblies of 8 Burkholderia
      mallei strains that were isolated in Turkey.
AU  - Daligault HE et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01234-15.

PMID- 25414490
VI  - 2
DP  - 2014
TI  - Whole-Genome Assemblies of 56 Burkholderia Species.
PG  - e01106-14
AB  - Burkholderia is a genus of betaproteobacteria that includes three notable human pathogens: B.
      cepacia, B. pseudomallei, and B. mallei. While B. pseudomallei and
      B. mallei are considered potential biowarfare agents, B. cepacia infections are
      largely limited to cystic fibrosis patients. Here, we present 56 Burkholderia
      genomes from 8 distinct species.
AU  - Daligault HE et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01106-14.

PMID- 25342679
VI  - 2
DP  - 2014
TI  - Whole-Genome Yersinia sp. Assemblies from 10 Diverse Strains.
PG  - e01055-14
AB  - Yersinia spp. are animal pathogens, some of which cause human disease. We sequenced 10
      Yersinia isolates (from six species: Yersinia enterocolitica, Y.
      fredericksenii, Y. kristensenii, Y. pestis, Y. pseudotuberculosis, and Y.
      ruckeri) to high-quality draft or complete status. The genomes range in size from
      3.77 to 4.94 Mbp.
AU  - Daligault HE et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01055-14.

PMID- 25342684
VI  - 2
DP  - 2014
TI  - Complete Genome Assembly of Corynebacterium sp. Strain ATCC 6931.
PG  - e01074-14
AB  - The genus Corynebacterium is best known for the pathogen C. diphtheriae; however, it contains
      mostly commensal and nonpathogenic, as well as several opportunistic,
      pathogens. Here, we present the 2.47-Mb scaffolded assembly of the type strain,
      Corynebacterium sp. ATCC 6931 (NCTC 1914), as deposited into GenBank under
      accession number CP008913.
AU  - Daligault HE
AU  - Davenport KW
AU  - Minogue TD
AU  - Bishop-Lilly KA
AU  - Bruce DC
AU  - Chain PS
AU  - Coyne SR
AU  - Frey KG
AU  - Jaissle J
AU  - Koroleva GI
AU  - Ladner JT
AU  - Li PE
AU  - Meincke L
AU  - Munk AC
AU  - Palacios GF
AU  - Redden CL
AU  - Johnson SL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01074-14.

PMID- 25291763
VI  - 2
DP  - 2014
TI  - Draft Genome Assembly of Klebsiella pneumoniae Type Strain ATCC 13883.
PG  - e00939-14
AB  - Klebsiella pneumoniae is a common cause of antibiotic-resistant bacterial infections in
      immunocompromised individuals. Here, we present the 5.54-Mb
      scaffolded assembly of the type strain K. pneumoniae type strain ATCC 13883, as
      deposited in GenBank under accession no. JOOW00000000.
AU  - Daligault HE
AU  - Davenport KW
AU  - Minogue TD
AU  - Bishop-Lilly KA
AU  - Bruce DC
AU  - Chain PS
AU  - Coyne SR
AU  - Frey KG
AU  - Jaissle J
AU  - Koroleva GI
AU  - Ladner JT
AU  - Lo CC
AU  - Meincke L
AU  - Munk AC
AU  - Palacios GF
AU  - Redden CL
AU  - Johnson SL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00939-14.

PMID- 25237030
VI  - 2
DP  - 2014
TI  - Complete Genome Assembly of a Quality Control Reference Isolate, Moraxella catarrhalis Strain ATCC 25240.
PG  - e00938-14
AB  - Generally an opportunistic pathogen in the United States, Moraxella catarrhalis has acquired
      resistance to multiple antibacterial/antimicrobial agents. Here, we
      present the complete 1.9-Mb genome of M. catarrhalis strain ATCC 25240, as
      deposited in NCBI under the accession number CP008804.
AU  - Daligault HE
AU  - Davenport KW
AU  - Minogue TD
AU  - Bishop-Lilly KA
AU  - Bruce DC
AU  - Chain PS
AU  - Coyne SR
AU  - Frey KG
AU  - Jaissle J
AU  - Koroleva GI
AU  - Ladner JT
AU  - Lo CC
AU  - Meincke L
AU  - Munk C
AU  - Palacios GF
AU  - Redden CL
AU  - Johnson SL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00938-14.

PMID- 25237025
VI  - 2
DP  - 2014
TI  - Draft Genome Assembly of Bordetella bronchiseptica ATCC 10580, a Historical Canine Clinical Isolate.
PG  - e00916-14
AB  - We present the scaffolded genome of Bordetella bronchiseptica ATCC 10580, assembled into 98
      contigs. This 5.1-Mb assembly (68.2% G+C content) contains
      4,870 coding regions. The strain was originally isolated from canine lung tissue
      and is used in quality control testing.
AU  - Daligault HE
AU  - Davenport KW
AU  - Minogue TD
AU  - Bishop-Lilly KA
AU  - Bruce DC
AU  - Chain PS
AU  - Coyne SR
AU  - Frey KG
AU  - Jaissle J
AU  - Koroleva GI
AU  - Ladner JT
AU  - Lo CC
AU  - Meincke L
AU  - Munk C
AU  - Palacios GF
AU  - Redden CL
AU  - Johnson SL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00916-14.

PMID- 25258272
VI  - 2
DP  - 2014
TI  - Draft Genome Assembly of Ralstonia pickettii Type Strain K-288 (ATCC 27853).
PG  - e00973-14
AB  - We present the genome assembly of Ralstonia pickettii K-288 (ATCC 27511), consisting of 27
      contigs placed into a single scaffold. This 4.76-Mbp genome has
      64.0% G+C content and 4,425 coding sequences. Because this is the type strain,
      inclusion of its data set among other Ralstonia genomes should provide a
      historical genomic perspective.
AU  - Daligault HE
AU  - Davenport KW
AU  - Minogue TD
AU  - Broomall SM
AU  - Bruce DC
AU  - Chain PS
AU  - Coyne SR
AU  - Gibbons HS
AU  - Jaissle J
AU  - Lo CC
AU  - Meincke L
AU  - Munk AC
AU  - Rosenzweig CN
AU  - Johnson SL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00973-14.

PMID- 25291774
VI  - 2
DP  - 2014
TI  - Genome Assembly of Serratia marcescens Type Strain ATCC 13880.
PG  - e00967-14
AB  - Serratia marcescens ATCC 13880 is the type strain of the species and a commonly used quality
      control strain. Here, we present the annotated genome assembly of
      5.13 Mbp (59.8% G+C content) as submitted to NCBI under accession no.
      JOVM00000000.
AU  - Daligault HE
AU  - Davenport KW
AU  - Minogue TD
AU  - Broomall SM
AU  - Bruce DC
AU  - Chain PS
AU  - Coyne SR
AU  - Gibbons HS
AU  - Jaissle J
AU  - Rosenzweig CN
AU  - Scholz M
AU  - Teshima H
AU  - Johnson SL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00967-14.

PMID- 10739241
VI  - 9
DP  - 2000
TI  - Substrate-assisted catalysis: Molecular basis and biological significance.
PG  - 1-9
AB  - Substrate-assisted catalysis (SAC) is the process by which a functional group in a substrate
      contributes to catalysis by an enzyme.  SAC has been demonstrated for representatives of three
      major enzyme classes: serine proteases, GTPases, and type II restriction endonucleases, as
      well as lysozyme and hexose-1-phosphate uridylyltransferase.  Morover, structure-based
      predictions of SAC have been made for many additional enzymes.  Examples of SAC include both
      naturally occurring enzymes such as type II restriction endonucleases as well as engineered
      enzymes including serine proteases.  In the latter case, a functional group from a substrate
      can substitute for a catalytic residue replaced by site-directed mutagenesis. From a protein
      engineering perspective, SAC provides a strategy for drastically changing enzyme substrate
      specificity or even the reaction catalyzed.  From a biological viewpoint, SAC contributes
      significantly to the activity of some enzymes and may represent a functional intermediate in
      the evolution of catalysis.  This review focuses on advances in engineering enzyme specificity
      and activity by SAC, together with the biological significance of this phenomenon.
AU  - Dall'Acqua W
AU  - Carter P
PT  - Journal Article
TA  - Protein Sci.
JT  - Protein Sci.
SO  - Protein Sci. 2000 9: 1-9.

PMID- 26988062
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of 'Acidibacillus ferrooxidans' ITV01, a Novel Acidophilic  Firmicute Isolated from a Chalcopyrite Mine Drainage Site in Brazil.
PG  - e01748-15
AB  - Here, we report the draft genome sequence of 'Acidibacillus ferrooxidans' strain  ITV01, a
      ferrous iron- and sulfide-mineral-oxidizing, obligate heterotrophic, and
      acidophilic bacterium affiliated with the phylum Firmicutes. Strain ITV01 was
      isolated from neutral drainage from a low-grade chalcopyrite from a mine in
      northern Brazil.
AU  - Dall'Agnol H
AU  - Nancucheo I
AU  - Johnson DB
AU  - Oliveira R
AU  - Leite L
AU  - Pylro VS
AU  - Holanda R
AU  - Grail B
AU  - Carvalho N
AU  - Nunes GL
AU  - Tzotzos G
AU  - Fernandes GR
AU  - Dutra J
AU  - Orellana SC
AU  - Oliveira G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01748-15.

PMID- 27811087
VI  - 4
DP  - 2016
TI  - Genome Sequence of Paraburkholderia nodosa Strain CNPSo 1341, a N2-Fixing Symbiont of the Promiscuous Legume Phaseolus vulgaris.
PG  - e01073-16
AB  - Paraburkholderia nodosa CNPSo 1341 is a N2-fixing symbiont of Phaseolus vulgaris  isolated
      from an undisturbed soil of the Brazilian Cerrado. Its draft genome
      contains 8,614,032 bp and 8,068 coding sequences (CDSs). Nodulation and
      N2-fixation genes were clustered in the genome that also contains several genes
      of secretion systems and quorum sensing.
AU  - Dall'Agnol RF
AU  - Costa MR
AU  - Ribeiro RA
AU  - Delamuta JR
AU  - Chueire LM
AU  - Hungria M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01073-16.

PMID- 27417831
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of the Hyperthermophilic and Piezophilic Archeon Thermococcus piezophilus CDGST, Able To Grow under Extreme Hydrostatic Pressures.
PG  - e00610-16
AB  - We report the genome sequence of Thermococcus superprofundus strain CDGS(T), a new piezophilic
      and hyperthermophilic member of the order Thermococcales isolated
      from the world's deepest hydrothermal vents, at the Mid-Cayman Rise. The genome
      is consistent with a heterotrophic, anaerobic, and piezophilic lifestyle.
AU  - Dalmasso C
AU  - Oger P
AU  - Courtine D
AU  - Georges M
AU  - Takai K
AU  - Maignien L
AU  - Alain K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00610-16.

PMID- 
VI  - 0
DP  - 1987
TI  - Mechanisms of bacteriophage insensitivity in the lactic streptococci.
PG  - 259-268
AB  - The mesophilic lactic streptococci, which comprise Streptococcus cremoris, S. lactis, and S.
      lactis subsp. diacetylactis, are of major industrial importance as components of starter
      cultures used in the manufacture of a variety of fermented dairy products, e.g., cheeses,
      lactic butter, cultured buttermilk, sour cream, and quarg.  Bacteriophage attack has been
      recognized since the 1930s as the most serious cause of starter culture inhibition in
      commercial practice.  The consequence may be significant economic loss due to downgrading of
      product or, in severe cases, total loss of the fermentation.  The vulnerability of dairying,
      in contrast to other modern industrial fermentations, to phages exists partly because the
      substrate, milk, cannot be sterilized for biochemical reasons, and in addition, the starter
      culture must perform in large mechanized and automated units that demand consistent,
      predictable acid production to ensure high-quality end products with the desired flavor and
      texture characteristics.
AU  - Daly C
AU  - Fitzgerald G
PT  - Journal Article
TA  - Streptococcal Genetics
JT  - Streptococcal Genetics
SO  - Streptococcal Genetics 1987 0: 259-268.

PMID- 8879402
VI  - 70
DP  - 1996
TI  - Biotechnology of lactic acid bacteria with special reference to bacteriophage resistance.
PG  - 99-110
AB  - Lactic acid bacteria play an important role in many food and feed fermentations.  In recent
      years major advances have been made in unravelling the genetic and molecular basis of
      significant industrial traits of lactic acid bacteria.  Bacteriophages which can infect and
      destroy lactic acid bacteria pose a particularly serious threat to dairy fermentations that
      can result in serious economic losses.  Consequently, these organisms and the mechanisms by
      which they interact with their hosts have received much research attention.  This paper
      reviews some of the key discoveries over the years that have led us to our current
      understanding of bacteriophages themselves and the means by which their disruptive influence
      may be minimized.
AU  - Daly C
AU  - Fitzgerald GF
AU  - Davis R
PT  - Journal Article
TA  - Antonie Van Leeuwenhoek
JT  - Antonie Van Leeuwenhoek
SO  - Antonie Van Leeuwenhoek 1996 70: 99-110.

PMID- 17373858
VI  - 5
DP  - 2007
TI  - Protein Oxidation Implicated as the Primary Determinant of Bacterial Radioresistance.
PG  - e92
AB  - In the hierarchy of cellular targets damaged by ionizing radiation (IR), classical models of
      radiation toxicity place DNA at the top. Yet, many
      prokaryotes are killed by doses of IR that cause little DNA damage. Here
      we have probed the nature of Mn-facilitated IR resistance in Deinococcus
      radiodurans, which together with other extremely IR-resistant bacteria
      have high intracellular Mn/Fe concentration ratios compared to
      IR-sensitive bacteria. For in vitro and in vivo irradiation, we
      demonstrate a mechanistic link between Mn(II) ions and protection of
      proteins from oxidative modifications that introduce carbonyl groups.
      Conditions that inhibited Mn accumulation or Mn redox cycling rendered D.
      radiodurans radiation sensitive and highly susceptible to protein
      oxidation. X-ray fluorescence microprobe analysis showed that Mn is
      globally distributed in D. radiodurans, but Fe is sequestered in a region
      between dividing cells. For a group of phylogenetically diverse
      IR-resistant and IR-sensitive wild-type bacteria, our findings support the
      idea that the degree of resistance is determined by the level of oxidative
      protein damage caused during irradiation. We present the case that
      protein, rather than DNA, is the principal target of the biological action
      of IR in sensitive bacteria, and extreme resistance in Mn-accumulating
      bacteria is based on protein protection.
AU  - Daly MJ
AU  - Gaidamakova EK
AU  - Matrosova VY
AU  - Vasilenko A
AU  - Zhai M
AU  - Leapman RD
AU  - Lai B
AU  - Ravel B
AU  - Li SM
AU  - Kemner KM
AU  - Fredrickson JK
PT  - Journal Article
TA  - PLoS Biology
JT  - PLoS Biology
SO  - PLoS Biology 2007 5: e92.

PMID- 22504811
VI  - 78
DP  - 2012
TI  - Complete Sequence Analysis of Two Methanotroph-Specific repABC-Containing Plasmids from Methylocystis sp. Strain SC2.
PG  - 4373-4379
AB  - The complete nucleotide sequences of two large, low-copy-number plasmids of 229.6
      kb (pBSC2-1) and 143.5 kb (pBSC2-2) were determined during assembly of the
      whole-genome shotgun sequences of the methane-oxidizing bacterium Methylocystis
      sp. strain SC2. The physical existence of the two plasmids in strain SC2 was
      confirmed by pulsed-field gel electrophoresis followed by Southern hybridization.
      Both plasmids have a conserved replication module of the repABC system and carry
      genes involved in their faithful maintenance and conjugation. In addition, they
      contain genes that might be involved in essential metabolic processes. These
      include several heavy metal resistance genes and copper transport genes in
      pBSC2-1 and a complete nitrous oxide reductase operon and a pmoC singleton in
      pBSC2-2, the latter encoding the PmoC subunit of particulate methane
      monooxygenase.
AU  - Dam B
AU  - Kube M
AU  - Dam S
AU  - Reinhardt R
AU  - Liesack W
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2012 78: 4373-4379.

PMID- 17371843
VI  - 27
DP  - 2007
TI  - Biological functions of DNA methyltransferase 1 require its methyltransferase activity.
PG  - 3891-3899
AB  - DNA methyltransferase 1 (DNMT1) has been reported to interact with a wide variety of factors
      and to contain intrinsic transcriptional
      repressor activity. When a conservative point mutation was introduced
      at the key catalytic residue, mutant DNMT1 failed to rescue any of the
      phenotypes of Dnmt1-null embryonic stem (ES) cells, which indicated
      that the biological functions of DNMT1 are exerted through the
      methylation of DNA. ES cells that expressed the mutant protein did not
      survive differentiation. Intracisternal A-particle family
      retrotransposons were no longer methylated and were transcribed at high
      levels. The proper localization of DNMT1 depended on normal genomic
      methylation, and we discuss the implications of this finding for
      epigenetic dysregulation in cancer.
AU  - Damelin M
AU  - Bestor TH
PT  - Journal Article
TA  - Mol. Cell. Biol.
JT  - Mol. Cell. Biol.
SO  - Mol. Cell. Biol. 2007 27: 3891-3899.

PMID- Not carried by PubMed...
VI  - 88
DP  - 1988
TI  - Characterization of a restriction enzyme isolated from a hydrothermal vent community bacterium, Hyphomonas jannaschiana.
PG  - 213
AB  - A restriction endonuclease has been isolated and purified from Hyphomonas
      jannaschiana.  The enzyme, HjaI, was purified using an FPLC equipped with a
      Mono Q column.  Yields of several thousand units of enzyme activity per gram of
      cells were obtained.  Optimal activity was achieved in 25 mM Tris-HCl (pH-7.8),
      100 mM NaCl, 10 mM MgCl/2, 100 micro g/ml BSA, 2 mM 2-mercaptoethanol at 37C.
      This enzyme was inactivated by incubation at 65C.  By comparing the
      fragmentation patterns of pBR322 and lambda DNA to computer generated patterns
      provided by New England Biolabs, the recognition sequence was found to be
      GATATC.  HjaI is an isoschizomer of EcoRV.  Cleavage of DNA by this enzyme
      produced blunt ended fragments.  Furthermore, DNA isolated from H. jannaschiana
      was not cleaved by EcoRV.
AU  - Danaher R
AU  - Stein DC
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1988 88: 213.

PMID- Not carried by PubMed...
VI  - 0
DP  - 1988
TI  - Characterization of a restriction endonuclease and the cloning of its corresponding DNA methylase from the thermal vent bacterium Hyphomonas jannaschiana.
PG  - 25
AB  - The marine bacterium H. jannaschiana produces a restriction enzyme, HjaI, that
      was purified by column chromatography.  Maximal enzyme activity occurred in 25
      mM Tris-HCl (pH-9.0), 100 mM NaCl, 10 mM MgCl2, 100 micrograms/ml BSA, 2 mM
      2-mercaptoethanol at 37C.  The recognition sequence was found to be GATATC, as
      determined by comparing banding patterns obtained after digesting lambda DNA
      with those predicted from its DNA sequence.  HjaI produces blunt ended DNA
      fragments, as measured by a digestion/ligation scheme.  DNA isolated from H.
      jannaschiana was not cleaved by EcoRV, an isoschizomer of HjaI.  The
      corresponding methylase (M.HjaI) was cloned into E. coli methylase accepting
      host (DH5 mcr).  H. jannaschiana chromosomal DNA was partially digested with
      and inserted into the PstI site of pBR322.  Plasmid DNA was isolated from the
      entire gene bank, digested with EcoRV, and transformed back into DH5 mcr.
      M.HjaI clones were identified based on their plasmid DNA being partially
      protected against cleavage by EcoRV.  Several plasmids were identified that
      were partially resistant to EcoRV, and all shared a common 8 Kb PstI fragment.
AU  - Danaher R
AU  - Stein DC
PT  - Journal Article
TA  - Abstr. 1st Intl. Symp. Marine Mol. Biol.
JT  - Abstr. 1st Intl. Symp. Marine Mol. Biol.
SO  - Abstr. 1st Intl. Symp. Marine Mol. Biol. 1988 0: 25.

PMID- 2197177
VI  - 89
DP  - 1990
TI  - Expression of cloned restriction and modification genes, hjaIRM from Hyphomonas jannaschiana in Escherichia coli.
PG  - 129-133
AB  - A type-II RM system, HjaI, was identified in the marine bacterium, Hyphomonas
      jannaschiana.  The ENase recognizes GATATC, and DNA fragments generated after
      cleavage with this enzyme contain blunt ends.  A DNA fragment encoding these
      enzymes was cloned and expressed in Escherichia coli, although the level of
      expression of the cloned genes was low.  DNA methylated by M.HjaI was not
      restricted by the Mcr or Mrr restriction systems of E. coli.  Although H.
      jannaschiana is a marine bacterium isolated near the thermal vents on the floor
      of the Pacific Ocean, the biochemical properties of the ENase were similar to
      those of EcoRV, an isoschizomer isolated from E. coli.
AU  - Danaher RJ
AU  - Stein DC
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1990 89: 129-133.

PMID- 29301890
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Rhodococcus sp. Strain NCIMB 12038, a Naphthalene-Degrading Bacterium.
PG  - e01420-17
AB  - We report here the draft genome sequence of Rhodococcus sp. strain NCIMB 12038, an
      industrially important bacterium, possessing a large and diverse repertoire of
      genes involved in the biotransformation of various organic compounds, including
      naphthalene.
AU  - Dandare SU
AU  - Skvortsov T
AU  - Arkhipova K
AU  - Allen CCR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01420-17.

PMID- 10954595
VI  - 28
DP  - 2000
TI  - Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames.
PG  - 3278-3288
AB  - Four years after the original sequence submission, we have re-annotated the genome of
      Mycoplasma pneumoniae to incorporate novel data. The total number of ORFs has been increased
      from 677 to 688 (10 new proteins were predicted in intergenic regions, two further were newly
      identified by mass spectrometry and one protein ORF was dismissed) and the number of RNAs from
      39 to 42 genes. For 19 of the now 35 tRNAs and for six other functional RNAs the exact genome
      positions were re-annotated and two new tRNA(Leu) and a small 200 nt RNA were identified.
      Sixteen protein reading frames were extended and eight shortened. For each ORF a consistent
      annotation vocabulary has been introduced. Annotation reasoning, annotation categories and
      comparisons to other published data on M. pneumoniae functional assignments are given.
      Experimental evidence includes 2-dimensional gel electrophoresis in combination with mass
      spectrometry as well as gene expression data from this study. Compared to the original
      annotation, we increased the number of proteins with predicted functional features from 349 to
      458. The increase includes 36 new predictions and 73 protein assignments confirmed by the
      published literature. Furthermore, there are 23 reductions and 30 additions with respect to
      the previous annotation. mRNA expression data support transcription of 184 of the functionally
      unassigned reading frames.
AU  - Dandekar T
AU  - Huynen M
AU  - Regula JT
AU  - Ueberle B
AU  - Zimmermann CU
AU  - Andrade MA
AU  - Doerks T
AU  - Sanchez-Pulido L
AU  - Snel B
AU  - Suyama M
AU  - Yuan YP
AU  - Herrmann R
AU  - Bork P
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2000 28: 3278-3288.

PMID- 25540353
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Violacein-Producing Marine Bacterium Pseudoalteromonas sp. 520P1.
PG  - e01346-14
AB  - Here, we report a draft 5.25-Mb genome sequence of Pseudoalteromonas sp. 520P1, a marine
      violacein-producing bacterium isolated from the Pacific coast of Japan.
      Genome annotation by BLAST searches revealed the presence of one acylhomoserine
      lactone (AHL) synthase (luxI) and five AHL receptor protein (luxR) gene homologs.
AU  - Dang HT
AU  - Yotsumoto K
AU  - Enomoto K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01346-14.

PMID- 2832380
VI  - 170
DP  - 1988
TI  - Distribution and diversity of hsd genes in Escherichia coli and other enteric bacteria.
PG  - 1775-1782
AB  - We screened Salmonella typhimurium, Citrobacter freundii, Klebsiella
      pneumoniae, Shigella boydii, and many isolates of Escherichia coli for DNA
      sequences homologous to those encoding each of two unrelated type I restriction
      and modification systems (EcoK and EcoA).  Both K- and A-related hsd genes were
      identified, but never both in the same strain.  S. typhimurium encodes three
      restriction and modification systems, but its DNA hybridized only to the
      K-specific probe which we know to identify the StySB system.  No homology to
      either probe was detected in the majority of E. coli strains, but in C.
      freundii, we identified homology to the A-specific probe.  We cloned this
      region of the C. freundii genome and showed that it encoded a functional,
      A-related restriction system whose specificity differs from those of known type
      I enzymes.  Sequences immediately flanking the hsdK genes of E.coli K-12 and
      the hsdA genes of E. coli 15T- were shown to be homologous, indicating similar
      or even identical positions in their respective chromosomes.  E. coli C has no
      known restriction system, and the organization of its chromosome is consistent
      with deletion of the three hsd genes and their neighbor, mcrB.
AU  - Daniel AS
AU  - Fuller-Pace FV
AU  - Legge DM
AU  - Murray NE
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1988 170: 1775-1782.

PMID- 28619812
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Six Enterococcus faecalis Strains Isolated from Malaysian Clinical and Environmental Origins.
PG  - e00553-17
AB  - Enterococcus faecalis is known to cause a variety of nosocomial infections, including urinary
      tract infections. Antibiotic resistance and virulence
      properties in this species are of public concern. The draft genome sequences of
      six E. faecalis strains isolated from clinical and environmental sources in
      Malaysia are presented here.
AU  - Daniel DS
AU  - Gan HM
AU  - Lee SM
AU  - Dykes GA
AU  - Rahman S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00553-17.

PMID- 26586892
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Prosthecomicrobium hirschii ATCC 27832T.
PG  - e01355-15
AB  - We report the draft genome sequence of Prosthecomicrobium hirschii ATCC 27832T, an
      alphaproteobacterium with remarkable cellular morphologies. The chromosome
      comprises 6,484,983 bp in six scaffolds with a G+C content of 69%, and 6,066
      potential coding sequences.
AU  - Daniel JJ
AU  - Givan SA
AU  - Brun YV
AU  - Brown PJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01355-15.

PMID- Not carried by PubMed...
VI  - 208
DP  - 1994
TI  - Specificity of DNA cleavage by the type IIs restriction enzyme, HphI.
PG  - 66
AB  - Type IIs restriction enzymes are DNA-cleaving proteins that bind to short (4-8 base pair)
      sequences of double-helical DNA and cleave at positions distant from the recognition site.
      HphI is a type IIs restriction enzyme that recognizes the nonpalindromic sequence
      5'-GGTGA-3' and is reported to hydrolyze the DNA backbone 8/7 base pairs away from the
      recognition site. We will report interesting effects of varying substrate size and sequence on
      the DNA-cleavage reaction of HphI.
AU  - Daniels JS
AU  - Gates KS
PT  - Journal Article
TA  - ACS Abstracts
JT  - ACS Abstracts
SO  - ACS Abstracts 1994 208: 66.

PMID- 12634054
VI  - 327
DP  - 2003
TI  - Subunit assembly for DNA cleavage by restriction endonuclease SgrAI.
PG  - 579-591
AB  - The SgrAI endonuclease usually cleaves DNA with two recognition sites more rapidly than DNA
      with one site, often converting the former directly to
      the products cut at both sites. In this respect, SgrAI acts like the
      tetrameric restriction enzymes that bind two copies of their target sites
      before cleaving both sites concertedly. However, by analytical
      ultracentrifugation, SgrAI is a dimer in solution though it aggregates to
      high molecular mass species when bound to its specific DNA sequence. Its
      reaction kinetics indicate that it uses different mechanisms to cleave DNA
      with one and with two SgrAI sites. It cleaves the one-site DNA in the
      style of a dimeric restriction enzyme acting at an individual site,
      mediating neither interactions in trans, as seen with the tetrameric
      enzymes, nor subunit associations, as seen with the monomeric enzymes. In
      contrast, its optimal reaction on DNA with two sites involves an
      association of protein subunits: two dimers bound to sites in cis may
      associate to form a tetramer that has enhanced activity, which then
      cleaves both sites concurrently. The mode of action of SgrAI differs from
      all restriction enzymes characterised previously, so this study extends
      the range of mechanisms known for restriction endonucleases.
AU  - Daniels LE
AU  - Wood KM
AU  - Scott DJ
AU  - Halford SE
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2003 327: 579-591.

PMID- Not included in PubMed...
VI  - 10
DP  - 1984
TI  - Restriction and modification of halophage S45 in Halobacterium.
PG  - 133-136
AB  - A newly isolated group B1 bacteriophage, Halophage S45, is restricted and
      modified in vivo by strains of Halobacterium.  Three strain-specific activities
      have been observed.  Two of these occur in the same bacterial strain and appear
      to be due to different kinds of enzymatic activities.  One of the restriction
      specificities is shown to be associated with a strain-specific endonuclease
      active on unmodified halobacterial DNA.
AU  - Daniels LL
AU  - Wais AC
PT  - Journal Article
TA  - Curr. Microbiol.
JT  - Curr. Microbiol.
SO  - Curr. Microbiol. 1984 10: 133-136.

PMID- 10495945
VI  - 35
DP  - 1999
TI  - The plasmid carrying a temperature-sensitive mutation in the DNA-methylase gene of the PstI system: Effect on host cells at nonpermissive temperature.
PG  - 574-586
AB  - Temperature-sensitive (ts) derivatives of plasmid pRMP1, a derivative of PBR322 containing
      restriction and modification (RM) genes of the PstI system, were obtained using hydroxylamine
      mutagenesis. One of the isolated plasmids responsible for the inhibition of Escherichia coli
      cell growth at 42 degrees C, pRMPts, was analyzed in this work. Cells of Rec+ strains carrying
      this plasmid were unable to divide at 42 degrees C and formed long non-septated filaments that
      died upon prolonged cultivation. Cells of the RecA- strains carrying pRMPts did not form
      filaments at 42 degrees C and rapidly disappeared. On agar media with or without ampicillin,
      Rec+ and RecA- strains with this plasmid formed colonies of temperature-resistant (tr)
      derivatives with frequencies ranging from 1.5 x 10^-4 to 4 x 10^-6 in independent clones. The
      structure of plasmids from cells of tr- derivatives of Rec+ and RecA- strains carrying plasmid
      pRMPts was analyzed by the set of restriction enzymes. Reversions to the temperature-resistant
      phenotype were shown to result from the following events: (1) the insertional inactivation of
      the PstI restriction enzyme gene in pRMPts (the insertion of the IS1 element); (2) deletions
      in plasmid DNA fragments that partially or completely cover the restriction enzyme gene; (3)
      point mutations; and (4) others. The effect of the chromosomal sulA mutation on the
      maintenance of the ts-plasmid in bacterial cells was studied at 42 degrees C. High efficiency
      loss of the plasmid was detected in pRMPts-carrying Rec+ cells with the sulA::Tn5 mutation
      grown in liquid and solid nutrient media at this temperature.  Under similar conditions,
      plasmid loss was not detected in SulA+ cells. On the basis of the data obtained, it is
      concluded that the ts-mutation is located in the DNA-methylase gene of plasmid pRMPts. Mutant
      DNA methylase was unable to methylate all sites in the chromosomal DNA at 42 degrees C. Some
      of the unmethylated sites can be digested with the PstI enzyme, which leads to the induction
      of SOS response in Rec+ cells or to total mortality in cells with the recA phenotype.
AU  - Danilevich VN
AU  - Livshits VA
PT  - Journal Article
TA  - Genetika
JT  - Genetika
SO  - Genetika 1999 35: 574-586.

PMID- 23599289
VI  - 1
DP  - 2013
TI  - Genome Sequence of the Pathogenic Bacterium Vibrio vulnificus Biotype 3.
PG  - e00136-13
AB  - We report the first genome sequence of the pathogenic Vibrio vulnificus biotype 3. This draft
      genome sequence of the environmental strain VVyb1(BT3), isolated in
      Israel, provides a representation of this newly emerged clonal group, which
      reveals higher similarity to the clinical strains of biotype 1 than to the
      environmental ones.
AU  - Danin-Poleg Y
AU  - Elgavish S
AU  - Raz N
AU  - Efimov V
AU  - Kashi Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00136-13.

PMID- 26205875
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Environmental Bacterium Vibrio vulnificus CladeA-yb158.
PG  - e00754-15
AB  - We report the genome sequence of the environmental Vibrio vulnificus biotype 1_cladeA. This
      draft genome of the CladeA-yb158 strain, isolated in Israel,
      represents this newly emerged clonal group that contains both clinical and
      environmental strains.
AU  - Danin-Poleg Y
AU  - Raz N
AU  - Roig FJ
AU  - Amaro C
AU  - Kashi Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00754-15.

PMID- 25301654
VI  - 2
DP  - 2014
TI  - Genome Sequence of Nitratireductor basaltis Strain UMTGB225, a Marine Bacterium Isolated from a Green Barrel Tunicate in Bidong Island, Malaysia.
PG  - e01015-14
AB  - Nitratireductor basaltis strain UMTGB225 is a Gram-negative bacterium isolated from a marine
      tunicate found in Bidong Island, Terengganu, Malaysia. In this
      study, the genome of Nitratireductor basaltis UMTGB225 was sequenced to gain
      insight into the role of this bacterium and its association with tunicate hosts
      in a coral reef habitat.
AU  - Danish-Daniel M
AU  - Gan HY
AU  - Gan HM
AU  - Saari NA
AU  - Usup G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01015-14.

PMID- 27795265
VI  - 4
DP  - 2016
TI  - Genome Sequence of Bacillus sp. Strain UMTAT18 Isolated from the Dinoflagellate Alexandrium tamiyavanichii Found in the Straits of Malacca.
PG  - e01106-16
AB  - Bacillus sp. strain UMTAT18 was isolated from the harmful dinoflagellate Alexandrium
      tamiyavanichii Its genome consists of 5,479,367 bp with 5,546 open
      reading frames, 102 tRNAs, and 29 rRNAs. Gene clusters for biosynthesis of
      nonribosomal peptides, bacteriocin, and lantipeptide were identified. It also
      contains siderophore and genes related to stress tolerance.
AU  - Danish-Daniel M
AU  - Ming GH
AU  - Mohd NME
AU  - Sung YY
AU  - Usup G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01106-16.

PMID- 4332003
VI  - 68
DP  - 1971
TI  - Specific cleavage of simian virus 40 DNA by restriction endonuclease of Hemophilus influenzae.
PG  - 2913-2917
AB  - A bacterial restriction endonuclease has been used to produce specific
      fragments of SV40 DNA.  Digestion of DNA from plaque-purified stocks of SV40
      with the restriction endonuclease from Hemophilus influenzae gave ll fragments
      resolvable by polyacrylamide gel electrophoresis, eight of which were equimolar
      with the original DNA.  The fragments ranged from about 6.5 x 10/5 to 7.4 x
      10/4 daltons, as determined by electron microscopy, DNA content, or
      electrophoretic mobility.
AU  - Danna K
AU  - Nathans D
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1971 68: 2913-2917.

PMID- 
VI  - 154
DP  - 2010
TI  - Daniel Nathans.
PG  - 338-354
AB  - Dr. Daniel Nathans, the brilliant and reticent Nobel Prize-winning scientist who was regarded
      by many of his peers as the conscience of the Johns Hopkins University, died on 16 November
      1999 of leukemia at his home.  He was seventy-one.  Proud and passionate about ideas, Dr.
      Nathans helped Hopkins sustain its sense of tradition during a time that brought wrenching
      changes to academic medical centers.  In addition to reaching and conducting research, Dr.
      Nathans served the university as a valued adviser and interim president.  "He was the wise man
      of the medical center and he was seen that way," said former Hopkins medical dean Michael M.E.
      Johns, now chancellor for health affairs at Emory University in Atlanta.  "He walked quietly
      but carried the responsibility of the respect he had very, very thoughtfully."  Dr. William R.
      Broady, president of the Johns Hopkins University, said, "Dan Nathans was an extraordinary
      human being.  He was brilliant, of course... But as one who had the privilege of knowing Dan
      well, I was always most impressed with the man - modest, soft-spoken, unassuming, even
      self-effacing." Colleagues described Dr. Nathans as a man who taught by example and by
      encouragement, and as a researcher of vision and intellectual vigor.  "The great scientist can
      separate the wheat from the chaff.  One of the great things in research is to know what
      questions to ask, what subjects to focus on," said Dr. Solomon H. Snyder, the director of
      Hopkins's neuroscience department.  "He would ask the very best questions."
AU  - Danna KJ
PT  - Journal Article
TA  - Proc. Amer. Phil. Soc.
JT  - Proc. Amer. Phil. Soc.
SO  - Proc. Amer. Phil. Soc. 2010 154: 338-354.

PMID- 4343955
VI  - 69
DP  - 1972
TI  - Bidirectional replication of simian virus 40 DNA.
PG  - 3097-3100
AB  - SV40 (Simian Virus 40) DNA was pulse-labeled with [3H]thymidine in infected
      monkey cells, and the distribution of label within newly completed molecules
      was determined by analysis of specific fragments produced by restriction
      endonuclease from Hemophilus influenzae.  From these data, an order of
      synthesis or temporal order of the fragments was deduced.  Comparison of the
      temporal order with the physical order of the fragments in the SV40 DNA
      molecule indicates a correspondence in thehse orders for two separate groups of
      fragments.  From an analysis of the results, we conclude that SV40 DNA
      replication begins at a specific site and proceeds bidirectionally, terminating
      about halfway around the circular molecule from the initiation point.
AU  - Danna KJ
AU  - Nathans D
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1972 69: 3097-3100.

PMID- 28357980
VI  - 66
DP  - 2017
TI  - Manual curation and reannotation of the genomes of Clostridium difficile 630Deltaerm and C. difficile 630.
PG  - 286-293
AB  - PURPOSE: We resequenced the genome of Clostridium difficile 630Deltaerm (DSM
      28645), a model strain commonly used for the generation of insertion mutants.
      METHODOLOGY: The genome sequence was obtained by a combination of single-molecule
      real-timeand Illumina sequencing technology. RESULTS: Detailed manual curation
      and comparison to the previously published genomic sequence revealed sequence
      differences including inverted regions and the presence of plasmid pCD630. Manual
      curation of our previously deposited genome sequence of the parental strain 630
      (DSM 27543) led to an improved genome sequence. In addition, the sequence of the
      transposon Tn5397 was completely identified. We manually revised the current
      manual annotation of the initial sequence of strain 630 and modified either gene
      names, gene product names or assigned EC numbers of 57 % of genes. The number of
      hypothetical and conserved hypothetical proteins was reduced by 152. This
      annotation was used as a template to annotate the most recent genome sequences of
      the strains 630Deltaerm and 630. CONCLUSION: Based on the genomic analysis,
      several new metabolic features of C. difficile are proposed and could be
      supported by literature and subsequent experiments.
AU  - Dannheim H
AU  - Riedel T
AU  - Neumann-Schaal M
AU  - Bunk B
AU  - Schober I
AU  - Sproer C
AU  - Chibani CM
AU  - Gronow S
AU  - Liesegang H
AU  - Overmann J
AU  - Schomburg D
PT  - Journal Article
TA  - J. Med. Microbiol.
JT  - J. Med. Microbiol.
SO  - J. Med. Microbiol. 2017 66: 286-293.

PMID- 24371205
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Pediococcus pentosaceus Strain SL4.
PG  - e01106-13
AB  - Pediococcus pentosaceus SL4 was isolated from a Korean fermented vegetable product, kimchi. We
      report here the whole-genome sequence (WGS) of P. pentosaceus
      SL4. The genome consists of a 1.79-Mb circular chromosome (G+C content of 37.3%)
      and seven distinct plasmids ranging in size from 4 kb to 50 kb.
AU  - Dantoft SH
AU  - Bielak EM
AU  - Seo JG
AU  - Chung MJ
AU  - Jensen PR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01106-13.

PMID- Not carried by PubMed...
VI  - 53
DP  - 1993
TI  - Analysis of a protein: DNA interface; the effect of altered DNA substrates on EcoRI methylase function.
PG  - 5180B
AB  - EcoRI methyltransferase (MTase) binds to its double stranded recognition site 5'-GAATTC-3'

      and methylates it at the inner adenosine of each strand using S-adenosyl-L-methionine as the

      methyl donor. The Mtase is unperturbed by hemi-methylation at either inner adenosine in

      synthetic substrates, facilitating the study of substrates harboring modified bases at unique

      positions. Using this strategy the contributions of the N2 amino groups of guanosine and the

      C5 methyl groups of thymine toward specificity were investigated.

      

      As a result largely of changes in KM-DNA, deoxyinosine substitution for guanosine at either

      position in the M.EcoRI recognition site reduces the specificity constant (kcat/KM-DNA) 13 and

      39 fold. Thus methylation, which occurs in the major groove, is sensitive to both of these

      minor groove modifications. The specificity constant obtained from the double substituted

      substrate (14 fold below the control) indicates that there may be structural "communication"

      between these sites.

      

      The MTase is insensitive to removal of either one of the outer methyl groups by substitution

      of deoxyuridine for the outer thymine residues. When either the inner thymine residue opposite

      the hemi-methylation or both inner thymidine residues are substituted with deoxyuridine, the

      KM-DNA is 5 to 10 times larger than for the control substrate leading to a specificity

      constant that is 2 to 9 times larger.

      

      Comparisons of entropic and enthalpic data clearly show that there are structural

      perturbations within all of these modified substrates.

      

      The results indicate that not only are there effects of functional group removal on MTase

      function, but also structural change in the substrate beyond the altered residue is observed.

      Substitutions which reduce enzyme specificity were coupled with ones that are fairly silent in

      several different combinations. The resulting substrate could not only regain some of its lost

      specificity, but could also become a better substrate than the control. Thus, structural

      changes within the DNA substrate caused by functional group alterations can have a more

      profound effect on specificity than the removal of a protein:DNA contact.

      

AU  - Danzitz MJ
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1993 53: 5180B.

PMID- Not carried by PubMed...
VI  - 196
DP  - 1988
TI  - Investigations of EcoRI methylase contacts with its DNA substrate.
PG  - 95
AB  - The interactions between DNA binding proteins and their DNA substrates have
      been analyzed by many researchers during the past decade.  Much of this
      interest stems from the fact that DNA binding proteins are involved in a myriad
      of biologically significant events.  The monomeric EcoRI methylase recognizes
      the double stranded DNA sequence GAATTC and methylates the second adenine of
      this site.  This methylation event protects the site from cleavage by the
      corresponding dimeric endonuclease.  The portion of the DNA substrate which is
      protected by EcoRI methylase binding has been determined with the use of the
      hydroxyl radical DNA footprinting technique.  The ability of this enzyme to
      discriminate its preferred recognition site from modified sites has also been
      investigated kinetically by comparisons of specificity constants (kcat/Km).
AU  - Danzitz MJ
AU  - Reich NO
PT  - Journal Article
TA  - ACS Abstracts
JT  - ACS Abstracts
SO  - ACS Abstracts 1988 196: 95.

PMID- 2927145
VI  - 13D
DP  - 1989
TI  - Characterization of a protein-DNA interface:  DNA substrate functionalties important for EcoRI methylase specificity.
PG  - 84
AB  - EcoRI methylase is a monomeric 38,050 dalton enzyme requiring the cofactor
      S-adenosylmethionine (AdoMet) and its DNA substrate for activity.  The methylase recognizes
      the double stranded DNA sequence 5'-GAATTC-3' and methylates the second adenine of each
      strand.  Details about the DNA protein interface of a DNA methylase or any monomeric DNA
      binding protein have yet to be determined.  Hydroxyl radical footprinting experiments of
      recognition site containing oligonucleotides complexed with the methylase alone or with the
      methylase and sinefungin (an AdoMet analog and methylase inhibitor) have been carried out.
      These experiments have shown the sugar phosphate backbone regions in and around the
      recognition site which are protected by the methylase both with and without sinefungin
      present.  Some differences in both the binding pattern and affinity have been observed between
      these complexes.  Specific functionalities have been removed from the substrate at defined
      locations in the recognition site by the incorporation of non-standard nucleotides, such as
      uracil.  The kinetic parameters obtained with these substrates have allowed us to evaluate the
      importance of specific functional groups in substrate recognition (in the uracil example the
      methyl group of each thymidine).  The effect of single asymmetric substitutions on specificity
      and catalysis are being dissected out using this approach.  The thermal denaturation
      characteristics of the modified substrates are being used to probe for additional substrate
      structural changes.
AU  - Danzitz MJ
AU  - Reich NO
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1989 13D: 84.

PMID- 7694036
VI  - 9
DP  - 1993
TI  - Mechanism of expression of DNA repair gene vsr, an Escherichia coli gene that overlaps the DNA cystosine methylase gene, dcm.
PG  - 823-833
AB  - The DNA cytosine methylase gene of Escherichia coli, dcm, overlaps an open reading frame (ORF)
      that continues in +1 register past the end of the dcm. This ORF codes for a gene, vsr, that is
      required for a T:G to C:G base mismatch correction process. In this study, mutants that affect
      the level of expression of the two genes were constructed and characterized. Further, a
      previously isolated mutant, dcm-6, was cloned and mutations within it were identified.
      Northern blots were used to identify dcm-specific RNA species in wild type and dcm-6 cells.
      Based on these studies we conclude that there is a six-codon overlap between vsr and dcm. The
      two proteins appear to be made from a single RNA transcript and translation of dcm is required
      for the efficient synthesis of Vsr. Further, Vsr is active by itself and may not be produced
      as a fusion with Dcm. This is the first example of chromosomal genes that overlap in their
      coding regions and produce proteins with distinct functions.
AU  - Dar ME
AU  - Bhagwat AS
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1993 9: 823-833.

PMID- 19654054
VI  - 1794
DP  - 2009
TI  - Mutational analysis of the CG recognizing DNA methyltransferase SssI: Insight into enzyme-DNA interactions.
PG  - 1654-1662
AB  - To characterize important steps of DNA methylation by M.SssI, a prokaryotic DNA-(cytosine
      C5)methyltransferase (C5-MTase) sharing the
      specificity of eukaryotic C5-MTases (5'-CG-3'), ten amino acids,
      selected on the basis of sequence alignments and a computational model,
      were subjected to mutational analysis. Wild-type and mutant M.SssI
      variants were studied to determine methylation activity, DNA binding
      affinity, capacity to induce base flipping, and ability to form
      covalent complex with a DNA substrate containing the mechanism-based
      inhibitor 2-pyrimidinone. Wild-type M.SssI induced strong fluorescence
      when bound to substrate DNA containing 2-aminopurine in place of the
      target cytosine, indicating flipping of the target base. Reduced
      fluorescence, moderate, or drastic loss of methyltransferase activity
      and reduced DNA binding suggest the involvement of the conserved 5745
      (motif IV), 8232 (motif VIII, QxRx (R) under bar, and T313 (variable
      region, conserved (T) under barL), as well as of the non-conserved Q147
      in base flipping. Replacement of E186 (motif VI, (E) under bar NV) and
      8230 (motif VIII, Qx (R) under bar xR) with alanine resulted in loss of
      methyltransferase activity without impairing DNA binding affinity.
      These data are consistent with the catalytic role of E186 and 8230, and
      provide, for the first time, experimental support for the essential
      function of the hitherto not investigated invariant arginine of motif
      VIII in C5-MTases.
AU  - Darii MV
AU  - Cherepanova NA
AU  - Subach OM
AU  - Kirsanova OV
AU  - Rasko T
AU  - Slaska-Kiss K
AU  - Kiss A
AU  - Deville-Bonne D
AU  - Reboud-Ravaux M
AU  - Gromova ES
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 2009 1794: 1654-1662.

PMID- 
VI  - 41
DP  - 2007
TI  - Isolation and site-directed mutagenesis of DNA methyltransferase SssI.
PG  - 110-117
AB  - Prokaryotic DNA methyltransferase SssI (M.SssI) methylates cytosines at C5 in CpG sequences.
      Bacterial strains that produced M.SssI and its
      mutants as His(6)-tagged proteins were constructed. To verify the role
      of Ser300 in recognizing the CpG sequence by the enzyme, Ser300 was
      replaced by Gly or Pro. The substitutions had virtually no effect on
      DNA binding and methylation by M.SssI apart from a slight decrease in
      binding in the case of S300P. It was assumed that no contact with DNA
      is formed by the side chain of Ser300 and the carbonyl oxygen and amide
      nitrogen of its peptide bonds. In addition, Ala was substituted for
      highly conserved Val188, presumably involved in stabilization of the
      flipped-out cytosine during the reaction. The substitution decreased
      fivefold the dissociation constant of the enzyme-substrate complex and
      halved the initial rate of DNA methylation. Despite the lack of a
      considerable effect of V188A, it was assumed that Val188 does form a
      contact with the target cytosine, but such a contact is formed with Ala
      in the case of the V188A mutant.
AU  - Darii MV
AU  - Kirsanova OV
AU  - Drutsa VL
AU  - Kochetkov SN
AU  - Gromova ES
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2007 41: 110-117.

PMID- 24600039
VI  - 78
DP  - 2014
TI  - Bacterial Genome Instability.
PG  - 1-39
AB  - Bacterial genomes are remarkably stable from one generation to the next but are plastic on an
      evolutionary time scale, substantially shaped by horizontal gene transfer, genome
      rearrangement, and the activities of mobile DNA elements. This implies the existence of a
      delicate balance between the maintenance of genome stability and the tolerance of genome
      instability. In this review, we describe the specialized genetic elements and the endogenous
      processes that contribute to genome instability. We then discuss the consequences of genome
      instability at the physiological level, where cells have harnessed instability to mediate
      phase and antigenic variation, and at the evolutionary level, where horizontal gene transfer
      has played an important role. Indeed, this ability to share DNA sequences has played a major
      part in the evolution of life on Earth. The evolutionary plasticity of bacterial genomes,
      coupled with the vast numbers of bacteria on the planet, substantially limits our ability to
      control disease.
AU  - Darmon E
AU  - Leach DRF
PT  - Journal Article
TA  - Microbiol. Mol. Biol. Rev.
JT  - Microbiol. Mol. Biol. Rev.
SO  - Microbiol. Mol. Biol. Rev. 2014 78: 1-39.

PMID- 24336374
VI  - 1
DP  - 2013
TI  - High-Quality Draft Genome Sequences of Xanthomonas axonopodis pv. glycines Strains CFBP 2526 and CFBP 7119.
PG  - e01036-13
AB  - We report here the high-quality draft genome sequences of two strains of Xanthomonas
      axonopodis pv. glycines, the causal agent of bacterial pustule on
      soybeans. Comparison of these genomes with those of phylogenetically closely
      related pathovars of Xanthomonas spp. will help to understand the mechanisms
      involved in host specificity and adaptation to host plants.
AU  - Darrasse A
AU  - Bolot S
AU  - Serres-Giardi L
AU  - Charbit E
AU  - Boureau T
AU  - Fisher-Le SM
AU  - Briand M
AU  - Arlat M
AU  - Gagnevin L
AU  - Koebnik R
AU  - Noel LD
AU  - Carrere S
AU  - Jacques MA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01036-13.

PMID- 8387444
VI  - 127
DP  - 1993
TI  - Sequence of the Salmonella typhimurium StyLT1 restriction-modification genes: homologies with EcoP1 and EcoP15 type-III R-M systems and presence of helicase domains.
PG  - 105-110
AB  - The StyLTI restriction-modification (R-M) system of Salmonella typhimurium has recently been
      suggested to belong to the type-III R-M systems [De Backer and Colson. Gene 97 (1991)
      103-107]. The nucleotide sequences of StyLTI mod and res have been determined. Two closely
      adjacent open reading frames were found 12 bp apart with coding capacities of 651 (Mod) and
      982 (Res) amino acids (aa), respectively. The genes, lying in the same direction of
      transcription in the mod-res order, are transcribed as distinct units. The deduced aa
      sequences reveal homologies with known type-III enzymes from the Escherichia coli P1 prophage,
      E. coli P15 plasmid and Bacillus cereus chromosome. In addition, the StyLTI restriction
      endonuclease (ENase), like other type-I and type-III ENases, contains sequence motifs
      characteristic of superfamily-II helicases, which may be involved in DNA unwinding at the
      cleavage site.
AU  - Dartois V
AU  - De Backer O
AU  - Colson C
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1993 127: 105-110.

PMID- 27409077
VI  - 11
DP  - 2016
TI  - The Genomic Sequence of the Oral Pathobiont Strain NI1060 Reveals Unique Strategies for Bacterial Competition and Pathogenicity.
PG  - E0158866
AB  - Strain NI1060 is an oral bacterium responsible for periodontitis in a murine
      ligature-induced disease model. To better understand its pathogenicity, we have
      determined the complete sequence of its 2,553,982 bp genome. Although closely
      related to Pasteurella pneumotropica, a pneumonia-associated rodent commensal
      based on its 16S rRNA, the NI1060 genomic content suggests that they are
      different species thriving on different energy sources via alternative metabolic
      pathways. Genomic and phylogenetic analyses showed that strain NI1060 is distinct
      from the genera currently described in the family Pasteurellaceae, and is likely
      to represent a novel species. In addition, we found putative virulence genes
      involved in lipooligosaccharide synthesis, adhesins and bacteriotoxic proteins.
      These genes are potentially important for host adaption and for the induction of
      dysbiosis through bacterial competition and pathogenicity. Importantly, strain
      NI1060 strongly stimulates Nod1, an innate immune receptor, but is defective in
      two peptidoglycan recycling genes due to a frameshift mutation. The in-depth
      analysis of its genome thus provides critical insights for the development of
      NI1060 as a prime model system for infectious disease.
AU  - Darzi Y
AU  - Jiao Y
AU  - Hasegawa M
AU  - Moon H
AU  - Nunez G
AU  - Inohara N
AU  - Raes J
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2016 11: E0158866.

PMID- 25838486
VI  - 3
DP  - 2015
TI  - Deciphering the Genome Sequences of the Hydrophobic Cyanobacterium Scytonema tolypothrichoides VB-61278.
PG  - e00228-15
AB  - Scytonema tolypothrichoides VB-61278, a terrestrial cyanobacterium, can be exploited to
      produce commercially important products. Here, we report for the
      first time a 10-Mb draft genome assembly of S. tolypothrichoides VB-61278, with
      214 scaffolds and 7,148 putative protein-coding genes.
AU  - Das A
AU  - Panda A
AU  - Singh D
AU  - Chandrababunaidu MM
AU  - Mishra GP
AU  - Bhan S
AU  - Adhikary SP
AU  - Tripathy S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00228-15.

PMID- 30104693
VI  - 8
DP  - 2018
TI  - Extensive genomic diversity among Mycobacterium marinum strains revealed by whole genome sequencing.
PG  - 12040
AB  - Mycobacterium marinum is the causative agent for the tuberculosis-like disease
      mycobacteriosis in fish and skin lesions in humans. Ubiquitous in its
      geographical distribution, M. marinum is known to occupy diverse fish as hosts.
      However, information about its genomic diversity is limited. Here, we provide the
      genome sequences for 15 M. marinum strains isolated from infected humans and
      fish. Comparative genomic analysis of these and four available genomes of the M.
      marinum strains M, E11, MB2 and Europe reveal high genomic diversity among the
      strains, leading to the conclusion that M. marinum should be divided into two
      different clusters, the "M"- and the "Aronson"-type. We suggest that these two
      clusters should be considered to represent two M. marinum subspecies. Our data
      also show that the M. marinum pan-genome for both groups is open and expanding
      and we provide data showing high number of mutational hotspots in M. marinum
      relative to other mycobacteria such as Mycobacterium tuberculosis. This high
      genomic diversity might be related to the ability of M. marinum to occupy
      different ecological niches.
AU  - Das S
AU  - Pettersson BM
AU  - Behra PR
AU  - Mallick A
AU  - Cheramie M
AU  - Ramesh M
AU  - Shirreff L
AU  - DuCote T
AU  - Dasgupta S
AU  - Ennis DG
AU  - Kirsebom LA
PT  - Journal Article
TA  - Sci. Rep.
JT  - Sci. Rep.
SO  - Sci. Rep. 2018 8: 12040.

PMID- 26941228
VI  - 8
DP  - 2016
TI  - The Mycobacterium phlei genome: expectations and surprises.
PG  - 975-985
AB  - Mycobacterium phlei, a non-tuberculosis mycobacterial species was first described in 1898-99.
      We present the complete genome sequence for the M. phlei CCUG21000T type strain and the draft
      genomes for four additional strains. The genome size for all five is 5.3 Mb with 69.4% GC
      content. This is approximately 0.35 Mbps smaller than the previously reported M. phlei RIVM
      draft genome. The size difference is attributed partly to large bacteriophage sequence
      fragments in the M. phlei RIVM genome. Comparative analysis revealed: i) a CRISPR system
      similar to Type-1E (cas3) in M. phlei RIVM; ii) genes involved in polyamine metabolism and
      transport (potAD, potF) that are absent in other mycobacteria, and iii) strain-specific
      variations in the number of sigma-factor genes. Moreover, M. phlei has as many as 82 mce
      (mammalian cell entry) homologs and many of the horizontally acquired genes in M. phlei are
      present in other environmental bacteria including mycobacteria that share similar habitat.
      Phylogenetic analysis based on 693 Mycobacterium core genes present in all complete
      mycobacterial genomes suggested that its closest neighbor is Mycobacterium smegmatis JS623 and
      Mycobacterium rhodesiae NBB3 while it is more distant to M. smegmatis mc2 155.
AU  - Das S
AU  - Pettersson BM
AU  - Behra PR
AU  - Ramesh M
AU  - Dasgupta S
AU  - Bhattacharya A
AU  - Kirsebom LA
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2016 8: 975-985.

PMID- 25838485
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Bioactive-Compound-Producing Cyanobacterium Tolypothrix  campylonemoides Strain VB511288.
PG  - e00226-15
AB  - We report here the draft genome sequence of Tolypothrix campylonemoides VB511288, isolated
      from building facades in Santiniketan, India. The members of this genus
      produce several compounds of commercial importance. The draft assembly is
      10,627,177 bases in 135 scaffolds, and it contains 7,886 protein-coding genes,
      994 pseudogenes, 18 rRNA genes, and 76 tRNA genes.
AU  - Das S
AU  - Singh D
AU  - Madduluri M
AU  - Chandrababunaidu MM
AU  - Gupta A
AU  - Adhikary SP
AU  - Tripathy S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00226-15.

PMID- 
VI  - 16
DP  - 2005
TI  - Origin and evolution of inteins and other hint domains.
PG  - 211-231
AB  - The intein protein family is part of the Hint superfamily, named after the characteristic
      structure fold first identified in Hedgehog and intein protein domains.  Four characterized
      Hint domain families are currently known: Hog-Hint, intein, and two types of bacterial
      intein-like domains.  Together with sharing the same structural fold and common sequence
      features, Hint domains have similar biochemical activities.  The domains post-translationally
      process the proteins in which they are present by protein-splicing, self-cleavage or ligation
      activities.  Hint domains are 130 to 160 amino acids long, sharing 4-6 conserved sequence
      motifs.  The Hint protein fold is a compact, relatively flat, symmetrical structure, mainly
      composed of b-strands, with its N- and C-termini close together.  Inteins usually include
      additional homing-endonuclease and DNA-binding domains, not necessary for protein splicing,
      which mediate the homing of the intein gene.  Species from the three domains of life, Eukarya,
      Bacteria and Archaea, include Hint domains.  While inteins are apparently limited to
      unicellular eukaryotes and prokaryotes, Hog-Hint domains are present in multicellular animals.
      BIL domains and inteins overlap in their phylogenetic distributions, both are present in
      bacteria, but in different types of proteins.  Data gathered on Hint domains since their
      discovery in 1990 have identified their biochemical activity, their genetics and evolution.
      Apparently, each Hint family has its own distinct biological role.  Nevertheless, many facets
      of Hint domains are still unknown or debated.
AU  - Dassa B
AU  - Pietrokovski S
PT  - Journal Article
TA  - Nucleic Acids Mol. Biol.
JT  - Nucleic Acids Mol. Biol.
SO  - Nucleic Acids Mol. Biol. 2005 16: 211-231.

PMID- 26404597
VI  - 3
DP  - 2015
TI  - Near-Complete Genome Sequence of the Cellulolytic Bacterium Bacteroides (Pseudobacteroides) cellulosolvens ATCC 35603.
PG  - e01022-15
AB  - We report the single-contig genome sequence of the anaerobic, mesophilic, cellulolytic
      bacterium, Bacteroides cellulosolvens. The bacterium produces a particularly elaborate
      cellulosome system, wherein the types of cohesin-dockerin  interactions are opposite of other
      known cellulosome systems: cell-surface attachment is thus mediated via type-I interactions,
      whereas enzymes are integrated via type-II interactions.
AU  - Dassa B
AU  - Utturkar S
AU  - Hurt RA
AU  - Klingeman DM
AU  - Keller M
AU  - Xu J
AU  - Reddy YH
AU  - Borovok I
AU  - Rozman GI
AU  - Lamed R
AU  - Zhivin O
AU  - Bayer EA
AU  - Brown SD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01022-15.

PMID- 12616525
VI  - 88
DP  - 2003
TI  - Biochemical fractionation reveals association of DNA methyltransferase (Dnmt) 3b With Dnmt1 and that of Dnmt 3a with a histone H3 methyltransferase and Hdac1.
PG  - 855-864
AB  - De novo DNA methyltransferases, Dnmt3a and 3b, were purified by fractionation of S-100 extract
      from mouse lymphosarcoma cells through
      several chromatographic matrices followed by glycerol density gradient
      centrifugation. Dnmt3a was separated from Dnmt3b and Dnmt1 in the first
      column, Q-Sepharose whereas Dnmt3b co-purified with Dnmt1 after further
      fractionation through Mono-S and Mono-Q columns and glycerol density
      gradient centrifugation. Following purification, the majority of de novo
      DNA methyltransfearse activity was associated with Dnmt3b/Dnmt1 fractions.
      By contrast, the fractions containing Dnmt3a alone exhibited markedly
      reduced activity, which correlated with diminished expression of this
      isoform in these cells. Histone deacetylase 1(Hdac1) cofractionated with
      Dnmt3a throughout purification whereas Hdac1 was separated from
      Dnmt3b/Dnmt1 following chromatography on Mono-Q column. Dnmt3a purified
      through glycerol gradient centrifugation was also associated with a
      histone H3 methyltransferase (HMTase) activity whereas purified
      Dnmt3b/Dnmt1 was devoid of any HMTase activity. The activity of this
      HMTase was abolished when lysine 9 of N-terminal histone H3 peptide was
      replaced by leucine whereas mutation of lysine 4 to leucine inhibited this
      activity only partially. This is the first report on the identification of
      a few key co-repressors associated with endogenous Dnmt3a and of a complex
      containing Dnmt3b and a minor form of Dnmt1 following extensive
      biochemical fractionation.
AU  - Datta J
AU  - Ghoshal K
AU  - Sharma SM
AU  - Tajima S
AU  - Jacob ST
PT  - Journal Article
TA  - J. Cell. Biochem.
JT  - J. Cell. Biochem.
SO  - J. Cell. Biochem. 2003 88: 855-864.

PMID- 16322236
VI  - 65
DP  - 2005
TI  - Physical and functional interaction of DNA methyltransferase 3A with Mbd3 and Brg1 in mouse lymphosarcoma cells.
PG  - 10891-10900
AB  - Dnmt3a and Dnmt3b are de novo DNA methyltransferases that also act as transcriptional
      repressors independent of methyltransferase activity.
      To elucidate the underlying mechanism of transcriptional repression,
      Dnmt3a was purified from mouse lymphosarcoma cells (P1798) by extensive
      fractionation on five different chromatographic matrices followed by
      glycerol density gradient centrifugation. Liquid chromatography
      electrospray tandem mass spectrometry analysis of Dnmt3a-associated
      polypeptides identified the methyl CpG binding protein Mbd3, histone
      deacetylase 1(Hdac1), and components of Brg1 complex (Brg1, Baf155, and
      Baf57) in the purified preparation. Association of Dnmt3a with Mbd3 and
      Brg1 was confirmed by coinummoprecipitation and coimmunolocalization
      studies. Glutathione S-transferase pulldown assay showed that the
      NH2-terminal ATRX homology domain of Dnmt3a interacts with the methyl
      CpG binding domain of Mbd3 and with both bromo and ATPase domains of
      Brg1. Chromatin immunoprecipitation assay revealed that all three
      proteins are associated with transcriptionally silent methylated
      metallothionein (MT-I) promoter in the mouse lymphosarcoma cells. To
      understand the functional significance of their association with the
      promoter, their role on the MT-I promoter activity was analyzed by
      transient transfection assay. The results showed that Mbd3 and Dnmt3a
      specifically inhibited the methylated promoter, and the catalytic
      activity of Dnmt3a was dispensable for the suppression. In contrast,
      the wild-type but not the ATPase-inactive mutant of Brg1 suppressed
      MT-I promoter irrespective of its methylation status, implicating
      involvement of ATP-dependent chromatin remodeling in the process.
      Coexpression of two of the three interacting proteins at a time
      augmented their repressor function. This study shows physical and
      functional interaction of Dnmt3a with components of nucleosome
      remodeling machinery.
AU  - Datta J
AU  - Majumder S
AU  - Bai SM
AU  - Ghoshal K
AU  - Kutay H
AU  - Smith DS
AU  - Crabb JW
AU  - Jacob ST
PT  - Journal Article
TA  - Cancer Res.
JT  - Cancer Res.
SO  - Cancer Res. 2005 65: 10891-10900.

PMID- 8975608
VI  - 62
DP  - 1996
TI  - Analysis of the enterohemorrhagic Escherichia coli 0157 DNA region containing lambdoid phage gene p and Shiga-like toxin structural genes.
PG  - 791-797
AB  - In this study, we determined the nucleotide sequence of the p gene contained within a 5-kb
      EcoRI restriction fragment cloned from Shiga-like toxin II (SLT-II)-converting phage 933W of
      Escherichia coli O157:H7 strain EDL933. The p gene was 702 bp long and had 95.3% sequence
      similarity to the p gene of phage lambda. Multiple hybridization patterns were obtained when
      genomic DNA fragments were hybridized with both p and slt-I, slt-II, or slt-IIc sequences. All
      O157 isolates also possessed an analog of lambda gene p which was not linked with either slt-I
      or slt-II. Restriction fragment length polymorphism comparisons of clinical O157 isolates and
      derivatives undergoing genotype turnover during infection were made, and loss of large DNA
      fragments that hybridized with slt-II and p sequences was observed. To further analyze the DNA
      region containing the p and slt genes, we amplified fragments by using PCR with one primer
      complementary to p and the other complementary to either the slt-I or the slt-II gene. PCR
      analysis with enterohemorrhagic E. coli O157 and non-O157 strains yielded PCR products that
      varied in size between 5.1 and 7.8 kb. These results suggest that even within O157 isolates,
      the genomes of SLT-converting phages differ.  The methods described here may assist in further
      investigation of SLT-encoding phages and their role in the epidemiology of infection with
      enterohemorrhagic E. coli.
AU  - Datz M
AU  - Janetzki-Mittmann C
AU  - Franke S
AU  - Gunzer F
AU  - Schmidt H
AU  - Karch H
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1996 62: 791-797.

PMID- 18450817
VI  - 36
DP  - 2008
TI  - Chemical mapping of cytosines enzymatically flipped out of the DNA helix.
PG  - e57
AB  - Haloacetaldehydes can be employed for probing unpaired DNA structures involving cytosine and
      adenine residues. Using an enzyme that was structurally proven to flip its target cytosine out
      of the DNA helix, the HhaI DNA methyltransferase (M.HhaI), we demonstrate the suitability of
      the chloroacetaldehyde modification for mapping extrahelical (flipped-out) cytosine bases in
      protein-DNA complexes. The generality of this method was verified with two other DNA
      cytosine-5 methyltransferases, M.AluI and M.SssI, as well as with two restriction
      endonucleases, R.Ecl18kI and R.PspGI, which represent a novel class of base-flipping enzymes.
      Our results thus offer a simple and convenient laboratory tool for detection and mapping of
      flipped-out cytosines in protein-DNA complexes.
AU  - Daujotyte D
AU  - Liutkeviciute Z
AU  - Tamulaitis G
AU  - Klimasauskas S
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2008 36: e57.

PMID- 15274924
VI  - 12
DP  - 2004
TI  - HhaI DNA methyltransferase uses the protruding Gln237 for active flipping of its target cytosine.
PG  - 1047-1055
AB  - Access to a nucleotide by its rotation out of the DNA helix (base flipping) is used by
      numerous DNA modification and repair enzymes.  Despite extensive studies of the paradigm HhaI
      methyltransferase, initial events leading to base flipping remained elusive.  Here we
      demonstrate that the replacement of the target C:G pair with the 2-aminopurine:T pair in the
      DNA or shortening of the side chain of Gln237 in the protein severely perturb base flipping,
      but retain specific DNA binding.  Kinetic analyses and molecular modeling suggest that a
      steric interaction between the protruding side chain of Gln237 and the target cytosine in
      B-DNA reduces the energy barrier for flipping by 3 kcal/mol.  Subsequent stabilization of an
      open state by further 4 kcal/mol is achieved through specific hydrogen bonding of the side
      chain to the orphan guanine.  Gln237 thus plays a key role in actively opening the target C:G
      pair by a ?push-and-bind? mechanism.
AU  - Daujotyte D
AU  - Serva S
AU  - Vilkaitis G
AU  - Merkiene E
AU  - Venclovas C
AU  - Klimasauskas S
PT  - Journal Article
TA  - Structure
JT  - Structure
SO  - Structure 2004 12: 1047-1055.

PMID- 12736373
VI  - 16
DP  - 2003
TI  - Solubility engineering of the HhaI methyltransferase.
PG  - 295-301
AB  - DNA methylation is involved in epigenetic control of numerous cellular processes in
      eukaryotes, however, many mechanistic aspects of this
      phenomenon are not yet understood. A bacterial prototype cytosine-C5
      methyltransferase, M.HhaI, serves as a paradigm system for structural and
      mechanistic studies of biological DNA methylation, but further analysis of
      the 37 kDa protein is hampered by its insufficient solubility (0.15 mM).
      To overcome this problem, three hydrophobic patches on the surface of
      M.HhaI that are not involved in substrate interactions were subjected to
      site-specific mutagenesis. Residues M51 or V213 were substituted by polar
      amino acids of a similar size, and/or the C-terminal tetrapeptide FKPY was
      replaced by a single glycine residue (Delta324G). Two out of six mutants,
      delta324G and V213S/delta324G, showed improved solubility in initial
      analyses and were purified to homogeneity using a newly developed
      procedure. Biochemical studies of the engineered methyltransferases showed
      that the deletion mutant delta324G retained identical DNA binding, base
      flipping and catalytic properties as the wild-type enzyme. In contrast,
      the engineered enzyme showed (i) a significantly increased solubility
      (>0.35 mM), (ii) high-quality 2D-[(15)N,(1)H] TROSY NMR spectra, and (iii)
      (15)N spin relaxation times evidencing the presence of a monomeric
      well-folded protein in solution.
AU  - Daujotyte D
AU  - Vilkaitis G
AU  - Manelyte L
AU  - Skalicky J
AU  - Szyperski T
AU  - Klimasauskas S
PT  - Journal Article
TA  - Protein Eng.
JT  - Protein Eng.
SO  - Protein Eng. 2003 16: 295-301.

PMID- 1809336
VI  - 11
DP  - 1991
TI  - Cloning, restriction digestion and DNA labeling of large DNA fragments (>1 kb) in the presence of remelted SeaPlaque GTG agarose gels.
PG  - 784-790
AB  - Large DNA fragments (>1 kb), separated in low melting temperature SeaPlaque GTG
      agarose gels, can be enzymatically processed directly in the presence of this
      agarose (in-gel).  Time saving protocols are discussed for in-gel processing of
      large DNA fragments in the presence of remelted SeaPlaque GTG agarose,
      including cloning into pUC18, nick translation, random priming and restriction
      digestion.  These in-gel molecular biology techniques are as efficient as those
      using DNA recovered from agarose.  The effects of UV irradiation, Mg2+
      concentration and agarose concentration on selected in-gel protocols are also
      discussed.
AU  - Daum HA
AU  - White HW
AU  - Seidell CM
AU  - Johnson PA
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 1991 11: 784-790.

PMID- 25767217
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequence for Methicillin-Resistant Staphylococcus aureus Strain ATCC BAA-1680.
PG  - e00011-15
AB  - We report here the whole-genome sequence of the USA300 strain of methicillin-resistant
      Staphylococcus aureus (MRSA), designated ATCC BAA-1680, and
      commonly referred to as community-associated MRSA (CA-MRSA). This clinical MRSA
      isolate is commercially available from the American Type Culture Collection
      (ATCC) and is widely utilized as a control strain for research applications and
      clinical diagnosis. The isolate was propagated in ATCC medium 18, tryptic soy
      agar, and has been utilized as a model S. aureus strain in several studies,
      including MRSA genetic analysis after irradiation with 470-nm blue light.
AU  - Daum LT
AU  - Bumah VV
AU  - Masson-Meyers DS
AU  - Khubbar M
AU  - Rodriguez JD
AU  - Fischer GW
AU  - Enwemeka CS
AU  - Gradus S
AU  - Bhattacharyya S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00011-15.

PMID- 15293946
VI  - 159
DP  - 2004
TI  - Bme585I [5'-CCCGC(4/6)-3'], a new isoschizomer of restriction endonuclease FauI, isolated from a strain of Bacillus mesentericus.
PG  - 129-133
AB  - Bme585I is a new member of the restriction endonuclease type IIS family. It was partially
      purified from the heterothrophic, mesophilic
      bacterial strain Bacillus mesentericus 585 by ammonium sulphate
      precipitation and phosphocellulose column chromatography. Bme585I is a
      monomeric protein with a molecular mass of 62 kD. The enzyme is active
      over a broad pH range from 7.0 to 8.8, has a temperature optimum of
      37 degrees C and tolerance of NaCl. in reaction buffer from 0 to 400 mM.
      Bme585I recognizes the asymmetric sequence 5'-CCCGC(4/6)-3' and is
      therefore an isoschizomer of restriction endonuclease FauI.
AU  - Davalieva K
AU  - Ziberovski J
AU  - Efremov GD
PT  - Journal Article
TA  - Microbiol. Res.
JT  - Microbiol. Res.
SO  - Microbiol. Res. 2004 159: 129-133.

PMID- 25291764
VI  - 2
DP  - 2014
TI  - Whole-genome sequences of nine francisella isolates.
PG  - e00941-14
AB  - Primarily a zoonotic disease, Francisella tularensis is a fastidious intracellular pathogen
      and is listed as a CDC category A pathogen with notably
      high pathogenicity. Here we present the scaffolded genome assemblies of nine
      Francisella strains: eight F. tularensis and one F. philomiragia.
AU  - Davenport KW et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00941-14.

PMID- 25377697
VI  - 2
DP  - 2014
TI  - Complete Genome Assembly of Staphylococcus epidermidis AmMS 205.
PG  - e01059-14
AB  - Staphylococcus epidermidis causes a large number of catheter-related sepsis infections
      annually in the United States. We present the 2.54-Mbp complete genome
      assembly of reference strain S. epidermidis AmMS 205, including a single 37.7-kbp
      plasmid. The annotated assembly is available in GenBank under accession numbers
      CP009046 and CP009047.
AU  - Davenport KW
AU  - Daligault HE
AU  - Minogue TD
AU  - Bishop-Lilly KA
AU  - Broomall SM
AU  - Bruce DC
AU  - Chain PS
AU  - Coyne SR
AU  - Frey KG
AU  - Gibbons HS
AU  - Jaissle J
AU  - Redden CL
AU  - Rosenzweig CN
AU  - Scholz MB
AU  - Teshima H
AU  - Johnson SL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01059-14.

PMID- 25258271
VI  - 2
DP  - 2014
TI  - Whole-Genome Sequence of Listeria monocytogenes Type Strain 53 XXIII.
PG  - e00970-14
AB  - Listeria monocytogenes causes the food-borne illness listeriosis that primarily infects
      'vulnerable' groups (e.g., elderly adults, pregnant women, very young
      children, and the immunocompromised). We sequenced the genome of L. monocytogenes
      XXIII (ATCC 15313) and assembled it into a single scaffold (three contigs) and
      deposited the annotated assembly into GenBank as accession no. JOOX00000000.
AU  - Davenport KW
AU  - Daligault HE
AU  - Minogue TD
AU  - Bishop-Lilly KA
AU  - Bruce DC
AU  - Chain PS
AU  - Coyne SR
AU  - Frey KG
AU  - Jaissle J
AU  - Koroleva GI
AU  - Ladner JT
AU  - Li PE
AU  - Palacios GF
AU  - Redden CL
AU  - Scholz MB
AU  - Teshima H
AU  - Johnson SL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00970-14.

PMID- 25342682
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Type Strain Pasteurella multocida subsp. multocida ATCC 43137.
PG  - e01070-14
AB  - Soft-tissue infection by Pasteurella multocida in humans is usually associated with a dog- or
      cat-related injury, and these infections can become aggressive. We
      sequenced the type strain P. multocida subsp. multocida ATCC 43137 into a single
      closed chromosome consisting of 2,271,840 bp (40.4% G+C content), which is
      currently available in the NCBI GenBank under the accession number CP008918.
AU  - Davenport KW
AU  - Daligault HE
AU  - Minogue TD
AU  - Bishop-Lilly KA
AU  - Bruce DC
AU  - Chain PS
AU  - Coyne SR
AU  - Frey KG
AU  - Jaissle J
AU  - Koroleva GI
AU  - Ladner JT
AU  - Lo CC
AU  - Palacios GF
AU  - Redden CL
AU  - Scholz MB
AU  - Teshima H
AU  - Johnson SL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01070-14.

PMID- 25237026
VI  - 2
DP  - 2014
TI  - Draft Genome Assembly of Delftia acidovorans Type Strain 2167.
PG  - e00917-14
AB  - The Delftia acidovorans 2167 (ATCC 15668, Delftia type strain) genome was sequenced into a
      6-contig scaffolded assembly of 6.78-Mb. This environmental
      microbe, previously named to both the Comamonas and Pseudomonas genera, is an
      opportunistic pathogen and often the subject of phylogenetic placement debates.
AU  - Davenport KW
AU  - Daligault HE
AU  - Minogue TD
AU  - Bishop-Lilly KA
AU  - Bruce DC
AU  - Chain PS
AU  - Coyne SR
AU  - Frey KG
AU  - Jaissle J
AU  - Koroleva GI
AU  - Ladner JT
AU  - Palacios GF
AU  - Redden CL
AU  - Scholz MB
AU  - Teshima H
AU  - Johnson SL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00917-14.

PMID- 25258273
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Stenotrophomonas maltophilia Type Strain 810-2 (ATCC  13637).
PG  - e00974-14
AB  - An emerging nosocomial pathogen, Stenotrophomonas maltophila has a high mortality rate in
      those it infects. Here, we present the complete genome sequence of
      Stenotrophomonas maltophilia 810-2 (ATCC 13637), the type strain of the species.
      The 5-Mb (66.1% G+C content) genome has been deposited in NCBI under accession
      number CP008838.
AU  - Davenport KW
AU  - Daligault HE
AU  - Minogue TD
AU  - Broomall SM
AU  - Bruce DC
AU  - Chain PS
AU  - Coyne SR
AU  - Gibbons HS
AU  - Jaissle J
AU  - Li PE
AU  - Rosenzweig CN
AU  - Scholz MB
AU  - Johnson SL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00974-14.

PMID- 25146140
VI  - 2
DP  - 2014
TI  - Draft Genome Assembly of Acinetobacter baumannii ATCC 19606.
PG  - e00832-14
AB  - Acinetobacter baumannii is an emerging nosocomial pathogen, and therefore high-quality genome
      assemblies for this organism are needed to aid in detection,
      diagnostic, and treatment technologies. Here we present the improved draft
      assembly of A. baumannii ATCC 19606 in two scaffolds. This 3,953,621-bp genome
      contains 3,750 coding regions and has a 39.1% G+C content.
AU  - Davenport KW
AU  - Daligault HE
AU  - Minogue TD
AU  - Bruce DC
AU  - Chain PS
AU  - Coyne SR
AU  - Jaissle JG
AU  - Koroleva GI
AU  - Ladner JT
AU  - Li PE
AU  - Palacios GF
AU  - Scholz MB
AU  - Teshima H
AU  - Johnson SL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00832-14.

PMID- 14661275
VI  - 4
DP  - 2003
TI  - DNA mismatch-specific base flipping by a bisacridine macrocycle.
PG  - 1326-1331
AB  - Most, if not all, enzymes that chemically modify nucleobases in DNA flip their target base
      from the inside of the double helix into an extrahelical
      position. This energetically unfavorable conformation is partly stabilized
      by specific binding of the apparent abasic site being formed. Thus, DNA
      base-flipping enzymes, like DNA methyltransferases and DNA glycosylases,
      generally bind very strongly to DNA containing abasic sites or abasic-site
      analogues. The macrocyclic bisacridine BisA has previously been shown to
      bind abasic sites. Herein we demonstrate that it is able to specifically
      recognize DNA base mismatches and most likely induces base flipping.
      Specific binding of BisA to DNA mismatches was studied by thermal
      denaturation experiments by using short duplex oligodeoxynucleotides
      containing central TT, TC, or TG mismatches or a TA match. In the presence
      of the macrocycle a strong increase in the melting temperature of up to
      7.1 degrees C was observed for the mismatch-containing duplexes, whereas
      the melting temperature of the fully matched duplex was unaffected.
      Furthermore, BisA binding induced an enhanced reactivity of the mispaired
      thymine residue in the DNA toward potassium permanganate oxidation. A
      comparable reactivity has previously been observed for a TT target base
      mismatch in the presence of DNA methyltransferase M.TaqI. This similarity
      to a known base-flipping enzyme suggests that insertion of BisA into the
      DNA helix displaces the mispaired thymine residue into an extrahelical
      position, where it should be more prone to chemical oxidation. Thus, DNA
      base flipping does not appear to be limited to DNA-modifying enzymes but
      it is likely to also be induced by a small synthetic molecule binding to a
      thermodynamically weakened site in DNA.
AU  - David A
AU  - Bleimling N
AU  - Beuck C
AU  - Lehn JM
AU  - Weinhold E
AU  - Teulade-Fichou MP
PT  - Journal Article
TA  - Chembiochem
JT  - Chembiochem
SO  - Chembiochem 2003 4: 1326-1331.

PMID- 26358587
VI  - 3
DP  - 2015
TI  - Genome Sequences of Klebsiella variicola Isolates from Dairy Animals with Bovine  Mastitis from Newfoundland, Canada.
PG  - e00938-15
AB  - Klebsiella variicola was recently reported as an emerging and/or previously misidentified
      species associated with opportunistic infections in humans. Here, we report the draft genome
      sequences of K. variicola isolates from two animals with clinical mastitis from a dairy farm
      in Newfoundland, Canada.
AU  - Davidson FW
AU  - Whitney HG
AU  - Tahlan K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00938-15.

PMID- 23950125
VI  - 1
DP  - 2013
TI  - Genome Sequence of an Epidemic Isolate of Mycobacterium abscessus subsp. bolletii from Rio de Janeiro, Brazil.
PG  - e00617-13
AB  - Multiple isolates of Mycobacterium abscessus subsp. bolletii, collectively called BRA100, were
      associated with outbreaks of postsurgical skin infections across
      various regions of Brazil from 2003 to 2009. We announce the draft genome
      sequence of a newly sequenced BRA100 strain, M. abscessus subsp. bolletii
      CRM-0020, isolated from a patient in Rio de Janeiro, Brazil.
AU  - Davidson RM
AU  - Reynolds PR
AU  - Farias-Hesson E
AU  - Duarte RS
AU  - Jackson M
AU  - Strong M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00617-13.

PMID- 
VI  - 24
DP  - 2001
TI  - Immobilization of the restriction enzymes HaeIII and HindIII on porous silica particles via a glutaraldehyde linkage for the micro-digestion of dsDNA with analysis by capillary electrophoresis.
PG  - 10-16
AB  - Solid-phase DNA restriction digest reactors have been developed consisting of silica particles
      modified with a covalently tethered
      restriction enzyme. This solid-phase restriction reactor enables
      digestion and separation of minute quantities of DNA with minimal
      reagent consumption. In this study, the restriction enzymes, HaeIII,
      PstI, and HindIII, were successfully immobilized via glutaraldehyde
      linkages to porous silica micro-particles. Studies were carried out to
      examine the impact of immobilization on enzymatic activity. Digestions
      of phiX174-RF DNA phage and SV40 viral DNA were performed with the
      immobilized enzymes by placing the silica particles in solution with
      the target DNA with digestion times of 120 min and 240 min
      respectively. The digests were analyzed off-line using capillary
      electrophoresis (CE) with laser-induced fluorescence (LIF) detection.
      Timed studies were performed to establish optimal conditions for
      complete digestion. Digests utilizing immobilized HaeIII and HindIII
      were similar in composition to homogeneous, free solution digests. PstI
      showed no evidence of activity upon immobilization. The immobilized
      restriction enzymes could also be used for multiple rounds of
      digestion; however, longer incubation times were required for
      successive runs probably due to partial denaturation of the restriction
      enzyme. Digests also were prepared and isolated by use of a simple
      micro-spin column consisting of a layer of immobilized enzyme-coated
      silica on a molecular weight cut-off filter. Using this approach,
      digestion times were comparable to solution digests as previously
      mentioned; however, enzyme reuse and reaction product isolation was
      facilitated.
AU  - Davidson YY
AU  - Soper SA
AU  - Margolis S
AU  - Sander LC
PT  - Journal Article
TA  - J. Sep. Sci.
JT  - J. Sep. Sci.
SO  - J. Sep. Sci. 2001 24: 10-16.

PMID- 21269504
VI  - 12
DP  - 2011
TI  - Comparative analysis and supragenome modeling of twelve Moraxella catarrhalis clinical isolates.
PG  - 70
AB  - BACKGROUND: M. catarrhalis is a gram-negative, gamma-proteobacterium and
      an opportunistic human pathogen associated with otitis media (OM) and
      exacerbations of chronic obstructive pulmonary disease (COPD). With direct
      and indirect costs for treating these conditions annually exceeding $33
      billion in the United States alone, and nearly ubiquitous resistance to
      beta-lactam antibiotics among M. catarrhalis clinical isolates, a greater
      understanding of this pathogen's genome and its variability among isolates
      is needed. RESULTS: The genomic sequences of ten geographically and
      phenotypically diverse clinical isolates of M. catarrhalis were determined
      and analyzed together with two publicly available genomes. These twelve
      genomes were subjected to detailed comparative and predictive analyses
      aimed at characterizing the supragenome and understanding the metabolic
      and pathogenic potential of this species. A total of 2383 gene clusters
      were identified, of which 1755 are core with the remaining 628 clusters
      unevenly distributed among the twelve isolates. These findings are
      consistent with the distributed genome hypothesis (DGH), which posits that
      the species genome possesses a far greater number of genes than any single
      isolate. Multiple and pair-wise whole genome alignments highlight limited
      chromosomal re-arrangement. CONCLUSIONS: M. catarrhalis gene content and
      chromosomal organization data, although supportive of the DGH, show modest
      overall genic diversity. These findings are in stark contrast with the
      reported heterogeneity of the species as a whole, as wells as to other
      bacterial pathogens mediating OM and COPD, providing important insight
      into M. catarrhalis pathogenesis that will aid in the development of novel
      therapeutic regimens.
AU  - Davie JJ
AU  - Earl J
AU  - de Vries SP
AU  - Ahmed A
AU  - Hu FZ
AU  - Bootsma HJ
AU  - Stol K
AU  - Hermans PW
AU  - Wadowsky RM
AU  - Ehrlich GD
AU  - Hays JP
AU  - Campagnari AA
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2011 12: 70.

PMID- 10525405
VI  - 292
DP  - 1999
TI  - The DNA translocation and ATPase activities of restriction-deficient mutants of EcoKI.
PG  - 787-796
AB  - EcoKI, a type I restriction enzyme, specifies DNA methyltransferase, ATPase, endonuclease and
      DNA translocation activities. One subunit (HsdR) of the oligomeric enzyme contributes to those
      activities essential for restriction. These activities involve ATP-dependent DNA translocation
      and DNA cleavage. Mutations that change amino acids within recognisable motifs in HsdR impair
      restriction. We have used an in vivo assay to monitor the effect of these mutations on DNA
      translocation. The assay follows the EcoKI-dependent entry of phage T7 DNA from the phage
      particle into the host cell. Earlier experiments have shown that mutations within the seven
      motifs characteristic of the DEAD-box family of proteins that comprise known or putative
      helicases severely impair the ATPase activity of purified enzymes. We find that the mutations
      abolish DNA translocation in vivo. This provides evidence that these motifs are relevant to
      the coupling of ATP hydrolysis to DNA translocation. Mutations that identify an endonuclease
      motif similar to that found at the active site of type II restriction enzymes and other
      nucleases have been shown to abolish DNA nicking activity.  When conservative changes are made
      at these residues, the enzymes lack nuclease activity but retain the ability to hydrolyse ATP
      and to translocate DNA at wild-type levels. It has been speculated that nicking may be
      necessary to resolve the topological problems associated with DNA translocation by type I
      restriction and modification systems. Our experiments show that loss of the nicking activity
      associated with the endonuclease motif of EcoKI has no effect on ATPase activity in vitro or
      DNA translocation of the T7 genome in vivo.
AU  - Davies GP
AU  - Kemp P
AU  - Molineux IJ
AU  - Murray NE
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1999 292: 787-796.

PMID- 10390354
VI  - 290
DP  - 1999
TI  - On the structure and operation of type I DNA restriction enzymes.
PG  - 565-579
AB  - Type I DNA restriction enzymes are large, molecular machines possessing DNA methyltransferase,
      ATPase, DNA translocase and endonuclease activities. The ATPase, DNA translocase and
      endonuclease activities are specified by the restriction (R) subunit of the enzyme. We
      demonstrate that the R subunit of the Eco KI type I restriction enzyme comprises several
      different functional domains. An N-terminal domain contains an amino acid motif identical with
      that forming the catalytic site in simple restriction endonucleases, and changes within this
      motif lead to a loss of nuclease activity and abolish the restriction reaction. The central
      part of the R subunit contains amino acid sequences characteristic of DNA helicases. We
      demonstrate, using limited proteolysis of this subunit, that the helicase motifs are contained
      in two domains. Secondary structure prediction of these domains suggests a structure that is
      the same as the catalytic domains of DNA helicases of known structure. The C-terminal region
      of the R subunit can be removed by elastase treatment leaving a large fragment, stable in the
      presence of ATP, which can no longer bind to the other subunits of Eco KI suggesting that this
      domain is required for protein assembly. Considering these results and previous models of the
      methyltransferase part of these enzymes, a structural and operational model of a type I DNA
      restriction enzyme is presented.
AU  - Davies GP
AU  - Martin I
AU  - Sturrock SS
AU  - Cronshaw A
AU  - Murray NE
AU  - Dryden DTF
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1999 290: 565-579.

PMID- 9776741
VI  - 26
DP  - 1998
TI  - EcoKI with an amino acid substitution in any one of seven DEAD-box motifs has impaired ATPase and endonuclease activities.
PG  - 4828-4836
AB  - For type I restriction systems, recently determined nucleotide sequences predict conserved
      amino acids in the subunit that is essential for restriction but not modification (HsdR). The
      conserved sequences emphasize motifs characteristic of the DEAD-box family of proteins which
      comprises putative helicases, and they identify a new candidate for motif IV. We provide
      evidence based on an analysis of EcoKI which supports both the relevance of DEAD-box motifs to
      the mechanism of restriction and the new definition of motif IV. Amino acid substitutions
      within the newly identified motif IV and those in six other previously identified DEAD-box
      motifs, but not in the original motif IV, confer restriction-deficient phenotypes. We have
      examined the relevance of the DEAD-box motifs to the restriction pathway by determining the
      steps permitted in vitro by the defective enzymes resulting from amino acid substitutions in
      each of the seven motifs. EcoKI purified from the seven restriction-deficient mutants binds to
      an unmethylated target sequence and, in the presence of AdoMet, responds to ATP by undergoing
      the conformational change essential for the pathway of events leading to DNA cleavage. The
      seven enzymes have little or no ATPase activity and no endonuclease activity, but they retain
      the ability to nick unmodified DNA, though at reduced rates. Nicking of a DNA strand could
      therefore be an essential early step in the restriction pathway, facilitating the
      ATP-dependent translocation of DNA, particularly if this involves DNA helicase activity.
AU  - Davies GP
AU  - Powell LM
AU  - Webb JL
AU  - Cooper LP
AU  - Murray NE
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1998 26: 4828-4836.

PMID- 2497965
VI  - 2
DP  - 1989
TI  - DNA restriction and modification systems in Neisseria gonorrhoeae.
PG  - S78-S82
AB  - A review.  Introduces new nomenclature.
AU  - Davies JK
PT  - Journal Article
TA  - Clin. Microbiol. Rev.
JT  - Clin. Microbiol. Rev.
SO  - Clin. Microbiol. Rev. 1989 2: S78-S82.

PMID- 6245338
VI  - 177
DP  - 1980
TI  - A relationship between plasmid structure, structural lability, and sensitivity to site-specific endonucleases in Neisseria gonorrhoeae.
PG  - 251-260
AB  - Nearly all gonococcal strains carry a small "phenotypically cryptic" plasmid of
      approximately 4,200 basepairs.  A detailed physical map of this plasmid has
      been constructed, revealing the presence of numerous putative inverted repeats.
      These studies also revealed the presence on the plasmid of rercognition
      sequences for several site-specific endonucleases (particularly HpaII, MspI and
      AluI) that are particularly resistant to cleavage, and confirmed previous
      reports of structural lability.  Both the sites that are resistant to cleavage,
      and the observed structural variation are association with the inverted
      repetitive sequences.
AU  - Davies JK
AU  - Normark S
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1980 177: 251-260.

PMID- 19168609
VI  - 191
DP  - 2009
TI  - A Novel Integrative Conjugative Element Mediates Genetic Transfer from Group G Streptococcus to Other -Hemolytic Streptococci.
PG  - 2257-2265
AB  - Lateral gene transfer is a significant contributor to the ongoing
      evolution of many bacterial pathogens, including beta-hemolytic
      streptococci. Here we provide the first characterization of a novel
      integrative conjugative element (ICE), ICESde3396, from Streptococcus
      dysgalactiae subsp. equisimilis (group G streptococcus [GGS]), a bacterium
      commonly found in the throat and skin of humans. ICESde3396 is 64 kb in
      size and encodes 66 putative open reading frames. ICESde3396 shares 38
      open reading frames with a putative ICE from Streptococcus agalactiae
      (group B streptococcus [GBS]), ICESa2603. In addition to genes involves in
      conjugal processes, ICESde3396 also carries genes predicted to be involved
      in virulence and resistance to various metals. A major feature of
      ICESde3396 differentiating it from ICESa2603 is the presence of an 18-kb
      internal recombinogenic region containing four unique gene clusters, which
      appear to have been acquired from streptococcal and nonstreptococcal
      bacterial species. The four clusters include two cadmium resistance
      operons, an arsenic resistance operon, and genes with orthologues in a
      group A streptococcus (GAS) prophage. Streptococci that naturally harbor
      ICESde3396 have increased resistance to cadmium and arsenate, indicating
      the functionality of genes present in the 18-kb recombinogenic region. By
      marking ICESde3396 with a kanamycin resistance gene, we demonstrate that
      the ICE is transferable to other GGS isolates as well as GBS and GAS. To
      investigate the presence of the ICE in clinical streptococcal isolates, we
      screened 69 isolates (30 GGS, 19 GBS, and 20 GAS isolates) for the
      presence of three separate regions of ICESde3396. Eleven isolates
      possessed all three regions, suggesting they harbored ICESde3396-like
      elements. Another four isolates possessed ICESa2603-like elements. We
      propose that ICESde3396 is a mobile genetic element that is capable of
      acquiring DNA from multiple bacterial sources and is a vehicle for
      dissemination of this DNA through the wider beta-hemolytic streptococcal
      population.
AU  - Davies MR
AU  - Shera J
AU  - Van Domselaar GH
AU  - Sriprakash KS
AU  - McMillan DJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2009 191: 2257-2265.

PMID- 23434113
VI  - 16
DP  - 2013
TI  - Entering the era of bacterial epigenomics with single molecule real time DNA sequencing.
PG  - 192-198
AB  - DNA modifications, such as methylation guide numerous critical biological processes, yet
      epigenetic information has not routinely been collected as part of
      DNA sequence analyses. Recently, the development of single molecule real time
      (SMRT) DNA sequencing has enabled detection of modified nucleotides (e.g. 6mA,
      4mC, 5mC) in parallel with acquisition of primary sequence data, based on
      analysis of the kinetics of DNA synthesis reactions. In bacteria, genome-wide
      mapping of methylated and unmethylated loci is now feasible. This technological
      advance sets the stage for comprehensive, mechanistic assessment of the effects
      of bacterial DNA methyltransferases (MTases)-which are ubiquitous, extremely
      diverse, and largely uncharacterized-on gene expression, chromosome structure,
      chromosome replication, and other fundamental biological processes. SMRT
      sequencing also enables detection of damaged DNA and has the potential to uncover
      novel DNA modifications.
AU  - Davis BM
AU  - Chao MC
AU  - Waldor MK
PT  - Journal Article
TA  - Curr. Opin. Microbiol.
JT  - Curr. Opin. Microbiol.
SO  - Curr. Opin. Microbiol. 2013 16: 192-198.

PMID- 7771761
VI  - 67
DP  - 1995
TI  - Protein splicing -- the lengths some proteins will go to.
PG  - 131-137
AB  - We review the recently discovered phenomenon of protein splicing which
      is the excision of an inernal protein sequence at the protein level rather than at the RNA
      level. The means by which examples of protein splicing have been idenified are described,
      and the similarities of the internally spliced protein products (or inteins) are discussed.
      Comparisons are made between inteins and group I RNA introns.  We describe the
      evidence supporting excision of inteins by a post-translational autocatalytic reaction of a
      full
      length polypeptide precursor, rather than by RNA splicing.  An examination is made of
      some of the proposed mechanism schemes and the evidence supporting them is presented.
AU  - Davis EO
AU  - Jenner PJ
PT  - Journal Article
TA  - Antonie Van Leeuwenhoek
JT  - Antonie Van Leeuwenhoek
SO  - Antonie Van Leeuwenhoek 1995 67: 131-137.

PMID- 1423588
VI  - 71
DP  - 1992
TI  - Protein splicing in the maturation of M. tuberculosis RecA protein: a mechanism for tolerating a novel class of intervening sequence.
PG  - 201-210
AB  - The M. tuberculosis recA locus comprises an 85 kd open reading frame but produced 38 kd RecA
      and 47 kd products in E. coli. No RNA processing was detected; rather, an 85 kd precursor
      protein was spliced, releasing a 47 kd spacer protein, and joining its terminal fragments to
      form mature RecA protein. "Spacer" protein was also produced in M. tuberculosis and from a
      hybrid spacer-LacZa fusion molecule. Mutagenesis at codon wobble positions at one splice
      junction showed that protein rather than nucleotide sequence determined splicing activity.
      Other mutants defined additional regions needed for splicing and allowed processing to be
      followed. Splicing was essential for RecA activity in E. coli. The possibility that splicing
      is a manifestation of a novel class of genetic element is discussed.
AU  - Davis EO
AU  - Jenner PJ
AU  - Brooks PC
AU  - Colston MJ
AU  - Sedgwick SG
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1992 71: 201-210.

PMID- 1909321
VI  - 173
DP  - 1991
TI  - Novel structure of the recA locus of Mycobacterium tuberculosis implies processing of the gene product.
PG  - 5653-5662
AB  - A fragment of Mycobacterium tuberculosis DNA containing recA-like sequences was identified by
      hybridization with the Escherichia coli recA gene and cloned. Although no expression was
      detected from its own promoter in E. coli, expression from a vector promoter partially
      complemented E. coli recA mutants for recombination, DNA repair, and mutagenesis, but not for
      induction of phage lambda. This clone produced a protein which cross-reacts with antisera
      raised against the E. coli RecA protein and was approximately the same size. However, the
      nucleotide sequence of the cloned fragment revealed the presence of an open reading frame for
      a protein about twice the size of other RecA proteins and the cloned product detected by
      Western blotting (immunoblotting). The predicted M. tuberculosis RecA protein sequence was
      homologous with RecA sequences from other bacteria, but this homology was not dispersed;
      rather it was localized to the first 254 and the last 96 amino acids, with the intervening 440
      amino acids being unrelated. Furthermore, the junctions of homology were in register with the
      uninterrupted sequence of the E. coli RecA protein. Identical restriction fragments were found
      in the genomic DNAs of M. tuberculosis H37Rv and H37Ra and of M. bovis BCG. It is concluded
      that the ancestral recA gene of these species diversified via an insertional mutation of at
      least 1,320 bp of DNA. Possible processing mechanisms for synthesizing a normal-size RecA
      protein from this elongated sequence are discussed.
AU  - Davis EO
AU  - Sedgwick SG
AU  - Colston MJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1991 173: 5653-5662.

PMID- 7508863
VI  - 13
DP  - 1994
TI  - Evidence of selection for protein introns in the recAs of pathogenic mycobacteria.
PG  - 699-703
AB  - Protein introns are recently discovered genetic elements whose intervening sequences are
      removed from a precursor protein by an unusual protein splicing intron, and the religation of
      the amino- and carboxy-terminal fragments of the precursor. The recA gene of Mycobacterium
      tuberculosis contains one such element and we now show that the other major mycobacterial
      pathogen, Mycobacterium leprae, also possesses a protein intron in its recA, although other
      mycobacterial recA genes do not. However, these two protein introns are different in size,
      sequence and location of insertion of their coding sequences into the recAs of M. tuberculosis
      and M. leprae, indicating that acquisition of the protein introns has occurred independently
      in the two species, and thus suggesting that there has been selection for splicing in the
      maturation of RecA in the pathogenic mycobacteria. The M. leprae protein intron provides an
      example of conditional protein splicing, splicing occurring in M. leprae itself but not when
      expressed in Escherichia coli, unlike most previously described protein introns. These
      observations suggest that protein introns may perform a function for their host, rather than
      being just selfish elements.
AU  - Davis EO
AU  - Thangaraj HS
AU  - Brooks PC
AU  - Colston MJ
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1994 13: 699-703.

PMID- 25146136
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Hawaiian Sea Slug Symbiont Vibrio sp. Strain ER1A.
PG  - e00820-14
AB  - Bacteria belonging to the genus Vibrio are prevalent in the marine environment and are known
      for forming symbiotic relationships with hosts. Vibrio sp. strain
      ER1A is a dominant symbiont of the Hawaiian sea slug, Elysia rufescens. Here we
      report the draft genome sequence of Vibrio sp. ER1A.
AU  - Davis J
AU  - Hill RT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00820-14.

PMID- 23833133
VI  - 1
DP  - 2013
TI  - Genome Sequence of Streptomyces viridosporus Strain T7A ATCC 39115, a Lignin-Degrading Actinomycete.
PG  - e00416-13
AB  - We announce the availability of the genome sequence of Streptomyces viridosporus  strain T7A
      ATCC 39115, a plant biomass-degrading actinomycete. This bacterium is
      of special interest because of its capacity to degrade lignin, an underutilized
      component of plants in the context of bioenergy. It has a full complement of
      genes for plant biomass catabolism.
AU  - Davis JR et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00416-13.

PMID- 22493203
VI  - 194
DP  - 2012
TI  - Genome Sequence of Amycolatopsis sp. Strain ATCC 39116, a Plant Biomass-Degrading Actinomycete.
PG  - 2396-2397
AB  - We announce the availability of a high-quality draft of the genome sequence of Amycolatopsis
      sp. strain 39116, one of few bacterial species that are known to
      consume the lignin component of plant biomass. This genome sequence will further
      ongoing efforts to use microorganisms for the conversion of plant biomass into
      fuels and high-value chemicals.
AU  - Davis JR
AU  - Goodwin LA
AU  - Woyke T
AU  - Teshima H
AU  - Bruce D
AU  - Detter C
AU  - Tapia R
AU  - Han S
AU  - Han J
AU  - Pitluck S
AU  - Nolan M
AU  - Mikhailova N
AU  - Land ML
AU  - Sello JK
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2396-2397.

PMID- 8467964
VI  - 7
DP  - 1993
TI  - Eludication of sites flanking CpG dinucleotides important in the regulation of mammalian cytosine DNA methyltransferase.
PG  - A1291
AB  - It is known that methylation of cytosines in eukaryotes occurs only at cytosines within CpG
      dinucleotides. However, not every CpG site in eukaryotic DNA is methylated, giving rise to
      various patterns of methylation for different types of cells and stages of development. How
      this variability is established is not well understood, but methylation of genes at particular
      sites has been shown to inhibit their expression. To examine the possibility that sequences
      flanking CpG dinucleotides act differentially in the regulation of mammalian cytosine
      methyltransferase, a number of dissimilar CpG flanking sequences on various substrates have
      been examined. Through use of gel-shift and methylation data carried out on plasmid pBR322 and
      SV40 viral DNA, sites of facilitated methyltransferase-DNA interaction have been determined.
      Footprinting assays currently being employed will reveal sites critical to recognition and
      catalysis. Characterization of the protein-DNA interactions involved with the mammalian
      methyltransferase may lead to new insights into its gene regulatory mechanism.
AU  - Davis M
AU  - Guorong X
AU  - Glickman G
AU  - Reich N
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1993 7: A1291.

PMID- 24029757
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Staphylococcus aureus Tager 104, a Sequence Type 49 Ancestor.
PG  - e00706-13
AB  - We report here the complete genome sequence of Staphylococcus aureus Tager 104, originally
      isolated from a cutaneous abscess in 1947 by Morris Tager. Sequence
      typing of the strain revealed its membership in sequence type 49 (ST49), a
      previously unknown multilocus sequence type (MLST) in clinical samples.
AU  - Davis R
AU  - Hossain MJ
AU  - Liles MR
AU  - Panizzi P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00706-13.

PMID- 8481004
VI  - 59
DP  - 1993
TI  - ScrFI restriction-modification system of Lactococcus lactis subsp. cremoris UC503: Cloning and Characterization of two ScrFI methylase genes.
PG  - 777-785
AB  - Two genes from the total genomic DNA of dairy starter culture Lactococcus lactis subsp.
      cremoris UC503, encoding ScrFI modification enzymes, have been cloned and expressed in
      Escherichia coli. No homology between the two methyase genes was detected, and inverse
      polymerase chain reaction of flanking chromosomal DNA indicated that both were linked on the
      Lactococcus genome. Neither clone encoded the cognate endonuclease. The DNA sequence of one of
      the methylase genes (encoded by pCI931M) was determined and consisted of an open reading frame
      1,170 bp long, which could encode a protein of 389 amino acids (Mr,44.5). The amino acid
      sequence contained the highly characteristic motifs of an m5C methylase. Extensive regions of
      homology were observed with the methylases of NlaX, EcoRII, and Dcm.
AU  - Davis R
AU  - Van der Lelie D
AU  - Mercenier A
AU  - Daly C
AU  - Fitzgerald GF
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1993 59: 777-785.

PMID- 26494665
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Spiroplasma kunkelii Strain CR2-3x, Causal Agent of Corn Stunt Disease in Zea mays L.
PG  - e01216-15
AB  - Spiroplasma kunkelii causes corn stunt disease of Zea mays L. in the Americas. Here, we report
      the nucleotide sequence of the 1,463,926-bp circular chromosome and four plasmids of strain
      CR2-3x. This information will facilitate studies of Spiroplasma pathogenicity and evolutionary
      adaptations to transkingdom parasitism in plants and insect vectors.
AU  - Davis RE
AU  - Shao J
AU  - Dally EL
AU  - Zhao Y
AU  - Gasparich GE
AU  - Gaynor BJ
AU  - Athey JC
AU  - Harrison NA
AU  - Donofrio N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01216-15.

PMID- 28428304
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Spiroplasma citri Strain R8-A2T, Causal Agent of Stubborn Disease in Citrus Species.
PG  - e00206-17
AB  - Spiroplasma citri causes stubborn disease in Citrus spp. and diseases in other plants. Here,
      we report the nucleotide sequence of the 1,599,709-bp circular
      chromosome and two plasmids of S. citri strain R8-A2T This information will
      facilitate analyses to understand spiroplasmal pathogenicity and evolutionary
      adaptations to lifestyles in plants and arthropod hosts.
AU  - Davis RE
AU  - Shao J
AU  - Zhao Y
AU  - Gasparich GE
AU  - Gaynor BJ
AU  - Donofrio N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00206-17.

PMID- 26586899
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Spiroplasma turonicum Strain Tab4cT, a Parasite of a  Horse Fly, Haematopota sp. (Diptera: Tabanidae).
PG  - e01367-15
AB  - Spiroplasma turonicum was isolated from a Haematopota sp. fly in France. We report the
      nucleotide sequence of the circular chromosome of strain Tab4cT. The
      genome information will facilitate evolutionary studies of spiroplasmas,
      including symbionts of insects and ticks and pathogens of plants, insects,
      crustaceans, and humans.
AU  - Davis RE
AU  - Shao J
AU  - Zhao Y
AU  - Gasparich GE
AU  - Gaynor BJ
AU  - Donofrio N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01367-15.

PMID- 26940863
VI  - 17
DP  - 2016
TI  - Complete genome of Staphylococcus aureus Tager 104 provides evidence of its relation to modern systemic hospital-acquired strains.
PG  - 179
AB  - BACKGROUND: Staphylococcus aureus (S. aureus) infections range in severity due to
      expression of certain virulence factors encoded on mobile genetic elements (MGE).
      As such, characterization of these MGE, as well as single nucleotide
      polymorphisms, is of high clinical and microbiological importance. To understand
      the evolution of these dangerous pathogens, it is paramount to define reference
      strains that may predate MGE acquisition. One such candidate is S. aureus Tager
      104, a previously uncharacterized strain isolated from a patient with impetigo in
      1947. RESULTS: We show here that S. aureus Tager 104 can survive in the
      bloodstream and infect naive organs. We also demonstrate a procedure to construct
      and validate the assembly of S. aureus genomes, using Tager 104 as a
      proof-of-concept. In so doing, we bridged confounding gap regions that limited
      our initial attempts to close this 2.82 Mb genome, through integration of data
      from Illumina Nextera paired-end, PacBio RS, and Lucigen NxSeq mate-pair
      libraries. Furthermore, we provide independent confirmation of our segmental
      arrangement of the Tager 104 genome by the sole use of Lucigen NxSeq libraries
      filled by paired-end MiSeq reads and alignment with SPAdes software. Genomic
      analysis of Tager 104 revealed limited MGE, and a nuSabeta island configuration
      that is reminiscent of other hospital acquired S. aureus genomes. CONCLUSIONS:
      Tager 104 represents an early-branching ancestor of certain hospital-acquired
      strains. Combined with its earlier isolation date and limited content of MGE,
      Tager 104 can serve as a viable reference for future comparative genome studies.
AU  - Davis RW IV
AU  - Brannen AD
AU  - Hossain MJ
AU  - Monsma S
AU  - Bock PE
AU  - Nahrendorf M
AU  - Mead D
AU  - Lodes M
AU  - Liles MR
AU  - Panizzi P
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2016 17: 179.

PMID- 10937489
VI  - 2
DP  - 2000
TI  - Development of a transformation and gene reporter system for group II, non-proteolytic Clostridium botulinum type B strains.
PG  - 59-69
AB  - Non-proteolytic, Group II strains of Clostridium botulinum are of particular concern to the
      food industry because of their ability to survive and grow in REPFEDs (refrigerated processed
      foods of extended durability). Their analysis would benefit from the availability of a gene
      transfer system. In the present study we have been able, for the first time, to demonstrate
      transformation in a representative Group II strain, ATCC 25765. Initial attempts to transform
      ATCC 25765 with existing clostridial cloning vectors (pMTL540E and pMTL500E) were, however,
      prevented by a restriction barrier. Through a combination of classical and molecular
      approaches we were able to show that strain ATCC 25765 possesses a restriction endonuclease
      (CboI) and a methylase activity (M.CboI) which have the same specificity as MspI and M.MspI,
      respectively. CboI cleaves the palindrome 5'-CCGG-3' to generate a 3'-GC sticky end, whilst
      M.CboI specifically methylates the external C residue. An E. coli host was generated which
      expressed a Bacillus subtilis methylase enzyme (M.BsuFI) with equivalent specificity to
      M.CboI. Plasmids (pMTL540E and pMTL500E) prepared in this strain were subsequently shown to be
      capable of transforming ATCC 25765. The highest frequencies (0.8 X 10^4) transformants per
      microg of DNA) were obtained when cells were cultivated in media supplemented with 1% (w/v)
      glycine, and when the electroporation was undertaken at 10 kV/cm, 25 microF and at 400 ohms.
      Having developed an effective transformation procedure, we went on to construct reporter
      cassettes based on the Thermanaerobacterium sulfurigenes lacZ and the Vibrio fischeri luxAB
      genes. Using the former, and promoter regions isolated from the botulinum toxin genes, we have
      obtained preliminary evidence that reporter genes may be used to evaluate the physiological
      factors that affect toxin production in the food environment.
AU  - Davis TO
AU  - Henderson I
AU  - Brehm JK
AU  - Minton NP
PT  - Journal Article
TA  - J. Mol. Microbiol. Biotechnol.
JT  - J. Mol. Microbiol. Biotechnol.
SO  - J. Mol. Microbiol. Biotechnol. 2000 2: 59-69.

PMID- 430589
VI  - 29
DP  - 1979
TI  - Restriction insensitivity in bacteriophage T5.  I. Genetic characterization of mutants sensitive to EcoRI restriction.
PG  - 11-16
AB  - Unmodified bacteriophage T5 is able to grow normally on bacterial hosts carrying three
      different Escherichia coli restriction systems, EcoK, EcoPI, and EcoRI.  Under the same
      conditions, the plating efficiency of bacteriophage lambda is less than 10^-9.  At least in
      the case of EcoRI, this lack of in vivo restriction is not due to lack of restriction sites on
      the T5 DNA molecule.  These observations suggest that bacteriophage T5 specifies one or more
      restriction protection systems.  Mutants (ris) of T5 have been isolated which confer
      sensitivity to EcoRI restriction but not to EcoK or EcoPI.  The mutations are located in the
      pre-early region of the genetic map but are too far apart to be alleles of a single gene.
      Complementation studies show that the ris mutants can be helped to grow on the
      EcoRI-restricting host by coinfection with T5+.  This result provides evidence for a
      restriction protection function but does not necessarily show that the ris mutants are
      defective in such a system.
AU  - Davison J
AU  - Brunel F
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1979 29: 11-16.

PMID- 26472842
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Rhodococcus rhodochrous Strain KG-21, a Soil Isolate from Oil Fields of Krishna-Godavari Basin, India.
PG  - e01201-15
AB  - Here, we present the 6.1-Mb draft genome sequence of Rhodococcus rhodochrous strain KG-21, a
      soil isolate from the oil fields of Krishna-Godavari Basin in Andhra Pradesh, India. This
      genomic resource may help in the identification of the gene(s) involved in hydrocarbon
      degradation and their possible deployment for bioremediation.
AU  - Dawar C
AU  - Aggarwal RK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01201-15.

PMID- 26044433
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Hydrocarbon-Degrading Pseudomonas putida Strain KG-4, Isolated from Soil Samples Collected from Krishna-Godavari Basin in India.
PG  - e00590-15
AB  - We report here the 5.58-Mb draft genome of Pseudomonas putida strain KG-4 obtained from the
      oil fields of the Krishna-Godavari basin, Andhra Pradesh,
      India. The genome sequence is expected to facilitate identification and
      understanding of genes associated with hydrocarbon metabolism, which can help in
      developing strategies for managing oil spills and bioremediation.
AU  - Dawar C
AU  - Aggarwal RK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00590-15.

PMID- 24973023
VI  - 56
DP  - 2014
TI  - Improving the Efficiency of Transposon Mutagenesis in Salmonella Enteritidis by Overcoming Host-Restriction Barriers.
PG  - 1004-1010
AB  - Transposon mutagenesis using transposome complex is a powerful method for functional genomics
      analysis in diverse bacteria by creating a large number of random mutants to prepare a
      genome-saturating mutant library. However, strong host restriction barriers can lead to
      limitations with species- or strain-specific restriction-modification systems. The purpose of
      this study was to enhance the transposon mutagenesis efficiency of Salmonella Enteritidis to
      generate a larger number of random insertion mutants. Host-adapted Tn5 DNA was used to form a
      transposome complex, and this simple approach significantly and consistently improved the
      efficiency of transposon mutagenesis, resulting in a 46-fold increase in the efficiency as
      compared to non-adapted transposon DNA fragments. Random nature of Tn5 insertions was
      confirmed by high-throughput sequencing of the Tn5-junction sequences. The result based on S.
      Enteritidis in this study should find broad applications in preparing a comprehensive mutant
      library of other species using transposome complex.
AU  - Dawoud TM
AU  - Jiang T
AU  - Mandal RK
AU  - Ricke SC
AU  - Kwon YM
PT  - Journal Article
TA  - Mol. Biotechnol.
JT  - Mol. Biotechnol.
SO  - Mol. Biotechnol. 2014 56: 1004-1010.

PMID- 3470568
VI  - 11C
DP  - 1987
TI  - Characterization of three EcoRI endonuclease mutants with altered DNA-Protein contacts designed to change specificity.
PG  - 205
AB  - Mutants of the EcoRI endonuclease were created by site directed mutagenesis in
      an attempt to alter specificity.  The mutations were chosen, based on the
      crystal structure, to change the hydrogen bonding characteristics of the amino
      acid side chains responsible for recognition of the canonical DNA sequence.
      The mutants generated were Glu144->Asp(ED144), Arg145->Lys(RK145), and
      Arg200->Lys(RK200).  These were purified to homogeneity.  We measured kcat and
      Km on pBR322 and pBR322 lacking the RI site.  We also determined the salt and
      pH optima.  All of the mutants cleave the canonical sequence; however, they all
      accumulate the nicked intermediate.  Linear DNA production by ED144 is
      increased at low salt to a nearly wildtype level.  kcat values are well below
      wildtype kcat in RK145 and RK200.  The specificity constants (kcat/Km) are
      different from wildtype.  Canonical to noncanonical kcat/Km ratios indicate
      altered specificity.  Ed144 has increased specificity for the canonical site.
      The rate limiting step in the wildtype is the off rate from nonspecific DNA
      after cleavage.  If this step is also limitiing in the mutants, then hydrogen
      bonds involved in recognition of the canonical site are normally made to some
      extent in nonspecific DNA.  Completely changing specificity is difficult or
      perhaps impossible to accomplish by making a single amino acid change.  One
      might expect enzymes to have a structure resistsant to specificity changes by a
      single amino acid substitution, especially if a specificity change would be a
      lethal event.
AU  - Day JP
AU  - Reich NO
AU  - Hager P
AU  - Rosenberg J
AU  - McClarin JA
AU  - Grable J
AU  - Boyer HW
AU  - Greene PJ
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1987 11C: 205.

PMID- 25035322
VI  - 2
DP  - 2014
TI  - Genome Sequence of Bacillus thuringiensis subsp. kurstaki Strain HD-1.
PG  - e00613-14
AB  - We report here the complete genome sequence of Bacillus thuringiensis subsp. kurstaki strain
      HD-1, which serves as the primary U.S. reference standard for all
      commercial insecticidal formulations of B. thuringiensis manufactured around the
      world.
AU  - Day M
AU  - Ibrahim M
AU  - Dyer D
AU  - Bulla L Jr
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00613-14.

PMID- 25720688
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequences of the Archetypal K1 Escherichia coli Neonatal Isolate RS218 and Contemporary Neonatal Bacteremia Clinical Isolates SCB11, SCB12, and SCB15.
PG  - e01598-14
AB  - Neonatal bacteremia Escherichia coli strains commonly belong to the K1 capsular type. Their
      ability to cause invasive neonatal disease appears to be determined by other virulence factors
      that have yet to be identified. We report here the genome sequences of four E. coli neonatal
      bacteremia isolates, including that of  the archetypal strain RS218.
AU  - Day MW
AU  - Jackson LA
AU  - Akins DR
AU  - Dyer DW
AU  - Chavez-Bueno S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01598-14.

PMID- 321803
VI  - 21
DP  - 1977
TI  - UV-induced alleviation of K-specific restriction of bacteriophage lambda.
PG  - 1249-1251
AB  - A partial release of K-specific restriction of phage lambda grown in
      Escherichia coli C was observed when E. coli K strains AB1157 (having wild-type
      repair of UV-produced DNA damage) and AB1886 (uvrA) were irradiated with UV
      light before infection.  The effect occurred in AB1886 at lower UV fluences
      than it did in AB1157.  Little or no release of restriction was observed when
      AB2463 (recA) or AB2494 (lex-1) was used.  Such release of restriction appears
      to be another of the UV-induced phenomena associated with SOS repair.
AU  - Day RS
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1977 21: 1249-1251.

PMID- 27274785
VI  - 11
DP  - 2016
TI  - Complete genome sequence of Streptococcus agalactiae strain GBS85147 serotype of  type Ia isolated from human oropharynx.
PG  - 39
AB  - Streptococcus agalactiae, also referred to as Group B Streptococcus, is a frequent resident of
      the rectovaginal tract in humans, and a major cause of
      neonatal infection. The pathogen can also infect adults with underlying disease,
      particularly the elderly and immunocompromised ones. In addition, S. agalactiae
      is a known fish pathogen, which compromises food safety and represents a zoonotic
      hazard. This study provides valuable structural, functional and evolutionary
      genomic information of a human S. agalactiae serotype Ia (ST-103) GBS85147 strain
      isolated from the oropharynx of an adult patient from Rio de Janeiro, thereby
      representing the first human isolate in Brazil. We used the Ion Torrent PGM
      platform with the 200 bp fragment library sequencing kit. The sequencing
      generated 578,082,183 bp, distributed among 2,973,022 reads, resulting in an
      approximately 246-fold mean coverage depth and was assembled using the Mira
      Assembler v3.9.18. The S. agalactiae strain GBS85147 comprises of a circular
      chromosome with a final genome length of 1,996,151 bp containing 1,915
      protein-coding genes, 18 rRNA, 63 tRNA, 2 pseudogenes and a G + C content of
      35.48 %.
AU  - de Aguiar EL et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 39.

PMID- 27795240
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a Novel Mucilaginibacter Member Isolated from Brazilian  Amazon Soil.
PG  - e01033-16
AB  - Bacteria from the Mucilaginibacter genus are still poorly understood, although their
      importance has been shown by recent reports describing great quantities of
      biofilms produced in their colonies. We report the draft genome sequence of a
      novel Mucilaginibacter member, comprising 8 contigs, totaling 5,478,589 bp and
      4,876 predicted coding sequences.
AU  - de Alencar SA
AU  - Costa FS
AU  - Rodrigues GR
AU  - Barreto CC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01033-16.

PMID- 28408673
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Methicillin-Resistant Staphylococcus aureus Strain LC33  Isolated from Human Breast Milk.
PG  - e00154-17
AB  - Here, we report the draft genome sequence of Staphylococcus aureus strain LC33, isolated from
      human breast milk in Brazil. This microorganism has been typed as
      ST1/t127/sccmecV. To our knowledge, this is the first draft genome sequence of a
      methicillin-resistant S. aureus strain isolated from human breast milk.
AU  - de Almeida JB
AU  - de Carvalho SP
AU  - de Freitas LM
AU  - Guimaraes AM
AU  - do Nascimento NC
AU  - Dos Santos AP
AU  - Messick JB
AU  - Timenetsky J
AU  - Marques LM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00154-17.

PMID- 25999579
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Linezolid-Susceptible Staphylococcus haemolyticus Sh29/312/L2, a Clonal Derivative of a Linezolid-Resistant Clinical Strain.
PG  - e00494-15
AB  - We report the whole-genome sequence (WGS) of an in vitro susceptible derivative revertant
      mutant from a bloodstream isolate involved in a nosocomial outbreak in
      Brazil. The WGS comprises 2.5 Mb with 2,500 protein-coding sequences, 16rRNA
      genes, and 60 tRNA genes.
AU  - de Almeida LM
AU  - Pires C
AU  - Cerdeira LT
AU  - de Oliveira TG
AU  - McCulloch JA
AU  - Perez-Chaparro PJ
AU  - Sacramento AG
AU  - Brito AC
AU  - da Silva JL
AU  - de Araujo MR
AU  - Lincopan N
AU  - Martin MJ
AU  - Gilmore MS
AU  - Mamizuka EM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00494-15.

PMID- 26184948
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Noninvasive Streptococcus pyogenes M/emm28 Strain STAB10015, Isolated from a Child with Perianal Dermatitis in French Brittany.
PG  - e00806-15
AB  - We report here the complete genome sequence of a noninvasive strain of Streptococcus pyogenes
      M/emm28, isolated from perianal dermatitis in a child. The genome is composed of 1,950,454 bp,
      with a G+C content of 38.2%, and it has 1,925 identified coding sequences and harbors two
      intact prophages and a new integrating conjugative element (ICE).
AU  - de Andrade-Barboza S
AU  - Meygret A
AU  - Vincent P
AU  - Moullec S
AU  - Soriano N
AU  - Lagente V
AU  - Minet J
AU  - Kayal S
AU  - Faili A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00806-15.

PMID- 2467142
VI  - 13D
DP  - 1989
TI  - Molecular nature of the restriction-modification system LT of Salmonella typhimurium.
PG  - 212
AB  - Restriction-modification (R-M) system LT is present in most Salmonella strains.
      Its genes are chromosomally located near proC.  We have cloned these genes and
      determined some properties of the coded enzymes.  On appropriate S. typhimurium
      strains, the phage vector lambda EMBL4 was very strongly restricted by LT.
      This allowed the selection of a lambda clone carrying the modification gene and
      therefore immune to the LT restriction.  This gene was subcloned into plasmid
      vectors and expressed in E. coli.  A restricting recombinant clone was isolated
      from a plasmid genomic library of S. typhimurium made in a modifying host
      strain.  This clone proved to contain a plasmid harboring the genes coding for
      both restriction and modification activities.  In contrast with other studied
      R-M systems, the introduction of LT genes into a nonmodifying host is lethal,
      probably because of self-restriction of the chromosomal DNA.  The sequence of
      the recognition site of the LT enzymes was found to be 5' GAGAC 3'.  It is
      characteristic of type III R-M systems (5 bp long, asymmetric, adenine present
      on only one strand).  The methylated base is the 5' adenine.
AU  - De Backer O
AU  - Colson C
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1989 13D: 212.

PMID- 1846862
VI  - 173
DP  - 1991
TI  - Transfer of the genes for the StyLTI restriction-modification system of Salmonella typhimurium to strains lacking modification ability results in death of the recipient cells and degradation of their DNA.
PG  - 1328-1330
AB  - The genes encoding the restriction-modification system, StyLTI, of Salmonella
      typhimurium were inserted in vivo into the conjugative plasmid pULB21.  This
      allowed us to transfer the StyLTI genes at a very high frequency and to monitor
      the fate of recipient cells after mating.  Transfer of the StyLTI restriction
      and modification genes into a modificationless recipient was lethal and
      resulted in degradation of the cell's DNA.  This indicates that, in contrast to
      any other known restriction-modification systems, StyLTI cannot be established
      after horizontal transfer into a naive host.
AU  - De Backer O
AU  - Colson C
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1991 173: 1328-1330.

PMID- 1846861
VI  - 173
DP  - 1991
TI  - Two-step cloning and expression in Escherichia coli of the DNA restriction-modification system StyLTI of Salmonella typhimurium.
PG  - 1321-1327
AB  - The StyLTI restriction-modification system is common to most strains of the
      genus Salmonella, including Salmonella typhimurium.  We report here the
      two-step cloning of the genes controlling the StyLTI system.  The StyLTI
      methylase gene (mod) was cloned first.  Then, the companion endonuclease gene
      (res) was introduced on a compatible vector.  A strain of S. typhimurium
      sensitive to the coliphage lambda was constructed and used to select
      self-modifying recombinant phages from a Res-Mod+ S. typhimurium genomic
      library in the lambda EMBL4 cloning vector.  The methylase gene of one of these
      phages was then subcloned in pBR328 and transferred into Escherichia coli.  In
      the second step, the closely linked endonuclease and methylase genes were
      cloned together on a single DNA fragment inserted in pACYC184 and introduced
      into the Mod+ E. coli strain obtained in the first step.  Attemps to transform
      Mod- E. coli or S. typhimurium strains with this Res+ Mod+ plasmid were
      unsuccessful, whereas transformation of Mod+ strains occured at a normal
      frequency.  This can be understood if the introduction of the StyLTI genes into
      naive hosts is lethal because of degradation of host DNA by restriction
      activity; in contrast to most restriction-modification systems, StyLTI could
      not be transferred into naive hosts without killing them.  In addition, it was
      found that strains containing only the res gene are viable and lack restriction
      activity in the absence of the companion mod gene.  This suggests that
      expression of the StyLTI endonuclease activity requires at least one
      polypeptide involved in the methylation activity, as is the case for types I
      and III restriction-modification systems but not for type II systems.
AU  - De Backer O
AU  - Colson C
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1991 173: 1321-1327.

PMID- 1995420
VI  - 97
DP  - 1991
TI  - Identification of the recognition sequence for the M.StyLTI methyltransferase of Salmonella typhimurium LT7: an asymmetric site typical of type-III enzymes.
PG  - 103-107
AB  - The StyLTI restriction-modification (R-M) system is encoded by chromosomal
      genes of Salmonella typhimurium LT7.  We report here the identification of the
      nucleotide (nt) sequence methylated by the StyLTI modification
      methyltransferase (M.StyLTI).  This enzyme was partially purified from an
      Escherichia coli strain expressing the cloned M.StyLTI-encoding gene, but
      lacking StyLTI restriction activity, and used to methylate DNAs of known
      sequence, using S-adenosyl-[methyl-3H]-methionine as the methyl donor.  The
      [3H]methylated DNA was then digested with various endonucleases.  Examination
      of labelled and unlabelled restriction fragments allowed us to map the M.StyLTI
      sites in perfectly defined regions of the DNA.  Comparison of the nt sequences
      of DNA segments with or without M.StyLTI sites permitted us to identify the
      asymmetric and nondegenerate pentanucleotide, 5'-CAG(A*)G-3'/3'-GTCTC-5', as
      the StyLTI sequence.  M.StyLTI was found to methylate only the 3' A (see
      asterisk) in the upper strand of this sequence.  Thus, M.StyLTI recognises and
      methylates the DNA in a manner very similar to that of the three known type-III
      MTases, M.EcoPI, M.EcoP15, and M.HinfIII.  This strongly suggests that StyLTI
      constitutes a fourth type-III R-M system.
AU  - De Backer O
AU  - Colson C
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1991 97: 103-107.

PMID- 25522320
VI  - 10
DP  - 2014
TI  - Dissemination of cephalosporin resistance genes between Escherichia coli strains  from farm animals and humans by specific plasmid lineages.
PG  - e1004776
AB  - Third-generation cephalosporins are a class of beta-lactam antibiotics that are often used for
      the treatment of human infections caused by Gram-negative
      bacteria, especially Escherichia coli. Worryingly, the incidence of human
      infections caused by third-generation cephalosporin-resistant E. coli is
      increasing worldwide. Recent studies have suggested that these E. coli strains,
      and their antibiotic resistance genes, can spread from food-producing animals,
      via the food-chain, to humans. However, these studies used traditional typing
      methods, which may not have provided sufficient resolution to reliably assess the
      relatedness of these strains. We therefore used whole-genome sequencing (WGS) to
      study the relatedness of cephalosporin-resistant E. coli from humans, chicken
      meat, poultry and pigs. One strain collection included pairs of human and
      poultry-associated strains that had previously been considered to be identical
      based on Multi-Locus Sequence Typing, plasmid typing and antibiotic resistance
      gene sequencing. The second collection included isolates from farmers and their
      pigs. WGS analysis revealed considerable heterogeneity between human and
      poultry-associated isolates. The most closely related pairs of strains from both
      sources carried 1263 Single-Nucleotide Polymorphisms (SNPs) per Mbp core genome.
      In contrast, epidemiologically linked strains from humans and pigs differed by
      only 1.8 SNPs per Mbp core genome. WGS-based plasmid reconstructions revealed
      three distinct plasmid lineages (IncI1- and IncK-type) that carried cephalosporin
      resistance genes of the Extended-Spectrum Beta-Lactamase (ESBL)- and AmpC-types.
      The plasmid backbones within each lineage were virtually identical and were
      shared by genetically unrelated human and animal isolates. Plasmid
      reconstructions from short-read sequencing data were validated by long-read DNA
      sequencing for two strains. Our findings failed to demonstrate evidence for
      recent clonal transmission of cephalosporin-resistant E. coli strains from
      poultry to humans, as has been suggested based on traditional, low-resolution
      typing methods. Instead, our data suggest that cephalosporin resistance genes are
      mainly disseminated in animals and humans via distinct plasmids.
AU  - de Been M
AU  - Lanza VF
AU  - de Toro M
AU  - Scharringa J
AU  - Dohmen W
AU  - Du Y
AU  - Hu J
AU  - Lei Y
AU  - Li N
AU  - Tooming-Klunderud A
AU  - Heederik DJ
AU  - Fluit AC
AU  - Bonten MJ
AU  - Willems RJ
AU  - de la Cruz F
AU  - van Schaik W
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2014 10: e1004776.

PMID- 10632891
VI  - 35
DP  - 2000
TI  - The length of a tetranucleotide repeat tract in Haemophilus influenzae determines the phase variation rate of a gene with homology to type III DNA methyltransferases.
PG  - 211-222
AB  - Haemophilus influenzae is an obligate commensal of the upper respiratory tract of humans that
      uses simple repeats (microsatellites) to alter gene expression. The mod gene of H. influenzae
      strain Rd has homology to DNA methyltransferases of type III restriction/modification systems
      and has 40 tetranucleotide (5'-AGTC) repeats within its open reading frame. This gene was
      found in 21 out of 23 genetically distinct H. influenzae strains, and in 13 of these strains
      the locus contained repeats. H. influenzae strains were constructed in which a lacZ reporter
      was fused to a chromosomal copy of mod downstream of the repeats. Phase variation occurred at
      a high frequency in strains with the wild-type number of repeats. Mutation rates were derived
      for similarly engineered strains, containing different numbers of repeats. Rates increased
      linearly with tract length over the range 17-38 repeat units. The majority of tract
      alterations were insertions or deletions of one repeat unit with a 2:1 bias towards
      contractions of the tract. These results demonstrate the number of repeats to be an important
      determinant of phase variation rate in H. influenzae for a gene containing a microsatellite.
AU  - De Bolle X
AU  - Bayliss CD
AU  - Field D
AU  - van de Ven T
AU  - Saunders NJ
AU  - Hood DW
AU  - Moxon ER
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2000 35: 211-222.

PMID- 26950322
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a Salmonella enterica subsp. enterica Serovar Gallinarum bv. Gallinarum Isolate Associated with Fowl Typhoid Outbreaks in Brazil.
PG  - e00019-16
AB  - Salmonella enterica subsp. enterica serovar Gallinarum bv. Gallinarum strains are bird
      pathogens causing fowl typhoid (FT). Isolate BR_RS12 was obtained from a
      poultry flock with FT in 2014. The sequencing of this genome will enable to track
      the origin of the recent outbreaks in Brazil.
AU  - De Carli S
AU  - Graf T
AU  - Mayer FQ
AU  - Cibulski S
AU  - Lehmann FK
AU  - Fonseca AS
AU  - Ikuta N
AU  - Lunge VR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00019-16.

PMID- 28408675
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Two Clinical Methicillin-Resistant Staphylococcus aureus Strains Isolated from Healthy Children in Brazil.
PG  - e00158-17
AB  - We report here the draft genome sequences of two community-associated methicillin-resistant
      Staphylococcus aureus (CA-MRSA) strains, C18 and C80,
      isolated from healthy children from day care centers. To our knowledge, these are
      the first draft genome sequences of CA-MRSA ST398/CC398/SccmecV and CA-MRSA
      ST5/CC5/SccmecIVa isolated from healthy children in Brazil.
AU  - de Carvalho SP
AU  - de Almeida JB
AU  - de Freitas LM
AU  - Guimaraes AM
AU  - do Nascimento NC
AU  - Dos Santos AP
AU  - Messick JB
AU  - Timenetsky J
AU  - Marques LM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00158-17.

PMID- 29371355
VI  - 6
DP  - 2018
TI  - Genome Sequence of Rhizobium sullae HCNT1 Isolated from Hedysarum coronarium Nodules and Featuring Peculiar Denitrification Phenotypes.
PG  - e01518-17
AB  - The genome sequence of Rhizobium sullae strain HCNT1, isolated from root nodules  of the
      legume Hedysarum coronarium growing in wild stands in Tuscany, Italy, is
      described here. Unlike other R. sullae strains, this isolate features a truncated
      denitrification pathway lacking NO/N2O reductase activity and displaying high
      sensitivity to nitrite under anaerobic conditions.
AU  - de Diego-Diaz B
AU  - Treu L
AU  - Campanaro S
AU  - da Silva DV
AU  - Basaglia M
AU  - Favaro L
AU  - Casella S
AU  - Squartini A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01518-17.

PMID- 29348354
VI  - 6
DP  - 2018
TI  - Genome Sequence of Enterococcus mundtii EM01, Isolated from Bombyx mori Midgut and Responsible for Flacherie Disease in Silkworms Reared on an Artificial Diet.
PG  - e01495-17
AB  - The whole genome sequence of Enterococcus mundtii strain EM01 is reported here. The isolate
      proved to be the cause of flacherie in Bombyx mori To date, the
      genomes of 11 other E. mundtii strains have been sequenced. EM01 is the only
      strain that displayed active pathological effects on its associated animal
      species.
AU  - de Diego-Diaz B
AU  - Treu L
AU  - Campanaro S
AU  - da Silva DV
AU  - Saviane A
AU  - Cappellozza S
AU  - Squartini A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01495-17.

PMID- 1655710
VI  - 173
DP  - 1991
TI  - Use of cloned DNA methylase genes to increase the frequency of transfer of foreign genes into Xanthomonas campestris pv. malvacearum.
PG  - 6421-6427
AB  - In vitro-packaged cosmid libraries of DNA from the bacterium Xanthomonas
      campestris pv. malvacearum were restricted 200- to 1,000-fold when introduced
      into Mcr+ strains of Escherichia coli compared with restriction in the Mcr-
      strain HB101.  Restriction was predominantly associated with the mcrBC+ gene in
      E. coli.  A plasmid (pUFR052) encoding the XmaI and XmaIII DNA methylases was
      isolated from an X. campestris pv. malvacearum library by a screening procedure
      utilizing Mcr+ and Mcr- E. coli strains.  Transfer of plasmids from E. coli
      strains to X. campestris pv. malvacearum by conjugation was enhanced by up to
      five orders of magnitude when the donor cells contained pUFR052 as well as the
      plasmid to be transferred.  Subcloning of pUFR052 revealed that at least two
      regions of the plasmid were required for full modification activity.  Use of
      such modifier plasmids is a simple, novel method that may allow the efficient
      introduction of genes into any organism in which restriction systems provide a
      potent barrier to such gene transfer.
AU  - De Feyter R
AU  - Gabriel DW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1991 173: 6421-6427.

PMID- 29301884
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Marinobacter sp. Strain ANT_B65, Isolated from Antarctic Marine Sponge.
PG  - e01404-17
AB  - Marinobacter sp. strain ANT_B65 was isolated from sponge collected in King George Island,
      Antarctica. The draft genome of 4,173,840 bp encodes 3,743 protein-coding
      open reading frames. The genome will provide insights into the strain's potential
      use in the production of natural products.
AU  - de Franca P
AU  - Camilo E
AU  - Fantinatti-Garboginni F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01404-17.

PMID- 19370165
VI  - 5
DP  - 2009
TI  - Alliance of Proteomics and Genomics to Unravel the Specificities of Sahara Bacterium.
PG  - e1000434
AB  - To better understand adaptation to harsh conditions encountered in hot arid deserts, we report
      the first complete genome sequence and proteome analysis of a bacterium, Deinococcus deserti
      VCD115, isolated from Sahara surface sand. Its genome consists of a 2.8-Mb chromosome and
      three large plasmids of 324 kb, 314 kb, and 396 kb. Accurate primary genome annotation of its
      3,455 genes was guided by extensive proteome shotgun analysis. From the large corpus of MS/MS
      spectra recorded, 1,348 proteins were uncovered and semiquantified by spectral counting. Among
      the highly detected proteins are several orphans and Deinococcus-specific proteins of unknown
      function. The alliance of proteomics and genomics highthroughput techniques allowed
      identification of 15 unpredicted genes and, surprisingly, reversal of incorrectly predicted
      orientation of 11 genes. Reversal of orientation of two Deinococcus-specific radiation-induced
      genes, ddrC and ddrH, and
      identification in D. deserti of supplementary genes involved in manganese import extend our
      knowledge of the radiotolerance toolbox of Deinococcaceae. Additional genes involved in
      nutrient import and in DNA repair (i.e., two extra recA, three translesion DNA polymerases, a
      photolyase) were also identified and found to be expressed under standard growth conditions,
      and, for these DNA repair genes, after exposure of the cells to UV. The supplementary nutrient
      import and DNA repair genes are likely important for survival and adaptation of D. deserti to
      its nutrient-poor, dry, and UV-exposed extreme environment.
AU  - De Groot A
AU  - Dulermo R
AU  - Ortet P
AU  - Blanchard L
AU  - Guerin P
AU  - Fernandez B
AU  - Vacherie B
AU  - Dossat C
AU  - Jolivet E
AU  - Siguier P
AU  - Chandler M
AU  - Barakat M
AU  - Dedieu A
AU  - Barbe V
AU  - Heulin T
AU  - Sommer S
AU  - Achouak W
AU  - Jean A
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2009 5: e1000434.

PMID- 7804245
VI  - 41
DP  - 1994
TI  - Evidence for the ancestral origin of group I introns in the SSUrDNA of Naegleria spp.
PG  - 457-463
AB  - The sequence variation within the group I intron in five Naegleria spp. was studied and
      compared with the sequence variation within the flanking small subunit ribosomal DNA.
      Considerable sequence divergence was observed in the introns as well as in the rDNA.  In the
      intron deletions and insertions are only detected in the sequence contributing to the
      secondary structure, not in the open reading frame.  Most of the sequence variation is
      detected in the unpaired loops.  In the case of nucleotide substitution in helices,
      compensating base pair changes were observed.  The sequence variation does not induce
      variation in the secondary structure model.  The phylogenetic tree based on the intron
      sequences is similar to the tree based on the flanking rDNA sequences.  This observation
      indicates that the intron might have been acquired at an early stage in evolution, and lost in
      the majority of Naegleria spp.
AU  - De Jonckheere JF
PT  - Journal Article
TA  - J. Eukaryot. Microbiol.
JT  - J. Eukaryot. Microbiol.
SO  - J. Eukaryot. Microbiol. 1994 41: 457-463.

PMID- 25767247
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Five Spore-Forming Food Isolates of Bacillus pumilus.
PG  - e01539-14
AB  - Here, we report the draft genome sequences of five food isolates of Bacillus pumilus, a
      spore-forming Gram-positive bacterium.
AU  - de Jong A
AU  - van Heel AJ
AU  - Montalban-Lopez M
AU  - Krawczyk AO
AU  - Berendsen EM
AU  - Wells-Bennik M
AU  - Kuipers OP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01539-14.

PMID- 2824782
VI  - 196
DP  - 1987
TI  - Proteins encoded by the DpnII restriction gene cassette:  Two methylases and an endonuclease.
PG  - 457-469
AB  - Proteins encoded by three genes in the DpnII restriction enzyme cassette of
      Streptococcus pneumoniae were purified and characterized.  Large amounts of the
      proteins were produced by subcloning the cassette in an Escherichia coli
      expression system.  All three proteins appear to be dimers composed of
      identical polypeptide subunits.  One is the DpnII endonuclease, and the other
      two are DNA adenine methylases active at 5'GATC3' sites.  Inactivation of
      enzyme activity by insertions into the genes and comparison of the DNA sequence
      with the amino-terminal sequence of amino acid residues in the proteins
      demonstrated the following correspondence between genes and enzymes.  The
      promoter-proximal gene in the operon, dpnM, encodes a 33000 Mr polypeptide that
      gives rise to a potent DNA methylase.  The next gene, dpnA, encodes the 31000
      Mr polypeptide of a weaker and less-specific methylase.  The third gene, dpnB,
      encodes the 34000 Mr polypeptide of the endonuclease.  Although the
      endonuclease polypeptide is initiated from an ordinary ribosome-binding site,
      each of the methylase polypeptides begins at an atypical site with a consensus
      sequence entirely different from that of Shine & Dalgarno.  This presumptive
      novel ribosome-binding site is well recognized in both S. pneumoniae and E.
      coli.
AU  - de la Campa AG
AU  - Kale P
AU  - Springhorn SS
AU  - Lacks SA
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1987 196: 457-469.

PMID- 2844782
VI  - 263
DP  - 1988
TI  - Proteins encoded by the DpnI restriction gene cassette.
PG  - 14696-14702
AB  - Insertion mutations in the DpnI gene cassette of Streptococcus pneumoniae
      indicated that the two genes it contains, dpnC and dpnD, were transcribed from
      an adjacent promoter and that only dpnC was necessary for expression of the
      DpnI endonuclease.  Large amounts of the DpnI endonuclease were produced from
      the cloned cassette in an Escherichia coli expression system, and the enzyme
      was purified to homogeneity.  The DpnI endonuclease is composed of a single
      polypeptide of 30 kDa, which, as shown by NH2-terminal sequencing of the
      protein, is encoded by the entire dpnC open reading frame.  the native protein
      sedimented as a monomer of 30 kDa in 0.5 M NaCl.  A protein composed of a
      20-kDa polypeptide, which is presumably encoded by dpnD, was also produced in
      large amounts.  It was partially purified, but its function is unknown.
      Examination of the predicted amino acid sequence of DpnI revealed a potential
      metal-containing, DNA-binding finger structure.  It is suggested that this
      structure provides the specificity for recognition of the methylated DNA
      sequence, 5'-GmATC-3', that is cleaved by the DpnI endonuclease.
AU  - de la Campa AG
AU  - Springhorn SS
AU  - Kale P
AU  - Lacks SA
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1988 263: 14696-14702.

PMID- 26112781
VI  - 3
DP  - 2015
TI  - Complete Genome Sequences of Field Isolates of Mycobacterium bovis and Mycobacterium caprae.
PG  - e00247-15
AB  - Here we report the complete genome sequences of field isolates of Mycobacterium bovis and the
      related mycobacterial species, Mycobacterium caprae. The genomes of
      three M. bovis (MB1, MB3, MB4) and one M. caprae (MB2) field isolates with
      different virulence, prevalence, and host distribution phenotypes were sequenced.
AU  - de la Fuente J
AU  - Diez-Delgado I
AU  - Contreras M
AU  - Vicente J
AU  - Cabezas-Cruz A
AU  - Manrique M
AU  - Tobes R
AU  - Lopez V
AU  - Romero B
AU  - Dominguez L
AU  - Garrido JM
AU  - Juste R
AU  - Gortazar C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00247-15.

PMID- 23704184
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Moderately Halophilic Bacterium Pseudoalteromonas ruthenica Strain CP76.
PG  - e00268-13
AB  - Pseudoalteromonas ruthenica strain CP76, isolated from a saltern in Spain, is a moderately
      halophilic bacterium belonging to the Gammaproteobacteria. Here we
      report the draft genome sequence, which consists of a 4.0-Mb chromosome, of this
      strain, which is able to produce the extracellular enzyme haloprotease CPI.
AU  - de la Haba RR
AU  - Sanchez-Porro C
AU  - Leon MJ
AU  - Papke RT
AU  - Ventosa A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00268-13.

PMID- 10566865
VI  - 5
DP  - 1999
TI  - Antibiotic resistance as a stress response: complete sequencing of a large number of chromosomal loci in Staphylococcus aureus strain COL that impact   on the expression of resistance to methicillin.
PG  - 163-175
AB  - Tn551 inactivation has identified several determinants--fem or auxiliary genes--that, in
      addition to the mecA gene, are also critical for the
      expression of high-level and homogeneous resistance to methicillin.
      Genetic and/or biochemical analysis has shown that of the nearly dozen aux
      mutations described so far most are in genes involved in cell wall
      synthesis (murE, pbp2, glmM, glnR, femA/B, llm, etc.) or in complex
      regulatory functions (sigmaB), suggesting that optimal expression of
      resistance may involve the cooperative functioning of a number of genes in
      cell wall metabolism as well as stress response. The exact mechanism of
      these functions is not known. In an attempt to explore this unusual aspect
      of methicillin resistance more fully, a Tn551 transposon library,
      constructed in the background of the highly and homogeneously
      methicillin-resistant Staphylococcus aureus strain COL, was screened for
      all independent insertional mutants in which the level of methicillin
      resistance of the parental strain (MIC, 1,600 microg/ml) was reduced by at
      least 15-fold and up to 500-fold. We now describe the sequencing of 21
      Tn551-inactivated genes and their vicinities in 23 new auxiliary mutants
      that have been studied before. Using the inverted polymerase chain
      reaction (IPCR), we amplified fragments corresponding to the right and
      left junction of the Tn551 insertions, which were then sequenced by primer
      walking. The two largest groups of these new auxiliary genes encoded
      either proteins of unknown functions (6 genes) or showed homology with
      genes encoding proteins involved with putative sensory/regulatory
      activities (7 genes: protein kinases, ABC transporters, and a catabolite
      control protein). Sequencing upstream and downstream allowed the
      identification of a number of additional open reading frames, some of
      which may also include functions relevant for the expression of antibiotic
      resistance.
AU  - De Lencastre H
AU  - Wu SW
AU  - Pinho MG
AU  - Ludovice AM
AU  - Filipe S
AU  - Gardete S
AU  - Sobral R
AU  - Gill S
AU  - Chung M
AU  - Tomasz A
PT  - Journal Article
TA  - Microb. Drug Resist.
JT  - Microb. Drug Resist.
SO  - Microb. Drug Resist. 1999 5: 163-175.

PMID- 26404608
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Pelosinus fermentans JBW45, a Member of a Remarkably  Competitive Group of Negativicutes in the Firmicutes Phylum.
PG  - e01090-15
AB  - The genome of Pelosinus fermentans JBW45, isolated from a chromium-contaminated site in
      Hanford, Washington, USA, has been completed with PacBio sequencing. Nine copies of the rRNA
      gene operon and multiple transposase genes with identical sequences resulted in breaks in the
      original draft genome and may suggest genomic instability of JBW45.
AU  - De Leon KB
AU  - Utturkar SM
AU  - Camilleri LB
AU  - Elias DA
AU  - Arkin AP
AU  - Fields MW
AU  - Brown SD
AU  - Wall JD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01090-15.

PMID- 22965085
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Pelosinus fermentans JBW45, Isolated during In Situ Stimulation for Cr(VI) Reduction.
PG  - 5456-5457
AB  - Pelosinus fermentans JBW45 is an anaerobic, lactate-fermenting bacterium isolated from
      Cr(VI)-contaminated groundwater at the Hanford Nuclear Reservation 100-H site (Washington)
      that was collected after stimulation with a polylactate compound. The genome sequence of this
      organism will provide insight into the metabolic potential of a predominant population during
      stimulation for metal-reducing conditions.
AU  - De Leon KB
AU  - Young ML
AU  - Camilleri LB
AU  - Brown SD
AU  - Skerker JM
AU  - Deutschbauer AM
AU  - Arkin AP
AU  - Fields MW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5456-5457.

PMID- 30533909
VI  - 7
DP  - 2018
TI  - Near-Complete Genome Sequences of Streptomyces sp. Strains AC1-42T and AC1-42W, Isolated from Bat Guano from Cabalyorisa Cave, Mabini, Pangasinan, Philippines.
PG  - e00904-18
AB  - Streptomyces sp. strains AC1-42T and AC1-42W, isolated from bat guano from Cabalyorisa Cave,
      Mabini, Pangasinan, Philippines, are active against Bacillus
      subtilis subsp. subtilis KCTC 3135(T). The near-complete genome sequences
      reported here represent a possible source of ribosomally synthesized,
      posttranslationally modified peptides, such as lantipeptides, bacteriocins,
      linaridin, and a lasso peptide.
AU  - De Leon MP
AU  - Park AY
AU  - Montecillo AD
AU  - Siringan MAT
AU  - Rosana ARR
AU  - Kim SG
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e00904-18.

PMID- 23682152
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Pseudomonas veronii Strain 1YdBTEX2.
PG  - e00258-13
AB  - Pseudomonas veronii strain 1YdBTEX2 was isolated from a benzene-contaminated site. Here we
      report the draft genome sequence of 1YdBTEX2 and its genes
      associated with aromatic metabolism. The broad catabolic potential of this strain
      is consistent with the environment from which it was isolated.
AU  - de Lima-Morales D
AU  - Chaves-Moreno D
AU  - Jarek M
AU  - Vilchez-Vargas R
AU  - Jauregui R
AU  - Pieper DH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00258-13.

PMID- 2830237
VI  - 170
DP  - 1988
TI  - An exocytoplasmic endonuclease with restriction function in Streptomyces antibioticus.
PG  - 1339-1345
AB  - Streptomyces antibioticus produces a strong endo-DNase which is located between
      the cytoplasmic membrane and the cell wall.  All DNA substrates assayed,
      including the chromosomal DNA of this species and several bacteriophage DNAs,
      were completely degraded in vitro by the enzyme.  The rate of synthesis of the
      nuclease depended on the growth medium.  In NBG medium, in which the enzyme is
      not produced, the size of lytic plaques of several actinophages was larger than
      that in GYM or GAE medium, in which synthesis of the nuclease takes place late
      in growth.  In addition, one of the phages assayed, PhiA6, showed a diminution
      of its efficiency of plating in GYM medium with respect to that in NBG medium;
      another phage, PhiA9, grew in NBG medium but not in the other two media.  It is
      postulated that the presence of the host nuclease, together with the capability
      of the particular phage to adsorb on S. antibioticus of different growth
      phases, determines the efficiency of growth and the plaque size of the phages
      on productive media.  This hypothesis was confirmed when the growth of PhiA6
      and PhiA9 in a mutant of S. antibioticus lacking the endonuclease activity was
      analyzed.  It is concluded that the enzyme can assume, under some
      circumstances, a role in in vivo restriction.
AU  - de los Reyes-Gavilan CG
AU  - Aparicio JF
AU  - Barbes C
AU  - Hardisson C
AU  - Sanchez J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1988 170: 1339-1345.

PMID- 16348347
VI  - 56
DP  - 1990
TI  - Evidence for a plasmid-linked restriction-modification system in Lactobacillus helveticus.
PG  - 3412-3419
AB  - The presence of a restriction-modification (R/M) system against two
      bacteriophages, 328-B1 and hv, was demonstrated in three Lactobacillus
      helveticus strains, CNRZ 1094, CNRZ 1095, and CNRZ 1096.  In addition, the
      burst size of phage 328-B1 in the three restrictive strains CNRZ 1094, CNRZ
      1095, and CNRZ 1096 was reduced with respect to the values obtained in its
      propagating strain, CNRZ 328.  Heating at 60C did not inactivate the R/M
      system.  Nonrestrictive variants from CNRZ 1094 were easily obtained under
      several culture conditions, but treatment with novobiocin at 42C followed by
      storage at -20C resulted in drastic elimination of the R+/M+ phenotype from all
      clones tested.  Electrophoretic analysis of CNRZ 1084 nonrestrictive variants
      revealed the concomitant loss of a 34-kb plasmid.  Four EcoRI fragments from
      the 34-kb plasmid were cloned in the Escherichia coli vector pACYC184.  The use
      of one or several of these fragments as probes confirmed the plasmidic location
      of the genes responsible for the R/M system.  These probes also showed the
      presence of R/M plasmids in the two other restriction strains, CNRZ 1095 and
      CNRZ 1096.  Lactose-fermenting ability and/or proteolytic capacity was not
      linked to the 34-kb plasmid.
AU  - de los Reyes-Gavilan CG
AU  - Limsowtin GKY
AU  - Sechaud L
AU  - Veaux M
AU  - Accolas J-P
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1990 56: 3412-3419.

PMID- 29408032
VI  - 214
DP  - 2018
TI  - Transposon-associated lincosamide resistance lnu(C) gene identified in Brachyspira hyodysenteriae ST83.
PG  - 51-55
AB  - Treatment of Swine Dysentery (SD) caused by Brachyspira hyodysenteriae (B. hyodysenteriae) is
      carried out using antimicrobials such as macrolides, lincosamides and pleuromutilins leading
      to the selection of resistant strains.  Whole genome sequencing of a multidrug-resistant B.
      hyodysenteriae strain called BH718 belonging to sequence type (ST) 83 revealed the presence of
      the lincosamide resistance gene lnu(C) on the small 1724-bp transposon MTnSag1. The strain
      also contains an A to T substitution at position 2058 (A2058T) in the 23S rRNA gene which is
      known to be associated with macrolide and lincosamide resistance in B. hyodysenteriae. Testing
      of additional strains showed that those containing lnu(C) exhibited a higher minimal
      inhibitory concentration (MIC) of lincomycin
      (MIC64 mg/L) compared to strains lacking lnu(C), even if they also harbor the A2058T mutation.
      Resistance to pleuromutilins could not be explained by the presence of already reported
      mutations in the 23S rRNA gene and in the ribosomal protein L3. This study shows that B.
      hyodysenteriae has the ability to acquire mobile genetic elements conferring resistance to
      antibiotics.
AU  - De Luca S
AU  - Nicholson P
AU  - Magistrali CF
AU  - Garcia-Martin AB
AU  - Rychener L
AU  - Zeeh F
AU  - Frey J
AU  - Perreten V
PT  - Journal Article
TA  - Vet. Microbiol.
JT  - Vet. Microbiol.
SO  - Vet. Microbiol. 2018 214: 51-55.

PMID- 22374951
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Clinical Isolate Pantoea ananatis LMG 5342.
PG  - 1615-1616
AB  - The enterobacterium Pantoea ananatis is an ecologically versatile species. It has been found
      in the environment, as plant epiphyte and endophyte, as an emerging
      phytopathogen, and as a presumptive, opportunistic human pathogen. Here, we
      report the complete genome sequence of P. ananatis LMG 5342, isolated from a
      human wound.
AU  - De Maayer P
AU  - Chan WY
AU  - Rezzonico F
AU  - Buhlmann A
AU  - Venter SN
AU  - Blom J
AU  - Goesmann A
AU  - Frey JE
AU  - Smits TH
AU  - Duffy B
AU  - Coutinho TA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1615-1616.

PMID- 20348253
VI  - 192
DP  - 2010
TI  - Genome sequence of Pantoea ananatis LMG20103, the causative agent of Eucalyptus blight and dieback.
PG  - 2936-2937
AB  - Pantoea ananatis is a Gram-negative plant pathogen that causes disease on a broad range of
      host plants, including pineapple, maize, rice, onion, melons, and Eucalyptus, and has been
      implicated in several cases of human disease. Here, we report the genome sequence of P.
      ananatis LMG20103
      isolated from diseased Eucalyptus in South Africa.
AU  - De Maayer P
AU  - Chan WY
AU  - Venter SN
AU  - Toth IK
AU  - Birch PR
AU  - Joubert F
AU  - Coutinho TA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 2936-2937.

PMID- 24903881
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Geobacillus sp. Strains CAMR5420 and CAMR12739.
PG  - e00567-14
AB  - Thermophilic Geobacillus spp. can efficiently hydrolyze hemicellulose polymers and are
      therefore of interest in biotechnological applications. Here we report
      the genome sequences of two hemicellulolytic strains, Geobacillus sp. CAMR12739
      and CAMR5420.
AU  - De Maayer P
AU  - Williamson CE
AU  - Vennard CT
AU  - Danson MJ
AU  - Cowan DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00567-14.

PMID- 25744985
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of a New Delhi Metallo-beta-Lactamase-5 (NDM-5)-Producing Multidrug-Resistant Escherichia coli Isolate.
PG  - e00017-15
AB  - A multidrug-resistant Escherichia coli isolate from an abdominal lesion displayed resistance
      to all beta-lactams tested, including carbapenems, in addition to
      macrolides, fluoroquinolones, and tetracycline. Sequence analyses demonstrated
      the presence of blaNDM-5 in addition to at least 13 genes and 6 efflux pumps
      associated with antibiotic resistance.
AU  - de Man TJ
AU  - Perry KA
AU  - Avillan JJ
AU  - Rasheed JK
AU  - Limbago BM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00017-15.

PMID- 26988052
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Mycobacterium wolinskyi, a Rapid-Growing Species of Nontuberculous Mycobacteria.
PG  - e00138-16
AB  - Mycobacterium wolinskyi is a nonpigmented, rapidly growing nontuberculous mycobacterium
      species that is associated with bacteremia, peritonitis, infections
      associated with implants/prostheses, and skin and soft tissue infections often
      following surgical procedures in humans. Here, we report the first functionally
      annotated draft genome sequence of M. wolinskyi CDC_01.
AU  - de Man TJ
AU  - Perry KA
AU  - Lawsin A
AU  - Coulliette AD
AU  - Jensen B
AU  - Toney NC
AU  - Limbago BM
AU  - Noble-Wang J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00138-16.

PMID- 27660781
VI  - 4
DP  - 2016
TI  - High-Quality Draft Genome Sequence of the Multidrug-Resistant Clinical Isolate Enterococcus faecium VRE16.
PG  - e00992-16
AB  - Specific lineages of the commensal bacterium Enterococcus faecium belonging to CC17,
      especially ST412, have been isolated from patients in several hospitals
      worldwide and harbor antibiotic resistance genes and virulence factors. Here, we
      report a high-quality draft genome sequence and highlight features of E. faecium
      VRE16, a representative of this ST.
AU  - de Mello SS
AU  - Van Tyne D
AU  - Dabul AN
AU  - Gilmore MS
AU  - Camargo IL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00992-16.

PMID- 27834701
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Brevibacterium linens SMQ-1335.
PG  - e01242-16
AB  - Brevibacterium linens is one of the main bacteria found in the smear of surface-ripened
      cheeses. The genome of the industrial strain SMQ-1335 was
      sequenced using PacBio. It has 4,209,935 bp, a 62.6% G+C content, 3,848 open
      reading frames, and 61 structural RNAs. A new type I restriction-modification
      system was identified.
AU  - de Melo AG
AU  - Labrie SJ
AU  - Dumaresq J
AU  - Roberts RJ
AU  - Tremblay DM
AU  - Moineau S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01242-16.

PMID- 26203342
VI  - 10
DP  - 2015
TI  - High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Burkholderia sp. strain UYPR1.413.
PG  - 31
AB  - Burkholderia sp. strain UYPR1.413 is an aerobic, motile, Gram-negative, non-spore-forming rod
      that was isolated from a root nodule of Parapiptadenia
      rigida collected at the Angico plantation, Mandiyu, Uruguay, in December 2006. A
      survey of symbionts of P. rigida in Uruguay demonstrated that this species is
      nodulated predominantly by Burkholderia microsymbionts. Moreover, Burkholderia
      sp. strain UYPR1.413 is a highly efficient nitrogen fixing symbiont with this
      host. Currently, the only other sequenced isolate to fix with this host is
      Cupriavidus sp. UYPR2.512. Therefore, Burkholderia sp. strain UYPR1.413 was
      selected for sequencing on the basis of its environmental and agricultural
      relevance to issues in global carbon cycling, alternative energy production, and
      biogeochemical importance, and is part of the GEBA-RNB project. Here we describe
      the features of Burkholderia sp. strain UYPR1.413, together with sequence and
      annotation. The 10,373,764 bp high-quality permanent draft genome is arranged in
      336 scaffolds of 342 contigs, contains 9759 protein-coding genes and 77 RNA-only
      encoding genes.
AU  - De Meyer SE
AU  - Fabiano E
AU  - Tian R
AU  - Van Berkum P
AU  - Seshadri R
AU  - Reddy T
AU  - Markowitz V
AU  - Ivanova N
AU  - Pati A
AU  - Woyke T
AU  - Howieson J
AU  - Kyrpides N
AU  - Reeve W
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 31.

PMID- 26203327
VI  - 10
DP  - 2015
TI  - High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Cupriavidus sp. strain UYPR2.512.
PG  - 13
AB  - Cupriavidus sp. strain UYPR2.512 is an aerobic, motile, Gram-negative, non-spore-forming rod
      that was isolated from a root nodule of Parapiptadenia
      rigida grown in soils from a native forest of Uruguay. Here we describe the
      features of Cupriavidus sp. strain UYPR2.512, together with sequence and
      annotation. The 7,858,949 bp high-quality permanent draft genome is arranged in
      365 scaffolds of 369 contigs, contains 7,411 protein-coding genes and 76 RNA-only
      encoding genes, and is part of the GEBA-RNB project proposal.
AU  - De Meyer SE
AU  - Fabiano E
AU  - Tian R
AU  - Van Berkum P
AU  - Seshadri R
AU  - Reddy T
AU  - Markowitz V
AU  - Ivanova NN
AU  - Pati A
AU  - Woyke T
AU  - Howieson J
AU  - Kyrpides NC
AU  - Reeve W
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 13.

PMID- 29074646
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Mesorhizobium sophorae ICMP 19535T, a Highly Specific, Nitrogen-Fixing Symbiont of New Zealand Endemic Sophora spp.
PG  - e00958-17
AB  - We report here the complete genome sequence of Mesorhizobium sophorae ICMP 19535T This strain
      was isolated from Sophora microphylla root nodules and can nodulate
      and fix nitrogen with this host and also with Sophora prostrata, Sophora
      longicarinata, and Clianthus puniceus The genome consists of 8.05 Mb.
AU  - De Meyer SE
AU  - Nguyen DT
AU  - Wang P
AU  - Andrews M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00958-17.

PMID- 26478786
VI  - 10
DP  - 2015
TI  - High-quality permanent draft genome sequence of the Mimosa asperata - nodulating  Cupriavidus sp. strain AMP6.
PG  - 80
AB  - Cupriavidus sp. strain AMP6 is an aerobic, motile, Gram-negative, non-spore-forming rod that
      was isolated from a root nodule of Mimosa asperata
      collected in Santa Ana National Wildlife Refuge, Texas, in 2005. Mimosa asperata
      is the only legume described so far to exclusively associates with Cupriavidus
      symbionts. Moreover, strain AMP6 represents an early-diverging lineage within the
      symbiotic Cupriavidus group and has the capacity to develop an effective
      nitrogen-fixing symbiosis with three other species of Mimosa. Therefore, the
      genome of Cupriavidus sp. strain AMP6 enables comparative analyses of symbiotic
      trait evolution in this genus and here we describe the general features, together
      with sequence and annotation. The 7,579,563 bp high-quality permanent draft
      genome is arranged in 260 scaffolds of 262 contigs, contains 7,033 protein-coding
      genes and 97 RNA-only encoding genes, and is part of the GEBA-RNB project
      proposal.
AU  - De Meyer SE
AU  - Parker M
AU  - Van Berkum P
AU  - Tian R
AU  - Seshadri R
AU  - Reddy TB
AU  - Markowitz V
AU  - Ivanova N
AU  - Pati A
AU  - Woyke T
AU  - Kyrpides N
AU  - Howieson J
AU  - Reeve W
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 80.

PMID- 26388968
VI  - 10
DP  - 2015
TI  - High-quality permanent draft genome sequence of the Lebeckia - nodulating Burkholderia dilworthii strain WSM3556(T).
PG  - 64
AB  - Burkholderia dilworthii strain WSM3556(T) is an aerobic, motile, Gram-negative,
      non-spore-forming rod that was isolated from an effective N2-fixing root nodule of Lebeckia
      ambigua collected near Grotto Bay Nature Reserve, in the Western Cape of South Africa, in
      October 2004. This plant persists in infertile and deep sandy soils with acidic pH, and is
      therefore an ideal candidate for a perennial based agriculture system in Western Australia.
      WSM3556(T) thus represents a potential inoculant quality strain for L. ambigua for which we
      describe the general features, together with genome sequence and annotation. The 7,679,067 bp
      high-quality permanent draft genome is arranged in 140 scaffolds of 141 contigs,  contains
      7,059 protein-coding genes and 64 RNA-only encoding genes, and is part of the GEBA-RNB project
      proposal.
AU  - De Meyer SE
AU  - Tian R
AU  - Seshadri R
AU  - Ivanova N
AU  - Pati A
AU  - Markowitz V
AU  - Woyke T
AU  - Yates R
AU  - Howieson J
AU  - Kyrpides N
AU  - Reeve W
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 64.

PMID- 26478785
VI  - 10
DP  - 2015
TI  - High-quality permanent draft genome sequence of the Lebeckia ambigua-nodulating Burkholderia sp. strain WSM4176.
PG  - 79
AB  - Burkholderia sp. strain WSM4176 is an aerobic, motile, Gram-negative, non-spore-forming rod
      that was isolated from an effective N2-fixing root nodule
      of Lebeckia ambigua collected in Nieuwoudtville, Western Cape of South Africa, in
      October 2007. This plant persists in infertile, acidic and deep sandy soils, and
      is therefore an ideal candidate for a perennial based agriculture system in
      Western Australia. Here we describe the features of Burkholderia sp. strain
      WSM4176, which represents a potential inoculant quality strain for L. ambigua,
      together with sequence and annotation. The 9,065,247 bp high-quality-draft genome
      is arranged in 13 scaffolds of 65 contigs, contains 8369 protein-coding genes and
      128 RNA-only encoding genes, and is part of the GEBA-RNB project proposal
      (Project ID 882).
AU  - De Meyer SE
AU  - Tian R
AU  - Seshadri R
AU  - Reddy T
AU  - Markowitz V
AU  - Ivanova N
AU  - Pati A
AU  - Woyke T
AU  - Kyrpides N
AU  - Yates R
AU  - Howieson J
AU  - Reeve W
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 79.

PMID- 24994795
VI  - 2
DP  - 2014
TI  - Genome Sequence of Streptomyces wadayamensis Strain A23, an Endophytic Actinobacterium from Citrus reticulata.
PG  - e00625-14
AB  - The actinobacterium Streptomyces wadayamensis A23 is an endophyte of Citrus reticulata that
      produces the antimycin and mannopeptimycin antibiotics, among
      others. The strain has the capability to inhibit Xylella fastidiosa growth. The
      draft genome of S. wadayamensis A23 has ~7.0 Mb and 6,006 protein-coding
      sequences, with a 73.5% G+C content.
AU  - de Oliveira LG
AU  - Tormet GGD
AU  - Samborsky M
AU  - Marcon J
AU  - Araujo WL
AU  - de Azevedo JL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00625-14.

PMID- 25573928
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Vibrio fluvialis Strains 560 and 539, Isolated from Environmental Samples.
PG  - e01344-14
AB  - Vibrio fluvialis is a halophilic bacterium found in many environments and is mainly associated
      with sporadic cases and outbreaks of gastroenteritis in humans.
      Here, we describe the genome sequences of environmental strains of V. fluvialis
      560 (Vf560) and V. fluvialis 539 (Vf539) possessing a variant of the integrative
      and conjugative element (ICE) SXT for the first time in Brazil and South America.
AU  - de Oliveira-Veras AA et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01344-14.

PMID- 23991251
VI  - 8
DP  - 2013
TI  - Complete genome sequence of Streptococcus agalactiae strain SA20-06, a fish pathogen associated to meningoencephalitis outbreaks.
PG  - 188-197
AB  - Streptococcus agalactiae (Lancefield group B; GBS) is the causative agent of
      meningoencephalitis in fish, mastitis in cows, and neonatal sepsis in humans.
      Meningoencephalitis is a major health problem for tilapia farming and is
      responsible for high economic losses worldwide. Despite its importance, the
      genomic characteristics and the main molecular mechanisms involved in virulence
      of S. agalactiae isolated from fish are still poorly understood. Here, we present
      the genomic features of the 1,820,886 bp long complete genome sequence of S.
      agalactiae SA20-06 isolated from a meningoencephalitis outbreak in Nile tilapia
      (Oreochromis niloticus) from Brazil, and its annotation, consisting of 1,710
      protein-coding genes (excluding pseudogenes), 7 rRNA operons, 79 tRNA genes and
      62 pseudogenes.
AU  - de Padua-Pereira U et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 188-197.

PMID- 25377699
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Non-O1 and Non-O139 Vibrio cholerae Strain VCC19.
PG  - e01094-14
AB  - Vibrio cholerae O1 is the causative agent of cholera and is ubiquitous in the aquatic
      environment, while V. cholerae strains non-O1 and non-O139 are recognized
      as causative agents of sporadic and localized outbreaks of diarrhea. Here, we
      report the complete sequence of a non-O1 and non-O139 V. cholerae strain (VCC19),
      which was isolated from the environment in Brazil. The sequence includes the
      integrative conjugative element (ICE). This paper is the first report of the
      presence of such an element in a V. cholerae strain isolated in Brazil.
AU  - de Sa PC
AU  - Da Silva ML
AU  - Carneiro AR
AU  - Gomes JC
AU  - Dias LM
AU  - Alves JT
AU  - De Oliveira VAA
AU  - Barauna RA
AU  - Das Gracas DA
AU  - Matte MH
AU  - Sato MI
AU  - Hachich EM
AU  - Matte GR
AU  - Ramos RT
AU  - Silva A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01094-14.

PMID- 29674547
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Pseudomonas sp. Strain 382 and Pantoea coffeiphila 342, Endophytic Bacteria Isolated from Brazilian Guarana [Paullinia cupana (Mart.)  Ducke].
PG  - e00287-18
AB  - Pseudomonas sp. strain 382 and Pantoea coffeiphila 342 are two endophytic bacterial strains
      isolated from Paullinia cupana (guarana) seeds. Their draft
      genome sizes were 5.96 and 6.38 Mbp, with 315 and 266 scaffolds and 52% and 62%
      GC content, respectively.
AU  - de Siqueira KA
AU  - Liotti RG
AU  - Mendes TAO
AU  - Soares MA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00287-18.

PMID- 29650581
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of the Mercury-Resistant Strain Acinetobacter baumannii I43.
PG  - e00283-18
AB  - Here, we report the draft genome sequence of the Acinetobacter baumannii strain I43, which is
      highly resistant to mercury. The Illumina-based sequence analysis
      revealed a genome of approximately 4,520,353 bp composed of 4,091 coding
      sequences.
AU  - de Siqueira KA
AU  - Mello IS
AU  - Pietro-Souza W
AU  - Mendes TAO
AU  - Soares MA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00283-18.

PMID- 22689236
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of the Nitrogen-Fixing Symbiotic Bacterium Bradyrhizobium elkanii 587.
PG  - 3547-3548
AB  - The draft sequence of the genome of Bradyrhizobium elkanii 587 is presented. This was obtained
      using Illumina Next-Gen DNA sequencing combined with Sanger
      sequencing. Genes for the pathways involved in biological nitrogen fixation (the
      nif gene cluster), nod genes including nodABC, and genes for the type III protein
      secretion system (T3SS) are present.
AU  - de Souza JA
AU  - Tieppo E
AU  - Magnani GS
AU  - Alves LM
AU  - Cardoso RL
AU  - Cruz LM
AU  - de Oliveira LF
AU  - Raittz RT
AU  - de Souza EM
AU  - Pedrosa FO
AU  - Lemos EG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3547-3548.

PMID- 25838497
VI  - 3
DP  - 2015
TI  - Genome of Rhizobium sp. UR51a, Isolated from Rice Cropped in Southern Brazilian Fields.
PG  - e00249-15
AB  - Rhizobium sp. UR51a is a Gram-negative bacterium isolated from roots of rice plants, and it
      presents plant growth-promoting abilities. The nutrient uptake in
      rice plants inoculated with UR51a was satisfactory. The genome of strain UR51a is
      composed of 5,233,443-bp and harbors 5,079 coding sequences.
AU  - de Souza R
AU  - Sant'Anna FH
AU  - Ambrosini A
AU  - Tadra-Sfeir M
AU  - Faoro H
AU  - Pedrosa FO
AU  - Souza EM
AU  - Passaglia LM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00249-15.

PMID- 25838496
VI  - 3
DP  - 2015
TI  - Genome of Pseudomonas sp. FeS53a, a Putative Plant Growth-Promoting Bacterium Associated with Rice Grown in Iron-Stressed Soils.
PG  - e00248-15
AB  - Pseudomonas sp. FeS53a was isolated from the roots of rice plants cultivated in one area with
      a well-established history of iron toxicity. The FeS53a genome
      sequence provides the genetic basis for understanding its lifestyle and survival
      in association with rice in conditions of iron toxicity.
AU  - de Souza R
AU  - Sant'Anna FH
AU  - Ambrosini A
AU  - Tadra-Sfeir M
AU  - Faoro H
AU  - Pedrosa FO
AU  - Souza EM
AU  - Passaglia LM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00248-15.

PMID- 23469362
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Herbaspirillum huttiense subsp. putei IAM 15032, a Strain Isolated from Well Water.
PG  - e00252-12
AB  - Here we report the one-scaffold draft genome of subsp. strain 7-2 (IAM 15032), which was
      isolated from well water.
AU  - de Souza V
AU  - Piro VC
AU  - Faoro H
AU  - Tadra-Sfeir MZ
AU  - Chicora VK
AU  - Guizelini D
AU  - Weiss V
AU  - Vialle RA
AU  - Monteiro RA
AU  - Steffens MB
AU  - Marchaukoski JN
AU  - Pedrosa FO
AU  - Cruz LM
AU  - Chubatsu LS
AU  - Raittz RT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00252-12.

PMID- 28495764
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Geobacillus sp. LEMMY01, a Thermophilic Bacterium Isolated from the Site of a Burning Grass Pile.
PG  - e00200-17
AB  - We report here the 3,586,065-bp draft genome of Geobacillus sp. LEMMY01, which was isolated
      (axenic culture) from a thermophilic chemolitoautotrophic consortium
      obtained from the site of a burning grass pile. The genome contains biosynthetic
      gene clusters coding for secondary metabolites, such as terpene and lantipeptide,
      confirming the biotechnological potential of this strain.
AU  - de Souza YPA
AU  - da Mota FF
AU  - Rosado AS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00200-17.

PMID- 27979940
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Enterococcus faecalis Strain UCD-PD3.
PG  - e01386-16
AB  - Here, we present the draft genome sequence of Enterococcus faecalis strain UCD-PD3. The
      assembly contains 2,861,314 bp in 73 contigs. This strain was
      isolated from a feral domestic cat (Felis catus) anal sac secretion sample, as
      part of a project on isolating and characterizing the microbes present in feline
      anal sacs.
AU  - De Vries DR
AU  - Martin AL
AU  - Ganz HH
AU  - Eisen JA
AU  - Coil DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01386-16.

PMID- Not included in PubMed...
VI  - 152
DP  - 1989
TI  - Isolation and characterization of Paracoccus denitrificans mutants with increased conjugation frequencies and pleiotropic loss of a (nGATCn) DNA-modifying property.
PG  - 52-57
AB  - A selection scheme was devised to isolate Paracoccus denitrificans mutants with
      increased recipient qualities in transfer experiments, using broad host range
      plasmids.  In some of the mutants obtained, a DNA modifying activity that
      prevents the activity of the restriction endonucleases BamHI and BglII on
      isolated P. denitrificans DNA had simultaneously been lost.  From a detailed
      analysis of the restriction properties of the enzymes Sau3AI, MboI and DpnI, it
      was concluded that a subset of GATC sequences in P. denitrificans DNA may be
      methylated at an unusual position.  It was concluded that P. denitrificans
      possesses at least one potent host-dependent restriction/modification system
      which affects conjugation.  In addition to the class of enhanced transfer
      mutants, at least one other class of enhanced transfer mutants with unknown
      defect(s) was isolated.  Strains, in which the two mutant classes were
      combined, exhibited transfer frequencies which were significantly higher than
      strains containing either mutation alone.  Such double mutant strains appeared
      to be well suited for future experiments like complementation analysis,
      transposon mutagenesis and gene replacement by homologous recombination.
AU  - de Vries GE
AU  - Harms N
AU  - Hoogendijk J
AU  - Stouthamer AH
PT  - Journal Article
TA  - Arch. Microbiol.
JT  - Arch. Microbiol.
SO  - Arch. Microbiol. 1989 152: 52-57.

PMID- 28619801
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Sphingomonas sp. Strain Sph1(2015), Isolated from a Fouled Membrane Filter Used To Produce Drinking Water.
PG  - e00517-17
AB  - We report here the high-quality draft genome sequence of Sphingomonas sp. strain  Sph1(2015),
      isolated from a fouled reverse osmosis membrane used for the
      production of high-quality drinking water. The draft sequence provides insights
      into the modus operandi of this strain to form biofilms on membrane surfaces.
      This knowledge offers tools to develop novel antifouling strategies.
AU  - de Vries HJ
AU  - Marshall IPG
AU  - Schreiber L
AU  - Plugge CM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00517-17.

PMID- 12426350
VI  - 184
DP  - 2002
TI  - Transcriptional phase variation of a Type III restriction-modification system in Helicobacter pylori.
PG  - 6615-6623
AB  - Phase variation is important in bacterial pathogenesis, since it generates
      antigenic variation for the evasion of immune responses and provides a
      strategy for quick adaptation to environmental changes. In this study, a
      Helicobacter pylori clone, designated MOD525, was identified that
      displayed phase-variable lacZ expression. The clone contained a
      transcriptional lacZ fusion in a putative type III DNA methyltransferase
      gene (mod, a homolog of the gene JHP1296 of strain J99), organized in an
      operon-like structure with a putative type III restriction endonuclease
      gene (res, a homolog of the gene JHP1297), located directly upstream of
      it. This putative type III restriction-modification system was common in
      H. pylori, as it was present in 15 out of 16 clinical isolates. Phase
      variation of the mod gene occurred at the transcriptional level both in
      clone MOD525 and in the parental H. pylori strain 1061. Further analysis
      showed that the res gene also displayed transcriptional phase variation
      and that it was cotranscribed with the mod gene. A homopolymeric cytosine
      tract (C tract) was present in the 5' coding region of the res gene.
      Length variation of this C tract caused the res open reading frame (ORF)
      to shift in and out of frame, switching the res gene on and off at the
      translational level. Surprisingly, the presence of an intact res ORF was
      positively correlated with active transcription of the downstream mod
      gene. Moreover, the C tract was required for the occurrence of
      transcriptional phase variation. Our finding that translation and
      transcription are linked during phase variation through slipped-strand
      mispairing is new for H. pylori.
AU  - De Vries N
AU  - Duinsbergen D
AU  - Kuipers EJ
AU  - Pot RGJ
AU  - Wiesenekker P
AU  - Penn CW
AU  - Van Vliet AHM
AU  - Vandenbroucke-Grauls CMJE
AU  - Kusters JG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2002 184: 6615-6623.

PMID- 
VI  - 118
DP  - 2000
TI  - Phase variation in a type III restriction-modification system of Helicobacter pylori.
PG  - A736
AB  - The on- and off-switching of the expression of virulence factors (phase variation) plays an
      important role in the pathogenesis of many bacterial infections.  LPS phase variation in
      Helicobacter pylori occurs at the translational level and has been studied well.  In contrast,
      phase variation at the transcriptional level has not been demonstrated in H. pylori.
      Therefore, we investigated transcriptional on- and off-switching of gene expression in H.
      pylori.  Methods: A library with random genomic transcriptional lacZ fusions in H. pylori
      strain 1061 (HP1061) was screened for mutants that showed blue and white sectored colonies on
      X-Gal.  As the X-Gal substrate is converted into a blue product when the lacZ gene is
      expressed into the beta-galactosidase, sectored colonies indicate transcriptional phase
      variation.  Results: One HP1061 mutant displayed frequent on- and off-switching of lacZ
      expression.  The on-to-off switch frequency was 2.67%, while the off-to-on frequency was
      0.75%.  Sequencing revealed that the lacZ gene was fused to a putative type III methylase gene
      (mod).  RNA spot blot hybridization demonstrated that specific lacZ and mod probes bound to
      mRNA from blue colonies, but not to mRNA from white colonies.  This proved that mod switched
      on and off a the transcriptional level.  An open reading frame, encoding a putative type III
      restriction enzyme gene (res), is located immediately upstream of mod and contains a
      polynucleotide C-tract.  This C-tract, which may cause phase variation of res through
      translational frameshifts, might indirectly act on the transcription of mod.  However,
      sequence analysis showed that the number of cytosines in res was not related to the on- or
      off-status of mod. Conclusion: In H. pylori, the putative type III methylase gene, mod,
      displays phase variation at the transcriptional level.  It is known that methylation of
      promoter sequences can affect the transcription of bacterial virulence factors.  We propose a
      specific role of mod and related restriction-modification systems in H. pylori in the
      regulation of virulence genes.
AU  - de Vries N
AU  - Duinsbergen D
AU  - Kuipers EJ
AU  - Wiesenekker P
AU  - Vandenbroucke-Grauls CM
AU  - Kusters JG
PT  - Journal Article
TA  - Gastroenterology
JT  - Gastroenterology
SO  - Gastroenterology 2000 118: A736.

PMID- 
VI  - 47
DP  - 2000
TI  - Transcriptional phase variation in a type III restriction modification system of Helicobacter pylori.
PG  - A17
AB  - Phase variation of virulence genes is important in the pathogenesis of many bacterial
      infections.  So far, phase variation at the transcriptional level has not been demonstrated in
      H. pylori.  Here, we report for the first time transcriptional phase variation in H. pylori.
      An H. pylori 1061 library with random genomic transcriptional lacZ fusions was screened for
      transformants showing blue, white and sectored colonies on X-Gal.  This phenotype indicated a
      fusion of lacZ to a gene displaying transcriptional phase variation.  In one transformant
      showing sectored colonies, lacZ was inserted in a putative type III methylase gene (mod).  An
      endonuclease gene (res) was located immediately upstream of mod and contained a C-tract, which
      may cause translational frameshifting.  Blue colonies tended to have 14 Cs, which results in
      the translation of res.  In contrast, white colonies contained C-tract lengths leading to
      disruption of the open reading frame.  RNA spot blots and RT-PCR indicated that mod displayed
      transcriptional phase variation, as mod mRNA was only present in blue colonies, and not in
      white colonies.  Res was transcribed both in blue and in white colonies.  In H. pylori 1061 a
      type III methylase gene displays transcriptional phase variation.  Translational frameshifting
      of the upstream endonuclease gene may be involved in the regulation of mod phase variation.
      Since DNA methylation can affect the transcription of bacterial virulence factors, we propose
      that mod and related restriction-modification systems play a role in the regulation of the
      expression of virulence genes in H. pylori.
AU  - de Vries N
AU  - Duinsbergen D
AU  - Kuipers EJ
AU  - Wiesenekker P
AU  - Vandenbroucke-Grauls CMJ
AU  - Kusters JG
PT  - Journal Article
TA  - Gut
JT  - Gut
SO  - Gut 2000 47: A17.

PMID- Not included in PubMed...
VI  - 128
DP  - 1980
TI  - Are sequence-specific deoxyribonucleases of value as taxonomic markers of cyanobacterial species?
PG  - 242-247
AB  - Three nucleotide sequence-specific deoxyribonucleases present in extracts of
      Anabaena subcylindrica have been purified and characterized.  Endo R AsuI
      recognizes and cleaves the nucleotide sequence G^GNCC (Hughes et al., 1980)
      while Endo R AsuII and III split the sequences TT^CGAA and GPu^CGPyC,
      respectively (this paper).  An Anabaena strain "Waterbury" converging
      genetically at the 30-35% level with both A. subcylindrica and A. cylindrica
      (as judged by DNA-DNA hybridization in vitro) was shown to possess the
      endonuclease pattern typical for A. cylindrica (de Waard et al., 1978).  The
      usefulness of these specific endonucleases as taxonomic markers for the
      classifiction of cyanobacteria is discussed.
AU  - de Waard A
AU  - Duyvesteyn M
PT  - Journal Article
TA  - Arch. Microbiol.
JT  - Arch. Microbiol.
SO  - Arch. Microbiol. 1980 128: 242-247.

PMID- 103749
VI  - 96
DP  - 1978
TI  - A new sequence-specific endonuclease from Anabaena cylindrica.
PG  - 106-110
AB  - The isolation of sequence-specific endodeoxyribonucleases from the cyanophytes
      Anabaena variabilis (ATCC 27892), Anabaena subcylindrica (CCAP 1403/4b) and
      Anabaena catenula (CCAP 1403/1) has been reported.  We have found a new
      endonuclease from Anabaena cylindrica (CCAP 1403/2a) and describe here the
      procedure of its isolation as well as the elucidation of the nucleotide
      sequences: 5' G Pu ^ C G Py C 3' 3' C Py G C ^ Pu G 5' recognized by the
      purified enzyme AcyI.
AU  - de Waard A
AU  - Korsuize J
AU  - van Beveren CP
AU  - Maat J
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1978 96: 106-110.

PMID- 109315
VI  - 101
DP  - 1979
TI  - Two sequence-specific endonucleases from Anabaena oscillarioides.
PG  - 71-76
AB  - There has been an increasing number of reports on sequence-specific
      endodeoxyribonucleases (endo.R.) in cyanobacteria (blue-green algae).  As their
      cleavage specificities have proven to be different from those of the many
      bacterial restriction enzymes already characterized, these new enzymes have
      been useful additions to the ever expanding endo R. catalog.  We report here
      the isolation of two such endonucleases from one strain of Anabaena
      oscillarioides (AosI and II) which cleave the nucleotide sequences 5'TGC^GCA3'
      and 5'GPu^CGPyC3', respectively.
AU  - de Waard A
AU  - van Beveren CP
AU  - Duyvesteyn M
AU  - van Ormondt H
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1979 101: 71-76.

PMID- Not included in PubMed...
VI  - 180
DP  - 1985
TI  - Purification and characterization of endonucleases DraII and III from Deinococcus radiophilus.
PG  - 219-223
AB  - Deinococcus radiophilus strain ATCC 27603 contains, apart from endonuclease
      DraI, two additional sequence-specific endonucleases.  These enzymes,
      designated DraII and DraIII, recognize nucleotide sequences with novel
      specificities, PuG^GNCCPy and CACNNN^GTG, respectively.
AU  - de Wit CM
AU  - Dekker BMM
AU  - Neele AC
AU  - de Waard A
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1985 180: 219-223.

PMID- 12077294
VI  - 99
DP  - 2002
TI  - Zinc finger as distance determinant in the flexible linker of intron  endonuclease I-TevI.
PG  - 8554-8561
AB  - l-Tevl, the phage T4 td intron-encoded endonuclease, recognizes a  lengthy DNA target and
      initiates intron mobility by introducing a
      double-strand break in the homing site. The enzyme uses both sequence and
      distance determinants to cleave the DNA 23-25 bp upstream of the intron
      insertion site. l-Tevl consists of an N-terminal catalytic domain and a
      C-terminal DNA-binding domain separated by a long, flexible linker. The
      DNA-binding domain consists of three subdomains: a zinc finger, a
      minor-groove binding a-helix, and a helix-turn-helix. In this study, a
      mutational analysis was undertaken to assess the roles of these subdomains
      in substrate binding and cleavage. Surprisingly, the zinc finger is not
      required for DNA binding or catalysis. Rather, the zinc finger is a
      component of the linker and directs the catalytic domain to cleave the
      homing site at a fixed distance from the intron insertion site. When the
      cleavage site (CS) is shifted outside a given range, wild-type l-Tevl
      defaults to the fixed distance, whereas zinc-finger mutants have lost the
      distance determinant and search out the displaced cleavage sequences.
      Although counterintuitive, a protein containing a 19-aa deletion of the
      zinc finger can extend further than can wild-type l-Tevl to cleave a
      distant CS sequence, and a Cys-to-Ala mutant of the ligands for zinc,
      nominally a longer protein, can retract to cleave at a closer CS sequence.
      Models are presented for the novel function of the zinc finger, as a
      molecular constraint, whereby intramolecular protein-protein interactions
      position the catalytic domain by "catalytic clamp" and/or
      "linker-organizer" mechanisms.
AU  - Dean AB
AU  - Stanger MJ
AU  - Dansereau JT
AU  - Van Roey P
AU  - Derbyshire V
AU  - Belfort M
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2002 99: 8554-8561.

PMID- 3005073
VI  - 13
DP  - 1985
TI  - Recent advances in high-performance liquid affinity chromatography columns.
PG  - 1055-1058
AB  - For the initial isolation of restriction endonucleases from crude extracts we
      have found that 1 ml of quaternary aminoethyl 'Mono-Q' strong anion-exchange
      column is ideal.  All the restriction enzymes we studies were eluted between
      0.2 and 0.6m-KCl.  This has enabled us to get to up a rapid screening program
      for novel type-II restriction endonuclease activities.  the profile of enzyme
      activities from an extract of a cyanobacterium Nostoc SA, incubated with lambda
      DNA, shows four separate restriction enzymes of different specificity.  These
      enzyme fractions were separately digested with other DNA substrates.  These and
      other experiments lead us to conclude that the enzymes were NspSAI
      (C-Y-C-G-R-G), NspSAII (G-G-T-N-A-C-C), NspSAIII (C-C-A-T-G-G), NspSAIV
      (G-G-A-T-C-C) and were isoschizomers of AvaI, BstEII, NcoI and BamHI,
      respectively.  The distribution of cytosines and guanines in each cutting site
      is interestingly consistent.  We have found that the purity of these and other
      enzymes after a single Mono Q column step is sufficient not only for
      characterization of their specificity on a series of substrates, but also to
      carry out analysis of the termini of the cutting sites using a modified form of
      M13 sequencing.
AU  - Dean PDC
AU  - Walker JNB
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 1985 13: 1055-1058.

PMID- 29051254
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Lactobacillus acidophilus Strain ATCC 53544.
PG  - e01138-17
AB  - Here we present the complete genome sequence of Lactobacillus acidophilus ATCC 53544. The
      assembly contains 1,991,906 bp and is 99.7% similar to L. acidophilus
      NCFM. This strain was isolated from a rectal swab specimen of an infant and has
      previously been used as a feed supplement for animals.
AU  - Dean SN
AU  - Vora GJ
AU  - Walper SA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01138-17.

PMID- 22180812
VI  - 5
DP  - 2011
TI  - Complete genome sequence of 'Enterobacter lignolyticus' SCF1.
PG  - 69-85
AB  - In an effort to discover anaerobic bacteria capable of lignin degradation, we isolated
      'Enterobacter lignolyticus' SCF1 on minimal media with alkali lignin as
      the sole source of carbon. This organism was isolated anaerobically from tropical
      forest soils collected from the Short Cloud Forest site in the El Yunque National
      Forest in Puerto Rico, USA, part of the Luquillo Long-Term Ecological Research
      Station. At this site, the soils experience strong fluctuations in redox
      potential and are net methane producers. Because of its ability to grow on lignin
      anaerobically, we sequenced the genome. The genome of 'E. lignolyticus' SCF1 is
      4.81 Mbp with no detected plasmids, and includes a relatively small arsenal of
      lignocellulolytic carbohydrate active enzymes. Lignin degradation was observed in
      culture, and the genome revealed two putative laccases, a putative peroxidase,
      and a complete 4-hydroxyphenylacetate degradation pathway encoded in a single
      gene cluster.
AU  - Deangelis KM
AU  - D'Haeseleer P
AU  - Chivian D
AU  - Fortney JL
AU  - Khudyakov J
AU  - Simmons B
AU  - Woo H
AU  - Arkin AP
AU  - Davenport KW
AU  - Goodwin L
AU  - Chen A
AU  - Ivanova N
AU  - Kyrpides NC
AU  - Mavromatis K
AU  - Woyke T
AU  - Hazen TC
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 5: 69-85.

PMID- 7959053
VI  - 150
DP  - 1994
TI  - Positive selection of recombinant plasmids based on the EcoK restriction activity of Escherichia coli K-12.
PG  - 197-198
AB  - We have constructed a pTZ19R-derived vector which allows efficient positive selection of
      recombinant plasmids. The system uses the EcoK restriction activity of Escherichia coli K-12
      to select against non-recombinant plasmids. The vector contains an EcoK site which, if deleted
      or disrupted by ligating a DNA fragment, yields recombinant plasmids that are no longer
      suceptible to EcoK restriction when transformed into a restriction-proficient E. coli host.
AU  - DeBacker O
AU  - Chomez P
AU  - DePlaen E
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1994 150: 197-198.

PMID- 18556790
VI  - 190
DP  - 2008
TI  - Insights into plant cell wall degradation from the genome sequence of the soil bacterium Cellvibrio japonicus.
PG  - 5455-5463
AB  - The plant cell wall, which consists of a highly complex array of interconnecting
      polysaccharides, is the most abundant source of organic
      carbon in the biosphere. Microorganisms that degrade the plant cell wall
      synthesize an extensive portfolio of hydrolytic enzymes that display
      highly complex molecular architectures. To unravel the intricate
      repertoire of plant cell wall-degrading enzymes synthesized by the
      saprophytic soil bacterium Cellvibrio japonicus, we sequenced and analyzed
      its genome, which predicts that the bacterium contains the complete
      repertoire of enzymes required to degrade plant cell wall and storage
      polysaccharides. Approximately one-third of these putative proteins (57)
      are predicted to contain carbohydrate binding modules derived from 13 of
      the 49 known families. Sequence analysis reveals approximately 130
      predicted glycoside hydrolases that target the major structural and
      storage plant polysaccharides. In common with that of the colonic
      prokaryote Bacteroides thetaiotaomicron, the genome of C. japonicus is
      predicted to encode a large number of GH43 enzymes, suggesting that the
      extensive arabinose decorations appended to pectins and xylans may
      represent a major nutrient source, not just for intestinal bacteria but
      also for microorganisms that occupy terrestrial ecosystems. The results
      presented here predict that C. japonicus possesses an extensive range of
      glycoside hydrolases, lyases, and esterases. Most importantly, the genome
      of C. japonicus is remarkably similar to that of the gram-negative marine
      bacterium, Saccharophagus degradans 2-40(T). Approximately 50% of the
      predicted C. japonicus plant-degradative apparatus appears to be shared
      with S. degradans, consistent with the utilization of plant-derived
      complex carbohydrates as a major substrate by both organisms.
AU  - DeBoy RT
AU  - Mongodin EF
AU  - Fouts DE
AU  - Tailford LE
AU  - Khouri H
AU  - Emerson JB
AU  - Mohamoud Y
AU  - Watkins K
AU  - Henrissat B
AU  - Gilbert HJ
AU  - Nelson KE
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2008 190: 5455-5463.

PMID- 19558513
VI  - 11
DP  - 2009
TI  - Metagenomic approach studying the taxonomic and functional diversity of the bacterial community in a mesotrophic lake (Lac du Bourget - France).
PG  - 2412-2424
AB  - The main goals of this work were to identify the metabolic pathways of the
      bacterial community in a lacustrine ecosystem and to establish links
      between taxonomic composition and the relative abundances of these
      metabolic pathways. For this purpose, we analysed a 16S rRNA gene library
      obtained by gene amplification together with a sequence library of both
      insert ends on c. 7700 fosmids. Whatever the library used, Actinobacteria
      was the most abundant bacterial group, followed by Proteobacteria and
      Bacteroidetes. Specific aquatic clades such as acI and acIV
      (Actinobacteria) or LD12 and GOBB-C201 (Alphaproteobacteria) were found in
      both libraries. From comparative analysis of metagenomic libraries, the
      metagenome of this lake was characterized by overrepresentation of genes
      involved in the degradation of xenobiotics mainly associated with
      Alphaproteobacteria. Actinobacteria were mainly related to metabolic
      pathways involved in nucleotide metabolism, cofactors, vitamins, energy,
      replication and repair. Betaproteobacteria appeared to be characterized by
      the presence of numerous genes implicated in environmental information
      processing (membrane transport and signal transduction) whereas glycan and
      carbohydrate metabolism pathways were overrepresented in Bacteroidetes.
      These results prompted us to propose hypotheses on the ecological role of
      these bacterial classes in lacustrine ecosystems.
AU  - Debroas D
AU  - Humbert JF
AU  - Enault F
AU  - Bronner G
AU  - Faubladier F
AU  - Cornillot C
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2009 11: 2412-2424.

PMID- 6256608
VI  - 179
DP  - 1980
TI  - The ral gene of phage lambda.
PG  - 75-80
AB  - The lambda ral function modulates the restriction and modification activities
      of the Escherichia coli K12 and B restriction enzymes (Zabeau et al., 1980).
      In order to further analyse this function, ral deficient mutants have been
      isolated, using a method which exploits the property of the strong mutagen
      N-methyl-N'-nitro-N-nitrosoguanidine (N.G.) to induce multiple closely linked
      mutations.  Hence, mutagenized phages carrying mutations in one locus were
      frequently found to contain additional mutations in adjacent loci.  This very
      efficient mutagenesis procedure enabled us to isolate 27 independent Ral
      deficient mutants.  Seven mutants were found to affect the ral gene directly
      and were located between the genes N and cIII.  Detailed mapping of two of
      these mutants showed that the lambda ral gene is located at position 70.6-70.9%
      on the physical map.  The isolation and characterization of these mutants
      further supports the conclusion that ral is a gene different from the N gene,
      and demonstrates that the ral gene product is responsible for both
      counteracting restriction and enhancing modification.
AU  - Debrouwere L
AU  - Zabeau M
AU  - Van Montagu M
AU  - Schell J
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1980 179: 75-80.

PMID- 23409265
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Nitrate- and Phosphate-Accumulating Bacillus sp. Strain MCC0008.
PG  - e00189-12
AB  - Here, we report the draft genome sequence of the nitrate- and phosphate-accumulating Bacillus
      sp. strain MCC0008, isolated from a consortium
      enriched from municipal sewage in nitrate broth (HiMedia M439). The total size of
      the genome is 5,609,456 bp, with a G+C content of 35.1%.
AU  - Debroy S
AU  - Bhattacharjee A
AU  - Thakur AR
AU  - Raychaudhuri S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00189-12.

PMID- 23469363
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of a Nitrate- and Phosphate-Removing Bacillus sp., WBUNB009.
PG  - e00254-12
AB  - The draft genome sequence (5,868,741 bp) of a nitrate- and phosphate-removing sp., WBUNB009,
      isolated from a raw sewage canal in nitrate broth (Himedia M439)
      with a G+C content of 34.9% is reported. It removes 60.23% nitrate and 96%
      phosphate within 16 h at 37 degrees C.
AU  - Debroy S
AU  - Mukherjee P
AU  - Roy S
AU  - Thakur AR
AU  - Raychaudhuri S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00254-12.

PMID- 23469361
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of a Phosphate-Accumulating Bacillus sp., WBUNB004.
PG  - e00251-12
AB  - The draft genome sequence of a nitrate- and phosphate-removing, Gram-positive sp. with optimum
      growth at 37 degrees C and pH 7 in nitrate broth (HiMedia M439)
      isolated from rhizosphere of a water lily, with a genome size of 5,465,157 bp and
      a G+C content of 35.0%, is reported here.
AU  - Debroy S
AU  - Mukherjee P
AU  - Roy S
AU  - Thakur AR
AU  - Raychaudhuri S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00251-12.

PMID- 24699952
VI  - 2
DP  - 2014
TI  - Genome Sequence and Methylome of Soil Bacterium Gemmatirosa kalamazoonensis KBS708T, a Member of the Rarely Cultivated Gemmatimonadetes Phylum.
PG  - e00226-14
AB  - Bacteria belonging to the phylum Gemmatimonadetes are found in a wide variety of  environments
      and are particularly abundant in soils. Here, we present the complete genome sequence and
      methylation pattern of the newly described Gemmatirosa kalamazoonensis type strain.
AU  - Debruyn JM
AU  - Radosevich M
AU  - Wommack KE
AU  - Polson SW
AU  - Hauser LJ
AU  - Fawaz MN
AU  - Korlach J
AU  - Tsai YC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00226-14.

PMID- 10786852
VI  - 6
DP  - 2000
TI  - Expression of the Naegleria intron endonuclease is dependent on a functional group I self-cleaving ribozyme.
PG  - 616-627
AB  - NaSSU1 is a complex nuclear group I intron found in several species of Naegleria, consisting
      of a large self-splicing group I ribozyme (NaGIR2), which itself is interrupted by a small,
      group I-like ribozyme (NaGIR1) and an open reading frame (ORF) coding for a homing
      endonuclease. The GIR1 ribozyme cleaves in vitro transcripts of NaSSU1 at two internal
      processing sites about 400 nt downstream of the 5' end of the intron, proximal to the
      endonuclease ORF. Here we demonstrate that self-cleavage of the excised intron also occurs in
      vivo in Naegleria gruberi, generating an ORF-containing RNA that possesses a short leader with
      a sequence element likely to be involved in gene expression. To assess the functional
      significance of self-cleavage, we constructed a genetic system in Saccharomyces cerevisiae.
      First, a mutant yeast strain was selected with a mutation in all the rRNA genes, rendering the
      rDNA resistant to cleavage by the Naegleria endonuclease. Active endonuclease, which is
      otherwise lethal, could be expressed readily in these cells. Endonuclease activity also could
      be detected in extracts of yeast harboring plasmids in which the endonuclease ORF was embedded
      in its native context in the intron. Analysis of the RNA from these yeast cells showed that
      the excised intron RNA was processed as in N. gruberi. A mutant intron constructed to prevent
      self-cleavage of the RNA failed to express endonuclease activity. These results support the
      hypothesis that the NaGIR1-catalyzed self-cleavage of the intron RNA is a key event in
      expression of the endonuclease.
AU  - Decatur WA
AU  - Johansen S
AU  - Vogt VM
PT  - Journal Article
TA  - RNA
JT  - RNA
SO  - RNA 2000 6: 616-627.

PMID- 9537320
VI  - 392
DP  - 1998
TI  - The complete genome of the hyperthermophilic bacterium Aquifex aeolicus.
PG  - 353-358
AB  - Aquifex aeolicus was one of the earliest diverging, and is one of the most thermophilic,
      bacteria known. It can grow on hydrogen, oxygen, carbon dioxide, and mineral salts. The
      complex metabolic machinery needed for A. aeolicus to function as a chemolithoautotroph (an
      organism which uses an inorganic carbon source for biosynthesis and an inorganic chemical
      energy source) is encoded within a genome that is only one-third the size of the E. coli
      genome. Metabolic flexibility seems to be reduced as a result of the limited genome size. The
      use of oxygen (albeit at very low concentrations) as an electron acceptor is allowed by the
      presence of a complex respiratory apparatus. Although this organism grows at 95 degrees C, the
      extreme thermal limit of the Bacteria, only a few specific indications of thermophily are
      apparent from the genome. Here we describe the complete genome sequence of 1,551,335 base
      pairs of this evolutionarily and physiologically interesting organism.
AU  - Deckert G
AU  - Warren PV
AU  - Gaasterland T
AU  - Young WG
AU  - Lenox AL
AU  - Graham DE
AU  - Overbeek R
AU  - Snead MA
AU  - Keller M
AU  - Aujay M
AU  - Huber R
AU  - Feldman RA
AU  - Short JM
AU  - Olson GJ
AU  - Swanson RV
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1998 392: 353-358.

PMID- 
VI  - 46
DP  - 2010
TI  - New DNA methyltransferase M.AjnI from the bacterium Acinetobacter johnsonii R2 produces the 5'-m5CCWGG-3' sequence.
PG  - 849-853
AB  - Optimum conditions for the activity of the new DNA methylase in cell lysate were determined.
      Methylation of DNAs of bacteriophages lambda
      and T7 and plasmid pBR322 (dcm+) in the 5'-Cm5CWGG-3' region blocked
      M.AjnI activity. The specificity of M.AjnI was determined using lambda
      DNA methylated by this enzyme as well as computer modeling and data on
      the sensitivity of restriction endonucleases Mval, HinfI, and BstMAI to
      methylation.
AU  - Dedkov VS
PT  - Journal Article
TA  - Prikl. Biokhim. Mikrobiol.
JT  - Prikl. Biokhim. Mikrobiol.
SO  - Prikl. Biokhim. Mikrobiol. 2010 46: 849-853.

PMID- 
VI  - 0
DP  - 2009
TI  - Analysis of specificity of DNA-methyltransferase M.AspS9I in cell lysate by means of restriction endonuclease blocking.
PG  - 30-39
AB  - Specificity of DNA-methyltransferase M.AspS9I has been determined using cell lysate of
      Arthrobacter species S9.  To this end, we employed methylation sensitivity of restriction
      endonucleases and also modeling of the methylation process.  Modeling consisted of editing DNA
      sequences by substitution of letters for methylated bases and their complementary bases.
      Substrate DNA treated by M.AspS9I were used for studying of sensitivity of some restriction
      endonucleases to methylation.  Thus it was shown that the overlapping dcm-methylation did not
      block the M.AspS9I activity.  The suggested approach can appear universal and simple enough
      for determining DNA-methyltransferases specificity.
AU  - Dedkov VS
PT  - Journal Article
TA  - Biotekhnologiya
JT  - Biotekhnologiya
SO  - Biotekhnologiya 2009 0: 30-39.

PMID- 
VI  - 0
DP  - 2009
TI  - Defining specificity of DNA methyltransferase M.Bsc4I in cellular lysate by blocking restriction endonucleases and computer modeling.
PG  - 3-8
AB  - The specificity of DNA methyltransferase M.Bsc4I was determined in cellular lysate of Bacillus
      schlegelii 4.  The methylation sensitivity of restriction endonucleases and methylation
      modeling were used for this purpose.  Modeling consisted of editing DNA sequences using
      replacements of methylated bases and their complementary bases.  Substrate DNA treated with
      M.Bsc4I were used to study the sensitivity of some restrictases to methylation.  It was shown
      that M.Bsc4I methylated 5'-Cm4CNNNNNNNGG-3' and overlapping dcm-methylation blocked its
      activity.  The suggested approach would be universal and simple for determining the
      specificity of DNA methyltransferases.
AU  - Dedkov VS
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 2009 0: 3-8.

PMID- 
VI  - 4
DP  - 2004
TI  - Determining of G+C Content in Bacterial DNA using Restriction Endonucleases.
PG  - 77-82
AB  - Bacterial DNAs were cleaved by restriction endonucleases (restrictases) recognizing sequences
      of G and C or A and T nucleotides. Experimental curves were obtained for determination G+C
      content in bacterial DNA. The developed express-method is supposed to be helpful for
      restriction cleavage of bacterial lysates DNA, bacteria identification separation of microbial
      isolates in to strains and also for determining DNA methylases.
AU  - Dedkov VS
PT  - Journal Article
TA  - Biotekhnologiya
JT  - Biotekhnologiya
SO  - Biotekhnologiya 2004 4: 77-82.

PMID- 
VI  - 27
DP  - 2012
TI  - Novel M.BstC8I methyltransferase forms 5'-G(m5C)NNGC-3'. Investigation of restriction endonuclease sensitivity to M.BstC8I methylation.
PG  - 40-47
AB  - A novel M.BstC8I DNA methylase was detected in cell lysate of Bacillus stearothermophilus C8
      grown on Luria agar at 37A degrees C. DNA
      methylation of bacteriophages lambda and T7 in the 5'-G(m5C)NNGC-3'
      segment blocked the activity of the BstC8I restrictase. The specificity
      of the M.BstC8I was analyzed on methylated lambda DNA and using
      computer modeling and the data on the sensitivity of BstC8I, BsuRI,
      AjnI, and PvuII restrictases to methylation. The sensitivity of a
      number of restrictases to the novel type of methylation was shown. The
      results can be used for study of DNA methylation.
AU  - Dedkov VS
PT  - Journal Article
TA  - Mol. Genet. Microbiol. Virol.
JT  - Mol. Genet. Microbiol. Virol.
SO  - Mol. Genet. Microbiol. Virol. 2012 27: 40-47.

PMID- 
VI  - 0
DP  - 2010
TI  - New DNA methyltransferase M.AjnI from Acinetobacter johnsonii R2 produces 5'-m5CCWGG-3' sequence.
PG  - 36-40
AB  - 
AU  - Dedkov VS
PT  - Journal Article
TA  - Biotekhnologiya
JT  - Biotekhnologiya
SO  - Biotekhnologiya 2010 0: 36-40.

PMID- 10702987
VI  - 1
DP  - 2000
TI  - New rare-cutting restriction endonuclease SmiI from Streptococcus milleri recognizes 5'-ATTT/AAAT-3'.
PG  - 23-27
AB  - A new restriction endonuclease (restrictase) SmiI of type II was detected in the bacterial
      strain Streptococcus milleri. Cellular lysate enzyme cut T7 and adenovirus-2 DNAs at site
      5'-ATTT/AAAT-3' but not lambda DNA, which does not contain this sequence. Intensive aeration
      inhibited the growth of S. milleri. The content of restrictase in cells was the greatest
      during the logarithmic growth phase. A total of 20,000 units of SmiI were isolated from 4 g of
      cells by cellular extract fractionation with ammonium sulfate and subsequent chromatography on
      columns with Bio Gel A 0.5 m, heparin agarose, and phosphocellulose. The purified enzyme cut
      the synthetic oligonucleotide duplex in the center of the recognized site 5'-ATTT/AAAT-3'.
      SmiI restrictase is a true isoschizomer of the rare-cutting SwaI enzyme. SmiI belongs to a
      small group of enzymes which recognize octanucleotide sites and can be used for large-block
      fragmentation of DNA. Comparison of specificities of rare-cutting and other restrictases
      suggests that the enzymes recognizing octanucleotides can evolutionarily originate from
      enzymes recognizing both hexanucleotides and tetranucleotides.
AU  - Dedkov VS
AU  - Bondar TS
AU  - Shevchenco AV
AU  - Degtyarev SK
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 2000 1: 23-27.

PMID- 9628357
VI  - 379
DP  - 1998
TI  - Actinobacillus and Streptococcus: producers of isoschizomers of the restriction endonucleases R.HphI, R.SauI, R.NheI, R.MboI and R.SwaI.
PG  - 573-574
AB  - New restriction endonucleases have been found in microorganisms isolated from the microflora
      of human teeth.  The strain-producers are Actinobacillus suis and Streptococcus milleri.  The
      new enzymes are isoschizomers of the prototypes as follows: AsuHPI-HphI; AsuSAI-SauI;
      AsuNHI-NheI; AsuMBI and SmiMBI-MboI; SmiI-rare-cutter SwaI.
AU  - Dedkov VS
AU  - Degtyarev SK
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1998 379: 573-574.

PMID- 1317569
VI  - 28
DP  - 1992
TI  - Detection of restriction endonucleases in Streptomyces and Nocardia cells.
PG  - 309-313
AB  - A simple technique is proposed for the detection of restriction endonucleases in Streptomyces
      and Nocardia cells. The analysis was performed directly in the cells collected from colonies
      cultivated on Petri dishes with an innoculation loop. The cells were treated with lyzozyme,
      EDTA and Triton X-100. The lysates were tested for restriction endonucleases. The technique
      enables the detection of enzymes NcoI, NotI, NruI, Sfr303I, and SfiI in the lysates of the
      respective strains-producers.
AU  - Dedkov VS
AU  - Degtyarev SK
PT  - Journal Article
TA  - Prikl. Biokhim. Mikrobiol.
JT  - Prikl. Biokhim. Mikrobiol.
SO  - Prikl. Biokhim. Mikrobiol. 1992 28: 309-313.

PMID- 
VI  - 6
DP  - 2015
TI  - Cloning and Study of New DNA Methyltransferase M.FatI Modifying Cytosine in a Recognition Site CATG.
PG  - 1341-1348
AB  - A fragment of Flavobacterium aquatile NL3 DNA carrying the gene of DNA methyltransferase
      M.FatI was cloned in pUC19 plasmid. DNA was sequenced and M.FatI gene was analyzed. A
      recombinant strain Esherichia coli was grown up and the enzyme was purified. M.FatI
      specificity was determined by a blocking of some restriction endonucleases and computer
      modeling. It's well known that M.NlaIII produces 5'-C(m6A)TG-3', whereas FatI MTase
      modifies the cytosine residue with formation 5'-(m5C)ATG-3'. The sensitivity of restriction
      endonucleases to FatI-methylation has been studied.
AU  - Dedkov VS
AU  - Gonchar DA
AU  - Abdurashitov MA
AU  - Udalyeva SG
AU  - Urumceva LA
AU  - Chernukhin VA
AU  - Mutylo GV
AU  - Degtyarev SK
PT  - Journal Article
TA  - Res. J. Pharm. Biol. Chem. Sci.
JT  - Res. J. Pharm. Biol. Chem. Sci.
SO  - Res. J. Pharm. Biol. Chem. Sci. 2015 6: 1341-1348.

PMID- 
VI  - 32
DP  - 2015
TI  - Cloning and study of new DNA methyltransferase M.AluBI modifying adenine in a recognition site AGCT.
PG  - 3211-3216
AB  - A fragment of Arthrobacter luteus B DNA carrying the gene of new DNA methyltransferase M.AluBI
      was cloned and expressed in Escherichia coli. The recombinant plasmid pM.AluBI-16 contains the
      M.AluBI gene (1515 bp in length), corresponding to a protein of 504 amino acid residues. The
      amino acid sequence analysis showed that M.AluBI could be an adenine-(N6)-DNA
      methyltransferase. A recombinant strain was grown up and the enzyme was purified by a
      consecutive chromatography on P-11 Phosphocellulose, Heparin-Sepharose, Sephacryl S-200 and
      Hydroxyapatite. M.AluBI specificity was determined by the original method based on blocking of
      restriction endonucleases cleavage of overlapped sites and on computer modeling. It was first
      shown that AluBI MTase modifies the adenine residue with formation of 5&#180;-(m6A)GCT-3&#180;
      as opposed to its prototype, M.AluI, producing 5&#180;-AG(m5C)T-3&#180;. A comparative
      sensitivity analysis of different, well known restriction endonucleases to the methylation by
      M.AluBI and M.AluI was done using &#955; and T7 phage DNA. The newly acquired data on
      methylation sensitivity cold be useful for conducting experiments on DNA digestion with
      restriction endonucleases, and especially with the particular cleavage sensitivity pattern
      generated with the M.AluBI methyltransferase enzyme.
AU  - Dedkov VS
AU  - Gonchar DA
AU  - Abdurashitov MA
AU  - Udalyeva SG
AU  - Urumceva LA
AU  - Chernukhin VA
AU  - Shiryaeva EN
AU  - Degtyarev SK
PT  - Journal Article
TA  - Biotecnol. Apl.
JT  - Biotecnol. Apl.
SO  - Biotecnol. Apl. 2015 32: 3211-3216.

PMID- 
VI  - 12
DP  - 2016
TI  - New DNA methyltransferase M.AgsI produces TTSA(m6A).
PG  - 100-106
AB  - Agrococcus species 25 DNA was cloned in pUC19 plasmid of Escherichia coli. Cloned DNA fragment
      contained two Opened Reading Frames with 8 amino acid motives which belonged to amino DNA
      methyltransferases. Thus M.AgsI can be the first of subunit adenine-(N6)-DNA
      methyltransferase. The enzyme was purified from the recombinant strain by chromatography on
      P-11 Phosphocellulose, Heparin-Sepharose and Hydroxyapatite. M.AgsI specificity was determined
      by a study of protection of lambda DNA methylated with M.AgsI against cleavage with some
      restriction endonucleases. A sensitivity of restriction endonucleases to M.AgsI-methylation
      was studied.
AU  - Dedkov VS
AU  - Gonchar DA
AU  - Chernukhin VA
AU  - Abdurashitov MA
AU  - Udalyeva SG
AU  - Urumceva LA
AU  - Degtyarev SK
PT  - Journal Article
TA  - Biotechnology: an Indian Journal
JT  - Biotechnology: an Indian Journal
SO  - Biotechnology: an Indian Journal 2016 12: 100-106.

PMID- 
VI  - 5
DP  - 2002
TI  - FatI restriction endonuclease from Flavobacterium aquatile NL3 cleaves DNA at 5'-^CATG-3' site.
PG  - 3-7
AB  - 
AU  - Dedkov VS
AU  - Kileva EV
AU  - Popichenko DV
AU  - Degtyarev SK
PT  - Journal Article
TA  - Biotekhnologiya
JT  - Biotekhnologiya
SO  - Biotekhnologiya 2002 5: 3-7.

PMID- 
VI  - 2
DP  - 2012
TI  - A M.BssECI DNA Methyltransferase Forms 5 '-m4CCNNGG-3 '. Sensitivity of Restriction Endonucleases to the New Methylation.
PG  - 32-42
AB  - A novel DNA methyltransferase, M.BssECI, has been isolated and purified from Bacillus
      stearothermophilus EC cells. The enzyme methylates a
      surface cytosine residue in a 5'-CCNNGG-3' sequence with the formation
      of N4-methylcytosine, 5'-m4CCNNGG-3'. The approaches to enzyme
      isolation, purification (gel-filtration on a Biogel A-0,5m with the
      following chromatography on benzyl-DEAE-cellulose and
      heparin-Sepharose) and identification of the methylated DNA sequence
      were developed. The optimum conditions and the activity of the novel
      methyltransferase were determined using phage X. DNA on the basis of
      the BssECI restriction endonuclease blockage. A base that was
      methylated within the recognized sequence was detected using the
      [H-3]-labeling of the oligonucleotide duplex. The specificity of
      M.BssECI was investigated using self-methylated Adeno-2 DNA taking into
      account the sensitivity of the BssECI, MvaI and MspI restriction
      endonucleases to methylated DNA; computer modeling was also employed.
      The isolated enzyme can be used in studying of character of DNA
      methylation; in particular, it permitted to distinguish the
      m4C-methylated cytosine from m5C. DNAs of phages lambda and T7
      methylated by M.BssECI were applied to the investigation of the
      sensitivity of some restriction endonucleases to the methylation of
      their recognition sites.
AU  - Dedkov VS
AU  - Mikhnenkova NA
AU  - Djanobilova ZK
AU  - Tarasova MV
PT  - Journal Article
TA  - Biotekhnologiya
JT  - Biotekhnologiya
SO  - Biotekhnologiya 2012 2: 32-42.

PMID- 
VI  - 3
DP  - 2004
TI  - Restriction Endonuclease AjnI from Acinetobacter johnsonii R2, an Isoschizomer of EcoRII, recognizes 5'- CCWGG-3' and cleaves dcm-methylated sites.
PG  - 19-24
AB  - A producer of restriction endonuclease AjnI has been isolated from natural resources and
      identified as bacterial species Acinetobacter johnsonii R2. The restriction enzyme
      purification and estimation of its activity is described. It has been shown that AjnI produces
      DNA fragments with 5'-CCWGG sticky ends similar to EcoRII, but cleavage is not blocked by
      dcm-methylation. A new restriction endonuclease AjnI may be widely used in genetic
      engineering.
AU  - Dedkov VS
AU  - Mikhnenkova NA
AU  - Vlasenko LP
AU  - Tomilova JE
AU  - Kashirina JG
AU  - Gonchar DA
AU  - Degtyarev SK
PT  - Journal Article
TA  - Biotekhnologiya
JT  - Biotekhnologiya
SO  - Biotekhnologiya 2004 3: 19-24.

PMID- 
VI  - 1
DP  - 2003
TI  - Restriction endonuclease BmtI from Bacillus megaterium S2 cleaves DNA at 5'-GCTAG^C-3' site.
PG  - 11-15
AB  - A new strain producer of a BmtI restriction endonuclease (restrictase) has been found out and
      identified as bacteria species Bacillus
      megaterium S2. The scheme of purification and several characteristics
      of the enzyme are described. BmtI is a heteroschizomer of the well
      known NheI enzyme (recognition sequence 5'-GdwnarwCTAGC-3'). It
      produces DNA fragments with CTAG-3' extending ends. BmtI restrictase
      may be used in genetic engineering.
AU  - Dedkov VS
AU  - Nayakshina TN
AU  - Popichenko DV
AU  - Degtyarev SK
PT  - Journal Article
TA  - Biotekhnologiya
JT  - Biotekhnologiya
SO  - Biotekhnologiya 2003 1: 11-15.

PMID- 2628752
VI  - 11
DP  - 1989
TI  - SsrI - a Type II restriction endonuclease from Staphylococcus saprophyticus cells.
PG  - 24-27
AB  - The recognition sequence and cleavage site for restriction endonuclease SsrI have been
      determined, the latter being 5'-GTT^AAC-3'.  The enzyme was isolated from Staphyloccus
      saprophyticus and may be used in DNA investigation instead of its isoschizomer HpaI.
AU  - Dedkov VS
AU  - Prihodko GG
AU  - Puchkova LI
AU  - Serov GD
AU  - Rechkunova NI
AU  - Degtyarev SK
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1989 11: 24-27.

PMID- 7607535
VI  - 157
DP  - 1995
TI  - CciNI, an isoschizomer of NotI from Curtobacterium citreum recognizes 5'-GC/GGCCGC-3'.
PG  - 99-100
AB  - CciNI, an isoschizomer of NotI, has been isolated from Curtobacterium citreum.  The enzyme
      cleaves within the recognition sequence 5'-GC/GGCCGC-3' as indicated by the slash.
AU  - Dedkov VS
AU  - Rechkunova NI
AU  - Prihodko EA
AU  - Kileva EV
AU  - Kusner YS
AU  - Verchozina VA
AU  - Degtyarev SK
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 99-100.

PMID- Not carried by PubMed...
VI  - 1
DP  - 1990
TI  - Screening of strains producing restriction endonucleases in Lake Baikal.
PG  - 35-37
AB  - Screening of bacterial strains which produce restriction endonucleases was
      performed.  It was shown that strains Flavobacterium aquatile, Hafnia alvei,
      Acinetobacter calcoaceticus, Pseudomonas gladioli were producers of
      restrictases FauI, HalI and HalII, Aca I, PgaI, respectively.
AU  - Dedkov VS
AU  - Repin VE
AU  - Rechkunova NI
AU  - Degtyarev SK
AU  - Verhosina VA
AU  - Vinogradova TP
PT  - Journal Article
TA  - Izv. Sib. Otd. Akad. Nauk SSSR
JT  - Izv. Sib. Otd. Akad. Nauk SSSR
SO  - Izv. Sib. Otd. Akad. Nauk SSSR 1990 1: 35-37.

PMID- 
VI  - 6
DP  - 2003
TI  - Restriction endonucleases FalI and FalII from Flavobacterium aquatile Ob10 recognize 5'-(8/13)AAGN5CTT(13/8)-3' and 5'-CG^CG-3',  respectively.
PG  - 24-29
AB  - We have isolated from water supplies a strain Flavobacterium aquatile Ob10 which produces two
      restriction endonucleases FalI and FalII.  FalI is a new prototype and recognizes the DNA
      sequence that follows: 5'-(8/13)AAGN5CTT(13/8)-3'.  FalI is stimulated by
      S-adenosylmethionine and cleaves DNA on both sides of its recognition sequence.  Thus, FalI
      belongs to the BcgI-subtype of restriction endonucleases.  The recognition sequence for FalII
      restriction
      endonuclease is 5'-CG/CG-3' and this enzyme is thus an isoschizomer of FnuDII.
AU  - Dedkov VS
AU  - Sinichkina SA
AU  - Abdurashitov MA
AU  - Popichenko DV
AU  - Degtyarev SK
PT  - Journal Article
TA  - Biotekhnologiya
JT  - Biotekhnologiya
SO  - Biotekhnologiya 2003 6: 24-29.

PMID- 
VI  - 6
DP  - 2001
TI  - Restriction endonuclease ZraI from Zoogloea ramigera 11 recognizes 5'-GAC/GTC-3'.
PG  - 3-7
AB  - A producer of restriction endonuclease (restrictase) from natural isolates has been obtained
      and identified as bacteria species Zoogloea ramigera II, while the restrictase was named ZraI.
      The way of the purification and estimation of the enzyme activity is described.  It was shown
      that ZraI produces blunt ended DNA fragments.  The restrictase is promising for the wide use
      in gene engineering.
AU  - Dedkov VS
AU  - Sinichkina SA
AU  - Popichenko DV
AU  - Degtyarev SK
PT  - Journal Article
TA  - Biotekhnologiya
JT  - Biotekhnologiya
SO  - Biotekhnologiya 2001 6: 3-7.

PMID- 1964718
VI  - 0
DP  - 1990
TI  - Isolation of aquatic microorganisms producing the restriction endonucleases from the Black Sea.
PG  - 17-18
AB  - 300 clones of microorganisms isolated at different stations and from different
      depths in the Black Sea were screened for restriction endonucleases was found
      in 17 clones screened.  Three of them were identified to be Alteromonas
      haloplanktis Bl. Restriction endonuclease AhaBI is an isoschizomer of Sau96I.
      An identified Alteromonas haloplanktis clone B8 produces AhaB8I restriction
      endonuclease the prototype of which is KpnI.  Of the clones isolated three are
      Moraxella species B4 producing MspB4I restriction endonuclease analogous to
      BanI, three are Bacillus species producing BspB2I and one is Micrococcus lylae
      113 producing Mly1131 analogue of NarI, six Moraxella species B6 produce
      MspB6I.  The isolated producer strains may be used for isolation of
      above-mentioned restriction endonucleases.
AU  - Dedkov VS
AU  - Zernov YP
AU  - Rechkunova NI
AU  - Degtyarev SK
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1990 0: 17-18.

PMID- 25745010
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Methyloferula stellata AR4, an Obligate Methanotroph Possessing Only a Soluble Methane Monooxygenase.
PG  - e01555-14
AB  - Methyloferula stellata AR4 is an aerobic acidophilic methanotroph, which, in contrast to most
      known methanotrophs but similar to Methylocella spp., possesses
      only a soluble methane monooxygenase. However, it differs from Methylocella spp.
      by its inability to grow on multicarbon substrates. Here, we report the draft
      genome sequence of this bacterium.
AU  - Dedysh SN
AU  - Naumoff DG
AU  - Vorobev AV
AU  - Kyrpides N
AU  - Woyke T
AU  - Shapiro N
AU  - Crombie AT
AU  - Murrell JC
AU  - Kalyuzhnaya MG
AU  - Smirnova AV
AU  - Dunfield PF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01555-14.

PMID- 27516513
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Anoxybacillus suryakundensis Strain JS1T (DSM 27374T) Isolated from a Hot Spring in Jharkhand, India.
PG  - e00824-16
AB  - Anoxybacillus suryakundensis strain JS1(T), a facultative anaerobic, moderately thermophilic,
      alkalitolerant bacterium, was isolated from a hot spring. The
      estimated genome is 2.6 Mb and encodes 2,668 proteins.
AU  - Deep K
AU  - Poddar A
AU  - Whitman WB
AU  - Das SK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00824-16.

PMID- 4540599
VI  - 52
DP  - 1973
TI  - A simple assay for DNA restriction endonucleases.
PG  - 637-641
AB  - Recently several groups have used restriction enzymes to produce a limited
      number of unique, double stranded DNA fragments from the genome of SV40 virus
      and the double stranded replicative form of bacteriophage PhiX174.
AU  - DeFilippes FM
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 1973 52: 637-641.

PMID- 4599683
VI  - 58
DP  - 1974
TI  - A new method for isolation of a restriction enzyme from Haemophilus parainfluenzae.
PG  - 586-596
AB  - A rapid procedure which gives high yields of the restriction enzyme HpaI from
      Hemophilus parainfluenzae is described.  The procedure effectively removes a
      second restriction enzyme HpaII as well as exonucleolytic activity.  The
      optimal ionic conditions for the enzyme are similar to those found for one of
      the enzymes isolated from Hemophilus influenzae.  The enzyme is stable at 37C
      for several hours but it is rapidly inactivated at 60C.  Patterns are presented
      which show the electropohoretic separation of the digestion products of two
      viral DNAs by this enzyme.
AU  - DeFilippes FM
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1974 58: 586-596.

PMID- 24242100
VI  - 35
DP  - 2013
TI  - Ceci n'est pas une DNMT: Recently discovered functions of DNMT2 and their relation to methyltransferase activity (Comment on DOI 10.1002/bies.201300088).
PG  - 1024
AB  - 
AU  - Defossez P-A
PT  - Journal Article
TA  - Bioessays
JT  - Bioessays
SO  - Bioessays 2013 35: 1024.

PMID- 19451630
VI  - 106
DP  - 2009
TI  - Hamiltonella defensa, genome evolution of protective bacterial endosymbiont from pathogenic ancestors.
PG  - 9063-9068
AB  - Eukaryotes engage in a multitude of beneficial and deleterious interactions with bacteria.
      Hamiltonella defensa, an endosymbiont of
      aphids and other sap-feeding insects, protects its aphid host from attack
      by parasitoid wasps. Thus H. defensa is only conditionally beneficial to
      hosts, unlike ancient nutritional symbionts, such as Buchnera, that are
      obligate. Similar to pathogenic bacteria, H. defensa is able to invade
      naive hosts and circumvent host immune responses. We have sequenced the
      genome of H. defensa to identify possible mechanisms that underlie its
      persistence in healthy aphids and protection from parasitoids. The 2.1-Mb
      genome has undergone significant reduction in size relative to its closest
      free-living relatives, which include Yersinia and Serratia species
      (4.6-5.4 Mb). Auxotrophic for 8 of the 10 essential amino acids, H.
      defensa is reliant upon the essential amino acids produced by Buchnera.
      Despite these losses, the H. defensa genome retains more genes and
      pathways for a variety of cell structures and processes than do obligate
      symbionts, such as Buchnera. Furthermore, putative pathogenicity loci,
      encoding type-3 secretion systems, and toxin homologs, which are absent in
      obligate symbionts, are abundant in the H. defensa genome, as are
      regulatory genes that likely control the timing of their expression. The
      genome is also littered with mobile DNA, including phage-derived genes,
      plasmids, and insertion-sequence elements, highlighting its dynamic nature
      and the continued role horizontal gene transfer plays in shaping it.
AU  - Degnan PH
AU  - Yu Y
AU  - Sisneros N
AU  - Wing RA
AU  - Moran NA
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2009 106: 9063-9068.

PMID- 4581370
VI  - 123
DP  - 1973
TI  - Host controlled restriction and modification of bacteriophage mu and mu-promoted chromosome mobilization in Citrobacter freundii.
PG  - 283-288
AB  - Bacteriophage Mu grown on Escherichia coli K12 (Mu.K) is restricted by wild
      type Citrobacter freundii.  In two C. freundii mutants, where the restriction
      of foreign F' factors is absent (de Graaff and Stouthamer, 1971), the
      restriction for Mu.K., although at a lower level, still exists.  Consequently
      two host specificity systems exist in C. freundii, one affecting mainly the
      acceptance of foreign plasmid and chromosomal DNA and one affecting foreign DNA
      of bacteriophage Mu.  Mu is able to lysogenize C. freundii and to induce
      mutations at random in its chromosome.  Furthermore Mu is able to promote the
      mobilization of the C. freundii chromosome in strains carrying F' factors.  Mu
      promoted integration of F ts 114 lac+ into the C. freundii chromosome was
      observed, resulting in the formation of stable Hfr strains.  In this way it is
      possible to devise a method for chromosome transfer in other genera than E.
      coli to which plasmids of E. coli can be transferred, but in which no
      chromosome mobilization is possible because of poor DNA homology between the
      foreign plasmid and the host chromosome.
AU  - deGraaff J
AU  - Kreuning PC
AU  - van de Putte P
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1973 123: 283-288.

PMID- 1322531
VI  - 20
DP  - 1992
TI  - AclI, a new restriction endonuclease from Acinetobacter calcoaceticus recognizing 5'-AA^CGTT-3' .
PG  - 3787
AB  - AclI, a new restriction endonuclease, has been purified from Acinetobacter calcoaceticus M4.
      AclI recognizes the sequence 5'AA^CGTT3' and cleaves DNA as indicated. The enzyme was
      purified using the following chromatographic steps: 1) gel-filtration through biogel A-0.5m,
      2) DEAE-cellulose, 3) phosphocellulose, 4) heparin sepharose.
AU  - Degtyarev SK
AU  - Abdurashitov MA
AU  - Kolyhalov AA
AU  - Rechkunova NI
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 3787.

PMID- 2545213
VI  - 15
DP  - 1989
TI  - Immobilized oligonucleotides as affinity ligands for restriction endonucleases.
PG  - 358-362
AB  - Affinity chromatography of Type IIS restriction endonucleases is proposed. It is shown that
      endonucleases HgaI, FokI, and SfaNI have affinity to the matrix with immobilized
      oligonucleotides which contain the endonuclease's recognition sites resistant to hydrolysis.
AU  - Degtyarev SK
AU  - Belavin PA
AU  - Shishkina IG
AU  - Zarytova VF
AU  - Gavryuchenkova LP
AU  - Morozov SM
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1989 15: 358-362.

PMID- 10871355
VI  - 28
DP  - 2000
TI  - BtrI, a novel restriction endonuclease, recognises the non-palindromic sequence 5'-CACGTC(-3/-3)-3'.
PG  - e56
AB  - The recognition sequence and cleavage positions of a new restriction endonuclease BtrI
      isolated from Bacillus stearothermophilus SE-U62 have been determined.  BtrI belongs to a rare
      type IIQ of restriction endonucleases, which recognise non-palindromic nucleotide sequences
      and cleave DNA symmetrically within them.
AU  - Degtyarev SK
AU  - Belichenko OA
AU  - Lebedeva NA
AU  - Dedkov VS
AU  - Abdurashitov MA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2000 28: e56.

PMID- 1322532
VI  - 20
DP  - 1992
TI  - AcsI, a new restriction endonuclease from Arthrobacter citreus 310 recognizing 5'-Pu^AATTPy-3'.
PG  - 3789
AB  - AcsI, an isoschizomer of FsiI, has been purified from Arthrobacter citreus 310. AcsI
      recognizes the sequence 5'Pu^AATTPy3' and cleaves DNA as indicated by the arrow. The enzyme
      was purified using two chromatographic steps: phosphocellulose and heparin sepharose. The
      enzyme was free of contaminating nuclease activity. After 20-fold over-digestion on lambda DNA
      greater than 95% of the DNA fragments can be ligated and then recut by AcsI. Optimal
      conditions for AcsI activity are 10 mM Tris-HCl (pH 8.5), 10 mM MgCl2, 100 mM NaCl at 37C. The
      fragments produced by AcsI digestion of lambda and T7 DNAs match those predicted by cleavage
      at the sequence PuAATTPy.
AU  - Degtyarev SK
AU  - Kolyhalov AA
AU  - Rechkunova NI
AU  - Abdurashitov MA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 3789.

PMID- 2787154
VI  - 15
DP  - 1989
TI  - Determination of substrate specificity of restriction endonuclease FauI.
PG  - 130-132
AB  - The recognition sequence and cleavage point of restriction endonuclease FauI
      have been determined as 5'-CCCGC(4/6).  Not being an isoschizomer of any known
      restriction endonuclease, this enzyme may be used in genetic engineering.
AU  - Degtyarev SK
AU  - Kolyhalov AA
AU  - Rechkunova NI
AU  - Dedkov VS
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1989 15: 130-132.

PMID- 1645873
VI  - 19
DP  - 1991
TI  - Bsp1720I, an isoschizomer of EspI from Bacillus species 1720 recognizing 5'-GC^TNAGC-3'.
PG  - 2504
AB  - Bsp1720I, an isoschisomer of EspI (1) has been purified from Bacillus species 1720.  Bsp1720I
      recognizes the sequence 5'GC^TNAGC3' and cleaves DNA as indicated by the arrow.  The enzyme
      was purified using the following chromatographic steps: 1) gel-filtration through biogel A0.5
      m, 2) DEAE-cellulose, 3) phosphocellulose.  The enzyme was free of contaminating nuclease
      activity.  After 40-fold overdigestion on lambda DNA greater than 95% of the DNA fragments can
      be ligated and then recut by Bsp1720I.  Optimal conditions for Bsp1720I activity are 20 mM
      Tris-HCl (pH 7.5), 10 mM MgCl2, 100 mM NaCl at 37C. The fragments produced by Bsp1720I
      digestion of lambda DNA match those predicted by cleavage at the sequence GCTNAGC (figure 1,
      lane 2). The cleavage site was determined accordingly to earlier published procedure (2).  DNA
      of pUC 8 with the insert containing a Bsp1720I cleavage site (pVE27) was digested by the
      enzymes XmaI and PvuII; reaction products were labelled with [a-32P]dCTP by Klenow Fragment.
      350 bp DNA fragment was eluted from gel after electrophoresis in 6% PAAG, its structure and
      Bsp1720I hydrolysis site were determined (figure 2).  The results show that Bsp1720I cleaves
      DNA as indicated by arrows:
      5'-GC^TNAGC-3'
      3'-CGANT^CG-5'.
AU  - Degtyarev SK
AU  - Kolyhalov AA
AU  - Rechkunova NT
AU  - Tepavicharova II
AU  - Mechandjiska LI
AU  - Builieva EI
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 2504.

PMID- 2348824
VI  - 24
DP  - 1990
TI  - BsiI - A new unusual restriction endonuclease.
PG  - 244-247
AB  - The restriction endonuclease BsiI from Bacillus sphaericus was isolated.  The
      recognition sequence and cleavage point of enzyme BsiI have been determined as
      C^TCGTG
      GAGCA^C.
      This restriction endonuclease is not an isoschizomer of any known restriction
      endonucleases and differs from other enzymes: it hydrolyses DNA at an
      assymmetrical recognition sequence.
AU  - Degtyarev SK
AU  - Kolykhalov AA
AU  - Rechkunova NI
AU  - Dedkov VS
AU  - Zhilkin PA
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1990 24: 244-247.

PMID- 9099883
VI  - 187
DP  - 1997
TI  - Primary structure and strand specificity of BstF5I-1 DNA methyltransferase which recognizes 5'-GGATG-3'.
PG  - 217-219
AB  - The gene for BstF5I-1 DNA-methyltransferase (Mtase) from Bacillus stearothermophilus F5 (a
      FokI isoschizomer, recognizing 5'-GGATG-3') was cloned and its nucleotide sequence was
      determined.  Analysis of deduced amino acid sequence shows that M.BstF5I-1 belongs to D/21
      class of Mtases and has a little homology with M.FokI.  M.BstF5I-1 modifies only the upper
      strand of the recognition sequence (5'-GGATG-3').
AU  - Degtyarev SK
AU  - Netesova NA
AU  - Abdurashitov MA
AU  - Shevchenko AV
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1997 187: 217-219.

PMID- 9628355
VI  - 379
DP  - 1998
TI  - Cloning and characterization of the gene encoding M.FauI DNA methyltransferase.
PG  - 567-568
AB  - The enzymes of the FauI restriction-modification system from the Flavobacterium aquatile
      strain recognize the non-palindromic sequence 5'-CCCGC-3'/3'-GG-GCG-5'.  We have cloned
      the gene encoding the DNA modifying component of this system and determined its nucleotide
      sequence.  The deduced amino acid sequence contains ten conserved motifs characteristic for
      [cytosine-5] DNA methyltransferases.  Part of the gene sequence that encodes the putative
      target recognizing domain of the M.FauI shows some homology with the downstream region, thus
      indicating that duplication of the DNA segment was probably involved in the gene evolution.
AU  - Degtyarev SK
AU  - Netesova NA
AU  - Chizhikov VE
AU  - Abdurashitov MA
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1998 379: 567-568.

PMID- 3142485
VI  - 14
DP  - 1988
TI  - Determination of the substrate specificity of restriction endonuclease SfeI.
PG  - 848-849
AB  - The recognition sequence and cleavage site C^TRYAG of a new restriction
      endonuclease SfeI have been determined.
AU  - Degtyarev SK
AU  - Prihodko GG
AU  - Rechkunova NI
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1988 14: 848-849.

PMID- 8493116
VI  - 21
DP  - 1993
TI  - VspI methylase belongs to m6A-gamma class of adenine methylases.
PG  - 2015
AB  - We have successfully isolated a genomic clone of Vibrio species strain 343 which encodes
      methyltransferases and prevents plasmid and bacterial DNA degredation by restriction
      endonuclease VspI. There are three open reading frames starting from nucleotides #503, #57,
      #812 and ending at #1780, which encode 47.5, 45.5 and 36.1 kd proteins respectively. The
      Shine-Dalgarno signal are present in the last two open reading frames. Gel-filtration of
      native methylase VspI showed a molecular weight of 42.7 kd. Thus, the open reading frame of
      the methylase gene is #557-1780 and it encodes a 408 amino acid protein. The comparison of
      deduced amino acid structure of VspI methylase and others has been done according to
      Klimasauskas et al. According to mutual positions of two conservative domains this enzyme
      belongs to m6A-gamma class. M.VspI has a NPPW-motif instead of an NPPY one, but replacement of
      aromatic amino acid tyrosine by another aromatic amino acid tryptophan might be insignificant.
AU  - Degtyarev SK
AU  - Prikhodko EA
AU  - Prikhodko GG
AU  - Krasnykh VN
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 2015.

PMID- 8439575
VI  - 1172
DP  - 1993
TI  - Interaction of VspI and Tru9I restriction endonucleases with synthetic oligonucleotides.
PG  - 89-94
AB  - We describe the properties of two new restriction endonucleases VspI and Tru9I which recognize
      sequences AT^TAAT and T^TAA respectively. The molecular weights, subunit structure and
      steady-state kinetic constants of these enzymes for native and modified substrates have been
      determined. We have investigated the interaction of VspI and Tru9I with synthetic
      oligonucleotides containing modifications either within the recognition sites or around them.
      These modifications represent the substitution of different DNA deoxyribonucleosides by
      1,2-dideoxy-D-ribofuranose, which corresponds to loss of the heterocyclic base while the
      sugar-phosphate chain remains intact. The effects of the substitutions were analyzed by
      determining the steady-state kinetic values of the hydrolysis reaction by VspI and Tru9I. The
      enzymes exhibited Michaelis-Menten kinetics for hydrolyzable substrates. The initial rates
      (Vo) of hydrolysis of modified and unmodified strands of the duplexes varied as a result of
      these substitutions. The substrates for VspI and Tru9I which contain modifications around the
      bond to be hydrolyzed or within the complementary nucleosides were unreactive.
AU  - Degtyarev SK
AU  - Prikhodko EA
AU  - Rechkunova NI
AU  - Gorbunov YA
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1993 1172: 89-94.

PMID- 7607528
VI  - 157
DP  - 1995
TI  - Biochemical characterization of VspI methyltransferase.
PG  - 65-66
AB  - The gene (vspIM) encoding VspI methyltransferase (MTase) has previously been cloned and
      sequenced, and shown to belong to the gamma class of m6-adenine MTases.  Here it is shown that
      the MTase modifies the third adenine within the recognition sequence 5'-ATTAAT-3'.
AU  - Degtyarev SK
AU  - Prikhodko EA
AU  - Rechkunova NI
AU  - Prikhodko GG
AU  - Krasnykh VN
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 65-66.

PMID- Not carried by PubMed...
VI  - 14
DP  - 1988
TI  - Determination of purity of restriction endonucleases.
PG  - 102-105
AB  - A method for the determination of exonucleases and phosphatase impurities in preparations of
      restriction endonucleases using 5'-[32P]-labelled double-stranded 20-base long
      deoxyribooligonucleotides is suggested. Incubation of enzyme with substrate is carried out in
      restriction buffer with subsequent electrophoresis of the reaction mixture in 20%
      polyacrylamide in the presence of 7M urea and autoradiography of the gel.  The percent of
      label in oligonucleotide is determined.
AU  - Degtyarev SK
AU  - Rechkunova NI
PT  - Journal Article
TA  - Izv. Sib. Otd. Akad. Nauk SSSR
JT  - Izv. Sib. Otd. Akad. Nauk SSSR
SO  - Izv. Sib. Otd. Akad. Nauk SSSR 1988 14: 102-105.

PMID- Not carried by PubMed...
VI  - 15
DP  - 1989
TI  - Determination of substrate specificity of restriction endonucleases Bme18I and Kzo9I.
PG  - 25-26
AB  - The recognition sequence and cleavage point of restriction endonucleases Bme18I and Kzo9I have
      been determined as G^G(A/T) CC and ^GATC, respectively.
AU  - Degtyarev SK
AU  - Rechkunova NI
AU  - Grinev AA
AU  - Dedkov VS
PT  - Journal Article
TA  - Izv. Sib. Otd. Akad. Nauk SSSR
JT  - Izv. Sib. Otd. Akad. Nauk SSSR
SO  - Izv. Sib. Otd. Akad. Nauk SSSR 1989 15: 25-26.

PMID- 2216771
VI  - 18
DP  - 1990
TI  - II-Q restriction endonucleases - new class of type II enzymes.
PG  - 5807-5810
AB  - Unique restriction endonucleases Bpu10I and BsiI have been isolated from
      Bacillus pumilus and Bacillus sphaericus, respectively.  The recognition
      sequences and cleavage points of these enzymes have been determined as
      5'-CC^TNAGC-3'
      3'-GGANT^CG-5' for Bpu10I
      and
      5'-C^TCGTG-3'
      3'-GAGCA^C-5' for BsiI.
      Restriction endonucleases Bpu10I and BsiI represent a new class of enzymes
      which recognize nonpalindromic nucleotide sequences and hydrolyze DNA within
      the recognition sequences may be regarded as quasi-palindromic and the enzymes
      may be designated as type II-Q restriction endonucleases.
AU  - Degtyarev SK
AU  - Rechkunova NI
AU  - Kolyhalov AA
AU  - Dedkov VS
AU  - Zhilkin PA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 5807-5810.

PMID- 3036170
VI  - 13
DP  - 1987
TI  - Determination of substrate specificity of restriction endonuclease VneI.
PG  - 422-423
AB  - The recognition sequence and cleavage point of restriction endonuclease VneI
      have been determined as 5'-G^TGCAC.  This enzyme is not isoschizomer of any
      known restriction endonucleases and therefore may be widely used in
      investigation of DNA structure.
AU  - Degtyarev SK
AU  - Rechkunova NI
AU  - Netesova NA
AU  - Tchigikov VE
AU  - Malygin EG
AU  - Kochkin AV
AU  - Mikhajlov VV
AU  - Rasskazov VA
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1987 13: 422-423.

PMID- Not carried by PubMed...
VI  - 1
DP  - 1990
TI  - The recognition sequence and cleavage point of restriction endonuclease Bse 21 I.
PG  - 138-139
AB  - The recognition sequence and cleavage point of restriction endonuclease Bse21I
      have been determined as 5'-CC^TNAGG.  This enzyme is an isoschizomer of SauI
      and may replace it in investigation of DNA structure.
AU  - Degtyarev SK
AU  - Rechkunova NI
AU  - Repin VE
AU  - Kolyhalov AA
AU  - Netesov SV
PT  - Journal Article
TA  - Izv. Sib. Otd. Akad. Nauk SSSR
JT  - Izv. Sib. Otd. Akad. Nauk SSSR
SO  - Izv. Sib. Otd. Akad. Nauk SSSR 1990 1: 138-139.

PMID- 8396549
VI  - 131
DP  - 1993
TI  - Bsp24I, a new unusual restriction endonuclease.
PG  - 93-95
AB  - *

      A new restriction endonuclease, Bsp24I, from Bacillus species 24, recognizing:

      

         5'-^N8 GACNNNNNNTGGN12^-3'

         3'-^N13CTGNNNNNNACCN7^-5',

      

      has been isolated. Its specificity and cleavage points were determined.

      

AU  - Degtyarev SK
AU  - Rechkunova NI
AU  - Zernov YP
AU  - Dedkov VS
AU  - Chizikov VE
AU  - Van Calligan M
AU  - Williams R
AU  - Murray E
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1993 131: 93-95.

PMID- 3036169
VI  - 13
DP  - 1987
TI  - Determination of the substrate specificity of restriction endonuclease VspI.
PG  - 420-421
AB  - The recognition sequence and cleavage point of restriction endonuclease VspI
      have been determined as 5'-AT^TAAT.  This enzyme is not an isoschizomer of any
      known restriction endonucleases.  DNA pBR322 contains a single VspI recognition
      sequence in position 3539.  Therefore this enzyme may be used for cloning DNA
      in the VspI site in AmpR-gene of pBR322.
AU  - Degtyarev SK
AU  - Repin VE
AU  - Rechkunova NI
AU  - Tchigikov VE
AU  - Malygin EG
AU  - Mikhajlov VV
AU  - Rasskazov VA
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1987 13: 420-421.

PMID- 2290429
VI  - 24
DP  - 1990
TI  - Type II restriction enzymes:  Possible evolutionary links between the enzymes and their palindromic tetranucleotide recognition sequences.
PG  - 1393-1398
AB  - The distribution of restriction enzymes with tetranucleotide recognition sequences in nature
      was analyzed.  A rule for the conversion of these recognition sites was formulated, and a
      scheme showing the evolutionary links of restriction enzymes with their palindromic
      tetranucleotide sequences is proposed.
AU  - Degtyarev SK
AU  - Zernov YP
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1990 24: 1393-1398.

PMID- 2586500
VI  - 23
DP  - 1989
TI  - Determination of unusual substrate specificity of restriction endonuclease Bpu10I.
PG  - 1051-1056
AB  - A new enzyme Bpu10I was isolated form Bacillus pumilus.  This enzyme is not an isoschizomer of
      any known restriction endonucleases.  The search of possible recognition sequences was carried
      out in sequences ABCNiDEF (i=0-6) on substrate DNA lambda CI857, T7, pBR322.  The recognition
      sequence and cleavage sites of restriction endonuclease Bpu10I have been determined as
      CC^TNAGC
      GGANT^CG.
AU  - Degtyarev SK
AU  - Zilkin PA
AU  - Prihodko GG
AU  - Repin VE
AU  - Rechkunova NI
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1989 23: 1051-1056.

PMID- 10545092
VI  - 18
DP  - 1999
TI  - Crystal structure of MunI restriction endonuclease in complex with cognate DNA at 1.7 A resolution.
PG  - 5805-5816
AB  - The MunI restriction enzyme recognizes the palindromic hexanucleotide sequence C/AATTG (the
      '/' indicates the cleavage site).  The crystal structure of its active site mutant D83A
      bound to cognate DNA has been determined at 1.7 A resolution.  Base-specific contacts between
      MunI and DNA occur exclusively in the major groove. While DNA-binding sites of most other
      restriction enzymes are comprised of discontinuous sequence segments, MunI combines all
      residues involved in the base-specific contacts within one short stretch (residues R115-R121)
      located at the N-terminal region of the 3(10)4 helix. The outer CG base pair of the
      recognition sequence is recognized solely by R115 through hydrogen bonds made by backbone and
      side chain atoms to both bases. The mechanism of recognition of the central AATT nucleotides
      by MunI is similar to that of EcoRI, which recognizes the G/AATTC sequence. The local
      conformation of AATT deviates from the typical B-DNA form and is remarkably similar to
      EcoRI-DNA. It appears to be essential for specific hydrogen bonding and recognition by MunI
      and EcoRI.
AU  - Deibert M
AU  - Grazulis S
AU  - Janulaitis A
AU  - Siksnys V
AU  - Huber R
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1999 18: 5805-5816.

PMID- 10966652
VI  - 7
DP  - 2000
TI  - Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA.
PG  - 792-799
AB  - The crystal structure of the NgoMIV restriction endonuclease in complex with cleaved DNA has
      been determined at 1.6 A resolution. The crystallographic asymmetric unit contains a protein
      tetramer and two DNA molecules cleaved at their recognition sites. This is the first structure
      of a tetrameric restriction enzyme-DNA complex. In the tetramer, two primary dimers are
      arranged back to back with two oligonucleotides bound in clefts on opposite sides of the
      tetramer. The DNA molecules retain a B-type conformation and have an enclosed angle between
      their helical axes of 60 degrees. Sequence-specific interactions occur in both the major and
      minor grooves. Two Mg2+ ions are located close to the cleaved phosphate at the active site of
      NgoMIV. Biochemical experiments show that interactions between the recognition sites within
      the tetramer greatly increase DNA cleavage efficiency.
AU  - Deibert M
AU  - Grazulis S
AU  - Sasnauskas G
AU  - Siksnys V
AU  - Huber R
PT  - Journal Article
TA  - Nat. Struct. Biol.
JT  - Nat. Struct. Biol.
SO  - Nat. Struct. Biol. 2000 7: 792-799.

PMID- 7501438
VI  - 23
DP  - 1995
TI  - Restriction endonuclease BsoFI is sensitive to the 5'-methylation of deoxycytidines in its recognition sequence.
PG  - 4227-4228
AB  - The isoschizomeric restriction endonucleases Fnu4HI and BsoFI cleave DNA at 5'-GC/NGC-3'
      sequences.  Fnu4HI has been shown to be inhibited by 5'-CG-3' methylation in the sequences
      5'-GmCGGC-3' or 5'-GCGGmCG-3'.  We have now investigated the methylation sensitivity of
      BsoFI by testing its activity on plasmid DNA 5'-CG-3' methylated with the M.SssI DNA
      methyltransferase or on synthetic (CGG)n repetitive oligodeoxyribonucleotides which have been
      partly or completely C methylated.  The data demonstrate that BsoFI cannot cleave at its
      recognition sequence when it is completely 5'-CG-3' methylated.  These enzymes have proven
      to be useful in analyses of the methylation status in (CGG)n repeats of the human genome.
AU  - Deissler H
AU  - Genc B
AU  - Doerfler W
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1995 23: 4227-4228.

PMID- 27688330
VI  - 4
DP  - 2016
TI  - Genome Sequences of Nine Gram-Negative Vaginal Bacterial Isolates.
PG  - e00889-16
AB  - The vagina is home to a wide variety of bacteria that have great potential to impact human
      health. Here, we announce reference strains (now available through
      BEI Resources) and draft genome sequences for 9 Gram-negative vaginal isolates
      from the taxa Citrobacter, Klebsiella, Fusobacterium, Proteus, and Prevotella.
AU  - Deitzler GE
AU  - Ruiz MJ
AU  - Lu W
AU  - Weimer C
AU  - Park S
AU  - Robinson LS
AU  - Hallsworth-Pepin K
AU  - Wollam A
AU  - Mitreva M
AU  - Lewis WG
AU  - Lewis AL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00889-16.

PMID- 27688329
VI  - 4
DP  - 2016
TI  - Genome Sequences of 14 Firmicutes Strains Isolated from the Human Vagina.
PG  - e00888-16
AB  - Research on vaginal infections is currently limited by a lack of available fully  sequenced
      bacterial reference strains. Here, we present strains (now available
      through BEI Resources) and genome sequences for a set of 14 vaginal isolates from
      the phylum Firmicutes These genome sequences provide a valuable resource for
      future research in understanding the role of Gram-positive bacteria in vaginal
      health and disease.
AU  - Deitzler GE
AU  - Ruiz MJ
AU  - Weimer C
AU  - Park S
AU  - Robinson L
AU  - Hallsworth-Pepin K
AU  - Wollam A
AU  - Mitreva M
AU  - Lewis AL
AU  - Lewis WG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00888-16.

PMID- 9421500
VI  - 26
DP  - 1998
TI  - Three different group I introns in the nuclear large subunit ribosomal DNA of the amoeboflagellate Naegleria.
PG  - 456-461
AB  - We have amplified the large subunit ribosomal DNA of the 12 described Naegleria spp. and of 34
      other Naegleria lineages that might be distinct species.  Two strains yielded a product that
      is longer than 3 kb, which is the length of the LSUrDNA of all described Naegleria spp.
      Sequencing data revealed that the insert in one of these strains is a group I intron without
      an open reading frame, while the other strain contains two different group I introns, of which
      the second intron has an ORF of 175 amino acids.  In the latter ORF there is a conserved
      His-Cys box as in the homing endonucleases present in group I introns in the small subunit
      ribosomal DNA of Naegleria spp.  Although the group I introns in the LSUrDNA differ in
      sequence, they are more related to each other than they are to the group I introns in the
      SSUrDNA of Naegleria spp.  The three group I introns in the LSUrDNA in Naegleria are at
      different locations and are probably acquired by horizontal transfer, contrary to the SSUrDNA
      group I introns in this genus which are of ancestral origin and are transmitted vertically.
AU  - DeJonckheere JF
AU  - Brown S
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1998 26: 456-461.

PMID- 23070174
VI  - 57
DP  - 2013
TI  - Comparative sequence analysis of a multi-drug resistant plasmid from Aeromonas hydrophila.
PG  - 120-129
AB  - Aeromonas hydrophila is a pathogenic bacterium that has been implicated in fish,
      animal, and human disease. Recently, a multi-drug resistance (MDR) plasmid pR148
      was isolated from A. hydrophila obtained from a tilapia (Oreochromis niloticus)
      farm in Thailand. pR148 is a 165,906 bp circular plasmid containing 147 coding
      regions showing highest similarity to pNDM-1_Dok1, an MDR plasmid isolated from a
      human pathogen. It was also very similar to other IncA/C plasmids isolated from
      humans, animals, food, and fish. pR148 contains a mercuric resistance operon and
      encodes the complete set of genes for the type 4 secretion system. pR148 encodes
      for a Tn21 type transposon. This contains the drug resistance genes qacH,
      bla(OXA-10), aadA1, and sul1 in a class 1 integron; tetA and tetR in a transposon
      Tn1721; and catA2 and a duplicate sul1 in a locus showing 100% similarity to IncU
      plasmids isolated from fish. The bla(OXA-10) and aadA1 genes showed 100%
      similarity with those from the Acinetobacter baumannii AYE chromosomal genome.
      The similarity of pR148 to a human pathogen-derived plasmid indicates that the
      plasmids were either transferred between them or that they are derived from a
      common origin. Previous studies have shown that IncA/C plasmids retain a
      conserved backbone, while the accessory region points to lateral gene transfer.
      These observations point out the dangers of indiscriminate use of antibiotics in
      humans and in animals and the necessity of understanding how drug resistance
      determinants are disseminated and transferred.
AU  - Del Castillo CS
AU  - Hikima JI
AU  - Jang HB
AU  - Nho SW
AU  - Jung TS
AU  - Wongtavatchai J
AU  - Kondo H
AU  - Hirono I
AU  - Takeyama H
AU  - Aoki T
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2013 57: 120-129.

PMID- 23516201
VI  - 1
DP  - 2013
TI  - Genome Sequence of the Butanol Hyperproducer Clostridium saccharoperbutylacetonicum N1-4.
PG  - e0007013
AB  - Clostridium saccharoperbutylacetonicum is one of the most important acetone-butanol-ethanol
      (ABE)-generating industrial microorganisms and one of the
      few bacteria containing choline in its cell wall. Here, we report the draft
      genome sequence of C. saccharoperbutylacetonicum strain N1-4 (6.6 Mbp; G+C
      content, 29.4%) and the findings obtained from the annotation of the genome.
AU  - Del Cerro C
AU  - Felpeto-Santero C
AU  - Rojas A
AU  - Tortajada M
AU  - Ramon D
AU  - Garcia JL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0007013.

PMID- 23012286
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Methanotrophic Poly-beta-Hydroxybutyrate Producer Methylocystis parvus OBBP.
PG  - 5709-5710
AB  - Methylocystis parvus OBBP is an obligate methylotroph considered the type species of the genus
      Methylocystis. Two pmoCAB particulate methane monooxygenase operons
      and one additional singleton pmoC paralog were identified in the sequence. No
      evidence of genes encoding soluble methane monooxygenase was found. Comparison of
      M. parvus OBBP and Methylocystis sp. strain Rockwell (ATCC 49242) suggests that
      both species should be taxonomically classified in different genera.
AU  - Del Cerro C
AU  - Garcia JM
AU  - Rojas A
AU  - Tortajada M
AU  - Ramon D
AU  - Galan B
AU  - Prieto MA
AU  - Garcia JL
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5709-5710.

PMID- 10544268
VI  - 460
DP  - 1999
TI  - Characterization of a new variant DNA (cytosine-5)-methyltransferase unable to methylate double stranded DNA isolated from the marine annelid worm Chaetopterus variopedatus.
PG  - 380-384
AB  - The enzyme S-adenosylmethionine-DNA (cytosine-5)-methyltransferase has been identified, first
      time for invertebrates, in embryos of the marine polychaete annelid worm Chaetopterus
      variopedatus. The molecule has been isolated from embryos at 15 h of development. It is a
      single peptide of about 200 kDa molecular weight, cross-reacting with antibodies against sea
      urchin DNA methyltransferase. The enzymatic properties of the molecule are similar to those of
      Dnmt1 methyltransferases isolated from other organisms, but with the peculiarity to be unable
      to make 'de novo' methylation on double stranded DNA.
AU  - del Gaudio R
AU  - Di Giaimo R
AU  - Potenza N
AU  - Branno M
AU  - Aniello F
AU  - Geraci G
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1999 460: 380-384.

PMID- 368038
VI  - 137
DP  - 1979
TI  - Method for isolating restriction- and modificationless mutants of Escherichia coli K-12.
PG  - 673-676
AB  - A simple method is described for the selection and isolation of restriction- and
      modificationless mutants in Escherichia coli K-12 by using the following properties: (i) the
      temperature-sensitive repressor activity of phage lambda-cI857; (ii) a mutant of lambda phage
      defective in integration and the establishment of repression (lambda-b2cI); (iii) a virulent
      phage insensitive to the repressor activity.  The final yield of spontaneously arising rK- mK+
      and rK- mK- mutants from stationary-phase cultures was about 5% of the surviving cells.
AU  - Del Giudice L
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1979 137: 673-676.

PMID- 21304734
VI  - 3
DP  - 2010
TI  - Complete genome sequence of Intrasporangium calvum type strain (7 KIP).
PG  - 294-303
AB  - Intrasporangium calvum Kalakoutskii et al. 1967 is the type species of the genus
      Intrasporangium, which belongs to the actinobacterial family Intrasporangiaceae.
      The species is a Gram-positive bacterium that forms a branching mycelium, which
      tends to break into irregular fragments. The mycelium of this strain may bear
      intercalary vesicles but does not contain spores. The strain described in this
      study is an airborne organism that was isolated from a school dining room in
      1967. One particularly interesting feature of I. calvum is that the type of its
      menaquinone is different from all other representatives of the family
      Intrasporangiaceae. This is the first completed genome sequence from a member of
      the genus Intrasporangium and also the first sequence from the family
      Intrasporangiaceae. The 4,024,382 bp long genome with its 3,653 protein-coding
      and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea
      project.
AU  - Del Rio TG et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 3: 294-303.

PMID- 2536593
VI  - 56
DP  - 1989
TI  - Site-specific DNA endonuclease and RNA maturase activities of two homologous intron-encoded proteins from yeast mitochondria.
PG  - 431-444
AB  - Two introns of the mitochondrial genome 777-3A of S. cerevisiae, bI4 in cob and aI4 in cox1
      genes, contain ORFs that can be translated into two homologous proteins. We changed the UGA,
      AUA, and CUN codons of these ORFs to the universal genetic code, in order to study the
      functions of their translated products in E. coli and in yeast, by retargeting the nuclear
      encoded protein into mitochondria. The p27b14 protein has been shown to be required for the
      splicing of both introns bI4 and aI4. The homologous p28aI4 protein is highly toxic to E.
      coli. It can specifically cleave double-stranded DNA at a sequence representing the junction
      of the two fused flanking exons. We present evidence that this system is a good model for
      studying the role of mitochondrial intron-encoded proteins in the rearrangement of genetic
      information at both the RNA (RNA splicing-bI4 maturase) and DNA levels (intron
      transposition-aI4 transposase).
AU  - Delahodde A
AU  - Goguel V
AU  - Becam AM
AU  - Creusot F
AU  - Perea J
AU  - Banroques J
AU  - Jacq C
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1989 56: 431-444.

PMID- 26679591
VI  - 3
DP  - 2015
TI  - Genome Sequence of Bradyrhizobium tropiciagri Strain CNPSo 1112T, Isolated from a Root Nodule of Neonotonia wightii.
PG  - e01482-15
AB  - CNPSo 1112(T) is a nitrogen-fixing symbiont of perennial soybean, a tropical legume forage.
      Its draft genome indicates a large genome with a circular
      chromosome and 9,554 coding sequences (CDSs). Operons of nodulation, nitrogen
      fixation, and uptake hydrogenase were present in the symbiotic island, and the
      genome encompasses several CDSs of stress tolerance.
AU  - Delamuta JR
AU  - Gomes DF
AU  - Ribeiro RA
AU  - Chueire LM
AU  - Souza RC
AU  - Almeida LG
AU  - Vasconcelos AT
AU  - Hungria M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01482-15.

PMID- 27365354
VI  - 4
DP  - 2016
TI  - Genome Sequence of Bradyrhizobium stylosanthis Strain BR 446T, a Nitrogen-Fixing  Symbiont of the Legume Pasture Stylosanthes guianensis.
PG  - e00631-16
AB  - Bradyrhizobium stylosanthis BR 446(T) is a nitrogen-fixing symbiont of the tropical legume
      pasture Stylosanthes guianensis Its draft genome contains 8,801,717 bp and 8,239 coding
      sequences (CDSs). Several putative genes that might confer high competitiveness and
      saprophytic capacity under the stressful conditions of tropical soils were identified in the
      genome.
AU  - Delamuta JR
AU  - Ribeiro RA
AU  - Gomes DF
AU  - Souza RC
AU  - Chueire LM
AU  - Hungria M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00631-16.

PMID- 26383651
VI  - 3
DP  - 2015
TI  - Genome Sequence of Bradyrhizobium pachyrhizi Strain PAC48T, a Nitrogen-Fixing Symbiont of Pachyrhizus erosus (L.) Urb.
PG  - e01074-15
AB  - Bradyrhizobium pachyrhizi PAC48(T) has been isolated from a jicama nodule in Costa Rica. The
      draft genome indicates high similarity with that of Bradyrhizobium elkanii. Several coding
      sequences (CDSs) of the stress response might help in survival in the tropics. PAC48(T)
      carries nodD1 and nodK, similar to Bradyrhizobium (Parasponia) ANU 289 and a particular nodD2
      gene.
AU  - Delamuta JRM
AU  - Ribeiro RA
AU  - Gomes DF
AU  - Souza RC
AU  - Chueire LM
AU  - Hungria M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01074-15.

PMID- 23105075
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of a Nonhemolytic Fish-Pathogenic Streptococcus agalactiae  Strain.
PG  - 6341-6342
AB  - Streptococcus agalactiae is a significant Gram-positive bacterial pathogen of terrestrial and
      aquatic animals. A subpopulation of nonhemolytic strains which
      appear to be pathogenic only for poikilotherms exists. We report here the first
      draft genome sequence of a nonhemolytic S. agalactiae isolate recovered from a
      diseased fish.
AU  - Delannoy CM
AU  - Zadoks RN
AU  - Lainson FA
AU  - Ferguson HW
AU  - Crumlish M
AU  - Turnbull JF
AU  - Fontaine MC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6341-6342.

PMID- 26227606
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Human-Pathogenic Escherichia coli O26:H11 Strains Carrying the stx2 Gene Only and Circulating in France.
PG  - e00852-15
AB  - Shiga toxin-producing Escherichia coli (STEC) O26:H11 is one of the most frequent pathogens
      associated with diarrhea and hemolytic-uremic syndrome (HUS). In this
      report, we present the draft genome sequences of seven strains of STEC O26:H11
      carrying the stx2a or stx2d gene only and isolated in France from HUS patients.
AU  - Delannoy S
AU  - Mariani-Kurkdjian P
AU  - Bonacorsi S
AU  - Liguori S
AU  - Ison SA
AU  - Fach P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00852-15.

PMID- 24639510
VI  - 111
DP  - 2014
TI  - Molecular dissection of the evolution of carbapenem-resistant multilocus sequence type 258 Klebsiella pneumoniae.
PG  - 4988-4993
AB  - Infections caused by drug-resistant bacteria are a major problem worldwide.
      Carbapenem-resistant Klebsiella pneumoniae, most notably isolates classified as
      multilocus sequence type (ST) 258, have emerged as an important cause of hospital
      deaths. ST258 isolates are predominantly multidrug resistant, and therefore
      infections caused by them are difficult to treat. It is not known why the ST258
      lineage is the most prevalent cause of multidrug-resistant K. pneumoniae
      infections in the United States and other countries. Here we tested the
      hypothesis that carbapenem-resistant ST258 K. pneumoniae is a single genetic
      clone that has disseminated worldwide. We sequenced to closure the genomes of two
      ST258 clinical isolates and used these genomes as references for comparative
      genome sequencing of 83 additional clinical isolates recovered from patients at
      diverse geographic locations worldwide. Phylogenetic analysis of the SNPs in the
      core genome of these isolates revealed that ST258 K. pneumoniae organisms are two
      distinct genetic clades. This unexpected finding disproves the single-clone
      hypothesis. Notably, genetic differentiation between the two clades results from
      an approximately 215-kb region of divergence that includes genes involved in
      capsule polysaccharide biosynthesis. The region of divergence appears to be a
      hotspot for DNA recombination events, and we suggest that this region has
      contributed to the success of ST258 K. pneumoniae. Our findings will accelerate
      research on novel diagnostic, therapeutic, and vaccine strategies designed to
      prevent and/or treat infections caused by multidrug resistant K. pneumoniae.
AU  - Deleo FR
AU  - Chen L
AU  - Porcella SF
AU  - Martens CA
AU  - Kobayashi SD
AU  - Porter AR
AU  - Chavda KD
AU  - Jacobs MR
AU  - Mathema B
AU  - Olsen RJ
AU  - Bonomo RA
AU  - Musser JM
AU  - Kreiswirth BN
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2014 111: 4988-4993.

PMID- 26649149
VI  - 10
DP  - 2015
TI  - Genome sequence of the clover symbiont Rhizobium leguminosarum bv. trifolii strain CC275e.
PG  - 121
AB  - Rhizobium leguminosarum bv. trifolii strain CC275e is a highly effective, N2-fixing
      microsymbiont of white clover (Trifolium repens L.). The bacterium has
      been widely used in both Australia and New Zealand as a clover seed inoculant
      and, as such, has delivered the equivalent of millions of dollars of nitrogen
      into these pastoral systems. R. leguminosarum strain CC275e is a rod-shaped,
      motile, Gram-negative, non-spore forming bacterium. The genome was sequenced on
      an Illumina MiSeq instrument using a 2 x 150 bp paired end library and assembled
      into 29 scaffolds. The genome size is 7,077,367 nucleotides, with a GC content of
      60.9 %. The final, high-quality draft genome contains 6693 protein coding genes,
      close to 85 % of which were assigned to COG categories. This Whole Genome Shotgun
      project has been deposited at DDBJ/EMBL/GenBank under the accession JRXL00000000.
      The sequencing of this genome will enable identification of genetic traits
      associated with host compatibility and high N2 fixation characteristics in
      Rhizobium leguminosarum. The sequence will also be useful for development of
      strain-specific markers to assess factors associated with environmental fitness,
      competiveness for host nodule occupancy, and survival on legume seeds (New
      Zealand Ministry of Business, Innovation and Employment program, 'Improving
      forage legume-rhizobia performance' contract C10X1308 and DairyNZ Ltd.).
AU  - Delestre C
AU  - Laugraud A
AU  - Ridgway H
AU  - Ronson C
AU  - O'Callaghan M
AU  - Barrett B
AU  - Ballard R
AU  - Griffiths A
AU  - Young S
AU  - Blond C
AU  - Gerard E
AU  - Wakelin S
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 121.

PMID- 4583940
VI  - 124A
DP  - 1973
TI  - Restriction and modification of bacteriophages by Escherichia coli K12 involving a cryptic P1 prophage associated with different plasmids.
PG  - 173-178
AB  - By transducing hybrid plasmids with P1, two transductants were found to carry a cryptic P1
      phage closely associated with plasmids R(T), Ton or Col(VI), Trp.  The presence of these
      cryptic P1 phages was manifested by restriction and modification of phages T1 and T7.  Linkage
      on a single genetic structure of the cryptic P1 phage and the other extrachromosomal genes was
      demonstrated by associated transfer by conjugation and P1-transduction.  The two cryptic P1
      phages were not identical.
AU  - Delhalle E
PT  - Journal Article
TA  - Ann. Microbiol. (Paris)
JT  - Ann. Microbiol. (Paris)
SO  - Ann. Microbiol. (Paris) 1973 124A: 173-178.

PMID- 24699959
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Host-Restricted Salmonella enterica Serovar Abortusovis Strain SS44.
PG  - e00261-14
AB  - Salmonella enterica serovar Abortusovis is a pathogen strictly adapted to ovines, in which it
      causes abortion. To enhance our understanding of this pathogen, we assembled the first draft
      sequence of an S. Abortusovis genome (strain SS44). The obtained genomic data might facilitate
      the study of S. enterica evolution and host adaptation.
AU  - Deligios M
AU  - Bacciu D
AU  - Deriu E
AU  - Corti G
AU  - Bordoni R
AU  - De Bellis G
AU  - Leori GS
AU  - Rubino S
AU  - Uzzau S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00261-14.

PMID- 16439655
VI  - 311
DP  - 2006
TI  - Community genomics among stratified microbial assemblages in the ocean's interior.
PG  - 496-503
AB  - Microbial life predominates in the ocean, yet little is known about its genomic variability,
      especially along the depth continuum. We report here
      genomic analyses of planktonic microbial communities in the North Pacific
      Subtropical Gyre, from the ocean's surface to near-sea floor depths.
      Sequence variation in microbial community genes reflected vertical
      zonation of taxonomic groups, functional gene repertoires, and metabolic
      potential. The distributional patterns of microbial genes suggested
      depth-variable community trends in carbon and energy metabolism,
      attachment and motility, gene mobility, and host-viral interactions.
      Comparative genomic analyses of stratified microbial communities have the
      potential to provide significant insight into higher-order community
      organization and dynamics.
AU  - DeLong EF
AU  - Preston CM
AU  - Mincer T
AU  - Rich V
AU  - Hallam SJ
AU  - Frigaard NU
AU  - Martinez A
AU  - Sullivan MB
AU  - Edwards R
AU  - Brito BR
AU  - Chisholm SW
AU  - Karl DM
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2006 311: 496-503.

PMID- 21914889
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of the Pigmented Streptococcus thermophilus Strain JIM8232.
PG  - 5581-5582
AB  - Streptococcus thermophilus is a dairy species commonly used in the manufacture of cheese and
      yogurt. Here, we report the complete sequence of
      S. thermophilus strain JIM8232, isolated from milk and which produces a
      yellow pigment, an atypical trait for this bacterium.
AU  - Delorme C
AU  - Bartholini C
AU  - Luraschi M
AU  - Pons N
AU  - Loux V
AU  - Almeida M
AU  - Guedon E
AU  - Gibrat JF
AU  - Renault P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5581-5582.

PMID- 21742894
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of the clinical Streptococcus salivarius strain CCHSS3.
PG  - 5041-5042
AB  - Streptococcus salivarius is a commensal species commonly found in the human oral cavity and
      digestive tract, although it is also associated with
      human infections such as meningitis, endocarditis and bacteremia. Here, we
      report the complete sequence of S. salivarius strain CCHSS3 isolated from
      human blood.
AU  - Delorme C
AU  - Guedon E
AU  - Pons N
AU  - Cruaud C
AU  - Couloux A
AU  - Loux V
AU  - Chiapello H
AU  - Poyart C
AU  - Gautier C
AU  - Sanchez N
AU  - Almeida M
AU  - Kennedy S
AU  - Ehrlich SD
AU  - Gibrat JF
AU  - Wincker P
AU  - Renault P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5041-5042.

PMID- 11756688
VI  - 99
DP  - 2002
TI  - The genome sequence of the facultative intracellular pathogen Brucella melitensis.
PG  - 443-448
AB  - Brucella melitensis is a facultative intracellular bacterial pathogen that causes abortion in
      goats and sheep and Malta fever in humans. The genome of B. melitensis strain 16M was
      sequenced and found to contain 3,294,935 bp distributed over two circular chromosomes of
      2,117,144 bp and 1,177,787 bp encoding 3,197 ORFs. By using the bioinformatics suite ERGO,
      2,487 (78%) ORFs were assigned functions. The origins of replication of the two chromosomes
      are similar to those of other -proteobacteria. Housekeeping genes, including those involved in
      DNA replication, transcription, translation, core metabolism, and cell wall biosynthesis, are
      distributed on both chromosomes. Type I, II, and III secretion systems are absent, but genes
      encoding sec-dependent, sec-independent, and flagella-specific type III, type IV, and type V
      secretion systems as well as adhesins, invasins, and hemolysins were identified. Several
      features of the B. melitensis genome are similar to those of the symbiotic Sinorhizobium
      meliloti.
AU  - DelVecchio VG et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2002 99: 443-448.

PMID- 
VI  - 32
DP  - 1998
TI  - System controlling expression of antirestriction genes ardA and ardB of IncN transmission plasmid pKM101 (R46).
PG  - 208-213
AB  - A system regulating the expression of antirestriction genes ardA and ardB of transmission
      plasmid pKM101 (R46) was studied.  These phylogenetically distant genes are involved in
      protecting plasmid DNA from cell restriction enzymes and adapting to a new host after conjugal
      transfer.  The regulatory system involves two conserved upstream repeats, which flank the 5'
      end of ard and contain a potent promoter, and regulatory proteins ArdK and ArdR.  At least one
      of the proteins, ArdK, can bind with the promoter and act as a suppressor.  Both proteins
      control the expression of their own genes.  The regulatory system was assumed to trigger the
      coordinated expression of the ard genes and efficient synthesis of the Ard antirestriction
      proteins, which are essential to conjugal transfer of the plasmid and its adaptation to the
      new host.
AU  - Delver EP
AU  - Agofanova OV
AU  - Tupikova EE
AU  - Vorobeva EP
AU  - Belogurov AA
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1998 32: 208-213.

PMID- 1653225
VI  - 173
DP  - 1991
TI  - Nucleotide sequence of the Gene (ard) encoding the antirestriction protein of plasmid colIb-P9.
PG  - 5887-5892
AB  - The IncI1 plasmid ColIb-P9 was found to encode an antirestriction function.
      The relevant gene, and (alleviation of restriction of DNA), maps about 5 kb
      from the origin of transfer, in the region transferred early during bacterial
      conjugation.  Ard inhibits both restriction and modification by each of the
      four type I systems of Escherichia coli tested, but it had no effect on
      restriction by EcoRI, a type II system, or EcoP1, a type III system.  The
      nucleotide sequence of the ColIb ard gene was determined; the predicted
      molecular weight of the Ard polypeptide is 19,193.  The proposed polypeptide
      chain contains an excess of 25 negatively charged amino acids, suggesting that
      its overall character is very acidic.  Deletion analysis of the gene revealed
      that the Ard protein contained a distinct functional domain located in the
      COOH-terminal half of the polypeptide.  We suggest that the biological role of
      the ColIb Ard protein is associated with overcoming host-controlled restriction
      during bacterial conjugation.
AU  - Delver EP
AU  - Kotova VU
AU  - Zavilgelsky GB
AU  - Belogurov AA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1991 173: 5887-5892.

PMID- 20463886
VI  - 6
DP  - 2010
TI  - DNA adenine methylation is required to replicate both Vibrio cholerae chromosomes once per cell cycle.
PG  - e1000939
AB  - DNA adenine methylation is widely used to control many DNA transactions, including
      replication. In Escherichia coli, methylation serves to silence newly
      synthesized (hemimethylated) sister origins. SeqA, a protein that binds to
      hemimethylated DNA, mediates the silencing, and this is necessary to restrict
      replication to once per cell cycle. The methylation, however, is not essential
      for replication initiation per se but appeared so when the origins (oriI and
      oriII) of the two Vibrio cholerae chromosomes were used to drive plasmid
      replication in E. coli. Here we show that, as in the case of E. coli, methylation
      is not essential for oriI when it drives chromosomal replication and is needed
      for once-per-cell-cycle replication in a SeqA-dependent fashion. We found that
      oriII also needs SeqA for once-per-cell-cycle replication and, additionally, full
      methylation for efficient initiator binding. The requirement for initiator
      binding might suffice to make methylation an essential function in V. cholerae.
      The structure of oriII suggests that it originated from a plasmid, but unlike
      plasmids, oriII makes use of methylation for once-per-cell-cycle replication, the
      norm for chromosomal but not plasmid replication.
AU  - Demarre G
AU  - Chattoraj DK
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2010 6: e1000939.

PMID- 28935751
VI  - 5
DP  - 2017
TI  - Genome Sequence of Bacillus safensis Strain Ingolstadt Isolated from the Pectoralis Pouch of a Patient with Defibrillator-Related Surgery.
PG  - e01031-17
AB  - We report the draft genome sequence of clindamycin-resistant Bacillus safensis strain
      Ingolstadt isolated from a patient with bacterial colonization after heart
      surgery. The draft genome comprises 3.75 Mbp and harbors 3,793 predicted
      protein-encoding genes and a small plasmid.
AU  - Dematheis F
AU  - Antwerpen MH
AU  - Grass G
AU  - Walter MC
AU  - Borgmann S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01031-17.

PMID- 27738023
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Streptomyces sp. AVP053U2 Isolated from Styela clava, a  Tunicate Collected in Long Island Sound.
PG  - e00874-16
AB  - Streptomyces sp. AVP053U2 is a marine bacterium isolated from Styela clava, a tunicate
      collected in Long Island Sound. Here, we report a draft genome for this
      bacterium, which was found to contain a high capacity for secondary metabolite
      production based on analysis and identification of numerous biosynthetic gene
      clusters.
AU  - deMayo JA
AU  - Maas KR
AU  - Klassen JL
AU  - Balunas MJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00874-16.

PMID- 28814988
VI  - 12
DP  - 2017
TI  - The draft genome of the hyperthermophilic archaeon Pyrodictium delaneyi strain hulk, an iron and nitrate reducer, reveals the capacity for sulfate reduction.
PG  - 47
AB  - Pyrodictium delaneyi strain Hulk is a newly sequenced strain isolated from chimney samples
      collected from the Hulk sulfide mound on the main Endeavour
      Segment of the Juan de Fuca Ridge (47.9501 latitude, -129.0970 longitude, depth
      2200 m) in the Northeast Pacific Ocean. The draft genome of strain Hulk shared
      99.77% similarity with the complete genome of the type strain Su06T, which shares
      with strain Hulk the ability to reduce iron and nitrate for respiration. The
      annotation of the genome of strain Hulk identified genes for the reduction of
      several sulfur-containing electron acceptors, an unsuspected respiratory
      capability in this species that was experimentally confirmed for strain Hulk.
      This makes P. delaneyi strain Hulk the first hyperthermophilic archaeon known to
      gain energy for growth by reduction of iron, nitrate, and sulfur-containing
      electron acceptors. Here we present the most notable features of the genome of P.
      delaneyi strain Hulk and identify genes encoding proteins critical to its
      respiratory versatility at high temperatures. The description presented here
      corresponds to a draft genome sequence containing 2,042,801 bp in 9 contigs, 2019
      protein-coding genes, 53 RNA genes, and 1365 hypothetical genes.
AU  - Demey LM
AU  - Miller CR
AU  - Manzella MP
AU  - Spurbeck RR
AU  - Sandhu SK
AU  - Reguera G
AU  - Kashefi K
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 47.

PMID- 6097301
VI  - 49
DP  - 1984
TI  - Comparison of specific recognition sites of adenine and cytosine DNA-methyltransferase of Yersinia pestis EV 76C dam and dcm by Escherichia coli methylases.
PG  - 1594-1597
AB  - Using enzymatic modelling of in vitro methylation of chromosome DNAs from Yersinia pestis EV
      76, E. coli 834 and E. coli C600 RII by DNA methylases of EcoRII and EcoDam as well as of DNA
      hydrolysis of plasmid pBR 322 from the cells of Y. pestis EV 76, E. coli C600 and E. coli 834
      by restrictases of EcoRII and CfuI, it was found that cytosine DNA methylase from plaque
      bacteria does not correspond to the type of RII methylases of E. coli.  Adenine DNA methylase
      is related to E. coli methylases type dam and modified adenine in the nucleotide sequence of
      GATC.
AU  - Demidova GV
AU  - Goncharov EK
AU  - Tynianova VI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1984 49: 1594-1597.

PMID- 15817797
VI  - 151
DP  - 2005
TI  - Sau421, a Bcgl-like restriction-modification system encoded by the Staphylococcus aureus quadruple-converting phage phi 42.
PG  - 1301-1311
AB  - The serotype F phage 042 of Staphylococcus aureus is a triple-converting bacteriophage that
      encodes the staphylokinase gene
      (sak) and the enterotoxin A gene (entA). Lysogeny results in loss of
      expression of the chromosomal beta-haemolysin gene (hlb) (negative
      conversion), the expression of staphylokinase and enterotoxin A
      (positive conversion), and the acquisition of resistance to lysis by
      all 23 phages of the International Basic Set (IBS) of S. aureus typing
      phages. Until this study, the basis of 042 resistance to lysis by
      exogenous phages was unknown. The authors report here that phage 042
      encodes a restriction-modification (R-M) system, termed Sau42I,
      adjacent to and in the same orientation to the phage integrase gene
      int. The genes encoding Sau42I were cloned and sequenced, and found to
      consist of two overlapping reading frames, ORF S (specificity) and ORF
      RM (restriction-modification), in the same orientation. The ORFs share
      a high degree of DNA and amino acid sequence homology with the
      previously characterized BcgI R-M system of Bacillus coagulans.
      Expression of the cloned Sau421 ORF S and ORF RM in S. aureus 80CR3
      transformants from a plasmid vector conferred resistance to lysis by
      all 23 IBS phages. Similarly, transformants of S. aureus RN4220
      harbouring recombinant plasmids containing both ORFs were resistant to
      lysis by the IBS typing phages. However, transformants harbouring
      plasmids encoding either ORF S or ORF RM were susceptible to lysis by
      the IBS phages, and they had the same phage-susceptibility pattern as
      the respective parental isolates. In vitro analysis of crude and
      partially purified extracts of S. aureus transformants harbouring both
      the 042 ORF S and ORF RM genes indicated that Sau421 has endonuclease
      activity and requires co-factors Mg2+ and S-adenosylmethionine in order
      to function, and activity is optimized at pH 8, although the precise
      recognition sequence has yet to be determined. The findings of this
      study confirm that phi 42 is a quadruple-converting phage, believed to
      be the first described for S. aureus, and show that it encodes a novel
      R-M system termed Sau421.
AU  - Dempsey RM
AU  - Carroll D
AU  - Kong HM
AU  - Higgins L
AU  - Keane CT
AU  - Coleman DC
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2005 151: 1301-1311.

PMID- 21859443
VI  - 12
DP  - 2011
TI  - Genome sequencing reveals diversification of virulence factor content and possible host adaptation in distinct subpopulations of Salmonella enterica.
PG  - 425
AB  - BACKGROUND: Divergence of bacterial populations into distinct subpopulations is
      often the result of ecological isolation. While some studies have suggested the
      existence of Salmonella enterica subsp. enterica subclades, evidence for these
      subdivisions has been ambiguous. Here we used a comparative genomics approach to
      define the population structure of Salmonella enterica subsp. enterica, and
      identify clade-specific genes that may be the result of ecological
      specialization. RESULTS: Multi-locus sequence analysis (MLSA) and single
      nucleotide polymorphisms (SNPs) data for 16 newly sequenced and 30 publicly
      available genomes showed an unambiguous subdivision of S. enterica subsp.
      enterica into at least two subpopulations, which we refer to as clade A and clade
      B. Clade B strains contain several clade-specific genes or operons, including a
      beta-glucuronidase operon, a S-fimbrial operon, and cell surface related genes,
      which strongly suggests niche specialization of this subpopulation. An additional
      set of 123 isolates was assigned to clades A and B by using qPCR assays targeting
      subpopulation-specific SNPs and genes of interest. Among 98 serovars examined,
      approximately 20% belonged to clade B. All clade B isolates contained two
      pathogenicity related genomic islands, SPI-18 and a cytolethal distending toxin
      islet; a combination of these two islands was previously thought to be exclusive
      to serovars Typhi and Paratyphi A. Presence of beta-glucuronidase in clade B
      isolates specifically suggests an adaptation of this clade to the vertebrate
      gastrointestinal environment. CONCLUSIONS: S. enterica subsp. enterica consists
      of at least two subpopulations that differ specifically in genes involved in host
      and tissue tropism, utilization of host specific carbon and nitrogen sources and
      are therefore likely to differ in ecology and transmission characteristics.
AU  - den Bakker HC
AU  - Moreno-Switt AI
AU  - Govoni G
AU  - Cummings CA
AU  - Ranieri ML
AU  - Degoricija L
AU  - Hoelzer K
AU  - Rodriguez-Rivera LD
AU  - Brown S
AU  - Bolchacova E
AU  - Furtado MR
AU  - Wiedmann M
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2011 12: 425.

PMID- 24837381
VI  - 80
DP  - 2014
TI  - Comparative genomic and morphological analysis of Listeria phages isolated from farm environments.
PG  - 4616-4625
AB  - The genus Listeria is ubiquitous in the environment and includes the globally
      important foodborne pathogen Listeria monocytogenes. While the genomic diversity
      of Listeria has been well studied, considerably less is known about the genomic
      and morphological diversity of Listeria bacteriophages. In this study, we
      sequenced and analyzed the genomes of 14 Listeria phages mostly isolated from New
      York dairy farm environments, as well as one related Enterococcus faecalis phage,
      to obtain information on genome characteristics and diversity. We also examined
      12 of the phages by electron microscopy to characterize their morphology. These
      Listeria phages, based on gene orthology and morphology, together with previously
      sequenced Listeria phages could be classified into five orthoclusters, including
      one novel orthocluster. One orthocluster (I) consists of large genome (
      approximately 135 kb) myoviruses belonging to the genus "Twort-like viruses",
      three orthoclusters (II-IV) contain small genome (36-43 kb) siphoviruses with
      icosahedral heads, and the novel orthocluster V contains medium-sized genome (
      approximately 66 kb) siphoviruses with elongated heads. A novel orthocluster (VI)
      of E. faecalis phages, with medium-sized genomes ( approximately 56 kb), was
      identified which grouped together and shares morphological features with the
      novel Listeria phage orthocluster V. This new group of phages (i.e.,
      orthoclusters V and VI) is composed of putative lytic phages that may prove to be
      useful in phage-based applications for biocontrol, detection, and therapeutic
      purposes.
AU  - Denes T
AU  - Vongkamjan K
AU  - Ackermann HW
AU  - Moreno-Switt AI
AU  - Wiedmann M
AU  - den Bakker HC
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2014 80: 4616-4625.

PMID- 24471506
VI  - 86
DP  - 2014
TI  - Highly Sensitive Electrochemical Methyltransferase Activity Assay.
PG  - 2117-2123
AB  - A simple and highly sensitive electrochemical DNA methyltransferase (MTase) activity assay is
      presented in this report. The assay employs the electrocatalytic oxidation of ascorbic acid
      (AA) by a threading intercalator (N,N'-bis(3propylimidazole)-1,4,5,8-naphthalene diimide
      (PIND) functionalized with electrocatalytic redox Os(bpy)(2)Cl+ moieties (PIND-Os)). Briefly,
      a double-stranded DNA (ds-DNA) containing the symmetric sequence of 5'-CCGG-3' is first
      immobilized on a gold electrode. The electrode is then incubated with M.SssI CpG
      methyltransferase (M.SssI MTase) which catalyzes the methylation of the specific CpG
      dinucleotides, and the electrode is subsequently treated with a restriction endonuclease HpaII
      which recognizes the 5'-CCGG-3' sequence. Once the CpG site in the 5'-CCGG-3' is
      methylated, HpaII recognition is blocked. Higher M.SssI MTase activity leads to more CpG sites
      being methylated and consequently impedes more the restriction endonuclease HpaII digestion
      process. Thus, a larger amount of ds-DNA remains on the electrode surface after the HpaII.
      treatment. Thereafter, the electrode is incubated with PIND-Os during which PIND-Os
      specifically inserts itself between base pairs of ds-DNA and catalyzes the electrooxidation of
      AA. The methylation event corresponding to the MTase activity can therefore be monitored and
      amplified by the electrocatalytic oxidation of AA. A linear correlation between the catalytic
      oxidation current of AA and the activity of M.SssI MTase ranged from 0 to 120 U/mL with a
      current sensitivity of 0.046 mu A mL U-1 is obtained. The inhibitor screening ability of the
      developed MTase activity assay is also demonstrated.
AU  - Deng H
AU  - Yang X
AU  - Yeo SP
AU  - Gao Z
PT  - Journal Article
TA  - Anal. Chem.
JT  - Anal. Chem.
SO  - Anal. Chem. 2014 86: 2117-2123.

PMID- 9722504
VI  - 273
DP  - 1998
TI  - Multiple isoforms of DNA methyltransferase are encoded by the vertebrate cytosine DNA methyltransferase gene.
PG  - 22869-22872
AB  - This manuscript tests the hypothesis that multiple forms of cytosine-DNA methyltransferase are
      expressed in vertebrates in vivo.  Vertebrate genomes are distinguished by tissue- and
      gene-specific DNA methylation patterns.  Specific methylation patterns are believed to encode
      epigenetic information.  In distinction from the remarkable diversity of DNA methylation
      patterns, only one functional DNA MeTase cDNA has been identified to date in different
      vertebrate organisms.  Using reverse transcription-polymerase chain reaction and RNase
      protection analyses, we show that the methyltransferase domain of the rat DNA MeTase is
      alternatively spliced in vivo, generating different in-frame variants of DNA MeTase in
      specific tissues.  This process is developmentally regulated and is induced in PC12 cells by a
      known inducer of neuronal differentiation, nerve growth factor.  The data presented here point
      toward a new mechanism for generating diversity of DNA MeTases and possibly diverse DNA
      methylation patterns.
AU  - Deng J
AU  - Szyf M
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1998 273: 22869-22872.

PMID- 26634018
VI  - 10
DP  - 2015
TI  - Complete genome of Pseudomonas chlororaphis strain UFB2, a soil bacterium with antibacterial activity against bacterial canker pathogen of tomato.
PG  - 117
AB  - Strain UFB2 was isolated from a soybean field soil in Mississippi and identified  as a member
      of Pseudomonas chlororaphis. Strain UFB2 has a broad-spectrum
      antimicrobial activity against common soil-borne pathogens. Plate assays showed
      that strain UFB2 was especially efficient in inhibiting the growth of Clavibacter
      michiganensis 1-07, the causal agent of the devastating bacterial canker of
      tomato. Here, the complete genome sequence of P. chlororaphis strain UFB2 is
      reported and described. The strain UFB2 genome consists of a circular chromosome
      of 6,360,256 bp of which 87.86 % are protein-coding bases. Genome analysis
      revealed multiple gene islands encoding various secondary metabolites such as
      2,4-diacetylphloroglucinol. Further genome analysis will provide more details
      about strain UFB2 antibacterial activities mechanisms and the use of this strain
      as a potential biocontrol agent.
AU  - Deng P
AU  - Wang X
AU  - Baird SM
AU  - Lu SE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 117.

PMID- 12142430
VI  - 184
DP  - 2002
TI  - Genome sequence of Yersinia pestis KIM.
PG  - 4601-4611
AB  - We present the complete genome sequence of Yersinia pestis KIM, the etiologic agent of bubonic
      and pneumonic plague. The strain KIM, biovar Mediaevalis, is associated with the second
      pandemic, including the Black Death. The 4.6-Mb genome encodes 4,198 open reading frames
      (ORFs). The origin, terminus, and most genes encoding DNA replication proteins are similar to
      those of Escherichia coli K-12. The KIM genome sequence was compared with that of Y. pestis
      CO92, biovar Orientalis, revealing homologous sequences but a remarkable amount of genome
      rearrangement for strains so closely related. The differences appear to result from multiple
      inversions of genome segments at insertion sequences, in a manner consistent with present
      knowledge of replication and recombination. There are few differences attributable to
      horizontal transfer. The KIM and E. coli K-12 genome proteins were also compared, exposing
      surprising amounts of locally colinear "backbone," or synteny, that is not discernible at the
      nucleotide level. Nearly 54% of KIM ORFs are significantly similar to K-12 proteins, with
      conserved housekeeping functions. However, a number of E. coli pathways and transport systems
      and at least one global regulator were not found, reflecting differences in lifestyle between
      them. In KIM-specific islands, new genes encode candidate pathogenicity proteins, including
      iron transport systems, putative adhesins, toxins, and fimbriae.
AU  - Deng W et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2002 184: 4601-4611.

PMID- 12644504
VI  - 185
DP  - 2003
TI  - Comparative Genomics of Salmonella enterica Serovar Typhi Strains Ty2 and CT18.
PG  - 2330-2337
AB  - We present the 4.8-Mb complete genome sequence of Salmonella enterica serovar Typhi strain
      Ty2, a human-specific pathogen causing typhoid fever.
      A comparison with the genome sequence of recently isolated S. enterica
      serovar Typhi strain CT18 showed that 29 of the 4,646 predicted genes in
      Ty2 are unique to this strain, while 84 genes are unique to CT18. Both
      genomes contain more than 200 pseudogenes; 9 of these genes in CT18 are
      intact in Ty2, while 11 intact CT18 genes are pseudogenes in Ty2. A
      half-genome interreplichore inversion in Ty2 relative to CT18 was
      confirmed. The two strains exhibit differences in prophages, insertion
      sequences, and island structures. While CT18 carries two plasmids, one
      conferring multiple drug resistance, Ty2 has no plasmids and is sensitive
      to antibiotics.
AU  - Deng W
AU  - Liou SR
AU  - Plunkett IIIG
AU  - Mayhew GF
AU  - Rose DJ
AU  - Burland V
AU  - Kodoyianni V
AU  - Schwartz DC
AU  - Blattner FR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2003 185: 2330-2337.

PMID- 29464208
VI  - 4
DP  - 2018
TI  - Multi-heme cytochromes provide a pathway for survival in energy-limited environments.
PG  - eaao5682
AB  - Bacterial reduction of oxidized sulfur species (OSS) is critical for energy
      production in anaerobic marine subsurfaces. In organic-poor sediments, H2 has
      been considered as a major energy source for bacterial respiration. We identified
      outer-membrane cytochromes (OMCs) that are broadly conserved in sediment
      OSS-respiring bacteria and enable cells to directly use electrons from insoluble
      minerals via extracellular electron transport. Biochemical, transcriptomic, and
      microscopic analyses revealed that the identified OMCs were highly expressed on
      the surface of cells and nanofilaments in response to electron donor limitation.
      This electron uptake mechanism provides sufficient but minimum energy to drive
      the reduction of sulfate and other OSS. These results suggest a widespread
      mechanism for survival of OSS-respiring bacteria via electron uptake from solid
      minerals in energy-poor marine sediments.
AU  - Deng X
AU  - Dohmae N
AU  - Nealson KH
AU  - Hashimoto K
AU  - Okamoto A
PT  - Journal Article
TA  - Sci. Adv.
JT  - Sci. Adv.
SO  - Sci. Adv. 2018 4: eaao5682.

PMID- 23704182
VI  - 1
DP  - 2013
TI  - Genome Sequence of Salmonella enterica Serotype Tennessee Strain CDC07-0191, Implicated in the 2006-2007 Multistate Food-Borne Outbreak Linked to Peanut  Butter in the United States.
PG  - e00260-13
AB  - Salmonella enterica serotype Tennessee strain CDC07-0191 was isolated from the 2006-2007
      multistate food-borne outbreak linked to peanut butter in the United
      States. Here we report a high-quality draft assembly of the genome sequence of
      this strain, derived from a patient. This is the first reported high-quality
      draft genome sequence for S. enterica serotype Tennessee, which will enable
      in-depth studies of its transmission and virulence.
AU  - Deng X
AU  - Salazar JK
AU  - Frezet S
AU  - Maccannell D
AU  - Ribot EM
AU  - Fields PI
AU  - Fricke WF
AU  - Zhang W
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00260-13.

PMID- 27587824
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Vibrio alginolyticus ZJ-T.
PG  - e00912-16
AB  - Vibrio alginolyticus is a ubiquitous Gram-negative bacterium which is normally distributed in
      the coastal and estuarine environments. It has been suggested to
      be an opportunistic pathogen to both marine animals and humans, Here, the
      completed genome sequence of V. alginolyticus ZJ-T was determined by Illumina
      high-throughput sequencing.
AU  - Deng Y
AU  - Chen C
AU  - Zhao Z
AU  - Huang X
AU  - Yang Y
AU  - Ding X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00912-16.

PMID- 21317323
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Bacillus subtilis BSn5, an Endophytic Bacterium of Amorphophallus konjac with Antimicrobial Activity for the  Plant Pathogen Erwinia carotovora subsp. carotovora.
PG  - 2070-2071
AB  - Here, we present the complete genome sequence of Bacillus subtilis strain BSn5, isolated from
      Amorphophallus konjac calli tissue and showing strong
      inhibitory activity to Erwinia carotovora subsp. carotovora, which causes
      Amorphophallus soft rot disease and affects the industry development of
      this organism.
AU  - Deng Y
AU  - Zhu Y
AU  - Wang P
AU  - Zhu L
AU  - Zheng J
AU  - Li R
AU  - Ruan L
AU  - Peng D
AU  - Sun M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 2070-2071.

PMID- 11092734
VI  - 11
DP  - 2000
TI  - LldI, a plasmid-encoded type I restriction and modification system in Lactococcus lactis.
PG  - 239-245
AB  - A plasmid-encoded type I restriction and modification (R-M) system, designated LldI, was
      identified in Lactococcus lactis biovar diacetylactis LD10-1. LldI consists of three genes
      encoding endonuclease, methylase and specificity subunits, respectively. RT-PCR analysis
      revealed that the three genes are co-transcribed as a polycistronic mRNA in L. lactis. The
      specificity subunit of LldI differs significantly in the target recognition domains from those
      of other type I R-M systems, suggesting that LldI confers a novel specificity in L. lactis.
AU  - Deng YM
AU  - Liu CQ
AU  - Dunn NW
PT  - Journal Article
TA  - DNA Seq.
JT  - DNA Seq.
SO  - DNA Seq. 2000 11: 239-245.

PMID- 1579503
VI  - 20
DP  - 1992
TI  - Eco27kI, a new isoschizomer of AvaI from Escherichia coli.
PG  - 1992
AB  - A small collection (108) of Escherichia coli strains isolated in Kiev was surveyed for type II
      restriction endonucleases. 95 strains produced these enzymes; among them Eco27kI, a new
      isoschizomer of AvaI, recognized the palindromic sequence 5'-C/PyCGPuG-3'.
AU  - Denjmuchametov MM
AU  - Ruban NM
AU  - Zakharova MV
AU  - Beletzkaja IV
AU  - Kravetz AN
AU  - Solonin AS
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 1992.

PMID- 9744801
VI  - 433
DP  - 1998
TI  - The Ecl18kI restriction-modification system: cloning, expression, properties of the purified enzymes.
PG  - 233-236
AB  - Ecl18kI is a type II restriction-modification system isolated from Enterobacter cloaceae 18kI
      strain.  Genes encoding Ecl18kI methyltransferase (M.Ecl18kI) and Ecl18kI restriction
      endonuclease (R.Ecl18kI) have been cloned and expressed in Escherichia coli.  These enzymes
      recognize the 5'.../CCNGG...3' sequence in DNA; M.Ecl18kI methylates the C5 carbon atom of
      the inner dC residue and R.Ecl18kI cuts DNA as shown by the arrow.  The restriction
      endonuclease and the methyltransferase were purified from E. coli B834 [p18Ap1] cells to near
      homogeneity.  The restriction endonuclease is present in the solution as a tetramer, while the
      methyltransferase is a monomer.  The interactions of M.Ecl18kI and R.Ecl18kI with
      1,2-dideoxy-D-ribofuranose containing DNA duplexes were investigated.  The target base
      flipping-out mechanism is applicable in the case of M.Ecl18kI.  Correct cleavage of the abasic
      substrates by R.Ecl18kI is accompanied by non-canonical hydrolysis of the modified strand.
AU  - Denjmukhametov MM
AU  - Brevnov MG
AU  - Zakharova MV
AU  - Repyk AV
AU  - Solonin AS
AU  - Petrauskene OV
AU  - Gromova ES
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1998 433: 233-236.

PMID- 9454069
VI  - 31
DP  - 1997
TI  - Characterization of plasmids encoding type II restriction-modification systems, isoschizomers of SsoII.
PG  - 831-838
AB  - Five strains of Enterobacteriaceae family have been revealed that have
      restriction-modification systems of type II, isoschizomers of SsoII.  The genes coding for the
      restriction endonucleases and DNA methyltransferases are located on plasmids of two types. The
      plasmids differ in size, capacity for mobilization by conjugative plasmids, and structure of
      locus cer.  Recombinant two-plasmid strains were obtained containing plasmids with genes for
      Ecl18kI and EcoRII restriction endonucleases in the presence of DNA methyltransferase Ecl18kI.
      The stability of the two-plasmid system with the ecoRIIR and ecl18kIM genes implies similar
      mechanisms of concerted regulation of gene expression in the restriction-modification systems
      Ecl18kI and EcoRI.  Genes for Ecl18kI and SsoII restriction-modification systems have
      essentially the same sequence.
AU  - Denjmukhametov MM
AU  - Zakharova MV
AU  - Kravets AN
AU  - Pertsev AV
AU  - Sineva EV
AU  - Repik AV
AU  - Beletskaya IV
AU  - Gromova ES
AU  - Solonin AS
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1997 31: 831-838.

PMID- 27549662
VI  - 15
DP  - 2016
TI  - Functional genomic analyses of Enterobacter, Anopheles and Plasmodium reciprocal interactions that impact vector competence.
PG  - 425
AB  - BACKGROUND: Malaria exerts a tremendous socioeconomic impact worldwide despite
      current control efforts, and novel disease transmission-blocking strategies are
      urgently needed. The Enterobacter bacterium Esp_Z, which is naturally harboured
      in the mosquito midgut, can inhibit the development of Plasmodium parasites prior
      to their invasion of the midgut epithelium through a mechanism that involves
      oxidative stress. Here, a multifaceted approach is used to study the tripartite
      interactions between the mosquito, Esp_Z and Plasmodium, towards addressing the
      feasibility of using sugar-baited exposure of mosquitoes to the Esp_Z bacterium
      for interruption of malaria transmission. METHODS: The ability of Esp_Z to
      colonize Anopheles gambiae midguts harbouring microbiota derived from wild
      mosquitoes was determined by qPCR. Upon introduction of Esp_Z via nectar feeding,
      the permissiveness of colonized mosquitoes to Plasmodium falciparum infection was
      determined, as well as the impact of Esp_Z on mosquito fitness parameters, such
      as longevity, number of eggs laid and number of larvae hatched. The genome of
      Esp_Z was sequenced, and transcriptome analyses were performed to identify
      bacterial genes that are important for colonization of the mosquito midgut, as
      well as for ROS-production. A gene expression analysis of members of the
      oxidative defence pathway of Plasmodium berghei was also conducted to assess the
      parasite's oxidative defence response to Esp_Z exposure. RESULTS: Esp_Z persisted
      for up to 4 days in the An. gambiae midgut after introduction via nectar feeding,
      and was able to significantly inhibit Plasmodium sporogonic development.
      Introduction of this bacterium did not adversely affect mosquito fitness.
      Candidate genes involved in the selection of a better fit Esp_Z to the mosquito
      midgut environment and in its ability to condition oxidative status of its
      surroundings were identified, and parasite expression data indicated that Esp_Z
      is able to induce a partial and temporary shutdown of the ookinetes antioxidant
      response. CONCLUSIONS: Esp_Z is capable of inhibiting sporogonic development of
      Plasmodium in the presence of the mosquito's native microbiota without affecting
      mosquito fitness. Several candidate bacterial genes are likely mediating midgut
      colonization and ROS production, and inhibition of Plasmodium development appears
      to involve a shutdown of the parasite's oxidative defence system. A better
      understanding of the complex reciprocal tripartite interactions can facilitate
      the development and optimization of an Esp_Z-based malaria control strategy.
AU  - Dennison NJ
AU  - Saraiva RG
AU  - Cirimotich CM
AU  - Mlambo G
AU  - Mongodin EF
AU  - Dimopoulos G
PT  - Journal Article
TA  - Malar. J.
JT  - Malar. J.
SO  - Malar. J. 2016 15: 425.

PMID- 30533932
VI  - 7
DP  - 2018
TI  - Draft Genome Sequences of Escherichia coli Strains FP2 and FP3, Isolated from the Canada Goose (Branta canadensis).
PG  - e01079-18
AB  - Draft genomes of two strains of Escherichia coli, FP2 and FP3, isolated from the  feces of the
      Canada goose (Branta canadensis), were sequenced. Genome sizes were
      5.26 Mb with a predicted G+C content of 50.54% (FP2) and 5.07 Mb with a predicted
      G+C content of 50.41% (FP3).
AU  - Denny AL
AU  - Arruda SE
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e01079-18.

PMID- 19339031
VI  - 388
DP  - 2009
TI  - T4 phages against Escherichia coli diarrhea: potential and problems.
PG  - 21-30
AB  - A combination of in vitro and in vivo experiments with comparative phage
      genomics was used for the rational design of a phage cocktail against E.
      coli diarrhea. Orally applied T4 coliphages representing three different
      subgroups (T4-, RB49- and JS98-like phages) had no negative impact on the
      murine gut microbiota. T4 phages were found with high titers in the cecum
      and colon and lower titers in the small intestine, but were not detected
      in the blood, liver or spleen. No adverse effects were observed after
      one-month exposure to phage nor were serum anti-T4 antibodies detected. T4
      phages belonging to the same subgroup showed closely related genomes that
      differed by 12 (phage JS10 vs. JS98 reference) to 17 (phage JSE vs. RB49
      reference) insertion/deletions mostly representing single small ORFs.
      Bioinformatic analysis did not reveal undesired genes in the T4 genomes.
      Sequence variability was seen over the tail fibre genes, but the
      variability did not correlate with phage host range. The investigated T4
      phages were not only species- but also strain-specific, necessitating the
      use of phage cocktails consisting of 10 and 16 T4 phage isolates to cover
      half to two thirds of E. coli strains representing the five main
      pathotypes isolated from diarrhea patients.
AU  - Denou E
AU  - Bruttin A
AU  - Barretto C
AU  - Ngom-Bru C
AU  - Brussow H
AU  - Zuber S
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 2009 388: 21-30.

PMID- 9484440
VI  - 36
DP  - 1998
TI  - Complete sequence of the mitochondrial DNA of Chlamydomonas eugametos.
PG  - 285-295
AB  - The complete  nucleotide sequence of the Chlamydomonas eugametos mitochondrial genome has been
      determined (22,897 bp, 34.6% G+C).  The genes identified in this circular-mapping genome
      include those for apocytochrome b, subunit 1 of the cytochrome oxidase complex.  Subunits
      1,2,4,5, and 6 of the N dehydrogenase complex, discontinuous large and small subunit ribosomal
      rRNAs and three tRNAs whose anticodons CAU, CCA and UUG are specific for methionine,
      tryptophan and glutamine, respectively.  The C. eugametos mitochondrial DNA, therefore, shares
      almost the same reduced set of coding functions and similar unusual features of rRNA gene
      organization with the linear 15.8 kb mtDNA of Chlamydomonas reinhardtii, the only other
      completely sequenced chlamydomonadalean mtDNA.  However, sequence analysis of the C. eugametos
      mtDNA has revealed the following distinguishing features relative to those of C. reinhardtii:
      (1) the absence of a reverse transcriptase-like gene homologue, (2) the presence of an
      addition gene for tRNAmet that may be a pseudogene, (3) a completely different gene order, (4)
      transcription of all genes from the same mtDNA strand, (5) a lower G+ C content, (6) less
      pronounced bias in codon usage, and (7) nine group I introns, several of which contain open
      reading frames coding for potential maturases/endonucleases and two have a nucleotide at the
      5' or 3' splice site of the deduced precursor RNAs that deviates from highly conserved
      nucleotides reported in other group I introns.  The features of mitochondrial genome
      organization and gene content shared by C. eugametos and C. reinhardtii contrast with their
      green algal mtDNAs that have been characterized in detail.  The deep evolutionary divergence
      between these two Chlamydomonas taxa within the Chlamydomonadales suggests that their shared
      features of mitochondrial genome organization evolved prior to the origin of this group.
AU  - Denovan-Wright EM
AU  - Nedelcu AM
AU  - Lee RW
PT  - Journal Article
TA  - Plant Mol. Biol.
JT  - Plant Mol. Biol.
SO  - Plant Mol. Biol. 1998 36: 285-295.

PMID- 23144415
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Burkholderia phenoliruptrix BR3459a (CLA1), a Heat-Tolerant, Nitrogen-Fixing Symbiont of Mimosa flocculosa.
PG  - 6675-6676
AB  - The genus Burkholderia represents a challenge to the fields of taxonomy and phylogeny and,
      especially, to the understanding of the contrasting roles as
      either opportunistic pathogens or bacteria with biotechnological potential. Few
      genomes of nonpathogenic strains, especially of diazotrophic symbiotic bacteria,
      have been sequenced to improve understanding of the genus. Here, we contribute
      with the complete genome sequence of Burkholderia phenoliruptrix strain BR3459a
      (CLA1), an effective diazotrophic symbiont of the leguminous tree Mimosa
      flocculosa Burkart, which is endemic to South America.
AU  - deOliveira-Cunha C
AU  - Goda-Zuleta LF
AU  - Paula-deAlmeida LG
AU  - Prioli-Ciapina L
AU  - Lustrino-Borges W
AU  - Pitard RM
AU  - Baldani JI
AU  - Straliotto R
AU  - deFaria SM
AU  - Hungria M
AU  - Sousa-Cavada B
AU  - Mercante FM
AU  - Ribeiro-deVasconcelos AT
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6675-6676.

PMID- 3949011
VI  - 197
DP  - 1986
TI  - Selective phosphorylation of human DNA methyltransferase by protein kinase C.
PG  - 149-153
AB  - Human DNA methyltransferase, the enzyme thought to be responsible for the somatic inheritance
      of patterns of DNA methylation, is an effective substrate for phosphorylation by protein
      kinase C. This provides a plausible mechanistic link between the action of tumor promoting
      phorbol esters, which stimulate protein kinase C, and abnormal patterns of DNA methylation
      often observed in transformed cells.
AU  - DePaoli-Roach A
AU  - Roach PJ
AU  - Zucker KE
AU  - Smith SS
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1986 197: 149-153.

PMID- 12202768
VI  - 30
DP  - 2002
TI  - Dnmt3L is a transcriptional repressor that recruits histone deacetylase.
PG  - 3831-3838
AB  - The Dnmt3L protein belongs to the Dnmt3 family of DNA methyltransferases by virtue of its
      sequence homology in the plant homeodomain (PHD)-like motif. Dnmt3L is essential for the
      establishment of maternal genomic imprints and, given its lack of key methyltransferase
      motifs, is more likely to act as a regulator of methylation rather than as an enzyme that
      methylates DNA. Here, we show that Dnmt3L, like Dnmt3a and Dnmt3b, interacts both in vitro and
      in vivo with the histone deacetylase HDAC1. Consistent with the binding to a deacetylase,
      Dnmt3L purifies histone deacetylase activity from nuclear extracts. We find that Dnmt3L can
      repress transcription and that this repression is dependent on HDAC1 and is relieved by
      treatment with the HDAC inhibitor trichostatin A. Binding of Dnmt3L to HDAC1 as well as its
      repressive function require the PHD-like motif. Our results indicate that Dnmt3L plays a role
      in transcriptional regulation and that recruitment of the HDAC repressive machinery is a
      shared and conserved feature of the Dnmt3 family. The fact that, despite the absence of a
      methyltransferase domain, Dnmt3L retains the capacity to contact deacetylase further
      substantiates the notion that the Dnmts can repress transcription independently of their
      methylating activities.
AU  - Deplus R
AU  - Brenner C
AU  - Burgers WA
AU  - Putmans P
AU  - Kouzarides T
AU  - de Launoit Y
AU  - Fuks F
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2002 30: 3831-3838.

PMID- 12125824
VI  - 4
DP  - 2002
TI  - The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea.
PG  - 453-461
AB  - The Archaeon Methanosarcina mazei and related species are of great ecological importance as
      they are the only organisms fermenting acetate, methylamines and methanol to methane, carbon
      dioxide and ammonia (in case of methylamines). Since acetate is the precursor of 60% of the
      methane produced on earth these organisms contribute significantly to the production of this
      greenhouse gas, e.g. in rice paddies. The 4,096,345 base pairs circular chromosome of M. mazei
      is more than twice as large as the genomes of the methanogenic Archaea currently completely
      sequenced (Bult et al., 1996; Smith et al., 1997). 3,371 open reading frames (ORFs) were
      identified. Based on currently available sequence data 376 of these ORFs are
      Methanosarcina-specific and 1,043 ORFs find their closest homologue in the bacterial domain.
      544 of these ORFs reach significant similarity values only in the bacterial domain. They
      include 56 of the 102 transposases, and proteins involved in gluconeogenesis, proline
      biosynthesis, transport processes, DNA-repair, environmental sensing, gene regulation, and
      stress response. Striking examples are the occurrence of the bacterial GroEL/GroES chaperone
      system and the presence of tetrahydrofolate-dependent enzymes. These findings might indicate
      that lateral gene transfer has played an important evolutionary role in forging the physiology
      of this metabolically versatile methanogen.
AU  - Deppenmeier U et al
PT  - Journal Article
TA  - J. Mol. Microbiol. Biotechnol.
JT  - J. Mol. Microbiol. Biotechnol.
SO  - J. Mol. Microbiol. Biotechnol. 2002 4: 453-461.

PMID- 29037147
VI  - 18
DP  - 2017
TI  - De novo assembly of genomes from long sequence reads reveals uncharted territories of Propionibacterium freudenreichii.
PG  - 790
AB  - BACKGROUND: Propionibacterium freudenreichii is an industrially important bacterium granted
      the Generally Recognized as Safe (the GRAS) status, due to its
      long safe use in food bioprocesses. Despite the recognized role in the food
      industry and in the production of vitamin B12, as well as its documented
      health-promoting potential, P. freudenreichii remained poorly characterised at
      the genomic level. At present, only three complete genome sequences are available
      for the species. RESULTS: We used the PacBio RS II sequencing platform to
      generate complete genomes of 20 P. freudenreichii strains and compared them in
      detail. Comparative analyses revealed both sequence conservation and genome
      organisational diversity among the strains. Assembly from long reads resulted in
      the discovery of additional circular elements: two putative conjugative plasmids
      and three active, lysogenic bacteriophages. It also permitted characterisation of
      the CRISPR-Cas systems. The use of the PacBio sequencing platform allowed
      identification of DNA modifications, which in turn allowed characterisation of
      the restriction-modification systems together with their recognition motifs. The
      observed genomic differences suggested strain variation in surface piliation and
      specific mucus binding, which were validated by experimental studies. The
      phenotypic characterisation displayed large diversity between the strains in
      ability to utilise a range of carbohydrates, to grow at unfavourable conditions
      and to form a biofilm. CONCLUSION: The complete genome sequencing allowed
      detailed characterisation of the industrially important species, P.
      freudenreichii by facilitating the discovery of previously unknown features. The
      results presented here lay a solid foundation for future genetic and functional
      genomic investigations of this actinobacterial species.
AU  - Deptula P
AU  - Laine PK
AU  - Roberts RJ
AU  - Smolander OP
AU  - Vihinen H
AU  - Piironen V
AU  - Paulin L
AU  - Jokitalo E
AU  - Savijoki K
AU  - Auvinen P
AU  - Varmanen P
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2017 18: 790.

PMID- 24673340
VI  - 356
DP  - 2014
TI  - Genomic analysis of Pseudomonas aeruginosa PA96, the host of carbapenem resistance plasmid pOZ176.
PG  - 212-216
AB  - Pseudomonas aeruginosa PA96 is a clinical isolate from Guangzhou, China, that is
      multiresistant to antibiotics. We previously described the 500-kb IncP-2 plasmid, pOZ176 that
      encodes many resistance genes including the IMP-9 carbapenemase. Whole-genome sequencing of
      PA96 enabled characterization of its genomic islands, virulence factors, and chromosomal
      resistance genes. We filled gaps using PCR and used optical mapping to confirm the correct
      contig order. We automatically annotated the core genome and manually annotated the genomic
      islands. The genome is 6 444 091 bp and encodes 5853 ORFs. From the whole-genome sequence, we
      constructed a physical map and constructed a phylogenetic tree for comparison with sequenced
      P. aeruginosa strains. Analysis of known core genome virulence factors and resistance genes
      revealed few differences with other strains, but the major virulence island is closer to that
      of DK2 than to PA14. PA96 most closely resembles the environmental strain M18, and notably
      shares a common serotype, pyoverdin type, flagellar operon, type IV pilin, and several genomic
      islands with M18.
AU  - Deraspe M
AU  - Alexander DC
AU  - Xiong J
AU  - Ma JH
AU  - Low DE
AU  - Jamieson FB
AU  - Roy PH
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2014 356: 212-216.

PMID- 20605981
VI  - 78
DP  - 2010
TI  - Delineation and Analysis of Chromosomal Regions Specifying Yersinia pestis.
PG  - 3930-3941
AB  - Yersinia pestis, the causative agent of plague, has recently diverged from the less virulent
      enteropathogen Yersinia pseudotuberculosis. Its
      emergence has been characterized by massive genetic loss and
      inactivation and limited gene acquisition. The acquired genes include
      two plasmids, a filamentous phage, and a few chromosomal loci. The aim
      of this study was to characterize the chromosomal regions acquired by
      Y. pestis. Following in silico comparative analysis and PCR screening
      of 98 strains of Y. pseudotuberculosis and Y. pestis, we found that
      eight chromosomal loci (six regions [R1(pe) to R6(pe)] and two coding
      sequences [CDS1(pe) and CDS2(pe)]) specified Y. pestis. Signatures of
      integration by site specific or homologous recombination were
      identified for most of them. These acquisitions and the loss of
      ancestral DNA sequences were concentrated in a chromosomal region
      opposite to the origin of replication. The specific regions were
      acquired very early during Y. pestis evolution and were retained during
      its microevolution, suggesting that they might bring some selective
      advantages. Only one region (R3(pe)), predicted to carry a lambdoid
      prophage, is most likely no longer functional because of mutations.
      With the exception of R1(pe) and R2(pe), which have the potential to
      encode a restriction/modification and a sugar transport system,
      respectively, no functions could be predicted for the other Y.
      pestis-specific loci. To determine the role of the eight chromosomal
      loci in the physiology and pathogenicity of the plague bacillus, each
      of them was individually deleted from the bacterial chromosome. None of
      the deletants exhibited defects during growth in vitro. Using the
      Xenopsylla cheopis flea model, all deletants retained the capacity to
      produce a stable and persistent infection and to block fleas.
      Similarly, none of the deletants caused any acute flea toxicity. In the
      mouse model of infection, all deletants were fully virulent upon
      subcutaneous or aerosol infections. Therefore, our results suggest that
      acquisition of new chromosomal materials has not been of major
      importance in the dramatic change of life cycle that has accompanied
      the emergence of Y. pestis.
AU  - Derbise A
AU  - Chenal-Francisque V
AU  - Huon C
AU  - Fayolle C
AU  - Demeure CE
AU  - Chane-Woon-Ming B
AU  - Medigue C
AU  - Hinnebusch BJ
AU  - Carniel E
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2010 78: 3930-3941.

PMID- 9048944
VI  - 265
DP  - 1997
TI  - Two-domain structure of the td intron-encoded endonuclease I-TevI correlates with the two-domain configuration of the homing site.
PG  - 494-506
AB  - I-TevI, the T4 td intron-encoded endonuclease, catalyzes the first step in intron homing by
      making a double-strand break in the intronless allele within a sequence designated the homing
      site.  The 28 kDa enzyme, which interacts with the homing site over a span of 37 bp, binds as
      a monomer, contacting two domains of the substrate.  In this study, limited proteolysis
      experiments indicate that I-TevI consists of two domains that behave as discrete physical
      entities as judged by a number of functional and structural criteria.  Overexpression clones
      for each domain were constructed and the proteins were purified.  The carboxy-terminal domain
      has DNA-binding activity coincident with the primary binding region of the homing site and
      binds with the same affinity as the full-length enzyme.  The isolated amino-terminal domain,
      contains the conserved GIY-YIG motif, consistent with its being the catalytic domain.
      Furthermore, site-directed mutagenesis of a conserved arginine residue within the extended
      motif rendered the full-length protein catalytically inactive, although DNA-binding was
      maintained.  This is the first evidence that the GIY-YIG motif is important for catalytic
      activity.  An enzyme with an N-terminal catalytic domain and a C-terminal DNA-binding domain
      connected by a flexible linker is in accord with the bipartite structure of the homing site.
AU  - Derbyshire V
AU  - Kowalski JC
AU  - Dansereau JT
AU  - Hauer CR
AU  - Belfort M
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1997 265: 494-506.

PMID- 29954911
VI  - 6
DP  - 2018
TI  - Genome Sequences of Five Lactobacillus sp. Isolates from Traditional Turkish Sourdough.
PG  - e00616-18
AB  - A high level of variation in microflora can be observed in profiles of lactic acid bacteria
      (LAB) from sourdoughs. Here, we present draft genome sequences of
      Lactobacillus reuteri E81, L. reuteri LR5A, L. rhamnosus LR2, L. plantarum
      PFC-311, and the novel Lactobacillus sp. strain PFC-70, isolated from traditional
      Turkish backslopped wheat sourdoughs.
AU  - Dertli E
AU  - Skory CD
AU  - Simsek O
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00616-18.

PMID- 26514760
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Two New Zealand Xanthomonas campestris pv. campestris Isolates, ICMP 4013 and ICMP 21080.
PG  - e01247-15
AB  - Xanthomonas campestris pv. campestris is a necrotrophic bacterial pathogen of crucifers. We
      report here the draft genome sequences of isolates ICMP 4013 and
      ICMP 21080 from New Zealand. These sequences will facilitate the identification
      of race-specific factors in X. campestris pv. campestris.
AU  - Desai D
AU  - Li JH
AU  - van Zijll-de-Jong E
AU  - Braun R
AU  - Pitman A
AU  - Visnovsky S
AU  - Hampton J
AU  - Christey M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01247-15.

PMID- 28232437
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Mycoplasma pneumoniae Type 2 Reference Strain FH Using Single-Molecule Real-Time Sequencing Technology.
PG  - e01629-16
AB  - Mycoplasma pneumoniae type 2 strain FH was previously sequenced with Illumina (FH-Illumina)
      and 454 (FH-454) technologies according to Xiao et al. (2015) and
      Krishnakumar et al. (2010). Comparative analyses revealed differences in genomic
      content between these sequences, including a 6-kb region absent from the FH-454
      submission. Here, we present a complete genome sequence of FH sequenced with the
      Pacific Biosciences RSII platform.
AU  - Desai HP
AU  - Morrison SS
AU  - Diaz MH
AU  - Benitez AJ
AU  - Wolff BJ
AU  - Winchell JM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01629-16.

PMID- 23549920
VI  - 4
DP  - 2013
TI  - Evolutionary Genomics of Salmonella enterica Subspecies.
PG  - e00198-13
AB  - Six subspecies are currently recognized in Salmonella enterica. Subspecies I (subspecies
      enterica) is responsible for nearly all infections in humans and warm-blooded animals, while
      five other subspecies are isolated principally from coldblooded animals. We sequenced 21
      phylogenetically diverse strains, including two representatives from each of the previously
      unsequenced five subspecies and 11 diverse new strains from S. enterica subspecies enterica,
      to put this species into an evolutionary perspective. The phylogeny of the subspecies was
      partly obscured by abundant recombination events between lineages and a relatively short
      period of time within which subspeciation took place. Nevertheless, a variety of different
      tree-building methods gave congruent evolutionary tree topologies for subspeciation. A total
      of 285 gene families were identified that were recruited into subspecies enterica, and most of
      these are of unknown function. At least 2,807 gene families were identified in one or more of
      the other subspecies that are not found in subspecies I or Salmonella bongori. Among these
      gene families were 13 new candidate effectors and 7 new candidate fimbrial clusters. A third
      complete type III secretion system not present in subspecies enterica (I) isolates was found
      in both strains of subspecies salamae (II). Some gene families had complex taxonomies, such as
      the type VI secretion systems, which were recruited from four different lineages in five of
      six subspecies. Analysis of nonsynonymous-to-synonymous substitution rates indicated that the
      more-recently acquired regions in S. enterica are undergoing faster fixation rates than the
      rest of the genome. Recently acquired AT-rich regions, which often encode virulence functions,
      are under ongoing selection to maintain their high AT content.
AU  - Desai PT
AU  - Porwollik S
AU  - Long F
AU  - Cheng P
AU  - Wollam A
AU  - Bhonagiri-Palsikar V
AU  - Hallsworth-Pepin K
AU  - Clifton SW
AU  - Weinstock GM
AU  - McClelland M
PT  - Journal Article
TA  - MBio
JT  - MBio
SO  - MBio 2013 4: e00198-13.

PMID- 24923324
VI  - 6
DP  - 2014
TI  - Pangenome evidence for extensive interdomain horizontal transfer affecting lineage core and shell genes in uncultured planktonic thaumarchaeota and euryarchaeota.
PG  - 1549-1563
AB  - Horizontal gene transfer (HGT) is an important force in evolution, which may
      lead, among other things, to the adaptation to new environments by the import of
      new metabolic functions. Recent studies based on phylogenetic analyses of a few
      genome fragments containing archaeal 16S rRNA genes and fosmid-end sequences from
      deep-sea metagenomic libraries have suggested that marine planktonic archaea
      could be affected by high HGT frequency. Likewise, a composite genome of an
      uncultured marine euryarchaeote showed high levels of gene sequence similarity to
      bacterial genes. In this work, we ask whether HGT is frequent and widespread in
      genomes of these marine archaea, and whether HGT is an ancient and/or recurrent
      phenomenon. To answer these questions, we sequenced 997 fosmid archaeal clones
      from metagenomic libraries of deep-Mediterranean waters (1,000 and 3,000 m depth)
      and built comprehensive pangenomes for planktonic Thaumarchaeota (Group I
      archaea) and Euryarchaeota belonging to the uncultured Groups II and III
      Euryarchaeota (GII/III-Euryarchaeota). Comparison with available reference
      genomes of Thaumarchaeota and a composite marine surface euryarchaeote genome
      allowed us to define sets of core, lineage-specific core, and shell gene ortholog
      clusters for the two archaeal lineages. Molecular phylogenetic analyses of all
      gene clusters showed that 23.9% of marine Thaumarchaeota genes and 29.7% of
      GII/III-Euryarchaeota genes had been horizontally acquired from bacteria. HGT is
      not only extensive and directional but also ongoing, with high HGT levels in
      lineage-specific core (ancient transfers) and shell (recent transfers) genes.
      Many of the acquired genes are related to metabolism and membrane biogenesis,
      suggesting an adaptive value for life in cold, oligotrophic oceans. We
      hypothesize that the acquisition of an important amount of foreign genes by the
      ancestors of these archaeal groups significantly contributed to their divergence
      and ecological success.
AU  - Deschamps P
AU  - Zivanovic Y
AU  - Moreira D
AU  - Rodriguez-Valera F
AU  - Lopez-Garcia P
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2014 6: 1549-1563.

PMID- 1920448
VI  - 33
DP  - 1991
TI  - Counterselection of GATC sequences in enterobacteriophages by the components of the methyl-directed mismatch repair system.
PG  - 125-132
AB  - Weak to severe deficit of GATC sequences in the DNA of enterobacteriophages appears to be

      correlated with their undermethylation during growth in dam+ (GATC ade-methylase) bacteria.

      This observation is corroborated by the sequence analysis showing no evidence for

      site-specific mutagenicity of 6meAde. The MutH protein of the methyl-directed mismatch repair

      system recognizes and cleaves the undermethylated GATC sequences in the course of mismatch

      repair. To enquire whether the MutH function of the methyl-directed mismatch repair system

      participates in counterselection of GATC sequences in enterobacteriophages, we have studied

      the yield of bacteriophage PhiX174 containing either 0, 1, or 2 GATC sequences, in wild type,

      dam, and mut (H,L,S,U) Escherichia coli. Following transfection with unmethylated DNA

      containing two GATC sequences, a net decrease in the yield of infective particles was observed

      in all bacterial mutH+ dam- strains, whereas no detectable decrease was observed in bacteria

      infected by DNA without GATC sequence. This effect of the MutH function is maximum in wild

      type and mutL and mutS bacteria whereas the effect is not significant in mutU bacteria,

      suggesting an interaction of the helicase II with the MutH protein.

      

      However, in dam+ bacteria, the presence of GATC sequences leads to an increased yield of

      infective particles. The effect of GATC sequence and its Dam methylation system on phage yield

      in mutH- bacteria reveals that methylated GATC sequences are advantageous to the phage. These

      results suggest that the methyl-directed mismatch repair system, and in particular its MutH

      protein, may have participated in severe counterselection of GATC sequences from

      enterobacteriophages, presumably by DNA cleavage or by interfering with DNA replication or

      packaging when GATC sequences are undermethylated. Coevolution of the Dam and MutH proteins

      could then account for the loss of GATC sequences from DNA of bacteriophages growing in dam+

      hosts.

      

AU  - Deschavanne P
AU  - Radman M
PT  - Journal Article
TA  - J. Mol. Evol.
JT  - J. Mol. Evol.
SO  - J. Mol. Evol. 1991 33: 125-132.

PMID- 18305127
VI  - 46
DP  - 2008
TI  - Characterization of new Staphylococcal Cassette Chromosome mec (SCCmec) and topoisomerase genes in fluoroquinolone and methicillin-resistant Staphylococcus pseudintermedius.
PG  - 1818-1823
AB  - Fluoroquinolone and methicillin-resistant Staphylococcus pseudintermedius isolates harbor two
      new Staphylococcal Cassette Chromosome (SCCmec) which belong to class A, allotype 3 (SCCmec
      II-III) and to the new allotype 5 (SCCmec VII). Analysis of the complete nucleotide sequence
      of the topoisomerase loci gyrB/A and grlB/A revealed mutations involved in fluoroquinolone
      resistance.
AU  - Descloux S
AU  - Rossano A
AU  - Perreten V
PT  - Journal Article
TA  - J. Clin. Microbiol.
JT  - J. Clin. Microbiol.
SO  - J. Clin. Microbiol. 2008 46: 1818-1823.

PMID- 24051315
VI  - 1
DP  - 2013
TI  - Genome Sequence of Dehalobacter UNSWDHB, a Chloroform-Dechlorinating Bacterium.
PG  - e00720-13
AB  - The chloroform-respiring bacterium Dehalobacter UNSWDHB was isolated from subsurface soil
      contaminated with a mixture of organohalides, including
      chloroform. Here, we present its 3.2-Mb genome.
AU  - Deshpande NP
AU  - Wong YK
AU  - Manefield M
AU  - Wilkins MR
AU  - Lee M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00720-13.

PMID- 24482515
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Mycoplasma ovis Strain Michigan, a Hemoplasma of Sheep with Two Distinct 16S rRNA Genes.
PG  - e01235-13
AB  - We report the complete genome sequence of Mycoplasma ovis strain Michigan. Its single circular
      chromosome has 702,511 bp and contains 2 copies of the 16S rRNA
      gene, one corresponding to M. ovis and the other to 'Candidatus Mycoplasma
      haemovis.' All housekeeping genes and the 5S-23S rRNA genes are present in single
      copies.
AU  - Deshuillers PL
AU  - Santos AP
AU  - do Nascimento NC
AU  - Hampel JA
AU  - Bergin IL
AU  - Dyson MC
AU  - Messick JB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01235-13.

PMID- 11601904
VI  - 288
DP  - 2001
TI  - Comparative Genomics Reveals Close Genetic Relationships between Phages from Dairy Bacteria and Pathogenic Streptococci: Evolutionary Implications for Prophage-Host Interactions.
PG  - 325-341
AB  - The genome of the highly pathogenic M1 serotype Streptococcus pyogenes isolate SF370 contains
      eight prophage elements. Only prophage SF370.1 could be induced by mitomycin C treatment.
      Prophage SF370.3 showed a 33.5-kb-long genome that closely resembled the genome organization
      of the cos-site temperate Siphovirus r1t infecting the dairy bacterium Lactococcus lactis. The
      two-phage genomes shared between 60 and 70% nucleotide sequence identity over the DNA
      packaging, head and tail genes. Analysis of the SF370.3 genome revealed mutations in the
      replisome organizer gene that may prevent the induction of the prophage. The mutated phage
      replication gene was closely related to a virulence marker identified in recently emerged M3
      serotype S. pyogenes strains in Japan. This observation suggests that prophage genes confer
      selective advantage to the lysogenic host. SF370.3 encodes a hyaluronidase and a DNase that
      may facilitate the spreading of S. pyogenes through tissue planes of its human host. Prophage
      SF370.2 showed a 43-kb-long genome that closely resembled the genome organization of pac-site
      temperate Siphoviridae infecting the dairy bacteria S. thermophilus and L. lactis. Over part
      of the structural genes, the similarity between SF370.2 and S. thermophilus phage O1205
      extended to the nucleotide sequence level. SF370.2 showed two probable inactivating mutations:
      one in the replisome organizer gene and another in the gene encoding the portal protein.
      Prophage SF370.2 also encodes a hyaluronidase and in addition two very likely virulence
      factors: prophage-encoded toxins acting as superantigens that may contribute to the immune
      deregulation observed during invasive streptococcal infections. The superantigens are encoded
      between the phage lysin and the right attachment site of the prophage genome. The genes were
      nearly sequence identical with a DNA segment in S. equi, suggesting horizontal gene transfer.
      The trend for prophage genome inactivation was even more evident for the remaining five
      prophage sequences that showed massive losses of prophage DNA. In these prophage remnants only
      13-0.3 kb of putative prophage DNA was detected. We discuss the genomics data from S. pyogenes
      strain SF370 within the framework of Darwinian coevolution of prophages and lysogenic bacteria
      and suggest elements of genetic cooperation and elements of an arms race in this host-parasite
      relationship.
AU  - Desiere F
AU  - McShan WM
AU  - van Sinderen D
AU  - Ferretti JJ
AU  - Brussow H
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 2001 288: 325-341.

PMID- 23045486
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of the Ethanol-Producing Zymomonas mobilis subsp. mobilis Centrotype ATCC 29191.
PG  - 5966-5967
AB  - Zymomonas mobilis is an ethanologenic bacterium that has been studied for use in  biofuel
      production. Of the sequenced Zymomonas strains, ATCC 29191 has been
      described as the phenotypic centrotype of Zymomonas mobilis subsp. mobilis, the
      taxon that harbors the highest ethanol-producing Z. mobilis strains. ATCC 29191
      was isolated in Kinshasa, Congo, from palm wine fermentations. This strain is
      reported to be a robust levan producer, while in recent years it has been
      employed in studies addressing Z. mobilis respiration. Here we announce the
      finishing and annotation of the ATCC 29191 genome, which comprises one chromosome
      and three plasmids.
AU  - Desiniotis A
AU  - Kouvelis VN
AU  - Davenport K
AU  - Bruce D
AU  - Detter C
AU  - Tapia R
AU  - Han C
AU  - Goodwin LA
AU  - Woyke T
AU  - Kyrpides NC
AU  - Typas MA
AU  - Pappas KM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5966-5967.

PMID- 
VI  - 28
DP  - 2000
TI  - Targetted DNA distortion by EcoP15I DNA methyltransferase.
PG  - A309
AB  - EcoP15I DNA methyltransferase, a member of the type III restriction-modification system, binds
      to the sequence 5'-CAGCAG-3' transferring a methyl group from S-adenosyl-L-methionine to the
      second adenine.  We have investigated protein-DNA interactions in the methylase-DNA complex by
      three methods.  Determination of equilibrium dissociation constants indicated that the enzyme
      had higher affinity for DNA containing mismatches at the target base within the recognition
      sequence.  Potassium permanganate footprinting studies revealed that there was a
      hyper-reactive cleavage site coincident with adenine that is the target base for methylation.
      More importantly, to detect DNA conformational alterations within the enzyme-DNA complexes, we
      have used a fluorescence-based assay, when the enzyme bound to DNA containing 2-aminopurine
      substitutions within the cognate sequence, an 8-10 fold fluorescence enhancement resulting
      from enzymatic flipping of the target adenine was observed, fluorescence spectroscopy analysis
      showed that the changes attributable to structural distortion were specific for only the bases
      within the recognition sequence.  Interestingly, we observed that both the adenines in the
      recognition site appear to be structurally distorted to the same extent.  While the target
      adenine is probably flipped out of the DNA duplex, our results also suggest that fluorescence
      enhancements could be derived from protein-DNA interactions other than base flipping.  Taken
      together, our results support the proposed base flipping mechanism for adenine
      methyltransferases.
AU  - Desirazu NR
AU  - Reddy YV
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 2000 28: A309.

PMID- 12676953
VI  - 278
DP  - 2003
TI  - The methyl donor S-adenosylmethionine inhibits active demethylation of DNA: a candidate novel mechanism for the pharmacological effects of s-adenosylmethionine.
PG  - 20812-20820
AB  - S-Adenosylmethionine (AdoMet) is the methyl donor of numerous methylation reactions. The
      current model is that an increased concentration of AdoMet
      stimulates DNA methyltransferase reactions, triggering hypermethylation
      and protecting the genome against global hypomethylation, a hallmark of
      cancer. Using an assay of active demethylation in HEK 293 cells, we show
      that AdoMet inhibits active demethylation and expression of an ectopically
      methylated CMV-GFP (green fluorescent protein) plasmid in a dose-dependent
      manner. The inhibition of GFP expression is specific to methylated GFP;
      AdoMet does not inhibit an identical but unmethylated CMV-GFP plasmid.
      S-Adenosylhomocysteine (AdoHcy), the product of methyltransferase
      reactions utilizing AdoMet does not inhibit demethylation or expression of
      CMV-GFP. In vitro, AdoMet but not AdoHcy inhibits methylated DNA-binding
      protein 2/DNA demethylase as well as endogenous demethylase activity
      extracted from HEK 293, suggesting that AdoMet directly inhibits
      demethylase activity, and that the methyl residue on AdoMet is required
      for its interaction with demethylase. Taken together, our data support an
      alternative mechanism of action for AdoMet as an inhibitor of
      intracellular demethylase activity, which results in hypermethylation of
      DNA.
AU  - Detich N
AU  - Hamm S
AU  - Just G
AU  - Knox JD
AU  - Szyf M
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2003 278: 20812-20820.

PMID- 11335728
VI  - 276
DP  - 2001
TI  - A conserved 3'-untranslated element mediates growth regulation of DNA methyltransferase 1 and inhibits its transforming activity.
PG  - 24881-24890
AB  - Ectopic expression of DNA methyltransferase 1 (DNMT1) has been proposed to play an important
      role in cancer. dnmt1 mRNA is undetectable in
      growth-arrested cells but is induced upon entrance into the S phase of the cell cycle, and
      until now, the mechanisms responsible for this regulation were unknown. In this report, we
      demonstrate that the 3'-untranslated region (3'-UTR) of the dnmt1 mRNA can confer a
      growth-dependent regulation on its own message as well as a heterologous beta-globin mRNA Our
      results indicate that a 54-nucleotide highly conserved element within the 3'-UTR is necessary
      and sufficient to mediate this regulation. Cell-free mRNA decay experiments demonstrate that
      this element increases mRNA turnover rates and does so to a greater extent in the presence of
      extracts prepared from arrested cells. A specific RNA-protein complex is formed with the
      3'-UTR only in growth-arrested cells, and a UV cross-linking analysis revealed a 40-kDa
      protein (p40), the binding of which is dramatically increased in growth-arrested cells and is
      inversely correlated with dnmt1 mRNA levels as cells are induced into the cell cycle. Although
      ectopic expression of human DNMT1 lacking the 3'-UTR can transform NIH-3T3 cells, inclusion
      of the 3'-UTR prevents transformation. These
      results support the hypothesis that deregulated expression of DNMT1
      with the cell cycle is important for cellular transformation.
AU  - Detich N
AU  - Ramchandani S
AU  - Szyf M
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2001 276: 24881-24890.

PMID- 12177048
VI  - 277
DP  - 2002
TI  - Promoter-specific activation and demethylation by MBD2/demethylase.
PG  - 35791-35794
AB  - MBD2 is the only member of a family of methyl-CpG-binding proteins that has been reported to
      be both a transcriptional repressor and a DNA
      demethylase (dMTase). To understand the apparently contradictory function
      of MBD2/dMTase, we studied the effects of dMTase overexpression on the
      activity of various in vitro methylated promoters transiently transfected
      into HEK293 cells. We found that forced expression of a MBD2/dMTase
      expression vector (His-dMTase) differentially activated two methylated
      reporters, pSV40-CAT (the SV40 enhancerless promoter adjacent to the
      chloramphenicol acetyltransferase (CAT) reporter gene) and pGL2T+I4xTBRE
      (a region of the p21 promoter next to the luciferase reporter gene), in a
      time- and dose-dependent manner. His-dMTase increased pSV40-CAT expression
      by 3-10-fold after 96 h, while pGL2T+I4xTBRE expression was increased by
      2-3-fold after only 48 h and did not further increase at 96 h. Gene
      activation was not universal because no effect was seen with the p19-ARF
      promoter. We then assessed whether activation might be due to
      demethylation within the promoter region. Using bisulfite mapping, we
      found that exogenous expression of His-dMTase induced demethylation at 8
      of the 10 CpG sites within the SV40 promoter. The observation that
      His-dMTase increases the demethylase activity in the cells was also
      confirmed using an in vitro CpG demethylase assay with a mC32pG
      oligonucleotide substrate and purified Q-Sepharose fractions from HEK293
      cells transfected with His-dMTase or empty pcDNA3.1His vector. We propose
      that a single protein possessing both repressor and demethylase functions
      has evolved to coordinate a program that requires suppression of some
      methylated genes and activation of others.
AU  - Detich N
AU  - Theberge J
AU  - Szyf M
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2002 277: 35791-35794.

PMID- 945948
VI  - 72
DP  - 1976
TI  - Analysis of 5-methylcytosine in DNA.
PG  - 586-592
AB  - A method is described for the unambiguous rapid identification and quantitation of the minor
      base, 5-methylcytosine, in DNA using high resolution mass spectrometry.  This method can
      detect one 5-methylcytosine residue per 5500 nucleotides in Phi X174 DNA, in a sample of less
      than 10 micrograms and requires less than 1 micrograms of calf thymus DNA in which the molar
      ratio of 5-methylcytosine/cytosine is about 0.05.
AU  - Deutsch J
AU  - Razin A
AU  - Sedat J
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 1976 72: 586-592.

PMID- 1374836
VI  - 110
DP  - 1992
TI  - Detection of a CpA methylase in an insect system: Characterization and substrate specificity.
PG  - 103-111
AB  - a cytosine-specific DNA methyltransferase (EC 2.1.1.37) has been purified to near homogeneity
      from a mealybug (Planococcus lilacinus). The enzyme can methylate cytosine residues in CpG
      sequences as well as CpA sequences. The apparent molecular weight of the enzymes was estimated
      as 135,000 daltons by FPLC. The enzyme exhibits a processive mode of action and a salt
      dependance similar to mammalian methylases. Mealybug methylase exhibits a preference for
      denatured DNA substrates.
AU  - Devajyothi C
AU  - Brahmachari V
PT  - Journal Article
TA  - Mol. Cell. Biochem.
JT  - Mol. Cell. Biochem.
SO  - Mol. Cell. Biochem. 1992 110: 103-111.

PMID- 24407649
VI  - 2
DP  - 2014
TI  - Genome Sequence of the Mycorrhizal Helper Bacterium Pseudomonas fluorescens BBc6R8.
PG  - e01152-13
AB  - We report the draft genome sequence of the mycorrhizal helper bacterium Pseudomonas
      fluorescens strain BBc6R8. This is the first genome of a mycorrhizal
      helper bacterium. The draft genome contains 6,952,353 bp and is predicted to
      encode 6,317 open reading frames. Comparative genomic analyses will help to
      identify helper traits.
AU  - Deveau A
AU  - Gross H
AU  - Morin E
AU  - Karpinets T
AU  - Utturkar S
AU  - Mehnaz S
AU  - Martin F
AU  - Frey-Klett P
AU  - Labbe J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01152-13.

PMID- 26868408
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Pseudomonas sp. Strain ADP, a Bacterial Model for Studying the Degradation of the Herbicide Atrazine.
PG  - e01733-15
AB  - We report here the 7,259,392-bp draft genome of Pseudomonas sp. strain ADP. This  is a
      bacterial strain that was first isolated in the 1990s from soil for its
      ability to mineralize the herbicide atrazine. It has extensively been studied as
      a model to understand the atrazine biodegradation pathway. This genome will be
      used as a reference and compared to evolved populations obtained by experimental
      evolution conducted on this strain under atrazine selection pressure.
AU  - Devers-Lamrani M
AU  - Spor A
AU  - Mounier A
AU  - Martin-Laurent F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01733-15.

PMID- 20952566
VI  - 192
DP  - 2010
TI  - Genome of Helicobacter pylori Strain 908.
PG  - 6488-6489
AB  - Helicobacter pylori is a genetically diverse and coevolved pathogen inhabiting human gastric
      niches and leading to a spectrum of gastric
      diseases in susceptible populations. We describe the genome sequence of H.
      pylori 908, which was originally isolated from an African patient living
      in France who suffered with recrudescent duodenal ulcer disease. The
      strain was found to be phylogenetically related to H. pylori J99, and its
      comparative analysis revealed several specific genome features and novel
      insertion-deletion and substitution events. The genome sequence revealed
      several strain-specific deletions and/or gain of genes exclusively present
      in HP908 compared with different sequenced genomes already available in
      the public domain. Comparative and functional genomics of HP908 and its
      subclones will be important in understanding genomic plasticity and the
      capacity to colonize and persist in a changing host environment.
AU  - Devi SH
AU  - Taylor TD
AU  - Avasthi TS
AU  - Kondo S
AU  - Suzuki Y
AU  - Megraud F
AU  - Ahmed N
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 6488-6489.

PMID- 24233592
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of a Plant Growth-Promoting Rhizobacterium, Serratia fonticola Strain AU-P3(3).
PG  - e00946-13
AB  - Plant growth-promoting rhizobacteria (PGPR), found in the rhizospheric region of  plants, not
      only suppress plant disease, but also directly improve plant health
      by improving the availability of nutrients and by providing phytostimulants.
      Herein, we report the high-quality genome sequence of Serratia fonticola strain
      AU-P3(3), a PGPR of the pea plant, which confers phosphate solubilization,
      indole-3-acetic acid production, ammonia production, hydrogen cyanide (HCN)
      production, and siderophore production and also confers activity against
      Rhizoctonia species. The 5.02-Mb genome sequence contains genes related to plant
      growth promotion and biocontrol activities.
AU  - Devi U
AU  - Khatri I
AU  - Kumar N
AU  - Kumar L
AU  - Sharma D
AU  - Subramanian S
AU  - Saini AK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00946-13.

PMID- 24309742
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Plant-Growth-Promoting Rhizobacterium Serratia fonticola Strain AU-AP2C, Isolated from the Pea Rhizosphere.
PG  - e01022-13
AB  - Plant health can be augmented by plant-growth-promoting rhizobacteria (PGPR) that confer
      biofertilizer, phytostimulation, and biocontrol activities. Herein, we
      provide the high-quality draft genome sequence of Serratia fonticola strain
      AU-AP2C, a Gram-negative motile PGPR of the pea plant, conferring phosphate
      solubilization, ammonia production, and antifungal activity against Fusarium sp.
      The 4.9-Mb genome contains genes related to plant growth promotion and synthesis
      of siderophores.
AU  - Devi U
AU  - Khatri I
AU  - Kumar N
AU  - Sharma D
AU  - Subramanian S
AU  - Saini AK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01022-13.

PMID- 28963216
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of a Gordonia sp. Isolated from the Soil of a Red Alder Plant.
PG  - e01039-17
AB  - A Gordonia species was cultured from soil of a red alder (Alnus rubra) plant. Here we present
      the assembled and annotated genome sequence to aid investigations
      into the potential of this organism as a symbiont and comparative studies of the
      genus Gordonia.
AU  - Devitt NP
AU  - Herman B
AU  - Luchterhand RA
AU  - Costa MA
AU  - Jacobi JL
AU  - Davin LB
AU  - Lewis NG
AU  - Bell CJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01039-17.

PMID- 2892399
VI  - 42
DP  - 1988
TI  - The relative efficiency of restriction enzymes:  an update.
PG  - 179-182
AB  - The question of which restriction enzymes to use in screening newly cloned
      probes for RFLPs continues to come up.  The importance of this question is
      obvious when it is recognised that, as of this writing, more than 140
      restriction endonucleases are listed as commerically available.  By way of
      aiding the decision process, Wijsman (1984) produced a model with which the
      efficiency of any restriction enzyme relative to that of any other might be
      assessed.  The model involves a calculation of the relative efficiency (RE) of
      the enzyme, which takes into account the recognition sequence of the enzyme,
      the size of the DNA fragment being used to probe the digests, and the minimum
      restriction-fragment size detectable in the usual 0.7%-1.25% agarose gels.  RE
      is thus a unitless value by means of which any two or more enzymes might be
      compared.  All other things being equal, the higher the RE value the more
      efficient the enzyme is in detecting sequence variants.  In this letter this
      model is applied to an expanded and updated list of restriction enzymes, with
      the result that some apparently good screening candidates and a few poor
      candidates are observed.
AU  - Devor EJ
PT  - Journal Article
TA  - Am. J. Hum. Genet.
JT  - Am. J. Hum. Genet.
SO  - Am. J. Hum. Genet. 1988 42: 179-182.

PMID- 24158559
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Bacillus sp. Strain NSP2.1, a Nonhalophilic Bacterium Isolated from the Salt Marsh of the Great Rann of Kutch, India.
PG  - e00909-13
AB  - The 5.52-Mbp draft genome sequence of Bacillus sp. strain NSP2.1, a nonhalophilic bacterium
      isolated from the salt marsh of the Great Rann of Kutch, India, is
      reported here. An analysis of the genome of this organism will facilitate the
      understanding of its survival in the salt marsh.
AU  - Dey R
AU  - Pal KK
AU  - Sherathia D
AU  - Dalsania T
AU  - Savsani K
AU  - Patel I
AU  - Sukhadiya B
AU  - Mandaliya M
AU  - Thomas M
AU  - Ghorai S
AU  - Vanpariya S
AU  - Rupapara R
AU  - Rawal P
AU  - Saxena AK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00909-13.

PMID- 24115550
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Bacillus sp. Strain NSP9.1, a Moderately Halophilic Bacterium Isolated from the Salt Marsh of the Great Rann of Kutch, India.
PG  - e00835-13
AB  - We report the 4.52-Mbp draft genome sequence of Bacillus sp. strain NSP9.1, a moderately
      halophilic bacterium isolated from the salt marsh of the Great Rann of
      Kutch, India. Analysis of the genome of this organism will lead to a better
      understanding of the genes and metabolic pathways involved in imparting
      osmotolerance.
AU  - Dey R
AU  - Pal KK
AU  - Sherathia D
AU  - Dalsania T
AU  - Savsani K
AU  - Patel I
AU  - Thomas M
AU  - Ghorai S
AU  - Vanpariya S
AU  - Rupapara R
AU  - Rawal P
AU  - Sukhadiya B
AU  - Mandaliya M
AU  - Saxena AK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00835-13.

PMID- 24407641
VI  - 2
DP  - 2014
TI  - Insight into the First Draft Genome Sequence of the Genus Sediminibacillus, Sediminibacillus halophilus Strain NSP9.3.
PG  - e01133-13
AB  - We report the 3.98-Mbp first draft genome sequence of Sediminibacillus halophilus strain
      NSP9.3, a moderate halophile isolated from a seasonal salt marsh of the
      Great Rann of Kutch, India. Exploring the genome of this organism will facilitate
      the understanding of the mechanism(s) of osmotolerance and survival in
      differential osmolarity.
AU  - Dey R
AU  - Pal KK
AU  - Sherathia D
AU  - Sukhadiya B
AU  - Dalsania T
AU  - Patel I
AU  - Savsani K
AU  - Thomas M
AU  - Vanpariya S
AU  - Mandaliya M
AU  - Rupapara R
AU  - Rawal P
AU  - Ghorai S
AU  - Bhayani S
AU  - Shah A
AU  - Saxena AK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01133-13.

PMID- 24356848
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Obligate Halophilic Bacillus sp. Strain NSP22.2, Isolated from a Seasonal Salt Marsh of the Great Rann of Kutch, India.
PG  - e01104-13
AB  - Here, we report the 4.0-Mbp draft genome of an obligate halophile, Bacillus sp. strain
      NSP22.2, isolated from a seasonal salt marsh of the Great Rann of Kutch,
      India. To understand the mechanism(s) of obligate halophilism and to isolate the
      relevant gene(s), the genome of Bacillus sp. NSP22.2 was sequenced.
AU  - Dey R
AU  - Pal KK
AU  - Sherathia D
AU  - Vanpariya S
AU  - Patel I
AU  - Dalsania T
AU  - Savsani K
AU  - Sukhadiya B
AU  - Mandaliya M
AU  - Thomas M
AU  - Ghorai S
AU  - Rupapara R
AU  - Rawal P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01104-13.

PMID- 24657871
VI  - 80
DP  - 2014
TI  - Draft Genome Comparison of Representatives of the Three Dominant Genotype Groups of Dairy Bacillus licheniformis Strains.
PG  - 3453-3462
AB  - The spore-forming bacterium Bacillus licheniformis is a common contaminant of milk and milk
      products. Strains of this species isolated from dairy products can be differentiated into
      three major groups, namely, G, F1, and F2, using random amplification of polymorphic DNA
      (RAPD) analysis; however, little is known about the genomic differences between these groups
      and the identity of the fragments that make up their RAPD profiles. In this work we obtained
      high-quality draft genomes of representative strains from each of the three RAPD groups
      (designated strain G-1, strain F1-1, and strain F2-1) and compared them to each other and to
      B. licheniformis ATCC 14580 and Bacillus subtilis 168. Whole-genome comparison and multilocus
      sequence typing revealed that strain G-1 contains significant sequence variability and belongs
      to a lineage distinct from the group F strains. Strain G-1 was found to contain genes coding
      for a type I restriction modification system, urease production, and bacitracin synthesis, as
      well as the 8-kbp plasmid pFL7, and these genes were not present in strains F1-1 and F2-1. In
      agreement with this, all isolates of group G, but no group F isolates, were found to possess
      urease activity and antimicrobial activity against Micrococcus. Identification of RAPD band
      sequences revealed that differences in the RAPD profiles were due to differences in gene
      lengths, 3' ends of predicted primer binding sites, or gene presence or absence. This work
      provides a greater understanding of the phylogenetic and phenotypic differences observed
      within the B. licheniformis species.
AU  - Dhakal R
AU  - Seale R
AU  - Brent D
AU  - Hilton C
AU  - Craven H
AU  - Turner MS
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2014 80: 3453-3462.

PMID- 26893423
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Tepidimonas taiwanensis Strain MB2, a Chemolithotrophic  Thermophile Isolated from a Hot Spring in Central India.
PG  - e01723-15
AB  - Tepidimonas taiwanensis strain MB2 is a thermophile isolated from a hot spring located in
      central India. Here, we report a 28,49,160 bp draft genome sequence of
      Tepidimonas taiwanensis MB2. The genome shows properties of sulfur metabolism,
      nitrogen fixation, ammonia metabolism, assimilation of organic acids, and a wide
      variety of proteases.
AU  - Dhakan DB
AU  - Saxena R
AU  - Chaudhary N
AU  - Sharma VK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01723-15.

PMID- 25700411
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of a Cellulase-Producing Psychrotrophic Paenibacillus Strain, IHB B 3415, Isolated from the Cold Environment of the Western Himalayas,  India.
PG  - e01581-14
AB  - Paenibacillus sp. strain IHB B 3415 is a cellulase-producing psychrotrophic bacterium isolated
      from a soil sample from the cold deserts of Himachal Pradesh,  India. Here, we report an
      8.44-Mb assembly of its genome sequence with a G+C content of 50.77%. The data presented here
      will provide insights into the mechanisms of cellulose degradation at low temperature.
AU  - Dhar H
AU  - Swarnkar MK
AU  - Gulati A
AU  - Singh AK
AU  - Kasana RC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01581-14.

PMID- 380146
VI  - 96
DP  - 1979
TI  - Restriction in vivo.  IV. Effect of restriction of parental DNA on the expression of restriction alleviation systems in phage T4.
PG  - 404-411
AB  - Under restricting conditions expression of early T4 genes is determined in part by the
      location of the particular gene relative to the cleavage site.  Some genes are inactivated
      directly by cleavage of the DNA.  Other genes are inactivated by secondary exonucleolytic
      degradation of cleaved DNA.  A third class of genes continues to be expressed from the small
      fragments which remain after the exonucleolytic degradation of the cleaved fragments.
      Expression of phage genes coding for the inhibitors of the restriction endonuclease and
      restriction exonuclease are prevented by endonucleolytic cleavage and exonucleolytic
      degradation, respectively.
AU  - Dharmalingam K
AU  - Goldberg EB
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1979 96: 404-411.

PMID- 768782
VI  - 260
DP  - 1976
TI  - Mechanism localisation and control of restriction cleavage of phage T4 and lambda chromosomes in vivo.
PG  - 406-410
AB  - The primary action of restriction endonuclease, cleaving infecting DNA, has
      been demonstrated in vivo.  This primary cleavage is followed rapidly by
      hydrolysis of the cleaved DNA at its newly exposed termini.  Infecting viruses
      can inactivate cytoplasmic and membrane restriction endonucleases to prevent
      cleavage of unmodified DNA replicas.
AU  - Dharmalingam K
AU  - Goldberg EB
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1976 260: 406-410.

PMID- 6991879
VI  - 178
DP  - 1980
TI  - Restriction in vivo.  V. Induction of SOS functions in Escherichia coli by restricted T4 phage DNA and alleviation of restriction by SOS functions.
PG  - 51-58
AB  - Degradation products of restricted T4 DNA induced filamentation, mutagenesis,
      and to a lesser extent, synthesis of recA protein in wild type cells but not in
      recA, lexA or recBC mutants of Escherichia coli.  We conclude that the
      structural damage to the DNA caused by restriction cleavage and exonuclease V
      degradation can induce SOS functions.  Degradation of restricted
      nonglucosylated T4 DNA by exonuclease V delayed cell division and induced
      filament formation and mutagenesis in lexA+ but not in lexA- cells.  Delay of
      cell division was also dependent upon recA and recBC functions.  Such
      degradation of DNA also dramatically increased mutagenesis in tif- Sfi- cells
      at 42.  The synthesis of recA protein continued in the restricting host after
      infection by the nonglucosylated T4 phage, but enhanced synthesis is not
      induced to the extent seen in SOS induced tif cells grown at 42.  We also found
      that restriction of nonglucosylated T4 was alleviated in UV irradiated cells.
      The UV induced alleviation of rgl and rK restriction depended upon post
      irradiation protein synthesis and was not observed in recA, lexA or recBC
      mutants.
AU  - Dharmalingam K
AU  - Goldberg EB
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1980 178: 51-58.

PMID- 768783
VI  - 260
DP  - 1976
TI  - Phage-coded protein prevents restriction of unmodified progeny T4 DNA.
PG  - 454-455
AB  - None
AU  - Dharmalingam K
AU  - Goldberg EB
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1976 260: 454-455.

PMID- 6276366
VI  - 149
DP  - 1982
TI  - Physical mapping and cloning of bacteriophage T4 anti-restriction ednonuclease gene.
PG  - 694-699
AB  - We have proposed that the ability of T4 to produce non-glucosylated progeny
      after a single cycle of growth on a galU rglA rglB+ mutant of Escherichia coli
      is due to the inhibition of the rglB+ function by a phage-coded,
      anti-restriction endonuclease protein.  Based on this hypothesis, we screened
      T4 deletion mutants for failure to give a burst in this host.  The absence of
      an arn gene in phage mutants secondary infecting non-glucosylated phage from
      rglB-controlled cleavage.  A functional arn gene was cloned on plasmid pBR325,
      and the 0.8-kilobase insert DNA was shown to be homologous to the DNA missing
      in the arn deletion phage.
AU  - Dharmalingam K
AU  - Revel HR
AU  - Goldberg EB
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1982 149: 694-699.

PMID- 27491995
VI  - 4
DP  - 2016
TI  - Insights into the Genome Sequences of an N-Acyl Homoserine Lactone Molecule Producing Two Pseudomonas spp. Isolated from the Arctic.
PG  - e00767-16
AB  - We report for the first time the draft genome sequence of two psychrotrophic Pseudomonas
      species, Pseudomonas simiae RGCB 73 and Pseudomonas brenneri RGCB
      108, from the Arctic that produce more than one acyl homoserine lactone molecule
      of varied N-acyl length. The study confirms the presence of a LuxR-LuxI (type)
      mediated quorum-sensing system in both the Pseudomonas species and enables us to
      understand the role of quorum sensing in their survival in extremely cold
      environments.
AU  - Dharmaprakash A
AU  - Reghunathan D
AU  - Sivakumar KC
AU  - Prasannakumar M
AU  - Thomas S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00767-16.

PMID- 18498642
VI  - 7
DP  - 2008
TI  - A genomic search approach to identify esterases in Propionibacterium freudenreichii involved in the formation of flavour in Emmental cheese.
PG  - 16
AB  - ABSTRACT: BACKGROUND: Lipolysis is an important process of cheese ripening
      that contributes to the formation of flavour. Propionibacterium
      freudenreichii is the main agent of lipolysis in Emmental cheese; however,
      the enzymes involved produced by this species have not yet been
      identified. Lipolysis is performed by esterases (carboxylic ester
      hydrolases, EC 3.1.1.-) which are able to hydrolyse acylglycerols bearing
      short, medium and long chain fatty acids. The genome sequence of P.
      freudenreichii type strain CIP103027T was recently obtained in our
      laboratory.The aim of this study was to identify as exhaustively as
      possible the potential esterases in P. freudenreichii that could be
      involved in the hydrolysis of acylglycerols in Emmental cheese. The
      proteins identified were produced in a soluble and active form by
      heterologous expression in Escherichia coli for further study of their
      activity and specificity of hydrolysed substrates. RESULTS: The approach
      chosen was a genomic search approach that combined and compared four
      methods based on automatic and manual searches of homology and motifs
      among P. freudenreichii CIP103027T predicted proteins. Twenty-three
      putative esterases were identified in this step. Then a selection step
      permitted to focus the study on the 12 most probable esterases, according
      to the presence of the GXSXG motif of the alpha/beta hydrolase fold
      family. The 12 corresponding coding sequences were cloned in expression
      vectors, containing soluble N-terminal fusion proteins. The best
      conditions to express each protein in a soluble form were found thanks to
      an expression screening, using an incomplete factorial experimental
      design. Eleven out of the 12 proteins were expressed in a soluble form in
      E. coli and six showed esterase activity on 1-naphthyl acetate and/or
      propionate, as demonstrated by a zymographic method. CONCLUSION: We were
      able to demonstrate that our genomic search approach was efficient to
      identify esterases from the genome of a P. freudenreichii strain, more
      exhaustively than classical approaches. This study highlights the interest
      in using the automatic search of motifs, with the manual search of
      homology to previously characterised enzymes as a complementary method.
      Only further characterisations would permit the identification of the
      esterases of P. freudenreichii involved in the lipolysis in Emmental
      cheese.
AU  - Dherbecourt J
AU  - Falentin H
AU  - Canaan S
AU  - Thierry A
PT  - Journal Article
TA  - Microb. Cell Fact.
JT  - Microb. Cell Fact.
SO  - Microb. Cell Fact. 2008 7: 16.

PMID- 20610411
VI  - 186
DP  - 2010
TI  - Accidental Amplification and Inactivation of a Methyltransferase Gene Eliminates Cytosine Methylation in Mycosphaerella graminicola.
PG  - 67
AB  - A de novo search for repetitive elements in the genome sequence of the wheat pathogen
      Mycosphaerella graminicola identified a family of
      repeats containing a DNA cytosine methyltransferase sequence (MgDNMT).
      All 23 MgDNMT sequences identified carried signatures of repeat induced
      point mutation (RIP). All copies were subtelomeric in location except
      for one on chromosome 6. Synteny with M. fijiensis implied that the
      nontelomeric copy on chromosome 6 served as a template for subsequent
      amplifications. Southern analysis revealed that the MgDNMT sequence
      also was amplified in 15 additional M. graminicola isolates from
      various geographical regions. However, this amplification event was
      specific to M. graminicola; a search for MgDNMT homologs identified
      only a single, unmutated copy in the genomes of 11 other ascomycetes. A
      genome-wide methylation assay revealed that M. graminicola lacks
      cytosine methylation, as expected if its MgDNMT gene is inactivated.
      Methylation was present in several other species tested, including the
      closest known relatives of M. graminicola, species S1 and S2.
      Therefore, the observed changes most likely occurred within the past
      10,500 years since the divergence between M. graminicola and S1. Our
      data indicate that the recent amplification of a single-copy MgDNMT
      gene made it susceptible to RIP, resulting in complete loss of cytosine
      methylation in M. graminicola.
AU  - Dhillon B
AU  - Cavaletto JR
AU  - Wood KV
AU  - Goodwin SB
PT  - Journal Article
TA  - Genetics
JT  - Genetics
SO  - Genetics 2010 186: 67.

PMID- 19447908
VI  - 191
DP  - 2009
TI  - Complete Genome Sequence of Aggregatibacter (Haemophilus) aphrophilus NJ8700.
PG  - 4693-4694
AB  - We report the finished and annotated genome sequence of Aggregatibacter aphrophilus strain
      NJ8700, a strain isolated from the oral flora of a healthy individual, and discuss
      characteristics that may affect its dual roles in human health and disease. This strain has a
      rough appearance, and its genome contains genes encoding a type VI secretion system and
      several factors that may participate in host colonization.
AU  - Di Bonaventura MP
AU  - Desalle R
AU  - Pop M
AU  - Nagarajan N
AU  - Figurski DH
AU  - Fine DH
AU  - Kaplan JB
AU  - Planet PJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2009 191: 4693-4694.

PMID- 22965087
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Lactobacillus rossiae DSM 15814T.
PG  - 5460-5461
AB  - The draft genome sequence of Lactobacillus rossiae DSM 15814(T) (CS1, ATCC BAA-88) was
      determined by a whole-genome shotgun approach. Reads were assembled
      to a 2.9-Mb draft version. RAST genome annotation evidenced 2,723 predicted
      coding sequences. Many carbohydrate, amino acid, and amino acid derivative
      subsystem features were found.
AU  - Di Cagno R
AU  - De Angelis M
AU  - Cattonaro F
AU  - Gobbetti M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5460-5461.

PMID- 25146139
VI  - 2
DP  - 2014
TI  - Genome Sequence of Rhodococcus opacus Strain R7, a Biodegrader of Mono- and Polycyclic Aromatic Hydrocarbons.
PG  - e00827-14
AB  - Rhodococcus opacus strain R7 (CIP107348) degrades several mono- and polycyclic aromatic
      hydrocarbons. Here, we present the high-quality draft genome sequence of
      strain R7, consisting of 10,118,052 bp, with a G+C content of 67.0%, 9,602
      protein-coding genes, and 62 RNAs genes.
AU  - Di Gennaro P
AU  - Zampolli J
AU  - Presti I
AU  - Cappelletti M
AU  - D'Ursi P
AU  - Orro A
AU  - Mezzelani A
AU  - Milanesi L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00827-14.

PMID- 11470526
VI  - 272
DP  - 2001
TI  - DNA (cytosine-5) methyltransferase turnover and cellular localization in developing Paracentrotus lividus sea urchin embryo.
PG  - 199-208
AB  - The turnover and localization of the enzyme DNA (cytosine-5) methyltransferase (Dnmt1) were
      studied during Paracentrotus lividus sea urchin embryo development using antibody preparations
      against the NH(2) and COOH-terminal regions of the molecule. The antibodies reveal, by Western
      blots and whole-mount analyses, that the enzyme is differentially required during embryonic
      development. The changeover point is at blastula stage, where a proteolytic mechanism
      hydrolyses the enzyme present in all embryonic cells by removing a peptide of about 45 kDa
      from the amino terminal region of the 190 kDa enzyme initially synthesized on maternal
      transcripts. The resulting 145 kDa enzyme shows modified catalytic properties, different
      antibody reactivity and is rapidly destroyed in the few hours before gastrulation. At more
      advanced stages of development the enzyme is newly synthesized but only in particular cell
      types, among which are neurons. The data show that Dnmt1 is removed from embryonic cells
      before gastrulation to be synthesized again at different levels in different cell types,
      indicating that the concentration of Dnmt1 is critical for the various differentiated cells of
      the developing sea urchin embryo.
AU  - Di Giaimo R
AU  - Locascio A
AU  - Aniello F
AU  - Branno M
AU  - del Gaudio R
AU  - Potenza N
AU  - Geraci G
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 2001 272: 199-208.

PMID- 24810619
VI  - 54
DP  - 2014
TI  - Isolation and partial characterization of bacteriophages infecting Pseudomonas syringae pv. actinidiae, causal agent of kiwifruit bacterial canker.
PG  - 1-12
AB  - The phytopathogen Pseudomonas syringae pv. actinidiae (Psa) is the causal agent of bacterial
      canker of kiwifruit. In the last years, it has caused severe economic losses to Actinidia spp.
      cultivations, mainly in Italy and New Zealand. Conventional strategies adopted did not provide
      adequate control of infection. Phage therapy may be a realistic and safe answer to the urgent
      need for novel antibacterial agents aiming to control this bacterial pathogen. In this study,
      we described the isolation and characterization of two bacteriophages able to specifically
      infect Psa. phiPSA1, a member of the Siphoviridae family, is a temperate phage with a narrow
      host range, a long latency, and a burst size of 178; phiPSA2 is a lytic phage of Podoviridae
      family with a broader host range, a short latency, a burst size of 92 and a higher
      bactericidal activity as determined by the TOD value. The genomic sequence of phiPSA1 has a
      length of 51,090 bp and a low sequence homology with the other siphophages, whereas phiPSA2
      has a length of 40 472 bp with a 98% homology with Pseudomonas putida bacteriophage gh-1. Of
      the two phages examined, phiPSA2 may be considered as a candidate for phage therapy of
      kiwifruit disease, while phiPSA1 seems specific toward the recent outbreak's isolates and
      could be useful for Psa typing.
AU  - Di Lallo G
AU  - Evangelisti M
AU  - Mancuso F
AU  - Ferrante P
AU  - Marcelletti S
AU  - Tinari A
AU  - Superti F
AU  - Migliore L
AU  - D'Addabbo P
AU  - Frezza D
AU  - Scortichini M
AU  - Thaller MC
PT  - Journal Article
TA  - J. Basic Microbiol.
JT  - J. Basic Microbiol.
SO  - J. Basic Microbiol. 2014 54: 1-12.

PMID- 27340072
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of the First KPC-Type Carbapenemase-Positive Proteus mirabilis Strain from a Bloodstream Infection.
PG  - e00607-16
AB  - Sequencing of the blaKPC-positive strain Proteus mirabilis AOUC-001 was performed using both
      the MiSeq and PacBio RS II platforms and yielded a single molecule of
      4,272,433 bp, representing the complete chromosome. Genome analysis showed the
      presence of several acquired resistance determinants, including two copies of
      blaKPC-2 carried on a fragment of a KPC-producing plasmid previously described in
      Klebsiella pneumoniae.
AU  - Di Pilato V
AU  - Chiarelli A
AU  - Boinett CJ
AU  - Riccobono E
AU  - Harris SR
AU  - D'Andrea MM
AU  - Thomson NR
AU  - Rossolini GM
AU  - Giani T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00607-16.

PMID- 23928025
VI  - 69
DP  - 2014
TI  - Characterization of plasmid pAX22, encoding VIM-1 metallo-beta-lactamase, reveals a new putative mechanism of In70 integron mobilization.
PG  - 67-71
AB  - Objectives: VIM-type enzymes are among the most widespread acquired metallo-b-lactamases among
      Gramnegative pathogens. Integron In70 is a class 1 integron that has emerged as a successful
      genetic support for
      blaVIM-1 (one of themostprevalent blaVIM allelic variants) in
      Gram-negativenon-fermenters,andis usually chromosome borne. The objective of this study was to
      characterize plasmid pAX22 from Achromobacter xylosoxidans
      AX22, which represents the only In70-harbouring plasmid known so far, to gather insights into
      the mechanisms of evolution and dissemination of In70-like elements.
      Methods: The complete sequence of pAX22was obtained by pyrosequencing and assembled with Roche
      Newbler software. The draft sequence, completed using a PCR-based strategy, was annotated via
      the BASys tool and compared with known sequences using BLAST algorithms.
      Results: The backbone of pAX22 showed significant similarity with that of pNOR-2000, a
      blaVIM-2-harbouring plasmid from Pseudomonas aeruginosa, and with the TnCP23 transposon. The
      three elements differed from each other mainly by the class 1 integron cassette arrays and by
      some integron-associated structures. In pAX22, In70was associated with a novel putative
      transposon, Tn7017, composed of a defective Tn402-like transposon
      carrying In70 and the ISPa17 insertion sequence.
      Conclusion: Plasmid pAX22 belongs to a lineage of plasmids circulating among Gram-negative
      non-fermenters. In70 was probably acquired by pAX22 by transposition of Tn7017, revealing a
      novel putative mechanism of In70
      mobilization. Our results highlight the potential role that ISPa17couldhave in mobilizing
      defective Tn402-like transposons carrying class 1 integrons.
AU  - Di Pilato V
AU  - Pollini S
AU  - Rossolini GM
PT  - Journal Article
TA  - J. Antimicrob. Chemother.
JT  - J. Antimicrob. Chemother.
SO  - J. Antimicrob. Chemother. 2014 69: 67-71.

PMID- 28087584
VI  - 72
DP  - 2017
TI  - Emergence of Klebsiella variicola positive for NDM-9, a variant of New Delhi metallo-beta-lactamase, in an urban river in South Korea.
PG  - 1063-1067
AB  - Objectives: To examine the presence of pathogenic bacteria carrying New Delhi
      metallo-beta-lactamase in the environment and to characterize the genome
      structures of these strains. Methods: Phenotypic screening of antimicrobial
      susceptibility and WGS were conducted on three Klebsiella variicola strains
      possessing NDM-9 isolated from an urban river. Results: Three
      carbapenem-resistant K. variicola isolated from Gwangju tributary were found to
      possess bla NDM-9 genes. Antimicrobial susceptibility testing indicated
      resistance of these strains to aminoglycosides, carbapenems, cephems, folate
      pathway inhibitors, fosfomycin and penicillins, but susceptibility to
      fluoroquinolones, phenicols, tetracyclines and miscellaneous agents. WGS revealed
      that the 108 kb IncFII(Y)-like plasmids carry bla NDM-9 sandwiched between IS 15
      for the GJ1 strain, IS 26 for the GJ2 strain, IS 15D1 for the GJ3 strain and IS
      Vsa3 , and further bracketed by IS 26 and Tn AS3 along with the mercury
      resistance operon upstream and the class 1 integron composed of gene cassettes of
      aadA2 , dfrA12 and sul1 downstream. An aph(3')-Ia gene conferring resistance to
      aminoglycosides is located after the integrons. Chromosomally encoded bla LEN-13
      , fosA , aqxA and oqxB genes, as well as plasmid-mediated bla TEM-1B and bla
      CTX-M-65 encoding ESBL, ant(3')-Ia and mph (A) genes, were also identified.
      Conclusions: The findings of the present study provide us with the information
      that NDM-9 has been spreading into the environment. Dissemination of NDM-9 in the
      environment has raised a health risk alarm as this variant of NDM carries MDR
      genes with highly transferable mobile genetic elements, increasing the
      possibility of resistance gene transfer among microorganisms in the environment.
AU  - Di DY
AU  - Jang J
AU  - Unno T
AU  - Hur HG
PT  - Journal Article
TA  - J. Antimicrob. Chemother.
JT  - J. Antimicrob. Chemother.
SO  - J. Antimicrob. Chemother. 2017 72: 1063-1067.

PMID- 29025952
VI  - 5
DP  - 2017
TI  - Permanent Draft Genome Sequences for Mesorhizobium sp. Strains LCM 4576, LCM 4577, and ORS3428, Salt-Tolerant, Nitrogen-Fixing Bacteria Isolated from  Senegalese Soils.
PG  - e01154-17
AB  - The genus Mesorhizobium contains many species that are able to form nitrogen-fixing nodules on
      plants of the legume family. Here, we report the draft
      genome sequences for three Mesorhizobium strains. The genome sizes of strains LCM
      4576, LCM 4577, and ORS3428 were 7.24, 7.02, and 6.55 Mbp, respectively.
AU  - Diagne N
AU  - Swanson E
AU  - Pesce C
AU  - Fall F
AU  - Diouf F
AU  - Bakhoum N
AU  - Fall D
AU  - Faye MN
AU  - Oshone R
AU  - Simpson S
AU  - Morris K
AU  - Thomas WK
AU  - Moulin L
AU  - Diouf D
AU  - Tisa LS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01154-17.

PMID- 28385842
VI  - 5
DP  - 2017
TI  - Permanent Draft Genome Sequence of Ensifer sp. Strain LCM 4579, a Salt-Tolerant,  Nitrogen-Fixing Bacterium Isolated from Senegalese Soil.
PG  - e00117-17
AB  - The genus Ensifer (formerly Sinorhizobium) contains many species able to form nitrogen-fixing
      nodules on plants of the legume family. Here, we report the
      6.1-Mb draft genome sequence of Ensifer sp. strain LCM 4579, with a G+C content
      of 62.4% and 5,613 candidate protein-encoding genes.
AU  - Diagne N
AU  - Swanson E
AU  - Pesce C
AU  - Fall F
AU  - Diouf F
AU  - Bakhoum N
AU  - Fall D
AU  - Ndigue FM
AU  - Oshone R
AU  - Simpson S
AU  - Morris K
AU  - Thomas WK
AU  - Moulin L
AU  - Diouf D
AU  - Tisa LS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00117-17.

PMID- 28473386
VI  - 5
DP  - 2017
TI  - Permanent Draft Genome Sequence of Rhizobium sp. Strain LCM 4573, a Salt-Tolerant, Nitrogen-Fixing Bacterium Isolated from Senegalese Soils.
PG  - e00285-17
AB  - The genus Rhizobium contains many species that are able to form nitrogen-fixing nodules on
      plants of the legume family. Here, we report the 5.5-Mb draft genome
      sequence of the salt-tolerant Rhizobium sp. strain LCM 4573, which has a G+C
      content of 61.2% and 5,356 candidate protein-encoding genes.
AU  - Diagne N
AU  - Swanson E
AU  - Pesce C
AU  - Fall F
AU  - Diouf F
AU  - Bakhoum N
AU  - Fall D
AU  - Ndigue FM
AU  - Oshone R
AU  - Simpson S
AU  - Morris K
AU  - Thomas WK
AU  - Moulin L
AU  - Diouf D
AU  - Tisa LS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00285-17.

PMID- 22275102
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Marine Bacterium Vibrio campbellii DS40M4, Isolated from Open Ocean Water.
PG  - 904
AB  - Vibrio sp. strain DS40M4 is a marine bacterium that was isolated from open ocean water. In
      this work, using genomic taxonomy, we were able to
      classify this bacterium as V. campbellii. Our genomic analysis revealed
      that V. campbellii DS40M4 harbors genes related to iron transport,
      virulence, and environmental fitness, such as those encoding anguibactin
      and vanchrobactin biosynthesis proteins, type II, III, IV, and VI
      secretion systems, and proteorhodopsin.
AU  - Dias GM
AU  - Thompson CC
AU  - Fishman B
AU  - Naka H
AU  - Haygood MG
AU  - Crosa JH
AU  - Thompson FL
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 904.

PMID- 26950327
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequence of Corynebacterium pseudotuberculosis Strain 226, Isolated  from the Abscess of a Goat in California.
PG  - e00038-16
AB  - Corynebacterium pseudotuberculosis is the etiological agent of a caseous lymphadenitis
      disease. Herein, we present the first complete genome sequencing of
      C. pseudotuberculosis strain 226, isolated from an abscess of the sub-iliac lymph
      node of a goat from California (USA). The genome contains 2,138 coding sequences
      (CDSs), 12 rRNAs, 49 tRNAs, and 72 pseudogenes.
AU  - Dias LM
AU  - Alves JT
AU  - Veras AA
AU  - Barauna RA
AU  - Sa PH
AU  - Spier S
AU  - Edman JM
AU  - Guimaraes LC
AU  - Rocha FS
AU  - Ramos RT
AU  - Azevedo V
AU  - Silva A
AU  - Carneiro AR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00038-16.

PMID- Not included in PubMed...
VI  - 135
DP  - 1989
TI  - Isolation and characterization of actinophages infecting Streptomyces species and their interaction with host restriction-modification systems.
PG  - 1847-1856
AB  - Nine different phages, PhiA1 to PhiA9, were isolated from soil samples on
      Streptomyces antibioticus ATCC 11891, a strain which produces the macrolide
      antibiotic oleandomycin.  Each phage displayed a different host-range which did
      not extend beyond Streptomyces species.  Host-range was mainly limited by
      adsorption specificity and host-controlled restriction-modification systems.
      All the phages except PhiA3 and PhiA9 formed turbid plaques on S. antibioticus,
      but did not lysogenize this host.  However, three of the phages (PhiA5, PhiA7
      and PhiA8) were identified as temperate, since they were able to lysogenize
      other Streptomyces strains.  All of the phages were morphologically similar and
      belonged to group B of Bradley's classification.  They had polyhedral heads and
      long, non-contractile tails.  PhiA5, PhiA6 and PhiA7 had a base plate at the
      terminal end of the tail.  Analysis with restriction endonucleases indicated
      that the nine phages contained double-stranded DNA.  Hybridization studies
      between the phage genomes, together with results on genome structure, allowed
      classification of the phages into five groups: (I) PhiA2, PhiA4 and PhiA9, (II)
      PhiA3 and PhiA8, (III) PhiA7, (IV) PhiA5 and PhiA6, and (V) PhiA1.
AU  - Diaz LA
AU  - Hardisson C
AU  - Rodicio MR
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1989 135: 1847-1856.

PMID- 29773634
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Ochrobactrum haematophilum FI11154, Isolated from Kunu-Zaki, a Nigerian Millet-Based Fermented Food.
PG  - e00428-18
AB  - Ochrobactrum haematophilum FI11154 was isolated from kunu-zaki, a Nigerian traditional
      fermented millet-based food. Here, we present the first complete
      genome sequence of this species. The genome consists of five replicons and
      contains genes related to iron uptake and phosphatase activities.
AU  - Diaz M
AU  - Wegmann U
AU  - Akinyemi N
AU  - Oguntoyinbo FA
AU  - Sayavedra L
AU  - Mayer MJ
AU  - Narbad A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00428-18.

PMID- 28410368
VI  - 12
DP  - 2017
TI  - Comprehensive bioinformatics analysis of Mycoplasma pneumoniae genomes to investigate underlying population structure and type-specific determinants.
PG  - E0174701
AB  - Mycoplasma pneumoniae is a significant cause of respiratory illness worldwide.
      Despite a minimal and highly conserved genome, genetic diversity within the
      species may impact disease. We performed whole genome sequencing (WGS) analysis
      of 107 M. pneumoniae isolates, including 67 newly sequenced using the Pacific
      BioSciences RS II and/or Illumina MiSeq sequencing platforms. Comparative genomic
      analysis of 107 genomes revealed >3,000 single nucleotide polymorphisms (SNPs) in
      total, including 520 type-specific SNPs. Population structure analysis supported
      the existence of six distinct subgroups, three within each type. We developed a
      predictive model to classify an isolate based on whole genome SNPs called against
      the reference genome into the identified subtypes, obviating the need for genome
      assembly. This study is the most comprehensive WGS analysis for M. pneumoniae to
      date, underscoring the power of combining complementary sequencing technologies
      to overcome difficult-to-sequence regions and highlighting potential differential
      genomic signatures in M. pneumoniae.
AU  - Diaz MH
AU  - Desai HP
AU  - Morrison SS
AU  - Benitez AJ
AU  - Wolff BJ
AU  - Caravas J
AU  - Read TD
AU  - Dean D
AU  - Winchell JM
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2017 12: E0174701.

PMID- 29276571
VI  - 12
DP  - 2017
TI  - Draft genome sequence of Dethiosulfovibrio salsuginis DSM 21565(T) an anaerobic,  slightly halophilic bacterium isolated from a Colombian saline spring.
PG  - 86
AB  - A bacterium belonging to the phylum Synergistetes, genus Dethiosulfovibrio was isolated in
      2007 from a saline spring in Colombia. Dethiosulfovibrio salsuginis
      USBA 82(T) (DSM 21565(T)= KCTC 5659(T)) is a mesophilic, strictly anaerobic,
      slightly halophilic, Gram negative bacterium with a diderm cell envelope. The
      strain ferments peptides, amino acids and a few organic acids. Here we present
      the description of the complete genome sequencing and annotation of the type
      species Dethiosulfovibrio salsuginis USBA 82(T). The genome consisted of 2.68 Mbp
      with a 53.7% G + C. A total of 2609 genes were predicted and of those, 2543 were
      protein coding genes and 66 were RNA genes. We detected in USBA 82(T) genome six
      Synergistetes conserved signature indels (CSIs), specific for Jonquetella,
      Pyramidobacter and Dethiosulfovibrio. The genome of D. salsuginis contained, as
      expected, genes related to amino acid transport, amino acid metabolism and
      thiosulfate reduction. These genes represent the major gene groups of
      Synergistetes, related with their phenotypic traits, and interestingly, 11.8% of
      the genes in the genome belonged to the amino acid fermentation COG category. In
      addition, we identified in the genome some ammonification genes such as nitrate
      reductase genes. The presence of proline operon genes could be related to de novo
      synthesis of proline to protect the cell in response to high osmolarity. Our
      bioinformatics workflow included antiSMASH and BAGEL3 which allowed us to
      identify bacteriocins genes in the genome.
AU  - Diaz-Cardenas C
AU  - Lopez G
AU  - Alzate-Ocampo JD
AU  - Gonzalez LN
AU  - Shapiro N
AU  - Woyke T
AU  - Kyrpides NC
AU  - Restrepo S
AU  - Baena S
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 86.

PMID- 25359919
VI  - 2
DP  - 2014
TI  - Genome Sequence of Vibrio cholerae Strain O1 Ogawa El Tor, Isolated in Mexico, 2013.
PG  - e01123-14
AB  - We present the draft genome sequence of Vibrio cholerae InDRE 3140 recovered in 2013 during a
      cholera outbreak in Mexico. The genome showed the Vibrio 7th
      pandemic islands VSP1 and VSP2, the pathogenic islands VPI-1 and VPI-2, the
      integrative and conjugative element SXT/R391 (ICE-SXT), and both prophages CTXphi
      and RS1phi.
AU  - Diaz-Quinonez JA
AU  - Hernandez-Monroy I
AU  - Lopez-Martinez I
AU  - Ortiz-Alcantara J
AU  - Gonzalez-Duran E
AU  - Ruiz-Matus C
AU  - Kuri-Morales P
AU  - Ramirez-Gonzalez JE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01123-14.

PMID- 29437094
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Anaplasma phagocytophilum, A. marginale, and A. ovis Isolates from Different Hosts.
PG  - e01503-17
AB  - Here, we report the draft genome sequences of isolates of Anaplasma phagocytophilum, Anaplasma
      marginale, and Anaplasma ovis The genomes of A.
      phagocytophilum (human), A. marginale (cattle), and A. ovis (goat) isolates from
      the United States were sequenced and characterized. This is the first report of
      an A. ovis genome sequence.
AU  - Diaz-Sanchez S
AU  - Hernandez-Jarguin A
AU  - Fernandez-de-Mera IG
AU  - Alberdi P
AU  - Zweygarth E
AU  - Gortazar C
AU  - de la Fuente J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01503-17.

PMID- 26067968
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of the Linear Plasmid pJD12 Hosted by Micrococcus sp. D12, Isolated from a High-Altitude Volcanic Lake in Argentina.
PG  - e00627-15
AB  - The linear plasmid pDJ12 from Micrococcus D12, isolated from the high-altitude volcanic
      Diamante Lake in the northwest of Argentina, was completely sequenced
      and annotated. It is noteworthy that the element is probably conjugative and
      harbors genes potentially instrumental in coping with stress conditions that
      prevail in such an extreme environment.
AU  - Dib JR
AU  - Angelov A
AU  - Liebl W
AU  - Dobber J
AU  - Voget S
AU  - Schuldes J
AU  - Gorriti M
AU  - Farias ME
AU  - Meinhardt F
AU  - Daniel R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00627-15.

PMID- 25792053
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Thauera sp. Strain SWB20, Isolated from a Singapore Wastewater Treatment Facility Using Gel Microdroplets.
PG  - e00132-15
AB  - We report here the genome sequence of Thauera sp. strain SWB20, isolated from a Singaporean
      wastewater treatment facility using gel microdroplets (GMDs) and
      single-cell genomics (SCG). This approach provided a single clonal microcolony
      that was sufficient to obtain a 4.9-Mbp genome assembly of an ecologically
      relevant Thauera species.
AU  - Dichosa AE et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00132-15.

PMID- 19698104
VI  - 10
DP  - 2009
TI  - Community-wide analysis of microbial genome sequence signatures.
PG  - R85
AB  - BACKGROUND: Analyses of DNA sequences from cultivated microorganisms have
      revealed genome-wide, taxa-specific nucleotide compositional characteristics,
      referred to as genome signatures. These signatures have far-reaching implications
      for understanding genome evolution and potential application in classification of
      metagenomic sequence fragments. However, little is known regarding the
      distribution of genome signatures in natural microbial communities or the extent
      to which environmental factors shape them. RESULTS: We analyzed metagenomic
      sequence data from two acidophilic biofilm communities, including composite
      genomes reconstructed for nine archaea, three bacteria, and numerous associated
      viruses, as well as thousands of unassigned fragments from strain variants and
      low-abundance organisms. Genome signatures, in the form of tetranucleotide
      frequencies analyzed by emergent self-organizing maps, segregated sequences from
      all known populations sharing < 50 to 60% average amino acid identity and
      revealed previously unknown genomic clusters corresponding to low-abundance
      organisms and a putative plasmid. Signatures were pervasive genome-wide. Clusters
      were resolved because intra-genome differences resulting from translational
      selection or protein adaptation to the intracellular (pH approximately 5) versus
      extracellular (pH approximately 1) environment were small relative to
      inter-genome differences. We found that these genome signatures stem from
      multiple influences but are primarily manifested through codon composition, which
      we propose is the result of genome-specific mutational biases. CONCLUSIONS: An
      important conclusion is that shared environmental pressures and interactions
      among coevolving organisms do not obscure genome signatures in acid mine drainage
      communities. Thus, genome signatures can be used to assign sequence fragments to
      populations, an essential prerequisite if metagenomics is to provide ecological
      and biochemical insights into the functioning of microbial communities.
AU  - Dick GJ
AU  - Andersson AF
AU  - Baker BJ
AU  - Simmons SL
AU  - Thomas BC
AU  - Yelton AP
AU  - Banfield JF
PT  - Journal Article
TA  - Genome Biology
JT  - Genome Biology
SO  - Genome Biology 2009 10: R85.

PMID- 18344346
VI  - 74
DP  - 2008
TI  - Genomic insights into Mn(II) oxidation by the marine alphaproteobacterium Aurantimonas sp. strain SI85-9A1.
PG  - 2646-2658
AB  - Microbial Mn(II) oxidation has important biogeochemical consequences in
      marine, freshwater, and terrestrial environments, but many aspects of the
      physiology and biochemistry of this process remain obscure. Here, we
      report genomic insights into Mn(II) oxidation by the marine
      alphaproteobacterium Aurantimonas sp. strain SI85-9A1, isolated from the
      oxic/anoxic interface of a stratified fjord. The SI85-9A1 genome harbors
      the genetic potential for metabolic versatility, with genes for
      organoheterotrophy, methylotrophy, oxidation of sulfur and carbon
      monoxide, the ability to grow over a wide range of O(2) concentrations
      (including microaerobic conditions), and the complete Calvin cycle for
      carbon fixation. Although no growth could be detected under autotrophic
      conditions with Mn(II) as the sole electron donor, cultures of SI85-9A1
      grown on glycerol are dramatically stimulated by addition of Mn(II),
      suggesting an energetic benefit from Mn(II) oxidation. A putative Mn(II)
      oxidase is encoded by duplicated multicopper oxidase genes that have a
      complex evolutionary history including multiple gene duplication, loss,
      and ancient horizontal transfer events. The Mn(II) oxidase was most
      abundant in the extracellular fraction, where it cooccurs with a putative
      hemolysin-type Ca(2+)-binding peroxidase. Regulatory elements governing
      the cellular response to Fe and Mn concentration were identified, and 39
      targets of these regulators were detected. The putative Mn(II) oxidase
      genes were not among the predicted targets, indicating that regulation of
      Mn(II) oxidation is controlled by other factors yet to be identified.
      Overall, our results provide novel insights into the physiology and
      biochemistry of Mn(II) oxidation and reveal a genome specialized for life
      at the oxic/anoxic interface.
AU  - Dick GJ
AU  - Podell S
AU  - Johnson HA
AU  - Rivera-Espinoza Y
AU  - Bernier-Latmani R
AU  - McCarthy JK
AU  - Torpey JW
AU  - Clement BG
AU  - Gaasterland T
AU  - Tebo BM
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2008 74: 2646-2658.

PMID- 6273591
VI  - 149
DP  - 1981
TI  - Structure of a B-DNA dodecamer  II.  Influence of base sequence on helix structure.
PG  - 761-786
AB  - Detailed examination of the structure of the B-DNA dodecamer
      C-G-C-G-A-A-T-T-C-G-C-G, obtained by single-crystal X-ray analysis (Drew et
      al., 1981), reveals that the local helix parameters, twist, tilt and roll, are
      much more strongly influenced by base sequence than by crystal packing or any
      other external forces.  The central EcoRI restriction endonuclease recognition
      site, G-A-A-T-T-C, is a B helix with an average of 9.8 base-pairs per turn.  It
      is flanked on either side by single base-pair steps having aspects of an A-like
      helix character.  The dodecamer structure suggests several general principles,
      whose validity must be tested by other B-DNA analyses.  (1) When an external
      bending moment is applied to a B-DNA double helix, it bends smoothly, without
      kinks or breaks, and with relatively little effect on local helix parameters.
      (2) Purine-3', 5'-pyrimidine steps open their base planes towards the major
      groove, pyrimidine-purine steps open toward the minor groove, and homopolymer
      (Pur-Pur, Pyr-Pyr) steps resist rolling in either direction.  This behavior is
      related to the preference of pyrimidines for more negative glycosyl torsion
      angles.  (3) CpG steps have smaller helical twist angles than do GpC, as though
      in compensation for their smaller intrinsic base overlap.  Data on A-T steps
      are insufficient for generalization.  (4) G-C base-pairs have smaller propellor
      twist than A-T, and this arises mainly from interstrand base overlap rather
      than the presence of the third hydrogen bond.  (5) DNAase I cuts preferentially
      at positions of high helical twist, perhaps because of increased exposure of
      the backbone to attack.  The correlation of the digestion patterns in solution
      and helical twist in the crystal argues for the essential identity of the helix
      structure in the two environments.  (6) In the two places where the sequence
      TpCpG occurs, the C slips from under T in order to stack more efficiently over
      G.  At the paired bases of this CpG step, the G and C are tilted so the angle
      between base planes is splayed out to the outside of the helix.  This TpC is
      the most favored cutting site for DNAse I by a factor of 4-5 (Lomonossoff et
      al., 1981).  (7) The EcoRI restriction endonuclease and methylase both appear
      to prefer a cutting site of the type purine-purine-A-T-T-pyrimidine, involving
      two adjacent homopolymer triplets, and this may be a consequence of the
      relative stiffness of homopolymer base-stacking observed in the dodecamer.
AU  - Dickerson RE
AU  - Drew HR
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1981 149: 761-786.

PMID- 1326121
VI  - 257
DP  - 1992
TI  - Lithuanian biochemist builds enzyme empire.
PG  - 1473-1474
AB  - Vilnius -If you like to browse through laboratory catalogs looking for the latest equipment
      and reagents, you might have come across a surprising entry in the most recent offering from
      New England Biolabs.  There, on page 46, you'll find a whole set of new restriction enzymes
      -the enzymes that chop up DNA and are a vital part of every molecular biologist's toolbox.
      The surprise: The enzymes are all labeled "Made in Lithuania".  Lithuania? How could a small
      Baltic state, independent for less than a year, compete with hot shot Western biotech
      companies in supplying enzymes to the United States? Ask Rich Roberts, the former Cold Spring
      Harbor Laboratory molecular biologist who is now director of research for New England Biolabs
      and he will answer in a word: "Janulaitis".  Vidas Janulaitis (pronounced Yanoo-LITEis), he
      will tell you, is professor of biochemistry a the University of Vilnius, head of the Institute
      of Applied Enzymology -and creator of one of the world's largest collections of restriction
      enzymes, with more than 100 on offer.  He also appears to be the first successful
      biotechnology entrepreneur to emerge from the former Soviet Union -and New England Biolabs'
      competitors are well aware of his talents.  "Formidable", is how Jeremy Walker of Amersham
      International describes Janulaitis' contribution to the number of new restriction enzymes
      marketed each year.
AU  - Dickman S
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1992 257: 1473-1474.

PMID- 25768799
VI  - 11
DP  - 2015
TI  - The role of china in the global spread of the current cholera pandemic.
PG  - E1005072
AB  - Epidemics and pandemics of cholera, a severe diarrheal disease, have occurred
      since the early 19th century and waves of epidemic disease continue today.
      Cholera epidemics are caused by individual, genetically monomorphic lineages of
      Vibrio cholerae: the ongoing seventh pandemic, which has spread globally since
      1961, is associated with lineage L2 of biotype El Tor. Previous genomic studies
      of the epidemiology of the seventh pandemic identified three successive
      sub-lineages within L2, designated waves 1 to 3, which spread globally from the
      Bay of Bengal on multiple occasions. However, these studies did not include
      samples from China, which also experienced multiple epidemics of cholera in
      recent decades. We sequenced the genomes of 71 strains isolated in China between
      1961 and 2010, as well as eight from other sources, and compared them with 181
      published genomes. The results indicated that outbreaks in China between 1960 and
      1990 were associated with wave 1 whereas later outbreaks were associated with
      wave 2. However, the previously defined waves overlapped temporally, and are an
      inadequate representation of the shape of the global genealogy. We therefore
      suggest replacing them by a series of tightly delineated clades. Between 1960 and
      1990 multiple such clades were imported into China, underwent further
      microevolution there and then spread to other countries. China was thus both a
      sink and source during the pandemic spread of V. cholerae, and needs to be
      included in reconstructions of the global patterns of spread of cholera.
AU  - Didelot X
AU  - Pang B
AU  - Zhou Z
AU  - McCann A
AU  - Ni P
AU  - Li D
AU  - Achtman M
AU  - Kan B
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2015 11: E1005072.

PMID- Not included in PubMed...
VI  - 28
DP  - 1988
TI  - Cell localization of EcoRI endonuclease in Escherichia coli K-12.
PG  - 468-470
AB  - Cell compartmentation of EcoRI endonuclease was analyzed using either parental
      or tolA excretory strains of Escherichia coli.  Cells were subjected to various
      fractionation procedures such as osmotic shock or spheroplast formation.  Our
      results showed that EcoRI activity was almost entirely recovered into
      cytoplasmic fractions and consequently was not released into the extracellular
      medium by a tolA mutant.  These results did not support previous reports
      suggesting a periplasmic location for the EcoRI enzyme and did not allow to
      develop a simple method for EcoRI purification from culture supernatants of
      excretory mutants.
AU  - Didier S
AU  - Lazzaroni JC
AU  - Portalier R
PT  - Journal Article
TA  - Appl. Microbiol. Biotechnol.
JT  - Appl. Microbiol. Biotechnol.
SO  - Appl. Microbiol. Biotechnol. 1988 28: 468-470.

PMID- 
VI  - 
DP  - 2010
TI  - The structural basis of DNA recognition and base extrusion by a DNA cytosine-5 methyltransferase M.HaeIII.
PG  - 
AB  - The goal of this study is to elucidate the mechanism of sequence specific DNA recognition and
      base extrusion by DNA cytosine-5 methyltransferase from Haemophilus aegyptius M.Haelll. We
      have solved the crystal structure of the C71S mutant of M.Haelll in complex with the substrate
      DNA at 2.4A resolution (InC below for brevity). For the first time an X-ray structure reveals
      a fully intrahelical target cytosine
      poised for extrusion by a cytosine-5 methyltransferase. The target cytosine
      is destabilized, having lost most of its stacking interactions with both neighbouring bases
      and making longer hydrogen bonds with the complementary guanine. In addition the protein
      competes for Watson-Crick hydrogen bonding of the target base pair.  Both the protein and the
      DNA conformations are remarkably different from those in the structure where the target
      cytosine is extrahelical (ExC for brevity) [57]. In the ExC structure the cytosine 3 ' of the
      target base is the one forming a base pair with the guanine of the target base pair, whereas
      in the InC structure the bases within the
      recognition sequence stay correctly paired. The conformation of the DNA backbone 3' to the
      target cytosine changes significantly as well - it shifts further away from the protein. The
      catalytic loop of M.Haelll (residues 71-89) is retracted away from the DNA as well. The
      results suggest that M.Haelll actively participates in base flipping.  It destabilizes the
      target base by altering both stacking and Watson-Crick hydrogen bonding - two fundamental
      interactions that keep DNA bases intrahelical.  In order to elucidate the role of the
      intercalating residue Ile-221 in base extrusion,
      a glycine mutant was constructed. Its structure in complex with the specific DNA has been
      determined using X-ray crystallography. This structure is essentially identical to the ExC,
      suggesting that the extrahelical state, observed in ExC, can be achieved in the absence of the
      DNA helix stabilization provided by Ile-221.
AU  - Didovyk A
PT  - Journal Article
TA  - Ph.D. Thesis, Harvard University, USA
JT  - Ph.D. Thesis, Harvard University, USA
SO  - Ph.D. Thesis, Harvard University, USA 2010 : .

PMID- 23012373
VI  - 287
DP  - 2012
TI  - Structural Origins of DNA Target Selection and Nucleobase Extrusion by a DNA Cytosine Methyltransferase.
PG  - 40099-40105
AB  - Epigenetic methylation of cytosine residues in DNA is an essential element of genome
      maintenance and function in organisms ranging from
      bacteria to humans. DNA 5-cytosine methyltransferase enzymes (DCMTases)
      catalyze cytosine methylation via reaction intermediates in which the
      DNA is drastically remodeled, with the target cytosine residue extruded
      from the DNA helix and plunged into the active site pocket of the
      enzyme. We have determined a crystal structure of M.HaeIII DCMTase in
      complex with its DNA substrate at a previously unobserved state, prior
      to extrusion of the target cytosine and frameshifting of the DNA
      recognition sequence. The structure reveals that M.HaeIII selects the
      target cytosine and destabilizes its base-pairing through a precise,
      focused, and coordinated assault on the duplex DNA, which isolates the
      target cytosine from its nearest neighbors and thereby facilitates its
      extrusion from DNA.
AU  - Didovyk A
AU  - Verdine GL
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2012 287: 40099-40105.

PMID- 28183771
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Arcobacter sp. Strain LFT 1.7 Isolated from Great Scallop (Pecten maximus) Larvae.
PG  - e01617-16
AB  - Arcobacter sp. strain LFT 1.7 was isolated from great scallop (Pecten maximus) larvae.
      Analysis of the 16S rRNA gene sequence showed that strain LFT 1.7 formed
      an independent lineage in the genus Arcobacter The draft genome of LFT 1.7 was
      sequenced to determine the taxonomic position and ecological function of this
      strain.
AU  - Dieguez AL
AU  - Romalde JL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01617-16.

PMID- 28153896
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Neptuniibacter sp. Strains LFT 1.8 and ATR 1.1.
PG  - e01541-16
AB  - We present the draft genomes of two strains previously identified as Neptuniibacter sp. LFT
      1.8 (= CECT 8936 = DSM 100781) and ATR 1.1 (= CECT 8938 =
      DSM 100783) isolated from larvae of great scallops (Pecten maximus) and seawater,
      respectively. Both strains surely constitute two novel species in this genus,
      with putative applications for aromatic compound degradation.
AU  - Dieguez AL
AU  - Romalde JL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01541-16.

PMID- 3172240
VI  - 202
DP  - 1988
TI  - DNA curvature in native and modified EcoRI recognition sites and possible influence upon the endonuclease cleavage reaction.
PG  - 823-834
AB  - The ligation of a decadeoxynucleotide containing the EcoRI recognition site
      forms a series of multimers which appear to be curved based on observed
      anomalous gel migration in polyacrylamide gels.  The degree of DNA curvature
      present in the recognition sequence, based upon the observed migration anomaly,
      can be altered by modifications to the purine functional groups at the 2- and
      6-positions.  Deletion of the guanine 2-amino group, occurring in the minor
      groove of the B-DNA helix, is most effective in increasing the observed DNA
      curvature.  Conversely, the displacement of an amino group from the major
      groove to the minor groove eliminates curvature.  DNA curvature is also
      modulated by the exocyclic group at the purine 6-position with decreasing
      curvature observed when changing the amino group to a carbonyl or proton
      substitute.
AU  - Diekmann S
AU  - McLaughlin LW
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1988 202: 823-834.

PMID- 23071100
VI  - 30
DP  - 2013
TI  - The Rhizome of the Multidrug-Resistant Enterobacter aerogenes Genome Reveals How New 'Killer Bugs' Are Created because of a Sympatric Lifestyle.
PG  - 369-383
AB  - Here, we sequenced the 5,419,609 bp circular genome of an Enterobacter aerogenes
      clinical isolate that killed a patient and was resistant to almost all current
      antibiotics (except gentamicin) commonly used to treat Enterobacterial
      infections, including colistin. Genomic and phylogenetic analyses explain the
      discrepancies of this bacterium and show that its core genome originates from
      another genus, Klebsiella. Atypical characteristics of this bacterium (i.e.,
      motility, presence of ornithine decarboxylase, and lack of urease activity) are
      attributed to genomic mosaicism, by acquisition of additional genes, such as the
      complete 60,582 bp flagellar assembly operon acquired "en bloc" from the genus
      Serratia. The genealogic tree of the 162,202 bp multidrug-resistant conjugative
      plasmid shows that it is a chimera of transposons and integrative conjugative
      elements from various bacterial origins, resembling a rhizome. Moreover, we
      demonstrate biologically that a G53S mutation in the pmrA gene results in
      colistin resistance. E. aerogenes has a large RNA population comprising 8 rRNA
      operons and 87 cognate tRNAs that have the ability to translate transferred genes
      that use different codons, as exemplified by the significantly different codon
      usage between genes from the core genome and the "mobilome." On the basis of our
      findings, the evolution of this bacterium to become a "killer bug" with new
      genomic repertoires was from three criteria that are "opportunity, power, and
      usage" to indicate a sympatric lifestyle: "opportunity" to meet other bacteria
      and exchange foreign sequences since this bacteria was similar to sympatric
      bacteria; "power" to integrate these foreign sequences such as the acquisition of
      several mobile genetic elements (plasmids, integrative conjugative element,
      prophages, transposons, flagellar assembly system, etc.) found in his genome; and
      "usage" to have the ability to translate these sequences including those from
      rare codons to serve as a translator of foreign languages.
AU  - Diene SM
AU  - Merhej V
AU  - Henry M
AU  - El Filali A
AU  - Roux V
AU  - Robert C
AU  - Azza S
AU  - Gavory F
AU  - Barbe V
AU  - La Scola B
AU  - Raoult D
AU  - Rolain JM
PT  - Journal Article
TA  - Mol. Biol. Evol.
JT  - Mol. Biol. Evol.
SO  - Mol. Biol. Evol. 2013 30: 369-383.

PMID- 23661480
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Dietzia sp. Strain UCD-THP (Phylum Actinobacteria).
PG  - e00197-13
AB  - Here, we present the draft genome sequence of an actinobacterium, Dietzia sp. strain UCD-THP,
      isolated from a residential toilet handle. The assembly contains
      3,915,613 bp. The genome sequences of only two other Dietzia species have been
      published, those of Dietzia alimentaria and Dietzia cinnamea.
AU  - Diep AL
AU  - Lang JM
AU  - Darling AE
AU  - Eisen JA
AU  - Coil DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00197-13.

PMID- 16517273
VI  - 367
DP  - 2006
TI  - Complete genome sequence of USA300, an epidemic clone of community-acquired meticillin-resistant Staphylococcus aureus.
PG  - 731-739
AB  - BACKGROUND: USA300, a clone of meticillin-resistant Staphylococcus aureus, is a major source
      of community-acquired infections in the USA, Canada, and
      Europe. Our aim was to sequence its genome and compare it with those of
      other strains of S aureus to try to identify genes responsible for its
      distinctive epidemiological and virulence properties. METHODS: We
      ascertained the genome sequence of FPR3757, a multidrug resistant USA300
      strain, by random shotgun sequencing, then compared it with the sequences
      of ten other staphylococcal strains. FINDINGS: Compared with closely
      related S aureus, we noted that almost all of the unique genes in USA300
      clustered in novel allotypes of mobile genetic elements. Some of the
      unique genes are involved in pathogenesis, including Panton-Valentine
      leucocidin and molecular variants of enterotoxin Q and K. The most
      striking feature of the USA300 genome is the horizontal acquisition of a
      novel mobile genetic element that encodes an arginine deiminase pathway
      and an oligopeptide permease system that could contribute to growth and
      survival of USA300. We did not detect this element, termed arginine
      catabolic mobile element (ACME), in other S aureus strains. We noted a
      high prevalence of ACME in S epidermidis, suggesting not only that ACME
      transfers into USA300 from S epidermidis, but also that this element
      confers a selective advantage to this ubiquitous commensal of the human
      skin. INTERPRETATION: USA300 has acquired mobile genetic elements that
      encode resistance and virulence determinants that could enhance fitness
      and pathogenicity.
AU  - Diep BA
AU  - Gill SR
AU  - Chang RF
AU  - Phan TH
AU  - Chen JH
AU  - Davidson MG
AU  - Lin F
AU  - Lin J
AU  - Carleton HA
AU  - Mongodin EF
AU  - Sensabaugh GF
AU  - Perdreau-Remington F
PT  - Journal Article
TA  - Lancet
JT  - Lancet
SO  - Lancet 2006 367: 731-739.

PMID- 22241781
VI  - 40
DP  - 2012
TI  - The rotation-coupled sliding of EcoRV.
PG  - 4064-4070
AB  - It has been proposed that certain type II restriction enzymes (REs), such as EcoRV, track the
      helical pitch of DNA as they diffuse along DNA, a so-called
      rotation-coupled sliding. As of yet, there is no direct experimental observation
      of this phenomenon, but mounting indirect evidence gained from single-molecule
      imaging of RE-DNA complexes support the hypothesis. We address this issue by
      conjugating fluorescent labels of varying size (organic dyes, proteins and
      quantum dots) to EcoRV, and by fusing it to the engineered Rop protein scRM6.
      Single-molecule imaging of these modified EcoRVs sliding along DNA provides us
      with their linear diffusion constant (D(1)), revealing a significant size
      dependency. To account for the dependence of D(1) on the size of the EcoRV label,
      we have developed four theoretical models describing different types of motion
      along DNA and find that our experimental results are best described by
      rotation-coupled sliding of the protein. The similarity of EcoRV to other type II
      REs and DNA binding proteins suggests that this type of motion could be widely
      preserved in other biological contexts.
AU  - Dikic J
AU  - Menges C
AU  - Clarke S
AU  - Kokkinidis M
AU  - Pingoud A
AU  - Wende W
AU  - Desbiolles P
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: 4064-4070.

PMID- 2854808
VI  - 74
DP  - 1988
TI  - Genetic dissection of the methylcytosine-specific restriction system mcrB of Escherichia coli K-12.
PG  - 23-24
AB  - Meeting Abstract
AU  - Dila D
AU  - Raleigh EA
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 23-24.

PMID- 2203735
VI  - 172
DP  - 1990
TI  - Genetic and sequence organization of the mcrBC locus of Escherichia coli K-12.
PG  - 4888-4900
AB  - The mcrB (rglB) locus of Escherichia coli K-12 mediates sequence-specific restriction of
      cytosine-modified DNA.  Genetic and sequence analysis shows that the locus actually comprises
      two genes, mcrB and mcrC.  We show here that in vivo, McrC modifies the specificity of McrB
      restriction by expanding the range of modified sequences restricted.  That is, the sequences
      sensitive to McrB+-dependent restriction can be divided into two sets:  some modified
      sequences containing 5-methylcytosine are restricted by McrB+McrC+ cells.  The sequences
      restricted only by McrB+C+ include T-even bacteriophage containing 5-hydroxymethylcytosine
      (restriction of this phage is the RglB+ phenotype), some sequences containing
      N4-methylcytosine, and some sequences containing 5-methylcytosine.  The sequence codes for two
      polypeptides of 54 (McrB) and 42 (McrC) kilodaltons, whereas in vitro translation yields four
      products, of ~29 and ~49 (McrB) and of ~38 and ~40 (McrC) kilodaltons.  The McrB polypeptide
      sequence contains a potential GTP-binding motif, so this protein presumably binds the
      nucleotide cofactor.  The deduced McrC polypeptide is somewhat basic and may bind to DNA,
      consistent with its genetic activity as a modulator of the specificity of McrB.  At the
      nucleotide sequence level, the G+C content of mcrBC is very low for E. coli, suggesting that
      the genes may have been acquired recently during the evolution of the species.
AU  - Dila D
AU  - Sutherland E
AU  - Moran L
AU  - Slatko B
AU  - Raleigh EA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1990 172: 4888-4900.

PMID- 28684574
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Escherichia coli K-12 (ATCC 10798).
PG  - e00573-17
AB  - Here, we present the draft genome sequence of Escherichia coli ATCC 10798. E. coli ATCC 10798
      is a K-12 strain, one of the most well-studied model
      microorganisms. The size of the genome was 4,685,496 bp, with a G+C content of
      50.70%. This assembly consists of 62 contigs and the F plasmid.
AU  - Dimitrova D
AU  - Engelbrecht KC
AU  - Putonti C
AU  - Koenig DW
AU  - Wolfe AJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00573-17.

PMID- 23144377
VI  - 194
DP  - 2012
TI  - Genome Sequence of Staphylococcus arlettae Strain CVD059, Isolated from the Blood of a Cardiovascular Disease Patient.
PG  - 6615-6616
AB  - We have isolated a Staphylococcus arlettae strain, strain CVD059, from the blood  of a
      rheumatic mitral stenosis patient. Here, we report the genome sequence and
      potential virulence factors of this clinical isolate. The draft genome of S.
      arlettae CVD059 is 2,565,675 bp long with a G+C content of 33.5%.
AU  - Dinakaran V
AU  - Shankar M
AU  - Jayashree S
AU  - Rathinavel A
AU  - Gunasekaran P
AU  - Rajendhran J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6615-6616.

PMID- 12397175
VI  - 99
DP  - 2002
TI  - In vivo stabilization of the Dnmt1 (cytosine-5)-methyltransferase protein.
PG  - 14861-14866
AB  - The Dnmt1o form of the Dnmt1 (cytosine-5)-methyltransferase enzyme is synthesized and stored
      in the cytoplasm of the oocyte and is used after fertilization to maintain methylation
      patterns on imprinted genes. After implantation of the blastocyst, Dnmt1o is replaced by the
      Dnmt1 form, which has an additional 118 aa at its amino terminus. To investigate functional
      differences between Dnmt1o and Dnmt1, mice were generated with a mutant allele, Dnmt1(V),
      which synthesized Dnmt1o instead of Dnmt1 in all somatic cells. Homozygous Dnmt1(V) mice were
      phenotypically normal, and had normal levels of genomic methylation, indicating that Dnmt1o
      adopts the maintenance methyltransferase function of Dnmt1. Despite the apparent equivalence
      of Dnmt1o and Dnmt1 maintenance methyltransferase function in somatic cells, the Dnmt1o
      protein was found at high levels (with a corresponding high enzymatic activity) in Dnmt1(V)
      mice. In heterozygous Dnmt1(V)/+ embryonic stem cells and early embryos, equal steady-state
      levels of Dnmt1o and Dnmt1 proteins were produced from the Dnmt1(V) and the WT Dnmt1 alleles,
      respectively. However, in older embryos and adults, the Dnmt1(V) allele produced five times
      the steady-state level of protein of the WT Dnmt1 allele. The difference in Dnmt1o and Dnmt1
      levels is due to a developmentally regulated mechanism that degrades the Dnmt1 protein. The
      intrinsic stability of the Dnmt1o protein is the most likely reason for its use as a
      maternal-effect protein; stable ooplasmic stores of Dnmt1o would be available to traffick into
      the nuclei of the eight-cell stage embryo and maintain methylation patterns on alleles of
      imprinted genes during the fourth embryonic S phase.
AU  - Ding F
AU  - Chaillet JR
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2002 99: 14861-14866.

PMID- 12929092
VI  - 36
DP  - 2003
TI  - Conservation of Dnmt1o Cytosine methyltransferase in the marsupial Monodelphis domestica.
PG  - 209-213
AB  - Imprinted genes have been identified in both eutherian mammals and in marsupials. In eutherian
      species, there is a conservation of the
      imprinting process, both in terms of the genes imprinted and the
      epigenetic inheritance mechanism. In the mouse, the inheritance of gametic
      methylation patterns depends on an oocyte-derived isoform of the Dnmt1
      (cytosine-5)-methyltransferase protein, Dnmt1o, which functions during
      preimplantation development to maintain methylation patterns on imprinted
      alleles. To determine if this component of genomic imprinting is also
      found in marsupials, Dnmt1 isoforms were examined in somatic cells and
      germ cells of the South American opossum Monodelphis domestica. There is a
      Dnmt1o protein in Monodelphis oocytes that is synthesized, as in the
      mouse, from a different transcript than the somatic Dnmt1 protein. Thus,
      an essential component of imprinting in eutherian mammals is found in a
      marsupial species, suggesting that marsupials and eutherian mammals
      imprint their genes with the same methylation-dependent mechanism.
AU  - Ding F
AU  - Patel C
AU  - Ratnam S
AU  - McCarrey JR
AU  - Chaillet JR
PT  - Journal Article
TA  - Genesis
JT  - Genesis
SO  - Genesis 2003 36: 209-213.

PMID- 24526637
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Six Rhodobacter capsulatus Strains, YW1, YW2, B6, Y262, R121, and DE442.
PG  - e00050-14
AB  - Rhodobacter capsulatus is a model organism for studying a novel type of horizontal gene
      transfer mediated by a phage-like gene transfer agent (RcGTA).
      Here we report the draft genome sequences of six R. capsulatus strains that
      exhibit different RcGTA properties, including RcGTA overproducers, RcGTA
      nonproducers, and/or RcGTA nonreceivers.
AU  - Ding H
AU  - Moksa MM
AU  - Hirst M
AU  - Beatty JT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00050-14.

PMID- 27257205
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Bacillus cereus 905, a Plant Growth-Promoting Rhizobacterium of Wheat.
PG  - e00489-16
AB  - Bacillus cereus 905 is a plant growth-promoting rhizobacterium, isolated from wheat
      rhizosphere. The draft genome sequence of this strain is 5.39 Mb and
      harbors 5,412 coding sequences.
AU  - Ding H
AU  - Niu B
AU  - Fan H
AU  - Li Y
AU  - Wang Q
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00489-16.

PMID- 24994792
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Vibrio fortis Dalian14 Isolated from Diseased Sea Urchin (Strongylocentrotus intermedius).
PG  - e00409-14
AB  - Here, we report the draft genome sequence of Vibrio fortis Dalian14 isolated from diseased sea
      urchin (Strongylocentrotus intermedius) during disease outbreaks in
      North China. The availability of this genome sequence will facilitate the study
      of the mechanisms of pathogenicity and evolution of Vibrio species.
AU  - Ding J
AU  - Dou Y
AU  - Wang Y
AU  - Chang Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00409-14.

PMID- 21602346
VI  - 193
DP  - 2011
TI  - Whole genome sequences of four Brucella strains.
PG  - 3674-3675
AB  - Brucella melitensis and Brucella suis are intracellular pathogens to livestock and humans.
      Here we report four genome sequences, the virulent strain B. melitensis M28-12 and vaccine
      strains B. melitensis M5, M111 and B. suis S2 that show varied virulence and pathogenicity,
      which will help to design more effective brucellosis vaccine.
AU  - Ding J
AU  - Pan Y
AU  - Jiang H
AU  - Cheng J
AU  - Liu T
AU  - Qin N
AU  - Yang Y
AU  - Cui B
AU  - Chen C
AU  - Liu C
AU  - Mao K
AU  - Zhu B
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3674-3675.

PMID- 27014194
VI  - 7
DP  - 2016
TI  - Genomic Insight into the Host Endosymbiont Relationship of Endozoicomonas montiporae CL-33T with its Coral Host.
PG  - 251
AB  - The bacterial genus Endozoicomonas was commonly detected in healthy corals in many
      coral-associated bacteria studies in the past decade.  Although, it is likely to be a core
      member of coral microbiota, little is known about its ecological roles.  To decipher potential
      interactions between bacteria and their coral hosts, we sequenced and investigated the first
      culturable endozoicomonal bacterium from coral, the E. montiporae CL-33T.  Its genome had
      potential sign of ongoing genome erosion and gene exchange with its host.  Testosterone
      degradation and type III secretion system are commonly present in Endozoicomonas and may have
      roles to recognize and deliver effectors to their hosts.  Moreover, genes of eukaryotic ephrin
      ligand B2 are present in its genome; presumably this bacterium could move into coral cells via
      endocytosis after binding to coral's Eph receptors.  In addition, 7,8-dihydro-8-oxoguanine
      triphosphatase and isocitrate lyase are possible type III secretion effectors that might help
      coral to prevent mitochondrial dysfunction and promote gluconeogenesis, especially under
      stress conditions.  Based on all these findings, we inferred that E. montiporae was a
      facultative endosymbiont that can recognize, translocate, communicate and modulate its coral
      host.
AU  - Ding J-Y
AU  - Shiu J-H
AU  - Chen W-M
AU  - Chiang Y-R
AU  - Tang S-L
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2016 7: 251.

PMID- 24625874
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of the Extremely Halophilic Archaeon Haloarcula hispanica Strain N601.
PG  - e00178-14
AB  - Haloarcula hispanica has been widely used in haloarchaeal studies, particularly in the
      isolation of haloviruses. The genome of strain N601, a laboratory
      derivative of the type strain ATCC 33960, was sequenced. Several potentially
      significant differences from the published sequence of the type strain (CGMCC
      1.2049 = ATCC 33960) were observed.
AU  - Ding JY
AU  - Chiang PW
AU  - Hong MJ
AU  - Dyall-Smith M
AU  - Tang SL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00178-14.

PMID- 21705583
VI  - 193
DP  - 2011
TI  - Draft Genome Sequence of Paenibacillus elgii B69, a Strain with Broad Antimicrobial Activity.
PG  - 4537
AB  - Here, we report the draft genome sequence of Paenibacillus elgii B69, which was isolated from
      soil and with broad-spectrum antimicrobial
      activity. As far as we know, the P. elgii genome is the biggest one among
      Paenibacillus genus with genome sequence available. Multiple sets of genes
      related to antibiotic biosynthetic pathways have been found in the genome.
AU  - Ding R
AU  - Li Y
AU  - Qian C
AU  - Wu X
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4537.

PMID- 2211533
VI  - 172
DP  - 1990
TI  - Presence of N6-methyladenine in GATC sequences of Bacillus popilliae and Bacillus lentimorbus KLN2.
PG  - 6156-6159
AB  - Nine strains of Bacillus popilliae and Bacillus lentimorbus KLN2 contain N6-methyladenine in
      GATC sequences, as determined by using the restriction enzymes MboI and DpnI. Among eight
      other Bacillus species examined, all, except one strain of Bacillus brevis (ATCC 9999), lacked
      adenine methylation in GATC. A methylase with Escherichia coli dcm site specificity was not
      present in any of the Bacillus species studied.
AU  - Dingman DW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1990 172: 6156-6159.

PMID- 28572312
VI  - 5
DP  - 2017
TI  - Four Complete Paenibacillus larvae Genome Sequences.
PG  - e00407-17
AB  - Four complete genome sequences of genetically distinct Paenibacillus larvae strains have been
      determined. Pacific BioSciences single-molecule real-time
      (SMRT) sequencing technology was used as the sole method of sequence
      determination and assembly. The chromosomes exhibited a G+C content of 44.1 to
      44.2% and a molecular size range of 4.29 to 4.67 Mbp.
AU  - Dingman DW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00407-17.

PMID- 8680935
VI  - 4
DP  - 1995
TI  - Bacteriophage resistance in Lactococcus.
PG  - 297-314
AB  - Lactic acid bacteria are industrial micoorganisms used in many food fermentations.
      Lactococcus species are susceptible to bacteriophage infections that may result in slowed or
      failed fermentations.  A substantial amount of research has focused on characterizing natural
      mechanisms by which bacterial cells defend themselves against phage.  Numerous natural phage
      defense mechanisms have been identified and studied, and recent efforts have improved phage
      resistance by using molecular techniques.  The study of how phages overcome these resistance
      mechanisms is also an important objective.  New strategies to minimize the presence,
      virulence, and evolution of phage are being developed and are likely to be applied
      industrially.
AU  - Dinsmore PK
AU  - Klaenhammer TR
PT  - Journal Article
TA  - Mol. Biotechnol.
JT  - Mol. Biotechnol.
SO  - Mol. Biotechnol. 1995 4: 297-314.

PMID- 29496843
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Ezakiella peruensis Strain M6.X2, a Human Gut Gram-Positive Anaerobic Coccus.
PG  - e01487-17
AB  - We report here the draft genome sequence of Ezakiella peruensis strain M6.X2(T) The draft
      genome is 1,672,788 bp long and harbors 1,589 predicted
      protein-encoding genes, including 26 antibiotic resistance genes with 1 gene
      encoding vancomycin resistance. The genome also exhibits 1 clustered regularly
      interspaced short palindromic repeat region and 333 genes acquired by horizontal
      gene transfer.
AU  - Diop A
AU  - Diop K
AU  - Tomei E
AU  - Raoult D
AU  - Fenollar F
AU  - Fournier PE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01487-17.

PMID- 27856571
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Lactobacillus plantarum Kanjika 2007, Isolated from Kanjika, a South Indian Traditional Food.
PG  - e00924-16
AB  - The draft genome sequence of Lactobacillus plantarum Kanjika 2007, isolated from  the South
      Indian staple, medicinal, and traditional food kanjika, is reported
      here. The whole genome consists of 3.16 Mb with a G+C content of 44.7% and 3,009
      protein-coding genes, 78 tRNAs, and 4rRNAs (5S-23S-16S).
AU  - Divyashri G
AU  - Rajagopal K
AU  - Prapulla SG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00924-16.

PMID- 2838134
VI  - 4
DP  - 1988
TI  - Errors between sites in restriction site mapping.
PG  - 117-123
AB  - Restriction site mapping programs construct maps by generating permutations of
      fragments and checking for consistency.  Unfortunately many consistent maps
      often are obtained within the experimental error bounds, even though there is
      only one actual map.  A particularly efficient algorithm is presented that aims
      to minimize error bounds between restriction sites.  The method is generalized
      for linear and circular maps.  The time complexity is derived and execution
      times are given for multiple enzymes and a range of error bounds.
AU  - Dix TI
AU  - Kieronska DH
PT  - Journal Article
TA  - Comput. Appl. Biosci.
JT  - Comput. Appl. Biosci.
SO  - Comput. Appl. Biosci. 1988 4: 117-123.

PMID- 21304731
VI  - 3
DP  - 2010
TI  - Complete genome sequence of Syntrophothermus lipocalidus type strain (TGB-C1).
PG  - 268-275
AB  - Syntrophothermus lipocalidus Sekiguchi et al. 2000 is the type species of the genus
      Syntrophothermus. The species is of interest because of its strictly
      anaerobic lifestyle, its participation in the primary step of the degradation of
      organic maters, and for releasing products which serve as substrates for other
      microorganisms. It also contributes significantly to maintain a regular pH in its
      environment by removing the fatty acids through beta-oxidation. The strain is
      able to metabolize isobutyrate and butyrate, which are the substrate and the
      product of degradation of the substrate, respectively. This is the first complete
      genome sequence of a member of the genus Syntrophothermus and the second in the
      family Syntrophomonadaceae. Here we describe the features of this organism,
      together with the complete genome sequence and annotation. The 2,405,559 bp long
      genome with its 2,385 protein-coding and 55 RNA genes is a part of the Genomic
      Encyclopedia of Bacteria and Archaea project.
AU  - Djao OD et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 3: 268-275.

PMID- Not carried by PubMed...
VI  - 58
DP  - 1997
TI  - Development of a triggered suicide system for bacteriophage defense.
PG  - 1095B
AB  - A novel bacteriophage defense mechanism was developed for Lactococcus lactis where an
      inducible phage promoter was used to activate bacterial suicide system after the infection.
      The LlaIR+ restriction endonuclease was exploited as a lethal gene of a phage-inducible
      suicide system.  When expressed from a constitutive promoter, the LlaIR+ endonuclease was
      lethal across a wide range of Gram-positive bacteria, including L. lactis.  Lethality of the
      LlaIR+ was exploited to develop several novel, positive selection cloning vectors for these
      organisms.  A middle, phage-inducible promoter (Phi31P) from lytic lactococcal bacteriophage
      Phi31 was cloned upstream of the LlaIR+ on the high-copy plasmid (pTRK414H).  When L. lactis
      (pTRK414h) was infected with 10^7 pfu/ml phage in broth culture, at multiplicity of infection
      (MOI) of 0.1, no lysis was observed and the culture developed normally.  The efficiency of
      plaquing (EOP) for Phi31 on L. lactis (pTRK414H) was lowered to 10^-4.  Center of infection
      assays revealed that 85% of the infected L. lactis (pTRK414H) cells did not release progeny
      phage.  The burst size of Phi31 in L. lactis (pTRK414H) was 41, four-fold lower than in
      control cells.  The Phi31P/LlaIR+ cassette also inhibited four Phi31-recombinant derivatives,
      at levels at least ten-fold greater than Phi31.  However, mutant phages could be enriched that
      were less sensitive to the Phi31P/LlaIR+-encoded restriction.  These phages were altered in
      the strength and timing of Phi31P induction.  The efficiency of the Phi31P/LlaIR+-based
      suicide system was improved by increasing promoter strength, providing a restriction enhancer
      llaIC, and by combination with other abortive defenses, per31 and abiA.  When either per31 or
      abiA were combined with llaIC and Phi31P/LlaIR+, the EOP was reduced to <10^ -10 and virulent
      phages were eliminated from the infected population.  Broader application of bacterial suicide
      systems depends on the availability of phage-specific promoters.  A rapid method for isolation
      of these promoters, based on the "capping" activity of the vaccinia virus guanylytransferase,
      was developed in this study and used successfully to identify a phage-specific promoter from
      lytic lactococcal bacteriophage sk1.
AU  - Djordjevic GM
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1997 58: 1095B.

PMID- Not carried by PubMed...
VI  - 95
DP  - 1995
TI  - Positive selection, insertion cloning vectors for lactic acid bacteria based on a restriction endonuclease cassette.
PG  - 527
AB  - Lactococcus lactis contains numerous restriction and modification (R/M) systems of different
      specificity.  A novel IIS type R/M system has been characterized from the Lactococcus lactis
      conjugative plasmid pTR2030.  The LlaI operon is composed of six genes; the methylase gene
      llaM is followed by three genes (llaI.1, llaI.2, and llaI.3), all of which are essential for
      restriction activity.  We have successfully subcloned the llaI.1, llaI.2, and llaI.3 genes,
      without llaIM, as a suicide cassette into the E. coli-lactococcal shuttle vectors pTRKL2 and
      pBV5030.  A promoter (P6) from Lactobacillus acidophilus ATCC4356, which is functional in E.
      coli, lactococci, and lactobacilli, was cloned upstream of the three gene cassette.
      Restriction activity (R+) was evaluated in Escherichia coli and various lactic acid bacteria
      (LAB).  The R+ cassette was not functional in E. coli, but was lethal to L. lactis,
      Lactobacillus plantarum, Lactobacillus gasseri, Lactobacillus johnsonii, Enterococcus
      faecalis, and Carnobacterium pisicola.  The R+ suicide vector has several unique restriction
      cloning sites located within the R+ three gene cassette that can facilitate cloning, including
      NdeI, StuI, NarI and EcoRV.  Random genomic fragments from Lb. johnsonii were cloned into the
      NdeI site resulting in complete inactivation of R+ activity and providing unconditional
      selection for recombinant plasmids in surviving transformants.  These positive selection
      cloning vectors are the first for lactic acid bacteria that are based on a restriction
      endonuclease cassette.  Functional activity of the llaI genes in various lactic acid bacteria
      will also enable use of the R+ vector for positive screening of promoter and terminator
      sequences in these genera.
AU  - Djordjevic GM
AU  - Klaenhammer TR
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1995 95: 527.

PMID- 8693025
VI  - 35
DP  - 1996
TI  - Positive selection, cloning vectors for gram-positive bacteria based on a restriction endonuclease cassette.
PG  - 37-45
AB  - Lactococcus lactis contains numerous restriction and modification (R/M) systems of different
      specificities.  A novel IIS type R/M system encoded by the LlaI operon has previously been
      characterized from the L. lactis conjugative plasmid pTR2030.  The LlaI operon is composed of
      six genes: First, a small regulatory gene IIaIC precedes the methylase gene llaIM.  The
      following three genes, llaI.1, llaI.2, llaI.3, are all essential for restriction endonuclease
      activity and are designated as the restriction cassette llaIR.  The fourth open reading frame
      of unknown function follows the llaIR gene cassette.  We have successfully subcloned the three
      llaIR genes, llaI.1, llaI.2, and llaI.3, without llaIM, as a suicide cassette into the three
      shuttle vectors pTRKL2, pTRKH2, and pBV5030.  A promoter (P6) from Lactobacillus acidophilus
      ATCC4356, which is functional in E. coli, lactococci, and lactobacilli was cloned upstream of
      the three gene cassette.  Restriction activity was evaluated in Escherichia coli and several
      gram-positive bacteria.  The llaIR restriction cassette was not functional in E. coli, but its
      presence was lethal to L. lactis, Lactobacillus gasseri, Lactobacillus plantarum,
      Lactobacillus johnsonii, Lactobacillus acidophilus, Carnobacterium pisicola, Enterococcus
      faecalis, Bacillus subtilis, and Leuconostoc gelidum.  Several novel, positive selection
      cloning vectors were developed that can exploit unique cloning sites within the llaIR
      cassette.  Insertions in llaI.1 resulted in complete inactivation of restriction activity and
      provided unconditional selection for recombinant plasmids in surviving transformants.  These
      positive selection cloning vectors are the first for gram-positive bacteria that are based on
      a restriction endonuclease cassette.  Functional activity of the llaIR genes in various
      gram-positive bacteria would also enable use of these cloning vectors for positive selection
      of promoters, terminators, and regulatory sequences across these genera.
AU  - Djordjevic GM
AU  - Klaenhammer TR
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 1996 35: 37-45.

PMID- 9352925
VI  - 179
DP  - 1997
TI  - A triggered-suicide system designed as a defense against bacteriophages.
PG  - 6741-6748
AB  - A novel bacteriophage protection system for Lactococcus lactis based on a genetic trap, in
      which a strictly phage-inducible promoter isolated from the lytic phage Phi31 is used to
      activate a bacterial suicide system after infection, was developed.  The lethal gene of the
      suicide system consists of the three-gene restriction cassette LlaIR+, which is lethal across
      a wide range of gram-positive bacteria.  The phage-inducible trigger promoter (Phi31P) and the
      LlaIR+ restriction cassette were cloned in Escherichia coli on a high-copy-number replicon to
      generate pTRK414H.  Restriction activity was not apparent in E. coli or L. lactis prior to
      phage infection.  In phage challenges of L. lactis (pTRK414H) with Phi31, the efficiency of
      plaquing was lowered to a 10^-4 and accompanied by a fourfold reduction in burst size.
      Center-of-infection assays revealed that only 15% of infected cells released progeny phage.
      In addition to phage Phi31, the Phi31P/LlaIR+ suicide cassette also inhibited four
      Phi31-derived recombinant phages at levels at least 10-fold greater than that of Phi31.  The
      Phi31P/LlaIR+-based suicide system is a genetically engineered form of abortive infection that
      traps and eliminates phages potentially evolving in fermentation environments by destroying
      the phage genome and killing the propagation host.  This type of phage-triggered suicide
      system could be designed for any bacterium-phage combination, given a universal lethal gene
      and an inducible promoter which is triggered by the infecting bacteriophage.
AU  - Djordjevic GM
AU  - O'Sullivan DJ
AU  - Walker SA
AU  - Conkling MA
AU  - Klaenhammer TR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1997 179: 6741-6748.

PMID- 23499818
VI  - 112
DP  - 2013
TI  - Modeling bacterial immune systems: Strategies for expression of toxic - but useful - molecules.
PG  - 139-144
AB  - Protection of bacterial cells against virus infection requires expression of molecules that
      are able to destroy the incoming foreign
      DNA. However, these molecules can also be toxic for the host cell. In
      both restriction-modification (R-M), and the recently discovered
      CRISPR/Cas systems, the toxicity is (in part) avoided through rapid
      transition of the expression of the toxic molecules from 'OFF' to 'ON'
      state. In restriction-modification systems the rapid transition is
      achieved through a large binding cooperativity, and low translation
      rate of the control protein. On the other hand, CRISPR array expression
      in CRISPR/Cas systems involves a mechanism where a small decrease of
      unprocessed RNAs leads to a rapid increase of processed small RNAs.
      Surprisingly, this rapid amplification crucially depends on fast
      non-specific degradation of the unprocessed molecules by an
      unidentified nuclease, rather than on large cooperativity in protein
      binding. Furthermore, the major control elements that are responsible
      for fast transition of R-M and CRISPR/Cas systems from 'OFF' to 'ON'
      state, are also directly involved in increased stability of the steady
      states of these systems. We here discuss mechanisms that allow rapid
      transition of toxic molecules from the unproductive to the productive
      state in R-M and CRISPR/Cas systems. The main purpose of this
      discussion is to put relevant theoretical and experimental work in a
      perspective that points to general similarities in otherwise
      mechanistically very different bacterial immune systems.
AU  - Djordjevic M
PT  - Journal Article
TA  - Biosystems
JT  - Biosystems
SO  - Biosystems 2013 112: 139-144.

PMID- 23105091
VI  - 194
DP  - 2012
TI  - Genome Sequence of Paenibacillus alvei DSM 29, a Secondary Invader during European Foulbrood Outbreaks.
PG  - 6365
AB  - Paenibacillus alvei is known as a secondary invader during European foulbrood of  honeybees.
      Here, we announce the 6.83-Mb draft genome sequence of P. alvei type
      strain DSM 29. Putative genes encoding an antimicrobial peptide, a binary toxin,
      a mosquitocidal toxin, alveolysin, and different polyketides and nonribosomal
      peptides were identified.
AU  - Djukic M
AU  - Becker D
AU  - Poehlein A
AU  - Voget S
AU  - Daniel R
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6365.

PMID- 26227611
VI  - 3
DP  - 2015
TI  - First Insights into the Genome of Fructobacillus sp. EFB-N1, Isolated from Honey  Bee Larva Infected with European Foulbrood.
PG  - e00868-15
AB  - European foulbrood is a worldwide disease affecting the honey bee brood. Here, we report the
      draft genome sequence of Fructobacillus sp. EFB-N1, which was isolated
      from an infected honey bee larva derived from a Swiss European foulbrood
      outbreak. The genome consists of 68 contigs and harbors 1,629 predicted
      protein-encoding genes.
AU  - Djukic M
AU  - Daniel R
AU  - Poehlein A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00868-15.

PMID- 26203329
VI  - 10
DP  - 2015
TI  - High quality draft genome of Lactobacillus kunkeei EFB6, isolated from a German European foulbrood outbreak of honeybees.
PG  - 16
AB  - The lactic acid bacterium Lactobacillus kunkeei has been described as an inhabitant of
      fructose-rich niches. Here we report on the genome sequence of L.
      kunkeei EFB6, which has been isolated from a honeybee larva infected with
      European foulbrood. The draft genome comprises 1,566,851 bp and 1,417 predicted
      protein-encoding genes.
AU  - Djukic M
AU  - Poehlein A
AU  - Strauss J
AU  - Tann FJ
AU  - Leimbach A
AU  - Hoppert M
AU  - Daniel R
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 16.

PMID- 21914864
VI  - 193
DP  - 2011
TI  - Genome Sequence of Brevibacillus laterosporus LMG 15441, a Pathogen of Invertebrates.
PG  - 5535-5536
AB  - Here we announce the genome sequence of the bacterium Brevibacillus laterosporus LMG 15441,
      which is a pathogen of invertebrates. The genome
      consists of one chromosome and two circular plasmids. Sequence analysis
      revealed a large potential to produce polyketides, nonribosomal peptides,
      and toxins.
AU  - Djukic M
AU  - Poehlein A
AU  - Thurmer A
AU  - Daniel R
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5535-5536.

PMID- 12630344
VI  - 1
DP  - 2003
TI  - Comparative effectiveness of typing Staphylococcus aureus methicillin-resistant strains, isolated in Moscow hospitals, with the use of three collections of bacteriophages.
PG  - 3-9
AB  - The typing of S. aureus methicillin-resistant strains, isolated in different hospitals of
      Moscow; was carried out with the use of three
      collections of phages: the International Set of Phages; the set of phages
      of the International Center of S. aureus phage typing in London (L); and
      the experimental collection of phages of the Gamaleya Institute of
      Epidemiology and Microbiology in Moscow (M). In this study made with the
      use of both the phages of the International Diagnostic Set and phages L in
      the standard typing dose of 1 TP about 6% of the cultures under study
      proved to be sensitive. When the typing dose was increased to 100 TP the
      phages of the international diagnostic set lyzed 75.5% of the cultures.
      The typed strains were found to belong to phage types 77 (71.7%), 77/84/85
      (19.6%) and 94/96 (6.5%). At a concentration of 100 TP phages L lyzed
      83.7% of the cultures, but the dominating phage types could not be
      determined due to a great variety of phage markers. In contrast to the two
      preceding collections, the third phage collection M was composed in such a
      way that in the study of the investigated culture the specificity of its
      restriction modification was primarily evaluated and only then the
      presence of antiphage immunity was determined. This latter collection was
      used in the evaluation of 93.1% of the cultures. By the specificity of
      their restriction specification system the majority of them were
      classified with two new groups, heretofore not described. Only this
      collection M made it possible to differentiate epidemic and sporadic
      strains and to evaluate the epidemic situation in all 6 hospitals.
AU  - Dmitrenko OA
AU  - Sidorenko SV
AU  - Zhukhovitsky VG
AU  - Terekhova RV
AU  - Karabak VI
AU  - Tarasevich NN
AU  - Vasilyeva EI
AU  - Prokhorov VY
PT  - Journal Article
TA  - Zh. Mikrobiol. Epidemiol. Immunobiol.
JT  - Zh. Mikrobiol. Epidemiol. Immunobiol.
SO  - Zh. Mikrobiol. Epidemiol. Immunobiol. 2003 1: 3-9.

PMID- 24285648
VI  - 1
DP  - 2013
TI  - Genome Sequence of Mycoplasma parvum (Formerly Eperythrozoon parvum), a Diminutive Hemoplasma of the Pig.
PG  - e00986-13
AB  - We report the complete genome sequence of Mycoplasma parvum strain Indiana. Its circular
      chromosome is 564,395 bp, which is smaller than that of Mycoplasma
      genitalium, which was previously considered the smallest member of the
      Mollicutes. Comparative analyses of the genomes of M. parvum and Mycoplasma suis
      will provide novel insights into the molecular basis of their virulence.
AU  - do Nascimento NC
AU  - Dos Santos AP
AU  - Chu Y
AU  - Guimaraes AM
AU  - Pagliaro A
AU  - Messick JB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00986-13.

PMID- 22374945
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Mycoplasma haemocanis Strain Illinois.
PG  - 1605-1606
AB  - Mycoplasma haemocanis is a blood pathogen that may cause acute disease in immunosuppressed or
      splenectomized dogs. The genome of the strain Illinois is a
      single circular chromosome with 919,992 bp and a GC content of 35%. Analyses of
      the M. haemocanis genome will provide insights into its biology and in vitro
      cultivation requirements.
AU  - do Nascimento NC
AU  - Guimaraes AM
AU  - Santos AP
AU  - Sanmiguel PJ
AU  - Messick JB
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1605-1606.

PMID- 15246274
VI  - 325
DP  - 2004
TI  - Complete genomic DNA sequence of rock bream iridovirus.
PG  - 351-363
AB  - Iridovirus is a causative agent of epizootics among cultured rock bream
      (Oplegnathus fasciatus) in Korea. Here, we report the complete genomic
      sequence of rock bream iridovirus (RBIV). The genome of RBIV was 112080 bp
      long and contained at least 118 putative open reading frames (ORFs), and
      its genome organization was similar to that of infectious spleen and
      kidney necrosis virus (ISKNV). Of the RBIV's 118 ORFs, 85 ORFs showed
      60-99% amino acid identity to those of ISKNV. Phylogenetic analysis of
      major capsid protein (MCP), DNA repair protein RAD2, and DNA polymerase
      type-B family indicated that RBIV is closely related to red sea bream
      iridovirus (RSIV), Grouper sleepy disease iridovirus (GSDIV), Dwarf
      gourami iridovirus (DGIV), and ISKNV. The genome sequence provides useful
      information concerning the evolution and divergence of iridoviruses in
      cultured fish.
AU  - Do JW
AU  - Moon CH
AU  - Kim HJ
AU  - Ko MS
AU  - Kim SB
AU  - Son JH
AU  - Kim JS
AU  - An EJ
AU  - Kim MK
AU  - Lee SK
AU  - Han MS
AU  - Cha SJ
AU  - Park MS
AU  - Park MA
AU  - Lee JS
AU  - Kim YC
AU  - Choi DL
AU  - Kim JW
AU  - Park JW
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 2004 325: 351-363.

PMID- 25720682
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Enterotoxigenic Escherichia coli Siphophage Seurat.
PG  - e00044-15
AB  - Enterotoxigenic Escherichia coli (ETEC) is one of the leading causes of diarrhea in developing
      countries. Bacteriophage therapy has the potential to aid in the prevention and treatment of
      ETEC-related illness. To that end, we present here the complete genome of ETEC siphophage
      Seurat and describe its major features.
AU  - Doan DP
AU  - Lessor LE
AU  - Hernandez AC
AU  - Kuty EGF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00044-15.

PMID- 28223461
VI  - 8
DP  - 2017
TI  - Identification of a Pseudomonas aeruginosa PAO1 DNA Methyltransferase, Its Targets, and Physiological Roles.
PG  - e02312-16
AB  - DNA methylation is widespread among prokaryotes, and most DNA methylation reactions are
      catalyzed by adenine DNA methyltransferases, which are part of
      restriction-modification (R-M) systems. R-M systems are known for their role in
      the defense against foreign DNA; however, DNA methyltransferases also play
      functional roles in gene regulation. In this study, we used single-molecule
      real-time (SMRT) sequencing to uncover the genome-wide DNA methylation pattern in
      the opportunistic pathogen Pseudomonas aeruginosa PAO1. We identified a conserved
      sequence motif targeted by an adenine methyltransferase of a type I R-M system
      and quantified the presence of N6-methyladenine using liquid
      chromatography-tandem mass spectrometry (LC-MS/MS). Changes in the PAO1
      methylation status were dependent on growth conditions and affected P. aeruginosa
      pathogenicity in a Galleria mellonella infection model. Furthermore, we found
      that methylated motifs in promoter regions led to shifts in sense and antisense
      gene expression, emphasizing the role of enzymatic DNA methylation as an
      epigenetic control of phenotypic traits in P. aeruginosa Since the DNA
      methylation enzymes are not encoded in the core genome, our findings illustrate
      how the acquisition of accessory genes can shape the global P. aeruginosa
      transcriptome and thus may facilitate adaptation to new and challenging
      habitats.IMPORTANCE With the introduction of advanced technologies, epigenetic
      regulation by DNA methyltransferases in bacteria has become a subject of intense
      studies. Here we identified an adenosine DNA methyltransferase in the
      opportunistic pathogen Pseudomonas aeruginosa PAO1, which is responsible for DNA
      methylation of a conserved sequence motif. The methylation level of all target
      sequences throughout the PAO1 genome was approximated to be in the range of 65 to
      85% and was dependent on growth conditions. Inactivation of the methyltransferase
      revealed an attenuated-virulence phenotype in the Galleria mellonella infection
      model. Furthermore, differential expression of more than 90 genes was detected,
      including the small regulatory RNA prrF1, which contributes to a global
      iron-sparing response via the repression of a set of gene targets. Our finding of
      a methylation-dependent repression of the antisense transcript of the prrF1 small
      regulatory RNA significantly expands our understanding of the regulatory
      mechanisms underlying active DNA methylation in bacteria.
AU  - Doberenz S
AU  - Eckweiler D
AU  - Reichert O
AU  - Jensen V
AU  - Bunk B
AU  - Sproer C
AU  - Kordes A
AU  - Frangipani E
AU  - Luong K
AU  - Korlach J
AU  - Heeb S
AU  - Overmann J
AU  - Kaever V
AU  - Haussler S
PT  - Journal Article
TA  - MBio
JT  - MBio
SO  - MBio 2017 8: e02312-16.

PMID- 25301648
VI  - 2
DP  - 2014
TI  - Genome Sequence of the Sponge-Associated Ruegeria halocynthiae Strain MOLA R1/13b, a Marine Roseobacter with Two Quorum-Sensing-Based Communication Systems.
PG  - e00998-14
AB  - Ruegeria halocynthiae MOLA R1/13b is an alphaproteobacterium isolated from the Mediterranean
      sea sponge Crambe crambe. We report here the genome sequence and
      its annotation, revealing the presence of quorum-sensing genes. This is the first
      report of the full genome of a Ruegeria halocynthiae strain.
AU  - Doberva M
AU  - Sanchez-Ferandin S
AU  - Ferandin Y
AU  - Intertaglia L
AU  - Croue J
AU  - Suzuki M
AU  - Lebaron P
AU  - Lami R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00998-14.

PMID- 25278539
VI  - 2
DP  - 2014
TI  - Genome Sequence of Maribius sp. Strain MOLA 401, a Marine Roseobacter with a Quorum-Sensing Cell-Dependent Physiology.
PG  - e00997-14
AB  - Maribius sp. strain MOLA401 is an alphaproteobacterium isolated from a coral reef lagoon
      located in New Caledonia, France. We report the genome sequence and its
      annotation which, interestingly, reveals the presence of genes involved in quorum
      sensing. This is the first report of a full genome within the genus Maribius.
AU  - Doberva M
AU  - Sanchez-Ferandin S
AU  - Ferandin Y
AU  - Intertaglia L
AU  - Joux F
AU  - Lebaron P
AU  - Lami R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00997-14.

PMID- 2436149
VI  - 15
DP  - 1987
TI  - PFGE of human DNA: 5-azacytidine improves restriction.
PG  - 3183
AB  - Pulsed field gel electrophoresis of human DNA and the development of long-range restriction
      maps are frequently hampered by the cytosine methylation that occurs at CG dinucleotides in
      human DNA.  This methylation can interfere with restriction and change the size, number and
      concentration of fragments detected in Southern blots.  We have found that these effects,
      which vary at different loci and in different cell lines, can be partially overcome by growing
      cells in 5-azacytidine prior to DNA isolation.  This treatment increases the number of enzymes
      that can be used to map a locus; it can help distinguish between polymorphic methylation
      patterns and polymorphic restriction patterns; and it can establish distinguishing
      characteristics for particular restriction fragments.
AU  - Dobkin C
AU  - Ferrando C
AU  - Brown WT
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1987 15: 3183.

PMID- 12379716
VI  - 70
DP  - 2002
TI  - Genetic structure and distribution of four pathogenicity islands (PAI I(536) to PAI IV(536)) of uropathogenic Escherichia coli strain 536.
PG  - 6365-6372
AB  - For the uropathogenic Escherichia coli strain 536 (O6:K15:H31), the DNA
      sequences of three pathogenicity islands (PAIs) (PAI I(536) to PAI
      III(536)) and their flanking regions (about 270 kb) were determined to
      further characterize the virulence potential of this strain. PAI I(536) to
      PAI III(536) exhibit features typical of PAIs, such as (i) association
      with tRNA-encoding genes; (ii) G+C content differing from that of the host
      genome; (iii) flanking repeat structures; (iv) a mosaic-like structure
      comprising a multitude of functional, truncated, and nonfunctional
      putative open reading frames (ORFs) with known or unknown functions; and
      (v) the presence of many fragments of mobile genetic elements. PAI I(536)
      to PAI III(536) range between 68 and 102 kb in size. Although these
      islands contain several ORFs and known virulence determinants described
      for PAIs of other extraintestinal pathogenic E. coli (ExPEC) isolates,
      they also consist of as-yet-unidentified ORFs encoding putative virulence
      factors. The genetic structure of PAI IV(536), which represents the core
      element of the so-called high-pathogenicity island encoding a siderophore
      system initially identified in pathogenic yersiniae, was further
      characterized by sample sequencing. For the first time, multiple PAI
      sequences (PAI I(536) to PAI IV(536)) in uropathogenic E. coli were
      studied and their presence in several wild-type E. coli isolates was
      extensively investigated. The results obtained suggest that these PAIs or
      at least large fragments thereof are detectable in other pathogenic E.
      coli isolates. These results support our view that the acquisition of
      large DNA regions, such as PAIs, by horizontal gene transfer is an
      important factor for the evolution of bacterial pathogens.
AU  - Dobrindt U
AU  - Blum-Oehler G
AU  - Nagy G
AU  - Schneider G
AU  - Johann A
AU  - Gottschalk G
AU  - Hacker J
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2002 70: 6365-6372.

PMID- 6248417
VI  - 10
DP  - 1980
TI  - DNA protection with the DNA methylase M.BbvI from Bacillus brevis var. GB against cleavage by the restriction endonucleases PstI and PvuII.
PG  - 105-112
AB  - BamHI fragments of the Bacillus brevis var. GB plasmid pAD1 have been cloned in Escherichia
      coli HB101 using pBR322 plasmid as a vector.  The analysis of the recombinant plasmids showed
      that additional PstI sites had appeared in cloned fragments of pAD1.  Methylation of the
      recombinant plasmids in vitro by enzymes from B. brevis GB cells blocks cleavage at these
      additional PstI sites of cloned pAD1 fragments and at the PstI site of pBR322.  Among DNA
      methylases of B. brevis GB, the cytosine DNA methylase M.BbvI is the most likely agent
      modifying the recognition sequences of PstI.  The methylase can modify cytosine residues in
      PstI or PvuII sites if these recognition sequences are linked to G at 5'- or to C at
      3'-termini.  In particular, in vitro methylation of the SV40 DNA by B. brevis GB methylases
      protects one of the two PstI sites and two of the three PvuII sites.  The described effect of
      the protection of the specific PstI and PvuII sites may be used for physical mapping of
      genomes and DNA cloning.
AU  - Dobritsa AP
AU  - Dobritsa SV
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1980 10: 105-112.

PMID- 813785
VI  - 40
DP  - 1975
TI  - Methylation of phage 1P+f DNA of Bacillus brevis var. G-B.
PG  - 1269-1274
AB  - The DNA of a virulent mutant of temperate phage 1P+f of Bacillus brevis var.
      G-B belongs to the AT type (GC=34.5 mole %) and contains 5-methylcytosine (0.17
      mole %) and N6-methyl-adenine (0.32 mole %) as minor bases.  The amount of
      these bases in the phage DNA does not depend on the nature of the host (P- and
      S variants of B. brevis var. G-B).  In contrast to the host DNA and
      heterologous DNA of Pseudomonas aeruginosa the DNAs of phages 1P+f (P-) and
      1P+f (S) do not accept methyl groups during in vitro methylation by enzymes
      from B. brevis var. G-B cells.  Consequently, these phage DNAs are completely
      methylated in vivo.  The nature of the methylation of phage DNA in cells of
      different variants of B. brevis var. G-B is the same, i.e., dissociation of the
      culture is not accompanied by a change in the specificity of the methylation of
      the DNA.  In phage 1P+f DNA 5-methylcytosine is present in all of the
      pyrimidine isopliths; the maximum amount of this base (~27%) is found in the
      dipyrimidine clusters.  In the host DNA all of the 5-methylcytosine is located
      only in mono- and dipyrimidine fragments in a ratio of 1:1.  This means that
      the specificities of the methylation of the cytosine residues in the host and
      phage DNAs are different.  This difference is apparently due to the
      participation of some specific methylase, induced by phage 1P+f, in the
      methylation of the phage DNA.
AU  - Dobritsa AP
AU  - Mikhailov AA
AU  - Vanyushin BF
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1975 40: 1269-1274.

PMID- 24009124
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Streptomyces albulus Strain CCRC 11814, an {varepsilon}-Poly-L-Lysine-Producing Actinomycete.
PG  - e00696-13
AB  - Here, we report the draft genome sequence of Streptomyces albulus strain CCRC 11814, a
      soil-dwelling, Gram-positive bacterium. S. albulus produces
      epsilon-poly-l-lysine, which has diverse antimicrobial activity. The genome is
      9.43 Mb in size, with a G+C content of 72.2%, and contains 9,177 protein-coding
      sequences.
AU  - Dodd A
AU  - Swanevelder D
AU  - Featherston J
AU  - Rumbold K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00696-13.

PMID- 22210223
VI  - 78
DP  - 2012
TI  - Plasmid Localization and Organization of Melamine Degradation Genes in Rhodococcus sp. Strain Mel.
PG  - 1397-1403
AB  - Rhodococcus sp. strain Mel was isolated from soil by enrichment and grew in
      minimal medium with melamine as the sole N source with a doubling time of 3.5 h.
      Stoichiometry studies showed that all six nitrogen atoms of melamine were
      assimilated. The genome was sequenced by Roche 454 pyrosequencing to 13x
      coverage, and a 22.3-kb DNA region was found to contain a homolog to the melamine
      deaminase gene trzA. Mutagenesis studies showed that the cyanuric acid hydrolase
      and biuret hydrolase genes were clustered together on a different 17.9-kb contig.
      Curing and gene transfer studies indicated that 4 of 6 genes required for the
      complete degradation of melamine were located on an approximately 265-kb
      self-transmissible linear plasmid (pMel2), but this plasmid was not required for
      ammeline deamination. The Rhodococcus sp. strain Mel melamine metabolic pathway
      genes were located in at least three noncontiguous regions of the genome, and the
      plasmid-borne genes encoding enzymes for melamine metabolism were likely recently
      acquired.
AU  - Dodge AG
AU  - Wackett LP
AU  - Sadowsky MJ
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2012 78: 1397-1403.

PMID- 1958315
VI  - 372
DP  - 1991
TI  - Patterns of DNA methylation-evolutionary vestiges of foreign DNA inactivation as a host defense mechanism.
PG  - 557-564
AB  - The proposals in this review are based on experimental work on the integration
      of foreign DNA in mammalian cells, on the establishment of specific de novo
      patterns of DNA methylation, and on the inhibition of transcription by the
      sequence-specific methylation of promoter sequences.  It is suggested that
      eukaryotic cells have developed several mechanisms of defense against the
      uptake, integration, and continued expression of foreign DNA.  In the course of
      evolution and continuing at present, cells have been exposed to foreign DNA,
      entire genomes or fragments of them.  A particularly problematic organ system
      in that respect must be the digestive tract in higher organisms.  The defense
      mechanisms are thought to be the folling:  (1) degradation and/or excretion of
      foreign DNA; (ii) excision and loss of previously integrated DNA from the host
      genome; (iii) targeted inactivation of foreign genes by sequence-specific
      methylation.  Genes whose products could be advantageous to the transformed
      cells can somehow be selectively excluded from this silencing mechanism.  In
      part, the specificity of de novo methylation must reside in the DNA
      methyltransferase systems of the host cell.  However, nucleotide sequence,
      structure, and chromatin arrangement in the foreign DNA could also play an
      important role.  Since defense processes must have been activated many times in
      evolution, patterns of DNA methylation as they can be observed today, may
      represent vestiges of evolution, i.e. the sum total of selective de novo
      methylations, possibly demethylations, and mutations.  Could existing patterns
      of DNA methylation be altered during embryogenesis?  One has also to consider
      the possibility that the insertion and progressive methylation of foreign DNA
      can lead to alterations in the methylation of flanking host cell DNA-sequences
      abutting the site of integration.  It will be interesting to investigate to
      what extent these changes can contribute to the oncogenic transformation of
      cells, particularly after the insertion of foreign (viral) genomes in cells
      transformed by oncogenic viruses.
AU  - Doerfler W
PT  - Journal Article
TA  - Biol. Chem. Hoppe Seyler
JT  - Biol. Chem. Hoppe Seyler
SO  - Biol. Chem. Hoppe Seyler 1991 372: 557-564.

PMID- 24309743
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Bacillus thuringiensis Serovar Israelensis Strain HD-789.
PG  - e01023-13
AB  - Bacillus thuringiensis is an important microbial insecticide for controlling agricultural
      pests. We report the finished genome sequence of Bacillus
      thuringiensis serovar israelensis strain HD-789, which contains genes encoding 7
      parasporal crystals consisting of Cry4Aa3, Cry4Ba5 (2 genes), Cry10Aa3, Cry11Aa3,
      Cry60Ba3, and Cry60Aa3, plus 3 Cyt toxin genes and 1 hemagglutinin gene.
AU  - Doggett NA
AU  - Stubben CJ
AU  - Chertkov O
AU  - Bruce DC
AU  - Detter JC
AU  - Johnson SL
AU  - Han CS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01023-13.

PMID- 24976890
VI  - 9
DP  - 2013
TI  - Genome sequence of Phaeobacter inhibens type strain (T5(T)), a secondary metabolite producing representative of the marine Roseobacter clade, and  emendation of the species description of Phaeobacter inhibens.
PG  - 334-350
AB  - Strain T5(T) is the type strain of the species Phaeobacter inhibens Martens et al. 2006, a
      secondary metabolite producing bacterium affiliated to the
      Roseobacter clade. Strain T5(T) was isolated from a water sample taken at the
      German Wadden Sea, southern North Sea. Here we describe the complete genome
      sequence and annotation of this bacterium with a special focus on the secondary
      metabolism and compare it with the genomes of the Phaeobacter inhibens strains
      DSM 17395 and DSM 24588 (2.10), selected because of the close phylogenetic
      relationship based on the 16S rRNA gene sequences of these three strains. The
      genome of strain T5(T) comprises 4,130,897 bp with 3.923 protein-coding genes and
      shows high similarities in genetic and genomic characteristics compared to P.
      inhibens DSM 17395 and DSM 24588 (2.10). Besides the chromosome, strain T5(T)
      possesses four plasmids, three of which show a high similarity to the plasmids of
      the strains DSM 17395 and DSM 24588 (2.10). Analysis of the fourth plasmid
      suggested horizontal gene transfer. Most of the genes on this plasmid are not
      present in the strains DSM 17395 and DSM 24588 (2.10) including a nitrous oxide
      reductase, which allows strain T5(T) a facultative anaerobic lifestyle. The G+C
      content was calculated from the genome sequence and differs significantly from
      the previously published value, thus warranting an emendation of the species
      description.
AU  - Dogs M et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 9: 334-350.

PMID- 24501652
VI  - 9
DP  - 2013
TI  - Genome sequence of Phaeobacter daeponensis type strain (DSM 23529(T)), a facultatively anaerobic bacterium isolated from marine sediment, and emendation  of Phaeobacter daeponensis.
PG  - 142-159
AB  - TF-218(T) is the type strain of the species Phaeobacter daeponensis Yoon et al. 2007, a
      facultatively anaerobic Phaeobacter species isolated from tidal flats.
      Here we describe the draft genome sequence and annotation of this bacterium
      together with previously unreported aspects of its phenotype. We analyzed the
      genome for genes involved in secondary metabolite production and its anaerobic
      lifestyle, which have also been described for its closest relative Phaeobacter
      caeruleus. The 4,642,596 bp long genome of strain TF-218(T) contains 4,310
      protein-coding genes and 78 RNA genes including four rRNA operons and consists of
      five replicons: one chromosome and four extrachromosomal elements with sizes of
      276 kb, 174 kb, 117 kb and 90 kb. Genome analysis showed that TF-218(T) possesses
      all of the genes for indigoidine biosynthesis, and on specific media the strain
      showed a blue pigmentation. We also found genes for dissimilatory nitrate
      reduction, gene-transfer agents, NRPS/ PKS genes and signaling systems homologous
      to the LuxR/I system.
AU  - Dogs M et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 9: 142-159.

PMID- 8440479
VI  - 124
DP  - 1993
TI  - Escherichia coli host strains SURE and SRB fail to preserve a palindrome cloned in lambda phage: improved alternate host strains.
PG  - 29-35
AB  - We have attempted to produce Escherichia coli strains with the optimal combination of host
      mutations required for the construction of genomic libraries in lambda and cosmid vectors. For
      lambda vectors, we defined this as a strain that combined high efficiency of phage plating
      with optimal tolerance to DNA methylation and the ability to propagate recombinants containing
      regions of potential secondary structure. To optimize this latter property, we have tested a
      series of strains for the ability to propagate a lambda phage containing a palindromic
      sequence. These included an mcr- derivative of a strain shown by Ishiura et al. [J. Bacteriol.
      171 (1989)] 1068-1074] to allow optimal stability of inserts in cosmid clones. All the sbcC
      strains allowed plaque formation of the palindrome-containing lambda phage. However, while the
      palindrome-containing phage plated with reasonable efficiency of SURE (recB sbcC recJ umuC
      uvrC) and SRB (sbcC recJ umuC uvrC), the majority of phage recovered from these strains no
      longer required an sbcC host for subsequent plating. These two strains also gave poorer titres
      with a low-yielding phage clone from the huma Prader-Willi chromosome region. Optimal phage
      hosts appear to be those that are McrA (mcrBC-hse-mrr)combined with mutations in sbcC plus
      recBC or recD and without mutations in additional recombination functions such as recJ or recJ
      umuC uvrC.
AU  - Doherty JP
AU  - Lindeman R
AU  - Trent RJ
AU  - Graham MW
AU  - Woodcock DM
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1993 124: 29-35.

PMID- 28963217
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Streptomyces olivochromogenes NBRC 3561, a Bioactive Peptide-Producing Actinobacterium.
PG  - e01048-17
AB  - Recently, we found that Streptomyces olivochromogenes NBRC 3561 produced a bioactive peptide,
      so we sequenced its genome to clarify its biosynthesis. We
      report here the draft genome sequence of S. olivochromogenes NBRC 3561, in which
      40 potential secondary metabolite gene clusters were predicted by antiSMASH.
AU  - Dohra H
AU  - Miyake Y
AU  - Kodani S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01048-17.

PMID- 23969064
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Holospora undulata Strain HU1, a Micronucleus-Specific Symbiont of the Ciliate Paramecium caudatum.
PG  - e00664-13
AB  - Holospora undulata is a micronucleus-specific symbiont of the ciliate Paramecium  caudatum. We
      report here the draft genome sequence of H. undulata strain HU1.
      This genome information will contribute to the study of symbiosis between H.
      undulata and the host P. caudatum.
AU  - Dohra H
AU  - Suzuki H
AU  - Suzuki T
AU  - Tanaka K
AU  - Fujishima M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00664-13.

PMID- 27492001
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Planomonospora sphaerica JCM9374, a Rare Actinomycete.
PG  - e00779-16
AB  - Planomonospora sphaerica is a rare actinomycete that is a potential antibiotic producer. Here,
      we report the draft genome sequence of P. sphaerica strain
      JCM9374. This is the first genome report of a bacterium belonging to the genus
      Planomonospora The genome information of P. sphaerica will contribute to studies
      on the structure and function of antibiotics.
AU  - Dohra H
AU  - Suzuki T
AU  - Inoue Y
AU  - Kodani S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00779-16.

PMID- 19364803
VI  - 146
DP  - 2009
TI  - Reinvestigation of the Molecular Influence of Hypoxanthine on the DNA Cleavage Efficiency of Restriction Endonucleases BglII, EcoRI and BamHI.
PG  - 201-208
AB  - Hypoxanthine (Hyp), a deaminated base of adenine (Ade), can be employed as a good probe
      molecule to reveal the significance of the minor groove
      of guanine (Gua) in biomolecular interactions because Hyp possesses a
      similar structure to Gua lacking its 2-amino group. In this study, we
      examined cleavage efficiencies of restriction endonuclease enzymes on
      DNA substrates with Hyp in their recognition sequences. As a substrate
      for BglII, EcoRI and BamHI, 24-mer DNA oligomer with Hyp (in place of
      Gua) was prepared together with its complementary sequences with
      cytosine (Cyt) or thymine (Thy) as the counter base. At 37 degrees C
      incubation for 1h, BglII and EcoRI showed higher DNA cleavage
      reactivity on Hyp-containing DNA substrates than on normal ones,
      whereas BamHI showed lower values on Hyp-containing substrates. Such
      high cleavage performance of BglII and EcoRI on Hyp-containing DNA
      substrates is in contrast to the results obtained 20 years ago, in
      which short DNA substrates (8- or 10-mer) and low reaction temperatures
      (15-20 degrees C) were employed. These new results suggest that the
      lack of the exocyclic 2-amino group of Gua could contribute to enhanced
      recognition access of BglII and EcoRI to DNA substrates.
AU  - Doi A
AU  - Pack SP
AU  - Kodaki T
AU  - Makino K
PT  - Journal Article
TA  - J. Biochem. (Tokyo)
JT  - J. Biochem. (Tokyo)
SO  - J. Biochem. (Tokyo) 2009 146: 201-208.

PMID- 27257211
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Thiostrepton-Producing Streptomyces laurentii ATCC 31255.
PG  - e00360-16
AB  - Streptomyces laurentii ATCC 31255 produces thiostrepton, a thiopeptide class antibiotic. Here,
      we report the complete genome sequence for this strain, which
      contains a total of 8,032,664 bp, 7,452 predicted coding sequences, and a G+C
      content of 72.3%.
AU  - Doi K
AU  - Fujino Y
AU  - Nagayoshi Y
AU  - Ohshima T
AU  - Ogata S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00360-16.

PMID- 23950135
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Geobacillus kaustophilus GBlys, a Lysogenic Strain with  Bacteriophage OH2.
PG  - e00634-13
AB  - Geobacillus kaustophilus strain GBlys was isolated along with the bacteriophage OH2, which
      infects G. kaustophilus NBRC 102445(T). Here we present a draft
      sequence of this strain's genome, which consists of 216 contigs for a total of
      3,541,481 bp, 3,679 predicted coding sequences, and a G+C content of 52.1%.
AU  - Doi K
AU  - Mori K
AU  - Martono H
AU  - Nagayoshi Y
AU  - Fujino Y
AU  - Tashiro K
AU  - Kuhara S
AU  - Ohshima T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00634-13.

PMID- 23929467
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of D-Branched-Chain Amino Acid Producer Lactobacillus otakiensis JCM 15040T, Isolated from a Traditional Japanese Pickle.
PG  - e00546-13
AB  - Lactobacillus otakiensis strain JCM 15040(T) was isolated from an unsalted pickling solution
      used in the production of sunki, a traditional Japanese pickle.
      Here, we prepared a draft genome sequence for this strain consisting of 40
      contigs containing a total of 2,347,132 bp, 2,310 predicted coding sequences, and
      a G+C content of 42.4%.
AU  - Doi K
AU  - Mori K
AU  - Mutaguchi Y
AU  - Tashiro K
AU  - Fujino Y
AU  - Ohmori T
AU  - Kuhara S
AU  - Ohshima T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00546-13.

PMID- 23405350
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Pediococcus lolii NGRI 0510Q(T) Isolated from Ryegrass Silage.
PG  - e00156-12
AB  - Pediococcus lolii NGRI 0510Q(T) was isolated from ryegrass silage produced on Ishigaki Island,
      Okinawa Prefecture, Japan. Here we present a draft genome
      sequence for this strain, consisting of 103 contigs for a total of 2,047,078 bp,
      2,154 predicted coding sequences, and a G+C content of 42.1%.
AU  - Doi K
AU  - Mori K
AU  - Tashiro K
AU  - Fujino Y
AU  - Nagayoshi Y
AU  - Hayashi Y
AU  - Kuhara S
AU  - Ohshima T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00156-12.

PMID- 15247328
VI  - 32
DP  - 2004
TI  - In vitro selection of restriction endonucleases by in vitro compartmentalization.
PG  - e95
AB  - Restriction endonucleases are widely used in laboratory applications from recombinant DNA
      technology to diagnostics, but engineering of restriction
      enzymes by structure-guided design and in vivo directed evolution is at an
      early stage. Here, we report the use of an in vitro compartmentalization
      system for completely in vitro selection of restriction enzymes.
      Compartmentalization of a single gene in a rabbit reticulocyte in vitro
      transcription/translation system serves to isolate individually
      synthesized enzymes from each other. In each compartment, an active enzyme
      cleaves only its own encoding gene, whereas genes encoding inactive
      enzymes remain intact. Affinity selection of the cleaved DNA encoding
      active restriction endonucleases was accomplished by the use of
      streptavidin-immobilized beads and dUTP-biotin, which was efficiently
      incorporated into the cohesive end of the cleaved DNA using a DNA
      polymerase. We confirmed that genes encoding active restriction
      endonuclease FokI could be selected from a randomized library. This method
      overcomes the limitations of current in vivo technologies and should prove
      useful for rapid screening and evolution of novel restriction enzymes from
      diverse mutant libraries, as well as for studies of catalytic and
      evolutionary mechanisms of restriction enzymes.
AU  - Doi N
AU  - Kumadaki S
AU  - Oishi Y
AU  - Matsumura N
AU  - Yanagawa H
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2004 32: e95.

PMID- 
VI  - 5
DP  - 2005
TI  - In vitro selection of restriction enzyme and receptor ligands by microcapsulated cell free protein synthesis system.
PG  - 84-86
AB  - 
AU  - Doi N
AU  - Yanagawa H
PT  - Journal Article
TA  - Baiotekunoroji Janaru
JT  - Baiotekunoroji Janaru
SO  - Baiotekunoroji Janaru 2005 5: 84-86.

PMID- 25070096
VI  - 58
DP  - 2014
TI  - Whole-genome assembly of Klebsiella pneumoniae coproducing NDM-1 and OXA-232 carbapenemases using single-molecule, real-time sequencing.
PG  - 5947-5953
AB  - The whole-genome sequence of a carbapenem-resistant Klebsiella pneumoniae strain, PittNDM01,
      which coproduces NDM-1 and OXA-232 carbapenemases, was determined in
      this study. The use of single-molecule, real-time (SMRT) sequencing provided a
      closed genome in a single sequencing run. K. pneumoniae PittNDM01 has a single
      chromosome of 5,348,284 bp and four plasmids: pPKPN1 (283,371 bp), pPKPN2
      (103,694 bp), pPKPN3 (70,814 bp), and pPKPN4 (6,141 bp). The contents of the
      chromosome were similar to that of the K. pneumoniae reference genome strain MGH
      78578, with the exception of a large inversion spanning 23.3% of the chromosome.
      In contrast, three of the four plasmids are unique. The plasmid pPKPN1, an
      IncHI1B-like plasmid, carries the blaNDM-1, armA, and qnrB1 genes, along with
      tellurium and mercury resistance operons. blaNDM-1 is carried on a unique
      structure in which Tn125 is further bracketed by IS26 downstream of a class 1
      integron. The IncFIA-like plasmid pPKPN3 also carries an array of resistance
      elements, including blaCTX-M-15 and a mercury resistance operon. The ColE-type
      plasmid pPKPN4 carrying blaOXA-232 is identical to a plasmid previously reported
      from France. SMRT sequencing was useful in resolving the complex bacterial
      genomic structures in the de novo assemblies.
AU  - Doi Y
AU  - Hazen TH
AU  - Boitano M
AU  - Tsai YC
AU  - Clark TA
AU  - Korlach J
AU  - Rasko DA
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2014 58: 5947-5953.

PMID- 27688337
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Enterococcus faecalis Strain W11 Isolated from an Algal Food Product.
PG  - e01037-16
AB  - Here, we report the complete genome sequence of Enterococcus faecalis strain W11  isolated
      from an algal food product in Japan. This study should facilitate the
      identification of a novel mechanism of glycerol metabolic control in lactic acid
      bacteria.
AU  - Doi Y
AU  - Takizawa N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01037-16.

PMID- 29301892
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of a Violacein-Producing Iodobacter sp. from the Hudson Valley Watershed.
PG  - e01428-17
AB  - Iodobacter species are among a number of freshwater Gram-negative violacein-producing
      bacteria. Janthinobacterium lividum and Chromobacterium
      violaceum have had their whole genomes sequenced and annotated. This is the first
      report of a draft whole-genome sequence of a violacein-producing Iodobacter
      strain that was isolated from the Hudson Valley watershed.
AU  - Doing G
AU  - Perron GG
AU  - Jude BA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01428-17.

PMID- 10434023
VI  - 429
DP  - 1999
TI  - Effect of interaction between 5-azacytidine and DNA (cytosine-5) methyltransferase on C-to-G and C-to-T mutations in Escherichia coli.
PG  - 37-44
AB  - The purpose of this study was to determine the effect of the Dcm
      cytosine methyltransferase on 5-azacytidine (5-azaC) mutagenesis in
      Escherichia coli. We used a Lac reversion assay to measure C-to-G and C-
      to-T mutations at a single, methylatable cytosine in the lacZ gene, in
      the presence and absence of Dcm. C-to-G mutations are stimulated by 5-
      azaC but are largely independent of Dcm. In contrast, C-to-T mutations
      are not stimulated by 5-azaC in either wild type or dcm cells. However,
      in cells which contain Dcm but are defective in very short patch
      repair, the normally high frequency of spontaneous C-to-T mutations is
      decreased by the analog in a dose-dependent manner.
AU  - Doiron KM
AU  - Lavigne-Nicolas J
AU  - Cupples CG
PT  - Journal Article
TA  - Mutat. Res.
JT  - Mutat. Res.
SO  - Mutat. Res. 1999 429: 37-44.

PMID- 8763960
VI  - 178
DP  - 1996
TI  - Overexpression of vsr in Escherichia coli is mutagenic.
PG  - 4294-4296
AB  - Overexpression of vsr in Escherichia coli stimulates transition and frameshift mutations.  The
      pattern of mutations suggests that mutagenesis is due to saturation or inactivation of
      dam-directed mismatch repair.
AU  - Doiron KMJ
AU  - Viau S
AU  - Koutroumanis M
AU  - Cupples CG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1996 178: 4294-4296.

PMID- 26404586
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Two Commensal Enterococcus cecorum Strains Isolated from Chickens in Belgium.
PG  - e01108-15
AB  - Here, we report the draft genome sequences of two commensal Enterococcus cecorum  strains
      (1710s23 and 1711s24), cultivated from the ceca of healthy laying hens originating from
      different farms in Belgium.
AU  - Dolka B
AU  - Boyen F
AU  - Butaye P
AU  - Heidemann OR
AU  - Naundrup TIC
AU  - Christensen JP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01108-15.

PMID- 26383654
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Five Clinical Enterococcus cecorum Strains Isolated from Different Poultry Species in Poland.
PG  - e01082-15
AB  - Here, we report five draft genome sequences of Enterococcus cecorum strains that  were
      isolated from different bird species of affected poultry flocks (commercial  broilers [CB],
      broiler breeders [BB], commercial layers [CL], ducks [D], and geese [G]) in Poland.
AU  - Dolka B
AU  - Heidemann OR
AU  - Naundrup TIC
AU  - Christensen JP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01082-15.

PMID- 27469967
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Lactobacillus delbrueckii Strain #22 Isolated from a Patient with Short Bowel Syndrome and Previous d-Lactic Acidosis and  Encephalopathy.
PG  - e00747-16
AB  - d-Lactic acidosis with associated encephalopathy caused by overgrowth of intestinal lactic
      acid bacteria is a rarely diagnosed neurological complication
      of patients with short bowel syndrome. Here, we report the draft genome sequence
      of Lactobacillus delbrueckii strain #22 isolated from a patient with short bowel
      syndrome and previous d-lactic acidosis/encephalopathy.
AU  - Domann E
AU  - Fischer F
AU  - Glowatzki F
AU  - Fritzenwanker M
AU  - Hain T
AU  - Zechel-Gran S
AU  - Giffhorn-Katz S
AU  - Neubauer BA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00747-16.

PMID- 2981211
VI  - 260
DP  - 1985
TI  - Restriction nuclease digestions driven to completion by Escherichia coli RNA polymerase and T4 gene 32 protein.
PG  - 415-417
AB  - Restriction enzyme digestions of large scale DNA preparations often do not go
      to completion.  This is due to product inhibition by the newly generated ends
      of the digested DNA.  The addition of exogenous proteins that bind tightly to
      the free ends of DNA or to single-stranded DNA will relieve this inhibition.
      We show that a considerable savings on restriction nucleases can be attained by
      the addition of RNA polymerase or T4 gene 32 protein in stoichiometric amounts
      to the newly produced DNA ends.
AU  - Dombroski DF
AU  - Morgan AR
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1985 260: 415-417.

PMID- 26112794
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Two Toxigenic Corynebacterium ulcerans Strains.
PG  - e00699-15
AB  - Here, we present the draft genome sequences of two toxigenic Corynebacterium ulcerans strains
      isolated from two different patients: one from a blood sample
      and the other from a scar exudate following surgery. Although these two strains
      harbor the diphtheria toxin gene tox, no full prophage sequences were found in
      the flanking regions.
AU  - Domingo MC
AU  - Fournier E
AU  - Masse C
AU  - Charest H
AU  - Bernard K
AU  - Cote JC
AU  - Tremblay C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00699-15.

PMID- 24029758
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Bacillus pumilus CCMA-560, Isolated from an Oil-Contaminated Mangrove Swamp.
PG  - e00707-13
AB  - Bacillus pumilus strain CCMA-560 was isolated from an oil-contaminated mangrove swamp and was
      shown to produce biosurfactants. The strain appears to be capable
      of degrading some plant cell wall-related compounds, including hemicelluose and
      pectin. Genes for biopolymer export and polysaccharide intercellular adhesin
      synthesis were also annotated.
AU  - Domingos DF
AU  - Dellagnezze BM
AU  - Greenfield P
AU  - Reyes LR
AU  - Melo IS
AU  - Midgley DJ
AU  - Oliveira VM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00707-13.

PMID- 24179120
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Biosurfactant-Producing Bacterium Gordonia amicalis  Strain CCMA-559, Isolated from Petroleum-Impacted Sediment.
PG  - e00894-13
AB  - Gordonia amicalis strain CCMA-559 was isolated from an oil-contaminated mangrove  swamp and
      shown to produce biosurfactants. This strain is a strict aerobe that
      readily degrades an array of carbon sources, including N-acetylglucosamine,
      cellobiose, Tween 80, and 4-hydroxybenzoic acid, and, like other G. amicalis
      strains, likely desulfurizes dibenzothiophene.
AU  - Domingos DF
AU  - Dellagnezze BM
AU  - Greenfield P
AU  - Reyes LR
AU  - Melo IS
AU  - Midgley DJ
AU  - Oliveira VM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00894-13.

PMID- 11536360
VI  - 45
DP  - 2001
TI  - Differential effects of isomeric incorporation of fluorophenylalanines into PvuII endonuclease.
PG  - 55-61
AB  - Incorporation of fluorine into proteins has long served as a means of probing structure and
      function, yet there are few studies that examine the impact of fluorine substitution,
      particularly at locations distant from the active sites of enzymes. The flexibility of
      isomeric fluorine incorporation at Phe is used to explore subtle substitution effects on
      enzyme activity and conformation. The unnatural amino acids o-, m-, and p-fluorophenylalanines
      were incorporated biosynthetically into the representative PvuII restriction endonuclease.
      Interestingly, m-fluoro-Phe-PvuII endonuclease exhibits very similar conformational stability
      to that of the native enzyme, but it exhibits a reproducible, 2-fold higher average specific
      activity. Given the level of incorporation and the distribution of species, the species of
      modified enzyme responsible for this increase in specific activity is most likely even faster.
      Further, moving the fluorine atom from the meta- to the para-position of Phe results in a
      4-fold decrease in specific activity and a decrease in conformational stability of 1.5
      kcal/mol. Since none of the Phe residues in PvuII endonuclease lies near the DNA recognition
      or catalytic sites, this differential behavior alludes to the impact of subtle changes in
      enzyme conformation on endonuclease activity and suggests novel ways to influence catalytic
      behavior.
AU  - Dominguez MA Jr
AU  - Thornton KC
AU  - Melendez MG
AU  - Dupureur CM
PT  - Journal Article
TA  - Proteins
JT  - Proteins
SO  - Proteins 2001 45: 55-61.

PMID- 
VI  - 54
DP  - 2007
TI  - Population dynamics and Restriction-Modification (RM) systems in Helicobacter pylori.
PG  - 114
AB  - H. pylori is highly recombinant, but RMs provide a barrier to recombination and preserve
      species identity.  A strain with higher RM numbers is expected to have high barriers to
      recombination.  As human hosts mix, H. pylori strains recombine.  In Latin America we have
      evidence of an increasing dominance of European strains at the expense of Amerindian, and
      African strains.  We hypothesize that European strains of H. pylori have higher number
      methylases than Amerindian strains.  We compared the number of restriction sites (using
      pDRAW32) in 3406 bp DNA sequences from H. pylori strains from different geographic phylotypes.
      We also determined in vitro, the restriction profile of 16 RE to infer the number of active
      methylases.  The number of possible restriction sites for 16 RE on multilocus sequences from
      102 strains of diverse geographical origin did not vary among strain groups.  All strains had
      cognate sequences for at least 13 of the 16 tested RE.  Average restriction sites were 5.2;
      5.7; 6.1 and 6.3 for strains hpWAfrica, hpEurope, hspEAsia and hspAmerind respectively.  Only
      Hpy8I, HpyCH4IV, HpyCH4V, had variable number of restriction sites by strain group.  MLST
      sequences do not indicate a substantial variation in the number of RE cognate restriction
      sites between strain phylotypes.  Preliminary results indicate however that the number of
      active methylases is very variable among strains.  So far, based on restriction profiles to 17
      RE, 2 Amerindian strains show 0 and 4 methylases and one European strain shows 5 methylases.
      In conclusion, variations in RE activity in H. pylori populations do not seem to be due to
      differences in the number of restriction sites in the DNA, but rather to the number of active
      methylases.
AU  - Dominguez-Bello MG
AU  - Maldonado AL
PT  - Journal Article
TA  - Zoonoses Public Health
JT  - Zoonoses Public Health
SO  - Zoonoses Public Health 2007 54: 114.

PMID- 24029764
VI  - 1
DP  - 2013
TI  - Complete Genomic Sequence of 'Thermofilum adornatus' Strain 1910bT, a Hyperthermophilic Anaerobic Organotrophic Crenarchaeon.
PG  - e00726-13
AB  - The complete genomic sequence of a novel hyperthermophilic crenarchaeon, strain 1910b(T), was
      determined. The genome comprises a 1,750,259-bp circular chromosome
      containing single copies of 3 rRNA genes, 43 tRNA genes, and 1,896 protein-coding
      sequences. In silico genome-genome hybridization suggests the proposal of a novel
      species, 'Thermofilum adornatus' strain 1910b(T).
AU  - Dominova IN
AU  - Kublanov IV
AU  - Podosokorskaya OA
AU  - Derbikova KS
AU  - Patrushev MV
AU  - Toshchakov SV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00726-13.

PMID- 23868130
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Salinarchaeum sp. Strain HArcht-Bsk1T, Isolated from  Hypersaline Lake Baskunchak, Russia.
PG  - e00505-13
AB  - The complete genome sequence of a novel halophilic archaeon, Salinarchaeum sp. strain
      HArcht-Bsk1(T), was determined using next-generation sequencing. The
      genome comprises a 3,255,260-bp circular chromosome with a G+C content of 66.7%.
      Automatic annotation of the genome revealed a single rRNA operon, 45 tRNAs, and
      3,013 protein-coding gene sequences.
AU  - Dominova IN
AU  - Sorokin DY
AU  - Kublanov IV
AU  - Patrushev MV
AU  - Toshchakov SV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00505-13.

PMID- 22966191
VI  - 86
DP  - 2012
TI  - Complete Genomic Sequence of Erwinia amylovora Phage PhiEaH2.
PG  - 10899
AB  - Erwinia amylovora is the causative agent of fire blight, a serious disease of
      some Rosaceae plants. The newly isolated bacteriophage PhiEaH2 is able to lyse E.
      amylovora in the laboratory and has reduced the occurrence of fire blight cases
      in field experiments. This study presents the sequenced complete genome and
      analysis of phage PhiEaH2.
AU  - Domotor D
AU  - Becsagh P
AU  - Rakhely G
AU  - Schneider G
AU  - Kovacs T
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 2012 86: 10899.

PMID- 26494672
VI  - 3
DP  - 2015
TI  - Genome Sequences of Multidrug-Resistant Salmonella enterica Serovar Paratyphi B (dT+) and Heidelberg Strains from the Colombian Poultry Chain.
PG  - e01265-15
AB  - Salmonella enterica is a pathogen of significant public health importance that is frequently
      associated with foodborne illness. We report the whole-genome sequences of four
      multidrug-resistant Salmonella enterica serovar Paratyphi B and Heidelberg strains, isolated
      from the Colombian poultry chain. The isolates contain a variety of antimicrobial resistance
      genes for aminoglycosides, beta-lactams, fluoroquinolones, sulfonamides, tetracycline, and
      trimethoprim.
AU  - Donado-Godoy P
AU  - Bernal JF
AU  - Rodriguez F
AU  - Gomez Y
AU  - Agarwala R
AU  - Landsman D
AU  - Marino-Ramirez L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01265-15.

PMID- 10972825
VI  - 37
DP  - 2000
TI  - Overcoming the restriction barrier to plasmid transformation of Helicobacter pylori.
PG  - 1066-1074
AB  - Helicobacter pylori strains demonstrate substantial variability in the efficiency of
      transformation by plasmids from Escherichia coli, and many strains are completely resistant to
      transformation. Among the barriers to transformation are numerous strain-specific
      restriction-modification systems in H. pylori. We have developed a method to protect plasmid
      DNA from restriction by in vitro site-specific methylation using cell-free extracts of H.
      pylori before transformation. In two cases, plasmid DNA treated with cell-free extracts in
      vitro acquired the restriction pattern characteristic of genomic DNA from the source strain.
      Among three strains examined in detail, the transformation frequency by treated plasmid
      shuttle and suicide vectors was significantly increased compared with mock-treated plasmid
      DNA. The results indicate that the restriction barrier in H. pylori can be largely overcome by
      specific DNA methylation in vitro. The approach described should significantly enhance the
      ability to manipulate gene function in H. pylori and other organisms that have substantial
      restriction barriers to transformation.
AU  - Donahue JP
AU  - Israel DA
AU  - Peek RM
AU  - Blaser MJ
AU  - Miller GG
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2000 37: 1066-1074.

PMID- 11959452
VI  - 208
DP  - 2002
TI  - Inactivation of a Helicobacter pylori DNA methyltransferase alters dnaK operon expression following host-cell adherence.
PG  - 295-301
AB  - The Helicobacter pylori hpyIM gene encodes a type II DNA methyltransferase that is highly
      conserved among strains. To investigate the potential role of M.HpyI methyltransferase
      activity in controlling gene expression in H. pylori, we analyzed gene transcription profiles
      in wild-type strain J166 and an isogenic hpyIM mutant strain using gene arrays. This analysis
      showed that the expression of a majority of genes was unaffected by hpyIM mutation, especially
      in exponential phase cultures. However, in stationary phase cultures and in cells adherent to
      AGS gastric epithelial cells in vitro, loss of hpyIM function altered the expression of the
      stress-responsive dnaK operon. Complementation of the hpyIM mutation using a shuttle plasmid
      encoding a wild-type copy of the gene re-established the wild-type pattern of dnaK operon
      expression. These data suggested that hpyIM, encoding a DNA methyltransferase, may have a role
      in H. pylori physiology that supersedes its original function in a type II
      restriction-modification system.
AU  - Donahue JP
AU  - Israel DA
AU  - Torres VJ
AU  - Necheva AS
AU  - Miller GG
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2002 208: 295-301.

PMID- 
VI  - 
DP  - 2001
TI  - Restriction and modification systems.
PG  - 269-276
AB  - Prokaryotic restriction-modification (R-M) systems were first recognized in Escherichia coli
      nearly 50 years ago and are now known to be ubiquitous among bacterial species.  In general,
      R-M systems consist of two distinct enzymatic activities: first, a restriction endonuclease
      that cleaves DNA at a specific recognition sequence, and second, a DNA methyltransferase that
      methylates DNA at the same site and thus prevents cleavage by the cognate restriction enzyme.
      The genomic sequences of Helicobacter pylori strains J99 and 26695 have revealed that this
      bacterium contains an abundance of restriction and modification genes, some of which have been
      subsequently shown to function as authentic R-M systems or as partial systems, composed of the
      DNA methyltransferase component alone.  Interestingly, R-M genes comprise a significant
      percentage of H. pylori strain-specific genes and are more prevalent in H. pylori than in
      other bacterial species whose genomes have been fully sequenced.  R-M systems in H. pylori
      have been identified on the basis of sequence similarity to known restriction enzymes and
      methyltransferases, genetic organization, and specific enzyme isolation and characterization.
      This chapter summarizes the current state of knowledge regarding the structure and function of
      the large number of putative R-M genes and systems that are now recognized to be present in H.
      pylori.
AU  - Donahue JP
AU  - Peek RM Jr
PT  - Journal Article
TA  - Helicobacter pylori: Physiology and Genetics
JT  - Helicobacter pylori: Physiology and Genetics
SO  - Helicobacter pylori: Physiology and Genetics 2001 : 269-276.

PMID- 21034474
VI  - 11
DP  - 2010
TI  - Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species.
PG  - R107
AB  - BACKGROUND: Streptococcus pneumoniae is one of the most important causes of microbial diseases
      in humans. The genomes of 44 diverse strains of S. pneumoniae
      were analyzed and compared with strains of non-pathogenic streptococci of the
      Mitis group. RESULTS: Despite evidence of extensive recombination, the S.
      pneumoniae phylogenetic tree revealed six major lineages. With the exception of
      serotype 1, the tree correlated poorly with capsular serotype, geographical site
      of isolation and disease outcome. The distribution of dispensable genes--genes
      present in more than one strain but not in all strains--was consistent with
      phylogeny, although horizontal gene transfer events attenuated this correlation
      in the case of ancient lineages. Homologous recombination, involving short
      stretches of DNA, was the dominant evolutionary process of the core genome of S.
      pneumoniae. Genetic exchange occurred both within and across the borders of the
      species, and S. mitis was the main reservoir of genetic diversity of S.
      pneumoniae. The pan-genome size of S. pneumoniae increased logarithmically with
      the number of strains and linearly with the number of polymorphic sites of the
      sampled genomes, suggesting that acquired genes accumulate proportionately to the
      age of clones. Most genes associated with pathogenicity were shared by all S.
      pneumoniae strains, but were also present in S. mitis, S. oralis and S. infantis,
      indicating that these genes are not sufficient to determine virulence.
      CONCLUSIONS: Genetic exchange with related species sharing the same ecological
      niche is the main mechanism of evolution of S. pneumoniae. The open pan-genome
      guarantees the species a quick and economical response to diverse environments.
AU  - Donati C et al
PT  - Journal Article
TA  - Genome Biol.
JT  - Genome Biol.
SO  - Genome Biol. 2010 11: R107.

PMID- 11139614
VI  - 29
DP  - 2001
TI  - Structure of human DNMT2, an enigmatic DNA methyltransferase homolog that displays denaturant-resistant binding to DNA.
PG  - 439-448
AB  - DNMT2 is a human protein that displays strong sequence similarities to DNA
      (cytosine-5)-methyltransferases (m(5)C MTases) of both prokaryotes and eukaryotes. DNMT2
      contains all 10 sequence motifs that are conserved among m(5)C MTases, including the consensus
      S:-adenosyl-L-methionine-binding motifs and the active site ProCys dipeptide. DNMT2 has close
      homologs in plants, insects and Schizosaccharomyces pombe, but no related sequence can be
      found in the genomes of  Saccharomyces cerevisiae or Caenorhabditis elegans.  The crystal
      structure of a deletion mutant of DNMT2 complexed with S-adenosyl-L-homocysteine (AdoHcy) has
      been determined at 1.8 A resolution. The structure of the large domain that contains the
      sequence motifs involved in catalysis is remarkably similar to that of M.HhaI, a confirmed
      bacterial m(5)C MTase, and the smaller target recognition domains of DNMT2 and M.HhaI are also
      closely related in overall structure. The small domain of DNMT2 contains three short helices
      that are not present in M.HhaI. DNMT2 binds AdoHcy in the same conformation as confirmed m(5)C
      MTases and, while DNMT2 shares all sequence and structural features with m(5)C MTases, it has
      failed to demonstrate detectable transmethylase activity. We show here that homologs of DNMT2,
      which are present in some organisms that are not known to methylate their genomes, contain a
      specific target-recognizing sequence motif including an invariant CysPheThr tripeptide. DNMT2
      binds DNA to form a denaturant-resistant complex in vitro. While the biological function of
      DNMT2 is not yet known, the strong binding to DNA suggests that DNMT2 may mark specific
      sequences in the genome by binding to DNA through the specific target-recognizing motif.
AU  - Dong A
AU  - Yoder JA
AU  - Zhang X
AU  - Zhou L
AU  - Bestor TH
AU  - Cheng X
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2001 29: 439-448.

PMID- 15195996
VI  - 385
DP  - 2004
TI  - Structure of the Q237W mutant of HhaI DNA methyltransferase: an insight into protein-protein interactions.
PG  - 373-379
AB  - We have determined the structure of a mutant (Q237W) of HhaI DNA methyltransferase, complexed
      with the methyl-donor product AdoHcy. The
      Q237W mutant proteins were crystallized in the monoclinic space group
      C2 with two molecules in the crystallographic asymmetric unit.
      Protein-protein interface calculations in the crystal lattices suggest
      that the dimer interface has the specific characteristics for homodimer
      protein-protein interactions, while the two active sites are spatially
      independent on the outer surface of the dimer. The solution behavior
      suggests the formation of HhaI dimers as well. The same HhaI dimer
      interface is also observed in the previously characterized binary
      (M.HhaI-AdoMet) and ternary (M.HhaI-DNA-AdoHcy) complex structures,
      crystallized in different space groups. The dimer is characterized
      either by a noncrystallographic twofold symmetry or a crystallographic
      symmetry. The dimer interface involves three segments: the
      amino-terminal residues 2-8, the carboxy-terminal residues 313-327, and
      the linker (amino acids 179-184) between the two functional domains the
      catalytic methylation domain and the DNA target recognition domain.
      Both the amino and carboxyterminal segments are part of the methylation
      domain. We also examined protein-protein interactions of other
      structurally characterized DNA MTases, which are often found as a
      2-fold related dimer with the largest dimer interface area for the
      group-beta MTases. A possible evolutionary link between the Type I and
      Type II restriction-modification systems is discussed.
AU  - Dong AP
AU  - Zhou L
AU  - Zhang X
AU  - Stickel S
AU  - Roberts RJ
AU  - Cheng XD
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 2004 385: 373-379.

PMID- 24482512
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Sphingobium sp. Strain C100, a Polycyclic Aromatic Hydrocarbon-Degrading Bacterium from the Deep-Sea Sediment of the Arctic Ocean.
PG  - e01210-13
AB  - Sphingobium sp. strain C100 was isolated from a polycyclic aromatic hydrocarbon
      (PAH)-degrading consortium from the deep-sea sediment of the Arctic Ocean. It can
      degrade two- to four-ring PAHs at 25 degrees C. Here we present the draft genome
      sequence of this strain, which is 4,776,810 bp with a G+C content of 63.9%.
AU  - Dong C
AU  - Bai X
AU  - Lai Q
AU  - Xie Y
AU  - Chen X
AU  - Shao Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01210-13.

PMID- 24459272
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Marinomonas sp. Strain D104, a Polycyclic Aromatic Hydrocarbon-Degrading Bacterium from the Deep-Sea Sediment of the Arctic Ocean.
PG  - e01211-13
AB  - Marinomonas sp. strain D104 was isolated from a polycyclic aromatic hydrocarbon-degrading
      consortium enriched from deep-sea sediment from the Arctic
      Ocean. The draft genome sequence of D104 (approximately 3.83 Mbp) contains 62
      contigs and 3,576 protein-encoding genes, with a G+C content of 44.8%.
AU  - Dong C
AU  - Bai X
AU  - Lai Q
AU  - Xie Y
AU  - Chen X
AU  - Shao Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01211-13.

PMID- 25197471
VI  - 9
DP  - 2014
TI  - Complete genome sequence of Thalassolituus oleivorans R6-15, an obligate hydrocarbonoclastic marine bacterium from the Arctic Ocean.
PG  - 893-901
AB  - Strain R6-15 belongs to the genus Thalassolituus, in the family Oceanospirillaceae of
      Gammaproteobacteria. Representatives of this genus are
      known to be the obligate hydrocarbonoclastic marine bacteria. Thalassolituus
      oleivorans R6-15 is of special interest due to its dominance in the crude
      oil-degrading consortia enriched from the surface seawater of the Arctic Ocean.
      Here we describe the complete genome sequence and annotation of this strain,
      together with its phenotypic characteristics. The genome with size of 3,764,053
      bp comprises one chromosome without any plasmids, and contains 3,372
      protein-coding and 61 RNA genes, including 12 rRNA genes.
AU  - Dong C
AU  - Chen X
AU  - Xie Y
AU  - Lai Q
AU  - Shao Z
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 893-901.

PMID- 29074658
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Bacillus subtilis Strain CGMCC 12426, an Efficient Poly-gamma-Glutamate Producer.
PG  - e01163-17
AB  - Bacillus subtilis CGMCC 12426 is an efficient producer of poly-gamma-glutamate with regular
      stereochemistry. Here, the complete genome sequence of B. subtilis
      CGMCC 12426 is presented, which may facilitate the design of rational strategies
      for further strain improvements with industrial potential.
AU  - Dong H
AU  - Chang J
AU  - He X
AU  - Hou Q
AU  - Long W
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01163-17.

PMID- 20161730
VI  - 5
DP  - 2010
TI  - Engineering Clostridium Strain to Accept Unmethylated DNA.
PG  - e9038
AB  - It is difficult to genetically manipulate the medically and biotechnologically important genus
      Clostridium due to the existence of
      the restriction and modification (RM) systems. We identified and
      engineered the RM system of a model clostridial species, C.
      acetobutylicum, with the aim to allow the host to accept the
      unmethylated DNA efficiently. A gene CAC1502 putatively encoding the
      type II restriction endonuclease Cac8241 was identified from the genome
      of C. acetobutylicum DSM1731, and disrupted using the ClosTron system
      based on group II intron insertion. The resulting strain SMB009 lost
      the type II restriction endonuclease activity, and can be transformed
      with unmethylated DNA as efficiently as with methylated DNA. The
      strategy reported here makes it easy to genetically modify the
      clostridial species using unmethylated DNA, which will help to advance
      the understanding of the clostridial physiology from the molecular
      level.
AU  - Dong HJ et al
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2010 5: e9038.

PMID- 29424684
VI  - 4
DP  - 2018
TI  - Genome analysis of clinical multilocus sequence Type 11 Klebsiella pneumoniae from China.
PG  - e000149
AB  - The increasing prevalence of KPC-producing Klebsiella pneumoniae strains in clinical settings
      has been largely attributed to dissemination of organisms of
      specific multilocus sequence types, such as ST258 and ST11. Compared with the
      ST258 clone, which is prevalent in North America and Europe, ST11 is common in
      China but information regarding its genetic features remains scarce. In this
      study, we performed detailed genetic characterization of ST11 K. pneumoniae
      strains by analyzing whole-genome sequences of 58 clinical strains collected from
      diverse geographic locations in China. The ST11 genomes were found to be highly
      heterogeneous and clustered into at least three major lineages based on the
      patterns of single-nucleotide polymorphisms. Exhibiting five different capsular
      types, these ST11 strains were found to harbor multiple resistance and virulence
      determinants such as the blaKPC-2 gene, which encodes carbapenemase, and the
      yersiniabactin-associated virulence genes irp, ybt and fyu. Moreover, genes
      encoding the virulence factor aerobactin and the regulator of the mucoid
      phenotype (rmpA) were detectable in six genomes, whereas genes encoding
      salmochelin were found in three genomes. In conclusion, our data indicated that
      carriage of a wide range of resistance and virulence genes constitutes the
      underlying basis of the high level of prevalence of ST11 in clinical settings.
      Such findings provide insight into the development of novel strategies for
      prevention, diagnosis and treatment of K. pneumoniae infections.
AU  - Dong N
AU  - Zhang R
AU  - Liu L
AU  - Li R
AU  - Lin D
AU  - Chan EW
AU  - Chen S
PT  - Journal Article
TA  - Microbial Genomics
JT  - Microbial Genomics
SO  - Microbial Genomics 2018 4: e000149.

PMID- Not carried by PubMed...
VI  - 9
DP  - 1987
TI  - A simple and practical quantitative method for measuring the activity of restriction endonucleases.
PG  - 34-36
AB  - None
AU  - Dong Q
AU  - Cao X
AU  - Zou G
AU  - Zhu R
PT  - Journal Article
TA  - Yichuan
JT  - Yichuan
SO  - Yichuan 1987 9: 34-36.

PMID- 28138357
VI  - 12
DP  - 2017
TI  - Genome sequence of a high agarase-producing strain Flammeovirga sp. SJP92.
PG  - 13
AB  - Flammeovirga sp. SJP92 is a Gram-negative, aerobic, rod-shaped, non-motile and non-flagellated
      strain that belongs to the family Flammeovirgaceae of the class
      Cytophagia. The strain was isolated from the intestine of abalone, which produces
      many extracellular agarases and exhibits efficient degradation activities on
      various polysaccharides, especially agarose. Here we present the high-quality
      draft genome of Flammeovirga sp. SJP92, together with its phenotypic
      characteristics. The genome sequence is 8, 534, 834 bp, which comprised with one
      chromosome and no plasmid. It contained 6, 291 protein-coding and 99 RNA genes,
      including 93 tRNA, 5 rRNA and 1 ncRNA genes.
AU  - Dong Q
AU  - Ruan L
AU  - Shi H
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 13.

PMID- Not carried by PubMed...
VI  - 42
DP  - 1996
TI  - Chemical modification and inhibition kinetics of restriction endonuclease Bsp63I.
PG  - 237-240
AB  - Restriction endonuclease Bsp63I has been isolated and purified by affinity chromatography.
      The role of specific amino acid residues in Bsp63I was determined by chemical modification.
      Sulfhydryl groups were modified with p-chloromercuribenzoic acid, lysine residues with
      pyridoxal-5'-phosphate (PLP) and arginine residues with 2,3-butanedione.  The results show
      that these residues are related to the activity of Bsp63I.  Dynamic analysis shows that the
      type of PLP inhibition is analogous anticompetitive inhibition. *>
AU  - Dong Q
AU  - Zou G
AU  - Cao X
AU  - Zhu R
PT  - Journal Article
TA  - Wuhan Daxue Xuebao
JT  - Wuhan Daxue Xuebao
SO  - Wuhan Daxue Xuebao 1996 42: 237-240.

PMID- 28183756
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Lactobacillus plantarum CGMCC 8198.
PG  - e01559-16
AB  - We report the complete genome sequence of Lactobacillus plantarum CGMCC 8198, a novel
      probiotic strain isolated from fermented herbage. We have determined the
      complete genome sequence of strain L. plantarum CGMCC 8198, which consists of
      genes that are likely to be involved in dairy fermentation and that have
      probiotic qualities.
AU  - Dong QQ
AU  - Hu HJ
AU  - Luo XG
AU  - Wang QT
AU  - Gu XC
AU  - Zhou H
AU  - Zhou WJ
AU  - Ni XM
AU  - Zhang TC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01559-16.

PMID- 29051747
VI  - 8
DP  - 2017
TI  - pirAB(vp) -Bearing Vibrio parahaemolyticus and Vibrio campbellii Pathogens Isolated from the Same AHPND-Affected Pond Possess Highly Similar Pathogenic Plasmids.
PG  - 1859
AB  - Acute hepatopancreatic necrosis disease (AHPND) is a severe shrimp disease
      originally shown to be caused by virulent strains of Vibrio parahaemolyticus
      (VPAHPND). Rare cases of AHPND caused by Vibrio species other than V.
      parahaemolyticus were reported. We compared an AHPND-causing V. campbellii
      (VCAHPND) and a VPAHPND isolate from the same AHPND-affected pond. Both strains
      are positive for the virulence genes pirAB(vp) . Immersion challenge test with
      Litopenaeus vannamei indicated the two strains possessed similar pathogenicity.
      Complete genome comparison showed that the pirAB(vp) -bearing plasmids in the two
      strains were highly homologous, and they both shared high homologies with plasmid
      pVA1, the reported pirAB(vp) -bearing plasmid. Conjugation and DNA-uptake genes
      were found on the pVA1-type plasmids and the host chromosomes, respectively,
      which may facilitate the dissemination of pirAB(vp) . Novel variations likely
      driven by ISVal1 in the genetic contexts of the pirAB(vp) genes were found in the
      two strains. Moreover, the VCAHPND isolate additionally contains multiple
      antibiotic resistance genes, which may bring difficulties to control its future
      outbreak. The dissemination of the pirAB(vp) in non-parahaemolyticus Vibrio also
      rises the concern of missing detection in industrial settings since the isolation
      method currently used mainly targeting V. parahaemolyticus. This study provides
      timely information for better understanding of the causes of AHPND and molecular
      epidemiology of pirAB(vp) and also appeals for precautions to encounter the
      dissemination of the hazardous genes.
AU  - Dong X
AU  - Bi D
AU  - Wang H
AU  - Zou P
AU  - Xie G
AU  - Wan X
AU  - Yang Q
AU  - Zhu Y
AU  - Chen M
AU  - Guo C
AU  - Liu Z
AU  - Wang W
AU  - Huang J
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2017 8: 1859.

PMID- 22535934
VI  - 194
DP  - 2012
TI  - Genomic Comparison of Rickettsia helvetica and Other Rickettsia Species.
PG  - 2751
AB  - We report the complete and annotated genome sequence of Rickettsia helvetica strain C9P9,
      which was first isolated in 1979 from Ixodes ricinus ticks in
      Switzerland and is considered a human pathogen.
AU  - Dong X
AU  - El Karkouri K
AU  - Robert C
AU  - Gavory F
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2751.

PMID- 22933759
VI  - 194
DP  - 2012
TI  - Genome Sequence of Rickettsia australis, the Agent of Queensland Tick Typhus.
PG  - 5129
AB  - Rickettsia australis strain Phillips(T) was isolated in Queensland, Australia, in 1950. It is
      the tick-borne agent of Queensland tick typhus, a disease endemic in
      Australia. The 1.29-Mb genome sequence of this bacterium is highly similar to
      that of Rickettsia akari but contains two plasmids.
AU  - Dong X
AU  - El Karkouri K
AU  - Robert C
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5129.

PMID- 23209240
VI  - 194
DP  - 2012
TI  - Genomic Analysis of Rickettsia japonica Strain YHT.
PG  - 6992
AB  - Rickettsia japonica strain YH, isolated in 1984 in Japan, is the type strain of R. japonica,
      the tick-borne agent of Japanese spotted fever. Here, we report the
      1.33-Mb genome of this rickettsial species.
AU  - Dong X
AU  - El-Karkouri K
AU  - Robert C
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6992.

PMID- 27056217
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Tepidibacillus decaturensis Strain Z9, an Anaerobic, Moderately Thermophilic, and Heterotrophic Bacterium from the Deep Subsurface of   the Illinois Basin, USA.
PG  - e00190-16
AB  - The genome of the moderately thermophilic and halotolerant bacteriumTepidibacillus
      decaturensisstrain Z9 was sequenced. The draft genome
      comprises three scaffolds, for a total of 2.95 Mb. As the first sequenced genome
      within the genusTepidibacillus, 2,895 protein-coding genes, 52 tRNA genes, and 3
      rRNA operons were predicted.
AU  - Dong Y
AU  - Chang YJ
AU  - Sanford RA
AU  - Fouke BW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00190-16.

PMID- 28209821
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of an Isolate of Fusarium oxysporum f. sp. melongenae, the  Causal Agent of Fusarium Wilt of Eggplant.
PG  - e01597-16
AB  - Here, we present the genome sequence of an isolate (14004) of Fusarium oxysporum  f. sp.
      melongenae, an eggplant pathogen. The final assembly consists of 1,631
      scaffolds with 53,986,354 bp (G+C content, 46.4%) and 16,485 predicted genes.
AU  - Dong Z
AU  - Hsiang T
AU  - Luo M
AU  - Xiang M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01597-16.

PMID- 28209832
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of Three Multidrug-Resistant Clinical Isolates of Streptococcus pneumoniae Serotype 19A with Different Susceptibilities to the  Myxobacterial Metabolite Carolacton.
PG  - e01641-16
AB  - The full-genome sequences of three drug- and multidrug-resistant Streptococcus pneumoniae
      clinical isolates of serotype 19A were determined by PacBio
      single-molecule real-time sequencing, in combination with Illumina MiSeq
      sequencing. A comparison to the genomes of other pneumococci indicates a high
      nucleotide sequence identity to strains Hungary19A-6 and TCH8431/19A.
AU  - Donner J
AU  - Bunk B
AU  - Schober I
AU  - Sproer C
AU  - Bergmann S
AU  - Jarek M
AU  - Overmann J
AU  - Wagner-Dobler I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01641-16.

PMID- 2829967
VI  - 949
DP  - 1988
TI  - Bacteriophage T2 and T4, dam+ and damh and Eco dam+ methylation: preference at different sites.
PG  - 240-246
AB  - We present a method for determining preference for methylation at minor methylation sites. The
      target DNA sequence is first subjected to computer-assisted analysis to predict which
      restriction endonuclease(s) will generate fragments that will contain only one or two likely
      minor methylation site(s). The target DNA is then methylated in vitro with a radioactive
      methyl-group donor and subjected to digestion by the chosen restriction enzyme(s). The amount
      of radioactivity in the various fragments is determined, after separating them using
      polyacrylamide gel electrophoresis. We documented the effect of nearby bases on the
      methylation preference and the relative preference for methylation at some specific minor
      methylation sites.
AU  - Doolitle MM
AU  - Sirotkin K
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1988 949: 240-246.

PMID- 8390659
VI  - 90
DP  - 1993
TI  - The comings and goings of homing endonucleases and mobile introns.
PG  - 5379-5381
AB  - In this issue Belfort and coworkers report the isolation and characterization of a
      thermostable endonuclease from the archaebacterium Desulfurococcus mobilis. Remarkably, the
      enzyme is encoded in an intron in the single gene for 23S rRNA and is expressed only after the
      corresponding RNA segment is excised from the newly made rRNA. Archaebacterial introns are
      unique in that their excision is catalyzed by an enzyme. The endonuclease has a number of
      features characteristic of the homing endonucleases found in fungi and their organelles, and
      these have led the authors to wonder whether trans-kingdom gene transfer may have been
      involved. As the authors suggest, all of these topics--introns, archaebacteria, homing
      endonucleases, and horizontal transfers--are lightning rods for debate.
AU  - Doolittle RF
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1993 90: 5379-5381.

PMID- 11442348
VI  - 7
DP  - 2001
TI  - Annotated draft genomic sequence from a Streptococcus pneumoniae type 19F clinical isolate.
PG  - 99-125
AB  - The public availability of numerous microbial genomes is enabling the analysis of bacterial
      biology in great detail and with an unprecedented, organism-wide and taxon-wide, broad scope.
      Streptococcus pneumoniae is one of the most important bacterial pathogens throughout the
      world.  We present here sequences and functional annotations for 2.1-Mbp of pneumococcal DNA,
      covering more than 90% of the total estimated size of the genome.  The sequenced strain is a
      clinical isolate resistant to macrolides and tetracycline.  It carries a type 19F capsular
      locus, but multilocus sequence typing for several conserved genetic loci suggests that the
      strain sequence belongs to a pneumococcal lineage that most often expresses a serotype 15
      capsular polysaccharide.  A total of 2,046 putative open reading frames longer than 100 amino
      acids were identified (average of 1,009 bp per ORF), including all described two-component
      systems and aminoacyl tRNA synthetases.  Comparisons to other complete, or nearly complete,
      bacterial genomes were made and are presented in a graphical form for all the predicted
      proteins.
AU  - Dopazo J
AU  - Mendoza A
AU  - Herrero J
AU  - Caldara F
AU  - Humbert Y
AU  - Friedli L
AU  - Guerrier M
AU  - Grand-Schenk E
AU  - Gandin C
AU  - DeFrancesco M
AU  - Polissi A
AU  - Buell G
AU  - Feger G
AU  - Garcia E
AU  - Peitsch M
AU  - Garcia-Bustos JF
PT  - Journal Article
TA  - Microb. Drug Resist.
JT  - Microb. Drug Resist.
SO  - Microb. Drug Resist. 2001 7: 99-125.

PMID- 23766401
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences of Mycoplasma auris and Mycoplasma yeatsii, Two Species of the Ear Canal of Caprinae.
PG  - e00280-13
AB  - We report here the draft genome sequences of Mycoplasma auris and Mycoplasma yeatsii, two
      species commonly isolated from the external ear canal of Caprinae.
AU  - Dordet-Frisoni E et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00280-13.

PMID- 10066749
VI  - 274
DP  - 1999
TI  - High base pair opening rates in tracts of GC base pairs.
PG  - 6957-6962
AB  - Sequence-dependent structural features of the DNA double helix have a strong influence on the
      base pair opening dynamics. Here we report a detailed study of the kinetics of base pair
      breathing in tracts of GC base pairs in DNA duplexes derived from 1H NMR measurements of the
      imino proton exchange rates upon titration with the exchange catalyst ammonia. In the limit of
      infinite exchange catalyst concentration, the exchange times of the guanine imino protons of
      the GC tracts extrapolate to much shorter base pair lifetimes than commonly observed for
      isolated GC base pairs. The base pair lifetimes in the GC tracts are below 5 ms for almost all
      of the base pairs. The unusually rapid base pair opening dynamics of GC tracts are in striking
      contrast to the behavior of AT tracts, where very long base pair lifetimes are observed. The
      implication of these findings for the structural principles governing spontaneous helix
      opening as well as the DNA-binding.
AU  - Dornberger U
AU  - Leijon M
AU  - Fritzsche H
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1999 274: 6957-6962.

PMID- 9917393
VI  - 285
DP  - 1999
TI  - Genetic analysis of the base-specific contacts of BamHI restriction endonuclease.
PG  - 1515-1523
AB  - Here, we investigate the highly specific interaction of the BamHI endonuclease with its
      cognate recognition sequence GGATCC by determining which amino acid residues can be
      substituted at the DNA interface while maintaining specificity.  Mutational studies, together
      with the structural determination of the restriction endonuclease BamHI have revealed the
      amino acid residues which are involved in DNA catalysis and those which play a role in the
      specific binding of the enzyme to its cognate DNA recognition sequence.  Amino acid residues
      N116, S118, R122, D154 and R155 are involved in DNA sequence recognition and are located in
      the major groove in close proximity to the nucleotide bases comprising the recognition
      sequence.  Cassette mutagenesis of these amino acids, together with in vivo transcriptional
      interference selection, was used to identify an array of substitutions which maintain
      site-specific binding to the cognate GGATCC sequence.  This approach has demonstrated the
      extent of acceptable variation among amino acid residues which are directly involved in
      site-specific binding.  One variant, double mutant N116H, S118G was found to cleave DNA only
      when the adenine base in the recognition site is methylated.
AU  - Dorner LF
AU  - Bitinaite J
AU  - Whitaker RD
AU  - Schildkraut I
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1999 285: 1515-1523.

PMID- 7908739
VI  - 22
DP  - 1994
TI  - Direct selection of binding proficient/catalytic deficient variants of BamHI endonuclease.
PG  - 1068-1074
AB  - Variants of BamHI endonuclease in which the glutamate 113 residue has been changed to lysine
      or the aspartate 94 to asparagine were shown to behave as repressor molecules in vivo. This
      was demonstrated by placing a BamHI recognition sequence, GGATCC, positioned as an operator
      sequence in an antisense promoter for the aadA gene (spectinomycin resistance). Repression of
      this promoter relieved the inhibition of expression of spectinomycin resistance. This system
      was then used to select new binding proficient/cleavage deficient BamHI variants. The BamHI
      endonuclease gene was mutagenized either by exposure to hydroxylamine or by PCR. The
      mutagenized DNA was reintroduced into E.coli carrying the aadA gene construct, and
      transformants that conferred spectinomycin resistance were selected. Twenty SP'transformants
      were sequenced. Thirteen of these were newly isolated variants of the previously identified
      D94 and E113 residues which are known to be involved in catalysis. The remaining seven
      variants were all located at residue 111 and the glutamate 111 residue was shown to be
      involved with catalysis.
AU  - Dorner LF
AU  - Schildkraut I
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1994 22: 1068-1074.

PMID- 22123769
VI  - 193
DP  - 2011
TI  - Genome Sequences of Three Tunicamycin-Producing Streptomyces Strains, S. chartreusis NRRL 12338, S. chartreusis NRRL 3882, and S. lysosuperificus  ATCC 31396.
PG  - 7021-7022
AB  - We announce the sequencing of Streptomyces chartreusis NRRL 12338 and NRRL 3882 and
      Streptomyces lysosuperificus ATCC 31396. These are producers of
      tunicamycins, chartreusins, cephalosporins, holomycins, and calcimycin.
      The announced genomes, together with the published Streptomyces
      clavuligerus genome, will facilitate data mining of these secondary
      metabolites.
AU  - Doroghazi JR
AU  - Ju KS
AU  - Brown DW
AU  - Labeda DP
AU  - Deng Z
AU  - Metcalf WW
AU  - Chen W
AU  - Price NP
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 7021-7022.

PMID- 29371424
VI  - 359
DP  - 2018
TI  - Systematic discovery of antiphage defense systems in the microbial pangenome.
PG  - eaar4120
AB  - The arms race between bacteria and phages led to the development of sophisticated antiphage
      defense systems, including CRISPR-Cas and restriction-modification
      systems. Evidence suggests that unknown defense systems are located in 'defense
      islands' in microbial genomes. We comprehensively characterized the bacterial
      defensive arsenal by examining gene families that are clustered next to known
      defense genes in prokaryotic genomes. Candidate defense systems were
      systematically engineered and validated in model bacteria for their antiphage
      activities. We report nine previously unknown antiphage systems and one
      antiplasmid system that are widespread in microbes and strongly protect against
      foreign invaders. These include systems that adopted components of the bacterial
      flagella and condensin complexes. Our data also suggest a common, ancient
      ancestry of innate immunity components shared between animals, plants, and
      bacteria.
AU  - Doron S
AU  - Melamed S
AU  - Ofir G
AU  - Leavitt A
AU  - Lopatina A
AU  - Keren M
AU  - Amitai G
AU  - Sorek R
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2018 359: eaar4120.

PMID- 
VI  - 2000
DP  - 2000
TI  - Proteolytic control of restriction by the type I restriction enzyme EcoKI.
PG  - A177
AB  - Type I restriction systems are sophisticated molecular machines that methylate (modify) or cut
      duplex DNA depending upon the methylation status of their target sequences.  When unmodified
      DNA enters the bacterial cells this DNA is a substrate for restriction, a process in which
      extensive DNA translocation precedes DNA breakage.  An amino acid substitution in EcoKI, which
      changes a motif essential for the active site of the modification activity, leads to an enzyme
      that is unable to modify the DNA but retains the ability to recognize unmodified target
      sequences and make double-stranded breaks in the DNA.  In vivo, breakage of unmodified
      chromosomes is prevented by a posttranslational mechanism that depends on ClpXP-dependent
      proteolysis and leads to the degradation of the subunit within the restriction enzyme that is
      essential for restriction but not modification.  Analysis of mutants that affect different
      stages of the restriction reaction suggests a model in which the degradation occurs after the
      enzyme has recognized unmodified target sequences and initiated the DNA translocation that
      precedes DNA breakage.  The mechanisms that allow cells to distinguish between chromosomal and
      foreign DNA are under investigation.
AU  - Doronina VA
AU  - Murray NE
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 2000 2000: A177.

PMID- 11136462
VI  - 39
DP  - 2001
TI  - The proteolytic control of restriction activity in Escherichia coli K-12.
PG  - 416-428
AB  - The endonuclease activity of EcoKI is regulated by the ClpXP-dependent degradation of the
      subunit that is essential for restriction, but not modification.  We monitored proteolysis in
      mutants blocked at different steps in the restriction pathway.  Mutations that prevent DNA
      translocation render EcoKI refractory to proteolysis, whereas those that permit DNA
      translocation, but block endonuclease activity, do not.  Although proteolysis alleviates
      restriction in a mutant that lacks modification activity, some restriction activity remains;
      our evidence indicates residual EcoKI associated with the membrane fraction.  ClpXP protects
      the bacterial chromosome, but little effect was detected on unmodified foreign DNA within the
      cytoplasm of a restriction-proficient cell.  The molecular basis for the distinction between
      unmodified resident and foreign DNA remains to be determined.
AU  - Doronina VA
AU  - Murray NE
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2001 39: 416-428.

PMID- 29472329
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Bacillus sp. Strain UFRGS-B20, a Hydrocarbon Degrader.
PG  - e00052-18
AB  - Bacillus sp. strain UFRGS-B20 was isolated in 2012 from Brazilian land-farming soil
      contaminated with petrochemical oily sludge. This strain was subjected to
      hydrocarbon biodegradation tests, showing degradation rates of up to 60%. Here,
      we present the 6.82-Mb draft genome sequence of the strain, which contains 2,178
      proteins with functional assignments.
AU  - Dorr-de-Quadros P
AU  - Fulthorpe R
AU  - Saati R
AU  - Cerqueira V
AU  - Bento FM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00052-18.

PMID- 19783628
VI  - 191
DP  - 2009
TI  - Comparative genome analysis of Listeria bacteriophages reveals extensive mosaicism, programmed translational frameshifting, and a novel prophage insertion site.
PG  - 7206-7215
AB  - The genomes of six Listeria bacteriophages were sequenced and analyzed.
      Phages A006, A500, B025, P35, and P40 are members of the Siphoviridae and
      contain double-stranded DNA genomes of between 35.6 kb and 42.7 kb. Phage
      B054 is a unique myovirus and features a 48.2-kb genome. Phage B025
      features 3' overlapping single-stranded genome ends, whereas the other
      viruses contain collections of terminally redundant, circularly permuted
      DNA molecules. Phages P35 and P40 have a broad host range and lack
      lysogeny functions, correlating with their virulent lifestyle. Phages
      A500, A006, and B025 integrate into bacterial tRNA genes, whereas B054
      targets the 3' end of translation elongation factor gene tsf. This is the
      first reported case of phage integration into such an evolutionarily
      conserved genetic element. Peptide fingerprinting of viral proteins
      revealed that both A118 and A500 utilize +1 and -1 programmed
      translational frameshifting for generating major capsid and tail shaft
      proteins with C termini of different lengths. In both cases, the unusual
      +1 frameshift at the 3' ends of the tsh coding sequences is induced by
      overlapping proline codons and cis-acting shifty stops. Although Listeria
      phage genomes feature a conserved organization, they also show extensive
      mosaicism within the genome building blocks. Of particular interest is
      B025, which harbors a collection of modules and sequences with relatedness
      not only to other Listeria phages but also to viruses infecting other
      members of the Firmicutes. In conclusion, our results yield insights into
      the composition and diversity of Listeria phages and provide new
      information on their function, genome adaptation, and evolution.
AU  - Dorscht J
AU  - Klumpp J
AU  - Bielmann R
AU  - Schmelcher M
AU  - Born Y
AU  - Zimmer M
AU  - Calendar R
AU  - Loessner MJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2009 191: 7206-7215.

PMID- 26659671
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequence of a European Clone II and OXA-72-Producing Acinetobacter baumannii Strain from Serbia.
PG  - e01390-15
AB  - We report here the draft genome sequence of a carbapenem-resistant Acinetobacter  baumannii
      strain isolated from a patient, a strain which previously stayed in
      Serbia. This isolate possessed the blaOXA-72 carbapenemase gene. The draft genome
      sequence consists of a total length of 3.91 Mbp, with an average G+C content of
      38.8%.
AU  - Dortet L
AU  - Bonnin RA
AU  - Girlich D
AU  - Imanci D
AU  - Bernabeu S
AU  - Fortineau N
AU  - Naas T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01390-15.

PMID- 19433506
VI  - 37
DP  - 2009
TI  - Analyzing the forces binding a restriction endonuclease to DNA using a synthetic nanopore.
PG  - 4170-4179
AB  - Restriction endonucleases are used prevalently in recombinant DNA technology because they bind
      so stably to a specific target sequence and,
      in the presence of cofactors, cleave double-helical DNA specifically at a
      target sequence at a high rate. Using synthetic nanopores along with
      molecular dynamics (MD), we have analyzed with atomic resolution how a
      prototypical restriction endonuclease, EcoRI, binds to the DNA target
      sequence-GAATTC-in the absence of a Mg(2+) ion cofactor. We have
      previously shown that there is a voltage threshold for permeation of DNA
      bound to restriction enzymes through a nanopore that is associated with a
      nanonewton force required to rupture the complex. By introducing mutations
      in the DNA, we now show that this threshold depends on the recognition
      sequence and scales linearly with the dissociation energy, independent of
      the pore geometry. To predict the effect of mutation in a base pair on the
      free energy of dissociation, MD is used to qualitatively rank the
      stability of bonds in the EcoRI-DNA complex. We find that the second base
      in the target sequence exhibits the strongest binding to the protein,
      followed by the third and first bases, with even the flanking sequence
      affecting the binding, corroborating our experiments.
AU  - Dorvel B
AU  - Sigalov G
AU  - Zhao Q
AU  - Comer J
AU  - Dimitrov V
AU  - Mirsaidov U
AU  - Aksimentiev A
AU  - Timp G
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: 4170-4179.

PMID- 22965086
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Mycoplasma wenyonii Strain Massachusetts.
PG  - 5458-5459
AB  - Mycoplasma wenyonii is a hemotrophic mycoplasma that causes acute and chronic infections in
      cattle. Here, we announce the first complete genome sequence of
      this organism. The genome is a single circular chromosome with 650,228 bp and
      G+C% of 33.9. Analyses of M. wenyonii genome will provide insights into its
      biology.
AU  - Dos Santos AP
AU  - Guimaraes AM
AU  - do Nascimento NC
AU  - Sanmiguel PJ
AU  - Messick JB
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5458-5459.

PMID- 25059874
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Komagataeibacter rhaeticus Strain AF1, a High Producer of Cellulose, Isolated from Kombucha Tea.
PG  - e00731-14
AB  - Here, we present the draft genome sequence of Komagatabaeicter rhaeticus strain AF1, which was
      isolated from Kombucha tea and is capable of producing high levels
      of cellulose.
AU  - Dos Santos RA
AU  - Berretta AA
AU  - Barud HS
AU  - Ribeiro SJ
AU  - Gonzalez-Garcia LN
AU  - Zucchi TD
AU  - Goldman GH
AU  - Riano-Pachon DM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00731-14.

PMID- 26634755
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Komagataeibacter intermedius Strain AF2, a Producer of Cellulose, Isolated from Kombucha Tea.
PG  - e01404-15
AB  - Here, we present the draft genome sequence of Komagataeibacter intermedius strain AF2, which
      was isolated from Kombucha tea and is capable of producing cellulose,
      although at lower levels compared to another bacterium from the same environment,
      K. rhaeticus strain AF1.
AU  - Dos Santos RA
AU  - Berretta AA
AU  - Barud HS
AU  - Ribeiro SJ
AU  - Gonzalez-Garcia LN
AU  - Zucchi TD
AU  - Goldman GH
AU  - Riano-Pachon DM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01404-15.

PMID- Not carried by PubMed...
VI  - 18
DP  - 1988
TI  - Determination of the restriction-modification system of the polyvalent bacteriophage 821 in the cells of Staphylococcus-aureus strains.
PG  - 421
AB  - None
AU  - Doskar J
PT  - Journal Article
TA  - Scripta Fac. Sci. Nat. Univ. Purk. Brun.
JT  - Scripta Fac. Sci. Nat. Univ. Purk. Brun.
SO  - Scripta Fac. Sci. Nat. Univ. Purk. Brun. 1988 18: 421.

PMID- Not carried by PubMed...
VI  - 19
DP  - 1989
TI  - Characteristics of restriction-modification system of the polyvalent phage 812 in strains of staphylococcus aureus.
PG  - 391-401
AB  - On the basis of the study of restriction-deficient mutants (r-) a
      restriction-modification (RM) system concerning the polyvalent phage 812 has
      been characterized in some strains of S. aureus.  Capability to modify DNA of
      the phage 812 has been evidenced only in one of the total number of twelve r-
      mutant strains under study isolated earlier (Doskar and Rosypal 1986).
      Modification acquired by the polyvalent phage 812 in this mutant strain enables
      this phage to grow not only on the parent restrictive strain r+ but also on
      certain strains insensitive to the non-modified phage.  A similar pattern of
      sensitivity of these strains both to the modified phage and to certain
      host-range mutants of the phage of the phage 812 leads us to the conclusion
      that RM systems in these strains are similar and that the mutations widening
      the host-range of the polyvalent phage concern restriction-modification
      mechanisms.  Our attempt to detect restriction endonucleases of the class II in
      crude extracts from strains insensitive to the polyvalent phage 812 have not
      been successful.  RM system of the polyvalent phage 812 is believed not to be
      of class II because of the fact that most of r-mutants are
      modification-deficient.
AU  - Doskar J
PT  - Journal Article
TA  - Scripta Fac. Sci. Nat. Univ. Purk. Brun.
JT  - Scripta Fac. Sci. Nat. Univ. Purk. Brun.
SO  - Scripta Fac. Sci. Nat. Univ. Purk. Brun. 1989 19: 391-401.

PMID- 26868386
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a Klebsiella pneumoniae Carbapenemase-Positive Sequence  Type 111 Pseudomonas aeruginosa Strain.
PG  - e01663-15
AB  - Here, we report the draft genome sequence of a sequence type 111 Pseudomonas aeruginosa strain
      isolated in 2014 from a patient at the NIH Clinical Center.
      This P. aeruginosa strain exhibits pan-drug resistance and harbors the blaKPC-2
      gene, encoding the Klebsiella pneumoniae carbapenemase enzyme, on a plasmid.
AU  - Dotson GA
AU  - Dekker JP
AU  - Palmore TN
AU  - Segre JA
AU  - Conlan S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01663-15.

PMID- 2790034
VI  - 1009
DP  - 1989
TI  - Restriction endonuclease AfaI from Acidiphilium facilis, a new isoschizomer of RsaI: purification and properties.
PG  - 83-86
AB  - We have purified AfaI endonuclease, an isoschizomer of RsaI, from Acidiphilium
      facilis strain 28H.  The enzyme is homogeneous as judged by polyacrylamide gel
      electrophoresis, and composed of a single polypeptide chain with a molecular
      weight of 30,000.  AfaI endonuclease, like RsaI, recognizes the tetranucleotide
      sequence 5'-G-T-A-C-3', and cleaves between the T and A to produce blunt-ended
      fragments.  The yield of the enzyme is 50-100 times that of the RsaI, which is
      from a phototrophic bacterium, Rhodopseudomonas sphaeroides strain 28/5.
AU  - Dou D
AU  - Inagaki K
AU  - Kita K
AU  - Ohshima A
AU  - Hiraoka N
AU  - Kishimoto N
AU  - Sugio T
AU  - Tano T
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1989 1009: 83-86.

PMID- 2548154
VI  - 17
DP  - 1989
TI  - Protein-induced unwinding of DNA:  measurement by gel electrophoresis of complexes with DNA minicircles.  Application to restriction endonuclease EcoRI, catabolite gene activator protein and lac repressor.
PG  - 5173-5189
AB  - An electrophoretic procedure for the measurement of the helix unwinding induced
      by a sequence-specific protein is described.  The method, which was applied
      here to EcoRI, CAP and lac repressor, involved the migration of the complexes
      with positively and negatively supercoiled DNA minicircles carrying a single
      protein binding site.  Mobility shifts of complexes relative to naked DNAs
      appeared to be a result of 1) the unwinding; of 2) an increase in the molecular
      frictional coefficient, which led to a retardation; of 3) bending, in the
      particular case of CAP, which induced an acceleration; and of 4) looping, in
      the case of lac repressor, which also resulted in an acceleration.  Under
      conditions where the migration of the naked topoisomers was V-like (topoisomer
      mobility showed the same linear increase with both negative and positive
      supercoilings; Zivanovic et al. (1986) J. Mol. Biol., 192, 645-660), the
      protein unwinding contribution to mobility was assumed to be identical to that
      experimentally observed in the case of a thermal unwinding:  all negatively
      supercoiled topoisomers were retarded and all positively supercoiled
      topoisomers were accelerated to the same extent.  In contrast, the mobility
      contribution of the frictional term, as well as those of bending and looping,
      appeared to vary strongly with the magnitude of the supercoiling, but only
      weakly with its polarity.  As a consequence, these latter contributions may
      approximately cancel when one is measuring the difference between the shifts
      observed for two comigrating, negatively and positively supercoiled,
      topoisomers, allowing the unwinding to be calculated.  While estimates obtained
      for EcoRI, 23 +/- 3, and CAP, about 29, were in good agreement with previous
      measurements using topoisomerase I, the value found for lac repressor, 13 to
      16, was significantly smaller.
AU  - Douc-Rasy S
AU  - Kolb A
AU  - Prunell A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 5173-5189.

PMID- 22114185
VI  - 108
DP  - 2011
TI  - Binding and cleavage of DNA with the restriction enzyme EcoR1 using time-resolved second harmonic generation.
PG  - 19979-19984
AB  - The binding of EcoR1 to a 90-bp DNA duplex attached to colloidal microparticles and the
      subsequent cleavage by the enzyme was observed in real time and label-free with time-resolved
      second harmonic (SH) spectroscopy. This method provides a unique way to investigate
      biomolecular interactions based on its sensitivity to changes in structure and electrical
      charge on formation of a complex and subsequent dynamics. The binding of EcoR1 to the
      recognition sequence in DNA appears as a rapid increase in the SH signal, which is attributed
      to the enzyme-induced change in the DNA conformation, going from a rod-like to a bent shape.
      In the presence of the cofactor Mg(2+), the subsequent decay in the SH signal was monitored in
      real time as the following processes occurred: cleavage of DNA, dissociation of the enzyme
      from the DNA, and diffusion of the 74-bp fragment into the bulk solution leaving the 16-bp
      fragment attached to the microparticle. The observed decay was dependent on the concentration
      of Mg(2+), which functions as a cofactor and as an electrolyte. With SH spectroscopy the
      rehybridization dynamics between the rehybridized microparticle bound and free cleaved DNA
      fragments was observed in real time and label-free following the cleavage of DNA.
      Collectively, the experiments reported here establish SH spectroscopy as a powerful method to
      investigate equilibrium and time-dependent biological processes in a noninvasive and
      label-free way.
AU  - Doughty B
AU  - Kazer SW
AU  - Eisenthal KB
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2011 108: 19979-19984.

PMID- 15769873
VI  - 11
DP  - 2005
TI  - A C-terminal fragment of an intron-encoded maturase is sufficient for promoting group I intron splicing.
PG  - 437-446
AB  - Group I introns often encode proteins that catalyze site-specific DNA hydrolysis. Some of
      these proteins have acquired the ability to promote
      splicing of their cognate intron, but whether these two activities
      reside in different regions of the protein remains obscure. A crystal
      structure of I-AniI, a dual function intron-encoded protein, has shown
      that the protein has two pseudo-symmetric domains of equal size. Each
      domain contacts its DNA substrate on either side of two cleavage sites.
      As a first step to identify the RNA binding surface, the N- and
      C-terminal domains of I-AniI were separately expressed and tested for
      promoting the splicing of the mitochondrial (mt) COB pre-RNA. The
      N-terminal protein showed no splicing activation or RNA binding,
      suggesting that this domain plays a minimal role in activity or is
      improperly folded. Remarkably, the 16-kDa C-terminal half facilitates
      intron splicing with a rate similar to that of the full-length protein.
      Both the C-terminal fragment and full-length proteins bind tightly to
      the COB intron. RNase footprinting shows that the C-terminal and
      full-length proteins bind to the same regions and induce the same
      conformational changes in the COB intron. Together, these results show
      that the C-terminal fragment of I-AniI is necessary and sufficient for
      maturase activity and suggests that I-AniI acquired splicing function
      by utilizing a relatively small protein surface that likely represents
      a novel RNA binding motif. This fragment of I-AniI represents the
      smallest group I intron splicing cofactor described to date.
AU  - Downing ME
AU  - Brady KL
AU  - Caprara MG
PT  - Journal Article
TA  - RNA
JT  - RNA
SO  - RNA 2005 11: 437-446.

PMID- 29496835
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Enterobacter sp. Strain EA-1, an Electrochemically Active Microorganism Isolated from Tropical Sediment.
PG  - e00111-18
AB  - Enterobacter sp. strain EA-1 is an electrochemically active bacterium isolated from tropical
      sediment in Singapore. Here, the annotated draft genome assembly of
      the bacterium is reported. Whole-genome comparison indicates that Enterobacter
      sp. EA-1, along with a previously sequenced Enterobacter isolate from East Asia,
      forms a distinct clade within the Enterobacter genus.
AU  - Doyle LE
AU  - Williams RBH
AU  - Rice SA
AU  - Marsili E
AU  - Lauro FM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00111-18.

PMID- 16478204
VI  - 128
DP  - 2006
TI  - Directed evolution and substrate specificity profile of homing endonuclease I-SceI.
PG  - 2477-2484
AB  - The laboratory evolution of enzymes with tailor-made DNA cleavage specificities would
      represent new tools for manipulating genomes and may enhance our understanding of
      sequence-specific DNA recognition by nucleases.  Below we describe the development and
      successful application of an efficient in vivo positive and negative selection system that
      applies evolutionary pressure either to favor the cleavage of a desired target sequence or to
      disfavor the cleavage of nontarget sequences.  We also applied a previously described in vitro
      selection method to reveal the comprehensive substrate specificity profile of I-SceI homing
      endonucleases with altered DNA cleavage specificities.  The most highly evolved enzyme cleaves
      the target mutant DNA sequence with a selectivity that is comparable to wild-type I-SceI's
      preference for its cognate substrate.
AU  - Doyon JB
AU  - Pattanayak V
AU  - Meyer CB
AU  - Liu DR
PT  - Journal Article
TA  - J. Am. Chem. Soc.
JT  - J. Am. Chem. Soc.
SO  - J. Am. Chem. Soc. 2006 128: 2477-2484.

PMID- 29724843
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Mercury-Resistant Pseudomonas putida Strain DRA525.
PG  - e00370-18
AB  - We report here the draft genome sequence of Pseudomonas putida strain DRA525, isolated from
      mercury-contaminated soil. This strain shows resistance to mercury
      and multiple antibiotics, and its genome sequence contains several gene sets
      known to confer resistance to heavy metals enzymatically and through multidrug
      efflux pumps.
AU  - Drace K
AU  - Giangiuli S
AU  - LeSar C
AU  - Kiefer AM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00370-18.

PMID- 26494680
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Burkholderia cordobensis Type Strain LMG 27620, Isolated from Agricultural Soils in Argentina.
PG  - e01238-15
AB  - Bacteria of the genus Burkholderia are commonly found in diverse ecological niches in nature.
      We report here the draft genome sequence of Burkholderia cordobensis type strain LMG 27620,
      isolated from agricultural soil in Cordoba, Argentina. This strain harbors several genes
      involved in chitin utilization and phenol degradation, which make it an interesting candidate
      for biocontrol purposes and xenobiotic degradation in polluted environments.
AU  - Draghi WO
AU  - Mancini VUM
AU  - Wall LG
AU  - Zorreguieta A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01238-15.

PMID- 
VI  - 8
DP  - 2017
TI  - Fallacy of the unique genome: Sequence diversity within single Helicobacter pylori strains.
PG  - 0
AB  - 
AU  - Draper JL
AU  - Hansen LM
AU  - Bernick D
AU  - Abedrabbo S
AU  - Underwood JG
AU  - Kong N
AU  - Huang CB
AU  - Weis AM
AU  - Weimer BC
AU  - van Vliet AHM
AU  - Pourmand N
AU  - Solnick JV
AU  - Karplus K
PT  - Journal Article
TA  - MBio
JT  - MBio
SO  - MBio 2017 8: 0.

PMID- 28223462
VI  - 8
DP  - 2017
TI  - Fallacy of the Unique Genome: Sequence Diversity within Single Helicobacter pylori Strains.
PG  - e02321-16
AB  - Many bacterial genomes are highly variable but nonetheless are typically published as a single
      assembled genome. Experiments tracking bacterial genome
      evolution have not looked at the variation present at a given point in time.
      Here, we analyzed the mouse-passaged Helicobacter pylori strain SS1 and its
      parent PMSS1 to assess intra- and intergenomic variability. Using high sequence
      coverage depth and experimental validation, we detected extensive genome
      plasticity within these H. pylori isolates, including movement of the
      transposable element IS607, large and small inversions, multiple single
      nucleotide polymorphisms, and variation in cagA copy number. The cagA gene was
      found as 1 to 4 tandem copies located off the cag island in both SS1 and PMSS1;
      this copy number variation correlated with protein expression. To gain insight
      into the changes that occurred during mouse adaptation, we also compared SS1 and
      PMSS1 and observed 46 differences that were distinct from the within-genome
      variation. The most substantial was an insertion in cagY, which encodes a protein
      required for a type IV secretion system function. We detected modifications in
      genes coding for two proteins known to affect mouse colonization, the HpaA
      neuraminyllactose-binding protein and the FutB alpha-1,3 lipopolysaccharide (LPS)
      fucosyltransferase, as well as genes predicted to modulate diverse properties. In
      sum, our work suggests that data from consensus genome assemblies from single
      colonies may be misleading by failing to represent the variability present.
      Furthermore, we show that high-depth genomic sequencing data of a population can
      be analyzed to gain insight into the normal variation within bacterial
      strains.IMPORTANCE Although it is well known that many bacterial genomes are
      highly variable, it is nonetheless traditional to refer to, analyze, and publish
      'the genome' of a bacterial strain. Variability is usually reduced ('only
      sequence from a single colony'), ignored ('just publish the consensus'), or
      placed in the 'too-hard' basket ('analysis of raw read data is more robust'). Now
      that whole-genome sequences are regularly used to assess virulence and track
      outbreaks, a better understanding of the baseline genomic variation present
      within single strains is needed. Here, we describe the variability seen in
      typical working stocks and colonies of pathogen Helicobacter pylori model strains
      SS1 and PMSS1 as revealed by use of high-coverage mate pair next-generation
      sequencing (NGS) and confirmed by traditional laboratory techniques. This work
      demonstrates that reliance on a consensus assembly as 'the genome' of a bacterial
      strain may be misleading.
AU  - Draper JL
AU  - Hansen LM
AU  - Bernick DL
AU  - Abedrabbo S
AU  - Underwood JG
AU  - Kong N
AU  - Huang BC
AU  - Weis AM
AU  - Weimer BC
AU  - van Vliet AH
AU  - Pourmand N
AU  - Solnick JV
AU  - Karplus K
AU  - Ottemann KM
PT  - Journal Article
TA  - MBio
JT  - MBio
SO  - MBio 2017 8: e02321-16.

PMID- 8632478
VI  - 257
DP  - 1996
TI  - ATPase activity of the type IC restriction-modification system EcoR124II.
PG  - 960-969
AB  - We have investigated the ATPase activity of the type IC restriction-modification
      (R-M) system EcoR124II.  As with all type I R-M systems EcoR124II requires ATP hydrolysis to
      cut DNA.  We determined the KM for ATP to be 10^-5 to 10^-4 M.  By measuring ATP
      hydrolysis under different conditions and by simultaneously monitoring DNA restriction,
      methylation and ATP hydrolysis we propose that the order of events during restriction is: (1)
      binding of EcoR124II to a non-methylated recognition sequence, (2) start of DNA-dependent ATP
      hydrolysis which continues even after restriction is complete, (3) restriction of DNA, (4)
      methylation of the product.  Non-cleavable DNA substrates, such as recognition site containing
      oligonucleotides, also support ATP hydrolysis.  Methylation can also occur prior to ATP
      hydrolysis and prevent DNA degradation.
AU  - Dreier J
AU  - Bickle TA
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1996 257: 960-969.

PMID- 8980681
VI  - 264
DP  - 1996
TI  - DNA cleavage by the type IC restriction-modification enzyme EcoR124II.
PG  - 722-733
AB  - Type I restriction-modification systems bind to non-palindromic, bipartite recognition
      sequences.  Although these enzymes methylate specific adenine residues within their
      recognition sequences, they cut DNA at sites up to several thousand base-pairs away.  We have
      investigated the mechanism of how EcoR124II, a type IC restriction-modification system,
      selects the cleavage site.  Restriction studies with different DNA constructs revealed that
      circular DNA requires only one non-methylated recognition sequence to be cut, whereas linear
      DNA needs at least two such sites.  Cleavage of linear DNA is independent of site orientation.
      Further investigations of the linear substrates revealed a mechanism whereby the double-strand
      break is introduced between two recognition sequences.  We propose a model for the selection
      of restriction sites by type I enzymes where two EcoR124II complexes bind to two recognition
      sequences.  Lack of methylation at a site stimulates the enzyme to translocate DNA on both
      sides of the recognition sequence.  Thus the two complexes approach each other and, at the
      point where they meet, they interact to introduce a double-strand break in the DNA.
AU  - Dreier J
AU  - MacWilliams MP
AU  - Bickle TA
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1996 264: 722-733.

PMID- 378259
VI  - 562
DP  - 1979
TI  - The effect of differential methylation by Escherichia coli of plasmid DNA and phage T7 and lambda DNA on the cleavage by restriction endonuclease MboI from Moraxella bovis.
PG  - 418-428
AB  - The nucleotide sequence recognized and cleaved by the restriction endonuclease MboI is
      5'^GATC and is identical to the central tetranucleotide of the restriction sites of BamHI and
      BglII. Experiments on the restriction of DNA from Escherichia coli dam and dam+ confirm the
      notion that GATC sequences are adenosyl-methylated by the dam function of E. coli and thereby
      are made refractory to cleavage by MboI. On the basis of this observation the degree of dam
      methylation of various DNAs was examined by cleavage with MboI and other restriction
      endonuclease. In plasmid DNA essentially all of the GATC sequences are methylated by the dam
      function. The DNA of phage lambda is only partially methylated. Extended methylation is
      observed in the DNA of a substitution mutant of lambda, lambda gal8bio256, and in the lambda
      derived plasmid, lambda dv93, which is completely methylated. In contrast, phage T7 DNA is not
      methylated by dam. A suppression of dam methylation of T7 DNA appears to act only in cis since
      plasmid DNA replicated in a T7-infected cell is completely methylated. The results are
      discussed with respect to the participation of the dam methylase in different replication
      systems.
AU  - Dreiseikelmann B
AU  - Eichenlaub R
AU  - Wackernagel W
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1979 562: 418-428.

PMID- 6263867
VI  - 147
DP  - 1981
TI  - Absence in Bacillus subtilis and Staphylococcus aureus of the sequence-specific deoxyribonucleic acid methylation that is conferred in Escherichia coli K-12 by the dam and dcm enzymes.
PG  - 259-261
AB  - Restriction analysis of plasmid pHV14 deoxyribonucleic acid isolated from Escherichia coli
      K-12, Bacillus subtilis, and Staphylococcus aureus with restriction endonucleases MboI,
      Sau3AI, and EcoRII was used to study the methylation of those nucleotide sequences which in E.
      coli contain the major portions of N6-methyladenine and 5-methylcytosine.
AU  - Dreiseikelmann B
AU  - Wackernagel W
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1981 147: 259-261.

PMID- 2989796
VI  - 13
DP  - 1985
TI  - Structural junctions in DNA: the influence of flanking sequence on nuclease digestion specificities.
PG  - 4445-4467
AB  - When a protein binds to DNA, the affinity of this protein for its primary site
      of interaction may be influenced by the nature of flanking sequences.  This is
      thought to be a consequence of local cooperativity in the DNA molecule, where
      the conformation at one point along the helix can influence the conformation at
      another, and thereby modulate the free energy of protein-DNA recognition.In
      order to learn more about this procesas, we have carried out experiments of two
      sorts.  First, we have constructed sequences of the type (dA)11(dG)8, where the
      conformational preferences of the DNA molecule switch from one extreme to
      another over just a single base pair, and subjected them to digestion by DNAase
      I and DNAase II.  This is to learn whether the structure changes abruptly at
      the junction point, or more gradually with an influence extending into residues
      on either side.  Secondly, we have subjected long plasmid DNA to digestion by
      restriction enzymes Fnu DII, HaeIII, HhaI and MspI, to look for correlations
      between cutting rate and the identity of nucleotides on either side of the
      restriction site.  The influence of flanking sequence on nuclease digestion
      specificities is clearly evident in both kinds of experiment, but the rules
      governing this seem complex and not easily formulated.  The best that can be
      done at present is to divide the problem into two parts, "analogue" and
      "digital", representing sugar-phosphate and base components of recognition.
AU  - Drew HR
AU  - Travers A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1985 13: 4445-4467.

PMID- 13724384
VI  - 13
DP  - 1961
TI  - Genetic crosses between restricted and unrestricted phage T1 in lysogenic and nonlysogenic hosts.
PG  - 31-39
AB  - When Shigella dysenteriae is lysogenized by the phage P1, it becomes immune to
      infection with "ordinary" T1 phage ("restricted T1" or "rT1").  A
      host-controlled variant of T1 ("unrestricted T1" or "uT1") can multiply in the
      lysogenic S. dysenteriae.  Three-factor crosses were done between suitably
      marked strains of rT1 and uT1 in both lysogenic and nonlysogenic S.
      dysenteriae.  When lysogenic cells are infected with both rT1 and uT1, one
      finds some recombinants among the progeny, but few, if any phage bearing the
      genotype of the restricted parent.  The proportion of recombinants in the total
      yield is about one-eighth to one-twelfth that in control crosses (in
      nonlysogenic hosts) and is independent of the order of addition of either
      parent and of the time elapsing between the addition of each parent.  We infer,
      then, that (1) the genome of rT1 enters the lysogenic cells; (2) it is neither
      replicated nor is it destroyed; and (3) it can "mate" with genomes of uT1 which
      may be present.  The proportions of the various recombinant classes are
      unusual.  Complementary classes are not equal; certain markers may be recovered
      together with a high frequency, whereas certain others, more closely linked,
      are seldom found together.  Certain "double crossover" classes are more
      frequent than certain "single crossover" classes.  These observations can be
      explained in terms of a "copy choice" mechanism of recombination by assuming
      that the rT1 genome contains at least two "bad spots," the location of which
      can be determined approximately and which force a "switch" in replication from
      the restricted genome to the unrestricted genome.
AU  - Drexler H
AU  - Christensen JR
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1961 13: 31-39.

PMID- 1651485
VI  - 19
DP  - 1991
TI  - Casein is a potent enhancer for restriction enzyme activity.
PG  - 4295
AB  - Restriction enzymes class II are ATP independent and require magnesium ions for
      their activity.  Bovine serum albumin (BSA) and spermidine are added in some
      reaction buffers.  In our experience addition of spermidine sometimes causes
      severe problems with high molecular weight DNA and BSA has only a slight effect
      on enzyme activity.  Here we show that casein, the major protein component of
      milk is a potent stimulator of restriction enzyme activity.
AU  - Dreyer K
AU  - Schulte-Holthausen H
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 4295.

PMID- 4342633
VI  - 122
DP  - 1972
TI  - Host-controlled restriction and modification of phage r in Clostridium perfringens NCTC 8798 and some of its sporulation mutants.
PG  - 1117-1127
AB  - The development of phage r, a virulent bacteriophage, in a wild type strain of
      C. perfringens and in its sporulation mutants is described.  The phage is fully
      accepted by the wild type strain and most of the Spo mutants (r-m+).  Some
      mutants have altered host-controlled restriction and modification functions,
      i.e., the phage r is restricted and may be partially modified by the mutant
      strains.  Strains of phenotype r+m+/-, r+/-m+, r+/-m- and r-m- are described.
AU  - Dreyfus-Fourcade M
AU  - Sebald M
AU  - Zavadova M
PT  - Journal Article
TA  - Ann. Inst. Pasteur Microbiol.
JT  - Ann. Inst. Pasteur Microbiol.
SO  - Ann. Inst. Pasteur Microbiol. 1972 122: 1117-1127.

PMID- 28127419
VI  - 12
DP  - 2017
TI  - Towards long-read metagenomics: complete assembly of three novel genomes from bacteria dependent on a diazotrophic cyanobacterium in a freshwater lake  co-culture.
PG  - 9
AB  - Here we report three complete bacterial genome assemblies from a PacBio shotgun metagenome of
      a co-culture from Upper Klamath Lake, OR. Genome annotations and
      culture conditions indicate these bacteria are dependent on carbon and nitrogen
      fixation from the cyanobacterium Aphanizomenon flos-aquae, whose genome was
      assembled to draft-quality. Due to their taxonomic novelty relative to previously
      sequenced bacteria, we have temporarily designated these bacteria as incertae
      sedis Hyphomonadaceae strain UKL13-1 (3,501,508 bp and 56.12% GC), incertae sedis
      Betaproteobacterium strain UKL13-2 (3,387,087 bp and 54.98% GC), and incertae
      sedis Bacteroidetes strain UKL13-3 (3,236,529 bp and 37.33% GC). Each genome
      consists of a single circular chromosome with no identified plasmids. When
      compared with binned Illumina assemblies of the same three genomes, there was ~7%
      discrepancy in total genome length. Gaps where Illumina assemblies broke were
      often due to repetitive elements. Within these missing sequences were essential
      genes and genes associated with a variety of functional categories. Annotated
      gene content reveals that both Proteobacteria are aerobic anoxygenic phototrophs,
      with Betaproteobacterium UKL13-2 potentially capable of phototrophic oxidation of
      sulfur compounds. Both proteobacterial genomes contain transporters suggesting
      they are scavenging fixed nitrogen from A. flos-aquae in the form of ammonium.
      Bacteroidetes UKL13-3 has few completely annotated biosynthetic pathways, and has
      a comparatively higher proportion of unannotated genes. The genomes were detected
      in only a few other freshwater metagenomes, suggesting that these bacteria are
      not ubiquitous in freshwater systems. Our results indicate that long-read
      sequencing is a viable method for sequencing dominant members from low-diversity
      microbial communities, and should be considered for environmental metagenomics
      when conditions meet these requirements.
AU  - Driscoll CB
AU  - Otten TG
AU  - Brown NM
AU  - Dreher TW
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 9.

PMID- 26227602
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Lactobacillus agilis Strain Marseille.
PG  - e00840-15
AB  - We report the draft genome sequence of Lactobacillus agilis strain Marseille, isolated from
      stool samples of a child suffering from kwashiorkor. This strain
      can use two metabolic pathways allowing the assimilation of glucose and xylose.
      Here, we present the first draft genome of the Lactobacillus agilis species.
AU  - Drissi F
AU  - Labas N
AU  - Merhej V
AU  - Raoult D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00840-15.

PMID- 26227603
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Lactobacillus mucosae Strain Marseille.
PG  - e00841-15
AB  - Lactobacillus mucosae strain Marseille, isolated from stool samples of a child suffering from
      a malnutrition disorder called Kwashiorkor, produces bacteriocin
      and seems to have specific carbohydrate and lipid metabolisms different from
      those of other Lactobacillus organisms. The draft genome sequence of this strain
      is presented here.
AU  - Drissi F
AU  - Merhej V
AU  - Blanc-Tailleur C
AU  - Raoult D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00841-15.

PMID- 10821181
VI  - 263
DP  - 2000
TI  - Phenotypic and molecular characterization of conjugative antibiotic resistance plasmids isolated from bacterial communities of activated sludge.
PG  - 471-482
AB  - In order to isolate antibiotic resistance plasmids from bacterial communities found in
      activated sludge, derivatives of the
      3-chlorobenzoate-degrading strain Pseudomonas sp. B13, tagged with the
      green fluorescent protein as an identification marker, were used as
      recipients in filter crosses. Transconjugants were selected on agar
      plates containing 3-chlorobenzoate as the sole carbon source and the
      antibiotic tetracycline, streptomycin or spectinomycin, and were
      recovered at frequencies in the range of 10(-5) to 10(-8) per
      recipient. A total of 12 distinct plasmids, designated pB1-pB12, was
      identified. Their sizes ranged between 41 to 69 kb and they conferred
      various patterns of antibiotic resistance on their hosts. Two of the
      plasmids, pB10 and pB11, also mediated resistance to inorganic mercury.
      Seven of the 12 plasmids were identified as broad-host-range plasmids
      displaying extremely high transfer frequencies in filter crosses,
      ranging from 10^-1 to 10^-2 per recipient cell. Ten of the 12
      plasmids belonged to the IncP incompatibility group, based on replicon
      typing using IncP group-specific PCR primers. DNA sequencing of PCR
      amplification products further revealed that eight of the 12 plasmids
      belonged to the IncP beta subgroup, whereas two plasmids were
      identified as IncP alpha plasmids. Analysis of the IncP-specific PCR
      products revealed considerable differences among the IncP beta plasmids
      at the DNA sequence level. In order to characterize the gene 'load'
      of the IncP plasmids, restriction fragments were cloned and their DNA
      sequences established. A remarkable diversity of putative proteins
      encoded by these fragments was identified. Besides transposases and
      proteins involved in antibiotic resistance, two putative DNA invertases
      belonging to the Din family, a methyltransferase of a type I
      restriction/modification system, a superoxide dismutase. parts of a
      putative efflux system belonging to the RND family, and proteins of
      unknown function were identified.
AU  - Droge M
AU  - Puhler A
AU  - Selbitschka W
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 2000 263: 471-482.

PMID- 9461452
VI  - 26
DP  - 1998
TI  - The Escherichia coli MutL protein stimulates binding of Vsr and MutS to heteroduplex DNA.
PG  - 948-953
AB  - Vsr DNA mismatch endonuclease is the key enzyme of very short patch (VSP) DNA mismatch repair
      and nicks the T-containing strand at the site of a T-G mismatch in a sequence-dependent
      manner. MutS is part of the mutHLS repair system and binds to diverse mismatches in DNA. The
      function of the mutL gene product is currently unclear but mutations in the gene abolish
      mutHLS-dependent repair. The absence of MutL severely reduces VSP repair but does not abolish
      it. Purified MutL appears to act catalytically to bind Vsr to its substrate; one-hundredth of
      an equivalent of MutL is sufficient to bring about a significant effect. MutL enhances binding
      of MutS to its substrate 6-fold but does so in a stoichiometric manner. Mutational studies
      indicate that the MutL interaction region lies within the N-terminal 330 amino acids and that
      the MutL multimerization region is at the C-terminal end. MutL mutant monomeric forms can
      stimulate MutS binding.
AU  - Drotschmann K
AU  - Aronshtam A
AU  - Fritz H-J
AU  - Marinus MG
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1998 26: 948-953.

PMID- 11071947
VI  - 28
DP  - 2000
TI  - Biochemical characterization of I-CmoeI reveals that this H-N-H homing endonuclease shares functional similarities with H-N-H colicins.
PG  - 4566-4572
AB  - Endonuclease assays of the H-N-H proteins encoded by two group I introns in the Chlamydomonas
      moewusii chloroplast psbA gene revealed that the CmpsbA.1 intron specifies a site-specific DNA
      endonuclease, designated I-CmoeI. Like most previously reported intron-encoded endonucleases,
      I-CmoeI generates a double-strand break near the insertion site of its encoding intron,
      leaving 3' extensions of 4 nt. This enzyme was purified from Escherichia coli as a fusion
      protein with a His tag at its N-terminus. The recombinant protein (rI-CmoeI) requires a
      divalent alkaline earth cation for DNA cleavage (Mg(2+) > Ca(2+) > Sr(2+) > Ba(2+)).  It also
      requires a metal cofactor for DNA binding, a property shared with H-N-H colicins but not with
      the homing endonucleases characterized to date. rI-CmoeI binds its recognition sequence as a
      monomer, as revealed by gel retardation assays. K:(m) and k(cat) values of 100 +/- 40 pM and
      0.26 +/- 0.04 min(-1), respectively, were determined. Replacement of the first histidine of
      the H-N-H motif by an alanine residue abolishes both rI-CMOE:I activity and binding to its
      substrate. We propose that this conserved histidine residue plays a role in binding the metal
      cofactor and that such binding induces a structural modification of the enzyme which is
      required for DNA recognition.
AU  - Drouin M
AU  - Lucas P
AU  - Otis C
AU  - Lemieux C
AU  - Turmel M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2000 28: 4566-4572.

PMID- 22102579
VI  - 40
DP  - 2012
TI  - Novel non-specific DNA adenine methyltransferases.
PG  - 2119-2130
AB  - The mom gene of bacteriophage Mu encodes an enzyme that converts adenine to
      N(6)-(1-acetamido)-adenine in the phage DNA and thereby protects the viral genome from
      cleavage by a wide variety of restriction endonucleases. Mu-like prophage sequences present in
      Haemophilus influenzae Rd (FluMu), Neisseria meningitidis type A strain Z2491 (Pnme1) and H.
      influenzae biotype aegyptius ATCC 11116 do not possess a Mom-encoding gene. Instead, at the
      position occupied by mom in Mu they carry an unrelated gene that encodes a protein with
      homology to DNA adenine N(6)-methyltransferases (hin1523, nma1821, hia5, respectively).
      Products of the hin1523, hia5 and nma1821 genes modify adenine residues to N(6)-methyladenine,
      both in vitro and in vivo. All of these enzymes catalyzed extensive DNA methylation; most
      notably the Hia5 protein caused the methylation of 61% of the adenines in lambda DNA. Kinetic
      analysis of oligonucleotide methylation suggests that all adenine residues in DNA, with the
      possible exception of poly(A)-tracts, constitute substrates for the Hia5 and Hin1523 enzymes.
      Their potential 'sequence specificity' could be summarized as AB or BA (where B = C, G or
      T). Plasmid DNA isolated from Escherichia coli cells overexpressing these novel DNA
      methyltransferases was resistant to cleavage by many restriction enzymes sensitive to adenine
      methylation.
AU  - Drozdz M
AU  - Piekarowicz A
AU  - Bujnicki JM
AU  - Radlinska M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: 2119-2130.

PMID- 15332077
VI  - 11
DP  - 2004
TI  - Reeling in the bases.
PG  - 804-806
AB  - EcoR124I is a type I DNA restriction and modification enzyme. The single-molecule magnetic
      tweezers technique reveals that this
      sophisticated molecular machine is capable of moving thousands of base
      pairs of DNA in one binding event.
AU  - Dryden DT
PT  - Journal Article
TA  - Nat. Struct. Mol. Biol.
JT  - Nat. Struct. Mol. Biol.
SO  - Nat. Struct. Mol. Biol. 2004 11: 804-806.

PMID- 10917668
VI  - 27
DP  - 1999
TI  - The assembly of the EcoKI type I DNA restriction/modification enzyme and its interaction with DNA.
PG  - 691-696
AB  - 
AU  - Dryden DT
AU  - Davies GD
AU  - Martin I
AU  - Powell LM
AU  - Murray NE
AU  - Ellis DJ
AU  - Berge T
AU  - Edwardson JM
AU  - Henderson RM
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 1999 27: 691-696.

PMID- 21310716
VI  - 39
DP  - 2011
TI  - DNA translocation by type III restriction enzymes: a comparison of current models of their operation derived from ensemble and single-molecule  measurements.
PG  - 4525-4531
AB  - Much insight into the interactions of DNA and enzymes has been obtained using a number of
      single-molecule techniques. However, recent results  generated using two of these
      techniques-atomic force microscopy (AFM) and  magnetic tweezers (MT)-have produced apparently
      contradictory results when applied to the action of the ATP-dependent type III restriction
      endonucleases on DNA. The AFM images show extensive looping of the DNA  brought about by the
      existence of multiple DNA binding sites on each enzyme and enzyme dimerisation. The MT
      experiments show no evidence for looping being a requirement for DNA cleavage, but instead
      support a diffusive sliding of the enzyme on the DNA until an enzyme-enzyme collision occurs,
      leading to cleavage. Not only do these two methods appear to disagree, but also the models
      derived from them have difficulty explaining some ensemble biochemical results on DNA
      cleavage. In this 'Survey and Summary', we describe several different models put forward for
      the action of type III restriction enzymes and their inadequacies. We also attempt to
      reconcile the different models and indicate areas for further experimentation to elucidate the
      mechanism of these enzymes.
AU  - Dryden DT
AU  - Edwardson JM
AU  - Henderson RM
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2011 39: 4525-4531.

PMID- 11557806
VI  - 29
DP  - 2001
TI  - Nucleoside triphosphate-dependent restriction enzymes.
PG  - 3728-3741
AB  - The known nucleoside triphosphate-dependent restriction enzymes are hetero-oligomeric proteins
      that behave as molecular machines in response to their target sequences. They translocate DNA
      in a process dependent on the hydrolysis of a nucleoside triphosphate. For the ATP-dependent
      type I and type III restriction and modification systems, the collision of translocating
      complexes triggers hydrolysis of phosphodiester bonds in unmodified DNA to generate
      double-strand breaks. Type I endonucleases break the DNA at unspecified sequences remote from
      the target sequence, type III endonucleases at a fixed position close to the target sequence.
      Type I and type III restriction and modification (R-M) systems are notable for effective
      post-translational control of their endonuclease activity. For some type I enzymes, this
      control is mediated by proteolytic degradation of that subunit of the complex which is
      essential for DNA translocation and breakage. This control, lacking in the well-studied type
      II R-M systems, provides extraordinarily effective protection of resident DNA should it
      acquire unmodified target sequences. The only well-documented GTP-dependent restriction
      enzyme, McrBC, requires methylated target sequences for the initiation of phosphodiester bond
      cleavage.
AU  - Dryden DT
AU  - Murray NE
AU  - Rao DN
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2001 29: 3728-3741.

PMID- 
VI  - 
DP  - 1999
TI  - Bacterial DNA methyltransferases.
PG  - 283-340
AB  - There are four entries for DNA MTases in the E.C. database.  Classes 2.1.1.37 and 2.1.1.73
      both methylate carbon 5 of the cytosine base and differ in that the former group contains a
      large regulatory domain and is only found in multicellular eukarotes.  Classes 2.1.1.72 and
      2.1.1.113 act on the exocyclic amino groups of adenine and cytosine respectively.  Thus, three
      modifications carried out by MTases have now been identified. Cytosine can be modified at
      either the C5 or N4 position, and adenine at the N6 position.  These methylation sites are all
      in the major groove of B-form DNA which is also the region which allows the most effective
      recognition of a DNA sequence via hydrogen bonding and hydrophobic interactions.
AU  - Dryden DTF
PT  - Journal Article
TA  - S-Adenosylmethionine-dependent Methyltransferases: Structures and Functions.
JT  - S-Adenosylmethionine-dependent Methyltransferases: Structures and Functions.
SO  - S-Adenosylmethionine-dependent Methyltransferases: Structures and Functions. 1999 : 283-340.

PMID- 29138322
VI  - 114
DP  - 2017
TI  - Structures of the type I DNA restriction enzymes.
PG  - E10261-E10262
AB  - The article by Liu et al. (1) on the structure of type I
      DNA restriction and modification enzymes purports to
      significantly advance our understanding of these enzymes
      and proposes a model for their operation.
      While the partial structure of one of these enzymes
      is interesting and defines the interface between some
      of the subunits, the article contains many misinterpretations
      of the literature.
AU  - Dryden DTF
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2017 114: E10261-E10262.

PMID- 24119670
VI  - 21
DP  - 2013
TI  - The Architecture of Restriction Enzymes.
PG  - 1720-1721
AB  - In this issue of Structure, Lyumkis and colleagues describe a high resolution structure of a
      polymerized form of the SgrAl restriction enzyme, which shows that it forms a helical assembly
      with four enzyme molecules per turn of the helix. The DNA is arranged on the periphery of the
      protein helix pointing away from the helical axis.
AU  - Dryden DTF
PT  - Journal Article
TA  - Structure
JT  - Structure
SO  - Structure 2013 21: 1720-1721.

PMID- 
VI  - 8
DP  - 1997
TI  - Assembly of the multifunctional EcoKI DNA restriction enzyme in vitro.
PG  - 593-601
AB  - Type I DNA restriction/modification systems have been found in many strains of Escherichia
      coli and Salmonella enterica and several other gram negative and positive bacteria.  They
      maintain the modification of the host chromosome after DNA replication by methylating adenine
      bases on the newly synthesized DNA strand within specific DNA target sequences.  This
      methylation reaction is triggered by the recognition of targets which are methylated on the
      parental DNA stand.  If methylation is not detected on either strand then the restriction
      reaction is triggered.  Unmodified target sequences will exist on foreign DNA, usually of
      viral origin.  A type I system cleaves the foreign DNA thereby preventing (restricting) its
      replication and propagation.  In contrast to the widely used type II restriction/modification
      systems which have separate restriction endonucleases and modification methyltransferases, the
      type I systems combine both activities in one large oligomeric enzyme.
AU  - Dryden DTF
AU  - Cooper LP
AU  - Murray NE
PT  - Journal Article
TA  - Tech. Prot. Chem.
JT  - Tech. Prot. Chem.
SO  - Tech. Prot. Chem. 1997 8: 593-601.

PMID- 8514761
VI  - 268
DP  - 1993
TI  - Purification and characterization of the methyltransferase from the Type I restriction and modification system of Escherichia coli K12.
PG  - 13228-13236
AB  - The DNA methyltransferase component of the type I restriction and modification enzyme of
      Escherichia coli K12 has been purified. The active component, a trimer of molecular mass 170
      kDa consisting of one DNA recognition subunit(S) and two modification subunits(M), showed the
      expected preference for modifying a hemimethylated substrate rather than an unmethylated one.
      Small amounts of the dimers M2 and M1S1 were also isolated. Subunit rearrangements of the
      three protein species occurred on ion exchange and heparin-agarose chromatography.
      Denaturation of the trimer gave folding intermediates, and these and the dimer forms isolated
      during purification may reflect the assembly of the protein in vivo. Enzyme activity was
      recovered on refolding the denatured protein by dilution of the denaturant. A comparison of
      the predicted isoelectric points of all known S subunits of type I restriction and
      modification enzymes revealed values that correlated with the arrangement of type I systems in
      several families. Electrostatic interactions may explain the different subunit stoichiometries
      observed during purification of type I enzymes and the differing preferences for
      hemimethylated DNA displayed by the three type I families.
AU  - Dryden DTF
AU  - Cooper LP
AU  - Murray NE
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1993 268: 13228-13236.

PMID- 9033396
VI  - 36
DP  - 1997
TI  - The in vitro assembly of the EcoKI type I DNA restriction/modification enzyme and its in vivo implications.
PG  - 1065-1076
AB  - Type I DNA restriction/modification enzymes protect the bacterial cell from viral infection by
      cleaving foreign DNA which lacks N6-adenine methylation within a target sequence and
      maintaining the methylation of the targets on the host chromosome.  It has been noted that the
      genes specifying type I systems can be transferred to a new host lacking the appropriate,
      protective methylation without any adverse effect.  The modification phenotype apparently
      appears before the restriction phenotype, but no evidence for transcriptional or translational
      control of the genes and the resultant phenotypes has been found.  Type I enzymes contain
      three types of subunit, S for sequence recognition, M for DNA modification (methylation), and
      R for DNA restriction (cleavage), and can function solely as an M2S1 methylase or as a R2M2S1
      bifunctional methylase/nuclease.  We show that the methylase is not stable at the
      concentrations expected to exist in vivo, dissociating into free M subunit and M1S1, whereas
      the complete nuclease is a stable structure.  The M1S1 form can bind the R subunit as
      effectively as the M2S1 methylase but possesses no activity; therefore, upon establishment of
      the system in a new host, we propose that most of the R subunit will initially be trapped in
      an inactive complex until the methylase has been able to modify and protect the host
      chromosome.  We believe that the in vitro assembly pathway will reflect the in vivo situation,
      thus allowing the assembly process to at least partially explain the observations that the
      modification phenotype appears before the restriction phenotype upon establishment of a type I
      system in a new host cell.
AU  - Dryden DTF
AU  - Cooper LP
AU  - Thorpe PH
AU  - Byron O
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1997 36: 1065-1076.

PMID- Not carried by PubMed...
VI  - 27
DP  - 1999
TI  - The assembly of the EcoKI type I DNA restriction/modification enzyme and its interaction with DNA.
PG  - A87
AB  - Type I DNA restriction-modification enzymes protect the bacterial cell from viral infection by
      cleaving foreign DNA which lacks N6-adenine methylation within a target sequence and
      maintaining the methylation of the targets on the host chromosome.  They comprise three types
      of subunit, S M and R and can function solely as an M2S1 methylase or as an R2M2S1
      bifunctional methylase/nuclease.  The subunits contain domains related to those in other
      smaller methylases, nucleases and helicases.  The nuclease is a stable structure, whereas the
      methylase dissociates into nonfunctional forms M and M1S1 at the concentrations expected to
      exist in vivo.  The restriction reaction relies upon extensive DNA translocation driven by ATP
      hydrolysis prior to endonucleolytic DNA cleavage.  Cleavage occurs between two,
      widely-separated, target sites.  This is consistent with the translocation process causing the
      collision of two enzymes on the DNA.  However, atomic force microscopy has suggested that DNA
      binding induces dimerization of the enzyme prior to the initiation of translocation and that
      cleavage occurs once the DNA loop bound between the two enzymes has been pulled in towards the
      enzymes.
AU  - Dryden DTF
AU  - Davies GD
AU  - Powell LM
AU  - Murray NE
AU  - Ellis DJ
AU  - Berge T
AU  - Edwardson JM
AU  - Henderson RM
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 1999 27: A87.

PMID- 7552723
VI  - 2
DP  - 1995
TI  - Structural modelling of a type I DNA methyltransferase.
PG  - 632-635
AB  - Amino-acid sequence comparison and tertiary structure modelling suggest a structure for type I
      DNA methyltransferases and an evolutionary link to type II methyltransferases.
AU  - Dryden DTF
AU  - Sturrock SS
AU  - Winter M
PT  - Journal Article
TA  - Nat. Struct. Biol.
JT  - Nat. Struct. Biol.
SO  - Nat. Struct. Biol. 1995 2: 632-635.

PMID- 7607472
VI  - 157
DP  - 1995
TI  - Mutational analysis of conserved amino-acid motifs in EcoKI adenine methyltransferase.
PG  - 123-124
AB  - The EcoKI methyltransferase (M.EcoKI, MTase) contains the amino acid (aa) sequences AAGTA and
      NPPF believed to represent the two sequences that are strongly conserved in adenine MTases.
      We have analysed a mutation in the first sequence that abolishes cofactor binding and enzyme
      activity, and mutations in the second sequence that reduce or abolish activity without
      affecting cofactor and DNA binding.
AU  - Dryden DTF
AU  - Willcock DF
AU  - Murray NE
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 123-124.

PMID- 28726616
VI  - 23
DP  - 2017
TI  - Molecular Characterization of Corynebacterium diphtheriae Outbreak Isolates, South Africa, March-June 2015.
PG  - 1308-1315
AB  - In 2015, a cluster of respiratory diphtheria cases was reported from
      KwaZulu-Natal Province in South Africa. By using whole-genome analysis, we
      characterized 21 Corynebacterium diphtheriae isolates collected from 20 patients
      and contacts during the outbreak (1 patient was infected with 2 variants of C.
      diphtheriae). In addition, we included 1 cutaneous isolate, 2 endocarditis
      isolates, and 2 archived clinical isolates (ca. 1980) for comparison. Two novel
      lineages were identified, namely, toxigenic sequence type (ST) ST-378 (n = 17)
      and nontoxigenic ST-395 (n = 3). One archived isolate and the cutaneous isolate
      were ST-395, suggesting ongoing circulation of this lineage for >30 years. The
      absence of preexisting molecular sequence data limits drawing conclusions
      pertaining to the origin of these strains; however, these findings provide
      baseline genotypic data for future cases and outbreaks. Neither ST has been
      reported in any other country; this ST appears to be endemic only in South
      Africa.
AU  - du Plessis M et al
PT  - Journal Article
TA  - Emerg. Infect. Dis.
JT  - Emerg. Infect. Dis.
SO  - Emerg. Infect. Dis. 2017 23: 1308-1315.

PMID- 23021223
VI  - 151
DP  - 2012
TI  - Dual binding of chromomethylase domains to H3K9me2-containing nucleosomes directs DNA methylation in plants.
PG  - 167-180
AB  - DNA methylation and histone modification exert epigenetic control over gene expression. CHG
      methylation by CHROMOMETHYLASE3 (CMT3) depends on histone H3K9
      dimethylation (H3K9me2), but the mechanism underlying this relationship is poorly
      understood. Here, we report multiple lines of evidence that CMT3 interacts with
      H3K9me2-containing nucleosomes. CMT3 genome locations nearly perfectly correlated
      with H3K9me2, and CMT3 stably associated with H3K9me2-containing nucleosomes.
      Crystal structures of maize CMT3 homolog ZMET2, in complex with H3K9me2 peptides,
      showed that ZMET2 binds H3K9me2 via both bromo adjacent homology (BAH) and chromo
      domains. The structures reveal an aromatic cage within both BAH and chromo
      domains as interaction interfaces that capture H3K9me2. Mutations that abolish
      either interaction disrupt CMT3 binding to nucleosomes and show a complete loss
      of CMT3 activity in vivo. Our study establishes dual recognition of H3K9me2 marks
      by BAH and chromo domains and reveals a distinct mechanism of interplay between
      DNA methylation and histone modification.
AU  - Du J
AU  - Zhong X
AU  - Bernatavichute YV
AU  - Stroud H
AU  - Feng S
AU  - Caro E
AU  - Vashisht AA
AU  - Terragni J
AU  - Chin HG
AU  - Tu A
AU  - Hetzel J
AU  - Wohlschlegel JA
AU  - Pradhan S
AU  - Patel DJ
AU  - Jacobsen SE
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 2012 151: 167-180.

PMID- 
VI  - S
DP  - 2007
TI  - Rapid mapping of large DNA molecules using fluorescent labeled restriction enzyme.
PG  - 331A
AB  - Rapid DNA mapping at the single molecule level is a powerful tool for research and clinical
      application. We report here a development of new tags for high throughput mapping of large DNA
      based on our Direct Linear Analysis (DLA) technology. Double-stranded DNA molecules were
      stained with two fluorescent tags: a nonspecific intercalator for uniform backbone staining
      and a sequence-specific tag for physical mapping. These DNA molecules were then stretched by
      elongational flow to a linear conformation in a high-throughput microfluidic device, and the
      positions of site-specific tags were detected. We applied restriction enzymes for DNA tagging
      due to their unique features including high binding affinity, sequence specificity, and fast
      target localization. The restriction enzymes selected for tagging retained high binding
      efficiency in the presence of Ca++ after fluorescent-labeling; however, their cleavage
      function was inactivated. We show that DNA fragments ranging from 50-200 kb, or 16-66
      microns-long, can be tagged with fluorescently labeled AgeI or BamHI, intercalated, stretched
      to their contour length in our device, and then interrogated molecule by molecule. More than
      5,000 molecules could be analyzed through the microfluidic device in 10-15 minutes and
      identity of the DNA fragments revealed by tagging patterns as well as lengths. We analyzed
      multiple genomic DNA fragments from E. coli stains, demonstrating great potential of using
      this method to obtain information regarding DNA structure and to discriminate DNA fragments
      originated from different organisms.
AU  - Du L
AU  - Zhang M
AU  - Burton R
AU  - Spielberger K
AU  - Mollova E
AU  - Gilmanshin R
PT  - Journal Article
TA  - Biophys. J.
JT  - Biophys. J.
SO  - Biophys. J. 2007 S: 331A.

PMID- 26929335
VI  - 113
DP  - 2016
TI  - Human DNMT1 transition state structure.
PG  - 2916-2921
AB  - Human DNA methyltransferase 1 (DNMT1) maintains the epigenetic state of DNA by replicating CpG
      methylation signatures from parent to daughter strands, producing heritable methylation
      patterns through cell divisions. The proposed catalytic mechanism of DNMT1 involves
      nucleophilic attack of Cys1226 to cytosine (Cyt) C6, methyl transfer from
      S-adenosyl-l-methionine (SAM) to Cyt C5, and proton abstraction from C5 to form methylated CpG
      in DNA. Here, we report the subangstrom geometric and electrostatic structure of the major
      transition state (TS) of the reaction catalyzed by human DNMT1. Experimental kinetic isotope
      effects were used to guide quantum mechanical calculations to solve the TS structure. Methyl
      transfer occurs after Cys1226 attack to Cyt C6, and the methyl transfer step is chemically
      rate-limiting for DNMT1. Electrostatic potential maps were compared for the TS and ground
      states, providing the electronic basis for interactions between the protein and reactants at
      the TS. Understanding the TS of DNMT1 demonstrates the possibility of using similar analysis
      to gain subangstrom geometric insight into the complex reactions of epigenetic modifications.
AU  - Du Q
AU  - Wang Z
AU  - Schramm VL
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2016 113: 2916-2921.

PMID- 21551293
VI  - 193
DP  - 2011
TI  - Genome Sequence of Gluconacetobacter sp. Strain SXCC-1, Isolated from Chinese Vinegar Fermentation Starter.
PG  - 3395-3396
AB  - Gluconacetobacter are prominent bacteria during traditional vinegar fermentation. Here, we
      report a draft genome sequence of Gluconacetobacter
      sp. strain SXCC-1. This strain was isolated from fermentation starter
      (Daqu) that used for commercial production of Shanxi vinegar, the best
      known vinegar of China.
AU  - Du XJ
AU  - Jia SR
AU  - Yang Y
AU  - Wang S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3395-3396.

PMID- 23929487
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Lactococcus lactis subsp. lactis Strain YF11.
PG  - e00599-13
AB  - Lactococcus lactis subsp. lactis strain YF11 is a food preservative bacterium with a high
      capacity to produce nisin. Here, we announce the draft genome
      sequence of Lactococcus lactis subsp. lactis YF11 (2,527,433 bp with a G+C
      content of 34.81%).
AU  - Du Y
AU  - Song L
AU  - Feng W
AU  - Pei G
AU  - Zheng P
AU  - Yu Z
AU  - Sun J
AU  - Qiao J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00599-13.

PMID- 25555737
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Cellulolytic Bacterium Clavibacter sp. CF11, a Strain Producing Cold-Active Cellulase.
PG  - e01304-14
AB  - Clavibacter sp. strain CF11, which was isolated from soil at a tomato-planting greenhouse in
      Inner Mongolia, North China, has a high capability for producing
      cold-active cellulase at low temperatures. Here, we report the draft genome
      sequence of strain CF11, which comprises 2,437 protein-coding sequences and 49
      RNA-coding sequences.
AU  - Du Y
AU  - Yuan B
AU  - Zeng Y
AU  - Meng J
AU  - Li H
AU  - Wang R
AU  - Li G
AU  - Feng F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01304-14.

PMID- 21725015
VI  - 193
DP  - 2011
TI  - Draft Genome Sequence of the Novel Agar-Digesting Marine Bacterium HQM9.
PG  - 4557
AB  - Strain HQM9, an aerobic rod-shaped marine bacterium from red alga, can produce agarases and
      liquefy solid plating medium efficiently when agar
      was used as coagulant. Here we report the draft genome sequence of strain
      HQM9, which should be a novel species of Flavobacteriaceae, and initial
      findings from its preliminary analysis.
AU  - Du Z
AU  - Zhang Z
AU  - Miao T
AU  - Wu J
AU  - Lu G
AU  - Yu J
AU  - Xiao J
AU  - Chen G
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4557.

PMID- 23723402
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Agrobacterium sp. Strain UHFBA-218, Isolated from Rhizosphere Soil of Crown Gall-Infected Cherry Rootstock Colt.
PG  - e00302-13
AB  - We report here the draft genome sequence of the alphaproteobacterium Agrobacterium sp. strain
      UHFBA-218, which was isolated from rhizosphere soil of
      crown gall-infected cherry rootstock Colt. The draft genome of strain UHFBA-218
      consists of 112 contigs (5,425,303 bp) and 5,063 coding sequences with a G+C
      content of 59.8%.
AU  - Dua A
AU  - Sangwan N
AU  - Kaur J
AU  - Saxena A
AU  - Kohli P
AU  - Gupta AK
AU  - Lal R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00302-13.

PMID- 21914880
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Rickettsia heilongjiangensis, an Emerging Tick-Transmitted Human Pathogen.
PG  - 5564-5565
AB  - Rickettsia heilongjiangensis is an emerging tick-transmitted human pathogen causing
      far-Eastern spotted fever. Here we report the complete
      sequence and the main features of the genome of R. heilongjiangensis
      (strain 054).
AU  - Duan C
AU  - Tong Y
AU  - Huang Y
AU  - Wang X
AU  - Xiong X
AU  - Wen B
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5564-5565.

PMID- 25527293
VI  - 34
DP  - 2015
TI  - Specific but interdependent functions for Arabidopsis AGO4 and AGO6 in RNA-directed DNA methylation.
PG  - 581-592
AB  - Argonaute (AGO) family proteins are conserved key components of small RNA-induced silencing
      pathways. In the RNA-directed DNA methylation (RdDM) pathway in
      Arabidopsis, AGO6 is generally considered to be redundant with AGO4. In this
      report, our comprehensive, genomewide analyses of AGO4- and AGO6-dependent DNA
      methylation revealed that redundancy is unexpectedly negligible in the genetic
      interactions between AGO4 and AGO6. Immunofluorescence revealed that AGO4 and
      AGO6 differ in their subnuclear co-localization with RNA polymerases required for
      RdDM. Pol II and AGO6 are absent from perinucleolar foci, where Pol V and AGO4
      are co-localized. In the nucleoplasm, AGO4 displays a strong co-localization with
      Pol II, whereas AGO6 co-localizes with Pol V. These patterns suggest that RdDM is
      mediated by distinct, spatially regulated combinations of AGO proteins and RNA
      polymerases. Consistently, Pol II physically interacts with AGO4 but not AGO6,
      and the levels of Pol V-dependent scaffold RNAs and Pol V chromatin occupancy are
      strongly correlated with AGO6 but not AGO4. Our results suggest that AGO4 and
      AGO6 mainly act sequentially in mediating small RNA-directed DNA methylation.
AU  - Duan CG
AU  - Zhang H
AU  - Tang K
AU  - Zhu X
AU  - Qian W
AU  - Hou YJ
AU  - Wang B
AU  - Lang Z
AU  - Zhao Y
AU  - Wang X
AU  - Wang P
AU  - Zhou J
AU  - Liang G
AU  - Liu N
AU  - Wang C
AU  - Zhu JK
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 2015 34: 581-592.

PMID- 9160747
VI  - 89
DP  - 1997
TI  - Crystal structure of PI-SceI, a homing endonuclease with protein splicing activity.
PG  - 555-564
AB  - PI-SceI is a bifunctional yeast protein that propagates its mobile gene by catalyzing protein
      splicing and site-specific DNA double-strand cleavage.  Here, we report the 2.4 A crystal
      structure of the PI-SceI protein.  The structure is composed of two separate domains (I and
      II) with novel folds and different functions.  Domain I, which is elongated and formed largely
      from seven beta sheets, harbors the N and C termini residues and two His residues that are
      implicated in protein splicing.  Domain II, which is compact and is primarily composed of two
      similar alpha/beta motifs related by local two-fold symmetry, contains the putative nuclease
      active site with a cluster of two acidic residues and one basic residue commonly found in
      restriction endonucleases.  This report presents prototypic structures of domains with single
      endonuclease and protein splicing active sites.
AU  - Duan X
AU  - Gimble FS
AU  - Quiocho FA
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1997 89: 555-564.

PMID- 8969304
VI  - 264
DP  - 1996
TI  - Dynamic contributions to the DNA binding entropy of the EcoRI and EcoRV restriction endonucleases.
PG  - 546-555
AB  - Molecular dynamics simulations on DNA-EcoRI and DNA-EcoRV complexes suggest that the DNA
      within these complexes is significantly more ordered than free DNA.  Similarly, both the
      protein and the DNA are more ordered in the specific (cognate) DNA-EcoRV complex than they are
      in the non-cognate DNA-protein complex, consistent with recently proposed analogies between
      protein folding and sequence-specific DNA-protein recognition.  Analysis of the trajectories
      shows that the net entropy gain upon specific binding to be the result of opposing
      contributions.  Solvent release, which increases entropy versus configurational terms (as
      measured by the magnitude of the atomic fluctuations), and collective terms from tight
      coupling between the motions of the protein and the DNA.
AU  - Duan Y
AU  - Wilkosz P
AU  - Rosenberg JM
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1996 264: 546-555.

PMID- 28729265
VI  - 5
DP  - 2017
TI  - The Complete Genome Sequence of Trueperella pyogenes UFV1 Reveals a Processing System Involved in the Quorum-Sensing Signal Response.
PG  - e00639-17
AB  - We present here the complete genome sequence of Trueperella pyogenes UFV1. The 2.3-Mbp genome
      contains an extremely interesting AI-2 transporter and processing
      system related to the quorum-sensing signal response. This specific feature is
      described in this species for the first time and might be responsible for a new
      pathogenic behavior.
AU  - Duarte VDS
AU  - Treu L
AU  - Campanaro S
AU  - Dias RS
AU  - Silva CCD
AU  - Giacomini A
AU  - Corich V
AU  - de Paula SO
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00639-17.

PMID- 27056224
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the New Pathogen for Bivalve Larvae Vibrio bivalvicida.
PG  - e00216-16
AB  - Vibrio bivalvicidais a novel pathogen of bivalve larvae responsible for recent vibriosis
      outbreaks affecting shellfish hatcheries. Here, we announce the draft
      genome sequence ofV. bivalvicida605(T)and describe potential virulence factors.
AU  - Dubert J
AU  - Spinard EJ
AU  - Nelson DR
AU  - Gomez-Chiarri M
AU  - Romalde JL
AU  - Barja JL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00216-16.

PMID- 9115372
VI  - 25
DP  - 1997
TI  - Angle and locus of the bend induced by the MspI DNA methyltransferase in a sequence-specific complex with DNA.
PG  - 2025-2029
AB  - Bending of DNA induced by M.MspI, one of the m5C-DNA methyltransferases, has been investigated
      using circular permutation analysis.  The M.MspI Mtase induced sharp bends in DNA containing
      its recognition sequence 5'-CCGG-3' which was estimated to be 142 +/- 4 degrees and 132 +/-
      4 degrees for circularly permuted DNA fragments of 127 and 1459 bp respectively.  The bend
      center was found to be asymmetric with respect to the CCGG sequence and appeared to exclude
      the 'target cytosine'.  An estimate of -15 kcal/mol was obtained for the free energy
      associated with M.MspI-induced DNA bending.
AU  - Dubey AK
AU  - Bhattacharya SK
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1997 25: 2025-2029.

PMID- 18587865
VI  - 33
DP  - 1989
TI  - Stabilization of restriction endonuclease BamHI by cross-linking reagents.
PG  - 1311-1316
AB  - Bacillus amyloliquefaciens H produces a restriction endonuclease BamHI which is
      heat labile even at low temperatures.  Studies were conducted to enhance
      thermal stability of BamHI using cross-linking reagents, namely,
      glutaraldehyde, dimethyl adipimidate (DMA), dimethyl suberimidate (DMS), and
      dimethyl 3,3'-dithiobispropionimidate (DTBP).  Reaction with glutaraldehyde did
      not result in a preparation with enhanced thermal stability.  However, the
      DMA-, DMS-, and DTBP-cross-linked preparations of BamHI exhibited significant
      improvement in thermal stability.  Studies on thermal denaturation of the
      cross-linked enzyme preparations revealed that these do not follow a true
      first-order kinetics.  A possible deactivation scheme has been proposed in
      which the enzyme has been envisaged to go through a fully active but more
      susceptible transient state which, on prolonged heat exposure, exhibits a
      first-order decay kinetics.  At 35C, which is close to the optimum reaction
      temperature of 37C for BamHI activity, the half-life of DMA-, DMS-, and
      DTBP-cross-linked preparations were 4.0, 5.25, and 5.5 h, respectively, whereas
      the native enzyme exhibited a half-life of 1.2 h only.  The apparent values of
      deactivation rate constants for native, DMA-, DMS-, and DTBP-cross-linked BamHI
      were 1.13, 0.39, 0.29, and 0.26 h-1, respectively, at the same temperature, and
      the apparent values of activation energies for denaturation of native, DMA-,
      DMS-, and DTBP-cross-linked BamHI were 2.63, 5.24, 6.55, and 9.2 kcal/mol,
      respectively.  The DTBP-cross-linked BamHI was, therefore, the best heat-stable
      preparation among those tested.  The unusually low values of activation
      energies for denaturation of BamHI show their highly thermolabile nature
      compared to other commonly encountered enzymes such as trypsin, having
      activation energies of more than 40 kcal/mol for their denaturation.
AU  - Dubey AK
AU  - Bisaria VS
AU  - Mukhopadhyay SN
AU  - Ghose TK
PT  - Journal Article
TA  - Biotechnol. Bioeng.
JT  - Biotechnol. Bioeng.
SO  - Biotechnol. Bioeng. 1989 33: 1311-1316.

PMID- 1579450
VI  - 20
DP  - 1992
TI  - Purification and characteriation of the MspI DNA methyltransferase cloned and overexpressed in E. coli.
PG  - 1579-1585
AB  - The MspI restriction-modification system, which recognizes the sequence 5'-CCGG-3', has been
      previously cloned and sequenced. We subcloned the methyltransfearse gene (M.MspI) downstream
      of the ptac promoter in the multicopy vector pUC119 and overexpressed it in E. coli. Upon
      induction with IPTG, M.MspI constitutes more than 10% of cellular protein. A scheme has been
      devised to purify large amounts of biologically active M.MspI to apparent homogeneity from
      these overexpressing E. coli cells. Approximately 0.8 mg of pure M.MspI per gram of cells (wet
      weight) can be obtained. The apparent molecular weight of M.MspI is 49 kD, by SDS gel
      electrophoresis and 48-54 kD by gel filtration. At low concentrations (less than 0.4 mg/ml),
      the methyltransferase is a monomer in solution but at higher concentrations (greater than 3.0
      mg/ml) it exists predominantly as a dimer. Polyclonal antibodies raised against M.MspI
      cross-react with the DNA-methyltransferases of several other restriction-modification systems.
AU  - Dubey AK
AU  - Mollet B
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 1579-1585.

PMID- Not carried by PubMed...
VI  - 22
DP  - 1987
TI  - Sources, production, and purification of restriction enzymes.
PG  - 25-34
AB  - At present restriction enzymes are low volume, high value microbial products
      but information on their production, downstream processing, stability
      characteristics and applications have not been discussed from a
      biotechnological view point.  In this article an attempt has been made to bring
      out relevant information on restriction enzymes in collated form.
AU  - Dubey AK
AU  - Mukhopadhyay SN
AU  - Bisaria VS
AU  - Ghose TK
PT  - Journal Article
TA  - Process. Biochem.
JT  - Process. Biochem.
SO  - Process. Biochem. 1987 22: 25-34.

PMID- 1535704
VI  - 20
DP  - 1992
TI  - Sequence-specific DNA binding by the MspI DNA methyltransferase.
PG  - 3167-3173
AB  - The MspI methyltransferase (M.MspI) recognizes the sequence CCGG and catalyzes the formation
      of 5-methylcytosine at the first C-residue. We have investigated the sequence-specific
      DNA-binding properties of M.MspI under equilibrium conditions, using gel-mobility shift assays
      and DNaseI footprinting. M.MspI binds to DNA in a sequence-specific manner either alone or in
      the presence of the normal methyl donor S-adenosyl-L-methionine as well as the analogues,
      sinefungin and S-adenosyl-L-homocysteine. In the presence of S-adenosyl-L-homocysteine, M.MspI
      shows the highest binding affinity to DNA containing a hemimethylated recognition sequence
      (Kd=3.6x10-7M), but binds less well to unmethylated DNA (Kd=8.3x10-7M). Surprisingly it shows
      specific, although poor, binding to fully methylated DNA (Kd=4.2x10-6M). M.MspI binds
      approximately 5-fold more tightly to DNA containing its recognition sequence, CCGG, than to
      nonspecific sequences in the absence of cofactors. In the presence of S-adenosyl-L-methionine,
      S-adenosyl-L-homocysteine or sinefungin the discrimination between specific and nonspecific
      sequences increases up to 100-fold. DNaseI footprinting studies indicate that 16 base pairs of
      DNA are covered by M.MspI, with the recognition sequence CCGG located asymmetrically within
      the footprint.
AU  - Dubey AK
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 3167-3173.

PMID- 20173011
VI  - 61
DP  - 2011
TI  - Spirochaeta perfilievii sp. nov., an oxygen-tolerant, sulfide-oxidizing, sulfur-  and thiosulfate-reducing spirochaete isolated from a saline spring.
PG  - 110-117
AB  - A novel strain of fermenting, aerotolerant, chemo-organoheterotrophic spirochaete designated
      P(T) was isolated from a sulfur 'Thiodendron' mat in a saline spring
      at the Staraya Russa resort (Novgorod Region, Russia). Cells of strain P(T)
      exhibited a helical shape. The spirochaete required sulfide in the growth medium
      and was able to oxidize it non-enzymically to elemental sulfur via the
      interaction of H(2)O(2) with sulfide and deposit it in the periplasmic space.
      Growth occurred at 4-32 degrees C (optimum at 28-30 degrees C), pH 6.0-8.5
      (optimum pH 7.0-7.5), and in 0.1-1 M NaCl (optimum 0.35 M). The isolate used
      several sugars and polysaccharides as carbon or energy sources but did not use
      peptides, amino acids, organic acids or alcohols. The products of glucose
      fermentation were formate, acetate, ethanol, pyruvate, CO(2) and H(2). The
      genomic DNA G+C content was 41.7 mol%. 16S rRNA gene sequence analysis showed
      that strain P(T) fell within a group of species in the genus Spirochaeta,
      including Spirochaeta litoralis, S. isovalerica and S. cellobiosiphila, with
      which it shared less then 89 % sequence similarity. On the basis of its
      morphology, physiology and other phenotypic properties, as well as its
      phylogenetic position, the new isolate is considered to represent a novel species
      of the genus Spirochaeta, for which the name Spirochaeta perfilievii sp. nov. is
      proposed. The type strain is P(T) (=DSM 19205(T) =VKM B-2514(T)).
AU  - Dubinina G
AU  - Grabovich M
AU  - Leshcheva N
AU  - Rainey FA
AU  - Gavrish E
PT  - Journal Article
TA  - Int. J. Syst. Evol. Microbiol.
JT  - Int. J. Syst. Evol. Microbiol.
SO  - Int. J. Syst. Evol. Microbiol. 2011 61: 110-117.

PMID- 28935737
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Listeria monocytogenes Strain ATCC 7644.
PG  - e00970-17
AB  - Listeria monocytogenes is a Gram-positive, rod-shaped, non-spore-forming bacterium which is an
      important foodborne bacterial pathogen for humans worldwide
      with high mortality rates. Here, we report a 2,964,284-bp draft genome sequence
      of Listeria monocytogenes strain ATCC 7644 (American Type Culture Collection).
AU  - Duceppe MO
AU  - Carrillo C
AU  - Huang H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00970-17.

PMID- 
VI  - 0
DP  - 2008
TI  - Meganuclease engineering.
PG  - 38-42
AB  - 
AU  - Duchateau P
AU  - Grizot S
AU  - Paques F
PT  - Journal Article
TA  - BIOFUTUR
JT  - BIOFUTUR
SO  - BIOFUTUR 2008 0: 38-42.

PMID- 14528314
VI  - 21
DP  - 2003
TI  - The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens.
PG  - 1307-1313
AB  - Photorhabdus luminescens is a symbiont of nematodes and a broad-spectrum insect pathogen. The
      complete genome sequence of strain TT01 is 5,688,987
      base pairs (bp) long and contains 4,839 predicted protein-coding genes.
      Strikingly, it encodes a large number of adhesins, toxins, hemolysins,
      proteases and lipases, and contains a wide array of antibiotic
      synthesizing genes. These proteins are likely to play a role in the
      elimination of competitors, host colonization, invasion and bioconversion
      of the insect cadaver, making P. luminescens a promising model for the
      study of symbiosis and host-pathogen interactions. Comparison with the
      genomes of related bacteria reveals the acquisition of virulence factors
      by extensive horizontal transfer and provides clues about the evolution of
      an insect pathogen. Moreover, newly identified insecticidal proteins may
      be effective alternatives for the control of insect pests.
AU  - Duchaud E et al
PT  - Journal Article
TA  - Nat. Biotechnol.
JT  - Nat. Biotechnol.
SO  - Nat. Biotechnol. 2003 21: 1307-1313.

PMID- 17592475
VI  - 25
DP  - 2007
TI  - Complete genome sequence of the fish pathogen Flavobacterium psychrophilum.
PG  - 763-769
AB  - We report here the complete genome sequence of the virulent strain JIP02/86 (ATCC 49511) of
      Flavobacterium psychrophilum, a widely
      distributed pathogen of wild and cultured salmonid fish. The genome
      consists of a 2,861,988-base pair (bp) circular chromosome with 2,432
      predicted protein-coding genes. Among these predicted proteins, stress
      response mediators, gliding motility proteins, adhesins and many putative
      secreted proteases are probably involved in colonization, invasion and
      destruction of the host tissues. The genome sequence provides the basis
      for explaining the relationships of the pathogen to the host and opens new
      perspectives for the development of more efficient disease control
      strategies. It also allows for a better understanding of the physiology
      and evolution of a significant representative of the family
      Flavobacteriaceae, whose members are associated with an interesting
      diversity of lifestyles and habitats.
AU  - Duchaud E
AU  - Boussaha M
AU  - Loux V
AU  - Bernardet JF
AU  - Michel C
AU  - Kerouault B
AU  - Mondot S
AU  - Nicolas P
AU  - Bossy R
AU  - Caron C
AU  - Bessieres P
AU  - Gibrat JF
AU  - Claverol S
AU  - Dumetz F
AU  - Henaff ML
AU  - Benmansour A
PT  - Journal Article
TA  - Nat. Biotechnol.
JT  - Nat. Biotechnol.
SO  - Nat. Biotechnol. 2007 25: 763-769.

PMID- 3029706
VI  - 15
DP  - 1987
TI  - Isolation and purification of CeqI endonuclease, an isoschizomer of EcoRV.
PG  - 1334
AB  - None
AU  - Duda EG
AU  - Izsvak Z
AU  - Orosz A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1987 15: 1334.

PMID- 24501627
VI  - 8
DP  - 2013
TI  - Non contiguous-finished genome sequence of Pseudomonas syringae pathovar syringae strain B64 isolated from wheat.
PG  - 420-429
AB  - The Gram-negative gammaproteobacterium Pseudomonas syringae is one of the most wide-spread
      plant pathogens and has been repeatedly reported to cause significant
      damage to crop plantations. Research on this pathogen is very intensive, but most
      of it is done on isolates that are pathogenic to Arabidopsis, tomato, and bean.
      Here, we announce a high-quality draft genome sequence of Pseudomonas syringae
      pv. syringae B64 which is the first published genome of a P. syringae strain
      isolated from wheat up to date. The genome sequence will assist in gaining
      insights into basic virulence mechanisms of this pathogen which has a relatively
      small complement of type III effectors.
AU  - Dudnik A
AU  - Dudler R
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 420-429.

PMID- 23950121
VI  - 1
DP  - 2013
TI  - High-Quality Draft Genome Sequence of Pseudomonas syringae pv. Syringae Strain SM, Isolated from Wheat.
PG  - e00610-13
AB  - Pseudomonas syringae is one of the most widespread plant pathogens that can cause significant
      damage to crop plantations. Here, we announce a noncontiguous
      finished genome sequence of Pseudomonas syringae pv. syringae strain SM, isolated
      from hexaploid wheat. The genome sequence revealed the smallest described
      complement of type III effectors.
AU  - Dudnik A
AU  - Dudler R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00610-13.

PMID- 24723725
VI  - 2
DP  - 2014
TI  - Genome and Transcriptome Sequences of Pseudomonas syringae pv. syringae B301D-R.
PG  - e00306-14
AB  - Strains of the plant pathogen Pseudomonas syringae are commonly found in the phylosphere and
      are able to infect a number of agriculturally important crops. Here, we report a high-quality
      draft genome sequence of Pseudomonas syringae pv. syringae B301D-R, isolated from pears, which
      is a model strain for phytotoxin research in P. syringae.
AU  - Dudnik A
AU  - Dudler R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00306-14.

PMID- 12381401
VI  - 80
DP  - 2003
TI  - Salmonella DNA adenine methylase mutants prevent colonization of newly hatched chickens by homologous and heterologous serovars.
PG  - 153-159
AB  - Salmonella mutants lacking DNA adenine methylase (Dam) are highly attenuated for virulence and
      confer protection against oral challenge with
      homologous and heterologous Salmonella serovars in mice and chicken
      broilers. To determine whether vaccines based on Dam are efficacious in
      preventing early colonization of newly hatched chickens, a Salmonella
      typhimurium Dam(-) vaccine was evaluated for the protection of chicks
      against oral challenge with homologous and heterologous Salmonella
      serovars. Vaccination of chicks elicited protection 2 and 6 days
      post-challenge as evidenced by a significant reduction in colonization of
      the gastrointestinal tract (ileum, cecum and feces) and visceral organs
      (spleen and bursa) when challenged with homologous S. typhimurium.
      Moderate protection was observed following challenge with heterologous S.
      enteritidis and Salmonella O6, 14, 24:e, h-monophasic) serovars. These
      data suggest that Salmonella Dam mutant strains conferred
      cross-protection, presumably via competitive exclusion mechanisms that
      prevent superinfection of chicks by other Salmonella strains. Such
      protection may reduce pre-harvest Salmonella contamination in poultry,
      decreasing the potential for food-borne transmission of this pathogen to
      humans.
AU  - Dueger EL
AU  - House JK
AU  - Heithoff DM
AU  - Mahan MJ
PT  - Journal Article
TA  - Int. J. Food Microbiol.
JT  - Int. J. Food Microbiol.
SO  - Int. J. Food Microbiol. 2003 80: 153-159.

PMID- 11705984
VI  - 69
DP  - 2001
TI  - Salmonella DNA adenine methylase mutants elicit protective immune responses to homologous and heterologous serovars in chickens.
PG  - 7950-7954
AB  - Salmonella DNA adenine methylase (Dam) mutants that lack or
      overproduce Dam are highly attenuated for virulence in mice and confer
      protection against murine typhoid fever. To determine whether vaccines
      based on Dam are efficacious in poultry, a Salmonella Dam-vaccine was
      evaluated in the protection of chicken broilers against oral challenge
      with homologous and heterologous Salmonella serovars. A Salmonella
      enterica serovar Typhimurium Dam-vaccine strain was
      attenuated for virulence in day-of-hatch chicks more than 100,000-fold.
      Vaccination of chicks elicited cross-protective immune responses, as
      evidenced by reduced colonization (10- to 10,000-fold) of the
      gastrointestinal tract (ileum, cecum, and feces) and visceral organs
      (bursa and spleen) after challenge with homologous (Typhimurium F98)
      and heterologous (Enteritidis 4973 and S. enterica
      O6,14,24: e,h-monophasic) Salmonella serovars that are
      implicated in Salmonella infection of poultry. The
      protection conferred was observed for the organ or the maximum
      CFU/tissue/bird as a unit of analysis, suggesting that Dam mutant
      strains may serve as the basis for the development of efficacious
      poultry vaccines for the containment of Salmonella.
AU  - Dueger EL
AU  - House JK
AU  - Heithoff DM
AU  - Mahan MJ
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2001 69: 7950-7954.

PMID- 12804855
VI  - 21
DP  - 2003
TI  - Salmonella DNA adenine methylase mutants elicit early and late onset protective immune responses in calves.
PG  - 3249-3258
AB  - Salmonellosis is an important disease of livestock and Salmonella contamination of
      livestock-derived food products and effluents pose a
      significant risk to human health. Salmonella vaccines currently available
      to prevent salmonellosis in cattle have limited efficacy. Here we
      evaluated a Salmonella enterica serovar Typhimurium vaccine strain lacking
      the DNA adenine methylase (Dam) for safety and efficacy in calves.
      Vaccination was safe in calves, and following challenge with virulent
      Typhimurium 4 weeks post-immunization, vaccinated animals exhibited
      significantly lower mortality, diarrhea, and rectal temperatures, as well
      as reduced colonization of gastrointestinal tract and visceral organs
      compared to non-vaccinated control animals. Additionally, early onset
      protection (competitive exclusion) in vaccinated neonatal calves was
      demonstrated by attenuated clinical disease (as measured by rectal
      temperatures and attitude scores) and reduced mortality when challenged
      with virulent Typhimurium 24h after immunization. Taken together, these
      data suggest that vaccination with Salmonella Dam mutant strains confer
      significant protection against Salmonella infections in cattle via both
      adaptive immunity and competitive exclusion mechanisms.
AU  - Dueger EL
AU  - House JK
AU  - Heithoff DM
AU  - Mahan MJ
PT  - Journal Article
TA  - Vaccine
JT  - Vaccine
SO  - Vaccine 2003 21: 3249-3258.

PMID- 24874690
VI  - 2
DP  - 2014
TI  - Complete Genome of Rhodococcus pyridinivorans SB3094, a Methyl-Ethyl-Ketone-Degrading Bacterium Used for Bioaugmentation.
PG  - e00525-14
AB  - Here, we present the complete genome of Rhodococcus pyridinivorans SB3094, a
      methyl-ethyl-ketone (MEK)-degrading strain used for bioaugmentation relating to
      the treatment of wastewater contamination with petrochemical hydrocarbons. The
      genome highlights important features for bioaugmentation, including the genes
      involved in the degradation of MEK.
AU  - Dueholm MS
AU  - Albertsen M
AU  - D'Imperio S
AU  - Tale VP
AU  - Lewis D
AU  - Nielsen PH
AU  - Nielsen JL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00525-14.

PMID- 26067967
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of the Bacterium Aalborg_AAW-1, Representing a Novel Family within the Candidate Phylum SR1.
PG  - e00624-15
AB  - Here, we present the complete genome sequence of the candidate phylum SR1 bacterium
      Aalborg_AAW-1. Its 16S rRNA gene is only 85.5% similar to that of the
      closest relative, RAAC1_SR1, and the genome of Aalborg_AAW-1 consequently
      represents the first of a novel family within the candidate phylum SR1.
AU  - Dueholm MS
AU  - Albertsen M
AU  - Stokholm-Bjerregaard M
AU  - McIlroy SJ
AU  - Karst SM
AU  - Nielsen PH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00624-15.

PMID- 25212622
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Pseudomonas sp. UK4, a Model Organism for Studies of  Functional Amyloids in Pseudomonas.
PG  - e00898-14
AB  - Here, we present the complete genome of Pseudomonas sp. UK4. This bacterium was the first
      Pseudomonas strain shown to produce functional amyloids, and it
      represents a model organism for studies of functional amyloids in Pseudomonas
      (Fap).
AU  - Dueholm MS
AU  - Danielsen HN
AU  - Nielsen PH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00898-14.

PMID- 
VI  - 
DP  - 1988
TI  - DNA enzymes of Neisseria gonorrhoeae.
PG  - 251-256
AB  - Two gonococcal strains, the Dam+ strain D109, and the Dam- strain D211, were investigated for
      enzyme content. Enzymes were obtained from surface washes, by sonication and by osmotic shock.
      They were partially purified by precipitation and heparin-sepharose affinity chromatography.
      Endonuclease activity was assayed by using both dam-methylated and nonmethylated
      bacteriophage lambda DNA.  Two endonuclease activities that have not been previously described
      in the gonococcus were discovered.  One, designated R.NgoIX, is an isoschizomer of DpnI. [The
      enzyme named NgoIX has been renamed NgoDXVII. Enzymes with the specificity NgoX are mixtures
      of NgoI and NgoVIII specificities.]
AU  - Duff MK
AU  - Davies JK
PT  - Journal Article
TA  - Gonococci and Meningococci
JT  - Gonococci and Meningococci
SO  - Gonococci and Meningococci 1988 : 251-256.

PMID- 3150361
VI  - 74
DP  - 1988
TI  - Multiple restriction-modification systems in Neisseria gonorrhoeae.
PG  - 227-228
AB  - Meeting Abstract
AU  - Duff MK
AU  - Davies JK
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 227-228.

PMID- 12917486
VI  - 100
DP  - 2003
TI  - Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome.
PG  - 10020-10025
AB  - Prochlorococcus marinus, the dominant photosynthetic organism in the ocean, is found in two
      main ecological forms: high-light-adapted genotypes
      in the upper part of the water column and low-light-adapted genotypes at
      the bottom of the illuminated layer. P. marinus SS120, the complete genome
      sequence reported here, is an extremely low-light-adapted form. The genome
      of P. marinus SS120 is composed of a single circular chromosome of
      1,751,080 bp with an average G+C content of 36.4%. It contains 1,884
      predicted protein-coding genes with an average size of 825 bp, a single
      rRNA operon, and 40 tRNA genes. Together with the 1.66-Mbp genome of P.
      marinus MED4, the genome of P. marinus SS120 is one of the two smallest
      genomes of a photosynthetic organism known to date. It lacks many genes
      that are involved in photosynthesis, DNA repair, solute uptake,
      intermediary metabolism, motility, phototaxis, and other functions that
      are conserved among other cyanobacteria. Systems of signal transduction
      and environmental stress response show a particularly drastic reduction in
      the number of components, even taking into account the small size of the
      SS120 genome. In contrast, housekeeping genes, which encode enzymes of
      amino acid, nucleotide, cofactor, and cell wall biosynthesis, are all
      present. Because of its remarkable compactness, the genome of P. marinus
      SS120 might approximate the minimal gene complement of a photosynthetic
      organism.
AU  - Dufresne A et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2003 100: 10020-10025.

PMID- 169355
VI  - 96
DP  - 1975
TI  - Ligation of EcoRI endonuclease-generated DNA fragments into linear and circular structures.
PG  - 171-184
AB  - Double-stranded DNA fragments terminated at their 5'-ends by the
      single-stranded sequence pA-A-T-T-, generated by digestion of DNA with EcoRI
      restriction endonuclease, were ligated with Escherichia coli polynucleotide
      ligase under various conditions of temperature, concentration and time.  The
      linear and circular products of ligation were separated by electrophoresis in
      agarose gel and quantitated by densitometry.  The rate of ligation of
      (EcoRI-cleaved) simian virus (SV40) DNA at a concentration of 100 microgram/ml
      increased from 0C to 5C to 10C (6-fold increase overall); raising the
      temperature to 15C did not further increase the rate of ligation.  At the
      appropriate DNA concentrations, the predominant products of ligation are either
      linear concatemers that are integral multimers of the starting DNA fragment, or
      covalently closed circular structures of the monomeric DNA fragment.  Ligating
      a mixture of two different length DNA fragments gives rise to all of the
      possible expected recombinant molecules.  Linear or circular products of
      ligation were predicted by consideration of the total concentration of DNA
      termini, i, and the local concentration of one terminus in the neighborhood of
      the other on the same DNA molecule, j.  The parameter j is a function of the
      length of a DNA molecule, providing this length is greater than the random coil
      segment of DNA.  Experimentally it was found that circular structures are
      formed in significant amounts only under conditions when the value of j is
      several times greater than that of i.  When j = i, equal amounts of linear and
      circular products would be expected, but most of the molecules were ligated
      into linear concatemers.  No circular structure of a DNA fragment whose contour
      length l (6 x 10-2 microm) is smaller than the random coil segment value b
      (7.17 x 10-2 microm) was observed, while circular structures of the dimer of
      the same molecule (12 x 10-2 microm) were detected.
AU  - Dugaiczyk A
AU  - Boyer HW
AU  - Goodman HM
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1975 96: 171-184.

PMID- 4358949
VI  - 13
DP  - 1974
TI  - Physical identity of the SV40 deoxyribonucleic acid sequence recognized by the EcoRI restriction endonuclease and modification methylase.
PG  - 503-512
AB  - The EcoRI modification methylase introduces two methyl groups into one SV40 DNA
      molecule.  The only base methylated has been identified as N6-methyladenine.
      Both of the methyl groups are introduced into the same fragment (designated F,
      about 400 base pairs long) of a HindII endonuclease digest of SV40 DNA.  The
      EcoRI endonuclease makes one double-strand cleavage in SV40 DNA.  The site of
      this cleavage is also contained within the F fragment.  Analysis of
      dinucleoside monophosphates, trinucleoside diphosphates, and tetranucleoside
      triphosphates generated by partial digestion of the methylated DNA with
      pancreatic DNase I gives the following sequence of nucleotides at the site of
      methylation by the EcoRI methylase:  GpApm6ApTpTpC.  This sequence (with A in
      place of m6A) is also found at the site of phosphodiester-bond cleavage by the
      EcoRI restriction endonuclease.  Using [c-32P]rATP and polynucleotide kinase,
      SV40 DNA has been labeled in each strand with 32P specifically at the
      phosphodiester bonds cleaved by the EcoRI endonuclease.  The DNA was
      polymerized at 4o by hydrogen bonding of the cohesive termini of the EcoRI
      endonuclease break.  The labeled 5'-monophosphates at the staggered
      single-strand breaks were esterified with the adjacent 3'-hydroxyl groups by
      polynucleotide ligase at low temperature, and the covalently polymerized DNA
      was methylated by the EcoRI modification methylase using
      S-adenosyl-L-[methyl-3H]methionine.  Analysis of the radioactive labels in the
      mono- and dinucleotides from a partial digest of this double-labeled DNA
      identifies physically the same sequence of base pairs in SV40 DNA as the
      substrate site for the EcoRI endonuclease and for the EcoRI modification
      methylase.
AU  - Dugaiczyk A
AU  - Hedgpeth J
AU  - Boyer HW
AU  - Goodman HM
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1974 13: 503-512.

PMID- 4376004
VI  - 61
DP  - 1974
TI  - Location and nucleotide sequence of the site on SV40 DNA methylated by the EcoB modification methylase.
PG  - 1133-1140
AB  - The modification methylase from Escherichia coli strain B, EcoB, introduces two
      methyl groups into one SV40 DNA molecule.  The only base methylated has been
      identified as N6-methyladenine.  Digestion of the methylated SV40 DNA with two
      restriction endonucleases, one from Hemophilus influenzae, HindIII, and another
      from Hemophilus aegyptius, Hae, locates the methyl groups in the same DNA
      fragment, about 250 base pairs long, between 0.860 and 0.907 fractional lengths
      of SV40 DNA clockwise from the EcoRI site on the circular SV40 geneome.
      Analysis of dinucleoside monophosphates, trinucleoside diphosphates, and
      tetranucleoside triphosphates, generated by partial digestion of the methylated
      DNA with pancreatic DNaseI gave the following sequences of nucleotides at the
      site(s) of methylation by the EcoB methylase: 5'...C-m6A-G-C-T...3' and
      5'...T-G-m6A-A...3' These cannot be incorporated into a simple sequence with
      2-fold rotational symmetry.
AU  - Dugaiczyk A
AU  - Kimball M
AU  - Linn S
AU  - Goodman HM
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1974 61: 1133-1140.

PMID- 27908984
VI  - 4
DP  - 2016
TI  - Draft Anaplasma phagocytophilum Genome Sequences from Five Cows, Two Horses, and  One Roe Deer Collected in Europe.
PG  - e00950-16
AB  - Anaplasma phagocytophilum is a zoonotic tick-borne intracellular bacterium responsible for
      granulocytic anaplasmosis. As it is difficult to isolate and
      cultivate, only 20 A. phagocytophilum genomes have been sequenced to date. Here,
      we present eight A. phagocytophilum genome sequences obtained using alternative
      approaches based on sequence capture technology.
AU  - Dugat T
AU  - Rossignol MN
AU  - Rue O
AU  - Loux V
AU  - Marthey S
AU  - Moroldo M
AU  - Silaghi C
AU  - Hoper D
AU  - Frohlich J
AU  - Pfeffer M
AU  - Zweygarth E
AU  - Lagree AC
AU  - Boulouis HJ
AU  - Haddad N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00950-16.

PMID- 27445372
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Corynebacterium variabile Mu292, Isolated from Munster,  a French Smear-Ripened Cheese.
PG  - e00669-16
AB  - Here, we report the draft genome sequence of Corynebacterium variabile Mu292, which was
      originally isolated from the surface of Munster, a French smear-ripened
      cheese. This genome investigation will improve our knowledge on the molecular
      determinants potentially involved in the adaptation of this strain during the
      Munster-type cheese manufacturing process.
AU  - Dugat-Bony E
AU  - Sarthou AS
AU  - Loux V
AU  - Vidal M
AU  - Bonnarme P
AU  - Irlinger F
AU  - Layec S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00669-16.

PMID- 27231374
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Six Novel Bacterial Isolates from Chicken Ceca.
PG  - e00448-16
AB  - The chicken is the most common domesticated animal and the most abundant bird in  the world.
      However, the chicken gut is home to many previously uncharacterized
      bacterial taxa. Here, we report draft genome sequences from six bacterial
      isolates from chicken ceca, all of which fall outside any named species.
AU  - Duggett NA
AU  - Kay GL
AU  - Sergeant MJ
AU  - Bedford M
AU  - Constantinidou CI
AU  - Penn CW
AU  - Millard AD
AU  - Pallen MJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00448-16.

PMID- 26868390
VI  - 4
DP  - 2016
TI  - Six Pseudoalteromonas Strains Isolated from Surface Waters of Kabeltonne, Offshore Helgoland, North Sea.
PG  - e01697-15
AB  - Draft genomes are presented for 6 Pseudoalteromonas sp. strains isolated from surface waters
      at Kabeltonne, Helgoland, a long-term ecological research station
      in the North Sea. These strains contribute knowledge of the genomic underpinnings
      of a developing model system to study phage-host dynamics of a
      particle-associated ocean copiotroph.
AU  - Duhaime MB
AU  - Wichels A
AU  - Sullivan MB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01697-15.

PMID- 20613791
VI  - 5
DP  - 2011
TI  - Ecogenomics and genome landscapes of marine Pseudoalteromonas phage H105/1.
PG  - 107-121
AB  - Marine phages have an astounding global abundance and ecological impact.
      However, little knowledge is derived from phage genomes, as most of the
      open reading frames in their small genomes are unknown, novel proteins. To
      infer potential functional and ecological relevance of sequenced marine
      Pseudoalteromonas phage H105/1, two strategies were used. First,
      similarity searches were extended to include six viral and bacterial
      metagenomes paired with their respective environmental contextual data.
      This approach revealed 'ecogenomic' patterns of Pseudoalteromonas phage
      H105/1, such as its estuarine origin. Second, intrinsic genome signatures
      (phylogenetic, codon adaptation and tetranucleotide (tetra) frequencies)
      were evaluated on a resolved intra-genomic level to shed light on the
      evolution of phage functional modules. On the basis of differential codon
      adaptation of Phage H105/1 proteins to the sequenced Pseudoalteromonas
      spp., regions of the phage genome with the most 'host'-adapted proteins
      also have the strongest bacterial tetra signature, whereas the least
      'host'-adapted proteins have the strongest phage tetra signature. Such a
      pattern may reflect the evolutionary history of the respective phage
      proteins and functional modules. Finally, analysis of the structural
      proteome identified seven proteins that make up the mature virion, four of
      which were previously unknown. This integrated approach combines both
      novel and classical strategies and serves as a model to elucidate
      ecological inferences and evolutionary relationships from phage genomes
      that typically abound with unknown gene content.
AU  - Duhaime MB
AU  - Wichels A
AU  - Waldmann J
AU  - Teeling H
AU  - Glockner FO
PT  - Journal Article
TA  - ISME J.
JT  - ISME J.
SO  - ISME J. 2011 5: 107-121.

PMID- 6285204
VI  - 298
DP  - 1982
TI  - Single base substitution in an intron of oxidase gene compensates splicing defects of the cytochrome b gene.
PG  - 628-632
AB  - An extragenic suppressor mutation, mim2-1, which compensates yeast
      mitochondrial mutants deficient in splicing of the cytochrome b gene, has
      been mapped and sequenced. The mutation is due to a single G leads to A
      transition in the long open reading frame of the fourth intron of the
      oxidase subunit one gene. It causes the replacement of a glutamic codon by
      a lysine codon and the expression of a novel mRNA maturase active in
      splicing. Evolution and regulatory connections between homologous introns
      of nonhomologous genes are discussed.
AU  - Dujardin G
AU  - Jacq C
AU  - Slonimski PP
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1982 298: 628-632.

PMID- 
VI  - 16
DP  - 2005
TI  - Homing endonucleases and the yeast mitochondrial omega locus - A historical perspective.
PG  - 11-31
AB  - It was May 1985.  Outside the laboratory, near Paris, nature was exulting in its colorful
      mid-spring glory.  The last technical details and experimental pitfalls had been fixed in the
      preceding weeks.  Now, the site-specific endonucleolytic activity of the intron-encoded
      protein I that had been carefully engineered to express in Escherichia coli was detectable.
      According to my autoradiogram, it was cleaving the intron-less DNA exactly where I expected.
      This experiment opened the way to a series of yet unexpected developments, but for me it
      concluded a long and rather solitary quest.  Long, because the route that led to the first
      intron-encoded homing endonuclease, I-SceI according to the present nomenclature, had started
      no less than 15 years before, from a peculiarity of mitochondrial inheritance in yeast.
      Solitary, because, over this long period, the phenomenon that led to this discovery had
      remained a unique oddity of nature, limiting its interest for many.  Indeed, after the
      discovery of I-SceI, it took 3 additional years before the next examples of homing
      endonucleases could be identified, suggesting the generality of the phenomenon.  By this time,
      the enzymatic properties of I-SceI and its unusual specificity were already characterized, and
      it was clear that we were in the presence of a novel class of enzymes.
AU  - Dujon B
PT  - Journal Article
TA  - Nucleic Acids Mol. Biol.
JT  - Nucleic Acids Mol. Biol.
SO  - Nucleic Acids Mol. Biol. 2005 16: 11-31.

PMID- 2555264
VI  - 82
DP  - 1989
TI  - Group I introns as mobile genetic elements: facts and mechanistic speculations--a review.
PG  - 91-114
AB  - Group I introns form a structural and functional group of introns with widespread but
      irregular distribution among very diverse organisms and genetic systems. Evidence is now
      accumulating that several group I introns are mobile genetic elements with properties similar
      to those originally described for the omega system of Saccharomyces cerevisiae: mobile group I
      introns encode sequence-specific double-strand (ds) endoDNases, which recognize and cleave
      intronless genes to insert a copy of the intron by a ds-break repair mechanism. This mechanism
      results in: the efficient propagation of group I introns into their cognate sites; their
      maintenance at the site against spontaneous loss; and, perhaps, their transposition to
      different sites. The spontaneous loss of group I introns occurs with low frequency by an
      RNA-mediated mechanism. This mechanism eliminates introns defective for mobility and/or for
      RNA splicing. Mechanisms of intron acquisition and intron loss must create an equilibrium,
      which explains the irregular distribution of group I introns in various genetic systems.
      Furthermore, the observed distribution also predicts that horizontal transfer of intron
      sequences must occur between unrelated species, using vectors yet to be discovered.
AU  - Dujon B
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1989 82: 91-114.

PMID- 6156002
VI  - 20
DP  - 1980
TI  - Sequence of the intron and flanking exons of the mitochondrial 21S rRNA gene of yeast strains having different alleles at the omega and rib-1 loci.
PG  - 185-197
AB  - The complete nucleotide sequence has been determined for the intron, its junctions and the
      flanking exon regions of the 21S rRNA gene in three genetically characterized strains
      differing by their omega alleles (omega+, omega- and omega n) and by their
      chloramphenicol-resistant mutations at the rib-1 locus. Comparison of these DNA sequences
      shows that:  omega+ differs from omega- and omega n by the presence of the intron (1143bp), as
      well as by a second and unexpected mini-insert (66bp) located 156bp upstream within the exon,
      whose nature and functions are still unknown but whose striking palindromic structure may
      suggest a mitochondrial transposable element. The two mutations CR321 and CR323 correspond to
      two different monosubstitutions, 56bp apart in the omega- and omega n strains but separated by
      the intron in the omega+ strains. In relation to previous genetic results, a model is
      discussed assuming that the interactions of two different regions or genetic loci determine
      the chloramphenicol resistance, one of which contains the omega n mutations. A long
      uninterrupted coding sequence able to specify a 235 amino acid polypeptide exists within the
      intron. This remarkable observation gives new insight into the origin of the mitochondrial
      introns and raises the question of the possible functions of intron-encoded polypeptides.
      Finally, sequence comparisons with evolutionarily distant organisms, showing that different
      rRNA introns are inserted at different positions of an otherwise highly conserved region of
      the gene, suggest a recent insertion of these introns and a mechanism for splicing after the
      assembly of the large ribosomal subunit.
AU  - Dujon B
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1980 20: 185-197.

PMID- 
VI  - 0
DP  - 1986
TI  - Mitochondrial introns as mobile genetic elements: The role of intron-encoded proteins.
PG  - 5-27
AB  - Introns of organelle genes share distinctive RNA secondary structures that allow their
      classification into two known families. These structures are believed to play an essential
      role in splicing, and members of both structural classes have recently been shown to perform
      self-splicing reactions in vitro. In lower eukaryotes, many structured introns also contain
      long internal open reading frames (ORFs), which are able to code for hydrophilic proteins.
      Several properties of self-splicing structured introns suggest that they resemble mobile
      genetic elements, even though no actual transposition event involving these introns has yet
      been found. We report here on the characterization of two intron-encoded proteins that
      strongly support this attractive idea. First, we show that the class I intron of the 21S
      ribosomal RNA (rRNA) gene of Saccharomyces cerevisiae omega+ strains (r1 intron) encodes a
      specific transposase. This protein has been partially purified from Escherichia coli cells
      that overexpress it from an artificial universal code equivalent to the r1 intronic ORF. The
      omega transposase shows double-strand endonuclease activity in vitro. This activity creates a
      4-bp staggered cut with 3' OH overhangs within a specific sequence of the 21S rRNA gene of
      omega strains. It is precisely within this sequence that the r1 intron inserts by a
      duplicative transposition. Second, we report on the synthesis, in E. coli, of a putative
      reverse transcriptase encoded by the class II intron of the cytochrome b gene of
      Schizosaccharomyces pombe. This synthesis was obtained from E. coli expression vectors, using
      the class I intronic ORF linked to an artificial initiator sequence.
AU  - Dujon B
AU  - Colleaux L
AU  - Jacquier A
AU  - Michel F
AU  - Monteilhet C
PT  - Journal Article
TA  - Extrachromosomal elements in lower eukaryotes
JT  - Extrachromosomal elements in lower eukaryotes
SO  - Extrachromosomal elements in lower eukaryotes 1986 0: 5-27.

PMID- 3032144
VI  - 40
DP  - 1986
TI  - Mitochondrial introns as mobile genetic elements: the role of intron-encoded proteins.
PG  - 5-27
AB  - Introns of organelle genes share distinctive RNA secondary structures that allow
      their classification into two known families.  These structures are believed to play an
      essential role
      in splicing, and members of both structural classes have recently been shown to perform self-
      splicing reactions in vitro.  In lower eukaryotes, many structured introns also contain long
      internal
      open reading frames (ORFs), which are able to code for hydrophilic proteins.  Several
      properties
      of self-splicing structured introns suggest that they resemble mobile genetic elements, even
      though
      no actual transposition event involving these introns has yet been found.  We report here on
      the
      characterization of two intron-encoded proteins that strongly support this attractive idea.
      First, we
      show that the class I intron of the 21S ribosomal RNA (rRNA) gene of Saccharomyces cerevisiae
      omega+ strains (r1 intron) encodes a specific transposase.  This protein has been partially
      purified
      from Escherichia coli cells that overexpress it from an artificial universal code equivalent
      to the r1
      intronic ORF.  The omega transposase shows a double-strand endonuclease activity in vitro.
      This
      activity creates a 4-bp staggered cut with 3' OH overhangs within a specific sequence of the
      21S
      rRNA gene of omega- strains.  It is precisely within this sequence that the r1 intron inserts
      by a
      duplicative transposition.  Second, we report on the synthesis, in E. coli, of a putative
      reverse
      transcriptase encoded by the Class II intron of the cytochrome b gene of Schizosaccharomyces
      pombe.  This synthesis was obtained from E. coli expression vectors, using the class II
      intronic
      ORF linked to an artificial initiator sequence.  As further support of the idea that
      structured introns
      are mobile, we show, from a systematic screening of introns in various yeast species, that the
      r1
      intron has transposed into the ATPase subunit 9 gene of Kluyveromyces fragilis.  Structural
      features observed at the new intron homing site may be relevant to the transposition event.
AU  - Dujon B
AU  - Colleaux L
AU  - Jacquier A
AU  - Michel F
AU  - Monteilhet C
PT  - Journal Article
TA  - Basic Life Sci.
JT  - Basic Life Sci.
SO  - Basic Life Sci. 1986 40: 5-27.

PMID- 
VI  - 0
DP  - 1985
TI  - Mechanism of integration of an intron within a mitochondrial gene: a double strand break and the transposase function of an intron encoded protein as revealed by in vivo and in vitro assays.
PG  - 215-225
AB  - The intron of the mitochondrial 21S rRNA gene (rl intron) is optional in the yeast
      Saccharomyces cerevisiae, being found in some strains (omega+) but not in others (omega-) with
      no phenotypic difference related to its presence or absence. Crosses between omega+ strains
      and omega- strains determine a unique phenomenon that results in the integration of that
      intron into the previously intron minus copies of the 21S rRNA gene. This phenomenon resembles
      a duplicative transposition, with the intron itself representing the transposable element,
      except that the recipient site seems unique and that the transposition is accompanied by a
      unidirectional gene conversion affecting the genetic and molecular markers located in flanking
      exon sequences. In addition, the transposition is nearly quantitative, converting almost all
      intron minus copies of the 21S rRNA gene into intron plus copies, hence efficiently spreading
      that intron within the populations of interbreeding yeasts.
AU  - Dujon B
AU  - Cottarel G
AU  - Colleaux L
AU  - Betermier M
AU  - Jacquier A
AU  - D'Auriol L
AU  - Galibert F
PT  - Journal Article
TA  - Achievements and Perspectives of Mitochondrial Research. Volume II: Biogenesis.
JT  - Achievements and Perspectives of Mitochondrial Research. Volume II: Biogenesis.
SO  - Achievements and Perspectives of Mitochondrial Research. Volume II: Biogenesis. 1985 0: 215-225.

PMID- 30533901
VI  - 7
DP  - 2018
TI  - Draft Genome Sequence of Enterobacter cloacae 3F11 (Phylum Proteobacteria).
PG  - e00846-18
AB  - Presented here is the draft genome sequence of Enterobacter cloacae 3F11. This seed endophyte
      solubilizes rock phosphate and was isolated from Zea
      nicaraguensis. The genome contains 4,579,108 bp in 264 contigs.
AU  - Dumigan CR
AU  - Perry GE
AU  - Pauls KP
AU  - Raizada MN
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e00846-18.

PMID- 25278538
VI  - 2
DP  - 2014
TI  - High-Quality Draft Genome Sequence of Pseudomonas sp. BRG100, a Strain with Bioherbicidal Properties against Setaria viridis (Green Foxtail) and Other Pests   of Agricultural Significance.
PG  - e00995-14
AB  - Pseudomonas sp. BRG100 inhibits the growth of certain agricultural pests and is a potentially
      useful biopesticide for weeds and plant diseases. We have sequenced
      the 6.25-Mbp genome of this strain and assembled it into 4 scaffolds. Genome
      sequence comparisons revealed that this strain may represent a novel species of
      Pseudomonas.
AU  - Dumonceaux TJ
AU  - Town J
AU  - Links MG
AU  - Boyetchko S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00995-14.

PMID- 649568
VI  - 134
DP  - 1978
TI  - Biochemical and genetic properties of site-specific restriction endonucleases in Bacillus globigii.
PG  - 338-344
AB  - Bacillus globigii contains two site-specific endonucleases, BglI and BglII.  A
      rapid technique for selection of mutants deficient in each of these enzymes was
      developed using sensitivity to infection by bacteriophage SP50 as an indication
      of the levels of enzyme.  Mutants defective in BglI, BglII, and both BglI and
      BglII retained the wild-type modification phenotype.  Genetic and biochemical
      studies have established that these enzymes are involved in restriction in
      vivo.  Simplified purification procedures for BglI and BglII using these
      mutants are described.
AU  - Duncan CH
AU  - Wilson GA
AU  - Young FE
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1978 134: 338-344.

PMID- 24072860
VI  - 1
DP  - 2013
TI  - Genome Sequences of Three hpAfrica2 Strains of Helicobacter pylori.
PG  - e00729-13
AB  - We present the genome sequences of three hpAfrica2 strains of Helicobacter pylori, which are
      postulated to have evolved in isolation for many millennia in
      people of San ethnicity. Although previously considered to be ancestral to
      Helicobacter acinonychis, the hpAfrica2 strains differ markedly from H.
      acinonychis in their gene arrangement. These data provide new insights into
      Helicobacter evolution.
AU  - Duncan SS
AU  - Bertoli MT
AU  - Kersulyte D
AU  - Valk PL
AU  - Tamma S
AU  - Segal I
AU  - McClain MS
AU  - Cover TL
AU  - Berg DE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00729-13.

PMID- 16646971
VI  - 7
DP  - 2006
TI  - Phylogenomic analysis of the GIY-YIG nuclease superfamily.
PG  - 98
AB  - BACKGROUND: The GIY-YIG domain was initially identified in homing endonucleases and later in
      other selfish mobile genetic elements
      (including restriction enzymes and non-LTR retrotransposons) and in
      enzymes involved in DNA repair and recombination. However, to date no
      systematic search for novel members of the GIY-YIG superfamily or
      comparative analysis of these enzymes has been reported. RESULTS: We
      carried out database searches to identify all members of known GIY-YIG
      nuclease families. Multiple sequence alignments together with predicted
      secondary structures of identified families were represented as Hidden
      Markov Models (HMM) and compared by the HHsearch method to the
      uncharacterized protein families gathered in the COG, KOG, and PFAM
      databases. This analysis allowed for extending the GIY-YIG superfamily to
      include members of COG3680 and a number of proteins not classified in COGs
      and to predict that these proteins may function as nucleases, potentially
      involved in DNA recombination and/or repair. Finally, all old and new
      members of the GIY-YIG superfamily were compared and analyzed to infer the
      phylogenetic tree. CONCLUSION: An evolutionary classification of the
      GIY-YIG superfamily is presented for the very first time, along with the
      structural annotation of all (sub)families. It provides a comprehensive
      picture of sequence-structure-function relationships in this superfamily
      of nucleases, which will help to design experiments to study the mechanism
      of action of known members (especially the uncharacterized ones) and will
      facilitate the prediction of function for the newly discovered ones.
AU  - Dunin-Horkawicz S
AU  - Feder M
AU  - Bujnicki JM
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2006 7: 98.

PMID- 25523766
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Escherichia coli Strains Isolated from Septic Patients.
PG  - e01278-14
AB  - We present the draft genome sequences of six strains of Escherichia coli isolated from blood
      cultures collected from patients with sepsis. The strains were
      collected from two patient sets, those with a high severity of illness, and those
      with a low severity of illness. Each genome was sequenced by both Illumina and
      PacBio for comparison.
AU  - Dunitz MI
AU  - Coil DA
AU  - Jospin G
AU  - Eisen JA
AU  - Adams JY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01278-14.

PMID- 24762940
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Tatumella sp. Strain UCD-D_suzukii (Phylum Proteobacteria) Isolated from Drosophila suzukii Larvae.
PG  - e00349-14
AB  - Here we present the draft genome of Tatumella sp. strain UCD-D_suzukii, the first member of
      this genus to be sequenced. The genome contains 3,602,931 bp in 72 scaffolds. This strain was
      isolated from Drosophila suzukii larvae as part of a larger project to study the microbiota of
      D. suzukii.
AU  - Dunitz MI
AU  - James PM
AU  - Jospin G
AU  - Eisen JA
AU  - Coil DA
AU  - Chandler JA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00349-14.

PMID- 
VI  - 64
DP  - 2013
TI  - Genomic analysis and secondary metabolite production in Bacillus amyloliquefaciens AS 43.3: a biocontrol antagonist of Fusarium Head Blight.
PG  - 166-175
AB  - The complete genome of the biocontrol antagonist Bacillus amyloliquefaciens AS 43.3 is
      reported. B. amyloliquefaciens AS 43.3 has previously been shown to be effective in reducing
      Fusarium head blight in wheat. The 3.9Mbp genome was sequenced, assembled, and annotated.
      Genomic analysis of the strain identified 9 biosynthetic gene clusters encoding secondary
      metabolites associated with biocontrol activity. The analysis identified five non-ribosomal
      peptide synthetase clusters encoding three lipopeptides (surfactin, iturin, and fengycin), a
      siderophore (bacillibactin), and the antibiotic dipeptide bacilysin. In addition, three
      polyketide synthetase clusters were identified which encoded for the antibacterials:
      bacillaene, difficidin, and macrolactin. In addition to the non-ribosomal mediated
      biosynthetic clusters discovered, we identified a ribosomally encoded biosynthetic cluster
      that produces the antibiotic plantazolicin. To confirm the gene clusters were functional,
      cell-free culture supernatant was analyzed using LC=96MS/MS. The technique confirmed the
      presence of all nine metabolites or their derivatives. The study suggests the strain is most
      likely a member of the B. amyloliquefaciens subsp. plantarium clade. Comparative genomics of
      eight completed genomes of B. amyloliquefaciensidentify the core and pan-genomes for the
      species, including identifying genes unique to the biocontrol strains. This study demonstrates
      the growing importance of applying genomic-based studies to biocontrol organisms of plant
      pathogens which can enable the rapid identification of bioactive metabolites produced by a
      prospective biological control organism. In addition, this work provides a foundation for a
      mechanistic understanding of the B. amyloliquefaciens AS 43.3/Fusarium head blight biocontrol
      interaction.
AU  - Dunlap CA
AU  - Bowman MJ
AU  - Schisler DA
PT  - Journal Article
TA  - Biol. Control
JT  - Biol. Control
SO  - Biol. Control 2013 64: 166-175.

PMID- 
VI  - 0
DP  - 1971
TI  - Transduction and host controlled modification.  The role of the phage.
PG  - 223-233
AB  - Three unrelated general transducing phages of Pseudomonas aeruginosa have been
      studied to determine if the bacterial chromosomal fragments transferred in
      transduction are always susceptible to restriction.  Using restriction and
      modification mutants of the parent donor and recipient strains, to avoid
      effects on recombination resulting from non-homology, two of the phages, B3 and
      G101, were restricted for both their plaque forming and transducing properties.
      However, a third transducing phage, F116, showed no such restriction when
      transducing from a donor strain with a different DNA specificity to that of the
      recipient strain.  This immunity to restriction appears to be associated with
      the F115 phage genome and a variant of F116 has been found which, while immune
      to restriction of plaque forming ability, is not immune to restriction of its
      transducing ability.  The implication from these results is that a phage may be
      able to protect bacterial DNA from inactivation by the restriction mechanisms
      of host controlled modification.  With phage B3 a second type of immunity was
      found, in that not all bacterial markers showed the same reduction of
      transduction frequency caused by restriction and the results suggest an uneven
      distribution of recognition sites on the bacterial chromosome.
AU  - Dunn NW
AU  - Holloway BW
PT  - Journal Article
TA  - Informative molecules in biological systems.
JT  - Informative molecules in biological systems.
SO  - Informative molecules in biological systems. 1971 0: 223-233.

PMID- 10532373
VI  - 76
DP  - 1999
TI  - Group II introns and expression of conjugative transfer functions in lactic acid bacteria.
PG  - 77-88
AB  - The homologous lactococcal conjugative elements pRS01 and the sex factor of Lactococcus lactis
      strain 712 both contain a Group II intron within a gene believed to encode a conjugative
      relaxase enzyme. This enzyme is responsible for nicking of DNA at the origin of transfer
      (oriT) sequence of the sex factor DNA to initiate the strand transfer process. Group II
      introns have been studied in eukaryotes, and several of these elements in yeast mitochondrial
      genes have received considerable attention. These introns are relatively large in size and
      generally encode a protein within the intron sequence. In addition to splicing activity. Group
      II introns are mobile genetic elements. The intron-encoded proteins (IEPs) contain
      endonuclease and reverse transcriptase domains believed to play an enzymatic role in genetic
      mobility reactions, while a putative maturase domain is thought to promote splicing by
      stabilizing the folding of the intron RNA into an active ribozyme structure which carries out
      the splicing reaction. The lactococcal introns represent the first examples of Group II
      introns shown to be functional in vivo in prokaryotes. Because of the advantages of a
      bacterial system for genetic and molecular studies, the Ll.ltrB intron from pRS01 has
      attracted the attention of several laboratories interested in Group II intron biology.
      Recently, it has been shown that the system can be adapted to function in Escherichia coli
      (although at somewhat reduced efficiency). In addition, it has been recently proven that the
      best studied form of mobility, the homing of the intron into an intronless allele of the
      cognate exon gene, occurs via an RNA intermediate and does not require DNA homology or
      generalized host recombination functions. Current efforts are analysis of the role Ll.ltrB
      splicing in regulating expression of pRS01 conjugation functions. The lactococcal Group II
      introns represent the first demonstrated genetically mobile prokaryotic retroelements, and
      they also have considerable potential as genetic engineering tools for Lactic Acid Bacteria
      (LAB) and other organisms.
AU  - Dunny GM
AU  - McKay LL
PT  - Journal Article
TA  - Antonie Van Leeuwenhoek
JT  - Antonie Van Leeuwenhoek
SO  - Antonie Van Leeuwenhoek 1999 76: 77-88.

PMID- 18701646
VI  - 36
DP  - 2008
TI  - The structure of SgrAI bound to DNA; recognition of an 8 base pair target.
PG  - 5405-5416
AB  - The three-dimensional X-ray crystal structure of the 'rare cutting' type II restriction
      endonuclease SgrAI bound to cognate DNA is presented. SgrAI
      forms a dimer bound to one duplex of DNA. Two Ca(2+) bind in the enzyme
      active site, with one ion at the interface between the protein and DNA,
      and the second bound distal from the DNA. These sites are differentially
      occupied by Mn(2+), with strong binding at the protein-DNA interface, but
      only partial occupancy of the distal site. The DNA remains uncleaved in
      the structures from crystals grown in the presence of either divalent
      cation. The structure of the dimer of SgrAI is similar to those of Cfr10I,
      Bse634I and NgoMIV, however no tetrameric structure of SgrAI is observed.
      DNA contacts to the central CCGG base pairs of the SgrAI canonical target
      sequence (CR|CCGGYG, | marks the site of cleavage) are found to be very
      similar to those in the NgoMIV/DNA structure (target sequence G|CCGGC).
      Specificity at the degenerate YR base pairs of the SgrAI sequence may
      occur via indirect readout using DNA distortion. Recognition of the outer
      GC base pairs occurs through a single contact to the G from an arginine
      side chain located in a region unique to SgrAI.
AU  - Dunten PW
AU  - Little EJ
AU  - Gregory MT
AU  - Manohar VM
AU  - Dalton M
AU  - Hough D
AU  - Bitinaite J
AU  - Horton NC
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2008 36: 5405-5416.

PMID- 19307723
VI  - 65
DP  - 2009
TI  - The restriction enzyme SgrAI: structure solution via combination of poor MIRAS and MR phases.
PG  - 393-398
AB  - Uninterpretable electron-density maps were obtained using either MIRAS phases or MR phases in
      attempts to determine the structure of the type
      II restriction endonuclease SgrAI bound to DNA. While neither solution
      strategy was particularly promising (map correlation coefficients of
      0.29 and 0.22 with the final model, respectively, for the MIRAS and MR
      phases and Phaser Z scores of 4.0 and 4.3 for the rotation and
      translation searches), phase combination followed by density
      modification gave a readily interpretable map. MR with a distantly
      related model located a dimer in the asymmetric unit and provided the
      correct transformation to use in averaging electron density between
      SgrAI subunits. MIRAS data sets with low substitution and MR solutions
      from only distantly related models should not be ignored, as
      poor-quality starting phases can be significantly improved. The
      bootstrapping strategy employed to improve the initial MIRAS phases is
      described.
AU  - Dunten PW
AU  - Little EJ
AU  - Horton NC
PT  - Journal Article
TA  - Acta Crystallogr. D Biol. Crystallogr.
JT  - Acta Crystallogr. D Biol. Crystallogr.
SO  - Acta Crystallogr. D Biol. Crystallogr. 2009 65: 393-398.

PMID- 28572317
VI  - 5
DP  - 2017
TI  - Complete Genome Assembly of Pantoea stewartii subsp. stewartii DC283, a Corn Pathogen.
PG  - e00435-17
AB  - The phytopathogen Pantoea stewartii subsp. stewartii DC283 causes Stewart's wilt  disease in
      corn after transmission from the corn flea beetle insect vector. Here,
      we report that the complete annotated genome of P. stewartii DC283 has been fully
      assembled into one circular chromosome, 10 circular plasmids, and one linear
      phage.
AU  - Duong DA
AU  - Stevens AM
AU  - Jensen RV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00435-17.

PMID- 23820428
VI  - 4
DP  - 2013
TI  - CRISPR-Cas and restriction-modification systems are compatible and increase phage resistance.
PG  - 2087
AB  - Bacteria have developed a set of barriers to protect themselves against invaders such as phage
      and plasmid nucleic acids. Different prokaryotic defence systems exist and at least two of
      them directly target the incoming DNA: restriction-modification (R-M) and CRISPR-Cas systems.
      On their own, they are imperfect barriers to invasion by foreign DNA. Here, we show that R-M
      and CRISPR-Cas systems are compatible and act together to increase the overall phage
      resistance of a bacterial cell by cleaving their respective target sites. Furthermore, we show
      that the specific methylation of phage DNA does not impair CRISPR-Cas acquisition or
      interference activities. Taken altogether, both mechanisms can be leveraged to decrease phage
      contaminations in processes relying on bacterial growth and/or fermentation.
AU  - Dupuis M-E
AU  - Villion M
AU  - Magadan AH
AU  - Moineau S
PT  - Journal Article
TA  - Nat. Commun.
JT  - Nat. Commun.
SO  - Nat. Commun. 2013 4: 2087.

PMID- 
VI  - 12
DP  - 1999
TI  - Metal ion-dependent DNA-induced conformational changes in PvuII restriction endonucleases.
PG  - 43-47
AB  - Using 19F NMR spectroscopy as a solution structural probe, important preliminary
      conformational studies of the interactions between 3-fluorotyrosine-PvuII endonuclease and a
      cognate DNA are described.  Even at high microM to mM concentrations of enzyme and DNA, Ca(II)
      is required to observe enzyme conformational changes associated with the binding of a short
      oligonucleotide.  Further, these structural changes are global: The resonances of no fewer
      than 6 of the 10 3-fluorotyrosine residues per PvuII subunit shift by at least 0.1 ppm
      relative to the free enzyme, far more than can be accounted for as local effects of DNA
      binding.  Partial titration experiments are consistent with a slow off-rate for
      oligonucleotide binding and correspondingly slow (ms) exchange between free and DNA-bound
      conformations of enzyme.  These results demonstrate that this system provides a means to
      explore solution conformational aspects of restriction enzyme-DNA interactions.
AU  - Dupureur CM
PT  - Journal Article
TA  - SAAS Bulletin: Biochem. and Biotech.
JT  - SAAS Bulletin: Biochem. and Biotech.
SO  - SAAS Bulletin: Biochem. and Biotech. 1999 12: 43-47.

PMID- 16898413
VI  - 25
DP  - 2006
TI  - Unique P-31 spectral response to the formation of a specific restriction enzyme-DNA complex.
PG  - 747-764
AB  - Protein-induced distortion is a dramatic but not universally observed feature of
      sequence-specific DNA interactions. This is illustrated by
      the crystal structures of restriction enzyme-DNA complexes: While some
      of these structures exhibit DNA distortion, others do not. Among the
      latter is PvuII endonuclease, a small enzyme that is also amenable to
      NMR spectroscopic studies. Here P-31 NMR spectroscopy is applied to
      demonstrate the unique spectral response of DNA to sequence-specific
      protein interactions. The P-31 NMR spectrum of a noncognate DNA
      exhibits only spectral broadening upon the addition of enzyme. However,
      when enzyme is added to target DNA, a number of P-31 resonances ship
      dramatically. The magnitudes of the chemical shifts (2-3 ppm) are among
      the largest observed. Site-specific substitution with phosphoramidates
      and phosphorothioates are used analyze these effects. While such
      spectral features have been interpreted as indicative of DNA backbone
      distortions, FRET analysis indicates that this does not occur in
      PvuII-cognate DNA complexes in solution. The distinct P-31 spectral
      signature observed for cognate DNA mirrors that observed for the
      enzyme, underscoring the unique features of cognate complex formation.
AU  - Dupureur CM
PT  - Journal Article
TA  - Nucleosides Nucleotides Nucleic Acids
JT  - Nucleosides Nucleotides Nucleic Acids
SO  - Nucleosides Nucleotides Nucleic Acids 2006 25: 747-764.

PMID- 15794644
VI  - 44
DP  - 2005
TI  - NMR studies of restriction enzyme-DNA interactions: Role of conformation in sequence specificity.
PG  - 5065-5074
AB  - Sequence specific DNA binding proteins are thought to adopt distinct conformations when
      binding to target (cognate) and nontarget
      (noncognate) sequences. There is both biochemical and crystallographic
      evidence that this behavior is important in mediating sequence
      recognition by the Mg(II)-dependent Type II restriction enzymes.
      Despite this, there are few systematic comparisons of the structural
      behavior of these enzymes in various complexes. Here, H-1-N-15 HSQC NMR
      spectroscopy is applied to PvuII endonuclease (2 x 18 kDa) in an effort
      to better understand the relationship between sequence recognition and
      enzyme conformational behavior. Spectra of the free enzyme collected in
      the absence and presence of metal ions indicate that while there is a
      modest backbone conformational response upon binding Ca(II), this does
      not occur with Mg(II). Substrate binding itself is accompanied by very
      dramatic spectral changes consistent with a large-scale conformational
      response. HSQC spectra of the enzyme bound to cognate (specific) and
      noncognate (nonspecific) oligonucleotides in the presence of Ca(II) are
      dramatically distinct, revealing for the first time the structural
      uniqueness of a PvuII cognate complex in solution. The strong
      correlation between NMR spectral overlap and crystallographic data
      (C-alpha rmsd) permits characterization of the nonspecific Pvull
      complex as being more similar to the free enzyme than to the specific
      complex. Collectively, these data support the notion that it is the
      DNA, not the metal ion, which promotes a unique conformational response
      by the enzyme. It therefore follows that the principle role of metal
      ions in complex formation is one of driving substrate affinity and
      stability rather than conformationally priming the enzyme for substrate
      binding and sequence recognition. These results not only provide
      valuable insights into the mechanism of protein-DNA interactions but
      also demonstrate the utility of NMR spectroscopy in structure-function
      studies of these representative nucleic acid systems.
AU  - Dupureur CM
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2005 44: 5065-5074.

PMID- 10978180
VI  - 39
DP  - 2000
TI  - A catalytically deficient active site variant of PvuII endonuclease binds Mg(II) ions.
PG  - 10921-10927
AB  - In efforts to understand the mechanisms of many nucleic acid enzymes, the first site-directed
      mutations are made at conserved acidic active residues. Almost without exception, the low or
      null activities of the resulting variants are attributed to the importance of the acidic
      residue(s) to the ligation of required metal ions. Using Mg^25 NMR spectroscopy as a direct
      probe of metal ion binding and the homodimeric PvuII restriction endonuclease as a model
      system, this interpretation is examined and clarified. Our results indicate that Mg(II) binds
      wild-type PvuII endonuclease in the absence of DNA with a K(d,app) of 1.9 mM. Hill analysis
      yields an n(H) coefficient of 1.4, a value consistent with the binding of more than one Mg(II)
      ion per monomer active site. Variable pH studies indicate that two ionizable groups are
      responsible for Mg(II) binding by wild-type PvuII endonuclease near physiological pH. The
      pK(a,app) for these ionizations is 6.7, a value which is unusual for acidic residues but
      consistent with data obtained for critical groups in MunI endonuclease and a number of other
      hydrolases. To assign residues critical to ligating Mg(II), binding measurements were
      performed on the low activity catalytic site mutants E68A and D58A. As expected, E68A binds
      Mg(II) ions very weakly (K(d,app) approximately 40 mM), implicating Glu68 as critical to
      Mg(II) binding. Interestingly, while D58A has only residual specific activity, it retains an
      affinity for Mg(II) with a K(d,app) of 3.6 mM and exhibits a Hill coefficient of 0.7.
      Moreover, in this variant, multiple ionizable groups with pK(a,app) of 7.2 are involved in
      Mg(II) binding, suggesting a shuffling of Mg(II) ligands in the active site. These data
      indicate that Asp58 is important for the critical positioning of metal ion(s) required for
      catalysis.
AU  - Dupureur CM
AU  - Conlan LH
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2000 39: 10921-10927.

PMID- 11148032
VI  - 40
DP  - 2001
TI  - The PD ... (D/E)XK motif in restriction enzymes: A link between function and conformation.
PG  - 387-394
AB  - The active sites of Mg(II)-dependent nucleases feature a cluster of conserved charged residues
      which includes both acidic (Asp and Glu) and
      basic (Lys) side chains. In restriction enzymes, these side chains are
      part of the conserved PD...(D/E)XK functional sequence motif which has
      been implicated as being important in metal ion binding and catalytic
      steps. Recent work revealing the unusual behavior of the active site
      variant D58A of the representative PvuII endonuclease prompted
      speculation that the array of charged groups in the nuclease active
      site may also be linked to conformational behavior [Dupureur, C. M.
      and Conlan, L. H. (2000) Biochemistry 39, 10921-10927]. To address this
      issue, we analyzed the conformational behavior of active site variants
      of PvuII endonuclease using both NMR spectroscopic and thermodynamic
      methods. NMR spectroscopic analysis via F-19 and H-1-N-15 HSQC
      experiments indicates that a number of side chain and backbone amide
      groups are perturbed upon Ala substitution at conserved active site
      residues Asp58, Glu68, and Lys70. Spectral changes are particularly
      pronounced for the lowest-activity mutants (D58A and K70A). These
      changes are accompanied by perturbations in conformational stability.
      Ala substitution at each of these positions results in 2-5 kcal/mol of
      stabilization over the wild-type enzyme at pH 7.7, changes which
      constitute increases in DeltaG(d)(H2O) of 20-50%. The pH dependencies
      of mutant enzyme stabilities are distinct from those of the wild type,
      results which confirm that these ionizable groups strongly influence
      stability. Wild-type enzyme stability is correlated with the ionization
      of groups shown to be important to metal ion binding and orientation.
      Correlations between spectral changes and conformational stability
      indicate that the latter measurements may prove useful in the
      evaluation of site-directed mutant restriction enzymes. More
      importantly, these results indicate that structure-function
      relationships in restriction enzyme active sites can be complex, and
      that the ensemble of conserved charged residues which mediate DNA
      hydrolysis in Mg(II)-dependent nucleases constitutes a critical link
      between function and conformation.
AU  - Dupureur CM
AU  - Dominguez MA
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2001 40: 387-394.

PMID- 10103058
VI  - 261
DP  - 1999
TI  - Effects of divalent metal ions on the activity and conformation of native and 3-fluorotyrosine-PvuII endonucleases.
PG  - 261-268
AB  - The activities of restriction enzymes are important examples of Mg(II)-dependent hydrolysis of
      DNA. While a number of crystallographic studies of enzyme-DNA complexes have also involved
      metal ions, there have been no solution studies exploring the relationship between enzyme
      conformation and metal-ion binding in restriction enzymes.  Using PvuII restriction
      endonuclease as a model system, we have successfully developed biosynthetic fluorination and
      NMR spectroscopy as a solution probe of restriction-enzyme conformation.  The utility of this
      method is demonstrated with a study of metal-ion binding by PvuII endonuclease.  Replacement
      of 74% (+-10%) of the Tyr residues in PvuII endonuclease by 3-fluorotyrosine produces an
      enzyme with Mg(II)-supported specific activity and sequence specificity that is
      indistinguishable from that of the native enzyme.  Mn(II) supports residual activity of both
      the native and fluorinated enzymes; Ca(II) does not support activity in either enzyme, a
      result consistent with previous studies.  1H- and 19F-NMR spectroscopic studies reveal that
      while Mg(II) does not alter the enzyme conformation, the paramagnetic Mn(II) produces both
      short-range spectral broadening and longer range changes in chemical shift.  Most
      interestingly, Ca(II) binding perturbs a larger number of different resonances than Mn(II).
      Coupled with earlier mutagenesis studies that place Ca(II) in the active site these data
      suggest that the enzyme makes conformational adjustments to accommodate the distinct geometric
      preferences of Ca(II) and may play a role in the inability of this metal ion to support
      activity in restriction enzymes.
AU  - Dupureur CM
AU  - Hallman LM
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1999 261: 261-268.

PMID- 23766410
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Mycoplasma putrefaciens Strain 9231, One of the Agents of Contagious Agalactia in Goats.
PG  - e00354-13
AB  - Mycoplasma putrefaciens is one of the etiologic agents of contagious agalactia in goats. We
      report herein the complete genome sequence of Mycoplasma putrefaciens
      strain 9231.
AU  - Dupuy V et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00354-13.

PMID- 25323727
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Mycoplasma capricolum subsp. capripneumoniae Strain 9231-Abomsa.
PG  - e01067-14
AB  - Mycoplasma capricolum subsp. capripneumoniae is the etiological agent of contagious caprine
      pleuropneumonia. We report here the complete and annotated
      genome sequence of M. capricolum subsp. capripneumoniae strain 9231-Abomsa.
AU  - Dupuy V
AU  - Thiaucourt F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01067-14.

PMID- 22689244
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of the Purple Photosynthetic Bacterium Phaeospirillum molischianum DSM120, a Particularly Versatile Bacterium.
PG  - 3559-3560
AB  - Here we present the draft genome sequence of the versatile and adaptable purple photosynthetic
      bacterium Phaeospirillum molischianum DSM120. This study advances
      the understanding of the adaptability of this bacterium, as well as the
      differences between the Phaeospirillum and Rhodospirillum genera.
AU  - Duquesne K
AU  - Prima V
AU  - Ji B
AU  - Rouy Z
AU  - Medigue C
AU  - Talla E
AU  - Sturgis JN
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3559-3560.

PMID- 22493194
VI  - 194
DP  - 2012
TI  - Shotgun Genome Sequence of the Large Purple Photosynthetic Bacterium Rhodospirillum photometricum DSM122.
PG  - 2380
AB  - Here, we present the shotgun genome sequence of the purple photosynthetic bacterium
      Rhodospirillum photometricum DSM122. The photosynthetic apparatus of
      this bacterium has been particularly well studied by microscopy. The knowledge of
      the genome of this oversize bacterium will allow us to compare it with the other
      purple bacterial organisms to follow the evolution of the photosynthetic
      apparatus.
AU  - Duquesne K
AU  - Sturgis JN
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2380.

PMID- 16251401
VI  - 33
DP  - 2005
TI  - Zinc finger nucleases: custom-designed molecular scissors for genome engineering of plant and mammalian cells.
PG  - 5978-5990
AB  - Custom-designed zinc finger nucleases (ZFNs), proteins designed to cut at specific DNA
      sequences, are becoming powerful tools in gene targeting--the
      process of replacing a gene within a genome by homologous recombination
      (HR). ZFNs that combine the non-specific cleavage domain (N) of FokI
      endonuclease with zinc finger proteins (ZFPs) offer a general way to
      deliver a site-specific double-strand break (DSB) to the genome. The
      development of ZFN-mediated gene targeting provides molecular biologists
      with the ability to site-specifically and permanently modify plant and
      mammalian genomes including the human genome via homology-directed repair
      of a targeted genomic DSB. The creation of designer ZFNs that cleave DNA
      at a pre-determined site depends on the reliable creation of ZFPs that can
      specifically recognize the chosen target site within a genome. The
      (Cys2His2) ZFPs offer the best framework for developing custom ZFN
      molecules with new sequence-specificities. Here, we explore the different
      approaches for generating the desired custom ZFNs with high
      sequence-specificity and affinity. We also discuss the potential of
      ZFN-mediated gene targeting for 'directed mutagenesis' and targeted 'gene
      editing' of the plant and mammalian genome as well as the potential of
      ZFN-based strategies as a form of gene therapy for human therapeutics in
      the future.
AU  - Durai S
AU  - Mani M
AU  - Kandavelou K
AU  - Wu J
AU  - Porteus MH
AU  - Chandrasegaran S
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2005 33: 5978-5990.

PMID- 23712489
VI  - 99
DP  - 2013
TI  - Qualitative analysis of sequence specific binding of flavones to DNA using restriction endonuclease activity assays.
PG  - 530-537
AB  - Flavones, found in nature as secondary plant metabolites, have shown efficacy as anti-cancer
      agents. We have examined the binding of two
      flavones, 5,7-dihydroxy-3,6,8-trimethoxy-2-phenyl-4H-chromen-4-one
      (5,7-dihydroxy-3,6,8-trimethoxy flavone; FlavA) and
      3,5-dihydroxy-6,7,8-trimethoxy-2-phenyl-4H-chromen-4-one
      (3,5-dihydroxy-6,7,8-trimethoxy flavone; FlavB), to phiX174 RF DNA
      using restriction enzyme activity assays employing the restriction
      enzymes Alw44, AvaII, BssHII, DraI, MluI, NarI, NciI, NruI, PstI, and
      XhoI. These enzymes possess differing target and flanking sequences
      allowing for observation of sequence specificity analysis. Using
      restriction enzymes that cleave once with a mixture of supercoiled and
      relaxed DNA substrates provides for observation of topological effects
      on binding. FlavA and FlavB show differing sequence specificities in
      their respective binding to phiX. For example, with relaxed DNA, FlavA
      shows inhibition of cleavage with DraI (reaction site 5TTTAAA) but not
      BssHII (5GCGCGC) while FlavB shows the opposite results. Evidence for
      tolological specificity is also observed, Molecular modeling and
      conformational analysis of the flavones suggests that the phenyl ring
      of FlavB is coplanar with the flavonoid ring while the phenyl ring of
      FlavA is at an angle relative to the flavonoid ring. This may account
      for aspects of the observed sequence and topological specificities in
      the effects on restriction enzyme activity.
AU  - Duran E
AU  - Ramsauer VP
AU  - Ballester M
AU  - Torrenegra RD
AU  - Rodriguez OE
AU  - Winkle SA
PT  - Journal Article
TA  - Biopolymers
JT  - Biopolymers
SO  - Biopolymers 2013 99: 530-537.

PMID- 25063659
VI  - 80
DP  - 2014
TI  - Genomic Characterization and Transcriptional Studies of the Starch-Utilizing Strain Bifidobacterium adolescentis 22L.
PG  - 6080-6090
AB  - Bifidobacteria are members of the gut microbiota but the genetic basis for their adaptation to
      the human gut is poorly understood.  Analysis of the 2,203,222 bp genome of Bifidobacterium
      adolescentis 22L revealed a nutrient-acquisition strategy that targets diet/plant-derived
      glycans, in particular starch and starch-like carbohydrates.  Starch-like carbohydrates were
      shown to support the growth of B. acelescentis 22L.  Transcriptome profiling of 22L cultures
      grown under in vitro conditions or during colonization of the murine gut by RNAseq and qRT-PCR
      assays revealed the expression of a set of chromosomal loci responsible for starch metabolism
      as well as for pili production.  Such extracellular structures include so-called
      sortase-dependent and type IVb pili, which may be involved in gut colonization of 22L through
      adhesion to extracellular matrix proteins.
AU  - Duranti S
AU  - Turroni F
AU  - Lugli GA
AU  - Milani C
AU  - Viappiani A
AU  - Mangifesta M
AU  - Gioiosa L
AU  - Palanza P
AU  - van Sinderen D
AU  - Ventura M
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2014 80: 6080-6090.

PMID- 18245285
VI  - 190
DP  - 2008
TI  - The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse.
PG  - 2597-2606
AB  - Escherichia coli DH10B was designed for the propagation of large insert DNA library clones. It
      is used extensively, taking advantage of properties
      such as high DNA transformation efficiency and maintenance of large
      plasmids. The strain was constructed by serial genetic recombination
      steps, but the underlying sequence changes remained unverified. We report
      the complete genomic sequence of DH10B by using reads accumulated from the
      bovine sequencing project at Baylor College of Medicine and assembled with
      DNAStar's SeqMan genome assembler. The DH10B genome is largely colinear
      with that of the wild-type K-12 strain MG1655, although it is
      substantially more complex than previously appreciated, allowing DH10B
      biology to be further explored. The 226 mutated genes in DH10B relative to
      MG1655 are mostly attributable to the extensive genetic manipulations the
      strain has undergone. However, we demonstrate that DH10B has a 13.5-fold
      higher mutation rate than MG1655, resulting from a dramatic increase in
      insertion sequence (IS) transposition, especially IS150. IS elements
      appear to have remodeled genome architecture, providing homologous
      recombination sites for a 113,260-bp tandem duplication and an inversion.
      DH10B requires leucine for growth on minimal medium due to the deletion of
      leuLABCD and harbors both the relA1 and spoT1 alleles causing both
      sensitivity to nutritional downshifts and slightly lower growth rates
      relative to the wild type. Finally, while the sequence confirms most of
      the reported alleles, the sequence of deoR is wild type, necessitating
      reexamination of the assumed basis for the high transformability of DH10B.
AU  - Durfee T
AU  - Nelson R
AU  - Baldwin S
AU  - Plunkett G III
AU  - Burland V
AU  - Mau B
AU  - Petrosino JF
AU  - Qin X
AU  - Muzny DM
AU  - Ayele M
AU  - Gibbs RA
AU  - Csorgo B
AU  - Posfai G
AU  - Weinstock GM
AU  - Blattner FR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2008 190: 2597-2606.

PMID- 25197450
VI  - 9
DP  - 2014
TI  - Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade  possessing an unusually small genome.
PG  - 632-645
AB  - Strain HIMB11 is a planktonic marine bacterium isolated from coastal seawater in  Kaneohe Bay,
      Oahu, Hawaii belonging to the ubiquitous and versatile Roseobacter
      clade of the alphaproteobacterial family Rhodobacteraceae. Here we describe the
      preliminary characteristics of strain HIMB11, including annotation of the draft
      genome sequence and comparative genomic analysis with other members of the
      Roseobacter lineage. The 3,098,747 bp draft genome is arranged in 34 contigs and
      contains 3,183 protein-coding genes and 54 RNA genes. Phylogenomic and 16S rRNA
      gene analyses indicate that HIMB11 represents a unique sublineage within the
      Roseobacter clade. Comparison with other publicly available genome sequences from
      members of the Roseobacter lineage reveals that strain HIMB11 has the genomic
      potential to utilize a wide variety of energy sources (e.g. organic matter,
      reduced inorganic sulfur, light, carbon monoxide), while possessing a reduced
      number of substrate transporters.
AU  - Durham BP et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 632-645.

PMID- 1429469
VI  - 174
DP  - 1992
TI  - Molecular characterization of a second abortive phage resistance gene present in Lactococcus lactis subsp. lactis ME2.
PG  - 7463-7469
AB  - The fifth phage resistance factor from the prototype phage-insensitive strain Lactococcus
      lactis subsp. lactis ME2 has been characterized and sequenced. The genetic determinant for Prf
      (phage resistance five) was subcloned from the conjugative plasmid pTN20, which also encodes a
      restriction and modification system. Typical of other abortive resistance mechanisms, Prf
      reduces the efficiency of plaquing to 10-2 to 10-3 and decreases the plaque size and burst
      size of the small isometric-headed phage p2 in L. lactis subsp. lactis LM0230. However,
      normal-size plaques occurred at a frequency of 10-4 and contained mutant phages that were
      resistant to Prf, even after repeated propagation through a sensitive host. Prf does not
      prevent phage adsorption or promote restriction and modification activities, but 90% of Prf+
      cells infected with phage p2 die. Thus, phage infections in Prf+ cells are aborted. Prf is
      effective in both L. lactis subsp. lactis and L. lactis subsp. cremoris strains against
      several small isometric-headed phages but not against prolate-headed phages. The Prf
      determinant was localized by Tn5 mutagenesis and subcloning. DNA sequencing identified a
      1,056-nucleotide strutural gene designated abiC, Prf+ expression was obtained when abiC was
      subcloned into the lactococcal expression vector pMG36e, abiC is distinct from two other
      lactococcal abortive phage resistance genes, abiA (Hsp+, from L. lactis subsp. lactis ME2) and
      abi416 (Abi+, from L. lactis subsp. lactis IL416). Unlike abiA, the action of abiC does not
      appear to affect DNA replication. Thus, abiC represents a second abortive system found in ME2
      that acts at a different point of the phage lytic cycle.
AU  - Durmaz E
AU  - Higgins DL
AU  - Klaenhammer TR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1992 174: 7463-7469.

PMID- 17012400
VI  - 189
DP  - 2007
TI  - Abortive phage resistance mechanism AbiZ speeds the lysis clock to cause premature lysis of phage-infected Lactococcus lactis.
PG  - 1417-1425
AB  - The conjugative plasmid pTR2030 has been used extensively to confer phage resistance in
      commercial Lactococcus starter cultures. The
      plasmid harbors a 16-kb region, flanked by insertion sequence (IS)
      elements, that encodes the restriction/modification system L1aI and
      carries an abortive infection gene, abiA. The AbiA system inhibits both
      prolate and small isometric phages by interfering with the early stages
      of phage DNA replication. However, abiA alone does not account for the
      full abortive activity reported for pTR2030. In this study, a 7.5-kb
      region positioned within the IS elements and downstream of abiA was
      sequenced to reveal seven additional open reading frames (ORFs). A
      single ORF, designated abiZ, was found to be responsible for a
      significant reduction in plaque size and an efficiency of plaquing
      (EOP) of 10(-6), without affecting phage adsorption. AbiZ causes phage
      phi 31-infected Lactococcus lactis NCK203 to lyse 15 min early,
      reducing the burst size of phi 31 100-fold. Thirteen of 14 phages of
      the P335 group were sensitive to AbiZ, through reduction in either
      plaque size, EOP, or both. The predicted AbiZ protein contains two
      predicted transmembrane helices but shows no significant DNA
      homologies. When the phage phi 31 lysin and holin genes were cloned
      into the nisin-inducible shuttle vector pMSP3545, nisin induction of
      holin and lysin caused partial lysis of NCK203. In the presence of
      AbiZ, lysis occurred 30 min earlier. In holin-induced cells, membrane
      permeability as measured using propidium iodide was greater in the
      presence of AbiZ. These results suggest that AbiZ may interact
      cooperatively with holin to cause premature lysis.
AU  - Durmaz E
AU  - Klaenhammer TR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2007 189: 1417-1425.

PMID- 16534987
VI  - 61
DP  - 1995
TI  - A starter culture rotation strategy incorporating paired restriction/modification and abortive infection bacteriophage defenses in a single lactococcus lactis strain.
PG  - 1266-1273
AB  - Three derivatives of Lactococcus lactis subsp. lactis NCK203, each with a different pair of
      restriction/modification (R/M) and abortive infection (Abi) phage defense systems, were
      constructed and then rotated in repeated cycles of a milk starter culture activity test (SAT).
      The rotation proceeded successfully through nine successive SATs in the presence of phage and
      whey containing phage from previous cycles. Lactococcus cultures were challenged with 2 small
      isometric-headed phages, omega-31 and ul36, in one rotation series and with a composite of 10
      industrial phages in another series. Two native lactococcal R+/M+ plasmids, pTRK68 and pTRK11,
      and one recombinant plasmid, pTRK308, harboring a third distinct R/M system were incorporated
      into three NCK203 derivatives constructed separately for the rotation. The R+/M+ NCK203
      derivatives were transformed with high-copy-number plasmids encoding four Abi genes, abiA,
      abiC, per31, and per50. Various Abi and R/M combinations constructed in NCK203 were evaluated
      for their effects on cell growth, level of phage resistance, and retardation of phage
      development during repeated cycles of the SAT. The three NCK203 derivatives chosen for use in
      the SAT exhibited additive effects of the R/M and Abi phenotypes against sensitive phages. In
      such combinations, phage escaping restriction are prevented from completing their infective
      cycle by an abortive response that kills the host cell. The rotation series successfully
      controlled modified, recombinant, and mutant phages which were resistant to any one of the
      individual defense systems by presenting a different set of R/M and Abi defenses in the next
      test of the rotation.
AU  - Durmaz E
AU  - Klaenhammer TR
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1995 61: 1266-1273.

PMID- 18539811
VI  - 74
DP  - 2008
TI  - Genome sequence and characteristics of Lrm1, a prophage from industrial Lactobacillus rhamnosus strain M1.
PG  - 4601-4609
AB  - Prophage Lrm1 was induced with mitomycin C from an industrial Lactobacillus rhamnosus starter
      culture, M1. Electron microscopy of the
      lysate revealed relatively few intact bacteriophage particles among
      empty heads and disassociated tails. The defective Siphoviridae phage
      had an isometric bead of approximately 55 nm and noncontractile tail of
      about 275 nm with a small baseplate. In repeated attempts, the prophage
      could not be cured from L. rhamnosus M1, nor could a sensitive host be
      identified. Sequencing of the phage Lrm1 DNA revealed a genome of
      39,989 bp and a G+C content of 45.5%. A similar genomic organization
      and mosaic pattern of identities align Lrm1 among the closely related
      Lactobacillus casei temperate phages A2, Phi AT3, and LeaI and with L.
      rhamnosus virulent phage Lu-Nu. Of the 54 open reading frames (ORFs)
      identified, all but 8 shared homology with other phages of this group.
      Five unknown ORFs were identified that had no homologies in the
      databases nor predicted functions. Notably, Lrm1 encodes a putative
      endonuclease and a putative DNA methylase with homology to a methylase
      in Lactococcus lactis phage Tuc2009. Possibly, the DNA methylase,
      endonuclease, or other Lrm1 genes provide a function crucial to L.
      rhamnosus M1 survival, resulting in the stability of the defective
      prophage in its lysogenic state. The presence of a defective prophage
      in an industrial strain could provide superinfection immunity to the
      host but could also contribute DNA in recombination events to produce
      new phages potentially infective for the host strain in a large-scale
      fermentation environment.
AU  - Durmaz E
AU  - Miller MJ
AU  - Azcarate-Peril MA
AU  - Toon SP
AU  - Klaenhammer TR
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2008 74: 4601-4609.

PMID- 28982989
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Gordonia lacunae BS2T.
PG  - e00959-17
AB  - We report here the draft genome sequence of the soil bacterium Gordonia lacunae BS2T (= DSM
      45085T = JCM 14873T = NRRL B-24551T), isolated from an estuary in
      Plettenberg Bay, South Africa. Analysis of the draft genome revealed that more
      than 40% of the secondary metabolite biosynthetic genes encode new compounds.
AU  - Durrell K
AU  - Prins A
AU  - Le Roes-Hill M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00959-17.

PMID- 8437585
VI  - 236
DP  - 1993
TI  - Characterization of the cleavage site and the recognition sequence of the I-CreI DNA endonuclease encoded by the chloroplast ribosomal intron of Chlamydomonas reinhardtii.
PG  - 409-414
AB  - The chloroplast ribosomal intron of Chlamydomonas reinhardtii encodes a sequence-specific DNA
      endonuclease (I-CreI), which is most probably involved in the mobility of this intron. Here we
      show that I-CreI generates a 4 bp staggered cleavage just downstream of the intron insertion
      site. The I-CreI recognition sequence is 19-24 bp in size and is located asymmetrically around
      the intron insertion site. Screening of natural variants of the I-CreI recognition sequence
      indicates that the I-CreI endonuclease tolerates single and even multiple base changes within
      its recognition sequence.
AU  - Durrenberger F
AU  - Rochaix J-D
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1993 236: 409-414.

PMID- 1915304
VI  - 10
DP  - 1991
TI  - Chloroplast ribosomal intron of Chlamydomonas reinhardtii: in vitro self-splicing, DNA endonuclease activity and in vivo mobility.
PG  - 3495-3501
AB  - All chloroplast 23S ribosomal RNA genes of the unicellular alga Chlamydomonas reinhardtii
      contain an 888 bp group I intron with an internal open reading frame (ORF). A precursor RNA
      encompassing the intron with its 5' and 3' flanking sequences was shown to self-splice both
      during in vitro transcription and upon incubation of the isolated pre-RNA under self-splicing
      conditions. Expression of the internal ORF in Escherichia coli in the presence of a plasmid
      containing a cDNA corresponding to the intronless form of the 23S rRNA gene resulted in
      specific cleavage of the cDNA at or close to the exon junction sequence. To test whether this
      ORF-encoded double-strand DNA endonuclease is involved in intron mobility in vivo, the same
      ribosomal cDNA was stably integrated into the C. reinhardtii chloroplast genome using particle
      gun mediated transformation. All the transformants with the cDNA integrated at the expected
      site in the chloroplast genome had the intron precisely inserted at the artificial exon
      junction site. These experiments demonstrate that the chloroplast ribosomal intron of C.
      reinhardtii behaves as a ribozyme in vitro and also as a mobile genetic element in vivo
      provided a target site is present.
AU  - Durrenberger F
AU  - Rochaix J-D
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1991 10: 3495-3501.

PMID- 23788536
VI  - 1
DP  - 2013
TI  - Genome Sequence of the Bacillus subtilis Biofilm-Forming Transformable Strain PS216.
PG  - e00288-13
AB  - Bacillus subtilis PS216, a strain isolated in Slovenia, has been sequenced. PS216 is
      transformable and forms robust biofilms, making it useful for the study of
      competence regulation in an undomesticated bacterium.
AU  - Durrett R
AU  - Miras M
AU  - Mirouze N
AU  - Narechania A
AU  - Mandic-Mulec I
AU  - Dubnau D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00288-13.

PMID- 13888713
VI  - 5
DP  - 1962
TI  - Host Specificity of DNA Produced by Escherichia Coli:  II. Control over acceptance of DNA from infecting phage lambda.
PG  - 37-49
AB  - DNA of lambda.K (lambdaphage grown on E. coli strain K12) is shown to be
      degraded upon infection of the new host strains E. coli K12(P1) or E. coli B.
      This breakdown begins shortly after phage attachment and successful DNA
      injection.  32P label from the lambda.K DNA submitted to this degradation
      appears partly in acid-soluble components (organic and inorganic) and partly in
      acid-insoluble compounds.  The host cell survives such an infection and permits
      diffusion of a fraction of the degradation products into the medium, while
      probably re-using another fraction.  Genetic markers from lambda.K are rescued
      in K12(P1) host cells infected with both restricted lambda.K and unrestricted
      lambda.K(P1).  Since DNA breakdown competes in time with the rescue, the
      probability of marker rescue is high if the unrestricted phage infects first
      and low if the restricted phage infects first.  Only closely linked markers
      have a good chance to be rescued together.  The host specificity imparted to
      phage DNA by the bacterial strain on which it was produced is thought to be
      responsible for its recognition as incompatible with a new host strain.
      Bacterial mutants are described which, despite the presence of prophage P1,
      accept infecting lambda.K at relatively high rates.
AU  - Dussoix D
AU  - Arber W
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1962 5: 37-49.

PMID- 14292250
VI  - 11
DP  - 1965
TI  - Host specificity of DNA produced by Escherichia coli IV.  Host specificity of infectious DNA from bacteriophage lambda.
PG  - 238-246
AB  - DNA extracted with phenol from bacteriophage lambda gives rise to phage
      production after uptake by helper-infected, competent recipient cells (Kaiser,
      2962).  Under our experimental conditions, the number of infective centres
      obtained by infection of Escherichia coli K12 is about 10-3 per phage
      equivalent of DNA from lambda.K or from lambda.K(P1).  But on K12(P1) recipient
      cells only lambda-K(P1) DNA infects with an efficiency of 10-3, while lambda.K
      DNA gives about 100 times less infective centres.  The same factor of
      restriction for lambda.K is found in controls done by infection of the
      competent cells with intact phage particles instead of the phage DNA.
      Similarly, restrictions displayed by K12 against phage grown on E. coli B or E.
      coli C and those displayed by B against phage grown on K12 or C are found to
      hold true for DNA preparations.  E. coli C accepts all tested lambda DNA with
      about the same efficiency.  We conclude that the phenol extraction does not
      affect the host specificity of the phage DNA.  One cycle growth of lambda
      initiated by infection of K12 with lambda.K(P1) DNA confirms this result:  the
      parental P1-directed host specificity is transferred into the phage progeny,
      and it is found only in such phage particles that also inherit one strand of
      the infecting DNA molecule.  The stability of the association of DNA with its
      host specificity is further revealed by its resistance to various physical,
      chemical and enzymic treatments of the lambda DNA.  It is significant with
      respect to the understanding of the mechanism of competence of bacteria for
      infection with lambda DNA that only non-restricted phage acts as a good helper.
AU  - Dussoix D
AU  - Arber W
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1965 11: 238-246.

PMID- 
VI  - 
DP  - 1990
TI  - Cloning of the restriction-modification systems from Herpetosiphon giganteus Hpa1, Hpa2 and Hpg5 in E. coli - Characterization and comparative analysis of the genetic organization and structure.
PG  - 1-160
AB  - None - but this thesis shows that M.HgiBI, M.HgiDI, M.HgiDII and M.HgiGI are
      m5C-methylases.  Also, because SalI was used to select M.HgiDII gene and SalI
      can cleave when the last cytosine in the recognition sequence (GTCGAC) is m5C,
      M.HgiDII must methylate the first cytosine in the sequence.
AU  - Dusterhoft A
PT  - Journal Article
TA  - Ph.D. Thesis, Justus-Liebig University, Geissen, W. Germany
JT  - Ph.D. Thesis, Justus-Liebig University, Geissen, W. Germany
SO  - Ph.D. Thesis, Justus-Liebig University, Geissen, W. Germany 1990 : 1-160.

PMID- 2020544
VI  - 19
DP  - 1991
TI  - Stepwise cloning and molecular characterization of the HgiDI restriction-modification system from Herpetosiphon giganteus Hpa2.
PG  - 1049-1056
AB  - The restriction-modification system HgiDI from Herpetosiphon giganteus strain
      Hpa2 has been cloned in E. coli in a two-step procedure.  Selection of the
      methyltransferase (M.HgiDI) gene in vitro was performed using the heterologous
      restriction endonuclease AhaII, an isoschizomer of AcyI and HgiDI (GRCGYC).
      Cloning of the complete HgiDI endonuclease (R.HgiDI) gene could only be
      achieved in recipient cells harbouring a recombinant plasmid, which was
      expressing the corresponding methyltransferase and could thereby prevent the
      host from self-destruction of its genetic material.  The HgiDI
      restriction-modification system was sequenced and functionally correlated with
      two open reading frames of 309 (M) and 359 (R) codons.  In homology studies
      M.HgiDI showed significant similarities to 20 other m5C-methyltransferases and
      turned out to be the most compact enzyme of this group described so far.
      Initial attempts for overexpression of M.HgiDI and partial purification of
      R.HgiDI have been successful.
AU  - Dusterhoft A
AU  - Erdmann D
AU  - Kroger M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 1049-1056.

PMID- 2062638
VI  - 19
DP  - 1991
TI  - Isolation and genetic structure of the AvaII isoschizomeric restriction-modification system HgiBI from Herpetosiphon giganteus Hpg5:  M.HgiBI reveals high homology to M.BanI.
PG  - 3207-3211
AB  - The complete type II restriction-modification system HgiBI of Herpetosiphon
      giganteus strain Hpg5 recognizing the AvaII specific DNA sequence GGWCC has
      been cloned and expressed functionally active in Escherichia coli.  A
      considerable acceleration in cloning could be achieved by preparing a size
      restricted library after application of a related hybridization probe.  Both
      methyltransferase (437 codons) and restriction endonuclease gene (274 codons)
      were found to be encoded on a 3.6 kilobases ClaI/HincII fragment in the same
      transcriptional orientation separated by one triplet only.  Protein sequence
      comparisons revealed a close resemblance of M.HgiBI to the group of
      m5C-methyltransferases, especially to M.BanI from Bacillus aneurinolyticus with
      the related recognition sequence GGYRCC.  In contrast, no significant
      similarities have been observed for the associated endonuclease R.HgiBI with
      any other restriction enzyme described so far, even not with the isoschizomeric
      R.SinI from Salmonella infantis, or with R.BanI.
AU  - Dusterhoft A
AU  - Erdmann D
AU  - Kroger M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 3207-3211.

PMID- Not carried by PubMed...
VI  - 7
DP  - 1988
TI  - Site directed mutagenesis on the restriction endonuclease EcoRI using mixed oligonucleotides.
PG  - 737-740
AB  - The restriction endonuclease EcoRI could be modified via site directed
      mutagenesis at position Arg200.  Using the thiophosphate system we introduced
      either Lys, Glu or Gly in a one pot procedure.  Although G recognition should
      be affected, Lys200 showed wildtype specificity.
AU  - Dusterhoft A
AU  - Kroger M
PT  - Journal Article
TA  - Nucl. Nucl.
JT  - Nucl. Nucl.
SO  - Nucl. Nucl. 1988 7: 737-740.

PMID- 1937045
VI  - 106
DP  - 1991
TI  - Cloning, sequence and characterization of m5C-methyltransferase-encoding gene, hgiDIIM (GTCGAC), from Herpetosiphon giganteus strain Hpa2.
PG  - 87-92
AB  - We have cloned the gene (hgiDIIM) encoding the methyltransferase (MTase) of the SalI
      isoschizomeric restriction-modification (R-M) system, HgiDII (GTCGAC), into Escherichia coli.
      The hgiDIIM gene has been isolated from the same plasmid library of Herpetosiphon giganteus
      strain Hpa2, as was the previously cloned R-M system, HgiDI [AcyI/GRCGYC; Dusterhoft et al.,
      Nucl. Acids Res. 19 (1991) 1049-1056]. Sequencing and functional localization of hgiDIIM
      revealed an open reading frame (ORF) of 354 codons (39786 Da) with significant homologies to
      the group of m5C-, rather than the m4C-/m6A-, MTases. Subsequent cloning and analysis of
      adjacent chromosomal segments led to the identification of two additional ORFs upstream
      (ORF15, 139 codons) and downstream (ORF68, 611 codons) from hgiDIIM with the same
      transcriptional orientation as the hgiDIIM gene. However, the expected restriction enzyme
      function was not found in either of these ORFs.
AU  - Dusterhoft A
AU  - Kroger M
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1991 106: 87-92.

PMID- 27540063
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequences of Agricultural, Host-Associated Campylobacter coli and Campylobacter jejuni Strains.
PG  - e00833-16
AB  - We report here the genome sequences of four agricultural, multidrug-resistant Campylobacter
      spp.: C. coli 11601 and C. jejuni 11601MD, isolated from turkey
      cecum and jejunum, respectively, and C. coli 6067 and C. coli 6461, isolated from
      turkey-house water and swine feces, respectively. The genomes provide insights on
      Campylobacter antimicrobial resistance and host adaptations.
AU  - Dutta V
AU  - Altermann E
AU  - Olson J
AU  - Wray GA
AU  - Siletzky RM
AU  - Kathariou S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00833-16.

PMID- 27932656
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Two Historical Listeria monocytogenes Strains from Human Listeriosis Cases in 1933.
PG  - e01364-16
AB  - We report here the draft genome sequences of two Listeria monocytogenes strains from some of
      the earliest reported cases of human listeriosis in North America.
      The strains were isolated in 1933 from patients in Massachusetts and Connecticut,
      USA, and belong to the widely disseminated hypervirulent clonal complex 1 (CC1)
      and CC2.
AU  - Dutta V
AU  - Lee S
AU  - Ward TJ
AU  - Orwig N
AU  - Altermann E
AU  - Jima D
AU  - Parsons C
AU  - Kathariou S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01364-16.

PMID- 28495780
VI  - 5
DP  - 2017
TI  - Genome Sequences of Listeria monocytogenes Strains with Resistance to Arsenic.
PG  - e00327-17
AB  - Listeria monocytogenes frequently exhibits resistance to arsenic. We report here  the draft
      genome sequences of eight genetically diverse arsenic-resistant L.
      monocytogenes strains from human listeriosis and food-associated environments.
      The availability of these genomes will help elucidate the role of heavy-metal
      resistance in the ecology of L. monocytogenes.
AU  - Dutta V
AU  - Lee S
AU  - Ward TJ
AU  - Orwig N
AU  - Altermann E
AU  - Jima DD
AU  - Parsons C
AU  - Kathariou S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00327-17.

PMID- 28912327
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequence of the First Sequence Type 27 Brucella ceti Strain Isolated from European Waters.
PG  - e00988-17
AB  - Brucella spp. that cause marine brucellosis are becoming more important, as the disease
      appears to be more widespread than originally thought. Here, we report a
      whole and annotated genome sequence of Brucella ceti CRO350, a sequence type 27
      strain isolated from a bottlenose dolphin carcass found in the Croatian part of
      the northern Adriatic Sea.
AU  - Duvnjak S
AU  - Spicic S
AU  - Kusar D
AU  - Papic B
AU  - Reil I
AU  - Zdelar-Tuk M
AU  - Pavlinec Z
AU  - Duras M
AU  - Gomercic T
AU  - Hendriksen RS
AU  - Cvetnic Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00988-17.

PMID- 6244195
VI  - 111
DP  - 1980
TI  - A new sequence-specific endonuclease from a thermophilic cyanobacterium, Mastigocladus laminosus.
PG  - 423-426
AB  - The screening of a number of cyanobacteria (blue-green algae) for new
      sequence-specific deoxyribonucleases has been very rewarding.  We report here
      the purification of a new enzyme of this type from Mastigocladus laminosus
      (named MlaI) which recognizes and cleaves the nucleotide sequence TT^CGAA.
AU  - Duyvesteyn MGC
AU  - de Waard A
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1980 111: 423-426.

PMID- 6250895
VI  - 117
DP  - 1980
TI  - Two sequence-specific deoxyribonucleases from Rhodospirillum rubrum.
PG  - 241-246
AB  - The usefulness of sequence-specific endonucleases in solving fundamental
      problems in current molecular biology is well established.  The catalog of
      enzymes has increased steadily.  We report here the isolation and partial
      characterization of two enzymes from Rhodospirillum rubrum, endonucleases
      R.RruI and R.RruII.  The first enzyme is unique in that it recognizes and
      cleaves the hexanucleotide sequence AGT^ACT in DNA molecules of various origin.
      The latter enzyme (endo R.RruII) recognizes the nucleotide sequence CC(A/T)GG
      as does endo R.EcoRII; however, it cleaves the DNA within the site like the
      isoschizomer endo R.BstNI (CC^(A/T)GG).
AU  - Duyvesteyn MGC
AU  - de Waard A
AU  - van Ormondt H
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1980 117: 241-246.

PMID- 24317822
VI  - 1
DP  - 1981
TI  - Isolation and characterization of a sequence-specific deoxyriboendonuclease from Calothrix scopulorum.
PG  - 75-79
AB  - Sequence-specific deoxyriboendonucleases have been isolated from bacteria and
      fungi.  Except in a few cases the nucleotide sequences recognized by the
      cyanobacerial enzymes have been shown to be unique.  In this report we describe
      the isolation and characterization of an endonuclease (endo R. CscI) from a
      cyanobacterium, Calothrix scopulorum which cleaves the deoxynucleotide sequence
      CCGC^GG.  Isoschizomers have been found previously in a fungus and in two
      bacterial strains.
AU  - Duyvesteyn MGC
AU  - Korsuize J
AU  - de Waard A
PT  - Journal Article
TA  - Plant Mol. Biol.
JT  - Plant Mol. Biol.
SO  - Plant Mol. Biol. 1981 1: 75-79.

PMID- Not included in PubMed...
VI  - 134
DP  - 1983
TI  - Sequence-specific endonucleases in strains of Anabaena and Nostoc.
PG  - 276-281
AB  - The complements of restriction endonucleases of 12 strains of cyanobacteria were determined in
      cell-free extracts, and were compared with the complements of restriction activities assessed
      by measuring the relative efficiencies of plating of cyanophages on those cyanobacteria.  The
      hosts which were susceptible to all of the phages contained endo R.AvaI and endo R.AvaII, and
      in several cases probably endo R.AvaIII, or isoschizomers of these enzymes. Three hosts which
      were lysed by only a subset (1 or 3) of the phages contained different restriction
      endonucleases.  Anabaena sp. PCC 7120 showed apparent phenotypic restriction of phage AN-22
      grown in hosts with (isoschizomers of) AvaI, II and III, but no corresponding endonuclease has
      yet been detected in vitro.  Nostoc sp. ATCC 29131 (PCC 6705) was found to contain a
      restriction enzyme, NspBII, with hitherto unknown specificity, C A/C GC T/G G.
AU  - Duyvesteyn MGC
AU  - Korsuize J
AU  - de Waard A
AU  - Vonshak A
AU  - Wolk CP
PT  - Journal Article
TA  - Arch. Microbiol.
JT  - Arch. Microbiol.
SO  - Arch. Microbiol. 1983 134: 276-281.

PMID- 23355610
VI  - 41
DP  - 2013
TI  - Helicobacter pylori DprA alleviates restriction barrier for incoming DNA.
PG  - 3274-3288
AB  - Helicobacter pylori is a Gram-negative bacterium that colonizes human stomach and causes
      gastric inflammation. The species is naturally competent and displays remarkable diversity.
      The presence of a large number of restriction-modification (R-M) systems in this bacterium
      creates a barrier against natural transformation by foreign DNA. Yet, mechanisms that protect
      incoming double-stranded DNA (dsDNA) from restriction enzymes are not well understood. A
      DNA-binding protein, DNA Processing Protein A (DprA) has been shown to facilitate natural
      transformation of several Gram-positive and Gram-negative bacteria by protecting incoming
      single-stranded DNA (ssDNA) and promoting RecA loading on it. However, in this study, we
      report that H. pylori DprA (HpDprA) binds not only ssDNA but also dsDNA thereby conferring
      protection to both from various exonucleases and Type II restriction enzymes. Here, we
      observed a stimulatory role of HpDprA in DNA methylation through physical interaction with
      methyltransferases. Thus, HpDprA displayed dual functional interaction with H. pylori R-M
      systems by not only inhibiting the restriction enzymes but also stimulating
      methyltransferases. These results indicate that HpDprA could be one of the factors that
      modulate the R-M barrier during inter-strain natural transformation in H. pylori.
AU  - Dwivedi GR
AU  - Sharma E
AU  - Rao DN
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2013 41: 3274-3288.

PMID- 22689228
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Thermus sp. Strain RL, Isolated from a Hot Water Spring  Located atop the Himalayan Ranges at Manikaran, India.
PG  - 3534
AB  - Thermus sp. strain RL was isolated from a hot water spring (90 degrees C to 98 degrees C) at
      Manikaran, Himachal Pradesh, India. Here we report the draft genome
      sequence (20,36,600 bp) of this strain. The draft genome sequence consists of 17
      contigs and 1,986 protein-coding sequences and has an average G+C content of
      68.77%.
AU  - Dwivedi V
AU  - Sangwan N
AU  - Nigam A
AU  - Garg N
AU  - Niharika N
AU  - Khurana P
AU  - Khurana JP
AU  - Lal R
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3534.

PMID- 33837
VI  - 38
DP  - 1979
TI  - Interaction of HpaI endonuclease with chemically synthesized oligonucleotides.
PG  - 294
AB  - The octanucleotide dG-G-T-T-A-A-C-C is cleaved by the restriction endonuclease
      HpaI at the phosphodiester bond between thymidine and adenosine.
      Octanucleotides, containing modified nucleosides in the recognition sequence
      for HpaI, were chemically synthesized by our modified triester method.
      Interaction of the enzyme with dG-G-T-U-A-A-C-C, dG-G-T-U(Br)-A-A-C-C, and
      dG-I-T-T-A-A-C-C will be described.  An octanucleotide, in which the
      phosphodiester bond at the site of cleavage is replaced by its methyl
      phosphonate analogue, was also synthesized and is a reversible inhibitor of the
      HpaI endonuclease.
AU  - Dwyer PA
AU  - Riftina F
AU  - Agarwal KL
PT  - Journal Article
TA  - Fed. Proc.
JT  - Fed. Proc.
SO  - Fed. Proc. 1979 38: 294.

PMID- 6291587
VI  - 21
DP  - 1982
TI  - Interaction of the HpaI endonuclease with synthetic oligonucleotides.
PG  - 4693-4700
AB  - To determine which functional groups of bases within the grooves of
      double-helical DNA interact with the HpaI endonuclease, we have employed
      chemically synthesized octanucleotides containing base analogues.  The 5-methyl
      group of thymine was probed as a contact between the HpaI endonuclease and its
      recognition sequence by using the ologonucleotides d(G-G-T-T-A-A-C-C),
      d(G-G-T-U-A-A-C-C), and d(G-G-T-B-A-A-C-C).  The 2-amino group of guanine was
      probed as a contact for the HpaI endonuclease by using the octanucleotide
      d(G-I-T-T-A-A-C-C).  The HpaI endonuclease cleaves octanucleotides
      d(G-G-T-T-A-A-C-C) and d(G-G-T-B-A-A-C-C) according to Michaelis-Menten
      kinetics.  However, both the Km and turnover number for d(G-G-T-B-A-A-C-C) were
      severalfold lower than those for cleave of d(G-G-T-T-A-A-C-C).  In addition,
      d(G-G-T-U A-A-C-C) was not cleaved by HpaI endonuclease, suggesting that the
      5-methyl group of thymine is a contact between the HpaI endonuclease and its
      recognition sequence.  d(G-I-T-T-A-A-C-C) was not cleaved by the HpaI
      endonuclease which may be due in part to the low thermal stability of the
      duplex.  Nevertheless, our results suggest that the 2-amino group of guanine is
      a contact for the HpaI endonuclease.  A phosphate group 5' external to the HpaI
      recognition sequence has been identified as a contact between the HpaI
      endonuclease and DNA.  The HpaI endonuclease cleaved 5'-phosphorylated
      octanucleotide 30-fold faster than unphosphorylated octanucleotide.  In
      addition, the Km of the d(G-G-T-T-A-A-C-C) was 8000-fold higher than the Km of
      the phage f1 RFI DNA, suggesting that the octanucleotide is too short to take
      advantage of the entire DNA binding site of the enzyme.
AU  - Dwyer-Hallquist P
AU  - Kezdy FJ
AU  - Agarwal KL
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1982 21: 4693-4700.

PMID- 7690339
VI  - 131
DP  - 1993
TI  - Isolaton of Escherichia coli mutants lacking methylcytosine-dependent restriction systems for cloning extensively methylated frog virus 3 DNA.
PG  - 87-91
AB  - Many bacterial strains possess methylation-dependent restriction systems (MDRS) that
      demonstrate methylcytosine-dependent restriction endonuclease activity for the dinucleotide
      sequence, dCpdG. This makes these strains unsuitable for cloning methylated DNA. Some
      commercially available bacterial cells are recommended for cloning DNA fragments with
      methylated cytosines and adenines, e.g., Escherichia coli DH5-alphaMCR. Our attempts to clone
      frog virus 3 (FV3) DNA, which has the highest degree of cytosine methylation ever reported,
      using DH5-alphaMCR cells, were not successful. This and other observations suggested the
      existence of additional MDRS that have not yet been eliminated from DH5-alphaMCR cells. In
      order to isolate a mutant from this bacterial strain that is suitable to clone highly
      methylated FV3 DNA, we transformed these cells with a recombinant pUC19 plasmid containing a
      methylated 1.4-kb genomic DNA fragment from FV3, and selected for ampicillin (Ap) resistance.
      Three such attempts yielded only one colony that contained a fully methylated 1.4-kb FV3
      genomic DNA fragment. Furthermore, plasmid-cured Ap-sensitive colonies originating from this
      clone were isolated and have been successfully employed to clone the highly methylated FV3
      genomic DNA fragment.
AU  - Dy L
AU  - Chalasani S
AU  - Essani K
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1993 131: 87-91.

PMID- 24794723
VI  - 79
DP  - 2014
TI  - Expression of exogenous DNA methyltransferases: Application in molecular and cell biology.
PG  - 77-87
AB  - DNA methyltransferases might be used as powerful tools for studies in molecular and cell
      biology due to their ability to recognize and modify nitrogen bases in specific sequences of
      the genome. Methylation of the eukaryotic genome using exogenous DNA methyltransferases
      appears to be a promising approach for studies on chromatin structure. Currently, the
      development of new methods for targeted methylation of specific genetic loci using DNA
      methyltransferases fused with DNA-binding proteins is especially interesting. In the present
      review, expression of exogenous DNA methyltransferase for purposes of in vivo analysis of the
      functional chromatin structure along with investigation of the functional role of DNA
      methylation in cell processes are discussed, as well as future prospects for application of
      DNA methyltransferases in epigenetic therapy and in plant selection.
AU  - Dyachenko OV
AU  - Tarlachkov SV
AU  - Marinitch DV
AU  - Shevchuk TV
AU  - Buryanov YI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 2014 79: 77-87.

PMID- 26139716
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Bifidobacterium angulatum GT102 and Bifidobacterium adolescentis 150: Focusing on the Genes Potentially Involved in the Gut-Brain  Axis.
PG  - e00709-15
AB  - The draft genome sequences of Bifidobacterium angulatum GT102 and Bifidobacterium adolescentis
      150 strains isolated from the human intestinal microbiota are
      reported. Both strains are able to produce gamma-aminobutyric acid (GABA).
      Detailed genomes analysis will help to understand the role of GABA in the
      functioning of gut-brain axis.
AU  - Dyachkova MS
AU  - Klimina KM
AU  - Kovtun AS
AU  - Zakharevich NV
AU  - Nezametdinova VZ
AU  - Averina OV
AU  - Danilenko VN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00709-15.

PMID- 21701686
VI  - 6
DP  - 2011
TI  - Haloquadratum walsbyi: limited diversity in a global pond.
PG  - e20968
AB  - Background: Haloquadratum walsbyi commonly dominates the microbial flora of hypersaline
      waters. Its cells are extremely fragile squares requiring .14%(w/v) salt for growth,
      properties that should limit its dispersal and promote geographical isolation and divergence.
      To assess this, the genome sequences of two isolates recovered from sites at near maximum
      distance on Earth, were compared.  Principal Findings: Both chromosomes are 3.1 MB in size,
      and 84% of each sequence was highly similar to the other (98.6% identity), comprising the core
      sequence. ORFs of this shared sequence were completely synteneic (conserved in genomic
      orientation and order), without inversion or rearrangement. Strain-specific
      insertions/deletions could be precisely mapped, often allowing the genetic events to be
      inferred. Many inferred deletions were associated with short direct repeats (4- 20 bp).
      Deletion-coupled insertions are frequent, producing different sequences at identical
      positions. In cases where the inserted and deleted sequences are homologous, this leads to
      variant genes in a common synteneic background (as already described by others). Cas/CRISPR
      systems are present in C23T but have been lost in HBSQ001 except for a few spacer remnants.
      Numerous types of mobile genetic elements occur in both strains, most of which appear to be
      active, and with some specifically targetting others. Strain C23T carries two ,6 kb plasmids
      that show similarity to halovirus His1 and to sequences nearby halovirus/plasmid gene clusters
      commonly found in haloarchaea. Conclusions: Deletion-coupled insertions show that Hqr. walsbyi
      evolves by uptake and precise integration of foreign DNA, probably originating from close
      relatives. Change is also driven by mobile genetic elements but these do not by themselves
      explain the atypically low gene coding density found in this species. The remarkable genome
      conservation despite the presence of active systems for genome rearrangement implies both an
      efficient global dispersal system, and a high selective fitness for this species.
AU  - Dyall-Smith M
AU  - Pfeiffer F
AU  - Klee K
AU  - Palm P
AU  - Gross K
AU  - Schuster SC
AU  - Rampp M
AU  - Oesterhelt D
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2011 6: e20968.

PMID- 28818900
VI  - 5
DP  - 2017
TI  - Genome Sequence of an Australian Monophasic Salmonella enterica subsp. enterica Typhimurium Isolate (TW-Stm6) Carrying a Large Plasmid with Multiple  Antimicrobial Resistance Genes.
PG  - e00793-17
AB  - We report the genome sequence of a monophasic Salmonella enterica subsp. enterica Typhimurium
      strain (TW-Stm6) isolated in Australia that is similar to epidemic
      multidrug-resistant strains from Europe and elsewhere. This strain carries
      additional antibiotic and heavy-metal resistance genes on a large (275-kb) IncHI2
      plasmid.
AU  - Dyall-Smith ML
AU  - Liu Y
AU  - Billman-Jacobe H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00793-17.

PMID- 23516216
VI  - 1
DP  - 2013
TI  - Genome of the Haloarchaeon Natronomonas moolapensis, a Neutrophilic Member of a Previously Haloalkaliphilic Genus.
PG  - e0009513
AB  - The genus Natronomonas contains two species, one haloalkaliphile (N. pharaonis) and one
      neutrophile (N. moolapensis). Here, we report the genome sequence of N.
      moolapensis strain 8.8.11. The overall genome properties are similar for the two
      species. Only the neutrophile contains bacteriorhodopsin and a membrane
      glycolipid.
AU  - Dyall-Smith ML
AU  - Pfeiffer F
AU  - Oberwinkler T
AU  - Klee K
AU  - Rampp M
AU  - Palm P
AU  - Gross K
AU  - Schuster SC
AU  - Oesterhelt D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0009513.

PMID- 17209015
VI  - 189
DP  - 2007
TI  - Evidence for type III restriction and modification systems in Mycoplasma pulmonis.
PG  - 2197-2202
AB  - Mycoplasma pulmonis possesses a cassette of genes that are predicted to code for type III
      restriction and modification (R-M) enzymes. Transposon
      disruption of a gene predicted to code for the endonuclease subunit of the
      enzyme resulted in loss of R-M activity. Genomic data indicate that the
      cassette was acquired by horizontal gene transfer and possibly located on
      a mobile element.
AU  - Dybvig K
AU  - Cao Z
AU  - French CT
AU  - Yu H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2007 189: 2197-2202.

PMID- 9811902
VI  - 95
DP  - 1998
TI  - A family of phase-variable restriction enzymes with differing specificities generated by high-frequency gene rearrangements.
PG  - 13923-13928
AB  - The hsd genes of Mycoplasma pulmonis encode restriction and modification enzymes exhibiting a
      high degree of sequence similarity to the type I enzymes of enteric bacteria.  The S subunits
      of type I systems dictate the DNA sequence specificity of the holoenzyme and are required for
      both the restriction and the modification reactions.  The M. pulmonis chromosome has two hsd
      loci, both of which contains two hsdS genes each and are complex, site-specific DNA inversion
      systems.  Embedded within the coding regions of each hsdS gene are a minimum of three sites at
      which DNA inversions occur to generate extensive amino acid sequence variations in the
      predicted S subunits.  We show that the polymorphic hsdS genes produced by gene rearrangement
      encode a family of functional S subunits with differing DNA sequence specificities.  In
      addition to creating polymorphisms in hsdS sequences, DNA inversions regulate the
      phase-variable production of restriction activity because the other genes required for
      restriction activity (hsdR and hsdM) are expressed only from loci that are oriented
      appropriately in the chromosome relative to the hsd promoter.  These data cast doubt on the
      prevailing paradigms that restriction systems are either selfish or function to confer
      protection from invasion by foreign DNA.
AU  - Dybvig K
AU  - Sitaraman R
AU  - French CT
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1998 95: 13923-13928.

PMID- 6286600
VI  - 151
DP  - 1982
TI  - Cytosine methylation of the sequence GATC in a mycoplasma.
PG  - 1420-1424
AB  - Mycoplasma virus L2 is subject to host-specific restriction and modification in
      Acholeplasma laidlawii strains JA1 and K2.  We have examined the DNAs from both
      host cells and viruses propagated on these strains with respect to
      susceptibility to cleavage by restriction endonucleases and for DNA base
      modifications.  We show that, in strain K2 and L2 virus grown on K2 cells,
      cytosine in the sequence GATC is methylated to 5-methylcytosine and, although
      strain K2 and L2 viruses grown on K2 contain N6-methyladenine in their DNA,
      adenine in the sequence GATC is not methylated.  In contrast to K2, strain JA1
      and L2 virus grown on JA1 cells contain no detectable methylated bases.  It is
      not known which of the methylated bases in K2 is the basis for the K2
      restriction-modification system operative on L2 virus.
AU  - Dybvig K
AU  - Swinton D
AU  - Maniloff J
AU  - Hattman S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1982 151: 1420-1424.

PMID- 8905075
VI  - 50
DP  - 1996
TI  - Molecular biology of mycoplasmas.
PG  - 25-57
AB  - Although mycoplasmas lack cell walls, they are in many respects similar to the gram-positive
      bacteria with which they share a common ancestor.  The molecular biology of mycoplasmas is
      intriguing because the chromosome is uniquely small (<600 kb in some species) and extremely
      A-T rich (as high as 75 mol% in some species).  Perhaps to accommodate DNA with a lower G+C
      content, most mycoplasmas do not have the "universal" genetic code.  In these species, TGA is
      not a stop codon; instead it encodes tryptophan at a frequency 10 times greater than TGG, the
      usual codon for this amino acid.  Because of the presence of TGA codons, the translation of
      mycoplasmal proteins terminates prematurely when cloned genes are expressed in other
      eubacteria, such as Escherichia coli.  Many mycoplasmas possess strikingly dynamic chromosomes
      in which high-frequency changes result from errors in DNA repair or replication and from
      highly active recombination systems.  Often, high-frequency changes in the mycoplasmal
      chromosome are associated with antigenic and phase variation, which regulate the production of
      factors critical to disease pathogenesis.
AU  - Dybvig K
AU  - Voelker LL
PT  - Journal Article
TA  - Annu. Rev. Microbiol.
JT  - Annu. Rev. Microbiol.
SO  - Annu. Rev. Microbiol. 1996 50: 25-57.

PMID- 7934878
VI  - 12
DP  - 1994
TI  - Regulation of a restriction and modification system via DNA inversion in Mycoplasma pulmonis.
PG  - 547-560
AB  - An invertible DNA element of 6.8kb, designated the hsd1 locus, was identified in the
      chromosome of Mycoplasma pulmonis. Infection of host cells with mycoplasma virus P1 revealed
      that the organism's restriction and modification (R-M) properties are controlled by inversion
      of hsd1. The nucleotide sequence of hsd1 revealed several genes, the predicted amino acids of
      which bear striking similarity to the subunits of the type I R-M enzymes previously found only
      in enteric bacteria.
AU  - Dybvig K
AU  - Yu H
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1994 12: 547-560.

PMID- 27979936
VI  - 4
DP  - 2016
TI  - Complete Genome Sequences of Six Legionella pneumophila Isolates from Two Collocated Outbreaks of Legionnaires' Disease in 2005 and 2008 in  Sarpsborg/Fredrikstad, Norway.
PG  - e01367-16
AB  - Here, we report the complete genome sequences of Legionella pneumophila isolates  from two
      collocated outbreaks of Legionnaires' disease in 2005 and 2008 in
      Sarpsborg/Fredrikstad, Norway. One clinical and two environmental isolates were
      sequenced from each outbreak. The genome of all six isolates consisted of a 3.36
      Mb-chromosome, while the 2005 genomes featured an additional 68 kb-episome
      sharing high sequence similarity with the L. pneumophila Lens plasmid. All six
      genomes contained multiple mobile genetic elements including novel combinations
      of type-IVA secretion systems. A comparative genomics study will be launched to
      resolve the genetic relationship between the L. pneumophila isolates.
AU  - Dybwad M
AU  - Aarskaug T
AU  - Fykse EM
AU  - Henie ME
AU  - Blatny JM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01367-16.

PMID- 26744369
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of a Novel Clinical Isolate, Mycobacterium abscessus Strain NOV0213.
PG  - e01407-15
AB  - Mycobacterium abscessus is a rapid-growing species of nontuberculous mycobacteria that is
      frequently associated with opportunistic infections in humans. We determined the complete
      genome sequence of the M. abscessus strain NOV0213, which was isolated from a patient with
      tuberculosis-like disease and with various antibiotic resistances.
AU  - Dymova MA
AU  - Alkhovik OI
AU  - Evdokimova LS
AU  - Cherednichenko AG
AU  - Petrenko TI
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01407-15.

PMID- 24376271
VI  - 42
DP  - 2014
TI  - Editorial: NAR Surveys the Past, Present and Future of Restriction Endonucleases.
PG  - 1-2
AB  - In this issue, Nucleic Acids Research presents five Survey and Summary articles that describe
      the historical development of studies on restriction endonucleases and summarize much of our
      current understanding of this diverse and complex group of enzymes. The first of these
      articles, entitled 'Highlights of the DNA cutters: a short history of the restriction
      enzymes' (1), describes seminal studies on bacteriophage host restriction, details subsequent
      work on type I and type III enzymes that established the restriction-modification (RM)
      paradigm and summarizes other landmark events that led to restriction enzymes becoming a main
      driving force in the development of modern biotechnology and molecular medicine. Other Survey
      and Summary articles in this issue describe three of the major types of RM systems as they are
      understood today (2-4). The different types of RM systems-of which there are currently four-
      vary in their cofactor dependence, in the spatial relationship of DNA binding and cleavage
      sites and in the way in which endonuclease and modification activities are physically and
      mechanistically coupled to one another. The last of the Survey and Summary articles in this
      issue discusses RM systems in the broader context of toxin-antitoxin genetic systems, which
      exist in great variety throughout the microbial world (5).
AU  - Dynan W
AU  - Fox K
AU  - Stoddard B
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2014 42: 1-2.

PMID- 9469833
VI  - 26
DP  - 1998
TI  - Novel post-replicative DNA modification in Streptomyces: analysis of the preferred modification site of plasmid pIJ101.
PG  - 1248-1253
AB  - Both Streptomyces lividans and Streptomyces avermitilis have the ability to site  specifically
      modify their DNA, rendering it susceptible to in vitro
      Tris-dependent double-strand cleavage. We have cloned a 160 bp fragment
      containing the preferred modification site of plasmid pIJ101 and, employing an in
      vitro primer extension assay, determined that the modifications occur at guanine
      residues on either strand separated by 3 bp. These guanines are located within a
      6 bp palindromic 'core' sequence. A cloned copy of a 35 bp region of the plasmid
      containing this core sequence was not recognized by the modifying activity in
      vivo. To further investigate the nature of the site specificity a set of deletion
      mutants of the 160 bp sequence were analysed. This revealed that a substantial
      portion of this sequence is essential for authentic modification. The essential
      region contains three 13 bp direct repeats, the central one containing the core
      sequence, while the left-hand and right-hand copies overlap two potential
      stem-loop structures. Deletion of either left- or right-hand repeat structures
      abolishes modification within the core sequence, although the left-hand deletion
      resulted in modification at a secondary site within the right-hand direct repeat.
      These data support a post-replicative mechanism of modification, underlined by
      the observation that the modifications are not detected in single-stranded
      plasmid replication intermediates.
AU  - Dyson P
AU  - Evans M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1998 26: 1248-1253.

PMID- 21569803
VI  - 86
DP  - 2011
TI  - DIY series of genetic cassettes useful in construction of versatile = vectors specific for Alphaproteobacteria.
PG  - 166-174
AB  - We have developed a DIY (Do It Yourself) series of genetic casset=
      tes, which facilitate construction of novel versatile vectors for
      Alphaproteobacteria. All the cassettes are based on defined genetic
      modules derived from three natural plasmids of Paracoccus aminophilus JCM
      7686. We have constructed over 50 DIY cassettes, which differ in structure
      and specific features. All of them are functional in eight strains
      representing three orders of Alphaproteobacteria: Rhodobacterales,
      Rhizobiales and Caulobacterales. Besides various replication and
      stabilization systems, many of the cassettes also contain selective
      markers appropriate for Alphaproteobacteria (40 cassettes) and genetic
      modules responsible for mobilization for conjugal transfer (24 cassettes).
      All the DIY cassettes are bordered by different types of polylinkers,
      which facilitate vector construction. Using these DIY cassettes, we have
      created a set of compatible Escherichia coli-Alphaproteobacteria
      mobilizable shuttle vectors (high or low copy number in E. coli), which
      will greatly assist the genetic manipulation of Alphaproteobacteria.
AU  - Dziewit L
AU  - Adamczuk M
AU  - Szuplewska M
AU  - Bartosik D
PT  - Journal Article
TA  - J. Microbiol. Methods
JT  - J. Microbiol. Methods
SO  - J. Microbiol. Methods 2011 86: 166-174.

PMID- 25426110
VI  - 5
DP  - 2014
TI  - Plasmids of psychrophilic and psychrotolerant bacteria and their role in adaptation to cold environments.
PG  - 596
AB  - Extremely cold environments are a challenge for all organisms. They are mostly inhabited by
      psychrophilic and psychrotolerant bacteria, which employ various strategies to cope with the
      cold. Such harsh environments are often highly vulnerable to the influence of external factors
      and may undergo frequent dynamic changes. The rapid adjustment of bacteria to changing
      environmental conditions is crucial for their survival. Such 'short-term' evolution is often
      enabled by plasmids-extrachromosomal replicons that represent major players in horizontal gene
      transfer. The genomic sequences of thousands of microorganisms, including those of many
      cold-active bacteria have been obtained over the last decade, but the collected data have yet
      to be thoroughly analyzed. This report describes the results of a meta-analysis of the NCBI
      sequence databases to identify and characterize plasmids of psychrophilic and psychrotolerant
      bacteria. We have performed in-depth analyses of 66 plasmids, almost half of which are cryptic
      replicons not exceeding 10 kb in size. Our analyses of the larger plasmids revealed the
      presence of numerous genes, which may increase the phenotypic flexibility of their host
      strains. These genes encode enzymes possibly involved in (i) protection against cold and
      ultraviolet radiation, (ii) scavenging of reactive oxygen species, (iii) metabolism of amino
      acids, carbohydrates, nucleotides and lipids, (iv) energy production and conversion, (v)
      utilization of toxic organic compounds (e.g., naphthalene), and (vi) resistance to heavy
      metals, metalloids and antibiotics. Some of the plasmids also contain type II
      restriction-modification systems, which are involved in both plasmid stabilization and
      protection against foreign DNA. Moreover, approx. 50% of the analyzed plasmids carry genetic
      modules responsible for conjugal transfer or mobilization for transfer, which may facilitate
      the spread of these replicons among various bacteria, including across species boundaries.
AU  - Dziewit L
AU  - Bartosik D
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2014 5: 596.

PMID- 23479249
VI  - 17
DP  - 2013
TI  - Plasmid diversity in arctic strains of Psychrobacter spp.
PG  - 433-444
AB  - Six strains of Psychrobacter spp. isolated from guano of little auks collected on Spitsbergen
      island (Arctic) carried nine plasmids that
      were fully sequenced. These replicons (ranging in size from 2917 to
      14924 bp) contained either repA (ColE2-type) or repB (iteron-type)
      replication systems of a relatively narrow host range, limited to
      Psychrobacter spp. All but one of the plasmids carried predicted
      mobilization for conjugal transfer systems, encoding relaxases of the
      MOBQ, MOBV or MOBP families. The plasmids also contained diverse
      additional genetic load, including a type II restriction-modification
      system and a gene encoding a putative subunit C of alkyl hydroperoxide
      reductase (AhpC)-an antioxidant enzyme and major scavenger of reactive
      oxygen species. Detailed comparative sequence analyses, extended to all
      plasmids identified so far in psychrophilic bacteria, distinguished
      groups of the most ubiquitous replicons, which play a key role in
      horizontal gene transfer in cold environments.
AU  - Dziewit L
AU  - Cegielski A
AU  - Romaniuk K
AU  - Uhrynowski W
AU  - Szych A
AU  - Niesiobedzki P
AU  - Zmuda-Baranowska MJ
AU  - Zdanowski MK
AU  - Bartosik D
PT  - Journal Article
TA  - Extremophiles
JT  - Extremophiles
SO  - Extremophiles 2013 17: 433-444.

PMID- 22092764
VI  - 324
DP  - 2011
TI  - Functional characterization of the type II PamI restriction-modification system derived from plasmid pAMI7 of Paracoccus aminophilus JCM 7686.
PG  - 56-63
AB  - Plasmid pAMI7 of the methylotrophic bacterium Paracoccus aminophilus JCM 7686
      (Alphaproteobacteria) encodes a functional type II
      restriction-modification (R-M) system designated PamI. Homologous
      systems were identified in the genomes of distinct taxonomic groups of
      Bacteria and Archaea, which provides evidence that horizontal gene
      transfer has contributed to the wide dissemination of R-M modules -
      even between domains. Analysis of the cleavage specificity of the R.
      PamI endonuclease revealed that this protein is an isoschizomer of
      restriction enzyme NcoI. Interestingly, bioinformatic analyses suggest
      that R. PamI and NcoI are accompanied by methyltransferases of
      different methylation specificities (C5-methylcytosine and
      N4-methylcytosine methyltransferases, respectively), which possibly
      exemplifies recombinational shuffling of genes coding for individual
      components of R-M systems. The PamI system can stabilize plasmid pAMI7
      in a bacterial population, most probably at the postsegregational
      level. Therefore, it functions in an analogous manner to
      plasmid-encoded toxin-antitoxin (TA) systems. Since the TA system of
      pAMI7 is nonfunctional, it is highly probable that this lack is
      compensated by the stabilizing activity of PamI. This indicates the
      crucial role of the analyzed R-M system in the stable maintenance of
      pAMI7, which is, to our knowledge, the first report of 'symbiosis'
      between a R-M system and a plasmid in the Alphaproteobacteria.
AU  - Dziewit L
AU  - Kuczkowska K
AU  - Adamczuk M
AU  - Radlinska M
AU  - Bartosik D
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2011 324: 56-63.

PMID- 25187538
VI  - 88
DP  - 2014
TI  - Molecular Characterization of a Novel Temperate Sinorhizobium Bacteriophage, Phi LM21, Encoding DNA Methyltransferase with CcrM-Like Specificity.
PG  - 13111-13124
AB  - Phi LM21 is a temperate phage isolated from Sinorhizobium sp. strain LM21
      (Alphaproteobacteria). Genomic analysis and electron microscopy suggested that Phi LM21 is a
      member of the family Siphoviridae. The phage has an isometric head and a long noncontractile
      tail. The genome of Phi LM21 has 50,827 bp of linear double-stranded DNA encoding 72 putative
      proteins, including proteins responsible for the assembly of the phage particles, DNA
      packaging, transcription, replication, and lysis. Virion proteins were characterized using
      mass spectrometry, leading to the identification of the major capsid and tail components, tape
      measure, and a putative portal protein. We have confirmed the activity of two gene products, a
      lytic enzyme (a putative chitinase) and a DNA methyltransferase, sharing sequence specificity
      with the cell cycle-regulating methyltransferase (CcrM) of the bacterial host. Interestingly,
      the genome of Sinorhizobium phage Phi LM21 shows very limited similarity to other known phage
      genome sequences and is thus considered unique.IMPORTANCEProphages are known to play an
      important role in the genomic diversification of bacteria via horizontal gene transfer. The
      influence of prophages on pathogenic bacteria is very well documented. However, our knowledge
      of the overall impact of prophages on the survival of their lysogenic, nonpathogenic bacterial
      hosts is still limited. In particular, information on prophages of the agronomically important
      Sinorhizobium species is scarce. In this study, we describe the isolation and molecular
      characterization of a novel temperate bacteriophage, Phi LM21, of Sinorhizobium sp. LM21.
      Since we have not found any similar sequences, we propose that this bacteriophage is a novel
      species. We conducted a functional analysis of selected proteins. We have demonstrated that
      the phage DNA methyltransferase has the same sequence specificity as the cell cycle-regulating
      methyltransferase CcrM of its host. We point out that this phenomenon of mimicking the host
      regulatory mechanisms by viruses is quite common in bacteriophages.
AU  - Dziewit L
AU  - Oscik K
AU  - Bartosik D
AU  - Radlinska M
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 2014 88: 13111-13124.

PMID- 22675588
VI  - 5
DP  - 2011
TI  - High quality draft genome sequence of Segniliparus rugosus CDC 945(T)= (ATCC BAA-974(T)).
PG  - 389-397
AB  - Segniliparus rugosus represents one of two species in the genus Segniliparus, the sole genus
      in the family Segniliparaceae. A unique and interesting feature of
      this family is the presence of extremely long carbon-chain length mycolic acids
      bound in the cell wall. S. rugosus is also a medically important species because
      it is an opportunistic pathogen associated with mammalian lung disease. This
      report represents the second species in the genus to have its genome sequenced.
      The 3,567,567 bp long genome with 3,516 protein-coding and 49 RNA genes is part
      of the NIH Roadmap for Medical Research, Human Microbiome Project.
AU  - Earl AM
AU  - Desjardins CA
AU  - Fitzgerald MG
AU  - Arachchi HM
AU  - Zeng Q
AU  - Mehta T
AU  - Griggs A
AU  - Birren BW
AU  - Toney NC
AU  - Carr J
AU  - Posey J
AU  - Butler WR
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 5: 389-397.

PMID- 22493193
VI  - 194
DP  - 2012
TI  - Whole-Genome Sequences of Bacillus subtilis and Close Relatives.
PG  - 2378-2379
AB  - We sequenced four strains of Bacillus subtilis and the type strains for two closely related
      species, Bacillus vallismortis and Bacillus mojavensis. We report
      the high-quality Sanger genome sequences of B. subtilis subspecies subtilis
      RO-NN-1 and AUSI98, B. subtilis subspecies spizizenii TU-B-10(T) and DV1-B-1,
      Bacillus mojavensis RO-H-1(T), and Bacillus vallismortis DV1-F-3(T).
AU  - Earl AM
AU  - Eppinger M
AU  - Fricke WF
AU  - Rosovitz MJ
AU  - Rasko DA
AU  - Daugherty S
AU  - Losick R
AU  - Kolter R
AU  - Ravel J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2378-2379.

PMID- 17516660
VI  - 46
DP  - 2007
TI  - Mutability of an HNH nuclease imidazole general base and exchange of a deprotonation mechanism.
PG  - 7215-7225
AB  - Several unique protein folds that catalyze the hydrolysis of phosphodiester bonds have arisen
      independently in nature, including the
      PD(D/E)XK superfamily (typified by type II restriction endonucleases
      and many recombination and repair enzymes) and the HNH superfamily
      (found in an equally wide array of enzymes, including bacterial
      colicins and homing endonucleases). Whereas the identity and position
      of catalytic residues within the PD(D/E)XK superfamily are highly
      variable, the active sites of HNH nucleases are much more strongly
      conserved. In this study, the ability of an HNH nuclease to tolerate a
      mutation of its most conserved catalytic residue (its histidine general
      base), and the mechanism of the most active enzyme variant, were
      characterized. Conversion of this residue into several altered
      chemistries, glutamine, lysine, or glutamate, resulted in measurable
      activity. The histidine to glutamine mutant displays the highest
      residual activity and a pH profile similar to that of the wild-type
      enzyme. This activity is dependent on the presence of a neighboring
      imidazole ring, which has taken over as a less efficient general base
      for the reaction. This result implies that mutational pathways to
      alternative HNH-derived catalytic sites do exist but are not as
      extensively or successfully diverged or reoptimized in nature as
      variants of the PD(D/E)XK nuclease superfamily. This is possibly due to
      multiple steric constraints placed on the compact HNH motif, which is
      simultaneously involved in protein folding, DNA binding, and catalysis,
      as well as the use of a planar, aromatic imidazole group as a general
      base.
AU  - Eastberg JH
AU  - Eklund J
AU  - Monnat R
AU  - Stoddard BL
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2007 46: 7215-7225.

PMID- 17947319
VI  - 35
DP  - 2007
TI  - Thermodynamics of DNA target site recognition by homing endonucleases.
PG  - 7209-7221
AB  - The thermodynamic profiles of target site recognition have been surveyed for homing
      endonucleases from various structural families. Similar to
      DNA-binding proteins that recognize shorter target sites, homing
      endonucleases display a narrow range of binding free energies and
      affinities, mediated by structural interactions that balance the magnitude
      of enthalpic and entropic forces. While the balance of DeltaH and TDeltaS
      are not strongly correlated with the overall extent of DNA bending,
      unfavorable DeltaH(binding) is associated with unstacking of individual
      base steps in the target site. The effects of deleterious basepair
      substitutions in the optimal target sites of two LAGLIDADG homing
      endonucleases, and the subsequent effect of redesigning one of those
      endonucleases to accommodate that DNA sequence change, were also measured.
      The substitution of base-specific hydrogen bonds in a wild-type
      endonuclease/DNA complex with hydrophobic van der Waals contacts in a
      redesigned complex reduced the ability to discriminate between sites, due
      to nonspecific DeltaS(binding).
AU  - Eastberg JH
AU  - Smith AM
AU  - Zhao L
AU  - Ashworth J
AU  - Shen BW
AU  - Stoddard BL
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2007 35: 7209-7221.

PMID- 24459277
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Paenibacillus polymyxa CR1, a Plant Growth-Promoting  Bacterium Isolated from the Corn Rhizosphere Exhibiting Potential for Biocontrol,  Biomass Degradation, and Biofuel Production.
PG  - e01218-13
AB  - Here we report the complete genome sequence of the bacterium Paenibacillus polymyxa CR1
      (accession no. CP006941), which consists of one circular chromosome
      of 6,024,666 bp with 5,283 coding sequences (CDS), 87 tRNAs, and 12 rRNA operons.
      Data presented will allow for further insights into the mechanisms underpinning
      agriculturally and industrially relevant processes.
AU  - Eastman AW
AU  - Weselowski B
AU  - Nathoo N
AU  - Yuan ZC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01218-13.

PMID- 11179656
VI  - 195
DP  - 2001
TI  - Cloning, sequence analysis and heterologous expression of the DNA adenine-(N-6) methyltransferase from the human pathogen Actinobacillus actinomycetemcomitans.
PG  - 223-229
AB  - We cloned and sequenced the DNA adenine-N-6 methyltransferase gene of the human pathogen
      Actinobacillus actinomycetemcomitans (M.AacDAM).
      Restriction digestion shows that the enzyme methylates adenine in the
      sequence GATC. Expression of the enzyme in a DAM(-) background shows in
      vivo activity. A PSI-BLAST search revealed that M.AacDAM is most
      related to M.HindIV. M.EcoDAM, M.StyDAM. and M.Small. The ClustalW
      alignment shows highly conserved regions in the enzyme characteristic
      for type a MTases. Phylogenetic tree analysis shows a cluster of
      enzymes recognizing the sequence GATC, within a branch of orphan MTases
      harboring M.AacDAM, The cloning and sequencing of this first
      methyltransferase gene described for A. actinomycetemcomitans open the
      path for studies on the potential regulatory impact of DNA methylation
      on gene regulation and virulence in this organism.
AU  - Eberhard J
AU  - Oza J
AU  - Reich NO
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2001 195: 223-229.

PMID- 22773653
VI  - 78
DP  - 2012
TI  - Characterization of a novel microcin that kills enterohemorrhagic E. coli O157:H7 and O26.
PG  - 6592-6599
AB  - A novel phenotype was recently identified whereby specific strains of Escherichia
      coli inhibit competing E. coli via a mechanism that was designated
      "proximity-dependent inhibition" (PDI). PDI-expressing E. coli (PDI(+)) is known
      to inhibit susceptible E. coli strains (PDI(-)), including several
      enterohemorrhagic (EHEC) and enterotoxigenic (ETEC) strains. In this study every
      strain from a genetically diverse panel of E. coli O157:H7 (n=25) and additional
      strains of E. coli serovar O26 were susceptible to the PDI phenotype. Live-dead
      staining was consistent with inhibition by killing of susceptible cells.
      Comparative genome analysis identified the genetic component of PDI, which is
      composed of a plasmid-borne (Incl1) operon encoding a putative microcin and
      associated genes for transport, immunity, and microcin activation. Transfer of
      the plasmid to a PDI(-) strain resulted in transfer of the phenotype and deletion
      of the genes within the operon resulted in loss of the inhibition phenotype.
      Deletion of chromosomally encoded tolC also resulted in loss of the inhibitory
      phenotype and this confirmed that the putative microcin is most likely secreted
      via a type I secretion pathway. Deletion of an unrelated plasmid gene did not
      affect the PDI phenotype. Quantitative RT-PCR demonstrated that microcin
      expression is correlated with logarithmic-phase growth. The ability to inhibit a
      diversity of E. coli strains indicates this microcin may influence gut community
      composition and could be useful for control of important enteric pathogens.
AU  - Eberhart L
AU  - Deringer JR
AU  - Brayton KA
AU  - Sawant A
AU  - Besser TE
AU  - Call DR
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2012 78: 6592-6599.

PMID- 27634997
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Bordetella pertussis Strain VA-190 Isolated from a Vaccinated 10-Year-Old Patient with Whooping Cough.
PG  - e00972-16
AB  - The number of cases of pertussis has increased in the United States despite vaccination. We
      present the genome of an isolate of Bordetella pertussis from a
      vaccinated patient from Virginia. The genome was sequenced by long-read
      methodology and compared to that of a clinical isolate used for laboratory
      studies, D420.
AU  - Eby JC
AU  - Turner L
AU  - Nguyen B
AU  - Kang J
AU  - Neville C
AU  - Temple L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00972-16.

PMID- 3011544
VI  - 14
DP  - 1986
TI  - Action of restriction endonucleases on phosphorothioate DNA.
PG  - 204-205
AB  - Phosphorothioate analogues of nucleotides possess a number of properties which
      make then interesting compounds for biochemists (Eckstein, 1983).  One of these
      is the often slow rate of enzyme-catalysed hydrolysis of these analogues in
      comparson with the natural compounds.  Thus it has been shown that
      phosphorothioate internucleotidic linkages in DNA are either not or only slowly
      hydrolysed by exonuclease III and the 5' - 3' exonuclease activity of
      polymerase I.  An early observation indicated that at least some restriction
      endonucleases might hydrolyse such groups more slowly than the unmodified
      linkages (Vosberg & Eckstein, 1982).  As restriction endonucleases have found
      wide application in the manipulation of DNA and as this observation might offer
      the possibility of blocking specific sites in DNA against hydrolysis by these
      enzymes, it was decided to initiate a more detailed investigation on the
      interaction of restriction endonucleases with phosphorothioate-containing
      oligonucleotides and DNA.
AU  - Eckstein F
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 1986 14: 204-205.

PMID- 3014979
VI  - 471
DP  - 1986
TI  - Interaction of DNA containing phosphorothioate groups with restriction enzymes.
PG  - 217-225
AB  - Phosphorothioate analogues of nucleotides have become very valuable tools in
      enzymology.  The interest in these compounds is based on a variety of
      properties that distinguish them from the naturally occurring nucleotides.
      These are the generally slow rate of enzymatic hydrolysis of phosphorothioates,
      the chirality of the generally slow rate of enzymatic hydrolysis of
      phosphorothioates, the chirality of the phosphorous when the phosphorothioate
      is linked to two nonidentical groups, and the affinity to metal ions.  The
      various applications of phosphorothioate analogues of nucleotides to the study
      of enzyme mechanisms have been reviewed extensively in recent years.  In this
      article the effect of incorporation of phosphorothioate groups into DNA will be
      discussed.
AU  - Eckstein F
PT  - Journal Article
TA  - Ann. NY Acad. Sci.
JT  - Ann. NY Acad. Sci.
SO  - Ann. NY Acad. Sci. 1986 471: 217-225.

PMID- 17948013
VI  - 3
DP  - 2007
TI  - Phosphorothioation of DNA in bacteria.
PG  - 689-690
AB  - A phosphorothioate modificaiton of DNA has been identified in bacteria.  This first observed
      alteration of the DNA phosphate backbone opens many questions about themechanism of sulfur
      incoporation and the function of this modification.
AU  - Eckstein F
PT  - Journal Article
TA  - Nat. Chem. Biol.
JT  - Nat. Chem. Biol.
SO  - Nat. Chem. Biol. 2007 3: 689-690.

PMID- Not carried by PubMed...
VI  - 8
DP  - 1987
TI  - Cleavage of phosphorothioate-containing oligonucleotides and DNA by restriction endonucleases.
PG  - 23-27
AB  - The oligonucleotide d(GGsAATTCC) containing the recognition sequence of the
      EcoRI restriction endonuclease with a phosphorothioate group at the site of
      cleavage was synthesized by two approaches both based on the polymer support
      phophoroamidite method.  Only the Rp-diastereomer was cleaved by EcoRI, at a
      rate approximately 20 times slower than the all-phosphate-containing octamer.
      To study the interaction of restriction endonucleases with phosphorothioate
      internucleotide linkages double stranded M13mp2 DNA was prepared in which the
      (+)strand contained only phosphate groups but the (-)strand contained phosphate
      groups as well as base specifically introduced phosphorothioate groups of the
      Rp-configuration.  This hybrid DNA was cleaved by several restriction enzymes.
      The results obtained allow the classification of these enzymes into three
      groups:  those which produce nicked DNA as an isolatable intermediate, those
      where the nicked DNA is the final product and a third where ony linearised DNA
      can be detected.  Particularly the second class of enzymes should be of
      interest for the manipulation of DNA.
AU  - Eckstein F
AU  - Connolly BA
AU  - Potter VVL
PT  - Journal Article
TA  - Abteil. Chem.
JT  - Abteil. Chem.
SO  - Abteil. Chem. 1987 8: 23-27.

PMID- 24459283
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Highly Adherent Pseudomonas aeruginosa Small-Colony Variant SCV20265.
PG  - e01232-13
AB  - The evolution of small-colony variants within Pseudomonas aeruginosa populations  chronically
      infecting the cystic fibrosis lung is one example of the emergence of
      adapted subpopulations. Here, we present the complete genome sequence of the
      autoaggregative and hyperpiliated P. aeruginosa small-colony variant SCV20265,
      which was isolated from a cystic fi brosis (CF) patient.
AU  - Eckweiler D
AU  - Bunk B
AU  - Sproer C
AU  - Overmann J
AU  - Haussler S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01232-13.

PMID- 2044951
VI  - 5
DP  - 1991
TI  - The phage T4 nrdB intron: a deletion mutant of a version found in the wild.
PG  - 1032-1041
AB  - Bacteriophage T4 possesses three self-splicing group I introns. Two of the three introns are
      mobile elements; the third, in the gene encoding a subunit of the phage nucleotide reductase
      (nrdB), is not mobile. Because intron mobility offers a reasonable explanation for the
      paradoxical occurrence of large intervening sequences in a space-efficient eubacterial phage,
      it is puzzling that the nrdB intron is not mobile like its compatriots. We have discovered a
      larger nrdB intron in a closely related phage, and we infer from comparative sequence data
      that the T4 intron is a deletion mutant derived from this larger intron. This larger nrdB
      intron encodes an open reading frame of 269 codons, which we have cloned and overexpressed.
      The overexpressed protein shows a dsDNA endonuclease activity for the intronless nrdB gene,
      typical of mobile introns. Thus, we believe that all three introns of T4 are or were mobile
      "infectious introns" and that they have entered into and been maintained in the phage
      population by virtue of this efficient mobility.
AU  - Eddy SR
AU  - Gold L
PT  - Journal Article
TA  - Genes Dev.
JT  - Genes Dev.
SO  - Genes Dev. 1991 5: 1032-1041.

PMID- 1311841
VI  - 89
DP  - 1992
TI  - Artificial mobile DNA element constructed from the EcoRI endonuclease gene.
PG  - 1544-1547
AB  - There exist several examples of mobile group I introns.  These introns appear
      to use a straightforward mechanism to achieve highly site-specific and
      efficient insertion into homologous intronless genes.  Because the only
      intron-specific function required by the prevailing model for the mechanism  of
      intron mobility is the introduction of a site-specific double-stranded break in
      the intronless recipient DNA molecule, we reasoned that it should in principle
      be possible to construct an artificially mobile element from the gene for the
      restriction enzyme EcoRI that is capable of site-specific insertion at rates
      near those of authentic mobile introns.  The generality of the mobility
      mechanism may enable high-efficiency targeted gene replacements or disruptions
      in a variety of organisms.
AU  - Eddy SR
AU  - Gold L
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1992 89: 1544-1547.

PMID- 
VI  - 31
DP  - 2013
TI  - Genome engineering nucleases derived from GIY-YIG homing endonucleases.
PG  - 64-65
AB  - Efficient targeted manipulation of complex genomes requires highly specific endonucleases to
      generate double-strand breaks at defined locations.  The predominantly engineered nucleases,
      zinc-finger nucleases and TAL effector nucleases use the catalytic domain of FokI as the
      nuclease portion.  This domain, however, functions as a dimer to nonspecifically cleave DNA
      meaning that ZFNs and TALENs must be designed in head-to-head pairs to target a desired
      sequence.  To overcome this limitation and expand the toolbox of genome editing reagents, we
      used the N-terminal catalytic domain and interdomain linker of the monomeric GIY-YIG homing
      endonuclease I-TevI to create I-TevI-zinc-fingers, and I-TevI-TAL effectors.  We also made
      I-TevI fusions to LAGLIDADGs homing endonucleases.  All the three fusions showed activity on
      model substates on par with ZFNs and TALENs in yeast-based recombination assays.  These
      proof-of-concept experiments demonstrate that the catalytic domain of GIY-YIG homing
      endonucleases can be targeted to relevant loci by fusing the domain to characterize
      DNA-binding platforms.  Recent efforts have focused on improving the Tev-TAL platform by (1)
      understanding the spacing requirements between the nuclease cleavage site and the DNA binding
      site, (2) probing the DNA binding requirements of the I-TevI linker domain, and (3)
      demonstrating activity in mammalian systems.
AU  - Edgell D
AU  - Kleinstiver B
AU  - Wolfs JM
AU  - Wang L
AU  - Kolaczyk T
AU  - McDowell B
AU  - Bogdanove A
PT  - Journal Article
TA  - J. Biomol. Struct. Dyn.
JT  - J. Biomol. Struct. Dyn.
SO  - J. Biomol. Struct. Dyn. 2013 31: 64-65.

PMID- 
VI  - 16
DP  - 2005
TI  - Free-standing homing endonucleases of T-even phage: Freeloaders or functionaries?
PG  - 147-160
AB  - The ability of group I and II introns, and of inteins, to promote their own mobility to
      cognate genes lacking the intron or intein is a property that is now well documented in the
      scientific literature.  This so-called homing of introns and inteins is mediated by homing
      endonucleases encoded within the genetic elements.  Other chapters within this book have
      detailed the different classes of homing endonucleases, how homing endonuclease specifically
      recognize their target sequences, and the mechanisms of DNA cleavage.  This chapter deals with
      the surprising observation that homing endonucleases are not always found encoded within
      introns or inteins, and are often found inserted between genes.  Such free-standing homing
      endonucleases are particularly abundant in the well-studied Escherichia coli bacteriophage T4.
      In phage T4, the endonucleases themselves are mobile genetic elements, promoting their spread
      to related T-even phage genomes that lack the endonuclease gene by a double-strand break
      repair pathway.  This process is remarkably similar to endonuclease-mediated intron homing,
      and has been termed intronless homing.  Free-standing endonucleases have been identified in
      most sequenced genomes, but it is unlikely that all practice intronless homing, as some have
      been co-opted by cellular genomes to function in pathways unrelated to endonuclease mobility.
      Here, I will focus on free-standing endonucleases of phage genomes, and highlight differences
      in DNA-binding and cleavage strategies of intron-encoded versus free-standing endonucleases as
      it relates to promoting mobility between genomes.
AU  - Edgell DR
PT  - Journal Article
TA  - Nucleic Acids Mol. Biol.
JT  - Nucleic Acids Mol. Biol.
SO  - Nucleic Acids Mol. Biol. 2005 16: 147-160.

PMID- 19211047
VI  - 19
DP  - 2009
TI  - Selfish DNA: Homing Endonucleases Find a Home.
PG  - R115-R117
AB  - Self-splicing group I introns come in two flavours - those with a homing endonuclease to
      promote mobility of the intron, and those without an endonuclease. How homing endonucleases
      and self-splicing introns associate to form a composite selfish genetic element is a question
      of long-standing interest. Recent work has revealed that a shared characteristic of both
      introns and endonucleases, the targeting of conserved sequences, may provide the impetus for
      the evolution of composite mobile genetic elements.
AU  - Edgell DR
PT  - Journal Article
TA  - Curr. Biol.
JT  - Curr. Biol.
SO  - Curr. Biol. 2009 19: R115-R117.

PMID- 10986228
VI  - 182
DP  - 2000
TI  - Barriers to intron promiscuity in bacteria.
PG  - 5281-5289
AB  - The first bacterial intron, a self-splicing group I intron, was found to interrupt the
      thymidylate synthase (td) gene of the Escherichia coli phage T4.  The second and third
      bacterial group I introns were found to interrupt the aerobic (nrdB) and anaerobic (nrdD
      [initially named sunY]) ribonucleotide reductases of phage T4, and another group I intron was
      soon discovered in the DNA polymerase gene of SPO1, a Bacillus phage.  From this (admittedly)
      small sampling of phage genomes, one might have naively expected that group I introns would be
      abundant in phage or bacterial genomes, especially since subsequent laboratory experiments
      demonstrated that group I introns could propagate themselves (by a process called homing)
      throughout populations of intron-minus alleles with near 100% efficiency.  That a similar
      homing phenomenon had also been previously demonstrated for a group I intron in the large rRNA
      gene of yeast mitochondrial gave additional support to the notion that group I introns should
      be able to spread efficiently throughout populations.  However, this expected outcome has
      never been realized in natural phage populations; some phage populations harbor many introns,
      while other related phage populations harbor many introns, while other related phage
      populations are strangely lacking in any introns whatsoever.  Why do group I introns have an
      unusual distribution in phage and bacterial genomes, and what potential barriers might exist
      to prevent their spread?
AU  - Edgell DR
AU  - Belfort M
AU  - Shub DA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2000 182: 5281-5289.

PMID- 15361856
VI  - 11
DP  - 2004
TI  - Intron-encoded homing endonuclease I-TevI also functions as a transcriptional autorepressor.
PG  - 936-944
AB  - Customary binding sites of intron-encoded homing endonucleases lie within cognate intronless
      alleles, at the so-called homing sites. Here,
      we describe a novel, high-affinity binding site for I-TevI
      endonuclease, encoded within the group I td intron of phage T4. This
      site is an operator that overlaps the T4 late promoter, which drives
      I-TevI expression from within the td intron. I-TevI binds the operator
      and homing sites with equal affinity, and functions as a
      transcriptional autorepressor. Distinct sequence and spacing
      requirements of the catalytic domain result in reduced cleavage
      activity on operator DNA. Crystallographic studies showed that the
      overall interactions of the DNA-binding domain with the operator and
      homing sites are similar, but have some different hydrogen-bonding
      contacts. We present a model in which the flexibility in protein-DNA
      interactions allows I-TevI to bind variant intronless alleles to
      promote intron mobility while facilitating its function in
      autorepression, and thereby persistence in its host.
AU  - Edgell DR
AU  - Derbyshire V
AU  - Van Roey P
AU  - LaBonne S
AU  - Stanger MJ
AU  - Li Z
AU  - Boyd TM
AU  - Shub DA
AU  - Belfort M
PT  - Journal Article
TA  - Nat. Struct. Mol. Biol.
JT  - Nat. Struct. Mol. Biol.
SO  - Nat. Struct. Mol. Biol. 2004 11: 936-944.

PMID- 8723339
VI  - 6
DP  - 1996
TI  - Selfish DNA: The best defense is a good offense.
PG  - 385-388
AB  - The recent discovery of novel biochemical activities of intron-encoded endonucleases
      emphasizes the selfish nature of mobile genetic elements.
AU  - Edgell DR
AU  - Fast NM
AU  - Doolittle WF
PT  - Journal Article
TA  - Curr. Biol.
JT  - Curr. Biol.
SO  - Curr. Biol. 1996 6: 385-388.

PMID- 21029434
VI  - 7
DP  - 2010
TI  - Mobile DNA elements in T4 and related phages.
PG  - 290
AB  - Mobile genetic elements are common inhabitants of virtually every genome where they can exert
      profound influences on genome structure and function in addition to promoting their own spread
      within and between genomes. Phage T4 and related phage have long served as a model system for
      understanding the molecular mechanisms by which a certain class of mobile DNA, homing
      endonucleases, promote their spread. Homing endonucleases are site-specific DNA endonucleases
      that initiate mobility by introducing double-strand breaks at defined positions in genomes
      lacking the endonuclease gene, stimulating repair and recombination pathways that mobilize the
      endonuclease coding region. In phage T4, homing endonucleases were first discovered as encoded
      within the self-splicing td, nrdB and nrdD introns of T4. Genomic data has revealed that
      homing endonucleases are extremely widespread in T-even-like phage, as evidenced by the
      astounding fact that similar to 11% of the T4 genome encodes homing endonuclease genes, with
      most of them located outside of self-splicing introns. Detailed studies of the mobile td
      intron and its encoded endonuclease, I-TevI, have laid the foundation for genetic, biochemical
      and structural aspects that regulate the mobility process, and more recently have provided
      insights into regulation of homing endonuclease function. Here, we summarize the current state
      of knowledge regarding T4-encoded homing endonucleases, with particular emphasis on the
      td/I-TevI model system. We also discuss recent progress in the biology of free-standing
      endonucleases, and present areas of future research for this fascinating class of mobile
      genetic elements.
AU  - Edgell DR
AU  - Gibb EA
AU  - Belfort M
PT  - Journal Article
TA  - Virol. J.
JT  - Virol. J.
SO  - Virol. J. 2010 7: 290.

PMID- 11416170
VI  - 98
DP  - 2001
TI  - Related homing endonucleases I-BmoI and I-TevI use different strategies to cleave homologous recognition sites.
PG  - 7898-7903
AB  - A typical homing endonuclease initiates mobility of its group I intron by recognizing DNA both
      upstream and downstream of the intron insertion
      site of intronless alleles, preventing the endonuclease from binding
      and cleaving its own intron-containing allele. Here, we describe a
      GIY-YIG family homing endonuclease. I-BmoI, that possesses an unusual
      recognition sequence, encompassing 1 base pair upstream but 38 base
      pairs downstream of the intron insertion site. I-BmoI binds
      intron-containing and intronless substrates with equal affinity but can
      nevertheless discriminate between the two for cleavage. I-BmoI is
      encoded by a group I intron that interrupts the thymidylate synthase
      CTS) gene (thyA) of Bacillus mojavensis s87-18. This intron resembles
      one inserted 21 nucleotides further downstream in a homologous TS gene
      ltd) of Escherichia coli phage T4. I-TevI, the T4 td intron-encoded
      GIY-YIG endonuclease, is very similar to I-BmoI, but each endonuclease
      gene is inserted within a different position of its respective intron.
      Remarkably, I-TevI and I-BmoI bind a homologous stretch of TS-encoding
      DNA and cleave their intronless substrates in very similar positions.
      Our results suggest that each endonuclease has independently evolved
      the ability to distinguish intron-containing from intronless alleles
      while maintaining the same conserved recognition sequence centered on
      DNA-encoding active site residues of TS.
AU  - Edgell DR
AU  - Shub DA
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2001 98: 7898-7903.

PMID- 15491609
VI  - 343
DP  - 2004
TI  - Coincidence of cleavage sites of intron endonuclease I-TevI and critical sequences of the host thymidylate synthase gene.
PG  - 1231-1241
AB  - To maximize spread of their host intron or intein, many homing endonucleases recognize
      nucleotides that code for important and
      conserved amino acid residues of the target gene. Here, we examine the
      cleavage requirements for I-TevI, which binds a stretch of thymidylate
      synthase (TS) DNA that codes for functionally critical residues in the
      TS active site. Using an in vitro selection scheme, we identified two
      base-pairs in the I-TevI cleavage site region as important for cleavage
      efficiency. These were confirmed by comparison of I-TevI cleavage
      efficiencies on mutant and on wild-type substrates. We also showed that
      nicking of the bottom strand by I-TevI is not affected by mutation of
      residues surrounding the bottom-strand cleavage site, unlike other
      homing endonucleases. One of these two base-pairs is universally
      conserved in all TS sequences, and is identical with a previously
      identified cleavage determinant of I-BmoI, a related GIY-YIG
      endonuclease that binds a homologous stretch of TS-encoding DNA. The
      other base-pair is conserved only in a subset of TS genes that includes
      the I-TevI, but not the I-BmoI, target sequence. Both the I-TevI and
      I-BmoI cleavage site requirements correspond to functionally critical
      residues involved in an extensive hydrogen bond network within the TS
      active site. Remarkably, these cleavage requirements correlate with TS
      phylogeny in bacteria, suggesting that each endonuclease has
      individually adapted to efficiently cleave distinct TS substrates.
AU  - Edgell DR
AU  - Stanger MJ
AU  - Belfort M
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2004 343: 1231-1241.

PMID- 12781137
VI  - 13
DP  - 2003
TI  - Importance of a single base pair for discrimination between intron-containing and intronless alleles by endonuclease I-Bmol.
PG  - 973-978
AB  - Homing endonucleases initiate mobility of their host group I introns by binding to and
      cleaving lengthy recognition sequences that are typically
      centered on the intron insertion site (IS) of intronless alleles. Because
      the intron interrupts the endonucleases' recognition sequence,
      intron-containing alleles are immune to cleavage by their own
      endonuclease. I-TevI and I-BmoI are related GIY-YIG endonucleases that
      bind a homologous stretch of thymidylate synthase (TS)-encoding DNA but
      use different strategies to distinguish intronless from intron-containing
      substrates. I-TevI discriminates between substrates at the level of DNA
      binding, as its recognition sequence is centered on the intron IS. I-BmoI,
      in contrast, possesses a very asymmetric recognition sequence with respect
      to the intron IS, binds both intron-containing and intronless TS-encoding
      substrates, but efficiently cleaves only intronless substrate. Here, we
      show that I-BmoI is extremely tolerant of multiple substitutions around
      its cleavage sites and has a low specific activity. However, a single G-C
      base pair, at position -2 of a 39-base pair recognition sequence, is a
      major determinant for cleavage efficiency and distinguishes intronless
      from intron-containing alleles. Strikingly, this G-C base pair is
      universally conserved in phylogenetically diverse TS-coding sequences;
      this finding suggests that I-BmoI has evolved exquisite cleavage
      requirements to maximize the potential to spread to variant intronless
      alleles, while minimizing cleavage at its own intron-containing allele.
AU  - Edgell DR
AU  - Stanger MJ
AU  - Belfort M
PT  - Journal Article
TA  - Curr. Biol.
JT  - Curr. Biol.
SO  - Curr. Biol. 2003 13: 973-978.

PMID- 4553678
VI  - 9
DP  - 1972
TI  - Specific endonuclease R fragments of bacteriophage PhiX174 deoxyribonucleic acid.
PG  - 574-582
AB  - The restriction enzyme from Hemophilus influenzae, endonuclease R, cleaves
      PhiX174 replicative-form deoxyribonucleic acid (DNA) into at least 13 specific
      limit fragments.  The molecular weights of 12 of the fragments have been
      estimated by gel electrophoresis and electron microscopy.  Using the genetic
      assay for small fragments of PhiX DNA, we have shown that we can salvage
      markers from the endonuclease R PhiX-RF fragments.
AU  - Edgell MH
AU  - Hutchison CA III
AU  - Sclair M
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1972 9: 574-582.

PMID- 26893419
VI  - 4
DP  - 2016
TI  - High-Quality Draft Genome Sequence of Low-pH-Active Veillonella parvula Strain SHI-1, Isolated from Human Saliva within an In Vitro Oral Biofilm Model.
PG  - e01684-15
AB  - We announce here a draft genome sequence of Veillonella parvula strain SHI-1, obtained from
      healthy human saliva, discovered to be active at low pH using
      metatranscriptomics within an in vitro oral biofilm model. The genome is composed
      of 7 contigs, for a total of 2,200,064 bp.
AU  - Edlund A
AU  - Liu Q
AU  - Watling M
AU  - To TT
AU  - Bumgarner RE
AU  - He X
AU  - Shi W
AU  - McLean JS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01684-15.

PMID- 1459965
VI  - 174
DP  - 1992
TI  - Presence of methylated adenine in GATC Sequences in chromosomal DNAs from Campylobacter species.
PG  - 8156-8157
AB  - We digested chromosomal DNAs from 12 Campylobacter strains (C. jejuni, 4 strains; C. coli, 2
      strains; C. fetus subsp. fetus, 2 strains; C. hyointestinalis, 2 strains; and C. upsaliensis,
      2 strains) and from 4 Helicobacter strains (H. pylori, 2 strains: and H. mustelae, 2 strains)
      with HindIII, SstI, BamHI, DpnI, MboI, and Sau3AI. Restriction fragments were then separated
      by electrophoresis in 1% agarose or 10% polyacrylamide gels. Only DNAs from three
      Campylobacter species (C. jejuni, C. coli, and C. upsaliensis) were digested with DpnI (an
      enzyme that recognizes only methylated adenine in GATC sequences). We used MboI and Sau3AI to
      confirm these findings.
AU  - Edmonds P
AU  - Hall BM
AU  - Edwards WR
AU  - Hartline KM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1992 174: 8156-8157.

PMID- 25197478
VI  - 9
DP  - 2014
TI  - Non-contiguous finished genome sequence and description of Corynebacterium jeddahense sp. nov.
PG  - 987-1002
AB  - Corynebacterium jeddahense sp. nov., strain JCB(T), is the type strain of Corynebacterium
      jeddahense sp. nov., a new species within the genus
      Corynebacterium. This strain, whose genome is described here, was isolated from
      fecal flora of a 24-year-old Saudi male suffering from morbid obesity.
      Corynebacterium jeddahense is a Gram-positive, facultative anaerobic,
      nonsporulating bacillus. Here, we describe the features of this bacterium,
      together with the complete genome sequencing and annotation, and compare it to
      other member of the genus Corynebacterium. The 2,472,125 bp-long genome (1
      chromosome but not plasmid) contains 2,359 protein-coding and 53 RNA genes,
      including 1 rRNA operon.
AU  - Edouard S
AU  - Bibi F
AU  - Dhamodharan R
AU  - Lagier JC
AU  - Azhar EI
AU  - Robert C
AU  - Caputo A
AU  - Yasir M
AU  - Jiman-Fatani AA
AU  - Alawi M
AU  - Fournier PE
AU  - Raoult D
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 987-1002.

PMID- 25197469
VI  - 9
DP  - 2014
TI  - Genome sequence and description of Nesterenkonia massiliensis sp. nov. strain NP1(T.).
PG  - 866-882
AB  - Nesterenkonia massiliensis sp. nov., strain NP1(T), is the type strain of Nesterenkonia
      massiliensis sp. nov., a new species within the genus
      Nesterenkonia. This strain, whose genome is described here, was isolated from the
      feces of a 32-year-old French woman suffering from AIDS and living in Marseille.
      Nesterenkonia massiliensis is a Gram-positive aerobic coccus. Here, we describe
      the features of this bacterium, together with the complete genome sequencing and
      annotation. The 2,726,371 bp long genome (one chromosome but no plasmid) contains
      2,663 protein-coding and 51 RNA genes, including 1 rRNA operon.
AU  - Edouard S
AU  - Sankar S
AU  - Dangui NP
AU  - Lagier JC
AU  - Michelle C
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 866-882.

PMID- 28450499
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Uncultured Upland Soil Cluster Gammaproteobacteria Gives Molecular Insights into High-Affinity Methanotrophy.
PG  - e00047-17
AB  - Aerated soils form the second largest sink for atmospheric CH4 A near-complete genome of
      uncultured upland soil cluster Gammaproteobacteria that oxidize CH4 at
      <2.5 ppmv was obtained from incubated Antarctic mineral cryosols. This first
      genome of high-affinity methanotrophs can help resolve the mysteries about their
      phylogenetic affiliation and metabolic potential.
AU  - Edwards CR
AU  - Onstott TC
AU  - Miller JM
AU  - Wiggins JB
AU  - Wang W
AU  - Lee CK
AU  - Cary SC
AU  - Pointing SB
AU  - Lau MCY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00047-17.

PMID- 10337482
VI  - 26
DP  - 1999
TI  - Increasing DNA transfer efficiency by temporary inactivation of host restriction.
PG  - 892-900
AB  - E. coli and Salmonella typhimurium are widely used bacterial hosts for genetic manipulation of
      DNA from prokaryotes and eukaryotes.  Introduction of foreign DNA by electroporation or
      transduction into E. coli and Salmonella is limited by host restriction of incoming DNA by the
      recipient cells.  Here, we describe a simple method that temporarily inactivates host
      restriction, allowing high-frequency DNA transfer.  This technique might be readily applied to
      a wide range of bacteria to increase DNA transfer between strains and species.
AU  - Edwards RA
AU  - Helm RA
AU  - Maloy SR
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 1999 26: 892-900.

PMID- 25657265
VI  - 3
DP  - 2015
TI  - Genome Sequences of Two Pandoraea pnomenusa Isolates Recovered 11 Months Apart from a Cystic Fibrosis Patient.
PG  - e01389-14
AB  - Pandoraea is an emerging respiratory pathogen capable of causing chronic lung infections in
      people with cystic fibrosis (CF), but the clinical significance of
      this infection is ambiguous. We have sequenced and annotated the genomes of two
      multidrug-resistant Pandoraea pnomenusa isolates recovered 11 months apart from
      the same CF patient.
AU  - Ee R
AU  - Ambrose M
AU  - Lazenby J
AU  - Williams P
AU  - Chan KG
AU  - Roddam L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01389-14.

PMID- 27630623
VI  - 7
DP  - 2016
TI  - Novel methyltransferase recognition motif identified in Chania multitudinisentens RB-25T gen. nov., sp. nov.
PG  - 1362
AB  - DNA methylation, defined by the addition of a methyl group to adenine or cytosine bases in DNA
      catalyzed by DNA methyltransferases, is one of the most studied post-replicative DNA
      modification mechanism in bacteria.  The three forms of nucleotide methylation identified to
      date are: N6-methyladenine (m6A), N4-methylcytosine (m4C), and 5-methylcyosine (m5C).
AU  - Ee R
AU  - Lim Y-L
AU  - Yin W-F
AU  - See-Too W-S
AU  - Roberts RJ
AU  - Chan K-G
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2016 7: 1362.

PMID- 24699956
VI  - 2
DP  - 2014
TI  - De Novo Assembly of the Quorum-Sensing Pandoraea sp. Strain RB-44 Complete Genome Sequence Using PacBio Single-Molecule Real-Time Sequencing Technology.
PG  - e00245-14
AB  - We report the first complete genome sequence of Pandoraea sp. strain RB-44, which was found to
      possess quorum-sensing properties. To the best of our knowledge, this is the first
      documentation of both a complete genome sequence and quorum-sensing properties of a Pandoraea
      species.
AU  - Ee R
AU  - Lim YL
AU  - Yin WF
AU  - Chan KG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00245-14.

PMID- 25883299
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Enterobacter aerogenes, a DDE-Degrading and Plant Growth-Promoting Strain Isolated from Cucurbita pepo.
PG  - e00317-15
AB  - We report here the draft genome of Enterobacter aerogenes, a Gram-negative bacterium of the
      Enterobacteriaceae isolated from Cucurbita pepo root tissue.
      This bacterium shows 2,2-bis(p-chlorophenyl)-1,1-dichloroethylene (DDE)-degrading
      potential and plant growth-promoting capacity. An analysis of its 4.5-Mb draft
      genome will enhance the understanding of DDE degradation pathways and
      phytoremediation applications for DDE-contaminated soils.
AU  - Eevers N
AU  - Van Hamme JD
AU  - Bottos EM
AU  - Weyens N
AU  - Vangronsveld J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00317-15.

PMID- 25977415
VI  - 3
DP  - 2015
TI  - Sphingomonas taxi, Isolated from Cucurbita pepo, Proves to Be a DDE-Degrading and Plant Growth-Promoting Strain.
PG  - e00489-15
AB  - The draft genome of Sphingomonas taxi, a strain of the Sphingomonadaceae isolated from
      Cucurbita pepo root tissue, is presented. This Gram-negative bacterium shows
      2,2-bis(p-chlorophenyl)-1,1-dichloroethylene (DDE)-degrading potential and plant
      growth-promoting capacities. An analysis of its 3.9-Mb draft genome will enhance
      the understanding of DDE-degradation pathways and phytoremediation applications
      for DDE-contaminated soils.
AU  - Eevers N
AU  - Van Hamme JD
AU  - Bottos EM
AU  - Weyens N
AU  - Vangronsveld J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00489-15.

PMID- 25977414
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Methylobacterium radiotolerans, a DDE-Degrading and Plant Growth-Promoting Strain Isolated from Cucurbita pepo.
PG  - e00488-15
AB  - We announce the draft genome of Methylobacterium radiotolerans, a Gram-negative bacterium
      isolated from Cucurbita pepo roots. This strain shows
      2,2-bis(p-chlorophenyl)-1,1-dichloroethylene (DDE)-degrading potential and plant
      growth-promoting capacities. Analyses of its 6.8-Mb genome will improve our
      understanding of DDE-degradation pathways and aid in the deployment of
      phytoremediation technologies to remediate DDE-contaminated soils.
AU  - Eevers N
AU  - Van Hamme JD
AU  - Bottos EM
AU  - Weyens N
AU  - Vangronsveld J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00488-15.

PMID- 28450511
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Bordetella pertussis Pelita III, the Production Strain for an Indonesian Whole-Cell Pertussis Vaccine.
PG  - e00235-17
AB  - PT Bio Farma, the sole World Health Organization-approved Indonesian vaccine producer,
      manufactures a whole-cell whooping cough vaccine (wP) that, as part of
      a pentavalent diphtheria-tetanus-pertussis/hepatitis B/Haemophilus influenzae b
      (DTP/HB/Hib) vaccine, is used in Indonesia and many other countries. We report
      here the whole-genome sequence for Bordetella pertussis Pelita III, PT Bio
      Farma's wP production strain.
AU  - Efendi YS
AU  - Susanti D
AU  - Tritama E
AU  - Pasier ML
AU  - Niwan PGN
AU  - Raharso S
AU  - Iskandar AP
AU  - Giri-Rachman EA
AU  - Mukhopadhyay B
AU  - Purwantini E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00235-17.

PMID- 26472833
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Pathogenic Bacterium Vibrio vulnificus V252 Biotype  1, Isolated in Israel.
PG  - e01182-15
AB  - We report the genome sequence of the pathogenic Vibrio vulnificus biotype 1 clade B, which is
      suggested to have a common ancestor with biotype 3. This draft genome of the clinical strain
      V252, isolated in Israel, represents the clonal clade B group that contains both clinical and
      environmental strains.
AU  - Efimov V
AU  - Danin-Poleg Y
AU  - Green SJ
AU  - Elgavish S
AU  - Kashi Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01182-15.

PMID- 2976881
VI  - 214
DP  - 1988
TI  - Alleviation of type I restriction in adenine methylase (dam) mutants of Escherichia coli.
PG  - 313-316
AB  - The host-controlled EcoKI-restriction of unmodified phage lambda.O is alleviated in dam
      mutants of Escherichia coli by 100- to 300-fold. In addition, the EcoKI modification activity
      is substantially decreased in dam- strains. We show that type I restriction (EcoBI, EcoDI and
      EcoKI) is detectably alleviated in dam mutants. However, no relief of EcoRI restriction (Type
      II) occurs in dam- strains and only a slight effect of dam mutation on EcoPI restriction (Type
      III) is observed. We interpret the alleviation of the type I restriction in dam- strains to be
      a consequence of induction of the function which interferes with type I restriction systems.
AU  - Efimova EP
AU  - Delver EP
AU  - Belogurov AA
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1988 214: 313-316.

PMID- 2976882
VI  - 214
DP  - 1988
TI  - 2-aminopurine and 5-bromouracil induce alleviation of type I restriction in Escherichia coli:  Mismatches function as inducing signals?
PG  - 317-320
AB  - The EcoKI restriction of unmodified phage lambda is 1000-fold alleviated in Escherichia coli
      grown in the presence of base analogs 2-aminopurine (2AP) and 5-bromouracil (5BU). 2AP
      treatment of bacteria affects specifically the type I restriction systems (EcoAI, EcoBI, EcoDI
      and EcoKI) and does not influence type II (EcoRI) and type III (EcoP1) restriction.
      2AP-induced alleviation of restriction occurs in bacteria which are deficient in the SOS
      response (recA and lexA) and mismatch repair (mutH, mutL and mutS) and can be distinguished
      from the alleviation of restriction observed in dam-strains. We suggest that mismatches
      induced by 2AP and 5BU may function as an inducing signal for the alleviation of restriction
      observed in the presence of base analogs.
AU  - Efimova EP
AU  - Delver EP
AU  - Belogurov AA
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1988 214: 317-320.

PMID- 29074660
VI  - 5
DP  - 2017
TI  - Genome Sequence of Geobacillus stearothermophilus DSM 458, an Antimicrobial-Producing Thermophilic Bacterium, Isolated from a Sugar Beet  Factory.
PG  - e01172-17
AB  - This paper reports the full genome sequence of the antimicrobial-producing bacterium
      Geobacillus stearothermophilus DSM 458, isolated in a sugar beet
      factory in Austria. In silico analysis reveals the presence of a number of novel
      bacteriocin biosynthetic genes.
AU  - Egan K
AU  - Kelleher P
AU  - Field D
AU  - Rea MC
AU  - Ross RP
AU  - Cotter PD
AU  - Hill C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01172-17.

PMID- 25197483
VI  - 9
DP  - 2014
TI  - Complete genome sequence of the Radiation-Resistant bacterium Rubrobacter radiotolerans RSPS-4.
PG  - 1062-1075
AB  - Rubrobacter radiotolerans strain RSPS-4 is a slightly thermophilic member of the  phylum
      'Actinobacteria' isolated from a hot spring in Sao Pedro do Sul, Portugal.
      This aerobic and halotolerant bacterium is also extremely resistant to gamma and
      UV radiation, which are the main reasons for the interest in sequencing its
      genome. Here, we present the complete genome sequence of strain RSPS-4 as well as
      its assembly and annotation. We also compare the gene sequence of this organism
      with that of the type strain of the species R. radiotolerans isolated from a hot
      spring in Japan. The genome of strain RSPS-4 comprises one circular chromosome of
      2,875,491 bp with a G+C content of 66.91%, and 3 circular plasmids of 190,889 bp,
      149,806 bp and 51,047 bp, harboring 3,214 predicted protein coding genes, 46 tRNA
      genes and a single rRNA operon.
AU  - Egas C
AU  - Barroso C
AU  - Froufe HJ
AU  - Pacheco J
AU  - Albuquerque L
AU  - da Costa MS
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 1062-1075.

PMID- 27795247
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Enterobacter ludwigii NCR3, a Heavy Metal-Resistant Rhizobacterium.
PG  - e01076-16
AB  - We report here the draft genome of Enterobacter ludwigii NCR3, a Gram-negative bacterium
      isolated from the Carpobrotus rossii (Haw.) Schwantes rhizosphere. The
      analysis of the ~4.8-Mb draft genome shows that this strain harbors several genes
      associated with heavy metal resistance and plant growth-promoting activity,
      suggesting its potential application in microbe-assisted phytoremediation.
AU  - Egidi E
AU  - Wood JL
AU  - Aracic S
AU  - Kannan R
AU  - McDonald L
AU  - Bell CA
AU  - Fox EM
AU  - Liu W
AU  - Franks AE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01076-16.

PMID- 28596412
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Leifsonia sp. Strain NCR5, a Rhizobacterium Isolated from Cadmium-Contaminated Soil.
PG  - e00520-17
AB  - We report here the draft genome sequence of Leifsonia sp. strain NCR5, a Gram-positive
      actinomycete isolated from Carpobrotus rossii (Haw.) Schwantes
      rhizosphere. The de novo genome of Leifsonia sp. strain NCR5 was assembled with
      69 scaffolds and a G+C content of 69%, was 4.2 Mb in length, and contained 3,952
      coding sequences.
AU  - Egidi E
AU  - Wood JL
AU  - Fox EM
AU  - Liu W
AU  - Franks AE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00520-17.

PMID- 27795276
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Rhodococcus erythropolis NSX2, an Actinobacterium Isolated from a Cadmium-Contaminated Environment.
PG  - e01147-16
AB  - Rhodococcus erythropolis NSX2 is a rhizobacterium isolated from a heavy metal-contaminated
      environment. The 6.2-Mb annotated genome sequence shows that
      this strain harbors genes associated with heavy-metal resistance and xenobiotics
      degradation.
AU  - Egidi E
AU  - Wood JL
AU  - Fox EM
AU  - Liu W
AU  - Franks AE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01147-16.

PMID- 27688340
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Bacillus cereus LCR12, a Plant Growth-Promoting Rhizobacterium Isolated from a Heavy Metal-Contaminated Environment.
PG  - e01041-16
AB  - Bacillus cereus LCR12 is a plant growth-promoting rhizobacterium, isolated from a heavy
      metal-contaminated environment. The 6.01-Mb annotated genome sequence
      provides the genetic basis for revealing its potential application to remediate
      contaminated soils in association with plants.
AU  - Egidi E
AU  - Wood JL
AU  - Mathews E
AU  - Fox E
AU  - Liu W
AU  - Franks AE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01041-16.

PMID- 25635012
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Geobacter sp. Strain OR-1, an Arsenate-Respiring Bacterium Isolated from Japanese Paddy Soil.
PG  - e01478-14
AB  - Here, we report a draft genome sequence of Geobacter sp. strain OR-1, an arsenate-respiring
      bacterium isolated from Japanese paddy soil. It contained two
      distinct arsenic islands, one including genes for a respiratory arsenate
      reductase (Arr) as well as for arsenic resistance (arsD-arsA-acr3-arsR-arrA-arrB)
      and the second containing only genes for arsenic resistance.
AU  - Ehara A
AU  - Suzuki H
AU  - Amachi S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01478-14.

PMID- 24994802
VI  - 2
DP  - 2014
TI  - Draft genome sequence of strain q-1, an iodide-oxidizing alphaproteobacterium isolated from natural gas brine water.
PG  - e00659-14
AB  - Here we report the draft genome sequence of strain Q-1, an iodide (I(-))-oxidizing
      heterotrophic bacterium in the class Alphaproteobacteria
      isolated from natural gas brine water. The genome sequence contained a
      multicopper oxidase gene probably responsible for iodide oxidation. A
      photosynthetic gene cluster was found but genes for carbon-fixation were absent.
AU  - Ehara A
AU  - Suzuki H
AU  - Kanesaki Y
AU  - Yoshikawa H
AU  - Amachi S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00659-14.

PMID- 2987217
VI  - 260
DP  - 1985
TI  - Linear diffusion of restriction endonucleases on DNA.
PG  - 6160-6166
AB  - We have investigated the dependence of the rate of cleavage of DNA by EcoRI,
      HindIII, and BamHI on the chain length of the substrate.  In order to keep the
      influence of flanking sequences and of nonspecific binding identical for all
      substrates we have carried out all experiments with the same plasmid DNA which
      had been digested previously with a variety of different restriction enzymes to
      give a set of substrates of different lengths.  Our results show that depending
      on the buffer conditions long substrates are cleaved faster than small ones.
      We interpret these findings to mean that under certain conditions a linear
      diffusion of the enzymes on the DNA is involved in localizing the recognition
      sites.  For EcoRI the mean diffusion length is approximately 1000 base pairs at
      1 mM MgCl2 which can be shown by diffusion theory to correspond to a linear
      diffusion coefficient of 5.10-10 cm2 s-1.  At 10 mM MgCl2 the linear diffusion
      of EcoRI is negligible and does not lead to a significant enhancement of the
      rate of site localization.  In the presence of nonsaturating amounts of one of
      the prokaryotic histone-like protein Hu (NS 2) small and large DNa substrate
      are cleaved with identical rate by EcoRI indicating that other proteins bound
      to the DNA constitute a barrier across wich linear diffusion cannot take place.
      We conclude that linear diffusion, albeit detectable under certain conditions
      in vitro, probably is of little importance for the process of site localization
      in vivo.
AU  - Ehbrecht H-J
AU  - Pingoud A
AU  - Urbanke C
AU  - Maass G
AU  - Gualerzi C
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1985 260: 6160-6166.

PMID- 1138935
VI  - 395
DP  - 1975
TI  - Unusual properties of the DNA from Xanthomonas phage XP-12 in which 5-methylcytosine completely replaces cytosine.
PG  - 109-119
AB  - Xanthomonas phage XP-12 contains 5-methylcytosine completely replacing
      cytosine.  This substitution confers several unusual properties upon XP-12 DNA.
      The buoyant density of XP-12 DNA in CsCl gradients is 1.710 g/cm3, 0.016 g/cm3
      lower than that expected for a normal DNA with the same percentage of adenine
      plus thymine.  The melting temperature for XP-12 DNA in 0.012 M Na+ is the
      highest reported for any naturally occurring DNA, 83.2C, 6.1C higher than that
      of normal DNAs with the same percentage of adenine plus thymine.  Unlike the
      minor amounts of 5-methylcytosine found in most plant and animal DNAs, the
      5-methylcytosine residues of XP-12 derive their methyl group from the 3-carbon
      of serine instead of from the thiomethyl carbon of methionine.
AU  - Ehrlich M
AU  - Ehrlich K
AU  - Mayo JA
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1975 395: 109-119.

PMID- 4000939
VI  - 13
DP  - 1985
TI  - DNA methylation in thermophilic bacteria: N4-methylcytosine, 5-methylcytosine, and N6-methyladenine.
PG  - 1399-1412
AB  - While determining the minor and major base composition of the DNA from 17 types of
      thermophilic bacteria by high performance liquid chromatography (HPLC) of enzymatic digests,
      we have discovered a novel base, N4-methylcytosine (m4C). Its structure was proven by
      comparison of the DNA-derived nucleoside to the analogous authentic compound by HPLC, UV
      spectroscopy, and mass spectroscopy. Eight of the bacterial DNAs contained m4C. Only two
      contained the common minor base, 5-methylcytosine (m5C), and neither of these was from an
      extreme thermophile. The other prevalent modified base of bacterial DNA, N6-methyladenine
      (m6A), was found in nine of the DNAs. Restriction analysis revealed that four of the DNAs had
      dam-type (Gm6ATC) methylation patterns. Due to the propensity of m5C residues to be deaminated
      by heat to thymine residues and to inefficient repair of the resulting mismatched base pairs,
      thermophiles with optimal growth temperatures of >60C generally may avoid having m5C in their
      genomes. Instead, some of them have deamination-resistant m4C residues.
AU  - Ehrlich M
AU  - Gama-Sosa MA
AU  - Carreira LH
AU  - Ljungdahl LG
AU  - Kuo KC
AU  - Gehrke CW
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1985 13: 1399-1412.

PMID- 3527293
VI  - 6
DP  - 1986
TI  - DNA cytosine methylation and heat-induced deamination.
PG  - 387-393
AB  - The heat-induced conversion of 5-methylcytosine (m5C) residues to thymine residues and of
      cytosine to uracil residues in single-stranded DNA was studied.
      The calculated rates for deamination at 37 degrees C and pH 7.4 were
      approximately 9.5 X 10(-10) and 2.1 X 10(-10) sec-1, respectively.
      N4-Methyldeoxycytidine, which is in the DNA of certain thermophilic bacteria, was
      more heat-resistant than was deoxycytidine and much more than was
      5-methyldeoxycytidine. Thermophilic bacteria which contain N4-methylcytosine
      rather than m5C in their genomes may thereby largely avoid heat-induced mutation
      due to deamination, which is incurred by the many organisms that contain m5C in
      their DNA.
AU  - Ehrlich M
AU  - Norris KF
AU  - Wang RY
AU  - Kuo KC
AU  - Gehrke CW
PT  - Journal Article
TA  - Biosci. Rep.
JT  - Biosci. Rep.
SO  - Biosci. Rep. 1986 6: 387-393.

PMID- 6262918
VI  - 212
DP  - 1981
TI  - 5-Methylcytosine in eukaryotic DNA.
PG  - 1350-1357
AB  - A small portion of the cytosine residues in the DNA of higher eukaryotes as
      well as in that of many lower eukaryotes is methylated.  The resulting
      5-methylcytosine residues occur in specific sequences in the DNA, usually
      adjacent to guanine residues on the 3' side.  This methylation of eukaryotic
      DNA has been proposed to function in ways, including control of transcription,
      maintenance of chromosome structure, repair of DNA, establishment of preferred
      sites for mutation, oncogenic transformation, and, in certain systems,
      protection of DNA against enzymatic degradation.
AU  - Ehrlich M
AU  - Wang RY-H
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1981 212: 1350-1357.

PMID- 3029036
VI  - 169
DP  - 1987
TI  - N4-Methylcytosine as a minor base in bacterial DNA.
PG  - 939-943
AB  - The DNA base composition, including the minor base content, of 26 strains of
      bacteria was determined.  The studied bacteria are sources of widely used
      restriction endonucleases.  Approximately 35% of the bacterial DNAs contained
      N4-methylcytosine, about 60% contained 5-methylcytosine, and about 90% had
      N6-methyladenine.
AU  - Ehrlich M
AU  - Wilson GG
AU  - Kenneth CK
AU  - Gehrke CW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1987 169: 939-943.

PMID- 27540061
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Aeromonas sp. Strain EERV15.
PG  - e00811-16
AB  - We report here the draft genome sequence of Aeromonas sp. strain EERV15 isolated  from sand
      filter. The organism most closely related to Aeromonas sp. EERV15 is
      Aeromonas veronii B565, with an average 83% amino acid sequence similarity of
      putatively encoded protein open reading frames.
AU  - Ehsani E
AU  - Barrantes I
AU  - Vandermaesen J
AU  - Geffers R
AU  - Jarek M
AU  - Boon N
AU  - Springael D
AU  - Pieper DH
AU  - Vilchez-Vargas R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00811-16.

PMID- 25999565
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Rhodococcus sp. Strain 311R.
PG  - e00378-15
AB  - Here, we report the draft genome sequence of Rhodococcus sp. strain 311R, which was isolated
      from a site contaminated with alkanes and aromatic compounds. Strain
      311R shares 90% of the genome of Rhodococcus erythropolis SK121, which is the
      closest related bacteria.
AU  - Ehsani E
AU  - Jauregui R
AU  - Geffers R
AU  - Jareck M
AU  - Boon N
AU  - Pieper DH
AU  - Vilchez-Vargas R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00378-15.

PMID- 26586902
VI  - 3
DP  - 2015
TI  - First Draft Genome Sequence of the Acidovorax caeni sp. nov. Type Strain R-24608  (DSM 19327).
PG  - e01378-15
AB  - We report the draft genome sequence of the Acidovorax caeni type strain R-24608 that was
      isolated from activated sludge of an aerobic-anaerobic wastewater
      treatment plant. The closest strain to Acidovorax caeni strain R-24608 is
      Acidovorax sp. strain MR-S7 with a 55.4% (amino-acid sequence) open reading
      frames (ORFs) average similarity.
AU  - Ehsani E
AU  - Jauregui R
AU  - Geffers R
AU  - Jarek M
AU  - Boon N
AU  - Pieper DH
AU  - Vilchez-Vargas R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01378-15.

PMID- 29051258
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Typhimurium  Q1.
PG  - e01151-17
AB  - Here, we report the draft genome sequence of Salmonella enterica subsp. enterica  serovar
      Typhimurium strain Q1. The draft genome contains 4,793,493 bp in 149
      contigs.
AU  - Eichhorn I
AU  - Tedin K
AU  - Fulde M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01151-17.

PMID- 28935736
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Zoonotic Streptococcus canis Isolate G361.
PG  - e00967-17
AB  - Here, we report the draft genome sequence of an SCM-positive Streptococcus canis  strain,
      G361, isolated from a vaginal swab of a 40-year-old woman. The draft
      genome comprises 2,045,931 bp in 62 contigs.
AU  - Eichhorn I
AU  - van der Linden M
AU  - Jarek M
AU  - Fulde M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00967-17.

PMID- 9889119
VI  - 9
DP  - 1999
TI  - Mobile introns: Retrohoming by complete reverse splicing.
PG  - R11-R14
AB  - A mobile bacterial group II intron can integrate into DNA by the reverse splicing into a
      target site of its RNA transcript, which then acts as a template for DNA synthesis by an
      encoded reverse transcriptase.  Mobility does not require homologous recombination, which has
      important practical and evolutionary implications.
AU  - Eickbush TH
PT  - Journal Article
TA  - Curr. Biol.
JT  - Curr. Biol.
SO  - Curr. Biol. 1999 9: R11-R14.

PMID- 23723408
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Mannheimia haemolytica Strain 42548 from a Case of Bovine Respiratory Disease.
PG  - e00318-13
AB  - Mannheimia haemolytica is the major bacterial component in the bovine respiratory disease
      complex, which accounts for considerable economic losses to the cattle
      industry worldwide. The complete genome sequence of M. haemolytica strain 42548
      was determined. It has a size of 2.73 Mb and contains 2,888 genes, including
      several antibiotic resistance genes.
AU  - Eidam C
AU  - Poehlein A
AU  - Brenner MG
AU  - Kadlec K
AU  - Liesegang H
AU  - Brzuszkiewicz E
AU  - Daniel R
AU  - Sweeney MT
AU  - Murray RW
AU  - Watts JL
AU  - Schwarz S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00318-13.

PMID- 4911846
VI  - 2
DP  - 1968
TI  - Host-controlled restriction of T-even bacteriophages:  relation of four bacterial deoxyribonucleases to restriction.
PG  - 320-326
AB  - Escherichia coli strains B and K-12, which restrict growth of nonglucosylated
      T-even phage (T*phage), and nonrestricting strains (Shigella sonnei and mutants
      of E. coli B) were tested for levels of endonuclease I and exonucleases I,II,
      and III, by means of in vitro assays.  Cell-free extracts freed from
      deoxyribonucleic acid (DNA) were examined with three substrates: E. coli DNA,
      T*2 DNA, and T2 DNA.  Both restricting and nonrestricting strains had
      comparable levels of the four nuclease activities and had similar patterns of
      preference for the three substrates.  In addition, mutants of E. coli B and
      K-12 that lack endonuclease I were as effective as their respective wild types
      in restricting T* phage.
AU  - Eigner J
AU  - Block S
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1968 2: 320-326.

PMID- 22092679
VI  - 323
DP  - 2011
TI  - Adherence and motility characteristics of clinical Acinetobacter baumannii isolates.
PG  - 44-51
AB  - Acinetobacter baumannii continues to be a major health problem especially in
      hospital settings. Herein, features that may play a role in persistence and
      disease potential were investigated in a collection of clinical A. baumannii
      strains from Australia. Twitching motility was found to be a common trait in A.
      baumannii international clone I strains and in abundant biofilm formers, whereas
      swarming motility was only observed in isolates not classified within the
      international clone lineages. Bioinformatic analysis of the type IV fimbriae
      revealed a correlation between PilA sequence homology and motility. A high level
      of variability in adherence to both abiotic surfaces and epithelial cells was
      found. We report for the first time the motility characteristics of a large
      number of A. baumannii isolates and present a direct comparison of A. baumannii
      binding to nasopharyngeal and lung epithelial cells.
AU  - Eijkelkamp BA
AU  - Stroeher UH
AU  - Hassan KA
AU  - Papadimitrious MS
AU  - Paulsen IT
AU  - Brown MH
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2011 323: 44-51.

PMID- 22326849
VI  - 68
DP  - 2012
TI  - The complete genome sequences of four new IncN plasmids from wastewater treatment plant effluent provide new insights into IncN plasmid diversity and evolution.
PG  - 13-24
AB  - The dissemination of antibiotic resistance genes among bacteria often occurs by means of
      plasmids. Wastewater treatment plants (WWTP) were previously recognized as hot spots for the
      horizontal transfer of genetic material. One of the plasmid groups that is often associated
      with drug resistance is the incompatibility group IncN. The aim of this study was to gain
      insights into the diversity and evolutionary history of IncN plasmids by determining and
      comparing the complete genome sequences of the four novel multi-drug resistance plasmids
      pRSB201, pRSB203, pRSB205 and pRSB206 that were exogenously isolated from the final effluent
      of a municipal WWTP. Their sizes range between 42,875bp and 56,488bp and they share a common
      set of backbone modules that encode plasmid replication initiation, conjugative transfer, and
      plasmid maintenance and control. All plasmids are transferable at high rates between
      Escherichia coli strains, but did not show a broad host range. Different genes conferring
      resistances to ampicillin, streptomycin, spectinomycin, sulfonamides, tetracycline and
      trimethoprim were identified in accessory modules inserted in these plasmids. Comparative
      analysis of the four WWTP IncN plasmids and IncN plasmids deposited in the NCBI database
      enabled the definition of a core set of backbone genes for this group. Moreover, this approach
      revealed a close phylogenetic relationship between the IncN plasmids isolated from
      environmental and clinical samples. Phylogenetic analysis also suggests the existence of
      host-specific IncN plasmid subgroups. In conclusion, IncN plasmids likely contribute to the
      dissemination of resistance determinants between environmental bacteria and clinical strains.
      This is of particular importance since multi-drug resistance IncN plasmids have been
      previously identified in members of the Enterobacteriaceae that cause severe infections in
      humans.
AU  - Eikmeyer F
AU  - Hadiati A
AU  - Szczepanowski R
AU  - Wibberg D
AU  - Schneiker-Bekel S
AU  - Rogers LM
AU  - Brown CJ
AU  - Top EM
AU  - Puhler A
AU  - Schluter A
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 2012 68: 13-24.

PMID- 9214655
VI  - 3
DP  - 1997
TI  - Naegleria nucleolar introns contain two group I ribozymes with different functions in RNA splicing and processing.
PG  - 710-720
AB  - We have characterized the structural organization and catalytic properties of the large
      nucleolar group I introns (NaSSU1) of different Naegleria species N. jamiesoni, N. andersoni,
      N. italica, and N. gruberi.  NaSSU1 consists of three distinct RNA domains: an open reading
      frame encoding a homing-type endonuclease, and a small group I ribozyme (NaGIR1) inserted into
      the P6 loop of a second group I ribozyme (NaGIR2).  The two ribozymes have different functions
      in RNA splicing and processing.  NaGIR1 is an unusual self-cleaving group I ribozyme
      responsible for intron processing at two internal sites (IPS1 and IPS2), both close to the 5'
      end of the open reading frame.  This processing is hypothesized to lead to formation of a
      messenger RNA for the endonuclease.  Structurally, NaGIR2 is a typical group IC1 ribozyme,
      catalyzing intron excision and exon ligation reactions.  NaGIR2 is responsible for
      circularization of the excised intron, a reaction that generates full-length RNA circles of
      wild-type intron.  Although it is only distantly related in primary sequence, NaSSU1 RNA has a
      predicted organization and function very similar to that of the mobile group I intron DiSSU1
      of Didymium, the only other group I intron known to encode two ribozymes.  We propose that
      these twin-ribozyme introns define a distinct category of group I introns with a conserved
      structural organization and function.
AU  - Einvik C
AU  - Decatur WA
AU  - Embley TM
AU  - Vogt VM
AU  - Johansen S
PT  - Journal Article
TA  - RNA
JT  - RNA
SO  - RNA 1997 3: 710-720.

PMID- 12093901
VI  - 99
DP  - 2002
TI  - The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium.
PG  - 9509-9514
AB  - The complete genome of the green-sulfur eubacterium Chlorobium tepidum TLS was determined to
      be a single circular chromosome of 2,154,946 bp. This represents the first genome sequence
      from the phylum Chlorobia, whose members perform anoxygenic photosynthesis by the reductive
      tricarboxylic acid cycle. Genome comparisons have identified genes in C. tepidum that are
      highly conserved among photosynthetic species. Many of these have no assigned function and may
      play novel roles in photosynthesis or photobiology. Phylogenomic analysis reveals likely
      duplications of genes involved in biosynthetic pathways for photosynthesis and the metabolism
      of sulfur and nitrogen as well as strong similarities between metabolic processes in C.
      tepidum and many Archaeal species.
AU  - Eisen JA et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2002 99: 9509-9514.

PMID- 25931604
VI  - 3
DP  - 2015
TI  - Genome Sequence of the Acidophilic Iron Oxidizer Ferrimicrobium acidiphilum Strain T23T.
PG  - e00383-15
AB  - Extremely acidophilic iron-oxidizing bacteria have largely been characterized for the phyla
      Proteobacteria and Nitrospira. Here, we report the draft genome of an
      iron-oxidizing and -reducing heterotrophic mesophile of the Actinobacteria,
      Ferrimicrobium acidiphilum, which was isolated from an abandoned pyrite mine. The
      genome sequence comprises 3.08 Mb.
AU  - Eisen S
AU  - Poehlein A
AU  - Johnson DB
AU  - Daniel R
AU  - Schlomann M
AU  - Muhling M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00383-15.

PMID- 25931603
VI  - 3
DP  - 2015
TI  - Genome Sequence of the Acidophilic Ferrous Iron-Oxidizing Isolate Acidithrix ferrooxidans Strain Py-F3, the Proposed Type Strain of the Novel Actinobacterial   Genus Acidithrix.
PG  - e00382-15
AB  - Extremely acidophilic iron-oxidizing Gram-positive bacteria comprise species within the phyla
      Firmicutes and Actinobacteria. Here, we report the 4.02-Mb draft
      genome of Acidithrix ferrooxidans Py-F3, which was isolated from a stream
      draining an abandoned copper mine and proposed as the type species of a new genus
      of Actinobacteria.
AU  - Eisen S
AU  - Poehlein A
AU  - Johnson DB
AU  - Daniel R
AU  - Schlomann M
AU  - Muhling M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00382-15.

PMID- 
VI  - 
DP  - 2005
TI  - Development of a programmable restriction enzyme.
PG  - 1-116
AB  - 
AU  - Eisenschmidt K
PT  - Journal Article
TA  - Ph.D. Thesis, Germany
JT  - Ph.D. Thesis, Germany
SO  - Ph.D. Thesis, Germany 2005 : 1-116.

PMID- 12039534
VI  - 96
DP  - 2002
TI  - A fluorimetric assay for on-line detection of DNA cleavage by restriction endonucleases.
PG  - 185-191
AB  - We have developed an assay for online detection of DNA cleavage by restriction endonucleases,
      suitable for the high throughput screening of the activity and flanking sequence preference of
      restriction endonuclease variants. For this purpose oligodeoxynucleotides were used, labeled
      with either 6-FAM or TAMRA whose fluorescence is quenched by a neighboring DABCYL group. After
      endonucleolytic cleavage the products are too short to remain double-stranded and the
      fluorophor labeled strand is released with concomitant increase in fluorescence which can be
      easily quantified.
      Employing this method, cleavage reactions can be monitored continuously, allowing for fast
      detection of specific activity as well as determination of kinetic parameters. To demonstrate
      the reliability of our
      assay we measured K(M) and k(cat) values for the restriction endonuclease EcoRV and obtained
      results similar to those obtained with established assays. Moreover, our method makes it
      possible to observe
      the cleavage of two different substrates differing in the sequences flanking the EcoRV site
      and labeled with different fluorophors in competition in a single experiment. This assay can
      be carried out in a
      microplate format, which allows for the analysis of many restriction endonuclease variants in
      parallel.
AU  - Eisenschmidt K
AU  - Lanio T
AU  - Jeltsch A
AU  - Pingoud A
PT  - Journal Article
TA  - J. Biotechnol.
JT  - J. Biotechnol.
SO  - J. Biotechnol. 2002 96: 185-191.

PMID- 16356926
VI  - 33
DP  - 2005
TI  - Developing a programmed restriction endonuclease for highly specific DNA cleavage.
PG  - 7039-7047
AB  - Specific cleavage of large DNA molecules at few sites, necessary for the analysis of genomic
      DNA or for targeting individual genes in complex genomes, requires endonucleases of extremely
      high specificity. Restriction endonucleases (REase) that recognize DNA sequences of 4-C8 bp
      are not sufficiently specific for this purpose. In principle, the specificity of REases can be
      extended by fusion to sequence recognition modules, e.g. specific DNA-binding domains or
      triple-helix forming oligonucleotides (TFO). We have chosen to extend the specificity of
      REases using TFOs, given the combinatorial flexibility this fusion offers in addressing a
      short, yet precisely recognized restriction site next to a defined triple-helix forming site
      (TFS). We demonstrate here that the single chain variant of PvuII (scPvuII) covalently coupled
      via the bifunctional cross-linker N-(gamma-maleimidobutryloxy) succinimide ester to a TFO
      (5'-NH2-[CH2]6 or 12-MPMPMPMPMPPPPPPT-3', with M being 5-methyl-2'-deoxycytidine and P
      being 5-[1-propynyl]-2'-deoxyuridine), cleaves DNA specifically at the recognition site of
      PvuII (CAGCTG) if located in a distance of approximately one helical turn to a TFS
      (underlined) complementary to the TFO ('addressed' site:
      5'-TTTTTTTCTCTCTCTCN~10CAGCTG-3'), leaving 'unaddressed' PvuII sites intact. The
      preference for cleavage of an 'addressed' compared to an 'unaddressed' site is >1000-fold,
      if the cleavage reaction is initiated by addition of Mg2+ ions after preincubation of
      scPvuII-TFO and substrate in the absence of Mg2+ ions to allow triple-helix formation before
      DNA cleavage. Single base pair substitutions in the TFS prevent addressed DNA cleavage by
      scPvuII-TFO.
AU  - Eisenschmidt K
AU  - Lanio T
AU  - Simoncsits A
AU  - Jeltsch A
AU  - Pingoud V
AU  - Wende W
AU  - Pingoud A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2005 33: 7039-7047.

PMID- 10234783
VI  - 15
DP  - 1999
TI  - Functional analysis of HO gene in delayed homothallism in Saccharomyces cerevisiae wy2.
PG  - 451-458
AB  - Saccharomyces cerevisiae wy2 exhibits a novel life cycle, with delayed homothallism caused by
      a defective HO gene. In this strain, gradual diploidization occurs during successive
      subcultures. Three amino acids of wy2 HO were different from those of wild-type (wt) HO, which
      included a nonsense mutation (TAG) from Trp-292 and two amino acid changes of His-475 to Leu
      and Glu-530 to Lys. The ho gene of heterothallic strain CG379 was also sequenced in this
      study. Four amino acids of ho were different from those of HO. Among different amino acids in
      wy2 HO and ho, the alteration of His-475 to Leu was common between them. His-475 in HO was
      previously suggested to be involved in the DNA binding. We constructed a variety of chimeric
      HO genes by exchanging the corresponding restriction fragments generated from the wt HO, wy2
      HO and ho genes. These results and the site-directed mutagenesis studies allowed us to draw
      the following conclusions: (a) Gly-223 is essential for HO activity; (b) mutation of His-475
      to Leu significantly reduces the HO activity; (c) amber mutation (TAG) in wy2 HO car be
      suppressed inefficiently.
AU  - Ekino K
AU  - Kwon I
AU  - Goto M
AU  - Yoshino S
AU  - Furukawa K
PT  - Journal Article
TA  - Yeast
JT  - Yeast
SO  - Yeast 1999 15: 451-458.

PMID- 
VI  - 
DP  - 2005
TI  - Design and characterization of homing endonuclease I-PpoI variants with novel DNA sequence specificity.
PG  - 1-115
AB  - Homing endonucleases bind and cleave long DNA target sites with high degree of sequence
      specificity.  The homing endonuclease I-PpoI recognizes a 15 bp, semi-palindromic homing site
      sequence in the rDNA of all eukaryotes.  The co-crystal structure indicates taht a b-sheet in
      the major groove is responsible for most of the DNA-protein contacts that determine sequence
      specificity of the enzyme.  Base pair changes in the +/-6 position of the I-PpoI binding site
      disrupt cleavage.  To better understand the specificity at the +/- site, I have explored
      variants with altered specificity for a +6C/-6G change.  Three libraries of I-PpoI variants
      with varying degrees of rationally designed changes in the b-sheet were generated and screened
      for altered DNA sequence specificity to a +6C/-6G basepair change using a yeast one-hybrid
      assay.  A total of thirteen unique variants were isolated and characterized for binding
      affinity and cleavage activity on the WT site and the +6C/-6G site; the other seven variants
      had generally relaxed specificity or a higher affinity for the WT site.  Only one variant
      showed cleavage activity on the WT site and none of the variants cleaves the +6C/-6G site.
      Select variants were further investigated for their binding affinity for 4 other binding site
      sequences.  Five variants with single amino acid changes to the WT protein sequence and three
      variants with single amino acid changes to a protein variant with a specificity shift were
      generated and biochemically characterized for cleavage activity and binding affinity.  I-PpoI
      variant proteins provide insight into how DNA-protein contacts determine DNA sequence
      specificity.  A deeper understanding of homing endonuclease sequence specificity determinants
      and how specificity shifts occur will aid in the design and generation of homing endonuclease
      variants as useful tools for genomic research and therapy.
AU  - Eklund JL
PT  - Journal Article
TA  - Ph.D. Thesis, University of Washington, Seattle, USA
JT  - Ph.D. Thesis, University of Washington, Seattle, USA
SO  - Ph.D. Thesis, University of Washington, Seattle, USA 2005 : 1-115.

PMID- 17720708
VI  - 35
DP  - 2007
TI  - Altered target site specificity variants of the I-PpoI His-Cys box homing endonuclease.
PG  - 5839-5850
AB  - We used a yeast one-hybrid assay to isolate and characterize variants of the eukaryotic homing
      endonuclease I-PpoI that were able to bind a mutant,
      cleavage-resistant I-PpoI target or 'homing' site DNA in vivo. Native
      I-PpoI recognizes and cleaves a semi-palindromic 15-bp target site with
      high specificity in vivo and in vitro. This target site is present in the
      28S or equivalent large subunit rDNA genes of all eukaryotes. I-PpoI
      variants able to bind mutant target site DNA had from 1 to 8 amino acid
      substitutions in the DNA-protein interface. Biochemical characterization
      of these proteins revealed a wide range of site-binding affinities and
      site discrimination. One-third of variants were able to cleave target site
      DNA, but there was no systematic relationship between site-binding
      affinity and site cleavage. Computational modeling of several variants
      provided mechanistic insight into how amino acid substitutions that
      contact, or are adjacent to, specific target site DNA base pairs determine
      I-PpoI site-binding affinity and site discrimination, and may affect
      cleavage efficiency.
AU  - Eklund JL
AU  - Ulge UY
AU  - Eastberg J
AU  - Monnat RJ Jr
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2007 35: 5839-5850.

PMID- 23516181
VI  - 1
DP  - 2013
TI  - Whole-Genome Sequence of the Fish Virulent Strain Streptococcus iniae IUSA-1, Isolated from Gilthead Sea Bream (Sparus aurata) and Red Porgy (Pagrus pagrus).
PG  - e0002513
AB  - Streptococcus iniae is a major fish pathogen that produces invasive infections that result in
      economic losses in aquaculture. In this study, the draft genome
      sequence of Streptococcus iniae strain IUSA-1, isolated from a natural outbreak
      affecting gilthead sea bream (Sparus aurata) and red porgy (Pagrus pagrus), is
      presented.
AU  - El Aamri F
AU  - Acosta F
AU  - Real F
AU  - Padilla D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0002513.

PMID- 29192090
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Lactobacillus plantarum 10CH, a Potential Probiotic Lactic Acid Bacterium with Potent Antimicrobial Activity.
PG  - e01398-17
AB  - Lactobacillus plantarum 10CH is a bacteriocin-producing potential probiotic lactic acid
      bacterium (LAB) strain isolated from cheese. Its complete nucleotide
      sequence shows a single circular chromosome of 3.3 Mb, with a G+C content of
      44.51%, a 25-gene plantaricin bacteriocin gene cluster, and the absence of
      recognized virulence factors.
AU  - El Halfawy NM
AU  - El-Naggar MY
AU  - Andrews SC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01398-17.

PMID- 28663294
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Kingella negevensis SW7208426, the First European Strain of K. negevensis Isolated from a Healthy Child in Switzerland.
PG  - e00571-17
AB  - We report here the draft genome of Kingella negevensis strain SW7208426, isolated from the
      oropharynx of a healthy 6-year-old boy in Geneva, Switzerland. To our
      knowledge, this is the first genome report of the newly described K. negevensis
      species from Europe.
AU  - El Houmami N
AU  - Schrenzel J
AU  - Yagupsky P
AU  - Robert C
AU  - Ceroni D
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00571-17.

PMID- 25035318
VI  - 2
DP  - 2014
TI  - Genome Sequence of Lactobacillus delbrueckii subsp. lactis CNRZ327, a Dairy Bacterium with Anti-Inflammatory Properties.
PG  - e00328-14
AB  - Lactobacillus delbrueckii subsp. lactis CNRZ327 is a dairy bacterium with anti-inflammatory
      properties both in vitro and in vivo. Here, we report the
      genome sequence of this bacterium, which appears to contain no less than 215
      insertion sequence (IS) elements, an exceptionally high number regarding the
      small genome size of the strain.
AU  - El Kafsi H
AU  - Binesse J
AU  - Loux V
AU  - Buratti J
AU  - Boudebbouze S
AU  - Dervyn R
AU  - Hammani A
AU  - Maguin E
AU  - van de Guchte M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00328-14.

PMID- 27103706
VI  - 4
DP  - 2016
TI  - Genome Sequence of the Tick-Borne Pathogen Rickettsia raoultii.
PG  - e00157-16
AB  - ITALIC! Rickettsia raoultiiis a tick-associated spotted fever group (SFG) organism, causing
      scalp eschar and neck lymphadenopathy after tick bite (SENLAT)
      in humans. We report here the genome sequence of ITALIC! R. raoultiistrain
      Khabarovsk(T)(CSUR R3(T), ATCC VR-1596(T)), which was isolated from a ITALIC!
      Dermacentor silvarumtick collected in Russia.
AU  - El Karkouri K
AU  - Mediannikov O
AU  - Robert C
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00157-16.

PMID- 23388049
VI  - 10
DP  - 2013
TI  - Genome sequence and analysis of a broad-host range lytic bacteriophage that infects the Bacillus cereus group.
PG  - 48
AB  - ABSTRACT: BACKGROUND: Comparatively little information is available on members of
      the Myoviridae infecting low G+C content, Gram-positive host bacteria of the
      family Firmicutes. While numerous Bacillus phages have been isolated up till now
      only very few Bacillus cereus phages have been characterized in detail. RESULTS:
      Here we present data on the large, virulent, broad-host-range B. cereus phage
      vB_BceM_Bc431v3 (Bc431v3). Bc431v3 features a 158,618 bp dsDNA genome,
      encompassing 239 putative open reading frames (ORFs) and, 20 tRNA genes encoding
      17 different amino acids. Since pulsed-field gel electrophoresis indicated that
      the genome of this phage has a mass of 155-158 kb Bc431v3 DNA appears not to
      contain long terminal repeats that are found in the genome of Bacillus phage
      SPO1. CONCLUSIONS: Bc431v3 displays significant sequence similarity, at the
      protein level, to B. cereus phage BCP78, Listeria phage A511 and Enterococcus
      phage [latin capital letter o with stroke]EF24C and other morphologically related
      phages infecting Firmicutes such as Staphylococcus phage K and Lactobacillus
      phage LP65. Based on these data we suggest that Bc431v3 should be included as a
      member of the Spounavirinae; however, because of all the diverse taxonomical
      information has been addressed recently, it is difficult to determine the genus.
      The Bc431v3 phage contains some highly unusual genes such as gp143 encoding
      putative tRNAHis guanylyltransferase. In addition, it carries some genes that
      appear to be related to the host sporulation regulators. These are: gp098, which
      encodes a putative segregation protein related to FstK/SpoIIIE DNA transporters;
      gp105, a putative segregation protein; gp108, RNA polymerase sigma factor F/B;
      and, gp109 encoding RNA polymerase sigma factor G.
AU  - El-Arabi TF
AU  - Griffiths MW
AU  - She YM
AU  - Villegas A
AU  - Lingohr EJ
AU  - Kropinski AM
PT  - Journal Article
TA  - Virol. J.
JT  - Virol. J.
SO  - Virol. J. 2013 10: 48.

PMID- 2014266
VI  - 88
DP  - 1991
TI  - High expression of the DNA methyltransferase gene characterizes human neoplastic cells and progression stages of colon cancer.
PG  - 3470-3474
AB  - DNA methylation abnormalities occur consistently in human neoplasia including widespread
      hypomethylation and more recently recognized local increases in DNA methylation that hold
      potential for gene inactivation events. To study this imbalance further, we have cloned and
      localized to chromosome 19 a portion of the human DNA methyltransferase gene that codes for
      the enzyme catalyzing DNA methylation. Expression of this gene is low in normal human cells,
      significantly increased (30- to 50-fold by PCR analysis) in virally transformed cells, and
      strikingly elevated in human cancer cells (several hundredfold). In comparison to colon mucosa
      from patients without neoplasia, median levels of DNA methyltransferse transcripts are 15-fold
      increased in histologically normal nucosa from patients with cancers of the benign polyps that
      can precede cancers, 60-fold increased in the premalignant polyps, and >200-fold increased in
      the cancers. Thus, increases in DNA methyltansferase gene expression precede development of
      colonic neoplasia and continue during progression of colonic neoplasms. These increases may
      play a role in the genetic instability of cancer and mark early events in cell transformation.
AU  - El-Deiry WS
AU  - Nelkin BD
AU  - Celano P
AU  - Yen R-WC
AU  - Falco JP
AU  - Hamilton SR
AU  - Baylin SB
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1991 88: 3470-3474.

PMID- 25744991
VI  - 3
DP  - 2015
TI  - Genome Sequence of Pseudomonas azelaica Strain Aramco J.
PG  - e00037-15
AB  - We report here the draft genome sequence of Pseudomonas azelaica strain Aramco J  (7.3 Mbp; GC
      content, 61.9%), one of the few bacteria that can completely
      mineralize different hydroxybiphenyls, e.g., 2-hydroxybiphenyl,
      2,2'-dihydroxybiphenyl, and 3-hydroxybiphenyl. The findings obtained from its
      genome annotation suggest that this strain becomes a useful biocatalyst for
      aromatic bioconversions.
AU  - El-Said MM
AU  - Garcia JL
AU  - Martinez I
AU  - Del Cerro C
AU  - Nogales J
AU  - Diaz E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00037-15.

PMID- 11898342
VI  - 46
DP  - 2001
TI  - Isolation and characterization of two types of actinophage infecting Streptomyces scabies.
PG  - 519-526
AB  - Two types of actinophages, phiS and phiL, were isolated from soil samples by using
      Streptomyces scabies, a potato scab pathogen, as
      indicator strain. The phages were partially characterized according to
      their physicochemical properties, plaques and particles morphology, and
      their host range; this varied from narrow (for phiS) to wide (for
      phiL). The adsorption rate constants of the phiS and phiL were 3.44 and
      3.18 pL/min, and their burst sizes were 1.61 and 3.75 virions per mL,
      respectively. One-step growth indicated that phiS and phiL have a
      latent period of 1/2 h followed by a rise period of 1/2 h. The
      temperate character of these phages was tested in other isolates of
      Streptomyces. Four of the phages ( phiSS3, phiSS12, phiSS13 and
      phiSS17) were identified as temperate phages, since they were able to
      lysogenize SS3, SS12, SS13 and SS17. phiSS3, phiSS12 and, phiSS13 were
      homoimmune, and they were heteroimmune with respect to SS17. The
      restriction barriers of lysogenic isolates (SS12, SS13 and SS17)
      interfered with the blockage of plaque formation by phages ( phiSS12,
      phiSS13 or phiSS17) propagated on them, about 75 % of lysogenic
      isolates had restriction systems. The exposure of the lysogenic
      isolates (SS12, SS13 and SS17) to UV-irradiation prevented the possible
      restriction barriers of these isolates so that these barriers could be
      overcome.
AU  - El-Sayed ESA
AU  - El-Didamony G
AU  - Mansour K
PT  - Journal Article
TA  - Folia Microbiol. (Praha)
JT  - Folia Microbiol. (Praha)
SO  - Folia Microbiol. (Praha) 2001 46: 519-526.

PMID- 22740657
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Borrelia crocidurae.
PG  - 3723-3724
AB  - We announce the draft genome sequence of Borrelia crocidurae (strain Achema). The 1,557,560-bp
      genome (27% GC content) comprises one 919,477-bp linear chromosome
      and 638,083-bp plasmids that together carry 1,472 open reading frames, 32 tRNAs,
      and three complete rRNAs, with almost complete colinearity between B. crocidurae
      and Borrelia duttonii chromosomes.
AU  - Elbir H
AU  - Gimenez G
AU  - Robert C
AU  - Bergstrom S
AU  - Cutler S
AU  - Raoult D
AU  - Drancourt M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3723-3724.

PMID- 24407639
VI  - 2
DP  - 2014
TI  - Genome Sequence of the Asiatic Species Borrelia persica.
PG  - e01127-13
AB  - We report the complete genome sequence of Borrelia persica, the causative agent of tick-borne
      relapsing fever borreliosis on the Asian continent. Its genome of
      1,784,979 bp contains 1,850 open reading frames, three ribosomal RNAs, and 32
      tRNAs. One clustered regularly interspaced short palindromic repeat (CRISPR) was
      detected.
AU  - Elbir H
AU  - Larsson P
AU  - Normark J
AU  - Upreti M
AU  - Korenberg E
AU  - Larsson C
AU  - Bergstrom S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01127-13.

PMID- 24435869
VI  - 2
DP  - 2014
TI  - Genome Sequence of the Relapsing Fever Borreliosis Species Borrelia hispanica.
PG  - e01171-13
AB  - Borrelia hispanica is the etiological pathogen of tick-borne relapsing fever, transmitted to
      humans by infected Ornithodoros erraticus ticks. Here we present
      the 1,783,846-bp draft genome sequence, with an average G+C content of 28%. It
      has 2,140 open reading frames, 3 ribosomal RNAs, and 32 transfer RNAs.
AU  - Elbir H
AU  - Larsson P
AU  - Upreti M
AU  - Normark J
AU  - Bergstrom S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01171-13.

PMID- 24501641
VI  - 9
DP  - 2013
TI  - Staphylococcus aureus subsp. anaerobius strain ST1464 genome sequence.
PG  - 1-13
AB  - Staphylococcus aureus subsp. anaerobius is responsible for Morel's disease in animals and a
      cause of abscess in humans. It is characterized by a
      microaerophilic growth, contrary to the other strains of S. aureus. The
      2,604,446-bp genome (32.7% GC content) of S. anaerobius ST1464 comprises one
      chromosome and no plasmids. The chromosome contains 2,660 open reading frames
      (ORFs), 49 tRNAs and three complete rRNAs, forming one complete operon. The size
      of ORFs ranges between 100 to 4,600 bp except for two ORFs of 6,417 and 7,173 bp
      encoding segregation ATPase and non-ribosomal peptide synthase, respectively. The
      chromosome harbors Staphylococcus phage 2638A genome and incomplete
      Staphylococcus phage genome PT1028, but no detectable CRISPRS. The antibiotic
      resistance gene for tetracycline was found although Staphylococcus aureus subsp.
      anaerobius is susceptible to tetracycline in-vitro. Intact oxygen detoxification
      genes encode superoxide dismutase and cytochrome quinol oxidase whereas the
      catalase gene is impaired by a stop codon. Based on the genome, in-silico
      multilocus sequence typing indicates that S. aureus subsp. anaerobius emerged as
      a clone separated from all other S. aureus strains, illustrating host-adaptation
      linked to missing functions. Availability of S. aureus subsp. anaerobius genome
      could prompt the development of post-genomic tools for its rapid discrimination
      from S. aureus.
AU  - Elbir H
AU  - Robert C
AU  - Nguyen TT
AU  - Gimenez G
AU  - El Sanousi SM
AU  - Flock JI
AU  - Raoult D
AU  - Drancourt M
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 9: 1-13.

PMID- 28302772
VI  - 5
DP  - 2017
TI  - Chromosome and Megaplasmid Sequences of Borrelia anserina (Sakharoff 1891), the Agent of Avian Spirochetosis and Type Species of the Genus.
PG  - e00018-17
AB  - Sequences of the linear chromosome and plasmids of Borrelia anserina, the cause of avian
      spirochetosis of poultry, revealed a smaller genome than those of other
      Borrelia spp. transmitted by argasid ticks. Missing or disrupted genes included a
      dam methylase and those in the pathway for synthesis of phospholipids from
      glycerol.
AU  - Elbir H
AU  - Sitlani P
AU  - Bergstrom S
AU  - Barbour AG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00018-17.

PMID- 29163426
VI  - 8
DP  - 2017
TI  - Sugar Metabolism of the First Thermophilic Planctomycete Thermogutta terrifontis: Comparative Genomic and Transcriptomic Approaches.
PG  - 2140
AB  - Xanthan gum, a complex polysaccharide comprising glucose, mannose and glucuronic  acid
      residues, is involved in numerous biotechnological applications in
      cosmetics, agriculture, pharmaceuticals, food and petroleum industries.
      Additionally, its oligosaccharides were shown to possess antimicrobial,
      antioxidant, and few other properties. Yet, despite its extensive usage, little
      is known about xanthan gum degradation pathways and mechanisms. Thermogutta
      terrifontis, isolated from a sample of microbial mat developed in a terrestrial
      hot spring of Kunashir island (Far-East of Russia), was described as the first
      thermophilic representative of the Planctomycetes phylum. It grows well on
      xanthan gum either at aerobic or anaerobic conditions. Genomic analysis unraveled
      the pathways of oligo- and polysaccharides utilization, as well as the mechanisms
      of aerobic and anaerobic respiration. The combination of genomic and
      transcriptomic approaches suggested a novel xanthan gum degradation pathway which
      involves novel glycosidase(s) of DUF1080 family, hydrolyzing xanthan gum backbone
      beta-glucosidic linkages and beta-mannosidases instead of xanthan lyases,
      catalyzing cleavage of terminal beta-mannosidic linkages. Surprisingly, the genes
      coding DUF1080 proteins were abundant in T. terrifontis and in many other
      Planctomycetes genomes, which, together with our observation that xanthan gum
      being a selective substrate for many planctomycetes, suggest crucial role of
      DUF1080 in xanthan gum degradation. Our findings shed light on the metabolism of
      the first thermophilic planctomycete, capable to degrade a number of
      polysaccharides, either aerobically or anaerobically, including the
      biotechnologically important bacterial polysaccharide xanthan gum.
AU  - Elcheninov AG
AU  - Menzel P
AU  - Gudbergsdottir SR
AU  - Slesarev AI
AU  - Kadnikov VV
AU  - Krogh A
AU  - Bonch-Osmolovskaya EA
AU  - Peng X
AU  - Kublanov IV
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2017 8: 2140.

PMID- 1614885
VI  - 20
DP  - 1992
TI  - Isolation and characterization of restriction endonuclease BcuAI from Bacillus cereus A.
PG  - 2898
AB  - Restriction endonuclease BcuAI, an isoschizomer of AvaII (Figure 1), has been purified from
      Bacillus cereus A. The procedure of isolation of BcuAI included the fractionation with
      ammonium sulfate and column chromatography on DEAE-Sepharose (elution buffer 10 mM
      K-phosphate, pH 7.4, 0.1 mM EDTA, 1 mM DTT, 0.0-1.0 M KCl; elution zone of enzyme activity
      0.2-0.3 M KCl). 1400 u. BcuAI can be obtained from 1 g. of wet cells. BcuAI showed maximal
      activity at 30-37C, pH between 7.6-8.2, MgCl2 concentration in the range of 5-10 mM and at
      high ionic strength.
AU  - Eldarov MA
AU  - Karpichev IV
AU  - Samko OT
AU  - Anikeitcheva NV
AU  - Kalugin AA
AU  - Khoroshoutina EB
AU  - Sokolov NN
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 2898.

PMID- 1614883
VI  - 20
DP  - 1992
TI  - Characterization of BciBII, an isoschizomer of BstNI from a strain of Bacillus circulans B.
PG  - 2896
AB  - BciBII, an isoschizomer of BstNI (figure 1) has been isolated from Bacillus circulans B. The
      enzyme was purified by precipitation with polyethylenimine, ammonium sulfate and subsequent
      column chromatography on DEAE-sepharose, Blue sepharose and phosphocellulose. Restriction
      endonuclease BciBII showed maximal activity at 37C, pH between 7.4-7.8, MgCl2 concentration in
      the range of 8-12 mM and at high ionic strenghth.
AU  - Eldarov MA
AU  - Karpichev IV
AU  - Samko OT
AU  - Anikeitcheva NV
AU  - Kalugin AA
AU  - Khoroshoutina EB
AU  - Sokolov NN
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 2896.

PMID- 9914504
VI  - 259
DP  - 1999
TI  - I-NjaI, a nuclear intron-encoded homing endonuclease from Naegleria, generates a pentanucleotide 3' cleavage-overhang within a 19 base-pair partially symmetric DNA recognition site.
PG  - 281-288
AB  - Different species of the amoebo-flagellate Naegleria harbor optional group I introns in the
      nuclear ribosomal DNA that contain open reading frames.  Intron proteins from Naegleria
      jamiesoni, Naegleria andersoni, and Naegleria italica (named I-NjaI, I-NanI and I-NitI,
      respectively) were expressed in Escherichia coli and found to be isoschizomeric homing
      endonucleases that specifically recognize and cleave intron-lacking homologous alleles of
      ribosomal DNA.  The I-NjaI endonuclease was affinity purified, characterized in more detail,
      and found to generate five-nucleotide 3' staggered ends at the intron insertion site which
      differs from the ends generated by all other known homing endonucleases.  The recognition site
      was delimited and found to cover an ~19 base-pair partially symmetric sequence spanning both
      the cleavage site and the intron insertion site.  The palindromic feature was supported by
      mutational analysis of the target DNA.  All single-site substitutions within the recognition
      sequence were cleaved by the purified I-NjaI endonuclease, but at different efficiencies.  The
      center for symmetry and cleavage was found to be completely degenerate in specificity, which
      resembles that of the subclass IIW bacterial restriction enzymes.
AU  - Elde M
AU  - Haugen P
AU  - Willassen NP
AU  - Johansen S
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1999 259: 281-288.

PMID- 11106439
VI  - 267
DP  - 2000
TI  - Functional characterization of isoschizomeric His-Cys box homing endonucleases from Naegleria.
PG  - 7257-7266
AB  - Several species within the amoeboflagellate genus Naegleria harbor an optional ORF containing
      group I introns in their nuclear small subunit ribosomal DNA. The different ORFs encode homing
      endonucleases with 65 to 95% identity at the amino-acid level. I-NjaI, I-NanI and I-NitI, from
      introns in Naegleria jamiesoni, N. andersoni and N. italica, respectively, were analyzed in
      more detail and found to be isoschizomeric endonucleases that recognize and cleave an
      approximately 19-bp partially symmetrical sequence, creating a pentanucleotide 3' overhang
      upon
      cleavage. The optimal conditions for cleavage activity with respect to temperature, pH, salt
      and divalent metal ions were investigated. The optimal cleavage temperature for all three
      endonucleases was found to be 37 degrees C and the activity was dependent on the concentration
      of NaCl with an optimum at 200 mM. Divalent metal ions, primarily Mg2+, are essential for
      Naegleria endonuclease activity. Whereas both Mn2+ and Ca2+ could substitute for Mg2+, but
      with a slower cleavage rate, Zn2+ was unable to support cleavage. Interestingly, the pH
      dependence of DNA cleavage was found to vary significantly between the I-NitI and
      I-NjaI/I-NanI endonucleases with optimal pH values at 6.5 and 9, respectively. Site-directed
      mutagenesis of conserved I-NjaI residues strongly supports the hypothesis that Naegleria
      homing endonucleases share a similar zinc-binding structure and active site with the His-Cys
      box homing endonuclease I-PpoI.
AU  - Elde M
AU  - Willassen NP
AU  - Johansen S
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 2000 267: 7257-7266.

PMID- 29256426
VI  - 127
DP  - 2017
TI  - Fatal fibrino-hemorrhagic bronchopneumonia associated with Morganella morganii in a bottlenose dolphin: a case report.
PG  - 41-47
AB  - A 5 yr old, 184 kg, and 262 cm total length female bottlenose dolphin Tursiops
      truncatus was found dead in a display after bloody discharge from the blowhole
      was observed 3 h prior to death. Pathological examination revealed fibrinous
      bronchopneumonia with prominent areas of necrosis (sequestra) and numerous
      Gram-negative bacilli within alveoli and in blood vessels of the lungs and liver
      and between muscle fibers. The cause of death was attributed to septicemia.
      Often, cases of fibrinous bronchopneumonia are characterized by bacteremia in the
      latter stages of infection, resulting in the death of the animal. Septicemia
      likely accounts for the ecchymoses and petechiae noted on the spleen, pancreas,
      forestomach, lungs, visceral peritoneum, and small intestine. Additional lesions
      included hemothorax, stable red frothy fluid in the trachea, and lymphoid
      depletion in the spleen and lymph nodes. Pure growth of Morganella morganii was
      isolated from the lungs, blood, liver, and blowhole mucosa. Sequencing of 16s
      rRNA of the isolated bacteria showed more than 99.6% identity with M. morganii
      strain FDAARGOS_172. To our knowledge, this is the first report of fatal
      fibrinonecrotizing bronchopneumonia associated with M. morganii infection in a
      cetacean.
AU  - Elfadl AK
AU  - Lee SW
AU  - Kim JH
AU  - Lee KL
AU  - Arif-Ullah HM
AU  - Chung MJ
AU  - Ghim SG
AU  - Lee EJ
AU  - Kim YD
AU  - Kim SM
AU  - Jeon SG
AU  - Lim JH
AU  - Choi HJ
AU  - Park JK
AU  - Jeong KS
PT  - Journal Article
TA  - Dis. Aquat. Org.
JT  - Dis. Aquat. Org.
SO  - Dis. Aquat. Org. 2017 127: 41-47.

PMID- 25789551
VI  - 5
DP  - 2015
TI  - Highly Iterated Palindromic Sequences (HIPs) and Their Relationship to DNA Methyltransferases.
PG  - 921-948
AB  - The sequence GCGATCGC (Highly Iterated Palindrome, HIP1) is commonly found in high frequency
      in cyanobacterial genomes. An important clue to its function may
      be the presence of two orphan DNA methyltransferases that recognize internal
      sequences GATC and CGATCG. An examination of genomes from 97 cyanobacteria, both
      free-living and obligate symbionts, showed that there are exceptional cases in
      which HIP1 is at a low frequency or nearly absent. In some of these cases, it
      appears to have been replaced by a different GC-rich palindromic sequence,
      alternate HIPs. When HIP1 is at a high frequency, GATC- and CGATCG-specific
      methyltransferases are generally present in the genome. When an alternate HIP is
      at high frequency, a methyltransferase specific for that sequence is present. The
      pattern of 1-nt deviations from HIP1 sequences is biased towards the first and
      last nucleotides, i.e., those distinguish CGATCG from HIP1. Taken together, the
      results point to a role of DNA methylation in the creation or functioning of HIP
      sites. A model is presented that postulates the existence of a GmeC-dependent
      mismatch repair system whose activity creates and maintains HIP sequences.
AU  - Elhai J
PT  - Journal Article
TA  - Life
JT  - Life
SO  - Life 2015 5: 921-948.

PMID- 11454303
VI  - 8
DP  - 2001
TI  - Determination of bias in the relative abundance of oligonucleotides in DNA sequences.
PG  - 151-175
AB  - Different statistical measures of bias of oligonucleotide sequences in DNA sequences were
      compared, both by theoretical analysis and according to their abilities to predict the
      relative abundances of oligonucleotides in the genome of Escherichia coli. The expected
      frequency of an oligonucleotide calculated from a maximal order Markov model was shown to be a
      degenerate case of the expected frequency calculated from biases of all subwords arising when
      noncontiguous subwords exhibit no bias. Since (at least in E, coli) noncontiguous sequences
      exhibit significant bias, the total compositional bias
      approach is expected to represent biases in genomic sequences more
      faithfully than Markov approaches. In fact, the efficacy of statistics
      based on Markov analysis even at the highest order were inferior in
      predicting actual frequencies of oligonucleotides to methods that
      factored out biases of internal subwords with gaps. Using total
      compositional bias as a measure of relative abundance, tetranucleotide
      and hexanucleotide palindromes were found to be distributed differently
      from nonpalindromic sequences, with their means shifted somewhat
      towards underrepresentation, A subpopulation of palindromic
      hexanucleotides, however, was highly underrepresented, and this group
      consisted almost entirely of targets for Type II restriction enzymes
      found within strains of E, coli, Sites recognized by Type I
      endonucleases from related strains were not markedly biased, and with
      pentanucleotides, palindromic and nonpalindromic sequences had nearly
      identical distributions. The loss of restriction sites may be explained
      by the free transfer of plasmids encoding restriction enzymes and
      episodic selection for the presence of the enzymes.
AU  - Elhai J
PT  - Journal Article
TA  - J. Comput. Biol.
JT  - J. Comput. Biol.
SO  - J. Comput. Biol. 2001 8: 151-175.

PMID- 8051018
VI  - 176
DP  - 1994
TI  - Conduction of pEC22, a plasmid coding for MR.EcoT22I, mediated by a resident Tn3-like transposon, Tn5396.
PG  - 5059-5067
AB  - pEC22 is a small plasmid that encodes the restriction-modification system MR.EcoT22I.
      Restriction and functional analysis of the plasmid identified the positions of genes encoding
      that system. The plasmid is able to be conducted by conjugal plasmids, a process mediated by a
      transposon contained within pEC22. This cryptic transposon, called Tn5396, was isolated from
      pEC22 and partially sequenced. The sequence of Tn5396 is for the most part typical of
      transposons of the Tn3 family and is most similar to that of Tn1000. The transposon differs
      from closely related transposons in that it lacks well-conserved sequences in the
      inverted-repeat region and has an unusually long terminal inverted repeat. Consideration of
      regions of internal sequence similarity in this and other transposons in the Tn3 family
      supports a theory of the mechanism by which the ends of Tn3-like transposons may maintain
      substantial identity between their inverted repeats over the course of evolutionary time.
AU  - Elhai J
AU  - Cai Y
AU  - Wolk CP
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1994 176: 5059-5067.

PMID- 9068647
VI  - 179
DP  - 1997
TI  - Reduction of conjugal transfer efficiency by three restriction activities of Anabaena sp. strain PCC 7120.
PG  - 1998-2005
AB  - The efficiency of conjugal transfer of plasmids from Escherichia coli to the cyanobacterium
      Anabaena sp. strain PCC 7120 was quantitated as a function of the number of restriction sites
      for the restriction enzymes carried by the recipient.  In addition to the previously
      recognized isoschizomers of AvaI and AvaII, PCC 7120 was found to possess an isoschizomer of
      AvaIII.  Plasmids modified in E. coli with methylases that protect in vitro against
      restriction by the three enzymes were transferred with high efficiency, nearly independent of
      the number of restriction sites on the plasmid.  Plasmids left unprotected against one of the
      three restriction enzymes were transferred with lower efficiencies.  For low numbers of sites,
      the efficiency of conjugal transfer decreased as an exponential function of the number of
      unprotected sites.  The methods presented may be used to increase the efficiency of conjugal
      transfer into restriction-competent bacteria.
AU  - Elhai J
AU  - Vepritskiy A
AU  - Muro-Pastor AM
AU  - Flores E
AU  - Wolk CP
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1997 179: 1998-2005.

PMID- 20851897
VI  - 192
DP  - 2010
TI  - Complete Genome Sequence of the Cellulolytic Thermophile Caldicellulosiruptor obsidiansis OB47T.
PG  - 6099-6100
AB  - Caldicellulosiruptor obsidiansis OB47(T) (ATCC BAA-2073, JCM 16842) is an extremely
      thermophilic, anaerobic bacterium capable of hydrolyzing
      plant-derived polymers through the expression of
      multidomain/multifunctional hydrolases. The complete genome sequence
      reveals a diverse set of carbohydrate-active enzymes and provides further
      insight into lignocellulosic biomass hydrolysis at high temperatures.
AU  - Elkins JG et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 6099-6100.

PMID- 18535141
VI  - 105
DP  - 2008
TI  - A korarchaeal genome reveals insights into the evolution of the Archaea.
PG  - 8102-8107
AB  - The candidate division Korarchaeota comprises a group of uncultivated microorganisms that, by
      their small subunit rRNA phylogeny, may have
      diverged early from the major archaeal phyla Crenarchaeota and
      Euryarchaeota. Here, we report the initial characterization of a member of
      the Korarchaeota with the proposed name, "Candidatus Korarchaeum
      cryptofilum," which exhibits an ultrathin filamentous morphology. To
      investigate possible ancestral relationships between deep-branching
      Korarchaeota and other phyla, we used whole-genome shotgun sequencing to
      construct a complete composite korarchaeal genome from enriched cells. The
      genome was assembled into a single contig 1.59 Mb in length with a G + C
      content of 49%. Of the 1,617 predicted protein-coding genes, 1,382 (85%)
      could be assigned to a revised set of archaeal Clusters of Orthologous
      Groups (COGs). The predicted gene functions suggest that the organism
      relies on a simple mode of peptide fermentation for carbon and energy and
      lacks the ability to synthesize de novo purines, CoA, and several other
      cofactors. Phylogenetic analyses based on conserved single genes and
      concatenated protein sequences positioned the korarchaeote as a deep
      archaeal lineage with an apparent affinity to the Crenarchaeota. However,
      the predicted gene content revealed that several conserved cellular
      systems, such as cell division, DNA replication, and tRNA maturation,
      resemble the counterparts in the Euryarchaeota. In light of the known
      composition of archaeal genomes, the Korarchaeota might have retained a
      set of cellular features that represents the ancestral archaeal form.
AU  - Elkins JG et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2008 105: 8102-8107.

PMID- 23580711
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of the Hyperthermophilic Sulfate-Reducing Bacterium Thermodesulfobacterium geofontis OPF15T.
PG  - e00162-13
AB  - Thermodesulfobacterium geofontis OPF15(T) (ATCC BAA-2454, JCM 18567) was isolated from
      Obsidian Pool, Yellowstone National Park, and grows optimally at 83 degrees
      C. The 1.6-Mb genome sequence was finished at the Joint Genome Institute and has
      been deposited for future genomic studies pertaining to microbial processes and
      nutrient cycles in high-temperature environments.
AU  - Elkins JG et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00162-13.

PMID- 23593012
VI  - 9
DP  - 2013
TI  - Comparative genomics of wolbachia and the bacterial species concept.
PG  - E1003381
AB  - The importance of host-specialization to speciation processes in obligate
      host-associated bacteria is well known, as is also the ability of recombination
      to generate cohesion in bacterial populations. However, whether divergent strains
      of highly recombining intracellular bacteria, such as Wolbachia, can maintain
      their genetic distinctness when infecting the same host is not known. We first
      developed a protocol for the genome sequencing of uncultivable endosymbionts.
      Using this method, we have sequenced the complete genomes of the Wolbachia
      strains wHa and wNo, which occur as natural double infections in Drosophila
      simulans populations on the Seychelles and in New Caledonia. Taxonomically, wHa
      belong to supergroup A and wNo to supergroup B. A comparative genomics study
      including additional strains supported the supergroup classification scheme and
      revealed 24 and 33 group-specific genes, putatively involved in host-adaptation
      processes. Recombination frequencies were high for strains of the same supergroup
      despite different host-preference patterns, leading to genomic cohesion. The
      inferred recombination fragments for strains of different supergroups were of
      short sizes, and the genomes of the co-infecting Wolbachia strains wHa and wNo
      were not more similar to each other and did not share more genes than other A-
      and B-group strains that infect different hosts. We conclude that Wolbachia
      strains of supergroup A and B represent genetically distinct clades, and that
      strains of different supergroups can co-exist in the same arthropod host without
      converging into the same species. This suggests that the supergroups are
      irreversibly separated and that barriers other than host-specialization are able
      to maintain distinct clades in recombining endosymbiont populations. Acquiring a
      good knowledge of the barriers to genetic exchange in Wolbachia will advance our
      understanding of how endosymbiont communities are constructed from vertically and
      horizontally transmitted genes.
AU  - Ellegaard KM
AU  - Klasson L
AU  - Naslund K
AU  - Bourtzis K
AU  - Andersson SG
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2013 9: E1003381.

PMID- 27231369
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Klebsiella quasipneumoniae subsp. similipneumoniae Strain ATCC 700603.
PG  - e00438-16
AB  - Klebsiella quasipneumoniae subsp. similipneumoniae strain ATCC 700603, formerly known as K.
      pneumoniae K6, is known for producing extended-spectrum
      beta-lactamase (ESBL) enzymes that can hydrolyze oxyimino-beta-lactams, resulting
      in resistance to these drugs. We herein report the complete genome of strain ATCC
      700603 and show that the ESBL genes are plasmid-encoded.
AU  - Elliott AG
AU  - Ganesamoorthy D
AU  - Coin L
AU  - Cooper MA
AU  - Cao MD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00438-16.

PMID- 16188275
VI  - 353
DP  - 2005
TI  - Mechanism of the Escherichia coli DNA T:G-mismatch endonuclease (Vsr protein) probed with thiophosphate-containing oligodeoxynucleotides.
PG  - 692-703
AB  - The mechanism of the Escherichia coli DNA T:G mismatch endonuclease (Vsr) has been
      investigated using oligodeoxynucleotides substituted, at the scissile phosphate, with isomeric
      phosphorothioates and a 3'-phosphorothiolate. Binding and kinetic data with the
      phosphorothioates/phosphorothiolate indicate that the two magnesium ions, which constitute
      essential co-factors, are required to stabilise the extra negative charge developed on the
      phosphate as the transition state is formed. Additionally one of the magnesium ions serves to
      activate the leaving group (the non-bridging 3'-oxygen atom of the scissile phosphate) during
      the hydrolysis reaction. Stereochemical analysis, using the R(p) phosphorothioate isomer,
      indicates that Vsr carries out a hydrolytic reaction with inversion of stereochemistry at
      phosphorus, compatible with an in-line attack of water and a pentacovalent transition state
      with trigonal bipyramidal geometry. In conjunction with structures of Vsr bound to its
      products, these data allow the reconstruction of the enzyme-substrate complex and a
      comprehensive description of the hydrolysis mechanism.
AU  - Elliott SL
AU  - Brazier J
AU  - Cosstick R
AU  - Connolly BA
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2005 353: 692-703.

PMID- 2544564
VI  - 171
DP  - 1989
TI  - Cloning, genetic characterization, and nucleotide sequence of the hemA-prfA operon of Salmonella typhimurium.
PG  - 3948-3960
AB  - The first step in heme biosynthesis is the formation of 5-aminolevulinic acid (ALA). Mutations
      in two genes, hemA and hemL, result in auxotrophy for ALA in Salmonella typhimurium, but the
      roles played by these genes and the mechanism of ALA synthesis are not understood. I have
      cloned and sequenced the S. typhimurium hemA gene. The predicted polypeptide sequence for the
      HemA protein shows no similarity to known ALA synthases, and no ALA synthase activity was
      detected in extracts prepared from strains carrying the cloned hemA gene. Genetic analysis,
      DNA sequencing of amber mutations, and maxicell studies proved that the open reading frame
      identified in the DNA sequence encodes HemA. Another surprising finding of this study is that
      hemA lies directly upstream of prfA, which encodes peptide chain release factor 1 (RF-1). A
      hemA::Kan insertion mutation, constructed in vitro, was transferred to the chromosome and used
      to show that these two genes form an operon. The hemA gene ends with an amber codon,
      recognized by RF-1. I suggest a model for autogenous control of prfA expression by translation
      reinitiation.
AU  - Elliott T
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1989 171: 3948-3960.

PMID- 9886284
VI  - 6
DP  - 1999
TI  - Direct observation of DNA translocation and cleavage by the EcoKI endonuclease using atomic force microscopy.
PG  - 15-17
AB  - Type I DNA restriction and modification enzymes such as EcoKI are multimeric enzymes that
      cleave DNA molecules lacking an appropriate pattern of methylation on a target sequence,
      thereby protecting the host bacterium from invasion by foreign DNA.  The reaction involves the
      initial recognition of an unmethylated DNA target sequence with the aid of the cofactor
      S-adenosyl methionine.  Recognition is followed by extensive ATP-dependent translocation of
      the DNA in both directions toward the enzyme, which remains bound at the target sequence.
      Eventually, endonucleolytic cleavage of the DNA occurs.  Recently, protein complexes with
      nucleic acids have been imaged successfully using fluid tapping-mode atomic force microscopy.
      In this study, we have used AFM to explore the type I DNA restriction and modification
      pathway, and specifically to follow the ATP-dependent translocation and cleavage of a single
      plasmid by the EcoKI enzyme complex under near-physiological conditions.
AU  - Ellis DJ
AU  - Dryden DT
AU  - Berge T
AU  - Edwardson JM
AU  - Henderson RM
PT  - Journal Article
TA  - Nat. Struct. Biol.
JT  - Nat. Struct. Biol.
SO  - Nat. Struct. Biol. 1999 6: 15-17.

PMID- 18025092
VI  - 76
DP  - 2008
TI  - Genomic comparison of virulent Rickettsia rickettsii Sheila Smith and avirulent Rickettsia rickettsii Iowa.
PG  - 542-550
AB  - Rickettsia rickettsii is an obligate intracellular pathogen that is the causative agent of
      Rocky Mountain spotted fever. To identify genes
      involved in the virulence of R. rickettsii, the genome of an avirulent
      strain, R. rickettsii Iowa, was sequenced and compared to the genome of
      the virulent strain R. rickettsii Sheila Smith. R. rickettsii Iowa is
      avirulent in a guinea pig model of infection and displays altered plaque
      morphology with decreased lysis of infected host cells. Comparison of the
      two genomes revealed that R. rickettsii Iowa and R. rickettsii Sheila
      Smith share a high degree of sequence identity. A whole-genome alignment
      comparing R. rickettsii Iowa to R. rickettsii Sheila Smith revealed a
      total of 143 deletions for the two strains. A subsequent single-nucleotide
      polymorphism (SNP) analysis comparing Iowa to Sheila Smith revealed 492
      SNPs for the two genomes. One of the deletions in R. rickettsii Iowa
      truncates rompA, encoding a major surface antigen (rickettsial outer
      membrane protein A [rOmpA]) and member of the autotransporter family, 660
      bp from the start of translation. Immunoblotting and immunofluorescence
      confirmed the absence of rOmpA from R. rickettsii Iowa. In addition, R.
      rickettsii Iowa is defective in the processing of rOmpB, an
      autotransporter and also a major surface antigen of spotted fever group
      rickettsiae. Disruption of rompA and the defect in rOmpB processing are
      most likely factors that contribute to the avirulence of R. rickettsii
      Iowa. Genomic differences between the two strains do not significantly
      alter gene expression as analysis of microarrays revealed only four
      differences in gene expression between R. rickettsii Iowa and R.
      rickettsii strain R. Although R. rickettsii Iowa does not cause apparent
      disease, infection of guinea pigs with this strain confers protection
      against subsequent challenge with the virulent strain R. rickettsii Sheila
      Smith.
AU  - Ellison DW
AU  - Clark TR
AU  - Sturdevant DE
AU  - Virtaneva K
AU  - Porcella SF
AU  - Hackstadt T
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2008 76: 542-550.

PMID- 8095080
VI  - 17C
DP  - 1993
TI  - Characterization of I-PpoI, an intron-encoded endonuclease from Physarum polycephalum.
PG  - 177
AB  - The genetic mobility of group I introns is dependent upon the site-specific endonucleases
      which they encode. We have characterized several properties of I-PpoI, the endonuclease that
      mediates "homing" of intron 3 (PpLSU3) in the nuclear ribosomal DNA (rDNA) of the slime mold
      Physarum polycephalum. From deletion analysis, we conclude that the minimum recognition site
      is a sequence of 15 bp, which is partially symmetric. The purified enzyme behaves as a dimer
      in gel filtration and sedimentation. We have studied the interaction of I-PpoI with DNA by
      bandshift analysis, MPE footprinting and DMS protection. The enzyme, which binds in the major
      groove, protects ca. 21bp of DNA surrounding the cleavage site. The I-PpoI recognition site is
      present in the nuclear rDNA of all eucaryotes. In yeast, expression of the enzyme is lethal,
      presumably because of cleavage of rDNA repeats on chromosome XII. By pulse field gel analysis,
      this is the only chromosome cut in vitro. Yeast mutants that survive the lethal effects of the
      endonuclease occur at surprisingly high frequencies, and are of at least two classes. The
      first consists of cells carrying point mutations in the recognition sequence. All ca. 150
      copies of the rDNA are mutant, as evidenced by the inability of I-PpoI to cleave the rDNA in
      vitro. The second class consists of cells in which the intron has become inserted into all
      copies of the rDNA. These cells express active endonuclease.
AU  - Ellison EL
AU  - Muscarella DE
AU  - Vogt VM
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1993 17C: 177.

PMID- 8246971
VI  - 13
DP  - 1993
TI  - Interaction of the intron-encoded mobility endonuclease I-PpoI with its target site.
PG  - 7531-7539
AB  - Endonucleases encoded by mobile group I introns are highly specific DNases that induce a
      double-strand break near the site to which the intron moves. I-PpoI from the acellular slime
      mold Physarum polycephalum mediates the mobility of intron 3 (Pp LSU3) in the extrachromosomal
      nuclear ribosomal DNA of this organism. We showed previously that cleavage by I-PpoI creates a
      four-base staggered cut near the point of intron insertion. We have now characterized several
      further properties of the endonuclease. As determined by deletion analysis, the minimal target
      site recognized by I-PpoI was a sequence of 13 to 15 bp spanning the cleavage site. The
      purified protein behaved as a globular dimer in sedimentation and gel filtration. In gel
      mobility shift assays in the presence of EDTA, I-PpoI formed a stable and specific complex
      with DNA, dissociating with a half-life of 45 minutes. By footprinting and interference assays
      with methidiumpropyl-EDTA-intron(II), I-PpoI contacted a 22-to 24-bp stretch of DNA. The
      endonuclease protected most of the purines found in both the major and minor grooves of the
      DNA helix from modification by dimethylsulfate (DMS). However, the reactivity to DMS was
      enhanced at some purines, suggesting that binding leads to a conformational change in the DNA.
      The pattern of DMS protection differed fundamentally in the two partially symmetrical halves
      of the recognition sequence.
AU  - Ellison EL
AU  - Vogt VM
PT  - Journal Article
TA  - Mol. Cell. Biol.
JT  - Mol. Cell. Biol.
SO  - Mol. Cell. Biol. 1993 13: 7531-7539.

PMID- 12503319
VI  - 33
DP  - 2002
TI  - Restriction enzyme recognition sequence search program.
PG  - 1322-1326
AB  - A critical and difficult part of characterizing restriction enzymes and methylases is the
      identification of recognition sequences.  To simplify this process, we have developed a
      plasmid transformation method along with a computer program named RM search that determines
      the exact recognition sequences for given restriction and modification systems.
AU  - Ellrott KP
AU  - Kasarjian JKA
AU  - Jiang T
AU  - Ryu J
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 2002 33: 1322-1326.

PMID- 28572320
VI  - 5
DP  - 2017
TI  - Complete Genome Sequencing of Streptomyces sp. Strain MOE7, Which Produces an Extracellular Polysaccharide with Antioxidant and Antitumor Activities.
PG  - e00442-17
AB  - Streptomyces sp. strain MOE7 is a Gram-positive filamentous bacterium isolated from
      agricultural soil in Columbia, Missouri, USA. Strain MOE7 produces an
      extracellular polysaccharide with antioxidant and antitumor activities. Through
      PacBio RSII sequencing, the MOE7 genome was found to be a linear chromosome of
      8,399,509 bp with 6,782 protein-coding sequences.
AU  - Elnahas MO
AU  - De Leon KB
AU  - Amin MA
AU  - Hussein MMD
AU  - Ali AE
AU  - Wall JD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00442-17.

PMID- 25540012
VI  - 79
DP  - 2014
TI  - Increasing DNA substrate specificity of the EcoDam DNA-(adenine N-6)-methyltransferase by site-directed mutagenesis.
PG  - 1262-1266
AB  - DNA methylation catalyzed by DNA methyltransferases (MTases) is widespread in prokaryotes. In
      an attempt to find EcoDam variants with enhanced preference for hemimethylated DNA, the L122,
      P134, and V133 residues were replaced with other amino acids using site directed mutagenesis,
      and the catalytic activity of all variants on unmethylated and hemimethylated substrates was
      studied. Our results showed that, in addition to L122A, the L122S and L122A/V133L EcoDam
      variants were able to sense the methylation status of the 5'-GATC-3' double-stranded target
      recognition site and methylated only hemimethylated DNA.
AU  - Elsawy H
AU  - Chahar S
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 2014 79: 1262-1266.

PMID- 25540012
VI  - 79
DP  - 2014
TI  - Increasing DNA substrate specificity of the EcoDam DNA-(adenine N-6)-methyltransferase by site-directed mutagenesis.
PG  - 1262-1266
AB  - DNA methylation catalyzed by DNA methyltransferases (MTases) is widespread in prokaryotes. In
      an attempt to find EcoDam variants with enhanced preference for hemimethylated DNA, the L122,
      P134, and V133 residues were replaced with other amino acids using site directed mutagenesis,
      and the catalytic activity of all variants on unmethylated and hemimethylated substrates was
      studied. Our results showed that, in addition to L122A, the L122S and L122A/V133L EcoDam
      variants were able to sense the methylation status of the 5'-GATC-3' double-stranded target
      recognition site and methylated only hemimethylated DNA.
AU  - Elsawy H
AU  - Chahar S
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2014 79: 1262-1266.

PMID- 28982993
VI  - 5
DP  - 2017
TI  - High-Quality Genome Sequence of Bacillus anthracis Strain 14RA5914 Isolated during an Outbreak in Germany in 2014.
PG  - e01002-17
AB  - Bacillus anthracis is a zoonotic agent causing anthrax, a notifiable disease in animals. The
      last anthrax outbreak among cattle in Germany occurred in April 2014
      in Saxony-Anhalt. Here we report a high-quality genome sequence of the Bacillus
      anthracis strain 14RA5914 Dobichau isolated from the spleen of a dead cow.
AU  - Elschner MC
AU  - Busch A
AU  - Schliephake A
AU  - Gaede W
AU  - Zuchantke E
AU  - Tomaso H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01002-17.

PMID- 28280033
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of a Burkholderia pseudomallei Strain Isolated from a Pet Green Iguana in Prague, Czech Republic.
PG  - e01761-16
AB  - Burkholderia pseudomallei was isolated from pus from an abscess of a pet iguana living in a
      private household in Prague, Czech Republic. This paper presents the
      complete genome sequence of B. pseudomallei strain VB976100.
AU  - Elschner MC
AU  - Thomas P
AU  - El-Adawy H
AU  - Mertens K
AU  - Melzer F
AU  - Hnizdo J
AU  - Stamm I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01761-16.

PMID- 27908988
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of a Burkholderia mallei Isolate Originating from a Glanderous Horse from the Kingdom of Bahrain.
PG  - e01296-16
AB  - Burkholderia mallei is a zoonotic agent causing glanders, a notifiable disease in equines.
      During the past decades glanders emerged, and the Kingdom of Bahrain
      reported outbreaks to the World Organization of Animal Health in 2010 and 2011.
      This paper presents the complete genome sequence of the Burkholderia mallei
      strain 11RR2811 Bahrain1.
AU  - Elschner MC
AU  - Thomas P
AU  - Melzer F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01296-16.

PMID- 11493004
VI  - 311
DP  - 2001
TI  - DNA cleavage reactions by type II restriction enzymes that require two copies of their recognition sites.
PG  - 503-514
AB  - Several type II restriction endonucleases interact with two copies of their target sequence
      before they cleave DNA. Three such enzymes,
      NgoMIV, Cfr10I and NaeI, were tested on plasmids with one or two copies
      of their recognition sites, and on catenanes containing two interlinked
      rings of DNA with one site in each ring. The enzymes showed distinct
      patterns of behaviour. NgoMIV and NaeI cleaved the plasmid with two
      sites faster than that with one site and the catenanes at an
      intermediate rate, while Cfr10I gave similar steady-state rates on all
      three substrates. Both Cfr10I and NgoMIV converted the majority of the
      substrates with two sites directly to the products cut at both sites,
      while NaeI cleaved just one site at a time. All three enzymes thus
      synapse two DNA sites through three-dimensional space before cleaving
      DNA. With Cfr10I and NgoMIV, both sites are cleaved in one turnover, in
      a manner consistent with their tetrameric structures, while the
      cleavage of a single site by NaeI indicates that the second site acts
      not as a substrate but as an activator, as reported previously. The
      complexes spanning two sites have longer lifetimes on catenanes with
      one site in each ring than on circular DNA with two sites, which
      indicates that the catenanes have more freedom for site juxtaposition
      than plasmids with sites in cis.
AU  - Embleton ML
AU  - Siksnys V
AU  - Halford SE
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2001 311: 503-514.

PMID- 15123420
VI  - 339
DP  - 2004
TI  - Dynamics of DNA loop capture by the Sfil restriction endonuclease on supercoiled and relaxed DNA.
PG  - 53-66
AB  - The SfiI endonuclease is a prototype for DNA looping. It binds two copies of its recognition
      sequence and, if Mg2+ is present, cuts both
      concertedly. Looping was examined here on supercoiled and relaxed forms
      of a 5.5 kb plasmid with three SfiI sites: sites 1 and 2 were separated
      by 0.4 kb, and sites 2 and 3 by 2.0 kb. SfiI converted this plasmid
      directly to the products cut at all three sites, though DNA species
      cleaved at one or two sites were formed transiently during a burst
      phase. The burst revealed three sets of doubly cut products,
      corresponding to the three possible pairings of sites. The equilibrium
      distribution between the different loops was evaluated from the burst
      phases of reactions initiated by adding MgCl2 to SfiI bound to the
      plasmid. The short loop was favored over the longer loops, particularly
      on supercoiled DNA. The relative rates for loop capture were assessed
      after adding SfiI to solutions containing the plasmid and MgCl2. On
      both supercoiled and relaxed DNA, the rate of loop capture across 0.4
      kb was only marginally faster than over 2.0 kb or 2.4 kb. The relative
      strengths and rates of looping were compared to computer simulations of
      conformational fluctuations in DNA. The simulations concurred broadly
      with the experimental data, though they predicted that increasing site
      separations should cause a shallower decline in the equilibrium
      constants than was observed but a slightly steeper decline in the rates
      for loop capture. Possible reasons for these discrepancies are
      discussed.
AU  - Embleton ML
AU  - Vologodskii AV
AU  - Halford SE
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2004 339: 53-66.

PMID- 10369761
VI  - 289
DP  - 1999
TI  - Specificity from the synapsis of DNA elements by the SfiI endonuclease.
PG  - 785-797
AB  - The synapsis of DNA sites is a prerequisite for the reactions of many proteins that act at
      specific DNA sequences. The requirement for synapsis was investigated by analysing the
      reactions of SfiI, a tetrameric restriction enzyme that cleaves DNA only after interacting
      with two recognition sites. In the presence of Mg2+, oligonucleotide duplexes with the cognate
      recognition sequence were cleaved rapidly, with cooperative kinetics, while non-cognate
      duplexes were not cleaved. In the absence of Mg2+, the primary complex formed by SfiI with
      cognate DNA contained two duplexes synapsed by the tetramer: a secondary complex containing
      one duplex was seen only at elevated SfiI concentrations. In contrast, the principal complex
      with non-cognate DNA contained one duplex bound to SfiI. Pairs of non-cognate duplexes, or one
      cognate and one non-cognate duplex, generally failed to form synaptic complexes. On adding
      Mg2+to complexes with cognate DNA, cleavage occurred much more rapidly in the synaptic complex
      than in the secondary complex. DNA synapsis thus acts to enhance the specificity of SfiI for
      its recognition sequence, by demanding two cognate sites for a catalytically active complex
      and by excluding non-cognate sites from the synaptic complex.
AU  - Embleton ML
AU  - Williams SA
AU  - Watson MA
AU  - Halford SE
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1999 289: 785-797.

PMID- 1475202
VI  - 20
DP  - 1992
TI  - A group I intron in the small subunit ribosomal RNA gene from Naegleria andersoni ssp. andersoni strain PPMFB-6.
PG  - 6411
AB  - PCR reactions designed to amplify the entire small subunit (SSU) ribosomal RNA gene from
      Naegleria species for phylogenetic analyses, demonstrated a single band of approximately 2 kb
      in most species but a band of approximately 3.2 kb in strains of Naegleria andersoni,
      Naegleria andersoni ssp. andersoni and Naegleria australiensis ssp. italica.  The extra length
      in N.andersoni spp. andersoni strain PPMFB-6 is due to an insertion of approximately 1277 base
      pairs in the coding sequence of the rRNA gene.  The insertion is sited near the tip of helix
      19 immediately prior to the conserved SSU rRNA sequence CC-AG.  Extraction and sizing of total
      rRNA by gel electrophoresis revealed that the insertion was removed in vivo to produce a
      mature SSU rRNA of the same size as strains lacking the insertion in their SSU gene.  The
      insertion in N.andersoni ssp. andersoni was amplified and directly sequenced using a linear
      PCR reaction.  Sequence analysis revealed that it contains motifs which identify it as a group
      I intron.  Thus, the short sequences P, Q, R and S, which represent the conserved core
      structure of group I introns, are all present and they occur in that order.  The intron also
      contains a long open reading frame situated between R and S, which codes for a putative
      protein of unknown function and containing 245 amino acids.  Group I introns are rare in
      nuclear SSU rRNA genes and have hitherto only been reported in Ustilago maydis, Pneumocytis
      carini and Ankistrodesmus stipitatus.  The introns in these taxa are all small (394-480
      bases), they do not contain long open reading frames, and they are inserted at different
      positions in the SSU rRNA gene.  Furthermore, Naegleria branches at a point in the eukaryote
      phylogenetic tree which is much deeper than these taxa.  Thus, our observation significantly
      extends the phylogenetic range of group I introns in Eukaryote nuclear SSU genes.
AU  - Embley TM
AU  - Dyal P
AU  - Kilvington S
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 6411.

PMID- 11282624
VI  - 67
DP  - 2001
TI  - Molecular characterization of a theta replication plasmid and its use for development of a two-component food-grade cloning system for Lactococcus lactis.
PG  - 1700-1709
AB  - pCD4, a small, highly stable theta-replicating lactococcal plasmid, was
      used to develop a food-grade cloning system. Sequence analysis revealed
      five open reading frames and two putative cis-acting regions. None appears
      to code for undesirable phenotypes with regard to food applications.
      Functional analysis of the replication module showed that only the
      cis-acting ori region and the repB gene coding for the replication
      initiator protein were needed for the stable replication and maintenance
      of pCD4 derivatives in Lactococcus lactis. A two-component food-grade
      cloning system was derived from the pCD4 replicon. The vector pVEC1, which
      carries the functional pCD4 replicon, is entirely made up of L. lactis DNA
      and has no selection marker. The companion pCOM1 is a repB-deficient pCD4
      derivative that carries an erythromycin resistance gene as a dominant
      selection marker. The pCOM1 construct can only replicate in L. lactis if
      trans complemented by the RepB initiator provided by pVEC1. Since only the
      cotransformants that carry both pVEC1 and pCOM1 can survive on plates
      containing erythromycin, pCOM1 can be used transiently to select cells
      that have acquired pVEC1. Due to the intrinsic incompatibility between
      these plasmids, pCOM1 can be readily cured from the cells grown on an
      antibiotic-free medium after the selection step. The system was used to
      introduce a phage resistance mechanism into the laboratory strain MG1363
      of L. lactis and two industrial strains. The introduction of the antiphage
      barrier did not alter the wild-type plasmid profile of the industrial
      strains. The phenotype was stable after 100 generations and conferred an
      effective resistance phenotype against phages of the 936 and c2 species.
AU  - Emond E
AU  - Ee EL
AU  - Drolet G
AU  - Moineau S
AU  - LaPointe G
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2001 67: 1700-1709.

PMID- 9097424
VI  - 63
DP  - 1997
TI  - Phenotypic and genetic characterization of the bacteriophage abortive infection mechanism AbiK from Lactococcus lactis.
PG  - 1274-1283
AB  - The natural plasmid pSRQ800 isolated from Lactococcus lactis subsp. lactis W1 conferred strong
      phage resistance against small isometric phages of the 936 and P335 species when introduced
      into phage-sensitive L. lactis strains.  It had very limited effect on prolate phages of the
      c2 species.  The phage resistance mechanism encoded on pSRQ800 is a temperature-sensitive
      abortive infection system (Abi).  Plasmid pSRQ800 was mapped, and the Abi genetic determinant
      was localized on a 4.5-kb EcoRI fragment.  Cloning and sequencing of the 4.5-kb fragment
      allowed the identification of two large open reading frames.  Deletion mutants showed that
      only orf1 was needed to produce the Abi phenotype.  orf1 (renamed abiK) coded for a predicted
      protein of 599 amino acids (AbiK) with an estimated molecular size of 71.4 kDa and a pI of
      7.98.  DNA and protein sequence alignment programs found no significant homology with
      databases.  However, a database query based on amino acid composition suggested that AbiK
      might be in the same protein family as AbiA.  No phage DNA replication nor phage structural
      protein production was detected in infected AbiK+ L. lactis cells.  This system is believed to
      act at or prior to phage DNA replication.  When cloned into a high-copy vector, AbiK
      efficiency increased 100-fold.  AbiK provides another powerful tool that can be used in
      controlling phages during lactococcal fermentations.
AU  - Emond E
AU  - Holler BJ
AU  - Boucher I
AU  - Vandenbergh PA
AU  - Vedamuthu ER
AU  - Kondo JK
AU  - Moineau S
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1997 63: 1274-1283.

PMID- 25480167
VI  - 175
DP  - 2014
TI  - Variants of a genomic island in Aeromonas salmonicida subsp. salmonicida link isolates with their geographical origins.
PG  - 68-76
AB  - Aeromonas salmonicida subsp. salmonicida is a fish pathogen. Analysis of its
      genomic characteristics is required to determine the worldwide distribution of
      the various populations of this bacterium. Genomic alignments between the 01-B526
      pathogenic strain and the A449 reference strain have revealed a 51-kb chromosomal
      insertion in 01-B526. This insertion (AsaGEI1a) has been identified as a new
      genomic island (GEI) bearing prophage genes. PCR assays were used to detect this
      GEI in a collection of 139 A. salmonicida subsp. salmonicida isolates. Three
      forms of this GEI (AsaGEI1a, AsaGEI1b, AsaGEI2a) are now known based on this
      analysis and the sequencing of the genomes of seven additional isolates. A new
      prophage (prophage 3) associated with AsaGEI2a was also discovered. Each GEI
      appeared to be strongly associated with a specific geographic region. AsaGEI1a
      and AsaGEI2a were exclusively found in North American isolates, except for one
      European isolate bearing AsaGEI2a. The majority of the isolates bearing AsaGEI1b
      or no GEI were from Europe. Prophage 3 has also a particular geographic
      distribution and was found only in North American isolates. We demonstrated that
      A. salmonicida subsp. salmonicida possesses unsuspected elements of genomic
      heterogeneity that could be used as indicators to determine the geographic
      origins of isolates of this bacterium.
AU  - Emond-Rheault JG
AU  - Vincent AT
AU  - Trudel MV
AU  - Brochu F
AU  - Boyle B
AU  - Tanaka KH
AU  - Attere SA
AU  - Jubinville E
AU  - Loch TP
AU  - Winters AD
AU  - Faisal M
AU  - Frenette M
AU  - Derome N
AU  - Charette SJ
PT  - Journal Article
TA  - Vet. Microbiol.
JT  - Vet. Microbiol.
SO  - Vet. Microbiol. 2014 175: 68-76.

PMID- 29518238
VI  - 46
DP  - 2018
TI  - The DNMT3A R882H mutant displays altered flanking sequence preferences.
PG  - 3130-3139
AB  - The DNMT3A R882H mutation is frequently observed in acute myeloid leukemia (AML). It is
      located in the subunit and DNA binding interface of DNMT3A and has been
      reported to cause a reduction in activity and dominant negative effects. We
      investigated the mechanistic consequences of the R882H mutation on DNMT3A showing
      a roughly 40% reduction in overall DNA methylation activity. Biochemical assays
      demonstrated that R882H does not change DNA binding affinity, protein stability
      or subnuclear distribution of DNMT3A. Strikingly, DNA methylation experiments
      revealed pronounced changes in the flanking sequence preference of the
      DNMT3A-R882H mutant. Based on these results, different DNA substrates with
      selected flanking sequences were designed to be favored or disfavored by R882H.
      Kinetic analyses showed that the R882H favored substrate was methylated by R882H
      with 45% increased rate when compared with wildtype DNMT3A, while methylation of
      the disfavored substrate was reduced 7-fold. Our data expand the model of the
      potential carcinogenic effect of the R882H mutation by showing CpG site specific
      activity changes. This result suggests that R882 is involved in the indirect
      readout of flanking sequence preferences of DNMT3A and it may explain the
      particular enrichment of the R882H mutation in cancer patients by revealing
      mutation specific effects.
AU  - Emperle M
AU  - Rajavelu A
AU  - Kunert S
AU  - Arimondo PB
AU  - Reinhardt R
AU  - Jurkowska RZ
AU  - Jeltsch A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2018 46: 3130-3139.

PMID- 26517665
VI  - 110
DP  - 2015
TI  - Genomic analysis of a nontoxigenic, invasive Corynebacterium diphtheriae strain from Brazil.
PG  - 817-819
AB  - We report the complete genome sequence and analysis of an invasive
      Corynebacterium diphtheriae strain that caused endocarditis in Rio de Janeiro,
      Brazil. It was selected for sequencing on the basis of the current relevance of
      nontoxigenic strains for public health. The genomic information was explored in
      the context of diversity, plasticity and genetic relatedness with other
      contemporary strains.
AU  - Encinas F
AU  - Marin MA
AU  - Ramos JN
AU  - Vieira VV
AU  - Mattos-Guaraldi AL
AU  - Vicente AC
PT  - Journal Article
TA  - Memorias do Instituto Oswaldo Cruz
JT  - Memorias do Instituto Oswaldo Cruz
SO  - Memorias do Instituto Oswaldo Cruz 2015 110: 817-819.

PMID- 2985609
VI  - 260
DP  - 1985
TI  - The DNA restriction endonuclease of Escherichia coli B.  I. Studies of the DNA translocation and the ATPase activities.
PG  - 5720-5728
AB  - Electron microscopic examination of DNA intermediates formed by the restriction
      endonuclease of Escherichia coli B revealed supercoiled loops that are
      presumably formed during an ATP-dependent DNA translocation process in which
      the enzyme remains bound to the recognition site while tracking along the DNA
      helix to a cleavage site.  The rate of DNA translocation during this process is
      at least 5000 base pairs/min at 37C.  Even after all cleavages have been
      completed, complexes are seen that contain terminal loops or loop plus tail
      structures.  During this later phase of the reaction, ATP is hydrolyzed at a
      rate which is dependent upon the size of the largest possible loop (or loop
      plus tail); this ATP hydrolysis can be terminated by one double-strand cleavage
      within the loop region between the recognition site and the terminus.  To
      explain these results, it is hypothesized that after cleavage the enzyme cycles
      between a tracking (and possibly backtracking) mode which is fueled by ATP
      hydrolysis and a relatively long static period in which ATP hydrolysis does not
      occur.  While tracking, the enzyme would be bound both to the recognition site
      and to a distal site but, while static, the enzyme would be bound only at the
      recognition site of nonlooped molecules.  This postnuclease phase of the
      reaction is hypothesized to reflect a reaction whereby the enzyme initially
      scans DNA molecules before making a strand cleavage.
AU  - Endlich B
AU  - Linn S
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1985 260: 5720-5728.

PMID- 2985610
VI  - 260
DP  - 1985
TI  - The DNA restriction endonuclease of Escherichia coli B.  II.  Further studies of the structure of DNA intermediates and products.
PG  - 5729-5738
AB  - The DNA intermediates and final products formed by the Type I restriction
      endonuclease, EcoB, were further characterized.  DNA cleaved on only one strand
      (hemi-restricted DNA) contains gaps of approximately 70-100 nucleotides, while
      the fully restricted products contain 3'-single-stranded tails averaging
      approximately 70-100 nucleotides for each strand cleaved.  The gaps and tails
      are formed with the release of an equal number of nucleotides as small
      oligonucleotides that are soluble in acid.  After purification, neither the
      hemi-restricted nor the fully restricted DNAs are cleaved again by EcoB.  There
      is no apparent specificity for which strand of a duplex is initially cleaved by
      EcoB, nor is there specificity with respect to the composition of the
      3'-terminal nucleotide formed on the DNA or the 3'- or 5'-terminal nucleotides
      of the acid-soluble oligonucleotides released during DNA cleavage.  The
      structure formed at the 5' terminus of the DNA product which blocks
      phosphorylation by T4 polynucleotide kinase remains unknown, but its removal
      with phage lambda exonuclease allows at least some reutilization of recognition
      sites by EcoB as well as phosphorylation of the newly formed 5' termini.  To
      explain the complex mechanism of this enzyme, it is suggested that the
      unidentified 5'-tails prevent wasteful rerestriction from occurring, whereas
      the 3'-single-stranded tails create DNA which, when nonhomologous to
      chromosomal DNA, cannot be rescued because such tails are not a substrate for
      DNA polymerases.  However, when homologous chromosomal DNA exists, the randomly
      cleaved large fragments with these tails can easily be assimilated by
      recA-mediated genetic recombination, thus stimulating DNA exchange between
      related organisms.
AU  - Endlich B
AU  - Linn S
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1985 260: 5729-5738.

PMID- Not carried by PubMed...
VI  - 14
DP  - 1981
TI  - Type I restriction enzymes.
PG  - 137-156
AB  - Many bacteria contain enzymatic systems that act to restrict the expression of
      foreign DNA introduced through phage infection, conjugation, or transformation.
      This phenomenon of host-controlled specificity was first described in the
      early 1950s by Luria and Human, who studied T-even phages, and by Bertani and
      Weigle, who investigated the restriction of the host ranges of lambda and P2
      phages.  It was observed that a particular phage could have widely different
      efficiencies of infection on several closely related bacterial strains, but
      when phages that had initially plated with low efficiency were replated on the
      same bacterial strain, the efficiency of infection increased dramatically.
      This modification of host range was not a hereditary genetic adaptation,
      however, since it could be lost by subsequent propagation of the phage in
      another bacterial strain.  It was subsequently shown that the host-specificity
      system described by Luria and Human was unique to the T-even phages, whereas
      the system described by Bertani and Weigle was more widespread.  The type I
      restriction-modification systems described in this review are of the latter,
      more general, class.  Modification of the T-even phages involves the
      glycosylation of hydroxymethylcytosine residues, and has been reviewed
      elsewhere.  Further investigation of lambda phage host specificity by Arber and
      coworkers led to the hypothesis of a molecular mechanism in which special DNA
      sequences are acted upon by appropriate restriction and modification enzymnes.
      Foreign DNA that happens to contain such specific sequences is cleaved by a
      restriction endonuclease upon entering the cell.  When these same sequence
      exist in the bacterium's own DNA, however, they are protected by a modification
      methylase that imparts methylase that imparts methyl groups to bases within the
      sequences, rendering them resistant to endonuclease action.  This hypothesis
      was substantiated in the late 1960s when restriction endonucleases from the E.
      coli strains K and B were discovered and isolated in highly purified form.
      These nucleases were genetically identified as the restriction enzymes and
      observed to be complex in terms of cofactor requirements, subunit composition,
      and interactions with the DNA substrate.  Other restriction enzymes were soon
      isolated from other bacteria such as Haemophilus influenzae.  Many of these
      endonucleases have distinctly different properties from those of the E. coli B
      and K nucleases, and are distinguished as two additional types of restriction
      endonucleases.  Whether all of these latter enzymes function in situ in a
      restriction capacity is not clear.
AU  - Endlich B
AU  - Linn S
PT  - Journal Article
TA  - The Enzymes
JT  - The Enzymes
SO  - The Enzymes 1981 14: 137-156.

PMID- 15202882
VI  - 69
DP  - 2004
TI  - Design and synthesis of photochemically controllable restriction endonuclease BamHI by manipulating the salt-bridge network in the dimer  interface.
PG  - 4292-4298
AB  - The strategy for the design of photochemically controllable enzymes by manipulating the dimer
      interface is described. Employing a restriction
      endonuclease BamHI, the selective incorporation of amino acids having a
      photoremovable 6-nitroveratryl group into the specific position
      (Lys132) in the dimer interface of the BamHI mutant (H133A) was
      performed. The activity of the photofunctionalized BamHI mutant was
      significantly suppressed, and the following photoirradiation induced
      the recovery of the activity. In addition, uncaging of the
      6-nitroveratryl group introduced to Lys132 did not seriously reduce the
      catalytic activity and affinity for the substrate. These results
      indicate that the activity of the enzyme can be effectively regulated
      by caging and uncaging of the specific amino acid in the dimer
      interface using the photoremovable group.
AU  - Endo M
AU  - Nakayama K
AU  - Majima T
PT  - Journal Article
TA  - J. Org. Chem.
JT  - J. Org. Chem.
SO  - J. Org. Chem. 2004 69: 4292-4298.

PMID- 409849
VI  - 114
DP  - 1977
TI  - Analysis of Drosophila melanogaster Satellite IV with restriction endonuclease MboII.
PG  - 441-449
AB  - The products of digestion of Drosophila melanogaster satellite IV DNA with
      restriction endonuclease MboII have been analysed and found to be consistent
      with a repeating pentamer sequence (A-G-A-A-G)n for satellite IV.  More than
      95% of the satellite DNA is digested to fragments less than 25 base-pairs in
      length, suggesting that the DNA sequence is highly conserved.
AU  - Endow SA
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1977 114: 441-449.

PMID- 875030
VI  - 112
DP  - 1977
TI  - Two restriction-like enzymes from Xanthomonas malvacearum.
PG  - 521-529
AB  - Two sequence-specific endonucleases, XmaI and XmaII, have been purified from
      Xanthomonas malvacearum.  XmaI makes cuts in bacteriophage lambda and
      adenovirus-2 DNA identical with those produced by SmaI, a restriction-like
      enzyme previously isolated from Serratia marcescens Sb.XmaI cleaves within the
      sequence 5'-C^-C-C-G-G-G-3' 3'-G-G-G-C-G-^C-5' at the sites indicated by the
      arrows.  XmaII is an isoschizomer of the specific endonuclease PstI previously
      isolated from Providencia stuartii.
AU  - Endow SA
AU  - Roberts RJ
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1977 112: 521-529.

PMID- 26044416
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Biowarfare Simulant Bacillus atrophaeus Strain 930029.
PG  - e00491-15
AB  - We report here the draft genome sequence of Bacillus atrophaeus strain 930029. Strain 930029
      shows evidence of drift, based on a comparison to the corresponding
      source strain publicly available today.
AU  - Eng C
AU  - Blouin Y
AU  - Ding N
AU  - Larigauderie G
AU  - Ramisse V
AU  - Pujol C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00491-15.

PMID- 25977435
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequence and Annotation of Octopine-Utilizing Pseudomonas kilonensis (Previously P. fluorescens) Strain 1855-344.
PG  - e00463-15
AB  - Here, we report the whole-genome sequence and annotation of Pseudomonas kilonensis 1855-344
      (previously known as P. fluorescens 1855-344). The genome
      contains an octopine oxidase gene cluster consistent with the ability to utilize
      octopine. A biosynthetic gene cluster was identified for mangotoxin and
      aryl-polyene using the antiSMASH server.
AU  - Eng WW
AU  - Gan HM
AU  - Gan HY
AU  - Hudson AO
AU  - Savka MA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00463-15.

PMID- 3030192
VI  - 53
DP  - 1987
TI  - Plasmid transformation of Streptomyces tendae after heat attenuation of restriction.
PG  - 1-3
AB  - Streptomyces tendae ATCC 31160 produces nikkomycin, a fungicide and insecticide
      that inhibits chitin synthases.  Exposure of S. tendae protoplasts to 50C for
      30 min is required for transformation (10-2 thiostrepton-resistant
      transformants per microgram of DNA) with plasmid pIJ702 or pIJ680 from
      Streptomyces lividans.  pIJ702 and pIJ680 DNA isolated from the S. tendae
      transformants is efficient (10-6 to 10-7 transformants per microgram DNA) in
      subsequent transformations of S. tendae protoplasts generated at 30C.  PstI
      fails to cut the single PstI site in pIJ702 and cuts only one of the two PstI
      sites in pIJ680 DNA isolated from S. tendae transformants.  Digests of plasmid
      DNA mixtures showed that plasmid DNA from S. tendae does not inhibit PstI
      activity.  pIJ702 and pIJ680 DNA from S. tendae transformants was used to
      transform S. lividans to show that plasmid DNA remains unchanged, except for
      modification at some PstI sites in S. tendae, as a consequence of passage
      through S. tendae.  The DNA modification is lost when S. lividans is
      transformed with plasmid DNA from S. tendae transformants.  Since S. tendae
      modifies only some PstI sites, it appears the modification (presumably
      restriction activity also) activity in S. tendae recognizes a sequence that
      includes or overlaps the PstI hexanucleotide recognition sequence.
AU  - Engel P
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1987 53: 1-3.

PMID- 25527542
VI  - 81
DP  - 2015
TI  - Gut symbionts from distinct hosts exhibit genotoxic activity via divergent colibactin biosynthetic pathways.
PG  - 1502-1512
AB  - Secondary metabolites produced by nonribosomal peptide synthetase (NRPS) or
      polyketide synthase (PKS) pathways are chemical mediators of microbial
      interactions in diverse environments. However, little is known about their
      distribution, evolution, and functional roles in bacterial symbionts associated
      with animals. A prominent example is "colibactin", a largely unknown family of
      secondary metabolites produced by Escherichia coli via a hybrid NRPS-PKS
      biosynthetic pathway, inflicting DNA damage upon eukaryotic cells and
      contributing to colorectal cancer and tumor formation in the mammalian gut. Thus
      far, homologs of this pathway have only been found in closely related
      Enterobacteriaceae, while a divergent variant of this gene cluster was recently
      discovered in a marine alphaproteobacterial Pseudovibrio strain. Herein, we
      sequenced the genome of Frischella perrara PEB0191, a bacterial gut symbiont of
      honey bees, and identified a homologous colibactin biosynthetic pathway related
      to those found in Enterobacteriaceae. We show that the colibactin genomic island
      (GI) has conserved gene synteny and biosynthetic module architecture across F.
      perrara, Enterobacteriaceae and the Pseudovibrio strain. Comparative metabolomics
      analyses of F. perrara and E. coli further reveal that these two bacteria produce
      related colibactin pathway-dependent metabolites. Finally, we demonstrate that F.
      perrara, like E. coli, causes DNA damage in eukaryotic cells in vitro in a
      colibactin pathway-dependent manner. Together, these results support that
      divergent variants of the colibactin biosynthetic pathway are widely distributed
      among bacterial symbionts, producing related secondary metabolites and likely
      endowing its producer with functional capabilities important for diverse
      symbiotic associations.
AU  - Engel P
AU  - Vizcaino MI
AU  - Crawford JM
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2015 81: 1502-1512.

PMID- 28684575
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Escherichia coli K-12 (ATCC 29425).
PG  - e00574-17
AB  - A draft genome sequence for Escherichia coli ATCC 29425 was investigated. The size of the
      genome was 4,608,319 bp, with an observed G+C content of 50.68%. This
      assembly consisted of 80 contigs, with an average coverage of 122.2x, including
      one contig representative of the complete genome for the temperate phage P1.
AU  - Engelbrecht KC
AU  - Putonti C
AU  - Koenig DW
AU  - Wolfe AJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00574-17.

PMID- 
VI  - 8
DP  - 2003
TI  - iceA genotypes may play a role in acquiring metronidazole resistance in Helicobacter pylori.
PG  - 356
AB  - Homologous recombination contributes to the extraordinary genetic diversity of Helicobacter
      pylori.  Recently, evidence of in vivo horizontal gene transfer was detected in the rdxA gene,
      which is involved in metronidazole resistance.  This bacterium possesses a large number of
      restriction - modification systems that afford protection against transforming DNA, apparently
      regulating the natural transformation of H. pylori.  The newly discovered virulence factor
      icaA exists in two variants, iceA1 which encodes an NlaIIIR homologue restriction enzyme and
      iceA2.  In this study, we evaluated the relationship between the metronidazole resistance and
      iceA genotypes in 76 H. pylori strains.  We determined metronidazole MIC values of H. pylori
      strains by agar dilution.  Following DNA purification iceA genotypes of H. pylori strains were
      determined by using PCR.  Thirty-eight (50.0%) out of 76 H. pylori strains were found
      metronidazole resistant.  MIC50 was 8 and MIC90 value was 128 ug/ml.  Forty-eight (63.2%) and
      19 (25.0%) of the strains were typed as iceA1 and iceA2, respectively.  Whereas, 9 (11.8%)
      strains yielded PCR products of unexpected length and typed as iceA1a/2a.  No significant
      difference was found between metronidazole MIC values of iceA1 and iceA2 strains.
      Metronidazole MIC values of iceA1a/2a strains were marginally lower than iceA2 strains
      (Mann-Whitney p=0.075).  We conclude that, restriction-modification systems may play an
      important role in acquiring metronidazole resistance in H. pylori.  The organization of iceA
      locus in iceA1a/2a strains should be further evaluated.
AU  - Engin D
AU  - Hascelik G
PT  - Journal Article
TA  - Helicobacter
JT  - Helicobacter
SO  - Helicobacter 2003 8: 356.

PMID- 11254386
VI  - 307
DP  - 2001
TI  - The energetics of the interaction of BamHI endonuclease with its recognition site GGATCC.
PG  - 619-636
AB  - The interaction of BamHI endonuclease with DNA has been studied crystallographically, but has
      not been characterized rigorously in solution. The enzyme binds in solution as a homodimer to
      its recognition site GGATCC. Only six base-pairs are directly recognized, but binding affinity
      (in the absence of the catalytic cofactor Mg(2+)) increases 5400-fold as oligonucleotide
      length increases from 10 to 14 bp. Binding is modulated by sequence context outside the
      recognition site, varying about 30-fold from the best (GTG or TAT) to the worst (CGG)
      flanking triplets. BamHI, EcoRI and EcoRV endonucleases all have different context
      preferences, suggesting that context affects binding by influencing the free energy levels of
      the complexes rather than that of the free DNA. Ethylation interference footprinting in the
      absence of divalent metal shows a localized and symmetrical pattern of phosphate contacts,
      with strong contacts at NpNpNpGGApTCC. In the presence of Mg(2+), first-order cleavage rate
      constants are identical in the two GGA half-sites, are the same for the two nicked
      intermediates and are unaffected by substrate length in the range 10-24 bp. DNA binding is
      strongly enhanced by mutations D94N, E111A or E113K, by binding of Ca(2+) at the active site,
      or by deletion of the scissile phosphate GpGATCC, indicating that a cluster of negative
      charges at the catalytic site contributes at least 3-4 kcal/mol of unfavorable binding free
      energy. This electrostatic repulsion destabilizes the enzyme-DNA complex and favors metal ion
      binding and progression to the transition state for cleavage.
AU  - Engler LE
AU  - Sapienza P
AU  - Dorner LF
AU  - Kucera R
AU  - Schildkraut I
AU  - Jen-Jacobson L
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2001 307: 619-636.

PMID- 9193002
VI  - 269
DP  - 1997
TI  - Specific binding by EcoRV endonuclease to its DNA recognition site GATATC.
PG  - 82-101
AB  - Restriction endonuclease EcoRV has been reported to be unable to distinguish its specific DNA
      site, GATATC, from non-specific DNA sites in the absence of the catalytic cofactor Mg2+, and
      thus to exercise sequence specificity solely in the catalytic step.  In contrast, we show here
      that under appropriate conditions of pH and salt concentration, specific complexes with
      oligonucleotides containing the GATATC site can be detected by either filter-binding or
      gel-retardation.  Equilibrium binding constants (KA) are easily measured by both direct
      equilibrium and equilibrium-competition methods.  The preference for "specific" over
      "non-specific" binding at pH 7 in the absence of divalent cations is about 1000-fold (per mole
      of oligonucleotide) or 12,000-fold (per mole of binding sites).  Ethylation-interference
      footprinting shows that the "specific" complex includes strong contacts to the phosphate
      groups GpApTpApTC.  Specific DNA binding is strongly pH-dependent, decreasing about 15-fold
      for each increase of one pH unit above pH 6, but non-specific binding is not; thus, binding
      specificity decreases with increasing pH.  Gel retardation and filter-binding at pH values
      less than 7 yielded essentially identical values of KA for specific-site binding, but at pH>7
      gel retardation significantly underestimates KA.  Specific-site binding is stimulated about
      700-fold by Ca2+ (not a cofactor for cleavage), but with non-cleavable 3'-phosphorothioate
      and 4'-thiodeoxyribose derivatives whose response to Ca2+ is similar to that of the parent
      oligonucleotide, Mg2+ stimulates binding only fourfold and twofold, respectively.  Thus,
      binding specificity is not dramatically enhanced by Mg2+.  Taking into account discrimination
      in binding and in the first-order rate constant for phosphodiester bond scission, the overall
      discrimination exercised against the incorrect site GTTATC is about 10^7-fold.  EcoRV
      endonuclease is thus not a "new paradigm" for site-specific interaction without binding
      specificity, but like other type II restriction endonucleases achieves sequence specificity by
      discriminating both in DNA binding and in catalysis.
AU  - Engler LE
AU  - Welch KK
AU  - Jen-Jacobson L
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1997 269: 82-101.

PMID- 20633563
VI  - 266
DP  - 2010
TI  - Restriction-modification systems and bacteriophage invasion: Who wins?
PG  - 550-559
AB  - The success of a phage that infects a bacterial cell possessing a restriction-modification
      (R-M) system depends on the activities of the
      host methyltransferase and restriction endonuclease, and the number of
      susceptible sites in the phage genome. However, there is no model
      describing this dependency and linking it to observable parameters such
      as the fraction of surviving cells under excess phage, or probability
      of plating at low amount of phages. We model the phage infection of a
      cell with a R-M system as a pure birth process with a killing state. We
      calculate the transitional probabilities and the stationary
      distribution for this process. We generalize the model developed for a
      single cell to the case of multiple identical cells invaded by a
      Poisson-distributed number of phages. The R-M enzyme activities are
      assumed to be constant, time-dependent, or random. The obtained results
      are used to estimate the ratio of the methyltransferase and
      endonuclease activities from the observed fraction of surviving cells.
AU  - Enikeeva FN
AU  - Severinov KV
AU  - Gelfand MS
PT  - Journal Article
TA  - J. Theor. Biol.
JT  - J. Theor. Biol.
SO  - J. Theor. Biol. 2010 266: 550-559.

PMID- 12771221
VI  - 31
DP  - 2003
TI  - A novel engineered meganuclease induces homologous recombination in yeast and mammalian cells.
PG  - 2952-2962
AB  - Homologous gene targeting is the ultimate tool for reverse genetics, but its use is often
      limited by low efficiency. In a number of recent studies,
      site- specific DNA double-strand breaks (DSBs) have been used to induce
      efficient gene targeting. Engineering highly specific, dedicated DNA
      endonucleases is the key to a wider usage of this technology. In this
      study, we present two novel, chimeric meganucleases, derived from homing
      endonucleases. The first one is able to induce recombination in yeast and
      mammalian cells, whereas the second cleaves a novel (chosen) DNA target
      site. These results are a first step toward the generation of custom
      endonucleases for the purpose of targeted genome engineering.
AU  - Epinat JC
AU  - Arnould S
AU  - Chames P
AU  - Rochaix P
AU  - Desfontaines D
AU  - Puzin C
AU  - Patin A
AU  - Zanghellini A
AU  - Paques F
AU  - Lacroix E
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2003 31: 2952-2962.

PMID- 21705586
VI  - 193
DP  - 2011
TI  - Genome Sequences of the Biotechnologically Important Bacillus megaterium Strains QM B1551 and DSM319.
PG  - 4199-4213
AB  - Bacillus megaterium is deep-rooted in the Bacillus phylogeny, making it an evolutionarily key
      species and of particular importance in understanding
      genome evolution, dynamics, and plasticity in the bacilli. B. megaterium
      is a commercially available, nonpathogenic host for the biotechnological
      production of several substances, including vitamin B(12), penicillin
      acylase, and amylases. Here, we report the analysis of the first complete
      genome sequences of two important B. megaterium strains, the plasmidless
      strain DSM319 and QM B1551, which harbors seven indigenous plasmids. The
      5.1-Mbp chromosome carries approximately 5,300 genes, while QM B1551
      plasmids represent a combined 417 kb and 523 genes, one of the largest
      plasmid arrays sequenced in a single bacterial strain. We have documented
      extensive gene transfer between the plasmids and the chromosome. Each
      strain carries roughly 300 strain-specific chromosomal genes that account
      for differences in their experimentally confirmed phenotypes. B.
      megaterium is able to synthesize vitamin B(12) through an
      oxygen-independent adenosylcobalamin pathway, which together with other
      key energetic and metabolic pathways has now been fully reconstructed.
      Other novel genes include a second ftsZ gene, which may be responsible for
      the large cell size of members of this species, as well as genes for gas
      vesicles, a second beta-galactosidase gene, and most but not all of the
      genes needed for genetic competence. Comprehensive analyses of the global
      Bacillus gene pool showed that only an asymmetric region around the origin
      of replication was syntenic across the genus. This appears to be a
      characteristic feature of the Bacillus spp. genome architecture and may be
      key to their sporulating lifestyle.
AU  - Eppinger M et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4199-4213.

PMID- 16789826
VI  - 2
DP  - 2006
TI  - Who ate whom? Adaptive Helicobacter genomic changes that accompanied a host jump from early humans to large felines.
PG  - e120
AB  - Helicobacter pylori infection of humans is so old that its population genetic structure
      reflects that of ancient human migrations. A closely
      related species, Helicobacter acinonychis, is specific for large felines,
      including cheetahs, lions, and tigers, whereas hosts more closely related
      to humans harbor more distantly related Helicobacter species. This
      observation suggests a jump between host species. But who ate whom and
      when did it happen? In order to resolve this question, we determined the
      genomic sequence of H. acinonychis strain Sheeba and compared it to
      genomes from H. pylori. The conserved core genes between the genomes are
      so similar that the host jump probably occurred within the last 200,000
      (range 50,000-400,000) years. However, the Sheeba genome also possesses
      unique features that indicate the direction of the host jump, namely from
      early humans to cats. Sheeba possesses an unusually large number of highly
      fragmented genes, many encoding outer membrane proteins, which may have
      been destroyed in order to bypass deleterious responses from the feline
      host immune system. In addition, the few Sheeba-specific genes that were
      found include a cluster of genes encoding sialylation of the bacterial
      cell surface carbohydrates, which were imported by horizontal genetic
      exchange and might also help to evade host immune defenses. These results
      provide a genomic basis for elucidating molecular events that allow
      bacteria to adapt to novel animal hosts.
AU  - Eppinger M
AU  - Baar C
AU  - Linz B
AU  - Raddatz G
AU  - Lanz C
AU  - Keller H
AU  - Morelli G
AU  - Gressmann H
AU  - Achtman M
AU  - Schuster SC
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2006 2: e120.

PMID- 23516226
VI  - 1
DP  - 2013
TI  - Whole-Genome Draft Sequences of 26 Enterohemorrhagic Escherichia coli O157:H7 Strains.
PG  - e0013412
AB  - First identified in 1982, Escherichia coli O157:H7 is the dominant enterohemorrhagic serotype
      underlying food-borne human infections in North
      America. Here, we report the genomes of twenty-six strains derived from patients
      and the bovine reservoir. These resources enable detailed whole-genome
      comparisons and permit investigations of genotypic and phenotypic plasticity.
AU  - Eppinger M
AU  - Daugherty S
AU  - Agrawal S
AU  - Galens K
AU  - Sengamalay N
AU  - Sadzewicz L
AU  - Tallon L
AU  - Cebula TA
AU  - Mammel MK
AU  - Feng P
AU  - Soderlund R
AU  - Tarr PI
AU  - Debroy C
AU  - Dudley EG
AU  - Fraser CM
AU  - Ravel J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0013412.

PMID- 19820101
VI  - 191
DP  - 2009
TI  - Draft Genome Sequences of Yersinia pestis Isolates From Natural Foci of Endemic Plague in China.
PG  - 7628-7629
AB  - To gain insights into the evolutionary origin, emergence and pathogenicity of the etiologic
      agent of plague, we have sequenced the genomes of four  Yersinia pestis strains isolated from
      the zoonotic rodent reservoir in  endemic plague foci in China (24). These resources enable
      in-depth studies  of Y. pestis sequence variations, and detailed whole genome comparisons of
      very closely related genomes from the supposed site of the origin and emergence of global
      pandemics of plague.
AU  - Eppinger M
AU  - Guo Z
AU  - Sebastian Y
AU  - Song Y
AU  - Lindler LE
AU  - Yang R
AU  - Ravel J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2009 191: 7628-7629.

PMID- 21421787
VI  - 77
DP  - 2011
TI  - Genome Signatures of Escherichia coli O157:H7 Isolates from the Bovine Host Reservoir.
PG  - 2916-2925
AB  - Cattle comprise a main reservoir of Shiga toxin-producing Escherichia coli
      O157:H7 (STEC). The significant differences in host prevalence,
      transmissibility, and virulence phenotypes among strains from bovine and
      human sources are of major interest to the public health community and
      livestock industry. Genomic analysis revealed divergence into three
      lineages: lineage I and lineage I/II strains are commonly associated with
      human disease, while lineage II strains are overrepresented in the
      asymptomatic bovine host reservoir. Growing evidence suggests that
      genotypic differences between these lineages, such as polymorphisms in
      Shiga toxin subtypes and synergistically acting virulence factors, are
      correlated with phenotypic differences in virulence, host ecology, and
      epidemiology. To assess the genomic plasticity on a genome-wide scale, we
      have sequenced the whole genome of strain EC869, a bovine-associated E.
      coli O157:H7 isolate. Comparative phylogenomic analysis of this key
      isolate enabled us to place accurately bovine lineage II strains within
      the genetically homogenous E. coli O157:H7 clade. Identification of
      polymorphic loci that are anchored both in the chromosomal backbone and
      horizontally acquired regions allowed us to associate bovine genotypes
      with altered virulence phenotypes and host prevalence. This study
      catalogued numerous novel lineage II-specific genome signatures, some of
      which appear to be associated intimately with the altered pathogenic
      potential and niche adaptation within the bovine rumen. The presented
      extended list of polymorphic markers is valuable in the development of a
      robust typing system critical for forensic, diagnostic, and
      epidemiological studies of this emerging human pathogen.
AU  - Eppinger M
AU  - Mammel MK
AU  - Leclerc JE
AU  - Ravel J
AU  - Cebula TA
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2011 77: 2916-2925.

PMID- 24201203
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Fish Pathogen Piscirickettsia salmonis.
PG  - e00926-13
AB  - Piscirickettsia salmonis is a Gram-negative intracellular fish pathogen that has  a
      significant impact on the salmon industry. Here, we report the genome sequence
      of P. salmonis strain LF-89. This is the first draft genome sequence of P.
      salmonis, and it reveals interesting attributes, including flagellar genes,
      despite this bacterium being considered nonmotile.
AU  - Eppinger M
AU  - McNair K
AU  - Zogaj X
AU  - Dinsdale EA
AU  - Edwards RA
AU  - Klose KE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00926-13.

PMID- 
VI  - 
DP  - 1991
TI  - Cloning of restriction-modification systems from Herpetosiphon giganteus Hpg9 and Hpg24 in E. coli - Characterization and comparative analysis of the genetic organization and structure.
PG  - 1-204
AB  - None
AU  - Erdmann D
PT  - Journal Article
TA  - Ph.D. Thesis, Justus-Liebig University, Geissen, W. Germany
JT  - Ph.D. Thesis, Justus-Liebig University, Geissen, W. Germany
SO  - Ph.D. Thesis, Justus-Liebig University, Geissen, W. Germany 1991 : 1-204.

PMID- 1662609
VI  - 202
DP  - 1991
TI  - Cloning and molecular characterization of the HgiCI restriction/modification system from Herpetosiphon giganteus Hpg9 reveals high similarity to BanI.
PG  - 1247-1256
AB  - The genes coding for the GGYRCC specific restriction/modification system HgiCI from
      Herpetosiphon giganteus Hpg9 have been cloned in Escherichia coli in three steps. As an
      initial step, the methyltransferase gene could be obtained after heterologous in vitro
      selection of a plasmid gene bank by cleavage with the isoschizomeric restriction endonuclease
      BanI. The adjacent endonuclease gene was cloned following Southern blot analysis of flanking
      genomic regions. The two genes code for polypeptides of 420 amino acids (M.HgiCI) and 345
      amino acids (R.HgiCI). Establishing a functional endonuclease gene could only be achieved
      using a tightly regulated expression system or by methylation of the genomic DNA prior to
      transformation of the endonuclease gene. The methyltransferase M.HgiCI shows significant
      similarities to the family of 5-methylcytidine methyltransferases. Striking similarities could
      be found with both the isoschizomeric endonuclease and methyltransferase of the BanI
      restriction/modification system from Bacillus aneurinolyticus.
AU  - Erdmann D
AU  - Dusterhoft A
AU  - Kroger M
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1991 202: 1247-1256.

PMID- 1644308
VI  - 117
DP  - 1992
TI  - Stepwise cloning and genetic organization of the seemingly unclonable HgiCII restriction-modification system from Herpetosiphon giganteus strain Hpg9, using PCR technique.
PG  - 15-22
AB  - The genes, hgiCIIR and hgiCIIM, that encode the HgiCII restriction and modification (R-M)
      system from Herpetosiphon giganteus strain Hpg9, an AvaII isoschizomer recognizing the
      sequence, CCA/TCC, were cloned in Escherichia coli. Cloning the respective hgiCIIM gene was
      achieved via in vitro selection both from a Sau3AI- and an NheI-generated plasmid gene library
      using AvaII, a commercially available isoschizomer of HgiCII. However, all attempts to clone
      the closely linked hgiCIIR and M genes in a single step resulted in deletions spanning parts
      of the coding region of hgiCIIR. Therefore, cloning of the missing 3'-terminal part of this
      gene was achieved by applying the inverse polymerase-chain-reaction technique. All attempts to
      construct an enzymatically active R.HgiCII failed; only the inactivated hgiCIIR gene could be
      cloned. Sequencing of the hgiCIIRM region (carrying predesigned small mutations in the R gene)
      disclosed three open reading frames (ORFs):one small ORF preceding the methyltransferase
      (MTase)-encoding gene, plus those encoding M.HgiCII (49620 Da) and R.HgiCII (30891 Da).
      M.HgiCII exhibits the common motif of ten conserved amino-acid blocks typically found within
      the group of m5C-MTases. The R-M system of HgiCII reveals strong homologies to the
      isoschizomeric R-M system of HgiBI from H. giganteus strain Hpg5, which in contrast, could be
      cloned in one step.
AU  - Erdmann D
AU  - Horst G
AU  - Dusterhoft A
AU  - Kroger M
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1992 117: 15-22.

PMID- 27340066
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence for a Clinical Isolate of Vancomycin-Resistant Enterococcus faecalis.
PG  - e00584-16
AB  - We report here the draft genome sequence of a multidrug-resistant Enterococcus faecalis
      strain, isolated from a patient at the University of Colorado Hospital.
      The genome assembly is 3,040,186 bp in length with 37.6% GC content. This isolate
      encodes eleven resistance genes, including those for glycopeptide,
      aminoglycoside, macrolide-lincosamide-streptogramin, and tetracycline resistance.
AU  - Erickson KE
AU  - Madinger NE
AU  - Chatterjee A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00584-16.

PMID- 28153899
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Clinical Isolates of Multidrug-Resistant Acinetobacter  baumannii.
PG  - e01547-16
AB  - We report here the draft genome sequences of two clinically isolated Acinetobacter baumannii
      strains. These samples were obtained from patients at the
      University of Colorado Hospital in 2007 and 2013 and encode an estimated 20 and
      13 resistance genes, respectively.
AU  - Erickson KE
AU  - Madinger NE
AU  - Chatterjee A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01547-16.

PMID- 25745002
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of 'Candidatus Methylacidiphilum kamchatkense' Strain Kam1, a Thermoacidophilic Methanotrophic Verrucomicrobium.
PG  - e00065-15
AB  - 'Candidatus Methylacidiphilum kamchatkense' strain Kam1 is an aerobic methane-oxidizing
      thermoacidophilic bacterium belonging to the Verrucomicrobia
      phylum. It was recovered from an acidic geothermal site in Uzon Caldera,
      Kamchatka, Russian Federation. Its genome possesses three complete pmoCAB gene
      clusters encoding particulate methane monooxygenase enzymes and a complete
      Calvin-Benson-Bassham cycle for carbon assimilation.
AU  - Erikstad HA
AU  - Birkeland NK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00065-15.

PMID- 28450872
VI  - 8
DP  - 2017
TI  - Comparative Analysis of Ralstonia solanacearum Methylomes.
PG  - 504
AB  - Ralstonia solanacearum is an important soil-borne plant pathogen with broad geographical
      distribution and the ability to cause wilt disease in many
      agriculturally important crops. Genome sequencing of multiple R. solanacearum
      strains has identified both unique and shared genetic traits influencing their
      evolution and ability to colonize plant hosts. Previous research has shown that
      DNA methylation can drive speciation and modulate virulence in bacteria, but the
      impact of epigenetic modifications on the diversification and pathogenesis of R.
      solanacearum is unknown. Sequencing of R. solanacearum strains GMI1000 and UY031
      using Single Molecule Real-Time technology allowed us to perform a comparative
      analysis of R. solanacearum methylomes. Our analysis identified a novel
      methylation motif associated with a DNA methylase that is conserved in all
      complete Ralstonia spp. genomes and across the Burkholderiaceae, as well as a
      methylation motif associated to a phage-borne methylase unique to R. solanacearum
      UY031. Comparative analysis of the conserved methylation motif revealed that it
      is most prevalent in gene promoter regions, where it displays a high degree of
      conservation detectable through phylogenetic footprinting. Analysis of hyper- and
      hypo-methylated loci identified several genes involved in global and virulence
      regulatory functions whose expression may be modulated by DNA methylation.
      Analysis of genome-wide modification patterns identified a significant
      correlation between DNA modification and transposase genes in R. solanacearum
      UY031, driven by the presence of a high copy number of ISrso3 insertion sequences
      in this genome and pointing to a novel mechanism for regulation of transposition.
      These results set a firm foundation for experimental investigations into the role
      of DNA methylation in R. solanacearum evolution and its adaptation to different
      plants.
AU  - Erill I
AU  - Puigvert M
AU  - Legrand L
AU  - Guarischi-Sousa R
AU  - Vandecasteele C
AU  - Setubal JC
AU  - Genin S
AU  - Guidot A
AU  - Valls M
PT  - Journal Article
TA  - Front. Plant Sci.
JT  - Front. Plant Sci.
SO  - Front. Plant Sci. 2017 8: 504.

PMID- 16857943
VI  - 313
DP  - 2006
TI  - Genome of Rice Cluster I archaea--the key methane producers in the rice rhizosphere.
PG  - 370-372
AB  - Rice fields are a global source of the greenhouse gas methane, which is
      produced by methanogenic archaea, and by methanogens of Rice Cluster I
      (RC-I) in particular. RC-I methanogens are not yet available in pure
      culture, and the mechanistic reasons for their prevalence in rice fields
      are unknown. We reconstructed a complete RC-I genome (3.18 megabases)
      using a metagenomic approach. Sequence analysis demonstrated an
      aerotolerant, H2/CO2-dependent lifestyle and enzymatic capacities for
      carbohydrate metabolism and assimilatory sulfate reduction, hitherto
      unknown among methanogens. These capacities and a unique set of
      antioxidant enzymes and DNA repair mechanisms as well as
      oxygen-insensitive enzymes provide RC-I with a selective advantage over
      other methanogens in its habitats, thereby explaining the prevalence of
      RC-I methanogens in the rice rhizosphere.
AU  - Erkel C
AU  - Kube M
AU  - Reinhardt R
AU  - Liesack W
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2006 313: 370-372.

PMID- Not included in PubMed...
VI  - 115
DP  - 1993
TI  - DNA methylation through a locally upaired intermediate.
PG  - 12583-12584
AB  - Methylation of DNA serves essential roles in mammalian development and in bacterial resistance
      to viral pathogens. In this process, a DNA (cytosine-5)-methyltransferase (DCMtase) mediates
      delivery of a methyl group from S-adenosyl-L-methionine to the 5-position of cytosine residues
      in DNA. DCMtases operate by conjugate addition of a cysteine thiolate to the 6-carbon (C6) of
      the substrate cytosine followed by transfer of a methyl group to C5. __-Elimination
      regenerates the free enzyme (Figure 1). We have noted that the stereoelectronic attack
      trajectories for thiolate addition and methyl transfer cannot be accommodated in a canonical
      B-form duplex, suggesting that DCMtases cause transient helical disruption during the
      catalytic event. Here we report evidence in favor of DCMtase-induced distortion of DNA and
      propose a structural model for the enzyme-DNA intermediate.
AU  - Erlanson DA
AU  - Chen L
AU  - Verdine GL
PT  - Journal Article
TA  - J. Am. Chem. Soc.
JT  - J. Am. Chem. Soc.
SO  - J. Am. Chem. Soc. 1993 115: 12583-12584.

PMID- Not included in PubMed...
VI  - 53
DP  - 1997
TI  - Selective base-pair destabilization enhances binding of a DNA methyltransferase.
PG  - 12041-12056
AB  - Disulfide crosslinks were introduced into the minor groove of DNA using the convertible
      nucleoside approach.  Depending upon the length of the tether, the modified base pairs were
      either stabilized or destabilized.  When the base-pairs were destabilized, the oligonucleotide
      was bound by a unmodified oligonucleotide.  Insights into the mechanism of DCMtases are
      discussed.
AU  - Erlanson DA
AU  - Wolfe SA
AU  - Chen L
AU  - Verdine GL
PT  - Journal Article
TA  - Tetrahedron
JT  - Tetrahedron
SO  - Tetrahedron 1997 53: 12041-12056.

PMID- 
VI  - 106
DP  - 2006
TI  - Mutations within the catalytic site of DNA methyltransferase (Dam) of Aeromonas hydrophila reverts the virulence of the dam-overproducing strain to that of the wild-type bacterium.
PG  - 76
AB  - A. hydrophila is an opportunistic human pathogen. In our recently published studies, we
      demonstrated that DNA adenine methyltransferase (Dam) of A. hydrophila is crucial for
      bacterial viability, and that it affects virulence of the bacterium by altering biological
      activities associated with type 2 and type 3 secreted proteins. Overall, overproduction of Dam
      in A. hydrophila using an arabinose-inducible pBAD vector attenuated bacterial virulence in a
      mouse model of infection. In this study, we demonstrated that the virulence potential of
      Dam-overproducing strain of A. hydrophila was reverted back to that of the wild-type (WT)
      bacterium when the catalytic site of Dam was mutated. Using Altered Sites in vitro Mutagenesis
      System, we mutated aspartic acid (D) and tyrosine (Y) residues to alanine (A) within the
      conserved catalytic motif (DPPY) of Dam. To confirm that the mutated enzyme lost its
      methyltransferase (MTase) activity, we transformed pBAD/dam*D/A, pBAD/dam*Y/A, and
      pBAD/damnative (as a control) recombinant plasmids into E. coli GM33 (Dam-) strain. Genomic
      DNA (gDNA) isolated from either the E. coli GM33 (pBAD/dam*D/A) or the E. coli GM33
      (pBAD/dam*Y/A) strain grown in the presence of arabinose was sensitive to DpnII digestion and
      resistant to DpnI restriction endonuclease cutting. These data verified that the gDNA were not
      methylated as the gDNA from E. coli GM33 strain with pBAD/damnative plasmid which exhibited
      opposite sensitivity to DpnI and resistance to DpnII digestion. Overproduction of mutated Dam
      in A. hydrophila resulted in bacterial motility, T3SS-associated cytotoxicity as well as
      hemolytic and cytotoxic activity associated with the cytotoxic enterotoxin and that of the
      protease activity similar to that of the WT bacterium which harbored the pBAD vector alone. In
      addition, we noted that lactone production, an indicator of quorum sensing, was increased when
      the native dam gene was over-expressed, with its levels returning to that of the WT bacterium
      when the damgene was mutated. Taken together, our data indicated that MTase activity is
      essential for altered virulence of A. hydrophila.
AU  - Erova T
AU  - Sha J
AU  - Fadl A
AU  - Khajanchi B
AU  - Chopra A
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 2006 106: 76.

PMID- 16988254
VI  - 74
DP  - 2006
TI  - Mutations within the catalytic motif of DNA adenine methyltransferase (Dam) of Aeromonas hydrophila cause the virulence of the Dam-overproducing strain to revert to that of the wild-type phenotype - bacterium DNA denine-methyltransferase catalytic.
PG  - 5763-5772
AB  - AUTHOR ABSTRACT - In this study, we demonstrated that the methyltransferase activity
      associated with Dam was essential for
      attenuation of Aeromonas hydrophila virulence. We mutated aspartic acid
      and tyrosine residues to alanine within the conserved DPPY catalytic
      motif of Dam and transformed the pBAD/dam(D/A), pBAD/dam(Y/A), and
      pBAD/damA(AhSSu) (with the native dam gene) recombinant plasmids into
      the Escherichia coli GM33 (dam-deficient) strain. Genomic DNA (gDNA)
      isolated from either of the E. coli GM33 strains harboring the pBAD
      vector with the mutated dam gene was resistant to DpnI digestion and
      sensitive to DpnII restriction endonuclease cutting. These findings
      were contrary to those with the gDNA of E. coli GM33 strain containing
      the pBAD/dam(AhSSU) plasmid, indicating nonmethylation of E. coli gDNA
      with mutated Dam. Overproduction of mutated Dam in A. hydrophild
      resulted in bacterial motility, hemolytic and cytotoxic activities
      associated with the cytotoxic enterotoxin (Act), and protease activity
      similar to that of the wild-type (WT) bacterium, which harbored the
      pBAD vector and served as a control strain. On the contrary,
      overproduction of native Dam resulted in decreased bacterial motility,
      increased Act-associated biological effects, and increased protease
      activity. Lactone production, an indicator of quorum sensing, was
      increased when the native dam gene was overexpressed, with its levels
      returning to that of the control strain when the dam gene was mutated.
      These effects of Dam appeared to be mediated through a regulatory
      glucose-inhibited division A protein. Infection of mice with the
      mutated Dam-overproducing strains resulted in mortality rates similar
      to those for the control strain, with 100% of the animals dying within
      2 to 3 days with two 50% lethal doses (LD(50)s) of the WT bacterium.
      Importantly, immunization of mice with a native-Dam-overproducing
      strain at the same LD50 did not result in any lethality and provided
      protection to animals after subsequent challenge with a lethal dose of
      the control strain.
AU  - Erova TE
AU  - Fadl AA
AU  - Sha J
AU  - Khajanchi BK
AU  - Pillai LL
AU  - Kozlova EVCAK
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2006 74: 5763-5772.

PMID- 22391092
VI  - 498
DP  - 2012
TI  - DNA adenine methyltransferase (Dam) controls the expression of the cytotoxic enterotoxin (act) gene of Aeromonas hydrophila via tRNA modifying enzyme-glucose-inhibited division protein (GidA).
PG  - 280-287
AB  - Aeromonas hydrophila is both a human and animal pathogen, and the cytotoxic enterotoxin (Act)
      is a crucial virulence factor of this bacterium because of its associated hemolytic,
      cytotoxic, and enterotoxic activities.
      Previously, to define the role of some regulatory genes in modulating Act production, we
      showed that deletion of a glucose-inhibited division gene (gidA) encoding tRNA methylase
      reduced Act levels, while overproduction
      of DNA adenine methyltransferase (Dam) led to a concomitant increase in Act-associated
      biological activities of a diarrheal isolate SSU of A.  hydrophila. Importantly, there are
      multiple GATC binding sites for Dam within an upstream sequence of the gidA gene and one such
      target site in the act gene upstream region.  We showed the dam gene to be essential for the
      viability of A. hydrophila SSU, and, therefore, to better understand
      the interaction of the encoding genes, Dam and GidA, in act gene regulation, we constructed a
      gidA in-frame deletion mutant of Escherichia coli GM28 (dam+) and GM33 (Adam) strains. We then
      tested the expressional activity of the act and gidA genes by using a promoterless pGlow-TOPO
      vector containing a
      reporter green fluorescent protein (GFP). Our data indicated that in GidA+ strains of E. coli,
      constitutive methylation of the GATC site(s) by Dam negatively regulated act and gidA gene
      expression as measured by
      GFP production. However, in the AgidA strains, irrespective of the presence or absence of
      constitutively active Dam, we did not observe any alteration in the expression of the act gene
      signifying the role of GidA in positively
      regulating Act production. To determine the exact mechanism of how Dam and GidA influence Act,
      a real-time quantitative PCR (RT-qPCR) assay was performed. The analysis indicated an increase
      in gidA and act gene expression in the A. hydrophila Dam-overproducing strain, and these data
      matchedwith Act production in the E. coli GM28 strain. Thus, the extent of DNA methylation
      caused by constitutive versus overproduction of Dam, as well as possible conformation of DNA
      influence the expression of act and gidA genes in A. hydrophila SSU.  Our results indicate
      that the act gene is under the control of both Dam and GidA modification methylases, and Dam
      regulates Act production via GidA.
AU  - Erova TE
AU  - Kosykh VG
AU  - Sha J
AU  - Chopra AK
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 2012 498: 280-287.

PMID- 16368997
VI  - 74
DP  - 2005
TI  - DNA adenine methyltransferase influences the virulence of Aeromonas hydrophila.
PG  - 410-424
AB  - Among the various virulence factors produced by Aeromonas hydrophila, a type II secretion
      system (T2SS)-secreted cytotoxic enterotoxin (Act) and the T3SS are crucial in the
      pathogenesis of Aeromonas-associated infections. Our laboratory molecularly characterized both
      Act and the T3SS from a diarrheal isolate, SSU of A. hydrophila, and defined the role of some
      regulatory genes in modulating the biological effects of Act. In this study, we cloned,
      sequenced, and expressed the DNA adenine methyltransferase gene of A. hydrophila SSU
      (dam(AhSSU)) in a T7 promoter-based vector system using Escherichia coli ER2566 as a host
      strain, which could alter the virulence potential of A. hydrophila. Recombinant Dam,
      designated as M.AhySSUDam, was produced as a histidine-tagged fusion protein and purified from
      an E. coli cell lysate using nickel affinity chromatography. The purified Dam had
      methyltransferase activity, based on its ability to transfer a methyl group from
      S-adenosyl-l-methionine to N(6)-methyladenine-free lambda DNA and to protect methylated lambda
      DNA from digestion with DpnII but not against the DpnI restriction enzyme. The dam gene was
      essential for the viability of the bacterium, and overproduction of Dam in A. hydrophila SSU,
      using an arabinose-inducible, P(BAD) promoter-based system, reduced the virulence of this
      pathogen. Specifically, overproduction of M.AhySSUDam decreased the motility of the bacterium
      by 58%. Likewise, the T3SS-associated cytotoxicity, as measured by the release of lactate
      dehydrogenase enzyme in murine macrophages infected with the Dam-overproducing strain, was
      diminished by 55% compared to that of a control A. hydrophila SSU strain harboring the pBAD
      vector alone. On the contrary, cytotoxic and hemolytic activities associated with Act as well
      as the protease activity in the culture supernatant of a Dam-overproducing strain were
      increased by 10-, 3-, and 2.4-fold, respectively, compared to those of the control A.
      hydrophila SSU strain. The Dam-overproducing strain was not lethal to mice (100% survival)
      when given by the intraperitoneal route at a dose twice that of the 50% lethal dose, which
      within 2 to 3 days killed 100% of the animals inoculated with the A. hydrophila control
      strain. Taken together, our data indicated alteration of A. hydrophila virulence by
      overproduction of Dam.
AU  - Erova TE
AU  - Pillai L
AU  - Fadl AA
AU  - Sha J
AU  - Wang SF
AU  - Galindo CL
AU  - Chopra AK
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2005 74: 410-424.

PMID- 26972562
VI  - 14
DP  - 2016
TI  - Restriction-Modification systems interplay causes avoidance of GATC site in prokaryotic genomes.
PG  - 1641003
AB  - Palindromes are frequently underrepresented in prokaryotic genomes. Palindromic 5[Formula: see
      text]-GATC-3[Formula: see text] site is a recognition site of
      different Restriction-Modification (R-M) systems, as well as solitary
      methyltransferase Dam. Classical GATC-specific R-M systems methylate GATC and
      cleave unmethylated GATC. On the contrary, methyl-directed Type II restriction
      endonucleases cleave methylated GATC. Methylation of GATC by Dam
      methyltransferase is involved in the regulation of different cellular processes.
      The diversity of functions of GATC-recognizing proteins makes GATC sequence a
      good model for studying the reasons of palindrome avoidance in prokaryotic
      genomes. In this work, the influence of R-M systems and solitary proteins on the
      GATC site avoidance is described by a mathematical model. GATC avoidance is
      strongly associated with the presence of alternate (methyl-directed or classical
      Type II R-M system) genes in different strains of the same species, as we have
      shown for Streptococcus pneumoniae, Neisseria meningitidis, Eubacterium rectale,
      and Moraxella catarrhalis. We hypothesize that GATC avoidance can result from a
      DNA exchange between strains with different methylation status of GATC site
      within the process of natural transformation. If this hypothesis is correct, the
      GATC avoidance is a sign of a DNA exchange between bacteria with different
      methylation status in a mixed population.
AU  - Ershova A
AU  - Rusinov I
AU  - Vasiliev M
AU  - Spirin S
AU  - Karyagina A
PT  - Journal Article
TA  - J. Bioinform. Comput. Biol.
JT  - J. Bioinform. Comput. Biol.
SO  - J. Bioinform. Comput. Biol. 2016 14: 1641003.

PMID- 22965118
VI  - 40
DP  - 2012
TI  - Solitary restriction endonucleases in prokaryotic genomes.
PG  - 10107-10115
AB  - Prokaryotic restriction-modification (R-M) systems defend the host cell from the  invasion of
      a foreign DNA. They comprise two enzymatic activities: specific DNA
      cleavage activity and DNA methylation activity preventing cleavage. Typically,
      these activities are provided by two separate enzymes: a DNA methyltransferase
      (MTase) and a restriction endonuclease (RE). In the absence of a corresponding
      MTase, an RE of Type II R-M system is highly toxic for the cell. Genes of the R-M
      system are linked in the genome in the vast majority of annotated cases. There
      are only a few reported cases in which the genes of MTase and RE from one R-M
      system are not linked. Nevertheless, a few hundreds solitary RE genes are present
      in the Restriction Enzyme Database (http://rebase.neb.com) annotations. Using the
      comparative genomic approach, we analysed 272 solitary RE genes. For 57 solitary
      RE genes we predicted corresponding MTase genes located distantly in a genome. Of
      the 272 solitary RE genes, 99 are likely to be fragments of RE genes. Various
      explanations for the existence of the remaining 116 solitary RE genes are also
      discussed.
AU  - Ershova AS
AU  - Karyagina AS
AU  - Vasiliev MO
AU  - Lyashchuk AM
AU  - Lunin VG
AU  - Spirin SA
AU  - Alexeevski AV
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: 10107-10115.

PMID- 26567582
VI  - 80
DP  - 2015
TI  - Role of Restriction-Modification Systems in Prokaryotic Evolution and Ecology.
PG  - 1373-1386
AB  - Restriction-modification (R-M) systems are able to methylate or cleave DNA depending on
      methylation status of their recognition site. It allows them to protect bacterial cells from
      invasion by foreign DNA. Comparative analysis of a large number of available bacterial genomes
      and methylomes clearly demonstrates that the role of R-M systems in bacteria is wider than
      only defense. R-M systems maintain heterogeneity of a bacterial population and are involved in
      adaptation of bacteria to change in their environmental conditions. R-M systems can be
      essential for host colonization by pathogenic bacteria. Phase variation and intragenomic
      recombinations are sources of the fast evolution of the specificity of R-M systems. This
      review focuses on the influence of R-M systems on evolution and ecology of prokaryotes.
AU  - Ershova AS
AU  - Rusinov IS
AU  - Spirin SA
AU  - Karyagina AS
AU  - Alexeevski AV
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 2015 80: 1373-1386.

PMID- 9200708
VI  - 36
DP  - 1997
TI  - Rapid-reaction analysis of plasmid DNA cleavage by the EcoRV restriction endonuclease.
PG  - 7567-7576
AB  - Rapid-reaction methods have been used previously to identify intermediates in the reaction of
      the EcoRV restriction endonuclease on oligonucleotide substrates.  In this study, the pathway
      on macromolecular DNA was elucidated by using the quench-flow method to analyze EcoRV
      reactions on a plasmid with one recognition site.  Some reactions were carried out by first
      allowing the EcoRV enzyme to bind nonspecifically to the DNA and then initiating DNA cleavage
      by adding magnesium ions.  The subsequent transfer of the enzyme from nonspecific to specific
      sites was extremely rapid, at a random walk rate of at least 5 x 10^5 base pairs per second.
      The two strands of the DNA at the EcoRV recognition site were then cleaved sequentially, at
      rates that were faster than the turnover number of the enzyme.  The rates recorded for the
      cleavage steps were direct measurements of phosphodiester hydrolysis, while the turnover is
      limited by the dissociation of the product cleaved in both strands.  Other reactions were
      initiated by adding EcoRV and MgCl2 to the DNA: these are the processes observed in reactions
      starting from DNA-bound enzyme but also the bimolecular association of the protein with the
      plasmid.  The association rate was limited by diffusion but its rate constant, 1.2 x 10^8 M-1
      s-1, was unusually small for the binding of a protein to DNA.  The slowness of this
      diffusion-controlled process may be due to a rapid oscillation of the protein between closed
      and open conformations, with only the open form capable of binding DNA.
AU  - Erskine SG
AU  - Baldwin GS
AU  - Halford SE
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1997 36: 7567-7576.

PMID- 7821558
VI  - 22
DP  - 1994
TI  - Fluorescent substrates for the EcoRV restriction endonuclease.
PG  - 299s
AB  - In the presence of Mg2+, the EcoRV restriction endonuclease cleaves DNA specifically at the
      sequence GAT/ATC (where / denotes the point of scission). Even the change of a single base
      pair within this sequence will lead to a million fold reduction of EcoRV activity.
      Paradoxically, gel retardation experiments in the absence of Mg2+ show that, unlike EcoRI and
      many other type II restriction endonucleases, EcoRV binds to DNA without any sequence
      preference. The specificity of EcoRV is in fact dependent on the production of a high affinity
      binding site for Mg2+ between the protein and the cognate DNA. X-ray crystal structures show
      that the cognate DNA adopts a highly distorted, kinked conformation in its complex with EcoRV,
      in contrast to noncognate DNA which retains a B-like conformation. The difference between the
      delta-G0 for the binding of cognate and noncognate sequences is near to zero and hence the
      energy from the additional contacts with the specific DNA appears to be neutralized by the
      unfavorable energy change from the distortion of the DNA. In addition, the crystal structures
      show that the protein itself must undergo a conformation change before it can bind DNA.
      Therefore, during one cycle of DNA cleavage, the EcoRV protein will undergo several
      conformational changes: due first to binding nonspecific DNA and then specific DNA, and later
      by the sequence of events leading to cleavage and product release.
AU  - Erskine SG
AU  - Halford SE
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 1994 22: 299s.

PMID- 9480767
VI  - 275
DP  - 1998
TI  - Reactions of the EcoRV restriction endonuclease with fluorescent oligodeoxynucleotides: identical equilibrium constants for binding to specific and non-specific DNA.
PG  - 759-772
AB  - The EcoRV restriction endonuclease cleaves DNA specifically at its recognition sequence in the
      presence of magnesium ions, but several studies have indicated that it binds to DNA in the
      absence of Mg2+ without any preference for its recognition site.  However, specific binding to
      the recognition site has also been reported.  To distinguish between these reports,
      oligodeoxynucleotides were tagged with either dansyl or eosin fluorophores at their 5'
      termini and annealed to form duplexes of 12 to 16 base-pairs.  For each length of duplex, one
      derivative had the EcoRV recognition sequence while another lacked this sequence.  For the
      duplexes with the recognition site, the fluorophores had no effect on DNA cleavage rates by
      EcoRV in the presence of Mg2+.  The binding of the specific and non-specific duplexes to EcoRV
      in the absence of Mg2+ was measured by fluorescence resonance energy transfer and by
      fluorescence depolarization.  In both procedures, the signal from the specific complex
      differed from the complex with non-specific DNA, with the depolarization data indicating that
      non-specific DNA bound to EcoRV retains a higher rotational freedom than specific DNA.  Even
      so, the equilibrium constant for the binding of specific DNA was identical, within error
      limits, to that for non-specific DNA.
AU  - Erskine SG
AU  - Halford SE
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1998 275: 759-772.

PMID- 7607481
VI  - 157
DP  - 1995
TI  - Interactions of the EcoRV restriction endonuclease with fluorescent oligodeoxynucleotides.
PG  - 153-156
AB  - A self-complementary dodecadeoxyribonucleotide that contains the recognition sequence for the
      R.EcoRV Enase was synthesized with a primary amino group at its 5' terminus.  The 5' amino
      function was labeled with the fluorescent dye 5-[dimethylamino] napthalene-1-sulfonyl
      chloride.  The labeled oligodeoxyribonucleotide in its duplex form was shown to be a suitable
      substrate for kinetic studies on the ENase and that no significant dye-DNA or dye-protein
      interactions occurred.  Finally, the binding of R.EcoRV to the labeled DNA was followed by
      detecting the fluorescence resonance energy transfer between the tryptophans of the protein
      and the fluorescent labels of the DNA.
AU  - Erskine SG
AU  - Halford SE
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 153-156.

PMID- Not included in PubMed...
VI  - 6
DP  - 1980
TI  - Isolation of the site-specific endonuclease EcoRI with the aid of an immunoabsorbent.
PG  - 1361-1369
AB  - A simple and satisfactorily reproducible method of isolating the site-specific endonuclease
      EcoRI which is based on the chromatography of the enzyme on a column filled with antibodies
      immobilized on Sepharose 4B is described.  The binding of the enzyme to the antibodies is
      carried out directly from a cell extract, and after the support has been washed free from
      unbound protein the enzyme is eluted.  The isolation of the homogeneous enzyme (20,000
      activity units per 1g of biomass) takes place in one stage and lasts 3 h.  The preparation
      obtained is stable on storage in 50% glycerol at -15C for more than six months.  The paper
      also describes a method of purifying the endonuclease EcoRI to the homogeneous state in two
      chromatographic stages:  in columns containing phosphocellulose and Sephadex G-150.  The
      enzyme obtained by this method contains no nonspecific nucleases and possesses a specific
      activity of 750,000 activity units/mg of protein (3750 activity units per 1g of biomass).
AU  - Eruslanov BV
AU  - Kramarov VM
AU  - Smolyanivov VV
AU  - Borovik RV
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1980 6: 1361-1369.

PMID- 8759842
VI  - 178
DP  - 1996
TI  - Cloning of a Neisseria meningitidis gene for L-lactate dehydrogenase (L-LDH): evidence for a second meningococcal L-LDH with different   regulation.
PG  - 4807-4813
AB  - We report the cloning of lldA, a Neisseria meningitidis gene for L-lactate dehydrogenase
      (L-LDH). Escherichia coli contains a single L-LDH gene
      (lldD) in the lld operon (previously lct). E. coli grown in complex media
      does not have L-LDH activity, but the activity is induced by growth in
      defined medium with L-lactate as the carbon source. In contrast,
      meningococci contain at least one L-LDH in addition to the lldA gene
      product. These enzymes are active in meningococci grown in complex media
      and are not dependent on growth in L-lactate. The predicted amino acid
      sequence of lldA is homologous to that of E. coli lldD and of other
      prokaryotic and eukaryotic flavin mononucleotide-containing enzymes that
      catalyze the oxidation of L-lactate and other small alpha-hydroxy acids. A
      mutant with a deletion in lldA was found to have reduced L-LDH activity.
      However, this mutant was able to grow on L-lactate, indicating that a
      second L-LDH must exist. Activity of the lldA enzyme was affected by
      growth conditions, being increased by growth on a defined medium with
      either L-lactate or pyruvate as the carbon source. For meningococci grown
      on a complex medium, activity of the lldA enzyme was increased by growth
      on plates or in well-aerated broth. A second L-lactate-oxidizing activity
      was seen in bacteria grown in poorly aerated broth. Neisseria gonorrhoeae
      contains a homolog of lldA. As for meningococci, mutation of the
      gonococcal lldA reduced L-LDH activity but did not affect growth on
      L-lactate.
AU  - Erwin AL
AU  - Gotschlich EC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1996 178: 4807-4813.

PMID- 18065541
VI  - 190
DP  - 2008
TI  - Analysis of genetic relatedness of Haemophilus influenzae isolates by multilocus sequence typing.
PG  - 1473-1483
AB  - The gram-negative bacterium Haemophilus influenzae is a human-restricted
      commensal of the nasopharynx that can also be associated with disease. The
      majority of H. influenzae respiratory isolates lack the genes for capsule
      production and are nontypeable (NTHI). Whereas encapsulated strains are
      known to belong to serotype-specific phylogenetic groups, the structure of
      the NTHI population has not been previously described. A total of 656 H.
      influenzae strains, including 322 NTHI strains, have been typed by
      multilocus sequence typing and found to have 359 sequence types (ST). We
      performed maximum-parsimony analysis of the 359 sequences and calculated
      the majority-rule consensus of 4,545 resulting equally most parsimonious
      trees. Eleven clades were identified, consisting of six or more ST on a
      branch that was present in 100% of trees. Two additional clades were
      defined by branches present in 91% and 82% of trees, respectively. Of
      these 13 clades, 8 consisted predominantly of NTHI strains, three were
      serotype specific, and 2 contained distinct NTHI-specific and
      serotype-specific clusters of strains. Sixty percent of NTHI strains have
      ST within one of the 13 clades, and eBURST analysis identified an
      additional phylogenetic group that contained 20% of NTHI strains. There
      was concordant clustering of certain metabolic reactions and putative
      virulence loci but not of disease source or geographic origin. We conclude
      that well-defined phylogenetic groups of NTHI strains exist and that these
      groups differ in genetic content. These observations will provide a
      framework for further study of the effect of genetic diversity on the
      interaction of NTHI with the host.
AU  - Erwin AL
AU  - Sandstedt SA
AU  - Bonthuis PJ
AU  - Geelhood JL
AU  - Nelson KL
AU  - Unrath WC
AU  - Diggle MA
AU  - Theodore MJ
AU  - Pleatman CR
AU  - Mothershed EA
AU  - Sacchi CT
AU  - Mayer LW
AU  - Gilsdorf JR
AU  - Smith AL
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2008 190: 1473-1483.

PMID- 21705604
VI  - 193
DP  - 2011
TI  - Genome Sequence of Streptomyces sp. Strain Tu6071.
PG  - 4278-4279
AB  - Streptomyces sp. Tu6071 is a soil-dwelling bacterium which has a highly active isoprenoid
      biosynthesis. Isoprenoids are important precursors for
      biopharmaceutical molecules such as antibiotics or anticancer agents,
      e.g., landomycin. Streptomyces sp. Tu6071 produces the industrially
      important terpene glycosides phenalinolactones, which have antibacterial
      activity against several Gram-positive bacteria. The availability of the
      genome sequence of Streptomyces sp. Tu6071 allows for understanding the
      biosynthesis of these pharmaceutical molecules and will facilitate
      rational genome modification to improve industrial use.
AU  - Erxleben A
AU  - Wunsch-Palasis J
AU  - Gruning BA
AU  - Luzhetska M
AU  - Bechthold A
AU  - Gunther S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4278-4279.

PMID- 28302771
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of a Multidrug-Resistant Strain of Enterococcus faecalis, PM01, Isolated from the Nest of an American Bushtit, Psaltriparius minimus.
PG  - e00017-17
AB  - Pathogenic microorganisms associated with avian nests may detrimentally impact parental health
      and nest success for the nest primary users, potentially
      neighboring avian or terrestrial species, including humans. Here, we report the
      genome sequence of Enterococcus faecalis strain PM01, isolated from a failed nest
      of American bushtits, Psaltriparius minimus.
AU  - Esani S
AU  - Constable JV
AU  - Van Laar TA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00017-17.

PMID- 27257196
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Oral Bacterium Streptococcus mutans JH1140.
PG  - e00472-16
AB  - Streptococcus mutans JH1140 is an oral bacterium known to produce the bacteriocin mutacin
      1140, and the strain has been genetically engineered to combat dental
      caries. Here, we report the 2.0-Mb draft genome of S. mutans JH1140. This genome
      provides new insights into the strain's superior colonization properties and its
      utility in replacement therapy.
AU  - Escano J
AU  - Deng P
AU  - Lu SE
AU  - Smith L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00472-16.

PMID- 27881546
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Two 'Haemophilus quentini' Isolates Recovered from Two  Different Patients' Blood Cultures.
PG  - e01321-16
AB  - Here, we present the draft genome sequences of two strains (K068 and C860) of the genospecies
      'Haemophilus quentini' The isolates were recovered from blood
      cultures of a newborn neonate and an elderly patient with septicemia in Ontario,
      Canada.
AU  - Eshaghi A
AU  - Soares D
AU  - Tsang R
AU  - Richardson D
AU  - Kus JV
AU  - Patel SN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01321-16.

PMID- 26512312
VI  - 10
DP  - 2015
TI  - High-quality permanent draft genome sequence of Bradyrhizobium sp. strain WSM1743 - an effective microsymbiont of an Indigofera sp. growing in Australia.
PG  - 87
AB  - Bradyrhizobium sp. strain WSM1743 is an aerobic, motile, Gram-negative, non-spore-forming rod
      that can exist as a soil saprophyte or as a legume
      microsymbiont of an Indigofera sp. WSM1743 was isolated from a nodule recovered
      from the roots of an Indigofera sp. growing 20 km north of Carnarvon in
      Australia. It is slow growing, tolerates up to 1 % NaCl and is capable of growth
      at 37 degrees C. Here we describe the features of Bradyrhizobium sp. strain
      WSM1743, together with genome sequence information and its annotation. The
      8,341,956 bp high-quality permanent draft genome is arranged into 163 scaffolds
      and 167 contigs, contains 7908 protein-coding genes and 75 RNA-only encoding
      genes and was sequenced as part of the Root Nodule Bacteria chapter of the
      Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Eshraghi L
AU  - De Meyer SE
AU  - Tian R
AU  - Seshadri R
AU  - Ivanova N
AU  - Pati A
AU  - Markowitz V
AU  - Woyke T
AU  - Kyrpides NC
AU  - Tiwari R
AU  - Yates R
AU  - Howieson J
AU  - Reeve W
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 87.

PMID- 11046140
VI  - 20
DP  - 2000
TI  - Multiple homing pathways used by yeast mitochondrial group II introns.
PG  - 8432-8446
AB  - The yeast mitochondrial DNA group II introns aI1 and aI2 are retroelements that insert site
      specifically into intronless alleles by a process called homing. Here, we used patterns of
      flanking marker coconversion in crosses with wild-type and mutant aI2 introns to distinguish
      three coexisting homing pathways: two that were reverse transcriptase (RT) dependent
      (retrohoming) and one that was RT independent. All three pathways are initiated by cleavage of
      the recipient DNA target site by the intron-encoded endonuclease, with the sense strand
      cleaved by partial or complete reverse splicing, and the antisense strand cleaved by the
      intron-encoded protein.  The major retrohoming pathway in standard crosses leads to insertion
      of the intron with unidirectional coconversion of upstream exon sequences. This pattern of
      coconversion suggests that the major retrohoming pathway is initiated by target DNA-primed
      reverse transcription of the reverse-spliced intron RNA and completed by double-strand break
      repair (DSBR) recombination with the donor allele. The RT-independent pathway leads to
      insertion of the intron with bi-directional coconversion and presumably occurs by a
      conventional DSBR recombination mechanism initiated by cleavage of the recipient DNA target
      site by the intron-encoded endonuclease, as for group I intron homing. Finally, some mutant
      DNA target sites shift up to 43% of retrohoming to another pathway not previously detected for
      aI2 in which there is no coconversion of flanking exon sequences. This new pathway presumably
      involves synthesis of a full-length cDNA copy of the inserted intron RNA, with completion by a
      repair process independent of homologous recombination, as found for the Lactococcus lactis
      Ll.LtrB intron. Our results show that group II intron mobility can occur by multiple pathways,
      the ratios of which depend on the characteristics of both the intron and the DNA target site.
      This remarkable flexibility enables group II introns to use different recombination and repair
      enzymes in different host cells.
AU  - Eskes R
AU  - Liu L
AU  - Ma H
AU  - Chao MY
AU  - Dickson L
AU  - Lambowitz AM
AU  - Perlman PS
PT  - Journal Article
TA  - Mol. Cell. Biol.
JT  - Mol. Cell. Biol.
SO  - Mol. Cell. Biol. 2000 20: 8432-8446.

PMID- 9118229
VI  - 88
DP  - 1997
TI  - Mobility of yeast mitochondrial group II introns: Engineering a new site specificity and retrohoming via full reverse splicing.
PG  - 865-874
AB  - The mobile group II introns aI1 and aI2 of yeast mtDNA encode endonuclease activities that
      cleave intronless DNA target sites to initiate mobility by target DNA-primed reverse
      transcription.  For aI2, sense-strand cleavage occurs mainly by a partial reverse splicing
      reaction, whereas for aI1, complete reverse splicing occurs, leading to insertion of the
      linear intron RNA into double-stranded DNA.  Here, we show that aI1 homing and reverse
      splicing depend on the EBS1 (RNA)/IBS1(DNA) pairing and that target specificity can be changed
      by compensatory changes in the target site and the donor intron.  Using well-marked strains to
      follow coconversion of flanking DNA, we show that homing occurs by both RT-dependent and
      -independent pathways.  Remarkably, in most RT-dependent events, the reverse spliced intron is
      the initial template for first-strand cDNA synthesis.
AU  - Eskes R
AU  - Yang J
AU  - Lambowitz AM
AU  - Perlman PS
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1997 88: 865-874.

PMID- 
VI  - 
DP  - 1973
TI  - The host-controlled restriction enzyme of Escherichia coli B.
PG  - 1-191
AB  - The restriction endonuclease of Escherichia coli B has been
      purified and is free of non-specific endonuclease.  On sucrose gradients it
      sediments in a broad band with an S20,w of 11 through 18.  As judged by
      polyacrylamide gel electrophoresis the enzyme exists in at leas two active
      forms, each of which possesses three nonidentical polypeptides, alpha,
      beta, and gamma, of molecular weights 135,000, 60,000 and 55,000,
      respectively.  The molecular weights of these two forms have been estimated
      to be around 200,000 and 700,000.  Combining this information with
      estimates of the ratios of subunits present in each form suggests that the
      molecular formulae of the two forms are alpha1beta1gamma1 and
      alpha2beta4gamma2, respectively.  The subunits, beta and gamma, are
      indistinguishable by polyacrylamide gel electrophoresis from the two
      subunits found in the modification methylase of Escherichia coli B.
AU  - Eskin B
PT  - Journal Article
TA  - Ph.D. Thesis, University of California, Berkeley, USA
JT  - Ph.D. Thesis, University of California, Berkeley, USA
SO  - Ph.D. Thesis, University of California, Berkeley, USA 1973 : 1-191.

PMID- 4576514
VI  - 11
DP  - 1973
TI  - Host-controlled modification and restriction of bacteriophage T7 by Escherichia coli B.
PG  - 1020-1023
AB  - T7 phage resists Escherichia coli B host-controlled modification and
      restriction in vivo, but its DNA carries roughly five sites which are
      susceptible to the purified enzymes.
AU  - Eskin B
AU  - Lautenberger JA
AU  - Linn S
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1973 11: 1020-1023.

PMID- 4265567
VI  - 247
DP  - 1972
TI  - The deoxyribonucleic acid modification and restriction enzymes of Escherichia coli B. III.  Studies of the restriction adenosine triphosphatase.
PG  - 6192-6196
AB  - The restriction endonuclease of Escherichia coli B catalyzes a massive
      hydrolysis of ATP to ADP and Pi. The ATPase requires S-adenosylmethionine and
      DNA containing unmodified restriction sites.  The apparent Km for fd
      replicative form DNA is 20 microM DNA nucleotide, and ATP is half-saturating at
      100 microM.  Like the nuclease, the ATPase is inhibited strongly by
      S-adenosylethionine and 5'-methylthioadenosine, but only weakly by
      S-adenosylhomocysteine.  The hydrolysis of ATP continues long after DNA
      degradation has ceased.  Whereas no ATPase is observed when restricted DNA but
      no unmodified DNA is present in a reaction mixture, restricted DNA is required
      for the maintenance of ATPase once initiated.  A hypothetical scheme is
      presented which involves the conversion of the enzyme during DNA hydrolysis
      from a form capable of nuclease activity to one catalyzing the breakdown of
      ATP.
AU  - Eskin B
AU  - Linn S
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1972 247: 6192-6196.

PMID- 4568607
VI  - 247
DP  - 1972
TI  - The deoxyribonucleic acid modification and restriction enzymes of Escherichia coli B. II. Purification, subunit structure, and catalytic properties of the restriction endonuclease.
PG  - 6183-6191
AB  - The restriction endonuclease of Escherichia coli B has been purified and is
      free of nonspecific endonuclease.  On sucrose gradients it sediments in a broad
      band with an S20,w of 11 through 18.  As judged by polyacrylamide gel
      electrophoresis the enzyme exists in at least two active forms, each of which
      possess three nonidentical polypeptides, a, b, and c, of molecular weights
      135,000, 60,000 and 55,000, respectively.  The subunits, b, and c, are
      indistinguishable by polyacrylamide gel electrophoresis from the two subunits
      found in the modification methylase of E. coli B.  ATP is half-saturating at 80
      to 100 lM, S-adenosylmethionine has an apparent Km of 0.3 to 0.4 microM, and fd
      replicative form DNA is saturating at greater than 10 to 20 microM
      DNA-nucleotide.  S-adenosylethionine and 5'-methylthioadenosine, but not
      S-adenosylhomocysteine are potent inhibitors of the enzyme.  Modified DNA
      inhibits by 50% when added in a 5-fold excess over unmodified substrate.  The
      restriction nuclease activity ceases after 5 or 10 min, and the enzyme does not
      appear to turn over in the nuclease reaction.  The cleaved DNA product is not
      adenylylated, phosphorylated, or methylated during hydrolysis.  It is
      susceptible to lambda-exonuclease, exonuclease III, the recBC nuclease, and,
      after denaturation, exonuclease I.  These results imply that the termini of the
      restricted DNA have hydroxyl and 5'-phosphoryl groups, and that they have a
      duplex structure.  However, restricted DNA cannot be phosphorylated by
      polynucleotide kinase, even after treatment of the DNA with alkaline
      phosphatase.  Finally, in order to make the enzyme more accessible, relatively
      rapid assay procedures are suggested which are based on the ATPase activity of
      the enzyme, or on the rendering of circular DNA to a linear form which is
      susceptible to the recBC nuclease.
AU  - Eskin B
AU  - Linn S
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1972 247: 6183-6191.

PMID- 5337837
VI  - 93
DP  - 1967
TI  - Susceptibility of different coliphage genomes to host-controlled variation.
PG  - 835-844
AB  - Twenty-eight coliphages were studied for their susceptibility to four systems
      of host control variation in Escherichia coli.  Both temperate and virulent
      phages were studied, including phages with ribonucleic acid, double- and
      single-stranded deoxyribonucleic acid (DNA) and glucosylated DNA.  The systems
      examined were E. coli C-K, K-B, B-K, and K-K(P1).  The C-K, K-B, and B-K
      systems affected temperate phages and nonlysogenizing mutants derived from
      temperate phages.  In general, these systems did not restrict virulent phages.
      Phage 21e, a variant of phage 21, lost the ability to undergo restriction in
      the C-K and B-K systems, but retained susceptibility to the K-B and K-K(P(1)
      systems.  This suggests that the genetic site(s) on the phage, as well as in
      the host, determines susceptibility to host-controlled variation.  Both
      temperate and dependent virulent phages were susceptible to the host control
      system resulting from the presence of prophage P1.  The autonomous and small
      virulents were not susceptible.  In a given system, the various susceptible
      phages differed widely in their efficiency of plating on the restricting host.
      If the few infections that occur arise in rare special cells, then different
      populations of special cells are available to different phage species.  For
      most phage types, when a susceptible phage infected a nonrestricting host, the
      progeny showed the specificity appropriate to that host. Behavior of T3 was
      exceptional, however,  When T3 obtained from E. coli K infected E. coli C or B,
      some of the progeny phages retained K host specificity, whereas others acquired
      the specificity of the new host.
AU  - Eskridge RW
AU  - Weinfeld H
AU  - Paigen K
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1967 93: 835-844.

PMID- 29700147
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Plant Growth-Promoting Burkholderia sp. Strain BE12, Isolated from the Rhizosphere of Maize.
PG  - e00299-18
AB  - Burkholderia sp. strain BE12, isolated from a French agricultural soil, possesses antifungal
      activity against a set of phytopathogenic fungi and has friendly
      interactions with grapevine. Here, we present the draft genome sequence of BE12,
      along with genes related to plant growth-promoting traits and siderophores that
      this strain contains, supporting its plant growth and antifungal activities.
AU  - Esmaeel Q
AU  - Sanchez L
AU  - Robineau M
AU  - Dorey S
AU  - Clement C
AU  - Jacquard C
AU  - Barka EA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00299-18.

PMID- 15220328
VI  - 279
DP  - 2004
TI  - Human DNA methyltransferase 1 is required for maintenance of the histone H3 modification pattern.
PG  - 37175-37184
AB  - DNA methyltransferase 1 (DNMT1) plays an essential role in murine development and is thought
      to be the enzyme primarily responsible for
      maintenance of the global methylation status of genomic DNA. However,
      loss of DNMT1 in human cancer cells affects only the methylation status
      of a limited number of pericentromeric sequences. Here we show that
      human cancer cells lacking DNMT1 display at least two important
      differences with respect to wild type cells: a profound disorganization
      of nuclear architecture, and an altered pattern of histone H3
      modification that results in an increase in the acetylation and a
      decrease in the dimethylation and trimethylation of lysine 9.
      Additionally, this phenotype is associated with a loss of interaction
      of histone deacetylases (HDACs) and HP1 (heterochromatin protein 1)
      with histone H3 and pericentromeric repetitive sequences (satellite 2).
      Our data indicate that DNMT1 activity, via maintenance of the
      appropriate histone H3 modifications, contributes to the preservation
      of the correct organization of large heterochromatic regions.
AU  - Espada J
AU  - Ballestar E
AU  - Fraga MF
AU  - Garea AV
AU  - Juarranz A
AU  - Stockert JC
AU  - Robertson KD
AU  - Fuks FO
AU  - Esteller M
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2004 279: 37175-37184.

PMID- 22391530
VI  - 56
DP  - 2012
TI  - Carriage of an ACME II Variant may have contributed to MRSA ST239-like Strain Replacement in Liverpool Hospital, Sydney, Australia.
PG  - 3380-3383
AB  - Approximately 39% of MRSA ST239-like bloodstream isolates from Liverpool Hospital
      (1997-2008) carry an arginine catabolic mobile element (ACME). Whole genome
      sequencing revealed that an ACME II variant is located between orfX and SCCmec
      III, and based on pulsed-field gel electrophoresis patterns and temporal
      relationships of all ST239-like isolates (n=360), ACME carriage may have
      contributed to sub-pulsotype strain replacement.
AU  - Espedido BA
AU  - Steen JA
AU  - Barbagiannakos T
AU  - Mercer J
AU  - Paterson DL
AU  - Grimmond SM
AU  - Cooper MA
AU  - Gosbell IB
AU  - van Hal SJ
AU  - Jensen SO
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2012 56: 3380-3383.

PMID- 22374955
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Pseudomonas psychrotolerans L19, Isolated from Copper Alloy Coins.
PG  - 1623-1624
AB  - We report the draft genome sequence of Pseudomonas psychrotolerans strain L19, isolated from a
      European 50-cent copper alloy coin. Multiple genes potentially involved in copper resistance
      were identified; however, it is unknown if these copper ion resistance determinants contribute
      to prolonged survival of this strain on dry metallic copper.
AU  - Esperito-Santo C
AU  - Lin Y
AU  - Hao X
AU  - Wei G
AU  - Rensing C
AU  - Grass G
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1623-1624.

PMID- 28860262
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of Two Pseudomonas aeruginosa Strains Isolated from Children with Bacteremia.
PG  - e00927-17
AB  - Two Pseudomonas aeruginosa strains isolated from children with bacteremia in Mexico City were
      sequenced using PacBio RS-II single-molecule real-time (SMRT)
      technology. The strains consist of a 7.0- to 7.4-Mb chromosome, with a high
      content of mobile elements, and variation in the genetic content of class 1
      integron In1409.
AU  - Espinosa-Camacho LF
AU  - Delgado G
AU  - Miranda-Novales G
AU  - Soberon-Chavez G
AU  - Alcaraz LD
AU  - Morales-Espinosa R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00927-17.

PMID- 28883139
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of Four Extensively Drug-Resistant Pseudomonas aeruginosa Strains, Isolated from Adults with Ventilator-Associated Pneumonia at   a Tertiary Referral Hospital in Mexico City.
PG  - e00925-17
AB  - Four extensively drug-resistant Pseudomonas aeruginosa strains, isolated from patients with
      pneumonia, were sequenced using PacBio RS-II single-molecule
      real-time (SMRT) technology. Genome sequence analysis identified great
      variability among mobile genetic elements, as well as some previously undescribed
      genomic islands and new variants of class 1 integrons (In1402, In1403, In1404,
      and In1408).
AU  - Espinosa-Camacho LF
AU  - Delgado G
AU  - Soberon-Chavez G
AU  - Alcaraz LD
AU  - Castanon J
AU  - Morales-Espinosa R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00925-17.

PMID- 
VI  - 93
DP  - 2012
TI  - Mining for restriction endonucleases in Nicaragua.
PG  - 49-62
AB  - The Molecular Biology Center at the University of Central America in Nicaragua (CBM-UCA) was
      founded in 1999 to strengthen biotechnology research capacity and education in Nicaragua and
      the Central American region.  One of the first projects launched by the CBM-UCA was
      bio-prospecting for key industrial enzymes.  This ongoing study seeks to discover and
      characterize restriction enzymes (RE) in bacteria, and to create a database of microorganisms
      isolated and identified by 16S rDNA sequencing methodology.  In this paper we highlight the
      importance of studying the extreme environmental conditions for building knowledge of
      Nicaraguan biodiversity through modern molecular biology techniques such as metagenomics.  The
      isolation of prototype enzymes such as EcoRV and ClaI is presented as an update and extension
      of previously undertaken work.
AU  - Espinoza-Miranda SS
AU  - Gomez-Rodriguez JA
AU  - Huete-Perez JA
PT  - Journal Article
TA  - Encuentro
JT  - Encuentro
SO  - Encuentro 2012 93: 49-62.

PMID- 22461546
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of the Shrimp Pathogen Vibrio harveyi CAIM 1792.
PG  - 2104
AB  - Vibrio harveyi is a Gram-negative bacterium found in tropical and temperate marine
      environments as a free-living organism or in association with aquatic
      animals. We report the first sequenced genome of a Vibrio harveyi strain, CAIM
      1792, the etiologic agent of the 'bright red' syndrome of the Pacific white
      shrimp Litopenaeus vannamei.
AU  - Espinoza-Valles I
AU  - Soto-Rodriguez S
AU  - Edwards RA
AU  - Wang Z
AU  - Vora GJ
AU  - Gomez-Gil B
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2104.

PMID- 8710508
VI  - 24
DP  - 1996
TI  - The complete nucleotide sequence of bacteriophage HP1 DNA.
PG  - 2360-2368
AB  - The complete nucleotide sequence of the temperate phage HP1 of Haemophilus influenzae was
      determined. The phage contains a linear, double-stranded genome of 32 355 nt with cohesive
      termini. Statistical methods were used to identify 41 probable protein coding segments
      organized into five plausible transcriptional units. Regions encoding proteins involved in
      recombination, replication, transcriptional control, host cell lysis and phage production were
      identified. The sizes of proteins in the mature HP1 particle were determined to assist in
      identifying genes for structural proteins. Similarities between HP1 coding sequences and those
      in databases, as well as similar gene organizations and control mechanisms, suggest that HP1
      is a member of the P2-like phage family, with strong similarities to coliphages P2 and 186 and
      some similarity to the retronphage Ec67.
AU  - Esposito D
AU  - Fitzmaurice WP
AU  - Benjamin RC
AU  - Goodman SD
AU  - Waldman AS
AU  - Socca JJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1996 24: 2360-2368.

PMID- 2467142
VI  - 13D
DP  - 1989
TI  - An animal virus-induced DNA-methyltransferase.
PG  - 222
AB  - The DNA genome of frog virus 3 (FV3), an iridovirus, is highly methylated; more
      than 20% of cytosine residues are methylated at the 5-carbon position.
      Methylation of the viral DNA occurs in the cytoplasm of infected cells by an
      FV3-specified DNA-methyltransferase (DNA-mt).  To determine the role of this
      enzyme in virus replication and gene expression we have isolated a number of
      FV3 mutants defective in the expression of DNA-mt activity.  Combined genetic
      and biochemical analyses of one of the mutants have revealed a 26K polypeptide
      associated with DNA-mt activity.  Attempts to purify the 26K polypeptide have
      resulted in co-purification of two other polypeptides.  30K and 18K, along with
      the 26K one.  Additional experiments directed toward identifying DNA-mt
      activity with the individual polypeptides, together with reconstitution
      experiments, have indicated that at least two polypeptides (26K and 18K) are
      required for functional DNA-mt activity.  These data support the conclusion
      that FV3-induced DNA-mt, unlike any known eukaryotic DNA-mt, resides in a
      complex of at least two polypeptides.
AU  - Essani K
AU  - Goorha R
AU  - Granoff A
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1989 13D: 222.

PMID- 2445102
VI  - 161
DP  - 1987
TI  - Mutation in a DNA-binding protein reveals an association between DNA-methyltransferase activity and a 26,000-Da polypeptide in frog virus 3-infected cells.
PG  - 211-217
AB  - The DNA of frog virus 3, an iridovirus, is highly methylated; more than 20% of the cytosine
      bases are methylated at the 5-carbon position by an FV3-induced DNA methyltransferase.  To
      determine the role of this enzyme in virus replication and regulation of gene expression, we
      have analyzed an FV3 mutant that lacks DNA-mt activity and is resistant to 5-azacytidine (an
      inhibitor of DNA-mt).  Comparative polypeptide analysis using cytoplasmic extracts from the
      wild-type FV3 and mutant-infected cells, revealed that a single protein of 26,000 molecular
      weight was altered in the mutant-infected cells.  The altered polypeptide migrated faster in
      SDS-polyacrylamide gel as compared to the wild-type FV3 26K protein.  Five spontaneous
      revertants derived from the mutant regained the migrational characteristic of the wild-type
      26K protein, DNA-mt activity, and methylation of their DNA.  We further show that the 26K
      polypeptide is a DNA-binding protein and that 80% of the enzyme activity can be eluted from an
      ssDNA affinity column.  Taken together, these data support the conclusion that the 26K
      polypeptide is associated with DNA-mt activity.
AU  - Essani K
AU  - Goorha R
AU  - Granoff A
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1987 161: 211-217.

PMID- 15143064
VI  - 279
DP  - 2004
TI  - The coupling of tight DNA binding and base flipping: identification of a conserved structural motif in base flipping enzymes.
PG  - 31419-31428
AB  - Val(121) is positioned immediately above the extrahelical cytosine in HhaI DNA C(5)-cytosine
      methyltransferase, and replacement with alanine
      dramatically interferes with base flipping and catalysis. DNA binding and
      k(cat) are decreased 10^5-fold for the Val(121) --> Ala mutant that has a
      normal circular dichroism spectrum and AdoMet affinity. The magnitude of
      this loss of function is comparable with removal of the essential
      catalytic Cys(81). Surprisingly, DNA binding is completely recovered
      (increase of 10^5-fold) with a DNA substrate lacking the target cytosine
      base (abasic). Thus, interfering with the base flipping transition results
      in a dramatic loss of binding energy. Our data support an induced fit
      mechanism in which tight DNA binding is coupled to both base flipping and
      protein loop rearrangement. The importance of the proximal protein segment
      (His(127)-Thr(132)) in maintaining this critical interaction between
      Val(121) and the flipped cytosine was probed with single site alanine
      substitutions. None of these mutants are significantly altered in
      secondary structure, AdoMet or DNA affinity, k(methylation),
      k(inactivation), or k(cat). Although Val(121) plays a critical role in
      both extrahelical base stabilization and catalysis, its position and
      mobility are not influenced by individual residues in the adjacent peptide
      region. Structural comparisons with other DNA methyltransferases and DNA
      repair enzymes that stabilize extrahelical nucleotides reveal a motif that
      includes a positively charged or polar side chain and a hydrophobic
      residue positioned adjacent to the target DNA base and either the 5'- or
      3'-phosphate.
AU  - Estabrook RA
AU  - Lipson R
AU  - Hopkins B
AU  - Reich N
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2004 279: 31419-31428.

PMID- 17005571
VI  - 281
DP  - 2006
TI  - Observing an induced-fit mechanism during sequence-specific DNA methylation.
PG  - 37205-37214
AB  - The characterization of conformational changes that drive induced-fit mechanisms and their
      quantitative importance to enzyme specificity are
      essential for a full understanding of enzyme function. Here, we report on
      M.HhaI, a sequence-specific DNA cytosine C(5) methyltransferase that
      reorganizes a flexible loop (residues 80-100) upon binding cognate DNA as
      part of an induced-fit mechanism. To directly observe this approximately
      26A conformational rearrangement and provide a basis for understanding its
      importance to specificity, we replaced loop residues Lys-91 and Glu-94
      with tryptophans. The double mutants W41F/K91W and W41F/E94W are
      relatively unperturbed in kinetic and thermodynamic properties. W41F/E94W
      shows DNA sequence-dependent changes in fluorescence: significant changes
      in equilibrium and transient state fluorescence that occur when the enzyme
      binds cognate DNA are absent with nonspecific DNA. These real-time,
      solution-based results provide direct evidence that binding to cognate DNA
      induces loop reorganization into the closed conformer, resulting in the
      correct assembly of the active site. We propose that M.HhaI scans
      nonspecific DNA in the loop-open conformer and rearranges to the closed
      form once the cognate site is recognized. The fluorescence data exclude
      mechanisms in which loop motion precedes base flipping, and we show loop
      rearrangements are directly coupled to base flipping, because the
      sequential removal of single hydrogen bonds within the target
      guanosine:cytosine base pair results in corresponding changes in loop
      motion.
AU  - Estabrook RA
AU  - Reich N
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2006 281: 37205-37214.

PMID- 30533936
VI  - 7
DP  - 2018
TI  - Draft Genome Sequence of Enterobacter sp. Strain OLF, a Colonizer of Olive Flies.
PG  - e01068-18
AB  - Enterobacter sp. strain OLF colonizes laboratory-reared and wild individuals of the olive
      fruit fly Bactrocera oleae. The 5.07-kbp genome sequence of
      Enterobacter sp. strain OLF encodes metabolic pathways that allow the bacterium
      to partially supplement the diet of the olive fly when its dominant endosymbiont,
      Erwinia dacicola, is absent.
AU  - Estes AM
AU  - Hearn DJ
AU  - Nadendla S
AU  - Pierson EA
AU  - Dunning HJC
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e01068-18.

PMID- 24336367
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Salmonella enterica subsp. enterica Serotype Saintpaul Strain S-70, Isolated from an Aquatic Environment.
PG  - e01016-13
AB  - Salmonella is a pathogen of worldwide importance, causing disease in a vast range of hosts,
      including humans. We report the genome sequence of Salmonella enterica
      subsp. enterica serotype Saintpaul strain S-70, isolated from an aquatic
      environment.
AU  - Estrada-Acosta M
AU  - Medrano-Felix A
AU  - Jimenez M
AU  - Gomez-Gil B
AU  - Leon-Felix J
AU  - Amarillas L
AU  - Chaidez C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01016-13.

PMID- 28385835
VI  - 5
DP  - 2017
TI  - Genome Sequence of a Toxin-Positive Clostridium difficile Strain Isolated from Murine Feces.
PG  - e00088-17
AB  - Herein, we report the genome sequence of a Clostridium difficile strain isolated  from the
      feces of antibiotic-treated C57BL/6 mice. We have named this strain,
      which differs considerably from those of the previously sequenced C. difficile
      strains, LEM1.
AU  - Etienne-Mesmin L
AU  - Chassaing B
AU  - Adekunle O
AU  - Mattei LM
AU  - Edwards AN
AU  - McBride SM
AU  - Bushman FD
AU  - Gewirtz AT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00088-17.

PMID- 
VI  - 106
DP  - 2014
TI  - Elucidating Restriction Endonucleases Reaction Mechanisms via Dwell-Time Distribution Analysis.
PG  - 22A
AB  - We have developed a Total Internal Reflection Fluorescence microscopy based assay that allows
      us to simultaneously measure the length of the catalytic cycle for hundreds of restriction
      endonuclease molecules in one experiment.  We stably attach thousands of short duplex DNA
      molecules, each labeled with a single quantum dot semiconductor nanocrystal, to a passivated
      glass surface within a flow channel.  The disappearance of a quantum dot indicates that its
      DNA tether has been cleaved.  We introduce restriction endonuclease molecules into the channel
      in the absence of magnesium, which permits binding to, but not cleavage of the surface
      immobilized DNA substrate.  When buffer containing magnesium is introduced into the flow
      channel, DNA cleavage by the pre-bound restriction endonuclease molecules is initiated.  This
      synchronization allows us to measure the lag time between the introduction of magnesium and
      the completion of DNA cleavage for the entire population of enzymes.  Analysis of the
      dwell-time distributions can provide insights into the DNA cleavage mechanism.  Our
      observations suggest that EcoRV, a dimeric Type II restriction endonuclease that cleaves the
      palindromic sequence GAT/ATCF (where / is the cut site), requires two kinetic steps to
      complete duplex cleavage after prebinding.  However, dwell-time distributions suggest that
      BcnI, which is active as a monomer and cleaves the pseudopalindromic sequence 5'-CC/SGG-5'
      (where S stands for C or G), requires more than four kinetic steps to complete duplex
      cleavage.  Furthermore, experiments performed with strand-specific DNA substrates suggest that
      the number of steps indicated by the dwell-time distribution depends on which strand of the
      recognition site must be cleaved to result in quantum dot release.  By designing additional
      substrates that mimic the various intermediate states, we plan to dissect the mechanism by
      which BcnI cleaves each strand of the intact restriction site.
AU  - Etson CM
AU  - Todorov P
AU  - Walt DR
PT  - Journal Article
TA  - Biophys. J.
JT  - Biophys. J.
SO  - Biophys. J. 2014 106: 22A.

PMID- 
VI  - 102
DP  - 2012
TI  - Single-Molecule Studies of Restriction Endonuclease Kinetics.
PG  - 486A
AB  - Under optimal conditions, restriction endonucleases are capable of mediating remarkably
      specific DNA cleavage. This quality makes the restriction endonuclease an indispensible tool
      for genetic modification and manipulation.  However, the mechanism by which restriction
      endonucleases effectively discriminate between their cognate site and other DNA sequences is
      not fully understood. Under certain conditions, many restriction endonucleases display 'star
      activity' - relaxed specificity resulting in DNA cleavage at sequences that differ from their
      normal recognition sequence - but the mechanism by which specificity is relaxed is not fully
      understood. Although at least 600 of the almost 4000 restriction endonucleases that have been
      identified are commercially available in purified form, DNA cleavage kinetics of only a few of
      these enzymes have been studied in detail. We have developed a fluorescence-based approach
      with which we can track the progress of the cleavage reaction in real time, and simultaneously
      determine the values of the kinetic constants for a particular restriction endonuclease at a
      specific sequence. Modeling restriction endonuclease-mediated DNA cleavage as a
      Michaelis-Menten-like process, we expected reaction rates to display a hyperbolic dependence
      on substrate concentration, but our measurements deviate from this dependence, especially
      under conditions associated with increased star activity (such as low ionic strength). These
      observations suggest that substrate inhibition may be a part of the reaction mechanism under
      normal conditions, and that star activity may be a result of an increase in the population of
      this pathway. Using high density arrays of femtoliter-sized reaction
      vessels created by selectively etching bundled optical fibers, we can
      observe the cleavage activity of hundreds of individual restriction endonuclease molecules in
      solution. By characterizing the population distribution of single-enzyme turnover rates under
      a variety of conditions, we hope to gain insight into the reaction mechanisms of both specific
      cleavage and star activity.
AU  - Etson CM
AU  - Wilburn F
AU  - Moody T
AU  - Fashakin V
AU  - Walt DR
PT  - Journal Article
TA  - Biophys. J.
JT  - Biophys. J.
SO  - Biophys. J. 2012 102: 486A.

PMID- 25614569
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Enterobacter sp. Strain UCD-UG_FMILLET (Phylum Proteobacteria).
PG  - e01461-14
AB  - Here, we present the draft genome of Enterobacter sp. strain UCD-UG_FMILLET. This strain is an
      endophyte isolated from the roots of finger millet, an Afro-Indian
      cereal crop. The genome contains 4,801,411 bp in 53 scaffolds.
AU  - Ettinger CL
AU  - Mousa WM
AU  - Raizada MN
AU  - Eisen JA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01461-14.

PMID- 25614570
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Burkholderia gladioli Strain UCD-UG_CHAPALOTE (Phylum Proteobacteria).
PG  - e01462-14
AB  - Here, we present the draft genome of Burkholderia gladioli strain UCD-UG_CHAPALOTE. This
      strain is an endophyte isolated from surface sterilized
      seeds of an ancient Mexican landrace of corn, Chapalote. The genome contains
      8,527,129 bp in 109 scaffolds.
AU  - Ettinger CL
AU  - Shehata HR
AU  - Johnston-Monje D
AU  - Raizada MN
AU  - Eisen JA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01462-14.

PMID- 15476804
VI  - 343
DP  - 2004
TI  - Mechanistic insights from the structures of HincII bound to cognate DNA cleaved from addition of Mg2+ and Mn2+.
PG  - 833-849
AB  - The three-dimensional X-ray crystal structures of HincII bound to cognate DNA containing
      GTCGAC and Mn2+ or Mg2+, at 2.50 Angstrom and
      2.95 Angstrom resolution, respectively, are presented. In both
      structures, the DNA is found cleaved, and the positions of the
      active-site groups, cleaved phosphate group, and 3' oxygen atom of the
      leaving group are in very similar positions. Two highly occupied Mn2+
      positions are found in each active site of the four
      crystallographically independent subunit copies in the HincII/DNA/Mn2+
      structure. The manganese ion closest to the previously identified
      single Ca2+ position of HincII is shifted 1.7 Angstrom and has lost
      direct ligation to the active-site aspartate residue, Asp127. A
      Mn2+-ligated water molecule in a position analogous to that seen in the
      HincII/DNA/Ca2+ structure, and proposed to be the attacking
      nucleophile, is beyond hydrogen bonding distance from the active-site
      lysine residue, Lys129, but remains within hydrogen bonding distance
      from the proRp oxygen atom of the phosphate group 3' to the scissile
      phosphate group. In addition, the position of the cleaved phosphate
      group is on the opposite side of the axis connecting the two metal ions
      relative to that found in the BamHI/product DNA/Mn2+ structure.
      Mechanistic implications are discussed, and a model for the
      two-metal-ion mechanism of DNA cleavage by HincII is proposed.
AU  - Etzkorn C
AU  - Horton NC
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2004 343: 833-849.

PMID- 15491133
VI  - 43
DP  - 2004
TI  - Ca2+ binding in the active site of HincII: implications for the catalytic mechanism.
PG  - 13256-13270
AB  - The 2.8 A crystal structure of the type II restriction endonuclease HincII bound to Ca(2+) and
      cognate DNA containing GTCGAC is presented. The DNA is
      uncleaved, and one calcium ion is bound per active site, in a position
      previously described as site I in the related blunt cutting type II
      restriction endonuclease EcoRV [Horton, N. C., Newberry, K. J., and
      Perona, J. J. (1998) Proc. Natl. Acad. Sci. U.S.A. 95 (23), 13489-13494],
      as well as that found in other related enzymes. Unlike the site I metal in
      EcoRV, but similar to that of PvuII, NgoMIV, BamHI, BglII, and BglI, the
      observed calcium cation is directly ligated to the pro-S(p) oxygen of the
      scissile phosphate. A calcium ion-ligated water molecule is well
      positioned to act as the nucleophile in the phosphodiester bond cleavage
      reaction, and is within hydrogen bonding distance of the conserved active
      site lysine (Lys 129), as well as the pro-R(p) oxygen of the phosphate
      group 3' of the scissile phosphate, suggesting possible roles for these
      groups in the catalytic mechanism. Kinetic data consistent with an
      important role for the 3'-phosphate group in DNA cleavage by HincII are
      presented. The previously observed sodium ion [Horton, N. C., Dorner, L.
      F., and Perona, J. J. (2002) Nat. Struct. Biol. 9, 42-47] persists in the
      active sites of the Ca(2+)-bound structure; however, kinetic data show
      little effect on the single-turnover rate of DNA cleavage in the absence
      of Na(+) ions.
AU  - Etzkorn C
AU  - Horton NC
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2004 43: 13256-13270.

PMID- 17085578
VI  - 189
DP  - 2007
TI  - M.SpyI, a DNA methyltransferase encoded on a mefA chimeric element, modifies the genome of Streptococcus pyogenes.
PG  - 1044-1054
AB  - While screening the clonality of Streptococcus pyogenes isolates from an outbreak of
      erythromycin-resistant pharyngitis in Pittsburgh, PA, we found
      a correlation between the presence of the chimeric element Phi10394.4
      (carrying the macrolide efflux gene, mefA) and genomic DNA being resistant
      to cleavage by SmaI restriction endonuclease. A search of the open reading
      frames in Phi10394.4 identified a putative type II
      restriction-modification (R-M) cassette containing a cytosine
      methyltransferase gene (spyIM). Heterologous expression of the cloned
      spyIM gene, as well as allelic-replacement experiments, showed that the
      action of this methyltransferase (M.SpyI) was responsible for the
      inhibition of SmaI digestion of genomic DNA in the Phi10394.4-containing
      isolates. Analysis of the methylation patterns of streptococcal genomic
      DNA from spyIM-positive strains, a spyIM deletion mutant, and a
      spyIM-negative strain determined that M.SpyI specifically recognized and
      methylated the DNA sequence to generate 5'-C(m)CNGG. To our knowledge,
      this is the first methyltransferase gene from S. pyogenes to be cloned and
      to have its activity characterized. These results reveal why pulsed field
      gel electrophoresis analysis of SmaI-digested genomic DNA cannot be used
      to analyze the clonality of some streptococci containing Phi10394.4 and
      may explain the inability of previous epidemiological studies to use SmaI
      to analyze DNAs from macrolide-resistant streptococci. The presence of the
      SpyI R-M cassette in Phi10394.4 could impart a selective advantage to host
      strain survival and may provide another explanation for the observed
      increase in macrolide-resistant streptococci.
AU  - Euler CW
AU  - Ryan PA
AU  - Martin JM
AU  - Fischetti VA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2007 189: 1044-1054.

PMID- 26081630
VI  - 6
DP  - 2015
TI  - Genetic Stabilization of the Drug-Resistant PMEN1 Pneumococcus Lineage by Its Distinctive DpnIII Restriction-Modification System.
PG  - e00173-15
AB  - The human pathogen Streptococcus pneumoniae (pneumococcus) exhibits a high degree of genomic
      diversity and plasticity. Isolates with high genomic similarity are
      grouped into lineages that undergo homologous recombination at variable rates.
      PMEN1 is a pandemic, multidrug-resistant lineage. Heterologous gene exchange
      between PMEN1 and non-PMEN1 isolates is directional, with extensive gene transfer
      from PMEN1 strains and only modest transfer into PMEN1 strains.
      Restriction-modification (R-M) systems can restrict horizontal gene transfer, yet
      most pneumococcal strains code for either the DpnI or DpnII R-M system and
      neither limits homologous recombination. Our comparative genomic analysis
      revealed that PMEN1 isolates code for DpnIII, a third R-M system syntenic to the
      other Dpn systems. Characterization of DpnIII demonstrated that the endonuclease
      cleaves unmethylated double-stranded DNA at the tetramer sequence 5' GATC 3', and
      the cognate methylase is a C5 cytosine-specific DNA methylase. We show that
      DpnIII decreases the frequency of recombination under in vitro conditions, such
      that the number of transformants is lower for strains transformed with
      unmethylated DNA than in those transformed with cognately methylated DNA.
      Furthermore, we have identified two PMEN1 isolates where the DpnIII endonuclease
      is disrupted, and phylogenetic work by Croucher and colleagues suggests that
      these strains have accumulated genomic differences at a higher rate than other
      PMEN1 strains. We propose that the R-M locus is a major determinant of genetic
      acquisition; the resident R-M system governs the extent of genome plasticity.
      IMPORTANCE: Pneumococcus is one of the most important community-acquired
      bacterial pathogens. Pneumococcal strains can develop resistance to antibiotics
      and to serotype vaccines by acquiring genes from other strains or species. Thus,
      genomic plasticity is associated with strain adaptability and pneumococcal
      success. PMEN1 is a widespread and multidrug-resistant highly pathogenic
      pneumococcal lineage, which has evolved over the past century and displays a
      relatively stable genome. In this study, we characterize DpnIII, a
      restriction-modification (R-M) system that limits recombination. DpnIII is
      encountered in the PMEN1 lineage, where it replaces other R-M systems that do not
      decrease plasticity. Our hypothesis is that this genomic region, where different
      pneumococcal lineages code for variable R-M systems, plays a role in the
      fine-tuning of the extent of genomic plasticity. It is possible that well-adapted
      lineages such as PMEN1 have a mechanism to increase genomic stability, rather
      than foster genomic plasticity.
AU  - Eutsey RA
AU  - Powell E
AU  - Dordel J
AU  - Salter SJ
AU  - Clark TA
AU  - Korlach J
AU  - Ehrlich GD
AU  - Hiller NL
PT  - Journal Article
TA  - MBio
JT  - MBio
SO  - MBio 2015 6: e00173-15.

PMID- 
VI  - 125
DP  - 2010
TI  - Implications of fast-time scale dynamics of human DNA/RNA cytosine methyltransferases (DNMTs) for protein function.
PG  - 407-418
AB  - The role of protein dynamics in the control of substrate recognition, catalysis, and
      protein-protein interactions is often underestimated. Recently, a number of studies have
      examined the contribution of protein dynamics to the thermodynamics of ligand binding in
      detail,
      mostly using NMR relaxation measurements and molecular dynamics (MD) simulations. The results
      unequivocally demonstrate that conformational dynamics play a pivotal role in the properties
      and functions of proteins, and
      ignoring this contribution is likely to lead to substantial errors when explaining the
      biological function of proteins and in predictions of the binding affinities of their cognate
      ligands. However, the details of the interplay between structure and dynamics and the way it
      affects the biological function of the target protein remain poorly understood. In
      this study, the changes in fast (picosecond-to-nanosecond time scale) dynamics of catalytic
      domains of four human cytosine DNA methyltransferases (DNMTs) were studied using molecular
      dynamics (MD) simulations. The results
      provide insight into the protein dynamics changes that occur upon binding of the cofactor,
      S-adenosylmethionine (SAM). Contrary to expectations, increased amplitude of motions of
      backbone amide (N-H) and terminal heavy
      atom (C-C) bond vectors was observed in all studied DNMTs upon binding of SAM. These results
      imply that the cofactor binding causes a global increase in the extent of protein dynamics in
      the short time scale. This global
      dynamic change constitutes a favourable entropic contribution to the free energy of SAM
      binding. These results suggest that cytosine DNA methyltransferases may exploit changes in
      their fast scale dynamics to reduce the entropic cost of the substrate binding.
AU  - Evans DA
AU  - Bronowska AK
PT  - Journal Article
TA  - Theor. Chem. Acc.
JT  - Theor. Chem. Acc.
SO  - Theor. Chem. Acc. 2010 125: 407-418.

PMID- 8081502
VI  - 140
DP  - 1994
TI  - Characterization of the Streptomyces-lividans-type site-specific DNA modification system in the avermectin-producer Streptomyces avermitilis permits investigation of two novel giant linear plasmids, pSA1 and pSA2.
PG  - 1367-1371
AB  - The degradation of Streptomyces avermitilis DNA samples analysed by conventional pulsed-field
      gel electrophoresis was shown to be due to Tris-dependent, double-strand cleavage.  Using
      alternative electrophoretic conditions, separation of intact DNA molecules was achieved,
      permitting the identification of two novel giant linear plasmids: the 100 kb pSA1 and 250 kb
      pSA2.  Use of pSA2 DNA as a probe showed that pSA1 does not cross-hybridize, indicating that
      the plasmids are not closely related.  The site-specificity of the DNA modifications, which
      render the DNA susceptible to Tris-dependent cleavage, was found to be essentially identical
      to that of similar modifications found in the DNA of S. lividans.
AU  - Evans M
AU  - Kaczmarek FS
AU  - Stutzman-Engwall K
AU  - Dyson P
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 1994 140: 1367-1371.

PMID- 24903882
VI  - 2
DP  - 2014
TI  - Complete Genome Sequences of Salmonella enterica Serovar Heidelberg Strains Associated with a Multistate Food-Borne Illness Investigation.
PG  - e01154-13
AB  - Next-generation sequencing is being evaluated for use with food-borne illness investigations,
      especially when the outbreak strains produce patterns that cannot
      be discriminated from non-outbreak strains using conventional procedures. Here we
      report complete genome assemblies of two Salmonella enterica serovar Heidelberg
      strains with a common pulsed-field gel electrophoresis pattern isolated during an
      outbreak investigation.
AU  - Evans PS
AU  - Luo Y
AU  - Muruvanda T
AU  - Ayers S
AU  - Hiatt B
AU  - Hoffman M
AU  - Zhao S
AU  - Allard MW
AU  - Brown EW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01154-13.

PMID- 9827992
VI  - 7
DP  - 1998
TI  - Semisynthesis of cytotoxic proteins using a modified protein splicing element.
PG  - 2256-2264
AB  - Two cytotoxic proteins, bovine pancreatic ribonuclease A (RNase A), and a restriction
      endonuclease from Haemophilus parainfluenzae (HpaI), were produced using a novel semisynthetic
      approach that utilizes a protein splicing element, an intein, to generate a reactive thioester
      at the C-terminus of a recombinant protein. Nucleophilic attack on this thioester by the
      N-terminal cysteine of a synthetic peptide ultimately leads to the ligation of the two
      reactants through a native peptide bond. This strategy was used to produce RNase A and HpaI by
      isolating inactive truncated forms of these proteins, the first 109 and 223 amino acids of
      RNase A and HpaI, respectively, as fusion proteins consisting of the target protein, an
      intein, and a chitin binding domain. Thiol-induced cleavage of the precursor led to the
      liberation of the target protein with a C-terminal thioester-tag. Addition of synthetic
      peptides representing the amino acids missing from the truncated forms led to the generation
      of full-length products that displayed catalytic activity indicative of the wild-type enzymes.
      The turnover numbers and Km for ligated and renatured RNase A were 8.2 s(-1) and 1.5 mM, in
      good agreement with reported values of 8.3 s(-1) and 1.2 mM (Hodges & Merrifield, 1975).
      Ligated HpaI had a specific activity of 0.5-1.5 x 10(6) U/mg, which compared favorably with
      the expected value of 1-2 x 10(6) U/mg (J. Benner, unpubl. obs.). Besides assisting in the
      production of cytotoxic proteins, this technique could allow the easy insertion of unnatural
      amino acids into a protein sequence.
AU  - Evans TC Jr
AU  - Benner J
AU  - Xu MQ
PT  - Journal Article
TA  - Protein Sci.
JT  - Protein Sci.
SO  - Protein Sci. 1998 7: 2256-2264.

PMID- 17630395
VI  - 282
DP  - 2007
TI  - Study of bacteriophage T4-encoded dam DNA (Adenine-N-6)-methyltransferase binding with substrates by rapid laser  UV cross-linking.
PG  - 26067-26076
AB  - DNA methyltransferases of the Dam family ( including bacteriophage T4-encoded Dam DNA
      (adenine- N-6)-methyltransferase ( T4Dam)) catalyze
      methyl group transfer from S-adenosyl-L-methionine ( AdoMet), producing
      S-adenosyl-Lhomocysteine ( AdoHcy) and methylated adenine residues in
      palindromic GATC sequences. In this study, we describe the application
      of direct ( i. e. no exogenous cross-linking reagents) laser UV
      cross-linking as a universal non-perturbing approach for studying the
      characteristics of T4Dam binding with substrates in the equilibrium and
      transient modes of interaction. UV irradiation of the enzyme center dot
      substrate complexes using an Nd3(+): yttrium aluminum garnet laser at
      266nm resulted in up to 3 and > 15% yields of direct T4Dam
      cross-linking to DNA and AdoMet, respectively. Consequently, we were
      able to measure equilibrium constants and dissociation rates for enzyme
      center dot substrate complexes. In particular, we demonstrate that both
      reaction substrates, specific DNA and AdoMet( or product AdoHcy),
      stabilized the ternary complex. The improved substrate affinity for the
      enzyme in the ternary complex significantly reduced dissociation rates
      ( up to 2 orders of magnitude). Several of the parameters obtained (
      such as dissociation rate constants for the binary T4Dam center dot
      AdoMet complex and for enzyme complexes with a non-fluorescent
      hemimethylated DNA duplex) were previously inaccessible by other means.
      However, where possible, the results of laser UV cross-linking were
      compared with those of fluorescence analysis. Our study suggests that
      rapid laser UV cross-linking efficiently complements standard DNA
      methyltransferase-related tools and is a method of choice to probe
      enzyme-substrate interactions in cases in which data cannot be acquired
      by other means.
AU  - Evdokimov AA
AU  - Sclavi B
AU  - Zinoviev VV
AU  - Malygin EG
AU  - Hattman S
AU  - Buckle M
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2007 282: 26067-26076.

PMID- 
VI  - 43
DP  - 2009
TI  - Design of oligonucleotide inhibitors for human DNA methyltransferase 1.
PG  - 418-425
AB  - Mammalian DNA methyltransferase 1 (Dnmt1) is responsible for copying the DNA methylation
      pattern during cell division. Since Dnmt1 plays an
      important role in carcinogenesis, it is of particular interest to
      search for its specific inhibitors. To design oligonucleotide
      inhibitors of human Dnmt1, a number of singlestranded, double-stranded,
      and hairpin DNA structures containing a canonical or a modified Dnmt1
      recognition site (5'-CG) were constructed on the basis of a 22-nt
      sequence. Structural features such as a C:A mismatch,
      phosphorothioates, and hairpins proved capable of incrementally
      increasing the oligonucleotide affinity for Dnmt1. An improvement of
      inhibitory properties was also achieved by replacing the target
      cytosine with 5,6-dihydro-5-azacytosine, 5-methyl-2-pyrimidinone, or
      6-methyl-pyrrolo-[2,3-d]-2-pyrimidinone. The concentration that caused
      50% inhibition of methylation of 1 mu M poly(dI-dC) center dot
      poly(dI-dC), a conventional DNA substrate, was approximately 10(-7) M
      for the most efficient oligonucleotides. Under the same in vitro
      conditions, these oligonucleotide inhibitors demonstrated a
      substantially stronger effect compared to known Dnmt1 inhibitors, which
      were used as controls.
AU  - Evdokimov AA
AU  - Zinoviev VV
AU  - Kuznetsov VV
AU  - Netesova NA
AU  - Malygin EG
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2009 43: 418-425.

PMID- 12391849
VI  - 36
DP  - 2002
TI  - The Kinetic Mechanism of Phage T4 DNA-[N6-Adenine]-Methyltransferase.
PG  - 849-861
AB  - Kinetic analysis of methyl group transfer from S-adenosyl-L-methionine to the GATC recognition
      site catalyzed by the phage T4 DNA-[N6-adenine]-methyltransferase [EC 2.1.1.72] showed that
      the reverse reaction is at least 500 times lower than the direct one.  The overall pattern of
      product inhibition corresponds to an ordered steady-state mechanism following the sequence
      SAM/DNA/metDNA/SAH/.  Pronounced inhibition was observed at high concentrations of the
      20-meric substrate duplex, which may be attributed to formation of a dead-end complex
      MTase-SAH-DNA.  In contrast, high SAM concentrations proportionally accelerated the reaction.
      Thus, the reaction may include a stage whereby the binding of SAM and the release of SAH are
      united into one concerted event.  Computer fitting of alternative kinetic schemes to the
      aggregate of experimental data revealed that the most plausible mechanism involves
      isomerization of the enzyme.
AU  - Evdokimov AA
AU  - Zinoviev VV
AU  - Malygin EG
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2002 36: 849-861.

PMID- 11221270
VI  - 26
DP  - 2000
TI  - Effect of S-adenosyl-L-methionine and its analogues on site-specific binding of DNA-(adenine-N6)-methyltransferase of T4 phage with the oligonucleotide substrate.
PG  - 797-800
AB  - Using fluorescence of 2-aminopurine-substituted oligonucleotide duplexes, "flipping" of the
      target base in the process of interaction of T4 DNA-(adenine-N6)-methyltransferase (EC
      2.1.1.72) with the substrate double-stranded DNA was revealed.  It was shown that
      S-adenosyl-L-methionine, the methyl group donor, induces the reorientation of the enzyme
      relative to the asymmetrically modified recognition site.
AU  - Evdokimov AA
AU  - Zinoviev VV
AU  - Malygin EG
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 2000 26: 797-800.

PMID- 11687585
VI  - 277
DP  - 2002
TI  - Bacteriophage T4 Dam DNA-[N6-adenine]Methyltransferase. Kinetic evidence for a catalytically essential conformational change in the ternary complex.
PG  - 279-286
AB  - We carried out a steady state kinetic analysis of the bacteriophage T4
      DNA-[N(6)-adenine]methyltransferase (T4 Dam) mediated methyl group transfer reaction from
      S-adenosyl-l-methionine (AdoMet) to Ade in the palindromic recognition sequence, GATC, of a
      20-mer oligonucleotide duplex. Product inhibition patterns were consistent with a steady
      state-ordered bi-bi mechanism in which the order of substrate binding and product (methylated
      DNA, DNA(Me) and S-adenosyl-l-homocysteine, AdoHcy) release was AdoMet, DNA, DNA(Me), Hcy. A
      strong reduction in the rate of methylation was observed at high concentrations of the
      substrate 20-mer DNA duplex. In contrast, increasing substrate AdoMet concentration led to
      stimulation in the reaction rate with no evidence of saturation. We propose the following
      model. Free T4 Dam (initially in conformational form E) randomly interacts with substrates
      AdoMet and DNA to form a ternary T4 Dam-AdoMet-DNA complex in which T4 Dam has isomerized to
      conformational state F, which is specifically adapted for catalysis. After the chemical step
      of methyl group transfer from AdoMet to DNA, product DNA(Me) dissociates relatively rapidly
      (k(off) = 1.7 s(-1)) from the complex. In contrast, dissociation of product AdoHcy proceeds
      relatively slowly (k(off) = 0.018 s(-1)), indicating that its release is the rate-limiting
      step, consistent with k(cat) = 0.015 s(-1). After AdoHcy release, the enzyme remains in the F
      conformational form and is able to preferentially bind AdoMet (unlike form E, which randomly
      binds AdoMet and DNA), and the AdoMet-F binary complex then binds DNA to start another
      methylation cycle. We also propose an alternative pathway in which the release of AdoHcy is
      coordinated with the binding of AdoMet in a single concerted event, while T4 Dam remains in
      the isomerized form F. The resulting AdoMet-F binary complex then binds DNA, and another
      methylation reaction ensues. This route is preferred at high AdoMet concentrations.
AU  - Evdokimov AA
AU  - Zinoviev VV
AU  - Malygin EG
AU  - Schlagman SL
AU  - Hattman S
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2002 277: 279-286.

PMID- 2996656
VI  - 100
DP  - 1985
TI  - Inheritance and phenotypic expression of plasmids coding EcoRI restriction endonuclease in Vibrio cholerae cells.
PG  - 472-474
AB  - Restriction endonucleases are widely used nowadays to clone DNA fragments of different origin
      with the aid of vector molecules of plasmids and bacteriophages.  The process of DNA
      recombination, in which restriction endonucleases take part, also takes place in vitro.  The
      obtaining of hybrid molecules in vivo, due to the action of restriction endonucleases can in
      many cases facilitate the task of cloning foreign DNA in bacterial cells.  For instance, by
      means of a technique based on completion of a recA-independent recombination process,
      EcoRI-dependent cloning of DNA has been carried out in Escherichia coli cells in vivo, so that
      it was possible to obtain plasmids carrying recB+C+ genes or enterotoxin Ent genes.
      Reproduction of this process in Vibrio cholerae opens up a new approach to the obtaining of
      recombinant plasmids carrying genes of V. cholerae and, in particular, genes responsible for
      the leading pathogenetic sign of V. cholerae, namely toxin formation.  For this purpose it was
      necessary to transfer into V. cholerae cells a plsmid coding restriction endonuclease EcoRI,
      to preserve it in V. cholerae cells, and to express EcoRI activity in them.  The aim of this
      investigaton was to construct such a plasmid and to investigate the phenotypic expression of
      its genetic determinants in V. cholerae cells.
AU  - Evdokimova NM
AU  - Aleshkin GI
AU  - Skavronskaya AG
PT  - Journal Article
TA  - Biull. Eksp. Biol. Med.
JT  - Biull. Eksp. Biol. Med.
SO  - Biull. Eksp. Biol. Med. 1985 100: 472-474.

PMID- 28408684
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Fish Pathogen Flavobacterium columnare Strain CSF-298-10.
PG  - e00173-17
AB  - We announce here the draft genome assembly of Flavobacterium columnare CSF-298-10, a strain
      isolated from an outbreak of columnaris disease at a
      commercial trout farm in Hagerman Valley, Idaho, USA. The complete genome
      consists of 13 contigs totaling 3,284,579 bp, with an average G+C content of
      31.5% and 2,933 predicted coding genes.
AU  - Evenhuis JP
AU  - LaPatra SE
AU  - Graf J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00173-17.

PMID- 
VI  - 
DP  - 1990
TI  - Structure-function analysis of the EcoRI DNA Methylase.
PG  - 1-190
AB  - The structural characteristics of the E. coli EcoRI methylase involved in methyl transfer from
      S-adenosyl-L-methionine to DNA and in binding these moities were analyzed. This study provides
      a "picture" of the methylase structure binding regions, critical residues and catalytic state.
      Not much structure-function information is available about DNA methylases or S-
      adenosyl-L-methionine binding enzymes. For DNA methylases, little is known about
      protein-cofactor interactions or the mechanisms of methyl transfer to DNA. Information about
      the E. coli EcoRI methylase is of interest since S-adenosyl-L-methionine is the methyl group
      donor for a large range of enzymes and the importance of DNA methylation is becoming
      increasingly obvious. Determination of structure-function relationships used traditional and
      innovative protein chemistries. These included proteolytic patterns, photoaffinity labeling
      with [methyl-3H]8-azido-S-adenosyl-L-methionine, chemical modification of cysteine and
      histidine residues, fluorescence spectroscopy and mass spectrometry.
AU  - Everett EA
PT  - Journal Article
TA  - Ph.D. Thesis, Univ. of California, Santa Barbara
JT  - Ph.D. Thesis, Univ. of California, Santa Barbara
SO  - Ph.D. Thesis, Univ. of California, Santa Barbara 1990 : 1-190.

PMID- 2170393
VI  - 265
DP  - 1990
TI  - Identification of a critical cysteine in EcoRI DNA methyltransferase by mass spectrometry.
PG  - 17713-17719
AB  - EcoRI DNA methyltransferase (MTase) is rapidly inactivated by N-ethylmaleimide
      with concomitant incorporation of 2 mol of N-ethyl[2-3H]maleimide/mol of
      functional monomer.  Preincubation of the enzyme with either
      S-adenosylmethionine or DNA reduces the rate of activity loss, whereas
      preincubation with DNA and the S-adenosylmethionine analog sinefungin
      completely protects the enzyme from inactivation.  An endo proteinase Glu-C
      digest of N-ethyl[2-3H]maleimide-modified enzyme was prepared and separated by
      high pressure liquid chromatography.  Modified and unmodified
      cysteine-containing peptides were located and identified by radioactivity, mass
      spectrometry, and tandem mass spectrometry.  In the absence of any ligands,
      cysteines 25, 116, and 223 are modified by N-ethylmaleimide; in the presence of
      DNA and sinefungin Cys-223 is essentially unmodified.  Thus, N-ethylmaleimide
      modification of Cys-223 in EcoRI DNA MTase is responsible for the loss of
      enzyme activity.  Cys-223 is preceded by Asn, and this (or Cys-Asn) occurs with
      high frequency in adenine and cytosine (N-4) DNA MTases.  Direct involvement of
      cysteine in methyl transfer reactions to adenine N-6 and cytosine N-4 is
      supported by the similarity of the reactions catalyzed by adenine N-6 and
      cytosine N-4 DNA MTases, the frequent presence of Asn-flanking Cys, and the
      importance of Cys-223 to EcoRI MTase function.
AU  - Everett EA
AU  - Falick AM
AU  - Reich NO
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1990 265: 17713-17719.

PMID- 3192615
VI  - 107
DP  - 1988
TI  - Determination of the EcoRI methylase Adomet binding region.
PG  - 854a
AB  - Although S-Adenosylmethionine (Adomet) is a methyl group donor in many
      enzymatic reactions including DNA methylation, structural features of DNA
      methylases necessary for Adomet binding and DNA methylation have not yet been
      determined.  Investigating structural determinants of activity is critical in
      understanding methylation and its role in gene expression, DNA repair,
      restriction-modification and carcinogenesis.  Our research involves the E. coli
      EcoRI methylase which transfers the methyl group from Adomet to the second
      adenine in GAATC DNA sequences.  Methylation protects the site from cleavage by
      the corresponding endonuclease.  We have synthesized an Adomet photoaffinity
      analog, 3H8-AzidoAdomet, which binds specifically to the Adomet site with
      similar binding and catalytic constants.  Covalent modification of the binding
      site with 3H8-AzAdomet and subsequent chromatographic, electrophoretic,
      autoradiographic and sequence analyses of proteolytic digests are being
      employed in isolating the methylase portion critical for Adomet binding.  A
      peptide segment of the Adomet binding site to which 3H8-AzAdomet binds has been
      obtained and is being identified along with the covalently modified amino acid
      residue or residues.
AU  - Everett EA
AU  - Reich NO
PT  - Journal Article
TA  - J. Cell Biol.
JT  - J. Cell Biol.
SO  - J. Cell Biol. 1988 107: 854a.

PMID- Not carried by PubMed...
VI  - 196
DP  - 1988
TI  - Determination of the EcoRI methylase Adomet binding region.
PG  - 94
AB  - Although S-Adenosylmethionine (Adomet) is a methyl group donor in many
      enzymatic reactions including DNA methylation, structural features of DNA
      methylases necessary for Adomet binding and DNA methylation have not yet been
      determined.  Investigating structural determinants of activity is critical in
      understanding methylation and its role in gene expression, DNA repair,
      restriction-modification and carcinogenesis.  Our research involves the E. coli
      EcoRI methylase which transfers the methyl group from Adomet to the second
      adenine in GAATTC DNA sequences.  Methylation protects the site from cleavage
      by the corresponding endonuclease.  We have synthesized an Adomet photoaffinity
      analog.  3H8-AzidoAdomet, which binds specifically to the Adomet site with
      similar binding and catalytic constants.  Covalent modification of the binding
      site with 3H8-AzAdomet and subsequent chromatographic, electrophoretic,
      autoradiographic and sequence analyses of proteolytic digests are being
      employed in isolating the methylase portion critical for Adomet binding.  A
      peptide segment of the Adomet binding site to which 3H8-AzAdomet binds has been
      obtained and is being identified along with the covalently modified amino acid
      residue or residues.
AU  - Everett EA
AU  - Reich NO
PT  - Journal Article
TA  - ACS Abstracts
JT  - ACS Abstracts
SO  - ACS Abstracts 1988 196: 94.

PMID- 2803296
VI  - 164
DP  - 1989
TI  - EcoRI DNA methylase activity is eliminated upon histidine residue modification.
PG  - 233-237
AB  - The E. coli EcoRI DNA methylase activity is completely eliminated in five
      minutes upon incubation with the histidine residue specific reagent diethyl
      pyrocarbonate.  In that two moles of N-ethoxyformylimidazole per mole of
      methylase are detected spectroscopically upon inactivation and activity is not
      restored by hydroxylamine, it is likely that activity loss is due to double
      modification of a single histidine residue.  This information is critical in
      determining the enzymatic mechanism, causes of the pH-activity curve, designing
      protein mutants and interpreting previous structure-function data.
AU  - Everett EA
AU  - Reich NO
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1989 164: 233-237.

PMID- 10438738
VI  - 181
DP  - 1999
TI  - An unspliced group I intron in 23S rRNA links chlamydiales, chloroplasts, and mitochondria.
PG  - 4734-4740
AB  - Chlamydia was the only genus in the order Chlamydiales until the
      recent characterization of Simkania negevensis Z(T) and Parachlamydia
      acanthamoebae strains. The present study of Chlamydiales 23S ribosomal
      DNA (rDNA) focuses on a naturally occurring group I intron in the I-
      CpaI target site of 23S rDNA from S. negevensis. The intron, SnLSU. 1,
      belonged to the IB4 structural subgroup and was most closely related to
      large ribosomal subunit introns that express single-motif, LAGLIDADG
      endonucleases in chloroplasts of algae and in mitochondria of amoebae.
      RT-PCR and electrophoresis of in vivo rRNA indicated that the intron
      was not spliced out of the 23S rRNA. The unspliced 658-nt intron is the
      first group I intron to be found in bacterial rDNA or rRNA, and it may
      delay the S. negevensis developmental replication cycle by affecting
      ribosomal function.
AU  - Everett KD
AU  - Kahane S
AU  - Bush RM
AU  - Friedman MG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1999 181: 4734-4740.

PMID- 27559430
VI  - 11
DP  - 2016
TI  - Permanent draft genome of strain ESFC-1: ecological genomics of a newly discovered lineage of filamentous diazotrophic cyanobacteria.
PG  - 53
AB  - The nonheterocystous filamentous cyanobacterium, strain ESFC-1, is a recently described member
      of the order Oscillatoriales within the Cyanobacteria. ESFC-1
      has been shown to be a major diazotroph in the intertidal microbial mat system at
      Elkhorn Slough, CA, USA. Based on phylogenetic analyses of the 16S RNA gene,
      ESFC-1 appears to belong to a unique, genus-level divergence; the draft genome
      sequence of this strain has now been determined. Here we report features of this
      genome as they relate to the ecological functions and capabilities of strain
      ESFC-1. The 5,632,035 bp genome sequence encodes 4914 protein-coding genes and 92
      RNA genes. One striking feature of this cyanobacterium is the apparent lack of
      either uptake or bi-directional hydrogenases typically expected within a
      diazotroph. Additionally, a large genomic island is found that contains numerous
      low GC-content genes and genes related to extracellular polysaccharide production
      and cell wall synthesis and maintenance.
AU  - Everroad RC
AU  - Stuart RK
AU  - Bebout BM
AU  - Detweiler AM
AU  - Lee JZ
AU  - Woebken D
AU  - Prufert-Bebout L
AU  - Pett-Ridge J
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 53.

PMID- 23908279
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of an Oscillatorian Cyanobacterium, Strain ESFC-1.
PG  - e00527-13
AB  - The nonheterocystous filamentous cyanobacterium strain ESFC-1 has recently been isolated from
      a marine microbial mat system, where it was identified as belonging
      to a recently discovered lineage of active nitrogen-fixing microorganisms. Here,
      we report the draft genome sequence of this isolate. The assembly consists of 3
      scaffolds and contains 5,632,035 bp with a GC content of 46.5%.
AU  - Everroad RC
AU  - Woebken D
AU  - Singer SW
AU  - Burow LC
AU  - Kyrpides N
AU  - Woyke T
AU  - Goodwin L
AU  - Detweiler A
AU  - Prufert-Bebout L
AU  - Pett-Ridge J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00527-13.

PMID- 26430051
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Four Genetically Distinct Human Isolates of Streptococcus dysgalactiae subsp. equisimilis.
PG  - e01139-15
AB  - beta-Hemolytic group C and group G streptococci (GCS-GGS; Streptococcus dysgalactiae subsp.
      equisimilis) emerged as human pathogens in the late 1970s. We report here the draft genome
      sequences of four genetically distinct human strains of GCS-GGS isolated between the 1960s and
      1980s. Comparative analysis of these genomes may provide a deeper understanding of GCS-GGS
      genome and virulence evolution.
AU  - Evers C
AU  - Patel K
AU  - Petrosyan V
AU  - Morrison C
AU  - Varghese V
AU  - Chu RA
AU  - Baig A
AU  - Thompson EJ
AU  - Chase M
AU  - Hu PC
AU  - Kalia A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01139-15.

PMID- 6139814
VI  - 219
DP  - 1983
TI  - Inference problems in population genetics:  DNA sequences, restriction endonucleases and ascertainment sampling.
PG  - 223-239
AB  - A major trend of population genetics theory in the 1970s was the increased
      emphasis on inductive arguments, based on observed genetic data, rather than on
      deductive arguments based on theory and models.  This occurred in part because
      the deductive theory had largely fulfilled its role of describing evolution as
      a genetic process, and in part because of the increasing amounts of data
      available on the genetic constitution of natural populations.  Inference
      procedures raise difficulties not present in the deductive theory.  Often
      conditional arguments are necessary since the data often must fulfil some
      condition to be observed.  Different inference procedures, having different
      efficiencies, apply for data from different apparatuses.  Care must be taken in
      deciding what it is the inference concerns.  These problems are illustrated by
      reference to restriction endonuclease techniques and ascertainment sampling.
AU  - Ewens WJ
PT  - Journal Article
TA  - Proc. R. Soc. Lond. B Biol. Sci.
JT  - Proc. R. Soc. Lond. B Biol. Sci.
SO  - Proc. R. Soc. Lond. B Biol. Sci. 1983 219: 223-239.

PMID- 27587807
VI  - 4
DP  - 2016
TI  - Genome Sequence of Avian Escherichia coli Strain IHIT25637, an Extraintestinal Pathogenic E. coli Strain of ST131 Encoding Colistin Resistance Determinant  MCR-1.
PG  - e00863-16
AB  - Sequence type 131 (ST131) is one of the predominant Escherichia coli lineages among
      extraintestinal pathogenic E. coli (ExPEC) that causes a variety of
      diseases in humans and animals and frequently shows multidrug resistance. Here,
      we report the first genome sequence of an ST131-ExPEC strain from poultry
      carrying the plasmid-encoded colistin resistance gene mcr-1.
AU  - Ewers C
AU  - Gottig S
AU  - Bulte M
AU  - Fiedler S
AU  - Tietgen M
AU  - Leidner U
AU  - Heydel C
AU  - Bauerfeind R
AU  - Semmler T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00863-16.

PMID- 8198576
VI  - 201
DP  - 1994
TI  - Evidence for a site-specific endonuclease in yeast mitochondria which recognizes the sequence 5'GCCCGGC.
PG  - 208-214
AB  - We have discovered a mitochondrial, site-specific DNase in Saccharomyces cerevisiae with
      properties like that of a type II restriction endonuclease. The enzyme, termed SceIII, cleaves
      the palindromic sequence, 5'GCCGGC, to give 3' ends recessed by 4 bases. SceIII is the first
      restriction-like endonuclease to be described in yeast mitochondria.
AU  - Ezekiel UR
AU  - Zassenhaus P
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1994 201: 208-214.

PMID- 17890317
VI  - 104
DP  - 2007
TI  - MicroRNA-29 family reverts aberrant methylation in lung cancer by targeting DNA methyltransferases 3A and 3B.
PG  - 15805-15810
AB  - MicroRNAs (miRNAs) are small, noncoding RNAs that regulate expression of many genes. Recent
      studies suggest roles of miRNAs in
      carcinogenesis. We and others have shown that expression profiles of
      miRNAs are different in lung cancer vs. normal lung, although the
      significance of this aberrant expression is poorly understood. Among
      the reported down-regulated miRNAs in lung cancer, the miRNA (miR)-29
      family (29a, 29b, and 29c) has intriguing complementarities to the
      3'-UTRs of DNA methyltransferase (DNMT)3A and -3B (de novo
      methyltransferases), two key enzymes involved in DNA methylation, that
      are frequently up-regulated in lung cancer and associated with poor
      prognosis. We investigated whether miR-29s could target DNMT3A and -B
      and whether restoration of miR-29s could normalize aberrant patterns of
      methylation in non-small-cell lung cancer. Here we show that expression
      of miR-29s is inversely correlated to DNMT3A and -3B in lung cancer
      tissues, and that miR-29s directly target both DNMT3A and -3B. The
      enforced expression of miR-29s in lung cancer cell lines restores
      normal patterns of DNA methylation, induces reexpression of
      methylation-silenced tumor suppressor genes, such as FHIT and WWOX, and
      inhibits tumorigenicity in vitro and in vivo. These findings support a
      role of miR-29s in epigenetic normalization of NSCLC, providing a
      rationale for the development of miRNA-based strategies for the
      treatment of lung cancer.
AU  - Fabbri M
AU  - Garzon R
AU  - Cimmino A
AU  - Liu Z
AU  - Zanesi N
AU  - Callegari E
AU  - Liu S
AU  - Alder H
AU  - Costinean S
AU  - Fernandez-Cymering C
AU  - Volinia S
AU  - Guler G
AU  - Morrison CD
AU  - Chan KK
AU  - Marcucci G
AU  - Calin GA
AU  - Huebner K
AU  - Croce CM
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2007 104: 15805-15810.

PMID- 
VI  - 12
DP  - 1998
TI  - Characterization of the Bacillus amyloliquefaciens HI methyltransferase.
PG  - A1446
AB  - Type II DNA methyltransferases are part of bacterial restriction-modification systems.
      Methyltransferases function as monomers, recognize a palindromic DNA sequence and use
      S-adenosyl-methionine as the methyl donor.  The Bacillus amyloliquefaciens methyltransferase
      is a 49 kDa protein which methylates the N4 position of cytosine in the DNA sequence GGATCC.
      Protein sequence alignment shows that M.BamHI has structural homology to M.TaqI.  The
      carboxyl-terminal region of M.BamHI also contains a region showing 72% identity to the
      predicted DNA binding region of M.DpnA.  Here, we report the properties of truncated proteins
      missing either the N or C terminus amino acids.  These truncated proteins have been tested for
      SAM and DNA binding as well as methylation activity.  However, specificity appears to be
      relaxed. In contrast, deletion of the carboxyl-terminus removes both DNA binding and
      methylating activity although SAM binding activity is retained.  The peptide produced from in
      vitro transcription/translation of the carboxyl-terminal region is being tested for DNA
      binding activity.  These results assign the DNA binding activity of M.BamHI to the
      carboxyl-terminal of the protein as predicted from sequence alignment studies.  The N-terminus
      region is necessary for increasing the specificity of the enzyme.
AU  - Fabian JS
AU  - Mattson T
AU  - Bazar LS
AU  - Chirikjian JG
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1998 12: A1446.

PMID- 9279140
VI  - 11
DP  - 1997
TI  - Characterization of the Bacillus amyloliquefaciens HI methyltransferase.
PG  - A900
AB  - Type II DNA methyltransferases are part of bacterial restriction-modification systems.  Most
      of the Mtases function as monomers, recognize a palindromic DNA sequence and use
      S-Adenosyl-Methionine as the methyl donor.  The Bacillus amyloliquefaciens methyltransferase
      is a 49kDa protein which methylates at the N4 position of cytosine in the sequence GGATCC.
      Crystal structures of three DNA Mtases show that they are folded into two domains.  The
      C-terminal domain is responsible for specific recognition and binding of the target DNA
      sequence.  The N-terminal domain contains the catalytic site formed by the conserved motif IV
      (NPPY in M.TaqI and PCQ in M.HhaI and M.HaeIII) and a deep cleft that harbors the cofactor
      SAM.  Crystal structures have also revealed that these enzymes extrude the target base from
      the double helix into the catalytic pocket where the methyl transfer occurs.  Partial
      proteolytic digestion of the BamHI methylase using Proteinase K generates a 38kDa peptide
      fragment that maintains methylase activity in vitro.  N-terminal peptide sequencing indicates
      that the fragment is missing 103 amino acids from the N-terminal end.  Gel shift assays
      indicate that the 38kDa fragment is able to interact with the DNA in a sequence dependent
      manner.  Preliminary kinetic analysis of the proteolytic fragment shows a decreased Km, Kcat
      and Vmax.  We are currently constructing C-terminal deletion mutants and will test them for
      methylase and DNA binding activity.
AU  - Fabian JS
AU  - Mattson T
AU  - Chirikjian JG
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1997 11: A900.

PMID- 8682220
VI  - 10
DP  - 1996
TI  - Comparative study of the biochemical properties of cellular and viral DNA-methyltransferases from Bacillus amyloliquefaciens H1.
PG  - A1103
AB  - Methyltransferases (Mtases) are a class of enzymes which place methyl groups onto a variety of
      substrates using S-adenosyl-methionine as a cofactor.  In prokaryotes, Mtases are often part
      of a restriction-modification system in which their role is to protect the host DNA from
      cleavage by the restriction enzyme.  Bacillus amyloliquefaciens HI contains two distinct
      methyltransferases (M.BamHI and M.BamHII) which recognize and methylate the same double
      stranded DNA sequence 5'-GGATCC-3'.  Both methylases have been cloned, sequenced, purified and
      characterized.  The two Mtases have little primary amino acid sequence homology, and therefore
      provide an ideal model for a variety of comparative studies.  The cellular enzyme (M.BamHI),
      is active as a 49KD monomer and methylates the exocyclic N4 nitrogen of the internal cytosine.
      M.BamHI, associated with a prophage, is a 31KD monomeric enzyme that also methylates the
      internal cytosine, although it is not yet known if it has an N4 or a C5 methylation activity.
      Time course experiments will be presented indicating that the specific activity of the viral
      methyltransferase (M.BamHII) is significantly greater than that of the cellular methylase
      (M.BamHI).  The nature of this difference in activity is being investigated.  Gel shift
      experiments will be presented that allow a comparison of the dissociation constants.  If the
      activity of either BamHI or BamHII is similar to that for HhaI, which extrudes the target base
      from the double helix, one might expect a bilobal conformation of the enzyme, at least when
      associated with its target sequence.  The results of limited proteolysis experiments designed
      to address this possibility will also be presented.
AU  - Fabian JS
AU  - Mattson T
AU  - Chirikjian JG
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1996 10: A1103.

PMID- 28860260
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequence of Streptococcus agalactiae Strain S13, Isolated from a Fish Eye from a Nile Tilapia Farm in Southern Brazil.
PG  - e00917-17
AB  - Streptococcus agalactiae is an important pathogen to world aquaculture due to its high
      mortality rates in fish farms and consequent economic losses. Our study
      presents the complete genome sequence of strain S13, isolated from a tilapia farm
      outbreak in southern Brazil.
AU  - Facimoto CT
AU  - Chideroli RT
AU  - Goncalves DD
AU  - Carmo AOD
AU  - Kalaphotakis E
AU  - Pereira UP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00917-17.

PMID- 27014193
VI  - 7
DP  - 2016
TI  - Why close a bacterial genome? The plasmid of Alteromonas macleodii HOT1A3 is a vector for inter-specific transfer of a flexible genomic island.
PG  - 248
AB  - Genome sequencing is rapidly becoming a staple technique in environmental and clinical
      microbiology, yet computational challenges still remain, leading to many draft genomes which
      are typically fragmented into many contigs.  We sequenced and completely assembled the genome
      of a marine heterotrophic bacterium, Alteromonas macleodii HOT1A3, and compared its full
      genome to several draft genomes obtained using different reference-based and denovo methods.
      In general, the denovo assemblies clearly outperformed the reference-based orhybridones,
      covering >99%of the genes and representing essentially all of the gene functions.  However,
      only the fully closed genome(4.5Mbp) allowed us to identify the presence of a large, 148 kbp
      plasmid, pAM1A3.  While HOT1A3 belongs to A. macleodii, typically found in surface waters
      (surface ecotype), this plasmid consists of an almost complete flexible genomic island(fGI),
      containing many genes involved in metal resistance previously identified in the genomes of
      Alteromonas mediterranea (deep ecotype).  Indeed, similar to A. mediterranea, A. macleodii
      HOT1A3 grows at concentrations of zinc, mercury, and copper that are inhibitory for other A.
      macleodii strains.  The presence of a plasmid encoding almost an entire fGI suggests that
      wholesale genomic exchange between heterotrophic marine bacteria belonging to related but
      ecologically different populations is not uncommon.
AU  - Fadeev E
AU  - De Pascale F
AU  - Vezzi A
AU  - Hubner S
AU  - Aharonovich D
AU  - Sher D
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2016 7: 248.

PMID- 17682042
VI  - 75
DP  - 2007
TI  - Overproduction of DNA adenine methyltransferase alters motility, invasion, and the lipopolysaccharide O-antigen composition of Yersinia enterocolitica.
PG  - 4990-4997
AB  - DNA adenine methyltransferase not only regulates basic cellular functions but also interferes
      with the proper expression of virulence factors in various pathogens.  We showed previously
      that for the human pathogen Yersinia enterocolitica, overproduction of Dam results in
      increased invasion of epithelial cells.  Since invasion and motility are coordinately
      regulated in Y. enterocolitica, we analyzed the motility of a Dam-overproducting (DamOP)
      strain and found it to be highly motile.  In DamOP strains, the operon encoding the master
      regulator of flagellum biosynthesis, flh DC, is upregulated.  We show that the increased
      invasion is not due to enhanced expression of known and putative Y. enterocolitica invasion
      and adhesion factors, such as Inv, YadA, Ail, Myf fibrils, Pil, or Flp pili.  However,
      overproduction of Dam results in an increased amount of rough lipopolysaccharide molecules
      lacking O-antigen side chains, this implies that reduced steric hindrance by LPS might
      contribute to increased invasion by a Y. enterocolitica DamOP strain.  Our data add an
      important new aspect to the various virulence-associated phenotypes influenced by DNA
      methylation in Y. enterocolitica and indicate that Dam targets regulatory processes modulating
      the composition and function of the bacterial surface.
AU  - Faelker S
AU  - Schilling J
AU  - Schmidt MA
AU  - Heusipp G
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2007 75: 4990-4997.

PMID- 16000719
VI  - 151
DP  - 2005
TI  - DNA methylation in Yersinia enterocolitica: Role of the DNA adenine methyltransferase in mismatch repair and regulation of virulence factors.
PG  - 2291-2299
AB  - DNA adenine methyltransferase plays an important role in physiological processes of
      Gram-negative bacteria such as mismatch repair and replication.  In addition, Dam regulates
      the expression of virulence genes in various species.  The authors cloned the dam gene of
      Yersinia enterocolitica and showed that Dam is essential for viability.  Dam overproduction in
      Y. enterocolitica resulted in an increased frequency of spontaneous mutation and decreased
      resistance to 2-aminopurine; however, these effects were only marginal compared to the effect
      of overproduction of Escherichia coli-derived Dam in Y. enterocolitica, implying different
      roles or activities of Dam in mismatch repair of the two species.  These differences in Dam
      function are not the cause for the essentiality of Dam in Y. enterocalitica, as Dam of E. coli
      can complement a dam defect in Y. enterocolitica.  Instead, Dam seems to interfere with
      expression of essential genes.  Furthermore, Dam mediates virulence of Y. enterocolitica.  Dam
      overproduction results in increased tissue culture invasion of Y. enterocolitica, while the
      expression of specifically in vivo-expressed genes is not altered.
AU  - Faelker S
AU  - Schmidt MA
AU  - Heusipp G
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2005 151: 2291-2299.

PMID- 29449378
VI  - 6
DP  - 2018
TI  - Complete Genome Sequences of Six Listeria monocytogenes Sequence Type 9 Isolates  from Meat Processing Plants in Norway.
PG  - e00016-18
AB  - Listeria monocytogenes is a foodborne pathogen that causes the often-fatal disease
      listeriosis. We present here the complete genome sequences of six L.
      monocytogenes isolates of sequence type 9 (ST9) collected from two different meat
      processing facilities in Norway. The genomes were assembled using Illumina and
      Nanopore sequencing data.
AU  - Fagerlund A
AU  - Langsrud S
AU  - Moen B
AU  - Heir E
AU  - Moretro T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00016-18.

PMID- 18276641
VI  - 36
DP  - 2008
TI  - Computer design of obligate heterodimer meganucleases allows efficient cutting of custom DNA sequences.
PG  - 2163-2173
AB  - Meganucleases cut long (>12 bp) unique sequences in genomes and can be used to induce targeted
      genome engineering by homologous recombination
      in the vicinity of their cleavage site. However, the use of natural
      meganucleases is limited by the repertoire of their target sequences,
      and considerable efforts have been made to engineer redesigned
      meganucleases cleaving chosen targets. Homodimeric meganucleases such
      as I-CreI have provided a scaffold, but can only be modified to
      recognize new quasi-palindromic DNA sequences, limiting their general
      applicability. Other groups have used dimer-interface redesign and
      peptide linkage to control heterodimerization between related
      meganucleases such as I-DmoI and I-CreI, but until now there has been
      no application of this aimed specifically at the scaffolds from
      existing combinatorial libraries of I-CreI. Here, we show that
      engineering meganucleases to form obligate heterodimers results in
      functional endonucleases that cut non-palindromic sequences. The
      protein design algorithm (FoldX v2.7) was used to design specific
      heterodimer interfaces between two meganuclease monomers, which were
      themselves engineered to recognize different DNA sequences. The new
      monomers favour functional heterodimer formation and prevent homodimer
      site recognition. This design massively increases the potential
      repertoire of DNA sequences that can be specifically targeted by
      designed I-CreI meganucleases and opens the way to safer targeted
      genome engineering.
AU  - Fajardo-Sanchez E
AU  - Stricher F
AU  - Paques F
AU  - Isalan M
AU  - Serrano L
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2008 36: 2163-2173.

PMID- 16169924
VI  - 15
DP  - 2005
TI  - Living with two extremes: conclusions from the genome sequence of Natronomonas pharaonis.
PG  - 1336-1343
AB  - Natronomonas pharaonis is an extremely haloalkaliphilic archaeon that was isolated from
      salt-saturated lakes of pH 11. We sequenced its 2.6-Mb
      GC-rich chromosome and two plasmids (131 and 23 kb). Genome analysis
      suggests that it is adapted to cope with severe ammonia and heavy metal
      deficiencies that arise at high pH values. A high degree of nutritional
      self-sufficiency was predicted and confirmed by growth in a minimal medium
      containing leucine but no other amino acids or vitamins. Genes for a
      complex III analog of the respiratory chain could not be identified in the
      N. pharaonis genome, but respiration and oxidative phosphorylation were
      experimentally proven. These studies identified protons as coupling ion
      between respiratory chain and ATP synthase, in contrast to other
      alkaliphiles using sodium instead. Secretome analysis predicts many
      extracellular proteins with alkaline-resistant lipid anchors, which are
      predominantly exported through the twin-arginine pathway. In addition, a
      variety of glycosylated cell surface proteins probably form a protective
      complex cell envelope. N. pharaonis is fully equipped with archaeal signal
      transduction and motility genes. Several receptors/transducers signaling
      to the flagellar motor display novel domain architectures. Clusters of
      signal transduction genes are rearranged in haloarchaeal genomes, whereas
      those involved in information processing or energy metabolism show a
      highly conserved gene order.
AU  - Falb M
AU  - Pfeiffer F
AU  - Palm P
AU  - Rodewald K
AU  - Hickmann V
AU  - Tittor J
AU  - Oesterhelt D
PT  - Journal Article
TA  - Genome Res.
JT  - Genome Res.
SO  - Genome Res. 2005 15: 1336-1343.

PMID- 24503984
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Textile Azo Dye-Decolorizing and -Degrading Pseudomonas  aeruginosa Strain PFK10, Isolated from the Common Effluent Treatment Plant of the  Ankleshwar Industrial Area of Gujarat, India.
PG  - e00019-14
AB  - Here, we report the draft genome sequence of Pseudomonas aeruginosa strain PFK10, isolated
      from the common effluent treatment plant (CETP) of the Ankleshwar
      industrial area of Gujarat, India. The 6.04-Mb draft genome sequence of strain
      PFK10 provides information about the genes encoding enzymes that enable the
      strain to decolorize and degrade textile azo dye.
AU  - Faldu PR
AU  - Kothari VV
AU  - Kothari CR
AU  - Rawal CM
AU  - Domadia KK
AU  - Patel PA
AU  - Bhimani HD
AU  - Raval VH
AU  - Parmar NR
AU  - Nathani NM
AU  - Koringa PG
AU  - Joshi CG
AU  - Kothari RK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00019-14.

PMID- 23969059
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences of Five Strains of Lactobacillus acidophilus, Strain CIP 76.13T, Isolated from Humans, Strains CIRM-BIA 442 and CIRM-BIA 445, Isolated  from Dairy Products, and Strains DSM 20242 and DSM 9126 of Unknown Origin.
PG  - e00658-13
AB  - Lactobacillus acidophilus is a natural inhabitant of mammalian gastrointestinal systems and is
      used in dairy and pharmaceutical products. Five draft genome
      sequences, covering 1,995,790 nucleotides (nt) on average, are divided into 19 to
      34 scaffolds covering 1,995 to 2,053 genes. The draft genome sequences were
      compared to the sequence of the L. acidophilus NCFM dairy strain.
AU  - Falentin H
AU  - Cousin S
AU  - Clermont D
AU  - Creno S
AU  - Ma L
AU  - Chuat V
AU  - Loux V
AU  - Rudiger P
AU  - Bizet C
AU  - Bouchier C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00658-13.

PMID- 20668525
VI  - 5
DP  - 2010
TI  - The complete genome of Propionibacterium freudenreichii CIRM-BIA1, a hardy actinobacterium with food and probiotic applications.
PG  - e11748
AB  - BACKGROUND: Propionibacterium freudenreichii is essential as a ripening culture in Swiss-type
      cheeses and is also considered for its probiotic use. This species
      exhibits slow growth, low nutritional requirements, and hardiness in many
      habitats. It belongs to the taxonomic group of dairy propionibacteria, in
      contrast to the cutaneous species P. acnes. The genome of the type strain, P.
      freudenreichii subsp. shermanii CIRM-BIA1 (CIP 103027(T)), was sequenced with an
      11-fold coverage. METHODOLOGY/PRINCIPAL FINDINGS: The circular chromosome of 2.7
      Mb of the CIRM-BIA1 strain has a GC-content of 67% and contains 22 different
      insertion sequences (3.5% of the genome in base pairs). Using a proteomic
      approach, 490 of the 2439 predicted proteins were confirmed. The annotation
      revealed the genetic basis for the hardiness of P. freudenreichii, as the
      bacterium possesses a complete enzymatic arsenal for de novo biosynthesis of
      aminoacids and vitamins (except panthotenate and biotin) as well as sequences
      involved in metabolism of various carbon sources, immunity against phages,
      duplicated chaperone genes and, interestingly, genes involved in the management
      of polyphosphate, glycogen and trehalose storage. The complete biosynthesis
      pathway for a bifidogenic compound is described, as well as a high number of
      surface proteins involved in interactions with the host and present in other
      probiotic bacteria. By comparative genomics, no pathogenicity factors found in P.
      acnes or in other pathogenic microbial species were identified in P.
      freudenreichii, which is consistent with the Generally Recognized As Safe and
      Qualified Presumption of Safety status of P. freudenreichii. Various pathways for
      formation of cheese flavor compounds were identified: the Wood-Werkman cycle for
      propionic acid formation, amino acid degradation pathways resulting in the
      formation of volatile branched chain fatty acids, and esterases involved in the
      formation of free fatty acids and esters. CONCLUSIONS/SIGNIFICANCE: With the
      exception of its ability to degrade lactose, P. freudenreichii seems poorly
      adapted to dairy niches. This genome annotation opens up new prospects for the
      understanding of the P. freudenreichii probiotic activity.
AU  - Falentin H
AU  - Deutsch SM
AU  - Jan G
AU  - Loux V
AU  - Thierry A
AU  - Parayre S
AU  - Maillard MB
AU  - Dherbecourt J
AU  - Cousin FJ
AU  - Jardin J
AU  - Siguier P
AU  - Couloux A
AU  - Barbe V
AU  - Vacherie B
AU  - Wincker P
AU  - Gibrat JF
AU  - Gaillardin C
AU  - Lortal S
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2010 5: e11748.

PMID- 26779303
VI  - 11
DP  - 2016
TI  - Permanent draft genome sequence of the probiotic strain Propionibacterium freudenreichii CIRM-BIA 129 (ITG P20).
PG  - 6
AB  - Propionibacterium freudenreichii belongs to the class Actinobacteria (Gram positive with a
      high GC content). This 'Generally Recognized As Safe' (GRAS)
      species is traditionally used as (i) a starter for Swiss-type cheeses where it is
      responsible for holes and aroma production, (ii) a vitamin B12 and propionic acid
      producer in white biotechnologies, and (iii) a probiotic for use in humans and
      animals because of its bifidogenic and anti-inflammatory properties. Until now,
      only strain CIRM-BIA1T had been sequenced, annotated and become publicly
      available. Strain CIRM-BIA129 (commercially available as ITG P20) has
      considerable anti-inflammatory potential. Its gene content was compared to that
      of CIRM-BIA1 T. This strain contains 2384 genes including 1 ribosomal operon, 45
      tRNA and 30 pseudogenes.
AU  - Falentin H
AU  - Deutsch SM
AU  - Loux V
AU  - Hammani A
AU  - Buratti J
AU  - Parayre S
AU  - Chuat V
AU  - Barbe V
AU  - Aury JM
AU  - Jan G
AU  - Le Loir Y
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 6.

PMID- 24435871
VI  - 2
DP  - 2014
TI  - Genome Sequence of Lactococcus lactis subsp. lactis bv. diacetylactis LD61.
PG  - e01176-13
AB  - Lactococcus lactis is widely used in the dairy industry. We report the draft genome sequence
      of L. lactis subsp. lactis bv. diacetylactis LD61, an industrial
      and extensively studied strain. In contrast to the closely related and
      plasmidless strain IL1403, LD61 contains 6 plasmids, and the genome sequence
      provides additional information related to adaptation to the dairy environment.
AU  - Falentin H
AU  - Naquin D
AU  - Loux V
AU  - Barloy-Hubler F
AU  - Loubiere P
AU  - Nouaille S
AU  - Lavenier D
AU  - Le Bourgeois P
AU  - Francois P
AU  - Schrenzel J
AU  - Hernandez D
AU  - Even S
AU  - Le Loir Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01176-13.

PMID- 24762941
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Phage-Like Plasmid pECOH89, Encoding CTX-M-15.
PG  - e00356-14
AB  - A nonconjugative and nontypable plasmid of a clinical Escherichia coli isolate expressing
      resistance to extended-spectrum cephalosporins (ESCs) was isolated and sequenced. The plasmid
      pECOH89 contains a CTX-M-15 resistance cassette and comprises 111,741 bp, with strong homology
      to bacteriophage-like plasmids and to the Salmonella-specific bacteriophage SSU5.
AU  - Falgenhauer L
AU  - Yao Y
AU  - Fritzenwanker M
AU  - Schmiedel J
AU  - Imirzalioglu C
AU  - Chakraborty T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00356-14.

PMID- 4899007
VI  - 100
DP  - 1969
TI  - Restriction in genetic crosses between Escherichia coli and Shigella flexneri.
PG  - 540-541
AB  - Shigella flexneri restricts Escherichia coli deoxyribonucleic acid (DNA) and
      can modify phage DNA so that it is restricted in E. coli.
AU  - Falkow S
AU  - Formal SB
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1969 100: 540-541.

PMID- 22720917
VI  - 95
DP  - 2012
TI  - Novel conjugative plasmids from the natural isolate Lactococcus lactis subspecies cremoris DPC3758: A repository of genes for the potential improvement of dairy starters.
PG  - 3593-3608
AB  - A collection of 17 natural lactococcal isolates from raw milk cheeses were studied in terms of
      their plasmid distribution, content, and
      diversity. All strains in the collection harbored an abundance of
      plasmids, including Lactococcus lactis ssp. cremoris DPC3758, whose
      8-plasmid complement was selected for sequencing. The complete
      sequences of pAF22 (22,388 kb), pAF14 (14,419 kb), pAF12 (12,067 kb),
      pAF07 (7,435 kb), and pAF04 (3,801 kb) were obtained, whereas gene
      functions of technological interest were mapped to pAF65 (65 kb) and
      pAF45 (45 kb) by PCR. The plasmids of L. lactis DPC3758 were found to
      encode many genes with the potential to improve the technological
      properties of dairy starters. These included 3 anti-phage
      restriction/modification (R/M) systems (1 of type I and 2 of type II)
      and genes for immunity/resistance to nisin, lacticin 481, cadmium, and
      copper. Regions encoding conjugative/mobilization functions were
      present in 6 of the 8 plasmids, including those containing the R/M
      systems, thus enabling the food-grade transfer of these mechanisms to
      industrial strains. Using cadmium selection, the sequential stacking of
      the R/M plasmids into a plasmid-free host provided the recipient with
      increased protection against 936- and c2-type phages. The association
      of food-grade selectable markers and mobilization functions on L.
      lactis DPC3758 plasmids will facilitate their exploitation to obtain
      industrial strains with enhanced phage protection and robustness. These
      natural plasmids also provide another example of the major role of
      plasmids in contributing to host fitness and preservation within its
      ecological niche.
AU  - Fallico V
AU  - Ross RP
AU  - Fitzgerald GF
AU  - McAuliffe O
PT  - Journal Article
TA  - J. Dairy Sci.
JT  - J. Dairy Sci.
SO  - J. Dairy Sci. 2012 95: 3593-3608.

PMID- 23950118
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Virulent Clostridium chauvoei Reference Strain JF4335.
PG  - e00593-13
AB  - Clostridium chauvoei is the etiological agent of blackleg, a disease of cattle and sheep with
      high mortality rates, causing severe economic losses in livestock
      production. Here, we report the draft genome sequence of the virulent C. chauvoei
      strain JF4335 (2.8 Mbp and 28% G+C content) and the annotation of the genome.
AU  - Falquet L
AU  - Calderon-Copete SP
AU  - Frey J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00593-13.

PMID- 25323717
VI  - 2
DP  - 2014
TI  - Complete Genome Sequences of Virulent Mycoplasma capricolum subsp. capripneumoniae Strains F38 and ILRI181.
PG  - e01041-14
AB  - Contagious caprine pleuropneumonia (CCPP) caused by Mycoplasma capricolum subsp.
      capripneumoniae is a severe epidemic affecting mainly domestic Caprinae species
      but also affects wild Caprinae species. M. capricolum subsp. capripneumoniae
      belongs to the 'Mycoplasma mycoides cluster.' The disease features prominently in
      East Africa, in particular Kenya, Tanzania, and Ethiopia. CCPP also endangers
      wildlife and thus affects not only basic nutritional resources of large
      populations but also expensively built-up game resorts in affected countries.
      Here, we report the complete sequences of two M. capricolum subsp.
      capripneumoniae strains: the type strain F38 and strain ILRI181 isolated druing a
      recent outbreak in Kenya. Both genomes have a G+C content of 24% with sizes of
      1,016,760 bp and 1,017,183 bp for strains F38 and ILRI181, respectively.
AU  - Falquet L
AU  - Liljander A
AU  - Schieck E
AU  - Gluecks I
AU  - Frey J
AU  - Jores J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01041-14.

PMID- 1727392
VI  - 6
DP  - 1992
TI  - Molecular dynamic-based prediction of DNA structure changes in DNA sequence and correlation to substrate specificity in EcoRI DNA methyltransferase.
PG  - A221
AB  - The object of this computational investigation is to determine the structural
      consequences of single base-pair substitutions in the canonical site GAATTC of
      14 base-pair oligonucleotide duplexes.  The computational schemes reported
      herein are guided by the earlier approaches established by Kollman and
      co-workers and include 100 picoseconds of molecular dynamics.  The atomic
      trajectories are analyzed for temporal variations of the phosphodiester and
      glycosidic torsion angles and the helicoidal parameters using both AMBER (1986)
      AMBER 3.0, UCSF) and Dials and Windows (J. Biomol. Str. Dyn., 6, 669(1989))
      algorithms.  We first performed two computations using the crystal structure of
      the Dickerson dodecamer and the standard Arnott B-DNA structure as the starting
      points.  The average backbone torsion angles alpha, beta, gamma, delta,
      epsilon, chi 1, chi 2 taken over the entire simulation time show 3% difference
      between the two structures, suggesting convergence towards a unique final
      structure.  The degree of agreement is even greater for the average helical
      twist omega.  These results corroborate Kollman's earlier report, therefore
      establishing the validity of our approach.  In view of our ongoing
      investigation with a series of 14 base-pair oligonucleotides (Biochemistry
      (1991) 30, 2933-2939; Nucleic Acids Research, in press), the sequence
      d(GGCGGAATTCGCGG) was subjected to 100 picoseconds of molecular dynamics.  The
      calculated backbone torsion angles show good agreement with the identical
      conformational values obtained from an earlier calculation on the dodecamer.
      In view of these consistencies, we have used the results from this later
      computation to gauge the structural variations that result from single
      base-pair substitutions within the canonical site GAATTC of d(GGCGGAATTCGCGG).
      It is hoped that these structural differences will ultimately help elucidate
      the mechanisms that describe the enzyme-DNA binding and catalysis for EcoRI
      methyltransferase.
AU  - Falsafi S
AU  - Reich N
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1992 6: A221.

PMID- 21183663
VI  - 193
DP  - 2010
TI  - Genome sequence of Bacillus subtilis subsp. spizizenii gtP20b isolated from the Indian Ocean.
PG  - 1276
AB  - Bacillus subtilis is a model organism of aerobic spore-forming Gram-positive bacteria and is
      of great industrial significance as the source of diverse novel functional molecules. Here we
      present to our knowledge the first genome sequence of a Bacillus subtilis strain gtP20b
      isolated from the marine environment. A subset of candidate genes and gene clusters were
      identified, which are potentially involved in production of diverse functional molecules like
      novel ribosomal and non-ribosomal antimicrobial peptides. The genome sequence described in
      this paper is due to its high strain-specificity of great importance for basic as well as
      applied researches on marine organisms.
AU  - Fan L
AU  - Bo S
AU  - Chen H
AU  - Ye W
AU  - Kleinschmidt K
AU  - Baumann HI
AU  - Imhoff JF
AU  - Kleine M
AU  - Cai D
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 193: 1276.

PMID- 21571991
VI  - 193
DP  - 2011
TI  - Draft genome sequence of a marine Streptomyces sp. strain PP-C42, isolated from the Baltic Sea.
PG  - 3691-3692
AB  - Streptomyces, a branch of aerobic Gram-positive bacteria represents the largest genus of
      actinobacteria. The streptomycetes are characterized by a
      complex secondary metabolism and produce over two-thirds of the clinically
      used natural antibiotics today. Here we report the draft genome sequence
      of a Streptomyces strain PP-C42 isolated from the marine environment. A
      subset of unique genes and gene clusters for diverse secondary metabolites
      as well as antimicrobial peptides (AMPs) could be identified from the
      genome, showing great promise as a source for novel bioactive compounds.
AU  - Fan L
AU  - Liu Y
AU  - Li Z
AU  - Baumann HI
AU  - Kleinschmidt K
AU  - Ye W
AU  - Imhoff JF
AU  - Kleine M
AU  - Cai D
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3691-3692.

PMID- 30505390
VI  - 13
DP  - 2018
TI  - High-quality-draft genome sequence of the heavy metal resistant and exopolysaccharides producing bacterium Mucilaginibacter pedocola TBZ30(T).
PG  - 34
AB  - Mucilaginibacter pedocola TBZ30(T) (= CCTCC AB 2015301(T) = KCTC 42833(T)) is a Gram-
      negative, rod-shaped, non-motile and non-spore-forming bacterium isolated
      from a heavy metal contaminated paddy field. It shows resistance to multiple
      heavy metals and can adsorb/remove Zn(2+) and Cd(2+) during cultivation. In
      addition, strain TBZ30(T) produces exopolysaccharides (EPS). These features make
      it a great potential to bioremediate heavy metal contamination and biotechnical
      application. Here we describe the genome sequence and annotation of strain
      TBZ30(T). The genome size is 7,035,113 bp, contains 3132 protein-coding genes
      (2736 with predicted functions), 50 tRNA encoding genes and 14 rRNA encoding
      genes. Putative heavy metal resistant genes and EPS associated genes are found in
      the genome.
AU  - Fan X
AU  - Tang J
AU  - Nie L
AU  - Huang J
AU  - Wang G
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2018 13: 34.

PMID- 29074656
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Pseudomonas fluorescens Strain ITEM 17298, Associated with Cheese Spoilage.
PG  - e01141-17
AB  - Pseudomonas fluorescens is a genetically and phenotypically heterogeneous species that is
      often reported as a spoiler of fresh foods, but it has recently been
      implicated in clinical infection. In this study, we sequenced the genome of P.
      fluorescens strain ITEM 17298, isolated from mozzarella cheese and able to cause
      several alterations under cold storage.
AU  - Fanelli F
AU  - Liuzzi VC
AU  - Quintieri L
AU  - Mule G
AU  - Baruzzi F
AU  - Logrieco AF
AU  - Caputo L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01141-17.

PMID- 23138224
VI  - 30
DP  - 2012
TI  - Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing.  LID - 10.1038/nbt.2432 [doi].
PG  - 1232
AB  - Single-molecule real-time (SMRT) DNA sequencing allows the systematic detection of chemical
      modifications such as methylation but has not previously been applied on a genome-wide scale.
      We used this approach to detect 49,311 putative 6-methyladenine (m6A) residues and 1,407
      putative 5-methylcytosine (m5C) residues in the genome of a pathogenic Escherichia coli
      strain. We obtained strand-specific information for methylation sites and a quantitative
      assessment of the frequency of methylation at each modified position. We deduced the sequence
      motifs recognized by the methyltransferase enzymes present in this strain without prior
      knowledge of their specificity. Furthermore, we found that deletion of a phage-encoded
      methyltransferase-endonuclease (restriction-modification; RM) system induced global
      transcriptional changes and led to gene amplification, suggesting that the role of RM systems
      extends beyond protecting host genomes from foreign DNA.
AU  - Fang G et al
PT  - Journal Article
TA  - Nat. Biotechnol.
JT  - Nat. Biotechnol.
SO  - Nat. Biotechnol. 2012 30: 1232.

PMID- 22740676
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Pseudomonas aeruginosa Strain ATCC 27853.
PG  - 3755
AB  - Pseudomonas aeruginosa is a common bacterium that can cause disease. The versatility of
      Pseudomonas aeruginosa enables the organism to infect damaged
      tissues or those with reduced immunity which cause inflammation and sepsis. Here
      we report the genome sequence of the strain ATCC 27853.
AU  - Fang X
AU  - Fang Z
AU  - Zhao J
AU  - Zou Y
AU  - Li T
AU  - Wang J
AU  - Guo Y
AU  - Chang D
AU  - Su L
AU  - Ni P
AU  - Liu C
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3755.

PMID- 23144371
VI  - 194
DP  - 2012
TI  - First Genome Sequence of a Burkholderia pseudomallei Isolate in China, Strain BPC006, Obtained from a Melioidosis Patient in Hainan.
PG  - 6604-6605
AB  - Melioidosis, caused by Burkholderia pseudomallei, is considered to be endemic to  Northern
      Australia and Southeast Asia, with high mortality and relapse rates,
      regardless of powerful antibiotic therapy. Here we report the first genome
      sequence of Burkholderia pseudomallei strain BPC006, obtained from a melioidosis
      patient in Hainan, China. The genome sizes of the 2 chromosomes were determined
      to be 4,001,777 bp and 3,153,284 bp.
AU  - Fang Y
AU  - Huang Y
AU  - Li Q
AU  - Chen H
AU  - Yao Z
AU  - Pan J
AU  - Gu J
AU  - Tang B
AU  - Wang HG
AU  - Yu B
AU  - Tong YG
AU  - Zou QM
AU  - Mao XH
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6604-6605.

PMID- 765154
VI  - 61
DP  - 1976
TI  - Detection of restriction endonucleases with a lac repressor-lac operator filter binding assay.
PG  - 237-239
AB  - The use of restriction enzymes as experimental tools has progressed rapidly
      within the last several years.  The purification of these enzymes, however,
      often poses a problem: since acid-soluable material is normally not released a
      convenient assay for enzyme activity does not exist.  Thus, gel electrophoresis
      or viscometry of digested DNA has often been employed to detect restriction
      enzymes during purification.  These methods are, however, time consuming and
      involve large quantities of DNA and/or expensive equipment.  We report here a
      test for restriction enzymes that avoids these complications; the test is
      inexpensive, rapid and can be done with very small quantities of DNA (0.02
      microgram per test is normally sufficient).
AU  - Fanning TG
AU  - Kreutzfeldt H-J
AU  - Davies RW
AU  - Schreier PH
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1976 61: 237-239.

PMID- 27635009
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Enterococcus mundtii QAUEM2808, Isolated from Dahi, a Fermented Milk Product.
PG  - e00995-16
AB  - Enterococcus mundtii QAUEM2808 has been isolated from dahi, an indigenous fermented milk
      product of Pakistan. Here, we report the draft genome sequence for
      this strain, which consists of 160 contigs corresponding to 2,957,514 bp and a
      G+C content of 38.5%.
AU  - Farah N
AU  - Mehdi A
AU  - Soomro SI
AU  - Soomro NI
AU  - Tareb R
AU  - Desmasures N
AU  - Vernoux JP
AU  - Bakhtiar SM
AU  - Imran M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00995-16.

PMID- 23792745
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Aeromonas diversa Type Strain.
PG  - e00330-13
AB  - We present here the first genome sequence of the Aeromonas diversa type strain (CECT 4254(T)).
      This strain was isolated from the leg wound of a patient in New
      Orleans (Louisiana) and was originally described as enteric group 501 and
      distinguished from A. schubertii by DNA-DNA hybridization and phenotypical
      characterization.
AU  - Farfan M
AU  - Spataro N
AU  - Sanglas A
AU  - Albarral V
AU  - Loren JG
AU  - Bosch E
AU  - Fuste MC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00330-13.

PMID- 21602338
VI  - 193
DP  - 2011
TI  - Genome sequence of Sphingomonas sp. S17, isolated from an alkaline, hyperarsenic and hypersaline volcanic-associated lake at high altitude in the Argentinean Puna.
PG  - 3686-3687
AB  - The High-Altitude Andean Lakes (HAAL) in the Argentinian Puna-High Andes region represent an
      almost unexplored ecosystem exposed to extreme
      conditions (high UV irradiation, hypersalinity, drastic temperature
      changes, desiccation, high pH). Here we present the first genome sequence
      isolated from this extreme environment, a Sphingomonas sp.
AU  - Farias ME
AU  - Revale S
AU  - Mancini E
AU  - Ordonez O
AU  - Turjanski A
AU  - Cortez N
AU  - Vazquez MP
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3686-3687.

PMID- 24530704
VI  - 541
DP  - 2014
TI  - Comparative whole genome analysis of six diagnostic brucellaphages.
PG  - 115-122
AB  - Whole genome sequencing of six diagnostic brucellaphages, Tbilisi (Tb), Firenze
      (Fz), Weybridge (Wb), S708, Berkeley (Bk) and R/C, was followed with genomic
      comparisons including recently described genomes of the Tb phage from Mexico
      (TbM) and Pr phage to elucidate genomic diversity and candidate host range
      determinants. Comparative whole genome analysis revealed high sequence
      homogeneity among these brucellaphage genomes and resolved three genetic groups
      consistent with defined host range phenotypes. Group I was composed of Tb and Fz
      phages that are predominantly lytic for Brucella abortus and Brucella neotomae;
      Group II included Bk, R/C, and Pr phages that are lytic mainly for B. abortus,
      Brucella melitensis and Brucella suis; Group III was composed of Wb and S708
      phages that are lytic for B. suis, B. abortus and B. neotomae. We found that the
      putative phage collar protein is a variable locus with features that may be
      contributing to the host specificities exhibited by different brucellaphage
      groups. The presence of several candidate host range determinants is illustrated
      herein for future dissection of the differential host specificity observed among
      these phages.
AU  - Farlow J
AU  - Filippov AA
AU  - Sergueev KV
AU  - Hang J
AU  - Kotorashvili A
AU  - Nikolich MP
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 2014 541: 115-122.

PMID- 28007853
VI  - 4
DP  - 2016
TI  - Genome Sequence of the Soviet/Russian Bacillus anthracis Vaccine Strain 55-VNIIVViM.
PG  - e01401-16
AB  - Bacillus anthracis strain 55-VNIIVViM is a live-attenuated nonencapsulated Soviet/Russian
      veterinary anthrax vaccine strain. We report here the genome of 55-VNIIVViM and confirm its
      phylogenetic placement in the global population structure of B. anthracis.
AU  - Farlow J
AU  - Kotorashvili A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01401-16.

PMID- 2537951
VI  - 17
DP  - 1989
TI  - Improved chemistry for oligodeoxyribonucleotide synthesis substantially improves restriction enzyme cleavage of a synthetic 35-mer.
PG  - 1231-1245
AB  - Two DNA duplexes of identical sequence and 35 nt in length were synthesized by
      an original and a highly improved version of phosphoramidite chemistry.  By
      base composition analysis, DNA synthesized by improved chemistry (termed
      DMTS-imp) contained no detectable modified bases while DNA synthesized by the
      original chemistry (termed DMTS-std) had a large number of modifications.
      Under optimal reaction conditions, HhaI and RsaI cleaved the DMTS-std duplex to
      76-77% completion and the DMTS-imp duplex to 96-99% completion.  Restriction
      analysis and piperidine treatment yielded estimates of approx. 3.0% modified
      nucleotides in DMTS-std and approx. 1.0% in DMTS-imp.  Overall, the
      improvements in chemistry inreased the restriction efficiency of synthetic DNA
      up to 10-fold.
AU  - Farrance IK
AU  - Eadie JS
AU  - Ivarie R
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 1231-1245.

PMID- Not included in PubMed...
VI  - 71
DP  - 1994
TI  - A fast restriction enzyme experiment for the undergraduate biochemistry lab.
PG  - 1095-1096
AB  - We recently updated out laboratory curriculum to include some popular and important techniques
      of molecular biology. We have designed a rapid experiment using restriction enzymes that can
      be done in one three-hour lab period. This experiment is one of the highlights of the course,
      and almost every student gets positive results.
AU  - Farrell SO
PT  - Journal Article
TA  - J. Chem. Educ.
JT  - J. Chem. Educ.
SO  - J. Chem. Educ. 1994 71: 1095-1096.

PMID- 23527001
VI  - 8
DP  - 2013
TI  - The Complete Genome and Phenome of a Community-Acquired Acinetobacter baumannii.
PG  - e58628
AB  - Many sequenced strains of Acinetobacter baumannii are established nosocomial pathogens capable
      of resistance to multiple antimicrobials.
      Community-acquired A. baumannii in contrast, comprise a minor
      proportion of all A. baumannii infections and are highly susceptible to
      antimicrobial treatment. However, these infections also present acute
      clinical manifestations associated with high reported rates of
      mortality. We report the complete 3.70 Mbp genome of A. baumannii
      D1279779, previously isolated from the bacteraemic infection of an
      Indigenous Australian; this strain represents the first
      community-acquired A. baumannii to be sequenced. Comparative analysis
      of currently published A. baumannii genomes identified twenty-four
      accessory gene clusters present in D1279779. These accessory elements
      were predicted to encode a range of functions including polysaccharide
      biosynthesis, type I DNA restriction-modification, and the metabolism
      of novel carbonaceous and nitrogenous compounds. Conversely, twenty
      genomic regions present in previously sequenced A. baumannii strains
      were absent in D1279779, including gene clusters involved in the
      catabolism of 4-hydroxybenzoate and glucarate, and the A. baumannii
      antibiotic resistance island, known to bestow resistance to multiple
      antimicrobials in nosocomial strains. Phenomic analysis utilising the
      Biolog Phenotype Microarray system indicated that A. baumannii D1279779
      can utilise a broader range of carbon and nitrogen sources than
      international clone I and clone II nosocomial isolates. However,
      D1279779 was more sensitive to antimicrobial compounds, particularly
      beta-lactams, tetracyclines and sulphonamides. The combined genomic and
      phenomic analyses have provided insight into the features
      distinguishing A. baumannii isolated from community-acquired and
      nosocomial infections.
AU  - Farrugia DN
AU  - Elbourne LDH
AU  - Hassan KA
AU  - Eijkelkamp BA
AU  - Tetu SG
AU  - Brown MH
AU  - Shah BS
AU  - Peleg AY
AU  - Mabbutt BC
AU  - Paulsen IT
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2013 8: e58628.

PMID- Not carried by PubMed...
VI  - 30
DP  - 1987
TI  - Isolation and partial purification of a restriction endonuclease from Pseudomonas ovalis.
PG  - 390-392
AB  - A restriction endonuclease, PovI, has been isolated and partially purified from
      Pseudomonas ovalis by high speed centrifugation and fractionation on a column
      of Biogel followed by dialysis and ion exchange chromatography on a
      phosphocellulose column.  The presence of the restriction endonuclease was
      detected by a simple assay procedure using agarose slab gel electrophoresis.
AU  - Faruqi AF
AU  - Ahmed N
PT  - Journal Article
TA  - Pak. J. Sci. Ind. Res.
JT  - Pak. J. Sci. Ind. Res.
SO  - Pak. J. Sci. Ind. Res. 1987 30: 390-392.

PMID- 25792059
VI  - 3
DP  - 2015
TI  - Genome Sequence of Bacillus anthracis Isolated from an Anthrax Burial Site in Pollino National Park, Basilicata Region (Southern Italy).
PG  - e00141-15
AB  - A Bacillus anthracis strain was isolated from a burial-site in Pollino National Park where a
      bovine died of anthrax and was buried in 2004. We report the first
      genome sequence of B. anthracis isolated in the Basilicata region (southern
      Italy), which is the highest risk area of anthrax infection in Italy.
AU  - Fasanella A
AU  - Braun P
AU  - Grass G
AU  - Hanczaruk M
AU  - Aceti A
AU  - Serrecchia L
AU  - Leonzio G
AU  - Tolve F
AU  - Georgi E
AU  - Antwerpen M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00141-15.

PMID- 12383256
VI  - 269
DP  - 2002
TI  - Dnmt3a and Dnmt1 functionally cooperate during de novo methylation of DNA.
PG  - 4981-4984
AB  - Dnmt3a is a de novo DNA methyltransferase that modifies unmethylated DNA. In contrast Dnmt1
      shows high preference for hemimethylated DNA. However, Dnmt1 can be activated for the
      methylation of unmodified DNA. We show here that the Dnmt3a and Dnmt1 DNA methyltransferases
      functionally cooperate in de novo methylation of DNA, because a fivefold stimulation of
      methylation activity is observed if both enzymes are present. Stimulation is observed if
      Dnmt3a is used before Dnmt1, but not if incubation with Dnmt1 precedes Dnmt3a, demonstrating
      that methylation of the DNA by Dnmt3a stimulates Dnmt1 and that no physical interaction of
      Dnmt1 and Dnmt3a is required. If Dnmt1 and Dnmt3a were incubated together a slightly increased
      stimulation is observed that could be due to a direct interaction of these enzymes. In
      addition, we show that Dnmt1 is stimulated for methylation of unmodified DNA if the DNA
      already carries some methyl groups. We conclude that after initiation of de novo methylation
      of DNA by Dnmt3a, Dnmt1 becomes activated by the pre-existing methyl groups and further
      methylates the DNA. Our data suggest that Dnmt1 also has a role in de novo methylation of DNA.
      This model agrees with the biochemical properties of these enzymes and provides a mechanistic
      basis for the functional cooperation of different DNA MTases in de novo methylation of DNA
      that has also been observed in vivo.
AU  - Fatemi M
AU  - Hermann A
AU  - Gowher H
AU  - Jeltsch A
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 2002 269: 4981-4984.

PMID- 11399088
VI  - 309
DP  - 2001
TI  - The activity of the murine DNA methyltransferase Dnmt1 is controlled by interaction of the catalytic domain with the N-terminal part of the enzyme leading to an allosteric activation of the enzyme after binding to methylated DNA.
PG  - 1189-1199
AB  - The mammalian DNA methyltransferase Dnmt1 is responsible for the maintenance of the pattern of
      DNA methylation in vivo. It is a large multidomain enzyme comprising 1620 amino acid residues.
      We have purified and characterized individual domains of Dnmt1 (NLS-containing domain, NlsD,
      amino acid residues: 1-343; replication foci-directing domain, 350-609; Zn-binding domain
      (ZnD), 613-748; polybromo domain, 746-1110; and the catalytic domain (CatD), 1124-1620). CatD,
      ZnD and NlsD bind to DNA, demonstrating the existence of three independent DNA-binding sites
      in Dnmt1. CatD shows a preference for binding to hemimethylated CpG-sites; ZnD prefers
      methylated CpGs; and NlsD specifically binds to CpG-sites, but does not discriminate between
      unmethylated and methylated DNA. These results are not compatible with the suggestion that the
      target recognition domain of Dnmt1 resides in the N terminus of the enzyme. We show by
      protein-protein interaction assays that ZnD and CatD interact with each other. The isolated
      catalytic domain does not methylate DNA, neither alone nor in combination with other domains.
      Full-length Dnmt1 was purified from baculovirus-infected insect cells. Under the experimental
      conditions, Dnmt1 has a strong (50-fold) preference for hemimethylated DNA. Dnmt1 is
      stimulated to methylate unmodified CpG sites by the addition of fully methylated DNA. This
      effect is dependent on Zn, suggesting that binding of methylated DNA to ZnD triggers the
      allosteric activation of the catalytic center of Dnmt1. The allosteric activation model can
      explain kinetic data obtained by others. It suggests that Dnmt1 might be responsible for
      spreading of methylation, a process that is observed during aging and carcinogenesis but may
      be important for de novo methylation of DNA.
AU  - Fatemi M
AU  - Hermann A
AU  - Pradhan S
AU  - Jeltsch A
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2001 309: 1189-1199.

PMID- 
VI  - 
DP  - 1999
TI  - Structure and evolution of AdoMet-dependent methyltransferases.
PG  - 1-38
AB  - A review of many different types of SAM-sependent Mtases, including DNA methyltransferases,
      RNA methyltransferases and many others.
AU  - Fauman EB
AU  - Blumenthal RM
AU  - Cheng X
PT  - Journal Article
TA  - S-Adenosylmethionine-dependent Methyltransferases: Structures and Functions.
JT  - S-Adenosylmethionine-dependent Methyltransferases: Structures and Functions.
SO  - S-Adenosylmethionine-dependent Methyltransferases: Structures and Functions. 1999 : 1-38.

PMID- 21515775
VI  - 193
DP  - 2011
TI  - Genome sequence of Rhizobium etli CNPAF512, a nitrogen-fixing symbiont isolated from bean root nodules in Brazil.
PG  - 3158-3159
AB  - Rhizobium etli is a Gram-negative soil-dwelling alpha-proteobacterium that carries out
      symbiotic biological nitrogen fixation in close association
      with legume hosts. R. etli strains exhibit high sequence divergence and
      are geographically structured, with a potentially dramatic influence on
      the outcome of symbiosis. Here, we present the genome sequence of R. etli
      CNPAF512, a Brazilian isolate from bean nodules. We anticipate that the
      availability of genome sequences of R. etli strains from distinctly
      different areas will provide valuable new insights into the geographic
      mosaic of the R. etli pangenome and the evolutionary dynamics that shape
      it.
AU  - Fauvart M
AU  - Sanchez-Rodriguez A
AU  - Beullens S
AU  - Marchal K
AU  - Michiels J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3158-3159.

PMID- 30344890
VI  - 13
DP  - 2018
TI  - Draft genomes of 'Pectobacterium peruviense' strains isolated from fresh water in France.
PG  - 27
AB  - Bacteria belonging to the genus Pectobacterium are responsible for soft rot disease on a wide
      range of cultivated crops. The 'Pectobacterium peruviense'
      specie, recently proposed inside the Pectobacterium genus, gathers strains
      isolated from potato tubers cultivated in Peru at high altitude. Here we report
      the draft genome sequence of two strains belonging to 'P. peruviense' isolated
      from river water in France indicating that the geographic distribution of this
      specie is likely to be larger than previously anticipated. We compared these
      genomes with the one published from the 'P. peruviense' specie type strain
      isolated in Peru.
AU  - Faye P
AU  - Bertrand C
AU  - Pedron J
AU  - Barny MA
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2018 13: 27.

PMID- 2717401
VI  - 17
DP  - 1989
TI  - The GTm6AC sequence is overwound and bent.
PG  - 2541-2556
AB  - By a combination of distance constraints obtained from NMR spectra and
      molecular mechanics calculations we have determined the three dimensional
      structure of the self-complementary decanucleotide d(CGCGTm6ACGCG).
      Methylation of an adenine at a position 3' to T induces significant
      conformational changes relative to B-DNA.  This arises from the close proximity
      of the four methyl groups in the large groove in the centre of the sequence.
      The helical twist between the two T.m6A base pairs is found to be 45, as for
      D-DNA, and is accompanied by a high negative value of the wedge roll angle
      between these base pairs.  The overall nonzero wedge roll observed shows that
      the helix is bent.  These constraints appear to be material for the absence of
      the sequence T-m6A in natural DNAs.
AU  - Fazakerley GV
AU  - Gabarro-Arpa J
AU  - Lebret M
AU  - Guy A
AU  - Guschlbauer W
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 2541-2556.

PMID- 3477454
VI  - 167
DP  - 1987
TI  - A two-dimensional H-NMR study of the dam methylase site:  comparison between the hemimethylated GATC sequence, its unmethylated analogue and a hemimethylated CATG sequence:  The sequence dependence of methylation upon base-pair lifetimes.
PG  - 397-404
AB  - We report two-dimensional NOE (NOESY) spectra on the sequence d(GCGATCATGG) d(CCATGATCGC)
      which contains the unmethylated dam site. As expected the DNA adopts a B-form conformation but
      appears to be distorted at the TG step of the second strand. This distorsion, probably
      bending, is not seen on the opposite strand. When the first strand is methylated on adenine in
      the GATC or CATG sequence the NOESY spectra indicate little or no change in the conformation.
      However the single strand-duplex change is slowed down to the slow-exchange region on a proton
      NMR time scale. We have assigned the exchangeable imino and cytidine amino resonances of the
      three duplexes. From the imino linewidths as a function of temperature, we observe that the
      unmethylated and the hemimethylated Gm6ATC duplexes melt normally from the ends. However, this
      is not so for the hemimethylated Cm6ATG duplex which, apart from the terminal base pairs,
      melts cooperatively and at high temperature. In spectra recorded in H2O a second duplex is
      observed, for the Gm6ATC sequence, which we have not been able to identify. It is however
      unlikely to be a hairpin structure. Ultraviolet-melting curves also indicate the presence of
      two transitions for this duplex. The effect of methylation upon base-pair lifetimes has been
      studied by comparing the above three duplexes. Little effect is observed upon methylation in
      the GATC sequence but a drastic increase in the lifetimes of all base pairs is observed upon
      methylation in the CATG sequence.
AU  - Fazakerley GV
AU  - Quignard E
AU  - Teoule R
AU  - Guy A
AU  - Guschlbauer W
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1987 167: 397-404.

PMID- 27811100
VI  - 4
DP  - 2016
TI  - Complete Whole-Genome Sequence of Salmonella enterica subsp. enterica Serovar Java NCTC5706.
PG  - e01219-16
AB  - Salmonellae are a significant cause of morbidity and mortality globally. Here, we report the
      first complete genome sequence for Salmonella enterica subsp. enterica
      serovar Java strain NCTC5706. This strain is of historical significance, having
      been isolated in the pre-antibiotic era and was deposited into the National
      Collection of Type Cultures in 1939.
AU  - Fazal MA
AU  - Alexander S
AU  - Burnett E
AU  - Deheer-Graham A
AU  - Oliver K
AU  - Holroyd N
AU  - Parkhill J
AU  - Russell JE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01219-16.

PMID- 29217794
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Lactobacillus salivarius SGL 03, a Novel Potential Probiotic Strain.
PG  - e01340-17
AB  - In this work, we report the draft genome sequence of Lactobacillus salivarius SGL 03, a novel
      potential probiotic strain isolated from healthy infant stools.
      Antibiotic resistance analysis revealed the presence of a tetracycline resistance
      gene without elements potentially responsible for interspecific horizontal gene
      transfer.
AU  - Federici F
AU  - Manna L
AU  - Rizzi E
AU  - Galantini E
AU  - Marini U
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01340-17.

PMID- 11943171
VI  - 514
DP  - 2002
TI  - N6-Adenine DNA-methyltransferase in wheat seedlings.
PG  - 305-308
AB  - The N(6)-adenine DNA-methyltransferase was isolated from the vacuolar vesicle fraction of
      wheat coleoptiles. In the presence of S-adenosyl-L-methionine the enzyme de novo methylates
      the first adenine residue in the TGATCA sequence in the single- or double-stranded DNA
      substrates but it prefers single-stranded structures. Wheat adenine DNA-methyltransferase
      (wadmtase) is a Mg(2+)- or Ca(2+)-dependent enzyme with a maximum activity at pH 7.5-8.0.
      Wadmtase seems to be responsible for mitochondrial DNA modification that might be involved in
      the regulation of replication of mitochondria in plants.
AU  - Fedoreyeva LI
AU  - Vanyushin BF
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 2002 514: 305-308.

PMID- 19232054
VI  - 74
DP  - 2009
TI  - SsoII-like DNA-methyltransferase Ecl18kI: Interaction between regulatory and methylating functions.
PG  - 85-91
AB  - The interaction of DNA-methyltransferase Ecl18kI (M.Ecl18kI) with a fragment of promoter
      region of restriction-modification system SsoII
      was studied. It is shown that dissociation constants of M.Ecl18kI and
      M.SsoII complexes with DNA ligand carrying a regulatory site previously
      characterized for M.SsoII have comparable values. A deletion derivative
      of M.Ecl18kI, Delta(72-379)Ecl18kI, representing the N-terminal protein
      region responsible for regulation, was obtained. It is shown that such
      polypeptide fragment has virtually no interaction with the regulatory
      site. Therefore, the existence of a region responsible for methylation
      is necessary for maintaining M.Ecl18kI regulatory function. The
      properties of methyl-transferase NlaX, which is actually a natural
      deletion derivative of M.Ecl18kI and M.SsoII lacking the first 70 amino
      acid residues and not being able to regulate gene expression of the
      SsoII restriction-modification system, were studied. The ability of
      mutant forms of M.Ecl18kI incorporating single substitutions in regions
      responsible for regulation and methylation to interact with both sites
      of DNA recognition was characterized. The data show a correlation
      between DNA-binding activity of two M.Ecl18kI regions-regulatory and
      methylating.
AU  - Fedotova EA
AU  - Protsenko AS
AU  - Zakharova MV
AU  - Lavrova NV
AU  - Alekseevsky AV
AU  - Oretskaya TS
AU  - Karyagina AS
AU  - Solonin AS
AU  - Kubareva EA
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2009 74: 85-91.

PMID- 6339942
VI  - 302
DP  - 1983
TI  - Expression of a bacterial modification methylase gene in yeast.
PG  - 266-268
AB  - Methylation of specific cytosines in the DNA is generally believed to play some
      role in the regulation of gene expression in eukaryotes.  However, some
      eukaryotes, such as Drosophila and yeast (S. Hattman, personal communication)
      seem not to contain 5-methylcytosine in their DNA.  It would be interesting to
      test, how gene expression in such organisms would respond to the methylation of
      specific cytosines in the genome.  As a first step towards this goal, we have
      introduced the gene encoding the Bacillus sphaericus R modification methylase,
      which methylates the internal cytosine within the recognition sequence 5'-GGCC,
      into yeast cells.  Southern-type hybridization to DNAs isolated from the
      transformed yeast clones revealed that the yeast plasmid carrying the
      prokaryotic methylase gene, as well as the two chromosomal genes tested (his3
      and leu2) were methylated, whereas the bulk of the yeast DNA remained largely
      unmethylated.  This indicates that the Bacillus sphaericus modification
      methylase was expressed in yeast but it modified only certain parts of the
      yeast DNA.
AU  - Feher Z
AU  - Kiss A
AU  - Venetianer P
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1983 302: 266-268.

PMID- 3074009
VI  - 74
DP  - 1988
TI  - In vivo methylation of yeast DNA by prokaryotic DNA methyltransferases.
PG  - 193-195
AB  - No detectable amounts of methylated bases are present in the DNA of the yeast, Saccharomyces
      cerevisiae.  This feature and the availability of an Escherichia coli-yeast cloning system
      make yeast an excellent host to study the factors affecting de novo DNA methylation, as well
      as their attendant effects in a eukaryotic cell.  Earlier, Feher et al. (1983) observed
      heterologous expression of the Bacillus sphaericus RI DNA-cytosine methyltransferase in yeast.
      Methylation of two known chromosomal genes was detected, while the bulk DNA remained largely
      unmethylated.  Heterologous expression of the E. coli DNA (N6-adenine)methyltransferase gene
      (dam) in yeast was reported by Brooks et al. (1983) and Hoekstra and Malone (1985; 1986).
AU  - Feher Z
AU  - Schlagman SL
AU  - Miner Z
AU  - Hattman S
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 193-195.

PMID- 2692855
VI  - 16
DP  - 1989
TI  - The UV excision-repair system of Saccharomyces cerevisiae is involved in the removal of methylcytosines formed in vivo by a cloned prokaryotic DNA methyltransferase.
PG  - 461-464
AB  - DNA methyltransferase activity is not normally found in yeast.  To investigate
      the response of Saccharomyces cerevisiae to the presence of methylated bases,
      we introduced the Bacillus subtilis SPR phage DNA-[cytosine-5]
      methyltransferase gene on the shuttle vector, YEp51.  The methyltransferase
      gene was functionally expressed in yeast under the control of the inducible
      yeast GAL10 promoter.  Following induction we observed a time-dependent
      methylation of yeast DNA in RAD+ and rad2 mutant strains; the rad2 mutant is
      defective in excision-repair of UV-induced DNA damage.  Analysis of restriction
      endonuclease digestion patterns revealed that the relative amount of methylated
      DNA was greater in the excision defective rad2 mutant than in the RAD+ strain.
      These data indicate that the yeast excision-repair system is capable of
      recognizing and removing m5C residues.
AU  - Feher Z
AU  - Schlagman SL
AU  - Miner Z
AU  - Hattman S
PT  - Journal Article
TA  - Curr. Genet.
JT  - Curr. Genet.
SO  - Curr. Genet. 1989 16: 461-464.

PMID- 1977248
VI  - 145
DP  - 1990
TI  - Expression of prokaryotic DNA methyltransferase genes in yeast.
PG  - 343
AB  - DNA methyltransferase activity is not normally found in yeast. To investigate the response of
      Saccharomyces cerevisiae to the presence of methylated bases, we introduced two phage-encoded
      DNA methyltransferase genes on the shuttle vector, YEp51. The Bacillus subtilis phage SPR
      enzyme methylates cytosine residues in three distinct recognition sequences [GGCC, CCGG, and
      CC(A/T)GG], whereas the Escherichia coli phage T4 Dam enzyme methylates adenines primarily in
      GATC sequences. Both phage-encoded genes were functionally expressed in yeast under the
      control of the inducible yeast GAL10 promoter. DNA methyltransferase activity was assayed by
      determining the susceptibility of yeast DNA to cleavage by restriction endonucleases:
      resistance to HaeIII and sensitivity to DpnI indicate SPR- and T4 Dam-specific in vivo
      methylation, respectively. Following induction of the GAL10 promoter we observed a
      time-dependent methylation of yeast DNA in the RAD+, as well as rad2 and rad3 mutant strains;
      these rad mutant strains are defective in excision-repair. Analysis of the restriction
      endonuclease digestion patterns revealed that the relative amount of high molecular weight
      methylated DNA was greater in the excision-defective rad mutants than in the RAD+ strain.
      Furthermore, after methyltransferase gene expression was turned off (by the addition of
      glucose to previously induced cells), we observed a decrease in methylation in the RAD+, but
      not in the DNA of the rad mutant. These data indicate that the yeast excision-repair system is
      capable of recognizing and removing m5C and m6A residues. All of our plasmid constructions
      contain more than one AUG initiation codon at the 5' end of the mRNA transcript and some of
      the AUGs are followed by an in-frame stop codon. Since we observed expression of the
      methyltransferase genes, it would appear that, in yeast, one or two short ORFs in the leader
      region do not necessarily prevent translation of a downstream gene.
AU  - Feher Z
AU  - Schlagman SL
AU  - Miner Z
AU  - Hattman S
PT  - Journal Article
TA  - Zentralbl. Mikrobiol.
JT  - Zentralbl. Mikrobiol.
SO  - Zentralbl. Mikrobiol. 1990 145: 343.

PMID- 16043691
VI  - 102
DP  - 2005
TI  - Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000.
PG  - 11064-11069
AB  - The complete genomic sequence of Pseudomonas syringae pv. syringae B728a (Pss B728a) has been
      determined and is compared with that of P. syringae
      pv. tomato DC3000 (Pst DC3000). The two pathovars of this economically
      important species of plant pathogenic bacteria differ in host range and
      other interactions with plants, with Pss having a more pronounced
      epiphytic stage of growth and higher abiotic stress tolerance and Pst
      DC3000 having a more pronounced apoplastic growth habitat. The Pss B728a
      genome (6.1 Mb) contains a circular chromosome and no plasmid, whereas the
      Pst DC3000 genome is 6.5 mbp in size, composed of a circular chromosome
      and two plasmids. Although a high degree of similarity exists between the
      two sequenced Pseudomonads, 976 protein-encoding genes are unique to Pss
      B728a when compared with Pst DC3000, including large genomic islands
      likely to contribute to virulence and host specificity. Over 375
      repetitive extragenic palindromic sequences unique to Pss B728a when
      compared with Pst DC3000 are widely distributed throughout the chromosome
      except in 14 genomic islands, which generally had lower GC content than
      the genome as a whole. Content of the genomic islands varies, with one
      containing a prophage and another the plasmid pKLC102 of Pseudomonas
      aeruginosa PAO1. Among the 976 genes of Pss B728a with no counterpart in
      Pst DC3000 are those encoding for syringopeptin, syringomycin, indole
      acetic acid biosynthesis, arginine degradation, and production of ice
      nuclei. The genomic comparison suggests that several unique genes for Pss
      B728a such as ectoine synthase, DNA repair, and antibiotic production may
      contribute to the epiphytic fitness and stress tolerance of this organism.
AU  - Feil H et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2005 102: 11064-11069.

PMID- 19693100
VI  - 4
DP  - 2010
TI  - Microbial community genomics in eastern Mediterranean Sea surface waters.
PG  - 78-87
AB  - Offshore waters of the eastern Mediterranean Sea are one of the most oligotrophic regions on
      Earth in which the primary productivity is phosphorus limited. To study the unexplored
      function and physiology of microbes inhabiting this system, we have analyzed a genomic library
      from the eastern Mediterranean Sea surface waters by sequencing both termini of nearly 5000
      clones. Genome recruitment strategies showed that the majority of high-scoring pairs
      corresponded to genomes from the Alphaproteobacteria (SAR11-like and Rhodobacterales),
      Cyanobacteria (Synechococcus and high-light
      adapted Prochlorococcus) and diverse uncultured Gammaproteobacteria. The community structure
      observed, as evaluated by both protein similarity scores or metabolic potential, was similar
      to that found in the euphotic zone of the ALOHA station off Hawaii but very different from
      that of deep aphotic
      zones in both the Mediterranean Sea and the Pacific Ocean. In addition, a strong enrichment
      toward phosphate and phosphonate uptake and utilization metabolism was also observed.
AU  - Feingersch R
AU  - Suzuki MT
AU  - Shmoish M
AU  - Sharon I
AU  - Sabehi G
AU  - Partensky F
AU  - Beja O
PT  - Journal Article
TA  - ISME J.
JT  - ISME J.
SO  - ISME J. 2010 4: 78-87.

PMID- 22000740
VI  - 302
DP  - 2012
TI  - DNA sequence analysis of the composite plasmid pTC conferring virulence and antimicrobial resistance for porcine enterotoxigenic Escherichia coli.
PG  - 4-9
AB  - In this study the plasmid pTC, a 90kb self-conjugative virulence plasmid
      of the porcine enterotoxigenic Escherichia coli (ETEC) strain EC2173
      encoding the STa and STb heat-stable enterotoxins and tetracycline
      resistance, has been sequenced in two steps. As a result we identified
      five main distinct regions of pTC: (i) the maintenance region responsible
      for the extreme stability of the plasmid, (ii) the TSL (toxin-specific
      locus comprising the estA and estB genes) which is unique and
      characteristic for pTC, (iii) a Tn10 transposon, encoding tetracycline
      resistance, (iv) the tra (plasmid transfer) region, and (v) the colE1-like
      origin of replication. It is concluded that pTC is a self-transmissible
      composite plasmid harbouring antibiotic resistance and virulence genes.
      pTC belongs to a group of large conjugative E. coli plasmids represented
      by NR1 with a widespread tra backbone which might have evolved from a
      common ancestor. This is the first report of a completely sequenced animal
      ETEC virulence plasmid containing an antimicrobial resistance locus,
      thereby representing a selection advantage for spread of pathogenicity in
      the presence of antimicrobials leading to increased disease potential.
AU  - Fekete PZ
AU  - Brzuszkiewicz E
AU  - Blum-Oehler G
AU  - Olasz F
AU  - Szabo M
AU  - Gottschalk G
AU  - Hacker J
AU  - Nagy B
PT  - Journal Article
TA  - Int. J. Med. Microbiol.
JT  - Int. J. Med. Microbiol.
SO  - Int. J. Med. Microbiol. 2012 302: 4-9.

PMID- 29674534
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of 'Nocardia suismassiliense' Strain S-137 (CSUR P4007).
PG  - e00212-18
AB  - 'Nocardia suismassiliense' strain S-137 isolated from Sus scrofa feces exhibits a 9.4-Mb
      (67.1% GC content) draft genome sequence containing 8,658 protein-coding
      genes, 66 tRNAs, and 9 rRNAs. In silico DNA-DNA hybridization confirmed strain
      S-137 as representative of a new species, 'Nocardia suismassiliense,' closely
      related to N. tenerifensis and N. brasiliensis.
AU  - Fellag M
AU  - Levasseur A
AU  - Delerce J
AU  - Bittar F
AU  - Marie JL
AU  - Davoust B
AU  - Drancourt M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00212-18.

PMID- 21745816
VI  - 39
DP  - 2011
TI  - The USP7/Dnmt1 complex stimulates the DNA methylation activity of Dnmt1 and regulates the stability of UHRF1.
PG  - 8355-8365
AB  - Aberrant DNA methylation is often associated with cancer and the formation of tumors; however,
      the underlying mechanisms, in particular the
      recruitment and regulation of DNA methyltransferases remain largely
      unknown. In this study, we identified USP7 as an interaction partner of
      Dnmt1 and UHRF1 in vivo. Dnmt1 and USP7 formed a soluble dimer complex
      that associated with UHRF1 as a trimeric complex on chromatin. Complex
      interactions were mediated by the C-terminal domain of USP7 with the
      TS-domain of Dnmt1, whereas the TRAF-domain of USP7 bound to the
      SRA-domain of UHRF1. USP7 was capable of targeting UHRF1 for
      deubiquitination and affects UHRF1 protein stability in vivo. Furthermore,
      Dnmt1, UHRF1 and USP7 co-localized on silenced, methylated genes in vivo.
      Strikingly, when analyzing the impact of UHRF1 and USP7 on Dnmt1-dependent
      DNA methylation, we found that USP7 stimulated both the maintenance and de
      novo DNA methylation activity of Dnmt1 in vitro. Therefore, we propose a
      dual role of USP7, regulating the protein turnover of UHRF1 and
      stimulating the enzymatic activity of Dnmt1 in vitro and in vivo.
AU  - Felle M
AU  - Joppien S
AU  - Nemeth A
AU  - Diermeier S
AU  - Thalhammer V
AU  - Dobner T
AU  - Kremmer E
AU  - Kappler R
AU  - Langst G
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2011 39: 8355-8365.

PMID- 1676153
VI  - 19
DP  - 1991
TI  - A genotypic mutation system measuring mutations in restriction recognition sequences.
PG  - 2913-2919
AB  - The RFLP/PCR approach (restriction fragment length polymorphism/polymerase
      chain reaction) to genotypic mutation analysis described here measures
      mutations in restriction recognition sequences.  Wild-type DNA is restricted
      before the resistant, mutated sequences are amplified by PCR and cloned.  We
      tested the capacity of this experimental design to isolate a few copies of a
      mutated sequence of the human c-Ha-ras1 gene from a large excess of wild-type
      DNA.  For this purpose we constructed a 272 bp fragment with 2 mutations in the
      PvuII recognition sequence 1727-1732 and studied the rescue by RFLP/PCR of a
      few copies of this PvuII mutant standard.  Following amplification with
      Taq-polymerase induced bp changes were quantitated by hybridization with
      specific oligonucleotide probes.  Our results indicate that 10 PvuII mutant
      standard copies can be rescued from 10/8 to 10/9 wild-type sequences.  Taq
      polymerase errors originating from unrestricted, residual wild-type DNA were
      sequence dependent and consisted mostly of transversions originating at G.C bp.
      In contrast to a doubly mutated standard the capacity to rescue single bp
      mutations by RFLP/PCR is limited by Taq-polymerase errors.  Therefore, we
      assessed the capacity of our protocol to isolate a G to T transversion mutation
      at base pair 1698 of the MspI-site 1695-1698 of the c-Ha-ras1 gene from excess
      wild-type ras1 DNA.  We found that 100 copies of the mutated ras1 fragment
      could be readily rescued from 10/8 copies of wild-type DNA.
AU  - Felley-Bosco E
AU  - Pourzand C
AU  - Zijlstra J
AU  - Amstad P
AU  - Cerutti P
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 2913-2919.

PMID- 19173286
VI  - 106
DP  - 2009
TI  - Dimerization of DNA methyltransferase 1 is mediated by its regulatory domain.
PG  - 521-528
AB  - DNA methylation is a major epigenetic modification and plays a crucial role in the regulation
      of gene expression. Within the family of DNA
      methyltransferases (Dnmts), Dnmt3a and 3b establish methylation marks during early
      development, while Dnmt1 maintains methylation
      patterns after DNA replication. The maintenance function of Dnmt1 is regulated by its large
      regulatory N-terminal domain that interacts with
      other chromatin factors and is essential for the recognition of hemi-methylated DNA.
      Gelfiltration analysis showed that purified Dnmt1 elutes
      at an apparent molecular weight corresponding to the size of a dimer. With protein interaction
      assays we could show that Dnmt1 interacts with
      itself through its N-terminal regulatory domain. By deletion analysis and
      co-immunoprecipitations we mapped the dimerization domain to
      the targeting sequence TS that is located in the center of the N-terminal domain (amino acids
      310-629) and was previously shown to mediate
      replication independent association with heterochromatin at chromocenters. Further mutational
      analyses suggested that the dimeric complex
      has a bipartite interaction interface and is formed in a head-to-head orientation. Dnmt1 dimer
      formation could facilitate the discrimination of
      hemi-methylated target sites as has been found for other palindromic DNA sequence recognizing
      enzymes. These results assign an additional
      function to the TS domain and raise the interesting question how these functions are spatially
      and temporarily co-ordinated.
AU  - Fellinger K
AU  - Rothbauer U
AU  - Felle M
AU  - Laengst G
AU  - Leonhardt H
PT  - Journal Article
TA  - J. Cell. Biochem.
JT  - J. Cell. Biochem.
SO  - J. Cell. Biochem. 2009 106: 521-528.

PMID- 27056239
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Three European Laboratory Derivatives from Enterohemorrhagic Escherichia coli O157:H7 Strain EDL933, Including Two Plasmids.
PG  - e01331-15
AB  - Escherichia coliO157:H7 EDL933, isolated in 1982 in the United States, was the first
      enterohemorrhagicE. coli(EHEC) strain sequenced. Unfortunately, European
      labs can no longer receive the original strain. We checked three European EDL933
      derivatives and found major genetic deviations (deletions, inversions) in two
      strains. All EDL933 strains contain the cryptic EHEC-plasmid, not reported
      before.
AU  - Fellner L
AU  - Huptas C
AU  - Simon S
AU  - Muhlig A
AU  - Scherer S
AU  - Neuhaus K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01331-15.

PMID- 27408681
VI  - 10
DP  - 2015
TI  - Permanent draft genome sequence of sulfoquinovose-degrading Pseudomonas putida strain SQ1.
PG  - 42
AB  - Pseudomonas putida SQ1 was isolated for its ability to utilize the plant sugar sulfoquinovose
      (6-deoxy-6-sulfoglucose) for growth, in order to define its
      SQ-degradation pathway and the enzymes and genes involved. Here we describe the
      features of the organism, together with its draft genome sequence and annotation.
      The draft genome comprises 5,328,888 bp and is predicted to encode 5,824
      protein-coding genes; the overall G + C content is 61.58 %. The genome annotation
      is being used for identification of proteins that might be involved in SQ
      degradation by peptide fingerprinting-mass spectrometry.
AU  - Felux AK
AU  - Franchini P
AU  - Schleheck D
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 42.

PMID- 24994798
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of a Novel Streptomyces griseorubens Strain, JSD-1, Active  in Carbon and Nitrogen Recycling.
PG  - e00650-14
AB  - Streptomyces griseorubens JSD-1, isolated from compost-treated soil, is able to utilize
      lignocellulose and nitrate as its sole carbon and nitrogen source for
      growth. Here, we announce the draft genome map of this actinomycete. The genes
      participating in lignocellulose and nitrate metabolism were picked out and
      identified.
AU  - Feng H
AU  - Zhi Y
AU  - Sun Y
AU  - Wei X
AU  - Luo Y
AU  - Zhou P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00650-14.

PMID- 26517369
VI  - 10
DP  - 2015
TI  - Sequencing and Analysis of the Pseudomonas fluorescens GcM5-1A Genome: A Pathogen Living in the Surface Coat of Bursaphelenchus xylophilus.
PG  - E0141515
AB  - It is known that several bacteria are adherent to the surface coat of pine wood
      nematode (Bursaphelenchus xylophilus), but their function and role in the
      pathogenesis of pine wilt disease remains debatable. The Pseudomonas fluorescens
      GcM5-1A is a bacterium isolated from the surface coat of pine wood nematodes. In
      previous studies, GcM5-1A was evident in connection with the pathogenicity of
      pine wilt disease. In this study, we report the de novo sequencing of the GcM5-1A
      genome. A 600-Mb collection of high-quality reads was obtained and assembled into
      sequence contigs spanning a 6.01-Mb length. Sequence annotation predicted 5,413
      open reading frames, of which 2,988 were homologous to genes in the other four
      sequenced P. fluorescens isolates (SBW25, WH6, Pf0-1 and Pf-5) and 1,137 were
      unique to GcM5-1A. Phylogenetic studies and genome comparison revealed that
      GcM5-1A is more closely related to SBW25 and WH6 isolates than to Pf0-1 and Pf-5
      isolates. Towards study of pathogenesis, we identified 79 candidate virulence
      factors in the genome of GcM5-1A, including the Alg, Fl, Waa gene families, and
      genes coding the major pathogenic protein fliC. In addition, genes for a complete
      T3SS system were identified in the genome of GcM5-1A. Such systems have proved to
      play a critical role in subverting and colonizing the host organisms of many
      gram-negative pathogenic bacteria. Although the functions of the candidate
      virulence factors need yet to be deciphered experimentally, the availability of
      this genome provides a basic platform to obtain informative clues to be addressed
      in future studies by the pine wilt disease research community.
AU  - Feng K
AU  - Li R
AU  - Chen Y
AU  - Zhao B
AU  - Yin T
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2015 10: E0141515.

PMID- 24675852
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Bacillus subtilis QH-1, a Chromium-Reducing Bacterial Strain Isolated in Qinghai Province, China.
PG  - e00182-14
AB  - Bacillus subtilis strain QH-1, a chromium-reducing bacterial strain, was isolated from a soil
      sample from a chromium-containing slag heap. The draft genome
      sequence of this bacterium is 4,034,036 bp in length, with a G+C content of
      43.71%, and it is predicted to contain 4,082 protein-coding genes.
AU  - Feng L
AU  - Ma T
AU  - Zhang J
AU  - Xu F
AU  - Shi L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00182-14.

PMID- 19115014
VI  - 3
DP  - 2008
TI  - A recalibrated molecular clock and independent origins for the cholera pandemic clones.
PG  - E4053
AB  - Cholera, caused by Vibrio cholerae, erupted globally from South Asia in 7
      pandemics, but there were also local outbreaks between the 6(th)
      (1899-1923) and 7(th) (1961-present) pandemics. All the above are serotype
      O1, whereas environmental or invertebrate isolates are antigenically
      diverse. The pre 7th pandemic isolates mentioned above, and other minor
      pathogenic clones, are related to the 7(th) pandemic clone, while the
      6(th) pandemic clone is in the same lineage but more distantly related,
      and non-pathogenic isolates show no clonal structure. To understand the
      origins and relationships of the pandemic clones, we sequenced the genomes
      of a 1937 prepandemic strain and a 6(th) pandemic isolate, and compared
      them with the published 7(th) pandemic genome. We distinguished mutational
      and recombinational events, and allocated these and other events, to
      specific branches in the evolutionary tree. There were more mutational
      than recombinational events, but more genes, and 44 times more base pairs,
      changed by recombination. We used the mutational single-nucleotide
      polymorphisms and known isolation dates of the prepandemic and 7(th)
      pandemic isolates to estimate the mutation rate, and found it to be 100
      fold higher than usually assumed. We then used this to estimate the
      divergence date of the 6(th) and 7(th) pandemic clones to be about 1880.
      While there is a large margin of error, this is far more realistic than
      the 10,000-50,000 years ago estimated using the usual assumptions. We
      conclude that the 2 pandemic clones gained pandemic potential
      independently, and overall there were 29 insertions or deletions of one or
      more genes. There were also substantial changes in the major integron,
      attributed to gain of individual cassettes including copying from within,
      or loss of blocks of cassettes. The approaches used open up new avenues
      for analysing the origin and history of other important pathogens.
AU  - Feng L
AU  - Reeves PR
AU  - Lan R
AU  - Ren Y
AU  - Gao C
AU  - Zhou Z
AU  - Ren Y
AU  - Cheng J
AU  - Wang W
AU  - Wang J
AU  - Qian W
AU  - Li D
AU  - Wang L
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2008 3: E4053.

PMID- 17372208
VI  - 104
DP  - 2007
TI  - Genome and proteome of long-chain alkane degrading Geobacillus thermodenitrificans NG80-2 isolated from a deep-subsurface oil reservoir.
PG  - 5602-5607
AB  - The complete genome sequence of Geobacillus thermodenitrificans NG80-2, a thermophilic
      bacillus isolated from a deep oil reservoir in Northern
      China, consists of a 3,550,319-bp chromosome and a 57,693-bp plasmid. The
      genome reveals that NG80-2 is well equipped for adaptation into a wide
      variety of environmental niches, including oil reservoirs, by possessing
      genes for utilization of a broad range of energy sources, genes encoding
      various transporters for efficient nutrient uptake and detoxification, and
      genes for a flexible respiration system including an aerobic branch
      comprising five terminal oxidases and an anaerobic branch comprising a
      complete denitrification pathway for quick response to dissolved oxygen
      fluctuation. The identification of a nitrous oxide reductase gene has not
      been previously described in Gram-positive bacteria. The proteome further
      reveals the presence of a long-chain alkane degradation pathway; and the
      function of the key enzyme in the pathway, the long-chain alkane
      monooxygenase LadA, is confirmed by in vivo and in vitro experiments. The
      thermophilic soluble monomeric LadA is an ideal candidate for treatment of
      environmental oil pollutions and biosynthesis of complex molecules.
AU  - Feng L
AU  - Wang W
AU  - Cheng J
AU  - Ren Y
AU  - Zhao G
AU  - Gao C
AU  - Tang Y
AU  - Liu X
AU  - Han W
AU  - Peng X
AU  - Liu R
AU  - Wang L
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2007 104: 5602-5607.

PMID- 22247537
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Salmonella enterica Serovar Pullorum RKS5078.
PG  - 744
AB  - Salmonella enterica serovar Pullorum is a chicken-adapted pathogen, causing pullorum disease.
      Its strict host adaptation has been suspected to
      result in gene decay. To validate this hypothesis and identify the decayed
      genes, we sequenced the complete genome of S. Pullorum RKS5078. We found
      263 pseudogenes in this strain and conducted functional analyses of the
      decayed genes.
AU  - Feng Y
AU  - Xu HF
AU  - Li QH
AU  - Zhang SY
AU  - Wang CX
AU  - Zhu DL
AU  - Cao FL
AU  - Li YG
AU  - Johnston RN
AU  - Zhou J
AU  - Liu GR
AU  - Liu SL
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 744.

PMID- 23516341
VI  - 9
DP  - 2013
TI  - Detecting DNA modifications from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic.
PG  - e1002935
AB  - DNA modifications such as methylation and DNA damage can play critical regulatory roles in
      biological systems. Single molecule, real time (SMRT) sequencing technology generates DNA
      sequences as well as DNA polymerase kinetic information that can be used for the direct
      detection of DNA modifications. We demonstrate that local sequence context has a strong impact
      on DNA polymerase kinetics in the neighborhood of the incorporation site during the DNA
      synthesis reaction, allowing for the possibility of estimating the expected kinetic rate of
      the enzyme at the incorporation site using kinetic rate information collected from existing
      SMRT sequencing data (historical data) covering the same local sequence contexts of interest.
      We develop an Empirical Bayesian hierarchical model for incorporating historical data. Our
      results show that the model could greatly increase DNA modification detection accuracy, and
      reduce requirement of control data coverage. For some DNA modifications that have a strong
      signal, a control sample is not even needed by using historical data as alternative to
      control. Thus, sequencing costs can be greatly reduced by using the model. We implemented the
      model in a R package named seqPatch, which is available at
      https://github.com/zhixingfeng/seqPatch.
AU  - Feng Z
AU  - Fang G
AU  - Korlach J
AU  - Clark T
AU  - Luong K
AU  - Zhang X
AU  - Wong W
AU  - Schadt E
PT  - Journal Article
TA  - PLOS Comp. Biol.
JT  - PLOS Comp. Biol.
SO  - PLOS Comp. Biol. 2013 9: e1002935.

PMID- 25404133
VI  - 42
DP  - 2014
TI  - qDNAmod: a statistical model-based tool to reveal intercellular heterogeneity of  DNA modification from SMRT sequencing data.
PG  - 13488-13499
AB  - In an isogenic cell population, phenotypic heterogeneity among individual cells is common and
      critical for survival of the population under different environment conditions. DNA
      modification is an important epigenetic factor that can regulate phenotypic heterogeneity. The
      single molecule real-time (SMRT) sequencing technology provides a unique platform for
      detecting a wide range of DNA modifications, including N6-methyladenine (6-mA),
      N4-methylcytosine (4-mC) and 5-methylcytosine (5-mC). Here we present qDNAmod, a novel
      bioinformatic tool for genome-wide quantitative profiling of intercellular heterogeneity of
      DNA modification from SMRT sequencing data. It is capable of estimating proportion of isogenic
      haploid cells, in which the same loci of the genome are differentially modified. We tested the
      reliability of qDNAmod with the SMRT sequencing data of Streptococcus pneumoniae strain ST556.
      qDNAmod detected extensive intercellular heterogeneity of DNA methylation (6-mA) in a clonal
      population of ST556. Subsequent biochemical analyses revealed that the recognition sequences
      of two type I restriction-modification (R-M) systems are responsible for the intercellular
      heterogeneity of DNA methylation initially identified by qDNAmod. qDNAmod thus represents a
      valuable tool for studying intercellular phenotypic heterogeneity from genome-wide DNA
      modification.
AU  - Feng Z
AU  - Li J
AU  - Zhang JR
AU  - Zhang X
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2014 42: 13488-13499.

PMID- 7687328
VI  - 364
DP  - 1993
TI  - Group II self-splicing introns in bacteria.
PG  - 358-361
AB  - Like nuclear premessenger introns, group II self-splicing introns are excised from primary
      transcripts as branched molecules, containing a 2'-5' phosphodiester bond.  For this reason,
      it is widely believed that the ribozyme (catalytic RNA) core of group II introns, or some
      evolutionarily related molecule, gave rise to the RNA components of the spliceosomal splicing
      machinery of the eukaryotic nucleus.  One difficulty with this hypothesis has been the
      restricted distribution of group II introns.  Unlike group I self-splicing introns, which
      interrupt not only organelle primary transcripts, but also some bacterial and nuclear genes,
      group II introns seemed to be confined to mitochondrial and chloroplast genomes.  We now
      report the discovery of group II introns both in cyanobacteria (the ancestors of chloroplasts)
      and the gamma subdivision of purple bacteria, or proteobacteria, whose alpha subdivision
      probably gave rise to mitochondria.  At least one of these introns actually self-splices in
      vitro.
AU  - Ferat J-L
AU  - Michel F
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1993 364: 358-361.

PMID- 11710099
VI  - 1
DP  - 2000
TI  - Inhibition of sequence-specific protein-DNA interaction and restriction endonuclease cleavage via triplex stabilization by poly(L-lysine)-graft-dextran copolymer.
PG  - 186-193
AB  - Triplex stabilization by poly(L-lysine)-graft-dextran copolymer within a mammalian gene
      promoter inhibits the DNA binding activity of nuclear proteins from HeLa cells as well as
      restriction endonuclease cleavage at physiological pH and ionic conditions in vitro.
      Electrophoretic mobility shift assays using a 30-mer homopurine-homopyrimidine stretch
      (located between -165 and -146 bp) of the promoter is engineered at the BamHI and PstI sites
      of a plasmid DNA, copolymer-mediated triplex stabilization also remarkably competes
      endonuclease activity of BamHI.  Finally, the triplex-stabilizing efficiency of the copolymer
      is remarkably higher than that of spermine and benzo[e]pyridoindole.  Our results indicate
      that the copolymer, regardless of the length of the target duplex, stabilizes triplexes for
      significant inhibition of protein-DNA interaction and endonuclease activity.  Since stable
      triplex formation within a short region out of a long native duplex is a prerequisite to
      confer the therapeutic potential of antigene strategy, triplex stabilization on a long target
      duplex and inhibition of nuclear protein - DNA interaction may open the possible in vivo
      applicability of the copolymer.
AU  - Ferdous A
AU  - Akaike T
AU  - Maruyama A
PT  - Journal Article
TA  - Biomacromolecules
JT  - Biomacromolecules
SO  - Biomacromolecules 2000 1: 186-193.

PMID- 19376874
VI  - 191
DP  - 2009
TI  - Genomic sequencing reveals regulatory mutations and recombinational events in the widely used MC4100 lineage of Escherichia coli K-12.
PG  - 4025-4029
AB  - The genome of an Escherichia coli MC4100 strain with a lambda placMu50
      fusion revealed numerous regulatory differences from MG1655, including one
      that arose during laboratory storage. The 194 mutational differences
      between MC4100(MuLac) and other K-12 sequences were mostly allocated to
      specific lineages, indicating the considerable mutational divergence
      between K-12 strains.
AU  - Ferenci T
AU  - Zhou Z
AU  - Betteridge T
AU  - Ren Y
AU  - Liu Y
AU  - Feng L
AU  - Reeves PR
AU  - Wang L
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2009 191: 4025-4029.

PMID- 17332005
VI  - 59
DP  - 2007
TI  - Interspecies spread of CTX-M-32 extended-spectrum {beta}-lactamase and the role of the insertion sequence IS1 in down-regulating blaCTX-M gene expression.
PG  - 841-847
AB  - OBJECTIVES: To characterize the extended-spectrum beta-lactamases (ESBLs)
      as well as their genetic environment in different isolates of
      Enterobacteriaceae from a patient with repeated urinary tract infections.
      METHODS: Two isolates of Escherichia coli and one Proteus mirabilis, all
      with ESBL phenotypes, were studied. Conjugation experiments and
      restriction fragment length polymorphisms (RFLPs) were performed. Cloning
      of the bla genes was by plasmid restriction and fragments ligation.
      Antibiotic susceptibility testing was by Etest. The genetic environment
      was analysed by direct sequencing of the DNA surrounding the bla gene.
      RT-PCR was performed to study the differences in the bla(CTX-M) gene
      expression. RESULTS: The bla gene was transferred by conjugation from the
      three clinical isolates, which by RFLP showed the same plasmid. The bla
      gene and surrounding sequences were cloned, an approximately 9 kbp AccI
      fragment was sequenced and the bla(CTX-M-32) gene was identified. The MICs
      of ceftazidime for transconjugants and transformants bearing the
      bla(CTX-M-32) gene were lower than those previously reported. Analysis of
      the DNA surrounding the ESBL gene revealed a new genetic structure with
      two insertion sequences, IS5 and IS1, located immediately upstream of the
      bla(CTX-M-32) gene; IS1 was located between the bla gene and IS5, and
      within the -10 and -35 promoter boxes of the bla(CTX-M-32) gene.
      Microbiological and biochemical studies revealed lower bla(CTX-M-32) gene
      expression in bacterial isolates with IS1 between the promoter boxes.
      CONCLUSIONS: Data suggest putative in vivo horizontal bla(CTX-M-32) gene
      transfer between two different genera of Enterobacteriaceae. A new complex
      structure, IS5-IS1, was detected upstream of the bla gene and IS1
      negatively modulated expression of the bla(CTX-M-32) gene because its
      location modified the bla promoter region.
AU  - Fernandez A
AU  - Gil E
AU  - Cartelle M
AU  - Perez A
AU  - Beceiro A
AU  - Mallo S
AU  - Tomas MM
AU  - Perez-Llarena FJ
AU  - Villanueva R
AU  - Bou G
PT  - Journal Article
TA  - J. Antimicrob. Chemother.
JT  - J. Antimicrob. Chemother.
SO  - J. Antimicrob. Chemother. 2007 59: 841-847.

PMID- 9628353
VI  - 379
DP  - 1998
TI  - Analysis of DNA methylation processes related to the inhibition of DNA synthesis by 5-azacytidine in Streptomyces antibioticus ETH 7451.
PG  - 559-562
AB  - 5-Azacytidine inhibits DNA synthesis and to a lesser proportion RNA synthesis in S.
      antibioticus.  The biosynthesis of proteins is not affected.  The main inhibitory effect of
      5-azacytidine on DNA and RNA synthesis is probably caused by its incorporation into newly
      synthesized DNA or RNA and the formation of covalent complexes between cytosine-specific
      methyltransferases and the modified DNA or RNA templates.  To analyze whether such effects
      could occur at the oriC region of S. antibioticus we analyzed the methylation status of this
      region using the bisulphite assisted genomic sequencing method.  One of the cytosine residues
      found to be partially methylated was contained within a unique NaeI sequence (GCCGGC) in oriC.
      Subsequent analysis shows chromosomal DNA from S. antibioticus to be resistant to R.NaeI
      restriction indicating that this strain contains a NaeI-specific cytosine C5-methyltransferase
      activity.  Following 5-azacytidine treatment the NaeI site within the oriC region becomes
      partially demethylated.  Our results suggest that some of the 5-azacytidine effects on DNA and
      RNA synthesis might indeed be related to the complex formation and inhibition of a
      cytosine-specific DNA methyltransferase.
AU  - Fernandez M
AU  - Olek A
AU  - Walter J
AU  - Sanchez J
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1998 379: 559-562.

PMID- 7541762
VI  - 157
DP  - 1995
TI  - Effect of  5-azacytidine and sinefungin on Streptomyces development.
PG  - 221-223
AB  - The effect of two DNA-methyltransferase inhibitors, 5-azacytidine (5azaC) and sinefungin (Sf),
      on the development of Streptomyces antibioticus ETH7451 (Sa) was studied. Pulse labeling
      experiments and SDS-PAGE analysis of proteins from cells grown in sporulation synthetic medium
      showed that both inhibitors affect a limited number of systems. Synthesis of the antibiotic
      rhodomycin was increased in the presence of 5azaC. 5azaC also stimulated the production of
      actinorhodin in cultures of S. coelicolor A3(2) grown in minimal medium. The analog did not
      affect the expression of whiB and whiG, two sporulation genes from S. coelicolor A3(2) whose
      homologues are present in Sa. Overall results indicated that 5azaC and Sf affect specific
      events associated with differentiation and secondary metabolism in Streptomyces.
AU  - Fernandez M
AU  - Soliveri J
AU  - Novella IS
AU  - Yebra MJ
AU  - Barbes C
AU  - Sanchez J
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 221-223.

PMID- 23682139
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Steroid Degrader Rhodococcus ruber Strain Chol-4.
PG  - e00215-13
AB  - The whole-genome shotgun sequence of Rhodococcus ruber strain Chol-4 is presented here. This
      organism was shown to be able to grow using many steroids as the sole carbon and energy
      sources. These sequence data will help us to further explore the metabolic abilities of this
      versatile degrader.
AU  - Fernandez-de-Las-Heras L
AU  - Alonso S
AU  - de la Vega-de-Leon A
AU  - Xavier D
AU  - Perera J
AU  - Navarro-Llorens JM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00215-13.

PMID- 29545291
VI  - 6
DP  - 2018
TI  - Whole-Genome Sequences of Two Arthrobacter Strains Isolated from a Holm Oak Rhizosphere Affected by Wildfire.
PG  - e00071-18
AB  - We report here the draft genome sequences of two Arthrobacter strains isolated from a holm oak
      forest affected by wildfire. Both strains were shown to act as
      plant growth promoters, with AFG20 being a member of the most abundant group
      found in this soil and AFG7.2 being the strain with the highest indole-3-acetic
      acid production level.
AU  - Fernandez-Gonzalez AJ
AU  - Lasa AV
AU  - Fernandez-Lopez M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00071-18.

PMID- 26159536
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of the Two Unrelated Macrolide-Resistant Corynebacterium argentoratense Strains CNM 463/05 and CNM 601/08, Isolated from Patients in the  University Hospital of Leon, Spain.
PG  - e00765-15
AB  - Corynebacterium argentoratense has been associated mainly with infections in the  human
      respiratory tract. Genome sequencing of two unrelated clinical
      macrolide-resistant strains, CNM 463/05 and CNM 601/08, revealed the presence of
      the antibiotic resistance gene erm(X) allocated to a specific genomic region with
      100% similarity to the widely distributed transposable element Tn5432.
AU  - Fernandez-Natal MI
AU  - Soriano F
AU  - Acedo A
AU  - Hernandez M
AU  - Tauch A
AU  - Rodriguez-Lazaro D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00765-15.

PMID- 25999560
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Corynebacterium kroppenstedtii CNM633/14 and CNM632/14, Multidrug-Resistant and Antibiotic-Sensitive Isolates from Nodules of  Granulomatous Mastitis Patients.
PG  - e00525-15
AB  - Corynebacterium kroppenstedtii has been associated with infections of the female  breast.
      Genome sequencing of two strains revealed a specific genomic island in
      the multidrug-resistant isolate CNM633/14 with similarity to the R plasmid
      pJA144188 of Corynebacterium resistens DSM 45100, being indicative of the
      horizontal transfer of antibiotic resistance genes to C. kroppenstedtii.
AU  - Fernandez-Natal MI
AU  - Soriano F
AU  - Ariza-Miguel J
AU  - Marrodan-Ciordia T
AU  - Acedo A
AU  - Hernandez M
AU  - Tauch A
AU  - Rodriguez-Lazaro D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00525-15.

PMID- 28082506
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of JVAP01T, the Type Strain of the Novel Species Acinetobacter dijkshoorniae.
PG  - e01480-16
AB  - Here, we report the draft genome sequence of the type strain of Acinetobacter dijkshoorniae, a
      novel human pathogen within the Acinetobacter
      calcoaceticus-Acinetobacter baumannii (ACB) complex. Strain JVAP01T has an
      estimated genome size of 3.9 Mb, exhibits a 38.8% G+C content, and carries a
      plasmid with the blaNDM-1 carbapenemase gene.
AU  - Fernandez-Orth D
AU  - Cosgaya C
AU  - Telli M
AU  - Mosqueda N
AU  - Mari-Almirall M
AU  - Roca I
AU  - Vila J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01480-16.

PMID- 27313301
VI  - 4
DP  - 2016
TI  - Draft Whole-Genome Sequences of Three Lactobacillus plantarum Food Isolates.
PG  - e00560-16
AB  - Lactobacillus plantarum is a widespread member of the Lactobacillus genus and frequently
      isolated from spoiled acidified food products. Here, we report the
      draft genome sequences of three L. plantarum food isolates.
AU  - Fernandez-Ramirez MD
AU  - Boekhorst J
AU  - de Jong A
AU  - Kuipers OP
AU  - Abee T
AU  - Nierop-Groot MN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00560-16.

PMID- 27939676
VI  - 49
DP  - 2017
TI  - Multi-omics approach to study global changes in a triclosan-resistant mutant strain of Acinetobacter baumannii ATCC 17978.
PG  - 74-80
AB  - Acinetobacter baumannii AB042, a triclosan-resistant mutant strain, was examined
      for modulated gene expression using whole-genome sequencing, transcriptomics and
      proteomics in order to understand the mechanism of triclosan resistance as well
      as its impact on A. baumannii. Data revealed modulated expression of the fatty
      acid metabolism pathway, co-factors known to play a role in the synthesis of
      fatty acids, as well as several transcriptional regulators. The membrane
      composition of the mutant revealed a decrease in C18 with a corresponding
      increase in C16 fatty acids compared with the parent strain A. baumannii ATCC
      17978. These data indicate that A. baumannii responds to triclosan by altering
      the expression of genes involved in fatty acid metabolism, antibiotic resistance
      and amino acid metabolism.
AU  - Fernando DM
AU  - Chong P
AU  - Singh M
AU  - Spicer V
AU  - Unger M
AU  - Loewen PC
AU  - Westmacott G
AU  - Kumar A
PT  - Journal Article
TA  - Int. J. Antimicrob. Agents
JT  - Int. J. Antimicrob. Agents
SO  - Int. J. Antimicrob. Agents 2017 49: 74-80.

PMID- 25136007
VI  - 58
DP  - 2014
TI  - Triclosan can select for an AdeIJK-overexpressing mutant of Acinetobacter baumannii ATCC 17978 that displays reduced susceptibility to multiple antibiotics.
PG  - 6424-6431
AB  - In order to determine if triclosan can select for mutants of Acinetobacter
      baumannii ATCC 17978 that display reduced susceptibilities to antibiotics, we
      isolated a triclosan-resistant mutant, A. baumannii AB042, by serial passaging of
      A. baumannii ATCC 17978 in growth medium supplemented with triclosan. The
      antimicrobial susceptibility of AB042 was analyzed by the 2-fold serial dilution
      method. Expression of five different resistance-nodulation-division (RND)
      pump-encoding genes (adeB, adeG, adeJ, A1S_2818, and A1S_3217), two outer
      membrane porin-encoding genes (carO and oprD), and the MATE family pump-encoding
      gene abeM was analyzed using quantitative reverse transcriptase (qRT) PCR. A.
      baumannii AB042 exhibited elevated resistance to multiple antibiotics, including
      piperacillin-tazobactam, doxycycline, moxifloxacin, ceftriaxone, cefepime,
      meropenem, doripenem, ertapenem, ciprofloxacin, aztreonam, tigecycline, and
      trimethoprim-sulfamethoxazole, in addition to triclosan. Genome sequencing of A.
      baumannii AB042 revealed a (116)G-->V mutation in fabI, the gene encoding the
      target enzyme for triclosan. Expression analysis of efflux pumps showed
      overexpression of the AdeIJK pump, and sequencing of adeN, the gene that encodes
      the repressor of the adeIJK operon, revealed a 73-bp deletion which would cause a
      premature termination of translation, resulting in an inactive truncated AdeN
      protein. This work shows that triclosan can select for mutants of A. baumannii
      that display reduced susceptibilities to multiple antibiotics from chemically
      distinct classes in addition to triclosan resistance. This multidrug resistance
      can be explained by the overexpression of the AdeIJK efflux pump.
AU  - Fernando DM
AU  - Xu W
AU  - Loewen PC
AU  - Zhanel GG
AU  - Kumar A
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2014 58: 6424-6431.

PMID- 25013144
VI  - 2
DP  - 2014
TI  - Complete Genome Sequences of Two Central European Brucella suis bv. 2 Haplotype 2c Strains Isolated from Wild Boars.
PG  - e00686-14
AB  - The Brucella suis haplotype 2c is commonly isolated from wild boars and domestic  pigs across
      Central Europe, though it is rarely described in the Iberian Peninsula. We report here the
      complete and annotated genome sequences of two haplotype 2c strains isolated from wild boars
      in the northeast region of Spain, above the Ebro River.
AU  - Ferreira AC
AU  - Tenreiro R
AU  - Correa-de-Sa MI
AU  - Dias R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00686-14.

PMID- 24994794
VI  - 2
DP  - 2014
TI  - Complete Genome Sequences of Three Iberian Brucella suis Biovar 2 Strains Isolated from Wild Boars.
PG  - e00618-14
AB  - Brucella suis biovar 2 is the most common biovar isolated from wild boars (Sus scrofa)
      associated with transmission to outdoor-reared pigs in Europe. We report here the complete and
      annotated genome sequences of three strains isolated from wild boars in Portugal and Spain and
      belonging to the Iberian clone (haplotypes 2d and 2e).
AU  - Ferreira AC
AU  - Tenreiro R
AU  - Correa-de-Sa MI
AU  - Dias R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00618-14.

PMID- 29930053
VI  - 6
DP  - 2018
TI  - Genome Sequence of Listeria monocytogenes 2542, a Serotype 4b Strain from a Cheese-Related Outbreak in Portugal.
PG  - e00540-18
AB  - We report here the draft genome sequence of Listeria monocytogenes 2542, a serotype 4b
      clinical strain recovered from a placental sample during a
      cheese-related listeriosis outbreak in Portugal.
AU  - Ferreira V
AU  - Magalhaes R
AU  - Almeida G
AU  - Cabanes D
AU  - Fritzenwanker M
AU  - Chakraborty T
AU  - Hain T
AU  - Teixeira P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00540-18.

PMID- 25125643
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Microbacterium sp. Strain CH12i, Isolated from Shallow Groundwater in Cape Hallett, Antarctica.
PG  - e00789-14
AB  - The Antarctic continent is largely covered by an expansive ice sheet, but it harbors diverse
      terrestrial and aquatic habitats in the coastal ice-free
      continental margins. Here we present the draft genome of Microbacterium sp.
      CH12i, which was isolated from hypersaline, alkaline, and nutrient-rich
      groundwater from Cape Hallett, northern Victoria Land, Antarctica.
AU  - Ferreras ER
AU  - De Maayer P
AU  - Makhalanyane TP
AU  - Guerrero LD
AU  - Aislabie JM
AU  - Cowan DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00789-14.

PMID- 11296296
VI  - 98
DP  - 2001
TI  - Complete genome sequence of an M1 strain of Streptococcus pyogenes.
PG  - 4658-4663
AB  - The 1,852,442-bp sequence of an M1 strain of Streptococcus pyogenes, a Gram-positive pathogen,
      has been determined and contains 1,752 predicted protein-encoding genes. Approximately
      one-third of these genes have no identifiable function, with the remainder falling into
      previously characterized categories of known microbial function. Consistent with the
      observation that S. pyogenes is responsible for a wider variety of human disease than any
      other bacterial species, more than 40 putative virulence-associated genes have been
      identified. Additional genes have been identified that encode proteins likely associated with
      microbial "molecular mimicry" of host characteristics and involved in rheumatic fever or acute
      glomerulonephritis. The complete or partial sequence of four different bacteriophage genomes
      is also present, with each containing genes for one or more previously undiscovered
      superantigen-like proteins. These prophage-associated genes encode at least six potential
      virulence factors, emphasizing the importance of bacteriophages in horizontal gene transfer
      and a possible mechanism for generating new strains with increased pathogenic potential.
AU  - Ferretti JJ et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2001 98: 4658-4663.

PMID- 1962209
VI  - 254
DP  - 1991
TI  - Selective cleavage of human DNA: RecA-assisted restriction endonuclease (RARE) cleavage.
PG  - 1494-1497
AB  - Current methods for sequence-specific cleavage of large segments of DNA are
      severely limited because of the paucity of possible cleavage sites.  A method
      is described whereby any EcoRI site can be targeted for specific cleavage.  The
      technique is based on the ability of RecA protein from Escherichia coli to pair
      an oligonucleotide to its homologous sequence in duplex DNA and to form a
      three-stranded complex.  This complex is protected from EcoRI methylase; after
      methylation and RecA protein removal, EcoRI restriction enzyme cleavage was
      limited to the site previously protected from methylation.  When pairs of
      oligonucleotides are used, a specific fragment can be cleaved out of genomes.
      The method was tested on lambda phage, Escherichia coli, and human DNA.
      Fragments exceeding 500 kilobases in length and yields exceeding 80 percent
      could be obtained.
AU  - Ferrin LJ
AU  - Camerini-Otero RD
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1991 254: 1494-1497.

PMID- 6300409
VI  - 159
DP  - 1982
TI  - Structure of the central spacer region of extrachromosomal ribosomal DNA in Physarum polycephalum.
PG  - 359-381
AB  - We have analyzed the sequence organization of the central spacer region of the
      extrachromosomal ribosomal DNA from two strains of the acellular slime mold
      Physarum polycephalum.  It had been inferred previously from electron
      microscopy that this region, which comprises about one third of the 60 kb++
      palindromic rDNA, contains a complex series of inverted repetitious sequences.
      By partial digestion of end-labeled fragments isolated from purified rDNA and
      from rDNA fragments cloned in Escherichia coli, we have constructed a detailed
      restriction map of this region.  The 22 kb of spacer DNA of each half molecule
      of rDNA contains the following elements:  (a) two separate regions, one of 1.1
      kb and one of 2.1 kb, composed of many direct repeats of the same 30 base-pair
      unit; (b) a region of 4.4 kb composed of a complex series of inverted repeats
      of a 310 base-pair unit; (c) another region of 1.6 kb composed of inverted
      repeats of the same 310 base-pair unit located directly adjacent to the center
      of the rDNA; (d) two copies of a unique sequence of 0.85 kb, which probably
      cocntains a replication origin.  Some of the CpG sequences in the spacer resist
      cleavage by certain restriction endonucleases and thus appear to be methylated.
      The lack of perfect symmetry about the central axis and the arrangement of
      inverted repeated sequences explain the complex pattern of branches and forks
      of the fold-back molecules previously observed by electron microscopy.
      Comparison of the rDNA restriction maps from the two strains of Physarum
      suggests that the repeat units in the spacer are undergoing concerted
      evolution.  We propose a model to explain the evolutionary origin of the
      several palindromic axes in the Physarum rDNA spacer.
AU  - Ferris PJ
AU  - Vogt VM
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1982 159: 359-381.

PMID- 1663864
VI  - 68
DP  - 1991
TI  - Factors affecting the digestion of restriction endonucleases in situ.
PG  - 45-51
AB  - The influence of incubation buffers and glycerol on the enzyme activity of naked DNA of lambda
      phage and mouse, and of mouse chromosomal DNA was investigated. The results obtained varied in
      part from previously known data, but confirmed the importance of these factors in determining
      the patterns of in situ restriction enzyme digestion so far attributed exclusively to
      endonuclease activity.
AU  - Ferrucci L
AU  - Rossino R
AU  - Mezzanotee R
PT  - Journal Article
TA  - Cytobios
JT  - Cytobios
SO  - Cytobios 1991 68: 45-51.

PMID- 25337710
VI  - 9
DP  - 2014
TI  - An emerging Mycoplasma associated with trichomoniasis, vaginal infection and disease.
PG  - E110943
AB  - Humans are colonized by thousands of bacterial species, but it is difficult to
      assess the metabolic and pathogenic potential of the majority of these because
      they have yet to be cultured. Here, we characterize an uncultivated vaginal
      mycoplasma tightly associated with trichomoniasis that was previously known by
      its 16S rRNA sequence as "Mnola." In this study, the mycoplasma was found almost
      exclusively in women infected with the sexually transmitted pathogen Trichomonas
      vaginalis, but rarely observed in women with no diagnosed disease. The genomes of
      four strains of this species were reconstructed using metagenome sequencing and
      assembly of DNA from four discrete mid-vaginal samples, one of which was obtained
      from a pregnant woman with trichomoniasis who delivered prematurely. These
      bacteria harbor several putative virulence factors and display unique metabolic
      strategies. Genes encoding proteins with high similarity to potential virulence
      factors include two collagenases, a hemolysin, an O-sialoglycoprotein
      endopeptidase and a feoB-type ferrous iron transport system. We propose the name
      "Candidatus Mycoplasma girerdii" for this potential new pathogen.
AU  - Fettweis JM
AU  - Serrano MG
AU  - Huang B
AU  - Brooks JP
AU  - Glascock AL
AU  - Sheth NU
AU  - Strauss JF III
AU  - Jefferson KK
AU  - Buck GA
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2014 9: E110943.

PMID- 21629720
VI  - 5
DP  - 2011
TI  - PCR-based identification of Klebsiella pneumoniae subsp. rhinoscleromatis, the agent of rhinoscleroma.
PG  - E1052
AB  - Rhinoscleroma is a chronic granulomatous infection of the upper airways caused by
      the bacterium Klebsiella pneumoniae subsp. rhinoscleromatis. The disease is
      endemic in tropical and subtropical areas, but its diagnosis remains difficult.
      As a consequence, and despite available antibiotherapy, some patients evolve
      advanced stages that can lead to disfiguration, severe respiratory impairment and
      death by anoxia. Because identification of the etiologic agent is crucial for the
      definitive diagnosis of the disease, the aim of this study was to develop two
      simple PCR assays. We took advantage of the fact that all Klebsiella pneumoniae
      subsp. rhinoscleromatis isolates are (i) of capsular serotype K3; and (ii) belong
      to a single clone with diagnostic single nucleotide polymorphisms (SNP). The
      complete sequence of the genomic region comprising the capsular polysaccharide
      synthesis (cps) gene cluster was determined. Putative functions of the 21 genes
      identified were consistent with the structure of the K3 antigen. The K3-specific
      sequence of gene Kr11509 (wzy) was exploited to set up a PCR test, which was
      positive for 40 K3 strains but negative when assayed on the 76 other Klebsiella
      capsular types. Further, to discriminate Klebsiella pneumoniae subsp.
      rhinoscleromatis from other K3 Klebsiella strains, a specific PCR assay was
      developed based on diagnostic SNPs in the phosphate porin gene phoE. This work
      provides rapid and simple molecular tools to confirm the diagnostic of
      rhinoscleroma, which should improve patient care as well as knowledge on the
      prevalence and epidemiology of rhinoscleroma.
AU  - Fevre C
AU  - Passet V
AU  - Deletoile A
AU  - Barbe V
AU  - Frangeul L
AU  - Almeida AS
AU  - Sansonetti P
AU  - Tournebize R
AU  - Brisse S
PT  - Journal Article
TA  - PLoS Neglected Trop. Dis.
JT  - PLoS Neglected Trop. Dis.
SO  - PLoS Neglected Trop. Dis. 2011 5: E1052.

PMID- 10919786
VI  - 66
DP  - 2000
TI  - A genomic sample sequence of the entomopathogenic bacterium Photorhabdus luminescens W14: Potential implications for virulence.
PG  - 3310-3329
AB  - Photorhabdus luminescens is a pathogenic bacterium that lives in the guts of insect-pathogenic
      nematodes. After invasion of an insect host
      by a nematode, bacteria are released from the nematode gut and help
      kill the insect, in which both the bacteria and the nematodes
      subsequently replicate. However, the bacterial virulence factors
      associated with this 'symbiosis of pathogens' remain largely obscure.
      In order to identify genes encoding potential virulence factors, we
      performed approximately 2,000 random sequencing reads from a P.
      luminescens W14 genomic library. We then compared the sequences
      obtained to sequences in existing gene databases and to the Escherichia
      coli K-12 genome sequence. Here we describe the different classes of
      potential virulence factors found. These factors include genes that
      putatively encode Tc insecticidal toxin complexes, Rbi-like toxins,
      proteases and lipases, colicin and pyocins, and various antibiotics.
      They also include a diverse array of secretion (e.g., type III), iron
      uptake, and lipopolysaccharide production systems. We speculate on the
      potential functions of each of these gene classes in insect infection
      and also examine the extent to which the invertebrate pathogen P,
      luminescens shares potential antivertebrate virulence factors. The
      implications for understanding both the biology of this insect pathogen
      and links between the evolution of vertebrate virulence factors and the
      evolution of invertebrate virulence factors are discussed.
AU  - Ffrench-Constant RH
AU  - Waterfield N
AU  - Burland V
AU  - Perna NT
AU  - Daborn PJ
AU  - Bowen D
AU  - Blattner FR
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2000 66: 3310-3329.

PMID- 
VI  - 39
DP  - 1998
TI  - Inhibition of DNA (cytosine-5) methyltransferase (Mtase) by selenium compounds, determined by an improved method for Mtase and global DNA methylation.
PG  - 88
AB  - Organoselenium compounds such as benzyl selenocyanate and
      1,4-phenylenebis(methylene)selenocyanate are efficient chemopreventive agents, inhibiting a
      variety of chemically induced tumors in animal models at both the initiation and
      postinitiation stages.  Because several lines of evidence suggest that inhibition of Mtase in
      tumor cells may be a sufficient condition for the suppression or reversion of carcinogenesis,
      we examined the effects of sodium selenite, BSC, p-XSC and benzyl thiocyanate on Mtase
      activity in extracts from human colon carcinomas, and in HCT116 human colon carcinoma cells in
      culture.  For this purpose, we developed an improved assay of the enzyme, in which label
      derived from S-adenosyl[methyl-3H]methionine is specifically determined in
      5-methyldeoxycytidine by HPLC with radioflow detection.  Selenite, BSC and p-XSC inhibited
      Mtase extracted from a human colon carcinoma with IC50s of 3.8, 8.1, and 5.2 uM, respectively.
      BTC had no effect.  Selenite, BSC and p-XSC also strongly inhibited the growth and Mtase
      activity of HCT116 cells.  We suggest that inhibition of Mtase may be central to the mechanism
      of chemoprevention by selenium compounds at the stage of postinitiation.
AU  - Fiala ES
AU  - Staretz ME
AU  - Pandya G
AU  - El-Bayoumy K
AU  - Hamilton SR
PT  - Journal Article
TA  - Proc. Amer. Assoc. Cancer Res.
JT  - Proc. Amer. Assoc. Cancer Res.
SO  - Proc. Amer. Assoc. Cancer Res. 1998 39: 88.

PMID- 9600343
VI  - 19
DP  - 1998
TI  - Inhibition of DNA cytosine methyltransferase by chemopreventive selenium compounds, determined by an improved assay for DNA cytosine methyltransferase and DNA cytosine methylation.
PG  - 597-604
AB  - The organoselenium compounds benzyl selenocyanate and 1,4-phenylenebis(methylene)selenocyanate
      as well as sodium selenite, are effective chemopreventive agents for various chemically
      induced tumors in animal models at both the initiation and postinitiation stages.  The
      mechanisms involved at the postinitiation stage are not clear.  Because several lines of
      evidence indicate that inhibition of excess DNA (cytosine-5)-methyltransferase may be a
      sufficient factor for the suppression or reversion of carcinogenesis, we examined the effects
      of sodium selenite, Bsc, p-XSC and benzyl thiocyanate, the sulfur analog of BSC, on Mtase
      activity in nuclear extracts of human colon carcinomas, and of p-XSC on the Mtase activity of
      HCT116 human colon carcinoma cells in culture.  For this purpose, we developed an improved
      Mtase assay, in which the incorporation of the methyl-[3-H] group from
      S-adenosyl[methyl-3H]methionine into deoxycytidine of poly(dI-dC)-poly(dI-dC), is specifically
      determined by HPLC with radioflow detection after enzymatic hydrolysis, enhancing specificity
      and reliability.  In a variation, using SssI methyltransferase and labeled
      S-adenosylmethionine, the overall methylation status of DNA in various tissues can also be
      compared. Selenite, BSC and p-XSC inhibited Mtase extracted from a human colon carcinoma with
      IC50S of 3.8, 8.1 and 5.2 uM, respectively; BTC had no effect.  P-XSC also inhibited the Mtase
      activity and growth of human colon carcinoma HCT116 cells, with an IC50 of ~20 uM.  The
      improved Mtase assay should prove to be a reliable method for screening potential Mtase
      inhibitors, especially using cells in culture.  We suggest that inhibition of Mtase may be a
      major mechanism of chemoprevention by selenium compounds at the postinitiation stage of
      carcinogenesis.
AU  - Fiala ES
AU  - Staretz ME
AU  - Pandya GA
AU  - El-Bayoumy K
AU  - Hamilton SR
PT  - Journal Article
TA  - Carcinogenesis
JT  - Carcinogenesis
SO  - Carcinogenesis 1998 19: 597-604.

PMID- 24019991
VI  - 7
DP  - 2013
TI  - Genome of the marine alphaproteobacterium Hoeflea phototrophica type strain (DFL-43(T)).
PG  - 440-448
AB  - Hoeflea phototrophica Biebl et al. 2006 is a member of the family Phyllobacteriaceae in the
      order Rhizobiales, which is thus far only partially
      characterized at the genome level. This marine bacterium contains the
      photosynthesis reaction-center genes pufL and pufM and is of interest because it
      lives in close association with toxic dinoflagellates such as Prorocentrum lima.
      The 4,467,792 bp genome (permanent draft sequence) with its 4,296 protein-coding
      and 69 RNA genes is a part of the Marine Microbial Initiative.
AU  - Fiebig A
AU  - Pradella S
AU  - Petersen J
AU  - Michael V
AU  - Pauker O
AU  - Rohde M
AU  - Goker M
AU  - Klenk HP
AU  - Wagner-Dobler I
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 7: 440-448.

PMID- 24019989
VI  - 7
DP  - 2013
TI  - Genome of the R-body producing marine alphaproteobacterium Labrenzia alexandrii type strain (DFL-11(T)).
PG  - 413-426
AB  - Labrenzia alexandrii Biebl et al. 2007 is a marine member of the family Rhodobacteraceae in
      the order Rhodobacterales, which has thus far only partially
      been characterized at the genome level. The bacterium is of interest because it
      lives in close association with the toxic dinoflagellate Alexandrium lusitanicum.
      Ultrastructural analysis reveals R-bodies within the bacterial cells, which are
      primarily known from obligate endosymbionts that trigger 'killing traits' in
      ciliates (Paramecium spp.). Genomic traits of L. alexandrii DFL-11(T) are in
      accordance with these findings, as they include the reb genes putatively involved
      in R-body synthesis. Analysis of the two extrachromosomal elements suggests a
      role in heavy-metal resistance and exopolysaccharide formation, respectively. The
      5,461,856 bp long genome with its 5,071 protein-coding and 73 RNA genes consists
      of one chromosome and two plasmids, and has been sequenced in the context of the
      Marine Microbial Initiative.
AU  - Fiebig A
AU  - Pradella S
AU  - Petersen J
AU  - Pauker O
AU  - Michael V
AU  - Lunsdorf H
AU  - Goker M
AU  - Klenk HP
AU  - Wagner-Dobler I
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 7: 413-426.

PMID- 24501632
VI  - 8
DP  - 2013
TI  - Genome sequence of the reddish-pigmented Rubellimicrobium thermophilum type strain (DSM 16684(T)), a member of the Roseobacter clade.
PG  - 480-490
AB  - Rubellimicrobium thermophilum Denner et al. 2006 is the type species of the genus
      Rubellimicrobium, a representative of the Roseobacter clade within the
      Rhodobacteraceae. Members of this clade were shown to be abundant especially in
      coastal and polar waters, but were also found in microbial mats and sediments.
      They are metabolically versatile and form a physiologically heterogeneous group
      within the Alphaproteobacteria. Strain C-Ivk-R2A-2(T) was isolated from colored
      deposits in a pulp dryer; however, its natural habitat is so far unknown. Here we
      describe the features of this organism, together with the draft genome sequence
      and annotation and novel aspects of its phenotype. The 3,161,245 bp long genome
      contains 3,243 protein-coding and 45 RNA genes.
AU  - Fiebig A
AU  - Riedel T
AU  - Gronow S
AU  - Petersen J
AU  - Klenk HP
AU  - Goker M
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 480-490.

PMID- 29650574
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of the Intimin-Positive Enteropathogenic Escherichia albertii Strain MBT-EA1, Isolated from Lettuce.
PG  - e00255-18
AB  - The genome of the intimin (eae)-harboring Escherichia albertii strain MBT-EA1, isolated from
      lettuce in Germany, was sequenced. Sequence analysis showed the
      assembled draft genome size to be 4,560,948 bp, containing a predicted total of
      4,414 protein-encoding genes, 11 rRNAs, and 82 tRNAs. Furthermore, three plasmid
      sequences were found.
AU  - Fiedler G
AU  - Brinks E
AU  - Bohnlein C
AU  - Cho GS
AU  - Koberg S
AU  - Kabisch J
AU  - Franz CMAP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00255-18.

PMID- 26682961
VI  - 71
DP  - 2015
TI  - Tigecycline resistance in clinical isolates of Enterococcus faecium is mediated by an upregulation of plasmid-encoded tetracycline determinants tet(L) and tet(M).
PG  - 871-881
AB  - OBJECTIVES: Tigecycline represents one of the last-line therapeutics to combat
      multidrug-resistant bacterial pathogens, including VRE and MRSA. The German National Reference
      Centre for Staphylococci and Enterococci has received 73 tigecycline-resistant Enterococcus
      faecium and Enterococcus faecalis isolates in recent years. The precise mechanism of how
      enterococci become resistant to tigecycline remains undetermined. This study documents an
      analysis of the role of efflux pumps in tigecycline resistance in clinical isolates of
      Enterococcus spp. METHODS: Various tigecycline MICs were found for the different isolates
      analysed. Tigecycline-resistant strains were analysed with respect to genome and transcriptome
      differences by means of WGS and RT-qPCR. Genes of interest were cloned and expressed in
      Listeria monocytogenes for verification of their functionality. RESULTS: Detailed comparative
      whole-genome analyses of three isogenic strains, showing different levels of tigecycline
      resistance, revealed the major facilitator superfamily (MFS) efflux pump TetL and the
      ribosomal protection protein TetM as possible drug resistance proteins. Subsequent RT-qPCR
      confirmed up-regulation of the respective genes. A correlation of gene copy number and level
      of MIC was inferred from further qPCR analyses. Expression of both tet(L) and tet(M) in L.
      monocytogenes unequivocally demonstrated the potential to increase tigecycline MICs upon
      acquisition of either locus. CONCLUSIONS: Our results indicate that increased expression of
      two tetracycline resistance determinants, a tet(L)-encoded MFS pump and a tet(M)-encoded
      ribosomal protection protein, is capable of conferring tigecycline resistance in enterococcal
      clinical isolates.
AU  - Fiedler S
AU  - Bender JK
AU  - Klare I
AU  - Halbedel S
AU  - Grohmann E
AU  - Szewzyk U
AU  - Werner G
PT  - Journal Article
TA  - J. Antimicrob. Chemother.
JT  - J. Antimicrob. Chemother.
SO  - J. Antimicrob. Chemother. 2015 71: 871-881.

PMID- 24482506
VI  - 2
DP  - 2014
TI  - First Complete Genome Sequence of Escherichia albertii Strain KF1, a New Potential Human Enteric Pathogen.
PG  - e00004-14
AB  - Escherichia albertii has been recently recognized as an emerging human and bird enteric
      pathogen. Here, we report the first complete chromosome nucleotide
      sequence of a clinical isolate of E. albertii strain KF1, which may provide
      information about the pathogenic potential of this new species and the mechanisms
      of evolution of enteropathogenic Escherichia spp.
AU  - Fiedoruk K
AU  - Daniluk T
AU  - Swiecicka I
AU  - Murawska E
AU  - Sciepuk M
AU  - Leszczynska K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00004-14.

PMID- 18464787
VI  - 26
DP  - 2008
TI  - The minimum information about a genome sequence (MIGS) specification.
PG  - 541-547
AB  - With the quantity of genomic data increasing at an exponential rate, it is imperative that
      these data be captured electronically, in a standard
      format. Standardization activities must proceed within the auspices of
      open-access and international working bodies. To tackle the issues
      surrounding the development of better descriptions of genomic
      investigations, we have formed the Genomic Standards Consortium (GSC).
      Here, we introduce the minimum information about a genome sequence (MIGS)
      specification with the intent of promoting participation in its
      development and discussing the resources that will be required to develop
      improved mechanisms of metadata capture and exchange. As part of its wider
      goals, the GSC also supports improving the 'transparency' of the
      information contained in existing genomic databases.
AU  - Field D et al
PT  - Journal Article
TA  - Nat. Biotechnol.
JT  - Nat. Biotechnol.
SO  - Nat. Biotechnol. 2008 26: 541-547.

PMID- 17827313
VI  - 73
DP  - 2007
TI  - Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil.
PG  - 7059-7066
AB  - Recent studies have highlighted the surprising richness of soil bacterial
      communities; however, bacteria are not the only microorganisms found in
      soil. To our knowledge, no study has compared the diversities of the four
      major microbial taxa, i.e., bacteria, archaea, fungi, and viruses, from an
      individual soil sample. We used metagenomic and small-subunit RNA-based
      sequence analysis techniques to compare the estimated richness and
      evenness of these groups in prairie, desert, and rainforest soils. By
      grouping sequences at the 97% sequence similarity level (an operational
      taxonomic unit [OTU]), we found that the archaeal and fungal communities
      were consistently less even than the bacterial communities. Although total
      richness levels are difficult to estimate with a high degree of certainty,
      the estimated number of unique archaeal or fungal OTUs appears to rival or
      exceed the number of unique bacterial OTUs in each of the collected soils.
      In this first study to comprehensively survey viral communities using a
      metagenomic approach, we found that soil viruses are taxonomically diverse
      and distinct from the communities of viruses found in other environments
      that have been surveyed using a similar approach. Within each of the four
      microbial groups, we observed minimal taxonomic overlap between sites,
      suggesting that soil archaea, bacteria, fungi, and viruses are globally as
      well as locally diverse.
AU  - Fierer N
AU  - Breitbart M
AU  - Nulton J
AU  - Salamon P
AU  - Lozupone C
AU  - Jones R
AU  - Robeson M
AU  - Edwards RA
AU  - Felts B
AU  - Rayhawk S
AU  - Knight R
AU  - Rohwer F
AU  - Jackson RB
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2007 73: 7059-7066.

PMID- 28209833
VI  - 5
DP  - 2017
TI  - Metagenome-Assembled Draft Genome Sequence of a Novel Microbial Stenotrophomonas  maltophilia Strain Isolated from Caenorhabditisremanei Tissue.
PG  - e01646-16
AB  - Stenotrophomonas maltophilia is a Gram-negative aerobic bacterium and emerging nosocomial
      pathogen. Here, we present a draft genome sequence for an S.
      maltophilia strain assembled from a metagenomic DNA extract isolated from a
      laboratory stock of the nematode worm Caenorhabditis remanei.
AU  - Fierst JL
AU  - Murdock DA
AU  - Thanthiriwatte C
AU  - Willis JH
AU  - Phillips PC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01646-16.

PMID- 10767527
VI  - 246
DP  - 2000
TI  - Genetic organization and heterogeneity of the iceA locus of Helicobacter pylori.
PG  - 59-68
AB  - The genetic organization and sequence heterogeneity of the iceA locus of Helicobacter pylori
      was studied, and the existence of two distinct gene families, iceA1 and iceA2, at this locus
      was confirmed. iceA1 has significant sequence homology to nlaIIIR, encoding an endonuclease in
      Neisseria lactamica, but the similarity at the protein level is limited, due to frameshift
      mutations of iceA1 in most H. pylori strains. In only five of the 19 iceA1 strains studied, a
      full-length open reading frame (ORF), capable of encoding a 228aa protein, with 52% homology
      to NlaIII was observed. The region upstream of iceA2 is highly variable in length, containing
      up to 15 copies of 8bp tandem repeats. iceA2 can encode proteins of 24, 59, 94, or 129 amino
      acids, consisting of 14 and 10aa domains, conserved in all iceA2 strains, flanking 0, 1, 2, or
      3 copies of a 35aa cassette. This 35aa cassette consists of domains of 13, 16 and 6aa,
      respectively. The 13aa and 6aa domains are highly conserved, but the 16aa domain exists in two
      variants. In total, five distinct iceA2 subtypes were defined. Database searches did not
      reveal any homologous sequences. Recombinant IceA1 and IceA2 proteins were expressed in
      Escherichia coli, confirming the predicted ORFs. Genotype-specific PCR primers permitted iceA
      genotyping in 318 (99.1%) of a worldwide collection of 321 H. pylori strains. The conserved
      sizes of the amplification products confirmed the worldwide distribution of discrete variants
      of iceA1 and iceA2.
AU  - Figueiredo C
AU  - Quint WG
AU  - Sanna R
AU  - Sablon E
AU  - Donahue JP
AU  - Xu Q
AU  - Miller GG
AU  - Peek RM
AU  - Blaser MJ
AU  - van Doorn L
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 2000 246: 59-68.

PMID- 25323710
VI  - 2
DP  - 2014
TI  - Complete Genome Sequences of Fish Pathogenic Weissella ceti Strains WS74 and WS105.
PG  - e01014-14
AB  - We describe here the genome sequencing and annotation of Weissella ceti strains WS74 and
      WS105, isolated from diseased rainbow trout in Brazil. The two genomes
      were sequenced with an Ion Torrent personal genome machine (PGM) using a fragment
      library. The genomes of strains WS74 and WS105 consist of circular chromosomes
      1,389,513 bp and 1,390,396 bp long, respectively, both presenting a G+C content
      of 40.75%.
AU  - Figueiredo HC
AU  - Leal CA
AU  - Dorella FA
AU  - Carvalho AF
AU  - Soares SC
AU  - Pereira FL
AU  - Azevedo VA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01014-14.

PMID- 26798105
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequence of Francisella noatunensis subsp. orientalis Strain FNO01 Isolated from Diseased Nile Tilapia in Brazil.
PG  - e01603-15
AB  - This paper describes the complete genome sequence of Francisella noatunensis subsp. orientalis
      strain FNO01, which was isolated during the first outbreak of
      francisellosis in cultured Nile tilapia in Brazil. The genome is composed of a
      circular chromosome with 1,859,830 bp and a G+C content of ~32%.
AU  - Figueiredo HC
AU  - Leal CA
AU  - Pereira FL
AU  - Soares SC
AU  - Goncalves LA
AU  - Dorella FA
AU  - Carvalho AF
AU  - Azevedo VA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01603-15.

PMID- 25146147
VI  - 2
DP  - 2014
TI  - Whole-Genome Sequence of Weissella ceti Strain WS08, Isolated from Diseased Rainbow Trout in Brazil.
PG  - e00851-14
AB  - We report here the complete genome sequence of Weissella ceti strain WS08, an emerging
      pathogen to farm-raised rainbow trout. The genome of strain WS08 is
      composed of a circular chromosome with 1,355,853 bp and a G+C content of 40.78%.
AU  - Figueiredo HC
AU  - Leal G
AU  - Pereira FL
AU  - Soares SC
AU  - Dorella FA
AU  - Carvalho AF
AU  - Pereira UP
AU  - Azevedo VA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00851-14.

PMID- 16302067
VI  - 100
DP  - 2005
TI  - The neuraminidase gene is present in the non-toxigenic Vibrio cholerae Amazonia strain: a different allele in comparison to the pandemic strains.
PG  - 563-569
AB  - The neuraminidase gene, nanH, is present in the O1, non-toxigenic Vibrio
      cholerae Amazonia strain. Its location has been assigned to a 150 kb NotI
      DNA fragment, with the use of pulsed-field gel electrophoresis and DNA
      hybridization. This NotI fragment is positioned inside 630 kb SfiI and
      1900 kb I-CeuI fragments of chromosome 1. Association of the pathogenicity
      island VPI-2, carrying nanH and other genes, with toxigenic strains has
      been described by other authors. The presence of nanH in a non-toxigenic
      strain is an exception to this rule. The Amazonia strain nanH was
      sequenced (Genbank accession No. AY825932) and compared to available V.
      cholerae sequences. The sequence is different from those of pandemic
      strains, with 72 nucleotide substitutions. This is the first description
      of an O1 strain with a different nanH allele. The most variable domain of
      the Amazonia NanH is the second lectin wing, comprising 13 out of 17 amino
      acid substitutions. Based on the presence of nanH in the same region of
      the genome, and similarity of the adjacent sequences to VPI-2 sequences,
      it is proposed that the pathogenicity island VPI-2 is present in this
      strain.
AU  - Figueiredo SC
AU  - Neves-Borges AC
AU  - Coelho A
PT  - Journal Article
TA  - Memorias do Instituto Oswaldo Cruz
JT  - Memorias do Instituto Oswaldo Cruz
SO  - Memorias do Instituto Oswaldo Cruz 2005 100: 563-569.

PMID- 16954322
VI  - 50
DP  - 2006
TI  - DNA methylase activity as a marker for the presence of a family of phage-like elements conferring efflux-mediated macrolide resistance in  streptococci.
PG  - 3689-3694
AB  - Recently, two related chimeric genetic elements (Tn1207.3 and Phi10394.4) were shown to carry
      the macrolide efflux gene mef in Streptococcus
      pyogenes (group A streptococci [GAS]). The dissemination of elements
      belonging to the Tn1207.3/Phi10394.4 family in recent isolates of GAS,
      Streptococcus dysgalactiae subsp. equisimilis, Streptococcus pneumoniae,
      and Streptococcus agalactiae recovered in Portugal was surveyed. In total,
      149 GAS, 18 S. pneumoniae, 4 S. dysgalactiae subsp. equisimilis, and 5 S.
      agalactiae isolates from infections, presenting the M phenotype of
      macrolide resistance and containing the mef gene, were screened for the
      presence of Tn1207.3/Phi10394.4 by PCR targeting open reading frames
      (ORFs) specific for these related elements. All the GAS isolates tested
      and one of the S. dysgalactiae subsp. equisimilis isolates carried
      Tn1207.3. However, neither of these elements was found in the isolates of
      the other streptococcal species. It was also noted that the DNAs of the
      isolates carrying Tn1207.3 were resistant to cleavage by the endonuclease
      SmaI. Cloning and expression of ORF12 of Tn1207.3 in Escherichia coli
      showed that it encoded a methyltransferase that rendered DNA refractory to
      cleavage by SmaI (M.Spy10394I). Using this characteristic as a marker for
      the presence of the Tn1207.3/Phi10394.4 family, we reviewed the literature
      and concluded that these genetic elements are widely distributed among
      tetracycline-susceptible GAS isolates presenting the M phenotype from
      diverse geographic origins and may have played an important role in the
      dissemination of macrolide resistance in this species.
AU  - Figueiredo TA
AU  - Aguiar SI
AU  - Melo-Cristino J
AU  - Ramirez M
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2006 50: 3689-3694.

PMID- 26316637
VI  - 3
DP  - 2015
TI  - Genome Sequence of Aeribacillus pallidus Strain GS3372, an Endospore-Forming Bacterium Isolated in a Deep Geothermal Reservoir.
PG  - e00981-15
AB  - The genome of strain GS3372 is the first publicly available strain of Aeribacillus pallidus.
      This endospore-forming thermophilic strain was isolated from a deep geothermal reservoir. The
      availability of this genome can contribute  to the clarification of the taxonomy of the
      closely related Anoxybacillus, Geobacillus, and Aeribacillus genera.
AU  - Filippidou S
AU  - Jaussi M
AU  - Junier T
AU  - Wunderlin T
AU  - Jeanneret N
AU  - Regenspurg S
AU  - Li PE
AU  - Lo CC
AU  - Johnson S
AU  - McMurry K
AU  - Gleasner CD
AU  - Vuyisich M
AU  - Chain PS
AU  - Junier P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00981-15.

PMID- 26067952
VI  - 3
DP  - 2015
TI  - Genome Sequence of Anoxybacillus geothermalis Strain GSsed3, a Novel Thermophilic Endospore-Forming Species.
PG  - e00575-15
AB  - Anoxybacillus geothermalis strain GSsed3 is an endospore-forming thermophilic bacterium
      isolated from filter deposits in a geothermal site. This novel species
      has a larger genome size (7.2 Mb) than that of any other Anoxybacillus species,
      and it possesses genes that support its phenotypic metabolic characterization and
      suggest an intriguing link to metals.
AU  - Filippidou S
AU  - Jaussi M
AU  - Junier T
AU  - Wunderlin T
AU  - Roussel-Delif L
AU  - Jeanneret N
AU  - Vieth-Hillebrand A
AU  - Vetter A
AU  - Regenspurg S
AU  - Johnson SL
AU  - McMurry K
AU  - Gleasner CD
AU  - Lo CC
AU  - Li P
AU  - Vuyisich M
AU  - Chain PS
AU  - Junier P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00575-15.

PMID- 26316638
VI  - 3
DP  - 2015
TI  - Genome Sequence of Bacillus alveayuensis Strain 24KAM51, a Halotolerant Thermophile Isolated from a Hydrothermal Vent.
PG  - e00982-15
AB  - Bacillus alveayuensis strain 24KAM51 was isolated from a marine hydrothermal vent in Milos,
      Greece. Its genome depicts interesting features of halotolerance and resistance to heavy
      metals.
AU  - Filippidou S
AU  - Wunderlin T
AU  - Junier T
AU  - Jeanneret N
AU  - Johnson S
AU  - McMurry K
AU  - Gleasner CD
AU  - Lo CC
AU  - Li PE
AU  - Vuyisich M
AU  - Chain PS
AU  - Junier P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00982-15.

PMID- 22689241
VI  - 194
DP  - 2012
TI  - Genome Sequence of Fibrella aestuarina BUZ 2T, a Filamentous Marine Bacterium.
PG  - 3555
AB  - Fibrella aestuarina BUZ 2(T) is the type strain of the recently characterized genus Fibrella.
      Here we report the draft genome sequence of this strain, which
      consists of a single scaffold representing the chromosome (with 11 gaps) and a
      161-kb circular plasmid.
AU  - Filippini M
AU  - Qi W
AU  - Blom J
AU  - Goesmann A
AU  - Smits TH
AU  - Bagheri HC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3555.

PMID- 22843583
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Filamentous Bacterium Fibrisoma limi BUZ 3T.
PG  - 4445
AB  - Fibrisoma limi strain BUZ 3(T), a Gram-negative bacterium, was isolated from coastal mud from
      the North Sea (Fedderwardersiel, Germany) and characterized
      using a polyphasic approach in 2011. The genome consists of a chromosome of about
      7.5 Mb and three plasmids.
AU  - Filippini M
AU  - Qi W
AU  - Jaenicke S
AU  - Goesmann A
AU  - Smits TH
AU  - Bagheri HC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4445.

PMID- 25838491
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Clostridium botulinum B2 450 Strain from Wound Botulism  in a Drug User in Italy.
PG  - e00238-15
AB  - Here, we report the draft genome sequence of Clostridium botulinum B2 450, responsible for the
      first reported case of wound botulism in a drug user in
      Italy.
AU  - Fillo S
AU  - Giordani F
AU  - Anselmo A
AU  - Fortunato A
AU  - Palozzi AM
AU  - De Santis R
AU  - Ciammaruconi A
AU  - Spagnolo F
AU  - Anniballi F
AU  - Fiore A
AU  - Auricchio B
AU  - De Medici D
AU  - Lista F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00238-15.

PMID- 29773639
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Streptococcus suis Strain SsRC-1, a Human Isolate from a Fatal Case of Toxic Shock Syndrome.
PG  - e00447-18
AB  - Streptococcus suis is an economically important pathogen in the pig industry and  is also an
      emerging zoonotic agent responsible for severe infections in humans.
      Here, we report the genome sequence of S. suis strain SsRC-1. Specifically, this
      strain was a serotype 2 and was isolated from a human fatal case of toxic shock
      syndrome (TSS) in Italy.
AU  - Fillo S
AU  - Mancini F
AU  - Anselmo A
AU  - Fortunato A
AU  - Rezza G
AU  - Lista F
AU  - Ciervo A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00447-18.

PMID- 11481431
VI  - 98
DP  - 2001
TI  - The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti.
PG  - 9889-9894
AB  - Analysis of the 1,683,333-nt sequence of the pSymB megaplasmid from the symbiotic N(2)-fixing
      bacterium Sinorhizobium meliloti revealed that the
      replicon has a high gene density with a total of 1,570 protein-coding
      regions, with few insertion elements and regions duplicated elsewhere in
      the genome. The only copies of an essential arg-tRNA gene and the minCDE
      genes are located on pSymB. Almost 20% of the pSymB sequence carries genes
      encoding solute uptake systems, most of which were of the ATP-binding
      cassette family. Many previously unsuspected genes involved in
      polysaccharide biosynthesis were identified and these, together with the
      two known distinct exopolysaccharide synthesis gene clusters, show that
      14% of the pSymB sequence is dedicated to polysaccharide synthesis. Other
      recognizable gene clusters include many involved in catabolic activities
      such as protocatechuate utilization and phosphonate degradation. The
      functions of these genes are consistent with the notion that pSymB plays a
      major role in the saprophytic competence of the bacteria in the soil
      environment.
AU  - Finan TM
AU  - Weidner S
AU  - Wong K
AU  - Buhrmester J
AU  - Chain P
AU  - Vorholter FJ
AU  - Hernandez-Lucas I
AU  - Becker A
AU  - Cowie A
AU  - Gouzy J
AU  - Golding B
AU  - Puhler A
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2001 98: 9889-9894.

PMID- 24336377
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Serratia sp. Strain ATCC 39006, a Model Bacterium for Analysis of the Biosynthesis and Regulation of Prodigiosin, a Carbapenem, and Gas  Vesicles.
PG  - e01039-13
AB  - Serratia sp. strain ATCC 39006 is a Gram-negative bacterium and a member of the
      Enterobacteriaceae that produces various bioactive secondary metabolites,
      including the tripyrrole red pigment prodigiosin and the beta-lactam antibiotic
      1-carbapenen-2-em-3-carboxylic acid (a carbapenem). This strain is the only
      member of the Enterobacteriaceae known to naturally produce gas vesicles, as
      flotation organelles. Here we present the genome sequence of this strain, which
      has served as a model for analysis of the biosynthesis and regulation of
      antibiotic production.
AU  - Fineran PC
AU  - Iglesias CMC
AU  - Ramsay JP
AU  - Wilf NM
AU  - Cossyleon D
AU  - McNeil MB
AU  - Williamson NR
AU  - Monson RE
AU  - Becher SA
AU  - Stanton JA
AU  - Brugger K
AU  - Brown SD
AU  - Salmond GP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01039-13.

PMID- 18398449
VI  - 4
DP  - 2008
TI  - Metagenomic analysis of human diarrhea: viral detection and discovery.
PG  - e1000011
AB  - Worldwide, approximately 1.8 million children die from diarrhea annually,
      and millions more suffer multiple episodes of nonfatal diarrhea. On
      average, in up to 40% of cases, no etiologic agent can be identified. The
      advent of metagenomic sequencing has enabled systematic and unbiased
      characterization of microbial populations; thus, metagenomic approaches
      have the potential to define the spectrum of viruses, including novel
      viruses, present in stool during episodes of acute diarrhea. The detection
      of novel or unexpected viruses would then enable investigations to assess
      whether these agents play a causal role in human diarrhea. In this study,
      we characterized the eukaryotic viral communities present in diarrhea
      specimens from 12 children by employing a strategy of "micro-mass
      sequencing" that entails minimal starting sample quantity (<100 mg stool),
      minimal sample purification, and limited sequencing (384 reads per
      sample). Using this methodology we detected known enteric viruses as well
      as multiple sequences from putatively novel viruses with only limited
      sequence similarity to viruses in GenBank.
AU  - Finkbeiner SR
AU  - Allred AF
AU  - Tarr PI
AU  - Klein EJ
AU  - Kirkwood CD
AU  - Wang D
PT  - Journal Article
TA  - PLoS Pathog.
JT  - PLoS Pathog.
SO  - PLoS Pathog. 2008 4: e1000011.

PMID- 8389441
VI  - 21
DP  - 1993
TI  - Isolation and identification by sequence homology of a putative cytosine methyltransferase from Arabidopsis thaliana.
PG  - 2383-2388
AB  - A plant cytosine methyltransferase cDNA was isolated using degenerate oligonucleotides, based
      on homology between prokaryote and mouse methyltransferases, and PCR to amplify a short
      fragment of a methyltansferase gene. A fragment of the predicted size was amplified from
      genomic DNA from Arabidopsis thaliana. Overlapping cDNA clones, some with homology to the PCR
      amplifed fragment, were identified and sequenced. The assembled nucleic acid sequence is 4720
      bp and encodes a protein of 1534 amino acids which has significant homology to prokaryote and
      mammalian cytosine methyltransferases. Like mammalian methylases, this enzyme has a C terminal
      methyltransferase domain linked to a second larger domain. The Arabidopsis methylase has eight
      of the ten conserved sequence motifs found in prokaryote cytosine-5 methyltransferases and
      shows 50% homology to the murine enzyme in the methyltransferase domain. The amino terminal
      domain is only 24% homologous to the murine enzyme and lacks the zinc binding region that has
      been found in methyltransferases from both mouse and man. In contrast to mouse where a single
      methyltransferase gene has been identified, a small multigene family with homology to the
      region amplified in PCR has been identified in Arabidopsis thaliana.
AU  - Finnegan EJ
AU  - Dennis ES
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 2383-2388.

PMID- 15012234
VI  - 49
DP  - 1998
TI  - DNA methylation in plants.
PG  - 223-247
AB  - Methylation of cytosine residues in DNA provides a mechanism of gene control.  There are two
      classes of methyltransferase in Arabidopsis; one has a carboxy-terminal methyltransferase
      domain fused to an amino-terminal regulatory domain and is similar to mammalian
      methyltransferases.  The second class apparently lacks an amino-terminal domain and is less
      well conserved.  Methylcytosine can occur at any cytosine residue, but it is likely that
      clonal transmission of methylation patterns only occurs for cytosines in strand-symmetrical
      sequences CpG and CpNpG.  In plants, as in mammals, DNA methylation has dual roles in defense
      against invading DNA and transposable elements and in gene regulation.  Although originally
      reported as having no phenotypic consequence, reduced DNA methylation disrupts normal plant
      development.
AU  - Finnegan EJ
AU  - Genger RK
AU  - Peacock WJ
AU  - Dennis ES
PT  - Journal Article
TA  - Annu. Rev. Plant Physiol. Plant Mol. Biol.
JT  - Annu. Rev. Plant Physiol. Plant Mol. Biol.
SO  - Annu. Rev. Plant Physiol. Plant Mol. Biol. 1998 49: 223-247.

PMID- 10999404
VI  - 43
DP  - 2000
TI  - Plant DNA methyltransferases.
PG  - 189-201
AB  - DNA methylation is an important modification of DNA that plays a role in genome management and
      in regulating gene expression during
      development. Methylation is carried out by DNA methyltransferases which
      catalyse the transfer of a methyl group to bases within the DNA helix.
      Plants have at least three classes of cytosine methyltransferase which
      differ in protein structure and function. The METI family, homologues
      of the mouse Dnmt1 methyltransferase, most likely function as
      maintenance methyltransferases, but may also play a role in de novo
      methylation. The chromomethylases, which are unique to plants, may
      preferentially methylate DNA in heterochromatin; the remaining class,
      with similarity to Dnmt3 methyltransferases of mammals, are putative de
      novo methyltransferases. The various classes of methyltransferase may
      show differential activity on cytosines in different sequence contexts.
      Chromomethylases may preferentially methylate cytosines in CpNpG
      sequences while the Arabidopsis METI methyltransferase shows a
      preference for cytosines in CpG sequences. Additional proteins, for
      example DDM1, a member of the SNF2/SWI2 family of chromatin remodelling
      proteins, are also required for methylation of plant DNA.
AU  - Finnegan EJ
AU  - Kovac KA
PT  - Journal Article
TA  - Plant Mol. Biol.
JT  - Plant Mol. Biol.
SO  - Plant Mol. Biol. 2000 43: 189-201.

PMID- 8710891
VI  - 93
DP  - 1996
TI  - Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development.
PG  - 8449-8454
AB  - Arabidopsis plants transformed with an antisense construct of an Arabidopsis methyltransferase
      cDNA (METI) have reduced cytosine methylation in CG dinucleotides. Methylation levels in
      progeny of five independent transformants ranged from 10% to 100% of the wild type. Removal of
      the antisense construct by segregation in sexual crosses did not fully restore methylation
      patterns in the progeny, indicating that methylation patterns are subject to meiotic
      inheritance in Arabidopsis. Plants with decreased methylation displayed a number of phenotypic
      and developmental abnormalities, including reduced apical dominance, smaller plant size,
      altered leaf size and shape, decreased fertility, and altered flowering time. Floral organs
      showed homeotic transformations that were associated with ectopic expression of the floral
      homeotic genes AGAMOUS and APETALA3 in leaf tissue. These observations suggest that DNA
      methylation plays an important role in regulating many developmental pathways in plants and
      that the developmental abnormalities seen in the methyltransferase antisense plants may be due
      to dysregulation of gene expression.
AU  - Finnegan EJ
AU  - Peacock WJ
AU  - Dennis ES
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1996 93: 8449-8454.

PMID- 23961312
VI  - 8
DP  - 2013
TI  - Complete genome sequence of Desulfocapsa sulfexigens, a marine deltaproteobacterium specialized in disproportionating inorganic sulfur  compounds.
PG  - 58-68
AB  - Desulfocapsa sulfexigens SB164P1 (DSM 10523) belongs to the deltaproteobacterial  family
      Desulfobulbaceae and is one of two validly described members of its genus.
      This strain was selected for genome sequencing, because it is the first marine
      bacterium reported to thrive on the disproportionation of elemental sulfur, a
      process with a unresolved enzymatic pathway in which elemental sulfur serves both
      as electron donor and electron acceptor. Furthermore, in contrast to its
      phylogenetically closest relatives, which are dissimilatory sulfate-reducers, D.
      sulfexigens is unable to grow by sulfate reduction and appears metabolically
      specialized in growing by disproportionating elemental sulfur, sulfite or
      thiosulfate with CO2 as the sole carbon source. The genome of D. sulfexigens
      contains the set of genes that is required for nitrogen fixation. In an acetylene
      assay it could be shown that the strain reduces acetylene to ethylene, which is
      indicative for N-fixation. The circular chromosome of D. sulfexigens SB164P1
      comprises 3,986,761 bp and harbors 3,551 protein-coding genes of which 78% have a
      predicted function based on auto-annotation. The chromosome furthermore encodes
      46 tRNA genes and 3 rRNA operons.
AU  - Finster KW
AU  - Kjeldsen KU
AU  - Kube M
AU  - Reinhardt R
AU  - Mussmann M
AU  - Amann R
AU  - Schreiber L
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 58-68.

PMID- 9207033
VI  - 25
DP  - 1997
TI  - Footprint analysis of the BspRI DNA methyltransferase -- DNA interaction.
PG  - 2841-2846
AB  - The interaction between the GGCC-specific BspRI DNA methyltransferase (M.BspRI) and substrate
      DNA was studied with footprinting techniques usiung a DNA fragment that was unmodified on both
      strands.  Footprinting with DNase I revealed an ~14 bp protected region.  Footprinting with
      dimethylsulfate detected major groove interactions with the guanine bases of the recognition
      sequence.  Reaction with 1,10-phenanthroline-copper did not show protection, suggesting that
      minor groove interactions play little role in sequence-specific recognition by M.BspRI.
      Hydroxyl radical footprinting revealed a protected stretch of 6 nt.  The hydroxyl radical
      footprint of M.BspRI differs markedly from the footprint reported for the HhaI and SssI
      methyltransferases.  The pattern of protection from dimethylsulfate and hydroxyl radicals
      suggests that the interactions of M.BspRI with DNA are similar to those detected in the
      co-crystal structure of the HaeIII methyltransferase.
AU  - Finta C
AU  - Kiss A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1997 25: 2841-2846.

PMID- 7590323
VI  - 164
DP  - 1995
TI  - Purification of the KpnI DNA methyltransferase and photolabeling of the enzyme with S-adenosyl-L-methionine.
PG  - 65-69
AB  - An Escherichia coli strain overproducing the KpnI DNA methyltransferase (M.KpnI) was
      constructed by cloning the kpnIM gene downstream from the inducible T7 phage omega 10
      promoter.  A method involving three chromatographic steps has been developed to purify M.KpnI
      to homogeneity.  The purified enzyme has a pH optimum around 7.3 and is inhibited by salts.
      M.KpnI can be photolabeled by UV-irradiation of the enzyme in the presence of
      S-adenosyl-L-[methyl-3H]methionine ([methyl-3H]AdoMet).  Photolabeling results from a specific
      interaction betweeen M.KpnI and AdoMet, as indicated by the dependence of photolabeling on
      native enzyme conformation and by the inhibitory effect of the AdoMet analogs, sinefungin and
      S-adenosyl-L-homocysteine (AdoHcy).
AU  - Finta C
AU  - Sulima U
AU  - Venetianer P
AU  - Kiss A
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 164: 65-69.

PMID- 23908289
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Brazilian Toxic Bloom-Forming Cyanobacterium Microcystis aeruginosa Strain SPC777.
PG  - e00547-13
AB  - Microcystis aeruginosa strain SPC777 is an important toxin-producing cyanobacterium, isolated
      from a water bloom of the Billings reservoir (Sao Paulo
      State, Brazil). Here, we report the draft genome sequence and initial findings
      from a preliminary analysis of strain SPC777, including several gene clusters
      involved in nonribosomal and ribosomal synthesis of secondary metabolites.
AU  - Fiore MF
AU  - Alvarenga DO
AU  - Varani AM
AU  - Hoff-Risseti C
AU  - Crespim E
AU  - Ramos RT
AU  - Silva A
AU  - Schaker PD
AU  - Heck K
AU  - Rigonato J
AU  - Schneider MP
AU  - Jeong H
AU  - Sim YM
AU  - Kim HJ
AU  - Lee YJ
AU  - Lee DW
AU  - Lim SK
AU  - Lee SJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00547-13.

PMID- 20861000
VI  - 39
DP  - 2011
TI  - DNA intercalation without flipping in the specific ThaI-DNA complex.
PG  - 744-754
AB  - The PD-(D/E)XK type II restriction endonuclease ThaI cuts the target sequence CG/CG with blunt
      ends. Here, we report the 1.3 A resolution
      structure of the enzyme in complex with substrate DNA and a sodium or
      calcium ion taking the place of a catalytic magnesium ion. The structure
      identifies Glu54, Asp82 and Lys93 as the active site residues. This agrees
      with earlier bioinformatic predictions and implies that the PD and (D/E)XK
      motifs in the sequence are incidental. DNA recognition is very unusual:
      the two Met47 residues of the ThaI dimer intercalate symmetrically into
      the CG steps of the target sequence. They approach the DNA from the minor
      groove side and penetrate the base stack entirely. The DNA accommodates
      the intercalating residues without nucleotide flipping by a doubling of
      the CG step rise to twice its usual value, which is accompanied by drastic
      unwinding. Displacement of the Met47 side chains from the base pair
      midlines toward the downstream CG steps leads to large and compensating
      tilts of the first and second CG steps. DNA intercalation by ThaI is
      unlike intercalation by HincII, HinP1I or proteins that bend or repair
      DNA.
AU  - Firczuk M
AU  - Wojciechowski M
AU  - Czapinska H
AU  - Bochtler M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2011 39: 744-754.

PMID- 6577261
VI  - 191
DP  - 1983
TI  - Genetic and physical studies of restriction-deficient mutants of the Inc FIV plasmids R124 and R124/3.
PG  - 145-153
AB  - R124 and R124/3 are R plasmids that carry the genes for two different
      restriction and modification systems.  The phenotype of strains carrying either
      of these plasmids along with the F'lac+ plasmid, is restriction-deficient
      (Res-).  The Res- phenotype is not due to selection of preexisting mutants but
      rather to a complex mutational event caused by the F plasmid.
      Restriction-deficient mutants carry extensive deletions and other DNA
      rearrangements.  Tn7 insertion is used to locate the restriction gene.  Many of
      the Res- mutants are genetically unstable and revert at exceptionally high
      frequencies.  Reversion is accompanied by DNA rearrangements which result in a
      net gain of 9kb of DNA.  F- derivatives of F+ which do not cause
      restriction-deficiency but do cause deletion were used to distinguish between
      the DNA rearrangements associated with restriction-deficiency and those
      associated with deletion.  From Res+ revertants of strains carrying F'lac+ and
      R124 or R124/3 we have isolated F plasmids that now carry the genes for the
      R124 or R124/3 restriction and modification systems.  It is suggested that
      interaction between part of the F plasmid and that segment of the R plasmid
      which controls the switch in Res-Mod specificity which has been observed
      (Glover et al. 1983) is responsible for the production of
      restriction-deficiency.
AU  - Firman K
AU  - Creasey WA
AU  - Watson G
AU  - Price C
AU  - Glover SW
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1983 191: 145-153.

PMID- 
VI  - 1
DP  - 2000
TI  - The role of subunit assembly in the functional control of Type I restriction-modification enzymes.
PG  - 35-41
AB  - Type I restriction-modification enzymes are multifunctional, multisubunit enzymes that provide
      their host bacteria with protection
      against invading DNA. This protection is accomplished through a very
      efficient cleavage of foreign DNA using a complex mechanism involving
      hydrolysis of ATP and subsequent translocation of the substrate DNA. In
      addition, the same enzymes provide protection for the host chromosome
      against cleavage by methylating the target recognition sites. However,
      the restriction (cleavage) activity of the enzyme must be carefully
      controlled both in terms of what constitutes substrate DNA ("foreign"
      versus "host") and the timing of the two activities when transferred to
      a new host (modification must precede restriction to allow
      establishment of the R-M system). The mechanism by which the enzyme
      differentiates between "foreign" and "host" DNA is described and we
      discuss recent evidence showing post-translational control as the
      primary mechanism for temporal control of restriction. The importance
      of subunit assembly in these processes is detailed and extended to
      include novel assemblies with unexpected function.
AU  - Firman K
AU  - Dutta C
AU  - Weiserova M
AU  - Janscak P
PT  - Journal Article
TA  - Mol. Biol. Today
JT  - Mol. Biol. Today
SO  - Mol. Biol. Today 2000 1: 35-41.

PMID- 3006102
VI  - 14
DP  - 1985
TI  - The EcoR124 and EcoR124/3 restriction and modification systems:  cloning the genes.
PG  - 224-234
AB  - The Escherichia coli plasmid R124 codes for a type I restriction and
      modification system EcoR124 and carries genetic information, most probably in
      the form of a "silent copy", for the expression of a different R-M specificity
      R124/3.  Characteristic DNA rearrangements have been shown to accompany the
      switch in specificity from R124 to R124/3 and vice versa.  We have cloned a
      14.2-kb HindIII fragment from R124 and shown that it contains the hsdR, hsdM,
      and hsdS genes which code for the EcoR124 R-M system.  An equivalent fragment
      from the plasmid R124/3 following the switch in R-M specificity has also been
      cloned and shown to contain the genes coding for the EcoR124/3 R-M system.
      These fragments, however, lack a component present on the wild-type plasmid
      essential for the switch in specificity.  Restriction fragment maps and
      preliminary heteroduplex analysis indicate the near identity of the genes that
      encode the two different DNA recognition specificities.  Transposon mutagenesis
      was used to locate the positions of the hsdR, hsdM, and hsdS genes on the
      cloned fragments in conjunction with complementation tests for gene function.
      Indirect evidence indicates that hsdR is expressed from its own promoter and
      that hsdM and hsdS are expressed from a single promoter, unidirectionally.
AU  - Firman K
AU  - Price C
AU  - Glover SW
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 1985 14: 224-234.

PMID- 10790375
VI  - 19
DP  - 2000
TI  - Measuring motion on DNA by the type I restriction endonuclease EcoR124I using triplex displacement.
PG  - 2094-2102
AB  - The type I restriction enzyme EcoR124I cleaves DNA following extensive linear translocation
      dependent upon ATP hydrolysis. Using protein-directed displacement of a DNA triplex, we have
      determined the kinetics of one-dimensional motion without the necessity of measuring DNA or
      ATP hydrolysis. The triplex was pre-formed specifically on linear DNA, 4370 bp from an
      EcoR124I site, and then incubated with endonuclease. Upon ATP addition, a distinct lag phase
      was observed before the triplex-forming oligonucleotide was displaced with exponential
      kinetics. As the distance between type I and triplex sites was shortened, the lag time
      decreased whilst the displacement reaction remained exponential. This is indicative of
      processive DNA translocation followed by collision with the triplex and oligonucleotide
      displacement. A linear relationship between lag duration and inter-site distance gives a
      translocation velocity of 400 +/- 32 bp/s at 20 degrees C. Furthermore, the data can only be
      explained by bi-directional translocation. An endonuclease with only one of the two HsdR
      subunits responsible for motion could still catalyse translocation. The reaction is less
      processive, but can 'reset' in either direction whenever the DNA is released.
AU  - Firman K
AU  - Szczelkun MD
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 2000 19: 2094-2102.

PMID- 3019129
VI  - 39
DP  - 1986
TI  - DNA Contamination in Commercial Restriction Endonucleases.
PG  - 145
AB  - None
AU  - Firnhaber C
AU  - Gerber M
AU  - Tooley K
AU  - Scoggin C
PT  - Journal Article
TA  - Am. J. Hum. Genet.
JT  - Am. J. Hum. Genet.
SO  - Am. J. Hum. Genet. 1986 39: 145.

PMID- 29122865
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Burkholderia contaminans 293K04B, an Endosymbiont of the Sponge-Derived Fungus Stachylidium bicolor.
PG  - e01142-17
AB  - Here, we present the draft genome of the endofungal symbiotic bacterium Burkholderia
      contaminans 293K04B, isolated from Stachylidium bicolor 293K04
      (Ascomycota). The fungus was originally isolated from the sponge Callyspongia cf.
      C. flammeaS. bicolor 293K04 produces the endolides A-B, bioactive cyclic peptides
      possibly biosynthesized by its endobacterium B. contaminans 293K04B.
AU  - Fisch KM
AU  - Silva PC
AU  - Genilloud O
AU  - Almeida C
AU  - Schaberle TF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01142-17.

PMID- 28347402
VI  - 6
DP  - 2017
TI  - Chlamydia trachomatis-containing vacuole serves as deubiquitination platform to stabilize Mcl-1 and to interfere with host defense.
PG  - e21465
AB  - Obligate intracellular Chlamydia trachomatis replicate in a membrane-bound
      vacuole called inclusion, which serves as a signaling interface with the host
      cell. Here, we show that the chlamydial deubiquitinating enzyme (Cdu) 1 localizes
      in the inclusion membrane and faces the cytosol with the active deubiquitinating
      enzyme domain. The structure of this domain revealed high similarity to mammalian
      deubiquitinases with a unique alpha-helix close to the substrate-binding pocket.
      We identified the apoptosis regulator Mcl-1 as a target that interacts with Cdu1
      and is stabilized by deubiquitination at the chlamydial inclusion. A chlamydial
      transposon insertion mutant in the Cdu1-encoding gene exhibited increased Mcl-1
      and inclusion ubiquitination and reduced Mcl-1 stabilization. Additionally,
      inactivation of Cdu1 led to increased sensitivity of C. trachomatis for IFNgamma
      and impaired infection in mice. Thus, the chlamydial inclusion serves as an
      enriched site for a deubiquitinating activity exerting a function in selective
      stabilization of host proteins and protection from host defense.
AU  - Fischer A
AU  - Harrison KS
AU  - Ramirez Y
AU  - Auer D
AU  - Chowdhury SR
AU  - Prusty BK
AU  - Sauer F
AU  - Dimond Z
AU  - Kisker C
AU  - Scott-Hefty P
AU  - Rudel T
PT  - Journal Article
TA  - eLife
JT  - eLife
SO  - eLife 2017 6: e21465.

PMID- 23469346
VI  - 1
DP  - 2013
TI  - Genome Sequence of Mycoplasma feriruminatoris sp. nov., a Fast-Growing Mycoplasma Species.
PG  - e00216-12
AB  - Members of the ' cluster' represent important livestock pathogens worldwide. We report the
      genome sequence of sp. nov., the closest relative to the ' cluster'
      and the fastest-growing species described to date.
AU  - Fischer A
AU  - Santana-Cruz I
AU  - Giglio M
AU  - Nadendla S
AU  - Drabek E
AU  - Vilei EM
AU  - Frey J
AU  - Jores J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00216-12.

PMID- 26516405
VI  - 10
DP  - 2015
TI  - High quality draft genomes of the Mycoplasma mycoides subsp. mycoides challenge strains Afade and B237.
PG  - 89
AB  - Members of the Mycoplasma mycoides cluster' represent important livestock pathogens
      worldwide. Mycoplasma mycoides subsp. mycoides is the etiologic agent
      of contagious bovine pleuropneumonia (CBPP), which is still endemic in many parts
      of Africa. We report the genome sequences and annotation of two frequently used
      challenge strains of Mycoplasma mycoides subsp. mycoides, Afade and B237. The
      information provided will enable downstream 'omics' applications such as
      proteomics, transcriptomics and reverse vaccinology approaches. Despite the
      absence of Mycoplasma pneumoniae like cyto-adhesion encoding genes, the two
      strains showed the presence of protrusions. This phenotype is likely encoded by
      another set of genes.
AU  - Fischer A
AU  - Santana-Cruz I
AU  - Hegerman J
AU  - Gourle H
AU  - Schieck E
AU  - Lambert M
AU  - Nadendla S
AU  - Wesonga H
AU  - Miller RA
AU  - Vashee S
AU  - Weber J
AU  - Meens J
AU  - Frey J
AU  - Jores J
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 89.

PMID- 27103722
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of 'Candidatus Phytoplasma oryzae' Strain Mbita1, the Causative Agent of Napier Grass Stunt Disease in Kenya.
PG  - e00297-16
AB  - Phytoplasmas are bacterial plant pathogens with devastating impact on agricultural production
      worldwide. In eastern Africa, Napier grass stunt disease
      causes serious economic losses in the smallholder dairy industry. This draft
      genome sequence of ' ITALIC! CandidatusPhytoplasma oryzae' strain Mbita1 provides
      insight into its genomic organization and the molecular basis of pathogenicity.
AU  - Fischer A
AU  - Santana-Cruz I
AU  - Wambua L
AU  - Olds C
AU  - Midega C
AU  - Dickinson M
AU  - Kawicha P
AU  - Khan Z
AU  - Masiga D
AU  - Jores J
AU  - Schneider B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00297-16.

PMID- 20974979
VI  - 107
DP  - 2010
TI  - Giant virus with a remarkable complement of genes infects marine zooplankton.
PG  - 19508-19513
AB  - As major consumers of heterotrophic bacteria and phytoplankton, microzooplankton are a
      critical link in aquatic foodwebs. Here, we show that a major marine microflagellate grazer is
      infected by a giant virus, Cafeteria roenbergensis virus (CroV), which has the largest genome
      of any described marine virus (approximately 730 kb of doublestranded DNA). The central 618-kb
      coding part of this AT-rich genome contains 544 predicted protein-coding genes; putative early
      and late promoter motifs have been detected and assigned to 191 and 72 of them, respectively,
      and at least 274 genes were expressed during infection. The diverse coding potential of CroV
      includes predicted translation factors, DNA repair enzymes such as DNA mismatch repair protein
      MutS and two photolyases, multiple ubiquitin pathway components, four intein elements, and 22
      tRNAs. Many genes including isoleucyl-tRNA synthetase, eIF-2y, and an Elp3- like histone
      acetyltransferase are usually not found in viruses. We also discovered a 38-kb genomic region
      of putative bacterial origin, which encodes several predicted carbohydrate metabolizing
      enzymes, including an entire pathway for the biosynthesis of 3- deoxy-D-manno-octulosonate, a
      key component of the outer membrane in Gram-negative bacteria. Phylogenetic analysis indicates
      that CroV is a nucleocytoplasmic large DNA virus, with Acanthamoeba polyphaga mimivirus as its
      closest relative, although less than one-third of the genes of CroV have homologs in
      Mimivirus. CroV is a highly complex marine virus and the only virus studied in genetic detail
      that infects one of the major groups of predators in the oceans.
AU  - Fischer MG
AU  - Allen MJ
AU  - Wilson WH
AU  - Suttle CA
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2010 107: 19508-19513.

PMID- 24767410
VI  - 15
DP  - 2014
TI  - A comprehensive analysis of Helicobacter pylori plasticity zones reveals that they are integrating conjugative elements with intermediate integration specificity.
PG  - 310
AB  - BACKGROUND: The human gastric pathogen Helicobacter pylori is a paradigm for
      chronic bacterial infections. Its persistence in the stomach mucosa is
      facilitated by several mechanisms of immune evasion and immune modulation, but
      also by an unusual genetic variability which might account for the capability to
      adapt to changing environmental conditions during long-term colonization. This
      variability is reflected by the fact that almost each infected individual is
      colonized by a genetically unique strain. Strain-specific genes are dispersed
      throughout the genome, but clusters of genes organized as genomic islands may
      also collectively be present or absent. RESULTS: We have comparatively analysed
      such clusters, which are commonly termed plasticity zones, in a high number of H.
      pylori strains of varying geographical origin. We show that these regions contain
      fixed gene sets, rather than being true regions of genome plasticity, but two
      different types and several subtypes with partly diverging gene content can be
      distinguished. Their genetic diversity is incongruent with variations in the rest
      of the genome, suggesting that they are subject to horizontal gene transfer
      within H. pylori populations. We identified 40 distinct integration sites in 45
      genome sequences, with a conserved heptanucleotide motif that seems to be the
      minimal requirement for integration. CONCLUSIONS: The significant number of
      possible integration sites, together with the requirement for a short conserved
      integration motif and the high level of gene conservation, indicates that these
      elements are best described as integrating conjugative elements (ICEs) with an
      intermediate integration site specificity.
AU  - Fischer W
AU  - Breithaupt U
AU  - Kern B
AU  - Smith SI
AU  - Spicher C
AU  - Haas R
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2014 15: 310.

PMID- 7607471
VI  - 157
DP  - 1995
TI  - Selection of mutations altering specificity in restriction-modification enzymes using the bacteriophage P22 challenge-phage system.
PG  - 119-121
AB  - A method for selecting mutants of site-specific DNA-binding proteins has been applied to the
      study of the EcoRI and RsrI restriction-modification enzymes.  Catalytically inactive variants
      of both endonucleases are shown to function as pseudo-repressors in the bacteriophage P22
      challenge-phage assay, and, upon further mutagenesis of the gene encoding R.EcoRI, a variant
      of that enzyme has been selected which appears to bind EcoRI-methylated GAATTC sequences to
      the exclusion of unmethylated sites: this specificity is the opposite of that belonging to the
      native enzyme.  Variants of the EcoRI methylase have also been found that lack either
      catalytic activity or both binding and catalytic activities.
AU  - Fisher EW
AU  - Yang M-T
AU  - Jeng S-T
AU  - Gardner JF
AU  - Gumport RI
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 119-121.

PMID- 8467964
VI  - 7
DP  - 1993
TI  - Isolation of a mutant EcoRI endonuclease with enhanced affinity for duplex methylated d(GAATTC).
PG  - A1290
AB  - The EcoRI endonuclease, one of the best characterized type II restriction endonucleases,
      cleaves duplex DNA at the sequence GAATTC with extreme specificity, catalyzing incorrect
      cleavage fewer than once in 10 to the 7th binding events. A companion DNA methyltransferase
      uniquely methylates the inner adenosine residue of the same sequence, inhibiting recognition
      of the site by the endonuclease. We have applied the bacteriophage P22 challenge-phage system
      to the selection of a mutant of the endonuclease which binds the methylated sequence in
      preference to the normal, unmethylated target sequence. The challenge-phage assay links
      survival of the infected cell to the presence of a protein capable of binding a cloned
      recognition sequence of the user's choice, and permits selection of mutant proteins with this
      capability from a randomly mutagenized population. In this case a methylated EcoRI site was
      chosen as the target recognition sequence by including in the host cells a plasmid bearing the
      EcoRI methylase gene. We have isolated a mutant of EcoRI endonuclease, generated by
      hydroxylamine treatment of a plasmid encoding a catalytically inactive form of the enzyme
      (E111Q), which binds the methylated site tightly enough to form a stable lysogen in
      challenge-phage assays. The challenge-phage data suggests that the mutant protein requires the
      methyl group for binding, because cells lacking the EcoRI methylase gene are unable to form
      lysogens. Current efforts are directed toward identifying the mutational change and examining
      by gel mobility shift assays whether the mutant protein discriminates the methylated from the
      unmethylated site in vitro. This work was supported in part by a grant (GM25621) from the
      National Institute of Health to R.I.G.
AU  - Fisher EW
AU  - Yang MT
AU  - Gardner JF
AU  - Gumport RI
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1993 7: A1290.

PMID- 14715927
VI  - 32
DP  - 2004
TI  - Characterization of cytosine methylated regions and 5-cytosine DNA methyltransferase (Ehmeth) in the protozoan parasite Entamoeba histolytica.
PG  - 287-297
AB  - The DNA methylation status of the protozoan parasite Entamoeba histolytica was heretofore
      unknown.  In the present study, we developed a new technique, based on the affinity of
      methylated DNA to 5-methyl-cytosine antibodies, to identify methylated DNA in this parasite.
      Ribosomal. DNA and ribosomal DNA circles were isolated by this method and we confirmed the
      validity of our approach by sodium bisulfite sequencing.  We also report the identification
      and the characterization of a gene, Ehmeth, encoding a DNA methyltransferase strongly
      homologous to the human DNA methyltransferase 2 (Dnmt2).  Immunofluorescence microscopy using
      an antibody raised against a recombinant Ehmeth showed that Ehmeth is concentrated in the
      nuclei of trophozoites.  The recombinant Ehmeth has a weak but significant methyltransferase
      activity when E. histolytica genomic DNA is used as substrate.  5-Azacytidine (5-AzaC), an
      inhibitor of DNA methyltransferase, was used to study in vivo the role of DNA methylation in
      E. histolytica.  Genomic DNA of trophozoites grown with 5-AzaC (23 uM) was undermethylated and
      the ability of 5-AzaC-treated trophozoites to kill mammalian cells or to cause liver abscess
      in hamsters was strongly impaired.
AU  - Fisher O
AU  - Siman-Tov R
AU  - Ankri S
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2004 32: 287-297.

PMID- 21818284
VI  - 6
DP  - 2011
TI  - Core proteome of the minimal cell: comparative proteomics of three mollicute species.
PG  - E21964
AB  - Mollicutes (mycoplasmas) have been recognized as highly evolved prokaryotes with
      an extremely small genome size and very limited coding capacity. Thus, they may
      serve as a model of a 'minimal cell': a cell with the lowest possible number of
      genes yet capable of autonomous self-replication. We present the results of a
      comparative analysis of proteomes of three mycoplasma species: A. laidlawii, M.
      gallisepticum, and M. mobile. The core proteome components found in the three
      mycoplasma species are involved in fundamental cellular processes which are
      necessary for the free living of cells. They include replication, transcription,
      translation, and minimal metabolism. The members of the proteome core seem to be
      tightly interconnected with a number of interactions forming core interactome
      whether or not additional species-specific proteins are located on the periphery.
      We also obtained a genome core of the respective organisms and compared it with
      the proteome core. It was found that the genome core encodes 73 more proteins
      than the proteome core. Apart of proteins which may not be identified due to
      technical limitations, there are 24 proteins that seem to not be expressed under
      the optimal conditions.
AU  - Fisunov GY
AU  - Alexeev DG
AU  - Bazaleev NA
AU  - Ladygina VG
AU  - Galyamina MA
AU  - Kondratov IG
AU  - Zhukova NA
AU  - Serebryakova MV
AU  - Demina IA
AU  - Govorun VM
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2011 6: E21964.

PMID- 22330677
VI  - 180
DP  - 2012
TI  - Full-Genome Dissection of an Epidemic of Severe Invasive Disease Caused by a Hypervirulent, Recently Emerged Clone of Group A Streptococcus.
PG  - 1522-1534
AB  - Group A Streptococcus (GAS) causes an exceptionally broad range of infections in humans, from
      relatively mild pharyngitis and skin infections to life-threatening necrotizing fasciitis and
      toxic shock syndrome. An epidemic of severe invasive human infections caused by type emm59
      GAS, heretofore an exceedingly rare cause of disease, spread west to east across Canada over a
      3-year period (2006 to 2008). By sequencing the genomes of 601 epidemic, historic, and other
      emm59 organisms, we discovered that a recently emerged, genetically distinct emm59 clone is
      responsible for the Canadian epidemic. Using near-real-time genome sequencing, we were able to
      show spread of the Canadian epidemic clone into the United States. The extensive genome data
      permitted us to identify patterns of geographic dissemination as well as links between emm59
      subclonal lineages that cause infections. Mouse and nonhuman primate models of infection
      demonstrated that the emerged clone is unusually virulent. Transmission of epidemic emm59
      strains may have occurred primarily by skin contact, as suggested by an experimental model of
      skin transmission. In addition, the emm59 strains had a significantly impaired ability to
      persist in human saliva and to colonize the oropharynx of mice, and seldom caused human
      pharyngitis. Our study contributes new information to the rapidly emerging field of molecular
      pathogenomics of bacterial epidemics and illustrates how full-genome data can be used to
      precisely illuminate the landscape of strain dissemination during a bacterial epidemic.
AU  - Fittipaldi N
AU  - Beres SB
AU  - Olsen RJ
AU  - Kapur V
AU  - Shea PR
AU  - Watkins ME
AU  - Cantu CC
AU  - Laucirica DR
AU  - Jenkins L
AU  - Flores AR
AU  - Lovgren M
AU  - Ardanuy C
AU  - Linares J
AU  - Low DE
AU  - Tyrrell GJ
AU  - Musser JM
PT  - Journal Article
TA  - Am. J. Pathol.
JT  - Am. J. Pathol.
SO  - Am. J. Pathol. 2012 180: 1522-1534.

PMID- 23337890
VI  - 133
DP  - 2013
TI  - Propionibacterium acnes Strain Populations in the Human Skin Microbiome Associated with Acne.
PG  - 2152-2160
AB  - The human skin microbiome has important roles in skin health and disease.
      However, bacterial population structure and diversity at the strain level is
      poorly understood. We compared the skin microbiome at the strain level and genome
      level of Propionibacterium acnes, a dominant skin commensal, between 49 acne
      patients and 52 healthy individuals by sampling the pilosebaceous units on their
      noses. Metagenomic analysis demonstrated that although the relative abundances of
      P. acnes were similar, the strain population structures were significantly
      different in the two cohorts. Certain strains were highly associated with acne,
      and other strains were enriched in healthy skin. By sequencing 66 previously
      unreported P. acnes strains and comparing 71 P. acnes genomes, we identified
      potential genetic determinants of various P. acnes strains in association with
      acne or health. Our analysis suggests that acquired DNA sequences and bacterial
      immune elements may have roles in determining virulence properties of P. acnes
      strains, and some could be future targets for therapeutic interventions. This
      study demonstrates a previously unreported paradigm of commensal strain
      populations that could explain the pathogenesis of human diseases. It underscores
      the importance of strain-level analysis of the human microbiome to define the
      role of commensals in health and disease.Journal of Investigative Dermatology
      advance online publication, 28 February 2013; doi:10.1038/jid.2013.21.
AU  - Fitz-Gibbon S
AU  - Tomida S
AU  - Chiu BH
AU  - Nguyen L
AU  - Du C
AU  - Liu M
AU  - Elashoff D
AU  - Erfe MC
AU  - Loncaric A
AU  - Kim J
AU  - Modlin RL
AU  - Miller JF
AU  - Sodergren E
AU  - Craft N
AU  - Weinstock GM
AU  - Li H
PT  - Journal Article
TA  - J. Invest. Dermatol.
JT  - J. Invest. Dermatol.
SO  - J. Invest. Dermatol. 2013 133: 2152-2160.

PMID- 11792869
VI  - 99
DP  - 2002
TI  - Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum.
PG  - 984-989
AB  - We determined and annotated the complete 2.2-megabase genome sequence of Pyrobaculum
      aerophilum, a facultatively aerobic nitrate-reducing hyperthermophilic (Topt=100 C)
      crenarchaeon.  Clues were found suggesting explanations of the organism's surprising
      intolerance to sulfur, which may aid in the development of methods for genetic studies of the
      organism.  Many interesting features worthy of further genetic studies were revealed.  Whole
      genome computational analysis confirmed experiments showing that P. aerophilum (and perhaps
      all crenarchaea) lack 5' untranslated regions in their mRNAs and thus appear not to use a
      ribosome-binding site (Shine-Delgarno)-based mechanism for translation initiation at the 5'
      end of transcripts.  Inspection of the lengths and distribution of mononucleotide
      repeat-tracts revealed some interesting features.  For instance, it was seen that
      mononucleotide repeat-tracts of Gs (or Cs) are highly unstable, a pattern expected for an
      organism deficient in mismatch repair.  This result, together with an independent study on
      mutation rates, suggests a "mutator" phenotype.
AU  - Fitz-Gibbon ST
AU  - Ladner H
AU  - Kim U-J
AU  - Stetter KO
AU  - Simon MI
AU  - Miller JH
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2002 99: 984-989.

PMID- 8586236
VI  - 85
DP  - 1995
TI  - Bacteriophage resistance in Lactococcus: Molecular characterization of the ScrFI restriction/modification system from Lactococcus lactis subsp. cremoris UC503.
PG  - 581-590
AB  - Members of the genus Lactococcus are used as starter cultures in the manufacture of a range of
      ripened and unripened fermented dairy products such as cheese, lactic butter and cottage
      cheese.  In many cases the production of these foods is concentrated in large manufacturing
      units where starter cultures are used on a more or less continuous and intensive basis.  In
      such modern, highly efficient manufacturing regimes, poor starter performance is undesirable.
      Thus, considerable effort has been targeted to successfully eliminate those factors, such as
      poor milk quality, which could have a negative impact on the activity of the starter culture.
      While there has been considerable success in countering the major problem of bacteriophage
      infection in cheese plants, phage still represent a very significant threat to the efficient
      performance of lactococcal starter cultures.  Obvious physical approaches such as careful
      design of manufacturing plants, aseptic handling of cultures and proper separation of whey
      from the culture preparation area have had considerable success but on their own will not
      guarantee a phage-free environment.  A further approach has been to examine the cultures
      themselves and to use isolates which display inherent resistance to phage.  Thus, carefully
      selected strains, exhibiting considerable levels of natural resistance to phage, have been
      included in defined starter culture systems used in many parts of the world, particularly for
      Cheddar cheese production.  These defined systems have proved to be quite successful in
      countering phage, especially when they are combined with good sanitization and asepsis
      regimes.  The quest for lactococcal hosts exhibiting high levels of resistance to phage has
      stimulated the analysis of phage/host interactions at a fundamental level.  One outcome of
      this research has been the recognition that some of these hosts possess one or more specific
      mechanisms which can confer on the host significant levels of resistance to phage.  These are
      usually, although not always, plasmid-encoded and quite often these plasmids are
      self-transmissible.  In general, three distinct types of resistance have been identified:
      adsorption inhibition, abortive infection (Abi) and restriction/modification (R/M).  Since the
      topic of phage resistance in lactococci has been reviewed in considerable depth in a number of
      recent publications, these specific areas will not be discussed in detail.  The major emphasis
      of this paper will be on the molecular analysis of the ScrFI R/M system, which mediates
      insensitivity to phage in vivo and has a number of unusual and interesting features.
AU  - Fitzgerald GF
AU  - Twomey DP
AU  - Daly C
AU  - Coffey AG
PT  - Journal Article
TA  - Genetics and Molecular Biology of Streptococci, Lactococci, and Enterococci
JT  - Genetics and Molecular Biology of Streptococci, Lactococci, and Enterococci
SO  - Genetics and Molecular Biology of Streptococci, Lactococci, and Enterococci 1995 85: 581-590.

PMID- 17023017
VI  - 358
DP  - 2007
TI  - Sequence and annotation of the 314-kb MT325 and the 321-kb FR483 viruses that infect Chlorella Pbi.
PG  - 459-471
AB  - Viruses MT325 and FR483, members of the family Phycodnaviridae, genus Chlorovirus, infect the
      fresh water, unicellular, eukaryotic, chlorella-like green alga, Chlorella Pbi. The 314,335-bp
      genome of MT325 and the 321,240-bp genome of FR483 are the first viruses that infect Chlorella
      Pbi to have their genomes sequenced and annotated. Furthermore, these genomes are the two
      smallest chlorella virus genomes sequenced to date, MT325 has 331 putative protein-encoding
      and 10 tRNA-encoding genes and FR483 has 335 putative protein-encoding and 9 tRNA-encoding
      genes. The protein-encoding genes are almost evenly distributed on both strands, and
      intergenic space is minimal. Approximately 40% of the viral gene products resemble entries in
      public databases, including some that are the first of their kind to be detected in a virus.
      For example, these unique gene products include an aquaglyceroporin in MT325, a potassium ion
      transporter protein and an alkyl sulfatase in FR483, and a dTDP-glucose pyrophosphorylase in
      both viruses. Comparison of MT325 and FR483 protein-encoding genes with the prototype
      chlorella virus PBCV-1 indicates that approximately 82% of the genes are present in all three
      viruses.
AU  - Fitzgerald LA
AU  - Graves MV
AU  - Li X
AU  - Feldblyum T
AU  - Hartigan J
AU  - Van Etten JL
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 2007 358: 459-471.

PMID- 17027058
VI  - 358
DP  - 2007
TI  - Sequence and annotation of the 369-kb NY-2A and the 345-kb AR158 viruses that infect Chlorella NC64A.
PG  - 472-484
AB  - Viruses NY-2A and AR158, members of the family Phycodnaviridae, genus
      Chlorovirus, infect the fresh water, unicellular, eukaryotic,
      chlorella-like green alga, Chlorella NC64A. The 368,683-bp genome of NY-2A
      and the 344,690-bp genome of AR158 are the two largest chlorella virus
      genomes sequenced to date; NY-2A contains 404 putative protein-encoding
      and 7 tRNA-encoding genes and AR158 contains 360 putative protein-encoding
      and 6 tRNA-encoding genes. The protein-encoding genes are almost evenly
      distributed on both strands, and intergenic space is minimal. Two of the
      NY-2A genes encode inteins, the large subunit of ribonucleotide reductase
      and a superfamily II helicase. These are the first inteins to be detected
      in the chlorella viruses. Approximately 40% of the viral gene products
      resemble entries in the public databases, including some that are
      unexpected for a virus. These include GDP-d-mannose dehydratase, fucose
      synthase, aspartate transcarbamylase, Ca(++) transporting ATPase and
      ubiquitin. Comparison of NY-2A and AR158 protein-encoding genes with the
      prototype chlorella virus PBCV-1 indicates that 85% of the genes are
      present in all three viruses.
AU  - Fitzgerald LA
AU  - Graves MV
AU  - Li X
AU  - Feldblyum T
AU  - Nierman WC
AU  - Van Etten JL
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 2007 358: 472-484.

PMID- 1322530
VI  - 20
DP  - 1992
TI  - Rapid shotgun cloning utilizing the two base recognition endonuclease CviJI.
PG  - 3753-3762
AB  - A new approach has been developed for the rapid fragmentation and fractionation of DNA into a
      size suitable for shotgun cloning and sequencing. The restriction endonuclease CviJI normally
      cleaves the recognition sequence PuGCPy between the G and C to leave blunt ends. Atypical
      reaction conditions which alter the specificity of this enzyme (CviJI**) yield a quasi-random
      distribution of DNA fragments from the small molecule pUC19 (2686 base pairs). To
      quantitatively evaluate the randomness of this fragmentation strategy, a CviJI** digest of
      pUC19 was size fractionated by a rapid gel filtration method and directly ligated, without end
      repair, to a lacZ minus M13 cloning vector. Sequence analysis of 76 clones showed that CviJI**
      restricts PyGCPy and PuCGPu, in addition to PuGCPy sites, and that new sequence data is
      accumulated at a rate consistent with random fragmentation. Advantages of this approach
      compared to sonication and agarose gel fractionation include: smaller amounts of DNA are
      required (0.2-0.5 ug instead of 2-5 ug), fewer steps are involved (no pre-ligation, end
      repair, chemical extraction, or agarose gel electrophoresis and elution are needed), and
      higher cloning efficiencies are obtained (CviJI** digested and column fractionated DNA
      transforms 3-16 times more efficiently than sonicated, end-repaired, and agarose fractionated
      DNA).
AU  - Fitzgerald MC
AU  - Skowron P
AU  - Van Etten JL
AU  - Smith LM
AU  - Mead DA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 3753-3762.

PMID- 26631971
VI  - 5
DP  - 2015
TI  - Re-engineering cellular physiology by rewiring high-level global regulatory genes.
PG  - 17653
AB  - Knowledge of global regulatory networks has been exploited to rewire the gene
      control programmes of the model bacterium Salmonella enterica serovar
      Typhimurium. The product is an organism with competitive fitness that is superior
      to that of the wild type but tuneable under specific growth conditions. The
      paralogous hns and stpA global regulatory genes are located in distinct regions
      of the chromosome and control hundreds of target genes, many of which contribute
      to stress resistance. The locations of the hns and stpA open reading frames were
      exchanged reciprocally, each acquiring the transcription control signals of the
      other. The new strain had none of the compensatory mutations normally associated
      with alterations to hns expression in Salmonella; instead it displayed
      rescheduled expression of the stress and stationary phase sigma factor RpoS and
      its regulon. Thus the expression patterns of global regulators can be adjusted
      artificially to manipulate microbial physiology, creating a new and resilient
      organism.
AU  - Fitzgerald S
AU  - Dillon SC
AU  - Chao TC
AU  - Wiencko HL
AU  - Hokamp K
AU  - Cameron AD
AU  - Dorman CJ
PT  - Journal Article
TA  - Sci. Rep.
JT  - Sci. Rep.
SO  - Sci. Rep. 2015 5: 17653.

PMID- 6298711
VI  - 10
DP  - 1982
TI  - ScrFI: a new sequence-specific endonuclease from Streptococcus cremoris.
PG  - 8171-8179
AB  - A novel sequence-specific endonuclease has been isolated from Streptococcus cremoris F. ScrFI
      recognizes the sequence:5'CC^NGG3'3'GGN^CC5'and cleaves as indicated by the arrow.  It is
      the first enzyme to recognize this sequence and the first endonuclease reported from the
      lactic streptococci used in dairy fermentations.
AU  - Fitzgerlad GF
AU  - Daly C
AU  - Brown LR
AU  - Gingeras TR
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1982 10: 8171-8179.

PMID- 27811091
VI  - 4
DP  - 2016
TI  - Genome Sequences of Eight Bacterial Species Found in Coculture with the Haptophyte Chrysochromulina tobin.
PG  - e01162-16
AB  - The microalgal division Haptophyta uses a range of nutritional sourcing, including mixotrophy.
      The genome of a member of this taxon, Chrysochromulina
      tobin, suggests that interactions with its bacterial cohort are critical for C.
      tobin physiology. Here, we report the genomes of eight bacterial species in
      coculture with C. tobin.
AU  - Fixen KR
AU  - Starkenburg SR
AU  - Hovde BT
AU  - Johnson SL
AU  - Deodato CR
AU  - Daligault HE
AU  - Davenport KW
AU  - Harwood CS
AU  - Cattolico RA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01162-16.

PMID- 23682147
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Curtobacterium flaccumfaciens Strain UCD-AKU (Phylum Actinobacteria).
PG  - e00244-13
AB  - Here we present the draft genome of an actinobacterium, Curtobacterium flaccumfaciens strain
      UCD-AKU, isolated from a residential carpet. The genome
      assembly contains 3,692,614 bp in 130 contigs. This is the first member of the
      Curtobacterium genus to be sequenced.
AU  - Flanagan JC
AU  - Lang JM
AU  - Darling AE
AU  - Eisen JA
AU  - Coil DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00244-13.

PMID- 767337
VI  - 251
DP  - 1976
TI  - Modification and restriction of T-even bacteriophages.
PG  - 1561-1570
AB  - Using the single-stranded circular DNA of bacteriophage fd as template,
      double-stranded circular DNA has been prepared in vitro with either 5-
      hydroxymethylcytosine ([hmdC]DNA) or cytosine ([dC]DNA) in the product strand.
      Extracts prepared from Escherichia coli cells restrictive to T-even phage containing
      nonglucosylated DNA degrade [hmdC]DNA to acid-soluble material in vitro, but do not
      degrade [dC]DNA.  In contrast, extracts prepared from E. coli K12 rglA- rglB-, a strain
      permissive to T-even phage containing nonglucosylated DNA, do not degrade [hmdC]DNA
      or [dC]DNA.  In addition, glucosylation of the [hmdC]DNA renders it resistant to
      degradation by extracts from restrictive strains.  The conversion of [hmdC]DNA to acid-
      soluble material in vitro consists of an HmCyt-specific endonucleolytic cleavage requiring
      the presence of the RglB gene product to form a linear molecule, followed by a non-
      HmCyt-specific hydrolysis of the linear DNA to acid-soluble fragments, catalyzed in part
      by exonuclease V.  The RglB protein present in extracts of E. coli K12 rglA- rglB+ has
      been purified 200-fold by complementation with extracts from E. coli K12 rglA- rglB-.
      The purified RglB protein does not contain detectable HmCyt-specific endonuclease or
      exonuclease activity.  In vitro endonucleolytic cleavage of [hmdC]DNA thus requires
      additional factors present in cell extracts.
AU  - Fleischman RA
AU  - Campbell JL
AU  - Richardson CC
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1976 251: 1561-1570.

PMID- 4944630
VI  - 68
DP  - 1971
TI  - Analysis of host range restriction in Escherichia coli treated with toluene.
PG  - 2527-2531
AB  - Escherichia coli cells treated with toluene replicate DNA when they are
      provided with deoxyribonucleoside 5'-triphosphates, ATP, Mg++, and K+.
      However, when deoxycytidine 5'-triphosphate is replaced by hydroxymethyl
      deoxycytidine 5'-triphosphate, incorporation of nucleotides into
      acid-precipitable material by toluene-treated strains restrictive to
      nonglucosylated T-even phage is reduced to less than 5% of that normally
      observed.  Even when dCTP is present in the reaction mixture, a similar effect
      of the hydroxymethyl analogue on DNA replication is observed.  In contrast,
      toluene-treated E. coli K12 r6-r2,4-, a strain permissive to the
      nonglucosylated T-even phage, incorporates hydroxymethyl deoxycytosine into its
      DNA, and replication proceeds at only a slightly reduced rate in the presence
      of the hydroxymethyl deoxycytidine 5'-triphosphate.  The presence of the
      hydroxymethyl deoxycytidine 5'-triphosphate in the reaction mixture does not
      lead to degradation of preexisting DNA of the restrictive host, but it does
      lead to an irreversible inhibition of further DNA replication; the inhibition
      is observed only when the hydroxymethyl deoxycytidine 5'-triphosphate is
      present during replication.  Thus phage-specific enzymes are not necessary for
      the incorporation of hydroxymethylcytosine into phage DNA, and the restrictive
      mechanism, present in the host cell before infection, can recognize
      hydroxymethylcytosine residues in its own DNA, as well as the DNA of the T-even
      phage.
AU  - Fleischman RA
AU  - Richardson CC
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1971 68: 2527-2531.

PMID- 7542800
VI  - 269
DP  - 1995
TI  - Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.
PG  - 496-512
AB  - An approach for genome analysis based on sequencing and assembly of unselected pieces of DNA
      from the whole chromosome has been applied to obtain the complete nucleotide sequence
      (1,830,137 base pairs) of the genome from the bacterium Haemophilus influenzae Rd.  This
      approach eliminates the need for initial mapping efforts and is therefore applicable to the
      vast array of microbial species for which genome maps are unavailable.  The H. influenzae Rd
      genome sequence (Genome Sequence Database accession number L42023) represents the only
      complete genome sequence from a free-living organism.
AU  - Fleischmann RD et al
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1995 269: 496-512.

PMID- 21261822
VI  - 1
DP  - 2008
TI  - Development and validation of an approach to produce large-scale quantities of CpG-methylated plasmid DNA.
PG  - 62-67
AB  - The prokaryotic CpG-specific DNA methylase from Spiroplasma, SssI methylase, has been
      extensively used to methylate plasmid DNA in vitro
      to investigate the effects of methylation in vertebrate systems.
      Currently available methods to produce CpG-methylated plasmid DNA have
      certain limitations and cannot generate large quantities of methylated
      DNA without cost or problems of purity. Here we describe an approach in
      which the SssI methylase gene has been introduced into the Escherichia
      coli bacterial genome under the control of an inducible promoter.
      Plasmid DNA propagated in this bacterium under conditions which induce
      the methylase gene result in significant (> 90%) CpG methylation.
      Methylated DNA produced by this approach behaves similarly to
      methylated DNA produced in vitro using the purified methylase. The
      approach is scalable allowing for the production of milligram
      quantities of methylated plasmid DNA.
AU  - Fletcher BS
PT  - Journal Article
TA  - Micro. Biotech.
JT  - Micro. Biotech.
SO  - Micro. Biotech. 2008 1: 62-67.

PMID- 9351205
VI  - 155
DP  - 1997
TI  - High efficiency intergeneric conjugal transfer of plasmid DNA from Escherichia coli to methyl DNA-restricting streptomycetes.
PG  - 223-229
AB  - Many streptomycetes, including S. coelicolor A3(2), possess a potent methyl-specific
      restriction which can present an effective barrier to the
      introduction of heterologous DNA. We have compared the efficiency of intergeneric
      conjugal transfer of different types of plasmids to S. coelicolor and S. lividans
      66 using two E. coli donors: the standard, methylation proficient strain S17-1,
      and the methylation deficient donor, ET12567(pUB307). We demonstrate that the
      methylation deficient donor can yield > 10(4)-fold more S. coelicolor
      exconjugants than the standard donor. In the case of pSET152 derivatives, which
      integrate into the host chromosome by site-specific recombination, up to 10% of
      streptomycete spores in the conjugation mixture inherit the plasmid. The
      conjugation procedure is efficient enough to obtain exconjugants with 'suicide'
      delivery plasmids and therefore provides a simple route for conducting gene
      disruptions in methyl DNA-restricting streptomycetes, and possibly other
      bacteria.
AU  - Flett F
AU  - Mersinias V
AU  - Smith CP
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1997 155: 223-229.

PMID- 438777
VI  - 110
DP  - 1979
TI  - A common host specificity in the restriction and modification of a bacteriophage by three distinct Streptomyces species.
PG  - 465-467
AB  - Restriction/modification of bacteriophage is a well characterized phenomenon in many bacterial
      species and has been identified among streptomycetes in Streptomyces albus G, Streptomyces
      griseus Kr. 15 and Streptomyces coelicolor.  Direct correlation between bacterial restriction
      of bacteriophage and a specific endonuclease has only been demonstrated for a few species,
      including one Streptomyces species.  The discovery of extrachromosomal elements in
      Streptomyces opened up the possibility of detecting such an element carrying
      restriction/modification, as has been shown to occur in eubacteria.
AU  - Flett F
AU  - Wotton SF
AU  - Kirby R
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1979 110: 465-467.

PMID- 9665136
VI  - 394
DP  - 1998
TI  - DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI.
PG  - 96-101
AB  - Homing endonucleases are a diverse collection of proteins that are encoded by genes with
      mobile, self-splicing introns.  They have also been identified in self-splicing inteins
      (protein introns).  These enzymes promote the movement of the DNA sequences that encode them
      from one chromosome location to another; they do this by making a site-specific double-strand
      break at a target site in an allele that lacks the corresponding mobile intron.  The target
      site recognized by these small endonucleases are generally long (14-44 base pairs).  Four
      families of homing endonucleases have been identified, including the LAGLIDADG, the His-Cys
      box, the GIY-YIG and the H-N-H endonucleases.  The first identified His-Cys box homing
      endonuclease was I-PpoI from the slime mould Physarum polycephalum.  Its gene residues in one
      of only a few nuclear introns known to exhibit genetic mobility.  Here we report the structure
      of the I-PpoI homing endonuclease bound to homing-site DNA determined to 1.8 Angstroms
      resolution.  I-PpoI displays an elongated fold of dimensions 25 x 35 x 80 Angstroms, with
      mixed alpha/beta topology.  Each I-PpoI monomer contains three antiparallel beta-sheets
      flanked by two long alpha-helices and a long carboxy-terminal tail, and is stabilized by two
      bound zinc ions 15 Angstroms apart.  The enzyme possesses a new zinc-bound fold and
      endonuclease active site.  The structure has been determined in both uncleaved substrate and
      cleaved product complexes.
AU  - Flick KE
AU  - Jurica MS
AU  - Monnat RJ Jr
AU  - Stoddard BL
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1998 394: 96-101.

PMID- 9416623
VI  - 6
DP  - 1997
TI  - Crystallization and preliminary X-ray studies of I-PpoI: A nuclear, intron-encoded homing endonuclease from Physarum polycephalum.
PG  - 2677-2680
AB  - The homing endonuclease I-PpoI is encoded by an optional third intron, Pp LSU 3, found in
      nuclear, extrachromosomal copies of the Physarum polycephalum 26S rRNA gene.  This
      endonuclease promotes the lateral transfer or "homing" of its encoding intron by recognizing
      and cleaving a partially symmetric, 15 bp homing site in 26S rDNA alleles that lack the Pp LSU
      3 intron.  The open reading frame encoding I-PpoI has been subcloned, and the endonuclease has
      been overproduced in E. coli.  Purified recombinant I-PpoI has been co-crystallized with a 21
      bp homing site DNA duplex.  The crystals belong to space group P3I21, with unit cell
      dimensions a=b=114 A, c= 89 A.  The results of initial X-ray diffraction experiments indicate
      that the asymmetric unit contains an enzyme homodimer and one duplex DNA molecule, and that
      the unit cell has a specific volume of 3.4 A3/dalton.  These experiments also provide strong
      evidence that I-PpoI contains several bound zinc ions as part of its structure.
AU  - Flick KE
AU  - McHugh D
AU  - Heath JD
AU  - Stephens KM
AU  - Monnat RJ Jr
AU  - Stoddard BL
PT  - Journal Article
TA  - Protein Sci.
JT  - Protein Sci.
SO  - Protein Sci. 1997 6: 2677-2680.

PMID- 3010238
VI  - 14
DP  - 1986
TI  - Role of thymidine residues in DNA recognition by the EcoRI and EcoRV restriction endonucleases.
PG  - 3463-3474
AB  - We have synthesized a series of oligonucleotides containing the EcoRI (GAATTC)
      or EcoRV (GATATC) recognition site within which or adjacent to which thymidine
      was substituted by uridine or derivatives of uridine.  The effects of these
      substitutions on the rate of the EcoRI and EcoRV catalyzed cleavage reaction
      were investigated.  Our results show that most of the substitutions within the
      site are quite well tolerated by EcoRI, not, however, by EcoRV.  We conclude
      that the thymin residues most likely are not dirctly involved in the
      recognition process of the EcoRI reaction.  In contrast, they are major points
      of contact, between substrate and enzym in the EcoRV reaction.  The effects of
      substitutions in the position adjacent to the recognition site is also markedly
      different for EcoRI and EcoRV.  Here, EcoRI seems to be considerably more
      selective than EcoRV.
AU  - Fliess A
AU  - Wolfes H
AU  - Rosenthal A
AU  - Schwellnus K
AU  - Blocker H
AU  - Frank R
AU  - Pingoud A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1986 14: 3463-3474.

PMID- 3062581
VI  - 16
DP  - 1988
TI  - Analysis of the recognition mechanism involved in the EcoRV catalyzed cleavage of DNA using modified oligodeoxynucleotides.
PG  - 11781-11793
AB  - We have prepared a series of undecadeoxynucleotides that contain changes in the
      functional group pattern present within the EcoRV recognition site - GATATC -.
      Oligonucleotides were synthesized on solid phase using normal and modified
      beta-cyanoethylphosphoramidites and analyzed in steady state cleavage
      experiments with the EcoRV restriction endonuclease.  The following groups
      appear to interact strongly with the enzyme, since their modification or
      substitution renders the oligonucleotides refractory to cleavage:  the
      exocyclic NH2-groups of both A residues, the N7 of the first A residue, the
      exocyclic NH2-group of the C residue and the CH3-groups of both T residues.
      The exocyclic NH-group of the G residue supports effective recognition, since
      its absence lowers the kcat of the cleavage reaction.  The N7 of the second A
      residue and the C5 position of the C residue apparently are not recognized by
      EcoRV; their substitution by -CH- or modification with -Br or -CH3 does not
      considerably change the rate of cleavage.  All oligonucleotides investigated
      compete with the unmodified substrate for binding to the enzyme.  We conclude
      that EcoRV recognizes its substrate presumably through hydrogen bonds to the
      exocyclic NH2-group and the N7 of the first A residue, the exocyclic NH2-groups
      of the second A and the C residue, as well as through hydrophobic interactions
      with both T residues.
AU  - Fliess A
AU  - Wolfes H
AU  - Seela F
AU  - Pingoud A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1988 16: 11781-11793.

PMID- 24407644
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Streptomyces niveus NCIMB 11891, Producer of the Aminocoumarin Antibiotic Novobiocin.
PG  - e01146-13
AB  - Streptomyces niveus NCIMB 11891 is the producer of the gyrase inhibitor novobiocin, which
      belongs to the aminocoumarin class of antibiotics. The genome
      sequence of this strain was found to contain, besides the gene cluster for
      novobiocin, a putative gene cluster for the macrolactam antibiotic BE-14106 and
      further secondary metabolite gene clusters.
AU  - Flinspach K
AU  - Ruckert C
AU  - Kalinowski J
AU  - Heide L
AU  - Apel AK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01146-13.

PMID- 26089430
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Sedimenticola thiotaurini Strain SIP-G1, a Polyphosphate- and Polyhydroxyalkanoate-Accumulating Sulfur-Oxidizing  Gammaproteobacterium Isolated from Salt Marsh Sediments.
PG  - e00671-15
AB  - We report the closed genome sequence of Sedimenticola thiotaurini strain SIP-G1 and an unnamed
      plasmid obtained through PacBio sequencing with 100% consensus
      concordance. The genome contained several distinctive features not found in other
      published Sedimenticola genomes, including a complete nitrogen fixation pathway,
      a complete ethanolamine degradation pathway, and an alkane-1-monooxygenase.
AU  - Flood BE
AU  - Jones DS
AU  - Bailey JV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00671-15.

PMID- 29773637
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Celeribacter baekdonensis Strain LH4, a Thiosulfate-Oxidizing Alphaproteobacterial Isolate from Gulf of Mexico  Continental Slope Sediments.
PG  - e00434-18
AB  - We report here the closed genome sequences of Celeribacter baekdonensis strain LH4 and five
      unnamed plasmids obtained through PacBio sequencing with 99.99%
      consensus concordance. The genomes contained several distinctive features not
      found in other published Celeribacter genomes, including the potential to
      aerobically degrade styrene and other phenolic compounds.
AU  - Flood BE
AU  - Leprich D
AU  - Bailey JV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00434-18.

PMID- 25941374
VI  - 112
DP  - 2015
TI  - Sequence type 1 group B Streptococcus, an emerging cause of invasive disease in adults, evolves by small genetic changes.
PG  - 6431-6436
AB  - The molecular mechanisms underlying pathogen emergence in humans is a critical
      but poorly understood area of microbiologic investigation. Serotype V group B
      Streptococcus (GBS) was first isolated from humans in 1975, and rates of invasive
      serotype V GBS disease significantly increased starting in the early 1990s. We
      found that 210 of 229 serotype V GBS strains (92%) isolated from the bloodstream
      of nonpregnant adults in the United States and Canada between 1992 and 2013 were
      multilocus sequence type (ST) 1. Elucidation of the complete genome of a 1992
      ST-1 strain revealed that this strain had the highest homology with a GBS strain
      causing cow mastitis and that the 1992 ST-1 strain differed from serotype V
      strains isolated in the late 1970s by acquisition of cell surface proteins and
      antimicrobial resistance determinants. Whole-genome comparison of 202 invasive
      ST-1 strains detected significant recombination in only eight strains. The
      remaining 194 strains differed by an average of 97 SNPs. Phylogenetic analysis
      revealed a temporally dependent mode of genetic diversification consistent with
      the emergence in the 1990s of ST-1 GBS as major agents of human disease.
      Thirty-one loci were identified as being under positive selective pressure, and
      mutations at loci encoding polysaccharide capsule production proteins, regulators
      of pilus expression, and two-component gene regulatory systems were shown to
      affect the bacterial phenotype. These data reveal that phenotypic diversity among
      ST-1 GBS is mainly driven by small genetic changes rather than extensive
      recombination, thereby extending knowledge into how pathogens adapt to humans.
AU  - Flores AR et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2015 112: 6431-6436.

PMID- 7607511
VI  - 157
DP  - 1995
TI  - Saturation mutagenesis of His114 of EcoRI reveals relaxed-specificity mutants.
PG  - 295-301
AB  - EcoRI recognizes and cleaves DNA at GAATTC sites and is one of the best characterized
      sequence-specific restriction endonucleases (ENases).  In previous studies, an EcoRI mutant,
      which exhibited relaxed substrate specificity and cleaved both canonical and EcoRI star sites,
      was isolated.  This mutant enzyme has Tyr instead of His114.  Here, we subjected residue 114
      of the EcoRI ENase to saturation mutagenesis.  The resulting mutant enzymes were characterized
      both in vivo and in vitro, resulting in the identification of mutants with canonical (H114K,
      Q, D, I) or relaxed (H114Y, F, S, T) specificity, as well as one mutant with severely impaired
      activity (H114P).  In the X-ray structure of an EcoRI-substrate complex, His 114 is located
      between the catalytic and recognition regions of EcoRI and may directly contact the DNA
      phosphate backbone.  Based on our genetic and biochemical findings and the X-ray structure, we
      propose that His114 participates in substrate recognition and catalysis, either directly, via
      protein-DNA interactions, or indirectly, by mediating conformational changes that trigger DNA
      cleavage in response to substrate recognition.
AU  - Flores H
AU  - Osuna J
AU  - Heitman J
AU  - Soberon X
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 295-301.

PMID- 22300630
VI  - 99
DP  - 2012
TI  - Comparative genomic analysis of two brucellaphages of distant origins.
PG  - 233-240
AB  - Here, we present the first complete genome sequence of brucellaphage Tbilisi (Tb)
      and compared it with that of Pr, a broad host-range brucellaphage recently
      isolated in Mexico. The genomes consist of 41,148bp (Tb) and 38,253bp (Pr), they
      differ mainly in the region encoding structural proteins, in which the genome of
      Tb shows two major insertions. Both genomes share 99.87% nucleotide identity, a
      high percentage of identity among phages isolated at so globally distant
      locations and temporally different occasions. Sequence analysis revealed 57
      conserved ORFs, three transcriptional terminators and four putative
      transcriptional promoters. The co-occurrence of an ORF encoding a putative
      DnaA-like protein and a putative oriC-like origin of replication was found in
      both brucellaphages genomes, a feature not described in any other phage genome.
      These elements suggest that DNA replication in brucellaphages differs from other
      phages, and might resemble that of bacterial chromosomes.
AU  - Flores V
AU  - Lopez-Merino A
AU  - Mendoza-Hernandez G
AU  - Guarneros G
PT  - Journal Article
TA  - Genomics
JT  - Genomics
SO  - Genomics 2012 99: 233-240.

PMID- 22933752
VI  - 194
DP  - 2012
TI  - Genome Sequence of Lactococcus garvieae IPLA 31405, a Bacteriocin-Producing, Tetracycline-Resistant Strain Isolated from a Raw-Milk Cheese.
PG  - 5118-5119
AB  - This work describes the draft genome sequence of Lactococcus garvieae IPLA 31405, isolated
      from a traditional Spanish cheese. The genome contains a
      lactose-galactose operon, a bacteriocin locus, two integrated phages, a
      transposon harboring an active tet(M) gene, and two theta-type plasmid replicons.
      Genes encoding virulence factors were not recorded.
AU  - Florez AB
AU  - Reimundo P
AU  - Delgado S
AU  - Fernandez E
AU  - Alegria A
AU  - Guijarro JA
AU  - Mayo B
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5118-5119.

PMID- 29659807
VI  - 10
DP  - 2018
TI  - The Genome Sequence of 'Candidatus Fokinia solitaria': Insights on Reductive Evolution in Rickettsiales.
PG  - 1120-1126
AB  - "Candidatus Fokinia solitaria" is an obligate intracellular endosymbiont of a
      unicellular eukaryote, a ciliate of the genus Paramecium. Here, we present the
      genome sequence of this bacterium and subsequent analysis. Phylogenomic analysis
      confirmed the previously reported positioning of the symbiont within the
      "Candidatus Midichloriaceae" family (order Rickettsiales), as well as its high
      sequence divergence from other members of the family, indicative of fast sequence
      evolution. Consistently with this high evolutionary rate, a comparative genomic
      analysis revealed that the genome of this symbiont is the smallest of the
      Rickettsiales to date. The reduced genome does not present flagellar genes, nor
      the pathway for the biosynthesis of lipopolysaccharides (present in all the other
      so far sequenced members of the family "Candidatus Midichloriaceae") or genes for
      the Krebs cycle (present, although not always complete, in Rickettsiales). These
      results indicate an evolutionary trend toward a stronger dependence on the host,
      in comparison with other members of the family. Two alternative scenarios are
      compatible with our results; "Candidatus Fokinia solitaria" could be either a
      recently evolved, vertically transmitted mutualist, or a parasite with a high
      host-specificity.
AU  - Floriano AM
AU  - Castelli M
AU  - Krenek S
AU  - Berendonk TU
AU  - Bazzocchi C
AU  - Petroni G
AU  - Sassera D
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2018 10: 1120-1126.

PMID- 27979949
VI  - 4
DP  - 2016
TI  - Genome Sequence of the Poly-3-Hydroxybutyrate Producer Clostridium acetireducens  DSM 10703.
PG  - e01399-16
AB  - Here, we report the genome sequence of Clostridium acetireducens (DSM 10703T), a  strictly
      anaerobic bacterium capable of fermenting acetate and leucine to
      butyrate, isovalerate, and poly-3-hydroxybutyrate. The draft genome consists of a
      circular chromosome with a size of 2.4 Mb and harbors 2,239 predicted
      protein-encoding genes.
AU  - Fluchter S
AU  - Poehlein A
AU  - Schiel-Bengelsdorf B
AU  - Daniel R
AU  - Durre P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01399-16.

PMID- 20453866
VI  - 7
DP  - 2010
TI  - Direct detection of DNA methylation during single-molecule, real-time sequencing.
PG  - 461-465
AB  - We describe the direct detection of DNA methylation, without bisulfite conversion, through
      single-molecule, real-time (SMRT) sequencing. In SMRT sequencing, DNA polymerases catalyze the
      incorporation of fluorescently labeled nucleotides into complementary nucleic acid strands.
      The arrival times and durations of the resulting fluorescence pulses yield information about
      polymerase kinetics and allow direct detection of modified nucleotides in the DNA template,
      including N6-methyladenine, 5-methylcytosine and 5-hydroxymethylcytosine.  Measurement of
      polymerase kinetics is an intrinsic part of SMRT sequencing and does not adversely affect
      determination of primary DNA sequence. The various modifications affect polymerase kinetics
      differently, allowing discrimination between them. We used these kinetic signatures to
      identify adenine methylation in genomic samples and found that, in combination with circular
      consensus
      sequencing, they can enable single-molecule identification of epigenetic
      modifications with base-pair resolution. This method is amenable to long read
      lengths and will likely enable mapping of methylation patterns in even highly
      repetitive genomic regions.
AU  - Flusberg BA
AU  - Webster DR
AU  - Lee JH
AU  - Travers KJ
AU  - Olivares EC
AU  - Clark TA
AU  - Korlach J
AU  - Turner SW
PT  - Journal Article
TA  - Nat. Methods
JT  - Nat. Methods
SO  - Nat. Methods 2010 7: 461-465.

PMID- Not carried by PubMed...
VI  - 58
DP  - 1998
TI  - Murine DNA cytosine C-5 methyltransferase: Insights into epigenetic control. from enzymological studies.
PG  - 3614B
AB  - The processes that contribute to mammalian development are numerous.  Genomic methylation
      patterns change dynamically with each differentiating cell division.  The enzyme responsible
      for DNA methylation is essential for normal development.  A precise functional description is
      catalysis and epigenesis. A rigorous DNA binding assay defined how sequences flanking CpG
      dideoxynucleotides affect the stability of the enzyme:DNA complex.  Oligonucleotides form
      reversible 1:1 complexes with the enzyme sequence-specifically.  A guanine/cytosine-rich
      sequence that mimics the GC-box boundthree-fold more tightly than the adenine/thymine rich
      cyclic AMP responsive element.  Binding discrimination between hemi- and unmethylated forms
      was small and single-stranded substrates bound more weakly than double-stranded DNA.  An in
      vitro screening method selected for CpG flanking sequence preferences from a large, divergent
      population.  After five iterative rounds of increasing selective pressure,
      guanosine/cytosine-rich sequences were abundant.  The enzyme uses sequence-dependent
      conformational features over two helical turns for discrimination, rather than specific base
      interactions.  The constants KmDNA, kcat, and kmethylation were determined.  The rate limiting
      step for most substrates was the methylation step itself.  Contrastingly, hemimethylated
      substrates exhibited burst kinetics, consistent with a rapid methylation event followed by a
      slower step which determines kcat.  Large substrates with multiple recognition sites do not
      show burst kinetics and have turnover constants of 30 hr-1.  Maintenance of genomic
      methylation patterns is preferred over de novo establishment of new patterns.  Four types of
      steady-state analyses were used to identify the order of substrate addition and product
      release.  Steady-state initial velocity studies including product and dead-end inhibition
      studies support an ordered Bi-Bi kinetic model in which DNA binds first, followed by
      S-adenosyl methionine and then release of S-adenosyl homocysteine.
AU  - Flynn J
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1998 58: 3614B.

PMID- 9636703
VI  - 279
DP  - 1998
TI  - DNA binding discrimination of the murine DNA cytosine-C5 methyltransferase.
PG  - 101-116
AB  - Mammalian DNA cytosine-C5 methyltransferase modifies the CpG dinucleotide in the context of
      many different genomic sequences.  A rigorous DNA binding assay was developed for the murine
      enzyme and used to define how sequences flanking the CpG dinucleotide affect the stability of
      the enzyme:DNA complex.  Oligonucleotides containing a single CpG site form reversible 1:1
      complexes with the enzyme that are sequence-specific.  A guanine/cytosine-rich 30 base-pair
      sequence, a mimic of the GC-box cis-element, bound threefold more tightly than an
      adenine/thymine-rich sequence, a mimic of the cyclic AMP responsive element.  However, the
      binding discrimination between hemi- and unmethylated forms of these DNA substrates was small,
      as we previously observed at the KmDNA level.  Single-stranded substrates are bound much more
      weakly than double-stranded DNA forms.  An in vitro screening method was used to select for
      CpG flanking sequence preferences of the DNA methyltransferase from a large, divergent
      population of DNA substrates.  After five interactive rounds of increasing selective pressure,
      guanosine/cytosine-rich sequences were abundant and contributed to binding stabilization for
      at least 12 base-pairs on either side of a central CpG.  Our results suggest a read-out of
      sequence-dependent conformational features, such as helical flexibility, minor groove
      dimensions and critical phosphate orientation and mobility, rather than interactions with
      specific bases over the course of two complete helical turns.  Thus, both studies reveal a
      preference for guanosine/cytosine deoxynucleotides flanking the cognate CpG.  The enzyme
      specificity for similar sequences in the genome may contribute to the in vivo functions of
      this vital enzyme.
AU  - Flynn J
AU  - Azzam R
AU  - Reich N
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1998 279: 101-116.

PMID- 12477724
VI  - 278
DP  - 2003
TI  - A potent cell-active allosteric inhibitor of murine DNA cytosine C5 methyltransferase.
PG  - 8238-8243
AB  - The major DNA cytosine methyltransferase isoform in mouse erythroleukemia cells, Dnmt1,
      exhibits potent dead-end inhibition with a single-stranded
      nucleic acid by binding to an allosteric site on the enzyme. The
      previously reported substrate inhibition with double-stranded substrates
      also involves binding to an allosteric site. Thus, both forms of
      inhibition involve ternary enzyme-DNA-DNA complexes. The inhibition
      potency of the single-stranded nucleic acid is determined by the sequence,
      length, and most appreciably the presence of a single 5-methylcytosine
      residue. A single-stranded phosphorothioate derivative inhibits DNA
      methylation activity in nuclear extracts. Mouse erythroleukemia cells
      treated with the phosphorothioate inhibitor show a significant decrease in
      global genomic methylation levels. Inhibitor treatment of human colon
      cancer cells causes demethylation of the p16 tumor suppressor gene and
      subsequent p16 re-expression. Allosteric inhibitors of mammalian DNA
      cytosine methyltransferases, representing a new class of molecules with
      potential therapeutic applications, may be used to elucidate novel
      epigenetic mechanisms that control development.
AU  - Flynn J
AU  - Fang JY
AU  - Mikovits JA
AU  - Reich NO
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2003 278: 8238-8243.

PMID- 8652507
VI  - 35
DP  - 1996
TI  - Murine DNA cytosine-C5 methyltransferase: pre-steady- and steady-state kinetic analysis with regulatory DNA sequences.
PG  - 7308-7315
AB  - We present the first description of KmDNA, KdDNA, kcat, and kmethylation for a mammalian DNA
      methyltransferase.  Homogeneous, 190 000 MrDNA (cytosine-5-)-methyltransferase isolated from
      mouse erythroleukemia cells has turnover constants of 0.15-0.59 h-1 with single-stranded and
      unmethylated double-stranded oligonucleotides containing a single CpG dinucleotide.  These
      substrates were designed to mimic DNA transcriptional cis elements previously reported to have
      cytosine C-5-methylated regulation.  The rate-limiting step for these substrates is the
      methylation step itself.  In contrast, hemimethylated double-stranded substrates show burst
      kinetics, consistent with a rapid methylation event (3 h-1) followed by a slower step which
      determines steady-state kcat.  Hemimethylated and unmethylated double-stranded DNA shows
      similar binding affinities; these results reveal the molecular basis for the enzyme's
      preference for hemimethylated DNA to be the methyl transfer step.  Substrates with multiple
      recognition sites do not show burst kinetics and have turnover rate constants of 6 h-1.
      Catalytic turnover for the mammalian enzyme is thus approximately 10-fold slower than that for
      the related bacterial enzymes.  Our combined results show quantitatively that one enzyme is
      certainly capable of both maintenance and de novo methylation and that maintenance of the
      genomic methylation pattern is preferred over the de novo establishment of new patterns.
      Direct comparison of the mammalian enzyme with the bacterial DNA cytosine-C5
      methyltransferase, M.SssI, indicates dramatic differences in preferences for single-stranded,
      double-stranded, and hemimethylated double-stranded substrates.  Moreover, the specificity
      hierarchy shown for the M.SssI is derived from very different changes in Km and catalysis than
      those observed for the mammalian DCMTase.  These results demonstrate that the M.SssI, and
      perhaps other DNA cytosine methyltransferases from bacteria, is functionally dissimilar to the
      mammalian enzyme.
AU  - Flynn J
AU  - Glickman JF
AU  - Reich NO
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1996 35: 7308-7315.

PMID- 9790680
VI  - 37
DP  - 1998
TI  - Murine DNA (cytosine-5-)-methyltransferase: Steady-state and substrate trapping analyses of the kinetic mechanism.
PG  - 15162-15169
AB  - DNA (cytosine-5-)-methyltransferase is essential for viable mammalian development and has a
      central function in the determination and maintenance of epigenetic methylation patterns.
      Steady-state and substrate trapping studies were performed to better understand how the enzyme
      functions.  The catalytic efficiency was dependent on substrate DNA length.  A 14-fold
      increase in KmDNA was observed as the length decreased from 5000 to 100 base pairs and kcat
      decreased by a third.  Steady-state analyses were used to identify the order of substrate
      addition onto the enzyme and the order of product release.  Double-reciprocal patterns of
      velocity versus substrate concentration intersected far from the origin and were nearly
      parallel.  The kinetic mechanism does not appear to change when the DNA substrate is either
      6250 or 100 base pairs in length.  Isotope trapping studies showed that the initial enzyme -
      AdoMet complex was not catalytically competent; however, the initial enzyme-poly(dI.dC-dI.dC)
      complex was observed to be competent for catalysis.  Product inhibition studies also support a
      sequential ordered bi-bi kinetic mechanism in which DNA binds to the enzyme first, followed by
      S-adenosyl-L-methionine, and then the products S-adenosyl-L-homocysteine and methylated DNA
      are released.  The proposed mechanism is similar to the mechanism proposed for M.HhaI, a
      bacterial DNA (cytosine-5-)-methyltransferase.  Evidence for an enzyme - DNA-DNA ternary
      complex is also presented.
AU  - Flynn J
AU  - Reich N
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1998 37: 15162-15169.

PMID- 8467964
VI  - 7
DP  - 1993
TI  - Identification of flanking sequence dependence of DNA recognition for mammalian DNA cytosine methyltransferase.
PG  - A1219
AB  - Mammalian DNA cytosine 5-methyltransferase (DNA Mtase) is a DNA modification enzyme which has
      been implicated to have an important role in gene regulation. Cytosines in the context of the
      dinucleotide CpG are differentially methylated in the different tissue types of higher
      eukaryotes. The pattern of methylation throughout the genome is believed to be heritable and
      important for the development of differentiated cell types. The aim of our studies are to
      answer to what extent sequences flanking a CpG determine the binding and catalytic activity of
      DNA Mtase. Our procedure uses a random population of oligonucleotide substrates which contain
      a central CpG dinucleotide flanked by 12 base pair degenerate regions on each side. The
      degenerate regions have been made such that no additional CpG's can be introduced into the
      oligos and contain equivalent proportions of all permutations. Partially purified enzyme was
      used to create ternary complexes with cofactors and 32P end labeled DNA. Complexes using the
      cofactors S-Adenosyl methionine, S-adenosyl homocysteine or sinefungin were shown to mobility
      shift the double stranded DNA in polyacrylamide gels. The addition of DNA Mtase specific
      antibodies to the reaction supershifts the DNA to a less mobile complex. The shifted DNA was
      isolated and amplified by the polymerase chain reaction. When subjecting this DNA to further
      rounds of selection preferential DNA flanking sequences survive. Through this application of
      in vitro genetics CpG flanking sequence dependencies are being resolved.
AU  - Flynn J
AU  - Reich NO
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1993 7: A1219.

PMID- 26798114
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Gammaproteobacterial Methanotrophs Isolated from Marine Ecosystems.
PG  - e01629-15
AB  - The genome sequences of Methylobacter marinus A45, Methylobacter sp. strain BBA5.1, and
      Methylomarinum vadi IT-4 were obtained. These aerobic methanotrophs
      are typical members of coastal and hydrothermal vent marine ecosystems.
AU  - Flynn JD et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01629-15.

PMID- 2116348
VI  - 69
DP  - 1990
TI  - Isolation and characterization of two sequence-specific endonucleases from the cyanobacterium Synechocystis sp. PCC 6308.
PG  - 105-108
AB  - The first two restriction endonucleases to be characterized in the cyanobacterium
      Synechocystis sp. PCC 6308 are described.  SynI, an AvaII isoschizomer, recognizes the base
      sequence 5'-GG[AT]CC-3'.  SynII, an XmnI isoschizomer, recognizes the sequence
      5'-GAANNNNTTC-3'.
AU  - Foerg E
AU  - Saporito L
AU  - Huang S
AU  - Yang J
AU  - Allen MM
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1990 69: 105-108.

PMID- 28505234
VI  - 65
DP  - 2017
TI  - Increased Risk for Meningococcal Disease Among Men Who Have Sex With Men in the United States, 2012-2015.
PG  - 756-763
AB  - Background: Several clusters of serogroup C meningococcal disease among men who
      have sex with men (MSM) have been reported in the United States in recent years.
      The epidemiology and risk of meningococcal disease among MSM is not well
      described. Methods: All meningococcal disease cases among men aged 18-64 years
      reported to the National Notifiable Disease Surveillance System between January
      2012 and June 2015 were reviewed. Characteristics of meningococcal disease cases
      among MSM and men not known to be MSM (non-MSM) were described. Annualized
      incidence rates among MSM and non-MSM were compared through calculation of the
      relative risk and 95% confidence intervals. Isolates from meningococcal disease
      cases among MSM were characterized using standard microbiological methods and
      whole-genome sequencing. Results: Seventy-four cases of meningococcal disease
      were reported among MSM and 453 among non-MSM. Annualized incidence of
      meningococcal disease among MSM was 0.56 cases per 100000 population, compared to
      0.14 among non-MSM, for a relative risk of 4.0 (95% confidence interval [CI],
      3.1-5.1). Among the 64 MSM with known status, 38 (59%) were infected with human
      immunodeficiency virus (HIV). HIV-infected MSM had 10.1 times (95% CI, 6.1-16.6)
      the risk of HIV-uninfected MSM. All isolates from cluster-associated cases were
      serogroup C sequence type 11. Conclusions: MSM are at increased risk for
      meningococcal disease, although the incidence of disease remains low. HIV
      infection may be an important factor for this increased risk. Routine vaccination
      of HIV-infected persons with a quadrivalent meningococcal conjugate vaccine in
      accordance with Advisory Committee on Immunization Practices recommendations
      should be encouraged.
AU  - Folaranmi TA et al
PT  - Journal Article
TA  - Clin. Infect. Dis.
JT  - Clin. Infect. Dis.
SO  - Clin. Infect. Dis. 2017 65: 756-763.

PMID- 10623722
VI  - 74
DP  - 2000
TI  - Widespread distribution of a group I intron and its three deletion derivatives in the lysin gene of streptococcus thermophilus bacteriophages.
PG  - 611-618
AB  - Of 62 Streptococcus thermophilus bacteriophages isolated from various ecological settings,
      half contain a lysin gene interrupted by a group IA2 intron. Phage mRNA splicing was
      demonstrated. Five phages possess a variant form of the intron resulting from three distinct
      deletion events located in the intron-harbored open reading frame (orf 253). The predicted orf
      253 gene sequence showed a significantly lower GC content than the surrounding intron and
      lysin gene sequences, and the predicted protein shared a motif with endonucleases found in
      phages from both gram-positive and gram-negative bacteria. A comparison of the phage lysin
      genes revealed a clear division between intron-containing and intron-free alleles, leading to
      the establishment of a 14-bp consensus sequence associated with intron possession. The
      conserved intron was not found elsewhere in the phage or S. thermophilus bacterial genomes.
      Folding of the intron RNA revealed secondary structure elements shared with other phage
      introns: first, a 38-bp insertion between regions P3 and P4 that can be folded into two
      stem-loop structures (shared with introns from Bacillus phage SPO1 and relatives); second, a
      conserved P7.2 region (shared with all phage introns); third, the location of the stop codon
      from orf 253 in the P8 stem (shared with coliphage T4 and Bacillus phage SPO1 introns);
      fourth, orf 253, which has sequence similarity with the H-N-H motif of putative endonuclease
      genes found in introns from Lactococcus, Lactobacillus, and Bacillus phages.
AU  - Foley S
AU  - Bruttin A
AU  - Brussow H
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 2000 74: 611-618.

PMID- Not carried by PubMed...
VI  - 0
DP  - 1990
TI  - Biosynthesis and distribution of methylcytosine in wheat DNA.  How different are plant DNA methyltransferases?
PG  - 199-210
AB  - One reason for the high methylcytosine content of plant DNA may lie in the
      specificity and activity of plant DNA methyltransferases.  We have analyzed the
      properties of the DNA methylase system previously purified from wheat embryo
      and find that it differs markedly enough from the known mammalian enzymes to
      establish a plant-specific type of DNA methyltransferase.  These differences
      reside, inter alia, in molecular weight, specificity towards DNA substrates of
      varying methylation, and insensitivity towards inhibition by 5-azacytidine.
AU  - Follman H
AU  - Balzer H-J
AU  - Schleicher R
PT  - Journal Article
TA  - Nucleic Acid Methylation
JT  - Nucleic Acid Methylation
SO  - Nucleic Acid Methylation 1990 0: 199-210.

PMID- 28302790
VI  - 5
DP  - 2017
TI  - Complete Genome and Methylome Analysis of Psychrotrophic Bacterial Isolates from  Lake Untersee in Antarctica.
PG  - e01753-16
AB  - This paper describes the complete genome sequences and methylome analysis of six
      psychrotrophic strains isolated from perennially ice-covered Lake Untersee in
      Antarctica.
AU  - Fomenkov A
AU  - Akimov VN
AU  - Vasilyeva LV
AU  - Andersen DT
AU  - Vincze T
AU  - Roberts RJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01753-16.

PMID- 
VI  - 280
DP  - 2013
TI  - Molecular dissection of the methylome of Burkholderia cenocepacia J2315.
PG  - 72-73
AB  - B. cenocepacia is a pathogenic gram-negative bacterium that often causes an opportunistic
      infection in cystic fibrosis patients.  It is highly antibiotic-resistant, transmissible, and
      often lethal.  Although genome sequences of several strains are available, the study of this
      organism, like many pathogens, has been relatively limited, and genetic study is difficult.
      The aim of this work was to analyze the genomic DNA methylation patterns from the sequenced
      strain, J2315, and identify specificities of putative DNA methyltransferases.  This might
      facilitate the development of an efficient transformation system to enhance genetic studies of
      this strain.  We took advantage of the recently developed platform for single-molecule real
      time sequencing by Pacific Biosciences.  This next generation sequencing technology allowed us
      not only to perform high throughput DNA sequencing, but also to identify the epigenetic status
      of the DNA using the polymerase's kinetic signature on the template during the reaction.  The
      kinetic signature analysis of B. cenocepacia J2315 genomic DNA revealed three modified motifs.
      Additionally, a number of ORF's encoding putative DNA methyltransferases were cloned into
      plasmid vectors, and their specificities were determined using SMRT sequecing.  A type III
      restriction-modificaiton system called M.BceJI resulted in m6A modification in the recognition
      sequence CA-CAG.  98.4% of all CACAG sequences in the genome were modified on just one strand
      as indicated, which is typical of a Type III methyltransferase.  Cloning ORF BCAL3494 showed
      it to be the gene responsible.  The genomic motif GTWWAC, containing a symmetrical
      double-stranded m6A modification, was 95.7% modified in the genome and was caused by the
      product of ORF BCAL992 and was called M.BceJIV.  Another modified motif with m4C modification
      was detected at the low rate of 4.8% within the eight base pair motif GCGGCCGC.  This was
      probably caused by the product of ORF BCAL1036, although when this was cloned and expressed at
      high levels the central tetranucleotide GGCC was m4C modified at high levels.  We called this
      methyltransferase M.BceJII.  Surprisingly, we also detected an unusual kinetic signature on
      the G base that is also associated with the four base core of the GCGGCCGC motif.  We still do
      not know which enzyme is responsible for this G modification.  Preliminary results suggest
      that M.BceJORF178P might also lead to G modification on the first base in the sequence GGNNTA
      albeit with a low IPD ratio in vitro.  This enzyme is highly toxic in E. coli, which has so
      far made a determination of its specificity very difficult.  One rather interesting
      methyltransferase is encoded by ORF pBCA072, which is located on a plasmid.  It results in
      single-stranded, non-specific m6A modification, but was only detected on plasmid DNA.  We have
      called this enzyme M.BceJIII.  A similar enzyme has been found on an E. coli plasmid and both
      could possibly play a restricted role during DNA replication.  The M and S subunits of a
      putative Type I restriction-modification system BceJORF418P have been cloned, but no
      modifications were detected either on genomic or plasmid DNA indicating that the system is
      probably inactive in this strain.
AU  - Fomenkov A
AU  - Clark T
AU  - Spittle K
AU  - Anton BM
AU  - Vincze T
AU  - Korlach J
AU  - Roberts RJ
PT  - Journal Article
TA  - FEBS J.
JT  - FEBS J.
SO  - FEBS J. 2013 280: 72-73.

PMID- 25700417
VI  - 3
DP  - 2015
TI  - Complete genome sequence and methylome analysis of Bacillus strain X1.
PG  - e01593-14
AB  - Bacillus strain X1 is the source strain for the restriction enzyme BstXI. Its complete
      sequence and full methylome was determined using single-molecule real-time (SMRT) sequencing.
AU  - Fomenkov A
AU  - Lunnen KD
AU  - Zhu Z
AU  - Anton BP
AU  - Wilson GG
AU  - Vincze T
AU  - Roberts RJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01593-14.

PMID- 28654677
VI  - 12
DP  - 2017
TI  - EcoBLMcrX, a classical modification-dependent restriction enzyme in Escherichia coli B: Characterization in vivo and in vitro with a new approach to cleavage  site determination.
PG  - e0179853
AB  - Here we characterize the modification-dependent restriction enzyme (MDE) EcoBLMcrX in vivo, in
      vitro and in its genomic environment. MDE cleavage of
      modified DNAs protects prokaryote populations from lethal infection by
      bacteriophage with highly modified DNA, and also stabilizes lineages by reducing
      gene import when sparse modification occurs in the wrong context. The function
      and distribution of MDE families are thus important. Here we describe the
      properties of EcoBLMcrX, an enzyme of the E. coli B lineage, in vivo and in
      vitro. Restriction in vivo and the genome location of its gene, ecoBLmcrX, were
      determined during construction and sequencing of a B/K-12 hybrid, ER2566. In
      classical restriction literature, this B system was named r6 or rglAB. Like many
      genome defense functions, ecoBLmcrX is found within a genomic island, where gene
      content is variable among natural E. coli isolates. In vitro, EcoBLMcrX was
      compared with two related enzymes, BceYI and NhoI. All three degrade fully
      cytosine-modified phage DNA, as expected for EcoBLMcrX from classical T4 genetic
      data. A new method of characterizing MDE specificity was developed to better
      understand action on fully-modified targets such as the phage that provide major
      evolutionary pressure for MDE maintenance. These enzymes also cleave plasmids
      with m5C in particular motifs, consistent with a role in lineage-stabilization.
      The recognition sites were characterized using a site-ranking approach that
      allows visualization of preferred cleavage sites when fully-modified substrates
      are digested. A technical constraint on the method is that ligation of
      one-nucleotide 5' extensions favors G:C over A:T approximately five-fold. Taking
      this bias into account, we conclude that EcoBLMcrX can cleave 3' to the modified
      base in the motif Rm5C|. This is compatible with, but less specific than, the
      site reported by others. Highly-modified site contexts, such as those found in
      base-substituted virulent phages, are strongly preferred.
AU  - Fomenkov A
AU  - Sun Z
AU  - Dila DK
AU  - Anton BP
AU  - Roberts RJ
AU  - Raleigh EA
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2017 12: e0179853.

PMID- 29700149
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of the Freshwater Bacterium Beggiatoa leptomitoformis Strain D-401.
PG  - e00311-18
AB  - Here, we report the complete closed genome sequence and methylome analysis of Beggiatoa
      leptomitoformis strain D-401 (DSM 14945, UNIQEMU 779), which is quite
      different from the previously described Beggiatoa leptomitoformis neotype strain
      D-402(T) (DSM 14946, UNIQEM U 779) with regard to morphology and lithotrophic
      growth in the presence of thiosulfate.
AU  - Fomenkov A
AU  - Sun Z
AU  - Vincze T
AU  - Dubinina G
AU  - Orlova M
AU  - Tarlachkov SV
AU  - Anton BP
AU  - Grabovich MY
AU  - Roberts RJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00311-18.

PMID- 28336599
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence and Methylome Analysis of Acinetobacter calcoaceticus 65.
PG  - e00060-17
AB  - Acinetobacter calcoaceticus 65 is the original source strain for the restriction  enzyme
      Acc65I. Its complete sequence and full methylome were determined using
      single-molecule real-time (SMRT) sequencing.
AU  - Fomenkov A
AU  - Vincze T
AU  - Degtyarev SK
AU  - Roberts RJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00060-17.

PMID- 26744373
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of a Strain of Azospirillum thiophilum Isolated from a Sulfide Spring.
PG  - e01521-15
AB  - We report the complete, closed genome sequence and complete methylome of Azospirillum
      thiophilum strain BV-S(T).
AU  - Fomenkov A
AU  - Vincze T
AU  - Grabovich M
AU  - Anton BP
AU  - Dubinina G
AU  - Orlova M
AU  - Belousova E
AU  - Roberts RJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01521-15.

PMID- 26659680
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of the Freshwater Colorless Sulfur Bacterium Beggiatoa leptomitiformis Neotype Strain D-402T.
PG  - e01436-15
AB  - In this report, we announce the availability of a complete closed genome sequence and
      methylome analysis of Beggiatoa leptomitiformis neotype strain D-402(T) (DSM
      14946, UNIQEM U 779).
AU  - Fomenkov A
AU  - Vincze T
AU  - Grabovich MY
AU  - Dubinina G
AU  - Orlova M
AU  - Belousova E
AU  - Roberts RJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01436-15.

PMID- 28860255
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequence and Methylome Analysis of the Freshwater Colorless Sulfur Bacterium Thioflexothrix psekupsii D3.
PG  - e00904-17
AB  - In this report, we announce the availability of a whole-genome sequence and methylome analysis
      of Thioflexothrix psekupsii strain D3.
AU  - Fomenkov A
AU  - Vincze T
AU  - Grabovich MY
AU  - Dubinina G
AU  - Orlova M
AU  - Belousova E
AU  - Roberts RJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00904-17.

PMID- 29439055
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence and Methylome Analysis of Bacillus caldolyticus NEB414.
PG  - e01605-17
AB  - Bacillus caldolyticus NEB414 is the original source strain for the restriction enzyme BclI.
      Its complete sequence and full methylome were determined using
      single-molecule real-time sequencing.
AU  - Fomenkov A
AU  - Vincze T
AU  - Mersha F
AU  - Roberts RJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01605-17.

PMID- 8036170
VI  - 22
DP  - 1994
TI  - The 'endo-blue method' for direct cloning of restriction endonuclease genes in E. coli.
PG  - 2399-2403
AB  - A new E. coli strain has been constructed that contains the dinD1::LacZ+ fusion and is
      deficient in methylation-dependent restriction systems (McrA-, McrBC-, Mrr-). This strain has
      been used to clone restriction endonuclease genes directly into E. coli. When E. coli cells
      are not fully protected by the cognate methylase, the restriction enzyme damages the DNA in
      vivo and induces the SOS response. The SOS-induced cells form blue colonies on indicator
      plates containing X-gal. Using this method the genes coding for the thermostable restriction
      enzymes TaqI (5'TCGA3') and Tth111I (5'GACNNNGTC3') have been successfully cloned in E.
      coli. The new strain will be useful to clone other genes involved in DNA metabolism.
AU  - Fomenkov A
AU  - Xiao J-P
AU  - Dila D
AU  - Raleigh E
AU  - Xu S-Y
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1994 22: 2399-2403.

PMID- 7607513
VI  - 157
DP  - 1995
TI  - Isolation of temperature-sensitive mutants of the BamHI restriction endonuclease.
PG  - 303-310
AB  - Two heat-sensitive R.BamHI mutants, T157I and P173L, and one cold-sensitive R.BamHI mutant,
      T114I, were isolated after chemical mutagenesis of the bamhIR gene that codes for the
      restriction endonuclease BamHI (R.BamHI).  The thermosensitivity of T114I, T157I and P173L is
      revealed by the 10/2-10/3 lower plating efficiency at the non-permissive temperature of
      strains bearing these alleles.  The conditional-lethal phenotype can be rescued by
      introduction of the cognate bamhIM gene into the same cell.  The mutant enzymes induce the SOS
      response in vivo and display reduced phage restriction activity.  The P173L protein, when
      expressed at 30oC and purified, shows reduced thermostability at 65oC.  T157I and P173L
      mutants yield different intermediates during partial trypsin digestion.  The
      conditional-lethal BamHI mutants could be used to deliver in vivo DNA cleavage and for further
      isolation of relaxed-specificity mutants.
AU  - Fomenkov A
AU  - Xu S-Y
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 303-310.

PMID- 3143102
VI  - 16
DP  - 1988
TI  - Isolation and properties of a new site specific endonuclease Bme142I from Bacillus megaterium 142.
PG  - 10399
AB  - A new type II restriction endonuclease, Bme142I, was partially purified and characterized from
      Bacillus megaterium 142.  It has been seen in a crude extract, because this bacterial strain
      does not have significant amounts of contaminating nucleases.  The enzyme was purified by
      chromatography on phosphocellulose P11 (elution buffer - 10 mM K-phosphate, pH 7.0, 0.1 mM
      EDTA, 2 mM DTT, 0.2 - 1 M NaCl) and hydroxyapatite (elution buffer - 0.01 - 0.5 M K-phosphate,
      pH 7.0, 1 mM EDTA, 2 mM DTT).  Yield of enzyme is 2000 units per gram of wet cells.  The
      enzyme is stable in elution buffer and may be stored at -20C after addition of glycerol to
      50%.  The recognition site was determined from the cleavage pattern of pBR322 plasmid.  The
      5'-end nucleotide is G.  This has been shown by incubation of the 5'-end labelled DNA
      fragments with nuclease P1 followed by thin-layer chromatography on a PEI cellulose plate.
      The points of cleavage of the recognition site were determined by the Maxam-Gilbert method.
      In contrast to its isoschizomer, the restriction endonuclease HaeII, which cleaves the same
      recognition site to produce a 4 base 3' extension, the Bme142I produces blunt-ended DNA
      fragments:
      5' PuGC^GCPy 3'
      3' PyCG^CGPu 5'.
AU  - Fomenkov AI
AU  - Kramarov VM
AU  - Andreev LV
AU  - Mochalov VV
AU  - Smolyaninov VV
AU  - Matvienko NI
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1988 16: 10399.

PMID- 22887671
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of the Hydrocarbon-Degrading and Emulsan-Producing Strain Acinetobacter venetianus RAG-1T.
PG  - 4771-4772
AB  - We report the draft genome sequence of Acinetobacter venetianus strain RAG-1(T),  which is
      able to degrade hydrocarbons and to synthesize a powerful biosurfactant
      (emulsan) that can be employed for oil removal and as an adjuvant for vaccine
      delivery. The genome sequence of A. venetianus RAG-1(T) might be useful for
      bioremediation and/or clinical purposes.
AU  - Fondi M
AU  - Orlandini V
AU  - Emiliani G
AU  - Papaleo MC
AU  - Maida I
AU  - Perrin E
AU  - Vaneechoutte M
AU  - Dijkshoorn L
AU  - Fani R
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4771-4772.

PMID- 23105071
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of the Volatile Organic Compound-Producing Antarctic Bacterium Arthrobacter sp. Strain TB23, Able To Inhibit Cystic Fibrosis Pathogens  Belonging to the Burkholderia cepacia Complex.
PG  - 6334-6335
AB  - Arthrobacter sp. strain TB23 was isolated from the Antarctic sponge Lissodendoryx nobilis.
      This bacterium is able to produce antimicrobial compounds and volatile
      organic compounds (VOCs) that inhibit the growth of other Antarctic bacteria and
      of cystic fibrosis opportunistic pathogens, respectively. Here we report the
      draft genome sequence of Arthrobacter sp. TB23.
AU  - Fondi M
AU  - Orlandini V
AU  - Maida I
AU  - Perrin E
AU  - Papaleo MC
AU  - Emiliani G
AU  - de Pascale D
AU  - Parrilli E
AU  - Tutino ML
AU  - Michaud L
AU  - Lo GA
AU  - Fani R
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6334-6335.

PMID- 21965534
VI  - 40
DP  - 2012
TI  - Creating highly specific nucleases by fusion of active restriction endonucleases and catalytically inactive homing endonucleases.
PG  - 847-860
AB  - Zinc-finger nucleases and TALE nucleases are produced by combining a specific DNA-binding
      module and a non-specific DNA-cleavage module,
      resulting in nucleases able to cleave DNA at a unique sequence. Here a new
      approach for creating highly specific nucleases was pursued by fusing a
      catalytically inactive variant of the homing endonuclease I-SceI, as DNA
      binding-module, to the type IIP restriction enzyme PvuII, as cleavage
      module. The fusion enzymes were designed to recognize a composite site
      comprising the recognition site of PvuII flanked by the recognition site
      of I-SceI. In order to reduce activity on PvuII sites lacking the flanking
      I-SceI sites, the enzymes were optimized so that the binding of I-SceI to
      its sites positions PvuII for cleavage of the composite site. This was
      achieved by optimization of the linker and by introducing amino acid
      substitutions in PvuII which decrease its activity or disturb its dimer
      interface. The most specific variant showed a more than 1000-fold
      preference for the addressed composite site over an unaddressed PvuII
      site. These results indicate that using a specific restriction enzyme,
      such as PvuII, as cleavage module, offers an alternative to the otherwise
      often used catalytic domain of FokI, which by itself does not contribute
      to the specificity of the engineered nuclease.
AU  - Fonfara I
AU  - Curth U
AU  - Pingoud A
AU  - Wende W
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: 847-860.

PMID- 29472339
VI  - 6
DP  - 2018
TI  - Genome Sequence of Azospirillum brasilense REC3, Isolated from Strawberry Plants.
PG  - e00089-18
AB  - The genome sequence of a plant growth-promoting bacterium and biocontrol agent, Azospirillum
      brasilense REC3, isolated from strawberry roots, is reported here.
      The A. brasilense REC3 total genome contains 7,229,924 bp and has a G+C content
      of 68.7 mol%.
AU  - Fontana CA
AU  - Salazar SM
AU  - Bassi D
AU  - Puglisi E
AU  - Lovaisa N
AU  - Toffoli LM
AU  - Pedraza R
AU  - Cocconcelli PS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00089-18.

PMID- 26847889
VI  - 4
DP  - 2016
TI  - Genome Sequence of Acidovorax avenae Strain T10_61 Associated with Sugarcane Red  Stripe in Argentina.
PG  - e01669-15
AB  - Red stripe of sugarcane in Argentina is a bacterial disease caused by Acidovorax  avenae. The
      genome sequence from the first isolate of this bacterium in Argentina
      is presented here. The draft genome of the A. avenae T10_61 strain contains
      5,646,552 bp and has a G+C content of 68.6 mol%.
AU  - Fontana PD
AU  - Fontana CA
AU  - Bassi D
AU  - Puglisi E
AU  - Salazar SM
AU  - Vignolo GM
AU  - Coccocelli PS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01669-15.

PMID- 26543121
VI  - 3
DP  - 2015
TI  - Genome Sequence of Citrobacter sp. CtB7.12, Isolated from the Gut of the Desert Subterranean Termite Heterotermes aureus.
PG  - e01290-15
AB  - The draft genome of Citrobacter sp. CtB7.12, isolated from termite gut, is presented here.
      This organism has been reported as a cellulolytic bacterium,
      which is biotechnologically important because it can be used as a gene donor for
      the ethanol and biofuel industries.
AU  - Fontes-Perez H
AU  - Olvera-Garcia M
AU  - Chavez-Martinez A
AU  - Rodriguez-Almeida FA
AU  - Arzola-Alvarez CA
AU  - Sanchez-Flores A
AU  - Corral-Luna A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01290-15.

PMID- 28495773
VI  - 5
DP  - 2017
TI  - New Sequence Types of Vibrio parahaemolyticus Isolated from a Malaysian Aquaculture Pond, as Revealed by Whole-Genome Sequencing.
PG  - e00302-17
AB  - The acquisition of Photorhabdus insect-related (Pir) toxin-like genes in Vibrio
      parahaemolyticus has been linked to hepatopancreatic necrosis disease in shrimp.
      We report the whole-genome sequences of genetically virulent and avirulent V.
      parahaemolyticus isolated from a Malaysian aquaculture pond and show that they
      represent previously unreported sequence types of V. parahaemolyticus.
AU  - Foo SM
AU  - Eng WWH
AU  - Lee YP
AU  - Gui K
AU  - Gan HM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00302-17.

PMID- 23405357
VI  - 1
DP  - 2013
TI  - Genome Sequence of Klebsiella pneumoniae Ecl8, a Reference Strain for Targeted Genetic Manipulation.
PG  - e00027-12
AB  - We report the genome sequence of Klebsiella pneumoniae subsp. pneumoniae Ecl8, a  spontaneous
      streptomycin-resistant mutant of strain ECL4, derived from NCIB 418.
      K. pneumoniae Ecl8 has been shown to be genetically tractable for targeted gene
      deletion strategies and so provides a platform for in-depth analyses of this
      species.
AU  - Fookes M
AU  - Yu J
AU  - De Majumdar S
AU  - Thomson N
AU  - Schneiders T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00027-12.

PMID- 25146134
VI  - 2
DP  - 2014
TI  - Whole-Genome Sequence of Serratia symbiotica Strain CWBI-2.3T, a Free-Living Symbiont of the Black Bean Aphid Aphis fabae.
PG  - e00767-14
AB  - The gammaproteobacterium Serratia symbiotica is one of the major secondary symbionts found in
      aphids. Here, we report the draft genome sequence of S.
      symbiotica strain CWBI-2.3(T), previously isolated from the black bean aphid
      Aphis fabae. The 3.58-Mb genome sequence might provide new insights to understand
      the evolution of insect-microbe symbiosis.
AU  - Foray V
AU  - Grigorescu AS
AU  - Sabri A
AU  - Haubruge E
AU  - Lognay G
AU  - Francis F
AU  - Fauconnier ML
AU  - Hance T
AU  - Thonart P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00767-14.

PMID- 4919758
VI  - 104
DP  - 1970
TI  - Degradation of enteric bacterial deoxyribonucleic acid by the Escherichia coli B restriction endonuclease.
PG  - 594-595
AB  - the deoxyribonucleic acid of five different genera of enteric microorganisms
      was shown to be degraded by the Escherichia coli B restriction endonuclease.
AU  - Ford E
AU  - Boyer HW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1970 104: 594-595.

PMID- 8478933
VI  - 230
DP  - 1993
TI  - Effects of co-factor and deoxycytidine substituted oligonucleotides upon sequence-specific interations between MspI DNA methyltransferase and DNA.
PG  - 779-786
AB  - MspI methyltransferase (M.MspI) catalyses the transfer of a methyl group from
      S-adenosyl-L-methionine to the C-5 position of the outer deoxycytidine base in the DNA
      sequence 5'-CCGG-3'. Recombinant M.MspI when expressed and purified as a translational
      fusion with glutathione-S-transferase, shows all of the properties of the wild-type enzyme. We
      report the kinetic analysis of M.MspI binding to DNA, which suggests a two-stage methylation
      process, whose initial DNA binding rate is governed by the presence of a positively charged
      sulphonium centre of the coafactor. Results are also presented that indicate that M.MspI binds
      preferentially to hemi-methylated DNA and that full methylation of either deoxycytidine on
      both strands significantly impairs sequence-specific protein-DNA interactions. Furthermore,
      the importance of the 4-amino group of the inner deoxycytidine for sequence-specific
      protein-DNA interactions is demonstrated by substituting deoxycytidine with
      2-pyrimidinone-1-beta-D-2-deoxyriboside. In addition, we detail the intrinsic structural
      elements of a cofactor, required to enhance the binding of M.MspI to its recognition sequence
      by using S-adenosyl-L-methionine and a range of derivatives.
AU  - Ford K
AU  - Taylor C
AU  - Connolly B
AU  - Hornby DP
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1993 230: 779-786.

PMID- 10103248
VI  - 65
DP  - 1999
TI  - Identification of four phage resistance plasmids from Lactococcus lactis subsp. cremoris HO2.
PG  - 1540-1547
AB  - The bacteriophage-host sensitivity patterns of 16 strains of Lactococcus lactis originally
      isolated from a mixed strain Cheddar cheese starter culture were determined.  Using phages
      obtained from cheese factory whey, four of the strains were found to be highly phage
      resistant.  One of these isolates, Lactococcus lactis subsp. cremoris HO2, was studied in
      detail to determine the mechanisms responsible for the phage insensitivity phenotypes.
      Conjugal transfer of plasmid DNA from strain HO2 allowed a function to be assigned to four of
      its six plasmids.  A 460kb molecule, designated pCI646, was found to harbor the lactose
      utilization genes, while this and plasmids of 58 kb (pCI658), 42 kb (pCI642), and 4.5 kb
      (pCI605) were shown to be responsible for the phage resistance phenotypes observed against the
      small isometric-headed phage omega-712 (936 phage species) and the prolate-headed phage
      omega-c2 (c2 species).  PCI658 was found to mediate an adsorption-blocking mechanism and was
      also responsible for the fluffy pellet phenotype of cells containing the molecule.  PCI642 and
      pCI605 were both shown to be required for the operation of a restriction-modification system.
AU  - Forde A
AU  - Daly C
AU  - Fitzgerald GF
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1999 65: 1540-1547.

PMID- 10532374
VI  - 76
DP  - 1999
TI  - Bacteriophage defence systems in lactic acid bacteria.
PG  - 89-113
AB  - The study of the interactions between lactic acid bacteria and their bacteriophages has been a
      vibrant and rewarding research activity for a considerable number of years. In the more recent
      past, the application of molecular genetics for the analysis of phage-host relationships has
      contributed enormously to the unravelling of specific events which dictate insensitivity to
      bacteriophage infection and has revealed that while they are complex and intricate in nature,
      they are also extremely effective. In addition, the strategy has laid solid foundations for
      the construction of phage resistant strains for use in commercial applications and has
      provided a sound basis for continued investigations into existing, naturally-derived and
      novel, genetically-engineered defence systems. Of course, it has also become clear that phage
      particles are highly dynamic in their response to those defence systems which they do
      encounter and that they can readily adapt to them as a consequence of their genetic
      flexibility and plasticity. This paper reviews the exciting developments that have been
      described in the literature regarding the study of phage-host interactions in lactic acid
      bacteria and the innovative approaches that can be taken to exploit this basic information for
      curtailing phage infection.
AU  - Forde A
AU  - Fitzgerald GF
PT  - Journal Article
TA  - Antonie Van Leeuwenhoek
JT  - Antonie Van Leeuwenhoek
SO  - Antonie Van Leeuwenhoek 1999 76: 89-113.

PMID- 25126841
VI  - 9
DP  - 2014
TI  - The complete genome sequence of Escherichia coli EC958: a high quality reference sequence for the globally disseminated multidrug resistant E. coli O25b:H4-ST131 clone.
PG  - E104400
AB  - Escherichia coli ST131 is now recognised as a leading contributor to urinary
      tract and bloodstream infections in both community and clinical settings. Here we
      present the complete, annotated genome of E. coli EC958, which was isolated from
      the urine of a patient presenting with a urinary tract infection in the Northwest
      region of England and represents the most well characterised ST131 strain.
      Sequencing was carried out using the Pacific Biosciences platform, which provided
      sufficient depth and read-length to produce a complete genome without the need
      for other technologies. The discovery of spurious contigs within the assembly
      that correspond to site-specific inversions in the tail fibre regions of
      prophages demonstrates the potential for this technology to reveal dynamic
      evolutionary mechanisms. E. coli EC958 belongs to the major subgroup of ST131
      strains that produce the CTX-M-15 extended spectrum beta-lactamase, are
      fluoroquinolone resistant and encode the fimH30 type 1 fimbrial adhesin. This
      subgroup includes the Indian strain NA114 and the North American strain JJ1886. A
      comparison of the genomes of EC958, JJ1886 and NA114 revealed that differences in
      the arrangement of genomic islands, prophages and other repetitive elements in
      the NA114 genome are not biologically relevant and are due to misassembly. The
      availability of a high quality uropathogenic E. coli ST131 genome provides a
      reference for understanding this multidrug resistant pathogen and will facilitate
      novel functional, comparative and clinical studies of the E. coli ST131 clonal
      lineage.
AU  - Forde BM
AU  - Ben Zakour NL
AU  - Stanton-Cook M
AU  - Phan MD
AU  - Totsika M
AU  - Peters KM
AU  - Chan KG
AU  - Schembri MA
AU  - Upton M
AU  - Beatson SA
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2014 9: E104400.

PMID- 21352581
VI  - 10
DP  - 2011
TI  - Genome sequences and comparative genomics of two Lactobacillus ruminis strains from the bovine and human intestinal tracts.
PG  - S13
AB  - Background: The genus Lactobacillus is characterized by an extraordinary degree of phenotypic
      and genotypic
      diversity, which recent genomic analyses have further highlighted. However, the choice of
      species for sequencing
      has been non-random and unequal in distribution, with only a single representative genome from
      the L. salivarius
      clade available to date. Furthermore, there is no data to facilitate a functional genomic
      analysis of motility in the
      lactobacilli, a trait that is restricted to the L. salivarius clade.
      Results: The 2.06 Mb genome of the bovine isolate Lactobacillus ruminis ATCC 27782 comprises a
      single circular
      chromosome, and has a G+C content of 44.4%. In silico analysis identified 1901 coding
      sequences, including genes
      for a pediocin-like bacteriocin, a single large exopolysaccharide-related cluster, two sortase
      enzymes, two CRISPR
      loci and numerous IS elements and pseudogenes. A cluster of genes related to a putative pilin
      was identified, and
      shown to be transcribed in vitro. A high quality draft assembly of the genome of a second L.
      ruminis strain, ATCC
      25644 isolated from humans, suggested a slightly larger genome of 2.138 Mb, that exhibited a
      high degree of
      synteny with the ATCC 27782 genome. In contrast, comparative analysis of L. ruminis and L.
      salivarius identified a
      lack of long-range synteny between these closely related species. Comparison of the L.
      salivarius clade core
      proteins with those of nine other Lactobacillus species distributed across 4 major
      phylogenetic groups identified
      the set of shared proteins, and proteins unique to each group.
      Conclusions: The genome of L. ruminis provides a comparative tool for directing functional
      analyses of other
      members of the L. salivarius clade, and it increases understanding of the divergence of this
      distinct Lactobacillus
      lineage from other commensal lactobacilli. The genome sequence provides a definitive resource
      to facilitate
      investigation of the genetics, biochemistry and host interactions of these motile intestinal
      lactobacilli.
AU  - Forde BM
AU  - Neville BA
AU  - O'Donnell MM
AU  - Riboulet-Bisson E
AU  - Claesson MJ
AU  - Coughlan A
AU  - Ross RP
AU  - O'Toole PW
PT  - Journal Article
TA  - Microb. Cell Fact.
JT  - Microb. Cell Fact.
SO  - Microb. Cell Fact. 2011 10: S13.

PMID- 26578678
VI  - 6
DP  - 2015
TI  - Lineage-Specific Methyltransferases Define the Methylome of the Globally Disseminated Escherichia coli ST131 Clone.
PG  - e01602-15
AB  - Escherichia coli sequence type 131 (ST131) is a clone of uropathogenic E. coli that has
      emerged rapidly and disseminated globally in both clinical and community
      settings. Members of the ST131 lineage from across the globe have been
      comprehensively characterized in terms of antibiotic resistance, virulence
      potential, and pathogenicity, but to date nothing is known about the methylome of
      these important human pathogens. Here we used single-molecule real-time (SMRT)
      PacBio sequencing to determine the methylome of E. coli EC958, the
      most-well-characterized completely sequenced ST131 strain. Our analysis of 52,081
      methylated adenines in the genome of EC958 discovered three m6A methylation
      motifs that have not been described previously. Subsequent SMRT sequencing of
      isogenic knockout mutants identified the two type I methyltransferases (MTases)
      and one type IIG MTase responsible for m6A methylation of novel recognition
      sites. Although both type I sites were rare, the type IIG sites accounted for
      more than 12% of all methylated adenines in EC958. Analysis of the distribution
      of MTase genes across 95 ST131 genomes revealed their prevalence is highly
      conserved within the ST131 lineage, with most variation due to the presence or
      absence of mobile genetic elements on which individual MTase genes are located.
      IMPORTANCE: DNA modification plays a crucial role in bacterial regulation.
      Despite several examples demonstrating the role of methyltransferase (MTase)
      enzymes in bacterial virulence, investigation of this phenomenon on a
      whole-genome scale has remained elusive until now. Here we used single-molecule
      real-time (SMRT) sequencing to determine the first complete methylome of a strain
      from the multidrug-resistant E. coli sequence type 131 (ST131) lineage. By
      interrogating the methylome computationally and with further SMRT sequencing of
      isogenic mutants representing previously uncharacterized MTase genes, we defined
      the target sequences of three novel ST131-specific MTases and determined the
      genomic distribution of all MTase target sequences. Using a large collection of
      95 previously sequenced ST131 genomes, we identified mobile genetic elements as a
      major factor driving diversity in DNA methylation patterns. Overall, our analysis
      highlights the potential for DNA methylation to dramatically influence gene
      regulation at the transcriptional level within a well-defined E. coli clone.
AU  - Forde BM
AU  - Phan MD
AU  - Gawthorne JA
AU  - Ashcroft MM
AU  - Stanton-Cook M
AU  - Sarkar S
AU  - Peters KM
AU  - Chan KG
AU  - Chong TM
AU  - Yin WF
AU  - Upton M
AU  - Schembri MA
AU  - Beatson SA
PT  - Journal Article
TA  - MBio
JT  - MBio
SO  - MBio 2015 6: e01602-15.

PMID- 16466269
VI  - 110
DP  - 2006
TI  - Physical nature of interactions within the active site of cytosine-5-methyltransferase.
PG  - 2308-2313
AB  - The physical nature of interactions within the active site of cytosine-5-methyltransferase
      (CMT) was studied using a
      variation-perturbation energy decomposition scheme defining a sequence
      of approximate intermolecular interaction energy models. These models
      have been used to analyze the catalytic activity of residues
      constituting cytosine-5-methyltransferase active site as well their
      role in the binding group of de novo designed inhibitors. Our results
      indicate that Glu119, Arg163, and Arg165 appear to play the dominant
      role in stabilizing the protonated transition state structure and their
      influence can be qualitatively approximated by electrostatic
      interactions alone. The stabilization of neutral structures of the
      alternative reaction pathway is small, which might suggest the
      protonated pathway as preferred by the enzyme. Exchange and
      delocalization terms are negligible in most cases, or they cancel each
      other to some extent. Interactions of inhibitors with the CMT active
      site are dominated by electrostatic multipole contributions in analogy
      with previously studied transition state analogue inhibitors of leucyl
      aminopeptidase.
AU  - Forde GK
AU  - Kedzierski P
AU  - Sokalski WA
AU  - Forde AE
AU  - Hill GA
AU  - Leszczynski J
PT  - Journal Article
TA  - J. Phys. Chem. A
JT  - J. Phys. Chem. A
SO  - J. Phys. Chem. A 2006 110: 2308-2313.

PMID- 22416128
VI  - 109
DP  - 2012
TI  - DNA methylation dynamics, metabolic fluxes, gene splicing, and alternative phenotypes in honey bees.
PG  - 4968-4973
AB  - In honey bees (Apis mellifera), the development of a larva into either a queen or worker
      depends on differential feeding with royal jelly and involves epigenomic
      modifications by DNA methyltransferases. To understand the role of DNA
      methylation in this process we sequenced the larval methylomes in both queens and
      workers. We show that the number of differentially methylated genes (DMGs) in
      larval head is significantly increased relative to adult brain (2,399 vs. 560)
      with more than 80% of DMGs up-methylated in worker larvae. Several highly
      conserved metabolic and signaling pathways are enriched in methylated genes,
      underscoring the connection between dietary intake and metabolic flux. This
      includes genes related to juvenile hormone and insulin, two hormones shown
      previously to regulate caste determination. We also tie methylation data to
      expressional profiling and describe a distinct role for one of the DMGs encoding
      anaplastic lymphoma kinase (ALK), an important regulator of metabolism. We show
      that alk is not only differentially methylated and alternatively spliced in Apis,
      but also seems to be regulated by a cis-acting, anti-sense non-protein-coding
      transcript. The unusually complex regulation of ALK in Apis suggests that this
      protein could represent a previously unknown node in a process that activates
      downstream signaling according to a nutritional context. The correlation between
      methylation and alternative splicing of alk is consistent with the recently
      described mechanism involving RNA polymerase II pausing. Our study offers
      insights into diet-controlled development in Apis.
AU  - Foret S
AU  - Kucharski R
AU  - Pellegrini M
AU  - Feng S
AU  - Jacobsen SE
AU  - Robinson GE
AU  - Maleszka R
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2012 109: 4968-4973.

PMID- 18786820
VI  - 112
DP  - 2008
TI  - The mitochondrial genome of the phytopathogenic basidiomycete Moniliophthora perniciosa is 109 kb in size and contains a stable integrated plasmid.
PG  - 1136-1152
AB  - We present here the sequence of the mitochondrial genome of the basidiomycete phytopathogenic
      hemibiotrophic fungus Moniliophthora perniciosa, causal agent of the Witches' Broom Disease
      in Theobroma cacao.
      The DNA is a circular molecule of 109,103 base pairs, with 31.9% GC, and is the largest
      sequenced so far. This size is due essentially to the presence of numerous non-conserved
      hypothetical ORFs. It contains the 14 genes coding for proteins involved in the oxidative
      phosphorylation, the two rRNA genes, one ORF coding for a ribosomal protein (rps3), and a set
      of 26 tRNA genes that recognize codons for all amino acids. Seven homing endonucleases are
      located inside introns. Except atp8, all conserved known genes are in the same orientation.
      Phylogenetic analysis based on the cox genes agrees with the commonly accepted fungal
      taxonomy. An uncommon feature of this mitochondrial genome is the presence of a region that
      contains a set of four, relatively small, nested, inverted repeats enclosing two genes coding
      for polymerases with an invertron-type structure and three conserved hypothetical genes
      interpreted as the stable integration of a mitochondrial linear plasmid. The integration of
      this plasmid seems to be a recent evolutionary event that could have implications in fungal
      biology. This sequence is available under GenBank accession number AY376688.
AU  - Formighieri EF et al
PT  - Journal Article
TA  - Mycol. Res.
JT  - Mycol. Res.
SO  - Mycol. Res. 2008 112: 1136-1152.

PMID- 25035335
VI  - 2
DP  - 2014
TI  - Genome Sequence of Pseudomonas mandelii PD30.
PG  - e00713-14
AB  - The genome sequence of Pseudomonas mandelii PD30 is reported in this announcement. The genes
      for the reduction of nitrate to dinitrogen were
      identified in the genome assembly and subsequently used in gene expression
      research.
AU  - Formusa PA
AU  - Hsiang T
AU  - Habash MB
AU  - Lee H
AU  - Trevors JT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00713-14.

PMID- 27587829
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequence of Aeromonas hydrophila Strain AH-1 (Serotype O11).
PG  - e00920-16
AB  - Aeromonas hydrophila is an emerging pathogen of aquatic and terrestrial animals,  including
      humans. Here, we report the whole-genome sequence of the septicemic A.
      hydrophila AH-1 strain, belonging to the serotype O11, and the first mesophilic
      Aeromonas with surface layer (S-layer) to be sequenced.
AU  - Forn-Cuni G
AU  - Tomas JM
AU  - Merino S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00920-16.

PMID- 27587828
VI  - 4
DP  - 2016
TI  - Genome Sequence of Aeromonas hydrophila Strain AH-3 (Serotype O34).
PG  - e00919-16
AB  - Aeromonas hydrophila is an emerging pathogen of poikilothermic animals, from fish to mammals,
      including humans. Here, we report the whole-genome sequence of the A.
      hydrophila AH-3 strain, isolated from a fish farm goldfish septicemia outbreak in
      Spain, with a characterized polar and lateral flagellum glycosylation pattern.
AU  - Forn-Cuni G
AU  - Tomas JM
AU  - Merino S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00919-16.

PMID- Not carried by PubMed...
VI  - 208
DP  - 1994
TI  - The effect of AT and GC sequence specific minor groove binding agents on restriction endonuclease activity.
PG  - 97
AB  - The naturally occuring DNA minor groove-binders, netropsin and distamycin A, recognize (A/T)4
      and (A/T)5 sequences respectively. These ligands have well-documented effects on proteins such
      as restriction endonucleases and transcription factors whose DNA recognition sequences have
      high A/T content. We have investigated the ability of two synthetic imidazole containing and
      G/C selective oligopeptides to interfere with the catalytic activity of restriction
      endonucleases, and compared this with the effects of netropsin and distamycin. The
      endonucleases were chosen to have either A/T rich (EcoRI, EcoRV) or G/C rich (BalI, NruI,
      Fnu4HI, BanII) recognition sequences. An agarose gel assay was used to measure the degree of
      cleavage of 32P-labelled DNA in the presence or absence of minor groove-binding ligand, and
      ligand-DNA binding data was obtained using methidium-propyl EDTA (MPE) footprinting
      methodology. The results from these studies will be presented.
AU  - Forrow S
AU  - Lee M
AU  - Souhami RL
AU  - Hartley JA
PT  - Journal Article
TA  - ACS Abstracts
JT  - ACS Abstracts
SO  - ACS Abstracts 1994 208: 97.

PMID- 7728903
VI  - 96
DP  - 1995
TI  - The effect of AT and GC sequence specific minor groove-binding agents on restriction endonuclease activity.
PG  - 125-142
AB  - The ability of the naturally occurring A/T specific DNA minor groove binders netropsin and
      distamycin A and two synthetic G/C selective oligopeptide analogues (1 and 2), to interfere
      with the catalytic activity of restriction endonucleases has been investigated. Enzymes were
      chosen to have A/T rich (EcoRI, EcoRV) or G/C rich (BalI, NruI) recognition sequences. An
      agarose gel assay was used to measure the cleavage of 32P-labelled DNA and ligand-DNA binding
      data was obtained using methidium-propyl EDTA footprinting. Netropsin and distamycin bind at
      the recognition sites, and dose-dependently inhibited cleavage by, EcoRI and EcoRV, (EcoRI >
      EcoRV). They were also more effective at inhibiting the catalytic activity of BalI than either
      1 or 2. NruI was inhibited by distamycin and 2, but not by netropsin or 1. DNA footprinting
      revealed that neither 1 or 2 bound to the BalI or NruI recognition sequences under the
      conditions used whereas netropsin and distamycin footprint at adjacent sites. 1 binds to two
      of the three recognition sequences for the enzyme Fnu4HI (GCNGC) in the fragment studied and
      was shown to inhibit DNA cleavage only at these two sites. 2 binds strongly to two GGGCTC
      sequences which are recognition sites for the enzyme BanII. In this case a pronounced
      stimulation of cleavage was observed in the presence of 2 over a wide dose range. The results
      indicate that enzyme inhibition does not necessarily result from simultaneous occupancy of a
      common site, or at nearby flanking sequences, and in some circumstances, a pronounced
      stimulation of enzyme cleavage can occur.
AU  - Forrow SM
AU  - Lee M
AU  - Souhami RL
AU  - Hartley JA
PT  - Journal Article
TA  - Chem. Biol. Interact.
JT  - Chem. Biol. Interact.
SO  - Chem. Biol. Interact. 1995 96: 125-142.

PMID- 24847883
VI  - 509
DP  - 2014
TI  - Bacterial phylogeny structures soil resistomes across habitats.
PG  - 612-616
AB  - Ancient and diverse antibiotic resistance genes (ARGs) have previously been
      identified from soil, including genes identical to those in human pathogens.
      Despite the apparent overlap between soil and clinical resistomes, factors
      influencing ARG composition in soil and their movement between genomes and
      habitats remain largely unknown. General metagenome functions often correlate
      with the underlying structure of bacterial communities. However, ARGs are
      proposed to be highly mobile, prompting speculation that resistomes may not
      correlate with phylogenetic signatures or ecological divisions. To investigate
      these relationships, we performed functional metagenomic selections for
      resistance to 18 antibiotics from 18 agricultural and grassland soils. The 2,895
      ARGs we discovered were mostly new, and represent all major resistance
      mechanisms. We demonstrate that distinct soil types harbour distinct resistomes,
      and that the addition of nitrogen fertilizer strongly influenced soil ARG
      content. Resistome composition also correlated with microbial phylogenetic and
      taxonomic structure, both across and within soil types. Consistent with this
      strong correlation, mobility elements (genes responsible for horizontal gene
      transfer between bacteria such as transposases and integrases) syntenic with ARGs
      were rare in soil by comparison with sequenced pathogens, suggesting that ARGs
      may not transfer between soil bacteria as readily as is observed between human
      pathogens. Together, our results indicate that bacterial community composition is
      the primary determinant of soil ARG content, challenging previous hypotheses that
      horizontal gene transfer effectively decouples resistomes from phylogeny.
AU  - Forsberg KJ
AU  - Patel S
AU  - Gibson MK
AU  - Lauber CL
AU  - Knight R
AU  - Fierer N
AU  - Dantas G
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2014 509: 612-616.

PMID- 794836
VI  - 3
DP  - 1976
TI  - Kinetic studies on the cleavage of adenovirus DNA by restriction endonuclease EcoRI.
PG  - 3255-3269
AB  - The kinetics of cleavage of DNA from Adenovirus Type 1 (Ad1), Type 5 (Ad5) and
      Type 6 (Ad6) by restriction endonuclease EcoRI was investigated by quantitative
      evaluation of the fluorescence from ethidium stained DNA fragments separated on
      agarose gels.  The apparent rate constants of cleavage at different cleavage
      sites have been determined and large differences in the cleavage sites of the
      individual sites within one type of DNA were found.  From the kinetics of
      cleavage information on the sequence of the DNA fragments can be obtained.  The
      order of the fragments A,B,C,D of Ad6 DNA obtained after complete cleavage by
      restriction endonuclease EcoRI was found to be ADCB; the order of the
      corresponding fragments A,B,C of Ad1 and Ad5 DNA was found to be ACB.
AU  - Forsblom S
AU  - Rigler R
AU  - Ehrenberg M
AU  - Pettersson U
AU  - Philipson L
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1976 3: 3255-3269.

PMID- 29650583
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Four Clinical Legionella pneumophila Isolates from Ontario, Canada.
PG  - e00295-18
AB  - Legionella pneumophila outbreak investigations require the development of reliable typing
      methods to better understand the genetic relationships of the
      isolates involved. Here, we report the draft genome sequences of four clinical
      Legionella pneumophila isolates obtained between 2000 and 2012 in Ontario,
      Canada.
AU  - Fortuna A
AU  - Ramnarine R
AU  - Li A
AU  - Fittipaldi N
AU  - Frantz C
AU  - Mallo GV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00295-18.

PMID- 7505062
VI  - 262
DP  - 1993
TI  - Abnormal chromosome behavior in Neurospora mutants defective in DNA methylation.
PG  - 1737-1741
AB  - The function and regulation of DNA methylation in eukaryotes remain unclear. Genes affecting
      methylation were identified in the fungus Neurospora crassa. A mutation in one gene, dim-2,
      resulted in the loss of all detectable DNA methylation. Abnormal segregation of the
      methylation defects in crosses led to the discovery that the methylation mutants frequently
      generate strains with extra chromosomes or chromosomal parts. Starvation for
      S-adenosylmethionine, the presumed methyl group donor for DNA methylation, also produced
      aneuploidy. These results suggest that DNA methylation plays a role in the normal control of
      chromosome behavior.
AU  - Foss HM
AU  - Roberts CJ
AU  - Claeys KM
AU  - Selker EU
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1993 262: 1737-1741.

PMID- 21304672
VI  - 2
DP  - 2010
TI  - Complete genome sequence of Xylanimonas cellulosilytica type strain (XIL07T).
PG  - 1-8
AB  - Xylanimonas cellulosilytica Rivas et al. 2003 is the type species of the genus Xylanimonas of
      the actinobacterial family Promicromonosporaceae. The species X. cellulosilytica is of
      interest because of its ability to hydrolyze cellulose and xylan. Here we describe the
      features of this organism, together with the complete genome sequence, and annotation. This is
      the first complete genome sequence of a member of the large family Promicromonosporaceae, and
      the 3,831,380 bp long genome (one chromosome plus an 88,604 bp long plasmid) with its 3485
      protein-coding and 61 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea
      project.
AU  - Foster B et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 2: 1-8.

PMID- 15780005
VI  - 3
DP  - 2005
TI  - The Wolbachia genome of Brugia malayi: endosymbiont evolution within a human pathogenic nematode.
PG  - E121
AB  - Complete genome DNA sequence and analysis is presented for Wolbachia, the
      obligate alpha-proteobacterial endosymbiont required for fertility and survival
      of the human filarial parasitic nematode Brugia malayi. Although, quantitatively,
      the genome is even more degraded than those of closely related Rickettsia
      species, Wolbachia has retained more intact metabolic pathways. The ability to
      provide riboflavin, flavin adenine dinucleotide, heme, and nucleotides is likely
      to be Wolbachia's principal contribution to the mutualistic relationship, whereas
      the host nematode likely supplies amino acids required for Wolbachia growth.
      Genome comparison of the Wolbachia endosymbiont of B. malayi (wBm) with the
      Wolbachia endosymbiont of Drosophila melanogaster (wMel) shows that they share
      similar metabolic trends, although their genomes show a high degree of genome
      shuffling. In contrast to wMel, wBm contains no prophage and has a reduced level
      of repeated DNA. Both Wolbachia have lost a considerable number of membrane
      biogenesis genes that apparently make them unable to synthesize lipid A, the
      usual component of proteobacterial membranes. However, differences in their
      peptidoglycan structures may reflect the mutualistic lifestyle of wBm in contrast
      to the parasitic lifestyle of wMel. The smaller genome size of wBm, relative to
      wMel, may reflect the loss of genes required for infecting host cells and
      avoiding host defense systems. Analysis of this first sequenced endosymbiont
      genome from a filarial nematode provides insight into endosymbiont evolution and
      additionally provides new potential targets for elimination of cutaneous and
      lymphatic human filarial disease.
AU  - Foster J et al
PT  - Journal Article
TA  - PLoS Biology
JT  - PLoS Biology
SO  - PLoS Biology 2005 3: E121.

PMID- 9537396
VI  - 180
DP  - 1998
TI  - Levels of the Vsr endonuclease do not regulate stationary-phase reversion of a Lac- frameshift allele in Escherichia coli.
PG  - 1944-1946
AB  - Vsr endonuclease, which initiates very short patch repair, has been hypothesized to regulate
      mutation in stationary-phase cells.  Overexpression of Vsr does dramatically increase the
      stationary-phase reversion of a Lac- frameshift allele, but the absence of Vsr has no effect.
      Thus, at least in this case, Vsr has no regulatory role in stationary-phase mutation, and the
      effects of Vsr overproduction are likely to be artifactual.
AU  - Foster PL
AU  - Rosche WA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1998 180: 1944-1946.

PMID- 25377717
VI  - 2
DP  - 2014
TI  - Genome Sequence of Borrelia crocidurae Strain 03-02, a Clinical Isolate from Senegal.
PG  - e01150-14
AB  - The draft genome sequence of Borrelia crocidurae strain 03-02, a blood isolate from a febrile
      Senegalese patient, comprises a 920,021-bp linear chromosome
      (27.7% G+C content), 32 tRNAs, 818 open reading frames, and one cluster of
      regularly interspaced short palindromic repeats. Its genotype differs from that
      of the Achema reference strain.
AU  - Fotso FA
AU  - Mediannikov O
AU  - Padmanabhan R
AU  - Robert C
AU  - Fournier PE
AU  - Raoult D
AU  - Drancourt M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01150-14.

PMID- 28596408
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Serratia proteamaculans MFPA44A14-05, a Model Organism for the Study of Meat and Seafood Spoilage.
PG  - e00491-17
AB  - In this study, we present a draft genome sequence of Serratia proteamaculans MFPA44A14-05.
      This strain was isolated from a spoiled organic
      modified-atmosphere-packed beef carpaccio. The draft genome sequence will
      contribute to the understanding of the role of the S. proteamaculans species in
      meat and seafood spoilage.
AU  - Fougy L
AU  - Coeuret G
AU  - Champomier-Verges MC
AU  - Chaillou S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00491-17.

PMID- 
VI  - 17
DP  - 2012
TI  - Epigenetic Drug Discovery: Targeting DNA Methyltransferases (vol 17, pg 2, 2012).
PG  - 700
AB  - Foulks, J.M.; Parnell, K.M.; Nix, R.N.; Chau, S.; Swierczek, K.; Saunders, M.; Wright, K.;
      Hendrickson, T.F.; Ho, K.K.; McCullar, M.V.; Kanner, S.B. Epigenetic Drug Discovery: Targeting
      DNA Methyltransferases. J. Biomol. Screen. 2012, 17, 2-17. (Original doi:
      10.1177/1087057111421212).
AU  - Foulks JM
AU  - Parnell KM
AU  - Chau S
AU  - Swierczek K
AU  - Saunders M
AU  - Wright K
AU  - Hendrickson TF
AU  - McCullar MV
AU  - Kanner SB
PT  - Journal Article
TA  - J. Biomol. Screen.
JT  - J. Biomol. Screen.
SO  - J. Biomol. Screen. 2012 17: 700.

PMID- 19379498
VI  - 10
DP  - 2009
TI  - Analysis of the Rickettsia africae genome reveals that virulence acquisition in Rickettsia species may be explained by genome reduction.
PG  - 166
AB  - ABSTRACT: BACKGROUND: The Rickettsia genus includes 25 validated species,
      17 of which are proven human pathogens. Among these, the pathogenicity
      varies greatly, from the highly virulent R. prowazekii, which causes
      epidemic typhus and kills its arthropod host, to the mild pathogen R.
      africae, the agent of African tick-bite fever, which does not affect the
      fitness of its tick vector. RESULTS: We evaluated the clonality of R.
      africae in 70 patients and 155 ticks, and determined its genome sequence,
      which comprises a circular chromosome of 1,278,540 bp including a tra
      operon and an unstable 12,377-bp plasmid. To study the genetic
      characteristics associated with virulence, we compared this species to R.
      prowazekii, R. rickettsii and R. conorii. R. africae and R. prowazekii
      have, respectively, the less and most decayed genomes. Eighteen genes are
      present only in R. africae including one with a putative protease domain
      upregulated at 37degreesC. CONCLUSION: Based on these data, we speculate
      that a loss of regulatory genes causes an increase of virulence of
      rickettsial species in ticks and mammals. We also speculate that in
      Rickettsia species virulence is mostly associated with gene loss.
AU  - Fournier PE
AU  - El Karkouri K
AU  - Leroy Q
AU  - Robert C
AU  - Giumelli B
AU  - Renesto P
AU  - Socolovschi C
AU  - Parola P
AU  - Audic S
AU  - Raoult D
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2009 10: 166.

PMID- 22374949
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Rickettsia slovaca, the Agent of Tick-Borne Lymphadenitis.
PG  - 1612
AB  - The present study reports the complete and annotated genome sequence of the human pathogen
      Rickettsia slovaca strain 13-B, which was isolated from a Dermacentor
      tick in Slovakia in 1968. The 1.27-Mb genome provides further insights into the
      acquisition of virulence related to genome reduction in Rickettsia species.
AU  - Fournier PE
AU  - El Karkouri K
AU  - Robert C
AU  - Medigue C
AU  - Raoult D
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1612.

PMID- 23045489
VI  - 194
DP  - 2012
TI  - Genomic Comparison of Kingella kingae Strains.
PG  - 5972
AB  - Kingella kingae is a betaproteobacterium from the order Neisseriales, and it is an agent of
      invasive infections in children. We sequenced the genome from the
      septic arthritis strain 11220434. It is composed of a 1,990,794-bp chromosome but
      no plasmid, and it contains 2,042 protein-coding genes and 52 RNA genes,
      including 3 rRNA genes.
AU  - Fournier PE
AU  - Rouli L
AU  - El Karkouri K
AU  - Nguyen TT
AU  - Yagupsky P
AU  - Raoult D
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5972.

PMID- 16415984
VI  - 2
DP  - 2006
TI  - Comparative genomics of multidrug resistance in Acinetobacter baumannii.
PG  - e7
AB  - Acinetobacter baumannii is a species of nonfermentative gram-negative bacteria commonly found
      in water and soil. This organism was susceptible
      to most antibiotics in the 1970s. It has now become a major cause of
      hospital-acquired infections worldwide due to its remarkable propensity to
      rapidly acquire resistance determinants to a wide range of antibacterial
      agents. Here we use a comparative genomic approach to identify the
      complete repertoire of resistance genes exhibited by the
      multidrug-resistant A. baumannii strain AYE, which is epidemic in France,
      as well as to investigate the mechanisms of their acquisition by
      comparison with the fully susceptible A. baumannii strain SDF, which is
      associated with human body lice. The assembly of the whole shotgun genome
      sequences of the strains AYE and SDF gave an estimated size of 3.9 and 3.2
      Mb, respectively. A. baumannii strain AYE exhibits an 86-kb genomic region
      termed a resistance island--the largest identified to date--in which 45
      resistance genes are clustered. At the homologous location, the SDF strain
      exhibits a 20 kb-genomic island flanked by transposases but devoid of
      resistance markers. Such a switching genomic structure might be a hotspot
      that could explain the rapid acquisition of resistance markers under
      antimicrobial pressure. Sequence similarity and phylogenetic analyses
      confirm that most of the resistance genes found in the A. baumannii strain
      AYE have been recently acquired from bacteria of the genera Pseudomonas,
      Salmonella, or Escherichia. This study also resulted in the discovery of
      19 new putative resistance genes. Whole-genome sequencing appears to be a
      fast and efficient approach to the exhaustive identification of resistance
      genes in epidemic infectious agents of clinical significance.
AU  - Fournier PE
AU  - Vallenet D
AU  - Barbe V
AU  - Audic S
AU  - Ogata H
AU  - Poirel L
AU  - Richet H
AU  - Robert C
AU  - Mangenot S
AU  - Abergel C
AU  - Nordmann P
AU  - Weissenbach J
AU  - Raoult D
AU  - Claverie JM
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2006 2: e7.

PMID- 9872396
VI  - 440
DP  - 1998
TI  - The complete sequence of the mitochondrial genome of Saccharomyces cerevisiae.
PG  - 325-331
AB  - The currently available yeast mitochondrial DNA (mtDNA) sequence is incomplete, contains many
      errors and is derived from several polymorphic
      strains. Here, we report that the mtDNA sequence of the strain used for
      nuclear genome sequencing assembles into a circular map of 85,779 bp which
      includes 10 kb of new sequence. We give a list of seven small hypothetical
      open reading frames (ORFs). Hot spots of point mutations are found in
      exons near the insertion sites of optional mobile group I intron-related
      sequences. Our data suggest that shuffling of mobile elements plays an
      important role in the remodelling of the yeast mitochondrial genome.
AU  - Foury F
AU  - Roganti T
AU  - Lecrenier N
AU  - Purnelle B
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1998 440: 325-331.

PMID- 29097459
VI  - 5
DP  - 2017
TI  - Genome Sequence of Piezophilic Bacterium Desulfovibrio profundus Strain 500-1, Isolated from a Deep Sediment Layer in the Japan Sea.
PG  - e01181-17
AB  - Piezophilic Desulfovibrio profundus strain 500-1 was isolated in the Japan Sea from a sediment
      layer at 500-m depth under a water column of 1,000 m. Here, we
      report the genome sequence of this strain, which includes a 4,168,905-bp circular
      chromosome and two plasmids of 42,836 bp and 6,167 bp.
AU  - Fouteau S
AU  - Guerin T
AU  - Magdelenat G
AU  - Roumagnac M
AU  - Bartoli M
AU  - Ollivier B
AU  - Dolla A
AU  - Barbe V
AU  - Pradel N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01181-17.

PMID- 15660156
VI  - 3
DP  - 2005
TI  - Major structural differences and novel potential virulence mechanisms from the genomes in multiple Campylobacter species.
PG  - e15
AB  - Sequencing and comparative genome analysis of four strains of Campylobacter including C. lari
      RM2100, C. upsaliensis RM3195, and C. coli RM2228 has revealed major structural differences
      that are associated with the insertion of phage- and plasmid-like genomic islands, as well as
      major variations in the lipooligosaccharide complex. Poly G tracts are longer, are greater in
      number, and show greater variability in C. upsaliensis than in the other species. Many genes
      involved in host colonization, including racR/S, cadF, cdt, ciaB, and flagellin genes, are
      conserved across the species, but variations that appear to be species specific are evident
      for a lipooligosaccharide locus, a capsular (extracellular) polysaccharide locus, and a novel
      Campylobacter putative licABCD virulence locus. The strains also vary in their metabolic
      profiles, as well as their resistance profiles to a range of antibiotics. It is evident that
      the newly identified hypothetical and conserved hypothetical proteins, as well as
      uncharacterized two-component regulatory systems and membrane proteins, may hold additional
      significant information on the major differences in virulence among the species, as well as
      the specificity of the strains for particular hosts.
AU  - Fouts DE et al
PT  - Journal Article
TA  - PLoS Biology
JT  - PLoS Biology
SO  - PLoS Biology 2005 3: e15.

PMID- 18654632
VI  - 4
DP  - 2008
TI  - Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice.
PG  - E1000141
AB  - We report here the sequencing and analysis of the genome of the
      nitrogen-fixing endophyte, Klebsiella pneumoniae 342. Although K.
      pneumoniae 342 is a member of the enteric bacteria, it serves as a model
      for studies of endophytic, plant-bacterial associations due to its
      efficient colonization of plant tissues (including maize and wheat, two of
      the most important crops in the world), while maintaining a mutualistic
      relationship that encompasses supplying organic nitrogen to the host
      plant. Genomic analysis examined K. pneumoniae 342 for the presence of
      previously identified genes from other bacteria involved in colonization
      of, or growth in, plants. From this set, approximately one-third were
      identified in K. pneumoniae 342, suggesting additional factors most likely
      contribute to its endophytic lifestyle. Comparative genome analyses were
      used to provide new insights into this question. Results included the
      identification of metabolic pathways and other features devoted to
      processing plant-derived cellulosic and aromatic compounds, and a robust
      complement of transport genes (15.4%), one of the highest percentages in
      bacterial genomes sequenced. Although virulence and antibiotic resistance
      genes were predicted, experiments conducted using mouse models showed
      pathogenicity to be attenuated in this strain. Comparative genomic
      analyses with the presumed human pathogen K. pneumoniae MGH78578 revealed
      that MGH78578 apparently cannot fix nitrogen, and the distribution of
      genes essential to surface attachment, secretion, transport, and
      regulation and signaling varied between each genome, which may indicate
      critical divergences between the strains that influence their preferred
      host ranges and lifestyles (endophytic plant associations for K.
      pneumoniae 342 and presumably human pathogenesis for MGH78578). Little
      genome information is available concerning endophytic bacteria. The K.
      pneumoniae 342 genome will drive new research into this less-understood,
      but important category of bacterial-plant host relationships, which could
      ultimately enhance growth and nutrition of important agricultural crops
      and development of plant-derived products and biofuels.
AU  - Fouts DE
AU  - Tyler HL
AU  - DeBoy RT
AU  - Daugherty S
AU  - Ren Q
AU  - Badger JH
AU  - Durkin AS
AU  - Huot H
AU  - Shrivastava S
AU  - Kothari S
AU  - Dodson RJ
AU  - Mohamoud Y
AU  - Khouri H
AU  - Roesch LF
AU  - Krogfelt KA
AU  - Struve C
AU  - Triplett EW
AU  - Methe BA
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2008 4: E1000141.

PMID- 17675301
VI  - 35
DP  - 2007
TI  - Haemophilus influenzae phasevarions have evolved from type III DNA restriction systems into epigenetic regulators of gene expression.
PG  - 5242-5252
AB  - Phase variably expressed (randomly switching) methyltransferases associated with type III
      restriction-modification (R-M) systems have been
      identified in a variety of pathogenic bacteria. We have previously shown
      that a phase variable methyltransferase (Mod) associated with a type III
      R-M system in Haemophilus influenzae strain Rd coordinates the random
      switching of expression of multiple genes, and constitutes a phase
      variable regulon-'phasevarion'. We have now identified the recognition
      site for the Mod methyltransferase in H. influenzae strain Rd as
      5'-CGAAT-3'. This is the same recognition site as the previously described
      HinfIII system. A survey of 59 H. influenzae strains indicated significant
      sequence heterogeneity in the central, variable region of the mod gene
      associated with target site recognition. Intra- and inter-strain
      transformation experiments using Mod methylated or non-methylated
      plasmids, and a methylation site assay demonstrated that the sequence
      heterogeneity seen in the region encoding target site specificity does
      correlate to distinct target sites. Mutations were identified within the
      res gene in several strains surveyed indicating that Res is not
      functional. These data suggest that evolution of this type III R-M system
      into an epigenetic mechanism for controlling gene expression has, in some
      strains, resulted in loss of the DNA restriction function.
AU  - Fox KL
AU  - Dowideit SJ
AU  - Erwin AL
AU  - Srikhanta YN
AU  - Smith AL
AU  - Jennings MP
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2007 35: 5242-5252.

PMID- 17714447
VI  - 65
DP  - 2007
TI  - Phase variable type III restriction-modification systems of host-adapted bacterial pathogens.
PG  - 1375-1379
AB  - Phase variation, the high-frequency on/off switching of gene expression, is a common feature
      of host-adapted bacterial pathogens. Restriction-modification (R-M) systems, which are
      ubiquitous among bacteria, are classically assigned the role of cellular defence against
      invasion of foreign DNA. These enzymes are not obvious candidates for phase variable
      expression, a characteristic usually associated with surface-expressed molecules subject to
      host immune selection. Despite this, numerous type III R-M systems in bacterial pathogens
      contain repetitive DNA motifs that suggest the potential for phase variation. Several roles
      have been proposed for phase variable R-M systems based on DNA restriction function. However,
      there is now evidence in several important human pathogens, including Haemophilus influenzae,
      Neisseria meningitidis and Neisseria gonorrhoeae, that these systems are 'phasevarions'
      (phasevariable regulons) controlling expression of multiple genes via a novel epigenetic
      mechanism.
AU  - Fox KL
AU  - Srikhanta YN
AU  - Jennings MP
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2007 65: 1375-1379.

PMID- 2844179
VI  - 155
DP  - 1988
TI  - DNAse I footprinting of restriction enzymes.
PG  - 779-785
AB  - DNAse I footprint of restriction enzymes has been achieved by using calcium
      containing digestion buffers so that the enzymes bind to but do not cleave DNA.
      EcoRI produces a footprint 17 bases long, overestimating the region of contact
      with DNA by about 7-8 base pairs.  Restriction enzymes HaeIII and HinP1I
      generate smaller footprints of 15 and 13 base pairs respectively.
AU  - Fox KR
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1988 155: 779-785.

PMID- 10871403
VI  - 28
DP  - 2000
TI  - Recognition of GT mismatches by Vsr mismatch endonuclease.
PG  - 2535-2540
AB  - The Vsr mismatch endonuclease recognises the sequence CTWGG (W=A or T) in which the indicated
      thymine is paired with guanine and nicks the DNA backbone on the 5'-side of the mispaired
      thymine.  By using base analogues of G and T we have explored the functional groups on the
      mismatch pair which are recognized by the enzyme.  Removal of the thymine 5-methyl group
      causes a 60% reduction in activity, while removing the 2-amino group of guanine reduces
      cleavage by 90%.  Placing 2-aminopurine or nebularine opposite T generates mismatches which
      are cut at a much lower rate (0.1%).  When either base is removed, generating a pseudoabasic
      site (1',2'-dideoxyribose), the enzyme still produces site-specific cleavage, but at only 1%
      of the original rate.  Although TT and CT mismatches at this position are cleaved at a low
      rate (~1%), mismatches with other bases (such as GA and AC) and Watson-Crick base pairs are
      not cleaved by the enzyme.  There is also no cleavage when the mismatched T is replaced with
      difluorotoluene.
AU  - Fox KR
AU  - Allinson SL
AU  - Sahagun-Krause H
AU  - Brown T
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2000 28: 2535-2540.

PMID- 12626718
VI  - 31
DP  - 2003
TI  - The affinity of different MBD proteins for a specific methylated locus depends on their intrinsic binding properties.
PG  - 1765-1774
AB  - The methyl-CpG binding domain (MBD) family of proteins was defined based on sequence
      similarity in their DNA binding domains. In light of their
      high degree of conservation, it is of inherent interest to determine the
      genomic distribution of these proteins, and their associated co-repressor
      complexes. One potential determinant of specificity resides in differences
      in the intrinsic DNA binding properties of the various MBD proteins. In
      this report, we use a capillary electrophoretic mobility shift assay
      (CEMSA) with laser-induced fluorescence (LIF) and neutral capillaries to
      calculate MBD-DNA binding affinities. MBD proteins were assayed on pairs
      of methylated and unmethylated duplex oligos corresponding to the promoter
      regions of the BRCA1, MLH1, GSTP1 and p16(INK4a) genes, and binding
      affinities for each case were calculated by Scatchard analyses. With the
      exception of mammalian MBD3 and Xenopus MBD3 LF, all the MBD proteins
      showed higher affinity for methylated DNA (in the nanomolar range) than
      for unmethylated DNA (in the micromolar range). Significant differences
      between MBD proteins in the affinity for methylated DNA were observed,
      ranging within two orders of magnitude. By mutational analysis of MBD3 and
      using CEMSA, we demonstrate the critical role of specific residues within
      the MBD in conferring selectivity for methylated DNA. Interestingly, the
      binding affinity of specific MBD proteins for methylated DNA fragments
      from naturally occurring sequences are affected by local methyl-CpG
      spacing.
AU  - Fraga MF
AU  - Ballestar E
AU  - Montoya G
AU  - Taysavang P
AU  - Wade PA
AU  - Esteller M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2003 31: 1765-1774.

PMID- 29773636
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of a 'Candidatus Liberibacter europaeus' Strain Assembled from Broom Psyllids (Arytainilla spartiophila) from New Zealand.
PG  - e00430-18
AB  - Here, we report the draft genome sequence of 'Candidatus Liberibacter europaeus'  ASNZ1,
      assembled from broom psyllids (Arytainilla spartiophila) from New Zealand.
      The assembly comprises 15 contigs, with a total length of 1.33 Mb and a G+C
      content of 33.5%.
AU  - Frampton RA
AU  - Thompson SM
AU  - Kalamorz F
AU  - David C
AU  - Addison SM
AU  - Smith GR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00430-18.

PMID- 11551826
VI  - 33
DP  - 2001
TI  - Five novel alternatively spliced transcripts of DNA (cytosine-5) methyltransferase 2 in human peripheral blood leukocytes.
PG  - 1104-1115
AB  - Alternative splicing of RNA molecules transcribed from DNA (cytosine-5) methyltransferases has
      been proposed as a mechanism by which methylation is able to effect diverse biological
      processes in higher eukaryotes. This study has investigated transcriptional versatility of DNA
      (cytosine-5) methyltransferase 2, which may methylate cytosine residues within 5'-CCTGG-3'
      pentanucleotides in regions of the human genome devoid of 5'-CG-3' methylation. Five novel
      splice variants of DNA (cytosine-5) methyltransferase 2 were identified in the peripheral
      blood leukocytes of healthy subjects following cloning and sequencing of RT-PCR products
      amplified using gene specific oligodeoxyribonucleotide primers. The generation of some of
      these splice variants may be influenced by the formation of secondary structures within
      pre-mRNA due to the repetition of sequences flanking alternatively spliced exons in a reverse
      and complementary orientation on the same strand. These findings enable novel approaches to
      investigate the role of RNA secondary structures in alternative splicing. The DNA (cytosine-5)
      methyltransferase 2 splice variants are generated in all the major cell types of peripheral
      blood, as well as in neoplastic lymphoid cells indicating that they are unlikely to generate
      proteins involved in control of the cell cycle or cellular differentiation. Interestingly, the
      gene products generated by some splice variants completely or partially lack highly conserved
      amino acid motifs shown to be important for the catalysis of cytosine  methylation. The
      possibility cannot be excluded, therefore, that alternative splicing of DNA (cytosine-5)
      methyltransferase 2 pre-mRNA may generate protein isoforms which have different methylating
      capabilities or which are involved in biological processes other than the catalysis of
      cytosine methylation.
AU  - Franchina M
AU  - Hooper J
AU  - Kay PH
PT  - Journal Article
TA  - Int. J. Biochem. Cell Biol.
JT  - Int. J. Biochem. Cell Biol.
SO  - Int. J. Biochem. Cell Biol. 2001 33: 1104-1115.

PMID- 11034545
VI  - 19
DP  - 2000
TI  - Evidence that cytosine residues within 5'-CCTGG-3' pentanucleotides can be methylated in human DNA independently of the methylating system that modifies 5'-CG-3' dinucleotides.
PG  - 521-526
AB  - In contrast to the complex sequence specificities of the prokaryotic DNA methylating systems,
      the mammalian machinery identified thus far methylates cytosine residues within the context of
      a 5'-CG-3' dinucleotide. To explore the possibility that cytosine residues that do not
      precede guanine may be independently methylated in mammalian DNA, we have examined a region of
      the human myogenic gene, Myf-3, which is not targeted by the methylating system that
      methylates 5'-CG-3' dinucleotides. Our investigations have revealed cytosine methylation
      within the 5'-CCTGG-3' pentanucleotides specified by the 0.8-kb Myf-3 probe. We have also
      found that in DNA from neoplastic cells, in which 5'-CG-3' dinucleotides within Myf-3 become
      abnormally hypermethylated, cytosine residues within 5'-CCTGG-3' pentanucleotides are not
      methylated. Moreover, methylation of 5'-CCTGG-3' pentanucleotides was not detected within
      the closely related Myf-4 gene, which is normally 5'-CG-3' hypermethylated. These findings
      indicate the existence of a system that methylates 5'-CCTGG-3' pentanucleotides
      independently of the system that methylates cytosine residues within 5'-CG-3' dinucleotides.
      It is possible that the 5'-CCTGG-3' methylating system influences the fate of foreign
      integrated DNA.
AU  - Franchina M
AU  - Kay PH
PT  - Journal Article
TA  - DNA Cell Biol.
JT  - DNA Cell Biol.
SO  - DNA Cell Biol. 2000 19: 521-526.

PMID- 10799969
VI  - 50
DP  - 2000
TI  - Allele-specific variation in the gene copy number of human cytosine 5-methyltransferase.
PG  - 112-117
AB  - Previously, we have identified two alternate allelic forms of cytosine 5-methyltransferase,
      5-MT I and 5-MT II, specified by polymorphic fragments of 1.5 and 1.1 kb, respectively. In the
      presence study, a 0.8-kb genomic probe was prepared which was confirmed to be included within
      the polymorphic fragments. The 0.8-kb probe hybridised with greater intensity to the 1.1-kb
      fragment than the 1.5-kb fragment. Densitometric analysis indicated that there is 1 copy of
      5-MT associated with 5-MT I, whereas there may be 1-4 copies of the gene associated with the
      5-MT II allele. Segregation studies demonstrated that the multiple copies of 5-MT II are
      inherited in a Mendelian fashion. These results allow novel approaches to investigating the
      underlying mechanisms of cytosine methylation and gene duplication.
AU  - Franchina M
AU  - Kay PH
PT  - Journal Article
TA  - Hum. Hered.
JT  - Hum. Hered.
SO  - Hum. Hered. 2000 50: 112-117.

PMID- 29097478
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Staphylococcus aureus 4185, a Strain That Produces Aureocyclicin 4185.
PG  - e01249-17
AB  - The draft genome sequence of the aureocyclicin 4185-producing strain Staphylococcus aureus
      4185 is presented. The assembly contains 2,789,721 bp and a
      G+C content of 32.8%. Genome analysis allowed us to determine the complete
      sequence of the bacteriocinogenic plasmid pRJ101 and to find another bacteriocin
      gene cluster encoded on the bacterial chromosome.
AU  - Francisco MS
AU  - Farias FM
AU  - Santos INS
AU  - Marques-Bastos SLS
AU  - Albano RM
AU  - Bastos MDCF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01249-17.

PMID- 27932645
VI  - 4
DP  - 2016
TI  - Complete Genome Sequences of the Endophytic Streptomyces Strains EN16, EN23, and  EN27, Isolated from Wheat Plants.
PG  - e01342-16
AB  - The complete genome sequences of three endophytic Streptomyces species were compared. Strains
      EN16, EN23, and EN27 were isolated from surface-sterilized
      roots of wheat plants from South Australia. In field trials, these strains are
      effective in suppressing fungal root diseases of wheat when added as spore
      coatings to wheat seed.
AU  - Franco CM
AU  - Araujo R
AU  - Adetutu E
AU  - Tobe SS
AU  - Mallya S
AU  - Paul B
AU  - Satyamoorthy K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01342-16.

PMID- 28619813
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of the Endophytic Streptomyces sp. Strains LUP30 and LUP47B, Isolated from Lucerne Plants.
PG  - e00556-17
AB  - The complete genome sequences of two endophytic Streptomyces sp. strains, LUP30 and LUP47B,
      were analyzed. These strains were isolated from surface-sterilized
      roots of lucerne plants from South Australia and were found to promote the growth
      of the rhizobial partner in vitro and significantly increased nodulation and
      nitrogen fixation in lucerne plants.
AU  - Franco CMM
AU  - Adetutu EM
AU  - Le HX
AU  - Ballard RA
AU  - Araujo R
AU  - Tobe SS
AU  - Paul B
AU  - Mallya S
AU  - Satyamoorthy K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00556-17.

PMID- 27469966
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Agrobacterium rhizogenes Strain NCPPB2659.
PG  - e00746-16
AB  - This work reports the draft genome sequence of Agrobacterium rhizogenes strain NCPPB2659 (also
      known as strain K599). The assembled genome contains 5,277,347 bp, composed of one circular
      chromosome, the pRi2659 virulence plasmid, and 17 scaffolds pertaining to the linear
      chromosome. The wild-type strain causes hairy root disease in dicots and has been used to make
      transgenic hairy root cultures and composite plants (nontransgenic shoots with transgenic
      roots). Disarmed variants of the strain have been used to produce stable transgenic monocot
      and dicot plants.
AU  - Franco JAV
AU  - Collier R
AU  - Wang Y
AU  - Huo N
AU  - Gu Y
AU  - Thilmony R
AU  - Thomson JG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00746-16.

PMID- 26404600
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence and Gene Annotation of Stemphylium lycopersici Strain CIDEFI-216.
PG  - e01069-15
AB  - Stemphylium lycopersici is a plant-pathogenic fungus that is widely distributed throughout the
      world. In tomatoes, it is one of the etiological agents of gray leaf spot disease. Here, we
      report the first draft genome sequence of S. lycopersici, including its gene structure and
      functional annotation.
AU  - Franco ME
AU  - Lopez S
AU  - Medina R
AU  - Saparrat MC
AU  - Balatti P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01069-15.

PMID- 26868405
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Vibrio sp. Strain Evh12, a Bacterium Retrieved from the  Gorgonian Coral Eunicella verrucosa.
PG  - e01729-15
AB  - To shed light on the associations established between Vibrio species and soft corals in
      coastal ecosystems, we report here the draft genome sequence of Vibrio
      sp. strain Evh12, a bacterium that has been isolated from the gorgonian coral
      Eunicella verrucosa and that shows antagonistic activity against Escherichia
      coli.
AU  - Franco T
AU  - Califano G
AU  - Goncalves AC
AU  - Cucio C
AU  - Costa R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01729-15.

PMID- 2557624
VI  - 86
DP  - 1989
TI  - Sequence-specific recognition and cleavage of duplex DNA via triple-helix formation by oligonucleotides covalently linked to a phenanthroline-copper chelate.
PG  - 9702-9706
AB  - Homopyrimidine oligodeoxynucleotides recognize the major groove of the DNA double helix at
      homopurine-homopyrimidine sequences by forming local triple helices. Phenanthroline was
      covalently attached to the 5' end of an 11-mer homopyrimidine oligonuceotide of sequence
      d(TTTCCTCCTCT). Simian virus 40 DNA, which contains a single target site for this
      oligonucleotide, was used as a substrate for the phenanthroline-oligonucleotide conjugate. In
      the presence of copper ions and a reducing agent, a single specific double-strand cleavage
      site was observed at 20oC by agarose gel electrophoresis. The efficiency of double-strand
      cleavage was >70% at 20oC and pH 7.4. Secondary cleavage sites were observed when binding of
      the oligonucleotide to mismatched sequences was allowed to take place at low temperature. The
      exact location of the cleavage sites was determined by polyacrylamide gel electrophoresis of
      denatured fragments by using both simian virus 40 DNA and a synthetic DNA fragment containing
      the target sequence. The asymmetric distribution of the cleavage sites on the two strands
      revealed that the cleavage reaction took place in the minor groove even though the
      phenanthroline linker was located in the major groove. Linkers of different lengths were used
      to tether phenanthroline to the oligonucleotide and their relative efficacies of DNA cleavage
      were compared. Based on these comparative studies and on model building, it is proposed that
      the phenanthroline ring carried by the oligonucleotide intercalates from the major groove and
      that copper chelation locks the complex in place from within the minor groove where the
      cleavage reaction occurs.
AU  - Francois J-C
AU  - Saison-Behmoaras T
AU  - Barbier C
AU  - Chassignol M
AU  - Thuong NT
AU  - Helene C
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1989 86: 9702-9706.

PMID- 2558728
VI  - 28
DP  - 1989
TI  - Inhibition of restriction endonuclease cleavage via triple helix formation by homopyrimidine oligonucleotides.
PG  - 9617-9619
AB  - A 17-mer homopyrimidine oligonucleotide was designed to bind to the major
      groove of SV40 DNA at a 17 base pair homopurine-homopyrimidine sequence via
      Hoogsteen base pairing.  This sequence contains the recognition site for the
      class II-S restriction enzyme Ksp632I.  The oligonucleotide was shown to
      inhibit enzymatic cleavage under conditions that allow for triple helix
      formation.  Inhibition is sequence-specific and occurs in the micromolar
      concentration range.  Triple helix formation by oligonucleotides opens new
      possibilities for sequence-specific regulation of gene expression.
AU  - Francois J-C
AU  - Saison-Behmoaras T
AU  - Thuong NT
AU  - Helene C
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1989 28: 9617-9619.

PMID- 26779178
VI  - 6
DP  - 2015
TI  - The Complete Genome Sequence of the Murine Pathobiont Helicobacter typhlonius.
PG  - 1549
AB  - BACKGROUND: Immuno-compromised mice infected with Helicobacter typhlonius are used to model
      microbially inducted inflammatory bowel disease (IBD). The specific
      mechanism through which H. typhlonius induces and promotes IBD is not fully
      understood. Access to the genome sequence is essential to examine emergent
      properties of this organism, such as its pathogenicity. To this end, we present
      the complete genome sequence of H. typhlonius MIT 97-6810, obtained through
      single-molecule real-time sequencing. RESULTS: The genome was assembled into a
      single circularized contig measuring 1.92 Mbp with an average GC content of
      38.8%. In total 2,117 protein-encoding genes and 43 RNA genes were identified.
      Numerous pathogenic features were found, including a putative pathogenicity
      island (PAIs) containing components of type IV secretion system,
      virulence-associated proteins and cag PAI protein. We compared the genome of H.
      typhlonius to those of the murine pathobiont H. hepaticus and human pathobiont H.
      pylori. H. typhlonius resembles H. hepaticus most with 1,594 (75.3%) of its genes
      being orthologous to genes in H. hepaticus. Determination of the global
      methylation state revealed eight distinct recognition motifs for adenine and
      cytosine methylation. H. typhlonius shares four of its recognition motifs with H.
      pylori. CONCLUSION: The complete genome sequence of H. typhlonius MIT 97-6810
      enabled us to identify many pathogenic features suggesting that H. typhlonius can
      act as a pathogen. Follow-up studies are necessary to evaluate the true nature of
      its pathogenic capabilities. We found many methylated sites and a plethora of
      restriction-modification systems. The genome, together with the methylome, will
      provide an essential resource for future studies investigating gene regulation,
      host interaction and pathogenicity of H. typhlonius. In turn, this work can
      contribute to unraveling the role of Helicobacter in enteric disease.
AU  - Frank J
AU  - Dingemanse C
AU  - Schmitz AM
AU  - Vossen RH
AU  - van Ommen GJ
AU  - den Dunnen JT
AU  - Robanus-Maandag EC
AU  - Anvar SY
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2015 6: 1549.

PMID- 26079637
VI  - 17
DP  - 2015
TI  - Ocean's twelve: Flagellar and biofilm chromids in the multipartite genome of Marinovum algicola DG898 exemplify functional compartmentalization.
PG  - 4019-4034
AB  - The marine bacterium Marinovum algicola DG898 is a representative of the
      Roseobacter group (Rhodobacteraceae, Alphaproteobacteria) and harbors a for
      Proteobacteria unprecedented wealth of eleven extrachromosomal replicons (ECRs).
      The relevance of ECRs has previously been exemplified by photosynthesis and
      biofilm plasmids, but the evolutionary forces for the emergence of multipartite
      genomes are largely unknown. The newly established genome revealed the
      exceptional metabolic potential of Marinovum and its adaptation to the
      phycosphere. Comparative codon usage analyses allowed the identification of eight
      chromids and three plasmids. Functional gene clustering is documented by the
      52-kb biofilm chromid that is required for surface attachment. The most
      conspicuous finding is the presence of a highly expressed chromid-encoded
      flagellum gene cluster (FGC, fla2) that is indispensable for swimming motility.
      M. algicola DG898 harbors an additional chromosome-encoded flagellum (fla1) with
      unknown function. Comprehensive phylogenetic analyses revealed the presence of a
      third FGC type (fla3) in Rhodobacteraceae and indicated the transmission of
      complete FGCs via conjugation. The current Marinovum study indicates a functional
      correlation of the intracellular fla2-chromid localization and the subcellular
      positioning of the flagellum. The proposed mechanism might represent - apart from
      horizontal transfer - a novel driving force for the emergence of multipartite
      genomes.
AU  - Frank O
AU  - Goker M
AU  - Pradella S
AU  - Petersen J
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2015 17: 4019-4034.

PMID- 25197473
VI  - 9
DP  - 2014
TI  - Complete genome sequence of the Phaeobacter gallaeciensis type strain CIP 105210(T) (= DSM 26640(T) = BS107(T)).
PG  - 914-932
AB  - Phaeobacter gallaeciensis CIP 105210(T) (= DSM 26640(T) = BS107(T)) is the type strain of the
      species Phaeobacter gallaeciensis. The genus Phaeobacter belongs to
      the marine Roseobacter group (Rhodobacteraceae, Alphaproteobacteria). Phaeobacter
      species are effective colonizers of marine surfaces, including frequent
      associations with eukaryotes. Strain BS107(T) was isolated from a rearing of the
      scallop Pecten maximus. Here we describe the features of this organism, together
      with the complete genome sequence, comprising eight circular replicons with a
      total of 4,448 genes. In addition to a high number of extrachromosomal replicons,
      the genome contains six genomic island and three putative prophage regions, as
      well as a hybrid between a plasmid and a circular phage. Phylogenomic analyses
      confirm previous results, which indicated that the originally reported P.
      gallaeciensis type-strain deposit DSM 17395 belongs to P. inhibens and that CIP
      105210(T) (= DSM 26640(T)) is the sole genome-sequenced representative of P.
      gallaeciensis.
AU  - Frank O
AU  - Pradella S
AU  - Rohde M
AU  - Scheuner C
AU  - Klenk HP
AU  - Goker M
AU  - Petersen J
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 914-932.

PMID- Not included in PubMed...
VI  - 48
DP  - 1994
TI  - Polymorphism of bacterial restriction-modification systems: the advantage of diversity.
PG  - 1470-1477
AB  - Bacterial restriction-modification systems provide defense against foreign DNA by using a self
      versus nonself recognition mechanism. A great diversity of recognition motifs is maintained in
      natural populations. Circumstantial evidence suggests that defense against bacteriophage
      viruses favors this diversity. (1) Bacterial restriction enzymes can destroy invading phage
      DNA. (2) Phage DNA can mimic the host's self-recognition mechanism. The ability of the virus
      to pose as a mimic favors diversification of the host's recognition motif. Other observations
      suggest that restriction modification (RM) does not provide any significant defensive
      advantages in mature communities. (1) In laboratory experiments, bacteria evolve resistance to
      phage by mutation and selection of the receptors to which phage adsorb. The outcome of these
      experiments is a community dominated by bacteria with receptor-based resistance, with a low
      abundance of phage and susceptible bacteria. (2) Phage are rare and receptor-based resistance
      is common in samples from natural communities. I present a model that shows two factors
      determine community composition: resources and RM diversity. Communities in resource-rich
      habitats are dominated by receptor-based resistance and support few phage; communities in poor
      habitats are dominated by restriction-modification defense and relatively abundant phage. RM
      diversity is itself a direct cause of community composition. As diversity increases from a low
      level, the abundance of phage increases and the relative abundance of receptor-based
      resistance declines. Further increases in diversity cause a crash in phage abundance, yielding
      a stable community of diverse RM types but an absence of the selective pressure--the
      phage--that drove the diversification. Empirical studies must sample a range of resource
      levels and RM diversity to analyze the forces that determine community composition.
AU  - Frank SA
PT  - Journal Article
TA  - Evolution
JT  - Evolution
SO  - Evolution 1994 48: 1470-1477.

PMID- 
VI  - 
DP  - 1983
TI  - Sequence-specific recognition of DNA by the HinfI restriction endonuclease.
PG  - 1-92
AB  - A method has been developed for measuring association constants of DNA-protein
      complexes using gel chromatography.  It is suitable for the study of a variety
      of systems and can be used over a wide range of concentrations.  This technique
      has been used to study the sequence-specific interaction of the HinfI
      restriction endonuclease with DNA.  HinfI has a monomer molecular weight of
      31000 daltons and appears to be active as a dimer.  Its turnover number is 25
      sites cleaved min-1 dimer-1 and its Km is less than 1x10-11M.  The protein was
      found to bind to supercoiled plasmid molecules with an observed free energy of
      association of -13.9 kcal mole-1.  The binding decreases at concentrations of
      NaCl above 50mM and this dependence corresponds to the apparent release of 3.4
      ion pairs.  The affinity of the nuclease for its site was found to be
      independent of pH over the range studied and showed a small dependence on
      temperature.  When the degenerate middle position of the HinfI recognition
      site, 5'GANTC, was varied, no change was observed in the binding constant.  The
      salt and pH dependencies of the cleavage reaction are similar to those of the
      binding constants and each of the degenerate sites studied was equally well
      cleaved.  Linear fragments containing the site are bound as tightly as
      supercoiled molecules.  The enzyme binds to non-specific DNA about 6 orders of
      magnitude more weakly than to its site and is unable to bind to DNA methylated
      at the A position of its recognition site.
AU  - Frankel AD
PT  - Journal Article
TA  - Ph.D. Thesis, Johns Hopkins University, USA
JT  - Ph.D. Thesis, Johns Hopkins University, USA
SO  - Ph.D. Thesis, Johns Hopkins University, USA 1983 : 1-92.

PMID- 2990540
VI  - 24
DP  - 1985
TI  - Measurement of DNA-protein equilibria using gel chromatography:  application to the HinfI restriction endonuclease.
PG  - 3049-3054
AB  - A method is described for measuring equilibrium constants of DNA-protein
      interactions using gel chromatography.  This technique has been used to study
      the sequence-specific interaction of the HinfI restriction endonuclease with
      DNA.  HinfI has a monomeric molecular weight of 31000 and exists as a dimer in
      its active form.  The protein binds to supercoiled DNA molecules containing its
      recognition site with an apparent free energy of -13.9 kcal/mol of sites.  This
      interaction is highly salt sensitive and causes a release of 3.4 ion pairs.
      The affinity of the nuclease for its recognition site is largely independent of
      both pH (6.5-8.5) and temperature (7-35C) and was not affected by variations in
      the degenerate middle position of the site.  Linear DNA fragments containing
      the HinfI recognition site were bound as tightly as supercoiled molecules.
      Binding to nonspecific DNA sites or to methylated DNA sites was approximately 6
      orders of magnitude weaker.  In general, enzyme activity and binding affinity
      parallel each other.
AU  - Frankel AD
AU  - Ackers GK
AU  - Smith HO
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1985 24: 3049-3054.

PMID- 6268796
VI  - 146
DP  - 1981
TI  - Restriction and modification enzymes detect no allosteric changes in DNA with bound lac repressor or RNA polymerase.
PG  - 611-619
AB  - A 203 base-pair fragment containing the lac operator/promoter region of
      Escherichia coli was inserted into the EcoRI site of the plasmid vector pKC7.
      Rates of restriction endonuclease cleavage of the flanking EcoRI sites and of
      several other restriction sites on the DNA molecule were then compared in the
      presence and absence of bound RNA polymerase or lac repressor.  The rates were
      identical whether or not protein had been bound, even for sites as close as 40
      base-pairs from a protein binding site.  No difference was detected using
      supercoiled, nicked circular, or linear DNA substrates.  No apparent change in
      the rates of methylation of EcoRI sites by EcoRI methylase was produced by
      binding the regulatory proteins.
AU  - Frankel AD
AU  - Smith HO
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1981 146: 611-619.

PMID- 5367368
VI  - 14
DP  - 1969
TI  - Genetic evidence for restriction targets in the DNA of phages lambda and Phi80.
PG  - 151-157
AB  - The phenomenon of restriction, recently reviewed in depth by Arber (1968) and
      by Arber and Linn (1969), is observed as the inactivation of a genome following
      transfer from one host to another.  Thus, phages propagated on one host may
      form plaques on a second host with an efficiency lower than that on the first.
      Those progeny phages which do emerge from the second host generally will have
      become modified so that they are no longer restricted in that host.  This
      modification is not replicated, and is diluted out upon further propagation of
      the phages in the first host.  The ability of a bacterium to restrict or to
      modify depends upon three linked bacterial cistrons:  one required for
      restriction, the second for modification and the third required for both
      functions and determining the specificity of each (Glover, Schell, Symonds &
      Stacey, 1963; Wood, 1966, Boyer & Roulland-Dussoix, 1969; Glover & Colson,
      1969).  Restriction of a phage by a bacterium was shown some years ago to be
      exerted directly upon the DNA of the phage after it is injected into the
      bacterial cell (Dussoix & Arber, 1962).  Restricting enzymes have now been
      purified and found to act at only a limited number of sites in the target DNA
      molecule, making double-strand breaks (Meselson & Yuan, 1968; Linn & Arber,
      1968; Roulland-Dussoix & Boyer, 1969).  Subsequent degradation in vivo
      presumably occurs by non-specific nuclease action on these fragments.
      Comparison of the restriction properties of several phages has now led to
      observations of a genetic nature which confirm the conclusion, based on
      biochemical evidence, that restriction is directed at target sites localized
      within the phage genome.  The restriction system of E. coli K12 is far more
      active on phage lambda than on the related phage Phi80.  The restriction
      properties of these phages are unaffected by each other in a trans
      complementation test.  Rather, the restriction properties can be exchanged only
      by genetic recombination, behaving as a small set of mappable restriction
      targets.  Sensitivity of lambda to K restriction can be lost by genetic
      deletion.
AU  - Franklin NC
AU  - Dove WF
PT  - Journal Article
TA  - Genet. Res.
JT  - Genet. Res.
SO  - Genet. Res. 1969 14: 151-157.

PMID- 8514410
VI  - 61
DP  - 1993
TI  - Nucleotide sequence encoding the mannose-fucose-resistant hemagglutinin of Vibrio cholerae O1 and construction of a mutant.
PG  - 3032-3037
AB  - The region of DNA encoding the mannose-fucose-resistant hemagglutinin (MFRHA) of Vibrio
      cholerae O1 has been localized, and the nucleotide sequence has been determined. The region
      contains a single open reading frame encoding 230 amino acids, corresponding to a protein of
      26.9 kDa. The N terminus of this protein is atypical for a protein localized in the outer
      membrane. A mutant lacking MFRHA activity has been constructed by allelic exchange after
      inactivation via the insertion of a kanamycin resistance gene cartridge. The MFRHA-negative
      mutant has been assessed for virulence in the infant mouse cholera model. This mutant shows a
      marked defect in its ability to persist in the infant mouse gut and is incapable of competing
      with the wild-type organism, even when given in 25-fold excess. This defect also leads to a >
      100-fold increase in the 50% lethal dose. These data suggest that the MFRHA is an important
      colonization factor in the infant mouse model.
AU  - Franzon VL
AU  - Barker A
AU  - Manning PA
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 1993 61: 3032-3037.

PMID- 7569993
VI  - 270
DP  - 1995
TI  - The minimal gene complement of Mycoplasma genitalium.
PG  - 397-403
AB  - The complete nucleotide sequence (580,070 base pairs) of the Mycoplasma genitalium genome, the
      smallest known genome of any free-living organism, has been determined by whole-genome random
      sequencing and assembly.  A total of only 470 predicted coding regions were identified that
      include genes required for DNA replication, transcription and translation, DNA repair,
      cellular transport, and energy metabolism.  Comparison of this genome to that of Haemophilus
      influenzae suggests that differences in genome content are reflected as profound differences
      in physiology and metabolic capacity between these two organisms.
AU  - Fraser CM et al
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1995 270: 397-403.

PMID- 9403685
VI  - 390
DP  - 1997
TI  - Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi.
PG  - 580-586
AB  - The genome of the bacterium Borrelia burgdorferi B31, the aetiologic agent of Lyme disease,
      contains a linear chromosome of 910,725 base pairs and at least 17 linear and circular
      plasmids with a combined size of more than 53,000 base pairs.  The chromosome contains 853
      genes encoding a basic set of proteins for DNA replication, transcription, translation, solute
      transport and energy metabolism, but, like Mycoplasma genitalium, it contains no genes for
      cellular biosynthetic reactions.  Because B. burgdorferi and M. genitalium are distantly
      related eubacteria, we suggest that their limited metabolic capacities reflect convergent
      evolution by gene loss from more metabolically competent progenitors.  Of 430 genes on 11
      plasmids, most have no known biological function; 39% of plasmid genes are paralogues that
      form 47 gene families.  The biological significance of the multiple plasmid-encoded genes is
      not clear, although they may be involved in antigenic variation or immune evasion.
AU  - Fraser CM et al
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1997 390: 580-586.

PMID- 9665876
VI  - 281
DP  - 1998
TI  - Complete genome sequence of Treponema pallidum, the syphilis spirochete.
PG  - 375-388
AB  - The complete genome sequence of Treponema pallidum was determined and shown to be 1,138,006
      pairs containing 1041 predicted coding sequences (open reading frames).  Systems for DNA
      replication, transcription, translation, and repair are intact, but catabolic and biosynthetic
      activities are minimized.  The number of identifiable transporters is small, and no
      phosphoenolpyruvate: phosphotransferase carbohydrate transporters were found.  Potential
      virulence factors include a family of 12 potential membrane proteins and several putative
      hemolysins.  Comparison of the T. pallidum genome sequence with that of another pathogenic
      spirochete, Borrelia burgdorferi, the agent of Lyme disease, identified unique and common
      genes and substantiates the considerable diversity observed among pathogenic spirochetes.
AU  - Fraser CM et al
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1998 281: 375-388.

PMID- 21593412
VI  - 108
DP  - 2011
TI  - Twists and turns of DNA methylation.
PG  - 8919-8920
AB  - DNA methylation, the post-replicative transfer of a methyl group to the C5 position of
      cytosine bases, was the first epigenetic modification identified and has been intensively
      studied for more than half a century.  By now it is clear that Dnmt1, the major eukaryotic DNA
      methyltransferase, faithfully maintains genome-wide methylation patterns and plays an
      essential role in the epigenetic network controlling gene expression and genome stability
      during development.  However, the molecular mechanisms that ultimately control DNA methylation
      still remain elusive.  This is, in part, attributable to the remarkable complexity of the DNA
      methylation reaction, the apparent involvement of several inter- and intra-molecular protein
      interactions, and the limited structural information.  The crystal structure of Dnmt1
      presented in PNAS now provides detailed insights into the inner workings and possible
      regulation of one of the most intriguing enzymes.
AU  - Frauer C
AU  - Leonhardt H
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2011 108: 8919-8920.

PMID- 19129216
VI  - 37
DP  - 2009
TI  - A versatile non-radioactive assay for DNA methyltransferase activity and DNA binding.
PG  - e22
AB  - We present a simple, non-radioactive assay for DNA methyltransferase activity and DNA binding.
      As most proteins are studied as GFP fusions in
      living cells, we used a GFP binding nanobody coupled to agarose beads (GFP
      nanotrap) for rapid one-step purification. Immobilized GFP fusion proteins
      were subsequently incubated with different fluorescently labeled DNA
      substrates. The absolute amounts and molar ratios of GFP fusion proteins
      and bound DNA substrates were determined by fluorescence spectroscopy. In
      addition to specific DNA binding of GFP fusion proteins, the enzymatic
      activity of DNA methyltransferases can also be determined by using suicide
      DNA substrates. These substrates contain the mechanism-based inhibitor
      5-aza-dC and lead to irreversible covalent complex formation. We obtained
      covalent complexes with mammalian DNA methyltransferase 1 (Dnmt1), which
      were resistant to competition with non-labeled canonical DNA substrates,
      allowing differentiation between methyltransferase activity and DNA
      binding. By comparison, the Dnmt1(C1229W) catalytic site mutant showed
      DNA-binding activity, but no irreversible covalent complex formation. With
      this assay, we could also confirm the preference of Dnmt1 for
      hemimethylated CpG sequences. The rapid optical read-out in a multi-well
      format and the possibility to test several different substrates in direct
      competition allow rapid characterization of sequence-specific binding and
      enzymatic activity.
AU  - Frauer C
AU  - Leonhardt H
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: e22.

PMID- 28663299
VI  - 5
DP  - 2017
TI  - Multiple Genome Sequences of Exopolysaccharide-Producing, Brewery-Associated Lactobacillus brevis Strains.
PG  - e00585-17
AB  - Lactobacillus brevis represents one of the most relevant beer-spoiling bacteria.  Besides
      strains causing turbidity and off flavors upon growth and metabolite
      formation, this species also comprises strains that produce exopolysaccharides
      (EPSs), which increase the viscosity of beer. Here, we report the complete genome
      sequences of three EPS-producing, brewery-associated L. brevis strains.
AU  - Fraunhofer ME
AU  - Geissler AJ
AU  - Jakob F
AU  - Vogel RF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00585-17.

PMID- 24072870
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Staphylococcus aureus 6850, a Highly Cytotoxic and Clinically Virulent Methicillin-Sensitive Strain with Distant Relatedness to  Prototype Strains.
PG  - e00775-13
AB  - Staphylococcus aureus is a frequent human commensal bacterium and pathogen. Here  we report
      the complete genome sequence of strain 6850 (spa type t185; sequence
      type 50 [ST50]), a highly cytotoxic and clinically virulent methicillin-sensitive
      strain from a patient with complicated S. aureus bacteremia associated with
      osteomyelitis and septic arthritis.
AU  - Fraunholz M
AU  - Bernhardt J
AU  - Schuldes J
AU  - Daniel R
AU  - Hecker M
AU  - Sinha B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00775-13.

PMID- 29674540
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of 116 Campylobacter jejuni Strains Isolated from Humans,  Animals, Food, and the Environment in Brazil.
PG  - e00250-18
AB  - Campylobacter jejuni is a major zoonotic pathogen that causes foodborne gastroenteritis
      worldwide. However, clinical cases of campylobacteriosis have
      been underreported and underdiagnosed in Brazil. Herein, we describe the draft
      genome sequences of 116 C. jejuni strains isolated from diverse sources in
      Brazil.
AU  - Frazao MR
AU  - Cao G
AU  - Medeiros MIC
AU  - Duque SDS
AU  - Leon MS
AU  - Allard MW
AU  - Falcao JP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00250-18.

PMID- 6328307
VI  - 309
DP  - 1984
TI  - Kinked DNA in crystalline complex with EcoRI endonuclease.
PG  - 327-331
AB  - The 3 angstrom electron density map of a co-crystalline recognition complex
      between EcoRI endonuclease and the oligonucleotide TCGCGAATTCGCG reveals that a
      tight, complementary interface between the enzyme and the major groove of the
      DNa is the major determinant of sequence specificity.  The DNA contains a
      torsional kink and other departures from the B conformation which unwind the
      DNA and thereby widen the major groove in the recognition site.
AU  - Frederick CA
AU  - Grable J
AU  - Melia M
AU  - Samudzi C
AU  - Jen-Jacobson L
AU  - Wang B-C
AU  - Greene P
AU  - Boyer HW
AU  - Rosenberg JM
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1984 309: 327-331.

PMID- 2846582
VI  - 263
DP  - 1988
TI  - Methylation of the EcoRI recognition site does not alter DNA conformation:  The crystal structure of d(CGCGAm6ATTCGCG) at 2.0-A resolution.
PG  - 17872-17879
AB  - Methylation of nucleic acid bases is known to prevent the cleavage of DNA by
      restriction endonucleases.  The effect on the conformation of the DNA molecule
      itself and hence its interactions with other DNA binding proteins has been a
      subject of general interest.  To help address this question, we have solved the
      crystal structure at 2.0 A of the methylated dodecamer, d(CGCGAm6ATTCGCG),
      which contains the EcoRI recognition sequence and have compared the
      conformation of the methylated molecule with that of its nonmethylated
      counterpart.  This methylation produces a bulky hydrophobic patch on the floor
      of the major groove of B-DNA which plays an important role in the mechanism of
      inhibition of EcoRI restriction activity.  However, with the exception of small
      perturbations in the immediate vicinity of the methyl groups, the structure is
      virtually unchanged.  Given the lack of a conformational change upon
      methylation, we have extended this thesis of the recognition process to other
      types of restriction systems and found that different restriction enzymes seem
      to have their own characteristic protein-DNA interactions.  The relative
      spatial orientations of methylation sites and cleavage sites must play a major
      role in ordering protein secondary structure elements as well as
      subunit-subunit interactions along the DNA strand.
AU  - Frederick CA
AU  - Quigley GJ
AU  - van der Marel GA
AU  - van Boom JH
AU  - Wang AH-J
AU  - Rich A
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1988 263: 17872-17879.

PMID- 11035019
VI  - 276
DP  - 2001
TI  - DNA recognition by the methyl-CpG binding domain of MeCP2.
PG  - 3353-3360
AB  - The methyl-CpG binding domain (MBD) of the transcriptional repressor MeCP2 has been proposed
      to recognize a single symmetrically methylated CpG base pair via hydrophobic patches on an
      otherwise positively charged DNA binding surface. We have tested this binding model by
      analysis of mutant derivatives of the MeCP2 MBD in electrophoretic mobility shift assays
      complemented by NMR structural analysis. Exposed arginine side chains on the binding face, in
      particular Arg-111, were found to be critical for binding. Arg-111 was found to interact with
      the conserved aspartate side chain Asp-121, which is proposed to orientate the arginine side
      chain to allow specific contacts with the DNA. The conformational flexibility of the
      disordered B-C loop region, which forms part of the binding face, was also shown to be
      important. In contrast, mutation of the exposed hydrophobic side chains had a less severe
      effect on DNA binding. This suggests that the Arg-111 side chain may contribute to
      sequence-specific recognition of the CpG site rather than simply making nonspecific contacts
      with the phosphate backbone. The majority of missense mutations within the MBD found in the
      human genetic disorder Rett syndrome were shown or predicted to affect folding of the domain
      rather than the DNA recognition event directly.
AU  - Free A
AU  - Wakefield RI
AU  - Smith BO
AU  - Dryden DT
AU  - Barlow PN
AU  - Bird AP
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2001 276: 3353-3360.

PMID- 24501630
VI  - 8
DP  - 2013
TI  - Genome sequence of the phage-gene rich marine Phaeobacter arcticus type strain DSM 23566(T.).
PG  - 450-464
AB  - Phaeobacter arcticus Zhang et al. 2008 belongs to the marine Roseobacter clade whose members
      are phylogenetically and physiologically diverse. In contrast to
      the type species of this genus, Phaeobacter gallaeciensis, which is well
      characterized, relatively little is known about the characteristics of P.
      arcticus. Here, we describe the features of this organism including the annotated
      high-quality draft genome sequence and highlight some particular traits. The
      5,049,232 bp long genome with its 4,828 protein-coding and 81 RNA genes consists
      of one chromosome and five extrachromosomal elements. Prophage sequences
      identified via PHAST constitute nearly 5% of the bacterial chromosome and
      included a potential Mu-like phage as well as a gene-transfer agent (GTA). In
      addition, the genome of strain DSM 23566(T) encodes all of the genes necessary
      for assimilatory nitrate reduction. Phylogenetic analysis and intergenomic
      distances indicate that the classification of the species might need to be
      reconsidered.
AU  - Freese HM et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 450-464.

PMID- 28912769
VI  - 8
DP  - 2017
TI  - Adaptation of Surface-Associated Bacteria to the Open Ocean: A Genomically Distinct Subpopulation of Phaeobacter gallaeciensis Colonizes Pacific Mesozooplankton.
PG  - 1659
AB  - The marine Roseobacter group encompasses numerous species which occupy a large
      variety of ecological niches. However, members of the genus Phaeobacter are
      specifically adapted to a surface-associated lifestyle and have so far been found
      nearly exclusively in disjunct, man-made environments including shellfish and
      fish aquacultures, as well as harbors. Therefore, the possible natural habitats,
      dispersal and evolution of Phaeobacter spp. have largely remained obscure.
      Applying a high-throughput cultivation strategy along a longitudinal Pacific
      transect, the present study revealed for the first time a widespread natural
      occurrence of Phaeobacter in the marine pelagial. These bacteria were found to be
      specifically associated to mesoplankton where they constitute a small but
      detectable proportion of the bacterial community. The 16S rRNA gene sequences of
      18 isolated strains were identical to that of Phaeobacter gallaeciensis
      DSM26640(T) but sequences of internal transcribed spacer and selected genomes
      revealed that the strains form a distinct clade within P. gallaeciensis. The
      genomes of the Pacific and the aquaculture strains were highly conserved and had
      a fraction of the core genome of 89.6%, 80 synteny breakpoints, and differed 2.2%
      in their nucleotide sequences. Diversification likely occurred through neutral
      mutations. However, the Pacific strains exclusively contained two active Type I
      restriction modification systems which is commensurate with a reduced acquisition
      of mobile elements in the Pacific clade. The Pacific clade of P. gallaeciensis
      also acquired a second, homolog phosphonate transport system compared to all
      other P. gallaeciensis. Our data indicate that a previously unknown, distinct
      clade of P. gallaeciensis acquired a limited number of clade-specific genes that
      were relevant for its association with mesozooplankton and for colonization of
      the marine pelagial. The divergence of the Pacific clade most likely was driven
      by the adaptation to this novel ecological niche rather than by geographic
      isolation.
AU  - Freese HM
AU  - Methner A
AU  - Overmann J
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2017 8: 1659.

PMID- 29194520
VI  - 9
DP  - 2017
TI  - Trajectories and Drivers of Genome Evolution in Surface-Associated Marine Phaeobacter.
PG  - 3297-3311
AB  - The extent of genome divergence and the evolutionary events leading to speciation of marine
      bacteria have mostly been studied for (locally) abundant, free-living
      groups. The genus Phaeobacter is found on different marine surfaces, seems to
      occupy geographically disjunct habitats, and is involved in different biotic
      interactions, and was therefore targeted in the present study. The analysis of
      the chromosomes of 32 closely related but geographically spread Phaeobacter
      strains revealed an exceptionally large, highly syntenic core genome. The
      flexible gene pool is constantly but slightly expanding across all Phaeobacter
      lineages. The horizontally transferred genes mostly originated from bacteria of
      the Roseobacter group and horizontal transfer most likely was mediated by gene
      transfer agents. No evidence for geographic isolation and habitat specificity of
      the different phylogenomic Phaeobacter clades was detected based on the sources
      of isolation. In contrast, the functional gene repertoire and physiological
      traits of different phylogenomic Phaeobacter clades were sufficiently distinct to
      suggest an adaptation to an associated lifestyle with algae, to additional
      nutrient sources, or toxic heavy metals. Our study reveals that the evolutionary
      trajectories of surface-associated marine bacteria can differ significantly from
      free-living marine bacteria or marine generalists.
AU  - Freese HM
AU  - Sikorski J
AU  - Bunk B
AU  - Scheuner C
AU  - Meier-Kolthoff JP
AU  - Sproer C
AU  - Gram L
AU  - Overmann J
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2017 9: 3297-3311.

PMID- 15797202
VI  - 15
DP  - 2005
TI  - Controlling DNA methylation: many roads to one modification.
PG  - 191-199
AB  - Genetic, biochemical and cytological studies on DNA methylation in several eukaryotic
      organisms have resulted in leaps of understanding in the past three years. Discoveries of
      mechanistic links between DNA methylation and histone methylation, and between these processes
      and RNA interference (RNAi) machineries have reinvigorated the field. The details of the
      connections between DNA methylation, histone modifications and RNA silencing remain to be
      elucidated, but it is already clear that no single pathway accounts for all DNA methylation
      found in eukaryotes. Rather, different taxa use one or more of several general mechanisms to
      control methylation. Despite recent progress, classic questions remain, including: What are
      the signals for DNA methylation? Are 'de novo' and 'maintenance' methylation truly
      separate processes? How is DNA methylation regulated?
AU  - Freitag M
AU  - Selker EU
PT  - Journal Article
TA  - Curr. Opin. Genet. Dev.
JT  - Curr. Opin. Genet. Dev.
SO  - Curr. Opin. Genet. Dev. 2005 15: 191-199.

PMID- 12072568
VI  - 99
DP  - 2002
TI  - A cytosine methyltransferase homologue is essential for repeat-induced point mutation in Neurospora crassa.
PG  - 8802-8807
AB  - During sexual development, Neurospora crassa inactivates genes in duplicated DNA segments by a
      hypermutation process, repeat-induced point mutation (RIP). RIP introduces C:G to T:A
      transition mutations and creates targets for subsequent DNA methylation in vegetative tissue.
      The mechanism of RIP and its relationship to DNA methylation are not fully understood.
      Mutations in DIM-2, a DNA methyltransferase (DMT) responsible for all known cytosine
      methylation in Neurospora, does not prevent RIP. We used RIP to disrupt a second putative DMT
      gene in the Neurospora genome and tested mutants for defects in DNA methylation and RIP. No
      effect on DNA methylation was detected in the tissues that could be assayed, but the mutants
      showed recessive defects in RIP. Duplications of the am and mtr genes were completely stable
      in crosses homozygous for the mutated potential DMT gene, which we call rid (RIP defective).
      The same duplications were inactivated normally in heterozygous crosses. Disruption of the rid
      gene did not noticeably affect fertility, growth, or development. In contrast, crosses
      homozygous for a mutation in a related gene in Ascobolus immersus, masc1, reportedly fail to
      develop and heterozygous crosses reduce methylation induced premeiotically .  We isolated
      homologues of rid from Neurospora tetrasperma and Neurospora intermedia to identify conserved
      regions. Homologues possess all motifs characteristic of eukaryotic DMTs and have large
      distinctive C- and N-terminal domains.
AU  - Freitag M
AU  - Williams RL
AU  - Kothe GO
AU  - Selker EU
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2002 99: 8802-8807.

PMID- 29326217
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Bifidobacterium Strains N4G05 and N5G01, Isolated from  the Human Vaginal Microbiome.
PG  - e01433-17
AB  - We report here the draft genome sequences of Bifidobacterium strains N4G05 and N5G01, isolated
      from the human vaginal microbiome. Genome sequences were obtained
      by de novo assembly from high-quality reads. Both strains were closely related to
      Bifidobacterium kashiwanohense based on barcode marker sequences and average
      nucleotide identity analysis.
AU  - Freitas AC
AU  - Hill JE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01433-17.

PMID- Not carried by PubMed...
VI  - 0
DP  - 1998
TI  - DNA inversions regulate a family of phase-variable restriction and modification enzymes in Mycoplasma pulmonis.
PG  - 274-275
AB  - Mycoplasma pulmonis is a murine pathogen that produces chronic disease in the reproductive and
      respiratory tracts and joints.  The ability to undergo rapid phenotypic changes is probably an
      important pathogenic attribute allowing the organism to quickly adapt to a changing
      environment.  The hsd1 and hsd2 loci of M. pulmonis are highly homologous, site-specific DNA
      inversion systems that encode proteins exhibiting significant amino acid similarity with the
      type I restriction and modification systems of enteric bacteria.  DNA inversions regulate
      transcription of the hsdS genes, acting as an on/off switches controlling which particular
      hsdS genes are expressed in the cell.  The hsdS genes encode the S subunits which dictate the
      sequence specificity of the type I holoenzyme.  We hypothesized that the various hsdS genes
      that can be induced by DNA inversion encode S subunits with different DNA recognition
      specificities, resulting in the production of R-M enzymes with different specificities.  To
      test this possibility, cultures of M. pulmonis was subcloned using filter cloning methods.
      R-M properties were examined by quantitating PFU of mycoplasma virus P1 on lawns of each
      individual subclone.  The R-M properties of over 100 subclones have been examined thus far.
      Subclones have been divided into five groups, each with unique R-M properties.  Group I is R-M
      negative.  Southern blot and hsd mRNA transcription anlayses suggest that R-M systems are
      "off" in these subclones because the hsd1 and hsd2 loci are oriented in the chromosome such
      that the hsdR and hsdM genes (encoding the R and M subunits of the type I holoenzyme) are not
      transcribed.  Groups II, III, IV and V are R-M positive, with the specificity of the R-M
      activity of each group being distinct.  Gene analyses (Southern hybridization, PCR and
      nucleotide sequencing indicate that different hsdS genes are transcribed in the different
      groups, explaining the unique R-M properties of each group.  These results indicate that M.
      pulmonis possesses a novel family of phase-variable R-M enzymes.  Because hsd inversions have
      previously been correlated with other gene rearrangements that regulate the phase-variable
      production of the V-1 surface proteins, it is possible that R-M enzymes in this system have an
      important but undefined role in disease pathogenesis.
AU  - French CT
AU  - Sitaraman R
AU  - Dybvig K
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1998 0: 274-275.

PMID- 23723405
VI  - 1
DP  - 2013
TI  - Genome of the Psychrophilic Bacterium Bacillus psychrosaccharolyticus, a Potential Source of 2'-Deoxyribosyltransferase for Industrial Nucleoside  Synthesis.
PG  - e00309-13
AB  - Here we report the draft genome sequence of Bacillus psychrosaccharolyticus, a cold-adapted
      bacterium with biotechnological interest. The genome contains genes
      related to the ability of this microorganism to grow at low temperatures and
      includes a nucleoside 2'-deoxyribosyltransferase, which can be used in the
      industrial synthesis of modified nucleosides with therapeutic activity.
AU  - Fresco-Taboada A
AU  - Del Cerro C
AU  - Fernandez-Lucas J
AU  - Arroyo M
AU  - Acebal C
AU  - Garcia JL
AU  - de la Mata I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00309-13.

PMID- Not carried by PubMed...
VI  - 343
DP  - 1992
TI  - Screening for novel class-II restriction endonucleases.
PG  - 123-124
AB  - More than 1500 class-II restriction endonucleases have been isolated from eu- and
      archaebacteria. In addition only a few restriction enzymes were described from eukaryotic
      sources like virus infected chlorella-like green algae. These enzymes represent more than 170
      different sequence specificities. Class-II restriction endonucleases are important tools in
      recombinant DNA technology. In addition restriction enzymes recognizing octa- and
      heptanucleotide sequences are necessary for the mapping of genomes because they produce very
      large fragments that can be resolved by pulse field gel electrophoresis. Our aim was to find
      and characterize new restriction enzymes and determine the specificities with respect to their
      recognition sequence and cleavage position.
AU  - Frey B
AU  - Kahle C
AU  - Zolch C
AU  - Kaluza K
AU  - Herz G
AU  - Lechner M
AU  - Auer J
AU  - Schmitz G
PT  - Journal Article
TA  - Fresenius Z. Anal. Chem.
JT  - Fresenius Z. Anal. Chem.
SO  - Fresenius Z. Anal. Chem. 1992 343: 123-124.

PMID- 1641345
VI  - 20
DP  - 1992
TI  - AspEI, a novel Eam11051 isoschizomer from Aureobacterium species recognizing 5'-GACnnn/nnGTC-3' .
PG  - 3782
AB  - We have isolated AspEI, a novel class II restriction endonuclease from Aureobacterium species
      3676 recognizing the palindromic sequence 5'-GACnnn/nnGTC-3' generating a 3'-protruding
      mononucleotide. With respect to its isoschizomer from Eam1105I, the novel enzyme can be easily
      isolated in high purity because of its occurrence as a single restriction enzyme in the
      Aureobacterium strain and the presence of high specific activity even in the crude extract. A
      comparison of cleavage patterns experimentally obtained with AspEI on standard lambda,
      phiX174RF, pBR322, T7 and Ad2 DNAs of known nucleotide sequence, with computer-derived mapping
      data predicts the sequence 5'-GACn5GTC-3'. The cut positions within the AspEI recognitin
      site were determined according to the enzymatic sequencing approach.
AU  - Frey B
AU  - Kaluza K
AU  - Auer J
AU  - Stratidakis I
AU  - Rina M
AU  - Bouriotis V
AU  - Schmitz G
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 3782.

PMID- 25342690
VI  - 2
DP  - 2014
TI  - Full-Genome Assembly of Reference Strain Providencia stuartii ATCC 33672.
PG  - e01082-14
AB  - A member of the normal human gut microflora, Providencia stuartii is of clinical  interest due
      to its role in nosocomial infections of the urinary tract and
      because it readily acquires antibiotic resistance. Here, we present the complete
      genome of P. stuartii strain ATCC 33672, consisting of a 4.28-Mbp chromosome and
      a 48.9-kbp plasmid.
AU  - Frey KG
AU  - Bishop-Lilly KA
AU  - Daligault HE
AU  - Davenport KW
AU  - Bruce DC
AU  - Chain PS
AU  - Coyne SR
AU  - Chertkov O
AU  - Freitas T
AU  - Jaissle J
AU  - Koroleva GI
AU  - Ladner JT
AU  - Minogue TD
AU  - Palacios GF
AU  - Redden CL
AU  - Xu Y
AU  - Johnson SL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01082-14.

PMID- 29348343
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Coxiella burnetii Historical Strain Leningrad-2, Isolated from Blood of a Patient with Acute Q Fever in Saint Petersburg, Russia.
PG  - e01464-17
AB  - This is the announcement of a draft genome sequence of Coxiella burnetii strain Leningrad-2,
      phase I. The strain, which is mildly virulent in infected guinea
      pigs, was isolated in 1957 from the blood of a patient with acute Q fever in
      Leningrad (now Saint Petersburg), Russia.
AU  - Freylikhman O
AU  - Kiselev A
AU  - Kazakov S
AU  - Sergushichev A
AU  - Panferova Y
AU  - Tokarevich N
AU  - Kostareva A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01464-17.

PMID- 21602358
VI  - 193
DP  - 2011
TI  - Comparative genomics of 28 Salmonella enterica isolates: evidence for CRISPR-mediated adaptive sublineage evolution.
PG  - 3556-3568
AB  - Despite extensive surveillance, food-borne Salmonella enterica infections
      continue to be a significant burden on public health systems worldwide. As
      the S. enterica species comprises sublineages that differ greatly in
      antigenic representation, virulence, and antimicrobial resistance
      phenotypes, a better understanding of the species' evolution is critical
      for the prediction and prevention of future outbreaks. The roles that
      virulence and resistance phenotype acquisition, exchange, and loss play in
      the evolution of S. enterica sublineages, which to a certain extent are
      represented by serotypes, remains mostly uncharacterized. Here, we compare
      17 newly sequenced and phenotypically characterized nontyphoidal S.
      enterica strains to 11 previously sequenced S. enterica genomes to carry
      out the most comprehensive comparative analysis of this species so far.
      These phenotypic and genotypic data comparisons in the phylogenetic
      species context suggest that the evolution of known S. enterica
      sublineages is mediated mostly by two mechanisms, (i) the loss of coding
      sequences with known metabolic functions, which leads to functional
      reduction, and (ii) the acquisition of horizontally transferred phage and
      plasmid DNA, which provides virulence and resistance functions and leads
      to increasing specialization. Matches between S. enterica clustered
      regularly interspaced short palindromic repeats (CRISPR), part of a
      defense mechanism against invading plasmid and phage DNA, and plasmid and
      prophage regions suggest that CRISPR-mediated immunity could control
      short-term phenotype changes and mediate long-term sublineage evolution.
      CRISPR analysis could therefore be critical in assessing the evolutionary
      potential of S. enterica sublineages and aid in the prediction and
      prevention of future S. enterica outbreaks.
AU  - Fricke WF
AU  - Mammel MK
AU  - McDermott PF
AU  - Tartera C
AU  - White DG
AU  - Leclerc JE
AU  - Ravel J
AU  - Cebula TA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3556-3568.

PMID- 19648374
VI  - 75
DP  - 2009
TI  - Antimicrobial resistance-conferring plasmids with similarity to virulence plasmids from avian pathogenic Escherichia coli strains in Salmonella enterica serovar Kentucky isolates from poultry.
PG  - 5963-5971
AB  - Salmonella enterica, a leading cause of food-borne gastroenteritis
      worldwide, may be found in any raw food of animal, vegetable, or fruit
      origin. Salmonella serovars differ in distribution, virulence, and host
      specificity. Salmonella enterica serovar Kentucky, though often found in
      the food supply, is less commonly isolated from ill humans. The
      multidrug-resistant isolate S. Kentucky CVM29188, isolated from a chicken
      breast sample in 2003, contains three plasmids (146,811 bp, 101,461 bp,
      and 46,121 bp), two of which carry resistance determinants (pCVM29188_146
      [strAB and tetRA] and pCVM29188_101 [bla(CMY-2) and sugE]). Both
      resistance plasmids were transferable by conjugation, alone or in
      combination, to S. Kentucky, Salmonella enterica serovar Newport, and
      Escherichia coli recipients. pCVM29188_146 shares a highly conserved
      plasmid backbone of 106 kb (>90% nucleotide identity) with two virulence
      plasmids from avian pathogenic Escherichia coli strains (pAPEC-O1-ColBM
      and pAPEC-O2-ColV). Shared avian pathogenic E. coli (APEC) virulence
      factors include iutA iucABCD, sitABCD, etsABC, iss, and iroBCDEN. PCR
      analyses of recent (1997 to 2005) S. Kentucky isolates from food animal,
      retail meat, and human sources revealed that 172 (60%) contained similar
      APEC-like plasmid backbones. Notably, though rare in human- and
      cattle-derived isolates, this plasmid backbone was found at a high
      frequency (50 to 100%) among S. Kentucky isolates from chickens within the
      same time span. Ninety-four percent of the APEC-positive isolates showed
      resistance to tetracycline and streptomycin. Together, our findings of a
      resistance-conferring APEC virulence plasmid in a poultry-derived S.
      Kentucky isolate and of similar resistance/virulence plasmids in most
      recent S. Kentucky isolates from chickens and, to lesser degree, from
      humans and cattle highlight the need for additional research in order to
      examine the prevalence and spread of combined virulence and resistance
      plasmids in bacteria in agricultural, environmental, and clinical
      settings.
AU  - Fricke WF
AU  - McDermott PF
AU  - Mammel MK
AU  - Zhao S
AU  - Johnson TJ
AU  - Rasko DA
AU  - Fedorka-Cray PJ
AU  - Pedroso A
AU  - Whichard JM
AU  - Leclerc JE
AU  - White DG
AU  - Cebula TA
AU  - Ravel J
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2009 75: 5963-5971.

PMID- 16385054
VI  - 188
DP  - 2006
TI  - The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis.
PG  - 642-658
AB  - Methanosphaera stadtmanae has the most restricted energy metabolism of all methanogenic
      archaea. This human intestinal inhabitant can generate methane only by reduction of methanol
      with H2 and is dependent on acetate as a carbon source. We report here the genome sequence of
      M. stadtmanae, which was found to be composed of 1,767,403 bp with an average G+C content of
      28% and to harbor only 1,534 protein-encoding sequences (CDS). The genome lacks 37 CDS present
      in the genomes of all other methanogens. Among these are the CDS for synthesis of
      molybdopterin and for synthesis of the carbon monoxide dehydrogenase/acetyl-coenzyme A
      synthase complex, which explains why M. stadtmanae cannot reduce CO2 to methane or oxidize
      methanol to CO2 and why this archaeon is dependent on acetate for biosynthesis of cell
      components. Four sets of mtaABC genes coding for methanol:coenzyme M methyltransferases were
      found in the genome of M. stadtmanae. These genes exhibit homology to mta genes previously
      identified in Methanosarcina species. The M. stadtmanae genome also contains at least 323 CDS
      not present in the genomes of all other archaea. Seventy-three of these CDS exhibit high
      levels of homology to CDS in genomes of bacteria and eukaryotes. These 73 CDS include 12 CDS
      which are unusually long (>2,400 bp) with conspicuous repetitive sequence elements, 13 CDS
      which exhibit sequence similarity on the protein level to CDS encoding enzymes involved in the
      biosynthesis of cell surface antigens in bacteria, and 5 CDS which exhibit sequence similarity
      to the subunits of bacterial type I and III restriction-modification systems.
AU  - Fricke WF
AU  - Seedorf H
AU  - Henne A
AU  - Kruer M
AU  - Liesegang H
AU  - Hedderich R
AU  - Gottschalk G
AU  - Thauer RK
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2006 188: 642-658.

PMID- 25043002
VI  - 513
DP  - 2014
TI  - Optimization of lag time underlies antibiotic tolerance in evolved bacterial populations.
PG  - 418-421
AB  - The great therapeutic achievements of antibiotics have been dramatically undercut by the
      evolution of bacterial strategies that overcome antibiotic stress. These strategies fall into
      two classes. 'Resistance' makes it possible for a microorganism to grow in the constant
      presence of the antibiotic, provided that the concentration of the antibiotic is not too high.
      'Tolerance' allows a microorganism to survive antibiotic treatment, even at high antibiotic
      concentrations, as long as the duration of the treatment is limited. Although both resistance
      and tolerance are important reasons for the failure of antibiotic treatments, the evolution of
      resistance is much better understood than that of tolerance. Here we followed the evolution of
      bacterial populations under intermittent exposure to the high concentrations of antibiotics
      used in the clinic and characterized the evolved strains in terms of both resistance and
      tolerance. We found that all strains adapted by specific genetic mutations, which became fixed
      in the evolved populations. By monitoring the phenotypic changes at the population and
      single-cell levels, we found that the first adaptive change to antibiotic stress was the
      development of tolerance through a major adjustment in the single-cell lag-time distribution,
      without a change in resistance. Strikingly, we found that the lag time of bacteria before
      regrowth was optimized to match the duration of the antibiotic-exposure interval. Whole genome
      sequencing of the evolved strains and restoration of the wild-type alleles allowed us to
      identify target genes involved in this antibiotic-driven phenotype: 'tolerance by lag'
      (tbl). Better understanding of lag-time evolution as a key determinant of the survival of
      bacterial populations under high antibiotic concentrations could lead to new approaches to
      impeding the evolution of antibiotic resistance.
AU  - Fridman O
AU  - Goldberg A
AU  - Ronin I
AU  - Shoresh N
AU  - Balaban NQ
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2014 513: 418-421.

PMID- 9989607
VI  - 443
DP  - 1999
TI  - Cleavage experiments with deoxythymidine 3',5'-bis-(p-nitrophenyl phosphate) suggest that the homing endonuclease I-PpoI follows the same mechanism of phosphodiester bond hydrolysis as the non-specific Serratia nuclease.
PG  - 209-214
AB  - We show here that two nucleases, Serratia nuclease and I-PpoI, with contrasting specificities,
      i.e. non-specific vs. highly sequence specific, share a structurally similar active site
      region with conservation of the catalytically relevant histidine and asparagine residues.  On
      the basis of a comparison of the available structures and biochemical data for wild type and
      mutant variants of Serratia nuclease and I-PpoI we propose that both enzymes have a catalytic
      mechanism, a proposition that is supported by our finding that both enzymes accept
      deoxythymidine 3',5'-bis-(p-nitrophenyl phosphate) as a substrate and cleave it in an
      identical manner.  According to this mechanism a histidine residue functions as a general base
      and Mg2+ bound to an asparagine residue as a Lewis acid in phosphodiester bond cleavage.
AU  - Friedhoff P
AU  - Franke I
AU  - Krause KL
AU  - Pingoud A
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1999 443: 209-214.

PMID- 11316811
VI  - 276
DP  - 2001
TI  - Sau3AI, a monomeric type II restriction endonuclease that dimerizes on the DNA and thereby induces DNA loops.
PG  - 23581-23588
AB  - Here, we report that Sau3AI, an unusually large type II restriction enzyme with sequence
      homology to the mismatch repair protein MutH, is a monomeric enzyme as shown by gel filtration
      and ultracentrifugation. Structural similarities in the N- and C-terminal halves of the
      protein suggest that Sau3AI is a pseudo-dimer, i.e. a polypeptide with two similar domains.
      Since Sau3AI displays a nonlinear dependence of cleavage activity on enzyme concentration and
      a strong preference for substrates with two recognition sites over those with only one, it is
      likely that the functionally active form of Sau3AI is a dimer of a pseudo-dimer. Indeed,
      electron microscopy studies demonstrate that two distant recognition sites are brought
      together through DNA looping induced by the simultaneous binding of two Sau3AI molecules to
      the DNA. We suggest that the dimeric form of Sau3AI supplies two DNA-binding sites, one that
      is associated with the catalytic center and one that serves as an effector site.
AU  - Friedhoff P
AU  - Lurz R
AU  - Lueder G
AU  - Pingoud A
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2001 276: 23581-23588.

PMID- 144900
VI  - 4
DP  - 1977
TI  - Studies on the biological role of DNA methylation:  III.  Role in excision of one-genome long single-stranded Phi X174 DNA.
PG  - 3483-3496
AB  - Accumulation of replicative intermediates of the bacteriophage Phi X174 was
      observed in E. coli C infected cells when phage DNA methylation has been
      inhibited by nicotinamide or when cells were infected with a
      temperature-sensitive mutant in gene A.  Analysis of the accumulating
      replicative intermediates by electron microscopy revealed that these molecules
      are composed of double-stranded DNA rings with multiple-genome length
      single-stranded "tails".  These results suggest that the single
      5-methylcytosine residue present in the phage DNA serves as a recognition site
      for the gene A protein mediating the excision of one-genome long phage DNA.
AU  - Friedman J
AU  - Friedmann A
AU  - Razin A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1977 4: 3483-3496.

PMID- 136644
VI  - 3
DP  - 1976
TI  - Studies on the biological role of DNA methylation.  II.  Role of Phi X174 DNA methylation in the process of viral progeny DNA synthesis.
PG  - 2665-2675
AB  - In vivo inhibition of bacteriophage Phi X174 DNA methylation by nicotinamide resulted in the
      accumulation of replicative intermediates with multiple-genome length single-stranded "tails".
      These abnormal replicative intermediates could not be chased into viral single-stranded
      circular DNA.  The effect of nicotinamide on phage maturation and accumulation of abnormal
      replicative intermediates could be reversed by washing out the inhibitor.  The results suggest
      that the single methyl group present in the viral DNA serves as a recognition site for a
      specific endonuclease, probably the gene A protein product, that is responsible for the
      excision of the single-stranded one-genome long viral DNA, before final maturation of the
      virus occurs.
AU  - Friedman J
AU  - Razin A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1976 3: 2665-2675.

PMID- 2580836
VI  - 260
DP  - 1985
TI  - The irreversible binding of Azacytosine-containing DNA fragments to bacterial DNA (cytosine-5)methyltransferases.
PG  - 5698-5705
AB  - DNA containing 5-azacytosine is an irreversible inhibitor of DNA
      (cytosine-5)methyltransferase.  This paper describes the binding of DNA
      methyltransferase to 32P-labeled fragments of DNA containing 5-azacytosine.
      The complexes were identified by gel electrophoresis.The EcoRII
      methyltransferase specified by the R15 plasmid was purified from Escherichia
      coli B(R15).  This enzyme methylates the second C in the sequence CCAGG and has
      a molecular mass of 60,000 Da.  Specific binding of enzyme to DNA fragments
      could be detected if either excess unlabeled DNA or 0.8% sodium dodecyl sulfate
      was added to the reaction mixture prior to electrophoresis.  Binding was
      dependent upon the presence of both the CCAGG sequence and azacytosine in the
      DNA fragment.  S-Adenosylmethionine stimulated the formation of the complex.
      The complex was stable to 6M urea but could be digested with pronase.  These
      DNA fragments could be used to detect the presence of several different
      methyltransferases in crude extracts of E. coli.  No DNA protein complexes
      could be detected in E. coli B extracts, a strain that contains no
      DNA(cytosine-5)methyltransferases.  The chromosomally determined methylase with
      the same specificity as the purified EcoRII methylase could be detected in
      crude extracts of E. coli K12 strains.  The MspI methylase cloned in E. coli
      HB101 could also be detected in crude extracts.  These enzymes are the only
      proteins that bind azacytosine-containing DNA in crude extracts of E. coli.
AU  - Friedman S
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1985 260: 5698-5705.

PMID- 91371
VI  - 89
DP  - 1979
TI  - The effect of 5-azacytidine on E. coli DNA methylase.
PG  - 1328-1333
AB  - 5-Azacytidine, when added to growing E. coli K12, causes a decrease in DNA
      methylation assayed in vitro.  This decrease is greater when E. coli DNA is
      used as substrate than when calf thymus DNA is used.  The decrease in activity
      is not due to the inhibition of protein synthesis caused by this drug, since
      neither chloramphenicol nor rifampin causes a decrease in enzyme activity.  The
      effect is specific for the DNA(cytosine-5)methylase; the methylation of adenine
      is not affected.  The concentration of drug that inhibits the DNA methylase by
      50% is the same concentration that inhibits cell growth by 50%.
AU  - Friedman S
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1979 89: 1328-1333.

PMID- 6164911
VI  - 19
DP  - 1981
TI  - The inhibition of DNA(Cytosine-5)methylases by 5-azacytidine:  The effect of azacytosine-containing DNA.
PG  - 314-320
AB  - DNA extracted from Escherichia coli grown in the presence of 5-azacytidine
      (azaC-DNA) inhibits the DNA(cytosine-5)methyltransferase extracted from E. coli
      K12 cells without affecting the DNA(adenine-N6)methyltransferase present in
      these same cells.  The inhibition is time-dependent and the rate of inhibition
      can be decreased by addition of substrate DNA.  The inhibitory capacity of the
      DNA is destroyed by incubation with pancreatic deoxyribonuclease or micrococcal
      nuclease; however, the inhibited enzyme cannot be reactivated by treatment with
      these enzymes.  The cytosine methylases methylate only double-stranded DNA.
      Similarly, the inhibitory DNA loses activity if it is heat-denatured, and
      regains activity upon reannealing.  The DNA will also inhibit the EcoRII and
      HpaII modification methylases which also synthesize 5-methylcytosine in DNA.
      Digestion of the inhibitory DNA with the respective restriction endonuclease
      destroys, in part, the inhibitory activity of the DNA for the respective
      methylase.  Base analysis indicated that 5-azacytidine replaced 8.4% of the
      cytosine in the azaC-DNA.  These results suggest that DNA containing
      5-azacytidine irreversibly inhibits DNA(cytosine-5)methylases.
AU  - Friedman S
PT  - Journal Article
TA  - Mol. Pharmacol.
JT  - Mol. Pharmacol.
SO  - Mol. Pharmacol. 1981 19: 314-320.

PMID- Not carried by PubMed...
VI  - 91
DP  - 1991
TI  - Adducts of the EcoRII methylase and 5-fluorocytosine-containing DNA.
PG  - A436
AB  - We have investigated the properties of the adduct formed between the EcoRII
      methyltransferase and DNA containing 5-fluorocytosine.  A polymer of CCCA/TGGG
      containing 75% substitution of cytosine by 5-fluorocytosine was synthesized
      labeled with alpha-32P dATP.  Irreversible inhibition of the enzyme by the DNA
      occurred over a 5 h time course.  This inhibition only occurred in the presence
      of AdoMet.  The DNA was methylated by the enzyme when incubated with
      (methyl-3H)AdoMet with a similar time course.  Digestion with DNase I yielded
      an adduct that was stable to boiling in 1% SDS but was unstable to a pH <5 and
      to ultrafiltration.  However, if the adduct were digested with trypsin a
      portion of the DNA remained bound to a peptide as defined by its altered
      mobility.  The adduct was therefore treated with staphylococcal protease and
      the products purified by HPLC.  The radioactive peak containing both 32P was
      further purified by polyacrylamide gel electrophoresis.  The region containing
      32P was subjected to peptide sequencing for 20 cycles.  A sequence was obtained
      which included a region of the protein that contains cysteine 186, a residue
      that we had previously identified as being susceptible to photolabeling with
      AdoMet and therefore part of the active site.
AU  - Friedman S
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1991 91: A436.

PMID- 2423968
VI  - 14
DP  - 1986
TI  - Binding of the EcoRII methylase to azacytosine-containing DNA.
PG  - 4543-4556
AB  - Binding of DNA (cytosine-5) methyltransferases to azacytosine containing DNA is
      stimulated by the presence of S-adenosyl-methionine or its analogs sinefungin
      or S-adenosyl-L-homocysteine.  Methylation of the DNA is therefore not
      necessary for binding to occur.  There is no relationship between the affinity
      of the analog for the EcoRII enzyme and its ability to stimulate binding.  The
      DNA-enzyme complex partially dissociates on incubation in 0.1% sodium dodecyl
      sulfate and 0.5 M ammonium acetate.  Some of this DNA could again form a tight
      complex with enzyme, indicating that DNA-enzyme complex formation is
      reversible.  Binding occurs when the second cytosine in the sequence CCAGG is
      substituted by azacytosine.  This is the cytosine that would normally be
      methylated by the enzyme.  The binding is therefore due to specific interaction
      of the methylase with azacytosine at the site it would normally methylate.
AU  - Friedman S
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1986 14: 4543-4556.

PMID- 1620620
VI  - 20
DP  - 1992
TI  - Binding of the EcoRII methyltransferase to 5-fluorocytosine-containing DNA.  Isolation of a bound peptide.
PG  - 3241-3248
AB  - The properties of the interaction of 5-fluorocytosine-containing DNA with the EcoRII
      methyltransferase were studied. The DNA used was either a polymer synthesized in vitro, or a
      20-mer containing one CCA/TGG sequence. The DNA could be methylated by the enzyme. In the
      process the enzyme formed a tight binding adduct with the DNA that could be identified by
      sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Enzyme activity was inhibited by
      this interaction. The 20-mer could be used to titrate the active site of the enzyme. The DNA
      polymer formed a tight binding complex that could be identified following digestion of the DNA
      with pancreatic deoxyribonuclease or micrococcal nuclease. A peptide-DNA adduct could be
      isolated after digestion of the EcoRII-DNA adduct with staphylococcal protease V8 by high
      pressure liquid chromatography and polyacrylamide gel electrophoresis. Sequencing of the
      peptide indicated the DNA bound to a region of the protein that is conserved in all
      procaryotic DNA(cytosine-5)-methyltransferases. We have previously shown that this region
      contains a cysteine that can be photomethylated with adenosylmethionine. This region, in
      addition to forming part of, or being adjacent to, the AdoMet binding site, also forms part of
      the DNA binding site.
AU  - Friedman S
AU  - Ansari N
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 3241-3248.

PMID- 6205659
VI  - 33
DP  - 1984
TI  - Effect of 5-azacytidine on deoxyribonucleic acid methylation in Escherichia coli K12.
PG  - 2675-2679
AB  - 5-azacytidine inhibits Escherichia coli DNA (cytosine-5) methylase when added to growing
      cells.  The time-course of recovery of methylase activity and the appearance of
      5-methylcytosine in DNA following removal of the drug was studied.  When E. coli K12 was
      treated with 5-azacytidine for 30 min, DNA (cytosine-5) methylase levels decreased to less
      than 10% of control levels and slowly recovered to control levels for three generations after
      treatment and returned to control levels after six generations of growth.  In contrast,
      beta-galactosidase levels in induced cells, which declined to 66% of control one generation
      after treatment, returned to control by the third generation of growth.  The rate of induction
      of beta-galactosidase had returned to the control rate two generations after growth resumed.
      Since azacytidine-containing DNA inhibits DNA-cytosine methylases in vitro, the prolonged
      inhibition of cytosine methylation in E. coli K12 following treatment with the drug could be
      due to the persistence of the drug in DNA and thus inhibition of newly synthesized enzymes.
AU  - Friedman S
AU  - Cheong LC
PT  - Journal Article
TA  - Biochem. Pharmacol.
JT  - Biochem. Pharmacol.
SO  - Biochem. Pharmacol. 1984 33: 2675-2679.

PMID- 7691793
VI  - 175
DP  - 1993
TI  - Induction of EcoRII methyltranserase:  Evidence for autogenous control.
PG  - 6293-6298
AB  - The cytosine analog 5-azacytidline kills Escherichia coli cells that carry plamids expressing
      EcoRII DNA (cytosine 5)methyltransferase under control of its own promoter. We previously
      showed that this enzyme binds tightly to azacytidine-containing DNA in vitro and proposed that
      such binding is lethal in vivo. In support of this proposal, we now show that the enzyme
      sediments with the nucleoid of azabytidine-treated cells. Azacytidine treatment led to an
      increase in the amount of enzyme, and this increase required sequences in the ecoRIIM promoter
      region. Enzyme inducibility correlated with drug sensitivity: plasmids carrying the
      methyltransferase gene but lacking the wild-type promoter did not confer sensitivity. These
      results suggested that the ecoRIIM gene was under autogenous control. Transcriptional
      ecoRIIM' -lacZ fusions in E. coli were, therefore, constructed. They showed that expression
      from the ecoRIIM promoter was reversed by treating the cells with azacytidine. These results
      provide evidence that the expression of the ecoRIIM gene is under autogenous regulation and
      that call death induced by azacytidine is due, in part, to the disruption of autoregulation.
AU  - Friedman S
AU  - Som S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1993 175: 6293-6298.

PMID- 1923825
VI  - 19
DP  - 1991
TI  - The core element of the EcoRII methylase as defined by protease digestion and deletion analysis.
PG  - 5403-5408
AB  - Binding of the EcoRII DNA methyltransferase to azacytosine-containing DNA
      protects the enzyme from digestion by proteases.  The limit digest yields a
      product having a Mr, on SDS-PAGE 20% less than the intact protein.  The N
      terminus of the tryptic digestion product was sequenced and found to be missing
      the N terminal 82 amino acids.  Under the conditions used unbound enzyme was
      digested to small peptides.  Protection of the enzyme undergoes major
      conformational changes when bound to DNA.  The trypsin sensitive region of the
      EcoRII methyltransferase occurs prior to the first constant region shared with
      other procaryotic DNA(cytosine-5)methyltransferases.  To determine if this
      region played a role in substrate binding or specificity, N-terminal deletion
      mutants were studied.  Deletion of 97 amino acids resulted in a decrease of
      enzyme activity.  Further deletions caused a complete loss of activity.  Enzyme
      deleted through amino acid 85 was purified and found to have the same
      specificity as wild type however there was an increase in Km for both
      S-adenosylmethionine (AdoMet) and DNA of 27 and 18 fold respectively.  The
      N-terminus of the EcoRII methylase, although a variable region present in many
      procaryotic DNA(cytosine-5)methylases, plays no role in determining enzyme
      specificity, although it does contribute to the interaction with both AdoMet
      and DNA.
AU  - Friedman S
AU  - Som S
AU  - Yang L-F
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 5403-5408.

PMID- 11004560
VI  - 1480
DP  - 2000
TI  - Specificity of DNA binding and methylation by the M.FokI DNA methyltransferase.
PG  - 145-159
AB  - The M.FokI adenine-N(6) DNA methyltransferase recognizes the asymmetric DNA sequence
      GGATG/CATCC. It consists of two domains each containing all motifs characteristic for
      adenine-N(6) DNA methyltransferases. We have studied the specificity of DNA-methylation by
      both domains using 27 hemimethylated oligonucleotide substrates containing recognition sites
      which differ in one or two base pairs from GGATG or CATCC. The N-terminal domain of M.FokI
      interacts very specifically with GATG-sequences, because only one of the altered sites is
      modified. In contrast, the C-terminal domain shows lower specificity. It prefers
      CATCC-sequences but only two of the 12 star sites (i.e. sites that differ in 1 bp from the
      recognition site) are not accepted and some star sites are modified with rates reduced only
      2-3-fold. In addition, GGATGC- and CGATGC-sites are modified which differ at two positions
      from CATCC. DNA binding experiments show that the N-terminal domain preferentially binds to
      hemimethylated GGATG/C(m)ATCC sequences whereas the C-terminal domain binds to DNA with higher
      affinity but without specificity. Protein-protein interaction assays show that both domains of
      M.FokI are in contact with each other. However, several DNA-binding experiments demonstrate
      that DNA-binding of both domains is mutually exclusive in full-length M.FokI and both domains
      do not functionally influence each other. The implications of these results on the molecular
      evolution of type IIS restriction/modification systems are discussed.
AU  - Friedrich T
AU  - Fatemi M
AU  - Gowhar H
AU  - Leismann O
AU  - Jeltsch A
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 2000 1480: 145-159.

PMID- 9628340
VI  - 379
DP  - 1998
TI  - Functional mapping of the EcoRV DNA methyltransferase by random mutagenesis and screening for catalytically inactive mutants.
PG  - 475-480
AB  - M.EcoRV is an alpha-adenine DNA methyltransferase.  According to structure predictions, the
      enzyme consists of a catalytic domain, which has a structure similar to all other
      DNA-methyltransferases, and a smaller DNA-recognition domain.  We have investigated this
      enzyme by random mutagenesis, using error-prone PCR, followed by selection for catalytically
      inactive mutants.  20 single mutants were identified that are completely inactive in vivo as
      His6- and GST-fusion proteins.  13 of them could be overexpressed and purified.  All of these
      mutants are also inactive in vitro.  5 of the mutations are located near the putative binding
      site for a flipped adenine residue (C192R, D193G, E212G, W231R, N239H).  All of these variants
      bind to DNA, demonstrating the importance of this region of the protein in catalysis.  Only
      the W231R mutant could be purified with high yields.  It binds to DNA and AdoMet and, thus,
      behaves like a bona fine active site mutant.  According to the structure prediction Trp231
      corresponds to Val121 in M.HhaI, which forms a hydrophobic contact to the flipped target
      cytosine.  4 of the remaining purified variants are located within a small region of the
      putative DNA-recognition domain (F115S, F117L, S121P, C122Y).  F117L, S121P and C122Y are
      unable to bind to DNA, suggesting a critical role of this region in DNA binding.  Taken
      together, these results are in good agreement with the structural model of M.EcoRV.
AU  - Friedrich T
AU  - Roth M
AU  - Helm-Kruse S
AU  - Jeltsch A
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1998 379: 475-480.

PMID- 26067981
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Tannerella forsythia Type Strain ATCC 43037.
PG  - e00660-15
AB  - Tannerella forsythia is an oral pathogen implicated in the development of periodontitis. Here,
      we report the draft genome sequence of the Tannerella
      forsythia strain ATCC 43037. The previously available genome of this designation
      (NCBI reference sequence NC_016610.1) was discovered to be derived from a
      different strain, FDC 92A2 (= ATCC BAA-2717).
AU  - Friedrich V
AU  - Pabinger S
AU  - Chen T
AU  - Messner P
AU  - Dewhirst FE
AU  - Schaffer C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00660-15.

PMID- 5158743
VI  - 17
DP  - 1971
TI  - Association of chloramphenicol resistance of group A streptococci with host-controlled restriction and modification of bacteriophages.
PG  - 1573-1576
AB  - Bacteriophages grown on chloramphenicol (CM)-sensitive group A streptococci
      plate efficiently only on other CM-sensitive strains, while phages propagated
      on CM-resistant strains plate well only on CM-resistant hosts.  Data are
      presented showing that the phages are subject to host-controlled modification
      and restriction, and that these processes are related to the CM resistance
      level of the host.
AU  - Friend PL
PT  - Journal Article
TA  - Can. J. Microbiol.
JT  - Can. J. Microbiol.
SO  - Can. J. Microbiol. 1971 17: 1573-1576.

PMID- 20865039
VI  - 5
DP  - 2010
TI  - Genomic Characterization of Campylobacter jejuni Strain M1.
PG  - e12253
AB  - Campylobacter jejuni strain M1 (laboratory designation 99/308) is a rarely
      documented case of direct transmission of C. jejuni from chicken to a
      person, resulting in enteritis. We have sequenced the genome of C. jejuni
      strain M1, and compared this to 12 other C. jejuni sequenced genomes
      currently publicly available. Compared to these, M1 is closest to strain
      81116. Based on the 13 genome sequences, we have identified the C. jejuni
      pan-genome, as well as the core genome, the auxiliary genes, and genes
      unique between strains M1 and 81116. The pan-genome contains 2,427 gene
      families, whilst the core genome comprised 1,295 gene families, or about
      two-thirds of the gene content of the average of the sequenced C. jejuni
      genomes. Various comparison and visualization tools were applied to the 13
      C. jejuni genome sequences, including a species pan- and core genome plot,
      a BLAST Matrix and a BLAST Atlas. Trees based on 16S rRNA sequences and on
      the total gene families in each genome are presented. The findings are
      discussed in the background of the proven virulence potential of M1.
AU  - Friis C
AU  - Wassenaar TM
AU  - Javed MA
AU  - Snipen L
AU  - Lagesen K
AU  - Hallin PF
AU  - Newell DG
AU  - Toszeghy M
AU  - Ridley A
AU  - Manning G
AU  - Ussery DW
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2010 5: e12253.

PMID- 28818885
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Two Gammaproteobacterial Methanotrophs Isolated from Rice Ecosystems.
PG  - e00526-17
AB  - The genomes of the aerobic methanotrophs 'Methyloterricola oryzae' strain 73aT and
      Methylomagnum ishizawai strain 175 were sequenced. Both strains were isolated
      from rice plants. Methyloterricola oryzae strain 73aT represents the first
      isolate of rice paddy cluster I, and strain 175 is the second representative of
      the recently described genus Methylomagnum.
AU  - Frindte K et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00526-17.

PMID- 27013038
VI  - 4
DP  - 2016
TI  - Draft Whole-Genome Sequences of Salmonella enterica subsp. enterica Serovars Enteritidis, Veneziana, and Salford, Isolated from Herbs.
PG  - e00134-16
AB  - Salmonellais a foodborne pathogen found in a wide variety of sources. Here, we report draft
      genome sequences of threeSalmonella entericasubsp.entericaserovars
      found in herbs: Enteritidis, Veneziana, and Salford, with the latter two being
      extremely rare in California.
AU  - Frink S
AU  - Morales C
AU  - Kiang D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00134-16.

PMID- 1123074
VI  - 52
DP  - 1975
TI  - Preparative purification of lambda-DNA fragments obtained after EcoRI digestion.
PG  - 121-126
AB  - The study of the expression, and structure of bacterial or eukaryotic genes, as
      well as the study of the interaction of a particular gene with specific
      proteins, require the isolation of individual genes, or groups of genes.  In
      bacteria, this can be done with specialized transducing phages, whose DNA is
      hydrolysed by restriction enzymes, and the interesting DNA fragment is then
      purified.  In a previous publication, the purification of the E. coli lac gene,
      via the DNA of a lac tranducing lambda bacteriophage has been reported.  In the
      present work, we describe the purification of all the EcoRI digestion products
      of the DNA of two mutants of lambda bacteriophage.  Two methods have been used:
      polyacrylamide gel electrophoresis, and isopycnic centrifugation in cesium
      sulfate gradients in the presence of silver ions.  As will be seen, the proper
      combination of both methods allows the purification of all fragments of lambda
      genomes with either two, or six sites sensitive to EcoRI digestion.
AU  - Fritsch A
AU  - Tiollais P
AU  - Buc H
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1975 52: 121-126.

PMID- 15551873
VI  - 385
DP  - 2004
TI  - A monomeric mutant of restriction endonuclease EcoRI nicks DNA without sequence specificity.
PG  - 975-985
AB  - We have mutated the monomer-monomer interface of the restriction endonuclease EcoRI in order
      to destabilize the homodimer and to stabilize heterodimers. Mutations of Leu158 to charged
      amino acid
      residues result in strong destabilization of the dimer. The largest
      effect was detected for the L158D mutant which is monomeric even at
      higher concentrations. It unspecifically degrades DNA by cleaving both
      single strands independently every 15 nucleotides on the average.
      Although cleavage is reproducible, it is not determined by nucleotide
      sequence but by general properties like conformation or deformability
      as has been found for other unspecific nucleases.
      Mutations of Ile230, which is in direct contact with Leu158 of the
      other subunit, cause structural changes with the loss of about ten
      percent alpha-helix content, but interfere only marginally with
      homodimerization and double strand cleavage. Again the mutation to
      aspartate shows the strongest effects. Mixtures of single mutants, one
      containing aspartate at one of the two positions and the other lysine
      at the corresponding position, form heterodimers. These are mainly
      stabilized compared to the homodimers by reestablishment of the
      wildtype hydrophobic interaction at the not mutated residues while an
      interaction of aspartate and lysine seems energetically unfavorable in
      this structural context.
AU  - Fritsche P
AU  - Alves J
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 2004 385: 975-985.

PMID- 9821960
VI  - 438
DP  - 1998
TI  - Asn141 is essential for DNA recognition by EcoRI restriction endonuclease.
PG  - 66-70
AB  - The amino acid residue Asn141 of the restriction endonuclease EcoRI was proposed to make three
      hydrogen bonds to both adenine residues within the recognition sequence GAATTC.  We have
      mutated Asn141 to alanine, aspartate, serine, and tyrosine.  Only the serine mutant is active
      under normal buffer conditions although 1000-fold less than wild-type EcoRI.  The alanine and
      aspartate mutants can be activated by Mn2+.  At acidic pH the latter mutant becomes even more
      active than the wild-type enzyme in the presence of Mn2+.  We conclude that Asn141 is
      essential for DNA recognition and that serine can partly substitute it.
AU  - Fritz A
AU  - Kuster W
AU  - Alves J
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1998 438: 66-70.

PMID- 28336601
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Murine Bacterial Isolate Lactobacillus murinus EF-1.
PG  - e00077-17
AB  - Screening for lysogenic lactobacilli in rat fecal samples has identified Lactobacillus murinus
      EF-1. Whole-genome sequencing revealed a 2.30-Mb draft
      genome with 39.6% G+C content and 2,196 open reading frames. PHAST analysis
      identified three intact prophages of 26.1 kb, 25.4 kb, and 49.6 kb in size.
AU  - Fritz E
AU  - Miller MJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00077-17.

PMID- 27688319
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of the Probiotic Enterococcus faecalis Symbioflor 1 Clones DSM16430 and DSM16434.
PG  - e01061-16
AB  - The probiotic Symbioflor 1 is a historical concoction of 10 isolates of Enterococcus faecalis
      Pulsed-field gel electrophoresis revealed two groups: one
      comprising eight identical clones (DSM16430, DSM16432, DSM16433, DSM16435 to
      DSM16439) and a further two isolates (DSM16431, DSM16434) with marginally
      different profiles. Here, we report a comparative analysis of the draft genome
      sequences of representative isolates.
AU  - Fritzenwanker M
AU  - Chakraborty A
AU  - Hain T
AU  - Zimmermann K
AU  - Domann E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01061-16.

PMID- 27445377
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence and Complete Plasmid Sequence of Acinetobacter lwoffii F78, an Isolate with Strong Allergy-Protective Properties.
PG  - e00685-16
AB  - The hygiene hypothesis states that the tremendous increase in atopic diseases correlates
      significantly with less contact to microbes in childhood. Here, we
      report the draft genome sequence of Acinetobacter lwoffii F78, a rural cowshed
      isolate with strong allergy-protective properties that contains an 8,579-bp
      plasmid.
AU  - Fritzenwanker M
AU  - Hain T
AU  - Kesper DA
AU  - Harb H
AU  - Renz H
AU  - Domann E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00685-16.

PMID- 23405346
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of the Probiotic Enterococcus faecalis Symbioflor 1 Clone DSM 16431.
PG  - e00165-12
AB  - Here, we report the complete and annotated genome sequence of the probiotic Enterococcus
      faecalis Symbioflor 1 clone DSM 16431, included in a commercial
      probiotic product used for more than 50 years without any reports of infection.
      This sequence will provide new insights into the biology of this nonpathogenic
      and probiotic microorganism.
AU  - Fritzenwanker M
AU  - Kuenne C
AU  - Billion A
AU  - Hain T
AU  - Zimmermann K
AU  - Goesmann A
AU  - Chakraborty T
AU  - Domann E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00165-12.

PMID- 6086461
VI  - 28
DP  - 1984
TI  - Purification of restriction endonuclease XcyI from Xanthomonas cyanopsidis.
PG  - 331-335
AB  - A new type II restriction endonuclease XcyI, purified from Xanthomonas cyanopsidis 13D5, is an
      isoschizomer of SmaI and XmaI that cleaves at the nucleotide sequence 5'-C^CCGG-3' of
      double-stranded DNA. The single restriction activity present in this strain permits rapid
      purification of 8000 units of cleavage activity from 10 g of freshly harvested cells. The
      resulting XcyI preparation is free of contaminating nuclease activities that interfere with in
      vitro manipulation of DNA.
AU  - Froman BE
AU  - Tait RC
AU  - Kado CI
AU  - Rodriguez RL
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1984 28: 331-335.

PMID- 1542678
VI  - 89
DP  - 1992
TI  - A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands.
PG  - 1827-1831
AB  - The modulation of DNA-protein interactions by methylation of protein-binding
      sites in DNA and the occurrence in genomic imprinting, X chromosome
      inactivation, and fragile X syndrome of different methylation patterns in DNA
      of different chromosomal origin have underlined the need to establish
      methylation patterns in individual strands of particular genomic sequences.  We
      report a genomic sequencing method that provides positive identification of
      5-methylcytosine residues and yields strand-specific sequences of individual
      molecules in genomic DNA.  The method utilizes bisulfite-induced modification
      of genomic DNA, under conditions whereby cytosine is converted to uracil, but
      5-methylcytosine remains nonreactive.  The sequence under investigation is then
      amplified by PCR with two sets of strand-specific primers to yield a pair of
      fragments, one from each strand, in which all uracil and thymine residues have
      been amplified as thymine and only 5-methylcytosine residues have been
      amplified as cytosine.  The PCR products can be sequenced directly to provide a
      strand-specific average sequence for the population of molecules or can be
      cloned and sequenced to provide methylation maps of single DNA molecules.  We
      tested the method by defining the methylation status within single DNA strands
      of two closely spaced CpG dinucleotides in the promoter of the human kininogen
      gene.  During the analysis, we encountered in sperm DNA an unusual methylation
      pattern, which suggests that the high methylation level of single-copy
      sequences in sperm may be locally modulated by binding of protein factors in
      germ-line cells.
AU  - Frommer M
AU  - McDonald LE
AU  - Millar DS
AU  - Collis CM
AU  - Watt F
AU  - Grigg GW
AU  - Molloy PL
AU  - Paul CL
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1992 89: 1827-1831.

PMID- 3132485
VI  - 71
DP  - 1988
TI  - Plasmid-mediated reduced phage sensitivity in Streptococcus lactis KR5.
PG  - 275-284
AB  - The phage insensitivity of Streptococcus lactis KR5 was evaluated for its
      possible linkage to plasmid DNA.  This strain possessed plasmids of
      40,29,26,21,16.5,10.5,7.8, and 1.5 Mdal.  Plasmid curing using novobiocin
      resulted in derivatives with increased sensitivity to prolate-headed phage,
      suggesting the involvement of plasmid DNA in phage insensitivity.
      Transformation of S. lactis LM0230 protoplasts with the KR5 plasmid DNA pool
      produced transformants containing a plasmid of about 27 Mdal.  These
      erythromycin-resistant transformants were lactose-positive phage-sensitive or
      were lactose-negative and exhibited a reduced sensitivity to phage.  Agarose
      gel electrophoresis and restriction endonuclease digestion analysis showed the
      17-Mdal plasmid band to be composed of two distinct plasmids of 26 Mdal (pBF61)
      and 29 Mdal (pBF62), which coded for reduced phage sensitivity and
      lactose-positive phenotypes, respectively.  The mechanisms of reduced phage
      sensitivity encoded by pBF61 included a restriction/modification system and a
      mechanism that resulted in reduced plaque size independent of incubation
      temperature.  These results further support the involvement of plasmid DNA in
      the mechanisms for reduced phage sensitivity in dairy streptococci.
AU  - Froseth BR
AU  - Harlander SK
AU  - McKay LL
PT  - Journal Article
TA  - J. Dairy Sci.
JT  - J. Dairy Sci.
SO  - J. Dairy Sci. 1988 71: 275-284.

PMID- 9020157
VI  - 272
DP  - 1997
TI  - Interference with DNA methyltransferase activity and genome methylation during F9 teratocarcinoma stem cell differentiation induced by polyamine depletion.
PG  - 4359-4366
AB  - When ornithine decarboxylase, the initial and highly regulated enzyme in polyamine
      biosynthesis, is irreversibly inactivated by alpha-difluoromethylornithine, F9 teratocarcinoma
      stem cells are depleted of putrescine and spermidine and as a result differentiate into a cell
      type which phenotypically resembles the parietal endoderm cells of the early mouse embryo.
      Simultaneously the level of decarboxylated S-adenosylmethionine (dcAdoMet), the amino propyl
      group donor in spermidine and spermine synthesis, increases dramatically, as the aminopropyl
      group acceptor molecules (putrescine and spermidine) become limiting.  When this excessive
      accumulation of dcAdoMet is prevented by specific inhibition of the AdoMet decarboxylase
      activity, the differentiative effect is counteracted, despite the fact that the extent of
      polyamine depletion remains almost identical.  Therefore, it may be concluded that dcAdoMet
      plays an important role in the induction of differentiation.  Moreover, this key metabolite
      acts as a competitive inhibitor of DNA methyltransferase and is therefore capable of
      interfering with the maintenance methylation of newly replicated DNA.  During the course of F9
      cell differentiation, the highly methylated genome is gradually demethylated, and its pattern
      of gene expression is changed.  Our present findings, that the DNA remains highly methylated
      and that the differentiative process is counteracted when the build-up of dcAdoMet is
      prevented, provide strong evidence for a causative relation between the level of cdAdoMet and
      the state of DNA methylation as well as cell differentiation.
AU  - Frostesjo L
AU  - Holm I
AU  - Grahn B
AU  - Page AW
AU  - Bestor TH
AU  - Heby O
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1997 272: 4359-4366.

PMID- 25125652
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Staphylococcus chromogenes Strain MU 970, Isolated from  a Case of Chronic Bovine Mastitis.
PG  - e00835-14
AB  - Coagulase-negative staphylococcal species are a common cause of subclinical bovine mastitis,
      with Staphylococcus chromogenes being one of the most frequently
      identified species in these cases. The draft genome sequence of an S. chromogenes
      isolate (MU 970) recovered from the milk of a cow with a chronic intramammary
      infection is reported here.
AU  - Fry PR
AU  - Calcutt MJ
AU  - Foecking MF
AU  - Hsieh HY
AU  - Suntrup DG
AU  - Perry J
AU  - Stewart GC
AU  - Middleton JR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00835-14.

PMID- 8622949
VI  - 93
DP  - 1996
TI  - Homing events in the gyrA gene of some mycobacteria.
PG  - 3410-3415
AB  - The A subunit of DNA gyrase in Mycobacterium leprae, unlike its
      counterpart in Mycobacterium tuberculosis, is produced by protein splicing as its gene,
      gyrA, harbors a 1260-bp in-frame insertion encoding an intein, a putative homing
      endonuclease.  Analysis of the gyrA locus from different mycobacterial species revealed the
      presence of inteins in Mycobacterium flavescens, Mycobacterium gordonae, and
      Mycobacterium kansasii but not in 10 other pathogenic or saprophytic mycobacteria.  In all
      four cases where intein coding sequences were found, they were localized in the same
      position in gyrA, immediately downstream of the codon for the key active-site residue Tyr-
      130.  The intein products were similar, but not identical, in sequence and the splice
      junctions displayed all the features found in other polypeptides known to be produced by
      protein splicing from a precursor protein.  Paired motifs, found in homing endonucleases
      encoded by some group I RNA introns, and inteins showing endonuclease activity, were
      present in the gyrA inteins as were other intein-specific signatures.  Some strains of
      M.flavescens, M. gordonae, and M. kansasii were shown by PCR analysis to have
      inteinless gyrA genes, in contrast to the situation in M. leprae where all the isolates
      possessed insertions in gyrA.  Sequencing of the corresponding regions revealed that,
      although the GyrA protein sequence was conserved, the nucleotide sequences differed in
      gyrA genes with and without inteins, suggesting that the homing endonuclease displays
      sequence specificity.
AU  - Fsihi H
AU  - Vincent V
AU  - Cole ST
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1996 93: 3410-3415.

PMID- 22442664
VI  - 7
DP  - 2012
TI  - Statistical Inference of In Vivo Properties of Human DNA Methyltransferases from Double-Stranded Methylation Patterns.
PG  - e32225
AB  - DNA methyltransferases establish methylation patterns in cells and transmit these patterns
      over cell generations, thereby influencing each
      cell's epigenetic states. Three primary DNA methyltransferases have
      been identified in mammals: DNMT1, DNMT3A and DNMT3B. Extensive in
      vitro studies have investigated key properties of these enzymes, namely
      their substrate specificity and processivity. Here we study these
      properties in vivo, by applying novel statistical analysis methods to
      double-stranded DNA methylation patterns collected using
      hairpin-bisulfite PCR. Our analysis fits a novel Hidden Markov Model
      (HMM) to the observed data, allowing for potential bisulfite conversion
      errors, and yields statistical estimates of parameters that quantify
      enzyme processivity and substrate specificity. We apply this model to
      methylation patterns established in vivo at three loci in humans: two
      densely methylated inactive X (Xi)-linked loci (FMR1 and G6PD), and an
      autosomal locus (LEP), where methylation densities are tissue-specific
      but moderate. We find strong evidence for a high level of processivity
      of DNMT1 at FMR1 and G6PD, with the mean association tract length being
      a few hundred base pairs. Regardless of tissue types, methylation
      patterns at LEP are dominated by DNMT1 maintenance events, similar to
      the two Xi-linked loci, but are insufficiently informative regarding
      processivity to draw any conclusions about processivity at that locus.
      At all three loci we find that DNMT1 shows a strong preference for
      adding methyl groups to hemi-methylated CpG sites over unmethylated
      sites. The data at all three loci also suggest low (possibly 0)
      association of the de novo methyltransferases, the DNMT3s, and are
      consequently uninformative about processivity or preference of these
      enzymes. We also extend our HMM to reanalyze published data on mouse
      DNMT1 activities in vitro. The results suggest shorter association
      tracts (and hence weaker processivity), and much longer non-association
      tracts than human DNMT1 in vivo.
AU  - Fu AQ
AU  - Genereux DP
AU  - Stoger R
AU  - Burden AF
AU  - Laird CD
AU  - Stephens M
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2012 7: e32225.

PMID- 29472324
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Xanthomonas arboricola pv. juglandis Strain DW3F3, Isolated from a Juglans regia L. Bacterial Blighted Fruitlet.
PG  - e00023-18
AB  - Here, we report the complete genome sequence of Xanthomonas arboricola pv. juglandis DW3F3, a
      strong pathogenic strain isolated from blighted walnut
      immature fruit (Juglans regia L. cv. Qingxiang). The genome consists of a single
      chromosome (5,144 kb).
AU  - Fu B
AU  - Chen Q
AU  - Wei M
AU  - Zhu J
AU  - Zou L
AU  - Li G
AU  - Wang L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00023-18.

PMID- 27587825
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of the d-Amino Acid Catabolism Bacterium Phaeobacter sp. Strain JL2886, Isolated from Deep Seawater of the South China Sea.
PG  - e00913-16
AB  - Phaeobacter sp. strain JL2886, isolated from deep seawater of the South China Sea, can
      catabolize d-amino acids. Here, we report the complete genome sequence
      of Phaeobacter sp. JL2886. It comprises ~4.06 Mbp, with a G+C content of 61.52%.
      A total of 3,913 protein-coding genes and 10 genes related to d-amino acid
      catabolism were obtained.
AU  - Fu Y
AU  - Wang R
AU  - Zhang Z
AU  - Jiao N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00913-16.

PMID- 28963199
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Bacillus thuringiensis Serovar rongseni Reference Strain SCG04-02, a Strain Toxic to Plutella xylostella.
PG  - e00691-17
AB  - Bacillus thuringiensis (Bt) is widely used to control agricultural and forestry pests, though
      there are only a few available complete genome sequences of the Bt
      reference strain. Here, we report the complete genome sequence of B.
      thuringiensis serovar rongseni reference strain SCG04-02, which is toxic to
      Plutella xylostella.
AU  - Fu Y
AU  - Wu Y
AU  - Yuan Y
AU  - Gao M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00691-17.

PMID- 28912316
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Bacillus thuringiensis subsp. aizawai HD133.
PG  - e00909-17
AB  - We report here the 6,512,057-bp draft genome sequence of Bacillus thuringiensis subsp. aizawai
      HD133. This strain contains at least 6 cry genes and 13 candidate
      biosynthetic gene clusters.
AU  - Fu Z
AU  - Xiao R
AU  - Luo R
AU  - Hu Z
AU  - Yang H
AU  - Guo Z
AU  - Lei P
AU  - Shan S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00909-17.

PMID- 17299055
VI  - 104
DP  - 2007
TI  - Characterization of a marine gammaproteobacterium capable of aerobic anoxygenic photosynthesis.
PG  - 2891-2896
AB  - Members of the gammaproteobacterial clade NOR5/OM60 regularly form an abundant
      part, up to 11%, of the bacterioplankton community in coastal systems during the
      summer months. Here, we report the nearly complete genome sequence of one
      cultured representative, Congregibacter litoralis strain KT71, isolated from
      North Sea surface water. Unexpectedly, a complete photosynthesis superoperon,
      including genes for accessory pigments, was discovered. It has a high sequence
      similarity to BAC clones from Monterey Bay [Beja O, Suzuki MT, Heidelberg JF,
      Nelson WC, Preston CM, et al. (2002) Nature 415:630-633], which also share a
      nearly identical gene arrangement. Although cultures of KT71 show no obvious
      pigmentation, bacteriochlorophyll a and spirilloxanthin-like carotenoids could be
      detected by HPLC analysis in cell extracts. The presence of two potential BLUF
      (blue light using flavin adenine dinucleotide sensors), one of which was found
      adjacent to the photosynthesis operon in the genome, indicates a light- and
      redox-dependent regulation of gene expression. Like other aerobic anoxygenic
      phototrophs (AAnPs), KT71 is able to grow neither anaerobically nor
      photoautotrophically. Cultivation experiments and genomic evidence show that KT71
      needs organic substrates like carboxylic acids, oligopeptides, or fatty acids for
      growth. The strain grows optimally under microaerobic conditions and actively
      places itself in a zone of approximately 10% oxygen saturation. The genome
      analysis of C. litoralis strain KT71 identifies the gammaproteobacterial marine
      AAnPs, postulated based on BAC sequences, as members of the NOR5/OM60 clade. KT71
      enables future experiments investigating the importance of this group of
      gammaproteobacterial AAnPs in coastal environments.
AU  - Fuchs BM
AU  - Spring S
AU  - Teeling H
AU  - Quast C
AU  - Wulf J
AU  - Schattenhofer M
AU  - Yan S
AU  - Ferriera S
AU  - Johnson J
AU  - Glockner FO
AU  - Amann R
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2007 104: 2891-2896.

PMID- 6253357
VI  - 10
DP  - 1980
TI  - Identification of palindromic sequences recognized by restriction endonucleases, as based on the tabularized sequencing data for seven viral and plasmid DNAs.
PG  - 357-370
AB  - Computer search  of DNA sequences for phages PhiX174, G4, M13 and fd, plasmids
      pBR322 and pA3, and virus SV40, was employed to prepare tables specifying the
      size classes and frequencies of DNA segments located between all possible
      tetra-, penta, and hexanucleotide palindromes.  As described earlier (Fuchs et
      al., 1978), these tables permit identifying sequences recognized by most of the
      restriction endonucleases.  The effect of sequencing errors on the accuracy of
      the present identification method is evaluated.  Only four of the 224 listed
      sequences do not appear in any of the seven DNAs, leading to discussion (see
      Appendix) on the natural sequence distribution.
AU  - Fuchs C
AU  - Rosenvold E
AU  - Honigman A
AU  - Szybalski W
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1980 10: 357-370.

PMID- 215495
VI  - 4
DP  - 1978
TI  - A simple method for identifying the palindromic sequences recognized by restriction endonucleases: the nucleotide sequence of the AvaII site.
PG  - 1-23
AB  - Tables specifying the frequencies, distances between and positions of all
      possible tetra-, penta-, and hexanucleotide palindromes*** in PhiX174 and SV40
      viral DNAs were prepared by a computer search of their base sequences.  A
      simple method based on these tables is described for identifying the sequence
      recognized by any specific restriction endonuclease.  The method requires
      experimental determination of the number and approximate sizes of the fragments
      obtained by digestion of PhiX174 RF and SV40 DNAs.  Using this method we
      identified the sequence for the AvaII restriction endonuclease as 5'-GG(AT)CC.
AU  - Fuchs C
AU  - Rosenvold EC
AU  - Honigman A
AU  - Szybalski W
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1978 4: 1-23.

PMID- 6250945
VI  - 10
DP  - 1980
TI  - Characterization of a site-specific restriction endonuclease SphI from Streptomyces phaeochromogenes.
PG  - 39-46
AB  - A new type-II restriction endonuclease SphI, has been partially purified from
      Streptomyces phaeochromogenes.  SphI recognizes the hexanucleotide sequence
      5'-GCATG^C and cleaves it at the postiion marked by the arrow.  This nucleotide
      sequence is present twice in SV40 DNA, four times in lambda DNA and only once
      in the cloning vehicles pBR322, pBR325, pBR327 and PBR328.
AU  - Fuchs LY
AU  - Covarrubias L
AU  - Escalante L
AU  - Sanchez S
AU  - Bolivar F
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1980 10: 39-46.

PMID- 6312262
VI  - 100
DP  - 1983
TI  - Guide to the Use of Type II Restriction  Endonucleases.
PG  - 3-38
AB  - Type II restriction endonucleases are DNases that recognize specific
      oligonucleotide sequences, make double-strand cleavages, and generate unique,
      equal molar fragments of a DNA molecule.  By the nature of their controllable,
      predictable, infrequent, and site-specific cleavage of DNA, restriction
      endonucleases proved to be extremely useful as tools in dissecting, analyzing,
      and reconfiguring genetic information at the molecular level.  Over 350
      different restriction endonucleases have been isolated from a wide variety of
      prokaryotic sources, representing at least 85 different recognition sequences.
      A number of excellent reviews detail the variety of restriction enzymes and
      their sources, their purification and determination of their sequence
      specificity, ad their physical properties, kinetics, and reaction mechanism.
      Here we provide a summary, based on the literature and our experience in this
      laboratory, emphasizing the practical aspects for using restriction
      endonucleases as tools.  This review focuses on the reaction, its components
      and the conditions that affect enzymic activity and sequence fidelity, methods
      for terinating the reaction, some reaction variations, and a troubleshooting
      guide to help identify and solve restriction endonuclease-related problems.
AU  - Fuchs R
AU  - Blakesley R
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1983 100: 3-38.

PMID- Not carried by PubMed...
VI  - 19
DP  - 1982
TI  - Expression of the genes for the Pst restriction-modification enzymes after cloning into a temperature-sensitive replication plasmid.
PG  - 523
AB  - Our objective was to develop a model system to study the use of an
      overexpression plasmid to increase synthesis of a restriction enzyme in
      Escherichia coli.  We chose the restriction (PstI)-modification system of
      Providencia stuartii that has been cloned into the HindIII site of pBR322
      (Walder, et al., 1981, P.N.A.S. 78:1503).  One hybrid plasmid, designated
      pPst102, contained a 5.9 kb insert with an internal HindIII site, producing 1.9
      and 4.0 kb fragments.  Although both enzymes were specified by the 4.0 kb
      fragment, the genes were poorly expressed in E. coli.  We subcloned the Pst
      genes into a temperature sensitive runaway plasmid (pBEU I) and transformed E.
      coli HB101.  Four independent transformants were isolated and characterized:
      pRF I (1.9 kb insert); pRF 2 (4.0 kb insert); pRF 3 and pRF 4 (4.9 kb insert).
      All four strains were subjected to temperature shifts to allow for
      overexpression of the plasmid.  Crude cell extracts were prepared and examined
      for PstI.  When the PstI activity of E. coli/pPst 102 is assigned a value
      enzymatic activities were estimated in the four strains: pRF I <0.5; pRF 2
      <0.5; pRF3 <0.5; pRF 4-10.0.  These results demonstrate that the overexpression
      plasmid produces a 10-fold increase in the activity of PstI in E. coli.
      Furthermore, this system provides a basis for studying the regulation of the
      PstI gene.
AU  - Fuchs R
AU  - Kane JF
PT  - Journal Article
TA  - Miami BioTechnology Winter Symposium
JT  - Miami BioTechnology Winter Symposium
SO  - Miami BioTechnology Winter Symposium 1982 19: 523.

PMID- 18425509
VI  - 79
DP  - 2008
TI  - Insertion sequence-based cassette PCR: cultivation-independent isolation of gamma-hexachlorocyclohexane-degrading genes from soil DNA.
PG  - 627-632
AB  - gamma-Hexachlorocyclohexane (gamma-HCH) is a highly chlorinated pesticide
      that has caused serious environmental problems. Based on the frequently
      observed association of insertion sequence IS6100 with lin genes for
      gamma-HCH degradation in several gamma-HCH-degrading bacterial strains
      isolated to date, DNA fragments flanked by two copies of IS6100 were
      amplified by nested polymerase chain reaction (PCR) technique using a DNA
      sample extracted from soil contaminated with HCH. Four distinct DNA
      fragments with sizes of 6.6, 2.6, 1.6, and 1.3 kb were obtained, three of
      which carried lin genes: the 6.6-kb fragment carried linD and linE as well
      as linR; the 2.6-kb fragment showed a truncated form of linF; and the
      1.6-kb fragment carried linB. Our approach, named as insertion sequence
      (IS)-based cassette PCR, was successful in the isolation of the lin genes
      from HCH-contaminated soil without cultivation of host cells and is
      applicable for the culture-independent isolation of other functional genes
      bordered by other IS elements.
AU  - Fuchu G
AU  - Ohtsubo Y
AU  - Ito M
AU  - Miyazaki R
AU  - Ono A
AU  - Nagata Y
AU  - Tsuda M
PT  - Journal Article
TA  - Appl. Microbiol. Biotechnol.
JT  - Appl. Microbiol. Biotechnol.
SO  - Appl. Microbiol. Biotechnol. 2008 79: 627-632.

PMID- 6810062
VI  - 186
DP  - 1982
TI  - Restriction and modification in Bacillus subtilis 168: Regulation of hsrM(nonB) expression in spoOA mutants and effects on permissiveness for Phi15 and Phi105 phages.
PG  - 118-121
AB  - Gene hsrM (nonB) of Bacillus subtilis 168, causing non-permissiveness to phage
      SP10 (Saito et al. 1979) and reduced plating efficiency of unmodified phage
      Phi105, is responsible for non-permissiveness of B. subtilis 168 for phages
      Phi15 and PZA.  Upon transformation to sporulation deficiency (allele spoOA) B.
      subtilis 168 becomes permissive for Phi15 and PAZ and loses the ability to
      restrict Phi105.  spoOA str-1 double transformants of B. subtilis 168, however,
      retain the restriction 168 and non-permissiveness for Phi15 and PZA phages, in
      spite of their Spo- phenotype.  Therefore it appears that a functional product
      of the spoOA gene is required for expression of gene hsrM in wild-type
      bacteria, but is not essential in streptomycin-resistant bacteria.  Phage
      genomes (PZA) were trapped in spores of the restriction deficient strain with
      much higher efficiency than in the wild-type.
AU  - Fucik V
AU  - Grunnerova H
AU  - Zadrazil S
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1982 186: 118-121.

PMID- 27563040
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of a Cylindrospermopsin-Producing Cyanobacterium, Cylindrospermopsis raciborskii CS505, Containing a Circular Chromosome and a  Single Extrachromosomal Element.
PG  - e00823-16
AB  - Cylindrospermopsis raciborskii is a freshwater cyanobacterium producing bloom events and
      toxicity in drinking water source reservoirs. We present the first
      genome sequence for C. raciborskii CS505 (Australia), containing one 4.1-Mbp
      chromosome and one 110-Kbp plasmid having G+C contents of 40.3% (3933 genes) and
      39.3% (111 genes), respectively.
AU  - Fuentes-Valdes JJ
AU  - Plominsky AM
AU  - Allen EE
AU  - Tamames J
AU  - Vasquez M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00823-16.

PMID- 30344889
VI  - 13
DP  - 2018
TI  - Draft genome sequences of Cylindrospermopsis raciborskii strains CS-508 and MVCC14, isolated from freshwater bloom events in Australia and Uruguay.
PG  - 26
AB  - Members of the genus Cylindrospermopsis represent an important environmental and  health
      concern. Strains CS-508 and MVCC14 of C. raciborskii were isolated from
      freshwater reservoirs located in Australia and Uruguay, respectively. While
      CS-508 has been reported as non-toxic, MVCC14 is a saxitoxin (STX) producer. We
      annotated the draft genomes of these C. raciborskii strains using the assembly of
      reads obtained from Illumina MiSeq sequencing. The final assemblies resulted in
      genome sizes close to 3.6 Mbp for both strains and included 3202 ORFs for CS-508
      (in 163 contigs) and 3560 ORFs for MVCC14 (in 99 contigs). Finally, both the
      average nucleotide identity (ANI) and the similarity of gene content indicate
      that these two genomes should be considered as strains of the C. raciborskii
      species.
AU  - Fuentes-Valdes JJ
AU  - Soto-Liebe K
AU  - Perez-Pantoja D
AU  - Tamames J
AU  - Belmar L
AU  - Pedros-Alio C
AU  - Garrido D
AU  - Vasquez M
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2018 13: 26.

PMID- 2932844
VI  - 143
DP  - 1985
TI  - Plating efficiencies of modified lambda-bio particles on temperature-sensitive hsd mutants of Escherichia coli K12.
PG  - 352-356
AB  - Two mutants of Escherichia coli K12 that are temperature sensitive in cell growth and lambda
      phage production are shown to contain at least two mutations.  One of the mutations in each of
      the isolates is in the hsd locus, and modification and restriction of lambda exhibits
      temperature sensitivity. One of the hsd mutations causes plaque formation by modified
      lambda-bio particles that do not contain an intact ral gene to be temperature dependent.
AU  - Fuerst CR
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1985 143: 352-356.

PMID- 14521907
VI  - 310
DP  - 2003
TI  - Distribution of potential type II restriction sites (palindromes) in prokaryotes.
PG  - 280-285
AB  - Restriction-modification systems are used as a defensive mechanism against inappropriate
      invasion of foreign DNA. The recognition sequences for the
      common type II restriction enzymes and their corresponding methylases are
      usually palindromes. In this study, we identified the most over- and
      underrepresented words in DNA of four bacteria: Escherichia coli, Bacillus
      subtilis, Clostridium perfringens, and Pseudomonas aeruginosa. Using
      maximum order Markov chain analysis, we found that palindromic words were
      most often more underrepresented than their non-palindromic counterparts.
      No strict rule for the intragenic palindrome content could be derived, but
      for three of the bacteria there was a weak correlation between codon usage
      bias and palindrome content. A clear drop in palindrome counts was
      observed in the Shine-Dalgarno region for B. subtilis and C. perfringens,
      but not in E. coli or P. aeruginosa. It was also shown that palindromes in
      eubacteria and archaebacteria seem to occur slightly more infrequently
      than expected on the basis of the genomic GC-content, but some exceptions
      to this principle exist.
AU  - Fuglsang A
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 2003 310: 280-285.

PMID- 25999557
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Pseudomonas aeruginosa KF702 (NBRC 110665), a Polychlorinated Biphenyl-Degrading Bacterium Isolated from Biphenyl-Contaminated   Soil.
PG  - e00517-15
AB  - Pseudomonas aeruginosa KF702 (NBRC 110665) utilizes biphenyl as a sole source of  carbon and
      degrades polychlorinated biphenyls (PCBs). Here, we report the
      7,167,540-bp draft genome sequence of KF702, which contains 6,714 coding
      sequences and a 65.8 mol% G+C content. The strain possesses genes for biphenyl
      catabolism and other genes that mediate degradation of various aromatic
      compounds.
AU  - Fujihara H
AU  - Yamazoe A
AU  - Hosoyama A
AU  - Suenaga H
AU  - Kimura N
AU  - Hirose J
AU  - Watanabe T
AU  - Futagami T
AU  - Goto M
AU  - Furukawa K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00517-15.

PMID- 25977441
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Pseudomonas abietaniphila KF701 (NBRC110664), a Polychlorinated Biphenyl-Degrading Bacterium Isolated from Biphenyl-Contaminated   Soil.
PG  - e00473-15
AB  - Pseudomonas abietaniphila KF701 utilizes biphenyl as a sole source of carbon and  degrades
      polychlorinated biphenyls (PCBs). Here, we report the 6,886,250-bp draft
      genome sequence of KF701, which contains 6,315 coding sequences and 59.4 mol% G+C
      content. The strain possesses genes for biphenyl catabolism and other genes that
      mediate the degradation of benzoate, salicylate, and phenol.
AU  - Fujihara H
AU  - Yamazoe A
AU  - Hosoyama A
AU  - Suenaga H
AU  - Kimura N
AU  - Hirose J
AU  - Watanabe T
AU  - Futagami T
AU  - Goto M
AU  - Furukawa K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00473-15.

PMID- 22972351
VI  - 76
DP  - 2012
TI  - Molecular Cloning, Expression, and Characterization of Starfish DNA (Cytosine-5)-methyltransferases.
PG  - 1661-1671
AB  - To determine whether and if so how a DNA methylation-dependent epigenetic mechanism for
      transcriptional gene silencing functions in
      Echinoderms, we cloned and sequenced dnmt1 and dnmt3 cDNAs of the
      starfish Asterina pectinifera. Since the Strongylocentrotus purpuratus
      genome has only two loci of DNA (cytosine-5)-methyltransferase genes
      encoding Dnmt1 and Dnmt3, they might constitute a sufficient set of
      timid genes in Echinoderms. The starfish Dnmt3 whose cDNA we cloned
      showed highest homology to a mammalian Dnmt3a2 splicing variant.
      Essentially all the characteristic motifs and sequences of the
      mammalian counterparts were found in the starfish Dnmts as well, except
      that a typical PCNA binding domain motif was lacking in the starfish
      Dnmt1. RT-PCR analysis indicated that the dnmt1 mRNA exists in both
      ovary and oocytes, but its levels in other tissues were very low or
      almost negligible. In contrast, the dnmt3 mRNA was detected only in the
      ovary, and not at all in the oocytes. The size of a dnmt1 transcript
      was about 6.5 kb on Northern blot analysis. On heterologous expression,
      the starfish Dnmt1 protein was expressed in insect cells in
      catalytically active form.
AU  - Fujihara Y
AU  - Miyasako H
AU  - Kato K
AU  - Hayashi T
AU  - Toraya T
PT  - Journal Article
TA  - Biosci. Biotechnol. Biochem.
JT  - Biosci. Biotechnol. Biochem.
SO  - Biosci. Biotechnol. Biochem. 2012 76: 1661-1671.

PMID- 25720677
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Talaromyces cellulolyticus Strain Y-94, a Source of Lignocellulosic Biomass-Degrading Enzymes.
PG  - e00014-15
AB  - Talaromyces cellulolyticus (formerly Acremonium cellulolyticus) is a promising fungus for
      cellulase production. Here, we present the draft genome sequence of T. cellulolyticus strain
      Y-94. The genome is 36.4 Mbp long and contains genes for several enzymes involved in the
      degradation of lignocellulosic biomass, including cellulases, hemicellulases, pectinases, and
      amylases.
AU  - Fujii T
AU  - Koike H
AU  - Sawayama S
AU  - Yano S
AU  - Inoue H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00014-15.

PMID- 25792049
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Lactococcus lactis subsp. lactis JCM 5805T, a Strain That Induces Plasmacytoid Dendritic Cell Activation.
PG  - e00113-15
AB  - Lactococcus lactis subsp. lactis JCM 5805(T) is a dairy lactic acid bacterium that induces
      plasmacytoid dendritic cell (pDC) activation. Here, we report the
      2.55-Mb draft genome and annotation of Lactococcus lactis JCM 5805(T). This
      genome information will provide further insights into the mechanisms underlying
      the immunomodulatory function of this strain.
AU  - Fujii T
AU  - Tomita Y
AU  - Ikushima S
AU  - Horie A
AU  - Fujiwara D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00113-15.

PMID- 27932651
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Probiotic Lactobacillus acidophilus Strain L-55 Isolated from a Healthy Human Gut.
PG  - e01357-16
AB  - Probiotic Lactobacillus acidophilus L-55 was isolated from a healthy human gut. Here, we
      report the draft genome sequence of this organism.
AU  - Fujii Y
AU  - Toh H
AU  - Matsubara T
AU  - Tomida S
AU  - Nguyen CT
AU  - Mimura I
AU  - Nakamura S
AU  - Morita H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01357-16.

PMID- 4956424
VI  - 4
DP  - 1965
TI  - On the nature of the deoxyribonucleic acid methylases.  Biological evidence for the multiple nature of the enzymes.
PG  - 2849-2855
AB  - The minor components of DNA of several bacterial species were determined by growing the
      organisms in the presence of [methyl-14C]methionine and analyzing the labeled bases by isotope
      dilution.  The DNA's were found to contain either 6-methylaminopurine or both
      6-methylaminopurine and 5-methylcytosine.  The interaction of extracts derived from some of
      these organisms with a variety of DNA's was also examined.  The results of these studies
      suggest that the DNA methylases as well as the substrate DNA's possess directive specificity
      regarding the pattern of methylation.  The findings confirm that the DNA methylases are
      species specific and also demonstrate the existence of two types of DNA methylases: one
      capable of methylating adenine and the other cytosine.  Infection by T2 bacteriophage elevates
      the DNA methylase activity of both E. coli B and E. coli K12.  Extracts of E. coli B can
      methylate only adenine of DNA, whereas in E. coli K12 two methylating capacities are normally
      present, producing 5-methylcytosine and 6-methylaminopurine.  However, on phage infection only
      the level of the adenine methylase was elevated.
AU  - Fujimoto D
AU  - Srinivasan PR
AU  - Borek E
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1965 4: 2849-2855.

PMID- 12202760
VI  - 30
DP  - 2002
TI  - Sequence-specific protection of plasmid DNA from restriction endonuclease hydrolysis by pyrrole-imidazole-cyclopropapyrroloindole conjugates.
PG  - 3748-3753
AB  - The pyrrole-imidazole (Py-Im) triamide-cyclopropapyrroloindole (CPI) conjugates ImPyImLDu86
      (7) and ImImPyLDu86 (14) were synthesized and their alkylating activities and inhibitory
      effects on DNA hydrolysis by restriction endonucleases were examined. Sequencing gel analysis
      demonstrated that conjugates 7 and 14 specifically alkylated DNA at 5'-CGCGCG-3' and
      5'-PyGGCCPu-3', respectively. Agarose gel electrophoresis indicated that incubation of a
      supercoiled plasmid, pSPORT I (4109 bp), with conjugate 7 effectively inhibited its hydrolysis
      by BssHII (5'-G_CGCGC-3'), whereas conjugate 14 had no effect on this hydrolysis. These
      results suggest that conjugate 7 sequence-specifically inhibits the hydrolysis of DNA by
      BssHII. Sequence-specific alkylation by the Py-Im triamide-CPI conjugates was further
      confirmed by inhibition of the Eco52I (5'-C_GGCCG-3') hydrolysis of conjugate 14-treated
      pQBI PGK (5387 bp). In clear contrast, hydrolysis of pQB1 PGK by DraI (3'-TTT_AAA-3') was
      not inhibited by 5 micro M conjugate 14. That ImImPy did not inhibit the hydrolysis of pQB1
      PGK indicates that covalent bond formation is necessary for inhibition. A similar experiment,
      using linear pQBI PGK, achieved the same extent of protection of the DNA with approximately
      half the concentration of conjugate 14 as was required to protect supercoiled DNA from
      hydrolysis.
AU  - Fujimoto K
AU  - Iida H
AU  - Kawakami M
AU  - Bando T
AU  - Tao Z-F
AU  - Sugiyama H
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2002 30: 3748-3753.

PMID- 
VI  - 47
DP  - 2006
TI  - Characterization of DNA methyltransferase genes in Brassica rapa.
PG  - S238
AB  - Cytosine methylation is an epigenetic process that plays a role in regulating gene expression.
      Plants have at least three classes of cytosine methyltransferase, i.e., MET1 class of
      methyltransferase, Chromomethylases, and de novo DNA methyltransferase.  In our study three
      putative methyltransferase genes, BrMET1a, BrMET1b, and BrCMT were isolated from genome
      library of Brassica rapa.  Identities of amino acid sequences between BrMET1a and atMET1 and
      between BrMET1b and AtMET1 were 72.0% and 66.7%, respectively.  Pfam analysis using deduced
      amino acid sequence showed the presence of BAH domain, CHROMO domain, and methyltransferase
      domain in BrCMT.  RT-PCR analysis revealed the expression of BrMET1a, BrMET1b, and BrCMT.
      These results suggested that these three genes function as methyltransferase in B. rapa.
AU  - Fujimoto R
AU  - Sasaki T
AU  - Nishio T
PT  - Journal Article
TA  - Plant Cell Physiol.
JT  - Plant Cell Physiol.
SO  - Plant Cell Physiol. 2006 47: S238.

PMID- 17038795
VI  - 81
DP  - 2006
TI  - Characterization of DNA methyltransferase genes in Brassica rapa.
PG  - 235-242
AB  - DNA methylation is essential for normal development and plays important roles in regulating
      gene expression in plants. Analysis of the key
      enzymes catalyzing DNA methylation is important to understand
      epigenetic phenomena. In this study, three putative methyltransferase
      genes, BrMET1a, BrMET1b, and BrCMT, were isolated from a genome library
      of Brassica rapa. Structural conservation of the amino acid sequence
      between BrMET1a/BrMET1b and AtMET1 and that between BrCMT and AtCMT3
      suggests that they may function as DNA methyltransferase. BrMET1a was
      expressed in vegetative and reproductive organs, while BrMET1b was
      expressed only in pistils, indicating that these two genes have
      different functions. BrCMT was expressed especially in stamens at the
      stage of 2-4 days before anthesis. We isolated three DNA
      methyltransferase genes in Brassica rapa and indicated differences of
      expression patterns of these DNA methyltransferase genes and expression
      levels in different tissues and developmental stages, suggesting that
      these genes might play important roles in epigenetic gene regulation in
      B. rapa.
AU  - Fujimoto R
AU  - Sasaki T
AU  - Nishio T
PT  - Journal Article
TA  - Genes Genet. Syst.
JT  - Genes Genet. Syst.
SO  - Genes Genet. Syst. 2006 81: 235-242.

PMID- 25523772
VI  - 2
DP  - 2014
TI  - Genome Sequence of the Deep-Sea Denitrifier Pseudomonas sp. Strain MT-1, Isolated from the Mariana Trench.
PG  - e01313-14
AB  - Pseudomonas sp. strain MT-1 was the first deep-sea denitrifier isolated and characterized from
      mud recovered from a depth of 11,000 m in the Mariana Trench.
      We report here the genome sequence of this bacterium, which contributes to our
      understanding of denitrification and bioenergetics in the deep sea.
AU  - Fujinami S
AU  - Oikawa Y
AU  - Araki T
AU  - Shinmura Y
AU  - Midorikawa R
AU  - Ishizaka H
AU  - Kato C
AU  - Horikoshi K
AU  - Ito M
AU  - Tamegai H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01313-14.

PMID- 24501628
VI  - 8
DP  - 2013
TI  - Complete genome sequence of Ilumatobacter coccineum YM16-304(T.).
PG  - 430-440
AB  - Ilumatobacter coccineum YM16-304(T) (=NBRC 103263(T)) is a novel marine actinobacterium
      isolated from a sand sample collected at a beach in Shimane
      Prefecture, Japan. Strain YM16-304(T) is the type strain of the species.
      Phylogenetically, strain YM16-304(T) is close to Ilumatobacter nonamiense
      YM16-303(T) (=NBRC 109120(T)), Ilumatobacter fluminis YM22-133(T) and some
      uncultured bacteria including putative marine sponge symbionts. Whole genome
      sequence of these species has not been reported. Here we report the complete
      genome sequence of strain YM16-304(T). The 4,830,181 bp chromosome was predicted
      to encode a total of 4,291 protein-coding genes.
AU  - Fujinami S
AU  - Takarada H
AU  - Kasai H
AU  - Sekine M
AU  - Omata S
AU  - Harada T
AU  - Fukai R
AU  - Hosoyama A
AU  - Horikawa H
AU  - Kato Y
AU  - Nakazawa H
AU  - Fujita N
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 430-440.

PMID- 24855304
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Potassium-Dependent Alkaliphilic Bacillus sp. Strain TS-2, Isolated from a Jumping Spider.
PG  - e00458-14
AB  - The potassium-dependent alkaliphilic Bacillus sp. strain TS-2 was isolated from the mashed
      extract of a jumping spider, and its draft genome sequence was
      obtained. Comparative genomic analysis with a previously sequenced
      sodium-dependent alkaliphilic Bacillus species may reveal potassium-dependent
      alkaline adaptation mechanisms.
AU  - Fujinami S
AU  - Takeda K
AU  - Onodera T
AU  - Satoh K
AU  - Sano M
AU  - Narumi I
AU  - Ito M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00458-14.

PMID- 24356828
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Sodium-Independent Alkaliphilic Microbacterium sp. Strain TS-1.
PG  - e01043-13
AB  - Alkaliphilic Microbacterium sp. strain TS-1, newly isolated from the jumping spider, showed
      Na(+)-independent growth and motility. Here, we report the draft
      genome sequence of this bacterium, which may provide beneficial information for
      Na(+)-independent alkaline adaptation mechanisms.
AU  - Fujinami S
AU  - Takeda K
AU  - Onodera T
AU  - Satoh K
AU  - Sano M
AU  - Narumi I
AU  - Ito M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01043-13.

PMID- 25189580
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Calcium-Dependent Paenibacillus sp. Strain TCA20, Isolated from a Hot Spring Containing a High Concentration of Calcium Ions.
PG  - e00866-14
AB  - Calcium-dependent Paenibacillus sp. strain TCA20 was isolated from a water sample of a hot
      spring containing a high concentration of calcium ions. Here, we report
      the draft genome sequence of this bacterium, which may be the basis for the
      research of calcium ion homeostasis.
AU  - Fujinami S
AU  - Takeda-Yano K
AU  - Onodera T
AU  - Satoh K
AU  - Sano M
AU  - Takahashi Y
AU  - Narumi I
AU  - Ito M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00866-14.

PMID- 26337893
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Methylobacterium sp. ME121, Isolated from Soil as a Mixed Single Colony with Kaistia sp. 32K.
PG  - e01005-15
AB  - Methylobacterium sp. ME121 was isolated from soil as a mixed single colony with Kaistia sp.
      32K, and its growth was enhanced by coculture. Here, we report the draft genome sequence of
      Methylobacterium sp. ME121, which may contribute to the  study of the molecular mechanisms
      underlying this phenomenon.
AU  - Fujinami S
AU  - Takeda-Yano K
AU  - Onodera T
AU  - Satoh K
AU  - Shimizu T
AU  - Wakabayashi Y
AU  - Narumi I
AU  - Nakamura A
AU  - Ito M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01005-15.

PMID- 28153912
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Thermus thermophilus TMY, Isolated from a Geothermal  Power Plant.
PG  - e01596-16
AB  - Thermus thermophilus TMY (JCM 10668) was isolated from silica scale formed at a geothermal
      power plant in Japan. Here, we report the complete genome sequence for
      this strain, which contains a chromosomal DNA of 2,121,526 bp with 2,500
      predicted genes and a pTMY plasmid of 19,139 bp, with 28 predicted genes.
AU  - Fujino Y
AU  - Nagayoshi Y
AU  - Ohshima T
AU  - Ogata S
AU  - Doi K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01596-16.

PMID- 2932679
VI  - 13
DP  - 1985
TI  - Sequence of the T4 recombination gene, uvsX, and its comparison with that of the recA gene of Escherichia coli.
PG  - 7473-7481
AB  - We have determined the nucleotide sequence of the uvsX gene of
      bacteriophage T4 which is involved in DNA recombination and damage repair,
      and whose product catalyzes in vitro reactions related to recombination
      process in analogous manners to E. coli recA gene product. The coding
      region consisted of 1170 nucleotides directing the synthesis of a
      polypeptide of 390 amino acids in length with a calculated molecular
      weight of 43,760. Amino acid composition, the sequence of seven
      NH2-terminal amino acids and molecular weight of the protein deduced from
      the nucleotide sequence were consistent with the data from the analysis of
      the purified uvsX protein. The nucleotide sequence and the deduced amino
      acid sequence were compared with those of the recA gene. Although a
      significant homology was not found in the nucleotide sequences, the amino
      acid sequences included 23% of identical and 15% of conservatively
      substituted residues.
AU  - Fujisawa H
AU  - Yonesaki T
AU  - Minagawa T
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1985 13: 7473-7481.

PMID- 20203057
VI  - 17
DP  - 2010
TI  - Genomic Structure of an Economically Important Cyanobacterium, Arthrospira (Spirulina) platensis NIES-39.
PG  - 85-103
AB  - A filamentous non-N-2-fixing cyanobacterium, Arthrospira (Spirulina) platensis, is an
      important organism for industrial applications and as
      a food supply. Almost the complete genome of A. platensis NIES-39 was
      determined in this study. The genome structure of A. platensis is
      estimated to be a single, circular chromosome of 6.8 Mb, based on
      optical mapping. Annotation of this 6.7 Mb sequence yielded 6630
      protein-coding genes as well as two sets of rRNA genes and 40 tRNA
      genes. Of the protein-coding genes, 78% are similar to those of other
      organisms; the remaining 22% are currently unknown. A total 612 kb of
      the genome comprise group II introns, insertion sequences and some
      repetitive elements. Group I introns are located in a protein-coding
      region. Abundant restriction-modification systems were determined.
      Unique features in the gene composition were noted, particularly in a
      large number of genes for adenylate cyclase and haemolysin-like
      Ca2+-binding proteins and in chemotaxis proteins. Filament-specific
      genes were highlighted by comparative genomic analysis.
AU  - Fujisawa T et al
PT  - Journal Article
TA  - DNA Res.
JT  - DNA Res.
SO  - DNA Res. 2010 17: 85-103.

PMID- 
VI  - 208
DP  - 2000
TI  - Phylogenetic characterization of endosymbionts in three hydrothermal vent mussels: influence on host distributions.
PG  - 147-155
AB  - 
AU  - Fujiwara Y
AU  - Takai K
AU  - Uematsu K
AU  - Tsuchida S
AU  - Hunt JC
AU  - Hashimoto J
PT  - Journal Article
TA  - Mar. Ecol. Prog. Ser.
JT  - Mar. Ecol. Prog. Ser.
SO  - Mar. Ecol. Prog. Ser. 2000 208: 147-155.

PMID- 28818905
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Mycobacterium stephanolepidis.
PG  - e00810-17
AB  - Mycobacterium stephanolepidis is a rapid-growing nonpigmented species isolated from marine
      teleost fish (Stephanolepis cirrhifer) and is closely related to
      Mycobacterium chelonae Here, we report the complete sequence of its genome,
      comprising a 4.9-Mb chromosome. The sequence represents essential data for future
      phylogenetic and comparative genome studies of this fish pathogen.
AU  - Fukano H
AU  - Yoshida M
AU  - Katayama Y
AU  - Omatsu T
AU  - Mizutani T
AU  - Kurata O
AU  - Wada S
AU  - Hoshino Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00810-17.

PMID- 29798927
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Mycobacterium montefiorense Isolated from Japanese Black Salamander (Hynobius nigrescens).
PG  - e00448-18
AB  - Mycobacterium montefiorense is a member of the Mycobacterium simiae complex, the  largest
      group of nontuberculous mycobacteria. Here, we report the genome sequence
      of M. montefiorense isolate BS, isolated from diseased Japanese black salamander
      (Hynobius nigrescens) reared in an aquarium in Japan. This is the first reported
      case of an M. montefiorense infection in an amphibian.
AU  - Fukano H
AU  - Yoshida M
AU  - Shimizu A
AU  - Iwao H
AU  - Katayama Y
AU  - Omatsu T
AU  - Mizutani T
AU  - Kurata O
AU  - Wada S
AU  - Hoshino Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00448-18.

PMID- 23544154
VI  - 8
DP  - 2013
TI  - Genomic Analysis by Deep Sequencing of the Probiotic Lactobacillus brevis KB290 Harboring Nine Plasmids Reveals Genomic Stability.
PG  - e60521
AB  - We determined the complete genome sequence of Lactobacillus brevis KB290, a probiotic lactic
      acid bacterium isolated from a traditional Japanese fermented vegetable. The genome contained
      a 2,395,134-bp chromosome that housed 2,391 protein-coding genes and nine plasmids that
      together accounted for 191 protein-coding genes. KB290 contained no virulence factor genes,
      and several genes related to presumptive cell wall-associated polysaccharide biosynthesis and
      the stress response were present in L. brevis KB290 but not in the closely related L. brevis
      ATCC 367. Plasmid-curing experiments revealed that the presence of plasmid pKB290-1 was
      essential for the strain's gastrointestinal tract tolerance and tendency
      to aggregate. Using next-generation deep sequencing of current and 18-year-old stock strains
      to detect low frequency variants, we evaluated genome stability. Deep sequencing of four
      periodic KB290 culture stocks with more than 1,000-fold coverage revealed 3 mutation sites and
      37 minority variation sites, indicating long-term stability and providing a useful method for
      assessing the stability of industrial bacteria at the nucleotide level.
AU  - Fukao M
AU  - Oshima K
AU  - Morita H
AU  - Toh H
AU  - Suda W
AU  - Kim SW
AU  - Suzuki S
AU  - Yakabe T
AU  - Hattori M
AU  - Yajima N
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2013 8: e60521.

PMID- 10615135
VI  - 24
DP  - 2000
TI  - DNA methyltransferase Dnmt1 associates with histone deacetylase activity.
PG  - 88-91
AB  - The DNA methyltransferase Dnmt1 is responsible for cytosine methylation in mammals and has a
      role in gene silencing. DNA methylation represses genes partly by recruitment of the
      methyl-CpG-binding protein MeCP2, which in turn recruits a histone deacetylase activity. Here
      we show that Dnmt1 is itself associated with histone deacetylase activity in vivo. Consistent
      with this association, we find that one of the known histone deacetylases, HDAC1, has the
      ability to bind Dnmt1 and can purify methyltransferase activity from nuclear extracts. We have
      identified a transcriptional repression domain in Dnmt1 that functions, at least partly, by
      recruiting histone deacetylase activity and shows homology to the repressor domain of the
      trithorax-related protein HRX (also known as MLL and ALL-1). Our data show a more direct
      connection between DNA methylation and histone deacetylation than was previously considered.
      We suggest that the process of DNA methylation, mediated by Dnmt1, may depend on or generate
      an altered chromatin state via histone deacetylase activity.
AU  - Fuks F
AU  - Burgers WA
AU  - Brehm A
AU  - Hughes-Davies L
AU  - Kouzarides T
PT  - Journal Article
TA  - Nat. Genet.
JT  - Nat. Genet.
SO  - Nat. Genet. 2000 24: 88-91.

PMID- 11350943
VI  - 20
DP  - 2001
TI  - Dnmt3a binds deacetylases and is recruited by a sequence-specific repressor to silence transcription.
PG  - 2536-2544
AB  - The Dnmt3a DNA methyltransferase is essential for mammalian development and is responsible for
      the generation of genomic methylation patterns, which lead to transcriptional silencing. Here,
      we show that Dnmt3a associates with RP58, a DNA-binding transcriptional repressor protein
      found at transcriptionally silent heterochromatin. Dnmt3a acts as a co-repressor for RP58 in a
      manner that does not require its de novo methyltransferase activity. Like other characterized
      co-repressors, Dnmt3a associates with the histone deacetylase HDAC1 using its ATRX-homology
      domain. This domain of Dnmt3a represents an independent transcriptional repressor domain whose
      silencing functions require HDAC activity. These results identify Dnmt3a as a co-repressor
      protein carrying deacetylase activity and show that Dnmt3a can be targeted to specific
      regulatory foci via its association with DNA-binding transcription factors.
AU  - Fuks F
AU  - Burgers WA
AU  - Godin N
AU  - Kasai M
AU  - Kouzarides T
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 2001 20: 2536-2544.

PMID- 19025584
VI  - 9
DP  - 2008
TI  - Cell death upon epigenetic genome methylation: a novel function of methyl-specific deoxyribonucleases.
PG  - R163
AB  - Background Alteration in epigenetic methylation can affect gene expression and
      other processes. In Prokaryota, DNA methyltransferase genes frequently
      move between genomes and present a potential threat. A methyl-specific
      deoxyribonuclease, McrBC, of Escherichia coli cuts invading methylated
      DNAs. Here we examined whether McrBC competes with genome methylation
      systems through host killing by chromosome cleavage.
      Results
      McrBC inhibited the establishment of a plasmid carrying a PvuII
      methyltransferase gene but lacking its recognition sites, likely
      through the lethal cleavage of chromosomes that become methylated.
      Indeed, its phage-mediated transfer caused McrBC-dependent chromosome
      cleavage. Its induction led to cell death accompanied by chromosome
      methylation, cleavage and degradation. RecA/RecBCD functions affect the
      chromosome processing and, together with SOS response, reduce the
      lethality. Our evolutionary/genomic analyses of mcrBC homologs revealed
      (i) wide distribution in Prokaryota, (ii) frequent distant horizontal
      transfer and linkage with mobility-related genes, (iii) diversification
      in the DNA binding domain. In these features, McrBCs resemble Type II
      restriction-modification systems, which behave as selfish mobile
      elements maintaining their frequency by host killing. McrBCs are
      frequently found linked with a methyltransferase homolog, which
      suggests a functional association.
      Conclusions
      Our experiments indicate McrBC can respond to genome methylation
      systems by host killing. Combined with our evolutionary/genomic
      analyses, they support our hypothesis McrBCs have evolved as mobile
      elements competing with specific genome methylation systems through
      host killing. To our knowledge, this represents the first report of a
      defense system against epigenetic systems through cell death.
AU  - Fukuda E
AU  - Kaminska KH
AU  - Bujnicki JM
AU  - Kobayashi I
PT  - Journal Article
TA  - Genome Biology
JT  - Genome Biology
SO  - Genome Biology 2008 9: R163.

PMID- 
VI  - 81
DP  - 2006
TI  - Suicidal defense against an epigenetic system: a role for a Type IV methyl-dependent restriction enzyme.
PG  - 408
AB  - Attack on the host cell chromosome by restriction enzymes is a subject of various biological
      interactions. When several Type II restriction-modification gene complexes enter a new host
      cell, they try to avoid chromosome breakage and cell killing by expressing the modification
      enzyme first. Once they establish themselves, they attack the host chromosome when their
      presence is threatened. Through this postsegregational killing strategy, they force their
      maintenance on the host. On the other
      hand, Escherichia coli cells employ a Type IV restriction enzyme McrBC, which recognizes
      methylated DNAs and cleaves DNA between two of these recognition sites. We hypothesize that
      McrBC serves for suicidal defense against invasion of specific DNA methylation systems. In
      this work, we analyze host attack by McrBC. We demonstrate McrBC-mediated abortion of
      establishment of a modification enzyme gene in E. coli. We also demonstrate McrBC-dependent
      cell death and chromosomal DNA degradation following genome methylation by RM systems. These
      results support our hypothesis. To our knowledge, this represents the first example of direct
      suicidal defense against an epigenetic system.
AU  - Fukuda E
AU  - Kobayashi I
PT  - Journal Article
TA  - Genes Genet. Syst.
JT  - Genes Genet. Syst.
SO  - Genes Genet. Syst. 2006 81: 408.

PMID- 25212615
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Polychlorinated Biphenyl Degrader Comamonas testosteroni TK102 (NBRC 109938).
PG  - e00865-14
AB  - Comamonas testosteroni TK102 (NBRC 109938; JCM 19603) can utilize biphenyl as a sole carbon
      source and degrade polychlorinated biphenyls (PCBs). The complete
      nucleotide sequence of the TK102 genome was determined. TK102 possesses several
      integrative and conjugative element-like regions, and one of them carries
      biphenyl-degradative genes.
AU  - Fukuda K
AU  - Hosoyama A
AU  - Tsuchikane K
AU  - Ohji S
AU  - Yamazoe A
AU  - Fujita N
AU  - Shintani M
AU  - Kimbara K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00865-14.

PMID- 21270894
VI  - 469
DP  - 2011
TI  - Bifidobacteria can protect from enteropathogenic infection through production of acetate.
PG  - 543-547
AB  - The human gut is colonized with a wide variety of microorganisms,
      including species, such as those belonging to the bacterial genus Bifidobacterium, that have
      beneficial effects on human physiology and pathology1-3. Among the most distinctive benefits
      of bifidobacteria are modulation of host defence responses and protection against infectious
      diseases4-6. Nevertheless, the molecular mechanisms underlying these effects have barely been
      elucidated. To investigate these mechanisms, we used mice associated with certain
      bifidobacterial strains and a simplified model of lethal infection with enterohaemorrhagic
      Escherichia coli O157:H7, together with an integrated 'omics' approach. Here we show that
      genes encoding an ATP-binding-cassette-type carbohydrate transporter present in certain
      bifidobacteria contribute to protecting mice against death induced by E. coli O157:H7. We
      found that this effect can be attributed, at least in part, to increased production of acetate
      and that translocation of the E. coli O157:H7 Shiga toxin from the gut lumen to the blood was
      inhibited. We propose that acetate produced by protective bifidobacteria improves intestinal
      defence mediated by epithelial cells and thereby protects the host against lethal infection.
AU  - Fukuda S
AU  - Toh H
AU  - Hase K
AU  - Oshima K
AU  - Nakanishi Y
AU  - Yoshimura K
AU  - Tobe T
AU  - Clarke JM
AU  - Topping DL
AU  - Suzuki T
AU  - Taylor TD
AU  - Itoh K
AU  - Kikuchi J
AU  - Morita H
AU  - Hattori M
AU  - Ohno H
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2011 469: 543-547.

PMID- 12839620
VI  - 8
DP  - 2003
TI  - VDE-initiated intein homing in Saccharomyces cerevisiae proceeds in a meiotic recombination-like manner.
PG  - 587-602
AB  - BACKGROUND: Inteins and group I introns found in prokaryotic and eukaryotic organisms
      occasionally behave as mobile genetic elements.
      During meiosis of the yeast Saccharomyces cerevisiae, the site-specific
      endonuclease encoded by VMA1 intein, VDE, triggers a single double-strand
      break (DSB) at an inteinless allele, leading to VMA1 intein homing.
      Besides the accumulating information on the in vitro activity of VDE, very
      little has been known about the molecular mechanism of intein homing in
      yeast nucleus. RESULTS: We developed an assay to detect the product of
      VMA1 intein homing in yeast genome. We analysed mutant phenotypes of RecA
      homologs, Rad51p and Dmc1p, and their interacting proteins, Rad54p and
      Tid1p, and found that they all play critical roles in intein inheritance.
      The absence of DSB end processing proteins, Sae2p and those in the
      Mre11-Rad50-Xrs2 complex, also causes partial reduction in homing
      efficiency. As with meiotic recombination, crossover events are frequently
      observed during intein homing. We also observed that the absence of
      premeiotic DNA replication caused by hydroxyurea (HU) or clb5delta
      clb6delta mutation reduces VDE-mediated DSBs. CONCLUSION: The repairing
      system working in intein homing shares molecular machinery with meiotic
      recombination induced by Spo11p. Moreover, like Spo11p-induced DNA
      cleavage, premeiotic DNA replication is a prerequisite for a VDE-induced
      DSB. VMA1 intein thus utilizes several host factors involved in meiotic
      and recombinational processes to spread its genetic information and
      guarantee its progeny through establishment of a parasitic relationship
      with the organism.
AU  - Fukuda T
AU  - Nogami S
AU  - Ohya Y
PT  - Journal Article
TA  - Genes Cells
JT  - Genes Cells
SO  - Genes Cells 2003 8: 587-602.

PMID- 
VI  - 80
DP  - 2005
TI  - Strategies of VDE for propagation in yeast nuclear genome.
PG  - 438
AB  - VDE, a homing endonuclease in Saccharomyces cerevisiae, is encoded by a mobile intein within
      the nuclear gene, VMA1.  VDE causes double-strand  break at the 31-bp VDE-recognition sequence
      in intein-less VMA1 allele during meiosis. The DSB is then repaired using the
      intein-containing allele as a template, leading to the conversion of intein-less allele to
      intein-containing allele. These processes are called "homing", by which VDE spreads throughout
      the population.  The study on DSB repair process of homing revealed that VDE-introduced DSB is
      repaired by homologous recombination system working in meiotic recombination as if it is one
      of the programmed meiotic DSBs.  To elucidate the meiosis-specificity of DSB formation by VDE,
      we examined several possibilities.  We found that none of expression, endonuclease activity,
      and nuclear import necessarily regulates the meiosis-specific DSB by VDE.  On the other hand,
      chromatin structure around VRS alters during meiosis. Chromatin immunoprecipitation revealed
      that VDE loading onto VRS occurs only when chromatin changes around VRS.  These results raise
      the possibility that chromatin configuration, which is modulated by the intrinsic property of
      VRS, reulates the meiosis-specific integration of VDE.  Thus, several host factors are
      involved in homing at meiosis-specific DSB formation and DSB repair processes to increase the
      copy number of VDE.
AU  - Fukuda T
AU  - Ohta K
AU  - Ohya Y
PT  - Journal Article
TA  - Genes Genet. Syst.
JT  - Genes Genet. Syst.
SO  - Genes Genet. Syst. 2005 80: 438.

PMID- 16757746
VI  - 5
DP  - 2006
TI  - Investigation of the mechanism of meiotic DNA cleavage by VMA1-derived endonuclease uncovers a meiotic alteration in chromatin structure  around the target site.
PG  - 981-990
AB  - VMA1-derived endonuclease (VDE), a homing endonuclease in Saccharomyces cerevisiae, is encoded
      by the mobile intein-coding sequence within the
      nuclear VMA1 gene. VDE recognizes and cleaves DNA at the 31-bp VDE
      recognition sequence (VRS) in the VMA1 gene lacking the intein-coding
      sequence during meiosis to insert a copy of the intein-coding sequence
      at the cleaved site. The mechanism underlying the meiosis specificity
      of VMA1 intein-coding sequence homing remains unclear. We studied
      various factors that might influence the cleavage activity in vivo and
      found that VDE binding to the VRS can be detected only when DNA
      cleavage by VDE takes place, implying that meiosis-specific DNA
      cleavage is regulated by the accessibility of VDE to its target site.
      As a possible candidate for the determinant of this accessibility, we
      analyzed chromatin structure around the VRS and revealed that local
      chromatin structure near the VRS is altered during meiosis. Although
      the meiotic chromatin alteration exhibits correlations with DNA binding
      and cleavage by VDE at the VMA1 locus, such a chromatin alteration is
      not necessarily observed when the VRS is embedded in ectopic gene loci.
      This suggests that nucleosome positioning or occupancy around the VRS
      by itself is not the sole mechanism for the regulation of
      meiosis-specific DNA cleavage by VDE and that other mechanisms are
      involved in the regulation.
AU  - Fukuda T
AU  - Ohta K
AU  - Ohya Y
PT  - Journal Article
TA  - Euk. Cell
JT  - Euk. Cell
SO  - Euk. Cell 2006 5: 981-990.

PMID- 15710748
VI  - 15
DP  - 2005
TI  - Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes.
PG  - 352-363
AB  - The genus Thermococcus, comprised of sulfur-reducing hyperthermophilic archaea, belongs to the
      order Thermococcales in Euryarchaeota along with
      the closely related genus Pyrococcus. The members of Thermococcus are
      ubiquitously present in natural high-temperature environments, and are
      therefore considered to play a major role in the ecology and metabolic
      activity of microbial consortia within hot-water ecosystems. To obtain
      insight into this important genus, we have determined and annotated the
      complete 2,088,737-base genome of Thermococcus kodakaraensis strain KOD1,
      followed by a comparison with the three complete genomes of Pyrococcus
      spp. A total of 2306 coding DNA sequences (CDSs) have been identified,
      among which half (1165 CDSs) are annotatable, whereas the functions of 41%
      (936 CDSs) cannot be predicted from the primary structures. The genome
      contains seven genes for probable transposases and four virus-related
      regions. Several proteins within these genetic elements show high
      similarities to those in Pyrococcus spp., implying the natural occurrence
      of horizontal gene transfer of such mobile elements among the order
      Thermococcales. Comparative genomics clarified that 1204 proteins,
      including those for information processing and basic metabolisms, are
      shared among T. kodakaraensis and the three Pyrococcus spp. On the other
      hand, among the set of 689 proteins unique to T. kodakaraensis, there are
      several intriguing proteins that might be responsible for the specific
      trait of the genus Thermococcus, such as proteins involved in additional
      pyruvate oxidation, nucleotide metabolisms, unique or additional metal ion
      transporters, improved stress response system, and a distinct restriction
      system.
AU  - Fukui T
AU  - Atomi H
AU  - Kanai T
AU  - Matsumi R
AU  - Fujiwara S
AU  - Imanaka T
PT  - Journal Article
TA  - Genome Res.
JT  - Genome Res.
SO  - Genome Res. 2005 15: 352-363.

PMID- 25657271
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of the Unclassified Iron-Oxidizing, Chemolithoautotrophic Burkholderiales Bacterium GJ-E10, Isolated from an Acidic  River.
PG  - e01455-14
AB  - Burkholderiales bacterium GJ-E10, isolated from the Tamagawa River in Akita Prefecture, Japan,
      is an unclassified, iron-oxidizing chemolithoautotrophic
      bacterium. Its single circular genome, consisting of 3,276,549 bp, was sequenced
      by using three types of next-generation sequencers and the sequences were then
      confirmed by PCR-based Sanger sequencing.
AU  - Fukushima J
AU  - Tojo F
AU  - Asano R
AU  - Kobayashi Y
AU  - Shimura Y
AU  - Okano K
AU  - Miyata N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01455-14.

PMID- 28428313
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Two Hydrogenogenic Carboxydotrophic Bacteria, Carboxydocella sp. Strains JDF658 and ULO1, Isolated from Two Distinct Volcanic  Fronts in Japan.
PG  - e00242-17
AB  - Hydrogenogenic carboxydotrophs may provide hydrogen as primary energy for the microbial
      community via carbon monoxide oxidation. To investigate the genetics of
      carbon monoxide metabolism, we report here the draft genome sequences of the
      hydrogenogenic carboxydotrophs Carboxydocella sp. strains JDF658 (2.60 Mbp; G+C
      content, 49.2%) and ULO1 (2.70 Mbp; G+C content, 48.8%).
AU  - Fukuyama Y
AU  - Oguro T
AU  - Omae K
AU  - Yoneda Y
AU  - Yoshida T
AU  - Sako Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00242-17.

PMID- 28232442
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Carboxydothermus pertinax and C. islandicus, Hydrogenogenic Carboxydotrophic Bacteria.
PG  - e01648-16
AB  - Carboxydothermus spp. are some of the most studied carbon monoxide-oxidizing anaerobic
      thermophiles. For further investigation into the carbon monoxide
      metabolism of Carboxydothermus spp., we report here the draft genome sequences of
      the hydrogenogenic carboxydotrophs Carboxydothermus pertinax (2.47 Mb; G+C
      content, 40.7%) and C. islandicus (2.39 Mb; G+C content, 42.0%).
AU  - Fukuyama Y
AU  - Omae K
AU  - Yoneda Y
AU  - Yoshida T
AU  - Sako Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01648-16.

PMID- 25697504
VI  - 43
DP  - 2015
TI  - Restriction-modification system with methyl-inhibited base excision and abasic-site cleavage activities.
PG  - 2841-2852
AB  - The restriction-modification systems use epigenetic modification to distinguish between self
      and nonself DNA. A modification enzyme transfers a methyl group to a base in a specific DNA
      sequence while its cognate restriction enzyme introduces breaks in DNA lacking this methyl
      group. So far, all the restriction enzymes hydrolyze phosphodiester bonds linking the monomer
      units of DNA. We recently reported that a restriction enzyme (R.PabI) of the PabI superfamily
      with half-pipe fold has DNA glycosylase activity that excises an adenine base in the
      recognition sequence (5'-GTAC). We now found a second activity in this enzyme: at the
      resulting apurinic/apyrimidinic (AP) (abasic) site (5'-GT#C, # = AP), its AP lyase activity
      generates an atypical strand break. Although the lyase activity is weak and lacks sequence
      specificity, its covalent DNA-R.PabI reaction intermediates can be trapped by NaBH4 reduction.
      The base excision is not coupled with the strand breakage and yet causes restriction because
      the restriction enzyme action can impair transformation ability of unmethylated DNA even in
      the absence of strand breaks in vitro. The base excision of R.PabI is inhibited by methylation
      of the target adenine base. These findings expand our understanding of genetic and epigenetic
      processes linking those in prokaryotes and eukaryotes.
AU  - Fukuyo M
AU  - Nakano T
AU  - Zhang Y
AU  - Furuta Y
AU  - Ishikawa K
AU  - Watanabe-Matsui M
AU  - Yano H
AU  - Hamakawa T
AU  - Ide H
AU  - Kobayashi I
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2015 43: 2841-2852.

PMID- 6091134
VI  - 81
DP  - 1984
TI  - Genetic recombination can generate altered restriction specificity.
PG  - 6095-6099
AB  - A recombinant strain, isolated following the transduction of an Escherichia
      coli recipient carrying the Salmonella typhimurium (SB) specificity genes with
      DNA from a donor having the Salmonella potsdam (SP) specificity, was shown
      [Bullas, L.R., Colson, C. and Van Pel, A. (1976) J. Gen. Microbiol. 95,
      166-172] to have neither SB nor SP specificity but to encode a novel
      restriction specificity, SQ.  The heteroduplex analysis of the hsdS
      (specificity) genes of the SB and SP restriction and modification systems
      described here identifies a conserved sequence of around 100 base pairs flanked
      by two nonhomologous regions each of approximately 500 base pairs.  This
      organization parallels that previously deduced from the DNA sequences of the
      hsdS genes of the related E. coli K-12, B, and D restriction systems.  The
      present heteroduplex analyses further show that the hsdS gene conferring the SQ
      specificity deserves one nonhomologous region from the SB gene and the other
      from the SP gene, as predicted from genetic exchange within the conserved
      sequence.  This finding supports the idea that two domains of an hsdS
      polypeptide, which are different for each specificity, may correlate with two
      regions of the DNA sequence recognized.  It has been shown that the recognition
      sequences for E. coli K-12 and B each consist of two short oligonucleotide
      sequences interrupted by a nonspecific sequence.  A similar organization is
      suggested for the Salmonella specificity systems, providing the potential for
      evolutionary diversification of restriction specificities as a result of
      recombination within the conserved sequence of the hsdS gene.
AU  - Fuller-Pace FV
AU  - Bullas LR
AU  - Delius H
AU  - Murray NE
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1984 81: 6095-6099.

PMID- 3001317
VI  - 186
DP  - 1985
TI  - EcoA and EcoE:  Alternatives to the EcoK Family of Type I Restriction and Modification Systems of Escherichia coli.
PG  - 65-75
AB  - The genes (hsd A) encoding EcoA, a restriction and modification system first
      identified in Escherichia coli 15T-, behave in genetic crosses as alleles of
      the genes (hsd K) encoding the archetypal type I restriction and modification
      system of E. coli K12.  Nevertheless, molecular experiments have failed to
      detect relatedness between the A and K systems.  We have cloned the hsd A genes
      and have identified, on the basis of DNA homology, related genes (hsd E)
      conferring a new specificity to a natural isolate of E. coli.  We show that the
      overall organization of the genes encoding EcoA and EcoE closely parallels that
      for EcoK.  Each enzyme is encoded by three genes, of which only one, hsdS,
      confers the specificity of DNA interaction.  The three genes are in the same
      order as those encoding EcoK, i.e. hsdR, hsdM and hsdS and, similarly, they
      include a promter between hsdR and hsdM from which the M and S genes can be
      transcribed.  The evidence indicates that EcoA and EcoE are type I restriction
      and modification enzymes, but they appear to identify an alternative family to
      EcoK.  For both families, the hsdR polypeptide is by far the largest, but the
      sizes of the other two polypeptides are reversed, with the smallest polypeptide
      of EcoK being the product of hsdS, and the smallest for the EcoA family being
      the product of hsdM.  Physiologically, the A restriction and modification
      system differs from that of K and its relatives, in that A-specific methylation
      of unmodified DNA is particularly effective.
AU  - Fuller-Pace FV
AU  - Cowan GM
AU  - Murray NE
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1985 186: 65-75.

PMID- 3025838
VI  - 83
DP  - 1986
TI  - Two DNA recognition domains of the specificity polypeptides of a family of type I restriction enzymes.
PG  - 9368-9372
AB  - The hsd genes of Salmonella typhimurium and Salmonella potsdam encode related
      type I restriction and modification systems designated SB and SP, respectively;
      the polypeptide encoded by the hsdS gene dictates the DNA sequence recognized.
      The hsdS genes of the SB and SP systems have a conserved sequence of around 100
      base pairs flanked by two nonhomologous (variable) regions of around 500 base
      pairs.  Recombination between the hsdS genes of SB and SP generated a system
      (SQ) with a different recognition specificity.  We have localized the position
      of the crossover in the central conserved region by analysis of nucleotide
      sequences.  Concomitant with the generation of a new combination of flanking
      variable regions is the recombination of minor differences in the central
      conserved region.  A polypeptide domain encoded on the 5' side of the crossover
      dictates recognition of the trinucleotide component of the target sequence, and
      a second domain encoded on the 3' side of the crossover, similarly governs
      recognition of the tetra- or penta-nucleotide component.  Our analysis
      implicates at least parts of the variable regions in the determination of the
      specificity of interaction between protein and DNA.  Furthermore, the
      trinucleotide components of the recognition sequences of S. typhimurium and
      Escherichia coli K-12 are identical, and the 5' segments of their hsdS genes
      are strikingly homologous rather than variable.
AU  - Fuller-Pace FV
AU  - Murray NE
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1986 83: 9368-9372.

PMID- 26450720
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Mariprofundus ferrooxydans Strain JV-1, Isolated from Loihi Seamount, Hawaii.
PG  - e01118-15
AB  - Mariprofundus ferrooxydans strain JV-1 was isolated in 1998 from Loihi Seamount,  Hawaii.
      Here, we present the draft genome of strain JV-1, which shows similarity  to other sequenced
      Mariprofundus isolates, strains PV-1 and M34.
AU  - Fullerton H
AU  - Hager KW
AU  - Moyer CL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01118-15.

PMID- 
VI  - 
DP  - 2006
TI  - Functional analysis of the two subunits of DNA methyltransferase EcoHK31I.
PG  - 1-224
AB  - Methylation of cytosine residues in DNA occurs in diverse organisms from bacteria to humans.
      In higher eukaryotic organisms cytosine-C5 methyltransferase is the only type of DNA MTase and
      it plays an important role in controlling a number of cellular processes including
      transcription, genomic imprinting and DNA repair.  In bacteria, there are three types of
      MTases, mC4-, mC5- and mA6-, classified according to the methylation site of the DNA.  MTase
      and its cognate restriction endonuclease form restriction-modification system.  The role of
      MTase is to protect the host from its own ENase digestion while the ENase acts to degrade the
      invasion of foreign DNA.  Sequence comparison of nearly 50 bacterial mC5-MTases has shown that
      these enzymes share an overall common protein architecture.  Ten conserved motifs (I to X),
      each 10 to 20 amino acids in length, have been identified, five of which are highly conserved
      (I, IV, VI, VIII and X).  In addition, all of these enzymes have a hypervariable region lying
      between motifs VIII and IX.  It is called the target recognition domain, and is responsible
      for the specificity of DNA recognition and the choice of base to be methylated.  All
      mC5-MTases are monomeric enzymes, except M. EcoHK31I and M.AquI which are MTases composed of
      two polypeptides.  M.EcoHK31I is a mC5-MTase which recognizes the sequence 5-YGGCCR-3' and
      consists of polypeptide a and b, with the latter gene encoded in an alternative reading frame
      of the former.  All of the conserved motifs in mC5-MTases can be found in polypeptide a,
      except motif IX, which is located in polypeptide b.  Both polypeptides are required for in
      vitro methylation.  Since both of the polypeptides a and b of M.EcoHK31I are sequenced and
      cloned into the expression vector separately, the role of DNA recognition and subunits
      interaction of individual polypeptides can be studied.  By electromobility shift assay, we
      found that polypeptides a and b complex recognize specific double strand oligos substrate.
      Polypeptide a-DNA formed aggregates and polypeptide b alone did not bind DNA.  Therefore,
      polypeptide b assists the proper binding of polypeptide a to DNA substrate.  Complex of
      polypeptide a and a polypeptide b variant with N-terminal deletion of 41 amino acids showed a
      16-fold reduction in methylation activity.  Further deletion resulted in an inactive MTase. By
      surface plasmon resonance assay, the dissociation equilibrium constant of polypeptides a and b
      complex was found to be 56.2nM and the KD for polypeptide a and deltaN46-polypeptide b complex
      was increased by about 95 folds, contributing by a drastic decrease in dissociate rate
      constant and an increase in association rate constant.  This indicated that the N-terminal
      region of polypeptide b takes part in subunit interaction.  To pinpoint which amino acid
      residues located at the variable region of polypeptide a are important for DNA binding and
      subunits interaction, "charge-to-alanine scanning mutagenesis" were performed on 16 charge
      residues between Asp213 and Glu271 in the small domain.  It was found that the five charge
      residues upstream of motif X are not required for activity.  For other residues except K225,
      E240 and D245, the protein is active when the same charge is maintained.
AU  - Fung WT
PT  - Journal Article
TA  - Ph.D. Thesis, Chinese Univ. of Hong Kong, China
JT  - Ph.D. Thesis, Chinese Univ. of Hong Kong, China
SO  - Ph.D. Thesis, Chinese Univ. of Hong Kong, China 2006 : 1-224.

PMID- 16740121
VI  - 387
DP  - 2006
TI  - Functional studies of the small subunit of EcoHK31I DNA methyltransferase.
PG  - 507-513
AB  - EcoHK311 DNA methyltransferase recognizes the sequence 5'-YGGCCR-3' and adds a methyl group
      to the fifth position of the internal cytosine to
      protect the DNA from cleavage by its cognate endonuclease. M.EcoHK311
      is composed of polypeptides alpha and beta. Polypepticle beta only
      contains the conserved IX motif of the C5-MTase family, and provides a
      unique example to show that this motif alone may be dislocated to
      another polypeptide. By electromobility shift assay, we found that the
      alpha/beta complex recognizes specific oligonucleotide substrates.
      Polypeptide alpha formed aggregates with DNA, while polypeptide p alone
      did not bind DNA. Therefore, polypeptide beta assists in the proper
      binding of polypeptide alpha to DNA substrate. The complex of
      polypeptide alpha and a polypeptide beta variant with an N-terminal
      deletion of 41 amino acids showed a 16-fold reduction in methylation
      activity. Further deletion resulted in an inactive methyltransferase.
      The dissociation equilibrium constant (K-d) of the alpha/beta complex
      was 56.4 nM, while the K-d value for the alpha/Delta N46-polypeptide
      beta complex was increased approximately 95-fold, caused by a drastic
      decrease in dissociate rate constant (k(d)) and an increase in the
      association rate constant (k(a)). This indicates that the N-terminal
      region of polypeptide beta takes part in subunit interaction, while the
      C-terminal region is involved in DNA binding.
AU  - Fung WT
AU  - Sze KH
AU  - Lee KF
AU  - Shaw PC
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 2006 387: 507-513.

PMID- 24526642
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Tomitella biformata AHU 1821T, Isolated from a Permafrost Ice Wedge in Alaska.
PG  - e00066-14
AB  - Tomitella biformata AHU 1821(T) was isolated and cultured from a permafrost ice wedge, aged
      presumably about 25,000 years, in the Fox permafrost tunnel (64.952
      degrees N 147.617 degrees W), Alaska. These genome data provide the basis for
      investigating T. biformata AHU 1821(T), identified as a long-term survivor of the
      extremely cold and closed environment.
AU  - Funo K
AU  - Kitagawa W
AU  - Tanaka M
AU  - Sone T
AU  - Asano K
AU  - Kamagata Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00066-14.

PMID- 28963215
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Type Strain Pseudomonas umsongensis DSM 16611.
PG  - e01038-17
AB  - Here, we report the draft genome sequence of Pseudomonas umsongensis type strain  DSM 16611.
      The assembly consists of 14 contigs containing 6,701,403 bp with a GC
      content of 59.73%.
AU  - Furmanczyk EM
AU  - Kaminski MA
AU  - Dziembowski A
AU  - Lipinski L
AU  - Sobczak A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01038-17.

PMID- 28963214
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Type Strain Pseudomonas jessenii DSM 17150.
PG  - e01035-17
AB  - We present the draft genome sequence of Pseudomonas jessenii type strain DSM 17150. The
      assembly consists of 13 contigs, contains 6,537,206 bp, and has a GC
      content of 59.7%.
AU  - Furmanczyk EM
AU  - Kaminski MA
AU  - Dziembowski A
AU  - Lipinski L
AU  - Sobczak A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01035-17.

PMID- 11267775
VI  - 196
DP  - 2001
TI  - Isolation and characterization of type IIS restriction endonuclease from Neisseria cuniculi ATCC 14688.
PG  - 171-176
AB  - Neisseria cuniculi produces the restriction enzyme NcuI which is an isoschizomer of MboII. We
      have demonstrated that NcuI recognizes a
      pentanucleotide sequence (5'-GAAGA-3'/3'-CTTCT-5'), and cleaves the DNA
      8 and 7 nucleotides downstream from the recognition site leaving a
      single 3'-protruding nucleotide. We have purified this enzyme to
      electrophoretic homogeneity using a four-step chromatographic procedure.
      NcuI endonuclease is a monomeric protein with an Mr = 48,000 +/- 1,000
      under denaturing conditions. The properties of NcuI are consistent with
      those for MboII, the position of the cleavage site being identical and
      the pH profile and divalent cation requirements being similar.
      Moreover, NcuI cross-reacts strongly with anti-MboII serum suggesting
      the presence of similar antigenic determinants. We have determined the
      sequence of 20 N-terminal amino acids for NcuI and concluded that this
      sequence is identical to the N-terminal portion of the MboII enzyme.
AU  - Furmanek B
AU  - Gromek K
AU  - Sektas M
AU  - Kaczorowski T
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2001 196: 171-176.

PMID- 17306509
VI  - 158
DP  - 2007
TI  - Molecular characterization of the DNA methyltransferase M1.NcuI from Neisseria cuniculi ATCC 14688.
PG  - 164-174
AB  - The methyltransferase M1.NcuI is a member of the restriction-modification system in Neisseria
      cuniculi ATCC14688 and recognizes the asymmetric
      pentanucleotide sequence 5'-GAAGA-3'/3'-CTTCT-5'. We purified M1.NcuI to
      electrophoretic homogeneity using a four-step chromatographic procedure.
      M1.NcuI is a protein with M(r)=32,000+/-1000 under denaturing conditions.
      It modifies the recognition sequence by transferring the methyl group from
      S-adenosyl-l-methionine to the 3' adenine of the pentanucleotide sequence
      5'-GAAGA-3'. M1.NcuI, like many other methyltransferases, occurs as a
      monomer in solution, as determined by gel filtration. Divalent cations
      inhibit the methylation activity of M1.NcuI. Optimal enzyme activity was
      observed at a pH of 8.0. M1.NcuI cross-reacted with anti-M1.MboII serum
      which reflects the similarity of M1.NcuI with M1.MboII at the amino acid
      level. The gene coding for the enzyme, designated ncuIM1, was cloned,
      sequenced and overexpressed in Escherichia coli. The structural gene is
      780 nucleotides in length coding for a protein of 259 amino acids (M(r)
      30,098). The presence and distribution of nine highly conserved amino acid
      sequence motifs and a putative target recognition domain in the enzyme
      structure suggest that M1.NcuI, similar to M1.MboII and M1.HpyAII, belongs
      to N(6)-adenine beta-class DNA methyltransferases.
AU  - Furmanek B
AU  - Sektas M
AU  - Wons E
AU  - Kaczorowski T
PT  - Journal Article
TA  - Res. Microbiol.
JT  - Res. Microbiol.
SO  - Res. Microbiol. 2007 158: 164-174.

PMID- 24315209
VI  - 169
DP  - 2014
TI  - Phenotypic and molecular characteristics of an Aeromonas hydrophila strain isolated from the River Nile.
PG  - 547-552
AB  - Aeromonas hydrophila, an inhabitant of aquatic ecosystems found in most parts of  the world,
      has considerable virulence potential. The polymerase chain reaction
      technique was used to assay for the presence of five virulence factor genes:
      haemolytic toxins aerA and ahh1, elastase ahyB, the enterotoxin act, and the
      polar flagella flaA/flaB in the A. hydrophila strain isolated from the River
      Nile. Drug screening showed high levels of resistance to beta-lactam antibiotics
      and tetracycline. Slime production was determined by the Congo red agar plate
      test. The isolate produced two restriction enzymes named AehI and AehII which are
      isoschizomers of XhoI and StuI respectively. The complete nucleotide sequence of
      the cryptic plasmid pAhy2.5 (2524 bp) from this strain was determined. Sequence
      analysis revealed the presence of two open reading frames (ORFs) encoding
      putative proteins. The protein coded by ORF1 is homologous with Rep proteins of
      plasmids belonging to the pC194 family, which are known to replicate by the
      rolling-circle mechanism. The putative double-strand origin of replication and a
      region with palindromic sequences that could function as a single-strand origin
      were detected in pAhy2.5.
AU  - Furmanek-Blaszk B
PT  - Journal Article
TA  - Microbiol. Res.
JT  - Microbiol. Res.
SO  - Microbiol. Res. 2014 169: 547-552.

PMID- 19332813
VI  - 155
DP  - 2009
TI  - M1.Mboll and M2.Mboll type IIS methyltransferases: different specificities, the same target.
PG  - 1111-1121
AB  - Methylation of a base in a specific DNA sequence protects the DNA from nucleolytic cleavage by
      restriction enzymes recognizing the same
      sequence. The Mboll restriction-modification (R-M) system of Moraxella
      bovis ATCC 10900 consists of a restriction endonuclease gene and two
      methyltransferase genes. The enzymes encoded by this system recognize
      an asymmetrical sequence 5'-GAAGA-3'/3'-CTTCT-5'. M1.Mboll modifies the
      last adenine in the recognition sequence 5'-GAAGA-3' to
      N-6-methyladenine. A second methylase, M2.Mboll, was cloned and
      purified to electrophoretic homogeneity using a four-step
      chromatographic procedure. It was demonstrated that M2.Mboll modifies
      the internal cytosine in the recognition sequence 3'-CTTCT-5', yielding
      N-4-methylcytosine, and moreover is able to methylate single-stranded
      DNA. The protein exists in solution as a monomer of molecular mass 30
      000 +/- 1000 Da under denaturing conditions, Divalent cations (Ca2+,
      Mg2+, Mn2+, and Zn2+) inhibit M2.Mboll methylation activity. It was
      found that the isomethylomer M2.Ncul from Neisseria cuniculi ATCC 14688
      behaves in the same manner. Functional analysis showed that the
      complete Mboll R-M system, consisting of two methyltransferases genes
      and the mbollR gene, is the most stable and the least harmful to
      bacterial cells.
AU  - Furmanek-Blaszk B
AU  - Boratynski R
AU  - Zolcinska N
AU  - Sektas M
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2009 155: 1111-1121.

PMID- 25724535
VI  - 362
DP  - 2015
TI  - The SfaNI restriction-modification system from Enterococcus faecalis NEB215 is located on a putative mobile genetic element.
PG  - fnv028
AB  - A type IIS restriction-modification (R-M) system SfaNI from Enterococcus faecalis NEB215 has
      been characterized. The sfaNIM gene was cloned by the methylase
      selection method. Methyltransferase SfaNI, a protein of 695 amino acids, consists
      of two domains responsible for different DNA-strand recognition and modification,
      and a putative DNA-binding HTH domain located in the N-terminal part of the
      protein. The sfaNIR gene, located adjacent to the gene of the cognate
      modification methyltransferases, encodes a protein of 648 amino acids. The enzyme
      has been purified to apparent homogeneity and its biochemical characteristics
      have been described. The R-M system SfaNI is flanked by a transposase gene at its
      5(') end, and a cassette chromosome recombinase (ccr) gene complex, encoding
      serine recombinases CcrA and CcrB, at the 3(') end. Both proteins are
      specifically involved in genome rearrangement and are widely distributed among
      staphylococcal species. These results suggested that the R-M system SfaNI is
      present on the putative mobile element.
AU  - Furmanek-Blaszk B
AU  - Sektas M
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2015 362: fnv028.

PMID- 29674545
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Five Staphylococcus aureus Strains Isolated from Clinically Healthy Cows in the Russian Federation.
PG  - e00275-18
AB  - We present here the draft genome sequences of five Staphylococcus aureus strains  isolated
      from milk samples from clinically healthy cows in the Russian
      Federation. Four of them were determined to be sequence type 97 (ST-97), and one
      was determined to be ST-22. All the strains are characterized by their genome
      possessing genes that code for enterotoxins and cytotoxins.
AU  - Fursova KK
AU  - Artem'eva OA
AU  - Nikanova DA
AU  - Larin AK
AU  - Zinovieva NA
AU  - Brovko FA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00275-18.

PMID- 26632218
VI  - 70
DP  - 2015
TI  - [Diversity in genome and epigenome of Helicobacter pylori].
PG  - 383-389
AB  - Helicobacter pylori infects human stomach and cause various gastric diseases including gastric
      cancer. The species is also known for rapid evolution and wide
      geographical diversity of genome sequence. Our team sequenced whole genome
      sequences of H. pylori strains isolated from Japanese patients and compared with
      whole genome sequences of H. pylori strains with other geographic origin and
      found that not only the gene repertoire but also genome structures and epigenetic
      modifications such as DNA methylations had large diversity with various
      mechanisms. Genome inversion events were geography specific and some of them were
      found to occur with gene duplication at their termini. DNA methylation states of
      H. pylori genomes suggested that they are diversified by both existence/absence
      repertoire of methyltransferase genes and by the movement of target recognition
      domain in the methyltransferase genes. Omics analysis revealed that methylation
      target sequence and transcriptome status are actually diversified by the domain
      sequence movement. We suggested that H. pylori utilizes these genome structure
      and methylome diversity for its adaptive evolution.
AU  - Furuta Y
PT  - Journal Article
TA  - Nihon Saikingaku Zasshi
JT  - Nihon Saikingaku Zasshi
SO  - Nihon Saikingaku Zasshi 2015 70: 383-389.

PMID- 
VI  - 84
DP  - 2009
TI  - Search for genomic rearrangements related to restriction-modification systems through genome comparison.
PG  - 441
AB  - We are proposing that restriction-modification systems are mobile element and the data which
      supports the hypothesis is accumulating.  For example, Type II restriction modification
      inserted in genome with long target duplication was found by the intra-genomic comparison
      analysis of Helicobacter pylori. First, we searched for more genome rearrangements related to
      restriction-modification systems by comprehensive bacterial intra-genomic comparison analysis
      and found the examples of (i) insertion with long target duplication of another type of
      restriction-modification systems, (ii) alleles consisted of different types of
      restriction-modification systems and (iii) alleles which have diversity in recognition
      domains. Next, we searched for the restriction-modification systems which are flanked by
      repeat sequences and found that restriction-modifiction systems are flanked by repeats much
      frequently than other genes significantly.  By the genome comparison analysis of those repeats
      flanked restriction-modification systems, we found that the transposon like structure of
      restriction-modification, which was flanked by long inverted repeats, was inserted with short
      direct repeats in the genome.
AU  - Furuta Y
AU  - Abe K
AU  - Kobayashi I
PT  - Journal Article
TA  - Genes Genet. Syst.
JT  - Genes Genet. Syst.
SO  - Genes Genet. Syst. 2009 84: 441.

PMID- 20071371
VI  - 38
DP  - 2010
TI  - Genome comparison and context analysis reveals putative mobile forms of restriction-modification systems and related rearrangements.
PG  - 2428-2443
AB  - The mobility of restriction-modification (RM) gene complexes and their association with genome
      rearrangements is a subject of active
      investigation. Here we conducted systematic genome comparisons and genome
      context analysis on fully sequenced prokaryotic genomes to detect
      RM-linked genome rearrangements. RM genes were frequently found to be
      linked to mobility-related genes such as integrase and transposase
      homologs. They were flanked by direct and inverted repeats at a
      significantly high frequency. Insertion by long target duplication was
      observed for I, II, III and IV restriction types. We found several RM
      genes flanked by long inverted repeats, some of which had apparently
      inserted into a genome with a short target duplication. In some cases,
      only a portion of an apparently complete RM system was flanked by inverted
      repeats. We also found a unit composed of RM genes and an integrase
      homolog that integrated into a tRNA gene. An allelic substitution of a
      Type III system with a linked Type I and IV system pair, and allelic
      diversity in the putative target recognition domain of Type IIG systems
      were observed. This study revealed the possible mobility of all types of
      RM systems, and the diversity in their mobility-related organization.
AU  - Furuta Y
AU  - Abe K
AU  - Kobayashi I
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2010 38: 2428-2443.

PMID- 21533192
VI  - 6
DP  - 2011
TI  - Domain Movement within a Gene: A Novel Evolutionary Mechanism for Protein Diversification.
PG  - e18819
AB  - A protein function is carried out by a specific domain localized at a specific position. In
      the present study, we report that, within a gene, a
      specific amino acid sequence can move between a certain position and
      another position. This was discovered when the sequences of
      restriction-modification systems within the bacterial species Helicobacter
      pylori were compared. In the specificity subunit of Type I
      restriction-modification systems, DNA sequence recognition is mediated by
      target recognition domain 1 (TRD1) and TRD2. To our surprise, several
      sequences are shared by TRD1 and TRD2 of genes (alleles) at the same locus
      (chromosomal location); these domains appear to have moved between the two
      positions. The gene/protein organization can be represented as
      x-(TRD1)-y-x-(TRD2)-y, where x and y represent repeat sequences. Movement
      probably occurs by recombination at these flanking DNA repeats. In
      accordance with this hypothesis, recombination at these repeats also
      appears to decrease two TRDs into one TRD or increase these two TRDs to
      three TRDs (TRD1-TRD2-TRD2) and to allow TRD movement between genes even
      at different loci. Similar movement of domains between TRD1 and TRD2 was
      observed for the specificity subunit of a Type IIG restriction enzyme.
      Similar movement of domain between TRD1 and TRD2 was observed for Type I
      restriction-modification enzyme specificity genes in two more eubacterial
      species, Streptococcus pyogenes and Mycoplasma agalactiae. Lateral domain
      movements within a protein, which we have designated DOMO (domain
      movement), represent novel routes for the diversification of proteins.
AU  - Furuta Y
AU  - Kawai M
AU  - Uchiyama I
AU  - Kobayashi I
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2011 6: e18819.

PMID- 
VI  - 
DP  - 2011
TI  - Restriction-modification systems as mobile epigenetic elements.
PG  - 85-103
AB  - Transfer of mobile genetic elements between prokaryotes is limited by restriction-modification
      systems.  Restriction-modification systems consist of a modification enzyme that
      epigenetically methylates a specific DNA sequence, and a restriction endonuclease (restriction
      enzyme) that cuts DNA lacking this epigenetic mark.  These elements were discovered because
      they attack mobile genetic elements.  However, recent studies have revealed that they are
      themselves mobile.  In some cases, the mobility of restriction-modification systems is through
      symbiosis with other forms of mobile elements.  In other cases, movement is unlinked to other
      mobile elements.  The systems may insert into the genome with long and variable target
      duplication, or into the intergenic region of an operon.  Insertion of
      restriction-modification systems induces other genome rearrangements such as amplification and
      inversion.  Even a domain within a protein can be the unit of mobility: some
      restriction-modification system subunits that recognize a target DNA sequence contain mobile
      amino acid sequences that can apparently move between different domains of a protein through
      recombination of DNA sequences encoding them.  This mobility extends the biological
      significance of restriction-modification systems beyond defense: the systems define, and
      sometimes even force, epigenetic order on a genome.  The multilevel conflicts involving these
      mobile epigenetic elements may drive prokaryotic evolution.
AU  - Furuta Y
AU  - Kobayashi I
PT  - Journal Article
TA  - Bacterial Integrative Mobile Genetic Elements
JT  - Bacterial Integrative Mobile Genetic Elements
SO  - Bacterial Integrative Mobile Genetic Elements 2011 : 85-103.

PMID- 22821560
VI  - 40
DP  - 2012
TI  - Movement of DNA sequence recognition domains between non-orthologous proteins.
PG  - 9218-9232
AB  - Comparisons of proteins show that they evolve through the movement of domains. However, in
      many cases, the underlying mechanisms remain
      unclear. Here, we observed the movements of DNA recognition domains
      between non-orthologous proteins within a prokaryote genome.
      Restriction-modification (RM) systems, consisting of a
      sequence-specific DNA methyltransferase and a restriction enzyme,
      contribute to maintenance/evolution of genomes/epigenomes. RM systems
      limit horizontal gene transfer but are themselves mobile. We compared
      Type III RM systems in Helicobacter pylori genomes and found that
      target recognition domain (TRD) sequences are mobile, moving between
      different orthologous groups that occupy unique chromosomal locations.
      Sequence comparisons suggested that a likely underlying mechanism is
      movement through homologous recombination of similar DNA sequences that
      encode amino acid sequence motifs that are conserved among Type III DNA
      methyltransferases. Consistent with this movement, incongruence was
      observed between the phylogenetic trees of TRD regions and other
      regions in proteins. Horizontal acquisition of diverse TRD sequences
      was suggested by detection of homologs in other Helicobacter species
      and distantly related bacterial species. One of these RM systems in H.
      pylori was inactivated by insertion of another RM system that likely
      transferred from an oral bacterium. TRD movement represents a novel
      route for diversification of DNA-interacting proteins.
AU  - Furuta Y
AU  - Kobayashi I
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: 9218-9232.

PMID- 23481556
VI  - 2
DP  - 2012
TI  - Mobility of DNA sequence recognition domains in DNA methyltransferases suggests epigenetics-driven adaptive evolution.
PG  - 292-296
AB  - DNA methylation is one of the best studied epigenetic modifications observed in prokaryotes as
      well as eukaryotes. It affects nearby gene expression. Most DNA
      methylation reactions in prokaryotes are catalyzed by a DNA methyltransferase,
      the modification enzyme of a restriction-modification (RM) system. Its target
      recognition domain (TRD) recognizes a specific DNA sequence for methylation. In
      this commentary, we review recent evidence for movement of TRDs between
      non-orthologous genes and movement within a gene. These movements are likely
      mediated by DNA recombination machinery, and are expected to alter the
      methylation status of a genome. Such alterations potentially lead to changes in
      global gene expression pattern and various phenotypes. The targets of natural
      selection in adaptive evolution might be these diverse methylomes rather than
      diverse genome sequences, the target according to the current paradigm in
      biology. This 'epigenetics-driven adaptive evolution' hypothesis can explain
      several observations in the evolution of prokaryotes and eukaryotes.
AU  - Furuta Y
AU  - Kobayashi I
PT  - Journal Article
TA  - Mobile Genet. Elements
JT  - Mobile Genet. Elements
SO  - Mobile Genet. Elements 2012 2: 292-296.

PMID- 25978460
VI  - 10
DP  - 2015
TI  - Microevolution of Virulence-Related Genes in Helicobacter pylori Familial Infection.
PG  - e0127197
AB  - Helicobacter pylori, a bacterial pathogen that can infect human stomach causing gastritis,
      ulcers and cancer, is known to have a high degree of genome/epigenome
      diversity as the result of mutation and recombination. The bacteria often infect
      in childhood and persist for the life of the host. One of the reasons of the
      rapid evolution of H. pylori is that it changes its genome drastically for
      adaptation to a new host. To investigate microevolution and adaptation of the H.
      pylori genome, we undertook whole genome sequencing of the same or very similar
      sequence type in multi-locus sequence typing (MLST) with seven genes in members
      of the same family consisting of parents and children in Japan. Detection of
      nucleotide substitutions revealed likely transmission pathways involving
      children. Nonsynonymous (amino acid changing) mutations were found in
      virulence-related genes (cag genes, vacA, hcpDX, tnfalpha, ggt, htrA and the
      collagenase gene), outer membrane protein (OMP) genes and other cell
      surface-related protein genes, signal transduction genes and
      restriction-modification genes. We reconstructed various pathways by which H.
      pylori can adapt to a new human host, and our results raised the possibility that
      the mutational changes in virulence-related genes have a role in adaptation to a
      child host. Changes in restriction-modification genes might remodel the methylome
      and transcriptome to help adaptation. This study has provided insights into H.
      pylori transmission and virulence and has implications for basic research as well
      as clinical practice.
AU  - Furuta Y
AU  - Konno M
AU  - Osaki T
AU  - Yonezawa H
AU  - Ishige T
AU  - Imai M
AU  - Shiwa Y
AU  - Shibata-Hatta M
AU  - Kanesaki Y
AU  - Yoshikawa H
AU  - Kamiya S
AU  - Kobayashi I
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2015 10: e0127197.

PMID- 
VI  - 88
DP  - 2013
TI  - Methylome diversification through changes in the sequence specificity of DNA methyltransferases.
PG  - 347
AB  - Helicobacter pylori, a human gastric pathogen, have a large number of DNA methyltransferase
      genes with each strain carrying a unique repertoire.  Previous genome comparison works
      suggested that these methyltransferases often change DNA sequence specificity through movement
      of amino-acid sequences in the target recognition domains between genes and within a gene
      (Domain Movement).  By Single-Molecule Real-Time sequencing technology, we detected methylated
      DNA sites throughout several closely related genomes.  We successfully deduced DNA sequence
      motifs for methylation and assigned each of them to a specific amino-acid sequence group of
      target recognition domains in the specificity determinant genes.  Overall, the methylome
      turned out to be quite variable among the closely-related strains, although there are
      hypermethylated loci in all the strains.  As expected from their effects on gene expression,
      knockout of a specificity gene led to changes in the transcriptome.  These results provide
      evidence for proposed mechanisms of sequence-specificity changes in the DNA methyltransferases
      and lend support to the concept of epigenetics-driven adaptive evolution.
AU  - Furuta Y
AU  - Namba H
AU  - Shibata T
AU  - Nishiyama T
AU  - Shigenobu S
AU  - Suzuki Y
AU  - Sugano S
AU  - Hasebe M
AU  - Kobayashi I
PT  - Journal Article
TA  - Genes Genet. Syst.
JT  - Genes Genet. Syst.
SO  - Genes Genet. Syst. 2013 88: 347.

PMID- 24722038
VI  - 10
DP  - 2014
TI  - Methylome Diversification through Changes in DNA Methyltransferase Sequence Specificity.
PG  - e1004272
AB  - Epigenetic modifications such as DNA methylation have large effects on gene expression and
      genome maintenance. Helicobacter pylori, a human gastric pathogen,
      has a large number of DNA methyltransferase genes, with different strains having
      unique repertoires. Previous genome comparisons suggested that these
      methyltransferases often change DNA sequence specificity through domain
      movement-the movement between and within genes of coding sequences of target
      recognition domains. Using single-molecule real-time sequencing technology, which
      detects N6-methyladenines and N4-methylcytosines with single-base resolution, we
      studied methylated DNA sites throughout the H. pylori genome for several closely
      related strains. Overall, the methylome was highly variable among closely related
      strains. Hypermethylated regions were found, for example, in rpoB gene for RNA
      polymerase. We identified DNA sequence motifs for methylation and then assigned
      each of them to a specific homology group of the target recognition domains in
      the specificity-determining genes for Type I and other restriction-modification
      systems. These results supported proposed mechanisms for sequence-specificity
      changes in DNA methyltransferases. Knocking out one of the Type I specificity
      genes led to transcriptome changes, which suggested its role in gene expression.
      These results are consistent with the concept of evolution driven by DNA
      methylation, in which changes in the methylome lead to changes in the
      transcriptome and potentially to changes in phenotype, providing targets for
      natural or artificial selection.
AU  - Furuta Y
AU  - Namba-Fukuyo H
AU  - Shibata TF
AU  - Nishiyama T
AU  - Shigenobu S
AU  - Suzuki Y
AU  - Sugano S
AU  - Hasebe M
AU  - Kobayashi I
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2014 10: e1004272.

PMID- 15184674
VI  - 101
DP  - 2004
TI  - Genome sequence of Picrophilus torridus and its implications for life around pH 0.
PG  - 9091-9096
AB  - The euryarchaea Picrophilus torridus and Picrophilus oshimae are able to grow around pH 0 at
      up to 65 C, thus they represent the most thermoacidophilic organisms known. Several features
      that may contribute to the thermoacidophilic survival strategy of P. torridus were deduced
      from analysis of its 1.55-megabase genome. P. torridus has the smallest genome among
      nonparasitic aerobic microorganisms growing on organic substrates and simultaneously the
      highest coding density among thermoacidophiles. An exceptionally high ratio of secondary over
      ATP-consuming primary transport systems demonstrates that the high proton concentration in the
      surrounding medium is extensively used for transport processes. Certain genes that may be
      particularly supportive for the extreme lifestyle of P. torridus appear to have been
      internalized into the genome of the Picrophilus lineage by horizontal gene transfer from
      crenarchaea and bacteria. Finally, it is noteworthy that the thermoacidophiles from
      phylogenetically distant branches of the Archaea apparently share an unexpectedly large pool
      of genes.
AU  - Futterer O
AU  - Angelov A
AU  - Liesegang H
AU  - Gottschalk G
AU  - Schleper C
AU  - Schepers B
AU  - Dock C
AU  - Antranikian G
AU  - Liebl W
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2004 101: 9091-9096.

PMID- 11732923
VI  - 40
DP  - 2001
TI  - Probing the general base catalysis in the first step of BamHI action by computer simulations.
PG  - 15017-15023
AB  - BamHI is a type II restriction endonuclease that catalyzes the scission of the phoshodiester
      bond in the GAGTCC cognate sequence in the presence of two divalent metal ions. The first step
      of the reaction is the preparation of water for nucleophilic attack by Glu-113, which has been
      proposed to abstract the proton from the attacking water molecule. Alternatively, the
      3'-phosphate group to the susceptible phosphodiester bond has been suggested to play a role
      as the general base. The two hypotheses have been tested by computer simulations using the
      semiempirical protein dipoles Langevin dipoles (PDLD/S) method. Deprotonation of water by
      Glu-113 has been found to be less favorable by 5.7 kcal/mol than metal-catalyzed deprotonation
      with a concomitant proton transfer to bulk solvent. The preparation of the nucleophile by the
      3'-phosphate group is less favorable by 12.3 kcal/mol. These results suggest that both the
      general base and the substrate-assisted mechanisms in the first step of BamHI action are less
      likely than the metal-catalyzed reaction. The metal ions in the active site of BamHI make the
      largest contributions to the reduction of the free energy of hydroxide ion formation. On the
      basis of these findings we propose that the first step of endonuclease catalysis does not
      require a general base; rather, the essential attacking nucleophile in BamHI catalytic action
      is stabilized by the metal ions.
AU  - Fuxreiter M
AU  - Osman R
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2001 40: 15017-15023.

PMID- 
VI  - 666-7
DP  - 2003
TI  - Computational approaches to restriction endonucleases.
PG  - 469-479
AB  - Type II restriction endonucleases catalyze phosphodiester bond hydrolysis in bacteria to
      protect the host cell from invading phage DNA.  Due to their exquisite sequence selectivity
      type II restriction endonucleases serve as excellent model systems for studying protein -
      nucleic acid interactions.  Crystal structures of the PD-(D/E)XK superfamily revealed a common
      a/b core motif and similar active site.  In contrast, these enzymes show little sequence
      similarity and use different strategies to interact with their substrate DNA.  Computational
      approaches have been applied to unify the mechanism of restriction endonucleases and
      rationalize their diversity.  The first step of type II restriction endonuclease catalysis has
      been studied on BamHI by semi-microscopic version of the Protein Dipoles Langevin Dipoles
      method.  The substrate-assisted catalysis and the general base mechanism have been concluded
      as less likely than the metal-catalyzed reaction.  A general model for catalysis has been
      proposed based on the group contributions to the reduction of the activation free energy.
      Factors contributing to structural stability of PD-(D/E)XK type II restriction endonucleases
      have been analyzed to elucidate evolutionary relationship between these enzymes.  Residues
      playing role in catalysis and recognition were highly correlated with those participating in
      stabilization centers.  Thus the main functional motifs were concluded to be evolutionary more
      conserved than other parts of the structure.  This observation is consistent with the proposal
      that these enzymes have developed from a common ancestor with divergent evolution.
AU  - Fuxreiter M
AU  - Osman R
AU  - Simon I
PT  - Journal Article
TA  - Theochem.
JT  - Theochem.
SO  - Theochem. 2003 666-7: 469-479.

PMID- 12142452
VI  - 11
DP  - 2002
TI  - Protein stability indicates divergent evolution of PD-(D/E)XK type II restriction endonucleases.
PG  - 1978-1983
AB  - Type II restriction endonucleases recognize 4-8 base-pair-long DNA sequences and catalyze
      their cleavage with remarkable specificity.
      Crystal structures of the PD-(DE)XK superfamily revealed a common
      alpha/beta core motif and similar active site. In contrast, these
      enzymes show little sequence similarity and use different strategies to
      interact with their substrate DNA. The intriguing question is whether
      this enzyme family could have evolved from a common origin. In our
      present work, protein structure stability elements were analyzed and
      compared in three parts of PD-(DE)XK type II restriction endonucleases:
      (1) core motif, (2) active-site residues, and (3) residues playing role
      in DNA recognition. High correlation was found between the active-site
      residues and those stabilization factors that contribute to preventing
      structural decay. DNA recognition sites were also observed to
      participate in stabilization centers. It indicates that recognition
      motifs and active sites in PD-(DE)XK type II restriction endonucleases
      should have been evolutionary more conserved than other parts of the
      structure. Based on this observation it is proposed that PD-(DE)XK type
      II restriction endonucleases have developed from a common ancestor with
      divergent evolution.
AU  - Fuxreiter M
AU  - Simon I
PT  - Journal Article
TA  - Protein Sci.
JT  - Protein Sci.
SO  - Protein Sci. 2002 11: 1978-1983.

PMID- 28183764
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Halolamina pelagica CDK2 Isolated from Natural Salterns  from Rann of Kutch, Gujarat, India.
PG  - e01593-16
AB  - Halolamina pelagica strain CDK2, a halophilic archaeon (growth range 1.36 to 5.12 M NaCl), was
      isolated from rhizosphere of wild grasses of hypersaline soil of the
      Rann of Kutch, Gujarat, India. Its draft genome contains 2,972,542 bp and 3,485
      coding sequences, depicting genes for halophilic serine proteases and trehalose
      synthesis.
AU  - Gaba S
AU  - Singh RN
AU  - Abrol S
AU  - Yadav AN
AU  - Saxena AK
AU  - Kaushik R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01593-16.

PMID- 7536414
VI  - 307
DP  - 1995
TI  - The mechanism of inhibition of DNA (cytosine-5-)-methyltransferases by 5-azacytosine is likely to involve methyl transfer to the inhibitor.
PG  - 87-92
AB  - The mechanism of inhibition of DNA (cytosine-5-)-methyltransferases by the mechanism-based
      inhibitor 5-azacytosine has remained unclear, mainly because of the unavailability of a
      substrate in which the inhibitor, but not normal cytosine, is present at the target site. We
      synthesized an oligonucleotide duplex containing a single target site for the EcoRII
      methyltransferase, in which the target base is 5-azacytosine. This substrate formed a stable
      covalent complex with EcoRII methyltransferase in the absence and in the presence of the
      cofactor S-adenosylmethionine. The complex formed in the presence of the cofactor was
      resistant to SDS and moderate heat treatment, and a methyl group was incorporated into the
      complex. Enzyme titration and kinetic studies of inhibition suggest that methyl transfer to
      the complex occurred only during the first turnover of the reaction. These results suggest
      that, when the enzyme binds to 5-azacytosine in the presence of the cofactor, a methyl group
      is transferred to the N-5 position of the base, resulting in the inactivation of the enzyme.
AU  - Gabbara S
AU  - Bhagwat AS
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 1995 307: 87-92.

PMID- 1526995
VI  - 267
DP  - 1992
TI  - Interaction of EcoRII endonuclease with DNA substrates containing single recognition sites.
PG  - 18623-18630
AB  - EcoRII is unusual among type II restriction enzymes in that, while it cleaves substrates such
      as pBR322 and bacteriophage lambda that contain several recognition sites for the enzyme
      efficiently, substrates such as the genomes of bacteriophages T3 and T7 which contain a small
      number of recognition sites are cut poorly by it. Interestingly, pBR322, or a short DNA duplex
      containing a single site for the enzyme, can activate the enzyme to cleave resistant
      substrates. We show here that at low concentrations, activator short duplexes are themselves
      cleaved poorly by the enzyme. Further, the reaction shows substrate cooperativity, and at high
      concentration, the duplexes are both activators and good substrates for the enzyme. This
      supports the model that the activation of EcoRII involves binding of more than one DNA
      molecule and provides a simple system to study the mechanism of activation. Using a gel
      mobility shift assay, we show that the enzyme forms sequence-specific, methylation-sensitive
      complexes with the duplexes in the absence of activating DNA. Therefore, resistance of the
      short duplexes to the enzyme at low concentrations cannot be due to an inability of the enzyme
      to bind the duplexes. Interestingly, these complexes are stable in the presence of Mg2+, the
      cofactor for the enzyme, and the complexes obtained in the presence of Mg2+ do not contain DNA
      that is cleaved by the enzyme. The inefficient step in the action of EcoRII on resistant
      substrates must occur subsequent to initial substrate binding and it is this step that the
      activating DNA must regulate.
AU  - Gabbara S
AU  - Bhagwat AS
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1992 267: 18623-18630.

PMID- 7612633
VI  - 34
DP  - 1995
TI  - Cytosine methyltransferase from Escherichia coli in which active site cysteine is replaced with serine is partially active.
PG  - 8914-8923
AB  - EcoRII methyltransferase (M.EcoRII) catalyzes the transfer of methyl groups from
      S-adenosyl-L-methionine (SAM) to C-5 position of second cytosine in the DNA sequence
      5'-CCWGG (W=A or T).  The reaction is initiated by a nucleophilic attack of the C-6 target
      cytosine
      by a cysteine that is conserved among all cytosine methyltransferases.  We have replaced this
      cysteine in M.EcoRII with serine or alanine and purified the proteins to homogeneity.  The
      catalytic
      efficiency (Kcat/Km) of the mutant enzyme with serine (C186S) for methyl transfer is about
      10,000 times less than that of WT but is substantially higher than the efficiency of the C186A
      mutant.  We show that the WT enzyme and C186S mutant are proficient in exchange of proton at
      C-5 and that this activity is reduced in the mutant to the same extent as the methyl transfer
      activity.
      The C186S mutant is insensitive to a cysteine-specific inhibitor, and it transfers methyl
      groups to
      the same position of cytosine as the WT enzyme.  The ability of serine to act as a nucleophile
      in the
      enzyme reaction suggests that it - and probably the cysteine in the WT enzyme - is activated
      by a
      nearby base.  Like the WT enzyme, C186S forms stable SDS-resistant complexes with DNA
      containing 5-azacytosine; but unlike the WT enzyme, the mutant reacts faster with
      5-azacytosine
      than with normal cytosine.  Apparently, greater reactivity of 5-azacytosine assists the C186S
      mutant in catalysis.
AU  - Gabbara S
AU  - Sheluho D
AU  - Bhagwat AS
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1995 34: 8914-8923.

PMID- 8177221
VI  - 243
DP  - 1994
TI  - A DNA repair process in Escherichia coli corrects U:G and T:G mismatches to C:G at sites of cytosine methylation.
PG  - 244-248
AB  - Escherichia coli contains a base mismatch correction system called VSP repair that is known to
      correct T:G mismatches to C:G when they occur in certain sequence contexts. The preferred
      sequence context for this process is the site for methylation by the E. coli DNA cytosine
      methylase (Dcm). For this reason, VSP repair is thought to counteract potential mutagenic
      effects of deamination of 5-methylcytosine to thymine. We have developed a genetic reversion
      assay that quantitates the frequency of C to T mutations at Dcm sites and the removal of such
      mutations by DNA repair processes. Using this assay, we have studied the repair of U:G
      mismatches in DNA to C:G and have found that VSP repair is capable of correcting these
      mismatches. Although VSP repair substantially affects the reversion frequency, it may not be
      as efficient at correcting U:G mismatches as the uracil DNA glycosylase-mediated repair
      process.
AU  - Gabbara S
AU  - Wyszynski M
AU  - Bhagwat AS
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1994 243: 244-248.

PMID- Not carried by PubMed...
VI  - 55
DP  - 1994
TI  - Molecular mechanism and mutagenic effects of DNA 5-cytosine methyltransferases.
PG  - 403B-404B
AB  - DNA (C-S)cytosine methyltransferases (C5 methylases) catalyze the transfer of methyl group to
      position 5 of cytosine in DNA. This type of modification occurs in most organisms, from
      bacteria to humans. In prokaryotes C5 methylases function primarily in protecting the cell
      from viral invasions. In eukaryotes C5 methylases play important roles in the regulation of
      gene expression. All known cytosine methylases, including the mouse and the human methylases,
      share a strong sequence conservation, suggesting a common reaction mechanism. I used the
      Escherichia coli EcoRII methylase in this study as a model enzyme to understand the mechanism
      and function of all cytosine methylases. The reaction catalyzed by the methylase is proposed
      to occur in a Michael fashion. My data using cytosine analogs support this mechanism.
      Furthermore, I show that a cysteine conserved among all cytosine methylases is required for
      catalysis. This role is likely to be in the nucleophilic attack at carbon 6 of cytosine, a
      first step in the reaction. In support of this role substitution of the conserved cysteine by
      serine or alanine reduces kcat of methyl transferase activity by 4 and 6 orders of magnitude,
      respectively, but does not appreciably affect Km. While studying the properties of the mutants
      with serine and alanine changes, I found that the hydroxyl group of the serine, replacing the
      conserved cysteine, can covalently link to DNA. Sites of cytosine methylation are hot-spots
      for cytosine (C) to thymine (T) mutations. In humans such mutations are found to be the cause
      of genetic diseases and cancer. Using a genetic system based on the reversion of a mutation in
      a kanamycin-resistance gene, I show that EcoRII methylase can cause cytosine to uracil (U)
      deaminations at a site of cytosine methylation, and that the uracil formed can propagate in
      vivo to cause C:G to T:A transition mutations. Thus the enzyme-mediated C to U deamination is
      one pathway by which cytosine methylases cause C to T mutations. The contribution of the C to
      U to T pathway in C to T mutagenesis was assessed by analyzing the barriers to its occurrence.
AU  - Gabbara SS
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1994 55: 403B-404B.

PMID- 26586883
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Moderately Heat-Tolerant Lactococcus lactis subsp. lactis bv. diacetylactis Strain GL2 from Algerian Dromedary Milk.
PG  - e01334-15
AB  - Lactococcus lactis subsp. lactis bv. diacetylactis GL2 is a moderately thermotolerant lactic
      acid bacterium isolated from dromedary raw milk. Here, we
      present the draft genome sequence of this potential new dairy starter strain,
      which combines thermotolerance and the capacity to metabolize lactose, casein,
      and citrate.
AU  - Gabed N
AU  - Yang M
AU  - Bey BHM
AU  - Drici H
AU  - Gross R
AU  - Dandekar T
AU  - Liang C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01334-15.

PMID- 28596390
VI  - 5
DP  - 2017
TI  - Draft Genome of Halomonas lionensis RHS90T, a Stress-Tolerant Gammaproteobacterium Isolated from Mediterranean Sea Sediments.
PG  - e00311-17
AB  - Members of the genus Halomonas are physiologically versatile and harbor ecological adaptations
      enabling the colonization of contrasted environments. We
      present here the draft genome of Halomonas lionensis RHS90T, isolated from
      Mediterranean Sea sediments. Numerous genes related to stress tolerance, DNA
      repair, or external signal-sensing systems were predicted, which could represent
      selective advantages of this marine bacterium.
AU  - Gaboyer F
AU  - Maignien L
AU  - Jebbar M
AU  - Alain K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00311-17.

PMID- 28663303
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Phaeobacter leonis Type Strain 306, an Alphaproteobacterium Isolated from Mediterranean Sea Sediments.
PG  - e00312-17
AB  - Phaeobacter leonis strain 306T is an alphaproteobacterium isolated from Mediterranean Sea
      sediments. It belongs to the genus Phaeobacter, which was
      recently proposed and is still poorly characterized. In an effort to better
      understand the fundamental aspects of the microbiology of this genus, we present
      here the 4.82-Mb draft genome sequence of Phaeobacter leonis strain 306T.
AU  - Gaboyer F
AU  - Maignien L
AU  - Jebbar M
AU  - Alain K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00312-17.

PMID- 23209230
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Bacteriocin-Producing Strain Lactococcus garvieae DCC43.
PG  - 6976-6977
AB  - This work describes the draft genome sequence of Lactococcus garvieae DCC43. The  2.2-Mb draft
      genome contains 2,227 predicted protein-coding genes, among which is
      a region encoding the bacteriocin garvicin ML. No antibiotic resistance genes or
      capsule-related virulence genes were identified. Two plasmid replication regions
      indicate that this strain likely contains plasmids. Comparative genomics suggests
      that this strain displays a high degree of sequence variation from the previously
      sequenced L. garvieae strains.
AU  - Gabrielsen C
AU  - Brede DA
AU  - Hernandez PE
AU  - Nes IF
AU  - Diep DB
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6976-6977.

PMID- 25977421
VI  - 3
DP  - 2015
TI  - Genome Sequences of 11 Shiga Toxin-Producing Escherichia coli Strains.
PG  - e00418-15
AB  - Shiga toxin-producing Escherichia coli (STEC) strains are a common cause of both  sporadic
      infection and outbreaks of enteric disease in humans. Here, we present
      draft genome sequences of 11 STEC strains of different serotypes (O145, O121,
      O26, O177, and O-type unknown), that have been isolated from patients with
      enteric disease of various degrees of severity, in the years 2001 to 2014 at St.
      Olavs Hospital in Trondheim, Norway.
AU  - Gabrielsen C
AU  - Drablos F
AU  - Afset JE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00418-15.

PMID- 28082508
VI  - 5
DP  - 2017
TI  - Genome Sequence of Enterococcus faecalis Strain CG_E.
PG  - e01488-16
AB  - Enterococcus faecalis CG_E is a Gram-positive, lactic acid-producing coccus. The  draft genome
      of E. faecalis strain CG_E comprises 2,969,881 bp and exhibits a G+C
      content of 37.34%. The genome encodes 2,848 predicted protein-encoding and 97 RNA
      genes.
AU  - Gabris C
AU  - Poehlein A
AU  - Bengelsdorf FR
AU  - Daniel R
AU  - Durre P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01488-16.

PMID- 28082507
VI  - 5
DP  - 2017
TI  - Genome Sequence of Lactobacillus sunkii Strain CG_D.
PG  - e01487-16
AB  - Lactobacillus sunkii CG_D is a rod-shaped, Gram-positive, and heterofermentative  lactic acid
      bacterium. The draft genome of L. sunkii strain CG_D comprises
      2,794,637 bp with an average G+C content of 42.03%. The genome harbors 2,662
      predicted protein-encoding, and 71 RNA genes.
AU  - Gabris C
AU  - Poehlein A
AU  - Bengelsdorf FR
AU  - Daniel R
AU  - Durre P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01487-16.

PMID- 12680948
VI  - 36
DP  - 2003
TI  - Improvement of phage defence in Lactococcus lactis by introduction of the plasmid encoded restriction and modification system LlaAI.
PG  - 332-336
AB  - AIMS: To study the ability of the plasmid-encoded restriction and modification (R/M) system
      LlaAI to function as a bacteriophage resistance
      mechanism in Lactococcus lactis during milk fermentations. METHODS AND
      RESULTS: Plasmid pAIcat4, carrying the R/M system LlaAI and a
      chloramphenicol resistance cassette, was introduced into the plasmid-free
      strain L. lactis MG1614 and the industrial strain L. lactis 964. By
      measuring changes in conductivity the influence of different phage on the
      growth was determined. CONCLUSIONS: The plasmid-encoded R/M system LlaAI
      significantly improves the bacteriophage resistance of L. lactis during
      milk fermentations. SIGNIFICANCE AND IMPACT OF THE STUDY: It is essential
      to determine the potential of a phage defence mechanism in L. lactis
      starter culture strains during growth in milk before steps are taken to
      improve starter cultures. This study shows that LlaAI is useful for
      improvement of starter cultures.
AU  - Gabs S
AU  - Josephsen J
PT  - Journal Article
TA  - Lett. Appl. Microbiol.
JT  - Lett. Appl. Microbiol.
SO  - Lett. Appl. Microbiol. 2003 36: 332-336.

PMID- 23408850
VI  - 41
DP  - 2013
TI  - Site- and strand-specific nicking of DNA by fusion proteins derived from MutH and I-SceI or TALE repeats.
PG  - e83
AB  - Targeted genome engineering requires nucleases that introduce a highly specific double-strand
      break in the genome that is either processed by homology-directed repair in the presence of a
      homologous repair template or by non-homologous end-joining (NHEJ) that usually results in
      insertions or deletions. The error-prone NHEJ can be efficiently suppressed by 'nickases'
      that produce a single-strand break rather than a double-strand break. Highly specific nickases
      have been produced by engineering of homing endonucleases and more recently by modifying zinc
      finger nucleases (ZFNs) composed of a zinc finger array and the catalytic domain of the
      restriction endonuclease FokI. These ZF-nickases work as heterodimers in which one subunit has
      a catalytically inactive FokI domain. We present two different approaches to engineer highly
      specific nickases; both rely on the sequence-specific nicking activity of the DNA mismatch
      repair endonuclease MutH which we fused to a DNA-binding module, either a catalytically
      inactive variant of the homing endonuclease I-SceI or the DNA-binding domain of the TALE
      protein AvrBs4. The fusion proteins nick strand specifically a bipartite recognition sequence
      consisting of the MutH and the I-SceI or TALE recognition sequences, respectively, with a more
      than 1000-fold preference over a stand-alone MutH site. TALE-MutH is a programmable nickase.
AU  - Gabsalilow L
AU  - Schierling B
AU  - Friedhoff P
AU  - Pingoud A
AU  - Wende W
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2013 41: e83.

PMID- 1880713
VI  - 31
DP  - 1991
TI  - Host-controlled modification and restriction as a criterion of evaluating the therapeutical potential of Pseudomonas phage.
PG  - 101-106
AB  - The recently isolated phages Phi ST3 and Phi ST1 were compared as to their
      lysis behaviour in about 100 different P. aeruginosa strains.  The growth of
      Phi ST3 varies greatly in different host strains.  We demonstrated one case of
      non-classical, host-dependent modification and restriction.  Here the
      capability to adsorb, and consequently to reproduce in a given host strain
      differs, depending on which modification the phage acquired in its former host.
      The DNA-containing phage Phi ST1 displays stable lysis properties in the
      majority of the host strains.  This make Phi ST1 a candidate for therapeutic
      phage preparations.  One of the reasons for stable lysis properties is the
      apparent selection against recognition sites of restriction enzymes in its
      genome.
AU  - Gachechiladze KK
AU  - Balardshishvili NS
AU  - Adamia RS
AU  - Chanishvili TG
AU  - Kruger DH
PT  - Journal Article
TA  - J. Basic Microbiol.
JT  - J. Basic Microbiol.
SO  - J. Basic Microbiol. 1991 31: 101-106.

PMID- 9638880
VI  - 287
DP  - 1998
TI  - Phage restriction and the presence of small plasmids in Salmonella enteritidis.
PG  - 509-519
AB  - Between 1990-1994, a total of 16,505 S. enteritidis strains of human, animal and food origin
      were phage-typed, using the Hungarian scheme and the changes of incidence of the dominant
      phage types were monitored.  The incidence of PT1 (corresponding to Ward's PT1 was very high
      between 1990 and 1992 (67.9071.0% of the total S. enteritidis isolates), later, it decreased.
      The prevalence of PT6 (corresponding to Ward's PT4) was rare until 1992, then it gradually
      increased.  The phage type and plasmid content of 78 Salmonella enteritidis strains were
      determined.  Small plasmids were present in 59% of the isolates, together with a
      serotype-specific (38 MDa) plasmid.  A correlation was found between the presence of the small
      plasmid and phage restriction to two phages used for subdividing the Hungarian phage types 1
      (PT1) and 6 (PT6) of S. enteritidis (corresponding to PT1 and PT4 in Ward's typing scheme,
      respectively).
AU  - Gado I
AU  - Laszlo VG
AU  - Negy B
AU  - Milch H
AU  - Drin I
AU  - Awad-Masalmeh M
AU  - Horvath J
PT  - Journal Article
TA  - Zentralbl. Bakteriol.
JT  - Zentralbl. Bakteriol.
SO  - Zentralbl. Bakteriol. 1998 287: 509-519.

PMID- 22933757
VI  - 194
DP  - 2012
TI  - Genome Sequence of Enterococcus hirae (Streptococcus faecalis) ATCC 9790, a Model Organism for the Study of Ion Transport, Bioenergetics, and Copper Homeostasis.
PG  - 5126-5127
AB  - Enterococcus hirae ATCC 9790 is a Gram-positive lactic acid bacterium that has been used in
      basic research for over 4 decades. Here we report the sequence and
      annotation of the 2.8-Mb genome of E. hirae and its endemic 29-kb plasmid
      pTG9790.
AU  - Gaechter T
AU  - Wunderlin C
AU  - Schmidheini T
AU  - Solioz M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5126-5127.

PMID- 25081256
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Xanthomonas axonopodis pv. allii Strain CFBP 6369.
PG  - e00727-14
AB  - We report here the draft genome sequence of Xanthomonas axonopodis pv. allii strain CFBP 6369,
      the causal agent of bacterial blight of onion. The draft genome
      has a size of 5,425,942 bp and a G+C content of 64.4%.
AU  - Gagnevin L
AU  - Bolot S
AU  - Gordon JL
AU  - Pruvost O
AU  - Verniere C
AU  - Robene I
AU  - Arlat M
AU  - Noel LD
AU  - Carrere S
AU  - Jacques MA
AU  - Koebnik R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00727-14.

PMID- 20368802
VI  - 5
DP  - 2010
TI  - The genes coding for the conversion of carbazole to catechol are flanked by IS6100 elements in Sphingomonas sp. strain XLDN2-5.
PG  - E10018
AB  - BACKGROUND: Carbazole is a recalcitrant compound with a dioxin-like
      structure and possesses mutagenic and toxic activities. Bacteria respond
      to a xenobiotic by recruiting exogenous genes to establish a pathway to
      degrade the xenobiotic, which is necessary for their adaptation and
      survival. Usually, this process is mediated by mobile genetic elements
      such as plasmids, transposons, and insertion sequences. FINDINGS: The
      genes encoding the enzymes responsible for the degradation of carbazole to
      catechol via anthranilate were cloned, sequenced, and characterized from a
      carbazole-degrading Sphingomonas sp. strain XLDN2-5. The car gene cluster
      (carRAaBaBbCAc) and fdr gene were accompanied on both sides by two copies
      of IS6100 elements, and organized as
      IS6100::ISSsp1-ORF1-carRAaBaBbCAc-ORF8-IS6100-fdr-IS6100. Carbazole was
      converted by carbazole 1,9a-dioxygenase (CARDO, CarAaAcFdr), meta-cleavage
      enzyme (CarBaBb), and hydrolase (CarC) to anthranilate and
      2-hydroxypenta-2,4-dienoate. The fdr gene encoded a novel ferredoxin
      reductase whose absence resulted in lower transformation activity of
      carbazole by CarAa and CarAc. The ant gene cluster (antRAcAdAbAa) which
      was involved in the conversion of anthranilate to catechol was also
      sandwiched between two IS6100 elements as IS6100-antRAcAdAbAa-IS6100.
      Anthranilate 1,2-dioxygenase (ANTDO) was composed of a reductase (AntAa),
      a ferredoxin (AntAb), and a two-subunit terminal oxygenase (AntAcAd).
      Reverse transcription-PCR results suggested that carAaBaBbCAc gene
      cluster, fdr, and antRAcAdAbAa gene cluster were induced when strain
      XLDN2-5 was exposed to carbazole. Expression of both CARDO and ANTDO in
      Escherichia coli required the presence of the natural reductases for full
      enzymatic activity. CONCLUSIONS/SIGNIFICANCE: We predict that IS6100 might
      play an important role in the establishment of carbazole-degrading
      pathway, which endows the host to adapt to novel compounds in the
      environment. The organization of the car and ant genes in strain XLDN2-5
      was unique, which showed strong evolutionary trail of gene recruitment
      mediated by IS6100 and presented a remarkable example of rearrangements
      and pathway establishments.
AU  - Gai Z
AU  - Wang X
AU  - Liu X
AU  - Tai C
AU  - Tang H
AU  - He X
AU  - Wu G
AU  - Deng Z
AU  - Xu P
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2010 5: E10018.

PMID- 22038966
VI  - 193
DP  - 2011
TI  - Genome Sequence of Sphingobium yanoikuyae XLDN2-5, an Efficient Carbazole-Degrading Strain.
PG  - 6404-6405
AB  - Sphingobium yanoikuyae XLDN2-5 is an efficient carbazole-degrading strain. Carbazole-degrading
      genes are accompanied on both sides by two copies of
      IS6100 elements. Here, we describe the draft genome sequence of strain
      XLDN2-5, which may provide important clues as to how it recruited
      exogenous genes to establish pathways to degrade the xenobiotics.
AU  - Gai Z
AU  - Wang X
AU  - Tang H
AU  - Tai C
AU  - Tao F
AU  - Wu G
AU  - Xu P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6404-6405.

PMID- 22123766
VI  - 193
DP  - 2011
TI  - Genome Sequence of Sphingomonas elodea ATCC 31461, a Highly Productive Industrial Strain of Gellan Gum.
PG  - 7015-7016
AB  - The commercial gelling agent gellan gum is a heteropolysaccharide produced by Sphingomonas
      elodea ATCC 31461. However, the genes involved in the
      biosynthesis, regulation, and modification of gellan gum have not been
      fully characterized. Here we describe the draft genome sequence of stain
      ATCC 31461 and major findings from its annotation.
AU  - Gai Z
AU  - Wang X
AU  - Zhang X
AU  - Su F
AU  - Wang X
AU  - Tang H
AU  - Tai C
AU  - Tao F
AU  - Ma C
AU  - Xu P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 7015-7016.

PMID- 23105052
VI  - 194
DP  - 2012
TI  - Genome Sequence of Pseudomonas aeruginosa DQ8, an Efficient Degrader of n-Alkanes and Polycyclic Aromatic Hydrocarbons.
PG  - 6304-6305
AB  - Pseudomonas aeruginosa DQ8, which was isolated from the crude oil polluted soil in the Daqing
      oilfield of China, can efficiently degrade diesel, crude oil,
      n-alkanes, and polycyclic aromatic hydrocarbons (PAHs). Here, we present a 6.8-Mb
      assembly of its genome sequence. We have annotated 23 coding sequences (CDSs)
      responsible for catabolism of n-alkanes and PAHs.
AU  - Gai Z
AU  - Zhang Z
AU  - Wang X
AU  - Tao F
AU  - Tang H
AU  - Xu P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6304-6305.

PMID- Not carried by PubMed...
VI  - 48
DP  - 1988
TI  - Purification of BsuE methylase to investigate the role of DNA methylation in rat growth hormone gene expression.
PG  - 2876B
AB  - DNA methylation at specific cytosine bases is one mechanism believed to be
      involved in determining tissue specific gene expression.  A tissue specific
      methylation pattern has been observed for the rat growth hormone (rGH) gene.
      In rat pituitary tissue which expresses GH a CGCG sequence 144 basepairs
      upstream from the rGH transcription initiation site is unmethylated.  This site
      is methylated in rat liver, spleen and kidney which do not express GH.  We have
      directly tested the effect of site specific methylation at the CGCG site on rGH
      promoter activity.  1.5 kilobasepairs of rGH promoter sequences were inserted
      in front of two bacterial indicator genes Neo and CAT.  A CGCG specific
      methylase was isolated from Bacillus subtilis strain ISE15 by three column
      chromatography steps:  phosphocellulose, heparin-sepharose and DEAE-Sepharose.
      Its molecular weight was 41,000 by gel filtration.  It exhibits optimal
      activity in mM KCl, 50 mM Tris.HCl, pH 7.3-8.3 and 5 mM 2-mercaptoethanol.
      This enzyme was used to methylate the CGCG sequence in GH1 Neo and GH1.CAT.
      Methylated and unmethylated fusion genes were transferred into GH3 rat
      pituitary tissue culture cells by calcium-phosphate coprecipitation or
      electroporation.  Cells transfected with GH1 Neo were harvested after 2 days,
      replated at 5x10/5 cells/100 cm dish in selective media (400 ug/ml G418), and
      counted after 2 weeks.  Cells were harvested 36 hours after transfection with
      GH1.CAT and acetylation of 14C-chloramphenicol measured in whole cell extracts.
      BsuE methylation resulted in a 68% decrease in GH1-Neo fusion gene activity
      and in a lesser 44% decrease in the control RSV-Neo fusion gene activity.  The
      control methylase, HhaI, which has over twice as many sites on the plasmid,
      inhibited RS V-Neo and GH1-Neo activity by 81%-83%.  We conclude that extensive
      methylation can nonspecifically inhibit fusion gene expression.  BsuE
      methylation of GH1-CAT inhibited fusion gene expression by 49% while the
      control HhaI methylase had no inhibitory effect on GH1-CAT activity in
      transient expression assays.  In addition, neither BsuE or HhaI methylation had
      any inhibitory effect on RSV-CAT activity.  Thus, we conclude that methylation
      of the rGH promoter at CGCG sequences does specifically inhibit rGH promoter
      activity.
AU  - Gaido ML
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1988 48: 2876B.

PMID- 3127393
VI  - 263
DP  - 1988
TI  - Isolation and characterization of BsuE methyltransferase, a CGCG specific DNA methyltransferase from Bacillus subtilis.
PG  - 4832-4836
AB  - The DNA methyltransferase M.BsuEI that recognizes the sequence 5'-CGCG-3' has
      been isolated from Bacillus subtilis strain ISE15.  A 1600-fold purification of
      M.BsuEI was achieved by column chromatography on phosphocellulose,
      heparin-Sepharose, and DEAE-Sepharose.  DNA methyltransferase activity was
      monitored in the column eluants radiochemically by the transfer of tritiated
      methyl groups from radiolabeled S-adenosylmethionine to poly(dGdC)-poly(dGdC)
      DNA, a sensitive and specific substrate for M.BsuEI activity.  The DNA sequence
      specificity of this methyltransferase activity was confirmed enzymatically by
      demonstrating that M.BsuEI-methylated DNA was selectively protected from
      cleavage by the restriction enzyme isoschizomers, ThaI and FnuDII.  Purified
      M.BsuEI has an apparent molecular size of 41,000-43,000 as determined by gel
      filtration and migrates as a 41-kDa protein in a sodium dodecyl
      sulfate-poly-acrylamide gel.  DNA methylation by M.BsuEI is dependent upon the
      presence of S-adenosylmethionine and 2-mercaptoethanol.  M.BsuEI
      methyltransferase activity is optimal at 37C in the presence of 50 mM Tris-HCl,
      pH 7.8, 25 mM KCl, 6 micromolar S-adenosylmethionine, 5 mM 2-mercaptoethanol,
      and 10 mM EDTA.  M.BsuEI methylates the external cytidine in its recognition
      sequence in both linear and supercoiled DNA.  A unique property of M.BsuEI is
      its ability to methylate 5'-CGCG-3' in Z-DNA.
AU  - Gaido ML
AU  - Prostko CR
AU  - Strobl JS
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1988 263: 4832-4836.

PMID- 3034185
VI  - 46
DP  - 1987
TI  - Methylation sensitivity of the restriction enzymes FnuDII and AccII.
PG  - 338-340
AB  - The restriction enzymes FnuDII and AccII are isoschizomers of the DNA sequence
      5'-CGCG-3'.  We have determined that 5-methylcytidine at either cytidine
      position in this recognition sequence inhibits DNA cleavage by FnuDII and
      AccII.  A third isoschizomer, ThaI was previously shown to exhibit an identical
      methylation sensitivity.  It is remarkable that 3 restriction enzymes derived
      from diverse microbiological sources exhibit this identical methylation
      sensitivity.
AU  - Gaido ML
AU  - Strobl JS
PT  - Journal Article
TA  - Arch. Microbiol.
JT  - Arch. Microbiol.
SO  - Arch. Microbiol. 1987 46: 338-340.

PMID- 27795245
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Ureolytic Environmental Isolate Bacillus galactosidilyticus PL133.
PG  - e01067-16
AB  - We report here the 5.19-Mb draft genome sequence of Bacillus galactosidilyticus PL133 isolated
      from poultry litter. The isolate was an important member of the
      cultivable aerobic bacteria identified to have ureolytic activity, which is
      responsible for ammonia generation in poultry litter residue.
AU  - Gaiero JR
AU  - Formusa PA
AU  - Hsiang T
AU  - Nicol RW
AU  - Habash M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01067-16.

PMID- 27795244
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Ureolytic Environmental Isolate Staphylococcus sp. NA309.
PG  - e01066-16
AB  - We report the 2.7 Mb draft genome sequence of Staphylococcus sp. NA309 isolated from poultry
      litter. The isolate was a dominant member of the cultivable aerobic
      bacteria identified to have ureolytic activity, responsible for ammonia
      generation in poultry litter residue.
AU  - Gaiero JR
AU  - Hsiang T
AU  - Nicol RW
AU  - Habash M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01066-16.

PMID- 12364615
VI  - 30
DP  - 2002
TI  - PfoI, a unique type II restriction endonuclease that recognizes the sequence 5'-T/CCNGGA-3'.
PG  - e98
AB  - A new type II restriction endonuclease designated PfoI has been partially purified from
      Pseudomonas fluorescens biovar 126.  PfoI recognizes the interrupted hexanucleotide
      palindromic sequence 5'-T/CCNGGA-3' and cleaves DNA to produce protruding pentanucleotide
      5'-ends.
AU  - Gaigalas M
AU  - Maneliene Z
AU  - Kazlauskiene R
AU  - Petrusyte M
AU  - Janulaitis A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2002 30: e98.

PMID- 28572325
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of a Porcine Commensal, Rothia nasimurium, Encoding a Nonribosomal Peptide Synthetase Predicted To Produce the Ionophore Antibiotic  Valinomycin.
PG  - e00453-17
AB  - We report the draft whole-genome sequence of Rothia nasimurium isolated from a porcine tonsil.
      The genome encodes a nonribosomal peptide synthetase predicted to
      produce valinomycin, a cyclic dodecadepsipeptide ionophore. Previously,
      valinomycin was known to be produced only by Streptomyces species and isolates
      belonging to the Bacillus pumilus group.
AU  - Gaiser RA
AU  - Medema MH
AU  - Kleerebezem M
AU  - van Baarlen P
AU  - Wells JM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00453-17.

PMID- 27445390
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Chloroflexus sp. Strain isl-2, a Thermophilic Filamentous Anoxygenic Phototrophic Bacterium Isolated from the Strokkur Geyser,   Iceland.
PG  - e00714-16
AB  - We report here the draft genome sequence of the thermophilic filamentous anoxygenic
      phototrophic bacterium Chloroflexus sp. strain isl-2, which was
      isolated from the Strokkur geyser, Iceland, and contains 5,222,563 bp with a G+C
      content of 59.65%. The annotated genome sequence offers the genetic basis for
      understanding the strain's ecological role as a phototrophic bacterium within the
      bacterial community.
AU  - Gaisin VA
AU  - Ivanov TM
AU  - Kuznetsov BB
AU  - Gorlenko VM
AU  - Grouzdev DS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00714-16.

PMID- 
VI  - 38
DP  - 2007
TI  - Methylation of dna may be useful as a computational tool: Experimental evidence.
PG  - 1-14
AB  - Previously we have explained the abstract concept we call 'aqueous computing' and
      illustrated it with concrete wet lab results. Here, we
      explore the use of methylase enzymes to 'write' on double-stranded DNA
      molecules at sites where restriction enzymes will cut if, and only if,
      the sites have not previously been methylated. A site represents the
      bit zero (False, F) if the site has been methylated and the bit one
      (True, T) if it has not been methylated. 'Reading' is done by
      attempting a cut at each of the sites. We found 8 commercially
      available methylases and 8 corresponding restriction enzymes that would
      not cut after the action of one of the methylases. We were able to
      confirm that methylation by each of these 8 enzymes individually
      blocked cleavage only by I he restriction enzyme associated with that
      site and not any other enzyme. We I hen used these enzymes to approach
      a 3-variable, 4-clause satisfiability (SAT) problem using either
      plasmid DNA (pBluescript) or PCR product made from the region
      containing the restriction enzyme sites on the plasmid. Pairs of
      methylases were defined to represent each of the states of the
      operators p, q and r, one methylase for p and another for p', etc. We
      methylated the DNA in parallel at the two sites so either the p site
      was methylated (making p false) or the P' site was methylated (making
      p' false). We did that for the other two variables as well to create a
      set of logically consistent DNA fragments. Then we applied the 4
      clauses using restriction enzymes to cut DNA fragments that did riot
      satisfy them. At the end, we found evidence for intact DNA indicating
      an answer satisfying all of the clauses. To confirm the state of each
      of the Boolean operators, we used cleavage by the appropriate
      restriction enzyme. We found in the computation with both the plasmid
      and the PCR product, one site pair to show false in both sites; q and
      q', for instance. This should not be possible. We suspected incomplete
      cutting during the clauses by one of these restriction Enzymes,
      specifically BssHII In summary, we did successfully show the usefulness
      of DNA methylation in a scheme to do a mathematical computation. Thus,
      we have added to our arsenal of potential methods of performing DNA
      computing in the aqueous style.
AU  - Gal S
AU  - Monteith N
AU  - Shkalim S
AU  - Huang H
AU  - Head T
PT  - Journal Article
TA  - Current Developments in Mathematical Biology
JT  - Current Developments in Mathematical Biology
SO  - Current Developments in Mathematical Biology 2007 38: 1-14.

PMID- 28572323
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Staphylococcus epidermidis 1457.
PG  - e00450-17
AB  - Staphylococcus epidermidis 1457 is a frequently utilized strain that is amenable  to genetic
      manipulation and has been widely used for biofilm-related research. We
      report here the whole-genome sequence of this strain, which encodes 2,277
      protein-coding genes and 81 RNAs within its 2.4-Mb genome and plasmid.
AU  - Galac MR
AU  - Stam J
AU  - Maybank R
AU  - Hinkle M
AU  - Mack D
AU  - Rohde H
AU  - Roth AL
AU  - Fey PD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00450-17.

PMID- 12712197
VI  - 422
DP  - 2003
TI  - The genome sequence of the filamentous fungus Neurospora crassa.
PG  - 859-868
AB  - Neurospora crassa is a central organism in the history of twentieth-century genetics,
      biochemistry and molecular biology. Here, we
      report a high-quality draft sequence of the N. crassa genome. The
      approximately 40-megabase genome encodes about 10,000 protein-coding
      genes--more than twice as many as in the fission yeast Schizosaccharomyces
      pombe and only about 25% fewer than in the fruitfly Drosophila
      melanogaster. Analysis of the gene set yields insights into unexpected
      aspects of Neurospora biology including the identification of genes
      potentially associated with red light photobiology, genes implicated in
      secondary metabolism, and important differences in Ca2+ signalling as
      compared with plants and animals. Neurospora possesses the widest array of
      genome defence mechanisms known for any eukaryotic organism, including a
      process unique to fungi called repeat-induced point mutation (RIP). Genome
      analysis suggests that RIP has had a profound impact on genome evolution,
      greatly slowing the creation of new genes through genomic duplication and
      resulting in a genome with an unusually low proportion of closely related
      genes.
AU  - Galagan JE et al
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2003 422: 859-868.

PMID- 11932238
VI  - 12
DP  - 2002
TI  - The genome of Methanosarcina acetivorans reveals extensive metabolic and physiological diversity.
PG  - 532-542
AB  - Methanogenesis, the biological production of methane, plays a pivotal role in the global
      carbon cycle and contributes significantly to global warming. The majority of methane in
      nature is derived from acetate. Here we report the complete genome sequence of an
      acetate-utilizing methanogen, Methanosarcina acetivorans C2A. Methanosarcineae are the most
      metabolically diverse methanogens, thrive in a broad range of environments, and are unique
      among the Archaea in forming complex multicellular structures. This diversity is reflected in
      the genome of M. acetivorans. At 5,751,492 base pairs it is by far the largest known archaeal
      genome. The 4524 open reading frames code for a strikingly wide and unanticipated variety of
      metabolic and cellular capabilities. The presence of novel methyltransferases indicates the
      likelihood of undiscovered natural energy sources for methanogenesis, whereas the presence of
      single-subunit carbon monoxide dehydrogenases raises the possibility of nonmethanogenic
      growth. Although motility has not been observed in any Methanosarcineae, a flagellin gene
      cluster and two complete chemotaxis gene clusters were identified. The availability of genetic
      methods, coupled with its physiological and metabolic diversity, makes M. acetivorans a
      powerful model organism for the study of archaeal biology.
AU  - Galagan JE et al
PT  - Journal Article
TA  - Genome Res.
JT  - Genome Res.
SO  - Genome Res. 2002 12: 532-542.

PMID- 24976889
VI  - 9
DP  - 2013
TI  - Permanent draft genome sequences of the symbiotic nitrogen fixing Ensifer meliloti strains BO21CC and AK58.
PG  - 325-333
AB  - Ensifer (syn. Sinorhizobium) meliloti is an important symbiotic bacterial species that fixes
      nitrogen. Strains BO21CC and AK58 were previously investigated for
      their substrate utilization and their plant-growth promoting abilities showing
      interesting features. Here, we describe the complete genome sequence and
      annotation of these strains. BO21CC and AK58 genomes are 6,985,065 and 6,974,333
      bp long with 6,746 and 6,992 genes predicted, respectively.
AU  - Galardini M et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 9: 325-333.

PMID- 24578270
VI  - 2
DP  - 2014
TI  - Evidence of Clonal Expansion in the Genome of a Multidrug-Resistant Mycobacterium tuberculosis Clinical Isolate from Peru.
PG  - e00089-14
AB  - We report the genome sequence of Mycobacterium tuberculosis INS-MDR from Peru, a
      multidrug-resistant tuberculosis (MDR-TB) and Latin American-Mediterranean (LAM)
      lineage strain. Our analysis showed mutations related to drug resistance in the
      rpoB (D516V), katG (S315T), kasA (G269S), and pncA (Q10R) genes. Our evidence
      suggests that INS-MDR may be a clonal expansion related to the African strain KZN
      1435.
AU  - Galarza M
AU  - Tarazona D
AU  - Borda V
AU  - Agapito JC
AU  - Guio H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00089-14.

PMID- 10891275
VI  - 300
DP  - 2000
TI  - Conformational changes and cleavage by the homing endonuclease I-PpoI: A critical role for a leucine residue in the active site.
PG  - 877-887
AB  - The homing endonuclease I-PpoI severely bends its DNA target, resulting in significant
      deformations of the minor and major groove near the scissile phosphate groups. To study the
      role of conformational changes within the protein catalyst and the DNA substrate, we have
      determined the structure of the enzyme in the absence of bound DNA, performed gel retardation
      analyses of DNA binding and bending, and have mutagenized a leucine residue that contacts an
      adenine nucleotide at the site of cleavage. The structure of the L116A/DNA complex has been
      determined and the effects of the mutation on affinity and catalysis have been measured. The
      wild-type protein displays a rigid-body rotation of its individual subunits upon DNA binding.
      Homing site DNA is not detectably bent in the absence of protein, but is sharply bent in both
      the wild-type and L116A complexes. These results indicate that binding involves a large
      distortion of the DNA and a smaller change in protein conformation. Leucine 116 is critical
      for binding and catalysis: it appears to be important for forming a well-ordered protein-DNA
      complex at the cleavage site, for maximal deformation of the DNA, and for desolvation of the
      nucleotide bases that are partially unstacked in the enzyme complex.
AU  - Galburt EA
AU  - Chadsey MS
AU  - Jurica MS
AU  - Chevalier BS
AU  - Erho D
AU  - Tang W
AU  - Monnat RJ Jr
AU  - Stoddard BL
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2000 300: 877-887.

PMID- 10581547
VI  - 6
DP  - 1999
TI  - A novel endonuclease mechanism directly visualized for I-PpoI.
PG  - 1096-1099
AB  - A novel mechanism of DNA endonucleolytic cleavage has been visualized for the homing
      endonuclease I-PpoI by trapping the uncleaved enzyme-substrate complex and comparing it to the
      previously visualized product complex. This enzyme employs a unique single metal mechanism. A
      magnesium ion is coordinated by an asparagine residue and two DNA oxygen atoms and stabilizes
      the phosphoanion transition state and the 3'oxygen leaving group. A hydrolytic water molecule
      is activated by a histidine residue for an in-line attack on the scissile phosphate. A
      strained enzyme-substrate-metal complex is formed before cleavage, then relaxed during the
      reaction.
AU  - Galburt EA
AU  - Chevalier B
AU  - Tang W
AU  - Jurica MS
AU  - Flick KE
AU  - Monnat RJ Jr
AU  - Stoddard BL
PT  - Journal Article
TA  - Nat. Struct. Biol.
JT  - Nat. Struct. Biol.
SO  - Nat. Struct. Biol. 1999 6: 1096-1099.

PMID- 
VI  - 16
DP  - 2005
TI  - His-Cys box homing endonuclease.
PG  - 85-102
AB  - Homing endonucleases are often grouped into four families based on distinct sequence motifs.
      One of these families is known as the His-Cys box homing endonucleases and contains two
      clusters of conserved histidine and cysteine residues over a central 100 amino acid region.
      At last count, 23 members of this family had been identified.  The open reading frames of
      these proteins are contained within mobile group I introns found in nuclear rDNA genes of
      several protists.  The nuclear location of these introns and ORFs is currently unique among
      the homing endonuclease families and poses an intriguing puzzle regarding their expression
      from non-coding rRNA transcripts.  The best-studied member of the His-Cys box homing
      endonucleases is I-PpoI from the myxomycete Physarum polycephalum.  Following an introduction
      to all of the known members of the His-Cys box endonuclease family, much of the following
      chapter will outline the extensive characterization of  I-PpoI structure and function.
      Although our understanding of how I-PpoI is expressed in cells is still not fully complete,
      the means by which I-PpoI specifically recognizes a single cleavage site in the host genome to
      mediate homing of its host intron is widely accepted.  Details of DNA recognition and the
      catalytic mechanism of nucleolytic cleavage have been ascertained from both in vivo and in
      vitro activity assays as well as from extensive X-ray crystallographic structural analyses of
      the enzyme bound to its DNA substrate.
AU  - Galburt EA
AU  - Jurica MS
PT  - Journal Article
TA  - Nucleic Acids Mol. Biol.
JT  - Nucleic Acids Mol. Biol.
SO  - Nucleic Acids Mol. Biol. 2005 16: 85-102.

PMID- 10655603
VI  - 7
DP  - 2000
TI  - Restriction endonucleases: one of these things is not like the others.
PG  - 89-91
AB  - The crystal structure of the restriction endonuclease BglII in complex with its DNA target
      site has been determined. The DNA binding mode and chemistry of catalysis are observed to
      differ from BamHI which cleaves a similar target site. These observations indicate that more
      divergence has occurred within this family of proteins than originally thought.
AU  - Galburt EA
AU  - Stoddard BL
PT  - Journal Article
TA  - Nat. Struct. Biol.
JT  - Nat. Struct. Biol.
SO  - Nat. Struct. Biol. 2000 7: 89-91.

PMID- 12437341
VI  - 41
DP  - 2002
TI  - Catalytic mechanisms of restriction and homing endonucleases.
PG  - 13851-13860
AB  - The catalytic mechanisms of type II restriction endonucleases and homing endonucleases are
      discussed and compared. Brief reviews of the
      chemistry of phosphoryl transfers and canonical one-metal and two-metal
      endonucleolytic mechanisms are provided along with possible future
      directions in the study of endonuclease active sites. The discussion of
      type II restriction endonucleases is comprised of a description of the
      general architecture of the canonical active site structural motif
      followed by more in-depth examples of one- and two-metal mechanisms.
      The homing endonuclease section is comprised of four sections
      describing what is known regarding the cleavage mechanisms of the four
      group I intron homing endonuclease families: LAGLIDADG, His-Cys box,
      H-N-H, and GIY-YIG.
AU  - Galburt EA
AU  - Stoddard BL
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2002 41: 13851-13860.

PMID- 25700408
VI  - 3
DP  - 2015
TI  - Genome Sequence and Annotation of a Human Infection Isolate of Escherichia coli O26:H11 Involved in a Raw Milk Cheese Outbreak.
PG  - e01568-14
AB  - The consumption of raw milk cheese can expose populations to Shiga toxin-producing Escherichia
      coli (STEC). We report here the genome sequence of an E. coli O26:H11 strain isolated from
      humans during the first raw milk cheese outbreak described in France (2005).
AU  - Galia W
AU  - Mariani-Kurkdjian P
AU  - Loukiadis E
AU  - Blanquet-Diot S
AU  - Leriche F
AU  - Brugere H
AU  - Shima A
AU  - Oswald E
AU  - Cournoyer B
AU  - Thevenot-Sergentet D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01568-14.

PMID- 11474104
VI  - 293
DP  - 2001
TI  - The composite genome of the legume symbiont Sinorhizobium meliloti.
PG  - 668-672
AB  - The scarcity of usable nitrogen frequently limits plant growth. A tight metabolic association
      with rhizobial bacteria allows legumes to obtain nitrogen compounds by bacterial reduction of
      dinitrogen (N2) to ammonium (NH4+). We present here the annotated DNA sequence of the
      alpha-proteobacterium Sinorhizobium meliloti, the symbiont of alfalfa. The tripartite
      6.7-megabase (Mb) genome comprises a 3.65-Mb chromosome, and 1.35-Mb pSymA and 1.68-Mb pSymB
      megaplasmids. Genome sequence analysis indicates that all three elements contribute, in
      varying degrees, to symbiosis and reveals how this genome may have emerged during evolution.
      The genome sequence will be useful in understanding the dynamics of interkingdom associations
      and of life in soil environments.
AU  - Galibert F et al
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2001 293: 668-672.

PMID- 18835994
VI  - 190
DP  - 2008
TI  - Genetic dissection of the Francisella novicida restriction barrier.
PG  - 7830-7837
AB  - Francisella tularensis is the causative agent of tularemia and is a category A select agent.
      Francisella novicida, considered by some to be one of four subspecies of F. tularensis, is
      used as a model in pathogenesis studies because it causes a disease similar to tularemia in
      rodents but is not harmful to humans. F. novicida exhibits a strong restriction barrier which
      reduces the transformation frequency of foreign DNA up to 10(6)-fold. To identify the genetic
      basis of this barrier, we carried out a mutational analysis of restriction genes identified in
      the F. novicida genome. Strains carrying combinations of insertion mutations in eight
      candidate loci were created and assayed for reduced restriction of unmodified plasmid DNA
      introduced by transformation. Restriction was reduced by mutations in four genes,
      corresponding to two type I, one type II, and one type III restriction system. Restriction was
      almost fully eliminated in a strain in which all four genes were inactive. The strongest
      contributor to the restriction barrier, the type II gene, encodes an enzyme which specifically
      cleaves Dam-methylated DNA. Genome comparisons show that most restriction genes in the F.
      tularensis subspecies are pseudogenes, explaining the unusually strong restriction barrier in
      F. novicida and suggesting that restriction was lost during evolution of the human pathogenic
      subspecies. As part of this study, procedures were developed to introduce unmodified plasmid
      DNA into F. novicida efficiently, to generate defined multiple mutants, and to produce
      chromosomal deletions of multiple adjacent genes.
AU  - Gallagher LA
AU  - McKevitt M
AU  - Ramage ER
AU  - Manoil C
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2008 190: 7830-7837.

PMID- Not included in PubMed...
VI  - 26
DP  - 1985
TI  - Sequence-specific endonuclease from the transformable cyanobacterium Anacystis nidulans R2.
PG  - 317-321
AB  - Extracts of the transformable cyanobacterial strain Anacystis nidulans R2 were
      analyzed for the presence of restriction endonuclease.  One enzyme, AniI, was
      found and determined to be sequence-specific on the basis of its ability to
      cleave several Bacillus plasmids at a limited number of sites.  The activity of
      this enzyme is significantly reduced in extracts prepared from cell cultures
      grown at 38C.
AU  - Gallagher ML
AU  - Burke WF
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1985 26: 317-321.

PMID- Not carried by PubMed...
VI  - 87
DP  - 1987
TI  - Unique cyanobacterial recognition sequence for the restriction endonuclease AniI.
PG  - 224
AB  - In previous studies, we have shown that the transformable cyanobacterium
      Anacystis nidulans R2 possesses a sequence specific endonuclease AniI.
      Restriction digest patterns of site-specific endonucleases of cyanobacterial
      origin were compared with AniI generated digests to determine if AniI is an
      isoschizomer of any of these enzymes.  We have previously shown that pBR322 is
      not cleaved by AniI.  We determined that only eight characterized
      cyanobacterial restriction-endonucleases are unable to cleave pBR322.  These
      enzymes or isoschizomers of them, if commercially available, were obtained and
      used to digest plasmid DNA substrates.  Although several enzymes were not
      available, we were able to make a comparison based on published data which
      indicated the number of cleavage sities on various substrate DNA's.  None of
      the commercially available endonucleases produced restriction patterns similar
      to AniI digests.  None of the enzymes which were compared indirectly were found
      to have the same number of cleavage sites on PhiX174 substrate DNA.  We
      therefore conclude that the AniI recognition sequence is unique with respect to
      other cyanobacterial restriction endonucleases.
AU  - Gallagher ML
AU  - Burke WF
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1987 87: 224.

PMID- 27834716
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the Soil Isolate Lysinibacillus fusiformis M5, a Potential Hypoxanthine Producer.
PG  - e01272-16
AB  - Lysinibacillus fusiformis strain M5 is a potential hypoxanthine producer that was isolated
      from clay soil. Here, we present the draft genome sequence that was
      annotated in order to facilitate future studies of L. fusiformis M5.
AU  - Gallegos-Monterrosa R
AU  - Maroti G
AU  - Balint B
AU  - Kovacs AT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01272-16.

PMID- 11982335
VI  - 47
DP  - 2002
TI  - Parameters associated with cloning in Actinobacillus actinomycetemcomitans.
PG  - 138-147
AB  - Characterization of virulence traits in Actinobacillus actinomycetemcomitans requires the
      application of recombinant DNA
      techniques. To develop appropriate genetic tools it is necessary to
      identify suitable host-vector systems. The Current Study assessed
      cloning parameters in A. actinomycetemcomitans for two preciously
      described vectors. pDMG4 and pMMB67. It was determined that the maximum
      size of recombinant molecule that could be transferred to A.
      actinomycetemcomitans strain ATCC29522 via electroporation was 33 kb.
      The size limit for transformation of the same strain with ligation
      mixtures (direct cloning), however, was limited to 23-24 kb. Additional
      experiments included electroporation of various A.
      actinomycetemcomitans strains with plasmid DNA isolated from
      Escherichia coli and different A. actinomycetemcomitans sources.
      Differences in transformation efficiencies, suggested the presence of a
      restriction modification system for pDMG4 in some strains of A. actinomycetemcomitans. Cloning
      of portions of the enterococcal plasmid pJH1 into A. actinomycetemcomitans resulted in the
      insertion of the intact vector
      into the chromosome.
AU  - Galli DM
AU  - Kerr MS
AU  - Fair AD
AU  - Permpanich P
AU  - LeBlanc DJ
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 2002 47: 138-147.

PMID- 18955433
VI  - 19
DP  - 2009
TI  - Ortho-proteogenomics: multiple proteomes investigation through orthology and a new MS-based protocol.
PG  - 128-135
AB  - The progress in sequencing technologies irrigates biology with an ever-increasing
      number of genome sequences. In most cases, the gene repertoire is predicted in
      silico and conceptually translated into proteins. As recently highlighted, the
      predicted genes exhibit frequent errors, particularly in start codons, with a
      serious impact on subsequent biological studies. A new "ortho-proteogenomic"
      approach is presented here for the annotation refinement of multiple genomes at
      once. It combines comparative genomics with an original proteomic protocol that
      allows the characterization of both N-terminal and internal peptides in a single
      experiment. This strategy was applied to the Mycobacterium genus with
      Mycobacterium smegmatis as the reference, and identified 946 distinct proteins,
      including 443 characterized N termini. These experimental data allowed the
      correction of 19% of the characterized start codons, the identification of 29
      proteins missed during the annotation process, and the curation, thanks to
      comparative genomics, of 4328 sequences of 16 other Mycobacterium proteomes.
AU  - Gallien S
AU  - Perrodou E
AU  - Carapito C
AU  - Deshayes C
AU  - Reyrat JM
AU  - Van Dorsselaer A
AU  - Poch O
AU  - Schaeffer C
AU  - Lecompte O
PT  - Journal Article
TA  - Genome Res.
JT  - Genome Res.
SO  - Genome Res. 2009 19: 128-135.

PMID- 3020514
VI  - 14
DP  - 1986
TI  - Alkyl phosphotriester modified oligodeoxyribonucleotides.  V. Synthesis and absolute configuration of Rp and Sp diastereomers of an ethyl phosphotriester (Et) modified EcoRI recognition sequence, d[GGAA(Et)TTCC].
PG  - 7405-7420
AB  - Protected deoxynucleoside 3'-O-ethyl-N, N-diisopropylphosphoramidite reagents
      were prepared for use in the automated synthesis of ethyl phosphotriester (Et)
      modified oligonucleotides.  The title diastereomers were separated by
      reversed-phase HPLC, and chirality at phosphorus was assigned by an improved
      configurational correlation scheme that was verified by NMR spectroscopic
      studies (accompanying paper, Part VI).  This generally applicable correlation
      scheme involved (1.) enzymatic digestions of each diastereomer to give the
      corresponding diastereomer of d[A(Et)T]; (2.) phosphite triester sulfurization
      to obtain diastereomeric 0-ethyl phosphorothioates, d[AS(Et)T], which were
      separated by HPLC for (3.) stereoretentive oxidation with H2O2 to give
      d[A(Et)T], and (4.) stereoretentive de-ethylation with PhSH-Et3N to give
      diastereomeric phosphorothioates, d[AST], whose configurations at phosphorus
      had been assigned previously.  Neither the Rp-Rp nor Sp-Sp duplex,
      {d[GGAA(Et)TTCC]}2, was cleaved by EcoRI endonuclease under conditions that led
      to cleavage of both the unmodified duplex, [d(GGAATTCC)]2, and the mixture of
      diastereomeric phosphorothioate-modified duplexes, [d(GGAASTTCC)]2.  Cleavage
      of the latter substrates was Sp-selective.
AU  - Gallo KA
AU  - Shao KL
AU  - Phillips LR
AU  - Regan JB
AU  - Koziolkiewicz M
AU  - Uznanski B
AU  - Stec WJ
AU  - Zon G
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1986 14: 7405-7420.

PMID- 
VI  - 13
DP  - 2019
TI  - Hypervirulent Group A Streptococcus Emergence in an Acaspular Background is Associated with Marked Remodeling of the Bacterial Cell Surface.
PG  - e0207897
AB  - Inactivating mutations in the control of virulence two-component regulatory system (covRS)
      often account for the hypervirulent phenotype in severe, invasive group A streptococcal
      (GAS) infections. As CovR represses production of the anti-phagocytic hyaluronic acid capsule,
      high level capsule production is generally considered critical to the hypervirulent phenotype
      induced by CovRS inactivation. There have recently been large outbreaks of GAS
      strains lacking capsule, but there are currently no data on the virulence of covRS-mutated,
      acapsular strains in vivo. We investigated the impact of CovRS inactivation in acapsular
      serotype M4 strains using a wild-type (M4-SC-1) and a naturally-occurring CovS-inactivated
      strain (M4-LC-1) that contains an 11bp covS insertion. M4-LC-1 was significantly more virulent
      in a mouse bacteremia model but caused smaller lesions in a subcutaneous mouse
      model. Over 10% of the genome showed significantly different transcript levels in M4-LC-1
      vs. M4-SC-1 strain. Notably, the Mga regulon and multiple cell surface protein-encoding
      genes were strongly upregulateda finding not observed for CovS-inactivated, encapsulated
      M1 or M3 GAS strains. Consistent with the transcriptomic data, transmission electron
      microscopy revealed markedly altered cell surface morphology of M4-LC-1 compared to
      M4-SC-1. Insertional inactivation of covS in M4-SC-1 recapitulated the transcriptome and
      cell surface morphology. Analysis of the cell surface following CovS-inactivation revealed
      that the upregulated proteins were part of the Mga regulon. Inactivation of mga in M4-LC-1
      reduced transcript levels of multiple cell surface proteins and reversed the cell surface
      alterations
      consistent with the effect of CovS inactivation on cell surface composition being mediated
      by Mga. CovRS-inactivating mutations were detected in 20% of current invasive
      serotype M4 strains in the United States. Thus, we discovered that hypervirulent M4 GAS
      strains with covRS mutations can arise in an acapsular background and that such hypervirulence
      is associated with profound alteration of the cell surface.
AU  - Galloway-Pena J
AU  - DebRoy S
AU  - Brumlow C
AU  - Li X
AU  - Tran T
AU  - Horstmann N
AU  - Yao H
AU  - Chen K
AU  - Wang F
AU  - Pan B-F
AU  - Hawke D
AU  - Thompson E
AU  - Arias C
AU  - Fowler VG
AU  - Bhatti M
AU  - Kalia A
AU  - Flores AR
AU  - Shelburne SA
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2019 13: e0207897.

PMID- 27174263
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Bacillus licheniformis CG-B52, a Highly Virulent Bacterium of Pacific White Shrimp (Litopenaeus vannamei), Isolated from a  Colombian Caribbean Aquaculture Outbreak.
PG  - e00321-16
AB  - Bacillus licheniformis strain CG-B52 was isolated as the etiological agent producing a
      self-limited outbreak of high mortalities in commercial Litopenaeus
      vannamei culture ponds on the Colombian Caribbean coast in 2005. Here, we report
      its draft genome and three novel extrachromosomal elements that it harbors.
AU  - Galvez EJ
AU  - Carrillo-Castro K
AU  - Zarate L
AU  - Guiza L
AU  - Pieper DH
AU  - Garcia-Bonilla E
AU  - Salazar M
AU  - Junca H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00321-16.

PMID- 26607897
VI  - 3
DP  - 2015
TI  - Genome Sequence of the Banana Plant Growth-Promoting Rhizobacterium Bacillus amyloliquefaciens BS006.
PG  - e01391-15
AB  - Bacillus amyloliquefaciens is an important plant growth-promoting rhizobacterium  (PGPR). We
      report the first whole-genome sequence of PGPR Bacillus
      amyloliquefaciens evaluated in Colombian banana plants. The genome sequences
      encode genes involved in plant growth and defense, including bacteriocins,
      ribosomally synthesized antibacterial peptides, in addition to genes that provide
      resistance to toxic compounds.
AU  - Gamez RM
AU  - Rodriguez F
AU  - Bernal JF
AU  - Agarwala R
AU  - Landsman D
AU  - Marino-Ramirez L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01391-15.

PMID- 27151797
VI  - 4
DP  - 2016
TI  - Genome Sequence of the Banana Plant Growth-Promoting Rhizobacterium Pseudomonas fluorescens PS006.
PG  - e00329-16
AB  - Pseudomonas fluorescens is a well-known plant growth-promoting rhizobacterium (PGPR). We
      report here the first whole-genome sequence of PGPR P. fluorescens
      evaluated in Colombian banana plants. The genome sequences contains genes
      involved in plant growth and defense, including bacteriocins,
      1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, and genes that provide
      resistance to toxic compounds.
AU  - Gamez RM
AU  - Rodriguez F
AU  - Ramirez S
AU  - Gomez Y
AU  - Agarwala R
AU  - Landsman D
AU  - Marino-Ramirez L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00329-16.

PMID- 22933764
VI  - 194
DP  - 2012
TI  - Genome Sequence of Novosphingobium sp. Strain Rr 2-17, a Nopaline Crown Gall-Associated Bacterium Isolated from Vitis vinifera L. Grapevine.
PG  - 5137-5138
AB  - Novosphingobium sp. strain Rr 2-17 is an N-acyl homoserine lactone (AHL)-producing bacterium
      isolated from the crown gall tumor of a grapevine. To
      our knowledge, this is the first draft genome announcement of a plant-associated
      strain from the genus Novosphingobium.
AU  - Gan HM
AU  - Chew TH
AU  - Hudson AO
AU  - Savka MA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5137-5138.

PMID- 22933776
VI  - 194
DP  - 2012
TI  - Genome Sequence of Methylobacterium sp. Strain GXF4, a Xylem-Associated Bacterium Isolated from Vitis vinifera L. Grapevine.
PG  - 5157-5158
AB  - Methylobacterium sp. strain GXF4 is an isolate from grapevine. Here we present the sequence,
      assembly, and annotation of its genome, which may shed light on its
      role as a grapevine xylem inhabitant. To our knowledge, this is the first genome
      announcement of a plant xylem-associated strain of the genus Methylobacterium.
AU  - Gan HM
AU  - Chew TH
AU  - Hudson AO
AU  - Savka MA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5157-5158.

PMID- 22887664
VI  - 194
DP  - 2012
TI  - Genome Sequence of Hydrogenophaga sp. Strain PBC, a 4-Aminobenzenesulfonate-Degrading Bacterium.
PG  - 4759-4760
AB  - Hydrogenophaga sp. strain PBC is an effective degrader of 4-aminobenzenesulfonate isolated
      from textile wastewater. Here we present the assembly and annotation of
      its genome, which may provide further insights into its metabolic potential. This
      is the first announcement of the draft genome sequence of a strain from the genus
      Hydrogenophaga.
AU  - Gan HM
AU  - Chew TH
AU  - Tay YL
AU  - Lye SF
AU  - Yahya A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4759-4760.

PMID- 22933765
VI  - 194
DP  - 2012
TI  - Genome Sequence of Ralstonia sp. Strain PBA, a Bacterium Involved in the Biodegradation of 4-Aminobenzenesulfonate.
PG  - 5139-5140
AB  - Ralstonia sp. strain PBA was isolated from textile wastewater in a coculture with
      Hydrogenophaga sp. strain PBC. Here we present the assembly and annotation of its
      genome, which may provide further insights into the mechanism of its interaction
      with strain PBC during 4-aminobenzenesulfonate degradation.
AU  - Gan HM
AU  - Chew TH
AU  - Tay YL
AU  - Lye SF
AU  - Yahya A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5139-5140.

PMID- 28839032
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequences of Salmonella enterica subsp. enterica Serovar Typhimurium Strains TT6675 and TT9097 Employed in the Isolation and Characterization of a  Giant Phage Mutant Collection.
PG  - e00857-17
AB  - We report here the genome sequences of Salmonella enterica subsp. enterica serovar Typhimurium
      strains TT6675 and TT9097, which we utilize for genetic
      analyses of giant bacterial viruses. Our analyses identified several genetic
      variations between the two strains, most significantly confirming strain TT6675
      as a serine suppressor and TT9097 as a nonsuppressor.
AU  - Gan HM
AU  - Eng WWH
AU  - Barton MK
AU  - Adams LE
AU  - Samsudin NA
AU  - Bartl AJ
AU  - Hudson AO
AU  - Savka MA
AU  - Thomas JA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00857-17.

PMID- 23045494
VI  - 194
DP  - 2012
TI  - Genome Sequence of Acinetobacter baumannii AC12, a Polymyxin-Resistant Strain Isolated from Terengganu, Malaysia.
PG  - 5979-5980
AB  - Acinetobacter baumannii is a major cause of nosocomial infection worldwide. We report the
      draft genome sequence of A. baumannii AC12, a multidrug-resistant
      nosocomial strain with additional resistance to carbapenems and polymyxin. The
      genome data will provide insights into the genetic basis of antimicrobial
      resistance and its adaptive mechanism.
AU  - Gan HM
AU  - Lean SS
AU  - Suhaili Z
AU  - Thong KL
AU  - Yeo CC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5979-5980.

PMID- 30533933
VI  - 7
DP  - 2018
TI  - High-Quality Draft Genome Sequence of the Type Strain of Allorhizobium vitis, the Primary Causal Agent of Grapevine Crown Gall.
PG  - e01045-18
AB  - Using Illumina and Nanopore reads, we assembled a high-quality draft genome sequence of
      Allorhizobium vitis K309(T) (= ATCC 49767(T), = NCPPB 3554(T)), a
      phytopathogenic strain isolated from a grapevine in Australia. The hybrid
      approach generated 50% fewer contigs and a 3-fold increase in the N 50 value
      compared with the previous Illumina-only assembly.
AU  - Gan HM
AU  - Lee MVJ
AU  - Savka MA
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e01045-18.

PMID- 23045495
VI  - 194
DP  - 2012
TI  - Whole-Genome Sequence of Enterobacter sp. Strain SST3, an Endophyte Isolated from Jamaican Sugarcane (Saccharum sp.) Stalk Tissue.
PG  - 5981-5982
AB  - Enterobacter sp. strain SST3 is an endophytic bacterium isolated from Saccharum spp. Here we
      present its annotated draft genome that may shed light on its role
      as a bacterial endophyte of sugarcane. To our knowledge, this is the first genome
      announcement of a sugarcane-associated bacterium from the genus Enterobacter.
AU  - Gan HM
AU  - McGroty SE
AU  - Chew TH
AU  - Chan KG
AU  - Buckley LJ
AU  - Savka MA
AU  - Hudson AO
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5981-5982.

PMID- 28798179
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequences of Two Carbapenem-Resistant Klebsiella quasipneumoniae Strains Isolated from a Tertiary Hospital in Johor, Malaysia.
PG  - e00768-17
AB  - We report the whole-genome sequences of two carbapenem-resistant clinical isolates of
      Klebsiella quasipneumoniae subsp. similipneumoniae obtained from two
      different patients. Both strains contained three different extended-spectrum
      beta-lactamase genes and showed strikingly high pairwise average nucleotide
      identity of 99.99% despite being isolated 3 years apart from the same hospital.
AU  - Gan HM
AU  - Rajasekaram G
AU  - Eng WWH
AU  - Kaniappan P
AU  - Dhanoa A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00768-17.

PMID- 24625871
VI  - 2
DP  - 2014
TI  - High-Quality Draft Whole-Genome Sequences of Three Strains of Enterobacter Isolated from Jamaican Dioscorea cayenensis (Yellow Yam).
PG  - e00170-14
AB  - Here we report the whole-genome sequences of three endophytic bacteria, Enterobacter sp.
      strain DC1, Enterobacter sp. strain DC3, and Enterobacter sp.
      strain DC4, from root tubers of the yellow yam plant, Dioscorea cayenensis.
      Preliminary analyses suggest that the genomes of the three bacteria contain genes
      involved in acetoin and indole-3-acetic acid metabolism.
AU  - Gan HM
AU  - Triassi AJ
AU  - Wheatley MS
AU  - Savka MA
AU  - Hudson AO
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00170-14.

PMID- 25883290
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequencing and Annotation of Bacillus safensis RIT372 and Pseudomonas oryzihabitans RIT370 from Capsicum annuum (Bird's Eye Chili) and  Capsicum chinense (Yellow Lantern Chili), Respectively.
PG  - e00288-15
AB  - Here, we report the genome sequences of Bacillus safensis RIT372 and Pseudomonas
      oryzihabitans RIT370 from Capsicum spp. Annotation revealed gene clusters for the
      synthesis of bacilysin, lichensin, and bacillibactin and sporulation killing
      factor (skfA) in Bacillus safensis RIT372 and turnerbactin and carotenoid in
      Pseudomonas oryzihabitans RIT370.
AU  - Gan HY et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00288-15.

PMID- 24812212
VI  - 2
DP  - 2014
TI  - Whole-genome sequences of 13 endophytic bacteria isolated from shrub willow (salix) grown in geneva, new york.
PG  - e00288-14
AB  - Shrub willow, Salix spp. and hybrids, is an important bioenergy crop. Here we report the
      whole-genome sequences and annotation of 13 endophytic bacteria from
      stem tissues of Salix purpurea grown in nature and from commercial cultivars and
      Salix viminalis x Salix miyabeana grown in bioenergy fields in Geneva, New York.
AU  - Gan HY
AU  - Gan HM
AU  - Savka MA
AU  - Triassi AJ
AU  - Wheatley MS
AU  - Smart LB
AU  - Fabio ES
AU  - Hudson AO
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00288-14.

PMID- 25377711
VI  - 2
DP  - 2014
TI  - Whole-Genome Sequences of Five Oligotrophic Bacteria Isolated from Deep within Lechuguilla Cave, New Mexico.
PG  - e01133-14
AB  - Here, we report the whole-genome sequences and annotation of five oligotrophic bacteria from
      two sites within the Lechuguilla Cave in the Carlsbad Caverns
      National Park, NM. Three of the five genomes contain an acyl-homoserine lactone
      signal synthase ortholog (luxI) that is involved in cell-to-cell communication
      via quorum sensing.
AU  - Gan HY
AU  - Gan HM
AU  - Tarasco AM
AU  - Busairi NI
AU  - Barton HA
AU  - Hudson AO
AU  - Savka MA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01133-14.

PMID- 25814609
VI  - 3
DP  - 2015
TI  - Genome Sequence of Vibrio campbellii Strain UMTGB204, a Marine Bacterium Isolated from a Green Barrel Tunicate.
PG  - e00210-15
AB  - Vibrio campbellii strain UMTGB204 was isolated from a green barrel tunicate. The  genome of
      this strain comprises 5,652,224 bp with 5,014 open reading frames, 9
      rRNAs, and 116 tRNAs. It contains genes related to virulence and environmental
      tolerance. Gene clusters for the biosynthesis of nonribosomal peptides and
      bacteriocin were also identified.
AU  - Gan HY
AU  - Noor ME
AU  - Saari NA
AU  - Musa N
AU  - Mustapha B
AU  - Usup G
AU  - Danish-Daniel M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00210-15.

PMID- 110783
VI  - 139
DP  - 1979
TI  - Genetic recombination during transformation in Bacillus subtilis:  appearance of a deoxyribonucleic acid methylase.
PG  - 270-279
AB  - In Bacillus subtilis the ability to take up deoxyribonucleic acid (DNA) and
      undergo genetic transformation may coincide with the induction of defective
      phage(s) and the expression of possibly related cryptic genes.  A
      restriction-modification enzyme system appears to be expressed.  Targets of the
      restriction activity on the DNA can be blocked by methylation catalyzed by the
      methyl transferase.  It is shown that cellular DNA becomes progressively
      methylated and reaches the maximum level during the peak of competency.
      Deoxycytidine residues of both incoming donor and resident DNA are methylated.
      The possible participation of these enzymes in recombination and the general
      role of crytptic genes in inducible functions are discussed.
AU  - Ganesan AT
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1979 139: 270-279.

PMID- Not carried by PubMed...
VI  - 0
DP  - 1982
TI  - Uptake, restriction, modification and recombination of DNA molecules during transformation in B. subtilis.
PG  - 261-268
AB  - Bacillus subtilis can be subjected to regimens of growth conditions that would
      permit them to take up single, double and plasmid superhelical DNA molecules.
      We know very little of transport mechanisms the cell has in store to handle
      different types of molecules.
AU  - Ganesan AT
PT  - Journal Article
TA  - Molecular Cloning and Gene Regulation in Bacilli
JT  - Molecular Cloning and Gene Regulation in Bacilli
SO  - Molecular Cloning and Gene Regulation in Bacilli 1982 0: 261-268.

PMID- 26847887
VI  - 4
DP  - 2016
TI  - Draft Whole-Genome Sequence of Haemophilus ducreyi Strain AUSPNG1, Isolated from  a Cutaneous Ulcer of a Child from Papua New Guinea.
PG  - e01661-15
AB  - Haemophilus ducreyi has recently emerged as a leading cause of cutaneous ulcers in the
      yaws-endemic areas of Papua New Guinea and other South Pacific islands.
      Here, we report the draft genome sequence of the H. ducreyi strain AUSPNG1,
      isolated from a cutaneous ulcer of a child from Papua New Guinea.
AU  - Gangaiah D
AU  - Marinov GK
AU  - Roberts SA
AU  - Robson J
AU  - Spinola SM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01661-15.

PMID- 26147869
VI  - 9
DP  - 2015
TI  - Haemophilus ducreyi Cutaneous Ulcer Strains Are Nearly Identical to Class I Genital Ulcer Strains.
PG  - E0003918
AB  - BACKGROUND: Although cutaneous ulcers (CU) in the tropics is frequently
      attributed to Treponema pallidum subspecies pertenue, the causative agent of
      yaws, Haemophilus ducreyi has emerged as a major cause of CU in yaws-endemic
      regions of the South Pacific islands and Africa. H. ducreyi is generally
      susceptible to macrolides, but CU strains persist after mass drug administration
      of azithromycin for yaws or trachoma. H. ducreyi also causes genital ulcers (GU)
      and was thought to be exclusively transmitted by microabrasions that occur during
      sex. In human volunteers, the GU strain 35000HP does not infect intact skin;
      wounds are required to initiate infection. These data led to several questions:
      Are CU strains a new variant of H. ducreyi or did they evolve from GU strains? Do
      CU strains contain additional genes that could allow them to infect intact skin?
      Are CU strains susceptible to azithromycin? METHODOLOGY/PRINCIPAL FINDINGS: To
      address these questions, we performed whole-genome sequencing and antibiotic
      susceptibility testing of 5 CU strains obtained from Samoa and Vanuatu and 9
      archived class I and class II GU strains. Except for single nucleotide
      polymorphisms, the CU strains were genetically almost identical to the class I
      strain 35000HP and had no additional genetic content. Phylogenetic analysis
      showed that class I and class II strains formed two separate clusters and CU
      strains evolved from class I strains. Class I strains diverged from class II
      strains ~1.95 million years ago (mya) and CU strains diverged from the class I
      strain 35000HP ~0.18 mya. CU and GU strains evolved under similar selection
      pressures. Like 35000HP, the CU strains were highly susceptible to antibiotics,
      including azithromycin. CONCLUSIONS/SIGNIFICANCE: These data suggest that CU
      strains are derivatives of class I strains that were not recognized until
      recently. These findings require confirmation by analysis of CU strains from
      other regions.
AU  - Gangaiah D
AU  - Webb KM
AU  - Humphreys TL
AU  - Fortney KR
AU  - Toh E
AU  - Tai A
AU  - Katz SS
AU  - Pillay A
AU  - Chen CY
AU  - Roberts SA
AU  - Munson RS Jr
AU  - Spinola SM
PT  - Journal Article
TA  - PLoS Neglected Trop. Dis.
JT  - PLoS Neglected Trop. Dis.
SO  - PLoS Neglected Trop. Dis. 2015 9: E0003918.

PMID- 29954914
VI  - 6
DP  - 2018
TI  - Fifty-Six Draft Genome Sequences of 10 Lactobacillus Species from 22 Commercial Dietary Supplements.
PG  - e00621-18
AB  - Here, we present the genome sequences of 56 isolates of 10 species of the genus Lactobacillus
      that are considered beneficial components of the gut microbiota.
      The isolates examined were found in commercially available dietary supplements in
      the U.S. market.
AU  - Gangiredla J
AU  - Barnaba TJ
AU  - Mammel MK
AU  - Lacher DW
AU  - Elkins CA
AU  - Lampel KA
AU  - Whitehouse CA
AU  - Tartera C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00621-18.

PMID- 29242221
VI  - 5
DP  - 2017
TI  - Species-Wide Collection of Escherichia coli Isolates for Examination of Genomic Diversity.
PG  - e01321-17
AB  - Pathogenic and nonpathogenic Escherichia coli strains present a vast genomic diversity. We
      report the genome sequences of 2,244 E. coli isolates from multiple
      animal and environmental sources. Their phylogenetic relationships and potential
      risk to human health were examined.
AU  - Gangiredla J
AU  - Mammel MK
AU  - Barnaba TJ
AU  - Tartera C
AU  - Gebru ST
AU  - Patel IR
AU  - Leonard SR
AU  - Kotewicz ML
AU  - Lampel KA
AU  - Elkins CA
AU  - Lacher DW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01321-17.

PMID- 29724828
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Escherichia albertii, Escherichia fergusonii, and Strains Belonging to Six Cryptic Lineages of Escherichia spp.
PG  - e00271-18
AB  - We report here the genome sequences of 55 strains belonging to the genus Escherichia from
      multiple animal and environmental sources. These strains include
      representatives of Escherichia albertii, Escherichia fergusonii, and six
      additional genetically distinct lineages of Escherichia spp., one of which is
      newly discovered and is being reported for the first time here.
AU  - Gangiredla J
AU  - Mammel MK
AU  - Barnaba TJ
AU  - Tartera C
AU  - Gebru ST
AU  - Patel IR
AU  - Leonard SR
AU  - Kotewicz ML
AU  - Lampel KA
AU  - Elkins CA
AU  - Lacher DW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00271-18.

PMID- 28280024
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Lactobacillus reuteri 121, a Source of alpha-Glucan and  beta-Fructan Exopolysaccharides.
PG  - e01691-16
AB  - The probiotic bacterium Lactobacillus reuteri 121 is a well-known producer of diverse
      homoexopolysaccharides (alpha-glucans and beta-fructans) from sucrose and
      maltodextrins/starches of interest for food applications. Here, we report the
      draft genome sequence of this strain, with a focus on carbohydrate-active
      enzymes.
AU  - Gangoiti J
AU  - Meng X
AU  - Lammerts-van-Bueren A
AU  - Dijkhuizen L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01691-16.

PMID- 27284155
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Dietzia maris DSM 43672, a Gram-Positive Bacterium of the Mycolata Group.
PG  - e00542-16
AB  - Here, we report the draft genome sequence of Dietzia maris, known previously as Rhodococcus
      maris It is 3,505,372 bp in size with a G+C content of 73%. The draft
      genome sequence will improve our understanding of Dietzia maris related to other
      mycolata species and constitutes a basic tool for exploring the cell wall
      proteins.
AU  - Ganguly S
AU  - Jimenez-Galisteo G
AU  - Pletzer D
AU  - Winterhalter M
AU  - Benz R
AU  - Vinas M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00542-16.

PMID- 27795267
VI  - 4
DP  - 2016
TI  - High-Quality Draft Genome Sequence of Thermocrinis jamiesonii GBS1T Isolated from Great Boiling Spring, Nevada.
PG  - e01112-16
AB  - The draft genome of Thermocrinis jamiesonii GBS1T is 1,315,625 bp in 10 contigs and encodes
      1,463 predicted genes. The presence of sox genes and various
      glycoside hydrolases and the absence of uptake NiFe hydrogenases (hyaB) are
      consistent with a requirement for thiosulfate and suggest the ability to use
      carbohydrate polymers.
AU  - Ganji R et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01112-16.

PMID- 
VI  - 
DP  - 1988
TI  - Recognition domains of Type I restriction enzymes.
PG  - 
AB  - Type I restriction and modification enzymes recognize asymmetric, bipartite target sequences,
      the specificity of which is dictated by a single subunit encoded by the hsdS gene.  Within the
      K-family, the S genes of members with different specificities have been sequenced.
      Comparisons of these reveal two large variable regions, each of ~450 base pairs, separated by
      a highly conserved region of ~100 base pairs.  Recombination between the central conserved
      regions of two S genes, those of StySP and StySB, has produced a new S gene (StySQ) encoding a
      functional polypeptide that confers a novel, hybrid specificity.  In this thesis I describe
      the formation of a second recombinant S gene, StySJ, which is of reciprocal structure to
      StySQ.  StySJ recognizes a target sequence predicted by a model wherein each S polypeptide
      contains two structurally independent DNA recognition domains which act together in defining
      an enzyme's target sequence.  Site directed mutagenesis was then used to demonstrate that the
      variable N-terminal 150 amino acids of an S polypeptide alone constitute one DNA recognition
      domain.  Two S polypeptides, each deleted for a single recognition domain were also produced.
      Though showing no enzymatic activity in vivo, these truncated polypeptides were capable of
      inhibiting the activities of complete restriction and modification enzymes from their own
      family, but not from another.  This is interpreted as being due to the truncated S
      polypeptides binding other enzyme subunits, thereby disrupting the formation of functional
      complexes.
AU  - Gann AAF
PT  - Journal Article
TA  - Ph.D. Thesis
JT  - Ph.D. Thesis
SO  - Ph.D. Thesis 1988 : .

PMID- Not carried by PubMed...
VI  - 50
DP  - 1990
TI  - Recognition domains of type I restriction enzymes.
PG  - 4377B
AB  - Type I restriction and modification enzymes recognize asymmetric, bipartite target sequences,
      the specificity of which is dictated by a single subunit encoded by the HsdS gene.  Within the
      K-family, the S genes of members with different specificities have been sequenced (Gough and
      Murray, 1983; Gann et al. 1987).  Comparisons of these reveal two large variable regions, each
      of ~450 base pairs, separated by a highly conserved region of ~100 base pairs. Recombination
      between the central conserved regions of two S genes, those of StySP and StySB, has produced a
      new S gene (StySQ) encoding a functional polypeptide that confers a novel, hybrid specificity
      (Fuller-Pace et al., 1984; Nagaraja, et al. 1985).  In this thesis I describe the formation of
      a second recombinant S gene, StySJ, which is of reciprocal structure to StySQ.  StySJ
      recognizes a target sequence predicted by a model wherein each S polypeptide contains two
      structurally independent DNA recognition domains which act together in defining an enzyme's
      target sequence.  Site directed mutagenesis was then used to demonstrate that the variable
      N-terminal 150 amino acids of an S polypeptide alone constitute one DNA recognition domain.
      Two S polypeptides, each deleted for a single recognition domain were also produced.  Though
      showing no enzymatic activity in vivo, these truncated polypeptide were capable of inhibiting
      the activities of complete restriction and modification enzymes from their own family, but not
      from another.  This is interpreted as being due to the truncated S polypeptides binding other
      enzyme subunits, thereby disrupting the formation of function restriction complexes.
AU  - Gann AAF
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1990 50: 4377B.

PMID- 2838725
VI  - 1
DP  - 1987
TI  - Reassortment of DNA recognition domains and the evolution of new specificities.
PG  - 13-22
AB  - TypeI restriction enzymes comprise three subunits only one of which, the S polypeptide,
      dictates the specificity of the DNA sequence recognized. Recombination between two different
      hsdS genes, SP and SB, led to the isolation of a system, SQ, which had a different specificity
      from that of either parent. The finding that the nucleotide sequence recognized by SQ is a
      hybrid containing components from both the SP and SB target sequences suggested that DNA
      recognition is carried out by two separable domains within each specificity polypeptide.  To
      test this we have made the recombinant gene of reciprocal structure and demonstrate that it
      encodes a polypeptide whose recognition sequence, deduced in vivo, is as predicted by this
      model.  We also report the sequence of the SB specificity gene, so that information is now
      available for the five known members of this family of enzymes.  All show a similar
      organization of conserved and variable regions.  Comparisons of the predicted amino acid
      sequences reveal large non-conserved areas which may not even be structurally similar.  This
      is remarkable since these different S subunits are functionally identical, except for the
      specificity with respect to the DNA sequence with which they interact.  We discuss the
      correlation of the variation in polypeptide sequence with recognition specificities.
AU  - Gann AAF
AU  - Campbell AJB
AU  - Collins JF
AU  - Coulson AFW
AU  - Murray NE
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1987 1: 13-22.

PMID- 22887660
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Lactate-Utilizing Pseudomonas aeruginosa Strain XMG.
PG  - 4751-4752
AB  - Pseudomonas aeruginosa XMG, isolated from soil, utilizes lactate. Here we present a 6.45-Mb
      assembly of its genome sequence. Besides the lactate utilization
      mechanism of the strain, the genome sequence may also provide other useful
      information related to P. aeruginosa, such as identifying genes involved in
      virulence, drug resistance, and aromatic catabolism.
AU  - Gao C
AU  - Hu C
AU  - Ma C
AU  - Su F
AU  - Yu H
AU  - Jiang T
AU  - Dou P
AU  - Wang Y
AU  - Qin T
AU  - Lv M
AU  - Xu P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4751-4752.

PMID- 22031930
VI  - 86
DP  - 2012
TI  - A Novel Cyanophage with a Cyanobacterial Nonbleaching Protein A Gene in the Genome.
PG  - 236-245
AB  - A cyanophage, PaV-LD, has been isolated from harmful filamentous cyanobacterium
      Planktothrix agardhii in Lake Donghu, a shallow freshwater lake in China. Here,
      we present the cyanophage's genomic organization and major structural proteins.
      The genome is a 95,299-bp-long, linear double-stranded DNA and contains 142
      potential genes. BLAST searches revealed 29 proteins of known function in
      cyanophages, cyanobacteria, or bacteria. Thirteen major structural proteins
      ranging in size from 27 kDa to 172 kDa were identified by SDS-PAGE and
      mass-spectrometric analysis. The genome lacks major genes that are necessary to
      the tail structure, and the tailless PaV-LD has been confirmed by an electron
      microscopy comparison with other tail cyanophages and phages. Phylogenetic
      analysis of the major capsid proteins also reveals an independent branch of
      PaV-LD that is quite different from other known tail cyanophages and phages.
      Moreover, the unique genome carries a nonbleaching protein A (NblA) gene (open
      reading frame [ORF] 022L), which is present in all phycobilisome-containing
      organisms and mediates phycobilisome degradation. Western blot detection
      confirmed that 022L was expressed after PaV-LD infection in the host filamentous
      cyanobacterium. In addition, its appearance was companied by a significant
      decline of phycocyanobilin content and a color change of the cyanobacterial cells
      from blue-green to yellow-green. The biological function of PaV-LD nblA was
      further confirmed by expression in a model cyanobacterium via an integration
      platform, by spectroscopic analysis and electron microscopy observation. The data
      indicate that PaV-LD is an exceptional cyanophage of filamentous cyanobacteria,
      and this novel cyanophage will also provide us with a new vision of the
      cyanophage-host interactions.
AU  - Gao EB
AU  - Gui JF
AU  - Zhang QY
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 2012 86: 236-245.

PMID- 21398552
VI  - 193
DP  - 2011
TI  - Genome sequence of Acinetobacter baumannii MDR-TJ.
PG  - 2365-2366
AB  - Acinetobacter baumannii is a species of pathogenic bacteria, originally included in the
      aerobic gram-negative bacterium, which is resistant to most antibiotics. In this paper, the
      MDR-TJ strain was isolated by the Second Hospital of Tianjin Medical University, China, which
      was found resistant to penicillin, spore class, aminoglycosides, quinolones and also imipenem.
      The genome sequence of Acinetobacter baumannii strain MDR-TJ was determined using a
      combination of 454 pyrosequencing and paired-end sequencing performed by the Roche Genome
      Sequencer FLX Systems to generate a scaffolded assembly.
AU  - Gao F
AU  - Wang Y
AU  - Liu YJ
AU  - Wu XM
AU  - Lv X
AU  - Gan YR
AU  - Song SD
AU  - Huang H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 2365-2366.

PMID- 23144418
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Brucella canis Strain 118, a Strain Isolated from Canine.
PG  - 6680
AB  - Brucella canis infects several species of animals, and canine is the preferred host. Genome
      sequences of strains from different hosts are valuable for
      comparative analysis of host adaptation and microevolution. Here, we report the
      genome sequence of Brucella canis strain 118, a strain isolated from canine.
AU  - Gao G
AU  - Li J
AU  - Li T
AU  - Zhang Z
AU  - Wang L
AU  - Yuan X
AU  - Wang Y
AU  - Xu J
AU  - Ke Y
AU  - Huang L
AU  - Wang D
AU  - Chen Z
AU  - Xu X
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6680.

PMID- 29545288
VI  - 6
DP  - 2018
TI  - Genome Sequence of Corynebacterium pseudotuberculosis Strain KM01, Isolated from  the Abscess of a Goat in Kunming, China.
PG  - e00013-18
AB  - Caseous lymphadenitis (CLA) is an acute, pyogenic, and contagious disease of goat that imposes
      considerable economic losses for farmers, and it is caused by
      Corynebacterium pseudotuberculosis Herein, we introduce the genome sequencing of
      C. pseudotuberculosis strain KM01, isolated from an abscess of a Saanen goat from
      Kunming, China. The genome contains 2,198 genes, the total length of the genes
      was 2,337,666 bp, and the GC content was 52.18%. The number of tandem repeat
      sequences was 44, the total length of the tandem repeat sequences was 1,970 bp
      (0.0772% of the genome), the number of minisatellite DNAs was 36, and there were
      48 tRNAs and 12 rRNAs.
AU  - Gao H
AU  - Ma Y
AU  - Shao Q
AU  - Hong Q
AU  - Zheng G
AU  - Li Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00013-18.

PMID- 22815441
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of High-Siderophore-Yielding Pseudomonas sp. Strain HYS.
PG  - 4121
AB  - We sequenced the genome of the high-siderophore-yielding strain Pseudomonas sp. HYS and then
      analyzed its iron acquisition systems. The 5.6-Mb draft genome
      sequence has a special pattern of pyoverdine synthesis clusters and contains an
      hmuRSTUV heme uptake cluster, which has a homolog only in some strains of the
      order Enterobacteriales.
AU  - Gao J
AU  - Yu X
AU  - Xie Z
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4121.

PMID- 22843589
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Gluconobacter oxydans WSH-003, a Strain That Is Extremely Tolerant of Saccharides and Alditols.
PG  - 4455-4456
AB  - Gluconobacter oxydans is known for its incomplete oxidation of a wide range of alcohols,
      sugars, and acids in a bioprocess. The corresponding oxidation products
      are secreted almost completely into the medium. Here, we present the high-quality
      draft genome sequence of G. oxydans WSH-003, an industrial strain with both high
      l-sorbose productivity and extreme tolerance to saccharides and alditols.
AU  - Gao L
AU  - Zhou J
AU  - Liu J
AU  - Du G
AU  - Chen J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4455-4456.

PMID- 21399684
VI  - 6
DP  - 2011
TI  - Structure of HsdS Subunit from Thermoanaerobacter tengcongensis Sheds Lights on Mechanism of Dynamic Opening and Closing of Type I Methyltransferase.
PG  - e17346
AB  - Type I DNA methyltransferases contain one specificity subunit (HsdS) and two modification
      subunits (HsdM). The electron microscopy model of
      M.EcoKI-M2S1 methyltransferase shows a reasonable closed state of this
      clamp-like enzyme, but the structure of the open state is still
      unclear. The 1.95 angstrom crystal structure of the specificity subunit
      from Thermoanaerobacter tengcongensis (TTE-HsdS) shows an unreported
      open form inter-domain orientation of this subunit. Based on the
      crystal structure of TTE-HsdS and the closed state model of
      M.EcoKI-M2S1, we constructed a potential open state model of type I
      methyltransferase. Mutational studies indicated that two alpha-helices
      (aa30-59 and aa466-495) of the TTE-HsdM subunit are important
      inter-subunit interaction sites in the TTE-M2S1 complex. DNA binding
      assays also highlighted the importance of the C-terminal region of
      TTE-HsdM for DNA binding by the TTE-M2S1 complex. On the basis of
      structural analysis, biochemical experiments and previous studies, we
      propose a dynamic opening and closing mechanism for type I
      methyltransferase.
AU  - Gao P
AU  - Tang Q
AU  - An XM
AU  - Yan XX
AU  - Liang DC
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2011 6: e17346.

PMID- 18328078
VI  - 282
DP  - 2008
TI  - The biosynthetic genes encoding for the production of the dynemicin enediyne core in Micromonospora chersina ATCC53710.
PG  - 105-114
AB  - Dynemicin is a novel anthraquinone-fused member of the 10-membered
      enediyne antitumor antibiotic family. The development of a genetic system
      for the dynemicin producer Micromonospora chersina confirmed, for the
      first time, the requirement of the putative enediyne core biosynthetic
      genes (dynE8, U14 and U15) and a tailoring oxidase gene (orf23) for
      dynemicin production. Cloning and sequence analysis of a 76 kb of genomic
      sequence region containing dynE8 revealed a variety of genes conserved
      among known enediyne loci. Surprisingly, this fragment and flanking
      chromosomal DNA lacked any obvious genes encoding for the biosynthesis of
      the anthraquinone, suggesting that the location of genes encoding for the
      biosynthesis of the dynemicin enediyne core and the dynemicin
      anthraquinone are chromosomally distinct. The demonstrated trace
      production of a shunt product from mutant strain QGD23 (Deltaorf23) also
      sets the stage for subsequent studies to delineate the key steps in
      enediyne core biosynthesis and tailoring.
AU  - Gao Q
AU  - Thorson JS
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2008 282: 105-114.

PMID- 
VI  - 33
DP  - 2011
TI  - An investigation on the genetic background of  Nostoc flagelliforme by similarity analysis of its partial genomic DNA and  phylogenetic comparison of deduced related species.
PG  - 1301-1318
AB  - Nostoc flagelliforme, which is distributed on arid and semi-arid steppes of northwestern parts
      of China, has attracted increasing interest for its stress tolerance. In order to gain more
      insight into the genetic background of N. flagelliforme, we sequenced its partial genomic DNA
      for
      similarity analyses against current public databases, followed
      by phylogenetic comparison of N. flagelliforme and the potentially related species deduced
      from the similarity analyses. Approximately 430 kb genomic sequence (*5% of genome as a rough
      estimate) was determined from 106
      distinct genomic clones. Nucleotide BLAST showed that *23.1% of the partial genomic sequence
      was similar to N. punctiforme genomic DNA and *12.4% to its plasmid DNA. Similar protein
      search by online FASTA-protein program showed 46.2% of the similar proteins had their
      corresponding orthologs in N. punctiforme genome. Furthermore, phylogenetic comparison based
      on 16S rRNA
      sequences showed N. flagelliforme and N. punctiforme clustered closer among the deduced
      related species. These results indicated that N. punctiforme might also be potentially close
      neighbor species of N. flagelliforme, in addition to the formerly regarded close neighbor
      species N. commune
      and N. sphaeroids. In general, these data enriched our recognition of the evolutionary
      relationship between N. flagelliforme and other Nostoc species, especially N. punctiforme.
AU  - Gao X
AU  - Liu K
AU  - Qiu B-S
PT  - Journal Article
TA  - Acta Physiol. Plant.
JT  - Acta Physiol. Plant.
SO  - Acta Physiol. Plant. 2011 33: 1301-1318.

PMID- 25678942
VI  - 10
DP  - 2015
TI  - Draft genome sequence of Halomonas lutea strain YIM 91125(T) (DSM 23508(T)) isolated from the alkaline Lake Ebinur in Northwest China.
PG  - 1
AB  - Species of the genus Halomonas are halophilic and their flexible adaption to changes of
      salinity and temperature brings considerable potential biotechnology
      applications, such as degradation of organic pollutants and enzyme production.
      The type strain Halomonas lutea YIM 91125(T) was isolated from a hypersaline lake
      in China. The genome of strain YIM 91125(T) becomes the twelfth species sequenced
      in Halomonas, and the thirteenth species sequenced in Halomonadaceae. We
      described the features of H. lutea YIM 91125(T), together with the high quality
      draft genome sequence and annotation of its type strain. The 4,533,090 bp long
      genome of strain YIM 91125(T) with its 4,284 protein-coding and 84 RNA genes is a
      part of Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial
      genomes (KMG-I) project. From the viewpoint of comparative genomics, H. lutea has
      a larger genome size and more specific genes, which indicated acquisition of
      function bringing better adaption to its environment. DDH analysis demonstrated
      that H. lutea is a distinctive species, and halophilic features and nitrogen
      metabolism related genes were discovered in its genome.
AU  - Gao XY
AU  - Zhi XY
AU  - Li HW
AU  - Zhou Y
AU  - Lapidus A
AU  - Han J
AU  - Haynes M
AU  - Lobos E
AU  - Huntemann M
AU  - Pati A
AU  - Ivanova NN
AU  - Mavromatis K
AU  - Tindall BJ
AU  - Markowitz V
AU  - Woyke T
AU  - Klenk HP
AU  - Kyrpides NC
AU  - Li WJ
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 1.

PMID- 29567742
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Bacillus velezensis B6, a Rhizobacterium That Can Control Plant Diseases.
PG  - e00182-18
AB  - The draft genome of Bacillus velezensis strain B6, a rhizobacterium with good biocontrol
      performance isolated from soil in China, was sequenced. The assembly
      comprises 32 scaffolds with a total size of 3.88 Mb. Gene clusters coding either
      ribosomally encoded bacteriocins or nonribosomally encoded antimicrobial
      polyketides and lipopeptides in the genome may contribute to plant disease
      control.
AU  - Gao YH
AU  - Guo RJ
AU  - Li SD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00182-18.

PMID- 28385857
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Actinomyces hongkongensis HKU8T Isolated from Human Blood.
PG  - e01650-16
AB  - Members of the genus Actinomyces are strongly associated with human diseases. We  present here
      the complete genome sequence of Actinomyces hongkongensis HKU8T,
      which consists of one circular chromosome. The strain characteristically contains
      various genes encoding for enzymes involved in arylamidase utilization.
AU  - Gao YX
AU  - Zhou YY
AU  - Xie Y
AU  - Wang M
AU  - Wang SJ
AU  - Shen SG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01650-16.

PMID- 21914884
VI  - 193
DP  - 2011
TI  - Genome Sequence of Anaerophaga sp. Strain HS1, a Novel, Moderately Thermophilic, Strictly Anaerobic Bacterium Isolated from Hot Spring  Sediment.
PG  - 5572
AB  - Anaerophaga sp. strain HS1 was isolated from offshore hot spring sediment in Xiamen, China. It
      was identified as a novel, moderately thermophilic,
      strictly anaerobic bacterium affiliated with the family Marinilabiaceae
      and showed xylanase activity. Here, we describe the 3.88-Mb draft genome
      sequence of Anaerophaga sp. strain HS1 and the annotation analysis of
      related xylanase genes.
AU  - Gao Z
AU  - Liu X
AU  - Ruan L
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5572.

PMID- 25780497
VI  - 9
DP  - 2014
TI  - Genome sequence of Ensifer medicae Di28; an effective N2-fixing microsymbiont of  Medicago murex and M. polymorpha.
PG  - 4
AB  - Ensifer medicae Di28 is an aerobic, motile, Gram-negative, non-spore-forming rod  that can
      exist as a soil saprophyte or as a legume microsymbiont of Medicago spp.
      Di28 was isolated in 1998 from a nodule recovered from the roots of M. polymorpha
      growing in the south east of Sardinia (Italy). Di28 is an effective microsymbiont
      of the annual forage legumes M. polymorpha and M. murex and is capable of
      establishing a partially effective symbiotic association with the perennial M.
      sativa. Here we describe the features of E. medicae Di28, together with genome
      sequence information and its annotation. The 6,553,624 bp standard draft genome
      is arranged into 104 scaffolds of 104 contigs containing 6,394 protein-coding
      genes and 75 RNA-only encoding genes. This rhizobial genome is one of 100
      sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for
      Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.
AU  - Garau G
AU  - Terpolilli J
AU  - Hill Y
AU  - Tian R
AU  - Howieson J
AU  - Brau L
AU  - Goodwin L
AU  - Han J
AU  - Reddy T
AU  - Huntemann M
AU  - Pati A
AU  - Woyke T
AU  - Mavromatis K
AU  - Markowitz V
AU  - Ivanova N
AU  - Kyrpides N
AU  - Reeve W
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 4.

PMID- 22815440
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of the Antagonistic Rhizosphere Bacterium Serratia plymuthica Strain PRI-2C.
PG  - 4119-4120
AB  - Serratia plymuthica strain PRI-2C is a rhizosphere bacterial strain with antagonistic activity
      against different plant pathogens. Here we present the
      5.39-Mb (G+C content, 55.67%) draft genome sequence of S. plymuthica strain
      PRI-2C with the aim of providing insight into the genomic basis of its
      antagonistic activity.
AU  - Garbeva P
AU  - van Elsas JD
AU  - de Boer W
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4119-4120.

PMID- 27083266
VI  - 306
DP  - 2016
TI  - Genetic relatedness and virulence properties of enteropathogenic Escherichia coli strains of serotype O119:H6 expressing localized adherence or localized and aggregative adherence-like patterns on HeLa cells.
PG  - 152-164
AB  - Enteropathogenic Escherichia coli (EPEC) induce attaching and effacing (A/E) lesions in
      enterocytes and produce the bundle-forming pilus (BFP) contributing to
      the localized adherence (LA) pattern formation on HeLa cells. Enteroaggregative
      E. coli (EAEC) produce aggregative adherence (AA) on HeLa cells and form
      prominent biofilms. The ability to produce LA or AA is an important hallmark to
      classify fecal E. coli isolates as EPEC or EAEC, respectively. E. coli strains of
      serotype O119:H6 exhibit an LA+ phenotype and have been considered as comprising
      a clonal group of EPEC strains. However, we have recently identified O119:H6 EPEC
      strains that produce LA and an AA-like pattern concurrently (LA/AA-like+). In
      this study, we evaluated the relatedness of three LA/AA-like+ and three LA+
      O119:H6 strains by comparing their virulence and genotypic properties. We first
      found that the LA/AA-like+ strains induced actin accumulation in HeLa cells
      (indicative of A/E lesions formation) and formed biofilms on abiotic surfaces
      more efficiently than the LA+ strains. MLST analysis showed that the six strains
      all belong to the ST28 complex. All strains carried multiple plasmids, but as
      plasmid profiles were highly variable, this cannot be used to differentiate
      LA/AA-like+ and LA+ strains. We further obtained their draft genome sequences and
      the complete sequences of four plasmids harbored by one LA/AA-like+ strain.
      Analysis of these sequences and comparison with 37 fully sequenced E. coli
      genomes revealed that both O119:H6 groups belong to the E. coli phylogroup B2 and
      are very closely related with only 58-67 SNPs found between LA/AA-like+ and LA+
      strains. Search of the draft sequences of the six strains for adhesion-related
      genes known in EAEC and other E. coli pathotypes detected no genes specifically
      present in LA/AA-like+ strains. Unexpectedly however, we found that a large
      plasmid distinct from pEAF is responsible for the AA-like phenotype of the
      LA/AA-like+ strains. Although we have not identified any plasmid genes
      specifically present in all LA/AA-like+ strains and absent in the LA+ strains,
      these results suggest the presence of an unknown mechanism to promote the AA-like
      pattern production and biofilm formation by the LA/AA-like+ strains. Because
      their ability to produce A/E lesions and biofilm concomitantly could exacerbate
      the clinical condition of the patient and lead to persistent diarrhea, the
      mechanism underlying the enhanced biofilm formation by the LA/AA-like+ O119:H6
      strains and their spread and involvement in severe diarrheal diseases should be
      more intensively investigated.
AU  - Garcia BG
AU  - Ooka T
AU  - Gotoh Y
AU  - Vieira MAM
AU  - Yamamoto D
AU  - Ogura Y
AU  - Girao DM
AU  - Sampaio SCF
AU  - Melo AB
AU  - Irino K
AU  - Hayashi T
AU  - Gomes TAT
PT  - Journal Article
TA  - Int. J. Med. Microbiol.
JT  - Int. J. Med. Microbiol.
SO  - Int. J. Med. Microbiol. 2016 306: 152-164.

PMID- 24201205
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Nitrosospira sp. Strain APG3, a Psychrotolerant Ammonia-Oxidizing Bacterium Isolated from Sandy Lake Sediment.
PG  - e00930-13
AB  - Bacteria in the genus Nitrosospira play vital roles in the nitrogen cycle. Nitrosospira sp.
      strain APG3 is a psychrotolerant betaproteobacterial
      ammonia-oxidizing bacterium isolated from freshwater lake sediment. The draft
      genome revealed that it represents a new species of cluster 0 Nitrosospira, which
      is presently not represented by described species.
AU  - Garcia JC
AU  - Urakawa H
AU  - Le VQ
AU  - Stein LY
AU  - Klotz MG
AU  - Nielsen JL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00930-13.

PMID- 24526653
VI  - 2
DP  - 2014
TI  - Genome Sequence of Pseudomonas azelaica HBP1, Which Catabolizes 2-Hydroxybiphenyl Fungicide.
PG  - e01248-13
AB  - Pseudomonas azelaica HBP1 (DSM 8897) is one of the few bacteria able to completely mineralize
      the 2-hydroxybiphenyl biocide. Here, we report the draft
      genome sequence of this strain (7.4 Mbp; G+C content, 63.5%) and the findings
      obtained from its genome annotation.
AU  - Garcia JL
AU  - Rozas D
AU  - Del Cerro C
AU  - Nogales J
AU  - El-Said MM
AU  - Diaz E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01248-13.

PMID- 10535939
VI  - 96
DP  - 1999
TI  - Translocation and specific cleavage of bacteriophage T7 DNA in vivo by EcoKI.
PG  - 12430-12435
AB  - Infection of Escherichia coli containing the type I restriction enzyme EcoKI by bacteriophage
      T7 0.3 mutants leads to restriction during the late stages of genome entry and during DNA
      replication. Patterns of cleavage in vivo suggest that some cutting occurs near the midpoint
      of two recognition sites, consistent with the idea that EcoKI translocates DNA bidirectionally
      through itself and cuts when two enzyme molecules collide. Rapid ejection of a 0.3(+) T7
      genome from a bacteriophage lambda particle results in degradation of the infecting DNA by
      EcoKI, showing that the normal T7 DNA translocation process delays restriction. A unique
      recognition site inserted at the genomic left end allows EcoKI to function as a molecular
      motor and to translocate the remaining 39 kilobases of T7 DNA into the cell.
AU  - Garcia LR
AU  - Molineux IJ
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1999 96: 12430-12435.

PMID- 28473397
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Three Bacterial Isolates from Cultures of the Marine Diatom Thalassiosira rotula.
PG  - e00316-17
AB  - Phytoplankton often both provision and depend on heterotrophic bacteria. In order to
      investigate these relationships further, we sequenced draft genomes of three
      bacterial isolates from cultures of the marine diatom Thalassiosira rotula to
      identify metabolic functions that may support interactions with T. rotula.
AU  - Garcia NS
AU  - Yung CM
AU  - Davis KM
AU  - Rynearson T
AU  - Hunt DE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00316-17.

PMID- 18952876
VI  - 74
DP  - 2008
TI  - Isolation of new Stenotrophomonas bacteriophages and genomic characterization of temperate phage S1.
PG  - 7552-7560
AB  - Twenty-two phages that infect Stenotrophomonas species were isolated
      through sewage enrichment and prophage induction. Of them, S1, S3, and S4
      were selected due to their wide host ranges compared to those of the other
      phages. S1 and S4 are temperate siphoviruses, while S3 is a virulent
      myovirus. The genomes of S3 and S4, about 33 and 200 kb, were resistant to
      restriction digestion. The lytic cycles lasted 30 min for S3 and about 75
      min for S1 and S4. The burst size for S3 was 100 virions/cell, while S1
      and S4 produced about 75 virus particles/cell. The frequency of
      bacteriophage-insensitive host mutants, calculated by dividing the number
      of surviving colonies by the bacterial titer of a parallel, uninfected
      culture, ranged between 10(-5) and 10(-6) for S3 and 10(-3) and 10(-4) for
      S1 and S4. The 40,287-bp genome of S1 contains 48 open reading frames
      (ORFs) and 12-bp 5' protruding cohesive ends. By using a combination of
      bioinformatics and experimental evidence, functions were ascribed to 21
      ORFs. The morphogenetic and lysis modules are well-conserved, but no
      lysis-lysogeny switch or DNA replication gene clusters were recognized.
      Two major clusters of genes with respect to transcriptional orientation
      were observed. Interspersed among them were lysogenic conversion genes
      encoding phosphoadenosine phosphosulfate reductase and GspM, a protein
      involved in the general secretion system II. The attP site of S1 may be
      located within a gene that presents over 75% homology to a
      Stenotrophomonas chromosomal determinant.
AU  - Garcia P
AU  - Monjardin C
AU  - Martin R
AU  - Madera C
AU  - Soberon N
AU  - Garcia E
AU  - Meana A
AU  - Suarez JE
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2008 74: 7552-7560.

PMID- 8755524
VI  - 93
DP  - 1996
TI  - Sequence-specific recognition by cytosine C5 and adenine N6 DNA methyltransferases requires different deformations of DNA.
PG  - 7618-7622
AB  - DNA methyltransferases modify specific cytosines and adenines within 2-6 bp recognition
      sequences.  We used scanning force microscopy and gel shift analysis to show that M.HhaI, a
      cytosine C5 methyltransferase, causes only a 2 degree bend upon binding its recognition site.
      Our results are consistent with prior crystallographic analysis showing that the enzyme
      stabilizes an extrahelical base while leaving the DNA duplex otherwise unperturbed.  In
      contrast, similar analysis of M.EcoRI, an adenine N6 DNA methyltransferase, shows an average
      bend angle of approximately 52 degrees.  This distortion of DNA conformation by M.EcoRI is
      shown to be important for sequence-specific binding.
AU  - Garcia RA
AU  - Bustamante CJ
AU  - Reich NO
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1996 93: 7618-7622.

PMID- 11838638
VI  - 11
DP  - 2001
TI  - Synthesis of oligonucleotide inhibitors of DNA (cytosine-C5) methyltransferase containing 5-azacytosine residues at specific sites.
PG  - 369-378
AB  - The incorporation of 5-azacytosine residues into DNA causes potent inhibition of DNA
      (cytosine-C5) methyltransferases.  The synthesis of oligodeoxyribonucleotides incorporating
      single or multiple 5-aza-2'-deoxycytidine residues at precise sites was undertaken to
      generate an array of sequences containing the reactive 5-azacytosine base as specific target
      sites for enzymatic methylation.  Preparation of these modified oligonucleotides requires the
      use of 2-(p-nitrophenyl) ethyloxycarbonyl (NPEOC) groups for the protection of exocyclic amino
      functions.  These groups are removed under mild conditions, thus avoiding conventional
      protocols that are detrimental to the integrity of the 5-azacytosine ring.
AU  - Garcia RG
AU  - Brank AS
AU  - Christman JK
AU  - Marquez VE
AU  - Eritja R
PT  - Journal Article
TA  - Antisense Nucleic Acid Drug Dev.
JT  - Antisense Nucleic Acid Drug Dev.
SO  - Antisense Nucleic Acid Drug Dev. 2001 11: 369-378.

PMID- 21641281
VI  - 11
DP  - 2011
TI  - Meticillin-resistant Staphylococcus aureus with a novel mecA homologue in human and bovine populations in the UK and Denmark: a descriptive study.
PG  - 595-603
AB  - BACKGROUND: Animals can act as a reservoir and source for the emergence of
      novel meticillin-resistant Staphylococcus aureus (MRSA) clones in human
      beings. Here, we report the discovery of a strain of S aureus (LGA251)
      isolated from bulk milk that was phenotypically resistant to meticillin
      but tested negative for the mecA gene and a preliminary investigation of
      the extent to which such strains are present in bovine and human
      populations. METHODS: Isolates of bovine MRSA were obtained from the
      Veterinary Laboratories Agency in the UK, and isolates of human MRSA were
      obtained from diagnostic or reference laboratories (two in the UK and one
      in Denmark). From these collections, we searched for mecA PCR-negative
      bovine and human S aureus isolates showing phenotypic meticillin
      resistance. We used whole-genome sequencing to establish the genetic basis
      for the observed antibiotic resistance. FINDINGS: A divergent mecA
      homologue (mecA(LGA251)) was discovered in the LGA251 genome located in a
      novel staphylococcal cassette chromosome mec element, designated type-XI
      SCCmec. The mecA(LGA251) was 70% identical to S aureus mecA homologues and
      was initially detected in 15 S aureus isolates from dairy cattle in
      England. These isolates were from three different multilocus sequence type
      lineages (CC130, CC705, and ST425); spa type t843 (associated with CC130)
      was identified in 60% of bovine isolates. When human mecA-negative MRSA
      isolates were tested, the mecA(LGA251) homologue was identified in 12 of
      16 isolates from Scotland, 15 of 26 from England, and 24 of 32 from
      Denmark. As in cows, t843 was the most common spa type detected in human
      beings. INTERPRETATION: Although routine culture and antimicrobial
      susceptibility testing will identify S aureus isolates with this novel
      mecA homologue as meticillin resistant, present confirmatory methods will
      not identify them as MRSA. New diagnostic guidelines for the detection of
      MRSA should consider the inclusion of tests for mecA(LGA251). FUNDING:
      Department for Environment, Food and Rural Affairs, Higher Education
      Funding Council for England, Isaac Newton Trust (University of Cambridge),
      and the Wellcome Trust.
AU  - Garcia-Alvarez L et al
PT  - Journal Article
TA  - Lancet Infect Dis
JT  - Lancet Infect Dis
SO  - Lancet Infect Dis 2011 11: 595-603.

PMID- 22252815
VI  - 56
DP  - 2012
TI  - Klebsiella pneumoniae ST258 Producing KPC-3 Identified in Italy Carries Novel Plasmids and OmpK36/OmpK35 Porin Variants.
PG  - 2143-2145
AB  - A carbapenemase-resistant Klebsiella pneumoniae strain, clone ST258 producing
      KPC-3, was fully characterized. The entire plasmid content was investigated,
      thereby identifying plasmids of the IncFII(k) (two of them similar to pKPQIL and
      pKPN3, respectively), IncX, and ColE types, carrying a formidable set of
      resistance genes against toxic compounds, metals, and antimicrobial drugs and a
      novel iron(III) uptake system.
AU  - Garcia-Fernandez A
AU  - Villa L
AU  - Carta C
AU  - Venditti C
AU  - Giordano A
AU  - Venditti M
AU  - Mancini C
AU  - Carattoli A
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2012 56: 2143-2145.

PMID- 22479446
VI  - 7
DP  - 2012
TI  - Reconstructing viral genomes from the environment using fosmid clones: the case of haloviruses.
PG  - e33802
AB  - Background: Metaviriomes, the viral genomes present in an environment, have been studied by
      direct sequencing of the viral DNA or by cloning in small insert libraries. The short reads
      generated by both approaches make it very difficult to assemble and annotate such flexible
      genomic entities. Many environmental viruses belong to unknown groups or prey on uncultured
      and little known cellular lineages, and hence might not be present in databases.
      Methodology and Principal Findings: Here we have used a different approach, the cloning of
      viral DNA into fosmids before sequencing, to obtain natural contigs that are close to the size
      of a viral genome. We have studied a relatively low diversity extreme environment: saturated
      NaCl brines, which simplifies the analysis and interpretation of the data. Forty-two different
      viral genomes were retrieved, and some of these were almost complete, and could be tentatively
      identified as head-tail phages (Caudovirales).
      Conclusions and Significance: We found a cluster of phage genomes that most likely infect
      Haloquadratum walsbyi, the square archaeon and major component of the community in these
      hypersaline habitats. The identity of the prey could be confirmed by the presence of CRISPR
      spacer sequences shared by the virus and one of the available strain genomes. Other viral
      clusters detected appeared to prey on the Nanohaloarchaea and on the bacterium Salinibacter
      ruber, covering most of the diversity of microbes found in this type of environment. This
      approach appears then as a viable alternative to describe
      metaviriomes in a much more detailed and reliable way than by the more common approaches based
      on direct sequencing. An example of transfer of a CRISPR cluster including repeats and spacers
      was accidentally found supporting the dynamic nature and frequent transfer of this peculiar
      prokaryotic mechanism of cell protection.
AU  - Garcia-Heredia I
AU  - Martin-Cuadrado A-B
AU  - Mojica FJ
AU  - Santos F
AU  - Mira A
AU  - Anton J
AU  - Rodriguez-Valera F
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2012 7: e33802.

PMID- 26404596
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Entomopathogenic Bacterium Bacillus pumilus 15.1, a  Strain Highly Toxic to the Mediterranean Fruit Fly Ceratitis capitata.
PG  - e01019-15
AB  - We present the draft whole-genome sequence of the entomopathogenic Bacillus pumilus 15.1
      strain that consists of 3,795,691 bp and 3,776 predicted protein-coding genes. This genome
      sequence provides the basis for understanding the potential mechanism behind the toxicity and
      virulence of B. pumilus 15.1 against the Mediterranean fruit fly.
AU  - Garcia-Ramon DC
AU  - Palma L
AU  - Berry C
AU  - Osuna A
AU  - Vilchez S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01019-15.

PMID- 26847793
VI  - 17
DP  - 2016
TI  - Genomic analysis of the nitrate-respiring Sphingopyxis granuli (formerly Sphingomonas macrogoltabida) strain TFA.
PG  - 93
AB  - BACKGROUND: Sphingomonads are Alphaproteobacteria that belong to the
      Sphingomonas, Novosphingobium, Sphingopyxis or Sphingobium genera, They are
      physiologically diverse and broadly distributed in nature, playing important
      roles in oligotrophic environments and in the degradation of recalcitrant
      polyaromatic compounds, Sphingopyxis is a poorly studied genus of which only one
      representative (S. alaskensis RB2256) has been deeply characterized. In this
      paper we analyze the genomic features of S. granuli strain TFA (formerly
      Sphingomonas macrogoltabida) in comparison with the available Sphingopyxis
      sequenced genomes, to describe common characteristics of this genus and to
      highlight unique characteristics of strain TFA. RESULTS: The TFA genome has been
      assembled in a single circular chromosome of 4.7 Mb. Genomic sequence analysis
      and proteome comparison re-assigned the TFA strain to the Sphingopyxis genus and
      the S. granuli species. Some regions of the TFA genome show high similarity (ca.
      100 %) to other bacteria and several genomic islands have been detected. Pathways
      for aromatic compound degradation have been predicted but no growth of TFA has
      been detected using these as carbon or nitrogen sources. Genes for nitrate
      respiration have been identified as TFA exclusive. Experimental data on anaerobic
      growth of TFA using nitrate as a terminal electron acceptor are also provided.
      CONCLUSIONS: Sphingopyxis representatives form a compact phylogenetic group (with
      the exception of S. baekryungensis DSM 16222) that share several characteristics,
      such as being naturally resistant to streptomycin, having only one ribosomal
      operon, a low number of prophages and CRISPR sequences, absence of selenoproteins
      and presence of ectoin and other biosynthesis pathways for secondary metabolites.
      Moreover, the TFA genome organization shows evidence of the presence of putative
      integrative and conjugative elements (ICE) responsible for the acquisition of
      several characteristics by horizontal transfer mechanisms. Sphingopyxis
      representatives have been described as strict aerobes but anaerobic growth using
      nitrate as a terminal electron acceptor might confer an environmental advantage
      to the first S. granuli strain characterized at genomic level.
AU  - Garcia-Romero I
AU  - Perez-Pulido AJ
AU  - Gonzalez-Flores YE
AU  - Reyes-Ramirez F
AU  - Santero E
AU  - Floriano B
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2016 17: 93.

PMID- 27151809
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Vancomycin-Susceptible, Ampicillin-Intermediate Enterococcus faecium Strain D344RRF.
PG  - e01720-15
AB  - Enterococcus faecium is an important nosocomial pathogen, causing a substantial health burden
      due to high resistance to antibiotics and its ability to colonize
      the gastrointestinal tract. Here, we present the draft genome of
      vancomycin-susceptible, ampicillin-intermediate strain D344RRF, a
      rifampicin/fusidic acid-resistant and commonly used laboratory strain, which is
      useful in studying the transfer of antibiotic resistance.
AU  - Garcia-Solache M
AU  - Rice LB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01720-15.

PMID- 27151808
VI  - 4
DP  - 2016
TI  - Genome Sequence of the Multiantibiotic-Resistant Enterococcus faecium Strain C68  and Insights on the pLRM23 Colonization Plasmid.
PG  - e01719-15
AB  - Enterococcus faecium infections are a rising concern in hospital settings.
      Vancomycin-resistant enterococci colonize the gastrointestinal tract and replace
      nonresistant strains, complicating the treatment of debilitated patients. Here,
      we present a polished genome of the multiantibiotic-resistant strain C68, which
      was obtained as a clinical isolate and is a useful experimental strain.
AU  - Garcia-Solache M
AU  - Rice LB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01719-15.

PMID- 29650573
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Pseudomonas oceani DSM 100277(T), a Deep-Sea Bacterium.
PG  - e00254-18
AB  - Pseudomonas oceani DSM 100277(T) was isolated from deep seawater in the Okinawa Trough at 1390
      m. P. oceani belongs to the Pseudomonas pertucinogena group. Here,
      we report the draft genome sequence of P. oceani, which has an estimated size of
      4.1 Mb and exhibits 3,790 coding sequences, with a G+C content of 59.94 mol%.
AU  - Garcia-Valdes E
AU  - Gomila M
AU  - Mulet M
AU  - Lalucat J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00254-18.

PMID- 21304739
VI  - 3
DP  - 2010
TI  - Complete genome sequence of Marinobacter adhaerens type strain (HP15), a diatom-interacting marine microorganism.
PG  - 97-107
AB  - Marinobacter adhaerens HP15 is the type strain of a newly identified marine species, which is
      phylogenetically related to M. flavimaris, M. algicola, and M.
      aquaeolei. It is of special interest for research on marine aggregate formation
      because it showed specific attachment to diatom cells. In vitro it led to
      exopolymer formation and aggregation of these algal cells to form marine snow
      particles. M. adhaerens HP15 is a free-living, motile, rod-shaped, Gram-negative
      gammaproteobacterium, which was originally isolated from marine particles sampled
      in the German Wadden Sea. M. adhaerens HP15 grows heterotrophically on various
      media, is easy to access genetically, and serves as a model organism to
      investigate the cellular and molecular interactions with the diatom Thalassiosira
      weissflogii. Here we describe the complete and annotated genome sequence of M.
      adhaerens HP15 as well as some details on flagella-associated genes. M. adhaerens
      HP15 possesses three replicons; the chromosome comprises 4,422,725 bp and codes
      for 4,180 protein-coding genes, 51 tRNAs and three rRNA operons, while the two
      circular plasmids are ~187 kb and ~42 kb in size and contain 178 and 52
      protein-coding genes, respectively.
AU  - Gardes A
AU  - Kaeppel E
AU  - Shehzad A
AU  - Seebah S
AU  - Teeling H
AU  - Yarza P
AU  - Glockner FO
AU  - Grossart HP
AU  - Ullrich MS
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 3: 97-107.

PMID- 23661484
VI  - 1
DP  - 2013
TI  - Genome Sequences of Pseudomonas spp. Isolated from Cereal Crops.
PG  - e00209-13
AB  - Compared to those of dicot-infecting bacteria, the available genome sequences of  bacteria
      that infect wheat and barley are limited. Herein, we report the draft
      genome sequences of four pseudomonads originally isolated from these cereals.
      These genome sequences provide a useful resource for comparative analyses within
      the genus and for cross-kingdom analyses of plant pathogenesis.
AU  - Gardiner DM
AU  - Stiller J
AU  - Covarelli L
AU  - Lindeberg M
AU  - Shivas RG
AU  - Manners JM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00209-13.

PMID- 24744326
VI  - 2
DP  - 2014
TI  - Genome Sequence of Fusarium graminearum Isolate CS3005.
PG  - e00227-14
AB  - Fusarium graminearum is one of the most important fungal pathogens of wheat, barley, and maize
      worldwide. This announcement reports the genome sequence of a highly virulent Australian
      isolate of this species to supplement the existing genome of the North American F. graminearum
      isolate Ph1.
AU  - Gardiner DM
AU  - Stiller J
AU  - Kazan K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00227-14.

PMID- 22493191
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Model Hyperthermophilic Archaeon Thermococcus litoralis NS-C.
PG  - 2375-2376
AB  - The hyperthermophilic archaeon Thermococcus litoralis strain NS-C, first isolated in 1985, has
      been a foundational organism for archaeal research in biocatalysis,
      DNA replication, metabolism, and the discovery of inteins. Here, we present the
      genome sequence of T. litoralis with a focus on the replication machinery and
      inteins.
AU  - Gardner AF
AU  - Kumar S
AU  - Perler FB
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2375-2376.

PMID- 6299666
VI  - 1
DP  - 1982
TI  - Cloning and sequencing of restriction fragments generated by EcoRI*.
PG  - 109-115
AB  - Thirty-four EcoRI* sites have been identified on the nucleotide sequence of
      CaMV, following cloning of EcoRI* fragments in M13mp2.  From this sequencing
      data, we have deduced that EcoRI* recognizes sites at any one of the six
      positions in the recognition site, with the exception of A5T or T5A changes
      within the central tetramer.  The EcoRI* restriction patterns of PhiX174 and
      pBR322 are consistent with these recognition criteria.  Similarly, BamHI*
      cleavage of PhiX174 and SV40 (George et al., 1980) produces restriction
      patterns that are consistent with single-position degeneracy in the canonical
      BamHI recognition site.  Cohesive termini produced by EcoRI* cleavage were
      ligated into the EcoRI site of M13mp2, even when there was a base pair mismatch
      within the four nucleotide overlap.  Mismatches were corrected asymmetrically
      during subsequent replication of M13 in E. coli.
AU  - Gardner RC
AU  - Howarth AJ
AU  - Messing J
AU  - Shepherd RJ
PT  - Journal Article
TA  - DNA
JT  - DNA
SO  - DNA 1982 1: 109-115.

PMID- 28751407
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Campylobacter jejuni subsp. jejuni ATCC 35925.
PG  - e00743-17
AB  - Here, we report the complete genome sequence of Campylobacter jejuni ATCC 35925,  an avian
      isolate from Sweden. The genome gives insight into the ATCC 35925
      strain's remarkable ability to tolerate copper and its permissiveness to plasmid
      transformation.
AU  - Gardner SP
AU  - Kendall KJ
AU  - Taveirne ME
AU  - Olson JW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00743-17.

PMID- 22569516
VI  - 79
DP  - 2012
TI  - Barriers to Horizontal Gene Transfer in Campylobacter jejuni.
PG  - 19-42
AB  - Campylobacter jejuni is among the most frequent agent of food-borne gastroenteritis in the
      world, but its physiology and pathogenesis. is
      less well understood than other bacterial enteric pathogens. This is
      due in part to the incompatibility of the molecular tools that have
      enabled advances in the characterization of other bacterial species.
      Most notably, the dearth of plasmid-based complementation, reporter
      assays, and plasmid-based unmarked mutagenesis procedures in many of
      the type strains has hindered research progress. The techniques
      themselves are not inadequate in Cam pylobacter species, but rather the
      barrier to genetic transfer of these genetic constructs from
      non-Campylobacter cloning stains such as Escherichia coli. Here, we
      review the modes of genetic transfer in C. jejuni and review the
      current state of research into the mechanism of each. Also reviewed are
      two systems (CRISPR-Cas and restriction modification) that are common
      to many strains of C. jejuni and are at least partly responsible for
      these barriers.
AU  - Gardner SP
AU  - Olson JW
PT  - Journal Article
TA  - Adv. Appl. Microbiol.
JT  - Adv. Appl. Microbiol.
SO  - Adv. Appl. Microbiol. 2012 79: 19-42.

PMID- 171627
VI  - 2
DP  - 1975
TI  - Sequences spanning the EcoRI substrate site.
PG  - 1851-1865
AB  - Substrate recognition by the EcoRI restriction endonuclease was investigated by
      analysis of the nucleotide sequences at the sites of enzymatic cleavage in
      various DNA molecules.  5'-end labeling and homochromatographic fingerprinting
      led to the determination of a 17-base-pair sequence spanning the EcoRI site of
      simian virus 40 DNA and a 15-base-pair sequence overlapping the EcoRI site of
      ColE1 plasmid DNA.  Three other DNAs were similarly tested, although extended
      sequences were not determined in these cases.  The EcoRI site was shown to be
      the symmetric, double-stranded equivalent of -N-G-A-A-T-T-C-N-.
AU  - Garfin DE
AU  - Boyer HW
AU  - Goodman HM
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1975 2: 1851-1865.

PMID- 4366956
VI  - 59
DP  - 1974
TI  - Nucleotide sequences at the cleavage sites of two restriction endonucleases from Hemophilus parainfluenzae.
PG  - 108-116
AB  - The nucleotide sequences at the cleavage sites of two restriction endonucleases from
      Hemophilus parainfluenzae, HpaI and HpaII, have been determined.  Terminal labeling at both
      the 3'- and 5'-termini was used to show that the HpaI enzyme cleaves the sequence
      5'...N-G-T-T^pA-A-C-N...3' 3'...N-C-A-Ap^T-T-G-N...5' and the sequence cleaved by the
      HpaII enzyme is 5'...N-C^pC-G-G-N...3' 3'...N-G-G-Cp^C-N...5' where the arrows indicate
      the points of strand scission.
AU  - Garfin DE
AU  - Goodman HM
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1974 59: 108-116.

PMID- 
VI  - 9
DP  - 2014
TI  - Genomic Survey, Gene Expression Analysis and Structural Modeling Suggest Diverse Roles of DNA Methyltransferases in Legumes.
PG  - 14
AB  - DNA methylation plays a crucial role in development through inheritable gene silencing. Plants
      possess three types of DNA methyltransferases (MTases), namely Methyltransferase (MET),
      Chromomethylase (CMT) and Domains Rearranged Methyltransferase (DRM), which maintain
      methylation at CG, CHG and CHH sites. DNA MTases have not been studied in legumes so far.
      Here, we report the identification and analysis of putative DNA MTases in five legumes,
      including chickpea, soybean, pigeonpea, Medicago and Lotus. MTases in legumes could be
      classified in known MET, CMT, DRM and DNA nucleotide methyltransferases (DNMT2) subfamilies
      based on their domain organization. First three MTases represent DNA MTases, whereas DNMT2
      represents a transfer RNA (tRNA) MTase. Structural comparison of all the MTases in plants with
      known MTases in mammalian and plant systems have been reported to assign structural features
      in context of biological functions of these proteins. The structure analysis clearly specified
      regions crucial for protein-protein interactions and regions important for nucleosome binding
      in various domains of CMT and MET proteins. In addition, structural model of DRM suggested
      that circular permutation of motifs does not have any effect on overall structure of DNA
      methyltransferase domain. These results provide valuable insights into role of various domains
      in molecular recognition and should facilitate mechanistic understanding of their function in
      mediating specific methylation patterns. Further, the comprehensive gene expression analyses
      of MTases in legumes provided evidence of their role in various developmental processes
      throughout the plant life cycle and response to various abiotic stresses. Overall, our study
      will be very helpful in establishing the specific functions of DNA MTases in legumes.
AU  - Garg R
AU  - Kumari R
AU  - Tiwari S
AU  - Goyal S
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2014 9: 14.

PMID- 27609931
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Two Strains of Xanthomonas arboricola Isolated from Prunus persica Which Are Dissimilar to Strains That Cause Bacterial Spot Disease on Prunus spp.
PG  - e00974-16
AB  - The draft genome sequences of two strains of Xanthomonas arboricola, isolated from
      asymptomatic peach trees in Spain, are reported here. These strains are
      avirulent and do not belong to the same phylogroup as X. arboricola pv. pruni, a
      causal agent of bacterial spot disease of stone fruits and almonds.
AU  - Garita-Cambronero J
AU  - Palacio-Bielsa A
AU  - Lopez MM
AU  - Cubero J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00974-16.

PMID- 26823958
VI  - 11
DP  - 2016
TI  - Draft genome sequence for virulent and avirulent strains of Xanthomonas arboricola isolated from Prunus spp. in Spain.
PG  - 12
AB  - Xanthomonas arboricola is a species in genus Xanthomonas which is mainly comprised of plant
      pathogens. Among the members of this taxon, X. arboricola pv.
      pruni, the causal agent of bacterial spot disease of stone fruits and almond, is
      distributed worldwide although it is considered a quarantine pathogen in the
      European Union. Herein, we report the draft genome sequence, the classification,
      the annotation and the sequence analyses of a virulent strain, IVIA 2626.1, and
      an avirulent strain, CITA 44, of X. arboricola associated with Prunus spp. The
      draft genome sequence of IVIA 2626.1 consists of 5,027,671 bp, 4,720 protein
      coding genes and 50 RNA encoding genes. The draft genome sequence of strain CITA
      44 consists of 4,760,482 bp, 4,250 protein coding genes and 56 RNA coding genes.
      Initial comparative analyses reveals differences in the presence of structural
      and regulatory components of the type IV pilus, the type III secretion system,
      the type III effectors as well as variations in the number of the type IV
      secretion systems. The genome sequence data for these strains will facilitate the
      development of molecular diagnostics protocols that differentiate virulent and
      avirulent strains. In addition, comparative genome analysis will provide insights
      into the plant-pathogen interaction during the bacterial spot disease process.
AU  - Garita-Cambronero J
AU  - Palacio-Bielsa A
AU  - Lopez MM
AU  - Cubero J
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 12.

PMID- 24903863
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Xanthomonas arboricola pv. pruni Strain Xap33, Causal Agent of Bacterial Spot Disease on Almond.
PG  - e00440-14
AB  - We report the annotated genome sequence of Xanthomonas arboricola pv. pruni strain Xap33,
      isolated from almond leaves showing bacterial spot disease symptoms
      in Spain. The availability of this genome sequence will aid our understanding of
      the infection mechanism of this bacterium as well as its relationship to other
      species of the same genus.
AU  - Garita-Cambronero J
AU  - Sena-Velez M
AU  - Palacio-Bielsa A
AU  - Cubero J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00440-14.

PMID- 3074021
VI  - 74
DP  - 1988
TI  - Properties and subunit structure of EcoRV methyltransferase.
PG  - 73-76
AB  - Meeting Abstract
AU  - Garnett J
AU  - Halford SE
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 73-76.

PMID- 10846226
VI  - 146
DP  - 2000
TI  - Characterization of transposon Tn1549, conferring VanB-type resistance in Enterococcus spp.
PG  - 1481-1489
AB  - Transfer of VanB-type resistance to glycopeptides among enterococci has been reported to be
      associated with the movement of large chromosomal
      genetic elements or of plasmids. The authors report the characterization
      of the 34 kb transposon Tn1549 borne by a plasmid related to pAD1 and
      conferring vancomycin resistance in clinical isolates of Enterococcus spp.
      Tn1549 contained 30 ORFs and appeared to be organized like the Tn916
      family of conjugative transposons into three functional regions: (i) the
      right end, implicated in the excision-integration process; (ii) the
      central part, in which the vanB2 operon replaces the tet(M) gene; and
      (iii) the left extremity, in which eight of the 18 ORFs could be
      implicated in the conjugative transfer.
AU  - Garnier F
AU  - Taourit S
AU  - Glaser P
AU  - Courvalin P
AU  - Galimand M
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2000 146: 1481-1489.

PMID- 12788972
VI  - 100
DP  - 2003
TI  - The complete genome sequence of Mycobacterium bovis.
PG  - 7877-7882
AB  - Mycobacterium bovis is the causative agent of tuberculosis in a range of animal species and
      man, with worldwide annual losses to agriculture of $3
      billion. The human burden of tuberculosis caused by the bovine tubercle
      bacillus is still largely unknown. M. bovis was also the progenitor for
      the M. bovis bacillus Calmette-Guerin vaccine strain, the most widely used
      human vaccine. Here we describe the 4,345,492-bp genome sequence of M.
      bovis AF2122/97 and its comparison with the genomes of Mycobacterium
      tuberculosis and Mycobacterium leprae. Strikingly, the genome sequence of
      M. bovis is >99.95% identical to that of M. tuberculosis, but deletion of
      genetic information has led to a reduced genome size. Comparison with M.
      leprae reveals a number of common gene losses, suggesting the removal of
      functional redundancy. Cell wall components and secreted proteins show the
      greatest variation, indicating their potential role in host-bacillus
      interactions or immune evasion. Furthermore, there are no genes unique to
      M. bovis, implying that differential gene expression may be the key to the
      host tropisms of human and bovine bacilli. The genome sequence therefore
      offers major insight on the evolution, host preference, and pathobiology
      of M. bovis.
AU  - Garnier T et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2003 100: 7877-7882.

PMID- 26679575
VI  - 3
DP  - 2015
TI  - Genome Sequences of 11 Brucella abortus Isolates from Persistently Infected Italian Regions.
PG  - e01402-15
AB  - Bovine brucellosis, typically caused by Brucella abortus, has been eradicated from much of the
      developed world. However, the disease remains prevalent in
      southern Italy, persisting as a public and livestock health concern. We report
      here the whole-genome sequences of 11 isolates from cattle (Bos taurus) and water
      buffalo (Bubalus bubalis) that are representative of the current genetic
      diversity of B. abortus lineages circulating in Italy.
AU  - Garofolo G
AU  - Foster JT
AU  - Drees K
AU  - Zilli K
AU  - Platone I
AU  - Ancora M
AU  - Camma C
AU  - De Massis F
AU  - Calistri P
AU  - Di Giannatale E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01402-15.

PMID- 25477397
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Antibiotic-Resistant Commensal Escherichia coli.
PG  - e00873-14
AB  - Antimicrobial resistance is a significant public health issue. We report here the draft genome
      sequences of three drug-resistant strains of commensal Escherichia
      coli isolated from a single healthy college student. Each strain has a distinct
      genome, but two of the three contain an identical large plasmid with multiple
      resistance genes.
AU  - Garrett M
AU  - Parker J
AU  - Stephens CM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00873-14.

PMID- 20545752
VI  - 12
DP  - 2010
TI  - Metagenomic analyses of novel viruses and plasmids from a cultured environmental sample of hyperthermophilic neutrophiles.
PG  - 2918-2930
AB  - Summary Two novel viral genomes and four plasmids were assembled from an
      environmental sample collected from a hot spring at Yellowstone National
      Park, USA, and maintained anaerobically in a bioreactor at 85 degrees C
      and pH 6. The double-stranded DNA viral genomes are linear (22.7 kb) and
      circular (17.7 kb), and derive apparently from archaeal viruses HAV1 and
      HAV2. Genomic DNA was obtained from samples enriched in filamentous and
      tadpole-shaped virus-like particles respectively. They yielded few
      significant matches in public sequence databases reinforcing, further, the
      wide diversity of archaeal viruses. Several variants of HAV1 exhibit major
      genomic alterations, presumed to arise from viral adaptation to different
      hosts. They include insertions up to 350 bp, deletions up to 1.5 kb, and
      genes with extensively altered sequences. Some result from recombination
      events occurring at low complexity direct repeats distributed along the
      genome. In addition, a 33.8 kb archaeal plasmid pHA1 was characterized,
      encoding a possible conjugative apparatus, as well as three cryptic
      plasmids of thermophilic bacterial origin, pHB1 of 2.1 kb and two closely
      related variants pHB2a and pHB2b, of 5.2 and 4.8 kb respectively.
      Strategies are considered for assembling genomes of smaller genetic
      elements from complex environmental samples, and for establishing possible
      host identities on the basis of sequence similarity to host CRISPR immune
      systems.
AU  - Garrett RA
AU  - Prangishvili D
AU  - Shah SA
AU  - Reuter M
AU  - Stetter KO
AU  - Peng X
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2010 12: 2918-2930.

PMID- 27856581
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Curtobacterium sp. Strain ER1/6, an Endophytic Strain Isolated from Citrus sinensis with Potential To Be Used as a Biocontrol Agent.
PG  - e01264-16
AB  - Herein, we report a draft genome sequence of the endophytic Curtobacterium sp. strain ER1/6,
      isolated from a surface-sterilized Citrus sinensis branch, and it
      presented the capability to control phytopathogens. Functional annotation of the
      ~3.4-Mb genome revealed 3,100 protein-coding genes, with many products related to
      known ecological and biotechnological aspects of this bacterium.
AU  - Garrido LM
AU  - Alves JM
AU  - Oliveira LS
AU  - Gruber A
AU  - Padilla G
AU  - Araujo WL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01264-16.

PMID- 20190051
VI  - 192
DP  - 2010
TI  - Complete genome sequence of Bifidobacterium animalis subsp. lactis BB-12, a widely consumed probiotic strain.
PG  - 2467-2468
AB  - Bifidobacterium animalis subsp. lactis BB-12 is a commercially available probiotic strain used
      throughout the world in a variety of functional
      foods and dietary supplements. The benefits of BB-12 have been documented
      in a number of independent clinical trials. Determination of the complete
      genome sequence reveals a single circular chromosome of 1,942,198 bp with
      1,642 predicted protein-encoding genes, 4 rRNA operons, and 52 tRNA genes.
      Knowledge of this sequence will lead to insight into the specific features
      which give this strain its probiotic properties.
AU  - Garrigues C
AU  - Johansen E
AU  - Pedersen MB
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 2467-2468.

PMID- Not carried by PubMed...
VI  - 5
DP  - 1995
TI  - Molecular genetics of bacteriophage and natural phage defense systems in the genus Lactococcus.
PG  - 905-947
AB  - Bacteriophage infection of starter cultures used in a range of milk fermentation processes,
      particularly those involving Lactococcus lactis, poses a significant problem in industrial
      practice.  The application of genetic and molecular technologies to the study of lactococcal
      bacteriophages has proven to be very rewarding in terms of understanding the nature of phage
      with respect to their physical and genetic organisation.  The availability of the full genomic
      sequence of a number of phages provides an unambiguous basis for determining the relationship
      between them, for elucidating their evolutionary progression and will also yield strategies
      for obstructing successful phage proliferation on previously sensitive hosts.  The genetic
      analysis of plage/host interactions has also highlighted the presence of natural defense
      systems (e.g. adsorption blocking, inhibition of phage DNA entry, restriction modification and
      abortive infection) in lactococci.  A number of restriction modification systems and abortive
      infection mechanisms have been characterized at a molecular level and the genes involved have
      been cloned and sequenced.  Plasmid-encoded phage resistance mechanisms can be exploited to
      generate strains which can successfully counter phage proliferation and will provide a basis
      for understanding the complex interactions between phages and their target hosts at a
      molecular level.
AU  - Garvey P
AU  - van Sinderen D
AU  - Twomey DP
AU  - Hill C
AU  - Fitzgerald GF
PT  - Journal Article
TA  - Int. Dairy Journal
JT  - Int. Dairy Journal
SO  - Int. Dairy Journal 1995 5: 905-947.

PMID- 25858850
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the First Hypermucoviscous Klebsiella variicola Clinical Isolate.
PG  - e01352-14
AB  - An antibiotic-susceptible and hypermucoviscous clinical isolate of Klebsiella variicola (K.
      variicola 8917) was obtained from the sputum of an adult patient.
      This work reports the complete draft genome sequence of K. variicola 8917 with
      103 contigs and an annotation that revealed a 5,686,491-bp circular chromosome
      containing a total of 5,621 coding DNA sequences, 65 tRNA genes, and an average
      G+C content of 56.98%.
AU  - Garza-Ramos U
AU  - Silva-Sanchez J
AU  - Barrios H
AU  - Rodriguez-Medina N
AU  - Martinez-Barnetche J
AU  - Andrade V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01352-14.

PMID- 27389261
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a Hypermucoviscous Extended-Spectrum-beta-Lactamase-Producing Klebsiella quasipneumoniae subsp.  similipneumoniae Clinical Isolate.
PG  - e00475-16
AB  - A clinical isolate of extended-spectrum-beta-lactamase-producing Klebsiella quasipneumoniae
      subsp. similipneumoniae 06-219 with hypermucoviscosity phenotypes
      obtained from a urine culture of an adult patient was used for whole-genome
      sequencing. Here, we report the draft genome sequences of this strain, consisting
      of 53 contigs with an ~5.6-Mb genome size and an average G+C content of 57.36%.
      The annotation revealed 6,622 coding DNA sequences and 77 tRNA genes.
AU  - Garza-Ramos U
AU  - Silva-Sanchez J
AU  - Catalan-Najera J
AU  - Barrios H
AU  - Rodriguez-Medina N
AU  - Garza-Gonzalez E
AU  - Cevallos MA
AU  - Lozano L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00475-16.

PMID- 29519827
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of a Multidrug- and Colistin-Resistant mcr-1-Producing Escherichia coli Isolate from a Swine Farm in Mexico.
PG  - e00102-18
AB  - A colistin-resistant mcr-1-carrying Escherichia coli strain, RC2-007, was isolated from a
      swine farm in Mexico. This extraintestinal and uropathogenic
      strain of E. coli belongs to serotype O89:H9 and sequence type 744. Assembly and
      annotation resulted in a 4.9-Mb draft genome that revealed the presence of
      plasmid-mediated mcr-1-ISApI1 genes as part of a prophage.
AU  - Garza-Ramos U
AU  - Tamayo-Legorreta E
AU  - Arellano-Quintanilla DM
AU  - Rodriguez-Medina N
AU  - Silva-Sanchez J
AU  - Catalan-Najera J
AU  - Rocha-Martinez MK
AU  - Bravo-Diaz MA
AU  - Alpuche-Aranda C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00102-18.

PMID- 29051233
VI  - 5
DP  - 2017
TI  - High-Quality Whole-Genome Sequences of the Oligo-Mouse-Microbiota Bacterial Community.
PG  - e00758-17
AB  - The Oligo-Mouse-Microbiota (Oligo-MM12) is a community of 12 mouse intestinal bacteria to be
      used for microbiome research in gnotobiotic mice. We present here
      the high-quality whole genome sequences of the Oligo-MM12 strains, which were
      obtained by combining the accuracy of the Illumina platforms with the long reads
      of the PacBio technology.
AU  - Garzetti D
AU  - Brugiroux S
AU  - Bunk B
AU  - Pukall R
AU  - McCoy KD
AU  - Macpherson AJ
AU  - Stecher B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00758-17.

PMID- 29798919
VI  - 6
DP  - 2018
TI  - Complete Genome Sequencing of the Mouse Intestinal Isolate Escherichia coli Mt1B1.
PG  - e00426-18
AB  - Escherichia coli Mt1B1, a mouse isolate, is a facultative anaerobic bacterium which was shown
      to counteract Salmonella enterica serovar Typhimurium infection
      in a mouse model. In the present study, we describe the complete genome sequence
      of E. coli Mt1B1, composed of a 5.1-Mb chromosome and a 62.6-kb plasmid.
AU  - Garzetti D
AU  - Eberl C
AU  - Stecher B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00426-18.

PMID- 23846271
VI  - 1
DP  - 2013
TI  - Genome Sequences of Four Yersinia enterocolitica Bioserotype 4/O:3 Isolates from  Mammals.
PG  - e00466-13
AB  - We report here the complete genome sequences of four European Yersinia enterocolitica
      mammalian isolates of bioserotype 4/O:3. The genomes have an
      average size of 4.50 Mb, a G+C content of 47%, and between 4,231 and 4,330 coding
      sequences (CDSs). No relevant differences were detected by genome comparison
      between mammalian and human isolates.
AU  - Garzetti D
AU  - Heesemann J
AU  - Rakin A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00466-13.

PMID- 27081140
VI  - 4
DP  - 2016
TI  - Genome Sequence of Pseudomonas sp. HUK17, Isolated from Hexachlorocyclohexane-Contaminated Soil.
PG  - e00275-16
AB  - Pseudomonassp. HUK17 has been isolated from hexachlorocyclohexane (HCH) long-term contaminated
      soil. The genome of strain HUK17 was sequenced to elucidate its
      adaptation toward HCH and to evaluate the presence of pesticide degradation
      pathways. Here, we report the annotated draft genome sequence (~2.6 Mbp) of this
      strain.
AU  - Gasc C
AU  - Richard JY
AU  - Peyret P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00275-16.

PMID- 27081139
VI  - 4
DP  - 2016
TI  - Genome Sequence of Staphylococcus aureus Strain HUK16, Isolated from Hexachlorocyclohexane-Contaminated Soil.
PG  - e00274-16
AB  - Staphylococcus aureusstrain HUK16 has been isolated from hexachlorocyclohexane (HCH)-long-term
      contaminated soil. The genome of strain HUK16 was sequenced to
      understand the genetic basis of its adaptation to HCH and to find the potential
      metabolic pathways allowing it to degrade the pesticide. Here, we report the
      annotated draft genome sequence (~2.7 Mbp) of this strain.
AU  - Gasc C
AU  - Richard JY
AU  - Peyret P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00274-16.

PMID- 27081138
VI  - 4
DP  - 2016
TI  - Genome Sequence of Bacillus subtilis Strain HUK15, Isolated from Hexachlorocyclohexane-Contaminated Soil.
PG  - e00273-16
AB  - Bacillus subtilisstrain HUK15 has been isolated from hexachlorocyclohexane
      (HCH)-long-term-contaminated soil. The genome of strain HUK15 was sequenced to
      investigate its adaptation toward HCH and its potential capability to degrade the
      pesticide. Here, we report the annotated draft genome sequence (~4.3 Mbp) of this
      strain.
AU  - Gasc C
AU  - Richard JY
AU  - Peyret P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00273-16.

PMID- 
VI  - 276
DP  - 2009
TI  - Tetrameric restriction enzyme Cfr42I belongs to the GIY-YIG nuclease family.
PG  - 140-141
AB  - The GIY-YIG nuclease domain was originally identified in homing endonucleases and enzymes
      involved in DNA repair and recombination.  Despite wide distribution of this domain,
      biochemical and structural studies of GIY-YIG proteins are often hampered by their
      multi-domain organization and complex functional requirements.  Many of the GIY-YIG family
      enzymes are functional as monomers.  We show that the Cfr42I restriction endonuclease which
      belongs to the GIY-YIG family and recognizes the symmetric sequence 5'-CCGC/GG-3' ('/'
      indicates the cleavage site) is a tetramer in solution.  Moreover, biochemical and kinetic
      studies demonstrate that the Cfr42I tetramer is catalytically active only upon simultaneous
      binding of two copies of its recognition sequence.  In that respect Cfr42I resembles the
      homotetrameric Type IIF restriction enzymes that belong to the distinct PD-D/E)XK nuclease
      superfamily.  Unlike the PD-(D/E)XK enzymes, the GIY-YIG nuclease Cfr42I accommodates an
      extrmely wide selection of metal ion cofactors, including Mg2+, Mn2+, Co2+, Zn2+, Ni2+, Cu2+
      and Ca2+.  To our knowledge, Cfr42I is the first tetrameric GIY-YIG family enzyme.  Similar
      structural arrangement and phenotypes displayed by restriction enzymes belonging to the
      PD-(D/E)XK and GIY-YIG nuclease families point to the functional significance of
      tetramerization.  In order to understand structure-function relationship within Cfr42I
      restriction enzyme we aim to determine its 3D structure by X-ray crystallography.
AU  - Gasiunas G
AU  - Sasnaukas G
AU  - Tamulaitis G
AU  - Siksnys V
PT  - Journal Article
TA  - FEBS J.
JT  - FEBS J.
SO  - FEBS J. 2009 276: 140-141.

PMID- 18086711
VI  - 36
DP  - 2008
TI  - Tetrameric restriction enzymes: expansion to the GIY-YIG nuclease family.
PG  - 938-949
AB  - The GIY-YIG nuclease domain was originally identified in homing endonucleases and enzymes
      involved in DNA repair and recombination. Many of the GIY-YIG family enzymes are functional as
      monomers. We show here that the Cfr42I restriction endonuclease which belongs to the GIY-YIG
      family and recognizes the symmetric sequence 5'-CCGC/GG-3' ('/' indicates the cleavage
      site) is a tetramer in solution. Moreover, biochemical and kinetic studies provided here
      demonstrate that the Cfr42I tetramer is catalytically active only upon simultaneous binding of
      two copies of its recognition sequence. In that respect Cfr42I resembles the homotetrameric
      Type IIF restriction enzymes that belong to the distinct PD-(E/D)XK nuclease superfamily.
      Unlike the PD-(E/D)XK enzymes, the GIY-YIG nuclease Cfr42I accommodates an extremely wide
      selection of metal-ion cofactors, including Mg(2+), Mn(2+), Co(2+), Zn(2+), Ni(2+), Cu(2+) and
      Ca(2+). To our knowledge, Cfr42I is the first tetrameric GIY-YIG family enzyme. Similar
      structural arrangement and phenotypes displayed by restriction enzymes of the PD-(E/D)XK and
      GIY-YIG nuclease families point to the functional significance of tetramerization.
AU  - Gasiunas G
AU  - Sasnauskas G
AU  - Tamulaitis G
AU  - Urbanke C
AU  - Razaniene D
AU  - Siksnys V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2008 36: 938-949.

PMID- Not included in PubMed...
VI  - 38
DP  - 1983
TI  - Specific endonuclease Sau3239I from Streptomyces aureofaciens CCM 3239.
PG  - 315-319
AB  - In the research of relations of plasmid DNA to antibiotic production in
      Streptomyces aureofaciens also the prototrophic chlortetracycline (CTC)
      producing strain of S. aureofaciens CCM 3239 was studied.  In this strain the
      presence of plasmid DNA was proven (unpublished data).  After elimination of
      the plasmid there were considerations on using this strain as the acceptor of
      DNA transformation.  The possibility of detection of a restriction-modifying
      system on this extrachromosomal element as found in eubacteria, (Arber, 1974)
      remained open.  Detection of restrictase activity in S. aureofaciens CCM 3239
      was interest as restriction endonucleases were isolated from more than 15 types
      of Streptomyces (Roberts, 1982).  Restriction endonuclease, type II, was also
      found in the non-producing mutant of S. aureofaciens IKA 18/4 (Timko, et al.,
      1978).  The substrate specificity and the cleavage site of this enzyme, SauI,
      is described in the paper by Timko et al., (1981).
AU  - Gasperik J
AU  - Godany A
AU  - Hostinova E
AU  - Zelinka J
PT  - Journal Article
TA  - Biologia (Bratisl)
JT  - Biologia (Bratisl)
SO  - Biologia (Bratisl) 1983 38: 315-319.

PMID- 25767220
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Halomonas sp. KHS3, a Polyaromatic Hydrocarbon-Chemotactic Strain.
PG  - e00020-15
AB  - The draft genome sequence of Halomonas sp. KHS3, isolated from seawater from Mar  del Plata
      harbor, is reported. This strain is able to grow using aromatic
      compounds as a carbon source and shows strong chemotactic response toward these
      substrates. Genes involved in motility, chemotaxis, and degradation of aromatic
      hydrocarbons were identified.
AU  - Gasperotti AF
AU  - Studdert CA
AU  - Revale S
AU  - Herrera SMK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00020-15.

PMID- 9628368
VI  - 379
DP  - 1998
TI  - Escherichia coli bacteriophage T1 DNA methyltransferase appears to interact with Escherichia coli enolase.
PG  - 621-623
AB  - Infection of Escherichia coli cells with bacteriophage T1 induces synthesis of a
      bacteriophage-specific DNA methyltransferase with a specificity for adenine residues in the
      sequence 5'-GATC-3'.  Purification of M.EcoT1 allowed the determination of the coding
      sequence of the gene.  The peptide of the entire coding sequence was over-expressed as a
      histidine-hexapeptide tagged protein in E. coli.  Affinity purification using a Ni2+ chelating
      (Ni-NTA) resin yielded a recombinant enzyme with almost the same enzymatic properties as the
      protein purified from T1 infected E. coli cells.  Interestingly, in both purification
      procedures, a protein with a molecular weight of 50000 was found to copurify with M.EcoT1.
      The N-terminal amino acid sequence identified these proteins in both cases as E. coli enolase.
AU  - Gassner C
AU  - Schneider-Scherzer ES
AU  - Lottspeich F
AU  - Schweiger M
AU  - Auer B
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1998 379: 621-623.

PMID- 9348106
VI  - 378
DP  - 1997
TI  - The recognition of methylated DNA by the GTP-dependent restriction endonuclease McrBC resides in the N-terminal domain of McrB.
PG  - 975-982
AB  - McrBC is a GTP-dependent restriction endonuclease of E. coli K12, selectively directed against
      DNA containing modified cytosine residues.  McrB, one of its components, is responsible for
      the binding and, together with McrC, for the cleavage of DNAs containing two 5'-PumC sites
      separated by 40-80 base pairs.  Gel retardation assays with wild-type and mutant McrB reveal
      that (i) single 5'-PumC sites in DNA can be sufficient to elicit binding by McrB.  Binding to
      such substrates is, however, weak and strongly dependent on the sequence context of PumC
      sites.  (ii) Strong DNA binding (Kass ~ 10^7M-1) is dependent on the presence of at least two
      PumC sites, even if they are separated by less than 40 bp, and is modulated by the sequence
      context (-AmCCGGT->-AmCTc/gAGT->-AGGmCCT->-AAGmCTT-).  (iii) DNA binding by McrB is
      accompanied by formation of distinct multiple complexes whose distribution is modulated by
      GTP. (iv) McrC, which cannot bind DNA by itself, moderately stimulates the DNA binding of McrB
      and converts McrB-DNA complexes to large aggregates.  (v) Deletion of the C-terminal half of
      McrB, which harbors the three consensus sequences characteristic for guanine nucleotide
      binding proteins, leads to protein inactive in GTP binding and/or hydrolysis and in
      McrC-assisted DNA cleavage; the protein, however, remains fully competent in DNA binding.
      (vi) Mutations in McrB which lead to a reduction in GTP binding and/or hydrolysis can affect
      DNA binding, suggesting that the two activities are coupled in the full-length protein.
AU  - Gast FU
AU  - Brinkmann T
AU  - Pieper U
AU  - Kruger T
AU  - Noyer-Weidner M
AU  - Pingoud A
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1997 378: 975-982.

PMID- 29599151
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Two Epidemic OXA-48-Producing Klebsiella pneumoniae Clinical Strains Isolated during a Large Outbreak in Spain.
PG  - e00026-18
AB  - We report here the draft genome sequences of Klebsiella pneumoniae strains Kp1803 and Kp3380
      isolated during a large outbreak at A Coruna Hospital in Spain. The
      final genome assemblies for Kp1803 and Kp3380 comprise approximately 6.6 and 6.1
      Mb, respectively, and both strains have G+C contents of 57.2%.
AU  - Gato E
AU  - Alvarez-Fraga L
AU  - Vallejo JA
AU  - Rumbo-Feal S
AU  - Martinez-Guitian M
AU  - Beceiro A
AU  - Poza M
AU  - Bou G
AU  - Perez A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00026-18.

PMID- 9830015
VI  - 273
DP  - 1998
TI  - A short DNA methyltransferase isoform restores methylation in vivo.
PG  - 32725-32729
AB  - Two murine DNA methyltransferase isoforms (MTases) have been observed, a longer form in
      somatic and embryonic stem cells and a shorter form in oocytes and preimplantation embryos.
      While the longer MTase is associated with maintenance methyltransferase activity in
      replicating cells, little is known about the shorter form.  We present genetic and biochemical
      evidence that both isoforms are expressed from the same Dnmt1 gene by using different
      translation initiation sites in exons 1 and 4.  We further demonstrate that the shorter
      isoform can functionally rescue Dnmt1 null ES cells that have a hypomethylated genome.  These
      rescued ES cells differentiate in vivo into a variety of cell types, unlike the Dnmt1 null ES
      cells that die upon induction of differentiation.  These results show that the shorter isoform
      can substitute for the longer maintenance MTase in ES and differentiated cells.  Our data
      further indicate that the shorter MTase isoform found in oocytes is fully functional in vivo
      and may play an active role in the regulation of DNA methylation and the establishment of
      imprinting patterns.
AU  - Gaudet F
AU  - Talbot D
AU  - Leonhardt H
AU  - Jaenisch R
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1998 273: 32725-32729.

PMID- 29976612
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of the Bacterium Serratia marcescens SGAir0764, Isolated from Singapore Air.
PG  - e00637-18
AB  - Serratia marcescens strain SGAir0764 was isolated from a tropical air sample collected in
      Singapore. The complete genome, sequenced on the PacBio RS II
      platform, consists of one chromosome with 5.1 Mb and one plasmid with 76.4 kb.
      Genome annotation predicts 4,723 protein-coding genes, 89 tRNAs, and 22 rRNAs.
AU  - Gaultier NE et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00637-18.

PMID- 29976611
VI  - 6
DP  - 2018
TI  - Genome Sequence of Geobacillus thermoleovorans SGAir0734, Isolated from Singapore Air.
PG  - e00636-18
AB  - The thermophilic bacterium Geobacillus thermoleovorans was isolated from a tropical air sample
      collected in Singapore. The genome was sequenced on the
      PacBio RS II platform and consists of one chromosome with 3.6 Mb and one plasmid
      with 75 kb. The genome comprises 3,509 protein-coding genes, 88 tRNAs, and 27
      rRNAs.
AU  - Gaultier NE et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00636-18.

PMID- 25814591
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of the Hypervirulent Bacterium Clostridium difficile Strain G46, Ribotype 027.
PG  - e00073-15
AB  - Clostridium difficile is one of the leading causes of antibiotic-associated diarrhea in health
      care facilities worldwide. Here, we report the genome sequence
      of C. difficile strain G46, ribotype 027, isolated from an outbreak in Glamorgan,
      Wales, in 2006.
AU  - Gaulton T
AU  - Misra R
AU  - Rose G
AU  - Baybayan P
AU  - Hall R
AU  - Freeman J
AU  - Turton J
AU  - Picton S
AU  - Korlach J
AU  - Gharbia S
AU  - Shah H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00073-15.

PMID- 25349630
VI  - 6
DP  - 2014
TI  - Phase-variable restriction/modification systems are required for Helicobacter pylori colonization.
PG  - 35
AB  - Background: One mechanism utilized by bacterial pathogens for host adaptation and immune
      evasion is the generation of phenotypic diversity by the phasevarion that results from the
      differential expression of a suite of genes regulated by the activity of a phase-variable
      methyltransferase within a restriction modification (RM) system. Phasevarions are active in
      Helicobacter pylori, however there have been no studies investigating the significance of
      phase-variable RM systems on host colonization.Methods: Two mutant types incapable of phase
      variation were constructed; a clean deletion mutant ('DEL') and a mutant ('ON') where the
      homopolymeric repeat was replaced with a non-repeat synonymous sequence, resulting in
      expression of the full-length protein. The resulting mutants were assessed for their
      colonisation ability in the mouse model.Results: Five phase-variable genes encoding either
      methyltransferases or members of RM systems were found in H. pylori OND79. Our mutants fell
      into three categories; 1, those with little effect on colonization, 2, those where expression
      of the full-length protein was detrimental, 3, those where both mutations were
      detrimental.Conclusions: Our results demonstrated that phase-variable methyltransferases are
      critical to H. pylori colonization, suggesting that genome methylation and generation of
      epigenetic diversity is important for colonization and pathogenesis. The third category of
      mutants suggests that differential genome methylation status of H. pylori cell populations,
      achieved by the phasevarion, is essential for host adaptation. Studies of phase-variable RM
      mutants falling in the two other categories, not strictly required for colonization, represent
      a future perspective to investigate the role of phasevarion in persistence of H. pylori.
AU  - Gauntlett JC
AU  - Nilsson H-O
AU  - Fulurija A
AU  - Marshall BJ
AU  - Benghezal M
PT  - Journal Article
TA  - Gut Pathog.
JT  - Gut Pathog.
SO  - Gut Pathog. 2014 6: 35.

PMID- 29097470
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the First Confirmed Isolate of Multidrug-Resistant Mycobacterium tuberculosis in Tasmania.
PG  - e01230-17
AB  - The spread of multidrug-resistant (MDR) tuberculosis (TB) has become a major global challenge.
      In 2016, Tasmania recorded its first known incidence of MDR-TB.
      Here, we report the draft whole-genome sequence of the Mycobacterium tuberculosis
      isolate from this case, TASMDR1, and describe single-nucleotide polymorphisms
      associated with its drug resistance.
AU  - Gautam SS
AU  - Mac Aogain M
AU  - O'Toole RF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01230-17.

PMID- 2036685
VI  - 19
DP  - 1991
TI  - A group I intron in the chloroplast large subunit rRNA gene of Chlamydomonas eugametos encodes a double-strand endonuclease that cleaves the homing site of this intron.
PG  - 43-47
AB  - During interspecific crosses between Chlamydomonas eugametos and Chlamydomonas moewusii, an
      optional group I intron of 955 base pairs (CeLSU 5) in the C. eugametos chloroplast large
      subunit rRNA gene undergoes a duplicative transposition event which is associated with
      frequent co-conversion of flanking cpDNA sequences. In the present study, we show that the
      basic protein of 218 amino acids encoded by CeLSU 5 could mediate the phenomenon of intron
      transposition, also called intron homing. We overexpressed the ORF specifying this protein in
      E. coli using expression vectors that contain a C. moewusii cpDNA sequence encompassing the
      intron homing site. The expression product was found to exhibit a double-strand DNA
      endonuclease activity that is specific for the homing site. This activity was detected in vivo
      by self linearization of the expression plasmids.
AU  - Gauthier A
AU  - Turmel M
AU  - Lemieux C
PT  - Journal Article
TA  - Curr. Genet.
JT  - Curr. Genet.
SO  - Curr. Genet. 1991 19: 43-47.

PMID- 28254983
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Pseudomonas fluorescens ML11A, an Endogenous Strain from Brook Charr with Antagonistic Properties against Aeromonas salmonicida subsp.  salmonicida.
PG  - e01716-16
AB  - Pseudomonas fluorescens ML11A, isolated from brook charr, showed a strong in vitro inhibitory
      effect against Aeromonas salmonicida subsp. salmonicida, a
      bacterial fish pathogen. Its genome harbors gene clusters for siderophore and
      bacteriocin biosynthesis and shares 99% whole-genome identity with P. fluorescens
      A506, a biological control strain used in agriculture.
AU  - Gauthier J
AU  - Charette SJ
AU  - Derome N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01716-16.

PMID- 562751
VI  - 80
DP  - 1977
TI  - Analysis of calif-thymus satellite DNA:  evidence for specific methylation of cytosine in C-G sequences.
PG  - 175-183
AB  - Digestion of purified calf thymus satellite I (density = 1.714 g/cm3) with a
      series of restriction enzymes shows that modification in this satellite occurs
      preferentially in the sequence C-G. This was also shown to be the case in the
      other satellites and in bulk chromosomal calf thymus DNA.  Cloning of purified
      satellite I DNA in Escherichia coli makes sites, previously modified, available
      for cutting with certain restriction enzymes.  All these new sites contain the
      sequence C-G.  High-resolution mass spectroscopy establishes that the
      satellites contain a low concentration of 5-methylcytosine.  This infers that
      methylation which inhibits restriction enzyme cutting must occur preferentially
      in the sequence C-G.  Hybridization of cRNA of cloned satellite I DNA with the
      satellites III (density = 1.706 g/cm3) and IV (density = 1.710 g/cm3) shows
      that there is no or little sequence homology between these satellites.
      Digestion of calf thymus satellite I DNA with endoR.EcoRI and subsequent
      hybridization studies with the fragments shows two EcoRI fragments in addition
      to the usual 1400-base-pair EcoRI repeat unit.
AU  - Gautier F
AU  - Bunemann H
AU  - Grotjahn L
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1977 80: 175-183.

PMID- 16347351
VI  - 53
DP  - 1987
TI  - Plasmid-determined systems for restriction and modification activity and abortive infection in Streptococcus cremoris.
PG  - 923-927
AB  - Streptococcus cremoris strain IL964 possessed a restriction and modification
      (R/M) activity which resulted in a bacteriophage efficiency of plating 5x10-6.
      Phage sensitivity of protoplast-induced plasmid-cured derivatives indicated
      that two plasmids called pIL103 (5.7 kiobases) and pIL107 (15.2 kilobases) were
      each coding for one R/M system.  Plasmid pIL103-encoded R/M was ascertained by
      transfer into the plasmid-free, R-/M- strain IL1403 of S. lactis, using
      protoplast cotransformation.  This procedure failed for pIL107 because of some
      degree of incompatibility between pIL107 and the indicator plasmid pHV1301 used
      in cotransformation experiments.  We also observed that plasmid pIL105 (8.7
      kilobases) which showed no incidence of phage sensitivity in the parental
      strain IL964, mediated abortive infection in strain IL1403.  In 97% of the
      infected cells, the phage infection was abortive, while in the remaining 3%
      phages were produced with a decreased burst size (50 instead of 180).
AU  - Gautier M
AU  - Chopin M-C
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1987 53: 923-927.

PMID- Not included in PubMed...
VI  - 46
DP  - 1987
TI  - Cloning of three plasmid-determined systems for restriction/modification and abortive infection.
PG  - 44
AB  - We have previously described three plasmids encoding phage-defense mechanisms in Streptococcus
      lactis and S. cremoris. Plasmids pIL7 (33 kilobases) and pIL103 (5.7 kb) each encodes for a
      restriction/modification (R/M) system and pIL105 (9.5 kb) encodes phage abortive infection. We
      cloned each of these mechanisms into the plasmid-free, S. lactis strain IL1403. The entire
      small pIL103 plasmid was inserted into the single EcoRI site of vector plasmid pIL204.
      Recombinant DNA molecules formed were used in transformation of S. lactis IL1403 protoplasts.
      Transformants selected for the pIL204-conferred erythromycin resistance were checked for
      resistance to phage 66. All the phage-resistant clones harbored pIL103::pIL204 recombinant
      DNA. In some cases deletions occured allowing the isolation of a 3.5 kb fragment carrying
      genes coding for R/M activity. In the same way, the entire pIL105 plasmid together with
      abortive infection activity was cloned into the single XbaI site of plasmid vector pIL252. A
      6.5 kb fragment carrying genes coding for R/M activity was isolated from the large pIL7
      plasmid following partial digestion with Sau3A and insertion of the fragments into the single
      BamHI site of plasmid vector pIL252. Experiments are currently in progress to bring together
      the 3 cloned fragments on the same vector plasmid in order to stack phage defense mechanisms
      and construct strains improved in their phage resistance.
AU  - Gautier M
AU  - Veaux M
AU  - Chopin M-C
PT  - Journal Article
TA  - FEMS Microbiol. Rev.
JT  - FEMS Microbiol. Rev.
SO  - FEMS Microbiol. Rev. 1987 46: 44.

PMID- 22457715
VI  - 7
DP  - 2012
TI  - Origin of the Diversity in DNA Recognition Domains in Phasevarion Associated modA Genes of Pathogenic Neisseria and Haemophilus influenzae.
PG  - e32337
AB  - Phase variable restriction-modification (R-M) systems have been identified in a range of
      pathogenic bacteria. In some it has been
      demonstrated that the random switching of the mod (DNA
      methyltransferase) gene mediates the coordinated expression of multiple
      genes and constitutes a phasevarion (phase variable regulon). ModA of
      Neisseria and Haemophilus influenzae contain a highly variable, DNA
      recognition domain (DRD) that defines the target sequence that is
      modified by methylation and is used to define modA alleles. 18 distinct
      modA alleles have been identified in H. influenzae and the pathogenic
      Neisseria. To determine the origin of DRD variability, the 18 modA DRDs
      were used to search the available databases for similar sequences.
      Significant matches were identified between several modA alleles and
      mod gene from distinct bacterial species, indicating one source of the
      DRD variability was via horizontal gene transfer. Comparison of DRD
      sequences revealed significant mosaicism, indicating exchange between
      the Neisseria and H. influenzae modA alleles. Regions of high inter-and
      intra-allele similarity indicate that some modA alleles had undergone
      recombination more frequently than others, generating further
      diversity. Furthermore, the DRD from some modA alleles, such as modA12,
      have been transferred en bloc to replace the DRD from different modA
      alleles.
AU  - Gawthorne JA
AU  - Beatson SA
AU  - Srikhanta YN
AU  - Fox KL
AU  - Jennings MP
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2012 7: e32337.

PMID- 27979947
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Cloacibacterium normanense NRS-1 Isolated from Municipal Wastewater.
PG  - e01397-16
AB  - Cloacibacterium normanense is a Gram-negative bacterium recovered from untreated  human
      wastewater. Given its high abundance in wastewater and its apparent absence
      in human stool, it may contribute to biological phosphate removal. Here, we
      perform a whole-genome sequence of C. normanense NRS-1(T) and examine particular
      features of this draft genome.
AU  - Gay NR
AU  - Fleming E
AU  - Oh J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01397-16.

PMID- Not carried by PubMed...
VI  - 19
DP  - 1982
TI  - Synthesis of a specific sequence of DNA using restriction enzymes.
PG  - 526
AB  - The restriction enzyme MboII recognizes the DNA sequence GAAGA and cleaves the
      DNA eight bases downstream from this site, leaving a single 3' protruding base.
      There are no apparent sequence requirements in the stretch of DNA between the
      recognition sequence and the point of cleavage.  Using this property, a segment
      of DNA from one fragment can be transferred to another fragment.
AU  - Gayle R
AU  - Bennett G
PT  - Journal Article
TA  - Miami BioTechnology Winter Symposium
JT  - Miami BioTechnology Winter Symposium
SO  - Miami BioTechnology Winter Symposium 1982 19: 526.

PMID- 2820843
VI  - 54
DP  - 1987
TI  - Formation of MboII vectors and cassettes using asymmetric MboII linkers.
PG  - 221-228
AB  - Class-IIS restriction endonucleases such as MboII cleave DNA at a specified
      distance away from their recognition sequences.  This feature was exploited to
      cleave DNA at previously inaccessible locations by preparing special asymmetric
      linker/adapters containing the MboII recognition sequence.  These could be
      joined to DNA fragments and subsequently cleaved by MboII.  Attachment of a 3'
      phosphate to one of the two different oligodeoxynucleotides comprising the
      asymmetric duplex prevented ligation at the improper end of the linker.
      Plasmids were contructed containing a unique BamHI or BclI site between the
      recognition and cleavage site of MboII.  These sites were used to introduce a
      foreign fragment into the plasmid at a position permitting MboII to cleave
      within the newly inserted fragment.  Once cleaved at the unique MboII site,
      another DNA fragment was inserted.  DNA was thus inserted at a sequence not
      previously accessible to specific cleavage by a restriction enzyme.  A cassette
      containing an identifiable marker, the lac operator, between two oppositely
      oriented MboII/BamHI linkers was made and tested in a random insertion linker
      mutagenesis experiment.
AU  - Gayle RB
AU  - Auger EA
AU  - Gough GR
AU  - Gilham PT
AU  - Bennett GN
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1987 54: 221-228.

PMID- 24072859
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Vancomycin-Heteroresistant Staphylococcus epidermidis Strain UC7032, Isolated from Food.
PG  - e00709-13
AB  - Staphylococcus epidermidis strain UC7032 was isolated from ready-to-eat cured meat and is
      heteroresistant to glycopeptide antibiotics. The draft whole-genome
      analysis revealed that this strain shows common characteristics typical of
      strains that are involved in nosocomial infections.
AU  - Gazzola S
AU  - Pietta E
AU  - Bassi D
AU  - Fontana C
AU  - Puglisi E
AU  - Cappa F
AU  - Cocconcelli PS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00709-13.

PMID- 26450721
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Streptomyces ahygroscopicus subsp. wuyiensis CK-15, Isolated from Soil in Fujian Province, China.
PG  - e01125-15
AB  - We report the first high-quality draft genome sequence of an antibiotic (wuyiencin)-producing
      strain, Streptomyces ahygroscopicus subsp. wuyiensis CK-15, isolated from soil samples
      collected from Fujian Province, China. The 9.41-Mb genome comprises 8,311 protein-coding
      sequences, encodes 89 structural RNAs, and  shows a G+C content of 72.25%.
AU  - Ge B
AU  - Liu Y
AU  - Liu B
AU  - Zhang K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01125-15.

PMID- 21742880
VI  - 193
DP  - 2011
TI  - Draft genome sequence of Gordonia neofelifaecis NRRL B-59395, a cholesterol-degrading actinomycete.
PG  - 5045-5046
AB  - We report a draft sequence of the genome of Gordonia neofelifaecis NRRL B-59395, a
      cholesterol-degrading actinomycete isolated from fresh faeces
      of a clouded leopard (Neofelis nebulosa). As predicted, the reported
      genome contains several gene clusters for cholesterol degradation. This is
      the second available genome sequence of the family Gordoniaceae.
AU  - Ge F
AU  - Li W
AU  - Chen G
AU  - Liu Y
AU  - Zhang G
AU  - Yong B
AU  - Wang Q
AU  - Wang N
AU  - Huang Z
AU  - Li W
AU  - Wang J
AU  - Wu C
AU  - Xie Q
AU  - Liu G
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5045-5046.

PMID- 26893433
VI  - 4
DP  - 2016
TI  - High-Quality Draft Genome Sequence of Leucobacter sp. Strain G161, a Distinct and Effective Chromium Reducer.
PG  - e01760-15
AB  - Here, we report the genome sequence for Leucobacter sp. strain G161 due to its distinct and
      effective hexavalent chromium reduction under aerobic growth
      conditions, followed by facultative anaerobic incubation. The draft genome
      sequence of Leucobacter sp. G161 comprises 3,554,188 bp, with an average G+C
      content of 65.3%, exhibiting 3,341 protein-coding genes and 55 predicted RNA
      genes.
AU  - Ge S
AU  - Ai W
AU  - Dong X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01760-15.

PMID- 23472221
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of the Industrial Strain Gluconobacter oxydans H24.
PG  - e00003-13
AB  - is characterized by its ability to incompletely oxidize carbohydrates and alcohols. The high
      yields of its oxidation products and complete secretion into
      the medium make it important for industrial use. We report the finished genome
      sequence of H24, an industrial strain with high l-sorbose productivity.
AU  - Ge X
AU  - Zhao Y
AU  - Hou W
AU  - Zhang W
AU  - Chen W
AU  - Wang J
AU  - Zhao N
AU  - Lin J
AU  - Wang W
AU  - Chen M
AU  - Wang Q
AU  - Jiao Y
AU  - Yuan Z
AU  - Xiong X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00003-13.

PMID- 14998998
VI  - 279
DP  - 2004
TI  - Chromatin targeting of de novo DNA methyltransferases by the PWWP domain.
PG  - 25447-25454
AB  - DNA methylation patterns of mammalian genomes are generated in gametogenesis and early
      embryonic development. Two de novo DNA
      methyltransferases, Dnmt3a and Dnmt3b, are responsible for the process.
      Both enzymes contain a long N-terminal regulatory region linked to a
      conserved C-terminal domain responsible for the catalytic activity.
      Although a PWWP domain in the N-terminal region has been shown to bind
      DNA in vitro, it is unclear how the DNA methyltransferases access their
      substrate in chromatin in vivo. We show here that the two proteins are
      associated with chromatin including mitotic chromosomes in mammalian
      cells, and the PWWP domain is essential for the chromatin targeting of
      the enzymes. The functional significance of PWWP-mediated chromatin
      targeting is suggested by the fact that a missense mutation in this
      domain of human DNMT3B causes immunodeficiency, centromeric
      heterochromatin instability, facial anomalies (ICF) syndrome, which is
      characterized by loss of methylation in satellite DNA, pericentromeric
      instability, and immunodeficiency. We demonstrate that the mutant
      protein completely loses its chromatin targeting capacity. Our data
      establish the PWWP domain as a novel chromatin/chromosome-targeting
      module and suggest that the PWWP-mediated chromatin association is
      essential for the function of the de novo methyltransferases during
      development.
AU  - Ge YZ
AU  - Pu MT
AU  - Gowher H
AU  - Wu HP
AU  - Ding JP
AU  - Jeltsch A
AU  - Xu GL
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2004 279: 25447-25454.

PMID- 10547695
VI  - 53
DP  - 1999
TI  - Contributions of genome sequencing to understanding the biology of Helicobacter pylori.
PG  - 353-387
AB  - About half of the world's population carries Helicobacter pylori, a gram-negative, spiral
      bacterium that colonizes the human stomach. The link between H. pylori and, ulceration as well
      as its association with the development of both gastric cancer and mucosa-associated lymphoid
      tissue lymphoma in humans is a serious public health concern. The publication of the genome
      sequences of two stains of H. pylori gives rise to direct evidence on the genetic diversity
      reported previously with respect to gene organization and nucleotide variability from strain
      to strain. The genome size of H. pylori strain 26695 is 1,6697,867 bp and is 1,643,831 bp for
      strain J99. Approximately 89% of the predicted open reading frames are common to both of the
      strains, confirming H. pylori as a single species. A region containing approximately 45% of H.
      pylori strain-specific open reading frames, termed the plasticity zone, is present on the
      chromosomes, verifying that some strain variability exists. Frequent alteration of nucleotides
      in the third position of the triplet codons and various copies of insertion elements on the
      individual chromosomes appear to contribute to distinct polymorphic fingerprints among strains
      analyzed by restriction fragment length polymorphisms, random amplified polymorphic DNA
      method, and repetitive element-polymerase chain reaction. Disordered chromosomal locations of
      some genes seen by pulsed-field gel electrophoresis are likely caused by rearrangement or
      inversion of certain segments in the genomes. Cloning and functional characterization of the
      genes involved in acidic survival, vacuolating toxin, cag-pathogenicity island, motility,
      attachment to epithelial cells, natural transformation, and the biosynthesis of
      lipopolysaccharides have considerably increased our understanding of the molecular genetic
      basis for the pathogenesis of H. pylori. The homopolymeric nucleotide tracts and dinucleotide
      repeats, which potentially regulate the on- and off-status of the target genes by the
      strand-slipped mispairing mechanism, are often found in the genes encoding the outer-membrane
      proteins, in enzymes for lipopolysaccharide synthesis, and within DNA modification/restriction
      systems. Therefore, these genes may be involved in the H. pylori-host interaction.
AU  - Ge Z
AU  - Taylor DE
PT  - Journal Article
TA  - Annu. Rev. Microbiol.
JT  - Annu. Rev. Microbiol.
SO  - Annu. Rev. Microbiol. 1999 53: 353-387.

PMID- 10769153
VI  - 39
DP  - 2000
TI  - The dynamic impact of CpG methylation in DNA.
PG  - 4939-4946
AB  - Solid-state deuterium NMR is used to investigate perturbations of the local, internal dynamics
      in the EcoRI restriction binding site, -GAATTC- induced by cytidine methylation. Methylation
      of the cytidine base in this sequence is known to suppress hydrolysis by the EcoRI restriction
      enzyme. Previous solid-state deuterium NMR studies have detected large amplitude motions of
      the phosphate-sugar backbone at the AT-CG junction of the unmethylated DNA sequence. This
      study shows that methylation of the cytidine base in a CpG dinucleotide reduces the amplitudes
      of motions of the phosphate-sugar backbone. These observations suggest a direct link between
      suppression of the amplitudes of localized, internal motions of the sugar-phosphate backbone
      of the DNA and inhibition of restriction enzyme cleavage.
AU  - Geahigan KB
AU  - Meints GA
AU  - Hatcher ME
AU  - Orban J
AU  - Drobny GP
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2000 39: 4939-4946.

PMID- 12661157
VI  - 34
DP  - 2003
TI  - Selective protection of restriction endonuclease sites.
PG  - 512-523
AB  - A difficulty that is encountered when attempting to insert a PCR-amplified product or DNA
      fragment of interest into a particular vector is the
      presence within the insert of one or more internal restriction
      endonuclease (RE) sites identical to those selected for the flanks of the
      insert. Our method circumvents this problem by partially protecting
      internal RE sites while flanking sites for the same RE are cleaved. The
      amplified product is first heat denatured in the presence of excess
      amounts of perfectly complementary oligonucleotides that can anneal to the
      flanks of the insert. The mixture is allowed to anneal and is subsequently
      digested with the appropriate endonucleases. This results in the cleavage
      of the flanking RE sites while digestion at the internal RE site is not
      efficient. The mixture is subsequently heat denatured and column purified
      to remove the oligonucleotides. The product is then allowed to anneal and
      can be used directly in a ligation reaction with the plasmid vector. This
      method facilitates the construction of recombinant molecules by creating
      desired flanks while preserving internal RE sites.
AU  - Gebreyesus KH
AU  - Owens RA
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 2003 34: 512-523.

PMID- 1810110
VI  - 38
DP  - 1991
TI  - A mathematical method for the identification of the ATGCAT recognition sequence of a Streptococcus mutans restriction endonuclease.
PG  - 43-46
AB  - Taking advantage of a mathematical equation applied so far in different fields the calculation
      of ATGCAT recognition sequence of restriction endonuclease from Streptococcus mutans serotype
      C (SmuCI) is reported together with confirming computer and physical mapping data.
AU  - Geck P
AU  - Molnar A
AU  - Nasz I
PT  - Journal Article
TA  - Acta Microbiol. Hung.
JT  - Acta Microbiol. Hung.
SO  - Acta Microbiol. Hung. 1991 38: 43-46.

PMID- 1810111
VI  - 38
DP  - 1991
TI  - Identification of ATGCAT sequence at sites of SmuCI restriction endonuclease by computer and physical mapping of Adenovirus Type I DNA.
PG  - 47-53
AB  - Physical mapping of adenovirus type I DNA was carried out in order to analyze the recognition
      sequence of a novel Streptococcus restriction endonuclease. In addition to the new map and
      homology data on this poorly analyzed serotype, the result offers the definite evidence for
      the ATGCAT recognition sequence on adenovirus DNA and the physical map of cleavage points.
AU  - Geck P
AU  - Molnar A
AU  - Nasz I
PT  - Journal Article
TA  - Acta Microbiol. Hung.
JT  - Acta Microbiol. Hung.
SO  - Acta Microbiol. Hung. 1991 38: 47-53.

PMID- 2834907
VI  - 34
DP  - 1987
TI  - Elimination of non-specific nucleases from restriction endonuclease preparations by different binding on free DNA ligand.
PG  - 241-245
AB  - In the purification of a novel restriction endonuclease (an AvaIII
      isoschizomer, isolated in this laboratory) standard methods were insufficient
      to eliminate non-specific nuclease contaminations.  Taking advantage of the
      specific site recognition and binding of the restriction endonuclease on DNAs,
      a method is described for the simple extraction of non-specific nucleases.  DNA
      substrate without recognizable sites do not bind the restriction endonuclease,
      while non-specific nucleases are absorbed to, and eliminated with, the DNA via
      gel filtration chromatography under special conditions.
AU  - Geck P
AU  - Molnar A
AU  - Nasz J
PT  - Journal Article
TA  - Acta Microbiol. Hung.
JT  - Acta Microbiol. Hung.
SO  - Acta Microbiol. Hung. 1987 34: 241-245.

PMID- 24874674
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Bacillus cereus Strain BcFL2013, a Clinical Isolate Similar to G9241.
PG  - e00469-14
AB  - Bacillus cereus strains, such as G9241, causing anthrax-like illnesses have recently been
      discovered. We report the genome sequence of a clinical strain, B.
      cereus BcFL2013, which is similar to G9241, recovered from a patient in Florida.
AU  - Gee JE
AU  - Marston CK
AU  - Sammons SA
AU  - Burroughs MA
AU  - Hoffmaster AR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00469-14.

PMID- 12654010
VI  - 270
DP  - 2003
TI  - In vitro analysis of the relationship between endonuclease and maturase activities in the bi-functional group I intron-encoded protein, I-AniI.
PG  - 1543-1554
AB  - The AnCOB group I intron from Aspergillus nidulans encodes a homing DNA endonuclease called
      I-AniI which also functions as a maturase, assisting
      in AnCOB intron RNA splicing. In this investigation we biochemically
      characterized the endonuclease activity of I-AniI in vitro and utilized
      competition assays to probe the relationship between the RNA- and
      DNA-binding sites. Despite functioning as an RNA maturase, I-AniI still
      retains several characteristic properties of homing endonucleases
      including relaxed substrate specificity, DNA cleavage product retention
      and instability in the reaction buffer, which suggest that the protein has
      not undergone dramatic structural adaptations to function as an
      RNA-binding protein. Nitrocellulose filter binding and kinetic burst
      assays showed that both nucleic acids bind I-AniI with the same 1 : 1
      stoichiometry. Furthermore, in vitro competition activity assays revealed
      that the RNA substrate, when prebound to I-AniI, stoichiometrically
      inhibits DNA cleavage activity, yet in reciprocal experiments, saturating
      amounts of prebound DNA substrate fails to inhibit RNA splicing activity.
      The data suggest therefore that both nucleic acids do not bind the same
      single binding site, rather that I-AniI appears to contain two binding
      sites.
AU  - Geese WJ
AU  - Kwon YK
AU  - Wen XP
AU  - Waring RB
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 2003 270: 1543-1554.

PMID- 11350164
VI  - 308
DP  - 2001
TI  - A comprehensive characterization of a group IB intron and its encoded maturase reveals that protein-assisted splicing requires an almost intact intron RNA.
PG  - 609-622
AB  - The group I intron (AnCOB) of the mitochondrial apocytochrome b gene from Aspergillus nidulans
      encodes a bi-functional maturase protein that is also a DNA endonuclease. Although the AnCOB
      intron self-splices, the encoded maturase protein greatly facilitates splicing, in part, by
      stabilizing RNA tertiary structure. To determine their role in self-splicing and in
      protein-assisted splicing, several peripheral RNA sub-domains in the 313 nucleotide intron
      were deleted (P2, P9, P9.1) or truncated (P5ab, P6a). The sequence in two helices (P2 and P9)
      was also inverted. Except for P9, the deleted regions are not highly conserved among group I
      introns and are often dispensable for catalytic activity. Nevertheless, despite the very tight
      binding of AnCOB RNA to the maturase and the high activity of the bimolecular complex (the
      rate of 5' splice-site cleavage was >20 min(-1) with guanosine as the cofactor), the intron
      was surprisingly sensitive to these modifications. Several mutations inactivated splicing
      completely and virtually all impaired splicing to varying degrees. Mutants containing
      comparatively small deletions in various regions of the intron significantly decreased binding
      affinity (generally >10(4)-fold), indicating that none of the domains that remained
      constitutes the primary recognition site of the maturase. The data argue that tight binding
      requires tertiary interactions that can be maintained by only a relatively intact intron RNA,
      and that the binding mechanism of the maturase differs from those of two other
      well-characterized group I intron splicing factors, CYT-18 and Cpb2. A model is proposed in
      which the protein promotes widespread cooperative folding of an RNA lacking extensive initial
      tertiary structure.
AU  - Geese WJ
AU  - Waring RB
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2001 308: 609-622.

PMID- 5946625
VI  - 241
DP  - 1966
TI  - The enzymatic methylation of ribonucleic acid and deoxyribonucleic acid.
PG  - 1995-2006
AB  - An enzyme activity which leads to the degradation of S-adenosylmethionine appears after T3
      phage infection of Escherichia coli B.  The purification and properties of this activity have
      been described.  The enzyme catalyzes the conversion of S-adenosylmethionine to
      thiomethyladenosine and homoserine.  It has been suggested that a gamma-amino-butyrolactone is
      an intermediate in this reaction.  The enzyme appears only after infection with T3 phage.
      Infection with phages T1, T2, T4, T5, T6, T7, or lambda does not result in the appearance of
      any activity.  The rate of enzyme formation and the requirement for protein synthesis de novo
      suggests that this activity is similar to early enzymes formed after infection with the T-even
      phages.  The enzyme has been isolated both from normal phage T3-infected E. coli and from
      ultraviolet light-inactivated phage T3-infected E. coli.  In the later case, the specific
      activity of cell-free extracts was several-fold higher than extracts obtained from normal
      phage T3-infected cells.  Infection of e. coli with ultraviolet light-inactivated phage T3
      does not result in the cessation of host cell deoxyribonucleic or ribonucleic acid synthesis.
      Thus, newly synthesized DNA and RNA formed after infection with phage T3 are devoid of
      methylated bases.  Phage T2, grown in ultraviolet light-inactivated, phage T3-infected E.
      coli, is likewise devoid of methylated bases.  Such methyl-deficient T2 phage appears to be
      normal in its biological properties so far examined.
AU  - Gefter M
AU  - Hausmann R
AU  - Gold M
AU  - Hurwitz J
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1966 241: 1995-2006.

PMID- 27340511
VI  - 11
DP  - 2016
TI  - High-quality permanent draft genome sequence of Ensifer sp. PC2, isolated from a  nitrogen-fixing root nodule of the legume tree (Khejri) native to the Thar Desert of India.
PG  - 43
AB  - Ensifer sp. PC2 is an aerobic, motile, Gram-negative, non-spore-forming rod that  was isolated
      from a nitrogen-fixing nodule of the tree legume P. cineraria (L.)
      Druce (Khejri), which is a keystone species that grows in arid and semi-arid
      regions of the Indian Thar desert. Strain PC2 exists as a dominant saprophyte in
      alkaline soils of Western Rajasthan. It is fast growing, well-adapted to arid
      conditions and is able to form an effective symbiosis with several annual crop
      legumes as well as species of mimosoid trees and shrubs. Here we describe the
      features of Ensifer sp. PC2, together with genome sequence information and its
      annotation. The 8,458,965 bp high-quality permanent draft genome is arranged into
      171 scaffolds of 171 contigs containing 8,344 protein-coding genes and 139
      RNA-only encoding genes, and is one of the rhizobial genomes sequenced as part of
      the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and
      Archaea-Root Nodule Bacteria (GEBA-RNB) project proposal.
AU  - Gehlot HS et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 43.

PMID- 368070
VI  - 254
DP  - 1979
TI  - Recognition sequence of the dam methylase of Escherichia coli K12 and mode of cleavage of DpnI endonuclease.
PG  - 1408-1413
AB  - The recognition sequence for the dam methylase of Escherichia coli K12 has been determined
      directly by use of in vivo methylated ColE1 DNA or DNA methylated in vitro with purified
      enzyme. The methylase recognizes the symmetric tetranucleotide d(pG-A-T-C) and introduces two
      methyl groups per site in duplex DNA with the product of methylation being
      6-methylaminopurine. This work has also demonstrated that DpnI restriction endonuclease
      cleaves on the 3' side of the modified adenine within the methylated sequence to yield DNA
      fragments possessing fully base-paired termini. All sequences in ColE1 DNA methylated by the
      dam enzyme are subject to double strand cleavage by DpnI endonuclease. Therefore, this
      restriction enzyme can be employed for mapping the location of sequences possessing the dam
      modification.
AU  - Geier GE
AU  - Modrich P
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1979 254: 1408-1413.

PMID- 2499352
VI  - 28
DP  - 1989
TI  - Genetic engineering of EcoRI mutants with altered amino acid residues in the DNA binding site:  Physiochemical investigations give evidence for an altered monomer/dimer equilibrium for the Gln144Lys145 and Gln144Lys145Lys200 mutants.
PG  - 2667-2677
AB  - We have genetically engineered the Arg200 ->Lys mutant, the Glu144Arg145
      ->GlnLys double mutant, and the Glu144Arg145Arg200 ->GlnLysLys triple mutant of
      the EcoRI endonuclease in extension of previously published work on
      site-directed mutagenesis of the EcoRI endonuclease in which Glu144 had been
      exchanged for Gln and Arg145 for Lys [Wolfes et al. (1986) Nucleic Acids Res.
      14, 9063].  All these mutants carry modifications in the DNA binding site.
      Mutant EcoRI proteins were purified to homogeneity and characterized by
      physiochemical techniques.  All mutants have a very similar secondary structure
      composition.  However, whereas the Lys200 mutant is not impaired in its
      capacity to form a dimer, the Gln144Lys145 and Gln144Lys145Lys200 mutants have
      a very much decreased propensity to form a dimer or tetramer depending on
      concentration as shown by gel filtration and analytical ultracentrifugation.
      This finding may explain the results of isoelectric focusing experiments which
      show that these two mutants have a considerably more basic pI than expected for
      a protein in which an acidic amino acid was replaced by a neutral one.
      Furthermore, while wild-type EcoRI and the Lys200 mutant are denatured in an
      irreversible manner upon heating to 60C, the thermal denaturation process as
      shown by circular dichroism spectroscopy is fully reversible with the
      Gln144Lys145 double mutant and the Gln144Lys145Lys200 triple mutant.  All EcoRI
      endonuclease mutants described here have a residual enzymatic activity with
      wild-type specificity, since Escherichia coli cells overexpressing the mutant
      proteins can only survive in the presence of EcoRI methylase.  The detailed
      analysis of the enzymatic activity and specificity of the purified mutant
      proteins is the subject of the accompanying paper.
AU  - Geiger R
AU  - Ruter T
AU  - Alves J
AU  - Fliess A
AU  - Wolfes H
AU  - Pingoud V
AU  - Urbanke C
AU  - Maass G
AU  - Pingoud A
AU  - Dusterhoft A
AU  - Kroger M
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1989 28: 2667-2677.

PMID- 15148359
VI  - 32
DP  - 2004
TI  - Isolation and characterization of a novel DNA methyltransferase complex linking DNMT3B with components of the mitotic chromosome condensation machinery.
PG  - 2716-2729
AB  - Proper patterns of genome-wide DNA methylation, mediated by DNA methyltransferases DNMT1, -3A
      and -3B, are essential for embryonic development and genomic stability in mammalian cells. The
      de novo DNA methyltransferase DNMT3B is of particular interest because it is frequently
      overexpressed in tumor cells and is mutated in immunodeficiency, centromere instability and
      facial anomalies (ICF) syndrome. In order to gain a better understanding of DNMT3B, in terms
      of the targeting of its methylation activity and its role in genome stability, we
      biochemically purified endogenous DNMT3B from HeLa cells. DNMT3B co-purifies and interacts,
      both in vivo and in vitro, with several components of the condensin complex (hCAP-C, hCAP-E
      and hCAP-G) and KIF4A. Condensin mediates genome-wide chromosome condensation at the onset of
      mitosis and is critical for proper segregation of sister chromatids. KIF4A is proposed to be a
      motor protein carrying DNA as cargo. DNMT3B also interacts with histone deacetylase 1 (HDAC1),
      the co-repressor SIN3A and the ATP-dependent chromatin remodeling enzyme hSNF2H. Further more,
      DNMT3B co-localizes with condensin and KIF4A on condensed chromosomes throughout mitosis.
      These studies therefore reveal the first direct link between the machineries regulating DNA
      methylation and mitotic chromosome condensation in mammalian cells.
AU  - Geiman TM
AU  - Sankpal UT
AU  - Robertson AK
AU  - Chen Y
AU  - Mazumdar M
AU  - Heale J
AU  - Schmiesing JA
AU  - Kim W
AU  - Yokomori K
AU  - Zhao Y
AU  - Robertson KD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2004 32: 2716-2729.

PMID- 15120635
VI  - 318
DP  - 2004
TI  - DNMT3B interacts with hSNF2H chromatin remodeling enzyme, HDACs 1 and 2, and components of the histone methylation system.
PG  - 544-555
AB  - The non-random pattern of genome-wide DNA methylation in mammalian cells is established and
      maintained by DNA methyltransferases DNMT1,
      3A, and 3B. De novo DNA methyltransferase DNMT3B is critical for
      embryonic development and is mutated in ICF syndrome. Despite its
      importance in normal cellular functioning, little is known about how
      DNMT3B operates in the context of chromatin. Here we demonstrate that
      DNMT3B associates with four chromatin-associated enzymatic activities
      common to transcriptionally repressed, heterochromatic regions of the
      genome: DNA methyltransferase, histone deacetylase, ATPase, and histone
      methylase activities. By immunoprecipitation and GST pull-down, we show
      that DNMT3B interacts with HDAC1, HDAC2, HP1 proteins, Suv39h1, and the
      ATP-dependent chromatin remodeling enzyme hSNF2H. Endogenous hSNF2H is
      also associated with DNA methyltransferase activity. These proteins
      co-localize extensively with DNMT3B in heterochromatic regions. Our
      results therefore link DNMT3B to three other components of the
      epigenetic machinery and provide important insights into how DNA
      methylation patterns may be established within the chromatin
      environment.
AU  - Geiman TM
AU  - Sankpal UT
AU  - Robertson AK
AU  - Zhao YX
AU  - Zhao YM
AU  - Robertson KD
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 2004 318: 544-555.

PMID- 12826058
VI  - 50
DP  - 2003
TI  - Sequence analysis and characterization of plasmids from Streptococcus thermophilus.
PG  - 53-69
AB  - The nucleotide sequences of eight plasmids isolated from seven Streptococcus thermophilus
      strains have been determined. Plasmids pSt04,
      pER1-1, and pJ34 are related and replicate via a rolling circle mechanism.
      Plasmid pJ34 encodes for a replication initiation protein (RepA) and a
      small polypeptide with unknown function. Plasmids pSt04 and pER1-1 carry
      in addition to repA genes coding for small heat shock proteins (sHsp).
      Expression of these proteins is induced at elevated temperatures or low pH
      and increases the thermo- and acid resistance. Plasmids pER1-2 and pSt22-2
      show identical sequences with five putative open reading frames (ORFs).
      The gene products of ORF1 and ORF4 reveal some similarities to transposon
      encoded proteins of Bacillus subtilis and Tn916. ORF1 of plasmid pSt106
      encodes a protein similar to resolvases of different Gram-positive
      bacteria. Integrity of ORF2 and 3, encoding a putative DNA primase and a
      replication protein, is essential for replication. ORF1 to 3 of plasmid
      pSt08, which are organized in a tricistronic operon, encode a RepA
      protein, an adenosine-specific methyltransferase, and a type II
      restriction endonuclease. Another type II restriction-modification (R/M)
      system is encoded on plasmid pSt0 which is highly similar to those encoded
      on lactococcal plasmid pHW393 and B. subtilis plasmid pXH13. Plasmid-free
      derivatives of strains St0 and St08 show increased phage sensitivity,
      indicating that in the wild-type strains the R/M systems are functionally
      expressed. Recombinant plasmids based on the replicons of plasmids pSt04,
      pJ34, pSt106, pSt08, and pSt0, are able to replicate in Lactococcus lactis
      and B. subtilis, respectively, whereas constructs carrying pER1-2 only
      replicate in S. thermophilus.
AU  - Geis A
AU  - El Demerdash HA
AU  - Heller KJ
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 2003 50: 53-69.

PMID- 27563041
VI  - 4
DP  - 2016
TI  - Multiple Genome Sequences of the Important Beer-Spoiling Species Lactobacillus backii.
PG  - e00826-16
AB  - Lactobacillus backii is an important beer-spoiling species. Five strains isolated from four
      different breweries were sequenced using single-molecule real-time
      sequencing. Five complete genomes were generated, which will help to understand
      niche adaptation to beer and provide the basis for consecutive analyses.
AU  - Geissler AJ
AU  - Behr J
AU  - Vogel RF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00826-16.

PMID- 27795248
VI  - 4
DP  - 2016
TI  - Multiple Genome Sequences of Important Beer-Spoiling Lactic Acid Bacteria.
PG  - e01077-16
AB  - Seven strains of important beer-spoiling lactic acid bacteria were sequenced using
      single-molecule real-time sequencing. Complete genomes were obtained for
      strains of Lactobacillus paracollinoides, Lactobacillus lindneri, and Pediococcus
      claussenii The analysis of these genomes emphasizes the role of plasmids as the
      genomic foundation of beer-spoiling ability.
AU  - Geissler AJ
AU  - Behr J
AU  - Vogel RF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01077-16.

PMID- 9171096
VI  - 25
DP  - 1997
TI  - Avoidance of palindromic words in bacterial and archaeal genomes: a close connection with restriction enzymes.
PG  - 2430-2439
AB  - Short palindromic sequences (4, 5 and 6 bp palindromes) are avoided at a statistically
      significant level in the genomes of several bacteria, including the completely sequenced
      Haemophilus influenzae and Synechocystis sp. genomes and in the complete genome of the
      archaeon Methanococcus jannaschii.  In contrast, there is only moderate avoidance of
      palindromes in the small genome of the bacterium Mycoplasma genitalium and no detectable
      avoidance in the genomes of chloroplasts and mitochondria.  The sites for type II
      restriction-modification enzymes detected in the given species tend to be among the most
      avoided palindromes in a particular genome, indicating a direct connection between the
      avoidance of short oligonucleotide words and restriction-modification systems with the
      respective specificity.  Palindromes corresponding to sites for restriction enzymes from other
      species are also avoided, albeit less significantly, suggesting that in the course of
      evolution bacterial DNA has been exposed to a wide spectrum of restriction enzymes, probably
      as the result of lateral transfer mediated by mobile genetic elements, such as plasmids and
      prophages.  Palindromic words appear to accumulate in DNA once it becomes isolated from
      restriction-modification systems, as demonstrated by the case of organellar genomes.  By
      combining these observations with protein sequence analysis, we show that the most avoided
      4-palindrome and the most avoided 6-palindrome in the archaeon M. jannaschii are likely to be
      recognition sites for two novel restriction-modification systems.
AU  - Gelfand MS
AU  - Koonin EV
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1997 25: 2430-2439.

PMID- 909085
VI  - 114
DP  - 1977
TI  - Two sequence-specific endonucleases from Moraxella bovis.
PG  - 169-179
AB  - Two new sequence-specific endodeoxyribonucleases have been partially purified from Moraxella
      bovis. These restriction-like enzymes, MboI and MboII, each cleave bacteriophage lambda DNA
      and adenovirus-2 DNA at more than 50 sites. MboI recognizes the sequence 5'^G-A-T-C 3' 3'
      C-T-A-T^5' and cleaves at the sites indicated by the arrows. A specific endonuclease, MosI,
      has also been purified from Moraxella osloenis and recognizes the same sequence as MboI.
AU  - Gelinas RE
AU  - Myers PA
AU  - Roberts RJ
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1977 114: 169-179.

PMID- 909093
VI  - 114
DP  - 1977
TI  - A specific endonuclease from Brevibacterium albidum.
PG  - 433-440
AB  - A new restriction-like endonuclease, BalI, has been partially purified from
      Brevibacterium albidum.  This enzyme cleaves bacteriophage lambda DNA at least
      18 times and adenovirus-2 DNA at least 16 times, but does not cleave simian
      virus 40 DNA.  All sites cleaved by BalI are also cut by the specific
      endonuclease HaeIII from Haemophilus aegyptius.  The recognition sequence of
      BalI is 5'-T-G-G ^ C-C-A-3' 3'-A-C-C ^ G-G-T-5' and the cleavage site is
      indicated by the arrows.
AU  - Gelinas RE
AU  - Myers PA
AU  - Weiss GH
AU  - Roberts RJ
AU  - Murray K
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1977 114: 433-440.

PMID- 16963513
VI  - 91
DP  - 2006
TI  - Dynamics of single DNA looping and cleavage by Sau3AI and effect of tension applied to the DNA.
PG  - 4154-4165
AB  - Looping and cleavage of single DNA molecules by the two-site restriction endonuclease Sau3AI
      were measured with optical tweezers. A DNA template
      containing many recognition sites was used, permitting loop sizes from
      approximately 10 to 10,000 basepairs. At high enzyme concentration,
      cleavage events were detected within 5 s and nearly all molecules were
      cleaved within 5 min. Activity decreased approximately 10-fold as the DNA
      tension was increased from 0.03 to 0.7 pN. Substituting Ca(2+) for Mg(2+)
      blocked cleavage, permitting measurement of stable loops. At low tension,
      the initial rates of cleavage and looping were similar (approximately
      0.025 s(-1) at 0.1 pN), suggesting that looping is rate limiting. Short
      loops formed more rapidly than long loops. The optimum size decreased from
      approximately 250 to 45 basepairs and the average number of loops (in 1
      min) from 4.2 to 0.75 as tension was increased from 0.03 to 0.7 pN. No
      looping was detected at 5 pN. These findings are in qualitative agreement
      with recent theoretical predictions considering only DNA mechanics, but we
      observed weaker suppression with tension and smaller loop sizes. Our
      results suggest that the span and elasticity of the protein complex,
      nesting of loops, and protein-induced DNA bending and wrapping play an
      important role.
AU  - Gemmen GJ
AU  - Millin R
AU  - Smith DE
PT  - Journal Article
TA  - Biophys. J.
JT  - Biophys. J.
SO  - Biophys. J. 2006 91: 4154-4165.

PMID- 16723432
VI  - 34
DP  - 2006
TI  - DNA looping by two-site restriction endonucleases: heterogeneous probability distributions for loop size and unbinding force.
PG  - 2864-2877
AB  - Proteins interacting at multiple sites on DNA via looping play an important role in many
      fundamental biochemical processes. Restriction
      endonucleases that must bind at two recognition sites for efficient
      activity are a useful model system for studying such interactions. Here we
      used single DNA manipulation to study sixteen known or suspected two-site
      endonucleases. In eleven cases (BpmI, BsgI, BspMI, Cfr10I, Eco57I, EcoRII,
      FokI, HpaII, NarI, Sau3AI and SgrAI) we found that substitution of Ca2+
      for Mg2+ blocked cleavage and enabled us to observe stable DNA looping.
      Forced disruption of these loops allowed us to measure the frequency of
      looping and probability distributions for loop size and unbinding force
      for each enzyme. In four cases we observed bimodal unbinding force
      distributions, indicating conformational heterogeneity and/or complex
      binding energy landscapes. Measured unlooping events ranged in size from 7
      to 7500 bp and the most probable size ranged from less than 75 bp to
      nearly 500 bp, depending on the enzyme. In most cases the size
      distributions were in much closer agreement with theoretical models that
      postulate sharp DNA kinking than with classical models of DNA elasticity.
      Our findings indicate that DNA looping is highly variable depending on the
      specific protein and does not depend solely on the mechanical properties
      of DNA.
AU  - Gemmen GJ
AU  - Millin R
AU  - Smith DE
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2006 34: 2864-2877.

PMID- 16868081
VI  - 103
DP  - 2006
TI  - Tension-dependent DNA cleavage by restriction endonucleases: Two-site enzymes are "switched off" at low force.
PG  - 11555-11560
AB  - DNA looping occurs in many important protein-DNA interactions, including those regulating
      replication, transcription, and recombination. Recent
      theoretical studies predict that tension of only a few piconewtons acting
      on DNA would almost completely inhibit DNA looping. Here, we study
      restriction endonucleases that require interaction at two separated sites
      for efficient cleavage. Using optical tweezers we measured the dependence
      of cleavage activity on DNA tension with 15 known or suspected two-site
      enzymes (BfiI, BpmI, BsgI, BspMI, Cfr9I, Cfr10I, Eco57I, EcoRII, FokI,
      HpaII, MboII, NarI, SacII, Sau3AI, and SgrAI) and six one-site enzymes
      (BamHI, EcoRI, EcoRV, HaeIII, HindIII, and DNaseI). All of the one-site
      enzymes were virtually unaffected by 5 pN of tension, whereas all of the
      two-site enzymes were completely inhibited. These enzymes thus constitute
      a remarkable example of a tension sensing "molecular switch." A detailed
      study of one enzyme, Sau3AI, indicated that the activity decreased
      exponentially with tension and the decrease was approximately 10-fold at
      0.7 pN. At higher forces ( approximately 20-40 pN) cleavage by the
      one-site enzymes EcoRV and HaeIII was partly inhibited and cleavage by
      HindIII was enhanced, whereas BamHI, EcoRI, and DNaseI were largely
      unaffected. These findings correlate with structural data showing that
      EcoRV bends DNA sharply, whereas BamHI, EcoRI, and DNaseI do not. Thus,
      DNA-directed enzyme activity involving either DNA looping or bending can
      be modulated by tension, a mechanism that could facilitate mechanosensory
      transduction in vivo.
AU  - Gemmen GJ
AU  - Millin R
AU  - Smith DE
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2006 103: 11555-11560.

PMID- 28546493
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequence of the Bacteriophage-Sensitive Strain Campylobacter jejuni  NCTC12662.
PG  - e00409-17
AB  - Campylobacter jejuni NCTC12662 has been the choice bacteriophage isolation strain due to its
      susceptibility to C. jejuni bacteriophages. This trait makes it a good
      candidate for studying bacteriophage-host interactions. We report here the
      whole-genome sequence of NCTC12662, allowing future elucidation of the molecular
      mechanisms of phage-host interactions in C. jejuni.
AU  - Gencay YE
AU  - Sorensen MCH
AU  - Brondsted L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00409-17.

PMID- 22529932
VI  - 7
DP  - 2012
TI  - Complete Genome and Transcriptomes of Streptococcus parasanguinis FW213: Phylogenic Relations and Potential Virulence Mechanisms.
PG  - E34769
AB  - Streptococcus parasanguinis, a primary colonizer of the tooth surface, is also an
      opportunistic pathogen for subacute endocarditis. The complete genome of strain
      FW213 was determined using the traditional shotgun sequencing approach and
      further refined by the transcriptomes of cells in early exponential and early
      stationary growth phases in this study. The transcriptomes also discovered 10
      transcripts encoding known hypothetical proteins, one pseudogene, five
      transcripts matched to the Rfam and additional 87 putative small RNAs within the
      intergenic regions defined by the GLIMMER analysis. The genome contains five
      acquired genomic islands (GIs) encoding proteins which potentially contribute to
      the overall pathogenic capacity and fitness of this microbe. The differential
      expression of the GIs and various open reading frames outside the GIs at the two
      growth phases suggested that FW213 possess a range of mechanisms to avoid host
      immune clearance, to colonize host tissues, to survive within oral biofilms and
      to overcome various environmental insults. Furthermore, the comparative genome
      analysis of five S. parasanguinis strains indicates that albeit S. parasanguinis
      strains are highly conserved, variations in the genome content exist. These
      variations may reflect differences in pathogenic potential between the strains.
AU  - Geng J
AU  - Chiu CH
AU  - Tang P
AU  - Chen Y
AU  - Shieh HR
AU  - Hu S
AU  - Chen YY
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2012 7: E34769.

PMID- 21914897
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of the Ureolytic Streptococcus salivarius Strain 57.I.
PG  - 5596-5597
AB  - Streptococcus salivarius 57.I is one of the most abundant and highly ureolytic bacteria in the
      human mouth. It can utilize urea as the sole
      nitrogen source via the activity of urease. Complete genome sequencing of
      S. salivarius 57.I revealed a chromosome and a phage which are absent in
      strain SK126.
AU  - Geng J
AU  - Huang SC
AU  - Li S
AU  - Hu S
AU  - Chen YY
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5596-5597.

PMID- 21551302
VI  - 193
DP  - 2011
TI  - Complete genome sequence of Bacillus amyloliquefaciens LL3, which exhibits glutamic acid-independent production of poly-{gamma}-glutamic acid.
PG  - 3393-3394
AB  - Bacillus amyloliquefaciens is one of most prevalent Gram-positive aerobic spore-forming
      bacteria with the ability of synthesizing polysaccharides
      and polypeptides. Here, we report the complete genome sequence of B.
      amyloliquefaciens LL3, which was isolated from fermented food and presents
      the glutamic acid-independent production of poly-gamma-glutamic acid.
AU  - Geng W
AU  - Cao M
AU  - Song C
AU  - Xie H
AU  - Liu L
AU  - Yang C
AU  - Feng J
AU  - Zhang W
AU  - Jin Y
AU  - Du Y
AU  - Wang S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3393-3394.

PMID- 10579493
VI  - 41
DP  - 1999
TI  - Multiple DNA methyltransferase genes in Arabidopsis thaliana.
PG  - 269-278
AB  - Methylation of plant DNA occurs at cytosines in any sequence context, and as the Arabidopsis
      methyltransferase, METI, preferentially methylates cytosines in CG dinucleotides, it is likely
      that Arabidopsis has other methyltransferases with different target specificities. We have
      identified five additional genes encoding putative DNA methyltransferases. Three of these
      genes are very similar to METI throughout the coding region; these genes probably arose by a
      series of gene duplication events, the most recent giving rise to METIIa and METIIb. METIIa
      and b are expressed at low levels in vegetative and floral organs and the level of transcripts
      is not affected by the introduction of a METI antisense transgene, nor do the METII enzymes
      substitute for the reduced activity of METI in methylating CG dinucleotides. METIII is not
      essential as it encodes a truncated protein. Two other genes encode a second class of DNA
      methyltransferase with the conserved motifs characteristic of cytosine methyltransferases, but
      with little homology to the METI-like methyltransferases through the remainder of the protein.
      These two methyltransferases are characterized by the presence of a chromodomain inserted
      within the methyltransferase domain, suggesting that they may be associated with
      heterochromatin. Both these genes are transcribed at low levels in vegetative and reproductive
      tissues.
AU  - Genger RK
AU  - Kovac KA
AU  - Dennis ES
AU  - Peacock WJ
AU  - Finnegan EJ
PT  - Journal Article
TA  - Plant Mol. Biol.
JT  - Plant Mol. Biol.
SO  - Plant Mol. Biol. 1999 41: 269-278.

PMID- Not included in PubMed...
VI  - 80
DP  - 1989
TI  - A basic program to construct evolutionary trees from restriction endonuclease data.
PG  - 254
AB  - None
AU  - Gentzbittel L
AU  - Nicolas P
PT  - Journal Article
TA  - J. Hered.
JT  - J. Hered.
SO  - J. Hered. 1989 80: 254.

PMID- 1979079
VI  - 81
DP  - 1990
TI  - Improvement of "A BASIC program to construct evolutionary trees from restriction endonuclease data" with the use of PASCAL.
PG  - 491-492
AB  - None
AU  - Gentzbittel L
AU  - Nicolas P
PT  - Journal Article
TA  - J. Hered.
JT  - J. Hered.
SO  - J. Hered. 1990 81: 491-492.

PMID- 6248525
VI  - 255
DP  - 1980
TI  - Sequence-specific endonuclease BamHI.
PG  - 6521-6524
AB  - The specificity of cleavage of BamHI is altered in the presence of hydrophobic
      reagents, such as glycerol and M2SO.  The enzyme with altered specificity,
      designated BamHI.1, generated digestion patterns of various DNAs, which were
      distinct from those generated by BamHI.  Cleavage sites recognized in PhiX174
      RF DNA in the presence of these hydrophobic reagents are not related to the
      BamHI palindrome.  BamHI.1 appears to be an endogenous form of BamHI that can
      be expressed by altering the hydrophobicity of the reaction.
AU  - George J
AU  - Blakesley RW
AU  - Chirikjian JG
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1980 255: 6521-6524.

PMID- 673852
VI  - 5
DP  - 1978
TI  - Biospecific fractionation matrices for sequence specific endonucleases.
PG  - 2223-2232
AB  - Fractionation of several type II specific restriction endonucleases was
      achieved by separation on two novel biospecific matrices.  The matrices are
      pyran, a copolymer of divinyl ether of maleic anhydride, and Cibacron Blue
      F3Ga, a blue dye commonly used for the calibration of molecular sieves.  Both
      compounds are insolubilized by coupling to sepharose through a cyanogen bromide
      linkage and in their soluable form inhibit the restriction endonucleases which
      we have tested.  These affinity matrices can be used to obtain restriction
      endonucleases from crude extracts after removal of nucleic acids.  They have
      also proven to have a high capacity when used as subsequent step in enzyme
      purification.  Their additional advantage is the rapid development time and
      reusability of columns packed with the two matrices.
AU  - George J
AU  - Chirikjian JG
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1978 5: 2223-2232.

PMID- 6283522
VI  - 79
DP  - 1982
TI  - Sequence-specific endonuclease BamHI: Relaxation of sequence recognition.
PG  - 2432-2436
AB  - The effect of glycerol on the specificity of DNA cleavage by the restriction
      endonuclease BamHI has been examined.  In addition to the canonical G ^ G-A-T-C
      site, BamHI cuts DNA at several sites that we have named noncanonical BamHI.1
      sites.  The number of BamHI.1 sites is simian virus 40 and pBR322 was
      determined to be 13 for each DNA.  Cutting sites determined by DNA sequence
      analysis include G ^ G-A-A-C-C, G ^ G-C-T-C-C, G ^ G-G-T-C-C, and G-A-A-T-C-C
      with the complementary strand sequence assignments of G-G-T-T-C-C, G-G-A-G-C-C,
      G-G-A-C-C-C, and G-G-A-T-T-C.  The relaxation in specificity was related to
      hydrogen bond acceptor and donor sites in the recognition sequence, in an
      attempt to generate a model of BamHI recognition of cognate sites in DNA.
AU  - George J
AU  - Chirikjian JG
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1982 79: 2432-2436.

PMID- Not included in PubMed...
VI  - 40
DP  - 1981
TI  - Chemical modifications as structural probes for the recognition of DNA palindromes by BamHI and BglI.
PG  - 1848
AB  - BamHI and BglI have been previously purified to apparent homogeneity in our
      laboratory.  The catalytically active form of BamHI is a dimer comprised of two
      apparently identical subunits of 23,000 daltons.  In comparison the active form
      of BglI was isolated as a single polypeptide of 34,000 daltons.  Chemical
      modification of the enzyme and both oligonucleotide and plasmid DNA substrates
      have been undertaken.  Enzyme which has been reductively alkylated (lysine
      modification) with formaldehyde is inactivated.  In contrast when such
      modifications are performed in the presence of a DNA substrate enzymatic
      activity is maintained.  Likewise DNAs that contain no recognition sequences
      for BamHI confer little protection against activity losses.  This suggests that
      upon specific binding to DNA, at least one or a group of lysine residues, are
      protected from chemical modification. BamHI recognizes the palindromic sequence
      G^GATCC.  We have evidence to suggest that the information required for
      recognition specificity resides in the major groove of the DNA double helix.
      This recognition may involve the N6 position of adenine and the 04 position of
      thymine.  The involvement of N7 and N2 of guanine and N3 of adenine are under
      curretn investigation by chemical modification procedures.
AU  - George J
AU  - Hamada Y-YT
AU  - Chirikjian JG
PT  - Journal Article
TA  - Fed. Proc.
JT  - Fed. Proc.
SO  - Fed. Proc. 1981 40: 1848.

PMID- 2997207
VI  - 260
DP  - 1985
TI  - Sequence-specific BamHI endonuclease.
PG  - 14387-14392
AB  - Arginyl residues in BamHI endonuclease were examined because of their alleged
      role in proteins that contain nucleotide- or phosphate-binding sites.
      Butanedione, an arginine-specific reagent, inhibited the endonuclease in the
      presence of sodium borate.  The inhibition was decreased by preliminary
      incubation of the enzyme with DNA or competitive inhibitors which were the
      5'-phosphoryl deoxydinucleotide subsets of the BamHI recognition sequence.  The
      dinucleotide pdGpdG protected the enzyme most efficiently against the
      butanedione modification.  Dinucleotides that were unrelated to the recognition
      sequence failed to protect the enzyme from inactivation.  These studies
      indicate that arginine residues may reside in the enzyme's active site and
      might function in the sequence-specific recognition of the BamHI palindrome.
AU  - George J
AU  - Nardone G
AU  - Chirikjian JG
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1985 260: 14387-14392.

PMID- 28388689
VI  - 12
DP  - 2017
TI  - Whole genome sequencing of Brucella melitensis isolated from 57 patients in Germany reveals high diversity in strains from Middle East.
PG  - E0175425
AB  - Brucellosis, a worldwide common bacterial zoonotic disease, has become quite rare
      in Northern and Western Europe. However, since 2014 a significant increase of
      imported infections caused by Brucella (B.) melitensis has been noticed in
      Germany. Patients predominantly originated from Middle East including Turkey and
      Syria. These circumstances afforded an opportunity to gain insights into the
      population structure of Brucella strains. Brucella-isolates from 57 patients were
      recovered between January 2014 and June 2016 with culture confirmed brucellosis
      by the National Consultant Laboratory for Brucella. Their whole genome sequences
      were generated using the Illumina MiSeq platform. A whole genome-based SNP typing
      assay was developed in order to resolve geographically attributed genetic
      clusters. Results were compared to MLVA typing results, the current gold-standard
      of Brucella typing. In addition, sequences were examined for possible genetic
      variation within target regions of molecular diagnostic assays. Phylogenetic
      analyses revealed spatial clustering and distinguished strains from different
      patients in either case, whereas multiple isolates from a single patient or
      technical replicates showed identical SNP and MLVA profiles. By including WGS
      data from the NCBI database, five major genotypes were identified. Notably,
      strains originating from Turkey showed a high diversity and grouped into seven
      subclusters of genotype II. MLVA analysis congruently clustered all isolates and
      predominantly matched the East Mediterranean genetic clade. This study confirms
      whole-genome based SNP-analysis as a powerful tool for accurate typing of B.
      melitensis. Furthermore it allows special allocation and therefore provides
      useful information on the geographic origin for trace-back analysis. However, the
      lack of reliable metadata in public databases often prevents a resolution below
      geographic regions or country levels and corresponding precise trace-back
      analysis. Once this obstacle is resolved, WGS-derived bacterial typing adds an
      important method to complement epidemiological surveys during outbreak
      investigations. This is the first report of a detailed genetic investigation of
      an extensive collection of B. melitensis strains isolated from human cases in
      Germany.
AU  - Georgi E
AU  - Walter MC
AU  - Pfalzgraf MT
AU  - Northoff BH
AU  - Holdt LM
AU  - Scholz HC
AU  - Zoeller L
AU  - Zange S
AU  - Antwerpen MH
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2017 12: E0175425.

PMID- 
VI  - 274
DP  - 2007
TI  - Novel approaches to engineering sequence-specificity of DNA cytosine-5 methyltransferases.
PG  - 259
AB  - Bacterial DNA cytosine-5 methyltransferases (C5-MTases) recognize
      2-8 bp DNA sequences and transfer the methyl group from
      the cofactor S-adenosyl-L-methionine onto the C5 position of a
      cytosine residue in that particular target sequence. Besides their
      utmost biological importance, DNA MTases were shown to be
      useful tools for site-specific DNA labelling [1] and for the construction
      of bionanodevices [2]. Here we describe the conversion of the
      HhaI methyltransferase (M.HhaI), which recognizes the palindromic
      GCGC site, into a GCG-specific or CGC-specific MTases.
      Due to a non-palindromic nature of the new targets, such engineered
      MTases could be used for creating hemimethylated CpG sites
      in DNA, which are desired models for mechanistic studies of the
      maintenance of genomic methylation patterns in higher eukaryotes
      [3]. Numerous crystal structures available for M.HhaI show that
      the recognition of the GCGC target is accomplished by two recognition
      loops. Directed evolution and rational design approaches
      were employed to obtain variants with the novel substrate specificities.
      Interestingly, one of the most efficient MTase variants contains
      a mutation outside the recognition loops, which allows the
      formation of a non-specific contact to the phosphodiester backbone
      of the DNA. Our results thus demonstrate that new asymmetric
      target specificities can be created by alterations of the
      recognition elements in DNA MTases, and that de novo non-specific
      contacts can compensate for the loss of base-specific DNA
      interactions.
      References
      1. Lukinavicius, G, et al. (2007). J Am Chem Soc, DOI: 10.1021/
      ja0691876.
      2. Singer, E, et al. (2006). Nano Lett, 6(6): 1184.
      3. Vilkaitis, G, et al. (2005). J Biol Chem, 280(1): 64.
AU  - Gerasimaite R
AU  - Klimasauskas S
PT  - Journal Article
TA  - FEBS J.
JT  - FEBS J.
SO  - FEBS J. 2007 274: 259.

PMID- 21245034
VI  - 39
DP  - 2011
TI  - Direct observation of cytosine flipping and covalent catalysis in a DNA methyltransferase.
PG  - 3771-3780
AB  - Methylation of the five position of cytosine in DNA plays important roles in epigenetic
      regulation in diverse organisms including humans. The transfer of methyl groups from the
      cofactor S-adenosyl-l-methionine is carried out by methyltransferase enzymes. Using the
      paradigm bacterial methyltransferase M.HhaI we demonstrate, in a chemically unperturbed
      system, the first direct real-time analysis of the key mechanistic events-the flipping of the
      target cytosine base and its covalent activation; these changes were followed by monitoring
      the hyperchromicity in the DNA and the loss of the cytosine chromophore in the target
      nucleotide, respectively. Combined with studies of M.HhaI variants containing redesigned
      tryptophan fluorophores, we find that the target base flipping and the closure of the mobile
      catalytic loop occur simultaneously, and the rate of this concerted motion inversely
      correlates with the stability of the target base pair. Subsequently, the covalent activation
      of the target cytosine is closely followed by but is not coincident with the methyl group
      transfer from the bound cofactor. These findings provide new insights into the temporal
      mechanism of this physiologically important reaction and pave the way to in-depth studies of
      other base-flipping systems.
AU  - Gerasimaite R
AU  - Merkiene E
AU  - Klimasauskas S
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2011 39: 3771-3780.

PMID- 19783820
VI  - 37
DP  - 2009
TI  - A directed evolution design of a GCG-specific DNA hemimethylase.
PG  - 7332-7341
AB  - DNA cytosine-5 methyltransferases (C5-MTases) are valuable models to study sequence-specific
      modification of DNA and are becoming increasingly
      important tools for biotechnology. Here we describe a structure-guided
      rational protein design combined with random mutagenesis and selection to
      change the specificity of the HhaI C5-MTase from GCGC to GCG. The
      specificity change was brought about by a five-residue deletion and
      introduction of two arginine residues within and nearby one of the target
      recognizing loops. DNA protection assays, bisulfite sequencing and enzyme
      kinetics showed that the best selected variant is comparable to wild-type
      M.HhaI in terms of sequence fidelity and methylation efficiency, and
      supersedes the parent enzyme in transalkylation of DNA using synthetic
      cofactor analogs. The designed C5-MTase can be used to produce
      hemimethylated CpG sites in DNA, which are valuable substrates for studies
      of mammalian maintenance MTases.
AU  - Gerasimaite R
AU  - Vilkaitis G
AU  - Klimasauskas S
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: 7332-7341.

PMID- 26966215
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Bacillus methylotrophicus Strain B25, a Potential Plant Growth-Promoting Rhizobacterium.
PG  - e00058-16
AB  - The complete genome of Bacillus methylotrophicus strain B25, isolated in Switzerland, was
      sequenced. Its size is 3.85 Mb, and several genes that may
      contribute to plant growth-promoting activities were identified in silico.
AU  - Gerbore J
AU  - Brutel A
AU  - Lemainque A
AU  - Mairey B
AU  - Medigue C
AU  - Vallenet D
AU  - Lefort F
AU  - Grizard D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00058-16.

PMID- 2326190
VI  - 18
DP  - 1990
TI  - Perturbation of DNA hairpins containing the EcoRI recognition site by hairpin loops of varying size and composition: physical (NMR and UV) and enzymatic (EcoRI) studies.
PG  - 1489-1498
AB  - We have investigated loop-induced structural perturbation of the stem structure
      in hairpins d(GAATTCXnGAATTC) (X = A, T, and n = 3, 4, 5 and 6) that contain an
      EcoRI restriction site in close proximity to the hairpin loop.
      Oligonucleotides containing either a T3 or an A3 loop were not hydrolyzed by
      the restriction enzyme and also showed only weak binding to EcoRI in the
      absence of the cofactor Mg2+.  In contrast, hairpins with larger loops are
      hydrolyzed by the enzyme at the scission site next to the loop although the
      substrate with a A4 loop is significantly more resistant than the
      oligonucleotide containing a T4 loop.  The hairpin structures with 3 loop
      residues were found to be thermally most stable while larger hairpin loops
      resulted in structures with lower melting temperatures.  The T-loop hairpins
      are thermally more stable than the hairpins containing the same number of A
      residues in the loop.  As judged from proton NMR spectroscopy and the
      thermodynamic data, the base pair closest to the hairpin loop did form in all
      cases studied.  The hairpin loops did, however, affect the conformation of the
      stem structure of the hairpins.  From 31P and 1H NMR spectroscopy we conclude
      that the perturbation of the stem structure is stronger for smaller hairpin
      loops and that the extent of the perturbation is limited to 2 - 3 base pairs
      for hairpins with T3 or A4 loops.  Our results demonstrate that hairpin loops
      modulate the conformation of the stem residues close to the loop and that this
      in turn reduces the substrate activity for DNA sequence specific proteins.
AU  - Germann MW
AU  - Kalisch BW
AU  - Lundberg P
AU  - Vogel HJ
AU  - van de Sande JH
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 1489-1498.

PMID- 9923708
VI  - 76
DP  - 1998
TI  - NMR spectroscopic and enzymatic studies of DNA hairpins containing mismatches in the EcoRI recognition site.
PG  - 391-402
AB  - We have correlated the structural perturbations caused by DNA mismatches with the enzymatic
      data of the interaction of the restriction endonuclease EcoRI with DNA. Oligonucleotides
      d(CGAGAATTCTCA5GAXAATTCT) (X = G, A, T) and d(CGCGAATTYGCGT4CGCXAATTCGCG) (Y = C, X = G, T and
      Y = A, X = T) containing single mismatches within the EcoRI recognition site were
      characterized by NMR spectroscopy and by their EcoRI substrate properties. UV melting and gel
      electrophoresis studies confirm that the oligonucleotides form hairpin structures. The
      presence of either a CT or a CA mismatch results in markedly lower Tm and van't Hoff
      enthalpies compared with the fully base paired control. NMR imino proton spectra of these
      hairpins demonstrate that the perturbation caused by the two mispairs or a noncanonical AT
      pair is localized and limited to one or two base pairs on either side of the perturbation. The
      DNA hairpin structures containing single mismatches, and to a lesser extent also sequences
      with a single noncanonical base pair, are substrates for the restriction endonuclease. In
      addition to the strand scission at the nonperturbed GpA phosphodiester bond some cleavage is
      observed at the mismatched position. The interactions of the CA and CT mismatched hairpin with
      the enzyme are characterized by binding constants that are only 33 and 57 times lower,
      respectively, than that for the canonical sequence, corresponding to 8-10 kJ x mol(-1) less
      favorable free binding energy. This, taken together with the NMR data, indicates that the CA
      and CT mismatches have only small effects on the EcoRI recognition of the DNA substrate. We
      conclude that two out of the three hydrogen bonds that characterize the interaction of EcoRI
      with the CG base pair in the canonical sequence can still be formed for either the CT or CA
      mismatched recognition site.
AU  - Germann MW
AU  - Kalisch BW
AU  - Varnum JM
AU  - Vogel HJ
AU  - van de Sande JH
PT  - Journal Article
TA  - Biochem. Cell Biol.
JT  - Biochem. Cell Biol.
SO  - Biochem. Cell Biol. 1998 76: 391-402.

PMID- 24926044
VI  - 2
DP  - 2014
TI  - Yersinia pseudotuberculosis ST42 (O:1) Strain Misidentified as Yersinia pestis by Mass Spectrometry Analysis.
PG  - e00435-14
AB  - We report here the draft sequence of strain CEB14_0017, alias HIAD_DUP, recovered from a human
      patient and initially identified as Yersinia pestis by mass
      spectrometry analysis. Genotyping based on tandem repeat polymorphism assigned
      the strain to Yersinia pseudotuberculosis sequence type 42 (ST42). The total
      assembly length is 4,894,739 bp.
AU  - Gerome P
AU  - Le Fleche P
AU  - Blouin Y
AU  - Scholz HC
AU  - Thibault FM
AU  - Raynaud F
AU  - Vergnaud G
AU  - Pourcel C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00435-14.

PMID- 20138093
VI  - 81
DP  - 2010
TI  - Development of pooled suppression subtractive hybridization to analyze the pangenome of Staphylococcus aureus.
PG  - 56-60
AB  - We describe the development and application of a Pooled Suppression
      Subtractive Hybridization (PSSH) method to describe differences between
      the genomic content of a pool of clinical Staphylococcus aureus isolates
      and a sequenced reference strain. In comparative bacterial genomics,
      Suppression Subtractive Hybridization (SSH) is normally utilized to
      compare genomic features or expression profiles of one strain versus
      another, which limits its ability to analyze communities of isolates.
      However, a PSSH approach theoretically enables the user to characterize
      the entirety of gene content unique to a related group of isolates in a
      single reaction. These unique fragments may then be linked to individual
      isolates through standard PCR. This method was applied to examine the
      genomic diversity found in pools of S.aureus isolates associated with
      complicated bacteremia infections leading to endocarditis and
      osteomyelitis. Across four pools of 10 isolates each, four hundred and
      twenty seven fragments not found in or significantly divergent from the S.
      aureus NCTC 8325 reference genome were detected. These fragments could be
      linked to individual strains within its pool by PCR. This is the first use
      of PSSH to examine the S. aureus pangenome. We propose that PSSH is a
      powerful tool for researchers interested in rapidly comparing the genomic
      content of multiple unstudied isolates.
AU  - Gerrish RS
AU  - Gill AL
AU  - Fowler VG
AU  - Gill SR
PT  - Journal Article
TA  - J. Microbiol. Methods
JT  - J. Microbiol. Methods
SO  - J. Microbiol. Methods 2010 81: 56-60.

PMID- 29025938
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Bacillus velezensis GF610, a Producer of Potent Anti-Listeria Agents.
PG  - e01046-17
AB  - Bacillus velezensis GF610 was isolated from soil in Illinois, USA, and found to produce
      amyloliquecidin GF610, a potent two-component antimicrobial peptide. We
      report here the GF610 strain draft genome sequence, which contains 4.29 Mb and an
      overall GC content of 45.91%.
AU  - Gerst MM
AU  - Dudley EG
AU  - Xiaoli L
AU  - Yousef AE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01046-17.

PMID- 29348344
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Bacillus velezensis OSY-S3, a Producer of Potent Antimicrobial Agents Active against Bacteria and Fungi.
PG  - e01465-17
AB  - Bacillus velezensis OSY-S3 produces anti-Listeria, anti-Escherichia coli, and antifungal
      compounds. Additionally, fermentate of B. velezensis OSY-S3 culture
      removes Staphylococcus aureus biofilms effectively. The draft genome sequence of
      B. velezensis OSY-S3 reported here had a genome size of ~3.90 Mb and a G+C
      content of 46.5%.
AU  - Gerst MM
AU  - Yesil M
AU  - Yousef AE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01465-17.

PMID- 29449402
VI  - 6
DP  - 2018
TI  - High-Quality Draft Genome Sequences of Five Xanthomonas arboricola pv. fragariae  Isolates.
PG  - e01585-17
AB  - Xanthomonas arboricola pv. fragariae was described in 2001 as the causal agent of strawberry
      bacterial leaf blight. We report here the first draft whole-genome
      sequences of five X. arboricola pv. fragariae isolates from Italy and France.
AU  - Getaz M
AU  - Baeyen S
AU  - Blom J
AU  - Maes M
AU  - Cottyn B
AU  - Pothier JF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01585-17.

PMID- 28798165
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of Three Isolates of Xanthomonas fragariae, the Bacterium Responsible for Angular Leaf Spots on Strawberry Plants.
PG  - e00642-17
AB  - Xanthomonas fragariae is a worldwide-spread plant bacterial disease causing angular leaf
      spots, thus reducing the yield of production for strawberry fruits.
      Three isolates with various geographic and time origins were sequenced with
      long-read technology (PacBio) to generate finished genome sequences of virulent
      strains and observe the variability in their contents.
AU  - Getaz M
AU  - van der Wolf JM
AU  - Blom J
AU  - Pothier JF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00642-17.

PMID- 28495777
VI  - 5
DP  - 2017
TI  - Complete Annotated Genome Sequences of Two Shiga Toxin-Producing Escherichia coli Strains and One Atypical Enteropathogenic E. coli Strain, Isolated from Naturally  Colonized Cattle of German Origin.
PG  - e00321-17
AB  - Shiga toxin-producing Escherichia coli (STEC) strains are important zoonotic enteric pathogens
      with the main reservoir in cattle. Here, we present the genomes
      of two STEC strains and one atypical enteropathogenic E. coli strain from cattle
      origin, obtained during a longitudinal study in German cattle herds.
AU  - Geue L
AU  - Menge C
AU  - Berens C
AU  - Barth SA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00321-17.

PMID- 14597008
VI  - 50
DP  - 2003
TI  - Sequence and genetic organization of the 19.3-kb erythromycin- and dalfopristin-resistance plasmid pLME300 from Lactobacillus fermentum  ROT1.
PG  - 190-201
AB  - Lactobacillus fermentum ROT1 was isolated from a raw milk dairy product. It is resistant to
      novobiocin, tetracycline, erythromycin and
      dalfopristin. A chromosomal tetracycline-resistance determinant was
      identified as tetM. A 19,398-bp plasmid (pLME300), present in several
      erythromycin-resistant strains of Lb. fermentum, was isolated from strain
      ROT1 and completely sequenced. Based on putative open reading frames,
      pLME300 contains at least four different functional regions. In region I,
      ORF1 shows high homologies to replication proteins of different
      theta-replicating plasmids. In addition, a tandem repeat of a 22-bp
      sequence appears 4.5 times. In region II, ORF3 may code for a methylase,
      and ORF4 has homologies to Mrr restriction system proteins of Deinococcus
      radiodurans and Escherichia coli suggesting a restriction-modification
      system. Region III harbours antibiotic-resistance genes, coding for a
      macrolide-lincosamide-streptogramin B (MLS) methylase Erm(LF) and the
      streptogramin A acetyltransferase Vat(E), which is identical to Vat(E)
      from Enterococcus faecium. Furthermore, region III shows a 91% nucleotide
      sequence identity to an erm-vat linkage of E. faecium. Region IV carries
      ORFs that appear to be involved in plasmid mobilization as characterized
      by a putative origin of transfer and a mobilization protein. pLME300 is
      the largest completely sequenced multi-resistance plasmid isolated from
      any Lactobacillus strain so far.
AU  - Gfeller KY
AU  - Roth M
AU  - Melle L
AU  - Teuber M
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 2003 50: 190-201.

PMID- 20393571
VI  - 0
DP  - 2010
TI  - Metagenome of the Mediterranean deep chlorophyll maximum studied by direct and fosmid library 454 pyrosequencing.
PG  - 1-13
AB  - The deep chlorophyll maximum (DCM) is a zone of maximal photosynthetic activity, generally
      located toward the base of the photic zone in lakes and oceans. In the tropical waters, this
      is a permanent feature, but in the Mediterranean and other temperate waters, the DCM is a
      seasonal phenomenon. The metagenome from a single sample of a mature Mediterranean DCM
      community has been 454 pyrosequenced both directly and after cloning in fosmids. This study is
      the first to be carried out at this sequencing depth (ca. 600 Mb combining direct and fosmid
      sequencing) at any DCM. Our results indicate a microbial community massively dominated by the
      high-light-adapted Prochlorococcus marinus subsp. pastoris, Synechococcus sp., and the
      heterotroph Candidatus Pelagibacter. The sequences retrieved were remarkably similar to the
      existing genome of P. marinus subsp. pastoris with a nucleotide identity over 98%. Besides, we
      found a large number of cyanophages that could prey on this microbe, although sequence
      conservation was much lower. The high abundance of phage sequences in the cellular size
      fraction indicated a remarkably high proportion of cells suffering phage lytic attack. In
      addition, several fosmids clearly belonging to Group II Euryarchaeota were retrieved and
      recruited many fragments from the total direct DNA sequencing suggesting that this group might
      be quite abundant in this habitat. The comparison between the direct and fosmids sequencing
      revealed a bias in the fosmid libraries against low-GC DNA and specifically against the two
      most dominant members of the community, Candidatus Pelagibacter and P. marinus subsp.
      pastoris, thus unexpectedly providing a feasible method to obtain large genomic fragments from
      other less prevalent members of this community.
AU  - Ghai R
AU  - Martin-Cuadrado AB
AU  - Molto AG
AU  - Heredia IG
AU  - Cabrera R
AU  - Martin J
AU  - Verdu M
AU  - Deschamps P
AU  - Moreira D
AU  - Lopez-Garcia P
AU  - Mira A
AU  - Rodriguez-Valera F
PT  - Journal Article
TA  - ISME J.
JT  - ISME J.
SO  - ISME J. 2010 0: 1-13.

PMID- 7550453
VI  - 41
DP  - 1995
TI  - Inhibition of cleavage by restriction endonucleases due to modifications induced in SV40 DNA by methyl methanesulfonate.
PG  - 59-66
AB  - Methyl methanesulfonate (MMS), a direct mutagen, methylates DNA bases and causes distortions
      in DNA structure.  Supercoiled SV40 DNA was treated in vitro with varying concentrations of
      MMS from 0.001 mM to 10 mM MMS either for 30 min or 3 h and analyzed by electrophoresis in 1%
      neutral and alkaline agarose gels.  The electrophoretic mobility (EPM) of native DNA did not
      change after treatment with the mutagen, while alkaline gels revealed low MW DNA fragments due
      to single strand breaks at alkali-sensitive sites generated by the action of MMS.  By
      two-dimensional electrophoresis, we find that all three native DNA forms contain
      alkali-sensitive sites after treatment with MMS.  To examine the effect of base modification
      by MMS on DNA-protein interactions, we have used as probes, restriction endonucleases.  These
      cleave DNA in a sequence-specific manner, and their activity is dependent upon the methylation
      status of the substrate DNA.  We find that cleavage by these restriction endonucleases is
      inhibited due to methylation by MMS.
AU  - Ghaskadbi S
AU  - Bharathi S
AU  - Modak SP
PT  - Journal Article
TA  - Cell. Mol. Biol. Res.
JT  - Cell. Mol. Biol. Res.
SO  - Cell. Mol. Biol. Res. 1995 41: 59-66.

PMID- 24786955
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Photorhabdus luminescens Strain BA1, an Entomopathogenic Bacterium Isolated from Nematodes Found in Egypt.
PG  - e00396-14
AB  - Photorhabdus luminescens strain BA1 is an entomopathogenic bacterium that forms a symbiotic
      association with Heterorhabditis nematodes. We report here a 5.0-Mbp
      draft genome sequence for P. luminscens strain BA1, with a G+C content of 42.46%
      and 4,250 candidate protein-coding genes.
AU  - Ghazal S
AU  - Hurst SGIV
AU  - Morris K
AU  - Abebe-Akele F
AU  - Thomas WK
AU  - Badr UM
AU  - Hussein MA
AU  - Abouzaied MA
AU  - Khalil KM
AU  - Tisa LS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00396-14.

PMID- 26988056
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Photorhabdus luminescens subsp. laumondii HP88, an Entomopathogenic Bacterium Isolated from Nematodes.
PG  - e00154-16
AB  - Photorhabdus luminescens subsp. laumondii HP88 is an entomopathogenic bacterium that forms a
      symbiotic association with Heterorhabditis nematodes. We report here
      a 5.27-Mbp draft genome sequence for P. luminescens subsp. laumondii HP88, with a
      G+C content of 42.4% and containing 4,243 candidate protein-coding genes.
AU  - Ghazal S
AU  - Oshone R
AU  - Simpson S
AU  - Morris K
AU  - Abebe-Akele F
AU  - Thomas WK
AU  - Khalil KM
AU  - Tisa LS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00154-16.

PMID- 28912324
VI  - 5
DP  - 2017
TI  - Permanent Draft Genome Sequence of Photorhabdus temperata Strain Hm, an Entomopathogenic Bacterium Isolated from Nematodes.
PG  - e00974-17
AB  - Photorhabdus temperata strain Hm is an entomopathogenic bacterium that forms a symbiotic
      association with Heterorhabditis nematodes. Here, we report a 5.0-Mbp
      draft genome sequence for P. temperata strain Hm with a G+C content of 44.1% and
      containing 4,226 candidate protein-encoding genes.
AU  - Ghazal S
AU  - Swanson E
AU  - Simpson S
AU  - Morris K
AU  - Abebe-Akele F
AU  - Thomas WK
AU  - Khalil KM
AU  - Tisa LS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00974-17.

PMID- 23887909
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Pseudomonas fluorescens LMG 5329, a White Line-Inducing  Principle-Producing Bioindicator for the Mushroom Pathogen Pseudomonas tolaasii.
PG  - e00383-13
AB  - Pseudomonas tolaasii, the causative agent of Agaricus bisporus brown blotch disease, can be
      identified by the white line reaction, occurring upon
      confrontation of the tolaasin-producing mushroom pathogen with 'Pseudomonas
      reactans,' producing the lipopeptide white line-inducing principle (WLIP). The
      draft genome sequence of the WLIP-producing indicator Pseudomonas fluorescens
      strain LMG 5329 is reported here.
AU  - Ghequire MG
AU  - Rokni-Zadeh H
AU  - Zarrineh P
AU  - De Mot R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00383-13.

PMID- 27081131
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Pseudomonas putida BW11M1, a Banana Rhizosphere Isolate  with a Diversified Antimicrobial Armamentarium.
PG  - e00251-16
AB  - In this study, we report the draft genome ofPseudomonas putidaBW11M1, a banana rhizosphere
      isolate producing various antimicrobial compounds, including a
      lectin-like bacteriocin, an R-type tailocin, the cyclic lipopeptide xantholysin,
      and the fatty acid-derived pseudopyronine.
AU  - Ghequire MG
AU  - Swings T
AU  - Michiels J
AU  - Gross H
AU  - De Mot R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00251-16.

PMID- 26494679
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Cellulolytic and Xylanolytic Paenibacillus sp. A59, Isolated from Decaying Forest Soil from Patagonia, Argentina.
PG  - e01233-15
AB  - Paenibacillus sp. A59 was isolated from decaying forest soil in Argentina and characterized as
      a xylanolytic strain. We report the draft genome sequence of this isolate, with an estimated
      genome size of 7 Mb which harbor 6,424 coding sequences. Genes coding for hydrolytic enzymes
      involved in lignocellulose deconstruction were predicted.
AU  - Ghio S
AU  - Martinez CAI
AU  - Talia P
AU  - Grasso DH
AU  - Campos E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01233-15.

PMID- 27491997
VI  - 4
DP  - 2016
TI  - Permanent Draft Genome Sequence of Nocardia sp. BMG111209, an Actinobacterium Isolated from Nodules of Casuarina glauca.
PG  - e00770-16
AB  - Nocardia sp. strain BMG111209 is a non-Frankia actinobacterium isolated from root nodules of
      Casuarina glauca in Tunisia. Here, we report the 9.1-Mbp draft genome
      sequence of Nocardia sp. strain BMG111209 with a G + C content of 69.19% and
      8,122 candidate protein-encoding genes.
AU  - Ghodhbane-Gtari F et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00770-16.

PMID- 27491980
VI  - 4
DP  - 2016
TI  - Permanent Improved High-Quality Draft Genome Sequence of Nocardia casuarinae Strain BMG51109, an Endophyte of Actinorhizal Root Nodules of Casuarina glauca.
PG  - e00799-16
AB  - Here, we report the first genome sequence of a Nocardia plant endophyte, N. casuarinae strain
      BMG51109, isolated from Casuarina glauca root nodules. The
      improved high-quality draft genome sequence contains 8,787,999 bp with a 68.90%
      GC content and 7,307 predicted protein-coding genes.
AU  - Ghodhbane-Gtari F et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00799-16.

PMID- 23516212
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Frankia sp. Strain CN3, an Atypical, Noninfective (Nod-) Ineffective (Fix-) Isolate from Coriaria nepalensis.
PG  - e0008513
AB  - We report here the genome sequence of Frankia sp. strain CN3, which was isolated  from
      Coriaria nepalensis. This genome sequence is the first from the fourth
      lineage of Frankia, strains of which are unable to reinfect actinorhizal plants.
      At 10 Mb, it represents the largest Frankia genome sequenced to date.
AU  - Ghodhbane-Gtari F et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0008513.

PMID- 24874687
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Frankia sp. Strain BMG5.23, a Salt-Tolerant Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina  glauca Grown in Tunisia.
PG  - e00520-14
AB  - Nitrogen-fixing actinobacteria of the genus Frankia are symbionts of woody dicotyledonous
      plants termed actinorhizal plants. We report here a 5.27-Mbp draft genome sequence for Frankia
      sp. strain BMG5.23, a salt-tolerant nitrogen-fixing actinobacterium isolated from root nodules
      of Casuarina glauca collected in Tunisia.
AU  - Ghodhbane-Gtari F
AU  - Hurst SGIV
AU  - Oshone R
AU  - Morris K
AU  - Abebe-Akele F
AU  - Thomas WK
AU  - Ktari A
AU  - Salem K
AU  - Gtari M
AU  - Tisa LS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00520-14.

PMID- 
VI  - 79
DP  - 2010
TI  - Induced expression of EcoRI endonuclease as an active maltose-binding fusion protein in Escherichia coli.
PG  - 167-172
AB  - Among the numerous bacterial Type II restriction enzymes, EcoRI endonuclease is the most
      extensively studied and is widely used in
      recombinant DNA technology. Its heterologous overexpression as
      recombinant protein has already been studied. However, very limited
      information concerning its fused product is available thus far. In the
      present study, the EcoRI restriction endonuclease gene was cloned and
      expressed as a part of maltose-binding fusion protein under the control
      of strong inducible tac promoter in TB1 strain of Escherichia coli
      cells. Transformed cells containing pMALc2X-EcoRI recombinant plasmid
      were unable to grow under experimental conditions. However, fused EcoRI
      protein was purified (with the yield of 0.01 mg/l of bacterial culture)
      by affinity chromatography from E. coli cells induced at the late
      exponential phase of growth. Restriction quality test revealed that the
      purified product could restrict a control plasmid DNA in vitro.
AU  - Gholizadeh A
AU  - Faizi MH
AU  - Kohnehrouz BB
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2010 79: 167-172.

PMID- 19775076
VI  - 47
DP  - 2009
TI  - Carborundum-dependent entrance of EcoRI restriction enzyme into plant cells and specific cleavage of genomic DNA.
PG  - 684-689
AB  - In a basic research to determine the morpho-molecular interactions of plant tissues with EcoRI
      DNA restriction enzyme, it was demonstrated
      that this protein is capable of entering the sunflower and maize leaf
      cells using a plant tissue-abrading material and cleaving the genomic
      DNA at specific sites. This was inferred from the analysis of
      morphological patterns of EcoRI-treated leaf areas as well as using
      some molecular tests, including the cleavage pattern analysis of
      genomic DNA isolated from treated locations followed by ligation of
      cleaved fragments into EcoRI site of a DNA cloning vector system. The
      overall results indicated that the specific restriction of genomic DNA
      may happen following the entrance of EcoRI protein most likely into the
      nucleus of plant cells.
AU  - Gholizadeh A
AU  - Kohnehrouz BB
PT  - Journal Article
TA  - Indian J. Exp. Biol.
JT  - Indian J. Exp. Biol.
SO  - Indian J. Exp. Biol. 2009 47: 684-689.

PMID- 26112790
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequencing of Brevundimonas diminuta XGC1, Isolated from a Tuberculosis Patient in Gujarat, India.
PG  - e00686-15
AB  - We report the draft genome of Brevundimonas diminuta strain XGC1, isolated from a
      tuberculosis-infected patient in Gujarat, India. This study also reveals that the
      B. diminuta XGC1 strain has acquired mutation to confer resistance to quinolone
      drugs.
AU  - Ghosh A
AU  - Chandratre K
AU  - Chaudhary A
AU  - Chaudhary S
AU  - Badani N
AU  - Chaudhary PS
AU  - Dhawan D
AU  - Vudathala S
AU  - Chikara SK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00686-15.

PMID- 23516205
VI  - 1
DP  - 2013
TI  - Whole-Genome Sequencing of Micrococcus luteus Strain Modasa, of Indian Origin.
PG  - e0007613
AB  - The hydrocarbon-degrading bacterium Micrococcus luteus strain Modasa was isolated from
      contaminated soil from Modasa, North Gujarat, India. Whole-genome sequencing
      and analysis provide an insight into the potentially important genes responsible
      for bioremediation.
AU  - Ghosh A
AU  - Chaudhary SA
AU  - Apurva SR
AU  - Tiwari T
AU  - Gupta S
AU  - Singh AK
AU  - Katudia KH
AU  - Patel MP
AU  - Chikara SK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0007613.

PMID- 24423871
VI  - 42
DP  - 2014
TI  - Cellular localization and dynamics of the Mrr type IV restriction endonuclease of Escherichia coli.
PG  - 3908-3918
AB  - In this study, we examined the intracellular whereabouts of Mrr, a cryptic type IV restriction
      endonuclease of Escherichia coli K12, in response to different
      conditions. In absence of stimuli triggering its activity, Mrr was found to be
      strongly associated with the nucleoid as a number of discrete foci, suggesting
      the presence of Mrr hotspots on the chromosome. Previously established elicitors
      of Mrr activity, such as exposure to high (hydrostatic) pressure (HP) or
      expression of the HhaII methyltransferase, both caused nucleoid condensation and
      an unexpected coalescence of Mrr foci. However, although the resulting
      Mrr/nucleoid complex was stable when triggered with HhaII, it tended to be only
      short-lived when elicited with HP. Moreover, HP-mediated activation of Mrr
      typically led to cellular blebbing, suggesting a link between chromosome and
      cellular integrity. Interestingly, Mrr variants could be isolated that were
      specifically compromised in either HhaII- or HP-dependent activation,
      underscoring a mechanistic difference in the way both triggers activate Mrr. In
      general, our results reveal that Mrr can take part in complex spatial
      distributions on the nucleoid and can be engaged in distinct modes of activity.
AU  - Ghosh A
AU  - Passaris I
AU  - Tesfazgi MM
AU  - Rocha S
AU  - Vanoirbeek K
AU  - Hofkens J
AU  - Aertsen A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2014 42: 3908-3918.

PMID- 28774984
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of blaCTX-M-27-Encoding Escherichia coli Strain H105 of  Sequence Type 131 Lineage C1/H30R.
PG  - e00736-17
AB  - Escherichia coli sequence type 131 (ST131) is the most frequent antimicrobial-resistant
      lineage of E. coli, propagating extended-spectrum
      beta-lactamases (ESBL) worldwide. Recently, an alarming rate of increase in
      isolates of the sublineage C1/H30R-blaCTX-M-27 of ST131 in geographically distant
      countries was reported. Here, we present the complete genome sequence of the
      ST131 sublineage C1/H30R E. coli isolate harboring blaCTX-M-27 from Germany.
AU  - Ghosh H
AU  - Bunk B
AU  - Doijad S
AU  - Schmiedel J
AU  - Falgenhauer L
AU  - Sproer C
AU  - Imirzalioglu C
AU  - Overmann J
AU  - Chakraborty T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00736-17.

PMID- 15541279
VI  - 293
DP  - 2004
TI  - An improved method for utilization of peptide substrates for antibody characterization and enzymatic assays.
PG  - 85-95
AB  - Synthetic peptides have become an important tool in antibody production and enzyme
      characterization. The small size of peptides, however, has
      hindered their use in assays systems, such as Western blots, and as
      immunogens. Here, we present a facile method to improve the properties
      of peptides for multiple applications by ligating the peptides to
      intein-generated carrier proteins. The stoichiometric ligation of
      peptide and carrier achieved by intein-mediated protein ligation (IPL)
      results in the ligation product migrating as a single band on a
      SDS-PAGE gel. The carrier proteins, HhaI methylase (M.HhaI) and
      maltose-binding protein (MBP), were ligated to various peptides; the
      ligated carrier-peptide products gave sharp, reproducible bands when
      used as positive controls for antibodies raised against the same
      peptides during Western blot analysis. We further show that ligation of
      the peptide antigens to a different thioester-tagged carrier protein,
      paramyosin, produced immunogens for the production of antisera in
      rabbits or mice. Furthermore, we demonstrate the generation of a
      substrate for enzymatic assays by ligating a peptide containing the
      phosphorylation site for Abl protein tyrosine kinase to a carrier
      protein. This carrier-peptide protein was used as a kinase substrate
      that could easily be tested for phosphorylation using a phosphotyrosine
      antibody in Western blot analysis. These techniques do not require
      sophisticated equipment, reagents, or skills thereby providing a simple
      method for research and development.
AU  - Ghosh I
AU  - Sun L
AU  - Evans TC
AU  - Xu MQ
PT  - Journal Article
TA  - J. Immunol. Methods
JT  - J. Immunol. Methods
SO  - J. Immunol. Methods 2004 293: 85-95.

PMID- 25301646
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Sphingobacterium sp. Strain PM2-P1-29, a Tetracycline-Degrading TetX-Expressing Aerobic Bacterium Isolated from  Agricultural Soil.
PG  - e00963-14
AB  - The genome of Sphingobacterium sp. strain PM2-P1-29 was sequenced. The bacterium  contains a
      physiologically active tet(X) gene, encoding a tetracycline-degrading
      monooxygenase. To our knowledge, this is the only bacterium naturally harboring
      tet(X) for which tetracycline degradation has been demonstrated.
AU  - Ghosh S
AU  - LaPara TM
AU  - Sadowsky MJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00963-14.

PMID- 8065930
VI  - 22
DP  - 1994
TI  - Real time kinetics of restriction endonuclease cleavage monitored by fluorescence resonance energy transfer.
PG  - 3155-3159
AB  - The kinetics of PaeR7I endonuclease-catalysed cleavage reactions of fluorophor-labeled
      oligonucleotide substrates have been examined using fluorescence resonance energy transfer
      (FRET). A series of duplex substrates were synthesized with an internal CTCGAG PaeR7I
      recognition site and donor (fluorescein) and acceptor (rhodamine) dyes conjugated to the
      opposing 5' termini. The time-dependent increase in donor fluorescence resulting from
      restriction cleavage of these substrates was continuously monitored and the initial rate data
      was fitted to the Michaelis-Menten equation. The steady state kinetic parameters for these
      substrates were in agreement with the rate constants obtained from a gel electrophoresis-based
      fixed time point assay using radiolabeled substrates. The FRET method provides a rapid
      continuous assay as well as high sensitivity and reproducibility. These features should make
      the technique useful for the study of DNA-cleaving enzymes.
AU  - Ghosh SS
AU  - Eis PS
AU  - Blumeyer K
AU  - Fearon K
AU  - Millar DP
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1994 22: 3155-3159.

PMID- 2402435
VI  - 18
DP  - 1990
TI  - Analysis of substrate specificity of the PaeR7I endonuclease: effect of base methylation on the kinetics of cleavage.
PG  - 5063-5068
AB  - In murine cells expressing the PaeR7I endonuclease and methylase genes, the
      recognition sites (CTCGAG) of these enzymes can be methylated at the adenine
      residue by the PaeR7I methylase and at the internal cytosine by the mouse DNA
      methyltransferase.  Using nonadecameric duplex deoxyoligonucleotide substrates,
      the specificity of the PaeR7I endonuclease for unmethylated, hemi-methylated,
      and fully methylated N6-methyladenine (m6A) and C5-methylcytosine (m5C)
      versions of these substrates has been studied.  The Km, kcat, and Ki values for
      these model substrates have been measured and suggest that fully or
      hemi-m6A-methylated PaeR7I sites in the murine genome are completely protected.
      However, the reactivity of fully or hemi-m5C-methylated PaeR7I sites is
      depressed 2900- and 100-fold respectively, compared to unmodified PaeR7I sites.
      The implications of the kinetic constants of the PaeR7I endonuclease for these
      methylated recognition sites as they occur in murine cells expressing this
      endonuclease gene are discussed.
AU  - Ghosh SS
AU  - Obermiller PS
AU  - Kwoh TJ
AU  - Gingeras TR
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 5063-5068.

PMID- 21914874
VI  - 193
DP  - 2011
TI  - Whole-Genome Shotgun Sequencing of the Sulfur-Oxidizing Chemoautotroph Tetrathiobacter kashmirensis.
PG  - 5553-5554
AB  - The chemolithoautotrophic betaproteobacterium Tetrathiobacter kashmirensis belongs to the
      family Alcaligenaceae and is phylogenetically closely
      related to pathogens such as Taylorella and Bordetella species. While a
      complete inorganic sulfur oxidation gene cluster, soxCDYZAXWB, is present
      in its genome, pathogenicity islands or genes associated with virulence,
      disease, cellular invasion, and/or intracellular resistance are completely
      absent.
AU  - Ghosh W
AU  - George A
AU  - Agarwal A
AU  - Raj P
AU  - Alam M
AU  - Pyne P
AU  - Das Gupta SK
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5553-5554.

PMID- 24744342
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of the Treponema pallidum subsp. pallidum Sea81-4 Strain.
PG  - e00333-14
AB  - Using the rabbit model of syphilis, the Sea81-4 strain of Treponema pallidum subsp. pallidum
      has been found to be more likely than other strains to invade the central nervous system
      (CNS). To identify possible explanations for this important phenotype at the genomic level, we
      sequenced the Sea81-4 strain genome.
AU  - Giacani L
AU  - Iverson-Cabral SL
AU  - King JC
AU  - Molini BJ
AU  - Lukehart SA
AU  - Centurion-Lara A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00333-14.

PMID- 20348263
VI  - 192
DP  - 2010
TI  - Complete genome sequence and annotation of the Treponema pallidum subsp. pallidum Chicago strain.
PG  - 2645-2646
AB  - In syphilis research, the Nichols strain of Treponema pallidum, isolated in 1912, has been the
      most widely studied. Recently, important differences
      among T. pallidum strains emerged; therefore, we sequenced and annotated
      the Chicago strain genome to facilitate and encourage the use of this
      strain in studying the pathogenesis of syphilis.
AU  - Giacani L
AU  - Jeffrey BM
AU  - Molini BJ
AU  - Le HT
AU  - Lukehart SA
AU  - Centurion-Lara A
AU  - Rockey DD
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 2645-2646.

PMID- 24947562
VI  - 16
DP  - 2014
TI  - Dam methylation regulates the expression of SPI-5-encoded sopB gene in Salmonella enterica serovar Typhimurium.
PG  - 615-622
AB  - DNA adenine methylation is an essential factor in Salmonella virulence. Here, we investigate
      the involvement of DNA adenine methylase (Dam) in the expression and translocation of a
      SPI-5-encoded effector of S. Typhimurium. SopB expression and secretion were determined using
      SopB FLAG-tagged wild type and dam strains of S. Typhimurium. Western blot and quantitative
      reverse transcriptase PCR analysis showed that the dam mutant expresses lower levels of SopB
      protein and sopB mRNA than the wild type strain under SPI-1 and SPI-2 inducing conditions in
      vitro. SopB secretion was also considerably impaired in the absence of dam. In agreement with
      in vitro experiments, SopB synthesis in dam mutants recovered from infected epithelial cells
      and from murine mesenteric lymph nodes was reduced by 40% respect to the wild type strain (p <
      0.05). SopB translocation was neither detected in the cytosol of epithelial cells nor in the
      cytosol of cells isolated from mesenteric lymph nodes infected with the dam mutant. Taken
      together, our results demonstrate that, in S. Typhimurium, Dam methylation modulates the
      expression and translocation of SPI-5-encoded SopB effector.
AU  - Giacomodonato MN
AU  - Llana MN
AU  - Castaneda MR
AU  - Buzzola F
AU  - Garcia MD
AU  - Calderon MD
AU  - Sarnacki SH
AU  - Cerquetti MC
PT  - Journal Article
TA  - Microbes Infect.
JT  - Microbes Infect.
SO  - Microbes Infect. 2014 16: 615-622.

PMID- 10572629
VI  - 27
DP  - 1999
TI  - MboII endonuclease heat inactivation before agarose gel electrophoresis to prevent artifactual bands in restriction patterns.
PG  - 886-887
AB  - MboII restriction enzyme belongs to class-IIS endonucleases group.  Like all of the enzymes
      belonging to this class, MboII cleaves DNA at a specific distance from its recognition
      sequence and still binds to its recognition sequence after DNA has been cleaved, because
      binding and cleaving domains have separate functions.
AU  - Giammanco GM
AU  - Grimont F
AU  - Grimont PA
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 1999 27: 886-887.

PMID- 25676759
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Xylella fastidiosa CoDiRO Strain.
PG  - e01538-14
AB  - We determined the draft genome sequence of the Xylella fastidiosa CoDiRO strain,  which has
      been isolated from olive plants in southern Italy (Apulia). It is
      associated with olive quick decline syndrome (OQDS) and characterized by
      extensive scorching and desiccation of leaves and twigs.
AU  - Giampetruzzi A
AU  - Chiumenti M
AU  - Saponari M
AU  - Donvito G
AU  - Italiano A
AU  - Loconsole G
AU  - Boscia D
AU  - Cariddi C
AU  - Martelli GP
AU  - Saldarelli P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01538-14.

PMID- 26679584
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of CO33, a Coffee-Infecting Isolate of Xylella fastidiosa.
PG  - e01472-15
AB  - The draft genome sequence of Xylella fastidiosa CO33 isolate, retrieved from symptomatic
      leaves of coffee plant intercepted in northern Italy, is reported.
      The CO33 genome size is 2,681,926 bp with a GC content of 51.7%.
AU  - Giampetruzzi A
AU  - Loconsole G
AU  - Boscia D
AU  - Calzolari A
AU  - Chiumenti M
AU  - Martelli GP
AU  - Saldarelli P
AU  - Almeida RP
AU  - Saponari M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01472-15.

PMID- 28684573
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of the Olive-Infecting Strain Xylella fastidiosa subsp.  pauca De Donno.
PG  - e00569-17
AB  - We report here the complete and annotated genome sequence of the plant-pathogenic bacterium
      Xylella fastidiosa subsp. pauca strain De Donno. This strain was
      recovered from an olive tree severely affected by olive quick decline syndrome
      (OQDS), a devastating olive disease associated with X. fastidiosa infections in
      susceptible olive cultivars.
AU  - Giampetruzzi A
AU  - Saponari M
AU  - Almeida RPP
AU  - Essakhi S
AU  - Boscia D
AU  - Loconsole G
AU  - Saldarelli P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00569-17.

PMID- 18332421
VI  - 105
DP  - 2008
TI  - Helicobacter pylori evolution during progression from chronic atrophic gastritis to gastric cancer and its impact on gastric stem cells.
PG  - 4358-4363
AB  - We have characterized the adaptations of Helicobacter pylori to a rarely
      captured event in the evolution of its impact on host biology-the
      transition from chronic atrophic gastritis (ChAG) to gastric
      adenocarcinoma-and defined the impact of these adaptations on an
      intriguing but poorly characterized interaction between this bacterium and
      gastric epithelial stem cells. Bacterial isolates were obtained from a
      single human host colonized with a single dominant strain before and after
      his progression from ChAG to gastric adenocarcinoma during a 4-year
      interval. Draft genome assemblies were generated from two isolates, one
      ChAG-associated, the other cancer-associated. The cancer-associated strain
      was less fit in a gnotobiotic transgenic mouse model of human ChAG and
      better able to establish itself within a mouse gastric epithelial
      progenitor-derived cell line (mGEP) that supports bacterial attachment.
      GeneChip-based comparisons of the transcriptomes of mGEPs and a control
      mouse gastric epithelial cell line revealed that, upon infection, the
      cancer-associated strain regulates expression of GEP-associated signaling
      and metabolic pathways, and tumor suppressor genes associated with
      development of gastric cancer in humans, in a manner distinct from the
      ChAG-associated isolate. The effects on GEP metabolic pathways, some of
      which were confirmed in gnotobiotic mice, together with observed changes
      in the bacterial transcriptome are predicted to support aspects of an
      endosymbiosis between this microbe and gastric stem cells. These results
      provide insights about how H. pylori may adapt to and influence stem cell
      biology and how its intracellular residency could contribute to gastric
      tumorigenesis.
AU  - Giannakis M
AU  - Chen SL
AU  - Karam SM
AU  - Engstrand L
AU  - Gordon JI
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2008 105: 4358-4363.

PMID- 14563834
VI  - 54
DP  - 2003
TI  - Isolation and characterization of a maintenance DNA-methyltransferase gene from peach (Prunus persica [L.] Batsch): transcript localization in vegetative and reproductive meristems of triple buds.
PG  - 2623-2633
AB  - A cDNA coding for a DNA (cytosine-5)-methyltransferase (METase) was
      isolated from peach (Prunus persica [L.] Batsch) and the corresponding
      gene designated as PpMETI. The latter encoded a predicted polypeptide of
      1564 amino acid residues and harboured all the functional domains
      conserved in the maintenance METases group type I. PpMETI was a single
      copy in the cultivar Chiripa which was used as a model in the present
      study. Expression analyses revealed that PpMETI transcripts were more
      abundant in tissues with actively proliferating cells such as apical tips,
      uncurled leaves, elongating herbaceous stems, and small immature fruits.
      Peach plants bear bud clusters (triads or triple buds), consisting of two
      lateral and one central bud with floral and vegetative fates,
      respectively. PpMETI in situ hybridization was performed in triple buds
      during their entire developmental cycle. High and low levels of PpMETI
      transcript were related to burst and quiescence of vegetative growth,
      respectively. Message localization distinguished lateral from central buds
      during the meristem switch to the floral phase. In fact, the PpMETI
      message was abundant in the L1 layer of protruding domes, a morphological
      trait marking the beginning of floral transition. The PpMETI transcript
      was also monitored during organ flower formation. Altogether, these data
      suggest a relationship between DNA replication and PpMETI gene expression.
AU  - Giannino D
AU  - Mele G
AU  - Cozza R
AU  - Bruno L
AU  - Testone G
AU  - Ticconi C
AU  - Frugis G
AU  - Bitonti MB
AU  - Innocenti AM
AU  - Mariotti D
PT  - Journal Article
TA  - J. Exp. Bot.
JT  - J. Exp. Bot.
SO  - J. Exp. Bot. 2003 54: 2623-2633.

PMID- 27365345
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a New Zealand Rickettsia-Like Organism Isolated from Farmed Chinook Salmon.
PG  - e00503-16
AB  - We report here the draft genome sequence of a rickettsia-like organism, isolated  from a New
      Zealand Chinook salmon farm experiencing high mortality. The genome is approximately 3 Mb in
      size, has a G+C content of approximately 39.2%, and is predicted to contain 2,870 coding
      sequences.
AU  - Gias E
AU  - Draper J
AU  - Brosnahan CL
AU  - Orr D
AU  - McFadden A
AU  - Jones B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00503-16.

PMID- 20497330
VI  - 78
DP  - 2010
TI  - Better late than early: delayed translation of intron-encoded endonuclease I-TevI is required for efficient splicing of its host group I intron.
PG  - 35-46
AB  - The td group I intron interrupting the thymidylate synthase (TS) gene of phage T4 is a mobile
      intron that encodes the homing endonuclease
      I-TevI. Efficient RNA splicing of the intron is required to restore
      function of the TS gene, while expression of I-TevI from within the
      intron is required to initiate intron mobility. Three distinct layers
      of regulation temporally limit I-TevI expression to late in the T4
      infective cycle, yet the biological rationale for stringent regulation
      has not been tested. Here, we deleted key control elements to
      deregulate I-TevI expression at early and middle times post T4
      infection. Strikingly, we found that deregulation of I-TevI, or of a
      catalytically inactive variant, generated a thymidine-dependent
      phenotype that is caused by a reduction in td intron splicing.
      Prematurely terminating I-TevI translation restores td splicing,
      full-length TS synthesis, and rescues the thymidine-dependent
      phenotype. We suggest that stringent translational control of I-TevI
      evolved to prevent the ribosome from disrupting key structural elements
      of the td intron that are required for splicing and TS function at
      early and middle times post T4 infection. Analogous translational
      regulatory mechanisms in unrelated intron-open reading frame
      arrangements may also function to limit deleterious consequences on
      splicing and host gene function.
AU  - Gibb EA
AU  - Edgell DR
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2010 78: 35-46.

PMID- 18218864
VI  - 319
DP  - 2008
TI  - Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome.
PG  - 1215-1220
AB  - We have synthesized a 582,970-base pair Mycoplasma genitalium genome. This synthetic genome,
      named M. genitalium JCVI-1.0, contains all the genes of wild-type M. genitalium G37 except
      MG408, which was disrupted by an antibiotic marker to block pathogenicity and to allow for
      selection. To identify the genome as synthetic, we inserted "watermarks" at intergenic sites
      known to tolerate transposon insertions. Overlapping "cassettes" of 5 to 7 kilobases (kb),
      assembled from chemically synthesized oligonucleotides, were joined by in vitro recombination
      to produce intermediate assemblies of approximately 24 kb, 72 kb ("1/8 genome"), and 144 kb
      ("1/4 genome"), which were all cloned as bacterial artificial chromosomes in Escherichia coli.
      Most of these intermediate clones were sequenced, and clones of all four 1/4 genomes with the
      correct sequence were identified. The complete synthetic genome was assembled by
      transformation-associated recombination cloning in the yeast Saccharomyces cerevisiae, then
      isolated and sequenced. A clone with the correct sequence was identified. The methods
      described here will be generally useful for constructing large DNA molecules from chemically
      synthesized pieces and also from combinations of natural and synthetic DNA segments.
AU  - Gibson DG et al
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2008 319: 1215-1220.

PMID- 20488990
VI  - 329
DP  - 2010
TI  - Creation of a bacterial cell controlled by a chemically synthesized genome.
PG  - 52-56
AB  - We report the design, synthesis, and assembly of the 1.08-mega-base pair
      Mycoplasma mycoides JCVI-syn1.0 genome starting from digitized genome
      sequence information and its transplantation into a M. capricolum
      recipient cell to create new M. mycoides cells that are controlled only by
      the synthetic chromosome. The only DNA in the cells is the designed
      synthetic DNA sequence, including "watermark" sequences and other designed
      gene deletions and polymorphisms, and mutations acquired during the
      building process. The new cells have expected phenotypic properties and
      are capable of continuous self-replication.
AU  - Gibson DG et al
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2010 329: 52-56.

PMID- 27777651
VI  - 11
DP  - 2016
TI  - Draft genome sequence of the marine Rhodobacteraceae strain O3.65, cultivated from oil-polluted seawater of the Deepwater Horizon oil spill.
PG  - 81
AB  - The marine alphaproteobacterium strain O3.65 was isolated from an enrichment culture of
      surface seawater contaminated with weathered oil (slicks) from the
      Deepwater Horizon (DWH) oil spill and belongs to the ubiquitous, diverse and
      ecological relevant Roseobacter group within the Rhodobacteraceae. Here, we
      present a preliminary set of physiological features of strain O3.65 and a
      description and annotation of its draft genome sequence. Based on our data we
      suggest potential ecological roles of the isolate in the degradation of crude oil
      within the network of the oil-enriched microbial community. The draft genome
      comprises 4,852,484 bp with 4,591 protein-coding genes and 63 RNA genes. Strain
      O3.65 utilizes pentoses, hexoses, disaccharides and amino acids as carbon and
      energy source and is able to grow on several hydroxylated and substituted
      aromatic compounds. Based on 16S rRNA gene comparison the closest described and
      validated strain is Phaeobacter inhibens DSM 17395, however, strain O3.65 is
      lacking several phenotypic and genomic characteristics specific for the genus
      Phaeobacter. Phylogenomic analyses based on the whole genome support extensive
      genetic exchange of strain O3.65 with members of the genus Ruegeria, potentially
      by using the secretion system type IV. Our physiological observations are
      consistent with the genomic and phylogenomic analyses and support that strain
      O3.65 is a novel species of a new genus within the Rhodobacteraceae.
AU  - Giebel HA
AU  - Klotz F
AU  - Voget S
AU  - Poehlein A
AU  - Grosser K
AU  - Teske A
AU  - Brinkhoff T
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 81.

PMID- 12886019
VI  - 100
DP  - 2003
TI  - The genome sequence of Blochmannia floridanus: Comparative analysis of reduced genomes.
PG  - 9388-9393
AB  - Bacterial symbioses are widespread among insects, probably being one of the key factors of
      their evolutionary success. We present the complete
      genome sequence of Blochmannia floridanus, the primary endosymbiont of
      carpenter ants. Although these ants feed on a complex diet, this symbiosis
      very likely has a nutritional basis: Blochmannia is able to supply
      nitrogen and sulfur compounds to the host while it takes advantage of the
      host metabolic machinery. Remarkably, these bacteria lack all known genes
      involved in replication initiation (dnaA, priA, and recA). The
      phylogenetic analysis of a set of conserved protein-coding genes shows
      that Bl. floridanus is phylogenetically related to Buchnera aphidicola and
      Wigglesworthia glossinidia, the other endosymbiotic bacteria whose
      complete genomes have been sequenced so far. Comparative analysis of the
      five known genomes from insect endosymbiotic bacteria reveals they share
      only 313 genes, a number that may be close to the minimum gene set
      necessary to sustain endosymbiotic life.
AU  - Gil R
AU  - Silva FJ
AU  - Zientz E
AU  - Delmotte F
AU  - Gonzalez-Candelas F
AU  - Latorre A
AU  - Rausell C
AU  - Kamerbeek J
AU  - Gadau J
AU  - Holldobler B
AU  - Van Ham RC
AU  - Gross R
AU  - Moya A
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2003 100: 9388-9393.

PMID- 24336365
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Campylobacter fetus subsp. testudinum Strain 03-427T.
PG  - e01002-13
AB  - Campylobacter fetus subsp. testudinum has been isolated from reptiles and humans. This
      Campylobacter subspecies is genetically distinct from other C. fetus
      subspecies. Here, we present the first whole-genome sequence for this C. fetus
      subspecies.
AU  - Gilbert MJ
AU  - Miller WG
AU  - Yee E
AU  - Blaser MJ
AU  - Wagenaar JA
AU  - Duim B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01002-13.

PMID- 25146144
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Campylobacter iguaniorum Strain 1485ET, Isolated from a Bearded Dragon (Pogona vitticeps).
PG  - e00844-14
AB  - Campylobacter iguaniorum has been isolated from reptiles. This Campylobacter species is
      genetically related to Campylobacter fetus and Campylobacter
      hyointestinalis. Here we present the first whole-genome sequence for this
      species.
AU  - Gilbert MJ
AU  - Miller WG
AU  - Yee E
AU  - Kik M
AU  - Wagenaar JA
AU  - Duim B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00844-14.

PMID- 23050599
VI  - 13
DP  - 2012
TI  - The Caulobacter crescentus phage phiCbK: genomics of a canonical phage.
PG  - 542
AB  - ABSTRACT: BACKGROUND: The bacterium Caulobacter crescentus is a popular model for
      the study of cell cycle regulation and senescence. The large prolate siphophage
      phiCbK has been an important tool in C. crescentus biology, and has been studied
      in its own right as a model for viral morphogenesis. Although a system of some
      interest, to date little genomic information is available on phiCbK or its
      relatives. RESULTS: Five novel phiCbK-like C. crescentus bacteriophages,
      CcrMagneto, CcrSwift, CcrKarma, CcrRogue and CcrColossus, were isolated from the
      environment. The genomes of phage phiCbK and these five environmental phage
      isolates were obtained by 454 pyrosequencing. The phiCbK-like phage genomes range
      in size from 205 kb encoding 318 proteins (phiCbK) to 280 kb encoding 448
      proteins (CcrColossus), and were found to contain nonpermuted terminal
      redundancies of 10 to 17 kb. A novel method of terminal ligation was developed to
      map genomic termini, which confirmed termini predicted by coverage analysis. This
      suggests that sequence coverage discontinuities may be useable as predictors of
      genomic termini in phage genomes. Genomic modules encoding virion morphogenesis,
      lysis and DNA replication proteins were identified. The phiCbK-like phages were
      also found to encode a number of intriguing proteins; all contain a clearly
      T7-like DNA polymerase, and five of the six encode a possible homolog of the C.
      crescentus cell cycle regulator GcrA, which may allow the phage to alter the host
      cell's replicative state. The structural proteome of phage phiCbK was determined,
      identifying the portal, major and minor capsid proteins, the tail tape measure
      and possible tail fiber proteins. All six phage genomes are clearly related;
      phiCbK, CcrMagneto, CcrSwift, CcrKarma and CcrRogue form a group related at the
      DNA level, while CcrColossus is more diverged but retains significant similarity
      at the protein level. CONCLUSIONS: Due to their lack of any apparent relationship
      to other described phages, this group is proposed as the founding cohort of a new
      phage type, the phiCbK-like phages. This work will serve as a foundation for
      future studies on morphogenesis, infection and phage-host interactions in C.
      crescentus.
AU  - Gill JJ
AU  - Berry JD
AU  - Russell WK
AU  - Lessor L
AU  - Escobar-Garcia DA
AU  - Hernandez D
AU  - Kane A
AU  - Keene J
AU  - Maddox M
AU  - Martin R
AU  - Mohan S
AU  - Thorn AM
AU  - Russell DH
AU  - Young R
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2012 13: 542.

PMID- 15774886
VI  - 187
DP  - 2005
TI  - Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain.
PG  - 2426-2438
AB  - Staphylococcus aureus is an opportunistic pathogen and the major causative agent of numerous
      hospital- and community-acquired infections. Staphylococcus epidermidis has emerged as a
      causative agent of infections often associated with implanted medical devices. We have
      sequenced the  2.8-Mb genome of S. aureus COL, an early methicillin-resistant isolate, and the
      2.6-Mb genome of S. epidermidis RP62a, a methicillin-resistant biofilm isolate. Comparative
      analysis of these and other staphylococcal genomes was used to explore the evolution of
      virulence and resistance between these two species. The S. aureus and S. epidermidis genomes
      are syntenic throughout their lengths and share a core set of 1,681 open reading frames.
      Genome islands in nonsyntenic regions are the primary source of variations in pathogenicity
      and resistance. Gene transfer between staphylococci and low-GC-content gram-positive bacteria
      appears to have shaped their virulence and resistance profiles. Integrated plasmids in S.
      epidermidis carry genes encoding resistance to cadmium and species-specific LPXTG surface
      proteins. A novel genome island encodes multiple phenol-soluble modulins, a potential S.
      epidermidis virulence factor. S. epidermidis contains the cap operon, encoding the
      polyglutamate capsule, a major virulence factor in Bacillus anthracis. Additional phenotypic
      differences are likely the result of single nucleotide polymorphisms, which are most numerous
      in cell envelope proteins. Overall differences in pathogenicity can be attributed to genome
      islands in S. aureus which encode enterotoxins, exotoxins, leukocidins, and leukotoxins not
      found in S. epidermidis.
AU  - Gill SR et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2005 187: 2426-2438.

PMID- 19648375
VI  - 75
DP  - 2009
TI  - Mobilization of a Tn402-like class 1 integron with a novel cassette array via flanking miniature inverted-repeat transposable element-like structures.
PG  - 6002-6004
AB  - A Tn402-like class 1 integron was recovered from a prawn-associated
      bacterium. One of its cassettes included methionine sulfoxide reductase
      genes, the first example of such genes being captured by an integron. The
      integron was flanked by direct repeats that resemble miniature
      inverted-repeat transposable element sequences. Excision of the integron
      by homologous recombination through these sequences was demonstrated.
AU  - Gillings MR
AU  - Labbate M
AU  - Sajjad A
AU  - Giguere NJ
AU  - Holley MP
AU  - Stokes HW
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2009 75: 6002-6004.

PMID- 29051246
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of a Colistin-Resistant Escherichia coli Strain Harboring mcr-1 on an IncHI2 Plasmid in the United States.
PG  - e01095-17
AB  - We report here the incidental detection and complete genome sequence of a urinary Escherichia
      coli strain harboring mcr-1 and resistant to colistin in a New York
      patient returning from Portugal in 2016. This strain, with sequence type 1485
      (ST1485), was a non-extended-spectrum beta-lactamase (ESBL) and non-carbapenemase
      producer and carried the mcr-1 gene on an IncHI2 plasmid.
AU  - Gilrane VL
AU  - Lobo S
AU  - Huang W
AU  - Zhuge J
AU  - Yin C
AU  - Chen D
AU  - Alvarez KJ
AU  - Budhai A
AU  - Nadelman I
AU  - Dimitrova N
AU  - Fallon JT
AU  - Wang G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01095-17.

PMID- 
VI  - 3
DP  - 2006
TI  - Engineering homing endonucleases to modify complex genomes.
PG  - 33-50
AB  - Gene targeting to selected chromosomal loci is greatly stimulated when free DNA ends are
      created that initiate double-strand break repair.  Gene therapy reagents can be developed by
      engineering DNA endonucleases that cleave genomes at desired target sequences.  Homing
      endonucleases are naturally occurring rare-cutting enzymes that have well understood DNA
      binding and DNA cleavage properties.  Rational design methods as well as directed evolution
      strategies that involve genetic selections and screens using combinatorial libraries generate
      homing endonucleases with altered sequence specificities.  Molecular switches are being
      introduced into these enzymes to regulate their activity.  This article reviews the progress
      that has been made in constructing homing endonucleases for gene therapy and genome
      engineering, and discusses the challenges that remain.
AU  - Gimble FS
PT  - Journal Article
TA  - Gene Ther. Regul.
JT  - Gene Ther. Regul.
SO  - Gene Ther. Regul. 2006 3: 33-50.

PMID- 
VI  - 16
DP  - 2005
TI  - Engineering homing endonucleases for genomic applications.
PG  - 177-192
AB  - The rapid progress in molecular biology that has occurred over the last three decades is due
      in large part to the availability of sequence-specific nucleases.  These enzymes have been
      indispensable tools in recombinant DNA protocols.  Most notably, the type II bacterial
      restriction enzymes have permitted the rapid and low-cost production of recombinant DNAs for
      cloning and other methods.  One drawback of these enzymes, however, is the small size of their
      recognition sequences, which range in length from 4-8 base pairs.  An enzyme that recognizes a
      6-bp target sequence cleaves DNA on average approximately once every 4000 bp.  When these
      enzymes digest DNA from a mammalian genome, which is typically >100 megabases in length, many
      thousands of DNA fragments are generated, and purification of individual species from this
      pool is difficult.
AU  - Gimble FS
PT  - Journal Article
TA  - Nucleic Acids Mol. Biol.
JT  - Nucleic Acids Mol. Biol.
SO  - Nucleic Acids Mol. Biol. 2005 16: 177-192.

PMID- 10754232
VI  - 185
DP  - 2000
TI  - Invasion of a multitude of genetic niches by mobile endonuclease genes.
PG  - 99-107
AB  - Persistence of a mobile DNA element in a population reflects a balance between the ability of
      the host to eliminate the element and the ability of the element to survive and to disseminate
      to other individuals. In each of the three biological kingdoms, several families of a mobile
      DNA element have been identified which encode a single protein that acts on nucleic acids.
      Collectively termed homing endonuclease genes (HEGs), these elements employ varied strategies
      to ensure their survival. Some members of the HEG families have a minimal impact on host
      fitness because they associate with genes having self-splicing introns or inteins that remove
      the HEGs at the RNA or protein level. The HEG and the intron/intein gene spread throughout the
      population by a gene conversion process initiated by the HEG-encoded endonuclease called
      'homing' in which the HEG and intron/intein genes are copied to cognate alleles that lack
      them. The endonuclease activity also contributes to a high frequency of lateral transmission
      of HEGs between species as has been documented in plants and other systems. Other HEGs have
      positive selection value because the proteins have evolved activities that benefit their host
      organisms. The success of HEGs in colonizing diverse genetic niches results from the
      flexibility of the encoded endonucleases in adopting new specificities.
AU  - Gimble FS
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2000 185: 99-107.

PMID- 11600710
VI  - 29
DP  - 2001
TI  - Degeneration of a homing endonuclease and its target sequence in a wild yeast strain.
PG  - 4215-4223
AB  - Mobile introns and inteins self-propagate by 'homing', a gene conversion process initiated
      by site-specific homing endonucleases. The VMA intein, which encodes the PI-SceI endonuclease
      in Saccharomyces cerevisiae, is present in several different yeast strains. Surprisingly, a
      wild wine yeast (DH1-1A) contains not only the intein(+) allele, but also an inteinless allele
      that has not undergone gene conversion. To elucidate how these two alleles co-exist, we
      characterized the endonuclease encoded by the DH1-1A intein(+) allele and the target site in
      the intein(-) allele. Sequence analysis reveals seven mutations in the 31 bp recognition
      sequence, none of which occurs at positions that are individually critical for activity.
      However, binding and cleavage of the sequence by PI-SceI is reduced 10-fold compared to the S.
      cerevisiae target. The PI-SceI analog encoded by the DH1-1A intein(+) allele contains 11
      mutations at residues in the endonuclease and protein splicing domains. None affects protein
      splicing, but one, a R417Q substitution, accounts for most of the decrease in DNA cleavage and
      DNA binding activity of the DH1-1A protein. Loss of activity in the DH1-1A endonuclease and
      target site provides one explanation for co-existence of the intein(+) and intein(-) alleles.
AU  - Gimble FS
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2001 29: 4215-4223.

PMID- 16698541
VI  - 14
DP  - 2006
TI  - Broken symmetry in homing endonucleases.
PG  - 804-806
AB  - Homing DNA endonucleases are highly site-specific enzymes that initiate the transfer of mobile
      DNA elements. In this issue of Structure, Spiegel et al. report the structure of the I-CeuI
      homing enzyme and describe how a symmetric homodimeric enzyme acquired specificity for an
      asymmetric substrate.
AU  - Gimble FS
PT  - Journal Article
TA  - Structure
JT  - Structure
SO  - Structure 2006 14: 804-806.

PMID- 9804821
VI  - 273
DP  - 1998
TI  - Identification of lys-403 in the PI-SceI homing endonuclease as part of a symmetric catalytic center.
PG  - 30524-30529
AB  - Superposition of the PI-SceI and I-CreI homing endonuclease three-dimensional x-ray structures
      indicates general similarity between the I-CreI homodimer and the PI-SceI endonuclease domain.
      Saddle-shaped structures are present in each protein that are proposed to bind DNA. At the
      putative endonucleolytic active sites, the superposition reveals that two lysine (Lys-301 and
      Lys-403 in PI-SceI and Lys-98 and Lys-98' in I-CreI) and two aspartic acid residues (Asp-218
      and Asp-326 in PI-SceI and Asp-20 and Asp-20' in I-CreI) are related by 2-fold symmetry. The
      critical role of Lys-301, Asp-218, and Asp-326 in the PI-SceI reaction pathway was reported
      previously. Here, we demonstrate the significance of the active-site symmetry by showing that
      alanine substitution at Lys-403 reduces cleavage activity by greater than 50-fold but has
      little effect on the DNA binding activity of the mutant enzyme. Substitution of Lys-403 with
      arginine, which maintains the positive charge, has only a modest effect on activity.
      Interestingly, even though the Lys-301 and Lys-403 residues display pseudosymmetry, PI-SceI
      mutant proteins with substitutions at these positions have different behaviors. The presence
      of similar basic and acidic residues in many LAGLIDADG homing endonucleases suggests that
      these enzymes use a common reaction mechanism to cleave double-stranded DNA.
AU  - Gimble FS
AU  - Duan X
AU  - Hu D
AU  - Quiocho FA
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1998 273: 30524-30529.

PMID- 14643662
VI  - 334
DP  - 2003
TI  - Assessing the plasticity of DNA target site recognition of the PI-SceI homing endonuclease using a bacterial two-hybrid selection system.
PG  - 993-1008
AB  - The PI-SceI protein from Saccharomyces cerevisiae is a member of the LAGLIDADG family of
      homing endonucleases that have been used in genomic
      engineering. To assess the flexibility of the PI-SceI-binding interaction
      and to make progress towards the directed evolution of homing
      endonucleases that cleave specified DNA targets, we applied a two-hybrid
      method to select PI-SceI variants from a randomized expression library
      that bind to different DNA substrates. In particular, the codon for Arg94,
      which is located in the protein splicing domain and makes essential
      contacts to two adjacent base-pairs, and the codons for four proximal
      residues were randomized. There is little conservation of the wild-type
      amino acid residues at the five randomized positions in the variants that
      were selected to bind to the wild-type site, yet one of the purified
      derivatives displays DNA-binding specificity and DNA endonuclease activity
      that is similar to that of the wild-type enzyme. A spectrum of DNA-binding
      behaviors ranging from partial relaxation of specificity to marked shifts
      in target site recognition are present in variants selected to bind to
      sites containing mutations at the two base-pairs. Our results illustrate
      the inherent plasticity of the PI-SceI/DNA interface and demonstrate that
      selection based on DNA binding is an effective means of altering the DNA
      cleavage specificity of homing endonucleases. Furthermore, it is apparent
      that homing endonuclease target specificity derives, in part, from
      constraints on the flexibility of DNA contacts imposed by hydrogen bonds
      to proximal residues.
AU  - Gimble FS
AU  - Moure CM
AU  - Posey KL
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2003 334: 993-1008.

PMID- 7890714
VI  - 270
DP  - 1995
TI  - Substitutions in conserved dodecapeptide motifs that uncouple the DNA binding and DNA cleavage activities of PI-SceI endonuclease.
PG  - 5849-5856
AB  - The PI-SceI endonuclease from yeast belongs to a protein family whose members contain two
      conserved dodecapeptide motifs within their primary sequences. The function of two acidic
      residues within these motifs, Asp218 and Asp326, was examined by substituting alanine,
      asparagine, and glutamic acid residues at these positions. All of the purified mutant proteins
      bind to the PI-SceI recogniton site with the same affinity and specificity as the wild-type
      enzyme. By contrast, substituting alanine or asparagine amino acids at the two positions
      completely eliminates strand cleavage of substrate DNA, whereas substitution with glutamic
      acid markedly reduces the cleavage activity. Experiments using nicked substrates demonstrate
      that the wild-type enzyme shows no strand preference during cleavage. These results are
      consistent with a model in which both acidic residues are part of a single catalytic center
      that cleaves both DNA strands. Furthermore, substrate binding by wild-type PI-SceI stimulates
      hydroxyl radical or hydroxide ion attack at the cleavage site while binding by the
      alanine-substituted proteins either stimulates this attack significantly less or protects the
      DNA at this position. These findings are discussed in terms of possible reaction mechanisms
      for PI-SceI-mediated endonucleolytic cleavage.
AU  - Gimble FS
AU  - Stephens BW
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1995 270: 5849-5856.

PMID- 1534148
VI  - 357
DP  - 1992
TI  - Homing of a DNA endonuclease gene by meiotic gene conversion in Saccharomyces cerevisiae.
PG  - 301-306
AB  - An unusual protein splicing reaction joins the N-terminal segment (A) and the C-terminal
      segment (C) of the 119K primary translation product (ABC) of the yeast VMA1 gene to yield a
      69K vacuolar H+-ATPase subunit (AC) and an internal 50K polypeptide (B). This 50K protein is a
      site-specific DNA endonuclease that shares 34% indentity with the homothallic switching
      endonuclease. The site cleaved by the VMA1-derived endonuclease exists in a VMA1 allele that
      lacks the derived endonuclease segment of the open reading frame. Cleavage at this site only
      occurs during meiosis and initiates 'homing', a gentic event that converts a VMA1 allele
      lacking the endonuclease coding sequence into one that contains it.
AU  - Gimble FS
AU  - Thorner J
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1992 357: 301-306.

PMID- 8408039
VI  - 268
DP  - 1993
TI  - Purification and characterization of VDE, a site-specific endonuclease from the yeast Saccharomyces cerevisiae.
PG  - 21844-21853
AB  - The 119-kDa primary translation product of the VMA1 gene of Saccharomyces cerevisiae undergoes
      a self-catalyzed rearrangement (protein splicing) that excises an internal 50-kDa segment of
      the polypeptide and joins the amino-terminal and carboxyl-terminal segments to generate the
      69-kDa subunit of the vacuolar membrane-associated H+-ATPase. We have shown previously that
      the internal segment is a site-specific endonuclease (Gimble, F.S., and Thorner, J. (1992)
      Nature 357, 301-306). Here we describe methods for the high level expression and purification
      to near homogeneity of both the authentic VMA1-derived endonuclease (or VDE) from yeast (yield
      18%) and a recombinant form of VDE made in bacteria (yield 29%). Detailed characterization of
      these preparations demonstrated that the yeast-derived and bacterially produced enzymes were
      indistinguishable, as judged by: (a) behavior during purification; (b) apparent native
      molecular mass (50 kDa); (c) immunological reactivity; and (d) catalytic properties (specific
      activity; cleavage site recognition; and optima for pH, temperature, divalent cation and ionic
      strength). The minimal site required for VDE cleavage was delimited to a 30-base pair sequence
      within its specific substrate ( the VMA1 delvde allele).
AU  - Gimble FS
AU  - Thorner J
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1993 268: 21844-21853.

PMID- 8913299
VI  - 263
DP  - 1996
TI  - Substrate recognition and induced DNA distortion by the PI-SceI endonuclease, an enzyme generated by protein splicing.
PG  - 163-180
AB  - PI-SceI, a double-stranded DNA endonuclease from Saccharomyces cerevisiae, is generated by
      protein splicing of an intein, which is an internal polypeptide within a larger precursor
      protein.  The enzyme initiates the mobility of the intein by cleaving at inteinless alleles of
      the VMA1 gene.  Genetic and biochemical studies reveal that the enzyme makes numerous
      base-specific and phosphate backbone contacts with its 31 bp asymmetrical recognition site.
      This site can be divided into two regions, both of which contain nucleotides that are
      essential for cleavage by PI-SceI.  Region I contains the PI-SceI cleavage site while Region
      II includes an adjacent sequence that covers two helical turns.  Mutational, interference and
      DNA mobility shift analyses demonstrate that Region II is sufficient for high-affinity PI-SceI
      binding.  Within this region, PI-SceI uses primarily phosphate backbone and some major groove
      interactions to contact the DNA, while within Region I , protein binding involves
      predominantly major groove interactions that overlap and lie proximal to the cleavage site.
      Interestingly, DNA binding by PI-SceI induces DNA conformational changes within Region II that
      are entirely exclusive of Region I sequences.  Furthermore, additional distortion occurs when
      PI-SceI binds to Region I in conjunction with Region II.  The importance of this latter
      distortion in the cleavage pathway is underscored by substrate mutations at or near the
      cleavage site that reduce or eliminate both Region I DNA bending and substrate cleavage.
      Based on these findings, we propose a model in which sequence-specific contacts made by
      PI-SceI contribute to its localization to the cleavage site and to its stabilization of a DNA
      conformation that is required for catalysis.  Finally, we discuss how the recognition
      characteristics of PI-SceI may have allowed the evolution of other endonucleases with altered,
      but similar, specificities.
AU  - Gimble FS
AU  - Wang J
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1996 263: 163-180.

PMID- 
VI  - 0
DP  - 1991
TI  - Restriction-modification systems: Genetic sentries and useful systems in the study of molecular genetics.
PG  - 301-321
AB  - This chapter describes two important roles which restriction-modification
      systems have in molecular genetics.  The first of these roles concerns the
      operation of these systems as genetic sentries.  The second role involves the
      part which restriction-modification systems are playing in the study of several
      important topics in molecular genetics.
AU  - Gingeras TR
PT  - Journal Article
TA  - Modern Microbial Genetics
JT  - Modern Microbial Genetics
SO  - Modern Microbial Genetics 1991 0: 301-321.

PMID- 6249680
VI  - 8
DP  - 1980
TI  - Restriction endonucleases and their recognition sequences.
PG  - 397-398
AB  - None
AU  - Gingeras TR
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 1980 8: 397-398.

PMID- 
VI  - 4
DP  - 1982
TI  - The isolation and characterization of the E. coli dam methylase gene.
PG  - 329-340
AB  - The E. coli dam (DNA adenine methylase) codes for an enzyme which methylates the DNA sequence
      GATC. When DNA has been modified by dam it is no longer susceptible to endonucleolytic
      cleavage by the restriction endonuclease MboI. Several DNA methylases have been shown to be
      part of a restriction-modification system (Roberts, 1981). However, the dam methylase does not
      seem to be part of such a system. Rather, the dam methylase has been implicated as part of a
      post-replicational mismatch repair system in E. coli. In heteroduplex lambda DNA containing
      only one methylated strand, the repair system will correct the unmethylated strand to match
      the methylated strand. (Wagner and Meselson, 1976, Meselson et al., 1980). Fully methylated
      mismatched heteroduplexes are not corrected. In addition, it has been demonstrated that when
      the dam methylase is not produced (dam-) or is over-produced (damS), such E. coli strains are
      hypermutable. (Herman and Modrich, 1980). An additional function for the dam methylase in E.
      coli may involve its role in DNA replication. It has been shown that the sequence methylated
      by the dam methylase, GATC, occurs at a very high frequency (i.e., 11 times within 245 base
      pairs) at the E. coli origin of replication (J. Zyskind, personal communication). Furthermore,
      such sites have been shown to occur near or at the ends of Okazaki fragments (Gomez-Eichelmann
      and Lark, 1977). Because of the possible important roles that the dam methylasae plays in the
      biology of E. coli, as well as sharing an identical recognition sequence with a set of type II
      restriction and modification enzymes (MboI), we have isolated and characterized clones
      containing the dam methylase gene.
AU  - Gingeras TR
AU  - Blumenthal RM
AU  - Roberts RJ
AU  - Brooks JE
PT  - Journal Article
TA  - Metabolism and Enzymology of Nucleic Acids
JT  - Metabolism and Enzymology of Nucleic Acids
SO  - Metabolism and Enzymology of Nucleic Acids 1982 4: 329-340.

PMID- 6300841
VI  - 80
DP  - 1983
TI  - Cloned restriction/modification system from Pseudomonas aeruginosa.
PG  - 402-406
AB  - DNA fragments from Pseudomonas aeruginosa carrying the PaeR7 restriction/modification genes
      have been cloned in the plasmid vector pBR322 and propagated in Escherichia coli. A subclone
      (pPAORM3.8) has been constructed that contains the complete restriction/modification system on
      a 3.8-kilobase DNA fragment. Digestion of the pPAORM3.8 plasmid with nuclease BAL-31 has
      yielded two types of clones. One type contains an active methylase gene but no active
      endonuclease gene; such clones will modify the DNA but not restrict the growth of incoming
      phage in vivo. The second type contains an active endonuclease gene but no active methylase
      gene, as judged both by in vivo tests and by the activity of the cell extracts in vitro.
      Although extracts of cells containing these plasmids display restriction endonuclease
      activity, these bacteria are unable to restrict the growth of incoming phage. Furthermore,
      chromosomal and phage DNA isolated from these host cells are not protected against cleavage by
      PaeR7 in vitro. The properties of PaeR7 endonuclease and methylase enzymes have also been
      examined. The PaeR7 restriction endonuclease recognizes and cleaves the sequence C^T-C-G-A-G,
      as does XhoI. However, there exists a canonical XhoI site at 26.5% on the adenovirus 2
      genome which is totally refractory to PaeR7 cleavage but is cut by XhoI. Under conditions of
      low salt, high glycerol, and high enzyme concentrations, a "PaeR7*" activity is found that is
      similar to that observed for EcoRI. Finally, evidence is presented that the PaeR7 methylase
      modifies the adenine residue within the recognition sequence. the restriction enzyme, the
      third describes the purification procedure for the methylase and the fourth describes the
      recognition sequence of the methylase. In some cases, several references appear in one of
      these categories when independent groups have reached similar conclusions.
AU  - Gingeras TR
AU  - Brooks JE
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1983 80: 402-406.

PMID- 8095080
VI  - 17C
DP  - 1993
TI  - A spectrofluorometric method for measurement of restriction endonuclease activity based on fluorescence polarization.
PG  - 173
AB  - A method is described for monitoring the enzymatic activity of type II restriction
      endonucleases using fluorophore-labeled oligonucleotide substrates. Cleavage of the duplex
      oligonucleotide substrates, in which one strand is covalently labeled with fluorescein,
      results in a time-dependent change of fluorescence polarization due to the formation of short,
      labeled fragments which are single-stranded at the temperature of the assay. This non-isotopic
      homogeneous approach is extremely sensitive and is much simpler than the current radiolabeled
      procedures which require fixed timepoint assays and the use of filter binding or gel
      electrophoresis for kinetic analysis of the cleavage reaction. The PaeR7I endonuclease has
      been used as an example for the applicability of the method. The kinetic parameters for the
      hydrolysis of a fluorescein-modified oligonucleotide substrate of the enzyme have been
      determined by using this approach to follow reaction rates.
AU  - Gingeras TR
AU  - Ghosh S
AU  - Blumeyer K
AU  - Eis R
AU  - Millar D
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1993 17C: 173.

PMID- 6272209
VI  - 9
DP  - 1981
TI  - Two new restriction endonucleases from Proteus vulgaris.
PG  - 4525-4536
AB  - Two novel sequence-specific endonucleases have been isolated from Proteus
      vulgaris, ATCC 13315.  PvuI recognizes the sequence: 5' CGAT^CG 3' 3' GC^TAGC
      5' and PvuII recognizes the sequence: 5' CAG^CTG 3' 3' GTC^GAC 5' and cleave as
      indicated by the arrow.  PvuI is an isoschizomer of XorII, RshI, and XniI.  No
      enzyme with the specificity of PvuII has been described previously.
AU  - Gingeras TR
AU  - Greenough L
AU  - Schildkraut I
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1981 9: 4525-4536.

PMID- 724510
VI  - 5
DP  - 1978
TI  - A computer assisted method for the determination of restriction enzyme recognition sites.
PG  - 4105-4127
AB  - A computer program has been developed which aids in the determination of
      restriction enzyme recognition sequences.  This is achieved by cleaving DNAs of
      known sequence with a restriction endonuclease and comparing the fragmentation
      pattern with a computer-generated set of patterns.  The feasibility of this
      approach has been tested using fragmentation patterns of PhiX174 DNA produced
      by enzymes of both known and unknown specificity.  Recognition sequences are
      predicted for two restriction endonucleases (BbvI and SfaNI) using this method.
      In addition, recognition sequnces are predicted for two other new enzymes
      (PvuI and MstI) using another computer-assisted method.
AU  - Gingeras TR
AU  - Milazzo JP
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1978 5: 4105-4127.

PMID- 625054
VI  - 118
DP  - 1978
TI  - A new specific endonuclease present in Xanthomonas holcicola, Xanthomonas papavericola and Brevibacterium luteum.
PG  - 113-122
AB  - A new specific endonuclease, XhoI, has been partially purified from Xanthomonas
      holcicola.  This enzyme cleaves adenovirus-2 DNA at five sites, bacteriophage
      DNA at one site, PhiX174 DNA at one site, but does not cleave simian virus DNA.
      It recognizes the sequence 5'-C-^T-C-G-A-G-3' 3'-G-A-G-C-T^-C-5' and cuts at
      the sites indicated by the arrows.  Enzymes with identical specificity have
      also been found in Xanthomonas papavericola and Brevibacterium luteum.
AU  - Gingeras TR
AU  - Myers PA
AU  - Olson JA
AU  - Hanberg FA
AU  - Roberts RJ
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1978 118: 113-122.

PMID- 
VI  - 5
DP  - 1984
TI  - Organization and expression of a type II restriction-modification system from Pseudomonas aeruginosa.
PG  - 267-275
AB  - A series of BAL-31 deletion mutants have been generated affecting both the structural and
      regulatory regions of the PaeR7 restriction-modification system. This system is organized as
      an operon with both the genes sharing a common regulatory region. Deletions in this regulatory
      region lead to a gradient of expression levels for both enzymes. Most striking is the
      observation that depressed levels of expression of endonuclease, as exemplified by both
      pPAOR1.9 and pPAOdel1.3, result in clones that do not restrict infecting phage.
      Cotransformation of pPAOR1.9 and pPACYCM2.7 into the same host did not result in recovery of a
      restriction phenotype. Consequently, phage restriction seems to be critically dependent on the
      levels of endonuclease produced, and not on the effect of an active methylase gene. DNA
      sequences of the control region of this system indicate two PaeR7 sites which are located in a
      critical position in the PaeR7 operon to determine if the levels of methylase are sufficient
      to protect both the plasmid and the DNA of the host cell. The effect of methylation on these
      sites during transcription is being studied as another possible means of controlling
      expression in this system.
AU  - Gingeras TR
AU  - Theriault G
AU  - Brooks JE
PT  - Journal Article
TA  - Metabolism and Enzymology of Nucleic Acids
JT  - Metabolism and Enzymology of Nucleic Acids
SO  - Metabolism and Enzymology of Nucleic Acids 1984 5: 267-275.

PMID- 27056235
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of an Escherichia coli O8:H19 Sequence Type 708 Strain Isolated from a Holstein Dairy Cow with Metritis.
PG  - e00261-16
AB  - We present here the genome sequence ofEscherichia coliO8:H19 strain KCJ852, belonging to
      multilocus sequence type (MLST) 708, isolated from the uterus of a
      cow with a bovine postpartum uterine infection known as metritis. Genomic
      investigation of KCJ852 will help us understand its virulence potential.
AU  - Ginn A
AU  - Ma Z
AU  - Galvao KN
AU  - Jeong KC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00261-16.

PMID- 17895969
VI  - 2
DP  - 2007
TI  - Paradoxical DNA Repair and Peroxide Resistance Gene Conservation in Bacillus pumilus SAFR-032.
PG  - e928
AB  - BACKGROUND: Bacillus spores are notoriously resistant to unfavorable conditions such as UV
      radiation, gamma-radiation, H(2)O(2), desiccation,
      chemical disinfection, or starvation. Bacillus pumilus SAFR-032 survives
      standard decontamination procedures of the Jet Propulsion Lab spacecraft
      assembly facility, and both spores and vegetative cells of this strain
      exhibit elevated resistance to UV radiation and H(2)O(2) compared to other
      Bacillus species. PRINCIPAL FINDINGS: The genome of B. pumilus SAFR-032
      was sequenced and annotated. Lists of genes relevant to DNA repair and the
      oxidative stress response were generated and compared to B. subtilis and
      B. licheniformis. Differences in conservation of genes, gene order, and
      protein sequences are highlighted because they potentially explain the
      extreme resistance phenotype of B. pumilus. The B. pumilus genome includes
      genes not found in B. subtilis or B. licheniformis and conserved genes
      with sequence divergence, but paradoxically lacks several genes that
      function in UV or H(2)O(2) resistance in other Bacillus species.
      SIGNIFICANCE: This study identifies several candidate genes for further
      research into UV and H(2)O(2) resistance. These findings will help explain
      the resistance of B. pumilus and are applicable to understanding
      sterilization survival strategies of microbes.
AU  - Gioia J et al
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2007 2: e928.

PMID- 17015664
VI  - 188
DP  - 2006
TI  - The Genome Sequence of Mannheimia haemolytica A1: Insights into Virulence, Natural Competence, and Pasteurellaceae Phylogeny.
PG  - 7257-7266
AB  - The draft genome sequence of Mannheimia haemolytica A1, the causative agent of bovine
      respiratory disease complex (BRDC), is presented. Strain
      ATCC BAA-410, isolated from the lung of a calf with BRDC, was the DNA
      source. The annotated genome includes 2,839 coding sequences, 1,966 of
      which were assigned a function and 436 of which are unique to M.
      haemolytica. Through genome annotation many features of interest were
      identified, including bacteriophages and genes related to virulence,
      natural competence, and transcriptional regulation. In addition to
      previously described virulence factors, M. haemolytica encodes adhesins,
      including the filamentous hemagglutinin FhaB and two trimeric
      autotransporter adhesins. Two dual-function
      immunoglobulin-protease/adhesins are also present, as is a third
      immunoglobulin protease. Genes related to iron acquisition and drug
      resistance were identified and are likely important for survival in the
      host and virulence. Analysis of the genome indicates that M. haemolytica
      is naturally competent, as genes for natural competence and DNA uptake
      signal sequences (USS) are present. Comparison of competence loci and USS
      in other species in the family Pasteurellaceae indicates that M.
      haemolytica, Actinobacillus pleuropneumoniae, and Haemophilus ducreyi form
      a lineage distinct from other Pasteurellaceae. This observation was
      supported by a phylogenetic analysis using sequences of predicted
      housekeeping genes.
AU  - Gioia J
AU  - Qin X
AU  - Jiang H
AU  - Clinkenbeard K
AU  - Lo R
AU  - Liu Y
AU  - Fox GE
AU  - Yerrapragada S
AU  - McLeod MP
AU  - McNeill TZ
AU  - Hemphill L
AU  - Sodergren E
AU  - Wang Q
AU  - Muzny DM
AU  - Homsi FJ
AU  - Weinstock GM
AU  - Highlander SK
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2006 188: 7257-7266.

PMID- 21304715
VI  - 2
DP  - 2010
TI  - Two genome sequences of the same bacterial strain, Gluconacetobacter diazotrophicus PAl 5, suggest a new standard in genome sequence submission.
PG  - 309-317
AB  - Gluconacetobacter diazotrophicus PAl 5 is of agricultural significance due to its ability to
      provide fixed nitrogen to plants. Consequently, its genome sequence
      has been eagerly anticipated to enhance understanding of endophytic nitrogen
      fixation. Two groups have sequenced the PAl 5 genome from the same source (ATCC
      49037), though the resulting sequences contain a surprisingly high number of
      differences. Therefore, an optical map of PAl 5 was constructed in order to
      determine which genome assembly more closely resembles the chromosomal DNA by
      aligning each sequence against a physical map of the genome. While one sequence
      aligned very well, over 98% of the second sequence contained numerous
      rearrangements. The many differences observed between these two genome sequences
      could be owing to either assembly errors or rapid evolutionary divergence. The
      extent of the differences derived from sequence assembly errors could be assessed
      if the raw sequencing reads were provided by both genome centers at the time of
      genome sequence submission. Hence, a new genome sequence standard is proposed
      whereby the investigator supplies the raw reads along with the closed sequence so
      that the community can make more accurate judgments on whether differences
      observed in a single stain may be of biological origin or are simply caused by
      differences in genome assembly procedures.
AU  - Giongo A
AU  - Tyler HL
AU  - Zipperer UN
AU  - Triplett EW
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 2: 309-317.

PMID- 25814616
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequence of Clostridium botulinum A2B3 87, a Highly Virulent Strain  Involved in a Fatal Case of Foodborne Botulism in Italy.
PG  - e00237-15
AB  - Here, we report the genome sequence of a rare bivalent strain of Clostridium botulinum, A2B3
      87. The strain was isolated from a foodborne botulism case that
      occurred in Italy in 1995. The case was characterized by rapid evolution of the
      illness and failure of conventional treatments.
AU  - Giordani F
AU  - Fillo S
AU  - Anselmo A
AU  - Palozzi AM
AU  - Fortunato A
AU  - Gentile B
AU  - Pittiglio V
AU  - Spagnolo F
AU  - Anniballi F
AU  - Fiore A
AU  - Auricchio B
AU  - De Medici D
AU  - Lista F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00237-15.

PMID- 2049093
VI  - 177
DP  - 1991
TI  - Purification and properties of a novel DNA methyltransferase from cultured rice cells.
PG  - 711-719
AB  - DNA methyltransferase activity has been observed in a total crude homogenate of rice cells
      grown in suspension culture using either native plant DNA or, under the conditions used, the
      more responsive hemimethylated poly (dI-MedC).poly(dI-dC).  Using the latter substrate we have
      purified an enzyme fraction 380-fold by salt extraction of chromatin, DEAE cellulose and
      phosphocellulose.  This purified fraction showed enzyme activity only with poly
      (dI-MedC).poly(dI-dC) thus suggesting the occurrence in plants of a DNA methyltransferase
      specific for hemimethylated DNA.  A Mr value of 54,000 was calculated on the basis of the
      sedimentation coefficient which was determined by sucrose density gradient centrifugation.
      Apparent Km values for poly(dI-MedC).poly(dI-dC) and S-adenosyl-L-methionine were found to be
      17 ug/ml and 2.6 uM, respectively.
AU  - Giordano M
AU  - Mattachini ME
AU  - Cella R
AU  - Pedrali-Noy G
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1991 177: 711-719.

PMID- 27340058
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence and Gene Annotation of the Uropathogenic Bacterium Proteus  mirabilis Pr2921.
PG  - e00564-16
AB  - Here, we report the genome sequence of Proteus mirabilis Pr2921, a uropathogenic  bacterium
      that can cause severe complicated urinary tract infections. After gene
      annotation, we identified two additional copies of ucaA, one of the most studied
      fimbrial protein genes, and other fimbriae related-proteins that are not present
      in P. mirabilis HI4320.
AU  - Giorello FM
AU  - Romero V
AU  - Farias J
AU  - Scavone P
AU  - Umpierrez A
AU  - Zunino P
AU  - Sotelo SJR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00564-16.

PMID- 23449845
VI  - 7
DP  - 2012
TI  - Complete genome sequence of Thermovibrio ammonificans HB-1(T), a thermophilic, chemolithoautotrophic bacterium isolated from a deep-sea hydrothermal vent.
PG  - 82-90
AB  - type strain HB-1 is a thermophilic (T: 75 degrees C), strictly anaerobic,
      chemolithoautotrophic bacterium that was isolated from an active, high
      temperature deep-sea hydrothermal vent on the East Pacific Rise. This organism
      grows on mineral salts medium in the presence of CO/H, using NO or S as electron
      acceptors, which are reduced to ammonium or hydrogen sulfide, respectively. is
      one of only three species within the genus , a member of the family , and it
      forms a deep branch within the phylum . Here we report the main features of the
      genome of strain HB-1 (DSM 15698).
AU  - Giovannelli D et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 7: 82-90.

PMID- 22180817
VI  - 5
DP  - 2011
TI  - Draft genome sequence of Caminibacter mediatlanticus strain TB-2, an epsilonproteobacterium isolated from a deep-sea hydrothermal vent.
PG  - 135-143
AB  - Caminibacter mediatlanticus strain TB-2(T) [1], is a thermophilic, anaerobic,
      chemolithoautotrophic bacterium, isolated from the walls of an active deep-sea
      hydrothermal vent chimney on the Mid-Atlantic Ridge and the type strain of the
      species. C. mediatlanticus is a Gram-negative member of the Epsilonproteobacteria
      (order Nautiliales) that grows chemolithoautotrophically with H(2) as the energy
      source and CO(2) as the carbon source. Nitrate or sulfur is used as the terminal
      electron acceptor, with resulting production of ammonium and hydrogen sulfide,
      respectively. In view of the widespread distribution, importance and
      physiological characteristics of thermophilic Epsilonproteobacteria in deep-sea
      geothermal environments, it is likely that these organisms provide a relevant
      contribution to both primary productivity and the biogeochemical cycling of
      carbon, nitrogen and sulfur at hydrothermal vents. Here we report the main
      features of the genome of C. mediatlanticus strain TB-2(T).
AU  - Giovannelli D
AU  - Ferriera S
AU  - Johnson J
AU  - Kravitz S
AU  - Perez-Rodriguez I
AU  - Ricci J
AU  - O'Brien C
AU  - Voordeckers JW
AU  - Bini E
AU  - Vetriani C
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 5: 135-143.

PMID- 16109880
VI  - 309
DP  - 2005
TI  - Genome streamlining in a cosmopolitan oceanic bacterium.
PG  - 1242-1245
AB  - The SAR11 clade consists of very small, heterotrophic marine alpha-proteobacteria that are
      found throughout the oceans, where they
      account for about 25% of all microbial cells. Pelagibacter ubique, the
      first cultured member of this clade, has the smallest genome and encodes
      the smallest number of predicted open reading frames known for a
      free-living microorganism. In contrast to parasitic bacteria and archaea
      with small genomes, P. ubique has complete biosynthetic pathways for all
      20 amino acids and all but a few cofactors. P. ubique has no pseudogenes,
      introns, transposons, extrachromosomal elements, or inteins; few paralogs;
      and the shortest intergenic spacers yet observed for any cell.
AU  - Giovannoni SJ
AU  - Tripp HJ
AU  - Givan S
AU  - Podar M
AU  - Vergin KL
AU  - Baptista D
AU  - Bibbs L
AU  - Eads J
AU  - Richardson TH
AU  - Noordewier M
AU  - Rappe MS
AU  - Short JM
AU  - Carrington JC
AU  - Mathur EJ
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2005 309: 1242-1245.

PMID- 25997461
VI  - 12
DP  - 2015
TI  - The C-terminal region of the RNA helicase CshA is required for the interaction with the degradosome and turnover of bulk RNA in the opportunistic pathogen Staphylococcus aureus.
PG  - 658-674
AB  - Staphylococcus aureus is a versatile opportunistic pathogen that adapts readily to a variety
      of different growth conditions. This adaptation requires a rapid regulation of gene expression
      including the control of mRNA abundance. The CshA DEAD-box RNA helicase was previously shown
      to be required for efficient turnover of the agr quorum sensing mRNA. Here we show by
      transcriptome-wide RNA sequencing and microarray analyses that CshA is required for the
      degradation of bulk mRNA.
      Moreover a subset of mRNAs is significantly stabilised in absence of CshA.
      Deletion of the C-terminal extension affects RNA turnover similar to the full deletion of the
      cshA gene. In accordance with RNA decay data, the C-terminal region of CshA is required for an
      RNA-independent interaction with components of the RNA degradation machinery. The C-terminal
      truncation of CshA reduces its ATPase activity and this reduction cannot be compensated at
      high RNA concentrations. Finally, the deletion of the C-terminal extension does affect growth
      at low temperatures, but to a significantly lesser degree than the full deletion, indicating
      that the core of the helicase can assume a partial function and opening the possibility that
      CshA is involved in different cellular processes.
AU  - Giraud C
AU  - Hausmann S
AU  - Lemeille S
AU  - Prados J
AU  - Redder P
AU  - Linder P
PT  - Journal Article
TA  - RNA Biol.
JT  - RNA Biol.
SO  - RNA Biol. 2015 12: 658-674.

PMID- 25081258
VI  - 2
DP  - 2014
TI  - Draft Genomes of Three Strains Representative of the Bacillus anthracis Diversity Found in France.
PG  - e00736-14
AB  - We report here the draft genomes of three Bacillus anthracis strains isolated in  France:
      08-8_20 (A.Br.001/002), 99-100 (A.Br.011/009), and 00-82 (B.Br CNEVA).
      The total lengths of assemblies are 5,440,708 bp, 5,446,472 bp, and 5,436,014 bp
      for 08-8_20, 99-100, and 00-82, respectively.
AU  - Girault G
AU  - Parisot N
AU  - Peyretaillade E
AU  - Peyret P
AU  - Derzelle S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00736-14.

PMID- 28705969
VI  - 5
DP  - 2017
TI  - First Draft Genome for a Burkholderia mallei Isolate Originating from a Glanderous Mule from Brazil.
PG  - e00579-17
AB  - Burkholderia mallei is the etiological agent of glanders. Here, we present the draft genome
      sequence of Burkholderia mallei strain 16-2438_BM#8 that was
      isolated from a mule found dead in Pernambuco, northeast Brazil. It is the first
      available genomic sequence from a strain isolated on the American continent.
AU  - Girault G
AU  - Woudstra C
AU  - Martin B
AU  - Vorimore F
AU  - Lucia-de-Assis-Santana V
AU  - Fach P
AU  - Madani N
AU  - Laroucau K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00579-17.

PMID- 21149627
VI  - 55
DP  - 2011
TI  - A diversity of clavulanic acid-inhibited extended-spectrum {beta}-lactamases in Aeromonas sp. from the Seine River, Paris, France.
PG  - 1256-1261
AB  - Environmental Aeromonas sp. isolates resistant to ceftazidime were
      recovered during an environmental survey performed with water samples from
      the Seine River, in Paris, France, in November 2009. Selected isolates
      were identified by sequencing of the 16S rRNA and rpoB genes. PCR and
      cloning experiments were used to identify
      broad-spectrum-beta-lactamase-encoding genes and their genetic context.
      Clavulanic acid-inhibited extended-spectrum-beta-lactamase (ESBL) genes
      were identified in 71% of the Aeromonas sp. isolates. A variety of ESBL
      genes were detected, including bla(VEB-1a), bla(SHV-12), bla(PER-1),
      bla(PER-6), bla(TLA-2), and bla(GES-7), suggesting an aquatic reservoir of
      those ESBL genes. Moreover, the repeated elements and different insertion
      sequences were identified in association with the bla(PER-6) and the
      bla(VEB-1a) genes, respectively, indicating a wide diversity of
      mobilization events, making Aeromonas spp. a vehicle for ESBL
      dissemination.
AU  - Girlich D
AU  - Poirel L
AU  - Nordmann P
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2011 55: 1256-1261.

PMID- 22156421
VI  - 78
DP  - 2012
TI  - Carbapenem-Hydrolyzing GES-5-Encoding Gene on Different Plasmid Types Recovered from a Bacterial Community in a Sewage Treatment Plant.
PG  - 1292-1295
AB  - Plasmids pRSB113 and pRSB115 were recovered from an activated sludge bacterial
      community of a municipal wastewater treatment plant in Germany. Both plasmids
      carry the same bla(GES-5) carbapenemase gene, located within two distinct class 1
      integrons. These plasmids have different backbones, belong to different
      incompatibility groups, and could replicate in both Pseudomonas aeruginosa and
      Escherichia coli.
AU  - Girlich D
AU  - Poirel L
AU  - Szczepanowski R
AU  - Schluter A
AU  - Nordmann P
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2012 78: 1292-1295.

PMID- 22253610
VI  - 8
DP  - 2012
TI  - A Half-Century of Inspiration: An Interview with Hamilton Smith.
PG  - e1002466
AB  - In 1962, Hamilton Smith abandoned a career in medicine to follow his passion for the emerging
      field of molecular biology; within six years, he had made the discovery of a lifetime.  As a
      new Johns Hopkins faculty member, Smith, together with his first graduate student, Kent
      Wilcox, geared up to study recombination in vitro but instead discoverd the restriction enzyme
      "R" in Haemophilus influenzae.  By cobbling together crude techniques, Smith, along with
      Wilcox and later Tom Kelly, showed the R cleaves DNA at a specific recognition sequence, a
      palindromic site, yielding blunt-ended DNA fragments.  Now known as HindII, R proved to be the
      first of an enormous class of Type II restriction enzymes, and as such, presaged gene cloning,
      allowed DNA to be reproducibly fragmented and then sequenced, and enabled physical mapping of
      genomes.  Smith went on to discover DNA methylases that constitute the other half of the
      bacterial host restriction and modification systems, as hypothesized by Werner Arber of
      Switzerland.  Together with Arber and his Hopkins colleague Daniel Nathans, who first used the
      enzyme on SV40 DNA and demonstrated discrete bands on a tube gel, Smith shared the Nobel Prize
      for Physiology or Medicine in 1978.
AU  - Gitschier J
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2012 8: e1002466.

PMID- 26159534
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequences of Multidrug-Resistant Escherichia coli Strains Sharing the Same Sequence Type (ST410) and Isolated from Human and Avian Sources in  Italy.
PG  - e00757-15
AB  - Extraintestinal pathogenic Escherichia coli (ExPEC) is involved in a wide spectrum of human
      diseases. Chickens have been suggested as reservoirs for
      fluoroquinolone (FQ)-resistant ExPEC strains. Here, we report the whole-genome
      sequences of 4 E. coli strains sharing the same sequence type (ST) (ST410) and
      that were isolated from human and avian sources in Italy.
AU  - Giufre M
AU  - Accogli M
AU  - Graziani C
AU  - Busani L
AU  - Cerquetti M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00757-15.

PMID- 28360180
VI  - 5
DP  - 2017
TI  - First Whole-Genome Sequence of a Haemophilus influenzae Type e Strain Isolated from a Patient with Invasive Disease in Italy.
PG  - e00059-17
AB  - In the present era of conjugate vaccines against Haemophilus influenzae type b,
      non-vaccine-preventable strains are of concern. Here, we report the first
      whole-genome sequence of an invasive H. influenzae type e strain. This genomic
      information will enable further investigations on encapsulated non-type b H.
      influenzae strains.
AU  - Giufre M
AU  - Cardines R
AU  - Cerquetti M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00059-17.

PMID- 25814593
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequences of Nonencapsulated Haemophilus influenzae Strains Isolated in Italy.
PG  - e00110-15
AB  - Haemophilus influenzae is an important human pathogen involved in invasive disease. Here, we
      report the whole-genome sequences of 11 nonencapsulated H.
      influenzae (ncHi) strains isolated from both invasive disease and healthy
      carriers in Italy. This genomic information will enrich our understanding of the
      molecular basis of ncHi pathogenesis.
AU  - Giufre M
AU  - De Chiara M
AU  - Censini S
AU  - Guidotti S
AU  - Torricelli G
AU  - De Angelis G
AU  - Cardines R
AU  - Pizza M
AU  - Muzzi A
AU  - Cerquetti M
AU  - Soriani M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00110-15.

PMID- 25953181
VI  - 3
DP  - 2015
TI  - Genome Sequences of Pseudoalteromonas Strains ATCC BAA-314, ATCC 70018, and ATCC  70019.
PG  - e00390-15
AB  - The assembly and annotation of the draft genome sequences for Pseudoalteromonas strains ATCC
      BAA314, ATCC 700518, and ATCC 700519 reveal candidates for promoting
      symbiosis between Pseudoalteromonas strains and eukaryotes. Groups of genes
      generally associated with virulence are present in all three strains, suggesting
      that these bacteria may be pathogenic under specific circumstances.
AU  - Givan SA
AU  - Zhou MY
AU  - Bromert K
AU  - Bivens N
AU  - Chapman LF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00390-15.

PMID- 23640198
VI  - 1
DP  - 2013
TI  - Whole-Genome Sequences of Streptococcus tigurinus Type Strain AZ_3a and S. tigurinus 1366, a Strain Causing Prosthetic Joint Infection.
PG  - e00210-12
AB  - Streptococcus tigurinus, a novel member of the Streptococcus mitis group, was recently
      identified as a causative agent of invasive infections. We report the
      complete genome sequences of the S. tigurinus type strain AZ_3a and S. tigurinus
      strain 1366. The genome sequences assist in the characterization of virulence
      determinants of S. tigurinus.
AU  - Gizard Y
AU  - Zbinden A
AU  - Schrenzel J
AU  - Francois P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00210-12.

PMID- 26272576
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Acinetobacter calcoaceticus Strain GK1, a Hydrocarbon-Degrading Plant Growth-Promoting Rhizospheric Bacterium.
PG  - e00909-15
AB  - The 3.94-Mb draft genome of Acinetobacter calcoaceticus GK1, a hydrocarbonoclastic plant
      growth-promoting Gram-negative rhizospheric bacterium,
      is presented here. Isolated at the Ford Motor Company site in Genk, Belgium, from
      poplar trees planted on a diesel-contaminated plume, GK1 is useful for enhancing
      hydrocarbon phytoremediation.
AU  - Gkorezis P
AU  - Bottos EM
AU  - Van Hamme JD
AU  - Franzetti A
AU  - Abbamondi GR
AU  - Balseiro-Romero M
AU  - Weyens N
AU  - Rineau F
AU  - Vangronsveld J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00909-15.

PMID- 26701084
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Arthrobacter sp. Strain SPG23, a Hydrocarbon-Degrading and Plant Growth-Promoting Soil Bacterium.
PG  - e01517-15
AB  - We report here the 4.7-Mb draft genome of Arthrobacter sp. SPG23, a hydrocarbonoclastic
      Gram-positive bacterium belonging to the Actinobacteria,
      isolated from diesel-contaminated soil at the Ford Motor Company site in Genk,
      Belgium. Strain SPG23 is a potent plant growth promoter useful for diesel fuel
      remediation applications based on plant-bacterium associations.
AU  - Gkorezis P
AU  - Bottos EM
AU  - Van Hamme JD
AU  - Thijs S
AU  - Rineau F
AU  - Franzetti A
AU  - Balseiro-Romero M
AU  - Weyens N
AU  - Vangronsveld J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01517-15.

PMID- 25657268
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Acinetobacter oleivorans PF1, a Diesel-Degrading and Plant-Growth-Promoting Endophytic Strain Isolated from Poplar Trees Growing on a   Diesel-Contaminated Plume.
PG  - e01430-14
AB  - We report the 3.7-Mb draft genome of Acinetobacter oleivorans strain PF1, a
      hydrocarbonoclastic Gram-negative bacterium in the class Gammaproteobacteria,
      isolated from poplar trees growing on a diesel-contaminated plume at the Ford
      Motor Company site in Genk, Belgium. Strain PF1 is a potent plant-growth
      promoter, useful for diesel fuel phytoremediation applications.
AU  - Gkorezis P
AU  - Rineau F
AU  - Van Hamme J
AU  - Franzetti A
AU  - Daghio M
AU  - Thijs S
AU  - Weyens N
AU  - Vangronsveld J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01430-14.

PMID- 27340073
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Bacillus licheniformis Strain GB2, a Hydrocarbon-Degrading and Plant Growth-Promoting Soil Bacterium.
PG  - e00608-16
AB  - We report the 4.39 Mb draft genome of Bacillus licheniformis GB2, a hydrocarbonoclastic
      Gram-positive bacterium of the family Bacillaceae, isolated
      from diesel-contaminated soil at the Ford Motor Company site in Genk, Belgium.
      Strain GB2 is an effective plant-growth promoter useful for diesel fuel
      remediation applications based on plant-bacterium associations.
AU  - Gkorezis P
AU  - Van Hamme J
AU  - Bottos E
AU  - Thijs S
AU  - Balseiro-Romero M
AU  - Monterroso C
AU  - Kidd PS
AU  - Rineau F
AU  - Weyens N
AU  - Sillen W
AU  - Vangronsveld J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00608-16.

PMID- 26950324
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Pantoea ananatis GB1, a Plant-Growth-Promoting Hydrocarbonoclastic Root Endophyte, Isolated at a Diesel Fuel Phytoremediation  Site Planted with Populus.
PG  - e00028-16
AB  - We report the 4.76-Mb draft genome of Pantoea ananatis GB1, a Gram-negative bacterium of the
      family Enterobacteriaceae, isolated from the roots of poplars
      planted for phytoremediation of a diesel-contaminated plume at the Ford Motor
      Company site in Genk, Belgium. Strain GB1 promotes plant growth in various hosts
      and metabolizes hydrocarbons.
AU  - Gkorezis P
AU  - Van Hamme JD
AU  - Bottos EM
AU  - Thijs S
AU  - Balseiro-Romero M
AU  - Monterroso C
AU  - Kidd PS
AU  - Rineau F
AU  - Weyens N
AU  - Vangronsveld J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00028-16.

PMID- 15983137
VI  - 33
DP  - 2005
TI  - Codon usage comparison of novel genes in clinical isolates of Haemophilus influenzae.
PG  - 3644-3658
AB  - A similarity statistic for codon usage was developed and used to compare novel gene sequences
      found in clinical isolates of Haemophilus influenzae with a reference set of 80 prokaryotic,
      eukaryotic and viral genomes. These analyses were performed to obtain an indication as to
      whether individual genes were Haemophilus-like in nature, or if they probably had more
      recently entered the H.influenzae gene pool via horizontal gene transfer from other species.
      The average and SD values were calculated for the similarity statistics from a study of the
      set of all genes in the H.influenzae Rd reference genome that encoded proteins of 100 amino
      acids or longer. Approximately 80% of Rd genes gave a statistic indicating that they were most
      like other Rd genes. Genes displaying codon usage statistics >1 SD above this range were
      either considered part of the highly expressed group of H.influenzae genes, or were considered
      of foreign origin. An alternative determinant for identifying genes of foreign origin was when
      the similarity statistics produced a value that was much closer to a non-H.influenzae
      reference organism than to any of the Haemophilus species contained in the reference set.
      Approximately 65% of the novel sequences identified in the H.influenzae clinical isolates
      displayed codon usages most similar to Haemophilus sp. The remaining novel sequences produced
      similarity statistics closer to one of the other reference genomes thereby suggesting that
      these sequences may have entered the H.influenzae gene pool more re
AU  - Gladitz J
AU  - Shen K
AU  - Antalis P
AU  - Hu FZ
AU  - Post JC
AU  - Ehrlich GD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2005 33: 3644-3658.

PMID- 25414502
VI  - 2
DP  - 2014
TI  - Genome Sequences of Vibrio navarrensis, a Potential Human Pathogen.
PG  - e01188-14
AB  - Vibrio navarrensis is an aquatic bacterium recently shown to be associated with human illness.
      We report the first genome sequences of three V. navarrensis
      strains obtained from clinical and environmental sources. Preliminary analyses of
      the sequences reveal that V. navarrensis contains genes commonly associated with
      virulence in other human pathogens.
AU  - Gladney LM
AU  - Katz LS
AU  - Knipe KM
AU  - Rowe LA
AU  - Conley AB
AU  - Rishishwar L
AU  - Marino-Ramirez L
AU  - Jordan IK
AU  - Tarr CL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01188-14.

PMID- 29898509
VI  - 626
DP  - 2018
TI  - Survival of antibiotic resistant bacteria following artificial solar radiation of secondary wastewater effluent.
PG  - 1005-1011
AB  - Urban wastewater treatment plant effluents represent one of the major emission sources of
      antibiotic-resistant
      bacteria(ARB)in natural aquatic environments.  In this study,the effect of artificial solar
      radiation on total culturable heterotrophic bacteria and ARB(including
      amoxicillin-resistant,ciprofloxacin-resistant,rifampicin-
      resistant,sulfamethoxazole-resistant,and tetracycline-resistant bacteria)present in secondary
      effluent was investigated.  Artificial solar radiation was effective in inactivating the
      majority of environmental bacteria, however,
      the proportion of strains with ciprofloxacin-resistance and rifampicin-resistance increased in
      the surviving populations. Isolates of Pseudomonas putida, Serratia marcescens, and
      Stenotrophomonas maltophilia nosocomial path-
      ogens were identified as resistant to solar radiation and to atleast three antibiotics. Draft
      genome sequencing and typing revealed isolates carrying multiple resistance genes; where S.
      maltophilia (resistant to all studied antibiotics)sequence type was similar to strains
      isolated in blood infections. Results from this study confirm that
      solar radiation reduces total bacterial load in secondary effluent, but may indirectly
      increase the relative abundance of ARB.
AU  - Glady-Croue J
AU  - Niu X-Z
AU  - Ramsay JP
AU  - Watkin E
AU  - Murphy RJT
AU  - Croue J-P
PT  - Journal Article
TA  - Sci. Total Environ.
JT  - Sci. Total Environ.
SO  - Sci. Total Environ. 2018 626: 1005-1011.

PMID- 27834713
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Corynebacterium amycolatum Strain ICIS 53 Isolated from  a Female Urogenital Tract.
PG  - e01267-16
AB  - This report describes the draft genome sequence of Corynebacterium amycolatum strain ICIS 53,
      isolated from the reproductive tract of a healthy woman. The size
      of the genome was 2,460,257 bp (58.98% G+C content). Annotation revealed 2,173
      coding sequences, including 2,076 proteins, 7 rRNA genes, and 53 tRNA genes.
AU  - Gladysheva IV
AU  - Cherkasov SV
AU  - Khlopko YA
AU  - Plotnikov AO
AU  - Gogoleva NE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01267-16.

PMID- 28912325
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Vaginal Isolate Corynebacterium amycolatum ICIS 9.
PG  - e00975-17
AB  - Corynebacterium amycolatum ICIS 9 was isolated from a vaginal smear of a healthy  woman. Here,
      we report the draft genome sequence of C. amycolatum ICIS 9, which
      will be useful for further studies of specific genetic features of this strain
      and for understanding its probiotic properties.
AU  - Gladysheva IV
AU  - Khlopko YA
AU  - Cherkasov SV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00975-17.

PMID- 11679669
VI  - 294
DP  - 2001
TI  - Comparative genomics of Listeria species.
PG  - 849-852
AB  - Listeria monocytogenes is a food-borne pathogen with a high mortality rate that has also
      emerged as a paradigm for intracellular parasitism. We present and compare the genome
      sequences of L. monocytogenes (2,944,528 base pairs) and a nonpathogenic species, L. innocua
      (3,011,209 base pairs). We found a large number of predicted genes encoding surface and
      secreted proteins, transporters, and transcriptional regulators, consistent with the ability
      of both species to adapt to diverse environments. The presence of 270 L. monocytogenes and 149
      L. innocua strain-specific genes (clustered in 100 and 63 islets, respectively) suggests that
      virulence in Listeria results from multiple gene acquisition and deletion events.
AU  - Glaser P et al
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2001 294: 849-852.

PMID- 12354221
VI  - 45
DP  - 2002
TI  - Genome sequence of Streptococcus agalactiae, a pathogen causing invasive neonatal disease.
PG  - 1499-1513
AB  - Streptococcus agalactiae is a commensal bacterium colonizing the intestinal tract of a
      significant proportion of the human population.
      However, it is also a pathogen which is the leading cause of invasive
      infections in neonates and causes septicaemia, meningitis and pneumonia.
      We sequenced the genome of the serogroup III strain NEM316, responsible
      for a fatal case of septicaemia. The genome is 2,211,485 base pairs long
      and contains 2118 protein coding genes. Fifty-five per cent of the
      predicted genes have an ortholog in the Streptococcus pyogenes genome,
      representing a conserved backbone between these two streptococci. Among
      the genes in S. agalactiae that lack an ortholog in S. pyogenes, 50% are
      clustered within 14 islands. These islands contain known and putative
      virulence genes, mostly encoding surface proteins as well as a number of
      genes related to mobile elements. Some of these islands could therefore be
      considered as pathogenicity islands. Compared with other pathogenic
      streptococci, S. agalactiae shows the unique feature that pathogenicity
      islands may have an important role in virulence acquisition and in genetic
      diversity.
AU  - Glaser P
AU  - Rusniok C
AU  - Buchrieser C
AU  - Chevalier F
AU  - Frangeul L
AU  - Msadek T
AU  - Zouine M
AU  - Couve E
AU  - Lalioui L
AU  - Poyart C
AU  - Trieu-Cuot P
AU  - Kunst F
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2002 45: 1499-1513.

PMID- 21217001
VI  - 193
DP  - 2011
TI  - Genome Sequence of the Plant-Pathogenic Bacterium Dickeya dadantii 3937.
PG  - 2076-2077
AB  - Dickeya dadantii is a plant-pathogenic enterobacterium responsible for the soft rot disease of
      many plants of economic importance. We present here
      the sequence of strain 3937, a strain widely used as a model system for
      research on the molecular biology and pathogenicity of this group of
      bacteria.
AU  - Glasner JD et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 2076-2077.

PMID- 18986251
VI  - 21
DP  - 2008
TI  - Niche-specificity and the variable fraction of the Pectobacterium pan-genome.
PG  - 1549-1560
AB  - We compare genome sequences of three closely related soft-rot pathogens that vary
      in host range and geographical distribution to identify genetic differences that
      could account for lifestyle differences. The isolates compared, Pectobacterium
      atrosepticum SCRI1043, P. carotovorum WPP14, and P. brasiliensis 1692, represent
      diverse lineages of the genus. P. carotovorum and P. brasiliensis genome contigs,
      generated by 454 pyrosequencing ordered by reference to the previously published
      complete circular chromosome of P. atrosepticum genome and each other, account
      for 96% of the predicted genome size. Orthologous proteins encoded by P.
      carotovorum and P. brasiliensis are approximately 95% identical to each other and
      92% identical to P. atrosepticum. Multiple alignment using Mauve identified a
      core genome of 3.9 Mb conserved among these Pectobacterium spp. Each core genome
      is interrupted at many points by species-specific insertions or deletions
      (indels) that account for approximately 0.9 to 1.1 Mb. We demonstrate that the
      presence of a hrpK-like type III secretion system-dependent effector protein in
      P. carotovorum and P. brasiliensis and its absence from P. atrosepticum is
      insufficient to explain variability in their response to infection in a plant.
      Additional genes that vary among these species include those encoding peptide
      toxin production, enzyme production, secretion proteins, and antibiotic
      production, as well as differences in more general aspects of gene regulation and
      metabolism that may be relevant to pathogenicity.
AU  - Glasner JD
AU  - Marquez-Villavicencio M
AU  - Kim HS
AU  - Jahn CE
AU  - Ma B
AU  - Biehl BS
AU  - Rissman AI
AU  - Mole B
AU  - Yi X
AU  - Yang CH
AU  - Dangl JL
AU  - Grant SR
AU  - Perna NT
AU  - Charkowski AO
PT  - Journal Article
TA  - Mol. Plant Microbe Interact.
JT  - Mol. Plant Microbe Interact.
SO  - Mol. Plant Microbe Interact. 2008 21: 1549-1560.

PMID- 
VI  - 0
DP  - 1992
TI  - Enzymatic properties and biological functions of VSR DNA mismatch endonuclease.
PG  - 165-173
AB  - The protein encoded by the vsr gene of E. coli K-12 was produced by construction and
      expression of a chimeric gene. The corresponding fusion protein contains b-lactamase as the
      N-terminal and the Vsr gene product as the C-terminal component. Enzymological studies of the
      fusion protein reveal the Vsr gene product as the first known example of a DNA mismatch
      endonuclease. Its substrate recognition properties are characterized by a combination of
      sequence and structure specificity as follows. Vsr endonuclease recognizes T/G mismatches in
      sequence contexts related to the cognate sequence of Dcm DNA cytosine methyltransferase and
      cleaves the phosphodiester bond on the 5' side of the mismatched T residue, forming a
      phosphorylated 5' end (Hennecke et al. 1991, Nature 353: 775-778). Studies concerning the
      influence of individual functional groups of the mismatched bases on substrate recognition and
      the detailed requirements of DNA sequence context are reported. The enzymology of Vsr
      endonuclease is summarized and its biological role is discussed.
AU  - Glasner W
AU  - Hennecke F
AU  - Fritz HJ
PT  - Journal Article
TA  - Structural tools for the analysis of protein-nucleic acid complexes advances in life sciences.
JT  - Structural tools for the analysis of protein-nucleic acid complexes advances in life sciences.
SO  - Structural tools for the analysis of protein-nucleic acid complexes advances in life sciences. 1992 0: 165-173.

PMID- 7823316
VI  - 245
DP  - 1995
TI  - Substrate preferences of Vsr DNA mismatch endonuclease and their consequences for the evolution of the Escherichia coli K-12 genome.
PG  - 1-7
AB  - The substrate spectrum of Vsr DNA mismatch endonuclease of Escherichia coli K-12 was
      investigated using fluorescence-labelled oligonucleotide substrates and a DNA sequencer for
      detection and quantification of substrates and reaction products. Fourteen substrates were
      found to be processed by the enzyme, which differ in one or two positions from the canonical
      pentanucleotide sequence CTA/TGG (T mismatched to G). Relative second-order rate constants of
      these substrates were determined in groups of four by multiple substrate kinetics and compared
      to the underrepresentation of the corresponding pentanucleotides in the E. coli K-12 genome.
      The high quality of correlation further establishes active mutagenesis by VSP repair as a
      significant driving force of the evolution of the E. coli K-12 genome and provides clues to
      its possible selective value.
AU  - Glasner W
AU  - Merkl R
AU  - Schellenberger V
AU  - Fritz HJ
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1995 245: 1-7.

PMID- 11048724
VI  - 407
DP  - 2000
TI  - The complete sequence of the mucosal pathogen Ureaplasma urealyticum.
PG  - 757-762
AB  - The comparison of the genomes of two very closely related human mucosal pathogens, Mycoplasma
      genitalium and Mycoplasma pneumoniae, has helped define the essential functions of a
      self-replicating minimal cell, as well as what constitutes a mycoplasma.  Here we report the
      complete sequence of a more distant phylogenetic relative of those bacteria, Ureaplasma
      urealyticum (parvum biovar), which is also a mucosal pathogen of humans.  It is the third
      mycoplasma to be sequenced, and has the smallest sequenced prokaryotic genome except for M.
      genitalium.  Although the U. urealyticum genome is similar to the two sequenced mycoplasma
      genomes, features make this organism unique among mycoplasmas and all bacteria.  Almost all
      ATP synthesis is the result of urea hydrolysis, which generates an energy-producing
      electrochemical gradient.  Some highly conserved eubacterial enzymes appear not to be encoded
      by U. urealyticum, including the cell-division protein FtsZ, chaperonins GroES and GroEL, and
      ribonucleoside-diphosphate reductase.  U. urealyticum has six closely related iron
      transporters, which apparently arose through gene duplication, suggesting that it has a kind
      of respiration system not present in other small genome bacteria.  The genome is only 25.5%
      G+C in nucleotide content, and the G+C content of individual genes may predict how essential
      those genes are to ureaplasma survival.
AU  - Glass JI
AU  - Lefkowitz EJ
AU  - Glass JS
AU  - Heiner CR
AU  - Chen EY
AU  - Cassell GH
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2000 407: 757-762.

PMID- 3025680
VI  - 10
DP  - 1985
TI  - Identification of the plasmid pLG13 coding for the DNA modification-restriction system EcoRV and properties of strains carrying this plasmid.
PG  - 39-42
AB  - 
AU  - Glatman LI
AU  - Iablokova MB
AU  - Kravets AI
AU  - Terekhov AA
AU  - Samoilenko II
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1985 10: 39-42.

PMID- 2560908
VI  - 34
DP  - 1989
TI  - Systems of DNA restriction-modification.
PG  - 932-938
AB  - None
AU  - Glatman LI
AU  - Kravets AN
PT  - Journal Article
TA  - Antibiot. Khimioter
JT  - Antibiot. Khimioter
SO  - Antibiot. Khimioter 1989 34: 932-938.

PMID- 6250778
VI  - 252
DP  - 1980
TI  - New DNA modification-restriction plasmid system detected in a clinical strain of Escherichia coli.
PG  - 993-995
AB  - 
AU  - Glatman LI
AU  - Moroz AF
AU  - Iablokova MB
AU  - Rebentish BA
AU  - Kholmina GV
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1980 252: 993-995.

PMID- 6261280
VI  - 4
DP  - 1980
TI  - A novel plasmid-mediated DNA restriction-modification system in E. coli.
PG  - 350-351
AB  - R plasmids from 101 clinical isolates were transferred to E. coli J62 by conjugation and
      tested for the presence of R plasmid-mediated restriction-modification DNA systems.  Thirty R
      plasmids were found to inhibit phage lambda vir development.  Ten plasmids determined
      restriction-modification system; nine of them proved identical with R.M. EcoRII.  One
      transconjugant, E. coli J62 pLG74, was shown to have a restriction-modification system
      different from all the known R plasmid-mediated systems.  Site-specific endonuclease has been
      isolated from E. coli J62 pLG74 which differed from all the known restriction endonucleases in
      the number of cleavage sites on phages lambda, phiX 174, virus SV40, plasmid pBR322 DNA
      molecules.
AU  - Glatman LI
AU  - Moroz AF
AU  - Yablokova MB
AU  - Rebentish BA
AU  - Kcholmina GV
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 1980 4: 350-351.

PMID- 2194120
VI  - 3
DP  - 1990
TI  - New site-specific endodesoxyribonuclease EcoHI.
PG  - 32
AB  - A new Type II site-specific endonuclease, EcoHI, has been isolated from a strain of
      Escherichia coli and characterized.  Restriction endonuclease EcoHI recognizes the nucleotide
      sequence C C (C/G) G'G with the cleavage site between the fourth and fifth nucleotides.  It
      is an isoschizomer of the restriction endonuclease CauII.  The yield of enzyme is 2500 units
      of activity per 1 g of biomass.  The producing strain Escherichia coli HI is nonpathogenic,
      easily grown with the antiobiotic resistance markers allowing the strain to be cultivated
      under selective conditions.
AU  - Glatman LI
AU  - Terekhov AA
AU  - Kalnin KV
AU  - Bolotin AP
AU  - Rebentish BA
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1990 3: 32.

PMID- 24604654
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Corynebacterium falsenii DSM 44353 To Study the Evolution of Corynebacterium Cluster 3 Species.
PG  - e00158-14
AB  - Corynebacterium falsenii is a member of the natural microflora of wild and domesticated birds
      and is rarely detected in human clinical specimens. The
      chromosomal sequence of the type strain C. falsenii DSM 44353 comprises 2,677,607
      bp and provides detailed insights into the evolution of Corynebacterium species
      assigned to the highly diverse cluster 3.
AU  - Glaub A
AU  - Bomholt C
AU  - Gravermann K
AU  - Brinkrolf K
AU  - Albersmeier A
AU  - Ruckert C
AU  - Tauch A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00158-14.

PMID- 21304681
VI  - 2
DP  - 2010
TI  - Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034).
PG  - 87-95
AB  - Chitinophaga pinensis Sangkhobol and Skerman 1981 is the type strain of the species which is
      the type species of the rapidly growing genus Chitinophaga in
      the sphingobacterial family 'Chitinophagaceae'. Members of the genus Chitinophaga
      vary in shape between filaments and spherical bodies without the production of a
      fruiting body, produce myxospores, and are of special interest for their ability
      to degrade chitin. Here we describe the features of this organism, together with
      the complete genome sequence, and annotation. This is the first complete genome
      sequence of a member of the family 'Chitinophagaceae', and the 9,127,347 bp long
      single replicon genome with its 7,397 protein-coding and 95 RNA genes is part of
      the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Glavina Del Rio T et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 2: 87-95.

PMID- 7873177
VI  - 17
DP  - 1994
TI  - Increasing proportions of uracil in DNA substrates increases inhibition of restriction enzyme digests.
PG  - 1086-1090
AB  - Techniques that rely upon the incorporation of uracil into DNA are being published with
      increasing frequency, especially in PCR protocols. We report here the efficiency of 18 type II
      restriction enzymes to digest PCR amplicons synthesized with varying proportions of TTP to
      dUTP in the PCR mixture. We find that most enzymes with A:T/U bp in their recognition site
      digest the amplicons less efficiently as the percentage of dUTP in the reaction mixture is
      increased. This effect is most dramatic when the proportion of dUTP in the nucleotide mixture
      exceeds 50%. All but one of the enzymes which fail to digest amplicons that are synthesized
      with 100% dUTP digest some amplicons which are synthesized with 90% dUTP.
AU  - Glenn TC
AU  - Waller DR
AU  - Braun MJ
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 1994 17: 1086-1090.

PMID- Not carried by PubMed...
VI  - 58
DP  - 1997
TI  - The murine DNA methyltransferase: Purification, heterologous expression, steady-state kinetics and post-translational processing.
PG  - 1265B
AB  - The mammalian DNA methyltransferase catalyzes the transfer of methyl groups from S-adenosyl
      methionine to the C5-cytosine within the d(CpG) dinucleotides of double-stranded DNA.  DNA
      methylation is critical for normal embryonic development, and regulates gene expression by
      controlling the binding of proteins to the regulatory regions of DNA.  Despite the biological
      importance of this enzyme, the DNA methyltransferase itself has not been characterized in
      detail, with respect to size, steady-state kinetic parameters, post-translational
      modifications and N-terminal sequence.  This lack of information has been due to the
      difficulty in  the purification of suitable quantities of the protein for enzymological and
      biochemical studies.  The murine erthroleukemia cell-derived DNA methyltransferase (300-800
      micrograms) of 3 x 10^10 cells grown in 10 liter cultures.  The recombinant enzyme was
      expressed as a fusion protein containing a nickel-affinity leader peptide using a baculovirus
      expression system.  Expression was 50-fold higher per cell than in the MEL-cells.  The
      recombinant enzyme (1-2mg) was purified from 5 x 10^8 Sf21 cells using immobilized nickel
      affinity chromatography.  The steady-state kinetic parameters of kcat, Km for the substrate,
      double-stranded poly(dI-dC) and the cofactor, S-adenosylmethionine were determined for both
      the MEL cell-derived and the recombinant DNA methyltransferases, demonstrating that the two
      enzymes were functionally similar.  The DNA methyltransferase was a noticeably slow enzyme
      (kcat, 7/hr); however, based on an estimate of the number of DNA methyltransferase molecules
      per nucleus, there should be enough methyltransferase activity to account for the levels of
      DNA methylation in a vertebrate cell.  Metabolic labeling experiments revealed that the DNA
      methyltransferase was post-translationally phosphorylated on serine/threonine residues, and
      peptide mapping using HPLC-electrospray mass spectrometry resulted in the identification of a
      single, predominant phosphorylation site on the MEL-derived DNA methyltransferase in the
      domain responsible for targeting of the enzyme to the replication foci.  Data demonstrating a
      single start of translation at the first methionine, as revised by a newly reported cDNA, is
      presented.
AU  - Glickman JF
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1997 58: 1265B.

PMID- 9016766
VI  - 230
DP  - 1997
TI  - Purification and characterization of recombinant baculovirus-expressed mouse DNA methyltransferase.
PG  - 280-284
AB  - DNA methylation is essential for normal embryonic development in mice.  An understanding of
      how DNA methylation is controlled is largely dependent upon the isolation and characterization
      of the cellular components of the DNA methylation system.  The enzyme which methylates DNA in
      eukaryotic cells is a C-5 cytosine DNA methyltransferase.  Historically, the characterization
      of this enzyme has been limited by its availability and purity.  Here, we present a
      single-step purification of 4 mg of baculovirus-expressed mouse DNA methyltransferase
      containing a nickel-affinity leader peptide.  The recombinant DNA methyltransferase copurified
      with inhibitory RNA, which was removed by treatment with ribonuclease A.  Like its
      non-recombinant counterpart, the recombinant enzyme is activated by hemi-methylation.  A
      direct steady-state kinetic comparison between the recombinant baculovirus-expressed enzyme
      with its MEL cell-derived counterpart is presented.
AU  - Glickman JF
AU  - Flynn J
AU  - Reich NO
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1997 230: 280-284.

PMID- 9211941
VI  - 272
DP  - 1997
TI  - Peptide mapping of the murine DNA methyltransferase reveals a major phosphorylation site and the start of translation.
PG  - 17851-17857
AB  - The murine DNA methyltransferase catalyzes the transfer of methyl groups from
      S-adenosylmethionine to cytosines within d(CpG) dinucleotides.  The enzyme is necessary for
      normal embryonic development and is implicated in a number of important processes, including
      the control of gene expression and cancer.  Metabolic labeling and high pressure liquid
      chromatography-electrospray ionization-mass spectrometry (HPLC-ESI-MS) were performed on DNA
      methyltransferase purified from murine erythroleukemia cells.  Serine 514 was identified as a
      major phosphorylation site that lies in a domain required for targeting of the enzyme to the
      replication foci.  These results present a potential mechanism for the regulation of DNA
      methylation.  HPLC-ESI-MS peptide mapping data demonstrated that the purified murine DNA
      methyltransferase protein contains the N-terminal regions predicted by the recently revised
      5' gene sequences.  The evidence suggests a start of translation at the first predicted
      methionine, with no alternate translational start sites.  Our peptide mapping results provide
      a more detailed structural characterization of the DNA methyltransferase that will facilitate
      future structure/function studies.
AU  - Glickman JF
AU  - Pavlovich JG
AU  - Reich NO
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1997 272: 17851-17857.

PMID- 7980570
VI  - 204
DP  - 1994
TI  - Baculovirus-mediated high level expression of a mammalian DNA methyltransferase.
PG  - 1003-1008
AB  - The murine C-5 cytosine DNA methyltransferase (Mtase, E.C.2.1.1.37) containing a hexahistidine
      affinity leader peptide has been expressed at levels which are at least 50-fold higher than
      previously reported.  The recombinant enzyme has activity levels similar to the wild-type
      enzyme.  The recombinant polypeptide binds to and elutes from a nickel affinity resin (IMAC
      resin).  No dramatic differences in post-translational modification between the wild-type and
      recombinant enzyme were observed.  The recombinant system will be useful in performing
      site-directed mutagenesis and will facilitate enzymological and biological investigations of
      this enzyme.
AU  - Glickman JF
AU  - Reich NO
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1994 204: 1003-1008.

PMID- 8467964
VI  - 7
DP  - 1993
TI  - The expression of the murine DNA cytosine methyltransferase in cultured cells from Spodoptera frugiperda using a recombinant Baculovirus.
PG  - A1291
AB  - The murine DNA methyltransferase (MTase, EC 2.1.1.371) is a 169.6 kD enzyme which transfers
      methyl groups from the S-adenosyl methionine cofactor to the 5' carbon of cytosine in DNA.
      DNA methylation in mammals has been implicated in the regulation of gene expression,
      immunoglobulin gene re-arrangement, X-chromosome inactivation and carcinogenesis. We have
      expressed the MTase in cultured insect cells using a lethal linear baculovirus system. Our
      data indicates 100-fold enhancement in MTase expression over previous methods. This system
      will enable us to perform more precise enzymology on the MTase because prior studies were
      limited by the quantity of purified enzyme available. To our knowledge, this is the largest
      nuclear protein expressed using the baculovirus system. We are currently optimizing the
      expression system and investigating the role of post-translational modification and
      sub-cellular localization in the regulation of function of MTase function.
AU  - Glickman JF
AU  - Reich NO
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1993 7: A1291.

PMID- 26377311
VI  - 15
DP  - 2015
TI  - Potential mechanisms of attenuation for rifampicin-passaged strains of Flavobacterium psychrophilum.
PG  - 179
AB  - BACKGROUND: Flavobacterium psychrophilum is the etiologic agent of bacterial coldwater disease
      in salmonids. Earlier research showed that a
      rifampicin-passaged strain of F. psychrophilum (CSF 259-93B.17) caused no disease
      in rainbow trout (Oncorhynchus mykiss, Walbaum) while inducing a protective
      immune response against challenge with the virulent CSF 259-93 strain. We
      hypothesized that rifampicin passage leads to an accumulation of genomic
      mutations that, by chance, reduce virulence. To assess the pattern of phenotypic
      and genotypic changes associated with passage, we examined proteomic, LPS and
      single-nucleotide polymorphism (SNP) differences for two F. psychrophilum strains
      (CSF 259-93 and THC 02-90) that were passaged with and without rifampicin
      selection. RESULTS: Rifampicin resistance was conveyed by expected mutations in
      rpoB, although affecting different DNA bases depending on the strain. One
      rifampicin-passaged CSF 259-93 strain (CR) was attenuated (4 % mortality) in
      challenged fish, but only accumulated eight nonsynonymous SNPs compared to the
      parent strain. A CSF 259-93 strain passaged without rifampicin (CN) accumulated
      five nonsynonymous SNPs and was partially attenuated (28 % mortality) compared to
      the parent strain (54.5 % mortality). In contrast, there were no significant
      change in fish mortalities among THC 02-90 wild-type and passaged strains,
      despite numerous SNPs accumulated during passage with (n = 174) and without
      rifampicin (n = 126). While only three missense SNPs were associated with
      attenuation, a Ser492Phe rpoB mutation in the CR strain may contribute to further
      attenuation. All strains except CR retained a gliding motility phenotype. Few
      proteomic differences were observed by 2D SDS-PAGE and there were no apparent
      changes in LPS between strains. Comparative methylome analysis of two strains (CR
      and TR) identified no shared methylation motifs for these two strains.
      CONCLUSION: Multiple genomic changes arose during passage experiments with
      rifampicin selection pressure. Consistent with our hypothesis, unique
      strain-specific mutations were detected for the fully attenuated (CR), partially
      attenuated (CN) and another fully attenuated strain (B17).
AU  - Gliniewicz K
AU  - Wildung M
AU  - Orfe LH
AU  - Wiens GD
AU  - Cain KD
AU  - Lahmers KK
AU  - Snekvik KR
AU  - Call DR
PT  - Journal Article
TA  - BMC Microbiol.
JT  - BMC Microbiol.
SO  - BMC Microbiol. 2015 15: 179.

PMID- 15547252
VI  - 32
DP  - 2004
TI  - Comparative analysis of the Borrelia garinii genome.
PG  - 6038-6046
AB  - Three members of the genus Borrelia (B.burgdorferi, B.garinii, B.afzelii) cause tick-borne
      borreliosis. Depending on the Borrelia species involved,
      the borreliosis differs in its clinical symptoms. Comparative genomics
      opens up a way to elucidate the underlying differences in Borrelia
      species. We analysed a low redundancy whole-genome shotgun (WGS) assembly
      of a B.garinii strain isolated from a patient with neuroborreliosis in
      comparison to the B.burgdorferi genome. This analysis reveals that most of
      the chromosome is conserved (92.7% identity on DNA as well as on amino
      acid level) in the two species, and no chromosomal rearrangement or larger
      insertions/deletions could be observed. Furthermore, two collinear
      plasmids (lp54 and cp26) seem to belong to the basic genome inventory of
      Borrelia species. These three collinear parts of the Borrelia genome
      encode 861 genes, which are orthologous in the two species examined. The
      majority of the genetic information of the other plasmids of
      B.burgdorferii is also present in B.garinii although orthology is not easy
      to define due to a high redundancy of the plasmid fraction. Yet, we did
      not find counterparts of the B.burgdorferi plasmids lp36 and lp38 or their
      respective gene repertoire in the B.garinii genome. Thus, phenotypic
      differences between the two species could be attributable to the presence
      or absence of these two plasmids as well as to the potentially positively
      selected genes.
AU  - Glockner G
AU  - Lehmann R
AU  - Romualdi A
AU  - Pradella S
AU  - Schulte-Spechtel U
AU  - Schilhabel M
AU  - Wilske B
AU  - Suhnel J
AU  - Platzer M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2004 32: 6038-6046.

PMID- 12835416
VI  - 100
DP  - 2003
TI  - Complete genome sequence of the marine planctomycete Pirellula sp. strain 1.
PG  - 8298-8303
AB  - Pirellula sp. strain 1 ("Rhodopirellula baltica") is a marine representative of the globally
      distributed and environmentally important
      bacterial order Planctomycetales. Here we report the complete genome
      sequence of a member of this independent phylum. With 7.145 megabases,
      Pirellula sp. strain 1 has the largest circular bacterial genome sequenced
      so far. The presence of all genes required for heterolactic acid
      fermentation, key genes for the interconversion of C1 compounds, and 110
      sulfatases were unexpected for this aerobic heterotrophic isolate.
      Although Pirellula sp. strain 1 has a proteinaceous cell wall, remnants of
      genes for peptidoglycan synthesis were found. Genes for lipid A
      biosynthesis and homologues to the flagellar L- and P-ring protein
      indicate a former Gram-negative type of cell wall. Phylogenetic analysis
      of all relevant markers clearly affiliates the Planctomycetales to the
      domain Bacteria as a distinct phylum, but a deepest branching is not
      supported by our analyses.
AU  - Gloeckner FO
AU  - Kube M
AU  - Bauer M
AU  - Teeling H
AU  - Lombardot T
AU  - Ludwig W
AU  - Gade D
AU  - Beck A
AU  - Borzym K
AU  - Heitmann K
AU  - Rabus R
AU  - Schlesner H
AU  - Amann R
AU  - Reinhardt R
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2003 100: 8298-8303.

PMID- 16914037
VI  - 7
DP  - 2006
TI  - Comparative genome analysis: Selection pressure on the Borrelia vls cassettes is essential for infectivity.
PG  - 211
AB  - ABSTRACT: BACKGROUND: At least three species of Borrelia burgdorferi sensu lato (Bbsl) cause
      tick-borne Lyme disease. Previous work including the
      genome analysis of B. burgdorferi B31 and B. garinii PBi suggested a
      highly variable plasmid part. The frequent occurrence of duplicated
      sequence stretches, the observed plasmid redundancy, as well as the mainly
      unknown function and variability of plasmid encoded genes rendered the
      relationships between plasmids within and between species largely
      unresolvable. RESULTS: To gain further insight into Borreliae genome
      properties we completed the plasmid sequences of B. garinii PBi, added the
      genome of a further species, B. afzelii PKo, to our analysis, and compared
      for both species the genomes of pathogenic and apathogenic strains. The
      core of all Bbsl genomes consists of the chromosome and two plasmids
      collinear between all species. We also found additional groups of
      plasmids, which share large parts of their sequences. This makes it very
      likely that these plasmids are relatively stable and share common
      ancestors before the diversification of Borrelia species. The analysis of
      the differences between B. garinii PBi and B. afzelii PKo genomes of low
      and high passages revealed that the loss of infectivity is accompanied in
      both species by a loss of similar genetic material. Whereas B. garinii PBi
      suffered only from the break-off of a plasmid end, B. afzelii PKo lost
      more material, probably an entire plasmid. In both cases the vls gene
      locus encoding for variable surface proteins is affected. CONCLUSIONS: The
      complete genome sequences of a B. garinii and a B. afzelii strain
      facilitates further comparative studies within the genus Borrellia. Our
      study shows that loss of infectivity can be traced back to only one single
      event in B. garinii PBi: the loss of the vls cassettes possibly due to
      error prone gene conversion. Similar albeit extended losses in B. afzelii
      PKo support the hypothesis that infectivity of Borrelia species depends
      heavily on the evasion from the host response.
AU  - Gloeckner G
AU  - Schulte-Spechtel U
AU  - Schilhabel M
AU  - Felder M
AU  - Suehnel J
AU  - Wilske B
AU  - Platzer M
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2006 7: 211.

PMID- Not included in PubMed...
VI  - 41
DP  - 1978
TI  - Genetics of the R-M systems in Haemophilus.
PG  - 123
AB  - The genus Haemophilus is an extremely rich source of restriction endonucleases of both type I
      and type II.  Altogether 22 such enzymes have been detected and partially characterized.
      About half of these enzymes have been isolated from Haemophilus influenzae and each of the H.
      influenzae serotypes a, b, c, d, e and f are believed to possess restriction and modification
      (R-M) systems.  The R-M systems from serotypes a, b, d, e and f have been analyzed genetically
      and the restriction endonucleases from serotypes a, f (HinaII, HinaIII and HinfIII) have been
      partially characterized.  All of the evidence indicates that the enzymes which form part of
      the H. influenzae R-M systems are type I enzymes and their role appears to be similar to that
      of other restriction endonucleases that can be detected by in vivo tests.  Type II restriction
      endonucleases have been isolated from all of the H. influenzae serotypes other than serotype a
      and characterized using bacteriophage lambda or other well-defined DNA molecules as substrate.
      These enzymes do not appear to form part of recognized R-M systems and they have little or no
      activity on Haemophilus phage DNA.
AU  - Glover SW
PT  - Journal Article
TA  - Heredity
JT  - Heredity
SO  - Heredity 1978 41: 123.

PMID- 6249678
VI  - 8
DP  - 1980
TI  - Restriction Endonucleases.  Genetics of restriction/modification systems.
PG  - 395-400
AB  - Three different types of restriction/modification system are now recognized: type I, type II
      and type III.  The genetics of type-I systems has been investigated by several groups of
      workers and there is common agreement that three genes are involved: hsdS, hsdR and hsdM.  The
      specificity of the system is determined by the product of the hsdS gene.  Mutations in the
      hsdS gene produce an r-m- phenotype; mutations in the hsdR gene produce an r-m+ phenotype and
      mutations in the hsdM gene produce an r-m- phenotype.  Several such systems have been
      recognized and analysed genetically in Escherichia coli and in Salmonella typhimurium.
      Complementation tests employing partial diploids constructed by using F' strains show that
      the E. coli systems K and B and the S. typhimurium system SB are functionally related, and
      mapping experiments show that they are genetically allelic.  It has been shown that
      restriction endonucleases isolated from type-I systems have the three different polypeptide
      subunits that the three-gene model predicts, and that type-I-modification methylases have the
      two subunits expected from the genetic model.  However, unambiguous assignment of polypeptide
      subunit to coding gene is still lacking. No convincing evidence for regulatory-gene functions
      has been obtained so far.
AU  - Glover SW
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 1980 8: 395-400.

PMID- 4921184
VI  - 15
DP  - 1970
TI  - Functional analysis of host-specificity mutants in Escherichia coli.
PG  - 237-250
AB  - Evidence from a functional analysis of host-specificity mutants in merodiploids
      is presented which supports the suggestion that three genes, hss, hsr and hsm,
      are necessary for the expression of host-controlled restriction and
      modification.  The host-specificity phenotype expressed by the merodiploids
      provides evidence that at least two genes, hss and hsr, are concerned in the
      expression of host-specific restriction of DNA and one of these genes, hss, is
      responsible for the strain specificity of the restriction enzyme.  A class of
      modification-deficient mutants isolated from restriction-deficient,
      modification-proficient mutants, was also tested for complementation in
      merodiploids and the phenotype of these merodiploids provides evidence that at
      least two genes, hss and hsm, are concerned in the expression of host-specific
      modification of DNA and one of these genes, hss, is responsible for the strain
      specificity of the modification enzyme.  How these three genes function at the
      molecular level is discussed in terms of models based on the interaction of
      subunits to form oligomeric enzymes.
AU  - Glover SW
PT  - Journal Article
TA  - Genet. Res.
JT  - Genet. Res.
SO  - Genet. Res. 1970 15: 237-250.

PMID- 4878053
VI  - 53
DP  - 1968
TI  - Host specificity in F' heterogenotes of Escherichia coli.
PG  - i-ii
AB  - Host-controlled modification of DNA in strains of Escherichia coli has two
      clearly defined characteristics.  First, modification, a process which acts
      directly on DNA and involves the specific alteration of certain base sequences
      by methylation.  As a result, the DNA synthesized in a particular strain may
      carry a characteristic, strain-specific pattern.  Secondly, restriction, a
      process which may lead to the rapid degradation of DNA introduced into a cell
      of different host strain specificity.  The host specificities of E. coli strain
      K12 and E. coli strain B are different such that DNA from K12 may be degraded
      in B and vice versa.  In both strains mutants have been isolated which either
      have lost the ability to restrict but are still able to modify DNA, or have
      lost both the ability to restrict and to modify DNA.  The genetic location of
      both these mutations has been determined in E. coli K and E. coli B.  Both
      mutations map in the thr-leu region.  An F' factor from E. coli K12 carrying
      thr-leu and the genes determining host specificity has been used to examine the
      host-specificity properties of diploids.  Restriction was assayed simply by
      measuring the efficiency of plating of bacteriophage lambda grown on either E.
      coli K or E. coli B and designated lambda.K and lambda.B respectively.
      Modification was assayed again indirectly by growing phage lambda on the
      diploid strains and measuring its efficiency of plating on standard indicator
      strains.  The results obtained so far indicate that:  1) In strain K the
      wild-type alleles are dominant to both of the mutants described above.  2) The
      diploid K/K may plate lambda.B less efficiently than the haploid strain K.  3)
      The diploid K/B restricts both lambda.K and lambda.B.  4) The diploid K/B
      produces lambda particles which are able to plate on both strains K and B.  5)
      The diploid constructed between K and a mutant of B deficient in both
      restriction and modification is indistinguishable from the haploid K strain.
      6) The diploid constructed between K and a mutant of B deficient in restriction
      only, restricts both lambda.K and lambda.B and produces lambda particles which
      are able to plate on both strains K and B.  These results will be discussed in
      relation to the several models which have been proposed to explain the genetic
      basis of host-controlled modification of DNA.
AU  - Glover SW
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1968 53: i-ii.

PMID- 4894745
VI  - 13
DP  - 1969
TI  - Genetics of host-controlled restriction and modification in Eschericia coli.
PG  - 227-240
AB  - In recent years many aspects of the processes of restriction and modification
      which characterize the host controlled modification (CM) of bacteriophages in
      Escherica coli have been clarified (reviewed by Arber (1965a) and Klein
      (1965)).  In this paper we describe:  (i) the results of genetic experiments
      which locate the sites of these mutations close to the serB locus, (ii) the
      results of genetic crosses between different HCM mutants, and (iii) the results
      of experiments designed to elucidate the number of functional units involved in
      the control of HCM and the relationships between them.
AU  - Glover SW
AU  - Colson C
PT  - Journal Article
TA  - Genet. Res.
JT  - Genet. Res.
SO  - Genet. Res. 1969 13: 227-240.

PMID- 5326492
VI  - 7
DP  - 1966
TI  - Stable and unstable alterations of the host-induced modification properties of Escherichia coli B, K and C.
PG  - 223-234
AB  - The system of host-induced modification (HIM) in E. coli B, K and C (Arber &
      Dussoix, 1962) has the following properties.  Normal K, which is able to
      restrict phage lambda grown in either B or C and confers a K-specific
      modification to lambda-DNA synthesized in it, can be represented as K r+m+.
      Similarly, normal B can be represented as B r+m+, indicating that it restricts
      phage lambda grown in either K or C and that it confers a B-specific
      modification to lambda-DNA synthesized in it.  Strain C accepts phage lambda
      grown in K, B or C without restriction.  Recently the genes controlling
      restriction and modification have been mapped close to the marker threonine and
      on the opposite side of it to leucine (Colson, Glover, Symonds & Stacey, 1965).
      In the course of this work, strains were isolated which had HIM properties
      unlike those of B, K or C.  These strains display different patterns of HIM.
      One such pattern can be represented as B r-m+, indicating that the ability to
      restrict lambda grown in K or C has been lost while the ability to confer the
      B-specific modification is retained.  Another can be represented as K r-m- or B
      r-m-:  these strains have lost the ability to restrict lambda.C and to confer
      respectively either the K- or the B-specific modificatiton.  Others are more
      complex and comprise strains which on first isolation appear to bear HIM
      properties intermediate between those of B,K and C, but which on further
      analysis turn out to be unstable.  We shall describe the isolation of these
      strains and present some details of their behaviour.
AU  - Glover SW
AU  - Colson C
PT  - Journal Article
TA  - Genet. Res.
JT  - Genet. Res.
SO  - Genet. Res. 1966 7: 223-234.

PMID- Not included in PubMed...
VI  - 6
DP  - 1965
TI  - The breakdown of the restriction mechanism in zygotes of Escherichia coli.
PG  - 153-155
AB  - A few cells in a culture of E. coli K or E. coli B, usually about 1 in 10-4,
      permit the growth of the restricted phage lambda.C (Arber & Dussoix, 1962).
      Such cells may be genetically different from the majority of the cells in the
      culture or they may be temporarily in such a physiological condition that the
      restriction mechanism breaks down or cannot be expressed.  Mutants which are
      genetically unable to restrict the growth of phage normally restricted by
      wild-type cells have been isolated (Glover et al., 1963; Colson et al., 1964;
      Wood, 1964).  But several environmental factors are known which decrease the
      capacity of wild-type bacteria to restrict the growth of unmodified phage
      particles (Luria, 1953; Lederberg, 1957; Uetake et al., 2964).  We shall report
      here observations which suggest that E. coli zygotes are in a special
      physiological condition such that their ability to restrict phage is reduced by
      more than a factor of 100.
AU  - Glover SW
AU  - Colson C
PT  - Journal Article
TA  - Genet. Res.
JT  - Genet. Res.
SO  - Genet. Res. 1965 6: 153-155.

PMID- 
VI  - 0
DP  - 1982
TI  - Genetic control of DNA specificity.
PG  - 331-338
AB  - The plasmid R124 codes for a unique restriction and modification (RM) system and the
      derivative plasmid R124/3 codes for an RM system with a different DNA specificity.  Evidence
      has been obtained that the genes coding for each RM system are carried by both R124 and R124/3
      and that normally only one set of genes is expressed.  The mechanism that ensues that only one
      set of genes is expressed has been investigated in a series of experiments in which a plasmid
      expressing the genes for the R124 RM system and a plasmid expressing the genes for the R124/3
      can be transposed to F plasmids that are compatible with the R factors.  The results of these
      experiments indicate that a trans-acting regulatory mechanism coded for by a resident plasmid
      switches off the expression of RM genes on an introduced plasmid.  Evidence is also presented
      for an additional trans-acting regulatory mechanism which can switch on the expression of the
      alternative set of genes carried by the introduced plasmid.  The regulatory mechanism(s)
      controlling the switch in expression of R124 and R124/3 RM genes involves a physical
      rearrangement of DNA segments, and a possible model for this regulatory mechanism is
      discussed.
AU  - Glover SW
AU  - Firman K
PT  - Journal Article
TA  - Genetic Exchange
JT  - Genetic Exchange
SO  - Genetic Exchange 1982 0: 331-338.

PMID- Not included in PubMed...
VI  - 41
DP  - 1978
TI  - A novel class of restriction-deficient mutants.
PG  - 122-123
AB  - R124 is a unique R factor in compatability group F IV which confers tetracycline resistance
      (Tc) and carries the genes for a restriction-modification (R-M) system.  R124/3 is a
      derivative plasmid which determines a R-M system of different biological specificity to R124.
      During experiments designed to isolate restriction-deficient (r-) mutants of these R factors
      in which F-lac+.0 was transferred to R124 or R124/3 carrying bacteria virtually all of the
      colonies isolated were restriction-deficient.  Restriction-deficient mutants can be isolated
      just as readily following transfer of these R factors to F-lac+ carrying bacteria.  Many of
      the restriction-deficient mutants isolated are also modification-deficient and some
      unexpectedly express the modifications characteristic of both R124 and R124/3.  Evidence is
      presentd to indicate that the restriction-deficient phenotype of these R factors is not
      dependent on the continued presence of F-lac+ which lead to their isolation and that other
      F-prime factors can interact with R124 to produce r- mutants also at very high frequency.
      Many of these r- mutants show high "reversion" frequencies to r+ and evidence is presented to
      indicate that mutation to Tc sensitivity may also arise frequently following transfer to
      F-lac+ to R+ bacteria.  These results are discussed in relation to what is known about the DNA
      of the plasmid molecules from studies conducted by Dr. S.G. Hughes.
AU  - Glover SW
AU  - Firman K
PT  - Journal Article
TA  - Heredity
JT  - Heredity
SO  - Heredity 1978 41: 122-123.

PMID- 6343803
VI  - 190
DP  - 1983
TI  - The alternate expression of two restriction and modification systems.
PG  - 65-69
AB  - Plasmids R124 and R124/3 carry genes coding for two different R-M systems and
      normally only one set of genes is expressed.  These genes can be translocated
      to F plasmids that are compatible with the R factors and in strains carrying
      these F plasmids and an R factor a transacting regulatory mechanism switches
      off the expression of R-M genes on the introduced plasmid.  Additionally the
      unexpressed genes on the introduced plasmid are expressed.  The regulatory
      mechanism controlling the alternative expression of R124 and R124/3 R-M genes
      involves a physical rearrangement of DNA sequences.
AU  - Glover SW
AU  - Firman K
AU  - Watson G
AU  - Price C
AU  - Donaldson S
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1983 190: 65-69.

PMID- 4536917
VI  - 46
DP  - 1972
TI  - Host specificity of DNA in Haemophilus influenzae:  Restriction and modification in strain Rd.
PG  - 1610-1617
AB  - Wild type strains of Haemophilus influenzae Rd consist of two phenotypic
      classes of bacteria which differ in their abilities to restrict and modify
      phage HP1.  Each of these classes r- m- and r+ m+ is unstable and segregates
      several percent of bacteria of the alternative phenotype.  In addition stable
      r- m- bacteria occur spontaneously in r+ m+ cultures and an r- m+ mutant was
      isolated after mutagenesis of an r+ m+ strain.
AU  - Glover SW
AU  - Piekarowicz A
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1972 46: 1610-1617.

PMID- Not included in PubMed...
VI  - 4
DP  - 1963
TI  - The control of host-induced modification by phage P1.
PG  - 480-482
AB  - The phenomenon of host-induced modification has two facets, restriction and
      modification.  Recently these two processes have been clarified by Arber and
      Dussoix in the system where phage lambda multiplies either in Escherichia coli
      K12, or in K12 cells lysogenic for the phage P1.  The phage lambda.K is
      accepted only by 1 in 10-4 recipient K(P1) cells; these produce modified
      lambda.P1 phage particles, which then are able to infect either K or K(P1)
      cells with an efficiency of one.  In a beautiful series of experiments Arber
      and Dussoix showed that modification must be a process which acts directly on
      the DNA of phage lambda, and that where unmodified lambda-DNA enters K(P1)
      cells it is rapidly degraded into small molecular weight fragments.  These
      findings led Arber to the generalization that modification should affect all
      forms of DNA which are synthesized in K(P1) cells, and that restriction would
      apply to all DNA that can be transferred from K to K(P1).  He was able to
      demonstrate that restriction and modification did occur during the transfer of
      the bacterial genome in conjugation, and also during the transfer of DNA by
      transforming principle and by transduction (Arber & Dussoix, 1962, Dussoix &
      Arber, 1962; Arber, 1962).  In this note we shall first present some data
      extending Arber's observations to the transfer of a variety of episomes, and
      then show how these results can be utilized to demonstrate that the roles of
      restriction and modification imposed by P1 are under independent genetic
      control.
AU  - Glover SW
AU  - Schell J
AU  - Symonds N
AU  - Stacey KA
PT  - Journal Article
TA  - Genet. Res.
JT  - Genet. Res.
SO  - Genet. Res. 1963 4: 480-482.

PMID- 2679559
VI  - 164
DP  - 1989
TI  - Observation of arginyl-deoxyoligonucleotide interactions in TaqI endonuclease by detection of specific 1H NMR signals from 140 kD [Nn1, Nn2, 15N Arg]TaqI/oligomer complexes.
PG  - 88-93
AB  - Proton and nitrogen signals of the guanidinium amines in [Nn1, Nn2 15N Arg]TaqI
      endonuclease were observed using isotope filtered experiments and proton
      detected H{15N} heterocorrelated two dimensional NMR spectroscopy.  These
      rapidly exchanging protons could be detected in the free enzyme only at pH 4.5;
      at pH 8.5, no signals were measured after extensive signal averaging.  Addition
      of deoxyribonucleotide oligomers resulted in the appearance of two groups of
      signals at about 5.8 and 7.5 ppm.  Since these signals are independent of the
      presence of cognate sequence or Mg2+, it is assumed they represent nonspecific
      arginyl-DNA interactions.  This labeling/NMR approach provides a new method for
      investigating the role of arginine in protein-DNA interactions.
AU  - Glushka J
AU  - Barany F
AU  - Cowburn D
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1989 164: 88-93.

PMID- 26769922
VI  - 4
DP  - 2016
TI  - Genome Sequence of Listeria monocytogenes Strain F6540 (Sequence Type 360) Collected from Food Samples in Ontario, Canada.
PG  - e01507-15
AB  - Comparative genomic analysis between pathogenic and nonpathogenic Listeria monocytogenes
      strains provides a good model for studying the virulence of this
      organism. Here, we report the genome sequence of the nonpathogenic L.
      monocytogenes strain F6540 (sequence type 360) identified specifically in food
      samples in Ontario, Canada, in 2010.
AU  - Gnaneshan S
AU  - Hsueh YC
AU  - Liang L
AU  - Teatero S
AU  - Fittipaldi N
AU  - Mallo GV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01507-15.

PMID- 29301493
VI  - 19
DP  - 2018
TI  - Pacbio sequencing of copper-tolerant Xanthomonas citri reveals presence of a chimeric plasmid structure and provides insights into reassortment and shuffling of transcription activator-like effectors among X. citri strains.
PG  - 16
AB  - BACKGROUND: Xanthomonas citri, a causal agent of citrus canker, has been a
      well-studied model system due to recent availability of whole genome sequences of
      multiple strains from different geographical regions. Major limitations in our
      understanding of the evolution of pathogenicity factors in X. citri strains
      sequenced by short-read sequencing methods have been tracking plasmid reshuffling
      among strains due to inability to accurately assign reads to plasmids, and
      analyzing repeat regions among strains. X. citri harbors major pathogenicity
      determinants, including variable DNA-binding repeat region containing
      Transcription Activator-like Effectors (TALEs) on plasmids. The long-read
      sequencing method, PacBio, has allowed the ability to obtain complete and
      accurate sequences of TALEs in xanthomonads. We recently sequenced Xanthomonas
      citri str. Xc-03-1638-1-1, a copper tolerant A group strain isolated from
      grapefruit in 2003 from Argentina using PacBio RS II chemistry. We analyzed
      plasmid profiles, copy number and location of TALEs in complete genome sequences
      of X. citri strains. RESULTS: We utilized the power of long reads obtained by
      PacBio sequencing to enable assembly of a complete genome sequence of strain
      Xc-03-1638-1-1, including sequences of two plasmids, 249 kb (plasmid harboring
      copper resistance genes) and 99 kb (pathogenicity plasmid containing TALEs). The
      pathogenicity plasmid in this strain is a hybrid plasmid containing four TALEs.
      Due to the intriguing nature of this pathogenicity plasmid with Tn3-like
      transposon association, repetitive elements and multiple putative sites for
      origins of replication, we might expect alternative structures of this plasmid in
      nature, illustrating the strong adaptive potential of X. citri strains. Analysis
      of the pathogenicity plasmid among completely sequenced X. citri strains, coupled
      with Southern hybridization of the pathogenicity plasmids, revealed clues to
      rearrangements of plasmids and resulting reshuffling of TALEs among strains.
      CONCLUSIONS: We demonstrate in this study the importance of long-read sequencing
      for obtaining intact sequences of TALEs and plasmids, as well as for identifying
      rearrangement events including plasmid reshuffling. Rearrangement events, such as
      the hybrid plasmid in this case, could be a frequent phenomenon in the evolution
      of X. citri strains, although so far it is undetected due to the inability to
      obtain complete plasmid sequences with short-read sequencing methods.
AU  - Gochez AM
AU  - Huguet-Tapia JC
AU  - Minsavage GV
AU  - Shantaraj D
AU  - Jalan N
AU  - Strauss A
AU  - Lahaye T
AU  - Wang N
AU  - Canteros BI
AU  - Jones JB
AU  - Potnis N
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2018 19: 16.

PMID- 15259773
VI  - 49
DP  - 2004
TI  - Characterization of a complex restriction-modification system detected in Staphylococcus aureus and Streptococcus agalactiae strains isolated  from infections of domestic animals.
PG  - 307-314
AB  - Characterization of classic type II restriction-modification systems (RMS) (restriction
      endonucleases and modification methyltransferases)
      was carried out in isolates of Staphylococcus aureus and Streptococcus
      agalactiae obtained from clinical material. Among the 100 isolates of
      S. aureus two different RMS type II were detected. The first was
      expressed in isolates 32 and 33 (Sau32 I and Sau33 I); the targeting
      sequence was determined as 5'-GGN CC-3' (Sau96 I isoschizomer). The
      second was found in isolates no. 90, 93, 96*, and 98 (Sau90 I, Sau93 I,
      Sau96* I, Sau98 I) and enzymes recognized sequence 5'-CTY RAG-3' (SmlI
      isoschizomer). Analysis of 40 isolates of S. agalactiae revealed only
      one RMS; it was detected in two isolates (no. 16 and 23; Sag16 I and
      Sag23 I). Restriction endonuclease expressed by these isolates cleaved
      DNA in sequence 5'-CTG CA/G-3' (PstI isoschizomer). In RMS-positive S.
      aureus and S. agalactiae isolates plasmid DNA capable of replication in
      Escherichia coli and Bacillus subtilis was also detected and isolated.
AU  - Godany A
AU  - Bukovska G
AU  - Farkasovska J
AU  - Brnakova Z
AU  - Dmitriev A
AU  - Tkacikova L
AU  - Ayele T
AU  - Mikula I
PT  - Journal Article
TA  - Folia Microbiol. (Praha)
JT  - Folia Microbiol. (Praha)
SO  - Folia Microbiol. (Praha) 2004 49: 307-314.

PMID- 11702402
VI  - 46
DP  - 2001
TI  - Connection between foreign DNA replication and induced expression of the restriction-modification system in Streptomyces aureofaciens.
PG  - 193-196
AB  - Tetracycline-producing strains of Streptomyces aureofaciens expressed the SauLPI
      restriction-modification system, which recognized the specific DNA sequence 5-GCCGGC-3'
      (isoschizomer NaeI).  The activation of the second R-M system SauLPII (5'-GAGCTC-3',
      isoschizomer of XhoI), which was silent during the growth cycle, after a foreign DNA transfer
      into this strain was observed.  This phenomenon was tentatively explained as a response of the
      cells against the exogenous DNA entering the cells.  The involvement of a SOS-like response in
      induction of R-M system genes in S. aureofaciens strains has been considered.
AU  - Godany A
AU  - Farkasovska J
AU  - Bukovska G
AU  - Timko J
PT  - Journal Article
TA  - Folia Microbiol. (Praha)
JT  - Folia Microbiol. (Praha)
SO  - Folia Microbiol. (Praha) 2001 46: 193-196.

PMID- 9026438
VI  - 138
DP  - 1996
TI  - Characterization of an XhoI isoschizomer in Streptomyces aureofaciens after actinophage infection.
PG  - 123-127
AB  - After infection of tetracycline producing strains of S. aureofaciens with
      actinophages Mu1/6 and B1 some phage resistant colonies were obtained in each experiment.
      These colonies expressed a new restriction-modification (RM) system of type II, which  was
      different from the common RM system (SauLPI) of these strains recognizing the  sequence
      GCCGGC.  This new RM system was not detected before in parental strains.   The new
      endonuclease was purified from a phage resistant strain of S. aureofaciens B96,  using two
      step column chromatography to the grade without non specific nucleolytic  activity.  SauLPII
      endonuclease recognized and cleaved the palindromic hexanucleotide  sequence 5'-C/TCGAG-3',
      thus it was a true isoschizomer of XhoI.
AU  - Godany A
AU  - Pristas P
AU  - Oktavcova B
AU  - Farkosovska J
AU  - Ziffova M
AU  - Sevcikova B
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1996 138: 123-127.

PMID- 10570167
VI  - 96
DP  - 1999
TI  - Recurrent invasion and extinction of a selfish gene.
PG  - 13880-13885
AB  - Homing endonuclease genes show super-Mendelian inheritance, which allows them to spread in
      populations even when they are of no benefit to the host organism. To test the idea that
      regular horizontal transmission is necessary for the long-term persistence of these genes, we
      surveyed 20 species of yeasts for the omega-homing endonuclease gene and associated group I
      intron. The status of omega could be categorized into three states (functional, nonfunctional,
      or absent), and status was not clustered on the host phylogeny. Moreover, the phylogeny of
      omega differed significantly from that of the host, strong evidence of horizontal
      transmission. Further analyses indicate that horizontal transmission is more common than
      transposition, and that it occurs preferentially between closely related species. Parsimony
      analysis and coalescent theory suggest that there have been 15 horizontal transmission events
      in the ancestry of our yeast species, through simulations indicate that this value is probably
      an underestimate. Overall, the data support a cyclical model of invasion, degeneration, and
      loss, followed by reinvasion, and each of these transitions is estimated to occur about once
      every 2 million years. The data are thus consistent with the idea that frequent horizontal
      transmission is necessary for the long-term persistence of homing endonuclease genes, and
      further, that this requirement limits these genes to organisms with easily accessible germ
      lines. The data also show that mitochondrial DNA sequences are transferred intact between
      yeast species; if other genes do not show such high levels of horizontal transmission, it
      would be due to lack of selection, rather than lack of opportunity.
AU  - Goddard MR
AU  - Burt A
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1999 96: 13880-13885.

PMID- 21350155
VI  - 331
DP  - 2011
TI  - Molecular biology. Preference by exclusion.
PG  - 1017-1018
AB  - DNA methylation is a modification that controls gene expression and contributes to mammalian
      development, aging, and cancer cell biology.  In mice and humans, the addition of a methyl
      group to a cytosine within a cytosine-guanine dinucleotide is catalyzed by DNA
      methyltransferase enzymes DNMT3A, DNMT3B, or DNMT1.  The latter is the main "maintenance
      methylase" because it adds a methyl group primarily to double-strand DNA that is already
      methylated on one strand (hemimethylated).  How DNMT1 prefers hemimethylated over unmethylated
      DNA, in contrast to DNMT3A and DNMT3B, has not been clear.  On page 1036 of this issue, Song
      et al. present the crystal structures of human and mouse DNMT1 in complex with unmethylated
      DNA, providing an explanation for the mechanism of substrate selection by this crucial enzyme.
AU  - Godley LA
AU  - Mondragon A
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2011 331: 1017-1018.

PMID- 960577
VI  - 73
DP  - 1976
TI  - A catalogue of cleavages of PhiX174, S13, G4, and ST-1 DNA by 26 different restriction endonucleases.
PG  - 561-567
AB  - The number of cleavages produced in PhiX174, S12, G4, and ST-1 double-stranded
      RFI DNA by 26 different enzymes is given.  Some enzymes, but not all, produce
      similar-sized fragments from PhiX174 and S13 DNA, but all enzymes produce
      completely different-sized fragments from G4 and ST-1 compared with PhiX174.
      PhiX174 RFI is cleaved once to linear RFIII DNA by PstI, AvaI, and XhoI (BluI).
      S13 RFI is cleaved once by PstI, AvaI, and MboI; G4 RF is cleaved once by
      EcoRI, KpnI, PstI, and BglII; and ST-1 RFI DNA is cleaved once by KpnI and BglI
      and BglII.  The sites of these single cleavages have been mapped.  At least
      eight enzymes cleave single-stranded PhiX174 DNA as well as PhiX174
      double-stranded DNA.
AU  - Godson GN
AU  - Roberts RJ
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1976 73: 561-567.

PMID- 11175899
VI  - 8
DP  - 2001
TI  - Structure of the N6-adenine DNA methyltransferase M.TaqI in complex with DNA and a cofactor analog.
PG  - 121-125
AB  - The 2.0 angstrom crystal structure of the N6-adenine DNA methyltransferase M.TaqI in complex
      with specific DNA and a non-reactive cofactor analog reveals a previously unrecognized
      stabilization of the extrahelical target base.  To catalyze the transfer of the methyl group
      from the cofactor S-adenosyl-L-methionine to the 6-amino group of adenine within the
      double-stranded DNA sequence 5'-TCGA-3', the target nucleoside is rotated out of the DNA
      helix.  Stabilization of the extrahelical conformation is achieved by DNA compression
      perpendicular to the DNA helix axis at the target base pair position and relocation of the
      partner base thymine in an interstrand Pi-stacked position, where it would sterically overlap
      with an inner-helical target adenine.  The extrahelical target adenine is specifically
      recognized in the active site, and the 6-amino group of adenine donates two hydrogen bonds to
      Asn 105 and Pro 106, which both belong to the conserved catalytic motif IV of N6-adenine DNA
      methyltransferases.  These hydrogen bonds appear to increase the partial negative charge of
      the N6 atom of adenine and activate it for direct nucleophilic attack on the methyl group of
      the cofactor.
AU  - Goedecke K
AU  - Pignot M
AU  - Goody RS
AU  - Scheidig AJ
AU  - Weinhold E
PT  - Journal Article
TA  - Nat. Struct. Biol.
JT  - Nat. Struct. Biol.
SO  - Nat. Struct. Biol. 2001 8: 121-125.

PMID- 30533891
VI  - 7
DP  - 2018
TI  - Draft Genome Sequence of the Psychrotolerant Bacterium Kurthia sibirica ATCC 49154(T).
PG  - e00841-18
AB  - The aerobic, Gram-positive, psychrotolerant bacterium Kurthia sibirica was first  isolated
      from the stomach and intestinal contents of the Magadan mammoth
      recovered from the permafrost in eastern Siberia in 1977. K. sibirica was
      sequenced, and the predicted genome size is 3,496,665 bp, with 36.42% G+C
      content.
AU  - Goen AE
AU  - Silverwood T
AU  - Underriner A
AU  - Trachtenberg AM
AU  - Kelley C
AU  - MacLea KS
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e00841-18.

PMID- 365688
VI  - 3
DP  - 1978
TI  - SstI: A restriction endonuclease from Streptomyces sp. stanford.
PG  - 347-352
AB  - A strain of Streptomyces has been isolated which is a convenient source of a
      new restriction endonuclease.  The enzyme has been prepared from extracts of
      these cells and its cleavage sites localized on phage lambda DNA.  The enzyme,
      termed SstI, produces cohesive ends and should be useful for molecular cloning
      experiments.
AU  - Goff SP
AU  - Rambach A
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1978 3: 347-352.

PMID- 12419742
VI  - 13
DP  - 2002
TI  - DNA methyltransferase inhibitors-state of the art.
PG  - 1699-1716
AB  - Background: DNA methylation is the addition of a methyl group to the 5 position of cytosine.
      It is an epigenetic process with several effects, including chromatin structure modulation,
      transcriptional repression and the suppression of transposable elements.  In malignancy,
      methylation patterns change, resulting in global hypomethylation with regional
      hypermethylation.  This can lead to genetic instability and the repression of tumor suppressor
      genes.
      Design: A review of the DNA methyltransferase inhibitor literature was conducted.
      Results: DNA methylation inhibitors have demonstrated the ability to inhibit hypermethylation,
      restore suppressor gene expression and exert antitumor effects in in vitro and in vivo
      laboratory models.  Four inhibitors, which are analogs of the nucleoside deoxycytidine, have
      been clinically tested: 5-azacytidine, 5-aza-2'-deoxycytidine, 1-beta-D-arabinofuranosyl-5
      -azacytosine and dihydro-5-azacytidine.  The first two have demonstrated encouraging
      antileukemic activity but little activity in solid tumors, while the latter two are no longer
      under study due to lack of efficacy.  A fifth agent, MG98, is an antisense
      oligodeoxynucleotide directed against the 3' untranslated region of the DNA
      methyltransferase-1 enzyme mRNA, and is now under phase II study.
      Conclusions: While some positive clinical results with DNA methyltransferase inhibitors have
      been seen, a definitive clinical role for these agents will most likely require combination
      therapy, and good phase III studies are needed.
AU  - Goffin J
AU  - Eisenhauer E
PT  - Journal Article
TA  - Ann. Oncol.
JT  - Ann. Oncol.
SO  - Ann. Oncol. 2002 13: 1699-1716.

PMID- 28572319
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Escherichia coli BLR(DE3), a recA-Deficient Derivative of E. coli BL21(DE3).
PG  - e00441-17
AB  - Escherichia coli BLR(DE3) is a commercially available recA-deficient derivative of BL21(DE3),
      one of the most widely used strains for recombinant protein
      expression. Here, we present the full-genome sequence of BLR(DE3) and highlight
      additional differences with its parent strain BL21(DE3) which were previously
      unreported but may affect its physiology.
AU  - Goffin P
AU  - Dehottay P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00441-17.

PMID- 30240834
VI  - 66
DP  - 2018
TI  - Genome-wide analysis of Borrelia turcica and 'Candidatus Borrelia tachyglossi' shows relapsing fever-like genomes with unique genomic links to Lyme disease Borrelia.
PG  - 72-81
AB  - Borrelia are tick-borne bacteria that in humans are the aetiological agents of
      Lyme disease and relapsing fever. Here we present the first genomes of B. turcica
      and B. tachyglossi, members of a recently described and rapidly expanding
      Borrelia clade associated with reptile (B. turcica) or echidna (B. tachyglossi)
      hosts, transmitted by hard ticks, and of unknown pathogenicity. Borrelia
      tachyglossi and B. turcica genomes are similar to those of relapsing fever
      Borrelia species, containing a linear ~ 900kb chromosome, a single long (> 70kb)
      linear plasmid, and numerous short (< 40kb) linear and circular plasmids, as well
      as a suite of housekeeping and macronutrient biosynthesis genes which are not
      found in Lyme disease Borrelia. Additionally, both B. tachyglossi and B. turcica
      contain paralogous vsp and vlp proteins homologous to those used in the
      multiphasic antigen-switching system used by relapsing fever Borrelia to evade
      vertebrate immune responses, although their number was greatly reduced compared
      to human-infectious species. However, B. tachyglossi and B. turcica chromosomes
      also contain numerous genes orthologous to Lyme disease Borrelia-specific genes,
      demonstrating a unique evolutionary, and potentially phenotypic link between
      these groups. Borrelia tachyglossi and B. turcica genomes also have unique
      genetic features, including degraded and deleted tRNA modification genes, and an
      expanded range of macronutrient salvage and biosynthesis genes compared to
      relapsing fever and Lyme disease Borrelia. These genomes and genomic comparisons
      provide an insight into the biology and evolutionary origin of these Borrelia,
      and provide a valuable resource for future work.
AU  - Gofton AW
AU  - Margos G
AU  - Fingerle V
AU  - Hepner S
AU  - Loh SM
AU  - Ryan U
AU  - Irwin P
AU  - Oskam CL
PT  - Journal Article
TA  - Infect. Genet. Evol.
JT  - Infect. Genet. Evol.
SO  - Infect. Genet. Evol. 2018 66: 72-81.

PMID- 17101053
VI  - 6
DP  - 2006
TI  - Inteins, introns, and homing endonucleases: recent revelations about the life cycle of parasitic genetic elements.
PG  - 94
AB  - Self splicing introns and inteins that rely on a homing endonuclease for propagation are
      parasitic genetic elements. Their life-cycle and
      evolutionary fate has been described through the homing cycle.
      According to this model the homing endonuclease is selected for
      function only during the spreading phase of the parasite. This phase
      ends when the parasitic element is fixed in the population. Upon
      fixation the homing endonuclease is no longer under selection, and its
      activity is lost through random processes. Recent analyses of these
      parasitic elements with functional homing endonucleases suggest that
      this model in its most simple form is not always applicable.
      Apparently, functioning homing endonuclease can persist over long
      evolutionary times in populations and species that are thought to be
      asexual or nearly asexual. Here we review these recent findings and
      discuss their implications. Reasons for the long-term persistence of a
      functional homing endonuclease include: More recombination (sexual and
      as a result of gene transfer) than previously assumed for these
      organisms; complex population structures that prevent the element from
      being fixed; a balance between active spreading of the homing
      endonuclease and a decrease in fitness caused by the parasite in the
      host organism; or a function of the homing endonuclease that increases
      the fitness of the host organism and results in purifying selection for
      the homing endonuclease activity, even after fixation in a local
      population. In the future, more detailed studies of the population
      dynamics of the activity and regulation of homing endonucleases are
      needed to decide between these possibilities, and to determine their
      relative contributions to the long term survival of parasitic genes
      within a population. Two outstanding publications on the amoeba
      Naegleria group I intron (Wikmark et al. BMC Evol Biol 2006, 6: 39) and
      the PRP8 inteins in ascomycetes (Butler et al. BMC Evol Biol 2006, 6:
      42) provide important stepping stones towards integrated studies on how
      these parasitic elements evolve through time together with, or despite,
      their hosts.
AU  - Gogarten JP
AU  - Hilario E
PT  - Journal Article
TA  - BMC Evol. Biol.
JT  - BMC Evol. Biol.
SO  - BMC Evol. Biol. 2006 6: 94.

PMID- 12142479
VI  - 56
DP  - 2002
TI  - Inteins: Structure, function, and evolution.
PG  - 263-287
AB  - Inteins are genetic elements that disrupt the coding sequence of genes. However, in contrast
      to introns, inteins are transcribed and translated
      together with their host protein. Inteins appear most frequently in
      Archaea, but they are found in organisms belonging to all three domains of
      life and in viral and phage proteins. Most inteins consist of two domains:
      One is involved in autocatalytic splicing, and the other is an
      endonuclease that is important in the spread of inteins. This review
      focuses on the evolution and technical application of inteins and only
      briefly summarizes recent advances in the study of the catalytic
      activities and structures of inteins. In particular, this review considers
      inteins as selfish or parasitic genetic elements, a point of view that
      explains many otherwise puzzling aspects of inteins.
AU  - Gogarten JP
AU  - Senejani AG
AU  - Zhaxybayeva O
AU  - Olendzenski L
AU  - Hilario E
PT  - Journal Article
TA  - Annu. Rev. Microbiol.
JT  - Annu. Rev. Microbiol.
SO  - Annu. Rev. Microbiol. 2002 56: 263-287.

PMID- 1310149
VI  - 12
DP  - 1992
TI  - Connections between RNA splicing and DNA intron mobility in yeast mitochondria: RNA maturase and DNA endonuclease switching experiments.
PG  - 696-705
AB  - The intron-encoded proteins bI4 RNA maturase and aI4 DNA endonuclease can
      be faithfully expressed in yeast cytoplasm from engineered forms of their
      mitochondrial coding sequences. In this work we studied the relationships
      between these two activities associated with two homologous intron-encoded
      proteins: the bI4 RNA maturase encoded in the fourth intron of the
      cytochrome b gene and the aI4 DNA endonuclease (I-SceII) encoded in the
      fourth intron of the gene coding for the subunit I of cytochrome oxidase.
      Taking advantage of both the high recombinogenic properties of yeast and
      the similarities between the two genes, we constructed in vivo a family of
      hybrid genes carrying parts of both RNA maturase and DNA endonuclease
      coding sequences. The presence of a sequence coding for a mitochondrial
      targeting peptide upstream from these hybrid genes allowed us to study the
      properties of their translation products within the mitochondria in vivo.
      We thus could analyze the ability of the recombinant proteins to
      complement RNA maturase deficiencies in different strains. Many
      combinations of the two parental intronic sequences were found in the
      recombinants. Their structural and functional analysis revealed the
      following features. (i) The N-terminal half of the bI4 RNA maturase could
      be replaced in total by its equivalent from the aI4 DNA endonuclease
      without affecting the RNA maturase activity. In contrast, replacing the
      C-terminal half of the bI4 RNA maturase with its equivalent from the aI4
      DNA endonuclease led to a very weak RNA maturase activity, indicating that
      this region is more differentiated and linked to the maturase activity.
      (ii) None of the hybrid proteins carrying an RNA maturase activity kept
      the DNA endonuclease activity, suggesting that the latter requires the
      integrity of the aI4 protein. These observations are interesting because
      the aI4 DNA endonuclease is known to promote the propagation, at the DNA
      level, of the aI4 intron, whereas the bI4 RNA maturase, which is required
      for the splicing of its coding intron, also controls the splicing process
      of the aI4 intron. We propose a scenario for the evolution of these
      intronic proteins that relies on a switch from DNA endonuclease to RNA
      maturase activity.
AU  - Goguel V
AU  - Delahodde A
AU  - Jacq C
PT  - Journal Article
TA  - Mol. Cell. Biol.
JT  - Mol. Cell. Biol.
SO  - Mol. Cell. Biol. 1992 12: 696-705.

PMID- 25999554
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Jeotgalibacillus soli DSM 23228, a Bacterium Isolated from Alkaline Sandy Soil.
PG  - e00512-15
AB  - Jeotgalibacillus soli, a bacterium capable of degrading N-acyl homoserine lactone, was
      isolated from a soil sample in Portugal. J. soli constitutes the
      only Jeotgalibacillus species isolated from a non-marine source. Here, the draft
      genome, several interesting glycosyl hydrolases, and its putative N-acyl
      homoserine lactonases are presented.
AU  - Goh KM
AU  - Chan KG
AU  - Yaakop AS
AU  - Chan CS
AU  - Ee R
AU  - Tan WS
AU  - Gan HM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00512-15.

PMID- 17322187
VI  - 153
DP  - 2007
TI  - The complete genome sequence of Clostridium difficile phage {phi}C2 and comparisons to {phi}CD119 and inducible prophages of CD630.
PG  - 676-685
AB  - The complete genomic sequence of a previously characterized temperate
      phage of Clostridium difficile, C2, is reported. The genome is 56 538 bp
      and organized into 84 putative ORFs in six functional modules. The head
      and tail structural proteins showed similarities to that of C. difficile
      phage CD119 and Streptococcus pneumoniae phage EJ-1, respectively.
      Homologues of structural and replication proteins were found in prophages
      1 and 2 of the sequenced C. difficile CD630 genome. A putative holin
      appears unique to the C. difficile phages and was functional when
      expressed in Escherichia coli. Nucleotide sequence comparisons of C2 to
      CD119 and the CD630 prophage sequences showed relatedness between C2 and
      the prophages, but less so to CD119. C2 integrated into a gene encoding a
      putative transcriptional regulator of the gntR family. C2, CD119 and CD630
      prophage 1 genomes had a Cdu1-attP-integrase arrangement, suggesting that
      the pathogenicity locus (PaLoc) of C. difficile, flanked by cdu1, has
      phage origins. The attP sequences of C2, CD119 and CD630 prophages were
      dissimilar. C2-related sequences were found in 84 % of 37 clinical C.
      difficile isolates and typed reference strains.
AU  - Goh S
AU  - Ong PF
AU  - Song KP
AU  - Riley TV
AU  - Chang BJ
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2007 153: 676-685.

PMID- 9089393
VI  - 121
DP  - 1997
TI  - Effects of 2'-substituents of the first deoxyguanosine residue in the recognition sequence on EcoRI restriction endonuclease activity.
PG  - 219-224
AB  - The effects of 2'-substituents of the first deoxyguanosine on EcoRI activity were examined
      using synthetic octadeoxynucleotides d(GG*AATTCC) containing 2'-substituted derivatives (G*),
      i.e., 2'-fluoro-2'-deoxyguanosine (dGfl), 2'-chloro-2'-deoxyguanosine (dGcl), and
      guanosine (rG).  The overall structures of the octamers were very similar, as shown by CD and
      UV measurements, although their EcoRI reactivities were very different: 100% in 60 min for
      d(GGAATTCC) and d(GGflAATTCC), 5% in 24h for d[G(rG)AATTCC], and no cleavage at all in 24h for
      d(GGclAATTCC).  However, the kinetics showed the octamers exhibit similar binding-affinity to
      the enzyme (10^6-10^7 M).  31P-NMR analysis suggested the modified octamers change the
      phosphate backbone conformation in a duplex, since an unusual downfield-shifted signal in the
      spectra was commonly observed for the modified octamers at low temperature (i.e., a single
      strand state), which was shifted upfield at high temperature (i.e., a single strand state).
      The order of the differences was dGcl>rG>dGfl-containing octamers, coinciding with that of the
      vdW volume of 2'-substituents (Cl>OH>F) and the cleavage reactivities.  These findings
      suggest the steric hindrance by the 2'-substituents causes a conformational change of the
      phosphate backbone close to the scissile bond, and then interferes with the EcoRI reaction.
AU  - Gohda K
AU  - Matsuo N
AU  - Oda Y
AU  - Ikehara M
AU  - Uesugi S
PT  - Journal Article
TA  - J. Biochem. (Tokyo)
JT  - J. Biochem. (Tokyo)
SO  - J. Biochem. (Tokyo) 1997 121: 219-224.

PMID- 27284151
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Two Heat-Resistant Mutant Strains (A52 and B41) of the  Photosynthetic Hydrogen-Producing Bacterium Rhodobacter capsulatus.
PG  - e00531-16
AB  - The draft genome sequences of two heat-resistant mutant strains, A52 and B41, derived from
      Rhodobacter capsulatus DSM 1710, and with different hydrogen
      production levels, are reported here. These sequences may help understand the
      molecular basis of heat resistance and hydrogen production in R. capsulatus.
AU  - Gokce A
AU  - Cakar ZP
AU  - Yucel M
AU  - Ozcan O
AU  - Sencan S
AU  - Sertdemir I
AU  - Erguner B
AU  - Yuceturk B
AU  - Sarac A
AU  - Yuksel B
AU  - Ozturk Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00531-16.

PMID- 21886866
VI  - 4
DP  - 2011
TI  - Complete genome sequence of the acetate-degrading sulfate reducer Desulfobacca acetoxidans type strain (ASRB2).
PG  - 393-401
AB  - Desulfobacca acetoxidans Elferink et al. 1999 is the type species of the genus Desulfobacca,
      which belongs to the family Syntrophaceae in the class
      Deltaproteobacteria. The species was first observed in a study on the competition
      of sulfate-reducers and acetoclastic methanogens for acetate in sludge. D.
      acetoxidans is considered to be the most abundant acetate-degrading sulfate
      reducer in sludge. It is of interest due to its isolated phylogenetic location in
      the 16S rRNA-based tree of life. This is the second completed genome sequence of
      a member of the family Syntrophaceae to be published and only the third genome
      sequence from a member of the order Syntrophobacterales. The 3,282,536 bp long
      genome with its 2,969 protein-coding and 54 RNA genes is a part of the Genomic
      Encyclopedia of Bacteria and Archaea project.
AU  - Goker M et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 4: 393-401.

PMID- 22675590
VI  - 5
DP  - 2011
TI  - Complete genome sequence of the termophilic sulfur-reducer Desulfurobacterium thermolithotrophum type strain (BSA) from a deep-sea hydrothermal vent.
PG  - 407-415
AB  - Desulfurobacterium thermolithotrophum L'Haridon et al. 1998 is the type species of the ge-nus
      Desulfurobacterium which belongs to the family Desulfurobacteriaceae. The species is of
      interest because it represents the first thermophilic bacterium that can act as a primary
      pro-ducer in the temperature range of 45-75oC (optimum 70oC) and is incapable of growing
      un-der microaerophilic conditions. Strain BSAT preferentially synthesizes high-melting-point
      fatty acids (C18 and C20) which is hypothesized to be a strategy to ensure the functionality
      of the membrane at high growth temperatures. This is the second completed genome sequence of a
      member of the family Desulfurobacteriaceae and the first sequence from the genus
      Desulfurobacterium. The 1,541,968 bp long genome harbors 1,543 protein-coding and 51 RNA genes
      and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Goker M et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 5: 407-415.

PMID- 22768366
VI  - 6
DP  - 2012
TI  - Genome sequence of the moderately thermophilic, amino-acid-degrading and sulfur-reducing bacterium Thermovirga lienii type strain (Cas60314(T)).
PG  - 230-239
AB  - Thermovirga lienii Dahle and Birkeland 2006 is a member of the genus Thermovirga  in the
      genomically moderately well characterized phylum 'Synergistetes'. Members
      of this relatively recently proposed phylum 'Synergistetes' are of interest
      because of their isolated phylogenetic position and their diverse habitats, e.g.
      from humans to oil wells. The genome of T. lienii Cas60314(T) is the fifth genome
      sequence (third completed) from this phylum to be published. Here we describe the
      features of this organism, together with the complete genome sequence and
      annotation. The 1,999,646 bp long genome (including one plasmid) with its 1,914
      protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria
      and Archaea project.
AU  - Goker M et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 6: 230-239.

PMID- 25197486
VI  - 9
DP  - 2014
TI  - Genome sequence of the Thermotoga thermarum type strain (LA3(T)) from an African  solfataric spring.
PG  - 1105-1117
AB  - Thermotoga thermarum Windberger et al. 1989 is a member to the genomically well characterized
      genus Thermotoga in the phylum 'Thermotogae'. T. thermarum is of
      interest for its origin from a continental solfataric spring vs. predominantly
      marine oil reservoirs of other members of the genus. The genome of strain LA3T
      also provides fresh data for the phylogenomic positioning of the
      (hyper-)thermophilic bacteria. T. thermarum strain LA3(T) is the fourth sequenced
      genome of a type strain from the genus Thermotoga, and the sixth in the family
      Thermotogaceae to be formally described in a publication. Phylogenetic analyses
      do not reveal significant discrepancies between the current classification of the
      group, 16S rRNA gene data and whole-genome sequences. Nevertheless, T. thermarum
      significantly differs from other Thermotoga species regarding its iron-sulfur
      cluster synthesis, as it contains only a minimal set of the necessary proteins.
      Here we describe the features of this organism, together with the complete genome
      sequence and annotation. The 2,039,943 bp long chromosome with its 2,015
      protein-coding and 51 RNA genes is a part of the Genomic Encyclopedia of Bacteria
      and Archaea project.
AU  - Goker M et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 1105-1117.

PMID- 25197484
VI  - 9
DP  - 2014
TI  - Genome sequence of the mud-dwelling archaeon Methanoplanus limicola type strain (DSM 2279(T)), reclassification of Methanoplanus petrolearius as Methanolacinia  petrolearia and emended descriptions of the genera Methanoplanus and  Methanolacinia.
PG  - 1076-1088
AB  - Methanoplanus limicola Wildgruber et al. 1984 is a mesophilic methanogen that was isolated
      from a swamp composed of drilling waste near Naples, Italy, shortly
      after the Archaea were recognized as a separate domain of life. Methanoplanus is
      the type genus in the family Methanoplanaceae, a taxon that felt into disuse
      since modern 16S rRNA gene sequences-based taxonomy was established.
      Methanoplanus is now placed within the Methanomicrobiaceae, a family that is so
      far poorly characterized at the genome level. The only other type strain of the
      genus with a sequenced genome, Methanoplanus petrolearius SEBR 4847(T), turned
      out to be misclassified and required reclassification to Methanolacinia. Both,
      Methanoplanus and Methanolacinia, needed taxonomic emendations due to a
      significant deviation of the G+C content of their genomes from previously
      published (pre-genome-sequence era) values. Until now genome sequences were
      published for only four of the 33 species with validly published names in the
      Methanomicrobiaceae. Here we describe the features of M. limicola, together with
      the improved-high-quality draft genome sequence and annotation of the type
      strain, M3(T). The 3,200,946 bp long chromosome (permanent draft sequence) with
      its 3,064 protein-coding and 65 RNA genes is a part of the G enomic E ncyclopedia
      of B acteria and Archaea project.
AU  - Goker M et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 1076-1088.

PMID- 21304693
VI  - 3
DP  - 2010
TI  - Complete genome sequence of Ignisphaera aggregans type strain (AQ1.S1).
PG  - 66-75
AB  - Ignisphaera aggregans Niederberger et al. 2006 is the type and sole species of genus
      Ignisphaera. This archaeal species is characterized by a coccoid-shape and
      is strictly anaerobic, moderately acidophilic, heterotrophic hyperthermophilic
      and fermentative. The type strain AQ1.S1(T) was isolated from a near neutral,
      boiling spring in Kuirau Park, Rotorua, New Zealand. This is the first completed
      genome sequence of the genus Ignisphaera and the fifth genome (fourth type
      strain) sequence in the family Desulfurococcaceae. The 1,875,953 bp long genome
      with its 2,009 protein-coding and 52 RNA genes is a part of the Genomic
      Encyclopedia of Bacteria and Archaea project.
AU  - Goker M et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 3: 66-75.

PMID- 21304694
VI  - 3
DP  - 2010
TI  - Complete genome sequence of Olsenella uli type strain (VPI D76D-27C).
PG  - 76-84
AB  - Olsenella uli (Olsen et al. 1991) Dewhirst et al. 2001 is the type species of the genus
      Olsenella, which belongs to the actinobacterial family Coriobacteriaceae.
      The species is of interest because it is frequently isolated from dental plaque
      in periodontitis patients and can cause primary endodontic infection. The species
      is a Gram-positive, non-motile and non-sporulating bacterium. The strain
      described in this study was isolated from human gingival crevices. This is the
      first completed sequence of the genus Olsenella and the fifth sequence from a
      member of the family Coriobacteriaceae. The 2,051,896 bp long genome with its
      1,795 protein-coding and 55 RNA genes is a part of the Genomic Encyclopedia of
      Bacteria and Archaea project.
AU  - Goker M et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 3: 76-84.

PMID- 21475588
VI  - 4
DP  - 2011
TI  - Complete genome sequence of Isosphaera pallida type strain (IS1B).
PG  - 63-71
AB  - Isosphaera pallida (ex Woronichin 1927) Giovannoni et al. 1995 is the type species of the
      genus Isosphaera. The species is of interest because it was the
      first heterotrophic bacterium known to be phototactic, and it occupies an
      isolated phylogenetic position within the Planctomycetaceae. Here we describe the
      features of this organism, together with the complete genome sequence and
      annotation. This is the first complete genome sequence of a member of the genus
      Isosphaera and the third of a member of the family Planctomycetaceae. The
      5,472,964 bp long chromosome and the 56,340 bp long plasmid with a total of 3,763
      protein-coding and 60 RNA genes are part of the Genomic Encyclopedia of Bacteria
      and Archaea project.
AU  - Goker M et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 4: 63-71.

PMID- 21677857
VI  - 4
DP  - 2011
TI  - Complete genome sequence of Odoribacter splanchnicus type strain (1651/6).
PG  - 200-209
AB  - Odoribacter splanchnicus (Werner et al. 1975) Hardham et al. 2008 is the type species of the
      genus Odoribacter, which belongs to the family Porphyromonadaceae
      in the order 'Bacteroidales'. The species is of interest because members of the
      Odoribacter form an isolated cluster within the Porphyromonadaceae. This is the
      first completed genome sequence of a member of the genus Odoribacter and the
      fourth sequence from the family Porphyromonadaceae. The 4,392,288 bp long genome
      with its 3,672 protein-coding and 74 RNA genes and is a part of the Genomic
      Encyclopedia of Bacteria and Archaea project.
AU  - Goker M et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 4: 200-209.

PMID- 25792047
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of a Highly Virulent Strain of the Plant Pathogen Dickeya solani, IFB0099.
PG  - e00109-15
AB  - Dickeya solani is an important bacterial pathogen of potato cultivars in Europe.  Here, we
      present the draft genome of D. solani strain IFB0099 isolated from
      potato in Poland that shows a high level of pectinolytic activity and a high
      virulence. This genome sequence is 5,094,121 bp and contains 4,365 protein-coding
      sequences.
AU  - Golanowska M
AU  - Galardini M
AU  - Bazzicalupo M
AU  - Hugouvieux-Cotte-Pattat N
AU  - Mengoni A
AU  - Potrykus M
AU  - Slawiak M
AU  - Lojkowska E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00109-15.

PMID- 14206593
VI  - 52
DP  - 1964
TI  - The enzymatic methylation of RNA and DNA, VIII.  Effects of bacteriophage  infection on the activity of the methylating enzymes.
PG  - 292-297
AB  - We, as well as others, have previously reported on the presence in Escherichia coli of several
      enzymes which catalyze the transfer of methyl groups from S-adenosylmethionine to sRNA,
      ribosomal RNA, and DNA.  Although the biological function of the methylated bases which these
      enzymes produce is still obscure, the species and strain specificity of the methylation
      reactions suggest that they provide a basis for a recognition mechanism.  The virulent
      bacteriophage-host cell system is an example of a phenomenon involving recognition by the host
      of a foreign nucleic acid; in some instances, phage DNA is rapidly synthesized while the host
      DNA is rapidly degraded.  If methylated bases are involved in controlling such a recognition
      mechanism, then a study of the methylated base content of DNA's of various bacteriophages
      grown in different hosts might provide a clue as to the biological function of the methylating
      enzymes.  In order to establish a suitable system for further investigation, we have studied
      the effects of phage infection on the activities of the various methylating enzymes in the
      host cell.  This communication summarizes such studies.  It has been found that while the RNA
      methylases are apparently unchanged, DNA methylation activity increases markedly after
      infection with T2.  In contrast, T3 infection induces an enzyme which cleaves
      S-adenosylmethionine to thiomethyladenosine and homoserine.
AU  - Gold M
AU  - Hausmann R
AU  - Maitra U
AU  - Hurwitz J
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1964 52: 292-297.

PMID- 14257620
VI  - 239
DP  - 1964
TI  - The enzymatic methylation of ribonucleic acid and deoxyribonucleic acid. V. Purification and properties of the deoxyribonucleic acid-methylating activity of Escherichia coli.
PG  - 3858-3865
AB  - The classical investigations of Wyatt, and Dunn and Smith, established the existence of
      5-methylcytosine and 6-methylaminopurine as constituents of  the deoxyribonucleic acid of
      higher plants and animals, and of bacteria and bacterial viruses, respectively.  Until
      recently, the biochemical pathways for the  incorporation of these "trace bases" into
      deoxyribonucleic acid was unknown although it had been shown that the deoxyribonucleoside
      triphosphate of 5-methylcytosine could quantitatively replace deoxycytidine triphosphate as a
      substrate for the enzyme deoxyribonucleic acid polymerase.  The discovery that the
      glucosylation of A of the T-even bacteriophages and methylation of soluble ribonucleic acid
      occurred at the polynucleotide level suggested that the incorporation of methyl groups might
      also take place after polymerization in the biosynthesis of DNA.  In previous communications
      from this laboratory, the presence of an enzyme activity of Escherichia coli which catalyzes
      the transfer of methyl groups to cytosine and adenine moieties of a variety of DNAs has been
      reported.  This reaction can be presented by the following equation.  DNA +
      S-adenosylmethionine  + DNA methylase  gives methyl-DNA (containing 5-methylcytosine and
      6-methylaminopurine) + S-adenosylhomocysteine.  In this report the purification and properties
      of this enzyme activity are described.
AU  - Gold M
AU  - Hurwitz J
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1964 239: 3858-3865.

PMID- 16578536
VI  - 50
DP  - 1963
TI  - THE ENZYMATIC METHYLATION OF RNA AND DNA, II. ON THE SPECIES SPECIFICITY OF THE METHYLATION ENZYMES.
PG  - 164-169
AB  - There is evidence that methylated bases in DNA and sRNA are not randomly distributed in
      polynucleotide chains.  In wheat germ DNA, the two 6-aminopyrimidines, cytosine and
      5-methylcytosine, do not appear to substitute randomly for each other, as determined by
      chemical analysis of oligonucleotides.  This specificity appears to be related to the direct
      methylation of deoxycytidylate of DNA at the polynucleotide level, as has also been found to
      apply to the origin of the base, 6-methylaminopurine.  These observations are in keeping with
      the incorporation studies of Bessman et al. with the DNA polymerase system.  This enzyme
      readily catalyzes the incorporation of dCMP and 5-methyl dCMP into DNA without distinguishing
      between these deoxynucleotides, and therefore does not appear responsible for localization of
      methylated bases.  In RNA, the methylated bases are uniquely localized to soluble RNA as
      indicated by a large body of information.  Here, RNA polymerase, the enzyme which appears to
      synthesize all RNA species from a DNA template of normal cells, lacks specificity in
      differentiating between methylated bases and normal bases.  Thus, for example, ribothymidylate
      is readily incorporated into RNA in place of uridylate with the same nearest neighbor
      frequency.  However, the distribution of methylated bases of sRNA is not random, and analyses
      of purified sRNA molecules, specific for particular amino acids, indicate that they contain
      varied amounts as well as different methylated bases.  As in the case of DNA, this specific
      distribution of methylated bases has been explained by the observation that methylation occurs
      at the polynucleotide level rather than the mononucleotide stage.  While with DNA it appears
      that methylation is catalyzed by a single enzyme, in the case of sRNA many enzymes are
      involved.  To date, 5 different enzymes catalyzing specific methylation reactions with sRNA
      have been isolated.
AU  - Gold M
AU  - Hurwitz J
AU  - Anders M
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1963 50: 164-169.

PMID- 13948644
VI  - 11
DP  - 1963
TI  - The enzymatic methylation of RNA and DNA.
PG  - 107-114
AB  - The methionine origin of the methyl group of the "trace bases" of Escherichia coli and ascites
      cells has been demonstrated by Borek et al. and Biswas et al.  Fleissner and Borek have
      recently reported that extracts of E. coli catalyse the transfer of the methyl group from
      C14-methyl-labeled methionine to E. coli soluble RNA provided this S-RNA was isolated from a
      methionine auxotroph which continues to synthesize RNA when deprived of its essential amino
      acid.  Although the DNA dependent RNA polymerase system incorporated ribothymidylate from
      ribothymidine triphosphate into RNA specifically in place of uridylate, no demonstrable
      phosphorylation of ribothymidylate was detected in extracts of E. coli.  These observations,
      and especially the report of Fleissner and Borek, suggest that the trace nucleotide
      ribothymidylate, is synthesized at the polynucleotide level.
AU  - Gold M
AU  - Hurwitz J
AU  - Anders M
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1963 11: 107-114.

PMID- 25359909
VI  - 2
DP  - 2014
TI  - Whole-Genome Shotgun Sequence of Bacillus mojavensis Strain RRC101, an Endophytic Bacterium Antagonistic to the Mycotoxigenic Endophytic Fungus Fusarium  verticillioides.
PG  - e01090-14
AB  - Here, we report the whole-genome shotgun sequence of Bacillus mojavensis strain RRC101,
      isolated from a maize kernel. This strain is antagonistic to the
      mycotoxigenic plant pathogen Fusarium verticillioides and grows within maize
      tissue, suggesting potential as an endophytic biocontrol agent.
AU  - Gold SE
AU  - Blacutt AA
AU  - Meinersmann RJ
AU  - Bacon CW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01090-14.

PMID- 25452498
VI  - 34
DP  - 2015
TI  - BREX is a novel phage resistance system widespread in microbial genomes.
PG  - 169-183
AB  - The perpetual arms race between bacteria and phage has resulted in the evolution  of efficient
      resistance systems that protect bacteria from phage infection. Such
      systems, which include the CRISPR-Cas and restriction-modification systems, have
      proven to be invaluable in the biotechnology and dairy industries. Here, we
      report on a six-gene cassette in Bacillus cereus which, when integrated into the
      Bacillus subtilis genome, confers resistance to a broad range of phages,
      including both virulent and temperate ones. This cassette includes a putative
      Lon-like protease, an alkaline phosphatase domain protein, a putative RNA-binding
      protein, a DNA methylase, an ATPase-domain protein, and a protein of unknown
      function. We denote this novel defense system BREX (Bacteriophage Exclusion) and
      show that it allows phage adsorption but blocks phage DNA replication.
      Furthermore, our results suggest that methylation on non-palindromic TAGGAG
      motifs in the bacterial genome guides self/non-self discrimination and is
      essential for the defensive function of the BREX system. However, unlike
      restriction-modification systems, phage DNA does not appear to be cleaved or
      degraded by BREX, suggesting a novel mechanism of defense. Pan genomic analysis
      revealed that BREX and BREX-like systems, including the distantly related Pgl
      system described in Streptomyces coelicolor, are widely distributed in ~10% of
      all sequenced microbial genomes and can be divided into six coherent subtypes in
      which the gene composition and order is conserved. Finally, we detected a phage
      family that evades the BREX defense, implying that anti-BREX mechanisms may have
      evolved in some phages as part of their arms race with bacteria.
AU  - Goldfarb T
AU  - Sberro H
AU  - Weinstock E
AU  - Cohen O
AU  - Doron S
AU  - Charpak-Amikam Y
AU  - Afik S
AU  - Ofir G
AU  - Sorek R
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 2015 34: 169-183.

PMID- 23144384
VI  - 194
DP  - 2012
TI  - Whole-Genome Sequence of Livestock-Associated ST398 Methicillin-Resistant Staphylococcus aureus Isolated from Humans in Canada.
PG  - 6627-6628
AB  - Despite reports of high colonization rates of ST398 livestock-associated methicillin-resistant
      Staphylococcus aureus (LA-MRSA) among pigs and pig farmers,
      the incidence of LA-MRSA infection in the general population in Canada appears to
      be rare in comparison to that in some European countries. In this study, the
      complete genome sequence of a Canadian representative LA-MRSA isolate (08BA02176)
      from a human postoperative surgical site infection was acquired and compared to
      the sequenced genome of an LA-MRSA isolate (S0385) from Europe to identify
      genetic traits that may explain differences in the success of these particular
      strains in some locales.
AU  - Golding GR
AU  - Bryden L
AU  - Levett PN
AU  - McDonald RR
AU  - Wong A
AU  - Graham MR
AU  - Tyler S
AU  - Van Domselaar G
AU  - Mabon P
AU  - Kent H
AU  - Butaye P
AU  - Smith TC
AU  - Kadlec K
AU  - Schwarz S
AU  - Weese SJ
AU  - Mulvey MR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6627-6628.

PMID- 12971987
VI  - 3
DP  - 2003
TI  - Analysis of DNA (cytosine 5) methyltransferase mRNA sequence and expression in bovine preimplantation embryos, fetal and adult tissues.
PG  - 551-558
AB  - Mammalian preimplantation development is a critical stage for establishment of the genomic
      methylation pattern and proper function of
      the enzymes responsible for this appear essential for normal development.
      To date, the vast majority of work concerning the developmental expression
      of the DNA cytosine 5-methyltansferases (Dnmts) has been conducted in
      mice. Here we report the sequence and expression of the Dnmt family during
      bovine preimplantation and fetal development. Bovine Dnmt mRNAs display
      strong sequence homology to those of human and mouse and similar to other
      species, exist as multiple isoforms. Two of these splice variants, which
      have been termed Dnmt2gamma and Dnmt3a4, represent previously unreported
      sequence combinations. Work presented here demonstrates early bovine
      embryos express mRNA coding for the somatic form of Dnmt1 and that this
      transcript fractionates with the ribosome. Unlike the murine model, mRNA
      encoding the de novo methyltransferases, Dnmt3a and 3b are present during
      preimplantation development and can also be found in the ribosomal
      subcellular fraction. Further, results of Real Time PCR analysis indicate
      significant differences in Dnmt mRNA expression levels exist among
      different tissue types as well as between fetal and adult stages.
      Recently, it has been postulated that the cause of abnormal methylation
      observed in cloned embryos may be due in part to misexpression of the
      Dnmt1o isoform during preimplantation development. Work presented here
      raises new and significant hypotheses that must be considered both
      regarding the cadre of DNA methyltranferases that direct epigenetic
      programming during normal development and regarding the implication of
      abnormal DNMT expression in cloned embryos.
AU  - Golding MC
AU  - Westhusin ME
PT  - Journal Article
TA  - Gene Expr. Patterns
JT  - Gene Expr. Patterns
SO  - Gene Expr. Patterns 2003 3: 551-558.

PMID- 24762932
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Trueperella pyogenes, Isolated from the Infected Uterus  of a Postpartum Cow with Metritis.
PG  - e00194-14
AB  - Trueperella pyogenes is a common commensal bacterium and an opportunistic pathogen associated
      with chronic purulent disease, particularly in ruminants. We report here the genome sequence
      of a T. pyogenes isolate from a severe case of bovine metritis. This is the first full record
      of a T. pyogenes genome.
AU  - Goldstone RJ
AU  - Amos M
AU  - Talbot R
AU  - Schuberth HJ
AU  - Sandra O
AU  - Sheldon IM
AU  - Smith DG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00194-14.

PMID- 24994791
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Escherichia coli MS499, Isolated from the Infected Uterus of a Postpartum Cow with Metritis.
PG  - e00217-14
AB  - Specific Escherichia coli strains associated with bovine postpartum uterine infection have
      recently been described. Many recognized virulence factors are
      absent in these strains; therefore, to define a prototypic strain, we report here
      the genome sequence of E. coli isolate MS499 from a cow with the postpartum
      disease metritis.
AU  - Goldstone RJ
AU  - Talbot R
AU  - Schuberth HJ
AU  - Sandra O
AU  - Sheldon IM
AU  - Smith DG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00217-14.

PMID- 25035329
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Respiratory and Urinary Tract Isolates of Acinetobacter baumannii from the Same Patient.
PG  - e00692-14
AB  - Acinetobacter baumannii is a frequent hospital-acquired human pathogen. This report describes
      the draft genome sequences of two distinct A. baumannii clinical
      isolates from the same patient. A comparison of the genomes revealed differences
      in antibiotic resistance and will enable the determination of genomic differences
      responsible for virulence at each body site.
AU  - Golemboski D
AU  - Eardly BD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00692-14.

PMID- 11875980
VI  - 28
DP  - 2002
TI  - M.BstF5I-4, the fourth DNA-methyltransferase of the BstF5I restriction-modification system from Bacillus stearothermophilus F5.
PG  - 84-86
AB  - The fourth DNA-methyltransferase of the BstF5I restriction-modification (RM) system from
      Bacillus stearothermophilus F5 (M.BstF5I-4) was discovered, which modifies the adenine residue
      within the upper strand of the recognition site 5'-GGATG-3'/5'-CATCC-3'. Thus, unlike
      other known RM systems, the BstF5I RM system comprises four genes encoding
      DNA-methyltransferases, three of which possess the same substrate specificity and methylate
      adenine within the 5'-GGATG sequence.
AU  - Golikova LN
AU  - Gutorov VV
AU  - Evdokimov AA
AU  - Shchelkunov SN
AU  - Gonchar DA
AU  - Okhapkina SS
AU  - Degtyarev SK
AU  - Netesova NA
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 2002 28: 84-86.

PMID- 10867922
VI  - 34
DP  - 2000
TI  - Multiplicity of site-specific DNA-methyltransferases of the BstF5I restriction modification system from Bacillus stearothermophilus F5.
PG  - 443-447
AB  - A fragment located downstream of the genes for DNA methyltransferases of Bacillus
      stearothermophilus F5 (M.BstF5I-I and M.BstF5I-2) was
      sequenced. The fragment contains a gene for another methylase,
      M.BstF5I-3, structurally and functionally similar to the N-terminal
      domain of M.FokI. Thus, in contrast to other restriction-modification
      systems, the BstF5I system includes three methylases, two being
      homologous to the individual M.FokI domains.
AU  - Golikova LN
AU  - Netosova NA
AU  - Gutorov VV
AU  - Belavin PA
AU  - Abdurashitov MA
AU  - Gonchar DA
AU  - Degtyarev SK
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2000 34: 443-447.

PMID- 15952895
VI  - 74
DP  - 2005
TI  - Eukaryotic cytosine methyltransferases.
PG  - 481-514
AB  - Large-genome eukaryotes use heritable cytosine methylation to silence promoters, especially
      those associated with transposons and imprinted
      genes. Cytosine methylation does not reinforce or replace ancestral
      gene regulation pathways but instead endows methylated genomes with the
      ability to repress specific promoters in a manner that is buffered
      against changes in the internal and external environment. Recent
      studies have shown that the targeting of de novo methylation depends on
      multiple inputs; these include the interaction of repeated sequences,
      local states of histone lysine methylation, small RNAs and components
      of the RNAi pathway, and divergent and catalytically inert cytosine
      methyltransferase homologues that have acquired regulatory roles. There
      are multiple families of DNA (cytosine-5) methyltransferases in
      eukaryotes, and each family appears to be controlled by different
      regulatory inputs. Sequence-specific DNA-binding proteins, which
      regulate most aspects of gene expression, do not appear to be involved
      in the establishment or maintenance of genomic methylation patterns.
AU  - Goll MG
AU  - Bestor TH
PT  - Journal Article
TA  - Annu. Rev. Biochem.
JT  - Annu. Rev. Biochem.
SO  - Annu. Rev. Biochem. 2005 74: 481-514.

PMID- 25838470
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Lactobacillus plantarum Strain B21, a Bacteriocin-Producing Strain Isolated from Vietnamese Fermented Sausage Nem Chua.
PG  - e00055-15
AB  - Lactobacillus plantarum strain B21 was isolated from Vietnamese sausage (nem chua) and
      demonstrated broad antimicrobial activity due to the production of
      bacteriocins. Here, we report the complete genome sequence of this strain
      (3,284,260 bp).
AU  - Golneshin A
AU  - Adetutu E
AU  - Ball AS
AU  - May BK
AU  - Van TT
AU  - Smith AT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00055-15.

PMID- 29025928
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Lactobacillus plantarum Strain A6, a Strong Acid Producer Isolated from a Vietnamese Fermented Sausage (Nem Chua).
PG  - e00987-17
AB  - Lactobacillus plantarum strain A6, a strong acid producer, was isolated from a Vietnamese
      fermented sausage (nem chua). Here, we report the genome sequence of
      this strain (3,368,579 bp).
AU  - Golneshin A
AU  - Gor MC
AU  - Van TTH
AU  - May B
AU  - Moore RJ
AU  - Smith AT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00987-17.

PMID- 16358732
VI  - 39
DP  - 2005
TI  - Determination and analysis of the primary structure of NM.BstSEI operon from Bacillus stearothermophilus SE-589 which produces N.BstSEI site-specific nickase.
PG  - 960-964
AB  - Nucleotide sequence of Bacillus stearothermophilus SE-589 DNA fragment which includes an
      operon for site-specific NM-system with a gene for BstSEI nickase has been determined.
      Analysis of the regions adjacent to nickase gene has revealed two genes encoding DNA
      methyltransferases, which belong to different classes. Three genes which form system operon
      are separated with short open reading frames (ORFs). Analysis of these ORFs has shown that
      they encode polypeptides which are homologous to different parts of BstSEI nickase, NatB
      protein and arginase. A difference in GC-content of the beginning and ending regions of the
      cloned DNA fragment as well as presence of short ORFs similar to genes for known proteins may
      indicate that NM.BstSEI system operon has evolved by horizonthal DNA transfer.
AU  - Gololobova NS
AU  - Okhapkina SS
AU  - Abdurashitov MA
AU  - Degtyarev SK
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2005 39: 960-964.

PMID- 29348330
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Escherichia coli Bacteriophage PGT2.
PG  - e01370-17
AB  - Bacteriophage PGT2 was isolated from horse feces by using an uncharacterized Escherichia coli
      strain, 7s, isolated from the same sample as the host.
      Bacteriophage PGT2 and a related phage, phiKT, which was previously isolated from
      the same source, are likely to represent a new genus within the Autographivirinae
      subfamily of the Podoviridae family of viruses.
AU  - Golomidova AK
AU  - Kulikov EE
AU  - Kudryavtseva AV
AU  - Letarov AV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01370-17.

PMID- 19729506
VI  - 37
DP  - 2009
TI  - Structural mechanisms for the 5'-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII.
PG  - 6613-6624
AB  - EcoRII restriction endonuclease is specific for the 5'-CCWGG sequence (W stands for A or T);
      however, it shows no activity on a single recognition site. To activate cleavage it requires
      binding of an additional target site as an allosteric effector. EcoRII dimer consists of three
      structural units: a central catalytic core, made from two copies of the C-terminal domain
      (EcoRII-C), and two N-terminal effector DNA binding domains (EcoRII-N). Here, we report
      DNA-bound EcoRII-N and EcoRII-C structures, which show that EcoRII combines two radically
      different structural mechanisms to interact with the effector and substrate DNA. The catalytic
      EcoRII-C dimer flips out the central T:A base pair and makes symmetric interactions with the
      CC:GG half-sites. The EcoRII-N effector domain monomer binds to the target site asymmetrically
      in a single defined orientation which is determined by specific hydrogen bonding and van der
      Waals interactions with the central T:A pair in the major groove. The EcoRII-N mode of the
      target site recognition is shared by the large class of higher plant transcription factors of
      the B3 superfamily.
AU  - Golovenko D
AU  - Manakova E
AU  - Tamulaitiene G
AU  - Grazulis S
AU  - Siksnys V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: 6613-6624.

PMID- 24423868
VI  - 42
DP  - 2014
TI  - Structural insight into the specificity of the B3 DNA-binding domains provided by the co-crystal structure of the C-terminal fragment of BfiI restriction enzyme.
PG  - 4113-4122
AB  - The B3 DNA-binding domains (DBDs) of plant transcription factors (TF) and DBDs of EcoRII and
      BfiI restriction endonucleases (EcoRII-N and BfiI-C) share a common
      structural fold, classified as the DNA-binding pseudobarrel. The B3 DBDs in the
      plant TFs recognize a diverse set of target sequences. The only available
      co-crystal structure of the B3-like DBD is that of EcoRII-N (recognition sequence
      5'-CCTGG-3'). In order to understand the structural and molecular mechanisms of
      specificity of B3 DBDs, we have solved the crystal structure of BfiI-C
      (recognition sequence 5'-ACTGGG-3') complexed with 12-bp cognate oligoduplex.
      Structural comparison of BfiI-C-DNA and EcoRII-N-DNA complexes reveals a
      conserved DNA-binding mode and a conserved pattern of interactions with the
      phosphodiester backbone. The determinants of the target specificity are located
      in the loops that emanate from the conserved structural core. The BfiI-C-DNA
      structure presented here expands a range of templates for modeling of the
      DNA-bound complexes of the B3 family of plant TFs.
AU  - Golovenko D
AU  - Manakova E
AU  - Zakrys L
AU  - Zaremba M
AU  - Sasnauskas G
AU  - Grazulis S
AU  - Siksnys V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2014 42: 4113-4122.

PMID- 19429552
VI  - 75
DP  - 2009
TI  - Community genomic and proteomic analyses of chemoautotrophic iron-oxidizing 'Leptospirillum rubarum' (Group II) and 'Leptospirillum ferrodiazotrophum' (Group III) bacteria in acid mine drainage biofilms.
PG  - 4599-4615
AB  - We analyzed near-complete population (composite) genomic sequences for
      coexisting acidophilic iron-oxidizing Leptospirillum group II and III
      bacteria (phylum Nitrospirae) and an extrachromosomal plasmid from a
      Richmond Mine, Iron Mountain, CA, acid mine drainage biofilm. Community
      proteomic analysis of the genomically characterized sample and two other
      biofilms identified 64.6% and 44.9% of the predicted proteins of
      Leptospirillum groups II and III, respectively, and 20% of the predicted
      plasmid proteins. The bacteria share 92% 16S rRNA gene sequence identity
      and >60% of their genes, including integrated plasmid-like regions. The
      extrachromosomal plasmid carries conjugation genes with detectable
      sequence similarity to genes in the integrated conjugative plasmid, but
      only those on the extrachromosomal element were identified by proteomics.
      Both bacterial groups have genes for community-essential functions,
      including carbon fixation and biosynthesis of vitamins, fatty acids, and
      biopolymers (including cellulose); proteomic analyses reveal these
      activities. Both Leptospirillum types have multiple pathways for osmotic
      protection. Although both are motile, signal transduction and
      methyl-accepting chemotaxis proteins are more abundant in Leptospirillum
      group III, consistent with its distribution in gradients within biofilms.
      Interestingly, Leptospirillum group II uses a methyl-dependent and
      Leptospirillum group III a methyl-independent response pathway. Although
      only Leptospirillum group III can fix nitrogen, these proteins were not
      identified by proteomics. The abundances of core proteins are similar in
      all communities, but the abundance levels of unique and shared proteins of
      unknown function vary. Some proteins unique to one organism were highly
      expressed and may be key to the functional and ecological differentiation
      of Leptospirillum groups II and III.
AU  - Goltsman DS
AU  - Denef VJ
AU  - Singer SW
AU  - VerBerkmoes NC
AU  - Lefsrud M
AU  - Mueller RS
AU  - Dick GJ
AU  - Sun CL
AU  - Wheeler KE
AU  - Zemla A
AU  - Baker BJ
AU  - Hauser L
AU  - Land M
AU  - Shah MB
AU  - Thelen MP
AU  - Hettich RL
AU  - Banfield JF
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2009 75: 4599-4615.

PMID- 15385458
VI  - 72
DP  - 2004
TI  - Structural organization of the pFra virulence-associated plasmid of rhamnose-positive Yersinia pestis.
PG  - 5613-5621
AB  - The 137,036-bp plasmid pG8786 from rhamnose-positive Yersinia pestis G8786
      isolated from the high mountainous Caucasian plague focus in Georgia is an
      enlarged form of the pFra virulence-associated plasmid containing genes
      for synthesis of the antigen fraction 1 and phospholipase D. In addition
      to the completely conserved genes of the pFra backbone, pG8786 contains
      two large regions consisting of 4,642 and 32,617 bp, designated regions 1
      and 2, respectively. Region 1 retains a larger part of Salmonella enterica
      serovar Typhi plasmid pHCM2 resembling the backbone of pFra replicons,
      while region 2 contains 25 open reading frames with high levels of
      similarity to the transfer genes of the F-like plasmids. Surprisingly,
      region 1 is also present in the pFra plasmid of avirulent Y. pestis strain
      91001 isolated in Inner Mongolia, People's Republic of China. Despite the
      fact that some genes typically involved in conjugative transfer of the
      F-like replicons are missing in pG8786, we cannot exclude the possibility
      that pG8786 might be transmissive under certain conditions. pG8786 seems
      to be an ancient form of the pFra group of plasmids that were conserved
      due to the strict geographical isolation of rhamnose-positive Y. pestis
      strains in the high mountainous Caucasian plague locus.
AU  - Golubov A
AU  - Neubauer H
AU  - Nolting C
AU  - Heesemann J
AU  - Rakin A
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2004 72: 5613-5621.

PMID- 23599290
VI  - 1
DP  - 2013
TI  - Genome Sequence of Thalassolituus oleivorans MIL-1 (DSM 14913T).
PG  - e00141-13
AB  - Thalassolituus oleivorans is one of the most prevalent marine gammaproteobacteria in microbial
      communities, emerging after oil spills in coastal, estuarine, and
      surface seawaters. Here, we present the assembled genome of strain T. oleivorans
      MIL-1 (DSM 14913(T)), which is 3,920,328 bp with a G+C content of 46.6%.
AU  - Golyshin PN
AU  - Werner J
AU  - Chernikova TN
AU  - Tran H
AU  - Ferrer M
AU  - Yakimov MM
AU  - Teeling H
AU  - Golyshina OV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00141-13.

PMID- 28680072
VI  - 8
DP  - 2017
TI  - 'ARMAN' archaea depend on association with euryarchaeal host in culture and in situ.
PG  - 60
AB  - Intriguing, yet uncultured 'ARMAN'-like archaea are metabolically dependent on other members
      of the microbial community. It remains uncertain though which hosts
      they rely upon, and, because of the lack of complete genomes, to what extent.
      Here, we report the co-culturing of ARMAN-2-related organism, Mia14, with
      Cuniculiplasma divulgatum PM4 during the isolation of this strain from acidic
      streamer in Parys Mountain (Isle of Anglesey, UK). Mia14 is highly enriched in
      the binary culture (ca. 10% genomic reads) and its ungapped 0.95 Mbp genome
      points at severe voids in central metabolic pathways, indicating dependence on
      the host, C. divulgatum PM4. Analysis of C. divulgatum isolates from different
      sites and shotgun sequence data of Parys Mountain samples suggests an extensive
      genetic exchange between Mia14 and hosts in situ. Within the subset of organisms
      with high-quality genomic assemblies representing the 'DPANN' superphylum, the
      Mia14 lineage has had the largest gene flux, with dozens of genes gained that are
      implicated in the host interaction.In the absence of complete genomes, the
      metabolic capabilities of uncultured ARMAN-like archaea have been uncertain.
      Here, Golyshina et al. apply an enrichment culture technique and find that the
      ungapped genome of the ARMAN-like archaeon Mia14 has lost key metabolic pathways,
      suggesting dependence on the host archaeon Cuniculiplasma divulgatum.
AU  - Golyshina OV
AU  - Toshchakov SV
AU  - Makarova KS
AU  - Gavrilov SN
AU  - Korzhenkov AA
AU  - La Cono V
AU  - Arcadi E
AU  - Nechitaylo TY
AU  - Ferrer M
AU  - Kublanov IV
AU  - Wolf YI
AU  - Yakimov MM
AU  - Golyshin PN
PT  - Journal Article
TA  - Nat. Commun.
JT  - Nat. Commun.
SO  - Nat. Commun. 2017 8: 60.

PMID- 21914899
VI  - 193
DP  - 2011
TI  - Genome Sequence of Mycobacterium bovis BCG Moreau, the Brazilian Vaccine Strain against Tuberculosis.
PG  - 5600-5601
AB  - Mycobacterium bovis bacillus Calmette-Guerin (BCG) is the only vaccine available against
      tuberculosis, and the strains used worldwide represent a
      family of daughter strains with distinct genotypic characteristics. Here
      we report the complete genome sequence of M. bovis BCG Moreau, the strain
      in continuous use in Brazil for vaccine production since the 1920s.
AU  - Gomes LH
AU  - Otto TD
AU  - Vasconcellos EA
AU  - Ferrao PM
AU  - Maia RM
AU  - Moreira AS
AU  - Ferreira MA
AU  - Castello-Branco LR
AU  - Degrave WM
AU  - Mendonca-Lima L
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5600-5601.

PMID- 26430044
VI  - 3
DP  - 2015
TI  - Genome Comparison of an Ancestral Isolate and a Modern Isolate of Mycobacterium tuberculosis of the Beijing Lineage from Sao Paulo, Brazil.
PG  - e01129-15
AB  - Mycobacterium tuberculosis of the Bejing subtype (MtbB) is transmitted efficiently in high
      burden countries for this genotype. A higher virulence was associated with isolates of the
      'modern' Beijing genotype sub-lineages when compared to 'ancient' ones. Here, we report
      the full genomes of the strain representing these two genotypes from Brazil, a country with a
      low incidence of MtbB.
AU  - Gomes LL
AU  - Marin MA
AU  - Lasunskaia E
AU  - Vasconcellos SE
AU  - Araujo ME
AU  - de Miranda AB
AU  - Suffys PN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01129-15.

PMID- 29903814
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Two Sporothrix schenckii Clinical Isolates Associated with Human Sporotrichosis in Colombia.
PG  - e00495-18
AB  - Sporothrix schenckii is a thermodimorphic fungal pathogen with a high genetic diversity. In
      this work, we present the assembly and similarity analysis of the
      whole-genome sequences of two clinical isolates from Colombia of S.
      schenckiisensu stricto.
AU  - Gomez OM
AU  - Alvarez LC
AU  - Munoz JF
AU  - Misas E
AU  - Gallo JE
AU  - Jimenez MDP
AU  - Arango M
AU  - McEwen JG
AU  - Hernandez O
AU  - Clay OK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00495-18.

PMID- 9130589
VI  - 1351
DP  - 1997
TI  - Isolation and nucleotide sequence of the gene encoding the XamI DNA methyltransferase of Xanthomonas campestris pv. amaranthicola.
PG  - 261-266
AB  - The gene (xamIM) encoding the DNA methyltransferase of the XamI restriction-modification
      system from Xanthomonas campestris pv. amaranthicola (M.XamI) has been cloned in Escherichia
      coli and its nucleotide sequence determined.  The sequence predicts a protein of 527 amino
      acids that contains nine conserved motifs characteristic of DNA amino methyltransferases.  In
      fact, M.XamI shows significant similarity with N6-adenine methyltransferases of the gamma
      group of amino methyltransferases, including M.SalI (from the isoschizomeric SalI
      restriction-modification system) and M.TaqI (the only N6-adenine methyltransferase for which a
      three-dimensional structure is available).  M.XamI and M.SalI share two highly conserved
      regions within the C-terminal domain, one of which aligns with one of the DNA recognition
      loops proposed for M.TaqI.  Analysis of the chromosomal DNA adjacent to xamIM led to the
      identification of an additional ORF (275 codons), downstream, in the same transcriptional
      orientation. Although some limited similarities between the SalI restriction enzyme and the
      product deduced from this ORF were found, the clone carrying xamIM did not express the
      expected endonuclease function.
AU  - Gomez P
AU  - Ribas-Aparicio RM
AU  - Pelaez AI
AU  - Gomez A
AU  - Rodicio MR
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1997 1351: 261-266.

PMID- 10398747
VI  - 172
DP  - 1999
TI  - Characterization of IS1389, a new member of the IS3 family of insertion sequences isolated from Xanthomonas campestris pv. amaranthicola.
PG  - 15-21
AB  - IS1389, a new insertion sequence belonging to the IS3 family, has been identified in
      Xanthomonas campestris pv. amaranthicola. The genome of this bacterium contains at least 11
      copies of the element, whereas no hybridizing sequences were detected in other Xanthomonas
      species [X. axonopodis, X. fragaridae, X. phaseoli, and X. (Stenotrophomonas) maltophila]. Two
      nearly identical copies of the element (IS1389-A and IS1389-B) were characterized. According
      to analysis of sequence alignments and similar structural features, IS1389 belongs to the
      IS407 subgroup of the IS3 family, which duplicates 4 bp of target DNA upon insertion. IS1389-A
      was found in the proximity of the modification gene of the XamI restriction-modification
      system.
AU  - Gomez P
AU  - Ribas-Aparicio RM
AU  - Pelaez AI
AU  - Rodicio MR
PT  - Journal Article
TA  - Arch. Microbiol.
JT  - Arch. Microbiol.
SO  - Arch. Microbiol. 1999 172: 15-21.

PMID- 27034493
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Two Sphingopyxis sp. Strains, Dominant Members of the Bacterial Community Associated with a Drinking Water Distribution System  Simulator.
PG  - e00183-16
AB  - We report the draft genomes of twoSphingopyxissp. strains isolated from a chloraminated
      drinking water distribution system simulator. Both strains are
      ubiquitous residents and early colonizers of water distribution systems. Genomic
      annotation identified a class 1 integron (intI1) gene associated with sulfonamide
      (sul1) and puromycin (pac) antibiotic resistance genes.
AU  - Gomez-Alvarez V
AU  - Pfaller S
AU  - Revetta RP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00183-16.

PMID- 26798093
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequences of Four Strains Closely Related to Members of the Mycobacterium chelonae Group, Isolated from Biofilms in a Drinking Water  Distribution System Simulator.
PG  - e01539-15
AB  - We report here the draft genome sequences of four Mycobacterium chelonae strains  from
      biofilms subjected to a 'chlorine burn' in a chloraminated drinking water
      distribution system simulator. These opportunistic pathogens have been detected
      in hospital and municipal water distribution systems, in which biofilms have been
      recognized as an important factor for their persistence.
AU  - Gomez-Alvarez V
AU  - Revetta RP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01539-15.

PMID- 26744376
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Six Mycobacterium immunogenum Strains Obtained from a Chloraminated Drinking Water Distribution System Simulator.
PG  - e01538-15
AB  - We report here the draft genome sequences of six Mycobacterium immunogenum strains isolated
      from a chloraminated drinking water distribution system
      simulator subjected to changes in operational parameters. M. immunogenum, a
      rapidly growing mycobacterium previously reported to be the cause of
      hypersensitivity pneumonitis from contaminated metalworking fluid aerosols, is
      becoming a public health concern.
AU  - Gomez-Alvarez V
AU  - Revetta RP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01538-15.

PMID- 20436956
VI  - 8
DP  - 2010
TI  - Proteorhodopsin phototrophy promotes survival of marine bacteria during starvation.
PG  - E1000358
AB  - Proteorhodopsins are globally abundant photoproteins found in bacteria in the
      photic zone of the ocean. Although their function as proton pumps with
      energy-yielding potential has been demonstrated, the ecological role of
      proteorhodopsins remains largely unexplored. Here, we report the presence and
      function of proteorhodopsin in a member of the widespread genus Vibrio, uncovered
      through whole-genome analysis. Phylogenetic analysis suggests that the Vibrio
      strain AND4 obtained proteorhodopsin through lateral gene transfer, which could
      have modified the ecology of this marine bacterium. We demonstrate an increased
      long-term survival of AND4 when starved in seawater exposed to light rather than
      held in darkness. Furthermore, mutational analysis provides the first direct
      evidence, to our knowledge, linking the proteorhodopsin gene and its biological
      function in marine bacteria. Thus, proteorhodopsin phototrophy confers a fitness
      advantage to marine bacteria, representing a novel mechanism for bacterioplankton
      to endure frequent periods of resource deprivation at the ocean's surface.
AU  - Gomez-Consarnau L
AU  - Akram N
AU  - Lindell K
AU  - Pedersen A
AU  - Neutze R
AU  - Milton DL
AU  - Gonzalez JM
AU  - Pinhassi J
PT  - Journal Article
TA  - PLoS Biology
JT  - PLoS Biology
SO  - PLoS Biology 2010 8: E1000358.

PMID- 17215843
VI  - 445
DP  - 2007
TI  - Light stimulates growth of proteorhodopsin-containing marine Flavobacteria.
PG  - 210-213
AB  - Proteorhodopsins are bacterial light-dependent proton pumps. Their discovery
      within genomic material from uncultivated marine bacterioplankton caused
      considerable excitement because it indicated a potential phototrophic function
      within these organisms, which had previously been considered strictly
      chemotrophic. Subsequent studies established that sequences encoding
      proteorhodopsin are broadly distributed throughout the world's oceans.
      Nevertheless, the role of proteorhodopsins in native marine bacteria is still
      unknown. Here we show, from an analysis of the complete genomes of three marine
      Flavobacteria, that cultivated bacteria in the phylum Bacteroidetes, one of the
      principal components of marine bacterioplankton, contain proteorhodopsin.
      Moreover, growth experiments in both natural and artificial seawater (low in
      labile organic matter, which is typical of the world's oceans) establish that
      exposure to light results in a marked increase in the cell yield of one such
      bacterium (Dokdonia sp. strain MED134) when compared with cells grown in
      darkness. Thus, our results show that the phototrophy conferred by
      proteorhodopsin can provide critical amounts of energy, not only for respiration
      and maintenance but also for active growth of marine bacterioplankton in their
      natural environment.
AU  - Gomez-Consarnau L
AU  - Gonzalez JM
AU  - Coll-Llado M
AU  - Gourdon P
AU  - Pascher T
AU  - Neutze R
AU  - Pedros-Alio C
AU  - Pinhassi J
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2007 445: 210-213.

PMID- 387741
VI  - 140
DP  - 1979
TI  - Deoxyribonucleic Acid Adenine and Cytosine Methylation in Salmonella typhimurium  and Salmonella typhi.
PG  - 574-579
AB  - The methylations of adenine in the sequence - GATC - and of the second cytosine in  the
      sequence - [Formula: see text] - were studied in Salmonella typhimurium and
      in Salmonella typhi. The study was carried out by using endonucleases which
      restrict the plasmid pBR322 by cleavage at the sequences - GATC - (DpnI and MboI)
      and - [Formula: see text] - (EcoRII). The restriction patterns obtained for this
      plasmid isolated from transformed S. typhimurium and S. typhi were compared with
      those of pBR322 isolated from Escherichia coli K-12. In E. coli K-12, adenines at
      the sequence - GATC - and the second cytosines at - [Formula: see text] - are met
      hylated by enzymes coded for by the genes dam and dem, respectively. From
      comparison of the restriction patterns obtained, it is concluded that S.
      typhimurium and S. typhi contain genes responsible for deoxyribonucleic acid
      methylation equivalent to E. coli K-12 genes dam and dcm.Images:
AU  - Gomez-Eichelmann MC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1979 140: 574-579.

PMID- 1657894
VI  - 173
DP  - 1991
TI  - Presence of 5-methylcytosine in CC(A/T)GG sequences (Dcm methylation) in DNAs from different bacteria.
PG  - 7692-7694
AB  - The presence of CC(A/T)GG sequences with methylated internal cytosine (Dcm methylation) was
      determined in DNA from different genera of eubacteria. This methylation was studied by using
      restriction enzymes EcoRII and BstNI, which cleave unmethylated or methylated CC(A/T)GG
      sequences. Dcm methylation was only detected in genera of the family Enterobacteriaceae
      closely related to Escherichia: Shigella, Citrobacter, Salmonella, and Klebsiella.
AU  - Gomez-Eichelmann MC
AU  - Levy-Mustri A
AU  - Ramirez-Santos J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1991 173: 7692-7694.

PMID- 8360914
VI  - 37
DP  - 1993
TI  - Methylated cytosine at Dcm (CCA/TGG) sites in Escherichia coli:  Possible function and evolutionary implications.
PG  - 11-24
AB  - The frequency and distribution of methylated cytosine (5-MeC) at CCA/TGG (Dcm sites) in 49 E.
      coli DNA loci (207,530 bp) were determined. Principal observations of this analysis were: (1)
      Dcm frequency was higher than expected from random occurrence but lower than calculated with
      Markov chain analysis; (2) CCTGG sites were found more frequently in coding than in noncoding
      regions, while the opposite was true for CCAGG sites; (3) Dcm site distribution does not
      exhibit any identifiably regular pattern on the chromosome; (4) Dcm sites at oriC are probably
      not important for accurate initiation of DNA replication; (5) 5-MeC in codons was more
      frequently found in first than in second and third positions; (6) there are probably few genes
      in which the mutation rate is determined mainly be DNA methylation. It is proposed that the
      function of Dcm methylase is to protect chromosomal DNA from restriction-enzyme EcoRII. The
      Dcm methylation contribution to determine frequency of oligonucleotides, mutation rate, and
      recombination level, and thus evolution of the E. coli genome, could be interpreted as a
      consequence of the acquisition of this methylation.
AU  - Gomez-Eichelmann MC
AU  - Ramirez-Santos J
PT  - Journal Article
TA  - J. Mol. Evol.
JT  - J. Mol. Evol.
SO  - J. Mol. Evol. 1993 37: 11-24.

PMID- 24604636
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Vibrio parahaemolyticus Strain M0605, Which Causes Severe Mortalities of Shrimps in Mexico.
PG  - e00055-14
AB  - Acute hepatopancreatic necrosis disease (AHPND), also known as early mortality syndrome (EMS),
      causes high mortalities in cultured shrimps in Asia (L. Tran et
      al., Dis. Aquat. Organ. 105:45-55, 2013, http://dx.doi.org/10.3354/dao02621).
      Here, we report the draft genome sequence of one Mexican strain of Vibrio
      parahaemolyticus that causes similar clinical signs in diseased shrimps.
AU  - Gomez-Gil B
AU  - Soto-Rodriguez S
AU  - Lozano R
AU  - Betancourt-Lozano M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00055-14.

PMID- 25125645
VI  - 2
DP  - 2014
TI  - High-Quality Draft Genomes of Two Vibrio parahaemolyticus Strains Aid in Understanding Acute Hepatopancreatic Necrosis Disease of Cultured Shrimps in  Mexico.
PG  - e00800-14
AB  - The high-quality draft genomes of two Vibrio parahaemolyticus strains, one that causes the
      acute hepatopancreatic necrosis disease (AHPND) in cultured shrimps
      (FIM-S1708(+)), and another that does not (FIM-S1392(-)) are reported. A
      chromosome-scale assembly for the FIM-S1392(-) genome is reported here. The
      analysis of the two genomes gives some clues regarding the genomic differences
      between the strains.
AU  - Gomez-Jimenez S
AU  - Noriega-Orozco L
AU  - Sotelo-Mundo RR
AU  - Cantu-Robles VA
AU  - Cobian-Guemes AG
AU  - Cota-Verdugo RG
AU  - Gamez-Alejo LA
AU  - Del Pozo-Yauner L
AU  - Guevara-Hernandez E
AU  - Garcia-Orozco KD
AU  - Lopez-Zavala AA
AU  - Ochoa-Leyva A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00800-14.

PMID- 21895912
VI  - 14
DP  - 2012
TI  - Genomic content of uncultured Bacteroidetes from contrasting oceanic provinces in the North Atlantic Ocean.
PG  - 52-66
AB  - Bacteroidetes are widespread in marine systems where they play a crucial role in
      organic matter degradation. Whole genome analysis of several strains has revealed
      a broad glycolytic and proteolytic potential. In this study, we used a targeted
      metagenomic approach to investigate the degradation capabilities of distinct
      Bacteroidetes clades from two contrasting regions of the North Atlantic Ocean,
      the Polar Biome (BPLR) and the North Atlantic Subtropical (NAST). We present here
      the analysis of 76 Bacteroidetes fosmids, of which 28 encode the 16S rRNA gene as
      phylogenetic marker, and their comparison to complete Bacteroidetes genomes.
      Almost all of the 16S rRNA harbouring fosmids belonged to clades that we
      previously identified in BPLR and NAST. The majority of sequenced fosmids could
      be assigned to Bacteroidetes affiliated with the class Flavobacteria. We also
      present novel genomic information on the classes Cytophagia and Sphingobacteria,
      suggesting a capability of the latter for attachment to algal surfaces. In our
      fosmid set we identified a larger potential for polysaccharide degradation and
      cell surface attachment in the phytoplankton-rich BPLR. Particularly, two
      flavobacterial fosmids, one affiliated with the genus Polaribacter, showed a
      whole armoury of enzymes that likely function in degradation of sulfated
      polysaccharides known to be major constituents of phytoplankton cell walls. Genes
      involved in protein and peptidoglycan degradation, although present in both
      fosmid sets, seemed to have a slight preponderance in NAST. This study provides
      support for the hypothesis of a distinct specialization among marine
      Bacteroidetes for the degradation of certain types of polymers.
AU  - Gomez-Pereira PR
AU  - Schuler M
AU  - Fuchs BM
AU  - Bennke C
AU  - Teeling H
AU  - Waldmann J
AU  - Richter M
AU  - Barbe V
AU  - Bataille E
AU  - Glockner FO
AU  - Amann R
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2012 14: 52-66.

PMID- 
VI  - 15
DP  - 2008
TI  - Bioprospeccion de enzimas de restriccion en bacterias de suelos y ambientes volcanicos de Nicaragua.
PG  - 70-87
AB  - 
AU  - Gomez-Rodriguez JA
AU  - Huete-Perez JA
PT  - Journal Article
TA  - Encuentro
JT  - Encuentro
SO  - Encuentro 2008 15: 70-87.

PMID- 26044424
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Toluene-Degrading Pseudomonas stutzeri Strain ST-9.
PG  - e00567-15
AB  - Strain ST-9 was isolated from toluene-contaminated soil (Samaria, Israel). The draft genome
      has an estimated size of 4.8 Mb, exhibits an average G+C content of
      60.37%, and is predicted to encode 4,183 proteins, including a gene cluster for
      aromatic hydrocarbon degradation. It is assigned to genomovar 3 of Pseudomonas
      stutzeri.
AU  - Gomila M
AU  - Busquets A
AU  - Garcia-Valdes E
AU  - Michael E
AU  - Cahan R
AU  - Nitzan Y
AU  - Lalucat J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00567-15.

PMID- 28798177
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Marine Bacterium Pseudomonas aestusnigri VGXO14T.<jour_book>Genome Announc.
PG  - e00765-17
AB  - The type strain of Pseudomonas aestusnigri (VGXO14), isolated from a crude oil-polluted marine
      sand sample, is a member of the P. pertucinogena phylogenetic
      group. Here, we report the genome sequence (3.83 Mb) of P. aestusnigri to gain
      insights into the biology and taxonomy of marine Pseudomonas spp. adapted to
      polluted marine habitats.
AU  - Gomila M
AU  - Mulet M
AU  - Lalucat J
AU  - Garcia-Valdes E
PT  - Journal Article
TA  - 
JT  - 
SO  -  2017 5: e00765-17.

PMID- 28385850
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Pseudomonas pachastrellae Strain CCUG 46540T, a Deep-Sea Bacterium.
PG  - e00136-17
AB  - Pseudomonas pachastrellae strain CCUG 46540T (KMM 330T) was isolated from a deep-sea sponge
      specimen collected in the Philippine Sea at a depth of 750 m. The
      draft genome has an estimated size of 4.0 Mb, exhibits a G+C content of 61.2
      mol%, and is predicted to encode 3,592 proteins, including pathways for the
      degradation of aromatic compounds.
AU  - Gomila M
AU  - Mulet M
AU  - Lalucat J
AU  - Garcia-Valdes E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00136-17.

PMID- 26021918
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Vibrio sp. Strain Vb278, an Antagonistic Bacterium Isolated from the Marine Sponge Sarcotragus spinosulus.
PG  - e00521-15
AB  - We report here the draft genome sequence of Vibrio sp. Vb278, a biofilm-producing strain
      isolated from the marine sponge Sarcotragus spinosulus, showing in vitro
      antibacterial activity. The annotated genome displays a range of symbiotic
      factors and the potential for the biosynthesis of several biologically active
      natural products.
AU  - Goncalves AC
AU  - Franco T
AU  - Califano G
AU  - Dowd SE
AU  - Pohnert G
AU  - Costa R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00521-15.

PMID- 27073591
VI  - 11
DP  - 2016
TI  - Complete genome sequences of Francisella noatunensis subsp. orientalis strains FNO12, FNO24 and FNO190: a fish pathogen with genomic clonal behavior.
PG  - 30
AB  - The genus Francisella is composed of Gram-negative, pleomorphic, strictly aerobic and
      non-motile bacteria, which are capable of infecting a variety of terrestrial
      and aquatic animals, among which Francisella noatunensis subsp. orientalis stands
      out as the causative agent of pyogranulomatous and granulomatous infections in
      fish. Accordingly, F. noatunensis subsp. orientalis is responsible for high
      mortality rates in freshwater fish, especially Nile Tilapia. In the current
      study, we present the genome sequences of F. noatunensis subsp. orientalis
      strains FNO12, FNO24 and FNO190. The genomes include one circular chromosome of
      1,859,720 bp, consisting of 32 % GC content, 1538 coded proteins and 363
      pseudogenes for FNO12; one circular chromosome of 1,862,322 bp, consisting of 32
      % GC content, 1537 coded proteins and 365 pseudogenes for FNO24; and one circular
      chromosome of 1,859,595 bp, consisting of 32 % GC content, 1539 coded proteins
      and 362 pseudogenes for FNO190. All genomes have similar genetic content,
      implicating a clonal-like behavior for this species.
AU  - Goncalves LA
AU  - de Castro SS
AU  - Pereira FL
AU  - Dorella FA
AU  - de Carvalho AF
AU  - de Freitas AGM
AU  - Leal CA
AU  - Azevedo V
AU  - Figueiredo HC
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 30.

PMID- 
VI  - 1
DP  - 2005
TI  - PspXI, a novel restriction endonuclease that recognizes the unusual  DNA sequence 5'-VC^TCGAGB-3'.
PG  - 18-23
AB  - We have discovered a bacterial strain Pseudomonas species X11 that produces the novel
      restriction endonuclease PspXI. This enzyme recognizes an unusual degenerate octanucleotide
      sequence 5'-VCTCGAGB-3', where V stands for A, C or G and B stands for T, C or G.  The PspXI
      restriction endonuclease preparation with concentration of 10000 units/ml was isolated using
      four chromatographic steps. PspXI cuts its recognition sequence between C and T producing
      cohesive ends compatible with those of produced by XhoI(5'-C^TCGAG-3') and
      SalI(5'-G^TCGAC-3') restriction endonucleases.
AU  - Gonchar DA
AU  - Abdurashitov MA
AU  - Belichenko OA
AU  - Dedkov VS
AU  - Mezentseva NV
AU  - Tomilova JE
AU  - Degtyarev SK
PT  - Journal Article
TA  - Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol.
JT  - Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol.
SO  - Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol. 2005 1: 18-23.

PMID- 17685226
VI  - 41
DP  - 2007
TI  - Sse9I restriction-modification system: Organization of genes and structural comparison of proteins.
PG  - 491-498
AB  - The nucleotide sequence was established for the operon of the Sse9I type II
      restriction-modification system of Sporosarcina species 9D.  The enzymes of the Sse9I system
      recognize the 5'-AATT-3' tetranucleotide.  The operon includes three genes,
      sse9IC-sse9IR-sse9IM, which are transcribed unidirectionally and code, respectively, for the
      controller protein (C.Sse9I), restriction endonuclease (R.Sse9I), and DNA methyltransferase
      (M.Sse9I).  The region immediately upstream of sse9IC was found to contain a conserved
      nucleotide sequence (C box) providing a binding site for C.Sse9I.  The amino acid sequences of
      C.Sse9I and R.Sse9I were compared with those of related proteins.  In the case of R.Sse9I, the
      highest homology was observed with the R.MunI (5'CAATTG-3') and R.EcoRI (5'GAATTC-3')
      regions that harbor the amino acid residues involved in recognizing the AATT inner
      tetranucleotide.  The sse9IR gene was cloned in an expression vector, and recombinant R.Sse9I
      was isolated.
AU  - Gonchar DA
AU  - Abdurashitov MA
AU  - Okhapkina SS
AU  - Shagin DA
AU  - Kileva EV
AU  - Degtyarev SK
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2007 41: 491-498.

PMID- 
VI  - 6
DP  - 2010
TI  - BlsI- and GlaI-PCR assays - a new method of DNA methylation study.
PG  - 5-12
AB  - Regulation of genes activity in mammalians genomes is based on DNA methylation of CG
      dinucleotides with formation of 5-methylcytosine (5mC) in both DNA strands.  Mammalian
      DNA-methyltransferases Dnmt1, Dnmt3a and Dnmt3b catalyze a reaction of DND methylation.  Dnmt1
      maintains DNA methylation pattern in vivo modifying a new strand after replication.  Dnmt3a
      and Dnmt3b are responsible for DNA methylation de novo and, likely, differ in their function
      and preferable region of modification.  Study of Dnmt3a and Dnmnt3b substrate specificity has
      shown that both enzymes methylate CG-dinucleotide4 mostly in DNA sequence PuCGPy.  At present
      time 5mC determination is represented mostly by a chemical treatment of DNA with sodium
      bisulphite, which results in cytosine transformation into uracil, and native DNA allows to
      locate positions of methylated cytosines in studied DNA.  Method of bisulphite conversion is
      quite expensive, time-consuming and often results in obtaining false positive data.  Because
      of substantial DNA degradation this method is used for analysis of only short (100 - 150 bp)
      DNA sequences.  Among enzymatic methods of 5mC determination, so called methyl-sensitive PCR
      assay is the most popular.  This method is based on inability of restriction enzymes, which
      contain CG dinucleotide in the recognition site, to cut this site if 5mC is present in the
      dinucleotide.  A subsequent PCR from primers, which are located around a chosen recognition
      site, produces a corresponding DNA fragment if there is a methylated CG-dinucleotide within
      this site.  On the contrary, DNA fragment is not produced in PCR if there is no methylated
      CG-dinucleotide in a recognition sequence of restriction enzyme.  Application of
      methyl-sensitive PCR assay is limited by a very short list of recognition sequences.  Recently
      we have discovered and characterized absolutely new enzymes BlsI and GlaI, which belong to the
      type of methyl-directed site-specific DNA endonucleases and cleave only methylated DNA.  GlaI
      recognizes DNA sequence 5'-Pu(5mC)GPy-3'/3'-PyG(5mC)Pu-5', whereas BlsI hydrolyzes DNA
      sequence 5'-GCNGC-3' if at least one 5-methylcytosine (N isn't considering) is present in
      each DNA strand of the recognition site.  In this work we have developed a new method of DNA
      methylation determination -
      BlsI- and GlaI-PCR assays, and have applied this method to study a methylation of regulation
      of tumor suppressor genes in DNA from different human cell lines.
AU  - Gonchar DA
AU  - Akishev AG
AU  - Degtyarev SK
PT  - Journal Article
TA  - Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol.
JT  - Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol.
SO  - Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol. 2010 6: 5-12.

PMID- 
VI  - 12
DP  - 2016
TI  - Cloning and characterization of a new site specific methyl-directed DNA endonuclease EcoBLI recognizing 5'-G(5mC)NGC-3'/3'-CGN(5mC)G-5'.
PG  - 175-181
AB  - A gene coding BisI, site specific 5mC-directed DNA endonuclease recognizing DNA sequence
      5'-G(5mC)NGC-3'/3'-CGN(5mC)G-5', was recently identified in the sequenced genome of the
      strain-producer Bacillus subtilis T30.  In this work we have undertaken a search of bisI gene
      homologues among the sequenced genomes of enterobacteria.  DNA analysis has revealed a small
      group of highly homologous ORFs with unknown function including one ORF in DNA of well-known
      strain E. coli.  This ORF WP 001276099.1 from E.coli BL21 (DE3) was amplified and cloned.  An
      obtained recombinant strain E.coli PEcoBLI produces MD-endonuclease named EcoBLI.  The new
      enzyme has the same substrate specificity as BisI MD-endonuclease.  Thus, ORF WP 001276099.1
      from E.coli BL21 (DE3) encodes site-specific  5mC-directed DNA-endonuclease EcoBLI recognizing
      and cleaving DNA sequence as indicated by arrows 5'-G(5mC)^NGC-3'/3'-CGN^(5mC)G-5'.
AU  - Gonchar DA
AU  - Chernukhin VA
AU  - Abdurashitov MA
AU  - Kileva EV
AU  - Dedkov VS
AU  - Mikhnenkova NA
AU  - Lomakovskaya EN
AU  - Udalyeva SG
AU  - Degtyarev SK
PT  - Journal Article
TA  - BTAIJ
JT  - BTAIJ
SO  - BTAIJ 2016 12: 175-181.

PMID- 9567290
VI  - 34
DP  - 1998
TI  - Restriction endonuclease Sse9I from Sporosarcina sp. strain 9D recognizes the 5'-AATT-3' DNA sequence.
PG  - 139-141
AB  - A new restriction endonuclease Sse9I was isolated from the bacterial strain Sporosarcina sp.
      9D. The enzyme belongs to type II restrictases and recognizes the tetranucleotide sequence
      5'-AATT-3'.  The enzyme cleaves DNA before the first adenine residue, so it is a true
      isoschizomer of Tsp509I restrictase.  However, unlike the prototype, Sse9I digests DNA at 55oC
      and loses its activity after 20 min storage at 65oC.
AU  - Gonchar DA
AU  - Dedkov VS
AU  - Verkhozina VA
AU  - Kusner YS
AU  - Shevchenko AV
AU  - Degtyarev SK
PT  - Journal Article
TA  - Prikl. Biokhim. Mikrobiol.
JT  - Prikl. Biokhim. Mikrobiol.
SO  - Prikl. Biokhim. Mikrobiol. 1998 34: 139-141.

PMID- 9511140
VI  - 2
DP  - 1998
TI  - Sse9I, a restriction endonuclease from Sporosarcina sp. 9D which recognizes the sequence 5'AATT-3'.
PG  - 32-34
AB  - Sse9I, a type II restriction endonuclease, has been isolated from Sporosarcina species 9D.
      The recognition sequence and cleavage point of restriction endonuclease Sse9I have been
      determined as 5'-/AATT-3'.  The new enzyme is an isoschizomer of Tsp509I, but its optimal
      incubation temperature is 55 C and it is inactivated at 65 C for 20 min.
AU  - Gonchar DA
AU  - Dedkov VS
AU  - Verkhozina VA
AU  - Kusner YS
AU  - Shevchenko AV
AU  - Degtyarev SK
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1998 2: 32-34.

PMID- 8759012
VI  - 24
DP  - 1996
TI  - Cloning and characterization of Sse9I DNA-methyltransferase recognizing 5'-AATT-3'.
PG  - 2790-2792
AB  - The gene from Sporosarcina species 9D encoding Sse9I DNA-methyltransferase (M.Sse9I) was
      cloned and expressed in Escherichia coli.  The recombinant plasmid pMSse-1 contains the
      M.Sse9I gene 1086 bp in length, corresponding to a protein of 362 amino acid residues.
      M.Sse9I recognizes the tetranucleotide sequence 5'-AATT-3' and modifies the second adenine
      within the recognition sequence.  The amino acid sequence of M.Sse9I was compared with those
      of other methylases.  According to mutual positions of four conservative domains the new
      enzyme belongs to a subgroup of D12 class.  This subgroup includes Sse9I, CviAII, NlaIII and
      N-terminal domains of LlaI, FokI and StsI DNA-methyltransferases.
AU  - Gonchar DA
AU  - Wolf YI
AU  - Degtyarev SK
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1996 24: 2790-2792.

PMID- 26868396
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Enterococcus faecium Strain 58m, Isolated from Intestinal Tract Content of a Woolly Mammoth, Mammuthus primigenius.
PG  - e01706-15
AB  - Enterococcus faecium 58m is a putative ancient nonpathogenic strain isolated from the
      intestinal content of an adult woolly mammoth (Mammuthus primigenius). Here,
      we report its draft genome sequence, consisting of 60 contigs. In silico genomic
      analysis was performed to determine the genetic features and pathogenic potential
      of this microorganism.
AU  - Goncharov A
AU  - Grigorjev S
AU  - Karaseva A
AU  - Kolodzhieva V
AU  - Azarov D
AU  - Akhremenko Y
AU  - Tarasova L
AU  - Tikhonov A
AU  - Masharskiy A
AU  - Zueva L
AU  - Suvorov A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01706-15.

PMID- 
VI  - 60
DP  - 2010
TI  - Antibiotic resistance of Escherichia coli O157:H7 isolated from cattle and sheep.
PG  - 489-494
AB  - A total of 102 Escherichia coli O157:H7 colonies recovered from 11 cattle and 14 sheep were
      collected and tested for their antibiotic resistance profiles using a disc diffusion method,
      according to the Clinical and Laboratory Standards Institute. Four (36.36 %) of the 11 cattle
      E. coli O157:H7 isolates were resistant to cephalothin, one (9.09 %) isolate was resistant to
      streptomycin, and one (9.09 %) to nalidixic acid. Two (14.28 %) of the 14 sheep E. coli
      O157:H7 isolates were resistant to sulphamethoxazole,
      one (7.14 %) isolate was resistant to sulphonamide compounds, and one (7.14 %) to
      streptomycin. All cattle and sheep isolates were found to be susceptible to
      cephazolin, gentamicin, ciprofloxacin, imipenem, trimethoprim/sulphamethoxazole,
      chloramphenicol, trimethoprim, and ceftiofur. Six cattle isolates were susceptible at a ratio
      of 54.54 %, and 11 (78.57 %) isolates from sheep were susceptible to all 20 antibiotics
      tested. As an overall result, 68 % of the E. coli O157:H7 isolates belonging to cattle and
      sheep were susceptible to all antibiotics tested. On the other hand, most of the E. coli
      O157:H7 isolates were intermediately resistant to streptomycin, cephalothin,
      sulphamethoxazole, ampicillin, and kanamycin.
AU  - Goncuoglu M
AU  - Aydin ND
AU  - Erol I
PT  - Journal Article
TA  - Ann. Microbiol. (Paris)
JT  - Ann. Microbiol. (Paris)
SO  - Ann. Microbiol. (Paris) 2010 60: 489-494.

PMID- 28126946
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Streptococcus iniae 89353, a Virulent Strain Isolated from Diseased Tilapia in Taiwan.
PG  - e01524-16
AB  - Streptococcus iniae 89353 is a virulent strain isolated from diseased tilapia in  Taiwan. The
      full-genome sequence of S. iniae 89353 is 2,098,647 bp. The revealed
      genome information will be beneficial for identification and understanding of
      potential virulence genes of Streptococcus iniae and possible immunogens for
      vaccine development against streptococcosis.
AU  - Gong HY
AU  - Wu SH
AU  - Chen CY
AU  - Huang CW
AU  - Lu JK
AU  - Chou HY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01524-16.

PMID- 22374961
VI  - 194
DP  - 2012
TI  - Genome Sequence of Comamonas testosteroni ATCC 11996, a Representative Strain Involved in Steroid Degradation.
PG  - 1633-1634
AB  - Comamonas testosteroni strains belong to the family of Comamonadaceae and are known for their
      ability to utilize steroid compounds as carbon source. Here, we
      present the draft genome sequence of strain ATCC 11996, with a G+C content of
      61.48%.
AU  - Gong W
AU  - Kisiela M
AU  - Schilhabel MB
AU  - Xiong G
AU  - Maser E
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1633-1634.

PMID- 9207015
VI  - 25
DP  - 1997
TI  - Structure of PvuII DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment.
PG  - 2702-2715
AB  - We have determined the structure of PvuII methyltransferase (M.PvuII) complexed with
      S-adenosyl-L-methionine (AdoMet) by multiwavelength anomalous diffraction, using a crystal of
      the selenomethionine-substituted protein.  M.PvuII catalyzes transfer of the methyl group from
      AdoMet to the exocyclic amino (N4) nitrogen of the central cytosine in its recognition
      sequence 5'-CAGCTG-3'.  The protein is dominated by an open alpha/beta-sheet stucture with a
      prominent V-shaped cleft: AdoMet and catalytic amino acids are located at the bottom of this
      cleft.  The size and the basic nature of the cleft are consistent with duplex DNA binding.
      The target (methylatable) cytosine, if flipped out of the double helical DNA as seen for DNA
      methyltransferases that generate 5-methylcytosine, would fit into the concave active site next
      to the AdoMet.  This M.PvuII alpha/beta-sheet structure is very similar to those of M.HhaI (a
      cytosine C5 methyltransferase) and M.TaqI (an adenine N6 methyltransferase), consistent with a
      model predicting that DNA methyltransferases share a common structural fold while having the
      major functional regions permuted into three distinct linear orders.  The main feature of the
      common fold is a seven-stranded beta-sheet (6/7/5/4/1/2/3/) formed by five parallel
      beta-strands and an antiparallel beta-hairpin.  The beta-sheet is flanked by size parallel
      alpha-helices, three on each side.  The AdoMet binding site is located at the C-terminal ends
      of strands beta1 and beta2 and the active site is at the C-terminal ends of strands beta4 and
      beta5 and the N-terminal end of strand beta7.  The AdoMet-protein interactions are almost
      identical among M.PvuII, M.HhaI and M.TaqI, as well as in an RNA methyltransferase and at
      least one small molecule methyltransferase.  The structural similarity among the active sites
      of M.PvuII, M.TaqI and M.HhaI reveals that catalytic amino acids essential for cytosine N4 and
      adenine N6 methylation coincide spatially with those for cytosine C5 methylation, suggesting a
      mechanism for amino methylation.
AU  - Gong W
AU  - O'Gara M
AU  - Blumenthal RM
AU  - Cheng X
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1997 25: 2702-2715.

PMID- 28116042
VI  - 12
DP  - 2017
TI  - High quality draft genome sequence of Janthinobacterium psychrotolerans sp. nov., isolated from a frozen freshwater pond.
PG  - 8
AB  - Strain S3-2T, isolated from sediment of a frozen freshwater pond, shares 99% 16S  rRNA gene
      sequence identity with strains of the genus Janthinobacterium. Strain
      S3-2T is a facultative anaerobe that lacks the ability to produce violacein but
      shows antibiotic resistance, psychrotolerance, incomplete denitrification, and
      fermentation. The draft genome of strain S3-2T has a size of ~5.8 Mbp and
      contains 5,297 genes, including 115 RNA genes. Based on the phenotypic properties
      of the strain, the low in silico DNA-DNA hybridization (DDH) values with related
      genomes (<35%), and the low whole genome-based average nucleotide identity (ANI)
      (<86%) with other strains within the genus Janthinobacterium, we propose that
      strain S3-2T is the type strain (= DSM 102223 = LMG 29653) of a new species
      within this genus. We propose the name Janthinobacterium psychrotolerans sp. nov.
      to emphasize the capability of the strain to grow at low temperatures.
AU  - Gong X
AU  - Skrivergaard S
AU  - Korsgaard BS
AU  - Schreiber L
AU  - Marshall IP
AU  - Finster K
AU  - Schramm A
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 8.

PMID- 28104657
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Desulfovibrio BerOc1, a Mercury-Methylating Strain.
PG  - e01483-16
AB  - Desulfovibrio BerOc1 is a sulfate-reducing bacterium isolated from the Berre lagoon (French
      Mediterranean coast). BerOc1 is able to methylate and demethylate mercury. The genome size is
      4,081,579 bp assembled into five contigs. We identified the hgcA and hgcB genes involved in
      mercury methylation, but not those responsible for mercury demethylation.
AU  - Goni-Urriza M
AU  - Gassie C
AU  - Bouchez O
AU  - Klopp C
AU  - Guyoneaud R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01483-16.

PMID- 23209244
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of the Copiotrophic Marine Bacterium Alteromonas macleodii Strain ATCC 27126T.
PG  - 6998
AB  - The genome of Alteromonas macleodii strain ATCC 27126(T) has been resequenced and closed into
      a single contig. We describe here the genome of this important and
      globally distributed marine bacterium.
AU  - Gonzaga A
AU  - Lopez-Perez M
AU  - Martin-Cuadrado AB
AU  - Ghai R
AU  - Rodriguez-Valera F
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6998.

PMID- 23212172
VI  - 4
DP  - 2012
TI  - Polyclonality of concurrent natural populations of Alteromonas macleodii.
PG  - 1360-1374
AB  - We have analyzed a natural population of the marine bacterium, Alteromonas macleodii, from a
      single sample of seawater to evaluate the genomic diversity
      present. We performed full genome sequencing of four isolates and 161 metagenomic
      fosmid clones, all of which were assigned to A. macleodii by sequence similarity.
      Out of the four strain genomes, A. macleodii deep ecotype (AltDE1) represented a
      different genome, whereas AltDE2 and AltDE3 were identical to the previously
      described AltDE. Although the core genome (~80%) had an average nucleotide
      identity of 98.51%, both AltDE and AltDE1 contained flexible genomic islands
      (fGIs), that is, genomic islands present in both genomes in the same genomic
      context but having different gene content. Some of the fGIs encode cell surface
      receptors known to be phage recognition targets, such as the O-chain of the
      lipopolysaccharide, whereas others have genes involved in physiological traits
      (e.g., nutrient transport, degradation, and metal resistance) denoting microniche
      specialization. The presence in metagenomic fosmids of genomic fragments
      differing from the sequenced strain genomes, together with the presence of new
      fGIs, indicates that there are at least two more A. macleodii clones present. The
      availability of three or more sequences overlapping the same genomic region also
      allowed us to estimate the frequency and distribution of recombination events
      among these different clones, indicating that these clustered near the genomic
      islands. The results indicate that this natural A. macleodii population has
      multiple clones with a potential for different phage susceptibility and
      exploitation of resources, within a seemingly unstructured habitat.
AU  - Gonzaga A
AU  - Martin-Cuadrado AB
AU  - Lopez-Perez M
AU  - Megumi-Mizuno C
AU  - Garcia-Heredia I
AU  - Kimes NE
AU  - Lopez-Garcia P
AU  - Moreira D
AU  - Ussery D
AU  - Zaballos M
AU  - Ghai R
AU  - Rodriguez-Valera F
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2012 4: 1360-1374.

PMID- 26220966
VI  - 6
DP  - 2015
TI  - Genomic Adaptations to the Loss of a Conserved Bacterial DNA Methyltransferase.
PG  - e00952-15
AB  - CcrM is an orphan DNA methyltransferase nearly universally conserved in a vast group of
      Alphaproteobacteria. In Caulobacter crescentus, it controls the
      expression of key genes involved in the regulation of the cell cycle and cell
      division. Here, we demonstrate, using an experimental evolution approach, that C.
      crescentus can significantly compensate, through easily accessible genetic
      changes like point mutations, the severe loss in fitness due to the absence of
      CcrM, quickly improving its growth rate and cell morphology in rich medium. By
      analyzing the compensatory mutations genome-wide in 12 clones sampled from
      independent DeltaccrM populations evolved for ~300 generations, we demonstrated
      that each of the twelve clones carried at least one mutation that potentially
      stimulated ftsZ expression, suggesting that the low intracellular levels of FtsZ
      are the major burden of DeltaccrM mutants. In addition, we demonstrate that the
      phosphoenolpyruvate-carbohydrate phosphotransfer system (PTS) actually modulates
      ftsZ and mipZ transcription, uncovering a previously unsuspected link between
      metabolic regulation and cell division in Alphaproteobacteria. We present
      evidence that point mutations found in genes encoding proteins of the PTS provide
      the strongest fitness advantage to DeltaccrM cells cultivated in rich medium
      despite being disadvantageous in minimal medium. This environmental sign
      epistasis might prevent such mutations from getting fixed under changing natural
      conditions, adding a plausible explanation for the broad conservation of CcrM.
      IMPORTANCE: In bacteria, DNA methylation has a variety of functions, including
      the control of DNA replication and/or gene expression. The cell cycle-regulated
      DNA methyltransferase CcrM modulates the transcription of many genes and is
      critical for fitness in Caulobacter crescentus. Here, we used an original
      experimental evolution approach to determine which of its many targets make CcrM
      so important physiologically. We show that populations lacking CcrM evolve
      quickly, accumulating an excess of mutations affecting, directly or indirectly,
      the expression of the ftsZ cell division gene. This finding suggests that the
      most critical function of CcrM in C. crescentus is to promote cell division by
      enhancing FtsZ intracellular levels. During this work, we also discovered an
      unexpected link between metabolic regulation and cell division that might extend
      to other Alphaproteobacteria.
AU  - Gonzalez D
AU  - Collier J
PT  - Journal Article
TA  - MBio
JT  - MBio
SO  - MBio 2015 6: e00952-15.

PMID- 24398711
VI  - 42
DP  - 2014
TI  - The functions of DNA methylation by CcrM in Caulobacter crescentus: a global approach.
PG  - 3720-3735
AB  - DNA methylation is involved in a diversity of processes in bacteria, including maintenance of
      genome integrity and regulation of gene expression. Here, using
      Caulobacter crescentus as a model, we exploit genome-wide experimental methods to
      uncover the functions of CcrM, a DNA methyltransferase conserved in most
      Alphaproteobacteria. Using single molecule sequencing, we provide evidence that
      most CcrM target motifs (GANTC) switch from a fully methylated to a
      hemi-methylated state when they are replicated, and back to a fully methylated
      state at the onset of cell division. We show that DNA methylation by CcrM is not
      required for the control of the initiation of chromosome replication or for DNA
      mismatch repair. By contrast, our transcriptome analysis shows that >10% of the
      genes are misexpressed in cells lacking or constitutively over-expressing CcrM.
      Strikingly, GANTC methylation is needed for the efficient transcription of dozens
      of genes that are essential for cell cycle progression, in particular for DNA
      metabolism and cell division. Many of them are controlled by promoters methylated
      by CcrM and co-regulated by other global cell cycle regulators, demonstrating an
      extensive cross talk between DNA methylation and the complex regulatory network
      that controls the cell cycle of C. crescentus and, presumably, of many other
      Alphaproteobacteria.
AU  - Gonzalez D
AU  - Kozdon JB
AU  - McAdams HH
AU  - Shapiro L
AU  - Collier J
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2014 42: 3720-3735.

PMID- 8081498
VI  - 140
DP  - 1994
TI  - The expression of the bstVIM gene from Bacillus stearothermophilus V is restricted to vegetative cell growth.
PG  - 1337-1340
AB  - The activity of BstVI DNA methyltransferase was monitored during the sporulative cycle of
      Bacillus stearothermophilus V. Significant methylase activity was found only in bacteria
      growing vegetatively. This was confirmed by Northern hybridization, which indicated that the
      bstVIM gene was not transcribed in cells undergoing sporulation. Supporting evidence came from
      experiments which demonstrated that the RNA polymerase holoenzyme from these cells did not
      recognize the promoter elements upstream of the bstVIM gene.
AU  - Gonzalez E
AU  - Padilla C
AU  - Saavedra C
AU  - Vasquez C
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 1994 140: 1337-1340.

PMID- 8370531
VI  - 131
DP  - 1993
TI  - Characterization of the bstVIRM genes encoding the Bacillus stearothermophilus V restriction-modification system.
PG  - 103-106
AB  - The nucleotide (nt) sequence of a 2.7-kb HindIII-EcoRI DNA fragment encoding the bstVIR and
      bstVIM genes has been determined. The sequence predicts a restriction endonuclease of 224
      amino acids (aa), Mr 25,104, and a methyltransferase of 561 aa, Mr 65,702. Both genes are
      aligned in the same orientation and are separated by a 102-nt intergenic region. No homology
      was found between R-BstVI and M-BstVI when their deduced aa sequences were compared.
      Significant similarity at the aa level was found, however, when both enzymes were compared to
      their equivalents in the paeR71RM system of Pseudomonas aeruginosa PAO303.
AU  - Gonzalez E
AU  - Vasquez C
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1993 131: 103-106.

PMID- 16505379
VI  - 103
DP  - 2006
TI  - The partitioned Rhizobium etli genome: Genetic and metabolic redundancy in seven interacting replicons.
PG  - 3834-3839
AB  - We report the complete 6,530,228-bp genome sequence of the symbiotic nitrogen fixing bacterium
      Rhizobium etli. Six large plasmids comprise
      one-third of the total genome size. The chromosome encodes most functions
      necessary for cell growth, whereas few essential genes or complete
      metabolic pathways are located in plasmids. Chromosomal synteny is
      disrupted by genes related to insertion sequences, phages, plasmids, and
      cell-surface components. Plasmids do not show synteny, and their orthologs
      are mostly shared by accessory replicons of species with multipartite
      genomes. Some nodulation genes are predicted to be functionally related
      with chromosomal loci encoding for the external envelope of the bacterium.
      Several pieces of evidence suggest an exogenous origin for the symbiotic
      plasmid (p42d) and p42a. Additional putative horizontal gene transfer
      events might have contributed to expand the adaptive repertoire of R.
      etli, because they include genes involved in small molecule metabolism,
      transport, and transcriptional regulation. Twenty-three putative sigma
      factors, numerous isozymes, and paralogous families attest to the
      metabolic redundancy and the genomic plasticity necessary to sustain the
      lifestyle of R. etli in symbiosis and in the soil.
AU  - Gonzalez V
AU  - Santamaria RI
AU  - Bustos P
AU  - Hernandez-Gonzalez I
AU  - Medrano-Soto A
AU  - Moreno-Hagelsieb G
AU  - Janga SC
AU  - Ramirez MA
AU  - Jimenez-Jacinto V
AU  - Collado-Vides J
AU  - Davila G
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2006 103: 3834-3839.

PMID- 19796133
VI  - 301
DP  - 2009
TI  - Characterization of the methyl-specific restriction system of Streptomyces coelicolor A3(2) and of the role played by laterally acquired nucleases.
PG  - 35-43
AB  - The methyl-specific restriction system of Streptomyces coelicolor A3(2) was analyzed by
      carrying out transformations with unmethylated and
      methylated pSET152 DNA. Streptomyces coelicolor was found to strongly
      restrict DNA methylated in vivo by the Dam, Dcm and Hsd modification
      systems of Escherichia coli. Hsd-modified DNA was restricted as
      strongly as Dam-modified DNA, even though there are significantly fewer
      sites on the plasmid; Dcm-modified plasmid was restricted more strongly
      then either Dam-or Hsd-modified DNA. Restriction of plasmid DNA
      modified in vitro by different methylases also showed a greater
      dependence on the methylated sequence than on the number of methylated
      sites. Streptomyces coelicolor mutants were constructed that lacked
      genes identified as the likely candidates for encoding methyl-specific
      restriction nucleases (the products of the SCO4213, SCO4631 and SCO2863
      genes, as well as the SCO3261-SCO3262 operon) that are located in the
      laterally acquired genomic islands of the S. coelicolor chromosome;
      these mutants showed partial alleviation of methylated DNA restriction.
      Cloning of these genes in the close relative Streptomyces lividans
      increased the restriction of methylated DNA by this species, confirming
      their role as part of the methyl-specific restriction system of S.
      coelicolor.
AU  - Gonzalez-Ceron G
AU  - Miranda-Olivares OJ
AU  - Servin-Gonzalez L
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2009 301: 35-43.

PMID- 30533938
VI  - 7
DP  - 2018
TI  - Closed Genome Sequences of Two Clostridium botulinum Strains Obtained by Nanopore Sequencing.
PG  - e01075-18
AB  - Here we report the genome sequences of two toxin-producing Clostridium botulinum  strains, one
      environmental sample (83F) and one clinical sample (CDC51232). The
      genomes were closed by a combination of long-read and short-read sequencing. The
      strains belong to C. botulinum sequence type 4 (ST4) and ST7, respectively.
AU  - Gonzalez-Escalona N
AU  - Haendiges J
AU  - Miller JD
AU  - Sharma SK
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e01075-18.

PMID- 24092795
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences of Two O104:H21 Escherichia coli Isolates Causing Hemorrhagic Colitis during a 1994 Montana Outbreak Provide Insight into Their  Pathogenicity.
PG  - e00805-13
AB  - We sequenced the genomes of two strains of O104:H21 enterohemorrhagic Escherichia coli (EHEC)
      isolated during an outbreak of hemorrhagic colitis in Montana in
      1994. These strains carried a plasmid that contains several virulence genes not
      present in pO157. The genome sequences will improve phylogenetic analysis of
      other non-O157 E. coli strains in the future.
AU  - Gonzalez-Escalona N
AU  - McFarland MA
AU  - Rump LV
AU  - Payne J
AU  - Andrzejewski D
AU  - Brown EW
AU  - Evans PS
AU  - Croley TR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00805-13.

PMID- 21551294
VI  - 193
DP  - 2011
TI  - Genome sequence of the clinical O4:K12 serotype Vibrio parahaemolyticus strain 10329.
PG  - 3405-3406
AB  - Vibrio parahaemolyticus is the leading cause of foodborne illnesses worldwide. Here we report
      a draft genome of V. parahaemolyticus strain
      Vp10329 of O4:K12 serotype. It belongs to the main U. S. West Coast clonal
      complex of V. parahaemolyticus (ST36) causing oyster-associated human
      illness. It contains the virulence determinants tdh and trh but appears to
      infect at much lower doses than V. parahaemolyticus strains with these
      same determinants from other areas such as the U.S. Gulf and Atlantic
      coasts.
AU  - Gonzalez-Escalona N
AU  - Strain EA
AU  - De Jesus AJ
AU  - Jones JL
AU  - Depaola A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3405-3406.

PMID- 25502671
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Bivalent Clostridium botulinum Strain IBCA10-7060, Encoding Botulinum Neurotoxin B and a New FA Mosaic Type.
PG  - e01275-14
AB  - Here we report the genome sequence of a Clostridium botulinum strain IBCA10-7060  producing
      botulinum neurotoxin serotype B and a new toxin serotype. Multilocus
      sequence typing analysis revealed that this strain belongs to a new sequence
      type, and whole-genome single nucleotide polymorphism analysis showed that this
      strain clustered with strains in lineage 2 from group I.
AU  - Gonzalez-Escalona N
AU  - Thirunavukkarasu N
AU  - Singh A
AU  - Toro M
AU  - Brown EW
AU  - Zink D
AU  - Rummel A
AU  - Sharma SK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01275-14.

PMID- 11439018
VI  - 310
DP  - 2001
TI  - DNA binding and cleavage selectivity of the Escherichia coli DNA G:T-mismatch endonuclease (vsr protein).
PG  - 501-508
AB  - The Escherichia coli vsr endonuclease recognises T:G base-pair mismatches in double-stranded
      DNA and initiates a repair pathway by
      hydrolysing the phosphate group 5' to the incorrectly paired T. The
      gene encoding the vsr endonuclease is next to the gene specifying the
      E. coli dcm DNA-methyltransferase; an enzyme that adds CH3 groups to
      the first dC within its target sequence CC[A/T]GG, giving
      C5MeC[A/T]GG. Deamination of the d(5Me)C results in CT[A/T]GG in
      which the first T is mis-paired with dG and it is believed that the
      endonuclease preferentially recognises T:G mismatches within the dcm
      recognition site. Here, the preference of the vsr endonuclease for
      bases surrounding the T:G mismatch has been evaluated. Determination of
      specificity constant (k(st)/K-D; k(st) = rate constant for single
      turnover, K-D = equilibrium dissociation constant) confirms vsr's
      preference for a T:G mismatch within a dcm sequence i.e. C (T) under
      bar [A/T]GG (the underlined T being mis-paired with dG) is the best
      substrate. However, the enzyme is capable of binding and hydrolysing
      sequences that differ from the dcm target site by a single base-pair
      (dcm star sites). Individual alteration of any of the four bases
      surrounding the mismatched T gives a substrate, albeit with reduced
      binding affinity and slowed turnover rates. The vsr endonuclease has a
      much lower selectivity for the dcm sequence than type II restriction
      endonucleases have for their target sites. The results are discussed in
      the light of the known crystal structure of the vsr protein and its
      possible physiological role.
AU  - Gonzalez-Nicieza R
AU  - Turner DP
AU  - Connolly BA
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2001 310: 501-508.

PMID- 21952541
VI  - 193
DP  - 2011
TI  - Genome Sequence of the Mycobacterium colombiense Type Strain, CECT 3035.
PG  - 5866-5867
AB  - We report the first whole-genome sequence of the Mycobacterium colombiense type strain, CECT
      3035, which was initially isolated from Colombian
      HIV-positive patients and causes respiratory and disseminated infections.
      Preliminary comparative analyses indicate that the M. colombiense lineage
      has experienced a substantial genome expansion, possibly contributing to
      its distinct pathogenic capacity.
AU  - Gonzalez-Perez M
AU  - Murcia MI
AU  - Landsman D
AU  - Jordan IK
AU  - Marino-Ramirez L
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5866-5867.

PMID- 27818776
VI  - 14
DP  - 2016
TI  - Deciphering the virulence factors of the opportunistic pathogen Mycobacterium colombiense.
PG  - 98-105
AB  - Mycobacterium avium complex (MAC) contains clinically important nontuberculous
      mycobacteria worldwide and is the second largest medical complex in the
      Mycobacterium genus after the Mycobacterium tuberculosis complex. MAC comprises
      several species that are closely phylogenetically related but diverse regarding
      their host preference, course of disease, virulence and immune response. In this
      study we provided immunologic and virulence-related insights into the M.
      colombiense genome as a model of an opportunistic pathogen in the MAC. By using
      bioinformatic tools we found that M. colombiense has deletions in the genes
      involved in p-HBA/PDIM/PGL, PLC, SL-1 and HspX production, and loss of the ESX-1
      locus. This information not only sheds light on our understanding the virulence
      mechanisms used by opportunistic MAC pathogens but also has great potential for
      the designing of species-specific diagnostic tools.
AU  - Gonzalez-Perez MN
AU  - Murcia MI
AU  - Parra-Lopez C
AU  - Blom J
AU  - Tauch A
PT  - Journal Article
TA  - New Microbes New Infect.
JT  - New Microbes New Infect.
SO  - New Microbes New Infect. 2016 14: 98-105.

PMID- 30072959
VI  - 9
DP  - 2018
TI  - Genome variation in the model halophilic bacterium Salinibacter ruber.
PG  - 1499
AB  - 
AU  - Gonzalez-Torres P
AU  - Gabaldon T
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2018 9: 1499.

PMID- 9113112
VI  - 386
DP  - 1997
TI  - Mutagenic and epigenetic effects of DNA methylation.
PG  - 107-118
AB  - Tumorigenesis begins with the disregulated growth of an abnormal cell that has acquired the
      ability to divide more rapidly than its normal counterparts.  Alterations in global levels and
      regional changes in the patterns of DNA methylation are among the earliest and most frequent
      events known to occur in human cancers.  These changes in methylation may impair the proper
      expression and/or function of cell-cycle regulatory genes and thus confer a selective growth
      advantage to affected cells.  Developments in the field of cancer research over the past few
      years have led to an increased understanding of the role DNA methylation may play in
      tumorigenesis.  Many of these studies have investigated two major mechanisms by which DNA
      methylation may lead to aberrant cell cycle control: (1) through the generation of transition
      mutations via deamination-driven events resulting in the inactivation of tumor suppressor
      genes, or (2) by altering levels of gene expression through epigenetic effects at CpG islands.
      The mechanisms by which the normal function of growth regulatory genes may become affected by
      the mutagenic and epigenetic properties of DNA methylation will be discussed in the framework
      of recent discoveries in the field.
AU  - Gonzalgo ML
AU  - Jones PA
PT  - Journal Article
TA  - Mutat. Res.
JT  - Mutat. Res.
SO  - Mutat. Res. 1997 386: 107-118.

PMID- 4631356
VI  - 70
DP  - 1973
TI  - Separation of specific segments of transforming DNA after treatment with endodeoxyribonuclease.
PG  - 503-506
AB  - Hemophilus parainfluenzae endodeoxyribonuclease was used to degrade the DNA of
      H. influenzae and to follow the biological activity of 14 markers associated
      with this DNA.  It was found that some H. influenzae markers were completely
      inactivated by endodeoxyribonuclease treatment, while others appeared to retain
      all or almost all of their original activity.  The bulk of the H. influenzae
      DNA was reduced to double-stranded pieces of the order of 0.8 1 Mdaltons.
      Velocity sedimentation of the DNA in sucrose gradients disclosed that markers
      that retained biological activity were present in DNA particles that were of
      the order of 1 Mdaltons or larger, and indicated a close correlation between
      the size of the DNA fragment and the amount of biological activity retained.
      These data suggest that H. parainfluenzae endodeoxyribonuclease breaks DNA at
      specific sites.  The nalr marker was shown to have twice as much biological
      activity after treatment with endodeoxyribonuclease when assayed at saturating
      DNA concentrations.  In the linear portion of the DNA dose-response curve, the
      biological activity of this marker was reduced 3- to 10-fold compared to
      untreated DNA (in accord with the reduced size of its DNA).  These data
      demonstrate a specific enrichment of the nalr marker by about 6- to 20-fold,
      and suggest a technique for the separation and purification of specific
      segments of DNA.
AU  - Goodgal SH
AU  - Gromkova R
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1973 70: 503-506.

PMID- 23405353
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Mycoplasma hyorhinis Strain SK76.
PG  - e00101-12
AB  - Mycoplasma hyorhinis is a eubacterium belonging to the Mollicutes class and is responsible for
      porcine respiratory and arthritic diseases. It is also the major
      contaminant of mammalian tissue cultures in laboratories worldwide. Here, we
      report the complete genome sequence of M. hyorhinis strain SK76.
AU  - Goodison S
AU  - Urquidi V
AU  - Kumar D
AU  - Reyes L
AU  - Rosser CJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00101-12.

PMID- 
VI  - 0
DP  - 1977
TI  - DNA site recognition by the EcoRI restriction endonuclease and modification methylase.
PG  - 239-259
AB  - None
AU  - Goodman HM
AU  - Greene PJ
AU  - Garfin DE
AU  - Boyer HW
PT  - Journal Article
TA  - Nucleic Acid - Protein Recognition
JT  - Nucleic Acid - Protein Recognition
SO  - Nucleic Acid - Protein Recognition 1977 0: 239-259.

PMID- 11743194
VI  - 294
DP  - 2001
TI  - Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58.
PG  - 2323-2328
AB  - Agrobacterium tumefaciens is a plant pathogen capable of transferring a defined segment of DNA
      to a host plant, generating a gall tumor. Replacing the transferred  tumor-inducing genes with
      exogenous DNA allows the introduction of any desired gene into the plant. Thus, A. tumefaciens
      has been critical for the development of modern plant genetics and agricultural biotechnology.
      Here we describe the genome of A. tumefaciens strain C58, which has an unusual structure
      consisting of one circular and one linear chromosome. We discuss genome architecture and
      evolution and additional genes potentially involved in virulence and metabolic parasitism of
      host plants.
AU  - Goodner B et al
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2001 294: 2323-2328.

PMID- 2119891
VI  - 63
DP  - 1990
TI  - A self-splicing group I intron in the DNA polymerase gene of Bacillus subtilis bacteriophage SPO1.
PG  - 417-424
AB  - We report a self-splicing intron in bacteriophage SPO1, whose host is the gram-positive
      Bacillus subtilis. The intron contains all the conserved features of primary sequence and
      secondary structure previously described for the group IA introns of eukaryotic organelles and
      the gram-negative bacteriophage T4. The SPO1 intron contains an open reading frame of 522
      nucleotides. As in the T4 introns, this open reading frame begins in a region that is looped
      out of the secondary structure, but ends in a highly conserved region of the intron core. The
      exons encode SPO1 DNA polymerase, which is highly similar to E. coli DNA polymerase I. The
      demonstration of self-splicing introns in viruses of both gram-positive and gram-negative
      eubacteria lends further evidence for their early origin in evolution.
AU  - Goodrich-Blair H
AU  - Scarlato V
AU  - Gott JM
AU  - Xu M-Q
AU  - Shub DA
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1990 63: 417-424.

PMID- 8095080
VI  - 17C
DP  - 1993
TI  - A site- and strand-specific intron-endonuclease is required for marker exclusion.
PG  - 177
AB  - The virulent Bacillus subtilis bacteriophage SPO1 and SP82 belong to a closely related family
      that contain hydroxymethyluracil (HMU) in place of thymine in their DNA. The DNA polymerase
      gene of these phage is interrupted by a self-splicing group I intron. We have characterized
      two endonucleases, I-HmuI (encoded by SPO1) and I-HmuII (encoded by SP82) that are encoded
      entirely within the DNA polymerase intron. Other intron-endonucleases are initiators of
      "intron homing". They introduce a double-strand cleavage specifically on intron-less alleles
      and repair of this cleavage, using the intron-plus allele as a template, results in two
      intron-plus copies of DNA via unidirectional gene conversion. The HMU-phage
      intron-endonucleases have several unique features. First, they are strand- as well as
      site-specific, introducing a nick in the noncoding strand 4 nucleotides (nt) (I-HmuI) or 54 nt
      (I-HmuII) downstream of the 3' splice site of the intron, within exon II of the DNA
      polymerase gene. Second, the endonucleases cleave intron-plus as well as intron-less DNA.
      Third, the endonucleases show a distinct preference, both in vitro and in vivo, for the DNA of
      the heterologous phage. These differences in the HMU intron-endonucleases could reflect a
      difference in function. Previous reports indicated that in mixed infections genetic markers of
      SP82 are more likely to be carried by progeny than those of SP01. This exclusion occurs over
      10 kilobases of DNA surrounding the DNA polymerase gene. We have found that expression of
      I-HmuII by SP82 is required for this exclusion process. We hypothesize that the intron homing
      mechanism of I-HmuII has been expanded to confer a selective advantage on its host in
      competition with close relatives.
AU  - Goodrich-Blair H
AU  - Shub DA
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1993 17C: 177.

PMID- 8565067
VI  - 84
DP  - 1996
TI  - Beyond homing: Competition between intron endonucleases confers a selective advantage on flanking genetic markers.
PG  - 211-221
AB  - The closely related B. subtilis bacteriophages SPO1 and SP82 have similar introns inserted
      into a conserved domain of their DNA polymerase genes.  These introns encode endonucleases
      with unique properties.  Other intron-encoded "homing" endonucleases cleave both strands of
      intronless DNA; subsequent repair results in unidirectional gene conversion to the
      intron-containing allele.  In contrast, the enzymes described here cleave one strand on both
      intron-containing and intronless targets at different distances from their common intron
      insertion site.  Most surprisingly, each enzyme prefers DNA of the heterologous phage.  The
      SP82-encoded endonuclease is responsible for exclusion of the SPO1 intron and flanking genetic
      markers from the progeny of mixed infections, a novel selective advantage imparted by an
      intron to the genome in which it resides.
AU  - Goodrich-Blair H
AU  - Shub DA
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1996 84: 211-221.

PMID- 7937082
VI  - 22
DP  - 1994
TI  - The DNA polymerase genes of several HMU-bacteriophages have similar group I introns with highly divergent open reading frames.
PG  - 3715-3721
AB  - A previous report described the discovery of a group I, self-splicing intron
      in the DNA
      polymerase gene of the Bacillus subtilis bacteriophage SPO1.  In this study, the DNA
      polymerase genes of
      three close relatives of SPO1: SP82, 2C and Phi e, were also found to be interrupted by an
      intron.  All of these
      introns have group I secondary structures that are extremely similar to one another in
      primary sequence.
      Each is interrupted by an open reading frame that, unlike the intron core or exon sequences,
      are highly
      diverged.  Unlike the relaives of Escherichia coli bacteriophage T4, most of which do not
      have introns, this
      intron seems to be common among the relatives of SPO1.
AU  - Goodrich-Blair H
AU  - Shub DA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1994 22: 3715-3721.

PMID- 15858783
VI  - 18
DP  - 2005
TI  - Recognition in action: flipping pyrimidine dimers.
PG  - 193-195
AB  - DNA bases are normally sheltered within a double helix, but enzymes that modify and repair DNA
      gain access by flipping individual bases out
      of the double helix.
AU  - Goodsell DS
PT  - Journal Article
TA  - J. Mol. Recognit.
JT  - J. Mol. Recognit.
SO  - J. Mol. Recognit. 2005 18: 193-195.

PMID- 11897876
VI  - 20
DP  - 2002
TI  - The molecular perspective: Restriction endonucleases.
PG  - 190-191
AB  - We live in a remarkable age. Physicians now have an unprecedented range of options for helping
      their patients. Surgery and radiology are using advanced technologies to pinpoint treatments.
      Chemotherapeutic approaches are showing ever-greater effectiveness and specificity,
      approaching the goal of a "magic bullet." And we are now entering a time when we can make
      changes at the most basic level, introducing changes directly into the genetic code. Gene
      therapy, the ability to introduce new genes into living cells, holds great promise for the
      treatment of many diseases, including cancer. Restriction endonucleases are the molecules that
      spawned the field of biotechnology, the first of the many molecular tools that make gene
      therapy a reality. Bacteria build restriction endonucleases to protect themselves from attack
      by viruses. These enzymes cleave DNA at a specific sequence of nucleotides: for instance, one
      enzyme from Escherichia coli cuts the sequence GAATTC and another enzyme from Bacillus
      amyloliquefaciens will not cut it, but instead cuts the similar sequence GGATCC. Each species
      of bacterium protects its own DNA at its personal sequence by adding a bulky methyl group on a
      few of the bases, so only invading viral DNA, which does not have the protective methyl
      groups, is chopped up and destroyed. There are hundreds of forms of these restriction enzymes,
      made by different bacteria to cut DNA at different sequences.
AU  - Goodsell DS
PT  - Journal Article
TA  - Stem Cells
JT  - Stem Cells
SO  - Stem Cells 2002 20: 190-191.

PMID- 11854550
VI  - 7
DP  - 2002
TI  - The Molecular Perspective: Restriction Endonucleases.
PG  - 82-83
AB  - We live in a remarkable age. Physicians now have an unprecedented range of options for helping
      their patients. Surgery and radiology are using advanced technologies to pinpoint treatments.
      Chemotherapeutic approaches are showing ever-greater effectiveness and specificity,
      approaching the goal of a "magic bullet." And we are now entering a time when we can make
      changes at the most basic level, introducing changes directly into the genetic code. Gene
      therapy, the ability to introduce new genes into living cells, holds great promise for the
      treatment of many diseases, including cancer. Restriction endonucleases are the molecules that
      spawned the field of biotechnology, the first of the many molecular tools that make gene
      therapy a reality. Bacteria build restriction endonucleases to protect themselves from attack
      by viruses. These enzymes cleave DNA at a specific sequence of nucleotides: for instance, one
      enzyme from Escherichia coli cuts the sequence GAATTC and another enzyme from Bacillus
      amyloliquefaciens will not cut it, but instead cuts the similar sequence GGATCC. Each species
      of bacterium protects its own DNA at its personal sequence by adding a bulky methyl group on a
      few of the bases, so only invading viral DNA, which does not have the protective methyl
      groups, is chopped up and destroyed. There are hundreds of forms of these restriction enzymes,
      made by different bacteria to cut DNA at different sequences.
AU  - Goodsell DS
PT  - Journal Article
TA  - The Oncologist
JT  - The Oncologist
SO  - The Oncologist 2002 7: 82-83.

PMID- 21695235
VI  - 7
DP  - 2011
TI  - Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis.
PG  - E1002070
AB  - The plant-pathogenic fungus Mycosphaerella graminicola (asexual stage:
      Septoria tritici) causes septoria tritici blotch, a disease that greatly
      reduces the yield and quality of wheat. This disease is economically
      important in most wheat-growing areas worldwide and threatens global food
      production. Control of the disease has been hampered by a limited
      understanding of the genetic and biochemical bases of pathogenicity,
      including mechanisms of infection and of resistance in the host. Unlike
      most other plant pathogens, M. graminicola has a long latent period during
      which it evades host defenses. Although this type of stealth pathogenicity
      occurs commonly in Mycosphaerella and other Dothideomycetes, the largest
      class of plant-pathogenic fungi, its genetic basis is not known. To
      address this problem, the genome of M. graminicola was sequenced
      completely. The finished genome contains 21 chromosomes, eight of which
      could be lost with no visible effect on the fungus and thus are
      dispensable. This eight-chromosome dispensome is dynamic in field and
      progeny isolates, is different from the core genome in gene and repeat
      content, and appears to have originated by ancient horizontal transfer
      from an unknown donor. Synteny plots of the M. graminicola chromosomes
      versus those of the only other sequenced Dothideomycete, Stagonospora
      nodorum, revealed conservation of gene content but not order or
      orientation, suggesting a high rate of intra-chromosomal rearrangement in
      one or both species. This observed "mesosynteny" is very different from
      synteny seen between other organisms. A surprising feature of the M.
      graminicola genome compared to other sequenced plant pathogens was that it
      contained very few genes for enzymes that break down plant cell walls,
      which was more similar to endophytes than to pathogens. The stealth
      pathogenesis of M. graminicola probably involves degradation of proteins
      rather than carbohydrates to evade host defenses during the biotrophic
      stage of infection and may have evolved from endophytic ancestors.
AU  - Goodwin SB et al
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2011 7: E1002070.

PMID- 26380646
VI  - 10
DP  - 2015
TI  - Improved-high-quality draft genome sequence of Rhodococcus sp. JG-3, a eurypsychrophilic Actinobacteria from Antarctic Dry Valley permafrost.
PG  - 61
AB  - The actinobacterium Rhodococcus sp. JG-3 is an aerobic, eurypsychrophilic, soil bacterium
      isolated from permafrost in the hyper arid Upper Dry Valleys of Antarctica. It is yellow
      pigmented, gram positive, moderately halotolerant and capable of growth from 30 degrees C down
      to at least -5 degrees C. The 5.28 Mb high-quality-draft genome is arranged into 6 scaffolds,
      containing 9 contigs and  4998 protein coding genes, with 64 % GC content. Increasing the
      availability of genome sequences from cold-adapted species is crucial to gaining a better
      understanding of the molecular traits of cold adaptation in microbes.
AU  - Goordial J
AU  - Raymond-Bouchard I
AU  - Ronholm J
AU  - Shapiro N
AU  - Woyke T
AU  - Whyte L
AU  - Bakermans C
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 61.

PMID- 6310398
VI  - 309
DP  - 1983
TI  - Prenatal Diagnosis of Sickle-Cell anemia in the First Trimester of Pregnancy.
PG  - 831-833
AB  - To investigate the usefulness of chorionic biopsy for prenatal diagnosis of
      sickle-cell anemia by restriction-endonuclease analysis of fetal DNA, we
      studies 30 pregnancies before elective abortion.  When the reproductibility of
      the technique for obtaining adequate DNA samples was established, we
      successfully applied the test to five pregnancies at risk for sickle-cell
      anemia.  In two cases, sickle-cell disease of the fetus led to a decision to
      terminate the pregnancy.  In three other cases, a normal or AS genotype was
      demonstrated.  One normal infant has been born, and one other pregnancy is
      continuing normally.  In one case in which fetal death was observed three weeks
      after ampling, placental abnormalties found on histologic examination were
      compatible with a chromosomal aberration.  Our study shows that chorionic
      biopsy is feasible for the prenatal diagnosis of sickle-cell disease before the
      10th gestational week.  If subsequent experience demonstrates this technique to
      be safe enough for mother and fetus, the ability to test in early pregnancy may
      make prenatal diagnosis acceptable to more couples at risk for serious genetic
      disorders.
AU  - Goossens MD
AU  - Dumez Y
AU  - Kaplan L
AU  - Lupker M
AU  - Chabret C
AU  - Henrion R
AU  - Rosa J
PT  - Journal Article
TA  - N. Engl. J. Med.
JT  - N. Engl. J. Med.
SO  - N. Engl. J. Med. 1983 309: 831-833.

PMID- 19258268
VI  - 53
DP  - 2009
TI  - Genetic organization of transposase regions surrounding blaKPC carbapenemase genes on plasmids from Klebsiella strains isolated in a New York City hospital.
PG  - 1998-2004
AB  - Carbapenem-resistant Klebsiella strains carrying Klebsiella pneumoniae
      carbapenemases (KPC) are endemic to New York City and are spreading across
      the United States and internationally. Recent studies have indicated that
      the KPC structural gene is located on a 10-kb plasmid-borne element
      designated Tn4401. Fourteen Klebsiella pneumoniae strains and one
      Klebsiella oxytoca strain isolated at a New York City hospital in 2005
      carrying either bla(KPC-2) or bla(KPC-3) were examined for isoforms of
      Tn4401. Ten of the Klebsiella strains contained a 100-bp deletion in
      Tn4401, corresponding to the Tn4401a isoform. The presence of this
      deletion adjacent to the upstream promoter region of bla(KPC) in Tn4401a
      resulted in a different -35 promoter sequence of TGGAGA than that of
      CTGATT present in isoform Tn4401b. Complete sequencing of one plasmid
      carrying bla(KPC) from each of three nonclonal isolates indicated the
      presence of genes encoding other types of antibiotic resistance
      determinants. The 70.6-kb plasmid from K. pneumoniae strain S9 carrying
      bla(KPC-2) revealed two identical copies of Tn4401b inserted in an inverse
      fashion, but in this case, one of the elements disrupted a group II
      self-splicing intron. In K. pneumoniae strain S15, the Tn4401a element
      carrying bla(KPC-2) was found on both a large 120-kb plasmid and a smaller
      24-kb plasmid. Pulsed-field gel electrophoresis results indicate that the
      isolates studied represent a heterogeneous group composed of unrelated as
      well as closely related Klebsiella strains. Our results suggest that
      endemic KPC-positive Klebsiella strains constitute a generally nonclonal
      population comprised of various alleles of bla(KPC) on several distinct
      plasmid genetic backgrounds. This study increases our understanding of the
      genetic composition of the evolving and expanding role of KPC-producing,
      healthcare-associated, gram-negative pathogens.
AU  - Gootz TD
AU  - Lescoe MK
AU  - Dib-Hajj F
AU  - Dougherty BA
AU  - He W
AU  - Della-Latta P
AU  - Huard RC
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2009 53: 1998-2004.

PMID- Not carried by PubMed...
VI  - 57
DP  - 1995
TI  - Molecular cloning and biochemical characterization of DsaV methyltransferase from Dactylococcopsis salina.
PG  - 121
AB  - The methyltransferase (Mtase) in the DsaV restriction-modification system methylates within
      5'-CCNGG sequences.  I have cloned the gene for this Mtase and characterized it.  The
      predicted sequence of the Mtase protein contains sequence motifs conserved among all
      cytosine-5 Mtases and is most similar to other Mtases that methylate CCNGG sequences -- namely
      M.ScrFI and M.SsoII.  The "variable" region within the three enzymes that methylate CCNGG can
      be aligned with the sequences of two enzymes that methylate CCWGG sequences.  Remarkably, two
      segments within this region contain significant similarity with the region of M.HhaI that is
      known to contact DNA bases.  These aligments suggest that many cytosine-5 Mtases are likely to
      interact with DNA using a similar structural framework.  I have developed a simple new method
      that can identify the base methylated by a sequence-specific DNA methyltransferase and have
      used it to identify the cytosine that is methylated by DsaV methyltransferase (M.DsaV) within
      its recognition sequence 5'-CCNGG.  The method utilizes the fact that exonuclease III of E.
      coli does not degrade DNA ends with 3' overhangs and cannot hydrolyze a phosphorothioate
      linkage.  DNA duplexes containing phosphorothioate linkages at specific positions were
      methylated with M.DsaV in the presence of [methyl-3H] S-adenosylmethionine and were subjected
      to exonuclease III digestion.  The pattern of [methyl-3H] dCMP release from the duplexes was
      consistent with the methylation of the internal cytosine in CCNGG, but not of the outer
      cytosine.  Methylation of CCWGG (W = A or T) sequences at the internal cytosines is native to
      E. coli and is not restricted by the modified cytosine restriction (Mcr) systems.
      Surprisingly, the gene for M.DsaV was significantly restricted by the McrBC system.  I
      interpret this to mean that M.DsaV may occasionally methylate at sequences other than CCNNGG
      or may occasionally methylate the outer cytosine in its recognition sequence.  I have also
      shown for the first time that M.EcoRII methylates at CCSGG sites and other non-canonical sites
      using a plasmid that substantially overproduces M.EcoRII.  This result suggests that C5
      methylates may occasionally methylate cellular DNA at non-canonical sites and that E. coli
      methylation specific restriction system and DNA mismatch correction systems may have evolved
      to accommodate this fact.
AU  - Gopal J
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1995 57: 121.

PMID- 7870587
VI  - 23
DP  - 1995
TI  - Determination of methylation specificity of DsaV methyltransferase by a simple biochemical method.
PG  - 29-35
AB  - We have developed a simple new method that can identify the base methylated by a
      sequence-specific DNA methyltransferase and have used it to identify the cytosine that is
      methylated by DsaV methyltransferase (M.DsaV) within its recognition sequence 5'-CCNGG. The
      method utilizes the fact that exonuclease III of E.coli does not degrade DNA ends with 3'
      overhangs and cannot hydrolyze a phosphorothioate linkage. DNA duplexes containing
      phosphorothioate linkages at specific positions were methylated with M.DsaV in the presence of
      [methyl-3H] S-adenosylmethionine and were subjected to exonuclease III digestion. The pattern
      of [methyl-3H] dCMP release from the duplexes was consistent with the methylation of the
      internal cytosine in CCNGG, but not of the outer cytosine. To establish the accuracy of this
      method, we confirmed the known specificity of EcoRII methyltransferase by the method. We also
      confirmed the specificity of M.DsaV using an established biochemical method that involves the
      use of a type IIS restriction enzyme. Methylation of CCWGG (W=A or T) sequences at the
      internal cytosines is native to E. coli and is not restricted by the modified cytosine
      restriction (Mcr) systems. Surprisingly, the gene for M.DsaV was significantly restricted by
      the McrBC system. We interpret this to mean that M.DsaV may occasionally methylate at
      sequences other than CCNGG or may occasionally methylate the outer cytosine in its recognition
      sequence.
AU  - Gopal J
AU  - Bhagwat AS
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1995 23: 29-35.

PMID- 7971279
VI  - 22
DP  - 1994
TI  - DsaV methyltransferase and its isoschizomers contain a conserved segment that is similar to the segment in HhaI methyltransferase that is in contact with DNA bases.
PG  - 4482-4488
AB  - The methyltransferase (MTase) in the DsaV restriction-modification system methylates within
      5'-CCNGG sequences. We have cloned the gene for this MTase and determined its sequence. The
      predicted sequence of the MTase protein contains sequence motifs conserved among all
      cytosine-5 MTases and is most similar to other MTases that methylate CCNGG sequences, namely
      M.ScrFI and M.SsoII. All three MTases methylate the internal cytosine within their recognition
      sequence. The 'variable' region within the three enzymes that methylate CCNGG can be aligned
      with the sequences of two enzymes that methylate CCWGG sequences. Remarkably, two segments
      within this region contain significant similarity with the region of M.HhaI that is known to
      contact DNA bases. These alignments suggest that many cytosine-5 MTases are likely to interact
      with DNA using a similar structural framework.
AU  - Gopal J
AU  - Yebra MJ
AU  - Bhagwat AS
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1994 22: 4482-4488.

PMID- 7607527
VI  - 157
DP  - 1995
TI  - Cloning and characterization of the gene encoding the DsaV methyltransferase.
PG  - 61-63
AB  - A gene encoding the M.DsaV methyltransferase was cloned and characterized.  The enzyme
      methylates the internal cytosines in the 5'-CCTGG recognition sequence, as determined by a
      novel rapid method employing 3H label and exonuclease III.
AU  - Gopal J
AU  - Yebra MJ
AU  - Bhagwat AS
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 61-63.

PMID- 
VI  - 
DP  - 2009
TI  - Functional characterization of the de novo DNA methyltransferase DNMT3B.
PG  - 1-215
AB  - DNA methylation is an epigenetic mark that is required for transcriptional repression in
      mammalian development, imprinting, and in the maintenance of genome stability. Genome-wide
      methylation patterns are established and maintained by three DNA methyltransferases (DNMTs)-
      DNMT1, DNMT3A, and DNMT3B. DNMT3B is specifically involved in silencing the satellite repeats
      at the centromeric and pericentromeric regions. The role of DNMT3B at the centromeric region
      is also emphasized by mitotic defects arising due to chromosome instability observed in ICF
      syndrome, a disease caused by germline mutations in DNMT3B. Although the mechanism of DNA
      methylation is well known, the targeting of DNA methylation and DNMT3B to certain genomic loci
      remains poorly understood. DNMT3B is also regulated by alternative splicing. Several DNMT3B
      splice variants are overexpressed in tumor cells and negatively regulate normal DNMT3B
      mediated DNA methylation. Therefore it is important to understand the significance of DNMT3B
      splice variants in development and tumorigenesis. In the present study, a yeast two-hybrid
      screening was performed and several novel DNMT3B protein interactions were identified. Of the
      several proteins identified, the interaction of DNMT3B with the mammalian chromatin associated
      factor MCAF and the chromodomain helicase DNA binding protein CHD3 were confirmed, and need
      further characterization. The interaction between DNMT3B and the constitutive centromeric
      protein CENP-C was confirmed in mammalian cells. Results from siRNA knock downs, bisulfite
      genomic sequencing and ChIP, demonstrate that CENP-C recruits DNA methylation and DNMT3B to
      both centromeric and pericentromeric satellite repeats. CENP-C and DNMT3B influence the
      histone modifications in satellite repeat regions, including marks characteristic of
      centromeric chromatin and disruption of this interaction causes elevated transcription of
      centromeric repeats. Loss of CENP-C or DNMT3B leads to elevated chromosome misalignment and
      segregation defects during mitosis. Taken together, the interaction between CENP-C and DNMT3B
      suggests a novel mechanism by which DNA methylation is targeted to discrete regions of the
      genome and contributes to chromosomal stability. In another study, a novel alternatively
      spliced form of DNMT3B lacking exon 5 was identified and characterized. This variant was
      termed DNMT3B3"5 because of its close resemblance with the ubiquitously expressed DNMT3B3
      isoform. The novel splice variant lacking exon 5 is highly expressed in pluripotent cells and
      neural tissues, and is conserved in the mouse and is re-expressed on converting differentiated
      mEFs into pluripotent iPS cells. DNMT3B3"5 also displays altered expression in human tumor
      cell lines as well as an altered subcellular localization. Ectopic overexpression of DNMT3B3"5
      resulted in repetitive element hypomethylation. Taken together, these results demonstrate that
      alternative splicing of exon 5 may play an important role in stem cell maintenance or
      differentiation and exon 5 could influence the functional properties of DNMT3B.
AU  - Gopalakrishnan S
PT  - Journal Article
TA  - Ph.D. Thesis, Univ. of Florida, Gainesville
JT  - Ph.D. Thesis, Univ. of Florida, Gainesville
SO  - Ph.D. Thesis, Univ. of Florida, Gainesville 2009 : 1-215.

PMID- 24604659
VI  - 2
DP  - 2014
TI  - Whole-Genome Sequences of Six Salmonella enterica Serovar Bovismorbificans Isolates Associated with a 2011 Multistate Hummus-Borne Outbreak.
PG  - e01239-13
AB  - We present six draft genome sequences of Salmonella enterica serovar Bovismorbificans from
      isolates associated with the 2011 hummus-borne multistate
      outbreak. All six genome sequences indicate the presence of two plasmids, one of
      which demonstrates similarity to the 93-kb pSLT2 IncF-type plasmid of Salmonella
      enterica serovar Typhimurium.
AU  - Gopinath G
AU  - Jean-Gilles BJ
AU  - Grim C
AU  - Blaylock M
AU  - Blackwell R
AU  - Merid S
AU  - Diallo A
AU  - Hanes D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01239-13.

PMID- 24604660
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Nine Salmonella enterica Serovar Bovismorbificans Isolates from Various Sources.
PG  - e01249-13
AB  - The sequences of nine genomes of Salmonella enterica serovar Bovismorbificans were compared to
      study the diversity and distribution of this emerging virulent
      serovar. These whole-genome sequences fill some gaps in knowledge of the
      diversity of the isolates used in this investigation.
AU  - Gopinath G
AU  - Jean-Gilles BJ
AU  - Grim C
AU  - Hanes D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01249-13.

PMID- 24309737
VI  - 1
DP  - 2013
TI  - Genome Sequences of Two Enterobacter pulveris Strains, 601/05T (=LMG 24057T =DSM  19144T) and 1160/04 (=LMG 24058 =DSM 19146), Isolated from Fruit Powder.
PG  - e00991-13
AB  - We report the draft genome sequences of the Enterobacter pulveris strains 601/05(T)
      (=LMG24057(T) =DSM19144(T)) and 1160/04 (=LMG24058 =DSM19146), isolated
      from fruit powder. The genome assemblies for the E. pulveris type strain,
      LMG24057, and strain LMG24058 have sizes of 4,708,624 and 4,811,103 bp and G+C
      contents of 56.6% and 56.5%, respectively.
AU  - Gopinath GR
AU  - Grim CJ
AU  - Tall BD
AU  - Mammel MK
AU  - Sathyamoorthy V
AU  - Trach LH
AU  - Chase HR
AU  - Fanning S
AU  - Stephan R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00991-13.

PMID- 6273824
VI  - 9
DP  - 1981
TI  - The effect of several nucleic acid binding drugs on the cleavage of d(GGAATTCC) and pBR322 by the EcoRI restriction endonuclease.
PG  - 6115-6127
AB  - The endonucleolytic action of the EcoRI restriction enzyme on the
      double-stranded oligonucleotide d(GGAATTCC) and the supercoiled plasmid DNA
      pBR322 is inhibited by actinomycin D, ethidium bromide, proflavin, distamycin A
      and netropsin.  Half-maximal inhibition is observed at around 100 micromolar
      concentrations for the intercalating drugs, and around 0.1 to 1 micromolar
      concentrations for netropsin and distamycin A.  The inhibitory activity of
      these drugs can be correlated with their affinity to the oligonucleotide and
      the plasmid DNA.  Since at high concentrations of the drugs a complete
      inhibition is observed, it is concluded that the effect of the drugs on the
      sterochemistry of the EcoRI site is such that recognition is excluded.
AU  - Goppelt M
AU  - Langowski J
AU  - Pingoud A
AU  - Haupt W
AU  - Urbanke C
AU  - Mayer H
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1981 9: 6115-6127.

PMID- 6245864
VI  - 104
DP  - 1980
TI  - The interaction of the EcoRI restriction endonuclease with its substrate:  A physico-chemical study employing natural and synthetic oligonucleotides and polynucleotides.
PG  - 101-107
AB  - The interaction of the EcoRI restriction endodeoxyribonuclease with
      polynucleotides has been studied in a qualitative manner by an affinity
      adsorption technique using polynucleotides immobilized on cellulose.  It is
      shown that EcoRI binds to single-stranded and double-stranded
      polyribonucleotides and polydeoxyribonucleotides.  Mg2+ ions are not required
      for binding.  In order to define differences between specific and non-specific
      binding we have investigated the interaction of EcoRI with d(TAAATG),
      d(TTACAT), d(GAATTC) and d(GGAATTCC).  We have synthesized for this purpose
      d(TAAATG), d(TTACAT) and d(GAATTC) by the diester approach.  d(GAATTC) and
      d(GGAATTCC) are self complementary.  Differential melting experiments show that
      the octanucleotide has a melting point of 28C under ionic conditions where the
      hexanucleotide is single-stranded even below 0C.  Correspondingly, the
      octanucleotide is cleaved by EcoRI, while the hexanucleotide is not.  The
      binding of oligonucleotides to EcoRI can be monitored by the circular dichroism
      of the enzyme.  Titrations show that in the absence of Mg2+ ions all
      oligonucleotides are bound with similar magnitude:  Ka - 10/7 M-1.  Complex
      formation is weakened with increasing temperature, corresponding to a delta Ho
      of -21 kJ/mol and increasing ionic strength, corresponding to an involvement of
      two ion-pair bonds between DNA and enzyme.  Mg2+ ions have no significant
      influence on the binding of d(TAAATG), d(TTACAT) and d(GAATTC) to the enzyme.
      The binding of d(GGAATTCC) to EcoRI is strengthened by a factor of 50 in the
      presence of Mg2+ ions, as measured by cleavage experiments using d(GAATTC) as a
      competing inhibitor in the enzymatic assay.
AU  - Goppelt M
AU  - Pingoud A
AU  - Maass G
AU  - Mayer H
AU  - Koster H
AU  - Frank R
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1980 104: 101-107.

PMID- 7920259
VI  - 3
DP  - 1994
TI  - Self-splicing group I and group II introns encode homologous (putative) DNA endonucleases of a new family.
PG  - 1117-1120
AB  - A new family of protein domains consisting of 50-80 amino acid residues is described.  It is
      composed of nearly 40 members, including domains encoded by plastid and phage group I introns;
      mitochondrial, plastid, and bacterial group II introns; eubacterial genomes and plasmids; and
      phages.  The name "EX1HH-HX3H" was coined for both domain and family.  It is based on 2 most
      prominent amino acid sequene motifs, each encompassing a pair of highly conserved histidine
      residues in a specific arrangement: EX1HH and HX3H.  The "His" motifs often alternate with
      amino- and carboxy-terminal motifs of a new type of Zn-finger-like structure
      CX2,4CX29-54[CH]X2,3[CH].  The EX1HH-HX3H domain in eubacterial E2-type bacteriocins and in
      phage RB3 (wild variant of phage T4) product of the nrdB group I intron was reported to be
      essential for DNA endonuclease activity of these proteins.  In other proteins, the EX1HH-HX3H
      domain is hypothesized to possess DNase activity as well.  Presumably, this activity promotes
      movement (rearrangement) of group I and group II introns encoding the EX1HH-HX3H domain and
      other gene targets.  In the case of Escherichia coli restrictase McrA and possibly several
      related proteins, it appears to mediate the restriction of alien DNA molecules.
AU  - Gorbalenya AE
PT  - Journal Article
TA  - Protein Sci.
JT  - Protein Sci.
SO  - Protein Sci. 1994 3: 1117-1120.

PMID- 1657645
VI  - 291
DP  - 1991
TI  - Endonuclease (R) subunits of type-I and type-III restriction-modification enzymes contain a helicase-like domain.
PG  - 277-281
AB  - A statistically significant amino acid sequence similarity is demonstrated
      between the endonuclease (R) subunit of the EcoKI restriction-modification
      (R-M) enzyme, and RNA and DNA helicases of the so-called 'DEAD' family.  It is
      further shown that all three known sequences of R subunits of type-I and
      type-III R-M enzymes contain the conserved amino acid sequence motifs typical
      of the previously described helicase superfamily II (1989) Nucl. Acids Res.
      17,4713-4730.  A hypothesis is proposed that these enzymes may exert helicase
      activity possibly required for local unwinding of DNA in the cleavage sites.
AU  - Gorbalenya AE
AU  - Koonin EV
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1991 291: 277-281.

PMID- 2835958
VI  - 13
DP  - 1987
TI  - Chemical synthesis and characteristics of oligonucleotide substrates for restriction endonuclease BamHI and methylase Eco dam.
PG  - 1629-1637
AB  - Oligodeoxyribonucleotides which form a number of duplexes, containing the recognition
      sequences for endonuclease BamHI and DNA methylase Eco dam, were synthesized by the
      phosphotriester approach. Furthermore, synthesis of 3'-phosphorylated
      oligodeoxyribonucleotides from corresponding S-methyl phosphorothioate triester oligomers is
      described. The synthetic duplexes are characterized by some defects in the recognition
      sequences for endonuclease BamHI and methylase Eco dam, viz. nick, absence of an
      internucleotide phosphate, modifications (including partial single-strandedness) of the
      recognition site. Interaction of the enzymes with these synthetic substrates was investigated.
AU  - Gorbunov YA
AU  - Zinovev VV
AU  - Rechkunova NI
AU  - Ovechkina LG
AU  - Popov SG
AU  - Malygin EG
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1987 13: 1629-1637.

PMID- 10320585
VI  - 32
DP  - 1999
TI  - Identification of variable regions in the genomes of tubercle bacilli using bacterial artificial chromosome arrays.
PG  - 643-655
AB  - Whole-genome comparisons of the tubercle bacilli were undertaken using ordered bacterial
      artificial chromosome (BAC) libraries of Mycobacterium
      tuberculosis and the vaccine strain, Mycobacterium bovis BCG-Pasteur,
      together with the complete genome sequence of M. tuberculosis H37Rv.
      Restriction-digested BAC arrays of M. tuberculosis H37Rv were used in
      hybridization experiments with radiolabelled M. bovis BCG genomic DNA to
      reveal the presence of 10 deletions (RD1-RD10) relative to M.
      tuberculosis. Seven of these regions, RD4-RD10, were also found to be
      deleted from M. bovis, with the three M. bovis BCG-specific deletions
      being identical to the RD1-RD3 loci described previously. The distribution
      of RD4-RD10 in Mycobacterium africanum resembles that of M. tuberculosis
      more closely than that of M. bovis, whereas an intermediate arrangement
      was found in Mycobacterium microti, suggesting that the corresponding
      genes may affect host range and virulence of the various tubercle bacilli.
      Among the known products encoded by these loci are a copy of the proposed
      mycobacterial invasin Mce, three phospholipases, several PE, PPE and
      ESAT-6 proteins, epoxide hydrolase and an insertion sequence. In a
      complementary approach, direct comparison of BACs uncovered a third class
      of deletions consisting of two M. tuberculosis H37Rv loci, RvD1 and RvD2,
      deleted from the genome relative to M. bovis BCG and M. bovis. These
      deletions affect a further seven genes, including a fourth phospholipase,
      plcD. In summary, the insertions and deletions described here have
      important implications for our understanding of the evolution of the
      tubercle complex.
AU  - Gordon SV
AU  - Brosch R
AU  - Billault A
AU  - Garnier T
AU  - Eiglmeier K
AU  - Cole ST
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1999 32: 643-655.

PMID- 
VI  - 50
DP  - 2011
TI  - Molecular mechanisms of bacteriophage resistance of lactic acid bacteria.
PG  - 265-273
AB  - Lactic acid bacteria (LAB) constitute a heterogeneous group of bacteria, which are found in
      diverse environments, such as the human body or plants, and are traditionally used to produce
      fermented food. Food bio-transformation in industrial processes increases the economical
      importance of LAB. However, conditions that exist in industrial facilities do not seem to be
      an optimal environment for bacteria. During technological processes, which take place in
      enclosed space, the intensity of physical (temperature shift), chemical (acids) or biological
      (phages) stress factors raises dramatically. In the dairy industry, bacteriophage
      contamination is regarded as a serious problem due to the disturbance or arrest of the
      production processes, which results in significant economical losses. It is well documented
      that LAB evolved defense systems against bacteriophages, which allow them to survive in harsh
      conditions. Therefore, bacteria used in food industry are selected for high level of
      bacteriophage resistance. According to the mode of action, natural bacterial defense systems
      against their predators were divided into 5 categories: (i) inhibition of phage adsorption,
      (ii) blocking of phage DNA injection, (iii) phage abortive infection systems, (iv) restriction
      modification systems, (v) CRISPR/Cas systems. Remarkably, the majority of known bacteriophage
      resistance systems are plasmid-encoded. In this context, future studies on phage resistance
      mechanisms as well as plasmid sequencing may have an impact on solving the problem of phage
      infections in the dairy industry.
AU  - Gorecki RK
AU  - Bardowski JK
PT  - Journal Article
TA  - Postepy Mikrobiologii
JT  - Postepy Mikrobiologii
SO  - Postepy Mikrobiologii 2011 50: 265-273.

PMID- 21789242
VI  - 6
DP  - 2011
TI  - Adaptative potential of the Lactococcus lactis IL594 strain encoded in its 7 plasmids.
PG  - e22238
AB  - The extrachromosomal gene pool plays a significant role both in evolution and in the
      environmental adaptation of bacteria.  The L. lactis subsp. lactis IL594 strain contains seven
      plasmids, named pIL1 to pIL7, and is the parental strain of the plasmidfree L. lactis IL1403,
      which is one of the best characterized lactococcal strains of LAB. Complete nucleotide
      sequences of pIL1 (6,382 bp), pIL2 (8,277 bp), pIL3 (19,244 bp), pIL4 (48,979), pIL5 (23,395),
      pIL6 (28,435 bp) and pIL7 (28,546) were
      established and deposited in the generally accessible database (GeneBank). Nine highly
      homologous repB-containing replicons, belonging to the lactococcal theta-type replicons, have
      been identified on the seven plasmids. Moreover, a putative region involved in conjugative
      plasmid mobilization was found on four plasmids, through identification of the
      presence of mob genes and/or oriT sequences. Detailed bioinformatic analysis of the plasmid
      nucleotide sequences provided new insight into the repertoire of plasmid-encoded functions in
      L. lactis, and indicated that plasmid genes from IL594 strain can be important for L. lactis
      adaptation to specific environmental conditions (e.g. genes coding for proteins involved in
      DNA repair or cold shock response) as well as for technological processes (e.g. genes encoding
      citrate and lactose utilization, oligopeptide transport, restriction-modification system).
      Moreover, global gene analysis indicated
      cooperation between plasmid- and chromosome-encoded metabolic pathways.
AU  - Gorecki RK
AU  - Koryszewska-Baginska A
AU  - Golebiewski M
AU  - Zylinska J
AU  - Grynberg M
AU  - Bardowski JK
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2011 6: e22238.

PMID- 26203328
VI  - 10
DP  - 2015
TI  - Draft genome sequence and characterization of Desulfitobacterium hafniense PCE-S.
PG  - 15
AB  - This genome report describes the draft genome and the physiological characteristics of
      Desulfitobacterium hafniense PCE-S, a Gram-positive bacterium
      known to dechlorinate tetrachloroethene (PCE) to dichloroethene by a PCE
      reductive dehalogenase. The draft genome has a size of 5,666,696 bp with a G + C
      content of 47.3%. The genome is very similar to the already sequenced
      Desulfitobacterium hafniense Y51 and the type strain DCB-2. We identified two
      complete reductive dehalogenase (rdh) genes in the genome of D. hafniense PCE-S,
      one of which encodes PceA, the PCE reductive dehalogenase, and is located on a
      transposon. Interestingly, this transposon structure differs from the
      PceA-containing transposon of D. hafniense Y51. The second rdh encodes an unknown
      reductive dehalogenase, highly similar to rdhA 7 found in D. hafniense DCB-2, in
      which the corresponding gene is disrupted. This reductive dehalogenase might be
      responsible for the reductive dechlorination of 2,4,5-trichlorophenol and
      pentachlorophenol, which is mediated by D. hafniense PCE-S in addition to the
      reductive dechlorination of PCE.
AU  - Goris T
AU  - Hornung B
AU  - Kruse T
AU  - Reinhold A
AU  - Westermann M
AU  - Schaap PJ
AU  - Smidt H
AU  - Diekert G
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 15.

PMID- 19897645
VI  - 192
DP  - 2010
TI  - A genomic island defines subspecies-specific virulence features of the host-adapted pathogen Campylobacter fetus subsp. venerealis.
PG  - 502-517
AB  - The pathogen Campylobacter fetus comprises two subspecies, C. fetus subsp.
      fetus and C. fetus subsp. venerealis. Although these taxa are highly
      related on the genome level, they are adapted to distinct hosts and
      tissues. C. fetus subsp. fetus infects a diversity of hosts, including
      humans, and colonizes the gastrointestinal tract. In contrast, C. fetus
      subsp. venerealis is largely restricted to the bovine genital tract,
      causing epidemic abortion in these animals. In light of their close
      genetic relatedness, the specific niche preferences make the C. fetus
      subspecies an ideal model system to investigate the molecular basis of
      host adaptation. In this study, a subtractive-hybridization approach was
      applied to the genomes of the subspecies to identify different genes
      potentially underlying this specificity. The comparison revealed a genomic
      island uniquely present in C. fetus subsp. venerealis that harbors several
      genes indicative of horizontal transfer and that encodes the core
      components necessary for bacterial type IV secretion. Macromolecular
      transporters of this type deliver effector molecules to host cells,
      thereby contributing to virulence in various pathogens. Mutational
      inactivation of the putative secretion system confirmed its involvement in
      the pathogenicity of C. fetus subsp. venerealis.
AU  - Gorkiewicz G
AU  - Kienesberger S
AU  - Schober C
AU  - Scheicher SR
AU  - Gully C
AU  - Zechner R
AU  - Zechner EL
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 502-517.

PMID- 23144376
VI  - 194
DP  - 2012
TI  - Draft Genome Sequences of Actinomyces timonensis Strain 7400942T and Its Prophage.
PG  - 6613-6614
AB  - A draft genome sequence of Actinomyces timonensis, an anaerobic bacterium isolated from a
      human clinical osteoarticular sample, is described here.
      CRISPR-associated proteins, insertion sequence, and toxin-antitoxin loci were
      found on the genome. A new virus or provirus, AT-1, was characterized.
AU  - Gorlas A
AU  - Gimenez G
AU  - Raoult D
AU  - Roux V
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6613-6614.

PMID- 22887657
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Methanomassiliicoccus luminyensis, the Largest Genome of a Human-Associated Archaea Species.
PG  - 4745
AB  - The present study describes the complete and annotated genome sequence of
      Methanomassiliicoccus luminyensis strain B10 (DSM 24529(T), CSUR P135), which was
      isolated from human feces. The 2.6-Mb genome represents the largest genome of a
      methanogenic euryarchaeon isolated from humans. The genome data of M. luminyensis
      reveal unique features and horizontal gene transfer events, which might have
      occurred during its adaptation and/or evolution in the human ecosystem.
AU  - Gorlas A
AU  - Robert C
AU  - Gimenez G
AU  - Drancourt M
AU  - Raoult D
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4745.

PMID- Not carried by PubMed...
VI  - 0
DP  - 1991
TI  - Synthesis of EcoRV restriction endonuclease in Escherichia coli continuous culture.  II. Effects of cultivation conditions on efficiency of thermoinduction of synthesis of cloned EcoRV restriction endonuclease.
PG  - 27-30
AB  - Effects of growth rate of recombinant cells of E. coli K802 (plLRV8) and of induction
      conditions on the efficiency of thermoinduction of synthesis of EcoRV restriction endonuclease
      cloned in PILRV8 plasmid controlled by the pR promoter of lambda phage were studied. The
      efficiency of thermoinduction was shown to be 2-2.5 times higher in E. coli cells growing with
      mu=0.35 h-1 than in fast growing cells with mu=0.6 h-1. Introduction of casamino acids did not
      influence the thermoinduction level in slow (mu=0.35 h-1) growing cells, but stimulated
      restrictase synthesis insignificantly in fast growing cells (mu=0.6 h-1). Addition of glucose
      and glucose + casamino acids into EcoRV induction medium resulted in lowering the
      thermoinduction efficiency of the PR promoter by 13-31%, respectively, as compared with
      induction on nutrient-deficient medium for slow growing cells. At the same time, addition of
      glucose while thermoinducing fast growing cells enhanced synthesis of EcoRV restrictase.
      Dynamics of the induced synthesis of EcoRV restriction endonuclease were observed to be
      different in fast and slow growing cultures of recombinant cells.
AU  - Gorlatova NV
AU  - Kryuchkova EG
AU  - Koltovaya NA
AU  - Dolgova IN
AU  - Ananyin VM
AU  - Velkov VV
PT  - Journal Article
TA  - Biotekhnologiya
JT  - Biotekhnologiya
SO  - Biotekhnologiya 1991 0: 27-30.

PMID- Not carried by PubMed...
VI  - 3
DP  - 1991
TI  - Synthesis of EcoRV restriction endonuclease by chemostatic cultivation of an Escherichia coli K 802 recombinant strain.  1. Effects of growth rate on expression of plasmid genes of EcoRV restriction endonuclease and beta-lactamase.
PG  - 34-38
AB  - Stability and expression of pILRV8 plasmid in E. coli cells growing on minimal
      glucose medium were studied in chemostatic mode within a wide range of dilution
      rates (D=0; V=0.1-0.6 hr-1) and in turbidostatic mode (Vmax=0.7 hr-1).  High
      segregational and structural stability was characteristic for the strain under
      these conditions.  Beta-lactamase and EcoRV restriction endonuclease determined
      by genes of pILRV8 plasmid were synthesized concertedly, activity increasing
      4-fold with increasing dilution rate in chemostatic mode.
AU  - Gorlatova NV
AU  - Kryukova EG
AU  - Koltovaya NA
AU  - Dolgova IN
AU  - Velkov VV
PT  - Journal Article
TA  - Biotekhnologiya
JT  - Biotekhnologiya
SO  - Biotekhnologiya 1991 3: 34-38.

PMID- 10702254
VI  - 275
DP  - 2000
TI  - Reactions of BglI and other Type II restriction endonucleases with discontinuous recognition sites.
PG  - 6928-6936
AB  - Type II restriction enzymes generally recognize continuous sequences of 4-8 consecutive base
      pairs on DNA, but some recognize discontinuous
      sites where the specified sequence is interrupted by a defined length
      of nonspecific DNA. To date, a mechanism has been established for only
      one type II endonuclease with a discontinuous site, SfiI at
      GGCCNNNNNGGCC (where N is any base). In contrast to orthodox enzymes
      such as EcoRV, dimeric proteins that act at a single site, SfiI is a
      tetramer that interacts with two sites before cleaving DNA. BglI has a
      similar recognition sequence (GCCNNNNNGGC) to SfiI but a crystal
      structure like EcoRV. BglI and several other endonucleases with
      discontinuous sites were examined to see if they need two sites for
      their DNA cleavage reactions. The enzymes included some with sites
      containing lengthy segments of nonspecific DNA, such as XcmI
      (CCANNNNNNNNNTGG). In all cases, they acted at individual sites.
      Elongated recognition sites do not necessitate unusual reaction
      mechanisms. Other experiments on BglI showed that it bound to and
      cleaved DNA in the same manner as EcoRV, thus further delineating a
      distinct group of restriction enzymes with similar structures and a
      common reaction mechanism.
AU  - Gormley NA
AU  - Bath AJ
AU  - Halford SE
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2000 275: 6928-6936.

PMID- 11729188
VI  - 277
DP  - 2002
TI  - The type IIs restriction endonuclease BspMI is a tetramer that acts concertedly at two copies of an asymmetric DNA sequence.
PG  - 4034-4041
AB  - Type IIs endonucleases recognize asymmetric DNA sequences and cleave both strands at fixed
      positions downstream of the sequence. Many type IIs enzymes, including BspMI, cleave
      substrates with two sites more rapidly than those with one site. They usually act sequentially
      on DNA with two sites, but BspMI converted such a substrate directly to the final products cut
      at both sites. The BspMI endonuclease was found to be a tetramer, in contrast to the monomeric
      structures for many type IIs enzymes. No change in subunit association occurred during the
      BspMI reaction. Plasmids with two BspMI sites were cleaved in cis, in reactions spanning sites
      in the same DNA, even when the sites were separated by just 38 bp. Plasmids with one BspMI
      site were cleaved in trans, with the enzyme bridging sites in separate DNA molecules: these
      slow reactions could be accelerated by adding a second DNA with the recognition sequence.
      Thus, whereas many type IIs enzymes dimerize before cleaving DNA, a process facilitated by two
      recognition sites in cis, the BspMI tetramer binds two copies of its recognition sequence
      before cleaving the DNA in both strands at both sites.
AU  - Gormley NA
AU  - Hillberg AL
AU  - Halford SE
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2002 277: 4034-4041.

PMID- 4631666
VI  - 56
DP  - 1973
TI  - [6N]Methyl adenine in the nuclear DNA of a eucaryote, Tetrahymena pyriformis.
PG  - 697-701
AB  - DNA isolated from macronuclei of the ciliate, Tetrahymena pyriformis, has been found to
      contain [6N]methyl adenine (MeAde); this represents the first clear demonstration of
      significant amounts of MeAde in the DNA of a eucaryote. The amounts of macronuclear MeAde
      differed slightly between different strains of Tetrahymena, with approximately 0.65-0.80% of
      the adenine bases being methylated. The MeAde content of macronuclear DNA did not seem to vary
      in different physiological states. The level of MeAde in DNA isolated from micronuclei, on the
      other hand, was quite low (at least tenfold lower than in macronuclear DNA).
AU  - Gorovsky MA
AU  - Hattman S
AU  - Pleger GL
PT  - Journal Article
TA  - J. Cell Biol.
JT  - J. Cell Biol.
SO  - J. Cell Biol. 1973 56: 697-701.

PMID- 28124151
VI  - 400
DP  - 2017
TI  - The Helicobacter pylori Methylome: Roles in Gene Regulation and Virulence.
PG  - 105-127
AB  - The methylome is defined as a map of DNA methylation patterns at single-base resolution. DNA
      methylation in bacteria was first discovered as a function of restriction-modification (R-M)
      systems. R-M systems in Helicobacter pylori, like those in other bacteria, are important
      host-specificity determinants that provide protection against foreign DNA. Moreover, the gene
      regulatory role of the methyltransferase (Mtase) unit of various Helicobacter pylori R-M
      systems is being increasingly recognized. Recent advances in the application of
      single-molecule real-time (SMRT) DNA sequencing to analyse DNA methylation have revealed for
      the first time comprehensive pictures of the genome-wide distribution of methylation sites in
      various strains of H. pylori. The methylomic data published so far have not only confirmed the
      significant inter-strain diversity of H. pylori Mtases and their DNA methylation profiles, but
      also identified numerous novel Mtase target recognition sites. The precise knowledge of the
      nucleotide sequence of Mtase recognition sites and their distribution within the H. pylori
      genome will in turn enable researchers to more readily test hypotheses on how H. pylori Mtases
      function to orchestrate gene regulation and/or modulate virulence. Methylomic studies hold
      promise for providing a deeper understanding into the roles of H. pylori Mtase and R-M systems
      in the physiology, epigenetics and possibly also pathogenesis of this important human
      pathogen. Consequently, the knowledge gained will provide crucial insights into the potential
      application of H. pylori methylomes as novel biomarkers for the prediction of disease outcome
      and/or antibiotic susceptibility.
AU  - Gorrell R
AU  - Kwok T
PT  - Journal Article
TA  - Curr. Top. Microbiol. Immunol.
JT  - Curr. Top. Microbiol. Immunol.
SO  - Curr. Top. Microbiol. Immunol. 2017 400: 105-127.

PMID- 29146854
VI  - 5
DP  - 2017
TI  - Complete Genomic Sequences of Two Salmonella enterica subsp. enterica Serogroup C2 (O:6,8) Strains from Central California.
PG  - e01234-17
AB  - Salmonella enterica subsp. enterica strains RM11060, serotype 6,8:d:-, and RM11065, serotype
      6,8:-:e,n,z15, were isolated from environmental samples
      collected in central California in 2009. We report the complete genome sequences
      of these two strains. These genomic sequences are distinct and will provide
      additional data to our understanding of S. enterica genomics.
AU  - Gorski L
AU  - Huynh S
AU  - Cooper KK
AU  - Parker CT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01234-17.

PMID- 26227608
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Streptomyces sp. Strain PBH53, Isolated from an Urban Environment.
PG  - e00859-15
AB  - We report the draft genome sequence of Streptomyces sp. strain PBH53, a strain isolated from
      an urban transit station in Ottawa, Canada. The analysis of the
      genome using the bioinformatics tool antiSMASH showed the presence of many unique
      natural product biosynthetic pathways.
AU  - Gosse JT
AU  - Hill P
AU  - Dowd SE
AU  - Boddy CN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00859-15.

PMID- 27445387
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Moraxella osloensis Strain KMC41, a Producer of 4-Methyl-3-Hexenoic Acid, a Major Malodor Compound in Laundry.
PG  - e00705-16
AB  - We report the complete genome sequence of Moraxella osloensis strain KMC41, isolated from
      laundry with malodor. The KMC41 genome comprises a 2,445,556-bp
      chromosome and three plasmids. A fatty acid desaturase and at least four
      beta-oxidation-related genes putatively associated with 4-methyl-3-hexenoic acid
      generation were detected in the KMC41 chromosome.
AU  - Goto T
AU  - Hirakawa H
AU  - Morita Y
AU  - Tomida J
AU  - Sato J
AU  - Matsumura Y
AU  - Mitani A
AU  - Niwano Y
AU  - Takeuchi K
AU  - Kubota H
AU  - Kawamura Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00705-16.

PMID- 26543123
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Porphyromonas gingivalis Strain Ando Expressing a 53-Kilodalton-Type Fimbrilin Variant of Mfa1 Fimbriae.
PG  - e01292-15
AB  - Periodontopathic Porphyromonas gingivalis strain Ando abundantly expresses a 53-kDa-type Mfa1
      fimbria. Here, we report the draft genome sequence of Ando, with
      a size of 2,229,994 bp, average G+C content of 48.4%, and 1,755 predicted
      protein-coding sequences.
AU  - Goto T
AU  - Nagano K
AU  - Hirakawa H
AU  - Tanaka K
AU  - Yoshimura F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01292-15.

PMID- 22740670
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Helicobacter cinaedi Strain PAGU611, Isolated in a Case of Human Bacteremia.
PG  - 3744-3745
AB  - We report the complete genome sequence of Helicobacter cinaedi strain PAGU611, isolated in a
      case of human bacteremia. The PAGU611 genome comprises a
      2,078,348-bp chromosome and a 23,054-bp plasmid. The chromosome contains a unique
      genomic island, encoding a type VI secretion system and clustered regularly
      interspaced short palindromic repeat (CRISPR) loci.
AU  - Goto T
AU  - Ogura Y
AU  - Hirakawa H
AU  - Tomida J
AU  - Morita Y
AU  - Akaike T
AU  - Hayashi T
AU  - Kawamura Y
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3744-3745.

PMID- 2467840
VI  - 2
DP  - 1988
TI  - Genes within genes: independent expression of phage T4 intron open reading frames and the genes in which they reside.
PG  - 1791-1799
AB  - The td, nrdB, and sunY introns of bacteriophage T4 each contain a long open reading frame
      (ORF). These ORFs are preceded by functional T4 late promoters and, in the case of the nrdB
      intron ORF, a functional middle promoter. Expression of phage-encoded intron ORF-lacZ fusions
      indicates that these T4 genes are highly regulated. The lack of translation of these ORFs from
      the early pre-mRAs can be accounted for by the presence of secondary structures that are
      absent from the late RNAs. Because translation of the intron ORFs could disrupt core
      structural elements required for pre-mRNA splicing, such regulation may be necessary to allow
      expression of the genes in which they reside.
AU  - Gott JM
PT  - Journal Article
TA  - Genes Dev.
JT  - Genes Dev.
SO  - Genes Dev. 1988 2: 1791-1799.

PMID- 1570334
VI  - 89
DP  - 1992
TI  - Telomere-proximal DNA in Saccharomyces cerevisiae is refractory to methyltransferase activity in vivo.
PG  - 4062-4065
AB  - Genes located near telomeres in Saccharomyces cerevisiae undergo position-effect variegation;
      their transcription is subject to reversible but mitotically heritable repression. This
      position effect and the finding that telomeric DNA is late replicating suggest that yeast
      telomeres exist in a heterochromatin-like state. Mutations in genes that suppress the
      telomeric position effect suggest that a special chromatin structure exists near chromosomal
      termini. Thus transcriptional repression may be explained by the inability of DNA binding
      proteins to access the DNA near telomeres. To test this hypothesis, the Escherichia coli Dam
      DNA methyltransferase, which modifies the sequence GATC, was introduced into S. cerevisiae
      cells. DNA sequences near the telomere were highly refractive to Dam methylation but were
      modified when located at positions more internal on the chromosome. Telomeric sequences were
      accessible to methyltransferase activity in strains that contained a mutation that suppressed
      the telomeric position effect. These data support the model that sequence-specific DNA binding
      proteins are excluded from telomere-proximal sequences in vivo and show that expression of DNA
      methyltransferase activity may serve as a useful tool for mapping chromosomal structural
      domains in vivo.
AU  - Gottschling DE
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1992 89: 4062-4065.

PMID- 23739050
VI  - 7
DP  - 2013
TI  - Comparative genomics of pathogenic lineages of Vibrio nigripulchritudo identifies virulence-associated traits.
PG  - 1985-1996
AB  - Vibrio nigripulchritudo is an emerging pathogen of farmed shrimp in New Caledonia
      and other regions in the Indo-Pacific. The molecular determinants of V.
      nigripulchritudo pathogenicity are unknown; however, molecular epidemiological
      studies have suggested that pathogenicity is linked to particular lineages. Here,
      we performed high-throughput sequencing-based comparative genome analysis of 16
      V. nigripulchritudo strains to explore the genomic diversity and evolutionary
      history of pathogen-containing lineages and to identify pathogen-specific genetic
      elements. Our phylogenetic analysis revealed three pathogen-containing V.
      nigripulchritudo clades, including two clades previously identified from New
      Caledonia and one novel clade comprising putatively pathogenic isolates from
      septicemic shrimp in Madagascar. The similar genetic distance between the three
      clades indicates that they have diverged from an ancestral population roughly at
      the same time and recombination analysis indicates that these genomes have, in
      the past, shared a common gene pool and exchanged genes. As each contemporary
      lineage is comprised of nearly identical strains, comparative genomics allowed
      differentiation of genetic elements specific to shrimp pathogenesis of varying
      severity. Notably, only a large plasmid present in all highly pathogenic (HP)
      strains encodes a toxin. Although less/non-pathogenic strains contain related
      plasmids, these are differentiated by a putative toxin locus. Expression of this
      gene by a non-pathogenic V. nigripulchritudo strain resulted in production of
      toxic culture supernatant, normally an exclusive feature of HP strains. Thus,
      this protein, here termed 'nigritoxin', is implicated to an extent that remains
      to be precisely determined in the toxicity of V. nigripulchritudo.
AU  - Goudenege D
AU  - Labreuche Y
AU  - Krin E
AU  - Ansquer D
AU  - Mangenot S
AU  - Calteau A
AU  - Medigue C
AU  - Mazel D
AU  - Polz MF
AU  - Le Roux F
PT  - Journal Article
TA  - ISME J.
JT  - ISME J.
SO  - ISME J. 2013 7: 1985-1996.

PMID- 6304321
VI  - 166
DP  - 1983
TI  - Sequence diversity among related genes for recognition of specific targets in DNA molecules.
PG  - 1-19
AB  - Escherichia coli strains K12 and B, and a new strain designed D, each encode a
      characteristic restriction and modification enzyme.  These enzymes (EcoK, EcoB
      and presumably EcoD) comprise three subunits of which one, that encoded by the
      so-called specificity gene (hsdS), is responsible for recognition of the DNA
      sequence speific to that system.  The other two subunits, encoded by hsdR and
      hsdM, are interchangeable between systems, and the available molecular evidence
      suggests that the hsdR and hsdM genes are highly conserved.  The DNA sequence
      of a segment of the hsd region that includes the hsdS gene has been determined
      for each of the three strains.  The hsdS gene varies in length from 1335 to
      1425 base-pairs and the only regions showing obvious homology, one of about 100
      base-pairs and a second of about 250 base-pairs, are highly conserved.  The
      remainder of each hsdS gene shares little, or no, homology with either of the
      other related specificity genes.  Thus, the specificity subunits, though
      components of a family of closely related enzymes with very similar functions,
      have remarkably dissimilar primary structure.
AU  - Gough JA
AU  - Murray NE
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1983 166: 1-19.

PMID- 5326110
VI  - 91
DP  - 1966
TI  - Methylated bases in the host-modified deoxyribonucleic acid of Escherichia coli and bacteriophage lambda.
PG  - 1460-1468
AB  - The deoxyribonucleic acid (DNA) from strains of Escherichia coli and phage
      lambda was examined to determine whether the types or amounts of
      methionine-derived methylated bases present correlated with the host-specific
      modification of that DNA.  The DNA of strain C600 (which has K-12 modification
      specificity) and of a modificationless mutant of C600 are similar in their
      content of 5-methylcytosine and 6-methylaminopurine.  Strains Bc251 and its
      Pl-lysogen differ in P1-controlled specificity, but they have the same content
      of 6-methylaminopurine, and both lack 5-methylcytosine in their DNA.  Phage
      lambda contains the same methylated bases as its host of origin, but in reduced
      amounts and in different proportions.  Although minor amounts of these
      methylated bases may have importance as a result of their location, the
      presence of the majority of these methylated bases is irrelevant to the
      specificity of host modification of DNA.
AU  - Gough M
AU  - Lederberg S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1966 91: 1460-1468.

PMID- 27081135
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Mycoplasma mycoides subsp. mycoides T1/44, a Vaccine  Strain against Contagious Bovine Pleuropneumonia.
PG  - e00263-16
AB  - Mycoplasma mycoidessubsp.mycoidesis the etiologic agent of contagious bovine pleuropneumonia.
      We report here the complete genome sequence of the strain T1/44,
      which is widely used as a live vaccine in Africa.
AU  - Gourgues G
AU  - Barre A
AU  - Beaudoing E
AU  - Weber J
AU  - Magdelenat G
AU  - Barbe V
AU  - Schieck E
AU  - Jores J
AU  - Vashee S
AU  - Blanchard A
AU  - Lartigue C
AU  - Sirand-Pugnet P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00263-16.

PMID- 24072865
VI  - 1
DP  - 2013
TI  - Whole-Genome Shotgun Sequencing of Rhodococcus erythropolis Strain P27, a Highly  Radiation-Resistant Actinomycete from Antarctica.
PG  - e00763-13
AB  - Here, we report the draft genome sequence of radiation-resistant Rhodococcus erythropolis
      strain P27, isolated from leaves of Deschampsia antarctica Desv. (Poaceae) in the Admiralty
      Bay area, Antarctica.
AU  - Gouvea-Taketani R
AU  - Domingues ZT
AU  - Soares-de-Melo I
AU  - Mendes R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00763-13.

PMID- 16547044
VI  - 188
DP  - 2006
TI  - Genomic Organization and Molecular Characterization of Clostridium difficile Bacteriophage {Phi}CD119.
PG  - 2568-2577
AB  - In this study, we have isolated a temperate phage (PhiCD119) from a
      pathogenic Clostridium difficile strain and sequenced and annotated its
      genome. This virus has an icosahedral capsid and a contractile tail
      covered by a sheath and contains a double-stranded DNA genome. It belongs
      to the Myoviridae family of the tailed phages and the order Caudovirales.
      The genome was circularly permuted, with no physical ends detected by
      sequencing or restriction enzyme digestion analysis, and lacked a cos
      site. The DNA sequence of this phage consists of 53,325 bp, which carries
      79 putative open reading frames (ORFs). A function could be assigned to 23
      putative gene products, based upon bioinformatic analyses. The PhiCD119
      genome is organized in a modular format, which includes modules for
      lysogeny, DNA replication, DNA packaging, structural proteins, and host
      cell lysis. The PhiCD119 attachment site attP lies in a noncoding region
      close to the putative integrase (int) gene. We have identified the phage
      integration site on the C. difficile chromosome (attB) located in a
      noncoding region just upstream of gene gltP, which encodes a carrier
      protein for glutamate and aspartate. This genetic analysis represents the
      first complete DNA sequence and annotation of a C. difficile phage.
AU  - Govind R
AU  - Fralick JA
AU  - Rolfe RD
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2006 188: 2568-2577.

PMID- 15226412
VI  - 32
DP  - 2004
TI  - One recognition sequence, seven restriction enzymes, five reaction mechanisms.
PG  - 3469-3479
AB  - The diversity of reaction mechanisms employed by Type II restriction enzymes was investigated
      by analysing the reactions of seven endonucleases at the same DNA sequence. NarI, KasI,
      Mly113I, SfoI, EgeI, EheI and BbeI cleave DNA at several different positions in the sequence
      5'-GGCGCC-3'. Their reactions on plasmids with one or two copies of this sequence revealed
      five distinct mechanisms. These differ in terms of the number of sites the enzyme binds, and
      the number of phosphodiester bonds cleaved per turnover. NarI binds two sites, but cleaves
      only one bond per DNA-binding event. KasI also cuts only one bond per turnover but acts at
      individual sites, preferring intact to nicked sites. Mly113I cuts both strands of its
      recognition sites, but shows full activity only when bound to two sites, which are then
      cleaved concertedly. SfoI, EgeI and EheI cut both strands at individual sites, in the manner
      historically considered as normal for Type II enzymes. Finally, BbeI displays an absolute
      requirement for two sites in close physical proximity, which are cleaved concertedly. The
      range of reaction mechanisms for restriction enzymes is thus larger than commonly imagined, as
      is the number of enzymes needing two recognition sites.
AU  - Gowers DM
AU  - Bellamy SRW
AU  - Halford SE
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2004 32: 3469-3479.

PMID- 12628933
VI  - 22
DP  - 2003
TI  - Protein motion from non-specific to specific DNA by three-dimensional routes aided by supercoiling.
PG  - 1410-1418
AB  - DNA-binding proteins are generally thought to locate their target sites by first associating
      with the DNA at random and then translocating to the
      specific site by one-dimensional (1D) diffusion along the DNA. We report
      here that non-specific DNA conveys proteins to their target sites just as
      well when held near the target by catenation as when co-linear with the
      target. Hence, contrary to the prevalent view, proteins move from random
      to specific sites primarily by three-dimensional (3D) rather than 1D
      pathways, by multiple dissociation/re-association events within a single
      DNA molecule. We also uncover a role for DNA supercoiling in target-site
      location. Proteins find their sites more readily in supercoiled than in
      relaxed DNA, again indicating 3D rather than 1D routes.
AU  - Gowers DM
AU  - Halford SE
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 2003 22: 1410-1418.

PMID- 16243975
VI  - 102
DP  - 2005
TI  - Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA.
PG  - 15883-15888
AB  - Proteins that act at specific DNA sequences bind DNA randomly and then translocate to the
      target site. The translocation is often ascribed to the protein sliding along the DNA while
      maintaining continuous contact with it. Proteins also can move on DNA by multiple cycles of
      dissociation/reassociation within the same chain. To distinguish these pathways, a strategy
      was developed to analyze protein motion between DNA sites. The strategy reveals whether the
      protein maintains contact with the DNA as it transfers from one site to another by sliding or
      whether it loses contact by a dissociation/reassociation step. In reactions at low salt, the
      test protein stayed on the DNA as it traveled between sites, but only when the sites were <50
      bp apart. Transfers of >30 bp at in vivo salt, and over distances of >50 bp at any salt,
      always included at least one dissociation step. Hence, for this enzyme, 1D sliding operates
      only over short distances at low salt, and 3D dissociation/reassociation is its main mode of
      translocation.
AU  - Gowers DM
AU  - Wilson GG
AU  - Halford SE
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2005 102: 15883-15888.

PMID- 11728730
VI  - 205
DP  - 2001
TI  - DNA from Aspergillus flavus contains 5-methylcytosine.
PG  - 151-155
AB  - DNA from Aspergillus sp. has been reported not to contain 5-methylcytosine. However, it has
      been found that Aspergillus nidulans responds to 5-azacytidine, a drug that is a strong
      inhibitor of DNA methyltransferases. Therefore, we have re-examined the occurrence of
      5-methylcytosine in DNA from Aspergillus flavus by using a highly sensitive and specific
      method for detection of modified bases in genomic DNA comprising high-performance liquid
      chromatography separation of nucleosides, labeling of the nucleoside with deoxynucleoside
      kinase and two-dimensional thin-layer chromatography. Our results show that 5-methylcytosine
      is present in DNA from A. flavus. We estimate the relative amounts of 5-methylcytosine to
      cytosine to be approximately 1/400.
AU  - Gowher H
AU  - Ehrlich KC
AU  - Jeltsch A
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2001 205: 151-155.

PMID- 11919202
VI  - 277
DP  - 2002
TI  - Molecular enzymology of the catalytic domains of the Dnmt3a and Dnmt3b DNA methyltransferases.
PG  - 20409-20414
AB  - The C-terminal domains of the mammalian DNA methyltransferases Dnmt1, Dnmt3a, and Dnmt3b
      harbor all the conserved motifs characteristic for
      cytosine-C5 methyltransferases. Whereas the isolated catalytic domain
      of Dnmt1 is inactive, we show here that the C-terminal domains of
      Dnmt3a and Dnmt3b are catalytically active. Neither Dnmt3a nor Dnmt3b
      shows a significant preference for the satellite 2 sequence, although
      Dnmt3b is required for methylation of these regions in vivo. However,
      the catalytic domain of Dnmt3a methylates DNA in a distributive
      reaction, whereas Dnmt3b is processive, which accelerates methylation
      of macromolecular DNA in vitro. This property could make Dnmt3b a
      preferred enzyme for methylation at satellite 2 repeats, since they are
      highly CG-rich. We have also analyzed the catalytic activities of six
      different mutations found in ICF (immunodeficiency, centromeric
      instability, and facial abnormalities) patients in the catalytic domain
      of Dnmt3b. Five of them display catalytic activities reduced by
      10-50-fold; one mutant was inactive in our assay (residual activity
      <1%). These results confirm that a reduced catalytic activity of Dnm3b
      causes ICF. However, the mutations in general do not completely
      abrogate catalytic activity. This finding may explain why ICF patients
      are viable, whereas nmt3b knock-out mice die during embryogenesis.
AU  - Gowher H
AU  - Jeltsch A
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2002 277: 20409-20414.

PMID- 11021972
VI  - 303
DP  - 2000
TI  - Molecular enzymology of the EcoRV DNA-(Adenine-N6)-methyltransferase: Kinetics of DNA binding and bending, kinetic mechanism and linear diffusion of the enzyme on DNA.
PG  - 93-110
AB  - The EcoRV DNA-(adenine-N(6))-methyltransferase recognizes GATATC sequences and modifies the
      first adenine residue within this site. We show here, that the enzyme binds to the DNA and the
      cofactor S-adenosylmethionine (AdoMet) in an ordered bi-bi fashion, with AdoMet being bound
      first. M.EcoRV binds DNA in a non-specific manner and the enzyme searches for its recognition
      site by linear diffusion with a range of approximately 1800 bp. During linear diffusion the
      enzyme continuously scans the DNA for the presence of recognition sites. Upon specific
      M.EcoRV-DNA complex formation a strong increase in the fluorescence of an oligonucleotide
      containing a 2-aminopurine base analogue at the GAT-2AP-TC position is observed which, most
      likely, is correlated with DNA bending. In contrast to the GAT-2AP-TC substrate, a G-2AP-TATC
      substrate in which the target base is replaced by 2-aminopurine does not show an increase in
      fluorescence upon M.EcoRV binding, demonstrating that 2-aminopurine is not a general tool to
      detect base flipping. Stopped-flow experiments show that DNA bending is a fast process with
      rate constants >10 s(-1).  In the presence of cofactor, the specific complex adopts a second
      conformation, in which the target sequence is more tightly contacted by the enzyme. M.EcoRV
      exists in an open and in a closed state that are in slow equilibrium. Closing the open state
      is a slow process (rate constant approximately 0.7 min(-1)) that limits the rate of DNA
      methylation under single turnover conditions. Product release requires opening of the closed
      complex which is very slow (rate constant approximately 0.05-0.1 min(-1)) and limits the rate
      of DNA methylation under multiple turnover conditions. M.EcoRV methylates DNA sequences
      containing more than one recognition site in a distributive manner. Since the dissociation
      rate from non-specific DNA does not depend on the length of the DNA fragment, DNA dissociation
      does not preferentially occur at the ends of the DNA.
AU  - Gowher H
AU  - Jeltsch A
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2000 303: 93-110.

PMID- 11399089
VI  - 309
DP  - 2001
TI  - Enzymatic properties of recombinant Dnmt3a DNA methyltransferase from mouse: the enzyme modifies DNA in a non-processive manner and also methylates non-CpG Sites.
PG  - 1201-1208
AB  - We present the first in vitro study investigating the catalytic properties of a mammalian de
      novo DNA methyltransferase. Dnmt3a from mouse was cloned and expressed in Escherichia coli. It
      was shown to be catalytically active in E. coli cells in vivo. The methylation activity of the
      purified protein was highest at pH 7.0 and 30 mM KCl. Our data show that recombinant Dnmt3a
      protein is indeed a de novo methyltransferase, as it catalyzes the transfer of methyl groups
      to unmethylated substrates with similar efficiency as to hemimethylated substrates. With
      oligonucleotide substrates, the catalytic activity of Dnmt3a is similar to that of Dnmt1: the
      Km values for the unmethylated and hemimethylated oligonucleotide substrates are 2.5 microM,
      and the k(cat) values are 0.05 h^-1 and 0.07 h^-1, respectively. The enzyme catalyzes the
      methylation of DNA in a distributive manner, suggesting that Dnmt3a and Dnmt1 may cooperate
      during de novo methylation of DNA. Further, we investigated the methylation activity of Dnmt3a
      at non-canonical sites. Even though the enzyme shows maximum activity at CpG sites, with
      oligonucleotide substrates, a high methylation activity was also found at CpA sites, which are
      modified only twofold slower than CpG sites. Therefore, the specificity of Dnmt3a is
      completely different from that of the maintenance methyltransferase Dnmt1, which shows a 40 to
      50-fold preference for hemimethylated over unmethylated CpG sites and has almost no
      methylation activity at non-CpG sites. Copyright 2001 Academic Press.
AU  - Gowher H
AU  - Jeltsch A
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2001 309: 1201-1208.

PMID- 11118227
VI  - 19
DP  - 2000
TI  - DNA of Drosophila melanogaster contains 5-methylcytosine.
PG  - 6918-6923
AB  - It is commonly accepted that the DNA of Drosophila melanogaster does not contain
      5-methylcytosine, which is essential in the development of most eukaryotes. We have developed
      a new, highly specific and sensitive assay to detect the presence of 5-methylcytosine in
      genomic DNA. The DNA is degraded to nucleosides, 5-methylcytosine purified by HPLC and, for
      detection by 1D- and 2D-TLC, radiolabeled using deoxynucleoside kinase and [-32P]ATP. Using
      this assay, we show here that 5- methylcytosine occurs in the DNA of D. melanogaster at a
      level of 1 in 1000-2000 cytosine residues in adult flies. DNA methylation is detectable in all
      stages of D. melanogaster development.
AU  - Gowher H
AU  - Leismann O
AU  - Jeltsch A
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 2000 19: 6918-6923.

PMID- 15671018
VI  - 280
DP  - 2005
TI  - Mechanism of stimulation of catalytic activity of Dnmt3A and Dnmt3B DNA-(cytosine-C5)-methyltransferases by Dnmt3L.
PG  - 13341-13348
AB  - Dnmt3L has been identified as a stimulator of the catalytic activity of de novo DNA
      methyltransferases. It is essential in the development of
      germ cells in mammals. We show here that Dnmt3L stimulates the
      catalytic activity of the Dnmt3A and Dnmt3B enzymes by directly binding
      to their respective catalytic domains via its own C-terminal domain.
      The catalytic activity of Dnmt3A and -3B was stimulated similar to
      15-fold, and Dnmt3L directly binds to DNA but not to
      S-adenosyl-L-methionine (AdoMet). Complex formation between Dnmt3A and
      Dnmt3L accelerates DNA binding by Dnmt3A 20-fold and lowers its Km for
      DNA. Interaction of Dnmt3L with Dnmt3A increases the binding of the
      coenzyme AdoMet to Dnmt3A, and it lowers the Km of Dnmt3A for AdoMet.
      On the basis of our data we propose a model in which the interaction of
      Dnmt3A with Dnmt3L induces a conformational change of Dnmt3A that opens
      the active site of the enzyme and promotes binding of DNA and the
      AdoMet. We demonstrate that the interaction of Dnmt3A and Dnmt3L is
      transient, and after DNA binding to Dnmt3A, Dnmt3L dissociates from the
      complex. Following dissociation of Dnmt3L, Dnmt3A adopts a closed
      conformation leading to slow rates of DNA release. Therefore, Dnmt3L
      acts as a substrate exchange factor that accelerates DNA and AdoMet
      binding to de novo DNA methyltransferases.
AU  - Gowher H
AU  - Liebert K
AU  - Hermann A
AU  - Xu GL
AU  - Jeltsch A
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2005 280: 13341-13348.

PMID- 16472822
VI  - 357
DP  - 2006
TI  - Mutational analysis of the catalytic domain of the murine Dnmt3a DNA-(cytosine C5)-methyltransferase.
PG  - 928-941
AB  - On the basis of amino acid sequence alignments and structural data of related enzymes, we have
      performed a mutational analysis of 14 amino
      acid residues in the catalytic domain of the murine Dnmt3a
      DNA-(cytosine C5)-methyltransferase. The target residues are located
      within the ten conserved amino acid sequence motifs characteristic for
      cytosine-C5 methyltransferases and in the putative DNA recognition
      domain of the enzyme (TRD). Mutant proteins were purified and tested
      for their catalytic properties and their abilities to bind DNA and
      AdoMet. We prepared a structural model of Dnmt3a. to interpret our
      results. We demonstrate that Phe50 (motif I) and Glu74 (motif II) are
      important for AdoMet binding and catalysis. D96A (motif III) showed
      reduced AdoMet binding but increased activity under conditions of
      saturation with S-adenosyl-L-methionine (AdoMet), indicating that the
      contact of Asp96 to AdoMet is not required for catalysis. R130A
      (following motif IV), R241A and R246A (in the TRD), R292A, and R297A
      (both located in front of motif X) showed reduced DNA binding. R130A
      displayed a strong reduction in catalytic activity and a complete
      change in flanking sequence preferences, indicating that Arg130 has an
      important role in the DNA interaction of Dnmt3a. R292A also displayed
      reduced activity and changes in the flanking sequence preferences,
      indicating a potential role in DNA contacts farther away from the CG
      target site. N167A (motif VI) and R202A (motif VIII) have normal AdoMet
      and DNA binding but reduced catalytic activity. While Asn167 might
      contribute to the positioning of residues from motif VI, according to
      structural data Arg202 has a role in catalysis of cytosine-C5
      methyltransferases. The R295A variant was catalytically inactive most
      likely because of destabilization of the hinge sub-domain of the
      protein.
AU  - Gowher H
AU  - Loutchanwoot P
AU  - Vorobjeva G
AU  - Handa V
AU  - Jurkowska RZ
AU  - Jurkowski TP
AU  - Jeltsch A
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2006 357: 928-941.

PMID- 16026162
VI  - 44
DP  - 2005
TI  - De novo methylation of nucleosomal DNA by the mammalian Dnmt1 and Dnmt3A DNA methyltransferases.
PG  - 9899-9904
AB  - In the cell, DNA is wrapped on histone octamers, which reduces its accessibility for DNA
      interacting enzymes. We investigated de novo
      methylation of nucleosomal DNA in vitro and show that the Dnmt3a and
      Dnmt1 DNA methyltransferases efficiently methylate nucleosomal DNA
      without dissociation of the histone octamer from the DNA. In contrast,
      the prokaryotic SssI DNA methyltransferase and the catalytic domain of
      Dnmt3a are strongly inhibited by nucleosomes. We also found that
      full-length Dnmt1 and Dnmt3a bind to nucleosomes much stronger than
      their isolated catalytic domains, demonstrating that the N-terminal
      parts of the MTases are required for the interaction with nucleosomes.
      Variations of the DNA sequence or the histone tails did not
      significantly influence the methylation activity of Dnmt3a. The
      observation that mammalian methyltransferases directly modify
      nucleosomal DNA provides an insight into the mechanisms by which
      histone tail and DNA methylation patterns can influence each other
      because the DNA methylation pattern can be established while histones
      remain associated to the DNA.
AU  - Gowher H
AU  - Stockdale CJ
AU  - Goyal R
AU  - Ferreira H
AU  - Owen-Hughes T
AU  - Jeltsch A
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2005 44: 9899-9904.

PMID- 17965600
VI  - 2
DP  - 2007
TI  - Phosphorylation of serine-515 activates the mammalian maintenance methyltransferase Dnmt1.
PG  - 155-160
AB  - DNA methyltransferase 1 methylates hemi-methylated CG sites generated during DNA replication.
      Serine 515 of this enzyme has been shown to be
      phosphorylated. To explore the importance of S515 phosphorylation, we
      generated mutants of Dnmt1 which removed the phosphorylation potential
      (S515A) or mimic phosphoserine (S515E), purified the proteins from
      insect cells and analyzed their DNA methylation activity in vitro. The
      S515E mutant was found to be active, while S515A mutant had severe loss
      in activity when compared to the wild type protein. The loss of
      activity of the S515A variant was not due to loss of DNA binding
      capacity. Furthermore, we show that a phosphorylated peptide whose
      sequence mimics the surrounding of Ser515 ((EKIYISKIVVE)-K-P) inhibited
      the activity of wild type Dnmt1 ten-fold more than the
      non-phosphorylated peptide. The inhibition was specific for Dnmt1 and
      for the particular peptide sequence. Our data suggest that
      phosphorylation of Ser515 is important for an interaction between the
      N-terminal domain of Dnmt1 and its catalytic domain that is necessary
      for activity and that this interaction is specifically disrupted by the
      phosphorylated peptide. We conclude that phosphorylation of Dnmt1 at
      Ser515 could be an important regulator of Dnmt1 activity during cell
      cycle and after proliferative stimuli.
AU  - Goyal R
AU  - Rathert P
AU  - Laser H
AU  - Gowher H
AU  - Jeltsch A
PT  - Journal Article
TA  - EPIGENETICS
JT  - EPIGENETICS
SO  - EPIGENETICS 2007 2: 155-160.

PMID- 16500889
VI  - 34
DP  - 2006
TI  - Accuracy of DNA methylation pattern preservation by the Dnmt1 methyltransferase.
PG  - 1182-1188
AB  - DNA methyltransferase 1 (Dnmt1) has a central role in copying the pattern of DNA methylation
      after replication which is one manifestation of
      epigenetic inheritance. With oligonculeotide substrates we show that mouse
      Dnmt1 has a 30- to 40-fold preference for hemimethylated DNA that is
      almost lost after addition of fully methylated oligonucleotides. Using
      long hemimethylated DNA substrates that carry defined methylation patterns
      and bisulfite analysis of the methylation reaction products, we show a
      15-fold preference for hemimethylated CG sites. Dnmt1 moves along the DNA
      in a random walk methylating hemimethylated substrates with high
      processivity (>50 sites are visited on average which corresponds to linear
      diffusion over 6000 bp). The frequency of skipping sites is very low
      (<0.3%) and there is no detectable flanking sequence preference. CGCTC
      sites tend to terminate the processive methylation of DNA by Dnmt1.
      Unmethylated DNA is modified non-processively with a preference for
      methylation at CCGG sites. We simulate the propagation of methylation
      patterns using a stochastic model with the specificity of Dnmt1 observed
      here and conclude that either methylation of several sites is required to
      propagate the methylation information over several cellular generations or
      additional epigenetic information must be used.
AU  - Goyal R
AU  - Reinhardt R
AU  - Jeltsch A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2006 34: 1182-1188.

PMID- 10520739
VI  - 9
DP  - 1998
TI  - Isolation and identification by sequence homology of a second putative C5-DNA-methyltransferase gene from Ascobolus immersus.
PG  - 109-112
AB  - I report the cloning of a new Ascobolus gene (masc 2) that potentially encodes a
      C5-DNA-methyltransferase. The putative protein exhibits the two domains characteristic of
      eukaryotic maintenance DNA-methyltransferase: a large N-terminal domain and a C-terminal
      domain containing all ten catalytic motifs arranged in the canonical order. A new type of
      eukaryotic DNA-methylase gene (masc 1) has been recently found in Ascobolus. Masc1 is
      essential for the de novo methylation and dispensable for methylation maintenance. The masc2
      gene could encode the methylase involved in this maintenance.
AU  - Goyon C
PT  - Journal Article
TA  - DNA Seq.
JT  - DNA Seq.
SO  - DNA Seq. 1998 9: 109-112.

PMID- 8021939
VI  - 240
DP  - 1994
TI  - Perpetuation of cytosine methylation in Ascobolus immersus implies a novel type of maintenance methylase.
PG  - 42-51
AB  - In the ascomycete Ascobolus immersus, duplicated DNA segments are subject to the methylation
      induced premeiotically (MIP) process. Affected sequences are heavily methylated at their
      cytosine residues. We used the bisulphite genomic sequencing method to determine the
      methylation status of every cytosine residue in a gene which had undergone MIP. Several
      individual DNA molecules, all issued from the replication of a single molecule initially
      subject to MIP, were sequenced. In each molecule, methylation extended over almost the whole
      length of the previously duplicated segment. The methylation extent was precisely delimited
      and constant in each of the molecules, leaving unmethylated a nearly 100-nucleotide region
      next to each end. In none of the molecules did methylation resulting from MIP extend beyond
      the ends. Although the DNA molecules were not all methylated with the same intensity, all
      cytosine residues in the methylated portion could be methylated, most of them belonging to
      non-symmetrical sequences. This finding contrasts with the situation in higher eukaryotes in
      which most, if not all, methylation is at short symmetrical sequences such as CpG or CpNpG,
      ensuring perpetuation of methylation. Methylation at non-symmetrical sequences implies that in
      A. immersus maintenance involves a novel sequence-non-specific methyltransferase.
AU  - Goyon C
AU  - Nogueira TIV
AU  - Faugeron G
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1994 240: 42-51.

PMID- 6400815
VI  - 1
DP  - 1984
TI  - Two-fold symmetry of crystalline DNA-EcoRI endonuclease recognition complexes.
PG  - 1149-1160
AB  - Recognition complexes between EcoRI endonuclease and either of two synthetic
      oligonucleotides (sequences CGCGAATTCGCG and TCGCGAATTCGCG) crystallize in
      space Group P321 with unit cell parameters a=128 and c=47 angstroms and a=118.4
      and c=49.7 angstroms, respectively.  Native diffraction data to 3 angstrom
      resolution have been collected from the form containing the tridecameric
      sequence.  Electrophoretic analyses of dissolved crystals demonstrate that this
      form contains DNA and protein in a ratio of one double helix per enzyme dimer.
      The most likely asymmetric unit contents are one 31,000 dalton enzyme subunit
      and one strand of DNA, yielding VM values of 3.1 cubic angstroms/dal and 2.8
      cubic angstroms/dal for the forms containing dodecameric and tridecameric DNA,
      respectively.  This implies that the DNA-protein complex possesses two-fold
      rotational symmetry, which has been incorporated in the crystalline lattice.
AU  - Grable J
AU  - Frederick CA
AU  - Samudzi C
AU  - Jen-Jacobson L
AU  - Lesser D
AU  - Greene P
AU  - Boyer HW
AU  - Itakura K
AU  - Rosenberg JM
PT  - Journal Article
TA  - J. Biomol. Struct. Dyn.
JT  - J. Biomol. Struct. Dyn.
SO  - J. Biomol. Struct. Dyn. 1984 1: 1149-1160.

PMID- Not included in PubMed...
VI  - 376
DP  - 1995
TI  - Transformation of the EcoRI restriction endonuclease to an enzyme with altered specificity: Development of a positive in vivo selection system.
PG  - S102
AB  - The EcoRI restriction endonuclease is one of the best studied enzymes so far.  It cleaves the
      DNA sequence G/AATTC with very high specificity.  All attempts to change the sequence
      specificity of this enzyme by using site-directed mutagenesis methods have not been successful
      until today.  This is caused by the redundancy of enzyme-substrate interactions leading to
      specific sequence recognition and cleavage.  Therefore, we have developed a positive in vivo
      selection system that allows screening for an active enzyme with altered specificity.
      Bacterial cells are transformed with a pool of plasmids containing the randomly mutated
      endonuclease gene.  In order to protect the host DNA from cleavage a methyltransferase
      corresponding to the altered specificity is required.  We used the MunI methylase which is
      specific for the cognate sequence CAATTG.  Selection is carried out by infecting the cells
      with a lambda phage, which carried a gene coding for a toxic protein.  The sequence of this
      gene was altered to generate several sites of the desired new specificity.  The transcription
      of the toxic gene is prevented only when a restriction activity with this specificity is
      present.
AU  - Grabowski G
AU  - Alves J
PT  - Journal Article
TA  - Biol. Chem. Hoppe Seyler
JT  - Biol. Chem. Hoppe Seyler
SO  - Biol. Chem. Hoppe Seyler 1995 376: S102.

PMID- 7607470
VI  - 157
DP  - 1995
TI  - Site-directed mutagenesis in the catalytic center of the restriction endonuclease EcoRI.
PG  - 113-118
AB  - The catalytic center of the restriction endonuclease (ENase) EcoRI is structurally homologous
      to that of EcoRV, BamHI and PvuII.  Each of these ENases contains a short motif of three to
      four amino acid (aa) residues which are positioned in a similar orientation to the scissile
      phosphodiester bond.  We have mutated these aa (Pro90, Asp91, Glu111 and Lys113) in EcoRI to
      determine their individual roles in catalysis.  The replacement of Asp91 and Lys113,
      respectively, by conservative mutations (Ala91, Asn91, Ala113, Gln113, His113 and Leu113)
      resulted in a reduction of binding affinity and complete loss of cleavage activity.  Only
      Lys113-Arg substitution still allows to cleave DNA, albeit with a rate reduced by at least
      four orders of magnitude.  Lys113 seems to stabilize the structure of the wild-type (wt) ENase
      since all five ENase variants with mutations at this position show a strongly enhanced
      tendency to aggregate.  The Ala and Gln mutants of Glu111 bind the recognition sequence
      slightly stronger than wt EcoRI and cleave it with a low, but detectable rate.  Only the
      Glu111-Lys mutant, in which the charge is reversed, shows neither binding nor cleavage
      activity.  Pro90 is not important for catalysis, because the Ala90 mutant cleaves DNA with an
      only slightly reduced rate.  Under star conditions, however, this mutant is even more active
      than wt EcoRI.  Therefore, the charged aa Asp91, Glu111 and Lys113 are essential for catalytic
      activity of the EcoRI ENase.  Differences in the individual contributions of these aa to
      binding and catalysis, as compared with results obtained with EcoRV and BamHI mutants, show
      that similar catalytic centers are used in a slightly different way by these three ENases.
AU  - Grabowski G
AU  - Jeltsch A
AU  - Wolfes H
AU  - Maass G
AU  - Alves J
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 113-118.

PMID- 8641414
VI  - 381
DP  - 1996
TI  - Asp-59 is not important for the catalytic activity of the restriction endonuclease EcoRI.
PG  - 106-110
AB  - The amino acid Asp-59 was proposed to be involved in EcoRI catalyzed DNA cleavage.  We have
      tested this hypothesis by site directed mutagenesis experiments.  The four mutants D59A, D59E,
      D59G, and D59N bind with similar stability to the specific recognition sequence as wild type
      EcoRI.  The D59E mutant cleaves DNA as fast as the wild type enzyme.  Specific activities of
      the other three mutants are five to tenfold lower.  Therefore, we conclude that Asp-59  is not
      involved in catalysis of the EcoRI restriction endonuclease.  Consequences for catalytic
      mechanisms of EcoRI and other restriction enzymes are discussed.
AU  - Grabowski G
AU  - Maass G
AU  - Alves J
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1996 381: 106-110.

PMID- Not included in PubMed...
VI  - 7
DP  - 1981
TI  - Restriction endonuclease TaqXI from Thermus aquaticus.
PG  - 628-630
AB  - A new restriction endonuclease TaqXI has been isolated from an unidentified
      strain of Thermus aquaticus.  The enzyme recognizes the pentanucleotide
      sequence CC(A/T)GG and cleaves it between C and A or T, the methylation of the
      C residue is not protecting the sequence from the cleavage.
AU  - Grachev SA
AU  - Mamaev SV
AU  - Gurevich AI
AU  - Igoshin AV
AU  - Kolosov MN
AU  - Slyusarenko AG
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1981 7: 628-630.

PMID- 22315421
VI  - 109
DP  - 2012
TI  - Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011.
PG  - 3065-3070
AB  - The degree to which molecular epidemiology reveals information about the sources  and
      transmission patterns of an outbreak depends on the resolution of the
      technology used and the samples studied. Isolates of Escherichia coli O104:H4
      from the outbreak centered in Germany in May-July 2011, and the much smaller
      outbreak in southwest France in June 2011, were indistinguishable by standard
      tests. We report a molecular epidemiological analysis using multiplatform
      whole-genome sequencing and analysis of multiple isolates from the German and
      French outbreaks. Isolates from the German outbreak showed remarkably little
      diversity, with only two single nucleotide polymorphisms (SNPs) found in isolates
      from four individuals. Surprisingly, we found much greater diversity (19 SNPs) in
      isolates from seven individuals infected in the French outbreak. The German
      isolates form a clade within the more diverse French outbreak strains. Moreover,
      five isolates derived from a single infected individual from the French outbreak
      had extremely limited diversity. The striking difference in diversity between the
      German and French outbreak samples is consistent with several hypotheses,
      including a bottleneck that purged diversity in the German isolates, variation in
      mutation rates in the two E. coli outbreak populations, or uneven distribution of
      diversity in the seed populations that led to each outbreak.
AU  - Grad YH et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2012 109: 3065-3070.

PMID- 27340076
VI  - 4
DP  - 2016
TI  - Genome Sequence of Streptomyces aureofaciens ATCC Strain 10762.
PG  - e00615-16
AB  - Streptomyces aureofaciens is a Gram-positive actinomycete that produces the antibiotics
      tetracycline and chlortetracycline. Here, we report the assembly and
      initial annotation of the draft genome sequence of S. aureofaciens ATCC strain
      10762.
AU  - Gradnigo JS
AU  - Somerville GA
AU  - Huether MJ
AU  - Kemmy RJ
AU  - Johnson CM
AU  - Oliver MG
AU  - Moriyama EN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00615-16.

PMID- 6314328
VI  - 80
DP  - 1983
TI  - Complete DNA methylation does not prevent polyoma and simian virus 40 virus early gene expression.
PG  - 6470-6474
AB  - The effect of DNA methylation on polyoma virus and simian virus 40 gene
      expression was investigated.  For this purpose, the cytosines of all C-G
      dinucleotides of the viral DNAs were methylated by the use of rat liver
      methylase and the completeness of methylation was verified by dinucleotide
      analysis and restriction endonuclease treatment.  The biological activity of
      unmethylated and fully methylated DNAs was tested by microinjecting them into
      tissue culture cells.  The functions analyzed included early and late viral
      gene expression, viral DNA replication, oncogenic transformation efficiency,
      and virus maturation.  No difference in any of these biological functions was
      observed between methylated and unmethylated DNA.  Early gene expression of
      methylated DNA is not the result of demethylation because viral DNA reextracted
      from the injected cells, under nonpermissive conditions, retained the
      methylation pattern of the input DNA.  In contrast, viral DNA extracted from
      transformed cells or from intact virus particles was partially or completely
      demethylated.
AU  - Graessmann M
AU  - Graessmann A
AU  - Wagner H
AU  - Werner E
AU  - Simon D
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1983 80: 6470-6474.

PMID- 27013043
VI  - 4
DP  - 2016
TI  - First Genome Sequence of a Mexican Multidrug-Resistant Acinetobacter baumannii Isolate.
PG  - e00156-16
AB  - Acinetobacter baumanniihas emerged as an important nosocomial pathogen worldwide. Here, we
      present the draft genome of the first multidrug-resistantA.
      baumanniiisolate, sampled from a tertiary hospital in Mexico City. This genome
      will provide a starting point for studying the genomic diversity of this species
      in Mexico.
AU  - Grana-Miraglia L
AU  - Lozano L
AU  - Castro-Jaimes S
AU  - Cevallos MA
AU  - Volkow P
AU  - Castillo-Ramirez S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00156-16.

PMID- 25001858
VI  - 15
DP  - 2014
TI  - Whole genome sequence comparison of vtx2-converting phages from Enteroaggregative Haemorrhagic Escherichia coli strains.
PG  - 574
AB  - BACKGROUND: Enteroaggregative Haemorrhagic E. coli (EAHEC) is a new pathogenic
      group of E. coli characterized by the presence of a vtx2-phage integrated in the
      genomic backbone of Enteroaggregative E. coli (EAggEC). So far, four distinct
      EAHEC serotypes have been described that caused, beside the large outbreak of
      infection occurred in Germany in 2011, a small outbreak and six sporadic cases of
      HUS in the time span 1992-2012. In the present work we determined the whole
      genome sequence of the vtx2-phage, termed Phi-191, present in the first described
      EAHEC O111:H2 isolated in France in 1992 and compared it with those of the
      vtx-phages whose sequences were available. RESULTS: The whole genome sequence of
      the Phi-191 phage was identical to that of the vtx2-phage P13374 present in the
      EAHEC O104:H4 strain isolated during the German outbreak 20 years later.
      Moreover, it was also almost identical to those of the other vtx2-phages of EAHEC
      O104:H4 strains described so far. Conversely, the Phi-191 phage appeared to be
      different from the vtx2-phage carried by the EAHEC O111:H21 isolated in the
      Northern Ireland in 2012.The comparison of the vtx2-phages sequences from EAHEC
      strains with those from the vtx-phages of typical Verocytotoxin-producing E. coli
      strains showed the presence of a 900 bp sequence uniquely associated with EAHEC
      phages and encoding a tail fiber. CONCLUSIONS: At least two different
      vtx2-phages, both characterized by the presence of a peculiar tail fiber-coding
      gene, intervened in the emergence of EAHEC. The finding of an identical
      vtx2-phage in two EAggEC strains isolated after 20 years in spite of the high
      variability described for vtx-phages is unexpected and suggests that such
      vtx2-phages are kept under a strong selective pressure.The observation that
      different EAHEC infections have been traced back to countries where EAggEC
      infections are endemic and the treatment of human sewage is often ineffective
      suggests that such countries may represent the cradle for the emergence of the
      EAHEC pathotype. In these regions, EAggEC of human origin can extensively
      contaminate the environment where they can meet free vtx-phages likely spread by
      ruminants excreta.
AU  - Grande L
AU  - Michelacci V
AU  - Tozzoli R
AU  - Ranieri P
AU  - Maugliani A
AU  - Caprioli A
AU  - Morabito S
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2014 15: 574.

PMID- 2041776
VI  - 19
DP  - 1991
TI  - Identification by computer sequence analysis of transcriptional regulator proteins in Dictyostelium discoideum and Serratia marcescens.
PG  - 2359-2362
AB  - We have performed computer searches in the database of known protein sequences
      for proteins similar in sequence to bacteriophage regulatory proteins of known
      3-D structure.  The searches are more selective than other methods due to the
      use of a length-dependent threshold in sequence similarity, above which
      structural homology is implied with high certainty.  Two probable DNA binding
      proteins were identified which are predicted to have a three-dimensional
      structure very similar to bacteriophage cro and repressor proteins.
      Approximate three-dimensional model coordinates are available from the authors.
      Both proteins contain the helix-turn-helix sequence motif typical of a wide
      class of DNA binding proteins and their function is deduced by analogy to
      sequence-similar proteins of known function.  We predict that the Y.SmaI
      protein in the restriction-modification enzyme gene locus of the
      enterobacterium serratia marcescens is a regulator of endonuclease expression;
      and, that the vegetative specific gene VSH7 of the slime mold dictyostelium
      discoideum codes for a regulator of gene expression specific for the slime mold
      growth phage before the onset of the developmental program.  Point mutations
      that would have a strong effect on growth regulation phenotype are suggested.
      The VSH7 protein would be the first eukaryotic representative of the cro /
      phage repressor class.
AU  - Grandori R
AU  - Sander C
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 2359-2362.

PMID- 2162051
VI  - 87
DP  - 1990
TI  - Differential plasmid rescue from transgenic mouse DNAs into Escherichia coli methylation-restriction mutants.
PG  - 4645-4649
AB  - Plasmids comprising transgene insertions in four lines of transgenic mice have been retrieved
      by plasmid rescue into a set of Escherichia coli strains with
      mutations in different members of the methylation-dependent restriction system
      (MDRS). Statistical analysis of plasmid rescue frequencies has revealed that the
      MDRS loci detect differential modifications of the transgene insertions among
      mouse lines that show distinctive patterns of transgene expression. Plasmids in
      mice that express hybrid insulin transgenes during development can be readily
      cloned into E. coli strains carrying mutations in two of the MDRS loci, mcrA and
      mcrB. In mice in which transgene expression is inappropriately delayed into
      adulthood, plasmids can only be cloned into E. coli that carry mutations in all
      known MDRS activities. Differential cloning frequencies in the presence or
      absence of the various methylation-dependent restriction genes represent a
      further way to distinguish regions of mammalian chromosomes. These multiply
      deficient E. coli strains will also facilitate the molecular cloning of modified
      chromosomal DNA.
AU  - Grant SG
AU  - Jessee J
AU  - Bloom FR
AU  - Hanahan D
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1990 87: 4645-4649.

PMID- 1510972
VI  - 31
DP  - 1992
TI  - Stereochemical outcome of the hydrolysis reaction catalyzed by the EcoRV restriction endonuclease.
PG  - 7855-7861
AB  - The stereochemical course of the reaction catalyzed by the EcoRV restriction and endonuclesae
      has been determined. This endonuclease recognizes GATATC sequences and cuts between the
      central T and dA bases. The Rp isomer of d(GACGATsATCGTC) (this dodecamer contains a
      phosphorothioate rather than the usual phosphate group between the central T and dA residues,
      indicated by the s) was a substrate for the endonuclease. Performing this reaction in H2[18O]
      gave [18O]dps(ATCGTC)(a pentamer containing an 18 O-labeled 5'-phosphorothioate) which was
      converted to [18O]dAMPS with nuclese P1. This deoxynucleoside 5'-[18O]phosphorothioate was
      sterospecifically converted to [18O]dATPalphaS with adenylate kinase and pyruvate kinase
      [Brody, R.S., & Frey, P.A.(1981) Biochemistry 20, 1245-1251]. Analysis of the position of the
      18O in this product by 31P NMR spectroscopy showed that it was in a bridging position between
      the alpha- and beta-phosphorus atoms. This indicates that the EcoRV hydrolysis proceeds with
      inversion of configuration at phosphorus. The simplest interpretation is that the mechanism of
      this endonuclease involves a direct in-line attack at phosphorus by H2O with a trigonal
      bipyramidal transition state. A covalent enzyme oligodeoxynucleotide species can be discounted
      as an intermediate. An identical result has been previously observed with the EcoRI
      endonuclease [Connolly,B.A., Eckstein,F., & Pingoud,A.(1984) J. Biol. Chem. 259, 10760-10763].
      X-ray crystallography has shown that both of these endonucleases contain a conserved array of
      amino acids at their active sites. Possible mechanistic roles for these conserved amino acids
      in the light of the stereochemical findings are discussed.
AU  - Grasby JA
AU  - Connolly BA
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1992 31: 7855-7861.

PMID- 26868410
VI  - 4
DP  - 2016
TI  - Genome Sequence of Bacillus pumilus Strain Bonn, Isolated from an Anthrax-Like Necrotic Skin Infection Site of a Child.
PG  - e01741-15
AB  - We report the draft genome sequence of Bacillus pumilus strain Bonn associated with human skin
      infection. B. pumilus Bonn was isolated from a carbuncle-like
      necrotic site, resembling cutaneous anthrax, on the back of the hand of a
      10-year-old child.
AU  - Grass G
AU  - Bierbaum G
AU  - Molitor E
AU  - Gotte N
AU  - Antwerpen M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01741-15.

PMID- 26564034
VI  - 3
DP  - 2015
TI  - Genome Sequence of Bacillus anthracis Larissa, Associated with a Case of Cutaneous Anthrax in Greece.
PG  - e01273-15
AB  - We report the genome sequence of Bacillus anthracis strain Larissa, isolated from a diseased
      sheep associated with a human case of cutaneous anthrax in Central
      Greece from 2012. Genome sequence analysis of strain Larissa may aid in
      describing phylogenetic relationships of B. anthracis isolates in Southeastern
      European countries.
AU  - Grass G
AU  - Hanczaruk M
AU  - Antwerpen M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01273-15.

PMID- 4910817
VI  - 2
DP  - 1968
TI  - Loss of host-controlled restriction of lambda bacteriophage in Escherichia coli following methionine deprivation.
PG  - 1368-1373
AB  - Lambda bacteriophages produced in Escherichia coli C (designated as lambda.C)
      are restricted in their ability to grow in E. coli K-12.  The rare successful
      infections that arise in the K-12 population occur in "special" cells which
      have lost their capacity to restrict lambda.C.  These infections yield modified
      progeny phage (designated as lambda.K) which unlike lambda.C, plate equally
      well on E. coli C and E. coli K-12.  When methionine, but no other amino acid,
      was removed from the growth medium of a mutant strain of E. coli K-12, the
      number of special cells rapidly increased 500- to 3,000-fold.  These new
      special cells retain their capacity to produce modified lambda.K progeny.  This
      conversion of restricting cells into special cells does not require the
      synthesis of new protein.  The special cells formed when methionine was removed
      from the culture did not revert into restricting cells when methionine was
      restored.  Such cells have also lost the ability to divide for at least 4 hr
      after methionine supplementation.  When methionine was restored, the remaining
      restricting cells, but not the special cells, immediately resumed growth.
      Removing methionine from cultures of E. coli B caused a similar increase in the
      number of special cells able to support the growth of lambda.C and lambda.K.
      However, when E. coli K-12 (P1) cultures were deprived of methionine, the
      number of special cells increased for lambda.C but not for lambda.K.  Thus,
      retention of the P1-restriction system, unlike the B- and the K-12 systems,
      does not require the presence of methionine.
AU  - Grasso RJ
AU  - Paigen K
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1968 2: 1368-1373.

PMID- 4876151
VI  - 36
DP  - 1968
TI  - The effect of amino acids on host-controlled restriction of lambda phage.
PG  - 1-8
AB  - Phage lambda grown in Escherichia coli C (lambda.C) plates with an efficiency
      of approximately 4 X 10-4 on log phage E. coli K12 grown in broth.  These few
      successful infections occur in "special cells" in the K12 population which have
      lost their ability to restrict lambda.C.  E. coli K12 grown in minimal medium
      has 30-50 times as many special cells.  Supplementation of minimal medium with
      an amino acid mixture reduced the frequency of special cells to that observed
      in broth cultures.  When amino acids were tested individually, the addition of
      either alainine or leucine alone to minimal medium reduced the special cell
      population.  This reduction in the frequency of special cells was reversed by
      the futher addition of several other amino acids to the growth medium.  Medium
      shift experiments with alanine and leucine suggest that these amino acids do
      not act at the time of infection; instead they determine the presence of a
      metabolic system involved in the expression of host-controlled restriction.
      Removal of methionine from K12 cultures containing an otherwise complete amino
      acid mixture caused an increase in the number of special cells.  Unlike the
      alanine and leucine effects, this increase was rapid and occurred in the
      presence of chloramphenicol.  Prolonged growth in methionine was required to
      restore the reduced special cell frequency.  It appears that the removal of
      methionine can convert a restricting cell into a special cell which is then
      incapable of undergoing cell division.  The various amino acid effects are
      specific to the K12-restriction system and do not influence the B- or
      P1-restriction systems of E. coli.
AU  - Grasso RJ
AU  - Paigen K
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1968 36: 1-8.

PMID- 4891221
VI  - 38
DP  - 1969
TI  - Loss of host-controlled restriction and modification of phage lambda in Escherichia coli K12 previously infected with UV-irradiated coli-phage T3.
PG  - 191-194
AB  - Host range properties of bacteriophages are altered not only by genetic
      mutation, but also by the process of host-controlled modification.
AU  - Grasso RJ
AU  - Paigen K
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1969 38: 191-194.

PMID- 26876161
VI  - 6
DP  - 2016
TI  - AnnoTALE: bioinformatic tools for identification, annotation, and nomenclature of TALEs from Xanthomonas genomic sequences.
PG  - 21077
AB  - Transcription activator-like effectors (TALEs) are virulence factors, produced by the
      bacterial plant pathogen Xanthomonas, that function as gene activators inside plant cells.
      Although the contribution of individual TALEs to infectivity has been shown, the specific
      roles of most TALEs, and the overall TALE diversity in Xanthomonas spp. is not known. TALEs
      possess a highly repetitive DNA-binding domain, which is notoriously difficult to sequence.
      Here, we describe an improved method for characterizing
      TALE genes by the use of PacBio sequencing. We present AnnoTALE, a suite of applications for
      the analysis and annotation of TALE genes from Xanthomonas genomes, and for grouping similar
      TALEs into classes. Based on these classes, we propose a unified nomenclature for Xanthomonas
      TALEs that reveals similarities pointing to related functionalities. This new classification
      enables us to compare related TALEs and to identify base substitutions responsible for the
      evolution of TALE specificities.
AU  - Grau J
AU  - Reschke M
AU  - Erkes A
AU  - Streubel J
AU  - Morgan RD
AU  - Wilson GG
AU  - Koebnik R
AU  - Boch J
PT  - Journal Article
TA  - Sci. Rep.
JT  - Sci. Rep.
SO  - Sci. Rep. 2016 6: 21077.

PMID- 25883287
VI  - 3
DP  - 2015
TI  - Genome Sequence of Mushroom Soft-Rot Pathogen Janthinobacterium agaricidamnosum.
PG  - e00277-15
AB  - Janthinobacterium agaricidamnosum causes soft-rot disease of the cultured button  mushroom
      Agaricus bisporus and is thus responsible for agricultural losses. Here,
      we present the genome sequence of J. agaricidamnosum DSM 9628. The 5.9-Mb genome
      harbors several secondary metabolite biosynthesis gene clusters, which renders
      this neglected bacterium a promising source for genome mining approaches.
AU  - Graupner K
AU  - Lackner G
AU  - Hertweck C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00277-15.

PMID- 8467964
VI  - 7
DP  - 1993
TI  - Site-directed mutagenesis of the gene encoding phage T4 dCMP hydroxymethylase.
PG  - A1197
AB  - The proposed roles of several amino acid residues in deoxycytidylate (dCMP) hydroxymethylase
      (CH) have been tested. CH catalyzes the formation of 5-hydroxymethyl-dCMP, an essential
      component of phage T4 DNA, from dCMP and methylenetetrahydrofolate (CH2THF). CH resemble
      thymidylate synthase (TS), an enzyme of known crystallographic structure, in both amino acid
      sequence and reaction catalyzed. Conversion of Cys148 to Asp, Gly, or Ser decreases CH
      activity at least 10/5-fold, consistent with a nucleophilic role for Cys148 (analogous to the
      catalytic Cys residue in TS). In TS, hydrogen bonds connect O4 and N3 of the substrate dUMP to
      an Asn. Conversion of the corresponding residue in CH, Asp179 to an Asn reverses the substrate
      preference of CH from dCMP to dUMP. Asp179 is proposed to stabilize covalent catalytic
      intermediates, by protonating N3 of the pyrimidine-CH adduct. CH is inactivated by
      5-fluoro-deoxyuridylate (FdUMP), a mechanism-based inactivator of TS, by formation of a
      ternary complex between enzyme, CH2THF and FdUMP. Replacement of Cys148 prevents formation of
      such a complex. The secondary equilibrium isotope effect upon the formation of the ternary
      complex, HK/TK, was measured using a mixture of 2(14C)-FdUMP and 6[3H]-FdUMP. The observed
      inverse effect is consistent with the formation of a covalent complex where C6 of FdUMP is sp3
      hybridized and covalently linked to the thiol of Cys148. The proposed roles of a number of
      other residues in CH are currently under investigation.
AU  - Graves KL
AU  - Butler MM
AU  - Hardy LW
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1993 7: A1197.

PMID- 23618714
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of MKD8, a Conjugal Recipient Mycobacterium smegmatis Strain.
PG  - e00148-13
AB  - We report an annotated draft genome sequence of the Mycobacterium smegmatis strain MKD8. This
      strain acts as a recipient during conjugation with the
      reference M. smegmatis strain mc(2)155. While the genomes of the two strains are
      colinear and have similar sizes, extensive genome-wide sequence variation
      suggests rich diversity within the M. smegmatis clade.
AU  - Gray TA
AU  - Palumbo MJ
AU  - Derbyshire KM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00148-13.

PMID- 11842098
VI  - 30
DP  - 2002
TI  - Crystal structure of the Bse634I restriction endonuclease: comparison of two enzymes recognizing the same DNA sequence.
PG  - 876-885
AB  - Crystal structures of Type II restriction endonucleases demonstrate a conserved common core
      and active site residues but diverse structural elements involved in DNA sequence
      discrimination. Comparative structural analysis of restriction enzymes recognizing the same
      nucleotide sequence might therefore contribute to our understanding of the structural
      diversity of specificity determinants within restriction enzymes. We have solved the crystal
      structure of the Bacillus stearothermophilus restriction endonuclease Bse634I by the multiple
      isomorphous replacement technique to 2.17 Angstroms resolution. Bse634I is an isoschisomer of
      the Cfr10I restriction enzyme whose crystal structure has been reported previously.
      Comparative structural analysis of the first pair of isoschisomeric enzymes revealed conserved
      structural determinants of sequence recognition and catalysis. However, conformations of the
      N-terminal subdomains differed between Bse634I/Cfr10I, suggesting a rigid body movement that
      might couple DNA recognition and catalysis. Structural similarities extend to the quaternary
      structure level: crystal contacts suggest that Bse634I similarly to Cfr10I is arranged as a
      tetramer. Kinetic analysis reveals that Bse634I is able to interact simultaneously with two
      recognition sites supporting the tetrameric architecture of the protein. Thus, restriction
      enzymes Bse634I, Cfr10I and NgoMIV, recognizing overlapping nucleotide sequences, exhibit a
      conserved tetrameric architecture that is of functional importance.
      * To whom correspondence should be addressed at: Institute of Biotechnolo
AU  - Grazulis S
AU  - Deibert M
AU  - Rimseliene R
AU  - Skirgaila R
AU  - Sasnauskas G
AU  - Lagunavicius A
AU  - Repin V
AU  - Urbanke C
AU  - Huber R
AU  - Siksnys V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2002 30: 876-885.

PMID- 16247004
VI  - 102
DP  - 2005
TI  - Structure of the metal-independent restriction enzyme BfiI reveals fusion of a specific DNA-binding domain with a nonspecific nuclease.
PG  - 15797-15802
AB  - Among all restriction endonucleases known to date, BfiI is unique in cleaving DNA in the
      absence of metal ions. BfiI represents a different
      evolutionary lineage of restriction enzymes, as shown by its crystal
      structure at 1.9-A resolution. The protein consists of two structural
      domains. The N-terminal catalytic domain is similar to Nuc, an
      EDTA-resistant nuclease from the phospholipase D superfamily. The
      C-terminal DNA-binding domain of BfiI exhibits a beta-barrel-like
      structure very similar to the effector DNA-binding domain of the
      Mg(2+)-dependent restriction enzyme EcoRII and to the B3-like DNA-binding
      domain of plant transcription factors. BfiI presumably evolved through
      domain fusion of a DNA-recognition element to a nonspecific nuclease akin
      to Nuc and elaborated a mechanism to limit DNA cleavage to a single
      double-strand break near the specific recognition sequence. The crystal
      structure suggests that the interdomain linker may act as an autoinhibitor
      controlling BfiI catalytic activity in the absence of a specific DNA
      sequence. A psi-blast search identified a BfiI homologue in a
      Mesorhizobium sp. BNC1 bacteria strain, a plant symbiont isolated from an
      EDTA-rich environment.
AU  - Grazulis S
AU  - Manakova E
AU  - Roessle M
AU  - Bochtler M
AU  - Tamulaitiene G
AU  - Huber R
AU  - Siksnys V
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2005 102: 15797-15802.

PMID- 16088825
VI  - 192
DP  - 2005
TI  - Genome Sequence of a Serotype M28 Strain of Group A Streptococcus: Potential New Insights into Puerperal Sepsis and Bacterial Disease   Specificity.
PG  - 760-770
AB  - Puerperal sepsis, a major cause of death of young women in Europe in the 1800s, was due
      predominantly to the gram-positive pathogen group A
      Streptococcus. Studies conducted during past decades have shown that
      serotype M28 strains are the major group A Streptococcus organisms
      responsible for many of these infections. To begin to increase our
      understanding of their enrichment in puerperal sepsis, we sequenced the
      genome of a genetically representative strain. This strain has genes
      encoding a novel array of prophage virulence factors, cell-surface
      proteins, and other molecules likely to contribute to host-pathogen
      interactions. Importantly, genes for 7 inferred extracellular proteins are
      encoded by a 37.4-kb foreign DNA element that is shared with group B
      Streptococcus and is present in all serotype M28 strains. Proteins encoded
      by the 37.4-kb element were expressed extracellularly and in human
      infections. Acquisition of foreign genes has helped create a
      disease-specialist clone of this pathogen.
AU  - Green NM
AU  - Zhang S
AU  - Porcella SF
AU  - Nagiec MJ
AU  - Barbian KD
AU  - Beres SB
AU  - Lefebvre RB
AU  - Musser JM
PT  - Journal Article
TA  - J. Infect. Dis.
JT  - J. Infect. Dis.
SO  - J. Infect. Dis. 2005 192: 760-770.

PMID- 6251833
VI  - 95
DP  - 1980
TI  - The isolation of a restriction enzyme from Bordetella pertussis.
PG  - 1282-1287
AB  - A restriction enzyme was isolated from Bordetella pertussis cells by a
      single-step purification procedure using chromatography on phosphocellulose.
      Different DNA molecules were digested with this enzyme; the fragmentation
      patterns obtained were compared to those obtained after digestion with the
      HindIII enzyme isolated from Haemophilus influenzae strain Rd.  It was
      concluded that the cleavage site specificities of these enzymes were identical.
AU  - Greenaway PJ
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1980 95: 1282-1287.

PMID- 17827295
VI  - 189
DP  - 2007
TI  - Genome sequence analysis of the emerging human pathogenic acetic acid bacterium Granulibacter bethesdensis.
PG  - 8727-8736
AB  - Chronic granulomatous disease (CGD) is an inherited immune deficiency characterized by
      increased susceptibility to infection with
      Staphylococcus, certain gram-negative bacteria, and fungi. Granulibacter
      bethesdensis, a newly described genus and species within the family
      Acetobacteraceae, was recently isolated from four CGD patients residing in
      geographically distinct locales who presented with fever and
      lymphadenitis. We sequenced the genome of the reference strain of
      Granulibacter bethesdensis, which was isolated from lymph nodes of the
      original patient. The genome contains 2,708,355 base pairs in a single
      circular chromosome, in which 2,437 putative open reading frames (ORFs)
      were identified, 1,470 of which share sequence similarity with ORFs in the
      nonpathogenic but related Gluconobacter oxydans genome. Included in the
      967 ORFs that are unique to G. bethesdensis are ORFs potentially important
      for virulence, adherence, DNA uptake, and methanol utilization. GC% values
      and best BLAST analysis suggested that some of these unique ORFs were
      recently acquired. Comparison of G. bethesdensis to other known CGD
      pathogens demonstrated conservation of some putative virulence factors,
      suggesting possible common mechanisms involved in pathogenesis in CGD.
      Genotyping of the four patient isolates by use of a custom microarray
      demonstrated genome-wide variations in regions encoding DNA uptake systems
      and transcriptional regulators and in hypothetical ORFs. G. bethesdensis
      is a genetically diverse emerging human pathogen that may have recently
      acquired virulence factors new to this family of organisms.
AU  - Greenberg DE
AU  - Porcella SF
AU  - Zelazny AM
AU  - Virtaneva K
AU  - Sturdevant DE
AU  - Kupko JJ
AU  - Barbian KD
AU  - Babar A
AU  - Dorward DW
AU  - Holland SM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2007 189: 8727-8736.

PMID- 3856713
VI  - 9B
DP  - 1985
TI  - Site-directed mutagenesis of the EcoRI endonuclease.
PG  - 94
AB  - The EcoRI endonuclease has been crystallized with its substrate and the X-ray
      structure has been solved to 3 angstroms (Nature 309: 327, 1984).  Sequence
      recognition is mediated by a series of hydrogen bonds between complementary
      surfaces of the protein and the major groove of the DNA.  We have used the
      crystallographic analysis to design putative specificity mutations in the
      endonuclease and to predict possible new specificities that might arise.  In
      particular, a glutamic acid residue which is postulated to interact with the N6
      positions of the adjacent adenines in the recognition sequence has been
      replaced with glutamic acid.  The predicted recognition sequence would contain
      a guanine in place of one of the adenines.  This alteration has been introduced
      into the endonuclease gene by means of mismatch primer mutagenesis.  The
      expression and characterization of the mutant protein is underway.
AU  - Greene P
AU  - Reich NO
AU  - McClarin J
AU  - Boyer HW
AU  - Rosenberg J
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1985 9B: 94.

PMID- 2851493
VI  - 68
DP  - 1988
TI  - Purification and characterization of the restriction endonuclease RsrI, an isoschizomer of EcoRI.
PG  - 43-52
AB  - Rhodobacter sphaeroides strain 630 produces restriction enzyme RsrI which is an
      isoschizoemr of EcoRI.  We have purified this enzyme and initiated a comparison
      with the EcoRI endonuclease.  The properties of RsrI are consistent with a
      reaction mechanism similar to that of EcoRI:  the position of cleavage within
      the -GAATTC- site is identical, the MgCl2 optimum for the cleavage is
      identical, and the pH profile is similar.  Methylation of the substrate
      sequence by the EcoRI methylase protects the site from cleavage by the RsrI
      endonuclease.  RsrI cross-reacts strongly with anti-EcoRI serum indicating
      three-dimensional structural similarities.  We have determined the sequence of
      34 N-terminal amino acids for RsrI and this sequence possesses significant
      similarity to the EcoRI N terminus.
AU  - Greene PJ
AU  - Ballard BT
AU  - Stephenson F
AU  - Kohr WJ
AU  - Rodriguez H
AU  - Rosenberg JM
AU  - Boyer HW
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 68: 43-52.

PMID- Not included in PubMed...
VI  - 7
DP  - 1974
TI  - The EcoRI restriction endonuclease.
PG  - 87-105
AB  - Type II bacterial restriction endonucleases have become increasingly useful in
      the analysis of small DNA genomes, while attempts to use the Type I restriction
      endonucleases have not been satisfactory because they appear to be less
      specific than originally imagined.  The current purification procedure for the
      EcoRI restriction endonuclease and some of its properties, as well as a
      procedure for partial purification of the related EcoRI modification methylase,
      are described.
AU  - Greene PJ
AU  - Betlach MC
AU  - Boyer HW
AU  - Goodman HM
PT  - Journal Article
TA  - Methods Mol. Biol.
JT  - Methods Mol. Biol.
SO  - Methods Mol. Biol. 1974 7: 87-105.

PMID- 7461146
VI  - 40
DP  - 1981
TI  - Genetic and molecular analysis of the EcoRI restriction and modification system.
PG  - 293
AB  - The structure and function of the EcoRI endonuclease and methylase are being
      studied in order to elucidate how proteins recognize specific DNA sequences.
      We have crystallized the EcoRI endonuclease and measured space group and unit
      cell parameters.  We plan to sequence the endonuclease and methylase by
      sequencing the DNA which encodes them.  The genes are closely linked on a
      multicopy plasmid, pMB1.  The approximate boundaries of the genes have been
      determined by cloning different restriction fragments.  Based on subunit
      molecular weight estimates of 36,000 daltons and 29,000 daltons for the
      methylase and endonuclease respectively, the required length of DNA for both
      structural genes is ~ 1800 base pairs.  A 2300 base pair restriction fragment
      has been shown to contain all of the information necessary for the expression
      of normal levels of both enzymes.  A detailed restriction map of this fragment
      has been prepared using the technique of end labeling followed by partial
      digestion.  DNA sequencing is underway using chain terminating inhibitors.
      Clones have been isolated with this fragment in both orientations relative to
      the lac promoter and operator in pBH20.  The effect of the lac control system
      on the specific activity of EcoRI enzymes suggests that the direction of
      transcription is from the endonuclease to the methylase.
AU  - Greene PJ
AU  - Boyer HW
PT  - Journal Article
TA  - Fed. Proc.
JT  - Fed. Proc.
SO  - Fed. Proc. 1981 40: 293.

PMID- 6257703
VI  - 256
DP  - 1981
TI  - Sequence Analysis of the DNA Encoding the EcoRI Endonuclease and Methylase.
PG  - 2143-2153
AB  - The EcoRI endonuclease and methylase recognize the same hexanucleotide substrate sequence.  We
      have determined the sequence of a fragment of DNA which encodes these enzymes using the
      chain-termination method of Sanger (Sanger, F., Nicklen, S., and Coulson, A.R. (1977) Proc.
      Natl. Acad. Sci. U.S.A. 74, 5463-5467).  The amino acid sequences of both enzymes were derived
      from the DNA sequence.  The coding regions selected include the only open translational frames
      of sufficient length to accommodate the enzymes.  They coincide with previously established
      gene boundaries and orientation.  The predicted amino acid sequences correlate well with
      analyses of the purified protein. Comparison of the nucleotide and protein sequences reveals
      no homology between the endonuclease and methylase which might provide insight into the origin
      of the restriction-modification system or the mechanism of common substrate recognition.
      Based on secondary structure predictions, the two enzymes also have grossly different
      molecular architecture.  The base composition of the sequence is 65% A + T, and the codon
      usage is signficantly different from that observed in several Escherichia coli chromosomal
      genes.  In some cases, frequently selected codons are recognized by minor tRNA species.  A
      spontaneous mutation in the endonuclease gene was isolated.  Serine replaces arginine at
      residue 187.  In crude extracts, EcoRI specific cleavage is ~0.3% wild type.
AU  - Greene PJ
AU  - Gupta M
AU  - Boyer HW
AU  - Brown WE
AU  - Rosenberg JM
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1981 256: 2143-2153.

PMID- 673857
VI  - 5
DP  - 1978
TI  - A general method for the purification of restriction enzymes.
PG  - 2373-2380
AB  - An abbreviated procedure has been developed for the purification of restriction
      endonucleases.  This procedure uses chromatography on phosphocellulose and
      hydroxylapatite and results in enzymes of sufficient purity to permit their use
      in the sequencing, molecular cloning, and physical mapping of DNA.
AU  - Greene PJ
AU  - Heyneker HL
AU  - Bolivar F
AU  - Rodriguez RL
AU  - Betlach MC
AU  - Covarrubias AA
AU  - Backman K
AU  - Russel DJ
AU  - Tait R
AU  - Boyer HW
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1978 5: 2373-2380.

PMID- 173854
VI  - 99
DP  - 1975
TI  - Restriction and modification of a self-complementary octanucleotide containing the EcoRI substrate.
PG  - 237-261
AB  - In order to study the interactions of the EcoRI restriction endonuclease and
      modification methylase with DNA, we have synthesized the self-complementary
      octanucleotide, pT-G-A-A-T-T-C-A, which contains the nucleotide sequence of the
      EcoRI substrate.  This octamer can act as a substrate for both the endonuclease
      and methylase; the enzymatic alteration of this molecule is the same as that of
      DNA, with cleavage and methylation both occurring at the same positions on
      either substrate.  The optimum temperature for the reaction of the
      octanucleotide with the endonuclease is 15C and that with the methylase is
      12.5C.  The optimum temperature for the reactions of both of the enzymes with
      DNA is 37C.  The low temperatures for reactions with the octanucleotide reflect
      the conditions under which this molecule can serve as a substrate for the
      enzymes.
AU  - Greene PJ
AU  - Poonian MS
AU  - Nussbaum AL
AU  - Tobias L
AU  - Garfin DE
AU  - Boyer HW
AU  - Goodman HM
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1975 99: 237-261.

PMID- 
VI  - 0
DP  - 1987
TI  - Structure and function of the EcoRI endonuclease.
PG  - 3-7
AB  - None
AU  - Greene PJ
AU  - Yanofsky S
AU  - Reich N
AU  - Day J
AU  - Hager P
AU  - Boyer HW
PT  - Journal Article
TA  - Protein Structure, Folding and Design 2
JT  - Protein Structure, Folding and Design 2
SO  - Protein Structure, Folding and Design 2 1987 0: 3-7.

PMID- 
VI  - 0
DP  - 1986
TI  - The effect of DNA-mediated restriction on conjugation in Neisseria gonorrhoeae.
PG  - 1-138
AB  - A derivative of the gonococcal shuttle-vector pLES2 containing the proAB genes of Neisseria
      gonorrhoeae strain KH45 was mobilized by the gonococcal conjugal plasmid into Escherichia coli
      recipients independent of the host strain restriction-modification phenotype.  Introduction of
      this plasmid into E. coli via conjugation does not result in deletions.  Expression of the
      proline biosynthesis genes was confirmed by cultivation of transconjugants on media devoid of
      proline.  The plasmid was mobilized to various gonococcal strains.  Transfer frequencies of
      10^-5 were obtained.  When isogenic crosses between the recipient D13 strain, and D13
      containing pLES4, were compared, transfer occurred at 10^-2.  The role of restriction during
      conjugation was investigated as an explanation for the increase in transfer efficiency.  The
      self-mobilizable plasmid pFT6, propagated in an R.NgoII-, M.NgoII- gonococcal strain, was used
      in filter matings with R.NgoII- M.NgoII+, R.NgoII+ M.NgoII+, and R.NgoII- M.NgoII- recipient
      strains.  The results demonstrated that the plasmid mobilized to the gonococcal recipients at
      equal frequencies, indicating that restriction was not a barrier to conjugation.  Introduction
      of pLES4 into commensal species of the Neisseriaceae via conjugation was unsuccessful.  A
      mechanism other than restriction is presented as a possible factor influencing conjugation in
      the gonococcus.
AU  - Gregoire ST
PT  - Journal Article
TA  - M.Sc. Thesis. Univ. Maryland.
JT  - M.Sc. Thesis. Univ. Maryland.
SO  - M.Sc. Thesis. Univ. Maryland. 1986 0: 1-138.

PMID- 12351230
VI  - 214
DP  - 2002
TI  - Plasmid pC present in Salmonella enterica serovar Enteritidis PT14b strains encodes a restriction modification system.
PG  - 195-198
AB  - Salmonella enterica serovar Enteritidis (S. enteritidis) possesses plasmids of different sizes
      and roles. Besides the serovar-specific
      virulence plasmid present in most field strains, S. enteritidis can
      harbour plasmids of low molecular mass whose biological role is poorly
      understood. We therefore sequenced plasmid pC present in S. enteritidis
      strains belonging to phage type PT14b. The size of plasmid was
      determined to be 5269 bp and it was predicted to encode four open
      reading frames (ORFs). The first two ORFs were found (initial 3230 bp)
      to be highly homologous to rom and mbeA genes of Co1E1 plasmid of
      Escherichia coli. Proteins encoded by the other two ORFs were 99%
      homologous to a restriction methylase and restriction endonuclease
      encoded by plasmid pECO29 of a field strain of E. coli. Using
      insertional mutagenesis we confirmed experimentally that the plasmid
      pC-encoded restriction modification system was functional and could
      explain the high resistance of S. enteritidis PT14b strains to phage
      infection.
AU  - Gregorova D
AU  - Pravcova M
AU  - Karpiskova R
AU  - Rychlik I
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2002 214: 195-198.

PMID- 20211223
VI  - 100
DP  - 2010
TI  - Rule-based simulation of temperate bacteriophage infection: Restriction-modification as a limiter to infection in bacterial populations.
PG  - 166-177
AB  - An individual-based model (IbM) for bacterial adaptation and evolution, COSMIC-Rules, has been
      employed to simulate interactions of virtual
      temperate bacteriophages (phages) and their bacterial hosts. Outcomes
      of infection mimic those of a phage such as lambda, which can enter
      either the lytic or lysogenic cycle, depending on the nutritional
      status of the host. Infection of different hosts possessing differing
      restriction and modification systems is also simulated. Phages
      restricted upon infection of one restricting host can be adapted (by
      host-controlled modification of the phage genome) and subsequently
      propagate with full efficiency on this host. However, such ability is
      lost if the progeny phages are passaged through a new host with a
      different restriction and modification system before attempted
      re-infection of the original restrictive host. The simulations show
      that adaptation and re-adaptation to a particular host-controlled
      restriction and modification system result in lower efficiency and
      delayed lysis of bacterial cells compared with infection of
      non-restricting host bacteria.
      Such biologically realistic simulations validate the use of the IbM
      approach to predicting behaviour of bacteriophages in bacterial
      populations. The applicability of the model for more complex scenarios
      aimed at predictive modelling of bacterial evolution in a changing
      environment and the implications for the spread of viruses in a wider
      context are discussed.
AU  - Gregory R
AU  - Saunders VA
AU  - Saunders JR
PT  - Journal Article
TA  - Biosystems
JT  - Biosystems
SO  - Biosystems 2010 100: 166-177.

PMID- 24459279
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Mycobacterium tuberculosis Strain MtURU-001, Isolated from a Rapidly Progressing Outbreak in Uruguay.
PG  - e01220-13
AB  - Despite efficient control programs, large clonal outbreaks of tuberculosis (TB) may arise in
      low-risk populations. Recently, an unusual TB outbreak was reported
      in Uruguay, reaching an elevated disease attack rate (53 to 69%). Here, we report
      the genome sequence of the Mycobacterium tuberculosis strain associated with this
      rapidly progressing outbreak, named MtURU-001.
AU  - Greif G
AU  - Iraola G
AU  - Berna L
AU  - Coitinho C
AU  - Rivas CM
AU  - Naya H
AU  - Robello C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01220-13.

PMID- 16938559
VI  - 410
DP  - 2006
TI  - DamID: Mapping of in vivo protein-genome interactions using tethered DNA adenine methyltransferase.
PG  - 342-359
AB  - A large variety of proteins bind to specific parts of the genome to regulate gene expression,
      DNA replication, and chromatin structure.
      DamID is a powerful method used to map the genomic interaction sites of
      these proteins in vivo. It is based on fusing a protein of interest to
      Escherichia coli DNA adenine methyltransferase (dam). Expression of
      this fusion protein in vivo leads to preferential methylation of
      adenines in DNA surrounding the native binding sites of the dam fusion
      partner. Because adenine methylation does not occur endogenously in
      most eukaryotes, it provides a unique tag to mark protein interaction
      sites. The adenine-methylated DNA fragments are isolated by selective
      polymerase chain reaction amplification and can be identified by
      microarray hybridization. We and others have successfully applied DamID
      to the genome-wide identification of interaction sites of several
      transcription factors and other chromatin-associated proteins. This
      chapter discusses DamID technology in detail, and a step-by-step
      experimental protocol is provided for use in Drosophila cell lines.
AU  - Greil F
AU  - Moorman C
AU  - van Steensel B
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 2006 410: 342-359.

PMID- 25323716
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Escherichia coli BW25113.
PG  - e01038-14
AB  - Escherichia coli BW25113 is the parent strain of the Keio collection comprising nearly 4,000
      single-gene deletion mutants. We report the complete 4,631,469-bp
      genome sequence of this strain and the key variations from the type strain E.
      coli MG1655.
AU  - Grenier F
AU  - Matteau D
AU  - Baby V
AU  - Rodrigue S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01038-14.

PMID- 25977423
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Four NDM-1-Producing Klebsiella pneumoniae Strains from a Health Care Facility in Northern California.
PG  - e00421-15
AB  - We report the draft genome sequences of Klebsiella pneumoniae strains from four patients at a
      northern California health care facility. All strains contained the
      New Delhi metallo-beta-lactamase (NDM1) carbapenemase with extended antibiotic
      resistance, including resistance to expanded-spectrum cephalosporins, imipenem,
      ertapenem, and meropenem. NDM gene alignments revealed that the resistance was
      plasmid encoded.
AU  - Greninger AL
AU  - Chorny I
AU  - Knowles S
AU  - Ng VL
AU  - Chaturvedi V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00421-15.

PMID- 26316632
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Mycobacterium heckeshornense Strain RLE.
PG  - e00930-15
AB  - We report here the draft genome sequence of Mycobacterium heckeshornense strain RLE isolated
      from a sputum sample from a patient with shortness of breath. This is the first draft genome
      sequence of M. heckeshornense.
AU  - Greninger AL
AU  - Cunningham G
AU  - Chiu CY
AU  - Miller S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00930-15.

PMID- 26205863
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Mycobacterium heraklionense Strain Davo.
PG  - e00807-15
AB  - We report the draft genome sequence of Mycobacterium heraklionense strain Davo, isolated from
      a fine-needle aspirate of a right-ankle soft-tissue mass. This is
      the first draft genome sequence of Mycobacterium heraklionense, a nonpigmented
      rapidly growing mycobacterium.
AU  - Greninger AL
AU  - Cunningham G
AU  - Chiu CY
AU  - Miller S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00807-15.

PMID- 26067960
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Mycobacterium obuense Strain UC1, Isolated from Patient  Sputum.
PG  - e00612-15
AB  - We report the draft genome sequence of Mycobacterium obuense strain UC1 from a patient sputum
      sample. This is the first draft genome sequence of Mycobacterium
      obuense, a rapidly growing scotochromogenic mycobacterium.
AU  - Greninger AL
AU  - Cunningham G
AU  - Hsu ED
AU  - Yu JM
AU  - Chiu CY
AU  - Miller S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00612-15.

PMID- 26112791
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Mycobacterium elephantis Strain Lipa.
PG  - e00691-15
AB  - We report the draft genome sequence of Mycobacterium elephantis strain Lipa from  a sputum
      sample of a patient with pulmonary disease. This is the first draft
      genome sequence of M. elephantis, a rapidly growing mycobacterium.
AU  - Greninger AL
AU  - Cunningham G
AU  - Yu JM
AU  - Hsu ED
AU  - Chiu CY
AU  - Miller S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00691-15.

PMID- 26067970
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Mycobacterium arupense Strain GUC1.
PG  - e00630-15
AB  - We report the draft genome sequence of Mycobacterium arupense strain GUC1 from a  sputum
      sample of a patient with bronchiectasis. This is the first draft genome
      sequence of Mycobacterium arupense, a rapidly growing nonchromogenic
      mycobacteria.
AU  - Greninger AL
AU  - Cunningham G
AU  - Yu JM
AU  - Hsu ED
AU  - Chiu CY
AU  - Miller S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00630-15.

PMID- 26383669
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Turicella otitidis TD1, Isolated from a Patient with Bacteremia.
PG  - e01060-15
AB  - We report the draft genome sequence of Turicella otitidis strain TD1, isolated from a central
      line catheter sample from a patient with a history of bowel obstruction. It contained several
      genetic determinants of multidrug-resistant phenotypes such as a cfrA 50S methyltransferase,
      two major facilitator superfamily-type drug resistance transporters, and a putative
      beta-lactamase.
AU  - Greninger AL
AU  - Kozyreva V
AU  - Truong CL
AU  - Graves M
AU  - Chaturvedi V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01060-15.

PMID- 26358603
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Kerstersia gyiorum CG1, Isolated from a Leg Ulcer.
PG  - e01036-15
AB  - We report the first draft genome sequence of Kerstersia gyiorum from a leg ulcer  of a patient
      with diabetes and osteomyelitis. The 3.94-Mb genome assembly included 3,428 annotated coding
      sequences with an N50 of 223,310 bp and a plasmid encoding a type IV secretion system gene and
      two antitoxin genes.
AU  - Greninger AL
AU  - Kozyreva V
AU  - Truong CL
AU  - Longoria R
AU  - Chaturvedi V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01036-15.

PMID- 27834718
VI  - 4
DP  - 2016
TI  - First Draft Genome Sequences of Neisseria sp. Strain 83E34 and Neisseria sp. Strain 74A18, Previously Identified as CDC Eugonic Fermenter 4b Species.
PG  - e01277-16
AB  - We report the first draft genome sequences of two isolates previously classified  as CDC EF-4b
      species, Neisseria sp. 83E34 and Neisseria sp. 74A18. Both strains
      were isolated from patients with animal bites and likely constitute novel
      genomospecies with average nucleotide identities of <95% to other sequenced
      strains.
AU  - Greninger AL
AU  - Streithorst J
AU  - Chiu CY
AU  - Miller S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01277-16.

PMID- 28360160
VI  - 5
DP  - 2017
TI  - First Complete Genome Sequence of Corynebacterium riegelii.
PG  - e00084-17
AB  - Here, we report the first complete genome sequence of Corynebacterium riegelii strain
      PUDD_83A45, isolated from the urine of a patient with urinary tract
      infection. The genome measured 2.56 Mb and contained no plasmid.
AU  - Greninger AL
AU  - Streithorst J
AU  - Chiu CY
AU  - Miller S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00084-17.

PMID- 22493197
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Persistent Salmonella enterica subsp. enterica Serotype Senftenberg Strain SS209.
PG  - 2385-2386
AB  - Salmonella enterica subsp. enterica serotype Senftenberg is an emerging serotype  in poultry
      production which has been found to persist in animals and the farm
      environment. We report the genome sequence and annotation of the SS209 strain of
      S. Senftenberg, isolated from a hatchery, which was identified as persistent in
      broiler chickens.
AU  - Grepinet O
AU  - Boumart Z
AU  - Virlogeux-Payant I
AU  - Loux V
AU  - Chiapello H
AU  - Gendrault A
AU  - Gibrat JF
AU  - Chemaly M
AU  - Velge P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2385-2386.

PMID- 22493198
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Invasive Salmonella enterica subsp. enterica Serotype Enteritidis Strain LA5.
PG  - 2387-2388
AB  - Salmonella enterica subsp. enterica serotype Enteritidis is one of the major causes of
      gastroenteritis in humans due to consumption of poultry derivatives.
      Here we report the whole-genome sequence and annotation, including the virulence
      plasmid, of S. Enteritidis LA5, which is a chicken isolate used by numerous
      laboratories in virulence studies.
AU  - Grepinet O
AU  - Rossignol A
AU  - Loux V
AU  - Chiapello H
AU  - Gendrault A
AU  - Gibrat JF
AU  - Velge P
AU  - Virlogeux-Payant I
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2387-2388.

PMID- 16217547
VI  - 1
DP  - 2005
TI  - Gain and loss of multiple genes during the evolution of Helicobacter pylori.
PG  - e43
AB  - Sequence diversity and gene content distinguish most isolates of Helicobacter pylori. Even
      greater sequence differences differentiate distinct populations of H. pylori from different
      continents, but it was not clear whether these populations also differ in gene content. To
      address this question, we tested 56 globally representative strains of H. pylori and four
      strains of Helicobacter acinonychis with whole genome microarrays. Of the weighted average of
      1,531 genes present in the two sequenced genomes, 25% are absent in at least one strain of H.
      pylori and 21% were absent or variable in H. acinonychis. We extrapolate that the core genome
      present in all isolates of H. pylori contains 1,111 genes. Variable genes tend to be small and
      possess unusual GC content; many of them have probably been imported by horizontal gene
      transfer. Phylogenetic trees based on the microarray data differ from those based on sequences
      of seven genes from the core genome. These discrepancies are due to homoplasies resulting from
      independent gene loss by deletion or recombination in multiple strains, which distort
      phylogenetic patterns. The patterns of these discrepancies versus population structure allow a
      reconstruction of the timing of the acquisition of variable genes within this species.
      Variable genes that are located within the cag pathogenicity island were apparently first
      acquired en bloc after speciation. In contrast, most other variable genes are of unknown
      function or encode restriction/modification enzymes, transposases, or outer membrane proteins.
      These seem to have been acquired prior to speciation of H. pylori and were subsequently lost
      by convergent evolution within individual strains. Thus, the use of microarrays can reveal
      patterns of gene gain or loss when examined within a phylogenetic context that is based on
      sequences of core genes.
AU  - Gressmann H
AU  - Linz B
AU  - Ghai R
AU  - Pleissner KP
AU  - Schlapbach R
AU  - Yamaoka Y
AU  - Kraft C
AU  - Suerbaum S
AU  - Meyer TF
AU  - Achtman M
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2005 1: e43.

PMID- 20037647
VI  - 4
DP  - 2009
TI  - High throughput sequencing and proteomics to identify immunogenic proteins of a new pathogen: the dirty genome approach.
PG  - E8423
AB  - BACKGROUND: With the availability of new generation sequencing
      technologies, bacterial genome projects have undergone a major boost.
      Still, chromosome completion needs a costly and time-consuming gap
      closure, especially when containing highly repetitive elements. However,
      incomplete genome data may be sufficiently informative to derive the
      pursued information. For emerging pathogens, i.e. newly identified
      pathogens, lack of release of genome data during gap closure stage is
      clearly medically counterproductive. METHODS/PRINCIPAL FINDINGS: We thus
      investigated the feasibility of a dirty genome approach, i.e. the release
      of unfinished genome sequences to develop serological diagnostic tools. We
      showed that almost the whole genome sequence of the emerging pathogen
      Parachlamydia acanthamoebae was retrieved even with relatively short reads
      from Genome Sequencer 20 and Solexa. The bacterial proteome was analyzed
      to select immunogenic proteins, which were then expressed and used to
      elaborate the first steps of an ELISA. CONCLUSIONS/SIGNIFICANCE: This work
      constitutes the proof of principle for a dirty genome approach, i.e. the
      use of unfinished genome sequences of pathogenic bacteria, coupled with
      proteomics to rapidly identify new immunogenic proteins useful to develop
      in the future specific diagnostic tests such as ELISA,
      immunohistochemistry and direct antigen detection. Although applied here
      to an emerging pathogen, this combined dirty genome sequencing/proteomic
      approach may be used for any pathogen for which better diagnostics are
      needed. These genome sequences may also be very useful to develop DNA
      based diagnostic tests. All these diagnostic tools will allow further
      evaluations of the pathogenic potential of this obligate intracellular
      bacterium.
AU  - Greub G
AU  - Kebbi-Beghdadi C
AU  - Bertelli C
AU  - Collyn F
AU  - Riederer BM
AU  - Yersin C
AU  - Croxatto A
AU  - Raoult D
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2009 4: E8423.

PMID- 25189587
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Pseudomonas sp. Strain JMM, a Sediment-Hosted Environmental Isolate.
PG  - e00879-14
AB  - Pseudomonas sp. strain JMM was isolated from the sediments of a natural water reservoir (pH, 6
      to 7) located at Chambyal village in Samba district of Jammu and
      Kashmir, India. Here we report the annotated draft genome sequence of strain JMM
      having 52 contigs with 5,884 genes and an average G+C content of 66.5%.
AU  - Grewal S
AU  - Vakhlu J
AU  - Gupta V
AU  - Sangwan N
AU  - Kohli P
AU  - Nayyar N
AU  - Rani P
AU  - Sance SS
AU  - Lal R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00879-14.

PMID- 8161538
VI  - 33
DP  - 1994
TI  - DNA mismatch binding and incision at modified guanine bases by extracts of mammalian cells: implications for tolerance to DNA methylation damage.
PG  - 4787-4793
AB  - Two activities involved in separate pathways for correcting G.T mispairs in DNA have been
      assayed on duplex substrates containing modified guanine bases. The first, the G.T mismatch
      incision activity, is specifically involved in short-patch repair of mispairs arising via
      deamination of 5-methylcytosine. The second activity can be detected by its ability to bind to
      G.T mispairs and may initiate correction by a long-patch mechanism. 6-Thioguanine and
      06-methylguanine paired with thymine were efficiently incised by cell extracts if the modified
      guanine was in a CpG dinucleotide. Incision was not observed when either purine was paired
      with cytosine. Extracts of cells that are tolerant both to methylation damage and to
      6-thioguanine in DNA also incised 6-thioguanine.T and O6-methylguanine.T base pairs. The data
      suggest that this activity is unlikely to contribute significantly to the biological effects
      of 06-methylguanine in DNA. A defect in this pathway is therefore unlikely to explain the
      cross-resistance of tolerant cells to the two base analogs in DNA. In binding assays,
      6-thioguanine-T base pairs were recognized efficiently and to an equivalent extent by the same
      protein complex as G.T mispairs. O6-methylguanine.T base pairs were also recognized but with
      reduced efficiency. No binding was observed to 6-thioguanine.C or O6-methylguanine.C base
      pairs. Recognition by the binding complex was essentially independent of the base immediately
      5' to the mismatched guanine but was somewhat more efficient if O6-methylguanine was preceded
      by a purine. Extracts of two tolerant lines with a known defect in G.T mismatch binding failed
      to form complexes with substrates containing the modified bases. The ability of the G.T
      binding factor to recognize both O6-methylguanine.T and 6-thioguanine.T pairs indicates that
      the long-patch repair pathway is more likely to be involved in mediating the cytotoxicity of
      the two-base analogs.
AU  - Griffin S
AU  - Branch P
AU  - Xu Y-Z
AU  - Karran P
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1994 33: 4787-4793.

PMID- 12409482
VI  - 30
DP  - 2002
TI  - AarI, a restriction endonuclease from Arthrobacter aurescens SS2-322, which recognizes the novel non-palindromic sequence 5'-CACCTGC(N)4/8-3'.
PG  - e123
AB  - A new type II restriction endonuclease AarI has been isolated from Arthrobacter aurescens
      SS2-322. AarI recognizes the non-palindromic heptanucleotide sequence 5'-CACCTGC(N)(4/8)-3'
      and makes a staggered cut at the fourth and eighth bases downstream of the target duplex
      producing a four base 5'-protruding end. AarI activity is stimulated by
      oligodeoxyribonucleotide duplexes containing an enzyme-specific recognition sequence.
AU  - Grigaite R
AU  - Maneliene Z
AU  - Janulaitis A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2002 30: e123.

PMID- 
VI  - 14
DP  - 2004
TI  - The integration of recognition and cleavage: X-ray structures of pre-transition state complex, post-reactive complex, and the DNA-free endonuclease.
PG  - 137-177
AB  - DNA has been selected as the biological information storage molecule for many reasons; one of
      which is its stability.  The rate of spontaneous hydrolysis of DNA (at 24oC and pH 7.4) was
      estimated at 5.7x10-14S-1; more recently, Radzicka and Wolfenden have estimated this value at
      1.7x10-13 s-1.  This corresponds to an estimated half-life of 130,000 years for a DNA
      phosphodiester bond in solution, placing DNA hydrolysis among the slowest of biochemical
      reactions in the absence of enzymes.
AU  - Grigorescu A
AU  - Horvath M
AU  - Wilkosz PA
AU  - Chandrasekhar K
AU  - Rosenberg JM
PT  - Journal Article
TA  - Nucleic Acids Mol. Biol.
JT  - Nucleic Acids Mol. Biol.
SO  - Nucleic Acids Mol. Biol. 2004 14: 137-177.

PMID- 
VI  - 86
DP  - 2004
TI  - A local folding transition coupled to site-specific binding in EcoRI restriction endonuclease.
PG  - 591a
AB  - Restriction endonuclease EcoRI is not only an invaluable tool in genetic engineering but also
      a paradigm for understanding the molecular
      mechanisms of protein-DNA recognition. Recent crystallographic data
      demonstrate that a major localized folding transition accompanies
      binding of the EcoRI restriction endonuclease to its cognate DNA site;
      this result is in accordance with previous biophysical studies which
      indicated a large conformational change taking place in the protein
      upon site-specific binding. The three-dimensional structure of the apo
      EcoRI enzyme reveals an unusual molecular architecture: a rigid
      scaffold with a small minidomain on top of it. In the absence of
      stabilizing inter-molecular contacts the minidomain does not adopt a
      well-ordered conformation. A structural analysis indicates that the
      metastability of this region of the protein is dictated by a
      combination of favorable and unfavorable tertiary interactions. The
      conformation of the minidomain observed in the specific protein-DNA
      complex is apparently stabilized by a set of favorable inter-molecular
      contacts. Many of these are highly specific contacts (recognition
      interactions) between the protein and the DNA substrate. All the amino
      acid substitutions that have been shown to alter (i.e. reduce) the DNA
      sequence specificity of the enzyme are localized in regions that
      exhibit low structural stability in the unbound protein. This, and
      other lines of evidence suggest that local native metastability is
      important for the molecular recognition function of the EcoRI
      endonuclease.
AU  - Grigorescu AA
AU  - Rosenberg JM
PT  - Journal Article
TA  - Biophys. J.
JT  - Biophys. J.
SO  - Biophys. J. 2004 86: 591a.

PMID- 23405317
VI  - 1
DP  - 2013
TI  - Draft Genome of the Nitrogen-Fixing Bacterium Pseudomonas stutzeri Strain KOS6 Isolated from Industrial Hydrocarbon Sludge.
PG  - e00072-12
AB  - Here we present a draft genome of Pseudomonas stutzeri strain KOS6. This strain was isolated
      from industrial hydrocarbon sludge as a diazotrophic microorganism.
      It represents one of the major parts of the culturable community of the waste and
      has potential importance for phytoremediation technology.
AU  - Grigoryeva TV
AU  - Laikov AV
AU  - Naumova RP
AU  - Manolov AI
AU  - Larin AK
AU  - Karpova IY
AU  - Semashko TA
AU  - Alexeev DG
AU  - Kostryukova ES
AU  - Muller R
AU  - Govorun VM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00072-12.

PMID- 25999578
VI  - 3
DP  - 2015
TI  - Genome Sequence of Cronobacter sakazakii Serogroup O:4, Sequence Type 4 Strain CDC 2009-03746, Isolated from a Fatal Case of Infantile Meningitis.
PG  - e00492-15
AB  - We report the draft genome sequence of a Cronobacter sakazakii serogroup O:4, sequence type 4
      strain, CDC 2009-03746 (=NM1240=2009-06-01), isolated from a
      fatal case of infantile meningitis. The draft genome has a size of 4,492,904 bp
      and a G+C% content of 56.7.
AU  - Grim CJ
AU  - Gopinath GR
AU  - Jarvis KG
AU  - Sathyamoorthy V
AU  - Trach LH
AU  - Chase HR
AU  - Tall BD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00492-15.

PMID- 24336376
VI  - 1
DP  - 2013
TI  - Genome Sequence of an Enterobacter helveticus Strain, 1159/04 (LMG 23733), Isolated from Fruit Powder.
PG  - e01038-13
AB  - We report the draft genome sequence of Enterobacter helveticus strain LMG 23733,  isolated
      from fruit powder. The draft genome assembly for E. helveticus strain
      LMG 23733 has a size of 4,635,476 bp and a G+C content of 55.9%.
AU  - Grim CJ
AU  - Gopinath GR
AU  - Mammel MK
AU  - Sathyamoorthy V
AU  - Trach LH
AU  - Chase HR
AU  - Tall BD
AU  - Fanning S
AU  - Stephan R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01038-13.

PMID- 20348258
VI  - 192
DP  - 2010
TI  - Genome Sequence of Hybrid Vibrio cholerae O1 MJ-1236, B-33, and CIRS101 and Comparative Genomics with V. cholerae.
PG  - 3524-3533
AB  - The genomes of Vibrio cholerae O1 Matlab variant MJ-1236, Mozambique O1 El Tor variant B33,
      and altered O1 El Tor CIRS101 were sequenced. All three
      strains were found to belong to the phylocore group 1 clade of V.
      cholerae, which includes the 7th-pandemic O1 El Tor and serogroup O139
      isolates, despite displaying certain characteristics of the classical
      biotype. All three strains were found to harbor a hybrid variant of CTXPhi
      and an integrative conjugative element (ICE), leading to their
      establishment as successful clinical clones and the displacement of
      prototypical O1 El Tor. The absence of strain- and group-specific genomic
      islands, some of which appear to be prophages and phage-like elements,
      seems to be the most likely factor in the recent establishment of
      dominance of V. cholerae CIRS101 over the other two hybrid strains.
AU  - Grim CJ
AU  - Hasan NA
AU  - Taviani E
AU  - Haley B
AU  - Chun J
AU  - Brettin TS
AU  - Bruce DC
AU  - Detter JC
AU  - Han CS
AU  - Chertkov O
AU  - Challacombe J
AU  - Huq A
AU  - Nair GB
AU  - Colwell RR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 3524-3533.

PMID- 27795288
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Vibrio (Listonella) anguillarum ATCC 14181.
PG  - e01185-16
AB  - We report the draft genome sequence of Vibrio anguillarum ATCC 14181, a Gram-negative,
      hemolytic, O2 serotype marine bacterium that causes mortality in
      mariculture species. The availability of this genome sequence will add to our
      knowledge of diversity and virulence mechanisms of Vibrio anguillarum as well as
      other pathogenic Vibrio spp.
AU  - Grim CJ
AU  - Schreier HJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01185-16.

PMID- 22689231
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Marine Bacterium Marinobacter hydrocarbonoclasticus SP17,  Which Forms Biofilms on Hydrophobic Organic Compounds.
PG  - 3539-3540
AB  - Marinobacter hydrocarbonoclasticus SP17 forms biofilms specifically at the interface between
      water and hydrophobic organic compounds (HOCs) that are used as
      carbon and energy sources. Biofilm formation at the HOC-water interface has been
      recognized as a strategy to overcome the low availability of these nearly
      water-insoluble substrates. Here, we present the genome sequence of SP17, which
      could provide further insights into the mechanisms of enhancement of HOCs
      assimilation through biofilm formation.
AU  - Grimaud R
AU  - Ghiglione JF
AU  - Cagnon C
AU  - Lauga B
AU  - Vaysse PJ
AU  - Rodriguez-Blanco A
AU  - Mangenot S
AU  - Cruveiller S
AU  - Barbe V
AU  - Duran R
AU  - Wu LF
AU  - Talla E
AU  - Bonin P
AU  - Michotey V
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3539-3540.

PMID- 1645867
VI  - 19
DP  - 1991
TI  - Inhibition of restriction enzyme cleavage of DNA modified with 7-deaza-dGTP.
PG  - 2791
AB  - DNA templates containing G+C rich regions or stable secondary structures can
      potentially pose problems for PCR amplification.  Incorporation of the
      structure destabilizing analogue, 7-deaza-dGTP into the PCR reaction allows
      successful amplification of such template sequences.  It has been reported that
      when 7-deaza-dGTP is substituted for dGTP in a DNA-fragment, the cleavage rate
      by the restriction enzyme EcoRI is reduced.  We find that EcoRI as well as
      other commonly used restriction enzymes will not cut DNA containing
      7-deaza-dGTP when it is incorporated into PCR product.  Substrates for the
      restriction enzymes were amplified by PCR using pUC19 and bacteriophage lambda
      sequences.  Each 100 microliter reaction contained 200 microM each of dATP,
      dCTP, dTTP, dGTP or 7-deaza-dGTP, 1 microM of each primer, 2.5 units Taq DNA
      Polymerase, 1 ng DNA template, 50 mM KCl, 10 mM Tris-HCl, pH 8.3 @ 37C, 1.5 mM
      MgCl2, 0.01% gelatin.  Five hundred nanograms of the PCR product from reactions
      containing either 7-deaza-dGTP or dGTP were incubated with commonly-used
      restriction enzymes.  Restriction digests were resolved on 1.2% agarose gels
      with ethidium bromide staining.  Table 1 summarizes the results of the
      restriction digests where 7-deaza-dGTP was substituted for dGTP in the PCR
      reaction.  For most enzymes tested, inclusion of 7-deaza-dGTP in the PCR
      product prevented the restriction enzyme from cutting the DNA.  It is not yet
      clear to us how this inhibition occurs.  We assume that the presence of the
      deaza residue in the recognition sequence affects proper binding and/or cutting
      of the DNA substrate.  As yet the details of the spatial interaction between
      the modified G residue and various restriction enzyme active/binding sites is
      unclear.  Inhibition of cutting can occur when the G residues are 5 prime (eg.
      EcoRI), 3 prime (eg. PstI), immediately adjacent (eg. SalI), or two bases away
      from the cut site (eg. AccI).  Three enzymes (XbaI, HindIII, MaeII) are not
      inhibited by the presence of modified G residues in their recognition sequence.
      We have no knowledge of how modified G residues may inhibit cutting from a
      complementary strand of DNA.  7-deaza-dGTP could be beneficial for applications
      such as cDNA cloning where multiple internal restriction sites are protected
      during linker digestion. This would be similar to the strategy of methylating
      cDNA prior to digestion with methyl-sensitive restriction enzymes.  Use of
      7-deaza-dGTP to this end may allow the use of a greater number of enzymes.
AU  - Grime SK
AU  - Martin RL
AU  - Holaway BL
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 2791.

PMID- 2165969
VI  - 90
DP  - 1990
TI  - Achilles' heel cleavage: creation of rare restriction sites in lambda phage genomes and evaluation of additional operators, repressors and restriction/modification systems .
PG  - 1-7
AB  - A novel technique for the creation of rare restriction sites was described by Koob et al.
      [Science 241 (1988) 1084-1086]. This technique, Achilles' heel cleavage (AC), relies on the
      use of a bound repressor molecule to protect only one of many identical restriction sites from
      a modification methyltransferase that inactivates all other restriction sites. The technique
      was applied to a small plasmid and shown to work efficiently with two repressor/operator
      systems: lac repressor/lacO operator and lambda repressor/lambda OL1 operator. Here, we have
      extended these results to a lac operator carried by a much larger vector, namely a 44-kb phage
      lambda construct. In addition, we have evaluated the effect of altering the stability of the
      lac repressor/lac operator complex by varying both the operator and the repressor. We have
      also evaluated several more restriction/modification systems (MboI, Dam, MspI and AluI) in
      addition to HhaI and HaeII used earlier. Finally, we extended the AC technique to a third
      system, that of the phage 434 repressor and a synthetic 434 operator. From our results we
      conclude that the ACT method should be applicable to the mapping of large genomes and to
      measuring the strength of operator-repressor interactions. AC could also be applied to
      identifying and evaluating many different DNA-binding proteins and their sites of action.
AU  - Grimes E
AU  - Koob M
AU  - Szybalski W
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1990 90: 1-7.

PMID- 28428288
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of the Streptococcus gallolyticus subsp. gallolyticus Strain DSM 16831.
PG  - e00108-17
AB  - Streptococcus gallolyticus subsp. gallolyticus DSM 16831 is an intriguing strain  because of
      its low virulent phenotype compared to other isolates. We present here
      the complete genome sequence for this strain isolated from koala feces.
AU  - Grimm I
AU  - Dumke J
AU  - Vollmer T
AU  - Hinse D
AU  - Ruckert C
AU  - Kalinowski J
AU  - Knabbe C
AU  - Dreier J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00108-17.

PMID- 9518476
VI  - 26
DP  - 1998
TI  - The protein splicing domain of the homing endonuclease PI-SceI is responsible for specific DNA binding.
PG  - 1857-1862
AB  - The homing endonuclease PI-SceI consists of a protein splicing domain (I) and an
      endonucleolytic domain (II).  To characterize the two domains with respect to their
      contribution to DNA recognition we cloned, purified and characterized the isolated domains.
      Both domains have no detectable endonucleolytic activity.  Domain I binds specifically to the
      PI-SceI recognition sequence, whereas domain II displays only weak non-specific DNA binding.
      In the specific complex with domain I the DNA is bent to a similar extent as observed with the
      initial complex formed between PI-SceI and DNA.  Our results indicate that protein splicing
      domain I is also involved in recognition of the DNA substrate.
AU  - Grindl W
AU  - Wende W
AU  - Pingoud V
AU  - Pingoud A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1998 26: 1857-1862.

PMID- 30054276
VI  - 293
DP  - 2018
TI  - Crystal structure of a novel domain of the motor subunit of the Type I restriction enzyme EcoR124 involved in complex assembly and DNA binding.
PG  - 15043-15054
AB  - Although EcoR124 is one of the better-studied Type I restriction-modification enzymes, it
      still presents many challenges to detailed analyses because of its
      structural and functional complexity and missing structural information. In all
      available structures of its motor subunit HsdR, responsible for DNA translocation
      and cleavage, a large part of the HsdR C terminus remains unresolved. The crystal
      structure of the C terminus of HsdR, obtained with a crystallization chaperone in
      the form of pHluorin fusion and refined to 2.45 A, revealed that this part of the
      protein forms an independent domain with its own hydrophobic core and displays a
      unique alpha-helical fold. The full-length HsdR model, based on the WT structure
      and the C-terminal domain determined here, disclosed a proposed DNA-binding
      groove lined by positively charged residues. In vivo and in vitro assays with a
      C-terminal deletion mutant of HsdR supported the idea that this domain is
      involved in complex assembly and DNA binding. Conserved residues identified
      through sequence analysis of the C-terminal domain may play a key role in
      protein-protein and protein-DNA interactions. We conclude that the motor subunit
      of EcoR124 comprises five structural and functional domains, with the fifth, the
      C-terminal domain, revealing a unique fold characterized by four conserved motifs
      in the IC subfamily of Type I restriction-modification systems. In summary, the
      structural and biochemical results reported here support a model in which the
      C-terminal domain of the motor subunit HsdR of the endonuclease EcoR124 is
      involved in complex assembly and DNA binding.
AU  - Grinkevich P
AU  - Sinha D
AU  - Iermak I
AU  - Guzanova A
AU  - Weiserova M
AU  - Ludwig J
AU  - Mesters JR
AU  - Ettrich RH
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2018 293: 15043-15054.

PMID- 20556856
VI  - 8
DP  - 2010
TI  - IDENTIFICATION OF CONSERVED FEATURES OF LAGLIDADG HOMING ENDONUCLEASES.
PG  - 453-469
AB  - LAGLIDADG family of homing endonucleases are rare-cutting enzymes which recognize long target
      sequences and are of great interest in genome
      engineering. Despite advances in homing endonuclease engineering,
      effective methods of broadening the range of cleaved sequences are
      still lacking. Here, we present a study of conserved structural
      features of LAGLIDADG homing endonucleases that might aid further
      development of such methods. The protein-DNA interface of LAGLIDADG
      homing endonucleases differs considerably with the particular nuclease,
      and the analysis of conserved protein-DNA interactions could not
      identify any residues crucial for DNA binding and common to most
      nucleases of the family. For the homing endonuclease PI-SceI, a
      comparison of structural and experimental data derived from literature
      helped to identify 23 residues that are likely to be important for DNA
      binding. Analysis of the LAGLIDADG domain dimerization interface
      allowed the choosing of six positions that contribute to dimerization
      specificity most, while comparison of 446 sequences of LAGLIDADG
      endonucleases revealed groups of residues in these positions that
      appear to be most favorable for dimerization.
AU  - Grishin A
AU  - Fonfara I
AU  - Alexeevski A
AU  - Spirin S
AU  - Zanegina O
AU  - Karyagina A
AU  - Alexeyevsky D
AU  - Wende W
PT  - Journal Article
TA  - J. Bioinform. Comput. Biol.
JT  - J. Bioinform. Comput. Biol.
SO  - J. Bioinform. Comput. Biol. 2010 8: 453-469.

PMID- 12537018
VI  - 21
DP  - 2002
TI  - Affinity modification of EcoRII DNA methyltransferase by the dialdehyde-substituted DNA duplexes: mapping the enzyme region that interacts with DNA.
PG  - 753-764
AB  - Affinity modification of EcoRII DNA methyltransferase (M.EcoRII) by DNA duplexes containing
      oxidized 2'-O-beta-D-ribofuranosylcytidine (Crib*) or 1-(beta-D-galactopyranosyl)thymine
      (Tgal*) residues was performed. Cross-linking yields do not change irrespective of whether
      active Crib* replaces an outer or an inner (target) deoxycytidine within the EcoRII
      recognition site. Chemical hydrolysis of M.EcoRII in the covalent cross-linked complex with
      the Tgal*-substituted DNA indicates the region Gly268-Met391 of the methylase that is likely
      to interact with the DNA sugar-phosphate backbone. Both specific and non-specific DNA interact
      with the same M.EcoRII region. Our results support the theoretically predicted DNA binding
      region of M.EcoRII.
AU  - Gritsenko OM
AU  - Koudan EV
AU  - Mikhailov SN
AU  - Ermolinsky BS
AU  - VanAerschot A
AU  - Herdewijn P
AU  - Gromova ES
PT  - Journal Article
TA  - Nucleosides Nucleotides Nucleic Acids
JT  - Nucleosides Nucleotides Nucleic Acids
SO  - Nucleosides Nucleotides Nucleic Acids 2002 21: 753-764.

PMID- 11200275
VI  - 19
DP  - 2000
TI  - Probing the MvaI methyltransferase region that interacts with DNA: Affinity labeling with the dialdehyde-containing DNA duplexes.
PG  - 1805-1820
AB  - Affinity labeling of methyltransferase MvaI by DNA duplexes containing oxidized
      2'-O-beta-D-ribofuranosylcytidine or 1-(beta-D-galactopyranosyl)thymine residues was
      performed. Partial chemical hydrolysis of the covalently bound methylase in the conjugates
      with the dialdehyde-containing DNA allowed us to determine the amino acid region in the C
      terminus of methylase MvaI that interacts with DNA.
AU  - Gritsenko OM
AU  - Mikhailov SN
AU  - Efimtseva EV
AU  - Van Aerschot A
AU  - Herdewijn P
AU  - Gromova ES
PT  - Journal Article
TA  - Nucleosides Nucleotides Nucleic Acids
JT  - Nucleosides Nucleotides Nucleic Acids
SO  - Nucleosides Nucleotides Nucleic Acids 2000 19: 1805-1820.

PMID- 15335920
VI  - 2
DP  - 1992
TI  - Homing in on an endosymbiotic endonuclease.
PG  - 450-452
AB  - The "spacer protein" generated by a type of protein splicing in yeast turns out to be an
      endonuclease with the precise DNA-sequence specificity to promote the spread of its own coding
      sequence.
AU  - Grivell LA
PT  - Journal Article
TA  - Curr. Biol.
JT  - Curr. Biol.
SO  - Curr. Biol. 1992 2: 450-452.

PMID- 8805219
VI  - 6
DP  - 1996
TI  - Transposition: Mobile introns get into line.
PG  - 48-51
AB  - Group II introns encode highly structured, frequently self-splicing RNAs; they are also mobile
      genetic elements.  This mobility has been found to involve DNA-primed reverse transcription,
      with similarities to retrotransposition and telomere maintenance.
AU  - Grivell LA
PT  - Journal Article
TA  - Curr. Biol.
JT  - Curr. Biol.
SO  - Curr. Biol. 1996 6: 48-51.

PMID- 21482539
VI  - 39
DP  - 2011
TI  - Context dependence between subdomains in the DNA binding interface of the I-CreI homing endonuclease.
PG  - 6124-6136
AB  - Homing endonucleases (HE) have emerged as precise tools for achieving gene targeting events.
      Redesigned HEs with tailored specificities can be used to cleave new sequences, thereby
      considerably expanding the number of targetable genes and loci. With HEs, as well as with
      other protein scaffolds, context dependence of DNA/protein interaction patterns remains one of
      the major limitations for rational engineering of new DNA binders. Previous studies have shown
      strong crosstalk between different residues and regions of the DNA binding interface. To
      investigate this phenomenon, we systematically combined mutations from three groups of amino
      acids in the DNA binding regions of the I-CreI HE. Our results confirm that important
      crosstalk occurs throughout this interface in I-CreI. Detailed analysis of success rates
      identified a nearest-neighbour effect, with a more pronounced level of dependence between
      adjacent regions. Taken together, these data suggest that combinatorial engineering does not
      necessarily require the identification of separable functional or structural regions, and that
      groups of amino acids provide acceptable building blocks that can be assembled, overcoming the
      context dependency of the DNA binding interface. Furthermore, the present work describes a
      sequential method to engineer tailored HEs, wherein three contiguous regions are individually
      mutated and assembled to create HEs with engineered specificity.
AU  - Grizot S
AU  - Duclert A
AU  - Thomas S
AU  - Duchateau P
AU  - Paques F
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2011 39: 6124-6136.

PMID- 20026587
VI  - 38
DP  - 2010
TI  - Generation of redesigned homing endonucleases comprising DNA-binding domains derived from two different scaffolds.
PG  - 2006-2018
AB  - Homing endonucleases have become valuable tools for genome engineering. Their sequence
      recognition repertoires can be expanded by modifying their
      specificities or by creating chimeric proteins through domain swapping
      between two subdomains of different homing endonucleases. Here, we show
      that these two approaches can be combined to create engineered
      meganucleases with new specificities. We demonstrate the modularity of the
      chimeric DmoCre meganuclease previously described, by successfully
      assembling mutants with locally altered specificities affecting both
      I-DmoI and I-CreI subdomains in order to create active meganucleases with
      altered specificities. Moreover these new engineered DmoCre variants
      appear highly specific and present a low toxicity level, similar to
      I-SceI, and can induce efficient homologous recombination events in
      mammalian cells. The DmoCre based meganucleases can therefore offer new
      possibilities for various genome engineering applications.
AU  - Grizot S
AU  - Epinat JC
AU  - Thomas S
AU  - Duclert A
AU  - Rolland S
AU  - Paques F
AU  - Duchateau P
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2010 38: 2006-2018.

PMID- 19584299
VI  - 37
DP  - 2009
TI  - Efficient targeting of a SCID gene by an engineered single-chain homing endonuclease.
PG  - 5405-5419
AB  - Sequence-specific endonucleases recognizing long target sequences are emerging as powerful
      tools for genome engineering. These endonucleases
      could be used to correct deleterious mutations or to inactivate viruses,
      in a new approach to molecular medicine. However, such applications are
      highly demanding in terms of safety. Mutations in the human RAG1 gene
      cause severe combined immunodeficiency (SCID). Using the I-CreI dimeric
      LAGLIDADG meganuclease as a scaffold, we describe here the engineering of
      a series of endonucleases cleaving the human RAG1 gene, including obligate
      heterodimers and single-chain molecules. We show that a novel single-chain
      design, in which two different monomers are linked to form a single
      molecule, can induce high levels of recombination while safeguarding more
      effectively against potential genotoxicity. We provide here the first
      demonstration that an engineered meganuclease can induce targeted
      recombination at an endogenous locus in up to 6% of transfected human
      cells. These properties rank this new generation of endonucleases among
      the best molecular scissors available for genome surgery strategies,
      potentially avoiding the deleterious effects of previous gene therapy
      approaches.
AU  - Grizot S
AU  - Smith J
AU  - Daboussi F
AU  - Prieto J
AU  - Redondo P
AU  - Merino N
AU  - Villate M
AU  - Thomas S
AU  - Lemaire L
AU  - Montoya G
AU  - Blanco FJ
AU  - Paques F
AU  - Duchateau P
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: 5405-5419.

PMID- 12867480
VI  - 185
DP  - 2003
TI  - Cytosine methylation by the SuaI restriction-modification system: implications for genetic fidelity in a hyperthermophilic archaeon.
PG  - 4657-4661
AB  - 5-methylcytosine in chromosomal DNA represents a potential source of frequent spontaneous
      mutation for hyperthermophiles. To determine the
      relevance of this threat for the archaeon Sulfolobus acidocaldarius, the
      mode of GGCC methylation by its restriction-modification system, SuaI, was
      investigated. Distinct isoschizomers of the SuaI endonuclease were used to
      probe the methylation state of GGCC in native S. acidocaldarius DNA. In
      addition, the methylation sensitivity of the SuaI endonuclease was
      determined with synthetic oligonucleotide substrates and modified natural
      DNAs. The results show that the SuaI system uses N(4) methylation to block
      cleavage of its recognition site, thereby avoiding the creation of G. T
      mismatches by spontaneous deamination at extremely high temperature.
AU  - Grogan DW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2003 185: 4657-4661.

PMID- 9298958
VI  - 36
DP  - 1997
TI  - Does the restriction endonuclease EcoRV employ a two-metal-ion mechanism for DNA cleavage?
PG  - 11389-11401
AB  - Two models for the catalytic mechanism of the restriction endonuclease EcoRV exist which
      differ in the number and function of metal ions proposed to be directly involved in catalysis.
      In one model, two metal ions bound by Glu45, Asp74, and Asp90 are assumed to have a direct
      catalytic function; in the other, only one metal ion bound by Asp74 and Asp90.  We show here
      that in the presence of Mn2+, the catalytic activity of an EcoRV-E45A mutant is only slightly
      reduced (1.8-fold) as compared to wild type EcoRV and that the single-turnover rate constant
      of DNA cleavage by E45A is reduced only 39-fold, whereas the D74A and D90A mutants are
      catalytically inactive under all conditions.  These findings make an important catalytic
      function of Glu45, like binding of an essential divalent metal ion, unlikely.  In addition, we
      have analyzed the dependence of the DNA cleavage rate by EcoRV and EcoRV mutants on the
      concentration of Mg2+ and Mn2+.  We found for the wild type enzyme a sigmoidal dependence of
      the rate of DNA cleavage on the concentration of Mg2+ or Mn2+, indicative of at least two
      metal ions involved in DNA binding and catalysis.  This, however, does not mean that EcoRV
      follows a two-metal-ion mechanism in DNA cleavage, because also for the E45A mutant a
      sigmoidal dependence of the rate of DNA cleavage on the Mg2+ concentration was found, making
      metal ion binding to the E45/D74 site unlikely.  In contrast, the Y219C mutant shows a
      hyperbolic dependence.  In agreement with results obtained earlier, these findings demonstrate
      binding of a Mg2+ ion at a site influenced by Tyr219, an amino acid residue that is far away
      from the active site.  Metal binding at this site does not have a catalytic role but rather
      supports specific DNA binding.  We conclude that on the basis of our data a two-metal-ion
      mechanism of DNA cleavage is unlikely for EcoRV and that the complex metal ion effects
      observed are due to metal ion binding at sites that are not directly involved in catalysis.
AU  - Groll DH
AU  - Jeltsch A
AU  - Selent U
AU  - Pingoud A
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1997 36: 11389-11401.

PMID- 27634989
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Streptomyces sp. Strain PTY087I2, Isolated from Styela canopus, a Panamanian Tunicate.
PG  - e00856-16
AB  - Streptomyces sp. PTY087I2 is a marine bacterium isolated from Styela canopus, a tunicate
      collected in Bocas del Toro, Panama. Here, we report a draft genome
      sequence for this bacterium, found to have 94.7% average nucleotide identity
      (ANI) with Streptomyces roseosporus NRRL 11379, and containing a diverse suite of
      secondary metabolite gene clusters.
AU  - Gromek SM
AU  - Sung AA
AU  - Klassen JL
AU  - Balunas MJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00856-16.

PMID- 4145862
VI  - 114
DP  - 1973
TI  - Restriction and modification of bacteriophage S2 in Haemophilus influenzae.
PG  - 1151-1157
AB  - The major conclusion from these studies is that variants of Haemophilus
      influenzae Rd which restrict and modify phage S2 are metastable and capable of
      giving rise to one another with high frequency.  Nonrestrictive RdS cells
      segregate spontaneously to the restricting, modifying phenotype in about 5% of
      the progeny of a single clone.  The restriction cells derived from RdS revert
      to the nonrestrictive phenotype in 15 to 25% of the progeny of a single clone.
      These frequencies are not appreciably affected by treatment with acriflavine or
      ethidium bromide, compounds which affect plasmid stability, or by
      nitrosoguanidine, a powerful mutagen.  The genetic locus for restriction and
      modification of bacteriophage S2 is found to have a chromosomal position
      between the biotin and proline loci.  Restriction-modification of phage S2 has
      been shown to be a function of its deoxyribonucleic acid (DNA) in that
      transfection with S2 phage DNA or prophage DNA is subject to host restriction
      and modification.  An enzyme preparation which contains endodeoxyribonuclease
      but no appreciable exonuclease activity, from mutant H. influenzae com-10 did
      not restrict phage S2.RdS DNA or prophage DNA transfecting activity, indicating
      that this endodeoxyribonuclease is not responsible for phage restriction.  A
      new restriction enzyme isolated from H. influenzae Rd was found to be the major
      enzyme involved in the restriction of bacteriophage S2.  The enzyme inactivated
      the transfecting activity of unmodified phage DNA but did not attack modified
      phage DNA.  Unlike endodeoxyribonuclease R, this enzyme requires adenosine
      triphosphate and S-adenosylmethionine.
AU  - Gromkova R
AU  - Bendler J
AU  - Goodgal S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1973 114: 1151-1157.

PMID- Not carried by PubMed...
VI  - 75
DP  - 1975
TI  - On the restriction-modification systems of Haemophilus aegyptius.
PG  - 103
AB  - In order to assess the role of type I and type II restriction systems in vivo
      in Haemophilus we have attempted to isolate mutants deficient in restriction
      and modification.  Because no mutants of the type II system were found in H.
      influenze Rd, H. aegyptius was used since it contained different type II
      restriction activities.  Bacteriophage S2 does not form plaques on wild type H.
      aegyptius although it is efficiently absorbed.  Mutants capable of plating S2
      with an efficiency of 10-7 were obtained.  Restriction was completely
      eliminated by three more stepwise mutagenic treatments.  Analysis of these
      mutants suggested that the wild type had at least three independent type I
      systems.  Mutants deficient in restriction-modification were also deficient in
      transforming activity.  The type II restriction systems of H. aegyptius did not
      restrict bacteriophage S2 from H. influenze although its DNA was attacked in
      vitro by purified type II restriction enzymes.  In the same way unmodified S2
      grown on H. aegyptius was not restricted in vivo by the type II restriction
      systems of H. influenzae Rd, but was excluded by its type I restriction system.
      These data support the conclusion that only type I restriction is involved in
      the exclusion of bacteriophage S2 in Haemophilus.  A type I activity was
      isolated from H. aegyptius and appears responsible for restriction of S2.
AU  - Gromkova R
AU  - Goodgal S
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1975 75: 103.

PMID- 
VI  - 0
DP  - 1974
TI  - On the role of restriction enzymes in transformation and transfection.
PG  - 209-215
AB  - None
AU  - Gromkova R
AU  - Goodgal SH
PT  - Journal Article
TA  - Mechanisms of recombination
JT  - Mechanisms of recombination
SO  - Mechanisms of recombination 1974 0: 209-215.

PMID- 1085299
VI  - 127
DP  - 1976
TI  - Biological Properties of a Haemophilus influenzae Restriction Enzyme, HindI.
PG  - 848-854
AB  - A type I restriction enzyme from Haemophilus influenzae, HindI, which requires
      adenosine 5'-triphosphate and 5-adenosyl methionine, was studied for its
      activity on transfecting and transforming deoxyribonucleic acid (DNA).  The
      enzyme reduced the size of unmodified bacteriophage S2 DNA from 37 Mdaltons to
      approximately 10 Mdaltons, but did not affect modified S2 DNA.  Unmodified
      transforming DNA was attacked in vitro by HindI; however, relatively low levels
      of inactivation were obtained for single markers, and linked transformants were
      inactivated as a function of the distance between markers. In contrast,
      unmodified bacterial DNA was not inactivated in vivo for either single or
      linked markers by the HindI restriction system, probably because the segments
      generated by HindI were still capable of being integrated in vivo.  The lack of
      preferential inactivation of markers by the enzyme suggests that it makes
      random breaks in the DNA.
AU  - Gromkova R
AU  - Goodgal SH
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1976 127: 848-854.

PMID- Not included in PubMed...
VI  - 34
DP  - 1975
TI  - On the effect of a restriction modification system on transformation in Haemophilus influenzae.
PG  - 588
AB  - Type I restriction enzymes, those that require ATP and S-adenosyl methionine
      for activity, have been isolated and shown to be responsible for restriction of
      bacteriophages S2 and HPlcl in Haemophilus. H. influenzae serotypes Rb and Rd
      have different Type I restriction and modification systems although their type
      II endodeoxyribonucleases have the same specificities.  The H. influenzae Rd
      system has been shown to reversibly segregate, with a high frequency, to a
      restriction modification deficient phenotype, however, the Rb system is stable
      and can be used to study the effect of the type I restriction modification
      system on bacterial transformation.  Mutants with different restriction and
      modification phenotypes were examined for their efficiency of transformation.
      The mutants studied included the first step mutants, r+/-m+, and r-m-; and the
      second step mutants r-m-, r-m+, and r-m+/- obtained by a second round of
      mutation.  A reduction in normal transforming activity ranging from 0.5 to 0.01
      was obtained with all mutants tested with the greatest reductions associated
      with the second step r-m- strains.  Transformation of mutants to the r+m+
      phenotype resulted in recovery of normal transforming efficiency, and,
      conversely transformation of r+m+ wild type recipients to the r-m- phenotype
      resulted in lowered transformability.  The mutants were found to have
      deficiences in their type I restriction and modification enzymes but no changes
      in their levels of type II restriction enzymes.
AU  - Gromkova R
AU  - Goodgal SH
PT  - Journal Article
TA  - Fed. Proc.
JT  - Fed. Proc.
SO  - Fed. Proc. 1975 34: 588.

PMID- 4334766
VI  - 109
DP  - 1972
TI  - Action of Haemophilus endodeoxyribonuclease on biologically active deoxyribonucleic acid.
PG  - 987-992
AB  - An enzyme similar to that described by Smith and Wilcox (15) for Haemophilus
      influenzae which attacks foreign deoxyribonucleic acid (DNA) but not its own
      has been isolated and purified from H. parainfluenzae.  The enzyme degrades
      foreign DNA to limited sizes and can destroy the transforming activity of H.
      influenzae and Bacillus subtilis DNA.  The enzyme can also destroy the
      biological activity of H. influenzae phage and prophage DNA.  On the other
      hand, the H. influenzae endodeoxyribonuclease can destroy the transforming
      activity of H. parainfluenzae DNA but not its own DNA.  It also attacks B.
      subtilis DNA and its transforming activity.
AU  - Gromkova R
AU  - Goodgal SH
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1972 109: 987-992.

PMID- 
VI  - 73
DP  - 1973
TI  - A restriction enzyme from Haemophilus influenzae requiring adenosine triphosphate and S-adenosyl methionine.
PG  - 72
AB  - The endodeoxyribonuclease isolated from H. influenzae does not attack H. influenzae DNA nor H.
      influenzae phage S2 transfecting activity.  Since there is restriction and modification of
      phage S2 in H. influenzae it was clear that another restriction system was present.  A new
      restriction activity (Hd) that destroys the transfecting activity of unmodified DNA from phage
      grown in nonrestrictive recipients and does not inactivate modified DNA has been purified from
      H. influenzae.  Unlike endo-R the enzyme activity which attacks phage DNA requires ATP and
      S-adenosyl methionine.  Transformation by foreign bacterial DNA was also inactivated by the Hd
      system.  This inactivation was stimulated by ATP and SAM.  The enzyme is considerably larger
      than endo-R; it elutes earlier in Bio-Gel fractionation, and sediments further in a glycerol
      sedimentation velocity gradient.  A similar enzyme has been isolated from H. influenzae Reid.
      Since the H. influenzae Reid enzyme can attack the DNA from phage grown in restrictive cells
      of H. influenzae, one can conclude that the H. influenzae and H. influenzae Reid restriction
      systems have different specificities.
AU  - Gromkova R
AU  - LaPorte J
AU  - Goodgal SH
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1973 73: 72.

PMID- 
VI  - 20
DP  - 1986
TI  - Interaction of EcoRII restriction and modification enzymes with synthetic fragments of DNA.
PG  - 22-32
AB  - A set of DNA duplexes containing repetitive recognition sites for restriction endonucleases
      EcoRII, EcoRI, and AluI, in which the phosphodiester bonds in the EcoRII cleavage sites were
      replaced by phosphoamide or unbreakable pyrophosphate bonds, was synthesized.  It was found
      that the restriction endonuclease EcoRII does not cleave the substrate at the phosphoamide
      bond.  Using substrates containing modified bonds in the EcoRII recognition sites in one of
      the strands, it was shown that this enzyme is capable of catalyzing single-strand breaks both
      in the dA- and in the dT-containing strand of the recognition site.  The restriction
      endonuclease EcoRII interacts with both strands of the recognition site of DNA, whereas
      cleavage of each of them occurs independently of the cleavage of the other.  Restriction
      endonucleases EcoRI and AluI specifically digest the synthesized substrates at the
      phosphodiester bonds; however, this cleavage is hindered if the modified bond is situated in
      the recognition site (EcoRI) or adjoins it (AluI).  For EcoRII and AluI this effect is more
      pronounced in the case of substrates with pyrophosphate bonds than with phosphoamide bonds.
AU  - Gromova ES
AU  - Elob AA
AU  - Kubareva EA
AU  - Metelev VG
AU  - Shabarova ZA
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1986 20: 22-32.

PMID- 3005844
VI  - 20
DP  - 1986
TI  - Interaction of EcoRII restriction and modification enzymes with synthetic fragments of DNA.  IV. DNA duplexes with phosphoamide and pyrophosphate internucleotide bonds -- substrates for the study of single-strand breaks.
PG  - 29-40
AB  - A set of DNA duplexes containing repetitive recognition sites for restriction
      endonucleases EcoRII, EcoRI, and AluI, in which the phosphodiester bonds in the EcoRII
      cleavage sites were replaced by phosphoamide or unbreakable pyrophosphate bonds, was
      synthesized.  It was found that the restriction endonuclease EcoRII does not cleave the
      substrate at the phosphoamide bond.  Using substrates containing modified bonds in the
      EcoRII recognition sites in one of the strands, it was shown that this enzyme is capable of
      catalyzing single-strand breaks both in the dA- and in the dT-containing strand of the
      recognition site.  The restriction endonuclease EcoRII interacts with both strands of the
      recognition site of DNA, whereas cleavage of each of them occurs independently of the
      cleavage of the other.  Restriction endonucleases EcoRI and AluI specifically digest the
      synthesized substrates at the phosphodiester bonds; however, this cleavage is hindered if
      the modified bond is situated in the recognition site (EcoRI) or adjoins it (AluI).  For
      EcoRII and AluI this effect is more pronounced in the case of substrates with
      pyrophosphate bonds than with phosphoamide bonds.
AU  - Gromova ES
AU  - Elob AA
AU  - Kubareva EA
AU  - Metelev VG
AU  - Shabarova ZA
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1986 20: 29-40.

PMID- 12723477
VI  - 37
DP  - 2003
TI  - Prokaryotic DNA methyltransferases: The structure and the mechanism of interaction with DNA.
PG  - 300-314
AB  - The review considers current views on the function of DNA methyltransferases (MTases) that
      belong to prokaryotic type II
      restriction-modification systems. A commonly accepted classification of
      MTases is described along with their primary and tertiary structures and
      molecular mechanisms of their specific interaction with DNA (including
      methylation). MTase inhibitors are also considered. Special emphasis is
      placed on the flipping of the target heterocyclic base out of the double
      helix and on the methods employed in its analysis. Base flipping is a
      fundamentally new type of DNA conformational changes and is also of
      importance in the case of other DNA-operating enzymes. MTases show unique
      sequence homology, and are similar in structure of functional centers and
      in the mechanism of methylation. These data contribute to the
      understanding of the general biological significance of methylation, since
      prokaryotic and eukaryotic MTases are structurally and functionally
      similar.
AU  - Gromova ES
AU  - Khoroshaev AV
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2003 37: 300-314.

PMID- 1665978
VI  - 4
DP  - 1991
TI  - Peculiarities of recognition of CCA/TGG sequences in DNA by restriction endonucleases MvaI and EcoRII.
PG  - 133-141
AB  - To elucidate the mechanism of action of restriction endonucleases MvaI and EcoRII a study was
      made of their interaction with a set of synthetic substrates in which the heterocyclic bases
      or the sugar-phosphate backbone has been modified; individual nucleotide residues had been
      removed or replaced with hydrocarbon bridges, and mismatched base pairs had been introduced.
      The groups of atoms in the heterocyclic bases and the phosphates in the recognition site that
      produce the most significant influence on the functioning of endonucleases MvaI and EcoRII
      were discerned. Profound differences were found in the functioning of the MvaI and EcoRII
      neoschizomers. The catalytic activity of EcoRII is significantly affected by any alteration in
      the recognition site structure and conformation, with a modification in one strand of the
      substrate causing the same decrease in the hydrolysis rate of both strands. Endonuclease MvaI
      is tolerant to a number of structural abnormalities; the latter sometimes affect only
      hydrolysis of one strand of the recognition site. The enzyme can preferentially cleave one of
      the substrate strands. Mismatched base pairs retard and sometimes block the hydrolysis. The
      effect depends on the particular enzyme, mismatch and its location.
AU  - Gromova ES
AU  - Kubareva EA
AU  - Vinogradova MN
AU  - Oretskaya TS
AU  - Shabarova ZA
PT  - Journal Article
TA  - J. Mol. Recognit.
JT  - J. Mol. Recognit.
SO  - J. Mol. Recognit. 1991 4: 133-141.

PMID- 1883910
VI  - 56
DP  - 1991
TI  - Cleavage of concatemeric substrates by restriction endonucleases MvaI and SsoII.
PG  - 552-559
AB  - The interaction of enzymes SsoII (^CCNGG) and MvaI (CC^A/TGG) with concatemeric
      duplexes used earlier to study EcoRII (CCA/TGG) was investigated with a view to
      elucidating the general principles of restriction endonuclease function.  A
      pattern common to all three enzymes was observed with DNA duplexes containing
      AA or TT pairs in the central position of the recognition site.  The AA pair
      blocks or substantially hinders the endonuclease action, whereas the TT pair is
      either less inhibitory or altogether inert.  SsoII, like EcoRII was able to
      processively cleave the concatemeric substrates and to interact with (or to be
      close to) the hydrogen in the 5th position of the outer dC residue of the
      recognition site.  MvaI was found to differ from EcoRII in the way they
      recognize and cleave the same nucleotide sequence.  The substrate-bound MvaI
      molecule is incapable of linear diffusion along the DNA.  Effective hydrolysis
      of dU- and m5dC-containing polymers rules out the participation of hydrophobic
      contacts of the enzyme with the methyl group of the dT residue and with the 5th
      hydrogen of the outer dC residue of the recognition site in DNA-protein
      interactions.
AU  - Gromova ES
AU  - Kubareva EA
AU  - Yolov AA
AU  - Akatova EA
AU  - Nikolskaya II
AU  - Shabarova ZA
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1991 56: 552-559.

PMID- 2824157
VI  - 295
DP  - 1987
TI  - Study of the DNA cleavage mechanism of the restriction endonuclease MvaI.
PG  - 1493-1497
AB  - None
AU  - Gromova ES
AU  - Kuchava EA
AU  - Pein C-D
AU  - Oreshkaya TS
AU  - Shabarova ZA
AU  - Check D
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1987 295: 1493-1497.

PMID- 7663428
VI  - 36
DP  - 1995
TI  - Kinetic studies of MvaI DNA methyltransferase interaction with modified oligonucleotide duplexes.
PG  - 247-255
AB  - We have measured steady-state kinetics of an N4-cytosine methylase, M.MvaI,
      using as substrates modified non-selfcomplementary tetradecanucleotide duplexes containing the
      CCWGG target sequence.  The inner or outer localisation of the dI residue in the MvaI
      recognition
      site seems to be of little importance since the specificity constants kcat/KM are only 2 to 7
      fold
      smaller than that of the canonical substrate.  Replacement of dG residues by dI in both
      strands
      resulted in a 25 to 60-fold decrease of the specificity constant.  Modifications of the
      phosphate
      backbone or opening of the sugar ring of one of the dG residues had only little influence on
      the
      action of M.MvaI.  The enzyme appears to be rather tolerant to different kinds of modification
      in its
      substrate in the minor groove.
AU  - Gromova ES
AU  - Oretskaya TS
AU  - Eritja R
AU  - Guschlbauer W
PT  - Journal Article
TA  - Biochem. Mol. Biol. Int.
JT  - Biochem. Mol. Biol. Int.
SO  - Biochem. Mol. Biol. Int. 1995 36: 247-255.

PMID- 1841289
VI  - 24
DP  - 1991
TI  - Study of the mechanism of EcoRII endonuclease activation with synthetic substrates.
PG  - 217-218
AB  - EcoRII restriction endonuclease is not able to cleave phage DNA with isolated EcoRII
      recognition sites.  However addition of the EcoRII sensitive DNA or short substrates may
      stimulate such a cleavage.  It has been suggested that EcoRII requires at least two
      recognition sites for its activation.  In order to substantiate the mechanism of
      EcoRII-substrate interaction we report a model system convenient for stimulation effect
      studies and the results of testing as activators a wide set of modified and unmodified DNA.
AU  - Gromova ES
AU  - Petrauskene OV
AU  - Kubareva EA
PT  - Journal Article
TA  - Nucleic Acids Symp. Ser.
JT  - Nucleic Acids Symp. Ser.
SO  - Nucleic Acids Symp. Ser. 1991 24: 217-218.

PMID- 2174177
VI  - 39
DP  - 1990
TI  - DNA-Protein interactions:  The use of synthetic oligo- and polynucleotides for studying single-stranded-DNA-binding proteins and restriction endonucleases.
PG  - 1-47
AB  - None
AU  - Gromova ES
AU  - Shabarova AZ
PT  - Journal Article
TA  - Prog. Nucleic Acid Res. Mol. Biol.
JT  - Prog. Nucleic Acid Res. Mol. Biol.
SO  - Prog. Nucleic Acid Res. Mol. Biol. 1990 39: 1-47.

PMID- 3034294
VI  - 13
DP  - 1987
TI  - DNA duplexes with phosphoamide bonds:  the interaction with EcoRII and SsoII restriction endonucleases.
PG  - 269-272
AB  - We studied the interaction of EcoRII and SsoII restriction endonucleases with
      synthetic DNA duplexes, containing 3'N -> 5'P and 3'P -> 5'N phosphoamide
      internucleotide bonds in one of the cleavage points.  Enzymatic hydrolysis of
      the modified strand of the duplexes is blocked in all cases.  The presence of
      phosphoamide bonds was found to reduce the rate of cleavage of the natural
      strand by EcoRII and to have no influence in case of SsoII.  Properties of the
      EcoRII endonuclease complex with its substrate, containing non-cleavable 3'N ->
      5'P internucleotide bonds in each cleavage point, were examined.  In the
      presence of Mg2+ ions the equilibrium association constant of the
      enzyme-substrate complex is 3-fold reduced, and the dissociation rate constant
      of the complex is increased by 1.5 times.
AU  - Gromova ES
AU  - Vinogradova MN
AU  - Uporova TM
AU  - Gryaznova OI
AU  - Isagulyants MG
AU  - Kosykh VG
AU  - Nikolskaya II
AU  - Shabarova ZA
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1987 13: 269-272.

PMID- 416358
VI  - 272
DP  - 1978
TI  - Methylation of single-stranded DNA in vitro introduces new restriction endonuclease cleavage sites.
PG  - 375-377
AB  - Restriction endonucleases recognise specific sequences in DNA, and these
      endonucleases, especially those which generate cohesive ends, have been widely
      used to clone DNA.  However, many DNAs lack sequences which are recognised by
      endonucleases such as EcoRI, HindIII or BamHI.  A general method of overcoming
      this problem has been described recently. This approach involves the synthesis
      of oligonucleotides sensitive to a specific endonuclease and the blunt end
      ligation of these molecules to the DNA to be cloned.  In contrast, we sought a
      method which avoids the insertion of addtional nucleotides into a DNA sequence,
      but depends on direct modification of DNA.  If a DNA sequence differs in only
      one base pair from the recognition sequence of a restriction endonuclease, a
      particular change of this base pair will generate the proper sequence.  Here we
      describe a way of generating restriction endonuclease cleavage sites by single
      base changes derived after in vitro methylation of single-stranded DNA.
AU  - Gronenborn B
AU  - Messing J
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1978 272: 375-377.

PMID- Not included in PubMed...
VI  - 46
DP  - 1991
TI  - Some properties of restriction endonucleases from Acetobacter pasteurianus.
PG  - 1103-1108
AB  - Restriction endonucleases ApaBI, ApaCI and ApaDI have been purified from three different
      strains of Acetobacter pasteurianus. The enzyme ApaBI recognized 35 cleavage sites on
      bacteriophage lambda DNA, 20 sites on adeno-virus-2 DNA and 2 sites on plasmid pBR322 DNA.
      The recognition sequence for this enzyme is
      5'-GCANNNNN/TGC-3'
      3'-CGT/NNNNNACG-5'
      The ApaCI enzyme is an isoschizomer of the restriction endonuclease BamHI. ApaDI is the
      third enzyme with 6 sites of cleavage on pBR 327 DNA, 7 sites on pAT 153 DNA more than 20
      sites on bacteriophage lambda DNA.
AU  - Grones J
AU  - Turna J
PT  - Journal Article
TA  - Biologia (Bratisl)
JT  - Biologia (Bratisl)
SO  - Biologia (Bratisl) 1991 46: 1103-1108.

PMID- 8457597
VI  - 1162
DP  - 1993
TI  - Some properties of restriction endonuclease ApaBI from Acetobacter pasteurianus.
PG  - 323-325
AB  - A number of restriction endonucleases have been isolated from many species of prokaryotes and
      their specificities documented. Recently, several restriction endonucleases have been isolated
      from Acetobacter genera. Up to date, two restriction endonucleases, ApaI and ApaLI have been
      isolated from Acetobacter pasteurianus cells. The isolation of a new restriction endonuclease,
      type-II ApaBI is described in this article.
AU  - Grones J
AU  - Turna J
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1993 1162: 323-325.

PMID- 1493903
VI  - 37
DP  - 1992
TI  - Isolation of a new restriction enzyme, ApaCI, an isoschizomer of BamHI produced by Acetobacter pasteurianus.
PG  - 353-356
AB  - A new Type II restriction endonuclease ApaCI purified from Acetobacter pasteurianus is an
      isoschizomer of BamHI that cleaves at the nucleotide sequence 5'-G/GATCC-3' of
      double-stranded DNA. The single restriction activity present in this strain permits the rapid
      purification of 30,000 units of cleavage activity from 10 g of freshly harvested cells. The
      resulting ApaCI preparation is free of contaminant nuclease activities that might interfere
      with in vitro manipulation of DNA.
AU  - Grones J
AU  - Turna J
PT  - Journal Article
TA  - Folia Microbiol. (Praha)
JT  - Folia Microbiol. (Praha)
SO  - Folia Microbiol. (Praha) 1992 37: 353-356.

PMID- 1630925
VI  - 20
DP  - 1992
TI  - ApaCI, an isoschizomer of BamHI isolated from Acetobacter pasteurianus.
PG  - 3513
AB  - 
AU  - Grones J
AU  - Turna J
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 3513.

PMID- 21304678
VI  - 2
DP  - 2010
TI  - Complete genome sequence of Veillonella parvula type strain (Te3).
PG  - 57-65
AB  - Veillonella parvula (Veillon and Zuber 1898) Prevot 1933 is the type species of the genus
      Veillonella in the family Veillonellaceae within the order
      Clostridiales. The species V. parvula is of interest because it is frequently
      isolated from dental plaque in the human oral cavity and can cause opportunistic
      infections. The species is strictly anaerobic and grows as small cocci which
      usually occur in pairs. Veillonellae are characterized by their unusual
      metabolism which is centered on the activity of the enzyme methylmalonyl-CoA
      decarboxylase. Strain Te3(T), the type strain of the species, was isolated from
      the human intestinal tract. Here we describe the features of this organism,
      together with the complete genome sequence, and annotation. This is the first
      complete genome sequence of a member of the large clostridial family
      Veillonellaceae, and the 2,132,142 bp long single replicon genome with its 1,859
      protein-coding and 61 RNA genes is part of the Genomic Encyclopedia of Bacteria
      and Archaea project.
AU  - Gronow S et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 2: 57-65.

PMID- 21475585
VI  - 4
DP  - 2011
TI  - Complete genome sequence of Paludibacter propionicigenes type strain (WB4).
PG  - 36-44
AB  - Paludibacter propionicigenes Ueki et al. 2006 is the type species of the genus Paludibacter,
      which belongs to the family Porphyromonadaceae. The species is of
      interest because of the position it occupies in the tree of life where it can be
      found in close proximity to members of the genus Dysgonomonas. This is the first
      completed genome sequence of a member of the genus Paludibacter and the third
      sequence from the family Porphyromonadaceae. The 3,685,504 bp long genome with
      its 3,054 protein-coding and 64 RNA genes consists of one circular chromosome and
      is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Gronow S et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 4: 36-44.

PMID- 21677856
VI  - 4
DP  - 2011
TI  - Complete genome sequence of Bacteroides salanitronis type strain (BL78).
PG  - 191-199
AB  - Bacteroides salanitronis Lan et al. 2006 is a species of the genus Bacteroides, which belongs
      to the family Bacteroidaceae. The species is of interest because it
      was isolated from the gut of a chicken and the growing awareness that the
      anaerobic microflora of the cecum is of benefit for the host and may impact
      poultry farming. The 4,308,663 bp long genome consists of a 4.24 Mbp chromosome
      and three plasmids (6 kbp, 19 kbp, 40 kbp) containing 3,737 protein-coding and
      101 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea
      project.
AU  - Gronow S et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 4: 191-199.

PMID- 18952874
VI  - 74
DP  - 2008
TI  - Enhanced Transformation Efficiency of Recalcitrant Bacillus cereus and Bacillus weihenstephanensis Isolates upon In Vitro Methylation of Plasmid DNA.
PG  - 7817-7820
AB  - Digestion patterns of chromosomal DNAs of Bacillus cereus and Bacillus weihenstephanensis
      strains suggest that Sau3AI-type restriction
      modification systems are widely present among the isolates tested. In
      vitro methylation of plasmid DNA was used to enhance poor plasmid
      transfer upon electroporation to recalcitrant strains that carry Sau3AI
      restriction barriers.
AU  - Groot MN
AU  - Nieboer F
AU  - Abee T
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2008 74: 7817-7820.

PMID- 
VI  - 41
DP  - 2013
TI  - Development of a universal radioactive DNA methyltransferase inhibition test for high-throughput screening and mechanistic studies.
PG  - 12
AB  - DNA methylation is an important epigenetic mark in eukaryotes, and aberrant pattern of this
      modification is involved in numerous diseases such as cancers. Interestingly, DNA methylation
      is reversible and thus is considered a promising therapeutic target. Therefore, there is a
      need for identifying new small inhibitors of C5 DNA methyltransferases (DNMTs). Despite the
      development of numerous in vitro DNMT assays, there is a lack of reliable tests suitable for
      high-throughput screening, which can also  ive insights into inhibitor mechanisms of action.
      We developed a new test based on scintillation proximity assay meeting these requirements.
      After optimizing our assay on human DNMT1 and calibrating it with two known inhibitors, we
      carried out S-Adenosyl-L-Methionine and DNA competition studies on three inhibitors and were
      able to determine each mechanism of action. Finally, we showed that our test was applicable to
      3 other methyltransferases sources: human DNMT3A, bacterial M. SssI and cellular extracts a s
      well.
AU  - Gros C
AU  - Chauvigne L
AU  - Poulet A
AU  - Menon Y
AU  - Ausseil F
AU  - Dufau I
AU  - Arimondo PB
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2013 41: 12.

PMID- 29291715
VI  - 19
DP  - 2018
TI  - Comparative genome and phenotypic analysis of three Clostridioides difficile strains isolated from a single patient provide insight into multiple infection of C. difficile.
PG  - 1
AB  - BACKGROUND: Clostridioides difficile infections (CDI) have emerged over the past
      decade causing symptoms that range from mild, antibiotic-associated diarrhea
      (AAD) to life-threatening toxic megacolon. In this study, we describe a multiple
      and isochronal (mixed) CDI caused by the isolates DSM 27638, DSM 27639 and DSM
      27640 that already initially showed different morphotypes on solid media.
      RESULTS: The three isolates belonging to the ribotypes (RT) 012 (DSM 27639) and
      027 (DSM 27638 and DSM 27640) were phenotypically characterized and high quality
      closed genome sequences were generated. The genomes were compared with seven
      reference strains including three strains of the RT 027, two of the RT 017, and
      one of the RT 078 as well as a multi-resistant RT 012 strain. The analysis of
      horizontal gene transfer events revealed gene acquisition incidents that sort the
      strains within the time line of the spread of their RTs within Germany. We could
      show as well that horizontal gene transfer between the members of different RTs
      occurred within this multiple infection. In addition, acquisition and exchange of
      virulence-related features including antibiotic resistance genes were observed.
      Analysis of the two genomes assigned to RT 027 revealed three single nucleotide
      polymorphisms (SNPs) and apparently a regional genome modification within the
      flagellar switch that regulates the fli operon. CONCLUSION: Our findings show
      that (i) evolutionary events based on horizontal gene transfer occur within an
      ongoing CDI and contribute to the adaptation of the species by the introduction
      of new genes into the genomes, (ii) within a multiple infection of a single
      patient the exchange of genetic material was responsible for a much higher genome
      variation than the observed SNPs.
AU  - Gross U
AU  - Brzuszkiewicz E
AU  - Gunka K
AU  - Starke J
AU  - Riedel T
AU  - Bunk B
AU  - Sproer C
AU  - Wetzel D
AU  - Poehlein A
AU  - Chibani C
AU  - Bohne W
AU  - Overmann J
AU  - Zimmermann O
AU  - Daniel R
AU  - Liesegang H
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2018 19: 1.

PMID- 2987827
VI  - 13
DP  - 1985
TI  - Two new restriction endonucleases DraII and DraIII from Deinococcus radiophilus.
PG  - 1517-1528
AB  - In addition to recently characterized DraI (1), two new Type II restriction
      endonucleases, DraII and DraIII, with novel site-specificities were isolated
      and purified from Deinococcus radiophilus ATCC 27603.  DraII and DraIII
      recognize the hepta- and nonanucleotide sequences(DraII)5'-Pu G ^ G N C C Py-3'
      3'-Py C C N G ^ G Pu-5'and(DraIII)5'-C A C N N N ^ G T G-3' 3'-G T G ^ N N N C
      A C-5'The cleavage sites within both strands are indicated by arrows.  The
      recognition sequences were established by mapping of the cleavage sites on
      pBR322 (DraII) and fd109 RF DNA (DraIII).  The sequence specificities were
      confirmed by computer-assisted restriction analyses of the generated fragment
      patterns of the sequenced DNA's of the bacteriophages lambda, PhiX174 RF,
      M13mp8 RF and fd109 RF, the viruses Adeno2 and SV40, and the plasmids pBR322
      and pBR328.  The cleavage positions within the recognition sequences were
      determined by sequencing experiments.
AU  - Grosskopf R
AU  - Wolf W
AU  - Kessler C
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1985 13: 1517-1528.

PMID- 22675578
VI  - 5
DP  - 2011
TI  - Draft genome sequence of strain HIMB100, a cultured representative of the SAR116 clade of marine Alphaproteobacteria.
PG  - 269-278
AB  - Strain HIMB100 is a planktonic marine bacterium in the class Alphaproteobacteria. This strain
      is of interest because it is one of the first known isolates from a globally ubiquitous clade
      of marine bacteria known as SAR116 within the family Rhodospirillaceae. Here we de-scribe
      preliminary features of the organism, together with the draft genome sequence and an-notation.
      This is the second genome sequence of a member of the SAR116 clade. The 2,458,945 bp genome
      contains 2,334 protein-coding and 42 RNA genes.
AU  - Grote J et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 5: 269-278.

PMID- 22203982
VI  - 109
DP  - 2012
TI  - Genome and physiology of a model Epsilonproteobacterium responsible for sulfide detoxification in marine oxygen depletion zones.
PG  - 506-510
AB  - Eutrophication and global climate change lead to expansion of hypoxia in the ocean, often
      accompanied by the production of hydrogen sulfide, which
      is toxic to higher organisms. Chemoautotrophic bacteria are thought to
      buffer against increased sulfide concentrations by oxidizing hydrogen
      sulfide before its diffusion to oxygenated surface waters. Model organisms
      from such environments have not been readily available, which has
      contributed to a poor understanding of these microbes. We present here a
      detailed study of 'Sulfurimonas gotlandica' str. GD1, an
      Epsilonproteobacterium isolated from the Baltic Sea oxic-anoxic interface,
      where it plays a key role in nitrogen and sulfur cycling. Whole-genome
      analysis and laboratory experiments revealed a high metabolic flexibility,
      suggesting a considerable capacity for adaptation to variable redox
      conditions. S. gotlandica str. GD1 was shown to grow
      chemolithoautotrophically by coupling denitrification with oxidation of
      reduced sulfur compounds and dark CO(2) fixation. Metabolic versatility
      was further suggested by the use of a range of different electron donors
      and acceptors and organic carbon sources. The number of genes involved in
      signal transduction and metabolic pathways exceeds those of other
      Epsilonproteobacteria. Oxygen tolerance and environmental-sensing systems
      combined with chemotactic responses enable this organism to thrive
      successfully in marine oxygen-depletion zones. We propose that S.
      gotlandica str. GD1 will serve as a model organism in investigations that
      will lead to a better understanding how members of the
      Epsilonproteobacteria are able to cope with water column anoxia and the
      role these microorganisms play in the detoxification of sulfidic waters.
AU  - Grote J
AU  - Schott T
AU  - Bruckner CG
AU  - Glockner FO
AU  - Jost G
AU  - Teeling H
AU  - Labrenz M
AU  - Jurgens K
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2012 109: 506-510.

PMID- 26893432
VI  - 4
DP  - 2016
TI  - First Complete Genome Sequence of Tenacibaculum dicentrarchi, an Emerging Bacterial Pathogen of Salmonids.
PG  - e01756-15
AB  - Tenacibaculum-like bacilli have recently been isolated from diseased sea-reared Atlantic
      salmon in outbreaks that took place in the XI region (Region de Aysen)
      of Chile. Molecular typing identified the bacterium as Tenacibaculum
      dicentrarchi. Here, we report the complete genome sequence of the AY7486TD
      isolate recovered during those outbreaks.
AU  - Grothusen H
AU  - Castillo A
AU  - Henriquez P
AU  - Navas E
AU  - Bohle H
AU  - Araya C
AU  - Bustamante F
AU  - Bustos P
AU  - Mancilla M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01756-15.

PMID- 29930073
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Roseomonas aestuarii Strain JR1/69-1-13 Isolated from Nitrate- and Radionuclide-Contaminated Groundwater in Russia.
PG  - e00583-18
AB  - The draft genome sequence of Roseomonas aestuarii strain JR1/69-1-13, an aerobic
      chemoorganotrophic bacterium isolated from nitrate- and radionuclide-contaminated
      groundwater in Russia, is presented here. The genome was annotated to elucidate
      the genomic basis for the strain's adaptation to the environment and its
      resistance to nitrate, heavy metals, and metalloids.
AU  - Grouzdev DS
AU  - Babich TL
AU  - Tourova TP
AU  - Sokolova DS
AU  - Abdullin RR
AU  - Poltaraus AB
AU  - Schevchenko MA
AU  - Toshchakov SV
AU  - Nazina TN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00583-18.

PMID- 24723706
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Magnetospirillum sp. Strain SO-1, a Freshwater Magnetotactic Bacterium Isolated from the Ol'khovka River, Russia.
PG  - e00235-14
AB  - Here, we present the draft genome sequence of Magnetospirillum sp. strain SO-1, a freshwater
      magnetotactic spirillum isolated from the sediments of the Ol'khovka River, Russia.
AU  - Grouzdev DS
AU  - Dziuba MV
AU  - Sukhacheva MS
AU  - Mardanov AV
AU  - Beletskiy AV
AU  - Kuznetsov BB
AU  - Skryabin KG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00235-14.

PMID- 30338027
VI  - 13
DP  - 2018
TI  - Draft genome sequences of 'Candidatus Chloroploca asiatica' and 'Candidatus Viridilinea mediisalina', candidate representatives of the Chloroflexales order:  phylogenetic and taxonomic implications.
PG  - 24
AB  - 'Candidatus Chloroploca asiatica' B7-9 and 'Candidatus Viridilinea mediisalina' Kir15-3F
      are mesophilic filamentous anoxygenic phototrophic bacteria from
      alkaline aquatic environments. Both bacteria became available in the last few
      years and only in stable enrichment culture. In this study, we report the draft
      genomic sequences of 'Ca. Chloroploca asiatica' B7-9 and 'Ca. Viridilinea
      mediisalina' Kir15-3F, which were assembled from metagenomes of their cultures
      with a fold coverage 86.3x and 163.8x, respectively. The B7-9 (5.8 Mb) and the
      Kir15-3F (5.6 Mb) draft genome harbors 4818 and 4595 predicted protein-coding
      genes, respectively. In this article, we analyzed the phylogeny of
      representatives of the Chloroflexineae suborder in view of the appearance of new
      genomic data. These data were used for the revision of earlier published
      group-specific conserved signature indels and for searching for novel signatures
      for taxons in the Chloroflexineae suborder.
AU  - Grouzdev DS
AU  - Rysina MS
AU  - Bryantseva IA
AU  - Gorlenko VM
AU  - Gaisin VA
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2018 13: 24.

PMID- 29930062
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of a Dissimilatory U(VI)-Reducing Bacterium, Shewanella xiamenensis Strain DCB2-1, Isolated from Nitrate- and Radionuclide-Contaminated Groundwater in Russia.
PG  - e00555-18
AB  - Here, we describe the draft genome sequence of Shewanella xiamenensis strain DCB2-1, isolated
      from nitrate- and radionuclide-contaminated groundwater. This
      strain is able to reduce nitrate, Tc(VII), Cr(VI), Fe(III), and U(VI), and its
      genome sequence contains several gene sets encoding denitrification, resistance
      to heavy metals, and reduction of metals and metalloids.
AU  - Grouzdev DS
AU  - Safonov AV
AU  - Babich TL
AU  - Tourova TP
AU  - Krutkina MS
AU  - Nazina TN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00555-18.

PMID- 29880595
VI  - 6
DP  - 2018
TI  - Genome Sequence of Methylotrophic Azospirillum sp. Strain B2, Isolated from a Raised Sphagnum Bog.
PG  - e00492-18
AB  - Azospirillum sp. strain B2 is a soil bacterium which was originally isolated from the
      Sosvyatskoe raised Sphagnum bog in Russia. Here, we present the approximately
      8-Mb draft genome sequence of Azospirillum sp. B2, with the aim of providing
      insight into the genomic basis of its ecological success in peatland settings.
AU  - Grouzdev DS
AU  - Tikhonova EN
AU  - Krutkina MS
AU  - Kravchenko IK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00492-18.

PMID- 24233584
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Lactobacillus fermentum Lf1, an Indian Isolate of Human  Gut Origin.
PG  - e00883-13
AB  - Lactobacillus fermentum is a normal inhabitant of the human gastrointestinal tract. Here, we
      report the draft genome sequence of an Indian isolate of the
      probiotic strain L. fermentum Lf1, isolated from the human gut.
AU  - Grover S
AU  - Sharma VK
AU  - Mallapa RH
AU  - Batish VK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00883-13.

PMID- 24265501
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Lactobacillus plantarum Strain Lp91, a Promising Indian  Probiotic Isolate of Human Gut Origin.
PG  - e00976-13
AB  - Lactobacillus plantarum is a highly versatile species among lactic acid bacteria  that has
      been widely isolated from highly diversified ecological niches,
      including the gastrointestinal tract. Here, we report the first draft genome
      sequence of an Indian isolate of the probiotic strain L. plantarum Lp91, isolated
      from human gut.
AU  - Grover S
AU  - Sharma VK
AU  - Mallapa RH
AU  - Batish VK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00976-13.

PMID- 6087579
VI  - 6
DP  - 1984
TI  - Growth and bioenergetic characteristics of Escherichia coli CK, capable of producing restriction endonuclease, under the conditions of batch cultivation.
PG  - 50-55
AB  - The conditions necessary for the controlled single and multicycle process of
      the batch cultivation of E. coli CK, capable of producing E. coli CK specific
      endonuclease, have been established.  This process can be regulated with
      respect to a number of parameters (temperature, pH, pO2, eH).  The possibility
      of using thermodynamic characteristics, calculated on the basis of the redox
      potential and disclosing the energetics of growth, for evaluating the
      effectiveness of controlled batch cultivation.  The optimum results have been
      obtained during the isolation of E. coli CK restriction endonuclease, active
      and containing no admixture of other endonucleases, at the period from the
      maximum specific growth rate to the end of the exponential growth phase, i.e.
      to the beginning of the stationary phase.
AU  - Gruber IM
AU  - Nikolskaya II
AU  - Uporova TM
AU  - Nisilevich VF
PT  - Journal Article
TA  - Zh. Mikrobiol. Epidemiol. Immunobiol.
JT  - Zh. Mikrobiol. Epidemiol. Immunobiol.
SO  - Zh. Mikrobiol. Epidemiol. Immunobiol. 1984 6: 50-55.

PMID- 11917035
VI  - 30
DP  - 2002
TI  - An in vivo selection system for homing endonuclease activity.
PG  - e29
AB  - Homing endonucleases are enzymes that catalyze the highly sequence-specific cleavage of DNA.
      We have developed an in vivo selection in Escherichia coli that links cell survival with
      homing endonuclease-mediated DNA cleavage activity and sequence specificity. Using this
      selection, wild-type and mutant variants of three homing endonucleases were characterized
      without requiring protein purification and in vitro analysis. This selection system may
      facilitate the study of sequence-specific DNA cleaving enzymes, and selections based on this
      work may enable the evolution of homing endonucleases with novel activities or specificities.
AU  - Gruen M
AU  - Chang K
AU  - Serbanescu I
AU  - Liu DR
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2002 30: e29.

PMID- 6269052
VI  - 9
DP  - 1981
TI  - Restriction enzyme digestion of hemimethylated DNA.
PG  - 2509-2515
AB  - Hemimethylated duplex DNA of the bacteriophage PhiX174 was synthesized using
      primed repair synthesis in vitro with E. coli DNA polymerase I followed by
      ligation to produce the covalently closed circular duplex (RFI).
      Single-stranded PhiX DNA was used as template, a synthetic oligonucleotide as
      primer and 5-methyldeoxycytidine-5'-triphosphate (5mdCTP) was used in place of
      dCTP.  The hemimethylated product was used as substrate for cleavage by various
      restriction enzymes.  Out of the 17 enzymes tests, only 5 (BstNI, TaqI, HincII,
      HinfI and HpaI) cleaved the hemimethylated DNA.  Two enzymes (MspI and HaeIII)
      were able to produce nicks on the unmethylated strand of the cleavage site.
      MspI, which is known to cleave at CCGG when the internal cytosine residue is
      methylated, does not cleave when both cytosines are methylated.  Another
      enzyme, ApyI, cleaves at the sequence CC(A/T)GG when the internal cytosine is
      methylated, but is inactive on hemimethylated DNA in which both cytosines are
      methylated.  Hemimethylated molecules should be useful for studying DNA
      methylation both in vivo and in vitro.
AU  - Gruenbaum Y
AU  - Cedar H
AU  - Razin A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1981 9: 2509-2515.

PMID- 28153904
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Pseudonocardia autotrophica Strain DSM 43083, an Efficient Producer of Peroxidases for Lignin Modification.
PG  - e01562-16
AB  - Pseudonocardia autotrophica strain DSM 43083 is a filamentous actinobacterium and was
      described to degrade or modify lignin. Here, we present its draft genome
      sequence, with a size of 5.8 Mb, to unravel the gene set coding for promising
      monooxygenases, dioxygenases, and DyP-type peroxidases associated with aromatic
      metabolism and lignin modification.
AU  - Grumaz C
AU  - Rais D
AU  - Kirstahler P
AU  - Vainshtein Y
AU  - Rupp S
AU  - Zibek S
AU  - Sohn K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01562-16.

PMID- 28705965
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Three Actinobacteria Strains Presenting New Candidate Organisms with High Potentials for Specific P450 Cytochromes.
PG  - e00532-17
AB  - The three Actinobacteria strains Streptomyces platensis DSM 40041, Pseudonocardia autotrophica
      DSM 535, and Streptomyces fradiae DSM 40063 were described to
      selectively oxyfunctionalize several drugs. Here, we present their draft genomes
      to unravel their gene sets encoding promising cytochrome P450 monooxygenases
      associated with the generation of drug metabolites.
AU  - Grumaz C
AU  - Vainshtein Y
AU  - Kirstahler P
AU  - Luetz S
AU  - Kittelmann M
AU  - Schroer K
AU  - Eggimann FK
AU  - Czaja R
AU  - Vogel A
AU  - Hilberath T
AU  - Worsch A
AU  - Girhard M
AU  - Urlacher VB
AU  - Sandberg M
AU  - Sohn K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00532-17.

PMID- 10666443
VI  - 28
DP  - 2000
TI  - MethTools-a toolbox to visualize and analyze DNA methylation data.
PG  - 1053-1058
AB  - The Bisulfite Genomic Sequencing technique has found wide acceptance for the generation of
      DNA-methylation maps with single-base resolution. The method is based on the selective
      deamination of cytosine to uracil (and subsequent conversion to thymine via PCR), whereas
      5-methylcytosine residues remain unchanged. Methylation maps are created by the comparison of
      bisulfite converted sequences with the untreated genomic sequence. 'MethTools' is a
      collection of software tools that replaces the time-consuming manual comparison process,
      generates graphical outputs of methylation patterns and methylation density, estimates the
      systematic error of the experiment and searches for conserved methylated nucleotide patterns.
      The programs are written in Perl 5 and C, and the source code can be downloaded. All tools run
      independently but the programs are interfaced. Thus, a script can perform the entire analysis
      procedure automatically. In addition, a web-based remote analysis service is offered. Both the
      source code and the remote analysis are available at http://genome.imb-jena.de/methtools/
AU  - Grunau C
AU  - Schattevoy R
AU  - Mache N
AU  - Rosenthal A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2000 28: 1053-1058.

PMID- 23788550
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Streptomyces viridochromogenes Strain Tu57, Producer of  Avilamycin.
PG  - e00384-13
AB  - Here we present the draft genome sequence of Streptomyces viridochromogenes Tu57. This strain
      is a producer of avilamycin A, an oligosaccharide antibiotic from the
      orthosomycin group, which is active against Gram-positive bacteria.
AU  - Gruning BA
AU  - Erxleben A
AU  - Hahnlein A
AU  - Gunther S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00384-13.

PMID- 3139036
VI  - 950
DP  - 1988
TI  - Reduced methyl group acceptance of 1-beta-D-arabinofuranosylcytosine-containing DNA polymers.
PG  - 366-373
AB  - Previous studies have shown that 1-beta-D-arabinofuranosylcytosine (ara-C) can
      induce differentiation of various malignant cells and that DNA methylation
      patterns become altered under ara-C treatment of those cells.  The aim of this
      study was to investigate whether this influence on DNA methylation is caused by
      a direct effect of DNA-incorporated ara-C molecules on nuclear DNA methylase.
      For this reason, we constructed various ara-C-substituted DNA polymers and used
      them as substrates for highly purified eukaryotic DNA methylase isolated from
      murine P815 mastocytoma cells.  The ara-C incorporation into DNA polymers was
      measured by either an ara-C-specific radioimmunoassay or by use of
      radioactive-labelled ara-C during the synthesis of those polymers.  We found an
      inverse correlation between the level of ara-C substitution of the DNA polymers
      and their methyl group acceptance.  Kinetic experiments performed with
      ara-C-modified DNA polymers pointed out that the mode of action of DNA
      methylase remains unaltered.  DNA methylase is neither detached nor fixed at an
      ara-C site, but is somehow hindered in its enzymatic activity, probably by
      slowing down the walking mechanism.  Hence, the previously observed
      hypermethylation of DNA of some eukaryotic cells, propagated in the presence of
      ara-C, is apparently not due to a direct effect of DNA-incorporated ara-C
      molecules on endogenous DNA methylase.
AU  - Grunwald S
AU  - Driever PH
AU  - Hoelzer D
AU  - Drahovsky D
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1988 950: 366-373.

PMID- 8463270
VI  - 268
DP  - 1993
TI  - Peptide splicing in the vacuolar ATPase subunit A from Candida tropicalis.
PG  - 7372-7381
AB  - Subunit A of the vacuolar proton pump appears to be responsible for the ATP hydrolysis which
      is coupled to the pumping of protons into a variety of intracellular acid compartments,
      including the fungal vacuole.  We report here the cloning and sequence determination of the
      gene encoding subunit A from Candida tropicalis.  Southern blot hybridization analysis
      indicates that there is a single gene which encodes this protein.  The gene contains a single
      intron at the extreme 5'-end  of the coding region.  The gene is predicted to encode a
      polypeptide of 1088 residues with a calculated molecular mass of 119,019 daltons, yet the
      mature polypeptide appears to be approximately 67 kDa, indicating that this protein probably
      undergoes the same sort of processing that is evidenced in the homologous protein from
      Saccharomyces cerevisiae in which an approximately 50-kDa polypeptide (the spacer) is spliced
      out of the mature protein.  The Candida gene, with and without this middle portion, has been
      expressed in S. cerevisiae and found to restore a Saccharomyces subunit A deletion mutant
      (tfp1-delta8) to apparently wild-type growth at pH 7.6, and normal vacuolar acidification.
      The peptide sequence of the two predicted mature ends is very similar to the sequences of the
      analogous proteins from Daucus carota, S. cerevisiae, and Neurospora crassa (60.5, 87.4, and
      72.9% identity, respectively), but the middle portion bears only very limited homology with
      the Saccharomyces protein sequence.  Processing of the gene product occurs in S. cerevisiae,
      Escherichia coli, and in rabbit reticulocyte-mediated in vitro translation, indicating that
      the excision is probably autocatalytic.  The limited sequence identity seen between the
      Saccharomyces and Candida spacer domains may considerably narrow the functionally important
      regions responsible for the excision event.
AU  - Gu HH
AU  - Xu J
AU  - Gallagher M
AU  - Dean GE
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1993 268: 7372-7381.

PMID- 28280031
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of a Polydroxyalkanoate-Synthesizing Bacterium, Bacillus sp. Strain PJC48, Isolated from Activated Sludge.
PG  - e01751-16
AB  - The genome sequence of a Bacillus strain is capable of synthesizing polyhydroxyalkanoates, and
      Bacillus sp. is considered a platform strain for the
      production of many biodegradable materials. Here, we present the sequence of the
      PJC48 strain genome, which is composed of three chromatin structures, an
      extracellular structure, and a cytoskeleton.
AU  - Gu JJ
AU  - Zhou Y
AU  - Lu JJ
AU  - Ye BC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01751-16.

PMID- 24926050
VI  - 2
DP  - 2014
TI  - Genome Sequence of the epsilon-Poly-l-Lysine-Producing Strain Streptomyces albulus NK660, Isolated from Soil in Gutian, Fujian Province, China.
PG  - e00532-14
AB  - We determined the complete genome sequence of a soil bacterium, Streptomyces albulus NK660. It
      can produce epsilon-poly-l-lysine, which has antimicrobial
      activity against a spectrum of microorganisms. The genome of S. albulus NK660
      contains a 9,360,281-bp linear chromosome and a 12,120-bp linear plasmid.
AU  - Gu Y
AU  - Yang C
AU  - Wang X
AU  - Geng W
AU  - Sun Y
AU  - Feng J
AU  - Wang Y
AU  - Quan Y
AU  - Che Y
AU  - Zhang C
AU  - Gong T
AU  - Zhang W
AU  - Gao W
AU  - Zuo Z
AU  - Song C
AU  - Wang S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00532-14.

PMID- 24625876
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence and Annotation of the Entomopathogenic Bacterium Xenorhabdus szentirmaii Strain DSM16338.
PG  - e00190-14
AB  - We report the genome sequence of Xenorhabdus szentirmaii DSM16338 (4.84 Mb), a symbiont of the
      entomopathogenic nematode Steinernema rarum. This strain produces
      antimicrobial activity.
AU  - Gualtieri M
AU  - Ogier JC
AU  - Pages S
AU  - Givaudan A
AU  - Gaudriault S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00190-14.

PMID- 23209229
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Bacillus thuringiensis Serovar Sichuansis Strain MC28.
PG  - 6975
AB  - Bacillus thuringiensis is an important microbial insecticide used in the control  of
      agricultural pests. Here we report the finished, annotated genome sequence of
      Bacillus thuringiensis serovar Sichuansis strain MC28, which can form parasporal
      crystals consisting of Cry4Cc1, Cry30Fa1, Cry53Ab1, Cry54Aa1, Cry54Ab1, Cry68Aa1,
      Cry69Aa1, Cry69Aa2, Cry70Ba1, Cyt1Da1, and Cyt2Aa3. It is also highly toxic to
      lepidopterous and dipterous insects.
AU  - Guan P
AU  - Ai P
AU  - Dai X
AU  - Zhang J
AU  - Xu L
AU  - Zhu J
AU  - Li Q
AU  - Deng Q
AU  - Li S
AU  - Wang S
AU  - Liu H
AU  - Wang L
AU  - Li P
AU  - Zheng A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6975.

PMID- 20668693
VI  - 5
DP  - 2010
TI  - Alteration of Sequence Specificity of the Type IIS Restriction Endonuclease BtsI.
PG  - e11787
AB  - The Type IIS restriction endonuclease BtsI recognizes and digests at GCAGTG(2/0). It comprises
      two subunits: BtsIA and BtsIB. The BtsIB
      subunit contains the recognition domain, one catalytic domain for
      bottom strand nicking and part of the catalytic domain for the top
      strand nicking. BtsIA has the rest of the catalytic domain that is
      responsible for the DNA top strand nicking. BtsIA alone has no activity
      unless it mixes with BtsIB to reconstitute the BtsI activity. During
      characterization of the enzyme, we identified a BtsIB mutant R119A
      found to have a different digestion pattern from the wild type BtsI.
      After characterization, we found that BtsIB(R119A) is a novel
      restriction enzyme with a previously unreported recognition sequence
      CAGTG(2/0), which is named as BtsI-1. Compared with wild type BtsI,
      BtsI-1 showed different relative activities in NEB restriction enzyme
      reaction buffers NEB1, NEB2, NEB3 and NEB4 and less star activity.
      Similar to the wild type BtsIB subunit, the BtsI-1 B subunit alone can
      act as a bottom nicking enzyme recognizing CAGTG(-/0). This is the
      first successful case of a specificity change among this restriction
      endonuclease type.
AU  - Guan SX
AU  - Blanchard A
AU  - Zhang PH
AU  - Zhu ZY
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2010 5: e11787.

PMID- 25146135
VI  - 2
DP  - 2014
TI  - Genome Sequence of a Xylella fastidiosa Strain Causing Sycamore Leaf Scorch Disease in Virginia.
PG  - e00773-14
AB  - Xylella fastidiosa causes bacterial leaf scorch in landscape trees including sycamore. We
      determined the draft genome of X. fastidiosa strain Sy-Va, isolated
      in Virginia from a sycamore tree displaying leaf scorch symptoms. The Sy-VA
      genome contains 2,477,829 bp, and has a G+C content of 51.64 mol%.
AU  - Guan W
AU  - Shao J
AU  - Davis RE
AU  - Zhao T
AU  - Huang Q
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00773-14.

PMID- 24604658
VI  - 2
DP  - 2014
TI  - Genome Sequence of a Xylella fastidiosa Strain Causing Mulberry Leaf Scorch Disease in Maryland.
PG  - e00916-13
AB  - Xylella fastidiosa causes bacterial leaf scorch in landscape trees, including mulberry. We
      determined the draft genome of the mulberry strain Mul-MD in order
      to gain a better understanding of the molecular basis of strain divergence, host
      specificity, nutrient requirements, and pathogenicity, as well as to develop
      genome-based specific detection methods.
AU  - Guan W
AU  - Shao J
AU  - Zhao T
AU  - Huang Q
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00916-13.

PMID- 25414501
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of an Obligately Methylotrophic Methanogen, Methanococcoides methylutens, Isolated from Marine Sediment.
PG  - e01184-14
AB  - Methanococcoides methylutens, the type species of the genus Methanococcoides, is  a slightly
      halophilic methanogenic archaeon with a methylotrophic metabolism.
      Here, we present the annotated draft genome sequence of M. methylutens, which
      comprises 2,508,511 bp with 2,482 coding sequences, 51 tRNA genes, and a G+C
      content of 42.5%.
AU  - Guan Y
AU  - Ngugi DK
AU  - Blom J
AU  - Ali S
AU  - Ferry JG
AU  - Stingl U
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01184-14.

PMID- 28883147
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of 64 Salmonella enterica Serotype Enteritidis Isolates Obtained from Wild Mice.
PG  - e00953-17
AB  - Salmonella enterica serotype Enteritidis is a foodborne pathogen of global concern, because it
      is frequently isolated from foods and patients. Draft genome
      sequences are reported here for 64 S Enteritidis strains isolated from the
      intestines and spleens of mice caught live on chicken farms in the U.S.
      Northeast. The availability of these genomes provides baseline information on the
      genomic diversity of S Enteritidis during the 1990s, when foodborne outbreaks
      traced to internal contamination of eggs were prevalent.
AU  - Guard J
AU  - Cao G
AU  - Kastanis GJ
AU  - Davison S
AU  - McClelland M
AU  - Sanchez LM
AU  - Zheng J
AU  - Brown E
AU  - Allard MW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00953-17.

PMID- 23516211
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Vibrio mimicus Strain CAIM 602T.
PG  - e0008413
AB  - Vibrio mimicus is a Gram-negative bacterium associated with gastrointestinal diseases in
      humans around the world. We report the complete genome sequence of
      the Vibrio mimicus strain CAIM 602(T) (CDC1721-77, LMG 7896(T), ATCC 33653(T)).
AU  - Guardiola-Avila I
AU  - Acedo-Felix E
AU  - Noriega-Orozco L
AU  - Yepiz-Plascencia G
AU  - Sifuentes-Romero I
AU  - Gomez-Gil B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0008413.

PMID- 26779304
VI  - 11
DP  - 2016
TI  - Complete genome sequence of the potato pathogen Ralstonia solanacearum UY031.
PG  - 7
AB  - Ralstonia solanacearum is the causative agent of bacterial wilt of potato. Ralstonia
      solanacearum strain UY031 belongs to the American phylotype IIB,
      sequevar 1, also classified as race 3 biovar 2. Here we report the completely
      sequenced genome of this strain, the first complete genome for phylotype IIB,
      sequevar 1, and the fourth for the R. solanacearum species complex. In addition
      to standard genome annotation, we have carried out a curated annotation of type
      III effector genes, an important pathogenicity-related class of genes for this
      organism. We identified 60 effector genes, and observed that this effector
      repertoire is distinct when compared to those from other phylotype IIB strains.
      Eleven of the effectors appear to be nonfunctional due to disruptive mutations.
      We also report a methylome analysis of this genome, the first for a R.
      solanacearum strain. This analysis helped us note the presence of a toxin gene
      within a region of probable phage origin, raising the hypothesis that this gene
      may play a role in this strain's virulence.
AU  - Guarischi-Sousa R
AU  - Puigvert M
AU  - Coll NS
AU  - Siri MI
AU  - Pianzzola MJ
AU  - Valls M
AU  - Setubal JC
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 7.

PMID- 1849078
VI  - 10
DP  - 1991
TI  - Increased protein flexibility leads to promiscuous protein-DNA interactions in type IC restriction-modification systems.
PG  - 951-957
AB  - We have investigated the role of a four amino acid element that is repeated twice and three
      times, respectively, in the specificity polypeptides of the two allelic
      restriction-modification systems EcoR124 and EcoR124/3. We had earlier shown that this
      difference in amino acid sequence between the two systems is solely responsible for the
      different DNA sequence specificities of the two systems. The effect of single amino acid
      substitutions and small insertion and deletion mutations on restriction activity and
      modification specificity was determined in vivo by phage infection assays and in vitro by
      methylation of DNA with purified modification methylases. Mutant restriction-modification
      systems with changes in the number and the length of the central amino acid repeats exhibited
      decreased restriction activity and in some cases relaxed substrate specificity. Our data
      strongly support the idea that the repetitive amino acid motif in the specificity polypeptides
      forms part of a flexible interdomain linker. It may be responsible for positioning on the DNA
      the two major specificity polypeptide domains which are thought to contact independently the
      half sites of the split recognition sequences typical for all type I restriction-modification
      systems.
AU  - Gubler M
AU  - Bickle TA
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1991 10: 951-957.

PMID- 1740108
VI  - 11
DP  - 1992
TI  - Recombination of constant and variable modules alters DNA sequence recognition by type IC restriction-modification enzymes.
PG  - 233-240
AB  - EcoR124I and EcoDXXI are allelic type I restriction-modification (R-M) systems
      whose specificity genes consist of common structural elements: two variable
      regions are separated by a constant, homologous region containing a number of
      repetitive sequence elements.  In vitro recombination of variable and constant
      elements has led to fully active, hybrid R-M systems exhibiting new and
      predictable target site specificities.  Methylation of synthetic DNA sequences
      with purified, hybrid modification methylases was used to confirm the proposed
      recognition sequences.  The results clearly demonstrate the correlation between
      protein domains and target site specificity.  Our data suggest that a bacterial
      population may switch the recognition sequences of its type I R-M system by
      single recombination events and thus is able to maintain a prokaryotic analogue
      of the immune system of variable specificity.
AU  - Gubler M
AU  - Braguglia D
AU  - Meyer J
AU  - Piekarowicz A
AU  - Bickle TA
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1992 11: 233-240.

PMID- 28408685
VI  - 5
DP  - 2017
TI  - Permanent Draft Genome Sequences of Three Frankia sp. Strains That Are Atypical,  Noninfective, Ineffective Isolates.
PG  - e00174-17
AB  - Here, we present draft genome sequences for three atypical Frankia strains (lineage 4) that
      were isolated from root nodules but are unable to reinfect
      actinorhizal plants. The genome sizes of Frankia sp. strains EUN1h, BMG5.36, and
      NRRL B16386 were 9.91, 11.20, and 9.43 Mbp, respectively.
AU  - Gueddou A
AU  - Swanson E
AU  - Ktari A
AU  - Nouioui I
AU  - Hezbri K
AU  - Ghodhbane-Gtari F
AU  - Simpson S
AU  - Morris K
AU  - Thomas WK
AU  - Sen A
AU  - Gtari M
AU  - Tisa LS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00174-17.

PMID- 21742871
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of the commensal Streptococcus salivarius strain JIM8777.
PG  - 5024-5025
AB  - The commensal bacterium Streptococcus salivarius is a prevalent species of the human
      oropharyngeal tract with an important role in oral ecology.
      Here, we report the complete 2.2-Mb genome sequence and annotation of
      strain JIM8777, which was recently isolated from the oral cavity of a
      healthy, dentate infant.
AU  - Guedon E
AU  - Delorme C
AU  - Pons N
AU  - Cruaud C
AU  - Loux V
AU  - Couloux A
AU  - Gautier C
AU  - Sanchez N
AU  - Layec S
AU  - Galleron N
AU  - Almeida M
AU  - van de Guchte M
AU  - Kennedy SP
AU  - Ehrlich SD
AU  - Gibrat JF
AU  - Wincker P
AU  - Renault P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5024-5025.

PMID- 22887674
VI  - 194
DP  - 2012
TI  - Genome Sequence of Parascardovia denticolens IPLA 20019, Isolated from Human Breast Milk.
PG  - 4776-4777
AB  - This work describes the draft genome of Parascardovia denticolens IPLA 20019, isolated from
      human milk. This species, usually isolated from caries lesions, is
      taxonomically related to the genus Bifidobacterium. The genetic information of
      IPLA 20019 enhances our understanding of the adaptation of this P. denticolens
      strain from human breast milk.
AU  - Gueimonde M
AU  - Bottacini F
AU  - van Sinderen D
AU  - Ventura M
AU  - Margolles A
AU  - Sanchez B
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4776-4777.

PMID- 23209243
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Immunomodulatory Strain Bifidobacterium bifidum LMG 13195.
PG  - 6997
AB  - In this work, we report the genome sequences of Bifidobacterium bifidum strain LMG13195.
      Results from our research group show that this strain is able to
      interact with human immune cells, generating functional regulatory T cells.
AU  - Gueimonde M
AU  - Ventura M
AU  - Margolles A
AU  - Sanchez B
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6997.

PMID- 27634985
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Lactococcus lactis subsp. lactis A12, a Strain Isolated from Wheat Sourdough.
PG  - e00692-16
AB  - We report here the complete genome sequence of Lactococcus lactis subsp. lactis strain A12, a
      strain isolated from sourdough. The circular chromosome and the
      four plasmids reveal genes involved in carbohydrate metabolism that are
      potentially required for the persistence of this strain in such a complex
      ecosystem.
AU  - Guellerin M
AU  - Passerini D
AU  - Fontagne-Faucher C
AU  - Robert H
AU  - Gabriel V
AU  - Loux V
AU  - Klopp C
AU  - Le Loir Y
AU  - Coddeville M
AU  - Daveran-Mingot ML
AU  - Ritzenthaler P
AU  - Le Bourgeois P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00692-16.

PMID- 1351960
VI  - 16E
DP  - 1992
TI  - Cloning, isolation, and characterization of the human T-cell DNA-cytosine 5-methyltransferase gene.
PG  - 179
AB  - DNA methylation can affect the latency of HIV and HTLV by effectively silencing
      transcriptional expression. Previous studies have shown that a CpG island in the HIV LTR, when
      methylated by the human DNA-cytosine 5-methyltransferase (MeTase), inactivates HIV
      transcription in cis. Further characterization of the methyltransferase enzyme is therefore of
      obvious interest. A human T-cell cDNA library from the cell line Jurkatt has been screened,
      using a murine DNA methyltransferase cDNA clone as a probe, and a clone of approximately 0.7
      Kb has been isolated (pMET2) and sequenced with 87% homology to an area in the 3' region of
      the murine cDNA. Based on the size of the mature protein (-172 Kdaltons), a gene of at least 5
      Kb is expected. Southern blot analysis of human genomic DNA yielded single fragments of 4.2 Kb
      to over 12 Kb, using the pMET2 fragment as a probe. Northern blot analysis has been employed
      to analyze transcriptional expression, and to determine the size of the methyltranferase
      message. A human genomic library has been screened and four putative clones isolated and shown
      positive by PCR analysis, using primers to pMET2. Southern analysis on phage DNA digested with
      XbaI yields fragments large enough to include a full-length copy of the gene. Sub-cloning into
      an expression vector is underway in order to obtain sequence information, and to further
      characterize this gene.
AU  - Guenthner C
AU  - Kim S
AU  - Bednarik DP
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1992 16E: 179.

PMID- 24459282
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Williamsia sp. Strain D3, Isolated From the Darwin Mountains, Antarctica.
PG  - e01230-13
AB  - Actinobacteria are the dominant taxa in Antarctic desert soils. Here, we describe the first
      draft genome of a member of the genus Williamsia (strain D3) isolated
      from Antarctic soil. The genome of this psychrotolerant bacterium may help to
      elucidate crucial survival mechanisms for organisms inhabiting cold desert soil
      systems.
AU  - Guerrero LD
AU  - Makhalanyane TP
AU  - Aislabie JM
AU  - Cowan DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01230-13.

PMID- 27811092
VI  - 4
DP  - 2016
TI  - Genome Sequence of Clostridium paraputrificum 373-A1 Isolated in Chile from a Patient Infected with Clostridium difficile.
PG  - e01178-16
AB  - Clostridium paraputrificum is a gut microbiota member reported in several cases of bacteremia
      and coinfections. So far, only one genome sequence of a C.
      paraputrificum (AGR2156) isolate is available. Here, we present the draft genome
      of C. paraputrificum strain 373-A1, isolated from stools from a patient with C.
      difficile infection.
AU  - Guerrero-Araya E
AU  - Plaza-Garrido A
AU  - Diaz-Yanez F
AU  - Pizaro-Guajardo M
AU  - Valenzuela SL
AU  - Meneses C
AU  - Gil F
AU  - Castro-Nallar E
AU  - Paredes-Sabja D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01178-16.

PMID- 2991196
VI  - 163
DP  - 1985
TI  - Determination of DNA Sequences Containing Methylcytosine in Bacillus subtilis Marburg.
PG  - 573-579
AB  - The methylcytosine-containing sequences in the DNA of Bacillus subtilis 168
      Marburg (Restriction-modification Type BSUM) were determined by three different
      methods: (i) examination of in vivo-methylated DNA by restriction enzyme
      digestion and, whenever possible, analysis for methycytosine at the 5' end;
      (ii) methylation in vitro of unmethylated DNA with B. subtilis DNA
      methyltransferase and determination of the methylated sites; and (iii) the
      methylatability of unmethylated DNA by B. subtilis methyltransferase after
      potential sites have been destroyed by digestion with restriction
      endonucleases.  The results obtained by these methods, taken together, show
      that methylcytosine was present only within the sequence 5'-TCGA-3'.  The
      presence of methylcytosine at the 5' end of the DNA fragments generated by
      restriction endonuclease AsuII digestion and the fact that in vivo-methylated
      DNA could not be digested by the enzyme XhoI showed that the recognition
      sequences of these two enzymes contained methylcytosine.  As these two enzymes
      recognized a similar sequence containing a 5' pyrimidine (Py) and a 3' purine
      (pu), 5'-PyTCGAPu'3', the possibility that methylcytosine is present in the
      complementary sequences 5'TTCGAG-3' and 5'CTCGAA-3' was postulated.  This was
      verified by the methylation in vitro, with B. subtilis enzyme, of a
      2.6-kilobase fragment of lambda DNA containing two such sites and devoid of
      AsuII or XhoI recognition sequences.  By analyzing the methylatable sites, it
      was found that in one of the two PyTCGAPu sequences, cytosine was methylated in
      vitro in both DNA strands.  It is concluded that the sequence 5'-PyTCGAPu'3' is
      methylated by the DNA methyltransferase (of cytosine) of B. subtilis Marburg.
AU  - Guha S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1985 163: 573-579.

PMID- 3150363
VI  - 74
DP  - 1988
TI  - DNA methyltransferase of Bacillus subtilis Marburg:  purification, properties and further evidence of specificity.
PG  - 77-81
AB  - Bacillus subtilis Marburg strain displays DNA methyltransferase activity. This enzyme, M.BsuM,
      methylates cytosine in the sequence 5'-YTCGAR-3' (Y=pyrimidine; R=purine). M.BsuM was
      purified from exponentially growing cells of B. subtilis 168M. This enzyme (45+/- 1 kDa) is
      monomeric and recognizes only double-stranded DNA. It is inhibited partially by Mg2+, Mn2+
      ions and spermidine and almost totally by sodium dodecyl sulfate, urea and agarose. This
      enzyme methylates specifically the three methylatable sites of the plasmid pBM3. Relaxation of
      specificity (star activity) was observed in the presence of organic solvents. A very low
      amount of M.BsuM was obtained in the standard Marburg strain. To obtain sufficient enzyme
      attempts are being made to clone the M.BsuM gene in Escherichia coli by using a constructed
      plasmid (pBM14) vector. Only one transformant containing a 3-kb insert and showing a low level
      of expression, was obtained.
AU  - Guha S
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 77-81.

PMID- 1641327
VI  - 20
DP  - 1992
TI  - Expression of Escherichia coli dam gene in Bacillus subtilis provokes DNA damage response: N6-methyladenine is removed by two repair pathways.
PG  - 3607-3615
AB  - The dam gene of Excherichia coli encodes a DNA methyltransferase that methylates the N6
      position of adenine in the sequence GATC. It was stably expressed from a shuttle vector in a
      repair- and recombination-proficient strain of Bacillus subtilis. In this strain the majority
      of plasmid DNA molecules was modified at dam sites whereas most chromosomal DNA remained
      unmethylated during exponential growth. During stationary phase the amount of unmethylated DNA
      increased, suggesting that methylated bases were being removed. An ultraviolet damage
      repair-deficient mutant (uvrB) contained highly methylated chromosomal and plasmid DNA. High
      levels of Dam methylation were detrimental to growth and viability of this mutant strain and
      some features of the SOS response were also induced. A mutant defective in the synthesis of
      adaptive DNA alkyltransferases and induction of the adaptive response (ada) also showed high
      methylation and properties similar to that of the dam gene expressing uvrB strain. When
      protein extracts from B. subtilis expressing the Dam methyltransferase or treated with
      N-methyl-N-nitro-N-nitroso-guanidine were incubated with [3H]-labelled Dam methylated DNA, the
      methyl label was bound to two proteins of 14 and 9 kD. Some free N6-methyladenine residues are
      excised by proteins involved in both excision (uvrB) and the adaptive response (ada) DNA
      repair pathways in B. subtilis.
AU  - Guha S
AU  - Guschlbauer W
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 3607-3615.

PMID- 1420312
VI  - 1132
DP  - 1992
TI  - Improved plasmids containing the Escherichia coli dam gene under the control of the tac promoter.
PG  - 309-310
AB  - We report the construction of a series of plasmids containing the dam gene under the control
      of the tac promoter. Cells containing these plasmids produce about 8 to 10-fold more Dam
      methyltransferase (Mtase) than the previously used plasmid pTP166 and avoid the use of a high
      temperature step necessary for the expression of Dam Mtase in the plasmid pDOX1 and thus
      allows its use for the study of thermosensitive mutants.
AU  - Guha S
AU  - Guschlbauer W
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1992 1132: 309-310.

PMID- 12167644
VI  - 277
DP  - 2002
TI  - The RecA intein of Mycobacterium tuberculosis promotes cleavage of ectopic DNA sites: Implications for the dispersal of inteins in natural populations.
PG  - 40352-40361
AB  - The RecA intein of Mycobacterium tuberculosis, a novel double-stranded DNA endonuclease,
      requires both Mn2+ and ATP for efficient cleavage of the inteinless recA allele. In this
      study, we show that Mg2+ alone was sufficient to stimulate PI-MtuI to cleave double-stranded
      DNA at ectopic sites. In the absence of Mg2+, PI-MtuI formed complexes with topologically
      different forms of DNA containing ectopic recognition sequences with equal affinity but failed
      to cleave DNA. We observed that PI-MtuI was able to inflict double-strand breaks robustly
      within the ectopic recognition sequence to generate either a blunt end or 1-2 nucleotide
      3'-hydroxyl overhangs. Mutational analyses of the presumptive metal-ion binding ligands
      (D122, D222 and E220) together with immunoprecipitation assays provided compelling evidence to
      link both the Mg2+- and Mn2+ and ATP-dependent endonuclease activities to PI-MtuI. The kinetic
      mechanism of PI-MtuI promoted cleavage of ectopic DNA sites proceeded through a sequential
      mechanism with transient accumulation of nicked circular duplex DNA as an intermediate.
      Together, these data suggest that PI-MtuI, like group II introns, might mediate ectopic DNA
      transposition and hence its lateral transfer in natural populations.
AU  - Guhan N
AU  - Muniyappa K
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2002 277: 40352-40361.

PMID- 12853636
VI  - 31
DP  - 2003
TI  - Mycobacterium tuberculosis RecA intein, a LAGLIDADG homing endonuclease, displays Mn2+ and DNA-dependent ATPase activity.
PG  - 4184-4191
AB  - Mycobacterium tuberculosis RecA intein (PI-MtuI), a LAGLIDADG homing endonuclease, displays
      dual target specificity in response to alternative
      cofactors. While both ATP and Mn(2+) were required for optimal cleavage of
      an inteinless recA allele (hereafter referred to as cognate DNA), Mg(2+)
      alone was sufficient for cleavage of ectopic DNA sites. In this study, we
      have explored the ability of PI-MtuI to catalyze ATP hydrolysis in the
      presence of alternative metal ion cofactors and DNA substrates. Our
      results indicate that PI-MtuI displays maximum ATPase activity in the
      presence of cognate but not ectopic DNA. Kinetic analysis revealed that
      Mn(2+) was able to stimulate PI-MtuI catalyzed ATP hydrolysis, whereas
      Mg(2+) failed to do so. Using UV crosslinking, limited proteolysis and
      amino acid sequence analysis, we show that (32)P-labeled ATP was bound to
      a 14 kDa peptide containing the putative Walker A motif. Furthermore, the
      limited proteolysis approach disclosed that cognate DNA was able to induce
      structural changes in PI-MtuI. Mutation of the presumptive metal
      ion-binding ligands (Asp122 and Asp222) in the LAGLIDADG motifs of PI-MtuI
      impaired its affinity for ATP, thus resulting in a reduction in or loss of
      its endonuclease activity. Together, these results suggest that PI-MtuI is
      a (cognate) DNA- and Mn(2+)-dependent ATPase, unique from the LAGLIDADG
      family of homing endonucleases, and implies a possible role for ATP
      hydrolysis in the recognition and/or cleavage of homing site DNA sequence.
AU  - Guhan N
AU  - Muniyappa K
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2003 31: 4184-4191.

PMID- 11850426
VI  - 277
DP  - 2002
TI  - Mycobacterium tuberculosis RecA intein possesses a novel ATP-dependent site-specific double-stranded DNA endonuclease activity.
PG  - 16257-16264
AB  - Mycobacterium tuberculosis recA harbors an intervening sequence in its open reading frame,
      presumed to encode an endonuclease (PI-MtuI) required for intein homing in inteinless recA
      allele. Although the protein-splicing ability of PI-MtuI has been characterized, the
      identification of its putative endonuclease activity has remained elusive. To investigate
      whether PI-MtuI possesses endonuclease activity, recA intervening sequence was cloned,
      overexpressed, and purified to homogeneity. Here we show that PI-MtuI bound both single- and
      double-stranded DNA with similar affinity but failed to cleave DNA in the absence of
      cofactors. Significantly, PI-MtuI nicked supercoiled DNA in the presence of alternative
      cofactors but required both Mn2+ and ATP to generate linear double-stranded DNA. We observed
      that PI-MtuI was able to inflict a staggered double-strand break 24 bp upstream of the
      insertion site in the inteinless recA allele. Similar to a few homing endonucleases, DNA
      cleavage by PI-MtuI was specific with an exceptionally long cleavage site spanning 22 bp. The
      kinetic mechanism of PI-MtuI promoted cleavage supports a sequential rather than concerted
      pathway of strand cleavage with the formation of nicked double-stranded DNA as an
      intermediate. Together, these results reveal that RecA intein is a novel Mn2+-ATP-dependent
      double-strand specific endonuclease, which is likely to be important for homing process in
      vivo.
AU  - Guhan N
AU  - Muniyappa K
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2002 277: 16257-16264.

PMID- 12870715
VI  - 38
DP  - 2003
TI  - Structural and functional characteristics of homing endonucleases.
PG  - 199-248
AB  - Mobile genetic elements constitute a remarkably diverse group of nonessential selfish genes
      that provide no apparent function to the host.
      These selfish genes have been implicated in host extinction, speciation
      and architecture of genetic systems. Homing endonucleases, encoded by the
      open reading frames embedded in introns or inteins of mobile genetic
      elements, possess double-stranded DNA-specific endonuclease activity. They
      inflict sequence-specific double-strand breaks at or near the homing site
      in intron- or intein-less allele. Subsequently, through nonreciprocal
      exchange the insertion sequence (intron or intein) is transferred from an
      intein- or intron-containing allele to an intein- or intron-less allele.
      The components of host double-strand break repair pathway are thought to
      finish the "homing" process. Several lines of evidence suggest that homing
      endonucleases are capable of promoting transposition into ectopic sites
      within or across genomes for their survival as well as dispersal in
      natural populations. The occurrence of inteins at high frequencies serves
      as instructive models for understanding the mechanistic aspects of the
      process of homing and its evolution. This review focuses on genetic,
      biochemical, structural, and phylogenetic aspects of homing endonucleases,
      and their comparison with restriction endonucleases.
AU  - Guhan N
AU  - Muniyappa K
PT  - Journal Article
TA  - Crit. Rev. Biochem. Mol. Biol.
JT  - Crit. Rev. Biochem. Mol. Biol.
SO  - Crit. Rev. Biochem. Mol. Biol. 2003 38: 199-248.

PMID- 26823575
VI  - 4
DP  - 2016
TI  - Draft Genome Assembly of a Filamentous Euendolithic (True Boring) Cyanobacterium, Mastigocoleus testarum Strain BC008.
PG  - e01574-15
AB  - Mastigocoleus testarum strain BC008 is a model organism used to study marine photoautotrophic
      carbonate dissolution. It is a multicellular, filamentous,
      diazotrophic, euendolithic cyanobacterium ubiquitously found in marine benthic
      environments. We present an accurate draft genome assembly of 172 contigs
      spanning 12,700,239 bp with 9,131 annotated genes with an average G+C% of 37.3.
AU  - Guida BS
AU  - Garcia-Pichel F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01574-15.

PMID- 
VI  - 0
DP  - 1982
TI  - Conjugative transfer of chromosomal R determinants in Streptococcus pneumoniae.
PG  - 88-92
AB  - 
AU  - Guild WR
AU  - Smith MD
AU  - Shoemaker NB
PT  - Journal Article
TA  - Microbiology-1982
JT  - Microbiology-1982
SO  - Microbiology-1982 1982 0: 88-92.

PMID- 26564039
VI  - 3
DP  - 2015
TI  - Genome Sequence of a Clinical Klebsiella pneumoniae Sequence Type 6 Strain.
PG  - e01311-15
AB  - We report here the genome sequence of Klebsiella pneumoniae CH1034, a sequence type 6 (ST6)
      strain isolated in 2012 from a central venous catheter of a
      hospitalized patient.
AU  - Guilhen C
AU  - Iltis A
AU  - Forestier C
AU  - Balestrino D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01311-15.

PMID- 27389274
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequencing of Two Bartonella bacilliformis Strains.
PG  - e00659-16
AB  - Bartonella bacilliformis is the causative agent of Carrion's disease, a highly endemic human
      bartonellosis in Peru. We performed a whole-genome assembly of two
      B. bacilliformis strains isolated from the blood of infected patients in the
      acute phase of Carrion's disease from the Cusco and Piura regions in Peru.
AU  - Guillen Y
AU  - Casadella M
AU  - Garcia-de-la-Guarda R
AU  - Espinoza-Culupu A
AU  - Paredes R
AU  - Ruiz J
AU  - Noguera-Julian M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00659-16.

PMID- 29930042
VI  - 6
DP  - 2018
TI  - Sequencing and Annotation of the Genome of Mycobacterium tuberculosis MYC004, a Strain Causing Meningitis in Mexico.
PG  - e00523-18
AB  - Mycobacterium tuberculosis strain MYC004 was isolated from a Mexican patient with tuberculous
      meningitis, the most aggressive form of tuberculosis. The draft
      genome sequence is the first of a meningeal strain of M. tuberculosis reported
      from Latin America and consists of 4,411,530 bp, including 4,251 protein-encoding
      genes.
AU  - Guillen-Nepita AL
AU  - Negrete-Paz AM
AU  - Vazquez-Marrufo G
AU  - Cruz-Hernandez A
AU  - Fresia P
AU  - Naya H
AU  - Vazquez-Garciduenas MS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00523-18.

PMID- 23105057
VI  - 194
DP  - 2012
TI  - Genome Sequence of 'Candidatus Mycoplasma haemolamae' Strain Purdue, a Red Blood  Cell Pathogen of Alpacas (Vicugna pacos) and Llamas (Lama glama).
PG  - 6312-6313
AB  - We report the complete genome sequence of 'Candidatus Mycoplasma haemolamae,' an  endemic
      red-cell pathogen of camelids. The single, circular chromosome has
      756,845 bp, a 39.3% G+C content, and 925 coding sequences (CDSs). A great
      proportion (49.1%) of these CDSs are organized into paralogous gene families,
      which can now be further explored with regard to antigenic variation.
AU  - Guimaraes AM
AU  - Toth B
AU  - Santos AP
AU  - do Nascimento NC
AU  - Kritchevsky JE
AU  - Messick JB
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6312-6313.

PMID- 25999553
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Mycobacterium bovis Strain SP38, a Pathogenic Bacterium  Isolated from a Bovine in Brazil.
PG  - e00511-15
AB  - We report a draft genome sequence of Mycobacterium bovis strain SP38, isolated from the lungs
      of a cow in Brazil. The assembly of reads resulted in 36 contigs
      in a total of approximately 4.37 Mb. Comparison of M. bovis strains sequenced to
      date will aid in understanding bovine tuberculosis in Brazil.
AU  - Guimaraes AM
AU  - Zimpel CK
AU  - Ikuta CY
AU  - do Nascimento NC
AU  - Dos Santos AP
AU  - Messick JB
AU  - Heinemann MB
AU  - Ferreira NJS
AU  - Brandao PE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00511-15.

PMID- 23704183
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Corynebacterium urealyticum Strain DSM 7111, Isolated from a 9-Year-Old Patient with Alkaline-Encrusted Cystitis.
PG  - e00264-13
AB  - Corynebacterium urealyticum is a common skin colonizer with potent urease activity. It is
      clinically recognized as an opportunistic pathogen causing
      urinary tract infections. The annotated genome sequence of strain DSM 7111,
      isolated from the urine of a young boy with an ectopic kidney, provides new
      insights into the pathomechanisms of this bacterium.
AU  - Guimaraes LC
AU  - Soares SC
AU  - Albersmeier A
AU  - Blom J
AU  - Jaenicke S
AU  - Azevedo V
AU  - Soriano F
AU  - Tauch A
AU  - Trost E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00264-13.

PMID- 27469956
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Toxigenic Corynebacterium ulcerans Strain 03-8664 Isolated from a Human Throat.
PG  - e00719-16
AB  - Corynebacterium ulcerans is an emergent pathogen infecting wild and domesticated  animals
      worldwide that may serve as reservoirs for zoonotic infections. In this
      study, we present the draft genome of C. ulcerans strain 03-8664. The draft
      genome has 2,428,683 bp, 2,262 coding sequences, and 12 rRNA genes.
AU  - Guimaraes LC
AU  - Viana MV
AU  - Benevides LJ
AU  - Mariano DC
AU  - Veras AA
AU  - Sa PH
AU  - Rocha FS
AU  - Vilas BPC
AU  - Soares SC
AU  - Barbosa MS
AU  - Guiso N
AU  - Badell E
AU  - Azevedo V
AU  - Ramos RT
AU  - Silva A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00719-16.

PMID- 27034486
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Corynebacterium ulcerans Strain 04-3911, Isolated from Humans.
PG  - e00171-16
AB  - Corynebacterium ulceransis a pathogenic bacterium infecting wild and domesticated animals;
      some infection cases in humans have increased throughout the world. The
      current study describes the draft genome of strain 04-3911, isolated from humans.
      The draft genome has 2,492,680 bp, 2,143 coding sequences, 12 rRNA genes, and 50
      tRNA genes.
AU  - Guimaraes LC
AU  - Viana MV
AU  - Benevides LJ
AU  - Mariano DC
AU  - Veras AA
AU  - Sa PH
AU  - Rocha FS
AU  - Vilas BPC
AU  - Soares SC
AU  - Barbosa MS
AU  - Guiso N
AU  - Badell E
AU  - Carneiro AR
AU  - Azevedo V
AU  - Ramos RT
AU  - Silva A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00171-16.

PMID- 27034487
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Toxigenic Corynebacterium ulcerans Strain 04-7514, Isolated from a Dog in France.
PG  - e00172-16
AB  - Here, we present the draft genome of toxigenicCorynebacterium ulceransstrain 04-7514. The
      draft genome has 2,497,845 bp, 2,059 coding sequences, 12 rRNA
      genes, 46 tRNA genes, 150 pseudogenes, 1 clustered regularly interspaced short
      palindromic repeat (CRISPR) array, and a G+C content of 53.50%.
AU  - Guimaraes LC
AU  - Viana MV
AU  - Benevides LJ
AU  - Mariano DC
AU  - Veras AA
AU  - Sa PH
AU  - Rocha FS
AU  - Vilas BPC
AU  - Soares SC
AU  - Barbosa MS
AU  - Guiso N
AU  - Badell E
AU  - Carneiro AR
AU  - Azevedo V
AU  - Ramos RT
AU  - Silva A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00172-16.

PMID- 26272565
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Picocyanobacterium Synechococcus sp. Strain GFB01, Isolated from a Freshwater Lagoon in the Brazilian Amazon.
PG  - e00876-15
AB  - We present the draft genome of the cyanobacterium strain Synechococcus sp. GFB01, the first
      genome sequencing of this genus isolated from South America. This draft
      genome consists of 125 contigs with a total size of 2,339,812 bp. Automatic
      annotation identified several genes involved with heavy metal resistance and
      natural transformation.
AU  - Guimaraes PI
AU  - Leao TF
AU  - de Melo AG
AU  - Ramos RT
AU  - Silva A
AU  - Fiore MF
AU  - Schneider MP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00876-15.

PMID- 7763729
VI  - 39
DP  - 1993
TI  - Restriction/modification in Streptococcus thermophilus: isolation and characterization of a type II restriction endonuclease Sth455I.
PG  - 216-220
AB  - Streptococcus thermophilus strain CNRZ 455 produces a type II restriction endonuclease
      designated Sth455I. This enzyme was isolated from cell extracts by anionic and cationic
      exchange chromatography. This yielded an enzyme preparation free of non-specific nucleases.
      The optimal reaction conditions for Sth455I are: MgCl2, 30 mM; pH range, 8-9; incubation
      temperature, 37-40oC; and high NaCl concentration, 100-200 mM. The results of single- and
      double-digestion experiments indicates that Sth455I is an isoschizomer of BstNI and EcoRII
      showing different sensitivity to methylation The enzyme exhibits restriction activity on the
      DNA of three bacteriophages of S. thermophilus and no activity on the phage lytic for strain
      CNRZ 455. The restriction/modification system associated with this strain is discussed.
AU  - Guimont C
AU  - Henry P
AU  - Linden G
PT  - Journal Article
TA  - Appl. Microbiol. Biotechnol.
JT  - Appl. Microbiol. Biotechnol.
SO  - Appl. Microbiol. Biotechnol. 1993 39: 216-220.

PMID- 22072651
VI  - 193
DP  - 2011
TI  - Genome Sequence of Bifidobacterium breve DPC 6330, a Strain Isolated from the Human Intestine.
PG  - 6799-6800
AB  - The draft genome of Bifidobacterium breve DPC 6330, isolated from an elderly patient, was
      determined. B. breve DPC 6330 was previously
      identified to synthesize the beneficial metabolite conjugated linoleic
      acid from free linoleic acid. The sequence will allow identification and
      characterization of the genetic determinants of its putative beneficial
      properties.
AU  - Guinane CM
AU  - Barrett E
AU  - Fitzgerald GF
AU  - van Sinderen D
AU  - Ross RP
AU  - Stanton C
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6799-6800.

PMID- 21533100
VI  - 6
DP  - 2011
TI  - Host Specific Diversity in Lactobacillus johnsonii as Evidenced by a Major Chromosomal Inversion and Phage Resistance Mechanisms.
PG  - e18740
AB  - Genetic diversity and genomic rearrangements are a driving force in bacterial evolution and
      niche adaptation. We sequenced and annotated
      the genome of Lactobacillus johnsonii DPC6026, a strain isolated from
      the porcine intestinal tract. Although the genome of DPC6026 is similar
      in size (1.97mbp) and GC content (34.8%) to the sequenced human isolate
      L. johnsonii NCC 533, a large symmetrical inversion of approximately
      750 kb differentiated the two strains. Comparative analysis among 12
      other strains of L. johnsonii including 8 porcine, 3 human and 1
      poultry isolate indicated that the genome architecture found in DPC6026
      is more common within the species than that of NCC 533. Furthermore a
      number of unique features were annotated in DPC6026, some of which are
      likely to have been acquired by horizontal gene transfer (HGT) and
      contribute to protection against phage infection. A putative type III
      restriction-modification system was identified, as were novel Clustered
      Regularly Interspaced Short Palindromic Repeats (CRISPR) elements.
      Interestingly, these particular elements are not widely distributed
      among L. johnsonii strains. Taken together these data suggest
      intra-species genomic rearrangements and significant genetic diversity
      within the L. johnsonii species and indicate towards a host-specific
      divergence of L. johnsonii strains with respect to genome inversion and
      phage exposure.
AU  - Guinane CM
AU  - Kent RM
AU  - Norberg S
AU  - Hill C
AU  - Fitzgerald GF
AU  - Stanton C
AU  - Ross RP
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2011 6: e18740.

PMID- 26823572
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Nine Strains of Ralstonia solanacearum Differing in Virulence to Eggplant (Solanum melongena).
PG  - e01415-15
AB  - Ralstonia solanacearum displays variability in its virulence to solanaceous crops. We report
      here the draft genome sequences of eight phylotype I strains and
      one phylotype III strain differing in virulence to the resistant eggplant
      genotype AG91-25. These data will allow the identification of virulence- and
      avirulence-related genes.
AU  - Guinard J
AU  - Vinatzer BA
AU  - Poussier S
AU  - Lefeuvre P
AU  - Wicker E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01415-15.

PMID- 28153905
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of 18 Psychrotolerant and 2 Thermotolerant Strains Representative of Particular Ecotypes in the Bacillus cereus Group.
PG  - e01568-16
AB  - Bacteria from the Bacillus cereus group exhibit genetic and physiological diversity through
      different ecotypes. Here, we present the draft genome sequences
      of 20 bacterial strains belonging to the contrasted psychrotolerant and
      thermotolerant ecotypes.
AU  - Guinebretiere MH
AU  - Loux V
AU  - Martin V
AU  - Nicolas P
AU  - Sanchis V
AU  - Broussolle V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01568-16.

PMID- 25081269
VI  - 2
DP  - 2014
TI  - Genome analysis of 17 extensively drug-resistant strains reveals new potential mutations for resistance.
PG  - e00759-14
AB  - We report the whole-genome sequence of an extensively drug-resistant (XDR) tuberculosis (TB)
      strain of Latin American-Mediterranean (LAM) lineage. This
      strain is phenotypically resistant to aminoglycosides, but carries no related
      mutations in rrs, tlyA, and eis. Through genome analysis comparison with 16 XDR
      strains, we found 218 non-synonymous single nucleotide polymorphisms (SNPs)
      shared that could confer resistance.
AU  - Guio H
AU  - Tarazona D
AU  - Galarza M
AU  - Borda V
AU  - Curitomay R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00759-14.

PMID- 26514770
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Herbaspirillum hiltneri N3 (DSM 17495), Isolated from Surface-Sterilized Wheat Roots.
PG  - e01288-15
AB  - We report the complete genome sequence of Herbaspirillum hiltneri N3 (DSM 17495), a member of
      the genus Herbaspirillum of the Betaproteobacteria. The genome is
      contained in a single chromosome, and analysis revealed that N3 lacks the whole
      nitrogen fixation (nif) gene cluster, confirming its inability to fix nitrogen.
AU  - Guizelini D
AU  - Saizaki PM
AU  - Coimbra NA
AU  - Weiss VA
AU  - Faoro H
AU  - Sfeir MZ
AU  - Baura VA
AU  - Monteiro RA
AU  - Chubatsu LS
AU  - Souza EM
AU  - Cruz LM
AU  - Pedrosa FO
AU  - Raittz RT
AU  - Marchaukoski JN
AU  - Steffens MB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01288-15.

PMID- 29051234
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of a Salmonella enterica Serovar Typhi Strain Resistant to  Fourth-Generation Cephalosporin and Fluoroquinolone Antibiotics.
PG  - e00850-17
AB  - Typhoid is endemic in developing countries. We report here the first draft genome sequence of
      a Salmonella enterica serovar Typhi clinical isolate from Pakistan
      exhibiting resistance to cefepime (a fourth-generation cephalosporin) and
      fluoroquinolone antibiotics, two of the last-generation therapies against this
      pathogen. The genome is ~4.8 Mb, with two putative plasmids.
AU  - Gul D
AU  - Potter RF
AU  - Riaz H
AU  - Ashraf ST
AU  - Wallace MA
AU  - Munir T
AU  - Ali A
AU  - Burnham CA
AU  - Dantas G
AU  - Andleeb S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00850-17.

PMID- 26337878
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of the Rhizobacterium Pseudomonas trivialis Strain IHBB745 with Multiple Plant Growth-Promoting Activities and Tolerance to Desiccation and Alkalinity.
PG  - e00943-15
AB  - The complete genome sequence of 6.45 Mb is reported here for Pseudomonas trivialis strain
      IHBB745 (MTCC 5336), which is an efficient, stress-tolerant, and broad-spectrum plant
      growth-promoting rhizobacterium. The gene-coding clusters predicted the genes for phosphate
      solubilization, siderophore production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase
      activity, indole-3-acetic acid  (IAA) production, and stress response.
AU  - Gulati A
AU  - Swarnkar MK
AU  - Vyas P
AU  - Rahi P
AU  - Thakur R
AU  - Thakur N
AU  - Singh AK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00943-15.

PMID- 28751380
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Bradyrhizobium sp. ORS285, a Photosynthetic Strain Able To Establish Nod Factor-Dependent or Nod Factor-Independent Symbiosis with  Aeschynomene Legumes.
PG  - e00421-17
AB  - Here, we report the complete genome sequence of Bradyrhizobium sp. strain ORS285, which is
      able to nodulate Aeschynomene legumes using two distinct strategies that
      differ in the requirement of Nod factors. The genome sequence information of this
      strain will help understanding of the different mechanisms of interaction of
      rhizobia with legumes.
AU  - Gully D
AU  - Teulet A
AU  - Busset N
AU  - Nouwen N
AU  - Fardoux J
AU  - Rouy Z
AU  - Vallenet D
AU  - Cruveiller S
AU  - Giraud E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00421-17.

PMID- 21398550
VI  - 193
DP  - 2011
TI  - Complete genome sequence of 'Vulcanisaeta moutnovskia' strain 768-28, a novel member of the hyperthermophilic crenarchaeal genus Vulcanisaeta.
PG  - 2355-2356
AB  - Strain 768-28 was isolated from a hot spring in Kamchatka, Russia and represents a novel
      member of the Vulcanisaeta genus. The complete genome sequence of this thermoacidophilic
      anaerobic crenarchaeon reveals genes for protein and carbohydrate-active enzymes, the
      Embden-Meyerhof and Entner-Doudoroff pathways for glucose metabolism, the tricarboxylic acid
      cycle, beta-oxidation of fatty acids, and sulfate reduction.
AU  - Gumerov VM
AU  - Mardanov AV
AU  - Beletsky AV
AU  - Prokofeva MI
AU  - Bonch-Osmolovskaya EA
AU  - Ravin NV
AU  - Skryabin KG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 2355-2356.

PMID- 28751405
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Vibrio gazogenes ATCC 43942.
PG  - e00733-17
AB  - Vibrio gazogenes ATCC 43942 has the potential to synthesize a plethora of metabolites which
      are of clinical and agricultural significance in response to
      environmental triggers. The complete genomic sequence of Vibrio gazogenes ATCC
      43942 is reported herein, contributing to the knowledge base of strains in the
      Vibrio genus.
AU  - Gummadidala PM
AU  - Holder ME
AU  - O'Brien JL
AU  - Ajami NJ
AU  - Petrosino JF
AU  - Mitra C
AU  - Chen YP
AU  - Decho AW
AU  - Chanda A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00733-17.

PMID- 11401710
VI  - 40
DP  - 2001
TI  - Variations in the surface proteins and restriction enzyme systems of Mycoplasma pulmonis in the respiratory tract of infected rats.
PG  - 1037-1044
AB  - Restriction and modification (R-M) systems are generally thought to protect bacteria from
      invasion by foreign DNA. This paper proposes the existence of an alternative role for the
      phase-variable R-M systems encoded by the hsd loci of Mycoplasma pulmonis. Populations of M.
      pulmonis cells that arose during growth in different environments were compared with respect
      to R-M activity and surface antigen production. When M. pulmonis strain X1048 was propagated
      in laboratory culture medium, > 95% of colony-forming units (cfu) lacked R-M activity and
      produced the variable surface protein VsaA. Mycoplasmas isolated from the nose of
      experimentally infected rats also lacked R-M activity and produced VsaA. In contrast, the cell
      population of mycoplasmas isolated from the lower respiratory tract of the infected rats was
      more complex. The most dramatic results were obtained for mycoplasmas isolated from the
      trachea. At 14 days postinfection, 38% of mycoplasma isolates produced a Vsa protein other
      than VsaA, and 34% of isolates had active restriction systems. These data suggest that
      differences in selection pressures in animal tissues affect the surface proteins and the R-M
      activity of the mycoplasmal cell population. We propose that variations in the production of
      R-M activity and cell surface proteins are important for the survival of the mycoplasma within
      the host.
AU  - Gumulak-Smith J
AU  - Teachman A
AU  - Tu AH
AU  - Simecka JW
AU  - Lindsey JR
AU  - Dybvig K
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2001 40: 1037-1044.

PMID- 23012278
VI  - 194
DP  - 2012
TI  - Draft Genome Sequences of Helicobacter pylori Isolates from Malaysia, Cultured from Patients with Functional Dyspepsia and Gastric Cancer.
PG  - 5695-5696
AB  - Helicobacter pylori is the main bacterial causative agent of gastroduodenal disorders and a
      risk factor for gastric adenocarcinoma and mucosa-associated
      lymphoid tissue (MALT) lymphoma. The draft genomes of 10 closely related H.
      pylori isolates from the multiracial Malaysian population will provide an insight
      into the genetic diversity of isolates in Southeast Asia. These isolates were
      cultured from gastric biopsy samples from patients with functional dyspepsia and
      gastric cancer. The availability of this genomic information will provide an
      opportunity for examining the evolution and population structure of H. pylori
      isolates from Southeast Asia, where the East meets the West.
AU  - Gunaletchumy SP
AU  - Teh X
AU  - Khosravi Y
AU  - Ramli NS
AU  - Chua EG
AU  - Kavitha T
AU  - Mason JN
AU  - Lee HT
AU  - Alias H
AU  - Zaidan NZ
AU  - Yassin NB
AU  - Tay LC
AU  - Rudd S
AU  - Mitchell HM
AU  - Kaakoush NO
AU  - Loke MF
AU  - Goh KL
AU  - Vadivelu J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5695-5696.

PMID- 1355085
VI  - 174
DP  - 1992
TI  - Cloning and linkage analysis of Neisseria gonorrhoeae DNA methyltransferases.
PG  - 5654-5660
AB  - We have cloned DNA methyltransferases (MTases) from various strains of Neisseria gonorrhoeae.
      Each of these clones represents a single specificity, indicating that the multiple gonococcal
      MTase specificities are encoded by monospecific MTases. The DNAs of five strains (FA5100, F62,
      MS11, Pgh3-2, and WR302) were digested with NheI, SpeI, or NheI plus SpeI and subjected to
      pulsed-field gel electrophoresis. The DNA MTase clones were used to probe Southern blots of
      these pulsed-field gels to determine whether the MTase genes are linked and whether there are
      stain-to-strain differences. The results indicate that none of these genes are closely linked,
      but variable hybridization patterns indicate that there exist restriction fragment length
      polymorphisms between the strains tested. Most of the chromosomal regions containing these
      restriction fragment length polymorphisms are clustered in regions containing gonococcal genes
      known or suspected to antigenically vary via genetic recombination.
AU  - Gunn JS
AU  - Piekarowicz A
AU  - Chien R
AU  - Stein DC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1992 174: 5654-5660.

PMID- 9321671
VI  - 25
DP  - 1997
TI  - The Neisseria gonorrhoeae S.NgoVIII restriction/modification system: a type IIs system homologous to the Haemophilus parahaemolyticus HphI restriction/modification system.
PG  - 4147-4152
AB  - Strains of Neisseria gonorrhoeae possess numerous restriction-modification systems.  One of
      these systems, which has been found in all strains tested, encodes the S.NgoVIII specificity
      (5' TCACC 3') R-M system.  We cloned two adjacent methyltransferase genes (dcmH and damH),
      each encoding proteins whose actions protect DNA from digestion by R.HphI or R.NgoBI (%'
      TCACC 3').  The damH gene product is a N6-methyladenine methyltransferase that recognizes
      this sequence.  We constructed a plasmid containing multiple copies of the S.NgoVIII sequence,
      grew it in the presence of damH and used the HPLC to demonstrate the presence of
      N6-methyladenine in the DNA.  A second plasmid, containing overlapping damH and Escherichia
      coli dam recognition sequences in combination with various restriction digests, was used to
      identify which adenine in the recognition sequence was modified by damH.  The predicted dcmH
      gene product is homologous to 5-methylcytosine methyltransferases.  The products of both the
      dcmH and damH genes, as well as an open reading frame downstream of the damH gene are highly
      similar to the Haemophilus parahaemolyticus hphIMC, hphIMA and hphIR gene products, encoding
      the HphI type IIs R-M system.  The S.NgoVIII R-M genes are flanked by a 97 bp direct repeat
      that may be involved in the mobility of this R-M system.
AU  - Gunn JS
AU  - Stein DC
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1997 25: 4147-4152.

PMID- 8406039
VI  - 132
DP  - 1993
TI  - Natural variation of the NgoII restriction-modification of Neisseria gonorrhoeae.
PG  - 15-20
AB  - The NgoII restriction-modification (R-M) system of Neisseria gonorrhoeae recognizes the
      sequence 5'-GGCC-3'. This system is encoded by two separate genes, dcmB for the
      methyltransferase (MTase) and dcrB for the restriction endonuclease (ENase). Three strains
      that vary in their NgoII phenotype were examined. Strain Pgh3-2 produced detectable levels of
      both enzymes, strain F62 lacked detectable levels of the dcrB gene product, and strain WR302
      failed to produce either gene product. Strains that lacked either enzyme activity still
      possessed the genes that encode them. Transcriptional fusions of dcrB in strains F62 and
      Pgh3-2 indicate that this gene is transcribed at nearly identical levels in each strain. The
      DNA encoding the NgoII R-M system was cloned from the three strains, and the nucleotide
      sequence was determined. The dcrB genes of WR302 and F62 possess the same frameshift mutation
      (base position 1435) which would result in a truncated protein. The WR302 dcmB was found to
      have a point mutation that changed Arg 288 (a residue that is conserved in all prokaryotic and
      phage cytosine MTases sequenced to date) to Trp.
      [ The enzyme called NgoII in this abstract has been renamed NgoCII, Jan/1998. ]
AU  - Gunn JS
AU  - Stein DC
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1993 132: 15-20.

PMID- 8709956
VI  - 251
DP  - 1996
TI  - Use of a non-selective transformation technique to construct a multiply restriction/modification-deficient mutant of Neisseria gonorrhoeae.
PG  - 509-517
AB  - A technique that allows for easy identification of transformants of Neisseria gonorrhoeae in
      the absence of selective pressure has been developed.  A suicide vector that contains a
      gonococcal DNA uptake sequence was constructed to aid in DNA uptake.  In this transformation
      procedure, a limiting number of cells is incubated with an excess amount of DNA, and the
      mixture is plated onto a non-selective medium.  At least 20% of the resulting colonies
      contained cells that had been transformed.  This strategy was utilized to construct specific
      deletions of the S.NgoI, II, IV, V, and VII restriction-modification (R/M) genes.  All five
      deletions were successfully incorporated into the chromosome of FA19, producing strain JUG029.
      Strain JUG029 could be transformed with non-methylated plasmid DNA while strain FA19 could not
      be transformed with such DNA.  The development of a simple, non-slective transformation
      technique, coupled with the construction of a strain that is more permissive for DNA-mediated
      transformation, will aid in genetic manipulations of the gonococcus.
AU  - Gunn JS
AU  - Stein DC
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1996 251: 509-517.

PMID- 26744606
VI  - 11
DP  - 2016
TI  - Complete genome sequence of Methanospirillum hungatei type strain JF1.
PG  - 2
AB  - Methanospirillum hungatei strain JF1 (DSM 864) is a methane-producing archaeon and is the type
      species of the genus Methanospirillum, which belongs to the
      family Methanospirillaceae within the order Methanomicrobiales. Its genome was
      selected for sequencing due to its ability to utilize hydrogen and carbon dioxide
      and/or formate as a sole source of energy. Ecologically, M. hungatei functions as
      the hydrogen- and/or formate-using partner with many species of syntrophic
      bacteria. Its morphology is distinct from other methanogens with the ability to
      form long chains of cells (up to 100 mum in length), which are enclosed within a
      sheath-like structure, and terminal cells with polar flagella. The genome of M.
      hungatei strain JF1 is the first completely sequenced genome of the family
      Methanospirillaceae, and it has a circular genome of 3,544,738 bp containing
      3,239 protein coding and 68 RNA genes. The large genome of M. hungatei JF1
      suggests the presence of unrecognized biochemical/physiological properties that
      likely extend to the other Methanospirillaceae and include the ability to form
      the unusual sheath-like structure and to successfully interact with syntrophic
      bacteria.
AU  - Gunsalus RP
AU  - Cook LE
AU  - Crable B
AU  - Rohlin L
AU  - McDonald E
AU  - Mouttaki H
AU  - Sieber JR
AU  - Poweleit N
AU  - Zhou H
AU  - Lapidus AL
AU  - Daligault HE
AU  - Land M
AU  - Gilna P
AU  - Ivanova N
AU  - Kyrpides N
AU  - Culley DE
AU  - McInerney MJ
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 2.

PMID- 26607886
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Campylobacter jejuni RM1285, a Rod-Shaped Morphological Variant.
PG  - e01361-15
AB  - Campylobacter jejuni is a spiral shaped Gram-negative food-borne bacterial pathogen of humans
      found on poultry products. Strain RM1285 is a rod-shaped variant of this species. The genome
      of RM1285 was determined to be 1,635,803 bp, with a G+C content of 30.5%.
AU  - Gunther NW IV
AU  - Bono JL
AU  - Needleman DS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01361-15.

PMID- 28935738
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Campylobacter jejuni RM1246-ERRC, Which Exhibits Resistance to Quaternary Ammonium Compounds.
PG  - e00978-17
AB  - Campylobacter jejuni strain RM1246-ERRC is a clinical isolate. In laboratory experiments,
      RM1246-ERRC exhibited greater resistance to the antimicrobial
      effects of quaternary ammonium compounds than other C. jejuni strains. The
      chromosome of RM1246-ERRC is 1,659,694 bp with a G+C content of 30.56%. The
      strain also possesses a 45,197-bp plasmid.
AU  - Gunther NW IV
AU  - Reichenberger ER
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00978-17.

PMID- 27125483
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of UV-Resistant Campylobacter jejuni RM3194, Including an 81.08-Kilobase Plasmid.
PG  - e00305-16
AB  - Campylobacter jejuni strain RM3194 was originally isolated from a human with enteritis and
      contains a novel 81,079-bp plasmid. RM3194 has exhibited superior
      survival compared to other Campylobacter jejuni strains when challenged with UV
      light. The chromosome of RM3194 was determined to be 1,651,183 bp, with a G+C
      content of 30.5%.
AU  - Gunther NW IV
AU  - Reichenberger ER
AU  - Bono JL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00305-16.

PMID- 6267072
VI  - 256
DP  - 1981
TI  - Restriction and modification in Bacillus subtilis:  Two DNA methyltransferases with BsuRI specificity.  I.  Purification and Physical Properties.
PG  - 9340-9345
AB  - Two S-adenosyl-L-methionine: DNA (cytosine 5)-methyltransferases, termed
      M.BsuRIa and M.BsuRIb, were purified 3,000- and 4,000-fold, respectively, from
      Bacillus subtilis strain OG3R (r+m+) by successive column chromatography.  The
      molecular weights determined by gel filtration were 37,000 for M.BsuRIa and
      40,000 for M.BsuRIb.  The sedimentation coefficients s20,w were 3.55 for both
      enzymes as determined by glycerol gradient centrifugation, corresponding to
      molecular weights of 43,000.  Analysis of the two methyltransferases by agarose
      gel electrophoresis, showed correspondence of the M.BsuRIa activity with one
      protein band at a molecular weight of 41,000, whereas M.BsuRIb activity was
      associated with two protein bands with molecular weights of 42,000 and 39,000,
      respectively.
AU  - Gunthert U
AU  - Freund M
AU  - Trautner TA
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1981 256: 9340-9345.

PMID- 6267073
VI  - 256
DP  - 1981
TI  - Restriction and modification in Bacillus subtilis:  Two DNA Methyltransferases with BsuRI specificity.  II.  Catalytic properties, substrate specificity, and mode of action.
PG  - 9346-9351
AB  - The properties of two DNA methyltransferases, termed M.BsuRIa and M.BsuRIb,
      whose isolation was described in the preceding paper (Gunthert, U., Freund, M.,
      and Trautner, T.A. (1981) J. Biol. Chem. 256: 9340-9345) were compared.  Both
      enzymes recognize the same target sequence in double-stranded DNA, leading to
      methylation of the internal cytosine:  5'GGC*C  The enzymes have identical
      reaction constants with their substrates, DNA (km = 2.7 nM for the 5'GGCC
      sequence), and S-adenosyl-L-methionine (km = 0.7 microM).  Initial rates of
      methyl group transfer were proportional to enzyme concentration over a range of
      50-fold, indicating absence of aggregation.  The enzymes are different in their
      ionic strength requirements using Tris-HCl, pH 8.4.  M.BsuRIa is most active at
      100 mM, M.BsuRIb at 440 mM.  As measured by incorporation kinetics and heat
      inactivation, M.BsuRIa is the more stable enzyme of the two.  Equilibrium
      dialysis was used to study the mode of methyl group transfer to the DNA with
      either enzyme.  The data indicate that initially S-adenosyl-L-methionine binds
      to methyltransferase.  This complex attaches to either modified or nonmodified
      DNA.  The methyl group will then be transfered to a nonmodified target
      sequence, leading to the disociation of enzyme and S-adenosyl-L-homocysteine
      from the DNA.
AU  - Gunthert U
AU  - Jentsch S
AU  - Freund M
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1981 256: 9346-9351.

PMID- 3093230
VI  - 159
DP  - 1986
TI  - Multispecific DNA methyltransferases from Bacillus subtilis phages Properties of wild-type and various mutant enzymes with altered DNA affinity.
PG  - 485-492
AB  - Temperate Bacillus subtilis phages SPR, Phi3T, d11 and SPbeta code for DNA
      methyltransferases, each having mutliple sequence specificities.  The SPR
      wild-type and various mutant methyltransferases were overproduced 1000-fold in
      Escherichia coli and were purified by three consecutive chromatographic steps.
      The stable form of these multispecific enzymes in solution are monomers with a
      relative molecular mass (Mr) of about 50,000.  The methyl-transfer kinetics of
      the SPR wild-type and mutant enzymes were determined with DNA substrates
      carrying either none or one of the three recognition sequences (GGCC, CCGG,
      CCA/TGG).  Evaluation of the catalytic properties for DNA and
      S-adenosylmethionine binding suggested that the NH2-terminal part of the
      protein is important for both non-sequence-specific DNA binding and
      S-adenosylmethionine binding as well as transfer of methyl groups.  On the
      other hand, mutations in the COOH-terminal part lead to weaker site-specific
      interactions of the enzyme.  Antibodies raised against the purified SPR enzyme
      specifically immunoprecipitated the Phi3T,d11 and SPbeta methyltransferases,
      but failed to precipitate the chromosomally coded enzymes from B. subtilis
      (BsuRI) and B. sphaericus (BspRI).  Immunoaffinity chromatography is an
      efficient purification step for the related phage methyltransferases.
AU  - Gunthert U
AU  - Lauster R
AU  - Reiners L
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1986 159: 485-492.

PMID- 824459
VI  - 20
DP  - 1976
TI  - Restriction and Modification in Bacillus subtilis: Inducibility of a DNA Methylating Activity in Nonmodifying Cells.
PG  - 188-195
AB  - The nonrestricting/nonmodifying strain Bacillus subtilis 222 (4-m-) can be
      induced to synthesize a DNA-modifying activity upon treatment with either
      mitomycin C (MC) or UV light.  This is shown by the following facts.  (i)
      Infection of MC-pretreated 222 cells with unmodified SPP1 phage yields about 3%
      modified phage that are resistant to restriction in B. subtilis R (r+m+).  The
      induced modifying activity causes the production of a small fraction of fully
      modified phage in a minority class of MC-treated host cells.  (ii) The
      MC-pretreated host cells contain a DNA cytosine methylating activity; both
      bacterial and phage DNAs have elevated levels of 5-methylcytosine.  (iii) The
      MC-induced methylation of SPP1 DNA takes place at the recognition nucleotide
      sequences of restriction endonuclease R from B. subtilis R.  (iv) Crude
      extracts of MC-pretreated 222 cells have enhanced DNA methyltransferase
      activities, with a substrate specificity similar to that found in modification
      enzymes present in (constituitively) modifying strains.
AU  - Gunthert U
AU  - Pawlek B
AU  - Stutz J
AU  - Trautner TA
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1976 20: 188-195.

PMID- 3108859
VI  - 15
DP  - 1987
TI  - Bacillus subtilis phage SPR codes for a DNA methyltransferase with triple sequence specificity.
PG  - 3689-3701
AB  - SPR, a temperate Bacillus subtilis phage, codes for a DNA methyltransferase
      that can methylate the sequences GGCC (or GGCC) and CCGG at the cytosines
      indicated.  We show here that it can also methylate the sequence CC(A/T)GG and
      protect it from cleavage with EcoRII and ApyI.  This methylation can be seen in
      vivo as well as in vitro with purified SPR methyltransferase.  SPR19 and SPR83
      are two mutant phages, defective in GGCC or CCGG methylation, respectively.
      These mutants have not lost their ability to methylate CC(A/T)GG sites.
      Mutation SPR26 has lost the ability to methylate all three sites.  Thus the SPR
      methyltransferase codes for three genetically distinguishable methylation
      abilities.
AU  - Gunthert U
AU  - Reiners L
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1987 15: 3689-3701.

PMID- 3011599
VI  - 41
DP  - 1986
TI  - Cloning and expression of Bacillus subtilis phage DNA methyltransferase genes in Escherichia coli and B. subtilis.
PG  - 261-270
AB  - The DNA methyltransferase (Mtase) genes of the temperate Bacillus subtilis
      phages SPR (wild type and various mutants), Phi3T, p11 and SBb have been cloned
      and expressed in Escherichia coli and B. subtilis host-plasmid vector systems.
      Mtase activity has been quantitated in these clones by performing in vitro
      methylation assays of cell-free extracts.  The four-phage Mtase genes differ in
      the amount of Mtase synthesized when transcribed from their genuine promoters.
      In B. subtilis as well as in E. coli the SPR Mtase is always produced in
      smaller amounts than the other phage Mtases.  Expression levels of the SPR
      Mtase are dependent on the strength of the upstream vector promoter sequences.
      Overproduction of the SPR wild-type and mutant enzymes was achieved in E. coli
      (inducible expression) by fusions to the lambda pL or the tac promoter and in
      B. subtilis (constitutive expression) by means of the phage SP02 promoter.
AU  - Gunthert U
AU  - Reiners L
AU  - Lauster R
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1986 41: 261-270.

PMID- 213280
VI  - 90
DP  - 1978
TI  - Restriction and modification in Bacillus subtilis. Localization of the methylated nucleotide in the BsuRI recognition sequence.
PG  - 581-583
AB  - Calf thymus DNA was methylated in vitro with cell extracts of Bacillus subtilis OG3R (r+m+)
      and S-adenosyl[Me-3H]methionine.  After depurination of the [3H]methylated DNA, the analysis
      of the pyrimidine dinucleotides revealed the following positions of the methylated nucleosides
      (indicated by an asterisk) with the BsuRI recognition sequence:
      5' dG-dG-dC*-dC
      dC-dC*-dG-dG 5'.
AU  - Gunthert U
AU  - Storm K
AU  - Bald R
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1978 90: 581-583.

PMID- 815782
VI  - 142
DP  - 1975
TI  - Restriction and modification in B. subtilis.
PG  - 185-191
AB  - The content of 5-methylcytosine (5MC) and 6-methyladenine (6MA) in modified and
      nonmodified DNAs from B. subtilis and B. subtilis phage SPP1 were determined.
      Non-modified SPP1-O DNA contains about 15 5MC residues/molecule.  Each modified
      SPP1-R DNA molecule carries 190 modification specific methyl groups.  This
      number is sufficient to account for modification of the 80 restriction sites in
      SPP1 DNA (Bron and Murray, 1975) against endo R.BsuR, assuming each modified
      site contains two 5MC residues.  Resistance of SPO1 DNA against endo R.BsuR
      restriction both in vivo and in vitro is probably not due to methylation of
      endo R.BsuR recognition sites.
AU  - Gunthert U
AU  - Stutz J
AU  - Klotz G
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1975 142: 185-191.

PMID- 6325095
VI  - 108
DP  - 1984
TI  - DNA methyltransferases of Bacillus subtilis and its bacteriophages.
PG  - 11-22
AB  - Postreplicative DNA methylation occurs with a high incidence in bacteria and may affect
      resident DNA and that of infecting bacteriophages. By far the most widespread role of DNA
      methylation is to provide the DNA with "modification" i.e., protection against the
      endonucleolytic attack of cellular restriction enzymes. Important aspects of this role in
      connection with type-I enzymes are discussed in the review of Suri et al. (this volume).
      Another well-studied physiological function of DNA methylation observed in Escherichia coli is
      its role in strand recognition for proofreading during DNA synthesis, which is covered in the
      review by Radman and Wagner (this volume). Some role of host-mediated DNA methylation is
      implemented in the regulation of gene expression of bacteriophage mu; this work is the subject
      of the review by Kahmann (this volume).
AU  - Gunthert U
AU  - Trautner TA
PT  - Journal Article
TA  - Curr. Top. Microbiol. Immunol.
JT  - Curr. Top. Microbiol. Immunol.
SO  - Curr. Top. Microbiol. Immunol. 1984 108: 11-22.

PMID- 10903206
VI  - 289
DP  - 2000
TI  - Group II introns designed to insert into therapeutically relevant DNA target sites in human cells.
PG  - 452-457
AB  - Mobile group II intron RNA's insert directly into DNA target sites and are then
      reverse-transcribed into genomic DNA by the associated intron-encoded protein.  Target site
      recognition involves modifiable base-pairing interactions between the intron RNA and a
      >14-nucleotide region of the DNA target site, as well as fixed interactions between the
      protein and flanking regions.  Here, we developed a highly efficient Escherichia coli genetic
      assay to determine detailed target site recognition rules for the Lactococcus lactis group II
      intron Ll.LtrB and to select introns that insert into desired target sites.  Using human
      immunodeficiency virus-type 1 (HIV-1) proviral DNA and the human CCR5 gene as examples, we
      show that group II introns can be retargeted to insert efficiently into virtually any target
      DNA and that the retargeted introns retain activity in human cells.  This work provides the
      practical basis for potential applications of targeted group II introns in genetic
      engineering, functional genomics, and gene therapy.
AU  - Guo H
AU  - Karberg M
AU  - Long M
AU  - Jones JP III
AU  - Sullenger B
AU  - Lambowitz AM
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2000 289: 452-457.

PMID- 9362497
VI  - 16
DP  - 1997
TI  - Group II intron endonucleases use both RNA and protein subunits for recognition of specific sequences in double-stranded DNA.
PG  - 6835-6848
AB  - Group II introns use intron-encoded reverse transcriptase, maturase and DNA endonuclease
      activities for site-specific insertion into DNA.  Remarkably, the endonucleases are
      ribonucleoprotein complexes in which the excised intron RNA cleaves the sense strand of the
      recipient DNA by reverse splicing, while the intron-encoded protein cleaves the antisense
      strand.  Here, studies with the yeast group II intron aI2 indicate that both the RNA and
      protein components of the endonuclease contribute to recognition of an ~30 bp DNA target site.
      Our results lead to a model in which the protein component first recognizes specific
      nucleotides in the most distal 5' exon region of the DNA target site (E2-21 to -11).  Binding
      of the protein then leads to DNA unwinding, enabling the intron RNA to base pair to a 13
      nucleotide DNA sequence (E2-12 to E3+1) for reverse splicing.  Antisense-strand cleavage
      requires additional interactions of the protein with the 3' exon DNA (E3 +1 to +10).  Our
      results show how enzymes can use RNA and protein subunits cooperatively to recognize specific
      sequences in double-stranded DNA.
AU  - Guo H
AU  - Zimmerly S
AU  - Perlman PS
AU  - Lambowitz AM
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1997 16: 6835-6848.

PMID- 
VI  - 7
DP  - 2003
TI  - Type II restriction endonucleases: Structures and applications.
PG  - 225-245
AB  - Restriction endonucleases are enzymes that recognize specific double-strand DNA sequences and
      cleave at a defined point within or close to that sequence.  These enzymes have become
      indispensable tools in modern biochemistry, recombinant DNA technology, genome mapping, and
      genetic manipulation.  Diverse recognition strategies and high specificity make restriction
      enzymes an ideal system for structural studies of DNA recognition and cleavage by proteins.
      For various applications such as DNA fingerprinting to study cancer or infectious diseases,
      there have also been long-standing interests in rational design of artificial restriction
      enzymes with desired specificities.  However, restriction enzymes have proven to be a
      difficult case for protein engineering.  In general initial attempts were not successful,
      mainly because the tight coupling of specific binding to catalysis was not fully understood.
      New structures reported reveal that these enzymes are more diverse than expected.  Comparisons
      of twelve available structures of Type II restriction enzyme/DNA complexes indicate that
      structural elements responsible for allosteric coupling of recognition to catalysis, as well
      as dimer structures, correlate well with their cleavage patterns on DNA.  It is thus likely
      that enzymes in the existing pool with different cleavage patterns reflect different control
      mechanisms that couple DNA recognition to DNA cleavage and/or dimer structures.  A systematic
      study of restriction enzymes with unique DNA cleavage patterns may illuminate alternative
      coupling mechanisms suitable for manipulation in order to create tailor-made restriction
      enzymes with desired specificities.
AU  - Guo H-C
PT  - Journal Article
TA  - Recent Res. Devel. Macromol.
JT  - Recent Res. Devel. Macromol.
SO  - Recent Res. Devel. Macromol. 2003 7: 225-245.

PMID- 
VI  - 14
DP  - 2004
TI  - Broad host range plasmid-based gene transfer system in the cyanobacterium Gloeobacter violaceus which lacks thylakoids.
PG  - 31-35
AB  - Gloeobacter violaceus, a cyanobacterium lack of thylakoids, is refractory to genetic
      manipulations because its cells are enveloped by
      a thick gelatinous sheath and in colonial form. In this study, a large
      number of single cells were obtained by repeated pumping with a syringe
      with the gelatinous sheath removed. And an exogenous broad host range
      plasmid pKT210 was conjugatively transferred into G. violaceus.
      Analyses with dot-blot hybridization and restriction mapping showed
      that the exogenous plasmid pKT210 had been introduced into G. violaceus
      and stably maintained with no alteration in its structure. pKT210
      extracted from G. violaceus exconjugants could be transformed into the
      mcr - mrr - E. coli strain DH10B but not the mcr(+) mrr(+) strain
      DH5alpha, which suggests that a methylase system may be present in G.
      violaceus.
AU  - Guo HT
AU  - Xu XD
PT  - Journal Article
TA  - Prog. Nat. Sci.
JT  - Prog. Nat. Sci.
SO  - Prog. Nat. Sci. 2004 14: 31-35.

PMID- 20447404
VI  - 400
DP  - 2010
TI  - Directed Evolution of an Enhanced and Highly Efficient FokI Cleavage Domain for Zinc Finger Nucleases.
PG  - 96-107
AB  - Zinc finger nucleases (ZFNs) are powerful tools for gene therapy and genetic engineering. The
      high specificity and affinity of these chimeric
      enzymes are based on custom-designed zinc finger proteins (ZFPs). To
      improve the performance of existing ZFN technology, we developed an in
      vivo evolution-based approach to improve the efficacy of the FokI cleavage
      domain (FCD). After multiple rounds of cycling mutagenesis and DNA
      shuffling, a more efficient nuclease variant (Sharkey) was generated. In
      vivo analyses indicated that Sharkey is >15-fold more active than
      wild-type FCD on a diverse panel of cleavage sites. Further, a mammalian
      cell-based assay showed a three to sixfold improvement in targeted
      mutagenesis for ZFNs containing derivatives of the Sharkey cleavage
      domain. We also identified mutations that impart sequence specificity to
      the FCD that might be utilized in future studies to further refine ZFNs
      through cooperative specificity. In addition, Sharkey was observed to
      enhance the cleavage profiles of previously published and newly selected
      heterodimer ZFN architectures. This enhanced and highly efficient cleavage
      domain will aid in a variety of ZFN applications in medicine and biology.
AU  - Guo J
AU  - Gaj T
AU  - Barbas CFIII
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2010 400: 96-107.

PMID- 22740668
VI  - 194
DP  - 2012
TI  - Genome sequences of three species in the family planctomycetaceae.
PG  - 3740-3741
AB  - Most of the species in the family Planctomycetaceae are of interest for their eukaryotic-like
      cell structures and characteristics of resistance to extreme
      environments. Here, we report draft genome sequences of three aquatic parasitic
      species of this family, Singulisphaera acidiphila (DSM 18658T), Schlesneria
      paludicola (DSM 18645T), and Zavarzinella formosa (DSM 19928T).
AU  - Guo M
AU  - Han X
AU  - Jin T
AU  - Zhou L
AU  - Yang J
AU  - Li Z
AU  - Chen J
AU  - Geng B
AU  - Zou Y
AU  - Wan D
AU  - Li D
AU  - Dai W
AU  - Wang H
AU  - Chen Y
AU  - Ni P
AU  - Fang C
AU  - Yang R
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3740-3741.

PMID- 29348342
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of the Crude Oil-Degrading and Biosurfactant-Producing Strain Cobetia sp. QF-1.
PG  - e01456-17
AB  - We report here the draft genome of Cobetia sp. QF-1, a cold-adapted bacterium isolated from
      crude oil-contaminated seawater of the Yellow Sea, China. This
      genome is approximately 4.1 Mb (G+C content, 57.44%) with 3,513 protein-coding
      sequences. Cobetia sp. QF-1 shows crude oil degradation and biosurfactant
      production activity at low temperature.
AU  - Guo P
AU  - Cao B
AU  - Qiu X
AU  - Lin J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01456-17.

PMID- 25103757
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Bacillus subtilis BAB-1, a Biocontrol Agent for Suppression of Tomato Gray Mold.
PG  - e00744-14
AB  - Bacillus subtilis BAB-1, isolated from cotton rhizosphere soil, is an excellent biocontrol
      agent for tomato gray mold. The genome of B. subtilis strain BAB-1 was
      fully sequenced and annotated, genes encoding the antifungal active compound were
      identified, and multiple sets of regulatory systems were found in the genome.
AU  - Guo Q
AU  - Li S
AU  - Lu X
AU  - Zhang X
AU  - Wang P
AU  - Ma P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00744-14.

PMID- 23558530
VI  - 1
DP  - 2013
TI  - Genome Sequencing of Bacillus subtilis Strain XF-1 with High Efficiency in the Suppression of Plasmodiophora brassicae.
PG  - e0006613
AB  - The genome of the rhizobacterium Bacillus subtilis XF-1 is 4.06 Mb in size and harbors 3,853
      coding sequences (CDS). Giant gene clusters were dedicated to the
      nonribosomal synthesis of antimicrobial lipopeptides and polyketides. Remarkably,
      XF-1 possesses a gene cluster involved in the synthesis of chitosanase that is
      related to the suppression of the pathogen Plasmodiophora brassicae.
AU  - Guo S
AU  - Mao Z
AU  - Wu Y
AU  - Hao K
AU  - He P
AU  - He Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0006613.

PMID- 21551299
VI  - 193
DP  - 2011
TI  - Complete genome of Pseudomonas mendocina NK-01, which synthesizes medium-chain-length polyhydroxyalkanoates and alginate oligosaccharides.
PG  - 3413-3414
AB  - Pseudomonas mendocina NK-01 can synthesize medium-chain-length polyhydroxyalkanoate (PHA(MCL))
      and alginate oligosaccharides (AO)
      simultaneously from glucose in the condition of limited nitrogen source.
      Here we report the complete sequence of the 5.4-Mbp genome of Pseudomonas
      mendocina NK-01, that was isolated from farmland soil in Tianjin, China.
AU  - Guo W
AU  - Wang Y
AU  - Song C
AU  - Yang C
AU  - Li Q
AU  - Li B
AU  - Su W
AU  - Sun X
AU  - Song D
AU  - Yang X
AU  - Wang S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3413-3414.

PMID- 28883132
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Natranaerobius trueperi DSM 18760T, an Anaerobic, Halophilic, Alkaliphilic, Thermotolerant Bacterium Isolated from a Soda Lake.
PG  - e00785-17
AB  - The anaerobic, halophilic, alkaliphilic, thermotolerant bacterium Natranaerobius  trueperi was
      isolated from a soda lake in Wadi An Natrun, Egypt. It grows
      optimally at 3.7 M Na+, pH 9.5, and 43 degrees C. The draft genome consists of
      2.63 Mb and is composed of 2,681 predicted genes. Genomic analysis showed that
      various genes are potentially involved in the adaptation mechanisms for osmotic
      stress, pH homeostasis, and high temperatures.
AU  - Guo X
AU  - Liao Z
AU  - Holtzapple M
AU  - Hu Q
AU  - Zhao B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00785-17.

PMID- 28935723
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Natronolimnobius baerhuensis CGMCC 1.3597T, an Aerobic Haloalkaliphilic Archaeon Isolated from a Soda Lake.
PG  - e00710-17
AB  - The haloalkaliphilic archaeon Natronolimnobius baerhuensis was isolated from a soda lake in
      Inner Mongolia (China), growing optimally at about 20% NaCl and pH
      9.0. The draft genome consists of approximately 3.91 Mb and contains 3,810
      predicted genes. Some genes that regulate intracellular osmotic stress and pH
      homeostasis were identified, providing insight into specific adaptations to this
      double-extreme environment.
AU  - Guo X
AU  - Liao Z
AU  - Yan Y
AU  - Holtzapple M
AU  - Hu Q
AU  - Zhao B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00710-17.

PMID- 25383530
VI  - 517
DP  - 2015
TI  - Structural insight into autoinhibition and histone H3-induced activation of DNMT3A.
PG  - 640-644
AB  - DNA methylation is an important epigenetic modification that is essential for various
      developmental processes through regulating gene expression, genomic
      imprinting, and epigenetic inheritance. Mammalian genomic DNA methylation is
      established during embryogenesis by de novo DNA methyltransferases, DNMT3A and
      DNMT3B, and the methylation patterns vary with developmental stages and cell
      types. DNA methyltransferase 3-like protein (DNMT3L) is a catalytically inactive
      paralogue of DNMT3 enzymes, which stimulates the enzymatic activity of Dnmt3a.
      Recent studies have established a connection between DNA methylation and histone
      modifications, and revealed a histone-guided mechanism for the establishment of
      DNA methylation. The ATRX-DNMT3-DNMT3L (ADD) domain of Dnmt3a recognizes
      unmethylated histone H3 (H3K4me0). The histone H3 tail stimulates the enzymatic
      activity of Dnmt3a in vitro, whereas the molecular mechanism remains elusive.
      Here we show that DNMT3A exists in an autoinhibitory form and that the histone H3
      tail stimulates its activity in a DNMT3L-independent manner. We determine the
      crystal structures of DNMT3A-DNMT3L (autoinhibitory form) and DNMT3A-DNMT3L-H3
      (active form) complexes at 3.82 and 2.90 A resolution, respectively. Structural
      and biochemical analyses indicate that the ADD domain of DNMT3A interacts with
      and inhibits enzymatic activity of the catalytic domain (CD) through blocking its
      DNA-binding affinity. Histone H3 (but not H3K4me3) disrupts ADD-CD interaction,
      induces a large movement of the ADD domain, and thus releases the autoinhibition
      of DNMT3A. The finding adds another layer of regulation of DNA methylation to
      ensure that the enzyme is mainly activated at proper targeting loci when
      unmethylated H3K4 is present, and strongly supports a negative correlation
      between H3K4me3 and DNA methylation across the mammalian genome. Our study
      provides a new insight into an unexpected autoinhibition and histone H3-induced
      activation of the de novo DNA methyltransferase after its initial genomic
      positioning.
AU  - Guo X
AU  - Wang L
AU  - Li J
AU  - Ding Z
AU  - Xiao J
AU  - Yin X
AU  - He S
AU  - Shi P
AU  - Dong L
AU  - Li G
AU  - Tian C
AU  - Wang J
AU  - Cong Y
AU  - Xu Y
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2015 517: 640-644.

PMID- 25908138
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Pseudoalteromonas sp. Strain ECSMB14103, Isolated from the East China Sea.
PG  - e00330-15
AB  - Pseudoalteromonas sp. strain ECSMB14103 was isolated from marine biofilms formed  on the East
      China Sea. The draft genome sequence comprises 4.11 Mp with a G+C
      content of 39.7%. The information from the draft genome will contribute to an
      understanding of bacteria-animal interaction.
AU  - Guo XP
AU  - Ding DW
AU  - Bao WY
AU  - Yang JL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00330-15.

PMID- 22628509
VI  - 194
DP  - 2012
TI  - Whole-Genome Sequence of Klebsiella pneumonia Strain LCT-KP214.
PG  - 3281
AB  - Klebsiella pneumoniae is a Gram-negative, nonmotile, encapsulated, lactose-fermenting,
      facultative anaerobic, rod-shaped bacterium found in the
      normal flora of the mouth, skin, and intestines. Here we present the fine-draft
      genome sequence of K. pneumoniae strain LCT-KP214, which originated from K.
      pneumoniae strain CGMCC 1.1736.
AU  - Guo Y
AU  - Cen Z
AU  - Zou Y
AU  - Fang X
AU  - Li T
AU  - Wang J
AU  - Chang D
AU  - Su L
AU  - Liu Y
AU  - Chen Y
AU  - Yang R
AU  - Liu C
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3281.

PMID- 23144397
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Rahnella aquatilis Strain HX2, a Plant Growth-Promoting  Rhizobacterium Isolated from Vineyard Soil in Beijing, China.
PG  - 6646-6647
AB  - Rahnella aquatilis strain HX2 is a plant growth-promoting, disease-suppressive rhizobacterium
      that was isolated from a vineyard soil in Beijing, China. Here, we
      report the genome sequence of this strain, which provides a valuable resource for
      future research examining the mechanisms of traits associated with plant growth
      promotion and biocontrol.
AU  - Guo Y
AU  - Jiao Z
AU  - Li L
AU  - Wu D
AU  - Crowley DE
AU  - Wang Y
AU  - Wu W
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6646-6647.

PMID- 22815458
VI  - 194
DP  - 2012
TI  - Genome of Helicobacter pylori Strain XZ274, an Isolate from a Tibetan Patient with Gastric Cancer in China.
PG  - 4146-4147
AB  - The infection rate of Helicobacter pylori is high all over the world, especially  in the
      Chinese Tibetan Plateau. Here, we report the genome sequence of
      Helicobacter pylori strain XZ274 isolated from a Tibetan patient with gastric
      cancer. The strain contains 1,634,138 bp with 1,654 coding sequences and a pXZ274
      plasmid of 22,406 bp with 26 coding sequences. This is the first complete genome
      sequence of Helicobacter pylori from the Tibetan Plateau in China.
AU  - Guo Y
AU  - Wang H
AU  - Li Y
AU  - Song Y
AU  - Chen C
AU  - Liao Y
AU  - Ren L
AU  - Guo C
AU  - Tong W
AU  - Shen W
AU  - Chen M
AU  - Mao X
AU  - Guo G
AU  - Zou Q
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4146-4147.

PMID- 21952548
VI  - 193
DP  - 2011
TI  - Genome Sequence of Duck Pathogen Mycoplasma anatis Strain 1340.
PG  - 5883-5884
AB  - Mycoplasma anatis, a member of the class Mollicutes, is the causative agent of a contagious
      infectious disease of domestic ducklings, wild
      birds, and eggs. Increasing reports show that coinfection of M. anatis
      with Escherichia coli results in substantial economic impacts on the duck
      farms in China. Here, we announce the first genome sequence of M. anatis.
AU  - Guo Z
AU  - Chen P
AU  - Ren P
AU  - Kuang S
AU  - Zhou Z
AU  - Li Z
AU  - Liu M
AU  - Shi D
AU  - Xiao Y
AU  - Wang X
AU  - Zhou R
AU  - Jin H
AU  - Bi D
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5883-5884.

PMID- 23599295
VI  - 1
DP  - 2013
TI  - Genome Sequence of Mycoplasma columbinum Strain SF7.
PG  - e00157-13
AB  - Mycoplasma columbinum is a member of nonglycolytic Mycoplasma species which can hydrolyze
      arginine. Increasingly research has revealed that M. columbinum is
      associated with respiratory disease of pigeons and that the respiratory disease
      symptoms could be eliminated via the use of mycoplasma treatment medicine. Here
      we report the genome sequence of M. columbinum strain SF7, which is the first
      genome report for M. columbinum.
AU  - Guo Z
AU  - Xu X
AU  - Zheng Q
AU  - Li T
AU  - Kuang S
AU  - Zhang Z
AU  - Chen Y
AU  - Lu X
AU  - Zhou R
AU  - Bi D
AU  - Jin H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00157-13.

PMID- Not carried by PubMed...
VI  - 3
DP  - 1991
TI  - Effects of organic solvents on the specificity and activity of restriction endonuclease Bsp63I and Bsp78I.
PG  - 135-138
AB  - 
AU  - Guolin A
AU  - Shiwen L
AU  - Yong Z
AU  - Mingyi Q
AU  - Tong Z
PT  - Journal Article
TA  - J. Wuhan Univ.
JT  - J. Wuhan Univ.
SO  - J. Wuhan Univ. 1991 3: 135-138.

PMID- 21742876
VI  - 193
DP  - 2011
TI  - Genome Sequence of Rheinheimera sp. Strain A13L, Isolated from Pangong Lake, India.
PG  - 5873-5874
AB  - Rheinheimera sp. strain A13L, which has antimicrobial activity, was isolated from alkaline
      brackish water of the high-altitude Pangong Lake of
      Ladakh, India. Here we report the draft genome sequence of Rhienheimera
      sp. strain A13L (4,523,491 bp with a G+C content of 46.23%). The genome is
      predicted to contain genes for marinocine and colicin V production, which
      may be responsible for the antimicrobial activity of the strain.
AU  - Gupta HK
AU  - Gupta RD
AU  - Singh A
AU  - Chauhan NS
AU  - Sharma R
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5873-5874.

PMID- 22398859
VI  - 94
DP  - 2012
TI  - Restriction endonucleases: natural and directed evolution.
PG  - 583-599
AB  - Type II restriction endonucleases (REs) are highly sequence-specific compared with other
      classes of nucleases. PD-(D/E)XK nucleases,
      initially represented by only type II REs, now comprise a large and
      extremely diverse superfamily of proteins and, although sharing a
      structurally conserved core, typically display little or no detectable
      sequence similarity except for the active site motifs. Sequence
      similarity can only be observed in methylases and few isoschizomers. As
      a consequence, REs are classified according to combinations of
      functional properties rather than on the basis of genetic relatedness.
      New alignment matrices and classification systems based on structural
      core connectivity and cleavage mechanisms have been developed to
      characterize new REs and related proteins. REs recognizing more than
      300 distinct specificities have been identified in RE database (REBASE:
      http://rebase.neb.com/cgi-bin/statlist) but still the need for newer
      specificities is increasing due to the advancement in molecular biology
      and applications. The enzymes have undergone constant evolution through
      structural changes in protein scaffolds which include random mutations,
      homologous recombinations, insertions, and deletions of coding DNA
      sequences but rational mutagenesis or directed evolution delivers
      protein variants with new functions in accordance with defined
      biochemical or environmental pressures. Redesigning through random
      mutation, addition or deletion of amino acids, methylation-based
      selection, synthetic molecules, combining recognition and cleavage
      domains from different enzymes, or combination with domains of
      additional functions change the cleavage specificity or substrate
      preference and stability. There is a growing number of patents awarded
      for the creation of engineered REs with new and enhanced properties.
AU  - Gupta R
AU  - Capalash N
AU  - Sharma P
PT  - Journal Article
TA  - Appl. Microbiol. Biotechnol.
JT  - Appl. Microbiol. Biotechnol.
SO  - Appl. Microbiol. Biotechnol. 2012 94: 583-599.

PMID- 25212614
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Plant Growth-Promoting Bacillus amyloliquefaciens Strain W2 Associated with Crocus sativus (Saffron).
PG  - e00862-14
AB  - Bacillus sp. strain W2 is a plant growth-promoting rhizobacterium isolated from saffron fields
      of Kashmir, India. Here, we report the draft genome sequence (3.9
      Mb) of Bacillus amyloliquefaciens strain W2 having 65 contigs (3, 997, 511 bp),
      4,163 coding sequences, and an average 46.45% GC content. Despite the 99%
      identity of the 16S rRNA gene with that of Bacillus amyloliquefaciens subsp.
      plantarum FZB42, the genome comparison revealed that only 48.7% of the W2 genome
      has homology with that of FZB42.
AU  - Gupta R
AU  - Vakhlu J
AU  - Agarwal A
AU  - Nilawe PD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00862-14.

PMID- 22189541
VI  - 39
DP  - 2012
TI  - Characterization of MspNI (G/GWCC) and MspNII (R/GATCY), novel thermostable Type II restriction endonucleases from Meiothermus sp., isoschizomers of AvaII and BstYI.
PG  - 5607-5614
AB  - MspNI and MspNII, isoschizomers of prototype Type II restriction endonucleases AvaII and
      BstYI, were extracted from an extreme thermophile bacterium belonging to the genus
      Meiothermus, isolated from the hot sulphur springs in north Himalayan region of India where
      temperature and pH ranged from 60 to 80C and 7.5 to 8.5, respectively. The two enzymes were
      purified to homogeneity using Cibacron-Blue 3GA Agarose, Q-Sepharose and SP-Sepharose
      chromatography and were homodimers with subunit molecular weights of 27 and 45 kDa,
      respectively. Restriction mapping and run-off sequencing of MspNI and MspNII cleaved pBR322
      DNA showed that they recognized and cleaved 5'-G/GWCC-3' and 5'-R/GATCY-3' sites,
      respectively.
      MspNI and MspNII worked optimally at 60 and 70C, 6 and 5 mM MgCl(2), respectively and showed
      no star activity in organic solvents. Both were resistant to sequence methylation and were
      stable up to 25 PCR cycles.
AU  - Gupta R
AU  - Xu S-Y
AU  - Sharma P
AU  - Capalsh N
PT  - Journal Article
TA  - Mol. Biol. Rep.
JT  - Mol. Biol. Rep.
SO  - Mol. Biol. Rep. 2012 39: 5607-5614.

PMID- 27587814
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Putten Strain CRJJGF_00159 (Phylum Gammaproteobacteria).
PG  - e00895-16
AB  - Here, we report a 4.90 Mbp draft genome sequence of Salmonella enterica subsp. enterica
      serovar Putten strain CRJJGF_00159 isolated from food animal in 2004.
AU  - Gupta SK
AU  - McMillan EA
AU  - Jackson CR
AU  - Desai PT
AU  - Porwollik S
AU  - McCleland M
AU  - Hiott LM
AU  - Humayoun SB
AU  - Frye JG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00895-16.

PMID- 27881547
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Salmonella enterica subsp. diarizonae Serovar 61:k:1,5,(7) Strain CRJJGF_00165 (Phylum Gammaproteobacteria).
PG  - e01322-16
AB  - Here, we report a 4.78-Mb draft genome sequence of the Salmonella enterica subsp. diarizonae
      serovar 61:k:1,5,(7) strain CRJJGF_00165 [also called S. enterica
      subsp. IIIb serovar 61:k:1,5,(7) strain CRJJGF_00165], isolated from ground beef
      in 2007.
AU  - Gupta SK
AU  - McMillan EA
AU  - Jackson CR
AU  - Desai PT
AU  - Porwollik S
AU  - McClelland M
AU  - Hiott LM
AU  - Humayoun SB
AU  - Barrett JB
AU  - Frye JG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01322-16.

PMID- 27634995
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Bardo Strain CRJJGF_00099 (Phylum Gammaproteobacteria).
PG  - e00964-16
AB  - Here, we report a 4.87-Mbp draft genome sequence of the multidrug-resistant (MDR) Salmonella
      enterica subsp. enterica serovar Bardo strain CRJJGF_00099, isolated
      from dairy cattle in 2005.
AU  - Gupta SK
AU  - McMillan EA
AU  - Jackson CR
AU  - Desai PT
AU  - Porwollik S
AU  - McClelland M
AU  - Hiott LM
AU  - Humayoun SB
AU  - Frye JG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00964-16.

PMID- 27417830
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Widemarsh Strain CRJJGF_00058 (Phylum Gammaproteobacteria).
PG  - e00604-16
AB  - Here, we report a 4.73 Mbp draft genome sequence of Salmonella enterica subsp. enterica
      serovar Widemarsh strain CRJJGF_00058, isolated from eggs in 2008.
AU  - Gupta SK
AU  - McMillan EA
AU  - Jackson CR
AU  - Desai PT
AU  - Porwollik S
AU  - McClelland M
AU  - Hiott LM
AU  - Humayoun SB
AU  - Frye JG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00604-16.

PMID- 27417829
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Lille Strain CRJJGF_000101 (Phylum Gammaproteobacteria).
PG  - e00603-16
AB  - Here, we report a 4.98 Mbp draft genome sequence of Salmonella enterica subsp. enterica
      serovar Lille strain CRJJGF_000101, isolated from ground beef in 2007.
AU  - Gupta SK
AU  - McMillan EA
AU  - Jackson CR
AU  - Desai PT
AU  - Porwollik S
AU  - McClelland M
AU  - Hiott LM
AU  - Humayoun SB
AU  - Frye JG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00603-16.

PMID- 27688320
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Orion Strain CRJJGF_00093 (Phylum Gammaproteobacteria).
PG  - e01063-16
AB  - Here, we report a 4.70-Mbp draft genome sequence of Salmonella enterica subsp. enterica
      serovar Orion strain CRJJGF_00093, isolated from a dog in 2005.
AU  - Gupta SK
AU  - McMillan EA
AU  - Jackson CR
AU  - Desai PT
AU  - Porwollik S
AU  - McClelland M
AU  - Hiott LM
AU  - Humayoun SB
AU  - Frye JG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01063-16.

PMID- 27389263
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Kiambu Strain CRJJGF_00061 (Phylum Gammaproteobacteria).
PG  - e00588-16
AB  - We report a 4.58 Mbp draft genome sequence of Salmonella enterica subsp. enterica serovar
      Kiambu strain CRJJGF_00061 isolated from cattle in 2004.
AU  - Gupta SK
AU  - McMillan EA
AU  - Jackson CR
AU  - Desai PT
AU  - Porwollik S
AU  - McClelland M
AU  - Hiott LM
AU  - Humayoun SB
AU  - Frye JG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00588-16.

PMID- 27609923
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Blockley Strain CRJJGF_00147 (Phylum Gammaproteobacteria).
PG  - e00954-16
AB  - Here, we report a 4.72-Mbp draft genome sequence of Salmonella enterica subsp. enterica
      serovar Blockley strain CRJJGF_00147, isolated from chicken rinse in
      2009.
AU  - Gupta SK
AU  - McMillan EA
AU  - Jackson CR
AU  - Desai PT
AU  - Porwollik S
AU  - McClelland M
AU  - Hiott LM
AU  - Humayoun SB
AU  - Frye JG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00954-16.

PMID- 26067164
VI  - 6
DP  - 2015
TI  - Structural basis of asymmetric DNA methylation and ATP-triggered long-range diffusion by EcoP15I.
PG  - 7363
AB  - Type III R-M enzymes were identified >40 years ago and yet there is no structural information
      on these multisubunit enzymes. Here we report the structure of a Type
      III R-M system, consisting of the entire EcoP15I complex (Mod2Res1) bound to DNA.
      The structure suggests how ATP hydrolysis is coupled to long-range diffusion of a
      helicase on DNA, and how a dimeric methyltransferase functions to methylate only
      one of the two DNA strands. We show that the EcoP15I motor domains are
      specifically adapted to bind double-stranded DNA and to facilitate DNA sliding
      via a novel 'Pin' domain. We also uncover unexpected 'division of labour', where
      one Mod subunit recognizes DNA, while the other Mod subunit methylates the target
      adenine-a mechanism that may extend to adenine N6 RNA methylation in mammalian
      cells. Together the structure sheds new light on the mechanisms of both helicases
      and methyltransferases in DNA and RNA metabolism.
AU  - Gupta YK
AU  - Chan SH
AU  - Xu SY
AU  - Aggarwal AK
PT  - Journal Article
TA  - Nat. Commun.
JT  - Nat. Commun.
SO  - Nat. Commun. 2015 6: 7363.

PMID- 22560991
VI  - 420
DP  - 2012
TI  - Structural Insights into the Assembly and Shape of Type III Restriction-Modification (R-M) EcoP15I Complex by Small-Angle X-ray Scattering.
PG  - 261-268
AB  - EcoP15I is the prototype of the Type III restriction enzyme family, composed of two
      modification (Mod) subunits to which two (or one)
      restriction (Res) subunits are then added. The Mod subunits are
      responsible for DNA recognition and methylation, while the Res subunits
      are responsible for ATP hydrolysis and cleavage. Despite extensive
      biochemical and genetic studies, there is still no structural
      information on Type III restriction enzymes. We present here
      small-angle X-ray scattering (SAXS) and analytical ultracentrifugation
      analysis of the EcoP15I holoenzyme and the Mod(2) subcomplex. We show
      that the Mod(2) subcomplex has a relatively compact shape with a radius
      of gyration (R-G) of similar to 37.4 angstrom and a maximal dimension
      of similar to 110 angstrom. The holoenzyme adopts an elongated crescent
      shape with an R-G of similar to 65.3 angstrom and a maximal dimension
      of similar to 218 angstrom. From reconstructed SAXS envelopes, we
      postulate that Mod(2) is likely docked in the middle of the holoenzyme
      with a Res subunit at each end. We discuss the implications of our
      model for EcoP15I. action, whereby the Res subunits may come together
      and form a 'sliding clamp' around the DNA.
AU  - Gupta YK
AU  - Yang L
AU  - Chan SH
AU  - Samuelson JC
AU  - Xu SY
AU  - Aggarwal AK
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2012 420: 261-268.

PMID- Not carried by PubMed...
VI  - 13
DP  - 1989
TI  - A buffer system suitable for most restriction enzymes.
PG  - 14-17
AB  - For the digestion of DNA samples by several restriction enzymes, the use of a
      single potassium glutamate buffer instead of different buffers recommended by
      the manufacturers was investigated.  Almost all of the restriction enzymes that
      we have tested to digest lambda DNA, showed the same activity with both buffer
      systems.  Thus the convenience of potassium glutamate buffer was clearly
      understood to be used with most restriction enzymes in place of the buffers
      recommended by the vendors.
AU  - Guray A
AU  - Erarslan A
AU  - Ozbilen O
PT  - Journal Article
TA  - DOGA TU J. Biol.
JT  - DOGA TU J. Biol.
SO  - DOGA TU J. Biol. 1989 13: 14-17.

PMID- 3074010
VI  - 74
DP  - 1988
TI  - The DNA and S-adenosylmethionine-binding regions of EcoDam and related methyltransferases.
PG  - 211-214
AB  - Previous comparison of the amino acid sequences of the GATC-methylating Escherichia coli Dam
      methyltransferase (MTase) with those of other adenine MTases (M.EcoRV, M.DpnII and T4Dam)
      localized four conserved regions. Regions III and IV have similarities with many other MTases.
      The sequence DPPY (or NPPY) is always present in region IV. It was suggested to be the AdoMet
      binding site. Publication of the nucleotide and amino acid sequences of M.CviBIII, M.DpnA and
      MutH give further credence to this assignment: M.DpnA, which also methylates GATC, has strong
      similarities with regions III and IV; M.CviBIII, a cytosine methylase, has a characteristic
      NPPY sequence in region IV, and only limited resemblance in region III; MutH, the
      GATC-specific endonuclease in DNA mismatch repair, has significant similarities uniquely in
      region III. The presently available evidence suggests that region III is the GAT(C) binding
      site and region IV is the AdoMet binding site. This hypothesis is strengthened by recent
      genetic findings.
AU  - Guschlbauer W
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 211-214.

PMID- 363177
VI  - 43
DP  - 1978
TI  - Sensitivity of chromosomal and plasmid E. coli DNA to restriction endonuclease EcoRII.
PG  - 1718-1720
AB  - It was shown that E. coli C, E. coli MRE 600 DNA, and also plasmid DNA of Col E1, RSF 2124
      from E. coli K-12, and plasmid DNA from E. coli MRE 600 were completely resistant against
      restriction endonuclease R. EcoRII.  Plasmid DNA's of Col E1, RSF 2124 amplified for 4 hours
      in the presence of chloramphenicol are sensitive to R.EcoRII but after 16-hour amplification
      in the presence of chloramphenicol these DNA's acquire complete resistance against R.EcoRII.
      These data point to the slower rate of modification of DNA in vivo by DC-methylases of EcoRII
      type in comparison with DNA methylase EcoRII.
AU  - Guseinov OA
AU  - Bogdarina IG
AU  - Kossykh VG
AU  - Buryanov YI
AU  - Baev AA
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1978 43: 1718-1720.

PMID- 22559230
VI  - 5
DP  - 2012
TI  - Dcm methylation is detrimental to plasmid transformation in Clostridium thermocellum.
PG  - 30
AB  - Background: Industrial production of biofuels and other products by cellulolytic
      microorganisms is of interest but hindered by the nascent
      state of genetic tools. Although a genetic system for Clostridium
      thermocellum DSM1313 has recently been developed, available methods
      achieve relatively low efficiency and similar plasmids can transform C.
      thermocellum at dramatically different efficiencies.
      Results: We report an increase in transformation efficiency of C.
      thermocellum for a variety of plasmids by using DNA that has been
      methylated by Escherichia coli Dam but not Dcm methylases. When
      isolated from a dam + dcm + E. coli strain, pAMG206 transforms C.
      thermocellum 100-fold better than the similar plasmid pAMG205, which
      contains an additional Dcm methylation site in the pyrF gene. Upon
      removal of Dcm methylation, transformation with pAMG206 showed a four-
      to seven-fold increase in efficiency; however, transformation
      efficiency of pAMG205 increased 500-fold. Removal of the Dcm
      methylation site from the pAMG205 pyrF gene via silent mutation
      resulted in increased transformation efficiencies equivalent to that of
      pAMG206. Upon proper methylation, transformation efficiency of plasmids
      bearing the pMK3 and pB6A origins of replication increased ca. three
      orders of magnitude.
      Conclusions: E. coli Dcm methylation decreases transformation
      efficiency in C. thermocellum DSM1313. The use of properly methylated
      plasmid DNA should facilitate genetic manipulation of this industrially
      relevant bacterium.
AU  - Guss AM
AU  - Olson DG
AU  - Caiazza NC
AU  - Lynd LR
PT  - Journal Article
TA  - Biotechnol. Biofuels.
JT  - Biotechnol. Biofuels.
SO  - Biotechnol. Biofuels. 2012 5: 30.

PMID- 8973353
VI  - 180
DP  - 1996
TI  - Cloning, expression and sequence analysis of the SphI restriction-modification system.
PG  - 107-112
AB  - SphI, a type II restriction-modification system from the bacterium Streptomyces
      phaeochromogenes, recognizes the sequence 5'-GCATGC.  The SphI methyltransferase encoding
      gene, sphIM, was cloned into Escherichia coli using Mtase selection to isolate the clone.
      However, none of these clones contained the restriction endonuclease gene.  Repeated attempts
      to clone the complete Enase gene along with sphIM in one step failed, presumably due to
      expression of SphI Enase gene, sphIR, in the presence of inadequate expression of sphIM.  The
      complete sphIR was finally cloned using a two-step process.  PCR was used to isolate the 3'
      end of sphIR from a library.  The intact sphIR, reconstructed under control of an inducible
      promoter, was introduced into an E. coli strain containing a plasmid with the NlaIII
      Mtase-encoding gene (nlaIIIM).  The nucleotide sequence of the SphI system was determined,
      analyzed and compared to previously sequenced R-M systems.  The sequence was also examined for
      features which would help explain why sphIR unlike other actinomycete Enase genes seemed to be
      expressed in E. coli.
AU  - Guthrie EP
AU  - Quinton-Jager T
AU  - Moran LS
AU  - Slatko BE
AU  - Kucera RB
AU  - Benner JS
AU  - Wilson GG
AU  - Brooks JE
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1996 180: 107-112.

PMID- 23209223
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Methanobacterium formicicum DSM 3637, an Archaebacterium Isolated from the Methane Producer Amoeba Pelomyxa palustris.
PG  - 6967-6968
AB  - Here is reported the draft genome sequence of Methanobacterium formicicum DSM 3637, which was
      isolated from the methane-producing amoeba Pelomyxa palustris.
      This bacterium was determined to be an endosymbiont living in the cytoplasm of P.
      palustris and the source of methane; however, the global characteristics of its
      genome suggest a free-living lifestyle rather than an endosymbiotic one.
AU  - Gutierrez G
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6967-6968.

PMID- 26089431
VI  - 3
DP  - 2015
TI  - Genome Sequence of Porticoccus hydrocarbonoclasticus Strain MCTG13d, an Obligate  Polycyclic Aromatic Hydrocarbon-Degrading Bacterium Associated with Marine Eukaryotic Phytoplankton.
PG  - e00672-15
AB  - Porticoccus hydrocarbonoclasticus strain MCTG13d is a recently discovered bacterium that is
      associated with marine eukaryotic phytoplankton and that almost
      exclusively utilizes polycyclic aromatic hydrocarbons (PAHs) as the sole source
      of carbon and energy. Here, we present the genome sequence of this strain, which
      is 2,474,654 bp with 2,385 genes and has an average G+C content of 53.1%.
AU  - Gutierrez T et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00672-15.

PMID- 25814607
VI  - 3
DP  - 2015
TI  - Genome Sequence of Polycyclovorans algicola Strain TG408, an Obligate Polycyclic  Aromatic Hydrocarbon-Degrading Bacterium Associated with Marine Eukaryotic  Phytoplankton.
PG  - e00207-15
AB  - Polycyclovorans algicola strain TG408 is a recently discovered bacterium associated with
      marine eukaryotic phytoplankton and exhibits the ability to
      utilize polycyclic aromatic hydrocarbons (PAHs) almost exclusively as sole
      sources of carbon and energy. Here, we present the genome sequence of this
      strain, which is 3,653,213 bp, with 3,477 genes and an average G+C content of
      63.8%.
AU  - Gutierrez T et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00207-15.

PMID- 27491994
VI  - 4
DP  - 2016
TI  - Genome Sequence of Arenibacter algicola Strain TG409, a Hydrocarbon-Degrading Bacterium Associated with Marine Eukaryotic Phytoplankton.
PG  - e00765-16
AB  - Arenibacter algicola strain TG409 was isolated from Skeletonema costatum and exhibits the
      ability to utilize polycyclic aromatic hydrocarbons as sole sources
      of carbon and energy. Here, we present the genome sequence of this strain, which
      is 5,550,230 bp with 4,722 genes and an average G+C content of 39.7%.
AU  - Gutierrez T et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00765-16.

PMID- 26184945
VI  - 3
DP  - 2015
TI  - Genome Sequence of Halomonas sp. Strain MCTG39a, a Hydrocarbon-Degrading and Exopolymeric Substance-Producing Bacterium.
PG  - e00793-15
AB  - Halomonas sp. strain MCTG39a was isolated from coastal sea surface water based on its ability
      to utilize n-hexadecane. During growth in marine medium the strain
      produces an amphiphilic exopolymeric substance (EPS) amended with glucose, which
      emulsifies a variety of oil hydrocarbon substrates. Here, we present the genome
      sequence of this strain, which is 4,979,193 bp with 4,614 genes and an average
      G+C content of 55.0%.
AU  - Gutierrez T et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00793-15.

PMID- 27609918
VI  - 4
DP  - 2016
TI  - Genome Sequence of Marinobacter sp. Strain MCTG268 Isolated from the Cosmopolitan Marine Diatom Skeletonema costatum.
PG  - e00937-16
AB  - Marinobacter sp. strain MCTG268 was isolated from the cosmopolitan marine diatom  Skeletonema
      costatum and can degrade oil hydrocarbons as sole sources of carbon
      and energy. Here, we present the genome sequence of this strain, which is
      4,449,396 bp with 4,157 genes and an average G+C content of 57.0%.
AU  - Gutierrez T et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00937-16.

PMID- 28860240
VI  - 5
DP  - 2017
TI  - Genome Sequence of Roseovarius sp. Strain MCTG156(2b) Isolated from a Phytoplankton Net Trawl on the Scottish West Coast.
PG  - e00837-17
AB  - Roseovarius sp. strain MCTG156(2b) was isolated from a phytoplankton net sample collected on
      the west coast of Scotland and was selected based on its ability to
      degrade polycyclic aromatic hydrocarbons. Here, we present the genome sequence of
      this strain, which is 5,113,782 bp, with 5,142 genes and an average G+C content
      of 60.7%.
AU  - Gutierrez T
AU  - Whitman WB
AU  - Huntemann M
AU  - Copeland A
AU  - Chen A
AU  - Vargese N
AU  - Kyrpides NC
AU  - Pillay M
AU  - Ivanova N
AU  - Mikhailova N
AU  - Mukherjee S
AU  - Stamatis D
AU  - Reddy TBK
AU  - Ngan CY
AU  - Chovatia M
AU  - Daum C
AU  - Shapiro N
AU  - Woyke T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00837-17.

PMID- 28798189
VI  - 5
DP  - 2017
TI  - Genome Sequence of Oceanicola sp. Strain MCTG156(1a), Isolated from a Scottish Coastal Phytoplankton Net Sample.
PG  - e00796-17
AB  - Oceanicola sp. strain MCTG156(1a) was isolated from a phytoplankton net sample collected on
      the west coast of Scotland and selected based on its ability to
      degrade polycyclic aromatic hydrocarbons. Here, we present the genome sequence of
      this strain, which comprises 3,881,122 bp with 3,949 genes and an average G+C
      content of 62.7%.
AU  - Gutierrez T
AU  - Whitman WB
AU  - Huntemann M
AU  - Copeland A
AU  - Chen A
AU  - Vargese N
AU  - Kyrpides NC
AU  - Pillay M
AU  - Ivanova N
AU  - Mikhailova N
AU  - Mukherjee S
AU  - Stamatis D
AU  - Reddy TBK
AU  - Ngan CY
AU  - Chovatia M
AU  - Daum C
AU  - Shapiro N
AU  - Woyke T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00796-17.

PMID- 25858838
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of a Helicobacter pylori Strain Isolated from a Patient with Diffuse Gastritis from a Region of High Cancer Risk in Colombia.
PG  - e00244-15
AB  - The draft genome sequence of one Colombian Helicobacter pylori strain is presented. This
      strain was isolated from a patient with diffuse gastritis from
      Tibana, Boyaca, a region with high gastric cancer risk.
AU  - Gutierrez-Escobar AJ
AU  - Bayona RM
AU  - Barragan VC
AU  - Trujillo CE
AU  - Bravo MM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00244-15.

PMID- 24609382
VI  - 42
DP  - 2014
TI  - Engineering nicking enzymes that preferentially nick 5-methylcytosine-modified DNA.
PG  - e77
AB  - N.Gamma is a strand-specific and site-specific DNA nicking enzyme (YCG downward arrowGT or AC
      upward arrowCGR). Here we describe the isolation of single and
      double mutants of N.Gamma with attenuated activity. The nicking domains (NDs) of
      E59A and 11 double mutants were fused to the 5mCG-binding domain of MBD2 and
      generated fusion enzymes that preferentially nick 5mCG-modified DNA. The CG
      dinucleotide can be modified by C5 methyltransferases (MTases) such as M.SssI,
      M.HhaI or M.HpaII to create composite sites AC upward arrowYGG N(8-15) 5mCG. We
      also constructed a fusion enzyme 2xMBD2-ND(N.BceSVIII) targeting more frequent
      composite sites AS upward arrowYS N(5-12) 5mCG in Mn2+ buffer. 5mCG-dependent
      nicking requires special digestion conditions in high salt (0.3 M KCl) or in Ni2+
      buffer. The fusion enzyme can be used to nick and label 5mCG-modified plasmid and
      genomic DNAs with fluorescently labeled Cy3-dUTP and potentially be useful for
      diagnostic applications, DNA sequencing and optical mapping of epigenetic
      markers. The importance of the predicted catalytic residues D89, H90, N106 and
      H115 in N.Gamma was confirmed by mutagenesis. We found that the wild-type enzyme
      N.Gamma prefers to nick 5mCG-modified DNA in Ni2+ buffer even though the nicking
      activity is sub-optimal compared to the activity in Mg2+ buffer.
AU  - Gutjahr A
AU  - Xu SY
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2014 42: e77.

PMID- 7987687
VI  - 317
DP  - 1994
TI  - Statistical significance of amino acid sequence similarity in type II DNA methyltransferases.
PG  - 20-24
AB  - The statistical significance of amino acid sequence similarities previously observed in type
      II DNA methyltransferases has been investigated. It is shown: (1) that the intramolecular
      similarities observed among various type II Mtases are not statistically significant and thus
      cannot be used to support a gene duplication model; (2) that the intermolecular similarities
      observed in a peptide in various type II adenine methylases are statistically confirmed; (3)
      that the similarities observed between MutH and these proteins for this peptide are not
      statistically significant and therefore cannot be used to propose a functional role in DNA
      recognition for this peptide.
AU  - Guyot J-B
AU  - Caudron B
PT  - Journal Article
TA  - C.R. Acad. Sci. III
JT  - C.R. Acad. Sci. III
SO  - C.R. Acad. Sci. III 1994 317: 20-24.

PMID- 8341592
VI  - 21
DP  - 1993
TI  - The role of the preserved sequences of Dam methylase.
PG  - 3183-3190
AB  - We have undertaken a site directed mutational analysis of two of the preserved regions in the
      amino acids sequence of Dam methylase in order to characterize their role. Mutations in region
      IV (sequence DPPY) abolish catalytic activity and greatly affect AdoMet crosslinking. Mutants
      in region III display a lowered specific activity with an unchanged AdoMet crosslinking
      capacity. We have also made a series of deletions both at the N and C terminal parts of the
      protein, which have been found to provide inactive enzyme. We discuss the significance of
      these results for the understanding of the functional properties of the enzyme.
AU  - Guyot JB
AU  - Grassi J
AU  - Hahn U
AU  - Guschlbauer W
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 3183-3190.

PMID- 28302776
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Three Closely Related Isolates of the Purple Nonsulfur  Bacterium Rhodovulum sulfidophilum.
PG  - e00029-17
AB  - We report here the draft genome sequences of three isolates of Rhodovulum sulfidophilum from a
      single population that will serve as a model system for
      understanding genomic traits that underlie metabolic variation within closely
      related marine purple nonsulfur bacteria in natural microbial communities.
AU  - Guzman MS
AU  - McGinley B
AU  - Santiago-Merced N
AU  - Gupta D
AU  - Bose A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00029-17.

PMID- 4974084
VI  - 32
DP  - 1968
TI  - Alteration of host specificity in Bacillus subtilis.
PG  - 297-301
AB  - Restriction of bacteriophages in host bacteria has been reported by many investigators, most
      of whom have observed the phenomenon to be associated with host-induced modification.  This
      report describes the restriction of bacteriophage without any apparent host-induced
      modification.  After a period of incubation at 53C, Bacillus subtilis 168 (ind-) cells were
      rendered permissive in their response to infection by phages SP-10 and SP-20.  Because phage
      SP-20 infected heated 168 cells with an efficiency 100 times greater than phage SP-10, most of
      the work described here was done with phage SP-20.
AU  - Gwinn DD
AU  - Lawton WD
PT  - Journal Article
TA  - Bacteriol. Rev.
JT  - Bacteriol. Rev.
SO  - Bacteriol. Rev. 1968 32: 297-301.

PMID- 22374964
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Vibrio fischeri SR5, a Strain Isolated from the Light Organ of the Mediterranean Squid Sepiola robusta.
PG  - 1639
AB  - Here, we describe the draft genome sequence of Vibrio fischeri SR5, a squid symbiotic isolate
      from Sepiola robusta in the Mediterranean Sea. This 4.3-Mbp
      genome sequence represents the first V. fischeri genome from an S. robusta
      symbiont and the first from outside the Pacific Ocean.
AU  - Gyllborg MC
AU  - Sahl JW
AU  - Cronin DCIII
AU  - Rasko DA
AU  - Mandel MJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1639.

PMID- 2585510
VI  - 209
DP  - 1989
TI  - Role of the hydrophobic effect in stability of site-specific protein-DNA complexes.
PG  - 801-816
AB  - The site-specific binding interaction of lac repressor with a symmetric
      operator sequence and of EcoRI endonuclease with its specific recognition site
      both exhibit a characteristic dependence of equilibrium binding constant (Kobs)
      on temperature, in which Kobs attains a relative maximum in the physiologically
      relevant temperature range.  This behavior, which appears to be quite general
      for site-specific protein-DNA interactions, is indicative of a large negative
      standard heat capacity change (DeltaCoP,obs) in the association process.  By
      analogy with model compound transfer studies and protein folding data, we
      propose that this DeltaCoP,obs results primarily from the removal of non-polar
      surface from water in the association process.  From DeltaCoP,obs we obtain
      semiquantitative information regarding the change in water-exposed non-polar
      surface area (DeltaAnp) and the corresponding hydrophobic driving force for
      association (DeltaGohyd):Delta Go hyd~8(+/- 1) x 10/1 DeltaCoP,obs~ -22 (+/-5)
      DeltaAnp.  We propose that removal of non-polar surface from water (the
      hydrophobic effect) and release of cations (the polyelectrolyte effect) drive
      the thermodynamically unfavorable processes (e.g. conformational distortions)
      necessary to achieve mutually complementary recognition surfaces (at a steric
      and functional-group level) in the specific complex.
AU  - Ha J-H
AU  - Spolar RS
AU  - Record MT
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1989 209: 801-816.

PMID- 10648549
VI  - 182
DP  - 2000
TI  - Native plasmids of Fusobacterium nucleatum: Characterization and use in development of genetic systems.
PG  - 1176-1180
AB  - Three native plasmids of Fusobacterium nucleatum were characterized, including DNA sequence
      analysis of one plasmid, pFN1. A shuttle plasmid, pHS17, capable of transforming Escherichia
      coli and F. nucleatum ATCC 10953 was constructed with pFN1. pHS17 was stably maintained in the
      F. nucleatum transformants, and differences in the transformation efficiencies suggested the
      presence of a restriction-modification system in F. nucleatum.
AU  - Haake SK
AU  - Yoder SC
AU  - Attarian G
AU  - Podkaminer K
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2000 182: 1176-1180.

PMID- 28729266
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Streptomyces sp. M1013, a Close Relative of Streptomyces ambofaciens and Streptomyces coelicolor.
PG  - e00643-17
AB  - We report the draft genome sequence of Streptomyces sp. M1013, a strain isolated  from the
      Medicago arborea rhizosphere in Izmir, Turkey. An average nucleotide
      identity (ANI) analysis reveals that this strain belongs to the same species as
      Streptomyces canus ATCC12647 and is closely related to Streptomyces ambofaciens
      and Streptomyces coelicolor.
AU  - Haas D
AU  - Gerbaud C
AU  - Sahin N
AU  - Pernodet JL
AU  - Lautru S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00643-17.

PMID- 18324396
VI  - 79
DP  - 2008
TI  - Subtractive hybridization and random arbitrarily primed PCR analyses of a benzoate-assimilating bacterium, Desulfotignum balticum.
PG  - 87-95
AB  - Subtractive hybridization (SH) and random arbitrarily primed PCR (RAP-PCR) were used to detect
      genes involved in anaerobic benzoate degradation by
      Desulfotignum balticum. Through SH, we obtained 121 DNA sequences specific
      for D. balticum but not for D. phosphitoxidans (a
      non-benzoate-assimilating species). Furthermore, RAP-PCR analysis showed
      that a 651-bp DNA fragment, having 55% homology with the solute-binding
      protein of the ABC transporter system in Methanosarcina barkeri, was
      expressed when D. balticum was grown on benzoate, but not on pyruvate. By
      shotgun sequencing of the fosmid clone (38,071 bp) containing the DNA
      fragment, 33 open reading frames (ORFs) and two incomplete ORFs were
      annotated, and several genes within this region corresponded to the DNA
      fragments obtained by SH. An 11.3-kb gene cluster (ORF10-17) revealed
      through reverse transcription-PCR showed homology with the ABC transporter
      system and TonB-dependent receptors, both of which are presumably involved
      in the uptake of siderophore/heme/vitamin B(12), and was expressed in
      response to growth on benzoate.
AU  - Habe H
AU  - Kobuna A
AU  - Hosoda A
AU  - Kouzuma A
AU  - Yamane H
AU  - Nojiri H
AU  - Omori T
AU  - Watanabe K
PT  - Journal Article
TA  - Appl. Microbiol. Biotechnol.
JT  - Appl. Microbiol. Biotechnol.
SO  - Appl. Microbiol. Biotechnol. 2008 79: 87-95.

PMID- 
VI  - 16
DP  - 2005
TI  - Function and evolution of HO and VDE endonucleases in fungi.
PG  - 161-175
AB  - The site-specific HO and VDE endonucleases are unusual members of a family of so-called group
      I LAGLIDADG homing endonucleases that are generally implicated in the homing of intron and
      intein sequences.  The great majority of these endonucleases are found in mitochondria and
      plastids of eukaryotes, but in budding yeast two members of this family apparently "escaped"
      into the nucleus.  In each case, the endonuclease creates a site-specific double-strand break
      in a target and promotes mobility of DNA sequences by homologous recombination requiring the
      Rad52 and Rad51 group of recombination proteins.  The HO endonuclease has been the subject of
      a great deal of interest, both because of its remarkable evolution and because of its great
      utility in the detailed analysis of DSB-mediated recombination.  Unlike most homing
      endonucleases, the HO endonuclease does not promote its own amplification, but rather
      catalyzes the switching/replacement of yeast's mating-type genes.  In addition, budding
      yeasts harbor the VDE endonuclease, which is found as an intein in the VMA1 gene.  VDE
      promotes its propagation from a VMA1 gene containing the VDE intein into a VMA1 gene lacking
      such a sequence.  VDE is remarkable also in sharing a close sequence and presumably
      evolutionary relationship with HO.
AU  - Haber JE
AU  - Wolfe KH
PT  - Journal Article
TA  - Nucleic Acids Mol. Biol.
JT  - Nucleic Acids Mol. Biol.
SO  - Nucleic Acids Mol. Biol. 2005 16: 161-175.

PMID- 3188833
VI  - 35
DP  - 1988
TI  - Restriction-modification like phenomenon observed in Mycobacterium smegmatis strains are consequences of natural polylysogeny.
PG  - 180-181
AB  - Titrating phage butyricum (By) on its original host, Mycobacterium smegmatis
      butyricum, and on M. smegmatis SN2 (SN2), phenomena similar to
      restriction-modification could be observed.  On the contrary, observations
      showing that By phages propagated on SN2 cells have altered morphological
      structure - instead of the icosahedral shape of the head of phage By, the head
      of phage By propagated on SN2 cells is elongated - could not be explained by
      the effect of DNA modification.  It has been assumed that the phenomena
      observed resulted as a consequence of natural lysogeny of the M. smegmatis
      strains.  This hypothesis was proved by biological methods and electron
      microscopic observations.  Phages with non-contractile tails of both types of
      head morphology were found to be present in lysates of M. smegmatis butyricum
      and SN2 cells, showing the polylysogenic property of their strains.
AU  - Haber K
AU  - Neumark T
AU  - Foldes I
PT  - Journal Article
TA  - Acta Microbiol. Hung.
JT  - Acta Microbiol. Hung.
SO  - Acta Microbiol. Hung. 1988 35: 180-181.

PMID- 4615158
VI  - 89
DP  - 1974
TI  - The bacteriophage P1 restriction endonuclease.
PG  - 545-563
AB  - The bacteriophage P1 restriction endonuclease has been purified from
      Escherichia coli lysogenic for P1.  This restriction endonuclease P has a
      sedimentation coefficient of 9.3S.  Unlike the E. coli K restriction
      endonuclease, endonuclease P does not require S-adenosylmethionine for breakage
      of DNA.  S-adenosylmethionine does, however, stimulate the rate of
      double-strand breakage of DNA by endonuclease P.  Hydrolysis of ATP by
      endonuclease P could not be detected under conditions in which the K
      restriction endonuclease massively degrades ATP.  The enzyme makes a limited
      number of double-strand breaks in unmodified or heterologously modified lambda
      DNA.  In the presence of S-adenosylmethionine, it does not cut every DNA
      molecule to the same extent.  Incubation of lambda DNA with excess amounts of
      the enzyme results in less breakage of the DNA than with smaller amounts of
      enzyme.  This effect is not seen in the absence of S-adenosylmethionine appears
      to be greater than the maximum amount of cutting in its presence.  This is most
      likely due to the modification methylase activity of P1 restriction
      endonuclease.
AU  - Haberman A
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1974 89: 545-563.

PMID- 4564204
VI  - 69
DP  - 1972
TI  - DNA modification methylase activity of Escherichia coli restriction endonucleases K and P.
PG  - 3138-3141
AB  - The highly purified restriction endonucleases of E. coli K and coliphage P1
      transfer methyl groups from S-adenosylmethionine to adenine residues of
      unmodified DNA.  Incubation of unmodified DNA with endonucleases K or P and
      S-adenosylmethionine renders the DNA resistant to restriction.  The enzymes,
      therefore, have both restriction endonuclease and modification methylase
      activities.
AU  - Haberman A
AU  - Heywood J
AU  - Meselson M
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1972 69: 3138-3141.

PMID- 28360179
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequence of Pseudomonas fluorescens EK007-RG4, a Promising Biocontrol Agent against a Broad Range of Bacteria, Including the Fire Blight  Bacterium Erwinia amylovora.
PG  - e00026-17
AB  - Here, we report the first draft whole-genome sequence of Pseudomonas fluorescens  strain
      EK007-RG4, which was isolated from the phylloplane of a pear tree. P.
      fluorescens EK007-RG4 displays strong antagonism against Erwinia amylovora, the
      causal agent for fire blight disease, in addition to several other pathogenic and
      non-pathogenic bacteria.
AU  - Habibi R
AU  - Tarighi S
AU  - Behravan J
AU  - Taheri P
AU  - Kjoller AH
AU  - Brejnrod A
AU  - Madsen JS
AU  - Sorensen SJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00026-17.

PMID- 6276293
VI  - 18
DP  - 1981
TI  - A site-specific DNA methylase from Escherichia coli K.
PG  - 295-297
AB  - A DNA methylase has been partially purified from E. coli K using heparin-agarose and
      DEAE-sephacel chromatography.  Plasmid pBR322 DNA was methylated by the enzyme and cleaved
      with restriction endonuclease HaeIII.  Among the DNA fragments obtained, only a few were
      methylated demonstrating that the enzyme recognizes specific sites on DNA.  Since all the
      EcoRII cleavage sites fall within the methylated fragments, the DNA methylase may be the
      cytosine methylase of E. coli K which is known to render the methylated sites resistant to
      EcoRII cleavage.
AU  - Hadi SM
PT  - Journal Article
TA  - Indian J. Biochem. Biophys.
JT  - Indian J. Biochem. Biophys.
SO  - Indian J. Biochem. Biophys. 1981 18: 295-297.

PMID- 6302281
VI  - 165
DP  - 1983
TI  - DNA restriction-modification enzymes of phage P1 and plasmid p15B.
PG  - 19-34
AB  - We have purified the type III restriction enzymes EcoPI and EcoP15 to
      homogeneity from bacteria that contain the structural genes for the enzymes
      cloned on small, multicopy plasmids and which overproduce the enzymes.  Both of
      the enzymes contain two different subunits.  The molecular weights of the
      subunits are the same for both enzymes and antibodies prepared against one
      enzyme cross-react with both subunits of the other.  Bacteria containing a
      plasmid derivative in which a large part of one of the structural genes has
      been deleted have a restriction- modification+ phenotype and contain only the
      smaller of the two subunits.  This subunit therefore must be the one that both
      recognizes the specific DNA sequence and methylates it in the modification
      reaction (the restriction enzyme itself also acts as a modification methylase).
      We have purified the PI and P15 modification subunits from these deletion
      derivatives and have shown that in vitro they have the expected properties:
      they are sequence-specific modification methylases.  In addition, we have
      demonstrated that strains carrying the full restriction/modification system
      also contain a pool of free modification subunits that might be responsible for
      in vivo modification.
AU  - Hadi SM
AU  - Bachi B
AU  - Iida S
AU  - Bickle TA
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1983 165: 19-34.

PMID- 231671
VI  - 134
DP  - 1979
TI  - DNA Recognition and Cleavage by the EcoP15 Restriction Endonuclease.
PG  - 655-666
AB  - EcoP15 is a restriction-modification enzyme coded by the P15 plasmid of
      Escherichia coli.  We have determined the sites recognized by this enzyme on
      pBR322 and simian virus 40 DNA.  The enzyme recognizes the sequence: 5'
      C-A-G-C-A-G 3'. . . . . . 3' G-T-C-G-T-C 5' for restriction, the enzyme cleaves
      the DNA 25 to 26 base-pairs 3' to this sequence and cleaves single-stranded 5'
      protrusions two bases long.
AU  - Hadi SM
AU  - Bachi B
AU  - Shepherd JCW
AU  - Yuan R
AU  - Ineichen K
AU  - Bickle TA
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1979 134: 655-666.

PMID- 1092685
VI  - 250
DP  - 1975
TI  - The role of S-adenosylmethionine in the cleavage of deoxyribonucleic acid by the restriction endonuclease from Escherichia coli K.
PG  - 4159-4164
AB  - The restriction endonuclease from Escherichia coli K specifically cleaves
      foreign DNA in the presence of S-adenosylmethionine, ATP, and Mg++.  The role
      of S-adenosylmethionine in this reaction has been studied by following the
      specific binding of the enzyme to unmodified DNA.  The results indicate that
      S-adenosylmethionine acts as an allosteric effector.  However, the
      rate-limiting step in the activation of the enzyme is not the binding of the
      effector itself, but an event subsequent to it.  The interaction of the
      S-adenosylmethionine with two mutant K restriction endonucleases isolated
      previously has also been investigated.  One of them, which is defective in
      restriction, can be activated in a manner similar to the wild type enzyme,
      while the other one, which lacks both restriction and modification activities
      (due to a mutation in the subunit responsible for DNA recognition), shows no
      such effect.
AU  - Hadi SM
AU  - Bickle TA
AU  - Yuan R
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1975 250: 4159-4164.

PMID- Not included in PubMed...
VI  - 29
DP  - 1973
TI  - Complementation in vitro by restriction enzymes from mutant strains E. coli K12.
PG  - 752
AB  - The restriction endonuclease from E. coli K12 has previously been shownw to a)
      bind and then cleave unmodified lambda DNA in the presence of SAM, ATP and
      Mg++, b) hydrolyze the ATP to ADP and inorganic phosphate in the course of the
      restriction reaction, and c) methylate unmodified lambda DNA when only SAM is
      present.  The restriction deficient mutant strains from E. coli K12, gamma
      K-mK+ and gamma K-mK- have been shown to complement in vivo to yield a wild
      type phenotype, gamma K+mK+.  Using a binding assay based on complementation in
      vitro between the two mutant extracts, the restriction endonucleases from the
      two mutant strains were purified extensively.  Complementation in vitro could
      be detected by specific binding and also by cleavage of the unmodified DNA when
      both mutant proteins were present.  Either mutant protein by itself showed no
      activity.  Studies on the methylase and ATPase activities of these mutant
      proteins, either alone or in combination are currently in progress.
AU  - Hadi SM
AU  - Yuan R
PT  - Journal Article
TA  - Experientia
JT  - Experientia
SO  - Experientia 1973 29: 752.

PMID- 4276461
VI  - 249
DP  - 1974
TI  - Complementation in vitro by mutant restriction enzymes from Escherichia coli K.
PG  - 4580-4586
AB  - Two mutant strains of Escherichia coli K, K-18 lacking restriction activity
      (endonucleolytic cleavage of foreign DNA), and the other, K-19 lacking both
      restriction and modification activities (specific DNA methylation that protects
      against the homologous restriction activity), complement in vivo to yield a
      wild type phenotype.  Although neither mutant extract alone binds unmodified
      DNA, the wild type extract and the mixture of mutant extracts do.  Retention of
      the DNA-enzyme complex on membrane filters was used as an assay to purify the
      two mutant restriction enzymes.  Both of these sediment like the wild type
      enzyme.  Complementation in vitro by the two mutant enzymes could be
      demonstrated by specific DNA binding, cleavage of the unmodified DNA, and
      restriction-dependent ATP hydrolysis.  All of these activities are absent in
      the individual mutant endonucleases but present in the wild type restriction
      endonuclease from E. coli K.  However, both mutant enzymes show an activity
      that hydrolyzes ATP which is different from that of the wild type enzyme since
      it does not require unmodified DNA, but is dependent on the presence of
      S-adenosylmethionine.
AU  - Hadi SM
AU  - Yuan R
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1974 249: 4580-4586.

PMID- 29326218
VI  - 6
DP  - 2018
TI  - First Draft Genome Sequences of Two Bartonella tribocorum Strains from Laos and Cambodia.
PG  - e01435-17
AB  - Bartonella tribocorum is a Gram-negative bacterium known to infect animals, and rodents in
      particular, throughout the world. In this report, we present the draft
      genome sequences of two strains of B. tribocorum isolated from the blood of a
      rodent in Laos and a shrew in Cambodia.
AU  - Hadjadj L
AU  - Jiyipong T
AU  - Bittar F
AU  - Morand S
AU  - Rolain JM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01435-17.

PMID- 27087892
VI  - 11
DP  - 2016
TI  - Non contiguous-finished genome sequence and description of Microbacterium gorillae sp. nov.
PG  - 32
AB  - Strain G3(T) (CSUR P207 = DSM 26203) was isolated from the fecal sample of a wild gorilla
      (Gorilla gorilla subsp gorilla) from Cameroon. It is a Gram-positive,
      facultative anaerobic short rod. This strain exhibits a 16S rRNA sequence
      similarity of 98.2 % with Microbacterium thalassium, the closest validly
      published Microbacterium species and member of the family Microbacteriaceae.
      Moreover, it shows a low MALDI-TOF-MS score (1.1 to 1.3) that does not allow any
      identification. Thus, it is likely that this strain represents a new species.
      Here we describe the phenotypic features of this organism, the complete genome
      sequence and annotation. The 3,692,770 bp long genome (one chromosome but no
      plasmid) contains 3,505 protein-coding and 61 RNA genes, including 4 rRNA genes.
      In addition, digital DNA-DNA hybridization values for the genome of the strain
      G3(T) against the closest Microbacterium genomes range between 19.7 to 20.5, once
      again confirming its new status as a new species. On the basis of these
      polyphasic data, consisting of phenotypic and genomic analyses, we propose the
      creation of Microbacterium gorillae sp. nov. that contains the strain G3(T).
AU  - Hadjadj L
AU  - Rathored J
AU  - Keita MB
AU  - Michelle C
AU  - Levasseur A
AU  - Raoult D
AU  - Fournier PE
AU  - Rolain JM
AU  - Bittar F
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 32.

PMID- 29954902
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of an Avian Native NDM-1-Producing Salmonella enterica subsp. enterica Serovar Corvallis Strain.
PG  - e00593-18
AB  - Carbapenems are an important class of beta-lactams and one of the last options for treating
      severe human infections. We present here the complete genome
      sequence of avian native carbapenemase-producing Salmonella enterica subsp.
      enterica serovar Corvallis strain 12-01738, harboring a blaNDM-1-carrying IncA/C2
      plasmid, isolated in 2012 from a wild bird (Milvus migrans) in Germany.
AU  - Hadziabdic S
AU  - Borowiak M
AU  - Bloch A
AU  - Malorny B
AU  - Szabo I
AU  - Guerra B
AU  - Kaesbohrer A
AU  - Fischer J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00593-18.

PMID- 29954918
VI  - 6
DP  - 2018
TI  - Complete Genome Sequences of Four Salmonella enterica subsp. enterica Serovar Senftenberg and Montevideo Isolates Associated with a 2016 Multistate Outbreak in the United States.
PG  - e00630-18
AB  - A multistate outbreak of 11 Salmonella infections linked to pistachio nuts occurred in 2016.
      In this announcement, we report the complete genome sequences
      of four Salmonella enterica subsp. enterica serovar Senftenberg and S. enterica
      subsp. enterica serovar Montevideo isolates from pistachios collected during the
      2016 outbreak investigation.
AU  - Haendiges J
AU  - Blessington T
AU  - Zheng J
AU  - Davidson G
AU  - Miller JD
AU  - Hoffmann M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00630-18.

PMID- 25103764
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Clinical Vibrio parahaemolyticus Strains Isolated in Maryland (2010 to 2013).
PG  - e00776-14
AB  - Vibrio parahaemolyticus is the leading cause of food-borne illnesses associated with the
      consumption of raw shellfish worldwide. Here, we report 45 draft genomes
      of V. parahaemolyticus. Thirty-five of them are strains that were isolated from
      clinical cases in the state of Maryland from 2010 to 2013. The remaining 10
      strains were historical isolates, isolated mostly from the West Coast of the
      United States during the period of 1988 to 2004. The availability of these
      genomes will allow for future phylogenetic analyses with other V.
      parahaemolyticus strains.
AU  - Haendiges J
AU  - Timme R
AU  - Allard M
AU  - Myers RA
AU  - Payne J
AU  - Brown EW
AU  - Evans P
AU  - Gonzalez-Escalona N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00776-14.

PMID- 26294637
VI  - 3
DP  - 2015
TI  - Genome Sequence of Devriesea agamarum, Isolated from Agamid Lizards with Dermatitis.
PG  - e00949-15
AB  - We report the genome sequence of Devriesea agamarum strain IMP2, isolated from the liver of a
      female Agama impalearis. This actinobacterium is associated with
      septicemia and dermatitis in agamid lizards. Availability of this genome sequence
      will contribute to the understanding of this pathogen's virulence.
AU  - Haesendonck R
AU  - Van Nieuwerburgh F
AU  - Haesebrouck F
AU  - Deforce D
AU  - Pasmans F
AU  - Martel A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00949-15.

PMID- 25110134
VI  - 118
DP  - 2014
TI  - I-OmiI and I-OmiII: Two intron-encoded homing endonucleases within the Ophiostoma minus rns gene.
PG  - 721-731
AB  - The mitochondrial small subunit ribosomal RNA (rns) gene of the ascomycetous fungus Ophiostoma
      minus [strain WIN(M)371] was found to contain a group IC2 and a group IIB1 intron at positions
      mS569 and mS952 respectively. Both introns have open reading frames (ORFs) embedded that
      encode double motif LAGLIDADG homing endonucleases (I-OmiI and I-OmiII respectively).
      Codon-optimized versions of I-OmiI and I-OmiII were synthesized for overexpression in
      Escherichia coli. The in vitro characterization of I-OmiII showed that it is a functional
      homing endonuclease that cleaves the rns target site two nucleotides upstream (sense strand)
      of the intron insertion site generating 4 nucleotide 3' overhangs. The endonuclease activity
      of I-OmiII was tested using linear and circular substrates and cleavage activity was evaluated
      at various temperatures. The I-OmiI protein was expressed in E. coli, but purification was
      difficult, thus the endonuclease activity of this protein was tested via in vivo assays.
      Overall this study showed that there are many native forms of functional homing endonucleases
      yet to be discovered among fungal mtDNA genomes.
AU  - Hafez M
AU  - Guha TK
AU  - Hausner G
PT  - Journal Article
TA  - Fungal Biol.
JT  - Fungal Biol.
SO  - Fungal Biol. 2014 118: 721-731.

PMID- 21816042
VI  - 12
DP  - 2011
TI  - Complete Genome Sequence of Brachyspira intermedia Reveals Unique Genomic Features in Brachyspira Species and Phage-mediated Horizontal Gene Transfer.
PG  - 395
AB  - ABSTRACT: BACKGROUND: Brachyspira spp. colonize the intestines of some
      mammalian and avian species and show different degrees of
      enteropathogenicity. Brachyspira intermedia can cause production losses in
      chickens and strain PWS/AT now becomes the fourth genome to be completed
      in the genus Brachyspira. RESULTS: 15 classes of unique and shared genes
      were analyzed in B. intermedia, B. murdochii, B. hyodysenteriae and B.
      pilosicoli. The largest number of unique genes was found in B. intermedia
      and B. murdochii. This indicates the presence of larger pan-genomes. In
      general, hypothetical protein annotations are overrepresented among the
      unique genes. A 3.2 kb plasmid was found in B. intermedia strain PWS/AT.
      The plasmid was also present in the B. murdochii strain but not in nine
      other Brachyspira isolates. Within the Brachyspira genomes, genes had been
      translocated and also frequently switched between leading and lagging
      strands, a process that can be followed by different AT-skews in the third
      positions of synonymous codons. We also found evidence that bacteriophages
      were being remodeled and genes incorporated into them. CONCLUSIONS: The
      accessory gene pool shapes species-specific traits. It is also influenced
      by reductive genome evolution and horizontal gene transfer. Gene-transfer
      events can cross both species and genus boundaries and bacteriophages
      appear to play an important role in this process. A mechanism for
      horizontal gene transfer appears to be gene translocations leading to
      remodeling of bacteriophages in combination with broad tropism.
AU  - Hafstrom T
AU  - Jansson DS
AU  - Segerman B
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2011 12: 395.

PMID- 29444255
VI  - 25
DP  - 2018
TI  - Identification of the DNA methyltransferases establishing the methylome of the cyanobacterium Synechocystis sp. PCC 6803.
PG  - 343-352
AB  - DNA methylation in bacteria is important for defense against foreign DNA, but is  also
      involved in DNA repair, replication, chromosome partitioning, and regulatory
      processes. Thus, characterization of the underlying DNA methyltransferases in
      genetically tractable bacteria is of paramount importance. Here, we characterized
      the methylome and orphan methyltransferases in the model cyanobacterium
      Synechocystis sp. PCC 6803. Single molecule real-time (SMRT) sequencing revealed
      four DNA methylation recognition sequences in addition to the previously known
      motif m5CGATCG, which is recognized by M.Ssp6803I. For three of the new
      recognition sequences, we identified the responsible methyltransferases.
      M.Ssp6803II, encoded by the sll0729 gene, modifies GGm4CC, M.Ssp6803III, encoded
      by slr1803, represents the cyanobacterial dam-like methyltransferase modifying
      Gm6ATC, and M.Ssp6803V, encoded by slr6095 on plasmid pSYSX, transfers methyl
      groups to the bipartite motif GGm6AN7TTGG/CCAm6AN7TCC. The remaining methylation
      recognition sequence GAm6AGGC is probably recognized by methyltransferase
      M.Ssp6803IV encoded by slr6050. M.Ssp6803III and M.Ssp6803IV were essential for
      the viability of Synechocystis, while the strains lacking M.Ssp6803I and
      M.Ssp6803V showed growth similar to the wild type. In contrast, growth was
      strongly diminished of the Deltasll0729 mutant lacking M.Ssp6803II. These data
      provide the basis for systematic studies on the molecular mechanisms impacted by
      these methyltransferases.
AU  - Hagemann M
AU  - Gartner K
AU  - Scharnagl M
AU  - Bolay P
AU  - Lott SC
AU  - Fuss J
AU  - Huettel B
AU  - Reinhardt R
AU  - Klahn S
AU  - Hess WR
PT  - Journal Article
TA  - DNA Res.
JT  - DNA Res.
SO  - DNA Res. 2018 25: 343-352.

PMID- 3470568
VI  - 11C
DP  - 1987
TI  - Analysis of noncanonical DNA cleavage by EcoRI endonuclease mutants.
PG  - 206
AB  - It has been proposed that DNA sequence specificity for the EcoRI endonuclease
      results from the formation of twelve hydrogen bonds between bases exposed at
      the major groove of the EcoRI site and six amino acid side chains (3 from each
      subunit) in the enzyme.  (Rosenberg and Greene, DNA 1, 117-124 (1982),
      Rosenberg et al., Science, in press) Conservative replacements in the 3 amino
      acids identified in the x-ray crystallographic structure as responsible for
      specificity were made (Glu 144 to Asp, Arg 145 to Lys, and Arg 200 to Lys).
      These changes failed to alter the site of primary cleavage.  However, all of
      these proteins nick noncanonical DNA sequences in pBR322 lacking the EcoRI
      site.  The location of these single strand cleavage sites is being determined
      for the wild type and mutant enzymes.  The identification of the sequences
      recognized by the different enzymes and the hierarchy of the rates at which
      these sequences are hydrolyzed will contribute to our understanding of how the
      endonuclease discriminates between DNA squences.
AU  - Hager PW
AU  - Boyer HW
AU  - Day JO
AU  - Reich NO
AU  - Greene P
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1987 11C: 206.

PMID- 2254311
VI  - 265
DP  - 1990
TI  - Probing the role of glutamic acid 144 in the EcoRI endonuclease using aspartic acid and glutamine replacements.
PG  - 21520-21526
AB  - The x-ray structure of the EcoRI endonuclease-DNA complex suggests that
      hydrogen bonds between amino acids, glutamic acid 144, arginine 145, and
      arginine 200, and major groove base moieties are the molecular determinants of
      specificity.  We have investigated residue 144 using aspartate and glutamine
      substitutions introduced by site-directed mutagenesis.  Substitution with
      glutamine results in a null phenotype (at least a 2000-fold reduction in
      activity).  On the other hand, the aspartic acid mutant (ED144) retained in
      vivo activity.  Substrate binding and catalytic studies were done with purified
      ED144 enzyme.  The affinity of the ED144 enzyme for the canonical sequence
      5'-GAATTC-3' is about 340-fold less than the wild-type (WT) enzyme, while its
      affinity for nonspecific DNA is about 50 times greater.  The ED144 enzyme
      cleaves one strand in the EcoRI site in plasmid pBR322 with a kcat/Km similar
      to WT.  In contrast to the WT enzyme, the ED144 enzyme dissociates after the
      first strand cleavage.  Partitioning between cleavage and dissociation at the
      first and second cleavage steps for the ED144 enzyme is extremely
      salt-sensitive.  The altered partitioning results largely from a
      destabilization of the enzyme-DNA complex, particularly the enzyme-nicked DNA
      complex, with only small changes in the respective cleavage rates.  The
      hydrogen bonds of Glu-144 are critical, they appear to act cooperatively with
      other specificity contacts to stabilize the enzyme-DNA complex.
AU  - Hager PW
AU  - Reich NO
AU  - Day JP
AU  - Coche TG
AU  - Boyer HW
AU  - Rosenberg JM
AU  - Greene PJ
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1990 265: 21520-21526.

PMID- 26112793
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Streptococcus pneumoniae Avery Strain A66.
PG  - e00697-15
AB  - We have used HiSeq 2000 technology to generate a draft genome sequence of Streptococcus
      pneumoniae strain A66. This is a common study strain used in
      investigations of pneumococcal bacterium-host interactions and was used in the
      seminal genetic studies of Avery et al.
AU  - Hahn C
AU  - Harrison EM
AU  - Parkhill J
AU  - Holmes MA
AU  - Paterson GK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00697-15.

PMID- 1964172
VI  - 136
DP  - 1990
TI  - Characterization of FP22, a large streptomycete bacteriophage with DNA insensitive to cleavage by many restriction enzymes.
PG  - 2395-2404
AB  - Bacteriophage FP22 has a very broad host range within streptomycetes and
      appeared to form lysogens of Streptomyces ambofaciens ATCC 15154.  FP22 shared
      strong cross-immunity and antibody cross-reactivity with bacteriophage P23, but
      not with seven other streptomycete bacteriophages.  FP22 particles had a head
      diameter of 71 nm and a tail length of 307 mm.  The FP22 genome was 131 kb,
      which is the largest bacteriophage genome reported for streptomycetes.  The G+C
      content of the genome was 46 mol% and restriction mapping indicated that FP22
      DNA had discrete ends.  NaCl- and pyrophosphate-resistant deletion mutants were
      readily isolated and the extent of the deletions defined at least 23 kb of
      dispensable DNA in two regions of the genome.  The DNA was not cleaved by most
      restriction endonucleases (or isoschizomers) which have been identified in the
      streptomycetes, including the tetranucleotide cutter MboI (GATC).
AU  - Hahn DR
AU  - McHenney MA
AU  - Baltz RH
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1990 136: 2395-2404.

PMID- 26380634
VI  - 10
DP  - 2015
TI  - High quality draft genome sequence of Flavobacterium rivuli type strain WB 3.3-2(T) (DSM 21788(T)), a valuable source of polysaccharide decomposing enzymes.
PG  - 46
AB  - Flavobacterium rivuli Ali et al. 2009 emend. Dong et al. 2013 is one of about 100 species in
      the genus Flavobacterium (family Flavobacteriacae, phylum Bacteroidetes) with a validly
      published name, and has been isolated from the spring of a hard water rivulet in Northern
      Germany. Including all type strains of the genus Myroides and Flavobacterium into the 16S rRNA
      gene sequence phylogeny revealed a clustering of members of the genus Myroides as a
      monophyletic group within the genus Flavobacterium. Furthermore, F. rivuli WB 3.3-2(T) and its
      next  relatives seem more closely related to the genus Myroides than to the type species of
      the genus Flavobacterium, F. aquatile. The 4,489,248 bp long genome with its 3,391
      protein-coding and 65 RNA genes is part of the G enomic E ncyclopedia of B acteria and A
      rchaea project. The genome of F. rivuli has almost as many genes encoding carbohydrate active
      enzymes (151 CAZymes) as genes encoding peptidases (177). Peptidases comprised mostly metallo
      (M) and serine (S) peptidases. Among CAZymes, 30 glycoside hydrolase families, 10 glycosyl
      transferase families, 7 carbohydrate binding module families and 7 carbohydrate esterase
      families were identified. Furthermore, we found four polysaccharide utilization loci (PUL) and
      one large CAZy rich gene cluster that might enable strain WB 3.3-2(T) to decompose plant and
      algae derived polysaccharides. Based on these results we propose F. rivuli as an interesting
      candidate for further physiological studies and the role of Bacteroidetes in the decomposition
      of complex polymers in the environment.
AU  - Hahnke RL et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 46.

PMID- 29622604
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of a New Ruminococcaceae Bacterium Isolated from Anaerobic Biomass Hydrolysis.
PG  - e00030-18
AB  - A new Ruminococcaceae bacterium, strain HV4-5-B5C, participating in the anaerobic digestion of
      grass, was isolated from a mesophilic two-stage laboratory-scale
      leach bed biogas system. The draft annotated genome sequence presented in this
      study and 16S rRNA gene sequence analysis indicated the affiliation of HV4-5-B5C
      with the family Ruminococcaceae outside recently described genera.
AU  - Hahnke S
AU  - Abendroth C
AU  - Langer T
AU  - Codoner FM
AU  - Ramm P
AU  - Porcar M
AU  - Luschnig O
AU  - Klocke M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00030-18.

PMID- 29146851
VI  - 5
DP  - 2017
TI  - Draft Whole-Genome Sequences of Periodontal Pathobionts Porphyromonas gingivalis, Prevotella intermedia, and Tannerella forsythia Contain Phase-Variable  Restriction-Modification Systems.
PG  - e01229-17
AB  - Periodontal disease comprises mild to severe inflammatory host responses to oral  bacteria
      that can cause destruction of the tooth-supporting tissue. We report
      genome sequences for 18 clinical isolates of Porphyromonas gingivalis, Prevotella
      intermedia, and Tannerella forsythia, Gram-negative obligate anaerobes that play
      a role in the periodontal disease process.
AU  - Haigh RD
AU  - Crawford LA
AU  - Ralph JD
AU  - Wanford JJ
AU  - Vartoukian SR
AU  - Hijazi K
AU  - Wade W
AU  - Oggioni MR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01229-17.

PMID- 27789640
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Burkholderia contaminans FFI-28, a Strain Isolated from a Contaminated Pharmaceutical Solution.
PG  - e01177-16
AB  - Burkholderia contaminans is a species of the Burkholderia cepacia complex, a group of bacteria
      that can grow in pharmaceutical products and are capable of
      infecting the immunocompromised and people with cystic fibrosis. Here, we report
      draft genome sequences for Burkholderia contaminans FFI-28, a strain isolated
      from a contaminated pharmaceutical solution.
AU  - Haim MS
AU  - Mollerach M
AU  - Van Domselaar G
AU  - Teves SA
AU  - Degrossi J
AU  - Cardona ST
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01177-16.

PMID- 2823077
VI  - 209
DP  - 1987
TI  - The effect of restriction on shotgun cloning and plasmid stability in Bacillus subtilis Marburg.
PG  - 335-342
AB  - Using the bifunctional cloning vehicle pHP13, which carries the replication
      functions of the cryptic Bacillus subtilis plasmid pTA1060, the effects of BsuM
      restriction on the efficiency of shotgun cloning of heterologous Escherichia
      coli DNA were studied.  In a restriction-deficient but modification-proficient
      mutant of B. subtilis, clones were obtained at a high frequency, comparable to
      frequencies normally obtained in E. coli (10/4 clones per microgram target
      DNA).  Large inserts were relatively abundant (26% of the clones contained
      inserts in the range of 6 to 15 kb), which resulted in a high average insert
      length (3.6 kb).  In the restriction-proficient B. subtilis strain, the class
      of large inserts was underrepresented.  Transformation of B. subtilis with E.
      coli-derived individual recombinant plasmids was affected by BsuM restriction
      in two ways.  First, the transforming activities of recombinant plasmids
      carrying inserts larger than 4kb, were, in comparison with the vector pHP13,
      reduced to varying degrees in the restricting host.  The levels of the
      reduction increased with insert length, resulting in a 7800-fold reduction for
      the largest plasmid used (pC23; insert length 16 kb).  Second, more than 80% of
      the pC23 transformants in the restricting strain contained a deleted plasmid.
      In the non-restricting strain, the transforming activities of the plasmids were
      fairly constant as a function of insert length (in the range of 0-16 kb), and
      no structural instability was observed.  It is concluded that for shotgun
      cloning in B. subtillis, the use of restriction-deficient strains is highly
      preferable.  Evidence is presented that in addition to XhoI other sequences are
      involved in BsuM restriction.  It is postulated that AsuII sites are additional
      target sites for BsuM restriction.
AU  - Haima P
AU  - Bron S
AU  - Venema G
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1987 209: 335-342.

PMID- 16936040
VI  - 188
DP  - 2006
TI  - Whole-Genome Sequence of Listeria welshimeri Reveals Common Steps in Genome Reduction with Listeria innocua as Compared to Listeria  monocytogenes.
PG  - 7405-7415
AB  - We present the complete genome sequence of Listeria welshimeri, a nonpathogenic member of the
      genus Listeria. Listeria welshimeri harbors a
      circular chromosome of 2,814,130 bp with 2,780 open reading frames.
      Comparative genomic analysis of chromosomal regions between L. welshimeri,
      Listeria innocua, and Listeria monocytogenes shows strong overall
      conservation of synteny, with the exception of the translocation of an
      F(o)F(1) ATP synthase. The smaller size of the L. welshimeri genome is the
      result of deletions in all of the genes involved in virulence and of
      "fitness" genes required for intracellular survival, transcription
      factors, and LPXTG- and LRR-containing proteins as well as 55 genes
      involved in carbohydrate transport and metabolism. In total, 482 genes are
      absent from L. welshimeri relative to L. monocytogenes. Of these, 249
      deletions are commonly absent in both L. welshimeri and L. innocua,
      suggesting similar genome evolutionary paths from an ancestor. We also
      identified 311 genes specific to L. welshimeri that are absent in the
      other two species, indicating gene expansion in L. welshimeri, including
      horizontal gene transfer. The species L. welshimeri appears to have been
      derived from early evolutionary events and an ancestor more compact than
      L. monocytogenes that led to the emergence of nonpathogenic Listeria spp.
AU  - Hain T et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2006 188: 7405-7415.

PMID- 27540054
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences for Seven Streptococcus parauberis Isolates from Wild Fish in the Chesapeake Bay.
PG  - e00741-16
AB  - Streptococcus parauberis is a pathogen of cattle and fish, closely related Streptococcus
      uberis and Streptococcus iniae We report the genomes of seven S.
      parauberis strains recovered from striped bass (Morone saxatilis) in the
      Chesapeake Bay. The availability of these genomes will allow comparative genomic
      analysis of Chesapeake Bay S. parauberis strains versus S. parauberis cultured
      from other animal hosts and geographic regions.
AU  - Haines A
AU  - Nebergall E
AU  - Besong E
AU  - Council K
AU  - Lambert O
AU  - Gauthier D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00741-16.

PMID- 1734524
VI  - 255
DP  - 1992
TI  - Predicted structural similarities of the DNA binding domains of c-Myc and endonuclease EcoRI.
PG  - 464-466
AB  - The c-Myc oncoprotein belongs to a family of proteins whose DNA binding domains
      contain a basic region-helix-loop-helix (bHLH) motif.  Systematic mutagenesis
      of c-Myc revealed that dimerized bHLH motifs formed a parallel four-helix
      bundle with the amino termini of helices 1 and 2 directed toward the inner and
      outer nucleotides of the DNA binding site, respectively.  Both the basic region
      and the carboxyl-terminal end of the loop contributed to DNA binding
      specificity.  The DNA binding domain of c-Myc may therefore be structurally
      similar to that of restriction endonuclease EcoRI.
AU  - Halazonetis TD
AU  - Kandil AN
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1992 255: 464-466.

PMID- Not included in PubMed...
VI  - 36
DP  - 1988
TI  - Identification and characterization of a novel restriction enzyme derived from Mycoplasma fermentans.
PG  - 404a
AB  - During our studies defining proteins that bind to the 5' regulatory regions of
      the human interleukin-2 receptor alpha chain (IL2Ralpha,p55, Tac antigen) gene,
      we have unexpectedly identified a new restriction enzyme specific for a
      sequence not cleaved by any known restriction enzyme.  Nuclear extracts from
      various cell lines were incubated with 32P-labeled DNA from the IL2Ralpha
      promoter region.  In the absence of any exogenous nuclease, extracts from
      Jurkat and MT-2 cells, but not from HeLa and HUT-102B2 cells, were capable of
      cleaving the DNA.  Subsequent analysis confirmed that only the Jurkat and MT-2
      T cells were infected with mycoplasma.  When extracts were prepared from the
      same Jurkat cell line cured with BM cycline, the activity was not present.  We
      have therefore concluded that the nuclease activity was derived from the
      mycoplasma rather than the T cells.  The mycoplasma strain containing both MT-2
      and Jurkat cells was identified as M. fermentans.  The new enzyme specifically
      recognizes the palindrome CAATTG, is inactivated by 15 min treatment at 65C, by
      proteinase K, and by 20 mM EDTA, and works optimally in low salt (<10mM NaCl)
      restriction enzyme buffer.  In conclusion, this enzyme recognizes a new
      recognition sequence and therefore has potential for general use in molecular
      biology.  In addition, it is possible that a rapid diagnostic test for
      mycoplasma may result from the use of mycoplasma specific restriction
      endonuclease assays on appropriate sequences of DNA.
AU  - Halden NF
AU  - Wolf JB
AU  - Cross SL
AU  - Leonard WJ
PT  - Journal Article
TA  - Clin. Res.
JT  - Clin. Res.
SO  - Clin. Res. 1988 36: 404a.

PMID- 2786191
VI  - 17
DP  - 1989
TI  - Identification of a novel site specific endonuclease produced by Mycoplasma fermentans:  discovery while characterizing DNA binding proteins in T lymphocyte cell lines.
PG  - 3491-3499
AB  - We have discovered a new restriction endonuclease, MfeI, in nuclear extracts
      from T cells contaminated with Mycoplasma fermentans.  This endonuclease was
      identified while studying proteins binding to the interleukin-2 receptor alpha
      chain gene promoter.  MfeI cuts at the recognition sequence C^AATTG generating
      EcoRI compatible cohesive ends.  Potential applications are discussed.
AU  - Halden NF
AU  - Wolf JB
AU  - Leonard WJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 3491-3499.

PMID- 28596391
VI  - 5
DP  - 2017
TI  - Draft Genome Report of Bacillus altitudinis SORB11, Isolated from the Indian Sector of the Southern Ocean.
PG  - e00339-17
AB  - Here, we present the draft genome sequence of Bacillus altitudinis SORB11, which  is tolerant
      to UV radiation. The strain was isolated from the Indian sector of
      the Southern Ocean at a depth of 3.8 km. The genome sequence information reported
      here for B. altitudinis SORB11 gives the basis of its UV resistance mechanism and
      provides data for further comparative studies with other bacteria resistant to UV
      radiation.
AU  - Halder U
AU  - Banerjee A
AU  - Chaudhry V
AU  - Varshney RK
AU  - Mantri S
AU  - Bandopadhyay R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00339-17.

PMID- 8195106
VI  - 176
DP  - 1994
TI  - Analysis of nonmethylated GATC sites in the Escherichia coli chromosome and identification of sites that are differentially methylated in response to environmental stimuli.
PG  - 3438-3441
AB  - Seven GATC sites that are nonmethylated in logarithmic growth phase cells using glycerol as a
      carbon source were isolated from the Escherichia coli chromosome.  Three of these GATC sites
      are located upstream of the operons gut, mtl, and ppiA, whereas DNA sequences adjacent to
      three other nonmethylated GATC sites are not homologous to previously identified genes.  The
      seventh nonmethylated GATC site is located downstream of uspA.  The protection of this site
      from DNA methylation requires leucine-responsive regulatory protein and is leucine responsive.
      The carbon source and the growth phase influenced the protection of the GATC site 5' of the
      ppiA gene.  The other five sites were protected under all the environmental conditions
      examined.
AU  - Hale WB
AU  - van der Woude MW
AU  - Low DA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1994 176: 3438-3441.

PMID- 24265497
VI  - 1
DP  - 2013
TI  - Genome Sequences of Clinical Vibrio cholerae Isolates from an Oyster-Borne Cholera Outbreak in Florida.
PG  - e00966-13
AB  - Between November 2010 and April 2011, 11 cases of cholera were identified and associated with
      the consumption of raw oysters harvested from Apalachicola Bay,
      Florida. The etiological agent was the ctxAB-positive Vibrio cholerae serogroup
      O75. The genome sequences of the isolates provide useful information and are
      deposited in the public genome databases.
AU  - Haley BJ
AU  - Choi SY
AU  - Hasan NA
AU  - Abdullah AS
AU  - Cebula TA
AU  - Huq A
AU  - Colwell RR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00966-13.

PMID- 27856587
VI  - 4
DP  - 2016
TI  - Genome Sequences of Two Salmonella enterica Serovar Kentucky Isolates Recovered from Poultry Carcasses in the United States.
PG  - e01289-16
AB  - We report here the draft genome sequences of two Salmonella enterica serovar Kentucky
      eBurstGroup 15 isolates collected from poultry carcasses in Georgia
      (USA).
AU  - Haley BJ
AU  - Kim SW
AU  - Liljebjelke K
AU  - Guard J
AU  - Van Kessel JA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01289-16.

PMID- 27660777
VI  - 4
DP  - 2016
TI  - Genome Sequence of a Novel Multiple-Antibiotic-Resistant Member of the Erysipelotrichaceae Family Isolated from a Swine Manure Storage Pit.
PG  - e00978-16
AB  - The swine gastrointestinal tract and stored swine manure may serve as reservoirs  of
      antibiotic resistance genes, as well as sources of novel bacteria. Here, we
      report the draft genome sequence of a novel taxon in the Erysipelotrichaceae
      family, isolated from a swine manure storage pit that is resistant to multiple
      antibiotics.
AU  - Haley BJ
AU  - Kim SW
AU  - Whitehead TR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00978-16.

PMID- 29051251
VI  - 5
DP  - 2017
TI  - Genome Sequences of Salmonella enterica subsp. enterica Serovar Kentucky Sequence Type 152 Isolated from Dairy Cows in the United States.
PG  - e01119-17
AB  - Salmonella enterica subsp. enterica serovar Kentucky (S. Kentucky) is frequently  isolated
      from dairy cows in the United States, but is an infrequent cause of
      human salmonellosis. To investigate the genomic features of S Kentucky strains
      isolated from a single dairy farm, the genomes of eight isolates were sequenced
      and added to the public domain.
AU  - Haley BJ
AU  - Luo Y
AU  - Wang C
AU  - Brown E
AU  - Allard M
AU  - Karns JS
AU  - Van Kessel JAS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01119-17.

PMID- 24762931
VI  - 2
DP  - 2014
TI  - Genome Sequences of Eight Salmonella enterica subsp. enterica Serovars Isolated from a Single Dairy Farm.
PG  - e00082-14
AB  - Here, we report draft genome sequences of 26 isolates of Salmonella enterica subsp. enterica,
      representing eight serotypes, which were isolated from cows in a Pennsylvania dairy herd, the
      farm on which they were reared, and the associated off-site heifer-raising facility over an
      8-year sampling period.
AU  - Haley BJ
AU  - Luo Y
AU  - Wang C
AU  - Pettengill J
AU  - Allard M
AU  - Brown E
AU  - Karns JS
AU  - Van Kessel JA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00082-14.

PMID- 26823571
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence and Methylome of Salmonella enterica subsp. enterica Cerro, a Frequent Dairy Cow Serovar.
PG  - e01350-15
AB  - Salmonella enterica subsp. enterica serovar Cerro is an infrequent pathogen of humans and
      other mammals but is frequently isolated from the hindgut of
      asymptomatic cattle in the United States. To further understand the genomic
      determinants of S. Cerro specificity for the bovine hindgut, the genome of
      isolate CFSAN001588 was fully sequenced and deposited in the GenBank database.
AU  - Haley BJ
AU  - Pirone C
AU  - Muruvanda T
AU  - Brown E
AU  - Allard M
AU  - Karns JS
AU  - Van Kessel JA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01350-15.

PMID- 
VI  - 3
DP  - 1986
TI  - Restriction enzymes in DNA-protein interactions.
PG  - 12-13
AB  - Within any organism from Escherichia coli to man, the genetic information is stored as a
      sequence of bases in the DNA but this constitutes only a blue-print for that organism.  The
      retrieval of the genetic information is absolutely dependent upon proteins that interact with
      the DNA.  The molecular basis of DNA-protein interactions is being studied by a group at the
      Bristol University who have used the EcoRI restriction endonuclease, an enzyme widely used in
      genetic engineering, as the test system.
AU  - Halford S
PT  - Journal Article
TA  - SERC Bulletin
JT  - SERC Bulletin
SO  - SERC Bulletin 1986 3: 12-13.

PMID- 
VI  - 
DP  - 1994
TI  - Restriction enzymes.
PG  - 954-956
AB  - Restriction enzymes are endonucleases that cleave DNA in response to a recognition site on the
      DNA.  The recognition site consists of a specific sequence of nucleotides in the DNA duplex,
      typically 4-8 base pairs long.  These endonucleases are found in many species of bacteria,
      where they function in restriction and modification systems.  The bacterial R/M system is
      analogous to an immune system, in that it enables the bacterium to distinguish its own DNA
      from foreign DNA and to eliminate the latter.  The discovery of restriction-modification
      systems followed the observation more than 30 years ago that a single cycle of phage growth in
      a particular bacterial host could alter the host range of the progeny phage; they had become
      'restricted' in their host range as a result of 'modification' in the original host.
      Restriction-modification is achieved by a combination of two enzyme activities: a modification
      methyltransferase and a restriction endonuclease.  The former transfers methyl groups from
      S-adenosylmethionine to specific bases within the recognition sequence, generally one in each
      strand: if one strand is already methylated, the second strand remains a substrate.  The
      latter cleaves the DNA but only if the recognition site is not methylated in either strand.
      Methylation of just one strand blocks restriction activity, so the bacterial DNA is protected
      from the endonuclease even after its semiconservative replication.  However, DNA that is
      foreign to the cell carrying the R/M system will lack the appropriate methylation and, if such
      DNA enters the cell, it is likely to be cleaved by the restriction enzyme.
AU  - Halford SE
PT  - Journal Article
TA  - Encyclopaedia of Molecular Biology
JT  - Encyclopaedia of Molecular Biology
SO  - Encyclopaedia of Molecular Biology 1994 : 954-956.

PMID- 
VI  - 31
DP  - 2009
TI  - The (billion dollar) consequences of studying why certain isolates of phage lambda infect only certain strains of E. coli: restriction enzymes.
PG  - 10-13
AB  - In 1953, Bertani and Weigle1 reported that samples of bacteriophage e that had been propagated
      on certain strains of Escherichia coli retained the ability to infect that same strain of E.
      coli but were unable to infect other strains. A contemporary version of their study is shown
      in Figure 1; phage e, obtained by infecting E. coli strain K (eK), is applied to two different
      E. coli strains, K and B. The eK particles infect E. coli K with an efficiency of 1: i.e.,
      every phage produces a plaque in a lawn of E. coli K cells. But the same preparation of eK
      shows a pathetic efficiency of infection on E. coli B, about 10-4: i.e., 10,000 phage
      particles yield just one plaque on the lawn of E. coli B cells. The phage obtained from the
      few productive infections of E. coli B (eB) are then tested against the same two strains, K
      and B. This time, the phage have largely lost the ability to infect E. coli K, as they now
      show an efficiency of 10-4 instead of 1, but they infect E. coli B much more readily than
      before, with an efficiency raised from 10-4 to 1.
AU  - Halford SE
PT  - Journal Article
TA  - Biochemist
JT  - Biochemist
SO  - Biochemist 2009 31: 10-13.

PMID- 6249682
VI  - 8
DP  - 1980
TI  - The specificity of the EcoRI restriction endonuclease.
PG  - 399-400
AB  - None
AU  - Halford SE
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 1980 8: 399-400.

PMID- Not included in PubMed...
VI  - 8
DP  - 1983
TI  - How does EcoRI cleave its recognition site on DNA?
PG  - 455-460
AB  - The two protein subunits of the EcoRI restriction enzyme interact symmetrically
      with the recognition site on DNA, so that each subunit is in position to cleave
      one strand of the DNA.  But each subunit seems to require a protein
      conformation change before it can cleave DNA.  Depending upon whether one or
      both subunits change conformation during the life-time of the enzyme-DNA
      complex, a single reaction of the EcoRI enzyme cleaves either one or both
      strands of the DNA.  Reaction profiles with other restriction enzymes differ
      from EcoRI, though the underlying mechanisms may be the same.
AU  - Halford SE
PT  - Journal Article
TA  - Trends Biochem. Sci.
JT  - Trends Biochem. Sci.
SO  - Trends Biochem. Sci. 1983 8: 455-460.

PMID- 10093713
VI  - 27
DP  - 1999
TI  - Restriction enzymes that act simultaneously at two DNA sites.
PG  - A88
AB  - The reaction of a type II restriction enzyme commonly results in DNA cleavage at a single
      site.  DNA with multiple recognition sites is cleaved by a succession of separate reactions at
      individual sites.  However, it has been discovered recently that many of the type II
      endonucleases can convert a substrate with two recognition sites directly into the product
      cleaved at both sites, without liberating DNA cut at a single site.  The coupled cleavage of
      two sites can be due to a processive mechanism involving the intramolecular transfer of the
      enzyme from one site to another.  Whilst such transfers have generally been considered to
      occur by "sliding", the linear diffusion of the protein along the DNA, studies on the EcoRV
      endonuclease have excluded "sliding" as a major pathway for intramolecular transfer and have
      indicated instead that the transfer occurs by "hopping", the dissociation of the protein from
      one site on the DNA followed by its reassociation to another site on the same molecule of DNA.
      In other cases, concerted action at two DNA sites is achieved by the restriction enzyme being
      unable to cleave DNA until it has bound to two copies of its recognition sequence, either by
      looping out the DNA between sites on the same DNA molecule or by bridging sites on separate
      molecules.  The SfiI endonuclease provides an illustration of the latter system.
AU  - Halford SE
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 1999 27: A88.

PMID- 11497991
VI  - 29
DP  - 2001
TI  - Hopping, jumping and looping by restriction enzymes.
PG  - 363-373
AB  - Type II restriction endonucleases recognize specific DNA sequences and cleave both strands of
      the DNA at fixed locations at or near their
      recognition sites. Many of these enzymes are dimeric proteins that
      recognize, in symmetrical fashion, palindromic DNA sequences. They
      generally catalyse independent reactions at each recognition site on
      the DNA, although in some cases they act processively; cutting the DNA
      first at one site, then translocating along the DNA to another site and
      cutting that before leaving the DNA. The way in which the degree of
      processivity varies with the length of DNA between the sites can reveal
      the mechanism of translocation. In contrast with the common view that
      proteins move along DNA by 'sliding', the principal mode of transfer of
      the EcoRV endonuclease is by 'hopping' and 'jumping', i.e. the
      dissociation of the protein from one site followed by its
      re-association with another site in the same DNA molecule, either close
      to or distant from the original site. Other type II restriction enzymes
      require two copies of their recognition sites for their DNA cleavage
      reactions. Many of these enzymes, such as SfiI, are tetramers with two
      DNA-binding surfaces. SfiI has no activity when bound to just one
      recognition site, and instead both DNA-binding surfaces have to be
      filled before it becomes active. Although the two sites can be on
      separate DNA molecules, SfiI acts optimally with two sites on the same
      DNA, where it traps the DNA between the sites in a loop. SfiI thus
      constitutes a test system for the analysis of DNA looping.
AU  - Halford SE
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 2001 29: 363-373.

PMID- 8095080
VI  - 17C
DP  - 1993
TI  - DNA recognition by EcoRV.
PG  - 152
AB  - In the presence of magnesium ions, the EcoRV restriction endonuclease cleaves DNA specifically
      at its recognition sequence, GATATC.  Sequences that differ from the recognition site by one
      base pair are cleaved at least a million times more slowly.  Yet, in binding to DNA in the
      absence of magnesium ions, the EcoRV restriction enzyme shows no sequence specificity.  The
      protein binds all sequences with equal affinity, and it can transfer readily from one site to
      another along the DNA molecule without dissociating from the DNA.  However, the DNA cleavage
      activity that is observed at any particular sequence is a function of the fractional
      saturation of the relevant enzyme-DNA complex with magnesium ions.  The observed difference in
      cleavage rates is due to the fact that the EcoRV enzyme has a high affinity for magnesium when
      it is located at its recognition site on DNA, but it has a low affinity for magnesium when it
      is located on any other DNA sequence.  Once it has bound the metal ion, the intrinsic activity
      of the EcoRV enzyme at noncognate sites is similar to that at the recognition site.  This
      mechanism can be correlated to the crystal structures of the EcoRV endonuclease that have been
      determined by F.K. Winkler.  Three structures were solved: the free enzyme in the absence of
      DNA; the specific complex at its recognition sequence, a nonspecific complex at a different
      DNA sequence.  The specific complex displays a large number of sequence-specific interactions
      between the protein and the DNA.  These are missing in the nonspecific complex.  But the
      additional interactions that are seen in the specific complex contribute nothing to the net
      free energy change for DNA binding.  Instead, all of the energy from the specific interactions
      is used to distort the DNA, and in other conformational changes: the structure of the specific
      DNA bound to EcoRV is extensively distorted while the nonspecific DNA is close to B-form.  The
      distortion results in only the specific complex being able to bind magnesium ions and to
      catalyse the reaction.  The communication between DNA recognition and catalysis thus seems to
      be mediated by the structure of the DNA itself.  This model is currently being tested by
      mutational analyses of EcoRV and by using fluorescence methods to monitor the conformational
      changes in the DNA and in the protein.
AU  - Halford SE
AU  - Baldwin GS
AU  - Vipond IB
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1993 17C: 152.

PMID- 10917669
VI  - 27
DP  - 1999
TI  - Restriction endonuclease reactions requiring two recognition sites.
PG  - 696-699
AB  - The standard perception of a restriction enzyme is of an endonuclease that recognizes a short
      palindrome of DNA and which cleaves both strands of the DNA at fixed locations in that
      sequence, in a reaction that requires only Mg2+ ions as a cofactor.  The perception thus
      refers to the type II restriction enzymes, as opposed to the type I and the type III systems.
      Many of the type II restriction enzymes conform to this perception.  Their recognition sites
      are often symmetrical palindromes, 4, 6 or occasionally 8 bp long, although in some instances
      the palindrome is interrupted by a fixed length of unspecified sequence.  They are usually
      dimers of identical subunits that interact symmetrically with their recognition sequences,
      even when the recognition site is an interrupted palindrome.  One active site in the dimer
      cleaves one strand of the DNA, while the second active site cleaves the symmetrically
      equivalent position in the other strand of the DNA.  The reactions of these enzymes are thus
      independent events at individual recognition sites, unless the enzyme hops along the DNA from
      one site to another.  The type II enzymes that match the standard perception include several
      well-characterized endonucleases, such as EcoRV, BglI and BamHI.
AU  - Halford SE
AU  - Bilcock DT
AU  - Stanford NP
AU  - Williams SA
AU  - Milsom SE
AU  - Gormley NA
AU  - Watson MA
AU  - Bath AJ
AU  - Embleton ML
AU  - Gowers DM
AU  - Daniels LE
AU  - Parry SH
AU  - Szczelkun MD
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 1999 27: 696-699.

PMID- 21428944
VI  - 39
DP  - 2011
TI  - The reaction mechanism of FokI excludes the possibility of targeting zinc finger nucleases to unique DNA sites.
PG  - 584-588
AB  - The FokI endonuclease is a monomeric protein with discrete DNA-recognition and catalytic
      domains. The latter has only one active site so, to cut both
      strands, the catalytic domains from two monomers associate to form a
      dimer. The dimer involving a monomer at the recognition site and another
      from free solution is less stable than that from two proteins tethered to
      the same DNA. FokI thus cleaves DNA with two sites better than one-site
      DNA. The two sites can be immediately adjacent, but they can alternatively
      be many hundreds of base pairs apart, in either inverted or repeated
      orientations. The catalytic domain of FokI is often a component of zinc
      finger nucleases. Typically, the zinc finger domains of two such nucleases
      are designed to recognize two neighbouring DNA sequences, with the
      objective of cutting the DNA exclusively between the target sequences.
      However, this strategy fails to take account of the fact that the
      catalytic domains of FokI can dimerize across distant sites or even at a
      solitary site. Additional copies of either target sequence elsewhere in
      the chromosome must elicit off-target cleavages.
AU  - Halford SE
AU  - Catto LE
AU  - Pernstich C
AU  - Rusling DA
AU  - Sanders KL
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 2011 39: 584-588.

PMID- 2835097
VI  - 27
DP  - 1988
TI  - Modes of DNA cleavage by the EcoRV restriction endonuclease.
PG  - 1771-1777
AB  - The mechanism of action ofthe EcoRV restriction endonuclease at its single
      recognition site on the plasmid pAT153 was analyzed by kinetic methods.  In
      reactions at pH 7.5, close to the optimum for this enzyme, both strands of the
      DNA were cut in a single concerted reaction:  DNA cut in only one strand of the
      duplex was neither liberated from the enzyme during the catalytic turnover nor
      accumulated as a steady-state intermediate.  In contrast, reactions at pH 6.0
      involved the sequential cutting of the two strands of the DNA.  Under these
      conditions, DNA cut in a single strand was an obligatory intermediate in the
      reaction pathway and a fraction of the nicked DNA dissociated from the enzyme
      during the turnover.  The different reaction profiles are shown to be
      consistent with a single mechanism in which the kinetic activity of each
      subunit of the dimeric protein is governed by its affinity for Mg2+ ions.  At
      pH 7.5, Mg2+ is bound to both subunits of the dimer for virtually the complete
      period of the catalytic turnover, while at pH 6.0 Mg2+ is bound transiently to
      one subunit at a time.  The kinetics of the EcoRV nuclease were unaffected by
      the DNA supercoiling.
AU  - Halford SE
AU  - Goodall AJ
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1988 27: 1771-1777.

PMID- 10966631
VI  - 7
DP  - 2000
TI  - Two are better than one.
PG  - 705-707
AB  - A crystal structure of a tetrameric restriction enzyme, NgoMIV, bound to two DNA duplexes has
      been determined.  Two subunits contact each duplex in much the same manner as a dimeric
      restriction enzyme recognizing a single site, but the dimeric units are packed back-to-back,
      placing the duplexes on opposite sides of the tetramer.  Interaction with two recognition
      sites, presumably via looping, enhances NgoMIV activity.
AU  - Halford SE
AU  - Gowers DM
AU  - Sessions RB
PT  - Journal Article
TA  - Nat. Struct. Biol.
JT  - Nat. Struct. Biol.
SO  - Nat. Struct. Biol. 2000 7: 705-707.

PMID- 6307279
VI  - 211
DP  - 1983
TI  - Single turnovers of the EcoRI restriction endonuclease.
PG  - 405-415
AB  - Single turnovers of the EcoRI restriction endonuclease, cleaving its recognition site on the
      covalently closed form of plasmid pMB9, were examined. Two methods were used to monitor the
      progress of the reactions: one involved quenching the reaction at various times followed by
      the electrophoretic separation of the products cleaved in one and in both strands of the
      duplex; the other employed a stopped-flow fluorimeter to measure the amount of ethidium
      bromide bound to the DNA as it changes when the DNA, cleaved in at least one strand,
      dissociates from the enzyme.  Two procedures were used to initiate the reactions.  For some,
      one solution containing the enzyme was mixed with a second containing both DNA and MgCl2: in
      these reactions, the fluorescence changed at the same rate as the cleavage of the first strand
      of the duplex. Other reactions were started by the addition of MgCl2 to a pre-equilibrium of
      enzyme and DNA: here, both strands of the DNA were cleaved faster than before, with the
      fluorescence signal now occurring at the same time as the cleavage of the second strand.  The
      different kinetics from the two assays and the two mixing procedures are consistent with the
      rates of these reactions being controlled by protein conformational changes.  These may affect
      either one subunit alone within the dimeric EcoRI enzyme, allowing the enzyme to cleave only
      one strand of the DNA in each turnover.  Alternatively, both subunits of the dimer may change,
      so that the enzyme then cleaves both strands during the life-time of one enzyme-DNA complex.
AU  - Halford SE
AU  - Johnson NP
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 1983 211: 405-415.

PMID- 6280676
VI  - 199
DP  - 1981
TI  - The EcoRI restriction endonuclease, covalently closed DNA and ethidium bromide.
PG  - 767-777
AB  - The reactions of the EcoRI restriction endonuclease on the covalently closed
      DNA of plamid pMB9 were studied in the presence of ethidium bromide.  At the
      concentrations of ethidium bromide tested, which covered the range over which
      the DNA is changed from negatively to positively supercoiled, the dye caused no
      alteration to the rate at which this enzyme cleaved the covalently closed DNA
      to yield the open-circle form, but the rate at which these open circles were
      cleaved to the linear product could be inhibited.  The fluorescence change,
      caused by ethidium bromide binding with different stoichiometries to covalently
      clodsed and open-circle DNA, provided a direct and sensitive signal for
      monitoring the cleavage of DNA by this enzyme.  This method was used for a
      steady-state kinetic analysis of the reaction catalysed by the EcoRI
      restriction enzyme.  Reaction mechanisms where a complex between DNA and Mg2+
      is the substrate for this enzyme were eliminated, and instead DNA and Mg2+ must
      bind to the enzyme in separate stages.  The requisite controls for this
      fluorimetric assay in both steady-state and transient kinetics studies, and its
      application to other enzymes that alter the structure of covalently closed DNA,
      are described.
AU  - Halford SE
AU  - Johnson NP
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 1981 199: 767-777.

PMID- 6263250
VI  - 191
DP  - 1980
TI  - The EcoRI restriction endonuclease with bacteriophage lambda DNA.  Equilibrium binding sites.
PG  - 593-604
AB  - The EcoRI restriction endonuclease was found by the filter binding technique to
      form stable complexes, in the absence of Mg2+, with the DNA from derivatives of
      bacteriophage lambda that either contain or lack EcoRI recognition sites.  The
      amount of complex formed at different enzyme concentrations followed a
      hyperbolic equilibrium-binding curve with DNA molecules containing EcoRI
      recognition sites, but a sigmoidal equilibrium-binding curve was obtained with
      a DNA molecule lacking EcoRI recognition sites.  The EcoRI enzyme displayed the
      same affinity for individual recognition sites on lambda DNA, even under
      conditions where it cleaves these sites at different rates.  The binding of the
      enzyme to a DNA molecule lacking EcoRI sites was decreased by Mg2+.  These
      observations indicate that (a) the EcoRI restriction enzyme binds
      preferentially to its recognition site on DNA, and that different reaction
      rates at different recognition sites are due to the rate of breakdown of this
      complex; (b) the enzyme also binds to other DNA sequences, but that two
      molecules of enzyme, in a different protein conformation, are involved in the
      formation of the complex at non-specific sequences; (c) the different
      affinities of the enzyme for the recognition site and for other sequences on
      DNA, coupled with the different protein conformations, account for the
      specificity of this enzyme for the cleavage of DNA at its recognition site; (d)
      the decrease in the affinity of the enzyme for DNA, caused by Mg2+, liberates
      binding energy from the DNA-protein complex that can be used in the catalytic
      reaction.
AU  - Halford SE
AU  - Johnson NP
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 1980 191: 593-604.

PMID- 6263249
VI  - 191
DP  - 1980
TI  - The EcoRI restriction endonuclease with bacteriophage lambda DNA.  Kinetic studies.
PG  - 581-592
AB  - The kinetics of the reactions of the EcoRI restriction endonuclease at
      individual recognition sites on the DNA from bacteriophage lambdawere found to
      differ markedly from site to site.  Under certain conditions of pH and ionic
      strength, the rates for the cleavage of the DNA were the same at each
      recognition site.  But under altered experimental conditions, different
      reaction rates were observed at each recognition site.  These results are
      consistent with a mechanism in which the kinetic stability of the complex
      between the enzyme and the recognition site on the DNA differs among the sites,
      due to the effect of interactions between the enzyme and DNA sequences
      surrounding each recognition site upon the transition state of the reaction.
      Reactions at individual sites on a DNA molecule containing more than one
      recognition site were found to be independent of each other, thus excluding the
      possibility of a processive mechanism for the EcoRI enzyme.  The consequences
      of these observations are discussed with regard to both DNA-protein
      interactions and to the application of restriction enzymes in the study of the
      structure of DNA molecules.
AU  - Halford SE
AU  - Johnson NP
AU  - Grinsted J
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 1980 191: 581-592.

PMID- 486086
VI  - 179
DP  - 1979
TI  - The reactions of the EcoRI and other restriction endonucleases.
PG  - 353-365
AB  - The reaction of the EcoRI restriction endonuclease was studied with both the
      plasmid pMB9 and DNA from bacteriophage lambda as the substrates.  With both
      circular and linear DNA molecules, the only reaction catalysed by the EcoRI
      restriction endonuclease was the hydrolysis of the phosphodiester bond within
      one strand of the recognition site on the DNA duplex.  The cleavage of both
      strands of the duplex was achieved only after two independent reactions, each
      involving a single-strand scission.  The reactivity of the enzyme for
      single-strand scissions was the same for both the first and the second cleavage
      within its recognition site.  No differences were observed between the
      mechanism of action on supercoiled and linear DNA substrates.  Other
      restriction endonucleases were tested against plasmid pMB9.  The HindIII
      restriction endonuclease cleaved DNA in the same manner as the EcoRI enzyme.
      However, in contrast with EcoRI, the SalI and the BamHI restriction
      endonucleases appeared to cleave both strands of the DNA duplex almost
      simultaneously.  The function of symmetrical DNA sequences and the conformation
      of the DNA involved in these DNA-protein interactions are discussed in the
      light of these observations.  The fact that the same reactions were observed on
      both supercoiled and linear DNA substrates implies that these interactions do
      not involve the unwinding of the duplex before catalysis.
AU  - Halford SE
AU  - Johnson NP
AU  - Grinsted J
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 1979 179: 353-365.

PMID- Not included in PubMed...
VI  - 14
DP  - 1986
TI  - Altered specificity of the EcoRV restriction endonuclease.
PG  - 260-261
AB  - Type II restriction endonucleases recognize specific sequences of nucleotides on DNA and, in
      the presence of Mg2+, cleave both strands of the DNA at fixed locations relative to the
      recognition site.  These enzymes generally show very high specificities: the rates at which
      they cleave their recognition sites can be several orders of magnitude faster than that for
      any cleavage at alternative DNA sequences.  However, in altered environments such as at high
      pH or in the presence of water-miscible organic solvents, many restriction enzymes show
      reduced specificity and cleave DNA at several sites in addition to the recognition site.  This
      phenomena was first observed with the EcoRI restriction enzyme, the altered activity at high
      pH being noted as EcoRI.  We describe here a similar alteration in the specificity of the
      EcoRV restriction enzyme and show that each additional site cleaved by EcoRV differs from the
      canonical EcoRV recognition sequence, 5'-G-A-T-A-T-C-3', by one nucleotide.
AU  - Halford SE
AU  - Lovelady BM
AU  - McCallum S
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 1986 14: 260-261.

PMID- 3011595
VI  - 41
DP  - 1986
TI  - Relaxed specificity of the EcoRV restriction endonuclease.
PG  - 173-181
AB  - The EcoRV restriction endonuclease normally shows a high specificity for its recognition site
      on DNA, GATATC. In standard reactions, it cleaves DNA at this site several orders of magnitude
      more readily than at any alternative sequence. But in the presence of dimethyl sulphoxide and
      at high pH, the EcoRV enzyme cleaves DNA at several sites that differ from its recognition
      site by one nucleotide. Of the 18 (3 x 6) possible sequences that differ from GATATC by one
      base, all were cleaved readily except for the following 4 sites: TATATC, CATATC, GATATA and
      GATATG. However, two of the sites that could be cleaved by EcoRV in the presence of dimethyl
      suphoxide, GAGATC and GATCTC, were only cleaved on DNA that lacked dam methylation: both
      contain the sequence GATC, the recognition site for the dam methylase of Escherichia coli.
AU  - Halford SE
AU  - Lovelady BM
AU  - McCallum SA
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1986 41: 173-181.

PMID- 15178741
VI  - 32
DP  - 2004
TI  - How do site-specific DNA-binding proteins find their targets?
PG  - 3040-3052
AB  - Essentially all the biological functions of DNA depend on site-specific DNA-binding proteins
      finding their targets, and therefore ?searching? through megabases of non-target DNA. In this
      article, we review current understanding of how this sequence searching is done. We review how
      simple diffusion through solution may be unable to account for the rapid rates of association
      observed in experiments on some model systems, primarily the Lac repressor. We then present a
      simplified version of the ?facilitated diffusion? model of Berg, Winter and von Hippel,
      showing how non-specific DNA?protein interactions may account for accelerated targeting, by
      permitting the protein to sample many binding sites per DNA encounter. We discuss the
      1-dimensional ?sliding? motion of protein along non-specific DNA, often proposed to be the
      mechanism of this multiple site sampling, and we discuss the role of short-range diffusive
      ?hopping? motions. We then derive the optimal range of sliding for a few physical situations,
      including simple models of chromosomes in vivo, showing that a sliding range of ~100bp before
      dissociation optimizes targeting in vivo. Going beyond first-order binding kinetics, we
      discuss how processivity, the interaction of a protein with two or more targets on the same
      DNA, can reveal the extent of sliding and we review recent experiments studying processivity
      using the restriction enzyme EcoRV. Finally, we discuss how single molecule techniques might
      be used to study the dynamics of DNA site-specific targeting of proteins.
AU  - Halford SE
AU  - Marko JF
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2004 32: 3040-3052.

PMID- 
VI  - 7
DP  - 1993
TI  - Mechanism of action of restriction endonuclease EcoRV.
PG  - 47-69
AB  - Type II restriction/modification (R/M) systems, such as EcoRV, consist of two enzymes that act
      at the same DNA sequence; a modification methyltransferase and a restriction endonuclease
      (Bennett and Halford 1989; Wilson and Murray 1991). For EcoRV, the recognition sequence is
      GATATC (Kholmina et al. 1980). The EcoRV modification enzyme methylates the first adenine
      within this sequence (Nwosu et al. 1988) while, in the presence of Mg2+ ions, the EcoRV
      restriction enzymes cleaves DNA specifically at this site (Schilkdraut et al. 1984). The
      endonuclease cuts both strands at the center of the sequence, to leave blunt-ended DNA
      fragments. However, prior methylation of the recognition site blocks restriction activity. The
      basic tenet of R/M systems is that, in vivo, the restriction enzyme cuts only DNA molecules
      that have not been exposed previously to the methyltransferase. Hence, they enable the cell to
      degrade foreign DNA entering the cell without destroying host DNA. E. coli strains carrying
      the EcoRV system show this phenotype (Bougueleret et al. 1984).
AU  - Halford SE
AU  - Taylor JD
AU  - Vermote CLM
AU  - Vipond IB
PT  - Journal Article
TA  - Nucl. Acids and Mol. Biol.
JT  - Nucl. Acids and Mol. Biol.
SO  - Nucl. Acids and Mol. Biol. 1993 7: 47-69.

PMID- 8004211
VI  - 30
DP  - 1994
TI  - Assays for restriction endonucleases using plasmid substrates.
PG  - 385-396
AB  - A type II restriction enzyme purchased from a commercial supplier comes with a specified
      number of units of enzyme activity. The units of restriction enzyme activity are defined by
      the minimal amount of enzyme needed to complete the digestion of 1 ug of bacteriophage lambda
      DNA in 1 h. These units are usually measured by making serial dilutions of the stock solution
      of the enzyme, adding 1 uL from each dilution to 1 ug of phage lambda DNA in a suitable
      buffer, incubating the reactions for 1 h at 37oC, and then analyzing the DNA by
      electrophoresis through agarose. This is, at best, a semiquantitative assay. It cannot yield
      quantitative data about the rate of the reaction of a restricton enzyme on a DNA substrate.
AU  - Halford SE
AU  - Taylor JD
AU  - Vermote CLM
AU  - Vipond IB
PT  - Journal Article
TA  - Methods Mol. Biol.
JT  - Methods Mol. Biol.
SO  - Methods Mol. Biol. 1994 30: 385-396.

PMID- 15139802
VI  - 33
DP  - 2004
TI  - Enzyme-mediated DNA looping.
PG  - 1-24
AB  - Most reactions on DNA are carried out by multimeric protein complexes that interact with two
      or more sites in the DNA and thus loop out the DNA
      between the sites. The enzymes that catalyze these reactions usually have
      no activity until they interact with both sites. This review examines the
      mechanisms for the assembly of protein complexes spanning two DNA sites
      and the resultant triggering of enzyme activity. There are two main routes
      for bringing together distant DNA sites in an enzyme complex: either the
      proteins bind concurrently to both sites and capture the intervening DNA
      in a loop, or they translocate the DNA between one site and another into
      an expanding loop, by an energy-dependent translocation mechanism. Both
      capture and translocation mechanisms are discussed here, with reference to
      the various types of restriction endonuclease that interact with two
      recognition sites before cleaving DNA.
AU  - Halford SE
AU  - Welsh AJ
AU  - Szczelkun MD
PT  - Journal Article
TA  - Annu. Rev. Biophys. Biomol. Struct.
JT  - Annu. Rev. Biophys. Biomol. Struct.
SO  - Annu. Rev. Biophys. Biomol. Struct. 2004 33: 1-24.

PMID- 26893411
VI  - 4
DP  - 2016
TI  - Genome Sequence of a Gram-Positive Diazotroph, Paenibacillus durus Type Strain ATCC 35681.
PG  - e00005-16
AB  - Here, we report the complete genome sequence of Paenibacillus durus type strain ATCC 35681,
      which can fix atmospheric nitrogen even in the presence of nitrate.
AU  - Halim MA
AU  - Rahman AY
AU  - Sim KS
AU  - Yam HC
AU  - Rahim AA
AU  - Ghazali AH
AU  - Najimudin N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00005-16.

PMID- 26981419
VI  - 7
DP  - 2016
TI  - Genome sequencing and annotation of multidrug resistant Mycobacterium tuberculosis (MDR-TB) PR10 strain.
PG  - 245-246
AB  - Here, we report the draft genome sequence and annotation of a multidrug resistant
      Mycobacterium tuberculosis strain PR10 (MDR-TB PR10) isolated from a patient diagnosed with
      tuberculosis. The size of the draft genome MDR-TB PR10 is 4.34 Mbp with 65.6% of G + C content
      and consists of 4637 predicted genes. The determinants were categorized by RAST into 400
      subsystems with 4286 coding sequences and 50 RNAs. The whole genome shotgun project has been
      deposited at DDBJ/EMBL/GenBank under the accession number CP010968.
AU  - Halim MZA
AU  - Jaafar MM
AU  - Teh LK
AU  - Ismail MI
AU  - Lee LS
AU  - Ngeow YF
AU  - Nor NM
AU  - Zainuddin ZF
AU  - Tang TH
AU  - Najimudin MN
AU  - Salleh MZ
PT  - Journal Article
TA  - Genomics Data
JT  - Genomics Data
SO  - Genomics Data 2016 7: 245-246.

PMID- 12381313
VI  - 323
DP  - 2002
TI  - Creation of an artificial bifunctional intein by grafting a homing endonuclease into a mini-intein.
PG  - 173-179
AB  - The majority of inteins are comprised of a protein splicing domain and a homing endonuclease
      domain. Experimental evidence has demonstrated that the splicing domain and the endonuclease
      domain in a bifunctional intein are largely independent of each other with respect to both
      structure and activity. Here, an artificial bifunctional intein has been created through the
      insertion of an existing homing endonuclease into a mini-intein that is naturally lacking this
      functionality. The gene for I-CreI, an intron-encoded homing endonuclease, was grafted into
      the monofunctional Mycobacterium xenopi GyrA intein at the putative site of the missing
      endonuclease. The resulting fusion protein was found to be capable of protein splicing similar
      to that of the parent intein. In addition, the protein demonstrated site-specific endonuclease
      activity that is characteristic of the I-CreI homing endonuclease. The function of each domain
      therefore remained unaffected by the presence of the other domain. This artificial fusion of
      the two domains is a potential novel mobile genetic element.
AU  - Hall MF
AU  - Noren CJ
AU  - Perler FB
AU  - Schildkraut I
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2002 323: 173-179.

PMID- 6292966
VI  - 36
DP  - 1982
TI  - Blockage of restriction endonuclease cleavage by thymine dimers.
PG  - 429-432
AB  - Viral DNAs were subjected to 254 nm irradiation and then digested with type II
      restriction endonucleases.  At the fluences used, irradiation inhibited
      cleavage by nucleases which recognize sites containing neighboring thymines.
      Cleavage by endonucleases with other recognition sequences was not affected.
      In viral and plasmid DNAs, this effect could be used to study thymine dimer
      formation at a few specific, mapped sites of defined base sequence.
AU  - Hall RK
AU  - Larcom LL
PT  - Journal Article
TA  - Photochem. Photobiol.
JT  - Photochem. Photobiol.
SO  - Photochem. Photobiol. 1982 36: 429-432.

PMID- 2185235
VI  - 172
DP  - 1990
TI  - The DNA adenine methyltransferase (dam+) gene of bacteriophage T4 reverses the mutator phenotype of an Escherichia coli dam mutant.
PG  - 2812-2813
AB  - The mutator phenotype of Escherichia coli dam mutants was found to be reversed
      by introduction of the bacteriophage T4 gene for DNA adenine methyltransferase.
      This precludes a direct role for the E. coli DNA adenine methyltransferase in
      mismatch repair, in addition to its role in strand discrimination, as suggested
      by earlier studies.
AU  - Hall RM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1990 172: 2812-2813.

PMID- 17114289
VI  - 103
DP  - 2006
TI  - Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum.
PG  - 18296-18301
AB  - Crenarchaeota are ubiquitous and abundant microbial constituents of soils, sediments, lakes,
      and ocean waters. To further describe the cosmopolitan
      nonthermophilic Crenarchaeota, we analyzed the genome sequence of one
      representative, the uncultivated sponge symbiont Cenarchaeum symbiosum. C.
      symbiosum genotypes coinhabiting the same host partitioned into two
      dominant populations, corresponding to previously described a- and b-type
      ribosomal RNA variants. Although they were syntenic, overlapping a- and
      b-type ribotype genomes harbored significant variability. A single tiling
      path comprising the dominant a-type genotype was assembled and used to
      explore the genomic properties of C. symbiosum and its planktonic
      relatives. Of 2,066 ORFs, 55.6% matched genes with predicted function from
      previously sequenced genomes. The remaining genes partitioned between
      functional RNAs (2.4%) and hypotheticals (42%) with limited homology to
      known functional genes. The latter category included some genes likely
      involved in the archaeal-sponge symbiotic association. Conversely, 525 C.
      symbiosum ORFs were most highly similar to sequences from marine
      environmental genomic surveys, and they apparently represent orthologous
      genes from free-living planktonic Crenarchaeota. In total, the C.
      symbiosum genome was remarkably distinct from those of other known Archaea
      and shared many core metabolic features in common with its free-living
      planktonic relatives.
AU  - Hallam SJ
AU  - Konstantinidis KT
AU  - Putnam N
AU  - Schleper C
AU  - Watanabe Y
AU  - Sugahara J
AU  - Preston C
AU  - de la Torre J
AU  - Richardson PM
AU  - DeLong EF
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2006 103: 18296-18301.

PMID- 16533068
VI  - 4
DP  - 2006
TI  - Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota.
PG  - e95
AB  - Marine Crenarchaeota represent an abundant component of oceanic microbiota with potential to
      significantly influence biogeochemical cycling in marine
      ecosystems. Prior studies using specific archaeal lipid biomarkers and
      isotopic analyses indicated that planktonic Crenarchaeota have the
      capacity for autotrophic growth, and more recent cultivation studies
      support an ammonia-based chemolithoautotrophic energy metabolism. We
      report here analysis of fosmid sequences derived from the uncultivated
      marine crenarchaeote, Cenarchaeum symbiosum, focused on the reconstruction
      of carbon and energy metabolism. Genes predicted to encode multiple
      components of a modified 3-hydroxypropionate cycle of autotrophic carbon
      assimilation were identified, consistent with utilization of carbon
      dioxide as a carbon source. Additionally, genes predicted to encode a near
      complete oxidative tricarboxylic acid cycle were also identified,
      consistent with the consumption of organic carbon and in the production of
      intermediates for amino acid and cofactor biosynthesis. Therefore, C.
      symbiosum has the potential to function either as a strict autotroph, or
      as a mixotroph utilizing both carbon dioxide and organic material as
      carbon sources. From the standpoint of energy metabolism, genes predicted
      to encode ammonia monooxygenase subunits, ammonia permease, urease, and
      urea transporters were identified, consistent with the use of reduced
      nitrogen compounds as energy sources fueling autotrophic metabolism.
      Homologues of these genes, recovered from ocean waters worldwide,
      demonstrate the conservation and ubiquity of crenarchaeal pathways for
      carbon assimilation and ammonia oxidation. These findings further
      substantiate the likely global metabolic importance of Crenarchaeota with
      respect to key steps in the biogeochemical transformation of carbon and
      nitrogen in marine ecosystems.
AU  - Hallam SJ
AU  - Mincer TJ
AU  - Schleper C
AU  - Preston CM
AU  - Roberts K
AU  - Richardson PM
AU  - DeLong EF
PT  - Journal Article
TA  - PLoS Biology
JT  - PLoS Biology
SO  - PLoS Biology 2006 4: e95.

PMID- 15353801
VI  - 305
DP  - 2004
TI  - Reverse methanogenesis: Testing the hypothesis with environmental genomics.
PG  - 1457-1462
AB  - Microbial methane consumption in anoxic sediments significantly impacts the global environment
      by reducing the flux of greenhouse gases from ocean to atmosphere. Despite its significance,
      the biological mechanisms controlling anaerobic methane oxidation are not well characterized.
      One current model suggests that relatives of methane-producing Archaea developed the capacity
      to reverse methanogenesis and thereby to consume methane to produce cellular carbon and
      energy. We report here a test of the "reverse-methanogenesis" hypothesis by genomic analyses
      of methane-oxidizing Archaea from deep-sea sediments. Our results show that nearly all genes
      typically associated with methane production are present in one specific group of archaeal
      methanotrophs. These genome-based observations support previous hypotheses and provide an
      informed foundation for metabolic modeling of anaerobic methane oxidation.
AU  - Hallam SJ
AU  - Putnam N
AU  - Preston CM
AU  - Detter JC
AU  - Rokhsar D
AU  - Richardson PM
AU  - DeLong EF
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2004 305: 1457-1462.

PMID- 26893415
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a Thermophilic Cyanobacterium from the Family Oscillatoriales (Strain MTP1) from the Chalk River, Colorado.
PG  - e01571-15
AB  - The draft genome (57.7% GC, 7,647,882 bp) of the novel thermophilic cyanobacterium MTP1 was
      determined by metagenomics of an enrichment culture. The
      genome shows that it is in the family Oscillatoriales and encodes multiple heavy
      metal resistances as well as the capacity to make exopolysaccharides.
AU  - Hallenbeck PC
AU  - Grogger M
AU  - Mraz M
AU  - Veverka D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01571-15.

PMID- 26893414
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the Photoheterotrophic Chloracidobacterium thermophilum  Strain OC1 Found in a Mat at Ojo Caliente.
PG  - e01570-15
AB  - Metagenomics of an enrichment culture from a New Mexico hot spring allowed the description of
      a draft genome of a Chloracidobacterium thermophilum strain for
      the first time outside Yellowstone National Park with a surprisingly high degree
      of identity with the type strain.
AU  - Hallenbeck PC
AU  - Grogger M
AU  - Mraz M
AU  - Veverka D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01570-15.

PMID- 11587935
VI  - 4
DP  - 2001
TI  - Playing Dr Jekyll and Mr Hyde: combined mechanisms of phase variation in bacteria.
PG  - 570-581
AB  - Phase variation is the adaptive process by which bacteria undergo frequent and reversible
      phenotypic changes resulting from genetic alterations in specific loci
      of their genomes. This process is crucial for the survival of pathogens and
      commensals in hostile and ever-changing host environments. Despite important
      differences in the molecular mechanisms that mediate and regulate phase
      variation, related strategies have evolved to generate high levels of genetic
      diversity through complex and combinatorial reshuffling of genetic information.
      Recent studies, supported by the emergence of global genomic approaches, have
      revealed that bacterial pathogens often use a combination of different mechanisms
      to vary the expression of a variety of biological functions, providing new
      insights into bacterial adaptation and virulence mechanisms. Recent advances in
      the understanding of the molecular mechanisms of phase variation are reviewed,
      and differences in these mechanisms outlined.
AU  - Hallet B
PT  - Journal Article
TA  - Curr. Opin. Microbiol.
JT  - Curr. Opin. Microbiol.
SO  - Curr. Opin. Microbiol. 2001 4: 570-581.

PMID- 15805518
VI  - 187
DP  - 2005
TI  - Completion of the genome sequence of Brucella abortus and comparison to the highly similar genomes of Brucella melitensis and Brucella suis.
PG  - 2715-2726
AB  - Brucellosis is a worldwide disease of humans and livestock that is caused by a number of very
      closely related classical Brucella species in the
      alpha-2 subdivision of the Proteobacteria. We report the complete genome
      sequence of Brucella abortus field isolate 9-941 and compare it to those
      of Brucella suis 1330 and Brucella melitensis 16 M. The genomes of these
      Brucella species are strikingly similar, with nearly identical genetic
      content and gene organization. However, a number of insertion-deletion
      events and several polymorphic regions encoding putative outer membrane
      proteins were identified among the genomes. Several fragments previously
      identified as unique to either B. suis or B. melitensis were present in
      the B. abortus genome. Even though several fragments were shared between
      only B. abortus and B. suis, B. abortus shared more fragments and had
      fewer nucleotide polymorphisms with B. melitensis than B. suis. The
      complete genomic sequence of B. abortus provides an important resource for
      further investigations into determinants of the pathogenicity and
      virulence phenotypes of these bacteria.
AU  - Halling SM
AU  - Peterson-Burch BD
AU  - Bricker BJ
AU  - Zuerner RL
AU  - Qing Z
AU  - Li LL
AU  - Kapur V
AU  - Alt DP
AU  - Olsen SC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2005 187: 2715-2726.

PMID- 28729254
VI  - 5
DP  - 2017
TI  - Finished Whole-Genome Sequences of Clostridium butyricum Toxin Subtype E4 and Clostridium baratii Toxin Subtype F7 Strains.
PG  - e00375-17
AB  - Clostridium butyricum and Clostridium baratii species have been known to produce  botulinum
      toxin types E and F, respectively, which can cause botulism, a rare but
      serious neuroparalytic disease. Here, we present finished genome sequences for
      two of these clinically relevant strains.
AU  - Halpin JL
AU  - Hill K
AU  - Johnson SL
AU  - Bruce DC
AU  - Shirey TB
AU  - Dykes JK
AU  - Luquez C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00375-17.

PMID- 28546482
VI  - 5
DP  - 2017
TI  - Finished Whole-Genome Sequence of Clostridium argentinense Producing Botulinum Neurotoxin Type G.
PG  - e00380-17
AB  - Here, we present a closed genome sequence for Clostridium argentinense strain 89G, the first
      strain identified to produce botulinum neurotoxin type G (BoNT/G).
      Although discovered in 1970, to date, there have been no reference quality
      sequences publicly available for this species.
AU  - Halpin JL
AU  - Hill K
AU  - Johnson SL
AU  - Bruce DC
AU  - Shirey TB
AU  - Dykes JK
AU  - Luquez C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00380-17.

PMID- 28546483
VI  - 5
DP  - 2017
TI  - Finished Whole-Genome Sequences of Two Clostridium botulinum Type A(B) Isolates.
PG  - e00381-17
AB  - Clostridium botulinum secretes a potent neurotoxin that causes devastating effects when
      ingested, including paralysis and death if not treated. In the
      United States, some clinically significant strains produce toxin type A while
      also harboring a silent B gene. These are the first two closed genome sequences
      published for this subset.
AU  - Halpin JL
AU  - Hill K
AU  - Johnson SL
AU  - Bruce DC
AU  - Shirey TB
AU  - Dykes JK
AU  - Luquez C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00381-17.

PMID- 21914873
VI  - 193
DP  - 2011
TI  - Genome Sequence of Lactobacillus salivarius NIAS840, Isolated from Chicken Intestine.
PG  - 5551-5552
AB  - Lactobacillus salivarius is a well-known lactic acid bacterium to which increasing attention
      has been paid recently for use as probiotics for
      humans and animals. L. salivarius NIAS840 was first isolated from broiler
      chicken feces, displaying antimicrobial activities against
      multidrug-resistant Staphylococcus aureus and Salmonella enterica serovar
      Typhimurium. Here, we report the genome sequence of L. salivarius NIAS840
      (2,046,557 bp) including a small plasmid and two megaplasmids.
AU  - Ham JS
AU  - Kim HW
AU  - Seol KH
AU  - Jang A
AU  - Jeong SG
AU  - Oh MH
AU  - Kim DH
AU  - Kang DK
AU  - Kim GB
AU  - Cha CJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5551-5552.

PMID- 21742881
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Bifidobacterium longum subsp. longum KACC 91563.
PG  - 5044
AB  - Bifidobacterium longum strains predominate the colonic microbiota of breast-fed infants. Here
      we report a complete genome sequence of B. longum
      subsp. longum KACC 91563 isolated from feces of neonates. A single
      circular chromosome of 2,385,301 bp contains 1,980 protein coding genes,
      56 tRNA genes, and 3 rRNA operons.
AU  - Ham JS
AU  - Lee T
AU  - Byun MJ
AU  - Lee KT
AU  - Kim MK
AU  - Han GS
AU  - Jeong SG
AU  - Oh MH
AU  - Kim DH
AU  - Kim H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5044.

PMID- 2788873
VI  - 17
DP  - 1989
TI  - LpnI, from Legionella pneumophila, is a neoschiozmer of HaeII.
PG  - 6417
AB  - LpnI is a Type II restriction endonuclease that was previously isolated from Legionella
      pneumophila strain 11 EJ and partially purified (1). Further purification by phosphocellulose
      and DNA-agrose chromatography, with an intermediate 50-75% ammonium sulphate
      concentration/fractionation step gave enzyme sufficiently pure for detailed characterization.
      LpnI cleaves pUC19 DNA at three sites. Double digests of pUC19 DNA with LpnI and either AatII,
      EcoRI, PvuI or RsaI mapped the LpnI cleavage site to approximately 230, 690 and 1090
      nucleotides. These sites lie close to those predicted for HaeII. Double digest between HaeII
      and LpnI on bacteriophage lambda DNA confirmed that these enzymes are isoschizomers (Fig 1a).
AU  - Hamablet L
AU  - Chen GC
AU  - Brown A
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 6417.

PMID- 25377709
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Lysinimicrobium mangrovi NBRC 105856T, Isolated from the Rhizosphere of a Mangrove.
PG  - e01131-14
AB  - Here, we report the draft genome sequence of the only species of the genus Lysinimicrobium,
      Lysinimicrobium mangrovi NBRC 105856(T), isolated from the
      rhizosphere of a mangrove. The first genomic sequence of this genus and species
      presented here will facilitate taxonomical, ecological, and functional studies of
      this rare actinobacterial group.
AU  - Hamada M
AU  - Ichikawa N
AU  - Oguchi A
AU  - Fujita N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01131-14.

PMID- 25883289
VI  - 3
DP  - 2015
TI  - Draft genome sequences of eight type strains of the genus demequina.
PG  - e00281-15
AB  - Here, we report the draft genome sequences of the type strains of Demequina aestuarii,
      Demequina aurantiaca, Demequina flava, Demequina globuliformis,
      Demequina lutea, Demequina oxidasica, Demequina salsinemoris, and Demequina
      sediminicola. The genome sequences presented here will facilitate taxonomical,
      ecological, and functional studies of members of the genus Demequina.
AU  - Hamada M
AU  - Ichikawa N
AU  - Oguchi A
AU  - Komaki H
AU  - Tamura T
AU  - Fujita N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00281-15.

PMID- 26337873
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Shellfish Larval Probiotic Bacillus pumilus RI06-95.
PG  - e00858-15
AB  - Bacillus pumilus RI06-95 is a marine bacterium isolated in Narragansett, Rhode Island, which
      has shown probiotic activity against marine pathogens in larval shellfish. We report the
      genome of B. pumilus RI06-95, which provides insight into the microbe's probiotic ability and
      may be used in future studies of the probiotic mechanism.
AU  - Hamblin M
AU  - Spinard E
AU  - Gomez-Chiarri M
AU  - Nelson DR
AU  - Rowley DC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00858-15.

PMID- 26679588
VI  - 3
DP  - 2015
TI  - Genome Sequence of Acinetobacter baumannii Strain D36, an Antibiotic-Resistant Isolate from Lineage 2 of Global Clone 1.
PG  - e01478-15
AB  - Multiply antibiotic-resistant Acinetobacter baumannii isolate D36 was recovered in Australia
      in 2008 and belongs to a distinct lineage of global clone 1 (GC1).
      Here, we present the complete 4.13 Mbp genome sequence (chromosome plus 4
      plasmids), generated via long read sequencing (PacBio).
AU  - Hamidian M
AU  - Hawkey J
AU  - Holt KE
AU  - Hall RM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01478-15.

PMID- 28860239
VI  - 5
DP  - 2017
TI  - Corrected Genome Sequence of Acinetobacter baumannii Strain AB0057, an Antibiotic-Resistant Isolate from Lineage 1 of Global Clone 1.
PG  - e00836-17
AB  - Extensively antibiotic-resistant Acinetobacter baumannii isolate AB0057 recovered in the
      United States in 2004 was one of the first global clone 1 isolates to be
      completely sequenced. Here, the complete 4.05-Mb genome sequence (chromosome and
      one plasmid) has been revised using Illumina HiSeq data and targeted sequencing
      of PCR products.
AU  - Hamidian M
AU  - Venepally P
AU  - Hall RM
AU  - Adams MD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00836-17.

PMID- 26044417
VI  - 3
DP  - 2015
TI  - Draft genomes of gammaproteobacterial methanotrophs isolated from terrestrial ecosystems.
PG  - e00515-15
AB  - Genome sequences of Methylobacter luteus, Methylobacter whittenburyi, Methylosarcina fibrata,
      Methylomicrobium agile, and Methylovulum miyakonense were generated. The strains represent
      aerobic methanotrophs typically isolated from various terrestrial ecosystems.
AU  - Hamilton R et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00515-15.

PMID- 28684569
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Lactobacillus paracasei DmW181, a Bacterium Isolated from Wild Drosophila.
PG  - e00545-17
AB  - The draft genome sequence of Lactobacillus paracasei DmW181, an anaerobic bacterium isolate
      from wild Drosophila flies, is reported here. Strain DmW181
      possesses genes for sialic acid and mannose metabolism. The assembled genome is
      3,201,429 bp, with 3,454 predicted genes.
AU  - Hammer AJ
AU  - Walters A
AU  - Carroll C
AU  - Newell PD
AU  - Chaston JM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00545-17.

PMID- 29371351
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of a blaCTX-M-1-Harboring Escherichia coli Isolate Recovered from Cattle in Germany.
PG  - e01476-17
AB  - We describe here the whole-genome sequence and basic characteristics of Escherichia coli
      isolate 15-AB01393, recovered from German beef within a national
      monitoring program in 2015. This isolate was identified as an
      extended-spectrum-beta-lactamase-producing E. coli strain of multilocus sequence
      type (MLST) ST58 harboring the antimicrobial resistance genes blaCTX-M-1, mph(A),
      sul2, dfrA5, strA, and strB.
AU  - Hammerl JA
AU  - Irrgang A
AU  - Grobbel M
AU  - Tenhagen BA
AU  - Kasbohrer A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01476-17.

PMID- 21697478
VI  - 85
DP  - 2011
TI  - Campylobacter jejuni Group III Phage CP81 Contains Many T4-Like Genes without Belonging to the T4-Type Phage Group: Implications for the Evolution of T4 Phages.
PG  - 8597-8605
AB  - CP81 is a virulent Campylobacter group III phage whose linear genome
      comprises 132,454 bp. At the nucleotide level, CP81 differs from other
      phages. However, a number of its structural and replication/recombination
      proteins revealed a relationship to the group II Campylobacter phages
      CP220/CPt10 and to T4-type phages. Unlike the T4-related phages, the CP81
      genome does not contain conserved replication and virion modules. Instead,
      the respective genes are scattered throughout the phage genome. Moreover,
      most genes for metabolic enzymes of CP220/CPt10 are lacking in CP81. On
      the other hand, the CP81 genome contains nine similar genes for homing
      endonucleases which may be involved in the attrition of the conserved gene
      order for the virion core genes of T4-type phages. The phage apparently
      possesses an unusual modification of C or G bases. Efficient cleavage of
      its DNA was only achieved with restriction enzymes recognizing pure A/T
      sites. Uncommonly, phenol extraction leads to a significant loss of CP81
      DNA from the aqueous layer, a property not yet described for other phages
      belonging to the T4 superfamily.
AU  - Hammerl JA
AU  - Jackel C
AU  - Reetz J
AU  - Beck S
AU  - Alter T
AU  - Lurz R
AU  - Barretto C
AU  - Brussow H
AU  - Hertwig S
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 2011 85: 8597-8605.

PMID- 22843857
VI  - 86
DP  - 2012
TI  - The Complete Genome Sequence of Bacteriophage CP21 Reveals Modular Shuffling in Campylobacter Group II Phages.
PG  - 8896
AB  - Campylobacter group II phages described so far share a high degree of sequence
      similarity. We report the 182,833-bp genomic sequence of the closely related
      group II phage CP21 and show that it has a completely different genomic
      organization. As in other group II phages, the CP21 genome is composed of large
      modules separated by long DNA repeat regions which obviously trigger
      recombination and modular shuffling.
AU  - Hammerl JA
AU  - Jackel C
AU  - Reetz J
AU  - Hertwig S
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 2012 86: 8896.

PMID- 18055592
VI  - 190
DP  - 2008
TI  - Genetic and functional properties of the self-transmissible Yersinia enterocolitica plasmid pYE854, which mobilizes the virulence plasmid pYV.
PG  - 991-1010
AB  - Yersinia strains frequently harbor plasmids, of which the virulence
      plasmid pYV, indigenous in pathogenic strains, has been thoroughly
      characterized during the last decades. Yet, it has been unknown whether
      the nonconjugative pYV can be transferred by helper plasmids naturally
      occurring in this genus. We have isolated the conjugative plasmids pYE854
      (95.5 kb) and pYE966 (70 kb) from a nonpathogenic and a pathogenic
      Yersinia enterocolitica strain, respectively, and demonstrate that both
      plasmids are able to mobilize pYV. The complete sequence of pYE854 has
      been determined. The transfer proteins and oriT of the plasmid reveal
      similarities to the F factor. However, the pYE854 replicon does not belong
      to the IncF group and is more closely related to a plasmid of
      gram-positive bacteria. Plasmid pYE966 is very similar to pYE854 but lacks
      two DNA regions of the larger plasmid that are dispensable for
      conjugation.
AU  - Hammerl JA
AU  - Klein I
AU  - Lanka E
AU  - Appel B
AU  - Hertwig S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2008 190: 991-1010.

PMID- 26205867
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Klebsiella oxytoca Isolates Originating from a Highly Contaminated Liquid Hand Soap Product.
PG  - e00820-15
AB  - In 2013, contaminated liquid soap was detected by routine microbiological monitoring of
      consumer products through state health authorities. Because of its
      high load of Klebsiella oxytoca, the liquid soap was notified via the European
      Union Rapid Alert System for Dangerous Non-Food Products (EU-RAPEX) and recalled.
      Here, we present two draft genome sequences and a summary of their general
      features.
AU  - Hammerl JA
AU  - Lasch P
AU  - Nitsche A
AU  - Dabrowski PW
AU  - Hahmann H
AU  - Wicke A
AU  - Kleta S
AU  - Dahouk SA
AU  - Dieckmann R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00820-15.

PMID- 2542898
VI  - 17
DP  - 1989
TI  - Characterization of a restriction enzyme from a strain of Neisseria gonorrhoea which recognizes 5'G^CCGGC3', an isoschizomer of NaeI.
PG  - 3320
AB  - A type II restriction enzyme, NgoAIV, has been isolated from a strain of Neisseria gonorrhoea.
      NgoAIV recognizes the palindromic sequence, 5'G^CCGGC3', and cleaves between the first G and
      C residues producing a 4- base 5' extension.
AU  - Hammond AW
AU  - Gerard GF
AU  - Campbell JH
AU  - Chatterjee DK
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 3320.

PMID- 2506530
VI  - 17
DP  - 1989
TI  - Characterization of NgoAIII, an isoschizomer of SstII from a strain of Neisseria gonorrhoea.
PG  - 6750
AB  - Note that this enzyme has been renamed NgoFIII because the strain it is from is
      FA1090 and not WR220, from which the NgoA series of enzymes have been reported.
AU  - Hammond AW
AU  - Gerard GF
AU  - Chatterjee DK
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 6750.

PMID- 1995432
VI  - 97
DP  - 1991
TI  - Cloning the KpnI restriction-modification system in Escherichia coli.
PG  - 97-102
AB  - The genes encoding the KpnI restriction and modification (R-M) system from
      Klebsiella pneumoniae, recognizing the sequence, 5'-GGTAC^C-3', were cloned and
      expressed in Escherichia coli.  Although the restriction endonuclease (ENase)-
      and methyltransferase (MTase)-encoding genes were closely linked, initial
      attempts to clone both genes as a single DNA fragment in a plasmid vector
      resulted in deletions spanning all or part of the gene coding for the ENase.
      Initial protection of the E. coli host with MTase expressed on a plasmid was
      required to stabilize a compatible plasmid carrying both the ENase- and the
      MTase-encoding genes on a single DNA fragment.  However, once established, the
      MTase activity can be supplied in cis to the kpnIR gene, without an extra copy
      of kpnIM.  A chromosomal map was generated localizing the kpnIR and kpnIM genes
      on 1.7-kb and 3.5-kb fragments, respectively.  A final E. coli strain was
      constructed, AH29, which contained two compatible plasmids: an inducible
      plasmid carrying the kpnIR gene which amplifies copy number at elevated
      temperatures and a pBR322 derivative expressing M.KpnI.  This strain produces
      approx. 10 million units of R.KpnI/g of wet-weight cells, which is several
      1000-fold higher than the level of R.KpnI produced by K. pneumoniae.  In
      addition, DNA methylated with M.KpnI in vivo does not appear to be restricted
      by the mcrA, mcrB or mrr systems of E. coli.
AU  - Hammond AW
AU  - Gerard GF
AU  - Chatterjee DK
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1991 97: 97-102.

PMID- 21304637
VI  - 1
DP  - 2009
TI  - Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3).
PG  - 54-62
AB  - Pedobacter heparinus (Payza and Korn 1956) Steyn et al. 1998 comb. nov. is the type species of
      the rapidly growing genus Pedobacter within the family
      Sphingobacteriaceae of the phylum 'Bacteroidetes'. P. heparinus is of interest,
      because it was the first isolated strain shown to grow with heparin as sole
      carbon and nitrogen source and because it produces several enzymes involved in
      the degradation of mucopolysaccharides. All available data about this species are
      based on a sole strain that was isolated from dry soil. Here we describe the
      features of this organism, together with the complete genome sequence, and
      annotation. This is the first report on a complete genome sequence of a member of
      the genus Pedobacter, and the 5,167,383 bp long single replicon genome with its
      4287 protein-coding and 54 RNA genes is part of the Genomic Encyclopedia of
      Bacteria and Archaea project.
AU  - Han C et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2009 1: 54-62.

PMID- 21304661
VI  - 1
DP  - 2009
TI  - Complete genome sequence of Kangiella koreensis type strain (SW-125).
PG  - 226-233
AB  - Kangiella koreensis (Yoon et al. 2004) is the type species of the genus and is of phylogenetic
      interest because of the very isolated location of the genus
      Kangiella in the gammaproteobacterial order Oceanospirillales. K. koreensis
      SW-125(T) is a Gram-negative, non-motile, non-spore-forming bacterium isolated
      from tidal flat sediments at Daepo Beach, Yellow Sea, Korea. Here we describe the
      features of this organism, together with the complete genome sequence, and
      annotation. This is the first completed genome sequence from the genus Kangiella
      and only the fourth genome from the order Oceanospirillales. This 2,852,073 bp
      long single replicon genome with its 2647 protein-coding and 48 RNA genes is part
      of the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Han C et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2009 1: 226-233.

PMID- 22675602
VI  - 6
DP  - 2012
TI  - Complete genome sequence of the sulfur compounds oxidizing chemolithoautotroph Sulfuricurvum kujiense type strain (YK-1(T)).
PG  - 94-103
AB  - Sulfuricurvum kujiense Kodama and Watanabe 2004 is the type species of the monotypic genus
      Sulfuricurvum, which belongs to the family Helicobacteraceae in
      the class Epsilonproteobacteria. The species is of interest because it is
      frequently found in crude oil and oil sands where it utilizes various reduced
      sulfur compounds such as elemental sulfur, sulfide and thiosulfate as electron
      donors. Members of the species do not utilize sugars, organic acids or
      hydrocarbons as carbon and energy sources. This genome sequence represents the
      type strain of the only species in the genus Sulfuricurvum. The genome, which
      consists of a circular chromosome of 2,574,824 bp length and four plasmids of
      118,585 bp, 71,513 bp, 51,014 bp, and 3,421 bp length, respectively, harboring a
      total of 2,879 protein-coding and 61 RNA genes and is a part of the Genomic
      Encyclopedia of Bacteria and Archaea project.
AU  - Han C et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 6: 94-103.

PMID- 21304738
VI  - 3
DP  - 2010
TI  - Complete genome sequence of Thermaerobacter marianensis type strain (7p75a).
PG  - 337-345
AB  - Thermaerobacter marianensis Takai et al. 1999 is the type species of the genus
      Thermaerobacter, which belongs to the Clostridiales family Incertae Sedis XVII.
      The species is of special interest because T. marianensis is an aerobic,
      thermophilic marine bacterium, originally isolated from the deepest part in the
      western Pacific Ocean (Mariana Trench) at the depth of 10.897m. Interestingly,
      the taxonomic status of the genus has not been clarified until now. The genus
      Thermaerobacter may represent a very deep group within the Firmicutes or
      potentially a novel phylum. The 2,844,696 bp long genome with its 2,375
      protein-coding and 60 RNA genes consists of one circular chromosome and is a part
      of the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Han C et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 3: 337-345.

PMID- 21886863
VI  - 4
DP  - 2011
TI  - Complete genome sequence of Treponema succinifaciens type strain (6091).
PG  - 361-370
AB  - Treponema succinifaciens Cwyk and Canale-Parola 1981 is of interest because this  strictly
      anaerobic, apathogenic member of the genus Treponema oxidizes
      carbohydrates and couples the Embden-Meyerhof pathway via activity of a
      pyruvate-formate lyase to the production of acetyl-coenzyme A and formate. This
      feature separates this species from most other anaerobic spirochetes. The genome
      of T. succinifaciens 6091(T) is only the second completed and published type
      strain genome from the genus Treponema in the family Spirochaetaceae. The
      2,897,425 bp long genome with one plasmid harbors 2,723 protein-coding and 63 RNA
      genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Han C et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 4: 361-370.

PMID- 21886864
VI  - 4
DP  - 2011
TI  - Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyR).
PG  - 371-380
AB  - Syntrophobotulus glycolicus Friedrich et al. 1996 is currently the only member of the genus
      Syntrophobotulus within the family Peptococcaceae. The species is of
      interest because of its isolated phylogenetic location in the genome-sequenced
      fraction of tree of life. When grown in pure culture with glyoxylate as carbon
      source the organism utilizes glyoxylate through fermentative oxidation, whereas,
      when grown in syntrophic co-culture with homoacetogenic or methanogenic bacteria,
      it is able to oxidize glycolate to carbon dioxide and hydrogen. No other organic
      or inorganic carbon source is utilized by S. glycolicus. The subdivision of the
      family Peptococcaceae into genera does not reflect the natural relationships,
      particularly regarding the genera most closely related to Syntrophobotulus. Both
      Desulfotomaculum and Pelotomaculum are paraphyletic assemblages, and the
      taxonomic classification is in significant conflict with the 16S rRNA data. S.
      glycolicus is already the ninth member of the family Peptococcaceae with a
      completely sequenced and publicly available genome. The 3,406,739 bp long genome
      with its 3,370 protein-coding and 69 RNA genes is a part of the Genomic
      Encyclopedia of Bacteria and Archaea project.
AU  - Han C et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 4: 371-380.

PMID- 16621833
VI  - 188
DP  - 2006
TI  - Pathogenomic Sequence Analysis of Bacillus cereus and Bacillus thuringiensis Isolates Closely Related to Bacillus anthracis.
PG  - 3382-3390
AB  - Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis are closely related
      gram-positive, spore-forming bacteria of the B. cereus
      sensu lato group. While independently derived strains of B. anthracis
      reveal conspicuous sequence homogeneity, environmental isolates of B.
      cereus and B. thuringiensis exhibit extensive genetic diversity. Here we
      report the sequencing and comparative analysis of the genomes of two
      members of the B. cereus group, B. thuringiensis 97-27 subsp. konkukian
      serotype H34, isolated from a necrotic human wound, and B. cereus E33L,
      which was isolated from a swab of a zebra carcass in Namibia. These two
      strains, when analyzed by amplified fragment length polymorphism within a
      collection of over 300 of B. cereus, B. thuringiensis, and B. anthracis
      isolates, appear closely related to B. anthracis. The B. cereus E33L
      isolate appears to be the nearest relative to B. anthracis identified thus
      far. Whole-genome sequencing of B. thuringiensis 97-27and B. cereus E33L
      was undertaken to identify shared and unique genes among these isolates in
      comparison to the genomes of pathogenic strains B. anthracis Ames and B.
      cereus G9241 and nonpathogenic strains B. cereus ATCC 10987 and B. cereus
      ATCC 14579. Comparison of these genomes revealed differences in terms of
      virulence, metabolic competence, structural components, and regulatory
      mechanisms.
AU  - Han CS et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2006 188: 3382-3390.

PMID- 21685284
VI  - 193
DP  - 2011
TI  - Draft Genome Sequence of Methylophaga aminisulfidivorans MPT.
PG  - 4265
AB  - Methylophaga aminisulfidivorans MP(T) is a restricted facultatively marine methylotrophic
      bacterium that grows on methanol, methylated amines,
      dimethyl sulfide, and dimethyl sulfoxide. Here we present the high-quality
      draft genome sequence of M. aminisulfidivorans MP(T) (KCTC 12909(T) = JCM
      14647(T)), consisting of a chromosome (3,092,085 bp) and a plasmid (16,875
      bp).
AU  - Han GH
AU  - Kim W
AU  - Chun J
AU  - Kim SW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4265.

PMID- 28935747
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Mycoplasma hyopneumoniae Strain KM014, a Clinical Isolate from South Korea.
PG  - e01012-17
AB  - Mycoplasma hyopneumoniae is the etiological agent of swine enzootic pneumonia, resulting in
      considerable economic losses in the swine industry. A few genome
      sequences of M. hyopneumoniae have been reported to date, implying that
      additional genome data are needed for further genetic studies. Here, we present
      the annotated genome sequence of M. hyopneumoniae strain KM014.
AU  - Han J
AU  - Park BS
AU  - Shin DJ
AU  - Song SY
AU  - Jeong YJ
AU  - Lee N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01012-17.

PMID- 22843593
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of the Metabolically Versatile Halophilic Archaeon Haloferax mediterranei, a Poly(3-Hydroxybutyrate-co-3-Hydroxyvalerate) Producer.
PG  - 4463-4464
AB  - Haloferax mediterranei, an extremely halophilic archaeon, has shown promise for production of
      poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) from unrelated
      cheap carbon sources. Here we report the complete genome (3,904,707 bp) of H.
      mediterranei CGMCC 1.2087, consisting of one chromosome and three megaplasmids.
AU  - Han J
AU  - Zhang F
AU  - Hou J
AU  - Liu X
AU  - Li M
AU  - Liu H
AU  - Cai L
AU  - Zhang B
AU  - Chen Y
AU  - Zhou J
AU  - Hu S
AU  - Xiang H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4463-4464.

PMID- 24330456
VI  - 55
DP  - 2013
TI  - CPRMethicillin resistant coagulase-negative staphylococci isolated from South Korean ducks exhibiting tremor.
PG  - 88
AB  - BACKGROUND: We describe coagulase-negative staphylococci (CoNS) isolates
      collected from ducklings exhibiting tremor in South Korea over the period of 2010
      to 2011. Screening of antimicrobial susceptibility and analysis of SCCmec
      elements of CoNS were also investigated. RESULTS: Staphylococcus cohnii was the
      most frequent staphylococcus (9 isolates) and S. sciuri (4 isolates), S. lentus
      (3 isolate), S. simulans (1 isolate) and S. epidermidis (1 isolate) were also
      detected. Among the 15 antimicrobials tested in this study, resistance against
      oxacillin (15 isolates, 83.3%) was most frequently observed, but only one isolate
      (SNUDS-1) possessed mecA. This isolate was shown to possess SCCmec type III; the
      type 3 ccr complex and the class A mec complex. CONCLUSIONS: Based on these
      results, isolate SNUDS-1 was shown to possess SCCmec type III; the type 3 ccr
      complex and the class A mec complex. Although the SCCmec type III is not
      predominant in human, MR-CoNS (Methicillin resistance Coagulase-negative
      staphylococci) in food animals should be monitored to prevent the dissemination
      of antimicrobial resistance genes and resistant pathogens to the community.
AU  - Han JE
AU  - Hwang SY
AU  - Kim JH
AU  - Shin SP
AU  - Jun JW
AU  - Chai JY
AU  - Park YH
AU  - Park SC
PT  - Journal Article
TA  - Acta Vet. Scand.
JT  - Acta Vet. Scand.
SO  - Acta Vet. Scand. 2013 55: 88.

PMID- 23405367
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of a Clinical Isolate, Aeromonas hydrophila SNUFPC-A8, from a Moribund Cherry Salmon (Oncorhynchus masou masou).
PG  - e00133-12
AB  - We present the genome of a clinical isolate, Aeromonas hydrophila SNUFPC-A8, from a moribund
      cherry salmon. The completed draft genome of this strain shows high
      sequence homology to the reference strain A. hydrophila ATCC 7966 (NC008570.1)
      and known plasmids pAsa2 and pAAk1 from other Aeromonas species (NC004925.1 and
      NC019014.1).
AU  - Han JE
AU  - Kim JH
AU  - Choresca C
AU  - Shin SP
AU  - Jun JW
AU  - Park SC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00133-12.

PMID- 24092786
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Aeromonas salmonicida subsp. achromogenes AS03, an Atypical Strain Isolated from Crucian Carp (Carassius carassius) in the Republic   of Korea.
PG  - e00791-13
AB  - We present the draft genome sequence of Aeromonas salmonicida subsp. achromogenes strain AS03,
      an atypical A. salmonicida strain that causes erythrodermatitis in
      crucian carp (Carassius carassius). This is the first genome sequence report of
      A. salmonicida subsp. achromogenes, one of the four subspecies of atypical A.
      salmonicida.
AU  - Han JE
AU  - Kim JH
AU  - Shin SP
AU  - Jun JW
AU  - Chai JY
AU  - Park SC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00791-13.

PMID- 21183664
VI  - 193
DP  - 2010
TI  - Complete genome sequence of the metabolically versatile plant growth-promoting endophyte, Variovorax paradoxus S110.
PG  - 1183-1190
AB  - Variovorax paradoxus is a microorganism of special interest due to its diverse metabolic
      capabilities, including the biodegradation of both
      biogenic compounds and anthropogenic contaminants. V. paradoxus also
      engages in mutually beneficial interactions with both bacteria and plants.
      The complete genome sequence of V. paradoxus S110 is composed of 6,754,997
      base pairs with 6,279 predicted protein-coding sequences within two
      circular chromosomes. The genomic analysis has revealed multiple metabolic
      features for autotrophic and heterotrophic lifestyles. These metabolic
      diversities enable independent survival as well as a symbiotic lifestyle.
      Consequently, S110 appears to have evolved into a superbly adaptable
      microorganism, able to survive in ever-changing environmental conditions.
      Based on our findings, we suggest V. paradoxus S110 as a potential
      candidate for agrobiotechnological applications, such as biofertilizer and
      biopesticide. Because it has many associations with other biota, it is
      also suited to serve as an additional model system for studies of
      microbe-plant and microbe-microbe interactions.
AU  - Han JI
AU  - Choi HK
AU  - Lee SW
AU  - Orwin PM
AU  - Kim J
AU  - Laroe SL
AU  - Kim TG
AU  - O'Neil J
AU  - Leadbetter JR
AU  - Lee SY
AU  - Hur CG
AU  - Spain JC
AU  - Ovchinnikova G
AU  - Goodwin L
AU  - Han C
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 193: 1183-1190.

PMID- 24158554
VI  - 1
DP  - 2013
TI  - Genome of the Root-Associated Plant Growth-Promoting Bacterium Variovorax paradoxus Strain EPS.
PG  - e00843-13
AB  - Variovorax paradoxus is a ubiquitous betaproteobacterium involved in plant growth promotion,
      the degradation of xenobiotics, and quorum-quenching activity. The
      genome of V. paradoxus strain EPS consists of a single circular chromosome of
      6,550,056 bp, with a 66.48% G+C content.
AU  - Han JI
AU  - Spain JC
AU  - Leadbetter JR
AU  - Ovchinnikova G
AU  - Goodwin LA
AU  - Han CS
AU  - Woyke T
AU  - Davenport KW
AU  - Orwin PM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00843-13.

PMID- 28254991
VI  - 5
DP  - 2017
TI  - Genome Sequence of Delftia acidovorans HK171, a Nematicidal Bacterium Isolated from Tomato Roots.
PG  - e01746-16
AB  - Delftia acidovorans strain HK171, isolated from tomato roots, exhibited nematicidal activity
      against Meloidogyne incognita Here, we present the genome
      sequence of D. acidovorans strain HK171, which consists of one circular
      chromosome of 6,430,384 bp, with 66.9% G+C content.
AU  - Han JW
AU  - Oh M
AU  - Choi GJ
AU  - Kim H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01746-16.

PMID- 23812535
VI  - 3
DP  - 2013
TI  - Extraordinary expansion of a Sorangium cellulosum genome from an alkaline milieu.
PG  - 2101
AB  - Complex environmental conditions can significantly affect bacterial genome size
      by unknown mechanisms. The So0157-2 strain of Sorangium cellulosum is an
      alkaline-adaptive epothilone producer that grows across a wide pH range. Here, we
      show that the genome of this strain is 14,782,125 base pairs, 1.75-megabases
      larger than the largest bacterial genome from S. cellulosum reported previously.
      The total 11,599 coding sequences (CDSs) include massive duplications and
      horizontally transferred genes, regulated by lots of protein kinases, sigma
      factors and related transcriptional regulation co-factors, providing the So0157-2
      strain abundant resources and flexibility for ecological adaptation. The
      comparative transcriptomics approach, which detected 90.7% of the total CDSs, not
      only demonstrates complex expression patterns under varying environmental
      conditions but also suggests an alkaline-improved pathway of the insertion and
      duplication, which has been genetically testified, in this strain. These results
      provide insights into and a paradigm for how environmental conditions can affect
      bacterial genome expansion.
AU  - Han K
AU  - Li ZF
AU  - Peng R
AU  - Zhu LP
AU  - Zhou T
AU  - Wang LG
AU  - Li SG
AU  - Zhang XB
AU  - Hu W
AU  - Wu ZH
AU  - Qin N
AU  - Li YZ
PT  - Journal Article
TA  - Sci. Rep.
JT  - Sci. Rep.
SO  - Sci. Rep. 2013 3: 2101.

PMID- 26473025
VI  - 10
DP  - 2015
TI  - Complete genome sequence of Mycobacterium tuberculosis K from a Korean high school outbreak, belonging to the Beijing family.
PG  - 78
AB  - Mycobacterium tuberculosis K, a member of the Beijing family, was first identified in 1999 as
      the most prevalent genotype in South Korea among clinical
      isolates of M. tuberculosis from high school outbreaks. M. tuberculosis K is an
      aerobic, non-motile, Gram-positive, and non-spore-forming rod-shaped bacillus. A
      transmission electron microscopy analysis displayed an abundance of lipid bodies
      in the cytosol. The genome of the M. tuberculosis K strain was sequenced using
      two independent sequencing methods (Sanger and Illumina). Here, we present the
      genomic features of the 4,385,518-bp-long complete genome sequence of M.
      tuberculosis K (one chromosome, no plasmid, and 65.59 % G + C content) and its
      annotation, which consists of 4194 genes (3447 genes with predicted functions),
      48 RNA genes (3 rRNA and 45 tRNA) and 261 genes with peptide signals.
AU  - Han SJ
AU  - Song T
AU  - Cho YJ
AU  - Kim JS
AU  - Choi SY
AU  - Bang HE
AU  - Chun J
AU  - Bai GH
AU  - Cho SN
AU  - Shin SJ
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 78.

PMID- 25564526
VI  - 43
DP  - 2015
TI  - Recognition and cleavage of 5-methylcytosine DNA by bacterial SRA-HNH proteins.
PG  - 1147-1159
AB  - SET and RING-finger-associated (SRA) domain is involved in establishment and maintenance of
      DNA methylation in eukaryotes. Proteins containing SRA domains
      exist in mammals, plants, even microorganisms. It has been established that
      mammalian SRA domain recognizes 5-methylcytosine (5mC) through a base-flipping
      mechanism. Here, we identified and characterized two SRA domain-containing
      proteins with the common domain architecture of N-terminal SRA domain and
      C-terminal HNH nuclease domain, Sco5333 from Streptomyces coelicolor and Tbis1
      from Thermobispora bispora. Both sco5333 and tbis1 cannot establish in methylated
      Escherichia coli hosts (dcm(+)), and this in vivo toxicity requires both SRA and
      HNH domain. Purified Sco5333 and Tbis1 displayed weak DNA cleavage activity in
      the presence of Mg(2+), Mn(2+) and Co(2+) and the cleavage activity was
      suppressed by Zn(2+). Both Sco5333 and Tbis1 bind to 5mC-containing DNA in all
      sequence contexts and have at least a preference of 100 folds in binding affinity
      for methylated DNA over non-methylated one. We suggest that linkage of
      methyl-specific SRA domain and weakly active HNH domain may represent a universal
      mechanism in competing alien methylated DNA but to maximum extent minimizing
      damage to its own chromosome.
AU  - Han T
AU  - Yamada-Mabuchi M
AU  - Zhao G
AU  - Li L
AU  - Liu G
AU  - Ou HY
AU  - Deng Z
AU  - Zheng Y
AU  - He X
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2015 43: 1147-1159.

PMID- 22965094
VI  - 194
DP  - 2012
TI  - Genome Sequence of Streptomyces auratus Strain AGR0001, a Phoslactomycin-Producing Actinomycete.
PG  - 5472-5473
AB  - Streptomyces auratus strain AGR0001 produces neophoslactomycin A, a novel analog  of
      phoslactomycin that possesses potent activity against some phytopathogenic
      fungi. Here, the draft genome sequence of S. auratus strain AGR0001 is presented,
      which would provide insight into the biosynthetic mechanism of neophoslactomycin
      A.
AU  - Han X
AU  - Li M
AU  - Ding Z
AU  - Zhao J
AU  - Ji K
AU  - Wen M
AU  - Lu T
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5472-5473.

PMID- 25999555
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of New Leprosy Agent Mycobacterium lepromatosis.
PG  - e00513-15
AB  - Mycobacterium lepromatosis is a newly discovered cause of leprosy. Here, we present a
      near-complete genome of M. lepromatosis from strain FJ924 obtained from
      a patient who died of leprosy. The genome contained 3,215,823 nucleotides and
      matched ~87% with the Mycobacterium leprae genome. This genome is likely the
      smallest of all mycobacterial genomes known to date.
AU  - Han XY
AU  - Mistry NA
AU  - Thompson EJ
AU  - Tang HL
AU  - Khanna K
AU  - Zhang L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00513-15.

PMID- 28798171
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Plant Growth-Promoting Bacterium Pseudomonas sp. SCPG-7, Isolated from Saline Soil.
PG  - e00702-17
AB  - Pseudomonas sp. SCPG-7 was isolated from saline soil. The strain can increase the germination
      rate of cotton seeds and promote the growth of cotton seedlings under
      salt stress conditions. The genome is 6,256,198 bp long, containing 5,672
      predicted open reading frames.
AU  - Han Y
AU  - Dai B
AU  - Zhou Y
AU  - Wu Z
AU  - Ye BC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00702-17.

PMID- 
VI  - 0
DP  - 1986
TI  - Mechanisms of DNA Transformation:  Restrictionlike effects in Transformation in Escherichia coli and Salmonella typhimurium.
PG  - 1-7
AB  - The introduction of naked DNA into Escherichia coli was first demonstrated by
      Mandel and Higa, who observed that incubation of a suspension of E. coli  cells
      and bacteriophage lambda DNA in a solution of CaCl2 at 0C resulted in the
      subsequent appearance of infectious centers.  They further showed that a heat
      pulse, in which the mixture of cells and DNA was briefly incubated at 42C,
      chilled on ice, and then diluted into growth medium, improved the frequency of
      transfection.  The general applicability of these conditions to DNA transfer
      was demonstrated by their use to effect plasmid transformation, in which
      circular plasmids carrying antibiotic resistance genes were stably established
      as replicating episomes; genetic transformation, in which linear E. coli DNA
      was transformed into auxotrophic strains to restore the mutant alleles; and
      transfection of other bacteriophages.  These observations proved to be
      applicable to DNA transformation of Salmonella typhimurium, suggesting that
      induction of the artificial or natural ability to take up DNA reflected general
      strutural or physiological features of these two closely related organisms.
      Most subsequent studies of DNA transformation have employed plasmids carrying
      antibiotic resistance genes, scoring transformation by the appearance of
      drug-resistant colonies under selective conditions.  Primary attention has been
      focused on E. coli, but it appears the observations are, in general, applicable
      to S. typhimurium as well.  Transformation with linear DNAs generally shows the
      same response to conditions, given the genetic distinction that linear DNA
      (chromosomal or bacteriophage) will most efficiently transform strains
      deficient in recBC nuclease, due to its degradative activity on the ends of DNA
      molecules.
AU  - Hanahan D
PT  - Journal Article
TA  - Escherichia coli and Salmonella typhimurium: Cellular and molecular biology.
JT  - Escherichia coli and Salmonella typhimurium: Cellular and molecular biology.
SO  - Escherichia coli and Salmonella typhimurium: Cellular and molecular biology. 1986 0: 1-7.

PMID- 24723717
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Growth-Promoting Endophyte Paenibacillus sp. P22, Isolated from Populus.
PG  - e00276-14
AB  - Paenibacillus sp. P22 is a Gram-negative facultative anaerobic endospore-forming  bacterium
      isolated from poplar hybrid 741 (female symbol[Populus alba x (P. davidiana + P. simonii) x P.
      tomentosa]). This bacterium shows strong similarities to Paenibacillus humicus, and important
      growth-promoting effects on in vitro grown explants of poplar hybrid 741 have been described.
AU  - Hanak AM
AU  - Nagler M
AU  - Weinmaier T
AU  - Sun X
AU  - Fragner L
AU  - Schwab C
AU  - Rattei T
AU  - Ulrich K
AU  - Ewald D
AU  - Engel M
AU  - Schloter M
AU  - Bittner R
AU  - Schleper C
AU  - Weckwerth W
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00276-14.

PMID- 11547565
VI  - 74
DP  - 2001
TI  - Inhibition of restriction enzyme's DNA sequence recognition by PUVA treatment.
PG  - 269-273
AB  - Applying various restriction enzymes on a specially designed 1.5 kb DNA fragment revealed that
      the inhibitory effects of psoralens + UVA
      irradiation (PUVA) treatment on restriction endonuclease activities are
      caused by recognition inhibition. In this study restriction enzymes
      that have a 5'-TpA sequence at the cleaving site (KpnI, XbaI, PmeI and
      DraI), and the noncleaving site (PacI) in recognition sites, or have
      two 5'-TpA sequences at the recognition site, and a nonspecific
      sequence between the recognition and the cleaving sites (BciVI), were
      inhibited by PUVA treatment. Most of the other restriction enzymes used
      in this study, which do not have a 5'-TpA sequence at their restriction
      site, were not inhibited by PUVA treatment, although a 5'-TpA sequence
      is located adjacent (SmaI) or very close (BamHI, SacI and PstI) to the
      recognition and cleaving sites for these enzymes. Because SphI, which
      does not have 5'-TpA at its restriction site, was strongly inhibited by
      PUVA treatment, the 5'-CpA sequence is suggested to be a new binding
      site of psoralens after UVA irradiation.
AU  - Hanawa F
AU  - Okamoto M
AU  - Towers GHN
PT  - Journal Article
TA  - Photochem. Photobiol.
JT  - Photochem. Photobiol.
SO  - Photochem. Photobiol. 2001 74: 269-273.

PMID- 2527357
VI  - 17
DP  - 1989
TI  - Nucleotide sequence of the dcm locus of Escherichia coli K12.
PG  - 5844
AB  - None
AU  - Hanck T
AU  - Gerwin N
AU  - Fritz H-J
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 5844.

PMID- 8441638
VI  - 21
DP  - 1993
TI  - Sequence-specific and mechanism-based crosslinking of Dcm DNA cytosine-C5 methyltransferase of E.coli K-12 to synthetic oligonucleotides containing 5-fluoro-2'-deoxycytidine.
PG  - 303-309
AB  - The product of the dcm gene is the only DNA cytosine-C5 methyltransferase of Escherichia coli
      K-12; it catalyses transfer of a methyl group from S-adenosyl methionine (SAM) to the C-5
      position of the inner cytosine residue of the cognate sequence CCA/TGG. Sequence-specific,
      covalent crosslinking of the enzyme to synthetic oligonucleotides containing
      5-fluoro-2'-deoxycytidine is demonstrated. This reaction is abolished if serine replaces the
      cysteine at residue #177 of the enzyme. These results lend strong support to a catalytic
      mechanism in which an enzyme sulfhydryl group undergoes Michael addition to the C5-C6 double
      bond, thus activating position C-5 of the substrate DNA cytosine residue for electrophilic
      attack by the methyl donor SAM. The enzyme is capable of self-methylation in a DNA-independent
      reaction requiring SAM and the presence of cysteine at position #177.
AU  - Hanck T
AU  - Schmidt S
AU  - Fritz HJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 303-309.

PMID- 8346027
VI  - 21
DP  - 1993
TI  - Synthesis and properties of oligodeoxynucleotides containing the analogue 2'-deoxy-4'-thiothymidine.
PG  - 3485-3491
AB  - The 2'-deoxythymidine analogue 2'-deoxy-4'thiothymidine has been incorporated, using
      standard methodology, into a series of dodecadeoxynucleotides containing the EcoRV restriction
      endonuclease recognition site (GATATC). The stability of these oligodeoxynucleotides and their
      ability to act as substrates for the restriction endonuclease and associated methylase have
      been compared with a normal unmodified oligodeoxynucleotide. No problems were encountered in
      the synthesis despite the presence of a potentially oxidisable sulfur atom in the sugar ring.
      The analogue had very little effect on the melting temperature of the self-complementary
      oligodeoxynucleotides so synthesised and all had a CD spectrum compatible with a B-DNA
      structure. The oligodeoxynucleotide containing one analogue in each strand within the
      recognition site, adjacent to the bond to be cleaved (i.e. GAXATC, where X is
      2'-deoxy-4'-thiothymidine), was neither a substrate for the endonuclease nor was recognized
      by the associated methylase. When still within the recognition hexanucleotide but two further
      residues removed from the site of cleavage (i.e. GATAXC), the oligodeoxynucleotide was a poor
      substrate for both the endonuclease and methylase. Binding of the oligodeoxynucleotide to the
      endonuclease was unaffected but the kcat value was only 0.03% of the value obtained for the
      parent oligodeoxynucleotide. These results show that the incorporation of
      2'-deoxy-4'-thionucleosides into synthetic oligodeoxynucleotides may shed light on subtle
      interations between proteins and their normal substrates and may also show why
      2'-deoxy-4'-thiothymidine itself is so toxic in cell culture.
AU  - Hancox EL
AU  - Connolly BA
AU  - Walker RT
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 3485-3491.

PMID- 9200709
VI  - 36
DP  - 1997
TI  - Kinetic analysis of a mutational hot spot in the EcoRV restriction endonuclease.
PG  - 7577-7585
AB  - The EcoRV endonuclease contacts the minor groove of DNA through a peptide loop encompassing
      residues 67-72.  This loop adapts to distorted DNA in the specific complex and to regular DNA
      in the nonspecific complex.  Random mutagenesis had previously identified glutamine 69 as the
      key component of the loop and this study reports on mutants with glutamate (Q69E), lysine
      (Q69K), or leucine (Q69L) at this position.  The mutants bound DNA specifically at the EcoRV
      recognition site in the presence of Ca2+, in the same manner as wild-type EcoRV.  In the
      absence of divalent metals, Q69K and Q69L showed the same nonspecific binding as native EcoRV
      while Q69E failed to bind DNA.  Glutamate at position 69 presumably repels nonspecific DNA
      whilst allowing the adaptations to specific DNA.  Both Q69E and Q69K had severely impaired DNA
      cleavage activities, while Q69L had a steady-state kcat within an order of magnitude of
      wild-type EcoRV though its primary product was nicked DNA, in contrast to double strand breaks
      by wild-type EcoRV.  The activity of Q69L required higher concentrations of Mg2+ than the
      wild-type and showed a sigmoidal dependence upon the Mg2+ concentration, indicating two metal
      ions per strand scission.  Transient kinetics on Q69L gave lower rate constants for
      phosphodiester hydrolysis than wild-type EcoRV and its reaction also involved a slow
      conformational change preceding DNA cleavage that had no equivalent with the wild-type.  Gln69
      in EcoRV thus plays key roles in the adjustments of the protein to varied DNA structures and
      in the alignment of the catalytic functions for DNA cleavage.
AU  - Hancox EL
AU  - Halford SE
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1997 36: 7577-7585.

PMID- 19389761
VI  - 155
DP  - 2009
TI  - Contribution of RecFOR machinery of homologous recombination to cell survival after loss of a restriction-modification gene complex.
PG  - 2320-2332
AB  - Loss of a type II restriction-modification gene complex, such as EcoRI, from a bacterial cell
      leads to death of its descendant cells through
      attack by residual restriction enzyme molecules on under-methylated target
      sites of newly synthesized chromosomes. Through such post-segregational
      host killing, these gene complexes force their maintenance on their host
      cells. This finding led to re-discovery of type II
      restriction-modification systems as selfish mobile elements. The host
      prokaryote cells were found to cope with such attacks through a variety of
      means. RecBCD pathway of homologous recombination in Escherichia coli
      repairs the lethal lesions on the chromosome while it destroys restricted
      non-self DNA. The recBCD homologs, however, appears very limited in
      distribution among bacterial genomes, while homologs of RecFOR proteins
      responsible for another pathway are widespread in eubacteria, just as the
      restriction-modification systems are. In the present work, therefore, we
      examined possible contribution of RecFOR pathway in cell survival after
      loss of a restriction-modification gene complex. A recF mutation reduced
      the survival in otherwise rec-positive background and, more severely, in a
      recBC sbcBC background. We also found that its effect is prominent in the
      presence of specific non-null mutant forms of RecBCD enzyme: the
      resistance to killing seen with recC1002, recC1004, recC2145 and recB2154
      is much reduced to the level of a null recBC allele when combined with a
      recF, recO or recR mutant allele. Such resistance was also dependent on
      RecJ and RecQ functions. UV resistance of these non-null recBCD mutants is
      also decreased by recF, recJ or recQ mutation. These results demonstrate
      that RecFOR pathway of recombination can greatly contribute to resistance
      to restriction-modification-mediated host killing depending on genetic
      backgrounds.
AU  - Handa N
AU  - Ichige A
AU  - Kobayashi I
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2009 155: 2320-2332.

PMID- 10735865
VI  - 182
DP  - 2000
TI  - Cellular responses to postsegregational killing by restriction-modification genes.
PG  - 2218-2229
AB  - Plasmids that carry one of several type II restriction modification gene complexes are known
      to show increased stability. The underlying mechanism was proposed to be the lethal attack by
      a restriction enzyme at chromosomal recognition sites in cells that had lost the restriction
      modification gene complex. In order to examine bacterial responses to this postsegregational
      cell killing, we analyzed the cellular processes following loss of the EcoRI restriction
      modification gene complex carried by a temperature-sensitive plasmid in an Escherichia coli
      strain that is wild type with respect to DNA repair. A shift to the nonpermissive temperature
      blocked plasmid replication, reduced the increase in viable cell counts and resulted in loss
      of cell viability. Many cells formed long filaments, some of which were multinucleated and
      others anucleated. In a mutant defective in RecBCD exonuclease/recombinase, these cell death
      symptoms were more severe and cleaved chromosomes accumulated. Growth inhibition was also more
      severe in recA, ruvAB, ruvC, recG, and recN mutants. The cells induced the SOS response in a
      RecBC-dependent manner. These observations strongly suggest that bacterial cells die as a
      result of chromosome cleavage after loss of a restriction modification gene complex and that
      the bacterial RecBCD/RecA machinery helps the cells to survive, at least to some extent, by
      repairing the cleaved chromosomes. These and previous results have led us to hypothesize that
      the RecBCD/Chi/RecA system serves to destroy restricted "nonself" DNA and repair restricted
      "self" DNA.
AU  - Handa N
AU  - Ichige A
AU  - Kusano K
AU  - Kobayashi I
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2000 182: 2218-2229.

PMID- 10572308
VI  - 81
DP  - 1999
TI  - Post-segregational killing by restriction modification gene complexes: Observations of individual cell deaths.
PG  - 931-938
AB  - Through a mechanism known as post-segregational killing, several plasmids mediate their stable
      maintenance by carrying genes that kill plasmid-free segregant cells. We demonstrated earlier
      that loss of plasmids carrying type II restriction modification (RM) gene complexes inhibits
      the propagation of a cell population and causes chromosome breakage. We now show the
      morphology of individual cells changes following loss of thermosensitive plasmids carrying
      EcoRI RM or PaeR7I RM after a shift to a non-permissive temperature. After a lag, many cells
      formed long filaments containing multiple nuclei as detected by DAPI staining. Several hours
      after the shift, many of these long filaments lacked nuclei. Fragmentation of chromosomal DNA
      down to 5 kb was detected by electrophoresis. These observations lend strong support to the
      concept of post-segregational cell killing by type II restriction modification gene complexes.
AU  - Handa N
AU  - Kobayashi I
PT  - Journal Article
TA  - Biochimie
JT  - Biochimie
SO  - Biochimie 1999 81: 931-938.

PMID- 16237019
VI  - 187
DP  - 2005
TI  - Type III restriction is alleviated by bacteriophage (RecE) homologous recombination function but enhanced by bacterial (RecBCD) function.
PG  - 7362-7373
AB  - Previous works have demonstrated that DNA breaks generated by restriction enzymes stimulate,
      and are repaired by, homologous recombination with an intact, homologous DNA region through
      the function of lambdoid bacteriophages lambda and Rac. In the present work, we examined the
      effect of bacteriophage functions, expressed in bacterial cells, on restriction of an
      infecting tester phage in a simple plaque formation assay. The efficiency of plaque formation
      on an Escherichia coli host carrying EcoRI, a type II restriction system, is not increased by
      the presence of Rac prophage-presumably because, under the single-infection conditions of the
      plaque assay, a broken phage DNA cannot find a homologue with which to recombine. To our
      surprise, however, we found that the efficiency of plaque formation in the presence of a type
      III restriction system, EcoP1 or EcoP15, is increased by the bacteriophage-mediated homologous
      recombination functions recE and recT of Rac prophage. This type III restriction alleviation
      does not depend on lar on Rac, unlike type I restriction alleviation. On the other hand,
      bacterial RecBCD-homologous recombination function enhances type III restriction. These
      results led us to hypothesize that the action of type III restriction enzymes takes place on
      replicated or replicating DNA in vivo and leaves daughter DNAs with breaks at nonallelic
      sites, that bacteriophage-mediated homologous recombination reconstitutes an intact DNA from
      them, and that RecBCD exonuclease blocks this repair by degradation from the restriction
      breaks.
AU  - Handa N
AU  - Kobayashi I
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2005 187: 7362-7373.

PMID- 
VI  - 75
DP  - 2000
TI  - Experimental genome evolution: Large-scale genome rearrangements associated with resistance of a chromosomal restriction-modification gene complex to replacement.
PG  - 381
AB  - Type II restriction enzymes are paired with modification enzymes that protect type II
      restriction sites from cleavage by methylating them.  A plasmid carrying a type II restriction
      modification gene complex is not easily replaced by an incompatible plasmid because loss of
      the former leads to cell death through chromosome cleavage.  In the present work, we looked to
      see if a chromosomally located restriction modification gene complex could be replaced by a
      homologous stretch of DNA.  We tried to replace the PaeR7I gene complex on the Escherichia
      coli chromosome by transducing a homologous stretch of PaeR7I-modified DNA.  The replacement
      efficiency of the restriction modification complex was lower than expected.  Some of the
      resulting recombinant clones retained the recipient restriction modification gene complex as
      well as the homologous DNA (donor allele), and slowly lost the donor allele in the absence of
      selection.  Analysis of their genome-wide rearrangements by Southern hybridization, inverse
      PCR, and sequence determination demonstrated the occurrence of unequal homologous
      recombination between copies of the transposon IS3.  It was strongly suggested that multiple
      rounds of unequal IS3-IS3 recombination caused large-scale duplication and inversion of the
      chromosome, and that only one of the duplicated copies of the recipient PaeR7I was replaced.
AU  - Handa N
AU  - Naito Y
AU  - Kobayashi I
PT  - Journal Article
TA  - Genes Genet. Syst.
JT  - Genes Genet. Syst.
SO  - Genes Genet. Syst. 2000 75: 381.

PMID- 11401700
VI  - 40
DP  - 2001
TI  - Experimental genome evolution: large-scale genome rearrangements associated with resistance to replacement of a chromosomal restriction-modification gene complex.
PG  - 932-940
AB  - Type II restriction enzymes are paired with modification enzymes that protect type II
      restriction sites from cleavage by methylating them. A plasmid carrying a type II
      restriction-modification gene complex is not easily replaced by an incompatible plasmid
      because loss of the former leads to cell death through chromosome cleavage. In the present
      work, we looked to see whether a chromosomally located restriction-modification gene complex
      could be replaced by a homologous stretch of DNA. We tried to replace the PaeR7I gene complex
      on the Escherichia coli chromosome by transducing a homologous stretch of PaeR7I-modified DNA.
      The replacement efficiency of the restriction-modification complex was lower than expected.
      Some of the resulting recombinant clones retained the recipient restriction-modification gene
      complex as well as the homologous DNA (donor allele), and slowly lost the donor allele in the
      absence of selection. Analysis of their genome-wide rearrangements by Southern hybridization,
      inverse polymerase chain reaction (iPCR) and sequence determination demonstrated the
      occurrence of unequal homologous recombination between copies of the transposon IS3. It was
      strongly suggested that multiple rounds of unequal IS3-IS3 recombination caused large-scale
      duplication and inversion of the chromosome, and that only one of the duplicated copies of the
      recipient PaeR7I was replaced.
AU  - Handa N
AU  - Nakayama Y
AU  - Sadykov M
AU  - Kobayashi I
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2001 40: 932-940.

PMID- 15854647
VI  - 348
DP  - 2005
TI  - Profound flanking sequence preference of Dnmt3a and Dnmt3b mammalian DNA methyltransferases shape the human epigenome.
PG  - 1103-1112
AB  - Mammalian DNA methyltransferases methylate cytosine residues within CG dinucleotides. By
      statistical analysis of published data of the Human
      Epigenome Project we have determined flanking sequences of up to
      +/- four base-pairs surrounding the central CG site that are
      characteristic of high (5'-CTTGCGCAAG-3') and low (5'-TGTTCGGTGG-3')
      levels of methylation in human genomic DNA. We have investigated the
      influence of flanking sequence on the catalytic activity of the Dnmt3a
      and Dnmt3b de novo DNA methyltransferases using a set of synthetic
      oligonucleotide substrates that covers all possible +/- 1 flanks
      in quantitative terms. Methylation kinetics experiments revealed a >13-fold difference between
      the preferred (RCGY) and disfavored +/-
      1 flanking base-pairs (YCGR). In addition, AT-rich flanks are preferred
      over GC-rich ones. These experimental preferences coincide with the
      genomic methylation patterns. Therefore, we have expanded our
      experimental analysis and found a >500-fold difference in the
      methylation rates of the consensus sequences for high and low levels of
      methylation in the genome. This result demonstrates a very pronounced
      flanking sequence preference of Dnmt3a and Dnmt3b. It suggests that the
      methylation pattern of human DNA is due, in part, to the flanking
      sequence preferences of the de novo DNA MTases and that flanking
      sequence preferences could be involved in the origin of CG islands.
      Furthermore, similar flanking sequence preferences have been found for
      the stimulation of the immune system by unmethylated CGs, suggesting a
      co-evolution of DNA MTases and the immune system.
AU  - Handa V
AU  - Jeltsch A
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2005 348: 1103-1112.

PMID- 29954912
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Streptomyces sp. Strain BSE7F, a Bali Mangrove Sediment Actinobacterium with Antimicrobial Activities.
PG  - e00618-18
AB  - The strain Streptomyces sp. BSE7F, a novel Streptomyces strain isolated from Indonesian
      mangrove sediment, displays antimicrobial activities against
      Gram-positive bacteria, Gram-negative bacteria, and yeast. Bioinformatic analysis
      of the genome sequence revealed the occurrence of 22 biosynthetic gene clusters
      disclosing the secondary metabolite capacity of strain BSE7F.
AU  - Handayani I
AU  - Ratnakomala S
AU  - Lisdiyanti P
AU  - Fahrurrozi AM
AU  - Wohlleben W
AU  - Mast Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00618-18.

PMID- Not included in PubMed...
VI  - 66
DP  - 1994
TI  - New technique for thermostability of restriction and modifying enzymes.
PG  - 103-104
AB  - Commentary on the use of trehalose to stabilize restriction enzymes
AU  - Handique AK
PT  - Journal Article
TA  - Curr. Sci.
JT  - Curr. Sci.
SO  - Curr. Sci. 1994 66: 103-104.

PMID- 23661489
VI  - 1
DP  - 2013
TI  - Genome Sequence of Hydrothermal Arsenic-Respiring Bacterium Marinobacter santoriniensis NKSG1T.
PG  - E00231-13
AB  - Marinobacter santoriniensis NKSG1(T) originates from metalliferous marine
      sediment. It can respire and redox cycle arsenic species and perform mixotrophic,
      nitrate-dependent Fe(II) oxidation. The genome sequence, reported here, will help
      further elucidate the genetic mechanisms underlying these and other potential
      biogeochemically relevant functions, such as arsenic and mercury resistance and
      hydrocarbon degradation.
AU  - Handley KM
AU  - Upton M
AU  - Beatson SA
AU  - Hery M
AU  - Lloyd JR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: E00231-13.

PMID- 25281541
VI  - 192
DP  - 2014
TI  - Cell physiology of the biotechnological relevant bacterium Bacillus pumilus-An omics-based approach.
PG  - 204-214
AB  - Members of the species Bacillus pumilus get more and more in focus of the biotechnological
      industry as potential new production strains. Based on exoproteome analysis, B. pumilus strain
      Jo2, possessing a high secretion capability, was chosen for an omics-based investigation. The
      proteome and metabolome of B. pumilus cells growing either in minimal or complex medium was
      analyzed. In total, 1542 proteins were identified in growing B. pumilus cells, among them 1182
      cytosolic proteins, 297 membrane and lipoproteins and 63 secreted proteins. This accounts for
      about 43% of the 3616 proteins encoded in the B. pumilus Jo2 genome sequence. By using GC-MS,
      IP-LC/MS and H NMR methods numerous metabolites were analyzed and assigned to reconstructed
      metabolic pathways. In the genome sequence a functional secretion system including the
      components of the Sec-and Tat-secretion machinery was found. Analysis of the exoproteome
      revealed secretion of about 70 proteins with predicted secretion signals. In addition,
      selected production-relevant genome features such as restriction modification systems and NRPS
      clusters of B. pumilus Jo2 are discussed. (C) 2014 Elsevier B.V. All rights reserved.
AU  - Handtke S
AU  - Volland S
AU  - Methling K
AU  - Albrecht D
AU  - Becher D
AU  - Nehls J
AU  - Bongaerts J
AU  - Maurer K-H
AU  - Lalk M
AU  - Liesegang H
AU  - Voigt B
AU  - Daniel R
AU  - Hecker M
PT  - Journal Article
TA  - J. Biotechnol.
JT  - J. Biotechnol.
SO  - J. Biotechnol. 2014 192: 204-214.

PMID- 26543106
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Bartonella ancashensis Strain 20.00, Isolated from the Blood of a Patient with Verruga Peruana.
PG  - e01217-15
AB  - Here we present the complete genome sequence of Bartonella ancashensis strain 20.00, isolated
      from the blood of a Peruvian patient with verruga peruana, known
      as Carrion's disease. Bartonella ancashensis is a Gram-negative bacillus,
      phylogenetically most similar to Bartonella bacilliformis, the causative agent of
      Oroya fever and verruga peruana.
AU  - Hang J
AU  - Mullins KE
AU  - Clifford RJ
AU  - Onmus-Leone F
AU  - Yang Y
AU  - Jiang J
AU  - Leguia M
AU  - Kasper MR
AU  - Maguina C
AU  - Lesho EP
AU  - Jarman RG
AU  - Richards AL
AU  - Blazes D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01217-15.

PMID- 2549808
VI  - 179
DP  - 1989
TI  - Controlled partial restriction digestions of DNA by competition with modification methyltransferases.
PG  - 357-360
AB  - Competitive reactions, using defined ratios of DNA restriction
      methyltransferase to endonuclease, are shown to result in reliable partial
      restriction digests of DNA.  This method is suitable over a wide range of DNA
      concentrations and works on DNA in liquid or embedded in agarose.  Simultaneous
      methylase/endonuclease reactions using endonucleases that cleave human DNA very
      infrequently, such as ClaI or NotI, should generate very large discrete DNA
      fragments suitable for physical mapping in the million base-pair range.
      Another possible application of methylase/endonuclease competitive reactions is
      the production of defined partial digests for making cosmid, lambda, or other
      genomic libraries.
AU  - Hanish J
AU  - McClelland M
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 1989 179: 357-360.

PMID- 2192360
VI  - 18
DP  - 1990
TI  - Methylase-limited partial NotI cleavage for physical mapping of genomic DNA.
PG  - 3287-3291
AB  - Partial cleavage of DNA with the restriction endonuclease NotI (5'...GC/GGCCGC...3') is an
      important technique for genomic mapping. However, partial genomic cleavage with this enzyme is
      impaired by the agarose matrix in which the DNA must be suspended. To solve this problem we
      have purified the blocking methylase M.BspRI (5'...GGmCC...3') for competititon digests with
      NotI. The resulting methylase-limited partial DNA cleavage is shown to be superior to standard
      techniques on bacterial genomic DNA.
AU  - Hanish J
AU  - McClelland M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 3287-3291.

PMID- 2903843
VI  - 5
DP  - 1988
TI  - Activity of DNA modification and restriction enzymes in KGB, a potassium glutamate buffer.
PG  - 105-107
AB  - The most abundant intracellular cation in bacteria is potassium, and the most abundant anion
      is glutamate. However, most recommended restriction endonuclease buffers contain Na+ and Cl-.
      Restriction endonucleases retain their ability to cleave DNA over a much broader range of
      potassium glutamate (KGlu) concentrations than NaCl concentrations. These facts encouraged us
      to investigate the possibility that we could use KGlu in an NaCl-free buffer and achieve
      normal levels of activity for all restriction endonuclease. In this paper we present data
      comparing the activity of 85 restriction endonucleases and 11 DNA methylases in a series of
      KGlu buffers (KGC) against that found under optimal conditions recommended by the vendors (New
      England Biolabs, Boehringer Mannheim Biochem., and International Biotech Inc.).
AU  - Hanish J
AU  - McClelland M
PT  - Journal Article
TA  - Gene Anal. Tech.
JT  - Gene Anal. Tech.
SO  - Gene Anal. Tech. 1988 5: 105-107.

PMID- 1850125
VI  - 19
DP  - 1991
TI  - Enzymatic cleavage of a bacterial chromosome at a transposon-inserted rare site.
PG  - 829-832
AB  - The sequential use of the methylase M.XbaI (5'-TCTAGm6A) and the methylation-dependent
      endonuclease DpnI (5'-Gm6A/TC) results in cleavage at 5'-TCTAGA/TCTAGA. This recognition
      sequence was introduced into a transposon derived from the Mu bacteriophage and transposed
      into the genome of the bacterium Salmonella typhimurium. M.XbaI methylation was provided in
      vivo by a plasmid containing the M.XbaI gene and the S. typhimurium genome was cleaved to
      completion by DpnI at one or more sites, depending on the number of transposon insertions. The
      resulting genomic fragments were resolved by pulsed-field electrophoresis. The potential use
      of single M.XbaI/DpnI cleavage sites as reference positions to map rare restriction sites is
      discussed.
AU  - Hanish J
AU  - McClelland M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 829-832.

PMID- 1889813
VI  - 10
DP  - 1991
TI  - Application of methylase-limited partial NotI cleavage for a long-range restriction map of the human ABL locus.
PG  - 681-685
AB  - The use of partial restriction digests for mapping complex genomes by
      pulsed-field gel electrophoresis has been limited by the difficulty of
      consistently obtaining these digests in agarose, which is a necessary matrix
      for high-molecular-weight DNA.  Enzyme cleavage in agarose is faster then
      diffusion for most of the enzymes which cleave infrequently.  We have developed
      a method for the production of partial digests in agarose for the endonuclease
      NotI (5' ...GC/GGCCGC...3') which circumvents the diffusion problem by using
      the blocking methylase M.BspRI (5' ...GGmCC...3'), which competes for the same
      sites.  Using various ratios of the methylase and endonuclease results in
      partial digests in any size range desired.  We report the successful
      application of this technique to the production of NotI partial digests of
      human genomic DNA for the mapping of the ABL locus of human chromosome 9.
AU  - Hanish J
AU  - Rebelsky M
AU  - McClelland M
AU  - Westbrook C
PT  - Journal Article
TA  - Genomics
JT  - Genomics
SO  - Genomics 1991 10: 681-685.

PMID- 1710498
VI  - 1074
DP  - 1991
TI  - The manipulation of DNA with restriction enzymes in low water systems.
PG  - 40-44
AB  - The cleavage of phage lambda DNA by the restriction enzyme HindIII in low water
      systems has been investigated.  Two types of low water systems have been
      studied - those which contain a surfactant in a reverse micelle environment and
      a surfactant-free system in which a solid support (celite) is used.  The effect
      of the surfactants themselves in a normal aqueous environment has also been
      studied.  Charged surfactants were found to greatly inhibit HindIII activity in
      aqueous buffer, while non-ionic surfactants did not affect either the activity
      or the specificity of the restriction enzyme.  The rate of cleavage by HindIII
      in a reverse micelle system consisting of sodium dioctylsulphosuccinate is very
      slow, however, in a Triton B system the expected fragments are observed.  In a
      surfactant-free low water environment, cleavage occurs at the expected sites
      but in a different order to that observed in normal aqueous systems.  These
      results sugest that DNA tertiary structure in low water systems is different to
      that in aqueous solution and that this influences cleavage by the restriction
      enzyme HindIII.
AU  - Hanley AB
AU  - Furniss CSM
AU  - Kwiatkowska CA
AU  - Mackie AR
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1991 1074: 40-44.

PMID- Not carried by PubMed...
VI  - 3
DP  - 1990
TI  - The cleavage of nucleic acids in reversed micelles using site specific endonucleases.
PG  - 253-258
AB  - Plasmid and lambda DNA molecules of between 2.2 and 48.5 kb pairs can be
      solubilised in n-hexane containing the surfactant sodium dioctyl sulfosuccinate
      (AOT) and aqueous buffers.  Linear lambda phage DNA fragments (2.2-23.1 kb
      pairs) and intact lambda bio 1 DNA (48.5 kb pairs) are efficiently cleaved by
      BamHI and EcoRI in systems containing 100 mM AOT.  Under these conditions,
      lambda bio 1 DNA undergoes regioselective restriction by HindIII at only one
      site but is completely cleaved when the surfactant concentration is lowered to
      50 mM.  Covalent closed circular plasmid DNA (pUC8, 2.73 kb pairs) is only
      partially linearised by EcoRI and BamHI in reversed micelles; HaeII cleavage
      affords both complete and partial restriction fragments.  The results suggest
      that the tertiary structures adopted by substrate DNA in reversed micelles
      influence the availability of restriction sites.
AU  - Hanley AB
AU  - Grinfeld E
AU  - Baxter RL
PT  - Journal Article
TA  - Biocatalysis
JT  - Biocatalysis
SO  - Biocatalysis 1990 3: 253-258.

PMID- 26184936
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of a Taxonomically Unique Neisseria Strain Isolated from a  Greater White-Fronted Goose (Anser albifrons) Egg on the North Slope of Alaska.
PG  - e00772-15
AB  - We report here the draft genome sequence of a unique Neisseria strain that was isolated from a
      greater white-fronted goose (Anser albifrons) egg. The sequencing
      was performed with an Illumina MiSeq system, and the sequence consists of 275
      contigs. The total genome is 2,397,978 bp long and has a G+C content of 46.4%.
AU  - Hansen CM
AU  - Choi SC
AU  - Parker J
AU  - Hueffer K
AU  - Chen J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00772-15.

PMID- 
VI  - 66
DP  - 2000
TI  - Mutations in the DNMT3B DNA methyltransferase gene cause the ICF syndrome.
PG  - 1724
AB  - Immunodeficiency, Centromeric instability and Facial anomalies are characteristics of a rare
      genetic disorder termed the ICF syndrome.  The centromeric instability of chromosomes 1, 9,
      and 16 is associated with the abnormal hypomethylation of their pericentromeric satellite
      regions.  Hypomethylation has also been reported for other types of heterochromatin, including
      the inactive X chromosome.  We examined these phenomena further at the molecular level and
      report here examples of extensive hypomethylation of these regions in ICF cells that are
      associated with nuclease hypersensitivity, advanced replication time and a variable escape
      from silencing for genes on the inactive X and Y chromosomes.  The ICF locus has been mapped
      to a 9 c-M region of chromosome 20 by homozygosity mapping.  By searching for homologies to
      known DNA methyltransferases, we identified a genomic sequence located in the ICF region that
      contains a full length homologue of the mouse DNMT3B methyltransferase gene.  The human
      sequence was used to screen ICF kindreds and we discovered mutations in 4 patients from 3
      families.  Restriction enzyme and bisulfite methylation analyses revealed extensive
      hypomethylation of 5' CpG islands at all 10 genes examined on the inactive X and 1 gene on
      the Y in two ICF females and 3 ICF males.  Abnormal hypomethylation in ICF was also associated
      with advanced replication time for several loci examined, including satellite II sequences.
      Consistent with these data, we discovered novel examples of escape from inactivation in
      untreated diploid fibroblasts and lymphoblasts from ICF patients for G5PD, MPP1, and SYBL1.
      This escape is variable, and appears to correlate with the degree of advanced replication time
      for these loci.  The ICF phenotype, therefore, is likely to involve abnormalities in gene
      silencing at multiple loci that arise from defects in methylation and late replication.  We
      found that the satellite hypomethylation defect in ICF cells can be complemented by somatic
      cell fusion to CHO cells.  We presume that this de novo methylation results from
      complementation of the defective human ICF gene with a functional hamster homologue and we
      sought to identify and localize DNA methyltransferases with de novo activity.  Dnmt3a and
      Dnmt3b are two very homologous DNA methyltransferases with de novo activity that were recently
      identified in the mouse.  Because the ICF locus maps to the proximal long arm of chromosome
      20, we searched the unfinished chromosome 20 sequence data at the Sanger Centre for homology
      to these genes and identified a PAC sequence containing a full length coding sequence that is
      highly homologous to the murine Dnmt3b gene.  The predicted DNMT38 sequence was verified by
      sequencing RT-PCR and PCR products amplified with derived primers.  We examined the DNMT3B
      gene in ICF patients for mutations and found three ICF-specific mutations: a T to G
      transversion resulting in a V726G missense substitution that is homozygous in the two affected
      brothers of Family 1, a CpG to CpA missense transition (A603T) that is heterozygous in the P4
      ICF female of Family 3, and an intronic CpG to CpA splice mutation resulting in an STP
      insertion before codon 897 that is homozygous in the P3 patient of Family 2 and heterozygous
      in the P4 patient of Family 3.  None of the mutations were present in over 200 normal
      chromosomes examined from unrelated individuals.  All three DNMT3B mutations are predicted to
      be in all major splice forms and occur in regions that are invariant among the DNMT3-like
      methyltransferases that have been identified in zebra-fish, mouse and man and are in or near
      regions of homology to certain bacteriophage methyltransferases.  These mutations all appear
      to be in the catalytic domain of the enzyme as they are within or near motifs present in
      nearly all m5C-methyltransferases.  Our observations of escape from X inactivation,
      complementation for the ICF methylation defect in somatic cells, and of DNMT3B mutations in
      ICF patients provide a useful model for examining the role of this enzyme in the establishment
      and maintenance of somatic methylation patterns.  This is the first example of a mutation in a
      human gene that alters DNA methylation patterns.
AU  - Hansen RS
AU  - Wijmenga C
AU  - D'Esposito M
AU  - Weemaes CMR
AU  - Gartier SM
PT  - Journal Article
TA  - Am. J. Hum. Genet.
JT  - Am. J. Hum. Genet.
SO  - Am. J. Hum. Genet. 2000 66: 1724.

PMID- 10588719
VI  - 96
DP  - 1999
TI  - The DNMT3B DNA methyltransferase gene is mutated in the ICF immunodeficiency syndrome.
PG  - 14412-14417
AB  - DNA methylation is an important regulator of genetic information in species ranging from
      bacteria to humans. DNA methylation appears to be critical for mammalian development because
      mice nullizygous for a targeted disruption of the DNMT1 DNA methyltransferase die at an early
      embryonic stage. No DNA methyltransferase mutations have been reported in humans until now. We
      describe here the first example of naturally occurring mutations in a mammalian DNA
      methyltransferase gene. These mutations occur in patients with a rare autosomal recessive
      disorder, which is termed the ICF syndrome, for immunodeficiency, centromeric instability, and
      facial anomalies. Centromeric instability of chromosomes 1, 9, and 16 is associated with
      abnormal hypomethylation of CpG sites in their pericentromeric satellite regions. We are able
      to complement this hypomethylation defect by somatic cell fusion to Chinese hamster ovary
      cells, suggesting that the ICF gene is conserved in the hamster and promotes de novo
      methylation. ICF has been localized to a 9-centimorgan region of chromosome 20 by homozygosity
      mapping. By searching for homologies to known DNA methyltransferases, we identified a genomic
      sequence in the ICF region that contains the homologue of the mouse Dnmt3b methyltransferase
      gene. Using the human sequence to screen ICF kindreds, we discovered mutations in four
      patients from three families. Mutations include two missense substitutions and a 3-aa
      insertion resulting from the creation of a novel 3' splice acceptor. None of the mutations
      were found in over 200 normal chromosomes. We conclude that mutations in the DNMT3B are
      responsible for the ICF syndrome.
AU  - Hansen RS
AU  - Wijmenga C
AU  - Luo P
AU  - Stanek AM
AU  - Canfield TK
AU  - Weemaes CM
AU  - Gartler SM
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1999 96: 14412-14417.

PMID- 6277926
VI  - 257
DP  - 1982
TI  - Evidence for translated intervening sequences in the mitochondrial genome of Saccharomyces cerevisiae.
PG  - 3218-3224
AB  - In yeast, the mitochondrial genes for subunit I of cytochrome oxidase (oxi3) and for
      apocytochrome b (cob) are known to be split. In some strains, the latter contains five
      intervening sequences, three of which coincide with clusters of mutational sites referred to
      in their order of transcription as the loci box3, 10, and 7, respectively. Mutations at the
      first of these result in the accumulation of novel, large polypeptides (apparent Mr = about
      43,000) believed to originate from a fusion of sequences found in the NH2-terminal segment of
      apocytochrome b to others encoded in the intervening sequence itself. We now provide evidence
      for close similarities of at least a part of translated intron sequences between (a) mutants
      in box7 in "long" form and "short" form strains (which lack the first three introns including
      the one for the box3 locus); (b) mutants in a subset of box7 mutants and those in box3, and
      (c) between intron sequences in box7 and a sequence presumably encoded in oxi3. These
      structural homologies presumably encoded in oxi3. These structural homologies have been
      analyzed and shown to be referable to sequence homologies in two proteins, one derived from
      the second intron (box3) in cob and the other from oxi3. The accumulation in certain cob
      mutants of proteins and of a transcript containing a sequence specified by oxi3 provides
      additional strong evidence for the previously suggested regulation of oxi3 by the penultimate,
      box7-containing intron of cob.
AU  - Hanson DK
AU  - Lamb MR
AU  - Mahler HR
AU  - Perlman PS
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1982 257: 3218-3224.

PMID- 28336586
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Tannerella forsythia Clinical Isolate 9610.
PG  - e00024-17
AB  - We present here the draft genome sequence of Tannerella forsythia 9610, a clinical isolate
      obtained from a periodontitis patient. The genome is composed of
      79 scaffolds with 82 contigs, for a length of 3,201,941 bp and a G+C of 47.3%.
AU  - Hanson-Drury S
AU  - To TT
AU  - Liu Q
AU  - Vo AT
AU  - Kim M
AU  - Watling M
AU  - Bumgarner RS
AU  - McLean JS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00024-17.

PMID- 2308821
VI  - 18
DP  - 1990
TI  - Site-specific inhibition of EcoRI restriction/modification enzymes by a DNA triple helix.
PG  - 157-161
AB  - The abilility of oligopyrimidines to inhibit, through triple helix formation,
      the specific protein-DNA interactions of the EcoRI restriction and modification
      enzymes (EcoRI and M.EcoRI) with their recognition sequence (GAATTC) was
      studied.  The oligonucleotides (CTT)4 and (CTT)8 formed triplexes in plasmids
      at (GAA)n repeats containing EcoRI sites.  Cleavage and methylation of EcoRI
      sites within these sequences were specifically inhibited by the
      oligonucleotides, whereas an EcoRI site adjacent to a (GAA)n sequence was
      inhibited much less.  Also, other EcoRI sites within the plasmid, or in
      exogenously added lambda DNA, were not inhibited.  These results demonstrate
      the potential of using triplex-forming oligonucleotides to block protein-DNA
      interactions at specific sites, and thus this technique may be useful in
      chromosome mapping and in the modulation of gene expression.
AU  - Hanvey JC
AU  - Shimizu M
AU  - Wells RD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 157-161.

PMID- 28729256
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Mycoplasma capricolum subsp. capripneumoniae Strain zly1309F, Isolated from Endangered Tibetan Antelope.
PG  - e00496-17
AB  - Mycoplasma capricolum subsp. capripneumoniae is an important pathogen of goats that causes
      contagious caprine pleuropneumonia. Here, we report the complete
      genome sequence of M. capricolum subsp. capripneumoniae strain zly1309F, isolated
      from a Tibetan antelope (Pantholops hodgsonii) in China.
AU  - Hao H
AU  - Chen S
AU  - Li Y
AU  - Sun H
AU  - Zhao P
AU  - Jian Y
AU  - Gao Y
AU  - Wu C
AU  - Liu Y
AU  - Chu Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00496-17.

PMID- 22628498
VI  - 194
DP  - 2012
TI  - The Genome of Plant Growth-Promoting Bacillus amyloliquefaciens subsp. plantarum  Strain YAU B9601-Y2 Contains a Gene Cluster for Mersacidin Synthesis.
PG  - 3264-3265
AB  - The genome of rhizobacterium Bacillus amyloliquefaciens subsp. plantarum YAU B9601-Y2 was 4.24
      Mb in size and harbored 3,991 coding sequences (CDS). Giant
      gene clusters were dedicated to nonribosomal synthesis of antimicrobial
      lipopeptides and polyketides. Remarkably, CAU B946 possessed a gene cluster
      involved in synthesis of mersacidin.
AU  - Hao K
AU  - He P
AU  - Blom J
AU  - Rueckert C
AU  - Mao Z
AU  - Wu Y
AU  - He Y
AU  - Borriss R
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3264-3265.

PMID- 27795249
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Bacillus pumilus PDSLzg-1, a Hydrocarbon-Degrading Bacterium Isolated from Oil-Contaminated Soil in China.
PG  - e01079-16
AB  - Bacillus pumilus strain PDSLzg-1, an efficient hydrocarbon-degrading bacterium, was isolated
      from oil-contaminated soil. Here, we present the complete sequence
      of its circular chromosome and circular plasmid. The genomic information is
      essential for the study of degradation of oil by B. pumilus PDSLzg-1.
AU  - Hao K
AU  - Li H
AU  - Li F
AU  - Guo P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01079-16.

PMID- 21264216
VI  - 6
DP  - 2011
TI  - Complete Sequencing and Pan-Genomic Analysis of Lactobacillus delbrueckii subsp bulgaricus Reveal Its Genetic Basis for Industrial Yogurt Production.
PG  - e15964
AB  - Lactobacillus delbrueckii subsp. bulgaricus (Lb. bulgaricus) is an important species of Lactic
      Acid Bacteria (LAB) used for cheese and
      yogurt fermentation. The genome of Lb. bulgaricus 2038, an industrial
      strain mainly used for yogurt production, was completely sequenced and
      compared against the other two ATCC collection strains of the same
      subspecies. Specific physiological properties of strain 2038, such as
      lysine biosynthesis, formate production, aspartate-related
      carbon-skeleton intermediate metabolism, unique EPS synthesis and
      efficient DNA restriction/modification systems, are all different from
      those of the collection strains that might benefit the industrial
      production of yogurt. Other common features shared by Lb. bulgaricus
      strains, such as efficient protocooperation with Streptococcus
      thermophilus and lactate production as well as well-equipped stress
      tolerance mechanisms may account for it being selected originally for
      yogurt fermentation industry. Multiple lines of evidence suggested that
      Lb. bulgaricus 2038 was genetically closer to the common ancestor of
      the subspecies than the other two sequenced collection strains,
      probably due to a strict industrial maintenance process for strain 2038
      that might have halted its genome decay and sustained a gene network
      suitable for large scale yogurt production.
AU  - Hao P
AU  - Zheng H
AU  - Yu Y
AU  - Ding G
AU  - Gu W
AU  - Chen S
AU  - Yu Z
AU  - Ren S
AU  - Oda M
AU  - Konno T
AU  - Wang S
AU  - Li X
AU  - Ji Z-S
AU  - Zhao G
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2011 6: e15964.

PMID- 22247533
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Plant Growth-Promoting Rhizobium Mesorhizobium amorphae, Isolated from Zinc-Lead Mine Tailings.
PG  - 736-737
AB  - Here, we describe the draft genome sequence of Mesorhizobium amorphae strain CCNWGS0123,
      isolated from nodules of Robinia pseudoacacia growing
      on zinc-lead mine tailings. A large number of metal(loid) resistance
      genes, as well as genes reported to promote plant growth, were identified,
      presenting a great future potential for aiding phytoremediation in
      metal(loid)-contaminated soil.
AU  - Hao X
AU  - Lin Y
AU  - Johnstone L
AU  - Baltrus DA
AU  - Miller SJ
AU  - Wei G
AU  - Rensing C
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 736-737.

PMID- 22275101
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Arsenite-Oxidizing Strain Agrobacterium tumefaciens 5A.
PG  - 903
AB  - Microbial transformations of arsenic influence its mobility and toxicity. We report the draft
      genome sequence of the arsenite-oxidizing strain
      Agrobacterium tumefaciens 5A isolated from an As-contaminated soil in the
      Madison River Valley, MT. A large number of metal (or metalloid)
      resistance genes, especially contributing to arsenite oxidation, were
      identified.
AU  - Hao X
AU  - Lin Y
AU  - Johnstone L
AU  - Liu G
AU  - Wang G
AU  - Wei G
AU  - McDermott T
AU  - Rensing C
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 903.

PMID- 21097614
VI  - 193
DP  - 2010
TI  - Complete Genome Sequence of Bifidobacterium longum subsp. longum BBMN68, a New Strain from Healthy Chinese Centenarian.
PG  - 787-788
AB  - Bifidobacterium longum subsp. longum BBMN68 was isolated from the fecal of healthy centenarian
      living in longevity area of BaMa, Guangxi, China.
      Here, we reported the main genome features of B. longum BBMN68 strain and
      the identification of several predicted proteins that tailored to the
      ecological niche of longevity.
AU  - Hao Y
AU  - Huang D
AU  - Guo H
AU  - Xiao M
AU  - An H
AU  - Zhao L
AU  - Zuo F
AU  - Zhang B
AU  - Hu S
AU  - Song S
AU  - Chen S
AU  - Ren F
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 193: 787-788.

PMID- 23599288
VI  - 1
DP  - 2013
TI  - Genome Sequence of a Freshwater Low-Nucleic-Acid-Content Bacterium, Betaproteobacterium Strain CB.
PG  - e00135-13
AB  - Betaproteobacterium strain CB is a typical minute freshwater bacterium, representing the
      small-cell bacteria that are numerically dominant in most
      freshwater environments. The genome of betaproteobacterium CB consists of a
      circular 2,045,720-bp chromosome, and the information we report will provide
      insights into the mechanisms underlying its survival and ecological function.
AU  - Hao Z
AU  - Li L
AU  - Liu J
AU  - Ren Y
AU  - Wang L
AU  - Bartlam M
AU  - Egli T
AU  - Wang Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00135-13.

PMID- 11732916
VI  - 40
DP  - 2001
TI  - Specific DNA Recognition by the Type II Restriction Endonuclease MunI: The Effect of pH.
PG  - 14960-14967
AB  - To investigate the effect of pH on sequence-specific binding, a thermodynamic characterization
      of the interaction of the protein MunI with a specific, and a nonspecific, oligonucleotide was
      performed. MunI is a type II restriction endonuclease which is able to bind specifically, but
      loses its enzymatic activity in the absence of magnesium ions. Comparison of the specific and
      nonspecific interactions at 10 and 25 degrees C shows that the latter is accompanied by a
      small change in enthalpy, and a negligible change in constant pressure heat capacity. On going
      through the pH range 5.75-9.0 at 25 degrees C, the affinity of specific complex formation is
      reduced by 20-fold. The interaction is accompanied by the protonation of groups assumed to be
      on the protein. Based on the simplest model that will fit the data, two distinct protonation
      events are observed. At low pH, two groups per protein molecule undergo protonation with a
      pK(a) of 6.0 and 6.9 in the free and bound forms, respectively. At high pH, a further
      independent protonation occurs involving two groups with pK(a) values of 8.9 and approximately
      10.7 in the free and bound forms, respectively. The change in heat capacity ranges from -2.7
      to -1.7 kJ mol(-)(1) K(-)(1) in going from pH 6.5 to 8.5. This range of variation of change in
      heat capacity can be accounted for by the effects of protonation of the interacting molecules.
      The change in heat capacity, calculated from surface area burial using a previously
      established relationship (1.15 kJ mol(-)(1) K(-)(1)), does not correlate well with the
      experimentally determined values.
AU  - Haq I
AU  - O'Brien R
AU  - Lagunavicius A
AU  - Siksnys V
AU  - Ladbury JE
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2001 40: 14960-14967.

PMID- 3009308
VI  - 22
DP  - 1985
TI  - Cloning and expression of EcoRI specific restriction modification system.
PG  - 252-254
AB  - RI-specific restriction-modification genes have been cloned in the multicopy
      plasmid pBR322.  Plasmid DNA, isolated from E. coli RY13, was cleaved with
      restriction enzyme BamHI and inserted at the BamHI site in pBR322 and cloned in
      E. coli HB101.  The recombinant DNA transnformants were selected by their
      resistance to ampicillin and sensitivity to tetracycline.  EcoRI-specific
      clones were identified by determining the efficiency of plating on
      transformants of modified and unmodified lambda phage.  Crude enzyme prepared
      from several of the transformants by dextran polyethylene glycol phase
      partition procedure yielded the same restriction pattern as the parental strain
      and purified EcoRI.
AU  - Haqqi TM
AU  - Ahmad S
AU  - Ahmad NS
AU  - Ahmad M
AU  - Hasnain A
AU  - Siddiqi M
AU  - Hadi SM
PT  - Journal Article
TA  - Indian J. Biochem. Biophys.
JT  - Indian J. Biochem. Biophys.
SO  - Indian J. Biochem. Biophys. 1985 22: 252-254.

PMID- 29903821
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Moorella sp. Strain Hama-1, a Novel Acetogenic Bacterium Isolated from a Thermophilic Digestion Reactor.
PG  - e00517-18
AB  - Moorella sp. strain Hama-1 was isolated from a thermophilic anaerobic digestion reactor
      treating poly(l-lactic acid). The strain is a thermophilic acetogen
      capable of lactate oxidation under anaerobic conditions. Here, we report the
      draft genome sequence of strain Hama-1, comprising 3.27 Mb in 48 contigs, with a
      G+C content of 56.6%.
AU  - Harada J
AU  - Yamada T
AU  - Giri S
AU  - Hamada M
AU  - Nobu MK
AU  - Narihiro T
AU  - Tsuji H
AU  - Daimon H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00517-18.

PMID- 26823579
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Nonhemolytic Streptococcus agalactiae Serotype V Strain 1, Isolated from the Buccal Cavity of a Canine.
PG  - e01612-15
AB  - The complete genome sequence from a nonhemolytic strain of Streptococcus agalactiae from the
      oral cavity of a canine was assembled. The genome is
      2,165,968 bp, contains 2,055 genes, and is classified as group B streptococcus
      (GBS) serotype V, strain 1. A comparison to other S. agalactiae sequences shows
      high gene synteny with human and bovine strains.
AU  - Harden LK
AU  - Morales KM
AU  - Hughey JR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01612-15.

PMID- 6088528
VI  - 259
DP  - 1984
TI  - Ethidium binding sites on plasmid DNA determined by photoaffinity labeling.
PG  - 11090-11097
AB  - Photoaffinity labeling of pBR322 with ethidium monoazide
      (8-azido-3-amino-5-ethyl-6-phenylphenanthridinium chloride) was used to provide evidence for
      the sequence specifity of ethidium binding to native DNA. DNA-drug interactions were examined
      at concentrations of eight covalently bound ethidium drugs per molecule of pBR322 (4363 base
      pairs). Restriction enzyme cutting was blocked by the covalent binding of a drug molecule at
      (or near) the enzyme recognition sequence. This phenomenon was observed with all restriction
      enzymes tested and was not limited to specific regions of the pBR322 molecule.
      Double-digestion experiments indicated that a drug molecule may bind 2 to 3 base pairs outside
      the recognition sequence and still block restriction enzyme digestion. Intact plasmid was
      treated with [3H] ethidium monoazide and digested with restriction enzymes. The amount of
      covalently-linked ethidium analog was quantitated for different restriction fragments and the
      G-C content of each fragment was determined from the DNA sequence. In approximately half of
      the fragments the drug appeared to preferentially bind at a G-C base pair. However, a
      preference for specific sequences such as 5'-C-G-3' was detected, as had been suggested by
      previous modeling studies with ethidium bromide. The other fragments were located in specific
      map regions of the plasmid and did not bind drug with a strict dependence on GC content
      suggesting that binding specificity may depend on more than one structural feature of the DNA.
AU  - Hardwick JM
AU  - von Sprecken RS
AU  - Yielding KL
AU  - Yielding LW
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1984 259: 11090-11097.

PMID- 25953175
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Bacillus megaterium Podophage Palmer.
PG  - e00358-15
AB  - Bacillus megaterium has been widely used as a research tool for decades. Its use  is on the
      rise as a recombinant protein production host and as a bioremediation
      bacterium. Bacteriophages against this bacterium may have biotechnological
      applications. Here, we describe the novel podophage Palmer, which infects B.
      megaterium.
AU  - Hargrove EC
AU  - Lopez MS
AU  - Hernandez AC
AU  - Kuty EGF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00358-15.

PMID- 26847891
VI  - 4
DP  - 2016
TI  - Complete Closed Genome Sequences of Salmonella enterica subsp. enterica Serotypes Anatum, Montevideo, Typhimurium, and Newport, Isolated from Beef, Cattle, and  Humans.
PG  - e01683-15
AB  - Salmonella enterica spp. are a diverse group of bacteria with a wide range of virulence
      potential. To facilitate genome comparisons across this virulence
      spectrum, we present eight complete closed genome sequences of four S. enterica
      serotypes (Anatum, Montevideo, Typhimurium, and Newport), isolated from various
      cattle samples and from humans.
AU  - Harhay DM
AU  - Bono JL
AU  - Smith TP
AU  - Fields PI
AU  - Dinsmore BA
AU  - Santovenia M
AU  - Kelley CM
AU  - Wang R
AU  - Harhay GP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01683-15.

PMID- 28983006
VI  - 5
DP  - 2017
TI  - Closed Genome Sequences of Seven Histophilus somni Isolates from Beef Calves with Bovine Respiratory Disease Complex.
PG  - e01099-17
AB  - Histophilus somni is a fastidious Gram-negative opportunistic pathogenic Pasteurellaceae that
      affects multiple organ systems and is one of the principal
      bacterial species contributing to bovine respiratory disease complex (BRDC) in
      feed yard cattle. Here, we present seven closed genome sequences isolated from
      three beef calves showing sign of BRDC.
AU  - Harhay GP
AU  - Harhay DM
AU  - Bono JL
AU  - Smith TPL
AU  - Capik SF
AU  - DeDonder KD
AU  - Apley MD
AU  - Lubbers BV
AU  - White BJ
AU  - Larson RL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01099-17.

PMID- 23682137
VI  - 1
DP  - 2013
TI  - Complete Closed Genome Sequences of Mannheimia haemolytica Serotypes A1 and A6, Isolated from Cattle.
PG  - e00188-13
AB  - Mannheimia haemolytica is a respiratory pathogen affecting cattle and related ruminants
      worldwide. M. haemolytica is commonly associated with bovine
      respiratory disease complex (BRDC), a polymicrobial multifactorial disease. We
      present the first two complete closed genome sequences of this species,
      determined using an automated assembly pipeline requiring no manual finishing.
AU  - Harhay GP
AU  - Koren S
AU  - Phillippy AM
AU  - McVey DS
AU  - Kuszak J
AU  - Clawson ML
AU  - Harhay DM
AU  - Heaton MP
AU  - Chitko-McKown CG
AU  - Smith TP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00188-13.

PMID- 24526647
VI  - 2
DP  - 2014
TI  - Complete Closed Genome Sequences of Three Bibersteinia trehalosi Nasopharyngeal Isolates from Cattle with Shipping Fever.
PG  - e00084-14
AB  - Bibersteinia trehalosi is a respiratory pathogen affecting cattle and related ruminants
      worldwide. B. trehalosi is closely related to Mannheimia haemolytica
      and is often associated with bovine respiratory disease complex (BRDC), a
      polymicrobial multifactorial disease. We present three complete closed genome
      sequences of this species generated using an automated assembly pipeline.
AU  - Harhay GP
AU  - McVey DS
AU  - Koren S
AU  - Phillippy AM
AU  - Bono J
AU  - Harhay DM
AU  - Clawson ML
AU  - Heaton MP
AU  - Chitko-McKown CG
AU  - Korlach J
AU  - Smith TP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00084-14.

PMID- 24526648
VI  - 2
DP  - 2014
TI  - Complete Closed Genome Sequences of Four Mannheimia varigena Isolates from Cattle with Shipping Fever.
PG  - e00088-14
AB  - Mannheimia varigena is an occasional respiratory pathogen of cattle and pigs. We  present the
      first four complete closed genome sequences of this species.
AU  - Harhay GP
AU  - Murray RW
AU  - Lubbers B
AU  - Griffin D
AU  - Koren S
AU  - Phillippy AM
AU  - Harhay DM
AU  - Bono J
AU  - Clawson ML
AU  - Heaton MP
AU  - Chitko-McKown CG
AU  - Smith TP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00088-14.

PMID- 26564032
VI  - 3
DP  - 2015
TI  - Genome Sequence of Salmonella enterica subsp. enterica Serovar Typhi Isolate PM016/13 from Untreated Well Water Associated with a Typhoid Outbreak in Pasir  Mas, Kelantan, Malaysia.
PG  - e01261-15
AB  - Salmonella enterica subsp. enterica serovar Typhi is a human-restricted pathogen  that causes
      typhoid fever. Even though it is a human-restricted pathogen, the bacterium is also isolated
      from environments such as groundwater and pond water. Here, we describe the genome sequence of
      the Salmonella enterica subsp. enterica serovar Typhi PM016/13 which was isolated from well
      water during a typhoid outbreak in Kelantan, Malaysia, in 2013.
AU  - Harish SM
AU  - Sim KS
AU  - Najimudin N
AU  - Aziah I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01261-15.

PMID- 26564035
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Typhi Isolate B/SF/13/03/195 Associated with a Typhoid Carrier in Pasir Mas, Kelantan,   Malaysia.
PG  - e01285-15
AB  - We report here the complete genome sequence of Salmonella enterica subsp. enterica serovar
      Typhi B/SF/13/03/195 obtained from a typhoid carrier, who is a food handler in Pasir Mas,
      Kelantan.
AU  - Harish SM
AU  - Sim KS
AU  - Nor FM
AU  - Hussin HM
AU  - Hamzah WM
AU  - Najimudin N
AU  - Aziah I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01285-15.

PMID- 24604655
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Antitrypanosomally Active Sponge-Associated Bacterium Actinokineospora sp. Strain EG49.
PG  - e00160-14
AB  - The marine sponge-associated bacterium Actinokineospora sp. strain EG49 produces  the
      antitrypanosomal angucycline-like compound actinosporin A. The draft genome
      of Actinokineospora sp. EG49 has a size of 7.5 megabases and a GC content of
      72.8% and contains 6,629 protein-coding sequences (CDS). antiSMASH predicted 996
      genes residing in 36 secondary metabolite gene clusters.
AU  - Harjes J
AU  - Ryu T
AU  - Abdelmohsen UR
AU  - Moitinho-Silva L
AU  - Horn H
AU  - Ravasi T
AU  - Hentschel U
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00160-14.

PMID- 21304705
VI  - 2
DP  - 2010
TI  - Complete genome sequence of Sebaldella termitidis type strain (NCTC 11300).
PG  - 220-227
AB  - Sebaldella termitidis (Sebald 1962) Collins and Shah 1986, is the only species in the genus
      Sebaldella within the fusobacterial family 'Leptotrichiaceae'. The sole
      and type strain of the species was first isolated about 50 years ago from
      intestinal content of Mediterranean termites. The species is of interest for its
      very isolated phylogenetic position within the phylum Fusobacteria in the tree of
      life, with no other species sharing more than 90% 16S rRNA sequence similarity.
      The 4,486,650 bp long genome with its 4,210 protein-coding and 54 RNA genes is
      part of the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Harmon-Smith M et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 2: 220-227.

PMID- 28338931
VI  - 9
DP  - 2017
TI  - Evolutionary Dynamics of Pathoadaptation Revealed by Three Independent Acquisitions of the VirB/D4 Type IV Secretion System in Bartonella.
PG  - 761-776
AB  - The alpha-proteobacterial genus Bartonella comprises a group of ubiquitous
      mammalian pathogens that are studied as a model for the evolution of bacterial
      pathogenesis. Vast abundance of two particular phylogenetic lineages of
      Bartonella had been linked to enhanced host adaptability enabled by
      lineage-specific acquisition of a VirB/D4 type IV secretion system (T4SS) and
      parallel evolution of complex effector repertoires. However, the limited
      availability of genome sequences from one of those lineages as well as other,
      remote branches of Bartonella has so far hampered comprehensive understanding of
      how the VirB/D4 T4SS and its effectors called Beps have shaped Bartonella
      evolution. Here, we report the discovery of a third repertoire of Beps associated
      with the VirB/D4 T4SS of B. ancashensis, a novel human pathogen that lacks any
      signs of host adaptability and is only distantly related to the two species-rich
      lineages encoding a VirB/D4 T4SS. Furthermore, sequencing of ten new Bartonella
      isolates from under-sampled lineages enabled combined in silico analyses and wet
      lab experiments that suggest several parallel layers of functional
      diversification during evolution of the three Bep repertoires from a single
      ancestral effector. Our analyses show that the Beps of B. ancashensis share many
      features with the two other repertoires, but may represent a more ancestral state
      that has not yet unleashed the adaptive potential of such an effector set. We
      anticipate that the effectors of B. ancashensis will enable future studies to
      dissect the evolutionary history of Bartonella effectors and help unraveling the
      evolutionary forces underlying bacterial host adaptation.
AU  - Harms A
AU  - Segers FH
AU  - Quebatte M
AU  - Mistl C
AU  - Manfredi P
AU  - Korner J
AU  - Chomel BB
AU  - Kosoy M
AU  - Maruyama S
AU  - Engel P
AU  - Dehio C
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2017 9: 761-776.

PMID- 28883129
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Zobellia sp. Strain OII3, Isolated from the Coastal Zone of the Baltic Sea.
PG  - e00737-17
AB  - Zobellia sp. strain OII3 was isolated from a marine environmental sample due to its
      heterotrophic lifestyle, i.e., using Escherichia coli cells as prey. It shows
      strong agar-lytic activity. The genome was assembled into 41 contigs with a total
      size of 5.4 Mb, revealing the genetic basis for natural product biosynthesis.
AU  - Harms H
AU  - Poehlein A
AU  - Thurmer A
AU  - Konig GM
AU  - Schaberle TF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00737-17.

PMID- 26868398
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Uncultured SAR324 Bacterium lautmerah10, Binned from a Red Sea Metagenome.
PG  - e01711-15
AB  - A draft genome of SAR324 bacterium lautmerah10 was assembled from a metagenome of a surface
      water sample from the Red Sea, Saudi Arabia. The genome is more
      complete and has a higher G+C content than that of previously sequenced SAR324
      representatives. Its genomic information shows a versatile metabolism that
      confers an advantage to SAR324, which is reflected in its distribution throughout
      different depths of the marine water column.
AU  - Haroon MF
AU  - Thompson LR
AU  - Stingl U
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01711-15.

PMID- 
VI  - 0
DP  - 1984
TI  - The interactions of mini-F with the plasmids R124 and R124/3.
PG  - 920
AB  - The Inc FIV plasmid R124 encodes a unique restriction and modification (R-M) system.  R124/3
      is a derivative plasmid which encodes an R-M system of different specificity.  When R124 or
      R124/3 are present in the same cell as the sex Factor F a restriction deficient (r-) phenotype
      results.  This r- phenotype reverts back to r+ with a frequency dependent upon the particular
      isolate.  When the F plasmids are isolated from these reverted strains they are found to
      encode the R-M system of the donor R124 or R124/3 plasmid.  The R-M system is translocated
      into the region of EcoRI fragments 5 and 7 of F, which encodes the Phi and Ori VI functions of
      F.  During this transfer of DNA some F DNA is lost.  Recent work with mini-F (cloned EcoRI
      fragments 5 and 7 of F) have shown that they alone do not result in the translocation of R-M
      genes from R124 or R124/3.  EcoRI fragments 5 and 7 of F when present in the same cell as R124
      or R124/3 result in a fraction of the cells expressing a r- phenotype which reverts back to a
      r+ phenotype.  This reversion process is not accompanied by any DNA transfer or rearrangement
      between F, R124, or R124/3 plasmids.  This strongly suggests that some other region of F is
      involved in the DNA rearrangement.  Studies with mini-F have also shown that under certain
      circumstances the rearrangement results in R124 expressing incF1 incompatability instead of
      the normal Inc FIV.
AU  - Harper SH
AU  - Firman K
AU  - Glover SW
PT  - Journal Article
TA  - Plasmids in Bacteria
JT  - Plasmids in Bacteria
SO  - Plasmids in Bacteria 1984 0: 920.

PMID- 27103725
VI  - 4
DP  - 2016
TI  - Genome Sequence of Aeromicrobium erythreum NRRL B-3381, an Erythromycin-Producing Bacterium of the Nocardioidaceae.
PG  - e00300-16
AB  - ITALIC! Aeromicrobium erythreumNRRL B-3381 has a 3,629,239-bp circular genome that has 72% G+C
      content. There are at least 3,121 coding sequences (CDSs), two
      rRNA gene operons, and 47 tRNAs. The genome and erythromycin ( ITALIC! ery)
      biosynthetic gene sequences provide resources for metabolic and combinatorial
      engineering of polyketides.
AU  - Harrell EA
AU  - Miller ES
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00300-16.

PMID- 1398028
VI  - 96
DP  - 1992
TI  - Plasmid involvement in the formation of a spontaneous bacteriophage insensitive mutant of Lactococcus lactis.
PG  - 135-141
AB  - Lactococcus lactis subsp. lactis biovar. diacetylactis DPC721 is a spontaneous bacteriophage
      insensitive mutant of stain DPC220, isolated after challenge with an industrial bacteriophage,
      phiD1. Plasmid analysis demonstrated that the bacteriophage insensitivity was associated with
      the absence of two native DPC220 plasmids (pAH82 and pAH33), and the presence of a novel
      plasmid (pAH90) in DPC721. The plasmids were transferred by conjugative mobilization to a
      plasmid free background where it was confirmed by restriction mapping that pAH90 is a
      co-integrate formed by the precise recombination of pAH82 and pAH33. The resistance phenotype
      encoded by pAH90 was also active against two bacteriophages homologous for the plasmid-free
      strain. Plasmid pAH90 was shown to encode at least two independent resistance mechanisms,
      including an adsorption-inhibition mechanism and a restriction and modification system. The
      adsorption-inhibition mechanism encoded by the co-integrate plasmid was specific for one of
      the phage used in this study.
AU  - Harrington A
AU  - Hill C
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1992 96: 135-141.

PMID- 23405332
VI  - 1
DP  - 2013
TI  - Genome Sequence of the Attenuated Carbosap Vaccine Strain of Bacillus anthracis.
PG  - e00067-12
AB  - The Bacillus anthracis Carbosap genome, which includes the pXO1 and pXO2 plasmids, has been
      shown to encode the major B. anthracis virulence factors, yet this strain's attenuation has
      not yet been explained. Here we report the draft genome sequence of this strain, and a
      comparison to fully virulent B. anthracis.
AU  - Harrington R
AU  - Ondov BD
AU  - Radune D
AU  - Friss MB
AU  - Klubnik J
AU  - Diviak L
AU  - Hnath J
AU  - Cendrowski SR
AU  - Blank TE
AU  - Karaolis D
AU  - Friedlander AM
AU  - Burans JP
AU  - Rosovitz MJ
AU  - Treangen T
AU  - Phillippy AM
AU  - Bergman NH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00067-12.

PMID- 25428968
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Pseudoalteromonas sp. Strain ND6B, an Oil-Degrading Isolate from Eastern Mediterranean Sea Water Collected at a Depth of 1,210  Meters.
PG  - e01212-14
AB  - Here, we report the draft genome of Pseudoalteromonas sp. strain ND6B, which is able to grow
      with crude oil as a carbon source. Strain ND6B was isolated from
      eastern Mediterranean Sea deep water at a depth of 1,210 m. The genome of strain
      ND6B provides insight into the oil-degrading ability of the Pseudoalteromonas
      species.
AU  - Harris AP
AU  - Techtmann SM
AU  - Stelling SC
AU  - Utturkar SM
AU  - Alshibli NK
AU  - Brown SD
AU  - Hazen TC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01212-14.

PMID- 
VI  - 2
DP  - 1999
TI  - Studying the function of methyltransferases using nucleotide analogue based random mutagenesis.
PG  - 209-212
AB  - The function of two methyltransferases M.SPR and M.HhaI have been investigated using a PCR
      based random mutagenesis procedure using nucleotide analogues with ambiguous base pairing
      properties.  The mutagenesis procedure was compared with traditional protocols in which
      manganese ions are introduced to decrease the fidelity of the DNA polymerase.
AU  - Harris VH
AU  - Hamilton A
AU  - Williams DM
AU  - Hornby DP
PT  - Journal Article
TA  - Collection Symposium Series
JT  - Collection Symposium Series
SO  - Collection Symposium Series 1999 2: 209-212.

PMID- 806078
VI  - 72
DP  - 1975
TI  - Electrophoretic separation of Bacillus subtilis genes.
PG  - 2207-2211
AB  - The cleavage of Bacillus subtilis DNA by EcoRI restriction endonuclease
      produces segments which retain various degrees of genetic transforming
      activity.  The active segments analyzed thus far, range in size from 23 to 3
      kilobases and can be partially separated by agarose gel electrophoresis.
      Various markers can thus be enriched from 30- to 60-fold.
AU  - Harris-Warrick RM
AU  - Elkana Y
AU  - Ehrlich SD
AU  - Lederberg J
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1975 72: 2207-2211.

PMID- 15968074
VI  - 187
DP  - 2005
TI  - Genomic sequence of an otitis media isolate of nontypeable Haemophilus influenzae: Comparative study with H. influenzae serotype d, strain KW20.
PG  - 4627-4636
AB  - In 1995, the Institute for Genomic Research completed the genome sequence of a rough
      derivative of Haemophilus influenzae serotype d, strain KW20. Although extremely useful in
      understanding the basic biology of H. influenzae, these data have not provided significant
      insight into disease caused by nontypeable H. influenzae, as serotype d strains are not
      pathogens. In contrast, strains of nontypeable H. influenzae are the primary pathogens of
      chronic and recurrent otitis media in children. In addition, these organisms have an important
      role in acute otitis media in children as well as other respiratory diseases. Such strains
      must therefore contain a gene repertoire that differs from that of strain Rd. Elucidation of
      the differences between these genomes will thus provide insight into the pathogenic mechanisms
      of nontypeable H. influenzae. The genome of a representative nontypeable H. influenzae strain,
      86-028NP, isolated from a patient with chronic otitis media was therefore sequenced and
      annotated. Despite large regions of synteny with the strain Rd genome, there are large
      rearrangements in strain 86-028NP's genome architecture relative to the strain Rd genome. A
      genomic island similar to an island originally identified in H. influenzae type b is present
      in the strain 86-028NP genome, while the mu-like phage present in the strain Rd genome is
      absent from the strain 86-028NP genome. Two hundred eighty open reading frames were identified
      in the strain 86-028NP genome that were absent from the strain Rd genome. These data provide
      new insight that complements and extends the ongoing analysis of nontypeable H. influenzae
      virulence determinants.
AU  - Harrison A
AU  - Dyer DW
AU  - Gillaspy A
AU  - Ray WC
AU  - Mungur R
AU  - Carson MB
AU  - Zhong H
AU  - Gipson J
AU  - Gipson M
AU  - Johnson LS
AU  - Lewis L
AU  - Bakaletz LO
AU  - Munson RS Jr
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2005 187: 4627-4636.

PMID- 26868403
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Pseudomonas syringae pv. syringae ALF3 Isolated from Alfalfa.
PG  - e01722-15
AB  - We report here the annotated draft genome sequence of Pseudomonas syringae pv. syringae strain
      ALF3, isolated in Wyoming. A comparison of this genome sequence
      with those of closely related strains of P. syringae adapted to other hosts will
      facilitate research into interactions between this pathogen and alfalfa.
AU  - Harrison J
AU  - Dornbusch MR
AU  - Samac D
AU  - Studholme DJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01722-15.

PMID- 26868395
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Two Strains of Xanthomonas arboricola pv. celebensis Isolated from Banana Plants.
PG  - e01705-15
AB  - We report here the annotated draft genome sequences of strains Xanthomonas arboricola pv.
      celebensis NCPPB 1832 and NCPPB 1630 (NCPPB, National Collection
      of Plant Pathogenic Bacteria), both isolated from Musa species in New Zealand.
      This will allow the comparison of genomes between phylogenetically distant
      xanthomonads that have independently converged with the ability to colonize
      banana plants.
AU  - Harrison J
AU  - Grant MR
AU  - Studholme DJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01705-15.

PMID- 29146840
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Mucoid Pseudomonas aeruginosa Clinical Isolate PA34.
PG  - e01307-17
AB  - Pseudomonas aeruginosa is a serious threat to patients suffering from cystic fibrosis. These
      organisms are exposed to a unique set of selective pressures
      within the lung. Here, we report the draft genome sequence of a mucoid P.
      aeruginosa clinical isolate obtained from a cystic fibrosis patient colonized
      with P. aeruginosa.
AU  - Harrison LB
AU  - Hanson ND
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01307-17.

PMID- 23405318
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Methicillin-Resistant Staphylococcus aureus Isolate  MRSA-M2.
PG  - e00037-12
AB  - We report the draft genome sequence of a methicillin-resistant strain of Staphylococcus
      aureus, designated MRSA-M2. This clinical isolate was obtained
      from an osteomyelitis patient undergoing treatment at the University of Texas
      Medical Branch (Galveston, TX). This strain is an ST30, spa type T019, agr III
      strain and has been utilized as a model S. aureus strain in a number of
      proteomic, transcriptomic, and animal model studies.
AU  - Harro JM
AU  - Daugherty S
AU  - Bruno VM
AU  - Jabra-Rizk MA
AU  - Rasko DA
AU  - Shirtliff ME
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00037-12.

PMID- Not included in PubMed...
VI  - 45
DP  - 1996
TI  - Characterization of a complex restriction/modification system detected in a Bifidobacterium longum strain.
PG  - 132-136
AB  - Two type-II restriction endonucleases, BloI and BloII, have been detected in a
      Bifidobacterium longum strain.  BloI is influenced by dam methylation: it cleaves dam- but not
      dam+ DNA.  It shows a temperature and pH optimum of 45oC and pH 7.5.  Restriction analysis
      and cloning experiments showed that the recognition sequence is RGATCY and that the enzyme
      cuts 5' to the guanine residue.  It is an isoschizomer of commercial enzymes, BstYI and XhoII.
      The second activity is not inhibited by dam methylation.  It has a temperature optimum between
      25oC and 30oC and shows a broad pH optimum between 4.5 and 7.0.  The activity is thermolabile
      and can be heat-killed by a 5 min incubation at 60oC.  Cloning and sequencing experiments
      revealed that its recognition sequence is CTGCAG and that it cuts 5' to the second guanine
      residue
      in the sequence.  This enzyme is the first described isoschizomer of PstI.
AU  - Hartke A
AU  - Benachour A
AU  - Boutibonnes P
AU  - Auffray Y
PT  - Journal Article
TA  - Appl. Microbiol. Biotechnol.
JT  - Appl. Microbiol. Biotechnol.
SO  - Appl. Microbiol. Biotechnol. 1996 45: 132-136.

PMID- 20333302
VI  - 5
DP  - 2010
TI  - The Complete Genome Sequence of Haloferax volcanii DS2, a Model Archaeon.
PG  - E9605
AB  - BACKGROUND: Haloferax volcanii is an easily culturable moderate halophile
      that grows on simple defined media, is readily transformable, and has a
      relatively stable genome. This, in combination with its biochemical and
      genetic tractability, has made Hfx. volcanii a key model organism, not
      only for the study of halophilicity, but also for archaeal biology in
      general. METHODOLOGY/PRINCIPAL FINDINGS: We report here the sequencing and
      analysis of the genome of Hfx. volcanii DS2, the type strain of this
      species. The genome contains a main 2.848 Mb chromosome, three smaller
      chromosomes pHV1, 3, 4 (85, 438, 636 kb, respectively) and the pHV2
      plasmid (6.4 kb). CONCLUSIONS/SIGNIFICANCE: The completed genome sequence,
      presented here, provides an invaluable tool for further in vivo and in
      vitro studies of Hfx. volcanii.
AU  - Hartman AL
AU  - Norais C
AU  - Badger JH
AU  - Delmas S
AU  - Haldenby S
AU  - Madupu R
AU  - Robinson J
AU  - Khouri H
AU  - Ren Q
AU  - Lowe TM
AU  - Maupin-Furlow J
AU  - Pohlschroder M
AU  - Daniels C
AU  - Pfeiffer F
AU  - Allers T
AU  - Eisen JA
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2010 5: E9605.

PMID- 22003571
VI  - 85
DP  - 1974
TI  - The effect of B specific restriction and modification of DNA on linkage relationships in f1 bacteriophage II.  Evidence for a heteroduplex intermediate in f1 recombination.
PG  - 357-369
AB  - We have analyzed the results of three gene II amber x gene II amber f1 phage
      crosses.  Each was done in a non-restricting (K) host, and in a restricting (B)
      host.  In each cross, only one parent was sensitive to B restriction.  The
      other parent was protected from B restriction, either because of a combination
      of genetic mutation at one site governing sensitivity to B restriction, and B
      specific modification at the other, or because of genetic mutation at both
      sites.  In all cases, B restriction resulted in the disruption of linkage
      relationships between the gene II region and the unselected sensitivity site
      markers.  Previously we have shown that when such crosses involve a protected
      parent which is B modified at both sensitivity sites, linkage relationships
      remain the same under restricting and non-restricting conditions.  Hence, the
      SB protection is conferred by mutation rather than modification.  Taken
      together, these results imply that, in a restricted cross, the B host
      specificity system can distinguish a protected parent which is B modified from
      one which is a sensitivity site mutant.  Since such a distinction could be made
      most easily on an intermediate structure containing hybrid DNA, we interpret
      these results in terms of a recombination mechanism mediated by an asymmetric
      heteroduplex.
AU  - Hartman N
AU  - Zinder ND
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1974 85: 357-369.

PMID- 22003570
VI  - 85
DP  - 1974
TI  - The effect of B specific restriction and modification of DNA on linkage relationships in f1 bacteriophage.  I.  Studies on the mechanism of B restriction in vivo.
PG  - 345-356
AB  - We have examined the effect of B specific restriction and modification of DNA
      on bacteriophage f1 recombination, using a procedure which enabled us to
      isolate the products of individual recombination events.  We have analyzed the
      results of a series of recombination experiments, each consisting of a cross
      between two gene II amber mutants, carried out both under conditions in which
      neither parent was restricted, and under conditions in which one parent was
      restricted while the other was protected from restriction because of B specific
      modification of its genome.  At least half of the recombination events under
      both restricting and nonrestricting conditions generated one parent and one
      recombinant.  By considering the ratio of recombinant types emerging wiwth each
      parent, linkage relationships between selected and unselected markers were
      established.  These linkage relationships remained the same under restricting
      and non-restricting conditions, except that under restricting conditions,
      neither the sensitive parent nor the class of recombinants normally associated
      with that parent was found.  We interpret this result as evidence that
      restriction cleavage does not occur at the sites governing sensitivity to B
      restriction, and perhaps is random.
AU  - Hartman N
AU  - Zinder ND
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1974 85: 345-356.

PMID- 19297
VI  - 80
DP  - 1977
TI  - A new restriction enzyme from Enterobacter cloacae (EclI).
PG  - 285-287
AB  - Deoxyribonucleases, which recognize specific nucleotide sequences in a duplex
      deoxypolynucleotide chain, are designated as restriction enzymes.  These
      enzymes, which may be partially involved in the phenomenon of genetic
      restriction, have been isolated from many bacterial species.  Among them are
      relatively few members of the large family of enterobacteriaceae.  We wish to
      report here the isolation of a restriction enzyme of type II from an
      Enterobacter cloacae strain.  As judged from the lambdacleavage pattern
      obtained with this enzyme, which is designated EclI, it recognizes a sequence
      different from that of a large variety of other type II restriction enzymes.
AU  - Hartmann H
AU  - Goebel W
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1977 80: 285-287.

PMID- 29371910
VI  - 13
DP  - 2018
TI  - Draft genome sequence of Streptomyces hyaluromycini MB-PO13(T), a hyaluromycin producer.
PG  - 2
AB  - Streptomyces hyaluromycini MB-PO13(T) (=NBRC 110483(T) = DSM 100105(T)) is type strain of the
      species, which produces a hyaluronidase inhibitor, hyaluromycin.
      Here, we report the draft genome sequence of this strain together with features
      of the organism and generation, annotation and analysis of the genome sequence.
      The 11.5 Mb genome of Streptomyces hyaluromycini MB-PO13(T) encoded 10,098
      putative ORFs, of which 5317 were assigned with COG categories. The genome
      harbored at least six type I PKS clusters, three type II PKS gene clusters, two
      type III PKS gene clusters, six NRPS gene clusters, and one hybrid PKS/NRPS gene
      cluster. The type II PKS gene cluster including
      2-amino-3-hydroxycyclopent-2-enone synthetic genes was identified to be
      responsible for hyaluromycin synthesis. We propose the biosynthetic pathway based
      on bioinformatic analysis.
AU  - Harunari E
AU  - Komaki H
AU  - Ichikawa N
AU  - Hosoyama A
AU  - Kimura A
AU  - Hamada M
AU  - Igarashi Y
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2018 13: 2.

PMID- 25477409
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Nicotinate-Metabolizing Soil Bacterium Bacillus niacini DSM 2923.
PG  - e01251-14
AB  - Bacillus niacini is a member of a small yet diverse group of bacteria able to catabolize
      nicotinic acid. We report here the availability of a draft genome for
      B. niacini, which we will use to understand the evolution of its namesake
      phenotype, which appears to be unique among the species in its phylogenetic
      neighborhood.
AU  - Harvey ZH
AU  - Snider MJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01251-14.

PMID- 24356839
VI  - 1
DP  - 2013
TI  - Genome Sequences of 28 Bordetella pertussis U.S. Outbreak Strains Dating from 2010 to 2012.
PG  - e01075-13
AB  - Despite the availability of highly effective vaccines, Bordetella pertussis incidence has been
      rapidly rising in highly vaccinated populations. Recent
      outbreaks have received media attention, feeding concerns about the emergence of
      dangerous new strains with increased virulence or that escape vaccine-induced
      immunity. To accelerate the study of this reemerging pathogen, we sequenced the
      genomes of 28 B. pertussis strains isolated during outbreaks from 2010 through
      2012, making both strains and sequence data available to the scientific
      community.
AU  - Harvill ET
AU  - Goodfield LL
AU  - Ivanov Y
AU  - Meyer JA
AU  - Newth C
AU  - Cassiday P
AU  - Tondella ML
AU  - Liao P
AU  - Zimmerman J
AU  - Meert K
AU  - Wessel D
AU  - Berger J
AU  - Dean JM
AU  - Holubkov R
AU  - Burr J
AU  - Liu T
AU  - Brinkac L
AU  - Kim M
AU  - Losada L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01075-13.

PMID- 24948754
VI  - 2
DP  - 2014
TI  - Genome Sequences of Nine Bordetella holmesii Strains Isolated in the United States.
PG  - e00438-14
AB  - An increasing number of pertussis-like cases are attributed to the emergent pathogen
      Bordetella holmesii. The genomes of 9 clinical isolates show that they
      are clonal, lack the virulence factors encoded by B. pertussis, and are more
      similar to nonpertussis bordetellae. New markers for B. holmesii can be developed
      using these sequences.
AU  - Harvill ET
AU  - Goodfield LL
AU  - Ivanov Y
AU  - Smallridge WE
AU  - Meyer JA
AU  - Cassiday PK
AU  - Tondella ML
AU  - Brinkac L
AU  - Sanka R
AU  - Kim M
AU  - Losada L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00438-14.

PMID- 20540756
VI  - 11
DP  - 2010
TI  - Drawing the line between commensal and pathogenic Gardnerella vaginalis through genome analysis and virulence studies.
PG  - 375
AB  - BACKGROUND: Worldwide, bacterial vaginosis (BV) is the most common vaginal
      disorder. It is associated with risk for preterm birth and HIV infection. The
      etiology of the condition has been debated for nearly half a century and the lack
      of knowledge about its cause and progression has stymied efforts to improve
      therapy and prevention. Gardnerella vaginalis was originally identified as the
      causative agent, but subsequent findings that it is commonly isolated from
      seemingly healthy women cast doubt on this claim. Recent studies shedding light
      on the virulence properties of G. vaginalis, however, have drawn the species back
      into the spotlight. RESULTS: In this study, we sequenced the genomes of a strain
      of G. vaginalis from a healthy woman, and one from a woman with bacterial
      vaginosis. Comparative analysis of the genomes revealed significant divergence
      and in vitro studies indicated disparities in the virulence potential of the two
      strains. The commensal isolate exhibited reduced cytotoxicity and yet the
      cytolysin proteins encoded by the two strains were nearly identical, differing at
      a single amino acid, and were transcribed at similar levels. The BV-associated
      strain encoded a different variant of a biofilm associated protein gene and
      demonstrated greater adherence, aggregation, and biofilm formation. Using filters
      with different pore sizes, we found that direct contact between the bacteria and
      epithelial cells is required for cytotoxicity. CONCLUSIONS: The results indicated
      that contact is required for cytotoxicity and suggested that reduced cytotoxicity
      in the commensal isolate could be due to impaired adherence. This study outlines
      two distinct genotypic variants of G. vaginalis, one apparently commensal and one
      pathogenic, and presents evidence for disparate virulence potentials.
AU  - Harwich MD Jr
AU  - Alves JM
AU  - Buck GA
AU  - Strauss JF III
AU  - Patterson JL
AU  - Oki AT
AU  - Girerd PH
AU  - Jefferson KK
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2010 11: 375.

PMID- 23281612
VI  - 13
DP  - 2012
TI  - Genomic sequence analysis and characterization of Sneathia amnii sp. nov.
PG  - S4
AB  - BACKGROUND: Bacteria of the genus Sneathia are emerging as potential pathogens of the female
      reproductive tract. Species of Sneathia, which were formerly grouped with Leptotrichia, can be
      part of the normal microbiota of the genitourinary tracts of men and women, but they are also
      associated with a variety of clinical conditions including bacterial vaginosis, preeclampsia,
      preterm labor, spontaneous abortion, post-partum bacteremia and other invasive infections.
      Sneathia species also exhibit a significant correlation with sexually transmitted diseases and
      cervical cancer. Because Sneathia species are fastidious and rarely cultured successfully in
      vitro; and the genomes of members of the genus had until now not been characterized, very
      little is known about the physiology or the virulence of these organisms. RESULTS: Here, we
      describe a novel species, Sneathia amnii sp. nov, which closely resembles bacteria previously
      designated "Leptotrichia amnionii". As part of the Vaginal Human Microbiome Project at VCU, a
      vaginal isolate of S. amnii sp. nov. was identified, successfully cultured and
      bacteriologically cloned. The biochemical characteristics and virulence properties of the
      organism were examined in vitro, and the genome of the organism was sequenced, annotated and
      analyzed. The analysis revealed a reduced circular genome of ~1.34 Mbp, containing ~1,282
      protein-coding genes. Metabolic reconstruction of the bacterium reflected its biochemical
      phenotype, and several genes potentially associated with pathogenicity were identified.
      CONCLUSIONS:
      Bacteria with complex growth requirements frequently remain poorly characterized and, as a
      consequence, their roles in health and disease are unclear. Elucidation of the physiology and
      identification of genes putatively involved in the metabolism and virulence of S. amnii may
      lead to a better understanding of the role of this potential pathogen in bacterial vaginosis,
      preterm birth, and other issues associated with vaginal and reproductive health.
AU  - Harwich MD Jr
AU  - Serrano MG
AU  - Fettweis JM
AU  - Alves JM
AU  - Reimers MA
AU  - Buck GA
AU  - Jefferson KK
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2012 13: S4.

PMID- 28280009
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Spiroplasma sp. NBRC 100390.
PG  - e00008-17
AB  - Spiroplasma sp. NBRC 100390 was initially described as a duplicate of S. atrichopogonis
      GNAT3597T (=ATCC BAA-520T) but later found to be different in the
      16S rDNA sequences. Here, we report the complete genome sequence of this
      bacterium to establish its identity and to facilitate future investigation.
AU  - Haryono M
AU  - Lo WS
AU  - Gasparich GE
AU  - Kuo CH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00008-17.

PMID- 3034737
VI  - 50
DP  - 1986
TI  - A novel multistep method for generating precise unidirectional deletions using BspMI, a class-IIS restriction enzyme.
PG  - 55-62
AB  - A novel approach is described that permits the introduction of unidirectional
      deletions into a cloned DNA fragment, in a precisely controlled manner.  The
      method is based on the use of a special vector and a class-IIS restriction
      endonuclease, BspMI, which produces staggered cuts 4 and 8 nucleotides (nt) to
      the 3' from its recognition site 5' -ACCTGC-3'.  The DNA fragment is inserted
      into the pUC19-based plasmid, which contains a unique BspMI recognition site,
      and the appropriate number of cleavage-and-deletion cycles is performed, each
      cycle removing 4 bp.  Since the recognition site is not affected by the BspMI
      cleavage, no recloning of the DNA fragment is necessary.  Each cycle consists
      of (i) BspMI cleavage, (ii) removal of the 4-nt single-stranded cohesive ends
      with mung bean nuclease (MB), and (iii) blunt-end ligation to recircularize the
      plasmid.  The shortened plasmid is reintroduced into the host, after one or
      after several such 4-bp deletion cycles.  When DNA is inserted into the
      multiple cloning site in the lacZ-alpha gene, the progress of 4-bp removal can
      be followed by determining the Lac phenotype, since removal of multiples of 3
      bp retains the reading frame while other kinds of deletions distort (or
      restore) the reading frame.  Loss of pre-existing restriction sites or creation
      of new ones also permits monitoring the progress of the deletion process.  The
      partial fill-in of the cohesive ends with less than four deoxyribonucleotide
      triphosphates, as mediated by Klenow fragment of E. coli DNA polymerase I
      (PolIk), would result in 1,2 or 3-bp deletions or additions in a given cleavage
      cycle, which permits one to create precise deletions.  An analogous series of
      cycles of BspMI cleavage employing a PolIk-mediated fill-in reaction instead of
      the MB digestion step, and followed by ligation, would permit one to synthesize
      various 4-bp direct-repeat sequences and desired variants of them.
AU  - Hasan N
AU  - Kim SC
AU  - Podhajska AJ
AU  - Szybalski W
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1986 50: 55-62.

PMID- 26021923
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Mycobacterium chelonae Type Strain ATCC 35752.
PG  - e00536-15
AB  - Mycobacterium chelonae is a rapidly growing opportunistic nontuberculous mycobacterial (NTM)
      species that causes infections in humans and other hosts.
      Here, we report the draft genome sequence of Mycobacterium chelonae type strain
      ATCC 35752, consisting of 4.89 Mbp, 63.96% G+C content, 4,489 protein-coding
      genes, 48 tRNAs, and 3 rRNA genes.
AU  - Hasan NA
AU  - Davidson RM
AU  - de Moura VC
AU  - Garcia BJ
AU  - Reynolds PR
AU  - Epperson LE
AU  - Farias-Hesson E
AU  - DeGroote MA
AU  - Jackson M
AU  - Strong M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00536-15.

PMID- 21078967
VI  - 107
DP  - 2010
TI  - Comparative genomics of clinical and environmental Vibrio mimicus.
PG  - 21134-21139
AB  - Whether Vibrio mimicus is a variant of Vibrio cholerae or a separate species has
      been the subject of taxonomic controversy. A genomic analysis was undertaken to
      resolve the issue. The genomes of V. mimicus MB451, a clinical isolate, and
      VM223, an environmental isolate, comprise ca. 4,347,971 and 4,313,453 bp and
      encode 3,802 and 3,290 ORFs, respectively. As in other vibrios, chromosome I
      (C-I) predominantly contains genes necessary for growth and viability, whereas
      chromosome II (C-II) bears genes for adaptation to environmental change. C-I
      harbors many virulence genes, including some not previously reported in V.
      mimicus, such as mannose-sensitive hemagglutinin (MSHA), and enterotoxigenic
      hemolysin (HlyA); C-II encodes a variant of Vibrio pathogenicity island 2
      (VPI-2), and Vibrio seventh pandemic island II (VSP-II) cluster of genes.
      Extensive genomic rearrangement in C-II indicates it is a hot spot for evolution
      and genesis of speciation for the genus Vibrio. The number of virulence regions
      discovered in this study (VSP-II, MSHA, HlyA, type IV pilin, PilE, and integron
      integrase, IntI4) with no notable difference in potential virulence genes between
      clinical and environmental strains suggests these genes also may play a role in
      the environment and that pathogenic strains may arise in the environment.
      Significant genome synteny with prototypic pre-seventh pandemic strains of V.
      cholerae was observed, and the results of phylogenetic analysis support the
      hypothesis that, in the course of evolution, V. mimicus and V. cholerae diverged
      from a common ancestor with a prototypic sixth pandemic genomic backbone.
AU  - Hasan NA
AU  - Grim CJ
AU  - Haley BJ
AU  - Chun J
AU  - Alam M
AU  - Taviani E
AU  - Hoq M
AU  - Munk AC
AU  - Saunders E
AU  - Brettin TS
AU  - Bruce DC
AU  - Challacombe JF
AU  - Detter JC
AU  - Han CS
AU  - Xie G
AU  - Nair GB
AU  - Huq A
AU  - Colwell RR
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2010 107: 21134-21139.

PMID- 27881537
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Mycobacterium chimaera Strain AH16.
PG  - e01276-16
AB  - Mycobacterium chimaera is a nontuberculous mycobacterial species that causes cardiovascular,
      pulmonary, and postsurgical infections. Here, we report the first
      complete genome sequence of M. chimaera This genome is 6.33 Mbp, with a G+C
      content of 67.56%, and encodes 4,926 protein-coding genes, as well as 74 tRNAs,
      one ncRNA, and three rRNA genes.
AU  - Hasan NA
AU  - Honda JR
AU  - Davidson RM
AU  - Epperson LE
AU  - Bankowski MJ
AU  - Chan ED
AU  - Strong M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01276-16.

PMID- 28774973
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Mycobacteriumchimaera Strain CDC2015-22-71.
PG  - e00693-17
AB  - Mycobacterium chimaera is a nontuberculous mycobacterium species commonly found in the
      environment. Here, we report the first complete genome sequence of a
      strain from the investigation of invasive infections following open-heart
      surgeries that used contaminated LivaNova Sorin Stockert 3T heater-cooler
      devices.
AU  - Hasan NA
AU  - Lawsin A
AU  - Perry KA
AU  - Alyanak E
AU  - Toney NC
AU  - Malecha A
AU  - Rowe LA
AU  - Batra D
AU  - Moulton-Meissner H
AU  - Miller JR
AU  - Strong M
AU  - Laufer HA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00693-17.

PMID- 28912319
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Mycobacterium chimaera SJ42, a Nonoutbreak Strain from an Immunocompromised Patient with Pulmonary Disease.
PG  - e00963-17
AB  - Mycobacterium chimaera, a nontuberculous mycobacterium (NTM) belonging to the Mycobacterium
      avium complex (MAC), is an opportunistic pathogen that can cause
      respiratory and disseminated disease. We report the complete genome sequence of a
      strain, SJ42, isolated from an immunocompromised male presenting with MAC
      pneumonia, assembled from Illumina and Oxford Nanopore data.
AU  - Hasan NA
AU  - Warren RL
AU  - Epperson LE
AU  - Malecha A
AU  - Alexander DC
AU  - Turenne CY
AU  - MacMillan D
AU  - Birol I
AU  - Pleasance S
AU  - Coope R
AU  - Jones SJM
AU  - Romney MG
AU  - Ng M
AU  - Chan T
AU  - Rodrigues M
AU  - Tang P
AU  - Gardy JL
AU  - Strong M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00963-17.

PMID- 29853509
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Saccharospirillum sp. Strain MSK14-1, Isolated from Surface Seawater Collected at Aburatsubo Inlet in Japan.
PG  - e00469-18
AB  - Here, we report the draft genome sequence of Saccharospirillum sp. strain MSK14-1, isolated
      from surface seawater collected at Aburatsubo Inlet in Japan.
      The genome sequence of strain MSK14-1 should contribute to our understanding of
      the characteristics of the genus Saccharospirillum.
AU  - Hasegawa M
AU  - Nakajima Y
AU  - Wong SK
AU  - Nakamura K
AU  - Ogura Y
AU  - Hayashi T
AU  - Kogure K
AU  - Yoshizawa S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00469-18.

PMID- 27895128
VI  - 85
DP  - 2017
TI  - Characterization of the pathogenicity of Streptococcus intermedius TYG1620 isolated from a human brain abscess based on the complete genome sequence with transcriptome analysis and transposon mutagenesis in a murine subcutaneous abscess model.
PG  - e00886-16
AB  - Streptococcus intermedius is known to cause periodontitis and pyogenic infections
      in the brain and liver. Here we report the complete genome sequence of strain
      TYG1620 (genome size: 2,006,877 bp; GC content: 37.6%; 2,020 predicted ORFs)
      isolated from a brain abscess in an infant. Comparative genome analysis of S.
      intermedius genome sequences suggested that TYG1620 carries a notable type VII
      secretion system (T7SS), two long-repeat regions and 19 ORFs for
      cell-wall-anchored proteins (CWAPs). To elucidate genes responsible for the
      pathogenicity of TYG1620, transcriptome analysis was performed in a murine
      subcutaneous abscess model. The results suggest that the expression of small
      hypothetical proteins similar to phenol-soluble modulin (PSM) beta1, a
      staphylococcal virulence factor, significantly increased in the abscess model. In
      addition, an experiment in a murine subcutaneous abscess model with random
      Tn-mutant attenuation suggested that Tn-mutants in 212 ORFs in the Tn-mutant
      library were attenuated in the murine abscess model (629 ORFs disrupted in
      total); the 212 ORFs are putatively essential for abscess formation.
      Transcriptome analysis identified 37 ORFs, including paralogs of the T7SS and
      putative glucan-binding CWAP in long-repeat regions, as upregulated and
      attenuated in vivo This study provides a comprehensive characterization of S.
      intermedius pathogenicity based on the complete genome sequence and a murine
      subcutaneous abscess model with transcriptome and Tn-mutagenesis, leading to
      identification of pivotal targets for vaccines or antimicrobial agents for the
      control of S. intermedius infections.
AU  - Hasegawa N
AU  - Sekizuka T
AU  - Sugi Y
AU  - Kawakami N
AU  - Ogasawara Y
AU  - Kato K
AU  - Yamashita A
AU  - Takeuchi F
AU  - Kuroda M
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2017 85: e00886-16.

PMID- 15590682
VI  - 280
DP  - 2005
TI  - Crystal structures of type II restriction endonuclease Eco0109I and its complex with cognate DNA.
PG  - 5605-5610
AB  - EcoO109I is a type II restriction endonuclease that recognizes the DNA sequence of RGGNCCY.
      Here we describe the crystal structures of
      EcoO109I and its complex with DNA. A comparison of the two structures
      shows that the catalytic domain moves drastically to capture the DNA.
      One metal ion and two water molecules are observed near the active site
      of the DNA complex. The metal ion is a Lewis acid that stabilizes the
      pentavalent phosphorus atom in the transition state. One water
      molecule, activated by Lys-126, attacks the phosphorus atom in an S(N)2
      mechanism, whereas the other water interacts with the W-leaving oxygen
      to donate a proton to the oxygen. EcoO109I is similar to EcoRI family
      enzymes in terms of its DNA cleavage pattern and folding topology of
      the common motif in the catalytic domain, but it differs in the manner
      of DNA recognition. Our findings propose a novel classification of the
      type II restriction endonucleases and lead to the suggestion that
      EcoO109I represents a new subclass of the EcoRI family.
AU  - Hashimoto H
AU  - Shimizu T
AU  - Imasaki T
AU  - Kato M
AU  - Shichijo N
AU  - Kita K
AU  - Sato M
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2005 280: 5605-5610.

PMID- 10957641
VI  - 56
DP  - 2000
TI  - Crystallographic study of intein homing endonuclease II encoded in the archaeal DNA polymerase gene.
PG  - 1185-1186
AB  - Intein homing endonucleases are proteins spliced out from a precursor protein and
      site-specific enzymes that make double-strand breaks in inteinless alleles. Crystals of intein
      homing endonuclease II from the hyperthermophilic archaeon Pyrococcus kodakaraensis strain
      KOD1 (PI-PkoII) have been grown at room temperature using ammonium sulfate as a precipitant.
      The diffraction pattern of the crystal extends to 3.0 A resolution at room temperature upon
      exposure to synchrotron X-rays at KEK-PF, Japan. The crystals have symmetry consistent with
      space group C222(1), with unit-cell parameters a = 107.6, b = 150.5, c = 146.8 A. A full set
      of X-ray diffraction data were collected to 3.0 A Bragg spacing from a native crystal with an
      overall R(merge) of 4.8% and a completeness of 96.6%.
AU  - Hashimoto H
AU  - Takahashi H
AU  - Nishioka M
AU  - Fujiwara S
AU  - Takagi M
AU  - Imanaka T
AU  - Inoue T
AU  - Kai Y
PT  - Journal Article
TA  - Acta Crystallogr. D Biol. Crystallogr.
JT  - Acta Crystallogr. D Biol. Crystallogr.
SO  - Acta Crystallogr. D Biol. Crystallogr. 2000 56: 1185-1186.

PMID- 8678306
VI  - 231
DP  - 1995
TI  - Quantitative determination of effective nibbling activities contaminating restriction endonuclease preparations.
PG  - 230-236
AB  - A simple and sensitive procedure with which to detect residual exonucleolytic nibbling
      activities contaminating restriction endonuclease preparations is described.  The procedure
      uses the kyosei-plasmid, pKF4, which confers kanamycin resistance and enforces streptomycin
      sensitivity encoded by the trp promoter/operator-driven rpsL+4amber (POtrp-rpsL+4am) gene onto
      Escherichia coli streptomycin-resistant, amber-suppressive, trp repressor-negative strains
      such as TH5.  When TH5 cells transformed by pKF4 were selected on agar medium containing
      kanamycin plus streptomycin, the efficiency of transformation plating was substantially lower
      than that on agar containing kanamycin alone.  However, when pKF4 DNA was digested by
      restriction enzymes that cut once per molecule within POtrp-rpsL+4am and religated, the
      plating efficiency increased depending on the degree of contamination of exonucleolytic
      nibbling activities in the enzyme preparations, due to deletion mutation at the ligation
      junction.  Plating efficiency was converted to "effective nibbling activity" corresponding to
      Bal31 nuclease-equivalent units.  Using this procedure, effective nibbling activities were
      detected in 17 of 34 commercial samples of restriction enzymes tested.  The method is simple
      and more sensitive than the procedures used by the commercial suppliers and it is applicable
      to the quality control testing of more than 100 restriction enzymes.
AU  - Hashimoto-Gotoh T
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 1995 231: 230-236.

PMID- 7590318
VI  - 164
DP  - 1995
TI  - Detection of exonuclease activities in restriction endonuclease preparations using an enforcement plasmid for kanamycin-resistance selection.
PG  - 41-44
AB  - A new enforcement (kyosei-) cloning plasmid vector, designated pKF4, was constructed which
      confers kanamycin resistance (KmR) and enforces streptomycin sensitivity (SmS).  Since it is
      important to employ restriction endonuclease (ENase) preparations free of exonuclease (Exo)
      activities for effective use of the kyosei-cloning procedure, ENases such as HpaI and SmaI
      purchased from four different suppliers were examined for possible contamination by
      exonucleases using pKF4.  The plasmid DNA was digested with either ENase, ligated and
      transformed into Escherichia coli mutants, rpsL, supE, trpR.  With pKF4 intact DNA (approx. 8
      ng), 2.3 x 10/5 KmR transformant and four KmRsmR transformant colonies were obtained: the
      efficiency of transformation plating (ETP) of the intact DNA was approx. 2 x 10-5.  On the
      other hand, the ETP values were significantly higher by one to three orders of magnitude when
      cut and rejoined DNAs were used under the same conditions in six out of either ENase samples
      examined.  The results indicate that even commercially supplied ENases, that should have
      passed their quality control test, could have been contaminated with Exo sufficient to
      interfere with effective use of the kyosei-cloning method.  Therefore, it is advisable to
      examine ENase samples for possible contamination with Exo activities, in order to choose the
      right preparations for this method at the beginning of the experiments.
AU  - Hashimoto-Gotoh T
AU  - Tsujimura A
AU  - Ogasahara Y
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 164: 41-44.

PMID- 27284135
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Mesorhizobium ciceri Strain CC1192, an Efficient Nitrogen-Fixing Microsymbiont of Cicer arietinum.
PG  - e00516-16
AB  - We report the complete genome sequence of Mesorhizobium ciceri strain CC1192, an  efficient
      nitrogen-fixing microsymbiont of Cicer arietinum (chickpea). The genome
      consists of 6.94 Mb distributed between a single chromosome (6.29 Mb) and a
      plasmid (0.65 Mb).
AU  - Haskett T
AU  - Wang P
AU  - Ramsay J
AU  - O'Hara G
AU  - Reeve W
AU  - Howieson J
AU  - Terpolilli J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00516-16.

PMID- 27284134
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Mesorhizobium ciceri bv. biserrulae Strain WSM1284, an Efficient Nitrogen-Fixing Microsymbiont of the Pasture Legume Biserrula  pelecinus.
PG  - e00514-16
AB  - We report the complete genome sequence of Mesorhizobium ciceri bv. biserrulae strain WSM1284,
      a nitrogen-fixing microsymbiont of the pasture legume Biserrula
      pelecinus The genome consists of 6.88 Mb distributed between a single chromosome
      (6.33 Mb) and a single plasmid (0.55 Mb).
AU  - Haskett T
AU  - Wang P
AU  - Ramsay J
AU  - O'Hara G
AU  - Reeve W
AU  - Howieson J
AU  - Terpolilli J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00514-16.

PMID- 15941775
VI  - 56
DP  - 2005
TI  - beta-Lactamases among extended-spectrum beta-lactamase (ESBL)-resistant Salmonella from poultry, poultry products and human patients in The Netherlands.
PG  - 115-121
AB  - OBJECTIVES: The purpose of this work was to study the genetic determinants
      responsible for extended-spectrum beta-lactamase (ESBL) resistance of
      Salmonella isolated from Dutch poultry, poultry meat and hospitalized
      humans. METHODS: Thirty-four ESBL-resistant Salmonella isolates from The
      Netherlands were tested towards 21 antimicrobial agents. PCR and
      sequencing were used to determine the underlying genetic determinants
      responsible for the ESBL phenotypes. The transferability of the ESBL
      phenotypes was tested by conjugation to a susceptible Salmonella enterica
      serovar Dublin and plasmid purification, restriction fragment length
      polymorphism (RFLP) and pulsed-field gel electrophoresis (PFGE) were
      employed to further characterize a subset of the isolates. RESULTS: A
      great genetic diversity was seen among the isolates. The bla(TEM-52) gene
      was most predominant and was found among Salmonella enterica serovars
      Blockley, Thomson, London, Enteritidis phage type 14b, Paratyphi B,
      Virchow and Typhimurium phage types 11 and 507. We also found the
      bla(TEM-20) gene in S. Paratyphi B var. Java and the bla(TEM-63) gene in
      S. Isangi. Furthermore, we detected the bla(CTX-M-28) gene in S. Isangi
      and the bla(CTX-M-3) gene in S. Typhimurium phage type 507. The
      bla(CTX-M-2) gene was identified in S. Virchow, which also contained a
      copy of the bla(SHV-2) gene and a copy of the bla(TEM-1) gene. The
      bla(SHV-12) gene was found alone in S. Concord and together with the
      bla(TEM-52) gene in S. Typhimurium. Finally, the bla(ACC-1) gene was
      cloned from a S. Bareilly isolate and was found to be present on
      indistinguishable plasmids in all S. Bareilly isolates examined as well as
      in a S. Braenderup isolate and a S. Infantis isolate. CONCLUSIONS: Our
      data underscore the diversity of ESBL genes in Salmonella enterica
      isolated from animals, food products and human patients.
AU  - Hasman H
AU  - Mevius D
AU  - Veldman K
AU  - Olesen I
AU  - Aarestrup FM
PT  - Journal Article
TA  - J. Antimicrob. Chemother.
JT  - J. Antimicrob. Chemother.
SO  - J. Antimicrob. Chemother. 2005 56: 115-121.

PMID- 26769946
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Arthrobacter sp. Strain LS16, Isolated from Agricultural Soils with Potential for Applications in Bioremediation and  Bioproducts.
PG  - e01586-15
AB  - Here we report the complete genomic sequence of the bacterium Arthrobacter sp. strain LS16,
      consisting of a single circular chromosome of 3.85 Mb with no
      identified plasmid. Data contained within will facilitate future genetic
      modification and engineering of the Arthrobacter sp. LS16 metabolic network to
      enhance traits relevant to bioremediation and bioproducts.
AU  - Hassan I
AU  - Eastman AW
AU  - Weselowski B
AU  - Mohamedelhassan E
AU  - Yanful EK
AU  - Yuan ZC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01586-15.

PMID- 24970833
VI  - 2
DP  - 2014
TI  - Genome Sequence of the Neurotoxigenic Clostridium butyricum Strain 5521.
PG  - e00632-14
AB  - Clostridium strains from six phylogenetic groups, C. botulinum groups I to IV, C. baratii, and
      C. butyricum, display the capacity to produce botulinum neurotoxin.
      Here, we present the genome sequence of a C. butyricum isolate, the
      neurotoxigenic strain 5521, which encodes the type E botulinum neurotoxin.
AU  - Hassan KA
AU  - Elbourne LD
AU  - Tetu SG
AU  - Johnson EA
AU  - Paulsen IT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00632-14.

PMID- 23516187
VI  - 1
DP  - 2013
TI  - Genome Sequence of the Group III Clostridium botulinum Strain Eklund-C.
PG  - e0004413
AB  - The neurotoxins produced by Clostridium botulinum strains are among the world's most potent
      toxins and are the causative agents of paralytic botulism. Here, we
      present the draft genome sequence of the group III C. botulinum strain Eklund-C,
      including a pseudolysogen-like bacteriophage that harbors the type C neurotoxin
      operon.
AU  - Hassan KA
AU  - Tetu SG
AU  - Elbourne LD
AU  - Johnson EA
AU  - Paulsen IT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0004413.

PMID- 23408795
VI  - 7
DP  - 2012
TI  - Complete genome sequence of Corynebacterium pseudotuberculosis biovar ovis strain P54B96 isolated from antelope in South Africa obtained by rapid next generation  sequencing technology.
PG  - 189-199
AB  - The Actinobacteria, Corynebacterium pseudotuberculosis strain P54B96, a nonmotile,
      non-sporulating and a mesophile bacterium, was isolated from liver,
      lung and mediastinal lymph node lesions in an antelope from South Africa. This
      strain is interesting in the sense that it has been found together with
      non-tuberculous mycobacteria (NTMs) which could nevertheless play a role in the
      lesion formation. In this work, we describe a set of features of C.
      pseudotuberculosis P54B96, together with the details of the complete genome
      sequence and annotation. The genome comprises of 2.34 Mbp long, single circular
      genome with 2,084 protein-coding genes, 12 rRNA, 49 tRNA and 62 pseudogenes and a
      G+C content of 52.19%. The analysis of the genome sequence provides means to
      better understanding the molecular and genetic basis of virulence of this
      bacterium, enabling a detailed investigation of its pathogenesis.
AU  - Hassan SS et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 7: 189-199.

PMID- 23012291
VI  - 194
DP  - 2012
TI  - Whole-genome sequence of Corynebacterium pseudotuberculosis strain Cp162, isolated from camel.
PG  - 5718-5719
AB  - Corynebacterium pseudotuberculosis is a pathogen of great veterinary and economic
      importance, since it affects livestock, mainly sheep and goats, worldwide,
      together with reports of its presence in camels in several Arabic, Asiatic, and
      East and West African countries, as well as Australia. In this article, we report
      the genome sequence of Corynebacterium pseudotuberculosis strain Cp162, collected
      from the external neck abscess of a camel in the United Kingdom.
AU  - Hassan SS et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5718-5719.

PMID- 25278537
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Devosia sp. Strain 17-2-E-8 and Devosia riboflavina Strain IFO13584.
PG  - e00994-14
AB  - Here we report the draft genome of Devosia sp. strain 17-2-E-8, isolated from Ontario
      agricultural soil (Canada) with promising deoxynivalenol
      biotransformation capabilities. In addition, we report the draft genome of
      Devosia riboflavina strain IFO13584, used as a control strain in our studies
      aimed at highlighting unique gene clusters involved in deoxynivalenol
      epimerization.
AU  - Hassan YI
AU  - Lepp D
AU  - He J
AU  - Zhou T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00994-14.

PMID- 26251505
VI  - 3
DP  - 2015
TI  - Insights into the Hydrocarbon Tolerance of Two Devosia Isolates, D. chinhatensis  Strain IPL18T and D. geojensis Strain BD-c194T, via Whole-Genome Sequence  Analysis.
PG  - e00890-15
AB  - Hexachlorocyclohexane (HCH) was among the most commonly used pesticides after the Second World
      War. The extensive use of this hydrocarbon for almost six decades
      has created a contamination problem on a global scale, and bioremediation methods
      are being extensively explored. The reported ability of some Devosia species to
      grow in the presence of appreciable amounts of hydrocarbons (2,000 mg/kg of
      contaminated soil) is attracting closer attention. Here, we report the de novo
      genome assembly of two hydrocarbon-tolerating Devosia isolates, D. chinhatensis
      strain IPL18(T) and D. geojensis strain BD-c194(T), as a first step toward
      understanding the metabolic pathways involved in their environmental adaptation
      and tolerance toward hydrocarbons.
AU  - Hassan YI
AU  - Lepp D
AU  - Li XZ
AU  - Zhou T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00890-15.

PMID- 25999556
VI  - 3
DP  - 2015
TI  - Genome Assemblies of Three Soil-Associated Devosia species: D. insulae, D. limi,  and D. soli.
PG  - e00514-15
AB  - Agricultural soils constitute highly diverse ecosystems with very rich bacterial  populations.
      Recent studies employing next-generation sequencing techniques have
      begun to explore the dynamics of bacterial species of such soils and utilized
      metagenomics approaches to understand how the diversity in soil microorganisms is
      affected or modified by agricultural practices. Understanding any microorganism's
      environmental adaptability in the genomic era starts by fully appreciating their
      encoding genome. Here, we report the draft genome sequences of three Devosia
      species based on three type strains that originated from soil samples: D. insulae
      strain DS-56, D. limi strain DSM17137, and D. soli strain GH2-10.
AU  - Hassan YI
AU  - Lepp D
AU  - Zhou T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00514-15.

PMID- 24501653
VI  - 9
DP  - 2013
TI  - Non-contiguous finished genome sequence and description of Halopiger djelfamassiliensis sp. nov.
PG  - 160-174
AB  - Halopiger djelfamassiliensis strain IIH2(T) sp. nov. is the type strain of Halopiger
      djelfamassiliensis sp. nov., a new species within the genus Halopiger.
      This strain, whose genome is described here, was isolated from evaporitic
      sediment of the hypersaline Lake Zahrez Gharbi in the Djelfa region (Algeria). H.
      Djelfamassiliensis is a Gram-negative, polymorphic-shaped and strictly aerobic
      archaeon. Here we describe the features of this organism, together with the
      complete genome sequence and annotation. The 3,771,216 bp long genome-contains
      3,761 protein-coding and 51 RNA genes, including 4 rRNA genes.
AU  - Hassani II
AU  - Robert C
AU  - Michelle C
AU  - Raoult D
AU  - Hacene H
AU  - Desnues C
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 9: 160-174.

PMID- 21467222
VI  - 108
DP  - 2011
TI  - Discovery of the curcumin metabolic pathway involving a unique enzyme in an intestinal microorganism.
PG  - 6615-6620
AB  - Polyphenol curcumin, a yellow pigment, derived from the rhizomes of a plant (Curcuma longa
      Linn) is a natural antioxidant exhibiting a variety of pharmacological activities and
      therapeutic properties. It has long been used as a traditional medicine and as a preservative
      and coloring agent in foods. Here, curcumin-converting microorganisms were isolated from human
      feces, the one exhibiting the highest activity being identified as Escherichia coli. We are
      thus unique in discovering that E. coli was able to act on curcumin. The curcumin-converting
      enzyme was purified from E. coli and characterized. The native enzyme had a molecular mass of
      about 82 kDa and consisted of two identical subunits. The enzyme has a narrow substrate
      spectrum, preferentially acting on curcumin. The microbial metabolism of curcumin by the
      purified enzyme was found to comprise a two-step reduction, curcumin being converted
      NADPH-dependently into an intermediate product, dihydrocurcumin, and then the end product,
      tetrahydrocurcumin. We named this enzyme 'NADPH-dependent curcumin/dihydrocurcumin
      reductase' (CurA). The gene (curA) encoding this enzyme was also identified. A homology
      search with the BLAST program revealed that a unique enzyme involved in curcumin metabolism
      belongs to the medium-chain dehydrogenase/reductase superfamily.
AU  - Hassaninasab A
AU  - Hashimoto Y
AU  - Tomita-Yokotani K
AU  - Kobayashi M
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2011 108: 6615-6620.

PMID- 29527191
VI  - 9
DP  - 2018
TI  - Pseudomonas rhizophila S211, a New Plant Growth-Promoting Rhizobacterium with Potential in Pesticide-Bioremediation.
PG  - 34
AB  - A number of Pseudomonas strains function as inoculants for biocontrol,
      biofertilization, and phytostimulation, avoiding the use of pesticides and
      chemical fertilizers. Here, we present a new metabolically versatile plant
      growth-promoting rhizobacterium, Pseudomonas rhizophila S211, isolated from a
      pesticide contaminated artichoke field that shows biofertilization, biocontrol
      and bioremediation potentialities. The S211 genome was sequenced, annotated and
      key genomic elements related to plant growth promotion and biosurfactant (BS)
      synthesis were elucidated. S211 genome comprises 5,948,515 bp with 60.4% G+C
      content, 5306 coding genes and 215 RNA genes. The genome sequence analysis
      confirmed the presence of genes involved in plant-growth promoting and
      remediation activities such as the synthesis of ACC deaminase, putative
      dioxygenases, auxin, pyroverdin, exopolysaccharide levan and rhamnolipid BS. BS
      production by P. rhizophila S211 grown on olive mill wastewater based media was
      effectively optimized using a central-composite experimental design and response
      surface methodology (RSM). The optimum conditions for maximum BS production yield
      (720.80 +/- 55.90 mg/L) were: 0.5% (v/v) inoculum size, 15% (v/v) olive oil mill
      wastewater (OMWW) and 40 degrees C incubation temperature at pH 6.0 for 8 days
      incubation period. Biochemical and structural characterization of S211 BS by
      chromatography and spectroscopy studies suggested the glycolipid nature of the
      BS. P. rhizophila rhamnolipid was stable over a wide range of temperature (40-90
      degrees C), pH (6-10), and salt concentration (up to 300 mM NaCl). Due to its
      low-cost production, emulsification activities and high performance in
      solubilization enhancement of chemical pesticides, the indigenous BS-producing
      PGPR S211 could be used as a promising agent for environmental bioremediation of
      pesticide-contaminated agricultural soils.
AU  - Hassen W
AU  - Neifar M
AU  - Cherif H
AU  - Najjari A
AU  - Chouchane H
AU  - Driouich RC
AU  - Salah A
AU  - Naili F
AU  - Mosbah A
AU  - Souissi Y
AU  - Raddadi N
AU  - Ouzari HI
AU  - Fava F
AU  - Cherif A
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2018 9: 34.

PMID- 25278531
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Mycoplasma canadense Strain HAZ 360_1 from Bovine Mastitic Milk in Japan.
PG  - e00984-14
AB  - Bovine mycoplasmal mastitis is spreading quickly among cows. Mycoplasma canadense, a causal
      species of bovine mastitis, reduces milk quality and quantity
      via the infiltration of numerous inflammatory cells. Presented here is the
      complete 693,241-bp genome sequence of M. canadense strain HAZ 360_1, which was
      isolated in Japan.
AU  - Hata E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00984-14.

PMID- 25883285
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Mycoplasma arginini Strain HAZ 145_1 from Bovine Mastitic Milk in Japan.
PG  - e00265-15
AB  - Mycoplasma arginini is a species sometimes isolated from bovine specimens, mastitic milk, etc.
      Its pathogenicity against cows, however, is unspecific,
      unlike other bovine mycoplasmas. Its whole-genome sequence is needed to
      comprehend its real image. We present here the 678,592-bp complete genome
      sequence of M. arginini strain HAZ 145_1.
AU  - Hata E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00265-15.

PMID- 25013143
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Mycoplasma californicum Strain HAZ160_1 from Bovine Mastitic Milk in Japan.
PG  - e00684-14
AB  - Bovine mycoplasmal mastitis is spreading quickly among cows. It often leads to clinical
      mastitis outbreaks and often results in huge economic losses. Mycoplasma
      californicum is an important causal species of bovine mastitis. Presented here is
      the 799,088-bp complete genome sequence of M. californicum strain HAZ160_1, which
      was isolated in Japan.
AU  - Hata E
AU  - Murakami K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00684-14.

PMID- 28963211
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Mycoplasma bovirhinis Strain HAZ141_2 from Bovine Nasal Discharge in Japan.
PG  - e01000-17
AB  - Mycoplasma bovirhinis, a mycoplasmal species involved in bovine respiratory diseases, is also
      a commensal microorganism that inhabits the bovine respiratory
      and reproductive organs. We present the complete 948,039-bp genome sequence of M.
      bovirhinis strain HAZ141_2, which was isolated from bovine nasal discharge in
      Japan.
AU  - Hata E
AU  - Nagai K
AU  - Murakami K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01000-17.

PMID- 28183755
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Mycoplasma bovigenitalium Strain HAZ 596 from a Bovine Vagina in Japan.
PG  - e01554-16
AB  - Mycoplasma bovigenitalium, a mycoplasmal species involved in various bovine diseases,
      including genital disease and mastitis, is also a commensal
      microorganism that inhabits the bovine genital organs. We present here the
      complete 853,553-bp genome sequence of M. bovigenitalium strain HAZ 596, which
      was isolated from a bovine vagina in Japan.
AU  - Hata E
AU  - Nagai K
AU  - Murakami K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01554-16.

PMID- 11934864
VI  - 129
DP  - 2002
TI  - Dnmt3L cooperates with the Dnmt3 family of de novo DNA methyltransferases to establish maternal imprints in mice.
PG  - 1983-1993
AB  - Genomic imprinting is regulated by differential methylation of the paternal and maternal
      genome. However, it remains unknown how parental imprinting is established during
      gametogenesis. In this study, we demonstrate that Dnmt3L, a protein sharing homology with DNA
      methyltransferases, Dnmt3a and Dnmt3b, but lacking enzymatic activity, is essential for the
      establishment of maternal methylation imprints and appropriate expression of maternally
      imprinted genes. We also show that Dnmt3L interacts with Dnmt3a and Dnmt3b and co-localizes
      with these enzymes in the nuclei of transfected cells, suggesting that Dnmt3L may regulate
      genomic imprinting via the Dnmt3 family enzymes. Consistent with this model, we show that
      [Dnmt3a(-/-), Dnmt3b()] mice also fail to establish maternal methylation imprints. In
      addition, both Dnmt3a and Dnmt3L are required for spermatogenesis. Together, our findings
      suggest that Dnmt3L may cooperate with Dnmt3 family methyltransferases to carry out de novo
      methylation of maternally imprinted genes in oocytes.
AU  - Hata K
AU  - Okano M
AU  - Lei H
AU  - Li E
PT  - Journal Article
TA  - Development
JT  - Development
SO  - Development 2002 129: 1983-1993.

PMID- 28684568
VI  - 5
DP  - 2017
TI  - Genome Sequence of Oxalobacter formigenes Strain HC-1.
PG  - e00533-17
AB  - The lack of Oxalobacter formigenes colonization of the human gut has been correlated with the
      formation of calcium oxalate kidney stones and also with the
      number of recurrent kidney stone episodes. Here, we present the genome sequence
      of HC-1, a human strain isolated from an individual residing in Iowa, USA.
AU  - Hatch M
AU  - Allison MJ
AU  - Yu F
AU  - Farmerie W
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00533-17.

PMID- 28705966
VI  - 5
DP  - 2017
TI  - Genome Sequence of Oxalobacter formigenes Strain OXCC13.
PG  - e00534-17
AB  - The lack of Oxalobacter formigenes colonization in the human gut is generally acknowledged as
      a risk factor for kidney stone formation since this microorganism
      can play an important role in oxalate homeostasis. Here, we present the genome
      sequence of OXCC13, a human strain isolated from an individual residing in
      Germany.
AU  - Hatch M
AU  - Allison MJ
AU  - Yu F
AU  - Farmerie W
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00534-17.

PMID- 22282335
VI  - 86
DP  - 2012
TI  - Complete Genome Sequences of 138 Mycobacteriophages.
PG  - 2382-2384
AB  - Bacteriophages are the most numerous biological entities in the biosphere, and
      although their genetic diversity is high, it remains ill defined.
      Mycobacteriophages-the viruses of mycobacterial hosts-provide insights into this
      diversity as well as tools for manipulating Mycobacterium tuberculosis. We report
      here the complete genome sequences of 138 new mycobacteriophages, which-together
      with the 83 mycobacteriophages previously reported-represent the largest
      collection of phages known to infect a single common host, Mycobacterium
      smegmatis mc(2) 155.
AU  - Hatfull GF
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 2012 86: 2382-2384.

PMID- 16789831
VI  - 2
DP  - 2006
TI  - Exploring the mycobacteriophage metaproteome: phage genomics as an educational platform.
PG  - e92
AB  - Bacteriophages are the most abundant forms of life in the biosphere and carry genomes
      characterized by high genetic diversity and mosaic
      architectures. The complete sequences of 30 mycobacteriophage genomes show
      them collectively to encode 101 tRNAs, three tmRNAs, and 3,357 proteins
      belonging to 1,536 "phamilies" of related sequences, and a statistical
      analysis predicts that these represent approximately 50% of the total
      number of phamilies in the mycobacteriophage population. These phamilies
      contain 2.19 proteins on average; more than half (774) of them contain
      just a single protein sequence. Only six phamilies have representatives in
      more than half of the 30 genomes, and only three-encoding tape-measure
      proteins, lysins, and minor tail proteins-are present in all 30 phages,
      although these phamilies are themselves highly modular, such that no
      single amino acid sequence element is present in all 30 mycobacteriophage
      genomes. Of the 1,536 phamilies, only 230 (15%) have amino acid sequence
      similarity to previously reported proteins, reflecting the enormous
      genetic diversity of the entire phage population. The abundance and
      diversity of phages, the simplicity of phage isolation, and the relatively
      small size of phage genomes support bacteriophage isolation and
      comparative genomic analysis as a highly suitable platform for
      discovery-based education.
AU  - Hatfull GF et al
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2006 2: e92.

PMID- 29439051
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Industrial Dairy Strain Streptococcus thermophilus DGCC 7710.
PG  - e01587-17
AB  - We report here the complete genome sequence of Streptococcus thermophilus DGCC 7710. S.
      thermophilus is widely used in industrial dairy production.
AU  - Hatmaker EA
AU  - Riley LA
AU  - O'Dell KB
AU  - Papanek B
AU  - Graveley BR
AU  - Garrett SC
AU  - Wei Y
AU  - Terns MP
AU  - Guss AM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01587-17.

PMID- 29930036
VI  - 6
DP  - 2018
TI  - Whole-Genome Sequencing and Annotation of a Drug-Resistant Extrapulmonary Clinical Isolate of Beijing Genotype Mycobacterium tuberculosis from Pune, India.
PG  - e00504-18
AB  - Whole-genome sequencing has emerged as a powerful tool to map genetic diversity among
      Mycobacterium tuberculosis isolates and identify the genomic signatures
      associated with drug resistance, pathogenesis, and disease transmission. Isolate
      LJ319 of the Mycobacterium tuberculosis complex (MTC)-Beijing genotype
      circulating in Maharashtra, India, which was obtained from the cerebrospinal
      fluid (CSF) of an immunocompetent patient, was subjected to whole-genome
      sequencing.
AU  - Hatolkar SM
AU  - Misra RN
AU  - Mahato R
AU  - Jadhav S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00504-18.

PMID- 14227035
VI  - 24
DP  - 1964
TI  - The functioning of T-even phages with unglucosylated DNA in restricting Escherichia coli host cells.
PG  - 333-348
AB  - The DNA of the T-even bacteriophages contains glucose bound to the pyrimidine
      base 5-hydroxymethylcytosine.  Modified forms of T-even phage, designated T*
      phage, which contain little or no glucose, are produced by growth in certain
      bacterial mutants blocked at some step in the synthesis of uridine
      diphosphoglucose.  The T* phage is able to grow on some strains of Shigella
      (permissive hosts) but grows poorly or not at all on various strains of
      Escherichia coli (restrictive hosts).  Evidence is presented that the DNA of T*
      phage undergoes extensive degradation to acid-soluble fragments following
      infection of restricting E. coli cells, whereas infection of E. coli with
      wild-type phage, or of Shigella with T* phage, causes very little degradation
      of phage DNA.  T* phage can perform certain functions after infection of
      restricting hosts.  In these respects the T* forms of phages T2,T4, and T6
      differ to some extent.  Also, phage T*2 can undergo extensive growth activation
      in E. coli cells in multiple infection, whereas T*4 and T*6 do not exhibit this
      multiplicity activation.  In mixed infection of E. coli B with the mutant
      T4am122, unable to induce synthesis of the enzyme
      deoxycytidylate-hydroxymethylase, T*2 and T*6 are capable of complementing the
      missing function, whereas T*4 cannot.  Evidence is presented that T* phages can
      in fact direct synthesis of some early enzymes in restricting hosts.  Despite
      the occurrence of some early enzyme synthesis, phage DNA synthesis does not
      occur after infection of restricting bacteria with T* phage except in the cells
      where restriction fails.  The ability of permissive hosts to support
      replication of T* phage is not due to an initial glucosylation of the incoming
      nonglucosylated DNA.
AU  - Hattman S
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1964 24: 333-348.

PMID- 4340808
VI  - 49
DP  - 1972
TI  - Methylation of adenine residues in bacteriophage T2 DNA.
PG  - 404-412
AB  - It has been previously shown that uP1 mutants, derived from phage T2 gt rP1, determine an
      altered form of the phage-induced DNA methylase. The uP1 enzyme methylates two- to threefold
      more adenine residues on phage DNA than does the wild-type methylase. The question of whether
      the presence of 5-hydroxymethylcytosine (HMC) in T2 DNA plays a role in determining methylase
      specificity was investigated. A triple amber mutantn was constructed which is defective in the
      synthesis of the enzymes, deoxycytidine triphosphatase (dCTPase) and deoxycytidylate
      hydroxymethylase (dCMP-HMase) as well as in the ability to degrade completely host DNA (genes
      56,42 and 47, respectively). In host cells lacking an amber suppressor (su-), the mutant is
      shown to synthesize DNA which contains cytosine (C) in place of HMC. This C-containing DNA has
      the same level of N6-methyladenine (MeAde) as observed in the HMC-containing DNA of T2 gt. rP1
      DNAs behaved similarly as substrates for in vitro methylation by extracts of phage-infected
      cells. These data indicate that the 5-hydroxymethyl group on HMC does not interfere with the
      activity of the wilde-type DNA methylase, nor does it enhance the activity of the uP1 enzyme.
AU  - Hattman S
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1972 49: 404-412.

PMID- 14921
VI  - 129
DP  - 1977
TI  - Partial purification of the Escherichia coli K-12 mec+ deoxyribonucleic acid-cytosine methylase:  in vitro methylation completely protects bacteriophage lambda deoxyribonucleic acid against cleavage by R.EcoRII.
PG  - 1330-1334
AB  - A procedure is described for the partial purification of the deoxyribonucleic
      acid (DNA)-cytosine methylases controlled by the RII plasmid and by the
      Escherichia coli mec+ gene.  The two enzymes exhibit similar but distinct
      chromatographic behavior on diethylaminoethyl-cellulose and phosphocellulose.
      Preliminary studies on the two methylases indicate that they are
      indistinguishable with respect to their Km for S-adenosylmethionine and their
      pH [in tris(hydroxymethyl)aminomethane buffer] and NaCl concentration optima.
      In vitro methylation of various phage lambda DNA substrates by the mec+ or RII
      enzyme modifies the DNA to a form that is completely resistant to
      double-stranded cleavage by the RII restriction endonuclease (R.EcoRII).  These
      results are consistent with our earlier proposal that the mec+ methylase
      recognizes RII host specificity sites.
AU  - Hattman S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1977 129: 1330-1334.

PMID- 6445426
VI  - 34
DP  - 1980
TI  - Specificity of the bacteriophage Mu mom+-controlled DNA modification.
PG  - 277-279
AB  - Bacteriophage Mu DNA was labeled after induction in the presence of
      [8-3H]adenine.  Purified DNA was enzymatically digested, and the 3H-labeled
      dinucleotides were isolated.  Approximately 15 to 20% of the adenine residues
      were modified to a new form, Ax, as observed previously (S. Hattman, J. Virol.
      32:468-475, 1979) in bulk DNA.  Paper electrophoretic analysis revealed that
      only two dinucleotide species contain Ax, namely, (Ax,C) and (Ax,G).  The
      observation that only C and G are the nearest neighbors of Ax is consistent
      with the proposal of Kahmann and Kamp (R. Kahmann and D. Kamp, J. Mol. Biol.,
      in press) that modification of Mu DNA occurs at the A residue within the
      pentanucleotide sequence 5'...(C/G)-A-(G/C)-N-Py...3'.
AU  - Hattman S
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1980 34: 277-279.

PMID- 4561202
VI  - 10
DP  - 1972
TI  - Plasmid-controlled variation in the content of methylated bases in bacteriophage lambda deoxyribonucleic acid.
PG  - 356-361
AB  - The N6-methyladenine (MeAde) and 5-methylcytosine (MeC) contents in deoxyribonucleic acid
      (DNA) of bacteriophage lambda has been analyzed as a function of host specificity. The
      following facts have emerged: (i) lambda grown on strains harboring the P1 prophage contain
      ca. 70 more MeAde residues/DNA molecule than lambda grown either in the P1-sensitive parent,
      or in a P1 immune-defective lysogen which does not confer P1 modification; (ii) lambda grown
      on strains harboring the N-3 drug-resistance factor contain ca. 60 more MeC residues/DNA
      molecule than lambda grown on the parental strain lacking the factor; (iii) lambda grown in
      Escherichia coli B strains is devoid of MeC, whereas lambda grown in a B (N-3) host contains a
      high level of MeC; (iv) the MeAde content in lambda DNA is not affected by the N-3 factor.
      These results suggest that P1 controls an adenine-specific DNA methylase, and that the N-3
      plasmid controls a cytosine-specific DNA methylase. The N-3 factor has been observed
      previously to direct cytosine-specific methylation of phage P22 DNA and E. coli B DNA in vivo;
      in vitro studies presented here demonstrate this activity.
AU  - Hattman S
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1972 10: 356-361.

PMID- 159363
VI  - 32
DP  - 1979
TI  - Unusual Modification of Bacteriophage Mu DNA.
PG  - 468-475
AB  - Bacteriophage mu DNA was labeled after induction in the presence of [2-3H]adenine or
      [8-3H]adenine. Both Mu mom+.dam+ DNA and Mu mom-.dam+ DNA have similar N6 -methyladenine
      (MeAde) contents, as well as similar frequencies of MeAde nearest neighbors. Both DNAs are
      sensitive to in vitro cleavage by R.DpnI but resistant to cleavage by R.DpnI but resistant to
      cleavage by R.DpnII. These results indicate that the mom+ protein does not alter the sequence
      specificity of the host dam+ methylase to produce MeAde at new sites. However, we have
      discovered a new modified base, denoted Ax, in Mu mom+.dam+ DNA; approximately 15% of the
      adenine residues are modified to Ax. Although the precise nature of the modification is not
      yet defined, analysis be electrophoresis and chromatography indicates that the N6-amino group
      is not the site of modification, and that the added moiety contains a free carboxyl group. Ax
      is not present in Mu mom+.dam+ or Mu mom-.dam+ phage DNA or in cellular DNA from unonduced Mu
      mom+.dam+ lysogens. These results suggest that expression of the dam+ and mom+ genes are
      required for the Ax modification and that this modification is responsible for protecting Mu
      DNA against certain restriction nucleases. Mu mom+.dam+ DNA and Mu mom-.dam- DNA contain a
      very low level of MeAde (ca. 1 MeAde per 5,000 adenine residues). Since the only nearest
      neighbor to MeAde appears to be cytosine, we suggest that the methylated sequence is
      5'...C-A-C...3' and that this methylation is mediated by the EcoK modification enzyme.
AU  - Hattman S
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1979 32: 468-475.

PMID- 4580913
VI  - 74
DP  - 1973
TI  - Plasmid-controlled variation in the content of methylated bases in single-stranded DNA phages M13 and fd.
PG  - 749-752
AB  - The N6-methyladenine and 5-methylcytosine contents in the DNA of bacteriophages
      M13 and fd have been analyzed.  The results are summarized as follows. (1)
      After growth in bacteria harboring the N-3 fi- drug resistance-factor, fd and
      M13 are observed to contain approximately 1 to 2 more 5-methylcytosine residues
      per DNA molecule than after rgrowth in the parental drug-sensitive host; no
      effect on the N6-methyladenine content is produced by the plasmid.  (2) After
      growth in bacteria harboring P1 prophage, fd and M13 are observed to contain
      approximately 2 to 3 more N6-methyladenine residues per DNA molecule than after
      growth in the parental P1-sensitive host; no apparent effect on the
      5-methylcytosine content was produced by the P1 plasmid.  (3) In agreement with
      others, fd carrying B-host specificity (fd.B) is observed to contain 2 more
      N6-methyladenine residues/DNA molecule than fd.K.
AU  - Hattman S
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1973 74: 749-752.

PMID- Not carried by PubMed...
VI  - 0
DP  - 1983
TI  - DNA Modification:  Methylation.
PG  - 152-155
AB  - None
AU  - Hattman S
PT  - Journal Article
TA  - Bacteriophage T4
JT  - Bacteriophage T4
SO  - Bacteriophage T4 1983 0: 152-155.

PMID- 5489224
VI  - 42
DP  - 1970
TI  - DNA methylation of T-even bacteriophages and of their nonglucosylated mutants:  its role in P1-directed restriction.
PG  - 359-367
AB  - The 6-methylaminopurine (MAP) content of bacteriophages T2,T4,T6 and their nonglucosylated gt
      mutants has been analyzed. Phage T2 contains 25% more MAP than T4; the nonglucosylated forms
      of T2 and T4 contain 30-100% more MAP than their respective wild-type parents; the level of
      MAP is affected by the growth temperature and by the level of glucosylation. T6 and its
      nonglucosylated mutants are devoid of MAP. Support for the hypothesis that methylation has a
      role in P1-directed restriction of gt mutants of T-even phages (Revel and Georgopoulos, 1969)
      is presented: (1) mutants of T2gt and T4gt insensitive to P1-restriction, designated uP1
      (Revel and Georgopoulos, 1969) contain hypermethylated DNA; (2) cells simultaneously infected
      with P1-sensitive T2gt or T6gt (designated rP1) and ultraviolet-irradiated T2gt uP1 yield
      progeny rP1 phage which contain hypermethylated DNA and are partially resistant to P1
      restriction. It is proposed that the uP1 mutations occur in the structural gene for phage DNA
      methylase. Methylation does not appear to be involved in the restriction of T2gt and T4gt by
      certain bacterial hosts that do not restrict T5gt (these bacteria are designated r6-r2,4+)
      because of the findings that (1) a T4gt mutant lacking MAP is still restricted in r6-r2,4+;
      (2) phenotypically methylated T6gt is accepted in r6-r2,4+.
AU  - Hattman S
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1970 42: 359-367.

PMID- 4934088
VI  - 7
DP  - 1971
TI  - Variation of 6-methylaminopurine content in bacteriophage P22 deoxyribonucleic acid as a function of host specificity.
PG  - 690-691
AB  - The 6-methylaminopurine (MAP) content of P22 deoxyribonucleic acid has been
      analyzed as a function of the host specificity it carries.  A 40 to 50%
      reduction in MAP level occurs as a result of growth in host cells defective in
      the ability to confer LT specificity.
AU  - Hattman S
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1971 7: 690-691.

PMID- Not carried by PubMed...
VI  - 14
DP  - 1981
TI  - DNA methylation.
PG  - 517-548
AB  - Almost all biological macromolecules undergo some form of processing event
      subsequent to their biosynthesis.  Polypeptides are specifically folded,
      cleaved, phosphorylated, acetylated, methylated, or covalently bound to other
      polypeptides.  RNA molecules are specifically cleaved, lengthened, spliced,
      methylated, thiolated, or otherwise base-modified.  These processes are
      obligatory events in the establishment of functional expression of these
      molecules.  It has been known for almost three decades that DNA is also subject
      to post-replication modification.  The main topic of this chapter is to
      consider the phenomenon of DNA methylation, its nature, distribution, analysis,
      specificity, and biological function.  In addition, I briefly review other DNA
      modifications known to occur among prokaryotes and eukaryotes.
AU  - Hattman S
PT  - Journal Article
TA  - The Enzymes
JT  - The Enzymes
SO  - The Enzymes 1981 14: 517-548.

PMID- 6752951
VI  - 79
DP  - 1982
TI  - DNA methyltransferase-dependent transcription of the phage Mu mom gene.
PG  - 5518-5521
AB  - The phage Mu mom gene controls an unusual DNA modification. Expression of the mom function
      requires an active host (dam+) DNA adenine methylase [S-adenosyl-L-methionine:DNA
      (6-aminopurine)-methyltranasferase]; in dam- hosts, Mu development is normal except that the
      viral DNA does not undergo the mom modification. The present communication compares
      transcription of the mom gene in dam+ versus dam- cells. 32P-labeled probes were prepared by
      nick-translation of a purified mom gene-containing restriction fragment and of virion DNA,
      respectively. These probes were hybridized with various RNAs blotted onto nitrocellulose
      filters (after fractionation by agarose gel electrophoresis). The salient findings are: (i)
      mom-specific RNA was readily detected in dam+ lysogenic cells, but only after induction of the
      Mu prophage; (ii) the level of mom RNA was decreased at least to 1/20th in induced dam- Mu
      lysogens; and (iii) little difference, if any, was observed between dam+ and dam- cells with
      respect to total Mu transcripts produced after prophage induction. These results are in accord
      with the known pattern of mom gene expression and Mu development. They show that the host
      (dam+) DNA adenine methylase activity is required for transcription of the mom gene. This
      represents a unique example where a DNA methylase exerts a positive regulatory role in mRNA
      transcription; alternative mechanisms for this process will be discussed.
AU  - Hattman S
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1982 79: 5518-5521.

PMID- 370402
VI  - 126
DP  - 1978
TI  - Sequence specificity of the P1 modification methylase (M.EcoP1) and the DNA methylase (M.Ecodam) controlled by the Escherichia coli dam gene.
PG  - 367-380
AB  - Labeled oligonucleotides have been fractionated from pancreatic DNase digests of DNA that had
      been methylated in vitro with the P1 modification enzyme (M.EcoP1) or with the DNA-adenine
      methylase (M.Ecodam) controlled by the Escherichia coli dam gene. The sequences of methylated
      oligonucleotides were established for M.Eco dam modification of calf thymus DNA. The results
      show that M.Ecodam methylates adenine residues contained in the twofold symmetrical sequence,
      5'...G-A-T-C...3'. The sequence for the site methylated by M.EcoP1 has also been deduced; we
      proposed that M.EcoP1 modification produces the following methylated pentameric sequence:
      5'...A-G-A*-C-Py...3' (where A* = N6 methyladenine and Py is C or T).
AU  - Hattman S
AU  - Brooks JE
AU  - Masurekar M
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1978 126: 367-380.

PMID- 4565547
VI  - 112
DP  - 1972
TI  - Location of the region controlling host specificity (hsII) with respect to drug resistance markers on the fi- R factor, N-3.
PG  - 1428-1430
AB  - The region controlling host specificity (hsII) has been mapped, by P22
      transduction, with respect to drug resistance markers carried on the fi- R
      factor, N-3.  The relative linear sequence of contransducible markers is
      Tc-Su-Sm-hsII.
AU  - Hattman S
AU  - Cousens L
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1972 112: 1428-1430.

PMID- 14060647
VI  - 50
DP  - 1963
TI  - Host-induced modification of T-even phages due to defective glucosylation of their DNA.
PG  - 297-300
AB  - None
AU  - Hattman S
AU  - Fukasawa T
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1963 50: 297-300.

PMID- 4550503
VI  - 69
DP  - 1972
TI  - Methylation of cytosine residues in DNA controlled by a drug resistance factor.
PG  - 187-190
AB  - The proportion of 5-methylcytosine (5MeCyt) and 6-methylaminopurine
      (N6-methyladenine, 6MeAde) in bacteriophage P22 DNA was analyzed as a function
      of the host-specificity the phage carried.  In the DNA of P22 grown in stsrains
      harboring the modifying drug-resistance-transfer-factor N-3, the 5MeCyt content
      was at least twice that after growth in strains lacking the factor.  In
      contrast, the 6MeAde level of P33 DNA was unaffected by the presence or absence
      of the factor.  The 6MeAde and 5MeCyt levels were unaffected by factors 222 and
      N-1, which do not modify phage DNA.  The 5MeCyt/6MeAde ratio was only slightly
      higher int he DNA of Salmonella strains that had received the N-3 factor.
      After transfer of the N-3 factor to Escherichia coli strain B, which normally
      lacks 5MeCyt, a high content of 5MeCyt is observed.  We conclude that the N-3
      factor controls a DNA methylase specific for cytosine residues.  If the N-3
      host specificity is imparted by cytosine methylation, this would be the first
      instance where a biological role for 5MeCyt has been elucidated.
AU  - Hattman S
AU  - Gold E
AU  - Plotnik A
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1972 69: 187-190.

PMID- 6305580
VI  - 47
DP  - 1983
TI  - Regulation of the DNA-modification function of bacteriophage Mu.
PG  - 647-653
AB  - The DNA-modification function of bacteriophage Mu, termed the mom function,
      presents very interesting examples of DNA modification and regulation of gene
      expression.  On both counts it sets new precedents.  The modification involved
      is new, and the expression of the mom gene appears to require methylation of
      sequences adjacent to the gene.
AU  - Hattman S
AU  - Goradia M
AU  - Monaghan C
AU  - Bukhari AI
PT  - Journal Article
TA  - Cold Spring Harb. Symp. Quant. Biol.
JT  - Cold Spring Harb. Symp. Quant. Biol.
SO  - Cold Spring Harb. Symp. Quant. Biol. 1983 47: 647-653.

PMID- 159962
VI  - 32
DP  - 1979
TI  - In vivo methylation of bacteriophage PhiX174 DNA.
PG  - 845-851
AB  - A mutant (designated mec-) has been isolated from Escherichia coli C which has
      lost DNA-cytosine methylase activity and the ability to protect phage lambda
      against in vivo restriction by the RII endonuclease.  This situation is
      analogous to that observed with an E. coli K-12 mec- mutant; thus, the E. coli
      C methylase appears to have overlapping sequence specificity with the K-12 and
      RII enzymes; (the latter methylases have been shown previously to recognize the
      same sequence).  Covalently closed, supertwisted double-stranded DNA (RFI) was
      isolated from C mec+ and C mec- cells infected with bacteriophage PhiX174.
      PhiX.mec- RFI is sensitive to in vitro cleavage by R.EcoRII and is cut twice to
      produce two fragments of almost equal size.  In contrast, PhiX.mec+ RFI is
      relatively resistant to in vitro cleavage by R.EcoRII.  R.BstI, which cleaves
      mec+/RII sites independent of the presence or absence of 5-methylcytosine,
      cleaves both forms of the RFI and produces two fragments similar in size to
      those with R.EcoRII.  These results demonstrate that PhiX.mec+ RFI is
      methylated in vivo by the host mec+ enzyme and that this methylation protects
      the DNA against cleavage by R.EcoRII.  This is consistent with the known
      location of two mec+/RII sequences (viz., 5' ... C-C-A/T-G-G ...3') on the
      PhiX174 map.  Mature single-stranded virion DNA was isolated from PhiX174
      propagated in C mec+ or C mec- in the presence of L-[methyl-3H]methionine.
      Paper chromatographic analyses of acid hydrolysates revealed that PhiX.mec+ DNA
      had a 10-fold-higher ratio of [3H]5-methylcytosine to [3H]cytosine compared to
      PhiX.mec-.  Since PhiX.mec+ contains, on the average, approximately 1
      5-methylcytosine residue per viral DNA, we conclude that methylation of PhiX174
      is mediated by the host mec+ enzyme only.  These results are not consistent
      with the conclusions of previous reports that PhiX174 methylation is mediated
      by a phage-induced enzyme and that methylation is essential for normal phage
      development.
AU  - Hattman S
AU  - Gribbin C
AU  - Hutchison CA
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1979 32: 845-851.

PMID- 712853
VI  - 124
DP  - 1978
TI  - Sequence specificity of DNA methylases from Bacillus amyloliquefaciens and Bacillus brevis.
PG  - 701-711
AB  - DNA methylation in Bacillus amyloliquefaciens strain H (Bam) and Bacillus
      brevis (Bbv) has been examined by a variety of techniques.  In vivo labelling
      studies revealed that Bam DNA contains no N6-methyladenine (MeAde), but
      contains 5-methylcytosine (MeCyt); approximately 0.7% of the cytosine residues
      are methylated.  DNA methylase activity was partially purified from both Bam
      and Bbv; the Bam enzyme preparation transferred methyl groups from
      S-adenosyl-L-[methyl-3H]methionine ([3H]AdoMet) to specific DNA cytosine
      residues only; in agreement with Vanyushin & Dobritsa (1975), the Bbv enzyme
      preparation methylated both DNA adenine and cytosine residues.  The (partial)
      sequence specificity of the methylases was determined by analyzing
      [3H]methyl-labelled dinucleotides obtained from enzymatic digests of DNA
      methylated in vitro.  Bam and Bbv each contain a DNA-cytosine methylase with
      overlapping sequence specificity; e.g. both enzymes produce G-C*, C*-A and
      C*-T.  This is consistent with a single, twofold symmetrical methylation
      sequence of 5'...G-C*-(A or T)-G-C...3'; this was observed by Vanyushin &
      Dobritsa (1975) for a different Bbv strain.  Bam contains a second DNA-cytosine
      methylase (not present in Bbv), which produces T-C* and C*-T.  We propose that
      this methylase is the BamI modification enzyme, and that the modified sequence
      is 5'...G-G-A-G-C*-C...3'.  Bbv appears to contain two DNA-adenine methylases
      which produce the (partial) methylated sequences, 5'...G-A*-T...3' and
      5'...A-A*-G...3', respectively; in the former case, all the G-A-T-C sites on
      Bbv DNA appear to be methylated.
AU  - Hattman S
AU  - Keister T
AU  - Gottehrer A
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1978 124: 701-711.

PMID- 15196891
VI  - 77
DP  - 2004
TI  - Bacteriophage T2Dam and T4Dam DNA-[N6-adenine]-methyltransferases.
PG  - 67-126
AB  - DNA mewthyltransferases are important enzymes that methylate DNA as a post replicative event.
      DNA MTases, encoded by both cellular and viral genes, catalyze methyl group transfer from
      S-adenosyl-L-methionine, producing S-adenosyl-L-homocysteine and methylated DNA.  The methyl
      group acceptor atom is either an exocyclic amino nitrogen (N6-Ade or N4-Cyt) or a ring carbon
      (C5-Cyt).  The DNA-[amino]-MTases [EC2.1.1.72 and 113]transfer methyl groups directly to the
      exocyclic nitrogen without the formation of a covalent enzyme-DNA intermediate, which occurs
      with the C5-Cyt MTases [EC2.1.73].  While most phokaryote DNA MTases are components of
      restriction-modification systems important in protecting cells from foreign DNAs, certain
      MTases do not have cognate restriction enzymes associated with them.  These include a family
      (Dam) of prokaryotic DNA-adenine MTases that methylate Ade in GATC sequences.  Several
      bacteriophages, such as T2 and T4, also encode Dam MTases.  Generally speaking, the Dam MTases
      are not essential for viability of bacteria or phage; however, they do have a variety of
      functions including regulation of transcription of certain genes, timing of DNA replication
      initiation, and protection against restriction endonucleases, and they play a crucial role in
      pathogenicity of intestinal bacteria.  Because they methylate specific nucleotide sequences,
      they provide excellent objects for studies on protein-DNA interactions.  Valuable insights
      into the organization/function of MTases have come from the identification of common motifs
      discovered by amino acid-seqence alignments.  The solution of a number of MTase crystal
      structures has added key details on the specific protein-DNA and protein-cofactor
      interactions.  However, genetic and biochemical analyses are essential for a more complete
      understanding of the functioning of these enzymes.  Here, we present results from all three
      approaches directed at characterizing the bacteriophage T2/T4 Dam DNA-[N6-adenine]-MTase.
AU  - Hattman S
AU  - Malygin EG
PT  - Journal Article
TA  - Prog. Nucleic Acid Res. Mol. Biol.
JT  - Prog. Nucleic Acid Res. Mol. Biol.
SO  - Prog. Nucleic Acid Res. Mol. Biol. 2004 77: 67-126.

PMID- 5331911
VI  - 30
DP  - 1966
TI  - Enzyme synthesis directed by nonglucosylated T-even bacteriophages in restriction hosts.
PG  - 427-438
AB  - Phage T2gt, defective in ability to initiate production of Alpha-glucosyl
      transferase, elicits the synthesis of other phage directed early enzymes in the
      host bacterium Escherichia coli B in which it cannot grow.  This early-enzyme
      synthesis is arrested at about the same time in infection with either T2gt or
      T2, despite the fact that T2gt DNA is apparently not replicated in E. coli B.
      A similar pattern of phage-enzyme synthesis is observed with other T even
      phages with nonglucosylated DNA.  Experiments with UV-irradiated phage and with
      inhibitors of protein synthesis indicate that the arrest of enzyme synthesis in
      infection with nonglucosylated phage is due not to the regulatory process
      operative in infection with normal phage, but to a different mechanism.  The
      evidence suggests that this mechanism is the rapid degradation of the
      nonglucosylated phage DNA.  The experiments also provide estimates for the
      half-life of phage-specific mRNA in the presence or absence of protein
      synthesis.
AU  - Hattman S
AU  - Revel HR
AU  - Luria SE
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1966 30: 427-438.

PMID- 4353870
VI  - 115
DP  - 1973
TI  - Isolation of a mutant of Escherichia coli defective in cytosine-specific deoxyribonucleic acid methylase activity and in partial protection of bacteriophage lambda against restriction by cells containing the N-3 drug-resistance factor.
PG  - 1103-1107
AB  - A mutant (designated mec-) of Escherichia coli F+ 100 endoI- su+ rk-mk+ has
      been isolated which is defective in cytosine-specific deoxyribonucleic acid
      (DNA) methylase activity.  The DNA of this mutant, as well as the DNA of phage
      lambda and fd propagated in it, is virtually devoid of 5-methyl-cytosine (MeC);
      in contrast, the mutation has no significant effect on the level of
      N6-methyladenine in DNA.  Phage lambda grown on the mec- mutant is more
      strongly restricted by N-3-containing cells than is lambda grown on the mec+
      parent.  These results suggest that methylation of certain cytosine residues by
      the E. coli K-12 enzyme partially protects lambda DNA from either the N-3
      restriction nuclease or against secondary degradation subsequent to
      N-3-specific degradation.  Analysis of the MeC level in viral and cellular DNA
      obtained from mec+, mec+ (mN3+), and mec- (mN3+) strains has led to the
      conclusion that the R-factor controlled DNA-cytosine methylase may be capable
      of methylating a sequence(s) which is a substrate for the K-12 enzyme.
AU  - Hattman S
AU  - Schlagman S
AU  - Cousens L
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1973 115: 1103-1107.

PMID- 776925
VI  - 127
DP  - 1976
TI  - Salmonella typhimurium SA Host Specificity System is based on Deoxyribonucleic Acid-Adenine Methylation.
PG  - 211-217
AB  - We have determined the nature of the deoxyribonucleic acid (DNA) modification
      governed by the SA host specificity system of Salmonella typhimurium.  Two
      lines of evidence indicate that SA modification is based on methylation of
      DNA-adenine residues.  (i) The SA+ locus of Salmonella was transferred into
      Escherichia coli B, a strain that does not contain 5-methylcytosine in its DNA;
      although the hybrid strain was able to confer SA modification, its DNA still
      did not contain 5-methylcytosine.  (ii) the N6-methyladenine content of phage L
      DNA was measured after growth in various host strains; phage lacking SA
      modification contained fewer N6-methyladenine residues per DNA.  We also
      investigated the possibility, suggested by others, that SA modification
      protects phage DNA against restriction by the RII host specificity system.
      Phages lambda, P3, and L were grown in various SA+ and SA- hosts and tested for
      their relative plating ability on strains containing or lacking RII
      restriction; the presence or absence of SA modification had no effect on RII
      restriction.  In vitro studies revealed, however, that Salmonella DNA is
      protected against cleavage by purified RII restriction endonuclease (R-EcoRII).
      This protection is not dependent on SA modification; rather, it appears to be
      due to methylation by a DNA-cytosine methylase which has overlapping
      specificity with the RII modification enzyme, but which is not involved in any
      other known host specificity system.
AU  - Hattman S
AU  - Schlagman S
AU  - Goldstein L
AU  - Frohlich M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1976 127: 211-217.

PMID- 641992
VI  - 119
DP  - 1978
TI  - Sequence specificity of the wild-type (dam+) and mutant (damh) forms of bacteriophage T2 DNA adenine methylase.
PG  - 361-376
AB  - Non-glucosylated, non-methylated phage T2 DNA was methylated in vitro with partially purified
      wild-type (dam+) or mutant (damh) T2 DNA adenine methylase. The radioactively labeled
      methyladenine-containing DNA was enzymatically degraded and the resulting oligonucleotides
      were separated according to chain length by DEAE-cellulose chromatography. Following
      "fingerprinting" by two-dimensional electrophoresis, we determined the sequence for vaious
      di-, tri- and tetranucleotides containing radioactive N6-methyldeoxyadenosine. From this
      analysis we conclude that both T2 dam+ and T2 damh contain the sequence 5'...G-mA-Py...3'.
AU  - Hattman S
AU  - van Ormondt H
AU  - de Waard A
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1978 119: 361-376.

PMID- 3902803
VI  - 164
DP  - 1985
TI  - Common evolutionary origin of the Phage T4 dam and host Escherichia coli dam DNA-adenine methyltransferase genes.
PG  - 932-937
AB  - We compared the known DNA nucleotide and encoded amino acid sequences of the Escherichia coli
      and bacteriophage T4 dam (DNA-adenine methyltransferase) genes. Despite the absence of any DNA
      sequence homology, there were four regions (11 to 33 residues long) of amino acid sequence
      homology containing 45 to 64% identity. These results suggest that the genes for these two
      enzymes have a common evolutionary origin.
AU  - Hattman S
AU  - Wilkinson J
AU  - Swinton D
AU  - Schlagman S
AU  - MacDonald PM
AU  - Mosig G
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1985 164: 932-937.

PMID- 10830953
VI  - 405
DP  - 2000
TI  - The DNA sequence of human chromosome 21.
PG  - 311-319
AB  - Chromosome 21 is the smallest human autosome. An extra copy of chromosome 21 causes Down
      syndrome, the most frequent genetic cause of significant mental retardation, which affects up
      to 1 in 700 live births. Several anonymous loci for monogenic disorders and predispositions
      for common complex disorders have also been mapped to this chromosome, and loss of
      heterozygosity has been observed in regions associated with solid tumours. Here we report the
      sequence and gene catalogue of the long arm of chromosome 21. We have sequenced 33,546,361
      base pairs (bp) of DNA with very high accuracy, the largest contig being 25,491,867 bp. Only
      three small clone gaps and seven sequencing gaps remain, comprising about 100 kilobases. Thus,
      we achieved 99.7% coverage of 21q. We also sequenced 281,116 bp from the short arm. The
      structural features identified include duplications that are probably involved in chromosomal
      abnormalities and repeat structures in the telomeric and pericentromeric regions. Analysis of
      the chromosome revealed 127 known genes, 98 predicted genes and 59 pseudogenes.
AU  - Hattori M et al
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2000 405: 311-319.

PMID- 26543125
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Nine Streptococcus suis Strains Isolated in the United  States.
PG  - e01301-15
AB  - Streptococcus suis is a swine pathogen responsible for economic losses to the pig industry
      worldwide. Additionally, it is a zoonotic agent that can cause severe
      infections in those in close contact with infected pigs and/or who consume
      uncooked or undercooked pork products. Here, we report nine draft genome
      sequences of S. suis.
AU  - Hau SJ
AU  - Bayles DO
AU  - Alt DP
AU  - Brockmeier SL
AU  - Frana TS
AU  - Nicholson TL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01301-15.

PMID- 29025944
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Nine Livestock-Associated Methicillin-Resistant Staphylococcus aureus Sequence Type 5 Isolates from Humans with Long-Term Swine  Contact.
PG  - e01079-17
AB  - Humans have been found to harbor livestock-associated methicillin-resistant Staphylococcus
      aureus (LA-MRSA) isolates. LA-MRSA isolates are considered adapted
      to colonizing livestock and less pathogenic in humans than their hospital- and
      community-acquired counterparts. Here, we present nine LA-MRSA sequence type 5
      isolates from veterinarians with long-term swine contact.
AU  - Hau SJ
AU  - Bayles DO
AU  - Alt DP
AU  - Davies PR
AU  - Haan JS
AU  - Nicholson TL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01079-17.

PMID- 28798188
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of a Livestock-Associated Methicillin-Resistant Staphylococcus aureus Sequence Type 5 Isolate from the United States.
PG  - e00791-17
AB  - Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) may be the largest
      MRSA reservoir outside the hospital setting. One concern with LA-MRSA
      is the acquisition of novel mobile genetic elements by these isolates. Here, we
      report the complete genome sequence of a swine LA-MRSA sequence type 5 isolate
      from the United States.
AU  - Hau SJ
AU  - Bayles DO
AU  - Alt DP
AU  - Frana TS
AU  - Nicholson TL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00791-17.

PMID- 28798187
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Livestock-Associated Methicillin-Resistant Staphylococcus aureus Sequence Type 398 Isolated from Swine in the United States.
PG  - e00790-17
AB  - Methicillin-resistant Staphylococcus aureus (MRSA) colonizes and causes disease in many animal
      species. Livestock-associated MRSA (LA-MRSA) isolates are
      represented by isolates of the sequence type 398 (ST398). These isolates are
      considered to be livestock adapted. This report provides the complete genome
      sequence of one swine-associated LA-MRSA ST398 isolate from the United States.
AU  - Hau SJ
AU  - Bayles DO
AU  - Alt DP
AU  - Frana TS
AU  - Nicholson TL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00790-17.

PMID- 29025945
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Nine Livestock-Associated Methicillin-Resistant Staphylococcus aureus Sequence Type 5 Isolates Obtained from Humans after  Short-Term Swine Contact.
PG  - e01080-17
AB  - Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) sequence type 5
      (ST5) has raised concerns surrounding the potential for these
      isolates to colonize or cause disease in humans with swine contact. Here, we
      report draft genome sequences for nine LA-MRSA ST5 isolates obtained from humans
      after short term swine contact.
AU  - Hau SJ
AU  - Bayles DO
AU  - Alt DP
AU  - Frana TS
AU  - Nicholson TL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01080-17.

PMID- 29097452
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of 14 Livestock-Associated Methicillin-Resistant Staphylococcus aureus Sequence Type 398 Isolates from Swine Farms in the United  States.
PG  - e01082-17
AB  - Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) is a bacterium
      carried by or obtained from swine and other livestock. The initial and
      predominant swine-associated LA-MRSA sequence type (ST) identified is ST398.
      Here, we present 14 draft genome sequences from LA-MRSA ST398 isolates found in
      the United States.
AU  - Hau SJ
AU  - Bayles DO
AU  - Alt DP
AU  - Frana TS
AU  - Nicholson TL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01082-17.

PMID- 29097451
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of 63 Swine-Associated Methicillin-Resistant Staphylococcus aureus Sequence Type 5 Isolates from the United States.
PG  - e01081-17
AB  - Methicillin-resistant Staphylococcus aureus colonizes humans and other animals such as swine.
      Livestock-associated methicillin-resistant Staphylococcus aureus
      (LA-MRSA) sequence type 5 (ST5) isolates are a public concern due to their
      pathogenicity and ability to acquire mobile genetic elements. This report
      presents draft genome sequences for 63 LA-MRSA ST5 isolates in the United States.
AU  - Hau SJ
AU  - Bayles DO
AU  - Alt DP
AU  - Frana TS
AU  - Nicholson TL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01081-17.

PMID- 28360167
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of Two Staphylococcus aureus Sequence Type 5 Isolates from California, USA.
PG  - e00099-17
AB  - Staphylococcus aureus causes a variety of human diseases ranging in severity. The
      pathogenicity of S. aureus can be partially attributed to the acquisition of
      mobile genetic elements. In this report, we provide two complete genome sequences
      from human clinical S. aureus isolates.
AU  - Hau SJ
AU  - Bayles DO
AU  - Alt DP
AU  - Nicholson TL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00099-17.

PMID- 28360166
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of 14 Staphylococcus aureus Sequence Type 5 Isolates from  California, USA.
PG  - e00098-17
AB  - Staphylococcus aureus is part of the human epithelial microbiota; however, it is  also a
      pathogen. The acquisition of mobile genetic elements plays a role in the
      virulence of S. aureus isolates and contributes to treatment failures. This
      report details the draft genome sequences of 14 clinical S. aureus isolates.
AU  - Hau SJ
AU  - Bayles DO
AU  - Alt DP
AU  - Nicholson TL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00098-17.

PMID- 29051244
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of One Methicillin-Sensitive and Seven Methicillin-Resistant Staphylococcus aureus Sequence Type 5 Isolates Obtained in   California.
PG  - e01084-17
AB  - Staphylococcus aureus is a commensal bacterium of humans that can cause a spectrum of
      diseases. An isolate's capacity to cause disease is partially
      attributed to the acquisition of novel mobile genetic elements. This report
      provides the draft genome sequence of one methicillin-susceptible and seven
      methicillin-resistant clinical human S. aureus isolates.
AU  - Hau SJ
AU  - Bayles DO
AU  - Alt DP
AU  - Nicholson TL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01084-17.

PMID- 29097453
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of 50 Methicillin-Resistant Staphylococcus aureus Sequence Type 5 Isolates Obtained from a U.S. Hospital.
PG  - e01083-17
AB  - Methicillin-resistant Staphylococcus aureus (MRSA) can be a commensal or pathogen in humans.
      Pathogenicity and disease are related to the acquisition of mobile
      genetic elements encoding virulence and antimicrobial resistance genes. Here, we
      report draft genome sequences for 50 clinical MRSA isolates from humans with
      MRSA-related disease.
AU  - Hau SJ
AU  - Bayles DO
AU  - Alt DP
AU  - Nicholson TL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01083-17.

PMID- 15069127
VI  - 32
DP  - 2004
TI  - The spread of LAGLIDADG homing endonuclease genes in rDNA.
PG  - 2049-2057
AB  - Group I introns that encode homing endonuclease genes (HEGs) are highly invasive genetic
      elements. Their movement into a homologous position in
      an intron-less allele is termed homing. Although the mechanism of
      homing is well understood, the evolutionary relationship between HEGs
      and their intron partners remains unclear. Here we have focused on the
      largest family of HEGs (encoding the protein motif, LAGLIDADG) to
      understand how HEGs and introns move in rDNA. Our analysis shows the
      phylogenetic clustering of HEGs that encode a single copy of the
      LAGLIDADG motif in neighboring, but often evolutionarily distantly
      related, group I introns. These endonucleases appear to have inserted
      into existing introns independent of ribozymes. In contrast, our data
      support a common evolutionary history for a large family of
      heterologous introns that encode HEGs with a duplicated LAGLIDADG
      motif. This finding suggests that intron/double-motif HEG elements can
      move into heterologous sites as a unit. Our data also suggest that a
      subset of the double-motif HEGs in rDNA originated from the duplication
      and fusion of a single-motif HEG encoded by present-day ribozymes in
      LSU rDNA.
AU  - Haugen P
AU  - Bhattacharya D
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2004 32: 2049-2057.

PMID- 11895434
VI  - 269
DP  - 2002
TI  - Characterization of the self-splicing products of two complex Naegleria LSU rDNA group I introns containing homing endonuclease genes.
PG  - 1641-1649
AB  - The two group I introns Nae.L1926 and Nmo.L2563, found at two different sites in nuclear LSU
      rRNA genes of Naegleria amoebo-flagellates, have been characterized in vitro. Their structural
      organization is related to that of the mobile Physarum intron Ppo.L1925 (PpLSU3) with ORFs
      extending the L1-loop of a typical group IC1 ribozyme. Nae.L1926, Nmo.L2563 and Ppo.L1925 RNAs
      all self-splice in vitro, generating ligated exons and full-length intron circles as well as
      internal processed excised intron RNAs. Formation of full-length intron circles is found to be
      a general feature in RNA processing of ORF-containing nuclear group I introns. Both Naegleria
      LSU rDNA introns contain a conserved polyadenylation signal at exactly the same position in
      the 3' end of the ORFs close to the internal processing sites, indicating an RNA polymerase
      II-like expression pathway of intron proteins in vivo. The intron proteins I-NaeI and I-NmoI
      encoded by Nae.L1926 and Nmo.L2563, respectively, correspond to His-Cys homing endonucleases
      of 148 and 175 amino acids. I-NaeI contains an additional sequence motif homologous to the
      unusual DNA binding motif of three antiparallel beta sheets found in the I-PpoI endonuclease,
      the product of the Ppo.L1925 intron ORF.
AU  - Haugen P
AU  - De Jonckheere JF
AU  - Johansen S
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 2002 269: 1641-1649.

PMID- 10654088
VI  - 36
DP  - 1999
TI  - Complex group-I introns in nuclear SSU rDNA of red and green algae: Evidence of homing-endonuclease pseudogenes in the Bangiophyceae.
PG  - 345-353
AB  - The green alga Scenedesmus pupukensis and the red alga Porphyra spiralis contain large
      group-IC1 introns in their nuclear small subunit
      ribosomal RNA genes due to the presence of open reading frames at the
      5' end of the introns. The putative 555 amino-acid Scenedesmus-encoded
      protein harbors a sequence motif resembling the bacterial S9 ribosomal
      proteins. The Porphyra intron self-splices in vitro, and generates both
      ligated exons and a full-length intron RNA circle. The Porphyra intron
      has an unusual structural organization by encoding a potential 149
      amino-acid homing-endonuclease-like protein on the complementary
      strand. A comparison between related group-I introns in the
      Bangiophyceae revealed homing-endonuclease-like pseudogenes due to
      frame-shifts and deletions in Porphyra and Bangia. The Scenedesmus and
      Porphyra introns provide new insights into the evolution and possible
      novel functions of nuclear group-I intron proteins.
AU  - Haugen P
AU  - Huss VAR
AU  - Nielsen H
AU  - Johansen S
PT  - Journal Article
TA  - Curr. Genet.
JT  - Curr. Genet.
SO  - Curr. Genet. 1999 36: 345-353.

PMID- 15661357
VI  - 21
DP  - 2005
TI  - The natural history of group I introns.
PG  - 111-119
AB  - There are four major classes of introns: self-splicing group I and group II introns, tRNA
      and/or archaeal introns and spliceosomal introns
      in nuclear pre-mRNA. Group I introns are widely distributed in
      protists, bacteria and bacteriophages. Group II introns are found in
      fungal and land plant mitochondria, algal plastids, bacteria and
      Archaea. Group II and spliceosomal introns share a common splicing
      pathway and might be related to each other. The tRNA and/or archaeal
      introns are found in the nuclear tRNA of eukaryotes and in archaeal
      tRNA, rRNA and mRNA. The mechanisms underlying the self-splicing and
      mobility of a few model group I introns are well understood. By
      contrast, the role of these highly distinct processes in the evolution
      of the 1500 group I introns found thus far in nature (e.g. in algae and
      fungi) has only recently been clarified. The explosion of new sequence
      data has facilitated the use of comparative methods to understand group
      I intron evolution in a broader context and to generate hypotheses
      about intron insertion, splicing and spread that can be tested
      experimentally.
AU  - Haugen P
AU  - Simon DM
AU  - Bhattacharya D
PT  - Journal Article
TA  - Trends Genet.
JT  - Trends Genet.
SO  - Trends Genet. 2005 21: 111-119.

PMID- 15891115
VI  - 33
DP  - 2005
TI  - The recent transfer of a homing endonuclease gene.
PG  - 2734-2741
AB  - The myxomycete Didymium iridis (isolate Panama 2) contains a mobile group I intron named
      Dir.S956-1 after position 956 in the nuclear small subunit (SSU) rRNA gene. The intron is
      efficiently spread through homing by the intron-encoded homing endonuclease I-DirI. Homing
      endonuclease genes (HEGs) usually spread with their associated introns as a unit, but
      infrequently also spread independent of introns (or inteins). Clear examples of HEG mobility
      are however sparse. Here, we provide evidence for the transfer of a HEG into a group I intron
      named Dir.S956-2 that is inserted into the SSU rDNA of the Costa Rica 8 isolate of D.iridis.
      Similarities between intron sequences that flank the HEG and rDNA sequences that flank the
      intron (the homing endonuclease recognition sequence) suggest that the HEG invaded the intron
      during the recent evolution in a homing-like event. Dir.S956-2 is inserted into the same SSU
      site as Dir.S956-1. Remarkably, the two group I introns encode distantly related splicing
      ribozymes with phylogenetically related HEGs inserted on the opposite strands of different
      peripheral loop regions. The HEGs are both interrupted by small spliceosomal introns that must
      be removed during RNA maturation.
AU  - Haugen P
AU  - Wikmark O-G
AU  - Vader A
AU  - Coucheron DH
AU  - Sjottem E
AU  - Johansen SD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2005 33: 2734-2741.

PMID- 25767233
VI  - 3
DP  - 2015
TI  - Genome Sequences of Mannheimia haemolytica Serotype A2 Isolates D171 and D35, Recovered from Bovine Pneumonia.
PG  - e00093-15
AB  - Here, we report two genomes, one complete and one draft, from isolates of serotype A2
      Mannheimia haemolytica recovered from pneumonic bovine lung.
AU  - Hauglund MJ
AU  - Tatum FM
AU  - Bayles DO
AU  - Maheswaran SK
AU  - Briggs RE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00093-15.

PMID- 25745008
VI  - 3
DP  - 2015
TI  - Genome Sequences of Serotype A6 Mannheimia haemolytica Isolates D174 and D38 Recovered from Bovine Pneumonia.
PG  - e00086-15
AB  - Here, we report two genomes, one complete and one draft, from virulent bovine strains of
      Mannheimia haemolytica serotype A6 recovered prior to the field usage
      of modern antimicrobial drugs.
AU  - Hauglund MJ
AU  - Tatum FM
AU  - Bayles DO
AU  - Maheswaran SK
AU  - Briggs RE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00086-15.

PMID- 24136851
VI  - 1
DP  - 2013
TI  - Genome Sequences of Mannheimia haemolytica Serotype A1 Strains D153 and D193 from Bovine Pneumonia.
PG  - e00848-13
AB  - Here we report two genome sequences, one complete and one draft, from virulent bovine strains
      of Mannheimia haemolytica serotype A1 recovered prior to the field
      usage of modern antimicrobial drugs.
AU  - Hauglund MJ
AU  - Tatum FM
AU  - Bayles DO
AU  - Maheswaran SK
AU  - Briggs RE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00848-13.

PMID- 24309741
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Psychrophilic and Alkaliphilic Rhodonellum psychrophilum Strain GCM71T.
PG  - e01014-13
AB  - Rhodonellum psychrophilum GCM71(T), isolated from the cold and alkaline submarine ikaite
      columns in the Ikka Fjord in Greenland, displays optimal growth at 5 to 10
      degrees C and pH 10. Here, we report the draft genome sequence of this strain,
      which may provide insight into the mechanisms of adaptation to these extreme
      conditions.
AU  - Hauptmann AL
AU  - Glaring MA
AU  - Hallin PF
AU  - Prieme A
AU  - Stougaard P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01014-13.

PMID- 22541164
VI  - 159
DP  - 2012
TI  - Comparative genomic analyses of the Taylorellae.
PG  - 195-203
AB  - Contagious equine metritis (CEM) is an important venereal disease of horses that
      is of concern to the thoroughbred industry. Taylorella equigenitalis is a
      causative agent of CEM but very little is known about it or its close relative
      Taylorella asinigenitalis. To reveal novel information about Taylorella biology,
      comparative genomic analyses were undertaken. Whole genome sequencing was
      performed for the T. equigenitalis type strain, NCTC11184. Draft genome sequences
      were produced for a second T. equigenitalis strain and for a strain of T.
      asinigenitalis. These genome sequences were analysed and compared to each other
      and the recently released genome sequence of T. equigenitalis MCE9. These
      analyses revealed that T. equigenitalis strains appear to be very similar to each
      other with relatively little strain-specific DNA content. A number of genes were
      identified that encode putative toxins and adhesins that are possibly involved in
      infection. Analysis of T. asinigenitalis revealed that it has a very similar gene
      repertoire to that of T. equigenitalis but shares surprisingly little DNA
      sequence identity with it. The generation of genome sequence information greatly
      increases knowledge of these poorly characterised bacteria and greatly
      facilitates study of them.
AU  - Hauser H
AU  - Richter DC
AU  - van Tonder A
AU  - Clark L
AU  - Preston A
PT  - Journal Article
TA  - Vet. Microbiol.
JT  - Vet. Microbiol.
SO  - Vet. Microbiol. 2012 159: 195-203.

PMID- 29371357
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Telmatospirillum siberiense 26-4b1, an Acidotolerant Peatland Alphaproteobacterium Potentially Involved in Sulfur Cycling.
PG  - e01524-17
AB  - The facultative anaerobic chemoorganoheterotrophic alphaproteobacterium Telmatospirillum
      siberiense 26-4b1 was isolated from a Siberian peatland. We
      report here a 6.20-Mbp near-complete high-quality draft genome sequence of T.
      siberiense that reveals expected and novel metabolic potential for the genus
      Telmatospirillum, including genes for sulfur oxidation.
AU  - Hausmann B
AU  - Pjevac P
AU  - Schreck K
AU  - Herbold CW
AU  - Daims H
AU  - Wagner M
AU  - Loy A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01524-17.

PMID- 5329749
VI  - 241
DP  - 1966
TI  - The enzymatic methylation of ribonucleic acid and deoxyribonucleic acid.
PG  - 1985-1994
AB  - Infection of Escherichia coli B with bacteriophages T1, T2, or T4 results in increase in the
      activity of deoxyribonucleic acid methylase assayed in crude extracts of the infected cells.
      The largest increase is observed after infection with T2 phage; T4 and T1 phages lead to
      smaller increases in that order of decreasing magnitude.  After infection with T3, T5, or T6
      phages, a decrease in activity was observed; T7 and lambda phages had no effect.  The kinetics
      of the increase in methylase activity after T2 infection is similar to those found with the
      "early enzymes" induced by T-even phages, and protein synthesis is necessary for the increase
      to occur.  The properties of the methylase activity of phage T2-infected bacteria suggest that
      it is a new phage-directed enzyme.
AU  - Hausmann R
AU  - Gold M
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1966 241: 1985-1994.

PMID- 
VI  - 83
DP  - 2005
TI  - Fungi vectored by the introduced bark beetle Tomicus piniperda in Ontario, Canada and comments on the taxonomy of Leptographium lundbergii, L. terebrantis, L. truncatum and L. wingfieldii.
PG  - 1222-1237
AB  - Fungi isolated from Tomicus piniperda (L.) galleries in infected trap logs, standing trees,
      and directly from insects were identified using morphological features and molecular data
      obtained from the mitochondrial and nuclear DNA region. Identified strains represented
      Leptographium wingfieldii Morelet, Leptographium procerum (Kendr.) Wingf., Leptographium
      lundbergii Lag.
AU  - Hausner G
AU  - Iranpour M
AU  - Kim J-J
AU  - Breuil C
AU  - Davis CN
AU  - Gibb EA
AU  - Reid J
AU  - Loewen PC
AU  - Hopkin AA
PT  - Journal Article
TA  - Can. J. Bot.
JT  - Can. J. Bot.
SO  - Can. J. Bot. 2005 83: 1222-1237.

PMID- 4616171
VI  - 1
DP  - 1974
TI  - Differences in susceptibility to restriction by E. coli B between various heteroduplex molecules of bacteriophage FD DNA.
PG  - 453-455
AB  - Fragments of B-modified bacteriophage fd sB1o sB2 RF DNA were prepared with the help of
      purified endonuclease R from Haemophilus parainfluenzae.  These were hybridized with
      unmodified circular single stranded fd DNA.  The resulting partial heteroduplex molecules were
      assayed for infectivity on competent cells of B-restricting and non-restricting strains of E.
      coli.  Three of such heteroduplexes originating from neighboring fragments on the physical map
      of fd RF DNA were shown to be more resistant to EcoB restriction than six others and the
      unmodified control.  It is suggested that the three corresponding vicinal fragments contain
      essential parts of the EcoB recognition site on this phage DNA.
AU  - Havelaar KJ
AU  - Korsuize J
PT  - Journal Article
TA  - Mol. Biol. Rep.
JT  - Mol. Biol. Rep.
SO  - Mol. Biol. Rep. 1974 1: 453-455.

PMID- 25189581
VI  - 2
DP  - 2014
TI  - Genome Sequences of Corynebacterium pseudotuberculosis Strains 48252 (Human, Pneumonia), CS_10 (Lab Strain), Ft_2193/67 (Goat, Pus), and CCUG 27541.
PG  - e00869-14
AB  - Here we report the genome sequencess of four Corynebacterium pseudotuberculosis strains. These
      include a strain isolated from a patient with C.
      pseudotuberculosis pneumonia (48252), a strain isolated from pus in goat
      (Ft_2193/67), a laboratory strain originating from strain Ft_2193/67 (CS_10), and
      the draft genome of an equine reference strain, CCUG 27541.
AU  - Havelsrud OE
AU  - Sorum H
AU  - Gaustad P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00869-14.

PMID- 24245509
VI  - 14
DP  - 2013
TI  - Evidence of microevolution of Salmonella Typhimurium during a series of egg-associated outbreaks linked to a single chicken farm.
PG  - 800
AB  - BACKGROUND: The bacterium Salmonella enterica serovar Typhimurium (S.
      Typhimurium) is one of the most frequent causes of foodborne outbreaks of
      gastroenteritis. Between 2005-2008 a series of S. Typhimurium outbreaks occurred
      in Tasmania, Australia, that were all traced to eggs originating from a single
      chicken farm. We sequenced the genomes of 12 isolates linked to these outbreaks,
      in order to investigate the microevolution of a pathogenic S. Typhimurium clone
      in a natural, spatiotemporally restricted population. RESULTS: The isolates,
      which shared a phage type similar to DT135 known locally as 135@ or 135a, formed
      a clade within the S. Typhimurium population with close similarity to the
      reference genome SL1334 (160 single nucleotide polymorphisms, or SNPs). Ten of
      the isolates belonged to a single clone (<23 SNPs between isolate pairs) which
      likely represents the population of S. Typhimurium circulating at the chicken
      farm; the other two were from sporadic cases and were genetically distinct from
      this clone. Divergence dating indicated that all 12 isolates diverged from a
      common ancestor in the mid 1990 s, and the clone began to diversify in 2003-2004.
      This clone spilled out into the human population several times between 2005-2008,
      during which time it continued to accumulate SNPs at a constant rate of 3-5 SNPs
      per year or 1x10-6 substitutions site-1 year-1, faster than the longer-term (~50
      year) rates estimated previously for S. Typhimurium. Our data suggest that
      roughly half of non-synonymous substitutions are rapidly removed from the S.
      Typhimurium population, after which purifying selection is no longer important
      and the remaining substitutions become fixed in the population. The S.
      Typhimurium 135@ isolates were nearly identical to SL1344 in terms of gene
      content and virulence plasmids. Their phage contents were close to SL1344, except
      that they carried a different variant of Gifsy-1, lacked the P2 remnant found in
      SL1344 and carried a novel P2 phage, P2-Hawk, in place SL1344's P2 phage
      SopEvarphi. DT135 lacks P2 prophage. Two additional plasmids were identified in
      the S. Typhimurium 135@ isolates, pSTM2 and pSTM7. Both plasmids were IncI1, but
      phylogenetic analysis of the plasmids and their bacterial hosts shows these
      plasmids are genetically distinct and result from independent plasmid acquisition
      events. CONCLUSIONS: This study provides a high-resolution insight into
      short-term microevolution of the important human pathogen S. Typhimurium. It
      indicates that purifying selection occurs rapidly in this population (</= 6
      years) and then declines, and provides an estimate for the short-term
      substitution rate. The latter is likely to be more relevant for foodborne
      outbreak investigation than previous estimates based on longer time scales.
AU  - Hawkey J
AU  - Edwards DJ
AU  - Dimovski K
AU  - Hiley L
AU  - Billman-Jacobe H
AU  - Hogg G
AU  - Holt KE
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2013 14: 800.

PMID- 6513830
VI  - 15
DP  - 1984
TI  - A possible model for the methylation of deoxycytidine in DNA.
PG  - 125-134
AB  - The modified base 5-methylcytidine has been found in the DNA of a number of
      different eukaryotic cells where it occurs principally in the dinucleotide
      sequence -CmpG- which is present as a palindrome in double-strand nucleic acid
      molecules.  There is considerable evidence to indicate and suggest that
      5-methylcytosine serves as a regulatory signal in eukaryotic gene expression.
      Replication of DNA containing -CmpG- gives rise to daughter DNA molecules
      containing new -CpG- dinucleotide sequences in which the cytidine residues are
      not methylated.  Methylation of these residues is carried out by a methylase
      enzyme using S-adenosyl-L-methionine as a specific methyl group donor.  This
      model discussed in the present communication tries to explain in chemical and
      biological terms the mechanism of the methylation reaction.  The first
      reactions of the scheme are well known through the work of other investigators.
      However, we introduce a new concept into our reaction mechanism by postulating
      the direct involvement of S-adenosyl-L-methionine in the reaction through its
      covalent attachment to the cytosine ring followed by a specific ring closure
      and methylation involving transfer of a hydride ion.  The model also gives a
      possible explanation of mechanism of interaction of dimethyl sulphoxide with
      the enzyme systems of certain eukaryotic cells, which are altered or changed in
      the regulation of gene expression by this chemical reagent.
AU  - Hawtrey AO
AU  - Ariatti M
PT  - Journal Article
TA  - Med. Hypotheses
JT  - Med. Hypotheses
SO  - Med. Hypotheses 1984 15: 125-134.

PMID- 2838807
VI  - 16
DP  - 1988
TI  - Synthesis of decadeoxyribonucleotides containing 5-modified uracils and their interactions with restriction endonucleases BglII, Sau3AI and MboI (Nucleosides and Nucleotides 82).
PG  - 4761-4776
AB  - Decadeoxyribonucleotides containing uracil, 5-bromouracil, 5-cyanouracil and 5-ethyluracil in
      recognition sequences of restriction endonucleases BglII, Sau3AI, MboI were synthesized.
      Decanucleotides containing 5-bromouracil in place of thymine had essentially the same
      susceptibility to all the restriction endonucleases.  Uracil-containing decanucleotides were
      however very resistant to attack.  Decanucleotides containing 5-cyanouracil in the recognition
      sequence were strongly resistant to hydrolysis by Sau3AI, but were hydrolysed by BglII and
      MboI as well as the parent decanucleotide.  Decanucleotides containing 5-ethyluracil were
      strongly resistant to hydrolysis by Sau3AI, but were partially resistant to hydrolysis by
      BglII and MboI.
AU  - Hayakawa T
AU  - Ono A
AU  - Ueda T
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1988 16: 4761-4776.

PMID- 21994924
VI  - 193
DP  - 2011
TI  - First draft genome sequence of a strain from the genus citricoccus.
PG  - 6092-6093
AB  - Bacteria of the genus Citricoccus have been isolated from ecological niches characterized by
      diverse abiotic stress conditions. Here we report
      the first genome draft of a strain of the genus Citricoccus isolated from
      the extremely oligotrophic Churince system in the Cuatro Cienegas Basin
      (CCB) in Coahuila, Mexico.
AU  - Hayano-Kanashiro C
AU  - Lopez-Arredondo DL
AU  - Cruz-Morales P
AU  - Alcaraz LD
AU  - Olmedo G
AU  - Barona-Gomez F
AU  - Herrera-Estrella L
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6092-6093.

PMID- 16738553
VI  - 2
DP  - 2006
TI  - Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110.
PG  - 2006.0007
AB  - With the goal of solving the whole-cell problem with Escherichia coli K-12 as a model cell,
      highly accurate genomes were determined for two closely related K-12 strains, MG1655 and
      W3110. Completion of the W3110 genome and comparison with the MG1655 genome revealed
      differences at 267 sites, including 251 sites with short, mostly single-nucleotide, insertions
      or deletions (indels) or base substitutions (totaling 358 nucleotides), in addition to 13
      sites with an insertion sequence element or defective prophage in only one strain and two
      sites for the W3110 inversion. Direct DNA sequencing of PCR products for the 251 regions with
      short indel and base disparities revealed that only eight sites are true differences. The
      other 243 discrepancies were due to errors in the original MG1655 sequence, including 79
      frameshifts, one amino-acid residue deletion, five amino-acid residue insertions, 73 missense,
      and 17 silent changes within coding regions. Errors in the original MG1655 sequence (<1 per
      13,000 bases) were mostly within portions sequenced with out-dated technology based on
      radioactive chemistry.
AU  - Hayashi K
AU  - Morooka N
AU  - Yamamoto Y
AU  - Fujita K
AU  - Isono K
AU  - Choi S
AU  - Ohtsubo E
AU  - Baba T
AU  - Wanner BL
AU  - Mori H
AU  - Horiuchi T
PT  - Journal Article
TA  - Mol. Syst. Biol.
JT  - Mol. Syst. Biol.
SO  - Mol. Syst. Biol. 2006 2: 2006.0007.

PMID- 11258796
VI  - 8
DP  - 2001
TI  - Complete genome sequence of Enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12.
PG  - 11-22
AB  - Escherichia coli O157:H7 is a major food-borne infectious pathogen that causes diarrhea,
      hemorrhagic colitis, and hemolytic uremic syndrome. Here we report the complete chromosome
      sequence of an O157:H7 strain isolated from the Sakai outbreak, and the results of genomic
      comparison with a benign laboratory strain, K-12 MG1655. The chromosome is 5.5 Mb in size, 859
      Kb larger than that of K-12. We identified a 4.1-Mb sequence highly conserved between the two
      strains, which may represent the fundamental backbone of the E. coli chromosome. The remaining
      1.4-Mb sequence comprises of O157:H7-specific sequences, most of which are horizontally
      transferred foreign DNAs. The predominant roles of bacteriophages in the emergence of O157:H7
      is evident by the presence of 24 prophages and prophage-like elements that occupy more than
      half of the O157:H7-specific sequences. The O157:H7 chromosome encodes 1632 proteins and 20
      tRNAs that are not present in K-12. Among these, at least 131 proteins are assumed to have
      virulence-related functions.  Genome-wide codon usage analysis suggested that the
      O157:H7-specific tRNAs are involved in the efficient expression of the strain-specific genes.
      A complete set of the genes specific to O157:H7 presented here sheds new insight into the
      pathogenicity and the physiology of O157:H7, and will open a way to fully understand the
      molecular mechanisms underlying the O157:H7 infection.
AU  - Hayashi T et al
PT  - Journal Article
TA  - DNA Res.
JT  - DNA Res.
SO  - DNA Res. 2001 8: 11-22.

PMID- 2507866
VI  - 3
DP  - 1989
TI  - Pseudomonas aeruginosa cytotoxin: the nucleotide sequence of the gene and the mechanism of activation of the protoxin.
PG  - 861-868
AB  - The gene encoding cytotoxin (ctx) was cloned from Pseudomonas aeruginosa 158 and
      the nucleotide sequence was determined. The structural gene of ctx encodes the
      procytotoxin of 286 amino acid residues with a molecular mass of 31,681 Daltons.
      Procytotoxin was activated by removal of 20 amino acid residues from the C
      terminus with trypsin. The cloned ctx gene was not expressed in either an
      Escherichia coli strain or a cytotoxin non-producing strain of P. aeruginosa. An
      expression system for the ctx gene was constructed by placing the structural gene
      of ctx downstream of tac promoter on a broad host-range vector plasmid.
AU  - Hayashi T
AU  - Kamio Y
AU  - Hishinuma F
AU  - Usami Y
AU  - Titani K
AU  - Terawaki Y
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1989 3: 861-868.

PMID- 26450733
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Enteropathogenic Escherichia coli, Isolated from the Bloody Stool Sample of a Common Marmoset (Callithrix jacchus).
PG  - e01161-15
AB  - Here, we report the draft genome sequence of Escherichia coli strain R811. This bacterium was
      isolated from the bloody stool sample of a common marmoset, and was categorized as
      enteropathogenic E. coli because it possessed eae.
AU  - Hayashimoto N
AU  - Morita H
AU  - Inoue T
AU  - Yasuda M
AU  - Yamamoto M
AU  - Itoh T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01161-15.

PMID- 28072419
VI  - 11
DP  - 2017
TI  - An acid-tolerant ammonia-oxidizing gamma-proteobacterium from soil.
PG  - 1130-1141
AB  - Nitrification, the microbial oxidation of ammonia to nitrate via nitrite, occurs
      in a wide range of acidic soils. However, the ammonia-oxidizing bacteria (AOB)
      that have been isolated from soil to date are acid-sensitive. Here we report the
      isolation and characterization of an acid-adapted AOB from an acidic agricultural
      soil. The isolated AOB, strain TAO100, is classified within the
      Gammaproteobacteria based on phylogenetic characteristics. TAO100 can grow in the
      pH range of 5-7.5 and survive in highly acidic conditions until pH 2 by forming
      cell aggregates. Whereas all known gammaproteobacterial AOB (gamma-AOB) species,
      which have been isolated from marine and saline aquatic environments, are
      halophiles, TAO100 is not phenotypically halophilic. Thus, TAO100 represents the
      first soil-originated and non-halophilic gamma-AOB. The TAO100 genome is
      considerably smaller than those of other gamma-AOB and lacks several genes
      associated with salt tolerance which are unnecessary for survival in soil. The
      ammonia monooxygenase subunit A gene of TAO100 and its transcript are higher in
      abundance than those of ammonia-oxidizing archaea and betaproteobacterial AOB in
      the strongly acidic soil. These results indicate that TAO100 plays an important
      role in the nitrification of acidic soils. Based on these results, we propose
      TAO100 as a novel species of a new genus, Candidatus Nitrosoglobus terrae.The
      ISME Journal advance online publication, 10 January 2017;
      doi:10.1038/ismej.2016.191.
AU  - Hayatsu M
AU  - Tago K
AU  - Uchiyama I
AU  - Toyoda A
AU  - Wang Y
AU  - Shimomura Y
AU  - Okubo T
AU  - Kurisu F
AU  - Hirono Y
AU  - Nonaka K
AU  - Akiyama H
AU  - Itoh T
AU  - Takami H
PT  - Journal Article
TA  - ISME J.
JT  - ISME J.
SO  - ISME J. 2017 11: 1130-1141.

PMID- 18445516
VI  - 91
DP  - 2008
TI  - Large-insert genome analysis technology detects structural variation in Pseudomonas aeruginosa clinical strains from cystic fibrosis patients.
PG  - 530-537
AB  - Large-insert genome analysis (LIGAN) is a broadly applicable,
      high-throughput technology designed to characterize genome-scale
      structural variation. Fosmid paired-end sequences and DNA fingerprints
      from a query genome are compared to a reference sequence using the Genomic
      Variation Analysis (GenVal) suite of software tools to pinpoint locations
      of insertions, deletions, and rearrangements. Fosmids spanning regions
      that contain new structural variants can then be sequenced. Clonal pairs
      of Pseudomonas aeruginosa isolates from four cystic fibrosis patients were
      used to validate the LIGAN technology. Approximately 1.5 Mb of inserted
      sequences were identified, including 743 kb containing 615 ORFs that are
      absent from published P. aeruginosa genomes. Six rearrangement breakpoints
      and 220 kb of deleted sequences were also identified. Our study expands
      the "genome universe" of P. aeruginosa and validates a technology that
      complements emerging, short-read sequencing methods that are better suited
      to characterizing single-nucleotide polymorphisms than structural
      variation.
AU  - Hayden HS
AU  - Gillett W
AU  - Saenphimmachak C
AU  - Lim R
AU  - Zhou Y
AU  - Jacobs MA
AU  - Chang J
AU  - Rohmer L
AU  - D'Argenio DA
AU  - Palmieri A
AU  - Levy R
AU  - Haugen E
AU  - Wong GK
AU  - Brittnacher MJ
AU  - Burns JL
AU  - Miller SI
AU  - Olson MV
AU  - Kaul R
PT  - Journal Article
TA  - Genomics
JT  - Genomics
SO  - Genomics 2008 91: 530-537.

PMID- 28983002
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of the Plant Pathogens Ralstonia solanacearum Type Strain K60 and R. solanacearum Race 3 Biovar 2 Strain UW551.
PG  - e01088-17
AB  - Ralstonia solanacearum is a globally distributed plant pathogen that causes bacterial wilt
      diseases of many crop hosts, threatening both sustenance farming
      and industrial agriculture. Here, we present closed genome sequences for the R.
      solanacearum type strain, K60, and the cool-tolerant potato brown rot strain R.
      solanacearum UW551, a highly regulated U.S. select agent pathogen.
AU  - Hayes MM
AU  - MacIntyre AM
AU  - Allen C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01088-17.

PMID- 27257202
VI  - 4
DP  - 2016
TI  - Draft Whole-Genome Sequences of 11 Bacillus cereus Food Isolates.
PG  - e00485-16
AB  - Bacillus cereus is a foodborne pathogen causing emetic and diarrheal-type syndromes. Here, we
      report the whole-genome sequences of 11 B. cereus food
      isolates.
AU  - Hayrapetyan H
AU  - Boekhorst J
AU  - de Jong A
AU  - Kuipers OP
AU  - Nierop GMN
AU  - Abee T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00485-16.

PMID- 168574
VI  - 72
DP  - 1975
TI  - Anatomy of herpes simplex virus DNA: Strain differences and heterogeneity in the locations of restriction endonuclease cleavage sites.
PG  - 1768-1772
AB  - Digestion of herpes simplex virus DNA by the HindII or EcoRI restriction
      endonucleases yielded 11 to 15 fragments with molecular weights between 2 and
      28 million.  The electrophoretic profiles obtained in 0.3% agarose gels with
      DNA fragments from nine different strains of herpes simplex virus type 1 could
      be readily differentiated from the patterns exhibited by the corresponding
      fragments from four separate strains of type 2 virus; however, within each
      serotype, the laboratory strains differed significantly among themselves and
      also from isolates passaged a minimum number of times outside the human host.
      Digestion of all DNAs of herpes simplex virus with either enzyme reproducibly
      generated two classes of fragments (major and minor) which differed in molar
      concentration.  Moreover, although the molecular weight of an intact herpes
      simplex 1 (F1) DNA molecule is approximately 98 Md, the summed molecular
      weights of all major and minor HindIII fragments totalled 160 Md, and the seven
      major fragments alone accounted for only 60 Md.  These unusual features
      indicate the existence of limited heterogeneity in the positions of cleavage
      sites along individual molecules.  We have eliminated the possibility that
      minor fragments arose from contamination with the defective DNA of high buoyant
      density which appears on serial undiluted passage of the virus.  In fact, this
      latter type of DNA was resistant to cleavage by HindIII and gave large amounts
      of only two species of EcoRI fragments, suggesting that the defective molecules
      consist of many tandem repeats of a small segment of viral DNA.  The
      heterogeneity in the viral DNA of normal density appears to be related to the
      structural organization of the molecules and does not necessarily imply
      differences in genetic content.
AU  - Hayward GS
AU  - Frenkel N
AU  - Roizman B
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1975 72: 1768-1772.

PMID- 24926061
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Nine Enteropathogenic Escherichia coli Strains from Kenya.
PG  - e00582-14
AB  - We report here the draft genome sequences of nine enteropathogenic Escherichia coli (EPEC)
      strains isolated from children in Kenya who died during
      hospitalization with diarrhea. Each of the isolates possess the EPEC adherence
      factor (EAF) plasmid encoding the bundle-forming pilus, which is characteristic
      of EPEC. These isolates represent diverse serogroups and EPEC phylogenomic
      lineages.
AU  - Hazen TH
AU  - Humphrys MS
AU  - Ochieng JB
AU  - Parsons M
AU  - Bopp CA
AU  - O'Reilly CE
AU  - Mintz E
AU  - Rasko DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00582-14.

PMID- 29472325
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of blaKPC-Containing Enterobacter aerogenes, Citrobacter freundii, and Citrobacter koseri Strains.
PG  - e00035-18
AB  - We report here the draft genome sequences of four blaKPC-containing bacteria identified as
      Klebsiella aerogenes, Citrobacter freundii, and Citrobacter koseri
      Additionally, we report the draft genome sequence of a K. aerogenes strain that
      did not contain a blaKPC gene but was isolated from the patient who had the
      blaKPC-2-containing K. aerogenes strain.
AU  - Hazen TH
AU  - Mettus RT
AU  - McElheny CL
AU  - Bowler SL
AU  - Doi Y
AU  - Rasko DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00035-18.

PMID- 22582383
VI  - 194
DP  - 2012
TI  - Genome Sequence of Klebsiella oxytoca 11492-1, a Nosocomial Isolate Possessing a  FOX-5 AmpC beta-Lactamase.
PG  - 3028-3029
AB  - Klebsiella oxytoca strain 11492-1 was isolated from a perianal swab culture from  a patient at
      the University of Maryland Medical Center in 2005. The K. oxytoca 11492-1 draft genome
      contains multiple antibiotic resistance genes, including a FOX-5 AmpC beta-lactamase encoded
      on a large IncA/C plasmid.
AU  - Hazen TH
AU  - Robinson GL
AU  - Harris AD
AU  - Rasko DA
AU  - Johnson JK
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3028-3029.

PMID- 23868135
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences of Three O157 Enteropathogenic Escherichia coli Isolates.
PG  - e00516-13
AB  - We report the draft genome sequences of three enteropathogenic Escherichia coli (EPEC)
      isolates that display the O157 serogroup but do not have the Shiga toxin
      genes (stx), which are characteristic of O157 enterohemorrhagic E. coli (EHEC).
      E. coli strain RN587/1 has the O157:H8 serotype and possesses the EAF plasmid
      characteristic of typical EPEC (J. B. Kaper, J. P. Nataro, and H. L. Mobley, Nat.
      Rev. Microbiol. 2:123-140, 2004). The other two isolates, strains C844-97 and
      C639-08, are both O157:H45 and possess the locus of enterocyte effacement (LEE)
      pathogenicity island; however, they do not contain the EAF plasmid or the
      stx-carrying phage.
AU  - Hazen TH
AU  - Sahl JW
AU  - Fraser CM
AU  - Donnenberg MS
AU  - Scheutz F
AU  - Rasko DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00516-13.

PMID- 22582382
VI  - 194
DP  - 2012
TI  - Draft Genome Sequences of the Diarrheagenic Escherichia coli Collection.
PG  - 3026-3027
AB  - We report the draft genome sequences of the collection referred to as the Escherichia coli
      DECA collection, which was assembled to contain representative isolates of the 15 most common
      diarrheagenic clones in humans
      (http://shigatox.net/new/). These genomes represent a valuable resource to the community of
      researchers who examine these enteric pathogens.
AU  - Hazen TH
AU  - Sahl JW
AU  - Redman JC
AU  - Morris CR
AU  - Daugherty SC
AU  - Chibucos MC
AU  - Sengamalay NA
AU  - Fraser-Liggett CM
AU  - Steinsland H
AU  - Whittam TS
AU  - Whittam B
AU  - Manning SD
AU  - Rasko DA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3026-3027.

PMID- 17921277
VI  - 73
DP  - 2007
TI  - Sequence Characterization and Comparative Analysis of Three Plasmids Isolated from Environmental Vibrio spp.
PG  - 7703-7710
AB  - The horizontal transfer of genes by mobile genetic elements such as
      plasmids and phages can accelerate genome diversification of Vibrio spp.,
      affecting their physiology, pathogenicity, and ecological character. In
      this study, sequence analysis of three plasmids from Vibrio spp.
      previously isolated from salt marsh sediment revealed the remarkable
      diversity of these elements. Plasmids p0908 (81.4 kb), p23023 (52.5 kb),
      and p09022 (31.0 kb) had a predicted 99, 64, and 32 protein-coding
      sequences and G+C contents of 49.2%, 44.7%, and 42.4%, respectively. A
      phylogenetic tree based on concatenation of the host 16S rRNA and rpoA
      nucleotide sequences indicated p23023 and p09022 were isolated from
      strains most closely related to V. mediterranei and V. campbellii,
      respectively, while the host of p0908 forms a clade with V. fluvialis and
      V. furnissii. Many predicted proteins had amino acid identities to
      proteins of previously characterized phages and plasmids (24 to 94%).
      Predicted proteins with similarity to chromosomally encoded proteins
      included RecA, a nucleoid-associated protein (NdpA), a type IV helicase
      (UvrD), and multiple hypothetical proteins. Plasmid p0908 had striking
      similarity to enterobacteria phage P1, sharing genetic organization and
      amino acid identity for 23 predicted proteins. This study provides
      evidence of genetic exchange between Vibrio plasmids, phages, and
      chromosomes among diverse Vibrio spp.
AU  - Hazen TH
AU  - Wu D
AU  - Eisen JA
AU  - Sobecky PA
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2007 73: 7703-7710.

PMID- 
VI  - 17
DP  - 2001
TI  - Structure and sequence analysis of cytosine DNA methyltransferase gene form infectious spleen and kidney necrosis virus.
PG  - 349-355
AB  - In the infectious spleen and kidney necrosis virus genome, an iridovirus, we have identified
      an open reading frame whose deduced amino acid sequence contains motifs characteristic of
      cytosine DNA methyltransferases.  The ORF consists of 684bp which codes for a protein of 227
      aa with a predicted molecular mass of 25,855 Da. Compared with some MTases found in bacteria,
      ISKNV MTase ORF contains the first four highly conserved  motifs of cytosine MTase, but the
      motif, responsible for DNA binding specificity, is missing.  Compared with 6 vertebrate
      iridoviruses, ISKNV is considered as a new group of Iridoviridae.  Partial sequences of 7
      vertebrate iridovirus MTases are highly conserved, they can be used to design primers to
      identify vertebrate iridovirus by PCR method.
AU  - He H
AU  - Deng M
AU  - He J
AU  - Weng S
PT  - Journal Article
TA  - Bingdu Xuebao
JT  - Bingdu Xuebao
SO  - Bingdu Xuebao 2001 17: 349-355.

PMID- 20525827
VI  - 192
DP  - 2010
TI  - The Complete Genome Sequence of Bacillus thuringiensis Mutant Strain BMB171.
PG  - 4074-4075
AB  - Bacillus thuringiensis is widely used as biopesticide for a long time. Here we report the
      finished and annotated genome sequence of B.
      thuringiensis mutant strain BMB171, a crystalliferous mutant strain
      obtained and stocked in our laboratory, with a high transformation
      frequency.
AU  - He J
AU  - Shao X
AU  - Zheng H
AU  - Li M
AU  - Wang S
AU  - Zhang Q
AU  - Li L
AU  - Liu Z
AU  - Sun M
AU  - Wang S
AU  - Yu Z
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 4074-4075.

PMID- 27151802
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Streptomyces venezuelae ATCC 15439, Producer of the Methymycin/Pikromycin Family of Macrolide Antibiotics, Using PacBio Technology.
PG  - e00337-16
AB  - Here, we report the complete genome sequence of Streptomyces venezuelae ATCC 15439, a producer
      of the methymycin/pikromycin family of macrolide antibiotics
      and a model host for natural product studies, obtained exclusively using PacBio
      sequencing technology. The 9.03-Mbp genome harbors 8,775 genes and 11 polyketide
      and nonribosomal peptide natural product gene clusters.
AU  - He J
AU  - Sundararajan A
AU  - Devitt NP
AU  - Schilkey FD
AU  - Ramaraj T
AU  - Melancon CEIII
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00337-16.

PMID- 21551307
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Bacillus thuringiensis subsp. chinensis strain CT-43.
PG  - 3407-3408
AB  - Bacillus thuringiensis is widely used as agricultural biopesticide for a long time. As a
      producing strain, B. thuringiensis subsp. chinensis strain
      CT-43 has high toxin to lepidopterous and dipterous insects. It can form
      various parasporal crystals consisting of Cry1Aa3, Cry1Ba1, Cry1Ia14,
      Cry2Aa9, and Cry2Ab1. During fermentation, it simultaneously generates
      vegetative insecticidal protein Vip3Aa10, as well as insecticidal
      nucleotide analogue thuringiensin. Here we report the finished, annotated
      genome sequence of B. thuringiensis strain CT-43.
AU  - He J
AU  - Wang J
AU  - Yin W
AU  - Shao X
AU  - Zheng H
AU  - Li M
AU  - Zhao Y
AU  - Sun M
AU  - Wang S
AU  - Yu Z
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3407-3408.

PMID- 11878882
VI  - 291
DP  - 2001
TI  - Complete genome analysis of the mandarin fish infectious spleen and kidney necrosis iridovirus.
PG  - 126-139
AB  - The nucleotide sequence of the infectious spleen and kidney necrosis virus
      (ISKNV) genome was determined and found to comprise 111,362 bp with a G+C
      content of 54.78%. It contained 124 potential open reading frames (ORFs)
      with coding capacities ranging from 40 to 1208 amino acids. The analysis
      of the amino acid sequences deduced from the individual ORFs revealed that
      35 of the 124 potential gene products of ISKNV show significant homology
      to functionally characterized proteins of other species. Some of the
      putative gene products of ISKNV showed significant homologies to proteins
      in the GenBank/EMBL/DDBJ databases including enzymes and structural
      proteins involved in virus replication, transcription, protein
      modification, and virus-host interaction. In addition, one major repeated
      sequence showing significant homology to the Red Sea bream iridovirus
      (RSIV) genome was identified. Based on the information obtained from
      biological properties (including histopathology, tissue tropisms, natural
      host range, and geographic distribution), physiochemical and physical
      properties, and genome analysis, we suggest that ISKNV, RSIV, sea bass
      iridovirus, grouper iridovirus, and African lampeye iridovirus may belong
      to a new genus of the Iridoviridae family and are tentatively referred to
      as cell hypertrophy iridoviruses.
AU  - He JG
AU  - Deng M
AU  - Weng SP
AU  - Li Z
AU  - Zhou SY
AU  - Long QX
AU  - Wang XZ
AU  - Chan SM
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 2001 291: 126-139.

PMID- 20368420
VI  - 107
DP  - 2010
TI  - Evolutionary dynamics of Clostridium difficile over short and long time scales.
PG  - 7527-7532
AB  - Clostridium difficile has rapidly emerged as the leading cause of antibiotic-associated
      diarrheal disease, with the transcontinental spread of
      various PCR ribotypes, including 001, 017, 027 and 078. However, the genetic
      basis for the emergence of C. difficile as a human pathogen is unclear. Whole
      genome sequencing was used to analyze genetic variation and virulence of a
      diverse collection of thirty C. difficile isolates, to determine both macro and
      microevolution of the species. Horizontal gene transfer and large-scale
      recombination of core genes has shaped the C. difficile genome over both short
      and long time scales. Phylogenetic analysis demonstrates C. difficile is a
      genetically diverse species, which has evolved within the last 1.1-85 million
      years. By contrast, the disease-causing isolates have arisen from multiple
      lineages, suggesting that virulence evolved independently in the highly epidemic
      lineages.
AU  - He M et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2010 107: 7527-7532.

PMID- 23357245
VI  - 164
DP  - 2012
TI  - Genome sequence of the plant growth promoting strain Bacillus amyloliquefaciens subsp plantarum B9601-Y2 and expression of mersacidin and other secondary metabolites.
PG  - 281-291
AB  - The plant-associated Bacillus amyloliquefaciens subsp. plantarum strain B9601-Y2, isolated
      from wheat rhizosphere, is a powerful plant
      growth-promoting rhizobacterium. Its relative large genome size of 4.24
      Mbp, exceeding that of other representatives of the B.
      amyloliquefaciens subsp. plantarum taxon, is mainly due to the presence
      of 18 DNA-islands containing remnants of phages, a unique restriction
      modification system, a gene cluster for mersacidin synthesis, and an
      orphan gene cluster devoted to non-ribosomal synthesis of an
      unidentified peptide. Like other members of the taxon, the Y2 genome
      contains giant gene clusters for non-ribosomal synthesis of the
      polyketides macrolactin, difficidin, and bacillaene, the antifungal
      lipopeptides bacillomycin D, and fengycin, the siderophore
      bacillibactin, and the dipeptide bacilysin. A gene cluster encoding
      enzymes for a degradative pathway with 2-keto-3-deoxygluconate and
      2-keto-3-deoxy-phosphogluconate as intermediates was explored by genome
      mining and found as being a unique feature for representatives of the
      plantarum subspecies. A survey of the Y2 genome against other B.
      amyloliquefaciens genomes revealed 130 genes only occurring in subsp.
      plantarum but not in subsp. amyloliquefaciens. Notably, the surfactin
      gene cluster is not functional due to a large deletion removing parts
      of the Srf synthetases B and C. Expression of polyketides,
      lipopeptides, mersacidin, and of the growth hormone indole-3-acetic
      acid in Y2 was demonstrated by matrix-assisted laser desorption
      ionization-time of flight mass spectroscopy and high-performance liquid
      chromatography, respectively.
AU  - He P
AU  - Hao K
AU  - Blom J
AU  - Rueckert C
AU  - Vater J
AU  - Mao Z
AU  - Wu Y
AU  - Hou M
AU  - He P
AU  - He Y
AU  - Borriss R
PT  - Journal Article
TA  - J. Biotechnol.
JT  - J. Biotechnol.
SO  - J. Biotechnol. 2012 164: 281-291.

PMID- 25988532
VI  - 5
DP  - 2015
TI  - Expression and purification of a single-chain Type IV restriction enzyme Eco94GmrSD and determination of its substrate preference.
PG  - 9747
AB  - The first reported Type IV restriction endonuclease (REase) GmrSD consists of GmrS and GmrD
      subunits. In most bacteria, however, the gmrS and gmrD genes are
      fused together to encode a single-chain protein. The fused coding sequence for
      ECSTEC94C_1402 from E. coli strain STEC_94C was expressed in T7 Express. The
      protein designated as Eco94GmrSD displays modification-dependent ATP-stimulated
      REase activity on T4 DNA with glucosyl-5-hydroxymethyl-cytosines (glc-5hmC) and
      T4gt DNA with 5-hydroxymethyl-cytosines (5hmC). A C-terminal 6xHis-tagged protein
      was purified by two-column chromatography. The enzyme is active in Mg(2+) and
      Mn(2+) buffer. It prefers to cleave large glc-5hmC- or 5hmC-modified DNA. In
      phage restriction assays, Eco94GmrSD weakly restricted T4 and T4gt, whereas T4
      IPI*-deficient phage (Deltaip1) were restricted more than 10(6)-fold, consistent
      with IPI* protection of E. coli DH10B from lethal expression of the closely
      homologous E. coli CT596 GmrSD. Eco94GmrSD is proposed to belong to the
      His-Asn-His (HNH)-nuclease family by the identification of a putative C-terminal
      REase catalytic site D507-H508-N522. Supporting this, GmrSD variants D507A,
      H508A, and N522A displayed no endonuclease activity. The presence of a large
      number of fused GmrSD homologs suggests that GmrSD is an effective phage
      exclusion protein that provides a mechanism to thwart T-even phage infection.
AU  - He X
AU  - Hull V
AU  - Thomas JA
AU  - Fu X
AU  - Gidwani S
AU  - Gupta YK
AU  - Black LW
AU  - Xu SY
PT  - Journal Article
TA  - Sci. Rep.
JT  - Sci. Rep.
SO  - Sci. Rep. 2015 5: 9747.

PMID- 17640271
VI  - 65
DP  - 2007
TI  - Analysis of a genomic island housing genes for DNA S-modification system in Streptomyces lividans 66 and its counterparts in other distantly related  bacteria.
PG  - 1034-1048
AB  - The complete sequence (92 770 bp) of a genomic island (GI) named SLG from Streptomyces
      lividans 66, encoding a novel DNA S-modification system (dnd), was
      determined. Its overall G+C content was 67.8%, lower than those of three
      sequenced Streptomyces genomes. Among 85 predicted open reading frames (ORFs) in
      SLG, 22 ORFs showed little homology with previously known proteins. SLG displays
      a mosaic structure composed of four modules, indicative of multiple recombination
      events in its formation. Spontaneous excision and circularization of SLG was
      observed, and the excision rate appeared to be induced at least fivefold by MNNG
      exposure. Using constructed mini-islands of SLG, we demonstrated that Slg01, a
      P4-like integrase, was sufficient to promote SLG integration, excision and
      circularization. Eleven counterpart dnd clusters, which also mapped to GIs in 10
      chromosomes and a plasmid, were found in taxonomically unrelated bacterial
      species from various geographic niches. Additionally, c. 10% of actinomycetes
      were found to possess a dnd cluster in a survey involving 74 strains. Comparison
      of dnd clusters in the 12 bacteria strongly suggests that these dnd-bearing
      elements might have evolved from a common ancestor similar to plasmid-originated
      chromosome II of Pseudoalteromonas haloplanktis TAC125.
AU  - He X
AU  - Ou HY
AU  - Yu Q
AU  - Zhou X
AU  - Wu J
AU  - Liang J
AU  - Zhang W
AU  - Rajakumar K
AU  - Deng Z
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2007 65: 1034-1048.

PMID- 28860235
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequence of the 1,4-Dioxane-Degrading Bacterium Mycobacterium dioxanotrophicus PH-06.
PG  - e00625-17
AB  - We report here the complete genome sequence of Mycobacterium dioxanotrophicus PH-06, which is
      capable of using 1,4-dioxane as a sole source of carbon and
      energy. The reported sequence will enable the elucidation of this novel metabolic
      pathway and the development of molecular biomarkers to assess bioremediation
      potential at contaminated sites.
AU  - He Y
AU  - Wei K
AU  - Si K
AU  - Mathieu J
AU  - Li M
AU  - Alvarez PJJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00625-17.

PMID- 25657275
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Campylobacter jejuni YH001 from Beef Liver, Which Contains a Novel Plasmid.
PG  - e01492-14
AB  - Campylobacter jejuni, commonly found in poultry and meat products, causes gastroenteritis in
      humans. Here, we report the complete genome sequence of a C.
      jejuni strain, YH001, isolated from retail beef liver. The genome is 1,712,361 bp
      and has a 30.5% G+C content and two plasmids of 46.5 kb and 4.4 kb.
AU  - He Y
AU  - Yan X
AU  - Reed S
AU  - Xie Y
AU  - Chen CY
AU  - Irwin P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01492-14.

PMID- 9468518
VI  - 273
DP  - 1998
TI  - Amino acid residues in both the protein splicing and endonuclease domains of the PI-SceI intein mediate DNA binding.
PG  - 4607-4615
AB  - A structure-based model describing the interaction of the two-domain PI-SceI endonuclease with
      its 31-base pair DNA substrate suggests that the endonuclease domain (domain II) contacts the
      cleavage site region of the substrate, while the protein splicing domain (domain I) interacts
      with a distal region that is sufficient for high affinity binding.  To support this model,
      alanine-scanning mutagenesis was used to assemble a set of 49 PI-SceI mutant proteins that
      were purified and assayed for their DNA binding and cleavage properties.  Fourteen mutant
      proteins were 4- to >500-fold less active than wild-type PI-SceI in cleavage assays, and one
      mutant (T225A) was 3-fold more active.  Alanine substitution at two positions in domain I
      reduces overall binding >60-fold by perturbing the interaction of PI-SceI with the minimal
      binding region.  Conversely, mutations in domain II have little effect on binding, reduce
      binding to the cleavage site region only, or affect binding to both regions.  Interestingly,
      substitutions at Lys301, which is part of the endonucleolytic active site, eliminate binding
      to the cleavage site region but permit contact with the minimal binding region.  This
      experimental evidence demonstrates that the protein splicing domain as well as the
      endonuclease domain is involved in binding of a DNA substrate with the requisite length.
AU  - He Z
AU  - Crist M
AU  - Yen H-C
AU  - Duan X
AU  - Quiocho FA
AU  - Gimble FS
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1998 273: 4607-4615.

PMID- Not carried by PubMed...
VI  - 16
DP  - 1989
TI  - Purification of BamHI DNA methylase and protection function of DNA methylation against restriction endonuclease BamHI.
PG  - 217-220
AB  - None
AU  - He Z
AU  - Jiang X
AU  - Xue J
AU  - Zheng W
PT  - Journal Article
TA  - Weishengwuxue Tongbao
JT  - Weishengwuxue Tongbao
SO  - Weishengwuxue Tongbao 1989 16: 217-220.

PMID- 1700369
VI  - 18
DP  - 1990
TI  - The use of 5-azacytidine to increase cleavage of methylation sensitive rare cutting restriction enzymes sites in amplified DNA.
PG  - 6147-6148
AB  - None
AU  - Heard E
AU  - Fried M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 6147-6148.

PMID- 9187655
VI  - 4
DP  - 1997
TI  - The structure of I-Crel, a group I intron-encoded homing endonuclease.
PG  - 468-476
AB  - The structure of I-Crel provides the first view of a protein encoded by a gene within an
      intron. This endonuclease recognizes a long DNA site approximately 20 base pairs in length and
      facilitates the lateral transfer of that intron. The protein exhibits a DNA-binding surface
      consisting of four antiparallel beta-strands that form a 20 A wide groove which is over 70 A
      long. The architecture of this fold is different from that of the TATA binding protein, TBP,
      which also contains an antiparallel beta-saddle. The conserved LAGLIDADG motif, which is found
      in many mobile intron endonucleases, maturases and inteins, forms a novel helical interface
      and contributes essential residues to the active site.
AU  - Heath PJ
AU  - Stephens KM
AU  - Monnat RJ Jr
AU  - Stoddard BL
PT  - Journal Article
TA  - Nat. Struct. Biol.
JT  - Nat. Struct. Biol.
SO  - Nat. Struct. Biol. 1997 4: 468-476.

PMID- 18990191
VI  - 70
DP  - 2008
TI  - A novel streptococcal integrative conjugative element involved in iron acquisition.
PG  - 1274-1292
AB  - In this study, we determined the function of a novel non-ribosomal peptide
      synthetase (NRPS) system carried by a streptococcal integrative
      conjugative element (ICE), ICESe2. The NRPS shares similarity with the
      yersiniabactin system found in the high-pathogenicity island of Yersinia
      sp. and is the first of its kind to be identified in streptococci. We
      named the NRPS product 'equibactin' and genes of this locus eqbA-N.
      ICESe2, although absolutely conserved in Streptococcus equi, the causative
      agent of equine strangles, was absent from all strains of the closely
      related opportunistic pathogen Streptococcus zooepidemicus. Binding of
      EqbA, a DtxR-like regulator, to the eqbB promoter was increased in the
      presence of cations. Deletion of eqbA resulted in a small-colony
      phenotype. Further deletion of the irp2 homologue eqbE, or the genes eqbH,
      eqbI and eqbJ encoding a putative ABC transporter, or addition of the iron
      chelator nitrilotriacetate, reversed this phenotype, implicating iron
      toxicity. Quantification of (55)Fe accumulation and sensitivity to
      streptonigrin suggested that equibactin is secreted by S. equi and that
      the eqbH, eqbI and eqbJ genes are required for its associated iron import.
      In agreement with a structure-based model of equibactin synthesis,
      supplementation of chemically defined media with salicylate was required
      for equibactin production.
AU  - Heather Z
AU  - Holden MT
AU  - Steward KF
AU  - Parkhill J
AU  - Song L
AU  - Challis GL
AU  - Robinson C
AU  - Davis-Poynter N
AU  - Waller AS
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2008 70: 1274-1292.

PMID- 25953160
VI  - 3
DP  - 2015
TI  - Complete Closed Genome Sequences of a Mannheimia haemolytica Serotype A1 Leukotoxin Deletion Mutant and Its Wild-Type Parent Strain.
PG  - e00417-15
AB  - Mannheimia haemolytica is a bacterial pathogen that secretes leukotoxin (LktA) which binds to
      leukocyte membranes via CD18, causing bacterial pneumonia in
      ruminants. We report the complete closed genome sequences of a leukotoxin mutant
      and its parent strain that are frequently used in respiratory disease studies.
AU  - Heaton MP
AU  - Harhay GP
AU  - Smith TP
AU  - Bono JL
AU  - Chitko-McKown CG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00417-15.

PMID- 21622738
VI  - 193
DP  - 2011
TI  - Genome sequence of the vertebrate gut symbiont Lactobacillus reuteri ATCC 53608.
PG  - 4015-4016
AB  - Lactobacillus reuteri inhabiting the gastrointestinal tract of a range of vertebrates is a
      true symbiont with established beneficial effects to the host. Here we describe the draft
      genome of L. reuteri ATCC 53608 strain isolated from pig. The genome sequence provides
      important insights into the evolutionary changes underlying host specialisation.
AU  - Heavens D
AU  - Tailford LE
AU  - Crossman L
AU  - Jeffers F
AU  - Mackenzie DA
AU  - Caccamo M
AU  - Juge N
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4015-4016.

PMID- 23929489
VI  - 1
DP  - 2013
TI  - Genome Sequence of the Cheese-Starter Strain Lactobacillus delbrueckii subsp. lactis CRL 581.
PG  - e00602-13
AB  - We report the genome sequence of Lactobacillus delbrueckii subsp. lactis CRL 581  (1,911,137
      bp, GC 49.7%), a proteolytic strain isolated from a homemade
      Argentinian hard cheese which has a key role in bacterial nutrition and releases
      bioactive health-beneficial peptides from milk proteins.
AU  - Hebert EM
AU  - Raya RR
AU  - Brown L
AU  - Font-de-Valdez G
AU  - Savoy-de-Giori G
AU  - Taranto MP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00602-13.

PMID- 22207745
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Bacteriocin-Producing Lactobacillus curvatus Strain CRL705.
PG  - 538-539
AB  - Lactobacillus curvatus is one of the most prevalent lactic acid bacteria found in fermented
      meat products. Here, we present the draft genome
      sequence of Lactobacillus curvatus CRL705, a bacteriocin producer strain
      isolated from an Argentinean artisanal fermented sausage, which consists
      of 1,833,251 bp (GC content, 41.9%) and two circular plasmids of 12,342 bp
      (pRC12; GC, 43.9%) and 18,664 bp (pRC18; GC, 34.4%).
AU  - Hebert EM
AU  - Saavedra L
AU  - Taranto MP
AU  - Mozzi F
AU  - Magni C
AU  - Nader ME
AU  - Font-de-Valdez G
AU  - Sesma F
AU  - Vignolo G
AU  - Raya RR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 538-539.

PMID- 21278298
VI  - 193
DP  - 2011
TI  - Genome sequence of Taylorella equigenitalis MCE9, the causative agent of contagious equine metritis.
PG  - 1785
AB  - Taylorella equigenitalis is the causative agent of contagious equine metritis (CEM), a
      sexually-transmitted infection of horses. We herein report the genome sequence of T.
      equigenitalis strain MCE9, isolated in 2005 from the urethral fossa of a 4-year-old stallion
      in France.
AU  - Hebert L
AU  - Moumen B
AU  - Duquesne F
AU  - Breuil MF
AU  - Laugier C
AU  - Batto JM
AU  - Renault P
AU  - Petry S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 1785.

PMID- 25428969
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Taylorella equigenitalis Strain MCE529, Isolated from a  Belgian Warmblood Horse.
PG  - e01214-14
AB  - Taylorella equigenitalis is the causative agent of contagious equine metritis (CEM), a
      sexually transmitted infection of horses. We herein report the genome
      sequence of T. equigenitalis strain MCE529, isolated in 2009 from the urethral
      fossa of a 15-year-old Belgian Warmblood horse in France.
AU  - Hebert L
AU  - Touzain F
AU  - de Boisseson C
AU  - Breuil MF
AU  - Duquesne F
AU  - Laugier C
AU  - Blanchard Y
AU  - Petry S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01214-14.

PMID- 4338039
VI  - 115
DP  - 1972
TI  - Phenotypic characterization of fi- R factors determining the restriction and modification hspII specificity.
PG  - 225-233
AB  - All known determinants of the restriction, modification specificity hspII are
      plasmids of the compatibility class N.  Two I-like R factors, R56 and R64 are
      able to interfere with the lytic cycle of phage lambda (in liberation of phage
      by lysogens or newly infected cells) by a different mechanism.
AU  - Hedges RW
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1972 115: 225-233.

PMID- 4558791
VI  - 71
DP  - 1972
TI  - R124, an fi+ R factor of a new compatibility class.
PG  - 403-405
AB  - The plasmids of Gram-negative bacteria can be classified as fi+ or fi-
      (Watanabe et al. 1964).  The former are capable of repressing the fertility
      functions, notably the production of sex pili, determined by the F factor
      (Nishimura, Ishibashi, Meynell & Hirota, 1967).  Most fi+ plasmids carry genes
      determining the production of sex pili similar to those determined by the F
      factor (F-like pili) in antigenic specificity and phage adsorption (Meynell &
      Datta, 1966; Lawn & Meynell, 1970; Dennison & Hedges, 1972).  Among the fi-
      plasmids a number of compatibility classes has been described (Watanabe, 1968;
      Datta & Hedges, 1971; Datta et al. 1971; Hedges & Datta, 1971).  Two plasmids
      belonging to the same compatibility class cannot stably co-exisit in a single
      cell.  Among the fi+ plasmids four compatibility classes have been described,
      three of which we propose to name as follows:  FI, the class including F,
      ColV2, ColV3 (MacFarren & Clowes, 1967) and R386 (Dennison, 1972); FII, the
      class including RI and many other fi+ R factors (Meynell, Meynell & Datta,
      1968); FIII, the class including ColB-K98 and ColB-K166 (Frydman & Meynell,
      1969); fourthly, the class including R62 (R62, though fi+, determines I-like
      pili and has the compatibility of a typical I-like plasmid) (lawn, Meynell,
      Meynell & Datta, 1967; N. Datta & R.W. Hedges, unpublished).  R124 is an fi+ R
      factor carrying tetracycline resistance and specifying F-like pili (Meynell &
      Datta, 1966).  It is the only fi+ R factor carrying tetracycline resistance and
      specifying F-like pili (Meynell & Datta, 1966).  It is the only fi+ R factor so
      far tested to determine restriction and modification of a number of DNA phages
      including lambda.  The specificity of this restriction, which is unique, is
      termed hsp I (Bannister & Glover, 1968).  Among the fi- R factors, all those
      capable of restriction or modification fall into a single compatibility group N
      (Hedges, 1972) and it seemed interesting to determine the compatibility
      specificity of R124.  In this paper we show that this plasmid co-exists stably
      with members of all the compatibility groups listed above and is thus the first
      example of a new compatibility group, FIV.
AU  - Hedges RW
AU  - Datta N
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1972 71: 403-405.

PMID- 4591318
VI  - 331
DP  - 1973
TI  - Hydrolysis of adenosine triphosphate accompanying interaction between Escherichia coli B restriction endonuclease and unmodified deoxyribonucleic acid.
PG  - 310-317
AB  - The Escherichia coli B restriction endonuclease hydrolyzes ATP to ADP and Pi in
      the presence of unmodified, double-strand DNA and Mg2+.  The requirements for
      maximum ATP hydrolysis are essentially the same as those for phosphodiester
      bond cleavage.  However, ATP is hydrolyzed under conditions where
      phosphodiester bond cleavage is prevented, namely, in the absence of
      S-adenosyl-L-methionine and in the presence of DNA which is resistant to the
      endonuclease by virtue of mutations.  ATP is shown to be necessary for the
      formation of the endonuclease-unmodified DNA complex.
AU  - Hedgpeth J
AU  - Boyer HW
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1973 331: 310-317.

PMID- 4343974
VI  - 69
DP  - 1972
TI  - DNA nucleotide sequence restricted by the RI Endonuclease.
PG  - 3448-3452
AB  - The sequence of DNA base pairs adjacent to the phosphodiester bonds cleaved by
      the RI restriction endonuclease in unmodified DNA from coliphage lambda has
      been determined.  The 5'-terminal nucleotide labeled with 32P and
      oligonucleotides up to the heptamer were analyzed from a pancreatic DNase
      digest.  The following sequence of nucleotides adjacent to the RI break made in
      lambda DNA was deduced from these data and from the 3'-dinucleotide sequence
      and nearest-neighbor analysis obtained from repair synthesis with the DNA
      polymerase of Rous sarcoma virus 5'....A/TpG^pApApTpTpCpT/A....3'
      3'....T/ApCpTpTpApAp^GpA/T....5' The RI endonuclease cleavage of the
      phosphodiester bonds (indicated by arrows) generates 5'-phosphodiester bonds
      (indicated by arrows) generates 5'-phosphoryls and short cohesive termini of
      four nucleotides, pApApTpT.  The most striking feature of the sequence is its
      symmetry.
AU  - Hedgpeth J
AU  - Goodman HM
AU  - Boyer HW
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1972 69: 3448-3452.

PMID- 26634758
VI  - 3
DP  - 2015
TI  - High-Quality Draft Genome Sequence of Kallotenue papyrolyticum JKG1T Reveals Broad Heterotrophic Capacity Focused on Carbohydrate and Amino Acid Metabolism.
PG  - e01410-15
AB  - The draft genome of Kallotenue papyrolyticum JKG1(T), a member of the order Kallotenuales,
      class Chloroflexia, consists of 4,475,263 bp in 4 contigs and
      encodes 4,010 predicted genes, 49 tRNA-encoding genes, and 3 rRNA operons. The
      genome is consistent with a heterotrophic lifestyle including catabolism of
      polysaccharides and amino acids.
AU  - Hedlund BP et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01410-15.

PMID- 11520613
VI  - 202
DP  - 2001
TI  - BceS1, a new addition to the type III restriction and modification family.
PG  - 189-193
AB  - The nucleotide sequence of an 11-kb chromosomal BglII fragment from Bacillus cereus American
      Type Culture Collection (ATCC) 10987 strain revealed two closely adjacent open reading frames
      organized in an operon, of which the deduced amino acids showed identity to the type III
      restriction and modification (R/M) subunits described in Gram-negative bacteria. An enhanced
      transcription level was revealed when the culture was grown in the presence of foreign DNA. A
      cell-free extract from this culture restricted pUC19, whereas from a plain medium the
      restriction was very weak. The in vitro methylation protected pUC 19 from restriction. The R/M
      system was designated BceS1 as this endonuclease required ATP and Mg(2+) as cofactors like
      other type III endonucleases. BceS1 is the first chromosomal type III R/M system characterized
      in a Gram-positive bacterium.
AU  - Hegna IK
AU  - Bratland H
AU  - Kolsto A
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2001 202: 189-193.

PMID- 1587478
VI  - 114
DP  - 1992
TI  - A type-II DNA restriction and modification system in Bacillus cereus?
PG  - 149-150
AB  - The deduced amino acid (aa) sequence of an open reading frame, present on a fragment of the
      Bacillus cereus ATCC10987 geneome, shows 29.3% identity within a 368-aa segment of the
      type-III EcoPI modification and restriction operon.
AU  - Hegna IK
AU  - Karlstrom ES
AU  - Lopez R
AU  - Kristensen T
AU  - Kolsto A-B
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1992 114: 149-150.

PMID- 5045302
VI  - 67
DP  - 1972
TI  - Mutants of bacteriophage T2 gt with altered DNA methylase activity.
PG  - 351-360
AB  - Certain non-glucosylated (gt) T-even bacteriophage mutants are restricted by
      prophage P1 (these are designated rP1).  Unrestricted mutants (uP1) have been
      shown earlier to contain hypermethylated DNA compared to their rP1 parent.  The
      DNA methylating enzyme induced by rP1 and uP1 phage has been partially purified
      by affinity chromatography on DNA cellulose. Both rP1 and uP1 methylase
      methylate adenine exclusively.  The uP1 methylase shows a greater thermal
      lability than the rP1 enzyme; both enzymic forms are stabilized against heat
      inactivation in the presence of substrate S-adenosylmethionine.  In terms of
      their ability to methylate non-viral cytosine-containing DNA's, rP1 and uP1
      methylase exhibit similar Km values and extents of methylation.  However, the
      uP1 methylase shows a higher affinity (lowered Km) and greater site recognition
      (higher extent of methylation) than the rP1 methylase with various T-even phage
      (5-hydroxymethylcytosine-containing) DNA's.  These results are consistent with
      the notion that mutation from rP1 to uP1 produces an alteration in the
      viral-induced DNA methylase.
AU  - Hehlmann R
AU  - Hattman S
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1972 67: 351-360.

PMID- 10952301
VI  - 406
DP  - 2000
TI  - DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae.
PG  - 477-483
AB  - Here we determine the complete genomic sequence of the gram negative, gamma-Proteobacterium
      Vibrio cholerae El Tor N16961 to be 4,033,460 base pairs (bp). The genome consists of two
      circular chromosomes of 2,961,146 bp and 1,072,314 bp that together encode 3,885 open reading
      frames. The vast majority of recognizable genes for essential cell functions (such as DNA
      replication, transcription, translation and cell-wall biosynthesis) and pathogenicity (for
      example, toxins, surface antigens and adhesins) are located on the large chromosome. In
      contrast, the small chromosome contains a larger fraction (59%) of hypothetical genes compared
      with the large chromosome (42%), and also contains many more genes that appear to have origins
      other than the gamma-Proteobacteria. The small chromosome also carries a gene capture system
      (the integron island) and host 'addiction' genes that are typically found on plasmids; thus,
      the small chromosome may have originally been a megaplasmid that was captured by an ancestral
      Vibrio species. The V. cholerae genomic sequence provides a starting point for understanding
      how a free-living, environmental organism emerged to become a significant human bacterial
      pathogen.
AU  - Heidelberg JF et al
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2000 406: 477-483.

PMID- 12368813
VI  - 20
DP  - 2002
TI  - Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis.
PG  - 1118-1123
AB  - Shewanella oneidensis is an important model organism for bioremediation studies because of its
      diverse respiratory capabilities, conferred in part by multicomponent, branched electron
      transport systems. Here we report the sequencing of the S. oneidensis genome, which consists
      of a 4,969,803-base pair circular chromosome with 4,758 predicted protein-encoding open
      reading frames (CDS) and a 161,613-base pair plasmid with 173 CDSs. We identified the first
      Shewanella lambda-like phage, providing a potential tool for further genome engineering.
      Genome analysis revealed 39 c-type cytochromes, including 32 previously unidentified in S.
      oneidensis, and a novel periplasmic [Fe] hydrogenase, which are integral members of the
      electron transport system. This genome sequence represents a critical step in the elucidation
      of the pathways for reduction (and bioremediation) of pollutants such as uranium (U) and
      chromium (Cr), and offers a starting point for defining this organism's complex electron
      transport systems and metal ion-reducing capabilities.
AU  - Heidelberg JF et al
PT  - Journal Article
TA  - Nat. Biotechnol.
JT  - Nat. Biotechnol.
SO  - Nat. Biotechnol. 2002 20: 1118-1123.

PMID- 2690008
VI  - 17
DP  - 1989
TI  - Cloning, characterization and heterologous expression of the SmaI restriction-modification system.
PG  - 9783-9796
AB  - The genes coding for the class-II Serratia marcescens restriction-modification
      system have been cloned and expressed in E. coli.  Recombinant clones
      restricted incoming phage only poorly; the recombinant plasmids, however,
      became fully modified in vivo, i.e. completely resistant against digestion with
      R.SmaI.  The determined nucleotide sequence of the cloned system revealed three
      open reading frames with lengths of 252 bp, 741 bp, and 876 bp.  Through
      various deletion experiments and an insertion-mutation experiment the 876 bp
      open reading frame could be assigned to the SmaI DNA modification enzyme and
      the 741 bp open reading frame to the SmaI restriction endonuclease.  Mapping of
      the transcription start sites of the genes revealed that the SmaI endonuclease
      is transcribed as a polycistronic mRNA together with a 252 bp long preceding
      open reading frame of unknown function.  No homology was found when comparing
      the amino acid sequence of M.SmaI with the published sequences of m5C-specific
      DNA modification methyltransferases.  On the other hand, a stretch of 14 amino
      acids in the C-proximal region of M.SmaI shows a signficant homology to the
      C-proximal amino acid sequences of the N6A-methyltransferases M.HinfI and
      M.DpnIIA and the N4C-methyltransferase M.PvuII.
AU  - Heidmann S
AU  - Seifert W
AU  - Kessler C
AU  - Domdey H
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 9783-9796.

PMID- 28684580
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of a Multidrug-Resistant, blaNDM-1-Expressing Klebsiella pneumoniae K66-45 Clinical Isolate from Norway.
PG  - e00601-17
AB  - Multidrug-resistant Klebsiella pneumoniae is a major cause of hospital-acquired infections.
      Here, we report the complete genome sequence of the
      multidrug-resistant, blaNDM-1-positive strain K. pneumoniae K66-45, isolated from
      a hospitalized Norwegian patient.
AU  - Heikal A
AU  - Samuelsen O
AU  - Kristensen T
AU  - Okstad OA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00601-17.

PMID- 29217796
VI  - 5
DP  - 2017
TI  - The Completed PacBio Single-Molecule Real-Time Sequence of Methylosinus trichosporium Strain OB3b Reveals the Presence of a Third Large Plasmid.
PG  - e01349-17
AB  - Presented here is the complete genome sequence of the well-studied Rhizobiales methanotroph
      Methylosinus trichosporium strain OB3b. The assembly contains
      5,183,433 bp, corresponding to a chromosome of 4,508,832 bp and three circular
      plasmids of 285,280 bp, 209,102 bp, and 180,219 bp.
AU  - Heil JR
AU  - Lynch MDJ
AU  - Cheng J
AU  - Matysiakiewicz O
AU  - D'Alessio M
AU  - Charles TC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01349-17.

PMID- 22478
VI  - 1
DP  - 1977
TI  - Specificity of cleavage by a restriction nuclease from Bacillus subtilis.
PG  - 291-303
AB  - The restriction nuclease from B. subtilis (Bsu) which cleaves in the middle of
      the tetra-nucleotide sequence 5'-GGCC-3'	 3'-CCGG-5' has been found to decrease
      its substrate specificity at high nuclease concentrations.  There are special
      conditions, high pH, low ionic strength, and high glycerol contents, which
      strongly enhance splitting with decreased specificity and also lead to
      splitting of single-stranded DNA.  By sequence analyses it is shown that the
      reduction in specificity of Bsu corresponds to cleavage predominantly at
      5'-GC-3' 3'-CG-5' sequences.  No comparable change in specificity has been
      observed in a restriction nuclease from Haemophilus aegyptius (HaeIII), an
      isoschizomer of Bsu.
AU  - Heininger K
AU  - Horz W
AU  - Zachau HG
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1977 1: 291-303.

PMID- 22465289
VI  - 161
DP  - 2012
TI  - Insights into the completely annotated genome of Lactobacillus buchneri CD034, a strain isolated from stable grass silage.
PG  - 153-166
AB  - Lactobacillus buchneri belongs to the group of heterofermentative lactic acid
      bacteria and is a common member of the silage microbiome. Here we report the
      completely annotated genomic sequence of L. buchneri CD034, a strain isolated
      from stable grass silage. The whole genome of L. buchneri CD034 was sequenced on
      the Roche Genome Sequencer FLX platform. It was found to consist of four
      replicons, a circular chromosome, and three plasmids. The circular chromosome was
      predicted to encode 2319 proteins and contains a genomic island and two prophages
      which significantly differ in G+C-content from the remaining chromosome. It
      possesses all genes for enzymes of a complete phosphoketolase pathway, whereas
      two enzymes necessary for glycolysis are lacking. This confirms the
      classification of L. buchneri CD034 as an obligate heterofermentative lactic acid
      bacterium. A set of genes considered to be involved in the lactate degradation
      pathway and genes putatively involved in the breakdown of plant cell wall
      polymers were identified. Moreover, several genes encoding putative S-layer
      proteins and two CRISPR systems, belonging to the subclasses I-E and II-A, are
      located on the chromosome. The largest plasmid pCD034-3 was predicted to encode
      57 genes, including a putative polysaccharide synthesis gene cluster, whereas the
      functions of the two smaller plasmids, pCD034-1 and pCD034-2, remain cryptic.
      Phylogenetic analysis based on sequence comparison of the conserved marker gene
      rpoA reveals that L. buchneri CD034 is more closely related to Lactobacillus
      hilgardii strains than to Lactobacillus brevis and Lactobacillus plantarum
      strains. Comparison of the L. buchneri CD034 core genome to other fully sequenced
      and closely related members of the genus Lactobacillus disclosed a high degree of
      conservation between L. buchneri CD034 and the recently sequenced L. buchneri
      strain NRRL B-30929 and a more distant relationship to L. buchneri ATCC 11577 and
      L. brevis ssp. gravesensis ATCC 27305, which cluster together with L. hilgardii
      type strain ATCC 8290. L. buchneri CD034 genome information will certainly
      provide the basis for further postgenome studies with the objective to optimize
      application of the strain in silage production.
AU  - Heinl S
AU  - Wibberg D
AU  - Eikmeyer F
AU  - Szczepanowski R
AU  - Blom J
AU  - Linke B
AU  - Goesmann A
AU  - Grabherr R
AU  - Schwab H
AU  - Puhler A
AU  - Schluter A
PT  - Journal Article
TA  - J. Biotechnol.
JT  - J. Biotechnol.
SO  - J. Biotechnol. 2012 161: 153-166.

PMID- 29724826
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Lelliottia nimipressuralis Type Strain SGAir0187, Isolated from Tropical Air Collected in Singapore.
PG  - e00231-18
AB  - Lelliottia nimipressuralis type strain SGAir0187 was isolated from tropical air samples
      collected in Singapore. The genome was assembled with an average coverage
      of 180-fold using Pacific Biosciences long reads and Illumina MiSeq paired-end
      reads. The genome measures 4.8 Mb and contains 4,424 protein-coding genes, 83
      tRNAs, and 25 rRNAs.
AU  - Heinle CE et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00231-18.

PMID- 28596410
VI  - 5
DP  - 2017
TI  - Genome Sequences for Streptomyces spp. Isolated from Disease-Suppressive Soils and Long-Term Ecological Research Sites.
PG  - e00493-17
AB  - We report here the high-quality genome sequences of three Streptomyces spp. isolated as part
      of a long-term study of microbial soil ecology. Streptomyces sp.
      strain GS93-23 was isolated from naturally disease-suppressive soil (DSS) in
      Grand Rapids, MN, and Streptomyces sp. strains S3-4 and 3211-3 were isolated from
      experimental plots in the Cedar Creek Ecosystem Science Reserve (CCESR).
AU  - Heinsch SC
AU  - Otto-Hanson L
AU  - Hsu SY
AU  - Kinkel L
AU  - Smanski MJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00493-17.

PMID- 8474115
VI  - 38
DP  - 1993
TI  - Characterisation of a Helicobacter pylori phage (HP1).
PG  - 245-249
AB  - The infection of two Helicobacter pylori strains with a
      phage-containing supernate of the lysogenic H. pylori strain IMMi 290/89
      resulted in a lytic cycle and propagation of phage HP1. In
      negatively-stained preparations, the empty phage heads measured 55-60 nm
      in diameter and mature heads measured 50 nm. The flexible, striated
      phage tail was c. 170 nm in length and 9.5 nm in diameter. The phage
      showed a mean density of 1.40 g/cm3 in sucrose-density gradients and
      contained double-stranded DNA c. 22,000 bp in length.
AU  - Heintschel von Heinegg E
AU  - Nalik HP
AU  - Schmid EN
PT  - Journal Article
TA  - J. Med. Microbiol.
JT  - J. Med. Microbiol.
SO  - J. Med. Microbiol. 1993 38: 245-249.

PMID- 19474347
VI  - 37
DP  - 2009
TI  - Physical and functional interactions between Escherichia coli MutL and the Vsr repair endonuclease.
PG  - 4453-4463
AB  - DNA mismatch repair (MMR) and very-short patch (VSP) repair are two pathways involved in the
      repair of T:G mismatches. To learn about
      competition and cooperation between these two repair pathways, we analyzed
      the physical and functional interaction between MutL and Vsr using
      biophysical and biochemical methods. Analytical ultracentrifugation
      reveals a nucleotide-dependent interaction between Vsr and the N-terminal
      domain of MutL. Using chemical crosslinking, we mapped the interaction
      site of MutL for Vsr to a region between the N-terminal domains similar to
      that described before for the interaction between MutL and the strand
      discrimination endonuclease MutH of the MMR system. Competition between
      MutH and Vsr for binding to MutL resulted in inhibition of the
      mismatch-provoked MutS- and MutL-dependent activation of MutH, which
      explains the mutagenic effect of Vsr overexpression. Cooperation between
      MMR and VSP repair was demonstrated by the stimulation of the Vsr
      endonuclease in a MutS-, MutL- and ATP-hydrolysis-dependent manner, in
      agreement with the enhancement of VSP repair by MutS and MutL in vivo.
      These data suggest a mobile MutS-MutL complex in MMR signalling, that
      leaves the DNA mismatch prior to, or at the time of, activation of
      downstream effector molecules such as Vsr or MutH.
AU  - Heinze RJ
AU  - Giron-Monzon L
AU  - Solovyova A
AU  - Elliot SL
AU  - Geisler S
AU  - Cupples CG
AU  - Connolly BA
AU  - Friedhoff P
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: 4453-4463.

PMID- 4598708
VI  - 59
DP  - 1974
TI  - Abolition of host cell restriction by high multiplicity of phage infection.
PG  - 356-370
AB  - When restricting host cells (Escherichia coli K12 or E. coli B) are infected
      first with a nonmodified lambda phage (called the helper phage) at high
      multiplicity and subsequently superinfected with a second nonmodified lambda
      vir phage (called the test phage), it can be shown that an increased number of
      infected cells produce a successful infection of phage which carry the virulent
      marker of the test phage.  This multiplicity effect has been studied both in
      normal and in recombination defective strains, in the presence or the absence
      of chloramphenicol and mitomycin C and in circumstances where the gene
      expression of the nonmodified helper phage was prevented by immunity.  The
      results indicate that the nonmodified helper-phage causes a temporary
      inactivation of the restricting system and that the multiplicity effect is not
      due to gene complementation or cooperation or to recombination.  Furthermore,
      this multiplicity effect can be observed in different hosts and with various
      nonmodified phages.  When similar experiments were performed with modified
      helper phage no multiplicity effect was observed.
AU  - Heip J
AU  - Rolfe B
AU  - Schell J
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1974 59: 356-370.

PMID- 15826660
VI  - 348
DP  - 2005
TI  - Site-specific DNA-nicking mutants of the heterodimeric restriction endonuclease R.BbvCI.
PG  - 631-640
AB  - The restriction enzyme R.BbvCI cleaves duplex DNA within a seven base-pair asymmetric
      recognition sequence, thus: CCTCAGC/GCGAGG -> CC^TCAGC/GC^TGAGG. We show that R.BbvCI
      comprises
      two different subunits, R-1 and R-2; that each subunit contains a
      catalytic site for DNA strand hydrolysis; and that these sites act
      independently and strand-specifically. In turn, each catalytic site was
      inactivated by mutagenesis to form dimeric enzymes in which only one
      bite remained functional. The altered enzymes hydrolyzed just one
      strand of the recognition sequence, nicking the DNA rather than
      cleaving it. Enzymes in which the catalytic site in the R-1 subunit
      remained functional nicked the bottom strand of the sequence, producing
      CCTCAGC/GC^TGAGG, while those in which the catalytic site
      in the R-2 subunit remained functional nicked the top strand, producing
      CC^TCAGC/GCTGAGG. These DNA-nicking enzymes could prove
      useful for investigation of DNA repair, recombination, and replication,
      and for laboratory procedures that initiate from nicks, such as DNA
      degradation, synthesis, and amplification.
AU  - Heiter DF
AU  - Lunnen KD
AU  - Wilson GG
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2005 348: 631-640.

PMID- 11598044
VI  - 69
DP  - 2001
TI  - Salmonella DNA adenine methylase mutants confer cross-protective immunity.
PG  - 6725-6730
AB  - Salmonella isolates that lack or overproduce DNA adenine methylase elicited a cross-protective
      immune response to different Salmonella serovars.  The protection afforded by the Salmonella
      enterica serovar Typhimurium Dam vaccine was greater than that elicited in mice that survived
      a virulent infection.  S. enterica serovar Typhimurium Dam mutant strains exhibited enhanced
      sensitivity to mediators of innate immunity such as antimicrobial peptides, bile, salts, and
      hydrogen peroxide.  Also, S. enterica serovar Typhimurium Dam- vaccines were not
      immunosuppressive; unlike wild-type vaccines, they failed to induce increased nitric oxide
      levels and permitted a subsequent robust humoral response to diptheria toxoid antigen in
      infected mice.  Dam mutant strains exhibited a low-grade persistence which, coupled with the
      nonimmunosuppression and the ectopic protein expression caused by altered levels of Dam, may
      provide an expanded source of potential antigens in vaccinated hosts.
AU  - Heithoff DM
AU  - Enioutina EY
AU  - Daynes RA
AU  - Sinsheimer RL
AU  - Low DA
AU  - Mahan MJ
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2001 69: 6725-6730.

PMID- 25448106
VI  - 33
DP  - 2015
TI  - Development of a Salmonella cross-protective vaccine for food animal production systems.
PG  - 100-107
AB  - Intensive livestock production is associated with increased Salmonella exposure, transmission,
      animal disease, and contamination of food and water supplies. Modified live Salmonella
      enterica vaccines that lack a functional DNA adenine methylase (Dam) confer cross-protection
      to a diversity of salmonellae in experimental models of murine, avian, ovine, and bovine
      models of salmonellosis. However, the commercial success of any vaccine is dependent upon the
      therapeutic index, the ratio of safety/efficacy. Herein, secondary virulence-attenuating
      mutations targeted to genes involved in intracellular and/or systemic survival were introduced
      into Salmonella dam vaccines to screen for vaccine candidates that were safe in the animal and
      the environment, while maintaining the capacity to confer cross-protective immunity to
      pathogenic salmonellae serotypes. Salmonella dam mgtC, dam sifA, and dam spvB vaccine strains
      exhibited significantly improved vaccine safety as evidenced by the failure to give rise to
      virulent revertants during the infective process, contrary to the parental Salmonella dam
      vaccine. Further, these vaccines exhibited a low grade persistence in host tissues that was
      associated with reduced vaccine shedding, reduced environmental persistence, and induction of
      cross-protective immunity to pathogenic serotypes derived from infected livestock. These data
      indicate that Salmonella dam double mutant vaccines are suitable for commercial applications
      against salmonellosis in livestock production systems. Reducing pre-harvest salmonellae load
      through vaccination will promote the health and productivity of livestock and reduce
      contamination of livestock-derived food products, while enhancing overall food safety. (C)
      2014 Elsevier Ltd. All rights reserved.
AU  - Heithoff DM
AU  - House JK
AU  - Thomson PC
AU  - Mahan MJ
PT  - Journal Article
TA  - Vaccine
JT  - Vaccine
SO  - Vaccine 2015 33: 100-107.

PMID- 
VI  - 102
DP  - 2002
TI  - Regulation of bacterial virulence by DNA methylation.
PG  - 73
AB  - Salmonella that lack or overproduce DNA adenine methylase (Dam) elicited a cross-protective
      immune response to different Salmonella
      serovars. Mice immunized with Dam mutant strains conferred
      significantly more protection than that conferred by mice exposed to a
      sub-lethal challenge with the virulent strain. In contrast to
      Salmonella and E. coli, Dam is essential for viability in Vibrio
      cholerae and Yersinia pseudotuberculosis; however, Dam overproduction
      is not lethal and significantly attenuated the virulence of both
      pathogens. Y. pseudotuberculosis mutants that overproduce Dam conferred
      fully protective immune responses and secreted several Yersinia outer
      proteins (Yops) under conditions that are nonpermissive for secretion
      in wild-type strains. Dam overproduction disrupted both the thermal and
      calcium regulation of the synthesis of the YopE cytotoxin, and relaxed
      the thermal but not the calcium dependence of YopE secretion. Because
      alterations of Dam activity attenuate such a diverse set of pathogenic
      organisms, the role of Dam in virulence may emerge as a general theme
      in bacterial pathogenesis.
AU  - Heithoff DM
AU  - Julio SM
AU  - Mahan MJ
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 2002 102: 73.

PMID- 
VI  - 101
DP  - 2001
TI  - The role of DNA adenine methylation in controlling bacterial virulence.
PG  - 59
AB  - Salmonella DNA adenine methylase (Dam) mutants are avirulent and are effective as live
      vaccines against murine typhoid fever. The role of
      Dam in virulence and in the elicitation of protective immune responses
      may rely on its capacity as a global regulator of gene expression. Dam
      was shown to regulate the expression of many genes that are induced
      during infection, and Dam- and Dam over-producer mutants expressed
      several proteins distinct from each other and from wild-type Salmonella
      grown in vitro. To explore whether Dam mutants were attenuated for
      virulence in pathogens other than Salmonella, we attempted to construct
      Dam-mutations in V. cholerae and Y. pseudotuberculosis. Dam is
      essential for viability in V. cholerae and in Yersinia. However, Dam
      overproduction in both organisms was not lethal and lead to reduced
      virulence in both organisms. Overproduction of Dam in Yersinia resulted
      in the ectopic secretion of Yersinia outer proteins (Yops) and a fully
      protective immune response in vaccinated mice. Since DNA adenine
      methylases are highly conserved in a wide variety of virulent bacteria,
      dysregulation of Dam activity is potentially a general strategy for the
      development of vaccines against varied bacterial pathogens.
AU  - Heithoff DM
AU  - Julio SM
AU  - Mahan MJ
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 2001 101: 59.

PMID- 10874736
VI  - 355
DP  - 2000
TI  - In vivo gene expression and the adaptive response: From pathogenesis to vaccines and antimicrobials.
PG  - 633-642
AB  - Microbial pathogens possess a repertoire of virulence determinants that each make unique
      contributions to fitness during infection. Analysis of
      these in vivo-expressed functions reveals the biology of the infection
      process, encompassing the bacterial infection strategies and the host
      ecological and environmental retaliatory strategies designed to combat
      them (e.g. thermal, osmotic, oxygen, nutrient and acid stress). Many of
      the bacterial virulence functions that contribute to a successful
      infection are normally only expressed during infection. A genetic
      approach was used to isolate mutants that ectopically expressed many of
      these functions in a laboratory setting. Lack of DNA adenine methylase
      (Dam) in Salmonella typhimurium abolishes the preferential expression
      of many bacterial virulence genes in host tissues. Dam- Salmonella were
      proficient in colonization of mucosal sites but were defective in
      colonization of deeper tissue sites. Additionally, Dam- mutants were
      totally avirulent and effective as live vaccines against murine typhoid
      fever. Since dam is highly conserved in many pathogenic bacteria that
      cause significant morbidity and mortality worldwide, Dams are
      potentially excellent targets for both vaccines and antimicrobials.
AU  - Heithoff DM
AU  - Sinsheimer RL
AU  - Low DA
AU  - Mahan MJ
PT  - Journal Article
TA  - Philos. Trans. R. Soc. Lond. B. Biol. Sci.
JT  - Philos. Trans. R. Soc. Lond. B. Biol. Sci.
SO  - Philos. Trans. R. Soc. Lond. B. Biol. Sci. 2000 355: 633-642.

PMID- 10320378
VI  - 284
DP  - 1999
TI  - An essential role for DNA adenine methylation in bacterial virulence.
PG  - 967-970
AB  - Salmonella typhimurium lacking DNA adenine methylase were fully proficient in colonization of
      mucosal sites but showed severe defects in colonization of deeper tissue sites.  These Dam-
      mutants were totally avirulent and were effective as live vaccines against murine typhoid
      fever.  Dam regulated the expression of at least 20 genes known to be induced during
      infection; a subset of these genes are among those activated by the PhoP global virulence
      regulator.  PhoP, in turn, affected Dam methylation at specific genomic sites, as evidenced by
      alterations in DNA methylation patterns.  Dam inhibitors are likely to have broad
      antimicrobial action, and Dam- derivatives of these pathogens may serve as live attenuated
      vaccines.
AU  - Heithoff DM
AU  - Sinsheimer RL
AU  - Low DA
AU  - Mahan MJ
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1999 284: 967-970.

PMID- 
VI  - 
DP  - 1989
TI  - On the repair of DNA breaks and the specificity of the EcoRI restriction enzyme.
PG  - 1-209
AB  - We would like to understand how proteins and enzymes interact with DNA.  We
      describe here our studies of the Mrr methylation dependent restriction enzyme,
      DNA single- and double-strand break repair in E. coli, and substrate
      recognition by the EcoRI endonuclease.  Many species of bacteria make
      restriction-modification systems to destroy foreign DNA that enters the cell.
      These systems usually consist of an endonuclease that cleaves a specific DNA
      sequence and a methylase which modifies the DNA to protect the host chromosome.
      We observed that when foreign site-specific methylases are expressed in E.
      coli, the SOS DNA repair response is induced.  This DNA damage is inflicted by
      E. coli restriction enzymes that cleave adenine (Mrr) or cytosine (McrB)
      methylated DNA.  The genes encoding four of the five known E. coli restriction
      systems lie clustered together, perhaps to coordinate or sequester the cellular
      defense system.  Several of these restriction systems differ between E. coli
      species, suggesting that their action may establish species boundaries.  The
      EcoRI endonuclease cleaves DNA molecules at the sequence GAATTC.  This enzyme
      is well characterized biochemically, the sequence of its gene is known, and the
      X-ray crystal structure of an EcoRI-DNA complex has been solved at 3 A
      resolution.  (McClarin, et al., 1986).  EcoRI serves as a paradigm for other
      restriction enzymes and as a model of DNA-protein interactions.  We took a
      genetic approach to study the EcoRI endonuclease.  We first asked if EcoRI DNA
      double-strand breaks are repaired in E. coli.  To this end, a series of
      temperature-sensitive EcoRI endouclease alleles were isolated.  Temperature
      shifts with these alleles revealed that in vivo DNA scission induces the E.
      coli SOS DNA  repair response.  However, neither SOS induction nor
      recombination are required to repair these lesions.  DNA ligase is required and
      may suffice to repair EcoRI breaks in the E. coli chromosome.  An in vivo DNA
      scission assay was devised based on the finding that DNA breaks induce the SOS
      response.  SOS induction was monitored with strains carrying the lactose operon
      fused to an SOS inducible promoter.  After DNA scission, these strains produce
      Beta-galactosidase and form blue colonies on X-Gal medium.  With this blue
      colony phenotype as a screen, two approaches were taken to isolate EcoRI
      mutants altered or disrupted in substrate specificity.  First, amino acids
      (E144, R200) implicated in substrate binding by the crystal structure were
      subjected to site-directed mutagenesis.  Of 50 of the 60 possible
      substitutions, several alleles retain weak endonuclease activity which, in vivo
      and in vitro, is of wild-type specificity.  Therefore the simple hydrogen bond
      model proposed from the crystal structure is insufficient to explain substrate
      recognition and additional interactions must participate in the
      substrate-enzyme complex.  In the second approach, mutants of an EcoRI ts
      allele were isolated which conditionally induce the SOS response and impair
      cell growth in spite of the normally protective methylase.  In vitro, these
      mutant proteins exhibit enhanced cleavage activity at EcoRI* sites, sequences
      which differ by one nucleotide from the normal recognition site and are also
      cleaved by the wild-type enzyme under altered buffer conditions.  Four of the
      five mutations of this type lie at the DNA-protein interface and may directly
      alter or disrupt substrate recognition.  One other (H114Y) lies far from the
      binding and cleavage sites.  This mutation falls three amino acids away from a
      previously described mutation, E111G (King et al., 1986, 1988), which severly
      impairs cleavage activity without altering DNA binding.  These two mutations
      support a model whereby DNA scission by the EcoRI endonuclease is
      allosterically activated upon substrate binding:  we suggest that the E111G
      mutation inhibits this conformational change while the H114Y mutation renders
      it more facile such that additional DNA sequences act as allosteric effectors
      and trigger cleavage.
AU  - Heitman J
PT  - Journal Article
TA  - Ph.D. Thesis, Rockefeller University, NY, USA
JT  - Ph.D. Thesis, Rockefeller University, NY, USA
SO  - Ph.D. Thesis, Rockefeller University, NY, USA 1989 : 1-209.

PMID- 7764063
VI  - 15
DP  - 1993
TI  - On the origins, structures and functions of restriction-modification enzymes.
PG  - 57-108
AB  - Typically, restriction-modification (RM) systems consist of two enzymes: an endonuclease that
      recognizes and cleaves a specific DNA sequence, and a methyltransferase that modifies the same
      sequence to protect the host chromosome from cleavage. These enzymes also play an important
      role in genetic engineering and provide insight into the basis of sequence-specific
      DNA-protein interactions. A growing number of type II restriction endonucleases and
      methyltransferases are being subjected to biochemical and genetic studies which, when combined
      with ongoing X-ray crystallographic analyses, promise to provide detailed models for
      mechanisms of DNA recognition and catalysis. Studies on anti-restriction systems, the repair
      of DNA-single- and double-strand breaks, and the roles of DNA lesions in recombination
      initiation, suggest RM systems may provoke genome rearrangements and assimilate foreign DNA
      into the host genome and point towards possible evolutionary sources of this interesting group
      of DNA metabolizing enzymes.
AU  - Heitman J
PT  - Journal Article
TA  - Genet. Eng. (N Y)
JT  - Genet. Eng. (N Y)
SO  - Genet. Eng. (N Y) 1993 15: 57-108.

PMID- 1445286
VI  - 14
DP  - 1992
TI  - How the EcoRI endonuclese recognizes and cleaves DNA.
PG  - 445-454
AB  - One popular recombinant DNA tool is the EcoRI endonuclease, which cleaves DNA at GAATTC sites
      and serves as a paradigm for sequence specific DNA-enzyme interactions. The recently revised
      X-ray crystal structure of an EcoRI-DNA complex reveals EcoRI employs novel DNA recognition
      motifs, a four a-helix bundle and two extended chains, which project into the major groove to
      contact substrate purines and pyrimidines. Interestingly, pyrimidine contacts had been
      predicted based on genetic and biochemical studies. Current work focuses on the EcoRI active
      site structure, enzyme and substrate conformational changes during catalysis, and
      host-restriction system interactions.
AU  - Heitman J
PT  - Journal Article
TA  - Bioessays
JT  - Bioessays
SO  - Bioessays 1992 14: 445-454.

PMID- 2695397
VI  - 85
DP  - 1989
TI  - Phage Trojan horses: a conditional expression system for lethal genes.
PG  - 193-197
AB  - The EcoRI restriction enzyme (ENase) cleaves DNA molecules within the sequence
      GAATTC.  Cells expressing this lethal activity normally make a second enzyme,
      the M.EcoRI methyltransferase (MTase), which protects their chromosomal DNA by
      modifying the EcoRI recognition sites.  To isolate mutants of the EcoRI ENase,
      its gene was cloned into a filamentous phage vector (M13mp18) under control of
      the lac promoter.  Normally, filamentous phages (M13, f1 and their derivatives)
      form turbid plaques by impairing the growth of their host cell without killing
      it.  In contrast, phages expressing the EcoRI ENase kill the host cell, but
      survive long enough to produce plaques which are very clear.  Expression of the
      M.EcoRI MTase rescues the host and restores turbid plaque formation.  EcoRI
      ENase mutants were isolated by screening for mutants that make turbid, instead
      of clear, plaques on an M- host.  This conditional expression system may be
      useful for cloning and mutating genes for other toxic proteins.
AU  - Heitman J
AU  - Fulford W
AU  - Model P
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1989 85: 193-197.

PMID- 10510229
VI  - 33
DP  - 1999
TI  - DNA nicks inflicted by restriction endonucleases are repaired by a RecA- and RecB-dependent pathway in Escherichia coli.
PG  - 1141-1151
AB  - Two mutants of the EcoRI endonuclease (R200K and E144C) predominantly nick only one strand of
      the DNA substrate. Temperature sensitivity of the mutant enzymes allowed us to study the
      consequences of inflicting DNA nicks at EcoRI sites in vivo. Expression of the EcoRI
      endonuclease mutants in the absence of the EcoRI methyltransferase induces the SOS DNA repair
      response and greatly reduces viability of recA56, recB21 and lexA3 mutant strains of
      Escherichia coli. In parallel studies, overexpression of the EcoRV endonuclease in cells also
      expressing the EcoRV methyltransferase was used to introduce nicks at non-cognate EcoRV sites
      in the bacterial genome. EcoRV overproduction was lethal in recA56 and recB21 mutant strains
      and moderately toxic in a lexA3 mutant strain. The toxic effect of EcoRV overproduction could
      be partially alleviated by introduction into the cells of multiple copies of the E. coli DNA
      ligase gene. These observations suggest that an increased number of DNA nicks can overwhelm
      the repair capacity of DNA ligase, resulting in the conversion of a proportion of DNA nicks
      into DNA lesions that require recombination for repair.
AU  - Heitman J
AU  - Ivanenko T
AU  - Kiss A
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1999 33: 1141-1151.

PMID- 3036779
VI  - 169
DP  - 1987
TI  - Site-specific methylases induce the SOS DNA repair response in Escherichia coli.
PG  - 3243-3250
AB  - Expression of the site-specific adenine methylase HhaII (GmeANTC, where me
      is methyl) or PstI (CTGCmeAG) induced the SOS DNA repair response in Escherichia
      coli. In contrast, expression of methylases indigenous to E. coli either did not induce SOS
      (EcoRI-GAmeATTC) or induced SOS to a lesser extent (dam-GmeATC). Recognition of
      adenine-methylated DNA required the product of a previously undescribed gene, which we
      named mrr (methylated adenine recognition and restriction). We suggest that mrr encodes
      an endonuclease that cleaves DNA containing N6-methyladenine and that DNA double-
      strand breaks induce the SOS response. Cytosine methylases foreign to E. coli (MspI
      [meCCGG], HaeIII [GGmeCC], BamHI [GGATmeCC],HhaI [GmeCGC],
      BsuRI[GGmeCC], and M.SPR) also induced SOS, whereas one indigenous to E. coli
      (EcoRII [CmeCA/TGG]) did not. SOS induction by cytosine methylation required the rglB
      locus, which encodes an endonuclease that cleaves DNA containing 5-hydroxymethyl- or
      5-methylcytosine (E. A. Raleigh and G. Wilson, Proc. Natl. Acad. Sci. USA 83:9070-
      9074, 1986).
AU  - Heitman J
AU  - Model P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1987 169: 3243-3250.

PMID- 2139225
VI  - 7
DP  - 1990
TI  - Substrate recognition by the EcoRI endonuclease.
PG  - 185-197
AB  - The EcoRI restriction endonuclease is one of the most widely used tools for
      recombinant DNA maniulations.  Because the EcoRI enzyme has been extremely well
      characterized biochemically and its structure is known at 3 angstrom resolution
      as an enzyme-DNA complex, EcoRI also serves as a paradigm for other restriction
      enzymes and as an important model of DNA-protein interactions.  To facilitate a
      genetic analysis of the EcoRI enzyme, we devised an in vivo DNA scission assay
      based on our finding that DNA double-strand breaks induce the Escherichia coli
      SOS response and thereby increase beta-galactosidase expression from SOS::lacZ
      gene fusions.  By site-directed mutagenesis, 50 of 60 possible point mutations
      were generated at three amino acids (E144, R145, and R200) implicated in
      substrate recognition by the crystal structure.  Although several of these
      mutant enzymes retain partial endonuclease activity, none are altered in
      substrate specificity in vivo or in vitro.  These findings argue that, in
      addition to the hydrogen bond interactions revealed by the crystal structure,
      the EcoRI enzyme must make additional contacts to recognize its substrate.
AU  - Heitman J
AU  - Model P
PT  - Journal Article
TA  - Proteins
JT  - Proteins
SO  - Proteins 1990 7: 185-197.

PMID- 2209548
VI  - 9
DP  - 1990
TI  - Mutants of the EcoRI endonuclease with promiscuous substrate specificity implicate residues involved in substrate recognition.
PG  - 3369-3378
AB  - The EcoRI restriction endonuclease cleaves DNA molecules at the sequence GAATTC. We devised a
      genetic screen to isolate EcoRI mutants with altered or broadened substrate specificity. In
      vitro, the purified mutant enzymes cleave both the wild-type substrate and sites which differ
      from this by one nucleotide (EcoRI star sites). These mutations identify four residues
      involved in substrate recognition and catalysis that are different from the amino acids
      proposed to recognize the substrate based on the EcoRI-DNA co-crystal structure. In fact,
      these mutations suppress EcoRI mutants altered at some of the proposed substrate binding
      residues (R145, R200). We argue that these mutations permit cleavage of additional DNA
      sequences either by perturbing or removing direct DNA-protein interactions or by facilitating
      conformational changes that allosterically couple substrate binding to DNA scission.
AU  - Heitman J
AU  - Model P
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1990 9: 3369-3378.

PMID- 1908806
VI  - 103
DP  - 1991
TI  - SOS induction as an in vivo assay of enzyme-DNA interactions.
PG  - 1-9
AB  - We have constructed strains which are convenient and sensitive indicators of
      DNA damage and describe their use.  These strains utilize an SOS::lacZ fusion
      constructed by Kenyon and Walker [Proc. Natl. Acad. Sci. USA 77 (1980)
      2819-2823] and respond to DNA damage by producing Beta-galactosidase.  They can
      be used to characterize restriction systems and screen for restriction
      endonuclease mutants.  Applications include the study of other enzymes involved
      in DNA metabolism, such as DNA methyltransferases, topoisomerases,
      recombinases, and DNA replication and repair enzymes.
AU  - Heitman J
AU  - Model P
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1991 103: 1-9.

PMID- 2648397
VI  - 86
DP  - 1989
TI  - Repair of the Escherichia coli chromosome after in vivo scission by the EcoRI endonuclease.
PG  - 2281-2285
AB  - We prepared a set of temperature-sensitive mutants of the EcoRI endonuclease.
      Under semipermissive conditions, Escherichia coli strains bearing these alleles
      form poorly growing colonies in which intracellular substrates are cleaved at
      EcoRI sites and the SOS DNA repair response is induced.  Strains defective in
      SOS induction (lexA3 mutant) or SOS induction and recombination (recA56 and
      recB21 mutants) are not more sensitive to this in vivo DNA scission, whereas
      strains deficient in DNA ligase (lig4 and lig ts7 mutants) are extremely
      sensitive.  We conclude that although DNA scission induces the SOS response,
      neither this induction nor recombination are required for repair.  DNA ligase
      is necessary and may be sufficient to repair EcoRI-mediated DNA breaks in the
      E. coli chromosome.
AU  - Heitman J
AU  - Zinder ND
AU  - Model P
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1989 86: 2281-2285.

PMID- Not carried by PubMed...
VI  - 51
DP  - 1990
TI  - On the repair of DNA breaks and the specificity of the EcoRI restriction enzyme.
PG  - 562B
AB  - We took a genetic approach to study the well characterized EcoRI restriction
      enzyme, an endonuclease that cleaves DNA molecules at the sequence GAATTC.
      First, a series of temperature-sensitive EcoRI endonuclease alleles were
      isolated.  Temperature shifts with these alleles revealed that in vivo DNA
      scission induces the E. coli SOS DNA repair response.  However, neither SOS
      induction nor recombination are required to repair these lesions.  DNA ligase
      is required and may suffice to repair EcoRI breaks in the E. coli chromosome.
      To monitor DNA scission in vivo we employed strains carrying the lactose operon
      fused to an SOS inducible promoter.  After DNA scission, these strains produce
      beta-galactosidase and form blue colonies on X-Gal medium.  Using this assay,
      two approaches were taken to isolate EcoRI mutants altered or disrupted in
      substrate specificity.  First, amino acids (E144, R145, R200) implicated in
      substrate binding by the crystal structure were subjected to site-directed
      mutagenesis.  Of 50 of the 60 possible substitutions, several alleles retain
      weak endonuclease activity which is of wild-type specificity.  Therefore the
      simple hydrogen bond model proposed from the crystal structure is insufficient
      to explain substrate recognition and additional interactions must participate
      in the substrate-enzyme complex.  In the second approach, mutants of an EcoRI
      ts allele were isolated which conditionally induce the SOS response in spite of
      the protective methylase.  These mutant proteins exhibit enhanced cleavage
      activity at EcoRI sites.  Four of five isolated mutations lie at the
      DNA-protein interface and may directly alter or disrupt substrate recognition.
      One other (H114Y) lies far from the binding or cleavage sites and falls three
      amino acids away from a previously described mutation, E111G (King et al, 1986,
      1988), which severely impairs DNA cleavage without altering DNA binding.  These
      mutations support a model whereby DNA scission by the EcoRI endonuclease is
      allosterically activated upon substrate binding: the E111G mutation may inhibit
      this conformational change while the H114Y mutation may render it more facile
      such that additional DNA sequences act as allosteric effectors and trigger
      cleavage.
AU  - Heitman JB
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1990 51: 562B.

PMID- 15699189
VI  - 151
DP  - 2005
TI  - Characterization of the flexible genome complement of the commensal Escherichia coli strain A0 34/86 (O83 : K24 : H31).
PG  - 385-398
AB  - Colonization by the commensal Escherichia coli strain A0 34/86 (O83 : K24 : H31) has proved to
      be safe and efficient in the prophylaxis and
      treatment of nosocomial infections and diarrhoea of preterm and newborn
      infants in Czech paediatric clinics over the past three decades. In
      searching for traits contributing to this beneficial effect related to the
      gut colonization capacity of the strain, the authors have analysed its
      genome by DNA-DNA hybridization to E. coli K-12 (MG1655) genomic DNA
      arrays and to 'Pathoarrays', as well as by multiplex PCR, bacterial
      artificial chromosome (BAC) library cloning and shotgun sequencing. Four
      hundred and ten E. coli K-12 ORFs were absent from A0 34/86, while 72 out
      of 456 genes associated with pathogenicity islands of E. coli and Shigella
      were also detected in E. coli A0 34/86. Furthermore, extraintestinal
      pathogenic E. coli-related genes involved in iron uptake and adhesion were
      detected by multiplex PCR, and genes encoding the HlyA and cytotoxic
      necrotizing factor toxins, together with 21 genes of the uropathogenic E.
      coli 536 pathogenicity island II, were identified by analysis of 2304
      shotgun and 1344 BAC clone sequences of A0 34/86 DNA. Multiple sequence
      comparisons identified 31 kb of DNA specific for E. coli A0 34/86; some of
      the genes carried by this DNA may prove to be implicated in the
      colonization capacity of the strain, enabling it to outcompete pathogens.
      Among 100 examined BAC clones roughly covering the A0 34/86 genome, one
      reproducibly conferred on the laboratory strain DH10B an enhanced capacity
      to persist in the intestine of newborn piglets. Sequencing revealed that
      this BAC clone carried gene clusters encoding gluconate and mannonate
      metabolism, adhesion (fim), invasion (ibe) and restriction/modification
      functions. Hence, the genome of this clinically safe and highly efficient
      colonizer strain appears to harbour many 'virulence-associated' genes.
      These results highlight the thin line between bacterial 'virulence' and
      'fitness' or 'colonization' factors, and question the definition of
      enterobacterial virulence factors.
AU  - Hejnova J
AU  - Dobrindt U
AU  - Nemcova R
AU  - Rusniok C
AU  - Bomba A
AU  - Frangeul L
AU  - Hacker J
AU  - Glaser P
AU  - Sebo P
AU  - Buchrieser C
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2005 151: 385-398.

PMID- 7763389
VI  - 4
DP  - 1993
TI  - Sequence-selective recognition and cleavage of double-helical DNA.
PG  - 29-36
AB  - Single sites within long double-helical DNA molecules can be recognized by a variety of
      mechanisms. Different strategies have been used to adapt sequence-specific recognition to
      sequence-specific cleavage of duplex DNA. Any nucleic acid can be converted into an artificial
      nuclease by the attachment of a cleaving reagent. Alternatively, a sequence-specific ligand
      can be used to protect a methylase recognition site from methylation. The protected site may
      then be cleaved selectively by a restriction endonuclease (the so-called 'Achilles heel'
      cleavage technique). Recent developments in this area have shown that it is possible to cleave
      chromosomal DNA at single sites within bacterial and eukaryotic genomes.
AU  - Helene C
PT  - Journal Article
TA  - Curr. Opin. Biotechnol.
JT  - Curr. Opin. Biotechnol.
SO  - Curr. Opin. Biotechnol. 1993 4: 29-36.

PMID- 26679590
VI  - 3
DP  - 2015
TI  - Genome Sequence of Bradyrhizobium viridifuturi Strain SEMIA 690T, a Nitrogen-Fixing Symbiont of Centrosema pubescens.
PG  - e01481-15
AB  - SEMIA 690(T) is a nitrogen-fixing symbiont of Centrosema pubescens, and comprises the recently
      described species Bradyrhizobium viridifuturi. Its draft genome
      indicates that it belongs to the Bradyrhizobium elkanii superclade. SEMIA 690(T)
      carries two copies of the regulatory nodD gene, and the nod and nif operons
      resemble those of Bradyrhizobium diazoefficiens.
AU  - Helene LC
AU  - Gomes DF
AU  - Delamuta JR
AU  - Ribeiro RA
AU  - Souza RC
AU  - Almeida LG
AU  - Vasconcelos AT
AU  - Hungria M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01481-15.

PMID- 28860263
VI  - 5
DP  - 2017
TI  - Genome Sequence of Rhizobium esperanzae Type Strain CNPSo 668, Isolated from Phaseolus vulgaris Nodules in Mexico.
PG  - e00935-17
AB  - Rhizobium esperanzae CNPSo 668T is a nitrogen-fixing symbiont of Phaseolus vulgaris isolated
      from Mexican soils. Its genome is estimated at 6,294,057 bp,
      with 6,219 coding sequences (CDSs) showing higher similarity (92.9%) with
      Rhizobium etli Three copies of the regulatory nodD, in addition to other
      nodulation genes, should define its host specificity.
AU  - Helene LCF
AU  - Ribeiro RA
AU  - Hungria M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00935-17.

PMID- 4372397
VI  - 14
DP  - 1974
TI  - Analysis of endonuclease R EcoRI fragments of DNA from lambdoid bacteriophages and other viruses by agarose-gel electrophoresis.
PG  - 1235-1243
AB  - By means of agarose-gel electrophoresis, endonuclease R EcoRI-generated
      fragments of DNA from various viruses were separated, their molecular weights
      were determined, and complete or partial fragment maps for lambda, Phi80, and
      hybrid phages were constructed.
AU  - Helling RB
AU  - Goodman HM
AU  - Boyer HW
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1974 14: 1235-1243.

PMID- 8541807
VI  - 11
DP  - 1995
TI  - DNA methylation in mycobacteria: absence of methylation at GATC (Dam) and CCA/TGG (Dcm) sequences.
PG  - 291-296
AB  - The presence of 6-methyladenine and 5-methylcytosine at Dam (GATC) and Dcm (CCA/TGG) sites in
      DNA of mycobacterial species was investigated using
      isoschizomer restriction enzymes. In all species examined, Dam and Dcm
      recognition sequences were not methylated indicating the absence of these
      methyltransferases. On the other hand, high performance liquid chromatographic
      analysis of genomic DNA from Mycobacterium smegmatis and Mycobacterium
      tuberculosis showed significant levels of 6-methyladenine and 5-methylcytosine
      suggesting the presence of DNA methyltransferases other than Dam and Dcm.
      Occurrence of methylation was also established by a sensitive genetic assay.
AU  - Hemavathy KC
AU  - Nagaraja V
PT  - Journal Article
TA  - FEMS Immunol Med Microbiol
JT  - FEMS Immunol Med Microbiol
SO  - FEMS Immunol Med Microbiol 1995 11: 291-296.

PMID- 21545095
VI  - 83
DP  - 2011
TI  - Characterizing DNA methyltransferases with an ultrasensitive luciferase-linked continuous assay.
PG  - 4996-5004
AB  - DNA (cytosine-5)-methyltransferases (DNMTs) catalyze the transfer of a methyl group from
      S-adenosyl-L-methionine (AdoMet) to the 5-position of cytosine residues and thereby silence
      transcription of regulated genes. DNMTs are important epigenetic targets. However, isolated
      DNMTs are weak catalysts and are difficult to assay. We report an ultrasensitive
      luciferase-linked continuous assay that converts the S-adenosyl-L-homocysteine product of DNA
      methylation to a quantifiable luminescent signal. Results with this assay are compared with
      the commonly used DNA labeling from [methyl-3H]AdoMet. A
      50-methylthioadenosine-adenosylhomocysteine nucleosidase is used to hydrolyze AdoHcy to
      adenine. Adenine phosphoribosyl transferase converts adenine to AMP and pyruvate
      orthophosphate dikinase converts AMP to ATP. Firefly luciferase gives a stable luminescent
      signal that results from continuous AMP recycling to ATP. This assay exhibits a broad dynamic
      range (0.1-1000 pmol of AdoHcy). The rapid response time permits continuous assays of DNA
      methylation detected by light output. The assay is suitable for high-throughput screening of
      chemical libraries for DNMT inhibition activity. The kinetic properties of human and bacterial
      CpG methyltransferases are characterized using this assay. Human catalytic domain DNMT3b
      activation byDNMT3L is shown to involve two distinct kinetic states that alter kcat but not Km
      for AdoMet. The assay is shown to be robust in the presence of high concentrations of the
      pyrimidine analogues 5-azacytidine and 5-azacytosine.
AU  - Hemeon I
AU  - Gutierrez JA
AU  - Ho M-C
AU  - Schramm VL
PT  - Journal Article
TA  - Anal. Chem.
JT  - Anal. Chem.
SO  - Anal. Chem. 2011 83: 4996-5004.

PMID- 20889752
VI  - 192
DP  - 2010
TI  - Sequencing of multiple clostridial genomes related to biomass conversion and biofuel production.
PG  - 6494-6496
AB  - Modern methods to develop microbe-based biomass conversion processes require a system-level
      understanding of the microbes involved. Clostridium
      species have long been recognized as ideal candidates for processes
      involving biomass conversion and production of various biofuels and other
      industrial products. To expand the knowledge base for clostridial species
      relevant to current biofuel production efforts, we have sequenced the
      genomes of 20 species spanning multiple genera. The majority of species
      sequenced fall within the class III cellulosome-encoding Clostridium and
      the class V saccharolytic Thermoanaerobacteraceae. Species were chosen
      based on representation in the experimental literature as model organisms,
      ability to degrade cellulosic biomass either by free enzymes or by
      cellulosomes, ability to rapidly ferment hexose and pentose sugars to
      ethanol, and ability to ferment synthesis gas to ethanol. The sequenced
      strains significantly increase the number of noncommensal/nonpathogenic
      clostridial species and provide a key foundation for future studies of
      biomass conversion, cellulosome composition, and clostridial systems
      biology.
AU  - Hemme CL et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 6494-6496.

PMID- 26586894
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Levilinea saccharolytica KIBI-1, a Member of the Chloroflexi Class Anaerolineae.
PG  - e01357-15
AB  - We report the draft genome sequence of Levilinea saccharolytica KIBI-1, a facultative
      anaerobic member of the Chloroflexi class Anaerolineae. While L.
      saccharolytica was characterized as an obligate anaerobe, genome analysis
      provides evidence for the presence of both aerobic respiration and partial
      denitrification pathways.
AU  - Hemp J
AU  - Ward LM
AU  - Pace LA
AU  - Fischer WW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01357-15.

PMID- 26586890
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Ornatilinea apprima P3M-1, an Anaerobic Member of the Chloroflexi Class Anaerolineae.
PG  - e01353-15
AB  - We report the draft genome sequence of Ornatilinea apprima P3M-1, a strictly anaerobic member
      of the Chloroflexi class Anaerolineae. This genome provides
      insight into the diversity of metabolism within the Anaerolineae, and the
      evolution of respiration within the Chloroflexi.
AU  - Hemp J
AU  - Ward LM
AU  - Pace LA
AU  - Fischer WW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01353-15.

PMID- 26586887
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Ardenticatena maritima 110S, a Thermophilic Nitrate- and Iron-Reducing Member of the Chloroflexi Class Ardenticatenia.
PG  - e01347-15
AB  - We report here the draft genome sequence of Ardenticatena maritima 110S, the first sequenced
      member of class Ardenticatenia of the phylum Chloroflexi. This
      thermophilic organism is capable of a range of physiologies, including aerobic
      respiration and iron reduction. It also encodes a complete denitrification
      pathway with a novel nitric oxide reductase.
AU  - Hemp J
AU  - Ward LM
AU  - Pace LA
AU  - Fischer WW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01347-15.

PMID- 8648625
VI  - 257
DP  - 1996
TI  - Uneven distribution of GATC motifs in the Escherichia coli chromosome, its plasmids and its phages.
PG  - 574-585
AB  - This work reconsiders the GATC motif distribution in a 1.6 Mb segment of the Escherichia coli
      genome, compared to its distribution in phages and plasmids.  At first sight the distribution
      of GATC words looks random.  But when a realistic model of the chromosome (made of average
      genes having the same codon usage as in the real chromosome), is used as a theoretical
      reference, strong biases are observed.  GATC pairs such as GATCNNGATC are under-represented
      while there is a strong positive selection for motifs separated by 10, 19, 70 and 1100 bp.
      The last class is the only one present in E. coli parasites.  It can be ascribed to the
      triggering sequences of the long-patch mismatch repair system.  The 6 bp class overlaps with
      the consensus of CAP (catabolite activator protein) and FNR (fumarate/nitrate regulator)
      binding sites, thus accounting for counter-selection.  The other classes, which could be
      targets for a nucleic acid binding protein, are almost always present inside protein coding
      sequences, and are members of clusters of GATC motifs.  Analysis of the genes containing these
      motifs suggests that they correspond to a regulatory process monitoring the shift from
      anaerobic to aerobic growth conditions  In particular this regulation, closing down
      transcription of a large number of genes involved in intermediary metabolism would be well
      suited for the cold and oxygen shift from the mammal's gut to the standard environmental
      conditions.  In this process the methylation status of GATC clusters would be very important
      for tuning transcription, and a DNA binding protein, probably a member of the cold-shock
      proteins family would be needed for alleviating the effects mediated by slackening of the pace
      of methylation during the shift.
AU  - Henaut A
AU  - Rouxel T
AU  - Gleizes A
AU  - Moszer I
AU  - Danchin A
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1996 257: 574-585.

PMID- 21060858
VI  - 6
DP  - 2010
TI  - The De Novo Cytosine Methyltransferase DRM2 Requires Intact UBA Domains and a Catalytically Mutated Paralog DRM3 during RNA-Directed DNA Methylation in Arabidopsis thaliana.
PG  - e1001182
AB  - Eukaryotic DNA cytosine methylation can be used to transcriptionally silence repetitive
      sequences, including transposons and retroviruses.
      This silencing is stable between cell generations as cytosine
      methylation is maintained epigenetically through DNA replication. The
      Arabidopsis thaliana Dnmt3 cytosine methyltransferase ortholog DOMAINS
      REARRANGED METHYLTRANSFERASE2 (DRM2) is required for establishment of
      small interfering RNA (siRNA) directed DNA methylation. In mammals PIWI
      proteins and piRNA act in a convergently evolved RNA-directed DNA
      methylation system that is required to repress transposon expression in
      the germ line. De novo methylation may also be independent of RNA
      interference and small RNAs, as in Neurospora crassa. Here we identify
      a clade of catalytically mutated DRM2 paralogs in flowering plant
      genomes, which in A. thaliana we term DOMAINS REARRANGED
      METHYLTRANSFERASE3 (DRM3). Despite being catalytically mutated, DRM3 is
      required for normal maintenance of non-CG DNA methylation,
      establishment of RNA-directed DNA methylation triggered by repeat
      sequences and accumulation of repeat-associated small RNAs. Although
      the mammalian catalytically inactive Dnmt3L paralogs act in an
      analogous manner, phylogenetic analysis indicates that the DRM and
      Dnmt3 protein families diverged independently in plants and animals. We
      also show by site-directed mutagenesis that both the DRM2 N-terminal
      UBA domains and C-terminal methyltransferase domain are required for
      normal RNA-directed DNA methylation, supporting an essential targeting
      function for the UBA domains. These results suggest that plant and
      mammalian RNA-directed DNA methylation systems consist of a combination
      of ancestral and convergent features.
AU  - Henderson IR
AU  - Deleris A
AU  - Wong W
AU  - Zhong XH
AU  - Chin HG
AU  - Horwitz GA
AU  - Kelly KA
AU  - Pradhan S
AU  - Jacobsen SE
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2010 6: e1001182.

PMID- 10802938
VI  - 249
DP  - 2000
TI  - Mammalian methyltransferases and methyl-CpG-binding domains: proteins involved in DNA methylation.
PG  - 55-74
AB  - The modified base 5-methylcytosine has been known to exist in mammalian DNA since 1950.  It
      wasn't until 1988 that the gene encoding the enzyme reponsible for the maintenance of
      5-methylcytosine in mammals, DNA-(cytosine-5) methyltransferase 1, was identified.  The
      following year, a protein activity was reported; it was able to bind DNA containing methylated
      cytosine followed by guanosine but, otherwise, it was indifferent to the sequence context.  A
      different protein activity, which was also capable of binding the sequence MeCpG, was
      identified in 1992, and the corresponding gene was cloned.  This provided the first molecular
      handle on MeCpG-binding proteins.  For the following 5 years, however, no further proteins
      were identified that were able to either methylate DNA or to bind specifically to methylated
      DNA.  The past 2 years have seen a flurry of activity in this field, with the reporting of
      three new candidate methyltransferases and four new candidate MeCPs.  Also developing is an
      ever-more-precise molecular picture of exactly how DNA methylation affects transcription. In
      this chapter, we will review that is known about the mammalian proteins involved in both
      methylating DNA and in interpreting the signal that DNA methylation represents.  For an
      evolutionary discussion of the known eukaryotic DNMTs, we refer the reader to a recent review
      by Colot and Rossignol.  In this review, we will only discuss MeCPs that do not require
      additional DNA sequence for specific binding to DNA.  For a summary of MeCPs in general we
      refer the reader to a review by Tate and Bird.
AU  - Hendrich B
AU  - Bird A
PT  - Journal Article
TA  - Curr. Top. Microbiol. Immunol.
JT  - Curr. Top. Microbiol. Immunol.
SO  - Curr. Top. Microbiol. Immunol. 2000 249: 55-74.

PMID- 9774669
VI  - 18
DP  - 1998
TI  - Identification and characterization of a family of mammalian methyl-CpG binding proteins.
PG  - 6538-6547
AB  - Methylation at the DNA sequence 5'-CpG is required for mouse development. MeCP2 and MBD1
      (formerly PCM1) are two known proteins that bind specifically to methylated DNA via a related
      amino acid motif and that can repress transcription. We describe here three novel human and
      mouse proteins (MBD2, MBD3, and MBD4) that contain the methyl-CpG binding domain. MBD2 and
      MBD4 bind specifically to methylated DNA in vitro. Expression of MBD2 and MBD4 tagged with
      green fluorescent protein in mouse cells shows that both proteins colocalize with foci of
      heavily methylated satellite DNA. Localization is disrupted in cells that have greatly reduced
      levels of CpG methylation. MBD3 does not bind methylated DNA in vivo or in vitro. MBD1, MBD2,
      MBD3, and MBD4 are expressed in somatic tissues, but MBD1 and MBD2 expression is reduced or
      absent in embryonic stem cells which are known to be deficient in MeCP1 activity. The data
      demonstrate that MBD2 and MBD4 bind specifically to methyl-CpG in vitro and in vivo and are
      therefore likely to be mediators of the biological consequences of the
      methylation signal.
AU  - Hendrich B
AU  - Bird A
PT  - Journal Article
TA  - Mol. Cell. Biol.
JT  - Mol. Cell. Biol.
SO  - Mol. Cell. Biol. 1998 18: 6538-6547.

PMID- 15466049
VI  - 186
DP  - 2004
TI  - Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis.
PG  - 6956
AB  - The genome sequence of the genetically tractable, mesophilic, hydrogenotrophic methanogen
      Methanococcus maripaludis contains 1,722 protein-coding genes in a single circular chromosome
      of 1,661,137 bp. Of the protein-coding genes (open reading frames [ORFs]), 44% were assigned a
      function, 48% were conserved but had unknown or uncertain functions, and 7.5% (129 ORFs) were
      unique to M. maripaludis. Of the unique ORFs, 27 were confirmed to encode proteins by the mass
      spectrometric identification of unique peptides. Genes for most known functions and pathways
      were identified. For example, a full complement of hydrogenases and methanogenesis enzymes was
      identified, including eight selenocysteine-containing proteins, with each being paralogous to
      a cysteine-containing counterpart. At least 59 proteins were predicted to contain iron-sulfur
      centers, including ferredoxins, polyferredoxins, and subunits of enzymes with various redox
      functions. Unusual features included the absence of a Cdc6 homolog, implying a variation in
      replication initiation, and the presence of a bacterial-like RNase HI as well as an RNase HII
      typical of the Archaea. The presence of alanine dehydrogenase and alanine racemase, which are
      uniquely present among the Archaea, explained the ability of the organism to use L- and
      D-alanine as nitrogen sources. Features that contrasted with the related organism
      Methanocaldococcus jannaschii included the absence of inteins, even though close homologs of
      most intein-containing proteins were encoded. Although two-thirds of the ORFs had their
      highest Blastp hits in Methanocaldococcus jannaschii, lateral gene transfer or gene loss has
      apparently resulted in genes, which are often clustered, with top Blastp hits in more
      distantly related groups.
AU  - Hendrickson EL et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2004 186: 6956.

PMID- 25524101
VI  - 3
DP  - 2014
TI  - Engineered Calcium-Precipitable Restriction Enzyme.
PG  - 969-971
AB  - We have developed a simple system for tagging and purifying proteins. Recent experiments have
      demonstrated that RTX (Repeat in Toxin) motifs from the adenylate cyclase toxin gene (CyaA) of
      B. pertussis undergo a conformational change upon binding calcium, resulting in precipitation
      of fused proteins and making this method a viable alternative for bioseparation. We have
      designed an iGEM Biobrick comprised of an RTX tag that can be easily fused to any protein of
      interest. In this paper, we detail the process of creating an RTX tagged version of the
      restriction enzyme EcoRI and describe a method for expression and purification of the
      functional enzyme.
AU  - Hendrix J
AU  - Read T
AU  - Lalonde J-F
AU  - Jensen PK
AU  - Heymann W
AU  - Lovelace E
AU  - Zimmermann SA
AU  - Brasino M
AU  - Rokicki J
AU  - Dowell RD
PT  - Journal Article
TA  - ACS Synth. Biol.
JT  - ACS Synth. Biol.
SO  - ACS Synth. Biol. 2014 3: 969-971.

PMID- 2985543
VI  - 162
DP  - 1985
TI  - Isolation of a Bacillus stearothermophilus mutant exhibiting increased thermostability in its restriction endonuclease.
PG  - 682-692
AB  - A procedure was developed for the selection of spontaneous mutants of Bacillus
      stearothermophilus NUB31 that are more efficient than the wild type in the
      restriction of phage at elevated temperatures.  Inactivation studies revealed
      that two mutants contained a more thermostable restriction enzyme and one
      mutant contained three times more enzyme than the wild type.  The restriction
      endonucleases from the wild type and one of the mutants were purified to
      apparent homogeneity.  The mutant enzyme was more thermostable than the
      wild-type enzyme.  The subunit molecular weight, amino acid composition,
      N-terminal and C-terminal amino acid residues, tryptic peptide map, and
      catalytic properties of the two enzymes were determined.  The two enzymes have
      similar catalytic properties, but the molecular size of the mutant enzyme is
      approximately 6 to 7 kilodaltons larger than that of the wild-type enzyme.  The
      mutant enzyme contains 54 additional amino acid residues, of which 26 to 28 are
      aspartate/asparagine, 8 to 15 are glutamate/glutamine, and 8 to 9 are tyrosine
      residues.  The two enzymes contained similar amounts of the other amino acids,
      identical N-terminal residues, and different C-terminal residues.  Tryptic
      peptide analyses revealed a high degree of homology between the two enzymes.
      The increased thermostability observed in the mutant enzyme appears to have
      been achieved by a mutation that resulted in the addition of amino acid
      residues to the wild-type enzyme.  A number of mechanisms are discussed that
      could account for the observed difference between the mutant and wild-type
      enzymes.
AU  - Hendrix JD
AU  - Welker NE
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1985 162: 682-692.

PMID- 25720684
VI  - 3
DP  - 2015
TI  - Genome Sequence of Salmonella Phage chi.
PG  - e01229-14
AB  - Salmonella bacteriophage chi is a member of the Siphoviridae family that gains entry into its
      host cells by adsorbing to their flagella. We report the complete  59,578-bp sequence of the
      genome of phage chi, which together with its relatives, exemplifies a largely unexplored type
      of tailed bacteriophage.
AU  - Hendrix RW
AU  - Ko CC
AU  - Jacobs-Sera D
AU  - Hatfull GF
AU  - Erhardt M
AU  - Hughes KT
AU  - Casjens SR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01229-14.

PMID- 10051617
VI  - 96
DP  - 1999
TI  - Evolutionary relationships among diverse bacteriophages and prophages: All the world's a phage.
PG  - 2192-2197
AB  - We report DNA and predicted protein sequence similarities, implying homology, among genes of
      double-stranded DNA (dsDNA) bacteriophages and prophages spanning a broad phylogenetic range
      of host bacteria. The sequence matches reported here establish genetic connections, not always
      direct, among the lambdoid phages of Escherichia coli, phage phiC31 of Streptomyces, phages of
      Mycobacterium, a previously unrecognized cryptic prophage, phiflu, in the Haemophilus
      influenzae genome, and two small prophage-like elements, phiRv1 and phiRv2, in the genome of
      Mycobacterium tuberculosis. The results imply that these phage genes, and very possibly all of
      the dsDNA tailed phages, share common ancestry. We propose a model for the genetic structure
      and dynamics of the global phage population in which all dsDNA phage genomes are mosaics with
      access, by horizontal exchange, to a large common genetic pool but in which access to the gene
      pool is not uniform for all phage.
AU  - Hendrix RW
AU  - Smith MCM
AU  - Burns RN
AU  - Ford ME
AU  - Hatfull GF
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1999 96: 2192-2197.

PMID- 22038965
VI  - 193
DP  - 2011
TI  - Genome Sequence of the Bacteriocin-Producing Oral Probiotic Streptococcus salivarius Strain M18.
PG  - 6402-6403
AB  - Streptococcus salivarius is a Gram-positive bacterial commensal and pioneer colonizer of the
      human oral cavity. Many strains produce
      ribosomally synthesized proteinaceous antibiotics (bacteriocins), and some
      strains have been developed for use as oral probiotics. Here, we present
      the draft genome sequence of the bacteriocin-producing oral probiotic S.
      salivarius strain M18.
AU  - Heng NC
AU  - Haji-Ishak NS
AU  - Kalyan A
AU  - Wong AY
AU  - Lovric M
AU  - Bridson JM
AU  - Artamonova J
AU  - Stanton JA
AU  - Wescombe PA
AU  - Burton JP
AU  - Cullinan MP
AU  - Tagg JR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6402-6403.

PMID- 28126938
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Weissella confusa MBF8-1, a Glucansucrase- and Bacteriocin-Producing Strain Isolated from a Homemade Soy Product.
PG  - e01497-16
AB  - We report here the draft genome sequence of Weissella confusa MBF8-1, an isolate  from a
      homemade fermented soybean product that produces sucrases and exhibits
      antibacterial (bacteriocin) activity. The draft genome of W. confusa MBF8-1
      comprises a 2.2-Mbp chromosome and a 17.8-kbp bacteriocin-encoding plasmid. Two
      putative glucansucrase genes were also identified.
AU  - Heng NC
AU  - Yeh CW
AU  - Malik A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01497-16.

PMID- 9584105
VI  - 149
DP  - 1998
TI  - A DNA methyltransferase homolog with a chromodomain exists in multiple polymorphic forms in Arabidopsis.
PG  - 307-318
AB  - Chromodomains are thought to mediate protein-protein interactions between chromatin
      components.  We have detected a chromodomain embedded within the catalytic region of a
      predicted Arabidopsis DNA methyltransferase that is diverged from other eukaryotic enzymes.
      The 791 residue "chromomethylase" is encoded by a floral transcript that is spliced from 20
      exons and is present at only ~1/10^-7 of total mRNA.  Genomic sequencing reveals an ancient
      haplotype split at CMT1 between Col-0 + Metz and the other ecotypes examined.  In the Col-0 +
      Metz haplotype, alternative mRNA processing at intron 13 truncates the coding region.  In Ler,
      RLD, and No-0, similar truncation is caused by insertion of an intact retrotransposon,
      Evelknievel, which is present as a single copy in Ler and RLD and is currently methylated and
      inactive.  Evelknievel is found at this site on a single branch that connects the Ler, RLD,
      and No-0 ecotypes but is absent from the genomes of all other ecotypes examined.  A stop codon
      within exon 6 of the Metz ecotype confirms that CMT1 is nonessential.  Nevertheless,
      comparison to CMT1 of Cardaminopsis arenosa, an outcrossing relative, indicates conservation
      for DNA methyltransferase function.  We discuss how allelic diversity of CMT1 may reflect
      loosened selective constraints in a self-fertilizing species such as Arabidopsis thaliana.
AU  - Henikoff S
AU  - Comai L
PT  - Journal Article
TA  - Genetics
JT  - Genetics
SO  - Genetics 1998 149: 307-318.

PMID- 
VI  - 61
DP  - 2000
TI  - Molecular and biochemical studies on a bifunctional group I intron encoded protein of yeast mitochondria.
PG  - 2899
AB  - Intron 4a (aI4a) of the yeast mitochondrial COXI gene is a mobile group I intron that contains
      a reading frame encoding both the homing endonuclease I-SceII and a latent maturase capable of
      splicing both aI4a and the fourth intron of the cytochrome b (COB) gene (bI4).  The aI4a
      reading frame is a member of a large gene family recognized by the presence of related
      dodecapeptide sequence motifs called P1 and P2.  In this study missense mutations of P1 and P2
      were placed in mtDNA by biolistic transformation and the effects of the mutations on intron
      mobility, I-SceII activity and maturase function were tested.  The mutations of P1 strongly
      affected intron mobility and I-SceII activity but had little or no effect on maturase
      function, while mutations of P2 affected splicing but not mobility or I-SceII activity.
      Surprisingly, the conditional (ts) mutations at P1 and P2 block one or the other function of
      the protein but not both.  This study indicates that the two functions depend on separate
      domains of the intron-encoded protein.  Normally splicing of the aI4a intron requires the bI4
      maturase.  In strains lacking the bI4 maturase, second site-suppressors that activate the aI4a
      maturase have been isolated; some map to the nuclear NAM2 gene (NAM2-1) and another to the
      aI4a ORF (MIM2-1, glu 117) and then transformed into yeast mitochondria.  These changes were
      designed to determine if activation of aI4a maturase results from the loss of a negative
      charge or the gain of a positive charge at the mim2 site.  Substitution of a positively
      charged amino acid (lys or arg) results in an active aI4a maturase, while the substitution of
      either a negatively charged amino acid (wild-type, glu) or a neutral amino acid (gln) was
      insufficient to activate the maturase.  These data show that the presence of a positive charge
      at the mim2 residue is sufficient to activate aI4a's latent maturase activity.  The mim2
      alleles were further characterized by assaying them for intron mobility.  All the mim2 alleles
      retain wild-type levels of intron mobility, indicating that they encode I-SceII activity.  The
      presence of both maturase and I-SceII activity in several alleles, (lys and arg) clearly
      demonstrates that both functions can co-exist within the same poly-peptide.  This study also
      characterizes several new in vitro DNA binding properties of I-SceII and speculates on their
      in vivo significance.
AU  - Henke RM
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 2000 61: 2899.

PMID- 7588637
VI  - 14
DP  - 1995
TI  - Maturase and endonuclease functions depend on separate conserved domains of the bifunctional protein encoded by the group I intron aI4a of yeast mitochondrial DNA.
PG  - 5094-5099
AB  - Intron 4a (aI4a) of the yeast mitochondrial COXI gene is a mobile group I intron that contains
      a reading frame encoding both the homing endonuclease I-SceII and a latent maturase capable
      of splicing both aI4a and the fourth intron of the cytochrome b (COB) gene (bI4).  The aI4a
      reading frame is a member of a large gene family recognized by the presence of related
      dodecapeptide sequence motifs called P1 and P2.  In this study, missense mutations of P1 and
      P2 were placed in mitochondrial DNA by biolistic transformation.  The effects of the mutations
      on intron mobility, endonuclease I-SceII activity and maturase function were tested.  The
      mutations of P1 strongly affected mobility and endonuclease I-SceII activity, but had little
      or no effect on maturase function; mutations of P2 affected splicing but not mobility or
      endonuclease I-SceII activity.  Surprisingly, the conditional (temperature-sensitive)
      mutations at P1 and P2 block one or the other function of the protein but not both.  This
      study indicates that the two functions depend on separate domains of the intron-encoded
      protein.
AU  - Henke RM
AU  - Butow RA
AU  - Perlman PS
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1995 14: 5094-5099.

PMID- 24675863
VI  - 2
DP  - 2014
TI  - Genome Sequence of the Octopine-Type Agrobacterium tumefaciens Strain Ach5.
PG  - e00225-14
AB  - We have sequenced the complete genome of the plant pathogen Agrobacterium tumefaciens strain
      LBA4213, a derivative of the wild-type strain A. tumefaciens
      Ach5 and the ancestor of A. tumefaciens strain LBA4404 used in genetic
      engineering. The genome consists of a circular chromosome and a linear
      chromosome, as well as a megaplasmid and a tumor-inducing plasmid.
AU  - Henkel CV
AU  - den Dulk-Ras A
AU  - Zhang X
AU  - Hooykaas PJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00225-14.

PMID- 26987727
VI  - 198
DP  - 2016
TI  - Classic spotlight: Bacteria versus phage--the Battle Rages!
PG  - 1007
AB  - Early studies of bacteriophages and their hosts revealed that
      some host strains were more resistant to certain phage isolates
      than were other closely related bacterial strains. Analysis of this
      phenomenon led to the discovery that many bacterial strains contain
      restriction/modification systems. Systems of this type include
      restriction endonucleases that cleave foreign DNA and modification
      enzymes that protect host DNA from cleavage. These restriction
      endonucleases provided the backbone for the development
      of DNA cloning technologies. Demonstration that bacterial
      hosts affected phage properties (1) and characterization of restriction
      and modification systems in Escherichia coli were provided
      in seminal papers by Luria and Human (1), Herbert
      Boyer (2), and Seymour Lederberg (3) in the Journal of Bacteriology
      (JB), as was demonstration that restriction occurs by
      DNA cleavage (4).
AU  - Henkin TM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2016 198: 1007.

PMID- 1944537
VI  - 253
DP  - 1991
TI  - The vsr gene product of E. coli K-12 is a strand- and sequence-specific DNA mismatch endonuclease.
PG  - 776-778
AB  - In Escherichia coli K-12, the Dcm methyltransferase catalyses methylation of the inner
      cytosine residue in the sequence CCA/TGG. Hydrolytic deamination of 5-methylcytosine bases in
      DNA leads to thymine residues, and hence to T/G mismatches, pre-mutagenic DNA lesions
      consisting of two natural DNA constituents and thus devoid of an obvious marker of the damaged
      DNA strand. These mismatches are corrected by the VSP repair pathway, which is characterized
      by very short patches of DNA repair synthesis. It depends on genes vsr and polA and is
      strongly stimulated by mutL and mutS. The vsr gene product (Vsr; Mr 18,000) was purified and
      characterized as a DNA mismatch endonuclease, a unique and hitherto unknown type of enzyme.
      Vsr endonuclease nicks double-stranded DNA within the sequence CTA/TGN or NTA/TGG next to the
      underlined thymidine residue, which is mismatched to 2'-deoxyguanosine. The incision is
      mismatch-dependent and strand-specific. These results illustrate how Vsr endonuclease
      initiates VSP mismatch repair.
AU  - Hennecke F
AU  - Kolmar H
AU  - Brundl K
AU  - Fritz H-J
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1991 253: 776-778.

PMID- 26607883
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Pseudomonas sp. Strain In5 Isolated from a Greenlandic Disease Suppressive Soil with Potent Antimicrobial Activity.
PG  - e01251-15
AB  - Pseudomonas sp. In5 is an isolate of disease suppressive soil with potent activity against
      pathogens. Its antifungal activity has been linked to a gene
      cluster encoding nonribosomal peptide synthetases producing the peptides
      nunamycin and nunapeptin. The genome sequence will provide insight into the
      genetics behind the antimicrobial activity of this strain.
AU  - Hennessy RC
AU  - Glaring MA
AU  - Michelsen CF
AU  - Olsson S
AU  - Stougaard P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01251-15.

PMID- 26184930
VI  - 3
DP  - 2015
TI  - Genome Sequence of Rhodococcus sp. Strain RD6.2 DSM 46800, a Methanesulfonate-Degrading Strain.
PG  - e00730-15
AB  - The complete genome sequence of a methanesulfonate-degrading strain, Rhodococcus  sp. strain
      RD6.2 DSM 46800, which was isolated from a brackish marsh sediment
      sample, is described here. This is the first reported genome of a
      nonproteobacterial strain using methanesulfonate (MSA) as a sole source of carbon
      and energy, which does not possess the conventional MSA-monooxygenase (MSAMO).
AU  - Henriques AC
AU  - De Marco P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00730-15.

PMID- 25953167
VI  - 3
DP  - 2015
TI  - Complete Genome Sequences of Two Strains of 'Candidatus Filomicrobium marinum,' a Methanesulfonate-Degrading Species.
PG  - e00160-15
AB  - Two novel methanesulfonate-degrading bacterial strains of 'Candidatus Filomicrobium marinum'
      (strains Y and W) were isolated from a marine water
      enrichment, and their complete genome sequences are presented here. These are the
      first full genomes reported for the genus Filomicrobium and for methanesulfonate
      (MSA)-degrading bacteria.
AU  - Henriques AC
AU  - De Marco P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00160-15.

PMID- 7768848
VI  - 177
DP  - 1995
TI  - Characterization of cotJ, a sigma E-controlled operon affecting the polypeptide composition of the coat of Bacillus subtilis spores.
PG  - 3394-3406
AB  - The outermost protective structure found in endospores of Bacillus subtilis is a thick protein
      shell known as the coat, which makes a key
      contribution to the resistance properties of the mature spore and also
      plays a role in its interaction with compounds able to trigger
      germination. The coat is organized as a lamellar inner layer and an
      electron-dense outer layer and has a complex polypeptide composition. Here
      we report the cloning and characterization of an operon, cotJ, located at
      about 62 degrees on the B. subtilis genetic map, whose inactivation
      results in the production of spores with an altered pattern of coat
      polypeptides. The cotJ operon was identified by screening a random library
      of lacZ transcriptional fusions for a conditional (inducer-dependent) Lac+
      phenotype in cells of a strain in which the structural gene (spoIIGB) for
      the early-acting, mother-cell-specific transcriptional factor sigma E was
      placed under the control of the IPTG
      (isopropyl-beta-D-thiogalactopyranoside)-inducible Pspac promoter.
      Sequence analysis of cloned DNA from the cotJ region complemented by
      genetic experiments revealed a tricistronic operon preceded by a strong
      sigma E-like promoter. Expression of an SP beta-borne cotJ-lacZ fusion
      commences at around h 2 of sporulation, as does expression of other sigma
      E-dependent genes, and shows an absolute requirement for sigma E. Studies
      with double-reporter strains bearing a cotJ-gusA fusion and lacZ fusions
      to other cot genes confirmed that expression of cotJ is initiated during
      sporulation prior to activation of genes known to encode coat structural
      proteins (with the sole exception of cotE). An in vitro-constructed
      insertion-deletion mutation in cotJ resulted in the formation of spores
      with no detectable morphological or resistance deficiency. However,
      examination of the profile of electrophoretically separated spore coat
      proteins from the null mutant revealed a pattern that was essentially
      identical to that of a wild-type strain in the range of 12 to 65 kDa,
      except for polypeptides of 17 and 24 kDa, the putative products of the
      second (cotJB) and third (cotJC) cistrons of the operon, that were missing
      or reduced in amount in the coat of the mutant. Polypeptides of the same
      apparent sizes are detected in spores of a cotE null mutant, on which
      basis we infer that the products of the cotJ operon are required for the
      normal formation of the inner layers of the coat or are themselves
      structural components of the coat. Because the onset of cotJ transcription is temporally
      coincident with the appearance of active sigmaE, we speculate that cotJ-encoded products may
      be involved in an early stage of coat assembly.
AU  - Henriques AO
AU  - Beall BW
AU  - Roland K
AU  - Moran CP Jr
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1995 177: 3394-3406.

PMID- 24285645
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Serratia fonticola UTAD54, a Carbapenem-Resistant Strain Isolated from Drinking Water.
PG  - e00970-13
AB  - Serratia fonticola UTAD54 is an environmental isolate that is resistant to carbapenems due to
      the presence of a class A carbapenemase and a
      metallo-beta-lactamase that are unique to this strain. Its draft genome sequence
      was obtained to clarify the molecular basis of its carbapenem resistance and
      identify the genomic context of its carbapenem resistance determinants.
AU  - Henriques I
AU  - Juca RRT
AU  - Barauna RA
AU  - de Sa PH
AU  - Marinho AD
AU  - Carneiro AR
AU  - Barbosa S
AU  - Pereira A
AU  - Alves A
AU  - Saavedra MJ
AU  - Egas C
AU  - Silva A
AU  - Correia A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00970-13.

PMID- 27834715
VI  - 4
DP  - 2016
TI  - Finished Genome Sequences of Xanthomonas fragariae, the Cause of Bacterial Angular Leaf Spot of Strawberry.
PG  - e01271-16
AB  - Xanthomonas fragariae is a foliar pathogen of strawberry that is of significant concern to
      nursery production of strawberry transplants and field production of
      strawberry fruit. Long-read sequencing was employed to generate finished genomes
      for two isolates (each with one chromosome and two plasmids) from symptomatic
      plants in northern California.
AU  - Henry PM
AU  - Leveau JH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01271-16.

PMID- 6297792
VI  - 32
DP  - 1983
TI  - Two intron sequences in yeast mitochondrial COX1 gene:  homology among URF-containing introns and strain-dependent variation in flanking exons.
PG  - 379-389
AB  - The DNA sequences of two optional introns in the gene for subunit I of cytochome c oxidase in
      yeast mitochondrial DNA have been determined. Both contain long unassigned reading frames
      (URFs). These display regions of amino acid homology with six other URFs, two of which encode
      proteins involved in mitochondrial RNA splicing. Such conserved regions may thus define
      functionally important domains of proteins involved in RNA processing. This homology also
      implies that these URFs had a common ancestral sequence, which has been duplicated and
      sipersed around the genome. Comparison of the flanking exons in the long strain KL14-4A with
      their unsplit counterpart in D273-10B reveals clustered sequence differences, which lead in
      D273-10B to codonas rearely used in exons. These differences may be linked to the loss or
      absence of one of the optional introns.
AU  - Hensgens LAM
AU  - Bonen L
AU  - de Haan M
AU  - van der Horst G
AU  - Grivell LA
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1983 32: 379-389.

PMID- 2203774
VI  - 265
DP  - 1990
TI  - The time-resolved kinetics of superhelical DNA cleavage by BamHI restriction endonuclease.
PG  - 15300-15307
AB  - The kinetics of the cleavage of superhelical plasmid DNA (pBR322) by the
      restriction endonuclease, BamHI, have been analyzed in terms of a compartmental
      model consistent with the chemistry first proposed by Rubin and Modrich (Rubin,
      R.A., and Modrich, P. (1978) Nucleic Acids Res. 5, 2991-2997) for analysis of
      the kinetics of the restriction endonuclease, EcoRI.  The model was defined in
      terms of two compartments representing DNA substrate (bound and free), two
      compartments representing nicked intermediate (bound and free), one compartment
      representing linear product, and one compartment for free enzyme.  A
      simultaneous analysis of concentration changes over time of the three DNA forms
      (superhelical, nicked, and linear) at six different enzyme concentrations was
      undertaken employing this compartmental model using SAAM (Simulation Analysis
      and Modeling) software.  Results showed that rate constants characterizing the
      association of enzyme with superhelical DNA (6.0 x 10/5M-1S-1) and nicked DNA
      (2.8 x 10/5M-1S-1) were similar in magnitude and rate constants characterizing
      cleavage of the first (1.2 x 10-2S-1) and second phosphodiester bonds (3.1 x
      10-2S-1) were also similar.  The analysis yields a kinetically determined
      equilibrium constant of 12.9 nM for the dissociation of nicked intermediate
      from the enzyme.  The rate constant describing the release of the nicked
      intermediate from the enzyme has a value of 3.7 x 10-3S-1.  By comparing the
      value of this release rate constant to the value of the constant describing the
      second cleavage event, it can be determined that only 10% of the nicked
      intermediate bound to the enzyme is released as free nicked DNA and that 90% of
      the nicked intermediate is processed to the linear form without being released.
      Hence, most of the DNA is cleaved as the result of a single enzyme-DNA
      recognition event.  No steady state assumptions were made in the analysis.  The
      approach was to directly solve the differential equations which described the
      kinetic processes using an interactive method.  This study demonstrates the
      usefulness of this approach for the analysis of kinetics of protein-DNA
      interactions for the restriction endonucleases.
AU  - Hensley P
AU  - Nardone G
AU  - Chirikjian JG
AU  - Wastney ME
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1990 265: 15300-15307.

PMID- 1647525
VI  - 19
DP  - 1991
TI  - Effects of 2-chloroadenine substitution in DNA on restriction endonuclease cleavage reactions.
PG  - 3143-3148
AB  - The purine analog, 2-chloro-2'-deoxyadenosine triphosphate (CldATP), was
      incorporated enzymatically in place of dATP into the minus strand of M13mp18
      duplex DNA.  Its effect on protein-DNA interactions was assessed by determining
      the amount of DNA cleavage by type II restriction endonucleases.  Substitution
      of chloroadenine (ClAde) for adenine (Ade) in DNA appreciably decreased the
      amount and rate of DNA cleavage of the minus strand when the analog was
      situated within the appropriate endonuclease recognition site.  ClAde residues
      flanking a restriction site had variable effects.  SmaI cleaved both
      ClAde-containing and control substrates with equal efficiency.  NarI, however,
      was stimulated 1.5-fold by the presence of ClAde outside its recognition site.
      The effects of analog incorporation on restriction enzyme cleavage of an
      opposing unsubstituted strand of duplex DNA was examined by enzymatically
      incorporating CldATP into complementary minus strand of a 36-base
      oligonucleotide.  Endonucleolytic cleavage of both plus and minus strands was
      reduced on 36-mers containing ClAde residues located within only the minus
      strand.  These data suggest that ClAde residues incorporated into a single DNA
      strand may have an appreciable effect of DNA-protein interactions that involve
      one or both strands of duplex DNA.
AU  - Hentosh P
AU  - McCastlain JC
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 3143-3148.

PMID- 2022628
VI  - 266
DP  - 1991
TI  - Enzymatic methylation of cytosine in DNA is prevented by adjacent 06-methylguanine residues.
PG  - 7985-7987
AB  - The effect of 06-alkylation of guanine residues on the enzymatic methylation of
      cytosine has been studied using synthetic oligonucleotides in which all
      guanines in cytosine-guanine sequences at potentially methylatable sites are
      replaced by 06-methylguanine.  In contrast with the unmodified forms, which
      showed high acceptance activity for methyl-3H-labeled groups from
      S-adenosyl-L-[methyl-3H]methionine in the presence of DNA methylase, the
      modified oligonucleotides were not substrates for the enzyme neither in the
      single-stranded or annealed forms.  In view of the importance of cytosine
      methylation in the down-regulation of certain genes, the potential to affect
      gene expression by this mechanism may be a contributory factor in the toxic and
      carcinogenic effects of chemical methylating agents.
AU  - Hepburn PA
AU  - Margison GP
AU  - Tisdale MJ
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1991 266: 7985-7987.

PMID- 2015298
VI  - 1088
DP  - 1991
TI  - Importance of the O6 position of guanine residues in the binding of DNA methylase to DNA.
PG  - 341-344
AB  - Methylation of Micrococcus lysodeikticus DNA by purified DNA methylase isolated
      from L1210 leukaemia cells is potently and specifically inhibited by both
      hetero and homoribo and deoxyribopolynucleotides containing guanine residues.
      The inhibitory effect is unaffected by chain length, but is abolished when the
      O6 residue of guanine is substituted as in poly[d(O6MeG)]20.  Potent inhibition
      is also shown by polyinosinic and polyxanthylic acids, but not by polyadenylic
      acid or by heteropolymers containing adenine and thymine.  These results
      suggest that the 6-position of the purine nucleus is important in binding of
      the DNA methylase to a particular region of the DNA duplex and that the
      hydrogen bonding properties of this group are important in enzyme recognition.
AU  - Hepburn PA
AU  - Tisdale MJ
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1991 1088: 341-344.

PMID- 21418497
VI  - 13
DP  - 2011
TI  - Genomic variations define divergence of water/wildlife-associated Campylobacter jejuni niche specialists from common clonal complexes.
PG  - 1549-1560
AB  - Although the major food-borne pathogen Campylobacter jejuni has been
      isolated from diverse animal, human and environmental sources, our
      knowledge of genomic diversity in C. jejuni is based exclusively on human
      or human food-chain-associated isolates. Studies employing multilocus
      sequence typing have indicated that some clonal complexes are more
      commonly associated with particular sources. Using comparative genomic
      hybridization on a collection of 80 isolates representing diverse sources
      and clonal complexes, we identified a separate clade comprising a group of
      water/wildlife isolates of C. jejuni with multilocus sequence types
      uncharacteristic of human food-chain-associated isolates. By genome
      sequencing one representative of this diverse group (C. jejuni 1336), and
      a representative of the bank-vole niche specialist ST-3704 (C. jejuni
      414), we identified deletions of genomic regions normally carried by human
      food-chain-associated C. jejuni. Several of the deleted regions included
      genes implicated in chicken colonization or in virulence. Novel genomic
      insertions contributing to the accessory genomes of strains 1336 and 414
      were identified. Comparative analysis using PCR assays indicated that
      novel regions were common but not ubiquitous among the water/wildlife
      group of isolates, indicating further genomic diversity among this group,
      whereas all ST-3704 isolates carried the same novel accessory regions.
      While strain 1336 was able to colonize chicks, strain 414 was not,
      suggesting that regions specifically absent from the genome of strain 414
      may play an important role in this common route of Campylobacter infection
      of humans. We suggest that the genomic divergence observed constitutes
      evidence of adaptation leading to niche specialization.
AU  - Hepworth PJ
AU  - Ashelford KE
AU  - Hinds J
AU  - Gould KA
AU  - Witney AA
AU  - Williams NJ
AU  - Leatherbarrow H
AU  - French NP
AU  - Birtles RJ
AU  - Mendonca C
AU  - Dorrell N
AU  - Wren BW
AU  - Wigley P
AU  - Hall N
AU  - Winstanley C
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2011 13: 1549-1560.

PMID- 29342160
VI  - 13
DP  - 2018
TI  - Expression of the lux genes in Streptococcus pneumoniae modulates pilus expression and virulence.
PG  - e0189426
AB  - Bioluminescence has been harnessed for use in bacterial reporter systems and for  in vivo
      imaging of infection in animal models. Strain Xen35, a bioluminescent
      derivative of Streptococcus pneumoniae serotype 4 strain TIGR4 was previously
      constructed for use for in vivo imaging of infections in animal models. We have
      shown that strain Xen35 is less virulent than its parent TIGR4 and that this is
      associated with the expression of the genes for bioluminescence. The expression
      of the luxA-E genes in the pneumococcus reduces virulence and down regulates the
      expression of the pneumococcal pilus.
AU  - Herbert JA
AU  - Mitchell AM
AU  - Ritchie R
AU  - Ma J
AU  - Ross-Hutchinson K
AU  - Mitchell TJ
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2018 13: e0189426.

PMID- 14659549
VI  - 229
DP  - 2003
TI  - Gene transfer into Clostridium difficile CD630 and characterisation of its methylase genes.
PG  - 103-110
AB  - Ignorance of pathogenesis in Clostridium difficile may be attributable to a lack of effective
      genetic tools. We have now shown that oriT-based
      shuttle vectors may be conjugated from Escherichia coli donors to the C.
      difficile strain CD630, at frequencies of around 10(-6) transconjugants
      per donor cell. Transfer is unaffected by either sequences present on the
      vector or its methylation status. Whilst the genome of this strain carries
      five methylase genes, there is no in silico or experimental evidence for
      cognate restriction enzymes. It would seem that the identified methylases
      do not participate in restriction-modification, and must, therefore,
      fulfil another role. A similar situation most likely applies to other
      clostridia.
AU  - Herbert M
AU  - O'Keeffe TA
AU  - Purdy D
AU  - Elmore M
AU  - Minton NP
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2003 229: 103-110.

PMID- 11349066
VI  - 69
DP  - 2001
TI  - Gene fragments distinguishing an epidemic-associated strain from a virulent prototype strain of Listeria monocytogenes belong to a distinct   functional subset of genes and partially cross-hybridize with other   Listeria species.
PG  - 3972-3979
AB  - Most major food-borne outbreaks of listeriosis in Europe and in the United States have been
      caused by genetically closely related Listeria
      monocytogenes strains of serotype 4b. In order to assess whether genomic
      loci exist that could underlie this increased epidemic potential, we
      subtracted the genome of the virulent prototype L. monocytogenes strain
      EGD from a prototype epidemic strain. A total of 39 DNA fragments
      corresponding to 20% of an estimated total of 150 to 190 kb of
      differential genome material were isolated. For 21 of these fragments, no
      function on the basis of homology could be predicted. Of the remaining 18
      fragments, 15 had homologies to bacterial surface proteins, some of which
      have been implicated in virulence mechanisms such as cell invasion,
      adhesion, or immune escape. Southern hybridization of arrays containing
      the epidemic-clone-specific DNA segments with genomic DNA of different L.
      monocytogenes strains was consistent with the current lineage division.
      Surprisingly, however, some of the fragments hybridized in a mosaic-like
      fashion to genomes of two other Listeria species, the animal pathogen L.
      ivanovii and the nonpathogen L. innocua. Taken together, our results
      provide a starting point for the identification of
      epidemic-trait-associated genes.
AU  - Herd M
AU  - Kocks C
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2001 69: 3972-3979.

PMID- 7007328
VI  - 145
DP  - 1981
TI  - Escherichia coli K-12 clones that overproduce dam methylase are hypermutable.
PG  - 644-646
AB  - A strain of Escherichia coli K-12 that overproduces dam methylase 50-fold was found to be
      hypermutable, and mutations which resulted in loss of excess methylase activity restored
      mutation frequencies to wild-type levels. These results are consistent with involvement of
      this deoxyribonucleic acid methylase in mismatch correction.
AU  - Herman GE
AU  - Modrich P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1981 145: 644-646.

PMID- 7037767
VI  - 257
DP  - 1982
TI  - Escherichia coli dam methylase physical and catalytic properties of the homogeneous enzyme.
PG  - 2605-2612
AB  - The Escherichia coli dam methylase has been purified 3000-fold to a purity of 95% from a clone
      which overproduces the enzyme 10- to 20-fold. Physical properties of enzyme purified from the
      overproducing clone were identical with those of enzyme previously obtained from a
      non-overproducing E. coli strain (Geier, G.E., and Modrich, P. (1979) J. Biol. Chem. 254,
      1408-1413). The methylase is comprised of a single polypeptide chain of Mr = 31,000 has an
      S20,W of 2.8 S, a Stokes radius of 24 A, and exists in solution as a monomer. Its aggregation
      state is not affected by the presence of S-adenosyl-L-methionine. The simple kinetic behavior
      of the methylase indicates that it functions as a monomer. Initial rates of methyl transfer
      are first order in enzyme concentration, and Michaelis-Menten behavior is obeyed with respect
      to both substrates. At 37C, in the presence of saturating DNA, the enzyme has a turnover
      number of 19 methyl transfers/min with a KM for S-adenosyl-L-methionine of 12.2 lM. At
      half-saturating S-adenosyl-L-methionine, the apparent KM for d(G-A-T-C) sites in ColE1 DNA is
      3.6NM. The mechanism of methyl transfer is also consistent with the monomer being the
      functional form of the enzyme. Studies with G4 RFI DNA (two d(G-A-T-C) sites) indicate that
      the methylase transfers 1 methyl group to a recognition site and then dissociates from this
      DNA prior to subsequent catalysis. It appears that kinetic parameters for methyl transfer to
      sites already modified on one DNA strand may be slightly more favorable than those for
      transfer to sites in which both strands are unmethylated.
AU  - Herman GE
AU  - Modrich P
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1982 257: 2605-2612.

PMID- 2467142
VI  - 13D
DP  - 1989
TI  - Introduction and expression of HhaI DNA methyltransferase in eukaryotic cells.
PG  - 223
AB  - DNA methylation abnormalities, which include both widespread hypomethylation
      and regional hypermethylation, hve been reported for many malignancies.  In
      culture, tumor cells often have increased DNA methyltransferase activity with
      unknown consequences.  To assess functional consequences of increased cytosine
      methylation in eukaryotic cells, we are using a constitutively expressed
      prokaryotic DNA methyltransferase enzyme in murine fibroblasts.  We inserted
      the cloned DNA sequence for the bacterial DNA methyltransferase M.HhaI
      (methylated sequence G^mCGC) into the retroviral expression vector pZIPneo
      SV(X).  Abundant G418 resistant colonies were produced in PA 317 amphotropic
      packaging cells after infection with either the pZIPneo SV(X) vector alone or
      M.HhaI inserted in the antisense direction.  However, insertion of M.HhaI in
      the sense orientation resulted in a total of two G418 resistant clones in 5
      independent experiments.  Southern and Northern blots probed with M.HhaI
      sequences demonstrated integration and expression.  Each M.HhaI clone in the
      sense orientation was tumorigenic in nude mice, and one of the clones was
      morphologically distinct from control PA 317 cells.  Other data suggest that
      constitutive expression of M.HhaI is often lethal to eukaryotic cells in
      culture, and may cause transformation of surviving cells.
AU  - Herman J
AU  - Nelkin B
AU  - Mabry M
AU  - Wilson G
AU  - Baylin S
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1989 13D: 223.

PMID- Not carried by PubMed...
VI  - 30
DP  - 1989
TI  - Introduction of prokaryotic HhaI DNA methyltransferase alters the phenotype of 3T3 cells.
PG  - 428
AB  - DNA methylation abnormalities are common in cancer.  Recently, we described
      hypermethylation on chromosome 11p (PNAS USA 85:5693-5697, 1988) which could
      result from the fact that tumor cells often have increased DNA
      methyltransferase activity.  To assess the functional consequences of
      increasing cytosine methylation capacity in eukaryotic cells, we have
      constitutively expressed two prokaryotic DNA methyltransferase enzymes in
      murine fibroblasts.  DNA sequences for the bacterial DNA methyltransferases
      M.HhaI (methylated sequence GmCGC), and M.HpaII (CmCGG) were introduced via the
      retroviral expression vector pZIPneo SV(X).  Abundant G418 resistant colonies,
      typically 60/experiment, were produced in PA317 amphotropic packaging cells
      after infection with the pZIPneo SV(X) vector alone, the M.HhaI inserted in the
      antisense direction, and M.HpaII in both directions.  However, insertion of
      M.HhaI in the sense orientation resulted in a total of only two G418 resistant
      clones in 5 independent experiments.  M.HhaI sequences were integrated and
      expressed in each clone.  Both clones were tumorigenic in nude mice, and one of
      the clones was morphologically distinct from control PA317 cells.  We also
      observed a similar discrepancy in the ability to select stably transfected Psi2
      cells used to infect the PA317 cells with the sense M.HhaI construct.  Our data
      suggest that constitutive expression of M.HhaI is most often lethal to 3T3
      cells in culture, and may cause transformation of those cells which survive.
AU  - Herman J
AU  - Nelkin B
AU  - Mabry M
AU  - Wilson G
AU  - Baylin S
PT  - Journal Article
TA  - Proc. Amer. Assoc. Cancer Res.
JT  - Proc. Amer. Assoc. Cancer Res.
SO  - Proc. Amer. Assoc. Cancer Res. 1989 30: 428.

PMID- 
VI  - 28
DP  - 2000
TI  - Molecular enzymology of the Dnmt1 DNA methyltransferase explains the mechanism of cis-spreading of DNA methylation.
PG  - A248
AB  - In mammals, methylation of DNA within CpG-sequences is involved in epigenetic control of gene
      expression, chromatin condensation and genetic imprinting.  So far, three active DNA
      methyltransferases have been identified in mice: Dnmt1 which is responsible for maintenance
      methylation, as well as Dnmt3a and 3b which are required for de novo methylation.  Methylation
      of DNA is essential in mammals because mice deficient in either Dnmt1, Dnmt3a or Dnmt3b die
      during development.  During tumorigenesis or aging, spreading of methylation is observed, i.e.
      starting from one modified CpG-site methylation spreads to neighboring CpGs until one region
      of the DNA is completely methylated.  The Dnmt1 enzyme consists of a catalytic domain (500
      amino acid residues) which closely resembles prokaryotic DNA-(cytosine-C5)-methyltransferases
      and a large regulatory N-terminal domain comprising about 1100 amino acid residues.  By
      cloning and characterizing several fragments of the Dnmt1 enzyme, we demonstrate that the
      N-terminal domain forms a DNA binding site distinct from the active center.  In kinetic assays
      with purified full-length Dnmt1, we show that binding of methylated CpGs to this additional
      DNA binding site allosterically activates the enzyme.  These enzymological properties of Dnmt1
      can explain the phenomenon of spreading of DNA methylation.
AU  - Hermann A
AU  - Fatemi M
AU  - Jeltsch A
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 2000 28: A248.

PMID- 15526163
VI  - 61
DP  - 2004
TI  - Biochemistry and biology of mammalian DNA methyltransferases.
PG  - 2571-2587
AB  - DNA methylation is a stable but not irreversible epigenetic signal that silences gene
      expression. It has a variety of important functions in mammals, including control of gene
      expression, cellular differentiation and development, preservation of chromosomal integrity,
      parental imprinting and X-chromosome inactivation. In addition, it has been implicated in
      brain function and the development of the immune system. Somatic alterations in genomic
      methylation patterns contribute to the etiology of human cancers and ageing. It is tightly
      interwoven with the modification of histone tails and other epigenetic signals. Here we review
      our current understanding of the molecular enzymology of the mammalian DNA methyltransferases
      Dnmt1, Dnmt3a, Dnmt3b and Dnmt2 and the roles of the enzymes in the above-mentioned biological
      processes.
AU  - Hermann A
AU  - Gowher H
AU  - Jeltsch A
PT  - Journal Article
TA  - Cell. Mol. Life Sci.
JT  - Cell. Mol. Life Sci.
SO  - Cell. Mol. Life Sci. 2004 61: 2571-2587.

PMID- 15339928
VI  - 279
DP  - 2004
TI  - The Dnmt1 DNA-(cytosine-C5)-methyltransferase methylates DNA processively with high preference for hemimethylated target sites.
PG  - 48350-48359
AB  - In the cell Dnmt1 is the major enzyme to maintain the pattern of DNA methylation after DNA
      replication. Evidence suggests the protein is
      located at the replication fork where it could directly modify nascent DNA
      immediately after replication. To elucidate the potential mechanism of
      this process, we investigate the processivity of DNA methylation and
      accuracy of copying an existing pattern of methylation in this study using
      purified Dnmt1 and hemimethylated substrate DNA. We demonstrate that Dnmt1
      methylates a hemimethylated 958mer substrate in a highly processive
      reaction. Fully methylated and unmethylated CG sites do not inhibit
      processive methylation of the DNA. Extending previous work, we show that
      unmethylated sites embedded in a hemimethylated context are modified at an
      approx. 24-fold reduced rate which demonstrates that the enzyme accurately
      copies existing patterns of methylation. Completely unmodified DNA is
      methylated even more slowly due to an allosteric activation of Dnmt1 by
      methylcytosine-containing DNA. Interestingly, Dnmt1 is not able to
      methylate hemimethylated CG sites on different strands of the DNA in a
      processive manner indicating that Dnmt1 keeps its orientation with respect
      to the DNA while methylating the CG sites on one strand of the DNA.
AU  - Hermann A
AU  - Goyal R
AU  - Jeltsch A
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2004 279: 48350-48359.

PMID- 12765016
VI  - 34
DP  - 2003
TI  - Methylation sensitivity of restriction enzymes interacting with GATC sites.
PG  - 924-930
AB  - DNA methylation plays an important role in many species ranging from bacteria to man, by
      controlling the expression of genes and protection of the genome from selfish DNA like
      transposons and viruses.  In E. coli and other gamma-proteobacteria, methylation of adenine
      residues (dam, DNA adenine methylation) occurs at GATC sites.  It serves to discriminate
      between parental and daughter strand during post-replicative mismatch repair, to coordinate
      cell cycle, DNA replication, and to regulate gene expression.  It also controls the
      pathogenicity of different gamma-proteobacteria.  To investigate the methylation state of DNA
      from various bacteria, archaea as well as lower and higher eukaryotes, digestion of the DNA
      with GATC-interacting restriction enzymes is often used.
AU  - Hermann A
AU  - Jeltsch A
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 2003 34: 924-930.

PMID- 12794065
VI  - 278
DP  - 2003
TI  - The human Dnmt2 has residual DNA-(cytosine-C5)-methyltransferase activity.
PG  - 31717-31721
AB  - The human Dnmt2 protein is one member of a protein family conserved from Schizosaccharomyces
      pombe and Drosophila melanogaster to Mus musculus and
      Homo sapiens. It contains all of the amino acid motifs characteristic for
      DNA-(Cytosine-C5) methyltransferases, and its structure is very similar to
      prokaryotic DNA methyltransferases. Nevertheless, so far all attempts to
      detect catalytic activity of this protein have failed. We show here by two
      independent assay systems that the purified Dnmt2 protein has weak DNA
      methyltransferase activity. Methylation was observed at CG sites in a
      loose ttnCGga(g/a) consensus sequence, suggesting that Dnmt2 has a more
      specialized role than other mammalian DNA methyltransferases.
AU  - Hermann A
AU  - Schmitt S
AU  - Jeltsch A
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2003 278: 31717-31721.

PMID- 24625873
VI  - 2
DP  - 2014
TI  - Genome Sequences of Sequence Type 45 (ST45) Persistent Methicillin-Resistant Staphylococcus aureus (MRSA) Bacteremia Strain 300-169 and ST45 Resolving MRSA  Bacteremia Strain 301-188.
PG  - e00174-14
AB  - Persistent methicillin-resistant Staphylococcus aureus (MRSA) bacteremia (positive blood
      cultures after >/=7 days) represents a challenging subset of
      invasive MRSA infections. The comparison of genome sequences of persistent
      (300-169) and resolving (301-188) MRSA bacteremia isolates with similar genetic
      background (sequence type 45 [ST45]) will help us to better understand underlying
      mechanisms of persistent MRSA bacteremia.
AU  - Hernandez D
AU  - Seidl K
AU  - Corvaglia AR
AU  - Bayer AS
AU  - Xiong YQ
AU  - Francois P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00174-14.

PMID- 24072856
VI  - 1
DP  - 2013
TI  - Whole-Genome Sequences of Staphylococcus aureus ST398 Strains of Animal Origin.
PG  - e00689-13
AB  - Staphylococcus aureus sequence type 398 (ST398) was originally associated with animal
      infections. We announce the complete genome sequences of two ST398
      methicillin-susceptible S. aureus strains from the livestock environment. These
      genome sequences assist in the characterization of interesting ST398 features
      relying on host tropism and epidemiological settings.
AU  - Hernandez D
AU  - van der Mee-Marquet N
AU  - Kluytmans J
AU  - Donnio PY
AU  - Quentin R
AU  - Corvaglia AR
AU  - Francois P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00689-13.

PMID- 28473380
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence and Assembly of a Lysobacter enzymogenes Strain with Biological Control Activity against Root Knot Nematodes.
PG  - e00271-17
AB  - Lysobacter enzymogenes strain B25, an isolate from an agricultural field, acts as a biological
      control agent against root knot nematodes in tomato plants. B25 also
      controls several fungal diseases and promotes plant growth under abiotic stress.
      We hereby report on the draft genome sequence and assembly of B25.
AU  - Hernandez I
AU  - Fernandez C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00271-17.

PMID- 27417832
VI  - 4
DP  - 2016
TI  - Draft Whole-Genome Sequence of the Type Strain Bacillus aquimaris TF12T.
PG  - e00640-16
AB  - Bacillus aquimaris TF12 is a Gram-positive bacteria isolated from a tidal flat of the Yellow
      Sea in South Korea. We report the draft whole-genome sequence of
      Bacillus aquimaris TF12, the type strain of a set of bacteria typically
      associated with marine habitats and with a potentially high biotechnology value.
AU  - Hernandez-Gonzalez IL
AU  - Olmedo-Alvarez G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00640-16.

PMID- 27417833
VI  - 4
DP  - 2016
TI  - Draft Whole-Genome Sequence of the Type Strain Bacillus horikoshii DSM 8719.
PG  - e00641-16
AB  - Members of the Bacillus genus have been extensively studied because of their ability to
      produce enzymes with high biotechnological value. Here, we report the
      draft of the whole-genome sequence of the type strain Bacillus horikoshii DSM
      8719, an alkali-tolerant strain.
AU  - Hernandez-Gonzalez IL
AU  - Olmedo-Alvarez G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00641-16.

PMID- 27738045
VI  - 4
DP  - 2016
TI  - Genome Sequence of the Photoarsenotrophic Bacterium Ectothiorhodospira sp. Strain BSL-9, Isolated from a Hypersaline Alkaline Arsenic-Rich Extreme Environment.
PG  - e01139-16
AB  - The full genome sequence of Ectothiorhodospira sp. strain BSL-9 is reported here. This purple
      sulfur bacterium encodes an arxA-type arsenite oxidase within the
      arxB2AB1CD gene island and is capable of carrying out 'photoarsenotrophy'
      anoxygenic photosynthetic arsenite oxidation. Its genome is composed of 3.5 Mb
      and has approximately 63% G+C content.
AU  - Hernandez-Maldonado J
AU  - Stoneburner B
AU  - Boren A
AU  - Miller L
AU  - Rosen M
AU  - Oremland RS
AU  - Saltikov CW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01139-16.

PMID- 25540337
VI  - 2
DP  - 2014
TI  - A Newly Sequenced Alcaligenes faecalis Strain: Implications for Novel Temporal Symbiotic Relationships.
PG  - e01246-14
AB  - We report here the draft genome sequence of Alcaligenes faecalis strain MOR02, a  bacterium
      that is able to colonize nematodes in a temporary fashion and kill
      insects for their own benefit. The availability of the genome should enable us to
      explain these phenotypes.
AU  - Hernandez-Mendoza A
AU  - Lozano-Aguirre BLF
AU  - Martinez-Ocampo F
AU  - Quiroz-Castaneda RE
AU  - Dantan-Gonzalez E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01246-14.

PMID- 25523778
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Organophosphorus Compound-Degrading Burkholderia zhejiangensis Strain CEIB S4-3.
PG  - e01323-14
AB  - Burkholderia species are widely distributed in the environment. A Burkholderia zhejiangensis
      strain was isolated from pesticide-contaminated soil from an
      agricultural field in Mexico and identified as an organophosphorus
      compound-degrading bacterium. In this study, we report the draft genome sequence
      of Burkholderia zhejiangensis strain CEIB S4-3.
AU  - Hernandez-Mendoza A
AU  - Martinez-Ocampo F
AU  - Lozano-Aguirre BLF
AU  - Popoca-Ursino EC
AU  - Ortiz-Hernandez L
AU  - Sanchez-Salinas E
AU  - Dantan-Gonzalez E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01323-14.

PMID- 26767092
VI  - 11
DP  - 2016
TI  - Draft Genome Sequence of the Biocontrol and Plant Growth-Promoting Rhizobacterium Pseudomonas fluorescens strain UM270.
PG  - 5
AB  - The Pseudomonas fluorescens strain UM270 was isolated form the rhizosphere of wild Medicago
      spp. A previous work has shown that this pseudomonad isolate was
      able to produce diverse diffusible and volatile compounds involved in plant
      protection and growth promotion. Here, we present the draft genome sequence of
      the rhizobacterium P. fluorescens strain UM270. The sequence covers 6,047,974 bp
      of a single chromosome, with 62.66 % G + C content and no plasmids. Genome
      annotations predicted 5,509 genes, 5,396 coding genes, 59 RNA genes and 110
      pseudogenes. Genome sequence analysis revealed the presence of genes involved in
      biological control and plant-growth promoting activities. We anticipate that the
      P. fluorescens strain UM270 genome will contribute insights about bacterial plant
      protection and beneficial properties through genomic comparisons among
      fluorescent pseudomonads.
AU  - Hernandez-Salmeron JE
AU  - Hernandez-Leon R
AU  - Orozco-Mosqueda MC
AU  - Valencia-Cantero E
AU  - Moreno-Hagelsieb G
AU  - Santoyo G
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 5.

PMID- 27284157
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Lysinibacillus sphaericus WHO Reference Strain 2362.
PG  - e00545-16
AB  - Lysinibacillus sphaericus is a species that contains strains widely used in the biological
      control of mosquitoes. Here, we present the complete 4.67-Mb genome of
      the WHO entomopathogenic reference strain L. sphaericus 2362, which is probably
      one of the most commercialized and studied strains. Genes coding for
      mosquitocidal toxin proteins were detected.
AU  - Hernandez-Santana A
AU  - Gomez-Garzon C
AU  - Dussan J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00545-16.

PMID- 29146853
VI  - 5
DP  - 2017
TI  - Genome Sequences of Four Subcluster L2 Mycobacterium Phages, Finemlucis, Miley16, Wilder, and Zakai.
PG  - e01233-17
AB  - Four subcluster L2 mycobacteriophages, Finemlucis, Miley16, Wilder, and Zakai, that infect
      Mycobacterium smegmatis mc(2)155 were isolated. The four phages are
      closely related to each other and code for 12 to 14 tRNAs and 130 to 132 putative
      protein-coding genes, including tyrosine integrases, cro, immunity repressors,
      and excise genes involved in the establishment of lysogeny.
AU  - Herren CD et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01233-17.

PMID- 2250018
VI  - 265
DP  - 1990
TI  - RNA splicing in Chlamydomonas chloroplasts.
PG  - 21134-21140
AB  - The 23 rRNA gene of the Chlamydomonas reinhardtii chloroplast contains an 888-base pair intron
      with structural features characteristic of Group I introns. The nuclear, chloroplast
      ribosome-deficient mutant of C. reinhardtii, ac20, overaccumulates an approx. 3.6-kilobase
      unspliced 23 S preRNA compared to wild-type cells. We have used [a-32P]GTP labeling of total
      RNA preparations from ac20 to rapidly determine that 23 S preRNA is capable of self-splicing.
      The ability of the 23 S intron (with flanking exon sequences) to correctly catalyze its own
      splicing was confirmed using RNA produced by in vitro transcription of cloned DNA. These
      results identify the first example of a self-splicing RNA of chloroplast origin.
AU  - Herrin DL
AU  - Chen Y-F
AU  - Schmidt GW
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1990 265: 21134-21140.

PMID- 27034479
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Two Kocuria Isolates, K. salsicia G1 and K. rhizophila  G2, Isolated from a Slaughterhouse in Denmark.
PG  - e00075-16
AB  - We report here the draft genome sequences ofKocuria salsiciaG1 andKocuria rhizophilaG2, which
      were isolated from a meat chopper at a small slaughterhouse
      in Denmark. The two annotated genomes are 2.99 Mb and 2.88 Mb in size,
      respectively.
AU  - Herschend J
AU  - Raghupathi PK
AU  - Roder HL
AU  - Sorensen SJ
AU  - Burmolle M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00075-16.

PMID- 27034478
VI  - 4
DP  - 2016
TI  - Genome Sequence of Kocuria palustris Strain W4.
PG  - e00074-16
AB  - We report the 3.09 Mb draft genome sequence ofKocuria palustrisW4, isolated from  a
      slaughterhouse in Denmark.
AU  - Herschend J
AU  - Raghupathi PK
AU  - Roder HL
AU  - Sorensen SJ
AU  - Burmolle M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00074-16.

PMID- 27034477
VI  - 4
DP  - 2016
TI  - Genome Sequence of Arthrobacter antarcticus Strain W2, Isolated from a Slaughterhouse.
PG  - e00073-16
AB  - We report the draft genome sequence ofArthrobacter antarcticusstrain W2, which was isolated
      from a wall of a small slaughterhouse in Denmark. The 4.43-Mb genome
      sequence was assembled into 170 contigs.
AU  - Herschend J
AU  - Raghupathi PK
AU  - Roder HL
AU  - Sorensen SJ
AU  - Burmolle M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00073-16.

PMID- 27609927
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the Xanthomonas bromi Type Strain LMG 947.
PG  - e00961-16
AB  - Here, we report the draft genome sequence of the Xanthomonas bromi type strain LMG 947, an
      important pathogen of bromegrasses (Bromus spp.). Comparative
      analysis with other Xanthomonas spp. that are pathogenic on forage grasses will
      assist the analysis of host-plant adaptation at the genome level.
AU  - Hersemann L
AU  - Wibberg D
AU  - Blom J
AU  - Widmer F
AU  - Kolliker R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00961-16.

PMID- 27536340
VI  - 11
DP  - 2016
TI  - Draft genome sequences of three Xanthomonas translucens pathovar reference strains (pv. arrhenatheri, pv. poae and pv. phlei) with different specificities  for forage grasses.
PG  - 50
AB  - As causal agents of bacterial wilt in pastures and meadows, bacteria of the species
      Xanthomonas translucens are a serious issue in forage grass production.
      So far, only little is known about host-pathogen interactions at the molecular
      level and the lack of comprehensive genome data impeded targeted breeding
      strategies towards resistant forage grass cultivars. Here we announce the draft
      genome sequences of three grass-pathogenic Xanthomonas translucens pathotype
      strains, i.e. pv. arrhenatheri LMG 727, pv. poae LMG 728 and pv. phlei LMG 730
      isolated from Arrhenatherum elatius (L.) P. Beauv. ex J. Presl & C. Presl
      (Switzerland), Poa trivialis L. (Switzerland) and Phleum pratense L. (Norway),
      respectively. The genomes of all three strains revealed a non-canonical type III
      secretion system and a set of 22 type III effectors as common virulence-related
      traits. Distinct inter-pathovar differences were observed for the
      lipopolysaccharide biosynthesis gene cluster and the presence of nonribosomal
      peptide synthetases.
AU  - Hersemann L
AU  - Wibberg D
AU  - Widmer F
AU  - Vorholter FJ
AU  - Kolliker R
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 50.

PMID- 12899832
VI  - 331
DP  - 2003
TI  - Sequence analysis of the genome of the temperate Yersinia enterocolitica phage PY54.
PG  - 605-622
AB  - The temperate Yersinia phage PY54 belongs to the unusual group of phages that replicate as
      linear plasmids with covalently closed ends. Besides
      Escherichia coli phage N15, PY54 is the only member of this group to be
      identified. We have determined the complete sequence (46,339 bp) of the
      PY54 genome. Bioinformatic analyses revealed 67 open reading frames (ORFs)
      with good coding potential located on both DNA strands. The comparison of
      the deduced PY54 gene products with known proteins encoded by other phages
      and bacteria along with functional studies have enabled us to assign the
      possible functions of 25 ORFs. In the left arm of the PY54 genome, we
      identified a number of ORFs that obviously code for head and tail
      proteins. Furthermore, this part of the phage genome contains genes
      probably involved in plasmid partitioning. Regarding the predicted gene
      functions and gene order, the PY54 and N15 left arms are similar. However,
      there are only weak DNA homologies and, in contrast to N15, the Yersinia
      phage harbours only a few ORFs related to genes found in lambdoid phages.
      The PY54 right arm comprises mainly regulatory genes as well as genes
      important for plasmid replication, DNA methylation, and host cell lysis.
      Out of 36 deduced products of the right arm, 13 revealed strongest
      database homologies to N15 proteins, of which the protelomerase and the
      Rep protein are exclusively homologous to their N15 counterparts. A number
      of PY54 genes essential for the lytic or lysogenic cycle were identified
      by functional analysis and characterization of phage mutants. In order to
      study transcription during the lytic and lysogenic stage, we analysed 34
      PY54 ORFs by reverse transcriptase (RT)-PCR. The phage transcription
      patterns in lysogenic bacteria and at the late lytic stage of infection
      are nearly identical. The reasons for this finding are spontaneous release
      of phages during lysogeny and a high rate of phages that lysogenize their
      Yersinia host upon infection.
AU  - Hertwig S
AU  - Klein I
AU  - Schmidt V
AU  - Beck S
AU  - Hammerl JA
AU  - Appel B
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2003 331: 605-622.

PMID- 9873067
VI  - 4
DP  - 1998
TI  - Protection of a restriction enzyme from heat inactivation by alpha-crystallin.
PG  - 29-32
AB  - To determine whether the chaperone activity of human alpha-crystallin can protect a
      restriction enzyme from heat inactivation.  The restriction enzyme NdeI was heated in the
      presence or absence of purified bovine alpha-crystallin.  Following heat treatment, the
      enzymatic activity of the heat treated samples was assayed by cleavage of plasmid DNA.  The
      extent of digestion was monitored by agarose gel electrophoresis and visualization of DNA
      fragments by ethidium bromide staining.  Heating of NdeI in the absence of alpha-crystallin
      resulted in inactivation.  However, NdeI heated in the presence of alpha-crystallin remained
      active.  Furthermore, an increased amount of alpha-crystallin provided a longer period of
      thermal protection.  The chaperone activity and thermo-protective effect of alpha-crystallin
      extend to protection of enzymatic activity, not merely the protection from thermally induced
      aggregation/denaturation.  In addition, inclusion of alpha-crystallin during some enzymatic
      reactions may be beneficial.
AU  - Hess JF
AU  - FitzGerald PG
PT  - Journal Article
TA  - Mol. Vis.
JT  - Mol. Vis.
SO  - Mol. Vis. 1998 4: 29-32.

PMID- 19055690
VI  - 11
DP  - 2009
TI  - Spreading antibiotic resistance through spread manure: characteristics of a novel plasmid type with low %G+C content.
PG  - 937-949
AB  - Bioactive amounts of antibiotics as well as resistant bacteria reach the
      soil through manure fertilization. We investigated plasmids that may
      stimulate the environmental spread and interspecies transfer of antibiotic
      resistance. After treatment of two soils with manure, either with or
      without the sulfonamide antibiotic sulfadiazine, a significant increase in
      copies of the sulfonamide resistance gene sul2 was detected by qPCR. All
      sul2 carrying plasmids, captured in Escherichia coli from soil, belonged
      to a novel class of self-transferable replicons. Manuring and sulfadiazine
      significantly increased the abundance of this replicon type in a
      chemically fertilized but not in an annually manured soil, as determined
      by qPCR targeting a transfer gene. Restriction patterns and antibiograms
      showed a considerable diversity within this novel plasmid group. Analysis
      of three complete plasmid sequences revealed a conserved 30 kbp backbone
      with only 36% G+C content, comprised of transfer and maintenance genes
      with moderate homology to plasmid pIPO2 and a replication module (rep and
      oriV) of other descent. The plasmids differed in composition of the
      27.0-28.3 kbp accessory region, each of which carried ISCR2 and several
      resistance genes. Acinetobacter spp. was identified as a potential host of
      such LowGC-type plasmids in manure and soil.
AU  - Heuer H
AU  - Kopmann C
AU  - Binh CT
AU  - Top EM
AU  - Smalla K
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2009 11: 937-949.

PMID- 15528648
VI  - 150
DP  - 2004
TI  - The complete sequences of plasmids pB2 and pB3 provide evidence for a recent ancestor of the IncP-1{beta} group without any accessory genes.
PG  - 3591-3599
AB  - The nucleotide sequences of the broad-host-range antibiotic resistance
      plasmids pB2 (61 kb) and pB3 (56 kb), which were isolated from a
      wastewater treatment plant, were determined and analysed. Both have a
      nearly identical IncP-1beta backbone, which diverged early from the
      sequenced IncP-1beta plasmids R751, pB10, pJP4, pADP1 and pUO1. In
      contrast to the latter plasmids, the pB2 and pB3 backbone does not seem to
      have undergone any deletions. The complete partition gene parA is located
      downstream of the mating pair formation (trb) module. A 14.4 kb or 19.0 kb
      mobile genetic element is present between traC and parA of pB3 and pB2,
      respectively. This region is typical for insertions in IncP-1beta
      plasmids, but the insertion site is unique. Both elements differ only by a
      duplication in pB2 of a tetA(C)-tetR-tnpA(IS26) fragment. The 5 bp target
      site duplication and the 26 bp inverted repeats flanking the mobile
      genetic elements are still intact, indicating that the insertion occurred
      recently. The element consists of three nested transposable elements: (i)
      a relict of a Tn402-like transposon with a gene for a new class D
      beta-lactamase (bla(NPS-2)); (ii) within that, another Tn402-like element
      with a class 1 integron harbouring the gene cassettes cmlA1 for a
      chloramphenicol efflux protein and aadA2 encoding a
      streptomycin/spectinomycin adenylyltransferase, and a copy of IS6100;
      (iii) into the integrase gene intI1 a tetracycline resistance module
      tetA(C)-tetR flanked by copies of IS26 is inserted. Interestingly, in
      contrast to all other IncP-1beta plasmids analysed so far, the oriV region
      between trfA and klcA is not interrupted by accessory genes, and there is
      no indication that previously inserted accessory genes have subsequently
      been deleted. The genes kluAB are also missing in that region and should
      thus be considered acquired genes. These findings, together with the fact
      that IncP-1beta plasmids acquired accessory elements at various positions
      in the backbone, suggest that IncP-1beta plasmids without any accessory
      genes exist in microbial communities. They must occasionally acquire
      accessory genes by transposition events, resulting in those plasmids that
      have been found based on selectable phenotypic traits.
AU  - Heuer H
AU  - Szczepanowski R
AU  - Schneiker S
AU  - Puhler A
AU  - Top EM
AU  - Schluter A
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2004 150: 3591-3599.

PMID- 9563837
VI  - 257
DP  - 1998
TI  - A stable shuttle vector system for efficient genetic complementation of Helicobacter pylori strains by transformation and conjugation.
PG  - 519-528
AB  - A versatile plasmid shuttle vector system was constructed, which is useful for genetic
      complementation of Helicobacter pylori strains or mutants with cloned genes of homologous or
      heterologous origin.  The individual plasmid vectors consist of the minimal essential genetic
      elements, including an origin of replication for Escherichia coli, a H. pylori-specific
      replicon originally identified on a small cryptic H. pylori plasmid, an oriT sequence and a
      multiple cloning site.  Shuttle plasmid pHel2 carries a chloramphenicol resistance cassette
      (catGC) and pHel3 contains a kanamycin resistance gene (aphA-3) as the selectable marker; both
      are functional in E. coli and H. pylori.  The shuttle plasmids were introduced into the H.
      pylori strain P1 by natural transformation.  An efficiency of 7.0 x 10^-7 and 4.7 x 10^-7
      transformants per viable recipient was achieved with pHel2 and pHel3, respectively, and both
      vectors showed stable, autonomous replication of H. pylori.  An approximately 100-fold higher
      H. pylori transformation rate was obtained when the shuttle vectors for transformation were
      isolated from the homologous H. pylori strain, rather than E. coli, indicating that DNA
      restriction and modification mechanisms play a crucial role in plasmid transformation.
      Interestingly, both shuttle vectors could also be mobilized efficiently from E. coli into
      different H. pylori recipients, with pHel2 showing an efficiency of 2.0 x 10^-5
      transconjugants per viable H. pylori P1 recipient.  Thus, DNA restriction seems to be strongly
      reduced or absent during conjugal transfer.  The functional complementation of a
      recA-deficient H. pylori mutant by the cloned H. pylori recA+ gene, and the expression of the
      heterologous green fluorescent protein in H. pylori demonstrate the general usefulness of this
      system, which will significantly facilitate the molecular analysis of H. pylori virulence
      factors in the future.
AU  - Heuermann D
AU  - Haas R
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1998 257: 519-528.

PMID- 44239
VI  - 88
DP  - 1979
TI  - Rhizobium lupini genetics.
PG  - 1-24
AB  - The purpose of this article is to review a genetic system that differs in many
      aspects to the well-known Escherichia coli system.  It is not the aim of the
      author to deal directly with the complex issues of Rhizobium symbiosis with
      Legumes nor with the problem of symbiotic nitrogen fixation by the Rhizobia.
      However, genetical investigations of the rhizobial strains involved may
      contribute to some understanding of the genetics of this complex system of
      symbiotic nitrogen fixation.  The mutants used in this study were obtained by
      mutagenesis of Rhizobium lupini strains isolated directly from Lupinus luteus
      root nodules in 1960.  These strains lost certain characteristics of the
      wild-type Rhizobium, especially its capacity to nodulate Lupins.  They are,
      however, characterized by high conjugational fertility, a prerequisite for the
      investigation of their genetics, by star formation, a recognition mechanism;
      and also by their bright yellow colony pigmentation.  This pigmentation arises
      from carotenoids localized in the plasma membrane of the cells which protect
      the cell's cytochromes from photoinactivation.  These three characteristics,
      conjugation, star formation, and carotenoid pigmentation, proved very useful
      for genetic investigation of these Rhizobium mutants.
AU  - Heumann W
PT  - Journal Article
TA  - Curr. Top. Microbiol. Immunol.
JT  - Curr. Top. Microbiol. Immunol.
SO  - Curr. Top. Microbiol. Immunol. 1979 88: 1-24.

PMID- 11847124
VI  - 21
DP  - 2002
TI  - The hemK gene in Escherichia coli encodes the N5-glutamine methyltransferase that modifies peptide release factors.
PG  - 769-778
AB  - Class 1 peptide release factors (RFs) in Escherichia coli are N5-methylated on the glutamine
      residue of the universally conserved GGQ motif. One other protein alone has been shown to
      contain N5-methylglutamine: E.coli ribosomal protein L3. We identify the L3 methyltransferase
      as YfcB and show that it methylates ribosomes from a yfcB strain in vitro, but not RF1 or RF2.
      HemK, a close orthologue of YfcB, is shown to methylate RF1 and RF2 in vitro. hemK is
      immediately downstream of and co-expressed with prfA. Its deletion in E.coli K12 leads to very
      poor growth on rich media and abolishes methylation of RF1. The activity of unmethylated RF2
      from K12 strains is extremely low due to the cumulative effects of threonine at position 246,
      in place of alanine or serine present in all other bacterial RFs, and the lack of
      N5-methylation of Gln252. Fast-growing spontaneous revertants in hemK K12 strains contain the
      mutations Thr246Ala or Thr246Ser in RF2. HemK and YfcB are the first identified
      methyltransferases modifying glutamine, and are widely distributed in nature.
AU  - Heurgue-Hamard V
AU  - Champ S
AU  - Engstrom A
AU  - Ehrenberg M
AU  - Buckingham RH
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 2002 21: 769-778.

PMID- 17126598
VI  - 297
DP  - 2007
TI  - DNA adenine methylation and bacterial pathogenesis.
PG  - 1-7
AB  - Methylation of DNA by the DNA adenine methyltransferase (Dam) provides an epigenetic signal
      that influences and regulates numerous physiological processes in the bacterial cell including
      chromosome replication, mismatch repair, transposition, and transcription. A growing number of
      reports describe a role for DNA adenine methylation in regulating the expression of various
      bacterial genes related to virulence in diverse pathogens, suggesting that DNA methylation may
      be a widespread and versatile regulator of virulence gene expression. Here, we summarize the
      current knowledge about the influence of DNA methylation on virulence functions and discuss
      perspectives for future research.
AU  - Heusipp G
AU  - Falker S
AU  - Schmidt MA
PT  - Journal Article
TA  - Int. J. Med. Microbiol.
JT  - Int. J. Med. Microbiol.
SO  - Int. J. Med. Microbiol. 2007 297: 1-7.

PMID- 27491982
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Eight Obligate Methane Oxidizers Occupying Distinct Niches Based on Their Nitrogen Metabolism.
PG  - e00421-16
AB  - The genome sequences of Methylomonas methanica (NCIMB 11130(T), R-45363, and R-45371),
      Methylomonas koyamae (R-45378, R-45383, and R-49807), Methylomonas
      lenta (R-45370), and Methylosinus sp. (R-45379) were obtained. These aerobic
      methanotrophs were isolated from terrestrial ecosystems, and their distinct
      phenotypes related to nitrogen assimilation and dissimilation were previously
      reported.
AU  - Heylen K
AU  - De Vos P
AU  - Vekeman B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00421-16.

PMID- 12710619
VI  - 53
DP  - 2003
TI  - Virgibacillus carmonensis sp. nov., Virgibacillus necropolis sp. nov. and Virgibacillus picturae sp. nov.
PG  - 501-511
AB  - A group of 13 strains was isolated from samples of biofilm formation on the mural
      paintings of the Servilia tomb (necropolis of Carmona, Spain) and the
      Saint-Catherine chapel (castle at Herberstein, Austria). The strains were
      subjected to a polyphasic taxonomic study, including (GTG)5-PCR, 16S rDNA
      sequence analysis, DNA-DNA hybridizations, DNA base ratio determination, analysis
      of fatty acids, polar lipids and menaquinones and morphological and biochemical
      characterization. In a phylogenetic tree based on neighbour-joining of 16S rDNA
      sequences, the strains are divided in two major groups, representing three novel
      species according to DNA-DNA relatedness, that are positioned at approximately
      equal distances from Virgibacillus and Salibacillus. After comparison of the
      novel results with existing data, the transfer of the species of Salibacillus to
      Virgibacillus is proposed, with the resulting new combinations Virgibacillus
      marismortui comb. nov. and Virgibacillus salexigens comb. nov. Additionally,
      three novel species are described, for which the names Virgibacillus carmonensis
      sp. nov., Virgibacillus necropolis sp. nov. and Virgibacillus picturae sp. nov.
      are proposed. The respective type strains are LMG 20964T (=DSM 14868T), LMG
      19488T (=DSM 14866T) and LMG 19492T (= DSM 14867T). Finally, an emended
      description of the genus Virgibacillus is given.
AU  - Heyrman J
AU  - Logan NA
AU  - Busse HJ
AU  - Balcaen A
AU  - Lebbe L
AU  - Rodriguez-Diaz M
AU  - Swings J
AU  - De Vos P
PT  - Journal Article
TA  - Int. J. Syst. Evol. Microbiol.
JT  - Int. J. Syst. Evol. Microbiol.
SO  - Int. J. Syst. Evol. Microbiol. 2003 53: 501-511.

PMID- 10911996
VI  - 5
DP  - 2000
TI  - Unexpected structural diversity in DNA recombination: the restriction endonuclease connection.
PG  - 1025-1034
AB  - Transposition requires a coordinated series of DNA breakage and joining reactions. The Tn7
      transposase contains two proteins: TnsA, which carries out DNA breakage at the 5' ends of the
      transposon, and TnsB, which carries out breakage and joining at the 3' ends of the
      transposon. TnsB is a member of the retroviral integrase superfamily whose hallmark is a
      conserved DDE motif. We report here the structure of TnsA at 2.4 A resolution. Surprisingly,
      the TnsA fold is that of a type II restriction endonuclease. Thus, Tn7 transposition involves
      a collaboration between polypeptides, one containing a DDE motif and one that does not. This
      result indicates that the range of biological processes that utilize restriction enzyme-like
      folds also includes DNA transposition.
AU  - Hickman AB
AU  - Li Y
AU  - Mathew SV
AU  - May EW
AU  - Craig NL
AU  - Dyda F
PT  - Journal Article
TA  - Mol. Cell
JT  - Mol. Cell
SO  - Mol. Cell 2000 5: 1025-1034.

PMID- 16846234
VI  - 45
DP  - 2006
TI  - Restriction enzyme kinetics monitored by UV linear dichroism.
PG  - 8912-8917
AB  - The use of linear dichroism (LD) spectroscopy for biological applications has been brought to
      the forefront recently by our
      development of thermostated microvolume Couette cells. We present a
      method for following the digestion of DNA by restriction endonucleases
      in real time without the use of any extrinsic dyes or labels. This is
      accomplished using linear dichroism spectroscopy (the differential
      absorbance of light polarized parallel and perpendicular to the sample
      orientation axis). The differential absorbance signal depends on the
      degree of alignment of the molecules. In this case the DNA is aligned
      by Couette flow (flowing the solution in the annular gap between two
      concentric cylinders), and we monitor the increase in alignment upon
      linearization of a circular DNA molecule. In addition, we observe a
      decrease in alignment upon further digestion and subsequent shortening
      of the DNA. Ten enzymes were investigated: seven enzymes with a single
      cut site (EcoRI, KpnI, NdeI, NotI, NruI, SmaI, XbaI), two enzymes with
      two cut sites (BstZ17I, EagI), and one enzyme with no cut site (ClaI).
      LD, as implemented in this new assay, is broadly applicable across a
      wide range of DNA-modifying enzymes and compounds and, as such, is a
      useful addition to the toolbox of biological characterization.
AU  - Hicks MR
AU  - Rodger A
AU  - Thomas CM
AU  - Batt SM
AU  - Dafforn TR
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2006 45: 8912-8917.

PMID- 21688832
VI  - 22
DP  - 2011
TI  - Restriction Endonuclease SsoII with Photoregulated Activity: A 'Molecular Gate' Approach.
PG  - 1366-1373
AB  - A novel method for regulating the activity of homodimeric
      proteins-"molecular gate" approach-was proposed and its usefulness illustrated for the type II
      restriction endonuclease SsoII (R.SsoII) as a model. The "molecular gate" approach is based on
      the modification of R.SsoII with azobenzene derivatives, which allows regulating DNA binding
      and cleavage via illumination with light. R. SsoII variants with single cysteine residues
      introduced at selected positions were obtained and modified with maleimidoazobenzene
      derivatives. A twofold change in the enzymatic activity after illumination with light of
      wavelengths of 365 and 470 nm, respectively,
      was demonstrated when one or two molecules of azobenzene derivatives were attached to the
      R.SsoII at the entrance of or within the DNA-binding site.
AU  - Hien L-T
AU  - Zatsepin TS
AU  - Schierling B
AU  - Volkov EM
AU  - Wende W
AU  - Pingoud A
AU  - Kubareva EA
AU  - Oretskaya TS
PT  - Journal Article
TA  - Bioconjugate Chem.
JT  - Bioconjugate Chem.
SO  - Bioconjugate Chem. 2011 22: 1366-1373.

PMID- 22327575
VI  - 78
DP  - 2012
TI  - Involvement of Two Latex-Clearing Proteins during Rubber Degradation and Insights into the Subsequent Degradation Pathway Revealed by the Genome Sequence of Gordonia polyisoprenivorans Strain VH2.
PG  - 2874-2887
AB  - The increasing production of synthetic and natural poly(cis-1,4-isoprene) rubber
      leads to huge challenges in waste management. Only a few bacteria are known to
      degrade rubber, and little is known about the mechanism of microbial rubber
      degradation. The genome of Gordonia polyisoprenivorans strain VH2, which is one
      of the most effective rubber-degrading bacteria, was sequenced and annotated to
      elucidate the degradation pathway and other features of this actinomycete. The
      genome consists of a circular chromosome of 5,669,805 bp and a circular plasmid
      of 174,494 bp with average GC contents of 67.0% and 65.7%, respectively. It
      contains 5,110 putative protein-coding sequences, including many candidate genes
      responsible for rubber degradation and other biotechnically relevant pathways.
      Furthermore, we detected two homologues of a latex-clearing protein, which is
      supposed to be a key enzyme in rubber degradation. The deletion of these two
      genes for the first time revealed clear evidence that latex-clearing protein is
      essential for the microbial utilization of rubber. Based on the genome sequence,
      we predict a pathway for the microbial degradation of rubber which is supported
      by previous and current data on transposon mutagenesis, deletion mutants, applied
      comparative genomics, and literature search.
AU  - Hiessl S
AU  - Schuldes J
AU  - Thurmer A
AU  - Halbsguth T
AU  - Broker D
AU  - Angelov A
AU  - Liebl W
AU  - Daniel R
AU  - Steinbuchel A
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2012 78: 2874-2887.

PMID- Not carried by PubMed...
VI  - 94
DP  - 1994
TI  - Isolation of a putative retriction/modification system from Campylobacter jejuni.
PG  - 224
AB  - Molecular studies of the Campylobacter jejuni genome can often prove difficult; one reason is

      that C. jejuni genomic DNA can be digested with only a small number of restriction

      endonucleases. Our goal was to isolate, characterize, and eventually disrupt a

      restriction/modification system in C. jejuni so that future genetic manipulation might prove

      easier.

      

      A lambda-zapII library was constructed using C. jejuni A74/O genomic DNA. The library was

      then transfected simultaneously with XL-1 blue and XL-1 Blue/pAN4, a plasmid containing the

      EcoRI loci in pBR322. Primary plaques were counted and compared from both transfection

      conditions; the number of plaques on XL-1 Blue were significantly higher than those on XL-1

      Blue/pAN4. Forty-two primary plaques were then picked from the XL-1 Blue/pAN4 lysates and

      again transfected using both XL-1 Blue and XL-1Blue/pAN4 lysates and again transfected using

      both XL-1 Blue and XL-1 Blue/pAN4. Primary plaques that gave similar lysate numbers when

      transfected into both E. coli were chosen on the hypothesis that they carried a C. jejuni

      restriction/modification system. Six of these secondary plaques were transfected into XL-1

      Blue for phage DNA isolation; isolated DNA was digested using a series of six restriction

      endonucleases. Only one of the six enzymes chosen allowed digestion of the phage DNA's.

      Future studies will include further characterization of the C. jejuni inserts to determine if

      a restriction/modification system is present.

      

AU  - Hiett K
AU  - Meinersmann R
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1994 94: 224.

PMID- 18362191
VI  - 52
DP  - 2008
TI  - Methicillin-resistant Staphylococcus saprophyticus Carrying Staphylococcal Cassette Chromosome mec (SCCmec) Have Emerged in Urogenital Tract  Infections.
PG  - 2061-2068
AB  - Staphylococcus saprophyticus is a uropathogenic bacterium that causes acute uncomplicated
      urinary tract infections (UTIs), particularly in
      female outpatients. We investigated the dissemination and antimicrobial
      susceptibility of 101 S. saprophyticus isolates from the genitourinary
      tracts of patients in Japan. Eight of these isolates were mecA-positive
      and showed beta-lactam resistance. Pulsed field gel electrophoresis (PFGE)
      showed that only some isolates were isogenic, indicating that the mecA
      gene was apparently acquired independently by mecA-positive isolates
      through staphylococcal cassette chromosome mec (SCCmec). Type
      determination of SCCmec by multiplex PCR showed non-typeable element in
      the 8 mecA-positive isolates. Sequence analysis of the entire SCCmec
      element from a prototype S. saprophyticus strain revealed that it is
      non-typeable with the current SCCmec classification due to the novel
      composition of the class A mec gene complex (IS431-mecA-mecR1-mecI genes)
      and the ccrA1/ccrB3 gene complex. Intriguingly, the attachment sites of
      SCCmec are similar to those of type I SCCmec in S. aureus NCTC 10442.
      Further, the genes around the mec gene complex are similar to those of
      type II/III SCCmec in S. aureus, while those around the ccr gene complex
      are similar to those of SCC15305RM found in S. saprophyticus ATCC 15305.
      In comparison with known SCCmec elements, this S. saprophyticus SCCmec is
      a novel type.
AU  - Higashide M
AU  - Kuroda M
AU  - Omura CT
AU  - Kumano M
AU  - Ohkawa S
AU  - Ichimura S
AU  - Ohta T
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2008 52: 2061-2068.

PMID- 26564045
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Desulfatitalea tepidiphila S28bFT.
PG  - e01326-15
AB  - Desulfatitalea tepidiphila S28bF(T) is a sulfate-reducing bacterium closely related to
      Desulfosarcina species. Here, the draft genome sequence of strain
      S28bF(T) is reported.
AU  - Higashioka Y
AU  - Kojima H
AU  - Watanabe T
AU  - Fukui M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01326-15.

PMID- Not carried by PubMed...
VI  - 87
DP  - 1987
TI  - Characterization of a cointegrate conjugal plasmid encoding phage restriction and modification activities in lactic streptococci.
PG  - 154
AB  - The conjugal plasmid pTN1060 (Tra+) encodes lactose-fermenting ability (Lac+),
      resistance to nisin (Nisr), and restriction and modification activities (R/M+)
      against phages of lactic streptococci.  Physical characterization of pTN1060
      revealed the plasmid was a cointegrate formed from pTR1040 (Lac+, Nisr) and a
      30 kb fragment that conferred Tra+ and R/M+ functions.  To identify the origin
      of the 30kb fragment, exconjugants from S. lactis N1 were characterized for
      Tra+ and R/M+ activities.  Exconjugants harboring either 60 Md pTN1060-like
      plasmids, or pTR1040 in combination with a 30 kb plasmid (pTN20) exhibited
      Lac+, Nisr, R/M+ and Tra+.  Phenotypic analysis, curing studies, and genetic
      transfer experiments with derivatives harboring pTN20 demonstrated a direct
      correlation of pTN20 with R/M+ activities and conjugal transfer ability.  pTN20
      probes hybridized with pTN1060 but not with pTR1040.  Restriction mapping
      further confirmed that pTN20 fragments were present in pTN1060.  The data
      demonstrated that pTN1060 was a cointegrate plasmid comprised of pTR1040 and
      pTN20.
AU  - Higgins DL
AU  - Sanozky-Dawes R
AU  - Klaenhammer TR
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1987 87: 154.

PMID- 2841286
VI  - 170
DP  - 1988
TI  - Restriction and modification activities from Streptococcus lactis ME2 are encoded by a self-transmissible plasmid, pTN20, that forms cointegrates during mobilization of lactose-fermenting ability.
PG  - 3435-3442
AB  - A self-transmissible (Tra+) plasmid encoding determinants for restriction and
      modification activities (R+/M+) from Streptococcus lactis ME2 was isolated and
      characterized.  The 28-kilobase (kb) plasmid (pTN20) was detected in
      lactose-fermenting (Lac+) transconjugants generated from matings between S.
      lactis N1, an ME2 variant, and a plasmid-free recipient, S. lactis LM2301.  The
      plaquing efficiencies of prolate- and small isometric-headed phages were
      reduced on transconjugants containing either pTN20 (R+/M+ Tra+) or 100-kb
      plasmids encoding Lac+, R+/M+, and Tra+.  Lac+ transconjugants which harbored
      pTR1040 (Lac+) and pTN20 (R+/M+) were phenotypically R-/M- and transferred Lac+
      at low frequency in subsequent matings to give rise to 100-kb R+/M+ plasmids.
      R+/M+ activities and high-frequency conjugal transfer ability were detected in
      Lac+ transconjugants that contained pTR1041 (Lac+) and pTN20 (R+/M+).  No
      100-kb R+/M+ plasmids were recovered after these matings, suggesting that
      pTR1041 was mobilized by pTN20 through a process that resembled plasmid
      donation.  pTR1041 was identical to pTR1040 but contained an additional 3.3-kb
      DNA fragment.  These data suggested that phenotypic expression of R+/M+ and
      Tra+ is affected by coresident Lac+ plasmids.  Restriction enzyme analysis and
      hybridization reactions demonstrated that the 100-kb R+/M+ plasmid was formed
      by a cointegration event between pTR1040 (Lac+) and pTN20 (R+/M+Tra+) during
      conjugal transfer via a conductive-type process.  This is the first report that
      defines self-transmissible restriction and modification plasmids in the lactic
      streptococci.
AU  - Higgins DL
AU  - Sanozky-Dawes RB
AU  - Klaenhammer TR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1988 170: 3435-3442.

PMID- 11410656
VI  - 29
DP  - 2001
TI  - The nicking endonuclease N.BstNBI is closely related to Type IIs restriction endonucleases MlyI and PleI.
PG  - 2492-2501
AB  - N.BstNBI is a nicking endonuclease that recognizes the sequence GAGTC and nicks the top strand
      preferentially. The Type IIs restriction endonucleases PleI and MlyI also recognize GAGTC, but
      cleave both DNA strands. Cloning and sequencing the genes encoding each of these three
      endonucleases discloses significant sequence similarities. Mutagenesis studies reveal a
      conserved set of catalytic residues among the three endonucleases, suggesting that they are
      closely related to each other. Furthermore, PleI and MlyI contain a single active site for DNA
      cleavage. The results from cleavage assays show that the reactions catalyzed by PleI and MlyI
      are sequential two step processes. The double-stranded DNA is first nicked on one DNA strand
      and then further cleaved on the second strand to form linear DNA. Gel filtration analysis
      shows that MlyI dimerizes in the presence of a cognate DNA and Ca(2+) whereas N.BstNBI remains
      a monomer, implicating dimerization as a requisite for the second strand cleavage. We suggest
      that N.BstNBI, MlyI and PleI diverged from a common ancestor and propose that N.BstNBI differs
      from MlyI and PleI in having an extremely limited second strand cleavage activity, resulting
      in a site-specific nicking endonuclease.
AU  - Higgins LS
AU  - Besnier C
AU  - Kong H
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2001 29: 2492-2501.

PMID- 27081137
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of 11 Clinical Isolates of Acinetobacter baumannii.
PG  - e00269-16
AB  - The development of multidrug-resistantAcinetobacter baumanniiis of serious concern in the
      hospital setting. Here, we report draft genome sequences of 11A.
      baumanniiisolates that were isolated from a single patient over a 65-day period,
      during which time the isolates exhibited increased antimicrobial resistance.
AU  - Higgins PG
AU  - Chan JZ
AU  - Seifert H
AU  - Pallen MJ
AU  - Millard AD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00269-16.

PMID- 27540059
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Nine Clinical Isolates of Vancomycin-Resistant Enterococci.
PG  - e00803-16
AB  - In 2012, there was an increase in vancomycin-resistant enterococci (VRE) isolated from the
      intensive care unit at the University Hospital of Cologne. Using
      whole-genome sequencing it was possible to establish that bloodstream infections
      with VRE were not the result of an outbreak or cross infections.
AU  - Higgins PG
AU  - Koehler D
AU  - Chan JZ
AU  - Cornely OA
AU  - Fatkenheuer G
AU  - Gillis M
AU  - Pallen MJ
AU  - Tien J
AU  - Seifert H
AU  - Vehreschild MJ
AU  - Millard AD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00803-16.

PMID- 17986343
VI  - 7
DP  - 2007
TI  - Subtle genetic changes enhance virulence of methicillin resistant and sensitive Staphylococcus aureus.
PG  - 99
AB  - ABSTRACT: BACKGROUND: Community acquired (CA) methicillin-resistant Staphylococcus aureus
      (MRSA) increasingly causes disease worldwide. USA300
      has emerged as the predominant clone causing superficial and invasive
      infections in children and adults in the USA. Epidemiological studies
      suggest that USA300 is more virulent than other CA-MRSA. The genetic
      determinants that render virulence and dominance to USA300 remain unclear.
      RESULTS: We sequenced the genomes of two pediatric USA300 isolates: one
      CA-MRSA and one CA-methicillin susceptible (MSSA), isolated at Texas
      Children's Hospital in Houston. DNA sequencing was performed by Sanger
      dideoxy whole genome shotgun (WGS) and 454 Life Sciences pyrosequencing
      strategies. The sequence of the USA300 MRSA strain was rigorously
      annotated. In USA300, MRSA 2685 chromosomal open reading frames were
      predicted and 3.1 and 27 kilobase (kb) plasmids were identified. USA300
      MSSA contained a 20 kb plasmid with some homology to the 27 kb plasmid.
      Two regions found in US300 MRSA were absent in USA300 MSSA. The USA300
      sequence was aligned with other sequenced S. aureus genomes and regions
      unique to USA300 MRSA were identified. CONCLUSIONS: USA300-MRSA is highly
      similar to other MRSA strains based on whole genome alignments and gene
      content, indicating that the differences in pathogenesis are due to subtle
      changes rather than to large-scale acquisition of virulence factor genes.
      The USA300 Houston isolate differs from another sequenced USA300 strain
      isolate, derived from a patient in San Francisco, in plasmid content and a
      number of sequence polymorphisms. Such differences will provide new
      insights into the evolution of pathogens.
AU  - Highlander SK et al
PT  - Journal Article
TA  - BMC Microbiol.
JT  - BMC Microbiol.
SO  - BMC Microbiol. 2007 7: 99.

PMID- 8921897
VI  - 178
DP  - 1996
TI  - The restriction-modification system of Pasteurella haemolytica is a member of a new family of type I enzymes.
PG  - 89-96
AB  - Genes encoding the type I restriction-modification (R-M) system of the bovine pathogen,
      Pasteurella haemolytica, have been identified immediately downstream of a locus that encodes a
      transcriptional activator of P. haemolytica leukotoxin expression.  Type I enzymes are encoded
      by three genes called hsdM, hsdS and hsdR, and have fallen into three groups, called Ia, Ib
      and Ic.  HsdS provides a sequence recognition function which in concert with HsdM forms an
      active methyltransferase (Mtase).  Inclusion of the HsdR subunit in the complex creates an
      active restriction endonuclease (Enase) capable of cleaving unmethylated target DNA.  The P.
      haemolytica hsdMSR genes were mapped using transposon Tn10d-Cam insertions, and bacteriophage
      restriction and modification assays in Escherichia coli.  We determined the nucleotide
      sequences of hsdM, hsdS and hsdR, and observed that the deduced amino acid (aa) sequences were
      very similar to predicted R-M subunits in the respiratory pathogen, Haemophilus influenzae.
      Phylogenetic comparisons of all known Hsd aa sequences placed the P. haemolytica and H.
      influenzae proteins into a new group which we labeled the Type Id R-M family.  Expression of
      the P. haemolytica R-M genes in E. coli was inefficient and is likely to be a consequence of
      the unusual codon usage in P. haemolytica genes.
AU  - Highlander SK
AU  - Garza O
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1996 178: 89-96.

PMID- 9284183
VI  - 65
DP  - 1997
TI  - A putative leucine zipper activator of Pasteurella haemolytica leukotoxin transcription and the potential for modulation of its synthesis by slipped-strand  mispairing.
PG  - 3970-3975
AB  - A Pasteurella haemolytica cosmid clone that activates leukotoxin transcription in Escherichia
      coli has been isolated. The activator locus, alxA, is part of a
      continuous open reading frame that includes the type I hsdM methylase gene. AlxA
      and HsdM peptides are processed from a precursor, and translation of the
      polyprotein can be modulated by slipped-strand mispairing across a
      pentanucleotide repeat, ACAGC, within the 5' end of alxA-hsdM. Extracts
      containing AlxA can bind to a leukotoxin promoter fragment.
AU  - Highlander SK
AU  - Hang VT
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 1997 65: 3970-3975.

PMID- 27151792
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Bacillus clausii AKU0647, a Strain That Produces Endo-beta-N-Acetylglucosaminidase A.
PG  - e00310-16
AB  - To comprehensively identify glycosyl hydrolase genes in the genome of Bacillus clausii strain
      AKU0647, which produces endo-beta-N-acetylglucosaminidase A
      (Endo-A), we conducted whole-genome shotgun sequencing. We identified several
      other putative glycosyl hydrolase genes apart from the Endo-A gene, and report
      these findings here.
AU  - Higuchi Y
AU  - Mori K
AU  - Suyama A
AU  - Huang Y
AU  - Tashiro K
AU  - Kuhara S
AU  - Takegawa K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00310-16.

PMID- 26450732
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Four Xanthomonas arboricola pv. juglandis Strains Associated with Walnut Blight in Chile.
PG  - e01160-15
AB  - Xanthomonas arboricola pv. juglandis is an important pathogen responsible for walnut blight
      outbreaks globally. Here, we report four draft genome sequences of  X. arboricola pv.
      juglandis strains isolated from Chilean walnut trees.
AU  - Higuera G
AU  - Gonzalez-Escalona N
AU  - Veliz C
AU  - Vera F
AU  - Romero J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01160-15.

PMID- 28063932
VI  - 483
DP  - 2017
TI  - Crystal structure of Deep Vent DNA polymerase.
PG  - 52-57
AB  - DNA polymerases are useful tools in various biochemical experiments. We have focused on the
      DNA polymerases involved in DNA replication including the
      unnatural base pair between 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds) and
      2-nitro-4-propynylpyrrole (Px). Many reports have described the different
      combinations between unnatural base pairs and DNA polymerases. As an example, for
      the replication of the Ds-Px pair, Deep Vent DNA polymerase exhibits high
      efficiency and fidelity, but Taq DNA polymerase shows much lower efficiency and
      fidelity. In the present study, we determined the crystal structure of Deep Vent
      DNA polymerase in the apo form at 2.5 A resolution. Using this structure, we
      constructed structural models of Deep Vent DNA polymerase complexes with DNA
      containing an unnatural or natural base in the replication position. The models
      revealed that the unnatural Ds base in the template-strand DNA clashes with the
      side-chain oxygen of Thr664 in Taq DNA polymerase, but not in Deep Vent DNA
      polymerase.
AU  - Hikida Y
AU  - Kimoto M
AU  - Hirao I
AU  - Yokoyama S
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 2017 483: 52-57.

PMID- 26868383
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the Fish Pathogen Mycobacterium pseudoshottsii Strain JCM15466, a Species Closely Related to M. marinum.
PG  - e01630-15
AB  - Mycobacterium pseudoshottsii is a slowly growing photochromogenic mycobacterium and fish
      pathogen isolated from wild marine fishes. M. pseudoshottsii closely
      resembles M. marinum, which is a human and animal pathogen. Here, we report the
      draft genome sequence of M. pseudoshottsii strain JCM15466, originally isolated
      from striped bass, Morone saxatilis.
AU  - Hikima J
AU  - Sakai M
AU  - Aoki T
AU  - Takeyama H
AU  - Hawke J
AU  - Mori K
AU  - Tashiro K
AU  - Kuhara S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01630-15.

PMID- 8604303
VI  - 24
DP  - 1996
TI  - Sequence analysis of 56 kb from the genome of the bacterium Mycoplasma pneumoniae comprising the dnaA region, the atp operon and a cluster of ribosomal protein genes.
PG  - 628-639
AB  - To sequence the entire 800 kilobase pair genome of the bacterium Mycoplasma pneumoniae, a
      plasmid library was established which contained the majority of the EcoRI fragments from M.
      pneumoniae.  The EcoRI fragments were subcloned from an ordered cosmid library comprising the
      complete M. pneumoniae genome.  Individual plasmid clones were sequenced in an ordered fashion
      mainly by primer walking.  We report here the initial results from the sequence analysis of
      about 56 kb comprising the dnaA region as a potential origin of replication, the ATPase operon
      and a region coding for a cluster of ribosomal protein genes.  The data were compared with the
      corresponding genes/operons from Bacillus subtilis, Escherichia coli, Mycoplasma capricolum
      and Mycoplasma gallisepticum.
AU  - Hilbert H
AU  - Himmelreich R
AU  - Plagens H
AU  - Herrmann R
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1996 24: 628-639.

PMID- 12488074
VI  - 92
DP  - 2003
TI  - Survey of restriction-modification systems and transformation in Mannheimia haemolytica and Pasteurella trehalosi.
PG  - 103-109
AB  - A significant obstacle to molecular studies of Mannheimia (Pasteurella) haemolytica, has been
      its resistance to genetic transformation. The lack
      of competence of many M. haemolytica strains has been attributed to the
      presence of restriction modification systems. In this study,
      representative strains of 12 M. haemolytica serotypes and four Pasteurella
      trehalosi serotypes were successfully transformed by electroporation using
      a recombinant vector derived from the native M. haemolytica A1 serotype
      plasmid pNSF2176. Transformation was achieved despite PCR-based evidence
      for the presence of genes encoding a type I restriction enzyme, phaI, and
      a type II restriction enzyme hsdM, in each of the M. haemolytica strains.
AU  - Hill AE
AU  - Lainson FA
PT  - Journal Article
TA  - Vet. Microbiol.
JT  - Vet. Microbiol.
SO  - Vet. Microbiol. 2003 92: 103-109.

PMID- Not included in PubMed...
VI  - 12
DP  - 1993
TI  - Bacteriophage and bacteriophage resistance in lactic acid bacteria.
PG  - 87-108
AB  - The study of bacteriophage-host interactions has been instrumental in the development of
      genetic systems in many genera, and laid many of the foundations of modern molecular genetics.
      Research into bacteriophage and bacteriophage resistance in the lactic acid bacteria has moved
      into a new and exciting dimension in recent years. Mechanisms such as adsorption inhibition,
      restriction and modification, and abortive infection which have been detected and described
      phenotypically over the past decade are now being subjected to molecular analysis, and this
      has led to a better understanding of the nature and variety of resistance systems employed by
      lactic acid bacteria to combat phage attack. In addition, analysis of different bacteriophage
      has increased our knowledge of these ubiquitous particles to the point where it is possible to
      construct novel phage resistances based on the phage genome itself. This review outlines the
      recent progress in the molecular analysis of bacteriophage, bacteriophage resistance and
      counter resistance, and the construction of novel resistance mechansims.
AU  - Hill C
PT  - Journal Article
TA  - FEMS Microbiol. Rev.
JT  - FEMS Microbiol. Rev.
SO  - FEMS Microbiol. Rev. 1993 12: 87-108.

PMID- Not carried by PubMed...
VI  - 76
DP  - 1996
TI  - Bacteriophage-host interactions and resistance mechanisms, analysis of the conjugative bacteriophage resistance plasmid pNP40.
PG  - 67-79
AB  - Research into bacteriophage and bacteriophage resistance in the lactic acid bacteria
      has moved into a new and exciting dimension in recent years.  Mechanisms such as adsorption
      inhibition, restriction and modification, and abortive infection which have been described
      phenotypically over the past decade are now being subjected to molecular analysis, and this
      has led
      to a better understanding of the nature and variety of resistance systems employed by lactic
      acid
      bacteria to combat phage attack.  In addition, analysis of different bacteriophage has
      increased our
      knowlege of these ubiquitous particles to the point where it is possible to construct novel
      phage
      resistances based on the phage genome.  This review will briefly outline the recent progress
      in the
      molecular analysis of bacteriophage-host interactions, bacteriophage resistance and counter
      resistance, and the construction of novel resistance mechanisms.  In particular, recent
      evidence
      regarding the mechanisms of resistance employed by the conjugative plasmid pNP40 will be
      described in some detail.  In addition, an instance will be described in which pNP40 has been
      used
      in the construction of phage resistant starters which have been successfully exploited by the
      dairy
      industry.
AU  - Hill C
AU  - Garvey P
AU  - Fitzgerald GF
PT  - Journal Article
TA  - Lait
JT  - Lait
SO  - Lait 1996 76: 67-79.

PMID- 
VI  - 23
DP  - 1990
TI  - Molecular characterization of a Type II methylase gene exchanged between pTR2030 and a virulent phage in Lactococci.
PG  - 167-168
AB  - None
AU  - Hill C
AU  - Miller L
AU  - Klaenhammer T
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 1990 23: 167-168.

PMID- 2389939
VI  - 56
DP  - 1990
TI  - Nucleotide sequence and distribution of the pTR2030 resistance determinant (hsp) which aborts bacteriophage infection in Lactococci.
PG  - 2255-2258
AB  - The lactococcal plasmid pTR2030 encodes resistance to bacteriophage attack via
      two mechanisms, an abortive-infection mechanism, designated Hsp, and a
      restriction and modification system.  We present the complete sequence of the
      hsp structural gene.  The gene is 1,887 base pairs in length and encodes a
      protein with a predicted molecular mass of 73.8 kilodaltons.  The upstream
      region was cloned in a promoter-screening vector and shown to direct the
      constitutive expression of the cat-86 gene.  An internal probe was used to
      determine the distribution of the hsp sequence in industrially significant
      lactococcal strains and to evaluate its relatedness to another lactococcal
      plasmid implicated in an abortive-infection-type mechanism, pNP40.  No homology
      was detected, suggesting that this gene is not widely distributed in
      lactococci.  Therefore, there are at least two independent abortive-infection
      genotypes in lactococci.
AU  - Hill C
AU  - Miller LA
AU  - Klaenhammer TR
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1990 56: 2255-2258.

PMID- 2121714
VI  - 172
DP  - 1990
TI  - Cloning, expression, and sequence determination of a bacteriophage fragment encoding bacteriophage resistance in Lactococcus lactis.
PG  - 6419-6426
AB  - A number of host-encoded phage resistance mechanisms have been described in
      lactococci.  However, the phage genome has not been exploited as a source of
      additional resistance determinants.  A 4.5-kb BamHI-HindIII fragment of phage
      nck202.50 (Phi50) was subcloned in streptococcus-Escherichia coli shuttle
      plasmid pSA3 and introduced into Lactoccus lactis NCK203 and MG1363 by
      protoplast transformation.  This cloned phage fragment directed a bacteriophage
      resistance phenotype designated Per (phage-encoded resistance).  Both Phi50 and
      a distantly related phage, nck202.48 (Phi48), formed small plaques on strain
      NCK213 at a slightly reduced efficiency of plaquing on the Per+ host.  The per
      locus was further reduced to a 1.4-kb fragment through in vitro deletion
      analysis.  The 1.4-kb fragment was sequenced, and the Per phenotype was found
      to be associated with a ca. 500-bp region rich in direct and inverted repeats.
      We present evidence that the Per region contains a phage origin of replication
      which, in trans, may interfere with phage replication by titration of DNA
      polymerase or other essential replication factors.  It was demonstrated that
      the Per+ activity was not detected against six independent phages which were
      previously shown to be sensitive to the Hsp+ mechanism.  The mutually exclusive
      resistance mechanisms could be combined to confer resistance to both types of
      phages (Hsp resistant and Per resistant) in a single host.  This is the first
      description in lactococci of a phage resistance phenotype, other than
      superinfection immunity, originating from a lactococcal phage genome.
AU  - Hill C
AU  - Miller LA
AU  - Klaenhammer TR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1990 172: 6419-6426.

PMID- 1906061
VI  - 173
DP  - 1991
TI  - In vivo genetic exchange of a functional domain from a Type II A methylase between lactococcal plasmid pTR2030 and a virulent bacteriophage.
PG  - 4363-4370
AB  - The conjugative plasmid pTR2030 confers bacteriophage resistance to lactococci by two
      independent mechanisms, an abortive infection mechanism (Hsp+) and a restriction and
      modification system (R+/M+).  pTR2030 transconjugants of lactococcal strains are used in the
      dairy industry to prolong the usefulness of mesophilic starter cultures.  One bacteriophage
      which has emerged against a pTR2030 transconjugant is not susceptible to either of the two
      defense systems encoded by the plasmid.  Phage nck202.50 (Phi50) is completely resistant to
      restriction by pTR2030.  A region of homology between pTR2030 Phi50 was subcloned, physically
      mapped, and sequenced.  A region of 1,273 bp was identical in both plasmid and phage,
      suggesting that the fragment had recently been transferred between the two genomes.  Sequence
      analysis confirmed that the transferred region encoded >55% of the amino domain of the
      structural gene for a type II methylase designated LlaI.  The LlaI gene is 1,869 bp in length
      and shows organizational similarities to the type II A methylase FokI.  In addition to the
      amino domain, upstream sequences, possibly containing the expression signals, were present on
      the phage genome.  The phage Phi50 fragment containing the methylase amino domain, designated
      LlaPI, when cloned onto the shuttle vector pSA3 was capable of modifying another phage genome
      in trans.  This is the first report of the genetic exchange between a bacterium and a phage
      which confers a selective advantage on the phage.  Definition of the LlaI system on pTR2030
      provides the first evidence that type II systems contribute to restriction and modification
      phenotypes during host-dependent replication of phages in lactococci.
AU  - Hill C
AU  - Miller LA
AU  - Klaenhammer TR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1991 173: 4363-4370.

PMID- 1857750
VI  - 25
DP  - 1991
TI  - The bacteriophage resistance plasmid pTR2030 forms high-molecular-weight multimers in Lactococci.
PG  - 105-112
AB  - Lactococcus lactis ME2 can transfer a 46-kb plasmid, pTR2030, which encodes
      abortive phage infection (Hsp) and restriction/modification (R/M) activities.
      pTR2030 can be detected as a monomeric plasmid in transconjugants at low copy
      number, but not in ME2.  pTR2030-specific probes were cloned and used to
      determine the location of the element in ME2.  No homology was observed between
      these pTR2030-specific probes and the CsCl-purified plasmid content of ME2.
      However, probes specific for pTR2030 hybridized strongly to a
      high-molecular-weight moiety, and not to chromosomal DNA, in total DNA isolated
      by a gentle lysis procedure.  The absence of junction fragments indicates that
      pTR2030 forms high-molecular-weight multimers in lactococci.  A phage-sensitive
      derivative of ME1, L. lactis N1, is cured of pTR2030 and no longer possesses
      the high-molecular-weight species.  When pTR2030 was reintroduced to N1 via
      conjugation, an ME2-like phage-insensitive phenotype was restored.  pTR2030
      could remain as a detectable monomeric plasmid in the N1 transconjugants or
      could revert to the high-molecular-weight structure.
AU  - Hill C
AU  - Miller LA
AU  - Klaenhammer TR
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 1991 25: 105-112.

PMID- 2508558
VI  - 55
DP  - 1989
TI  - The conjugative plasmid pTR2030 encodes two bacteriophage defense mechanisms in Lactococci, restriction modification (R+/M+) and abortive infection (Hsp+).
PG  - 2416-2419
AB  - pTR2030 is a conjugative plasmid which encodes resistance to bacteriophage in
      lactococci by a mechanism that aborts the phage infection (Hsp+).  Subcloning
      and in vivo deletion events showed that two independent mechanisms of
      resistance are located on a 13.6-kilobase BglII fragment cloned in pSA3; one
      mechanism is responsible for the abortive infection, and the other encodes a
      restriction modification system.  The introduction of pTR2030 or the
      recombinant plasmid pTK6 resulted in the loss of a resident restriction
      modification plasmid in Lactococcus lactis NCK202 which was not previously
      identified.
AU  - Hill C
AU  - Pierce K
AU  - Klaenhammer TR
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1989 55: 2416-2419.

PMID- 2504114
VI  - 55
DP  - 1989
TI  - Localization, cloning, and expression of genetic determinants for bacteriophage resistance (Hsp) from the conjugative plasmid pTR2030.
PG  - 1684-1689
AB  - Genetic determinants for a bacteriophage resistance mechanism (Hsp+) encoded by plasmid
      pTR2030 (46.2 kilobases [kb]) were localized by mapping an 11.5 -kb deletion that accompanied
      the transition of Lactococcus lactis LMA 12-4 transconjugants (M.E. Sanders, P.J. Leonard,
      W.D. Sing and T.R. Klaenhammer, Appl. Environ. Microbiol. 52:1001-1007, 1986) from phage
      resistance to phage sensitivity. The deleted 34.7-kb replicon (pTR2023, Hsp-) retained its
      conjugative ability, demonstrating that the phage resistance and conjugal transfer
      determinants were genetically distinct. The Hsp region of pTR2030, which was contained within
      a 13.6-kb BglII fragment, was cloned into the BamHI site of bacteriophage lambda EMBL3, and
      Hsp was subcloned into the Escherichia coli-Streptococcus shuttle vector pSa3. The recombinant
      plasmids pTK6 and pTK9 were recovered in E. coli HB101 and contained a 13.6-kb insert in
      opposite orientations. L. lactis MG1363 transformants carrying pTK6 or pTK9 exhibited a
      significant reduction in plaque size, in addition to a slight reduction in the efficiency of
      plaquing for both prolate and small isometric phages. Phenotypic reactions observed for the
      recombinant plasmids suggest that pTR2030-encoded Hsp acts similarly against both prolate and
      small isometric phages. Tn5 mutagenesis was used to define the region essential for the
      expression of the Hsp+ phenotype. Any of four insertions within a 3-kb region resulted in the
      loss of phagge resistance, whereas a further 26 insertions outside this locus had no effect on
      Hsp expression. In vitro deletion analysis confirmed that the 3-kb region contained all the
      information necessary for the observed resistance.
AU  - Hill C
AU  - Romero DA
AU  - McKenney DS
AU  - Finer KR
AU  - Klaenhammer TR
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1989 55: 1684-1689.

PMID- 10564824
VI  - 240
DP  - 1999
TI  - Cell to cell transmission of donor DNA overcomes differential incorporation of non-homologous and homologous markers in Neisseria gonorrhoeae.
PG  - 175-182
AB  - The neisseriae are naturally competent for DNA transformation. This genetic study examines
      whether the modification status of chromosomal donor DNA affects transformation of Neisseria
      gonorrhoeae to drug resistance. When a single modification system was inactivated, unmodified
      chromosomal donor DNA was not restricted when used to transform the cognate restriction+ host,
      irrespective of whether the donor DNA carried a point mutation (homologous marker) or a
      drug-resistance gene cassette (non-homologous marker). These observations contrasted
      transformations performed with unmodified plasmid donor DNAs, where the incoming DNA was
      excluded. However, during the study, it became apparent that certain strains of gonococci
      showed differential incorporation of non-homologous markers when compared with the
      incorporation of the homologous marker, even when the donor DNAs were prepared from parental
      strains. Differential incorporation of markers could be rescued either through cell to cell
      transmission of donor DNA, or by performing in vitro transformations with donor DNA
      preparations that were obtained from spent culture supernatants. Overall, the data indicate
      that, in addition to the exclusion of foreign DNA through the requirement for a genus-specific
      uptake sequence, gonococci appear capable of excluding DNA on the basis of homology.
AU  - Hill SA
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1999 240: 175-182.

PMID- 
VI  - 
DP  - 2005
TI  - Mechanism of DNA bending and its role in the specificity of EcoRV restriction endonuclease.
PG  - 1-160
AB  - Many DNA binding proteins involved in transcription, packaging and other processes bend their
      target sequences as part of their function.  The mechanism of DNA bending and its role in
      specificity, therefore, are topics of fundamental interest.  The homodimeric EcoRV restriction
      endonuclease, which recognizes the six base pair sequence GATATC, has emerged as one of the
      best studied nucleic acid binding proteins.  EcoRV bends the center TA step by 50 degrees to
      facilitate cleavage of the phosphodiester backbone.  A fluorescence resonance energy transfer
      assay was developed to monitor the DNA bending step, in addition to the binding and cleavage
      steps previously observed.  Bending of cognate DNA is rapid and appears to be simultaneous
      with binding.  Furthermore, no bending was observed in the absence of divalent metal. To
      elucidate the mechanism of DNA bending by EcoRV, electrostatic contacts between the protein
      and DNA were deleted.  This was done by mutating positively charged residues to alanine,
      replacing negatively charged DNA phosphates with uncharged methylphosphonates, and making both
      substitutions simultaneously.  It was found that asymmetric neutralization of the phosphate
      backbone improves DNA binding, bending, and cleavage, which indicates that DNA bending begins
      during the initial association process and has increasing importance throughout the catalytic
      pathway.  DNA bending was also stabilized by the diffuse charge present in the
      carboxy-terminal domain of each monomer, as observed by fluorescence in solution.  The crystal
      structure of a mutant lacking these domains also showed small changes at the active site,
      leading to destabilized binding of the divalent metal needed for catalysis.  To further
      understand how induced fit contributes to specificity, the transient kinetic techniques
      developed were used in partnership with x-ray crystallography to study discrimination against
      a noncognate sequence, GAATTC.  Again, binding and bending were simultaneous; however the bend
      angle decreased in response to a steric block at the center step.  The crystal structure
      showed that metal binding was disrupted, and this was suffient to reduce the cleavage rate
      105-fold.  Together, these studies demonstrate that specificity is coupled to catalysis by
      induced fit and partially establish the timing and mechanism of DNA bending by a site-specific
      nucleic acid enzyme.
AU  - Hiller DA
PT  - Journal Article
TA  - Ph.D. Thesis, Univ. of California, Santa Barbara
JT  - Ph.D. Thesis, Univ. of California, Santa Barbara
SO  - Ph.D. Thesis, Univ. of California, Santa Barbara 2005 : 1-160.

PMID- 14661948
VI  - 42
DP  - 2003
TI  - Simultaneous DNA binding and bending by EcoRV endonuclease observed by real-time fluorescence.
PG  - 14375-14385
AB  - The complete catalytic cycle of EcoRV endonuclease has been observed by combining fluorescence
      anisotropy with fluorescence resonance energy
      transfer (FRET) measurements. Binding, bending, and cleavage of substrate
      oligonucleotides were monitored in real time by rhodamine-x anisotropy and
      by FRET between rhodamine and fluorescein dyes attached to opposite ends
      of a 14-mer DNA duplex. For the cognate GATATC site binding and bending
      are found to be nearly simultaneous, with association and bending rate
      constants of (1.45-1.6) x 10(8) M(-1) s(-1). On the basis of the
      measurement of k(off) by a substrate-trapping approach, the equilibrium
      dissociation constant of the enzyme-DNA complex in the presence of
      inhibitory calcium ions was calculated as 3.7 x 10(-12) M from the kinetic
      constants. Further, the entire DNA cleavage reaction can be observed in
      the presence of catalytic Mg(2+) ions. These measurements reveal that the
      binding and bending steps occur at equivalent rates in the presence of
      either Mg(2+) or Ca(2+), while a slow decrease in fluorescence intensity
      following bending corresponds to k(cat), which is limited by the cleavage
      and product dissociation steps. Measurement of k(on) and k(off) in the
      absence of divalent metals shows that the DNA binding affinity is
      decreased by 5000-fold to 1.4 x 10(-8) M, and no bending could be detected
      in this case. Together with crystallographic studies, these data suggest a
      model for the induced-fit conformational change in which the role of
      divalent metal ions is to stabilize the sharply bent DNA in an orientation
      suitable for accessing the catalytic transition state.
AU  - Hiller DA
AU  - Fogg JM
AU  - Martin AM
AU  - Beechem JM
AU  - Reich NO
AU  - Perona JJ
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2003 42: 14375-14385.

PMID- 16981705
VI  - 45
DP  - 2006
TI  - Positively charged C-terminal subdomains of EcoRV endonuclease: contributions to DNA binding, bending, and cleavage.
PG  - 11453-11463
AB  - The carboxy-terminal subdomains of the homodimeric EcoRV restriction endonuclease each bear a
      net charge of +4 and are positioned on the inner
      concave surface of the 50 degree DNA bend that is induced by the enzyme. A
      complete kinetic and structural analysis of a truncated EcoRV mutant
      lacking these domains was performed to assess the importance of this
      diffuse charge in facilitating DNA binding, bending, and cleavage. At the
      level of formation of an enzyme-DNA complex, the association rate for the
      dimeric mutant enzyme was sharply decreased by 10(3)-fold, while the
      equilibrium dissociation constant was weakened by nearly 10(6)-fold
      compared with that of wild-type EcoRV. Thus, the C-terminal subdomains
      strongly stabilize the enzyme-DNA ground-state complex in which the DNA is
      known to be bent. Further, the extent of DNA bending as observed by
      fluorescence resonance energy transfer was also significantly decreased.
      The crystal structure of the truncated enzyme bound to DNA and calcium
      ions at 2.4 A resolution reveals that the global fold is preserved and
      suggests that a divalent metal ion crucial to catalysis is destabilized in
      the active site. This may explain the 100-fold decrease in the rate of
      metal-dependent phosphoryl transfer observed for the mutant. These results
      show that diffuse positive charge associated with the C-terminal
      subdomains of EcoRV plays a key role in DNA association, bending, and
      cleavage.
AU  - Hiller DA
AU  - Perona JJ
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2006 45: 11453-11463.

PMID- 16236314
VI  - 354
DP  - 2005
TI  - Non-cognate enzyme-DNA complex: structural and kinetic analysis of EcoRV endonuclease bound to the EcoRI recognition site GAATTC.
PG  - 121-136
AB  - The crystal structure of EcoRV endonuclease bound to non-cognate DNA at 2.0 angstroms
      resolution shows that very small structural adaptations are sufficient to ensure the extreme
      sequence specificity characteristic of restriction enzymes. EcoRV bends its specific GATATC
      site sharply by 50 degrees into the major groove at the center TA step, generating unusual
      base-base interactions along each individual DNA strand. In the symmetric non-cognate complex
      bound to GAATTC, the center step bend is relaxed to avoid steric hindrance caused by the
      different placement of the exocyclic thymine methyl groups. The decreased base-pair unstacking
      in turn leads to small conformational rearrangements in the sugar-phosphate backbone,
      sufficient to destabilize binding of crucial divalent metal ions in the active site. A second
      crystal structure of EcoRV bound to the base-analog GAAUTC site shows that the 50 degrees
      center-step bend of the DNA is restored. However, while divalent metals bind at high occupancy
      in this structure, one metal ion shifts away from binding at the scissile DNA phosphate to a
      position near the 3'-adjacent phosphate group. This may explain why the 10(4)-fold attenuated
      cleavage efficiency toward GAATTC is reconstituted by less than tenfold toward GAAUTC.
      Examination of DNA binding and bending by equilibrium and stopped-flow florescence quenching
      and fluorescence resonance energy transfer (FRET) methods demonstrates that the capacity of
      EcoRV to bend the GAATTC non-cognate site is severely limited, but that full bending of GAAUTC
      is achieved at only a threefold reduced rate compared with the cognate complex. Together, the
      structural and biochemical data demonstrate the existence of distinct mechanisms for ensuring
      specificity at the bending and catalytic steps, respectively. The limited conformational
      rearrangements observed in the EcoRV non-cognate complex provide a sharp contrast to the
      extensive structural changes found in a non-cognate BamHI-DNA crystal structure, thus
      demonstrating a diversity of mechanisms by which restriction enzymes are able to achieve
      specificity.
AU  - Hiller DA
AU  - Rodriguez AM
AU  - Perona JJ
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2005 354: 121-136.

PMID- 17675389
VI  - 189
DP  - 2007
TI  - Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: insights into the pneumococcal supragenome.
PG  - 8186-8195
AB  - The distributed-genome hypothesis (DGH) states that pathogenic bacteria
      possess a supragenome that is much larger than the genome of any single
      bacterium and that these pathogens utilize genetic recombination and a
      large, noncore set of genes as a means of diversity generation. We
      sequenced the genomes of eight nasopharyngeal strains of Streptococcus
      pneumoniae isolated from pediatric patients with upper respiratory
      symptoms and performed quantitative genomic analyses among these and nine
      publicly available pneumococcal strains. Coding sequences from all strains
      were grouped into 3,170 orthologous gene clusters, of which 1,454 (46%)
      were conserved among all 17 strains. The majority of the gene clusters,
      1,716 (54%), were not found in all strains. Genic differences per strain
      pair ranged from 35 to 629 orthologous clusters, with each strain's genome
      containing between 21 and 32% noncore genes. The distribution of the
      orthologous clusters per genome for the 17 strains was entered into the
      finite-supragenome model, which predicted that (i) the S. pneumoniae
      supragenome contains more than 5,000 orthologous clusters and (ii) 99% of
      the orthologous clusters ( approximately 3,000) that are represented in
      the S. pneumoniae population at frequencies of >or=0.1 can be identified
      if 33 representative genomes are sequenced. These extensive genic
      diversity data support the DGH and provide a basis for understanding the
      great differences in clinical phenotype associated with various
      pneumococcal strains. When these findings are taken together with previous
      studies that demonstrated the presence of a supragenome for Streptococcus
      agalactiae and Haemophilus influenzae, it appears that the possession of a
      distributed genome is a common host interaction strategy.
AU  - Hiller NL
AU  - Janto B
AU  - Hogg JS
AU  - Boissy R
AU  - Yu S
AU  - Powell E
AU  - Keefe R
AU  - Ehrlich NE
AU  - Shen K
AU  - Hayes J
AU  - Barbadora K
AU  - Klimke W
AU  - Dernovoy D
AU  - Tatusova T
AU  - Parkhill J
AU  - Bentley SD
AU  - Post JC
AU  - Ehrlich GD
AU  - Hu FZ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2007 189: 8186-8195.

PMID- 27856579
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence for a Urinary Isolate of Nosocomiicoccus ampullae.
PG  - e01248-16
AB  - A draft genome sequence for a urinary isolate of Nosocomiicoccus ampullae (UMB0853) was
      investigated. The size of the genome was 1,578,043 bp, with an
      observed G+C content of 36.1%. Annotation revealed 10 rRNA sequences, 40 tRNA
      genes, and 1,532 protein-coding sequences. Genome coverage was 727x and consisted
      of 32 contigs, with an N50 of 109,831 bp.
AU  - Hilt EE
AU  - Price TK
AU  - Diebel K
AU  - Putonti C
AU  - Wolfe AJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01248-16.

PMID- 25480686
VI  - 6
DP  - 2014
TI  - Global phylogenomic analysis of nonencapsulated Streptococcus pneumoniae reveals  a deep-branching classic lineage that is distinct from multiple sporadic lineages.
PG  - 3281-3294
AB  - The surrounding capsule of Streptococcus pneumoniae has been identified as a major virulence
      factor and is targeted by pneumococcal conjugate vaccines (PCV).
      However, nonencapsulated S. pneumoniae (non-Ec-Sp) have also been isolated
      globally, mainly in carriage studies. It is unknown if non-Ec-Sp evolve
      sporadically, if they have high antibiotic nonsusceptiblity rates and a unique,
      specific gene content. Here, whole-genome sequencing of 131 non-Ec-Sp isolates
      sourced from 17 different locations around the world was performed. Results
      revealed a deep-branching classic lineage that is distinct from multiple sporadic
      lineages. The sporadic lineages clustered with a previously sequenced, global
      collection of encapsulated S. pneumoniae (Ec-Sp) isolates while the classic
      lineage is comprised mainly of the frequently identified multilocus sequences
      types (STs) ST344 (n = 39) and ST448 (n = 40). All ST344 and nine ST448 isolates
      had high nonsusceptiblity rates to beta-lactams and other antimicrobials.
      Analysis of the accessory genome reveals that the classic non-Ec-Sp contained an
      increased number of mobile elements, than Ec-Sp and sporadic non-Ec-Sp.
      Performing adherence assays to human epithelial cells for selected classic and
      sporadic non-Ec-Sp revealed that the presence of a integrative conjugative
      element (ICE) results in increased adherence to human epithelial cells (P =
      0.005). In contrast, sporadic non-Ec-Sp lacking the ICE had greater growth in
      vitro possibly resulting in improved fitness. In conclusion, non-Ec-Sp isolates
      from the classic lineage have evolved separately. They have spread globally, are
      well adapted to nasopharyngeal carriage and are able to coexist with Ec-Sp. Due
      to continued use of PCV, non-Ec-Sp may become more prevalent.
AU  - Hilty M et al
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2014 6: 3281-3294.

PMID- 8948633
VI  - 24
DP  - 1996
TI  - Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae.
PG  - 4420-4449
AB  - The entire genome of the bacterium Mycoplasma pneumoniae M129 has been sequenced.  It has a
      size of 816,394 base pairs with an average G+C content of 40.0 mol%.  We predict 677 open
      reading frames (ORFs) and 39 genes coding for various RNA species.  Of the predicted ORFs,
      75.9% showed significant similarity to genes/proteins of other organisms while only 9.9% did
      not reveal any significant similarity to gene sequences in databases.  This permitted us
      tentatively to assign a functional classification to a large number of ORFs and to deduce the
      biochemical and physiological properties of this bacterium.  The reduction of the genome size
      of M.pneumoniae during its reductive evolution from ancestral bacteria can be explained by the
      loss of complete anabolic (e.g. no amino acid synthesis) and metabolic pathways.  Therefore,
      M.pneumoniae depends in nature on an obligate parasitic lifestyle which requires the provision
      of exogenous essential metabolites.  All the major classes of cellular processes and metabolic
      pathways are briefly described.  For a number of activities/functions present in M.pneumoniae
      according to experimental evidence, the corresponding genes could not be identified by
      similarity search.  For instance we failed to identify genes/proteins involved in motility,
      chemotaxis and management of oxidative stress.
AU  - Himmelreich R
AU  - Hilbert H
AU  - Plagens H
AU  - Pirkl E
AU  - Li B-C
AU  - Herrmann R
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1996 24: 4420-4449.

PMID- 9016618
VI  - 25
DP  - 1997
TI  - Comparative anlaysis of the genomes of the bacteria Mycoplasma pneumoniae and Mycoplasma genitalium.
PG  - 701-712
AB  - The sequenced genomes of the two closely related bacteria Mycoplasma genitalium and Mycoplasma
      pneumoniae were compared with emphasis on genome organization and coding capacity.  All the
      470 proposed open reading frames (ORFs) of the smaller M.genitalium genome (580 kb) were
      contained in the larger genome (816 kb) of M.pneumoniae.  There were some discrepancies in
      annotation, but inspection of the DNA sequences showed that the corresponding DNA was always
      present in M.pneumoniae.  The two genomes could be subdivided into six segments.  The order of
      orthologous genes was well conserved within individual segments but the order of these
      segments in both bacteria was different.  We explain the different organization of the
      segments by translocation via homologous recombination.  The translocations did not disturb
      the continuous bidirectional course of transcription in both genomes, starting at the proposed
      origin of replication.  The additional 236 kb in M.pneumoniae, compared with the M.genitalium
      genome, were coding for 209 proposed ORFs not identified in M.genitalium.  Of these ORFs, 110
      were amplifications of ORFs existing mainly as single copies in M.genitalium.  In addition, 23
      ORFs containing a copy of either one of the three repetitive DNA sequences RepMP2/3, RepMP4
      and RepMP5 were annotated in M.pneumoniae but not in M.genitalium, although similar DNA
      sequences were present.  The M.pneumoniae-specific genes included a restriction-modification
      system, two transport systems for carbohydrates, the complete set of three genes coding for
      the arginine dihydrolase pathway and 14 copies of the repetitive DNA sequence RepMP1 which
      were part of several different translated genes with unknown function.
AU  - Himmelreich R
AU  - Plagens H
AU  - Hilbert H
AU  - Reiner B
AU  - Herrmann R
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1997 25: 701-712.

PMID- 33837
VI  - 38
DP  - 1979
TI  - Purification and characterization of HpaI and HpaII.
PG  - 294
AB  - The restriction endonucleases from Haemophilus parainfluenzae, HpaI and HpaII,
      have been purified to homogeneity.  HpaI has been purified 10,000 fold and has
      a specific activity of 2.2 x 106 units/mg.  (1 unit corresponds to the amount
      of enzyme required to cleave 1 microgram of lambda DNA to completion in 60
      minutes.) HpaI has a monomer molecular weight of 29,000 daltons and exists as a
      58,000 dalton dimer under native conditions.  A specific volume (V) of 0.72
      cc/g used in the molecular weight determinations was calculated from the amino
      acid composition.  The sedimentation velocity is 3.61 x 10-13 sec.  A ratio of
      frictional coefficients (f/fo) was found to be 1.5 indicating an elongated
      molecule.  HpaII has been purified 8,000 fold and has a specific activity of
      1.8 x 106 units/mg.  (Same units as above.)  HpaII has a monomer molecular
      weight of 41,000 and exists as an 82,000 dalton dimer under native conditions.
      A specific volume (v) of 0.73 cc/g used in the molecular weight determinations
      was calculated from the amino acid composition.  The sedimentation velocity is
      4.45 x 10-13 sec.  A ratio of frictional coefficients (f/fo) was found to be
      1.45 indicating that HpaII is also an elongated molecule.
AU  - Hines JL
AU  - Agarwal KL
PT  - Journal Article
TA  - Fed. Proc.
JT  - Fed. Proc.
SO  - Fed. Proc. 1979 38: 294.

PMID- 6154863
VI  - 65
DP  - 1980
TI  - Preparation and properties of HpaI and HpaII endonucleases.
PG  - 153-163
AB  - Two restriction endonuclease activities, HpaI and HpaII, have been isolated
      from Haemophilus parainfluenzae.  Endonuclease HpaI has been isolated in
      homogeneous form, while HpaII has been purified free of contaminating nuclease
      and phosphatase activies.  HpaI recognizes the DNA sequence and cleaves the
      phosphodiester bonds in both strands as indicated.  HpaII recognizes the DNA
      sequence and cleaves the phosphodiester bonds in a staggered fashion as
      indicated.  The reaction products, in both cases, contain 5'-phosphoryl and
      3'-hydroxyl termini.
AU  - Hines JL
AU  - Chauncey TR
AU  - Agarwal KL
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1980 65: 153-163.

PMID- 12851384
VI  - 278
DP  - 2003
TI  - Kinetic analysis of the coordinated interaction of SgrAI restriction endonuclease with different DNA targets.
PG  - 40392-40399
AB  - SgrAI restriction endonuclease cooperatively interacts and cleaves two target sites that
      include both the canonical sites, CPuCCGGPyG, and the
      secondary sites, CPuCCGGPy(A/T/C). It has been observed that the cleaved
      canonical sites stimulate SgrAI cleavage at the secondary sites.
      Equilibrium binding studies show that SgrAI binds to its canonical sites
      with a high affinity (Ka = 4-8 x 10(10) M-1) and that it has a 15-fold
      lower affinity for the cleaved canonical sites and a 30-fold lower
      affinity for the secondary sites. Steady-state kinetics reveals substrate
      cooperativity for SgrAI cleavage on both canonical and secondary sites.
      The specificity of SgrAI for the secondary site CACCGGCT, as measured by
      kcat/K is about 500-fold lower than that for the canonical site CACCGGCG,
      but this difference is reduced to 10-fold in the presence of the cleaved
      canonical sites. The efficiency of canonical site cleavage also increases
      by 3-fold when the cleaved canonical sites are present in the reaction.
      Furthermore, the substrate cooperativity for SgrAI cleavage is abolished
      for both types of sites in the presence of cleaved canonical sites. These
      results indicate that target site cleavage occurs via a coordinated
      interaction of two SgrAI protein subunits, where the subunit bound to the
      cleaved site stimulates the cleavage of the uncut site bound by the other
      subunit. The free subunits of SgrAI have the flexibility to bind different
      target sites and, consequently, assemble into various catalytically active
      complexes, which differ in their catalytic efficiencies.
AU  - Hingorani-Varma K
AU  - Bitinaite J
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2003 278: 40392-40399.

PMID- 113797
VI  - 2
DP  - 1979
TI  - pMG7-mediated restriction of Pseudomonas aeruginosa phage DNAs is determined by a class II restriction endonuclease.
PG  - 387-393
AB  - A class II restriction endonuclease, PaeR7, has been isolated from a Pseudomonas aeruginosa
      strain containing the resistance plasmid pMG7. The activity cannot be isolated from an
      isogenic strain which does not contain this resistance plasmid. EndoR-PaeR7 requires Mg2+ for
      activity but does not require ATP or S-adenosyl-L-methionine. Specific digestion patterns are
      produced upon agarose gel electrophoresis of substrate DNAs which have been digested with the
      enzyme. The enzyme is the biochemical basis for the pMG7-mediated phage interference reported
      by Jacoby and Sutton (1977). DNAs isolated from restricted phages act as substrates for the
      enzyme while DNAs isolated from unrestricted phages and phages which have been modified by
      growth on strains containing pMG7 do not act as substrates for the enzyme.
AU  - Hinkle NF
AU  - Miller RV
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 1979 2: 387-393.

PMID- 6255448
VI  - 8
DP  - 1980
TI  - Physical and kinetic properties of the site specific endonuclease BamHI from Bacillus amyloliquefaciens.
PG  - 623-633
AB  - The site specific endonuclease BamHI which is composed of subunits of a
      molecular weight of 22,000 can aggregate to complexes of a molecular weight of
      36,0000.  It is an acidic protein with an iselectric point at pH 5.3.  Optimal
      activity is reached at 13 mM MgCl2.  A very simple method is presented to
      determine kinetic constants of restriction enzymes directly from agarose gel
      photographs without any further equipment applying the integrated Michaelis
      Menten equation.  With pJC 80 DNA as a substrate KM was found to be 3.6 10-10
      M.  The method can be used to redefine the unit activity of site specific
      endonucleases unambiguously.
AU  - Hinsch B
AU  - Kula M-R
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1980 8: 623-633.

PMID- 6269074
VI  - 9
DP  - 1981
TI  - Reaction kinetics of some important site-specific endonucleases.
PG  - 3159-3174
AB  - Reaction kinetics of the site-specific endonucleases BamHI, BglII, ClaI, EcoRI,
      HpaII, PstI, SalI, SmaI, and XorII were investigated employing some frequently
      used substrates.  Six of these enzymes could be analyzed under steady-state
      conditions.  Kinetic data were obtained from progres curves applying an
      integrated Michaelis-Menten equation.  KM ranged from 4 - 10-9M to 4 - 10-11 M.
      Activities also spanned two orders of magnitude.  In the case of ClaI the
      analysis of the pre-steady-state kinetics ("burst reaction") allowed the
      assessment of several rate constants.  The rate-limiting step is the very slow
      dissociation of the enzyme-product complex (0.22 min-1).  This complex is
      formed from the enzyme-bound nicked intermediate at a rate of about 6.  SmaI
      and XorII resembled ClaI in their kinetics.  The burst reaction can be used for
      the easy and unambiguous determination of molar concentrations of site-specific
      endonucleases in any preparation, which is free of non-specific DNases.
AU  - Hinsch B
AU  - Kula M-R
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1981 9: 3159-3174.

PMID- 6160464
VI  - 8
DP  - 1980
TI  - Binding of non-substrate nucleotides to a restriction endonuclease: a model for the interaction of Bam HI with its recognition sequence.
PG  - 2547-2559
AB  - The kinetic constants of the site-specific endonuclease Bam HI for various
      substrates were determined and binding of non-substrate nucleotides to the
      enzyme was studied.  Agarose gel assays in combination with an integrated
      Michaelis-Menten equation were used for the evaluation of data.  The turnover
      number was 2.2 min-1 at 37C with pJC80 DNA as the substrate.  It depends on the
      conformation and base composition of the substrate.  Michaelis constants also
      depend on substrate conformation.  Non-substrate polynucleotides were found to
      inhibit Bam competitively with KI ranging from 10-6 to >10-3 M depending on
      base composition, base pairing, and helix conformation.  Dinucleotides showed
      sequence-specific, competitive inhibition with KIs ranging from 10-5 to >10-3
      M.  Mononucleotides and -nucleosides acted noncompetitively.  Binding was
      influenced by the extent of phosphorylation, but not by the nature of the base.
      KIs varied between 10-3 and 10-2 M.  The results are discussed with respect to
      the recognition requirements of Bam HI.
AU  - Hinsch B
AU  - Mayer H
AU  - Kula M-R
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1980 8: 2547-2559.

PMID- 1645872
VI  - 19
DP  - 1991
TI  - Simple methods for making EcoK and McrA restrictionless mutants.
PG  - 2502
AB  - Restriction systems present a major obstacle to the cloning and expression of
      heterologous DNAs in bacteria such as E. coli.  Many modern cloning strains
      therefore carry disabling mutations in genes encoding restriction endonucleases
      to prevent degradation of these heterologous DNAs, however many laboratory
      strains of E. coli are not deficient in host restriction activity and are
      therefore inaccessible to foreign DNAs.  Here we describe simple methods for
      genetically eliminating EcoK and McrA restriction from E. coli that are
      generally applicable to strain improvement programs with other bacterial
      species.
AU  - Hiom K
AU  - Sedgwick SG
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 2502.

PMID- 1938927
VI  - 173
DP  - 1991
TI  - Cloning and structural characterization of the mcrA locus of Escherichia coli.
PG  - 7368-7373
AB  - Escherichia coli has DNA restriction systems which are able to recognize and
      attack modified cytosine residues in the DNA of incoming bacteriophages and
      plasmids.  The locus for the McrA/RglA system of modified cytosine restriction
      was located near the pin gene of the defective element, e14.  Hence, loss of
      the e14 element through abortive induction after UV irradiation caused a
      permanent loss of McrA restriction activity.  e14 DNA encoding McrA restriction
      was cloned and sequenced to reveal a single open reading frame of 831 bp with a
      predicted gene product of 31 kDa.  Clones expressing the complete open reading
      frame conferred both McrA and RglA phenotypes; however, a deletion derivative
      was found which complemented RglA restriction against nonglucosylated T6gt
      phage but did not complement for McrA restriction of methylated plasmid DNA.
      Possible explanations for this activity and a comparison with the different
      organization of the McrB/RglB restriction system are discussed.
AU  - Hiom K
AU  - Sedgwick SG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1991 173: 7368-7373.

PMID- 1655051
VI  - 73
DP  - 1991
TI  - Different mechanisms for SOS induced alleviation of DNA restriction in Escherichia coli.
PG  - 399-405
AB  - The alleviation of DNA restriction during the SOS response in Escherichia coli has been
      further investigated.  With the EcoK DNA restriction system UV irradiated wild-type cells show
      a 10^4-fold increase in ability to plate non-modified lambda phage and a 3-4 fold increase in
      transformation by non-modified plasmid DNA.  A role for the umuDC genes of E. coli in the
      process of SOS-induced restriction alleviation was identified by showing that a umuC122::Tn5
      mutant could alleviate EcoK restriction to only 5% that of wild-type levels.  Although umuDC
      are better characterized for their pivotal role in SOS induced mutagenesis, it is demonstrated
      here that umu-dependent alleviation of EcoK restriction is a transient process in which
      umu-dependent mutagenesis plays little part.  A second form of SOS induced alleviation of DNA
      restriction is described in this paper involving the McrA restriction system.  The mcrA gene
      is shown to be encoded within a defective prophage called e14 situated at the 25 min region on
      the Escherichia coli genetic map.  e14 is known to abortively excise from the chromosome after
      SOS induction and it is demonstrated in this report that mcrA is lost from the genome after
      SOS induction as part of e14.  This results in a co-ordinate decrease in the level of mcrA
      restriction within a population of cells.
AU  - Hiom K
AU  - Thomas SM
AU  - Sedgwick SG
PT  - Journal Article
TA  - Biochimie
JT  - Biochimie
SO  - Biochimie 1991 73: 399-405.

PMID- 1310522
VI  - 231
DP  - 1992
TI  - Alleviation of EcoK DNA restriction in Escherichia coli and involvement of umuDC activity.
PG  - 265-275
AB  - The activity of the EcoKI DNA restriction system of Escherichia coli reduces
      both the plating efficiency of unmodified phage lambda and the transforming
      ability of unmodified pBR322 plasmid DNA.  However, restriction can be
      alleviated in wild-type cells, by UV irradiation and expression of the SOS
      response, so that 10/3- to 10/4-fold increases in phage growth and fourfold
      increases in plasmid transformation occurred with unmodified DNA.  Restriction
      alleviation was found to be a transient effect because induced cells, which
      initially failed to restrict unmodified plasmid DNA, later restricted
      unmodified phage lambda.  Although the SOS response was needed for restriction
      alleviation, constitutive SOS induction, elicited genetically with a recA730
      mutation, did not alleviate restriction and UV irradiation was still needed.  A
      hitherto unsuspected involvement of the umuDC operon in this alleviation of
      restriction is characterized and, by differential complementation, was
      separated from the better known role of umuDC in mutagenic DNA repair.  The
      need for cleavage of UmuD for restriction alleviation was shown with plasmids
      encoding cleavable, cleaved, and non-cleavable forms of UmuD.  However, UV
      irradiation was still needed even when cleaved UmuD was provided.  The
      possibility that restriction alleviation occurs by a general inhibition of the
      EcoK restriction/modification complex was tested and discounted because
      modification of lambda was not reduced by UV irradiation.  An alternative idea,
      that restriction activity was competitively reduced by an increase in EcoK
      modification, was also discounted by the lack of any increase in the
      modification of lambda Ral-, a naturally undermodified phage.  Other possible
      mechanisms for restriction alleviation are discussed.
AU  - Hiom KJ
AU  - Sedgwick SG
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1992 231: 265-275.

PMID- 25416288
VI  - 56
DP  - 2015
TI  - Loss of Cytochrome cM Stimulates Cyanobacterial Heterotrophic Growth in the Dark.
PG  - 334-345
AB  - Although cyanobacteria are photoautotrophs, they have the capability for
      heterotrophic metabolism that enables them to survive in their natural habitat.
      However, cyanobacterial species that grow heterotrophically in the dark are rare.
      It remains largely unknown how cyanobacteria regulate heterotrophic activity. The
      cyanobacterium Leptolyngbya boryana grows heterotrophically with glucose in the
      dark. A dark-adapted variant dg5 isolated from the wild type (WT) exhibits
      enhanced heterotrophic growth in the dark. We sequenced the genomes of dg5 and
      the WT to identify the mutation(s) of dg5. The WT genome consists of a circular
      chromosome (6,176,364 bp), a circular plasmid pLBA (77,793 bp) and two linear
      plasmids pLBX (504,942 bp) and pLBY (44,369 bp). Genome comparison revealed three
      mutation sites. Phenotype analysis of mutants isolated from the WT by introducing
      these mutations individually revealed that the relevant mutation is a single
      adenine insertion causing a frameshift of cytM encoding Cyt cM. The respiratory
      oxygen consumption of the cytM-lacking mutant grown in the dark was significantly
      higher than that of the WT. We isolated a cytM-lacking mutant, DeltacytM, from
      another cyanobacterium Synechocystis sp. PCC 6803, and DeltacytM grew in the dark
      with a doubling time of 33 h in contrast to no growth of the WT. The respiratory
      oxygen consumption of DeltacytM grown in the dark was about 2-fold higher than
      that of the WT. These results suggest a suppressive role(s) for Cyt cM in
      regulation of heterotrophic activity.
AU  - Hiraide Y
AU  - Oshima K
AU  - Fujisawa T
AU  - Uesaka K
AU  - Hirose Y
AU  - Tsujimoto R
AU  - Yamamoto H
AU  - Okamoto S
AU  - Nakamura Y
AU  - Terauchi K
AU  - Omata T
AU  - Ihara K
AU  - Hattori M
AU  - Fujita Y
PT  - Journal Article
TA  - Plant Cell Physiol.
JT  - Plant Cell Physiol.
SO  - Plant Cell Physiol. 2015 56: 334-345.

PMID- 9400512
VI  - 350
DP  - 1997
TI  - Dissemination in Japanese hospitals of strains of Staphylococcus aureus heterogeneously resistant to vancomycin.
PG  - 1670-1673
AB  - BACKGROUND: Since the discovery of the vancomycin-resistant Staphylococcus aureus (VRSA)
      strain Mu50 (minimum inhibitory concentration [MIC] 8 mg/L),
      there has been concern about the potential spread of such strains
      throughout Japanese hospitals. Two important questions need to be
      answered: (1) what is the prevalence of VRSA, and (2) by what mechanism
      does vancomycin resistance occur. METHODS: The vancomycin susceptibilities
      of three methicillin-resistant S aureus (MRSA) strains (Mu50, Mu3, and H1)
      and the methicillin-susceptible S aureus type strain FDA209P were compared
      by MIC determinations and population analysis. Mu3 (MIC 3 mg/L) was
      isolated from the sputum of a patient with pneumonia after surgery who had
      failed vancomycin therapy. H1 (MIC 2 mg/L), which is a representative
      vancomycin-susceptible MRSA strain, was isolated from a patient with
      pneumonia who responded favourably to vancomycin therapy. Subclones of Mu3
      with increased resistance against vancomycin were selected with serial
      concentrations of vancomycin and their MICs were determined. The
      prevalence of VRSA and Mu3-like strains in Japanese hospitals was
      estimated by population analysis from 1149 clinical MRSA isolates obtained
      from 203 hospitals throughout Japan. The genetic traits of the Mu3 and
      Mu50 strains were compared with clonotypes of MRSA from around the world.
      FINDINGS: Mu3 and Mu50 had an identical pulsed-field gel electrophoresis
      banding pattern. When grown in a drug-free medium, Mu3 produced
      subpopulation of cells with varying degrees of vancomycin resistance, thus
      demonstrating natural heterogeneity, or variability, in susceptibility to
      vancomycin. In the presence of vancomycin, Mu3 produced subclones with
      resistance roughly proportional to the concentrations of vancomycin used.
      Selection of Mu3 with 8 mg/L or more of vancomycin gave rise to subclones
      with vancomycin resistance equal to that of Mu50 (MIC 8 mg/L) at a
      frequency of 1/1,000,000. During screening of Japanese MRSA strains, no
      strain of VRSA additional to Mu50 was found. The prevalence of MRSA
      isolates heterogeneously resistant to vancomycin was 20% in Juntendo
      University Hospital, 9.3% in the other seven university hospitals, and
      1.3% in non-university hospitals or clinics. INTERPRETATION:
      Heterogeneously resistant VRSA is a preliminary stage that allows
      development into VRSA upon exposure to vancomycin. Heterogeneously
      resistant VRSA was found in hospitals throughout Japan. This finding could
      explain, at least partly, the frequent therapeutic failure of MRSA
      infection with vancomycin in Japan.
AU  - Hiramatsu K
AU  - Aritaka N
AU  - Hanaki H
AU  - Kawasaki S
AU  - Hosoda Y
AU  - Hori S
AU  - Fukuchi Y
AU  - Kobayashi I
PT  - Journal Article
TA  - Lancet
JT  - Lancet
SO  - Lancet 1997 350: 1670-1673.

PMID- Not carried by PubMed...
VI  - 63
DP  - 1985
TI  - Site-Specific Restriction Endonucleases of Several Non-Pathogenic Bacteria.
PG  - 151-157
AB  - Seventy-one non-pathogenic bacterial strains were surveyed for the presence of Type II
      restriction endonucleases in aerobic culture. Five strains were found to contain specific
      enzymes: CflI from Cellulomonas flavignea, GalI from Gluconobacter albidus, GceI from
      Gluconobacter cerinus, HacI from Halococcus acetoinfaciens, and MflI from Microbacterium
      flavum. These enzymes cleaved respectively the sequences of 5'-CTGCA^G-3', 5'-CCGC^GG-3',
      5'-CCGC^GG-3', 5'-^GATC-3', and 5'Pu^GATCPy'3' at the positions indicated. HacI and
      MflI digested DNA from the Escherichia coli Dam-strain but not from the Dam+ strain,
      indicating that they react only with unmodified sequences. With NaCl or KCl, the optimal salt
      concentrations were 40-60 mM for CflI and 175-300mM for HacI; GalI and GceI did not require
      either salts. Activity was greatest at pH 7.1-7.5 for CflI and HacI, and pH 7.5-8.0 for GalI
      and GceI.
AU  - Hiraoka N
AU  - Kita K
AU  - Nakajima H
AU  - Kimizuka F
AU  - Obayashi A
PT  - Journal Article
TA  - J. Ferment. Technol.
JT  - J. Ferment. Technol.
SO  - J. Ferment. Technol. 1985 63: 151-157.

PMID- Not carried by PubMed...
VI  - 62
DP  - 1984
TI  - Purification and characterization of sequence-specific restriction endonuclease MflI.
PG  - 583-588
AB  - Class II restriction endonuclease MflI was purified 790-fold from the crude extract of
      Microbacterium flavum by chromatography on Phosphocellulose, DEAE-cellulose, and
      Heparin-sepharose columns. The purified preparation was free from non-specific nucleases and
      phosphatases. The enzyme required 7 to 20 mM Mg++ ions but not monovalent cations for its
      activity, and the maximum activity was obtained at pH 8.0-8.5 in the Tris-HCl buffer system.
      This enzyme recognized 5'-PuGATCPy-3' in DNA and cleaved between Pu and G in this sequence.
      However, MflI digested DNA from Escherichia coli Dam- strain, but not DNA from its Dam+ (wild
      type) strain, indicating that this enzyme only restricts the unmodified sequence.
AU  - Hiraoka N
AU  - Kita K
AU  - Nakajima H
AU  - Obayashi A
PT  - Journal Article
TA  - J. Ferment. Technol.
JT  - J. Ferment. Technol.
SO  - J. Ferment. Technol. 1984 62: 583-588.

PMID- 1417861
VI  - 188
DP  - 1992
TI  - Mutations at the putative junction sites of the yeast Vma1 protein, the catalytic subunit of the vacuolar membrane H+-ATPase, inhibit its processing by protein splicing.
PG  - 40-47
AB  - A single gene, VMA1, encodes the 69-kDa subunit of the vacuolar
      membrane H+-ATPase in the yeast Saccharomyces cerevisiae.  We have proposed that the
      subunit is synthesized as a precursor of 120 kDa (1,071 amino acids) and then converted to
      the 69-kDa form by an unusual processing reaction, which removes the internal domain of
      454 amino acids (residues 284-737) and joins the N- and C-terminal domains.  Cysteine to
      serine mutations at residues 284 and 738, the residues that bracket the internal domain,
      were introduced into the VMA1 gene by site-directed mutagenesis, and the mutant genes
      were expressed in a null vma1 mutant.  Cells harboring either of the mutant vma1 genes
      accumulate nonfunctional fragments of the subunit.  The mutation of Cys-284 inhibited the
      cleavage of the N-terminal junction site.  Cys-738 -> Ser mutation appeared to block the
      processing at both junction sites although the mutant gene yielded a small fraction of the
      functional 69-kDa subunit.
AU  - Hirata R
AU  - Anraku Y
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1992 188: 40-47.

PMID- 2139027
VI  - 265
DP  - 1990
TI  - Molecular structure of a gene, VMA1, encoding the catalytic subunit of H+-translocating adenosine triphosphatase from vacuolar membranes of Saccharomyces cerevisiae.
PG  - 6726-6733
AB  - Subunit alpha of the vacuolar membrane H+-translocating adenosine triphosphatase of the yeast
      Saccharomyces cerevisiae contains a catalytic site for ATP hydrolysis. N-terminal sequences of
      six tryptic peptides of the subunit were determined. Based on the peptide sequence
      information, a 39-base oligonucleotide probe was synthesized, and the gene encoding the
      subunit (VMA1) was isolated from a genomic DNA library by hybridization. The nucleotide
      sequence of the gene predicts a polypeptide of 1,071 amino acids with a calculated molecular
      mass of 118,635 daltons, which is much larger than the value 67 kDa estimated on sodium
      dodecyl sulfate-polyacrylamide gels. N- and C-terminal regions of the deduced sequence
      (residues 1-284 and 739-1,071) are very similar to those of the catalytic subunits of carrot
      (69 kDa) and Neurospora crassa (67 kDa) vacuolar membrane H+-ATPases (62 and 73% identity over
      600 residues, respectively). The homologous regions also show about 25% sequence identity over
      400 residues with beta-subunits of F0F1-ATPases. In contrast, the internal region containing
      454 amino acid residues (residues 285-738) shows no detectable sequence similarities to any
      known ATPase subunits and instead is similar to a yeast endonuclease encoded by the HO gene.
      None of the six tryptic peptides is located in this internal region. Northern blotting
      analysis detected a single mRNA of 3.5 kilobases, indicating that the gene has no introns.
      Although the reason for the discrepancy in molecular mass is unclear at present, these results
      suggest that a novel processing mechanism, which might involve a post-translational excision
      of the internal region followed by peptide ligation, operates on the yeast VMA1 product. The
      VMA1 gene has proved to be the same gene as the TFP1 gene whose dominant mutant allele
      (TFP1-408) confers a dominant trifluoperazine resistance and Ca2+-sensitive growth. This and
      our findings suggest that the vacuolar membrane H+-ATPase participates in maintenance of
      cytoplasmic Ca2+ homeostasis.
AU  - Hirata R
AU  - Ohsumi Y
AU  - Nakano A
AU  - Kawasaki H
AU  - Suzuki K
AU  - Anraku Y
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1990 265: 6726-6733.

PMID- 
VI  - 368
DP  - 2001
TI  - Molecules controlling genetic information, Part 4, Restriction endonucleases.
PG  - 52-54
AB  - 
AU  - Hirayama N
PT  - Journal Article
TA  - Gendai Kagaku
JT  - Gendai Kagaku
SO  - Gendai Kagaku 2001 368: 52-54.

PMID- 29674557
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Interpatient and Intrapatient Epidemiologically Linked  Neisseria gonorrhoeae Isolates.
PG  - e00319-18
AB  - Neisseria gonorrhoeae is the causative agent of gonorrhea and was identified by the World
      Health Organization as an urgent public health threat due to emerging
      antibiotic resistance. Here, we report 13 draft genome sequences of N.
      gonorrhoeae isolates derived from two epidemiologically linked cases from
      Austria.
AU  - Hirk S
AU  - Lepuschitz S
AU  - Cabal RA
AU  - Huhulescu S
AU  - Blaschitz M
AU  - Stoger A
AU  - Stadlbauer S
AU  - Hasenberger P
AU  - Indra A
AU  - Schmid D
AU  - Ruppitsch W
AU  - Allerberger F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00319-18.

PMID- 29674554
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Pseudomonas sp. Strain LLC-1 (NBRC 111237), Capable of Metabolizing Lignin-Derived Low-Molecular-Weight Compounds.
PG  - e00308-18
AB  - Pseudomonas sp. strain LLC-1 (NBRC 111237), isolated from soil, metabolizes lignin-derived
      low-molecular-weight compounds and utilizes vanillin and vanillic
      acid as its sole sources of carbon. Here, we report the draft genome sequence of
      Pseudomonas sp. strain LLC-1.
AU  - Hirose J
AU  - Tsuda N
AU  - Miyatake M
AU  - Yokoi H
AU  - Shimodaira J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00308-18.

PMID- 26494664
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Polychlorinated Biphenyl-Degrading Bacterium Pseudomonas stutzeri KF716 (NBRC 110668).
PG  - e01215-15
AB  - Pseudomonas stutzeri KF716 (NBRC 110668) utilizes biphenyl as a sole source of carbon and
      energy and degrades polychlorinated biphenyls. Here, we report the first draft genome sequence
      of a biphenyl-degrading strain of the species P. stutzeri.
AU  - Hirose J
AU  - Yamazoe A
AU  - Hosoyama A
AU  - Kimura N
AU  - Suenaga H
AU  - Watanabe T
AU  - Fujihara H
AU  - Futagami T
AU  - Goto M
AU  - Furukawa K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01215-15.

PMID- 26472850
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Polychlorinated Biphenyl-Degrading Bacterium Comamonas testosteroni KF712 (NBRC 110673).
PG  - e01214-15
AB  - We present a 5.89-Mb draft genome sequence of Comamonas testosteroni KF712 (NBRC  110673), a
      polychlorinated biphenyl degrader. The genome sequence clarified that  KF712 harbors the gene
      clusters coding for the catabolism of biphenyl and at least seven other aromatic compounds.
AU  - Hirose J
AU  - Yamazoe A
AU  - Hosoyama A
AU  - Kimura N
AU  - Suenaga H
AU  - Watanabe T
AU  - Fujihara H
AU  - Futagami T
AU  - Goto M
AU  - Furukawa K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01214-15.

PMID- 26988037
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Cyanobacterium Leptolyngbya sp. NIES-3755.
PG  - e00090-16
AB  - Cyanobacterial genus Leptolyngbya comprises genetically diverse species, but the  availability
      of their complete genome information is limited. Here, we isolated
      Leptolyngbya sp. strain NIES-3755 from soil at the Toyohashi University of
      Technology, Japan. We determined the complete genome sequence of the NIES-3755
      strain, which is composed of one chromosome and three plasmids.
AU  - Hirose Y
AU  - Fujisawa T
AU  - Ohtsubo Y
AU  - Katayama M
AU  - Misawa N
AU  - Wakazuki S
AU  - Shimura Y
AU  - Nakamura Y
AU  - Kawachi M
AU  - Yoshikawa H
AU  - Eki T
AU  - Kanesaki Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00090-16.

PMID- 25931605
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Cyanobacterium Geminocystis sp. Strain NIES-3709, Which Harbors a Phycoerythrin-Rich Phycobilisome.
PG  - e00385-15
AB  - The cyanobacterium Geminocystis sp. strain NIES-3709 accumulates a larger amount  of
      phycoerythrin than the related NIES-3708 strain does. Here, we determined the
      complete genome sequence of the NIES-3709 strain. Our genome data suggest that
      the different copy number of rod linker genes for phycoerythrin leads to the
      different phycoerythrin contents between the two strains.
AU  - Hirose Y
AU  - Katayama M
AU  - Ohtsubo Y
AU  - Misawa N
AU  - Iioka E
AU  - Suda W
AU  - Oshima K
AU  - Hanaoka M
AU  - Tanaka K
AU  - Eki T
AU  - Ikeuchi M
AU  - Kikuchi Y
AU  - Ishida M
AU  - Hattori M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00385-15.

PMID- 25953174
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Cyanobacterium Geminocystis sp. Strain NIES-3708, Which Performs Type II Complementary Chromatic Acclimation.
PG  - e00357-15
AB  - To explore the variation of the light-regulated genes during complementary chromatic
      acclimation (CCA), we determined the complete genome sequence of the
      cyanobacterium Geminocystis sp. strain NIES-3708. Within the light-regulated
      operon for CCA, we found genes for phycoerythrin but not phycocyanin, suggesting
      that this cyanobacterium modulates phycoerythrin composition only (type II CCA).
AU  - Hirose Y
AU  - Katayama M
AU  - Ohtsubo Y
AU  - Misawa N
AU  - Iioka E
AU  - Suda W
AU  - Oshima K
AU  - Hanaoka M
AU  - Tanaka K
AU  - Eki T
AU  - Ikeuchi M
AU  - Kikuchi Y
AU  - Ishida M
AU  - Hattori M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00357-15.

PMID- 24072863
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Micromonospora Strain L5, a Potential Plant-Growth-Regulating Actinomycete, Originally Isolated from Casuarina  equisetifolia Root Nodules.
PG  - e00759-13
AB  - Micromonospora species live in diverse environments and exhibit a broad range of  functions,
      including antibiotic production, biocontrol, and degradation of
      complex polysaccharides. To learn more about these versatile actinomycetes, we
      sequenced the genome of strain L5, originally isolated from root nodules of an
      actinorhizal plant growing in Mexico.
AU  - Hirsch AM et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00759-13.

PMID- 9042953
VI  - 403
DP  - 1997
TI  - Crystallization and preliminary X-ray analysis of restriction endonuclease FokI bound to DNA.
PG  - 136-138
AB  - FokI is a type IIs restriction endonuclease which recognizes an asymmetric DNA sequence and
      cleaves DNA a short distance away from the sequence.  The enzyme is bipartite in nature with
      its DNA recognition and cleavage functions located on distinct domains.  We report here
      cocrystals of the complete FokI enzyme (579 amino acids) bound to a 20-bp DNA fragment
      containing its recognition sequence.  The complex is amongst the largest protein-DNA complexes
      to be crystallized, and required macroseeding techniques for optimal crystal growth.  The
      cocrystals diffract to at least 2.8 Angstroms in resolution and belong to space group P21 with
      unit cell dimensions of a=67.9, b=119.8, c=69.1 Angstroms, b=96.6 degrees.  Using specific
      amino acid analysis we show that asymmetric unit contains a single FokI molecule bound to the
      20-bp DNA fragment.  This paper reports the first cocrystals of a type IIs restriction
      endonuclease.
AU  - Hirsch JA
AU  - Wah DA
AU  - Dorner LF
AU  - Shildkraut I
AU  - Aggarwal AK
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1997 403: 136-138.

PMID- 4885337
VI  - 102
DP  - 1968
TI  - Inhibition of modification and restriction for phages lambda and Tl by co-infecting T3.
PG  - 89-94
AB  - The host controlled modifications of phage lambda DNA by Escherichia coli B,K, and C(P1) can
      be suppressed by preinfecting the bacteria with UV-irradiated phage T3.  Since UV-irradiated
      T3 induces an enzyme which cleaves S-adenosylmethionine into homoserine and thiomethyl
      adenosine, and since S-adenosylmethionine is the only methyl group donor for DNA methylation,
      we conclude that methylation is a required step in the host controlled modification of
      lambda-DNA.  T3 itself successfully infects E. coli K and B with its nonmethylated DNA.  Also,
      restricted phage lambda or Tl will be accepted by the restrictive hosts E. coli B,K, and C(P1)
      if these are preinfected with UV-T3.  It thus appears that T3 is capable of blocking the
      restriction mechanisms in these hosts.  The inability of T3 to grow on C(P1) is not
      understood.  Since T3-DNA is restricted but not degraded into nucleotides by E. coli C(P1) we
      presume that degradation is not the initial step in restriction.
AU  - Hirsch-Kauffmann M
AU  - Sauerbier W
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1968 102: 89-94.

PMID- 21327935
VI  - 17
DP  - 2011
TI  - Dissemination of multiple MRSA clones among community-associated methicillin-resistant Staphylococcus aureus infections from Japanese children with impetigo.
PG  - 609-621
AB  - The proportion of MRSA strains that cause skin
      and soft infections has recently increased. In 3 months we
      have characterized 17 MRSA strains isolated from children
      with impetigo at a Japanese hospital. Seventeen MRSA
      strains belonged to 7 clones defined by clonal complex
      (CC) in MLST genotype and type of SCCmec, which were
      rarely identified among healthcare-associated MRSA: CC
      91-SCCmecIIb (4 strains); CC91-SCCmecIIn (2 strains);
      CC91-SCCmecIVa (2 strains); CC91-SCCmecV (4 strains);
      CC88-SCCmecIVg (3 strains); CC1-SCCmecIVc (1 strain);
      and CC5-SCCmecIVn (1 strain). Although one strain
      belonged to CC5, which has been commonly identified in
      healthcare-associated MRSA, it did not carry type II
      SCCmec, but carried type IV SCCmec. Fourteen of the 17
      strains carried exfoliative toxin a or b gene, and none
      carried Panton-Valentine leukocidine gene. Furthermore,
      we determined the entire nucleotide sequences of two type
      V SCCmec elements carried by strains JCSC5952, a CC91
      strain, and TSGH17, a Taiwanese CC59 strain. The structure
      of SCCmecJCSC5952 was more than 99% homologous
      in nucleotide identity with those of Taiwanese
      PVL-positive ST59 MRSA strains TSGH17 and PM1,
      which were designated as type V
AU  - Hisata K
AU  - Ito T
AU  - Matsunaga N
AU  - Komatsu M
AU  - Jin J
AU  - Li S
AU  - Watanabe S
AU  - Shimizu T
AU  - Hiramatsu K
PT  - Journal Article
TA  - J. Infect. Chemother.
JT  - J. Infect. Chemother.
SO  - J. Infect. Chemother. 2011 17: 609-621.

PMID- 28860242
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Systemically Disseminated Sequence Type 8 Staphylococcal Cassette Chromosome mec Type IVl Community-Acquired  Methicillin-Resistant Staphylococcus aureus.
PG  - e00852-17
AB  - Staphylococcus aureus JH4899, a community-acquired methicillin-resistant Staphylococcus aureus
      (CA-MRSA) isolate collected from a patient with
      systematically disseminated infection, is classified as sequence type 8 and
      carries the staphylococcal cassette chromosome mec type IVl (SCCmecIVl). It
      produces TSST-1, SEC, a newly discovered enterotoxin (SE1), and epidermal cell
      differentiation inhibitor A (EDIN-A). Here, we present the complete genome
      sequence of the chromosome and a plasmid harboring the se1 and ednA genes.
AU  - Hisatsune J
AU  - Hagiya H
AU  - Shiota S
AU  - Sugai M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00852-17.

PMID- 26988042
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Vancomycin-Intermediate Staphylococcus aureus Strain  MI (HIP5827).
PG  - e00123-16
AB  - We report the complete genome sequence of vancomycin-intermediate Staphylococcus  aureus
      (VISA) strain MI (HIP5827).
AU  - Hishinuma T
AU  - Katayama Y
AU  - Matsuo M
AU  - Sasaki T
AU  - Hiramatsu K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00123-16.

PMID- 23516194
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Actinomycete Rhodococcus sp. Strain AW25M09, Isolated from the Hadsel Fjord, Northern Norway.
PG  - e0005513
AB  - The cold-adapted Rhodococcus sp. strain AW25M09 was isolated from an Atlantic hagfish caught
      off the shore of northern Norway as part of an ongoing
      bioprospecting project that aims to identify novel bacteria with biotechnological
      potential. Here, we present the 5.8-Mb draft genome sequence, together with
      details regarding the origin of the strain and its sequence assembly.
AU  - Hjerde E
AU  - Pierechod MM
AU  - Williamson AK
AU  - Bjerga GE
AU  - Willassen NP
AU  - Smalas AO
AU  - Altermark B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0005513.

PMID- Not carried by PubMed...
VI  - 20
DP  - 1992
TI  - Screening of Rhodothermus marinus for restriction endonucleases.
PG  - 17
AB  - A screening of 43 Rhodothermus marinus strains for restriction endonucleases was done.  Two
      types of DNA substrates were used in the screening assay.  They were T7 DNA and lambda DNA.  A
      total of 27 strains (63%) showed cleavage of one or both substrates.  Restriction
      endonuclease positive strains were compared with a dendrogram based on a number of
      characteristics of the Rhodothermus marinus group genus.  The comparison revealed that
      restriction endonucleases exist in certain groups of strains.  Characterization of the
      restriction endonucleases indicate that all positive strains contain RmaI, an isoschizomer of
      MaeI and 3 strains contain a second restriction endonuclease, an isoschizomer of EcoRV as
      well.  RmaI, a type II restriction endonuclease, has been put on the market.
AU  - Hjorleifsdottir S
AU  - Pelursdottir S
AU  - Kristjansson JK
AU  - Korpela J
AU  - Torsti A-M
AU  - Mattila P
PT  - Journal Article
TA  - Thermophiles Sci. Technol.
JT  - Thermophiles Sci. Technol.
SO  - Thermophiles Sci. Technol. 1992 20: 17.

PMID- Not carried by PubMed...
VI  - 10
DP  - 1996
TI  - Screening for restriction endonucleases in aerobic, thermophilic eubacteria.
PG  - 13-18
AB  - A total of 216 Icelandic aerobic, heterotrophic, thermophiles belonging to three different
      genera were screened for type II restriction endonucleases.  The frequency of positive strains
      was 44% for both Thermus and Bacillus but 63% for Rhodothermus.  Approximately half of the
      enzymes from each group were characterised and a total of 14 different restriction enzymes
      were found.  In all cases they were isoschizomers of known enzymes.  Thermus contained 9
      different types, Bacillus 6 and Rhodothermus had 3.  This is the first time that isoschizomers
      of BspEI, BglI, EagI and EcoRV are found in Thermus and BstBI and EcoRV are found in
      Rhodothermus.
AU  - Hjorleifsdottir S
AU  - Petursdottir SK
AU  - Korpela J
AU  - Torsti A-M
AU  - Mattila P
AU  - Kristjansson JK
PT  - Journal Article
TA  - Biotechnol. Tech.
JT  - Biotechnol. Tech.
SO  - Biotechnol. Tech. 1996 10: 13-18.

PMID- 10715131
VI  - 39
DP  - 2000
TI  - Identification of the metal-binding sites of restriction endonucleases by Fe(2+)-mediated oxidative cleavage.
PG  - 3097-3105
AB  - Fenton chemistry [Fenton (1894) J. Chem. Soc. 65, 899-910] techniques were employed to
      identify the residues involved in metal binding located at the active sites of restriction
      endonucleases. This process uses transition metals to catalytically oxidize the peptide
      linkage that is in close proximity to the amino acid residues involved in metal ligation.
      Fe(2+) was used as the redox-active transition metal. It was expected that Fe(2+) would bind
      to the endonucleases at the Mg(2+)-binding site [Liaw et al. (1993) Biochemistry 32,
      7999-4003; Ermacora et al. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 6383-6387; Soundar and
      Colman (1993) J. Biol. Chem. 268, 5264-5271; Wei et al. (1994) Biochemistry 33, 7931-7936;
      Ettner et al. (1995) Biochemistry 34, 22-31; Hlavaty and Nowak (1997) Biochemistry 36,
      15515-15525). Fe(2+)-mediated oxidation was successfully performed on TaqI endonuclease,
      suggesting that this approach could be applied to a wide array of endonucleases [Cao and
      Barany (1998) J. Biol. Chem. 273, 33002-33010]. The restriction endonucleases BamHI, FokI,
      BglI, BglII, PvuII, SfiI, BssSI, BsoBI, EcoRI, EcoRV, MspI, and HinP1I were subjected to
      oxidizing conditions in the presence of Fe(2+) and ascorbate. All proteins were inactivated
      upon treatment with Fe(2+) and ascorbate. BamHI, FokI, BglI, BglII, PvuII, SfiI, BssSI, and
      BsoBI were specifically cleaved upon treatment with Fe(2+)/ascorbate. The site of
      Fe(2+)/ascorbate-induced protein cleavage for each enzyme was determined. The Fe(2+)-mediated
      oxidative cleavage of BamHI occurs between residues Glu77 and Lys78. Glu77 has been shown by
      structural and mutational studies to be involved in both metal ligation and catalysis [Newman
      et al. (1995) Science 269, 656-663; Viadiu and Aggarwal (1998) Nat. Struct. Biol. 5, 910-916;
      Xu and Schildkraut (1991) J. Biol. Chem. 266, 4425-4429]. The sites of
      Fe(2+)/ascorbate-induced cleavage for PvuII, FokI, BglI, and BsoBI agree with the
      metal-binding sites identified in their corresponding three-dimensional structures or from
      mutational studies [Cheng et al. (1994) EMBO J. 13, 3297-3935; Wah et al. (1997) Nature 388,
      97-100; Newman et al. (1998) EMBO J. 17, 5466-5476; Ruan et al. (1997) Gene 188, 35-39]. The
      metal-binding residues of BglII, SfiI, and BssSI are proposed based on amino acid sequencing
      of their Fe(2+)/ascorbate-generated cleavage fragments. These results suggest that Fenton
      chemistry may be a useful methodology in identifying amino acids involved in metal binding in
      endonucleases.
AU  - Hlavaty JJ
AU  - Benner JS
AU  - Hornstra LJ
AU  - Schildkraut I
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2000 39: 3097-3105.

PMID- 23723398
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences of Two Multidrug-Resistant Acinetobacter baumannii Strains of Sequence Type ST92 and ST96.
PG  - e00296-13
AB  - The global epidemiology of multidrug-resistant Acinetobacter baumannii is dominated by a
      limited number of clones. Here, we announce the draft genome
      sequences of two multidrug-resistant A. baumannii strains, 1H8 and 4A3,
      representing the major epidemic clones, sequence type 92 (ST92) and ST96,
      respectively.
AU  - Ho AY
AU  - Chow KH
AU  - Law PY
AU  - Tse H
AU  - Ho PL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00296-13.

PMID- 1989510
VI  - 284
DP  - 1991
TI  - Stereochemical studies of the C-methylation of deoxycytidine catalyzed by HhaI methylase and the N-methylation of deoxyadenosine catalyzed by EcoRI methylase.
PG  - 264-269
AB  - The steric course of methyl group transfer catalyzed by two DNA methylases, HhaI methylase,
      HhaI methylase, a DNA (cytosine-5) methyltransferase, and EcoRI methylase, which methylates at
      N6 of adenosine, has been studied with (methyl-R)- and (methyl-S)-[methyl-2H1,3H]
      adenosylmethionine as the methyl donor, using as substrates poly-d(GC) (HhaI) and the
      dodecamer oligonucleotide duplex d(CGCGAATTCGCG) (EcoRI), respectively. The methylated
      nucleotides were degraded to convert the chiral methyl groups into acetic acid for
      configurational analysis. It was found that both enzymatic reactions proceed with inversion of
      configuration of the methyl group.
AU  - Ho DK
AU  - Wu JC
AU  - Santi DV
AU  - Floss HG
PT  - Journal Article
TA  - Arch. Biochem. Biophys.
JT  - Arch. Biochem. Biophys.
SO  - Arch. Biochem. Biophys. 1991 284: 264-269.

PMID- 28619790
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Acinetobacter calcoaceticus CA16, a Bacterium Capable of Degrading Diesel and Lignin.
PG  - e00494-17
AB  - We report here the complete assembled genome sequence of Acinetobacter calcoaceticus CA16,
      which is capable of utilizing diesel and lignin as a sole
      carbon source. CA16 contains a 4,110,074-bp chromosome and a 5,920-bp plasmid.
      The assembled sequences will help elucidate potential metabolic pathways and
      mechanisms responsible for CA16's hydrocarbon degradation ability.
AU  - Ho MT
AU  - Weselowski B
AU  - Yuan ZC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00494-17.

PMID- 
VI  - 10
DP  - 2012
TI  - Genomic characterization of two new Salmonella bacteriophages: vB_SosS_Oslo and vB_SemP_Emek.
PG  - 18-23
AB  - Salmonella are classified on the basis of their surface antigens of which the O-antigen, which
      is the immunodominant portion of the lipopolysaccharide molecule, is highly variable among
      different strains.  Enzymes modifying O-antigenes are often encoded by prophages which
      represent the genomes of integrated temperate phages.  The expression of certain prophage
      genes by the lysogen can often result in the change in serotype of the host.  It was
      hypothesized that O-antigenes 14 and 20 of Salmonella strains might be encoded on prophages.
      This report outlines the isolation and sequencing of two novel bacteriophages,one from each fo
      Salmonella enterica serovars Oslo and Emek thought to have given rise to O-antigens 14 and 20,
      respectively.  Further analysis through lysogen isolation and serotyping has proven otherwise.
AU  - Ho N
AU  - Lingohr EJ
AU  - Villegas A
AU  - Cole L
AU  - Kropinski AM
PT  - Journal Article
TA  - Ann. Agrar. Sci.
JT  - Ann. Agrar. Sci.
SO  - Ann. Agrar. Sci. 2012 10: 18-23.

PMID- 27503649
VI  - 60
DP  - 2016
TI  - Emergence of ileS2-Carrying, Multidrug-Resistant Plasmids in Staphylococcus lugdunensis.
PG  - 6411-6414
AB  - Of 137 Staphylococcus lugdunensis isolates collected from two nephrology centers
      in Hong Kong, 10 (7.3%) and 3 (2.2%) isolates had high-level and low-level
      mupirocin resistance, respectively. Isolates with high-level resistance contained
      the plasmid-mediated ileS2 gene, while isolates with low-level resistance
      contained the mutation V588F within the chromosomal ileS gene. All but one of the
      ileS2-positive isolates belong to the predominating clone HKU1. Plasmids carrying
      the ileS2 gene were mosaic and also cocarry multiple other resistance
      determinants.
AU  - Ho PL
AU  - Liu MC
AU  - Chow KH
AU  - Tse CW
AU  - Lo WU
AU  - Mak SK
AU  - Lo WK
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2016 60: 6411-6414.

PMID- 24121549
VI  - 68
DP  - 2014
TI  - pIMP-PH114 Carrying bla IMP-4 in a Klebsiella pneumoniae Strain is Closely Related to Other Multidrug-Resistant IncA/C2 Plasmids.
PG  - 227-232
AB  - The IncA/C plasmids are broad host-range vehicles which have been associated with
      wide dissemination of CMY-2 among Enterobacteriaceae of human and animal origins.
      Acquired metallo-beta-lactamases (MBLs) such as the IMP-type enzymes are
      increasingly reported in multidrug-resistant Gram-negative bacteria worldwide,
      particularly in Enterobacteriaceae. We described the complete sequence of the
      first IMP-4-encoding IncA/C2 plasmid, pIMP-PH114 (151,885 bp), from a sequence
      type 1 Klebsiella pneumoniae strain that was recovered from a patient who was
      hospitalized in the Philippines. pIMP-PH114 consists of a backbone from the
      IncA/C2 plasmids, with the insertion of a novel Tn21-like class 1 integron
      composite structure (containing the cassette array bla IMP-4-qacG-aacA4-catB3,
      followed by a class C beta-lactamase bla DHA-1 and the mercury resistance operon,
      merRTPCADE) and a sul2-floR encoding region. Phylogenetic analysis of the IncA/C
      repA sequences showed that pIMP-PH114 formed a subgroup with other IncA/C
      plasmids involved in the international spread of CMY-2, TEM-24 and NDM-1.
      Identical bla IMP-4 arrays have been described among different Enterobacteriaceae
      and Acinetobacter spp. in China, Singapore and Australia but the genetic context
      is different. The broad host range of IncA/C plasmids may have facilitated
      dissemination of the bla IMP-4 arrays among different diverse groups of bacteria.
AU  - Ho PL
AU  - Lo WU
AU  - Chan J
AU  - Cheung YY
AU  - Chow KH
AU  - Yam WC
AU  - Lin CH
AU  - Que TL
PT  - Journal Article
TA  - Curr. Microbiol.
JT  - Curr. Microbiol.
SO  - Curr. Microbiol. 2014 68: 227-232.

PMID- 17496058
VI  - 60
DP  - 2007
TI  - Community emergence of CTX-M type extended-spectrum beta-lactamases among urinary Escherichia coli from women.
PG  - 140-144
AB  - OBJECTIVES: To conduct a territory-wide study of extended-spectrum
      beta-lactamases (ESBLs) among community isolates of urinary Escherichia
      coli from women in Hong Kong. METHODS: Up to 50 consecutive single-patient
      E. coli isolates, collected from 13 laboratories in 2004, were studied.
      The ESBLs were characterized by PCR sequencing using specific primers. The
      epidemiological relationship of the isolates was studied by PFGE and
      phylogenetic group PCRs. RESULTS: Forty-two ESBL producers were found
      among 600 consecutive isolates tested. The ESBL prevalence was 7.3%
      (15/205) for women aged 18-35 years, 5% (11/219) for women aged 36-50
      years, 6.3% (4/63) for women aged 51-64 years and 10.6% (12/113) for women
      aged >or=65 years (P=0.3). The ESBL-producing isolates were often
      multidrug-resistant and CTX-M-14 was found in 37 isolates, CTX-M-15 in 3
      isolates and CTX-M-3 in 2 isolates. PFGE revealed no significant clusters
      among the ESBL producers. Overall, CTX-M-14 producers were significantly
      more likely to belong to group D than non-ESBL producers [18/37 (48.6%)
      versus 13/57 (22.8%), P=0.009]. However, 7 of 13 (53.8%) CTX-M-14
      producers from women aged 18-35 years represented phylogenetic group B2,
      compared with 7 of 24 (29.2%) for women of all other ages (P=0.1).
      CONCLUSIONS: The study documented the community emergence of CTX-M as the
      predominant ESBL type among urinary isolates from women. The spread of
      CTX-M enzymes among isolates from young women is concerning and deserves
      close monitoring.
AU  - Ho PL
AU  - Poon WW
AU  - Loke SL
AU  - Leung MS
AU  - Chow KH
AU  - Wong RC
AU  - Yip KS
AU  - Lai EL
AU  - Tsang KW
PT  - Journal Article
TA  - J. Antimicrob. Chemother.
JT  - J. Antimicrob. Chemother.
SO  - J. Antimicrob. Chemother. 2007 60: 140-144.

PMID- 23144425
VI  - 194
DP  - 2012
TI  - Genome Sequence of Multidrug-Resistant Escherichia coli EC302/04, Isolated from a Human Tracheal Aspirate.
PG  - 6691-6692
AB  - Escherichia coli is an important etiologic agent of lower respiratory tract infections (LRTI).
      Multidrug-resistant E. coli EC302/04 was isolated from a
      tracheal aspirate, and its genome sequence is expected to provide insights into
      antimicrobial resistance as well as adaptive and virulence mechanisms of E. coli
      involved in LRTI.
AU  - Ho WS
AU  - Gan HM
AU  - Yap KP
AU  - Balan G
AU  - Yeo CC
AU  - Thong KL
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6691-6692.

PMID- 25879448
VI  - 16
DP  - 2015
TI  - The dnd operon for DNA phosphorothioation modification system in Escherichia coli is located in diverse genomic islands.
PG  - 199
AB  - Background: Strains of Escherichia coli that are non-typeable by pulsed-field gel
      electrophoresis (PFGE) due to in-gel degradation can influence their molecular
      epidemiological data. The DNA degradation phenotype (Dnd+) is mediated by the dnd
      operon that encode enzymes catalyzing the phosphorothioation of DNA, rendering
      the modified DNA susceptible to oxidative cleavage during a PFGE run. In this
      study, a PCR assay was developed to detect the presence of the dnd operon in
      Dnd+E. coli strains and to improve their typeability. Investigations into the
      genetic environments of the dnd operon in various E. coli strains led to the
      discovery that the dnd operon is harboured in various diverse genomic islands.
      Results: The dndBCDE genes (dnd operon) were detected in all Dnd+E. coli strains
      by PCR. The addition of thiourea improved the typeability of Dnd+E. coli strains
      to 100% using PFGE and the Dnd+ phenotype can be observed in both clonal and
      genetically diverse E. coli strains.Genomic analysis of 101 dnd operons from
      genome sequences of Enterobacteriaceae revealed that the dnd operons of the same
      bacterial species were generally clustered together in the phylogenetic tree.
      Further analysis of dnd operons of 52 E. coli genomes together with their
      respective immediate genetic environments revealed a total of 7 types of genetic
      organizations, all of which were found to be associated with genomic islands
      designated dnd-encoding GIs. The dnd-encoding GIs displayed mosaic structure and
      the genomic context of the 7 islands (with 1 representative genome from each type
      of genetic organization) were also highly variable, suggesting multiple
      recombination events. This is also the first report where two dnd operons were
      found within a strain although the biological implication is unknown.
      Surprisingly, dnd operons were frequently found in pathogenic E. coli although
      their link with virulence has not been explored. Conclusion: Genomic islands
      likely play an important role in facilitating the horizontal gene transfer of the
      dnd operons in E. coli with 7 different types of islands discovered so far.
      Electronic supplementary material: The online version of this article
      (doi:10.1186/s12864-015-1421-8) contains supplementary material, which is
      available to authorized users.
AU  - Ho WS
AU  - Ou HY
AU  - Yeo CC
AU  - Thong KL
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2015 16: 199.

PMID- 26793180
VI  - 6
DP  - 2016
TI  - The Complete Sequence and Comparative Analysis of a Multidrug-Resistance and Virulence Multireplicon IncFII Plasmid pEC302/04 from an Extraintestinal Pathogenic Escherichia coli EC302/04 Indicate Extensive Diversity of IncFII Plasmids.
PG  - 1547
AB  - Extraintestinal pathogenic Escherichia coli (ExPEC) that causes extraintestinal
      infections often harbor plasmids encoding fitness traits such as resistance and
      virulence determinants that are of clinical importance. We determined the
      complete nucleotide sequence of plasmid pEC302/04 from a multidrug-resistant E.
      coli EC302/04 which was isolated from the tracheal aspirate of a patient in
      Malaysia. In addition, we also performed comparative sequence analyses of 18
      related IncFIIA plasmids to determine the phylogenetic relationship and diversity
      of these plasmids. The 140,232 bp pEC302/04 is a multireplicon plasmid that bears
      three replication systems (FII, FIA, and FIB) with subtype of F2:A1:B1. The
      plasmid is self-transmissible with a complete transfer region. pEC302/04 also
      carries antibiotic resistance genes such as bla TEM-1 and a class I integron
      containing sul1, cml and aadA resistance genes, conferring multidrug resistance
      (MDR) to its host, E. coli EC302/04. Besides, two iron acquisition systems
      (SitABCD and IutA-IucABCD) which are the conserved virulence determinants of
      ExPEC-colicin V or B and M (ColV/ColBM)-producing plasmids were identified in
      pEC302/04. Multiple toxin-antitoxin (TA)-based addiction systems (i.e.,
      PemI/PemK, VagC/VagD, CcdA/CcdB, and Hok/Sok) and a plasmid partitioning system,
      ParAB, and PsiAB, which are important for plasmid maintenance were also found.
      Comparative plasmid analysis revealed only one conserved gene, the repA1 as the
      core genome, showing that there is an extensive diversity among the IncFIIA
      plasmids. The phylogenetic relationship of 18 IncF plasmids based on the core
      regions revealed that ColV/ColBM-plasmids and non-ColV/ColBM plasmids were
      separated into two distinct groups. These plasmids, which carry highly diverse
      genetic contents, are also mosaic in nature. The atypical combination of genetic
      materials, i.e., the MDR- and ColV/ColBM-plasmid-virulence encoding regions in a
      single ExPEC plasmid is rare but of clinical importance. Such phenomenon is
      bothersome when the plasmids are transmissible, facilitating the spread of
      virulence and resistance plasmids among pathogenic bacteria. Notably, certain TA
      systems are more commonly found in particular ExPEC plasmid types, indicating the
      possible relationships between certain TA systems and ExPEC pathogenesis.
AU  - Ho WS
AU  - Yap KP
AU  - Yeo CC
AU  - Rajasekaram G
AU  - Thong KL
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2016 6: 1547.

PMID- 9256423
VI  - 94
DP  - 1997
TI  - A protein encoded by a group I intron in Aspergillus nidulans directly assists RNA splicing and is a DNA endonuclease.
PG  - 8994-8999
AB  - Some group I introns self-splice in vitro, but almost all are thought to be assisted by
      proteins in vivo.  Mutational analysis has shown that the splicing of certain group I introns
      depends upon a maturase protein encoded by the intron itself.  However the effect of a protein
      on splicing can be indirect.  We now provide evidence that a mitochondrial intron-encoded
      protein from Aspergillus nidulans directly facilitates splicing in vitro.  This demonstrates
      that a maturase is an RNA splicing protein.  The protein-assisted reaction is as fast as that
      of any other known group I intron.  Interestingly the protein is also a DNA endonuclease, an
      activity required for intron mobilization.  Mobile elements frequently encode proteins that
      promote their propagation.  Intron-encoded proteins that also assist RNA splicing would
      facilitate both the transposition and horizontal transmission of introns.
AU  - Ho Y
AU  - Kim S-J
AU  - Waring RB
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1997 94: 8994-8999.

PMID- 10512698
VI  - 292
DP  - 1999
TI  - The maturase encoded by a group I intron from Aspergillus nidulans stabilizes RNA tertiary structure and promotes rapid splicing.
PG  - 987-1001
AB  - The AnCOB group I intron from Aspergillus nidulans self-splices, providing the
      Mg(2+)concentration is >/=15 mM. The splicing reaction is greatly stimulated by a maturase
      protein encoded within the intron itself. An initial structural and biochemical analysis of
      the splicing reaction has now been performed. The maturase bound rapidly to the precursor RNA
      (kon approximately 3x10^9 M^-1 min^-1) and remained tightly bound (koff</=0.04 min^-1). The
      catalytic step of 5' splice-site cleavage occurred at a rate of up to 11 min^-1 under single
      turnover conditions. The maturase- assisted reaction of heat-denatured RNA proceeded at a rate
      of about 1 min^-1, arguing that there are early steps of folding that cannot be readily
      facilitated by the protein. pH analysis revealed a biphasic profile with a pKa of 7.0. The
      rate of the maturase-assisted reaction was independent of the Mg(2+)concentration down to 3
      mM. Self-splicing in optimal Mg(2+)(>/=150 mM) was tenfold slower, in part because of the
      existence of an equilibrium between folded and partially folded RNA. In contrast, the maturase
      very effectively stabilized tertiary structure in 5 mM Mg(2+), a noticeable example being an
      interaction between the P8 helix and a GNRA sequence that constitutes the L2 terminal loop of
      the P2 helix. Formation of the 5' splice-site recognition helix was assisted by either the
      maturase or high concentrations of Mg(2+). The maturase was required during splicing so it is
      not a true chaperone. However, RNase protection assays and kinetic studies suggest that the
      maturase recognizes and facilitates folding of an intron with limited tertiary structure and
      even incomplete secondary structure.
AU  - Ho Y
AU  - Waring RB
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1999 292: 987-1001.

PMID- 26564046
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Burkholderia cenocepacia Strain 869T2, a Plant-Beneficial Endophytic Bacterium.
PG  - e01327-15
AB  - An endophytic bacterium, Burkholderia cenocepacia 869T2, isolated from vetiver grass, has
      shown its abilities for both in planta biocontrol and plant growth
      promotion. Its draft genome sequence was determined to provide insights into
      those metabolic pathways involved in plant-beneficial activity. This is the first
      genome report for endophytic B. cenocepacia.
AU  - Ho YN
AU  - Huang CC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01327-15.

PMID- 23105074
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Mycobacterium vaccae Type Strain ATCC 25954.
PG  - 6339-6340
AB  - Mycobacterium vaccae is a rapidly growing, nontuberculous Mycobacterium species that is
      generally not considered a human pathogen and is of major pharmaceutical
      interest as an immunotherapeutic agent. We report here the annotated genome
      sequence of the M. vaccae type strain, ATCC 25954.
AU  - Ho YS
AU  - Adroub SA
AU  - Abadi M
AU  - Al AB
AU  - Alkhateeb R
AU  - Gao G
AU  - Ragab A
AU  - Ali S
AU  - van Soolingen D
AU  - Bitter W
AU  - Pain A
AU  - Abdallah AM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6339-6340.

PMID- 23105073
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Mycobacterium fortuitum subsp. fortuitum Type Strain  DSM46621.
PG  - 6337-6338
AB  - Mycobacterium fortuitum is a member of the rapidly growing nontuberculous mycobacteria (NTM).
      It is ubiquitous in water and soil habitats, including
      hospital environments. M. fortuitum is increasingly recognized as an
      opportunistic nosocomial pathogen causing disseminated infection. Here we report
      the genome sequence of M. fortuitum subsp. fortuitum type strain DSM46621.
AU  - Ho YS
AU  - Adroub SA
AU  - Aleisa F
AU  - Mahmood H
AU  - Othoum G
AU  - Rashid F
AU  - Zaher M
AU  - Ali S
AU  - Bitter W
AU  - Pain A
AU  - Abdallah AM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6337-6338.

PMID- 24944333
VI  - 64
DP  - 2014
TI  - Brachybacterium ginsengisoli sp. nov., isolated from soil of a ginseng field.
PG  - 3063-3068
AB  - A novel Gram-staining-positive, aerobic bacterium, designed DCY80(T), was
      isolated from soil of a ginseng field in the Republic of Korea. 16S rRNA gene
      sequence analysis revealed that strain DCY80(T) belonged to the genus
      Brachybacterium (95.8-98.2 % similarity) and was most closely related to
      Brachybacterium faecium DSM 4810(T) (98.2 %). Colonies were circular, entire,
      low-convex, opaque and 0.5-1.0 mm in diameter after growth for 2 days on TSA at
      30 degrees C. Growth occurred at 4-34 degrees C (optimum, 25 degrees C), at pH
      5.0-10.0 (optimum, pH 6.5-7.0) and in the presence of 0-7.0 % NaCl. Strain
      DCY80(T) produced siderophores and was sensitive to penicillin G, erythromycin,
      cefazolin, oleandomycin, ceftazidime, vancomycin, tetracycline, novobiocin,
      carbamicillin, rifampicin and neomycin. The DNA G+C content was 71.0 mol%. Levels
      of DNA-DNA relatedness between strain DCY80(T) and B. faecium DSM 4810(T), B.
      paraconglomeratum KCTC 9916(T), B. saurashtrense DSM 23186(T) and B.
      conglomeratum KCTC 9915(T) were 46.9+/-0.5, 28.9+/-0.6, 20.4+/-0.9 and 17.3+/-0.4
      %, respectively. The cell-wall peptidoglycan of strain DCY80(T) contained
      meso-diaminopimelic acid as the diagnostic diamino acid. The menaquinones were
      MK-7 (85.8 %) and MK-8 (14.2 %). The major cellular fatty acids were anteiso-C15
      : 0 (69.1 %) and anteiso-C17 : 0 (12.2 %). Phosphatidylglycerol,
      diphosphatidylglycerol, an unidentified glycolipid, two unidentified
      phospholipids and five unidentified polar lipids were found. On the basis of our
      phenotypic and genotypic analyses, strain DCY80(T) represents a novel species of
      the genus Brachybacterium, for which the name Brachybacterium ginsengisoli sp.
      nov. is proposed (type strain DCY80(T) = KCTC 29226(T) = JCM 19356(T)).
AU  - Hoang VA
AU  - Kim YJ
AU  - Nguyen NL
AU  - Yang DC
PT  - Journal Article
TA  - Int. J. Syst. Evol. Microbiol.
JT  - Int. J. Syst. Evol. Microbiol.
SO  - Int. J. Syst. Evol. Microbiol. 2014 64: 3063-3068.

PMID- 22483584
VI  - 22
DP  - 2012
TI  - Development of rationally designed DNA N6 adenine methyltransferase inhibitors.
PG  - 3079-3082
AB  - A series of bisubstrate inhibitors for DNA N6 adenine methyltransferase (Dam) have been
      synthesized by linking an amine analogue of
      S-adenosylmethionine to an aryl moiety designed to probe the binding
      pocket of the DNA adenine base. An initial structure-activity
      relationship study has identified substituents that increase inhibitor
      potency to the similar to 10 mu M range and improve selectivity against
      the human cytosine methyltransferase Dnmt1.
AU  - Hobley G
AU  - McKelvie JC
AU  - Harmer JE
AU  - Howe J
AU  - Oyston PCF
AU  - Roach PL
PT  - Journal Article
TA  - Bioorg. Med. Chem. Lett.
JT  - Bioorg. Med. Chem. Lett.
SO  - Bioorg. Med. Chem. Lett. 2012 22: 3079-3082.

PMID- 6273787
VI  - 9
DP  - 1981
TI  - Restriction endonuclease EcaI from Enterobacter cloacae.
PG  - 4823-4832
AB  - Restriction endonuclease EcaI obtained from Enterobacter cloacae DSM30056
      recognizes the group of heptanucleotide palindromes 5'-G-^G-T-N-A-C-C-3', and
      on cleavage (arrow) produces fragments with 5' - terminal pentanucleotide
      extensions.  It is identical in specificity with restriction endonuclease
      BstEII from Bacillus stearothermophiulus ET.
AU  - Hobom G
AU  - Schwarz E
AU  - Melzer M
AU  - Mayer H
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1981 9: 4823-4832.

PMID- 2518929
VI  - 8
DP  - 2008
TI  - Generation of a restriction minus enteropathogenic Escherichia coli E2348/69 strain that is efficiently transformed with large, low copy plasmids.
PG  - 13
AB  - Background: Many microbes possess restriction-modification systems that protect them from
      parasitic DNA molecules. Unfortunately, the presence of a restriction-modification system in a
      given microbe also hampers genetic analysis. Although plasmids can be successfully conjugated
      into the enteropathogenic Escherichia coli strain E2348/69 and optimized protocols for
      competent cell preparation have been developed, we found that a large, low copy (similar to
      15) bioluminescent reporter plasmid, pJW15, that we modified for use in EPEC, was exceedingly
      difficult to transform into E2348/69. We reasoned that a restriction-modification system could
      be responsible for the low transformation efficiency of E2348/69 and sought to identify and
      inactivate the responsible gene(s), with the goal of creating an easily transformable strain
      of EPEC that could complement existing protocols for genetic manipulation of this important
      pathogen.Results: Using bioinformatics, we identified genes in the unfinished enteropathogenic
      Escherichia coli (EPEC) strain E2348/69 genome whose predicted products bear homology to the
      HsdM methyltransferases, HsdS specificity subunits, and HsdR restriction endonucleases of type
      I restriction-modification systems. We constructed a strain carrying a deletion of the
      conserved enzymatic domain of the EPEC HsdR homologue, NH4, and showed that its transformation
      efficiency was up to four orders of magnitude higher than that of the parent strain. Further,
      the modification capacity of NH4 remained intact, since plasmids that were normally
      recalcitrant to transformation into E2348/69 could be transformed upon passage through NH4.
      NH4 was unaffected in virulence factor production, since bundle forming pilus (BFP) subunits
      and type III secreted (T3S) proteins were present at equivalent levels to those seen in
      E2348/69. Further, NH4 was indistinguishable from E2348/69 in tissue culture infection model
      assays of localized adherence and T3S.Conclusion: We have shown that EPEC strain E2348/69
      utilizes a type 1 restriction- modification system to limit entry of new DNA. This
      restriction- modification system does not appear to be involved in virulence determinant
      expression or infection phenotypes. The hsdR mutant strain should prove useful in genetic
      analysis of the important diarrheal pathogen EPEC.
AU  - Hobson N
AU  - Price NL
AU  - Ward JD
AU  - Raivio TL
PT  - Journal Article
TA  - BMC Microbiol.
JT  - BMC Microbiol.
SO  - BMC Microbiol. 2008 8: 13.

PMID- 8467964
VI  - 7
DP  - 1993
TI  - Identification of a critical histidine in EcoRI DNA methyltransferase using protein modification and tandem mass spectrometry.
PG  - A1275
AB  - Diethyl pyrocarbonate (DEPC) is a known histidine specific reagent. Reaction of DEPC with
      EcoRI DNA methyltransferase causes a time-dependent loss of activity due to modification of a
      critical histidine(s) in the enzyme. The second order rate constant of the inactivation of the
      enzyme is 570 M-1s-1. A kinetic analysis of the inactivation by DEPC has been used to
      determine that only one of the seven histidines in the enzyme is critical. The number of
      critical histidines has also been determined spectrophotometrically. This analysis revealed
      that approximately 1.75 histidines are modified by DEPC-mediated inactivation suggests that
      the residue has a pKa of about 6.0. The modified histidines are being identified via tandem
      mass spectrometry methods in a novel LC-m.s. setup.
AU  - Hobson SD
AU  - Falick AM
AU  - Reich NO
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1993 7: A1275.

PMID- 16879640
VI  - 61
DP  - 2006
TI  - Role of pathogenicity island-associated integrases in the genome plasticity of uropathogenic Escherichia coli strain 536.
PG  - 584-595
AB  - The genome of uropathogenic Escherichia coli isolate 536 contains five well-characterized
      pathogenicity islands (PAIs) encoding key virulence
      factors of this strain. Except PAI IV(536), the four other PAIs of strain
      536 are flanked by direct repeats (DRs), carry intact integrase genes and
      are able to excise site-specifically from the chromosome. Genome screening
      of strain 536 identified a sixth putative asnW-associated PAI. Despite the
      presence of DRs and an intact integrase gene, excision of this island was
      not detected. To investigate the role of PAI-encoded integrases for the
      recombination process the int genes of each unstable island of strain 536
      were inactivated. For PAI I(536) and PAI II(536), their respective P4-like
      integrase was required for their excision. PAI III(536) carries two
      integrase genes, intA, encoding an SfX-like integrase, and intB, coding
      for an integrase with weak similarity to P4-like integrases. Only intB was
      required for site-specific excision of this island. For PAI V(536),
      excision could not be abolished after deleting its P4-like integrase gene
      but additional deletion of the PAI II(536)-specific integrase gene was
      required. Therefore, although all mediated by P4-like integrases, the
      activity of the PAI excision machinery is most often restricted to its
      cognate island. This work also demonstrates for the first time the
      existence of a cross-talk between integrases of different PAIs and shows
      that this cross-talk is unidirectional.
AU  - Hochhut B
AU  - Wilde C
AU  - Balling G
AU  - Middendorf B
AU  - Dobrindt U
AU  - Brzuszkiewicz E
AU  - Gottschalk G
AU  - Carniel E
AU  - Hacker J
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2006 61: 584-595.

PMID- 23144392
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Lactobacillus casei W56.
PG  - 6638
AB  - We announce the draft genome sequence of Lactobacillus casei W56 in one contig. This strain
      shows immunomodulatory and probiotic properties. The strain is also
      an ingredient of commercially available probiotic products.
AU  - Hochwind K
AU  - Weinmaier T
AU  - Schmid M
AU  - van Hemert S
AU  - Hartmann A
AU  - Rattei T
AU  - Rothballer M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6638.

PMID- 1475179
VI  - 20
DP  - 1992
TI  - Protein splicing removes intervening sequences in an archaea DNA polymerase.
PG  - 6153-6157
AB  - The Vent DNA polymerase gene from Thermococcus litoralis contains two in-frame insertions that
      must be spliced out to form the mature polymerase. Primer extension and cDNA PCR revealed no
      evidence of spliced RNA to account for this editing. In contrast, pulse-chase analysis
      indicated that expression constructs lacking the first insertion produced a protein precursor
      in Escherichia coli that was processed post-translationally to form polymerase and I-TliI, the
      endonuclease protein that is the product of the second insertion. At least one intermediate,
      which migrated more slowly than the precursor and may be branched, was also detected. Amino
      acid substitutions at the splice junction slowed or blocked the protein splicing reaction.
      Processing occurs in several heterologous systems, indicating either self-splicing or
      ubiquitous splicing factors. Processing occurs in a mutant lacking I-TliI endonuclease
      activity, establishing the independence of splicing and endonuclease activities.
AU  - Hodges RA
AU  - Perler FB
AU  - Noren CJ
AU  - Jack WE
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 6153-6157.

PMID- 1510946
VI  - 31
DP  - 1992
TI  - Cytosine methylation can induce local distortion in the structure of duplex DNA.
PG  - 7595-7599
AB  - Methyl groups at the C5 position of pyrimidines located within oligopurine-oligopyrimidine
      tracts in DNA have been shown previously to modulate curvature generated by those tracts.
      However, it was not known whether the influence of such methyl groups is consequent to the
      altered helical structure within the tracts themselves. In the current study, it is
      demonstrated that methylation of cytosines up to three base pairs away from a (dA)5(dT)5 tract
      (A-tract) can still result in alterations of the net curvature of the A-tract-containing DNA,
      as measured by alterations in electrophoretic mobility. This latter effect depends strongly on
      both the sequence of the non-A-tract DNA and the positions of the methylated C residues. The
      current results lend further support to the notion that the biological consequences of
      cytosine methylation may be effected through local alteration in DNA structure as well as
      through direct protein-DNA interactions.
AU  - Hodges-Garcia Y
AU  - Hagerman PJ
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1992 31: 7595-7599.

PMID- 2560930
VI  - 7
DP  - 1989
TI  - A rapid visual method for the identification of 4- or 6-base restriction endonuclease sites.
PG  - 148-149
AB  - In this report, we describe a rapid approach to identification of restriction
      endonuclease sites which makes computer searching unnecessary.  Increased speed
      is possible because searching with specific sequences is eliminated,
      substituting a one-time visual identification of palindromes.  These can be
      marked and identified with the aid of a chart at a later time.  In this manner,
      it is possible to identify 10-20 sites per minute with practice.  The technique
      will be especially useful for short pieces of DNA (2 kb or less), for newly
      published sequences, and for cloning experiments involving complex DNA
      constructions which are not readily available on a database.
AU  - Hodgson CP
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 1989 7: 148-149.

PMID- 23908282
VI  - 1
DP  - 2013
TI  - De Novo Assembly of the Streptomyces sp. Strain Mg1 Genome Using PacBio Single-Molecule Sequencing.
PG  - e00535-13
AB  - We report a draft genome assembly of Streptomyces sp. strain Mg1, a competitive soil isolate
      with multiple secondary metabolite gene clusters.
AU  - Hoefler BC
AU  - Konganti K
AU  - Straight PD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00535-13.

PMID- 3887134
VI  - 5
DP  - 1985
TI  - Expression of the Escherichia coli dam methylase in Saccharomyces cerevisiae:  Effect of in vivo adenine methylation on genetic recombination and mutation.
PG  - 610-618
AB  - The Escherichia coli DNA adenine methylase (dam) gene has been introduced into Saccharomyces
      cerevisiae on a yeast-E. coli shuttle vector. Sau3AI, MboI, and DpnI restriction enzyme
      digests and Southern hybridization analysis indicated that the dam gene is expressed in yeast
      cells and methylates GATC sequences. Analysis of digests of total genomic DNA indicated that
      some GATC sites are not sensitive to methylation. The failure to methylate may reflect an
      inaccessibility to the methylase due to chromosome structure. The effects of this in vivo
      methylation on the processes of recombination and mutation in mitotic cells were determined. A
      small but definite general increase was found in the frequency of mitotic recombination. A
      similar increase was observed for reversion of some auxotrophic markers; other markers
      demonstrated a small decrease in mutation frequency. The effects on mutation appear to be
      locus (or allele) specific. Recombination in meiotic cells was measured and was not detectably
      altered by the presence of 6-methyladenine in GATC sequences.
AU  - Hoekstra MF
AU  - Malone RE
PT  - Journal Article
TA  - Mol. Cell. Biol.
JT  - Mol. Cell. Biol.
SO  - Mol. Cell. Biol. 1985 5: 610-618.

PMID- 5340780
VI  - 2
DP  - 1965
TI  - The location of the restriction locus for lambda.K in Escherichia coli.
PG  - 204-212
AB  - Analysis of recombinants from E. coli K12 Hfr x E. coli B F- crosses showed
      that one locus on the chromososme of Escherichia coli, controlling restriction
      and probably also the modification of phage lambda, is located between the
      leading point of the Hfr H chromosome and the locus for threonine synthesis.
      The restriction locus also controls the restriction of the fertility factor of
      K12 and the restriction of chromosomal DNA of K12 in E. coli B.  The presence
      of the defective prophage X in E. coli B causes an additional restriction for
      phage lambda and for the fertility factor.
AU  - Hoekstra WPM
AU  - DeHaan PG
PT  - Journal Article
TA  - Mutat. Res.
JT  - Mutat. Res.
SO  - Mutat. Res. 1965 2: 204-212.

PMID- 18367473
VI  - 36
DP  - 2008
TI  - Presence and role of cytosine methylation in DNA viruses of animals.
PG  - 2825-2837
AB  - Nucleotide composition varies greatly among DNA viruses of animals, yet the evolutionary
      pressures and biological mechanisms driving these patterns are unclear. One of the most
      striking discrepancies lies in the frequency of CpG (the dinucleotide CG, linked by a
      phosphate group), which is underrepresented in most small DNA viruses (those with genomes
      below 10 kb) but not in larger DNA viruses. Cytosine methylation might be partially
      responsible, but research on this topic has focused on a few virus groups. For several viruses
      that integrate their genome into the host genome, the methylation status during this stage has
      been studied extensively, and the relationship between methylation and viral-induced tumor
      formation has been examined carefully. However, for actively replicating viruses-particularly
      small DNA viruses-the methylation status of CpG motifs is rarely known and the effects on the
      viral life cycle are obscure. In vertebrate host genomes, most cytosines at CpG sites are
      methylated, which in vertebrates acts to regulate gene expression and facilitates the
      recognition of unmethylated, potentially pathogen-associated DNA. Here we briefly introduce
      cytosine methylation before reviewing what is currently known about CpG methylation in DNA
      viruses.
AU  - Hoelzer K
AU  - Shackelton LA
AU  - Parrish CR
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2008 36: 2825-2837.

PMID- 1444272
VI  - 46
DP  - 1992
TI  - Replication cycle of Bacillus subtilis hydroxymethyluracil-containing phages.
PG  - 95-116
AB  - The present review focuses on phage 2C, a member of a family of virulent phages that multiply
      in Bacillus subtilis. The best known members of this group are SP01, Phie, H1, 2C, SP8, and
      Sp82, the genomes of which are made of double-stranded DNA of about 150 kilobase pairs (kbp).
      The two DNA strands have different buoyant densities. Moreover, thymine (T) is completely
      replaced by hydroxymethyluracil (hmUra). Comparison of the phage DNAs has shown that both base
      substitutions and deletions have contributed to the evolution of their genomes. In addition,
      all of the hmUra-phage genomes contain colinear redundant ends, amounting to 10% of total
      bases. Two lines of evidence suggest that the redundant ends of 2C DNA, in spite of extensive
      homology, contain unique sequences. Further studies focused on DNA replication during the
      lytic cycle. The semiconservative replication of the infecting viral genome is followed by
      extensive recombination. At the level of replication forks, viral DNA synthesis in
      permeabilized infected bacteria, was incorporated in small amounts into phage DNA. The
      putative primary origin of replication has been cloned and localized on the viral genome. Some
      viral promoters have been successfully cloned in Escherichia coli. These sequences, however,
      did not promote transcription in B. subtilis. The abnormal base might be required for promoter
      activity in the natural host.
AU  - Hoet PP
AU  - Coene MM
AU  - Cocito CG
PT  - Journal Article
TA  - Annu. Rev. Microbiol.
JT  - Annu. Rev. Microbiol.
SO  - Annu. Rev. Microbiol. 1992 46: 95-116.

PMID- 27836842
VI  - 83
DP  - 2017
TI  - Microdiversification of a Pelagic Polynucleobacter Species Is Mainly Driven by Acquisition of Genomic Islands from a Partially Interspecific Gene Pool.
PG  - e02266-16
AB  - Microdiversification of a planktonic freshwater bacterium was studied by comparing 37
      Polynucleobacter asymbioticus strains obtained from three
      geographically separated sites in the Austrian Alps. Genome comparison of nine
      strains revealed a core genome of 1.8 Mb, representing 81% of the average genome
      size. Seventy-five percent of the remaining flexible genome is clustered in
      genomic islands (GIs). Twenty-four genomic positions could be identified where
      GIs are potentially located. These positions are occupied strain specifically
      from a set of 28 GI variants, classified according to similarities in their gene
      content. One variant, present in 62% of the isolates, encodes a pathway for the
      degradation of aromatic compounds, and another, found in 78% of the strains,
      contains an operon for nitrate assimilation. Both variants were shown in
      ecophysiological tests to be functional, thus providing the potential for
      microniche partitioning. In addition, detected interspecific horizontal exchange
      of GIs indicates a large gene pool accessible to Polynucleobacter species. In
      contrast to core genes, GIs are spread more successfully across spatially
      separated freshwater habitats. The mobility and functional diversity of GIs allow
      for rapid evolution, which may be a key aspect for the ubiquitous occurrence of
      Polynucleobacter bacteria. IMPORTANCE: Assessing the ecological relevance of
      bacterial diversity is a key challenge for current microbial ecology. The
      polyphasic approach which was applied in this study, including targeted isolation
      of strains, genome analysis, and ecophysiological tests, is crucial for the
      linkage of genetic and ecological knowledge. Particularly great importance is
      attached to the high number of closely related strains which were investigated,
      represented by genome-wide average nucleotide identities (ANI) larger than 97%.
      The extent of functional diversification found on this narrow phylogenetic scale
      is compelling. Moreover, the transfer of metabolically relevant genomic islands
      between more distant members of the Polynucleobacter community provides important
      insights toward a better understanding of the evolution of these globally
      abundant freshwater bacteria.
AU  - Hoetzinger M
AU  - Schmidt J
AU  - Jezberova J
AU  - Koll U
AU  - Hahn MW
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2017 83: e02266-16.

PMID- 2838811
VI  - 16
DP  - 1988
TI  - The sensitivity of DNA cleavage by SpeI and ApaLI to methylation by M.EcoK.
PG  - 5206
AB  - During work on site-directed mutagenesis of the human interleukin-2 gene an
      EcoK site was created which overlapped recognition sequences for SpeI and ApaLI
      (Fig. 1a).  Isolation of the DNA from m+K strain DH1 and m-K strain HB101 and
      subsequent incubation with the two restriction endonucleases revealed that EcoK
      methylation completely or almost completely protected both DNA strands from
      cleavage by SpeI, but did not prevent cleavage of either strand by ApaLI (Fig.
      1b).  Thus, methylation of only one of the 5'-terminal A's of the SpeI site is
      sufficient to protect it against SpeI, whereas methylation of one of the two
      A's of the ApaLI sequence does not interfere with its cleavage by ApaLI.
AU  - Hofer B
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1988 16: 5206.

PMID- 6162159
VI  - 8
DP  - 1980
TI  - On the influence of thymidine analogues on the activity of phage fd promoters in vitro.
PG  - 6143-6162
AB  - RF I DNA of phage fd containing 5-bromo-deoxyuridine (br5Ud) or deoxyuridine
      (Ud) instead of deoxythymidine (Td) in the codogenic strand was synthesized in
      vitro.  The modified genomes could be cleaved by restriction endonuclease
      HpaII.  Although the recognition site of HpaII is CCGG, the cleavage rate was
      significantly reduced with Ud-containing DNA.  Both base substitutions altered
      the mobilities of several DNA fragments under the conditions of polyacrylamide
      gel electrophoresis.  The fragments containing binding sites for RNA polymerase
      were assayed for the rates of stable complex formation.  The substitution of Td
      for both, Ud and br5Ud, strongly influenced this parameter.  Thus the methyl
      group of Td has to be regarded as one of the sites in DNA which determine the
      rate of stable RNA polymerase binding and thereby possibly mediate promoter
      activity in vitro.  In most cases the rate of complex formation was decreased
      by Ud, but increased by br5Ud.
AU  - Hofer B
AU  - Koster H
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1980 8: 6143-6162.

PMID- 2798148
VI  - 17
DP  - 1989
TI  - The sensitivity of DNA cleavage by SnoI to methylation by M.EcoK.
PG  - 8009
AB  - None
AU  - Hofer B
AU  - Kuhlein B
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 8009.

PMID- 6285307
VI  - 10
DP  - 1982
TI  - Primary and secondary structure specificity of the cleavage of single-stranded DNA by endonuclease HinfI.
PG  - 2763-2773
AB  - The interaction of endonuclease HinfI with single-stranded fd DNA was examined.
      The sizes of the cleavage products indicate that the enzyme cuts this
      substrate at the same sequences as double-stranded DNA (GANTC).  To determine
      whether or not the recognition sites in a single-stranded DNA have to be
      present in double-stranded form in order to be cleaved, DNA fragments
      containing complementary or non-complementary HinfI sequences were prepared and
      tested as substrates.  The results suggest that completely base-paired
      recognition sites are necessary for cleavage.  Sequences surrounding the HinfI
      pentanucleotides significantly modulate the reaction rates.
AU  - Hofer B
AU  - Ruhe G
AU  - Koch A
AU  - Koster H
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1982 10: 2763-2773.

PMID- 29074674
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Two Brazilian Cyanobacterial Strains of Cylindrospermopsis raciborskii: Differences in Membrane Transporters, Saxitoxin  Production, and Antioxidant Activities.
PG  - e00879-17
AB  - We report here the draft genome sequences of two Brazilian strains of Cylindrospermopsis
      raciborskii, a saxitoxin-producer (CYRF) and a non-saxitoxin
      producer (CYLP), with each strain comprising one assembled scaffold. We revealed
      differences in the compositions of gene members coding for membrane transporters
      and antioxidant activities between the strains.
AU  - Hoffmann L
AU  - Ramos RJT
AU  - Guedes IA
AU  - Costa PF
AU  - Miguel CRD
AU  - Azevedo SMFOE
AU  - Silva R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00879-17.

PMID- 23405335
VI  - 1
DP  - 2013
TI  - Genome Sequences of Salmonella enterica Serovar Heidelberg Isolates Isolated in the United States from a Multistate Outbreak of Human Salmonella Infections.
PG  - e00004-12
AB  - Salmonella enterica is recognized as one of the most common bacterial agents of foodborne
      illness. We report draft genomes of four Salmonella serovar Heidelberg isolates associated
      with the recent multistate outbreak of human Salmonella Heidelberg infections linked to kosher
      broiled chicken livers in the United States in 2011. Isolates 2011K-1259 and 2011K-1232 were
      recovered from humans, whereas 2011K-1724 and 2011K-1726 were isolated from chicken liver.
      Whole genome sequence analysis of these isolates provides a tool for studying the short-term
      evolution of these epidemic clones and can be used for characterizing potentially new
      virulence factors.
AU  - Hoffmann M
AU  - Luo Y
AU  - Lafon PC
AU  - Timme R
AU  - Allard MW
AU  - McDermott PF
AU  - Brown EW
AU  - Zhao S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00004-12.

PMID- 24699967
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of a Multidrug-Resistant Salmonella enterica Serovar Typhimurium var. 5- Strain Isolated from Chicken Breast.
PG  - e00294-14
AB  - Volume 1, no. 6, e01068-13, 2013.  Page 2: The following should be added to the
      Acknowledgments.  "Research reported in this publication was supported by the Small Business
      Innovation Research Program (NIGMS) of the National Institutes of Health under award number
      R44GM105125 to R.J.R.  The content is solely the responsibility of the authors and does not
      necessarily represent the official views of the National Institutes of Health."
AU  - Hoffmann M
AU  - Muruvanda T
AU  - Allard MW
AU  - Korlach J
AU  - Roberts RJ
AU  - Timme R
AU  - Payne J
AU  - McDermott PF
AU  - Evans P
AU  - Meng J
AU  - Brown EW
AU  - Zhao S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00294-14.

PMID- 24356834
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of a Multidrug-Resistant Salmonella enterica Serovar Typhimurium var. 5- Strain Isolated from Chicken Breast.
PG  - e01068-13
AB  - Salmonella enterica subsp. enterica serovar Typhimurium is a leading cause of salmonellosis.
      Here, we report a closed genome sequence, including sequences of 3
      plasmids, of Salmonella serovar Typhimurium var. 5- CFSAN001921 (National
      Antimicrobial Resistance Monitoring System [NARMS] strain ID N30688), which was
      isolated from chicken breast meat and shows resistance to 10 different
      antimicrobials. Whole-genome and plasmid sequence analyses of this isolate will
      help enhance our understanding of this pathogenic multidrug-resistant serovar.
AU  - Hoffmann M
AU  - Muruvanda T
AU  - Allard MW
AU  - Korlach J
AU  - Roberts RJ
AU  - Timme R
AU  - Payne J
AU  - McDermott PF
AU  - Evans P
AU  - Meng J
AU  - Brown EW
AU  - Zhao S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01068-13.

PMID- 25359917
VI  - 2
DP  - 2014
TI  - First Fully Closed Genome Sequence of Salmonella enterica subsp. enterica Serovar Cubana Associated with a Food-Borne Outbreak.
PG  - e01112-14
AB  - Salmonella enterica subsp. enterica serovar Cubana (Salmonella serovar Cubana) is associated
      with human and animal disease. Here, we used third-generation,
      single-molecule, real-time DNA sequencing to determine the first complete genome
      sequence of Salmonella serovar Cubana CFSAN002050, which was isolated from fresh
      alfalfa sprouts during a multistate outbreak in 2012.
AU  - Hoffmann M
AU  - Muruvanda T
AU  - Pirone C
AU  - Korlach J
AU  - Timme R
AU  - Payne J
AU  - Evans P
AU  - Meng J
AU  - Brown EW
AU  - Allard MW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01112-14.

PMID- 26139714
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Agona 460004 2-1, Associated with a Multistate Outbreak in the United States.
PG  - e00690-15
AB  - Within the last several years, Salmonella enterica subsp. enterica serovar Agona  has been
      among the 20 most frequently isolated serovars in clinical cases of
      salmonellosis. In this report, the complete genome sequence of S. Agona strain
      460004 2-1 isolated from unsweetened puffed-rice cereal during a multistate
      outbreak in 2008 was sequenced using single-molecule real-time DNA sequencing.
AU  - Hoffmann M
AU  - Payne J
AU  - Roberts RJ
AU  - Allard MW
AU  - Brown EW
AU  - Pettengill JB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00690-15.

PMID- 22628505
VI  - 194
DP  - 2012
TI  - Genome Sequences of Five Salmonella enterica Serovar Heidelberg Isolates Associated with a 2011 Multistate Outbreak in the United States.
PG  - 3274-3275
AB  - Salmonella enterica serovar Heidelberg has caused numerous outbreaks in humans. Here, we
      report draft genomes of five isolates of serovar Heidelberg associated
      with the recent (2011) multistate outbreak linked to ground turkey in the United
      States. Isolates 2011K-1110 and 2011K-1132 were recovered from humans, while
      isolates 2011K-1138, 2011K-1224, and 2011K-1225 were recovered from ground
      turkey. Whole-genome sequence analysis of these isolates provides a tool for
      studying the short-term evolution of these epidemic clones.
AU  - Hoffmann M
AU  - Zhao S
AU  - Luo Y
AU  - Li C
AU  - Folster JP
AU  - Whichard J
AU  - Allard MW
AU  - Brown EW
AU  - McDermott PF
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3274-3275.

PMID- 16861657
VI  - 74
DP  - 2006
TI  - Unique features of a highly pathogenic Campylobacter jejuni strain.
PG  - 4694-4707
AB  - Campylobacter jejuni, a major human enteric pathogen, exhibits significant strain-to-strain
      differences which result in differences in pathogenic potential.  C. jejuni 81-176 is a highly
      virulent strain that exhibits unique pathogenic features and is used by many research
      laboratories.  We have determined the nucleotide sequence of its genome and compared it to the
      genomes of other sequenced C. jejuni strains.  We identified a number of unique genetic
      features which may confer specific metabolic and pathogenic properties on this strain.  We
      have also identified regions of the C. jejuni genome that are hot spots for the integration of
      horizontally acquired genetic material.  This information should help the understanding of the
      pathogenesis of C. jejuni and, in particular, the unique features of this highly pathogenic
      strain.
AU  - Hofreuter D
AU  - Tsai J
AU  - Watson RO
AU  - Novik V
AU  - Altman B
AU  - Benitez M
AU  - Clark C
AU  - Perbost C
AU  - Jarvie T
AU  - Du L
AU  - Galan JE
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2006 74: 4694-4707.

PMID- 23792739
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences for Ten Salmonella enterica Serovar Typhimurium Phage Type 135 Variants.
PG  - e00293-13
AB  - Salmonella enterica serovar Typhimurium (S. Typhimurium) is a common cause of gastroenteritis
      in humans. Here, we report the draft genome sequences of 10
      isolates of an S. Typhimurium phage type 135 variant that is linked to
      egg-associated outbreaks in Tasmania, Australia.
AU  - Hogg G
AU  - Dimovski K
AU  - Hiley L
AU  - Holt KE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00293-13.

PMID- 17550610
VI  - 8
DP  - 2007
TI  - Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains.
PG  - R103
AB  - BACKGROUND: The distributed genome hypothesis (DGH) posits that chronic
      bacterial pathogens utilize polyclonal infection and reassortment of genic
      characters to ensure persistence in the face of adaptive host defenses.
      Studies based on random sequencing of multiple strain libraries suggested
      that free-living bacterial species possess a supragenome that is much
      larger than the genome of any single bacterium. RESULTS: We derived high
      depth genomic coverage of nine nontypeable Haemophilus influenzae (NTHi)
      clinical isolates, bringing to 13 the number of sequenced NTHi genomes.
      Clustering identified 2,786 genes, of which 1,461 were common to all
      strains, with each of the remaining 1,328 found in a subset of strains;
      the number of clusters ranged from 1,686 to 1,878 per strain. Genic
      differences of between 96 and 585 were identified per strain pair.
      Comparisons of each of the NTHi strains with the Rd strain revealed
      between 107 and 158 insertions and 100 and 213 deletions per genome. The
      mean insertion and deletion sizes were 1,356 and 1,020 base-pairs,
      respectively, with mean maximum insertions and deletions of 26,977 and
      37,299 base-pairs. This relatively large number of small rearrangements
      among strains is in keeping with what is known about the transformation
      mechanisms in this naturally competent pathogen. CONCLUSION: A finite
      supragenome model was developed to explain the distribution of genes among
      strains. The model predicts that the NTHi supragenome contains between
      4,425 and 6,052 genes with most uncertainty regarding the number of rare
      genes, those that have a frequency of <0.1 among strains; collectively,
      these results support the DGH.
AU  - Hogg JS
AU  - Hu FZ
AU  - Janto B
AU  - Boissy R
AU  - Hayes J
AU  - Keefe R
AU  - Post JC
AU  - Ehrlich GD
PT  - Journal Article
TA  - Genome Biology
JT  - Genome Biology
SO  - Genome Biology 2007 8: R103.

PMID- 2602137
VI  - 17
DP  - 1989
TI  - Control of partial digestion combining the enzymes dam methylase and MboI.
PG  - 9571-9582
AB  - A method is described which allows the preparation of reproducible partial digests without
      previous establishment of the incubation conditions. It is based on a combined application of
      dam methylase and the restriction endonuclease MboI, both recognizing the sequence
      5'-GATC-3' but MboI unable to cut the methylated site. Due to their competition for the same
      substrate the DNA is partially digested with the size of the resulting fragments strongly
      dependent on the ratio of enzymes. The Km of the dam methylase was determined to be 115 ng
      DNA/microliter indicating a variance in fragment sizes generated at low DNA-concentrations.
      This effect is minimized above 150 ng/microliter. Any influence of digestion time is avoided,
      because the reaction runs until complete modification of all sites. The dependence on enzyme
      concentration and presence of agarose was checked. Knowledge of these parameters allows an
      accurate prediction of fragment sizes generated at different conditions. The technique was
      successfully used to construct libraries from different sources, in particular
      chromosome-specific libraries from small amounts of flow-sorted material.
AU  - Hoheisel JD
AU  - Nizetic D
AU  - Lehrach H
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 9571-9582.

PMID- 18931103
VI  - 191
DP  - 2009
TI  - The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients.
PG  - 261-277
AB  - Bacterial infections of the lungs of cystic fibrosis (CF) patients cause major complications
      in the treatment of this common genetic disease. Burkholderia
      cenocepacia infection is particularly problematic since this organism has high
      levels of antibiotic resistance, making it difficult to eradicate; the resulting
      chronic infections are associated with severe declines in lung function and
      increased mortality rates. B. cenocepacia strain J2315 was isolated from a CF
      patient and is a member of the epidemic ET12 lineage that originated in Canada or
      the United Kingdom and spread to Europe. The 8.06-Mb genome of this highly
      transmissible pathogen comprises three circular chromosomes and a plasmid and
      encodes a broad array of functions typical of this metabolically versatile genus,
      as well as numerous virulence and drug resistance functions. Although B.
      cenocepacia strains can be isolated from soil and can be pathogenic to both
      plants and man, J2315 is representative of a lineage of B. cenocepacia rarely
      isolated from the environment and which spreads between CF patients. Comparative
      analysis revealed that ca. 21% of the genome is unique in comparison to other
      strains of B. cenocepacia, highlighting the genomic plasticity of this species.
      Pseudogenes in virulence determinants suggest that the pathogenic response of
      J2315 may have been recently selected to promote persistence in the CF lung. The
      J2315 genome contains evidence that its unique and highly adapted genetic content
      has played a significant role in its success as an epidemic CF pathogen.
AU  - Holden MT et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2009 191: 261-277.

PMID- 17012393
VI  - 189
DP  - 2007
TI  - Complete genome of acute rheumatic fever-associated serotype M5 Streptococcus pyogenes strain manfredo.
PG  - 1473-1477
AB  - Comparisons of the 1.84-Mb genome of serotype M5 Streptococcus pyogenes strain Manfredo with
      previously sequenced genomes emphasized the role of
      prophages in diversification of S. pyogenes and the close relationship
      between strain Manfredo and MGAS8232, another acute rheumatic
      fever-associated strain.
AU  - Holden MT et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2007 189: 1473-1477.

PMID- 19948800
VI  - 192
DP  - 2010
TI  - Genome Sequence of a Recently Emerged, Highly Transmissible, Multi-Antibiotic- and Antiseptic-Resistant Variant of  Methicillin-Resistant Staphylococcus aureus, Sequence Type 239 (TW).
PG  - 888-892
AB  - The 3.1-Mb genome of an outbreak methicillin-resistant Staphylococcus aureus (MRSA) strain
      (TW20) contains evidence of recently acquired DNA,
      including two large regions (635 kb and 127 kb). The strain is resistant
      to a wide range of antibiotics, antiseptics, and heavy metals due to
      resistance genes encoded on mobile genetic elements and also mutations in
      housekeeping genes.
AU  - Holden MT
AU  - Lindsay JA
AU  - Corton C
AU  - Quail MA
AU  - Cockfield JD
AU  - Pathak S
AU  - Batra R
AU  - Parkhill J
AU  - Bentley SD
AU  - Edgeworth JD
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 888-892.

PMID- 15377794
VI  - 101
DP  - 2004
TI  - Genomic plasticity of the causative agent of melioidosis, Berkholderia pseudomallei.
PG  - 14240-14245
AB  - Burkholderia pseudomallei is a recognized biothreat agent and the causative agent of
      melioidosis. This Gram-negative bacterium exists as a soil saprophyte in melioidosis-endemic
      areas of the world and accounts for 20% of community-acquired septicaemias in northeastern
      Thailand where half of those affected die. Here we report the complete genome of B.
      pseudomallei, which is composed of two chromosomes of 4.07 megabase pairs and 3.17 megabase
      pairs, showing significant functional partitioning of genes between them. The large chromosome
      encodes many of the core functions associated with central metabolism and cell growth, whereas
      the small chromosome carries more accessory functions associated with adaptation and survival
      in different niches. Genomic comparisons with closely and more distantly related bacteria
      revealed a greater level of gene order conservation and a greater number of orthologous genes
      on the large chromosome, suggesting that the two replicons have distinct evolutionary origins.
      A striking feature of the genome was the presence of 16 genomic islands (GIs) that together
      made up 6.1% of the genome. Further analysis revealed these islands to be variably present in
      a collection of invasive and soil isolates but entirely absent from the clonally related
      organism B. mallei. We propose that variable horizontal gene acquisition by B. pseudomallei is
      an important feature of recent genetic evolution and that this has resulted in a genetically
      diverse pathogenic species.
AU  - Holden MTG et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2004 101: 14240-14245.

PMID- 15213324
VI  - 101
DP  - 2004
TI  - Complete genomes of two clinical Staphylococcus aureus strains: Evidence for the rapid evolution of virulence and drug resistance.
PG  - 9786-9791
AB  - Staphylococcus aureus is an important nosocomial and community-acquired pathogen. Its genetic
      plasticity has facilitated the evolution of many virulent and drug-resistant strains,
      presenting a major and constantly changing clinical challenge. We sequenced the ~2.8-Mbp
      genomes of two disease-causing S. aureus strains isolated from distinct clinical settings: a
      recent hospital-acquired representative of the epidemic methicillin-resistant S. aureus
      EMRSA-16 clone (MRSA252), a clinically important and globally prevalent lineage; and a
      representative of an invasive community-acquired methicillin-susceptible S. aureus clone
      (MSSA476). A comparative-genomics approach was used to explore the mechanisms of evolution of
      clinically important S. aureus genomes and to identify regions affecting virulence and drug
      resistance. The genome sequences of MRSA252 and MSSA476 have a well conserved core region but
      differ markedly in their accessory genetic elements. MRSA252 is the most genetically diverse
      S. aureus strain sequenced to date: ~6% of the genome is novel compared with other published
      genomes, and it contains several unique genetic elements. MSSA476 is methicillin-susceptible,
      but it contains a novel Staphylococcal chromosomal cassette (SCC) mec-like element (designated
      SCC476), which is integrated at the same site on the chromosome as SCCmec elements in MRSA
      strains but encodes a putative fusidic acid resistance protein. The crucial role that
      accessory elements play in the rapid evolution of S. aureus is clearly illustrated by
      comparing the MSSA476 genome with that of an extremely closely related MRSA community-acquired
      strain; the differential distribution of large mobile elements carrying virulence and
      drug-resistance determinants may be responsible for the clinically important phenotypic
      differences in these strains.
AU  - Holden MTG et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2004 101: 9786-9791.

PMID- 19603075
VI  - 4
DP  - 2009
TI  - Rapid Evolution of Virulence and Drug Resistance in the Emerging Zoonotic Pathogen Streptococcus suis.
PG  - e6072-e6072
AB  - Background: Streptococcus suis is a zoonotic pathogen that infects pigs and can occasionally
      cause serious infections in
      humans. S. suis infections occur sporadically in human Europe and North America, but a recent
      major outbreak has been
      described in China with high levels of mortality. The mechanisms of S. suis pathogenesis in
      humans and pigs are poorly
      understood.
      Methodology/Principal Findings: The sequencing of whole genomes of S. suis isolates provides
      opportunities to
      investigate the genetic basis of infection. Here we describe whole genome sequences of three
      S. suis strains from the same
      lineage: one from European pigs, and two from human cases from China and Vietnam. Comparative
      genomic analysis was
      used to investigate the variability of these strains. S. suis is phylogenetically distinct
      from other Streptococcus species for
      which genome sequences are currently available. Accordingly, ,40% of the ,2 Mb genome is
      unique in comparison to
      other Streptococcus species. Finer genomic comparisons within the species showed a high level
      of sequence conservation;
      virtually all of the genome is common to the S. suis strains. The only exceptions are three
      ,90 kb regions, present in the two
      isolates from humans, composed of integrative conjugative elements and transposons. Carried in
      these regions are coding
      sequences associated with drug resistance. In addition, small-scale sequence variation has
      generated pseudogenes in
      putative virulence and colonization factors.
      Conclusions/Significance: The genomic inventories of genetically related S. suis strains,
      isolated from distinct hosts and
      diseases, exhibit high levels of conservation. However, the genomes provide evidence that
      horizontal gene transfer has
      contributed to the evolution of drug resistance.
AU  - Holden MTG et al
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2009 4: e6072-e6072.

PMID- 23405354
VI  - 1
DP  - 2013
TI  - Genome Sequence of Pseudomonas sp. Strain Chol1, a Model Organism for the Degradation of Bile Salts and Other Steroid Compounds.
PG  - e00014-12
AB  - Bacterial degradation of steroid compounds is of high ecological and biotechnological
      relevance. Pseudomonas sp. strain Chol1 is a model organism for studying the degradation of
      the steroid compound cholate. Its draft genome sequence is presented and reveals one gene
      cluster responsible for the metabolism of steroid compounds.
AU  - Holert J
AU  - Alam I
AU  - Larsen M
AU  - Antunes A
AU  - Bajic VB
AU  - Stingl U
AU  - Philipp B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00014-12.

PMID- 23792744
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Leucobacter sp. Strain UCD-THU (Phylum Actinobacteria).
PG  - e00325-13
AB  - Here we present the draft genome of Leucobacter sp. strain UCD-THU. The genome contains
      3,317,267 bp in 11 scaffolds. This strain was isolated from a
      residential toilet as part of an undergraduate project to sequence reference
      genomes of microbes from the built environment.
AU  - Holland-Moritz HE
AU  - Bevans DR
AU  - Lang JM
AU  - Darling AE
AU  - Eisen JA
AU  - Coil DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00325-13.

PMID- 25146141
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Pyridinediol-Fermenting Bacterium Synergistes jonesii 78-1.
PG  - e00833-14
AB  - Here we present the draft genome of Synergistes jonesii 78-1, ATCC 49833, a member of the
      Synergistes phylum. This organism was isolated from the rumen of a
      Hawaiian goat and ferments pyridinediols. The assembly contains 2,747,397 bp in
      61 contigs.
AU  - Holland-Moritz HE
AU  - Coil DA
AU  - Badger JH
AU  - Dmitrov GI
AU  - Khouri H
AU  - Ward NL
AU  - Robb FT
AU  - Eisen JA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00833-14.

PMID- 29025934
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Salmonella enterica Serovar Senftenberg 070885 and Its Linalool-Adapted Mutant.
PG  - e01036-17
AB  - Here we report the genome sequences of both Salmonella Senftenberg 070885, a clinical isolate
      from the 2007 outbreak linked to basil, and its mutant
      linalool-adapted S Senftenberg (LASS). These draft genomes of S Senftenberg may
      enable the identification of bacterial genes responsible for resistance to basil
      oil.
AU  - Hollander A
AU  - Kalily E
AU  - Shachar D
AU  - Yaron S
AU  - Danin-Poleg Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01036-17.

PMID- 28360161
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Bacillus pumilus Strain GM3FR, an Endophyte Isolated from Aerial Plant Tissues of Festuca rubra L.
PG  - e00085-17
AB  - Here, we report the draft genome sequence of Bacillus pumilus GM3FR, an endophytic bacterium
      isolated from aerial plant tissues of Festuca rubra L. The
      draft genome consists of 3.5 Mb and harbors 3,551 predicted protein-encoding
      genes. The genome provides insights into the biocontrol potential of B. pumilus
      GM3FR.
AU  - Hollensteiner J
AU  - Poehlein A
AU  - Daniel R
AU  - Liesegang H
AU  - Vidal S
AU  - Wemheuer F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00085-17.

PMID- 29371354
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of the Endophyte Bacillus mycoides Strain GM5LP Isolated from Lolium perenne.
PG  - e01517-17
AB  - Bacillus mycoides GM5LP is a Gram-positive endophytic bacterium isolated from aerial plant
      tissues of Lolium perenne L. The 6.0-Mb draft genome harbors 6,132
      protein-coding sequences, some of which might be involved in the biosynthesis of
      antimicrobial substances.
AU  - Hollensteiner J
AU  - Poehlein A
AU  - Granzow S
AU  - Liesegang H
AU  - Daniel R
AU  - Vidal S
AU  - Wemheuer F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01517-17.

PMID- 28899808
VI  - 260
DP  - 2017
TI  - Complete genome sequence of the nematicidal Bacillus thuringiensis MYBT18247.
PG  - 48-52
AB  - The Gram-positive spore forming bacterium Bacillus thuringiensis MYBT18247 encodes three cry
      toxin genes, (cry6Ba2, cry6Ba3 and cry21-like) which are active
      against nematodes. For a better understanding of the evolution of virulence and
      cry toxins, we present here the complete genome sequence of Bacillus
      thuringiensis MYBT18247. Various additional virulence factors such as
      bacteriocins, proteases and hemolysins were identified. In addition, the
      methylome and the metabolic potential of the strain were analyzed and the strain
      phylogenetically classified.
AU  - Hollensteiner J
AU  - Poehlein A
AU  - Sproer C
AU  - Bunk B
AU  - Sheppard AE
AU  - Rosenstiel P
AU  - Schulenburg H
AU  - Liesegang H
PT  - Journal Article
TA  - J. Biotechnol.
JT  - J. Biotechnol.
SO  - J. Biotechnol. 2017 260: 48-52.

PMID- 28852435
VI  - 12
DP  - 2017
TI  - Complete Genome sequence of the nematicidal Bacillus thuringiensis MYBT18246.
PG  - 48
AB  - 10.1601/nm.5000 is a rod-shaped facultative anaerobic spore forming bacterium of  the genus
      10.1601/nm.4857. The defining feature of the species is the ability to
      produce parasporal crystal inclusion bodies, consisting of delta-endotoxins,
      encoded by cry-genes. Here we present the complete annotated genome sequence of
      the nematicidal 10.1601/nm.5000 strain MYBT18246. The genome comprises one
      5,867,749 bp chromosome and 11 plasmids which vary in size from 6330 bp to
      150,790 bp. The chromosome contains 6092 protein-coding and 150 RNA genes,
      including 36 rRNA genes. The plasmids encode 997 proteins and 4 t-RNA's. Analysis
      of the genome revealed a large number of mobile elements involved in genome
      plasticity including 11 plasmids and 16 chromosomal prophages. Three different
      nematicidal toxin genes were identified and classified according to the Cry toxin
      naming committee as cry13Aa2, cry13Ba1, and cry13Ab1. Strikingly, these genes are
      located on the chromosome in close proximity to three separate prophages.
      Moreover, four putative toxin genes of different toxin classes were identified on
      the plasmids p120510 (Vip-like toxin), p120416 (Cry-like toxin) and p109822 (two
      Bin-like toxins). A comparative genome analysis of 10.1601/nm.5000 MYBT18246 with
      three closely related 10.1601/nm.5000 strains enabled determination of the
      pan-genome of 10.1601/nm.5000 MYBT18246, revealing a large number of singletons,
      mostly represented by phage genes, morons and cryptic genes.
AU  - Hollensteiner J
AU  - Poehlein A
AU  - Sproer C
AU  - Bunk B
AU  - Sheppard AE
AU  - Rosentstiel P
AU  - Schulenburg H
AU  - Liesegang H
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 48.

PMID- 10447597
VI  - 36
DP  - 1999
TI  - The catalytic group-I introns of the psbA gene of Chlamydomonas reinhardtii: core structures, ORFs and evolutionary implications.
PG  - 69-78
AB  - The sequences and predicted secondary structures of the four catalytic group-I introns in the
      psbA gene of Chlamydomonas reinhardtii, Cr.psbA-1-Cr.psbA-4, have been determined. Cr.psbA-1
      and Cr.psbA-4 are subgroup-IA1 introns and have similar secondary structures, except at the
      3' end where Cr.psbA-1 contains a large inverted-repeat domain. Cr.psbA-4 is closely related
      to intron 1 of the Chlamydomonas moewusii psbA gene, with which it shares the same location,
      high nucleotide identity in the core, and an identically placed ORF that shows 58% amino-acid
      identity. Cr.psbA-2 is a subgroup-IA3 intron, and shows similarities to the Chlamydomonas
      eugametos rRNA intron, Ce.LSU-1. Cr.psbA-3 is a subgroup-IA2 intron, and is remarkably similar
      to the T4 phage intron, sunY.  Interestingly, a degenerate version of Cr.psbA-3 is located in
      the intergenic region between the chloroplast petA and petD genes. All four introns contain
      ORFs, which potentially code for basic proteins of 11-38 kDa. The ORFs in introns 2 and 3
      contain variants of the GIY-YIG motif; however, the Cr.psbA-2 ORF is free-standing, whereas
      the Cr.psbA-3 ORF is contiguous and in-frame with the upstream exon. The Cr.psbA-4 ORF
      contains an H-N-H motif, and possibly a GIY-YIG motif. These data indicate that the C.
      reinhardtii psbA introns have multiple origins, and illustrate some of the evolutionary DNA
      dynamics associated with group-I introns in Chlamydomonas.
AU  - Holloway SP
AU  - Deshpande NN
AU  - Herrin DL
PT  - Journal Article
TA  - Curr. Genet.
JT  - Curr. Genet.
SO  - Curr. Genet. 1999 36: 69-78.

PMID- 26380645
VI  - 10
DP  - 2015
TI  - Complete genome sequence of Vibrio anguillarum strain NB10, a virulent isolate from the Gulf of Bothnia.
PG  - 60
AB  - Vibrio anguillarum causes a fatal hemorrhagic septicemia in marine fish that leads to great
      economical losses in aquaculture world-wide. Vibrio anguillarum strain NB10 serotype O1 is a
      Gram-negative, motile, curved rod-shaped bacterium,  isolated from a diseased fish on the
      Swedish coast of the Gulf of Bothnia, and is slightly halophilic. Strain NB10 is a virulent
      isolate that readily colonizes fish skin and intestinal tissues. Here, the features of this
      bacterium are described and the annotation and analysis of its complete genome sequence is
      presented. The genome is 4,373,835 bp in size, consists of two circular chromosomes and one
      plasmid, and contains 3,783 protein-coding genes and 129 RNA  genes.
AU  - Holm KO
AU  - Nilsson K
AU  - Hjerde E
AU  - Willassen NP
AU  - Milton DL
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 60.

PMID- 26868392
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Hymenobacter sp. Strain AT01-02, Isolated from a Surface Soil Sample in the Atacama Desert, Chile.
PG  - e01701-15
AB  - Here, we report the 5.09-Mb draft genome sequence of Hymenobacter sp. strain AT01-02, which
      was isolated from a surface soil sample in the Atacama Desert, Chile. The isolate is extremely
      resistant to UV-C radiation and is able to accumulate high intracellular levels of Mn/Fe.
AU  - Holm-Hansen AC
AU  - Paulino-Lima IG
AU  - Fujishima K
AU  - Rothschild LJ
AU  - Jensen PR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01701-15.

PMID- 1711028
VI  - 173
DP  - 1991
TI  - Construction and use of Halobacterial shuttle vectors and further studies on Haloferax DNA gyrase.
PG  - 3807-3813
AB  - We report here on advances made in the construction of plasmid shuttle vectors suitable for
      genetic manipulations in both Escherichia coli and halobacteria. Starting with a 20.4-kb
      construct, pMDS1, new vectors were engineered which were considerably smaller yet retained
      several alternative cloning sites. A restriction barrier observed when plasmid DNA was
      transferred into Haloferax volcanii cells was found to operate via adenine methylation,
      resulting in a 10^3 drop in transformation efficiency and the loss of most constructs by
      incorporation of the resistance marker into the chromosome. Passing shuttle vectors through E.
      coli dam mutants effectively avoided this barrier. Deletion analysis revealed that the gene(s)
      for autonomous replication of pHK2 (the plasmid endogenous to Haloferax strain Aa2.2 and used
      in the construction of pMDS1) was located within a 4.2-kb SmaI-KpnI fragment. Convenient
      restriction sites were identified near the termini of the novobiocin resistance determinant
      (gyrB), allowing the removal of flanking sequences (including gyrA). These deletions did not
      appear to significantly affect transformation efficiencies or the novobiocin resistance
      phenotype of halobacterial transformants. Northern blot hybridization with strand- and
      gene-specific probes identified a single gyrB-gyrA transcript of 4.7 kb. This is the first
      demonstration in prokaryotes that the two subunits of DNA gyrase may be cotranscribed.
AU  - Holmes ML
AU  - Nuttall SD
AU  - Dyall-Smith ML
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1991 173: 3807-3813.

PMID- 24428166
VI  - 16
DP  - 2014
TI  - Contrasting genomic patterns and infection strategies of two co-existing Bacteroidetes podovirus genera.
PG  - 2501-2513
AB  - Bacterial viruses (phages) are abundant, ecologically important biological
      entities. However, our understanding of their impact is limited by model systems
      that are primarily not well represented in nature, e.g. Enterophages and their
      hosts. Here, we investigate genomic characteristics and infection strategies
      among six aquatic Bacteroidetes phages that represent two genera of exceptionally
      large ( approximately 70-75 kb genome) podoviruses, which were isolated from the
      same seawater sample using Cellulophaga baltica as host. Quantitative host range
      studies reveal that these genera have contrasting narrow (specialist) and broad
      (generalist) host ranges, with one-step growth curves revealing reduced burst
      sizes for the generalist phages. Genomic comparisons suggest candidate genes in
      each genus that might explain this host range variation, as well as provide
      hypotheses about receptors in the hosts. One generalist phage, phi38:1, was more
      deeply characterized, as its infection strategy switched from lytic on its
      original host to either inefficient lytic or lysogenic on an alternative host. If
      lysogenic, this phage was maintained extrachromosomally in the alternative host
      and could not be induced by mitomycin C. This work provides fundamental knowledge
      regarding phage-host ranges and their genomic drivers while also exploring the
      'host environment' as a driver for switching phage replication mode.
AU  - Holmfeldt K
AU  - Howard-Varona C
AU  - Solonenko N
AU  - Sullivan MB
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2014 16: 2501-2513.

PMID- 16125007
VI  - 29
DP  - 2005
TI  - New insights in the molecular biology and physiology of Streptococcus thermophilus revealed by comparative genomics.
PG  - 435-463
AB  - Streptoeoccus thermophilus is a major dairy starter used for the manufacture of yoghurt and
      cheese. The access to three genome
      sequences, comparative genomics and multilocus sequencing analyses
      suggests that this species recently emerged and is still undergoing a
      process of regressive evolution towards a specialised bacterium for
      growth in milk. Notably, S. thermophilus has maintained a
      well-developed nitrogen metabolism whereas its sugar catabolism has
      been subjected to a high level of degeneracy due to a paucity of carbon
      sources in milk. Furthermore, while pathogenic streptococci are
      recognised for a high capacity to expose proteins at their cell surface
      in order to achieve cell adhesion or to escape the host immune system,
      S. thermophilus has nearly lost this unique feature as well as many
      virulence-related functions. Although gene decay is obvious in S.
      thermophilus genome evolution, numerous small genomic islands, which
      were probably acquired by horizontal gene transfer, comprise important
      industrial phenotypic traits such as polysaccharide biosynthesis,
      bacteriocin production, restriction-modification systems or oxygen
      tolerance.
AU  - Hols P
AU  - Hancy F
AU  - Fontaine L
AU  - Grossiord B
AU  - Prozzi D
AU  - Leblond-Bourget N
AU  - Decaris B
AU  - Bolotin A
AU  - Delorme C
AU  - Ehrlich SD
AU  - Guedon E
AU  - Monnet W
AU  - Renault P
AU  - Kleerebezem M
PT  - Journal Article
TA  - FEMS Microbiol. Rev.
JT  - FEMS Microbiol. Rev.
SO  - FEMS Microbiol. Rev. 2005 29: 435-463.

PMID- 21813488
VI  - 3
DP  - 2011
TI  - A very early-branching Staphylococcus aureus lineage lacking the carotenoid pigment staphyloxanthin.
PG  - 881-895
AB  - Here we discuss the evolution of the northern Australian Staphylococcus aureus
      isolate MSHR1132 genome. MSHR1132 belongs to the divergent clonal complex 75
      lineage. The average nucleotide divergence between orthologous genes in MSHR1132
      and typical S. aureus is approximately sevenfold greater than the maximum
      divergence observed in this species to date. MSHR1132 has a small accessory
      genome, which includes the well-characterized genomic islands, nuSAalpha and
      nuSabeta, suggesting that these elements were acquired well before the expansion
      of the typical S. aureus population. Other mobile elements show mosaic structure
      (the prophage varphiSa3) or evidence of recent acquisition from a typical S.
      aureus lineage (SCCmec, ICE6013 and plasmid pMSHR1132). There are two differences
      in gene repertoire compared with typical S. aureus that may be significant clues
      as to the genetic basis underlying the successful emergence of S. aureus as a
      pathogen. First, MSHR1132 lacks the genes for production of staphyloxanthin, the
      carotenoid pigment that confers upon S. aureus its characteristic golden color
      and protects against oxidative stress. The lack of pigment was demonstrated in
      126 of 126 CC75 isolates. Second, a mobile clustered regularly interspaced short
      palindromic repeat (CRISPR) element is inserted into orfX of MSHR1132. Although
      common in other staphylococcal species, these elements are very rare within S.
      aureus and may impact accessory genome acquisition. The CRISPR spacer sequences
      reveal a history of attempted invasion by known S. aureus mobile elements. There
      is a case for the creation of a new taxon to accommodate this and related
      isolates.
AU  - Holt DC
AU  - Holden MT
AU  - Tong SY
AU  - Castillo-Ramirez S
AU  - Clarke L
AU  - Quail MA
AU  - Currie BJ
AU  - Parkhill J
AU  - Bentley SD
AU  - Feil EJ
AU  - Giffard PM
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2011 3: 881-895.

PMID- 22923403
VI  - 78
DP  - 2012
TI  - Identification of Cj1051c as a Major Determinant for the Restriction Barrier of Campylobacter jejuni Strain NCTC11168.
PG  - 7841-7848
AB  - Campylobacter jejuni is a leading cause of human diarrheal illness in the world, and research
      on it has benefitted greatly by the completion
      of several genome sequences and the development of molecular biology
      tools. However, many hurdles remain for a full understanding of this
      unique bacterial pathogen. One of the most commonly used strains for
      genetic work with C. jejuni is NCTC11168. While this strain is readily
      transformable with DNA for genomic recombination, transformation with
      plasmids is problematic. In this study, we have identified a
      determinant of this to be cj1051c, predicted to encode a
      restriction-modification type IIG enzyme. Knockout mutagenesis of this
      gene resulted in a strain with a 1,000-fold-enhanced transformation
      efficiency with a plasmid purified from a C. jejuni host. Additionally,
      this mutation conferred the ability to be transformed by plasmids
      isolated from an Escherichia coli host. Sequence analysis suggested a
      high level of variability of the specificity domain between strains and
      that this gene may be subject to phase variation. We provide evidence
      that cj1051c is active in NCTC11168 and behaves as expected for a type
      IIG enzyme. The identification of this determinant provides a greater
      understanding of the molecular biology of C. jejuni as well as a tool
      for plasmid work with strain NCTC11168.
AU  - Holt JP
AU  - Grant AJ
AU  - Coward C
AU  - Maskell DJ
AU  - Quinlan JJ
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2012 78: 7841-7848.

PMID- 22863732
VI  - 44
DP  - 2012
TI  - Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe.
PG  - 1056-1059
AB  - Shigella are human-adapted Escherichia coli that have gained the ability to invade the human
      gut mucosa and cause dysentery, spreading efficiently via
      low-dose fecal-oral transmission. Historically, S. sonnei has been predominantly
      responsible for dysentery in developed countries but is now emerging as a problem
      in the developing world, seeming to replace the more diverse Shigella flexneri in
      areas undergoing economic development and improvements in water quality.
      Classical approaches have shown that S. sonnei is genetically conserved and
      clonal. We report here whole-genome sequencing of 132 globally distributed
      isolates. Our phylogenetic analysis shows that the current S. sonnei population
      descends from a common ancestor that existed less than 500 years ago and that
      diversified into several distinct lineages with unique characteristics. Our
      analysis suggests that the majority of this diversification occurred in Europe
      and was followed by more recent establishment of local pathogen populations on
      other continents, predominantly due to the pandemic spread of a single, rapidly
      evolving, multidrug-resistant lineage.
AU  - Holt KE
AU  - Baker S
AU  - Weill FX
AU  - Holmes EC
AU  - Kitchen A
AU  - Yu J
AU  - Sangal V
AU  - Brown DJ
AU  - Coia JE
AU  - Kim DW
AU  - Choi SY
AU  - Kim SH
AU  - da Silveira WD
AU  - Pickard DJ
AU  - Farrar JJ
AU  - Parkhill J
AU  - Dougan G
AU  - Thomson NR
PT  - Journal Article
TA  - Nat. Genet.
JT  - Nat. Genet.
SO  - Nat. Genet. 2012 44: 1056-1059.

PMID- 25767221
VI  - 3
DP  - 2015
TI  - Genome Sequence of Acinetobacter baumannii Strain A1, an Early Example of Antibiotic-Resistant Global Clone 1.
PG  - e00032-15
AB  - Acinetobacter baumannii isolate A1 was recovered in the United Kingdom in 1982 and belongs to
      global clone 1 (GC1). Here, we present its complete 3.91-Mbp
      genome sequence, generated via a combination of short-read sequencing (Illumina),
      long-read sequencing (PacBio), and manual finishing.
AU  - Holt KE
AU  - Hamidian M
AU  - Kenyon JJ
AU  - Wynn MT
AU  - Hawkey J
AU  - Pickard D
AU  - Hall RM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00032-15.

PMID- 17384186
VI  - 189
DP  - 2007
TI  - Multidrug-Resistant Salmonella enterica Serovar Paratyphi A Harbors IncHI1 Plasmids Similar to Those Found in Serovar Typhi.
PG  - 4257-4264
AB  - Salmonella enterica serovars Typhi and Paratyphi A cause systemic
      infections in humans which are referred to as enteric fever.
      Multidrug-resistant (MDR) serovar Typhi isolates emerged in the 1980s, and
      in recent years MDR serovar Paratyphi A infections have become established
      as a significant problem across Asia. MDR in serovar Typhi is almost
      invariably associated with IncHI1 plasmids, but the genetic basis of MDR
      in serovar Paratyphi A has remained predominantly undefined. The DNA
      sequence of an IncHI1 plasmid, pAKU_1, encoding MDR in a serovar Paratyphi
      A strain has been determined. Significantly, this plasmid shares a common
      IncHI1-associated DNA backbone with the serovar Typhi plasmid pHCM1 and an
      S. enterica serovar Typhimurium plasmid pR27. Plasmids pAKU_1 and pHCM1
      share 14 antibiotic resistance genes encoded within similar mobile
      elements, which appear to form a 24-kb composite transposon that has
      transferred as a single unit into different positions into their IncHI1
      backbones. Thus, these plasmids have acquired similar antibiotic
      resistance genes independently via the horizontal transfer of mobile DNA
      elements. Furthermore, two IncHI1 plasmids from a Vietnamese isolate of
      serovar Typhi were found to contain features of the backbone sequence of
      pAKU_1 rather than pHCM1, with the composite transposon inserted in the
      same location as in the pAKU_1 sequence. Our data show that these serovar
      Typhi and Paratyphi A IncHI1 plasmids share highly conserved core DNA and
      have acquired similar mobile elements encoding antibiotic resistance genes
      in past decades.
AU  - Holt KE
AU  - Thomson NR
AU  - Wain J
AU  - Phan MD
AU  - Nair S
AU  - Hasan R
AU  - Bhutta ZA
AU  - Quail MA
AU  - Norbertczak H
AU  - Walker D
AU  - Dougan G
AU  - Parkhill J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2007 189: 4257-4264.

PMID- 7961638
VI  - 269
DP  - 1994
TI  - Location of putative binding and catalytic sites of NaeI by random mutagenesis.
PG  - 27286-27290
AB  - Endonuclease NaeI is a prototype for an unusual group of type II restriction endonucleases
      that must bind two DNA recognition sequences to cleave DNA. The naeIR gene, expressed from a
      Ptac promoter construct, was toxic to Escherichia coli in the absence of NaeI-sequence
      specific methylases. The naeIR gene was mutagenized with N-methyl-N'-nitrosoguanidine; four
      classes of NaeI variants were isolated in the absence of protecting methylase activity. Class
      I variants (T60I, E70K) lacked detectable cleavage activity, but displayed good
      sequence-specific DNA binding. Class II variants (D95N, G141D) displayed 1-5% of the wild-type
      cleavage activity and normal DNA binding. Class III variants (G131E, G131R/A219T, G236S,
      L241P, G245E, G245R, G250E, G270E) lacked both cleavage and binding activities. These results
      imply two amino acids (Thr-60, Glu-70) essential for catalysis. In addition, two domains are
      indicated in NaeI: one (Thr-60 to Gly-155) mediates substrate binding and catalysis, the other
      (Gly-197 to Gly-270) may mediate binding of the activating DNA sequence. Our results are
      compared with the active site residues of EcoRI, EcoRV, and BamHI.
AU  - Holtz JK
AU  - Topal MD
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1994 269: 27286-27290.

PMID- 15178416
VI  - 319
DP  - 2004
TI  - Cellular localization of type I restriction-modification enzymes is family dependent.
PG  - 375-380
AB  - Cellular localization of Type I restriction-modification enzymes EcoKI, EcoAI, and
      EcoR124I-the most frequently studied representatives of IA,
      113, and IC families-was analyzed by immunoblotting of subcellular
      fractions isolated from Escherichia coli strains harboring the
      corresponding hsd genes. EcoR124I shows characteristics similar to
      those of EcoKI. The complex enzymes are associated with the cytoplasmic
      membrane via DNA interaction as documented by the release of the Hsd
      subunits from the membrane into the soluble fraction following
      benzonase treatment. HsdR subunits of the membrane-bound enzymes EcoKI
      and EcoR124I are accessible, though to a different extent, at the
      external surface of cytoplasmic membrane as shown by trypsinization of
      intact spheroplasts. EcoAI strongly differs from EcoKI and EcoR124I,
      since neither benzonase nor trypsin affects its association with the
      cytoplasmic membrane. Possible reasons for such a different
      organization are discussed in relation of the control of the
      restriction-modification activities in vivo.
AU  - Holubova I
AU  - Vejsadova I
AU  - Firman K
AU  - Weiserovda M
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 2004 319: 375-380.

PMID- 10733903
VI  - 270
DP  - 2000
TI  - Localization of the Type I Restriction-Modification Enzyme EcoKI in the Bacterial Cell.
PG  - 46-51
AB  - To localise the type I restriction-modification (R-M) enzyme EcoKI within the bacterial cell,
      the Hsd subunits present in subcellular fractions were analysed using immunoblotting
      techniques. The endonuclease (ENase) as well as the methylase (MTase) were found to be
      associated with the cytoplasmic membrane. HsdR and HsdM subunits produced individually were
      soluble, cytoplasmic polypeptides and only became membrane-associated when coproduced with the
      insoluble HsdS subunit. The release of enzyme from the membrane fraction following benzonase
      treatment indicated a role for DNA in this interaction. Trypsinization of spheroplasts
      revealed that the HsdR subunit in the assembled ENase was accessible to protease, while HsdM
      and HsdS, in both ENase and MTase complexes, were fully protected against digestion. We
      postulate that the R-M enzyme EcoKI is associated with the cytoplasmic membrane in a manner
      that allows access of HsdR to the periplasmic space, while the MTase components are localised
      on the inner side of the plasma membrane.
AU  - Holubova I
AU  - Vejsadova S
AU  - Weiserova M
AU  - Firman K
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 2000 270: 46-51.

PMID- 18045423
VI  - 103
DP  - 2007
TI  - Potential of AbiS as defence mechanism determined by conductivity measurement.
PG  - 2382-2391
AB  - Aim: To compare pH and conductivity used in the determination of growth in reconstituted skim
      milk (RSM), to determine whether the presence of
      one or two plasmids in Lactococcus lactis had any influence on growth,
      and whether AbiS improved bacteriophages resistance of L. lactis.
      Methods and Results: Conductivity and pH were used to determine
      growth in RSM. A small increase in the generation time was found with
      increasing number of plasmids, while their size was unimportant. The
      introduction of a plasmid-encoding AbiS did only enhance the level of
      phage resistance significant when other plasmids encoding either AbiS1
      or the restriction modification system LlaBIII was present.
      Conclusions: The earliest detection of growth was observed by
      measuring pH, rather than conductance. The plasmid-encoded AbiS system
      has a potential to be used as a phage resistance mechanisms in L.
      lactis during milk fermentations, especially when combined with other
      anti-phage mechanisms.
      Significance and Impact of the Study: This study widened the
      knowledge about the influence of plasmid introduction on the growth
      rate of L. lactis, which is important for the construction of new
      strains. The level of protection against 936 groups of phages was only
      significant when the mechanism was present together with the RM system
      LlaBIII.
AU  - Holubova J
AU  - Josephsen J
PT  - Journal Article
TA  - J. Appl. Microbiol.
JT  - J. Appl. Microbiol.
SO  - J. Appl. Microbiol. 2007 103: 2382-2391.

PMID- 10329711
VI  - 274
DP  - 1999
TI  - Identification of the binding site for the extrahelical target base in N6-adenine DNA methyltransferases by photo-cross-linking with duplex oligodeoxyribonucleotides containing 5-iodouracil at the target position.
PG  - 15066-15072
AB  - DNA methyltransferases flip their target bases out of the DNA double helix for catalysis. Base
      flipping of C5-cytosine DNA methyltransferases was directly observed in the protein-DNA
      cocrystal structures of M.HhaI and M.HaeIII. Indirect structural evidence for base flipping of
      N6-adenine and N4-cytosine DNA methyltransferases was obtained by modeling DNA into the
      three-dimensional structures of M.TaqI and M.PvuII in complex with the cofactor. In addition,
      biochemical evidence of base flipping was reported for different N6-adenine DNA
      methyltransferases. As no protein-DNA cocrystal structure for the related N6-adenine and
      N4-cytosine DNA methyltransferases is available, we used light-induced photochemical
      cross-linking to identify the binding site of the extrahelical target bases. The N6-adenine
      DNA methyltransferases M.TaqI and M.CviBIII, which both methylate adenine within the
      double-stranded 5'-TCGA-3' DNA sequence, were photo-cross-linked to duplex
      oligodeoxyribonucleotides containing 5-iodouracil at the target position in 50-60% and almost
      quantitative yield, respectively. Proteolytic fragmentation of the M.CviBIII-DNA complex
      followed by Edman degradation and electrospray ionization mass spectrometry indicates
      photo-cross-linking to tyrosine 122. In addition, the mutant methyltransferases M.TaqI/Y108A
      and M.TaqI/F196A were photo-cross-linked with 6-fold and 2-fold reduced efficiency,
      respectively, which suggests that tyrosine 108 is the primary site of modification in M.TaqI.
      Our results indicate a close proximity between the extrahelical target base and tyrosine 122
      in M.CviBIII or tyrosine 108 in M.TaqI. As both residues belong to the conserved motif IV
      ((N/D/S)(P/I)P(Y/F/W)) found in all N6-adenine and N4-cytosine DNA as well as in N6-adenine
      RNA methyltransferases, a similar spatial relationship between the target bases and the
      aromatic amino acid residue within motif IV is expected for all these methyltransferases.
AU  - Holz B
AU  - Dank N
AU  - Eickhoff JE
AU  - Lipps G
AU  - Krauss G
AU  - Weinhold E
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1999 274: 15066-15072.

PMID- 9461471
VI  - 26
DP  - 1998
TI  - 2-Aminopurine as a fluorescent probe for DNA base flipping by methyltransferases.
PG  - 1076-1083
AB  - DNA base flipping, which was first observed for the C5-cytosine  methyltransferase M.HhaI,
      results in a complete removal of the stacking interactions between the target base and its
      neighboring bases.  We have investigated whether duplex oligodeoxynucleotides containing the
      fluorescent base analogue 2-aminopurine can be used to sense DNA base flipping.  Using M.HhaI
      as a paradigm for a base flipping enzyme, we find that the fluorescence intensity of duplex
      oligodeoxynucleotides containing 2-aminopurine at the target site is dramatically enhanced
      (54-fold) in the presence of M.HhaI.  Duplex oligodeoxynucleotides containing 2-aminopurine
      adjacent to the target cytosine show little fluorescence increase upon addition of M.HhaI.
      These results clearly demonstrate that duplex oligodeoxynucleotides containing 2-aminopurine
      at the target site can serve as fluorescence probes for base flipping.  Another enzyme
      hypothesized to use a base flipping mechanism is the N6-adenine DNA methyltransferase M.TaqI.
      Addition of M.TaqI to duplex oligodeoxynucleotides bearing 2-aminopurine at the target
      position, also results in a strongly enhanced fluorescence (13-fold), whereas addition to
      duplex oligodeoxynucleotides containing 2-aminopurine at the 3'- or 5'-neighboring position
      leads only to small fluorescence increases.  These results give the first experimental
      evidence that the adenine-specific DNA methyltransferase M.TaqI also flips its target base.
AU  - Holz B
AU  - Klimasauskas S
AU  - Serva S
AU  - Weinhold E
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1998 26: 1076-1083.

PMID- 9279140
VI  - 11
DP  - 1997
TI  - Fluorescence studies on the base flipping mechanism of the DNA methyltransferase M.TaqI.
PG  - A1151
AB  - The DNA methyltransferase from Thermus aquaticus catalyzes the methyl group transfer from
      S-adenosyl-L-methionine to the N6-position of adenine in the double-stranded DNA sequence
      5'-TCGA-3'.  A model of the ternary complex built with the crystal structure of M.TaqI-SAM
      complex and DNA duplex shows that the distance between the cofactor and the target adenine is
      too large to allow a direct methyl group transfer.  This distance can be decreased if the
      adenine rotates out of the DNA helix as described for a C5-DNA methyltransferase.  DNA
      containing the adenine analogue 2-aminopurine and intrinsic tryptophan fluorescence were used
      to examine such a base flipping mechanism for M.TaqI.  The fluorescence of 2-Ap is highly
      quenched in duplex DNA due to stacking of the neighboring bases.  Addition of M.TaqI to a DNA
      duplex with 2-Ap at the target site causes a large fluorescence increase which points to an
      extrahelical base in this complex.  In stopped-flow experiments this increase is single
      exponential with a rate constant of 20 s^-1.  Binding of DNA leads to a 30% increase of the
      tryptophan fluorescence intensity of M.TaqI.  This increase was resolved into two steps: a
      rapid first step (k+2 = 20 s-1) and a second step with a k+3 = 2 s-1.  Since both steps are
      not concentration dependent we suggest a very fast formation of an initial complex in a time
      scale not resolved by the stopped-flow method.  These data suggest that DNA binding of M.TaqI
      is at least a three step process, where the second step gives rise not only to a
      conformational change of the DNA methyltransferase but also of the DNA.
AU  - Holz B
AU  - Pues H
AU  - Wolcke J
AU  - Weinhold E
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1997 11: A1151.

PMID- 
VI  - 
DP  - 1999
TI  - Probes for DNA base flipping by DNA methyltransferases.
PG  - 337-345
AB  - In addition to the normal nucleobases adenine, thymine, guanine, and cytosine, the DNA of most
      organisms contains the methylated bases C5-methylcytosine, N6-methyladenine, or
      N4-methylcytosine.  These methylated bases are formed by DNA methyltransferases which catalyze
      the transfer of the activated methyl group from the cofactor S-adenosyl-L-methionine to the C5
      carbon of cytosine, the N6 nitrogen of adenine, or the N4 nitrogen of cytosine within specific
      DNA sequences.  Most DNA Mtases recognize palindromic DNA sequences, which contain two
      symmetry-related target bases.  After DNA replication, only the parental strand contains
      methylated bases (hemi-methylated DNA), and methylation of the daughter strand restores the
      fully methylated DNA.
AU  - Holz B
AU  - Weinhold E
PT  - Journal Article
TA  - Bioorganic Chemistry: Highlights and New Aspects
JT  - Bioorganic Chemistry: Highlights and New Aspects
SO  - Bioorganic Chemistry: Highlights and New Aspects 1999 : 337-345.

PMID- 20630873
VI  - 285
DP  - 2010
TI  - The Inherent Processivity of the Human de Novo Methyltransferase 3A (DNMT3A) Is Enhanced by DNMT3L.
PG  - 29091-29100
AB  - Human DNMT3A is responsible for de novo DNA cytosine methylation patterning during
      development. Here we show that DNMT3A methylates 5-8
      CpG sites on human promoters before 50% of the initially bound enzyme
      dissociates from the DNA. Processive methylation is enhanced 3-fold in
      the presence of DNMT3L, an inactive homolog of DNMT3A, therefore
      providing a mechanism for the previously described DNMT3L activation of
      DNMT3A. DNMT3A processivity on human promoters is also regulated by DNA
      topology, where a 2-fold decrease in processivity was observed on
      supercoiled DNA in comparison with linear DNA. These results are the
      first observation that DNMT3A utilizes this mechanism of increasing
      catalytic efficiency. Processive de novo DNA methylation provides a
      mechanism that ensures that multiple CpG sites undergo methylation for
      transcriptional regulation and silencing of newly integrated viral DNA.
AU  - Holz-Schietinger C
AU  - Reich NO
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2010 285: 29091-29100.

PMID- 22730298
VI  - 40
DP  - 2012
TI  - RNA modulation of the human DNA methyltransferase 3A.
PG  - 8550-8557
AB  - DNA methyltransferase 3A (DNMT3A) is one of two human de novo DNA methyltransferases essential
      for transcription regulation during cellular
      development and differentiation. There is increasing evidence that RNA plays a
      role in directing DNA methylation to specific genomic locations within mammalian
      cells. Here, we describe two modes of RNA regulation of DNMT3A in vitro. We show
      a single-stranded RNA molecule that is antisense to the E-cadherin promoter binds
      tightly to the catalytic domain in a structurally dependent fashion causing
      potent inhibition of DNMT3A activity. Two other RNA molecules bind DNMT3A at an
      allosteric site outside the catalytic domain, causing no change in catalysis. Our
      observation of the potent and specific in vitro modulation of DNMT3A activity by
      RNA supports in vivo data that RNA interacts with DNMT3A to regulate
      transcription.
AU  - Holz-Schietinger C
AU  - Reich NO
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: 8550-8557.

PMID- 18678653
VI  - 28
DP  - 2008
TI  - Direct interaction between DNA methyltransferase DIM-2 and HP1 is required for DNA methylation in Neurospora crassa.
PG  - 6044-6055
AB  - DNA methylation is involved in gene silencing and genomic stability in mammals, plants, and
      fungi. Genetics studies of Neurospora crassa have
      revealed that a DNA methyltransferase (DIM-2), a histone H3K9
      methyltransferase (DIM-5), and heterochromatin protein 1 (HP1) are
      required for DNA methylation. We explored the interrelationships of
      these components of the methylation machinery. A yeast two-hybrid
      screen revealed that HP1 interacts with DIM-2. We confirmed the
      interaction in vivo and demonstrated that it involves a pair of
      PXVXL-related motifs in the N-terminal region of DIM-2 and the chromo
      shadow domain of HP1. Both regions are essential for proper DNA
      methylation. We also determined that DIM-2 and HP1 form a stable
      complex independently of the trimethylation of histone H3K9, although
      the association of DIM-2 with its substrate sequences depends on
      trimethyl-H3K9. The DIM-2/HP1 complex does not include DIM-5. We
      conclude that DNA methylation in Neurospora is largely or exclusively
      the result of a unidirectional pathway in which DIM-5 methylates
      histone H3K9 and then the DIM-2/HP1 complex recognizes the resulting
      trimethyl-H3K9 mark via the chromo domain of HP1.
AU  - Honda S
AU  - Selker EU
PT  - Journal Article
TA  - Mol. Cell. Biol.
JT  - Mol. Cell. Biol.
SO  - Mol. Cell. Biol. 2008 28: 6044-6055.

PMID- 25059865
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Marine Cyanobacterium Synechococcus sp. Strain NKBG042902, Which Harbors a Homogeneous Plasmid Available for Metabolic  Engineering.
PG  - e00704-14
AB  - The marine cyanobacterium Synechococcus sp. strain NKBG042902 was isolated from coastal areas
      in Japan. Strain NKBG042902 has four plasmids: pSY8, pSY9, pSY10,
      and pSY11. Moreover, the hybrid plasmid pUSY02 containing pSY11 and Escherichia
      coli plasmid pUC18 was constructed for this strain. The genetic manipulation
      technique using pUSY02 was established for this strain and used in metabolic
      engineering. Here, we report the draft genome sequence of this strain, which has
      77 contigs comprising a total length of 3,319,479 bp, with a G+C content of
      49.4%.
AU  - Honda T
AU  - Liang Y
AU  - Arai D
AU  - Ito Y
AU  - Yoshino T
AU  - Tanaka T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00704-14.

PMID- 27516512
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Citrobacter freundii Strains CF04 and A41 Isolated from Moribund, Septicemic Giant Gourami (Osphronemus goramy) in Sri Lanka.
PG  - e00820-16
AB  - Citrobacter freundii is a Gram-negative opportunistic pathogen associated with many infectious
      conditions including septicemia in humans and animals. Here, we
      announce the draft genome sequences of two multidrug-resistant C. freundii
      strains (CF04 and A41) isolated from septicemic giant gourami (Osphronemus
      goramy) collected from aquaria in Sri Lanka.
AU  - Honein K
AU  - Jagoda SS
AU  - Arulkanthan A
AU  - Ushio H
AU  - Asakawa S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00820-16.

PMID- 29437097
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Aeromonas hydrophila Strain Ae25, Isolated from a Septicemic Moribund Koi Carp (Cyprinus carpio) in Sri Lanka.
PG  - e01523-17
AB  - Motile aeromonad septicemia caused by mesophilic strains of Aeromonas hydrophila  is a
      widespread problem in cultured freshwater fish. We announce here the draft
      genome sequence of the multidrug-resistant A. hydrophila strain Ae25, isolated
      from a koi carp (Cyprinus carpio) with motile aeromonad septicemia that was
      collected from an ornamental fish-breeding farm in Sri Lanka.
AU  - Honein K
AU  - Jagoda SSSS
AU  - Arulkanthan A
AU  - Ushio H
AU  - Asakawa S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01523-17.

PMID- 27389269
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the Endophytic Strain Rhodococcus kyotonensis KB10, a Potential Biodegrading and Antibacterial Bacterium Isolated from Arabidopsis  thaliana.
PG  - e00636-16
AB  - Rhodococcus kyotonensis KB10 is an endophytic bacterium isolated from Arabidopsis thaliana The
      organism showed mild antibacterial activity against the
      phytopathogen Pseudomonas syringae pv. tomato DC3000. This study reports the
      genome sequence of R. kyotonensis KB10. This bacterium contains an ectoine
      biosynthesis gene cluster and has the potential to degrade nitroaromatic
      compounds. The identified bacterium may be a suitable biocontrol agent and
      degrader of environmental pollutants.
AU  - Hong CE
AU  - Jo SH
AU  - Jeong H
AU  - Park JM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00636-16.

PMID- 28883145
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Endophytic Bacterium Variovorax paradoxus KB5, Which Has Antagonistic Activity against a Phytopathogen, Pseudomonas syringae pv.  tomato DC3000.
PG  - e00950-17
AB  - Variovorax paradoxus KB5, isolated from the inside of Arabidopsis thaliana leaves, showed
      antibacterial activity against the phytopathogen Pseudomonas
      syringae pv. tomato DC3000. Here, we report a draft genome sequence of V.
      paradoxus KB5, which contains a delftibactin-like nonribosomal peptide
      biosynthetic gene cluster.
AU  - Hong CE
AU  - Jo SH
AU  - Jo IH
AU  - Jeong H
AU  - Park JM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00950-17.

PMID- 28729274
VI  - 5
DP  - 2017
TI  - Genome Sequences of Two Shewanella spp. Isolated from the Gut of the Sea Cucumber Apostichopus japonicus (Selenka, 1867).
PG  - e00674-17
AB  - In this study, we sequenced the genomes of two Shewanella spp., newly isolated from the gut of
      the sea cucumber Apostichopus japonicus (Selenka, 1867). The
      whole-genome sequences reported here will expand the repertoire of genomic
      information for the members of the genus Shewanella and will provide important
      insights into their roles within microbial communities.
AU  - Hong HH
AU  - Choi H
AU  - Cheon S
AU  - Lee HG
AU  - Park C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00674-17.

PMID- 27313306
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Biofilm-Forming Strain Staphylococcus haemolyticus S167.
PG  - e00567-16
AB  - Staphylococcus haemolyticus S167 has the ability to produce biofilms in large quantities.
      Genomic analyses revealed information on the biofilm-related genes of
      S. haemolyticus S167. Detailed studies of biofilm formation at the molecular
      level could provide a foundation for biofilm control research.
AU  - Hong J
AU  - Kim J
AU  - Kim BY
AU  - Park JW
AU  - Ryu JG
AU  - Roh E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00567-16.

PMID- 23144374
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Pantoea sp. Strain A4, a Rafflesia-Associated Bacterium  That Produces N-Acylhomoserine Lactones as Quorum-Sensing Molecules.
PG  - 6610
AB  - Pantoea sp. strain A4 is a Gram-negative bacterium isolated from the Rafflesia flower. We
      present here, for the first time, the genome sequence of
      Rafflesia-associated Pantoea sp. strain A4, which exhibited quorum-sensing
      activity.
AU  - Hong KW
AU  - Gan HM
AU  - Low SM
AU  - Lee PK
AU  - Chong YM
AU  - Yin WF
AU  - Chan KG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6610.

PMID- 23105060
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Burkholderia sp. Strain GG4, a Betaproteobacterium That Reduces 3-Oxo-N-Acylhomoserine Lactones and Produces Different  N-Acylhomoserine Lactones.
PG  - 6317
AB  - Burkholderia sp. strain GG4, isolated from the ginger rhizosphere, possesses a unique
      N-acylhomoserine lactone (AHL)-modifying activity that reduces 3-oxo-AHLs
      to 3-hydroxy-AHLs. To the best of our knowledge, this is the first sequenced
      genome from a bacterium of the genus Burkholderia that shows both quorum-sensing
      and signaling confusion activities.
AU  - Hong KW
AU  - Koh CL
AU  - Sam CK
AU  - Yin WF
AU  - Chan KG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6317.

PMID- 23105061
VI  - 194
DP  - 2012
TI  - Whole-Genome Sequence of N-Acylhomoserine Lactone-Synthesizing and -Degrading Acinetobacter sp. Strain GG2.
PG  - 6318
AB  - Acinetobacter sp. strain GG2 is a quorum-sensing and quorum-quenching bacterium isolated from
      the ginger rhizosphere. It degrades a broad range of
      N-acylhomoserine lactone molecules via lactonase. The genome sequence of strain
      GG2 may provide insights on the regulation of quorum-sensing and quorum-quenching
      mechanisms in this bacterium.
AU  - Hong KW
AU  - Koh CL
AU  - Sam CK
AU  - Yin WF
AU  - Chan KG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6318.

PMID- 23115161
VI  - 194
DP  - 2012
TI  - Whole-Genome Sequence of Cupriavidus sp. Strain BIS7, a Heavy-Metal-Resistant Bacterium.
PG  - 6324
AB  - Cupriavidus sp. strain BIS7 is a Malaysian tropical soil bacterium that exhibits  broad
      heavy-metal resistance [Co(II), Zn(II), Ni(II), Se(IV), Cu(II), chromate,
      Co(III), Fe(II), and Fe(III)]. It is particularly resistant to Fe(II), Fe(III),
      and Zn(II). Here we present the assembly and annotation of its genome.
AU  - Hong KW
AU  - Thinagaran DA
AU  - Gan HM
AU  - Yin WF
AU  - Chan KG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6324.

PMID- 15378067
VI  - 22
DP  - 2004
TI  - The genome sequence of the capnophilic rumen bacterium Mannheimia succiniciproducens.
PG  - 1275-1281
AB  - The rumen represents the first section of a ruminant animal's stomach, where feed is
      collected and mixed with microorganisms for initial
      digestion. The major gas produced in the rumen is CO(2) (65.5 mol%), yet
      the metabolic characteristics of capnophilic (CO(2)-loving) microorganisms
      are not well understood. Here we report the 2,314,078 base pair genome
      sequence of Mannheimia succiniciproducens MBEL55E, a recently isolated
      capnophilic Gram-negative bacterium from bovine rumen, and analyze its
      genome contents and metabolic characteristics. The metabolism of M.
      succiniciproducens was found to be well adapted to the oxygen-free rumen
      by using fumarate as a major electron acceptor. Genome-scale metabolic
      flux analysis indicated that CO(2) is important for the carboxylation of
      phosphoenolpyruvate to oxaloacetate, which is converted to succinic acid
      by the reductive tricarboxylic acid cycle and menaquinone systems. This
      characteristic metabolism allows highly efficient production of succinic
      acid, an important four-carbon industrial chemical.
AU  - Hong SH
AU  - Kim JS
AU  - Lee SY
AU  - In YH
AU  - Choi SS
AU  - Rih JK
AU  - Kim CH
AU  - Jeong H
AU  - Hur CG
AU  - Kim JJ
PT  - Journal Article
TA  - Nat. Biotechnol.
JT  - Nat. Biotechnol.
SO  - Nat. Biotechnol. 2004 22: 1275-1281.

PMID- 26205864
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Caprolactam-Degrading Pseudomonas putida Strain SJ3.
PG  - e00810-15
AB  - Pseudomonas putida strain SJ3, which possesses caprolactam-degrading ability, was isolated
      from dyeing industry wastewater in Daegu, Republic of Korea. Here, we
      describe the draft genome sequence and annotation of the strain. The
      5,596,765-bp-long genome contains 4,293 protein-coding genes and 68 RNA genes
      with 61.70% G+C content.
AU  - Hong SJ
AU  - Park GS
AU  - Khan AR
AU  - Jung BK
AU  - Park YJ
AU  - Yoo NK
AU  - Lee C
AU  - Park CK
AU  - Shin JH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00810-15.

PMID- 25676754
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence and Annotation of the Insect Pathogenic Bacterium Xenorhabdus nematophila Strain C2-3, Isolated from Nematode Steinernema  carpocapsae in the Republic of Korea.
PG  - e01521-14
AB  - Xenorhabdus nematophila strain C2-3, which belongs to the family Enterobacteriaceae, was
      isolated from entomopathogenic nematodes collected in the
      Republic of Korea. Herein, we report a 4.38-Mbp draft genome sequence of X.
      nematophila strain C2-3, with a 43.6% G+C content. The RAST annotation analysis
      revealed 4,994 protein-coding sequences in the draft genome.
AU  - Hong SJ
AU  - Ullah I
AU  - Park GS
AU  - Jung BK
AU  - Choi J
AU  - Khan AR
AU  - Kim MC
AU  - Shin JH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01521-14.

PMID- 28495763
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Serratia marcescens Strains CAPREx SY13 and CAPREx SY21 Isolated from Yams.
PG  - e00191-17
AB  - Serratia marcescens strains CAPREx SY13 and CAPREx SY21 were isolated from Ghanaian yams from
      a London market. The draft genomes suggest that the strains
      are similar, with genomes of 5,308,004 and 5,157,134 bp and 59.35 and 59.62 G+C%,
      respectively. The genes necessary for prodigiosin biosynthesis were present in
      both strains.
AU  - Honger J
AU  - Monson RE
AU  - Rawlinson A
AU  - Salmond GPC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00191-17.

PMID- 18391199
VI  - 105
DP  - 2008
TI  - Complete genome of the uncultured Termite Group 1 bacteria in a single host protist cell.
PG  - 5555-5560
AB  - Termites harbor a symbiotic gut microbial community that is responsible for their ability to
      thrive on recalcitrant plant matter. The community comprises diverse microorganisms, most of
      which are as yet uncultivable; the detailed symbiotic mechanism remains unclear. Here, we
      present the first complete genome sequence of a termite gut symbiont-an uncultured bacterium
      named Rs-D17 belonging to the candidate phylum Termite Group 1 (TG1). TG1 is a dominant group
      in termite guts, found as intracellular   symbionts of various cellulolytic protists, without
      any physiological information. To acquire the complete genome sequence, we collected Rs-D17
      cells from only a single host protist cell to minimize their genomic  variation and performed
      isothermal whole-genome amplification. This
      strategy enabled us to reconstruct a circular chromosome (1,125,857 bp)
      encoding 761 putative protein-coding genes. The genome additionally contains 121 pseudogenes
      assigned to categories, such as cell wall biosynthesis, regulators, transporters, and defense
      mechanisms. Despite its apparent reductive evolution, the ability to synthesize 15 amino acids
      and various cofactors is retained, some of these genes having been duplicated. Considering
      that diverse termite-gut protists harbor TG1 bacteria, we suggest that this bacterial group
      plays a key role in the gut symbiotic system by stably supplying essential nitrogenous
      compounds deficient in lignocelluloses to their host protists and the termites. Our results
      provide a breakthrough to clarify the functions of and the interactions among the individual
      members of this multilayered symbiotic complex.
AU  - Hongoh Y
AU  - Sharma VK
AU  - Prakash T
AU  - Noda S
AU  - Taylor TD
AU  - Kudo T
AU  - Sakaki Y
AU  - Toyoda A
AU  - Hattori M
AU  - Ohkuma M
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2008 105: 5555-5560.

PMID- 19008447
VI  - 322
DP  - 2008
TI  - Genome of an Endosymbiont Coupling N2 Fixation to Cellulolysis within Protist Cells in Termite Gut.
PG  - 1108-1109
AB  - Termites harbor diverse symbiotic gut microorganisms, the majority of which are as yet
      uncultivable and their interrelationships unclear.  Here, we present the complete genome
      sequence of the uncultured Bacteroidales endosymbiont of the cellulolytic protest
      Pseudotrichonympha grassii, which accounts for 70% of the bacterial cells in the gut of the
      termite Coptotermes formosanus.  Functional annotation of the chromosome (1,114,206 base
      pairs) unveiled its ability to fix dinitrogen and recycle putative host nitrogen wastes for
      biosynthesis of diverse amino acids and cofactors, and import glucose and xylose as energy and
      carbon sources.  Thus, nitrogen fixation and cellulolysis are coupled within the protist's
      cells.  This highly evolved symbiotic system probably underlies the ability of the worldwide
      pest termites Coptotermes to use wood as their sole food.
AU  - Hongoh Y
AU  - Sharma VK
AU  - Prakash T
AU  - Noda S
AU  - Toh H
AU  - Taylor TD
AU  - Kudo T
AU  - Sakaki Y
AU  - Toyoda A
AU  - Hattori M
AU  - Ohkuma M
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2008 322: 1108-1109.

PMID- 15073316
VI  - 150
DP  - 2004
TI  - A DNA adenine methylase mutant of Shigella flexneri shows no significant attenuation of virulence.
PG  - 1073-1078
AB  - Mutants of Salmonella defective in DNA adenine methylase (dam) have been reported to be
      attenuated for virulence and to provide protective
      immunity when used as vaccine strains. To determine whether these
      observations could be extended to Shigella, a dam mutant of Shigella
      flexneri 2a was characterized and examined for the role of dam in
      pathogenesis. The Shigella dam mutant showed some unique
      characteristics; however, it retained virulence in vivo as well as in
      vitro. The mutant invaded cultured L2 monolayer cells as efficiently as
      the wild-type parent, but its intracellular growth was suppressed up to
      7 h post-invasion. Furthermore, the invading dam mutant formed smaller
      plaques in cell monolayers compared to the parent strain. However, the
      mutant produced keratoconjunctivitis in the Sereny test in guinea pigs
      only slightly more slowly than the wild-type. While the effect of the
      dam mutation on virulence was modest, the rate of spontaneous mutation
      in the dam mutant was 1000-fold greater compared with the wild-type.
      The virulence and high mutability displayed by the dam mutant of Sh.
      flexneri suggest that a general anti-bacterial pathogen vaccine
      strategy based on mutations in dam needs to be re-evaluated.
AU  - Honma Y
AU  - Fernandez RE
AU  - Maurelli AT
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2004 150: 1073-1078.

PMID- 8855319
VI  - 93
DP  - 1996
TI  - DNA repeats identify novel virulence genes in Hemophilus influenzae.
PG  - 11121-11125
AB  - The whole genome sequence (1.83 Mbp) of Haemophilus influenzae strain Rd was searched to
      identify tandem oligonucleotide repeat sequences.  Loss or gain of one or more nucleotide
      repeats through a recombination-independent slippage mechanism is known to mediate phase
      variation of surface molecules of pathogenic bacteria, including H. influenzae.  This
      facilitates evasion of host defenses and adaptation to the varying microenvironments of the
      host.  We reasoned that iterative nucleotides could identify novel genes relevant to
      microbe-host interactions.  Our search of the Rd genome sequence identified 9 novel loci with
      multiple (range 6-36, mean 22) tandem tetranucleotide repeats.  All were found to be located
      within putative open reading frames and included homologues of hemoglobin-binding proteins of
      Neisseria, a glycosyltransferase (lgtC gene product) of Neisseria, and an adhesin of Yersinia.
      These tetranucleotide repeat sequences were also shown to be present in two other
      epidemiologically different H. influenzae type b strains, although the number and distribution
      of repeats was different.  Further characterization of the lgtC gene showed that it was
      involved in phenotypic switching of a lipopolysaccharide epitope and that this variable
      expression was associated with changes in the number of tetranucleotide repeats.  Mutation of
      lgtC resulted in attenuated virulence of H., influenzae in an infant rate model of invasive
      infection.  These data indicate the rapidity, economy, and completeness with which whole
      genome sequences can be used to investigate the biology of pathogenic bacteria.
AU  - Hood DW
AU  - Deadman ME
AU  - Jennings MP
AU  - Bisercic M
AU  - Fleischmann RD
AU  - Venter JC
AU  - Moxon ER
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1996 93: 11121-11125.

PMID- Not carried by PubMed...
VI  - 5
DP  - 1993
TI  - Molecular Evolution: Sampling the New Synthesis.
PG  - 66-70
AB  - Contains a discussion of the evolution of restriction enzymes.
AU  - Hooper C
PT  - Journal Article
TA  - J. NIH Res.
JT  - J. NIH Res.
SO  - J. NIH Res. 1993 5: 66-70.

PMID- 16888362
VI  - 338
DP  - 2006
TI  - DNA methyltransferase probing of DNA-protein interactions.
PG  - 225-244
AB  - Effective methods of probing chromatin structure without disrupting DNA-protein interactions
      and associations are necessary for creating an accurate picture of chromatin and its processes
      in vivo.  Expression of cytidine-5 DNA methyltransferases (C5 DMTases) in Saccharomyces
      cerevisiae provides a powerful noninvasive method for asaying relative DNA accessibility in
      chromatin.  DNA MTases are occluded from protein-associated DNA based on the strength and span
      of the DNA-protein interation.  Ectopic regulation of C5 DMTase expression systems allows for
      minimal disruption of yeast physiology.  Methylated sites are detectd by bisulfite genomic
      sequencing, which leads to a positive signal corresponding to modified cytidine residues.
      High-resolution C5 DMTases with dinucleotide recognition specificity are shown to provide
      sufficient coverage to map interactions spanning a relatively short distance.
AU  - Hoose SA
AU  - Kladde MP
PT  - Journal Article
TA  - Methods Mol. Biol.
JT  - Methods Mol. Biol.
SO  - Methods Mol. Biol. 2006 338: 225-244.

PMID- 23887910
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Salmonella enterica Serovar Typhimurium U288.
PG  - e00467-13
AB  - Salmonella enterica serovar Typhimurium U288 has firmly established itself within the United
      Kingdom pig production industry. The prevalence of this highly
      pathogenic multidrug-resistant serovar at such a critical point in the food chain
      is therefore of great concern. To enhance our understanding of this
      microorganism, whole-genome and plasmid sequencing was performed.
AU  - Hooton SP
AU  - Timms AR
AU  - Moreton J
AU  - Wilson R
AU  - Connerton IF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00467-13.

PMID- 25540350
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Streptococcus agalactiae CNCTC 10/84, a Hypervirulent Sequence Type 26 Strain.
PG  - e01338-14
AB  - Streptococcus agalactiae (group B Streptococcus [GBS]) is a human pathogen with a propensity
      to cause neonatal infections. We report the complete genome sequence
      of GBS strain CNCTC 10/84, a hypervirulent clinical isolate frequently used to
      study GBS pathogenesis. Comparative analysis of this sequence may shed light on
      novel pathogenic mechanisms.
AU  - Hooven TA
AU  - Randis TM
AU  - Daugherty SC
AU  - Narechania A
AU  - Planet PJ
AU  - Tettelin H
AU  - Ratner AJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01338-14.

PMID- 15210696
VI  - 279
DP  - 2004
TI  - Simultaneous DNA binding, bending, and base flipping - Evidence for a novel M. EcoRI methyltransferase-DNA complex.
PG  - 37049-37060
AB  - We measured the kinetics of DNA bending by M.EcoRI using DNA labeled at both 5'-ends and
      observed changes in fluorescence resonance energy
      transfer. Although known to bend its cognate DNA site, energy transfer
      is decreased upon enzyme binding. This unanticipated effect is shown to
      be robust because we observe the identical decrease with different dye
      pairs, when the dye pairs are placed on the respective 3'-ends, the
      effect is cofactor- and protein-dependent, and the effect is observed
      with duplexes ranging from 14 through 17 base pairs. The same labeled
      DNA shows the anticipated increased energy transfer with EcoRV
      endonuclease, which also bends this sequence, and no change in energy
      transfer with EcoRI endonuclease, which leaves this sequence unbent. We
      interpret these results as evidence for an increased end-to-end
      distance resulting from M.EcoRI binding, mediated by a mechanism novel
      for DNA methyltransferases, combining DNA bending and an overall
      expansion of the DNA duplex. The M.EcoRI protein sequence is poorly
      accommodated into well defined classes of DNA methyltransferases, both
      at the level of individual motifs and overall alignment. Interestingly,
      M.EcoRI has an intercalation motif observed in the FPG DNA glycosylase
      family of repair enzymes. Enzyme-dependent changes in anisotropy and
      fluorescence resonance energy transfer have similar rate constants,
      which are similar to the previously determined rate constant for base
      flipping; thus, the three processes are nearly coincidental. Similar
      fluorescence resonance energy transfer experiments following
      AdoMet-dependent catalysis show that the unbending transition
      determines the steady state product release kinetics.
AU  - Hopkins BB
AU  - Reich NO
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2004 279: 37049-37060.

PMID- 144930
VI  - 22
DP  - 1977
TI  - Studies on restriction endonucleases.
PG  - 981-991
AB  - 
AU  - Horiuchi K
PT  - Journal Article
TA  - Tanpakushitsu Kakusan Koso
JT  - Tanpakushitsu Kakusan Koso
SO  - Tanpakushitsu Kakusan Koso 1977 22: 981-991.

PMID- 1102704
VI  - 95
DP  - 1975
TI  - Cleavage map of bacteriophage f1: Location of the Escherichia coli B-specific modification sites.
PG  - 147-165
AB  - Replicative form DNA of bacteriophage f1 was cleaved into specific fragments by
      two endonucleases isolated from Hemophilus aegyptius and an endonuclease
      isolated fom H. influenzae.  The fragments were ordered so as to construct a
      circular map of the phage f1 genome by: (1) digesting the isolated restriction
      fragments with a second restriction enzyme; and (2) testing in a transfection
      system for the ability of the fragments to rescue amber mutations contained on
      single-stranded viral DNA that was hybridized to a particular fragment.  The
      genome of bacteriophage f1 contains two SB sites, genetic sites which confer
      upon a DNA molecule susceptibility to the restriction-modification system of
      Escherichia coli B.  Each of these sites was located on a specific restriction
      fragment by transfection experiments.  In vitro modification of replicative
      form DNA of f1 and its SB mutants by endonuclease R. EcoB and the subsequent
      cleavage of the DNA by the Hemophilus endonucleases showed that the B-specific
      methylation occurs within at least 200 nucleotide pairs of the SB site.
AU  - Horiuchi K
AU  - Vovis GF
AU  - Enea V
AU  - Zinder ND
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1975 95: 147-165.

PMID- Not carried by PubMed...
VI  - 75
DP  - 1975
TI  - Cleavage mapping of the Escherichia coli B-specific modification sites of bacteriophage fl.
PG  - 225
AB  - Replicative form DNA (RF) of bacteriophage fl was cleaved into specific
      fragments by two endonucleases, R.HaeII and R.HaeIII, isolated from Hemophilus
      aegyptius and an endonuclease R.HindII isolated from H. influenzae.  The
      fragments were ordered so as to construct a circular map of the fl genome by:
      1) digesting the isolated restriction fragments with a second restriction
      enzyme; and 2) testing in a transfection system for the ability of the
      fragments to rescue amber mutations contained on single-strand viral DNA that
      was hybridized to a particular fragment.  Both of two SB sites, genetic sites
      which confer upon a DNA molecule susceptibility to the restriction-modification
      system of E. coli B, of fl were located on specific restriction fragments by
      transfection experiments.  In vitro modification of RF of fl and its SB mutants
      and the subsequent cleavage of the DNA by the Hemophilus endonucleases showed
      that the B-specific methylation occurs at, or very near, the SB site.
AU  - Horiuchi K
AU  - Vovis GF
AU  - Enea V
AU  - Zinder ND
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1975 75: 225.

PMID- 4272122
VI  - 249
DP  - 1974
TI  - Effect of deoxyribonucleic acid length on the adenosine triphosphatase activity of Escherichia coli restriction endonuclease B.
PG  - 543-552
AB  - Restriction endonuclease B possesses a DNA-dependent ATPase activity.  The ATP
      hydrolysis can continue for hours after the DNA hydrolysis has stopped and is
      due to a stable DNA-enzyme complex.  RF1 of bacteriophage f1 is much more
      active than its full length linear form (RFIII) in stimulating the ATP
      hydrolysis.  Experiments with lambda phage DNA sheared into various size
      molecules indicate that the ATPase activity is a direct function of the
      molecular weight of linear DNA in a range between 0.9 to 13 Mdaltons.  While
      sonicated, unmodified lambda DNA molecules (0.5 Md) fail to stimulate the
      ATPase activity, they do inhibit the intact DNA-stimulated ATP hydrolysis.  The
      results can be interpreted as follows. (a) Endonuclease R-B recognizes DNA at
      the SB sites; this recognition step is independent of DNA length.  (b) The
      probability that a linear DNA molecule is cleaved by an enzyme molecule bound
      to the DNA depends upon the length of the DNA: the greater the number of
      nucleotide pairs the higher the probability of cleavage.  Circularization of a
      small DNA duplex also increases the probability of cleavage.  One possible
      explanation is that the enzyme travels along the DNA molecule before cleaving
      the DNA.  If the enzyme reaches an end of the DNA molecule before cleavage
      occurs, the enzyme molecule is inactivated. (c) After DNA hydrolysis has
      occurred, the enzyme (or one of its components) remains on the DNA molecule and
      causes the massive ATP hydrolysis.
AU  - Horiuchi K
AU  - Vovis GF
AU  - Zinder ND
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1974 249: 543-552.

PMID- 4564208
VI  - 69
DP  - 1972
TI  - Cleavage of bacteriophage f1 DNA by the restriction enzyme of Escherichia coli.
PG  - 3220-3224
AB  - We studied the cleavage of the replicative form DNA (RFI) of bacteriophage f1
      and its SB mutants by purified restriction endonuclease of E. coli B.  The
      results indicate that: (i) Circular replicative forms are broken once to yield
      full-length linear molecules (RFIII).  Such linear molecules are less
      susceptible than RFI to endonuclease R-B.  (ii) The genetic sites (SB sites)
      that confer on the DNA susceptibility to B-restriction are not the actual sites
      of cleavage.  The number of possible cleavage sites is larger than the number
      of SB sites.  We conclude this because an RFIII molecule produced by
      endonuclease R-B from RFI of a mutant that has only one SB site can be
      circularized by denaturation and renaturation.  (iii) The SB site is not
      modified when the DNA is cleaved, since an SB site can be used repeatedly by
      endonuclease R-B; the RF III described in ii can be cleaved by the same enzyme
      after denaturation and renaturation.
AU  - Horiuchi K
AU  - Zinder N
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1972 69: 3220-3224.

PMID- 1058473
VI  - 72
DP  - 1975
TI  - Site-specific cleavage of single-stranded DNA by a Hemophilus restriction endonuclease.
PG  - 2555-2558
AB  - Single-stranded viral DNA of bacteriophage f1 is cleaved into specific
      fragments by endo R.HaeIII, a restriction endonuclease isolated from Hemophilus
      aegyptius.  The sites of the single strand cleavage correspond to those of the
      double strand cleavage.  A single-stranded DNA fragment containing only one
      HaeIII site is also cleaved by this enzyme.  This observation suggests that the
      reaction of single-stranded DNA cleavage does not require the formation of a
      symmetrical double-stranded structure that would result from the intramolecular
      base-pairing between two different HaeIII sites.  Other restriction
      endonucleases may also cleave single-stranded DNA.
AU  - Horiuchi K
AU  - Zinder ND
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1975 72: 2555-2558.

PMID- 25035323
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Streptomyces iranensis.
PG  - e00616-14
AB  - Streptomyces iranensis HM 35 has been shown to exhibit 72.7% DNA-DNA similarity to the
      important drug rapamycin (sirolimus)-producing Streptomyces rapamycinicus
      NRRL5491. Here, we report the genome sequence of HM 35, which represents a
      partially overlapping repertoire of secondary metabolite gene clusters with S.
      rapamycinicus, including the gene cluster for rapamycin biosynthesis.
AU  - Horn F
AU  - Schroeckh V
AU  - Netzker T
AU  - Guthke R
AU  - Brakhage AA
AU  - Linde J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00616-14.

PMID- 4916631
VI  - 10
DP  - 1970
TI  - Comparative experiments with DNA restriction factors Escherichia coli and Shigella sonnei.
PG  - 103-119
AB  - None
AU  - Horn G
AU  - Taubeneck U
PT  - Journal Article
TA  - Z. Allg. Mikrobiol.
JT  - Z. Allg. Mikrobiol.
SO  - Z. Allg. Mikrobiol. 1970 10: 103-119.

PMID- 26430030
VI  - 3
DP  - 2015
TI  - Mining Genomes of Three Marine Sponge-Associated Actinobacterial Isolates for Secondary Metabolism.
PG  - e01106-15
AB  - Here, we report the draft genome sequences of three actinobacterial isolates, Micromonospora
      sp. RV43, Rubrobacter sp. RV113, and Nocardiopsis sp. RV163 that had previously been isolated
      from Mediterranean sponges. The draft genomes were analyzed for the presence of gene clusters
      indicative of secondary metabolism using antiSMASH 3.0 and NapDos pipelines. Our findings
      demonstrated the chemical  richness of sponge-associated actinomycetes and the efficacy of
      genome mining in  exploring the genomic potential of sponge-derived actinomycetes.
AU  - Horn H
AU  - Hentschel U
AU  - Abdelmohsen UR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01106-15.

PMID- 26779305
VI  - 11
DP  - 2016
TI  - Draft genome of the Arabidopsis thaliana phyllosphere bacterium, Williamsia sp. ARP1.
PG  - 8
AB  - The Gram-positive actinomycete Williamsia sp. ARP1 was originally isolated from the
      Arabidopsis thaliana phyllosphere. Here we describe the general physiological
      features of this microorganism together with the draft genome sequence and
      annotation. The 4,745,080 bp long genome contains 4434 protein-coding genes and
      70 RNA genes. To our knowledge, this is only the second reported genome from the
      genus Williamsia and the first sequenced strain from the phyllosphere. The
      presented genomic information is interpreted in the context of an adaptation to
      the phyllosphere habitat.
AU  - Horn H
AU  - Keller A
AU  - Hildebrandt U
AU  - Kampfer P
AU  - Riederer M
AU  - Hentschel U
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 8.

PMID- 19082973
VI  - 16
DP  - 1993
TI  - DNA Methyltransferases (EC 2.1.1.72 and EC 2.1.1.73).
PG  - 201-211
AB  - DNA methyltransferases (Mtases) catalyze the transfer of the S-methyl group of
      S-adenosylmethionine (SAM) to deoxycytosine (dC) or deoxyadenine (dA) bases within defined DNA
      sequences. Individual enzymes are specific for one or the other base, and modify at the 6-NH2
      of dA(EC 2.1.1.72) or at the N4 or 5-C position of dC (EC 2.1.1.73) depending on the
      particular enzyme. The reaction is predominantly irreversible. Enzymes, such as
      O6-methylguanine DNA Mtase, that participate in DNA repair processes are not discussed.
AU  - Hornby DP
PT  - Journal Article
TA  - Methods Mol. Biol.
JT  - Methods Mol. Biol.
SO  - Methods Mol. Biol. 1993 16: 201-211.

PMID- Not included in PubMed...
VI  - 15
DP  - 1987
TI  - Characterization of EcoPI DNA adenine methylase.
PG  - 1039
AB  - Three categories of restriction and modification systems have been documented in bacteria and
      their phage.  Type I enzymes are complex multifunctional assemblies which catalyze DNA
      methylation, DNA hydrolysis, ATP hydrolysis and DNA topoisomerization.  Type II restriction
      and modification genes res and mod encode independent restriction endonuclease and DNA
      methylase activities which both recognize a common DNA sequence motif.  The latter enzymes are
      widely used in molecular cloning.  The most recent family to emerge is a functional hybrid
      between the previous types.  Thus EcoPI, a type III enzyme produced by phage PI is a tetramer
      of subunit stoichiometry (mod)2(res)2.  The methylase subunit recognizes and methylates the
      sequence AGACC at the central adenine, while the endonuclease subunit hydrolyses the DNA
      simultaneously some 25 base pairs downstream.  We are presently investigating the behavior of
      the enzyme on gels in the presence and absence of oligonucleotide duplexes and co-factors to
      elucidate the detailed mechanism of catalysis.
AU  - Hornby DP
AU  - Bickle TA
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 1987 15: 1039.

PMID- 9751641
VI  - 9
DP  - 1998
TI  - Protein-mediated base flipping.
PG  - 354-358
AB  - Since the discovery that the DNA methyltransferase M.HhaI utilizes a base flipping mechanism
      to expose its target cytosine during catalysis, this phenomenon has been observed in other
      nucleic acid modifying enzymes.  The crystallographic analyses of such enzyme-DNA complexes
      have revealed the molecular features of extrahelical base stabilization, but have been less
      informative about the flipping process itself.
AU  - Hornby DP
AU  - Ford GC
PT  - Journal Article
TA  - Curr. Opin. Biotechnol.
JT  - Curr. Opin. Biotechnol.
SO  - Curr. Opin. Biotechnol. 1998 9: 354-358.

PMID- 2820845
VI  - 54
DP  - 1987
TI  - High level expression of the EcoPI modification methylase gene and characterization of the gene product.
PG  - 239-245
AB  - We have cloned the gene coding for the EcoPI modification methylase in an
      expression system based on the phage lambda pL promoter and the cI857-coded
      thermoinducible repressor.  We have used this system to purify the enzyme on
      the 20-30 mg scale and have examined some of its enzymatic properties.  The
      enzyme is a tetramer of Mr 72000 subunits and is approximately 40%
      alpha-helical.  Experiments with the methyl donor, S-adenosyl methionine,
      radioactively labelled in different positions indicate that a methyl group is
      transferred to the enzyme during the reaction in what is most likely a covalent
      bond.
AU  - Hornby DP
AU  - Muller M
AU  - Bickle TA
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1987 54: 239-245.

PMID- 7957963
VI  - 355
DP  - 1994
TI  - The DNA recognition subunit of a DNA methyltransferase is predominantly a molten globule in the absence of DNA.
PG  - 57-60
AB  - Enzyme-catalysed DNA methylation provides an opportunity for the modulation of protein-DNA
      recognition in biological systems. Recently we have demonstrated that the smaller of the two
      subunits of the heterodimeric, cytosine-specific DNA methyltransferase, M.AquI, is largely
      responsible for sequence-specific DNA recognition. Here we present evidence from a series of
      NMR, fluorescence and circular dichroism spectroscopy experiments that the DNA binding subunit
      of M.AquI has the characteristics of a molten globule in the absence of the catalytic
      machinery. In this metastable state this subunit retains its ability to bind DNA in a
      sequence-specific manner. We believe this finding offers an insight into the structural
      flexibility which underpins the mechanism of action of these enzymes, and may provide a
      possible biological role for molten globules in protein function.
AU  - Hornby DP
AU  - Whitmarsh A
AU  - Pinarbasi H
AU  - Kelly SM
AU  - Price NC
AU  - Shore P
AU  - Baldwin GS
AU  - Waltho J
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1994 355: 57-60.

PMID- 8895589
VI  - 15
DP  - 1996
TI  - Counteracting the mutagenic effect of hydrolytic deamination of DNA 5-methylcytosine residues at high temperature: DNA mismatch N-glycosylase Mig.Mth of the thermophilic archaeon Methanobacterium thermoautotrophicum THF.
PG  - 5459-5469
AB  - Spontaneous hydrolytic deamination of DNA 5-methyl-cytosine residues gives rise to T/G
      mismatches which are pre-mutagenic lesions requiring DNA repair.  For fundamental reasons, the
      significance of this and other processes lowering genetic fidelity must be accentuated at
      elevated temperatures, making thermophilic organisms attractive objects for studying how cells
      cope with thermal noise threatening the integrity of their genetic information.  Gene mig of
      Methanobacterium thermoautotrophicum THF, an anaerobic archaeon with an optimal growth
      temperature of 65oC, was isolated and is product (Mig.Mth; EC3.2.2-) shown to be a
      T/G-selective DNA thymine N-glycosylase with the properties required for counteracting the
      mutagenic effect of hydrolytic 5-meC deamination.  The enzyme acts on T/G and U/G oppositions
      with similar efficiency; G/G, A/G, T/C and U/C are minor substrates; no other opposition of
      common nucleobases is attacked and no removal of U from single-stranded DNA is observed.
      Substrate preferences are modulated by sequence context.  Together with the results presented
      here, one example of an enzyme directed against the hydrolytic deamination damage of 5-meC is
      known from each of the three phylogenetic kingdoms; entry into the repair pathway is
      glycosylytic in the eukaryotic and the archaeal case, whereas the eubacterial repair starts
      with an endonucleolytic DNA incision.
AU  - Horst J-P
AU  - Fritz H-J
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1996 15: 5459-5469.

PMID- 28408672
VI  - 5
DP  - 2017
TI  - The Genome Sequence of Avibacterium paragallinarum Strain CL Has a Large Repertoire of Insertion Sequence Elements.
PG  - e00152-17
AB  - The draft genome sequence of Avibacterium paragallinarum strain CL serovar C is reported here.
      The genome comprises 154 contigs corresponding to 2.4 Mb with 41%
      G+C content and many insertion sequence (IS) elements, a characteristic not
      previously reported in A. paragallinarum.
AU  - Horta-Valerdi G
AU  - Sanchez-Alonso MP
AU  - Perez-Marquez VM
AU  - Negrete-Abascal E
AU  - Vaca-Pacheco S
AU  - Hernandez-Gonzalez I
AU  - Gomez-Lunar Z
AU  - Olmedo-Alvarez G
AU  - Vazquez-Cruz C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00152-17.

PMID- 
VI  - 14
DP  - 2004
TI  - Restriction endonucleases: Structure of the conserved catalytic core and the role of metal ions in DNA cleavage.
PG  - 361-392
AB  - Type II restriction endonucleases are a fascinating group of proteins.  With the REBase
      database currently listing ~3500 Type II REases having nearly 240 distinct DNA sequence
      specificities, they constitute one of the larger known families of enzymes.  These
      DNA-cleaving enzymes combine very high catalytic efficiencies (kcat/kuncat=~1016) with
      exquisite DNA sequence selectivity.  Restriction enzymes that are classified Type II cleave
      specifically within or close to their recognition sites, and do not require ATP hydrolysis for
      their nucleolytic activity.  DNA cleavage by these enzymes can result in DNA with either 5'
      or 3' overhangs or blunt ends.
AU  - Horton JR
AU  - Blumenthal RM
AU  - Cheng X
PT  - Journal Article
TA  - Nucleic Acids Mol. Biol.
JT  - Nucleic Acids Mol. Biol.
SO  - Nucleic Acids Mol. Biol. 2004 14: 361-392.

PMID- 9628337
VI  - 379
DP  - 1998
TI  - How is modification of the DNA substrate recognized by the PvuII restriction endonuclease?
PG  - 451-458
AB  - In restriction-modification systems, cleavage of substrate sites in cellular DNA by the
      restriction endonuclease is prevented by the action of a cognate methyltransferase that acts
      on the same substrate sites.  The PvuII restriction endonuclease has been structurally
      characterized in a complex with substrate DNA and as an apoenzyme.  We report here a
      structure, determined to 1.9 A resolution by crystallography, of a complex between R.PvuII and
      iodinated DNA.  The presence of an iodine at the 5-carbon of the methylatable cytosine results
      in the following changes in the protein: His84 moved away from the modified base; this
      movement was amplified in His85 and disrupts an intersubunit hydrogen bond; and the base
      modification disturbs the distribution of water molecules that associate with these histidine
      residues and the area of the scissile bond.  Considering these observations, hypotheses are
      given as to why a similar oligonucleotide, where a methyl group resides on the 5-carbon of the
      methylatable cytosine, is slowly cleaved by R.PvuII.
AU  - Horton JR
AU  - Bonventre J
AU  - Cheng X
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1998 379: 451-458.

PMID- 24895434
VI  - 42
DP  - 2014
TI  - Structure of 5-hydroxymethylcytosine-specific restriction enzyme, AbaSI, in complex with DNA.
PG  - 7947-7959
AB  - AbaSI, a member of the PvuRts1I-family of modification-dependent restriction endonucleases,
      cleaves deoxyribonucleic acid (DNA) containing
      5-hydroxymethylctosine (5hmC) and glucosylated 5hmC (g5hmC), but not DNA
      containing unmodified cytosine. AbaSI has been used as a tool for mapping the
      genomic locations of 5hmC, an important epigenetic modification in the DNA of
      higher organisms. Here we report the crystal structures of AbaSI in the presence
      and absence of DNA. These structures provide considerable, although incomplete,
      insight into how this enzyme acts. AbaSI appears to be mainly a homodimer in
      solution, but interacts with DNA in our structures as a homotetramer. Each AbaSI
      subunit comprises an N-terminal, Vsr-like, cleavage domain containing a single
      catalytic site, and a C-terminal, SRA-like, 5hmC-binding domain. Two N-terminal
      helices mediate most of the homodimer interface. Dimerization brings together the
      two catalytic sites required for double-strand cleavage, and separates the 5hmC
      binding-domains by approximately 70 A, consistent with the known activity of
      AbaSI which cleaves DNA optimally between symmetrically modified cytosines
      approximately 22 bp apart. The eukaryotic SET and RING-associated (SRA) domains
      bind to DNA containing 5-methylcytosine (5mC) in the hemi-methylated CpG
      sequence. They make contacts in both the major and minor DNA grooves, and flip
      the modified cytosine out of the helix into a conserved binding pocket. In
      contrast, the SRA-like domain of AbaSI, which has no sequence specificity,
      contacts only the minor DNA groove, and in our current structures the 5hmC
      remains intra-helical. A conserved, binding pocket is nevertheless present in
      this domain, suitable for accommodating 5hmC and g5hmC. We consider it likely,
      therefore, that base-flipping is part of the recognition and cleavage mechanism
      of AbaSI, but that our structures represent an earlier, pre-flipped stage, prior
      to actual recognition.
AU  - Horton JR
AU  - Borgaro JG
AU  - Griggs RM
AU  - Quimby A
AU  - Guan S
AU  - Zhang X
AU  - Wilson GG
AU  - Zheng Y
AU  - Zhu Z
AU  - Cheng X
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2014 42: 7947-7959.

PMID- 10903853
VI  - 300
DP  - 2000
TI  - PvuII endonuclease contains two calcium ions in active sites.
PG  - 1049-1056
AB  - Restriction endonucleases differ in their use of metal cofactors despite having remarkably
      similar folds for their catalytic regions. To explore this, we have characterized the
      interaction of endonuclease PvuII with the catalytically incompetent cation Ca(2+). The
      structure of a glutaraldehyde-crosslinked crystal of the endonuclease PvuII-DNA complex,
      determined in the presence of Ca(2+) at a pH of approximately 6.5, supports a two-metal
      mechanism of DNA cleavage by PvuII. The first Ca(2+) position matches that found in all
      structurally examined endonucleases, while the second position is similar to that of EcoRV but
      is distinct from that of BamHI and BglI. The location of the second metal in PvuII, unlike
      that in BamHI/BglI, permits no direct interaction between the second metal and the O3' oxygen
      leaving group. However, the interactions between the DNA scissile phosphate and the metals,
      the first metal and the attacking water, and the attacking water and DNA are the same in PvuII
      as they are in the two-metal models of BamHI and BglI, but are distinct from the proposed
      three-metal or the two-metal models of EcoRV.
AU  - Horton JR
AU  - Cheng X
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2000 300: 1049-1056.

PMID- 16524590
VI  - 358
DP  - 2006
TI  - Structure and Substrate Recognition of the Escherichia coli DNA Adenine Methyltransferase.
PG  - 559-570
AB  - The structure of the Escherichia coli Dam DNA-(adenine-N6)-methyltransferase in complex with
      cognate DNA was determined at 1.89 (A) over circle resolution in the presence of
      S-adenosyl-L-homocysteine. DNA recognition and the dynamics of base-flipping were studied by
      site-directed mutagenesis, DNA methylation kinetics and fluorescence stopped-flow experiments.
      Our data illustrate the mechanism of coupling of DNA recognition and base-flipping. Contacts
      to the non-target strand in the second (3') half of the GATC site are established by R124 to
      the fourth base-pair, and by L122 and P134 to the third base-pair. The aromatic ring of Y119
      intercalates into the DNA between the second and third base-pairs, which is essential for
      base-flipping to occur. Compared to previous published structures of bacteriophage T4 Dam,
      three major new observations are made in E. coli Dam. (1) The first Gua is recognized by K9,
      removal of which abrogates the first base-pair recognition. (2) The flipped target Ade binds
      to the surface of EcoDam in the absence of S-adenoSyl-L-methionine, which illustrates a
      possible intermediate in the base-flipping pathway. (3) The orphaned Thy residue displays
      structural flexibility by adopting an extrahelical or intrahelical position where it is in
      contact to N120.
AU  - Horton JR
AU  - Liebert K
AU  - Bekes M
AU  - Jeltsch A
AU  - Cheng XD
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2006 358: 559-570.

PMID- 15882618
VI  - 121
DP  - 2005
TI  - Transition from nonspecific to specific DNA interactions along the substrate-recognition pathway of Dam methyltransferase.
PG  - 349-361
AB  - DNA methyltransferases methylate target bases within specific nucleotide sequences. Three
      structures are described for bacteriophage T4 DNA-adenine methyltransferase (T4Dam) in ternary
      complexes with partially and fully specific DNA and a methyl-donor analog. We also report the
      effects of substitutions in the related Escherichia coli DNA methyltransferase (EcoDam),
      altering residues corresponding to those involved in specific interaction with the canonical
      GATC target sequence in T4Dam. We have identified two types of protein-DNA interactions:
      discriminatory contacts, which stabilize the transition state and accelerate methylation of
      the cognate site, and antidiscriminatory contacts, which do not significantly affect
      methylation of the cognate site but disfavor activity at noncognate sites. These structures
      illustrate the transition in enzyme-DNA interaction from nonspecific to specific interaction,
      suggesting that there is a temporal order for formation of specific contacts.
AU  - Horton JR
AU  - Liebert K
AU  - Hattman S
AU  - Jeltsch A
AU  - Cheng X
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 2005 121: 349-361.

PMID- 22848107
VI  - 40
DP  - 2012
TI  - Structure and cleavage activity of the tetrameric MspJI DNA modification-dependent restriction endonuclease.
PG  - 9763-9773
AB  - The MspJI modification-dependent restriction endonuclease recognizes 5-methylcytosine or
      5-hydroxymethylcytosine in the context of CNN(G/A) and cleaves both strands at fixed distances
      (N(12)/N(16)) away from the modified cytosine at the 3'-side. We determined the crystal
      structure of MspJI of Mycobacterium sp. JLS at 2.05-A resolution. Each protein monomer harbors
      two domains: an N-terminal DNA-binding domain and a C-terminal endonuclease. The N-terminal
      domain is structurally similar to that of the eukaryotic SET and RING-associated domain, which
      is known to bind to a hemi-methylated CpG dinucleotide. Four protein monomers are found in the
      crystallographic asymmetric unit. Analytical gel-filtration and ultracentrifugation
      measurements confirm that the protein exists as a tetramer in solution. Two monomers form a
      back-to-back dimer mediated by their C-terminal endonuclease domains. Two back-to-back dimers
      interact to generate a tetramer with two double-stranded DNA cleavage modules. Each cleavage
      module contains two active sites facing each other, enabling double-strand DNA cuts.
      Biochemical, mutagenesis and structural characterization suggest three different monomers of
      the tetramer may be involved respectively in binding the modified cytosine, making the first
      proximal N(12) cleavage in the same strand and then the second distal N(16) cleavage in the
      opposite strand. Both cleavage events require binding of at least a second recognition site
      either in cis or in trans.
AU  - Horton JR
AU  - Mabuchi MY
AU  - Cohen-Karni D
AU  - Zhang X
AU  - Griggs RM
AU  - Samaranayake M
AU  - Roberts RJ
AU  - Zheng Y
AU  - Cheng X
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: 9763-9773.

PMID- 9878366
VI  - 284
DP  - 1998
TI  - Asp34 of PvuII endonuclease is directly involved in DNA minor groove recognition and indirectly involved in catalysis.
PG  - 1491-1504
AB  - The PvuII restriction endonuclease is a homodimer that recognizes and cleaves the DNA sequence
      5'-CAGCTG-3' in double-stranded DNA, and the structure of this enzyme has been reported.  In
      the wild-type enzyme, Asp34 interacts with the internal guanine of the recognition sequence on
      the minor groove side.  The Asp34 codon was altered to specify Gly (D34G), and in vitro
      studies have revealed that the D34G protein has lost binding specificity for the central G.C
      base-pairs, and that it cuts the canonical sequence with 10^-4-fold reduced activity as
      compared to the wild-type enzyme.  We have now determined the structure at 1.59 angstroms
      resolution of the D34G PvuII endonuclease complexed with a 12 bp duplex deoxyoligonucleotide
      containing the cognate sequence.  The D34G alteration results in several structural changes
      relative to wild-type protein/DNA complexes.  First, the sugar moiety of the internal guanine
      changes from a C2'-endo to C3'-endo pucker while that of the 3' guanine changes from
      C3'-endo to C2'-endo pucker.  Second, the axial rise between the internal G.C base-pairs is
      reduced while that between the G.C and flanking base-pairs is expanded.  Third, two distinct
      monomeric active sites are observed that we refer to as being "primed" and "unprimed" for
      phosphodiester bond cleavage.  The primed and unprimed sites differ in the conformation of the
      Asp58 side-chain, and in the absence from unprimed sites of four networked water molecules.
      These water molecules, present in the primed site, have been implicated in the catalytic
      mechanism of this and other endonucleases; some of them can be replaced by the Mg2+ necessary
      for cleavage.  Taken together, these structural changes imply that the Asp34 side-chains from
      the two subunits maintain a distinct conformation of its DNA substrate, properly situating the
      target backbone phosphates and indirectly manipulating the active sites.  This provides some
      insight into how recognition of the specific DNA sequence is linked to catalysis by the highly
      specific restriction endonucleases, and reveals one way in which the structural conformation
      of the DNA is modulated coordinately with that of the PvuII protein.
AU  - Horton JR
AU  - Nastri HG
AU  - Riggs PD
AU  - Cheng X
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1998 284: 1491-1504.

PMID- 
VI  - 4
DP  - 2014
TI  - Structure and mutagenesis of the DNA modification-dependent restriction endonuclease AspBHI.
PG  - 9
AB  - The modification-dependent restriction endonuclease AspBHI recognizes 5-methylcytosine (5mC)
      in the double-strand DNA sequence context of (C/T)(C/G)(5mC) N(C/G) (N = any nucleotide) and
      cleaves the two strands a fixed distance (N-12/N-16) 3' to the modified cytosine. We
      determined the crystal structure of the homo-tetrameric AspBHI. Each subunit of the protein
      comprises two domains: an N-terminal DNA-recognition domain and a C-terminal DNA cleavage
      domain. The N-terminal domain is structurally similar to the eukaryotic SET and
      RING-associated (SRA) domain, which is known to bind to a hemi-methylated CpG dinucleotide.
      The C-terminal domain is structurally similar to classic Type II restriction enzymes and
      contains the endonuclease catalytic-site motif of DX(20)EAK. To understand how specific amino
      acids affect AspBHI recognition preference, we generated a homology model of the AspBHI-DNA
      complex, and probed the importance of individual amino acids by mutagenesis. Ser41 and Arg42
      are predicted to be located in the DNA minor groove 5' to the modified cytosine. Substitution
      of Ser41 with alanine (S41A) and cysteine (S41C) resulted in mutants with altered cleavage
      activity. All 19 Arg42 variants resulted in loss of endonuclease activity.
AU  - Horton JR
AU  - Nugent RL
AU  - Li A
AU  - Mabuchi MY
AU  - Fomenkov A
AU  - Cohen-Karni D
AU  - Griggs RM
AU  - Zhang X
AU  - Wilson GG
AU  - Zheng Y
AU  - Xu S-Y
AU  - Cheng X
PT  - Journal Article
TA  - Sci. Rep.
JT  - Sci. Rep.
SO  - Sci. Rep. 2014 4: 9.

PMID- 15273274
VI  - 32
DP  - 2004
TI  - Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase.
PG  - 3877-3886
AB  - Rotation of a DNA or RNA nucleotide out of the double helix and
      into a protein pocket ('base flipping') is a mechanistic feature common to
      some DNA/RNA-binding proteins. Here, we report the structure of HhaI
      methyltransferase in complex with DNA containing a south-constrained abasic
      carbocyclic sugar at the target site in the presence of the methyl donor
      byproduct AdoHcy. Unexpectedly, the locked south pseudosugar appears to be
      trapped in the middle of the flipping pathway via the DNA major groove,
      held in place primarily through Van der Waals contacts with a set of
      invariant amino acids. Molecular dynamics simulations indicate that the
      structural stabilization observed with the south-constrained pseudosugar
      will not occur with a north-constrained pseudosugar, which explains its
      lowered binding affinity. Moreover, comparison of structural transitions of
      the sugar and phosphodiester backbone observed during computational studies
      of base flipping in the M.HhaIM-DNA-AdoHcy ternary  complex indicate that the
      south-constrained pseudosugar induces a conformation on the phosphodiester
      backbone that corresponds to that of a discrete intermediate of the
      base-flipping pathway. As previous crystal structures of M.HhaI ternary
      complex with DNA displayed the flipped sugar moiety in the antipodal north
      conformation, we suggest that conversion of the sugar pucker from south to
      north beyond the middle of the pathway is an essential part of the
      mechanism through which flipping must proceed to reach its final
      destination. We also discuss the possibility of the south-constrained
      pseudosugar mimicking a transition state in the phosphodiester and sugar
      moieties that occurs during DNA base flipping in the presence of M.HhaI.
AU  - Horton JR
AU  - Ratner G
AU  - Banavali NK
AU  - Huang N
AU  - Choi Y
AU  - Maier MA
AU  - Marquez VE
AU  - MacKerell AD Jr
AU  - Cheng X
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2004 32: 3877-3886.

PMID- 25262349
VI  - 42
DP  - 2014
TI  - Modification-dependent restriction endonuclease, MspJI, flips 5-methylcytosine out of the DNA helix.
PG  - 12092-12101
AB  - MspJI belongs to a family of restriction enzymes that cleave DNA containing 5-methylcytosine
      (5mC) or 5-hydroxymethylcytosine (5hmC). MspJI is specific for the sequence 5(h)mC-N-N-G or A
      and cleaves with some variability 9/13 nucleotides downstream. Earlier, we reported the
      crystal structure of MspJI without DNA and proposed how it might recognize this sequence and
      catalyze cleavage. Here we report its co-crystal structure with a 27-base pair oligonucleotide
      containing 5mC. This structure confirms that MspJI acts as a homotetramer and that the
      modified cytosine is flipped from the DNA helix into an SRA-like-binding pocket. We expected
      the structure to reveal two DNA molecules bound specifically to the tetramer and engaged with
      the enzyme's two DNA-cleavage sites. A coincidence of crystal packing precluded this
      organization, however. We found that each DNA molecule interacted with two adjacent tetramers,
      binding one specifically and the other non-specifically. The latter interaction, which
      prevented cleavage-site engagement, also involved base flipping and might represent the
      sequence-interrogation phase that precedes specific recognition. MspJI is unusual in that DNA
      molecules are recognized and cleaved by different subunits. Such interchange of function might
      explain how other complex multimeric restriction enzymes act.
AU  - Horton JR
AU  - Wang H
AU  - Mabuchi MY
AU  - Zhang X
AU  - Roberts RJ
AU  - Zheng Y
AU  - Wilson GG
AU  - Cheng X
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2014 42: 12092-12101.

PMID- 25845600
VI  - 43
DP  - 2015
TI  - Structures of Escherichia coli DNA adenine methyltransferase (Dam) in complex with a non-GATC sequence: potential implications for methylation-independent  transcriptional repression.
PG  - 4296-4308
AB  - DNA adenine methyltransferase (Dam) is widespread and conserved among the
      gamma-proteobacteria. Methylation of the Ade in GATC sequences regulates diverse
      bacterial cell functions, including gene expression, mismatch repair and
      chromosome replication. Dam also controls virulence in many pathogenic
      Gram-negative bacteria. An unexplained and perplexing observation about
      Escherichia coli Dam (EcoDam) is that there is no obvious relationship between
      the genes that are transcriptionally responsive to Dam and the promoter-proximal
      presence of GATC sequences. Here, we demonstrate that EcoDam interacts with a
      5-base pair non-cognate sequence distinct from GATC. The crystal structure of a
      non-cognate complex allowed us to identify a DNA binding element, GTYTA/TARAC
      (where Y = C/T and R = A/G). This element immediately flanks GATC sites in some
      Dam-regulated promoters, including the Pap operon which specifies
      pyelonephritis-associated pili. In addition, Dam interacts with near-cognate GATC
      sequences (i.e. 3/4-site ATC and GAT). Taken together, these results imply that
      Dam, in addition to being responsible for GATC methylation, could also function
      as a methylation-independent transcriptional repressor.
AU  - Horton JR
AU  - Zhang X
AU  - Blumenthal RM
AU  - Cheng X
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2015 43: 4296-4308.

PMID- 16473850
VI  - 34
DP  - 2006
TI  - DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion.
PG  - 939-948
AB  - HinP1I recognizes and cleaves the palindromic tetranucleotide sequence G downward arrowCGC in
      DNA. We report three structures of HinP1I-DNA
      complexes: in the presence of Ca(2+) (pre-reactive complex), in the
      absence of metal ion (binary complex) and in the presence of Mg(2+)
      (post-reactive complex). HinP1I forms a back-to-back dimer with two active
      sites and two DNA duplexes bound on the outer surfaces of the dimer facing
      away from each other. The 10 bp DNA duplexes undergo protein-induced
      distortions exhibiting features of A-, B- and Z-conformations: bending on
      one side (by intercalation of a phenylalanine side chain into the major
      groove), base flipping on the other side of the recognition site (by
      expanding the step rise distance of the local base pair to Z-form) and a
      local A-form conformation between the two central C:G base pairs of the
      recognition site (by binding of the N-terminal helix in the minor groove).
      In the pre- and post-reactive complexes, two metals (Ca(2+) or Mg(2+)) are
      found in the active site. The enzyme appears to cleave DNA sequentially,
      hydrolyzing first one DNA strand, as seen in the post-reactive complex in
      the crystalline state, and then the other, as supported by the observation
      that, in solution, a nicked DNA intermediate accumulates before
      linearization.
AU  - Horton JR
AU  - Zhang X
AU  - Maunus R
AU  - Yang Z
AU  - Wilson GG
AU  - Roberts RJ
AU  - Cheng X
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2006 34: 939-948.

PMID- 
VI  - 122
DP  - 2000
TI  - Inhibition of EcoRV endonuclease by deoxyribo-3'-S-phosphorothiolates: A high-resolution X-ray crystallographic study.
PG  - 3314-3324
AB  - Three high-resolution structures of the restriction endonuclease EcoRV bound to a duplex DNA
      substrate analogue with deoxyribo-3'-S-phosphorothiolate linkages at both scissile phosphates
      are presented.  In each of these structures cocrystallized with Mg2+, Mn2+, or Ca2+ ions, the
      nonesterified pro-S oxygen of the scissile phosphate no longer directly ligates a divalent
      cation, as is observed for the unmodified complex.  Instead, one metal ion in all three
      structures is shifted toward the adjacent 3'-phosphate of the DNA, to occupy a position
      nearly identical to that previously observed in an EcoRV T93A/DNA/Ca2+ complex (N.C. Horton et
      al., Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 13489).  A second divalent metal ion in each
      structure bridges the carboxylate groups of Asp74 and Glu45 (74/45 site), as also seen in both
      wild-type and T93A cocrystals.  The uncleaved 3'-S-phosphorothiolate DNAs in these complexes
      are only slightly distorted from the conformation of the unmodified duplex.  Kinetic
      measurements show that the rate of the chemical step for analogue cleavage is severely reduced
      for each of the active metals Mg2+, Mn2+, and Co2+, and that the thiophilic Mn2+, Cd2+, and
      Zn2+ cations do not provide a measurable reconstitution of activity.  The inability of
      thiophilic metals to improve activity is consistent with models for catalysis derived from
      previous crystal structures, which indicate that ligation of a metal ion to the 3'-oxygen is
      mediated through an inner-sphere water molecule rather than by direct interaction.  The
      structures suggest that 3'-S-phosphorothiolate analogues resist cleavage because the bridging
      sulfur excludes inner-sphere ligation of divalent metal ions to any position on the scissile
      phosphate.  This distinguishes the inhibitory mechanism in EcoRV from that operative in the
      3'-5' exonuclease active site of DNA polymerase I (C.A. Brautigam et al., Biochemistry,
      1999, 38, 696), and likely as well from other enzymes which also catalyze phosphoryl transfer
      via direct metal ligation to the 3'-oxygen leaving group.
AU  - Horton NC
AU  - Connolly BA
AU  - Perona JJ
PT  - Journal Article
TA  - J. Am. Chem. Soc.
JT  - J. Am. Chem. Soc.
SO  - J. Am. Chem. Soc. 2000 122: 3314-3324.

PMID- 11742344
VI  - 9
DP  - 2002
TI  - Sequence selectivity and degeneracy of a restriction endonuclease mediated by DNA intercalation.
PG  - 42-47
AB  - The crystal structure of the HincII restriction endonuclease-DNA complex shows that degenerate
      specificity for blunt-ended cleavage at GTPyPuAC sequences arises from indirect readout of
      conformational preferences at the center pyrimidine-purine step. Protein-induced distortion of
      the DNA is accomplished by intercalation of glutamine side chains into the major groove on
      either side of the recognition site, generating bending by either tilt or roll at three
      distinct loci. The intercalated side chains propagate a concerted shift of all six target-site
      base pairs toward the minor groove, producing an unusual cross-strand purine stacking at the
      center pyrimidine-purine step. Comparison of the HincII and EcoRV cocrystal structures
      suggests that sequence-dependent differences in base-stacking free energies are a crucial
      underlying factor mediating protein recognition by indirect readout.
AU  - Horton NC
AU  - Dorner LF
AU  - Perona JJ
PT  - Journal Article
TA  - Nat. Struct. Biol.
JT  - Nat. Struct. Biol.
SO  - Nat. Struct. Biol. 2002 9: 42-47.

PMID- 10531503
VI  - 55
DP  - 1999
TI  - Crystallization and preliminary diffraction analysis of the HincII restriction endonuclease-DNA complex.
PG  - 1943-1945
AB  - Crystals of the 60 kDa dimeric HincII restriction enzyme bound to a 12 base-pair
      dyad-symmetric duplex DNA carrying the specific 5'-GTCGAC recognition site have been
      obtained. Crystals grew by hanging-drop vapor diffusion from solutions containing polyethylene
      glycol 4000 as precipitating agent. The rod-shaped crystals belong to space group I222 (or
      I2(1)2(1)2(1)), with unit-cell dimensions a = 66.9, b = 176.7, c = 256.0 A. There are most
      likely to be two dimeric complexes in the asymmetric unit. A complete native data set has been
      collected from a high-energy synchrotron source to a resolution of 2.5 A at 100 K, with an
      R(merge) of 4.8%.
AU  - Horton NC
AU  - Dorner LF
AU  - Schildkraut I
AU  - Perona JJ
PT  - Journal Article
TA  - Acta Crystallogr. D Biol. Crystallogr.
JT  - Acta Crystallogr. D Biol. Crystallogr.
SO  - Acta Crystallogr. D Biol. Crystallogr. 1999 55: 1943-1945.

PMID- 9811827
VI  - 95
DP  - 1998
TI  - Metal ion-mediated substrate-assisted catalysis in type II restriction endonucleases.
PG  - 13489-13494
AB  - The 2.15-Angstrom resolution cocrystal structure of EcoRV endonuclease mutant T93A complexed
      with DNA and Ca2+ ions reveals two divalent metals bound in one of the active sites.  One of
      these metals is ligated through an inner-sphere water molecule to the phosphate group located
      3' to the scissile phosphate.  A second inner-sphere water on this metal is positioned
      approximately in-line for attack on the scissile phosphate.  This structure corroborates the
      observation that the pro-SP phosphoryl oxygen on the adjacent 3' phosphate cannot be modified
      without severe loss of catalytic efficiency.  The structural equivalence of key groups,
      conserved in the active sites of EcoRV, EcoRI, PvuII, and BamHI endonucleases, suggests that
      ligation of a catalytic divalent metal ion to this phosphate may occur in many type II
      restriction enzymes.  Together with previous  cocrystal structures, these data allow
      construction of a detailed model for the pretransition state configuration in EcoRV.  This
      model features three divalent metal ions per active site and invokes assistance in the
      bond-making step by a conserved lysine, which stabilizes the attacking hydroxide ion
      nucleophile.
AU  - Horton NC
AU  - Newberry KJ
AU  - Perona JJ
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1998 95: 13489-13494.

PMID- 12196013
VI  - 41
DP  - 2002
TI  - Electrostatic contributions to site specific DNA cleavage by EcoRV endonuclease.
PG  - 10754-10763
AB  - Mutational analysis of amino acids at the periphery of the EcoRV endonuclease active site
      suggests that moderate-range electrostatic effects play a significant role in modulating the
      efficiency of phosphoryl transfer. Asp36 and Lys38 located on minor-groove binding surface
      loops approach within 7-9 angstroms of the scissile phosphates of the DNA. While the rates of
      single-site mutations removing the carboxylate or amine moieties at these positions are
      decreased 10^3-10^5-fold compared to that of wild-type EcoRV, we find that double mutants
      which rebalance the charge improve catalysis by up to 500-fold. Mutational analysis also
      suggests that catalytic efficiency is influenced by Lys173, which is buried at the base of a
      deep depression penetrating from a distal surface of the enzyme. The Lys173 amine group lies
      just 6 angstroms from the amine group of the conserved essential Lys92 side chain in the
      active site. Kinetic and crystallographic analyses of the EcoRV E45A mutant enzyme further
      show that the Glu45 carboxylate group facilitates an extensive set of conformational
      transitions which occur upon DNA binding. The crystal structure of E45A bound to DNA and Mn2+
      ions reveals significant conformational alterations in a small alpha-helical portion of the
      dimer interface located adjacent to the DNA minor groove. This leads to a tertiary
      reorientation of the two monomers as well as shifting of the key major-groove binding
      recognition loops. Because the Glu45 side chain does not appear to play a direct structural
      role in maintaining the active site, these rearrangements may instead originate in an altered
      electrostatic potential caused by removal of the negative charge. A Mn2+ binding site on the
      scissile phosphate is also disrupted in the E45A structure such that inner-sphere metal
      interactions made by the scissile DNA phosphate and conserved Asp90 carboxylate are each
      replaced with water molecules in the mutant. These findings argue against a proposed role for
      Asp36 as the general base in EcoRV catalysis, and reveal that the induced-fit conformational
      changes necessary for active site assembly and metal binding are significantly modulated by
      the electrostatic potential in this region.
AU  - Horton NC
AU  - Otey C
AU  - Lusetti S
AU  - Sam MD
AU  - Kohn J
AU  - Martin AM
AU  - Ananthnarayan V
AU  - Perona JJ
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2002 41: 10754-10763.

PMID- 9545372
VI  - 277
DP  - 1998
TI  - Role of protein-induced bending in the specificity of DNA recognition: crystal structure of EcoRV endonuclease complexes with d(AAAGAT) + d(ATCTT).
PG  - 779-787
AB  - The crystal structure of EcoRV endonuclease has been determined at 2.1 A resolution complexed
      to two five-base-pair DNA duplexes each containing the cognate recognition half-site.  The
      highly localized 50o bend into the major groove seen at the center TA-step of the continuous
      GATATC site is preserved in this discontinuous DNA complex lacking the scissile phosphates.
      Thus, this crystal structure provides evidence that covalent constraints associated with a
      continuous target site are not essential to enzyme-induced DNA bending, even when these
      constraints are removed directly at the locus of the bend.  The scissile phosphates are also
      absent in the crystal structure of EcoRV bound to the non-specific site TCGCGA, which shows a
      straight B-like conformation.  We conclude that DNA bending by EcoRV is governed only by the
      sequence and is not influenced by the continuity of the phosphodiester backbone.  Together
      with other data showing that cleavable non-cognate sites different by one or two base-pairs
      from GATATC, but does not bend non-specific sites that are less similar.  Structural and
      thermodynamic considerations suggest that the sequence-dependent energy cost of DNA bending is
      likely to play an important role in determining the specificity of EcoRV.  This differential
      cost is manifested at the binding step for bent non-cognate sequences and at the catalytic
      step for unbent non-specific sequences.
AU  - Horton NC
AU  - Perona JJ
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1998 277: 779-787.

PMID- 11276242
VI  - 8
DP  - 2001
TI  - Making the most of metal ions.
PG  - 290-293
AB  - Crystal structures of the homing endonuclease I-Crel bound to substrate DNA and divalent
      metals show that one metal ion is shared between the
      two active sites of the enzyme. This arrangement appears uniquely
      suited to the formation of double-stranded DNA breaks via a concerted
      reaction.
AU  - Horton NC
AU  - Perona JJ
PT  - Journal Article
TA  - Nat. Struct. Biol.
JT  - Nat. Struct. Biol.
SO  - Nat. Struct. Biol. 2001 8: 290-293.

PMID- 15170321
VI  - 43
DP  - 2004
TI  - DNA cleavage by EcoRV endonuclease: Two metal ions in three metal ion binding sites.
PG  - 6841-6857
AB  - Four crystal structures of EcoRV endonuclease mutants K92A and K38A provide new insight into
      the mechanism of DNA bending and the structural basis for metal-dependent phosphodiester bond
      cleavage. The removal of a key active site positive charge in the uncleaved K92A-DNA-M(2+)
      substrate complex results in binding of a sodium ion in the position of the amine nitrogen,
      suggesting a key role for a positive charge at this position in stabilizing the sharp DNA bend
      prior to cleavage. By contrast, two structures of K38A cocrystallized with DNA and Mn(2+) ions
      in different lattice environments reveal cleaved product complexes featuring a common, novel
      conformation of the scissile phosphate group as compared to all previous EcoRV structures. In
      these structures, the released 5'-phosphate and 3'-OH groups remain in close juxtaposition
      with each other and with two Mn(2+) ions that bridge the conserved active site carboxylates.
      The scissile phosphates are found midway between their positions in the prereactive substrate
      and postreactive product complexes of the wild-type enzyme. Mn(2+) ions occupy two of the
      three sites previously described in the prereactive complexes and are plausibly positioned to
      generate the nucleophilic hydroxide ion, to compensate for the incipient additional negative
      charge in the transition state, and to ionize a second water for protonation of the
      3'-oxyanion. Reconciliation of these findings with earlier X-ray and fluorescence studies
      suggests a novel mechanism in which a single initially bound metal ion in a third distinct
      site undergoes a shift in position together with movement of the scissile phosphate deeper
      into the active site cleft. This reconfigures the local environment to permit binding of the
      second metal ion followed by movement toward the pentacovalent transition state. The new
      mechanism suggested here embodies key features of previously proposed two- and three-metal
      catalytic models, and offers a view of the stereochemical pathway that integrates much of the
      copious structural and functional data that are available from exhaustive studies in many
      laboratories.
AU  - Horton NC
AU  - Perona JJ
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2004 43: 6841-6857.

PMID- 9705308
VI  - 273
DP  - 1998
TI  - Recognition of flanking DNA sequences by EcoRV endonuclease involves alternative patterns of water-mediated contacts.
PG  - 21721-21729
AB  - The 2.1-A cocrystal structure of EcoRV endonuclease bound to 5'-CGGGATATCCC, in a crystal
      lattice isomorphous with the cocrystallized undecamer 5'-AAAGATATCTT previously determined,
      shows novel base recognition in the major groove of the DNA flanking the GATATC target site.
      Lys104 of the enzyme interacts through water molecules with the exocyclic N-4 amino groups of
      flanking cytosines.  Steric exclusion of water molecule-binding sites by the 5'methyl group
      of thymine drives the adoption of alternative water-mediated contacts with AT versus GC
      flanks.  This structure provides a rare example of structural adaptability in the recognition
      of different DNA sequences by a protein and suggests preferred strategies for the expansion of
      target site specificity by EcoRV.
AU  - Horton NC
AU  - Perona JJ
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1998 273: 21721-21729.

PMID- 10801972
VI  - 97
DP  - 2000
TI  - Crystallographic snapshots along a protein-induced DNA-bending pathway.
PG  - 5729-5734
AB  - Two new high-resolution cocrystal structures of EcoRV endonuclease bound to DNA show that a
      large variation in DNA-bending angles is sampled in the ground state binary complex. Together
      with previous structures, these data reveal a contiguous series of protein conformational
      states delineating a specific trajectory for the induced-fit pathway. Rotation of the
      DNA-binding domains, together with movements of two symmetry-related helices binding in the
      minor groove, causes base unstacking at a key base-pair step and propagates structural changes
      that assemble the active sites. These structures suggest a complex mechanism for DNA bending
      that depends on forces generated by interacting protein segments, and on selective
      neutralization of phosphate charges along the inner face of the bent double helix.
AU  - Horton NC
AU  - Perona JJ
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2000 97: 5729-5734.

PMID- 
VI  - 78
DP  - 2000
TI  - Structural mechanism of phosphoryl transfer in EcoRV restriction endonuclease.
PG  - 417A
AB  - The structural mechanism of phosphoryl transfer in the type II restriction endonuclease EcoRV
      has been investigated using thermodynamic, kinetic, and crystallographic methods on modified
      substrates and site directed mutants.  A three metal ion mechanism has been proposed based on
      the observation of divalent cation binding sites in the enzyme active site.  pH rate profiles
      using Mg2+ and Mn2+ as the catalytic cofactor support the role of the metal ion in increasing
      the electrophilicity of the scissile phosphorus by direct ligation to the proS oxygen of the
      scissile phosphate.  Thio substitution at the 3'O position, in conjunction with metal
      substitution experiments, support the lack of direct metal ligation at this position.
      Structures of 3'S phosphorothiolate DNA containing the EcoRV cognate sequence, bound to
      EcoRV, and the divalent cations Ca2+, Mg2+ and Mn2+ show loss of direct ligation by the metal
      ion to the proS oxygen of the scissile phosphate, explaining the inability of EcoRV to cleave
      this modified substrate.  A structure of the mutant K38A bound to cognate DNA nd Mn2+ shows a
      new conformation of the scissile phosphate which is pulled deep into the active site, and
      suggests the conformation of an intermediate in the phosphoryl transfer reaction pathway.
AU  - Horton NC
AU  - Sam MD
AU  - Connolly BA
AU  - Perona JJ
PT  - Journal Article
TA  - Biophys. J.
JT  - Biophys. J.
SO  - Biophys. J. 2000 78: 417A.

PMID- 
VI  - 194
DP  - 2011
TI  - Genome sequence of Propionibacterium acnes Type II strain ATCC 11828.
PG  - 202-203
AB  - Propionibacterium acnes is an anaerobic Gram-positive bacterium that forms part of the normal
      human cutaneous microbiota and is occasionally associated with inflammatory diseases (I.
      Kurokawa et al., Exp. Dermatol. 18:821- 832, 2009). Here we present the complete genome
      sequence for the commercially available P. acnes type II reference strain ATCC 11828 (I. Nagy
      et al., Microbes Infect. 8:2195-2205, 2006) recovered from a subcutaneous abscess.
AU  - Horvath B
AU  - Hunyadkurti J
AU  - Voros A
AU  - Fekete C
AU  - Urban E
AU  - Kemeny L
AU  - Nagy I
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 194: 202-203.

PMID- 
VI  - 0
DP  - 2011
TI  - Protection against Foreign DNA.
PG  - 333-348
AB  - Bacteria rely on several defense systems that allow them to survive exposure to invading
      nucleic acids. Predatory exposure to abundant and ubiquitous viruses, combined with
      competition from a vast array of microbes, has lead to exogenous DNA exposure via
      transduction, conjugation, and transformation. Consequently, bacterial immune systems have
      been developed that allow the cell to recognize and distinguish incoming exogenous 'foreign'
      DNA, from endogenous 'self' DNA. These systems maintain genetic integrity, species identity,
      and genetic uniqueness, yet allow occasional exogenous DNA uptake and conservation of
      advantageous genetic material for adaptation to the environment. In addition to defense
      strategies such as prevention of adsorption, blocking of injection, and abortive infection,
      which are effective against phage, the chapter briefly addresses the well-characterized
      restriction-modification system (R-M), non-sugar-specific nucleases, and histone-like nucleoid
      structuring (H-NS). The chapter more specifically elaborates on clustered regularly
      interspaced short palindromic repeats (CRISPR). CRISPR/Cas, a recently described microbial
      system, provides acquired immunity against phages and plasmids by targeting nucleic acids in a
      sequence-specific manner. CRISPR features may be exploited for typing purposes, ecological and
      epidemiological studies, and also for enhancing phage resistance in bacteria.
AU  - Horvath P
AU  - Barrangou R
PT  - Journal Article
TA  - Bacterial Stress Responses, 2nd Edition
JT  - Bacterial Stress Responses, 2nd Edition
SO  - Bacterial Stress Responses, 2nd Edition 2011 0: 333-348.

PMID- 29895618
VI  - 293
DP  - 2018
TI  - The crystal structure of the Helicobacter pylori LlaJI.R1 N-terminal domain provides a model for site-specific DNA binding.
PG  - 11758-11771
AB  - Restriction modification systems consist of an endonuclease that cleaves foreign  DNA
      site-specifically and an associated methyltransferase that protects the
      corresponding target site in the host genome. Modification-dependent restriction
      systems, in contrast, specifically recognize and cleave methylated and/or
      glucosylated DNA. The LlaJI restriction system contains two 5-methylcytosine
      (5mC) methyltransferases (LlaJI.M1 and LlaJI.M2) and two restriction proteins
      (LlaJI.R1 and LlaJI.R2). LlaJI.R1 and LlaJI.R2 are homologs of McrB and McrC,
      respectively, which in Escherichia coli function together as a
      modification-dependent restriction complex specific for 5mC-containing DNA.
      Lactococcus lactis LlaJI.R1 binds DNA site-specifically, suggesting that the
      LlaJI system uses a different mode of substrate recognition. Here we present the
      structure of the N-terminal DNA-binding domain of Helicobacter pylori LlaJI.R1 at
      1.97-A resolution, which adopts a B3 domain fold. Structural comparison to B3
      domains in plant transcription factors and other restriction enzymes identifies
      key recognition motifs responsible for site-specific DNA binding. Moreover,
      biochemistry and structural modeling provide a rationale for how H. pylori
      LlaJI.R1 may bind a target site that differs from the 5-bp sequence recognized by
      other LlaJI homologs and identify residues critical for this recognition
      activity. These findings underscore the inherent structural plasticity of B3
      domains, allowing recognition of a variety of substrates using the same
      structural core.
AU  - Hosford CJ
AU  - Chappie JS
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2018 293: 11758-11771.

PMID- 411515
VI  - 479
DP  - 1977
TI  - Purification of cohesive-end-producing restriction endonuclease from Bacillus subtilis G.
PG  - 367-369
AB  - A new restriction endonuclease was partially purified from Bacillus subtilis G
      (IAM1247).  This restriction endonuclease (endonuclease RBsuG) seems to produce
      cohesive ends at its cleavage site.
AU  - Hoshino T
AU  - Uozumi T
AU  - Horinouchi S
AU  - Ozaki A
AU  - Beppu T
AU  - Arima K
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1977 479: 367-369.

PMID- 9513269
VI  - 156
DP  - 1997
TI  - Identification of restriction barriers in Pasteurella multocida.
PG  - 223-226
AB  - Several naturally occurring antibiotic resistance plasmids were isolated from Pasteurella
      multocida type D strains.  One plasmid, pPM1, was used to study transfer of DNA among P.
      multocida strains, and could be transferred into Escherichia coli and some P. multocida
      isolates.  However, pPM1 could only be transferred into the toxigenic P. multocida LFB3 at
      very low frequency.  Plasmid recovered from the electrotransformants could be transferred to
      LFB3 at high frequency.  These plasmid DNAs were resistant to PstI, and sensitive to DpnI
      digestion.  Sensitivity to DpnI was common to all the P. multocida DNAs, but resistance to
      PstI was confined to LFB3.  Plasmid pPM1 treated with PstI methylase was able to transform
      LFB3 at an increased frequency compared to unmethylated DNA, suggesting that LFB3 has a
      restriction system which cleaves at or near PstI sites.
AU  - Hoskins IC
AU  - Lax AJ
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1997 156: 223-226.

PMID- 11544234
VI  - 183
DP  - 2001
TI  - Genome of the bacterium Streptococcus pneumoniae strain R6.
PG  - 5709-5717
AB  - Streptococcus pneumoniae is among the most significant causes of bacterial disease in humans.
      Here we report the 2,038,615-bp genomic sequence of the gram-positive bacterium S. pneumoniae
      R6. Because the R6 strain is avirulent and, more importantly, because it is readily
      transformed with DNA from homologous species and many heterologous species, it is the
      principal platform for investigation of the biology of this important pathogen. It is also
      used as a primary vehicle for genomics-based development of antibiotics for gram-positive
      bacteria. In our analysis of the genome, we identified a large number of new uncharacterized
      genes predicted to encode proteins that either reside on the surface of the cell or are
      secreted. Among those proteins there may be new targets for vaccine and antibiotic
      development.
AU  - Hoskins J et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2001 183: 5709-5717.

PMID- 17719266
VI  - 10
DP  - 2007
TI  - Hypervariation and phase variation in the bacteriophage resistome.
PG  - 396-400
AB  - Most bacteria encode proteins for defence against infection by bacteriophages. The mechanisms
      that bring about phage defence are
      extremely diverse, suggesting frequent independent evolution of novel
      processes. Phage defence determinants are often plasmid or
      phage-encoded and many that are chromosomal show evidence of lateral
      transfer. Recent studies on restriction-modification (R-M) systems show
      that these genes are amongst the most rapidly evolving. Some bacteria
      have contingency genes that encode alternative target specificity
      determinants for Type I or Type III R-M systems, thus expanding the
      range of phages against which the host population is immune. The most
      counter-intuitive observation, however, is the prevalence of phase
      variation in many restriction systems, but recent arguments suggest
      that switching off expression of R-M systems can aid phage defence.
AU  - Hoskisson PA
AU  - Smith MCM
PT  - Journal Article
TA  - Curr. Opin. Microbiol.
JT  - Curr. Opin. Microbiol.
SO  - Curr. Opin. Microbiol. 2007 10: 396-400.

PMID- 25592393
VI  - 477
DP  - 2015
TI  - The phage growth limitation system in Streptomyces coelicolor A(3)2 is a toxin/antitoxin system, comprising enzymes with DNA methyltransferase, protein  kinase and ATPase activity.
PG  - 100-109
AB  - The phage growth limitation system of Streptomyces coelicolor A3(2) is an unusual
      bacteriophage defence mechanism. Progeny varphiC31 phage from an initial
      infection are thought to be modified such that subsequent infections are
      attenuated in a Pgl(+) host but normal in a Pgl(-) strain. Earlier work
      identified four genes required for phage resistance by Pgl. Here we demonstrate
      that Pgl is an elaborate and novel phage restriction system that, in part,
      comprises a toxin/antitoxin system where PglX, a DNA methyltransferase is toxic
      in the absence of a functional PglZ. In addition, the ATPase activity of PglY and
      a protein kinase activity in PglW are shown to be essential for phage resistance
      by Pgl. We conclude that on infection of a Pgl(+) cell by bacteriophage
      varphiC31, PglW transduces a signal, probably via phosphorylation, to other Pgl
      proteins resulting in the activation of the DNA methyltransferase, PglX and this
      leads to phage restriction.
AU  - Hoskisson PA
AU  - Sumby P
AU  - Smith MC
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 2015 477: 100-109.

PMID- 29519847
VI  - 6
DP  - 2018
TI  - Virulence-Related Genes Identified from the Genome Sequence of the Non-O1/Non-O139 Vibrio cholerae Strain VcN1, Isolated from Dhaka, Bangladesh.
PG  - e01513-17
AB  - We report here the first draft genome sequence of the non-O1/non-O139 Vibrio cholerae strain
      VcN1, isolated from Dhaka, Bangladesh. The data submitted to
      GenBank for this strain will contribute to advancing our understanding of this
      environmentally disseminated bacterium, including its virulence and its evolution
      as an important pathogen.
AU  - Hossain M
AU  - Alam M
AU  - Khaleque A
AU  - Islam S
AU  - Sadique A
AU  - Khan N
AU  - Halim Z
AU  - Sarker M
AU  - El-Sayed NM
AU  - Huq A
AU  - Ahsan GU
AU  - Colwell RR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01513-17.

PMID- 25414500
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Two Novel Aeromonas Species Recovered in Association with Cyanobacterial Blooms.
PG  - e01181-14
AB  - Aeromonas aquatica and Aeromonas lacus are two new species that have been found in association
      with cyanobacterial blooms from recreational Finnish lakes where
      adverse human health effects have been recorded. Here, we present the draft
      genome sequences of their type strains.
AU  - Hossain MJ
AU  - Beaz-Hidalgo R
AU  - Figueras MJ
AU  - Liles MR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01181-14.

PMID- 29930040
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Bacillus subtilis Strain MH1, Which Has a High Level  of Bacteriocin-Like Activity, Isolated from Soil in Bangladesh.
PG  - e00516-18
AB  - Bacillus subtilis MH1 demonstrates a high level of bacteriocin activity against several
      pathogenic bacteria. We announce here the full-genome sequence of strain
      MH1, isolated from soil in Bangladesh. This genome length is 4,094,053 bp, with
      43.5% GC content, 4,217 coding sequences (CDS), 10 rRNA, 84 tRNA, and 1
      transfer-messenger RNA (tmRNA).
AU  - Hossain MS
AU  - Akhter MZ
AU  - Hossain MM
AU  - Shishir MA
AU  - Khan SN
AU  - Hoq MM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00516-18.

PMID- 28729278
VI  - 5
DP  - 2017
TI  - High-Quality Genome Sequence of the Highly Resistant Bacterium Staphylococcus haemolyticus, Isolated from a Neonatal Bloodstream Infection.
PG  - e00683-17
AB  - Using Illumina HiSeq and PacBio technologies, we sequenced the genome of the
      multidrug-resistant bacterium Staphylococcus haemolyticus, originating from a
      bloodstream infection in a neonate. The sequence data can be used as an accurate
      reference sequence.
AU  - Hosseinkhani F
AU  - Emaneini M
AU  - van Leeuwen W
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00683-17.

PMID- 18873306
VI  - 175
DP  - 1948
TI  - The quantitative separation of purines, pyrimidines, and nucleosides by paper chromatography.
PG  - 315-332
AB  - The separation of amino acid mixtures by migration with
      organic solvents in filter paper has been successfully accomplished by
      many workers since it was first described by Consden, Gordon, and
      Martin.  Each amino acid travels in a more or less well defined spot in
      the body of uniformly migrating solvent and can be visualized in the
      dried paper as a local spot giving a color reaction with ninhydrin.  The
      present paper reports the separation of the purines and pyrimidines
      contained in nucleic acids, and several related compounds, by the
      movement of a boundary of n-butyl alcohol along paper strips.  Vischer
      and Chargaff have described the principal steps of a procedure for
      separating the two bases, guanine and adenine, from nucleic acid in a
      moving body of a quinoline-collidine mixture.  These purines were
      located in the paper by precipitation of mercury sulfide after formation
      of the insoluble mercury salts and washing in dilute acid.  After
      complete removal of the quinoline and collidine it was possible to
      identify the guanine and adenine by their absorption maxima in the
      ultraviolet range.
AU  - Hotchkiss RD
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1948 175: 315-332.

PMID- 19112458
VI  - 41
DP  - 2009
TI  - Protein demethylation required for DNA methylation.
PG  - 10-11
AB  - DNA methylation and histone modifications have essential roles in the transcriptional
      regulation of gene expression. Lysine-specific demethylase-1 (Lsd1), also called KDM1, is an
      enzyme with specificity toward the di and monomethylation states of lysine 4 and lysine 9 of
      histone H3 (H3K4 and H3K9), and of lysine 370 of p53 (ref. 1). Lsd1 serves transcriptional
      co-activator and co-repressor functions during development. On page 125 of this issue, En Li,
      Taiping Chen and colleagues3 identify DNA methyltransferase-1 (Dnmt1) as a novel substrate for
      Lsd1 and show that demethylation of Dnmt1 is required for the maintenance of global DNA
      methylation.
AU  - Hotz HR
AU  - Peters AH
PT  - Journal Article
TA  - Nat. Genet.
JT  - Nat. Genet.
SO  - Nat. Genet. 2009 41: 10-11.

PMID- 26067962
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Pseudoxanthomonas suwonensis Strain J1, a Cellulose-Degrading Bacterium Isolated from Leaf- and Wood-Enriched Soil.
PG  - e00614-15
AB  - We report here the complete genome sequence of the cellulose-degrading bacterium
      Pseudoxanthomonas suwonensis strain J1, isolated from soil enriched with rotten
      leaves and wood from the Zhong Mountain Scenic Area in Nanjing, China. This
      complete genome may contribute to further investigation of plant biomass
      degradation.
AU  - Hou L
AU  - Jiang J
AU  - Xu Z
AU  - Zhou Y
AU  - Leung FC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00614-15.

PMID- 29299111
VI  - 12
DP  - 2017
TI  - Genome sequence of Acuticoccus yangtzensis JL1095T (DSM 28604T) isolated from the Yangtze Estuary.
PG  - 91
AB  - Acuticoccus yangtzensis JL1095(T) is a proteobacterium from a genus belonging to  the family
      Rhodobacteraceae; it was isolated from surface waters of the Yangtze
      Estuary, China. This strain displays the capability to utilize aromatic and
      simple carbon compounds. Here, we present the genome sequence, annotations, and
      features of A. yangtzensis JL1095(T). This strain has a genome size of 5,043,263
      bp with a G + C content of 68.63%. The genome contains 4286 protein-coding genes,
      56 RNA genes, and 83 pseudo genes. Many of the protein-coding genes were
      predicted to encode proteins involved in carbon metabolism pathways, such as
      aromatic degradation and methane metabolism. Notably, a total of 31 genes were
      predicted to encode form II carbon monoxide dehydrogenases, suggesting potential
      for carbon monoxide oxidation. The genome analysis helps better understand the
      major carbon metabolic pathways of this strain and its role in carbon cycling in
      coastal marine ecosystems.
AU  - Hou L
AU  - Sun J
AU  - Xie X
AU  - Jiao N
AU  - Zhang Y
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 91.

PMID- 12758270
VI  - 317
DP  - 2003
TI  - A microarray method to evaluate the effect of CA mispairs on the accuracy of BstUI restriction endonuclease.
PG  - 276-279
AB  - Protein-DNA interaction is an essential event in many biological processes, such as
      transcription, replication, restriction, and modification.  The sequence selectivity of
      DNA-binding proteins plays an important role in controlling these processes in the cell.
      Understanding how DNA-binding proteins select the correct DNA sequence from the nonspecific
      sequences has attracted more and more interest in recent years.  Among DNA-binding proteins,
      restriction endonucleases are perhaps the most extreme in their DNA selectivity.  Research on
      the effects of sequence variations of the canonical recognition sites on the cleavage
      efficiency of restriction endonucleases is important for understanding its specificity.  These
      sequence variations include both a single base pair change and mispairs within the recognition
      site.  The former can result in over a million-fold decrease in activity, and the latter can
      impart a local destabilization on a double helix and affect the deformability and dynamic
      properties of the DNA at the mismatched site.
AU  - Hou P
AU  - Ji M
AU  - He N
AU  - Lu Z
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 2003 317: 276-279.

PMID- 14715253
VI  - 314
DP  - 2004
TI  - Microarray-based method to evaluate the accuracy of restriction endonucleases HpaII and MspI.
PG  - 110-117
AB  - A double-strand DNA (ds DNA) microarray was fabricated to analyze the structural perturbations
      caused by methylation and the different base
      mismatches in the interaction of the restriction endonucleases HpaII
      and MspI with DNA. First, a series of synthesized oligonucleotides were
      arrayed on the aldehyde-coated glass slides. Second, these
      oligonucleotides were hybridized with target sequences to obtain a ds DNA
      microarray, which includes several types of double strands with-the
      fully methylated, semi-methylated, and unmethylated canonical
      recognition sequences, semi-methylated and unmethylated base mismatches
      within the recognition sequences. The cleavage experiments were carried
      out under normal buffer conditions. The results indicated that MspI
      could partially cleave methylated and semi-methylated canonical
      recognition sequences. In contrast, HpaII could not cleave methylated
      and semi-methylated canonical recognition sequences. HpaII and MspI
      could both cleave the unmethylated canonical recognition sequence.
      However, HpaII could partially cleave the sequence containing one GG
      mismatch and not cleave other base mismatches in the corresponding
      recognition site. In contrast, MspI could not recognize the base
      mismatches within the recognition sequence. A good reproducibility was
      observed in several parallel experiments. The experiment indicates that
      the microarray technology has great potentials in high-throughput
      identifying important interactions between protein and DNA.
AU  - Hou P
AU  - Ji MJ
AU  - He NY
AU  - Lu ZH
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 2004 314: 110-117.

PMID- 26251486
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Delftia tsuruhatensis MTQ3, a Strain of Plant Growth-Promoting Rhizobacterium with Antimicrobial Activity.
PG  - e00822-15
AB  - Delftia tsuruhatensis MTQ3 is a plant growth-promoting rhizobacterium (PGPR) isolated from
      tobacco rhizosphere. Here, we report the draft genome sequence of
      D. tsuruhatensis MTQ3. Several functional genes related to antimicrobial activity
      and environment adaption have been found in the genome. This is the first genome
      sequence of D. tsuruhatensis related to PGPR.
AU  - Hou Q
AU  - Wang C
AU  - Guo H
AU  - Xia Z
AU  - Ye J
AU  - Liu K
AU  - Yang Y
AU  - Hou X
AU  - Liu H
AU  - Wang J
AU  - Du B
AU  - Ding Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00822-15.

PMID- 26294619
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Brevibacillus brevis DZQ7, a Plant Growth-Promoting Rhizobacterium with Broad-Spectrum Antimicrobial Activity.
PG  - e00831-15
AB  - Brevibacillus brevis DZQ7 is a plant growth-promoting rhizobacterium (PGPR) isolated from
      tobacco rhizosphere. Here, we report the draft genome sequence of
      B. brevis DZQ7. Several functional genes related to antimicrobial activity were
      identified in the genome.
AU  - Hou Q
AU  - Wang C
AU  - Hou X
AU  - Xia Z
AU  - Ye J
AU  - Liu K
AU  - Liu H
AU  - Wang J
AU  - Guo H
AU  - Yu X
AU  - Yang Y
AU  - Du B
AU  - Ding Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00831-15.

PMID- 15596722
VI  - 101
DP  - 2004
TI  - Genome sequence of the deep-sea {gamma}-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and   energy.
PG  - 18036-18041
AB  - We report the complete genome sequence of the deep-sea gamma-proteobacterium, Idiomarina
      loihiensis, isolated recently from a
      hydrothermal vent at 1,300-m depth on the Loihi submarine volcano, Hawaii.
      The I. loihiensis genome comprises a single chromosome of 2,839,318 base
      pairs, encoding 2,640 proteins, four rRNA operons, and 56 tRNA genes. A
      comparison of I. loihiensis to the genomes of other gamma-proteobacteria
      reveals abundance of amino acid transport and degradation enzymes, but a
      loss of sugar transport systems and certain enzymes of sugar metabolism.
      This finding suggests that I. loihiensis relies primarily on amino acid
      catabolism, rather than on sugar fermentation, for carbon and energy.
      Enzymes for biosynthesis of purines, pyrimidines, the majority of amino
      acids, and coenzymes are encoded in the genome, but biosynthetic pathways
      for Leu, Ile, Val, Thr, and Met are incomplete. Auxotrophy for Val and Thr
      was confirmed by in vivo experiments. The I. loihiensis genome contains a
      cluster of 32 genes encoding enzymes for exopolysaccharide and capsular
      polysaccharide synthesis. It also encodes diverse peptidases, a variety of
      peptide and amino acid uptake systems, and versatile signal transduction
      machinery. We propose that the source of amino acids for I. loihiensis
      growth are the proteinaceous particles present in the deep sea
      hydrothermal vent waters. I. loihiensis would colonize these particles by
      using the secreted exopolysaccharide, digest these proteins, and
      metabolize the resulting peptides and amino acids. In summary, the I.
      loihiensis genome reveals an integrated mechanism of metabolic adaptation
      to the constantly changing deep-sea hydrothermal ecosystem.
AU  - Hou S et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2004 101: 18036-18041.

PMID- 29853499
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Campylobacter fetus subsp. testudinum Strain 772, Isolated from Ascites of a Patient with Chronic Kidney Disease.
PG  - e00432-18
AB  - Campylobacter fetus subsp. testudinum originating in reptiles can cause invasive  infections
      in humans. Here, we present the whole-genome sequence of C. fetus
      subsp. testudinum strain 772, isolated from a human patient in China.
AU  - Hou SP
AU  - He P
AU  - Zhou Y
AU  - Wu XW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00432-18.

PMID- 8352729
VI  - 293
DP  - 1993
TI  - DNA substrate specificity of pea DNA methylase.
PG  - 617-624
AB  - DNA methylase, present in low-salt extracts of nuclei prepared from Pisum sativum shoot tips,
      methylates model DNA substrates containing CNG trinucleotides or CI dinucleotides only. The
      binding to the hemimethylated trinucleotide substrates is very much stronger and more
      persistent than the binding to the unmethylated substrates or to the hemimethylated
      dinucleotide substrate. When the DNA concentration is limiting, the rate of methyl-group
      transfer with the hemimethylated CNG substrate is much greater than that with the unmethylated
      CNG. However, the Vmax. is similar for the two CNG substrates. On fractionation using
      Q-Sepharose, two peaks of activity are seen with different relative activities using the di-
      and trinucleotide substrates. The relative activity with these substrates changes during
      purification, during plant growth and on heating at 35oC as well, indicating that more than
      one enzyme or more than one form of the enzyme may be present.
AU  - Houlston CE
AU  - Lindsay H
AU  - Pradhan S
AU  - Adams RLP
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 1993 293: 617-624.

PMID- 3022241
VI  - 14
DP  - 1986
TI  - Cloning the DdeI restriction-modification system using a two-step method.
PG  - 7939-7951
AB  - DdeI, a Type II restriction-modification system from the gram-negative
      anaerobic bacterium Desulfovibrio desulfuricans, recognizes the sequence CTNAG.
      The system has been cloned into E. coli in two steps.  First the methylase
      gene was cloned into pBR322 and a derivative expressing higher levels was
      constructed.  Then the endonuclease gene was located by Southern blot analyses;
      BamHI fragments large enough to contain the gene were cloned into pACYC184,
      introduced into a host containing the methylase gene, and screened for
      endonuclease activity.  Both genes are stably maintained in E. coli on separate
      but compatible plasmids.  The DdeI methylase is shown to be a cytosine
      methylase.  DdeI methylase clones decrease in viability as methylation activity
      increases in E. coli RR1 (our original cloning strain).  Therefore the DdeI
      system has been cloned and maintained in ER1467, a new E. coli cloning strain
      engineered to accept cytosine methylases.  Finally, it has been demonstrated
      that a very high level of methylation was necessary in the DdeI system for
      successful introduction of the active endonuclease gene into E. coli.
AU  - Howard KA
AU  - Card C
AU  - Benner JS
AU  - Callahan HL
AU  - Maunus R
AU  - Silber K
AU  - Wilson G
AU  - Brooks JE
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1986 14: 7939-7951.

PMID- 20802046
VI  - 192
DP  - 2010
TI  - Complete Genome Sequence of Staphylococcus aureus Strain JKD6008, an ST239 Clone of Methicillin-Resistant Staphylococcus aureus with  Intermediate-Level Vancomycin Resistance.
PG  - 5848-5849
AB  - We report here the complete 2.92-Mb genome sequence of a clinical isolate of
      methicillin-resistant Staphylococcus aureus subsp. aureus that
      demonstrates intermediate-level vancomycin resistance. The strain, named
      JKD6008, belongs to multilocus sequence type 239 and was isolated from the
      bloodstream of a patient in New Zealand in 2003.
AU  - Howden BP
AU  - Seemann T
AU  - Harrison PF
AU  - McEvoy CR
AU  - Stanton JA
AU  - Rand CJ
AU  - Mason CW
AU  - Jensen SO
AU  - Firth N
AU  - Davies JK
AU  - Johnson PD
AU  - Stinear TP
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 5848-5849.

PMID- 28450501
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of NDM-1-Producing Leclercia adecarboxylata.
PG  - e00135-17
AB  - Here, we provide the first draft genome sequence of NDM-1-producing Leclercia adecarboxylata,
      a human-opportunistic pathogen. The draft genome sequence
      consists of a total length of 5.13 Mbp, with an average G+C content of 55.2%.
AU  - Hoyos-Mallecot Y
AU  - Rojo-Martin MD
AU  - Bonnin RA
AU  - Creton E
AU  - Navarro MJM
AU  - Naas T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00135-17.

PMID- 10567546
VI  - 19
DP  - 1999
TI  - In vivo activity of murine de novo methyltransferases, Dnmt3a and Dnmt3b.
PG  - 8211-8218
AB  - The putative de novo methyltransferases, Dnmt3a and Dnmt3b, were reported to have weak
      methyltransferase activity in methylating the 3' long terminal repeat of Moloney murine
      leukemia virus in vitro. The activity of these enzymes was evaluated in vivo, using a stable
      episomal system that employs plasmids as targets for DNA methylation in human cells. De novo
      methylation of a subset of the CpG sites on the stable episomes is detected in human cells
      overexpressing the murine Dnmt3a or Dnmt3b1 protein.  This de novo methylation activity is
      abolished when the cysteine in the P-C motif, which is the catalytic site of cytosine
      methyltransferases, is replaced by a serine. The pattern of methylation on the episome is
      nonrandom, and different regions of the episome are methylated to different extents.
      Furthermore, Dnmt3a also methylates the sequence methylated by Dnmt3a on the stable episome in
      the corresponding chromosomal target. Overexpression of human DNMT1 or murine Dnmt3b does not
      lead to the same pattern or degree of de novo methylation on the episome as overexpression of
      murine Dnmt3a. This finding suggests that these three enzymes may have different targets or
      requirements, despite the fact that weak de novo methyltransferase activity has been
      demonstrated in vitro for all three enzymes. It is also noteworthy that both Dnmt3a and Dnmt3b
      proteins coat the metaphase chromosomes while displaying a more uniform pattern in the
      nucleus. This is the first evidence that Dnmt3a and Dnmt3b have de novo methyltransferase
      function in vivo and the first indication that the Dnmt3a and Dnmt3b proteins may have
      preferred target sites.
AU  - Hsieh C-L
PT  - Journal Article
TA  - Mol. Cell. Biol.
JT  - Mol. Cell. Biol.
SO  - Mol. Cell. Biol. 1999 19: 8211-8218.

PMID- 10648519
VI  - 182
DP  - 2000
TI  - Cloning, expression, and purification of a thermostable nonhomodimeric restriction enzyme, BslI.
PG  - 949-955
AB  - BslI is a thermostable type II restriction endonuclease with interrupted recognition sequence
      CCNNNNN/NNGG (/, cleavage position).  The BslI restriction-modification system from Bacillus
      species was cloned and expressed in Escherichia coli.  The system is encoded by three genes:
      the 2,739-bp BslI methylase gene (bslIM), the bslIRalpha gene, and the bslIRbeta gene.  The
      alpha and beta subunits of BslI can be expressed independently in E. coli in the absence of
      BslI methylase (M.BslI) protection.  BslI endonuclease activity can be reconstituted in vitro
      by mixing the two subunits together.  Gel filtration chromatography and native polyacrylamide
      gel electrophoresis indicated that BslI forms heterodimers (alphabeta), heterotetramers
      (alpha2beta2), and possibly oligomers in solution.  Two beta subunits can be cross-linked by a
      chemical cross-linking agent, indicating formation of heterotetramer BslI complex
      (alpha2beta2).  In DNA mobility shift assays, neither subunit alone can bind DNA.  DNA
      mobility shift activity was detected after mixing the two subunits together.  Because of the
      symmetric recognition sequence of the BslI endonuclease, we propose that its active form is
      alpha2beta2.  M.BslI contains nine conserved motifs of N-4 cytosine DNA methylases within the
      beta group of aminomethyltransferases.  Synthetic duplex deoxyoligonucleotides containing
      cytosine hemimethylated or fully methylated at N-4 in BslI sites in the first or second
      cytosine are resistant to BslI digestion.  C-5 methylation of the second cytosine on both
      strands within the recognition sequence also renders the site refractory to BslI digestion.
      Two putative zinc fingers are found in the alpha subunit of BslI endonuclease.
AU  - Hsieh P-C
AU  - Xiao J-P
AU  - O'Loane D
AU  - Xu S-Y
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2000 182: 949-955.

PMID- 10449766
VI  - 96
DP  - 1999
TI  - Two major forms of DNA (cytosine-5) methyltransferase in human somatic tissues.
PG  - 9751-9756
AB  - Thus far, only one major form of vertebrate DNA (cytosine-5) methyltransferase (CpG MTase, EC
      2.1.1.37) has been identified, cloned,
      and extensively studied. This enzyme, dnmt1, has been hypothesized to
      be responsible for most of the maintenance as well as the de novo
      methylation activities occurring in the somatic cells of vertebrates.
      We now report the discovery of another abundant species of CpG MTase in
      various types of human cell lines and somatic tissues. Interestingly,
      the mRNA encoding this CpG MTase results from alternative splicing of
      the primary transcript from the Dnmt1 gene, which incorporates in-frame
      an additional 48 nt. between exons 4 and 5. Furthermore, this 48-nt exon
      sequence is derived from the first, or the most upstream, copy of a set
      of seven different Alu repeats located in intron 4. The ratios of
      expression of this mRNA to the expression of the previously known,
      shorter Dnmt1 mRNA species, as estimated by semiquantitative reverse
      transcription-PCR analysis, range from two-thirds to three-sevenths.
      This alternative splicing scheme of the Dnmt1 transcript seems to be
      conserved in the higher primates. We suggest that the originally
      described and the recently discovered forms of CpG MTase be named dnmt1-
      a and dnmt1-b, respectively. The evolutionary and biological
      implications of this finding are discussed in relation to the cellular
      functions of the CpG residues and the CpG MTases.
AU  - Hsu DW
AU  - Lin MJ
AU  - Lee TL
AU  - Wen SC
AU  - Chen X
AU  - Shen CJ
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1999 96: 9751-9756.

PMID- 201281
VI  - 17
DP  - 1978
TI  - Altering the specificity of restriction endonuclease:  effect of replacing Mg2+ with Mn2+.
PG  - 131-138
AB  - In the presence of 100 mM Tris buffer (pH 7.5) and 1-10 mM Mg2+ EcoRI
      endonuclease cleaves DNA at a specific nucleotide sequence and in a
      characteristic way: -G^AATTC-.  But if Mg2+ is replaced by Mn2+, the
      specificity of the cleavage is relaxed and cleavages occur at many other sites;
      moreover, there appears to be a hierarchy of cleavage rates at the pseudo-EcoRI
      restriction sites.  For example, SV40 DNA is cleaved only once in the usual
      digestion conditions, but with Mn2+ more than ten cleavages are made; the five
      most rapidly cleaved SV40 DNA map locations are 0/1.0>0.93>0.33 ~0.49>0.25.
      Mn2+ also alters the restriction specificity of HindIII but not HpaII
      endonuclease.
AU  - Hsu M
AU  - Berg P
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1978 17: 131-138.

PMID- 1701261
VI  - 87
DP  - 1990
TI  - Retron for the 67-base multicopy single-stranded DNA from Escherichia coli: A potential transposable element encoding both reverse transcriptase and Dam methylase functions.
PG  - 9454-9458
AB  - The region (retron-Ec67) required for the biosynthesis of a branched-RNA linked multicopy
      single-stranded DNA (msDNA-Ec67) from a clinical isolate of Escherichia coli was mapped at a
      position equivalent to 19 min on the K-12 chromosome. The element containing the retron
      consisted of a unique 34-kilobase sequence that was flanked by direct repeats of a
      26-base-pair sequence found in the K-12 chromosomal DNA. This suggests that the 34-kilobase
      element was probably integrated into the E. coli genome by a mechanism related to
      transposition or phage integration. In the 34-kilobase sequence an open reading frame of 285
      residues was found, which displays 44% sequence identity with the E. coli Dam methylase.
      Interestingly, there are three GATC sequences, the site of Dam methylation, in the promoter
      region of the gene for reverse transcriptase.
AU  - Hsu M-Y
AU  - Inouye M
AU  - Inouye S
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1990 87: 9454-9458.

PMID- 26472836
VI  - 3
DP  - 2015
TI  - Comparison of Whole-Genome Sequences from Two Colony Morphovars of Burkholderia pseudomallei.
PG  - e01194-15
AB  - The entire genomes of two isogenic morphovars (vgh16W and vgh16R) of Burkholderia pseudomallei
      were sequenced. A comparison of the sequences from both strains indicates that they show
      99.99% identity, are composed of 22 tandem repeated sequences with <100 bp of indels, and have
      199 single-base variants.
AU  - Hsueh PT
AU  - Chen YS
AU  - Lin HH
AU  - Liu PJ
AU  - Ni WF
AU  - Liu MC
AU  - Chen YL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01194-15.

PMID- 26586873
VI  - 3
DP  - 2015
TI  - Genomic Sequence of Burkholderia multivorans NKI379, a Soil Bacterium That Inhibits the Growth of Burkholderia pseudomallei.
PG  - e01294-15
AB  - Burkholderia multivorans NKI379 is a soil bacterium that exhibits an antagonistic effect
      against the growth of Burkholderia pseudomallei, the causative agent of
      the infectious disease melioidosis. We report the draft genomic sequence of B.
      multivorans NKI379, which has a G+C content of 67% and 5,203 candidate
      protein-encoding genes.
AU  - Hsueh PT
AU  - Liu JK
AU  - Chen YL
AU  - Liu PJ
AU  - Ni WF
AU  - Chen YS
AU  - Wu KM
AU  - Lin HH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01294-15.

PMID- 21685282
VI  - 193
DP  - 2011
TI  - Genome Sequence of the 17{beta}-Estradiol-Utilizing Bacterium Sphingomonas Strain KC8.
PG  - 4266-4267
AB  - Sphingomonas strain KC8 is known for its ability to utilize 17beta-estradiol, a natural
      estrogen and an environmental
      endocrine-disrupting compound, as the sole carbon and energy source. Here,
      we report the draft genome sequence of the strain KC8 (4,074,265 bp, with
      a GC content of 63.7%) and major findings from its annotation.
AU  - Hu A
AU  - He J
AU  - Chu KH
AU  - Yu CP
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4266-4267.

PMID- 23908290
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Bisphenol A-Degrading Bacterium Sphingobium sp. Strain YL23.
PG  - e00549-13
AB  - Sphingobium sp. strain YL23, a novel bacterium isolated from sewage sludge of a domestic
      wastewater treatment plant, has been shown to completely degrade
      bisphenol A under aerobic conditions. Here, we describe a 3.8-Mb assembly of its
      genome sequence and major findings from its annotation.
AU  - Hu A
AU  - Lv M
AU  - Yu CP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00549-13.

PMID- Not carried by PubMed...
VI  - 15
DP  - 1994
TI  - NgoAIV--a new restriction endonuclease compared to its commercially available isoschizomers.
PG  - 42-43
AB  - The restriction endonuclease NaeI recognizes the sequence GCC^GGC and generates blunt-ended
      DNA fragments. However, NaeI demonstrates a strong site preference in its cleavage rate that
      may result in incomplete cleavage in some DNA. Therefore, there is a need to search for an
      isoschizomer to circumvent the problem. NgoAIV is an isoschizomer of NaeI that was purified
      from a strain of E. coli bearing the cloned NgoAIV gene from Neisseria gonorrhoea. NgoAIV
      cleaves between the first G and C residues, providing cohesive ends for more effective
      ligation. The enzyme has an apparent molecular weight of 31,000 Da on an SDS-PAGE gel.
AU  - Hu A-LW
PT  - Journal Article
TA  - BRL Focus
JT  - BRL Focus
SO  - BRL Focus 1994 15: 42-43.

PMID- 7056404
VI  - 41
DP  - 1982
TI  - Endonuclease NciI generates atypical termini.
PG  - 1119
AB  - Cleavage of DNA by the type II restriction endonuclease, NciI, produces termini
      that differ from those produced by most other type II enzymes.  This difference
      is manifested by the inability of T4 DNA ligase to ligate NciI generated
      termini, even under conditions that normally enhance ligation.  Tests for
      contaminating enzymes present in NciI preparations showed negligible levels of
      3' or 5' single or double strand specific exonucleases.  Similarly, no other
      endonuclease was detected in these preparations.  The presence of a ligation
      inhibitor in NciI preparations was eliminated by mixing DNA fragments produced
      by HpaII or TaqI with NciI fragments and measuring ligation.  Only the NciI
      generated fragments remained resistant to the ligation reaction precluding the
      presence of a nonspecific ligation inhibitor.  A successful ligation procedure
      was designed and included a two step incubation with T4 polynucleotide kinase
      and NciI formed fragments.  Step one utilized conditions that enhanced the
      inherent 3' phosphatase activity of T4 polynucleotide kinase.  The 2nd
      incubation step optimized the phosphorylation of the 5' hydroxyl terminus.  DNA
      fragments treated in this manner were ligated with more than a 50% efficiency
      under normal conditions.  The above result suggests that NciI cleaves DNA
      leaving a 3' phosphate and 5' hydroxyl, and explains the inability of T4 DNA
      ligase to ligate NciI generated fragments.
AU  - Hu AW
AU  - Marschel AH
PT  - Journal Article
TA  - Fed. Proc.
JT  - Fed. Proc.
SO  - Fed. Proc. 1982 41: 1119.

PMID- 10504231
VI  - 38
DP  - 1999
TI  - Mapping of a DNA binding region of the PI-SceI homing endonuclease by affinity cleavage and alanine-scanning mutagenesis.
PG  - 12621-12628
AB  - The PI-SceI protein is a member of the LAGLIDADG family of homing endonucleases that is
      generated by a protein splicing reaction. PI-SceI has a bipartite domain structure, and the
      protein splicing and endonucleolytic reactions are catalyzed by residues in domains I and II,
      respectively. Structural and mutational evidence indicates that both domains mediate DNA
      binding. Treatment of the protein with trypsin breaks a peptide bond within a disordered
      region of the endonuclease domain situated between residues Val-270 and Leu-280 and interferes
      with the ability of this domain to bind DNA. To identify specific residues in this region that
      are involved in DNA binding and/or catalysis, alanine-scanning mutagenesis was used to create
      a set of PI-SceI mutant proteins that were assayed for activity. One of these mutants, N281A,
      was >300-fold less active than wild-type PI-SceI, and two other proteins, R277A and N284A,
      were completely inactive. These decreases in cleavage activity parallel similar decreases in
      substrate binding by the endonuclease domains of these mutant proteins. We mapped the
      approximate position of the disordered region to one of the ends of the 31 base pair PI-SceI
      recognition sequence using mutant proteins that were substituted with cysteine at residues
      Asn-274 and Glu-283 and tethered to the chemical nuclease FeBABE. These mutational and
      affinity cleavage data strongly support a model of PI-SceI docked to its DNA substrate that
      suggests that one or more residues identified here are responsible for contacting base pair
      A/T(-)(9), which is essential for substrate binding.
AU  - Hu D
AU  - Crist M
AU  - Duan X
AU  - Gimble FS
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1999 38: 12621-12628.

PMID- 10644733
VI  - 275
DP  - 2000
TI  - Probing the Structure of the PI-SceI-DNA Complex by Affinity Cleavage and Affinity Photocross-linking.
PG  - 2705-2712
AB  - The PI-SceI protein is an intein-encoded homing endonuclease that initiates the mobility of
      its gene by making a double strand break at a single site in the yeast genome. The PI-SceI
      protein splicing and endonucleolytic active sites are separately located in each of two
      domains in the PI-SceI structure. To determine the spatial relationship between bases in the
      PI-SceI recognition sequence and selected PI-SceI amino acids, the PI-SceI-DNA complex was
      probed by photocross-linking and affinity cleavage methods. Unique solvent-accessible cysteine
      residues were introduced into the two PI-SceI domains at positions 91, 97, 170, 230, 376, and
      378, and the mutant proteins were modified with either 4-azidophenacyl bromide or iron
      (S)-1-(p-bromoacetamidobenzyl)-ethylenediaminetetraacetate (FeBABE). The phenyl azide-coupled
      proteins cross-linked to the PI-SceI target sequence, and the FeBABE-modified proteins cleaved
      the DNA proximal to the derivatized amino acid. The results suggest that an extended
      beta-hairpin loop in the endonuclease domain that contains residues 376 and 378 contacts the
      major groove near the PI-SceI cleavage site. Conversely, residues 91, 97, and 170 in the
      protein splicing domain are in close proximity to a distant region of the substrate. To
      interpret our results, we used a new PI-SceI structure that is ordered in regions of the
      protein that bind DNA. The data strongly support a model of the PI-SceI-DNA complex derived
      from this structure.
AU  - Hu D
AU  - Crist M
AU  - Duan X
AU  - Quiocho FA
AU  - Gimble FS
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2000 275: 2705-2712.

PMID- 22374957
VI  - 194
DP  - 2012
TI  - Genome Sequence of Streptomyces sp. Strain TOR3209, a Rhizosphere Microecology Regulator Isolated from Tomato Rhizosphere.
PG  - 1627
AB  - Streptomyces sp. strain TOR3209, isolated from tomato rhizosphere, can regulate the
      rhizosphere microecology of a variety of crops. Strain TOR3209 could improve
      plant systemic resistance and promote plant growth. Here, the genome sequence of
      strain TOR3209 is reported, providing the molecular biological basis of the
      regulation mechanism of rhizosphere microecology.
AU  - Hu D
AU  - Li X
AU  - Chang Y
AU  - He H
AU  - Zhang C
AU  - Jia N
AU  - Li H
AU  - Wang Z
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1627.

PMID- 27849586
VI  - 113
DP  - 2016
TI  - Origins of the current seventh cholera pandemic.
PG  - E7730-E7739
AB  - Vibrio cholerae has caused seven cholera pandemics since 1817, imposing terror on
      much of the world, but bacterial strains are currently only available for the
      sixth and seventh pandemics. The El Tor biotype seventh pandemic began in 1961 in
      Indonesia, but did not originate directly from the classical biotype
      sixth-pandemic strain. Previous studies focused mainly on the spread of the
      seventh pandemic after 1970. Here, we analyze in unprecedented detail the origin,
      evolution, and transition to pandemicity of the seventh-pandemic strain. We used
      high-resolution comparative genomic analysis of strains collected from 1930 to
      1964, covering the evolution from the first available El Tor biotype strain to
      the start of the seventh pandemic. We define six stages leading to the pandemic
      strain and reveal all key events. The seventh pandemic originated from a
      nonpathogenic strain in the Middle East, first observed in 1897. It subsequently
      underwent explosive diversification, including the spawning of the pandemic
      lineage. This rapid diversification suggests that, when first observed, the
      strain had only recently arrived in the Middle East, possibly from the Asian
      homeland of cholera. The lineage migrated to Makassar, Indonesia, where it gained
      the important virulence-associated elements Vibrio seventh pandemic island I
      (VSP-I), VSP-II, and El Tor type cholera toxin prophage by 1954, and it then
      became pandemic in 1961 after only 12 additional mutations. Our data indicate
      that specific niches in the Middle East and Makassar were important in generating
      the pandemic strain by providing gene sources and the driving forces for genetic
      events.
AU  - Hu D
AU  - Liu B
AU  - Feng L
AU  - Ding P
AU  - Guo X
AU  - Wang M
AU  - Cao B
AU  - Reeves PR
AU  - Wang L
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2016 113: E7730-E7739.

PMID- 9779579
VI  - 73
DP  - 1998
TI  - Isolation and characterization of a newly identified type II restriction endonuclease from a local Streptomyces sp. in Taiwan.
PG  - 231-241
AB  - Streptomyces chusanensis ZS-2, isolated from a soil sample in Chusan in Taiwan, was found to
      produce a new Type II restriction endonuclease. This restriction enzyme was designated as
      SchI. The purified enzyme was characterized as having a subunit mol wt of 28 kDa, and was
      apparently free from exonuclease activities. It cleaves the phosphodiester bond between the
      fourth C and the fifth G on the 5'-CCGCGG-3' sequence of DNAs, leaving a 2-nucleotide
      protruding end at its 3' site. This data suggests that SchI is an isoschizomer of SacII. In
      addition, based on the comparison between SchI and SacII regarding reaction parameters, it
      seems that SchI is a better choice of restriction enzyme for genetic analysis and mapping.
AU  - Hu K-Y
AU  - Wuu J-A
AU  - Kao M-C
AU  - Liu Y-T
AU  - Pai S-H
PT  - Journal Article
TA  - Appl. Biochem. Biotechnol.
JT  - Appl. Biochem. Biotechnol.
SO  - Appl. Biochem. Biotechnol. 1998 73: 231-241.

PMID- 25002488
VI  - 111
DP  - 2014
TI  - Mutation of a major CG methylase in rice causes genome-wide hypomethylation, dysregulated genome expression, and seedling lethality.
PG  - 10642-10647
AB  - Cytosine methylation at CG sites (mCG) plays critical roles in development, epigenetic
      inheritance, and genome stability in mammals and plants. In the dicot
      model plant Arabidopsis thaliana, methyltransferase 1 (MET1), a principal CG
      methylase, functions to maintain mCG during DNA replication, with its null
      mutation resulting in global hypomethylation and pleiotropic developmental
      defects. Null mutation of a critical CG methylase has not been characterized at a
      whole-genome level in other higher eukaryotes, leaving the generality of the
      Arabidopsis findings largely speculative. Rice is a model plant of monocots, to
      which many of our important crops belong. Here we have characterized a null
      mutant of OsMet1-2, the major CG methylase in rice. We found that seeds
      homozygous for OsMet1-2 gene mutation (OsMET1-2-/-), which directly segregated
      from normal heterozygote plants (OsMET1-2+/-), were seriously maldeveloped, and
      all germinated seedlings underwent swift necrotic death. Compared with wild type,
      genome-wide loss of mCG occurred in the mutant methylome, which was accompanied
      by a plethora of quantitative molecular phenotypes including dysregulated
      expression of diverse protein-coding genes, activation and repression of
      transposable elements, and altered small RNA profiles. Our results have revealed
      conservation but also distinct functional differences in CG methylases between
      rice and Arabidopsis.
AU  - Hu L
AU  - Li N
AU  - Xu C
AU  - Zhong S
AU  - Lin X
AU  - Yang J
AU  - Zhou T
AU  - Yuliang A
AU  - Wu Y
AU  - Chen YR
AU  - Cao X
AU  - Zemach A
AU  - Rustgi S
AU  - von Wettstein D
AU  - Liu B
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2014 111: 10642-10647.

PMID- 28663302
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of Two Salmonella enterica subsp. enterica Serovar Enteritidis Strains Isolated from Egg Products in the United States.
PG  - e00614-17
AB  - Egg-associated salmonellosis is an important public health problem in many countries. Here, we
      report the genome sequences, including plasmids, of two
      strains of Salmonella enterica subsp. enterica serovar Enteritidis isolated from
      egg products in 2012 and 2013 in the United States. This will provide more
      information and insight into the research about egg-associated salmonellosis.
AU  - Hu L
AU  - Zhang G
AU  - Allard MW
AU  - Yao K
AU  - Stones R
AU  - Hoffmann M
AU  - Brown EW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00614-17.

PMID- 9748454
VI  - 180
DP  - 1998
TI  - Structural organization of virulence-associated plasmids of Yersinia pestis.
PG  - 5192-5202
AB  - The complete nucleotide sequence and gene organization of the three virulence plasmids from
      Yersinia pestis KIM5 were determined. Plasmid
      pPCP1 (9,610 bp) has a GC content of 45.3% and encodes two previously
      known virulence factors, an associated protein, and a single copy of
      IS100. Plasmid pCD1 (70,504 bp) has a GC content of 44.8%. It is known to
      encode a number of essential virulence determinants, regulatory functions,
      and a multiprotein secretory system comprising the low-calcium response
      stimulation that is shared with the other two Yersinia species pathogenic
      for humans (Y. pseudotuberculosis and Y. enterocolitica). A new
      pseudogene, which occurs as an intact gene in the Y. enterocolitica and Y.
      pseudotuberculosis-derived analogues, was found in pCD1. It corresponds to
      that encoding the lipoprotein YlpA. Several intact and partial insertion
      sequences and/or transposons were also found in pCD1, as well as six
      putative structural genes with high homology to proteins of unknown
      function in other yersiniae. The sequences of the genes involved in the
      replication of pCD1 are highly homologous to those of the cognate plasmids
      in Y. pseudotuberculosis and Y. enterocolitica, but their localization
      within the plasmid differs markedly from those of the latter. Plasmid pMT1
      (100,984 bp) has a GC content of 50.2%. It possesses two copies of IS100,
      which are located 25 kb apart and in opposite orientations. Adjacent to
      one of these IS100 inserts is a partial copy of IS285. A single copy of an
      IS200-like element (recently named IS1541) was also located in pMT1. In
      addition to 5 previously described genes, such as murine toxin, capsule
      antigen, capsule anchoring protein, etc., 30 homologues to genes of
      several bacterial species were found in this plasmid, and another 44 open
      reading frames without homology to any known or hypothetical protein in
      the databases were predicted.
AU  - Hu P
AU  - Elliott J
AU  - McCready P
AU  - Skowronski E
AU  - Garnes J
AU  - Kobayashi A
AU  - Brubaker RR
AU  - Garcia E
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1998 180: 5192-5202.

PMID- 22628496
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Rubrivivax gelatinosus CBS.
PG  - 3262
AB  - Rubrivivax gelatinosus CBS, a purple nonsulfur photosynthetic bacterium, can grow
      photosynthetically using CO and N(2) as the sole carbon and nitrogen nutrients,
      respectively. R. gelatinosus CBS is of particular interest due to its ability to
      metabolize CO and yield H(2). We present the 5-Mb draft genome sequence of R.
      gelatinosus CBS with the goal of providing genetic insight into the metabolic
      properties of this bacterium.
AU  - Hu P
AU  - Lang J
AU  - Wawrousek K
AU  - Yu J
AU  - Maness PC
AU  - Chen J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3262.

PMID- 21572001
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Streptococcus suis Serotype 3 Strain ST3.
PG  - 3428-3429
AB  - Streptococcus suis is a zoonotic pathogen, causing economic loss in swine industry, and is
      also a threat to human health. To date, the mechanism of
      pathogenisis is not fully understood. Here, we report the complete genome
      sequence of S. suis strain ST3 of serotype 3, which provides opportunities
      to reveal genetic basis of infection of S. suis non-serotype 2 strains.
AU  - Hu P
AU  - Yang M
AU  - Zhang A
AU  - Wu J
AU  - Chen B
AU  - Hua Y
AU  - Yu J
AU  - Chen H
AU  - Xiao J
AU  - Jin M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3428-3429.

PMID- 21398551
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Streptococcus suis Serotype 14 Strain JS14.
PG  - 2375-2376
AB  - Streptococcus suis is an important zoonotic agent leading to a variety of diseases in swine
      and can be transmitted to human being upon close contact. Here, we report the complete genome
      sequence of S. suis serotype 14 strain JS14 which was isolated from a diseased pig in Jiangsu
      Province, China.
AU  - Hu P
AU  - Yang M
AU  - Zhang A
AU  - Wu J
AU  - Chen B
AU  - Hua Y
AU  - Yu J
AU  - Xiao J
AU  - Jin M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 2375-2376.

PMID- 28473383
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Riemerella anatipestifer Serotype 10 Strain HXb2.
PG  - e00278-17
AB  - The complete genome sequence of highly virulent Riemerella anatipestifer strain HXb2 was
      determined. The genome consisted of a single circular chromosome of
      2,425,237 bp containing 2,383 putative open reading frames (ORFs), 9 rRNA
      operons, and 40 tRNA genes.
AU  - Hu Q
AU  - Qi J
AU  - Bo H
AU  - Liu G
AU  - Tao M
AU  - Ding Y
AU  - Xue Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00278-17.

PMID- 26984839
VI  - 17
DP  - 2016
TI  - Antibiotic resistance mechanisms of Myroides sp.
PG  - 188-199
AB  - Bacteria of the genus Myroides (Myroides spp.) are rare opportunistic pathogens. Myroides sp.
      infections have been reported mainly in China. Myroides sp. is highly resistant to most
      available antibiotics, but the resistance mechanisms are not fully elucidated. Current strain
      identification methods based on biochemical traits are unable to identify strains accurately
      at the species level. While 16S ribosomal RNA (rRNA) gene sequencing can accurately achieve
      this, it fails to give information on the status and mechanisms of antibiotic resistance,
      because the 16S rRNA sequence contains no information on resistance genes, resistance islands
      or enzymes. We hypothesized that obtaining the whole genome sequence of Myroides sp., using
      next generation sequencing methods, would help to clarify the mechanisms of pathogenesis and
      antibiotic resistance, and guide antibiotic selection to treat Myroides sp. infections.  As
      Myroides sp. can survive in hospitals and the environment, there is a risk of nosocomial
      infections and
      pandemics. For better management of Myroides sp. infections, it is imperative to apply next
      generation sequencing technologies to clarify the antibiotic resistance mechanisms in these
      bacteria.
AU  - Hu S
AU  - Yuan S
AU  - Qu H
AU  - Jiang T
AU  - Zhou Y
AU  - Wang M
AU  - Ming D
PT  - Journal Article
TA  - J. Zhejiang Univ. Sci. B
JT  - J. Zhejiang Univ. Sci. B
SO  - J. Zhejiang Univ. Sci. B 2016 17: 188-199.

PMID- 21284892
VI  - 12
DP  - 2011
TI  - Comparative genomic and transcriptomic analysis revealed genetic characteristics related to solvent formation and xylose utilization in Clostridium acetobutylicum EA 2018.
PG  - 93
AB  - ABSTRACT: BACKGROUND: Clostridium acetobutylicum, a gram-positive and
      spore-forming anaerobe, is a major strain for the fermentative production
      of acetone, butanol and ethanol. But a previously isolated hyper-butanol
      producing strain C. acetobutylicum EA 2018 does not produce spores and has
      greater capability of solvent production, especially for butanol, than the
      type strain C. acetobutylicum ATCC 824. RESULTS: Complete genome of C.
      acetobutylicum EA 2018 was sequenced using Roche 454 pyrosequencing.
      Genomic comparison with ATCC 824 identified many variations which may
      contribute to the hyper-butanol producing characteristics in the EA 2018
      strain, including a total of 46 deletion sites and 26 insertion sites. In
      addition, transcriptomic profiling of gene expression in EA 2018 relative
      to that of ATCC824 revealed expression-level changes of several key genes
      related to solvent formation. For example, spo0A and adhEII have higher
      expression level, and most of the acid formation related genes have lower
      expression level in EA 2018. Interestingly, the results also showed that
      the variation in CEA_G2622 (CAC2613 in ATCC 824), a putative
      transcriptional regulator involved in xylose utilization, might accelerate
      utilization of substrate xylose. CONCLUSIONS: Comparative analysis of C.
      acetobutylicum hyper-butanol producing strain EA 2018 and type strain ATCC
      824 at both genomic and transcriptomic levels, for the first time,
      provides molecular-level understanding of non-sporulation, higher solvent
      production and enhanced xylose utilization in the mutant EA 2018. The
      information could be valuable for further genetic modification of C.
      acetobutylicum for more effective butanol production.
AU  - Hu S
AU  - Zheng H
AU  - Gu Y
AU  - Zhao J
AU  - Zhang W
AU  - Yang Y
AU  - Wang S
AU  - Zhao G
AU  - Yang S
AU  - Jiang W
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2011 12: 93.

PMID- 22525332
VI  - 22
DP  - 2012
TI  - Structural insights into DndE from Escherichia coli B7A involved in DNA phosphorothioation modification.
PG  - 1203-1206
AB  - DNA phosphorothioate modification, originally developed as an artificial tool to stabilize
      oligodeoxynucleotides against nuclease degradation, was recently found to be incorporated with
      sulfur into DNA backbone as a novel physiological variation by the five-gene dnd cluster
      (dndA-dndE) products in a sequence- and stereo-specific manner.  This PT modification causes
      the DNA degradation (Dnd) phenotype and is widespread and quantized in bacterial genomes,
      working as a part of a restriction modification system.  This modification can be specifically
      cleaved in vitro by type IV restriction endonuclease.  DndA works as a cysteine desulfurase
      and assembles DndC as a 4Fe-4S cluster protein.  DndC possesses ATP pyrophosphatase activity
      and is predicted to have 3'-phosphoadenosine-5'-phosphosulfate reductase activity, whereas
      DndB has homology to a group of transcriptional regulators.  DndD, known as SpfD in
      Pseudomonas fluorescens Pf0-1, has ATPase activity possibly related to DNA structure
      alteration of nicking during PT incorporation.  Sequence identity (46%) and similarity (61%)
      to phosphoribosylaminoimidazole carboxylase (NCAIR synthetase) from Anabaena variabilis
      suggest that DndE could be an NCAIR synthase analogue.  However, DndE may also act as a
      sulfotransferase due to a specific PAPS binding sequence AAVGK-TLLIHLHR contained in the
      C-terminus of DndE from Streptomyces lividans.  Therefore, the exact function of DndE remains
      unknown.
AU  - Hu W
AU  - Wang C
AU  - Liang J
AU  - Zhang T
AU  - Hu Z
AU  - Wang Z
AU  - Lan W
AU  - Li F
AU  - Wu H
AU  - Ding J
AU  - Wu G
AU  - Deng Z
AU  - Cao C
PT  - Journal Article
TA  - Cell Res.
JT  - Cell Res.
SO  - Cell Res. 2012 22: 1203-1206.

PMID- 
VI  - 54
DP  - 2002
TI  - Evaluation of DNA-binding ability of antibiotic DC-81 - indole conjugates by restriction endonuclease BamHI and molecular modeling studies.
PG  - 465-470
AB  - DC-81, an antitumor antibiotic produced by Streptomyces species, belongs to the
      pyrrolo-{2,1-c}{1,4}benzodiazepines which are potent inhibitors of nucleic acid synthesis
      because of their ability to recognize and bind to specific sequence of DNA to form a labile
      covalent adduct.  The hybrid agents comprised of DC-81 and indole carboxylate moiety 2 through
      carbon chain linkers (comprised of zero and two to four carbons) have been designed and
      synthesized by our group.  These compounds with DNA binding ability were determined by
      restriction endonuclease BamHI and molecular modeling studies.  The results demonstrated that
      DC-81 - IC hybrid 3c (with a three carbon chain linker) showed a higher DNA-binding affinity
      and gave rise to a maximal stabilization of the complex with DNA at the minor groove as
      compared to the other complexes formed with 3a, 3b and 3d.
AU  - Hu WP
AU  - Yu HS
AU  - Hsieh MC
AU  - Chen YC
AU  - Wang JJ
PT  - Journal Article
TA  - Chin. Pharm. J.
JT  - Chin. Pharm. J.
SO  - Chin. Pharm. J. 2002 54: 465-470.

PMID- 18296527
VI  - 190
DP  - 2008
TI  - Complete genome sequence of the mosquitocidal bacterium Bacillus sphaericus C3-41 and comparison with those of closely related Bacillus  species.
PG  - 2892-2902
AB  - Bacillus sphaericus strain C3-41 is an aerobic, mesophilic, spore-forming bacterium that has
      been used with great success in mosquito control
      programs worldwide. Genome sequencing revealed that the complete genome of
      this entomopathogenic bacterium is composed of a chromosomal replicon of
      4,639,821 bp and a plasmid replicon of 177,642 bp, containing 4,786 and
      186 potential protein-coding sequences, respectively. Comparison of the
      genome with other published sequences indicated that the B. sphaericus
      C3-41 chromosome is most similar to that of Bacillus sp. strain NRRL
      B-14905, a marine species that, like B. sphaericus, is unable to
      metabolize polysaccharides. The lack of key enzymes and sugar transport
      systems in the two bacteria appears to be the main reason for this
      inability, and the abundance of proteolytic enzymes and transport systems
      may endow these bacteria with exclusive metabolic pathways for a wide
      variety of organic compounds and amino acids. The genes shared between B.
      sphaericus C3-41 and Bacillus sp. strain NRRL B-14905, including mobile
      genetic elements, membrane-associated proteins, and transport systems,
      demonstrated that these two species are a biologically and
      phylogenetically divergent group. Knowledge of the genome sequence of B.
      sphaericus C3-41 thus increases our understanding of the bacilli and may
      also offer prospects for future genetic improvement of this important
      biological control agent.
AU  - Hu X
AU  - Fan W
AU  - Han B
AU  - Liu H
AU  - Zheng D
AU  - Li Q
AU  - Dong W
AU  - Yan J
AU  - Gao M
AU  - Berry C
AU  - Yuan Z
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2008 190: 2892-2902.

PMID- 25197460
VI  - 9
DP  - 2014
TI  - High quality draft genome sequence of Staphylococcus cohnii subsp. cohnii strain  hu-01.
PG  - 755-762
AB  - Staphylococcus cohnii subsp. cohnii belongs to the family Staphylococcaceae in the order
      Bacillales, class Bacilli and phylum Firmicutes. The increasing
      relevance of S. cohnii to human health prompted us to determine the genomic
      sequence of Staphylococcus cohnii subsp. cohnii strain hu-01, a
      multidrug-resistant isolate from a hospital in China. Here we describe the
      features of S. cohnii subsp. cohnii strain hu-01, together with the genome
      sequence and its annotation. This is the first genome sequence of the species
      Staphylococcus cohnii.
AU  - Hu X
AU  - Li A
AU  - Lv L
AU  - Yuan C
AU  - Guo L
AU  - Jiang X
AU  - Jiang H
AU  - Qian G
AU  - Zheng B
AU  - Guo J
AU  - Li L
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 755-762.

PMID- 29773631
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Staphylococcus microti DSM 22147, Isolated from the Common Vole.
PG  - e00420-18
AB  - Staphylococcus microti DSM 22147 was isolated from viscera of common voles (Microtus arvalis
      Pallas) with generalized Brucella microti infection in the
      Czech Republic. To the best of our knowledge, the genome sequence of the species
      S. microti has not been previously studied. The complete genome sequence of
      strain DSM 22147 includes a genome of 2,381,859 bp (38.0% GC content) without any
      plasmids.
AU  - Hu X
AU  - Shang Y
AU  - Guo J
AU  - Zhang H
AU  - Liang Y
AU  - Sun J
AU  - Yue F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00420-18.

PMID- 24948765
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of the p-Nitrophenol-Degrading Bacterium Pseudomonas putida DLL-E4.
PG  - e00596-14
AB  - The first complete genome sequence of a p-nitrophenol (PNP)-degrading bacterium is reported
      here. Pseudomonas putida DLL-E4, a Gram-negative bacterium isolated
      from methyl-parathion-polluted soil, can utilize PNP as the sole carbon and
      nitrogen source. P. putida DLL-E4 has a 6,484,062 bp circular chromosome that
      contains 5,894 genes, with a G+C content of 62.46%.
AU  - Hu X
AU  - Wang J
AU  - Wang F
AU  - Chen Q
AU  - Huang Y
AU  - Cui Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00596-14.

PMID- 26205872
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Staphylococcus sciuri subsp. sciuri Strain Z8, Isolated  from Human Skin.
PG  - e00714-15
AB  - Staphylococcus sciuri subsp. sciuri strain Z8 was isolated from a skin wound infection of a
      patient with infective endocarditis. To the best of our knowledge,
      the genome sequence of the species S. sciuri has not been previously studied. The
      complete genome sequence of strain Z8 includes a genome of 2,620,868 bp (32.43%
      GC content) without any plasmids.
AU  - Hu X
AU  - Zheng B
AU  - Jiang H
AU  - Kang Y
AU  - Cao Q
AU  - Ning H
AU  - Shang J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00714-15.

PMID- 30117799
VI  - 68
DP  - 2018
TI  - Acinetobacter wuhouensis sp. nov., isolated from hospital sewage.
PG  - 3212-3216
AB  - We recovered eight strains of the genus Acinetobacter from hospital sewage at
      West China Hospital in Chengdu, China. Based on the comparative analysis of the
      rpoB sequence, these strains formed a strongly supported and internally coherent
      cluster (intra-cluster identity of >/=98.0 %), which was clearly separated from
      all known Acinetobacter species (</=91.1 %). The eight strains also formed a
      tight and distinct cluster based on the genus-wide comparison of whole-cell mass
      fingerprints generated by matrix-assisted laser desorption/ionization
      time-of-flight mass spectrometry. In addition, the combination of their ability
      to assimilate 2,3-butanediol and phenylacetate, but not 4-hydroxybenzoate, and
      the inability to grow at 37 degrees C could distinguish these eight strains from
      all known Acinetobacter species. Whole-genomic sequencing has been performed for
      two selected strains, WCHA60(T) and WCHA62. There were 96.65 % average nucleotide
      identity (ANI) and 72 % in silico DNA-DNA hybridization (isDDH) values between
      WCHA60(T) and WCHA62, suggesting that the two strains indeed belonged to the same
      species. In contrast, the ANI and isDDH values between the two strains and the
      known Acinetobacter species were <83 and <30 %, respectively; both of which were
      far below the cut-off to define a bacterial species. Therefore, the eight strains
      should be considered to represent a novel species of the genus Acinetobacter, for
      which the name Acinetobacterwuhouensis sp. nov. is proposed. The type strain is
      WCHA60(T) (=CCTCC AB 2016204(T)=GDMCC 1.1100(T)=KCTC 52505(T)).
AU  - Hu Y
AU  - Feng Y
AU  - Qin J
AU  - Radolfova-Krizova L
AU  - Maixnerova M
AU  - Zhang X
AU  - Nemec A
AU  - Zong Z
PT  - Journal Article
TA  - Int. J. Syst. Evol. Microbiol.
JT  - Int. J. Syst. Evol. Microbiol.
SO  - Int. J. Syst. Evol. Microbiol. 2018 68: 3212-3216.

PMID- 18724694
VI  - 24
DP  - 2008
TI  - Phage resistance of Corynebacterium crenatum conferred by the restriction and modification system cglI.
PG  - 760-765
AB  - 
AU  - Hu Y
AU  - Li T
AU  - Yang Z
AU  - Zhang B
AU  - Li Y
PT  - Journal Article
TA  - Sheng Wu Gong Cheng Xue Bao
JT  - Sheng Wu Gong Cheng Xue Bao
SO  - Sheng Wu Gong Cheng Xue Bao 2008 24: 760-765.

PMID- 27795238
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a Pseudomonas sp. Strain Carrying blaIMP-25 and blaVIM-2 Carbapenemase Genes from Hospital Sewage.
PG  - e01027-16
AB  - Pseudomonas strain WCHP16 recovered from hospital sewage in West China Hospital,  Chengdu,
      China was found to carry two carbapenemase genes blaIMP-25 and blaVIM-2
      Here, we report its 5.7-Mb draft genome sequence, comprising 141 contigs and an
      average 59.53% G+C content. The genome contained 5,504 coding sequences and 67
      tRNA genes.
AU  - Hu Y
AU  - Wu W
AU  - Feng Y
AU  - Zhang X
AU  - Zong Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01027-16.

PMID- 24309735
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Deinococcus xibeiensis R13, a New Carotenoid-Producing Strain.
PG  - e00987-13
AB  - Deinococcus xibeiensis strain R13, isolated from radiation-contaminated soils, synthesizes a
      unique ketocarotenoid, deinoxanthin. Here, we present a 3.49-Mb
      assembly of its genome sequence, which can help us find the key genes of the
      deinoxanthin biosynthesis pathways and modify genes obtaining a high yield of the
      new carotenoid.
AU  - Hu Y
AU  - Xu X
AU  - Song P
AU  - Jiang L
AU  - Zhang Z
AU  - Huang H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00987-13.

PMID- 21742884
VI  - 193
DP  - 2011
TI  - Whole-Genome Sequence of a Multidrug-Resistant Clinical Isolate of Acinetobacter lwoffii.
PG  - 5549-5550
AB  - Acinetobacter lwoffii has been considered an opportunistic pathogen that can cause nosocomial
      infections in humans. Here, we present the genome
      sequence of A. lwoffii WJ10621, a multidrug-resistant clinical isolate
      that carries a plasmid with the NDM-1 resistance gene.
AU  - Hu Y
AU  - Zhang W
AU  - Liang H
AU  - Liu L
AU  - Peng G
AU  - Pan Y
AU  - Yang X
AU  - Zheng B
AU  - Gao GF
AU  - Zhu B
AU  - Hu H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5549-5550.

PMID- 24967843
VI  - 9
DP  - 2014
TI  - The first complete genome sequence of the class fimbriimonadia in the phylum armatimonadetes.
PG  - E100794
AB  - In this study, we present the complete genome of Fimbriimonas ginsengisoli Gsoil
      348T belonging to the class Fimbriimonadia of the phylum Armatimonadetes,
      formerly called as candidate phylum OP10. The complete genome contains a single
      circular chromosome of 5.23 Mb including a 45.5 kb prophage. Of the 4820 open
      reading frames (ORFs), 3,000 (62.2%) genes could be classified into Clusters of
      Orthologous Groups (COG) families. With the split of rRNA genes, strain Gsoil
      348T had no typical 16S-23S-5S ribosomal RNA operon. In this genome, the GC skew
      inversion which was usually observed in archaea was found. The predicted gene
      functions suggest that the organism lacks the ability to synthesize histidine,
      and the TCA cycle is incomplete. Phylogenetic analyses based on ribosomal
      proteins indicated that strain Gsoil 348T represents a deeply branching lineage
      of sufficient divergence with other phyla, but also strongly involved in
      superphylum Terrabacteria.
AU  - Hu ZY
AU  - Wang YZ
AU  - Im WT
AU  - Wang SY
AU  - Zhao GP
AU  - Zheng HJ
AU  - Quan ZX
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2014 9: E100794.

PMID- 
VI  - 0
DP  - 1998
TI  - Purification and characterization of the LlaGI restriction  enodnuclease from Lactococcus lactis subsp. cremoris G2.
PG  - P001
AB  - In the dairy industry, Lactococcus lactis are widely used as starter cultures in the
      manufacture of the dairy products.  Bacteriophage infection is a serious problem for the dairy
      industry.  To date, four categories of natural phage defense mechanisms have been identified
      in lactococci based on the mode of action: adsorption inhibition, penetration blocking,
      abortive infection, and restriction-modification system.  L. lactis subsp. cremoris G2 has
      previously been isolated and purified in our laboratory.  Strain G2, which encodes a type-II
      R-M endonuclease, designated LlaGI, contains at least five plasmids.  When L. lactis strain G2
      was cured from most of its plasmids, the specific nuclease activity was lost.  These results
      strongly indicate that the R-M system is plasmid-encoded.  LlaGI, an isoschizomer of NheI,
      which recognizes the palindromic DNA sequence 5'_GCTAGC_3' has been purified to homogeneity
      by a two-step procedure using ion-exchange and affinity chromatography.  The enzyme yield was
      in excess of 1000 units/g of wet cells.  The purified enzyme was free of nonspecific nuclease
      and requires only magnesium ion for its activity.  Physical properties indicate that LlaGI is
      present in solution as monomer of about 40kDa.
AU  - Hua NM
AU  - Karska-Wysocki B
AU  - Szatmari G
AU  - Mamet-Bratley MD
PT  - Journal Article
TA  - Life Sc. Confer. Ottawa
JT  - Life Sc. Confer. Ottawa
SO  - Life Sc. Confer. Ottawa 1998 0: P001.

PMID- 25540349
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Klebsiella pneumoniae Sequence Type 17, a Multidrug-Resistant Strain Isolated during Tigecycline Treatment.
PG  - e01337-14
AB  - Klbesiella pneumoniae is one of the most important human pathogens and frequently causes many
      diseases. To facilitate the comparative genome analysis in
      tigecycline resistance mechanism, we report the complete chromosomal sequence of
      a multidrug-resistance K. pneumoniae strain before tigecycline treatment for
      reference genome.
AU  - Hua X
AU  - Chen Q
AU  - Li X
AU  - Feng Y
AU  - Ruan Z
AU  - Yu Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01337-14.

PMID- 27587813
VI  - 4
DP  - 2016
TI  - Improved Complete Genome Sequence of the Extremely Radioresistant Bacterium Deinococcus radiodurans R1 Obtained Using PacBio Single-Molecule Sequencing.
PG  - e00886-16
AB  - The genome sequence of Deinococcus radiodurans R1 was published in 1999. We resequenced D.
      radiodurans R1 using PacBio and compared the sequence with the
      published one. Large insertions and single nucleotide polymorphisms (SNPs) were
      observed among the genome sequences. A more accurate genome sequence will be
      helpful to studies of D. radiodurans.
AU  - Hua X
AU  - Hua Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00886-16.

PMID- 23209232
VI  - 194
DP  - 2012
TI  - Genome Sequences of Two Multidrug-Resistant Acinetobacter baumannii Strains Isolated from a Patient before and after Treatment with Tigecycline.
PG  - 6979-6980
AB  - Acinetobacter baumannii is a Gram-negative bacterium which emerged as a significant nosocomial
      pathogen worldwide. To investigate the molecular basis of
      the tigecycline-resistant mechanism, we determined the genome sequences of two
      multidrug-resistant A. baumannii strains isolated from a patient before and after
      treatment with tigecycline.
AU  - Hua X
AU  - Zhou H
AU  - Jiang Y
AU  - Feng Y
AU  - Chen Q
AU  - Ruan Z
AU  - Yu Y
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6979-6980.

PMID- 10856254
VI  - 19
DP  - 2000
TI  - Crystal structure of NaeI - an evolutionary bridge between DNA endonuclease and topoisomerase.
PG  - 3110-3118
AB  - NaeI is transformed from DNA endonuclease to DNA topoisomerase and recombinase by a single
      amino acid substitution. The crystal structure of NaeI was solved at 2.3 A resolution and
      shows that NaeI is a dimeric molecule with two domains per monomer. Each domain contains one
      potential DNA recognition motif corresponding to either endonuclease or topoisomerase
      activity. The N-terminal domain core folds like the other type II restriction endonucleases as
      well as lambda-exonuclease and the DNA repair enzymes MutH and Vsr, implying a common
      evolutionary origin and catalytic mechanism. The C-terminal domain contains a catabolite
      activator protein (CAP) motif present in many DNA-binding proteins, including the type IA and
      type II topoisomerases. Thus, the NaeI structure implies that DNA processing enzymes evolved
      from a few common ancestors. NaeI may be an evolutionary bridge between endonuclease and DNA
      processing enzymes.
AU  - Huai Q
AU  - Colandene JD
AU  - Chen Y
AU  - Luo F
AU  - Zhao Y
AU  - Topal MD
AU  - Ke H
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 2000 19: 3110-3118.

PMID- 11473254
VI  - 8
DP  - 2001
TI  - Structure of NaeI-DNA complex reveals dual-mode DNA recognition and complete dimer rearrangement.
PG  - 665-669
AB  - NaeI, a novel DNA endonuclease, shows topoisomerase and recombinase activities when a Lys
      residue is substituted for Leu 43. The NaeI-DNA structure demonstrates that each of the two
      domains of NaeI recognizes one molecule of DNA duplex. DNA recognition induces dramatic
      rearrangements: narrowing the binding site of the Topo domain 16 angstroms to grip DNA,
      widening that
      of the Endo domain 8 angstroms to encircle and bend DNA 45 degrees for cleavage, and
      completely
      rebuilding the homodimer interface. The NaeI-DNA structure presents the first example of novel
      recognition of two copies of one DNA sequence by two different amino acid sequences and two
      different structural motifs in one polypeptide.
AU  - Huai Q
AU  - Colandene JD
AU  - Topal MD
AU  - Ke H
PT  - Journal Article
TA  - Nat. Struct. Biol.
JT  - Nat. Struct. Biol.
SO  - Nat. Struct. Biol. 2001 8: 665-669.

PMID- 8895094
VI  - 15
DP  - 1996
TI  - Splase: A new class IIS zinc-finger restriction endonuclease with specificity for Sp1 binding sites.
PG  - 481-489
AB  - A new restriction endonuclease, named Sp1ase, was constructed by genetically fusing the
      DNA-cleavage domain of the restriction endonuclease FokI with the zinc-finger DNA-binding
      domain of the transcription factor Sp1.  The resulting protein was expressed in Escherichia
      coli, partially purified, and shown to selectively digest plasmid DNA harboring consensus Sp1
      sites.  Sp1ase was also shown to selectively digest the long terminal repeat of the HIV-1 DNA
      at Sp1 sites.  Sp1ase recognizes a 10-bp DNA sequence and hydrolyzes phosphodiester bonds
      upstream of the binding sequence.  The binding specificity of Sp1ase makes this a "rare
      cutter" restriction enzyme which could be valuable in creating large DNA fragments for genome
      sequencing projects.  The result also presents the opportunity to create other restriction
      enzymes by altering the binding specificity of the zing-finger recognition helix.
AU  - Huang B
AU  - Schaeffer CJ
AU  - Li Q
AU  - Tsai M-D
PT  - Journal Article
TA  - J. Protein Chem.
JT  - J. Protein Chem.
SO  - J. Protein Chem. 1996 15: 481-489.

PMID- 26203343
VI  - 10
DP  - 2015
TI  - Complete genome sequence of Actinobacillus equuli subspecies equuli ATCC 19392(T).
PG  - 32
AB  - Actinobacillus equuli subsp. equuli is a member of the family Pasteurellaceae that is a common
      resident of the oral cavity and alimentary tract of healthy
      horses. At the same time, it can also cause a fatal septicemia in foals, commonly
      known as sleepy foal disease or joint ill disease. In addition, A. equuli subsp.
      equuli has recently been reported to act as a primary pathogen in breeding sows
      and piglets. To better understand how A. equuli subsp. equuli can cause disease,
      the genome of the type strain of A. equuli subsp. equuli, ATCC 19392(T), was
      sequenced using the PacBio RSII sequencing system. Its genome is comprised of
      2,431,533 bp and is predicted to encode 2,264 proteins and 82 RNAs.
AU  - Huang BF
AU  - Kropinski AM
AU  - Bujold AR
AU  - MacInnes JI
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 32.

PMID- 29472336
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Clostridium sp. Strain chh4-2 Isolated from Human Feces.
PG  - e00070-18
AB  - Here, we report the draft genome sequence of a Clostridium sp. strain isolated from a fecal
      sample of a 34-year-old adult male in Taiwan. This strain may
      represent a new bacterium, as suggested by a comparison based on whole-genome
      sequencing. The genome assembly comprised 6,089,737 bp, with a 45.63% G+C
      content.
AU  - Huang CH
AU  - Liou JS
AU  - Wang CL
AU  - Huang L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00070-18.

PMID- 29146835
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Bacillus cereus C1L, a Plant Growth-Promoting Rhizobacterium from the Rhizosphere of Formosa Lily in Taiwan.
PG  - e01290-17
AB  - Bacillus cereus C1L, a plant growth-promoting rhizobacterium, provides protection against
      fungal pathogens in monocot plants. To gain new insights into the
      biocontrol mechanisms used by this rhizobacterium, we determined the complete
      genome sequence of B. cereus C1L. One chromosome and three plasmids were
      identified with a total size of ~6.0 Mb.
AU  - Huang CJ
AU  - Zheng PX
AU  - Ou JY
AU  - Lin YC
AU  - Chen CY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01290-17.

PMID- 23105053
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Paenibacillus sp. Strain OSY-SE, a Bacterium Producing the Novel Broad-Spectrum Lipopeptide Antibiotic Paenibacterin.
PG  - 6306
AB  - A strain of Paenibacillus sp., OSY-SE, was isolated from soil and found to produce a novel
      lipopeptide antibiotic. The antibiotic, paenibacterin, is active
      against Gram-negative and Gram-positive bacterial pathogens. Paenibacterin is
      biosynthesized by a nonribosomal peptide synthetase pathway. Here we report the
      draft genome sequence of Paenibacillus sp. OSY-SE.
AU  - Huang E
AU  - Guo Y
AU  - Yousef AE
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6306.

PMID- 22887654
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Paenibacillus polymyxa OSY-DF, Which Coproduces a Lantibiotic, Paenibacillin, and Polymyxin E1.
PG  - 4739-4740
AB  - Paenibacillus polymyxa OSY-DF is a Gram-positive rod-shaped bacterium isolated from a
      fermented vegetable food. This bacterial strain displays potent
      antimicrobial activities against Gram-positive and Gram-negative pathogenic
      bacteria, attributed to the production of the lantibiotic paenibacillin and the
      colistin peptide polymyxin E1. Here we report the draft genome sequence of
      Paenibacillus polymyxa OSY-DF.
AU  - Huang E
AU  - Yousef AE
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4739-4740.

PMID- 4349491
VI  - 11
DP  - 1973
TI  - Analysis of simian virus 40 DNA with the restriction enzyme of Haemophilus aegyptius, endonuclease Z.
PG  - 508-514
AB  - Limited digestion of simian virus 40 (SV40) DNA from both small- and
      large-plaque strains with the restriction endonuclease Z from Haemophilus
      aegyptius yielded 10 specific fragments.  The number of nucleotide pairs for
      each fragment, determined by co-electrophoresis with PhiX174 RF fragments
      produced by endonuclease Z, ranges from 2,050 to 80.  The difference in the
      pattern between the large- and small-plaque strains is the disappearance of one
      fragment containing approximately 255 nucleotide pairs and the appearance of a
      new fragment with 145 nucleotide pairs.  This finding can be explained either
      by deletions or insertions totaling 110 nucleotide pairs.  Complementary RNA
      synthesized in vitro from the adeno-SV40 hybrid virus, strain ND-1, hybridized
      preferentially to four of the fragments of SV40 DNA.
AU  - Huang E-S
AU  - Newbold JE
AU  - Pagano JS
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1973 11: 508-514.

PMID- 29650579
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Raoultella ornithinolytica Strain HH3.
PG  - e00270-18
AB  - Raoultella ornithinolytica is a Gram-negative, nonmotile, encapsulated, and aerobic bacillus
      and an emerging hospital-related bacterial pathogen of humans.
      Here, we report a 5,977,517-bp draft genome sequence for Raoultella
      ornithinolytica strain HH3, isolated from a pretreatment sample collected at a
      Canadian wastewater treatment facility.
AU  - Huang H
AU  - Duceppe MO
AU  - Phipps-Todd B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00270-18.

PMID- 14612420
VI  - 23
DP  - 2003
TI  - The DIVa maturase binding site in the yeast group II intron aI2 is essential for intron homing but not for in vivo splicing.
PG  - 8809-8819
AB  - Splicing of the Saccharomyces cerevisiae mitochondrial DNA group II intron aI2 depends on the
      intron-encoded 62-kDa reverse transcriptase-maturase
      protein (p62). In wild-type strains, p62 remains associated with the
      excised intron lariat RNA in ribonucleoprotein (RNP) particles that are
      essential for intron homing. Studies of a bacterial group II intron showed
      that the DIVa substructure of intron domain IV is a high-affinity binding
      site for its maturase. Here we first present in vitro evidence extending
      that conclusion to aI2. Then, experiments with aI2 DIVa mutant strains
      show that the binding of p62 to DIVa is not essential for aI2 splicing in
      vivo but is essential for homing. Because aI2 splicing in the DIVa mutant
      strains remains maturase dependent, splicing must rely on other
      RNA-protein contacts. The p62 that accumulates in the mutant strains has
      reverse transcriptase activity, but fractionation experiments at high and
      low salt concentrations show that it associates more weakly than the
      wild-type protein with endogenous mitochondrial RNAs, and that phenotype
      probably explains the homing defect. Replacing the DIVa of aI2 with that
      of the closely related intron aI1 improves in vivo splicing but not
      homing, indicating that DIVa contributes to the specificity of the
      maturase-RNA interaction needed for homing.
AU  - Huang HR
AU  - Chao MY
AU  - Armstrong B
AU  - Wang Y
AU  - Lambowitz AM
AU  - Perlman PS
PT  - Journal Article
TA  - Mol. Cell. Biol.
JT  - Mol. Cell. Biol.
SO  - Mol. Cell. Biol. 2003 23: 8809-8819.

PMID- 26561516
VI  - 10
DP  - 2015
TI  - High quality draft genome sequence of the moderately halophilic bacterium Pontibacillus yanchengensis Y32(T) and comparison among Pontibacillus genomes.
PG  - 93
AB  - Pontibacillus yanchengensis Y32(T) is an aerobic, motile, Gram-positive, endospore-forming,
      and moderately halophilic bacterium isolated from a salt
      field. In this study, we describe the features of P. yanchengensis strain Y32(T)
      together with a comparison with other four Pontibacillus genomes. The 4,281,464
      bp high-quality-draft genome of strain Y32(T) is arranged into 153 contigs
      containing 3,965 protein-coding genes and 77 RNA encoding genes. The genome of
      strain Y32(T) possesses many genes related to its halophilic character, flagellar
      assembly and chemotaxis to support its survival in a salt-rich environment.
AU  - Huang J
AU  - Qiao ZX
AU  - Tang JW
AU  - Wang G
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 93.

PMID- 
VI  - 48
DP  - 2014
TI  - Developmental expression of Arabidopsis methyltransferase genes MET1, DRM2, and CMT3.
PG  - 681-687
AB  - Cytosine methylation is an epigenetic mark found in the genome of fungi, plants, and animals.
      DNA methylation is catalyzed by DNA methyltransferases. The function of DNA methyltransferases
      was shown to be highly conserved, but the biological role of these enzymes has not been
      clearly defined. We generated transgenic plants expressing METHYLTRANSFERASES::GUS reporter
      genes for three major DNA methyltransferases (MET1, DRM2 and CMT3) to gain insight into the
      potential physiological relevance of the individual members of the DNA methyltransferase
      family in Arabidopsis thaliana, and to investigate their expression patterns in detail. We
      found that METHYLTRANSFERASE::GUS genes display unique tissue, cell-type, and temporal
      patterns of expression throughout normal development, particularly in the flower. Our findings
      are supported by semi-quantitative reverse-transcription PCR, as well as by analyses of
      microarray databases. These data suggest that DNA methyltransferases may contribute to
      morphogenesis at every developmental stage and in every plant organ.
AU  - Huang J
AU  - Wang H
AU  - Liang W
AU  - Xie X
AU  - Guo G
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2014 48: 681-687.

PMID- 
VI  - 9
DP  - 2010
TI  - Roles of DNA methyltransferases in Arabidopsis development.
PG  - 8506-8514
AB  - DNA methylation plays a vital role during development in gene expression and chromatin
      organization. DNA methyl transferases catalyze the transfer of a methyl group to bases within
      the DNA helix. Plants differ from animals in having methylation at the sites of CHG and CHH.
      In plant, there are at least four classes of cytosine methyltransferase: MET1, CMT3, DRM and
      DNMT2. They show distinct expression patterns and levels in tissues and developmental stages
      and differential activity on cytosines in different sequence contexts. Mutations that cause
      severe loss of DNA methylation often leads to abnormal development. In the present review, we
      summarized recent findings of the three major DNA methyltransferases mutants playing vital
      role in development of Arabidopsis thaliana.
AU  - Huang JJ
AU  - Wang HH
AU  - Xie XJ
AU  - Zhang D
AU  - Liu Y
AU  - Guo GQ
PT  - Journal Article
TA  - Afr. J. Biotechnol.
JT  - Afr. J. Biotechnol.
SO  - Afr. J. Biotechnol. 2010 9: 8506-8514.

PMID- 24874673
VI  - 2
DP  - 2014
TI  - Genome Sequence of Sporolactobacillus terrae DSM 11697, the Type Strain of the Species.
PG  - e00465-14
AB  - Sporolactobacillus terrae DSM 11697 is the type strain of S. terrae. Here, we present a 3.2-Mb
      assembly of its genome sequence. As S. terrae is one of the
      important lactic acid bacteria, the genome sequence may provide insights into the
      molecular mechanism for its further microbial investigation.
AU  - Huang K
AU  - Ni J
AU  - Xu K
AU  - Tang H
AU  - Tao F
AU  - Xu P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00465-14.

PMID- 29371345
VI  - 6
DP  - 2018
TI  - Genome Sequence of Pseudomonas plecoglossicida Strain NZBD9.
PG  - e01412-17
AB  - Pseudomonas plecoglossicida NZBD9 is the causative agent of white nodules in cultured large
      yellow croaker in Fujian Province, China. We sequenced the genome
      of NZBD9 to gain a better understanding of the etiological agent. The genome
      sequence of the bacterium consists of 5.44 million bp, with a G+C content of
      61.9%.
AU  - Huang L
AU  - Zhao L
AU  - Su Y
AU  - Yan Q
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01412-17.

PMID- 6280151
VI  - 10
DP  - 1982
TI  - Digestion of highly modified bacteriophage DNA by restriction endonucleases.
PG  - 1579-1591
AB  - The ability of thirty Type II restriction endonucleases to cleave five
      different types of highly modified DNA has been examined.  The DNA substrates
      were derived from relatively large bacteriophage genomes which contain all or
      most of the cytosine or thymine residues substitutes at the 5-position.  These
      substituents were a proton (PBS1 DNA), a hydroxymethyl group (SP01 DNA), a
      methyl group (XP12 DNA), a glucosylated 4,5-dihydroxypentyl group (SP15 DNA).
      Although PBS1 DNA and SP01 DNA were digested by most of the enzymes, they were
      cleaved much more slowly than was normal DNA by many of them.
      5-Methyl-cytosine-rich XP12 DNA and the multiply modified T4 and SP15 DNAs were
      resistant to most of these endonucleases.  The only enzyme that cleaved all
      five of these DNAs was TaqI, which fragmented them extensively.
AU  - Huang L-H
AU  - Farnet CM
AU  - Ehrlich KC
AU  - Ehrlich M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1982 10: 1579-1591.

PMID- 7056404
VI  - 41
DP  - 1982
TI  - Digestion of highly modified phage DNA by restriction endonucleases.
PG  - 1199
AB  - The ability of thirty TypeII restriction endonucleases to cleave five different
      types of highly modified DNA has been examined.  The substrate DNAs were
      derived from relatively large bacteriophage genomes which contain all or most
      of the cytosine or thymine residues substituted at the 5-position.  These
      substituents were a proton (PBS1 DNA), a hydroxymethyl group (SP01 DNA), a
      methyl group (XP12 DNA), a glucosylated hydroxymethyl group (T4 DNA) or a
      phosphoglucuronated, glucosylated 4,5-dihydroxypentyl group (SP15 DNA).  While
      PBSI DNA and SP01 DNA were cleaved many times by most of the enzymes, they were
      cleaved much more slowly than was normal DNA by many of them.
      5-Methylcytosine-rich XP12 DNA and the multiply modified T4 and SP15 DNAs were
      resistant to most of the enzymes.  The only enzyme which cleaved all of these
      DNAs was TaqI; TaqI fragmented the five highly modified DNAs extensively.  The
      TaqI fragments from XP12 DNA were susceptible to ligation catalyzed by T4 DNA
      ligase.
AU  - Huang LH
AU  - Farnet C
AU  - Ehrlich KC
AU  - Ehrlich M
PT  - Journal Article
TA  - Fed. Proc.
JT  - Fed. Proc.
SO  - Fed. Proc. 1982 41: 1199.

PMID- 12506195
VI  - 100
DP  - 2003
TI  - Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase.
PG  - 68-73
AB  - DNA methylation, various DNA repair mechanisms, and possibly early events in the opening of
      DNA as required for transcription and replication are
      initiated by flipping of a DNA base out of the DNA double helix. The
      energetics and structural mechanism of base flipping in the presence of
      the DNA-processing enzyme, cytosine 5-methyltransferase from HhaI
      (M.HhaI), were obtained through molecular dynamics based upon free-energy
      calculations. Free-energy profiles for base flipping show that, when in
      the closed conformation, M.HhaI lowers the free-energy barrier to flipping
      by 17 kcalmol and stabilizes the fully flipped state. Flipping is shown to
      occur via the major groove of the DNA. Structural analysis indicates that
      flipping is facilitated by destabilization of the DNA double-helical
      structure and substitution of DNA base-pairing and base-stacking
      interactions with DNA-protein interactions. The fully flipped state is
      stabilized by DNA-protein interactions that are enhanced upon binding of
      coenzyme. This study represents an atomic detail description of the
      mechanism by which a protein facilitates specific structural distortion in
      DNA.
AU  - Huang N
AU  - Banavali NK
AU  - MacKerell AD Jr
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2003 100: 68-73.

PMID- 15571720
VI  - 345
DP  - 2005
TI  - Specificity in protein-DNA interactions: Energetic recognition by the (cytosine-C5)-methyltransferase from HhaI.
PG  - 265-274
AB  - Sequence-specific interactions between proteins and DNA are essential for a variety of
      biological functions. The
      (cytosine-C5)-methyltransferase from HhaI (M.HhaI) specifically
      modifies the second base in GCGC sequences, employing a
      base flipping mechanism to access the target base being chemically
      modified. The mechanism of sequence-specific recognition of M.HhaI is
      not evident based on crystallographic structures, leading to the
      suggestion that recognition is linked to the flipping event itself, a
      process that may be referred to as energetic recognition. Using
      computational methods, it is shown that the free energy barriers to
      flipping are significantly higher in non-cognate versus the cognate
      sequence, supporting the energetic recognition mechanism. Energetic
      recognition is imparted by two protein "selectivity filters" that
      function via a "web" of protein-DNA interactions in short-lived, high
      energy states present along the base flipping pathway. Other
      sequence-specific DNA binding proteins whose function involves
      significant distortion of DNA's conformation may use a similar
      recognition mechanism.
AU  - Huang N
AU  - MacKerell AD
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2005 345: 265-274.

PMID- Not carried by PubMed...
VI  - 42
DP  - 1996
TI  - Studies on chemical modification and kinetics of restriction endonuclease Bsp78I.
PG  - 233-236
AB  - Restriction endonuclease Bsp78I from Bacillus sphaericus 78 has been isolated and purified.
      The purified enzyme was found to be homogeneous.  Michaelis constant of the enzyme is 2.67 x
      10^-8mol /L (substrate is pBR322 DNA).  The role of specific amino acid residues in Bsp78I was
      assayed by chemical modifications.  Sulfhydryl groups were modified with
      p-chloromercuribenzoic acid, lysine residues with pyridoxal-5'-phosphate and arginine
      residues with 2,3-butanedione.  The results show that these residues are related to the
      activity of Bsp78I.
AU  - Huang N
AU  - Zou G
AU  - Cao X
AU  - Zhu R
PT  - Journal Article
TA  - Wuhan Daxue Xuebao
JT  - Wuhan Daxue Xuebao
SO  - Wuhan Daxue Xuebao 1996 42: 233-236.

PMID- 29700133
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Novosphingobium sp. Strain HII-3, a Bacterium Capable of Degrading the Cembranoid alpha(beta)-2,7,11-Cembratriene-4,6-Diol to Farnesal.
PG  - e00136-18
AB  - Novosphingobium sp. HII-3, the first bacterium confirmed to degrade the cembranoid
      alpha(beta)-2,7,11-cembratriene-4,6-diol to farnesal, was isolated
      from cured tobacco leaf in Henan, China. Here, we report the annotated draft
      genome sequence of strain HII-3, which has an estimated size of 4.45 Mb and
      comprises 4,072 coding sequences.
AU  - Huang S
AU  - Qian Y
AU  - Wei T
AU  - Jia C
AU  - Yang P
AU  - Mao D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00136-18.

PMID- 27231379
VI  - 4
DP  - 2016
TI  - First Complete Genome Sequence of a Subdivision 6 Acidobacterium Strain.
PG  - e00469-16
AB  - Although ubiquitous and abundant in soils, acidobacteria have mostly escaped isolation and
      remain poorly investigated. Only a few cultured representatives and
      just eight genomes of subdivisions 1, 3, and 4 are available to date. Here, we
      determined the complete genome sequence of strain HEG_-6_39, the first genome of
      Acidobacterium subdivision 6.
AU  - Huang S
AU  - Vieira S
AU  - Bunk B
AU  - Riedel T
AU  - Sproer C
AU  - Overmann J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00469-16.

PMID- 24482523
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Pseudomonas nitroreducens Strain TX1, Which Degrades Nonionic Surfactants and Estrogen-Like Alkylphenols.
PG  - e01262-13
AB  - Pseudomonas nitroreducens TX1 ATCC PTA-6168 was isolated from rice field drainage in Taiwan.
      The bacterium is of special interest because of its capability to use
      nonionic surfactants (alkylphenol polyethoxylates) and estrogen-like compounds
      (4-t-octylphenol and 4-nonylphenol) as a sole carbon source. This is the first
      report on the genome sequence of P. nitroreducens.
AU  - Huang SL
AU  - Chen H
AU  - Hu A
AU  - Tuan NN
AU  - Yu CP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01262-13.

PMID- 22328755
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Staphylococcus aureus M013, a pvl-Positive, ST59-SCCmec Type V Strain Isolated in Taiwan.
PG  - 1256-1257
AB  - We report the complete genome sequence of M013, a representative strain of a pvl-positive,
      sequence type 59-staphylococcal cassette chromosome mec type V
      (ST59-SCCmec type V) community-associated methicillin-resistant Staphylococcus
      aureus (CA-MRSA) clone in Taiwan. Comparison of M013 with the genomes of two
      CA-MRSA strains in the United States revealed major differences in the regions
      covering several genomic islands and prophages.
AU  - Huang TW
AU  - Chen FJ
AU  - Miu WC
AU  - Liao TL
AU  - Lin AC
AU  - Huang IW
AU  - Wu KM
AU  - Tsai SF
AU  - Chen YT
AU  - Lauderdale TL
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1256-1257.

PMID- 23658651
VI  - 8
DP  - 2013
TI  - Copy Number Change of the NDM-1 Sequence in a Multidrug-Resistant Klebsiella pneumoniae Clinical Isolate.
PG  - e62774
AB  - The genetic features of the antimicrobial resistance of a multidrug resistant Klebsiella
      pneumoniae strain harboring blaNDM-1
      were investigated to increase our understanding of the evolution of NDM-1. The strain, KPX,
      came from a Taiwanese patient with a hospitalization history in New Delhi. Complete DNA
      sequencing was performed; and the genes responsible for antimicrobial resistance were
      systematically examined and isolated by library screening. KPX harbored two resistance
      plasmids, pKPX-1 and pKPX-2, which are 250-kb and 141-kb in size, respectively, with blaNDM-1
      present on pKPX-1. The plasmid pKPX-1 contained genes associated with the IncR and IncF
      groups, while pKPX-2 belonged to the IncF family. Each
      plasmid carried multiple antimicrobial resistance genetic determinants. The gene responsible
      for resistance to carbapenems was found on pKPX-1 and that for resistance to aztreonam was
      found on pKPX-2. To our surprise, we discovered that blaNDM-1 exists on pKPX-1 as multiple
      copies in the form of tandem repeats. Amplification of blaNDM-1 was found to occur by
      duplication of an 8.6-kb unit, with the copy number of the repeat varying from colony to
      colony. This repeat sequence is identical to that of the pNDM-MAR except for two base
      substitutions. The copy number of blaNDM-1 of colonies under
      different conditions was assessed by Southern blotting and quantitative PCR. The blaNDM-1
      sequence was maintained in the presence of the antimicrobial selection; however, removal of
      antimicrobial selection led to the emergence of susceptible bacterial populations with a
      reduced copy number or even the complete loss of the blaNDM-1 sequence. The dynamic nature of
      the NDM-1 sequence provides a strong argument for judicious use of the broad-spectrum
      antimicrobials in order to reduce the development and spread of antimicrobial resistance among
      pathogens.
AU  - Huang TW
AU  - Chen TL
AU  - Chen YT
AU  - Lauderdale TL
AU  - Liao TL
AU  - Lee YT
AU  - Chen CP
AU  - Liu YM
AU  - Lin AC
AU  - Chang YH
AU  - Wu KM
AU  - Kirby R
AU  - Lai JF
AU  - Tan MC
AU  - Siu LK
AU  - Chang CM
AU  - Fung CP
AU  - Tsai SF
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2013 8: e62774.

PMID- 25676758
VI  - 3
DP  - 2015
TI  - Genome Sequence of Borrelia chilensis VA1, a South American Member of the Lyme Borreliosis Group.
PG  - e01535-14
AB  - Borrelia chilensis strain VA1 is a recently described South American member of the Borrelia
      burgdorferi sensu lato complex from Chile. Whole-genome sequencing
      analysis determined its linear chromosome and plasmids lp54 and cp26, confirmed
      its membership in the Lyme borreliosis group, and will open new research avenues
      regarding its pathogenic potential.
AU  - Huang W
AU  - Ojaimi C
AU  - Fallon JT
AU  - Travisany D
AU  - Maass A
AU  - Ivanova L
AU  - Tomova A
AU  - Gonzalez-Acuna D
AU  - Godfrey HP
AU  - Cabello FC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01535-14.

PMID- 6279321
VI  - 4
DP  - 1982
TI  - A simplified method for preparation of restriction endonuclease BamHI.
PG  - 60-62
AB  - A simplified method for preparation of restriction endonuclease BamHI was described.  With P11
      cellulose column chromatography, the exonuclease and nonspecific endonuclease activity in the
      crude extract could be removed and the activity of BamHI enriched by 10^5 fold.  The enzyme
      preparation thus made might be used for genetic manipulation.
AU  - Huang X
AU  - Jiang W
AU  - Zhang F
AU  - Liang Z
PT  - Journal Article
TA  - Zhongguo Yi Xue Ke Xue Yuan Xue Bao
JT  - Zhongguo Yi Xue Ke Xue Yuan Xue Bao
SO  - Zhongguo Yi Xue Ke Xue Yuan Xue Bao 1982 4: 60-62.

PMID- 26826230
VI  - 82
DP  - 2016
TI  - Characterization of a highly arginolytic Streptococcus species that potently antagonizes Streptococcus mutans.
PG  - 2187
AB  - The ability of certain oral biofilm bacteria to moderate pH through arginine metabolism by the
      arginine deiminase system (ADS) is a deterrent to the development of dental caries. Here, we
      characterize a novel Streptococcus strain, designated strain A12, isolated from supragingival
      dental plaque of a caries-free individual. A12 not only expressed the ADS pathway at high
      levels under a variety of conditions but also effectively inhibited growth and two
      intercellular signaling pathways of the dental caries pathogen Streptococcus mutans. A12
      produced copious amounts of H2O2 via the pyruvate oxidase enzyme that were sufficient to
      arrest the growth of S. mutans. A12 also produced a protease similar to challisin (Sgc) of
      Streptococcus gordonii that was able to block the competence-stimulating peptide (CSP)-ComDE
      signaling system, which is essential for bacteriocin production by S. mutans. Wild-type A12,
      but not an sgc mutant derivative, could protect the sensitive indicator strain Streptococcus
      sanguinis SK150 from killing by the bacteriocins of S. mutans. A12, but not S. gordonii, could
      also block the XIP (comX-inducing peptide) signaling pathway, which is the proximal regulator
      of genetic competence in S. mutans, but Sgc was not required for this activity. The complete
      genome sequence of A12 was determined, and phylogenomic analyses compared A12 to streptococcal
      reference genomes. A12 was most similar to Streptococcus australis and Streptococcus
      parasanguinis but sufficiently different that it may represent a new species. A12-like
      organisms may play crucial roles in the promotion of stable, health-associated oral biofilm
      communities by moderating plaque pH and interfering with the growth and virulence of caries
      pathogens.
AU  - Huang X
AU  - Palmer S
AU  - Ahn SJ
AU  - Richards VP
AU  - Williams ML
AU  - Nascimento MM
AU  - Burne RA
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2016 82: 2187.

PMID- 28428310
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Pseudomonas protegens H78, a Plant Growth-Promoting Rhizobacterium.
PG  - e00233-17
AB  - The plant growth-promoting rhizobacterium Pseudomonas protegens H78, which was isolated from
      the rhizosphere of oilseed rape in Shanghai, can produce a large
      array of antibiotics with a broad spectrum of activities. Here, we report the
      annotated complete genome sequence of P. protegens H78.
AU  - Huang X
AU  - Wang Z
AU  - Liu Y
AU  - Zhang X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00233-17.

PMID- 23773292
VI  - 14
DP  - 2013
TI  - High-throughput sequencing of methylated cytosine enriched by modification-dependent restriction endonuclease MspJI.
PG  - 56
AB  - Background: As a well-known epigenomic modification, DNA methylation is found to be common in
      plants and plays an important role in many
      biological processes. Relying on the unique feature of
      methylation-dependent digestion, the family of methylation-requiring
      restriction-like endonuclease, such as MspJI and its homologs, was
      suggested for a potential usage in methylation detection.
      Results: In this study, we combine MspJI digestion and
      electrophoretic band selection with next generation high-throughput
      sequencing technology to detect 5-methylcytosines in Arabidopsis
      genome. By developing a bioinformatics workflow to attribute the CNNR
      sites recognized by MspJI to the reference genome, we fulfilled the
      systematic assessment of this method.
      Conclusions: According to the assessment, here we provide the
      method for generating a detailed map of plant methylome that could be
      feasible, reliable and economical in methylation investigation.
AU  - Huang XJ
AU  - Lu HL
AU  - Wang JW
AU  - Xu LQ
AU  - Liu SY
AU  - Sun JH
AU  - Gao F
PT  - Journal Article
TA  - BMC Genet.
JT  - BMC Genet.
SO  - BMC Genet. 2013 14: 56.

PMID- 25977438
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Oleiagrimonas soli 3.5XT, a Type Species in a Newly Identified Genus, Isolated from an Oil Field in China.
PG  - e00469-15
AB  - Oleiagrimonas gudaosoli 3.5X(T) was isolated from an oil field and identified as  a new member
      of a novel genus. The draft genome sequence of this strain, which
      comprises 3,379,958 bp encoding 3,010 open reading frames (ORFs), can provide
      insight into the life style of this newly identified genus in
      petroleum-contaminated soil.
AU  - Huang Y
AU  - Fang T
AU  - Wang H
AU  - Zhou H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00469-15.

PMID- 2323503
VI  - 4
DP  - 1990
TI  - The inhibition of RecA-mediated strand exchange by adducts of azacytosine-containing DNA and EcoRII methylase.
PG  - A2294
AB  - Recovery of cells from treatment with 5-azacytidine is dependent on the recA,
      recBC pathway.  Cells containing DNA (cytosine-5) methylases which form tight
      binding complexes with azacytosine containing DNA (azaC-DNA) are more sensitive
      to the drug than cells lacking them.  We therefore studied the effect of these
      complexes on recA mediated strand exchange in vitro.  32P labelled 422 bp DNA
      fragment containing three binding sites for the EcoRII methylase and
      azacytosine in the (-) strand was prepared.  We investigated the effect of the
      EcoRII methylase on recA mediated strand exchange of the fragment with
      homologous M13 DNA by electrophoresis on agarose gels.  In the absence of the
      methylase, azaC-DNA has the same rate and extent of strand exchange as control
      DNA.  But in the presence of the methylase incorporation of duplexes into
      recA-ssDNA complexes is decreased from 80-90% to 10%, and strand exchange is
      completely inhibited.  Since there is no incorporation of duplexes with
      heterologous acceptor ssDNA, or in the absence of ATP, the incoporation of
      azaC-DNA duplexes in the presence of methylase is believed to occur by partial
      pairing of duplexes with homologous ssDNA leading to the formation of an
      inactive complex composed of the methylase, dsDNA and recA-ssDNA complexes.
AU  - Huang Y
AU  - Friedman S
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1990 4: A2294.

PMID- 1894630
VI  - 266
DP  - 1991
TI  - Inhibition of recA-mediated strand exchange by adducts of Azacytosine-containing DNA and the EcoRII methylase.
PG  - 17424-17429
AB  - Wild type Escherichia coli cells containing elevated levels of DNA (cytosine-5)
      methyltransferases have increased sensitivity to the toxic effects of
      5-azacytidine.  The methyltransferases form tight binding complexes with
      azacytosine in DNA which could interfere with the recA recBCD repair pathway
      which is largely responsible for cell survival after treatment with the drug.
      We therefore determined if these complexes interfered with recA-mediated strand
      exchange in vitro, 32P-labeled DNA fragments containing a single EcoRII site,
      with cytosine in the (-) strand replaced by 5-azacytosine, were prepared.  We
      investigated the effect of the EcoRII methyltransferase on recA-mediated strand
      exchange with homologous M13 DNA by electrophoresis in agarose gels.  In the
      absence of the methylase the rate and extent of strand exchange of
      azacytosine-containing DNA is the same as control DNA.  In the presence of the
      methyltransferase strand exchange is inhibited, but some incorporation of
      duplexes into recA-single-stranded DNA (ssDNA) complexes still occurs.  The
      formation of these complexes is dependent on the length of the fragment 3' to
      the methylase binding site on the strand complementary to the ssDNA.  The
      greater the length the greater the number of complexes that form.
      S-Adenosyl-L-methionine, which enhances binding of the methyltransferase to
      azacytosine-containing DNA, causes an increase in the inhibition of strand
      exchange and an increase in the number of inactive complexes formed.  The
      complexes can be dissociated with guanidinium chloride which denatures the
      methyltransferase and leads to release of the (+) strand.  The (-) strand
      remains associated with the ssDNA.  This result implies that a plectonemic
      joint is formed between recA-ssDNA complexes and azacytosine-containing
      DNA-methyltransferase complexes.  However, branch migration in these complexes
      is inhibited.  Denaturation of the methyltransferase allows branch migration to
      proceed to completion, releasing the (+) strand.
AU  - Huang Y
AU  - Friedman S
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1991 266: 17424-17429.

PMID- 29472343
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Sphingobacterium sp. Strain HMA12, Which Encodes Endo-beta-N-Acetylglucosaminidases and Can Specifically Hydrolyze  Fucose-Containing Oligosaccharides.
PG  - e01525-17
AB  - The genome sequence of the soil bacterium Sphingobacterium sp. strain HMA12, the  culture
      supernatant of which exhibited endo-beta-N-acetylglucosaminidase (ENGase)
      activity, was examined for ENGase-encoding genes. Here, we report the
      characterization of new genes of ENGases, obtained by whole-genome shotgun
      sequencing, that are capable of specifically hydrolyzing fucose-containing
      oligosaccharides.
AU  - Huang Y
AU  - Higuchi Y
AU  - Mori K
AU  - Yamashita R
AU  - Okino N
AU  - Tashiro K
AU  - Takegawa K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01525-17.

PMID- 23144396
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of the Fish Pathogen Vibrio harveyi Strain ZJ0603.
PG  - 6644-6645
AB  - Vibrio harveyi is an important pathogen that causes vibriosis in various aquatic  organisms.
      Here, we announce the draft genome sequence of V. harveyi strain
      ZJ0603, which was isolated from diseased Orange-spotted grouper (Epinephelus
      coioides) in Guangdong, China.
AU  - Huang Y
AU  - Jian J
AU  - Lu Y
AU  - Cai S
AU  - Wang B
AU  - Tang J
AU  - Pang H
AU  - Ding Y
AU  - Wu Z
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6644-6645.

PMID- 22374962
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Facultative Anaerobic Arsenite-Oxidizing and Nitrate-Reducing Bacterium Acidovorax sp. Strain NO1.
PG  - 1635-1636
AB  - Acidovorax sp. strain NO1, isolated from gold mine soil, was shown to be a facultative
      anaerobic arsenite-oxidizing and nitrate-reducing bacterium. The
      reported draft genome predicts the presence of genes involved in arsenic
      metabolism, nitrate reduction, phosphate transport, and multiple metal
      resistances and indicates putative horizontal gene transfer events.
AU  - Huang Y
AU  - Li H
AU  - Rensing C
AU  - Zhao K
AU  - Johnstone L
AU  - Wang G
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1635-1636.

PMID- 29800340
VI  - 73
DP  - 2018
TI  - Emergence of an XDR and carbapenemase-producing hypervirulent Klebsiella pneumoniae strain in Taiwan.
PG  - 20392046
AB  - Background: Carbapenemase-producing Klebsiella pneumoniae causes high mortality
      owing to the limited therapeutic options available. Here, we investigated an
      emergent carbapenem-resistant K. pneumoniae strain with hypervirulence found
      among KPC-2-producing strains in Taiwan. Methods: KPC-producing K. pneumoniae
      strains were collected consecutively from clinical specimens at the Taipei
      Veterans General Hospital between January 2012 and December 2014. Capsular types
      and the presence of rmpA/rmpA2 were analysed, and PFGE and MLST performed using
      these strains. The strain positive for rmpA/rmpA2 was tested in an in vivo mouse
      lethality study to verify its virulence and subjected to WGS to delineate its
      genomic features. Results: A total of 62 KPC-2-producing K. pneumoniae strains
      were identified; all of these belonged to ST11 and capsular genotype K47. One
      strain isolated from a fatal case with intra-abdominal abscess (TVGHCRE225)
      harboured rmpA and rmpA2 genes. This strain was resistant to tigecycline and
      colistin, in addition to carbapenems, and did not belong to the major cluster in
      PFGE. TVGHCRE225 exhibited high in vivo virulence in the mouse lethality
      experiment. WGS showed that TVGHCRE225 acquired a novel hybrid virulence plasmid
      harbouring a set of virulence genes (iroBCDN, iucABCD, rmpA and rmpA2, and iutA)
      compared with the classic ST11 KPC-2-producing strain. Conclusions: We identified
      an XDR ST11 KPC-2-producing K. pneumoniae strain carrying a hybrid virulent
      plasmid in Taiwan. Active surveillance focusing on carbapenem-resistant
      hypervirulent K. pneumoniae strains is necessary, as the threat to human health
      is imminent.
AU  - Huang YH
AU  - Chou SH
AU  - Liang SW
AU  - Ni CE
AU  - Lin YT
AU  - Huang YW
AU  - Yang TC
PT  - Journal Article
TA  - J. Antimicrob. Chemother.
JT  - J. Antimicrob. Chemother.
SO  - J. Antimicrob. Chemother. 2018 73: 20392046.

PMID- 10581261
VI  - 153
DP  - 1999
TI  - Role of exonucleolytic degradation in group I intron homing in phage T4.
PG  - 1501-1512
AB  - Homing of the phage T4 td intron is initiated by the intron-encoded endonuclease I-TevI, which
      cleaves the intronless allele 23 and 25 nucleotides upstream of the intron insertion site
      (IS). The distance between the I-TevI cleavage site (CS) and IS implicates endo- and/or
      exonuclease activities to resect the DNA segment between the IS and CS. Furthermore, 3' tails
      must presumably be generated for strand invasion by 5'-3' exonuclease activity. Three
      experimental approaches were used to probe for phage nucleases involved in homing: a
      comparative analysis of in vivo homing levels of nuclease-deficient phage, an in vitro assay
      of nuclease activity and specificity, and a coconversion analysis of flanking exon markers. It
      was thereby demonstrated that T4 RNase H, a 5'-3' exonuclease, T4 DNA exonuclease A (DexA)
      and the exonuclease activity of T4 DNA polymerase (43Exo), 3'-5' exonucleases, play a role
      in intron homing. The absence of these functions impacts not only homing efficiency but also
      the extent of degradation and flanking marker coconversion. These results underscore the
      critical importance of the 3' tail in intron homing, and they provide the first direct
      evidence of a role for 3' single-stranded DNA ends as intermediates in T4 recombination.
      Also, the involvement of RNase H, DexA, and 43Exo in homing provides a clear example of the
      harnessing of functions variously involved in phage nucleic acid metabolism for intron
      propagation.
AU  - Huang YJ
AU  - Parker MM
AU  - Belfort M
PT  - Journal Article
TA  - Genetics
JT  - Genetics
SO  - Genetics 1999 153: 1501-1512.

PMID- 26044425
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Agrobacterium tumefaciens Ach5.
PG  - e00570-15
AB  - Agrobacterium tumefaciens is a phytopathogenic bacterium that causes crown gall disease. The
      strain Ach5 was isolated from yarrow (Achillea ptarmica L.) and is
      the wild-type progenitor of other derived strains widely used for plant
      transformation. Here, we report the complete genome sequence of this bacterium.
AU  - Huang YY
AU  - Cho ST
AU  - Lo WS
AU  - Wang YC
AU  - Lai EM
AU  - Kuo CH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00570-15.

PMID- 1337330
VI  - 37
DP  - 1992
TI  - Biological function of DNA methylation.
PG  - 323-329
AB  - Structural and functional properties of prokaryotic DNA methyltransferases are summarized. The
      different aspects of the role of DNA methylation which influences DNA-protein interaction in
      restriction and modification of DNA and in mismatch repair, DNA replication and gene
      expression are discussed.
AU  - Hubacek J
PT  - Journal Article
TA  - Folia Microbiol. (Praha)
JT  - Folia Microbiol. (Praha)
SO  - Folia Microbiol. (Praha) 1992 37: 323-329.

PMID- 4589330
VI  - 79
DP  - 1973
TI  - Functional analysis of second-step host specificity mutations in unstable escherichia coli heterozygotes.
PG  - 257-264
AB  - From an Escherichia coli strain K12 carrying a temperature-sensitive host-specific
      modification (hsm) mutation, second-step mutants have been isolated that are completely
      deficient in modification and restriction. Complementation analysis has revealed that one
      group of these mutants is impaired in the specificity gene hss, while in the other group of
      mutant strains both mutations, i.e. the first-step temperature-sensitive and the second-step
      which impairs restriction and modification completely, are located in hsm. Analysis of the
      heterozygotes used in the complementation experiments suggested a cis- and tandem arrangement
      of the hs and leu genes in haploid, segregating exconjugants; however, the attachement of
      these genes to a cryptic plasmid was not excluded.
AU  - Hubacek J
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1973 79: 257-264.

PMID- 4916553
VI  - 50
DP  - 1970
TI  - Complementation analysis of temperature-sensitive host specificity mutations in Escherichia coli.
PG  - 111-127
AB  - A selection procedure was devised for the isolation of temperature-sensitive
      mutants of Escherichia coli K12 unable to restrict foreign DNA.  Many of the
      non-restricting mutants isolated also displayed temperature sensitivity in the
      modification of DNA.  The mutations were shown to map in the hs cluster of
      genes which determine the host specificity of DNA in E. coli.  The kinetics of
      inactivation of restriction showed that a short exposure to high temperature
      was sufficient to impair restriction of phage lambda DNA and that after shift
      to low temperature restriction did not return to the wild-type level until a
      period of growth had occurred.  One of the mutants was used as a starting
      strain from which further mutants were then selected for their inability to
      host-modify DNA.  Many of the mutants thus isolated, in addition to being
      impaired in modification, were found to be non-restricting at both high and low
      temperatures.  A complementation analysis of the mutants was carried out using
      an F' donor strain derived from E. coli B and carrying the host-specificity
      genes hssB+ hsr- hsm+.  In all but one of the F' merodiploids constructed
      between this F' and the temperature-sensitive host specificity mutants of E.
      coli K the temperature-sensitivity of the mutant phenotype was complemented and
      the merodiploids displayed K-and B-specific restriction and K- and B-specific
      modification.  From these results it is concluded that all of the
      temperature-sensitive mutants carry mutations in the hsm gene, and are hssK+
      hsr+ hsmts.  In addition it is argued that an hsm-directed polypeptide is
      required for restriction in addition to polypeptides directed by hssK and hsr.
      These results are discussed in terms of models based on the interaction of
      subunits to form oligomeric enzymes.
AU  - Hubacek J
AU  - Glover SW
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1970 50: 111-127.

PMID- 9821288
VI  - 43
DP  - 1998
TI  - The effect of recA mutation on the expression of EcoKI and EcoR124I hsd genes cloned in a multicopy plasmid.
PG  - 353-359
AB  - Type I restriction-modification endonucleases are composed of three subunits - HsdR, required
      for restriction, and HsdM and HsdS which can produce a separate DNA methyltransferase.  The
      HsdS subunit is required for DNA recognition.  In this paper we describe the effect of cloned
      EcoKI and EcoR124I hsd genes on the resulting R-M phenotype.  The variability in the
      expression of the wild type restriction phenotype after cloning of the wt hsd genes in a
      multicopy plasmid in Escherichia coli recA+ background suggests that the increased production
      of the restriction endonuclease from pBR322 is detrimental to the cell and this leads to the
      deletion of the cloned hsd genes from the hybrid plasmid and/or inactivation of the enzyme.
      The effect of a mutation in the E. coli recA gene on the expression of the R-M phenotype is
      described and discussed in relation to the role of the cell surface and the localization of
      the restriction endonuclease in the cell.
AU  - Hubacek J
AU  - Holubova I
AU  - Weiserova M
PT  - Journal Article
TA  - Folia Microbiol. (Praha)
JT  - Folia Microbiol. (Praha)
SO  - Folia Microbiol. (Praha) 1998 43: 353-359.

PMID- 
VI  - 0
DP  - 1985
TI  - Biological function of type I restriction enzymes.
PG  - 95-109
AB  - Type I restriction enzymes are structurally and functionally so complicated that it was often
      argued that they must perform some vital functions other than restriction and modification of
      DNA. Using a genetic approach that was found to be so fruitful in the past we analyzed
      temperature-sensitive (ts) mutations affecting restriction and modification. The concept of a
      gene, designated hsd.X, which seems to be located outside the hsd operon, was formulated and
      the role of its product in the regulation of expression of restriction and modification and in
      the initiation of DNA replication is discussed. Further, we tried to establish if the
      individual subunits of the type I restriction enzyme from E. coli K12 play some role in
      mini-Mu and Tn9 transposition mechanisms.
AU  - Hubacek J
AU  - Weiserova M
PT  - Journal Article
TA  - Gene Manipulation and Expression
JT  - Gene Manipulation and Expression
SO  - Gene Manipulation and Expression 1985 0: 95-109.

PMID- 6251160
VI  - 119
DP  - 1980
TI  - DNA restriction and modification in Escherichia coli: Functional analysis of the role of the dnaC(D) gene product.
PG  - 231-238
AB  - Escherichia coli strain PC-7 carries two independent temperature-sensitive mutations, one
      affecting the restriction and modification (R-M) phenotype and the other the DNAC(D)
      phenotype. The results of complementation and P1 transduction analysis of the mutation
      affecting the R-M phenotype implicate a fourth gene, designated hsdX, located close to the hsd
      three-gene complex. The properties of merodiploids constructed between appropriate recipients
      and F' elements with different mutations in hsdS, hsdR and hsdM genes might indicate that in
      strain PC-7 the temperature-sensitive products, determined by hsdR and hsdDK cistrons, are
      synthesized. The role of the temperature-sensitive dnaC(D) gene product in the formation of
      the restriction endonuclease was studied and no direct relation was found between the DnaC(D)
      and R-M phenotypes.
AU  - Hubacek J
AU  - Weiserova M
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1980 119: 231-238.

PMID- 7959434
VI  - 39
DP  - 1994
TI  - Restriction endonucleases R.EcoKI and R.EcoR124I are probably located in different environments within the bacterial cell.
PG  - 162-165
AB  - We describe the phenomenon of a transient state of R124I restriction deficiency after
      long-term storage of the E. coli [pCP1005] strain at 4oC, or after growth of the culture in
      synthetic M9 medium with the nonmutagenic solvent dimethyl sulfoxide. The unusual high
      reversion from the R+124 to the R-124 phenotype was observed only in E. coli strain
      transformed with the high-copy number plasmid pCP1005 carrying EcoR124I hsdR, M and S genes
      cloned, but not with strains carrying the natural conjugative plasmid R124. The effect of both
      treatments on the expression of EcoR124I phenotype in relation to the possible location of
      R.EcoR124I restriction endonuclease in E. coli is discussed.
AU  - Hubacek J
AU  - Weiserova M
AU  - Janscak P
AU  - Firman K
PT  - Journal Article
TA  - Folia Microbiol. (Praha)
JT  - Folia Microbiol. (Praha)
SO  - Folia Microbiol. (Praha) 1994 39: 162-165.

PMID- 2693592
VI  - 135
DP  - 1989
TI  - The location of a temperature-sensitive trans-dominant mutation and its effect on restriction and modification in Escherichia coli K12.
PG  - 3057-3065
AB  - An Escherichia coli K12 chromosomal EcoRI-BamHI fragment containing a mutant
      hsdS locus was cloned into plasmid pBR322.  The mcrB gene, closely linked to
      hsdS, was used for selection of clones with the inserted fragment using T4alpha
      gt57beta gt14 and lambda vir PvuII phages; the phage DNAs contain methylated
      cytosines and hence can be used to demonstrate McrB restriction.  For the
      efficient expression of the hsdS gene, a BglII fragment of phage lambda
      carrying the pR promoter was inserted into the BamHI site of the hybrid
      plasmid.  Under these conditions a trans-dominant effect of the hsdXts+d
      mutation on restriction and modification was detected.  Inactivation of the
      hsdS gene by the insertion of the lambda phage BglII fragment into the BglII
      site within this gene resulted in the disappearance of the trans-dominant
      effect.  When the cloned BamHI-EcoRI fragment was shortened by HpaI and EcoRI
      restriction enzymes, the trans-dominant effect was fully expressed.  The
      results indicate that the Xts+d mutation is located in the hsdS gene.  The
      effect of gene dosage of the HsdS subunit on the expression of Xts+d mutation
      was studied.  The results of complementation experiments, using F'-merodiploids
      or plasmid pBR322 with an inserted Xts+d mutation, support the idea that the
      HsdSts+d product competes with the wild-type HsdS product, and has a
      quantitatively different effect on restriction and modification.
AU  - Hubacek J
AU  - Zinkevich VE
AU  - Weiserova M
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1989 135: 3057-3065.

PMID- 27795246
VI  - 4
DP  - 2016
TI  - Draft Whole-Genome Sequence of a Haemophilus quentini Strain Isolated from an Infant in the United Kingdom.
PG  - e01075-16
AB  - Haemophilus quentini is a rare and distinct genospecies of Haemophilus that has been suggested
      as a cause of neonatal bacteremia and urinary tract infections in
      men. We present the draft whole-genome sequence of H. quentini MP1 isolated from
      an infant in the United Kingdom, aiding future identification and detection of
      this pathogen.
AU  - Hubbard AT
AU  - Davies SE
AU  - Baxter L
AU  - Thompson S
AU  - Collery MM
AU  - Hand DC
AU  - Fink CG
AU  - Thomas DJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01075-16.

PMID- 4091268
VI  - 150
DP  - 1985
TI  - DNA methyltransferases: Activity minigel analysis and determination with DNA covalently bound to a solid matrix.
PG  - 442-448
AB  - We describe two methods that facilitate detection and characterization of DNA
      methyltransferases: activity gel analysis and the use of DNA-cellulose or DNA-Sepharose in DNA
      methylation reactions.  The first permits identification of catalytic subunits, determination
      of the influence of proteolysis, and evolutionary or developmental studies.  The second allows
      accurate and fast determination of DNA methyltransferase activities in crude extracts and
      during purification.
AU  - Hubscher U
AU  - Pedrali-Noy G
AU  - Knust-Kron B
AU  - Doerfler W
AU  - Spadari S
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 1985 150: 442-448.

PMID- 24905728
VI  - 9
DP  - 2014
TI  - Resistance determinants and mobile genetic elements of an NDM-1-encoding Klebsiella pneumoniae strain.
PG  - E99209
AB  - Multidrug-resistant Enterobacteriaceae are emerging as a serious infectious
      disease challenge. These strains can accumulate many antibiotic resistance genes
      though horizontal transfer of genetic elements, those for beta-lactamases being
      of particular concern. Some beta-lactamases are active on a broad spectrum of
      beta-lactams including the last-resort carbapenems. The gene for the
      broad-spectrum and carbapenem-active metallo-beta-lactamase NDM-1 is rapidly
      spreading. We present the complete genome of Klebsiella pneumoniae ATCC BAA-2146,
      the first U.S. isolate found to encode NDM-1, and describe its repertoire of
      antibiotic-resistance genes and mutations, including genes for eight
      beta-lactamases and 15 additional antibiotic-resistance enzymes. To elucidate the
      evolution of this rich repertoire, the mobile elements of the genome were
      characterized, including four plasmids with varying degrees of conservation and
      mosaicism and eleven chromosomal genomic islands. One island was identified by a
      novel phylogenomic approach, that further indicated the cps-lps polysaccharide
      synthesis locus, where operon translocation and fusion was noted. Unique plasmid
      segments and mosaic junctions were identified. Plasmid-borne blaCTX-M-15 was
      transposed recently to the chromosome by ISEcp1. None of the eleven full copies
      of IS26, the most frequent IS element in the genome, had the expected 8-bp direct
      repeat of the integration target sequence, suggesting that each copy underwent
      homologous recombination subsequent to its last transposition event. Comparative
      analysis likewise indicates IS26 as a frequent recombinational junction between
      plasmid ancestors, and also indicates a resolvase site. In one novel use of
      high-throughput sequencing, homologously recombinant subpopulations of the
      bacterial culture were detected. In a second novel use, circular transposition
      intermediates were detected for the novel insertion sequence ISKpn21 of the ISNCY
      family, suggesting that it uses the two-step transposition mechanism of IS3.
      Robust genome-based phylogeny showed that a unified Klebsiella cluster contains
      Enterobacter aerogenes and Raoultella, suggesting the latter genus should be
      abandoned.
AU  - Hudson CM
AU  - Bent ZW
AU  - Meagher RJ
AU  - Williams KP
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2014 9: E99209.

PMID- 24029760
VI  - 1
DP  - 2013
TI  - Chromosome Sequence of Borrelia miyamotoi, an Uncultivable Tick-Borne Agent of Human Infection.
PG  - e00713-13
AB  - Borrelia miyamotoi is a newly recognized agent of human disease. B. miyamotoi strain LB-2001,
      an isolate from the tick Ixodes scapularis, was propagated in
      mice. The sequence of the chromosome was determined by next-generation sequencing
      of DNA isolated from whole blood. The sequence established that B. miyamotoi is a
      relapsing fever group species.
AU  - Hue F
AU  - Ghalyanchi LA
AU  - Barbour AG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00713-13.

PMID- 24926059
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Stenotrophomonas maltophilia Strain M30, Isolated from a Chronic Pressure Ulcer in an Elderly Patient.
PG  - e00576-14
AB  - Stenotrophomonas maltophilia is an emerging opportunistic pathogen with an increasing
      prevalence of multidrug-resistant strains. Here, we report the draft
      genome sequence of S. maltophilia strain M30, isolated from a pressure ulcer in
      an elderly patient.
AU  - Huedo P
AU  - Conchillo-Sole O
AU  - Yero D
AU  - Martinez-Servat S
AU  - Daura X
AU  - Gibert I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00576-14.

PMID- 26358605
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Napoli Strain SN310, Cause of a Multischool Outbreak in Milan, Italy, in 2014.
PG  - e01044-15
AB  - We report the draft genome sequence of Salmonella enterica subsp. enterica serovar Napoli
      strain SN310, isolated from a stool sample of an affected pupil during a multischool outbreak
      in 2014 in Milan, Italy. This represents the first  reported draft genome sequence of the
      emerging serovar Napoli.
AU  - Huedo P
AU  - Gori M
AU  - Scaltriti E
AU  - Morganti M
AU  - Casadei G
AU  - Amato E
AU  - Pontello M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01044-15.

PMID- 22675594
VI  - 6
DP  - 2012
TI  - Genome sequence of strain HIMB624, a cultured representative from the OM43 clade  of marine Betaproteobacteria.
PG  - 11-20
AB  - Strain HIMB624 is a planktonic marine bacterium within the family Methylophilaceae of the
      class Betaproteobacteria isolated from coastal seawater of Oahu, Hawaii. This strain is of
      interest because it is one of few known isolates from an abundant clade of Betaproteobacteria
      found in cultivation-independent studies of coastal seawater and freshwater environments
      around the globe, known as OM43. Here we describe some preliminary features of the organism,
      draft genome sequence and annotation, and comparative genomic analysis with one other
      sequenced member of this clade (strain HTCC2181). The 1,333,209 bp genome of strain HIMB624 is
      arranged in a single scaffold containing four contigs, and contains 1,381 protein encoding
      genes and 39 RNA genes.
AU  - Huggett MJ
AU  - Hayakawa DH
AU  - Rappe MS
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 6: 11-20.

PMID- 2228977
VI  - 172
DP  - 1990
TI  - Methylated DNA in Borrelia species.
PG  - 6602-6604
AB  - The DNA of Borrelia species was examined for the presence of methylated GATC
      sequences.  The relapsing-fever Borrelia sp., B. coriaceae, and only 3 of 22
      strains of B. burgdorferi contained adenine methylation systems.  B. anserina
      lacked an adenine methylation system.  Fundamental differences in DNA
      methylation exist among members of the genus Borrelia.
AU  - Hughes CAN
AU  - Johnson RC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1990 172: 6602-6604.

PMID- 26966198
VI  - 4
DP  - 2016
TI  - Genome Sequence of Stenotrophomonas maltophilia Strain SmAs1, Isolated From the Asian Malaria Mosquito Anopheles stephensi.
PG  - e00086-16
AB  - An isolate of Stenotrophomonas maltophilia was cultured from the Asian malaria vector
      Anopheles stephensi. Here, we present the annotated draft genome sequence
      of this S. maltophilia strain. This genomic resource will facilitate further
      characterization of bacteria associated with mosquitoes.
AU  - Hughes GL
AU  - Raygoza GJA
AU  - Koundal V
AU  - Rasgon JL
AU  - Mwangi MM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00086-16.

PMID- 26966197
VI  - 4
DP  - 2016
TI  - Genome Sequences of Staphylococcus hominis Strains ShAs1, ShAs2, and ShAs3, Isolated from the Asian Malaria Mosquito Anopheles stephensi.
PG  - e00085-16
AB  - Staphylococcus hominis is a culturable component of the bacterial microbiome of Anopheles
      stephensi. Here, we present the annotated draft genome sequences of
      three S. hominis isolates from A. stephensi. These genomic resources will
      facilitate experiments to further our understanding of the role of bacteria in
      mosquito biology.
AU  - Hughes GL
AU  - Raygoza GJA
AU  - Koundal V
AU  - Rasgon JL
AU  - Mwangi MM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00085-16.

PMID- 26888898
VI  - 54
DP  - 2016
TI  - Detection and Whole-Genome Sequencing of Carbapenemase-Producing Aeromonas hydrophila Isolates from Routine Perirectal Surveillance Culture.
PG  - 1167-1170
AB  - Perirectal surveillance cultures and a stool culture grewAeromonasspecies from
      three patients over a 6-week period and were without epidemiological links.
      Detection of theblaKPC-2gene in one isolate prompted inclusion of
      non-Enterobacteriaceaein our surveillance culture workup. Whole-genome sequencing
      confirmed that the isolates were unrelated and provided data
      forAeromonasreference genomes.
AU  - Hughes HY
AU  - Conlan SP
AU  - Lau AF
AU  - Dekker JP
AU  - Michelin AV
AU  - Youn JH
AU  - Henderson DK
AU  - Frank KM
AU  - Segre JA
AU  - Palmore TN
PT  - Journal Article
TA  - J. Clin. Microbiol.
JT  - J. Clin. Microbiol.
SO  - J. Clin. Microbiol. 2016 54: 1167-1170.

PMID- 
VI  - 
DP  - 1977
TI  - Studies of plasmid encoded restriction and modification systems.
PG  - 1-70
AB  - Within the general context of the distribution, role, and origin, of restriction and
      modification systems among plasmids, two plasmid encoded systems have been studied.  The
      EcoRII (hspII) system.  The sensitivity of the DNA of bacteriophage lambda to endo R.EcoRII in
      vitro was found to depend on the presence or absence of methylation introduced by the cytosine
      specific DNA methylase of E. coli K.  Subsequently, a revised minimum estimate for the number
      of cleavage sites for endo R.EcoRII and a map of these sites close to the ends of the lambda
      chromosome were made.  The EcoR124 (hspI) system.  The restriction and modification system
      carried by the plasmid R124 was shown to be different from the EcoRI system carried by plasmid
      RY5 (subsequently NTP13) with which it had previously been assumed to be identical.  Endo
      R.EcoR124 was isolated and found to be dependent on ATP and S-adenosylmethionine (it is a
      class I restriction endonuclease).  A derivative of R124 was isolated, by chance, which has
      acquired a restriction and modification system of novel specificity.  The derivative, R124/3,
      also has new cleavage sites for endo R.EcoRI and endo R.SalI in its DNA.  It is proposed that
      the new system, EcoR124/3 arose by recombination between the determinants of EcoK and EcoR124.
AU  - Hughes SG
PT  - Journal Article
TA  - Ph.D. Thesis, University of Edinburgh, Edinburgh, Scotland
JT  - Ph.D. Thesis, University of Edinburgh, Edinburgh, Scotland
SO  - Ph.D. Thesis, University of Edinburgh, Edinburgh, Scotland 1977 : 1-70.

PMID- 880215
VI  - 163
DP  - 1977
TI  - A map of the cleavage sites for endonuclease AvaI in the chromosome of bacteriophage lambda.
PG  - 503-509
AB  - The linear order of nine fragments generated by the action of endonuclease AvaI
      on the DNA of bacteriophage lambda was determined from the altered
      fragmentation patterns of bacteriophages containing known deletions and of
      hybrids of bacteriophages lambdaand U80.  Digestion of 5'-terminally
      32P-labelled bacteriophage-lambda DNA was used to identify the terminal
      fragments.  Measurement of relative fragment lengths permitted rough mapping of
      the endonuclease-AvaI cleavage sites relative to the ends of the
      bacteriophage-lambda chromosome.  The fragment order was confirmed and the map
      refined by analysis of the fragmentation of derivative phages containing single
      cleavage sites for endonuclease EcoRI.
AU  - Hughes SG
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 1977 163: 503-509.

PMID- 6246880
VI  - 185
DP  - 1980
TI  - The Isolation and Characterization of a Sequence-Specific Endonuclease from Anabaena subcylindrica.
PG  - 59-63
AB  - An endonuclease, AsuI, was isolated from extracts of Anabaena subcylindrica on
      the basis of gel-electrophoretic analysis of digests of bacteriophage-lambda
      DNA with the partially purified extracts.  The enzyme requires Mg2+, but no
      other cofactors.  Endonuclease AsuI recognizes the interrupted tetranucleotide
      sequence: 5'-G-^G-N-C-C-3'   -C-C-N-G^-G- and breaks the phosphodiester bonds
      indicated by the arrows to leave single-stranded trinucleotide projections at
      the 5'-termini of the DNA fragments.
AU  - Hughes SG
AU  - Bruce T
AU  - Murray K
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 1980 185: 59-63.

PMID- 1104876
VI  - 98
DP  - 1975
TI  - The sensitivity of bacteriophage lambda DNA to restriction endonuclease RII.
PG  - 645-647
AB  - Analysis of fragments of bacteriophage DNA produced by digestion with purified restriction
      endonuclease RII shows that DNA propagated in the presence of the cytosine-specific DNA
      methylase of Escherichia coli K is partially protected.  It is concluded that a fraction of
      the recognition sequences for EcoRII are methylated by this methylase which shares an element
      of sequence specificity with the RII restriction and modification enzymes.
AU  - Hughes SG
AU  - Hattman S
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1975 98: 645-647.

PMID- 6246881
VI  - 185
DP  - 1980
TI  - The Nucleotide Sequences Recognized by Endonucleases AvaI and AvaII from Anabaena variabilis.
PG  - 65-75
AB  - Determination of the 5'-terminal sequences flanking all the individual cleavage
      sites for endonuclease AvaI in bacteriophage-lambda DNA has shown that this
      enzyme recognizes the hexanucleotide sequence: 5'-C-^Y-C-G-R-G-3'
      G-R-G-C-Y-^C This sequence is cut as shown by the arrows to give
      single-stranded 5'-tetranucleotide protrusions (cohesive ends).  Endonucleases
      SmaI, XhoI and XmaI recognize different symmetrical subsets of this sequence
      and provide independent evidence for the occurrence of these subsets at
      particular endonuclease-AvaI cleavage sites in the bacteriophage-lambda genome.
      Further evidence for this structure came from the demonstration that DNA
      fragments generated by endonuclease AvaI can be ligated to form a discrete set
      of larger molecules and from nearest-neighbour analysis which showed that
      cytosine residues occurred at the 3'-side of cleavage points.  The observation
      that endonuclease AvaII recognized a subset of the sites recognized by AsuI
      [Hughes, Bruce & Murray (1979) Biochem. J. 185, 59-63] led to the deduction
      that AvaII recognizes the pentanucleotide sequence: 5'-G-^G-A-C-C-3'
      C-C-T-G-^G and breaks internucleotide bonds at the positions indicated by the
      arrows.
AU  - Hughes SG
AU  - Murray K
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 1980 185: 65-75.

PMID- 23961307
VI  - 8
DP  - 2013
TI  - Non-contiguous finished genome sequence and description of Brevibacillus massiliensis sp. nov.
PG  - 1-14
AB  - Brevibacillus massiliensis strain phR(T) sp. nov. is the type strain of B. massiliensis sp.
      nov., a new species within the genus Brevibacillus. This strain
      was isolated from the fecal flora of a woman suffering from morbid obesity. B.
      massiliensis is a Gram-positive aerobic rod-shaped bacterium. Here we describe
      the features of this organism, together with the complete genome sequence and
      annotation. The 5,051,018 bp long genome (1 chromosome but no plasmid) contains
      5,051 protein-coding and 84 RNA genes, and exhibits a G+C content of 53.1%.
AU  - Hugon P
AU  - Mishra AK
AU  - Lagier JC
AU  - Nguyen TT
AU  - Couderc C
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 1-14.

PMID- 23407456
VI  - 6
DP  - 2012
TI  - Non-contiguous finished genome sequence and description of Anaerococcus vaginalis.
PG  - 356-365
AB  - We report the properties of a draft genome sequence of the bacterium Anaerococcus vaginalis
      strain PH9, a species within the Anaerococcus genus. This strain, whose
      genome is described here, was isolated from the fecal flora of a 26-year-old
      woman suffering from morbid obesity. A. vaginalis is an obligate anaerobic
      coccus. Here we describe the features of this organism, together with the
      complete genome sequence and annotation. The 2,048,125-bp long (one chromosome
      but no plasmid) and contains 2,095 protein-coding and 38 RNA genes, including
      three rRNA genes.
AU  - Hugon P
AU  - Mishra AK
AU  - Robert C
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 6: 356-365.

PMID- 24019990
VI  - 7
DP  - 2013
TI  - Non contiguous-finished genome sequence and description of Alistipes obesi sp. nov.
PG  - 427-439
AB  - Alistipes obesi sp. nov. strain ph8(T) is the type strain of A. obesi, a new species within
      the genus Alistipes. This strain, whose genome is described here,
      was isolated from the fecal flora of a 26-year-old woman suffering from morbid
      obesity. A. obesi is an obligately anaerobic rod. Here we describe the features
      of this organism, together with the complete genome sequence and annotation. The
      3,162,233 bp long genome (1 chromosome but no plasmid) contains 2,623
      protein-coding and 49 RNA genes, including three rRNA genes.
AU  - Hugon P
AU  - Ramasamy D
AU  - Lagier JC
AU  - Rivet R
AU  - Couderc C
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 7: 427-439.

PMID- 24501634
VI  - 8
DP  - 2013
TI  - Non-contiguous finished genome sequence and description of Kallipyga massiliensis gen. nov., sp. nov., a new member of the family Clostridiales Incertae Sedis XI.
PG  - 500-515
AB  - Kallipyga massiliensis strain ph2(T) is the type strain of Kallipyga massiliensis gen. nov.,
      sp. nov., the type species of the new genus Kallipyga within the
      family Clostridiales Incertae Sedis XI. This strain, whose genome is described
      here, was isolated from the fecal flora of a 26-year-old woman suffering from
      morbid obesity. K. massiliensis is an obligate anaerobic coccus. Here we describe
      the features of this organism, together with the complete genome sequence and
      annotation. The 1,770,679 bp long genome (1 chromosome but no plasmid) contains
      1,575 protein-coding and 50 RNA genes, including 4 rRNA genes.
AU  - Hugon P
AU  - Ramasamy D
AU  - Robert C
AU  - Couderc C
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 500-515.

PMID- 22408247
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Streptomyces acidiscabies 84-104, an Emergent Plant Pathogen.
PG  - 1847
AB  - A draft genome sequence of the plant pathogen Streptomyces acidiscabies 84-104, an emergent
      plant pathogen, is presented here. The genome is among the largest of
      streptomycetes, at more than 11 Mb, and encodes a 100-kb pathogenicity island
      (PAI) shared with other plant-pathogenic streptomycetes. The presence of this
      conserved PAI, and the remnants of a conserved integrase/recombinase at its 3'
      end, supports the hypothesis that S. acidiscabies emerged as a plant pathogen as
      a result of this acquisition.
AU  - Huguet-Tapia JC
AU  - Loria R
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1847.

PMID- 26868406
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of the African Strain AXO1947 of Xanthomonas oryzae pv.  oryzae.
PG  - e01730-15
AB  - Xanthomonas oryzae pv. oryzae is the etiological agent of bacterial rice blight.  Three
      distinct clades of X. oryzae pv. oryzae are known. We present the complete
      annotated genome of the African clade strain AXO194 using long-read
      single-molecule PacBio sequencing technology. The genome comprises a single
      chromosome of 4,674,975 bp and encodes for nine transcriptional activator-like
      (TAL) effectors. The approach and data presented in this announcement provide
      information for complex bacterial genome organization and the discovery of new
      virulence effectors, and they facilitate target characterization of TAL
      effectors.
AU  - Huguet-Tapia JC
AU  - Peng Z
AU  - Yang B
AU  - Yin Z
AU  - Liu S
AU  - White FF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01730-15.

PMID- 25395638
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Dyella japonica Strain A8 Isolated from Malaysian Tropical Soil.
PG  - e01164-14
AB  - We previously identified and presented the draft genome of a Xanthomonadaceae bacterial strain
      Dyella japonica A8 which shows quorum-quenching activity. Here,
      we report the complete, closed genome sequence of this bacterium. This complete
      genome may help to further investigate the comparative quorum-quenching activity
      among D. japonica strains.
AU  - Hui RK
AU  - Chen JW
AU  - Chan KG
AU  - Leung FC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01164-14.

PMID- 25587010
VI  - 6
DP  - 2015
TI  - Genomic Avenue to Avian Colisepticemia.
PG  - e01681-14
AB  - Here we present an extensive genomic and genetic analysis of Escherichia coli strains of
      serotype O78 that represent
      the major cause of avian colisepticemia, an invasive infection caused by avian pathogenic
      Escherichia coli (APEC) strains. It is
      associated with high mortality and morbidity, resulting in significant economic consequences
      for the poultry industry. To understand
      the genetic basis of the virulence of avian septicemic E. coli, we sequenced the entire genome
      of a clinical isolate of serotype
      O78-O78:H19 ST88 isolate 789 (O78-9)-and compared it with three publicly available APEC O78
      sequences and one
      complete genome of APEC serotype O1 strain. Although there was a large variability in genome
      content between the APEC
      strains, several genes were conserved, which are potentially critical for colisepticemia. Some
      of these genes are present in multiple
      copies per genome or code for gene products with overlapping function, signifying their
      importance. A systematic deletion of
      each of these virulence-related genes identified three systems that are conserved in all
      septicemic strains examined and are critical
      for serum survival, a prerequisite for septicemia. These are the plasmid-encoded protein, the
      defective ETT2 (E. coli type 3
      secretion system 2) type 3 secretion system ETT2sepsis, and iron uptake systems. Strain O78-9
      is the only APEC O78 strain that
      also carried the regulon coding for yersiniabactin, the iron binding system of the Yersinia
      high-pathogenicity island. Interestingly,
      this system is the only one that cannot be complemented by other iron uptake systems under
      iron limitation and in serum.
AU  - Huja S
AU  - Oren Y
AU  - Trost E
AU  - Brzuszkiewicz E
AU  - Biran D
AU  - Blom J
AU  - Goesmann A
AU  - Gottschalk G
AU  - Hacker J
AU  - Ron EZ
AU  - Dobrindt U
PT  - Journal Article
TA  - MBio
JT  - MBio
SO  - MBio 2015 6: e01681-14.

PMID- 2013413
VI  - 98
DP  - 1991
TI  - High-level expression of a semisynthetic dam gene in Escherichia coli.
PG  - 83-88
AB  - We constructed a semisynthetic gene encoding a DNA-adenine-methyltransferase (Dam) that codes
      for the same amino acid sequence as the wild type (wt) Escherichia coli dam gene. Since for
      unknown reasons the entire wt sequence, from the start codon to the end of the gene, could not
      be cloned, a gene was constructed consisting of a chemically synthesized 5' portion and a 3'
      portion from the E. coli chromosome. Introduction of this semisynthetic gene into a suitable
      vector allows overproduction of E. coli Dam in mg amounts per liter E. coli culture, with
      optimum expression of the gene in the vector pJLA503. This plasmid places the target gene
      under control of the strong, tandemly arranged PR PL promoters from bacteriophage lambda,
      regulated by a temperature-sensitive lambda repressor. A rapid, two-column purification
      protocol is described that allows for very fast purification of the protein. The 32-kDa
      recombinant protein methylates the sequence GATC.
AU  - Hulsmann K-H
AU  - Quaas R
AU  - Georgalis Y
AU  - Saenger W
AU  - Hahn U
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1991 98: 83-88.

PMID- 22675579
VI  - 5
DP  - 2011
TI  - Complete genome of the onion pathogen Enterobacter cloacae EcWSU1.
PG  - 279-286
AB  - 
AU  - Humann JL
AU  - Wildung M
AU  - Cheng C-H
AU  - Lee T
AU  - Drew JC
AU  - Triplett EW
AU  - Main D
AU  - Schroeder BK
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 5: 279-286.

PMID- 25197457
VI  - 9
DP  - 2014
TI  - Complete genome of the switchgrass endophyte Enterobacter clocace P101.
PG  - 726-734
AB  - The Enterobacter cloacae complex is genetically very diverse. The increasing number of
      complete genomic sequences of E. cloacae is helping to determine the
      exact relationship among members of the complex. E. cloacae P101 is an endophyte
      of switchgrass (Panicum virgatum) and is closely related to other E. cloacae
      strains isolated from plants. The P101 genome consists of a 5,369,929 bp
      chromosome. The chromosome has 5,164 protein-coding regions, 100 tRNA sequences,
      and 8 rRNA operons.
AU  - Humann JL
AU  - Wildung M
AU  - Pouchnik D
AU  - Bates AA
AU  - Drew JC
AU  - Zipperer UN
AU  - Triplett EW
AU  - Main D
AU  - Schroeder BK
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 726-734.

PMID- 2837577
VI  - 200
DP  - 1988
TI  - Type III DNA restriction and modification systems EcoP1 and EcoP15.
PG  - 23-29
AB  - This paper presents the nucleotide sequence of the mod-res operon of phage P1,
      which encodes the two structural genes for the EcoP1 type III restriction and
      modification system.  We have also sequenced the mod gene of the allelic EcoP15
      system.  The mod gene product is responsible for binding the system-specific
      DNA recognition sequences in both restriction and modification:   it also
      catalyses the modification reaction.  A comparison of the two mod gene product
      sequences shows that they have conserved amino and carboxyl ends but have
      completely different sequences in the middle of the molecules.  Two alleles of
      the EcoP1 mod gene that are defective in modification but not in restriction
      were also sequenced.  The mutations in both alleles lie within the
      non-conserved regions.
AU  - Humbelin M
AU  - Suri B
AU  - Rao DN
AU  - Hornby DP
AU  - Eberle H
AU  - Pripfl T
AU  - Kenel S
AU  - Bickle TA
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1988 200: 23-29.

PMID- 21219459
VI  - 79
DP  - 2011
TI  - Characterization of Helicobacter pylori factors that control transformation frequency and integration length during inter-strain DNA  recombination.
PG  - 387-401
AB  - P>Helicobacter pylori is a genetically diverse bacterial species, owing in part to its natural
      competence for DNA uptake that facilitates
      recombination between strains. Inter-strain DNA recombination occurs
      during human infection and the H. pylori genome is in linkage
      equilibrium worldwide. Despite this high propensity for DNA exchange,
      little is known about the factors that limit the extent of
      recombination during natural transformation. Here, we identify
      restriction-modification (R-M) systems as a barrier to transformation
      with homeologous DNA and find that R-M systems and several components
      of the recombination machinery control integration length. Type II R-M
      systems, the nuclease nucT and resolvase ruvC reduced integration
      length whereas the helicase recG increased it. In addition, we
      characterized a new factor that promotes natural transformation in H.
      pylori, dprB. Although free recombination has been widely observed in
      H. pylori, our study suggests that this bacterium uses multiple systems
      to limit inter-strain recombination.
AU  - Humbert O
AU  - Dorer MS
AU  - Salama NR
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2011 79: 387-401.

PMID- 
VI  - 107
DP  - 2007
TI  - Functional characterization of HP0503: An adenine methyltransferase required for the virulence of Helicobacter pylori.
PG  - 39
AB  - Restriction-modification systems have traditionally been implicated in the protection of the
      bacterial genome from invading DNAs, but accumulating evidence suggests that they have other
      cellular functions. Helicobacter pylori contains a large number of these systems with at least
      23 identified. In silico genome analysis reveals that in many of these systems, the
      restriction-endonuclease component is inactive but the cognate methyltransferase retains full
      activity, implying that it confers a selective advantage to its host. In an effort to identify
      H. pylori factors required for the colonization of the mouse stomach, we identified HP0503, a
      protein of unknown function. Structure prediction algorithms revealed that HP0503 has a
      similar folding pattern to the adenine methyltransferase M.TaqI from Thermus aquaticus,
      leading us to hypothesize that HP0503 is a DNA methyltransferase required for the virulence of
      H. pylori. The methyltransferase activity of HP0503 was demonstrated using an engineered
      strain of E. coli defective in DNA methylation. Upon expression of HP0503 in this E. coli
      strain, genomic DNA methylation could be detected using antibodies recognizing methylated
      adenine. In addition, a point mutation in the predicted catalytic site of HP0503 completely
      abolished adenine methylation, further advocating its function as an adenine
      methyltransferase. To clarify the role of HP0503 in virulence, its DNA recognition site was
      determined. The restriction endonuclease Rsa I could digest genomic DNA from a HP0503 mutant
      strain but not WT, indicating that HP0503 acts on the same sequence as Rsa I, GTAC. This
      finding was confirmed by expressing HP0503 cognate endonuclease, HP0505, in E. coli, which
      cleaved DNA at GTAC sites. Interestingly, while GTAC sites are strongly avoided in the H.
      pylori genome (only 115 to 184 sites/genome), 16 of these sites are found within the 2 copies
      of the 3kbp DNA fragment encoding the 23S rRNA. We are currently testing the methylation
      status of HP0503 cognate sites and examining their impact on gene activity to probe the
      mechanism by which HP0503 confers a fitness advantage during stomach colonization.
AU  - Humbert O
AU  - Salama NR
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 2007 107: 39.

PMID- 18978016
VI  - 36
DP  - 2008
TI  - The Helicobacter pylori HpyAXII restriction-modification system limits exogenous DNA uptake by targeting GTAC sites but shows asymmetric  conservation of the DNA methyltransferase and restriction endonuclease  components.
PG  - 6893-6906
AB  - The naturally competent organism Helicobacter pylori encodes a large number of
      restriction-modification (R-M) systems that consist of a
      restriction endonuclease and a DNA methyltransferase. R-M systems are not
      only believed to limit DNA exchange among bacteria but may also have other
      cellular functions. We report a previously uncharacterized H. pylori type
      II R-M system, M.HpyAXII/R.HpyAXII. We show that this system targets GTAC
      sites, which are rare in the H. pylori chromosome but numerous in
      ribosomal RNA genes. As predicted, this type II R-M system showed
      attributes of a selfish element. Deletion of the methyltransferase
      M.HpyAXII is lethal when associated with an active endonuclease R.HpyAXII
      unless compensated by adaptive mutation or gene amplification. R.HpyAXII
      effectively restricted both unmethylated plasmid and chromosomal DNA
      during natural transformation and was predicted to belong to the novel
      'half pipe' structural family of endonucleases. Analysis of a panel of
      clinical isolates revealed that R.HpyAXII was functional in a small number
      of H. pylori strains (18.9%, n = 37), whereas the activity of M.HpyAXII
      was highly conserved (92%, n = 50), suggesting that GTAC methylation
      confers a selective advantage to H. pylori. However, M.HpyAXII activity
      did not enhance H. pylori fitness during stomach colonization of a mouse
      infection model.
AU  - Humbert O
AU  - Salama NR
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2008 36: 6893-6906.

PMID- 
VI  - 
DP  - 2010
TI  - Restriction-modification systems and the regulation of genetic exchange in Helicobacter pylori.
PG  - 1-127
AB  - Helicobacter pylori is a gram negative bacterial pathogen that colonizes the stomach of over
      half of the world population. Various pathologies are associated with H. pylori infection and
      include gastritis, peptic ulcers, gastric cancer and MALT lymphoma. H pylori is one of the
      most genetically diverse bacterial species known, a likely consequence of DNA recombination
      between H. pylori strains facilitated by their natural competence for DNA uptake. Inter-strain
      DNA recombination occurs in patients infected with multiple genetically distinct H. pylori
      isolates but the barriers that limit DNA exchange is this organism are not understood.
      Restriction-Modification (R-M) systems are made of a restriction endonuclease and a DNA
      methyltransferase, both of which target the same DNA sequence. These systems are generally
      believed to protect bacteria from bacteriophages invasion but their role in limiting
      inter-strain recombination remains unexplored. Over the course of my Thesis work, I first
      identified and characterized a novel H. pylori R-M system. I showed that this system targets
      the sequence GTAC and that it effectively restricts unmethylated DNA during natural
      transformation. After designing a novel genetic assay to quickly assess restriction
      endonuclease activity, I made the intriguing observation that the DNA methyltransferase
      activity is highly conserved as compared to the endonuclease activity in H. pylori, and
      suggested that DNA methylation has alternate roles in this organism. In the following chapter,
      I quantified the size of DNA exchanged during H. pylori inter-strain recombination and found
      that R-M systems reduce both recombination frequency and size. Several components of the DNA
      transformation and recombination pathways were also identified as regulators of transformation
      frequency and integration size during both homologous and homeologous DNA transformation. In
      the last chapter, I investigated whether DNA methylation controls gene transcription in H.
      pylori. Global transcriptional profiles of H. pylori bacteria were analyzed by microarrays in
      response to adenine methylation of the recognition sequences GTAC and TCGA. Transcriptional
      changes were observed in response to DNA methylation, but no correlation could be established
      with the distribution of methylation sites. Possible mechanisms of regulation by DNA
      methylation were considered.
AU  - Humbert OM
PT  - Journal Article
TA  - Ph.D. Thesis, University of Washington, Seattle, USA
JT  - Ph.D. Thesis, University of Washington, Seattle, USA
SO  - Ph.D. Thesis, University of Washington, Seattle, USA 2010 : 1-127.

PMID- 12576072
VI  - 313
DP  - 2003
TI  - Detection and analysis of enzymatic DNA methylation of oligonucleotide substrates by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.
PG  - 160-166
AB  - Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF) mass
      spectrometry was employed to analyze DNA
      methylation carried out by the Escherichia coli dam DNA methyltransferase
      using oligonucleotide substrates with molecular masses of 5000-10,000 Da
      per strand. The mass spectrometry assay offers several advantages: (i) it
      directly shows the methylation as the increase in the mass of the
      substrate DNA, (ii) it is nonradioactive, (iii) it is quantitative, and
      (iv) it can be automated for high-throughput applications. Since
      unmethylated and methylated DNA are detected, the ratio of methylation can
      be determined directly and accurately. Furthermore, the assay allows
      detection individually of the methylation of several substrates in
      competition, offering an ideal setup to analyze the specificity of DNA
      interacting with enzymes. We could not identify methylation at any
      noncanonical site, indicating that the dam MTase is a very specific
      enzyme. Finally, MALDI-TOF mass spectrometry permitted assessment of the
      number of methyl groups incorporated into each DNA strand, thereby,
      allowing study of mechanistic details such as the processivity of the
      methylation reaction. We provide evidence that the dam MTase modifies DNA
      in a processive reaction, confirming earlier findings.
AU  - Humeny A
AU  - Beck C
AU  - Becker CM
AU  - Jeltsch A
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 2003 313: 160-166.

PMID- 26692227
VI  - 16
DP  - 2015
TI  - Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium.
PG  - 1085
AB  - BACKGROUND: Clostridium autoethanogenum is an acetogenic bacterium capable of
      producing high value commodity chemicals and biofuels from the C1 gases present
      in synthesis gas. This common industrial waste gas can act as the sole energy and
      carbon source for the bacterium that converts the low value gaseous components
      into cellular building blocks and industrially relevant products via the action
      of the reductive acetyl-CoA (Wood-Ljungdahl) pathway. Current research efforts
      are focused on the enhancement and extension of product formation in this
      organism via synthetic biology approaches. However, crucial to metabolic
      modelling and directed pathway engineering is a reliable and comprehensively
      annotated genome sequence. RESULTS: We performed next generation sequencing using
      Illumina MiSeq technology on the DSM10061 strain of Clostridium autoethanogenum
      and observed 243 single nucleotide discrepancies when compared to the published
      finished sequence (NCBI: GCA_000484505.1), with 59.1 % present in coding regions.
      These variations were confirmed by Sanger sequencing and subsequent analysis
      suggested that the discrepancies were sequencing errors in the published genome
      not true single nucleotide polymorphisms. This was corroborated by the
      observation that over 90 % occurred within homopolymer regions of greater than 4
      nucleotides in length. It was also observed that many genes containing these
      sequencing errors were annotated in the published closed genome as encoding
      proteins containing frameshift mutations (18 instances) or were annotated despite
      the coding frame containing stop codons, which if genuine, would severely hinder
      the organism's ability to survive. Furthermore, we have completed a comprehensive
      manual curation to reduce errors in the annotation that occur through serial use
      of automated annotation pipelines in related species. As a result, different
      functions were assigned to gene products or previous functional annotations
      rejected because of missing evidence in various occasions. CONCLUSIONS: We
      present a revised manually curated full genome sequence for Clostridium
      autoethanogenum DSM10061, which provides reliable information for genome-scale
      models that rely heavily on the accuracy of annotation, and represents an
      important step towards the manipulation and metabolic modelling of this
      industrially relevant acetogen.
AU  - Humphreys CM et al
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2015 16: 1085.

PMID- 28935741
VI  - 5
DP  - 2017
TI  - Insights into the Genome of the Anaerobic Acetogen Sporomusa silvacetica DSM 10669.
PG  - e00983-17
AB  - Sporomusa silvacetica is a spore-forming, anaerobic acetogen isolated from soil derived from
      east central Germany. The genome contains genes of the
      Wood-Ljungdahl pathway required for carbon fixation and genes involved in the
      biosynthesis of the amino acid pyrrolysine. The genome (5.92 Mb) harbors 4,355
      predicted protein-encoding genes.
AU  - Humphreys JR
AU  - Daniel R
AU  - Poehlein A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00983-17.

PMID- 28935740
VI  - 5
DP  - 2017
TI  - Genome Sequence of the Homoacetogenic, Gram-Negative, Endospore-Forming Bacterium Sporomusa acidovorans DSM 3132.
PG  - e00981-17
AB  - Sporomusa acidovorans DSM 3132 is a strictly anaerobic, spore-forming and acetogenic
      bacterium, which was isolated from effluent of an alcohol distillation
      fermenter. The genome harbors genes involved in the Wood-Ljungdahl pathway for
      carbon fixation and several genes for glycerol metabolism. The genome (6.06 Mb)
      contains 4,506 predicted protein-encoding genes.
AU  - Humphreys JR
AU  - Daniel R
AU  - Poehlein A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00981-17.

PMID- 4544986
VI  - 58
DP  - 1974
TI  - Endonuclease R. Hind fragments of T7 DNA.
PG  - 25-31
AB  - Restriction enzyme endonuclease R. Hind of Haemophilus influenzae strain Rd,
      prepared by a rapid new method, was used to cleave bacteriophage T7 DNA into a
      minimum of 49 unique fragments which were separated on polyacrylamide gels.
      The fragments were estimated to fall within the size range of 100-200
      nucleotide pairs.
AU  - Humphries P
AU  - Gordon RL
AU  - McConnell DJ
AU  - Connolly P
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1974 58: 25-31.

PMID- 24903876
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Acetobacter aceti Strain 1023, a Vinegar Factory Isolate.
PG  - e00550-14
AB  - The genome sequence of Acetobacter aceti 1023, an acetic acid bacterium adapted to traditional
      vinegar fermentation, comprises 3.0 Mb (chromosome plus plasmids).
      A. aceti 1023 is closely related to the cocoa fermenter Acetobacter pasteurianus
      386B but possesses many additional insertion sequence elements.
AU  - Hung JE
AU  - Mill CP
AU  - Clifton SW
AU  - Magrini V
AU  - Bhide K
AU  - Francois JA
AU  - Ransome AE
AU  - Fulton L
AU  - Thimmapuram J
AU  - Wilson RK
AU  - Kappock TJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00550-14.

PMID- 10518555
VI  - 96
DP  - 1999
TI  - Drosophila proteins related to vertebrate DNA (5-cytosine) methyltransferases.
PG  - 11940-11945
AB  - DNA methylation at CpG residues is closely associated with a number of biological processes
      during vertebrate development. Unlike the vertebrates, however, several invertebrate species,
      including the Drosophila, do not have apparent DNA methylation in their genomes. Nor have
      there been reports on a DNA (5-cytosine) methyltransferase (CpG MTase) found in these
      invertebrates. We now present evidence for two CpG MTase-like proteins expressed in Drosophila
      cells. One of these, DmMTR1, is a protein containing peptide epitopes immunologically related
      to the conserved motifs I and IV in the catalytic domain of the mammalian dnmt1. DmMTR1 has an
      apparent molecular mass of 220 kDa and, similar to mammalian dnmt1, it also interacts in vivo
      with the proliferating cell nuclear antigen. During interphase of the syncytial Drosophila
      embryos, the DmMTR1 molecules are located outside the nuclei, as is dnmt1 in the mouse
      blastocyst. However, DmMTR1 appears to be rapidly transported into, and then out of the nuclei
      again, as the embryos undergo mitotic waves. Immunofluorescent data indicate that DmMTR1
      molecules "paint" the whole set of condensed Drosophila chromosomes throughout the mitotic
      phase, suggesting they may play an essential function in the cell-cycle regulated condensation
      of the Drosophila chromosomes. Through search in the genomic database, we also have identified
      a Drosophila polypeptide, DmMT2, that exhibits high sequence homology to the mammalian dnmt2
      and the yeast CpG MTase homolog pmt1. The expression of DmMT2 appears to be developmentally
      regulated. We discuss the evolutionary and functional implications of the discovery of these
      two Drosophila proteins related to mammalian CpG MTases.
AU  - Hung MS
AU  - Karthikeyan N
AU  - Huang B
AU  - Koo HC
AU  - Kiger J
AU  - Shen CJ
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1999 96: 11940-11945.

PMID- 29773623
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Azospirillum brasilense Strains Ab-V5 and Ab-V6, Commercially Used in Inoculants for Grasses and Legumes in Brazil.
PG  - e00393-18
AB  - Azospirillum brasilense strains Ab-V5 and Ab-V6 are largely used in commercial inoculants for
      grasses and legumes in Brazil. Their genomes were estimated at
      6,934,595 and 7,197,196 bp, respectively, and encompass genes related to nitrogen
      fixation, synthesis of phytohormones, and environmental adaptation. Although the
      strains differ in phenotypic properties, their genomes are highly similar.
AU  - Hungria M
AU  - Ribeiro RA
AU  - Nogueira MA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00393-18.

PMID- 22768362
VI  - 6
DP  - 2012
TI  - Complete genome sequence of the facultatively anaerobic, appendaged bacterium Muricauda ruestringensis type strain (B1(T)).
PG  - 185-193
AB  - Muricauda ruestringensis Bruns et al. 2001 is the type species of the genus Muricauda, which
      belongs to the family Flavobacteriaceae in the phylum
      Bacteroidetes. The species is of interest because of its isolated position in the
      genomically unexplored genus Muricauda, which is located in a part of the tree of
      life containing not many organisms with sequenced genomes. The genome, which
      consists of a circular chromosome of 3,842,422 bp length with a total of 3,478
      protein-coding and 47 RNA genes, is a part of the Genomic Encyclopedia of
      Bacteria and Archaea project.
AU  - Huntemann M et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 6: 185-193.

PMID- 23991250
VI  - 8
DP  - 2013
TI  - Genome sequence of the phylogenetically isolated spirochete Leptonema illini type strain (3055(T)).
PG  - 177-187
AB  - Leptonema illini Hovind-Hougen 1979 is the type species of the genus Leptonema, family
      Leptospiraceae, phylum Spirochaetes. Organisms of this family have a
      Gram-negative-like cell envelope consisting of a cytoplasmic membrane and an
      outer membrane. The peptidoglycan layer is associated with the cytoplasmic rather
      than the outer membrane. The two flagella of members of Leptospiraceae extend
      from the cytoplasmic membrane at the ends of the bacteria into the periplasmic
      space and are necessary for their motility. Here we describe the features of the
      L. illini type strain, together with the complete genome sequence, and
      annotation. This is the first genome sequence (finished at the level of Improved
      High Quality Draft) to be reported from of a member of the genus Leptonema and a
      representative of the third genus of the family Leptospiraceae for which complete
      or draft genome sequences are now available. The three scaffolds of the 4,522,760
      bp draft genome sequence reported here, and its 4,230 protein-coding and 47 RNA
      genes are part of the G enomic E ncyclopedia of Bacteria and Archaea project.
AU  - Huntemann M et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 177-187.

PMID- 21886857
VI  - 4
DP  - 2011
TI  - Complete genome sequence of the thermophilic sulfur-reducer Hippea maritima type  strain (MH(2)).
PG  - 303-311
AB  - Hippea maritima (Miroshnichenko et al. 1999) is the type species of the genus Hippea, which
      belongs to the family Desulfurellaceae within the class
      Deltaproteobacteria. The anaerobic, moderately thermophilic marine sulfur-reducer
      was first isolated from shallow-water hot vents in Matipur Harbor, Papua New
      Guinea. H. maritima was of interest for genome sequencing because of its isolated
      phylogenetic location, as a distant next neighbor of the genus Desulfurella.
      Strain MH(2) (T) is the first type strain from the order Desulfurellales with a
      completely sequenced genome. The 1,694,430 bp long linear genome with its 1,723
      protein-coding and 57 RNA genes consists of one circular chromosome and is a part
      of the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Huntemann M et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 4: 303-311.

PMID- 24558233
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Pseudomonas moraviensis R28-S.
PG  - e00035-14
AB  - We report the draft genome sequence of Pseudomonas moraviensis R28-S, isolated from the
      municipal wastewater treatment plant of Moscow, ID. The strain carries a
      native mercury resistance plasmid, poorly maintains introduced IncP-1 antibiotic
      resistance plasmids, and has been useful for studying the evolution of plasmid
      host range and stability.
AU  - Hunter SS
AU  - Yano H
AU  - Loftie-Eaton W
AU  - Hughes J
AU  - De Gelder L
AU  - Stragier P
AU  - De Vos P
AU  - Settles ML
AU  - Top EM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00035-14.

PMID- 23516218
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Myxococcus stipitatus Strain DSM 14675, a Fruiting Myxobacterium.
PG  - e0010013
AB  - Hallmarks of the myxobacteria include the formation of spore-filled fruiting bodies in
      response to starvation and synthesis of secondary metabolites.
      Myxococcus stipitatus forms morphologically highly distinct fruiting bodies and
      produces secondary metabolites with antibiotic or cytotoxic activities. Here, we
      present the 10.35-Mb genome sequence of M. stipitatus strain DSM 14675.
AU  - Huntley S
AU  - Kneip S
AU  - Treuner-Lange A
AU  - Sogaard-Andersen L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0010013.

PMID- 22582372
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of the Fruiting Myxobacterium Corallococcus coralloides  DSM 2259.
PG  - 3012-3013
AB  - Corallococcus coralloides, like most other myxobacteria, undergoes a developmental program
      culminating in the formation of fruiting bodies. C.
      coralloides fruiting bodies are morphologically distinct from those of other
      fruiting myxobacteria for which full-length genome sequences are available. The
      genome sequence of the 10.0-Mb C. coralloides genome is presented herein.
AU  - Huntley S
AU  - Zhang Y
AU  - Treuner-Lange A
AU  - Kneip S
AU  - Sensen CW
AU  - Sogaard-Andersen L
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3012-3013.

PMID- 21705602
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Propionibacterium acnes Type IB strain 6609.
PG  - 4561-4562
AB  - Propionibacterium acnes (P. acnes) is an anaerobic Gram-positive bacterium that forms part of
      the normal human cutaneous microbiota and is thought to
      play central role in acne vulgaris, a chronic inflammatory disease of the
      pilosebaceous unit (8). Here we present the whole genome sequence for the
      P. acnes Type IB strain 6609 isolated from a patient with inflammatory
      acne (15).
AU  - Hunyadkurti J
AU  - Feltoti Z
AU  - Horvath B
AU  - Nagymihaly M
AU  - Voros A
AU  - McDowell A
AU  - Patrick S
AU  - Urban E
AU  - Nagy I
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4561-4562.

PMID- 
VI  - 
DP  - 2017
TI  - Enterococcus faecalis genome defense systems and their impact on conjugative antibiotic resistance plasmid transfer.
PG  - 
AB  - Enterococcus faecalis is a Gram-positive bacterium that naturally colonizes humans and
      opportunistically causes life-threatening infections. Multidrug-resistant (MDR) E. faecalis
      strains
      have emerged that are replete with mobile genetic elements (MGEs). Considering that bacteria
      commonly possess two genome defense mechanisms to prevent MGE acquisition,
      restrictionmodification
      (R-M, analogous to an innate immune system) and CRISPR-Cas (adaptive immune
      system), we hypothesize that these barriers may have been compromised in MDR E. faecalis
      strains. However, little was known about the activities of E. faecalis R-M and CRISPR-Cas
      systems. In my dissertation, a functional E. faecalis OG1RF encoded R-M system was identified
      and its activity against MGEs was confirmed using both conjugation and transformation assays.
      This work was the first to demonstrate that R-M provides E. faecalis with significant defense
      capability against antibiotic resistance plasmids. Subsequently, the distribution of R-M
      systems
      in a larger collection of E. faecalis strains was studied. To predict the novel R-M systems, I
      developed an R-M prediction algorithm based on amino acid sequence homology, and
      successfully predicted new R-M systems in 75 E. faecalis genomes. Remarkably, some lineagevi
      i
      specific R-M systems were detected. Especially, hospital-adapted lineages were found to be
      enriched for certain R-M systems, suggesting that these bacteria can readily exchange DNA with
      each other. Another active form of genome defense in E. faecalis, namely CRISPR-Cas, has also
      been investigated. In experimental in vitro evolution studies, we observed that
      chromosomallyencoded
      CRISPR-Cas systems tend to be compromised upon enforced maintenance of antibiotic
      resistance plasmids possessing sequences targeted by CRISPR-Cas. Using deep sequencing, we
      found that CRISPR array alleles are naturally heterogeneous, which provides an evolutionary
      basis for compromised CRISPR-Cas under selection pressure. This work demonstrates that
      antibiotic use can inadvertently select for E. faecalis with enhanced abilities to acquire
      mobile
      genetic elements. Finally, I studied lytic enterococcal phages for their interactions with E.
      faecalis hosts. This work was undertaken because phage therapy is increasingly of interest as
      an
      alternative to antibiotics for infection treatment. The genome modification status of one
      novel
      enterococcal phage was characterized, and the phage was found to be modified at most cytosine
      residues. This phage evades E. faecalis R-M defense, most likely due to this ubiquitous genome
      modification. That the phage encodes an anti-R-M strategy is beneficial for phage therapy
      applications.
AU  - Huo W
PT  - Journal Article
TA  - Ph.D. Thesis
JT  - Ph.D. Thesis
SO  - Ph.D. Thesis 2017 : .

PMID- 25825433
VI  - 197
DP  - 2015
TI  - Genome modification in Enterococcus faecalis OG1RF assessed by bisulfite sequencing and single molecule real time sequencing.
PG  - 1939-1951
AB  - Enterococcus faecalis is a gram-positive bacterium that natively colonizes the human
      gastrointestinal tract and opportunistically causes life-threatening
      infections. Multidrug-resistant (MDR) E. faecalis strains have emerged, reducing
      treatment options for these infections. MDR E. faecalis have large genomes
      containing mobile genetic elements (MGEs) encoding antibiotic resistance and
      virulence determinants. Bacteria commonly possess genome defense mechanisms to
      block MGE acquisition, and we hypothesize that these mechanisms have been
      compromised in MDR E. faecalis. In restriction-modification (R-M) defense, the
      bacterial genome is methylated at cytosine (C) or adenine (A) residues by a
      methyltransferase (MTase) such that non-self DNA can be distinguished from self
      DNA. A cognate restriction endonuclease digests improperly modified non-self DNA.
      Little is known about R-M in E. faecalis. Here, we use genome resequencing to
      identify DNA modifications occurring in the oral isolate OG1RF. OG1RF has one of
      the smallest E. faecalis genomes sequenced to date, and possesses few MGEs.
      Single Molecule Real Time (SMRT) and bisulfite sequencing revealed that OG1RF has
      global 5-methylcytosine (m5C) methylation at 5' -GCWGC-3' motifs. A Type II R-M
      system confers the m5C modification, and disruption of this system impacts OG1RF
      electrotransformability and conjugative transfer of an antibiotic resistance
      plasmid. A second DNA MTase was poorly expressed in laboratory conditions but
      conferred global N4-methylcytosine (m4C) methylation at 5' -CCGG-'3 motifs when
      expressed in Escherichia coli. Based on our results, we conclude that R-M can act
      as a barrier to MGE acquisition and likely influences antibiotic resistance gene
      dissemination in the faecalis species. IMPORTANCE: The horizontal transfer of
      antibiotic resistance genes among bacteria is a critical public health concern.
      Enterococcus faecalis is an opportunistic pathogen causing life-threatening
      infections in humans. Multidrug resistance acquired by horizontal gene transfer
      limits treatment options for these infections. In this study, we use innovative
      DNA sequencing methodologies to investigate how a model strain of E. faecalis
      discriminates its own DNA from foreign DNA - i.e., self versus non-self
      discrimination. We also assess the role of an E. faecalis genome modification
      system in modulating conjugative transfer of an antibiotic resistance plasmid.
      These results are significant because they demonstrate that differential genome
      modification impacts horizontal gene transfer frequencies in E. faecalis.
AU  - Huo W
AU  - Adams HM
AU  - Zhang MQ
AU  - Palmer KL
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2015 197: 1939-1951.

PMID- Not included in PubMed...
VI  - 16
DP  - 1989
TI  - Separation and purification of restriction endonuclease MspI.
PG  - 235-236
AB  - None
AU  - Huo Y
AU  - Li P
PT  - Journal Article
TA  - Shengwu Huaxue Yu Shengwu Wuli Jinzhan
JT  - Shengwu Huaxue Yu Shengwu Wuli Jinzhan
SO  - Shengwu Huaxue Yu Shengwu Wuli Jinzhan 1989 16: 235-236.

PMID- 
VI  - 194
DP  - 2011
TI  - Complete genome sequence of Pelagibacterium halotolerans B2T.
PG  - 197-198
AB  - Pelagibacterium halotolerans B2T is a marine halotolerant bacterium that was isolated from a
      seawater sample collected from the East China Sea. Here, we present the complete genome
      sequence of the type strain P. halotolerans B2T, which consists of one chromosome (3,944,837
      bp; 61.4% G_C content) and one plasmid (4,050 bp; 56.1% G_C content). This is the first
      complete genome of a member of the Pelagibacterium genus.
AU  - Huo Y-Y
AU  - Cheng H
AU  - Han X-F
AU  - Jiang X-W
AU  - Sun C
AU  - Zhang X-Q
AU  - Zhu X-F
AU  - Liu Y-F
AU  - Li P-F
AU  - Ni P-X
AU  - Wu M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 194: 197-198.

PMID- 25945155
VI  - 9
DP  - 2014
TI  - High quality draft genome sequence of the heavy metal resistant bacterium Halomonas zincidurans type strain B6(T).
PG  - 30
AB  - Halomonas zincidurans strain B6(T) was isolated from a deep-sea heavy metal rich  sediment
      from the South Atlantic Mid-Ocean Ridge. The strain showed significant
      resistance to heavy metals, especially to zinc. Here we describe the genome
      sequence and annotation, as well as the features, of the organism. The genome
      contains 3,325 protein-coding genes (2,848 with predicted functions), 61 tRNA
      genes and 6 rRNA genes. H. zincidurans strain B6(T) encodes 31 genes related to
      heavy metal resistance. And HGT may play an important role in its adaption to the
      heavy metal rich environment. H. zincidurans strain B6(T) may have potential
      applications in the bioremediation of heavy metal-contaminated environments.
AU  - Huo YY
AU  - Li ZY
AU  - Cheng H
AU  - Wang CS
AU  - Xu XW
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 30.

PMID- 25614561
VI  - 3
DP  - 2015
TI  - Genome Sequences of the Listeria ivanovii subsp. ivanovii Type Strain and Two Listeria ivanovii subsp. londoniensis Strains.
PG  - e01440-14
AB  - We present the complete genomes of Listeria ivanovii subsp. ivanovii WSLC 3010 (ATCC
      19119(T)), Listeria ivanovii subsp. londoniensis WSLC 30151 (SLCC 8854),
      and Listeria ivanovii subsp. londoniensis WSLC 30167 (SLCC 6032), representing
      the type strain of the species and two strains of the same serovar but different
      properties, respectively.
AU  - Hupfeld M
AU  - Fouts DE
AU  - Loessner MJ
AU  - Klumpp J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01440-14.

PMID- 23103529
VI  - 18
DP  - 2013
TI  - Identification of Novel Bacterial M.SssI DNA Methyltransferase Inhibitors.
PG  - 348-355
AB  - DNA methylation is an important epigenetic regulator of gene expression. Abnormalities in DNA
      methylation patterns have been
      associated with various developmental and proliferative diseases,
      particularly cancer. Targeting DNA methyltransferases (DNMTs)
      represents a promising strategy for the treatment of such diseases.
      Current DNMT inhibitors suffer important drawbacks with respect to
      their efficacy, specificity, and toxicity. In this study, we have set
      up a robust in vitro bacterial M.SssI DNMT activity assay to
      systematically screen a collection of 26 240 compounds that were
      predicted to compete with the S-adenosyl-L-methionine (SAM) substrate
      of DNMT. This resulted in the identification of a novel set of
      structurally distinct inhibitors of M.SssI DNMT activity. Although
      molecular docking studies using an M.SssI homology model suggest that
      these compounds might compete with SAM binding, mode of activity (MoA)
      assays are still needed to confirm this hypothesis. Our set of novel
      M.SssI DNMT inhibitors, once confirmed in an orthogonal DNMT assay, may
      thus serve as a starting point to identify and characterize suitable
      lead candidates for further drug optimization.
AU  - Hupkes M
AU  - Azevedo R
AU  - Jansen H
AU  - van Zoelen EJ
AU  - Dechering KJ
PT  - Journal Article
TA  - J. Biomol. Screen.
JT  - J. Biomol. Screen.
SO  - J. Biomol. Screen. 2013 18: 348-355.

PMID- 9973559
VI  - 286
DP  - 1999
TI  - Mechanism-based inhibition of C5-cytosine DNA methyltransferases by 2-H pyrimidinone.
PG  - 389-401
AB  - DNA duplexes in which the target cytosine base is replaced by 2-H pyrimidinone have previously
      been shown to bind with a significantly greater affinity to C5-cytosine DNA methyltransferases
      than unmodified DNA.  Here, it is shown that 2-H pyrimidinone, when incorporated into DNA
      duplexes containing the recognition sites for M.HgaI-2 and M.MspI, elicits the formation of
      inhibitory covalent nucleoprotein complexes.  We have found that although covalent complexes
      are formed between 2-H pyrimidinone-modified DNA and both M.HgaI-2 and M.MspI, the kinetics of
      complex formation are quite distinct in each case.  Moreover, the formation of a covalent
      complex is still observed between 2-H pyrimidinone DNA and M.MspI in which the active-site
      cysteine residue is replaced by serine or threonine.  Covalent complex formation between
      M.MspI and 2-H pyrimidinone occurs as a direct result of nucleophilic attack by the residue at
      the catalytic position, which is enhanced by the absence of the 4-amino function in the base.
      The substitution of the catalytic cysteine residue by tyrosine or chemical modification of the
      wild-type enzyme with N-ethylmaleimide, abolishes covalent interaction.  Nevertheless the 2-H
      pyrimidinone-substituted duplex still binds to M.MspI with a greater affinity than a standard
      cognate duplex, since the 2-H pyrimidinone base is mis-paired with guanine.
AU  - Hurd PJ
AU  - Whitmarsh AJ
AU  - Baldwin GS
AU  - Kelly SM
AU  - Waltho JP
AU  - Price NC
AU  - Connolly BA
AU  - Hornby DP
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1999 286: 389-401.

PMID- 27187466
VI  - 8
DP  - 2016
TI  - The Draft Genome Sequence of the Yersinia entomophaga Entomopathogenic Type Strain MH96T.
PG  - 143
AB  - Here we report the draft genome of Yersinia entomophaga type strain MH96T. The genome shows
      93.8% nucleotide sequence identity to that of Yersinia nurmii type
      strain APN3a-cT, and comprises a single chromosome of approximately 4,275,531 bp.
      In silico analysis identified that, in addition to the previously documented Y.
      entomophaga Yen-TC gene cluster, the genome encodes a diverse array of toxins,
      including two type III secretion systems, and five rhs-associated gene clusters.
      As well as these multicomponent systems, several orthologs of known insect
      toxins, such as VIP2 toxin and the binary toxin PirAB, and distant orthologs of
      some mammalian toxins, including repeats-in-toxin, a cytolethal distending toxin,
      hemolysin-like genes and an adenylate cyclase were identified. The genome also
      contains a large number of hypothetical proteins and orthologs of known effector
      proteins, such as LopT, as well as genes encoding a wide range of proteolytic
      determinants, including metalloproteases and pathogen fitness determinants, such
      as genes involved in iron metabolism. The bioinformatic data derived from the
      current in silico analysis, along with previous information on the pathobiology
      of Y. entomophaga against its insect hosts, suggests that a number of these
      virulence systems are required for survival in the hemocoel and incapacitation of
      the insect host.
AU  - Hurst MR
AU  - Beattie A
AU  - Altermann E
AU  - Moraga RM
AU  - Harper LA
AU  - Calder J
AU  - Laugraud A
PT  - Journal Article
TA  - Toxins (Basel)
JT  - Toxins (Basel)
SO  - Toxins (Basel) 2016 8: 143.

PMID- 15262948
VI  - 186
DP  - 2004
TI  - Cloning Serratia entomophila antifeeding genes--a putative defective prophage active against the grass grub Costelytra zealandica.
PG  - 5116-5128
AB  - Serratia entomophila and Serratia proteamaculans (Enterobacteriaceae)
      cause amber disease in the grass grub Costelytra zealandica (Coleoptera:
      Scarabaeidae), an important pasture pest in New Zealand. Larval disease
      symptoms include cessation of feeding, clearance of the gut, amber
      coloration, and eventual death. A 155-kb plasmid, pADAP, carries the genes
      sepA, sepB, and sepC, which are essential for production of amber disease
      symptoms. Transposon insertions in any of the sep genes in pADAP abolish
      gut clearance but not cessation of feeding, indicating the presence of an
      antifeeding gene(s) elsewhere on pADAP. Based on deletion analysis of
      pADAP and subsequent sequence data, a 47-kb clone was constructed, which
      when placed in either an Escherichia coli or a Serratia background exerted
      strong antifeeding activity and often led to rapid death of the infected
      grass grub larvae. Sequence data show that the antifeeding component is
      part of a large gene cluster that may form a defective prophage and that
      six potential members of this prophage are present in Photorhabdus
      luminescens subsp. laumondii TTO1, a species which also has sep gene
      homologues.
AU  - Hurst MR
AU  - Glare TR
AU  - Jackson TA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2004 186: 5116-5128.

PMID- 25502670
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Photorhabdus temperata Strain Meg1, an Entomopathogenic  Bacterium Isolated from Heterorhabditis megidis Nematodes.
PG  - e01273-14
AB  - Photorhabdus temperata strain Meg1 is an entomopathogenic bacterium that forms a  symbiotic
      association with Heterorhabditis nematodes. We report here a 4.9-Mbp
      draft genome sequence for P. temperata strain Meg1, with a G+C content of 43.18%
      and containing 4,340 candidate protein-coding genes.
AU  - Hurst SG IV
AU  - Ghazal S
AU  - Morris K
AU  - Abebe-Akele F
AU  - Thomas WK
AU  - Badr UM
AU  - Hussein MA
AU  - AbouZaied MA
AU  - Khalil KM
AU  - Tisa LS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01273-14.

PMID- 24855310
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Frankia sp. Strain Thr, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina cunninghamiana Grown   in Egypt.
PG  - e00493-14
AB  - Nitrogen-fixing actinobacteria of the genus Frankia are symbionts of woody dicotyledonous
      plants termed actinorhizal plants. We report here a 5.3-Mbp draft
      genome sequence for Frankia sp. stain Thr, a nitrogen-fixing actinobacterium
      isolated from root nodules of Casuarina cunninghamiana collected in Egypt.
AU  - Hurst SGIV
AU  - Oshone R
AU  - Ghodhbane-Gtari F
AU  - Morris K
AU  - Abebe-Akele F
AU  - Thomas WK
AU  - Ktari A
AU  - Salem K
AU  - Mansour S
AU  - Gtari M
AU  - Tisa LS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00493-14.

PMID- 27257203
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a Mycobacterium africanum Clinical Isolate from Antioquia, Colombia.
PG  - e00486-16
AB  - Mycobacterium africanum is a member of the Mycobacterium tuberculosis complex. Most commonly
      found in West African countries, it has scarcely been described in
      South America. Here, we report the first genome sequence of a Colombian M.
      africanum clinical isolate. It is composed of 4,493,502 bp, with 4,069 genes.
AU  - Hurtado UA
AU  - Solano JS
AU  - Rodriguez A
AU  - Robledo J
AU  - Rouzaud F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00486-16.

PMID- 28428302
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of a Multidrug-Resistant Pseudomonas aeruginosa Strain Isolated from a Patient with a Urinary Tract Infection in Khartoum, Sudan.
PG  - e00203-17
AB  - Pseudomonas aeruginosa infection is difficult to treat due to the presence of antibiotic
      resistance determinants. Here, we report the genome sequence of a
      multidrug-resistant P. aeruginosa strain isolated from a patient with a urinary
      tract infection in 2015.
AU  - Hussain M
AU  - Suliman M
AU  - Ahmed A
AU  - Altayb H
AU  - Elneima E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00203-17.

PMID- 10591650
VI  - 286
DP  - 1999
TI  - Global transposon mutagenesis and a minimal mycoplasma genome.
PG  - 2165
AB  - Mycoplasma genitalium with 517 genes has the smallest gene complement of any independently
      replicating cell so far identified.  Global transposon mutagenesis was used to identify
      nonessential genes in an effort to learn whether the naturally occurring gene complement is a
      true minimal genome under laboratory growth conditions. The positions of 2209 transposon
      insertions in the completely sequenced genomes of M. genitalium and its close relative M.
      pneumoniae were determined by sequencing across the junction of the transposon and the genomic
      DNA. These junctions defined 1354 distinct sites of insertion that were not lethal.  The
      analysis suggests that 265 to 350 of the 480 protein-coding genes of M. genitalium are
      essential under laboratory growth conditions, including about 100 genes of unknown function.
AU  - Hutchison CA III
AU  - Peterson SN
AU  - Gill SR
AU  - Cline RT
AU  - White O
AU  - Fraser CM
AU  - Smith HO
AU  - Venter JC
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1999 286: 2165.

PMID- 28127420
VI  - 12
DP  - 2017
TI  - Permanent draft genome of Thiobacillus thioparus DSM 505T, an obligately chemolithoautotrophic member of the Betaproteobacteria.
PG  - 10
AB  - Thiobacillus thioparus DSM 505T is one of first two isolated strains of inorganic
      sulfur-oxidising Bacteria. The original strain of T. thioparus was lost almost
      100 years ago and the working type strain is Culture CT (=DSM 505T = ATCC 8158T)
      isolated by Starkey in 1934 from agricultural soil at Rutgers University, New
      Jersey, USA. It is an obligate chemolithoautotroph that conserves energy from the
      oxidation of reduced inorganic sulfur compounds using the Kelly-Trudinger pathway
      and uses it to fix carbon dioxide It is not capable of heterotrophic or
      mixotrophic growth. The strain has a genome size of 3,201,518 bp. Here we report
      the genome sequence, annotation and characteristics. The genome contains 3,135
      protein coding and 62 RNA coding genes. Genes encoding the transaldolase variant
      of the Calvin-Benson-Bassham cycle were also identified and an operon encoding
      carboxysomes, along with Smith's biosynthetic horseshoe in lieu of Krebs' cycle
      sensu stricto. Terminal oxidases were identified, viz. cytochrome c oxidase
      (cbb3, EC 1.9.3.1) and ubiquinol oxidase (bd, EC 1.10.3.10). There is a partial
      sox operon of the Kelly-Friedrich pathway of inorganic sulfur-oxidation that
      contains soxXYZAB genes but lacking soxCDEF, there is also a lack of the DUF302
      gene previously noted in the sox operon of other members of the 'Proteobacteria'
      that can use trithionate as an energy source. In spite of apparently not growing
      anaerobically with denitrification, the nar, nir, nor and nos operons encoding
      enzymes of denitrification are found in the T. thioparus genome, in the same
      arrangements as in the true denitrifier T. denitrificans.
AU  - Hutt LP
AU  - Huntemann M
AU  - Clum A
AU  - Pillay M
AU  - Palaniappan K
AU  - Varghese N
AU  - Mikhailova N
AU  - Stamatis D
AU  - Reddy T
AU  - Daum C
AU  - Shapiro N
AU  - Ivanova N
AU  - Kyrpides N
AU  - Woyke T
AU  - Boden R
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 10.

PMID- 27811105
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Alkaliphilus metalliredigens Strain QYMF, an Alkaliphilic and Metal-Reducing Bacterium Isolated from Borax-Contaminated  Leachate Ponds.
PG  - e01226-16
AB  - Alkaliphilus metalliredigens strain QYMF is an anaerobic, alkaliphilic, and metal-reducing
      bacterium associated with phylum Firmicutes QYMF was isolated from
      alkaline borax leachate ponds. The genome sequence will help elucidate the role
      of metal-reducing microorganisms under alkaline environments, a capability that
      is not commonly observed in metal respiring-microorganisms.
AU  - Hwang C et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01226-16.

PMID- 25614562
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Anaeromyxobacter sp. Fw109-5, an Anaerobic, Metal-Reducing Bacterium Isolated from a Contaminated Subsurface Environment.
PG  - e01449-14
AB  - We report the genome sequence of Anaeromyxobacter sp. Fw109-5, isolated from nitrate- and
      uranium-contaminated subsurface sediment of the Oak Ridge Integrated
      Field-Scale Subsurface Research Challenge (IFC) site, Oak Ridge Reservation, TN.
      The bacterium's genome sequence will elucidate its physiological potential in
      subsurface sediments undergoing in situ uranium bioremediation and natural
      attenuation.
AU  - Hwang C et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01449-14.

PMID- 17483805
VI  - 45
DP  - 2007
TI  - Recombinant expression and purification of functional XorII, a restriction endonuclease from Xanthomonas oryzae pv. oryzae.
PG  - 175-178
AB  - An endonuclease from Xanthomonas oryzae pathovar oryzae KACC 10331, XorII, was recombinantly
      produced in Escherichia coli using a T7
      system. XorII was purified using a combination of ion exchange and
      immobilized metal affinity chromatography (IMAC). An optimized washing
      protocol was carried out on an IMAC in order to obtain a high purity
      product. The final amount of purified XorII was approximately 2.5 mg/L
      of LB medium. The purified recombinant XorII was functional and showed
      the same cleavage pattern as PvuI. The enzyme activity tested the
      highest at 25 degrees C in 50 mM NaCl, 10 mM Tris-HCl, 10 mM MgCl2, and
      1 mM dithiothreitol at a pH of 7.9.
AU  - Hwang DK
AU  - Cho JY
AU  - Chae YK
PT  - Journal Article
TA  - J. Microbiol.
JT  - J. Microbiol.
SO  - J. Microbiol. 2007 45: 175-178.

PMID- 8036144
VI  - 22
DP  - 1994
TI  - SolI, a novel isoschizomer of BamHI isolated from Streptoverticillium olivoverticillatum.
PG  - 2197
AB  - SolI, a new type II restriction endonuclease has been purified from Streptoverticillium
      olivoverticillatum by chromatography on heparin-agarose and affigel-blue. The enzyme
      recognizes the palindromic hexanucleotide sequence of 5'-GGATCC-3' and cleaves after the
      first G to produce a 4 base 5'-extension.
AU  - Hwang H-Y
AU  - Yim J
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1994 22: 2197.

PMID- Not carried by PubMed...
VI  - 32
DP  - 1994
TI  - Characterization of a new type II restriction endonuclease isolated from Streptoverticillium olivoverticillatum.
PG  - 208-214
AB  - We screened many species from a wide variety of bacterial genera for a new type II restriction
      endonuclease.  The purification and characterization of SolI from a soil isolate,
      Streptoverticillum olivoverticillatum are described here.  The enzyme turned out to be an
      isoschizomer of BamHI.  It recognized the hexanucleotide sequence 5'-G/GATCC-3' and cleaved
      as shown by the arrow, generating a 4 base 5' extension.  Unlike its isoschizomer, BamHI, the
      activity was sensitive to dam methylation within the recognition sequence.  Following
      ammonium sulfate fractionation of the crude extract, heparin-agarose and Affi-gel Blue column
      chromatography were employed to purify the enzyme.  SolI required at least 0.2 mM of MgCl2 for
      the cleavage to occur.  The enzyme exhibited its maximal activity in the absence of NaCl, but
      was inhibited completely in the presence of 120mM NaCl.  The pH and temperature optima for
      activity were pH 8.6 and 40oC, respectively.  The molecular weight of SolI was estimated to be
      43,000 Da by Superose-12 gel filtration chromatography.
AU  - Hwang HY
AU  - Yim J
PT  - Journal Article
TA  - Korean J. Microbiol.
JT  - Korean J. Microbiol.
SO  - Korean J. Microbiol. 1994 32: 208-214.

PMID- 24948770
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Kitasatospora cheerisanensis KCTC 2395, Which Produces Plecomacrolide against Phytopathogenic Fungi.
PG  - e00604-14
AB  - Kitasatospora cheerisanensis KCTC 2395, which produces antifungal metabolites with bafilomycin
      derivatives, including bafilomycin C1-amide, was isolated from a
      soil sample at Mt. Jiri, South Korea. Here, we report its draft genome sequence,
      which contains 8.04 Mb with 73.6% G+C content and 7,810 protein-coding genes.
AU  - Hwang JY
AU  - Kim SH
AU  - Oh HR
AU  - Cho YJ
AU  - Chun J
AU  - Chung YR
AU  - Nam DH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00604-14.

PMID- 26404601
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Acetobacterium bakii DSM 8239, a Potential Psychrophilic Chemical Producer through Syngas Fermentation.
PG  - e01070-15
AB  - Acetobacterium bakii DSM 8239 is an anaerobic, psychrophilic, and chemolithoautotrophic
      bacterium that is a potential platform for producing commodity chemicals from syngas
      fermentation. We report here the draft genome sequence of A. bakii DSM 8239 (4.14 Mb) to
      elucidate its physiological and metabolic properties related to syngas fermentation.
AU  - Hwang S
AU  - Song Y
AU  - Cho BK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01070-15.

PMID- Not carried by PubMed...
VI  - 33
DP  - 1990
TI  - Character and function of restriction enzyme, EcoRI inhibiting substance extracted from spinach chloroplast and Chlamydomonas.
PG  - 217-223
AB  - Restriction enzyme inhibiting substance (REIS) extracted from spinach
      chloroplast and Chlamydomonas seems not to be proteinaceous, because its
      inhibiting activity was not lost by heat or trypsin treatment.  And it seems
      not to be lipid or polysaccharide, because its inhibiting activity was not lost
      by lipase or alpha-amylase treatment, respectively.  In Chlamydomonas,
      putrescine, spermidine and spermine were present.  The amount of putrescine was
      the smallest and that of spermine was the greatest.  But only spermine was
      contained in REIS and the activity of REIS.  It was proportional to the amount
      of spermine in REIS and it was hindered by Na+ ion.  So, the inhibiting
      activity of REIS seems to be deeply related to spermine contained in REIS.  But
      restriction enzyme inhibiting activity remained to the same extent although
      salts and spermine were eliminated by dialysis.
AU  - Hwang SB
AU  - Lee SH
PT  - Journal Article
TA  - Singmul Hakhoe Chi
JT  - Singmul Hakhoe Chi
SO  - Singmul Hakhoe Chi 1990 33: 217-223.

PMID- 27340060
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Dyella thiooxydans ATSB10, a Thiosulfate-Oxidizing Bacterium Isolated from Sunflower Fields in South Korea.
PG  - e00573-16
AB  - Dyella thiooxydans ATSB10 (KACC 12756(T) = LMG 24673(T)) is a thiosulfate-oxidizing bacterium
      isolated from rhizosphere soils of sunflower
      plants. In this study, we completely sequenced the genome of D. thiooxydans
      ATSB10 and identified the genes involved in thiosulfate oxidation and the
      metabolism of aromatic intermediates.
AU  - Hwangbo K
AU  - Um Y
AU  - Chung H
AU  - Yoo J
AU  - Kim KY
AU  - Madhaiyan M
AU  - Sa TM
AU  - Lee Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00573-16.

PMID- 27417835
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Bacillus velezensis CBMB205, a Phosphate-Solubilizing Bacterium Isolated from the Rhizoplane of Rice in the Republic of Korea.
PG  - e00654-16
AB  - Bacillus velezensis CBMB205 (= KACC 13105(T) = NCCB 100236(T)) was isolated from  the
      rhizoplane of rice (Oryza sativa L. cv. O-dae). According to previous
      studies, this bacterium has several genes that can promote plant growth, such as
      the phosphorus-solubilizing protein-coding gene. Here, we present the first
      complete genome of B. velezensis CBMB205.
AU  - Hwangbo K
AU  - Um Y
AU  - Kim KY
AU  - Madhaiyan M
AU  - Sa TM
AU  - Lee Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00654-16.

PMID- 26798096
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a 94-Year-Old Listeria monocytogenes Isolate, SLCC208.
PG  - e01572-15
AB  - We report here the draft genome sequence of Listeria monocytogenes strain SLCC208 from
      Seeliger's historical Special Listeria Culture Collection, initially
      cultured from a human case in France in 1921. This is, to our knowledge, the
      oldest L. monocytogenes isolate available and may be useful for comparative
      genomic studies of L. monocytogenes.
AU  - Hyden P
AU  - Pietzka A
AU  - Allerberger F
AU  - Springer B
AU  - Sensen C
AU  - Ruppitsch W
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01572-15.

PMID- 20359459
VI  - 70
DP  - 2010
TI  - Bacteriophage Host Range and Bacterial Resistance.
PG  - 217-248
AB  - Host range describes the breadth of organisms a parasite is capable of infecting, with limits
      on host range stemming from parasite, host, or environmental characteristics. Parasites can
      adapt to overcome host or environmental limitations, while hosts can adapt to control the
      negative impact of parasites. We consider these adaptations as they occur among bacteriophages
      (phages) and their bacterial hosts, since they are significant to phage use as antibacterials
      (phage therapy) or to protection of industrial ferments from phage attack. Initially, we
      address how phage host range can (and should) be defined plus summarize claims of host ranges
      spanning multiple bacterial genera. Subsequently, we review bacterial mechanisms of phage
      resistance. These include adsorption resistance, which results in reduced interaction between
      phage and bacterium; what we describe as 'restriction,' where bacteria live but phages die;
      and abortive infections, where both phage and bacterium die. Adsorption resistance includes
      loss of phage receptor molecules on hosts as welt as physical barriers hiding receptor
      molecules (e.g., capsules). Restriction mechanisms include phage-genome uptake blocks,
      superinfection immunity, restriction modification, and CRISPR, all of which function postphage
      adsorption but prior to terminal phage takeover of host metabolism. Standard laboratory
      selection methods, involving exposure of planktonic bacteria to high phage densities, tend to
      directly select for these prehost-takeover resistance mechanisms. Alternatively, resistance
      mechanisms that do not prevent bacterium death are less readily artificially selected.
      Contrasting especially bacteria mutation to adsorption resistance, these latter mechanisms
      likely are an underappreciated avenue of bacterial resistance to phage attack.
AU  - Hyman P
AU  - Abedon ST
PT  - Journal Article
TA  - Adv. Appl. Microbiol.
JT  - Adv. Appl. Microbiol.
SO  - Adv. Appl. Microbiol. 2010 70: 217-248.

PMID- 20418427
VI  - 76
DP  - 2010
TI  - Multiplex identification of microbes.
PG  - 3904-3910
AB  - We have adapted molecular inversion probe technology to identify
      microbes in a highly multiplexed procedure. This procedure does not
      require growth of the microbes. Rather, the technology employs DNA
      homology twice: once for the molecular probe to hybridize to its
      homologous DNA and again for the 20-mer oligonucleotide barcode on the
      molecular probe to hybridize to a commercially available molecular
      barcode array. As proof of concept, we have designed, tested, and
      employed 192 molecular probes for 40 microbes. While these particular
      molecular probes are aimed at our interest in the microbes in the human
      vagina, this molecular probe method could be employed to identify the
      microbes in any ecological niche.
AU  - Hyman RW
AU  - St-Onge RP
AU  - Allen EA
AU  - Miranda M
AU  - Aparicio AM
AU  - Fukushima M
AU  - Davis RW
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2010 76: 3904-3910.

PMID- 30533898
VI  - 7
DP  - 2018
TI  - Genome Sequence of a Plant Growth-Promoting Rhizobacterium, Pseudomonas sp. Strain 31-12.
PG  - e00947-18
AB  - We present here a draft genome sequence of Pseudomonas sp. strain 31-12, a plant
      growth-promoting rhizobacterium of several crop plants that was isolated from the
      rhizosphere of corn in southern Ontario, Canada.
AU  - Hynes RK
AU  - Dumonceaux TJ
AU  - Kangsopa J
AU  - Town JR
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e00947-18.

PMID- 26450734
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Exiguobacterium sp. Strain BMC-KP, an Environmental Isolate from Bryn Mawr, Pennsylvania.
PG  - e01164-15
AB  - Exiguobacterium sp. strain BMC-KP was isolated as part of a student environmental sampling
      project at Bryn Mawr College, PA. Sequencing of bacterial DNA assembled  a 3.32-Mb draft
      genome. Analysis suggests the presence of genes for tolerance to  cold and toxic metals, broad
      carbohydrate metabolism, and genes derived from phage.
AU  - Hyson P
AU  - Shapiro JA
AU  - Wien MW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01164-15.

PMID- 23991257
VI  - 8
DP  - 2013
TI  - Genome sequence of the moderately halophilic bacterium Salinicoccus carnicancri type strain Crm(T) (= DSM 23852(T)).
PG  - 255-263
AB  - Salinicoccus carnicancri Jung et al. 2010 belongs to the genus Salinicoccus in the family
      Staphylococcaceae. Members of the Salinicoccus are moderately
      halophilic and originate from various salty environments. The halophilic features
      of the Salinicoccus suggest their possible uses in biotechnological applications,
      such as biodegradation and fermented food production. However, the genus
      Salinicoccus is poorly characterized at the genome level, despite its potential
      importance. This study presents the draft genome sequence of S. carnicancri
      strain Crm(T) and its annotation. The 2,673,309 base pair genome contained 2,700
      protein-coding genes and 78 RNA genes with an average G+C content of 47.93 mol%.
      It was notable that the strain carried 72 predicted genes associated with
      osmoregulation, which suggests the presence of beneficial functions that
      facilitate growth in high-salt environments.
AU  - Hyun DW
AU  - Whon TW
AU  - Cho YJ
AU  - Chun J
AU  - Kim MS
AU  - Jung MJ
AU  - Shin NR
AU  - Kim JY
AU  - Kim PS
AU  - Yun JH
AU  - Lee J
AU  - Oh SJ
AU  - Bae JW
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 255-263.

PMID- 25858829
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Lactobacillus acidophilus FSI4, Isolated from Yogurt.
PG  - e00166-15
AB  - A new Lactobacillus acidophilus strain, FSI4, isolated from yogurt, was isolated  and
      sequenced in our laboratory. Our data, although supportive of previous
      conclusions regarding the remarkable stability of L. acidophilus species,
      indicate accumulating mutations in commercial L. acidophilus strains that warrant
      further study of the effect of damaged genes on the competitiveness of these
      bacteria in gut microbiota.
AU  - Iartchouk O
AU  - Kozyavkin S
AU  - Karamychev V
AU  - Slesarev A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00166-15.

PMID- 24558243
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Highly Nematicidal Bacillus thuringiensis DB27.
PG  - e00101-14
AB  - Here, we report the genome sequence of nematicidal Bacillus thuringiensis DB27, which provides
      first insights into the genetic determinants of its pathogenicity
      to nematodes. The genome consists of a 5.7-Mb chromosome and seven plasmids,
      three of which contain genes encoding nematicidal proteins.
AU  - Iatsenko I
AU  - Corton C
AU  - Pickard DJ
AU  - Dougan G
AU  - Sommer RJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00101-14.

PMID- 28408668
VI  - 5
DP  - 2017
TI  - Genome Sequence of Cobetia sp. Strain MM1IDA2H-1, a Hydrocarbon-Degrading and Biosurfactant-Producing Marine Bacterium.
PG  - e00132-17
AB  - Cobetia sp. strain MM1IDA2H-1 is a marine bacterium isolated from seawater samples that uses
      the heterocyclic aromatic hydrocarbon dibenzothiophene as the
      sole carbon source and produces a biosurfactant that inhibits bacterial quorum
      sensing. The Cobetia sp. MM1IDA2H-1 genome was sequenced, processed, assembled,
      and annotated for basic and applied studies.
AU  - Ibacache-Quiroga C
AU  - Canales C
AU  - Charifeh M
AU  - Dinamarca MA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00132-17.

PMID- 9322752
VI  - 196
DP  - 1997
TI  - A ColE1-type plasmid from Salmonella enteritidis encodes a DNA cytosine methyltransferase.
PG  - 145-158
AB  - The multicopy plasmid pFM366 was isolated from a virulent Salmonella enteritidis strain and
      was found to code for DNA methylase activity (Ibanez and Rotger, 1993). The present work was
      aimed at characterizing the genetic organization and functional of this 5.6 kb plasmid. We
      found pFM366 almost identical to the plasmid P4 isolated from Shigella sonnei, that encodes
      the SsoII restriction-modification system (Karyagina et al., 1993), and related to other
      ColE1-type plasmids. Examination of these plasmids revealed a common organization which
      suggests they were the result of similar recombinational events. The cytosine methylase of
      pFM366 is nearly identical to M. SsoII, whereas the gene encoding the restrictase homologous
      to R. SsoII is truncated and its product is inactive. The expression of the cytosine methylase
      encoded by pFM366 is strongly affected by deletion of regions located upstream and downstream
      of its ORF, and is negatively controlled by the rpoS gene in Escherichia coli. The methylase
      activity encoded by pFM366 induces the SOS response, which could be responsible for the
      observed delay in the growth of E. coli.
AU  - Ibanez M
AU  - Alvarez I
AU  - Rodriguez-Pena JM
AU  - Rotger R
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1997 196: 145-158.

PMID- 8339914
VI  - 109
DP  - 1993
TI  - Characterization of small cryptic plasmid from Salmonella enteritidis that affects the growth of Escherichia coli.
PG  - 225-230
AB  - We examined the plasmid content of 25 clinical isolates of Salmonella enteritidis, and
      detected the presence of small plasmids (3-5.3 kb) in 9 of them, alone, or in addition to the
      large, so-called virulence plasmid.  A 5.3-kb plasmid isolated as unique extrachromosomal DNA
      from a strain responsible for a high-mortality outbreak was characterized by restriction
      mapping and cloning.  The plasmid replicon was localized in a 1.7-kb fragment, that hybridized
      with three of the small plasmids detected in S. enteritidis, and with another small plasmid
      from Salmonella typhimurium.  A strain of Escherichia coli carrying this plasmid, or a cloned
      3.7-kb PvuII restriction fragment, showed a slower growth rate, especially in minimal medium,
      as well as a noticeable increase in DNA methyltransferase activity.
AU  - Ibanez M
AU  - Rotger R
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1993 109: 225-230.

PMID- 24926062
VI  - 2
DP  - 2014
TI  - Genome Sequences of Strain ATCC 29281 and Pin and Northern Red Oak Isolates of Lonsdalea quercina subsp. quercina.
PG  - e00584-14
AB  - Two bacteria identified as Lonsdalea quercina subsp. quercina were isolated from  oak trees
      showing symptoms of drippy blight. Here, we present their draft genome assemblies, as well as
      that of the type strain of this species. To our knowledge, these are the first published
      genome sequences of this subspecies of Lonsdalea quercina.
AU  - Ibarra-Caballero J
AU  - Zerillo MM
AU  - Snelling J
AU  - Cranshaw W
AU  - Boucher C
AU  - Tisserat N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00584-14.

PMID- 27979935
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Bacillus subtilis Ia1a, a New Strain for Poly-gamma-Glutamic Acid and Exopolysaccharide Production.
PG  - e01361-16
AB  - We report here the 4.092-Mb high-quality draft genome assembly of a newly isolated
      poly-gamma-glutamic acid-producing strain, Bacillus subtilis Ia1a. The
      genome sequence is considered a critical tool to facilitate the engineering of
      improved production strains. Exopolysaccharides and many industrially important
      enzymes can be produced by this new strain utilizing different carbon sources.
AU  - Ibrahim MH
AU  - Cress BF
AU  - Linhardt RJ
AU  - Koffas MA
AU  - Gross RA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01361-16.

PMID- 19361436
VI  - 387
DP  - 2009
TI  - Oligomeric structure diversity within the GIY-YIG nuclease family.
PG  - 10-16
AB  - The GIY-YIG nuclease domain has been identified in homing endonucleases, DNA repair and
      recombination enzymes, and restriction endonucleases.  The Type II restriction enzyme Eco29kI
      belongs to the GIY-YIG nuclease superfamily and, like most of other family members, including
      the homing endonuclease I-TevI, is a monomer. It recognizes the palindromic sequence
      5'-CCGC/GG-3' ('/' marks the cleavage position) and cuts it to generate 3'-staggered
      ends. The Eco29kI monomer, which contains a single active site, either has to nick
      sequentially individual DNA strands or has to form dimers or even higher-order oligomers upon
      DNA binding to make a double-strand break at its target site. Here, we provide experimental
      evidence that Eco29kI monomers dimerize on a single cognate DNA molecule forming the
      catalytically active complex. The mechanism described here for Eco29kI differs from that of
      Cfr42I isoschisomer, which also belongs to the GIY-YIG family but is functional as a tetramer.
      This novel mechanism may have implications for the function of homing endonucleases and other
      enzymes of the GIY-YIG family.
AU  - Ibryashkina EM
AU  - Sasnauskas G
AU  - Solonin AS
AU  - Zakharova MV
AU  - Siksnys V
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2009 387: 10-16.

PMID- 17626614
VI  - 7
DP  - 2007
TI  - Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily.
PG  - 48
AB  - The majority of experimentally determined crystal structures of type II restriction
      endonucleases exhibit a common PD-(D/E)XK fold.  Crystal structures have been also determined
      for single representatives of two other folds: PLD (R.BfiI) and half-pipe (R.PabI), and
      bioinformatics analyses supported by mutagenesis suggested that some REases belong to the HNH
      fold.  Our previous bioinformatic analysis suggested that REase R.Eco29kl shares sequence
      similarities with one more unrelated nuclease superfamily.  GIY-YIG, however so far no
      experimental data were available to support this prediction.  The determination of a crystal
      structure of the GIY-YIG domain of homing endonuclease I-TevI provided a template for modeling
      of R.Eco29kl and prompted us to validate the model experimentally. Using protein
      fold-recognition methods we generated a new alignment between R.Eco29kl and I-TevI, which
      suggested a reassignment of one of the putative catalytic residues.  A theoretical model of
      R.Eco29kl was constructed to illustrate its predicted three-dimensional fold and organization
      of the active site, comprising amino acid residues Y49, Y76, R104, H108, E142, and N154.  A
      series of mutants was constructed to generate amino acid substitutions of selected residues
      (Y49A, R104A, H108F, E142A and N154L) and the mutant proteins were examined for their ability
      to bind the DNA containing the Eco29kl site 5'-CCGCGG-3' and to catalyze the cleavage
      reaction.  Experimental data reveal that residues Y49, R104, E142, H108, and N154 are
      important for the nuclease activity of R.Eco29kl, while H108 and N154 are also important for
      specific DNA binding by this enzyme.
AU  - Ibryashkina EM
AU  - Zakharova MV
AU  - Baskunov VB
AU  - Bogdanova ES
AU  - Nagornykh MO
AU  - Den'mukhamedov MM
AU  - Melnik BS
AU  - Kolinski A
AU  - Gront D
AU  - Feder M
AU  - Solonin AS
AU  - Bujnicki JM
PT  - Journal Article
TA  - BMC Struct. Biol.
JT  - BMC Struct. Biol.
SO  - BMC Struct. Biol. 2007 7: 48.

PMID- 17904519
VI  - 363
DP  - 2007
TI  - In silco irestiriction landmairk genome scanning analysis of Xanthomonas oryzae pathovair oryzae MAFF 311018.
PG  - 852-856
AB  - We have developed a restriction landmark genome scanning (RLGS) system in silico, involving
      two-dimensional electrophoretic analysis of DNA by
      computer simulation that is based on the availability of whole-genome
      sequences for specific organisms. We applied the technique to the
      analysis of the Xanthomonas oryzae pathovar oryzae (Xoo) MAFF 311018,
      which causes bacterial blight in rice. The coverage that was found to
      be achievable using RLGS in silico, as a percentage of the genomic
      regions that could be detected, ranged from 44.5% to 72.7% per image.
      However, this reached a value of 96.7% using four images that were
      obtained with different combinations of landmark restriction enzymes.
      Interestingly, the signal intensity of some of the specific spots
      obtained was significantly lower than that of other surrounding spots
      when Mbol, which cleaves unmethylated 5'-GATC-3' sites, was used. DNA
      gel blot analysis with both DNA adenine methylase (Dam)-sensitive and
      -insensitive isoschizomers (Mbol and Sau3AI) revealed that Dam-mediated
      DNA adenine methylation had indeed occurred at these particular sites.
      These results suggest that a significant portion of the 5'-GATC-3'
      sites within the Xoo genome is stably methylated by Dam.
AU  - Ichida H
AU  - Maeda K
AU  - Ichise H
AU  - Matsuyama T
AU  - Abe T
AU  - Yoneyama K
AU  - Koba T
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 2007 363: 852-856.

PMID- 17250744
VI  - 274
DP  - 2007
TI  - DNA adenine methylation changes dramatically during establishment of symbiosis.
PG  - 951-962
AB  - The DNA adenine methylation status on specific 5'-GANTC-3' sites and its
      change during the establishment of plant-microbe interactions was
      demonstrated in several species of alpha-proteobacteria. Restriction
      landmark genome scanning (RLGS), which is a high-resolution two
      dimensional DNA electrophoresis method, was used to monitor the genomewide
      change in methylation. In the case of Mesorhizobium loti MAFF303099, real
      RLGS images obtained with the restriction enzyme MboI, which digests at
      GATC sites, almost perfectly matched the virtual RLGS images generated
      based on genome sequences. However, only a few spots were observed when
      the restriction enzyme HinfI was used, suggesting that most GANTC (HinfI)
      sites were tightly methylated and specific sites were unmethylated. DNA
      gel blot analysis with the cloned specifically unmethylated regions (SUMs)
      showed that some SUMs were methylated differentially in bacteroids
      compared to free-living bacteria. SUMs have also been identified in other
      symbiotic and parasitic bacteria. These results suggest that DNA adenine
      methylation may contribute to the establishment and/or maintenance of
      symbiotic and parasitic relationships.
AU  - Ichida H
AU  - Matsuyama T
AU  - Abe T
AU  - Koba T
PT  - Journal Article
TA  - FEBS J.
JT  - FEBS J.
SO  - FEBS J. 2007 274: 951-962.

PMID- 
VI  - 80
DP  - 2005
TI  - Stability of EcoRI restriction modification enzymes in vivo differentiates EcoRI restriction-modification system from other postsegregational cell killing systems.
PG  - 454
AB  - Certain Type II restriction modification gene systems can kill host cells when these gene
      systems are eliminated from the host cells.  Such ability to cause prostsegregational killing
      of host cells is the feature of bacterial addiction modules, each of which consists of toxin
      and antitoxin genes.  With these addiction modules, differential stability of toxin and
      antitoxin molecules in cells plays an essential role in execution of postsegregational
      killing.  We here examined in vivo stability of the EcoRI restriction enzyme (toxin) and
      modification enzyme (antitoxin) in Escherichia coli.  Using Western blot analysis and
      pulse-chase immunoprecipitation analysis, we demonstrated that both the EcoRI restriction
      enzyme and modification enzyme are as stable as bulk cellular proteins and that there is no
      marked difference in their stability.  We also monitored changes in cellular levels of the
      EcoRI restriction and modification enzyme during postsegregational killing.  Results from
      these analyses together suggest that the EcoRI gene system does not rely on differential
      stability between the toxin and the antitoxin molecules for execution of postsegregational
      cell killing.
AU  - Ichige A
AU  - Kobayashi I
PT  - Journal Article
TA  - Genes Genet. Syst.
JT  - Genes Genet. Syst.
SO  - Genes Genet. Syst. 2005 80: 454.

PMID- 16166522
VI  - 187
DP  - 2005
TI  - Stability of EcoRI Restriction-Modification Enzymes In Vivo Differentiates the EcoRI Restriction-Modification System from Other Postsegregational   Cell Killing Systems.
PG  - 6612-6621
AB  - Certain type II restriction modification gene systems can kill host cells when these gene
      systems are eliminated from the host cells. Such ability
      to cause postsegregational killing of host cells is the feature of
      bacterial addiction modules, each of which consists of toxin and antitoxin
      genes. With these addiction modules, the differential stability of toxin
      and antitoxin molecules in cells plays an essential role in the execution
      of postsegregational killing. We here examined in vivo stability of the
      EcoRI restriction enzyme (toxin) and modification enzyme (antitoxin), the
      gene system of which has previously been shown to cause postsegregational
      host killing in Escherichia coli. Using two different methods, namely,
      quantitative Western blot analysis and pulse-chase immunoprecipitation
      analysis, we demonstrated that both the EcoRI restriction enzyme and
      modification enzyme are as stable as bulk cellular proteins and that there
      is no marked difference in their stability. The numbers of EcoRI
      restriction and modification enzyme molecules present in a host cell
      during the steady-state growth were estimated. We monitored changes in
      cellular levels of the EcoRI restriction and modification enzymes during
      the postsegregational killing. Results from these analyses together
      suggest that the EcoRI gene system does not rely on differential stability
      between the toxin and the antitoxin molecules for execution of
      postsegregational cell killing. Our results provide insights into the
      mechanism of postsegregational killing by restriction-modification
      systems, which seems to be distinct from mechanisms of postsegregational
      killing by other bacterial addiction modules.
AU  - Ichige A
AU  - Kobayashi I
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2005 187: 6612-6621.

PMID- 21059706
VI  - 17
DP  - 2010
TI  - Genome Sequence of Kitasatospora setae NBRC 14216T: An Evolutionary Snapshot of the Family Streptomycetaceae.
PG  - 393-406
AB  - Kitasatospora setae NBRC 14216T (5KM-6054T) is known to produce setamycin (bafilomycin B1)
      possessing antitrichomonal activity. The genus Kitasatospora is morphologically similar to the
      genus Streptomyces, although they are distinguishable from each other on the basis of cell
      wall composition and the 16S rDNA sequence. We have determined the complete genome sequence of
      K. setae NBRC 14216T as the first Streptomycetaceae genome other than Streptomyces. The genome
      is a single linear chromosome of 8 783 278 bp with terminal inverted repeats of 127 148 bp,
      predicted to encode 7569 protein-coding genes, 9 rRNA operons, 1 tmRNA and 74 tRNA genes.
      Although these features resemble those of Streptomyces, genome-wide comparison of orthologous
      genes between K. setae and Streptomyces revealed smaller extent of synteny. Multilocus
      phylogenetic analysis based on amino acid sequences unequivocally placed K. setae outside the
      Streptomyces genus. Although many of the genes related to morphological differentiation
      identified in Streptomyces were highly conserved in K. setae, there were some differences such
      as the apparent absence of the AmfS (SapB) class of surfactant protein and differences in the
      copy number and variation of paralogous components involved in cell wall synthesis.
AU  - Ichikawa N et al
PT  - Journal Article
TA  - DNA Res.
JT  - DNA Res.
SO  - DNA Res. 2010 17: 393-406.

PMID- 25999558
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Pseudomonas aeruginosa Strain 8380, Isolated from the Human Gut.
PG  - e00520-15
AB  - Pseudomonas aeruginosa shows multidrug resistance, which is mainly attributable to its
      expression of xenobiotic efflux pumps. However, it is unclear how silent
      pumps are expressed in clinical isolates. Here, we sequenced the complete genome
      of P. aeruginosa strain 8380, which was isolated from a human gut.
AU  - Ichise YK
AU  - Kosuge T
AU  - Uwate M
AU  - Nakae T
AU  - Maseda H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00520-15.

PMID- 28705968
VI  - 5
DP  - 2017
TI  - Genome Sequence of Micromonospora sp. NBS 11-29, an Antibiotic and Hydrolytic Enzyme Producer, Isolated from River Sediment in Brazil.
PG  - e00552-17
AB  - The genus Micromonospora comprises actinomycetes with high biotechnological potential, due to
      their ability to produce secondary metabolites and enzymes. In
      this study, we report the draft genome sequence of Micromonospora sp. NBS 11-29,
      which showed antibacterial, cellulolytic, and xylanolytic activities under in
      vitro conditions.
AU  - Ichiwaki S
AU  - Costa ACMM
AU  - Silva EG
AU  - Rada LRM
AU  - Lima FR
AU  - Ortiz-Vera MP
AU  - Garrido LM
AU  - Sato MIZ
AU  - Araujo WL
AU  - Padilla G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00552-17.

PMID- 22395461
VI  - 7
DP  - 2012
TI  - Inhibition of MspI cleavage activity by hydroxymethylation of the CpG site A concern for DNA modification studies using restriction endonucleases.
PG  - 131-136
AB  - In mammalian genomic DNA, cytosine methylation predominantly occurs at CpG dinucleotides and
      provides epigenetic information. In some cells,
      5-methyl-cytosine (5-mC) can be further converted to
      5-hydroxymethyl-cytosine (5-hmC) by the ten-eleven translocation family
      of proteins. MspI restriction endonuclease has been used to analyze
      these modified cytosines. However, the kinetic analysis in this study
      revealed that MspI activity is dramatically decreased by symmetrical
      hydroxymethylation of its recognition sequence and partly inhibited by
      hemi-hydroxymethylation, whereas TaqI and HaeIII are relatively
      resistant to hydroxymethylation. Therefore, DNA modification studies
      that use MspI, for example, reduced representation bisulfite shotgun
      sequencing, quantitative analysis of 5-hmC and cleavage-sensitivity
      analysis, should be carefully interpreted.
AU  - Ichiyanagi K
PT  - Journal Article
TA  - EPIGENETICS
JT  - EPIGENETICS
SO  - EPIGENETICS 2012 7: 131-136.

PMID- 10891276
VI  - 300
DP  - 2000
TI  - Crystal structure of an archaeal intein-encoded homing endonuclease PI-PfuI.
PG  - 889-901
AB  - Inteins possess two different enzymatic activities, self-catalyzed protein splicing and
      site-specific DNA cleavage. These endonucleases, which are classified as part of the homing
      endonuclease family, initiate the mobility of their genetic elements into homologous alleles.
      They recognize long asymmetric nucleotide sequences and cleave both DNA strands in a monomer
      form. We present here the 2.1 A crystal structure of the archaeal PI-PfuI intein from
      Pyrococcus furiosus. The structure reveals a unique domain, designated here as the Stirrup
      domain, which is inserted between the Hint domain and an endonuclease domain. The
      horseshoe-shaped Hint domain contains a catalytic center for protein splicing, which involves
      both N and C-terminal residues. The endonuclease domain, which is inserted into the Hint
      domain, consists of two copies of substructure related by an internal pseudo 2-fold axis. In
      contrast with the I-CreI homing endonuclease, PI-PfuI possibly has two asymmetric catalytic
      sites at the center of a putative DNA-binding cleft formed by a pair of four-stranded
      beta-sheets. DNase I footprinting experiments showed that PI-PfuI covers more than 30 bp of
      the substrate asymmetrically across the cleavage site. A docking model of the DNA-enzyme
      complex suggests that the endonuclease domain covers the 20 bp DNA duplex encompassing the
      cleavage site, whereas the Stirrup domain could make an additional contact with another
      upstream 10 bp region. For the double-strand break, the two strands in the DNA duplex were
      cleaved by PI-PfuI with different efficiencies. We suggest that the cleavage of each strand is
      catalyzed by each of the two non-equivalent active sites.
AU  - Ichiyanagi K
AU  - Ishino Y
AU  - Ariyoshi M
AU  - Komori K
AU  - Morikawa K
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2000 300: 889-901.

PMID- 29496838
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Multidrug-Resistant Strain Citrobacter portucalensis MBTC-1222, Isolated from Uziza (Piper guineense) Leaves in Nigeria.
PG  - e00123-18
AB  - In this work, we report the draft whole-genome sequence of the multiply antibiotic-resistant
      Citrobacter portucalensis strain MBTC-1222 isolated from the
      uziza leafy vegetable in Nigeria. Sequence analysis showed the assembled genome
      size to be 4,881,935 bp, containing 4,603 protein-coding genes, 131 pseudogenes,
      7 rRNAs, 74 tRNAs, and 9 noncoding RNAs (ncRNAs).
AU  - Igbinosa EO
AU  - Rathje J
AU  - Habermann D
AU  - Brinks E
AU  - Cho GS
AU  - Franz CMAP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00123-18.

PMID- 30533887
VI  - 7
DP  - 2018
TI  - Genome Sequence of Oenococcus oeni UNQOe19, the First Fully Assembled Genome Sequence of a Patagonian Psychrotrophic Oenological Strain.
PG  - e00889-18
AB  - Oenococcus oeni UNQOe19 is a native strain isolated from a Patagonian pinot noir  wine
      undergoing spontaneous malolactic fermentation. Here, we present the 1.83-Mb
      genome sequence of O. oeni UNQOe19, the first fully assembled genome sequence of
      a psychrotrophic strain from an Argentinean wine.
AU  - Iglesias NG
AU  - Valdes LaHD
AU  - Olguin NT
AU  - Bravo-Ferrada BM
AU  - Brizuela NS
AU  - Tymczyszyn EE
AU  - Bibiloni H
AU  - Caballero AC
AU  - Delfederico L
AU  - Semorile L
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e00889-18.

PMID- 25700410
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Xanthomonas arboricola Strain 3004, a Causal Agent of Bacterial Disease on Barley.
PG  - e01572-14
AB  - We report here the annotated genome sequence of Xanthomonas arboricola strain 3004, isolated
      from barley leaves with symptoms of streak and capable of infecting other plant species. We
      sequenced the genome of X. arboricola strain 3004 to improve the understanding of molecular
      mechanisms of the pathogenesis and evolution of the genus Xanthomonas.
AU  - Ignatov AN
AU  - Kyrova EI
AU  - Vinogradova SV
AU  - Kamionskaya AM
AU  - Schaad NW
AU  - Luster DG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01572-14.

PMID- 6302279
VI  - 165
DP  - 1983
TI  - DNA Restriction-Modification Genes of Phage P1 and Plasmid p15B.
PG  - 1-18
AB  - The EcoP1 and EcoP15 DNA restriction-modification systems are coded by the related P1 prophage
      and p15B plasmid.  We have examined the organization of the genes for these systems using P1
      itself, "P1-P15" hybrid phages expressing the EcoP15 restriction specificity of p15B and
      cloned restriction fragments derived from these phage DNAs.  The results of transposon
      mutagenesis, restriction cleavage analysis, DNA heteroduplex analysis and in vitro
      transcription mapping allow the following conclusions to be drawn concerning the structural
      genes. (1) All of the genetic information necessary to specify either system is contained
      within a contiguous DNA segment of 5000 bases which encodes two genes.  One of them, necessary
      for both restriction and modification, we call mod and the other, required only for
      restriction (together with mod), we call res.  (2) The res gene is about 2800 bases long and
      at the heteroduplex level is largely identical for P1 and P15:  it shows a small region of
      partial nonhomology and some restriction cleavage site differences.  The mod gene is about
      2200 bases long and contains a 1200 base long region of non-homology between P1 and P15 toward
      the N-terminus of the gene.  The rest of the gene at this level of analysis is identical for
      the two systems.  (3) Each of the genes is transcribed in vitro from its own promoter.  It is
      possible that the res gene is also transcribed by readthrough from the mod promoter.
AU  - Iida S
AU  - Meyer J
AU  - Bachi B
AU  - Stalhammar-Carlemalm M
AU  - Schrickel S
AU  - Bickle TA
AU  - Arber W
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1983 165: 1-18.

PMID- 3029954
VI  - 157
DP  - 1987
TI  - Two DNA antirestriction systems of bacteriophage P1, darA, and darB:  characterization of darA- phages.
PG  - 156-166
AB  - Bacteriophage P1 is only weakly restricted when it infects cells carrying type
      I restriction and modification systems even though DNA purified from P1 phage
      particles is a good substrate for type I restriction enzymes in vitro.  Here we
      show that this protection against restriction is due to the products of two
      phage genes which we call darA and darB (dar for defense against restriction).
      Each of the dar gene products provides protection against a different subset of
      type I restriction systems.  The darA and darB gene products are found in the
      phage head and protect any DNA packaged into a phage head, including transduced
      chromosomal markers, from restriction.  The proteins must, therefore, be
      injected into recipient cells along with the DNA.  The proteins act strictly in
      cis.  For example, upon double infection of restricting cells with dar+ and
      dar- P1 phages, the dar+ genomes are protected from restriction while the
      dar-genomes are efficiently restricted.
AU  - Iida S
AU  - Streiff MB
AU  - Bickle TA
AU  - Arber W
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1987 157: 156-166.

PMID- 12354094
VI  - 7
DP  - 2002
TI  - PCNA clamp facilitates action of DNA cytosine methyltransferase 1 on hemimethylated DNA.
PG  - 997-1008
AB  - Proliferating cell nuclear antigen (PCNA) is a ring-shaped protein known as a processivity
      factor of DNA polymerase delta.  In addition to this role, PCNA interacts with a number of
      other proteins to increase their local concentration at replicated DNA sites.  DNA cytosine
      methyltransferase 1 (Dnmt1), which preserves epigenetic signals by completing the methylation
      of hemimethylated DNA aftr DNA replication, has been indicated as one of these PCNA binding
      proteins by a previous work.  However, the molecular mechanisms and functional significance of
      their association have not yet been studied.  Results: Dnmt1 can be readily isolated from
      nuclear extracts by PCNA affinity chromatography.  Studies of the interactions between the two
      proteins demonstrate that the N-terminal region of Dnmt1, which contains a typical PCNA
      binding
      motif, has core PCNA binding activity, and that the remaining portion of the protein exerts a
      negative influence on the interaction of Dnmt1 with PCNA.  The affinity of Dnmt1 for DNA is
      much higher for DNA bound by PCNA than for free DNA.  Furthermore, DNA methylation assays with
      hemimethylated DNA as a substrate revealed that PCNA clamp-bound DNA is methylated more
      efficiently by Dnmt1 than is free DNA.  Conclusion: These results provide the first
      biochemical evidence that physical interactions between PCNA and Dnmt1 facilitate the
      methylation of newly replicated DNA, on which PCNA remains associated as a functional clamp.
AU  - Iida T
AU  - Suetake I
AU  - Tajima S
AU  - Morioka H
AU  - Ohta S
AU  - Obuse C
AU  - Tsurimoto T
PT  - Journal Article
TA  - Genes Cells
JT  - Genes Cells
SO  - Genes Cells 2002 7: 997-1008.

PMID- 28302768
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Rhizobium sp. Strain TBD182, an Antagonist of the Plant-Pathogenic Fungus Fusarium oxysporum, Isolated from a Novel Hydroponics  System Using Organic Fertilizer.
PG  - e00007-17
AB  - Rhizobium sp. strain TBD182, isolated from a novel hydroponics system, is an antagonistic
      bacterium that inhibits the mycelial growth of Fusarium oxysporum
      but does not eliminate the pathogen. We report the draft genome sequence of
      TBD182, which may contribute to elucidation of the molecular mechanisms of its
      fungistatic activity.
AU  - Iida Y
AU  - Fujiwara K
AU  - Someya N
AU  - Shinohara M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00007-17.

PMID- Not included in PubMed...
VI  - 43
DP  - 1979
TI  - Recognition sequence of endonuclease R. BamNx from Bacillus amyloliquefaciens N.
PG  - 873-875
AB  - Recently, many site-specific deoxyribonucleases including restriction
      endonucleases which cleave DNA strands at unique sites have been isolated from
      various kinds of microorganisms.  Recognition nucleotide sequences on DNA have
      been determined for a number of them.  We have reported that Bacillus
      amyloliquefaciens N and many other Bacillus strains possess site-specific
      endonucleases.
AU  - Ikawa S
AU  - Shibata T
AU  - Ando T
PT  - Journal Article
TA  - Agric. Biol. Chem.
JT  - Agric. Biol. Chem.
SO  - Agric. Biol. Chem. 1979 43: 873-875.

PMID- 107391
VI  - 170
DP  - 1979
TI  - Host-Controlled modification and restriction in Bacillus subtilis.  Bsu168-System and BsuR-System in B. subtilis 168.
PG  - 123-127
AB  - A Bsu168-specific restriction deficient (r-1)6)8) mutant of Bacillus subtilis
      Marburg 168 was transformed to be BsuR-specific restriction proficient (r+R)
      with B. subtilis R DNA as efficiently as the Bsu168-specific restriction
      proficient (r+1)6)8) parental strain (hsrM+, hsdR-). We constructed
      r+Rm+Rr+1m6m8mm+1868 strain (ISMR4), r+Rm+Rr-1m6m8mm+1868 strain (ISR11) and
      r+Rm+Rr-1m6m8mm-1868 strain (ISR6) from strain 101 (r+1868m+1868), strain 1012
      (r-1868m+1868) and strain RM125 (r-1868m-1868), respectively by transformation
      with B. subtilis R DNA, and tested their restriction and modification
      activities on phage Phi105C.  The results show that the sites recognized by
      Bsu168-specific restriction and modification enzymes and the sites recognized
      by BsuR-specific ones are not overlapping. We conclude that the
      Bsu168-modification and restriction system and the BsuR-modification and
      restriction system are controlled independently by two distinct sets of genes
      in the r_Rm+R transformant of r+1868m+1868 strain B. subtilis 168.
AU  - Ikawa S
AU  - Shibata T
AU  - Ando T
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1979 170: 123-127.

PMID- 1018024
VI  - 80
DP  - 1976
TI  - The Site-specific Deoxyribonuclease from Bacillus pumilus (Endonuclease R.Bpu1387).
PG  - 1457-1460
AB  - A new site-specific endonuclease (DNase) was isolated from the cells of
      Bacillus pumilus AHU 1387 strain.  This enzyme (endonuclease R.Bpu 1387)
      introduced double-stranded scissions at unique sites on DNA's of coli phage
      lambda, lambda dvl, coli phage T7, Bacillus phage Phi105C, Bacillus phage SP10,
      and Simian Virus 40, in the presence of magnesium ion.  The activity was
      stimulated by the presence of NaCl.
AU  - Ikawa S
AU  - Shibata T
AU  - Ando T
PT  - Journal Article
TA  - J. Biochem. (Tokyo)
JT  - J. Biochem. (Tokyo)
SO  - J. Biochem. (Tokyo) 1976 80: 1457-1460.

PMID- 6246395
VI  - 177
DP  - 1980
TI  - Genetic studies on site-specific endodeoxyribonucleases in Bacillus subtilis:  Multiple modification and restriction systems in transformants of Bacillus subtilis 168.
PG  - 359-368
AB  - We transformed B. subtilis 168 with DNA from B. subtilis IAM1231, IAM1192 and
      ATCC6633.  When we examined the restriction activities of the transformants in
      vivo and in vitro using phage Phi105C we found the following: (1) Cells of
      either IAM1231 or IAM1192 have two modification and restriction systems
      (Bsu1231(1)-system and Bsu1231(II)-system in IAM1231, and Bsu1192(I)-system and
      Bsu1192(II)-systems in IAM1192), and cells of ATCC6633 have only one system
      (Bsu6633-system).  (2) The restriction enzymes of all of these five systems are
      site-specific endonucleases.  (3) The nucleotide sequence specifities of the
      enzymes involved in Bsu1231(I)-system, Bsu1192(I)-system and Bsu6633-system are
      the same; and those of Bsu1231(II)-system and Bsu1192(II)-system are the same.
      The sequence specificities of these two groups are different from each other
      and also different from those of the Bsu168-system of B. subtilis 168, the
      BsuR-system of B. subtilis R and the Bsu1247(I)-and Bsu1247(II)-systems which
      are systems of B. subtilis IAM1247.  (4) Transformants possessing four
      different modification and restriction systems (Bsu1231(I)-, Bsu1247(I)-, BsuR-
      and Bsu168-systems) were constructed.  (5) Transformation of two derivatives of
      168 that were mR+rR+ by DNA from IAM1231 produced 16 transformants that had the
      Bsu1231(II) restriction system, but had lost the BsuR system.  Transformation
      of a derivative of 168 that was m+1247(II)r+1247(II) by DNA from
      m+1231(II)r+1231(II)- or mR+rR+-derivative of 168 produced about 100 each of
      transformants that had the Bsu1231(II)-restriction system or the
      BsuR-restriction system.  But all these transformants lost the
      Bsu1247(II)-system.
AU  - Ikawa S
AU  - Shibata T
AU  - Ando T
AU  - Saito H
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1980 177: 359-368.

PMID- 6276670
VI  - 183
DP  - 1981
TI  - Chromosomal loci of genes controlling site-specific restriction endonucleases of Bacillus subtilis.
PG  - 1-6
AB  - We constructed transformants of B. subtilis 168 which acquired genes for
      site-specific restriction endonucleases.  These endonucleases originated from
      various strains of B. subtilis and were classified into five groups based on
      the specificity of the sequences recognized by the enzymes.  We examined the
      loci of genes for site-specific restriction endonucleases belonging to
      different groups:  hsrE determined Endo.R.Bsu1231(I), hsrB Endo.R.Bsu1247(I),
      hsrR Endo.R.BsuR and hsrC Endo.R.Bsu-1247(II).  One gene, hsrE, was located
      between sacA and purA by transduction crosses with phage PBS1, and another
      gene, hsrB, between hsrE and purA.  Genes hsrR and hsrC had been suggested to
      be allelic or closely linked by previous studies with transformation.  We
      located hsrR and hsrC between purB and tre.  Our previous observation and this
      study show that B. subtilis 168 has at least three independent loci on the
      chromosome for four genes for site-specific restriction endonucleases in
      addition to the locus for the original restriction activity (Bsu168-specific
      restriction) of strain 168.
AU  - Ikawa S
AU  - Shibata T
AU  - Matsumoto K
AU  - Iijima T
AU  - Saito H
AU  - Ando T
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1981 183: 1-6.

PMID- 12692562
VI  - 21
DP  - 2003
TI  - Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis.
PG  - 526-531
AB  - Species of the genus Streptomyces are of major pharmaceutical interest
      because they synthesize a variety of bioactive secondary metabolites. We
      have determined the complete nucleotide sequence of the linear chromosome
      of Streptomyces avermitilis. S. avermitilis produces avermectins, a group
      of antiparasitic agents used in human and veterinary medicine. The genome
      contains 9,025,608 bases (average GC content, 70.7%) and encodes at least
      7,574 potential open reading frames (ORFs). Thirty-five percent of the
      ORFs (2,664) constitute 721 paralogous families. Thirty gene clusters
      related to secondary metabolite biosynthesis were identified,
      corresponding to 6.6% of the genome. Comparison with Streptomyces
      coelicolor A3(2) revealed that an internal 6.5-Mb region in the S.
      avermitilis genome was highly conserved with respect to gene order and
      content, and contained all known essential genes but showed perfectly
      asymmetric structure at the oriC center. In contrast, the terminal regions
      were not conserved and preferentially contained nonessential genes.
AU  - Ikeda H
AU  - Ishikawa J
AU  - Hanamoto A
AU  - Shinose M
AU  - Kikuchi H
AU  - Shiba T
AU  - Sakaki Y
AU  - Hattori M
AU  - Omura S
PT  - Journal Article
TA  - Nat. Biotechnol.
JT  - Nat. Biotechnol.
SO  - Nat. Biotechnol. 2003 21: 526-531.

PMID- 12743753
VI  - 62
DP  - 2003
TI  - The Corynebacterium glutamicum genome: Features and impacts on biotechnological processes.
PG  - 99-109
AB  - Corynebacterium glutamicum has played a principal role in the progress of the amino acid
      fermentation industry. The complete genome sequence of the representative wild-type strain of
      C. glutamicum, ATCC 13032, has been determined and analyzed to improve our understanding of
      the molecular biology and physiology of this organism, and to advance the development of more
      efficient production strains. Genome annotation has helped in elucidation of the gene
      repertoire defining a desired pathway, which is accelerating pathway engineering. Post genome
      technologies such as DNA arrays and proteomics are currently undergoing rapid development in
      C. glutamicum. Such progress has already exposed new regulatory networks and functions that
      had so far been unidentified in this microbe. The next goal of these studies is to integrate
      the fruits of genomics into strain development technology. A novel methodology that merges
      genomics with classical strain improvement has been developed and applied for the
      reconstruction of classically derived production strains. How can traditional fermentation
      benefit from the C. glutamicum genomic data? The path from genomics to biotechnological
      processes is presented.
AU  - Ikeda M
AU  - Nakagawa S
PT  - Journal Article
TA  - Appl. Microbiol. Biotechnol.
JT  - Appl. Microbiol. Biotechnol.
SO  - Appl. Microbiol. Biotechnol. 2003 62: 99-109.

PMID- 29724849
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Petrimonas sp. Strain IBARAKI, Assembled from the Metagenome Data of a Culture Containing Dehalococcoides spp.
PG  - e00384-18
AB  - The complete genome sequence of Petrimonas sp. strain IBARAKI in a Dehalococcoides-containing
      culture was determined using the PacBio RS II
      platform. The genome is a single circular chromosome of 3,693,233 nucleotides
      (nt), with a GC content of 44%. This is the first genome sequence of a Petrimonas
      species.
AU  - Ikegami K
AU  - Aita Y
AU  - Shiroma A
AU  - Shimoji M
AU  - Tamotsu H
AU  - Ashimine N
AU  - Shinzato M
AU  - Ohki S
AU  - Nakano K
AU  - Teruya K
AU  - Satou K
AU  - Hirano T
AU  - Yohda M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00384-18.

PMID- 25197441
VI  - 9
DP  - 2014
TI  - Non-contiguous finished genome sequence and description of Halopiger goleamassiliensis sp. nov.
PG  - 956-959
AB  - Halopiger goleamassiliensis strain IIH3(T) sp. nov. is a novel, extremely halophilic archaeon
      within the genus Halopiger. This strain was isolated from an
      evaporitic sediment in El Golea Lake, Ghardaia region (Algeria). The type strain
      is strain IIH3(T). H. goleamassiliensis is moderately thermophilic, neutrophilic,
      non-motile and coccus-shaped. Here we describe the features of this organism,
      together with the complete genome sequence and annotation. The 3,906,923 bp long
      genome contains 3,854 protein-encoding genes and 49 RNA genes (1 gene is 16S
      rRNA, 1 gene is 23S rRNA, 3 genes are 5S rRNA, and 44 are tRNA genes).
AU  - Ikram HI
AU  - Catherine R
AU  - Caroline M
AU  - Didier R
AU  - Hocine H
AU  - Christelle D
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 956-959.

PMID- 29622612
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Lactobacillus plantarum subsp. plantarum Strain LB1-2, Isolated from the Hindgut of European Honeybees, Apis mellifera L., from  the Philippines.
PG  - e00209-18
AB  - Lactobacillus plantarum subsp. plantarum strain LB1-2, isolated from the hindgut  of European
      honeybees in the Philippines, is active against Paenibacillus larvae
      and has broad activity against several Gram-positive and Gram-negative bacteria.
      The complete genome sequence reported herein contains gene clusters for multiple
      bacteriocins and extensive gene inventories for carbohydrate metabolism.
AU  - Ilagan-Cruzada MFC
AU  - Rosana ARR
AU  - Montecillo AD
AU  - Sabino NG
AU  - Dalmacio IF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00209-18.

PMID- 26543112
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Multidrug-Resistant Clinical Isolate Mycobacterium tuberculosis 187.0, Used To Study the Effect of Drug Susceptibility Reversion by   the New Medicinal Drug FS-1.
PG  - e01272-15
AB  - Complete genome sequence of the multidrug-resistant clinical isolate Mycobacterium
      tuberculosis SCAID 187.0 containing several drug-resistance
      mutations is presented. This strain is used in experiments to study genomic and
      population changes leading to reversion of susceptibility to the 1st line
      anti-tuberculosis (TB) drugs under the influence of a new medicinal drug FS-1.
AU  - Ilin AI
AU  - Kulmanov ME
AU  - Korotetskiy IS
AU  - Akhmetova GK
AU  - Lankina MV
AU  - Shvidko SV
AU  - Reva ON
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01272-15.

PMID- 30338025
VI  - 13
DP  - 2018
TI  - One complete and three draft genome sequences of four Brochothrix thermosphacta strains, CD 337, TAP 175, BSAS1 3 and EBP 3070.
PG  - 22
AB  - Brochothrix thermosphacta is one of the dominant bacterial species associated with spoilage of
      chilled meat and seafood products through the production of
      various metabolites responsible for off-odors. However, metabolic pathways
      leading to meat and seafood spoilage are not all well known. The production of
      spoiling molecules seems to depend both on strains and on food matrix. Several B.
      thermosphacta genome sequences have been reported, all issued from meat isolates.
      Here, we report four genome sequences, one complete and three as drafts. The four
      B. thermosphacta strains CD 337, TAP 175, BSAS1 3, and EBP 3070 were isolated
      from different ecological niches (seafood or meat products either spoiled or not
      and bovine slaughterhouse). These strains known as phenotypically and genetically
      different were selected to represent intraspecies diversity. CD 337 genome is
      2,594,337 bp long, complete and circular, containing 2593 protein coding
      sequences and 28 RNA genes. TAP 175, BSAS1 3, and EBP 3070 genomes are arranged
      in 57, 83, and 71 contigs, containing 2515, 2668, and 2611 protein-coding
      sequences, respectively. These genomes were compared with two other B.
      thermosphacta complete genome sequences. The main genome content differences
      between strains are phages, plasmids, restriction/modification systems, and cell
      surface functions, suggesting a similar metabolic potential but a different niche
      adaptation capacity.
AU  - Illikoud N
AU  - Klopp C
AU  - Roulet A
AU  - Bouchez O
AU  - Marsaud N
AU  - Jaffres E
AU  - Zagorec M
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2018 13: 22.

PMID- 24215824
VI  - 64
DP  - 2014
TI  - Pelolinea submarina gen. nov., sp. nov., an anaerobic, filamentous bacterium of the phylum Chloroflexi isolated from subseafloor sediment.
PG  - 812-818
AB  - A novel, anaerobic filamentous bacterium, strain MO-CFX1(T), was isolated from a
      methanogenic community, which was originally established from subseafloor
      sediments collected from off the Shimokita Peninsula, Japan. Cells were
      non-spore-forming, non-motile, Gram-stain-negative and filamentous. The filaments
      were longer than 10 microm and 130-150 nm in width. Growth of the strain was
      observed at 10-37 degrees C (optimum 25-30 degrees C), at pH 5.5-8.5 (optimum pH
      7.0) and in 0-50 g NaCl l(-1) (optimum 15 g NaCl l(-1)). The strain was able to
      grow with a number of carbohydrates in the presence of yeast extract. The major
      cellular fatty acids were monounsaturated C18 : 1omega9, C16 : 1omega7 and
      saturated C18 : 0 and C16 : 0. The intact polar lipids of the strain were
      dominated by diacylglyceride and sphingolipid core lipid structures with
      monoglycosidic, mixed phosphomonoglycosidic and fatty-acid-modified
      monoglycosidic polar head groups. The G+C content of the genomic DNA was 52.4
      mol%. Based on the comparative 16S rRNA gene sequence analysis, strain MO-CFX1(T)
      was affiliated with the class Anaerolineae within the phylum Chloroflexi and was
      most closely related to Leptolinea tardivitalis YMTK-2(T) (sequence identity of
      91.0 %). Based on phenotypic and genetic properties of the novel isolate, we
      propose a novel species representing a new genus Pelolinea submarina gen. nov.,
      sp. nov., for strain MO-CFX1(T) ( = JCM 17238(T), = KCTC 5975(T)). This is the
      first formal description, to our knowledge, of an isolate of the phylum
      Chloroflexi from the deep-sea sedimentary environment.
AU  - Imachi H
AU  - Sakai S
AU  - Lipp JS
AU  - Miyazaki M
AU  - Saito Y
AU  - Yamanaka Y
AU  - Hinrichs KU
AU  - Inagaki F
AU  - Takai K
PT  - Journal Article
TA  - Int. J. Syst. Evol. Microbiol.
JT  - Int. J. Syst. Evol. Microbiol.
SO  - Int. J. Syst. Evol. Microbiol. 2014 64: 812-818.

PMID- 15502310
VI  - 60
DP  - 2004
TI  - Crystallization and preliminary X-ray diffraction analysis of homing endonuclease I-Tsp061I.
PG  - 2006-2008
AB  - Two crystal forms, rhombohedral and hexagonal, of a homing endonuclease from Thermoproteus sp.
      IC-061 (I-Tsp0611) were obtained by the
      hanging-drop and sitting-drop method, respectively. The hexagonal
      crystals belong to space group P6(3)22, with unit-cell parameters a = b
      = 111.4, c = 97.6 Angstrom, and diffract to 3.2 Angstrom resolution on
      beamline BL44 at SPring-8 (Harima, Japan). The rhombohedral crystals
      belong to space group R32, with unit-cell parameters a = b = 95.4, c =
      192.9 Angstrom, and diffract to 2.7 Angstrom resolution using a Cu
      Kalpha rotating-anode generator with an R-AXIS VII detector. The
      crystal asymmetric unit contained one protein molecule and the solvent
      contents of the two crystal forms were estimated to be 68.3 and 67.6%
      by volume, respectively.
AU  - Imagawa T
AU  - Nakayama H
AU  - Katunuma N
AU  - Sakuraba H
AU  - Ohshima T
AU  - Itoh T
AU  - Sako Y
AU  - Nomura N
AU  - Tsuge H
PT  - Journal Article
TA  - Acta Crystallogr. D Biol. Crystallogr.
JT  - Acta Crystallogr. D Biol. Crystallogr.
SO  - Acta Crystallogr. D Biol. Crystallogr. 2004 60: 2006-2008.

PMID- 25767227
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Nocardia seriolae Strain N-2927 (NBRC 110360), Isolated  as the Causal Agent of Nocardiosis of Yellowtail (Seriola quinqueradiata) in  Kochi Prefecture, Japan.
PG  - e00082-15
AB  - We report the draft genome sequence of Nocardia seriolae strain N-2927 (NBRC 110360), isolated
      from cultured yellowtail Seriola quinqueradiata. RAST
      annotation of the genome revealed 117 genes involved in the virulence, disease,
      and defense subsystem. Eleven of these genes were predicted as antibiotic
      resistance genes.
AU  - Imajoh M
AU  - Fukumoto Y
AU  - Yamane J
AU  - Sukeda M
AU  - Shimizu M
AU  - Ohnishi K
AU  - Oshima S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00082-15.

PMID- 26798107
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Erythromycin- and Oxytetracycline-Sensitive Nocardia seriolae Strain U-1 (NBRC 110359).
PG  - e01606-15
AB  - In Japan, the emergence of macrolide- and oxytetracycline-resistant strains of Nocardia
      seriolae has previously been reported. Here, we describe the draft
      genome sequence of N. seriolae strain U-1, isolated in 2011 from a diseased
      yellowtail in Kagoshima Prefecture. The draft genome does not have any genes
      responsible for macrolide and tetracycline resistance.
AU  - Imajoh M
AU  - Sukeda M
AU  - Shimizu M
AU  - Yamane J
AU  - Ohnishi K
AU  - Oshima S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01606-15.

PMID- 28774983
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Flavobacteriumpsychrophilum Strain SSADA-1411, Isolated  from an Ayu (Plecoglossus altivelis altivelis) Migrating Downriver To Spawn in  the Shimanto River, Kochi, Japan.
PG  - e00735-17
AB  - Here, we report the draft genome sequence and annotation of Flavobacterium psychrophilum
      strain SSADA-1411. This strain was isolated from the skin ulcer of
      an ayu (Plecoglossus altivelis altivelis) migrating downriver to spawn in the
      lower Shimanto River, in western Kochi Prefecture on Shikoku Island in Japan.
AU  - Imajoh M
AU  - Tsuji Y
AU  - Yamashita H
AU  - Ohgi M
AU  - Monno S
AU  - Ohnishi K
AU  - Horioka K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00735-17.

PMID- 29326209
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Escherichia coli Strain WG5.
PG  - e01403-17
AB  - Escherichia coli strain WG5 is a widely used host for phage detection, including  somatic
      coliphages employed as standard ISO method 10705-1 (2000). Here, we
      present the complete genome sequence of a commercial E. coli WG5 strain.
AU  - Imamovic L
AU  - Misiakou MA
AU  - van der Helm E
AU  - Panagiotou G
AU  - Muniesa M
AU  - Sommer MOA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01403-17.

PMID- 6268410
VI  - 117
DP  - 1981
TI  - Purification and properties of the restriction endonuclease BglII from Bacillus globigii.
PG  - 395-399
AB  - The restriction endonuclease BglII from Bacillus globigii has been purified to
      homogeneity.  The enzyme is a dimer of two subunits of Mr = 27000.  The
      reaction mechanism does not involve the accumulation of a DNA intermediate
      nicked in one strand and the enzyme is not affected by superhelical twists in
      the substrate DNA, indicating that DNA binding does not involve either winding
      or unwinding of the double helix.  Antibodies were prepared against BglII.
      These antibodies did not cross react with any other restriction endonucleases
      tested, including other enzymes from B. globigii or from closely related
      strains.  It is thus unlikely that type II restriction enzymes represent a
      closely related group of proteins.
AU  - Imber R
AU  - Bickle TA
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1981 117: 395-399.

PMID- 19678693
VI  - 48
DP  - 2009
TI  - Catalytic Mechanism of DNA Backbone Cleavage by the Restriction Enzyme EcoRV: A Quantum Mechanical/Molecular Mechanical Analysis.
PG  - 9061-9075
AB  - Endonucleases, Such as the restriction enzyme EcoRV, cleave the DNA backbone at a specific
      recognition sequence. We have investigated the
      catalytic mechanism of backbone phosphodiester hydrolysis by the
      restriction enzyme EcoRV by means of hybrid quantum
      mechanical/molecular mechanical calculations. An exhaustive computation
      of different reaction pathways is performed, thus generating a network
      of pathways. Comparison of the computed (AM1d/MM) enzymatic reaction
      pathways with an analogous mechanism for small-molecule model systems
      [AM1/d and B3LYP/6-31 + +G(d,p)] reveals that the transition barriers
      for associative hydrolysis, which is more probable in the model
      systems, are not lowered by the enzyme. Instead, a reaction mechanism
      which has mostly dissociative character is more likely. The protein
      environment is tuned to significantly electrostatically stabilize the
      transition state structures, The direct catalytic impact of essential
      residues is determined: The magnesium metal Ion activates a water
      molecule, thus facilitating protonation of the leaving group. A
      reduction of the coordination number of the magnesium metal ion from
      six to four upon the positioning of the attacking water molecule
      explains why larger metal ions, such as calcium, are not catalytically
      active. The nucleophile is generated by the transfer of a proton from
      the attacking water molecule to a carboxylic oxygen atom of aspartate
      90. The catalytic effect of lysine 92 involves proper positioning of
      the scissile phosphate group and, more importantly, stabilization of
      the metaphosphate intermediate in an orientation optimal for attack of
      the nucleophile.
AU  - Imhof P
AU  - Fischer S
AU  - Smith JC
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2009 48: 9061-9075.

PMID- 28798182
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Yersinia frederiksenii, Yersinia intermedia, and Yersinia kristensenii Strains from Brazil.
PG  - e00780-17
AB  - Yersinia enterocolitica-like strains are usually understudied. In this work, we reported the
      draft genome sequences of two Yersinia frederiksenii, two Yersinia
      intermedia, and two Yersinia kristensenii strains isolated from humans, animals,
      food, and the environment in Brazil. These draft genomes will provide better
      molecular characterizations of these species.
AU  - Imori PFM
AU  - Campioni F
AU  - Cao G
AU  - Kastanis G
AU  - Leon MS
AU  - Allard MW
AU  - Falcao JP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00780-17.

PMID- 30533892
VI  - 7
DP  - 2018
TI  - Draft Genome Sequence of Pseudomonas citronellolis LA18T, a Bacterium That Uses Levulinic Acid.
PG  - e00906-18
AB  - Pseudomonas citronellolis LA18T catabolizes levulinic acid (LA) from cellulosic biomass
      hydrolysate via acetyl-coenzyme A (acetyl-CoA) and propionyl-CoA. This
      study reports the 7.22-Mbp draft genome sequence of P. citronellolis LA18T. The
      draft genome sequence will aid the study of the LA catabolic pathway, which will
      allow for more applications of LA-utilizing bacteria.
AU  - Inaba T
AU  - Sato Y
AU  - Koike H
AU  - Hori T
AU  - Kanno M
AU  - Kimura N
AU  - Kirimura K
AU  - Habe H
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e00906-18.

PMID- 23640376
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Meiothermus ruber H328, Which Degrades Chicken Feathers, and Identification of Proteases and Peptidases Responsible for Degradation.
PG  - e00176-13
AB  - Meiothermus ruber H328 was isolated from Arima Hot Springs, Kobe, Japan, as a moderate
      thermophile. It has a strong ability to degrade intact chicken feathers.
      The enzymatic mechanism of the strain for feather degradation is unclear. The
      draft genome suggests potent enzyme candidates for degradation of keratin, a
      hard-to-degrade protein found in feathers.
AU  - Inada S
AU  - Watanabe K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00176-13.

PMID- Not included in PubMed...
VI  - 69
DP  - 1990
TI  - Isolation and characterization of restriction endonucleases from Acidiphilium sp. 16R and 22M.
PG  - 60-62
AB  - Restriction endonucleases (Asp16RI and Asp22MI) have been identified from the acidophilic
      bacteria Acidiphilium sp. 16R and 22M. The cleavage patterns with various DNAs show that both
      enzymes recognize the same sequence as the PvuI restriction endonuclease (5'-CGAT^CG-3'),
      which is from Proteus vulgaris ATCC 13315. Most of the catalytic properties observed for
      Asp16RI and Asp22MI were similar to those observed for PvuI. However, unlike PvuI both enzymes
      efficiently cleaved DNA in the absence of NaCl or KCl. The purification yield of Asp22MI is 60
      times that of PvuI.
AU  - Inagaki K
AU  - Dou D
AU  - Kita K
AU  - Hiraoka N
AU  - Kishimoto N
AU  - Sugio T
AU  - Tano T
PT  - Journal Article
TA  - J. Ferment. Bioeng.
JT  - J. Ferment. Bioeng.
SO  - J. Ferment. Bioeng. 1990 69: 60-62.

PMID- 7764267
VI  - 57
DP  - 1993
TI  - Restriction endonuclease Aor13HI from Acidiphilium organovorum 13H, a new isoschizomer of BspMII: Purification and characterization.
PG  - 1716-1721
AB  - A restriction endonuclease, Aor13HI, an isoschizomer of BspMII, was purified to homogeneity
      from cell extracts of Acidiphilium organovorum strain 13H. The enzyme has a molecular mass of
      60,000 daltons and consists of two subunits identical in molecular mass of 30,000 daltons.
      Aor13HI endonuclease, like BspMII, recognizes the palindromic six-base sequence
      5'-TCCGGA-3', and cleaves between the T and C to produce a four-base 5' extension. Aor13HI
      is not inhibited by dam-dependent methylation. The isoelectric point of the enzyme is 5.7.
      Aor13HI activity was maximum at pH 7.5, 100 mM KCI, 7.5-10mM MgC12 and 55 degrees C. The
      enzyme was stable up to 60 degrees C. The N-terminal amino acid sequence (30 residues) of
      Aor13HI did not show similarity with the sequence of other restriction endonuclease reported.
AU  - Inagaki K
AU  - Hikita T
AU  - Yanagidani S
AU  - Nomura Y
AU  - Kishimoto N
AU  - Tano T
AU  - Tanaka H
PT  - Journal Article
TA  - Biosci. Biotechnol. Biochem.
JT  - Biosci. Biotechnol. Biochem.
SO  - Biosci. Biotechnol. Biochem. 1993 57: 1716-1721.

PMID- 1956800
VI  - 19
DP  - 1991
TI  - AcpI, a novel isoschizomer of AsuII from Acidiphilium cryptum 25H, recognizes the sequence 5'TT^CGAA3'.
PG  - 6335
AB  - AcpI, a type II restriction endonuclease, has been isolated from Acidiphilium
      cryptum 25H.  AcpI, an isoschizomer of AsuII, recognizes the six base sequence
      5'TTCGAA3', and cleaves between the T and the C residues to produce a two base
      5' extension.
AU  - Inagaki K
AU  - Ito T
AU  - Sagawa H
AU  - Kotani H
AU  - Kishimoto N
AU  - Sugio T
AU  - Tano T
AU  - Tanaka H
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 6335.

PMID- 2235517
VI  - 18
DP  - 1990
TI  - Isolation and identification of restriction endonuclease Asp35HI from Acidiphilium species 35H.
PG  - 6155
AB  - None
AU  - Inagaki K
AU  - Kobayashi F
AU  - Dou D
AU  - Nomura Y
AU  - Kotani H
AU  - Kishimoto N
AU  - Sugio T
AU  - Tano T
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 6155.

PMID- 10920268
VI  - 128
DP  - 2000
TI  - Maintenance-type DNA methyltransferase is highly expressed in post-mitotic neurons and localized in the cytoplasmic compartment.
PG  - 315-321
AB  - Maintenance-type DNA methyltransferase (Dnmt1) is usually down-regulated in nonproliferating
      cells, In the present study, we
      detected significant expression of Dnmt1 protein in adult mouse brain
      where the majority of the cells are in a post-mitotic state. A
      significant amount of Dnmt1 protein was fractionated into the
      post-nuclear fraction for both cerebrum and cerebellum. The Dnmt1 in
      this fraction was enzymatically active. An immunofluorescence study
      revealed that Dnmt1 protein was mainly expressed in neurons and seemed
      to be localized in the cytoplasmic compartment, Primary culturing of
      neurons confirmed the expression and localization of Dnmt1 in the
      cytoplasmic compartment, The findings that the Dnmt1 transcript in the
      brain utilized the somatic-type exon and that the apparent size of the
      Dnmt1 protein in the cytoplasm was identical to that in proliferating
      culture cells indicate that the cytoplasmic Dnmt1 in neurons was of the
      somatic-type.
AU  - Inano K
AU  - Suetake I
AU  - Ueda T
AU  - Miyake Y
AU  - Nakamura M
AU  - Okada M
AU  - Tajima S
PT  - Journal Article
TA  - J. Biochem. (Tokyo)
JT  - J. Biochem. (Tokyo)
SO  - J. Biochem. (Tokyo) 2000 128: 315-321.

PMID- 25291773
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Flagellated Xanthomonas fuscans subsp. fuscans Strain CFBP 4884.
PG  - e00966-14
AB  - We report the draft genome sequence of the flagellated strain CFBP 4884 of Xanthomonas fuscans
      subsp. fuscans, which was isolated in an outbreak of common
      bacterial blight of beans along with non-flagellated strains. Comparative
      genomics will allow one to decipher the genomic diversity of strains cohabiting
      in epidemics.
AU  - Indiana A
AU  - Briand M
AU  - Arlat M
AU  - Gagnevin L
AU  - Koebnik R
AU  - Noel LD
AU  - Portier P
AU  - Darrasse A
AU  - Jacques MA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00966-14.

PMID- 28428294
VI  - 5
DP  - 2017
TI  - Complete and Assembled Genome Sequence of Lactobacillus plantarum RI-113 Isolated from Salami.
PG  - e00183-17
AB  - We present here the complete genome sequence of Lactobacillus plantarum RI-113, a strain
      isolated from salami, which was determined using single-molecule real-time
      sequencing.
AU  - Inglin RC
AU  - Meile L
AU  - Klumpp J
AU  - Stevens MJA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00183-17.

PMID- 28751390
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of 43 Lactobacillus Strains from the Species L. curvatus,  L. fermentum, L. paracasei, L. plantarum, L. rhamnosus, and L. sakei, Isolated  from Food Products.
PG  - e00632-17
AB  - The genome sequences of 43 Lactobacillus strains from the species L. curvatus, L. fermentum,
      L. paracasei, L. plantarum, L. rhamnosus, and L. sakei were determined
      using Illumina MiSeq.
AU  - Inglin RC
AU  - Meile L
AU  - Stevens MJA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00632-17.

PMID- 
VI  - 0
DP  - 2013
TI  - Genome inspector: A web tool for exploring bacterial genomes.
PG  - 5-16
AB  - Genome Inspector (GIN) is a new interactive web-based application for exploring bacterial
      genomes designed to provide users with a wide choice of options to facilitate the process of
      designing DNA primers for isolating genes from similar bacterial species and strains.  GIN
      employs a project-based approach in which users can select any given set of available genomes
      and perform a comprehensive bioinformatics analysis.  Currently, it encompasses the full set
      of annotated bacterial genomes available on GenBank, a total of 4300 files corresponding to
      over 740,000 annotated genes.  GIN allows new data to be added directly from GenBank as it is
      being generated, as well as new genome uploading for personal analysis.  The application
      interfaces were designed with potential users in mind to assist with their most common
      research goals.  Users can visually explore full circular genomes, search for similar regions
      in other species and strains, and visualize amplified genomic regions for several strains
      simultaneously.  This interactive tool allows for dynamic graphical exploration and refinement
      of search and exploration criteria.  Furthermore, it includes a multiple alignment algorithm
      (MUSCLE) to help researchers in the process of designing primers.  GIN is free and publicly
      available at http://gin.ul.pt/GIN2/index.php.
AU  - Inocencio T
AU  - Vital J
AU  - Vitor J
AU  - Falcao AO
PT  - Journal Article
TA  - Proc. InForum 2013
JT  - Proc. InForum 2013
SO  - Proc. InForum 2013 2013 0: 5-16.

PMID- 29748402
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Geobacter sulfurreducens Strain YM18, Isolated from River Sediment in Japan.
PG  - e00352-18
AB  - Geobacter sulfurreducens is known to be a dominant species in the anode biofilms  of microbial
      fuel cells. Here, we report the complete genome sequence of G.
      sulfurreducens strain YM18. Strain YM18 was isolated from a biofilm formed on an
      anode poised at -400 mV (versus an Ag/AgCl electrode) in a bioelectrochemical
      system.
AU  - Inoue K
AU  - Ogura Y
AU  - Kawano Y
AU  - Hayashi T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00352-18.

PMID- 5331504
VI  - 30
DP  - 1966
TI  - Phage P1 modification of bacterial DNA studied by generalized transduction.
PG  - 257-265
AB  - Mutants of P1 that either fail to cause restriction, r-m, or neither cause
      restriction nor modification, r-m-, were used to study the phage-induced
      modification of the bacterial chromosome of Escherichia coli K12 and the
      effects of modification on P1 generalized transduction.  The findings made were
      that: (1) the bacterial chromosomal markers transduced by P1 are not sensitive
      to restriction whereas the bacterial chromosomal markers transduced by P1 r-m-
      are sensitive to restriction; (2) the sensitivity to restriction differed for
      different markers; (3) all the regions of the bacterial chromosome tested
      appear to be modified; (4) modification can interfere with the transduction of
      certain markers in a way not associated with protection against restriction;
      (5) the modification of bacterial DNA can probably occur without DNA
      replication; (6) the sensitivity of lambda DNA to restriction is much greater
      than that of bacterial DNA when both are transferred by P1 transducing
      particles.  The implications of the results and limitations in interpreting
      them are discussed.
AU  - Inselburg J
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1966 30: 257-265.

PMID- 28280022
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Bifidobacterium longum W11 (LMG P-21586), Used as a Probiotic Strain.
PG  - e01659-16
AB  - We report the complete genome sequence of Bifidobacterium longum W11 (LMG P-21586) isolated
      from the intestinal microbiota of a healthy man. The analysis
      of the sequence may provide insights into the microbiological characteristics and
      the functional activity of this probiotic strain.
AU  - Inturri R
AU  - Ventura M
AU  - Ruas-Madiedo P
AU  - Lugli GA
AU  - Blandino G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01659-16.

PMID- 21110864
VI  - 11
DP  - 2010
TI  - The non-clonality of drug resistance in Beijing-genotype isolates of Mycobacterium tuberculosis from the Western Cape of South Africa.
PG  - 670
AB  - BACKGROUND: The Beijing genotype of M. tuberculosis is a virulent strain that is
      disseminating worldwide and has a strong association with drug resistance. In the
      Western Cape of South Africa, epidemiological studies have identified the R220
      cluster of the Beijing genotype as a major contributor to a recent outbreak of
      drug-resistant tuberculosis. Although the outbreak is considered to be due to
      clonal transmission, the relationship among drug resistant isolates has not yet
      been established. RESULTS: To better understand the evolution of drug resistance
      among these strains, 14 drug-resistant clinical isolates of the Beijing genotype
      were sequenced by whole-genome sequencing, including eight from R220 and six from
      a more ancestral Beijing cluster, R86, for comparison. While each cluster shares
      a distinct resistance mutation for isoniazid, mapping of other drug-resistance
      mutations onto a phylogenetic tree constructed from single nucleotide
      polymorphisms shows that resistance mutations to many drugs have arisen multiple
      times independently within each cluster of isolates. Thus, drug resistance among
      these isolates appears to be acquired, not clonally derived. This observation
      suggests that, although the Beijing genotype as a whole might have selective
      advantages enabling its rapid dissemination, the XDR isolates are relatively less
      fit and do not propagate well. Although it has been hypothesized that the
      increased frequency of drug resistance in some Beijing lineages might be caused
      by a mutator phenotype, no significant shift in synonymous substitution patterns
      is observed in the genomes. CONCLUSION: While MDR-TB is spreading by transmission
      in the Western Cape, our data suggests that further drug resistance (i.e. XDR-TB)
      at this stage is acquired.
AU  - Ioerger TR
AU  - Feng Y
AU  - Chen X
AU  - Dobos KM
AU  - Victor TC
AU  - Streicher EM
AU  - Warren RM
AU  - Gey-van-Pittius NC
AU  - Van Helden PD
AU  - Sacchettini JC
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2010 11: 670.

PMID- 136497
VI  - 96
DP  - 1976
TI  - Two restriction and modification systems in Staphylococcus aureus NCTC8325.
PG  - 277-281
AB  - The presence of two distinct host specificities in Staphylococcus aureus strain NCTC8325 was
      revealed by the isolation of restriction- and modification-deficient mutants.  The two host
      specificity systems, designated S1 and S2, are both active on phage 80 Mu Alpha but are not
      additive in their restricting activity.  Restriction-deficient, modification-proficient
      mutants were invariably affected in both restriction systems.  The functional relationship
      between these two systems is discussed.
AU  - Iordanescu S
AU  - Surdeanu M
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1976 96: 277-281.

PMID- 26067956
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Two Streptococcus pneumoniae Serotype 19F Sequence Type 271 Clinical Isolates with Low- and High-Level Cefotaxime Resistance.
PG  - e00605-15
AB  - We report here the draft genomes of two pneumococcal isolates in Hong Kong, CU_SPNE1_05 and
      CU_SPNE32_06. Strain CU_SPNE1_05 had a cefotaxime MIC of 1
      microg/ml, and CU_SPNE32_06 had an MIC of 32 microg/ml. Both strains belong to
      the multidrug-resistant serogroup 19, sequence type 271 (clonal complex
      3200/271).
AU  - Ip M
AU  - Ma H
AU  - Li C
AU  - Tsui S
AU  - Zhou H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00605-15.

PMID- 24744328
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Methicillin-Resistant Staphylococcus aureus CUHK_188 (ST188), a Health Care-Associated Bacteremic Isolate from Hong Kong.
PG  - e00255-14
AB  - We report the draft genome sequence of a methicillin-resistant Staphylococcus aureus strain
      designated CUHK_188, isolated from a bacteremic patient undergoing treatment at a university
      teaching hospital in Hong Kong. This strain belongs to sequence type 188 (ST188), with spa
      type t189 and staphylococcal cassette chromosome mec type V.
AU  - Ip M
AU  - Wang Z
AU  - Lam WY
AU  - Zhou H
AU  - Tsui S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00255-14.

PMID- 23908278
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Campylobacter fetus subsp. venerealis Biovar Intermedius, Isolated from the Prepuce of a Bull.
PG  - e00526-13
AB  - Campylobacter fetus subsp. venerealis is the causative agent of bovine genital
      campylobacteriosis, a sexually transmitted disease distributed worldwide. Campylobacter fetus
      subsp. venerealis biovar Intermedius strains differ in their biochemical behavior and are
      prevalent in some countries. We report the first genome sequence for this biovar, isolated
      from bull prepuce.
AU  - Iraola G
AU  - Perez R
AU  - Naya H
AU  - Paolicchi F
AU  - Harris D
AU  - Lawley TD
AU  - Rego N
AU  - Hernandez M
AU  - Calleros L
AU  - Carretto L
AU  - Velilla A
AU  - Morsella C
AU  - Mendez A
AU  - Gioffre A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00526-13.

PMID- 28729277
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Infantis Strain SPE101, Isolated from a Chronic Human Infection.
PG  - e00679-17
AB  - We report a 4.99-Mb draft genome sequence of Salmonella enterica subsp. enterica  serovar
      Infantis strain SPE101, isolated from feces of a 5-month-old breast-fed
      female showing diarrhea associated with severe dehydration and malnutrition. The
      infection prolonged for 6 months despite antibiotic treatment.
AU  - Iriarte A
AU  - Giner-Lamia J
AU  - Silva C
AU  - Betancor L
AU  - Astocondor L
AU  - Cestero JJ
AU  - Ochoa T
AU  - Garcia C
AU  - Puente JL
AU  - Chabalgoity JA
AU  - Garcia-Del Portillo F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00679-17.

PMID- 24812225
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Lactobacillus sucicola JCM 15457T, a Motile Lactic Acid  Bacterium Isolated from Oak Sap.
PG  - e00403-14
AB  - Here, we report the draft genome sequence of a motile lactic acid bacterium, Lactobacillus
      sucicola JCM 15457(T), isolated from oak sap. Motility-related
      genes and their organization in the annotated genome were broadly similar to
      those in the sequenced genomes of related lactobacilli.
AU  - Irisawa T
AU  - Oshima K
AU  - Suda W
AU  - Kitahara M
AU  - Sakamoto M
AU  - Kitamura K
AU  - Iida T
AU  - Hattori M
AU  - Ohkuma M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00403-14.

PMID- 22933766
VI  - 194
DP  - 2012
TI  - Genome Sequence of Staphylococcus equorum subsp. equorum Mu2, Isolated from a French Smear-Ripened Cheese.
PG  - 5141-5142
AB  - Staphylococcus equorum subsp. equorum is a member of the coagulase-negative staphylococcus
      group and is frequently isolated from fermented food products and
      from food-processing environments. It contributes to the formation of aroma
      compounds during the ripening of fermented foods, especially cheeses and
      sausages. Here, we report the draft genome sequence of Staphylococcus equorum
      subsp. equorum Mu2 to provide insights into its physiology and compare it with
      other Staphylococcus species.
AU  - Irlinger F
AU  - Loux V
AU  - Bento P
AU  - Gibrat JF
AU  - Straub C
AU  - Bonnarme P
AU  - Landaud S
AU  - Monnet C
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5141-5142.

PMID- 23766409
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Streptococcus agalactiae PR06.
PG  - e00351-13
AB  - Streptococcus agalactiae (group B streptococcus [GBS]) is a Gram-positive bacterium that was
      first recognized as a causative agent of bovine mastitis. S. agalactiae has subsequently
      emerged as a significant cause of human diseases. Here, we report the draft genome sequence of
      S. agalactiae PR06, which was isolated from a septicemic patient in a local hospital in
      Malaysia.
AU  - Irma-Syakina MZ
AU  - Teh LK
AU  - Salleh MZ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00351-13.

PMID- 20715267
VI  - 11
DP  - 2010
TI  - Analysis of the sorangicin gene cluster reinforces the utility of a combined phylogenetic/retrobiosynthetic analysis for deciphering natural product assembly by trans-AT PKS.
PG  - 1840-1849
AB  - The sorangicins are a group of polyketide antibiotics produced by several strains of the
      myxobacterium Sorangium cellulosum, whose activity is derived from inhibition of eubacterial
      RNA polymerase.  The core structure of sorangicins A and B, the metabolites of highest
      abundance, comprises a 31-membered lactone that exhibits many unusual features, including a
      tetra-substituted terahydropyran, a trisubstituted dihydropyran, and a signature C31-C36
      bicyclic ether moiety; sorangicin B lacks a hydroxyl group at C22 relative to sorangicin A.
      The sorangicins are the most potent myxobacterial antibiotics identified to date, exhibiting
      activity against both Gram-positive and Gram-negative species.  The corresponding glycosides
      are only poorly active, however, suggesting that this modification might serve to protect S.
      cellulosum from its own antibiotics.
AU  - Irschik H
AU  - Kopp M
AU  - Weissman KJ
AU  - Buntin K
AU  - Piel J
AU  - Muller R
PT  - Journal Article
TA  - Chembiochem
JT  - Chembiochem
SO  - Chembiochem 2010 11: 1840-1849.

PMID- 19364644
VI  - 19
DP  - 2009
TI  - Constrained (L-)-S-adenosyl-L-homocysteine (SAH) analogues as DNA methyltransferase inhibitors.
PG  - 2742-2746
AB  - Potent SAH analogues with constrained homocysteine units have been designed and synthesized as
      inhibitors of human DNMT enzymes. The five
      membered (2S,4S)-4-mercaptopyrrolidine-2-carboxylic acid, in 1a, was a
      good replacement for homocysteine, while the corresponding six-member
      counterpart was less active. Further optimization of 1a, changed the
      selectivity pro. le of these inhibitors. A Chloro substituent at the
      2-position of 1a, compound 1d, retained potency against DNMT1, while
      N-6 alkylation, compound 7a, conserved DNMT3b2 activity. The
      concomitant substitutions of 1a at both 2- and N-6 positions reduced
      activity against both enzymes.
AU  - Isakovic L
AU  - Saavedra OM
AU  - Llewellyn DB
AU  - Claridge S
AU  - Zhan LJ
AU  - Bernstein N
AU  - Vaisburg A
AU  - Elowe N
AU  - Petschner AJ
AU  - Rahil J
AU  - Beaulieu N
AU  - Gauthier F
AU  - MacLeod AR
AU  - Delorme D
AU  - Besterman JM
AU  - Wahhab A
PT  - Journal Article
TA  - Bioorg. Med. Chem. Lett.
JT  - Bioorg. Med. Chem. Lett.
SO  - Bioorg. Med. Chem. Lett. 2009 19: 2742-2746.

PMID- 10623539
VI  - 295
DP  - 2000
TI  - Engineered Zinc Finger Proteins that Respond to DNA Modification by HaeIII and HhaI Methyltransferase Enzymes.
PG  - 471-477
AB  - Zinc finger modules are capable of specifically interacting with DNA that contains
      5-methylcytosine (5-mC) in place of cytosine, suggesting that zinc finger-DNA binding could be
      regulated by extrinsic methylation of DNA. Here, we have used phage display to engineer zinc
      finger proteins that detect and discriminate DNA methylation by the prokaryotic enzymes HaeIII
      and HhaI. In these systems, zinc finger-DNA complexes are induced by DNA modification using
      the appropriate enzyme, which can therefore act as a switch. To further develop the
      specificity of the switch, zinc finger discrimination between 5-mC and thymine in DNA
      sequences is demonstrated despite the presence of the characteristic major groove methyl group
      that is common to both bases. Specificity was achieved using a DNA-binding strategy involving
      synergy between adjacent zinc fingers. We propose that engineered zinc fingers that recognise
      particular DNA modifications, such as sequence-specific DNA methylation, could be integrated
      into artificial regulatory circuits for the control of gene expression and other biological
      processes.
AU  - Isalan M
AU  - Choo Y
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2000 295: 471-477.

PMID- 22535930
VI  - 194
DP  - 2012
TI  - High-Quality Draft Genome Sequence of the Opitutaceae Bacterium Strain TAV1, a Symbiont of the Wood-Feeding Termite Reticulitermes flavipes.
PG  - 2744-2745
AB  - Microbial communities in the termite hindgut are essential for degrading plant material. We
      present the high-quality draft genome sequence of the Opitutaceae
      bacterium strain TAV1, the first member of the phylum Verrucomicrobia to be
      isolated from wood-feeding termites. The genomic analysis reveals genes coding
      for lignocellulosic degradation and nitrogen fixation.
AU  - Isanapong J et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2744-2745.

PMID- 6246113
VI  - 255
DP  - 1980
TI  - Mechanism of T4 phage restriction by plasmid Rts 1. Cleavage of T4 phage DNA by Rts 1-specific enzyme.
PG  - 4040-4047
AB  - Rts 1 is a plasmid which confers upon host bacteria the capacity to restrict T4 phage growth
      at 32oC but not at 42oC. This restriction was not dependent on cellular adenyl cyclase, while
      other phenotypes of Rts 1, such as the temperature-sensitive effect on host growth, were
      dependent on this enzyme. At 32"C, in Escherichia coli 2OSO/Rts 1 cells, 55 to 60% of the
      parental T4 phage DNA became acid-soluble within 5 to 10 min after infection,
      while in E. coli JC7623/Rts 1 cells, which lack exonuclease I and V, very little T4 DNA became
      acidsoluble.  The capacity of E. coli 2OSO/Rts 1 to degrade infecting T, DNA decreased 70%
      within 15 min after shifting the temperature to 42oC. Temperature shift up and down
      experiments in the presence of chloramphenicol showed that the protein responsible for T, DNA
      cleavage is thermosensitive, and once it is denatured it cannot regain its activity by
      lowering the temperature to 32oC in vivo. Alkaline sucrose gradient centrifugation revealed
      that the infecting Tq DNA was nicked in the presence of Rts 1 at 32"C, but not at 42oC in E.
      coli JC7623. The cell-free extract of E. coli JC7623/Rts 1 grown at 32oC contained an enzyme
      which converted Tq DNA to smaller but acid-insoluble fragments. This enzyme could not be
      detected in E. coli JC7623o r E. coli JC7623/Rts 1 grown at 42oC. The enzyme was rapidly
      inactivated when incubated at 42oC in vitro. Analysis of the reaction product by gel
      electrophoresis and alkaline and sodium dodecyl sulfate-neutral sucrose density gradient
      centrifugation, showed marked heterogeneity of the in vitro reaction product. This enzyme did
      not cleave either T7 DNA or nonglucosylated T4 DNA under the same experimental conditions.
      Only M$+ was required for its activity. These experiments suggest that the plasmid Rts 1 codes
      for a thermosensitive enzyme which specifically degrades glucosylated T, DNA, resulting in the
      restriction of T, phage growth at 32oC but not at 42oC. This enzyme, named Rts 1 endonuclease,
      was purified approximately 500-fold.
AU  - Ishaq M
AU  - Kaji A
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1980 255: 4040-4047.

PMID- 12801642
VI  - 310
DP  - 2003
TI  - Genomic organization and promoter analysis of the Dnmt3b gene.
PG  - 151-159
AB  - The Dnmt3b gene encodes a de novo DNA methyltransferase that is essential for normal mouse
      development. It is highly expressed in early embryos and
      embryonic stem (ES) cells but downregulated in most adult somatic tissues.
      To gain insight into the regulation of Dnmt3b, we have isolated a mouse
      genomic bacterial artificial chromosome clone that contains the Dnmt3b
      gene. Complete sequence analysis of the clone demonstrated that Dnmt3b
      consists of at least 24 exons and spans 38 kilobases. S1 nuclease analysis
      identified two adjacent transcriptional start sites located downstream of
      a unique TATA-like element in a CpG island. There was an unknown gene
      which we named mU(3) 17 kb upstream of the Dnmt3b locus, and it was
      transcribed ubiquitously and in the opposite direction of Dnmt3b.
      Transfection analysis revealed that the minimal promoter region containing
      an Sp1 site was active even in somatic cells, and that there were several
      repressor elements within 7.9 kb upstream of Dnmt3b downregulated this
      gene specifically in somatic cells but not in ES cells. These findings
      provide a basis for future detailed studies of the mechanisms controlling
      Dnmt3b expression.
AU  - Ishida C
AU  - Ura K
AU  - Hirao A
AU  - Sasaki H
AU  - Toyoda A
AU  - Sakaki Y
AU  - Niwa H
AU  - Li E
AU  - Kaneda Y
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 2003 310: 151-159.

PMID- 27563051
VI  - 4
DP  - 2016
TI  - Genome Sequence of Enterobacter cloacae Strain SENG-6, a Bacterium Producing Histo-Blood Group Antigen-Like Substances That Can Bind with Human Noroviruses.
PG  - e00893-16
AB  - Enterobacter sp. strain SENG-6, isolated from healthy human feces, produces histo-blood group
      antigen (HBGA)-like substances that can bind with human
      noroviruses. Based on the genome sequence analysis, strain SENG-6 belongs to the
      species Enterobacter cloacae The genome sequence of this strain should help
      identify genes associated with the production of HBGA-like substances.
AU  - Ishii S
AU  - Amarasiri M
AU  - Hashiba S
AU  - Yang P
AU  - Okabe S
AU  - Sano D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00893-16.

PMID- 22038961
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of the Denitrifying and N2O-Reducing Bacterium Pseudogulbenkiania sp. Strain NH8B.
PG  - 6395-6396
AB  - Pseudogulbenkiania sp. strain NH8B is a Neisseriales bacterium isolated from an agricultural
      field. This strain has strong denitrification and
      N(2)O reduction activities. Here, we report the finished and annotated
      genome sequence of this organism.
AU  - Ishii S
AU  - Tago K
AU  - Nishizawa T
AU  - Oshima K
AU  - Hattori M
AU  - Senoo K
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6395-6396.

PMID- 15466710
VI  - 101
DP  - 2004
TI  - The complete genomic sequence of Nocardia farcinica IFM 10152.
PG  - 14925-14930
AB  - We determined the genomic sequence of Nocardia farcinica IFM 10152, a clinical isolate, and
      revealed the molecular basis of its versatility.  The genome consists of a single circular
      chromosome of 6,021,225 bp with an average G+C content of 70.8% and two plasmids of 184,027
      (pNF1) and 87,093 (pNF2) bp with average G+C contents of 67.2% and 68.4%, respectively.  The
      chromosome encoded 5,674, putative protein-coding sequences, including many candidate genes
      for virulence and multidrug resistance as well as secondary metabolism.  Analyses of
      paralogous protein families suggest that gene duplications have resulted in a bacterium that
      can survive not only in soil environments but also in animal tissues, resulting in disease.
AU  - Ishikawa J
AU  - Yamashita A
AU  - Mikami Y
AU  - Hoshino Y
AU  - Kurita H
AU  - Hotta K
AU  - Shiba T
AU  - Hattori M
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2004 101: 14925-14930.

PMID- 21059708
VI  - 17
DP  - 2010
TI  - Conflicts targeting epigenetic systems and their resolution by cell death: novel concepts for methyl-specific and other restriction systems.
PG  - 325-342
AB  - Epigenetic modification of genomic DNA by methylation is important for defining the epigenome
      and the transcriptome in eukaryotes as well as in prokaryotes. In prokaryotes, the DNA
      methyltransferase genes often vary, are mobile, and are paired with the gene for a restriction
      enzyme. Decrease in a certain epigenetic methylation may lead to chromosome cleavage by the
      partner restriction enzyme, leading to eventual cell death. Thus, the pairing of a DNA
      methyltransferase and a restriction enzyme forces an epigenetic state to be maintained within
      the genome. Although restriction enzymes were originally discovered for their ability to
      attack invading DNAs, it may be understood because such DNAs show deviation from this
      epigenetic status. DNAs with epigenetic methylation, by a methyltransferase linked or unlinked
      with a restriction enzyme, can also be the target of DNases, such as McrBC of Escherichia
      coli, which was discovered because of its methyl-specific restriction. McrBC responds to
      specific genome methylation systems by killing the host bacterial cell through chromosome
      cleavage. Evolutionary and genomic analysis of McrBC homologues revealed their mobility and
      wide distribution in prokaryotes similar to restriction-modification systems. These findings
      support the hypothesis that this family of methyl-specific DNases evolved as mobile elements
      competing with specific genome methylation systems through host killing. These restriction
      systems clearly demonstrate the presence of conflicts between epigenetic systems.
AU  - Ishikawa K
AU  - Fukuda E
AU  - Kobayashi I
PT  - Journal Article
TA  - DNA Res.
JT  - DNA Res.
SO  - DNA Res. 2010 17: 325-342.

PMID- 
VI  - 83
DP  - 2008
TI  - Coupling of DNA replication and restriction: A type I restriction enzyme cleaves branched DNAs mimicing replication forks, in vitro.
PG  - 510
AB  - Coupling of DNA replication and restriction: A type I restriction enzyme cleaves branched DNAs
      mimicing replication forks, in vitro.  DNA cleavage by a restriction enzyme is prevented by
      methylation on the recognition sequence.  It has been imagined that DNA replication and
      restriction cleavage are coupled because unmethylated site will appear through replication
      fork passage.  In fact, we previously observed an example suggesting such a coupling between
      phage DNA replication and restriction, in vivo.  In the present study, we show that a purified
      type I restriction endonuclease cleaves DNAs with long branch mimicking replication forks, in
      the vicinity of the branch point dependent on an unmethylated recognition sequence.
      Relationship between type I restriction enzymnes and other enzymes known that they cleave
      branched DNA will be discussed.
AU  - Ishikawa K
AU  - Handa N
AU  - Kobayashi I
PT  - Journal Article
TA  - Genes Genet. Syst.
JT  - Genes Genet. Syst.
SO  - Genes Genet. Syst. 2008 83: 510.

PMID- 19357093
VI  - 37
DP  - 2009
TI  - Cleavage of a model DNA replication fork by a Type I restriction endonuclease.
PG  - 3531-3544
AB  - Cleavage of a DNA replication fork leads to fork restoration by recombination repair. In
      prokaryote cells carrying
      restriction-modification systems, fork passage reduces genome methylation
      by the modification enzyme and exposes the chromosome to attack by the
      restriction enzyme. Various observations have suggested a relationship
      between the fork and Type I restriction enzymes, which cleave DNA at a
      distance from a recognition sequence. Here, we demonstrate that a Type I
      restriction enzyme preparation cleaves a model replication fork at its
      branch. The enzyme probably tracks along the DNA from an unmethylated
      recognition site on the daughter DNA and cuts the fork upon encountering
      the branch point. Our finding suggests that these restriction-modification
      systems contribute to genome maintenance through cell death and indicates
      that DNA replication fork cleavage represents a critical point in genome
      maintenance to choose between the restoration pathway and the destruction
      pathway.
AU  - Ishikawa K
AU  - Handa N
AU  - Kobayashi I
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: 3531-3544.

PMID- 21441537
VI  - 39
DP  - 2011
TI  - Cleavage of a model DNA replication fork by a methyl-specific endonuclease.
PG  - 5489-5498
AB  - Epigenetic DNA methylation is involved in many biological processes. An epigenetic status can
      be altered by gain or loss of a DNA methyltransferase gene or its activity. Repair of DNA
      damage can also remove DNA methylation. In response to such alterations, DNA endonucleases
      that sense DNA methylation can act and may cause cell death. Here, we explored the possibility
      that McrBC, a methylation-dependent DNase of Escherichia coli, cleaves DNA at a replication
      fork. First, we found that in vivo restriction by McrBC of bacteriophage carrying a foreign
      DNA methyltransferase gene is increased in the absence of homologous recombination. This
      suggests that some cleavage events are repaired by recombination and must take place during or
      after replication. Next, we demonstrated that the enzyme can cleave a model DNA replication
      fork in vitro. Cleavage of a fork required methylation on both arms and removed one, the other
      or both of the arms. Most cleavage events removed the methylated sites from the fork. This
      result suggests that acquisition of even rarely occurring modification patterns will be
      recognized and rejected efficiently by modification-dependent restriction systems that
      recognize two sites. This process might serve to maintain an epigenetic status along the
      genome through programmed cell death.
AU  - Ishikawa K
AU  - Handa N
AU  - Sears L
AU  - Raleigh EA
AU  - Kobayashi I
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2011 39: 5489-5498.

PMID- 
VI  - 80
DP  - 2005
TI  - Discovery of a novel restriction endonuclease by genome comparison and application of a wheat-germ-based cell-free translation assay: PabI (5'GTA/C) from the hyperthermophilic archaeon Pyrococcus abyssi.
PG  - 454
AB  - To search for restriction endonucleasees, we used a novel plant-based cell-free translation
      procedure that bypasses the toxicity of these enzymes. To identify candidate genes, the
      related genomes of the hyperthermophilic archaea Pyrococcus abyssi and Pyrococcus horikoshii
      were compared. In line with the selfish mobile gene hypothesis for restriction-modification
      systems, apparent genome rearrangement around putative restriction genes serve as a selecting
      criterion.  Several candidate restriction genes were identified and expressed with a wheat
      germ-based cell-free protein synthesis system.  The resulting solution could be directly
      assayed for restriction activity.  We identified two deoxyribonucleases.  The novel enzymes
      was denoted as PabI, purified and found to recognize 5'GTAC and leave a 3TA overhang
      (5'GTA/C), a novel restriction enzyme-generated terminus.  PabI is active up to 90oC and
      optimally active at a pH of around 6 and in NaCl concentrations ranging from 100 to 200 mM.
      We predict that it has a novel three-dimensional structure.
AU  - Ishikawa K
AU  - Watanabe M
AU  - Kuroita T
AU  - Uchiyama I
AU  - Bujnicki J
AU  - Kawakami B
AU  - Tanokura M
AU  - Kobayashi I
PT  - Journal Article
TA  - Genes Genet. Syst.
JT  - Genes Genet. Syst.
SO  - Genes Genet. Syst. 2005 80: 454.

PMID- 16040595
VI  - 33
DP  - 2005
TI  - Discovery of a novel restriction endonuclease by genome comparison and application of a wheat-germ-based cell-free translation assay: PabI   (5'-GTA/C) from the hyperthermophilic archaeon Pyrococcus abyssi.
PG  - e112
AB  - To search for restriction endonucleases, we used a novel plant-based cell-free translation
      procedure that bypasses the toxicity of these
      enzymes. To identify candidate genes, the related genomes of the
      hyperthermophilic archaea Pyrococcus abyssi and Pyrococcus horikoshii were
      compared. In line with the selfish mobile gene hypothesis for
      restriction-modification systems, apparent genome rearrangement around
      putative restriction genes served as a selecting criterion. Several
      candidate restriction genes were identified and then amplified in such a
      way that they were removed from their own translation signal. During their
      cloning into a plasmid, the genes became connected with a plant
      translation signal. After in vitro transcription by T7 RNA polymerase, the
      mRNAs were separated from the template DNA and translated in a
      wheat-germ-based cell-free protein synthesis system. The resulting
      solution could be directly assayed for restriction activity. We identified
      two deoxyribonucleases. The novel enzyme was denoted as PabI, purified and
      found to recognize 5'-GTAC and leave a 3'-TA overhang (5'-GTA/C), a novel
      restriction enzyme-generated terminus. PabI is active up to 90 degrees C
      and optimally active at a pH of around 6 and in NaCl concentrations
      ranging from 100 to 200 mM. We predict that it has a novel 3D structure.
AU  - Ishikawa K
AU  - Watanabe M
AU  - Kuroita T
AU  - Uchiyama I
AU  - Bujnicki JM
AU  - Kawakami B
AU  - Tanokura M
AU  - Kobayashi I
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2005 33: e112.

PMID- Not included in PubMed...
VI  - 36
DP  - 1990
TI  - Purification of restriction endonuclease from Acetobacter pasteurianus IFO 13752 (ApaORI) and its properties.
PG  - 127-135
AB  - A restriction endonuclease, designated ApaORI, was purified from cell-free
      extracts of A. pasteurianus IFO 13752 by streptomycin treatment, ammonium
      sulfate fractionation, phosphocellulose treatment, hydroxylapatite and
      heparin-Sepharose CL-6B column chromatography, and gel filtration using a
      Superose 12 (HR10/30) column.  The purified enzyme was homogeneous on
      polyacrylamide gel disc electrophoresis.  The molecular weight of the purified
      enzyme was found by gel filtration to be 21,000 daltons.  The isoelectric point
      of the purified enzyme was neutral.  The purified enzyme cleaved lambda,
      PhiX174 RF I, M13mp7 RF I, and pBR322 DNAs at 18 or more, 2, 4 or more, and 4
      or more sites respectively.  The purified enzyme worked best at 37C and pH 7.5
      in a reaction mixture (50 micro liters) containing 1.0 microgram lambda DNA, 10
      mM Tris-HCl, 7 mM 2-mercaptoethanol, 7 mM MgCl2, and 50 mM NaCl.  However, the
      purified enzyme did not require NaCl for its reaction.  The purified enzyme
      recognizes the palindromic pentanucleotides 5'-CC (A or T)GG-3' and cuts
      between C and A (orT), producing 5'-cohesive mononucleotide extensions
      (isoschizomer of BstNI).
AU  - Ishikawa T
AU  - Yamada Y
PT  - Journal Article
TA  - J. Gen. Appl. Microbiol.
JT  - J. Gen. Appl. Microbiol.
SO  - J. Gen. Appl. Microbiol. 1990 36: 127-135.

PMID- 7708487
VI  - 23
DP  - 1995
TI  - Sse8647I, a new type II restriction endonuclease from a Streptomyces species cutting at 5'-AG/GWCCT-3'.
PG  - 742-744
AB  - We isolated and characterized a new type II restriction endonuclease which recognizes the
      palindromic heptanucleotide sequence 5'-AGGWCCT-3' and cleaves double-stranded DNA after the
      first G in the sequence from a microorganism belonging to Streptomyces species. This enzyme
      cleaves adenovirus 2 DNA at eight sites, but does not cleave lambda phage, pBR322, pUC18 and
      19, M13mp18 and 19, SV40, ColE1 and omega-X174 DNAs.
AU  - Ishino Y
AU  - Nomura Y
AU  - Kato I
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1995 23: 742-744.

PMID- Not carried by PubMed...
VI  - 36
DP  - 1995
TI  - Studies on restriction endonucleases of bacteria causing peroral infectious diseases.  I. Characterization of Hsd plasmid in Salmonella typhi.
PG  - 404-408
AB  - An Hsd (host specificity for DNA) plasmid designated pSTd4 was found in Salmonella Typhi D4,
      one of the standard phage typing strains.  The plasmid was introduced into E. coli K-12, and
      the restriction map of this plasmid was constructed.  The efficiency of plating of lambda-O
      phage was drastically reduced with pSTd4 as well as other small Hsd plasmids of
      Enterobacteriaceae origin.  The results clearly indicate that pSTd4 is a type-determining
      plasmid in S. Typhi D4.  We propose that rare phage types such as D4 carrying type-determining
      plasmids or lysogenic phages should be eliminated from the collection of standard phage
      typing strains of S. Typhi.
AU  - Ishiwata N
AU  - Tanimura A
AU  - Miyahara M
AU  - Mise K
PT  - Journal Article
TA  - Shokuhin Eiseigaku Zasshi
JT  - Shokuhin Eiseigaku Zasshi
SO  - Shokuhin Eiseigaku Zasshi 1995 36: 404-408.

PMID- 29053958
VI  - 68
DP  - 2017
TI  - Structure of the Dnmt1 Reader Module Complexed with a Unique Two-Mono-Ubiquitin Mark on Histone H3 Reveals the Basis for DNA Methylation Maintenance.
PG  - 350-360.e7
AB  - The proper location and timing of Dnmt1 activation are essential for DNA methylation
      maintenance. We demonstrate here that Dnmt1 utilizes
      two-mono-ubiquitylated histone H3 as a unique ubiquitin mark for its recruitment
      to and activation at DNA methylation sites. The crystal structure of the
      replication foci targeting sequence (RFTS) of Dnmt1 in complex with H3-K18Ub/23Ub
      reveals striking differences to the known ubiquitin-recognition structures. The
      two ubiquitins are simultaneously bound to the RFTS with a combination of
      canonical hydrophobic and atypical hydrophilic interactions. The C-lobe of RFTS,
      together with the K23Ub surface, also recognizes the N-terminal tail of H3. The
      binding of H3-K18Ub/23Ub results in spatial rearrangement of two lobes in the
      RFTS, suggesting the opening of its active site. Actually, incubation of Dnmt1
      with H3-K18Ub/23Ub increases its catalytic activity in vitro. Our results
      therefore shed light on the essential role of a unique ubiquitin-binding module
      in DNA methylation maintenance.
AU  - Ishiyama S et al
PT  - Journal Article
TA  - Mol. Cell
JT  - Mol. Cell
SO  - Mol. Cell 2017 68: 350-360.e7.

PMID- 28818906
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Aquitalea magnusonii Strain H3, a Plant Growth-Promoting Bacterium of Duckweed (Lemna minor).
PG  - e00812-17
AB  - Aquitalea magnusonii strain H3 is a promising plant growth-promoting bacterium for duckweed.
      Here, we report the draft genome sequence of strain H3 comprising
      4,750,601 bp in 73 contigs. Several genes associated with plant root colonization
      were identified.
AU  - Ishizawa H
AU  - Kuroda M
AU  - Ike M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00812-17.

PMID- 
VI  - 10
DP  - 2017
TI  - Evaluation of environmental bacterial communities as a factor affecting the growth of duckweed Lemna minor.
PG  - 0
AB  - 
AU  - Ishizawa H
AU  - Kuroda M
AU  - Morikawa M
AU  - Ike M
PT  - Journal Article
TA  - Biotechnol. Biofuels.
JT  - Biotechnol. Biofuels.
SO  - Biotechnol. Biofuels. 2017 10: 0.

PMID- 28104664
VI  - 5
DP  - 2017
TI  - First Complete Genome Sequence of Haemophilus influenzae Serotype a.
PG  - e01506-16
AB  - Haemophilus influenzae is an important human pathogen that primarily infects small children.
      In recent years, H. influenzae serotype a has emerged as a
      significant cause of invasive disease among indigenous populations. Here, we
      present the first complete whole-genome sequence of H. influenzae serotype a.
AU  - Iskander M
AU  - Hayden K
AU  - Van Domselaar G
AU  - Tsang R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01506-16.

PMID- 23788553
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of a Clinical Isolate of Mycobacterium tuberculosis Strain  PR05.
PG  - e00397-13
AB  - We report the annotated genome sequence of a clinical isolate, Mycobacterium tuberculosis
      strain PR05, which was isolated from the human cerebrospinal fluid
      of a patient diagnosed with tuberculosis.
AU  - Ismail A
AU  - Teh LK
AU  - Ngeow YF
AU  - Norazmi MN
AU  - Zainul ZF
AU  - Tang TH
AU  - Najimudin N
AU  - Salleh MZ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00397-13.

PMID- 25614574
VI  - 3
DP  - 2015
TI  - Draft genome sequence of calothrix strain 336/3, a novel h2-producing cyanobacterium isolated from a finnish lake.
PG  - e01474-14
AB  - We announce the draft genome sequence of Calothrix strain 336/3, an N2-fixing heterocystous
      filamentous cyanobacterium isolated from a natural habitat.
      Calothrix 336/3 produces higher levels of hydrogen than Nostoc punctiforme PCC
      73102 and Anabaena strain PCC 7120 and, therefore, is of interest for potential
      technological applications.
AU  - Isojarvi J
AU  - Shunmugam S
AU  - Sivonen K
AU  - Allahverdiyeva Y
AU  - Aro EM
AU  - Battchikova N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01474-14.

PMID- 
VI  - 28
DP  - 2000
TI  - In silico evidence for horizontal gene transfer of type II restriction-modification genes in Helicobacter pylori.
PG  - A185
AB  - Helicobacter pylori is a gram-negative bacteria associated with peptic ulcer disease and a
      risk factor for gastric cancer.  The organism is the first for which the complete genome
      sequences of two unrelated strains, 26695 and J99, has been published.  Analyses of these
      genomes have identified a high number of genes with homology to restriction and modification
      enzymes, many of which are strain specific.  Restriction-modification genes are widely
      distributed in bacteria and function in defense against invasion by foreign DNA.  Recent
      evidence also suggests their involvement in genomic rearrangement and evolution.  In order to
      gain insight into the role of R-M genes in H. pylori evolution, this study examined G+C
      content and codon bias of type II R-M genes in J99.  This strain consists of 4 paired type II
      R-M systems as well as 1 unpaired restriction enzyme and 15 unpaired modification enzymes.
      Compositional features of the codon positions for all 24 genes were determined with the
      program CODONTREE.  Overall G+C content in paired genes is higher for modification genes than
      restriction genes, suggesting a possible stepwise evolutionary process.  Three restriction and
      2 modification genes significantly deviate (P<0.05) in G+C content relative to the mean G+C
      content of the H. pylori genome.  Lastly, a distance matrix based on codon usage in paired R-M
      system genes was generated to test the hypothesis that a restriction gene is more closely
      related to its associated modification gene than to the modification genes of other paired R-M
      systems.  A UPGMA distance tree generated by the program NEIGHBOUR supports this hypothesis.
      These results provide in silico evidence that type II R-M genes in H. pylori J99, may have
      been acquired through horizontal gene transfer.
AU  - Isokpehi RD
AU  - Coker AO
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 2000 28: A185.

PMID- 11697346
VI  - 291S
DP  - 2001
TI  - Possible stepwise evolution of type II restriction-modification genes in Helicobacter pylori genome.
PG  - 94
AB  - Helicobacter pylori is a gram-negative bacteria associated with peptic ulcer disease.  The
      complete genome sequences of strains 26695 and J99 of the organism have been published and
      compared.  Analyses of these genomes have identified a high number of genes with homology to
      restriction and modification enzymes, many of which are strain specific and may have been
      acquired by horizontal gene transfer.  Restriction-Modification (R-M) genes are widely
      distributed in bacteria and function in defense against invasion by foreign DNA.  Recent
      evidence also suggests their involvement in genomic rearrangement and evolution.  In H.
      pylori, the modification genes may also regulate gene expression.  Variation in base
      composition of genes can provide evidence of the order of introduction of genes into a genome.
      Thus, in order to gain insight into the evolution of R-M genes in H. pylori genome, this study
      examined guanine and cytosine (G+C) content of the type II restriction genes (5 in 26695, 4 in
      J99) and modification genes (17 in 26695, 20 in J99).  In both strains, 4 pairs of R-M genes
      exist, two of which are unique to each strain.  All the type II R-M genes were retrieved from
      their respective databases and compositional features of the codon position were determined
      using a computer program CODONTREE.  In all the paired R-M genes, the overall G+C content of
      the modification gene is greater than its associated restriction gene, suggesting a possible
      stepwise evolutionary process.  Further studies such as time of introgression and amelioration
      of R-M genes in the genome could confirm their stepwise evolution.
AU  - Isokpehi RD
AU  - Coker AO
PT  - Journal Article
TA  - Int. J. Med. Microbiol.
JT  - Int. J. Med. Microbiol.
SO  - Int. J. Med. Microbiol. 2001 291S: 94.

PMID- 27365342
VI  - 4
DP  - 2016
TI  - Whole-Genome Shotgun Sequencing and Annotation of Mycobacterium tuberculosis MTB221/11 Isolated from a Cerebrospinal Fluid Sample in Malaysia.
PG  - e00376-16
AB  - Here, we report of the annotated genome sequence of Mycobacterium tuberculosis MTB221/11. The
      organism was isolated from the cerebrospinal fluid of a patient in Malaysia.
AU  - Issa R
AU  - Seradja VH
AU  - Abdullah MK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00376-16.

PMID- 27340055
VI  - 4
DP  - 2016
TI  - Annotated Sequence of Mycobacterium tuberculosis MTBR3/09 Isolated from a Sputum  Sample in Malaysia.
PG  - e00517-16
AB  - This is a report of the annotated genome sequence of Mycobacterium tuberculosis MTBR3/09. The
      organism was isolated from a sputum sample in Malaysia.
AU  - Issa R
AU  - Seradja VH
AU  - Abdullah MK
AU  - Abdul H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00517-16.

PMID- 27340054
VI  - 4
DP  - 2016
TI  - Annotated Whole-Genome Shotgun Sequence of Mycobacterium tuberculosis MTBR2/09 Isolated from a Sputum Sample in Malaysia.
PG  - e00515-16
AB  - Mycobacterium tuberculosis MTBR2/09 was isolated from a sputum sample from a male patient in
      Malaysia. This is a report of an annotated genome sequence of M.
      tuberculosis MTBR2/09.
AU  - Issa R
AU  - Seradja VH
AU  - Abdullah MK
AU  - Abdul H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00515-16.

PMID- 27340053
VI  - 4
DP  - 2016
TI  - Whole-Genome Shotgun Sequencing and Annotation of Mycobacterium tuberculosis MTBR1/09 Isolated from a Sputum Sample in Malaysia.
PG  - e00513-16
AB  - This is a report of an annotated genome sequence of Mycobacterium tuberculosis MTBR1/09. The
      organism was isolated from a sputum sample from a male patient in
      Malaysia.
AU  - Issa R
AU  - Seradja VH
AU  - Abdullah MK
AU  - Abdul H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00513-16.

PMID- 26925196
VI  - 11
DP  - 2016
TI  - Draft genome sequence of chloride-tolerant Leptospirillum ferriphilum Sp-Cl from  industrial bioleaching operations in northern Chile.
PG  - 19
AB  - Leptospirillum ferriphilum Sp-Cl is a Gram negative, thermotolerant, curved, rod-shaped
      bacterium, isolated from an industrial bioleaching operation in
      northern Chile, where chalcocite is the major copper mineral and copper
      hydroxychloride atacamite is present in variable proportions in the ore. This
      strain has unique features as compared to the other members of the species,
      namely resistance to elevated concentrations of chloride, sulfate and metals.
      Basic microbiological features and genomic properties of this biotechnologically
      relevant strain are described in this work. The 2,475,669 bp draft genome is
      arranged into 74 scaffolds of 74 contigs. A total of 48 RNA genes and 2,834
      protein coding genes were predicted from its annotation; 55 % of these were
      assigned a putative function. Release of the genome sequence of this strain will
      provide further understanding of the mechanisms used by acidophilic bacteria to
      endure high osmotic stress and high chloride levels and of the role of
      chloride-tolerant iron-oxidizers in industrial bioleaching operations.
AU  - Issotta F
AU  - Galleguillos PA
AU  - Moya-Beltran A
AU  - Davis-Belmar CS
AU  - Rautenbach G
AU  - Covarrubias PC
AU  - Acosta M
AU  - Ossandon FJ
AU  - Contador Y
AU  - Holmes DS
AU  - Marin-Eliantonio S
AU  - Quatrini R
AU  - Demergasso C
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 19.

PMID- 2374714
VI  - 18
DP  - 1990
TI  - Cloning, nucleotide sequence, and expression of the HincII restriction-modification system.
PG  - 3903-3911
AB  - Two genes, coding for the HincII from Haemophilus influenzae Rc
      restriction-modification system, were cloned and expressed in Escherichia coli
      RR1.  Their DNA sequences were determined.  The HincII methylase (M.HincII)
      gene was 1,506 base pairs (bp) long, corresponding to a protein of 502 amino
      acid residues (Mr=55,330).  The HincII endonuclease (R.HincII) gene was 774 bp
      long, corresponding to a protein of 258 amino acid residues (Mr=28,490).  The
      amino acid residues predicted from the R.HincII and the N-terminal amino acid
      sequence of the enzyme found by analysis were identical.  These methylase and
      endonuclease genes overlapped by 1 bp on the H. influenzae Rc chromosomal DNA.
      The clone, named E. coli RR1-Hinc, overproduced R.HincII.  The R.HincII
      activity of this clone was 1,000-fold that from H. influenzae Rc.  The amino
      acid sequence of M.HincII was compared with the sequences of four other
      adenine-specific type II methylases.  Important homology was found between the
      M.HincII and these other methylases.
AU  - Ito H
AU  - Sadaoka A
AU  - Kotani H
AU  - Hiraoka N
AU  - Nakamura T
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 3903-3911.

PMID- 1542567
VI  - 20
DP  - 1992
TI  - Cloning and expression of the HpaI restriction-modification genes.
PG  - 705-709
AB  - The genes from Haemophilus parainfluenzae encoding the HpaI
      restriction-modification system were cloned and expressed in Escherichia coli.
      From the DNA sequence, we predicted the HpaI endonuclease (R.HpaI) to have 254
      amino acid residues (Mr 29,630) and the HpaI methyltransferase (M.HpaI) to have
      314 amino acid residues (37,390).  The R.HpaI and M.HpaI genes overlapped by 16
      base pairs on the chromosomal DNA.  The genes had the same orientation.  The
      clone, named E. coli HB101-HPA2, overproduced R.HpaI.  R.HpaI activity from the
      clone was 100-fold that from H. parainfluenzae.  The amino acid sequence of
      M.HpaI was compared with those of other type II methyltransferases.
AU  - Ito H
AU  - Shimato H
AU  - Sadaoka A
AU  - Kotani H
AU  - Kimizuka F
AU  - Kato I
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 705-709.

PMID- 806480
VI  - 55
DP  - 1975
TI  - Susceptibility of non-thymine containing DNA to four bacterial restriction endonucleases.
PG  - 278-281
AB  - None
AU  - Ito J
AU  - Kawamura F
AU  - Duffy JJ
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1975 55: 278-281.

PMID- 107059
VI  - 5
DP  - 1979
TI  - Unusual base sequence arrangement in phage Phi29 DNA.
PG  - 1-7
AB  - Susceptibility of Bacillus subtilis phage Phi29 DNA to 34 different restriction
      endonucleases was determined.  Three enzymes, BglI, XbaI and BstEII, were found
      to cleave Phi29 DNA only once at specific sites.  The sites of these single
      cleavages have been mapped.  Thirteen enzymes did not cut Phi29 DNA.  Phi29
      HindIII DNA fragments inserted into pBR313 plasmid and propagated in
      Escherichia coli, were resistant to these restriction endonucleases.  This
      result suggests that the insusceptibility is due to the absence of the
      nucleotide sequences on Phi29 recognized by the enzymes, and not to the
      presence of modified nucleotides.
AU  - Ito J
AU  - Roberts RJ
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1979 5: 1-7.

PMID- 27738047
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Arenibacter sp. Strain C-21, an Iodine-Accumulating Bacterium Isolated from Surface Marine Sediment.
PG  - e01155-16
AB  - Arenibacter sp. strain C-21, isolated from surface marine sediment of Japan, accumulates
      iodine in the presence of glucose and iodide (I-). We report here the
      draft genome sequence of this strain to provide insight into the molecular
      mechanism underlying its iodine-accumulating ability.
AU  - Ito K
AU  - Nakajima N
AU  - Yamamura S
AU  - Tomita M
AU  - Suzuki H
AU  - Amachi S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01155-16.

PMID- 21778364
VI  - 333
DP  - 2011
TI  - Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine.
PG  - 1300-1303
AB  - 5-methylcytosine (5mC) in DNA plays an important role in gene expression, genomic imprinting,
      and suppression of transposable elements. 5mC can be converted to
      5-hydroxymethylcytosine (5hmC) by the Tet (ten eleven translocation) proteins.
      Here, we show that, in addition to 5hmC, the Tet proteins can generate
      5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) from 5mC in an enzymatic
      activity-dependent manner. Furthermore, we reveal the presence of 5fC and 5caC in
      genomic DNA of mouse embryonic stem cells and mouse organs. The genomic content
      of 5hmC, 5fC, and 5caC can be increased or reduced through overexpression or
      depletion of Tet proteins. Thus, we identify two previously unknown cytosine
      derivatives in genomic DNA as the products of Tet proteins. Our study raises the
      possibility that DNA demethylation may occur through Tet-catalyzed oxidation
      followed by decarboxylation.
AU  - Ito S
AU  - Shen L
AU  - Dai Q
AU  - Wu SC
AU  - Collins LB
AU  - Swenberg JA
AU  - He C
AU  - Zhang Y
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2011 333: 1300-1303.

PMID- 11302791
VI  - 45
DP  - 2001
TI  - Structural comparison of three types of Staphylococcal cassette chromosome mec integrated in the chromosome in methicillin-resistant Staphylococcus aureus.
PG  - 1323-1336
AB  - The beta-lactam resistance gene mecA of Staphylococcus aureus is carried by a novel mobile
      genetic element, designated staphylococcal cassette chromosome mec (SCCmec), identified in the
      chromosome of a Japanese methicillin-resistant S. aureus (MRSA) strain.  We now report
      identification of two additional types of mecA-carrying genetic elements found in the MRSA
      strains isolated in other countries of the world.  There were substantial differences in the
      size and nucleotide sequences between the elements and the SCCmec.  However, new elements
      shared the chromosomal integration site with the SCCmec.  Structural analysis of the new
      elements revealed that they possessed all of the salient features of the SCCmec: conserved
      terminal inverted repeats and direct repeats at the integration junction points, conserved
      genetic organization around the mecA gene, and the presence of cassette chromosome recombinase
      genes responsible for the movements of SCCmec.  The elements, therefore, were considered to
      comprise the SCCmeg family of staphylococcal mobile genetic elements together with the
      previously identified SCCmec.  Among 38 epidemic MRSA strains isolated in 20 countries, 34
      were shown to possess one of the three typical SCCmec elements on the chromosome.  Our
      findings indicated that there are at least three distinct MRSA clones in the world with
      different types of SCCmec in their chromosome.
AU  - Ito T
AU  - Katayama Y
AU  - Asada K
AU  - Mori N
AU  - Tsutsumimoto K
AU  - Tiensasitorn C
AU  - Hiramatsu K
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2001 45: 1323-1336.

PMID- 15215121
VI  - 48
DP  - 2004
TI  - Novel Type V Staphylococcal Cassette Chromosome mec Driven by a Novel Cassette Chromosome Recombinase, ccrC.
PG  - 2637-2651
AB  - Staphylococcal cassette chromosome mec (SCCmec) is a mobile genetic
      element composed of the mec gene complex, which encodes methicillin
      resistance, and the ccr gene complex, which encodes the recombinases
      responsible for its mobility. The mec gene complex has been classified
      into four classes, and the ccr gene complex has been classified into three
      allotypes. Different combinations of mec gene complex classes and ccr gene
      complex types have so far defined four types of SCCmec elements. Now we
      introduce the fifth allotype of SCCmec, which was found on the chromosome
      of a community-acquired methicillin-resistant Staphylococcus aureus strain
      (strain WIS [WBG8318]) isolated in Australia. The element shared the same
      chromosomal integration site with the four extant types of SCCmec and the
      characteristic nucleotide sequences at the chromosome-SCCmec junction
      regions. The novel SCCmec carried mecA bracketed by IS431
      (IS431-mecA-DeltamecR1-IS431), which is designated the class C2 mec gene
      complex; and instead of ccrA and ccrB genes, it carried a single copy of a
      gene homologue that encoded cassette chromosome recombinase. Since the
      open reading frame (ORF) was found to encode an enzyme which catalyzes the
      precise excision as well as site- and orientation-specific integration of
      the element, we designated the ORF cassette chromosome recombinase C
      (ccrC), and we designated the element type V SCCmec. Type V SCCmec is a
      small SCCmec element (28 kb) and does not carry any antibiotic resistance
      genes besides mecA. Unlike the extant SCCmec types, it carries a set of
      foreign genes encoding a restriction-modification system that might play a
      role in the stabilization of the element on the chromosome.
AU  - Ito T
AU  - Ma XX
AU  - Takeuchi F
AU  - Okuma K
AU  - Yuzawa H
AU  - Hiramatsu K
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2004 48: 2637-2651.

PMID- 29700164
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Mycobacterium virginiense Strain GF75, Isolated from the Mud of a Swine Farm in Japan.
PG  - e00362-18
AB  - Mycobacterium virginiense, a newly described species of the Mycobacterium terrae  complex, is
      a cause of tenosynovitis and osteomyelitis in the United States.
      Here, we report the 4,849,424-bp draft genome sequence of M. virginiense strain
      GF75, isolated from a mud sample taken from a Japanese swine farm.
AU  - Ito T
AU  - Maruyama F
AU  - Sawai K
AU  - Nozaki K
AU  - Otsu K
AU  - Ohya K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00362-18.

PMID- 10655332
VI  - 38
DP  - 2000
TI  - Sequence analysis and clinical significance of the iceA gene from Helicobacter pylori strains in Japan.
PG  - 483-488
AB  - The Helicobacter pylori iceA gene was recently identified as a genetic marker for the
      development of peptic ulcer in a Western population.  To assess the significance of iceA
      subtypes of H. pylori in relation to peptic ulcer, 140 Japanese clinical isolates (88 from
      Fukui and 52 from Okinawa) were characterized.  Sequence analysis of the iceA1 gene from 25
      representative Japanese strains was also carried out to identify the differences in iceA
      between the ulcer group and the gastritis group.  The iceA1 genotype was not correlated with
      the presence of peptide ulceration in either area.  In addition, sequence analysis led to
      identification of five deletions and five point mutations (a nonsense mutation or a 1-bp
      insertion) within the iceA1 open reading frame corresponding to previously published
      sequences.  These mutations were identified in both clinical groups (ulcer and gastritis
      groups) in each area.  Local DNA sequence analysis revealed that the endpoints of all five
      deletions coincided with direct repeats.  We also found four strains that carried longer iceA1
      open reading frames compared with that for strain 60190.  In conclusion, carriage of an iceA1
      strain does not seem to be a risk factor for peptic ulcer in Japanese subjects.  The critical
      mutations in the iceA1 gene in some isolates from patients with peptic ulcers suggested that
      IceA does not participate in the pathogenesis of peptic ulcer in Japan.  We also found
      deletion hot spots that were associated with direct repeats in iceA1 and that favored a
      small-deletion model of slipped mispairing events during replication.  We showed that iceA1
      sequence variations may be useful tools for analysis of the population genetics of H. pylori.
AU  - Ito Y
AU  - Azuma T
AU  - Ito S
AU  - Suto H
AU  - Miyaji H
AU  - Yamazaki Y
AU  - Kato T
AU  - Kohli Y
AU  - Keida Y
AU  - Kuriyama M
PT  - Journal Article
TA  - J. Clin. Microbiol.
JT  - J. Clin. Microbiol.
SO  - J. Clin. Microbiol. 2000 38: 483-488.

PMID- 9097040
VI  - 3
DP  - 1996
TI  - A 460-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 40.1-50.0 min region on the linkage map.
PG  - 379-392
AB  - The 465,813 base pair sequence corresponding to the 40.1-50.0 min region on the genetic map of
      Escherichia coli K-12 (W3110) was determined. Analysis of the sequence revealed that this
      region contained at least 466 potential open reading frames, of which 187 (40%) were
      previously reported, 105 (23%) were homologous to other known genes, 103 (22%) were identical
      or similar to hypothetical genes registered in databases, and the remaining 71 (15%) did not
      show a significant similarity to any other gene. At the 45.2-46.0 min region, we found a very
      large cluster of about 30 genes, whose functions are involved in the biosynthesis of
      polysaccharides as the components of outer membranes. In addition, we identified a new
      asn-tRNA gene, designated asnW, between the asnT and asnU genes and a new lysogenic phage
      attachment site as the cis-element.
AU  - Itoh T et al
PT  - Journal Article
TA  - DNA Res.
JT  - DNA Res.
SO  - DNA Res. 1996 3: 379-392.

PMID- 17028321
VI  - 174
DP  - 2006
TI  - Roles of PriA protein and double-strand DNA break repair functions in UV-induced restriction alleviation in Escherichia coli.
PG  - 2137-2149
AB  - It has been widely considered that. DNA modification protects the chromosome of bacteria E.
      coli K-12 against their own
      restriction-modification systems. Chromosomal DNA is protected from
      degradation by methylation of target sequences. However, when
      unmethylated target sequences are generated in the host chromosome, the
      endonuclease activity of the EcoKI restriction-modification enzyme is
      inactivated by the ClpXP protease and DNA is protected. This process is
      known as restriction alleviation (RA) and it can be induced by UV
      irradiation (UV-induced RA). It has been proposed that chromosomal
      Unmethylated target sequences, a signal for the cell to protect its own
      DNA, can be generated by homologous recombination during the repair of
      damaged DNA. In this study, we wanted to further investigate the
      genetic requirements for recombination proteins involved in the
      generation Of unmethylated target sequences. For this purpose, we
      monitored the alleviation of EcoKI restriction by measuring the
      survival of unmodified X in UV-irradiated cells. Our genetic analysis
      showed that UV-induced RA is dependent on the excision repair protein
      UvrA, the RecA-loading activity of the RecBCD enzyme, and the primosome
      assembly activity of the PriA helicase and is partially dependent on
      RecFOR proteins. On the basis of our results, we propose that
      Unmethylated target sequences are generated at the D-loop by the strand
      exchange of two hemi-methylated duplex DNAs and subsequent initiation
      of DNA replication.
AU  - Ivancic-Bace I
AU  - Vlasic I
AU  - Cogelja-Cajo G
AU  - Brcic-Kostic K
AU  - Salaj-Smic E
PT  - Journal Article
TA  - Genetics
JT  - Genetics
SO  - Genetics 2006 174: 2137-2149.

PMID- 16403429
VI  - 349
DP  - 2006
TI  - Restriction enzyme cleavage of fluorescently labeled DNA fragments - Analysis of the method and its usage in examination of digestion  completeness.
PG  - 277-284
AB  - Restriction enzymes have proven to be among the most valuable tools in molecular biology.  In
      this work, we demonstrate that the cleavage of fluorescently labeled, PCR-amplified DNA can be
      used as a simple and highly sensitive technique for detection of sequences present in a
      percentage as low as 0.6% in a DNA pool.  Due to the fact that fluorescent labeling of DNA
      fragments enables such sensitive detection and quantification of restriction enzyme cleavage,
      the method was further exploited in monitoring of the enzymatic digestion completeness and in
      determination of factors that influence restriction enzyme effectiveness.  We analyzed the
      activity of six restriction endonucleases; the percentage of uncleaved DNA fragments
      predominantly ranged between 2.0 and 2.5 and the highest value was 8.00%.  We conclude that,
      since the enzymatic digestion completeness may not always be assured, each assay based on
      restriction enzyme cleavage that is intended to be used in investigations of heterogeneity in
      a DNA pool should be constructed so that the presence of cleaved sequences is the indication
      of pool nonuniformity.  When the presence of uncleaved sequences indicates pool heterogeneity,
      the results could be misleading due to possible incompleteness of enzymatic cleavage.
AU  - Ivancic-Jelecki J
AU  - Baricevic M
AU  - Santak M
AU  - Forcic D
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 2006 349: 277-284.

PMID- 9628338
VI  - 379
DP  - 1998
TI  - Mutational analysis of the function of Met137 and Ile197, two amino acids implicated in sequence-specific DNA recognition by the EcoRI endonuclease.
PG  - 459-465
AB  - The gene encoding the EcoRI endonuclease was altered by site-directed mutagenesis to introduce
      multiple substitutions of M137 and I197, two amino acids which were suggested by the revised
      crystal structure to mediate recognition of the cytosines in the 5'-GAATTC-3' target
      sequence.  Eight substitutions of M137 and ten substitutions of I197 were isolated.  With the
      exception of M137W, M137P and M137K, all mutant enzymes retained enough activity to damage
      cellular DNA in the absence of the EcoRI methyltransferase.  All M137 replacements abolished
      the ability of the enzyme to restrict phage growth.  Conservative replacements at I197 (L, V)
      did not impair phage restriction, whereas non-conservative changes reduced (G, W) or abolished
      (D, P) restriction.  In general, substitutions at M137 were more deleterious than
      substitutions at I197.  Double mutants with combinations of M137G/A and I197G/A mutations
      exhibited a phenotype characteristic for the respective single M137 mutant.  Double mutants
      carrying combinations of the M137G/A replacements and substitutions at R200 were viable even
      in the absence of the methyltransferase, suggesting that disrupting contacts to both bases of
      the GC base pair inactivates the enzyme.  None of the replacements resulted in relaxed
      recognition specificity.  In summary, our findings are consistent with a role for M137 but do
      not support such a role for I197 in substrate recognition by the EcoRI endonuclease.
AU  - Ivanenko T
AU  - Heitman J
AU  - Kiss A
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1998 379: 459-465.

PMID- 28360896
VI  - 8
DP  - 2017
TI  - Comparative genomics of four Isosphaeraceae Planctomycetes: a common pool of plasmids and glycoside hydrolase genes shared by Paludisphaera borealis PX4T, Isosphaera pallida IS1BT, Singulisphaera acidiphila DSM 18658T, and strain SH-PL62.
PG  - 412
AB  - 
AU  - Ivanova AA
AU  - Naumoff DG
AU  - Miroshnikov KK
AU  - Liesack W
AU  - Dedysh SN
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2017 8: 412.

PMID- 24855296
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Marinobacter similis A3d10T and Marinobacter salarius R9SW1T.
PG  - e00442-14
AB  - Here, we present the draft genomes of Marinobacter similis A3d10(T), a potential  plastic
      biodegrader, and Marinobacter salarius R9SW1(T), isolated from
      radioactive waters. This genomic information will contribute information on the
      genetic basis of the metabolic pathways for the degradation of both plastic and
      radionuclides.
AU  - Ivanova EP
AU  - Ng HJ
AU  - Webb HK
AU  - Feng G
AU  - Oshima K
AU  - Hattori M
AU  - Ohkuma M
AU  - Sergeev AF
AU  - Mikhailov VV
AU  - Crawford RJ
AU  - Sawabe T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00442-14.

PMID- 21304646
VI  - 1
DP  - 2009
TI  - Complete genome sequence of Sanguibacter keddieii type strain (ST-74).
PG  - 110-118
AB  - Sanguibacter keddieii is the type species of the genus Sanguibacter, the only genus within the
      family of Sanguibacteraceae. Phylogenetically, this family is
      located in the neighborhood of the genus Oerskovia and the family
      Cellulomonadaceae within the actinobacterial suborder Micrococcineae. The strain
      described in this report was isolated from blood of apparently healthy cows. Here
      we describe the features of this organism, together with the complete genome
      sequence, and annotation. This is the first complete genome sequence of a member
      of the family Sanguibacteraceae, and the 4,253,413 bp long single replicon genome
      with its 3735 protein-coding and 70 RNA genes is part of the Genomic Encyclopedia
      of Bacteria and Archaea project.
AU  - Ivanova N et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2009 1: 110-118.

PMID- 21304648
VI  - 1
DP  - 2009
TI  - Complete genome sequence of Leptotrichia buccalis type strain (C-1013-b).
PG  - 126-132
AB  - Leptotrichia buccalis (Robin 1853) Trevisan 1879 is the type species of the genus, and is of
      phylogenetic interest because of its isolated location in the
      sparsely populated and neither taxonomically nor genomically adequately accessed
      family 'Leptotrichiaceae' within the phylum 'Fusobacteria'. Species of
      Leptotrichia are large, fusiform, non-motile, non-sporulating rods, which often
      populate the human oral flora. L. buccalis is anaerobic to aerotolerant, and
      saccharolytic. Here we describe the features of this organism, together with the
      complete genome sequence and annotation. This is the first complete genome
      sequence of the order 'Fusobacteriales' and no more than the second sequence from
      the phylum 'Fusobacteria'. The 2,465,610 bp long single replicon genome with its
      2306 protein-coding and 61 RNA genes is a part of the Genomic Encyclopedia of
      Bacteria and Archaea project.
AU  - Ivanova N et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2009 1: 126-132.

PMID- 21304674
VI  - 2
DP  - 2010
TI  - Complete genome sequence of Gordonia bronchialis type strain (3410).
PG  - 19-28
AB  - Gordonia bronchialis Tsukamura 1971 is the type species of the genus. G. bronchialis is a
      human-pathogenic organism that has been isolated from a large
      variety of human tissues. Here we describe the features of this organism,
      together with the complete genome sequence and annotation. This is the first
      completed genome sequence of the family Gordoniaceae. The 5,290,012 bp long
      genome with its 4,944 protein-coding and 55 RNA genes is part of the Genomic
      Encyclopedia of Bacteria and Archaea project.
AU  - Ivanova N et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 2: 19-28.

PMID- 21304682
VI  - 2
DP  - 2010
TI  - Complete genome sequence of Haliangium ochraceum type strain (SMP-2).
PG  - 96-106
AB  - Haliangium ochraceum Fudou et al. 2002 is the type species of the genus Haliangium in the
      myxococcal family 'Haliangiaceae'. Members of the genus
      Haliangium are the first halophilic myxobacterial taxa described. The cells of
      the species follow a multicellular lifestyle in highly organized biofilms, called
      swarms, they decompose bacterial and yeast cells as most myxobacteria do. The
      fruiting bodies contain particularly small coccoid myxospores. H. ochraceum
      encodes the first actin homologue identified in a bacterial genome. Here we
      describe the features of this organism, together with the complete genome
      sequence, and annotation. This is the first complete genome sequence of a member
      of the myxococcal suborder Nannocystineae, and the 9,446,314 bp long single
      replicon genome with its 6,898 protein-coding and 53 RNA genes is part of the
      Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Ivanova N et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 2: 96-106.

PMID- 21304698
VI  - 2
DP  - 2010
TI  - Complete genome sequence of Geodermatophilus obscurus type strain (G-20).
PG  - 158-167
AB  - Geodermatophilus obscurus Luedemann 1968 is the type species of the genus, which  is the type
      genus of the family Geodermatophilaceae. G. obscurus is of interest
      as it has frequently been isolated from stressful environments such as rock
      varnish in deserts, and as it exhibits interesting phenotypes such as lytic
      capability of yeast cell walls, UV-C resistance, strong production of
      extracellular functional amyloid (FuBA) and manganese oxidation. This is the
      first completed genome sequence of the family Geodermatophilaceae. The 5,322,497
      bp long genome with its 5,161 protein-coding and 58 RNA genes is part of the
      Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Ivanova N et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 2: 158-167.

PMID- 12721630
VI  - 423
DP  - 2003
TI  - Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis.
PG  - 87-91
AB  - Bacillus cereus is an opportunistic pathogen causing food poisoning manifested by diarrhoeal
      or emetic syndromes. It is closely related to the
      animal and human pathogen Bacillus anthracis and the insect pathogen
      Bacillus thuringiensis, the former being used as a biological weapon and
      the latter as a pesticide. B. anthracis and B. thuringiensis are readily
      distinguished from B. cereus by the presence of plasmid-borne specific
      toxins (B. anthracis and B. thuringiensis) and capsule (B. anthracis). But
      phylogenetic studies based on the analysis of chromosomal genes bring
      controversial results, and it is unclear whether B. cereus, B. anthracis
      and B. thuringiensis are varieties of the same species or different
      species. Here we report the sequencing and analysis of the type strain B.
      cereus ATCC 14579. The complete genome sequence of B. cereus ATCC 14579
      together with the gapped genome of B. anthracis A2012 enables us to
      perform comparative analysis, and hence to identify the genes that are
      conserved between B. cereus and B. anthracis, and the genes that are
      unique for each species. We use the former to clarify the phylogeny of the
      cereus group, and the latter to determine plasmid-independent
      species-specific markers.
AU  - Ivanova N et al
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2003 423: 87-91.

PMID- 21475591
VI  - 4
DP  - 2011
TI  - Complete genome sequence of Truepera radiovictrix type strain (RQ-24).
PG  - 91-99
AB  - Truepera radiovictrix Albuquerque et al. 2005 is the type species of the genus Truepera within
      the phylum 'Deinococcus/Thermus'. T. radiovictrix is of special
      interest not only because of its isolated phylogenetic location in the order
      Deinococcales, but also because of its ability to grow under multiple extreme
      conditions in alkaline, moderately saline, and high temperature habitats. Of
      particular interest is the fact that, T. radiovictrix is also remarkably
      resistant to ionizing radiation, a feature it shares with members of the genus
      Deinococcus. This is the first completed genome sequence of a member of the
      family Trueperaceae and the fourth type strain genome sequence from a member of
      the order Deinococcales. The 3,260,398 bp long genome with its 2,994
      protein-coding and 52 RNA genes consists of one circular chromosome and is a part
      of the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Ivanova N et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 4: 91-99.

PMID- 21886858
VI  - 4
DP  - 2011
TI  - Complete genome sequence of the extremely halophilic Halanaerobium praevalens type strain (GSL).
PG  - 312-321
AB  - Halanaerobium praevalens Zeikus et al. 1984 is the type species of the genus Halanaerobium,
      which in turn is the type genus of the family Halanaerobiaceae.
      The species is of interest because it is able to reduce a variety of
      nitro-substituted aromatic compounds at a high rate, and because of its ability
      to degrade organic pollutants. The strain is also of interest because it
      functions as a hydrolytic bacterium, fermenting complex organic matter and
      producing intermediary metabolites for other trophic groups such as
      sulfate-reducing and methanogenic bacteria. It is further reported as being
      involved in carbon removal in the Great Salt Lake, its source of isolation. This
      is the first completed genome sequence of a representative of the genus
      Halanaerobium and the second genome sequence from a type strain of the family
      Halanaerobiaceae. The 2,309,262 bp long genome with its 2,110 protein-coding and
      70 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea
      project.
AU  - Ivanova N et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 4: 312-321.

PMID- 28839039
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Anoxygenic Phototrophic Bacterium Phaeospirillum fulvum MGU-K5.
PG  - e00895-17
AB  - Phaeospirillum fulvum MGU-K5 is an anoxygenic, purple, photoheterotrophic, nonsulfur
      alphaproteobacterium. Unlike most purple nonsulfur bacteria, MGU-K5 is
      unable to grow aerobically under chemoorganotrophic conditions. Here, we present
      the draft genome sequence of P. fulvum to provide insights into its physiology.
AU  - Ivanovsky RN
AU  - Keppen OI
AU  - Lebedeva NN
AU  - Beletsky AV
AU  - Mardanov AV
AU  - Grouzdev DS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00895-17.

PMID- 3320959
VI  - 15
DP  - 1987
TI  - Thymine methyls and DNA-protein interactions.
PG  - 9975-9983
AB  - Evidence is summarized showing that thymine methyls are as important in the
      recognition of specific sequences by proteins as are the more widely recognized
      hydrogen bonding sites of bases in the major groove.  Strongest evidence has
      come from experiments using functional group mutagenesis in which thymines in a
      specific recognition sequence (e.g., promoters, operators and restriction
      sites) are replaced by oligonucleotide synthesis with methyl-free uracil or
      cytosine and 5-methylcytosine.  Such experiments have shown that thymine
      methyls can provide contact points via van der Waals interactions with amino
      acid side chains of specific DNA binding proteins.  Actual contact between a
      thymine methyl and carbons of a glutamine side chain has been observed in a
      cocrystal of the phage 434 repressor and its operator by X-ray analysis.  The
      issue of why thymine occurs in DNA is discussed in light of these findings.
AU  - Ivarie R
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1987 15: 9975-9983.

PMID- 1429443
VI  - 174
DP  - 1992
TI  - Regulation of the BamHI restriction-modification system by a small intergenic open reading frame, bamHIC, in both Escherichia coli and Bacillus subtilis.
PG  - 7194-7201
AB  - BamHI from Bacillus amyloliquefaciens H, is a type II restriction-modification system
      recognizing and cleaving the sequence G^GATCC. The BamHI restriction-modification system
      contains divergently transcribed endonuclease and methylase genes along with a small open
      reading frame oriented in the direction of the endonuclease gene. The small open reading frame
      has been designated bamHIC (for BamHI controlling element). It acts as both a positive
      activator of endonuclease expression and a negative repressor of methylase expression of BamHI
      clones in Escherichia coli. Methylase activity increased 15-fold and endonuclease activity
      decreased 100-fold when bamHIC was inactivated. The normal levels of activity for both
      methylase and endonuclease were restored by supplying bamHIC in trans. The BamHI
      restriction-modification system was transferred into Bacillus subtilis, where bamHIC also
      regulated endonuclease expression when present on multicopy plasmid vectors or integrated into
      the chromosome. In B. subtilis, disruption of bamHIC caused at least a 1,000-fold decrease in
      endonuclease activity; activity was partially restored by supplying bamHIC in trans.
AU  - Ives CL
AU  - Nathan PD
AU  - Brooks JE
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1992 174: 7194-7201.

PMID- 7592403
VI  - 177
DP  - 1995
TI  - The regulatory C proteins from different restriction-modification systems can cross-complement.
PG  - 6313-6315
AB  - The BamHI restriction-modification system contains a third gene, bamHIC, which positively
      regulates bamHIR.  Similar small genes from other systems were tested in vivo for their
      ability to cross-complement.  C.BamHI protein was identified, purified, and used to raise
      polyclonal antibodies.  Attempts to detect other C proteins in cell extracts by
      cross-reactivity with C.BamHI antibodies proved unsuccessful.
AU  - Ives CL
AU  - Sohail A
AU  - Brooks JE
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1995 177: 6313-6315.

PMID- 10481103
VI  - 179
DP  - 1999
TI  - Type II restriction endonucleases from Helicobacter pylori include an enzyme with a novel recognition sequence.
PG  - 175-180
AB  - Type II restriction endonuclease activities of Helicobacter pylori strain Roberts and of the
      type strain H. pylori NCTC 11637 were detected and analysed by conventional techniques. The
      endonucleases were partially purified, their optima for activity and their recognition and
      cleavage sites were determined. H. pylori (Roberts) contained at least two enzymes: HpyBI was
      an isoschizomer of RsaI (GT/AC) and HpyBII was of a novel specificity (GTN/NAC). H. pylori
      NCTC 11637 was found to contain an isoschizomer of EcoRV (HpyCI: GAT/ATC) and at least one
      other enzyme which was too unstable to characterise.
AU  - Ivic A
AU  - Jakeman KJ
AU  - Penn CW
AU  - Brown NL
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1999 179: 175-180.

PMID- 25502680
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Propane- and Butane-Oxidizing Actinobacterium Rhodococcus ruber IEGM 231.
PG  - e01297-14
AB  - We report a draft genome sequence of Rhodococcus ruber IEGM 231, isolated from a  water spring
      near an oil-extracting enterprise (Perm region, Russian Federation).
      This sequence provides important insights into the genetic mechanisms of propane
      and n-butane metabolism, organic sulfide and beta-sitosterol biotransformation,
      glycolipid biosurfactant production, and heavy metal resistance in
      actinobacteria.
AU  - Ivshina IB
AU  - Kuyukina MS
AU  - Krivoruchko AV
AU  - Barbe V
AU  - Fischer C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01297-14.

PMID- 1454552
VI  - 20
DP  - 1992
TI  - A restriction enzyme, BpuI is an isoschizomer of BanII.
PG  - 5850
AB  - We previously identified a type II restriction enzyme in extracts of Bacillus pumilus AHU1387
      and designated it BpuI (1,2), which recognizes the sequence GRGCYC and therefore may be an
      isoschizomer of HgiJII or BanII (3). In the present study, we examined the cleavage site of
      BpuI as well as the effect of methylation on the cleavage reaction in order to show that BpuI
      is an isoschizomer of BanII.
AU  - Iwabuchi M
AU  - Tajima S
AU  - Inoue T
AU  - Shibata T
AU  - Ando T
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 5850.

PMID- 14988487
VI  - 45
DP  - 2004
TI  - Improved genetic transformation of the thermophilic cyanobacterium, Thermosynechococcus elongatus BP-1.
PG  - 171-175
AB  - We improved genetic transformation of the thermophilic cyanobacterium, Thermosynechococcus
      elongatus BP-1, by combining electroporation with a
      top agar method. Transformation was also improved when a disruptant of a
      putative type I restriction endonuclease (tll2230) was used as recipient
      cells. In particular, some constructs, with which wild type has never been
      transformed, were successfully integrated into the tll2230-disruptant.
      Single-crossover recombination was detected more frequently than the
      double-crossover recombination. In accordance with the presence of all the
      homologs of pil genes in Synechocystis sp. PCC 6803, we found that T.
      elongatus is naturally transformable with exogenous DNA.
AU  - Iwai M
AU  - Katoh H
AU  - Katayama M
AU  - Ikeuchi M
PT  - Journal Article
TA  - Plant Cell Physiol.
JT  - Plant Cell Physiol.
SO  - Plant Cell Physiol. 2004 45: 171-175.

PMID- 21045313
VI  - 66
DP  - 2010
TI  - Crystallization and X-ray diffraction studies of DNA-free and DNA-bound forms of EcoO109I DNA methyltransferase.
PG  - 1528-1530
AB  - EcoO109I DNA methyltransferase (M.EcoO109I) is a type II modification enzyme from the EcoO109I
      restriction-modification system identified in
      Escherichia coli strain H709c. M.EcoO109I recognizes double-stranded
      RGGNCCY (where R = A or G, Y = T or C and N is any base) and transfers
      a methyl group to the C5 of the inner cytosines from
      S-adenosylmethionine. To reveal the mechanism of substrate recognition
      by M.EcoO109I, DNA-free and DNA-bound forms of M.EcoO109I were
      successfully crystallized. Crystals of the DNA-free and DNA-bound forms
      belonged to space groups P4(2)2(1)2, with unit-cell parameters a = b =
      120.5, c = 79.8 A, and P2(1), with unit-cell parameters a = 55.8, b =
      77.4, c = 117.4 A, beta = 93.5 degrees, respectively.
AU  - Iwamoto M
AU  - Hishiki A
AU  - Shimada T
AU  - Imasaki T
AU  - Tsuda J
AU  - Kita K
AU  - Shimizu T
AU  - Sato M
AU  - Hashimoto H
PT  - Journal Article
TA  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
JT  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
SO  - Acta Crystallogr. F Struct. Biol. Cryst. Commun. 2010 66: 1528-1530.

PMID- 1848653
VI  - 39
DP  - 1991
TI  - Selective inhibition of sequence-specific protein-DNA interactions by incorporation of 6-thioguanine:  Cleavage by restriction endonucleases.
PG  - 299-306
AB  - Incorporation of the antileukemic agent 6-thioguanine (TG) into cellular DNA
      has been demonstrated to be a major determinant of its cytotoxicity.  We have
      previously shown that complete replacement of G by TG within one DNA strand of
      the SV40 origin of replication can completely inhibit sequence-specific binding
      of the viral replication protein T antigen.  The aim of the present study was
      to determine the effect of more selective TG substitutions on DNA-protein
      interactions, by utilizing the simpler base recognition sequence motifs of
      restriction endonucleases.  In the first part of our study, we replaced G with
      TG in one or two of four possible sites within the duplex hexameric recognition
      sequence of BamHI (5'-G^GATCC-3'), by enzymatic extension of primed
      oligonucleotides.  This extension was stalled, but not completely inhibited, at
      locations where insertion of consecutive TG moieties was required.  Both
      strands of molecules containing a single substitution were cleaved by BamHI at
      reduced rates, with the substituted strand inhibited to a greater degree.  In
      molecules containing two substitutions, neither strand was cut by BamHI.  In
      contrast, we found that scission of these same mono- and disubstituted
      substrates by the less stringent isoschizomer MboI (5'-N^GATCN-3') was
      inhibited only slightly.  In the second part of our study, we investigated the
      effect of analog subsitution on scission by the type II-S enzymes AlwI and
      FokI, in order to separately determine the effects of restriction site
      modification versus scission site modification.  We found that the reactivity
      of these enzymes was completely abolished by TG substitution within the
      recognition site, whereas substitution at the scission site had no effect.  Our
      results demonstrate that infrequent TG substitutions within symmetric DNA
      sequences can inhibit sequence-specific interactions in an asymmetric fashion.
      In addition, although previous reports have shown that TG forms a relatively
      weak base pair with cytosine, it appears that the inhibition of restriction
      endonuclease-mediated cleavage resulting from TG incorporation is a function of
      the sequence requirements of the protein and not a general consequence of
      distrupted base-pairing at the recognition locus.  These data support the idea
      that the cytotoxic consequences of TG incorporation may be due to inhibition of
      sequence-specific protein-DNA interactions.
AU  - Iwaniec LM
AU  - Kroll JJ
AU  - Roethel WM
AU  - Maybaum J
PT  - Journal Article
TA  - Mol. Pharmacol.
JT  - Mol. Pharmacol.
SO  - Mol. Pharmacol. 1991 39: 299-306.

PMID- 27811101
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Klebsiella oxytoca Strain JKo3.
PG  - e01221-16
AB  - Klebsiella oxytoca can be either pathogenic or beneficial, depending on conditions. These
      opposing characteristics have not been fully elucidated. Here,
      we report the complete sequence of the K. oxytoca JKo3 genome, consisting of a
      single circular chromosome of 5,943,791 bp and four plasmids.
AU  - Iwase T
AU  - Ogura Y
AU  - Hayashi T
AU  - Mizunoe Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01221-16.

PMID- 27081127
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Klebsiella pneumoniae YH43.
PG  - e00242-16
AB  - We report here the complete genome sequence ofKlebsiella pneumoniaestrain YH43, isolated from
      sweet potato. The genome consists of a single circular chromosome
      of 5,520,319 bp in length. It carries 8 copies of rRNA operons, 86 tRNA genes,
      5,154 protein-coding genes, and thenifgene cluster for nitrogen fixation.
AU  - Iwase T
AU  - Ogura Y
AU  - Hayashi T
AU  - Mizunoe Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00242-16.

PMID- 18346280
VI  - 3
DP  - 2008
TI  - MutL homologs in restriction-modification systems and the origin of eukaryotic MORC ATPases.
PG  - 8
AB  - The provenance and biochemical roles of eukaryotic MORC proteins have remained poorly
      understood since the discovery of their prototype
      MORCI, which is required for meiotic nuclear division in animals. The
      MORC family contains a combination of a gyrase, histidine kinase, and
      MutL (GHKL) and S5 domains that together constitute a catalytically
      active ATPase module. We identify the prokaryotic MORCs and establish
      that the MORC family belongs to a larger radiation of several families
      of GHKL proteins (paraMORCs) in prokaryotes. Using contextual
      information from conserved gene neighborhoods we show that these
      proteins primarily function in restriction-modification systems, in
      conjunction with diverse superfamily II DNA helicases and
      endonucleases. The common ancestor of these GHKL proteins, MutL and
      topoisomerase ATPase modules appears to have catalyzed structural
      reorganization of protein complexes and concomitant DNA-superstructure
      manipulations along with fused or standalone nuclease domains.
      Furthermore, contextual associations of the prokaryotic MORCs and their
      relatives suggest that their eukaryotic counterparts are likely to
      carry out chromatin remodeling by DNA superstructure manipulation in
      response to epigenetic signals such as histone and DNA methylation.
      Reviewers: This article was reviewed by Arcady Mushegian and Gaspar
      Jekely.
AU  - Iyer LM
AU  - Abhiman S
AU  - Aravind L
PT  - Journal Article
TA  - Biol. Direct
JT  - Biol. Direct
SO  - Biol. Direct 2008 3: 8.

PMID- 21507349
VI  - 101
DP  - 2011
TI  - Natural History of Eukaryotic DNA Methylation Systems.
PG  - 25-104
AB  - Methylation of cytosines and adenines in DNA is a widespread epigenetic mark in both
      prokaryotes and eukaryotes. In eukaryotes, it has a profound influence on chromatin structure
      and dynamics. Recent advances in genomics and biochemistry have considerably elucidated the
      functions and provenance of these DNA modifications. DNA methylases appear to have emerged
      first in bacterial restriction-modification (R-M) systems from ancient RNA-modifying enzymes,
      in transitions that involved acquisition of novel catalytic residues and DNA-recognition
      features. DNA adenine methylases appear to have been acquired by ciliates, heterolobosean
      amoeboflagellates, and certain chlorophyte algae. Six distinct clades of cytosine methylases,
      including the DNMT1, DNMT2, and DNMT3 clades, were acquired by eukaryotes through independent
      lateral transfer of their precursors from bacteria or bacteriophages. In addition to these,
      multiple adenine and cytosine methylases were acquired by several families of eukaryotic
      transposons. In eukaryotes, the DNA-methylase module was often combined with distinct modified
      and unmodified peptide recognition domains and other modules mediating specialized
      interactions, for example, the RFD module of DNMT1 which contains a permuted Sm domain linked
      to a helix-turn-helix domain. In eukaryotes, the evolution of DNA methylases appears to have
      proceeded in parallel to the elaboration of histone-modifying enzymes and the RNAi system,
      with functions related to counter-viral and counter-transposon defense, and regulation of DNA
      repair and differential gene expression being their primary ancestral functions. Diverse DNA
      demethylation systems that utilize base-excision repair via DNA glycosylases and cytosine
      deaminases appear to have emerged in multiple eukaryotic lineages. Comparative genomics
      suggests that the link between cytosine methylation and DNA glycosylases probably emerged
      first in a novel R M system in bacteria. Recent studies suggest that the 5mC is not a terminal
      DNA modification, with enzymes of the Tet/JBP family of 2-oxoglutarate- and iron-dependent
      dioxygenases further hydroxylating it to form 5-hydroxy-methylcytosine (5hmC). These enzymes
      emerged first in bacteriophages and appear to have been transferred to eukaryotes on one or
      more occasions. Eukaryotes appear to have recruited three major types of DNA-binding domains
      (SRA/SAD, TAM/MBD, and CXXC) in discriminating DNA with methylated or unmethylated cytosines.
      Analysis of the domain architectures of these domains and the DNA methylases suggests that
      early in eukaryotic evolution they developed a close functional link with SET-domain
      methylases and Jumonji-related demethylases that operate on peptides in chromatin proteins. In
      several eukaryotes, other functional connections were elaborated in the form of various
      combinations between domains related to DNA methylation and those involved in ATP-dependent
      chromatin remodeling and RNAi. In certain eukaryotes, such as mammals and angiosperms, novel
      dependencies on the DNA methylation system emerged, which resulted in it affecting unexpected
      aspects of the biology of these organisms such as parent offspring interactions. In genomic
      terms, this was reflected in the emergence of new proteins related to methylation, such as
      Stella. The well-developed methylation systems of certain heteroloboseans, stramenopiles,
      chlorophytes, and haptophyte indicate that these might be new model systems to explore the
      relevance of DNA modifications in eukaryotes.
AU  - Iyer LM
AU  - Abhiman S
AU  - Aravind L
PT  - Journal Article
TA  - Prog. Mol. Biol. Transl. Sci.
JT  - Prog. Mol. Biol. Transl. Sci.
SO  - Prog. Mol. Biol. Transl. Sci. 2011 101: 25-104.

PMID- 19411852
VI  - 8
DP  - 2009
TI  - Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids.
PG  - 1698-1710
AB  - Modified bases in nucleic acids present a layer of information that directs biological
      function over and beyond the coding capacity of the
      conventional bases. While a large number of modified bases have been
      identified, many of the enzymes generating them still remain to be
      discovered. Recently, members of the 2-oxoglutarate- and
      iron(II)-dependent dioxygenase super-family, which modify diverse
      substrates from small molecules to biopolymers, were predicted and
      subsequently confirmed to catalyze oxidative modification of bases in
      nucleic acids. Of these, two distinct families, namely the AlkB and the
      kinetoplastid base J binding proteins (JBP) catalyze in situ hydroxylation
      of bases in nucleic acids. Using sensitive computational analysis of
      sequences, structures and contextual information from genomic structure
      and protein domain architectures, we report five distinct families of
      2-oxoglutarate- and iron(II)-dependent dioxygenase that we predict to be
      involved in nucleic acid modifications. Among the DNA-modifying families,
      we show that the dioxygenase domains of the kinetoplastid base J-binding
      proteins belong to a larger family that includes the Tet proteins,
      prototyped by the human oncogene Tet1, and proteins from basidiomycete
      fungi, chlorophyte algae, heterolobosean amoeboflagellates and
      bacteriophages. We present evidence that some of these proteins are likely
      to be involved in oxidative modification of the 5-methyl group of cytosine
      leading to the formation of 5-hydroxymethylcytosine. The Tet/JBP homologs
      from basidiomycete fungi such as Laccaria and Coprinopsis show large
      lineage-specific expansions and a tight linkage with genes encoding a
      novel and distinct family of predicted transposases, and a member of the
      Maelstrom-like HMG family. We propose that these fungal members are part
      of a mobile transposon. To the best of our knowledge, this is the first
      report of a eukaryotic transposable element that encodes its own
      DNA-modification enzyme with a potential regulatory role. Through a wider
      analysis of other poorly characterized DNA-modifying enzymes we also show
      that the phage Mu Mom-like proteins, which catalyze the
      N6-carbamoylmethylation of adenines, are also linked to diverse families
      of bacterial transposases, suggesting that DNA modification by
      transposable elements might have a more general presence than previously
      appreciated. Among the other families of 2-oxoglutarate- and
      iron(II)-dependent dioxygenases identified in this study, one which is
      found in algae, is predicted to mainly comprise of RNA-modifying enzymes
      and shows a striking diversity in protein domain architectures suggesting
      the presence of RNA modifications with possibly unique adaptive roles. The
      results presented here are likely to provide the means for future
      investigation of unexpected epigenetic modifications, such as
      hydroxymethyl cytosine, that could profoundly impact our understanding of
      gene regulation and processes such as DNA demethylation.
AU  - Iyer LM
AU  - Tahiliani M
AU  - Rao A
AU  - Aravind L
PT  - Journal Article
TA  - Cell Cycle
JT  - Cell Cycle
SO  - Cell Cycle 2009 8: 1698-1710.

PMID- 23814188
VI  - 41
DP  - 2013
TI  - Computational identification of novel biochemical systems involved in oxidation,  glycosylation and other complex modifications of bases in DNA.
PG  - 7635-7655
AB  - Discovery of the TET/JBP family of dioxygenases that modify bases in DNA has sparked
      considerable interest in novel DNA base modifications and their
      biological roles. Using sensitive sequence and structure analyses combined with
      contextual information from comparative genomics, we computationally characterize
      over 12 novel biochemical systems for DNA modifications. We predict previously
      unidentified enzymes, such as the kinetoplastid J-base generating
      glycosyltransferase (and its homolog GREB1), the catalytic specificity of
      bacteriophage TET/JBP proteins and their role in complex DNA base modifications.
      We also predict the enzymes involved in synthesis of hypermodified bases such as
      alpha-glutamylthymine and alpha-putrescinylthymine that have remained enigmatic
      for several decades. Moreover, the current analysis suggests that bacteriophages
      and certain nucleo-cytoplasmic large DNA viruses contain an unexpectedly diverse
      range of DNA modification systems, in addition to those using previously
      characterized enzymes such as Dam, Dcm, TET/JBP, pyrimidine hydroxymethylases,
      Mom and glycosyltransferases. These include enzymes generating modified bases
      such as deazaguanines related to queuine and archaeosine, pyrimidines comparable
      with lysidine, those derived using modified S-adenosyl methionine derivatives and
      those using TET/JBP-generated hydroxymethyl pyrimidines as biosynthetic starting
      points. We present evidence that some of these modification systems are also
      widely dispersed across prokaryotes and certain eukaryotes such as
      basidiomycetes, chlorophyte and stramenopile alga, where they could serve as
      novel epigenetic marks for regulation or discrimination of self from non-self
      DNA. Our study extends the role of the PUA-like fold domains in recognition of
      modified nucleic acids and predicts versions of the ASCH and EVE domains to be
      novel 'readers' of modified bases in DNA. These results open opportunities for
      the investigation of the biology of these systems and their use in biotechnology.
AU  - Iyer LM
AU  - Zhang D
AU  - Maxwell BA
AU  - Aravind L
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2013 41: 7635-7655.

PMID- 20543071
VI  - 192
DP  - 2010
TI  - Genome Sequence of a Cellulose Producing Bacterium, Gluconacetobacter hansenii ATCC 23769.
PG  - 4256-4257
AB  - The Gram-negative bacterium Gluconacetobacter hansenii is considered a model organism for
      studying cellulose synthesis. We have determined the
      genome sequence of the strain ATCC 23769.
AU  - Iyer PR
AU  - Geib SM
AU  - Catchmark J
AU  - Kao TH
AU  - Tien M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 4256-4257.

PMID- 27445376
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Rhizobium sp. GHKF11, Isolated from Farmland Soil in Pecan Grove, Texas.
PG  - e00682-16
AB  - Rhizobium sp. GHKF11 is an organophosphate-degrading bacterial strain that was isolated from
      farmland soil in Pecan Grove, Texas, USA. In addition to a capacity
      for pesticide degradation, GHKF11 shares conserved traits with other Rhizobium
      spp., including heavy metal resistance and transport genes that may have
      significant agricultural biotechnology applications.
AU  - Iyer R
AU  - Damania A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00682-16.

PMID- 27445375
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Exiguobacterium sp. KKBO11, Isolated Downstream of a Wastewater Treatment Plant in Houston, Texas.
PG  - e00681-16
AB  - Exiguobacterium sp. KKBO11, isolated near a wastewater treatment plant in Houston, Texas, USA,
      possesses a large number of genes involved in stress
      response and transport critical to survival in adverse environmental conditions.
      An unusually high copy number of RNA genes also possibly contributes to this
      microorganism's versatility by promoting nutrient uptake.
AU  - Iyer R
AU  - Damania A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00681-16.

PMID- 27417844
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Pseudomonas putida CBF10-2, a Soil Isolate with Bioremediation Potential in Agricultural and Industrial Environmental Settings.
PG  - e00670-16
AB  - Pseudomonas putida CBF10-2 is a microorganism isolated from farmland soil in Fairchild, TX,
      found to degrade high-impact xenobiotics, including
      organophosphate insecticides, petroleum hydrocarbons, and both monocyclic and
      polycyclic aromatics. The versatility of CBF10-2 makes it useful for multipurpose
      bioremediation of contaminated sites in agricultural and industrial environments.
AU  - Iyer R
AU  - Damania A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00670-16.

PMID- 27081147
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Pseudomonas stutzeri ODKF13, Isolated from Farmland Soil in Alvin, Texas.
PG  - e00293-16
AB  - Pseudomonas stutzeriODKF13 is a bacterial microorganism isolated from farmland soil in Alvin,
      Texas. This strain is notable for its naphthalene degradation and
      nitrogen fixation pathways and for its characterization as an organophosphate
      degrader of phosphotriester and phosphorothioate insecticides.
AU  - Iyer R
AU  - Damania A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00293-16.

PMID- 27081144
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Alkane-Degrading Acinetobacter venetianus JKSF02, Isolated from Contaminated Sediment of the San Jacinto River in Houston, Texas.
PG  - e00286-16
AB  - Acinetobacter venetianusJKSF02 was isolated from contaminated sediment in eastern Houston,
      Texas along the San Jacinto River. This microorganism specializes in
      n-alkane degradation and is well suited for bioremediation of the petroleum
      hydrocarbon deposited throughout the region by shipping and industrial activity
      from the Houston Ship Channel.
AU  - Iyer R
AU  - Damania A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00286-16.

PMID- 27081123
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the Broad-Spectrum Xenobiotic Degrader Achromobacter xylosoxidans ADAF13.
PG  - e00203-16
AB  - Achromobacter xylosoxidansADAF13, isolated from farmland soil, possesses a large  number of
      putative degradation genes and pathways that break down a wide variety
      of aromatic hydrocarbons, pesticides, endocrine disruptors, and other high-impact
      xenobiotics. These properties make this strain an excellent candidate for further
      development as a broad-spectrum bioremediation agent.
AU  - Iyer R
AU  - Damania A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00203-16.

PMID- 27174285
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Stenotrophomonas maltophilia CBF10-1, an Organophosphate-Degrading Bacterium Isolated from Ranch Soil in Fairchilds,  Texas.
PG  - e00378-16
AB  - Stenotrophomonas maltophilia CBF10-1 was isolated from a ranch in Fairchilds, Texas, USA. Its
      genome reveals a highly adaptable microorganism with a large
      complement of antibiotic and heavy metal resistance genes, efflux pumps,
      multidrug transporters, and xenobiotic degradation pathways.
AU  - Iyer R
AU  - Damania A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00378-16.

PMID- 27103720
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Organophosphate-Degrading Ochrobactrum anthropi FRAF13.
PG  - e00295-16
AB  - ITALIC! Ochrobactrum anthropiFRAF13 was isolated from farmland soil in Jersey Village, Texas.
      FRAF13 is a bacterial microorganism with broad antibiotic
      resistance that possesses a number of metal-dependent beta-lactam enzymes with
      secondary phosphotriesterase activity that can initiate the breakdown of
      organophosphate compounds.
AU  - Iyer R
AU  - Damania A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00295-16.

PMID- 27635050
VI  - 8
DP  - 2016
TI  - Comparison of intracellular 'Ca. Endomicrobium trichonymphae' genomovars illuminates the requirement and decay of defense systems against foreign DNA.
PG  - 3099-3107
AB  - "Candidatus Endomicrobium trichonymphae" (Bacteria; Elusimicrobia) is an obligate
      intracellular symbiont of the cellulolytic protist genus Trichonympha in the
      termite gut. A previous genome analysis of "Ca Endomicrobium trichonymphae"
      phylotype Rs-D17 (genomovar Ri2008), obtained from a Trichonympha agilis cell in
      the gut of the termite Reticulitermes speratus, revealed that its genome is small
      (1.1 Mb) and contains many pseudogenes; it is in the course of reductive genome
      evolution. Here we report the complete genome sequence of another Rs-D17
      genomovar, Ti2015, obtained from a different T. agilis cell present in an R.
      speratus gut. These two genomovars share most intact protein-coding genes and
      pseudogenes, showing 98.6% chromosome sequence similarity. However,
      characteristic differences were found in their defense systems, which comprised
      restriction-modification and CRISPR/Cas systems. The repertoire of intact
      restriction-modification systems differed between the genomovars, and two of the
      three CRISPR/Cas loci in genomovar Ri2008 are pseudogenized or missing in
      genomovar Ti2015. These results suggest relaxed selection pressure for
      maintaining these defense systems. Nevertheless, the remaining CRISPR/Cas system
      in each genomovar appears to be active; none of the "spacer" sequences (112 in
      Ri2008 and 128 in Ti2015) were shared whereas the "repeat" sequences were
      identical. Furthermore, we obtained draft genomes of three additional
      endosymbiotic Endomicrobium phylotypes from different host protist species, and
      discovered multiple, intact CRISPR/Cas systems in each genome. Collectively,
      unlike bacteriome endosymbionts in insects, the Endomicrobium endosymbionts of
      termite-gut protists appear to require defense against foreign DNA, although the
      required level of defense has likely been reduced during their intracellular
      lives.
AU  - Izawa K
AU  - Kuwahara H
AU  - Kihara K
AU  - Yuki M
AU  - Lo N
AU  - Ito T
AU  - Ohkuma M
AU  - Hongoh Y
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2016 8: 3099-3107.

PMID- 22675603
VI  - 6
DP  - 2012
TI  - Complete Genome Sequence of Clostridium clariflavum DSM 19732.
PG  - 104-115
AB  - Clostridium clariflavum is a Cluster III Clostridium within the family Clostridiaceae isolated
      from thermophilic anaerobic sludge (Shiratori et al,
      2009). This species is of interest because of its similarity to the model
      cellulolytic organism Clostridium thermocellum and for the ability of
      environmental isolates to break down cellulose and hemicellulose. Here we
      describe features of the 4,897,678 bp long genome and its annotation, consisting
      of 4,131 protein-coding and 98 RNA genes, for the type strain DSM 19732.
AU  - Izquierdo JA et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 6: 104-115.

PMID- 2539102
VI  - 258
DP  - 1989
TI  - Star activity and complete loss of specificity of CeqI endonuclease.
PG  - 301-303
AB  - Restriction endonuclease CeqI, an isoschizomer of EcoRV, exhibits star activity, a relaxation
      of specificity in the presence of Mn2+, dimethyl sulphoxide or glycerol. The enzyme cleaves a
      set of sequences that differ from the canonical GATATC by only one nucleotide in positions
      2,3,4 or 5. Two of these sequences are not cleaved if modified by dam methylase. A further
      loss of specificity can be observed in circumstances less favourable for the enzyme, namely
      low-ionic-strength buffers of pH values below 6.0 or above 9.4. This activity seems to cleave
      DNA at any sequence, producing a smear of well-defined bands. Partial renaturation of the
      denatured enzyme gives rise to a similar non-specific nuclease activity.
AU  - Izsvak Z
AU  - Duda E
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 1989 258: 301-303.

PMID- 1285828
VI  - 47
DP  - 1992
TI  - Purification and characterization of CeqI restriction endonuclease.
PG  - 830-834
AB  - CeqI, a type II restriction endonuclease, an isoschizomer of EcoRV was purified to apparent
      homogeneity by a combination of salt precipitation, ion exchange, dye affinity and hydrophobic
      interaction chromatographies. The crude enzyme was present in the form of large aggregates
      that could be pelleted by high speed centrifugation. The enzyme was not associated with
      cellular membranes, though non-ionic detergents lowered the apparent size of the aggregates.
      The purified enzymes also showed a tendency to form large molecular mass (66-600 kDa)
      complexes under physiological conditions, in the absence of cleavable DNA. The enzyme formed
      smaller complexes in the presence of DNA and non-ionic detergents and dissociated into
      subunits (and undergoes reversible loss of activity) in the presence of high concentrations of
      salts. According to SDS gel electrophoresis and sedimentation analysis the molecular mass of
      the monomer is 32+-2 kDa. The enzyme has a rather broad pH optimum, extending into the
      alkaline range and lost specifcity and activity in buffers below pH6.
AU  - Izsvak Z
AU  - Jobbagy Z
AU  - Duda E
PT  - Journal Article
TA  - Z. Naturforsch. C
JT  - Z. Naturforsch. C
SO  - Z. Naturforsch. C 1992 47: 830-834.

PMID- 9304804
VI  - 29
DP  - 1997
TI  - Cloning and characterization of the genes of the CeqI restriction-modification system.
PG  - 895-900
AB  - Two genes from Corynebacterium equii, a Gram-positive producing the CeqI
      restriction-modification enzymes were cloned and sequenced.  In vivo restriction experiments,
      DNA and amino acid sequence data suggest that the two genes code for the endonuclease and the
      methyltransferase enzymes.  However, when the two genes are expressed in E. coli, practically
      no enzyme activity can be detected in the supernatants of sonicated cells.  Based on the DNA
      sequence data CeqI restriction enodnuclease (an EcoRV isoschizomer) consists of 270 amino acid
      residues with a predicted molecular mass of 31.6 kDa, in good agreement with the previously
      measured 32+/- 2kDa.  The methyltansferase is 517 residues long (approx. 60 kDa).  The two
      genes are in opposite orientation and overlap by 37 base pairs on the chromosome.  The deduced
      amino acid sequence of the putative endonuclease gene revealed long stretches of hydrophobic
      amino acids, that may form the structural basis of the unusual aggregation properties of the
      restriction endonuclease.  The amino acid sequence of the methylase shows homologies with
      other type II methyltransferases.
AU  - Izsvak Z
AU  - Jobbagy Z
AU  - Takacs I
AU  - Duda E
PT  - Journal Article
TA  - Int. J. Biochem. Cell Biol.
JT  - Int. J. Biochem. Cell Biol.
SO  - Int. J. Biochem. Cell Biol. 1997 29: 895-900.

PMID- 21098248
VI  - 55
DP  - 2011
TI  - Whole-genome analysis of Salmonella enterica serovar Typhimurium T000240 reveals the acquisition of a genomic island involved in multidrug resistance via IS1 derivatives on the chromosome.
PG  - 623-630
AB  - Salmonella enterica serovar Typhimurium is frequently associated with
      life-threatening systemic infections, and the recent global emergence of
      multidrug resistance in S. enterica isolates from agricultural and clinical
      settings has raised concerns. In this study, we determined the whole-genome
      sequence of fluoroquinolone-resistant S. enterica serovar Typhimurium T000240
      strain (DT12) isolated from human gastroenteritis in 2000. Comparative genome
      analysis revealed that T000240 displays high sequence similarity to strain LT2,
      which was originally isolated in 1940, indicating that progeny of LT2 might be
      reemerging. T000240 possesses a unique 82-kb genomic island, designated as
      GI-DT12, which is composed of multidrug resistance determinants, including a
      Tn2670-like composite transposon (class 1 integron [intI1, bla(oxa-30), aadA1,
      qacEDelta1, and sul1], mercury resistance proteins, and chloramphenicol
      acetyltransferase), a Tn10-like tetracycline resistance protein (tetA), the
      aerobactin iron-acquisition siderophore system (lutA and lucABC), and an iron
      transporter (sitABCD). Since GI-DT12 is flanked by IS1 derivatives, IS1-mediated
      recombination likely played a role in the acquisition of this genomic island
      through horizontal gene transfer. The aminoglycoside-(3)-N-acetyltransferase
      (aac(3)) gene and a class 1 integron harboring the dfrA1 gene cassette
      responsible for gentamicin and trimethoprim resistance, respectively, were
      identified on plasmid pSTMDT12_L and appeared to have been acquired through
      homologous recombination with IS26. This study represents the first
      characterization of the unique genomic island GI-DT12 that appears to be
      associated with possible IS1-mediated recombination in S. enterica serovar
      Typhimurium. It is expected that future whole-genome studies will aid in the
      characterization of the horizontal gene transfer events for the emerging S.
      enterica serovar Typhimurium strains.
AU  - Izumiya H
AU  - Sekizuka T
AU  - Nakaya H
AU  - Taguchi M
AU  - Oguchi A
AU  - Ichikawa N
AU  - Nishiko R
AU  - Yamazaki S
AU  - Fujita N
AU  - Watanabe H
AU  - Ohnishi M
AU  - Kuroda M
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2011 55: 623-630.

PMID- 10978178
VI  - 39
DP  - 2000
TI  - Sequence-specific protection of duplex DNA against restriction and methylation enzymes by pseudocomplementary PNAs.
PG  - 10908-10913
AB  - A new generation of PNAs, so-called pseudocomplementary PNAs (pcPNAs) which are able to target
      the designated sites on duplex DNA with mixed
      sequence of purines and pyrimidines via double-duplex invasion mode,
      has recently been introduced. It has been demonstrated that appropriate
      pairs of decameric pcPNAs block an access of RNA polymerase to the
      corresponding promoter. Here, we show that this type of PNAs protects
      selected DNA sites containing all four nucleobases from the action of
      restriction enzymes and DNA methyltransferases. We have found that
      pcPNAs as short as octamers form stable and sequence-specific complexes
      with duplex DNA in a very salt-dependent manner. In accord with a
      strand-invasion mode of complex formation, the pcPNA binding proceeds
      much faster with supercoiled than with linear plasmids. The
      double-duplex invasion complexes selectively shield specific DNA sites
      from BclI restriction endonuclease and dam methylase. The
      pcPNA-assisted protection against enzymatic methylation is more
      efficient when the PNA-binding site embodies the methylase-recognition
      site rather than overlaps it. We conclude that pcPNAs may provide the
      robust tools allowing to sequence-specifically manipulate DNA duplexes
      in a virtually sequence-unrestricted manner.
AU  - Izvolsky KI
AU  - Demidov VV
AU  - Nielsen PE
AU  - Frank-Kamenetskii MD
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2000 39: 10908-10913.

PMID- 6086961
VI  - 51
DP  - 1984
TI  - Genetic and physiological studies of an Escherichia coli locus that restricts polynucleotide kinase- and RNA ligase-deficient mutants of bacteriophage T4.
PG  - 522-529
AB  - The RNA ligase and polynucleotide kinase of bacteriophage T4 are nonessential
      enzymes in most laboratory Escherichia coli strains.  However, T4 mutants which
      do not induce the enzymes are severely restricted in E. coli CTr5X, a strain
      derived from a clinical E. coli isolate.  We have mapped the restricting locus
      in E. coli CTr5X and have transduced it into other E. coli strains.  The
      restrictive locus seems to be a gene, or genes, unique to CTr5X or to be an
      altered form of a nonessential gene, since deleting the locus seems to cause
      loss of the phenotypes.  In addition to restricting RNA ligase- and
      polynucleotide kinase-deficient T4, the locus also restricts bacteriophages
      lambda and T4 with cytosine DNA.  When lambda or T4 with cytosine DNA infect
      strains with the prr locus, the phage DNA is injected, but phage genes are not
      expressed and the host cells survive.  These phenotypes are unlike anything yet
      described for a phage-host interaction.
AU  - Jabbar MA
AU  - Snyder L
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1984 51: 522-529.

PMID- 29889842
VI  - 13
DP  - 2018
TI  - Whole genome sequence and comparative analysis of Borrelia burgdorferi MM1.
PG  - e0198135
AB  - Lyme disease is caused by spirochaetes of the Borrelia burgdorferi sensu lato
      genospecies. Complete genome assemblies are available for fewer than ten strains
      of Borrelia burgdorferi sensu stricto, the primary cause of Lyme disease in North
      America. MM1 is a sensu stricto strain originally isolated in the midwestern
      United States. Aside from a small number of genes, the complete genome sequence
      of this strain has not been reported. Here we present the complete genome
      sequence of MM1 in relation to other sensu stricto strains and in terms of its
      Multi Locus Sequence Typing. Our results indicate that MM1 is a new sequence type
      which contains a conserved main chromosome and 15 plasmids. Our results include
      the first contiguous 28.5 kb assembly of lp28-8, a linear plasmid carrying the
      vls antigenic variation system, from a Borrelia burgdorferi sensu stricto strain.
AU  - Jabbari N
AU  - Glusman G
AU  - Joesch-Cohen LM
AU  - Reddy PJ
AU  - Moritz RL
AU  - Hood L
AU  - Lausted CG
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2018 13: e0198135.

PMID- 29097462
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Pasteurella multocida Serotype A Strain PMTB2.1 Isolated from Buffaloes That Died of Septicemia in Malaysia.
PG  - e01190-17
AB  - Pasteurella multocida causes pneumonic pasteurellosis and hemorrhagic septicemia  (HS) in
      large ruminants. In this study, we determined the complete genome
      sequence of P. multocida strain PMTB2.1 capsular serotype A isolated from
      buffaloes that died of septicemia.
AU  - Jabeen S
AU  - Yong YH
AU  - Abdullah FJF
AU  - Zakaria Z
AU  - Mat IN
AU  - Tan YC
AU  - Yee WY
AU  - Omar AR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01190-17.

PMID- 
VI  - 
DP  - 1983
TI  - Participation of outside DNA sequences in the EcoRI endonuclease reaction pathway.
PG  - 1-153
AB  - I have examined the kinetics of the interaction between EcoRI endonuclease and DNA as a model
      system for the study of recognition site location by sequence-specific DNA binding proteins.
      When the kinetics of interaction of nine linear DNA fragments derived from pBR322 and
      containing the EcoRI site in a central position were examined, the kinetic parameters
      governing both formation and decay of specific endonuclease-DNA complexes was found to
      increase 8-fold with increasing DNA chain length.  In contrast, equilibrium competition
      experiments demonstrated the intrinsic affinity for the recognition site was independent of
      DNA chain length for these molecules.  Thus, sequences outside the EcoRI site enhance the rate
      at which EcoRI endonuclease locates and leaves its recognition site without altering the
      intrinsic affinity of the enzyme for that site.  These results are in accord with a
      facilitated diffusion mechanism for site location, and indicate outside DNA sequences lie on
      the major kinetic pathway by which EcoRI endonuclease locates and leaves its recognition site.
      Competition cleavage experiments demonstrated that longer DNA molecules are preferentially
      cleaved by the endonuclease, suggesting outside DNA sequences also facilitate catalysis by the
      enzyme.  In accord with the view that DNHA sequences outside the EcoRI site are involved in
      the reaction pathway, the enzyme processively cleaves EcoRI sites separated by short distances
      on the same DNA chain.  The rate limiting step in EcoRI endonuclease catalysis has been
      examined by pre-steady state measurements.  Addition of endonuclease to saturating DNA
      resulted in a rapid initial burst of product formation.  This burst was stoichiometric with
      the amount of enzyme added and proves that steps up to and including double strand cleavage
      cannot be rate limiting in catalysis.  A similar burst was observed when EcoRI endonuclease
      was incubated with DNA in the absence of Mg2+, and cleavage  initiated by Mg2+ addition.  This
      latter burst quantitatively reflects the amount of site-specific enzyme-DNA complexes present
      at the time of Mg2+ addition, and has been utilized to assay site-specific binding.
AU  - Jack WE
PT  - Journal Article
TA  - Ph.D. Thesis
JT  - Ph.D. Thesis
SO  - Ph.D. Thesis 1983 : 1-153.

PMID- 2030964
VI  - 19
DP  - 1991
TI  - Overexpression, purification and crystallization of BamHI endonuclease.
PG  - 1825-1829
AB  - The type II restriction endonuclease BamHI has been expressed in E. coli,
      producing 100-fold more enzyme than the wild type Bacillus amyloliquefaciens H
      strain.  This high yield has facilitated purification to homogeneity of large
      amounts of the enzyme, along with its crystallization in a form which diffracts
      to at least 1.9 angstrom in X-ray analysis.
AU  - Jack WE
AU  - Greenough L
AU  - Dorner LF
AU  - Xu S-Y
AU  - Strzelecka T
AU  - Aggarwal AK
AU  - Schildkraut I
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 1825-1829.

PMID- 6765638
VI  - 1
DP  - 1981
TI  - Structures and mechanisms of EcoRI DNA restriction and modification enzymes.
PG  - 165-179
AB  - *

        I. Structural properties

       II. Catalytic properties

      III. Enzyme-substrate interactions

       IV. Cloning and the structural genes

      

AU  - Jack WE
AU  - Rubin RA
AU  - Newman A
AU  - Modrich P
PT  - Journal Article
TA  - Gene Amplif. Anal.
JT  - Gene Amplif. Anal.
SO  - Gene Amplif. Anal. 1981 1: 165-179.

PMID- 6287460
VI  - 79
DP  - 1982
TI  - Involvement of outside DNA sequences in the major kinetic path by which EcoRI endonuclease locates and leaves its recognition sequence.
PG  - 4010-4014
AB  - We have examined the kinetics of the interaction between endodeoxyribonuclease
      EcoRI (EC 3.1.23.13) and nine linear DNA fragments that range in size between
      34 and 6,200 base pairs and contain the EcoRI site of plasmid pBR322 in a
      central location.  The kinetic parameters governing both formation and decay of
      specific endonuclease DNA complexes increase 8-fold with increasing chain
      length over this size range.  In contrast, equilibrium competition experiments
      demonstrated that the intrinsic affinity of endonuclease for this recognition
      sequence is independent of DNA chain length over this size range.  In contrast,
      equilibrium competition experiments demonstrated that the intrinsic affinity of
      endonuclease for its recognition sequence is independent of DNA chain length
      over this range.  Thus, DNA sequences outside the recognition site enhance the
      rate at which EcoRI endonuclease locates or leaves its recognition site without
      affecting the intrinsic thermodynamic parameters of site-specific interaction.
      These results are consistent with a facilitated diffusion mechanism for
      specific DNA site location by this enzyme.
AU  - Jack WE
AU  - Terry BJ
AU  - Modrich P
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1982 79: 4010-4014.

PMID- 26404593
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Dichelobacter nodosus ATCC 25549, Strain VPI 2340 [11342], a Bacterium Causing Footrot in Sheep.
PG  - e01002-15
AB  - We report a draft genome sequence for Dichelobacter nodosus ATCC 25549, strain VPI 2340
      [11342], a causative agent of ovine footrot. The draft genome shares ~98% gene similarity with
      the available genome of D. nodosus strain VCS1703A but  is differentiated by extensive gene
      duplication and the absence of 13 particular  genes.
AU  - Jackson A
AU  - Humbert MV
AU  - Pandey A
AU  - Bratcher H
AU  - Christodoulides M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01002-15.

PMID- 4342968
VI  - 69
DP  - 1972
TI  - Biochemical method for inserting new genetic information into DNA of simian virus 40:  circular SV40 DNA molecules containing lambda phage genes and the galactose operon of Escherichia coli.
PG  - 2904-2909
AB  - We have developed methods for covalently joining duplex DNA molecules to one
      another and have used these techniques to construct circular dimers of SV40 DNA
      and to insert a DNA segment containing lambda phage genes and the galactose
      operon of E. coli into SV40 DNA.  The method involves:   (a) converting
      circular SV40 DNA to a linear form, (b) adding single-stranded
      homodeoxypolymeric extensions of defined composition and length to the 3' ends
      of one of the DNA strands with the enzyme terminal deoxynucleotidyl transferase
      (c) adding complementary homodeoxypolymeric extensions to the other DNA strand,
      (d) annealing the two DNA molecules to form a circular duplex structure, and
      (e) filling the gaps and sealing nicks in this structure with E. coli DNA
      polymerase and DNA ligase to form a covalently closed-circular DNA molecule.
AU  - Jackson DA
AU  - Symons RH
AU  - Berg P
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1972 69: 2904-2909.

PMID- 26769921
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of an Enterobacter Species Associated with Illnesses and Powdered Infant Formula.
PG  - e01479-15
AB  - This is the first report of the draft genome sequence of an Enterobacter species  that may
      have been transmitted from powdered infant formula (PIF) to infants,
      resulting in illness. Enterobacter spp. are currently permitted in PIF, but the
      transmission of this strain indicates that the microbiological criteria for PIF
      may need revision.
AU  - Jackson EE
AU  - Ogrodzki P
AU  - Pascoe B
AU  - Sheppard SK
AU  - Forsythe SJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01479-15.

PMID- 
VI  - 49
DP  - 2001
TI  - A novel use of bacterial transformation to discover new restriction enzymes in clinical E. coli strains.
PG  - 11A
AB  - Recent bacterial genome projects have revealed many new DNA sequences that encode restriction
      endonucleases and their corresponding methylases.  These findings suggest that many
      restriction enzymes have yet to be discovered.  Traditionally, restriction enzymes have been
      discovered by either the classical restriction and modification phenomena of bacteriophages or
      by direct enzyme assay.  To avoid the limitations of these traditional methods, we established
      a simple, quantitative R-M test based on plasmid transformation efficiency (plasmid R-M test)
      using DNA fragments derived from the E. coli phage Lambda.  This new plasmid R-M test works
      similarly to a traditional phage efficiency of plating assay, but is defined as efficiency of
      transformation.  A plasmid kit (p1-p6) was created by combining fragments of Lambda with the
      vector plasmid pMECA, which confers ampicillin resistance.  We used this new EOT method to
      test 250 E. coli strains obtained from 2 local hospitals.  Out of the 250 samples, 58 strains
      were ampicillin sensitive and were used for further study.  The plasmid pMECA and plasmids
      p1-p6 from the kit were transformed into these 58 strains.  Among those, 15 strains had a high
      rate of transformability and a suspected restriction-modification system.  The restriction
      results for these 15 strains were tabulated for p1-p6 by assigning a value of either (+) or
      (-).  Restriction (+) indicates the presence of a DNA recognition site, and thus no bacterial
      growth.  Restriction (-) indicates the absence of a recognition site, and presence of
      bacterial growth.  After comparing the restriction patterns of the 15 clinical strains with
      the restriction patterns of all known E. coli strains (173 listed in REBASE), we found one new
      restriction sequence pattern.  This novel pattern suggests a new DNA recognition sequence.  In
      order to identify this recognition sequence, we, in collaboration with UC Riverside engineers,
      developed a computer program designed to analyze the +/- restriction patterns.  This series of
      experiments indicates that the EOT test can be used to find new restriction enzymes in
      clinical E. coli samples.  We believe that this new method can be expanded to find new
      restriction enzymes and their recognition sequence in many types of bacteria.
AU  - Jackson SE
AU  - Koyama M
AU  - Ryu J
PT  - Journal Article
TA  - J. Invest. Med.
JT  - J. Invest. Med.
SO  - J. Invest. Med. 2001 49: 11A.

PMID- 26988046
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of emm4 Streptococcus pyogenes MEW427, a Throat Isolate  from a Child Meeting Clinical Criteria for Pediatric Autoimmune Neuropsychiatric   Disorders Associated with Streptococcus (PANDAS).
PG  - e00127-16
AB  - We report the complete genome assembly of the Streptococcus pyogenes type emm4 strain MEW427
      (also referred to as strain UM001 in the Pediatric Acute-Onset
      Neuropsychiatric Syndrome [PANS] Research Consortium), a throat isolate from a
      child with acute-onset neuropsychiatric symptoms meeting clinical criteria for
      PANDAS (pediatric autoimmune neuropsychiatric disorders associated with
      streptococcus). The genome length is 1,814,455 bp with 38.51% G+C%.
AU  - Jacob KM
AU  - Spilker T
AU  - LiPuma JJ
AU  - Dawid SR
AU  - Watson ME Jr
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00127-16.

PMID- Not carried by PubMed...
VI  - 49
DP  - 1988
TI  - Type II restriction-modification systems in Enterobacter aerogenes and Herpetosiphon giganteus.
PG  - 730B
AB  - The Type II modification methylase M.EaeI corresponding to the restriction
      endonuclease EaeI was partially purified from Enterobacter aerogenes PW201.
      The methylase converts the innermost cytosine residue in each strand of the
      family of related sequences recognised by EaeI (5'-PyGGCCPu-3') to
      5-methylcytosine.  M.EaeI protects these sites against cleavage by HaeIII and
      also protects overlapping 5'-CCGG-3 sites against cleavage by HpaII and MspI.
      Such protection may be useful in genetic manipulations.  Despite using a
      variety of cloning strategies, attempts to clone the EaeI
      restriction-modification system in Escherichia coli were unsuccessful.  It is
      now apparent that many of the problems encountered during these attempts can be
      explained by the existence in most E. coli strains of restriction systems which
      specifically restrict methylated DNA.  Possible evolutionary relationships
      between Type II restriction-modification systems were investigated in
      Herpetosiphon giganteus.  HgiJI from H. giganteus HFS101 has the recognition
      specificity 5'-GG(A/T)CC-3' and is the fifth isoschizomer of AvaII to have been
      identified in this genus.  The recognition specificities of HgiJII
      (5'-GPuGCPyC-3') and HgiAI (5'-G(A/T)GC(A/T)C-3') from H. giganteus strains
      HFS101 and HP1023 respectively are very similar and the DNAs from these strains
      are resistant to cleavage by both restriction endonucleases.  HgiAI and HgiJII
      may therefore be closely-related enzymes.  The potential role of Type II
      restriction-modification systems in limiting gene transfer between strains in
      this genus is also discussed.
AU  - Jacobs D
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1988 49: 730B.

PMID- 3467722
VI  - 238
DP  - 1986
TI  - Isolation and characterization of the M.EaeI modification methylase.
PG  - 613-616
AB  - Restriction endonucleases have found wide use in the analysis and restructuring of DNA
      molecules and as model systems for studying the interactions of proteins and DNA.  Many such
      activities have been characterized from a large number of bacterial genera (Roberts, 1985),
      and in virtually all cases examined a corresponding methylase is present that protects the
      bacterial DNA from cleavage (McClelland & Nelson, 1985).  These modification methylases have
      been less well-studied, presumably because they are of less importance as tools in the
      manipulation of DNA in vitro.  However, such methylases can be used to protect specific sites
      against cleavage by the cognate endonuclease, and they have been used to alter the number of
      target sites for non-cognate restriction endonucleases on DNA to generate novel specificities
      of cleavage (McClelland et al., 1984).We now report the specificity of the methylase M.EaeI
      corresponding to the endonuclease EaeI from Enterobacter aerogenes PW201 (Whitehead & Brown,
      1983).  We show that the methylase can be used to protect a subset of HaeIII recognition
      sequences from HaeIII cleavage and HpaII/MspI sites from HpaII or MspI cleavage.  Such
      protection may be useful in genetic manipulations.
AU  - Jacobs D
AU  - Brown NL
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 1986 238: 613-616.

PMID- 16714602
VI  - 74
DP  - 2006
TI  - Infectivity of the highly transformable BBE02(-) lp56(-) mutant of Borrelia burgdorferi, the Lyme disease spirochete, via ticks.
PG  - 3678-3681
AB  - Infectious Borrelia burgdorferi strains that have increased transformability with the shuttle
      vector pBSV2 were recently
      constructed by inactivating the gene encoding BBE02, a putative
      restriction-modification gene product expressed by the linear plasmid
      1p25 (Kawabata et al., Infect. Immun. 72:7147-7154, 2004). The absence
      of the linear plasmid 1p56, which carries another putative
      restriction-modification gene, further enhanced transformation rates.
      The infectivity of these mutants was assessed previously in mice that
      were inoculated with needle and syringe and was found to be equivalent
      to that of wild-type spirochetes. Here we examined the infectivity of
      spirochetes to ticks after capillary inoculation of Ixodes scapularis
      nymphs and the subsequent spirochetal infectivity to mice via ticks by
      using B. burgdorferi B31 clonal isolates lacking 1p56 and/or BBE02. The
      absence of 1p56 (but not BBE02) correlated with a lower number of
      spirochetes in ticks after feeding on mice; this plasmid thus may play
      a role, albeit not an essential one, in supporting spirochetal survival
      in the feeding tick. Importantly, however, the absence of 1p56 and
      BBE02 did not detectably influence infectivity to mice via ticks.
AU  - Jacobs MB
AU  - Norris SJ
AU  - Phillippi-Falkenstein KM
AU  - Philipp MT
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2006 74: 3678-3681.

PMID- 108695
VI  - 1
DP  - 1977
TI  - Restriction and modification determined by a Pseudomonas R plasmid.
PG  - 115-116
AB  - Pseudomonas plasmid pMG7 interferes with the propagation of bacteriophages B3, D3, F116, and
      G101 by determining a restriction and modification system.  This system also acts on plasmids
      RP-1 and RP8 to limit transfer into a pMG7+ recipient.
AU  - Jacoby GA
AU  - Sutton L
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 1977 1: 115-116.

PMID- 7178292
VI  - 8
DP  - 1982
TI  - Restriction-modification systems determined by Pseudomonas plasmids.
PG  - 141-147
AB  - Four additional Pseudomonas R plasmids determining the PaeR7
      restriction-modification system have been detected.  All are transfer deficient
      and appear to belong to the same incompatibility group.  The Pseudomonas
      fertility plasmid FP110 determines a different restriction-modification system
      and also inhibits the propagation of phage B39 by a separate mechanism.
      Pseudomonas R plasmid pMG73 has a third distinct restriction-modification
      specificity.  PaeFP110 and PaeR73 are proposed as designations for these new
      plasmid-determined systems for restriction and modification.
AU  - Jacoby GA
AU  - Sutton L
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 1982 8: 141-147.

PMID- 22334611
VI  - 40
DP  - 2012
TI  - Expanding LAGLIDADG endonuclease scaffold diversity by rapidly surveying evolutionary sequence space.
PG  - 4954-4964
AB  - LAGLIDADG homing endonucleases (LHEs) are a family of highly specific DNA endonucleases
      capable of recognizing target sequences approximately 20 bp in
      length, thus drawing intense interest for their potential academic,
      biotechnological and clinical applications. Methods for rational design of LHEs
      to cleave desired target sites are presently limited by a small number of
      high-quality native LHEs to serve as scaffolds for protein engineering-many are
      unsatisfactory for gene targeting applications. One strategy to address such
      limitations is to identify close homologs of existing LHEs possessing superior
      biophysical or catalytic properties. To test this concept, we searched public
      sequence databases to identify putative LHE open reading frames homologous to the
      LHE I-AniI and used a DNA binding and cleavage assay using yeast surface display
      to rapidly survey a subset of the predicted proteins. These proteins exhibited a
      range of capacities for surface expression and also displayed locally altered
      binding and cleavage specificities with a range of in vivo cleavage activities.
      Of these enzymes, I-HjeMI demonstrated the greatest activity in vivo and was
      readily crystallizable, allowing a comparative structural analysis. Taken
      together, our results suggest that even highly homologous LHEs offer a readily
      accessible resource of related scaffolds that display diverse biochemical
      properties for biotechnological applications.
AU  - Jacoby K
AU  - Metzger M
AU  - Shen BW
AU  - Certo MT
AU  - Jarjour J
AU  - Stoddard BL
AU  - Scharenberg AM
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: 4954-4964.

PMID- 24336373
VI  - 1
DP  - 2013
TI  - High-Quality Draft Genome Sequence of Xanthomonas alfalfae subsp. alfalfae Strain CFBP 3836.
PG  - e01035-13
AB  - We report the high-quality draft genome sequence of Xanthomonas alfalfae subsp. alfalfae
      strain CFBP 3836, the causal agent of bacterial leaf and stem spot in
      lucerne (Medicago sativa). Comparative genomics will help to decipher the
      mechanisms provoking disease and triggering the defense responses of this
      pathogen of the model legume Medicago truncatula.
AU  - Jacques MA
AU  - Bolot S
AU  - Charbit E
AU  - Darrasse A
AU  - Briand M
AU  - Arlat M
AU  - Gagnevin L
AU  - Koebnik R
AU  - Noel LD
AU  - Portier P
AU  - Carrere S
AU  - Boureau T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01035-13.

PMID- 3886163
VI  - 41
DP  - 1985
TI  - An intron-encoded protein is active in a gene conversion process that spreads an intron into a mitochondrial gene.
PG  - 383-394
AB  - The intron of the mitochondrial 21S rRNA gene of Saccharomyces cerevisiae possesses a long
      internal reading frame (ORF) that is conserved in various yeast species. In crosses between
      intron-plus and intron-minus variants, this intron determines a specific gene conversion
      phenomenon, which results in the integration of the intron sequence within all previously
      intron-minus copies of the gene. We show, from a frameshift mutant within the intron this ORF
      and from the need of mitochondrial protein synthesis, that ORF encodes a protein active in the
      gene conversion that spreads the intron within populations of interbreeding strains. This new
      intron function is reminiscent of the transposase encoded by mobile genetic elements and is
      discussed in relation to other intron functions.
AU  - Jacquier A
AU  - Dujon B
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1985 41: 383-394.

PMID- 6361491
VI  - 192
DP  - 1983
TI  - The intron of the mitochondrial 21S rRNA gene:  distribution in different yeast species and sequence comparison between Kluyveromyces thermotolerans and Saccharomyces cerevisiae.
PG  - 487-499
AB  - We have screened numerous different yeast species for the presence of sequences homologous to
      the intron of the mitochondrial 21S rRNA gene of Saccharomyces cerevisiae (intron r1) and
      found them in all Kluyveromyces species, some of the Saccharomyces species and none of the
      other yeasts tested. We have determined the nucleotide sequence of the r1-intron in K.
      thermotolerans and compared it with that of S. cerevisiae. The two introns are inserted at the
      same position within the 21S rRNA gene. They contain homologous internal open reading frames
      (ORFs) initiated at the same AUG codon which can be aligned over their entire length. Several
      silent multi-substitutions indicate that these intronic ORFs represent selectively conserved
      functional genes. Other intron segments, on the contrary, reveal short blocks of extensive
      homology separated by non-homologous stretches and/or additions-deletions. Comparison of our
      two yeast r1-introns with equivalent introns of N. crassa and A. nidulans mitochondria reveals
      that introns with very similar RNA secondary structures can accommodate different types of
      ORFs.
AU  - Jacquier A
AU  - Dujon B
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1983 192: 487-499.

PMID- 9446788
VI  - 242
DP  - 1998
TI  - Design of a combinatorial oligonucleotide library containing all possible hexamer palindromes: PCR synthesis and application for identifying restriction cleavage sites.
PG  - 297-302
AB  - An algorithm for designing a combinatorial library comprehensively representing all hexamer
      palindrome sequences at uniquely defined sites is described.  The expected size for such a
      library of 64 possible hexamer palindromes is 384 bases, which is reduced to 266 bases spread
      over 8 oligonucleotides through a linear overlap of rationally selected hexamer palindromes.
      The single stranded oligonucleotides of the designed sets were chemically synthesized and
      converted into corresponding duplex dimers using PCR primer-dimer method.  The utility of
      these duplex oligomers for identifying cleavage sites of restriction enzymes recognizing
      hexamer palindromes has been demonstrated using some representative enzymes.  The library is
      also useful for screening restriction enzymes with tetramer cleavage sites and identifying the
      "star" sites of restriction enzymes.  The sets of oligonucleotides with high information
      content, though designed for direct and unambiguous characterization of cleavage sites of
      isolated restriction enzymes, have potential applications as templates for characterizing
      sequence selective binding and interaction of small molecules nucleic acid.
AU  - Jadhav VR
AU  - Ganesh KN
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1998 242: 297-302.

PMID- 27284158
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Mycobacterium chelonae Type Strain CCUG 47445, a Rapidly Growing Species of Nontuberculous Mycobacteria.
PG  - e00550-16
AB  - Mycobacterium chelonae strains are ubiquitous rapidly growing mycobacteria associated with
      skin and soft tissue infections, cellulitis, abscesses,
      osteomyelitis, catheter infections, disseminated diseases, and postsurgical
      infections after implants with prostheses, transplants, and even hemodialysis
      procedures. Here, we report the complete genome sequence of M. chelonae type
      strain CCUG 47445.
AU  - Jaen-Luchoro D
AU  - Salva-Serra F
AU  - Aliaga-Lozano F
AU  - Segui C
AU  - Busquets A
AU  - Ramirez A
AU  - Ruiz M
AU  - Gomila M
AU  - Lalucat J
AU  - Bennasar-Figueras A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00550-16.

PMID- 27231356
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of the Mycobacterium immunogenum Type Strain CCUG 47286.
PG  - e00401-16
AB  - Here, we report the complete genome sequence of Mycobacterium immunogenum type strain CCUG
      47286, a nontuberculous mycobacterium. The whole genome has 5,573,781
      bp and covers as many as 5,484 predicted genes. This genome contributes to the
      task of closing the still-existing gap of genomes of rapidly growing
      mycobacterial type strains.
AU  - Jaen-Luchoro D
AU  - Segui C
AU  - Aliaga-Lozano F
AU  - Salva-Serra F
AU  - Busquets A
AU  - Gomila M
AU  - Ramirez A
AU  - Ruiz M
AU  - Moore ER
AU  - Lalucat J
AU  - Bennasar-Figueras A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00401-16.

PMID- 27908994
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of the Barley Pathogen Xanthomonas translucens pv. translucens DSM 18974T (ATCC 19319T).
PG  - e01334-16
AB  - We report here the complete 4.7-Mb genome sequence of Xanthomonas translucens pv. translucens
      DSM 18974T, which causes black chaff disease on barley (Hordeum
      vulgare). Genome data of this X. translucens type strain will improve our
      understanding of this bacterial species.
AU  - Jaenicke S
AU  - Bunk B
AU  - Wibberg D
AU  - Sproer C
AU  - Hersemann L
AU  - Blom J
AU  - Winkler A
AU  - Schatschneider S
AU  - Albaum SP
AU  - Kolliker R
AU  - Goesmann A
AU  - Puhler A
AU  - Overmann J
AU  - Vorholter FJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01334-16.

PMID- 18536921
VI  - 27
DP  - 2008
TI  - Methylation of chloroplast DNA does not affect viability and maternal inheritance in tobacco and may provide a strategy towards transgene containment.
PG  - 1377-1384
AB  - We report the integration of a type II restriction-methylase, mFokI, into the tobacco
      chloroplast genome and we demonstrate that the
      introduced enzyme effectively directs the methylation of its target
      sequence in vivo and does not affect maternal inheritance. We further
      report the transformation of tobacco with an E. coli dcm methylase
      targeted to plastids and we demonstrate efficient cytosine methylation
      of the plastid genome. Both adenosine methylation of FokI sites and
      cytosine methylation of dcm sites appeared phenotypically neutral. The
      ability to tolerate such plastid genome methylation is a pre-requisite
      for a proposed plant transgene containment system. In such a system, a
      chloroplast located, maternally inherited restriction methylase would
      provide protection from a nuclear-encoded, plastid targeted restriction
      endonuclease. As plastids are not paternally inherited in most crop
      species, pollen from such plants would carry the endonuclease transgene
      but not the corresponding methylase; the consequence of this should be
      containment of all nuclear transgenes, as pollination will only be
      viable in crosses to the appropriate transplastomic maternal
      background.
AU  - Jaffe B
AU  - Kovacs K
AU  - Andras C
AU  - Bodi Z
AU  - Liu Z
AU  - Fray RG
PT  - Journal Article
TA  - Plant Cell
JT  - Plant Cell
SO  - Plant Cell 2008 27: 1377-1384.

PMID- 27634998
VI  - 4
DP  - 2016
TI  - Genome Sequence of the Facultative Anaerobe Oerskovia enterophila DFA-19 (DSM 43852T).
PG  - e00973-16
AB  - Here, we report the draft genome sequence of Oerskovia enterophila DFA-19 (DSM 43852(T)), a
      facultative anaerobe soil bacterium, which was originally isolated
      from millipede feces and first described as Promicromonospora enterophila The
      genome consists of a circular chromosome comprising approximately 4.65 Mb and
      4,044 predicted protein-encoding genes.
AU  - Jag V
AU  - Poehlein A
AU  - Bengelsdorf FR
AU  - Daniel R
AU  - Durre P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00973-16.

PMID- 28484582
VI  - 12
DP  - 2017
TI  - Genome sequencing and description of Oerskovia enterophila VJag, an agar- and cellulose-degrading bacterium.
PG  - 30
AB  - A nonmotile, Gram-positive bacterium that shows an elongated and branching cell shape was
      isolated from soil samples from the botanical garden of Ulm University,
      Ulm, Germany. Here, the isolation procedure, identification, genome sequencing
      and metabolic features of the strain are described. Phylogenetic analysis allowed
      to identify the isolated strain as Oerskovia enterophila. The genus Oerskovia
      belongs to the family Cellulomonadaceae within the order Actinomycetales. The
      length of cells of O. enterophila ranges from 1 mum to 15 mum, depending on the
      growth phase. In the exponential growth phase, cells show an elongated and
      branching shape, whereas cells break up to round or coccoid elements in the
      stationary growth phase. The 4,535,074 bp long genome consists of 85 contigs with
      3918 protein-coding genes and 57 RNA genes. The isolated strain was shown to
      degrade numerous complex carbon sources such as cellulose, chitin, and starch,
      which can be found ubiquitously in nature. Moreover, analysis of the genomic
      sequence revealed the genetic potential to degrade these compounds.
AU  - Jag V
AU  - Poehlein A
AU  - Bengelsdorf FR
AU  - Daniel R
AU  - Durre P
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 30.

PMID- 2854807
VI  - 74
DP  - 1988
TI  - Distinct fractions of genomic DNA from cyanobacterium Nostoc commune that differ in the degree of methylation.
PG  - 197-201
AB  - Meeting Abstract
AU  - Jager K
AU  - Potts M
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 197-201.

PMID- 29301904
VI  - 6
DP  - 2018
TI  - Complete Genome Sequences of Three Streptococcus agalactiae Serotype Ia Isolates  Obtained from Disease Outbreaks in Nile Tilapia (Oreochromis niloticus).
PG  - e01432-17
AB  - This paper describes the whole-genome sequences for three Streptococcus agalactiae serotype Ia
      isolates. The isolates were recovered from the brains of
      clinically sick tilapia, Oreochromis niloticus, that were suffering from
      streptococcosis. One isolate was from tilapia in the United States and the other
      two from fish in China.
AU  - Jaglarz A
AU  - Gurgul A
AU  - Leigh WJ
AU  - Costa JZ
AU  - Thompson KD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01432-17.

PMID- 29439034
VI  - 6
DP  - 2018
TI  - Complete Genome Sequences of Three Fish-Associated Streptococcus agalactiae Isolates.
PG  - e00025-18
AB  - The whole-genome sequences are described here for three group B Streptococcus (GBS) (S.
      agalactiae) serotype Ib isolates obtained from tilapia (Oreochromis
      niloticus) farmed at sites in Honduras, Costa Rica, and the United States. The
      bacteria were isolated from the brains of fish displaying signs of
      streptococcosis.
AU  - Jaglarz A
AU  - Gurgul A
AU  - Leigh WJ
AU  - Costa JZ
AU  - Thompson KD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00025-18.

PMID- 24926056
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Aeromonas hydrophila Strain Ae34, Isolated from a Septicemic and Moribund Koi Carp (Cyprinus carpio koi), a Freshwater Aquarium  Fish.
PG  - e00572-14
AB  - Aeromonas hydrophila is an important opportunistic pathogen that infects a variety of aquatic
      and terrestrial animals, including humans. We report here the
      draft genome sequence of A. hydrophila Ae34, a multidrug-resistant isolate from
      the kidney of a moribund koi carp (Ciprinus carpio koi) with signs of hemorrhagic
      septicemia.
AU  - Jagoda SS
AU  - Tan E
AU  - Arulkanthan A
AU  - Kinoshita S
AU  - Watabe S
AU  - Asakawa S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00572-14.

PMID- 
VI  - 39
DP  - 1998
TI  - De novo DNA methyltransferase activity in a lung cancer cell line.
PG  - 95
AB  - In mammalian cells genomic methylation patterns are important for normal embryonic development
      and cell growth.  It has been proposed that distinct DNA methyltransferases are responsible
      for de novo and maintenance methylation, however, only one DNA methyltransferase with
      predominant maintenance activity has been identified in vertebrates so far.  In addition, the
      role of DNA methyltransferases in establishing aberrant patterns of DNA methylation in cancer
      remain poorly defined.  We have now tested both de novo and maintenance methylation activities
      in different cancer cell lines by using a DNA methyltransferase assay with polydldC
      (maintenance) and Drosophila genomic DNA (de novo) as substrates.  One lung cancer cell line,
      H249, had an abnormally high de novo methyltransferase activity.  Interestingly, treatment
      with 5-azadeoxycytidine reduced maintenance methylation activity in this cell, but did not
      affect de novo methylation activity.  Using gel filtration chromatography, we found that the
      peak activities of both maintenance and de novo methylation were detected in the same eluted
      fraction, suggesting that enzymes with similar molecular size, or the same enzyme, are
      responsible for maintenance and de novo methylation activities in this cell line.  Despite
      this in vitro de novo methyltransferase activity, several CpG islands which are commonly
      methylated in cancer remain methylation-free in this  cell line.  Thus, further investigation
      of this cancer cell line H249 may provide us further insights into the mechanisms of
      maintenance and de novo methylation, and their relation to aberrant methylation in cancer.
AU  - Jair K
AU  - Yen R-WC
AU  - Toyota M
AU  - Ho C
AU  - Baylin SB
AU  - Issa J-PJ
PT  - Journal Article
TA  - Proc. Amer. Assoc. Cancer Res.
JT  - Proc. Amer. Assoc. Cancer Res.
SO  - Proc. Amer. Assoc. Cancer Res. 1998 39: 95.

PMID- 28450509
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of a Biodesulfurizing Bacterium, Gordonia sp. Strain IITR100.
PG  - e00230-17
AB  - We report here the whole-genome sequence of a biodesulfurizing bacterium, Gordonia sp. strain
      IITR100. The bacterium has the unique ability to desulfurize
      both aliphatic and aromatic organosulfurs. The draft genome sequence will provide
      insights into the various genes and regulators involved in biodesulfurization and
      other catabolic pathways.
AU  - Jaishankar J
AU  - Singh P
AU  - Srivastava P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00230-17.

PMID- 30413737
VI  - 8
DP  - 2018
TI  - Genome Features and Biochemical Characteristics of a Robust, Fast Growing and Naturally Transformable Cyanobacterium Synechococcus elongatus PCC 11801 Isolated from India.
PG  - 16632
AB  - Cyanobacteria provide an interesting platform for biotechnological applications
      due to their efficient photoautotrophic growth, amenability to genetic
      engineering and the ability to grow on non-arable land. An ideal industrial
      strain of cyanobacteria would need to be fast growing and tolerant to high levels
      of temperature, light, carbon dioxide, salt and be naturally transformable. In
      this study, we report Synechococcus elongatus PCC 11801, a strain isolated from
      India that fulfills these requirements. The physiological and biochemical
      characteristics of PCC 11801 under carbon and light-limiting conditions were
      investigated. PCC 11801 shows a doubling time of 2.3 h, that is the fastest
      growth for any cyanobacteria reported so far under ambient CO2 conditions. Genome
      sequence of PCC 11801 shows genome identity of ~83% with its closest neighbors
      Synechococcus elongatus PCC 7942 and Synechococcus elongatus UTEX 2973. The
      unique attributes of PCC 11801 genome are discussed in light of the physiological
      characteristics that are needed in an industrial strain. The genome of PCC 11801
      shows several genes that do not have homologs in neighbor strains PCC 7942 and
      UTEX 2973, some of which may be responsible for adaptation to various abiotic
      stresses. The remarkably fast growth rate of PCC 11801 coupled with its
      robustness and ease of genetic transformation makes it an ideal candidate for the
      photosynthetic production of fuels and chemicals.
AU  - Jaiswal D
AU  - Sengupta A
AU  - Sohoni S
AU  - Sengupta S
AU  - Phadnavis AG
AU  - Pakrasi HB
AU  - Wangikar PP
PT  - Journal Article
TA  - Sci. Rep.
JT  - Sci. Rep.
SO  - Sci. Rep. 2018 8: 16632.

PMID- 28153890
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Pseudomonas hussainii Strain MB3, a Denitrifying Aerobic Bacterium Isolated from the Rhizospheric Region of Mangrove Trees in the Andaman   Islands, India.
PG  - e01527-16
AB  - The genome sequence of Pseudomonas hussainii MB3, isolated from the rhizospheric  region of
      mangroves in the Andaman Islands, is comprised of 3,644,788 bp and
      3,159 protein coding genes. Draft genome analysis indicates that MB3 is an
      aerobic bacterium capable of performing assimilatory sulfate reduction,
      dissimilatory nitrate reduction, and denitrification.
AU  - Jaiswal SK
AU  - Saxena R
AU  - Mittal P
AU  - Gupta A
AU  - Sharma VK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01527-16.

PMID- 27313296
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Moraxella catarrhalis Type Strain CCUG 353T.
PG  - e00552-16
AB  - Moraxella catarrhalis is a Gram-negative commensal and pathogenic bacterium found in the human
      respiratory tract. It is associated with otitis media and
      respiratory tract infections. Here, we report the draft genome sequence of M.
      catarrhalis type strain CCUG 353(T), composed of 18 contigs and a total size of
      1.89 Mb.
AU  - Jakobsson HE
AU  - Salva-Serra F
AU  - Thorell K
AU  - Gonzales-Siles L
AU  - Boulund F
AU  - Karlsson R
AU  - Sikora P
AU  - Engstrand L
AU  - Kristiansson E
AU  - Moore ER
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00552-16.

PMID- 28385844
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Six Strains of Streptococcus pneumoniae from Serotypes  5, 6A, 6B, 18C, 19A, and 23F.
PG  - e00125-17
AB  - Streptococcus pneumoniae is a pathogenic bacterium found most commonly in the respiratory
      tract of humans and is a common cause of pneumonia and bacterial
      meningitis. Here, we report the draft genome sequences of six S. pneumoniae
      strains: CCUG 1350, CCUG 7206, CCUG 11780, CCUG 33774, CCUG 35180, and CCUG
      35272.
AU  - Jakobsson HE
AU  - Salva-Serra F
AU  - Thorell K
AU  - Karlsson R
AU  - Gonzales-Siles L
AU  - Boulund F
AU  - Engstrand L
AU  - Kristiansson E
AU  - Moore ER
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00125-17.

PMID- 
VI  - 
DP  - 2007
TI  - Domain organization analysis of Type II restriction endonucleases.
PG  - 1-42
AB  - CONCLUSIONS 1. Two-domain organization of Type IIS REases R.Eco31I and R.Hin4II and Type IIP
      REase R.SdaI was identified by limited proteolysis. 2. The isolated N-domain of R.Eco31I was
      found to be responsible for the specific interaction with DNA. 3. The single HNH nuclease-like
      active site was identified in the C-domain of R.Eco31I. 4. Two R-M systems were cloned in E.
      coli: Hin4II of novel DNA specificity 5'-CCTTC(6/5) and SdaI that recognizes and cleave eight
      base DNA target, 5'-CCTGCA^GG. 5. The HNH nuclease-like active site was identified in the
      C-domain of R.Hin4II by bioinformatic methods.
AU  - Jakubauskas A
PT  - Journal Article
TA  - Ph.D. Thesis, Vilnius University
JT  - Ph.D. Thesis, Vilnius University
SO  - Ph.D. Thesis, Vilnius University 2007 : 1-42.

PMID- Not carried by PubMed...
VI  - 1
DP  - 1997
TI  - Construction and analysis of chimeric enzymes between type IIs restriction endonucleases Alw26I, Eco31I and Esp3I.
PG  - 26-30
AB  - Conserved regions I, III and IV were swapped between restriction endonucleases Alw26I, Eco31I
      and Esp3I, and 16 chimeric enzymes were constructed.  Only the hybrid enzyme
      Eco31I-(N-esp-Mva1269I) containing the N-terminus and conserved region I from Esp3I and the
      remaining part from Eco31I revealed the enzymatic activity of Eco31I specificity in crude
      lysate.  This indicates that the conserved region I belongs to the structural elements of
      Eco31I.  The four hybrid enzymes with swapped intermediate sequences between conserved regions
      III and IV and/or conserved region IV induce an SOS response in E. coli ER1992, which can be
      blocked with M.Alw26I methylase.  These results suggest that DNA lesions incurred by hybrid
      enzymes are site specific.
AU  - Jakubauskas A
AU  - Dauksaite V
PT  - Journal Article
TA  - Biologija
JT  - Biologija
SO  - Biologija 1997 1: 26-30.

PMID- 17499273
VI  - 370
DP  - 2007
TI  - Identification of a Single HNH Active Site in Type IIS Restriction Endonuclease Eco31I.
PG  - 157-169
AB  - Type IIS restriction endonuclease Eco31I is a "short-distance cutter", which cleaves DNA
      strands close to its recognition sequence, 5'-GGTCTC(1/5). Previously, it has been proposed
      that related endonucleases recognizing a common sequence core GTCTC possess two active sites
      for cleavage of both strands in the DNA substrate. Here, we present bioinformatic
      identification and experimental evidence for a single nuclease active site. We identified a
      short region of homology between Eco31I and HNH nucleases, constructed a three-dimensional
      model of the putative catalytic domain and validated our predictions by random and
      site-specific mutagenesis. The restriction mechanism of Eco31I is suggested by analogy to the
      mechanisms of phage T4 endonuclease VII and homing endonuclease I-PpoI. We propose that
      residues D311 and N334 coordinate the cofactor. H312 acts as a general base-activating water
      molecule for the nucleophilic attack. K337 together with R340 and D345 are located in close
      proximity to the active center and are essential for correct folding of catalytic motif, while
      D345 together with R264 and D273 could be directly involved in DNA binding. We also predict
      that the Eco31I catalytic domain contains a putative Zn-binding site, which is essential for
      its structural integrity. Our results suggest that the HNH-like active site is involved in the
      cleavage of both strands in the DNA substrate. On the other hand, analysis of site-specific
      mutants in the region, previously suggested to harbor the second active site, revealed its
      irrelevance to the nuclease activity. Thus, our data argue against the earlier prediction and
      indicate the presence of a single conserved active site in type IIS restriction endonucleases
      that recognize common sequence core GTCTC.
AU  - Jakubauskas A
AU  - Giedriene J
AU  - Bujnicki JM
AU  - Janulaitis A
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2007 370: 157-169.

PMID- 18848579
VI  - 61
DP  - 2009
TI  - Bioinformatic and partial functional analysis of pEspA and pEspB, two plasmids from Exiguobacterium arabatum sp nov RFL1109.
PG  - 52-64
AB  - The complete nucleotide sequences of two plasmids from Exiguobacterium arabatum sp. nov.
      RFL1109, pEspA (4563 bp) and pEspB (.38,945 bp), have
      been determined. Five ORFs were identified in the pEspA plasmid, and
      putative functions were assigned to two of them. Using deletion mapping
      approach, the Rep-independent replication region of pEspA, which
      functions in Bacillus subtilis, was localized within a 0.6 kb DNA
      region. Analysis of the pEspB sequence revealed 42 ORFs. From these,
      function of two genes encoding enzymes of the Lsp11091
      restriction-modification system was confirmed experimentally, while
      putative functions of another 18 ORFs were suggested based on
      comparative analysis. Three functional regions have been proposed for
      the pEspB plasmid: the putative conjugative transfer region, the region
      involved in plasmid replication and maintenance, and the region
      responsible for transposition of the IS21 family-like transposable
      elements.
AU  - Jakubauskas A
AU  - Kriukiene E
AU  - Trinkunaite L
AU  - Sapranauskas R
AU  - Jurenaite-Urbanaviciene S
AU  - Lubys A
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 2009 61: 52-64.

PMID- 18642930
VI  - 47
DP  - 2008
TI  - Domain organization and functional analysis of type IIS restriction endonuclease Eco31I.
PG  - 8546-8556
AB  - Type IIS restriction endonuclease Eco31I harbors a single HNH active site and cleaves both DNA
      strands close to its recognition sequence,
      5'-GGTCTC(1/5). A two-domain organization of Eco31I was determined by
      limited proteolysis. Analysis of proteolytic fragments revealed that
      the N-terminal domain of Eco31I is responsible for the specific DNA
      binding, while the C-terminal domain contains the HNH nuclease-like
      active site. Gel-shift and gel-filtration experiments revealed that a
      monomer of the N-terminal domain of Eco31I is able to bind a single
      copy of cognate DNA. However, in contrast to other studied type IIS
      enzymes, the isolated catalytic domain of Eco31I was inactive.
      Steady-state and transient kinetic analysis of Eco31I reactions was
      inconsistent with dimerization of Eco31I on DNA. Thus, we propose that
      Eco31I interacts with individual copies of its recognition sequence in
      its monomeric form and presumably remains a monomer as it cleaves both
      strands of double-stranded DNA. The domain organization and reaction
      mechanism established for Eco31I should be common for a group of
      evolutionary related type IIS restriction endonucleases Alw26I, BsaI,
      BsmAI, BsmBI and Esp3I that recognize DNA sequences bearing the common
      pentanucleotide 5'-GTCTC.
AU  - Jakubauskas A
AU  - Sasnauskas G
AU  - Giedriene J
AU  - Janulaitis A
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2008 47: 8546-8556.

PMID- 21908674
VI  - 193
DP  - 2011
TI  - Comparative genomic analysis of Xanthomonas axonopodis pv. citrumelo F1 causing citrus bacterial spot and related strains provides insights into  virulence and host-specificity.
PG  - 6342-6357
AB  - Xanthomonas axonopodis pv. citrumelo (Xacm) is a citrus pathogen causing citrus bacterial spot
      disease that is geographically restricted within the
      state of Florida. Illumina, 454 sequencing and optical mapping were used
      to obtain a complete genome sequence of Xacm strain F1, 4.9Mb in size. The
      strain lacks plasmids as compared to other citrus pathogens. Phylogenetic
      analysis revealed that this pathogen is very close to the tomato bacterial
      spot pathogen Xcv 85-10 with a completely different host range. We also
      compared Xacm to the genome of citrus canker pathogen Xac 306. Comparative
      genomic analysis showed differences in several gene clusters like Type 3
      effectors, Type 4 secretion system, lipopolysaccharide synthesis and
      others. In addition to pthA, effectors such as xopE3, xopAI and hrpW were
      absent in Xacm while present in Xac. These effectors might be responsible
      for survival and reduced virulence of this pathogen on citrus compared to
      Xac. We also identified unique effectors in Xacm that may be related to
      the different host range as compared to Xac. Xacm also lacks various genes
      such as syrE1, syrE2 and RTX toxin family genes, which were present in
      Xac. These may be associated with distinct virulence of Xacm and Xac.
      Comparison of the complete genome sequence of Xacm to Xac and Xcv provides
      valuable insights into the mechanism of bacterial virulence and
      host-specificity.
AU  - Jalan N
AU  - Aritua V
AU  - Kumar D
AU  - Yu F
AU  - Jones JB
AU  - Graham JH
AU  - Setubal JC
AU  - Wang N
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6342-6357.

PMID- 23682143
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Xanthomonas citri subsp. citri Strain Aw12879, a Restricted-Host-Range Citrus Canker-Causing Bacterium.
PG  - e00235-13
AB  - Xanthomonas citri subsp. citri causes citrus canker. The Asiatic strain has a broad host
      range, whereas the Wellington variant has a restricted host range.
      Here, we present the complete genome of X. citri subsp. citri strain A(W)12879.
      This study lays the foundation to further characterize the mechanisms for
      virulence and host range of X. citri.
AU  - Jalan N
AU  - Kumar D
AU  - Yu F
AU  - Jones JB
AU  - Graham JH
AU  - Wang N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00235-13.

PMID- 11191212
VI  - 38
DP  - 2000
TI  - Intragenic suppressors that restore the splicing and homing activities of the protein encoded by the second intron of the Saccharomyces capensis cyt b gene.
PG  - 276-282
AB  - The second (bi2) intron of the mitochondrial cyt b gene from Saccharomyces capensis encodes a
      bifunctional protein which acts both
      as a maturase, promoting intron splicing, and as a homing-endonuclease,
      I-ScaI, promoting intron mobility. In this work we isolated and
      characterized revertants from a respiratory-deficient mutant in which
      both functions of the protein have been lost. Intragenic revertants
      resulted mainly from monosubstitutions in the mutated codon and in one
      case from a distant second site mutation. All novel variants of the S.
      capensis bi2 intron-encoded protein are competent for the maturase
      activity but only two of them can partially complement the homing
      function.
AU  - Jamoussi K
AU  - Lazowska J
PT  - Journal Article
TA  - Curr. Genet.
JT  - Curr. Genet.
SO  - Curr. Genet. 2000 38: 276-282.

PMID- 29097476
VI  - 5
DP  - 2017
TI  - Genome Sequencing of Microbacterium sp. Yaish 1, a Bacterial Strain Isolated from the Rhizosphere of Date Palm Trees Affected by Salinity.
PG  - e01247-17
AB  - Microbacterium sp. strain Yaish 1 is a rhizospheric bacterium isolated from date  palm
      orchards with high soil salinity. The genome was sequenced, and genes coding
      for growth-promoting 1-aminocyclopropane-1-carboxylate (ACC) deaminase,
      siderophore-producing proteins, and tryptophan biosynthesis proteins were
      identified. Here, we report the draft whole-genome sequencing of the strain.
AU  - Jana GA
AU  - Al-Yahyai R
AU  - Yaish MW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01247-17.

PMID- 20042506
VI  - 84
DP  - 2010
TI  - Evidence for Multiple Recent Host Species Shifts among the Ranaviruses (Family Iridoviridae).
PG  - 2636-2647
AB  - Members of the genus Ranavirus (family Iridoviridae) have been recognized
      as major viral pathogens of cold-blooded vertebrates. Ranaviruses have
      been associated with amphibians, fish, and reptiles. At this time, the
      relationships between ranavirus species are still unclear. Previous
      studies suggested that ranaviruses from salamanders are more closely
      related to ranaviruses from fish than they are to ranaviruses from other
      amphibians, such as frogs. Therefore, to gain a better understanding of
      the relationships among ranavirus isolates, the genome of epizootic
      hematopoietic necrosis virus (EHNV), an Australian fish pathogen, was
      sequenced. Our findings suggest that the ancestral ranavirus was a fish
      virus and that several recent host shifts have taken place, with
      subsequent speciation of viruses in their new hosts. The data suggesting
      several recent host shifts among ranavirus species increase concern that
      these pathogens of cold-blooded vertebrates may have the capacity to cross
      numerous poikilothermic species barriers and the potential to cause
      devastating disease in their new hosts.
AU  - Jancovich JK
AU  - Bremont M
AU  - Touchman JW
AU  - Jacobs BL
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 2010 84: 2636-2647.

PMID- 14599794
VI  - 316
DP  - 2003
TI  - Genomic sequence of a ranavirus (family Iridoviridae) associated with salamander mortalities in North America.
PG  - 90-103
AB  - Disease is among the suspected causes of amphibian population declines, and an iridovirus and
      a chytrid fungus are the primary pathogens
      associated with amphibian mortalities. Ambystoma tigrinum virus (ATV) and
      a closely related strain, Regina ranavirus (RRV), are implicated in
      salamander die-offs in Arizona and Canada, respectively. We report the
      complete sequence of the ATV genome and partial sequence of the RRV
      genome. Sequence analysis of the ATV/RRV genomes showed marked similarity
      to other ranaviruses, including tiger frog virus (TFV) and frog virus 3
      (FV3), the type virus of the genus Ranavirus (family Iridoviridae), as
      well as more distant relationships to lymphocystis disease virus, Chilo
      iridescent virus, and infectious spleen and kidney necrosis virus.
      Putative open reading frames (ORFs) in the ATV sequence identified 24
      genes that appear to control virus replication and block antiviral
      responses. In addition, >50 other putative genes, homologous to ORFs in
      other iridoviral genomes but of unknown function, were also identified.
      Sequence comparison performed by dot plot analysis between ATV and itself
      revealed a conserved 14-bp palindromic repeat within most intragenic
      regions. Dot plot analysis of ATV vs RRV sequences identified several
      polymorphisms between the two isolates. Finally, a comparison of ATV and
      TFV genomic sequences identified genomic rearrangements consistent with
      the high recombination frequency of iridoviruses. Given the adverse
      effects that ranavirus infections have on amphibian and fish populations,
      ATV/RRV sequence information will allow the design of better diagnostic
      probes for identifying ranavirus infections and extend our understanding
      of molecular events in ranavirus-infected cells.
AU  - Jancovich JK
AU  - Mao J
AU  - Chinchar VG
AU  - Wyatt C
AU  - Case ST
AU  - Kumar S
AU  - Valente G
AU  - Subramanian S
AU  - Davidson EW
AU  - Collins JP
AU  - Jacobs BL
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 2003 316: 90-103.

PMID- 30519380
VI  - 13
DP  - 2018
TI  - Draft genomes of Cronobacter sakazakii strains isolated from dried spices bring unique insights into the diversity of plant-associated strains.
PG  - 35
AB  - Cronobacter sakazakii is a Gram-negative opportunistic pathogen that causes life- threatening
      infantile infections, such as meningitis, septicemia, and necrotizing
      enterocolitis, as well as pneumonia, septicemia, and urinary tract and wound
      infections in adults. Here, we report 26 draft genome sequences of C. sakazakii,
      which were obtained from dried spices from the USA, the Middle East, China, and
      the Republic of Korea. The average genome size of the C. sakazakii genomes was
      4393 kb, with an average of 4055 protein coding genes, and an average genome G +
      C content of 56.9%. The genomes contained genes related to carbohydrate transport
      and metabolism, amino acid transport and metabolism, and cell wall/membrane
      biogenesis. In addition, we identified genes encoding proteins involved in
      osmotic responses such as DnaJ, Aquaproin Z, ProQ, and TreF, as well as
      virulence-related and heat shock-related proteins. Interestingly, a metabolic
      island comprised of a variably-sized xylose utilization operon was found within
      the spice-associated C. sakazakii genomes, which supports the hypothesis that
      plants may serve as transmission vectors or alternative hosts for Cronobacter
      species. The presence of the genes identified in this study can support the
      remarkable phenotypic traits of C. sakazakii such as the organism's capabilities
      of adaptation and survival in response to adverse growth environmental conditions
      (e.g. osmotic and desiccative stresses). Accordingly, the genome analyses
      provided insights into many aspects of physiology and evolutionary history of
      this important foodborne pathogen.
AU  - Jang H et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2018 13: 35.

PMID- 29650569
VI  - 6
DP  - 2018
TI  - Whole-Genome Sequences of Cronobacter sakazakii Isolates Obtained from Foods of Plant Origin and Dried-Food Manufacturing Environments.
PG  - e00223-18
AB  - Here, we present draft genome sequences of 29 Cronobacter sakazakii isolates obtained from
      foods of plant origin and dried-food manufacturing facilities.
      Assemblies and annotations resulted in genome sizes ranging from 4.3 to 4.5 Mb
      and 3,977 to 4,256 gene-coding sequences with G+C contents of approximately
      57.0%.
AU  - Jang H
AU  - Addy N
AU  - Ewing L
AU  - Jean-Gilles BJ
AU  - Lee Y
AU  - Woo J
AU  - Negrete F
AU  - Finkelstein S
AU  - Tall BD
AU  - Lehner A
AU  - Eshwar A
AU  - Gopinath GR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00223-18.

PMID- 24855305
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Lactobacillus plantarum wikim18, Isolated from Korean Kimchi.
PG  - e00467-14
AB  - This report describes the draft genome sequence of Lactobacillus plantarum strain wikim18,
      isolated from the traditional Korean food kimchi. The reads generated by
      Ion Torrent PGM were assembled into 327 contigs. RAST annotation of the genome
      revealed 12 tRNAs and 3,316 protein-coding gene sequences.
AU  - Jang JY
AU  - Lim HI
AU  - Park HW
AU  - Choi HJ
AU  - Kim TW
AU  - Kang M
AU  - Lee JH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00467-14.

PMID- 
VI  - 22
DP  - 2000
TI  - Improved electrotransformation frequencies of Corynebacterium glutamicum using cell-surface mutantstransformation via electroporation using plasmid DNA.
PG  - 539-545
AB  - 6 Strains of Corynebacterium glutamicum were examined for electrotransformation using
      heterologous or homologous DNA. These were:
      AS019, a spontaneous rifampicin-resistant strain of ATCC 13059; MLB133
      and MLB194, auxotrophic cell surface mutants derived from ATCC 13059 by
      exposure to ethylmethane sulfonate; ATCC 13032; and RM3 and RM4,
      restriction modification mutants of ATCC 13032. Heterologous DNA was
      plasmid pCSL17 purified from Escherichia coli LE392. Homologous DNA was
      pCSL17 from C. glutamicum AS019. Transformation by electroporation
      involved a single pulse (2.5 kV, 25 uF) using a Gene-Pulser system,
      with subsequent culture on LBG medium containing glycine and
      isonicotinic acid hydrazide (INH). Transformation efficiency of MLB133
      was up to 100-fold higher than for AS019 and, when using heterologous
      derived DNA, MLB133 showed efficiencies comparable to, or better than,
      RM3 and RM4, demonstrating the importance of cell surface structures in
      impeding DNA uptake. MLB133 had a thinner cell wall than AS019, and
      growth in glycine or INH further diminished its thickness. The impact
      of glycine and INH on the mycolic composition of the strains is
      discussed. (20 ref)
AU  - Jang KH
AU  - Britz ML
PT  - Journal Article
TA  - Biotechnol. Lett.
JT  - Biotechnol. Lett.
SO  - Biotechnol. Lett. 2000 22: 539-545.

PMID- 8867385
VI  - 136
DP  - 1996
TI  - Analysis of nucleotide methylation in DNA from Corynebacterium glutamicum and related species.
PG  - 309-315
AB  - Plasmid DNA (pCSL17) isolated from Corynebacterium glutamicum transformed recipient McrBC+
      strains of Escherichia coli with lower efficiency than McrBC- strains, confirming a previous
      report by Tauch et al. which inferred that C. glutamicum DNA contains methylcytidine.
      Analysis of nucleotides in C. glutamicum-derived chromosomal and plasmid DNA failed to detect
      significant levels of methylated adenosine, but methylated cytidine was readily detected.
      Restriction enzymes which are inhibited by the presence of methylcytidine in their recognition
      sequence failed to cut pCSL17 from C. glutamicum, whereas enzymes which require methylation at
      adenosine in GATC sequences failed to cut.  Failure of HaeIII to cut two specific sites of C.
      glutamicum-derived pCSL17 identified the first cytidine in the sequence GGCCGC as one target
      of methylation in this species, which contains the methyltransferase recognition sequence.
      Although Brevibacterium lactofermentum-derived DNA showed a similar methylation pattern by
      HPLC analysis, HaeIII cleaved these GGCCGC sites, suggesting differences in the specificity of
      methylation between these two species.  Results for all analyses of B. flavum DNA were
      identical to those for C. glutamicum.
AU  - Jang KH
AU  - Chambers P
AU  - Britz ML
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1996 136: 309-315.

PMID- 
VI  - 11
DP  - 2001
TI  - Identification of a sequence containing methylated cytidine in Corynebacterium glutamicum and Brevibacterium flavum using bisulfite DNA derivatization and sequencing.
PG  - 819-824
AB  - The principal DNA modification systems of the amino-acid-producing bacteria Corynebacterium
      glutamicum AS019, Brevibacterium flavum BF4,
      and B. lactofermentum BL1 was investigated using two approaches;
      digestion of plasmid DNA isolated from these species using TseI and
      Fnu4HI, and sequence analysis of the putative methyltransferase target
      sites following the derivatization of DNA using metabisulfite
      treatment. The C. glutamicum and B. flavum strains showed similar
      digestion patterns to the two enzymes, indicating that the target for
      cytidine methyltransferase recognizes 5'-GCSGC-3' (where S is either G
      or C). Mapping the methylated cytidine sites by bisulfite
      derivatization, followed by PCR amplification and sequencing, was only
      possible when the protocol included an additional step eliminating any
      underivatized DNA after PCR amplification, thereby indicating that the
      derivatization was not 100% efficient. This may have been due to the
      high G-C content of this genus. It was confirmed that C. glutamicum
      AS019 and B. flavum BF4 methylated the cytidine in the Gm(5)CCGC
      sequences, yet there were no similar patterns of methylation in B.
      lactofermentum, which was consistent with the distinctive degradation
      pattern seen for the above enzymes. These findings demonstrate the
      successful application of a modified bisulfite derivatization method
      with the Corynebacterium species for determining methylation patterns,
      and showed that different species in the genus contain distinctive
      restriction and modification systems.
AU  - Jang KH
AU  - Chambers PJ
AU  - Britz ML
PT  - Journal Article
TA  - J. Microbiol. Biotechnol.
JT  - J. Microbiol. Biotechnol.
SO  - J. Microbiol. Biotechnol. 2001 11: 819-824.

PMID- 19722184
VI  - 5
DP  - 2009
TI  - Restriction-Enzyme-Coded Gold-Nanoparticle Probes for Multiplexed DNA Detection.
PG  - 2665-2668
AB  - The development of a multiplexed DNA detection assay has been of great interest in
      gene-expression profiling, drug screening, clinical diagnostics, and the detection of
      pathogens. However, it is still a challenging task to detect many different targets in one
      sample while retaining high target sensitivity. Restriction enzymes that can recognize and
      cleave specific double-stranded DNA (dsDNA) sequences have been widely used in molecular
      biology and genetic engineering.  Over 2000 site-specific endonucleases have been identified
      so far. Restriction enzymes have been used with DNA-modified gold nanoparticles (AuNPs) in
      various applications, such as release of the particle from the surface, conformational effects
      of nanoparticles on bioactivity, nanoparticle assembly and disassembly, and optimal conditions
      of efficient biomanipulation. The availability of numerous enzymatic restriction DNA sequences
      as well as the high specificity of restriction enzymes could be very useful aspects in a
      multiplexed DNA detection assay.
AU  - Jang KJ
AU  - Lee H
AU  - Jin HL
AU  - Park Y
AU  - Nam JM
PT  - Journal Article
TA  - Small
JT  - Small
SO  - Small 2009 5: 2665-2668.

PMID- 22628497
VI  - 194
DP  - 2012
TI  - Genome Sequence of Cold-Adapted Pseudomonas mandelii Strain JR-1.
PG  - 3263
AB  - Pseudomonas mandelii is a cold-adapted bacterium that can grow at 4 degrees C but not at 37
      degrees C. Here we report the draft genome sequence of P. mandelii
      strain JR-1.
AU  - Jang SH
AU  - Kim J
AU  - Kim J
AU  - Hong S
AU  - Lee C
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3263.

PMID- 20976608
VI  - 156
DP  - 2011
TI  - Complete nucleotide sequence of the temperate bacteriophage LBR48, a new member of the family Myoviridae.
PG  - 319-322
AB  - The complete genomic sequence of LBR48, a temperate bacteriophage induced
      from a lysogenic strain of Lactobacillus brevis, was found to be 48,211
      nucleotides long and to contain 90 putative open reading frames. Based on
      structural characteristics obtained from microscopic analysis and nucleic
      acid sequence determination, phage LBR48 can be classified as a member of
      the family Myoviridae. Analysis of the genome showed the conserved gene
      order of previously reported phages of the family Siphoviridae from lactic
      acid bacteria, despite low nucleotide sequence similarity. Analysis of the
      attachment sites revealed 15-nucleotide-long core sequences.
AU  - Jang SH
AU  - Yoon BH
AU  - Chang HI
PT  - Journal Article
TA  - Arch. Virol.
JT  - Arch. Virol.
SO  - Arch. Virol. 2011 156: 319-322.

PMID- 21551310
VI  - 193
DP  - 2011
TI  - Genome sequence of strain IMCC3088, a proteorhodopsin-containing marine bacterium belonging to the OM60/NOR5 clade.
PG  - 3415-3416
AB  - Strain IMCC3088, cultivated from the Yellow Sea, is a novel isolate belonging to the OM60/NOR5
      clade and is closely related to clone OM241,
      Congregibacter litoralis, and strain HTCC2080. Here the genome sequence of
      strain IMCC3088 is presented, showing the absence of photosynthetic gene
      clusters and the presence of proteorhodopsin.
AU  - Jang Y
AU  - Oh HM
AU  - Kang I
AU  - Lee K
AU  - Yang SJ
AU  - Cho JC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3415-3416.

PMID- 21602334
VI  - 193
DP  - 2011
TI  - Genome Sequence of Strain IMCC1989, a Novel Member of the Marine Gammaproteobacteria.
PG  - 3672-3673
AB  - Strain IMCC1989 is a novel member of the oligotrophic marine Gammaproteobateria (OMG) group,
      and is closely related with a symbiont
      group of genera Teredinibacter and 'Candidatus Endobugula'. Here we
      present the genome sequence of strain IMCC1989 that was isolated from the
      Yellow Sea by using dilution-to-extinction culturing.
AU  - Jang Y
AU  - Oh HM
AU  - Kim H
AU  - Kang I
AU  - Cho JC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3672-3673.

PMID- 29545297
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Vibrio parahaemolyticus Strain VP14, Isolated from a Penaeus vannamei Culture Farm.
PG  - e00149-18
AB  - Here, we report the draft genome sequence of an isolate of Vibrio parahaemolyticus, VP14,
      recovered from the gut of Penaeus vannamei shrimp farmed
      in southern India. The genome of VP14 comprised 5,224,046 bp with a GC content of
      45.3% and contained 5,326 genes, including 4,972 coding sequences.
AU  - Jangam AK
AU  - Bhuvaneswari T
AU  - Krishnan AN
AU  - Katneni VK
AU  - Avunje S
AU  - Grover M
AU  - Kumar S
AU  - Alavandi SV
AU  - Vijayan KK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00149-18.

PMID- 23012274
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Alkaliphilic Bacterium Nitritalea halalkaliphila Type Strain LW7, Isolated from Lonar Lake, India.
PG  - 5688-5689
AB  - An alkaliphilic bacterium, Nitritalea halalkaliphila LW7, which belongs to the family
      Cyclobacteriacae in the phylum Bacteroidetes, was isolated from Lonar Lake
      in Maharastra, India. Here we announce the draft genome sequence of the type
      strain LW7, which contains 3,633,701 bp with a G+C content of 48.58%.
AU  - Jangir PK
AU  - Singh A
AU  - Shivaji S
AU  - Sharma R
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5688-5689.

PMID- 23043000
VI  - 194
DP  - 2012
TI  - The genome sequence of the bacterium Streptomyces davawensis JCM 4913 and heterologous production of the unique antibiotic roseoflavin.
PG  - 6818-6827
AB  - Streptoymces davawensis JCM 4913 synthesizes the antibiotic roseoflavin, a structural
      riboflavin (vitamin B(2)) analog. Here we report the 9,466,619 base
      pair linear chromosome of S. davawensis JCM 4913 and a 89,331 base pair linear
      plasmid. The sequence has an average G + C content of 70.58% and contains six
      rRNA operons (16S-23S-5S) and 69 tRNA genes. The 8,616 predicted protein-coding
      sequences include 32 clusters coding for secondary metabolites several of which
      are unique to S. davawensis. The chromosome contains long terminal inverted
      repeats of 33,255 bp each and atypical telomeres. Sequence analysis with regard
      to riboflavin biosynthesis revealed three different patterns of gene organization
      in Streptomyces species. Heterologous expression of a set of genes present on a
      subgenomic fragment of S. davawensis resulted in the production of roseoflavin by
      the host Streptomyces coelicolor M1152. Phylogenetic analysis revealed that S.
      davawensis is a close relative to Streptomyces cinnabarinus and, much to our
      surprise, we found that the latter bacterium is a roseoflavin producer as well.
AU  - Jankowitsch F
AU  - Schwarz J
AU  - Ruckert C
AU  - Gust B
AU  - Szczepanowski R
AU  - Blom J
AU  - Pelzer S
AU  - Kalinowski J
AU  - Mack M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6818-6827.

PMID- 1727392
VI  - 6
DP  - 1992
TI  - Molecular cloning and expression of T-even phage specific restriction enzyme coded by drug resistance plasmid Rts1.
PG  - A216
AB  - Rts1 is a drug resistance factor which restricts the growth of T-even phages at
      32C but not at 42C (Ishaq & Kaji, 1980, J. Biol. Chem. 255:4040).  Using
      ampicillin and E. coli bacteriophage T4 double selection, a 2.4 kilobase (kb)
      EcoRI fragment of Rts1 DNA was cloned into pUC19 and pBluescript SK+ plasmids.
      The determinant carried by the insert codes for restriction of multiplication
      of T-even phages in E. coli 20SO.  The restriction phenomenon appeared
      independently from the orientation of the insert relative to the lac promoter
      of the carrier plasmids suggesting that the expression of the responsible
      determinant was controlled by its own promoter.  Nucleotide squence
      determination of the entire insert revealed the presence of two larger open
      reading frames (ORFs), both on the same DNA strand.  One, coding for 294 amino
      acids, proved to be related to phage restriction because deletions within this
      ORF by various restriction endonucleases inactivated the activity.  Unusaul
      feature of this ORF is that the distance between the most likely S.D. sequence
      and the ATG codon spans only two nucleotides.
AU  - Janosi L
AU  - Kaji A
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1992 6: A216.

PMID- 8078071
VI  - 242
DP  - 1994
TI  - Molecular cloning and expression of a novel hydroxymethylcytosine-specific restriction enzyme (PvuRts1I) modulated by glucosylation of DNA.
PG  - 45-61
AB  - The kanamycin resistance plasmid Rts1 restricts the growth of bacteriophage T2, T4 and T6. The
      DNA of these phage contains hydroxymethylcytosine (HMC) in place of regular cytosine and is
      modified by glycosylation. When HMC is not glucosylated, as in the DNA of glucosyl
      transferase-deficient T4 phage, this restriction becomes less apparent, a phenomenon not
      observed with any other known restriction systems. On the other hand, glucosylation of HMC to
      T6 phage leads to a less efficient restriction, while restriction of bacteriophage T2 remains
      unchanged. The modulating effect of glucose cannot be seen when cells contain a large amount
      of this enzyme, as in the case when multiple copies of its determinant are present in the
      cells. T-odd phage and bacteriophage lambda are not restricted by Rts1 suggesting that the
      restriction is specific to DNA containing HMC. The restriction phenotype is due to a single
      gene coding for a polypeptide of 293 amino acids. This enzyme has been named PvuRts1I. A gene
      with the sequence motifs similar to modification enzymes was found upstream of the gene coding
      for PvuRts1I. This gene, however, neither modifies the restriction phenotype of PvuRts1I, nor
      codes for detectable modification enzyme. T4 mutants with increased resistance to PvuRts1I
      appear to have deficiency in their beta-glucosyl transferase enzyme.
AU  - Janosi L
AU  - Yonemitsu H
AU  - Hong H
AU  - Kaji A
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1994 242: 45-61.

PMID- 23640377
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of the Probiotic Bifidobacterium thermophilum Strain RBL67.
PG  - e00191-13
AB  - Bifidobacterium thermophilum RBL67, an isolate from infant feces, exhibits bacteriocin-like
      antimicrobial activity against Listeria spp. and Salmonella spp.
      and protects HT29-MTX cells against Salmonella infection. Here, the complete
      genome sequence of the probiotic B. thermophilum strain RBL67 is presented.
AU  - Jans C
AU  - Lacroix C
AU  - Follador R
AU  - Stevens MJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00191-13.

PMID- 28935727
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of Lactobacillus curvatus KG6, L. curvatus MRS6, and Lactobacillus sakei FAM18311, Isolated from Fermented Meat Products.
PG  - e00915-17
AB  - The genomes of Lactobacillus curvatus KG6, L. curvatus MRS6, and Lactobacillus sakei FAM18311
      were sequenced and assembled using PacBio single-molecule
      real-time (SMRT) technology. The strains were isolated from Swiss fermented meat
      products. Circular chromosomes were of 1.98 Mbp (KG6), 2.11 Mbp (MRS6), and 1.95
      Mbp (FAM18311), with a G+C content of 41.3 to 42.0%.
AU  - Jans C
AU  - Lagler S
AU  - Lacroix C
AU  - Meile L
AU  - Stevens MJA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00915-17.

PMID- 8632480
VI  - 257
DP  - 1996
TI  - The type I restriction endonuclease R.EcoR124I: over-production and biochemical properties.
PG  - 977-991
AB  - In this paper we describe a two-plasmid system which allows over-production of
      the R.EcoR124I restriction endonuclease.  The endonuclease has been purified to homogeneity in
      milligram amounts and has been shown to be fully active for both restriction and modification.
      Unexpectedly, the enzyme was found to require only ATP and Mg2+ for ATPase activity and
      DNA cleavage; S-adenosyl methionine (SAM), which has been described as a cofactor of type I
      restriction enzymes, is not required by R.EcoR124I.  However, SAM was found to stimulate the
      rate of ATPase activity and DNA cleavage.  This may occur through an increase in specific DNA
      binding by R.EcoR124I in the presence of SAM, as indicated by our surface plasmon resonance
      experiments.  These functional differences from the well described R.EcoKI restriction
      endonuclease are reflected in a possible structural difference between the two enzymes, namely
      that
      the stoichiometry of R.EcoR124I appears to be R1M2S1 while that of R.EcoKI is R2M2S1.
      Supercoiled DNA with one or two SR124I recognition sites is cleaved by the same mechanism
      inferring cooperation between specifically bound and excess enzymes.  Nicked-circle DNA is an
      intermediate of cleavage reaction.  Cleavage of DNA was inhibited by an increased degree of
      negative supercoiling, which may reflect an increased difficulty for the enzyme to translocate
      the
      DNA.  Hemi-methylated DNA was the preferred substrate for methylation.
AU  - Janscak P
AU  - Abadjieva A
AU  - Firman K
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1996 257: 977-991.

PMID- 10656812
VI  - 295
DP  - 2000
TI  - DNA supercoiling during ATP-dependent DNA translocation by the type I restriction enzyme EcoAI.
PG  - 1089-1099
AB  - Type I restriction enzymes cleave DNA at non-specific sites far from their recognition
      sequence as a consequence of ATP-dependent DNA translocation past the
      enzyme. During this reaction, the enzyme remains bound to the recognition sequence and
      translocates DNA towards itself simultaneously from both directions, generating
      DNA loops, which appear to be supercoiled when visualised by electron microscopy. To further
      investigate the mechanism of DNA translocation by type I restriction
      enzymes, we have probed the reaction intermediates with DNA topoisomerases. A DNA
      cleavage-deficient mutant of EcoAI, which has normal DNA translocation and
      ATPase activities, was used in these DNA supercoiling assays. In the presence of eubacterial
      DNA topoisomerase I, which specifically removes negative supercoils, the
      EcoAI mutant introduced positive supercoils into relaxed plasmid DNA substrate in a reaction
      dependent on ATP hydrolysis. The same DNA supercoiling activity followed by
      DNA cleavage was observed with the wild-type EcoAI endonuclease. Positive supercoils were not
      seen when eubacterial DNA topoisomerase I was replaced by eukaryotic
      DNA topoisomerase I, which removes both positive and negative supercoils. Furthermore,
      addition of eukaryotic DNA topoisomerase I to the product of the supercoiling
      reaction resulted in its rapid relaxation. These results are consistent with a model in which
      EcoAI translocation along the helical path of closed circular DNA duplex
      simultaneously generates positive supercoils ahead and negative supercoils behind the moving
      complex in the contracting and expanding DNA loops, respectively. In addition,
      we show that the highly positively supercoiled DNA generated by the EcoAI mutant is cleaved by
      EcoAI wild-type endonuclease much more slowly than relaxed DNA. This
      suggests that the topological changes in the DNA substrate associated with DNA translocation
      by type I restriction enzymes do not appear to be the trigger for DNA
      cleavage.
AU  - Janscak P
AU  - Bickle TA
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2000 295: 1089-1099.

PMID- 9837717
VI  - 284
DP  - 1998
TI  - The DNA recognition subunit of the type IB restriction-modification enzyme EcoAI tolerates circular permutations of its polypeptide chain.
PG  - 937-948
AB  - The DNA specificity subunit (HsdS) of type I restriction-modification enzymes is composed of
      two independent target recognition domains and several regions whose amino acid sequence is
      conserved within an enzyme family.  The conserved regions participate in intersubunit
      interactions with two modification subunits (HsdM) and two restriction subunits (HsdR) to form
      the complete endonuclease.  It has been proposed that the domains of the HsdS subunit have a
      circular organization providing the required symmetry for their interaction with the other
      subunits and with the bipartite DNA target.  To test this model, we circularly permuted the
      HsdS subunit of the type IB R-M enzyme EcoAI at the DNA level by direct linkage of codons for
      original termini and introduction of new termini elsewhere along the N-terminal and central
      conserved regions.  By analysing the activity of mutant enzymes, two circularly permuted
      variants of HsdS that had termini located at equivalent positions in the N-terminal and
      central repeats, respectively, were found to fold into a functional DNA recognition subunit
      with wild-type specificity, suggesting a close proximity of the N and C termini in the native
      protein.  The wild-type HsdS subunit was purified to homogeneity and shown to form a stable
      trimeric complex with HsdM, M2S1, which was fully active as a DNA methyltransferase.  Gel
      electrophoretic mobility shift assays revealed that the HsdS protein alone was not able to
      form a specific complex with a 30-mer oligoduplex containing a single EcoAI recognition site.
      However, addition of stoichiometric amounts of hsdM to HsdS led to efficient specific DNA
      binding.  Our data provide evidence for the circular organization of domains of the HsdS
      subunit.  In addition, they suggest a possible role of hsdM subunits in the formation of this
      structure.
AU  - Janscak P
AU  - Bickle TA
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1998 284: 937-948.

PMID- 9742247
VI  - 26
DP  - 1998
TI  - Analysis of the subunit assembly of the type IC restriction-modification enzyme EcoR124I.
PG  - 4439-4445
AB  - Type I restriction-modification enzymes are composed of three different subunits, of which
      HsdS determines DNA specificity, HsdM is responsible for DNA methylation and HsdR is required
      for restriction.  The HsdM and hsdS subunits can also form an independent DNA
      methyltransferase with a subunit stoichiometry of M2S1.  We found that the purified EcoR124I
      R-M enzyme was a mixture of two species as detected by the presence of two differently
      migrating specific DNA-protein complexes in a gel retardation assay.  An analysis of protein
      subunits isolated from the complexes indicated that the larger species had a stoichiometry of
      R2M2S1 and the smaller species had a stoichiometry of R1M2S1.  In vitro analysis of subunit
      assembly revealed that while binding of the first HsdR subunit to the M2S1 complex with an
      apparent Kd of ~2.4 x 10^-7M.  Functional assays have shown that only the R2M2S1 complex is
      capable of DNA cleavage, however, the R1M2S1 complex retains ATPase activity.  The relevance
      of this situation is discussed in terms of the regulation of restriction activity in vivo upon
      conjugative transfer of a plasmid-born R-M system into an unmodified host cell.
AU  - Janscak P
AU  - Dryden DTF
AU  - Firman K
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1998 26: 4439-4445.

PMID- 10228175
VI  - 18
DP  - 1999
TI  - DNA translocation blockage, a general mechanism of cleavage site selection by type I restriction enzymes.
PG  - 2638-2647
AB  - Type I restriction enzymes bind to a specific DNA sequence and subsequently translocate DNA
      past the complex to reach a non-specific cleavage site.  We have examined several potential
      blocks to DNA translocation, such as positive supercoiling or a Holliday junction, for their
      ability to trigger DNA cleavage by type I restriction enzymes.  Introduction of positive
      supercoiling into plasmid DNA did not have a significant effect on the rate of DNA cleavage by
      EcoAI endonuclease nor on the enzyme's ability to select cleavage sites randomly throughout
      the DNA molecule.  Thus, positive supercoiling does not prevent DNA translocation.  EcoR124II
      endonuclease cleaved DNA at Holliday junctions present on both linear and negatively
      supercoiled substrates.  The latter substrate was cleaved by a single enzyme molecule at two
      sites, one on either side of the junction, consistent with a bi-directional translocation
      model.  Linear DNA molecules with two recognition sites for endonucleases from different type
      I families were cut between the sites when both enzymes were added simultaneously but not when
      a single enzyme was added.  We propose that type I restriction enzymes can track along a DNA
      substrate irrespective of its topology and cleave DNA at any barrier that is able to halt the
      translocation process.
AU  - Janscak P
AU  - MacWilliams MP
AU  - Sandmeier U
AU  - Nagaraja V
AU  - Bickle TA
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1999 18: 2638-2647.

PMID- 10373579
VI  - 27
DP  - 1999
TI  - Single amino acid substitutions in the HsdR subunit of the type IB restriction enzyme EcoAI uncouple the DNA translocation and DNA cleavage activities of the enzyme.
PG  - 2638-2643
AB  - Type I restriction enzymes bind to specific DNA sequences but subsequently translocate
      non-specific DNA past the complex in a reaction coupled to ATP hydrolysis and cleave DNA at
      any barrier that can halt the translocation process. The restriction subunit of these enzymes,
      HsdR, contains a cluster of seven amino acid sequence motifs typical of helicase superfamily
      II, that are believed to be relevant to the ATP-dependent DNA translocation. Alignment of all
      available HsdR sequences reveals an additional conserved region at the protein N-terminus with
      a consensus sequence reminiscent of the P-D...(D/E)-X-K catalytic motif of many type II
      restriction enzymes. To investigate the role of these conserved residues, we have produced
      mutants of the type IB restriction enzyme EcoAI. We have found that single alanine
      substitutions at Asp-61, Glu-76 and Lys-78 residues of the HsdR subunit abolished the
      enzyme's restriction activity but had no effect on its ATPase and DNA translocation
      activities, suggesting that these residues are part of the active site for DNA cleavage.
AU  - Janscak P
AU  - Sandmeier U
AU  - Bickle TA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1999 27: 2638-2643.

PMID- 11178902
VI  - 306
DP  - 2001
TI  - Subunit assembly and mode of DNA cleavage of the type III restriction endonucleases EcoP1I and EcoP15I.
PG  - 417-431
AB  - DNA cleavage by type III restriction endonucleases requires two inversely oriented asymmetric
      recognition sequences and results from
      ATP-dependent DNA translocation and collision of two enzyme molecules.
      Here, we characterized the structure and mode of action of the related
      EcoP1I and EcoP15I enzymes. Analytical ultracentrifugation and gel
      quantification revealed a common Res(2)Mod(2) subunit stoichiometry.
      Single alanine substitutions in the putative nuclease active site of
      ResP1 and ResP15 abolished DNA but not ATP hydrolysis, whilst a
      substitution in helicase motif VI abolished both activities. Positively
      supercoiled DNA substrates containing a pair of inversely oriented
      recognition sites were cleaved inefficiently, whereas the corresponding
      relaxed and negatively supercoiled substrates were cleaved efficiently,
      suggesting that DNA overtwisting impedes the convergence of the
      translocating enzymes. EcoP1I and EcoP15I could co-operate in DNA
      cleavage on a circular substrate containing several EcoP1I sites
      inversely oriented to a single EcoP15I site; cleavage occurred
      predominantly at the EcoP15I site. EcoP15I alone showed nicking
      activity on these molecules, cutting exclusively the top DNA strand at
      its recognition site. This activity was dependent on enzyme
      concentration and local DNA sequence. The EcoP1I nuclease mutant
      greatly stimulated the EcoP15I nicking activity, while the EcoP1I motif
      VI mutant did not. Moreover, combining an EcoP15I nuclease mutant with
      wild-type EcoP1I resulted in cutting the bottom DNA strand at the
      EcoP15I site. These data suggest that double-strand breaks result from
      top strand cleavage by a Res subunit proximal to the site of cleavage,
      whilst bottom strand cleavage is catalysed by a Res subunit supplied in
      trans by the distal endonuclease in the collision complex.
AU  - Janscak P
AU  - Sandmeier U
AU  - Szczelkun MD
AU  - Bickle TA
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2001 306: 417-431.

PMID- 10612739
VI  - 182
DP  - 2000
TI  - Two temperature-sensitive mutations in the DNA binding subunit of EcoKI with differing properties.
PG  - 99-104
AB  - Two temperature-sensitive mutations in the hsdS gene, which encodes the DNA specificity
      subunit of the type IA restriction-modification system EcoKI, designated Sts1 (Ser(340)Phe)
      and Sts2 (Ala(204)Thr) had a different impact on restriction-modification functions in vitro
      and in vivo. The enzyme activities of the Sts1 mutant were temperature-sensitive in vitro and
      were reduced even at 30 degrees C (permissive temperature). Gel retardation assays revealed
      that the Sts1 mutant had significantly decreased DNA binding, which was temperature-sensitive.
      In contrast the Sts2 mutant did not show differences from the wild-type enzyme even at 42
      degrees C. Unlike the HsdSts1 subunit, the HsdSts2 subunit was not able to compete with the
      wild-type subunit in assembly of the restriction enzyme in vivo, suggesting that the Sts2
      mutation affects subunit assembly. Thus, it appears that these two mutations map two important
      regions in HsdS subunit responsible for DNA-protein and protein-protein interactions,
      respectively.
AU  - Janscak P
AU  - Weiserova M
AU  - Hubacek J
AU  - Holubova I
AU  - Dutta CF
AU  - Firman K
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2000 182: 99-104.

PMID- 20233937
VI  - 192
DP  - 2010
TI  - Genome sequence of the edible cyanobacterium Arthrospira sp. PCC 8005.
PG  - 2465-2466
AB  - We determined the genome sequence of Arthrospira sp. PCC 8005, a cyanobacterial strain of
      great interest to the European Space Agency for
      its nutritive value and oxygenic properties in the Micro-Ecological Life
      Support System Alternative (MELiSSA) biological life support system for
      long-term manned missions into space.
AU  - Janssen PJ
AU  - Morin N
AU  - Mergeay M
AU  - Leroy B
AU  - Wattiez R
AU  - Vallaeys T
AU  - Waleron K
AU  - Waleron M
AU  - Wilmotte A
AU  - Quillardet P
AU  - de Marsac NT
AU  - Talla E
AU  - Zhang CC
AU  - Leys N
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 2465-2466.

PMID- 28495769
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Bacillus toyonensis VU-DES13, Isolated from Folsomia candida (Collembola: Entomobryidae).
PG  - e00287-17
AB  - We present here the draft genome of Bacillus toyonensis VU-DES13, which was isolated from the
      midgut of the soil-living springtail Folsomia candida Previous
      research revealed the presence of gene clusters for the biosynthesis of various
      secondary metabolites, including beta-lactam antibiotics, in the host's genome.
      The genome data are discussed in the light of the antimicrobial properties
      against fungi and oomycetes and a high level of beta-lactam resistance of the
      isolate.
AU  - Janssens TKS
AU  - de Boer TE
AU  - Agamennone V
AU  - Zaagman N
AU  - van Straalen NM
AU  - Roelofs D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00287-17.

PMID- 21951522
VI  - 13
DP  - 2011
TI  - Genome of alkaliphilic Bacillus pseudofirmus OF4 reveals adaptations that support the ability to grow in an external pH range from 7.5 to 11.4.
PG  - 3289-3309
AB  - Bacillus pseudofirmus OF4 is an extreme but facultative alkaliphile that grows
      non-fermentatively in a pH range from 7.5 to above 11.4 and can withstand large
      sudden increases in external pH. It is a model organism for studies of
      bioenergetics at high pH, at which energy demands are higher than at neutral pH
      because both cytoplasmic pH homeostasis and ATP synthesis require more energy.
      The alkaliphile also tolerates a cytoplasmic pH > 9.0 at external pH values at
      which the pH homeostasis capacity is exceeded, and manages other stresses that
      are exacerbated at alkaline pH, e.g. sodium, oxidative and cell wall stresses.
      The genome of B. pseudofirmus OF4 includes two plasmids that are lost from some
      mutants without viability loss. The plasmids may provide a reservoir of mobile
      elements that promote adaptive chromosomal rearrangements under particular
      environmental conditions. The genome also reveals a more acidic pI profile for
      proteins exposed on the outer surface than found in neutralophiles. A large array
      of transporters and regulatory genes are predicted to protect the alkaliphile
      from its overlapping stresses. In addition, unanticipated metabolic versatility
      was observed, which could ensure requisite energy for alkaliphily under diverse
      conditions.
AU  - Janto B et al
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2011 13: 3289-3309.

PMID- 
VI  - 17
DP  - 1989
TI  - Restriction Enzymes and their Applications.
PG  - 1-204
AB  - 
AU  - Janulaitis A
PT  - Journal Article
TA  - Trends in Science and Technology. Biotechnology series.
JT  - Trends in Science and Technology. Biotechnology series.
SO  - Trends in Science and Technology. Biotechnology series. 1989 17: 1-204.

PMID- 
VI  - 29
DP  - 1984
TI  - Restriction endonucleases.
PG  - 133-138
AB  - 
AU  - Janulaitis A
PT  - Journal Article
TA  - Zh. Vses. Khim.
JT  - Zh. Vses. Khim.
SO  - Zh. Vses. Khim. 1984 29: 133-138.

PMID- Not carried by PubMed...
VI  - 0
DP  - 1996
TI  - A novel approach to the study of DNA-protein interactions using related restriction endonucleases that recognize overlapping nucleotide sequences.
PG  - 28-31
AB  - Multiple attempts to change the specificity of restriction enzymes by substituting amino acids
      predicted by crystallographic analysis to be involved in substrate recognition have so far
      been unsuccessful.  In general, the results argue that the potential of this approach in study
      of RE is limited.  A novel approach to the analysis of such structure-function relationships
      is therefore suggested, which is based on the investigation of structurally related RE which
      recognize overlapping (but not identical) nucleotide sequences.  In an attempt to identify
      such RE, 22 genes encoding RE were cloned, sequenced, and their deduced amino acid sequences
      compared with those of previously described RE by computer analysis.  For the first time a
      group of 18 RE is demonstrated, which can be arranged in pairs (9 pairs) on the basis of
      significant overlap in recognition sequences, and some aa sequence similarity.  Indirect
      evidence is given to support the contention that members of each pair are structurally related
      to provide, in turn, the basis of a new model system for investigation of the role of
      structural changes in the development of changes in specificity.
AU  - Janulaitis A
PT  - Journal Article
TA  - Biologija
JT  - Biologija
SO  - Biologija 1996 0: 28-31.

PMID- 6299786
VI  - 151
DP  - 1983
TI  - A new sequence-specific endonuclease from Gluconobacter suboxydans.
PG  - 243-247
AB  - The isolation of sequence-specific endonucleases from Gluconobacter
      dioxyacetonicus (IAM 1814 and IAM 1840) and Gluconobacter oxydans sub.
      melanogenes (IAM 1836) has been reported.  We have examined six Gluconobacter
      suboxydans strains for the presence of the enzymes of this type and discovered
      in two of them restriction endonucleases of identical specificity (named GsuI
      and GsbI).Here, we describe the isolation procedure of the new site-specific
      endonuclease GsuI, which recognizes a hexanucleotide sequence 5' ...CTCCAG.
AU  - Janulaitis A
AU  - Bitinaite J
AU  - Jaskeleviciene B
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1983 151: 243-247.

PMID- 3074011
VI  - 74
DP  - 1988
TI  - Taxonomic specificity of restriction-modification enzymes.
PG  - 229-232
AB  - Meeting Abstract
AU  - Janulaitis A
AU  - Kazlauskiene R
AU  - Lazareviciute L
AU  - Gilvonauskaite R
AU  - Steponaviciene D
AU  - Jagelavicius M
AU  - Petrusyte M
AU  - Bitinaite J
AU  - Vezeviciute Z
AU  - Kiuduliene E
AU  - Butkus V
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 229-232.

PMID- 6884523
VI  - 161
DP  - 1983
TI  - Cytosine modification in DNA by BcnI methylase yields N4-methylcytosine.
PG  - 131-134
AB  - The means by which bacteria protect their own DNA from their restriction
      enzymes have not been fully investigated.  In all systems that have been
      studied, cells produce a modification methylase in addition to the retriction
      endonuclease.  Both enzymes recognize the same specific DNA sequence.  Not many
      DNA methylases were studied in detail, but all of those studied methylate
      either adenine to N6-methyladenine (m6A) or cytosine to 5-methylcytosine
      (m5C).Recently a site-specific endonuclease and methylase BcnI, both of which
      recognize the sequence 5'CC(C/G)GG, have been isolated from Bacillus
      centrosporus strain RFLI.  We here describe the property of MBcnI to methylate
      cytosine residues in DNA in vitro at the N4 position yielding N4-methylcytosine
      (m4C).  The same minor base in DNA isolated from B. centrosporus was detected.
      Such an unusual DNA modification is described for the first time.
AU  - Janulaitis A
AU  - Klimasauskas S
AU  - Petrusyte M
AU  - Butkus V
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1983 161: 131-134.

PMID- 6273230
VI  - 134
DP  - 1981
TI  - A new sequence-specific endonuclease from Streptococcus durans.
PG  - 172-174
AB  - Although a relatively large number of sequence-specific deoxyribonucleases
      (class II restriction endonucleases) is now available, new endonucleases with
      unique recognition sites are desirable, as they increase the flexibility of DNA
      analysis and recombinant techniques.  We report here the isolation from
      Streptococcus durans RFL 3 strain of a new enzyme (SduI) of this type, which
      recognizes hexanucleotide palindromic sequence 5'-G(G/A/T)-GC(C/A/T)C
      degenerated at two positions and consequently should cleave at the level of
      nine possible sites.
AU  - Janulaitis A
AU  - Marcinkeviciene L
AU  - Petrusyte M
AU  - Mironov A
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1981 134: 172-174.

PMID- Not included in PubMed...
VI  - 262
DP  - 1982
TI  - A specific endonuclease from Caulobacter fusiformis that cleaves only methylated DNA.
PG  - 241-244
AB  - None
AU  - Janulaitis A
AU  - Marcinkeviciene LY
AU  - Petrusyte MP
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1982 262: 241-244.

PMID- 6311623
VI  - 161
DP  - 1983
TI  - Three sequence-specific endonucleases from Escherichia coli RFL47.
PG  - 213-216
AB  - The characterization of the new restriction enzyme Eco47III recognizing a
      hexanucleotide palindromic sequence 5'AGC^GCT and cleaving, as indicated by the
      arrow, is reported.  It was isolated from Escherichia coli strain RFL47.
      Another two specific endonuclease Eco471 (isoschizomer of AvaII and Ecoz4711
      (isoschizomer of AsuI) were also found in this strain.  There are two Eco47III
      recognition sites on lambda DNA at 20997 and 37060 basepairs.  The central
      Eco47III fragment can be replaced by a cloned fragment in lambda vector mutant
      tR2 gene; i.e. lambda gt.
AU  - Janulaitis A
AU  - Petrusyte M
AU  - Butkus V
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1983 161: 213-216.

PMID- 1334260
VI  - 20
DP  - 1992
TI  - Purification and properties of the Eco57I restriction endonuclease and methylase-prototypes of a new class (type IV).
PG  - 6043-6049
AB  - The Eco57I restriction endonuclease and methylase were purified to homogeneity from the E.coli
      RR1 strain carrying the Eco57IRM genes on a recombinant plasmid. The molecular weight of the
      denaturated methylase is 63 kDa. The restriction endonuclease exists in a monomeric form with
      an apparent molecular weight of 104-108 kDa. R.Eco57I also possesses methylase activity. The
      methylation activities of both enzymes modify the outer A residue in the target sequence
      5'CTGAAG yielding N6-methyladenine. M.Eco57I modifies both strands of the substrate while
      R.Eco57I modifies only one. Only the methylase enzyme is stimulated by Ca2+. The restriction
      endonuclease shows an absolute requirement for Mg2+ and is stimulated by AdoMet. ATP has no
      influence on either activity of the enzymes. The subunit structure and enzymatic properties of
      the Eco57I enzymes distinguish them from all other restriction-modification enzymes that have
      been described previously. Therefore, RM.Eco57I may be regarded as a representative of a novel
      class of restriction-modification systems, and we propose to classify it as type IV.
AU  - Janulaitis A
AU  - Petrusyte M
AU  - Maneliene Z
AU  - Klimasauskas S
AU  - Butkus V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 6043-6049.

PMID- 6277689
VI  - 137
DP  - 1982
TI  - A new restriction endonuclease BcnI from Bacillus centrosporus RFL 1.
PG  - 178-180
AB  - Type II restriction endonucleases have proved to be an indispensable tool in
      DNA cloning and sequencing studies.  Over 200 individual enzymes with >60
      different specificities have been already described.  Here, we describe the
      purification and the determination of cleavage specificity of a novel type II
      restriction endonuclease from Bacillus centrosporus RFL 1.
AU  - Janulaitis A
AU  - Petrusyte MA
AU  - Jaskeleviciene BP
AU  - Krayev AS
AU  - Skryabin KG
AU  - Bayev AA
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1982 137: 178-180.

PMID- Not included in PubMed...
VI  - 257
DP  - 1981
TI  - A new restriction endonuclease BcnI from Bacillus centrosporus RFL1.
PG  - 749-750
AB  - Restriction endonucleases are finding wide use in the study of the structure
      and function of genomes and the production of recombinant DNA molecules.  At
      the present time, more than 50 restriction endonucleases with various substrate
      specificities are known; however, the search for new restriction enzymes, as
      before, is an urgent problem, since the detection of new restriction enzymes
      expands the experimenter's possibilities in solving the indicated problems.
AU  - Janulaitis A
AU  - Petrusyte MP
AU  - Jaskeleviciene BP
AU  - Krayev AS
AU  - Skryabin KG
AU  - Bayev AA
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1981 257: 749-750.

PMID- 6299887
VI  - 20
DP  - 1982
TI  - Cloning of the modification methylase gene of Bacillus centrosporus in Escherichia coli.
PG  - 197-204
AB  - The gene specifying a sequence-specific modification methylase of Bacillus centrosporus has
      been cloned in Escherichia coli using the restriction endonuclease HindIII and the plasmid
      pBR322.  The selection was based on detection of new methylation properties rendering
      recombinant plasmids carrying the methylase gene nonsusceptible to BcnI endonuclease cleavage.
      The presence of a 3.2-kb HindIII fragment in either orientation conferred BcnI resistance on
      the recombinant plasmids.  These results suggest that the BcnI methylase gene is expressed in
      E. coli under the control of a promoter located on the cloned fragment.  The relative level of
      BcnI methylase enzyme in E. coli was similar to that in B. centrosporus.  The recombinant
      clones do not exhibit any BcnI restriction-endonuclease activity.
AU  - Janulaitis A
AU  - Povilionis P
AU  - Sasnauskas K
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1982 20: 197-204.

PMID- Not included in PubMed...
VI  - 6
DP  - 1980
TI  - A new restriction endonuclease, CfrI from Citrobacter freundii.
PG  - 1746-1748
AB  - CfrI, a new site-specific restriction endonuclease, has been isolated from a
      Citrobacter freundii strain.  The enzyme recognizes the sequence 5'
      Py^G-G-C-C-Pu 3' Pu-C-C-G-G^Py in double-stranded DNA and cuts it between Py
      and G residues to give 5'-protruding tetranucleotide ends G-G-C-C.
AU  - Janulaitis A
AU  - Stakenas P
AU  - Jaskeleviciene B
AU  - Lebedenko EN
AU  - Berlin YA
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1980 6: 1746-1748.

PMID- 6617873
VI  - 161
DP  - 1983
TI  - A new site-specific endodeoxyribonuclease from Citrobacter freundii.
PG  - 210-212
AB  - Cfr10I, a site-specific endonuclease from Citrobacter freundii strain RFL10, was isolated. It
      recognizes and cleaves the family of related sequences: 5'Pu^CCGGPy to generate DNA fragments
      with 5' tetranucleotide extensions. Cfr10I may be useful in molecular cloning experiments,
      especially in conjunction with other enzymes which generate the same terminal extensions. ion
      have led to the detection of specific endodeoxyribonucleases (class II restriction
      endonucleases), distinguished by an exceptionally high substrate specificity, which served as
      the prerequisite for their use in molecular genetic and structural investigations of DNA.
AU  - Janulaitis A
AU  - Stakenas PS
AU  - Berlin YA
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1983 161: 210-212.

PMID- 6313311
VI  - 271
DP  - 1983
TI  - Distribution of specific endodeoxyribonucleases in various strains of Citrobacter freundii.
PG  - 483-485
AB  - The discovery of the phenomenon of host specificity at the beginning of the
      fifties and the investigation of its essence, realized in the discovery of
      enzymes of the restriction-modification systems, have made a large contribution
      to the development of modern molecular biology, genetics, and enzymology.  The
      search for and study of enzymes of restriction and modification have led to the
      detection of specific endodeoxyribonucleases (class II restriction
      endonucleases), distinguished by an exceptionally high substrate specificity,
      which served as the prerequisite for their use in molecular genetic and
      structural investigations of DNA.
AU  - Janulaitis A
AU  - Stakenas PS
AU  - Bitinaite JB
AU  - Jaskeleviciene BP
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1983 271: 483-485.

PMID- 6294607
VI  - 10
DP  - 1982
TI  - A new restriction endonuclease from Citrobacter freundii.
PG  - 6521-6530
AB  - CfrI, a new restriction endonuclease of unique substrate specificity, has been
      isolated from a Citrobacter freundii strain.  The enzyme recognizes a
      degenerated sequence PyGGCCPu in double-strand DNA and cleaves it between Py
      and G residues to yield 5'-protruding tetranucleotide ends GGCC.
AU  - Janulaitis A
AU  - Stakenas PS
AU  - Lebedenko EN
AU  - Berlin YA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1982 10: 6521-6530.

PMID- Not included in PubMed...
VI  - 18
DP  - 1983
TI  - Specificity of new restrictases and methylases.  Unusual modification of cytosine in position 4.
PG  - 115-129
AB  - Fourteen restrictases and four methylases were extracted and purified from 14 strains of
      independent origin of the species Citrobacter freundii and Escherichia coli. The nucleotide
      sequences recognized by the restrictases were determined by means of a comparison of the
      character of DNA cleavage by the investigated and known enzymes, by study of the cleavage
      frequency of substrates with a known primary structure, and by the mapping method. It was
      established that Cfr10I is a new prototype recognizing the sequence 5'PuCCGGPy. The other
      enzymes proved to be isoschizomers of known restrictases: Cfr5*, Cfr11I, Eco60I, and Eco61I
      are isoschizomers of EcoRII; Cfr4I, Cfr8I, and Cfr12T, Sau96I; Cfr6I, PvuII; Crf9I, SmaI;
      Eco6I, HgiJII; Eco32I, EcoRV; Eco52I, XmaIII; and Eco56I, NaeI. Several of these enzymes were
      demonstrated for the first time in E. coli and C. freundii. A study of the specificity of the
      methylases M.CfrI, M.Cfr6I, M.Cfr9I, and M.Cfr10I showed that these enzymes recognize the same
      nucleotide sequence as does the restrictase extracted from the same strain. Modification of
      DNA in vitro using M.CfrI and M.Cfr10I results in the production of 5-methylcytosine, and in
      the case of M.Cfr6I and M.Cfr9I, N4-methylcytosine. G, where M.HpaII methylates the inner,
      M.BsuFI/M.MspI the outer cytosine. Also the CCGG recognizing TRD of the multispecific B.
      subtilis phage SPR Mtase is distinct from that of the host enzyme, possibly indicating
      different requirements for TRDs operative in mono- and multispecific enzymes.
AU  - Janulaitis A
AU  - Stakenas PS
AU  - Petrusyte MP
AU  - Bitinaite JB
AU  - Klimasauskas SI
AU  - Butkus VV
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1983 18: 115-129.

PMID- 1334261
VI  - 20
DP  - 1992
TI  - Cloning and sequence analysis of the genes coding for Eco57I type IV restriction-modification enzymes.
PG  - 6051-6056
AB  - A 6.3 kb fragment of E.coli RFL57 DNA coding for the type IV restriction-modification system
      Eco57I was cloned and expressed in E.coli RR1. A 5775 bp region of the cloned fragment was
      sequenced which contains three open reading frames (ORF). The methylase gene is 1623 bp long,
      corresponding to a protein of 543 amino acids (62 kDa); the endonuclease gene is 2991 bp in
      length (997 amino acids, 117 kDa). The two genes are transcribed convergently from different
      strands with their 3'-ends separated by 69 bp. The third short open reading frame (186 bp, 62
      amino acids) has been indentified, that precedes and overlaps by 7 nucleotides the ORF
      encoding the methylase. Comparison of the deduced Eco57I endonuclease and methylase amino acid
      sequences revealed three regions of significant similarity. Two of them resemble the conserved
      sequence motifs characteristic of the DNA [adenine-N6] methylases. The third one shares
      similarity with corresponding regions of the PaeR71, TaqI, CviBIII, PstI, BamHI and HincII.
AU  - Janulaitis A
AU  - Vaisvila R
AU  - Timinskas A
AU  - Klimasauskas S
AU  - Butkus V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 6051-6056.

PMID- 6272608
VI  - 116
DP  - 1981
TI  - A spectrophotometric procedure for the determination of activity of restriction.
PG  - 116-122
AB  - A simple procedure basically applicable for the quantitative determination of
      activity of all restriction endonucleases is described.  Native DNA immobilized
      on cellulose is used as a substrate; after the treatment by restriction
      endonucleases this DNA is released to the solution.  Changes of the optical
      density of the solution containing solubilized DNA permit quantitative
      determination of the restriction endonuclease activity.
AU  - Janulaitis A
AU  - Vaitkevicius DP
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 1981 116: 116-122.

PMID- Not carried by PubMed...
VI  - 1
DP  - 1985
TI  - New methodical approach to development of technology for production of restriction endonucleases.  Development of scheme for isolation of homogeneous preparation of restrictase MvaI.
PG  - 39-51
AB  - Using restrictase MvaI isolated from Microccus varians RJL 19 cells a
      possibility has been investigated for selection of purification schemes of
      restrictases by means of study of binding of a specific enzyme with various
      sorbents (DEAE-cellulose, phosphocellulose, heparinsepharose, blue sepharose,
      Biorex 70 and SP-sephadex) under static conditions.  It has been illustrated
      that the character of interaction of the restrictase under the static
      conditions with various sorbents permits to predict its behavior under
      conditions of the column chromatography and select the effective sorbents,
      sequence of their application and conditions of conducting the column
      chromatography.  A highly effective scheme for purification of MvaI restrictase
      has been created which makes possible to produce electrophoretically
      homogeneous preparation of a specific enzyme as a result of just two stages of
      purification of the cell-free extract of M. varians RJL19 on phosphocellulose
      and blue sepharose.  The prospects of application of the recommended methodical
      approach for rapid development of a process for production on restrictases are
      discussed.
AU  - Janulaitis A
AU  - Vaitkevicius DP
PT  - Journal Article
TA  - Biotekhnologiya
JT  - Biotekhnologiya
SO  - Biotekhnologiya 1985 1: 39-51.

PMID- 23994162
VI  - 166
DP  - 2013
TI  - Expanding the diversity of oenococcal bacteriophages: Insights into a novel group based on the integrase sequence.
PG  - 331-340
AB  - Temperate bacteriophages are a contributor of the genetic diversity in the lactic
      acid bacterium Oenococcus oeni. We used a classification scheme for oenococcal
      prophages based on integrase gene polymorphism, to analyze a collection of
      Oenococcus strains mostly isolated in the area of Bordeaux, which represented the
      major lineages identified through MLST schemes in the species. Genome sequences
      of oenococcal prophages were clustered into four integrase groups (A to D) which
      were related to the chromosomal integration site. The prevalence of each group
      was determined and we could show that members of the intB- and intC-prophage
      groups were rare in our panel of strains. Our study focused on the so far
      uncharacterized members of the intD-group. Various intD viruses could be easily
      isolated from wine samples, while intD lysogens could be induced to produce
      phages active against two permissive O. oeni isolates. These data support the
      role of this prophage group in the biology of O. oeni. Global alignment of three
      relevant intD-prophages revealed significant conservation and highlighted a
      number of unique ORFs that may contribute to phage and lysogen fitness.
AU  - Jaomanjaka F
AU  - Ballestra P
AU  - Dols-Lafargue M
AU  - Le Marrec C
PT  - Journal Article
TA  - Int. J. Food Microbiol.
JT  - Int. J. Food Microbiol.
SO  - Int. J. Food Microbiol. 2013 166: 331-340.

PMID- 30533896
VI  - 7
DP  - 2018
TI  - Complete Genome Sequence of Lytic Oenococcus oeni Bacteriophage OE33PA.
PG  - e00818-18
AB  - Oenococcus oeni is the most common species of lactic acid bacteria associated with malolactic
      fermentation in wine. Here, we report the genome sequence of the
      lytic phage OE33PA (vB_OeS_OE33PA). It has a morphotype similar to that of
      members of the Siphoviridae family, a linear 39,866-bp double-stranded genome
      with cohesive ends, and 57 predicted open reading frames.
AU  - Jaomanjaka F
AU  - Claisse O
AU  - Philippe C
AU  - Le Marrec C
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e00818-18.

PMID- 26272563
VI  - 3
DP  - 2015
TI  - Genome Sequences of Three Oenococcus oeni Strains Isolated from Maipo Valley, Chile.
PG  - e00866-15
AB  - Oenococcus oeni is part of the microbial terroir involved in wine production. Here, we present
      three genome sequences of O. oeni strains isolated from
      spontaneous malolactic fermentation of cultivar Cabernet Sauvignon Maipo Valley,
      Chile.
AU  - Jara C
AU  - Romero J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00866-15.

PMID- 19740766
VI  - 37
DP  - 2009
TI  - High-resolution profiling of homing endonuclease binding and catalytic specificity using yeast surface display.
PG  - 6871-6880
AB  - Experimental analysis and manipulation of protein-DNA interactions pose unique biophysical
      challenges arising from the structural and chemical
      homogeneity of DNA polymers. We report the use of yeast surface display
      for analytical and selection-based applications for the interaction
      between a LAGLIDADG homing endonuclease and its DNA target. Quantitative
      flow cytometry using oligonucleotide substrates facilitated a complete
      profiling of specificity, both for DNA-binding and catalysis, with single
      base pair resolution. These analyses revealed a comprehensive segregation
      of binding specificity and affinity to one half of the pseudo-dimeric
      interaction, while the entire interface contributed specificity at the
      level of catalysis. A single round of targeted mutagenesis with tandem
      affinity and catalytic selection steps provided mechanistic insights to
      the origins of binding and catalytic specificity. These methods represent
      a dynamic new approach for interrogating specificity in protein-DNA
      interactions.
AU  - Jarjour J
AU  - West-Foyle H
AU  - Certo MT
AU  - Hubert CG
AU  - Doyle L
AU  - Getz MM
AU  - Stoddard BL
AU  - Scharenberg AM
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: 6871-6880.

PMID- 16787976
VI  - 22
DP  - 2006
TI  - Cleaver: software for identifying taxon specific restriction endonuclease recognition sites.
PG  - 2160-2161
AB  - Cleaver is an application for identifying restriction endonuclease recognition sites that
      occur in some taxa, but not in others.
      Differences in DNA fragment restriction patterns among taxa are the
      basis for many diagnostic assays for taxonomic identification and are
      used in procedures for removing the DNA of some taxa from pools of DNA
      from mixed sources. Cleaver analyses restriction digestion of groups of
      orthologous DNA sequences simultaneously to allow identification of
      differences in restriction pattern among the fragments derived from
      different taxa.
AU  - Jarman SN
PT  - Journal Article
TA  - Bioinformatics
JT  - Bioinformatics
SO  - Bioinformatics 2006 22: 2160-2161.

PMID- Not included in PubMed...
VI  - 208
DP  - 1987
TI  - Paucity of the Sau3AI recognition sequence (GATC) in the genome of Methanococcus voltae.
PG  - 191-194
AB  - High molecular weight genomic DNA isolated from the archaebacterium
      Methanococcus voltae by alkaline-SDS lysis was not effectively digested with
      the restriction enzyme Sau3AI, which recognizes the base sequence GATC.  M.
      voltae DNA was also resistant to digestion by MboI and BamHI which recognize
      sites containing the same GATC sequence.  Examination of a M. voltae genomic
      library prepared in Escherichia coli JM83 with a pUC vector revealed that the
      5-10 kb inserts were still resistant to Sau3AI digestion, indicating a likely
      lack of the GATC sequence in M. voltae DNA.
AU  - Jarrell KF
AU  - Julseth C
AU  - Pearson B
AU  - Kuzio J
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1987 208: 191-194.

PMID- 19897643
VI  - 192
DP  - 2010
TI  - Short-term Signatures of Evolutionary Change in the Salmonella enterica serovar Typhimurium 14028 Genome.
PG  - 560-567
AB  - Salmonella enterica serovar Typhimurium is a Gram-negative pathogen that causes
      gastroenteritis in humans and a typhoid-like disease in mice and is often used as a model for
      the disease promoted by the human-adapted S. enterica serovar Typhi. Despite its health
      importance, the only S. Typhimurium strain for which the complete genomic sequence has been
      determined is the avirulent LT2 strain, which is extensively used in genetic and physiologic
      studies. Here, we report the complete genomic sequence of the S. Typhimurium strain 14028s, as
      well as those of its progenitor and two additional derivatives. Comparison of these S.
      Typhimurium genomes revealed differences in the patterns of sequence evolution and the
      complete inventory of genetic alterations incurred in virulent and avirulent strains, as well
      as the sequence changes accumulated during laboratory passage of pathogenic organisms.
AU  - Jarvik T
AU  - Smillie C
AU  - Groisman EA
AU  - Ochman H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 560-567.

PMID- Not included in PubMed...
VI  - 39
DP  - 1993
TI  - Analysis of phage resistance mechanisms encoded by lactococcal plasmid pAJ2074.
PG  - 252-258
AB  - Lactococcal plasmid pAJ2074 is a 74-kb plasmid that confers phage resistance at 30oC against
      all lactococcal phages with prolate heads (referred to as prolate phage), and most small
      lactococcal phages with isometric heads (referred to as small isometric phage) that have been
      tested. The presence of pAJ2074 had no effect on phage adsorption or injection of phage DNA.
      Replication of prolate phage c2 DNA could not be detected in bacterial cells containing the
      plasmid up to 60 minutes after phage infection, whereas phage c2 DNA replication could be
      demonstrated at 20 minutes in the control strain. With pAJ2074 present there was no detectable
      growth of phage c2 and an 87% reduction in burst size for the small isometric phage sk1.
      Infective centres were reduced in the presence of pAJ2074 by 99% for phage c2 and by 93% for
      phage sk1. Plasmid pAJ2074 differed from pTR2030, in that the major effect of pAJ2074 was on
      prolate phage c2, rather than on the small isometric phage sk1, and no restriction and
      modification system could be detected. In addition, no DNA homology was detected between
      pAJ2074 and pTRK67 (derived from pTR2030). A recombinant plasmid pAJ88 containing an 8.4kb
      insert from pAJ2074 conferred an intermediate level of phage resistance. The DNA region that
      encoded reduced phage sensitivity was further defined by the subcloning of a 5.6kb EcoRV
      fragment that conferred resistance similar to pAJ88. The possibility of two phage-resistance
      mechanisms being encoded by pAJ2074 is discussed.
AU  - Jarvis AW
PT  - Journal Article
TA  - Can. J. Microbiol.
JT  - Can. J. Microbiol.
SO  - Can. J. Microbiol. 1993 39: 252-258.

PMID- 16347086
VI  - 51
DP  - 1986
TI  - Bacteriophage resistance conferred on lactic Streptococci by the conjugative plasmid pTR2030: Effects on small isometric-, large Isometric-,and prolate-headed Phages.
PG  - 1272-1277
AB  - A series of reactions between phages, sensitive hosts, and transconjugants where the
      sensitivity of small isometric-, large isometric-, and prolate-headed phages to
      pTR2030-induced phage resistance was evaluated in Streptococcus lactis and Streptococcus
      cremoris strains. Phage-resistant transconjugants were constructed in the desired hosts by
      conjugal transfer of lactose-fermenting ability (Lac+,pTR1040) and phage resistance (Hsp+
      pTR2030) from S. lactis TEK1. S. lactis and S. cremoris transconjugants harboring pTR2030 were
      resistant to all small isometric-headed phages examined. In contrast, prolate- and large
      isometric-headed phages were either not inhibited in the pTR2030 transconjugants or exhibited
      a reduction in plaque size without a reduction in the efficiency of plaquing. Small
      isometric-headed phages subject to pTR2030 induced inhibition shared no significant DNA
      homology with pTR2030, suggesting that phage immunity genes are not harbored on the plasmid or
      responsible for resistance. The general effectiveness of pTR2030 against small
      isometric-headed phages was highly significant since these are the phages which have been
      isolated most commonly from dairy fermentation plants.
AU  - Jarvis AW
AU  - Klaenhammer TR
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1986 51: 1272-1277.

PMID- 23594878
VI  - 3
DP  - 2013
TI  - Genomics and genetics of Sulfolobus islandicus LAL14/1, a model hyperthermophilic archaeon.
PG  - 130010
AB  - The 2 465 177 bp genome of Sulfolobus islandicus LAL14/1, host of the model rudivirus SIRV2,
      was sequenced. Exhaustive comparative genomic analysis of S. islandicus LAL14/1 and the nine
      other completely sequenced S. islandicus strains isolated from Iceland, Russia and USA
      revealed a highly syntenic common core genome of approximately 2 Mb and a long hyperplastic
      region containing most of the strain-specific genes. In LAL14/1, the latter region is enriched
      in insertion sequences, CRISPR (clustered regularly interspaced short palindromic repeats),
      glycosyl transferase genes, toxin-antitoxin genes and MITE (miniature invertedrepeat
      transposable elements). The tRNAgenes ofLAL14/1 are preferential targets for the integration
      of mobile elements but clusters of atypical genes (CAG) are also integrated elsewhere in the
      genome. LAL14/1 carries five CRISPR loci with 10 per
      cent of spacers matching perfectly or imperfectly the genomes of archaeal viruses and plasmids
      found in the Icelandic hot springs. Strikingly, theCRISPR_2 region of LAL14/1 carries an
      unusually long 1.9 kb spacer interspersed between two repeat regions and displays a high
      similarity to pING1-like conjugative plasmids. Finally, we have developed a genetic system for
      S. islandicus LAL14/1 and created DpyrEF and DCRISPR_1 mutants using double cross-over and
      pop-in/pop-out approaches, respectively. Thus,LAL14/1 is a promisingmodel to study virus-host
      interactions and the CRISPR/Cas defence mechanism in Archaea.
AU  - Jaubert C
AU  - Danioux C
AU  - Oberto J
AU  - Cortez D
AU  - Bize A
AU  - Krupovic M
AU  - She Q
AU  - Forterre P
AU  - Prangishvili D
AU  - Sezonov G
PT  - Journal Article
TA  - Open Biol.
JT  - Open Biol.
SO  - Open Biol. 2013 3: 130010.

PMID- 24652979
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Naphthalene Degrader Herbaspirillum sp. Strain RV1423.
PG  - e00188-14
AB  - Herbaspirillum sp. strain RV1423 was isolated from a site contaminated with alkanes and
      aromatic compounds and harbors the complete pathway for naphthalene
      degradation. The new features found in RV1423 increase considerably the
      versatility and the catabolic potential of a genus of bacteria previously
      considered mainly to be diazotrophic endophytes to plants.
AU  - Jauregui R
AU  - Rodelas B
AU  - Geffers R
AU  - Boon N
AU  - Pieper DH
AU  - Vilchez-Vargas R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00188-14.

PMID- Not carried by PubMed...
VI  - 75
DP  - 1995
TI  - Gene manipulation of Streptococcus bovis: progress and problems.
PG  - 654-655
AB  - In general, realization of the goals to control the digestive processes of
      ruminants via genetic manipulation of rumen bacteria, is limited mainly by little information
      about the genome of important rumen bacteria, development of suitable cloning system,
      stability of cloned DNA in rumen bacteria and in the whole rumen ecosystem as well.  In
      our cloning study, the Sau 3A fragments of chromosomal DNA of S. bovis AO 24/85 were
      ligated into BamHI site of shuttle vector pMX 39, as a host was used B. subtilis amy E-.
      The restriction analyses of the recombinant plasmid pJK 108 isolated from B. subtilis alpha-
      amylase positive clone showed that alpha-amylase gene was located within a 2.8 kb fragment of
      the S. bovis chromosomal DNA.  Looking for a suitable transformation system, we have
      transformed S. bovis AO 24/85 with plasmid pNZ12 by electroporation with  transformation
      efficiency 1.1 x 103 ug-1 DNA.  In our laboratory we tested more S. bovis  strains for their
      restriction activities.  We have developed a very simple, rapid and effective  method for
      testing of RE activity of rumen bacteria.  By this method we detected and then  isolated and
      characterized the restriction endonuclease SbvI, an isoschizomer of HaeIII,  from rumen
      amylolytic bacterium S. bovis III/1.  Enzyme SbvI recognizes the 4-bp  palindrome,
      5'-GGCC-3' and cleaves DNA after the second G in the sequence, producing blunt ends.
AU  - Javorsky P
AU  - Pravdova M
AU  - Vanat I
AU  - Pristas P
AU  - Styriak I
PT  - Journal Article
TA  - Can. J. Anim. Sci.
JT  - Can. J. Anim. Sci.
SO  - Can. J. Anim. Sci. 1995 75: 654-655.

PMID- 182213
VI  - 15
DP  - 1976
TI  - Arthrobacter luteus restriction endonuclease recognition sequence and its cleavage map of SV40 DNA.
PG  - 3612-3620
AB  - The nucleotide sequence at the cleavage site of the restriction endonuclease
      isolated from Arthrobacter luteus (Alu) has been determined.  The endonuclease
      cleaves at the center of a palindromic tetranucleotide sequence to give
      even-ended duplex DNA fragments phosphorylated at the 5'-end.  The endonuclease
      cleaves SV40 form I DNA into 32 fragments.  The order and sizes of these
      fragments have been determined to provide an Alu cleavage map of the SV40
      genome.
AU  - Jay E
AU  - Wu R
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1976 15: 3612-3620.

PMID- 26092468
VI  - 81
DP  - 2015
TI  - Pyrobaculum yellowstonensis str. WP30 respires on elemental sulfur and/or arsenate in circumneutral sulfidic geothermal sediments of Yellowstone National Park.
PG  - 5907-5916
AB  - Thermoproteales populations (phylum Crenarchaeota) are abundant in
      high-temperature (>70 degrees C) environments of Yellowstone National Park (YNP)
      and are important in mediating biogeochemical cycles of sulfur, arsenic, and
      carbon. The objectives of this study were to determine specific physiological
      attributes of the isolate Pyrobaculum yellowstonensis strain WP30, which was
      obtained from an elemental sulfur sediment (Joseph's Coat Hot Spring [JCHS] 80
      degrees C; pH 6.1, 135 muM As), and relate this organism to geochemical processes
      occurring in situ. Strain WP30 is a chemoorganoheterotroph and requires elemental
      sulfur and/or arsenate as electron acceptors. Growth in the presence of elemental
      sulfur and arsenate resulted in the formation of thioarsenates and polysulfides.
      The complete genome of this organism was sequenced (1.99 Mb, 58 % G+C), which
      revealed numerous metabolic pathways for the degradation of carbohydrates, amino
      acids, and lipids. Multiple dimethylsulfoxide molybdopterin (DMSO-MPT)
      oxidoreductase genes were identified, which are implicated in the reduction of
      sulfur and arsenic. Pathways for the de novo synthesis of nearly all required
      cofactors and metabolites were identified. Comparative genomics of P.
      yellowstonensis versus assembled metagenome sequence from JCHS showed that this
      organism is highly-related ( approximately 95 % average nucleotide identity) to
      in situ populations. The physiological attributes and metabolic capabilities of
      P. yellowstonensis provide an important foundation for developing an
      understanding of the distribution and function of these populations in YNP.
AU  - Jay ZJ
AU  - Beam JP
AU  - Dohnalkova A
AU  - Lohmayer R
AU  - Bodle B
AU  - Planer-Friedrich B
AU  - Romine M
AU  - Inskeep WP
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2015 81: 5907-5916.

PMID- 29192089
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Pseudomonas aeruginosa ATCC 9027, Originally Isolated from an Outer Ear Infection.
PG  - e01397-17
AB  - Pseudomonas aeruginosa ATCC 9027 was isolated in 1943 from a case of otitis externa and is
      commonly employed as a quality control strain for sterility,
      assessment of antibiofilm agents, and in vitro study of wound infection. Here, we
      present the 6.34-Mb draft genome sequence and highlight some pertinent genes that
      are associated with virulence.
AU  - Jayal A
AU  - Johns BE
AU  - Purdy KJ
AU  - Maddocks SE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01397-17.

PMID- 17623098
VI  - 8
DP  - 2007
TI  - Comparative genomic hybridizations reveal absence of large Streptomyces coelicolor genomic islands in Streptomyces lividans.
PG  - 229
AB  - BACKGROUND: The genomes of Streptomyces coelicolor and Streptomyces lividans bear a
      considerable degree of synteny. While S. coelicolor is the
      model streptomycete for studying antibiotic synthesis and differentiation,
      S. lividans is almost exclusively considered as the preferred host, among
      actinomycetes, for cloning and expression of exogenous DNA. We used whole
      genome microarrays as a comparative genomics tool for identifying the
      subtle differences between these two chromosomes. RESULTS: We identified
      five large S. coelicolor genomic islands (larger than 25 kb) and 18
      smaller islets absent in S. lividans chromosome. Many of these regions
      show anomalous GC bias and codon usage patterns. Six of them are in close
      vicinity of tRNA genes while nine are flanked with near perfect repeat
      sequences indicating that these are probable recent evolutionary
      acquisitions into S. coelicolor. Embedded within these segments are at
      least four DNA methylases and two probable methyl-sensing restriction
      endonucleases. Comparison with S. coelicolor transcriptome and proteome
      data revealed that some of the missing genes are active during the course
      of growth and differentiation in S. coelicolor. In particular, a pair of
      methylmalonyl CoA mutase (mcm) genes involved in polyketide precursor
      biosynthesis, an acyl-CoA dehydrogenase implicated in timing of
      actinorhodin synthesis and bldB, a developmentally significant regulator
      whose mutation causes complete abrogation of antibiotic synthesis belong
      to this category. CONCLUSION: Our findings provide tangible hints for
      elucidating the genetic basis of important phenotypic differences between
      these two streptomycetes. Importantly, absence of certain genes in S.
      lividans identified here could potentially explain the relative ease of
      DNA transformations and the conditional lack of actinorhodin synthesis in
      S. lividans.
AU  - Jayapal KP
AU  - Lian W
AU  - Glod F
AU  - Sherman DH
AU  - Hu WS
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2007 8: 229.

PMID- 2552319
VI  - 341
DP  - 1989
TI  - Restriction venture.
PG  - 272
AB  - India has launched its first venture capital company to make restriction enzymes.  Bangalore
      Genei Private Ltd has been set up by Dr. P.S. Babu, a theoretical physicist-turned-molecular
      biologist, and Dr. K. Prasad, an immunologist, both of whom have been associated with the
      Indian Institute of Science, Bangalore.  A large part of the funding for the company comes
      from the Technology Development and Information Company of India.  The new company will obtain
      the know-how for the manufacture of the enzymes from Astra Research Centre, Bangalore, which
      carries out research in medical biotechnology and is developing diagnostic kits for a variety
      of tropical diseases.  The Centre for Genetic Engineering will also assist the new company.
      Restriction enzymes are currently being imported by individual laboratories and in bulk
      quantities by the CSIR Centre for Biochemicals, New Delhi.  The new company will initially
      make the more important and commonly used restriction enzymes.
AU  - Jayaraman KS
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1989 341: 272.

PMID- 
VI  - 100
DP  - 2011
TI  - Phase variation and adaptation in bacteria: A 'Red Queen's Race'.
PG  - 1163-1171
AB  - In nature, bacteria are constantly exposed to many stressful conditions of life. This is
      particularly true of pathogens. Survival and
      adaptation under stressful conditions demand multiple strategies,
      genetic as well as phenotypic. Bacteria have many, pre-programmed,
      phenotypic stress response systems which can handle a limited number of
      stresses. Genetically, heritable as well as transient hypermutability
      mechanisms have been found to facilitate bacterial adaptation to varied
      and unpredictable stresses; these processes are not reviewed here.
      Instead, this article will focus on processes which do not increase
      global mutation rates but cause localized hypermutability in specific
      loci called contingency genes which have been identified particularly
      in pathogenic bacteria. These processes are collectively called phase
      and antigenic variations. Most of the contingency genes are involved in
      the synthesis or modification of surface-associated structures and
      enzymes. Phase variation in these genes involves high frequency,
      reversible, switching of their expression (on to off and off to on).
      The mechanisms of this switching are reviewed. However, some phase
      variable genes are not involved in the synthesis or modification of
      surface structures but are components of type I and type III
      restriction-modification (RM) systems. The on/off switching of these
      genes (type III RM genes) leads to regulation of expression of many
      unlinked genes, impacting several properties of cells. This novel type
      of control of multiple gene expression by phase variation has been
      named 'phasevarion'. The adaptive advantages of phase variation in
      contingency genes and phasevarions in the evasion of host immunity,
      virulence, niche adaptation and other phenomena are reviewed with some
      illustrative examples. Phase variation and bacterial adaptation have
      been likened to the 'Red Queen's Race' in Lewis Carrol's classic
      Through the Looking Glass.
AU  - Jayaraman R
PT  - Journal Article
TA  - Curr. Sci.
JT  - Curr. Sci.
SO  - Curr. Sci. 2011 100: 1163-1171.

PMID- 24072868
VI  - 1
DP  - 2013
TI  - Genome Sequence of Lactobacillus fermentum Strain MTCC 8711, a Probiotic Bacterium Isolated from Yogurt.
PG  - e00770-13
AB  - Lactobacillus fermentum strain MTCC 8711 is a lactic acid bacterium isolated from yogurt.
      Here, we describe the draft genome sequence and annotation of this
      strain. The 2,566,297-bp-long genome consisted of a single chromosome and seven
      plasmids. The genome contains 2,609 protein-coding and 74 RNA genes.
AU  - Jayashree S
AU  - Pooja S
AU  - Pushpanathan M
AU  - Vishnu U
AU  - Sankarasubramanian J
AU  - Rajendhran J
AU  - Gunasekaran P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00770-13.

PMID- 10319870
VI  - 22
DP  - 1999
TI  - Maintenance of genomic methylation requires a SW12/SNF2-like protein.
PG  - 94-97
AB  - Altering cytosine methylation by genetic means leads to a variety of developmental defects in
      mice, plants and fungi. Deregulation of cytosine methylation also has a role in human
      carcinogenesis. In some cases, these defects have been tied to the inheritance of epigenetic
      alterations (such as chromatin imprints and DNA methylation patterns) that do not involve
      changes in DNA sequence.  Using a forward genetic screen, we identified a gene (DDM1, decrease
      in DNA methylation) from the flowering plant Arabidopsis thaliana required to maintain normal
      cytosine methylation patterns. Additional ddm1 alleles (som4, 5, 6, 7, 8) were isolated in a
      selection for mutations that relieved transgene silencing (E.J.R., unpublished data). Loss of
      DDM1 function causes a 70% reduction of genomic cytosine methylation, with most of the
      immediate hypomethylation occurring in repeated sequences. In contrast, many low-copy
      sequences initially retain their methylation in ddm1 homozygotes, but lose methylation over
      time as the mutants are propagated through multiple generations by self-pollination. The
      progressive effect of ddm1 mutations on low-copy sequence methylation suggests that ddm1
      mutations compromise the efficiency of methylation of newly incorporated cytosines after DNA
      replication. In parallel with the slow decay of methylation during inbreeding, ddm1 mutants
      accumulate heritable alterations (mutations or stable epialleles) at dispersed sites in the
      genome that lead to morphological abnormalities. Here we report that DDM1 encodes a
      SWI2/SNF2-like protein, implicating chromatin remodelling as an important process for
      maintenance of DNA methylation and genome integrity.
AU  - Jeddeloh JA
AU  - Stokes TL
AU  - Richards EJ
PT  - Journal Article
TA  - Nat. Genet.
JT  - Nat. Genet.
SO  - Nat. Genet. 1999 22: 94-97.

PMID- 15582389
VI  - 14
DP  - 2004
TI  - Molecular mechanisms for multitasking: recent crystal structures of moonlighting proteins.
PG  - 663-668
AB  - Recently determined X-ray crystal structures of moonlighting proteins are helping to elucidate
      how a protein can evolve two different
      functions and, in some cases, switch between its two functions in
      response to cellular conditions. X-ray crystal structures of the I-Anil
      homing endonuclease/maturase and the PutA proline
      dehydrogenase/transcription factor have provided evidence that these
      proteins utilize separate protein surfaces for their multiple
      functions. Also, the structure of the DegP (HtrA) protease/chaperone
      has revealed information about the mechanism of its chaperone activity
      and suggests how the protein regulates its protease activity. Comparing
      the structure of eta-crystallin/retinal dehydrogenase with structures
      of its single-function enzyme homologs provides clues to changes in the
      protein structure that may have improved its ability to serve as a
      crystallin, but at the same time may have adversely affected its
      catalytic activity.
AU  - Jeffery CJ
PT  - Journal Article
TA  - Curr. Opin. Struct. Biol.
JT  - Curr. Opin. Struct. Biol.
SO  - Curr. Opin. Struct. Biol. 2004 14: 663-668.

PMID- 24675850
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of an Invasive Multidrug-Resistant Strain, Pseudomonas aeruginosa BK1, Isolated from a Keratitis Patient.
PG  - e00153-14
AB  - Pseudomonas aeruginosa infections are difficult to treat due to the presence of a multitude of
      virulence factors and antibiotic resistance. Here, we report the
      draft genome sequence of P. aeruginosa BK1, an invasive and multidrug-resistant
      strain, isolated from a bacterial keratitis patient in southern India.
AU  - Jeganathan LP
AU  - Prakash L
AU  - Sivakumar N
AU  - Antony A
AU  - Alqarawi S
AU  - Prajna L
AU  - Devarajan B
AU  - Mohankumar V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00153-14.

PMID- 14604787
VI  - 317
DP  - 2003
TI  - Maintenance of species identity and controlling speciation of bacteria: a new function for restriction/modification systems?
PG  - 13-16
AB  - Bacteria frequently exchange DNA among each other by horizontal gene transfer. However,
      maintenance of species identity and in particular
      speciation requires a certain barrier against an unregulated uptake of
      foreign DNA. Here it is suggested that formation of such a barrier is one
      important biological function of restriction/modification systems, in
      addition to the classical function of protection of bacteria against
      bacteriophage infection. This model explains the extreme variability and
      wide distribution of restriction/modification systems among prokaryotes,
      the prevalence of RM-systems in pathogenic bacteria and the existence of
      several RM-systems in single bacterial strains.
AU  - Jeltsch A
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 2003 317: 13-16.

PMID- 16570849
VI  - 301
DP  - 2006
TI  - Molecular enzymology of mammalian DNA methyltransferases.
PG  - 203-225
AB  - DNA methylation is an essential modification of DNA in mammals that is involved in gene
      regulation, development, genome defence and disease.
      In mammals 3 families of DNA methyltransferases (MTases) comprising (so
      far) 4 members have been found: Dnmt1, Dnmt2, Dnmt3A and Dnmt3B. In
      addition, Dnmt3L has been identified as a stimulator of the Dnmt3A and
      Dnmt3B enzymes. In this review the enzymology of the mammalian DNA
      MTases is described, starting with a depiction of the catalytic
      mechanism that involves covalent catalysis and base flipping.
      Subsequently, important mechanistic features of the mammalian enzyme
      are discussed including the specificity of Dnmt1 for hemimethylated
      target sites, the target sequence specificity of Dnmt3A, Dnmt3B and
      Dnmt2 and the flanking sequence preferences of Dnmt3A and Dnmt3B. In
      addition, the processivity of the methylation reaction by Dnmt1, Dnmt3A
      and Dnmt3B is reviewed. Finally, the control of the catalytic activity
      of mammalian MTases is described that includes the regulation of the
      activity of Dnmt1 by its N-terminal domain and the interaction of
      Dnmt3A and Dnmt3B with Dnmt3L. The allosteric activation of Dnmt1 for
      methylation at unmodified sites is described. Wherever possible,
      correlations between the biochemical properties of the enzymes and
      their physiological functions in the cell are indicated.
AU  - Jeltsch A
PT  - Journal Article
TA  - Curr. Top. Microbiol. Immunol.
JT  - Curr. Top. Microbiol. Immunol.
SO  - Curr. Top. Microbiol. Immunol. 2006 301: 203-225.

PMID- 11405235
VI  - 382
DP  - 2001
TI  - The cytosine N4-methyltransferase M.PvuII also modifies adenine residues.
PG  - 707-710
AB  - Methylation of DNA occurs at the C5 and N4 positions of cytosine and N6 of adenine. The
      chemistry of methylation is similar among methyltransferases specific for cytosine-N4 and
      adenine-N6. Moreover these enzymes have similar structures and active sites. Previously it has
      been demonstrated that the DNA-(adenine-N6)-methyltransferases M.EcoRV, M.EcoRI, E. coli dam
      and both domains of M.FokI also modify cytosine residues at the N4 position [Jeltsch et al.,
      J. Biol. Chem. 274 (1999), 19538-19544]. Here we show that the cytosine-N4 methyltransferase
      M.PvuII, which modifies the second cytosine in CAGCTG sequences, also methylates adenine
      residues in CAGATG/CAGCTG substrates in which the target cytosine is replaced by adenine in
      one strand of the recognition sequence. Therefore, adenine-N6 and cytosine-N4
      methyltransferases have overlapping target base specificities. These results demonstrate that
      the target base recognition by N-specific DNA methyltransferases is relaxed in many cases.
      Furthermore, it shows that the catalytic mechanisms of adenine-N6 and cytosine-N4
      methyltransferases are very similar.
AU  - Jeltsch A
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 2001 382: 707-710.

PMID- 11933228
VI  - 3
DP  - 2002
TI  - Beyond Watson and Crick: DNA methylation and molecular enzymology of DNA methyltransferases.
PG  - 274-293
AB  - DNA methyltransferases catalyze the transfer of a methyl group from S-adenosyl-L-methionine to
      cytosine or adenine bases in DNA. These
      enzymes challenge the Watson/Crick dogma in two instances: 1) They
      attach inheritable information to the DNA that is not encoded in the
      nucleotide sequence. This so-called epigenetic information has many
      important biological functions. In prokaryotes, DNA methylation is used
      to coordinate DNA replication and the cell cycle, to direct
      postreplicative mismatch repair, and to distinguish self and nonself
      DNA. In eukaryotes, DNA methylation contributes to the control of gene
      expression, the protection of the genome against selfish DNA,
      maintenance of genome integrity, parental imprinting, X-chromosome
      inactivation in mammals, and regulation of development, 2) The
      enzymatic mechanism of DNA methyltransferases is unusual, because these
      enzymes flip their target base out of the DNA helix and, thereby,
      locally disrupt the B-DNA helix. This review describes the biological
      functions of DNA methylation in bacteria, fungi, plants, and mammals.
      In addition, the structures and mechanisms of the DNA
      methyltransferases, which enable them to specifically recognize their
      DNA targets and to induce such large conformational changes of the DNA,
      are discussed.
AU  - Jeltsch A
PT  - Journal Article
TA  - Chembiochem
JT  - Chembiochem
SO  - Chembiochem 2002 3: 274-293.

PMID- 10368444
VI  - 49
DP  - 1999
TI  - Circular permutations in the molecular evolution of DNA methyltransferase.
PG  - 161-164
AB  - Circular permutations of genes during molecular evolution often are regarded as elusive,
      although a simple model can explain these rearrangements. The model assumes that first a gene
      duplication of the precursor gene occurs in such a way that both genes become fused in frame,
      leading to a tandem protein. After generation of a new start codon within the 5' part of the
      tandem gene and a stop at an equivalent position in the 3' part of the gene, a protein is
      encoded that represents a perfect circular permutation of the precursor gene product. The
      model is illustrated here by the molecular evolution of adenine-N6 DNA methyltransferases.
      Beta- and gamma-type enzymes of this family can be interconverted by a single circular
      permutation event. Interestingly, tandem proteins, proposed as evolutionary intermediates
      during circular permutation, can be directly observed in the case of adenine
      methyltransferases, because some enzymes belonging to type IIS, like the FokI
      methyltransferase, are built up by two fused enzymes, both of which are active independently
      of each other. The mechanism for circular permutation illustrated here is very easy and
      applicable to every protein. Thus, circular permutation can be regarded as a normal process in
      molecular evolution and a changed order of conserved amino acid motifs should not be
      interpreted to argue against divergent evolution.
AU  - Jeltsch A
PT  - Journal Article
TA  - J. Mol. Evol.
JT  - J. Mol. Evol.
SO  - J. Mol. Evol. 1999 49: 161-164.

PMID- 1618296
VI  - 304
DP  - 1992
TI  - On the catalytic mechanism of EcoRI and EcoRV.  A detailed proposal based on biochemical results, structural data and molecular modelling.
PG  - 4-8
AB  - EcoRI and EcoRV have a very similar active site, as is apparent from a comparison of the
      structures of their respective protein-DNA complexes.  Based on structural and mechanistic
      data, as well as detailed molecular modelling presented here, a mechanism for the DNA cleavage
      by these enzymes is suggested in which the attacking water molecule is activated by the
      phosphate group 3' to the scissile phosphodiester bond, and in which the leaving group is
      protonated by a water molecule associated with the essential cofactor, Mg2+.  The mechanism
      proposed may also apply to other nucleases.
AU  - Jeltsch A
AU  - Alves J
AU  - Maass G
AU  - Pingoud A
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1992 304: 4-8.

PMID- 8421302
VI  - 229
DP  - 1993
TI  - Mutational analysis of the function of Gln115 in the EcoRI restriction endonuclease, a critical amino acid for recognition of the inner thymidine residue in the sequence -GAATTC-and for coupling specific DNA binding to catalysis.
PG  - 221-234
AB  - The Gln115 residue of the EcoRI restriction endonuclease has been proposed to form a
      hydrophobic contact to the methyl group of the inner thymidine of the EcoRI recognition
      sequence -GAATTC- and to be involved in intramolecular hydrogen bonds to the mainchain at
      positions 140 and 143 as well as to the side-chain of Asn173. We have exchanged Gln115 for Ala
      and Glu by site-directed mutagenesis and analysed the purified mutant protein (Q115A and
      Q115E) biochemically and physico-chemically. Q115A and Q115E have the same secondary structure
      composition as wild-type EcoRI but are less stable towards thermal denaturation than the
      wild-type enzyme. In contrast to wild-type EcoRI the mutant proteins show a biphasic
      denaturation profile under alkaline pH, presumably because the amino acid exchange labilizes
      one part of the molecule, which unfolds before the rest of the protein is denatured. Q115A is
      catalytically inactive under normal buffer conditions, in part due to a diminished affinity
      towards DNA. At low ionic strength and alkaline pH, as well as in the presence of Mn2+, i.e.
      under conditions where wild-type EcoRI shows a relaxed specificity, Q115A is active, however
      not as much as wild-type EcoRI. Under these conditions it cleaves the canonical sequence
      -GAATTC- with the same kcat/km value as the sequence -GAAUTC-, which differs from the former
      sequence by a single methyl group, while wild-type EcoRI shows a tenfold lower kcat/Km for
      cleavage of -GAAUTC- than for -GAATTC-. Binding experiments, carried out in the absence of
      Mg2+, demonstrate that Q115A has a similar affinity toward -GAATTC- as to -GAAUTC-, while
      wild-type EcoRI binds to -GAATTC- with a tenfold preference over -GAAUTC-. On the basis of
      these thermodynamic and kinetic results it can be concluded that the hydrophobic contact
      between the gamma-methylene group of Gln115 and the methyl group of the inner thymidine
      contributes about 3 kJ/mol (0.7 kcal/mol) to the energy of interaction, both in the ground and
      the transition state, Q115E is catalytically inactive under normal buffer conditions, but
      becomes active at low ionic strength or in the presence of Mn2+. Different from Q15A, Q115E is
      inactive at alkaline pH and its DNA binding affinity is highest at acidic pH. The dependence
      of its DNA cleavage activity on pH, which is governed by a pKa of 7.35, can be attributed to
      the protonation of the newly introduced glutamic acid residue, if it is assumed that the
      carboxyl group is located in a non-polar environment and/or involved in a hydrogen bond as the
      donor. Taken together, these results demonstrate that Gln115, as suggested on the basis of the
      revised EcoRI-DNA co-crystal structure, interacts with the inner thymidine of the EcoRI
      recognition sequence and has a structure stabilizing role. In addition, our results suggest
      that Gln115 is crucial for coupling specific DNA binding to catalysis under normal buffer
      conditions and we suggest that this coupling is achieved because direct and indirect
      involvement of Gln115 in base recognition induces local conformational alterations of the
      C-terminal region of beta-strand beta3, which contains Lys113 and Glu111 that are constituents
      of the catalytic centre of EcoRI. Activation of the catalytic centre, therefore, could be
      triggered by Gln115.
AU  - Jeltsch A
AU  - Alves J
AU  - Oelgeschlager T
AU  - Wolfes H
AU  - Maass G
AU  - Pingoud A
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1993 229: 221-234.

PMID- 7890621
VI  - 270
DP  - 1995
TI  - A dodecapeptide comprising the extended chain-alpha-4 region of the restriction endonuclease EcoRI specifically binds to the EcoRI recognition site.
PG  - 5122-5129
AB  - The restriction endonuclease EcoRI binds and cleaves DNA containing GAATTC sequences with high
      specificity. According to the crystal structure, most of the specific contacts of the enzyme
      to the DNA are formed by the extended chain region and the first turn of alpha-helix alpha-4
      (amino acids 137-145). Here, we demonstrate that a dodecapeptide (WDGMAAGNAIER), which is
      identical in the underlined parts (M-R) of its sequence to EcoRI amino acids 137-145,
      specifically binds to GAATTC sequences. The peptide inhibits DNA cleavage by EcoRI but not by
      BamHI, BclI, EcoRV, HindIII, PacI, and XbaI. DNA cleavage by XbaI is slowed down at sites that
      partially overlap with EcoRI sites. The peptide inhibits cleavage of GAATTC sites by ApoI,
      which recognizes the sequence RAATTY. It interferes with DNA methylation by the EcoRI
      methyltransferase but not by the BamHI methyltransferase. It competes with EcoRI for DNA
      binding. Based on these results, the DNA binding constant of the peptide to GAATTC sequences
      was calculated to be 3 x 10/4 M-1. DNA binding is not temperature-dependent, suggesting that
      binding of the peptide is entropy-driven. As the peptide does not show any nonspecific binding
      to DNA, its DNA binding specificity is similar to that of EcoRI, in spite of the fact that the
      affinity is much smaller. These results suggest that contacts to the phosphate groups in EcoRI
      mainly provide binding affinity, whereas the specificity of EcoRI is based to a large extent
      on sequence-specific base contacts.
AU  - Jeltsch A
AU  - Alves J
AU  - Urbanke C
AU  - Maass G
AU  - Eickstein H
AU  - Lianshan Z
AU  - Bayer E
AU  - Pingoud A
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1995 270: 5122-5129.

PMID- 8378323
VI  - 90
DP  - 1993
TI  - Substrate-assisted catalysis in the cleavage of DNA by the EcoRI and EcoRV restriction enzymes.
PG  - 8499-8503
AB  - The crystal structure analyses of the EcoRI-DNA and EcoRV-DNA complexes do not provide clear
      suggestions as to which amino acid residues are responsible for the activation of water to
      carry out the DNA cleavage. Based on molecular modeling, we have proposed recently that the
      attacking water molecule is activated by the negatively charged pro-Rp phosphoryl oxygen of
      the phosphate group 3' to the scissile phosphodiester bond. We now present experimental
      evidence to support this proposal. (i) Oligodeoxynucleotide substrates lacking this phosphate
      group in one strand are cleaved only in the other strand. (ii) Oligodeoxynucleotide substrates
      carrying an H-phosphonate substitution at this position in both strands and, therefore,
      lacking a negatively charged oxygen at this position are cleaved at least four orders of
      magnitude more slowly than the unmodified substrate. These results are supported by other
      modification studies: oligodeoxynucleotide substrates with a phosphorothioate substitution at
      this position in both strands are cleaved only if the negatively charged sulfur is in the Rp
      configuration as shown for EcoRI [Koziolkiewics, M. and Stec, W.J. (1992) Biochemistry 31,
      9460-9466] and EcoRV (B.A. Connolly, personal communication). As the phosphate residue 3' to
      the scissile phosphodiester bond is not needed for strong DNA binding by both enzymes, these
      findings strongly suggest that this phosphate group plays an active role during catalysis.
      This proposal furthermore, give a straightforward explanation of why in the EcoRI-DNA and
      EcoRV-DNA complexes the DNA is distorted differently, but in each case the 3' phosphate group
      closely approaches the phosphate group that is attacked. Finally, an alternative mechanism for
      DNA cleavage involving two metal ions is unlikely in the light of our findings that both EcoRI
      and EcoRV and need only one Mg2+ per active site for cleavage.
AU  - Jeltsch A
AU  - Alves J
AU  - Wolfes H
AU  - Maass G
AU  - Pingoud A
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1993 90: 8499-8503.

PMID- 8068662
VI  - 33
DP  - 1994
TI  - Pausing of the restriction endonuclease EcoRI during linear diffusion on DNA.
PG  - 10215-10219
AB  - Linear diffusion is a mechanism to accelerate association rates beyond their three-dimensional
      diffusional limit. It is employed by the restriction endonuclease EcoRI as well as many other
      proteins interacting with specific DNA sequences to locate their target sites on the
      macromolecular substrate. In order to investigate biochemical and biophysical details of the
      linear diffusion process, we have developed a competitive cleavage assay which allows us to
      assess with great accuracy the influence of sequence, sequence context, and other structural
      features on the linear diffusion of EcoRI on DNA. We show here that linear diffusion is not a
      hopping but a sliding movement in which EcoRI follows the helical pitch of the DNA, because it
      does not "overlook" any cleavage site. Linear diffusion is slowed when EcoRI encounters sites
      on the DNA which resemble its recognition site ("star" sites). Pauses of up to 20 s are
      induced, depending on sequence and orientation of the star site. These data suggest that EcoRI
      can bind to DNA in two binding modes: one tight, specific, and immobile, leading to DNA
      cleavage, and another one loose and nonspecific, allowing for linear diffusion. Depending on
      the similarity between the recognition sequence and the DNA sequence being encountered by
      EcoRI, there will be a continuous transition between these binding modes. Other proteins bound
      to the DNA and irregular DNA structures such as bent DNA or a triple helix constitute a
      barrier than cannot easily be passed by EcoRI.
AU  - Jeltsch A
AU  - Alves J
AU  - Wolfes H
AU  - Maass G
AU  - Pingoud A
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1994 33: 10215-10219.

PMID- 10391886
VI  - 274
DP  - 1999
TI  - On the substrate specificity of DNA methyltransferases.
PG  - 19538-19544
AB  - Methylation of DNA is important in many organisms and essential in mammals. Nucleobases can be
      methylated at the adenine-N6, cytosine-N4, or cytosine-C5 atoms by specific DNA
      methyltransferases. We show here that the M.EcoRV, M.EcoRI, and Escherichia coli dam
      methyltransferases as well as the N- and C-terminal domains of the M. FokI enzyme, which were
      formerly all classified as adenine-N6 DNA methyltransferases, also methylate cytosine residues
      at position N4. Kinetic analyses demonstrate that the rate of methylation of cytosine residues
      by M.EcoRV and the M.FokI enzymes is reduced by only 1-2 orders of magnitude in relation to
      methylation of adenines. This result shows that although these enzymes methylate DNA in a
      sequence specific manner, they have a low substrate specificity with respect to the target
      base. This unexpected finding has implications on the mechanism of adenine-N6 DNA
      methyltransferases. Sequence comparisons suggest that adenine-N6 and cytosine-N4
      methyltransferases have changed their reaction specificity at least twice during evolution, a
      model that becomes much more likely given the partial functional overlap of both enzyme types.
      In contrast, methylation of adenine residues by the cytosine-N4 methyltransferase M.BamHI was
      not detectable. On the basis of our results, we suggest that adenine-N6 and cytosine-N4
      methyltransferases should be grouped into one enzyme family.
AU  - Jeltsch A
AU  - Christ F
AU  - Fatemi M
AU  - Roth M
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1999 274: 19538-19544.

PMID- 9480766
VI  - 275
DP  - 1998
TI  - Kinetics of methylation and binding of DNA by the EcoRV adenine-N6 methyltransferase.
PG  - 747-758
AB  - The EcoRV DNA methyltransferase specifically methylates the first adenine within its
      recognition sequence GATATC.  Methylation rates of DNA by this enzyme are strongly influenced
      by the length of oligonucleotide substrates employed.  In substrates >20 bp compared to a
      12mer substrate, the kcat/Km increases 100-fold, although the enzyme does not contact more
      than 12 base-pairs on the DNA.  Single-turnover rates are higher than kcat values.  M.EcoRV
      binding to DNA is fast but dissociation from the DNA is slow, demonstrating that the
      multiple-turnover rate is limited by the rate of product release.  The kinetics of DNA binding
      by M.EcoRV are not in accordance with the thermodynamic binding constant, suggesting that the
      M.EcoRV-DNA complex is involved in a slow conformational change.  The salt dependence of DNA
      binding is different for non-specific substrates (d ln(KAss)/d ln(cNaCl) = -2, indicative of
      electrostatic interactions) and specific substrates (d ln(KAss)/d ln(cNaCl)=+1, indicative of
      hydrophobic interactions).  This result demonstrates that the M.EcoRV-DNA complex has a
      different conformation in both binding modes.  M.EcoRV does not discriminate between
      hemimethylated and unmethylated substrates.  Using the 20mer we have analyzed the temperature
      and pH dependence of the single-turnover rate constant of M.EcoRV-DNA methylation by M.EcoRV
      which has an activation energy of 40 kJ/mol and its rate increases with increasing pH.  The pH
      dependence reveals the presence of an ionizable residue with a pKa of 7.9, which must be
      unprotonated for catalysis.  The rates of DNA methylation remain unchanged if an abasic site
      is introduced instead of the thymidine residue that is base-paired to the target adenine,
      demonstrating that flipping out the target adenine cannot contribute to the rate-limiting step
      of the enzymatic reaction.
AU  - Jeltsch A
AU  - Friedrich T
AU  - Roth M
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1998 275: 747-758.

PMID- 8238896
VI  - 213
DP  - 1993
TI  - A fast and accurate enzyme-linked immunosorbent assay for the determination of the DNA cleavage activity of restriction endonucleases.
PG  - 234-240
AB  - We have developed an assay procedure to monitor the cleavage of DNA substrates by restriction
      endonucleases. This procedures uses DNA substrates that are labeled with biotin on one 5' end
      and with an antigenic group, e.g., flourescein or digoxigenin, on the other 5' end. After
      incubation with the restriction enzyme, the reaction is stopped with EDTA and an aliquot is
      pipetted into the well of an avidin-coated microtiter plate. This imobilizes the unreacted
      substrate and the biotinylated cleavage product, whereas the other cleavage product labeled
      with the antigenic group is subsequently washed off. The unreacted substrate is detected by an
      enzyme-linked immunosorbent assay with an appropriate enzyme-linked anitbody. To test our
      assay we have measured the steady-state rate constants for cleavage of DNA by EcoRI yielding a
      kcat of 8.6 min and a Km of 150 nM, which are close to values measured with other assays. The
      advantage of this assay is that it is not only fast and accurate, but also very sensitive. It
      allows for many samples to be analyzed in parallel and lends itself to automation.
      Furthermore, this assay can be designed as a competitive assay, when two substrates carrying
      different antigenic groups are used. The usefulness of such a competitive assay is
      demonstrated by determining the influence of sequence context on the rate of DNA cleavage by
      EcoRI.
AU  - Jeltsch A
AU  - Fritz A
AU  - Alves J
AU  - Wolfes H
AU  - Pingoud A
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 1993 213: 234-240.

PMID- 
VI  - 28
DP  - 2000
TI  - Molecular enzymology of the DNA-(adenine-N6)-methyltransferase M.EcoRV: Kinetic mechanism, kinetics of DNA binding and bending, and linear diffusion.
PG  - A312
AB  - Methylation of DNA is important in many organisms and essential in mammals.  Nucleobases can
      be methylated at the adenine-N6, cytosine-N4 or cytosine-C5 atoms by specific DNA
      methyltransferases.  The M.EcoRV adenine-N6 DNA methyltransferase specifically transfers a
      methyl group from AdoMet to the first adenine within GATATC sequences.  We show here that
      substrate binding to the enzyme follows an ordered bi-bi mechanism with AdoMet binding before
      DNA.  After DNA binding a non-specific enzyme-DNA complex is formed that slides along the DNA
      for more than 1800 bps by linear diffusion.  Upon specific complex formation the DNA is bent
      in a fast process with rate constants >10s^-1.  The cofactor of the methylation reaction,
      S-adenosylmethionine, but not the product of the reaction, S-adenosylhomocysteine, promotes
      specific complex formation.  In the presence of cofactor, the specific complex can change into
      a second conformation, in which the target sequence is more tightly contacted by the enzyme.
      M.EcoRV exists in a slow equilibrium between an open and a closed conformation.  Cofactor
      binding to the apoenzyme shifts the conformational equilibrium to the open conformation
      thereby promoting DNA binding.  Formation of a closed enzyme-DNA complex is a slow process
      (rate constant < 0.7 min^-1), that limits the rate of DNA methylation under single turnover
      conditions.  Product release requires opening of the closed complex which is very slow (rate
      constant < 0.05-0.1 min^-1) and limits the multiple turnover rate constant.  Slow DNA release
      from the closed complex also explains the high efficiency of linear diffusion of M.EcoRV on
      DNA.
AU  - Jeltsch A
AU  - Gowhar H
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 2000 28: A312.

PMID- 
VI  - 
DP  - 2004
TI  - DNA Methyltransferases, Bacterial.
PG  - 644-651
AB  - DNA methylation has a number of important roles in bacteria including the control of gene
      expression, DNA replication, and the cell cycle.  In addition, it is involved in mismatch
      repair and protection of bacteria from foreign DNA in restriction modification systems.  DNA
      methyltransferases are the enzymes that methylate DNA.  They deposit methyl groups on DNA at
      the N6-position of adenine, or the N4- or C5-positions of cytosine in a sequence-specific
      reaction using S-adenosyl-L-methionine as the methyl group donor.  Their reaction mechanism
      includes rotating the target base completely out of the DNA helix in a biphasic process, where
      fast flipping of the base out of the double helix is followed by a slower binding of the
      flipped base into a hydrophobic pocket of the enzyme.  DNA MTases comprise two structural
      domains: the larger domain contains the cofactor-binding site and the binding pocket for the
      flipped base and the smaller domain is responsible for most of the sequence-specific contacts
      of the enzyme to the target site.  The structures of large domains from all known DNA MTases
      are similar, whereas the small domains are more heterogeneous in sequence and structure.  DNA
      MTases are an attractive model system to study how proteins recognize specific sequences of
      DNA and how the specificity of DNA recognition changes during molecular evolution.  In
      addition, they illustrate how the biochemical properties of the enzymes are related to their
      biological functions.  In this article, we shall describe the biological roles of DNA
      methylation in prokaryotes, discuss the chemistry of the enzymatic methylation reaction
      performed by the DNA methyltransferases (the focus of the review), and finally discuss aspects
      of the enzymology of this fascinating family of enzymes that reveal how these molecular
      machines perform their complicated biochemical tasks.
AU  - Jeltsch A
AU  - Gumport RI
PT  - Journal Article
TA  - Encyclopedia of Biological Chemistry
JT  - Encyclopedia of Biological Chemistry
SO  - Encyclopedia of Biological Chemistry 2004 : 644-651.

PMID- 27521372
VI  - 44
DP  - 2016
TI  - Allosteric control of mammalian DNA methyltransferases - a new regulatory paradigm.
PG  - 8556-8575
AB  - In mammals, DNA methylation is introduced by the DNMT1, DNMT3A and DNMT3B methyltransferases,
      which are all large multi-domain proteins containing a catalytic C-terminal domain and an
      N-terminal part with regulatory functions. Recently, two novel regulatory principles of DNMTs
      were uncovered. It was shown that their catalytic activity is under allosteric control of
      N-terminal domains with autoinhibitory function, the RFT and CXXC domains in DNMT1 and the ADD
      domain in DNMT3. Moreover, targeting and activity of DNMTs were found to be regulated in a
      concerted manner by interactors and posttranslational modifications (PTMs). In this review, we
      describe the structures and domain composition of the DNMT1 and DNMT3 enzymes, their DNA
      binding, catalytic mechanism, multimerization and the processes controlling their stability in
      cells with a focus on their regulation and chromatin targeting by PTMs, interactors and
      chromatin modifications. We propose that the allosteric regulation of DNMTs by autoinhibitory
      domains acts as a general switch for the modulation of the function of DNMTs, providing
      numerous possibilities for interacting proteins, nucleic acids or PTMs to regulate DNMT
      activity and targeting. The combined regulation of DNMT targeting and catalytic activity
      contributes to the precise spatiotemporal control of DNMT function and genome methylation in
      cells.
AU  - Jeltsch A
AU  - Jurkowska RZ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2016 44: 8556-8575.

PMID- 23663978
VI  - 117
DP  - 2013
TI  - Multimerization of the Dnmt3a DNA Methyltransferase and Its Functional Implications.
PG  - 445-464
AB  - The Dnmt3a DNA cytosine-C5 methyltransferase has been recently shown to exhibit a complex
      oligomerization and multimerization potential, the
      structural basis and functional implications of which will be the
      subject of this contribution. The enzyme forms a linear heterotetramer
      with Dnmt3L, in which the interaction of Dnmt3a and 3L stimulates the
      catalytic activity of Dnmt3a. Isolated Dnmt3a forms protein filaments
      that bind to several DNA molecules oriented in parallel, which plays an
      essential role in the location of the enzyme to heterochromatin. Dnmt3L
      disrupts Dnmt3a protein filaments and leads to a redistribution of the
      enzyme in cells toward euchromatin. Finally, Dnmt3a complexes and
      Dnmt3a/3L heterotetramers cooperatively multimerize on DNA forming
      protein DNA filaments. This leads to a preference of the enzyme for
      periodic methylation of DNA and supports its heterochromatic
      localization.
AU  - Jeltsch A
AU  - Jurkowska RZ
PT  - Journal Article
TA  - Prog. Mol. Biol. Transl. Sci.
JT  - Prog. Mol. Biol. Transl. Sci.
SO  - Prog. Mol. Biol. Transl. Sci. 2013 117: 445-464.

PMID- 17431611
VI  - 75
DP  - 2007
TI  - Application of DNA methyltransferases in targeted DNA methylation.
PG  - 1233-1240
AB  - DNA methylation is an essential epigenetic modification. In bacteria, it is involved in gene
      regulation, DNA repair, and control of cell cycle. In eukaryotes, it acts in concert with
      other epigenetic modifications to regulate gene expression and chromatin structure. In
      addition to these biological roles, DNA methyltransferases have several interesting
      applications in biotechnology, which are the main focus of this review, namely, (1) in vivo
      footprinting: as several bacterial DNA methyltransferases cannot methylate DNA bound to
      histone proteins, the pattern of DNA methylation after expression of DNA methyltransferases in
      the cell allows determining nucleosome positioning; (2) mapping the binding specificity of DNA
      binding proteins: after fusion of a DNA methyltransferase to a DNA-binding protein and
      expression of the fusion protein in a cell, the DNA methylation pattern reflects the
      DNA-binding specificity of the DNA-binding protein; and (3) targeted gene silencing: after
      fusion of a DNA methyltransferase to a suitable DNA-binding domain, DNA methylation can be
      directed to promoter regions of target genes. Thereby, gene expression can be switched off
      specifically, efficiently, and stably, which has a number of potential medical applications.
AU  - Jeltsch A
AU  - Jurkowska RZ
AU  - Jurkowski TP
AU  - Liebert K
AU  - Rathert P
AU  - Schlickenrieder M
PT  - Journal Article
TA  - Appl. Microbiol. Biotechnol.
JT  - Appl. Microbiol. Biotechnol.
SO  - Appl. Microbiol. Biotechnol. 2007 75: 1233-1240.

PMID- 7628720
VI  - 160
DP  - 1995
TI  - Evidence for an evolutionary relationship among type-II restriction endonucleases.
PG  - 7-16
AB  - Type-II restriction-modification (R-M) systems comprise two enzymes, a DNA methyltransferase
      (MTase) and a restriction endonuclease (ENase), each of which specifically interact with the
      same 4-8-bp sequence.  All type-II MTases share several amino acid (aa) sequence motifs, which
      makes an evolutionary relatedness among these enzymes probable.  The type-II ENases, in
      contrast, except for some homologous isoschizomers, do not share significant aa sequence
      similarity.  Therefore, ENases in general have been considered unrelated.  Here we show that
      in addition to the analysis of the genotype (aa sequence), a comparison of the phenotype
      (recognition sequence) of these enzymes can provide independent information regarding
      evolutionary relationships, and thereby, help to analyze the significance of weak aa sequence
      similarities.  Multistep Monte-Carlo analyses were employed to demonstrate that the
      recognition sequences of those ENases, which were found to be related by a progressive
      multiple aa sequence alignment, are more similar to each other than would be expected by
      chance.  This analysis supports the notion that not only type-II MTases, but also type-II
      ENases did not arise independently in evolution, but rather evolved from one or a few
      primordial DNA-modifying and DNA-cleaving enzymes, respectively.
AU  - Jeltsch A
AU  - Kroger M
AU  - Pingoud A
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 160: 7-16.

PMID- 7742329
VI  - 34
DP  - 1995
TI  - DNA binding specificity of the EcoRV restriction endonuclease is increased by Mg2+ binding to a metal ion binding site distinct from the catalytic center of the enzyme.
PG  - 6239-6246
AB  - In contrast to many other type II restriction endonucleases, EcoRV binds specifically to DNA
      only in the presence of Mg2+. According to the co-crystal structure of an EcoRV--DNA complex,
      Mg2+ ion(s) bind to the active site of EcoRV liganded by Glu45, Asp74, and Asp90. Here we
      present experimental evidence suggesting that the EcoRV--DNA complex also interacts with Mg2+
      ions at other sites: (i) We have prepared an EcoRV triple mutant, in which all acidic amino
      acids in the catalytic center are replaced by alanine. This mutant is catalytically inactive.
      It binds nonspecifically to DNA in the absence of Mg2+, whereas it binds specifically to DNA
      in the presence of Mg2+. This means that Mg2+ induces specific DNA binding in this mutant,
      although all Mg2+ ligands in the catalytic center are removed. Therefore, additional
      interactions between Mg2+ and the EcoRV--DNA complex probably occur at sites distinct from the
      catalytic center. (ii) We have measured the specific and nonspecific DNA binding constants of
      EcoRV and of the triple mutant in the presence and absence of Mg2+. Mg2+ reduces nonspecific
      binding by 3-4 orders of magnitude, presumably because Mg2+ ions bound to the DNA have to be
      released upon complex formation. In contrast, the specific binding of the wild-type enzyme and
      the triple mutant is increased in the presence of Mg2+. This result can only be explained if a
      Mg2+ ion binds to the specific EcoRV--DNA complex probably at a site distinct from the
      catalytic center. (iii) To locate additional metal ion binding sites in the EcoRV--DNA
      complex, we have determined the cleavage rates of several undecadeoxynucleotides which contain
      single phosphorothioate linkages in the presence of Mg2+ and Mn2+. It turned out that an
      oligodeoxynucleotide in which the first phosphate group within the GpATATC sequence (p3) is
      replaced by an Rp phosphorothioate is cleaved by a factor of 50 more readily in the presence
      of Mn2+ than with Mg2+. This result is interpreted to mean that p3, which is far away from the
      active site of EcoRV, interacts with a Mg2+ ion. (iv) We have produced the EcoRV Y219C mutant
      whose DNA cleavage activity compared to wild-type EcoRV is reduced by 3 orders of magnitude.
      It binds nonspecifically to DNA in the absence of Mg2+ but not detectably in the presence of
      Mg2+. Although the distinct role of Tyr219 is unclear at present, it must be pointed out that
      this amino acid is far away from the active site of EcoRV but located in close proximity to
      amino acid residues vis a vis p3. Hence, the behavior of this mutant also supports the
      conclusion that an important interaction between Mg2+ and the EcoRV--DNA complex occurs at a
      site distinct from the catalytic center.
AU  - Jeltsch A
AU  - Maschke H
AU  - Selent U
AU  - Wenz C
AU  - Kohler E
AU  - Connolly BA
AU  - Thorogood H
AU  - Pingoud A
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1995 34: 6239-6246.

PMID- 16679017
VI  - 31
DP  - 2006
TI  - Two substrates are better than one: dual specificities for Dnmt2 methyltransferases.
PG  - 306-308
AB  - Dnmt2 enzymes have been widely conserved during evolution and contain all of the signature
      motifs of DNA (cytosine-5)-methyltransferases;
      however, the DNA methyltransferase activity of these proteins is
      comparatively weak and their biochemical and functional properties
      remain enigmatic. Recent evidence now shows that Dnmt2 has a novel tRNA
      methyltransferase activity, raising the possibility that the biological
      roles of these proteins might be broader than previously thought. This
      finding has important implications for understanding the evolutionary
      relationships among these enzymes.
AU  - Jeltsch A
AU  - Nellen W
AU  - Lyko F
PT  - Journal Article
TA  - Trends Biochem. Sci.
JT  - Trends Biochem. Sci.
SO  - Trends Biochem. Sci. 2006 31: 306-308.

PMID- 9485362
VI  - 37
DP  - 1998
TI  - Kinetic characterization of linear diffusion of the restriction endonuclease EcoRV on DNA.
PG  - 2160-2169
AB  - We have examined the kinetic parameters of linear diffusion of EcoRV on DNA.  The data were
      analyzed by Monte Carlo simulations in which the efficiency of recognition of EcoRV sites
      during linear diffusion, the efficiency of linear diffusion, and the behavior of enzymes at
      the ends of linear DNA is explicitly treated.  The analysis of the dependence of linear
      diffusion on the concentrations of NaCl and MgCl2 shows that linear diffusion is maximal at 50
      mM NaCl under all concentrations of MgCl2 tested and increases with increasing concentrations
      of Mg2+ up to 10 mM, the highest concentration used in the test.  Under these conditions,
      EcoRV scans 2 x 10^6 bp during one binding event with a velocity of about 1.7 x 10^6 bp s-1.
      The enzyme tends to overlook cleavage sites at 1 mM but not at 10 mM MgCl2.  This result
      confirms the thermodynamic finding that EcoRV does not bind very specifically to DNA in the
      absence of Mg2+.  It demonstrates that there is a Mg2+-dependent continuous transition between
      a nonspecific and a specific binding mode of EcoRV to DNA.  By comparing cleavage rates of
      linear DNA whose ends are free or blocked, we have shown that EcoRV has a very low probability
      to fall off at the ends of linear DNA.  The enzyme rather is "reflected" and continues linear
      diffusion.  EcoRV does not cleave oligonucleotides containing two EcoRV sites processively.
      Consequently, dissociation of the enzyme from the cleavage products is not preceded by a
      transfer to nonspecific DNA, and linear diffusion is not involved in product dissociation in
      EcoRV.
AU  - Jeltsch A
AU  - Pingoud A
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1998 37: 2160-2169.

PMID- 8919860
VI  - 42
DP  - 1996
TI  - Horizontal gene transfer contributes to the wide distribution and evolution of type II restriction-modification systems.
PG  - 91-96
AB  - Restriction modification (RM) systems serve to protect bacteria against
      bacteriophages.  They comprise a restriction endonuclease activity that specifically cleaves
      DNA
      and a corresponding methyltransferase activity that specifically methylates the DNA, thereby
      protecting it from cleavage.  Such systems are very common in bacteria.  To find out whether
      the
      widespread distribution of RM systems is due to horizontal gene transfer, we have compared the
      codon usages of 29 type II RM systems with the average codon usage of their respective
      bacterial
      hosts.  Pronounced deviations in codon usage were found in six cases: EcoRI, EcoRV, KpnI,
      SinI, SmaI, and TthHB81.  They are interpreted as evidence for horizontal gene transfer in
      these
      cases.  As the methodology is expected to detect only one-fourth to one-third of all
      horizontal gene
      transfer events, this result implies that horizontal gene transfer had a considerable
      influence on the
      distribution and evolution of RM systems.  In all of these six cases the codon usage
      deviations of
      the restriction enzyme genes are much more pronounced than those of the methyltransferase
      genes.
      This result suggests that in these cases horizontal gene transfer had occurred sequentially
      with the
      gene for the methyltransferase being first acquired by the cell.  This can be explained by the
      fact
      that an active restriction endonuclease is highly toxic in cells whose DNA is not protected
      from
      cleavage by a corresponding methyltransferase.
AU  - Jeltsch A
AU  - Pingoud A
PT  - Journal Article
TA  - J. Mol. Evol.
JT  - J. Mol. Evol.
SO  - J. Mol. Evol. 1996 42: 91-96.

PMID- 11265290
VI  - 160
DP  - 2001
TI  - Methods for determining activity and specificity of DNA binding and DNA cleavage by class II restriction endonucleases.
PG  - 287-308
AB  - Restriction endonucleases coupled with DNA methyltransferases form the
      restriction-modification systems that occur ubiquitously among bacteria.  They protect
      bacterial cells against bacteriophage infection by cleaving incoming foreign DNA highly
      specifically if it contains the recognition sequence.  Cellular DNA is protected from cleavage
      by a specific methylation within the recognition sequence, which is introduced by the
      methyltransferase.  Restriction endonucleases recognize palindromic recognition sites, 4-8
      base pairs in length.  These enzymes are indispensable tools for genetic engineering.  The
      biology and biochemistry of type II restriction endonucleases has been reviewed recently and
      will be summarized only briefly here.  Type IIS restriction enzymes differ from type II
      enzymes in that they recognize an asymmetric recognition sequence.  Monomeric in solution,
      these enzymes consist of a DNA recognition domain and a catalytic domain.  Restriction
      endonucleases initiate DNA cleavage by binding nonspecifically to DNA.  Association of the
      enzymes to DNA is diffusion controlled, with rate constants in the order of 10^7-10^8
      M^-1s^-1.  In a series of dissociation and association steps and/or sliding along the DNA, the
      enzyme scans the DNA and searches for the recognition site in a one-dimensional diffusion
      process.  This process permits much faster target site location than would be possible via a
      three-dimensional search.  During recognition, conformational changes in the enzyme-DNA
      complex lead to the activation of the catalytic centers and cleavage of the DNA.
      Subsequently, the products are released, allowing for a new reaction cycle to take place.
      Often product release is the rate limiting step for multiple turnover cleavage reactions.
AU  - Jeltsch A
AU  - Pingoud AM
PT  - Journal Article
TA  - Methods Mol. Biol.
JT  - Methods Mol. Biol.
SO  - Methods Mol. Biol. 2001 160: 287-308.

PMID- 7607482
VI  - 157
DP  - 1995
TI  - Evidence for substrate-assisted catalysis in the DNA cleavage of several restriction endonucleases.
PG  - 157-162
AB  - Substrate-assisted catalysis was suggested to be involved in the DNA cleavage reaction of the
      restriction endonucleases (ENases) EcoRI and EcoRV, because experimental evidence exists that
      the phosphate group 3' to the scissile bond serves to deprotonate the attacking water.  Here,
      we have addressed the question whether this is a general mechanistic feature of the reactions
      catalyzed by ENases.  For this purpose, the cleavage rates of modified and unmodified
      oligodeoxyribonucleotides (oligos), in which the phosphate group 3' to the scissile bond is
      substituted by a methyl phosphonate, where measured for 17 enzymes.  Only five turned out not
      to be inhibited by this modification (BglII, BstI, BstYI, Cfr10I and MunI); all others cleave
      the modified substrate at a strongly reduced rate or not at all.  By employing a
      hemisubstituted oligo substrate we were able to further investigate the mechanism of
      inhibition of the latter group of ENases.  Some of them cleave the unmodified strand of the
      modified substrate with a nearly unaltered rate, whereas the modified strand is cleaved very
      slowly or not at all (BamHI, Bsp143I, Eco72I, MflI, NdeII, Sau3AI, XhoII).  The others (AluI,
      Cfr9I, DpnII, MboI, PvuII) cleave the modified strand of the modified substrate with a largely
      reduced rate or not at all.  These ENases, however, cleave the unmodified strand with a
      reduced rate, too.  Based on these results we conclude that BamHI, Bsp143I, Cfr9I, DpnII,
      Eco72I, MboI, MflI, NdeII, PvuII, Sau3AI and XhoII may possibly employ substrate assistance in
      catalysis.
AU  - Jeltsch A
AU  - Pleckaityte M
AU  - Selent U
AU  - Wolfes H
AU  - Siksnys V
AU  - Pingoud A
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 157-162.

PMID- 9918720
VI  - 285
DP  - 1999
TI  - Mutational analysis of target base flipping by the EcoRV adenine-N6 DNA methyltransferase.
PG  - 1121-1130
AB  - DNA methyltransferases flip their target base out of the DNA helix.  Here, we have
      investigated base flipping by wild-type EcoRV DNA methyltransferase and five M.EcoRV variants
      (D193A, Y196A, S229A, W231R and Y258A).  These variants bind to DNA and S-adenosyl-methionine
      but have a severely reduced catalytic efficiency or are catalytically inactive.  To measure
      base flipping three different assays were used, viz. analysis of the yields of
      photocrosslinking reactions between the enzymes and a substrate in which the target base is
      replaced by 5-iodouracil, analysis of the binding constants to substrates containing a
      mismatch base-pair at the target position and analysis of the salt dependence of specific
      complex formation.  Our data show that the Y196A, W231R and Y258A variants are not able to
      stabilize a flipped target base, suggesting that the aromatic amino acid residues (Tyr196,
      Trp231 and Tyr258) are involved in hydrophobic interactions with the flipped base.  The D193A
      variant behaves like wild-type M.EcoRV with respect to base flipping.  The fact that this
      variant is catalytically inactive indicates that Asp193 has a function in chemical catalysis.
      The S229A variant can better flip modified bases but does not tightly lock the flipped base
      into the adenine-binding pocket, suggesting that Ser229 could form a contact to the flipped
      adenine.
AU  - Jeltsch A
AU  - Roth M
AU  - Friedrich T
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1999 285: 1121-1130.

PMID- 8795041
VI  - 9
DP  - 1996
TI  - Structure prediction of the EcoRV DNA methyltransferase based on mutant profiling, secondary structure analysis, comparison with known structures of methyltransferases and isolation of catalytically inactive single mutants.
PG  - 413-423
AB  - The EcoRV DNA methyltransferase (M.EcoRV) is an alpha-adenine methyltransferase.  We have used
      two different programs to predict the secondary structure of M.EcoRV.  The resulting consensus
      prediction was tested by a mutant profiling analysis.  29 neutral mutations of M.EcoRV were
      generated by five cycles of random mutagenesis and selection for active variants to increase
      the reliability of the prediction and to get a secondary structure prediction for some
      ambiguously predicted regions.  The predicted consensus secondary structure elements could be
      aligned to the common topology of the structures of the catalytic domains of M.HhaI and
      M.TaqI.  In a complementary approach we have isolated nine catalytically inactive single
      mutants.  Five of these mutants contain an amino acid exchange within the catalytic domain of
      M.EcoRV (Val20-Ala, Lys81Arg, Cys192Arg, Asp193Gly, Trp231Arg).  The Trp231Arg mutant binds
      DNA similarly to wild-type M.EcoRV, but is catalytically inactive.  Hence this mutant behaves
      like a bona fide active site mutant.  According to the structure prediction, Trp231 is located
      in a loop at the putative active site of M.EcoRV.  The other inactive mutants were insoluble.
      They contain amino acid exchanges within the conserved amino acid motifs X, III or IV in
      M.EcoRV confirming the importance of these regions.
AU  - Jeltsch A
AU  - Sobotta T
AU  - Pingoud A
PT  - Journal Article
TA  - Protein Eng.
JT  - Protein Eng.
SO  - Protein Eng. 1996 9: 413-423.

PMID- 
VI  - 14
DP  - 2004
TI  - Sliding or hopping?  How restriction enzymes find their way on DNA.
PG  - 95-110
AB  - In this contribution, we discuss target site location of restriction endonucleases, which are
      extremely common among prokaryotes occurring in almost every species.  These enzymes
      specifically recognize and cleave short, often palindromic, sequences on bacteriophage or
      other kinds of foreign DNA.  By cleaving incoming DNA, they protect bacteria against
      bacteriophage infections acting like an immune system.  In addition, restriction endonucleases
      have an important role in the control of horizontal gene transfer and bacterial evolution.
      The cellular DNA is protected against nucleolytic attack by an accompanying DNA
      methyltransferase which recognizes the same nucleotide sequence and methylates one adenine or
      cytosine residue within the site.  Since restriction endonucleases and DNA methyltransferases
      are present at the same time in the cell, there is kinetic competition between them, which
      necessitates that the restriction enzyme finds its target site on an invading DNA faster than
      the methyltransferase.  In addition, fast target site location is also important, because the
      invading bacteriophage DNA has to be degraded before it gains control over the cellular
      metabolism.  Therefore, restriction enzymes were among the earliest examples where facilitated
      diffusion has been shown to be effective in target site location.  However, the actual
      mechanism of this process is still under debate; whereas most authors had proposed a sliding
      mechanism, this has recently been disputed by Halford and colleagues who favored a hopping
      process.
AU  - Jeltsch A
AU  - Urbanke C
PT  - Journal Article
TA  - Nucleic Acids Mol. Biol.
JT  - Nucleic Acids Mol. Biol.
SO  - Nucleic Acids Mol. Biol. 2004 14: 95-110.

PMID- 8890184
VI  - 15
DP  - 1996
TI  - Linear diffusion of the restriction endonuclease EcoRV on DNA is essential for the in vivo function of the enzyme.
PG  - 5104-5111
AB  - Linear diffusion along DNA is a mechanism of enhancing the association rates of proteins to
      their specific recognition sites on DNA.  It has been demonstrated for several proteins in
      vitro, but to date in no case in vivo.  Here we show that the restriction endonuclease EcoRV
      slides along the DNA, scanning ~1000 bp in one binding event.  This process is critically
      dependent on contacts between amino acid residues of the protein and the backbone of the DNA.
      The disruption of single hydrogen bonds and, in particular, the alteration of electrostatic
      interactions between amino acid side chains of the protein and phosphate groups of the DNA
      interfere with or abolish effective sliding.  The efficiency of linear diffusion is dependent
      on salt concentration, having a maximum at 50mM NaCl.  These results suggest that a
      nonspecific and mobile binding mode capable of linear diffusion is dependent on a subtle
      balance of forces governing the interaction of the enzyme and the DNA.  A strong correlation
      between the ability of EcoRV mutants to slide along the DNA in vitro and to protect
      Escherichia coli cells from phage infection demonstrates that linear diffusion occurs in vivo
      and is essential for effective phage restriction.
AU  - Jeltsch A
AU  - Wenz C
AU  - Stahl F
AU  - Pingoud A
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1996 15: 5104-5111.

PMID- 8771796
VI  - 14
DP  - 1996
TI  - Engineering novel restriction endonucleases: principles and applications.
PG  - 235-238
AB  - Restriction endonucleases cleave DNA with remarkable sequence specificity.  In this review, we
      summarize the status of, and prospects for, engineering restriction endonucleases with new
      specificities.  Such variants could be of considerable commercial value because restriction
      enzymes are among the most frequently used enzymes in molecular biology, and not all the
      desirable specificities are available.  While it has not yet been possible to effect
      specificity changes, mutants have been described that (1) exhibit relaxed specificity, (2)
      favor modified substrates over their natural substrates, (3) discriminate between cleavage
      sites located in different sequences, (4) prefer metal ions other than Mg2+ as cofactors for
      cleavage, or (5) possess site-specific DNA-nicking activity.
AU  - Jeltsch A
AU  - Wenz C
AU  - Wende W
AU  - Selent U
AU  - Pingoud A
PT  - Journal Article
TA  - Trends Biotechnol.
JT  - Trends Biotechnol.
SO  - Trends Biotechnol. 1996 14: 235-238.

PMID- 8538460
VI  - 259
DP  - 1995
TI  - Structural-perturbation approaches to thermodynamics of site-specific protein-DNA interactions.
PG  - 305-345
AB  - The solution of a large (and rapidly growing) number of crystal structures of site-specific
      protein-DNA complexes has given us extremely detailed views of the positional relationships at
      the interfaces between proteins and their "correct" DNA recognition sites.  This structural
      information identifies interactions between particular functional groups on the protein and
      particular functional groups on the DNA.  It is important to ask if the same proximity
      relationships and interactions pertain in solution.  Furthermore, structural information alone
      informs us about neither the quantitative contribution of each contact to the overall
      stability of the complex nor the role of the contacts, singly or in combination, in enabling
      the protein to discriminate between correct and incorrect DNA-binding sites.
AU  - Jen-Jacobson L
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1995 259: 305-345.

PMID- 9354759
VI  - 44
DP  - 1997
TI  - Protein-DNA recognition complexes: conservation of structure and binding energy in the transition state.
PG  - 153-180
AB  - This paper considers how enzymes that catalyze reactions at specific DNA sites have been
      engineered to overcome the problem of competitive inhibition by excess nonspecific binding
      sites on DNA.  The formation of a specific protein-DNA recognition complex is discussed from
      both structural and thermodynamic perspectives, and contrasted with formation of nonspecific
      complexes.  Evidence (from EcoRI and BamHI endonucleases) is presented that a wide variety of
      perturbations of the DNA substrate alter binding free energy but do not affect the free energy
      of activation for the chemical step; that is, many energetic factors contribute equally to the
      recognition complex and the transition-state complex.  This implies that the specific
      recognition complex bears a close resemblance to the transition-state complex, such that very
      tight binding to the recognition site on the DNA substrate does not inhibit catalysis, but
      instead provides energy that is efficiently utilized along the path to the transition state.
      It is suggested that this view can be usefully extended to "noncatalytic" site-specific
      DNA-binding proteins like transcriptional activators and general transcription factors.
AU  - Jen-Jacobson L
PT  - Journal Article
TA  - Biopolymers
JT  - Biopolymers
SO  - Biopolymers 1997 44: 153-180.

PMID- 
VI  - 12
DP  - 2000
TI  - Thermodynamic parameters of specific and nonspecific protein-DNA binding.
PG  - 143-160
AB  - Proteins that bind preferentially to specific recognition sites on DNA also bind more weakly
      to nonspecific DNA.  We have studied both specific and non-specific binding of the EcoRI and
      BamHI restriction endonucleases, and determined enthalpic and entropic contributions to
      binding free energy (delta G^o bind) using both the van't Hoff method and isothermal
      titration calorimetry.  Specific binding is characterized by a strongly negative delta C^o p
      and can be either enthalpy-driven or entropy-driven, depending on temperature.  Nonspecific
      binding has delta C^o = 0 and is enthalpy-driven.  A strongly negative delta C^o p is the
      "thermodynamic signature" of site-specific binding, because it reflects the characteristics of
      a tight complementary recognition interface: the burial of previously hydrated nonpolar
      surface and restriction of configurational-vibrational freedoms of protein, DNA, and water
      molecules trapped at the protein-DNA interface.  These factors are absent in nonspecific
      complexes.  We probed the contributions to delta C^o p by varying the sequence context
      surrounding the recognition site.  As delta G^o bind improves, delta C^o p, delta H^o and
      delta S^o all become more negative, and there is a linear correlation between delta H^o and
      delta S^o (enthalpy-entropy compensation).  Because these context variations do not change the
      protein-base or protein-phosphate contacts, the hydrophobic contribution or the number of
      trapped water molecules at the interface, we conclude that a better sequence context improves
      the "goodness of fit" in the interface and thus increases the magnitude of the negative
      configurational-vibrational contribution to delta C^o p.
AU  - Jen-Jacobson L
AU  - Engler LE
AU  - Ames JT
AU  - Kurpiewski MR
AU  - Grigorescu A
PT  - Journal Article
TA  - Supramol. Chem.
JT  - Supramol. Chem.
SO  - Supramol. Chem. 2000 12: 143-160.

PMID- 11080623
VI  - 8
DP  - 2000
TI  - Structural and thermodynamic strategies for site-specific DNA binding proteins.
PG  - 1015-1023
AB  - BACKGROUND: Site-specific protein-DNA complexes vary greatly in structural properties and in
      the thermodynamic strategy for achieving an appropriate binding free energy. A better
      understanding of the structural and energetic engineering principles might lead to rational
      methods for modification or design of such proteins.
      RESULTS: A novel analysis of ten site-specific protein-DNA complexes reveals a striking
      correspondence between the degree of imposed DNA distortion and the thermodynamic parameters
      of each system. For complexes with relatively undistorted DNA, favorable enthalpy change
      drives unfavorable entropy change, whereas for complexes with highly distorted DNA,
      unfavorable DeltaH^o is driven by favorable DeltaS^o. We show for the first time that
      protein-DNA associations have isothermal enthalpy-entropy compensation, distinct from
      temperature-dependent compensation, so DeltaH^o and DeltaS^o do not vary independently. All
      complexes have favorable DeltaH^o from direct protein-DNA recognition interactions and
      favorable DeltaS^o from water release.  Systems that strongly distort the DNA nevertheless
      have net unfavorable DeltaH^o as the result of molecular strain, primarily associated with the
      base pair destacking. These systems have little coupled protein folding and the strained
      interface suffers less immobilization, so DeltaS^o is net favorable. By contrast, systems with
      little DNA distortion have net favorable DeltaH^o, which must be counterbalanced by net
      unfavorable DeltaS^o, derived from loss of vibrational entropy (a result of isothermal
      enthalpy-entropy compensation) and from coupling between DNA binding and protein folding.
      CONCLUSIONS: Isothermal enthalpy-entropy compensation implies that a structurally optimal,
      unstrained fit is achieved only at the cost of entropically unfavorable immobilization,
      whereas an enthalpically weaker, strained interface entails smaller entropic penalties.
AU  - Jen-Jacobson L
AU  - Engler LE
AU  - Jacobson LA
PT  - Journal Article
TA  - Structure
JT  - Structure
SO  - Structure 2000 8: 1015-1023.

PMID- 8654385
VI  - 15
DP  - 1996
TI  - Structural adaptations in the interaction of EcoRI endonuclease with methylated GAATTC sites.
PG  - 2870-2882
AB  - We have studied the interaction of EcoRI endonuclease with oligonucleotides
      containing GAATTC sites bearing one or two adenine-N6-methyl groups, which would be in steric
      conflict with key protein side chains involved in recognition and/or catalysis in the
      canonical
      complex.  Single-strand methylation of either adenine produces small penalties in binding free
      energy (delta delta Gs ~ +1.4 kcal/mol), but elicits asymmetric structural adaptations in the
      complex, such that cleavage rate constants are strongly inhibited and unequal in the two DNA
      strands.  The dependences of cleavage rate constants on the concentration of the Mg2+ cofactor
      are
      unaltered.  When either adenine is methylated on both DNA strands, delta delta Gs
      (~+4kcal/mol)
      is larger than the expected sum of the delta delta Gs values for the single-strand
      methylations,
      because the asymmetric adaptations cannot occur.  Cleavage rate constants are reduced by
      600,000-fold for the biologically relevant GAmATTC/CTTmAAG site, but the
      GmAATTC/CTTAmAG site forms only a non-specific complex that cannot be cleaved.  These
      observations provide a detailed thermodynamic and kinetic explanation of how single-strand and
      double-strand methylation protect against endonuclease cleavage in vivo.  We propose that non-
      additive effects on binding and structural 'adaptations' are important in understanding how
      DNA
      methylation modulates the biological activities of non-catalytic DNA binding proteins.
AU  - Jen-Jacobson L
AU  - Engler LE
AU  - Lesser DR
AU  - Kurpiewski MR
AU  - Yee C
AU  - McVerry B
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1996 15: 2870-2882.

PMID- 6315732
VI  - 258
DP  - 1983
TI  - Coordinate ion pair formation between EcoRI endonuclease and DNA.
PG  - 14638-14646
AB  - The free energy of the binding reaction between EcoRI restriction endonuclease
      and a specific cognate dodecadeoxynucleotide (d(CGCGAATTCGCG)) has
      contributions from both electrostatic and nonelectrostatic components.  These
      contributions were dissected by measuring the effects of varying salt
      concentration on the equilibrium binding constant and applying the
      thermodynamic analyses of Record et al. (Record, M.T., Jr., Lohman, T.M., and
      deHaseth, P.L. (1976) J. Mol. Biol. 107: 145-158).  Endonuclease mutation S187
      (Arg 187 to Ser) (Greene, P.J., Gupta, M., Boyer, H.W., Brown, W.E., and
      Rosenberg, J.M. (1981) J. Biol. Chem. 256: 2143-2153) did not significantly
      affect the nonelectrostatic component but did perturb the electrostatic
      contribution to the binding energy (we are numbering the amino acid residues
      according to the DNA sequence).  The former was determined by extrapolating the
      linear portion of the salt dependence curve (0.125 to 0.25M KCl) to 1M ionic
      strength, with the same result for both wild type and S187 endonucleases at
      both pH 6.0 and 7.4 (-8.5 +- 1.5 kcal/mol or greater than 50% of the total
      binding free energy).  The slopes of these same curves yield estimates of eight
      ionic interactions between wild type endonuclease and the DNA at both pH
      values.  By contrast, binding of EcoRI-S187 to dodecanucleotide involves six
      charge-charge interactions at pH 6.0.  Only two ionic interactions are observed
      at pH 7.4.  This was unexpected since gel permeation chromatography
      demonstrated that the recognition complex for both wild type and S187 proteins
      contains an enzyme dimer and a DNA duplex.  EcoRI-S187 endonuclease retains
      wild type DNA sequence specificity, and the rate of the phosphodiester
      hydrolysis step is also unchanged.  Thus, electrostatic interactions are
      functionally separable from sequence recognition and strand cleavage.  Our
      results also establish that arginine 187 plays a key role in the electrostatic
      function and suggest that it might be located at the DNA-protein interface.
      The disproportionate loss of ion pairs at pH 7.4 can be rationalized by a model
      which suggests that six conformationally mobile ionic groups on the protein act
      in a coordinated manner during the interaction with DNA.
AU  - Jen-Jacobson L
AU  - Kurpiewski M
AU  - Lesser D
AU  - Grable J
AU  - Boyer HW
AU  - Rosenberg JM
AU  - Greene PJ
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1983 258: 14638-14646.

PMID- 3011275
VI  - 45
DP  - 1986
TI  - The enfolding arms of the EcoRI Endonuclease: role in DNA binding and cleavage.
PG  - 619-629
AB  - The N-terminal segments of the EcoRI endonuclease dimer form part of mobile
      "arms" that encircle DNA in the recognition complex.  By treating
      endonuclease-TCGCGAATTCGCG complexes with proteases, we have prepared a series
      of deletion derivatives lacking defined segments of the N-terminal region.  The
      5-12 segment is essential for DNA cleavage and forms one electrostatic
      interaction (per subunit) with DNA phosphate.  These ionic contacts are
      directly across the double helix from the scissile phosphodiester bonds; they
      thus may permit the enfolding arms to immobilize DNA in apposition to the
      catalytic cleft and/or contribute to the unusual "kinked" conformation of DNA
      in the complex.  Sequence specificity is fully retained when 28 residues are
      deleted from the N-terminus, but the complexes dissociate more rapidly.
AU  - Jen-Jacobson L
AU  - Lesser D
AU  - Kurpiewski M
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1986 45: 619-629.

PMID- 
VI  - 5
DP  - 1991
TI  - DNA sequence discrimination by EcoRI endonuclease.
PG  - 141-170
AB  - The EcoRI restriction endonuclease presents an especially informative case of specificity in
      protein-DNA interactions, because it exhibits extremely high sequence selectivity between its
      canonical recognition site GAATTC and related DNA sites that differ by as little as one base
      pair.  A gene-regulatory protein (the lac repressor) also shows stringent discrimination
      against single base-pair changes in Oc mutant sites.  By contrast, some bacteriophage
      repressors bind to a series of related operator DNA sites in a graduated fashion ("permissive
      discrimination"), yet discriminate stringently between operator and nonoperator DNA.
AU  - Jen-Jacobson L
AU  - Lesser DR
AU  - Kurpiewski MR
PT  - Journal Article
TA  - Nucleic Acids and Molecular Biology
JT  - Nucleic Acids and Molecular Biology
SO  - Nucleic Acids and Molecular Biology 1991 5: 141-170.

PMID- 14506863
VI  - 47
DP  - 2003
TI  - Identification of a novel DNA methyltransferase activity from Bacillus thuringiensis.
PG  - 144-145
AB  - A DNA methyltransferase activity was identified in a strain of Bacillus thuringiensis that was
      found to protect DNA from cleavage by the
      restriction endonuclease HaeIII at overlapping sites. Site-directed
      mutagenesis was used to confirm therecognition sequence of the
      methyltransferase as ACGGC.
AU  - Jenkinson E
AU  - Crickmore N
PT  - Journal Article
TA  - Curr. Microbiol.
JT  - Curr. Microbiol.
SO  - Curr. Microbiol. 2003 47: 144-145.

PMID- 11101665
VI  - 146
DP  - 2000
TI  - Gene transfer to clostridium cellulolyticum ATCC 35319.
PG  - 3071-3080
AB  - Although much is known about the bacterial cellulosome and its various protein components,
      their contributions to bacterial growth on cellulose and the process of cellulolysis in vivo
      cannot currently be assessed. To remedy this, the authors have developed gene transfer
      techniques for Clostridium cellulolyticum ATCC 35319. Firstly, transfer of Tn1545 has been
      obtained using an Enterococcus faecalis donor. Secondly, IncP-mediated conjugative
      mobilization of plasmids from Escherichia coli donors has also been achieved. The yield of
      transconjugants in both cases was low and was probably limited by the suboptimal growth
      conditions that must of necessity be employed for the co-culture of oligotrophic C.
      cellulolyticum with copiotrophic donors. A restriction endonuclease was detected in crude
      extracts of C. cellulolyticum. This enzyme, named CCE:I, is an isoschizomer of MSP:I (HPA:II).
      Electro-transformation was employed to establish plasmids containing the replication functions
      of pAMss1 (En. faecalis), pIM13 (Bacillus subtilis), pCB102 (Clostridium butyricum), pIP404
      (Clostridium perfringens) and pWV01 (Lactococcus lactis subsp. cremoris) in C. cellulolyticum.
      Transformants were only obtained if the DNA was appropriately methylated on the external C of
      the sequence 5'-CCGG-3' using either BSU:FI methylase in vivo or MSP:I methylase in vitro.
      Plasmids based on the pAMss1 and pIM13 replicons were more stably maintained than one based on
      the pCB102 replicon. Selection of transformants on solid medium led to low apparent
      transformation efficiencies (approx. 10(2) transformants per &mgr;g DNA) which might, in part,
      reflect the low plating efficiency of the organism. Selection of transformants in liquid
      medium led to a higher apparent yield of transformants (between 10(5) and 10(7) transformants
      per &mgr;g DNA). The methods developed here will pave the way for functional analysis of the
      various cellulosome components in vivo.
AU  - Jennert KC
AU  - Tardif C
AU  - Young DI
AU  - Young M
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2000 146: 3071-3080.

PMID- 28963219
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Methanobrevibacter smithii Isolate WWM1085, Obtained from a Human Stool Sample.
PG  - e01055-17
AB  - Methanobrevibacter smithii is a common inhabitant of the human gut. Here, we present a draft
      genome sequence of M. smithii isolate WWM1085, obtained from a
      human stool sample. This sequence will improve our understanding of the genetic
      diversity of this human-associated methanogen.
AU  - Jennings ME
AU  - Chia N
AU  - Boardman LA
AU  - Metcalf WW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01055-17.

PMID- 23469330
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Prepandemic Vibrio parahaemolyticus BB22OP.
PG  - e00002-12
AB  - The number of inflammatory gastroenteritis outbreaks due to the food-borne pathogen is rising
      sharply worldwide and in the United States in particular. Here
      we report the complete, annotated genome sequence of the prepandemic strain
      BB22OP and make some initial comparisons to the complete genome sequence for
      pandemic strain RIMD2210633.
AU  - Jensen RV
AU  - Depasquale SM
AU  - Harbolick EA
AU  - Hong T
AU  - Kernell AL
AU  - Kruchko DH
AU  - Modise T
AU  - Smith CE
AU  - McCarter LL
AU  - Stevens AM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00002-12.

PMID- 24698368
VI  - 58
DP  - 2014
TI  - Rapid and reliable method for identification of associated endonuclease cleavage and recognition sites.
PG  - 576-581
AB  - One barrier to cross during genetic engineering is the restriction-modification system found
      in many bacteria. In this study, we developed a fast and reliable method for mapping the
      recognition and cleavage site of the restriction endonucleases. Clostridium pasteurianum, a
      model organism for the study of nitrogen fixation, has been found to harbour at least two
      restriction-modification systems including the restriction endonucleases CpaPI, which is an
      isoschizomer of MboI and CpaAI. Dam-methylated DNA was used to isolate the activity of CpaAI.
      Exposing freshly prepared cell lysate to known nucleotide fragments and directly sequencing
      the pool of digested nucleotide fragments enabled identification of the cleavage sites in the
      fragments. By aligning the sequences adjacent to the cleavage site, it was possible to
      identify the recognition sequence. Using this method, we successfully located all CpaAI
      recognition and cleavage sites within the template sequence. By modifying DNA with both Dam
      and CpG methylases (M.SssI) and thereby preventing digestion by CpaPI and CpaAI, no further
      endonuclease activity was detected.Significance and Impact of the
      StudyRestriction-modification systems are important barriers to successful genetic
      modification in many bacterial species. In this study, we demonstrate an efficient and general
      applicable method for identifying endonuclease recognition and cleavage sites. For the study
      and the trails, the model organism for nitrogen fixation Clostridium pasteurianum was used.
      The method was proven to be reliable, and by modifying DNA at the identified sites, it is
      possible to prevent digestion.
AU  - Jensen TO
AU  - Kvist T
AU  - Mikkelsen MJ
AU  - Westermann P
PT  - Journal Article
TA  - Lett. Appl. Microbiol.
JT  - Lett. Appl. Microbiol.
SO  - Lett. Appl. Microbiol. 2014 58: 576-581.

PMID- 6195145
VI  - 156
DP  - 1983
TI  - Restriction and modification in Bacillus subtilis:  Sequence specificities of restriction/modification systems BsuM, BsuE, and BsuF.
PG  - 800-808
AB  - The sequence specificies of three Bacillus subtilis restriction/modification
      systems were established: (i) BsuM (CTCGAG), an isoschizomer to XhoI; (ii) BsuE
      (CGCG), an isoschizomer to FnuDII; and (iii) BsuF (CCGG), an isoschizomer to
      MspI, HpaII.  The BsuM modification enzyme methylates the 3' cytosine of the
      recognition sequence.  The BsuF modification enzyme methylates the 5' cytosine
      of the sequence, rendering such sites resistant to MspI degradation and leaving
      the majority of sites sensitive to HpaII degradation.
AU  - Jentsch S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1983 156: 800-808.

PMID- 6269059
VI  - 9
DP  - 1981
TI  - DNA methyltransferases affecting the sequence 5'CCGG.
PG  - 2753-2759
AB  - B. subtilis phage SPbeta and Moraxella sp. code for DNA methyl-transferases
      which methylate both cytosines of the sequence 5'CCGG.  Experiments using a B.
      subtilis strain whose DNA is sensitive to HpaII and resistant to MspI
      degradation, indicated that methylation of the outer C of this sequence
      provides protection against the restriction enzyme MspI.
AU  - Jentsch S
AU  - Gunthert U
AU  - Trautner TA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1981 9: 2753-2759.

PMID- Not carried by PubMed...
VI  - 0
DP  - 1980
TI  - Restriction and modification in B. subtilis:  Temperate phages SPbeta and Phi3T for BsuR specific methyltransferases.
PG  - 363-369
AB  - Genes for BsuR specific methyltransferases have been identified in the genomes
      of SPbeta and Phi3T.  Such genes are interchangeable between these two phages.
      Phages SPbeta and possibly also Phi3T code for additional methyltransferase(s)
      with different sequence specificities.
AU  - Jentsch S
AU  - Pawlek B
AU  - Noyer-Weidner M
AU  - Gunthert U
AU  - Trautner TA
PT  - Journal Article
TA  - Transformation 1980:  Proceedings of the Fifth European Meeting on Bacterial Transformation and Transfection
JT  - Transformation 1980:  Proceedings of the Fifth European Meeting on Bacterial Transformation and Transfection
SO  - Transformation 1980:  Proceedings of the Fifth European Meeting on Bacterial Transformation and Transfection 1980 0: 363-369.

PMID- 28302783
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Escherichia coli Strains Isolated at Calving from the Uterus, Vagina, Vulva, and Rectoanal Junction of a Dairy Cow That Later Developed  Metritis.
PG  - e01511-16
AB  - Escherichia coli is involved in the pathogenicity of metritis in cows. We report  here the
      genome sequences of E. coli strains isolated at calving from the uterus,
      vagina, vulva, and rectoanal junction of a dairy cow that later developed
      metritis. The genomic similarities will give an insight into phylogenetic
      relationships among strains.
AU  - Jeon SJ
AU  - Cunha F
AU  - Ginn A
AU  - Jeong KC
AU  - Galvao KN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01511-16.

PMID- 18974959
VI  - 46
DP  - 2008
TI  - DNA Adenine Methylation of sams1 Gene in Symbiont-Bearing Amoeba proteus.
PG  - 564-570
AB  - The expression of amoeba sams genes is switched from sams1 to sams2 when amoebae are infected
      with Legionella jeonii. To elucidate the
      mechanism for the inactivation of host sams1 gene by endosymbiotic
      bacteria, methylation states of the sams1 gene of D and xD amoebae was
      compared in this study. The sams1 gene of amoebae was methylated at an
      internal adenine residue of GATC site in symbiont-bearing xD amoebae
      but not in symbiont-free D amoebae, suggesting that the modification
      might have caused the inactivation of sams1 in xD amoebae. The sams1
      gene of xD amoebae was inactivated at the transcriptional level.
      Analysis of DNA showed that adenine residues in L. jeonii sams were
      also methylated, implying that L. jeonii bacteria belong to a Dam
      methylase-positive strain. In addition, both SAM and Met appeared to
      act as negative regulators for the expression of sams1 whereas the
      expression of sams2 was not affected in amoebae.
AU  - Jeon TJ
PT  - Journal Article
TA  - J. Microbiol.
JT  - J. Microbiol.
SO  - J. Microbiol. 2008 46: 564-570.

PMID- 28904743
VI  - 12
DP  - 2017
TI  - Complete genome sequence of the sulfur-oxidizing chemolithoautotrophic Sulfurovum lithotrophicum 42BKTT.
PG  - 54
AB  - A sulfur-oxidizing chemolithoautotrophic bacterium, Sulfurovum lithotrophicum 42BKTT, isolated
      from hydrothermal sediments in Okinawa, Japan, has been used
      industrially for CO2 bio-mitigation owing to its ability to convert CO2 into
      C5H8NO4- at a high rate of specific mitigation (0.42 g CO2/cell/h). The genome of
      S. lithotrophicum 42BKTT comprised of a single chromosome of 2217,891 bp with
      2217 genes, including 2146 protein-coding genes and 54 RNA genes. Here, we
      present its complete genome-sequence information, including information about the
      genes encoding enzymes involved in CO2 fixation and sulfur oxidation.
AU  - Jeon W
AU  - Priscilla L
AU  - Park G
AU  - Lee H
AU  - Lee N
AU  - Lee D
AU  - Kwon H
AU  - Ahn I
AU  - Lee C
AU  - Lee H
AU  - Ahn J
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 54.

PMID- 28254985
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Staphylococcus succinus 14BME20 Isolated from a Traditional Korean Fermented Soybean Food.
PG  - e01731-16
AB  - The complete genome sequence of Staphylococcus succinus 14BME20, isolated from a  Korean
      fermented soybean food and selected as a possible starter culture
      candidate, was determined. Comparative genome analysis with S. succinus CSM-77
      from a Triassic salt mine revealed the presence of strain-specific genes for
      lipid degradation in strain 14BME20.
AU  - Jeong DW
AU  - Lee JH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01731-16.

PMID- 19786035
VI  - 394
DP  - 2009
TI  - Genome Sequences of Escherichia coli B strains REL606 and BL21(DE3).
PG  - 644-652
AB  - Escherichia coli K-12 and B have been the subjects of classical experiments from which much of
      our understanding of molecular genetics has
      emerged. We present here complete genome sequences of two E. coli B
      strains, REL606, used in a long-term evolution experiment, and BL21(DE3),
      widely used to express recombinant proteins. The two genomes differ in
      length by 72,304 bp and have 426 single base pair differences, a seemingly
      large difference for laboratory strains having a common ancestor within
      the last 67 years. Transpositions by IS1 and IS150 have occurred in both
      lineages. Integration of the DE3 prophage in BL21(DE3) apparently
      displaced a defective prophage in the lambda attachment site of B. As
      might have been anticipated from the many genetic and biochemical
      experiments comparing B and K-12 over the years, the B genomes are similar
      in size and organization to the genome of E. coli K-12 MG1655 and have
      >99% sequence identity over approximately 92% of their genomes. E. coli B
      and K-12 differ considerably in distribution of IS elements and in
      location and composition of larger mobile elements. An unexpected
      difference is the absence of a large cluster of flagella genes in B, due
      to a 41 kbp IS1-mediated deletion. Gene clusters that specify the LPS
      core, O antigen, and restriction enzymes differ substantially, presumably
      because of horizontal transfer. Comparative analysis of 32 independently
      isolated E. coli and Shigella genomes, both commensals and pathogenic
      strains, identifies a minimal set of genes in common plus many
      strain-specific genes that constitute a large E. coli pan-genome.
AU  - Jeong H
AU  - Barbe V
AU  - Lee CH
AU  - Vallenet D
AU  - Yu DS
AU  - Choi SH
AU  - Couloux A
AU  - Lee SW
AU  - Yoon SH
AU  - Cattolico L
AU  - Hur CG
AU  - Park HS
AU  - Segurens B
AU  - Kim SC
AU  - Oh TK
AU  - Lenski RE
AU  - Studier FW
AU  - Daegelen P
AU  - Kim JF
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2009 394: 644-652.

PMID- 25359912
VI  - 2
DP  - 2014
TI  - Genome Sequence of the Plant Endophyte Bacillus pumilus INR7, Triggering Induced  Systemic Resistance in Field Crops.
PG  - e01093-14
AB  - Bacillus pumilus INR7 is an endophytic bacterium that has been commercialized as  a biological
      control product against soilborne pathogens as well as foliar
      pathogens by direct antagonism and induction of systemic resistance. In the
      current study, we provide the genome sequence and a possible explanation of the
      function of strain INR7.
AU  - Jeong H
AU  - Choi SK
AU  - Kloepper JW
AU  - Ryu CM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01093-14.

PMID- 28153898
VI  - 5
DP  - 2017
TI  - Genome Sequences of Bacillus thuringiensis Serovar kurstaki Strain BP865 and B. thuringiensis Serovar aizawai Strain HD-133.
PG  - e01544-16
AB  - We report the draft genome sequences of two insecticidal strains against lepidopteran pests,
      Bacillus thuringiensis serovar kurstaki strain BP865, an
      isolate from the South Korean phylloplane, and strain HD-133, a reference strain
      of B. thuringiensis serovar aizawai.
AU  - Jeong H
AU  - Choi SK
AU  - Park SH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01544-16.

PMID- 22328743
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Paenibacillus peoriae Strain KCTC 3763T.
PG  - 1237-1238
AB  - Paenibacillus peoriae is a potentially plant-beneficial soil bacterium and is a close relative
      to Paenibacillus polymyxa, the type species of the genus
      Paenibacillus. Herein, we present the 5.77-Mb draft genome sequence of the P.
      peoriae type strain with the aim of providing insight into the genomic basis of
      plant growth-promoting Paenibacillus species.
AU  - Jeong H
AU  - Choi SK
AU  - Park SY
AU  - Kim SH
AU  - Park SH
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1237-1238.

PMID- 29724846
VI  - 6
DP  - 2018
TI  - Genome Sequences of Two Cyanobacterial Strains, Toxic Green Microcystis aeruginosa KW (KCTC 18162P) and Nontoxic Brown Microcystis sp. Strain MC19, under  Xenic Culture Conditions.
PG  - e00378-18
AB  - Bloom-forming cyanobacteria pose concerns for the environment and the health of humans and
      animals by producing toxins and thus lowering water quality. Here, we
      report near-complete genome sequences of two Microcystis strains under xenic
      culture conditions, which were originally isolated from two separate freshwater
      reservoirs from the Republic of Korea.
AU  - Jeong H
AU  - Chun SJ
AU  - Srivastava A
AU  - Cui Y
AU  - Ko SR
AU  - Oh HM
AU  - Ahn CY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00378-18.

PMID- 22815459
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of the Plant Growth-Promoting Bacterium Bacillus siamensis  KCTC 13613T.
PG  - 4148-4149
AB  - Bacillus siamensis KCTC 13613(T), a novel halophilic Bacillus species isolated from a salted
      Thai food, produced antimicrobial compounds against plant pathogens
      and promoted plant growth by volatile emission. We determined the 3.8-Mb genome
      sequence of B. siamensis KCTC 13613(T) to reveal the plant-beneficial effect at
      the genomic level.
AU  - Jeong H
AU  - Jeong DE
AU  - Kim SH
AU  - Song GC
AU  - Park SY
AU  - Ryu CM
AU  - Park SH
AU  - Choi SK
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4148-4149.

PMID- 23950128
VI  - 1
DP  - 2013
TI  - Genome Sequence of Lysinibacillus sphaericus Strain KCTC 3346T.
PG  - e00625-13
AB  - Lysinibacillus sphaericus is a heterogeneous species that includes strains that produce
      mosquitocidal toxin proteins. Herein, we report the 4.56-Mb draft genome
      sequence of the nonpathogenic L. sphaericus strain KCTC 3346(T), which provides
      clues for the phylogenetic reassessment of L. sphaericus species and an
      understanding of its physiological properties.
AU  - Jeong H
AU  - Jeong DE
AU  - Sim YM
AU  - Park SH
AU  - Choi SK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00625-13.

PMID- 27103716
VI  - 4
DP  - 2016
TI  - Genome Sequence of the Endophytic Bacterium Bacillus thuringiensis Strain KB1, a  Potential Biocontrol Agent against Phytopathogens.
PG  - e00279-16
AB  - ITALIC! Bacillus thuringiensisis the most widely known microbial pesticide used in
      agricultural applications. Herein, we report a draft genome sequence of the
      endophytic bacterium ITALIC! Bacillus thuringiensisstrain KB1, which exhibits
      antagonism against phytopathogens.
AU  - Jeong H
AU  - Jo SH
AU  - Hong CE
AU  - Park JM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00279-16.

PMID- 25792055
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Escherichia coli Strain BL21.
PG  - e00134-15
AB  - Escherichia coli strain BL21 is one of the widely used bacterial hosts for high-level
      recombinant protein production and for other applications. Here, we
      present the complete genome sequence of a commercial version of the Escherichia
      coli BL21 strain.
AU  - Jeong H
AU  - Kim HJ
AU  - Lee SJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00134-15.

PMID- 26089433
VI  - 3
DP  - 2015
TI  - Genome Sequences of Pseudomonas amygdali pv. tabaci Strain ATCC 11528 and pv. lachrymans Strain 98A-744.
PG  - e00683-15
AB  - Certain pathovars of Pseudomonas amygdali, which is newly reclassified from Pseudomonas
      syringae by DNA-DNA hybridization and ribotyping, cause many serious
      diseases of major crop plants. Herein, we present draft genome sequences of P.
      amygdali pv. tabaci strain ATCC 11528 and P. amygdali pv. lachrymans strain
      98A-744.
AU  - Jeong H
AU  - Kloepper JW
AU  - Ryu CM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00683-15.

PMID- 26089427
VI  - 3
DP  - 2015
TI  - Genome Sequence of Rhizobacterium Serratia marcescens Strain 90-166, Which Triggers Induced Systemic Resistance and Plant Growth Promotion.
PG  - e00667-15
AB  - The rhizobacterium Serratia marcescens strain 90-166 elicits induced systemic resistance
      against plant pathogens and herbivores and promotes plant growth under
      greenhouse and field conditions. Strain 90-166 secretes volatile compounds,
      siderophores, salicylic acid, and quorum-sensing autoinducers as bacterial
      determinants toward plant health. Herein, we present its draft genome sequence.
AU  - Jeong H
AU  - Kloepper JW
AU  - Ryu CM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00667-15.

PMID- 26430040
VI  - 3
DP  - 2015
TI  - Genome Sequence of Antibiotic-Producing Bacillus amyloliquefaciens Strain KCTC 13012.
PG  - e01121-15
AB  - We report the 4.0-Mb draft genome sequence of Bacillus amyloliquefaciens (syn. Bacillus
      velezensis) KCTC 13012, which exhibits a broad spectrum of antagonistic  activity against
      bacteria and fungi and promotes plant growth as well. The genome contains an array of
      biosynthetic gene clusters for secondary metabolites that are comparable to those in Bacillus
      amyloliquefaciens subsp. plantarum FZB42(T).
AU  - Jeong H
AU  - Park SH
AU  - Choi SK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01121-15.

PMID- 24699954
VI  - 2
DP  - 2014
TI  - Genome Sequence of the Acrystalliferous Bacillus thuringiensis Serovar Israelensis Strain 4Q7, Widely Used as a Recombination Host.
PG  - e00231-14
AB  - Bacillus thuringiensis serovar israelensis is well known for its mosquitocidal activity and
      has long been used as a biopesticide. Herein, we present the genome sequence of B.
      thuringiensis serovar israelensis strain 4Q7, a plasmid-cured derivative with higher
      transformation efficiency than wild types.
AU  - Jeong H
AU  - Park SH
AU  - Choi SK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00231-14.

PMID- 27174273
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Four Plant Probiotic Bacillus Strains.
PG  - e00358-16
AB  - Here, we report the whole-genome sequences of four Bacillus strains that exhibit  plant
      probiotic activities. Three of them are the type strains of Bacillus
      endophyticus, 'Bacillus gaemokensis,' and Bacillus trypoxylicola, and the other,
      Bacillus sp. strain KCTC 13219, should be reclassified into a species belonging
      to the genus Lysinibacillus.
AU  - Jeong H
AU  - Park SH
AU  - Choi SK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00358-16.

PMID- 21742878
VI  - 193
DP  - 2011
TI  - Draft Genome Sequence of Paenibacillus polymyxa Type Strain (ATCC 842T), a Plant Growth-Promoting Bacterium.
PG  - 5026-5027
AB  - Paenibacillus polymyxa is an endospore-forming Gram-positive soil bacterium that is well-known
      for its ability to promote plant growth. Here
      we report the draft genome sequence of P. polymyxa ATCC 842(T), the type
      strain of the species P. polymyxa, and the family Paenibacillaceae. A
      repertoire of biosynthetic genes for antibiotics and hydrolytic enzymes
      accounts for its beneficial effects in rhizosphere to host plants it
      associates with.
AU  - Jeong H
AU  - Park SY
AU  - Chung WH
AU  - Kim SH
AU  - Kim N
AU  - Park SH
AU  - Kim JF
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5026-5027.

PMID- 23814036
VI  - 1
DP  - 2013
TI  - Genome Sequence of the Vancomycin-Producing Amycolatopsis orientalis subsp. orientalis Strain KCTC 9412T.
PG  - e00408-13
AB  - Amycolatopsis orientalis is the producer of vancomycin, a glycopeptide antibiotic that is used
      for the treatment of serious infections with Gram-positive bacteria.
      Here we present the next-generation sequencing (NGS)-based 9.06-Mb draft genome
      sequence of the type strain Amycolatopsis orientalis subsp. orientalis KCTC 9412
      (DSM 40040; ATCC 19795).
AU  - Jeong H
AU  - Sim YM
AU  - Kim HJ
AU  - Lee DW
AU  - Lim SK
AU  - Lee SJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00408-13.

PMID- 23908288
VI  - 1
DP  - 2013
TI  - Genome Sequences of Amycolatopsis orientalis subsp. orientalis Strains DSM 43388  and DSM 46075.
PG  - e00545-13
AB  - Strains of Amycolatopsis orientalis produce vancomycin or other related glycopeptide
      antibiotic compounds. Here we report the draft genome sequences of
      glycopeptide nonproducers Amycolatopsis orientalis subsp. orientalis DSM 43388
      and DSM 46075. Their genome information will provide insights into the
      acquisition and regulation of glycopeptide antibiotic resistance genes.
AU  - Jeong H
AU  - Sim YM
AU  - Kim HJ
AU  - Lee YJ
AU  - Lee DW
AU  - Lim SK
AU  - Lee SJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00545-13.

PMID- 25999562
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Bacillus subtilis Strain ATCC 6051a, a Potential Host for High-Level Secretion of Industrial Enzymes.
PG  - e00532-15
AB  - Bacillus subtilis ATCC 6051a (=KCTC 1028), which is less domesticated than strain 168, is
      widely used for the secretory expression of industrial enzymes. Herein,
      we present the complete genome sequence of the Bacillus subtilis strain ATCC
      6051a.
AU  - Jeong H
AU  - Sim YM
AU  - Park SH
AU  - Choi SK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00532-15.

PMID- 16352867
VI  - 33
DP  - 2005
TI  - Genomic blueprint of Hahella chejuensis, a marine microbe producing an algicidal agent.
PG  - 7066-7073
AB  - Harmful algal blooms, caused by rapid growth and accumulation of certain microalgae in the
      ocean, pose considerable impacts on marine environments,
      aquatic industries and even public health. Here, we present the
      7.2-megabase genome of the marine bacterium Hahella chejuensis including
      genes responsible for the biosynthesis of a pigment which has the lytic
      activity against a red-tide dinoflagellate. H.chejuensis is the first
      sequenced species in the Oceanospiralles clade, and sequence analysis
      revealed its distant relationship to the Pseudomonas group. The genome was
      well equipped with genes for basic metabolic capabilities and contained a
      large number of genes involved in regulation or transport as well as with
      characteristics as a marine heterotroph. Sequence analysis also revealed a
      multitude of genes of functional equivalence or of possible foreign
      origin. Functions encoded in the genomic islands include biosynthesis of
      exopolysacchrides, toxins, polyketides or non-ribosomal peptides, iron
      utilization, motility, type III protein secretion and pigmentation.
      Molecular structure of the algicidal pigment, which was determined through
      LC-ESI-MS/MS and NMR analyses, indicated that it is prodigiosin. In
      conclusion, our work provides new insights into mitigating algal blooms in
      addition to genetic make-up, physiology, biotic interactions and
      biological roles in the community of a marine bacterium.
AU  - Jeong H
AU  - Yim JH
AU  - Lee C
AU  - Choi SH
AU  - Park YK
AU  - Yoon SH
AU  - Hur CG
AU  - Kang HY
AU  - Kim D
AU  - Lee HH
AU  - Park KH
AU  - Park SH
AU  - Park HS
AU  - Lee HK
AU  - Oh TK
AU  - Kim JF
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2005 33: 7066-7073.

PMID- 22740672
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Hemolytic-Uremic Syndrome-Causing Strain Escherichia coli  NCCP15647.
PG  - 3747-3748
AB  - Enterohemorrhagic Escherichia coli (EHEC) causes a disease involving diarrhea, hemorrhagic
      colitis, and hemolytic-uremic syndrome (HUS). Here we present the
      draft genome sequence of NCCP15647, an EHEC isolate from an HUS patient. Its
      genome exhibits features of EHEC, such as genes for verotoxins, a type III
      secretion system, and prophages.
AU  - Jeong H
AU  - Zhao F
AU  - Igori D
AU  - Oh KH
AU  - Kim SY
AU  - Kang SG
AU  - Kim BK
AU  - Kwon SK
AU  - Lee CH
AU  - Song JY
AU  - Yu DS
AU  - Park MS
AU  - Cho SH
AU  - Kim JF
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3747-3748.

PMID- 29930044
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Bacillus subtilis Strain DKU_NT_03, Isolated from a Traditional Korean Food Using Soybean (Chung-gook-jang) for High-Quality Nattokinase Activity.
PG  - e00526-18
AB  - We present here the complete genome sequence of Bacillus subtilis strain DKU_NT_03 isolated
      from the traditional Korean food chung-gook-jang, which is
      made from soybeans. This strain was chosen to identify genetic factors with
      high-quality nattokinase activity.
AU  - Jeong HW
AU  - Bang MS
AU  - Lee YJ
AU  - Lee SJ
AU  - Lee SC
AU  - Shin JI
AU  - Oh CH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00526-18.

PMID- 29954917
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Chryseobacterium lactis NCTC11390(T) Isolated from Milk, Chryseobacterium oncorhynchi 701B-08(T) from Rainbow Trout, and Chryseobacterium viscerum 687B-08(T) from Diseased Fish.
PG  - e00628-18
AB  - The genus Chryseobacterium, belonging to the family Flavobacteriaceae, contains Gram-negative,
      yellow-pigmented, rod-shaped, and non-spore-forming bacterial
      species, which may be free living or parasitic. Here, we report draft genome
      sequences of type strains of three species of Chryseobacterium containing genes
      related to biological control and plant growth promotion.
AU  - Jeong JJ
AU  - Lee YJ
AU  - Pathiraja D
AU  - Park B
AU  - Choi IG
AU  - Kim KD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00628-18.

PMID- 29853508
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Bacillus megaterium KU143, Microbacterium testaceum KU313, and Pseudomonas protegens AS15, Isolated from Stored Rice Grains.
PG  - e00468-18
AB  - Bacillus megaterium KU143, Microbacterium testaceum KU313, and Pseudomonas protegens AS15 from
      stored rice grains exhibited antifungal activity against
      Aspergillus and Penicillium spp. predominant in stored rice. Here, we report
      their bacterial draft genomes, which contain genes related to biotic and abiotic
      stress management, as well as antimicrobial and insecticidal traits.
AU  - Jeong JJ
AU  - Moon HJ
AU  - Pathiraja D
AU  - Park B
AU  - Choi IG
AU  - Kim KD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00468-18.

PMID- 27795281
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Chryseobacterium artocarpi UTM-3T and Chryseobacterium  contaminans C26T, Isolated from Rhizospheres, and Chryseobacterium arthrosphaerae  CC-VM-7T, Isolated from the Feces of a Pill Millipede.
PG  - e01168-16
AB  - Species of the genus Chryseobacterium belonging to the family Flavobacteriaceae are nonmotile,
      yellow-pigmented, and rod-shaped bacteria, some of which were
      frequently isolated from soil or plant-related materials. Here, we present draft
      genome sequences of three type strains of Chryseobacterium, which contain genes
      related to plant growth promotion, colonization, or stress adaptation.
AU  - Jeong JJ
AU  - Park B
AU  - Oh JY
AU  - Mannaa M
AU  - Kim YJ
AU  - Hong JK
AU  - Choi IG
AU  - Kim KD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01168-16.

PMID- 27313310
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Chryseobacterium sp. Strain GSE06, a Biocontrol Endophytic Bacterium Isolated from Cucumber (Cucumis sativus).
PG  - e00577-16
AB  - Chryseobacterium sp. strain GSE06 is a biocontrol endophytic bacterium against the destructive
      soilborne oomycete Phytophthora capsici, which causes
      Phytophthora blight of pepper. Here, we present its draft genome sequence, which
      contains genes related to biocontrol traits, such as colonization, antimicrobial
      activity, plant growth promotion, and abiotic or biotic stress adaptation.
AU  - Jeong JJ
AU  - Park BH
AU  - Park H
AU  - Choi IG
AU  - Kim KD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00577-16.

PMID- 27103726
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a Biocontrol Rhizobacterium, Chryseobacterium kwangjuense Strain KJ1R5, Isolated from Pepper (Capsicum annuum).
PG  - e00301-16
AB  - Strain KJ1R5 of the rhizobacterium ITALIC! Chryseobacterium kwangjuenseis an effective
      biocontrol agent against Phytophthora blight of pepper caused by a
      destructive soilborne oomycete, ITALIC! Phytophthora capsici Here, we present the
      draft genome sequence of strain KJ1R5, which contains genes related to
      biocontrol, plant growth promotion, and environmental stress adaptation.
AU  - Jeong JJ
AU  - Park H
AU  - Park BH
AU  - Mannaa M
AU  - Sang MK
AU  - Choi IG
AU  - Kim KD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00301-16.

PMID- 29954909
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Phosphate-Solubilizing Chryseobacterium sp. Strain ISE14, a Biocontrol and Plant Growth-Promoting Rhizobacterium Isolated from Cucumber.
PG  - e00612-18
AB  - Chryseobacterium sp. strain ISE14 is a phosphate-solubilizing endophytic bacterium that
      exhibits plant growth promotion and biocontrol activities against
      Phytophthora blight and anthracnose on pepper. Here, we report the draft genome
      sequence of strain ISE14, which contains genes relating to phosphate
      solubilization, plant growth promotion, and biocontrol traits.
AU  - Jeong JJ
AU  - Sang MK
AU  - Pathiraja D
AU  - Park B
AU  - Choi IG
AU  - Kim KD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00612-18.

PMID- 19620278
VI  - 29
DP  - 2009
TI  - Selective Anchoring of DNA Methyltransferases 3A and 3B to Nucleosomes Containing Methylated DNA.
PG  - 5366-5376
AB  - Proper DNA methylation patterns are essential for mammalian development and differentiation.
      DNA methyltransferases (DNMTs) primarily establish
      and maintain global DNA methylation patterns; however, the molecular
      mechanisms for the generation and inheritance of methylation patterns
      are still poorly understood. We used sucrose density gradients of
      nucleosomes prepared by partial and maximum micrococcal nuclease
      digestion, coupled with Western blot analysis to probe for the
      interactions between DNMTs and native nucleosomes. This method allows
      for analysis of the in vivo interactions between the chromatin
      modification enzymes and their actual nucleosomal substrates in the
      native state. We show that little free DNA methyltransferase 3A and 3B
      (DNMT3A/3B) exist in the nucleus and that almost all of the cellular
      contents of DNMT3A/3B, but not DNMT1, are strongly anchored to a subset
      of nucleosomes. This binding of DNMT3A/3B does not require the presence
      of other well-known chromatin-modifying enzymes or proteins, such as
      proliferating cell nuclear antigen, heterochromatin protein 1,
      methyl-CpG binding protein 2, Enhancer of Zeste homolog 2, histone
      deacetylase 1, and UHRF1, but it does require an intact nucleosomal
      structure. We also show that nucleosomes containing methylated SINE and
      LINE elements and CpG islands are the main sites of DNMT3A/3B binding.
      These data suggest that inheritance of DNA methylation requires cues
      from the chromatin component in addition to hemimethylation.
AU  - Jeong S
AU  - Liang GN
AU  - Sharma S
AU  - Lin JC
AU  - Choi SH
AU  - Han H
AU  - Yoo CB
AU  - Egger G
AU  - Yang AS
AU  - Jones PA
PT  - Journal Article
TA  - Mol. Cell. Biol.
JT  - Mol. Cell. Biol.
SO  - Mol. Cell. Biol. 2009 29: 5366-5376.

PMID- 24831144
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Acid-Tolerant Clostridium drakei SL1T, a Potential Chemical Producer through Syngas Fermentation.
PG  - e00387-14
AB  - Clostridium drakei SL1(T) is a strictly anaerobic, H2-utilizing, and acid-tolerant acetogen
      isolated from an acidic sediment that is a potential
      platform for commodity chemical production from syngas fermentation. The draft
      genome sequence of this strain will enable determination of the acid resistance
      and autotrophic pathway of the acetogen.
AU  - Jeong Y
AU  - Song Y
AU  - Shin HS
AU  - Cho BK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00387-14.

PMID- 19449302
VI  - 238
DP  - 2009
TI  - Cytoplasmic Localization of Oocyte-Specific Variant of Porcine DNA Methyltransferase-1 During Early Development.
PG  - 1666-1673
AB  - DNA methyltransferase-1 (Dnmt1) is involved in the maintenance of genomic methylation
      patterns. Rather than full-length Dnmt1, mouse
      oocytes have a truncated variant called Dnmt1o. Immunofluorescence data
      showed that Dnmt1o localized to the cytoplasm, but this has not been
      confirmed using more direct methods. The cytoplasmic localization of
      Dnmt1o has been assigned to the main cause of global DNA demethylation
      in early mouse embryos. We studied localization of Dnmt1o in mouse and
      pig embryos. We identified pig Dnmt1o protein and its transcript with
      unique 5'-end sequence. Physically separating mouse and pig 2-cell
      embryos into their nuclear and cytoplasmic components demonstrated that
      Dnmt1o of both species localized to the cytoplasm. Cloned pig embryos
      had Dnmt1o as the main form, with no indication of somatic Dnmt1. These
      findings indicate that Dnmt1o is cytoplasmic during early development;
      its presence in both pig and mouse embryos further suggests that Dnmt1o
      is conserved in mammals. Developmental Dynamics 238:1666-1673, 2009.
AU  - Jeong YS
AU  - Oh KB
AU  - Park JS
AU  - Kim JS
AU  - Kang YK
PT  - Journal Article
TA  - Dev. Dyn.
JT  - Dev. Dyn.
SO  - Dev. Dyn. 2009 238: 1666-1673.

PMID- 26450729
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Nine Pseudomonas aeruginosa Strains, Including Eight Clinical Isolates.
PG  - e01154-15
AB  - We report on nine draft genomes of Pseudomonas aeruginosa isolates, assembled using a hybrid
      paired-end and Nextera mate-pair library approach. Eight are of clinical origin, and one is
      the ATCC 27853 strain. We also report their multilocus sequence types.
AU  - Jeraldo P
AU  - Cunningham SA
AU  - Quest D
AU  - Sikkink RA
AU  - O'Brien D
AU  - Eckloff BW
AU  - Patel R
AU  - Chia N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01154-15.

PMID- 26021920
VI  - 3
DP  - 2015
TI  - Draft genome sequences of 24 microbial strains assembled from direct sequencing from 4 stool samples.
PG  - e00526-15
AB  - The ability to assemble genomes from metagenomic sequencing avoids the need for culture and
      any associated culture biases. We assembled 24 essentially complete
      draft genomes from metagenomic pair-end and size-selected mate pair sequencing
      from 4 stool samples, 2 from subjects diagnosed with colorectal cancer and 2 from
      healthy controls.
AU  - Jeraldo P
AU  - Hernandez A
AU  - White BA
AU  - O'Brien D
AU  - Ahlquist D
AU  - Boardman L
AU  - Chia N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00526-15.

PMID- 18241920
VI  - 59
DP  - 2008
TI  - Comparative analysis of eight Arthrobacter plasmids.
PG  - 73-85
AB  - Despite the prevalence of Arthrobacter in the environment little is known
      about their plasmids, or the capacity of Arthrobacter plasmids to mediate
      horizontal gene transfer. In this study, we compared eight plasmids from
      five Arthrobacter strains in order to identify putative core maintenance
      genes for replication, segregation, and conjugation. Iteron like sequences
      were identified on some of the plasmids; however, no genes with obvious
      similarity to known replication sequences such as an origin of
      replication, or rep genes were identified. All eight plasmids contained a
      putative conjugation system. Genes with similarity to a relaxase, coupling
      protein, and various components of a type IV secretion system were
      identified on each plasmid; it appears that three different systems may be
      present. Putative parA partitioning genes were found in all of the
      plasmids. Each of the Arthrobacter strains examined contained a putative
      parB gene; however, of the three plasmids in Arthrobacter strain FB24 only
      one plasmid had a putative parB gene. Cluster analysis of many of the
      Arthrobacter genes suggested that they often formed branches within
      existing families of plasmid maintenance genes. Comparison of a
      concatenation of all the maintenance genes from each plasmid suggests that
      the eight Arthrobacter plasmids represent multiple evolutionary pathways.
AU  - Jerke K
AU  - Nakatsu CH
AU  - Beasley F
AU  - Konopka A
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 2008 59: 73-85.

PMID- 12427958
VI  - 148
DP  - 2002
TI  - Characterization of a novel Vibrio pathogenicity island (VPI-2) encoding neuraminidase (nanH) among toxigenic Vibrio cholerae isolates.
PG  - 3681-3693
AB  - Acquisition of virulence genes encoded on mobile genetic elements has played an important role
      in the emergence of pathogenic isolates of
      Vibrio cholerae, the causative agent of the diarrhoeal disease cholera.
      The genes encoding cholera toxin (ctxAB) the main cause of profuse
      secretory diarrhoea in cholera, are encoded on a filamentous
      bacteriophage CTXphi. The toxin coregulated pilus (TCP), an essential
      intestinal colonization factor, was originally designated as part of a
      pathogenicity island named the Vibrio pathogenicity island (VPI), but
      this island has more recently been proposed to be the genome of a
      filamentous phage, VPIphi. In this study, it is shown that nanH, which
      encodes neuraminidase, maps within a novel pathogenicity island
      designated VP1-2. The 57-3 kb VP1-2 has all of the characteristic
      features of a pathogenicity island, including the presence of a
      bacteriophage-like integrase (int), insertion in a tRNA gene (serine)
      and the presence of direct repeats at the chromosomal integration
      sites. Additionally, the G+C content of VP1-2 (42 mol%) is considerably
      lower than that of the entire genome (47 mol%). VPI-2 encodes several
      gene clusters, such as a restriction modification system (hsdR and
      hsdM) and genes required for the utilization of amino sugars (nan-nag
      region) as well as neuraminidase. To determine the distribution of
      VPI-2 among V. cholerae, 78 natural isolates were examined using PCR
      and Southern hybridization analysis for the presence of this region.
      All toxigenic V. cholerae 01 serogroup isolates examined contained
      VPI-2, whereas non-toxigenic isolates lacked the island. Of 14 V.
      cholerae 0139 serogroup isolates examined, only one strain, MO2,
      contained the entire 57-3 kb island, whereas 13 0139 isolates contained
      only a 20-0 kb region with most of the 5' region of VPI-2 which
      included nanH deleted in these strains.
AU  - Jermyn WS
AU  - Boyd EF
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2002 148: 3681-3693.

PMID- 23012285
VI  - 194
DP  - 2012
TI  - Draft Genome Sequences of Two Campylobacter jejuni Clinical Isolates, NW and D2600.
PG  - 5707-5708
AB  - The Campylobacter jejuni human clinical isolates NW and D2600 colonized C57BL/6
      interleukin-10-deficient (IL-10(-/-)) mice without inducing a robust inflammatory
      response (J. A. Bell et al., BMC Microbiol. 9:57, 2009). We announce draft genome
      sequences of NW and D2600 to facilitate comparisons with strains that induce
      gastrointestinal inflammation in this mouse model.
AU  - Jerome JP
AU  - Klahn BD
AU  - Bell JA
AU  - Barrick JE
AU  - Brown CT
AU  - Mansfield LS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5707-5708.

PMID- 15039089
VI  - 33
DP  - 2004
TI  - Mapping chromatin structure in vivo using DNA methyltransferases.
PG  - 68-80
AB  - Cytosine-5 DNA methyltransferases (C5 DMTases) are effective reagents for analyzing chromatin
      and footprinting DNA-bound factors in vivo.
      Cytosine methylation in accessible regions is assayed positively by the
      PCR-based technique of bisulfite sequencing. In this article, we
      outline two complementary uses for the DNA methyltransferase CviPI
      (M.CviPI, GC specificity) in probing chromatin organization. First, we
      describe the use of the naturally occurring, free enzyme as a
      diffusible probe to map changes in nucleosome structure and to
      footprint factor interactions at cis-regulatory sequences. In a second
      application, termed targeted gene methylation (TAGM), the DMTase is
      targeted via in-frame fusion to a DNA-binding factor. The rapid
      accumulation of DNA methylation enables highly sensitive detection of
      factor binding. Both strategies can be applied with any C5 DMTase, such
      as M.SssI, which also possesses a short-recognition specificity (CG). A
      description of methods for constructing C5 DMTase-expressing strains of
      Saccharomyces cerevisiae and analyzing chromatin regions is provided.
      We also include comprehensive protocols for the isolation and bisulfite
      treatment of genomic DNA as well as the subsequent bisulfite sequencing
      steps. Data demonstrating the efficacy of both DMTase probing
      techniques, theoretical considerations, and experimental analyses are
      presented at GAL1 and PHO5.
AU  - Jessen WJ
AU  - Dhasarathy A
AU  - Hoose SA
AU  - Carvin CD
AU  - Risinger AL
AU  - Kladde MP
PT  - Journal Article
TA  - Methods
JT  - Methods
SO  - Methods 2004 33: 68-80.

PMID- 8041711
VI  - 91
DP  - 1994
TI  - Snapshot blotting: transfer of nucleic acids and nucleoprotein complexes from electrophoresis gels to grids for electron microscopy.
PG  - 6870-6874
AB  - We present a technique, "snapshot blotting", for the electrophoretic transfer of nucleic acids
      and nucleoprotein complexes in gel electrophoresis bands onto highly stable carbon film-coated
      grids for imaging by electron microscopy.  The method permits structural analysis of
      macromolecular species that have been resolved by a gel mobility-shift assay.  To demonstrate
      the efficiency and integrity of the transfer process for a multiprotein-DNA assembly, we have
      imaged various species of prokaryotic transcription complex, using the cleavage-defective
      EcoRI(Q111) protein as an orientation marker and as a blockade of transcription elongation.
      Snapshot blotting should be of great utility in the structural characterization of nucleic
      acids and protein-nucleic acid interactions.
AU  - Jett SD
AU  - Bear DG
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1994 91: 6870-6874.

PMID- 23908295
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Persistent Cystic Fibrosis Isolate Pseudomonas aeruginosa Strain RP73.
PG  - e00568-13
AB  - Pseudomonas aeruginosa can establish lifelong chronic airway infections in cystic fibrosis
      (CF) patients. However, the genetic features associated with long-term
      persistence in the lung are not understood. We sequenced the genome of P.
      aeruginosa strain RP73, which was isolated after 16.9 years of chronic lung
      infection in a CF patient.
AU  - Jeukens J
AU  - Boyle B
AU  - Bianconi I
AU  - Kukavica-Ibrulj I
AU  - Tummler B
AU  - Bragonzi A
AU  - Levesque RC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00568-13.

PMID- 26227609
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Triclosan-Resistant Cystic Fibrosis Isolate Achromobacter xylosoxidans CF304.
PG  - e00865-15
AB  - Achromobacter xylosoxidans is an emerging opportunistic pathogen. Here, we present the genome
      sequence of cystic fibrosis isolate CF304. Assembly resulted
      in 29 contigs adding up to 6.3 Mbp. This is the second genome sequence for a
      cystic fibrosis isolate, and little is known about the genetic basis of
      pathogenicity in this organism.
AU  - Jeukens J
AU  - Freschi L
AU  - Kukavica-Ibrulj I
AU  - Nguyen D
AU  - Levesque RC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00865-15.

PMID- 26450741
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Two Lipopeptide-Producing Strains of Bacillus methylotrophicus.
PG  - e01176-15
AB  - Bacillus methylotrophicus is implicated in phytostimulation and disease suppression of
      agricultural and bioenergy crops. Here, we present the genome sequences of B. methylotrophicus
      strains B26 and OB9. Their assembly resulted in  26 and 24 contigs, respectively. These
      strains are well suited for comparative genomics studies and the evaluation of commercially
      valuable biomolecular compounds.
AU  - Jeukens J
AU  - Kukavica-Ibrulj I
AU  - Freschi L
AU  - Jabaji S
AU  - Levesque RC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01176-15.

PMID- 25481098
VI  - 194
DP  - 2015
TI  - A new prototype IIS/IIC/IIG endonuclease-methyltransferase TsoI from the thermophile Thermus scotoductus, recognising 5 '-TARCCA(N-11/9)-3 ' sequences.
PG  - 19-26
AB  - The Thermus sp. family of IIS/IIG/IIC enzymes includes the thermostable, bifunctional, fused
      restriction endonuclease (REase)-methyltransferases (MTase): TaqII, Tth111II/TthHB27I, TspGWI,
      TspDTI and TsoI. The enzymes are large proteins (approximately 120 kDa), their enzymatic
      activities are affected by S-adenosylmethionine (SAM), they recognise similar asymmetric
      cognate sites and cleave at a distance of 11/9 nucleotides (nt). The enzymes exhibit
      similarities of their amino acid (aa) sequences and DNA catalytic motifs. Thermus sp. enzymes
      are an example of functional aa sequence homologies among REases recognising different, yet
      related DNA sequences. The family consists of TspGWI- and TspDTI-subfamilies. TsoI appears to
      be a non-identical 'triplet', related to TspDTI and Tth11 1II/TthHB27I. The discovery of
      TsoI, purified from Thermus scotoductus, is described. This prototype, displaying a novel
      specificity, which was determined by: (i) cleavage of a reference plasmid and bacteriophage
      DNA, (ii) cleavage of custom PCR DNA substrates, (iii) run-off sequencing of cleavage products
      and (iv) shotgun cloning and sequencing of bacteriophage lambda (X) DNA digested with TsoI.
      The enzyme recognises a degenerated 5'-TARCCA-3' sequence, whereas DNA strands are cut 11/9
      nt downstream. The discovery of the TsoI prototype is of practical importance in
      biotechnology, as it extends the palette of cleavage specificities for gene cloning.
AU  - Jezewska-Frackowiak J
AU  - Lubys A
AU  - Vitkute J
AU  - Zakareviciene L
AU  - Zebrowska J
AU  - Krefft D
AU  - Skowron MA
AU  - Zylicz-Stachula A
AU  - Skowron PM
PT  - Journal Article
TA  - J. Biotechnol.
JT  - J. Biotechnol.
SO  - J. Biotechnol. 2015 194: 19-26.

PMID- 26205861
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Broad-Spectrum Antifungal Bacterium Burkholderia gladioli Strain NGJ1, Isolated from Healthy Rice Seeds.
PG  - e00803-15
AB  - We report here the draft genome sequence of Burkholderia gladioli strain NGJ1. The strain was
      isolated from healthy rice seeds and exhibits broad-spectrum
      antifungal activity against several agriculturally important pathogens, including
      Rhizoctonia solani, Magnaporthe oryzae, Venturia inaequalis, and Fusarium
      oxysporum.
AU  - Jha G
AU  - Tyagi I
AU  - Kumar R
AU  - Ghosh S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00803-15.

PMID- 2829965
VI  - 949
DP  - 1988
TI  - Investigation of the complexes of EcoRI endonuclease with decanucleotides containing canonical and modified recognition sequences using fluorescence and optical detection of magnetic resonance spectroscopy.
PG  - 189-194
AB  - The binding of EcoRI endonuclease to the oligonucleotides d(GCGAATTCGC) and
      d(GCGAA) (5BrdU) (5BrdU) d(CGC) has been investigated to determine whether
      stacking interactions occur between tryptophan residues and the DNA bases.
      Fluorescence binding isotherms show that the decamer containing the canonical
      and that containing the modified recognition sequence bind with comparable
      affinity.  Optically detected magnetic resonance spectra show limited
      perturbations of the Trp zero-field splitting parameters, which are assigned to
      electrical field effects.  No evidence for Trp stacking interactions has been
      found.
AU  - Jhon N-I
AU  - Casas-Finet JR
AU  - Maki AH
AU  - Modrich P
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1988 949: 189-194.

PMID- 23469349
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of the Piezophilic, Mesophilic, Sulfate-Reducing Bacterium Desulfovibrio hydrothermalis AM13(T.).
PG  - e00226-12
AB  - AM13 is a piezophilic, mesophilic, hydrogenotrophic sulfate-reducing bacterium collected from
      a deep-sea hydrothermal chimney on the East Pacific Rise (2,600 m
      depth, 13 degrees N). We report the genome sequence of this bacterium, which
      includes a 3,702,934-bp chromosome and a circular plasmid of 5,328 bp.
AU  - Ji B
AU  - Gimenez G
AU  - Barbe V
AU  - Vacherie B
AU  - Rouy Z
AU  - Amrani A
AU  - Fardeau ML
AU  - Bertin P
AU  - Alazard D
AU  - Leroy S
AU  - Talla E
AU  - Ollivier B
AU  - Dolla A
AU  - Pradel N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00226-12.

PMID- 26911736
VI  - 6
DP  - 2016
TI  - Bacterial cellulose synthesis mechanism of facultative anaerobe Enterobacter sp. FY-07.
PG  - 21863
AB  - Enterobacter sp. FY-07 can produce bacterial cellulose (BC) under aerobic and
      anaerobic conditions. Three potential BC synthesis gene clusters (bcsI, bcsII and
      bcsIII) of Enterobacter sp. FY-07 have been predicted using genome sequencing and
      comparative genome analysis, in which bcsIII was confirmed as the main
      contributor to BC synthesis by gene knockout and functional reconstitution
      methods. Protein homology, gene arrangement and gene constitution analysis
      indicated that bcsIII had high identity to the bcsI operon of Enterobacter sp.
      638; however, its arrangement and composition were same as those of BC
      synthesizing operon of G. xylinum ATCC53582 except for the flanking sequences.
      According to the BC biosynthesizing process, oxygen is not directly involved in
      the reactions of BC synthesis, however, energy is required to activate
      intermediate metabolites and synthesize the activator, c-di-GMP. Comparative
      transcriptome and metabolite quantitative analysis demonstrated that under
      anaerobic conditions genes involved in the TCA cycle were downregulated, however,
      genes in the nitrate reduction and gluconeogenesis pathways were upregulated,
      especially, genes in three pyruvate metabolism pathways. These results suggested
      that Enterobacter sp. FY-07 could produce energy efficiently under anaerobic
      conditions to meet the requirement of BC biosynthesis.
AU  - Ji K
AU  - Wang W
AU  - Zeng B
AU  - Chen S
AU  - Zhao Q
AU  - Chen Y
AU  - Li G
AU  - Ma T
PT  - Journal Article
TA  - Sci. Rep.
JT  - Sci. Rep.
SO  - Sci. Rep. 2016 6: 21863.

PMID- 27151796
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Zhouia amylolytica AD3, Isolated from Tidal Flat Sediment.
PG  - e00327-16
AB  - Zhouia amylolytica AD3 was isolated from tidal flat sediment at Taean, South Korea. We report
      here the draft genome sequence of Z. amylolytica AD3, which is
      the first report of a genome sequence of the genus Zhouia The genomic information
      will provide a better understanding of the physiology, adaptation, and evolution
      of Zhouia species.
AU  - Jia B
AU  - Jin HM
AU  - Lee HJ
AU  - Jeon CO
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00327-16.

PMID- 
VI  - 
DP  - 2007
TI  - Crystallographic and biochemical studies of mammalian de novo DNA methyltransferase Dnmt3.
PG  - 1-206
AB  - The mammalian DNA methyltransferase 3 (Dnmt3) family is responsible for de novo genomic
      methylation and consists of two active methyltransferases, Dnmt3a and Dnmt3b, and their
      homolog Dnmt3L. Structural and biochemical characterization have identified F261 of human
      DNMT3L as a key residue important for its homo-dimerization and its hetero-dimerization with
      Dnmt3a. This study provides a functional assessment for the tail-to-tail interface and key
      residues observed in the crystal structure of DNMT3L. A structure of the C-terminal domain of
      Dnmt3L in complex with the catalytic domain of active Dnmt3a has been determined in the
      presence of methyl donor analog AdoHcy. The complex structure showed that the heterodimer of
      Dnm3a-3L further dimerizes through Dnmt3a-3a interaction, forming a tetrameric enzyme complex
      with two active sites. Substitution of key residues from Dnmt3a-3a or Dnmt3a-3L interfaces
      eliminated the enzymatic activity of Dnmt3a. The functional implication of the molecular
      architecture of the Dnmt3a-Dnmt3L tetramer with two active sites is being proposed. This
      structure is the first of a genuine mammalian DNA methyltransferase as well as the first of
      any methyltransferase in complex with a regulator protein. This study indicates the complexity
      of mammalian Dnmt in comparison with bacterial enzymes in term of oligomeric state, substrate
      recognition and functional regulation.
AU  - Jia D
PT  - Journal Article
TA  - Ph.D. Thesis, Emory Univ., Atlanta, GA, USA
JT  - Ph.D. Thesis, Emory Univ., Atlanta, GA, USA
SO  - Ph.D. Thesis, Emory Univ., Atlanta, GA, USA 2007 : 1-206.

PMID- 17713477
VI  - 449
DP  - 2007
TI  - Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation.
PG  - 248-251
AB  - Genetic imprinting, found in flowering plants and placental mammals, uses DNA methylation to
      yield gene expression that is dependent on the parent of origin. DNA methyltransferase 3a
      (Dnmt3a) and its regulatory factor, DNA methyltransferase 3-like protein (Dnmt3L), are both
      required for the de novo DNA methylation of imprinted genes in mammalian germ cells. Dnmt3L
      interacts specifically with unmethylated lysine 4 of histone H3 through its amino-terminal PHD
      (plant homeodomain)-like domain. Here we show, with the use of crystallography, that the
      carboxy-terminal domain of human Dnmt3L interacts with the catalytic domain of Dnmt3a,
      demonstrating that Dnmt3L has dual functions of binding the unmethylated histone tail and
      activating DNA methyltransferase. The complexed C-terminal domains of
      Dnmt3a and Dnmt3L showed further dimerization through Dnmt3a-Dnmt3a
      interaction, forming a tetrameric complex with two active sites.
      Substitution of key non-catalytic residues at the Dnmt3a-Dnmt3L interface
      or the Dnmt3a-Dnmt3a interface eliminated enzymatic activity. Molecular
      modelling of a DNA-Dnmt3a dimer indicated that the two active sites are
      separated by about one DNA helical turn. The C-terminal domain of Dnmt3a
      oligomerizes on DNA to form a nucleoprotein filament. A periodicity in the
      activity of Dnmt3a on long DNA revealed a correlation of methylated CpG
      sites at distances of eight to ten base pairs, indicating that
      oligomerization leads Dnmt3a to methylate DNA in a periodic pattern. A
      similar periodicity is observed for the frequency of CpG sites in the
      differentially methylated regions of 12 maternally imprinted mouse genes.
      These results suggest a basis for the recognition and methylation of
      differentially methylated regions in imprinted genes, involving the
      detection of both nucleosome modification and CpG spacing.
AU  - Jia D
AU  - Jurkowska RZ
AU  - Zhang X
AU  - Jeltsch A
AU  - Cheng X
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2007 449: 248-251.

PMID- 27660775
VI  - 4
DP  - 2016
TI  - Genome Sequence of the Oral Probiotic Streptococcus salivarius JF.
PG  - e00971-16
AB  - Streptococcus salivarius is a nonpathogenic Gram-positive bacterium and the predominant
      colonizer of the oral microbiota. It finds a wide application in the
      prevention of upper respiratory tract infections, also reducing the frequency of
      other main pathogens. Here, we present the complete genome sequence of the oral
      probiotic S. salivarius JF.
AU  - Jia F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00971-16.

PMID- 27634996
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Lactobacillus oris J-1, a Potential Probiotic Isolated from the Human Oral Microbiome.
PG  - e00970-16
AB  - Lactobacilli can exert health-promoting effects in the human oral microbiome through many
      mechanisms, including pathogen inhibition, maintenance of microbial
      balance, immunomodulation, and enhancement of the epithelial barrier function.
      Here, we present the complete genome sequence of a potential probiotic,
      Lactobacillus oris J-1, that was isolated from the oral cavity of a health child.
AU  - Jia F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00970-16.

PMID- 28007860
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of the Industrial Bacterium Ketogulonicigenium vulgare SKV.
PG  - e01426-16
AB  - Ketogulonicigenium vulgare has been widely used in vitamin C two-step fermentation, which
      converts l-sorbose to 2-keto-l-gluonic acid. Here, the
      complete genome of K. vulgare SKV, which performs better fermentation production
      than K. vulgare Hbe602, is deciphered to understand the key differences in
      metabolism between K. vulgare strains SKV and Hbe602.
AU  - Jia N
AU  - Ding MZ
AU  - Du YZ
AU  - Feng S
AU  - Gao F
AU  - Yuan YJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01426-16.

PMID- 26248285
VI  - 10
DP  - 2015
TI  - Genome Sequence of Bacillus endophyticus and Analysis of Its Companion Mechanism in the Ketogulonigenium vulgare-Bacillus Strain Consortium.
PG  - E0135104
AB  - Bacillus strains have been widely used as the companion strain of
      Ketogulonigenium vulgare in the process of vitamin C fermentation. Different
      Bacillus strains generate different effects on the growth of K. vulgare and
      ultimately influence the productivity. First, we identified that Bacillus
      endophyticus Hbe603 was an appropriate strain to cooperate with K. vulgare and
      the product conversion rate exceeded 90% in industrial vitamin C fermentation.
      Here, we report the genome sequencing of the B. endophyticus Hbe603 industrial
      companion strain and speculate its possible advantage in the consortium. The
      circular chromosome of B. endophyticus Hbe603 has a size of 4.87 Mb with GC
      content of 36.64% and has the highest similarity with that of Bacillus megaterium
      among all the bacteria with complete genomes. By comparing the distribution of
      COGs with that of Bacillus thuringiensis, Bacillus cereus and B. megaterium, B.
      endophyticus has less genes related to cell envelope biogenesis and signal
      transduction mechanisms, and more genes related to carbohydrate transport and
      metabolism, energy production and conversion, as well as lipid transport and
      metabolism. Genome-based functional studies revealed the specific capability of
      B. endophyticus in sporulation, transcription regulation, environmental
      resistance, membrane transportation, extracellular proteins and nutrients
      synthesis, which would be beneficial for K. vulgare. In particular, B.
      endophyticus lacks the Rap-Phr signal cascade system and, in part, spore coat
      related proteins. In addition, it has specific pathways for vitamin B12 synthesis
      and sorbitol metabolism. The genome analysis of the industrial B. endophyticus
      will help us understand its cooperative mechanism in the K. vulgare-Bacillus
      strain consortium to improve the fermentation of vitamin C.
AU  - Jia N
AU  - Du J
AU  - Ding MZ
AU  - Gao F
AU  - Yuan YJ
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2015 10: E0135104.

PMID- 28596389
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Bacillus subtilis J-5, a Potential Biocontrol Agent.
PG  - e00275-17
AB  - Bacillus subtilis J-5 was isolated from tomato rhizosphere soil and exhibited strong
      inhibitory activity against Botrytis cinerea To shed light on the
      molecular mechanism underlying the biological control on phytopathogens, the
      whole genome of this strain was sequenced. Genes encoding antimicrobial compounds
      and the regulatory systems were identified in the genome.
AU  - Jia Z
AU  - Jin W
AU  - Huang Y
AU  - Song S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00275-17.

PMID- 23012293
VI  - 194
DP  - 2012
TI  - Genome Sequence of a Cold-Adaptable Sulfamethoxazole-Degrading Bacterium, Pseudomonas psychrophila HA-4.
PG  - 5721
AB  - Pseudomonas psychrophila HA-4 is a cold-adaptable, sulfamethoxazole-degrading bacterium. The
      genes related to its cold adaptation mechanism and
      sulfamethoxazole metabolism were unknown. We present the draft genome of strain
      HA-4. It could provide further insight into the sulfamethoxazole-degrading
      mechanism of strain HA-4.
AU  - Jiang B
AU  - Cui D
AU  - Li A
AU  - Gai Z
AU  - Ma F
AU  - Yang J
AU  - Ren N
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5721.

PMID- 23144406
VI  - 194
DP  - 2012
TI  - Genome Sequence of Borrelia garinii Strain NMJW1, Isolated from China.
PG  - 6660-6661
AB  - We announce the draft genome sequence of Borrelia garinii strain NMJW1, isolated  from Ixodes
      persulcatus in northeastern China. The 902,789-bp linear chromosome
      (28.4% GC content) contains 813 open reading frames, 33 tRNAs, and 4 complete
      rRNAs.
AU  - Jiang B
AU  - Yao H
AU  - Tong Y
AU  - Yang X
AU  - Huang Y
AU  - Jiang J
AU  - Cao W
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6660-6661.

PMID- 23618713
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Efficient Bioflocculant-Producing Bacterium Paenibacillus sp. Strain A9.
PG  - e00131-13
AB  - Paenibacillus sp. strain A9 is an important bioflocculant-producing bacterium, isolated from a
      soil sample, and is pale pink-pigmented, aerobic, and
      Gram-positive. Here, we report the draft genome sequence and the initial findings
      from a preliminary analysis of strain A9, which is a novel species of
      Paenibacillus.
AU  - Jiang BH
AU  - Liu JL
AU  - Hu XM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00131-13.

PMID- 22326795
VI  - 423
DP  - 2012
TI  - A bioluminescence assay for DNA methyltransferase activity based on methylation-resistant cleavage.
PG  - 224-228
AB  - DNA methyltransferase (MTase) is a kind of important regulatory factor in various biological
      processes. Current methods to investigate DNA
      MTase activity are still limited in the sensitivity and/or generality.
      Therefore, developing methods with high sensitivity and improved
      generality is needed. Here, we develop a new bioluminescence strategy
      based on methylation-resistant cleavage and protein expression in vitro
      to detect DNA MTase activity. In the strategy, Dam MTase was used as a
      model enzyme and Mbol as the methylation-resistant endonuclease, and
      luciferase reporter DNA (LR-DNA) was used as their action target.
      Because the completely methylated LR-DNA could be expressed as
      detectable luciferase, Dam MTase activity was quantified by measuring
      the luminescence intensity of the expressed luciferase. The assay
      provides a very low detection limit (0.08 U/ml) as well as a wide
      linear range (0.2-100 U/ml). Besides, the analysis mode has improved
      generality and could be extended to the detection of other DNA MTases
      and the corresponding inhibitor screening.
AU  - Jiang C
AU  - Yan CY
AU  - Huang C
AU  - Jiang JH
AU  - Yu RQ
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 2012 423: 224-228.

PMID- 28860247
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequence of Bacillus cereus AR156, a Potential Biocontrol Agent with High Soilborne Disease Biocontrol Efficacy and Plant Growth Promotion.
PG  - e00886-17
AB  - Bacillus cereus AR156 was originally isolated from the forest soil of Zhenjiang,  a city in
      China. To shed new light on the molecular mechanisms underlying the
      biological control of soilborne pathogens, the whole genome of this strain was
      sequenced. Here, we report the draft genome sequence of this strain, consisting
      of a single circularized contig measuring 5.66 Mb, with an average GC content of
      35.5% and 5,367 open reading frames.
AU  - Jiang CH
AU  - Chen Y
AU  - Yan F
AU  - Fan ZH
AU  - Guo JH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00886-17.

PMID- 18762393
VI  - 133
DP  - 2009
TI  - Identification and distribution of putative virulent genes in strains of Streptococcus suis serotype 2.
PG  - 309-316
AB  - In order to identify gene sequences unique to the virulent strains,
      suppression subtractive hybridization (SSH) was conducted using virulent
      Streptococcus suis type 2 (SS2) strain HA9801 and avirulent S. suis type 2
      strain T15. Thirty genomic regions were absent in T15, and the DNA
      sequences of these regions in HA9801 were determined. These DNA fragments,
      containing putative virulence genes, encoded 28 proteins that were
      homologous to proteins involved in various aspects of cellular surface
      structure, molecular synthesis, energy metabolism, regulation, transport
      systems and others of unknown function. According to the published SS2
      genomic sequence of the Chinese strain 98HAH33, PCR primers for 14
      significant DNA fragments were designed and used for detection of the
      distribution of these fragments in S. suis strains from different sources,
      serotypes, regions, groups and times. The results showed that these 14 DNA
      fragments were widely distributed in 37 detected SS2 strains, yet were
      absent among the avirulent strain T15. Moreover, these fragments could be
      detected in other serotypes of S. suis, but each serotype had a different
      distribution of the fragments.
AU  - Jiang H
AU  - Fan HJ
AU  - Lu CP
PT  - Journal Article
TA  - Vet. Microbiol.
JT  - Vet. Microbiol.
SO  - Vet. Microbiol. 2009 133: 309-316.

PMID- 
VI  - 25
DP  - 2000
TI  - Purification of restriction endonuclease Bsp63I by two step affinity chromatography.
PG  - 74-77
AB  - Restriction endonuclease Bsp63I has been isolated and purified by affinity chromatography on
      self-made DNA Sepharose4B and Cibacron Blue F3GA Sepharose 4B from Bacillus sphaericus 63.
      The purified enzyme was found to be homogenous as judged by polyacrylamide gel
      electrophoresis.  The specific activity of the enzyme is greater than 61400 units per mg
      protein and the yield of the purified enzyme is greater than 130 units per gram wet cells.
AU  - Jiang H
AU  - Zou G
AU  - Huang L
AU  - Zhu R
PT  - Journal Article
TA  - Xinan Shifan Daxue Xuebao, Ziran Kexueban
JT  - Xinan Shifan Daxue Xuebao, Ziran Kexueban
SO  - Xinan Shifan Daxue Xuebao, Ziran Kexueban 2000 25: 74-77.

PMID- 22965099
VI  - 194
DP  - 2012
TI  - Draft Genome Sequences of Enterobacter sp. Isolate Ag1 from the Midgut of the Malaria Mosquito Anopheles gambiae.
PG  - 5481
AB  - An isolate of Enterobacter sp. was obtained from the microbial community within the gut of the
      Anopheles gambiae mosquito, a major malaria vector in Africa. This
      genome was sequenced and annotated. The genome sequences will facilitate
      subsequent efforts to characterize the mosquito gut microbiome.
AU  - Jiang J
AU  - Alvarez C
AU  - Kukutla P
AU  - Yu W
AU  - Xu J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5481.

PMID- 23407619
VI  - 6
DP  - 2012
TI  - Complete genome sequence of Thauera aminoaromatica strain MZ1T.
PG  - 325-335
AB  - Thauera aminoaromatica strain MZ1T, an isolate belonging to genus Thauera, of the family
      Rhodocyclaceae and the class the Betaproteobacteria, has been
      characterized for its ability to produce abundant exopolysaccharide and degrade
      various aromatic compounds with nitrate as an electron acceptor. These
      properties, if fully understood at the genome-sequence level, can aid in
      environmental processing of organic matter in anaerobic cycles by
      short-circuiting a central anaerobic metabolite, acetate, from microbiological
      conversion to methane, a critical greenhouse gas. Strain MZ1T is the first strain
      from the genus Thauera with a completely sequenced genome. The 4,496,212 bp
      chromosome and 78,374 bp plasmid contain 4,071 protein-coding and 71 RNA genes,
      and were sequenced as part of the DOE Community Sequencing Program CSP_776774.
AU  - Jiang K et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 6: 325-335.

PMID- 26634017
VI  - 10
DP  - 2015
TI  - Complete genome sequence of Salinicoccus halodurans H3B36, isolated from the Qaidam Basin in China.
PG  - 116
AB  - Salinicoccus halodurans H3B36 is a moderately halophilic bacterium isolated from  a sediment
      sample of Qaidam Basin at 3.2 m vertical depth. Strain H3B36
      accumulate N (alpha)-acetyl-alpha-lysine as compatible solute against salinity
      and heat stresses and may have potential applications in industrial
      biotechnology. In this study, we sequenced the genome of strain H3B36 using
      single molecule, real-time sequencing technology on a PacBio RS II instrument.
      The complete genome of strain H3B36 was 2,778,379 bp and contained 2,853
      protein-coding genes, 12 rRNA genes, and 61 tRNA genes with 58 tandem repeats,
      six minisatellite DNA sequences, 11 genome islands, and no CRISPR repeat region.
      Further analysis of epigenetic modifications revealed the presence of 11,000
      m4C-type modified bases, 7,545 m6A-type modified bases, and 89,064 other modified
      bases. The data on the genome of this strain may provide an insight into the
      metabolism of N (alpha)-acetyl-alpha-lysine.
AU  - Jiang K
AU  - Xue Y
AU  - Ma Y
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 116.

PMID- 2059851
VI  - 7
DP  - 1991
TI  - A generic algorithm for finding restriction sites within DNA sequences.
PG  - 249-256
AB  - This paper describes a generic algorithm for finding restriction sites within
      DNA sequences.  The generality of the algorithm is made possible through the
      use of set theory.  Basic elements of DNA sequences, i.e. nucleotides (bases),
      are represented in sets, and DNA sequences, whether specific, ambiguous or even
      protein-coding, are represented as sequences of those sets.  The set
      intersection operation demonstrates its ability to perform pattern-matching
      correctly on various DNA sequences.  The performance analysis showed that the
      degree of complexity of the pattern matching is reduced from exponential to
      linear.  An example is given to show the actual and potential restriction
      sites, derived by the generic algorithm, in the DNA sequence template coding
      for a synthetic calmodulin.
AU  - Jiang K
AU  - Zheng J
AU  - Higgins SB
PT  - Journal Article
TA  - Comput. Appl. Biosci.
JT  - Comput. Appl. Biosci.
SO  - Comput. Appl. Biosci. 1991 7: 249-256.

PMID- 28074121
VI  - 12
DP  - 2017
TI  - Complete genome sequence and whole-genome phylogeny of Kosmotoga pacifica type strain SLHLJ1T from an East Pacific hydrothermal sediment.
PG  - 3
AB  - Kosmotoga pacifica strain SLHLJ1T is a thermophilic chemoorganoheterotrophic bacterium
      isolated from a deep-sea hydrothermal sediment. It belongs to the
      physiologically homogeneous Thermotogaceae family. Here, we describe the
      phenotypic features of K. pacifica together with its genome sequence and
      annotation. The chromosome has 2,169,170 bp, organized in one contig. A total of
      1897 candidate protein-encoding genes and 177 RNA genes were identified. The 16S
      rRNA gene sequence of this strain is distantly related to sequences of some
      relatives classified in the same genus (K. olearia 7.02% and K. shengliensis
      7.83%), with dissimilarity percentages close to the threshold generally described
      for genus delineation. Nevertheless, the percentage of conserved proteins (POCP),
      which is much higher than 50% (around 70%), together with phenotypic features of
      the isolates, confirm the affiliation all Kosmotoga species described so far to
      the same genus.
AU  - Jiang L
AU  - L'Haridon S
AU  - Jebbar M
AU  - Xu H
AU  - Alain K
AU  - Shao Z
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 3.

PMID- 23887916
VI  - 1
DP  - 2013
TI  - Genome Sequence of Thermus thermophilus ATCC 33923, a Thermostable Trehalose-Producing Strain.
PG  - e00493-13
AB  - Thermus thermophilus ATCC 33923 contains a thermostable enzyme that can efficiently catalyze
      the conversion of maltose into trehalose. Here we report a
      2.15-Mb assembly of its genome sequence and other useful information, including
      the coding sequences (CDS) responsible for biological processes such as DNA
      replication, DNA repair, and RNA maturation.
AU  - Jiang L
AU  - Lin M
AU  - Li X
AU  - Cui H
AU  - Xu X
AU  - Li S
AU  - Huang H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00493-13.

PMID- 24903865
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Defluviimonas indica Strain 20V17T, Isolated from a Deep-Sea Hydrothermal Vent Environment in the Southwest Indian Ocean.
PG  - e00479-14
AB  - Here, we present the draft genome sequence of Defluviimonas indica 20V17(T), which was
      isolated from a deep-sea hydrothermal vent chimney sample in the
      southwest Indian Ocean. The draft genome sequence contains 4,268,338 bp, with a
      G+C content of 66.33%.
AU  - Jiang L
AU  - Long M
AU  - Shao Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00479-14.

PMID- 23723404
VI  - 1
DP  - 2013
TI  - Genome Sequence of Clostridium tyrobutyricum ATCC 25755, a Butyric Acid-Overproducing Strain.
PG  - e00308-13
AB  - Clostridium tyrobutyricum ATCC 25755 is an efficient producer of butyric acid. Here we report
      a 3.01-Mb assembly of its genome sequence and other useful
      information, including the coding sequences (CDSs) responsible for an alternative
      pathway leading to acetate synthesis as well as a series of membrane transport
      systems.
AU  - Jiang L
AU  - Zhu L
AU  - Xu X
AU  - Li Y
AU  - Li S
AU  - Huang H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00308-13.

PMID- 22887665
VI  - 194
DP  - 2012
TI  - Whole-Genome Sequence of Staphylococcus hominis, an Opportunistic Pathogen.
PG  - 4761-4762
AB  - Staphylococcus hominis is a commensal coagulase-negative species of staphylococci. It has been
      considered a presumptive and opportunistic pathogen
      that causes nosocomial infections in humans. Here we present the draft genome
      sequence of S. hominis ZBW5, a multidrug-resistant strain isolated from a human
      skin sample, which provides opportunities to understand the mechanism and genetic
      basis of its pathogenesis.
AU  - Jiang S
AU  - Zheng B
AU  - Ding W
AU  - Lv L
AU  - Ji J
AU  - Zhang H
AU  - Xiao Y
AU  - Li L
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4761-4762.

PMID- 27445373
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Klebsiella variicola Strain KV321 Isolated from Rhizosphere Soil of Pisolithus tinctorius-Eucalyptus Mycorrhiza.
PG  - e00676-16
AB  - The draft genome sequences of Klebsiella variicola strain KV321, which was isolated from
      rhizosphere soil of Pisolithus tinctorius-Eucalyptus mycorrhiza,
      are reported here. The genome sequences contain genes involved in ABC transporter
      function in multiple-antibiotic drug resistance and colonization. This genomic
      analysis will help understand the genomic basis of K. variicola virulence genes
      and how the genes play a part in its interaction with other living organisms.
AU  - Jiang SF
AU  - Liu Y
AU  - Xiao MY
AU  - Ruan CJ
AU  - Lu ZJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00676-16.

PMID- 22275095
VI  - 194
DP  - 2012
TI  - Genome Sequence of Pseudomonas stutzeri SDM-LAC, a Typical Strain for Studying the Molecular Mechanism of Lactate Utilization.
PG  - 894-895
AB  - Pseudomonas stutzeri SDM-LAC is an efficient lactate utilizer with various applications in
      biocatalysis. Here we present a 4.2-Mb assembly of its
      genome. The annotated four adjacent genes form a lactate utilization
      operon, which could provide further insights into the molecular mechanism
      of lactate utilization.
AU  - Jiang T
AU  - Gao C
AU  - Su F
AU  - Zhang W
AU  - Hu C
AU  - Dou P
AU  - Zheng Z
AU  - Tao F
AU  - Ma C
AU  - Xu P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 894-895.

PMID- 22123770
VI  - 193
DP  - 2011
TI  - Genome Sequence of Halobiforma lacisalsi AJ5, an Extremely Halophilic Archaeon Which Harbors a bop Gene.
PG  - 7023-7024
AB  - The draft genome sequence (4,398,155 bp, with 65.35% G+C content) of Halobiforma lacisalsi
      AJ5, an extremely halophilic archaeon isolated from
      a salt lake, is reported here. This is the first genome report for a
      species of the Halobiforma genus.
AU  - Jiang X
AU  - Wang S
AU  - Cheng H
AU  - Huo Y
AU  - Zhang X
AU  - Zhu X
AU  - Han X
AU  - Ni P
AU  - Wu M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 7023-7024.

PMID- 23950124
VI  - 1
DP  - 2013
TI  - Genome Sequence of a Novel Polymer-Grade L-Lactate-Producing Alkaliphile, Exiguobacterium sp. Strain 8-11-1.
PG  - e00616-13
AB  - Exiguobacterium sp. strain 8-11-1 is a newly isolated alkaliphile, which was reported to
      efficiently produce l-lactate using NaOH as the neutralizing agent.
      Here, we present the first 2.9-Mb assembly of its genome sequence, which may
      provide useful information related to its efficient lactate production and sodium
      ion tolerance capacities.
AU  - Jiang X
AU  - Xue Y
AU  - Wang L
AU  - Yu B
AU  - Ma Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00616-13.

PMID- 25858830
VI  - 3
DP  - 2015
TI  - De Novo Whole-Genome Sequence of Micromonospora carbonacea JXNU-1 with Broad-Spectrum Antimicrobial Activity, Isolated from Soil Samples.
PG  - e00174-15
AB  - Micromonospora carbonacea JXNU-1 is an actinomycete with broad-spectrum antimicrobial
      activity, isolated from soil samples from the farmland in the area
      of Yaohu Lake in Nanchang, China. Here, we report the whole-genome sequence of M.
      carbonacea JXNU-1.
AU  - Jiang Y
AU  - Huang YH
AU  - Long ZE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00174-15.

PMID- 25908151
VI  - 3
DP  - 2015
TI  - Genome Sequence of a Versatile Aromatic Hydrocarbon-Degrading Bacterium, Arthrobacter sp. W1.
PG  - e00387-15
AB  - Arthrobacter sp. W1 is a versatile aromatic-degrading strain which can directly or
      cometabolically degrade various organic pollutants, such as phenol,
      naphthalene, carbazole, dibenzofuran, and dibenzothiophene. Here, we present a
      3.8-Mb draft genome sequence of strain W1, which may provide comprehensive
      genetic information for the application in environmental pollution remediation.
AU  - Jiang Y
AU  - Qu Y
AU  - Xu P
AU  - Tang H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00387-15.

PMID- 22287011
VI  - 78
DP  - 2012
TI  - Molecular Basis and Phylogenetic Implications of Deoxycylindrospermopsin Biosynthesis in the Cyanobacterium Raphidiopsis curvata.
PG  - 2256-2263
AB  - New insights into the distribution and biochemistry of the cyanotoxin
      cylindrospermopsin (CYN) have been provided by the recent determination of its
      biosynthesis gene cluster (cyr) in several cyanobacterial species. Raphidiopsis
      curvata CHAB1150 isolated from China was analyzed for CYN analogues. Only
      7-deoxy-CYN was detected in the cell extracts. The cyr gene cluster of R. curvata
      CHAB1150 was sequenced, and the cyr genes of this strain were found to have
      extremely high similarities (96% to 100%) to those from other nostocalean
      species. These species include Cylindrospermopsis raciborskii AWT205,
      Aphanizomenon sp. strain 10E6, and Aphanizomenon ovalisporum ILC-146. Insertion
      mutation was identified within the cyrI gene, and transcripts of cyrI and another
      functional gene cyrJ were detected in R. curvata CHAB1150. General congruence
      between the phylogenetic trees based on both cyr and 16S rrn was displayed.
      Neutral evolution was found on the whole sequences of the cyr genes, and 0 to 89
      negative selected codons were detected in each gene. Therefore, the function of
      CyrI is to catalyze the oxygenation of 7-deoxy-CYN in CYN biosynthesis. The
      transcripts of the mutated cyrI gene may result from polycistronic transcription.
      The high conservation of the cyr genes may be ascribed to purifying selection and
      horizontal gene transfer.
AU  - Jiang Y
AU  - Xiao P
AU  - Yu G
AU  - Sano T
AU  - Pan Q
AU  - Li R
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2012 78: 2256-2263.

PMID- 25377715
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Bacillus subtilis Strain NKYL29, an Antimicrobial-Peptide-Producing Strain from Soil.
PG  - e01140-14
AB  - Bacillus subtilis strain NKYL29 is an antimicrobial-peptide-producing strain isolated from the
      soil of Ranzhuang Tunnel in Hebei Province, China. Here, we
      present the draft genome of this strain, which provides the genetic basis for
      application of the antimicrobial peptide.
AU  - Jiang Y
AU  - Xu H
AU  - Li Y
AU  - Liu H
AU  - Yu L
AU  - Qiao M
AU  - Liu G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01140-14.

PMID- 16122562
VI  - 54
DP  - 2005
TI  - The complete sequence and analysis of the large virulence plasmid pSS of Shigella sonnei.
PG  - 149-159
AB  - The complete sequence of pSS, which is the large virulence plasmid of Shigella sonnei, was
      determined. The 214-kb plasmid is composed of
      segments of virulence-associated genes, the O-antigen gene clusters, a
      range of replication and maintenance genes, and large numbers of insertion
      sequence (IS) elements. Two hundred and forty-one open reading frames
      (ORFs) were identified, of which 117 are highly homologous to IS elements
      or transposases, 57 are homologous to known pathogenesis-associated
      proteins, and 30 are related to replication, plasmid maintenance, or other
      metabolic functions. Thirty-seven ORFs have no similarity to proteins with
      a known function, including two with no significant similarity to any
      hypothetical proteins. Interestingly, 10 ORFs encoding O-antigen gene
      clusters were identified on the plasmid and this is markedly different
      from most other Shigella spp. virulent plasmids. A novel toxin-antitoxin
      system, a series of stbDE homologs, was found on the plasmid immediately
      downstream of the replication region; the sole segregation stability
      system may be responsible for the instability of pSS. The pSS plasmid is a
      mixture of genes with different origins and functions. The sequence
      suggests a remarkable history of IS-mediated recombination and acquisition
      of DNA across a range of bacterial species.
AU  - Jiang Y
AU  - Yang F
AU  - Zhang X
AU  - Yang J
AU  - Chen L
AU  - Yan Y
AU  - Nie H
AU  - Xiong Z
AU  - Wang J
AU  - Dong J
AU  - Xue Y
AU  - Xu X
AU  - Zhu Y
AU  - Chen S
AU  - Jin Q
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 2005 54: 149-159.

PMID- 20547789
VI  - 54
DP  - 2010
TI  - Complete Nucleotide Sequence of Klebsiella pneumoniae Multidrug Resistance Plasmid pKP048, Carrying bla(KPC-2), bla(DHA-1), qnrB4, and armA.
PG  - 3967-3969
AB  - The Klebsiella pneumoniae multidrug resistance plasmid pKP048 was completely sequenced. This
      plasmid carries several important resistance
      determinants, such as bla(KPC-2), bla(DHA-1), qnrB4, and armA, which
      confer resistance to carbapenems, cephalosporins, fluoroquinolones, and
      aminoglycosides, respectively. Analysis of the finished 151,188-bp
      sequence data revealed 163 putative genes, 108 of which were assigned
      functions such as replication, stable inheritance, antibiotic
      resistance, a mobile element, conjugal transfer, and a
      restriction-modification system, showing the strong phylogenetic
      mosaicism and plasticity of the plasmid.
AU  - Jiang Y
AU  - Yu DL
AU  - Wei ZQ
AU  - Shen P
AU  - Zhou ZH
AU  - Yu YS
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2010 54: 3967-3969.

PMID- 21774254
VI  - 27
DP  - 2011
TI  - [Isolation and characterization of an iridovirus from sick giant salamander (Andrias davidianus)].
PG  - 274-282
AB  - A virus was isolated from cultured sick giant salmander (Andrias davidianus ) in
      a farm, Shanxi Province, China. Skin ulceration and necrosis of the distal limbs
      are main clinical symptoms. Virus propagated and caused CPE at 10 degrees C to 30
      degrees C in BF-2, CO, CHSE, FHM cells. The optimum condition of replication was
      in BF-2 cells at 25 degrees C. The virus was proved to be senstive to chloroform,
      heat, pH3 and pH10 treatment. Viral replication was inhibited by
      5-Fluoro-2-deoxyuridine (FUDR). These results indicated that the virus possessed
      an envelope and DNA as the genome. Electron-microscopic observation of
      thin-section showed numerous hexagonal viral particles measuring 130 nm to 150 nm
      in diameter orderly arranged in a lattice form in cytoplasm of BF-2 cells. The
      particles showed typical iridovirus morphology. A 413 bp fragment was amplified
      from the viral main capsid protein gene by PCR. The fragments was sequenced and
      analysed. The results showed the isolate shared more than 96% nucleotide identity
      with some Ranaviruses. We suggested that this virus was named as Andrias
      davidianus iridovirus (ADIV) tentatively.
AU  - Jiang YL
AU  - Zhang M
AU  - Jing HL
AU  - Gao LY
PT  - Journal Article
TA  - Bing Du Xue Bao
JT  - Bing Du Xue Bao
SO  - Bing Du Xue Bao 2011 27: 274-282.

PMID- 23144417
VI  - 194
DP  - 2012
TI  - Genome Sequences of the Primary Endosymbiont 'Candidatus Portiera aleyrodidarum'  in the Whitefly Bemisia tabaci B and Q Biotypes.
PG  - 6678-6679
AB  - 'Candidatus Portiera aleyrodidarum' is the obligate primary endosymbiotic bacterium of
      whiteflies, including the sweet potato whitefly Bemisia tabaci, and
      provides essential nutrients to its host. Here we report two complete genome
      sequences of this bacterium from the B and Q biotypes of B. tabaci.
AU  - Jiang ZF
AU  - Xia F
AU  - Johnson KW
AU  - Bartom E
AU  - Tuteja JH
AU  - Stevens R
AU  - Grossman RL
AU  - Brumin M
AU  - White KP
AU  - Ghanim M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6678-6679.

PMID- 29496834
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Streptomyces sp. Strain DH-12, a Soilborne Isolate from  the Thar Desert with Broad-Spectrum Antibacterial Activity.
PG  - e00108-18
AB  - Strain DH-12 exhibits broad-spectrum antibacterial activity toward Gram-positive  and
      Gram-negative pathogens. The 7.6-Mb draft genome sequence gives insight into
      the complete secondary metabolite production capacity and reveals genes
      putatively responsible for its antibacterial activity, as well as genes which
      enable the survival of the organism in an extreme arid environment.
AU  - Jiao J
AU  - Paterson J
AU  - Busche T
AU  - Ruckert C
AU  - Kalinowski J
AU  - Harwani D
AU  - Gross H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00108-18.

PMID- 28174619
VI  - 12
DP  - 2017
TI  - Complete genome sequence of Jiangella gansuensis strain YIM 002T (DSM 44835T), the type species of the genus Jiangella and source of new antibiotic compounds.
PG  - 21
AB  - Jiangella gansuensis strain YIM 002T is the type strain of the type species of the genus
      Jiangella, which is at the present time composed of five species, and
      was isolated from desert soil sample in Gansu Province (China). The five strains
      of this genus are clustered in a monophyletic group when closer actinobacterial
      genera are used to infer a 16S rRNA gene sequence phylogeny. The study of this
      genome is part of the GenomicEncyclopedia ofBacteria andArchaea project, and here
      we describe the complete genome sequence and annotation of this taxon. The genome
      of J. gansuensis strain YIM 002T contains a single scaffold of size 5,585,780 bp,
      which involves 149 pseudogenes, 4905 protein-coding genes and 50 RNA genes,
      including 2520 hypothetical proteins and 4 rRNA genes. From the investigation of
      genome sizes of Jiangella species, J. gansuensis shows a smaller size, which
      indicates this strain might have discarded too much genetic information to adapt
      to desert environment. Seven new compounds from this bacterium have recently been
      described; however, its potential should be higher, as secondary metabolite gene
      cluster analysis predicted 60 gene clusters, including the potential to produce
      the pristinamycin.
AU  - Jiao JY
AU  - Carro L
AU  - Liu L
AU  - Gao XY
AU  - Zhang XT
AU  - Hozzein WN
AU  - Lapidus A
AU  - Huntemann M
AU  - Reddy TB
AU  - Varghese N
AU  - Hadjithomas M
AU  - Ivanova NN
AU  - Goker M
AU  - Pillay M
AU  - Eisen JA
AU  - Woyke T
AU  - Klenk HP
AU  - Kyrpides NC
AU  - Li WJ
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 21.

PMID- 26139721
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Jiangella alkaliphila KCTC 19222T, Isolated from Cave Soil in Jeju, Republic of Korea.
PG  - e00721-15
AB  - We report the draft genome sequence of Jiangella alkaliphila KCTC 19222(T), isolated from cave
      soil in Jeju, Republic of Korea. This genome sequence,
      together with the previously sequenced J. gansuensis strain DSM 44835(T),
      identified from a desert environmental source, will give us a better
      understanding of the school of 'evolutionary taxonomy.'
AU  - Jiao JY
AU  - Liu L
AU  - Park DJ
AU  - Kim CJ
AU  - Xiao M
AU  - Chen J
AU  - Li L
AU  - Zhong JM
AU  - Zhao J
AU  - Li WJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00721-15.

PMID- 25944084
VI  - 108
DP  - 2015
TI  - Actinomadura amylolytica sp. nov. and Actinomadura cellulosilytica sp. nov., isolated from geothermally heated soil.
PG  - 75-83
AB  - Two aerobic, Gram-positive actinomycetes, designated YIM 77502(T) and YIM
      77510(T), were isolated from geothermally heated soil of Tengchong county, Yunnan
      province, south-west China. The taxonomic position of strains YIM 77502(T) and
      YIM 77510(T) were investigated by a polyphasic approach. Phylogenetic analyses
      based on 16S rRNA gene sequences showed that strains YIM 77502(T) and YIM
      77510(T) belong to the genus Actinomadura. Both strains form extensively-branched
      substrate and aerial mycelia which differentiated into short spore chains. The
      cell wall of the two strains contained meso-diaminopimelic acid, while the
      whole-cell sugars detected were glucose, madurose, mannose and rhamnose. The
      polar lipid profile of strain YIM 77502(T) was found to consist of
      diphosphatidylglycerol, phosphatidylinositol mannoside, phosphatidylinositol, two
      unidentified phospholipids and an unidentified polar lipid, while strain YIM
      77510(T) consisted of diphosphatidylglycerol, phosphatidylinositol mannoside and
      phosphatidylinositol. The respiratory quinones of strains YIM 77502(T) and YIM
      77510(T) were MK-9(H6) and MK-9(H8). The major fatty acids (>10 %) of strain YIM
      77502(T) were C17:0, iso-C16:0, C17:010-methyl and iso-C18:0, and those of strain
      YIM 77510(T) were iso-C16:0, C17:010-methyl and iso-C18:0. The G+C contents of
      strains YIM 77502(T) and YIM 77510(T) were determined to be 71.3 and 70.2 mol%,
      respectively. The DNA-DNA hybridization values of strains YIM 77502(T), YIM
      77510(T) and their closest phylogenetic neighbours Actinomadura echinospora BCRC
      12547(T) and Actinomadura umbrina KCTC 9343(T) were less than 70 %. Based on the
      morphological and physiological properties, and phylogenetic analyses, strains
      YIM 77502(T) and YIM 77510(T) are considered to represent two novel species of
      the genus Actinomadura, for which the names Actinomadura amylolytica sp. nov.
      (type strain YIM 77502(T) = DSM 45822(T) = CCTCC AA 2012024(T)) and Actinomadura
      cellulosilytica sp. nov. (type strain YIM 77510(T) = DSM 45823(T) = CCTCC AA
      2012023(T)) are proposed.
AU  - Jiao JY
AU  - Liu L
AU  - Zhou EM
AU  - Wei DQ
AU  - Ming H
AU  - Xian WD
AU  - Yuan CG
AU  - Zhong JM
AU  - Li WJ
PT  - Journal Article
TA  - Antonie Van Leeuwenhoek
JT  - Antonie Van Leeuwenhoek
SO  - Antonie Van Leeuwenhoek 2015 108: 75-83.

PMID- 25767219
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequence of 'Candidatus Rickettsia asemboensis' Strain NMRCii, Isolated from Fleas of Western Kenya.
PG  - e00018-15
AB  - Herein we present the draft genome sequence and annotation of 'Candidatus Rickettsia
      asemboensis' strain NMRCii. 'Ca. Rickettsia asemboensis' is
      phylogenetically related to but distinct from the flea-borne spotted fever
      pathogen Rickettsia felis. 'Ca. Rickettsia asemboensis' was initially identified
      in and subsequently isolated from Ctenocephalides cat and dog fleas from Kenya.
AU  - Jima DD
AU  - Luce-Fedrow A
AU  - Yang Y
AU  - Maina AN
AU  - Snesrud EC
AU  - Otiang E
AU  - Njenga K
AU  - Jarman RG
AU  - Richards AL
AU  - Hang J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00018-15.

PMID- 20639335
VI  - 192
DP  - 2010
TI  - Complete genome sequence of Lactobacillus fermentum CECT 5716, a probiotic strain isolated from human milk.
PG  - 4800
AB  - Lactobacillus fermentum is a heterofermentative lactic acid bacterium and is frequently
      isolated from mucosal surfaces of healthy humans.
      Lactobacillus fermentum CECT 5716 is a well-characterized probiotic strain
      isolated from human milk and, at present, is used in commercial infant
      formulas. Here, we report the complete and annotated genome sequence of
      this strain.
AU  - Jimenez E
AU  - Langa S
AU  - Martin V
AU  - Arroyo R
AU  - Martin R
AU  - Fernandez L
AU  - Rodriguez JM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 4800.

PMID- 20675488
VI  - 192
DP  - 2010
TI  - Complete genome sequence of Lactobacillus salivarius CECT 5713, a probiotic strain isolated from human milk and infant feces.
PG  - 5266-5267
AB  - Lactobacillus salivarius is a homofermentative lactic acid bacterium and is frequently
      isolated from mucosal surfaces of healthy humans. L. salivarius CECT 5713, a strain isolated
      simultaneously from breast milk and infant feces of a healthy mother-infant pair, has
      immunomodulatory, anti-inflammatory, and anti-infectious properties, as revealed by several in
      vitro and in vivo assays. Here, we report its complete and annotated genome sequence.
AU  - Jimenez E
AU  - Martin R
AU  - Maldonado A
AU  - Martin V
AU  - Gomez-de-Segura A
AU  - Fernandez L
AU  - Rodriguez JM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 5266-5267.

PMID- 22740680
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Bifidobacterium breve CECT 7263, a Strain Isolated from Human Milk.
PG  - 3762-3763
AB  - Bifidobacterium breve is an actinobacterium frequently isolated from colonic microbiota of
      breastfeeding babies. Here, we report the complete and annotated
      genome sequence of a B. breve strain isolated from human milk, B. breve CECT
      7263. The genome sequence will provide new insights into the biology of this
      potential probiotic organism and will allow the characterization of genes related
      to beneficial properties.
AU  - Jimenez E
AU  - Villar-Tajadura MA
AU  - Marin M
AU  - Fontecha J
AU  - Requena T
AU  - Arroyo R
AU  - Fernandez L
AU  - Rodriguez JM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3762-3763.

PMID- 24356843
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Bacillus toyonensis BCT-7112T, the Active Ingredient  of the Feed Additive Preparation Toyocerin.
PG  - e01080-13
AB  - Strain BCT-7112, previously identified as Bacillus cereus var. toyoi, is the type strain of
      the species Bacillus toyonensis, a novel species of the B. cereus
      group. The complete genome of this strain, which is the active ingredient of the
      feed additive preparation Toyocerin, has been sequenced and annotated to reveal
      the genetic properties of this probiotic organism with a long history of safe use
      in animal nutrition.
AU  - Jimenez G
AU  - Blanch AR
AU  - Tamames J
AU  - Rossello-Mora R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01080-13.

PMID- 26337890
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Bacterium Gordonia jacobaea, a New Member of the Gordonia Genus.
PG  - e00995-15
AB  - Gordonia jacobaea was isolated and characterized in the Department of Microbiology, University
      of Santiago de Compostela, in 2000. Here we present the  draft genome sequence of this
      species, which will improve our understanding of the diversity and the relation of the cell
      wall proteins of G. jacobaea with other mycolata.
AU  - Jimenez-Galisteo G
AU  - Villa TG
AU  - Vinuesa T
AU  - Vinas M
AU  - Dominguez A
AU  - Munoz E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00995-15.

PMID- 7937114
VI  - 22
DP  - 1994
TI  - New restriction endonuclease CviRI cleaves DNA at TG^CA sequences.
PG  - 3928-3929
AB  - A new type II restriction endonuclease, CviRI, was isolated from virus XZ-6E infected
      chlorella cells. CviRI is the first restriction endonuclease to recognize the sequence
      5'-TGCA-3' and cleaves DNA between the G and C residues to produce blunt-end termini.
      Methylation of the adenine or cytosine in 5'-TGCA-3' sequences prevents CviRI cleavage. Due
      to its sequence specificity, CviRI may be especially useful for detecting mutant alleles of
      many heritable human genetic diseases.
AU  - Jin A
AU  - Zhang Y
AU  - Xia Y
AU  - Traylor E
AU  - Nelson M
AU  - Van Etten JL
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1994 22: 3928-3929.

PMID- 22956494
VI  - 754
DP  - 2013
TI  - DNA Methyltransferases, DNA Damage Repair, and Cancer.
PG  - 3-29
AB  - The maintenance DNA methyltransferase (DNMT) 1 and the de novo methyltransferases DNMT3A and
      DNMT3B are all essential for mammalian development. DNA methylation, catalyzed by the DNMTs,
      plays an important role in maintaining genome stability. Aberrant expression of DNMTs and
      disruption of DNA methylation patterns are closely associated with many forms of cancer,
      although the exact mechanisms underlying this link remain elusive. DNA damage repair systems
      have evolved to act as a genome-wide surveillance mechanism to maintain chromosome integrity
      by recognizing and repairing both exogenous and endogenous DNA insults. Impairment of these
      systems gives rise to mutations and directly contributes to tumorigenesis. Evidence is
      mounting for a direct link between DNMTs, DNA methylation, and DNA damage repair systems,
      which provide new insight into the development of cancer. Like tumor suppressor genes, an
      array of DNA repair genes frequently sustain promoter hypermethylation in a variety of tumors.
      In addition, DNMT1, but not the DNMT3s, appear to function coordinately with DNA damage repair
      pathways to protect cells from sustaining mutagenic events, which is very likely through a DNA
      methylation-independent mechanism. This chapter is focused on reviewing the links between DNA
      methylation and the DNA damage response.
AU  - Jin B
AU  - Robertson KD
PT  - Journal Article
TA  - Adv. Exp. Med. Biol.
JT  - Adv. Exp. Med. Biol.
SO  - Adv. Exp. Med. Biol. 2013 754: 3-29.

PMID- 23782707
VI  - 13
DP  - 2013
TI  - Dynamics of fecal microbial communities in children with diarrhea of unknown etiology and genomic analysis of associated Streptococcus lutetiensis.
PG  - 141
AB  - BACKGROUND: The sequences of the 16S rRNA genes extracted from fecal samples
      provide insights into the dynamics of fecal microflora. This potentially gives
      valuable etiological information for patients whose conditions have been ascribed
      to unknown pathogens, which cannot be accomplished using routine culture methods.
      We studied 33 children with diarrhea who were admitted to the Children's Hospital
      in Shanxi Province during 2006. RESULTS: Nineteen of 33 children with diarrhea
      could not be etiologically diagnosed by routine culture and polymerase chain
      reaction methods. Eleven of 19 children with diarrhea of unknown etiology had
      Streptococcus as the most dominant fecal bacterial genus at admission. Eight of
      nine children whom three consecutive fecal samples were collected had
      Streptococcus as the dominant fecal bacterial genus, including three in the
      Streptococcus bovis group and three Streptococcus sp., which was reduced during
      and after recovery. We isolated strains that were possibly from the S. bovis
      group from feces sampled at admission, which were then identified as
      Streptococcus lutetiensis from one child and Streptococcus gallolyticus subsp.
      pasteurianus from two children. We sequenced the genome of S. lutetiensis and
      identified five antibiotic islands, two pathogenicity islands, and five unique
      genomic islands. The identified virulence genes included hemolytic toxin cylZ of
      Streptococcus agalactiae and sortase associated with colonization of pathogenic
      streptococci. CONCLUSIONS: We identified S. lutetiensis and S. gallolyticus
      subsp. pasteurianus from children with diarrhea of unknown etiology, and found
      pathogenic islands and virulence genes in the genome of S. lutetiensis.
AU  - Jin D
AU  - Chen C
AU  - Li L
AU  - Lu S
AU  - Li Z
AU  - Zhou Z
AU  - Jing H
AU  - Xu Y
AU  - Du P
AU  - Wang H
AU  - Xiong Y
AU  - Zheng H
AU  - Bai X
AU  - Sun H
AU  - Wang L
AU  - Ye C
AU  - Gottschalk M
AU  - Xu J
PT  - Journal Article
TA  - BMC Microbiol.
JT  - BMC Microbiol.
SO  - BMC Microbiol. 2013 13: 141.

PMID- 27313307
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Sphingobium yanoikuyae TJ, a Halotolerant Di-n-Butyl-Phthalate-Degrading Bacterium.
PG  - e00569-16
AB  - Sphingobium yanoikuyae TJ is a halotolerant di-n-butyl-phthalate-degrading bacterium, isolated
      from the Haihe estuary in Bohai Bay, Tianjin, China. Here, we
      report the 5.1-Mb draft genome sequence of this strain, which will provide
      insights into the diversity of Sphingobium spp. and the mechanism of phthalate
      ester degradation in the estuary.
AU  - Jin D
AU  - Zhu Y
AU  - Wang X
AU  - Kong X
AU  - Liu H
AU  - Wang Y
AU  - Deng Y
AU  - Jia M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00569-16.

PMID- 30533930
VI  - 7
DP  - 2018
TI  - Complete Genome Sequence of a Microcystin-Degrading Bacterium, Sphingosinicella microcystinivorans Strain B-9.
PG  - e00898-18
AB  - Sphingosinicella microcystinivorans strain B-9 has the ability to degrade cyanobacterial
      hepatotoxic cyclic peptides, microcystins, and nodularins. This is
      the first report of the complete genome sequence of the microcystin-degrading
      bacterium.
AU  - Jin H
AU  - Nishizawa T
AU  - Guo Y
AU  - Nishizawa A
AU  - Park HD
AU  - Kato H
AU  - Tsuji K
AU  - Harada KI
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e00898-18.

PMID- 21705606
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of the Polycyclic Aromatic Hydrocarbon-Degrading Bacterium Alteromonas sp. Strain SN2.
PG  - 4292-4293
AB  - Alteromonas sp. strain SN2, able to metabolize polycyclic aromatic hydrocarbons, was isolated
      from a crude oil-contaminated sea-tidal flat.
      Here we report the complete 4.97-Mb genome sequence and annotation of
      strain SN2. These will advance the understanding of strain SN2's
      adaptation to the sea-tidal flat ecosystem and its pollutant metabolic
      versatility.
AU  - Jin HM
AU  - Jeong H
AU  - Moon EJ
AU  - Math RK
AU  - Lee K
AU  - Kim HJ
AU  - Jeon CO
AU  - Oh TK
AU  - Kim JF
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4292-4293.

PMID- 25045662
VI  - 2014
DP  - 2014
TI  - Metadynamics Simulation Study on the Conformational Transformation of HhaI Methyltransferase: An Induced-Fit Base-Flipping Hypothesis.
PG  - 304563
AB  - DNA methyltransferases play crucial roles in establishing and maintenance of DNA methylation,
      which is an important epigenetic mark. Flipping the target cytosine out of the DNA helical
      stack and into the active site of protein provides DNA methyltransferases with an opportunity
      to access and modify the genetic information hidden in DNA. To investigate the conversion
      process of base flipping in the HhaI methyltransferase (M. HhaI), we performed different
      molecular simulation approaches on M.HhaI-DNA-S-adenosylhomocysteine ternary complex. The
      results demonstrate that the nonspecific binding of DNA to M. HhaI is initially induced by
      electrostatic interactions. Differences in chemical environment between the major and minor
      grooves determine the orientation of DNA. Gln237 at the target recognition loop recognizes the
      GCGC base pair from the major groove side by hydrogen bonds. In addition, catalytic loop
      motion is a key factor during this process. Our study indicates that base flipping is likely
      to be an 'induced-fit' process. This study provides a solid foundation for future studies on
      the discovery and development of mechanism-based DNA methyltransferases regulators.
AU  - Jin Lu
AU  - Ye F
AU  - Zhao D
AU  - Chen S
AU  - Zhu K
AU  - Zheng M
AU  - Jiang R-W
AU  - Jiang H
AU  - Luo C
PT  - Journal Article
TA  - Biomed Res. Int.
JT  - Biomed Res. Int.
SO  - Biomed Res. Int. 2014 2014: 304563.

PMID- 12384590
VI  - 30
DP  - 2002
TI  - Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157.
PG  - 4432-4441
AB  - We have sequenced the genome of Shigella flexneri serotype 2a, the most prevalent species and
      serotype that causes bacillary dysentery or shigellosis in man. The whole genome is composed
      of a 4 607 203 bp chromosome and a 221 618 bp virulence plasmid, designated pCP301. While the
      plasmid shows minor divergence from that sequenced in serotype 5a, striking characteristics of
      the chromosome have been revealed. The S.flexneri chromosome has, astonishingly, 314 IS
      elements, more than 7-fold over those possessed by its close relatives, the non-pathogenic K12
      strain and enterohemorrhagic O157:H7 strain of Escherichia coli. There are 13 translocations
      and inversions compared with the E.coli sequences, all involve a segment larger than 5 kb, and
      most are associated with deletions or acquired DNA sequences, of which several are likely to
      be bacteriophage-transmitted pathogenicity islands. Furthermore, S.flexneri, resembling
      another human-restricted enteric pathogen, Salmonella typhi, also has hundreds of pseudogenes
      compared with the E.coli strains. All of these could be subjected to investigations towards
      novel preventative and treatment strategies against shigellosis.
AU  - Jin Q et al
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2002 30: 4432-4441.

PMID- 20371518
VI  - 38
DP  - 2010
TI  - Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine.
PG  - e125
AB  - DNA cytosine-5 methylation is a well-studied epigenetic pathway implicated in gene expression
      control and disease pathogenesis. Different
      technologies have been developed to examine the distribution of
      5-methylcytosine (5mC) in specific sequences of the genome. Recently,
      substantial amounts of 5-hydroxymethylcytosine (5hmC), most likely derived
      from enzymatic oxidation of 5mC by TET1, have been detected in certain
      mammalian tissues. Here, we have examined the ability of several commonly
      used DNA methylation profiling methods to distinguish between 5mC and
      5hmC. We show that techniques based on sodium bisulfite treatment of DNA
      are incapable of distinguishing between the two modified bases. In
      contrast, techniques based on immunoprecipitation with anti-5mC antibody
      (methylated DNA immunoprecipitation, MeDIP) or those based on proteins
      that bind to methylated CpG sequences (e.g. methylated-CpG island recovery
      assay, MIRA) do not detect 5hmC and are specific for 5mC unless both
      modified bases occur in the same DNA fragment. We also report that several
      methyl-CpG binding proteins including MBD1, MBD2 and MBD4 do not bind to
      sequences containing 5hmC. Selective mapping of 5hmC will require the
      development of unique tools for the detection of this modified base.
AU  - Jin SG
AU  - Kadam S
AU  - Pfeifer GP
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2010 38: e125.

PMID- 9054434
VI  - 272
DP  - 1997
TI  - HO endonuclease cleaves MAT DNA in vitro by an inefficient stoichiometric reaction mechanism.
PG  - 7352-7359
AB  - Mating type switching in Saccharomyces cerevisiae initiates when HO endonuclease makes a
      double-stranded DNA break at the yeast MAT locus.  In this report, we characterize the
      fundamental biochemical properties of HO.  Using an assay that monitors cleavage of a MAT
      plasmid, we define an optimal in vitro reaction, showing in particular that the enzyme has a
      stringent requirement for zinc ions.  This suggests that zinc finger motifs present in HO are
      important for cleavage.  The most unexpected feature of HO, however, is its extreme
      inefficiency.  Maximal cleavage occurs when HO is present at a concentration of 1 molecule/3
      base pairs of substrate DNA.  Even under these conditions, complete digestion requires >2h.
      This inefficiency results from two characteristics of HO.  First, HO recycles slowly from
      cleaved product to new substrate, in part because the enzyme has an affinity for one end of
      its double strand break product.  Second, high levels of cleavage in the in vitro reaction
      correlate with the appearance of large protein-DNA aggregates.  At optimal HO concentrations,
      these latter aggregates, referred to as "florettes," have an ordered structure consisting of a
      densely staining central region and loops of radiating DNA.  These unusual properties may
      indicate that HO plays a role in other aspects of mating type switching subsequent to double
      strand break formation.
AU  - Jin Y
AU  - Binkowski G
AU  - Simon LD
AU  - Norris D
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1997 272: 7352-7359.

PMID- 
VI  - 272
DP  - 2005
TI  - On the DNA cleavage mechanism of Type I restriction enzymes.
PG  - 552
AB  - Although the DNA-cleavage mechanism of Type I restriction-modification enzymes has been
      extensively studied, the mode of how these enzymes introduce DNA double-strand breaks still
      remains elusive. In this work, DNA ends produced by EcoKI, EcoAI and EcoR124I, members of the
      Type IA, IB and IC families, respectively, have been characterized by cloning and sequencing
      of restriction products from reactions with a plasmid DNA substrate containing a single
      recognition site for each enzyme. We show that all three enzymes cut this DNA randomly with no
      preference for a particular base composition surrounding the cleavage site, producing both 5'-
      and 3'-overhangs of varying lengths. EcoAI preferentially generated 3''-overhangs of 2-3
      nucleotides, whereas EcoKI and EcoR124I displayed some preference for formation of
      5'-overhangs in a length of about 6-7 and 3-5 nucleotides, respectively. A mutant EcoAI
      endonuclease assembled from wild-type and nuclease-deficient restriction subunits generated a
      high proportion of nicked circular DNA, whereas the wild-type enzyme catalyzed efficient
      cleavage of both DNA strands. We conclude that Type I restriction enzymes require two
      restriction subunits to introduce DNA double-strand breaks, each providing one catalytic
      center for phosphodiester bond hydrolysis. Possible models for DNA cleavage are further
      studied and discussed.
AU  - Jindrova E
AU  - Schmid-Nuoffer S
AU  - Hamburger F
AU  - Janscak P
AU  - Bickle TA
PT  - Journal Article
TA  - FEBS J.
JT  - FEBS J.
SO  - FEBS J. 2005 272: 552.

PMID- 15788748
VI  - 33
DP  - 2005
TI  - On the DNA cleavage mechanism of Type I restriction enzymes.
PG  - 1760-1766
AB  - Although the DNA cleavage mechanism of Type I restriction-modification enzymes has been
      extensively studied, the mode of cleavage remains
      elusive. In this work, DNA ends produced by EcoKI, EcoAI and EcoR124I,
      members of the Type IA, IB and IC families, respectively, have been
      characterized by cloning and sequencing restriction products from the
      reactions with a plasmid DNA substrate containing a single recognition
      site for each enzyme. Here, we show that all three enzymes cut this
      substrate randomly with no preference for a particular base composition
      surrounding the cleavage site, producing both 5'- and 3'-overhangs of
      varying lengths. EcoAI preferentially generated 3'-overhangs of 2-3 nt,
      whereas EcoKI and EcoR124I displayed some preference for the formation of
      5'-overhangs of a length of approximately 6-7 and 3-5 nt, respectively. A
      mutant EcoAI endonuclease assembled from wild-type and nuclease-deficient
      restriction subunits generated a high proportion of nicked circular DNA,
      whereas the wild-type enzyme catalyzed efficient cleavage of both DNA
      strands. We conclude that Type I restriction enzymes require two
      restriction subunits to introduce DNA double-strand breaks, each providing
      one catalytic center for phosphodiester bond hydrolysis. Possible models
      for DNA cleavage are discussed.
AU  - Jindrova E
AU  - Schmid-Nuoffer S
AU  - Hamburger F
AU  - Janscak P
AU  - Bickle TA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2005 33: 1760-1766.

PMID- 24613968
VI  - 58
DP  - 2014
TI  - DNA-AuNPs based signal amplification for highly sensitive detection of DNA methylation, methyltransferase activity and inhibitor screening.
PG  - 40-47
AB  - A sensitive and selective electrochemical method was developed for the detection of DNA
      methylation, determination of DNA methyltransferase (MTase) activity and screening of MTase
      inhibitor. Methylene blue (MB) was employed as electrochemical indicator and DNA-modified gold
      nanoparticles (AuNPs) were used as signal amplification unit because the DNA strands in this
      composite have strong adsorption ability for MB. First, the thiolated single-stranded DNA S1
      was self-assembled on gold electrode, hybridization between the lower portion of DNA S1 and
      its complementary DNA S2 formed an identical double-stranded tetranucleotide target sequence
      for both DNA adenine methylation (Dam) MTase and methylation-resistant endonuclease Mbo I,
      then the upper portion of DNA S1 was hybridized with its complementary DNA S3 modified on
      AuNPs to bring the DNA S3-AuNPs amplification units onto the electrode. The DNA S1
      /S2/S3-AuNPs bioconjugate has lots of DNA strands, and they can adsorb abundant MB. Mbo I
      endounuclease could not cleave the identical target sequence after it was methylated by Dam
      MTase. On the contrary, the sequence without methylation could be cleaved, which would
      decrease the amount of adsorbed MB. The presence of redox-active MB was detected
      electrochemically by differential pulse voltammetry (DPV). Thus, the activity of Dam MTase and
      methylation status were sensitively converted to the DNA S3-AuNPs amplified DPV signals. The
      DPV signal demonstrated a linear relationship with logarithm of Dam concentration ranging from
      0.075 to 30 U/mL, achieving a detection limit of 0.02 U/mL (SIN=D3). Also, screening of Dam
      MTase inhibitor 5-fluorouracil was successfully investigated using this fabricated sensor.
AU  - Jing X
AU  - Cao X
AU  - Wang Li
AU  - Lan T
AU  - Li Y
AU  - Xie G
PT  - Journal Article
TA  - Biosensors and Bioelectronics
JT  - Biosensors and Bioelectronics
SO  - Biosensors and Bioelectronics 2014 58: 40-47.

PMID- 3008080
VI  - 14
DP  - 1986
TI  - Restriction endonucleases HindII and TaqI cleave DNA with mismatched nucleotides within their recognition sequences.
PG  - 1943-1949
AB  - Restriction endonucleases HindII and TaqI, but not SalI, were found to
      efficiently cleave synthetic hexdecanucleotide duplexes which contained either
      an A/C or a G/T mismatch within their respective restriction sites.
      Double-stranded M13 DNAs with identical mismatches were also cleaved under the
      assay conditions.  These results suggest that the distortion of the DNA duplex,
      caused by these purine/pyrimidine mismatches is not sufficiently large so as to
      interfere with the recognition and the subsequent cleavage of the DNA by these
      two enzymes.  HindII and SalI, but not TaqI, were furthermore shown to
      hydrolyze the two strands of the duplex with different rates.  The differences
      between the mode of recognition of their respective restriction sites by these
      three enzymes are discussed.
AU  - Jiricny J
AU  - Martin D
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1986 14: 1943-1949.

PMID- 3018674
VI  - 14
DP  - 1986
TI  - Oligonucleotide duplexes containing inosine, 7-deazainosine, tubercidin, nebularine and 7-deazanebularine as substrates for restriction endonucleases HindII, SalI and TaqI.
PG  - 6579-6590
AB  - Synthetic hexadecanucleotide duplexes containing a single purine nucleotide
      analogue in the recognition sites of the restriction endonucleases HindII, SalI
      and TaqI were used to investigate the restriction site determinants required by
      these enzymes for sequence recognition and phosphodiester bond cleavage.  The
      enzymes were, in general, unaffected by changes introduced into the minor
      groove of the helix.  SalI was found to be inhibited by the major groove
      modifications introduced into the fourth position of its recognition sequence
      GTCGAC.  HindII and TaqI were, by contrast, able to cleave the sites containing
      the analogues at this position.  TaqI and, to a lesser extent, HindII could
      also be shown to tolerate "mismatch analogues" at this site.
AU  - Jiricny J
AU  - Wood SG
AU  - Martin D
AU  - Ubasawa A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1986 14: 6579-6590.

PMID- 27081141
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Providencia heimbachae, Isolated from a Diabetic Foot Ulcer.
PG  - e00276-16
AB  - Providenciaspp. are ubiquitous Gram-negative bacteria of the familyEnterobacteriaceaethat are
      common opportunistic pathogens. In the present
      work, we have sequenced, annotated, and compared the draft genome ofProvidencia
      heimbachae, which was recovered from a diabetic foot ulcer. It is composed of
      4.22 Mb and encodes 3,843 protein-coding genes and 79 RNA genes, including 11
      rRNA genes.
AU  - Jneid J
AU  - Benamar S
AU  - Pagnier I
AU  - Levy PY
AU  - Lavigne JP
AU  - La Scola B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00276-16.

PMID- 28705978
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Pseudoalteromonas tetraodonis CSB01KR and Pseudoalteromonas lipolytica CSB02KR, Isolated from the Gut of the Sea Cucumber Apostichopus japonicus.
PG  - e00627-17
AB  - We present here the complete genome sequences of two newly isolated Pseudoalteromonas
      tetraodonis and Pseudoalteromonas lipolytica strains, isolated
      from the gut of the sea cucumber Apostichopus japonicus, to provide a useful
      means for facilitating the study of antibacterial, bacteriolytic, agarolytic, and
      algicidal activities of marine Pseudoalteromonas species.
AU  - Jo J
AU  - Choi H
AU  - Lee SG
AU  - Oh J
AU  - Lee HG
AU  - Park C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00627-17.

PMID- Not carried by PubMed...
VI  - 57
DP  - 1996
TI  - Evolutionary relationship of NaeI restriction endonuclease with DNA topisomerases.
PG  - 889
AB  - NaeI endonuclease must bind two DNA recognition sequences for cleavage
      to occur.  Therefore, DNAs containing NaeI recognition sequences without sufficient
      affinity to occupy one or the other DNA-binding sites are resistant to cleavage.  Tethering
      resistant and cleavable recognition sequences together caused a switch in their relative
      cleavabilities.  This switching implies that DNA cleavage occurs at the DNA-binding site
      with higher affinity for the resistant sequence.  The other DNA-binding site, with higher
      affinity for the cleavable sequence, acts as the effector DNA-binding site with little to no
      catalytic function.  Examination of the amino acid sequence of NaeI uncovered similarity to
      the active site of human ligase I, except for leucine 43 in NaeI instead of lysine essential
      for
      ligase activity.  Changing leucine 43 to lysine 43 (L43K) changed NaeI activity: NaeI-
      L43K relaxed supercoiled DNA to yield DNA topoisomers and recombined DNA to give
      dimeric molecule.  Interruption of the reactions of NaeI and NaeI-L43K with DNA
      demonstrated transient protein-DNA covalent complexes.  These findings imply coupled
      endonuclease and ligase domains and link NaeI endonuclease to the topoisomerase and
      recombinase protein families.  Glycerol gradient sedimentation of NaeI-L43K showed that
      the active conformation of NaeI-LA3K is a dimer.  The topoisomerase activity of NaeI-
      LA3K changed from processive to distributive with increasing cation concentration.  NaeI-
      L43K decatenated k-DNA and bonded the 5' end of the cleaved DNA.  These
      characteristics mimic those of the classic type II topoisomerases.  Also, the effects of
      topoisomerase drugs on NaeI-LA3K were determined.  NaeI-LA3K activity was
      specifically inhibited by eukaryotic topoisomerase II drugs daunorubicin, ellipticine, and
      m-AMSA.  Especially, the cleavage step of DNA relaxation by NaeI-LA3K was sensitively
      inhibited by these drugs, but the cleavage activity of wild-type NaeI was not.  Therefore,
      L43K amino acid change increased the sensitivity of NaeI protein to the drugs.  The
      increased sensitivity implies that protein-drug interaction is enhanced by the amino acid
      change and that the ligase-like active site, containing LA3K, provides a part of the drug
      binding pocket.
AU  - Jo K
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1996 57: 889.

PMID- 9580689
VI  - 26
DP  - 1998
TI  - Step-wise DNA relaxation and decatenation by NaeI-43K.
PG  - 2380-2384
AB  - NaeI protein was originally isolated for its restriction endonuclease properties.  NaeI was
      later discovered to either relax or cleave supercoiled DNA, depending upon whether NaeI
      position 43 contains a lysine (43K) or leucine (43L) respectively.  NaeI-43K DNA relaxation
      activity appears to be the product of coupling separate endonuclease and ligase domains within
      the same polypeptide.  Whereas NaeI relaxes supercoiled DNA like a topoisomerase, even forming
      a transient covalent intermediate with the substrate DNA, NaeI shows no obvious sequence
      similarity to the topoisomerases.  To further characterize the topoisomerase activity of NaeI,
      we report here that NaeI-43K changes the linking number of a single negatively supercoiled
      topoisomer of pBR322 by units of one and therefore is a type I topoisomerase.  Positively
      supercoiled pBR322 was resistant to NaeI-43K.  At low salt concentration NaeI-43K was
      processive; non-saturating amounts of enzyme relaxed a fraction of the DNA. At high salt
      concentration the same non-saturating amounts of NaeI-43K partially relaxed all the DNA in a
      step-wise fashion to give a Gaussian distribution of topoisomers, demonstrating a switch from
      a processive to a distributive mode of action.  NaeI-43K decatenated kinetoplast DNA
      containing nicked circles, implying that NaeI-43K can cleave opposite a nick.  The products of
      the reaction are decatenated nicked circles under both processive and distributive conditions.
      The behavior of NaeI-43K is consistent with that of a prokaryotic type I topoisomerase.
AU  - Jo K
AU  - Topal MD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1998 26: 2380-2384.

PMID- 8932368
VI  - 24
DP  - 1996
TI  - Effects on NaeI-DNA recognition of the leucine to lysine substitution that transforms restriction endonuclease NaeI to a topoisomerase: a model for restriction endonuclease evolution.
PG  - 4171-4175
AB  - Substituting lysine for leucine at position 43 (L43K) transforms NaeI from restriction
      endonuclease to topoisomerase and makes NaeI hypersensitive to intercalative anticancer drugs.
      Here we investigated DNA recognition by NaeI-L43K.  Using DNA competition and gel retardation
      assays, NaeI-L43K showed reduced affinity for DNA substrate and the ability to bind both
      single- and double-stranded DNA with a definite preference for the former.  Sedimentation
      studies showed that under native conditions NaeI-L43K, like NaeI, is a dimer.  Introduction of
      mismatched bases into double-stranded DNA significantly increased that DNA's ability to
      inhibit NaeI-L43K.  Wild-type NaeI showed no detectable binding of either single-stranded DNA
      or mismatched DNA over the concentration range studied.  These results demonstrate that the
      L43K substitution caused a significant change in recognition specificity by NaeI and imply
      that NaeI-L43K's topoisomerase activity is related to its ability to bind single-stranded and
      distorted regions in DNA.  A mechanism is proposed for the evolution of the NaeI
      restriction-modification system from a topoisomerase/ligase by a mutation that abolished
      religation activity and provided a needed change in DNA recognition.
AU  - Jo K
AU  - Topal MD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1996 24: 4171-4175.

PMID- 7892605
VI  - 267
DP  - 1995
TI  - DNA topoisomerase and recombinase activities in NaeI restriction endonuclease.
PG  - 1817-1820
AB  - NaeI endonuclease must bind to two DNA sequences for cleavage. Examination of the amino acid
      sequence of NaeI uncovered similarity to the active site of human DNA ligase I, except for
      leucine 43 in NaeI instead of the lysine essential for ligase activity. Changing leucine 43 to
      lysine 43 (L43K) changed NaeI activity: NaeI-L43K relaxed supercoiled DNA to yield DNA
      topisomers and recombined DNA to give dimeric molecules. Interruption of the reactions of NaeI
      and NaeI-L43K with DNA demonstrated transient protein-DNA covalent complexes. These findings
      imply coupled endonuclease and ligase domains and link NaeI endonuclease to the topoisomerase
      and recombinase protein families.
AU  - Jo K
AU  - Topal MD
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1995 267: 1817-1820.

PMID- 8756463
VI  - 35
DP  - 1996
TI  - Changing a leucine to a lysine residue makes NaeI endonuclease hypersensitive to DNA intercalative drugs.
PG  - 10014-10018
AB  - A single amino acid change transforms restriction enzyme NaeI to a topoisomerase and
      recombinase (NaeI-L43K) that shows no sequence similarity to these protein families.  This
      transformation appears to result from coupled endonuclease and ligase domains.  To further
      elucidate the relationship between NaeI-L43K and the topoisomerase protein family, we studied
      the effect of the topoisomerase inhibitors on NaeI-L43K activity.  The intercalative drugs
      amsacrine, ellipticine, and daunorubicin inhibited NaeI-L43K, whereas the nonintercalating
      drugs camptothecin, VP-16, and oxolinic acid did not.  Ethidium bromide also inhibited
      NaeI-L43K, implying that intercalation is responsible for its inhibition.  The effects of the
      intercalative drugs on the DNA cleavage steps of NaeI and NaeI-L43K were compared.  The drugs
      hardly inhibited DNA cleavage by wild type NaeI but completely inhibited DNA cleavage by
      NaeI-L43K.  This difference in inhibition demonstrates that the L43K amino acid change
      sensitized NaeI to these drugs.  Low concentrations of the intercalative drugs, except for
      ethidium bromide, enhance production of topoisomerase--DNA covalent intermediates but
      inhibited production of the NaeI-L43K-DNA covalent intermediate.  These results imply some
      unique differences between DNA relaxation by NaeI-L43K and DNA topoisomerase.  Concomitant
      with studying inhibition of the cleavage intermediate, NaeI-L53K was found to covalently bond
      with the 5' end of the cleaved DNA strand.
AU  - Jo K
AU  - Topal MD
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1996 35: 10014-10018.

PMID- 16159782
VI  - 187
DP  - 2005
TI  - Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition.
PG  - 6488
AB  - Pseudomonas syringae pv. phaseolicola, a gram-negative bacterial plant pathogen, is the causal
      agent of halo blight of bean. In this study, we report on the genome sequence of P. syringae
      pv. phaseolicola isolate 1448A, which encodes 5,353 open reading frames (ORFs) on one circular
      chromosome (5,928,787 bp) and two plasmids (131,950 bp and 51,711 bp). Comparative analyses
      with a phylogenetically divergent pathovar, P. syringae pv. tomato DC3000, revealed a strong
      degree of conservation at the gene and genome levels. In total, 4,133 ORFs were identified as
      putative orthologs in these two pathovars using a reciprocal best-hit method, with 3,941 ORFs
      present in conserved, syntenic blocks. Although these two pathovars are highly similar at the
      physiological level, they have distinct host ranges; 1448A causes disease in beans, and DC3000
      is pathogenic on tomato and Arabidopsis. Examination of the complement of ORFs encoding
      virulence, fitness, and survival factors revealed a substantial, but not complete, overlap
      between these two pathovars. Another distinguishing feature between the two pathovars is their
      distinctive sets of transposable elements. With access to a fifth complete pseudomonad genome
      sequence, we were able to identify 3,567 ORFs that likely comprise the core Pseudomonas genome
      and 365 ORFs that are P. syringae specific.
AU  - Joardar V et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2005 187: 6488.

PMID- 1520287
VI  - 286
DP  - 1992
TI  - Positive co-operative interaction between the subunits of CeqI restriction endonuclease.
PG  - 85-88
AB  - CeqI restriction endonuclease, an isoschizomer of EcoRV, forms complexes of 2-20 subunits
      under physiological conditions, in the absence of DNA. These molecules partially dissociate in
      the presence of DNA sequences recognized by CeqI or in the presence of non-ionic detergents.
      In solutions containing high concentrations of salts (e.g. 1M NaCl), the enzyme dissociated
      into subunits, concomitantly losing its activity. According to our experiments, it is the
      tetrameric form of the enzyme that binds the DNA and represents the catalytically active
      molecule. Analysis of the enzyme kinetics revealed a positive co-operative interaction between
      the subunits of the enzyme. Computer-assisted analysis of these data yielded a Hill
      coefficient of approx. 1.35, suggesting two binding sites per tetrameric enzyme molecule, two
      subunits per palindromic recognition site.
AU  - Jobbagy Z
AU  - Izsvak Z
AU  - Duda E
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 1992 286: 85-88.

PMID- 27516504
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Escherichia coli ER1821R, a Laboratory K-12 Derivative Engineered To Be Deficient in All Methylcytosine and Methyladenine  Restriction Systems.
PG  - e00763-16
AB  - We present here the complete genomic sequence of a rifampin-resistant derivative  of the
      Escherichia coli K-12 laboratory strain ER1821, engineered to be deficient
      in all known restriction systems, making it suitable for generating unbiased
      libraries from organisms with non-K-12 methylation patterns. The ER1821R genome
      is most closely related to that of DH1, another popular cloning strain (both
      derived from MM294), but is deleted for the e14 prophage (McrA(-)) and the
      immigration control (McrBC(-) EcoKI R(-) M(-) Mrr(-)) loci.
AU  - Jobling MG
AU  - Raleigh EA
AU  - Frank DN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00763-16.

PMID- 19395570
VI  - 75
DP  - 2009
TI  - Toward cloning of the magnetotactic metagenome: identification of magnetosome island gene clusters in uncultivated magnetotactic bacteria from different aquatic sediments.
PG  - 3972-3979
AB  - In this report, we describe the selective cloning of large DNA fragments
      from magnetotactic metagenomes from various aquatic habitats. This was
      achieved by a two-step magnetic enrichment which allowed the mass
      collection of environmental magnetotactic bacteria (MTB) virtually free of
      nonmagnetic contaminants. Four fosmid libraries were constructed and
      screened by end sequencing and hybridization analysis using heterologous
      magnetosome gene probes. A total of 14 fosmids were fully sequenced. We
      identified and characterized two fosmids, most likely originating from two
      different alphaproteobacterial strains of MTB that contain several
      putative operons with homology to the magnetosome island (MAI) of
      cultivated MTB. This is the first evidence that uncultivated MTB exhibit
      similar yet differing organizations of the MAI, which may account for the
      diversity in biomineralization and magnetotaxis observed in MTB from
      various environments.
AU  - Jogler C
AU  - Lin W
AU  - Meyerdierks A
AU  - Kube M
AU  - Katzmann E
AU  - Flies C
AU  - Pan Y
AU  - Amann R
AU  - Reinhardt R
AU  - Schuler D
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2009 75: 3972-3979.

PMID- 20406295
VI  - 12
DP  - 2010
TI  - Cultivation-independent characterization of 'Candidatus Magnetobacterium bavaricum' via ultrastructural, geochemical, ecological and metagenomic methods.
PG  - f2466-f2478
AB  - 'Candidatus Magnetobacterium bavaricum' is unusual among magnetotactic bacteria (MTB) in
      terms of cell size (8-10 microm long, 1.5-2 microm in diameter), cell architecture,
      magnetotactic behaviour and its distinct phylogenetic position in the deep-branching
      Nitrospira phylum. In the present study, improved magnetic enrichment techniques permitted
      high-resolution scanning electron microscopy and energy dispersive X-ray analysis, which
      revealed the intracellular organization of the magnetosome chains. Sulfur globule accumulation
      in the cytoplasm point towards a sulfur-oxidizing metabolism of 'Candidatus M. bavaricum'.
      Detailed analysis of 'Candidatus M. bavaricum' microhabitats revealed more complex
      distribution patterns than previously reported, with cells predominantly found in low oxygen
      concentration. No correlation to other geochemical parameters could be observed. In addition,
      the analysis of a metagenomic fosmid library revealed a 34 kb genomic fragment, which contains
      33 genes, among them the complete rRNA gene operon of 'Candidatus M. bavaricum' as well as a
      gene encoding a putative type IV RubisCO large subunit.
AU  - Jogler C
AU  - Niebler M
AU  - Lin W
AU  - Kube M
AU  - Wanner G
AU  - Kolinko S
AU  - Stief P
AU  - Beck AJ
AU  - de Beer D
AU  - Petersen N
AU  - Pan Y
AU  - Amann R
AU  - Reinhardt R
AU  - Schuler D
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2010 12: f2466-f2478.

PMID- 6308917
VI  - 23
DP  - 1983
TI  - Electron microscopy studies of DNA complexes with restriction endonuclease SalGI.
PG  - 197-201
AB  - The binding properties of the type II restriction endonuclease SalGI to the plasmid DNA pGW10
      has been investigated by electron microscopic studies.  Samples were spread by the BAC
      technique.  In the presence of magnesium, SalGI binds as dimers and tetramers to the specific
      recognition site 5'-G-T-C-G-A-C-3' and with lower rate to the sequence 5'-G-T-C-A-A-C-3',
      which represents the recognition site of the restriction endonucleases HindII and HincII.
AU  - Johannssen W
PT  - Journal Article
TA  - Z. Allg. Mikrobiol.
JT  - Z. Allg. Mikrobiol.
SO  - Z. Allg. Mikrobiol. 1983 23: 197-201.

PMID- Not carried by PubMed...
VI  - 20
DP  - 1988
TI  - Interaction of restriction endonuclease with DNA as revealed by electron microscopy.
PG  - 325-339
AB  - None
AU  - Johannssen W
PT  - Journal Article
TA  - Methods Microbiol.
JT  - Methods Microbiol.
SO  - Methods Microbiol. 1988 20: 325-339.

PMID- 231672
VI  - 134
DP  - 1979
TI  - Quaternary structure of the isolated restriction endonuclease EndoR.BglI from Bacillus globigii as revealed by electron microscopy.
PG  - 707-726
AB  - The restriction endonuclease EndoR.BglI was purified nearly to homogeneity.
      BglI samples, when negatively stained with 4% uranyl acetate, show two
      different particle projections in the electron microscope.  Projection A has an
      outer diameter of 22.5+/-0.8 nm and is composed of six intensity maxima
      arranged in a ring; the centre of the ring exhibits slightly visible additional
      substructures.  Projection B is also a ring; its outer diameter is 23.8+/-0.7
      nm; it does not show detailed fine structure, aside from a probable 10-fold
      rotational symmetry.  Variations of the negative staining technique (single
      carbon layer, 2% uranyl acetate; sandwich preparation with 4% uranyl acetate)
      revealed additional fine structural details for both projections.  From the
      electron microscopic observations, a model of the enzyme particle was developed
      containing 20 identical, biologically active monomers of molecular weight
      around 61,000 arranged as a pentagonal dodecahedron.  Tilting experiments
      established this structure decisively by interconversion of the different
      appearances of given particles in the expected way.  By sodium dodecyl
      sulphate/polyacrylamide gel electrophoresis, polyacrylamide gel electrophoresis
      in a continuous molecular sieve gradient and evaluation of negatively stained
      enzyme particles, a molecular weight of the monomer of 61,000 was estimated,
      resulting in a total enzyme particle molecular weight of 1.2x10/6 also
      determined by linear sucrose density-gradient centrifugation.
AU  - Johannssen W
AU  - Schutte H
AU  - Mayer F
AU  - Mayer H
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1979 134: 707-726.

PMID- 8415009
VI  - 21
DP  - 1993
TI  - A family of nuclear homing endonucleases.
PG  - 4405
AB  - Homing endonucleases from archaea introns, protein insertions, and the mobile group I introns
      from organelles share a common motif, the LAGLI-DADG motif. Sequence motifs like the
      zinc-finger and the BIY-YIG have been found in phage homing endonucleases. However, the only
      described nuclear homing endonuclease, the 18 kd I-Ppo protein has none of the above consensus
      sequences. This unclassified I-Ppo endonuclease is encoded by the mobile intron PpLSU3 found
      in the extrachromosomal ribosomal DNA (rDNA) of the myxomycete Physarum polycephalum.
      Recently, we have discovered two new group I intron elements from nuclear extrachromosomal
      rDNA that bears an apparent similarity to PpLSU3. The myxomycete Didymium iridis has a mobile
      group I intron that encodes a putative homing endonuclease I-Dir of 29kd, whereas the
      amoeba-flagellate Naegleria andersoni ssp andersoni contains a similar intron that encodes a
      putative homing endonuclease I-Naa of 28 kd. I-Dir, I-Naa and I-Ppo are all basic proteins
      with a theoretical isoelectric point of 9.5, 9.9 and 8.2, respectively. Furthermore, we could
      not identify any significant sequence similarity between these proteins and proteins in the
      GenBank and EMBL libraries, and they do not contain any of the sequence motifs (eg. LAGLI-DADG
      or GIY-YIG) found in other homing endonucleases. However, we have identified a conserved
      region among the nuclear homing endonucleases which consists of several His and Cys residues.
      Patterns of His and Cys residues have been associated with protein domains involved in
      metal-binding and interaction with nucleic acids, suggesting a similar function of the His-Cys
      Box. Database searches using the His-Cys box consensus sequence as the test sequence failed to
      identify homologous regions in other proteins. Furthermore, no significant sequence similarity
      is seen between I-Dir, I-Naa and I-Ppo outside this His-Cys Box (less than 10% identify). A
      comparison between three homologous intron-endcoded proteins from different species of
      Naegleria (identity between 85-96%;T.M.E., unpublished results) strongly support the His-Cys
      Box as a highly conserved region. Thus, we propose that the nuclear homing endonucleases are
      all members of the same family, identified by the His-Cys Box.
AU  - Johansen S
AU  - Embley TM
AU  - Willassen NP
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 4405.

PMID- 8124711
VI  - 76
DP  - 1994
TI  - An intron in the nuclear ribosomal DNA of Didymium iridis codes for a group I ribozyme and a novel ribozyme that cooperate in self-splicing.
PG  - 725-734
AB  - We have discovered a unique group I intron-like insertion (DiSSU) in the nuclear small subunit
      ribosomal RNA gene of the myxomycete Didymium iridis.  By sequence, DiSSU consists of a group
      I ribozyme at the 5' end, an open reading frame (ORF) in the middle, and novel element at the
      3' end.  Intron RNA self-splices in vitro to yield ten major processed RNAs, including a
      full-length circle.  The group I ribozyme can efficiently cleave at an internal processing
      site, which separates the group I ribozyme from the ORF.  Surprisingly, deletions that remove
      the entire group I ribozyme do not impair cleavage at the 3' splice site, implying that the
      3' element itself is a catalytic RNA.  Deletions that remove portions of the 3' element
      prevent utilization of the 5' splice site, suggesting that this element cooperates with the
      upstream group I ribozyme in splicing.  DiSSU appears to be the first example for the
      cooperative interaction of distinct ribozymes in RNA splicing.
AU  - Johansen S
AU  - Vogt VM
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1994 76: 725-734.

PMID- 27979938
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Extended-Spectrum-beta-Lactamase-Producing Escherichia coli Strain CCUG 62462, Isolated from a Urine Sample.
PG  - e01382-16
AB  - The draft genome sequence has been determined for an extended-spectrum-beta-lactamase
      (ESBL)-producing (blaCTX-M-15) Escherichia coli
      strain (CCUG 62462), composed of 119 contigs and a total size of 5.27 Mb. This E.
      coli is serotype O25b and sequence type 131, a pandemic clonal group, causing
      worldwide antimicrobial-resistant infections.
AU  - Johnning A
AU  - Jakobsson HE
AU  - Boulund F
AU  - Salva-Serra F
AU  - Moore ER
AU  - Ahren C
AU  - Karami N
AU  - Kristiansson E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01382-16.

PMID- 27056236
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Bacillus subtilis Strain CU1050, Which Is Sensitive to Phage SPbeta.
PG  - e00262-16
AB  - The Gram-positive bacteriumBacillus subtilisis used as a model organism to study  cellular and
      molecular processes. Here, we announce the complete genomic sequence
      ofB. subtilisstrain CU1050, derived fromB. subtilisstrain 168. CU1050 has
      historically been used to study suppressor mutations and phage biology,
      especially the lysogenic phage SPbeta.
AU  - Johnson CM
AU  - Grossman AD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00262-16.

PMID- 3006762
VI  - 25
DP  - 1986
TI  - Preparation and characterization of a viral DNA molecule containing a site-specific 2-aminofluorene adduct:  A new probe for mutagenesis by carcinogens.
PG  - 449-456
AB  - The synthetic oligonucleotide heptamer 5'-ATCCGTC-3' was reacted in vitro with
      N-acetoxy-N-(trifluoroacetyl)-2-aminofluorene and the resulting product
      isolated by reverse-phase high-performance liquid chromatography (HPLC).  This
      purified oligonucleotide, which was shown by chemical and enzymatic analysis to
      be a heptamer containing a single N-(deoxyguanin-8-yl)-2-aminofluorene adduct,
      was then used to situate the putatively mutagenic aminofluorene lesion within
      the genome of M13 mp9 by ligating it into a complementary single-stranded
      region located at a specific site in the negative strand of the duplex M13 mp9
      DNA molecule.  The presence of the adduct at the anticipated location was
      confirmed by taking advantage of the facts that AF adducts inhibit many
      restriction enzymes when located in or near their restriction sites and that
      the AF moiety should be contained within the HincII recognition sequence on M13
      mp9 DNA.  Upon attempted cleavage of the M13 DNA containing the site-specific
      AF adduct with HincII, we find that the large majority of the DNA remained
      circular, demonstrating the incorporation of the AF adduct in high yield into
      the DNA molecule at this location.  This system should prove useful in vivo for
      the study of mutagenesis by chemical carcinogens and in vitro to study the
      interaction of purified DNA metabolizing proteins with a template containing a
      site-specific lesion.
AU  - Johnson DL
AU  - Reid TM
AU  - Lee M-S
AU  - King CM
AU  - Romano LJ
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1986 25: 449-456.

PMID- 27034501
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Paenibacillus sp. Strain DMB5, Acclimatized and Enriched for Catabolizing Anthropogenic Compounds.
PG  - e00211-16
AB  - Here, we present the draft genome sequence ofPaenibacillussp. strain DMB5, isolated from
      polluted sediments of the Kharicut Canal, Vatva, India, having a
      genome size of 7.5 Mbp and 7,077 coding sequences. The genome of this
      dye-degrading bacterium provides valuable information on the microbe-mediated
      biodegradation of anthropogenic compounds.
AU  - Johnson J
AU  - Shah B
AU  - Jain K
AU  - Parmar N
AU  - Hinsu A
AU  - Patel N
AU  - Joshi CG
AU  - Madamwar D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00211-16.

PMID- 24503981
VI  - 2
DP  - 2014
TI  - Genome Sequences of Campylobacter jejuni 81-176 Variants with Enhanced Fitness Relative to the Parental Strain in the Chicken Gastrointestinal Tract.
PG  - e00006-14
AB  - Campylobacter jejuni is a major cause of food-borne infections in the United States due to its
      ability to asymptomatically colonize the gastrointestinal
      tracts of chickens. Using competition assays with parental C. jejuni 81-176,
      variants with consistently improved fitness in chicken ceca relative to the
      parental strain were identified and sequenced.
AU  - Johnson JG
AU  - Carpentier S
AU  - Spurbeck RR
AU  - Sandhu SK
AU  - Dirita VJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00006-14.

PMID- 25212620
VI  - 2
DP  - 2014
TI  - Genome Sequence of Klebsiella pneumoniae Respiratory Isolate IA565.
PG  - e00896-14
AB  - Klebsiella pneumoniae is a clinically significant opportunistic bacterial pathogen as well as
      a normal member of the human microbiota. K. pneumoniae strain
      IA565 was isolated from a tracheal aspirate at the University of Iowa Hospitals
      and Clinics. Here, we present the genome sequence of K. pneumoniae IA565.
AU  - Johnson JG
AU  - Spurbeck RR
AU  - Sandhu SK
AU  - Matson JS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00896-14.

PMID- 24994806
VI  - 2
DP  - 2014
TI  - Genome Sequence of Klebsiella pneumoniae Urinary Tract Isolate Top52.
PG  - e00668-14
AB  - Klebsiella pneumoniae is a significant cause of nosocomial infections, including
      ventilator-associated pneumonias and catheter-associated urinary tract
      infections. K. pneumoniae strain TOP52 #1721 (Top52) was isolated from a woman
      presenting with acute cystitis and subsequently characterized using various
      murine models of infection. Here we present the genome sequence of K. pneumoniae
      Top52.
AU  - Johnson JG
AU  - Spurbeck RR
AU  - Sandhu SK
AU  - Matson JS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00668-14.

PMID- 2784970
VI  - 32
DP  - 1989
TI  - Procainamide inhibits DNA methyltransferase.
PG  - S143
AB  - We have reported that T cells treated with procainamide (Pca) have
      hypomethylated DNA.  Pca can bind DNA, so we tested whether Pca inhibits T cell
      DNA methyltransferase.  DNA methyltransferase was partially purified from
      nuclei isolated from the human T cell leukemia line Jurkat.  Methyltransferase
      activity was measured by incubating the enzyme with Micrococcus luteus DNA and
      3H-S-adenosylmethionine (3H-SAM), then precipitating DNA onto fiberglass
      filters with ethanol and determining precipitated 3H.  A dose dependent
      inhibition of DNA methylation was observed, with 100 micromolar Pca inhibiting
      3H incorporation into DNA by 51+/-5% (mean +/1 SEM of three experiments, each
      performed in triplicate) (p<0.05).  Lineweaver-Burk analysis demonstrated
      competitive inhibition with DNA.  To test whether Pca is a nonspecific
      inhibitor of all transmethylation reactions, Jurkat cells were treated with Pca
      for four days, then incubated with 3H-SAM and 3H incorporation into membrane
      phospholipids measured.  No inhibition was observed.  These results demonstrate
      that Pca is a DNA methyltransferase inhibitor, and suggest that Pca inhibits
      Jurkat DNA methylation by selectively inhibiting this enzyme.
AU  - Johnson M
AU  - Scheinbart L
AU  - Pike M
AU  - Richardson B
PT  - Journal Article
TA  - Arthritis Rheum.
JT  - Arthritis Rheum.
SO  - Arthritis Rheum. 1989 32: S143.

PMID- 4700513
VI  - 11
DP  - 1973
TI  - Production of specific fragments of PhiX174 replicative form DNA by a restriction enzyme from Haemophilus parainfluenzae, endonuclease HP.
PG  - 596-599
AB  - A restriction endonuclease from Haemophilus parainfluenzae degrades Phi174
      replicative form DNA into eight specific fragments, ranging from 1,700 to 150
      base pairs and terminated specifically by deoxycytidylic acid.
AU  - Johnson PH
AU  - Lee AS
AU  - Sinsheimer RL
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1973 11: 596-599.

PMID- 28153911
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Tumor-Targeting Salmonella enterica Serovar Typhimurium Strain SL7207.
PG  - e01591-16
AB  - Salmonella enterica serovar Typhimurium strain SL7207 is a genetically modified derivative of
      strain SL1344, which preferentially accumulates in tumors and can
      be used as a vehicle for tissue-specific gene delivery in vivo Here, we report
      the draft genome sequence of SL7207, confirming a purported aroA deletion and
      four single-nucleotide polymorphisms compared to SL1344.
AU  - Johnson SA
AU  - Ormsby MJ
AU  - Wall DM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01591-16.

PMID- 25931592
VI  - 3
DP  - 2015
TI  - Complete genome sequences for 59 burkholderia isolates, both pathogenic and near  neighbor.
PG  - e00159-15
AB  - The genus Burkholderia encompasses both pathogenic (including Burkholderia mallei and
      Burkholderia pseudomallei, U.S. Centers for Disease Control and Prevention
      Category B listed), and nonpathogenic Gram-negative bacilli. Here we present full
      genome sequences for a panel of 59 Burkholderia strains, selected to aid in
      detection assay development.
AU  - Johnson SL et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00159-15.

PMID- 25931591
VI  - 3
DP  - 2015
TI  - Complete genome sequences for 35 biothreat assay-relevant bacillus species.
PG  - e00151-15
AB  - In 2011, the Association of Analytical Communities (AOAC) International released  a list of
      Bacillus strains relevant to biothreat molecular detection assays. We
      present the complete and annotated genome assemblies for the 15 strains listed on
      the inclusivity panel, as well as the 20 strains listed on the exclusivity panel.
AU  - Johnson SL et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00151-15.

PMID- 25931590
VI  - 3
DP  - 2015
TI  - Thirty-Two Complete Genome Assemblies of Nine Yersinia Species, Including Y. pestis, Y. pseudotuberculosis, and Y. enterocolitica.
PG  - e00148-15
AB  - The genus Yersinia includes three human pathogens, of which Yersinia pestis is responsible for
      >2,000 illnesses each year. To aid in the development of
      detection assays and aid further phylogenetic elucidation, we sequenced and
      assembled the complete genomes of 32 strains (across 9 Yersinia species).
AU  - Johnson SL et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00148-15.

PMID- 25931589
VI  - 3
DP  - 2015
TI  - Genome sequencing of 18 francisella strains to aid in assay development and testing.
PG  - e00147-15
AB  - Francisella tularensis is a highly infectious bacterium with the potential to cause high
      fatality rates if infections are untreated. To aid in the development
      of rapid and accurate detection assays, we have sequenced and annotated the
      genomes of 18 F. tularensis and Francisella philomiragia strains.
AU  - Johnson SL et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00147-15.

PMID- 29348328
VI  - 6
DP  - 2018
TI  - Correction for Johnson et al., 'Complete Genome Sequences for 35 Biothreat Assay-Relevant Bacillus Species'.
PG  - e01144-17
AB  - 
AU  - Johnson SL et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01144-17.

PMID- 25676747
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequences of 80 Environmental and Clinical Isolates of Burkholderia  pseudomallei.
PG  - e01282-14
AB  - Here, we present the draft genome sequences of 80 isolates of Burkholderia pseudomallei. The
      isolates represent clinical cases of melioidosis and
      environmental isolates from regions in Australia and Papua New Guinea where B.
      pseudomallei is endemic. The genomes provide further context for the diversity of
      the pathogen.
AU  - Johnson SL
AU  - Baker AL
AU  - Chain PS
AU  - Currie BJ
AU  - Daligault HE
AU  - Davenport KW
AU  - Davis CB
AU  - Inglis TJ
AU  - Kaestli M
AU  - Koren S
AU  - Mayo M
AU  - Merritt AJ
AU  - Price EP
AU  - Sarovich DS
AU  - Warner J
AU  - Rosovitz MJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01282-14.

PMID- 25977434
VI  - 3
DP  - 2015
TI  - Complete Genome Assemblies for Two Single-Chromosome Vibrio cholerae Isolates, Strains 1154-74 (Serogroup O49) and 10432-62 (Serogroup O27).
PG  - e00462-15
AB  - Here, we report the completed genome sequences for two non-O1/non-O139 Vibrio cholerae
      isolates. Each isolate has only a single chromosome, as opposed to the
      normal paradigm of two chromosomes found in all other V. cholerae isolates.
AU  - Johnson SL
AU  - Khiani A
AU  - Bishop-Lilly KA
AU  - Chapman C
AU  - Patel M
AU  - Verratti K
AU  - Teshima H
AU  - Munk AC
AU  - Bruce DC
AU  - Han CS
AU  - Xie G
AU  - Davenport KW
AU  - Chain P
AU  - Sozhamannan S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00462-15.

PMID- 26383665
VI  - 3
DP  - 2015
TI  - Finished Genome Assembly of Warm Spring Isolate Francisella novicida DPG 3A-IS.
PG  - e01046-15
AB  - We sequenced the complete genome of Francisella novicida DPG 3A-IS to closed and  finished
      status. This is a warm spring isolate recovered from Hobo Warm Spring (Utah, USA). The final
      assembly is available in NCBI under accession number CP012037.
AU  - Johnson SL
AU  - Minogue TD
AU  - Daligault HE
AU  - Wolcott MJ
AU  - Teshima H
AU  - Coyne SR
AU  - Davenport KW
AU  - Jaissle JG
AU  - Chain PS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01046-15.

PMID- 26383662
VI  - 3
DP  - 2015
TI  - Finished Genome Assembly of Yersinia pestis EV76D and KIM 10v.
PG  - e01024-15
AB  - Here, we sequenced the completed genome of Yersinia pestis EV76D and KIM 10v, two genomes used
      as references in assay development, to improved high-quality draft status.
AU  - Johnson SL
AU  - Minogue TD
AU  - Daligault HE
AU  - Wolcott MJ
AU  - Teshima H
AU  - Coyne SR
AU  - Davenport KW
AU  - Jaissle JG
AU  - Chain PS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01024-15.

PMID- 25593267
VI  - 3
DP  - 2015
TI  - Finished Genome Sequence of Bacillus cereus Strain 03BB87, a Clinical Isolate with B. anthracis Virulence Genes.
PG  - e01446-14
AB  - Bacillus cereus strain 03BB87, a blood culture isolate, originated in a 56-year-old male
      muller operator with a fatal case of pneumonia in 2003. Here we
      present the finished genome sequence of that pathogen, including a 5.46-Mb
      chromosome and two plasmids (209 and 52 Kb, respectively).
AU  - Johnson SL
AU  - Minogue TD
AU  - Teshima H
AU  - Davenport KW
AU  - Shea AA
AU  - Miner HL
AU  - Wolcott MJ
AU  - Chain PS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01446-14.

PMID- 27174264
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of a CTX-M-15-Producing Escherichia coli Strain from the H30Rx Subclone of Sequence Type 131 from a Patient with Recurrent Urinary Tract  Infections, Closely Related to a Lethal Urosepsis Isolate from the Patient's  Sister.
PG  - e00334-16
AB  - We report here the complete genome sequence, including five plasmid sequences, of Escherichia
      coli sequence type 131 (ST131) strain JJ1887. The strain was isolated
      in 2007 in the United States from a patient with recurrent cystitis, whose
      caregiver sister died from urosepsis caused by a nearly identical strain.
AU  - Johnson TJ
AU  - Aziz M
AU  - Liu CM
AU  - Sokurenko E
AU  - Kisiela DI
AU  - Paul S
AU  - Andersen P
AU  - Johnson JR
AU  - Price LB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00334-16.

PMID- 21602325
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Gallibacterium anatis strain UMN179, isolated from a laying hen with peritonitis.
PG  - 3676-3677
AB  - Gallibacterium anatis is a member of the normal flora of avian hosts and an important
      causative agent of peritonitis and salpingitis in laying hens. Here we report the availability
      of the first completed G. anatis genome sequence of strain UMN179, isolated from an Iowa
      laying hen with peritonitis.
AU  - Johnson TJ
AU  - Fernandez-Alarcon C
AU  - Bojesen AM
AU  - Nolan LK
AU  - Trampel DW
AU  - Seemann T
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3676-3677.

PMID- 25858844
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of a Carbapenem-Resistant Extraintestinal Pathogenic Escherichia coli Strain Belonging to the Sequence Type 131 H30R Subclade.
PG  - e00272-15
AB  - Here, we report the completed genome sequence of a carbapenem-resistant extraintestinal
      pathogenic Escherichia coli sequence type 131 (ST131) isolate,
      MNCRE44. The isolate was obtained in 2012 in Minnesota, USA, from a sputum sample
      from a hospitalized patient with multiple comorbidities, and it belongs to the
      H30R sublineage.
AU  - Johnson TJ
AU  - Hargreaves M
AU  - Shaw K
AU  - Snippes P
AU  - Lynfield R
AU  - Aziz M
AU  - Price LB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00272-15.

PMID- 16885466
VI  - 188
DP  - 2006
TI  - Complete DNA sequence of a ColBM plasmid from avian pathogenic Escherichia coli suggests that it evolved from closely related ColV virulence plasmids.
PG  - 5975-5983
AB  - Avian pathogenic Escherichia coli (APEC), an extraintestinal pathogenic E.
      coli causing colibacillosis in birds, is responsible for significant
      economic losses for the poultry industry. Recently, we reported that the
      APEC pathotype was characterized by possession of a set of genes contained
      within a 94-kb cluster linked to a ColV plasmid, pAPEC-O2-ColV. These
      included sitABCD, genes of the aerobactin operon, hlyF, iss, genes of the
      salmochelin operon, and the 5' end of cvaB of the ColV operon. However,
      the results of gene prevalence studies performed among APEC isolates
      revealed that these traits were not always linked to ColV plasmids. Here,
      we present the complete sequence of a 174-kb plasmid, pAPEC-O1-ColBM,
      which contains a putative virulence cluster similar to that of
      pAPEC-O2-ColV. These two F-type plasmids share remarkable similarity,
      except that they encode the production of different colicins;
      pAPEC-O2-ColV contains an intact ColV operon, and pAPEC-O1-ColBM encodes
      the colicins B and M. Interestingly, remnants of the ColV operon exist in
      pAPEC-O1-ColBM, hinting that ColBM-type plasmids may have evolved from
      ColV plasmids. Among APEC isolates, the prevalence of ColBM sequences
      helps account for the previously observed differences in prevalence
      between genes of the "conserved" portion of the putative virulence cluster
      of pAPEC-O2-ColV and those genes within its "variable" portion. These
      results, in conjunction with Southern blotting and probing of
      representative ColBM-positive strains, indicate that this "conserved"
      cluster of putative virulence genes is primarily linked to F-type
      virulence plasmids among the APEC isolates studied.
AU  - Johnson TJ
AU  - Johnson SJ
AU  - Nolan LK
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2006 188: 5975-5983.

PMID- 17293413
VI  - 189
DP  - 2007
TI  - The genome sequence of avian pathogenic Escherichia coli strain O1:K1:H7 shares strong similarities with human extraintestinal pathogenic E. coli  genomes.
PG  - 3228-3236
AB  - Escherichia coli strains that cause disease outside the intestine are known as extraintestinal
      pathogenic E. coli (ExPEC) and include human
      uropathogenic E. coli (UPEC) and avian pathogenic E. coli (APEC).
      Regardless of host of origin, ExPEC strains share many traits. It has been
      suggested that these commonalities may enable APEC to cause disease in
      humans. Here, we begin to test the hypothesis that certain APEC strains
      possess potential to cause human urinary tract infection through virulence
      genotyping of 1,000 APEC and UPEC strains, generation of the first
      complete genomic sequence of an APEC (APEC O1:K1:H7) strain, and
      comparison of this genome to all available human ExPEC genomic sequences.
      The genomes of APEC O1 and three human UPEC strains were found to be
      remarkably similar, with only 4.5% of APEC O1's genome not found in other
      sequenced ExPEC genomes. Also, use of multilocus sequence typing showed
      that some of the sequenced human ExPEC strains were more like APEC O1 than
      other human ExPEC strains. This work provides evidence that at least some
      human and avian ExPEC strains are highly similar to one another, and it
      supports the possibility that a food-borne link between some APEC and UPEC
      strains exists. Future studies are necessary to assess the ability of APEC
      to overcome the hurdles necessary for such a food-borne transmission, and
      epidemiological studies are required to confirm that such a phenomenon
      actually occurs.
AU  - Johnson TJ
AU  - Kariyawasam S
AU  - Wannemuehler Y
AU  - Mangiamele P
AU  - Johnson SJ
AU  - Doetkott C
AU  - Skyberg JA
AU  - Lynne AM
AU  - Johnson JR
AU  - Nolan LK
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2007 189: 3228-3236.

PMID- 23459610
VI  - 9
DP  - 2013
TI  - Programmed Protection of Foreign DNA from Restriction Allows Pathogenicity Island Exchange during Pneumococcal Transformation.
PG  - e1003178
AB  - In bacteria, transformation and restriction-modification (R-M) systems play potentially
      antagonistic roles. While the former, proposed as a
      form of sexuality, relies on internalized foreign DNA to create genetic
      diversity, the latter degrade foreign DNA to protect from bacteriophage
      attack. The human pathogen Streptococcus pneumoniae is transformable
      and possesses either of two R-M systems, DpnI and DpnII, which
      respectively restrict methylated or unmethylated double-stranded (ds)
      DNA. S. pneumoniae DpnII strains possess DpnM, which methylates dsDNA
      to protect it from DpnII restriction, and a second methylase, DpnA,
      which is induced during competence for genetic transformation and is
      unusual in that it methylates single-stranded (ss) DNA. DpnA was
      tentatively ascribed the role of protecting internalized plasmids from
      DpnII restriction, but this seems unlikely in light of recent results
      establishing that pneumococcal transformation was not evolved to favor
      plasmid exchange. Here we validate an alternative hypothesis, showing
      that DpnA plays a crucial role in the protection of internalized
      foreign DNA, enabling exchange of pathogenicity islands and more
      generally of variable regions between pneumococcal isolates. We show
      that transformation of a 21.7 kb heterologous region is reduced by more
      than 4 logs in dpnA mutant cells and provide evidence that the specific
      induction of dpnA during competence is critical for full protection. We
      suggest that the integration of a restrictase/ssDNA-methylase couplet
      into the competence regulon maintains protection from bacteriophage
      attack whilst simultaneously enabling exchange of pathogenicicy
      islands. This protective role of DpnA is likely to be of particular
      importance for pneumococcal virulence by allowing free variation of
      capsule serotype in DpnII strains via integration of DpnI capsule loci,
      contributing to the documented escape of pneumococci from capsule-based
      vaccines. Generally, this finding is the first evidence for a mechanism
      that actively promotes genetic diversity of S. pneumoniae through
      programmed protection and incorporation of foreign DNA.
AU  - Johnston C
AU  - Martin B
AU  - Granadel C
AU  - Polard P
AU  - Claverys JP
PT  - Journal Article
TA  - PLoS Pathog.
JT  - PLoS Pathog.
SO  - PLoS Pathog. 2013 9: e1003178.

PMID- 24021553
VI  - 21
DP  - 2013
TI  - Postreplication targeting of transformants by bacterial immune systems?
PG  - 516-521
AB  - Bacteria are constantly challenged by foreign genetic elements such as bacteriophages and
      plasmids. Several defense systems provide immunity against such attackers, including
      restriction modification (R M) systems and clustered, regularly interspaced short palindromic
      repeats (CRISPRs). These systems target attacking DNA and thus antagonize natural
      transformation, which relies on uptake of exogenous DNA to promote acquisition of new genetic
      traits. It is unclear how this antagonization occurs, becau e transforming DNA is single
      stranded, and thus resistant to these immune systems. Here, we propose a simple model whereby
      these systems limit transformation by attack of transformed chromosomes once double
      strandedness is restored by chromosomal replication.
AU  - Johnston C
AU  - Martin B
AU  - Polard P
AU  - Claverys J-P
PT  - Journal Article
TA  - Trends Microbiol.
JT  - Trends Microbiol.
SO  - Trends Microbiol. 2013 21: 516-521.

PMID- 28934361
VI  - 12
DP  - 2017
TI  - Restriction-modification mediated barriers to exogenous DNA uptake and incorporation employed by Prevotella intermedia.
PG  - e0185234
AB  - Prevotella intermedia, a major periodontal pathogen, is increasingly implicated in human
      respiratory tract and cystic fibrosis lung infections. Nevertheless, the
      specific mechanisms employed by this pathogen remain only partially characterized
      and poorly understood, largely due to its total lack of genetic accessibility.
      Here, using Single Molecule, Real-Time (SMRT) genome and methylome sequencing,
      bisulfite sequencing, in addition to cloning and restriction analysis, we define
      the specific genetic barriers to exogenous DNA present in two of the most
      widespread laboratory strains, P. intermedia ATCC 25611 and P. intermedia Strain
      17. We identified and characterized multiple restriction-modification (R-M)
      systems, some of which are considerably divergent between the two strains. We
      propose that these R-M systems are the root cause of the P. intermedia
      transformation barrier. Additionally, we note the presence of conserved Clustered
      Regularly Interspaced Short Palindromic Repeat (CRISPR) systems in both strains,
      which could provide a further barrier to exogenous DNA uptake and incorporation.
      This work will provide a valuable resource during the development of a genetic
      system for P. intermedia, which will be required for fundamental investigation of
      this organism's physiology, metabolism, and pathogenesis in human disease.
AU  - Johnston CD
AU  - Skeete CA
AU  - Fomenkov A
AU  - Roberts RJ
AU  - Rittling SR
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2017 12: e0185234.

PMID- 26893408
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Streptomyces silvensis ATCC 53525, a Producer of Novel Hormone Antagonists.
PG  - e00001-16
AB  - Streptomyces silvensis produces nonribosomal peptides that act as antagonists of  the human
      oxytocin and vasopressin receptors. Here, we present the genome
      sequence of S. silvensis ATCC 53525 and demonstrate that this organism possesses
      a number of additional biosynthetic gene clusters and might be a promising source
      for genome-guided drug discovery efforts.
AU  - Johnston CW
AU  - Li Y
AU  - Magarvey NA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00001-16.

PMID- 17995451
VI  - 410
DP  - 2008
TI  - Role of histidine residues in EcoP15I DNA methyltransferase activity as probed by chemical modification and site-directed mutagenesis.
PG  - 543-553
AB  - Towards understanding the catalytic mechanism of M.EcoP15I [EcoP15I MTase (DNA
      methyltransferase); an adenine methyltransferase], we
      investigated the role of histidine residues in catalysis. M.EcoP15I,
      when incubated with DEPC (diethyl pyrocarbonate), a histidine-specific
      reagent, shows a time- and concentration-dependent inactivation of
      methylation of DNA containing its recognition sequence of 5'-CAGCAG-3'.
      The loss of enzyme activity was accompanied by an increase in
      absorbance at 240 nm. A difference spectrum of modified versus native
      enzyme shows the formation of N-carbethoxyhistidine that is diminished
      by hydroxylamine. This, along with other experiments, strongly suggests
      that the inactivation of the enzyme by DEPC was specific for histidine
      residues. Substrate protection experiments show that pre-incubating the
      methylase with DNA was able to protect the enzyme from DEPC
      inactivation. Site-directed mutagenesis experiments in which the 15
      histidine residues in the enzyme were replaced individually with
      alanine corroborated the chemical modification studies and established
      the importance of His-335 in the methylase activity. No gross
      structural differences were detected between the native and H335A
      mutant MTases, as evident from CD spectra, native PAGE pattern or on
      gel filtration chromatography. Replacement of histidine with alanine
      residue at position 335 results in a mutant enzyme that is
      catalytically inactive and binds to DNA more tightly than the wild-type
      enzyme. Thus we have shown in the present study, through a combination
      of chemical modification and site-directed mutagenesis experiments,
      that His-335 plays an essential role in DNA methylation catalysed by
      M.EcoP15I.
AU  - Jois PS
AU  - Madhu N
AU  - Rao DN
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 2008 410: 543-553.

PMID- 
VI  - 4
DP  - 2004
TI  - Restriction endonucleases - a tool for DNA cleavage.
PG  - 239-245
AB  - 
AU  - Jomova K
AU  - Hegedusova A
AU  - Vollmannova A
PT  - Journal Article
TA  - Chem. Rozhlady
JT  - Chem. Rozhlady
SO  - Chem. Rozhlady 2004 4: 239-245.

PMID- 2549371
VI  - 217
DP  - 1989
TI  - The Escherichia coli dam gene is expressed as a distal gene of a new operon.
PG  - 85-96
AB  - DNA containing the Escherichia coli dam gene and sequences upstream from this gene were cloned
      from the Clarke-Carbon plasmids pLC29-47 and pLC13-42. Promoter activity was localized using
      pKO expression vectors and galactokinase assays to two regions, one 1650-2100 bp and the other
      beyond 2400 bp upstream of the dam gene. No promoter activity was detected immediately in
      front of this gene; plasmid pDam118, from which the nucleotide sequence of the dam gene was
      determined, is shown to contain the pBR322 promoter for the primer RNA from the pBR322 rep
      region present on a 76 bp Sau3A fragment inserted upstream of the dam gene in the correct
      orientation for dam expression. The nucleotide sequence upstream of dam has been determined.
      An open reading frame (ORF) is present between the nearest promoter region and the dam gene.
      Codon usage and base frequency analysis indicate that this is expressed as a protein of
      predicted size 46 kDa. A protein of size close to 46 kDa is expressed from this region,
      detected using minicell analysis. No function has been determined for this protein, and no
      significant homology exist between it and sequences in the PIR protein or GenBank DNA
      databases. This unidentified reading frame (URF) is termed urf-74.3, since it is an URF
      located at 74.3 min on the E. coli chromosome. Sequence comparisons between the regions
      upstream of urf-74.3 and the aroB gene show that the aroB gene is located immediately upstream
      of urf-74.3, and that the promoter activity nearest to dam is found within the aroB structural
      gene. This activity is relatively weak (about 15% of that of the E. coli gal operon promoter).
      The promoter activity detected beyond 2400 bp upstream of dam is likely to be that of the aroB
      gene, and is 3 to 4 times stronger than that found within the aroB gene. Three potential DnaA
      binding sites, each with homology of 8 of 9 bp, are present, two in the aroB promoter region
      and one just upstream of the dam gene. Expression through the site adjacent to the dam gene is
      enhanced 2- to 4-fold in dnaA mutants at 38C. Restriction site comparisons map these regions
      precisely on the Clarke-Carbon plasmids pLC13-42 and pLC29-47, and show that the E. coli ponA
      (mrcA) gene resides about 6 kb upstream of aroB.
AU  - Jonczyk P
AU  - Hines R
AU  - Smith DW
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1989 217: 85-96.

PMID- 21555588
VI  - 108
DP  - 2011
TI  - Genomic insights into the physiology and ecology of the marine filamentous cyanobacterium Lyngbya majuscula.
PG  - 8815-8820
AB  - Filamentous cyanobacteria of the genus Lyngbya are important contributors
      to coral reef ecosystems, occasionally forming dominant cover and
      impacting the health of many other co-occurring organisms. Moreover, they
      are extraordinarily rich sources of bioactive secondary metabolites, with
      35% of all reported cyanobacterial natural products deriving from this
      single pantropical genus. However, the true natural product potential and
      life strategies of Lyngbya strains are poorly understood because of
      phylogenetic ambiguity, lack of genomic information, and their close
      associations with heterotrophic bacteria and other cyanobacteria. To gauge
      the natural product potential of Lyngbya and gain insights into potential
      microbial interactions, we sequenced the genome of Lyngbya majuscula 3L, a
      Caribbean strain that produces the tubulin polymerization inhibitor
      curacin A and the molluscicide barbamide, using a combination of Sanger
      and 454 sequencing approaches. Whereas  approximately  293,000 nucleotides
      of the draft genome are putatively dedicated to secondary metabolism, this
      is far too few to encode a large suite of Lyngbya metabolites, suggesting
      Lyngbya metabolites are strain specific and may be useful in species
      delineation. Our analysis revealed a complex gene regulatory network,
      including a large number of sigma factors and other regulatory proteins,
      indicating an enhanced ability for environmental adaptation or microbial
      associations. Although Lyngbya species are reported to fix nitrogen,
      nitrogenase genes were not found in the genome or by PCR of genomic DNA.
      Subsequent growth experiments confirmed that L. majuscula 3L is unable to
      fix atmospheric nitrogen. These unanticipated life history characteristics
      challenge current views of the genus Lyngbya.
AU  - Jones AC et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2011 108: 8815-8820.

PMID- 28798167
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Sulfuriferula sp. Strain AH1, a Sulfur-Oxidizing Autotroph Isolated from Weathered Mine Tailings from the Duluth Complex in  Minnesota.
PG  - e00673-17
AB  - We report the closed and annotated genome sequence of Sulfuriferula sp. strain AH1. Strain AH1
      has a 2,877,007-bp chromosome that includes a partial Sox system
      for inorganic sulfur oxidation and a complete nitrogen fixation pathway. It also
      has a single 39,138-bp plasmid with genes for arsenic and mercury resistance.
AU  - Jones DS
AU  - Roepke EW
AU  - Hua AA
AU  - Flood BE
AU  - Bailey JV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00673-17.

PMID- 26769927
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Achromobacter piechaudii GCS2, Agrobacterium sp. Strain SUL3, Microbacterium sp. Strain GCS4, Shinella sp. Strain GWS1, and Shinella sp.   Strain SUS2 Isolated from Consortium with the Hydrocarbon-Producing Alga  Botryococcus br.
PG  - e01527-15
AB  - A variety of bacteria associate with the hydrocarbon-producing microalga Botryococcus braunii,
      some of which may influence its growth. We report here the
      genome sequences for Achromobacter piechaudii GCS2, Agrobacterium sp. strain
      SUL3, Microbacterium sp. strain GCS4, and Shinella sp. strains GWS1 and SUS2,
      isolated from a laboratory culture of B. braunii, race B, strain Guadeloupe.
AU  - Jones KJ
AU  - Moore K
AU  - Sambles C
AU  - Love J
AU  - Studholme DJ
AU  - Aves SJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01527-15.

PMID- 26430033
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of a Cyanotroph, Pseudomonas fluorescens NCIMB 11764, Employing Single-Molecule Real-Time Technology.
PG  - e01111-15
AB  - We report here the application of single-molecule real-time sequencing for determining the
      entire genome structure of the cyanotroph Pseudomonas fluorescens NCIMB 11764.
AU  - Jones LB
AU  - Kunz DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01111-15.

PMID- 2956428
VI  - 194
DP  - 1987
TI  - Mismatch repair of deaminated 5-methyl-cytosine.
PG  - 155-159
AB  - Deamination of 5-methyl-cytosine in double-stranded DNA produces a G.T mismatch.
      Heteroduplexes of bacteriophage lambda DNA containing a G.T mismatch at the site of G.5-meC
      base-pair in one of the parental phages were constructed and used to transfect Escherichia
      coli cells. Genetic analysis of the progeny phages derived from such heteroduplexes suggests
      that, in E. coli, mismatches resulting from the deamination of 5-methyl-cytosine are repaired
      by a system requiring the E. coli dcm methylase and some, but not all, of the functions of the
      E. coli methyl-directed mismatch repair system. The repair appears to act only on the G.T
      mismatch and acts specifically to restore the cytosine methylation sequence.
AU  - Jones M
AU  - Wagner R
AU  - Radman M
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1987 194: 155-159.

PMID- 8653676
VI  - 56
DP  - 1996
TI  - DNA methylation errors and cancer.
PG  - 2463-2467
AB  - It has become clear over the last few years that DNA methylation is essential for normal
      embryonic development and that alterations in DNA methylation are very common in cancer cells
      and are capable of directly modifying carcinogenesis.  Cytosine methylation is responsible for
      the induction of a surprisingly high percentage of disease-causing point mutations in tumor
      suppressor genes in somatic and germline cells.  This may either be due to the spontaneous
      deamination of 5-methylcytosine or to a more active process involving side reactions during
      the enzymatic modification of cytosine in DNA.  Current interest in the role of methylation
      has focused on the potential for abnormal methylation events to silence tumor suppressor
      genes, thus giving rise to a novel pathway to cause their progressive epigenetic inactivation.
      Random methylation of CpG islands not methylated in normal cells may contribute to the
      progressive inactivation of growth-inhibitory genes resulting in the clonal selection of cells
      with increasingly abnormal methylation patterns.  This model for gene inactivation during
      cancer development has important clinical implications, since it is possible to reactivate
      these dormant genes using inhibitors of DNA methylation and potentially restore growth control
      to cells.
AU  - Jones PA
PT  - Journal Article
TA  - Cancer Res.
JT  - Cancer Res.
SO  - Cancer Res. 1996 56: 2463-2467.

PMID- 9122155
VI  - 94
DP  - 1997
TI  - Altered DNA methylation and genome instability: A new pathway to cancer?
PG  - 2103-2105
AB  - DNA methylation is a mechanism for changing the base sequence of DNA without altering its
      coding function.  As a heritable, yet reversible, epigenetic change, it has the potential of
      altering gene expression and has profound developmental and genetic consequences.  The
      methylation reaction itself is mechanistically complex and involves the flipping of the target
      cytosine out of the intact double helix, so that the transfer of the methyl group from
      S-adenosylmethionine can occur in a cleft in the enzyme.  Cytosine methylation is inherently
      mutagenic, which presumably has led to the 80% suppression of the CpG methyl acceptor site in
      eukarytoic organisms, which methylate their genomes.  It contributes strongly to the
      generation of polymorphisms and germ-line mutations, and to transition mutations that
      inactivate tumor-suppressor genes.  Despite a 10- to 40-fold increase in the rate of
      transitions at methylated versus unmethylated cytosines, methylation is not only tolerated in
      several eukaryotes, but is actually required for the embryonic development of mammals.  The
      reasons 5-methylcytosine is essential for development remain obscure, but most probably relate
      to the well-documented ability of methylation, particularly the methylation of CpG-rich
      promoters, to block transcriptional activation.  Indeed, there is growing evidence that
      methylation plays a pivotal role in key developmental processes such as genomic imprinting and
      stabilization of X-chromosome inactivation.  It therefore is not surprising that alterations
      in this essential epigenetic system might play a role in carcinogenesis.
AU  - Jones PA
AU  - Gonzalgo ML
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1997 94: 2103-2105.

PMID- 11498574
VI  - 293
DP  - 2001
TI  - The role of DNA methylation in mammalian epigenetics.
PG  - 1068-1070
AB  - Genes constitute only a small proportion of the total mammalian genome, and the precise
      control of their expression in the presence of an overwhelming background of noncoding DNA
      presents a substantial problem for their regulation. Noncoding DNA, containing introns,
      repetitive elements, and potentially active transposable elements, requires effective
      mechanisms for its long-term silencing.  Mammals appear to have taken advantage of the
      possibilities afforded by cytosine methylation to provide a heritable mechanism for altering
      DNA-protein interactions to assist in such silencing.  Genes can be transcribed from
      methylation-free promoters even though adjacent transcribed and nontranscribed regions are
      extensively methylated. Gene promoters can be used and regulated while keeping noncoding DNA,
      including transposable elements, suppressed. Methylation is also used for long-term epigenetic
      silencing of X-linked and imprinted genes and can either increase or decrease the level of
      transcription, depending on whether the methylation inactivates a positive or negative
      regulatory element.
AU  - Jones PA
AU  - Takai D
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2001 293: 1068-1070.

PMID- 9620779
VI  - 19
DP  - 1998
TI  - Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription.
PG  - 187-191
AB  - CpG methylation in vertebrates correlates with alterations in chromatin structure and gene
      silencing.  Differences in DNA-methylation status are associated with imprinting phenomena and
      carcinogenesis.  In Xenopus laevis oocytes, DNA methylation dominantly silences transcription
      through the assembly of a repressive nucleosomal array.  Methylated DNA assembled into
      chromatin binds the transcriptional repressor MeCP2 which cofractionates with Sin3 and histone
      deacetylase.  Silencing conferred by MeCP2 and methylated DNA can be relieved by inhibition of
      histone deacetylase, facilitating the remodelling of chromatin and transcriptional activation.
      These results establish a direct casual relationship between DNA methylation-dependent
      transcription silencing and the modification of chromatin.
AU  - Jones PL
AU  - Veenstra GJC
AU  - Wade PA
AU  - Vermaak D
AU  - Kass SU
AU  - Landsberger N
AU  - Strouboulis J
AU  - Wolffe AP
PT  - Journal Article
TA  - Nat. Genet.
JT  - Nat. Genet.
SO  - Nat. Genet. 1998 19: 187-191.

PMID- 874454
VI  - 99
DP  - 1977
TI  - Host modification and restriction with a mycobacteriophage isolated from a pseudolysogenic Mycobacterium chelonei.
PG  - 389-395
AB  - A pseudolysogenic Mycobacterium chelonei and its phage Phi630 are described.  Phage Phi630 is
      the first mycobacteriophage reported to be resistant to the nonpolar solvents chloroform,
      dioxan and diethyl ether.  The phage had a latent period of 75 min, a rise period of 90 min
      and a burst size of 51.  Evidence is presented for host modification and restriction.  Phage
      Phi630A, grown on host strain M. chelonei F-630 Rg, plated on the alternative host M.
      smegmatis ATCC607 with an efficiency of plating of 10^-5 on the alternative host F-630 Rg.
      Phages Phi630A and Phi630B adsorbed equally well on their alternative hosts and on their
      indicator host strains.  The progeny of plaques from initial platings on the alternative host,
      when grown in the alternative host, exhibited a marked reduction in e.o.p. on their original
      host.
AU  - Jones WD Jr
AU  - Greenberg J
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1977 99: 389-395.

PMID- 26404585
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of a Pathogenic O86:H25 Sequence Type 57 Escherichia coli Strain Isolated from Poultry and Carrying 12 Acquired Antibiotic Resistance Genes.
PG  - e01107-15
AB  - Escherichia coli is a commensal bacterium that is frequently associated with
      multidrug-resistant zoonotic and foodborne infections. Here, we report the 5.6-Mbp draft
      genome sequence of an E. coli recovered from poultry, which encodes multiple acquired
      antibiotic resistance determinants, virulence factors, pathogenicity determinants, and mobile
      genetic elements.
AU  - Jones-Dias D
AU  - Manageiro V
AU  - Sampaio DA
AU  - Vieira L
AU  - Canica M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01107-15.

PMID- 
VI  - 20
DP  - 1999
TI  - Restriction endonuclease EcoRV mutants that switch metal ion requirement.
PG  - 109-111
AB  - Divalent metal ions, normally Mg2+, are essential for both DNA cleavage by the EcoRV
      restriction endonuclease at its recognition sequence, GATATC, and also for the enzyme's
      discrimination between this particular sequence and all other sequences.  In the absence of
      divalent metal ions, EcoRV demonstrates no catalytic activity, though it can still bind to DNA
      in a nonspecific manner with no preference in its recognition sequence.  The complex of EcoRV
      and its cognate DNA, however, has a high affinity for Mg2+ due to the distortion of the bound
      DNA, creating a metal-binding site between the protein and the DNA.
AU  - Joo EJ
AU  - Park WS
AU  - Kim SK
AU  - Bae YS
AU  - Moon BJ
PT  - Journal Article
TA  - Bull. Korean Chem. Soc.
JT  - Bull. Korean Chem. Soc.
SO  - Bull. Korean Chem. Soc. 1999 20: 109-111.

PMID- 21952546
VI  - 193
DP  - 2011
TI  - Genome Sequences for Five Strains of the Emerging Pathogen Haemophilus haemolyticus.
PG  - 5879-5880
AB  - We report the first whole-genome sequences for five strains, two carried and three pathogenic,
      of the emerging pathogen Haemophilus haemolyticus.
      Preliminary analyses indicate that these genome sequences encode markers
      that distinguish H. haemolyticus from its closest Haemophilus relatives
      and provide clues to the identity of its virulence factors.
AU  - Jordan IK et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5879-5880.

PMID- 11157209
VI  - 67
DP  - 2001
TI  - Efficient transformation system for Propionibacterium freudenreichii based on a novel vector.
PG  - 499-503
AB  - A 3.6-kb endogenous plasmid was isolated from a Propionibacterium freudenreichii strain and
      sequenced completely. Based on homologies with plasmids from other bacteria, notably a plasmid
      from Mycobacterium, a region harboring putative replicative functions was defined. Outside
      this region two restriction enzyme recognition sites were used for insertion of an Escherichia
      coli-specific replicon and an erythromycin resistance gene for selection in Propionibacterium.
      Hybrid vectors obtained in this way replicated in both E. coli and P. freudenreichii. Whereas
      electroporation of P. freudenreichii with vector DNA isolated from an E. coli transformant
      yielded 10 to 30 colonies per microgram of DNA, use of vector DNA reisolated from a
      Propionibacterium transformant dramatically increased the efficiency of transformation (> or
      =10(8) colonies per microgram of DNA). It could be shown that restriction-modification was
      responsible for this effect. The high efficiency of the system described here permitted
      successful transformation of Propionibacterium with DNA ligation mixtures.
AU  - Jore JPM
AU  - van Luijk N
AU  - Luiten RGM
AU  - van der Werf MJ
AU  - Pouwels PH
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2001 67: 499-503.

PMID- 28496941
VI  - 12
DP  - 2017
TI  - Chromosomal features of Escherichia coli serotype O2:K2, an avian pathogenic E. coli.
PG  - 33
AB  - Escherichia coli causing infection outside the gastrointestinal system are referred to as
      extra-intestinal pathogenic E. coli. Avian pathogenic E. coli is a
      subgroup of extra-intestinal pathogenic E. coli and infections due to avian
      pathogenic E. coli have major impact on poultry production economy and welfare
      worldwide. An almost defining characteristic of avian pathogenic E. coli is the
      carriage of plasmids, which may encode virulence factors and antibiotic
      resistance determinates. For the same reason, plasmids of avian pathogenic E.
      coli have been intensively studied. However, genes encoded by the chromosome may
      also be important for disease manifestation and antimicrobial resistance. For the
      E. coli strain APEC_O2 the plasmids have been sequenced and analyzed in several
      studies, and E. coli APEC_O2 may therefore serve as a reference strain in future
      studies. Here we describe the chromosomal features of E. coli APEC_O2. E. coli
      APEC_O2 is a sequence type ST135, has a chromosome of 4,908,820 bp (plasmid
      removed), comprising 4672 protein-coding genes, 110 RNA genes, and 156
      pseudogenes, with an average G + C content of 50.69%. We identified 82 insertion
      sequences as well as 4672 protein coding sequences, 12 predicated genomic
      islands, three prophage-related sequences, and two clustered regularly
      interspaced short palindromic repeats regions on the chromosome, suggesting the
      possible occurrence of horizontal gene transfer in this strain. The wildtype
      strain of E. coli APEC_O2 is resistant towards multiple antimicrobials, however,
      no (complete) antibiotic resistance genes were present on the chromosome, but a
      number of genes associated with extra-intestinal disease were identified.
      Together, the information provided here on E. coli APEC_O2 will assist in future
      studies of avian pathogenic E. coli strains, in particular regarding strain of E.
      coli APEC_O2, and aid in the general understanding of the pathogenesis of avian
      pathogenic E. coli.
AU  - Jorgensen SL
AU  - Kudirkiene E
AU  - Li L
AU  - Christensen JP
AU  - Olsen JE
AU  - Nolan L
AU  - Olsen RH
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 33.

PMID- 24503942
VI  - 9
DP  - 2014
TI  - Hundreds of circular novel plasmids and DNA elements identified in a rat cecum metamobilome.
PG  - E87924
AB  - Metagenomic approaches are widespread in microbiological research, but so far,
      the knowledge on extrachromosomal DNA diversity and composition has largely
      remained dependant on cultivating host organisms. Even with the emergence of
      metagenomics, complete circular sequences are rarely identified, and have
      required manual curation. We propose a robust in silico procedure for identifying
      complete small plasmids in metagenomic datasets from whole genome shotgun
      sequencing. From one very pure and exhaustively sequenced metamobilome from rat
      cecum, we identified a total of 616 circular sequences, 160 of which were
      carrying a gene with plasmid replication domain. Further homology analyses
      indicated that the majority of these plasmid sequences are novel. We confirmed
      the circularity of the complete plasmid candidates using an inverse-type PCR
      approach on a subset of sequences with 95% success, confirming the existence and
      length of discrete sequences. The implication of these findings is a broadened
      understanding of the traits of circular elements in nature and the possibility of
      massive data mining in existing metagenomic datasets to discover novel pools of
      complete plasmids thus vastly expanding the current plasmid database.
AU  - Jorgensen TS
AU  - Xu Z
AU  - Hansen MA
AU  - Sorensen SJ
AU  - Hansen LH
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2014 9: E87924.

PMID- 10631614
VI  - 4
DP  - 1999
TI  - Quantitative evaluation of metal ion binding to PvuII restriction endonuclease.
PG  - 814-823
AB  - Restriction enzymes are important examples of phosphodiester hydrolysis activity and as such
      have been of increasing interest to structural biologists. Much of the architecture of
      endonuclease active sites has been derived from X-ray crystallographic studies. These
      structures implicate conserved active site acidic residues and the scissile bond of the
      substrate as coordination ligands of required metal ions. Central to the development of
      restriction enzyme mechanism is our understanding of the role of metal ion binding in the
      reaction, an important feature of which is identifying the energetic contributions of the
      enzyme and the substrate to metal ion affinity. To begin to address this issue, isothermal
      titration calorimetry (ITC) and 19F NMR spectroscopy have been applied to evaluate metal ion
      binding by the representative PvuII endonuclease in the absence of substrate. In separate
      experiments, ITC data demonstrate that PvuII endonuclease binds 2.16 Mn(II) ions and 2.05
      Ca(II) metal ions in each monomer active site with Kd values of approximately 1 mM. While
      neither calorimetry nor protein NMR spectroscopy is directly sensitive to Mg(II) binding to
      the enzyme, Mn(II) competes with Mg(II) for common sites(s) on PvuII endonuclease.
      Substitution of the conserved active site carboxylate Glu68 with Ala resulted in a loss of
      affinity for both equivalents of both Ca(II) and Mn(II). Interestingly, the active site mutant
      D58A retained an affinity for Mn(II) with Kd approximately 2 mM. Mn(II) paramagnetic
      broadening in 19F spectra of wild-type and mutant 3-fluorotyrosine PvuII endonucleases are
      consistent with ITC results. Chemical shift analysis of 3-fluorotyrosine mutant enzymes is
      consistent with a perturbed conformation for D58A. Therefore, free PvuII endonuclease binds
      metal ions, and metal ion binding can precede DNA binding. Further, while Glu68 is critical to
      metal ion binding, Asp58 does not appear to be critical to the binding of at least one metal
      ion and appears to also have a role in structure. These findings provide impetus for exploring
      the roles of multiple metal ions in the structure and function of this representative
      endonuclease.
AU  - Jose TJ
AU  - Conlan LH
AU  - Dupureur CM
PT  - Journal Article
TA  - J. Biol. Inorg. Chem.
JT  - J. Biol. Inorg. Chem.
SO  - J. Biol. Inorg. Chem. 1999 4: 814-823.

PMID- 20709895
VI  - 192
DP  - 2010
TI  - Comparative genome biology of a serogroup B carriage and disease strain supports a polygenic nature of meningococcal virulence.
PG  - 5363-5377
AB  - Neisseria meningitidis serogroup B strains are responsible for most
      meningococcal cases in the industrialized countries, and strains belonging
      to the clonal complex ST-41/44 are among the most prevalent serogroup B
      strains in carriage and disease. Here, we report the first genome and
      transcriptome comparison of a serogroup B carriage strain from the clonal
      complex ST-41/44 to the serogroup B disease strain MC58 from the clonal
      complex ST-32. Both genomes are highly colinear, with only three major
      genome rearrangements that are associated with the integration of mobile
      genetic elements. They further differ in about 10% of their gene content,
      with the highest variability in gene presence as well as gene sequence
      found for proteins involved in host cell interactions, including Opc,
      NadA, TonB-dependent receptors, RTX toxin, and two-partner secretion
      system proteins. Whereas housekeeping genes coding for metabolic functions
      were highly conserved, there were considerable differences in their
      expression pattern upon adhesion to human nasopharyngeal cells between
      both strains, including differences in energy metabolism and stress
      response. In line with these genomic and transcriptomic differences, both
      strains also showed marked differences in their in vitro infectivity and
      in serum resistance. Taken together, these data support the concept of a
      polygenic nature of meningococcal virulence comprising differences in the
      repertoire of adhesins as well as in the regulation of metabolic genes and
      suggest a prominent role for immune selection and genetic drift in shaping
      the meningococcal genome.
AU  - Joseph B
AU  - Schneiker-Bekel S
AU  - Schramm-Gluck A
AU  - Blom J
AU  - Claus H
AU  - Linke B
AU  - Schwarz RF
AU  - Becker A
AU  - Goesmann A
AU  - Frosch M
AU  - Schoen C
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 5363-5377.

PMID- 25414494
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Halophilic and Highly Halotolerant Gammaproteobacteria Strain MFB021.
PG  - e01156-14
AB  - We report the 4.25-Mbp first draft sequence of Gammaproteobacteria strain MFB021, a moderate
      halophile isolated from petroleum-contaminated soil in Cochin, India.
      The genome of the strain MFB021 was sequenced to understand the mechanism of
      hydrocarbon degradation and the halophilicity of the bacterium.
AU  - Joseph TC
AU  - Baby A
AU  - Reghunathan D
AU  - Varghese AM
AU  - Murugadas V
AU  - Lalitha KV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01156-14.

PMID- 25414507
VI  - 2
DP  - 2014
TI  - First Draft Genome Sequence of a Member of the Genus Mangrovibacter, Isolated from an Aquaculture Farm in India.
PG  - e01209-14
AB  - Mangrovibacter sp. MFB070, a Gram-negative, facultatively anaerobic, nitrogen-fixing
      bacterium, was isolated from an aquaculture farm in Cochin,
      India. Here, we report the first draft genome sequence of a member of the genus
      Mangrovibacter, which may help us to elucidate the evolutionary status of this
      genus. The draft genome sequence of the Mangrovibacter sp. consists of 5,361,682
      bp, encoding 4,971 predicted coding sequences in 57 contigs.
AU  - Joseph TC
AU  - Varghese AM
AU  - Baby A
AU  - Reghunathan D
AU  - Murugadas V
AU  - Lalitha KV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01209-14.

PMID- 9631541
VI  - 163
DP  - 1998
TI  - Determination of the recognition sequence of the type II restriction endonuclease, LlaCI, from Lactococcus lactis W15.
PG  - 25-29
AB  - A new type II restriction endonuclease, called LlaCI, was partially purified from Lactococcus
      lactis subsp. Cremoris W15.  The characterization of the LlaCI endonuclease showed it to be an
      isoschizomer of HindIII, recognizing the sequence 5'-A/AGCTT-3'.  The cleavage site is
      indicated by the arrow.
AU  - Josephsen J
AU  - Jorgen-Jensen B
AU  - Nyengaard NR
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1998 163: 25-29.

PMID- 2112260
VI  - 23
DP  - 1990
TI  - Stacking of three different restriction and modification systems in Lactococcus lactis by cotransformation.
PG  - 71-75
AB  - Four plasmids encoding restriction and modification (R/M) systems are described
      that are different in the specificity of their restrictive activity toward the
      small isometric phage p2 and prolate phage c2.  The R/M plasmids were
      cotransformed into Lactococcus lactis MG1363 with pVS2, encoding resistance to
      chloramphenicol and erythromycin, to indicate successful transformation events.
      Analysis of cotransformants showed that three different R/M plasmids could be
      combined in L. lactis MG1363.  The efficiency at which phage plaqued on the
      transformants decreased as the number of R/M plasmids increased.  Some plasmid
      combinations were unstable suggesting replicon incompatibility.
AU  - Josephsen J
AU  - Klaenhammer T
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 1990 23: 71-75.

PMID- Not included in PubMed...
VI  - 59
DP  - 1989
TI  - Identification of three different plasmid-encoded restriction modification systems in Streptococcus-lactis subsp cremoris W56.
PG  - 161-166
AB  - Streptococcus lactis subsp. cremoris W56 (S. cremoris W56) is a strain partially resistant to
      phage attack. Derivatives which had lost either plasmid pJW563 or pJW566 no longer expressed
      the restriction and modification systems encoded by these plasmids. Genetic evidence for the
      correlation between the plasmids and the R/M systems was obtained by transformation. In
      addition, a third R/M system was discovered among the transformants and was shown to be
      encoded by pJW565. Thus, genetic evidence for at least 3 distinct R/M systems encoded by
      plasmids in S. cremoris W56 is presented. One of the R/M-systems showed stronger restriction
      of the isometric phage p2 than of the prolate phage c2. The other two systems restricted both
      classes of phages with equal efficiencies.
AU  - Josephsen J
AU  - Vogensen FK
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1989 59: 161-166.

PMID- 9687070
VI  - 37
DP  - 1998
TI  - Conserved sequence motifs in plant S-adenosyl-L-methionine-dependent methyltransferases.
PG  - 663-674
AB  - Plant S-adenosyl-L-methionine-dependent methyltransferases are the key enzymes in
      phenylpropanoid, flavonoid and many other metabolic pathways of biotechnological importance.
      Here we compiled the amino acid sequences of 56 SAM-Mtases from different plants and performed
      a computer analysis for the conserved sequence motifs that could possibly act as SAM-binding
      domains.  To date, genes or cDNAs encoding at least ten distinct groups of SAM-Mtases that
      utilize SAM and a variety of substrates have been reported from higher plants.  Three amino
      acid sequence motifs are conserved in most of these SAM-Mtases.  In addition, many conserved
      domains have been discovered in each group of O-methyltransferases that methylate specific
      substrates and may act as sites for substrate specificity in each enzyme.  Finally, a
      diagrammatic representation of the relationship between different OMTs is presented.  These
      SAM-Mtase sequence signatures will be useful in the identification of SAM-Mtase motifs in the
      hitherto unidentified proteins as well as for designing primers in the isolation of new
      SAM-Mtases from plants.
AU  - Joshi CP
AU  - Chiang VL
PT  - Journal Article
TA  - Plant Mol. Biol.
JT  - Plant Mol. Biol.
SO  - Plant Mol. Biol. 1998 37: 663-674.

PMID- 16675462
VI  - 281
DP  - 2006
TI  - Alteration of sequence specificity of the type II restriction endonuclease HincII through an indirect readout mechanism.
PG  - 23852-23869
AB  - The functional and structural consequences of a mutation of the DNA intercalating residue of
      HincII, Q138F, are presented. Modeling has
      suggested that the DNA intercalation by Gln-138 results in DNA
      distortions potentially used by HincII in indirect readout of its
      cognate DNA, GTYRAC ( Y = C or T, R = A or G) ( Horton, N. C., Dorner,
      L. F., and Perona, J. J. ( 2002) Nat. Struct. Biol. 9, 42 - 47).
      Kinetic data presented here indicate that the mutation of glutamine 138
      to phenylalanine ( Q138F) results in a change in sequence specificity
      at the center two base pairs of the cognate recognition site. We show
      that the preference of HincII for cutting, but not binding, the three
      cognate sites differing in the center two base pairs has been altered
      by the mutation Q138F. Five new crystal structures are presented
      including Q138F HincII bound to GTTAAC and GTCGAC both with and without
      Ca2+ as well as the structure of wild type HincII bound to GTTAAC. The
      Q138F HincII/DNA structures show conformational changes in the protein,
      bound DNA, and at the protein-DNA interface, consistent with the
      formation of adaptive complexes. Analysis of these structures and the
      effect of Ca2+ binding on the protein-DNA interface illuminates the
      origin of the altered specificity by the mutation Q138F in the HincII
      enzyme.
AU  - Joshi HK
AU  - Etzkorn C
AU  - Chatwell L
AU  - Bitinaite J
AU  - Horton NC
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2006 281: 23852-23869.

PMID- 23833141
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Arthrobacter crystallopoietes Strain BAB-32, Revealing Genes for Bioremediation.
PG  - e00452-13
AB  - Arthrobacter crystallopoietes strain BAB-32, a Gram-positive obligate aerobic actinobacterium
      having potential application in bioremediation and bioreduction
      of a few metals, was isolated from rhizosphere soil of Gandhinagar, Gujarat,
      India. The draft genome (4.3 Mb) of the strain revealed a few vital gene clusters
      involved in the metabolism of aromatic compounds, zinc, and sulfur.
AU  - Joshi MN
AU  - Pandit AS
AU  - Sharma A
AU  - Pandya RV
AU  - Desai SM
AU  - Saxena AK
AU  - Bagatharia SB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00452-13.

PMID- 23469348
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Halophilic Bacterium Halobacillus sp. Strain BAB-2008.
PG  - e00222-12
AB  - The sp. strain BAB-2008 is a moderately halophilic, rod-shaped, Gram-positive,
      orange-pigmented, carotenoid-producing bacterium isolated from saline soil near
      Zazam-Solar Park Road, Gujarat, India. Here we present the 3.7-Mb genome sequence
      to provide insights into its functional genomics and potential applications for
      carotenoid and enzyme production.
AU  - Joshi MN
AU  - Pandit AS
AU  - Sharma A
AU  - Pandya RV
AU  - Saxena AK
AU  - Bagatharia SB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00222-12.

PMID- 23472223
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Brevibacillus sp. Strain BAB-2500, a Strain That Might Play an Important Role in Agriculture.
PG  - e00021-13
AB  - A Gram-positive bacterium, sp. strain BAB-2500, was isolated as a lab contaminant in
      Gandhinagar, Gujarat, India. The draft genome (5.3 Mb) of the strain possesses
      genes for the reduction of arsenate and aluminum. These findings might provide
      insights into the utilization of this strain for improving crop production.
AU  - Joshi MN
AU  - Sharma A
AU  - Pandit AS
AU  - Pandya RV
AU  - Saxena AK
AU  - Bagatharia SB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00021-13.

PMID- 23105068
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Pontibacter sp. nov. BAB1700, a Halotolerant, Industrially Important Bacterium.
PG  - 6329-6330
AB  - Pontibacter sp. nov. BAB1700 is a halotolerant, Gram-negative, rod-shaped, pink-pigmented,
      menaquinone-7-producing bacterium isolated from sediments of a
      drilling well. The draft genome sequence of the strain, consisting of one
      chromosome of 4.5 Mb, revealed vital gene clusters involved in vitamin
      biosynthesis and resistance against various metals and antibiotics.
AU  - Joshi MN
AU  - Sharma AC
AU  - Pandya RV
AU  - Patel RP
AU  - Saiyed ZM
AU  - Saxena AK
AU  - Bagatharia SB
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6329-6330.

PMID- 21029741
VI  - 405
DP  - 2011
TI  - Evolution of I-SceI Homing Endonucleases with Increased DNA Recognition Site Specificity.
PG  - 185-200
AB  - Elucidating how homing endonucleases undergo changes in recognition site specificity will
      facilitate efforts to engineer proteins for gene therapy
      applications. I-SceI is a monomeric homing endonuclease that recognizes
      and cleaves within an 18-bp target. It tolerates limited degeneracy in its
      target sequence, including substitution of a C:G(+4) base pair for the
      wild-type A:T(+4) base pair. Libraries encoding randomized amino acids at
      I-SceI residue positions that contact or are proximal to A:T(+4) were used
      in conjunction with a bacterial one-hybrid system to select I-SceI
      derivatives that bind to recognition sites containing either the A:T(+4)
      or the C:G(+4) base pairs. As expected, isolates encoding wild-type
      residues at the randomized positions were selected using either target
      sequence. All I-SceI proteins isolated using the C:G(+4) recognition site
      included small side-chain substitutions at G100 and either contained
      (K86R/G100T, K86R/G100S and K86R/G100C) or lacked (G100A, G100T) a K86R
      substitution. Interestingly, the binding affinities of the selected
      variants for the wild-type A:T(+4) target are 4- to 11-fold lower than
      that of wild-type I-SceI, whereas those for the C:G(+4) target are
      similar. The increased specificity of the mutant proteins is also evident
      in binding experiments in vivo. These differences in binding affinities
      account for the observed  approximately 36-fold difference in target
      preference between the K86R/G100T and wild-type proteins in DNA cleavage
      assays. An X-ray crystal structure of the K86R/G100T mutant protein bound
      to a DNA duplex containing the C:G(+4) substitution suggests how sequence
      specificity of a homing enzyme can increase. This biochemical and
      structural analysis defines one pathway by which site specificity is
      augmented for a homing endonuclease.
AU  - Joshi R
AU  - Ho KK
AU  - Tenney K
AU  - Chen JH
AU  - Golden BL
AU  - Gimble FS
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2011 405: 185-200.

PMID- 14576111
VI  - 47
DP  - 2003
TI  - Tylosin Resistance in Arcanobacterium pyogenes Is Encoded by an Erm X Determinant.
PG  - 3519-3524
AB  - Arcanobacterium pyogenes, a commensal on the mucous membranes of many economically important
      animal species, is also a pathogen, causing
      abscesses of the skin, joints, and visceral organs as well as mastitis and
      abortion. In food animals, A. pyogenes is exposed to antimicrobial agents
      used for growth promotion, prophylaxis, and therapy, notably tylosin, a
      macrolide antibiotic used extensively for the prevention of liver
      abscessation in feedlot cattle in the United States. Of 48 A. pyogenes
      isolates, 11 (22.9%) exhibited inducible or constitutive resistance to
      tylosin (MIC of > or = 128 microg/ml). These isolates also exhibited
      resistance to other macrolide and lincosamide antibiotics, suggesting a
      macrolide-lincosamide resistance phenotype. Of the 11 resistant isolates,
      genomic DNA from nine hybridized to an erm(X)-specific probe. Cloning and
      nucleotide sequencing of the A. pyogenes erm(X) gene indicated that it was
      >95% similar to erm(X) genes from Corynebacterium and Propionibacterium
      spp. Eight of the erm(X)-containing A. pyogenes isolates exhibited
      inducible tylosin resistance, which was consistent with the presence of a
      putative leader peptide upstream of the erm(X) open reading frame. For at
      least one A. pyogenes isolate, 98-4277-2, erm(X) was present on a plasmid,
      pAP2, and was associated with the insertion sequence IS6100. pAP2 also
      carried genes encoding the repressor-regulated tetracycline efflux system
      determinant Tet 33. The repA gene from pAP2 was nonfunctional in
      Escherichia coli and at least one A. pyogenes isolate, suggesting that
      there may be host-encoded factors required for replication of this
      plasmid.
AU  - Jost BH
AU  - Field AC
AU  - Trinh HT
AU  - Songer JG
AU  - Billington SJ
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2003 47: 3519-3524.

PMID- 
VI  - 0
DP  - 1996
TI  - Mechanism of DNA demethylation in vertebrates and its biological significance.
PG  - 109-125
AB  - The aim of this chapter is to present some general features of site-specific and genome-wide
      demethylation.  Demethylation of DNA is part of the process responsible for the formation of
      specific methylation patterns.  The establishment of a CpG methylation pattern during
      embryonic development involves at least three components: DNA methyltransferase, a
      demethylation system (passive or active), and sequence-specific cis-trans controlling elements
      located on or near the CpG methylation sites.  The cis-trans controlling elements either
      enhance or inhibit the methylation of specific sequences.  Whether a given CpG site is
      methylated or not depends on the mole ratio of activities of the different factors involved
      and of their respective affinities for a specified CpG site on the DNA.  This concept of
      titratable factors is also valid for the cis-acting control elements.  For example, the
      introduction of DNA-binding sites for specific proteins into the cell could possibly titrate
      out protein factors and engender hypermethylation of the DNA.
AU  - Jost J-P
PT  - Journal Article
TA  - Epigenetic Mechanisms of Gene Regulation
JT  - Epigenetic Mechanisms of Gene Regulation
SO  - Epigenetic Mechanisms of Gene Regulation 1996 0: 109-125.

PMID- 8506318
VI  - 90
DP  - 1993
TI  - Nuclear extracts of chicken embryos promote an active demethylation of DNA by excision repair of 5-methyldeoxycytidine.
PG  - 4684-4688
AB  - Here I show that nuclear extracts of chicken embryos can promote the active demethylation of
      DNA.  The evidence shows that in hemimethylated DNA (i.e., methylated on one strand only)
      demethylation of 5mCpG occurs throughout nucleotide excision repair.  The first step of
      demethylation is the formation of specific nicks 5' from 5-methyldeoxycytidine.  Nicks are
      also observed in vitro on symmetrically methylated CpGs (i.e., methylated on both strands) but
      they result in breakage of the oligonucleotide with no repair.  No specific nicks are observed
      on the nonmethylated CpG. Nicks are strictly 5mCpG specific and do not occur on 5mCpC, 5mCpT,
      5mCpA, or 6mApT.  The effect of nonspecific nuclease(s) has been ruled out.  The nicking of
      mCpG takes place in the presence of 20 mM EDTA irrespective of the nature of the sequence
      surrounding the 5mCpG.  No methylcytosine glycosylase activity could be detected.  The repair
      is aphidicolin and N-ethylmaleimide resistant, suggesting a repair action by DNA polymerase
      beta.  In extracts of chicken embryos, the excision repair of mCpG is highest between the 6th
      and the 12th day of development, whereas it is barely detectable in nuclear extracts from
      different organs of adults.  The possible implications of 5mCpG endonuclease activity in
      active demethylation of DNA during differentiation is discussed.
AU  - Jost J-P
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1993 90: 4684-4688.

PMID- 9358164
VI  - 25
DP  - 1997
TI  - The RNA moiety of chick embryo 5-methylcytosine-DNA glycosylase targets DNA demethylation.
PG  - 4545-4550
AB  - We have previously shown that DNA demethylation by chick embryo 5-methylcytosine (5-MeC)-DNA
      glycosylase needs both protein and RNA.  RNA from enzyme purified by SDS-PAGE was isolated and
      cloned.  The clones have an insert ranging from 240 to 670 bp and contained on average one CpG
      per 14 bases.  All six clones tested had different sequences and did not have any sequence
      homology with any other known RNA.  RNase-inactivated 5-MeC-DNA glycosylase regained enzyme
      activity when incubated with recombinant RNA.  However, when recombinant RNA was incubated
      with the DNA substrate alone there was no demethylation activity.  Short sequences
      complementary to the labeled DNA substrate are present in the recombinant RNA.  Small
      synthetic oligoribonucleotides (11 bases long) complementary to the region of methylated CpGs
      of the hemimethylated double-stranded DNA substrate restore the activity of the
      RNase-inactivated 5-MeC-DNA glycosylase.  The corresponding oligodeoxyribonucleotide or the
      oligoribonucleotide complementary to the non-methylated strand of the same DNA substrate are
      inactive when incubated in the complementation test.  A minimum of 4 bases complementary of
      the CpG target sequence are necessary for reactivation of RNase-treated 5-MeC-DNA glycosylase.
      Complementation with double-stranded oligoribonucleotides does not restore 5-MeC-DNA
      glycosylase activity.  An excess of targeting oligoribonucleotides cannot change the
      preferential substrate specificity of the enzyme for hemimethylated double-stranded DNA.
AU  - Jost J-P
AU  - Fremont M
AU  - Siegmann M
AU  - Hofsteenge J
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1997 25: 4545-4550.

PMID- 8144502
VI  - 269
DP  - 1994
TI  - Transient DNA demethylation in differentiating mouse myoblasts correlates with higher activity of 5-methyldeoxycytidine excision repair.
PG  - 10040-10043
AB  - It has been recently shown that in developing chicken embryonic nuclear extracts there is a
      5-methyldeoxycytidine excision repair activity.  We show that in differentiating mouse
      myoblasts, a similar enzymatic reaction may be responsible for the genome-wide DNA
      demethylation (up to 50% of all CmCGG) occurring between the 3rd and 5th days of
      differentiation.  Furthermore, in differentiating myoblasts, there is first a 50% transient
      decrease in DNA methyltransferase activity and a 90% drop in the rate of DNA synthesis,
      followed by an increase in 5-methyl-CpG endonuclease and 5-methyldeoxycytidine excision repair
      activities.  As tested in vitro, the maximal activity of the 5-methyldeoxycytidine excision
      repair coincides with the maximal in vivo genome-wide DNA demethylation.  We also find that
      3-aminobenzamide, a potent inhibitor of ADP-ribosyltransferase, blocks the differentiation of
      myoblasts, the 5-methyldeoxycytidine excision repair activity, and the genome-wide
      demethylation.
AU  - Jost J-P
AU  - Jost Y-C
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1994 269: 10040-10043.

PMID- 7730351
VI  - 270
DP  - 1995
TI  - Mechanism of DNA demethylation in chicken embryos.
PG  - 9734-9739
AB  - We have previously shown that in developing chicken embryos and differentiating mouse
      myoblasts, the demethylation of 5-metCpGs occurs through the replacement of 5-methylcytosine
      by cytosine.  We have now purified over 30,000-fold a 5-methylcytosine-DNA glycosylase from
      12-day-old chicken embryos.  The enzyme copurifies with a mismatch-specific thymine-DNA
      glycosylase and an apyrimidic-endonuclease.  The reaction product of the highly purified
      5-methylcytosine-DNA glycosylase is 5-methylcytosine.  The copurified apyrimidic-endonuclease
      activity cleaves 3' from the apyrimidic sugar.  A 52.5-kDa peptide, isolated as a single band
      from preparative SDS-polyacrylamide gels, has both the 5-methylcytosine-DNA glycosylase and
      the mismatch-specific thymine-DNA glycosylase activities.  5-Methylcytosine-DNA glycosylase
      has an apparent pI of 5.5-7.5 and maximal activity between pH 6.5 and 7.5.  The Km for
      hemimethylated oligonucleotide substrate is 8 x 10^-8 M with a Vmax of 4 x 10^-11 mol/h/ug
      protein.  5-Methylcytosine-DNA glycosylase binds equally well to methylated and non-methylated
      DNA.  The enzyme reacts six times faster with the hemimethylated DNA than with the same
      bifilarly methylated DNA sequence, and single-stranded methylated DNA is not a substrate.  The
      action of the enzyme is distributive.
AU  - Jost J-P
AU  - Siegmann M
AU  - Sun L
AU  - Leung R
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1995 270: 9734-9739.

PMID- 10338142
VI  - 449
DP  - 1999
TI  - A re-investigation of the ribonuclease sensitivity of a DNA demethylation reaction in chicken embryo and G8 mouse myoblasts.
PG  - 251-254
AB  - Recently published results suggest that the ribonuclease sensitivity of the DNA demethylation
      reaction may be an experimental artifact due to the possible tight binding of the nucleases to
      the methylated DNA substrate. Using an improved protocol we show for two different systems
      that demethylation of hemi-methylated DNA is indeed sensitive to micrococcal nuclease,
      requires RNA and is not an experimental artifact.  The purified 5-MeC-DNA glycosylase from
      chicken embryos and G8 mouse myoblasts was first incubated for 5 min at 37 C with micrococcal
      nuclease in the presence of Ca2+  in the absence of the DNA substrate.  Upon blocking the
      nuclease activity by the addition of 25 mM EGTA, the DNA demethylation reaction was initiated
      by adding the labeled hemimethylated DNA substrate to the reaction mixture.  Under these
      conditions the DNA demethylation reaction was abolished.  In parallel controls, where the
      purified 5-MeC-DNA glycosylase was pre-incubated at 37 C with the nuclease, Ca2+ and EGTA or
      with the nuclease and EGTA, RNA was not degraded and no inhibition of the demethylation
      reaction was obtained.  As had already been shown for chicken embryos, the loss of 5-MeC-DNA
      glycosylase activity from G8 myoblasts following nuclease treatment can also be restored by
      the addition of synthetic RNA complementary to the methylated strand of the substrate DNA.  No
      reactivation of 5-MeC-DNA glycosylase is obtained by complementation with a random RNA
      sequence, the RNA sequence complementary to the non-methylated strand or DNA, thus ruling out
      a non-specific competition of the RNA for the binding of the nuclease to the labeled DNA
      substrate.
AU  - Jost J-P
AU  - Siegmann M
AU  - Thiry S
AU  - Jost Y-C
AU  - Benjamin D
AU  - Schwarz S
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1999 449: 251-254.

PMID- 25323725
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Raoultella planticola, Isolated from River Water.
PG  - e01061-14
AB  - We isolated Raoultella planticola from a river water sample, which was phenotypically
      indistinguishable from Escherichia coli on MI agar. The genome
      sequence of R. planticola was determined to gain information about its metabolic
      functions contributing to its false positive appearance of E. coli on MI agar. We
      report the first whole genome sequence of Raoultella planticola.
AU  - Jothikumar N
AU  - Kahler A
AU  - Strockbine N
AU  - Gladney L
AU  - Hill VR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01061-14.

PMID- 25323724
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Buttiauxella agrestis, Isolated from Surface Water.
PG  - e01060-14
AB  - MI agar is routinely used for quantifying Escherichia coli in drinking water. A suspect E.
      coli colony isolated from a water sample was identified as
      Buttiauxella agrestis. The whole genome sequence of B. agrestis was determined to
      understand the genetic basis for its phenotypic resemblance to E. coli on MI
      agar.
AU  - Jothikumar N
AU  - Kahler A
AU  - Strockbine N
AU  - Gladney L
AU  - Hill VR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01060-14.

PMID- Not carried by PubMed...
VI  - 29
DP  - 1988
TI  - Purification and characterization of restriction endonuclease CstI from Clostridium sticklandii.
PG  - 201-208
AB  - A type II restriction endonuclease CstI was purified to homogeneity from
      Clostridium sticklandii by phosphocellulose chromatography and preparative gel
      electrophoresis.  It was found that CstI was an isoschizomer of PstI which is
      widely used in molecular cloning.  Both CstI and PstI recognize and cleave the
      nucleotide sequence 5'-CTGCAG-3' of double stranded DNA.  Nucleotide sequence
      analysis revealed that both enzymes split the phosphodiester bond between A and
      G.  The molecular weight of CstI determined by disc gel electrophoresis was
      apparently 206,000.  The optimal pH, temperature, sodium chloride and magnesium
      ion concentrations of CstI were shown to be 7-9, 37-40C, 50-200 mM and 5 mM,
      respectively.  CstI is heat-labile.  When incubated at temperature higher than
      40C for 5 minutes, the enzyme lost its activity rapidly.
AU  - Jou T-W
AU  - Chen C-S
PT  - Journal Article
TA  - Bot. Bull. Acad. Sinica
JT  - Bot. Bull. Acad. Sinica
SO  - Bot. Bull. Acad. Sinica 1988 29: 201-208.

PMID- 23516200
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Mycobacterium bovis BCG Korea, the Korean Vaccine Strain for Substantial Production.
PG  - e0006913
AB  - Mycobacterium bovis bacillus Calmette-Guerin (BCG) is the only vaccine available  against
      tuberculosis, and the strains used worldwide represent a family of
      daughter strains with distinct genotypic characteristics. Here, we report the
      complete genome sequence of M. bovis BCG Korea, the strain that will be actually
      used in Korea for vaccine production.
AU  - Joung SM
AU  - Jeon SJ
AU  - Lim YJ
AU  - Lim JS
AU  - Choi BS
AU  - Choi IY
AU  - Yu JH
AU  - Na KI
AU  - Cho EH
AU  - Shin SS
AU  - Park YK
AU  - Kim CK
AU  - Kim HJ
AU  - Ryoo SW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0006913.

PMID- 26337883
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of an Alphaproteobacterium Associated with the Mediterranean Sponge Oscarella lobularis.
PG  - e00977-15
AB  - While sequencing DNA purified from the homoscleromorph sponge Oscarella lobularis, we detected
      a large number of reads with strong similarity to available alphaproteobacteria gene sequences
      of family Rhodobacteraceae. Here, we present the genome sequence of this putative sponge
      symbiont that we propose to designate as 'Candidatus Rhodobacter lobularis.'
AU  - Jourda C
AU  - Santini S
AU  - Rocher C
AU  - Le Bivic A
AU  - Claverie JM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00977-15.

PMID- 24762936
VI  - 2
DP  - 2014
TI  - Full-Genome Sequence of the Plant Growth-Promoting Bacterium Pseudomonas protegens CHA0.
PG  - e00322-14
AB  - We report the complete genome sequence of the free-living bacterium Pseudomonas protegens
      (formerly Pseudomonas fluorescens) CHA0, a model organism used in plant-microbe interactions,
      biological control of phytopathogens, and bacterial genetics.
AU  - Jousset A
AU  - Schuldes J
AU  - Keel C
AU  - Maurhofer M
AU  - Daniel R
AU  - Scheu S
AU  - Thuermer A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00322-14.

PMID- 12701689
VI  - 35
DP  - 2003
TI  - Optimising restriction enzyme cleavage of DNA derived from archival histopathological samples: an improved HUMARA assay.
PG  - 70-74
AB  - Aims: Our aim was to evaluate and optimise methylation-sensitive restriction enzyme assays for
      use in formalin-fixed, paraffin-embedded tissue (FFPET) samples, in order to improve the
      application of the HUMARA X-chromosome inactivation assay to FFPET samples.Methods: We
      extracted DNA from normal male colon and thyroid FFPET. Several DNA clean-up procedures and
      restriction enzyme buffer compositions were tested for two methylation-sensitive enzymes, HhaI
      and HpaII and a non-methylation-sensitive isoschizomere, MspI.Results: By including both a
      non-methylation-sensitive control enzyme and DNA from male archival specimens in our
      experiments, we were able to detect even subtle degrees of incomplete digestion. We showed
      that FFPET-derived DNA is a poor substrate for restriction enzymes, especially for
      methylation-sensitive restriction endonucleases. An optimised DNA clean-up protocol and
      restriction enzyme buffer-mix allowed us to achieve complete digestion.Conclusions: The
      combination of multiple, rigorous controls, DNA clean-up and restriction buffer optimisation
      increases the reliability of HUMARA-based X-chromosome inactivation analysis of FFPET samples.
      Analogous approaches are likely to allow optimisation of other restriction enzyme-based assays
      of FFPET samples.
AU  - Jovanovic L
AU  - Delahunt B
AU  - McIver B
AU  - Eberhardt NL
AU  - Grebe SKG
PT  - Journal Article
TA  - Pathology
JT  - Pathology
SO  - Pathology 2003 35: 70-74.

PMID- 26303235
VI  - 65
DP  - 2015
TI  - Luteipulveratus halotolerans sp. nov., a novel actinobacterium (Dermacoccaceae) from Sarawak, Malaysia.
PG  - 4113-4120
AB  - The taxonomic position of an actinobacterium strain, C296001T, isolated from a soil sample
      collected in Sarawak, Malaysia, was established using a polyphasic approach. Phylogenetically,
      strain C296001T is closely associated with the genus Luteipulveratus that forms a distinct
      monophyletic clade with the only described species, L. mongoliensis NBRC 105296T. The 16S rRNA
      gene sequence similarity between strain C296001T and L. mongoliensis is 98.7%. DNA-DNA
      hybridization results showed that the relatedness of strain C296001T to L. mongoliensis was
      only 21.5%. The G+C content of strain C296001T DNA is 71.7 mol%. Using a PacBio RS II system
      whole genome sequences for strains C296001T and NBRC 105296T were obtained. The determined
      genome sizes of 4.5 Mbps and 5.4 Mbps are similar to those of other Dermacoccaceae. The
      cell-wall peptidoglycan containing lysine, alanine, aspartic acid, glutamic acid and serine
      represents the peptidoglycan type A4alpha L-Lys-L-Ser-D-Asp. The major menaquinones are
      MK-8(H4), MK-8, and MK-8(H2). Phosphatidylglycerol, phosphatidylinositol,
      diphosphatidylglycerol and phosphoglycolipid are the polar lipids, while the whole-cell sugars
      are glucose, fucose and lower amount of ribose and galactose. The major fatty acids are
      iso-C16:0, anteiso-C17:0, iso-C16:1 H, anteiso-C17:1 omega9c, iso-C18:0, and C17:0 10-methyl.
      Chemotaxonomic analyses showed that C296001T had typical characteristics of members of the
      genus Luteipulveratus, with the main differences occurring in phenotypic characteristics.
      Based on the phenotypic and chemotaxonomic evidence, it is proposed that strain C296001T be
      classified as a novel species in the genus Luteipulveratus, for which the name Luteipulveratus
      halotolerans sp. nov. is recommended. The type strain is C296001T (=ATCC TSD-4T =JCM 30660T).
AU  - Juboi H
AU  - Basik AA
AU  - Shamsul SS
AU  - Arnold P
AU  - Schmitt EK
AU  - Sanglier JJ
AU  - Yeo TC
PT  - Journal Article
TA  - Int. J. Syst. Evol. Microbiol.
JT  - Int. J. Syst. Evol. Microbiol.
SO  - Int. J. Syst. Evol. Microbiol. 2015 65: 4113-4120.

PMID- 
VI  - 105
DP  - 2005
TI  - Mutation of a Campylobacter jejuni DNA methylase affects expression of multiple genes, motility, and epithelial cell adherence and invasion.
PG  - 79
AB  - Campylobacter jejuni causes over 2 million cases of severe bacterial gastroenteritis in the
      U.S. every year. Poultry flocks are ubiquitously and asymptomatically colonized with C.
      jejuni, and the most likely cause of human infection is via the consumption of contaminated
      poultry meat products as well as other foods cross contaminated during preparation, and
      contaminated water. C. jejuni is able to thrive at two different temperatures, 42oC (the core
      temperature of chickens) and 37oC (the core temperature of humans), thus there is likely to be
      temperature regulation of Campylobacter proteins for optimization of expression in each
      environment, including virulence factors important for human infection. We identified an
      ortholog of NCTC11168 cj1461 in C. jejuni strain 81-176 as a gene that was more highly
      expressed at 37oC than at 42oC. cj1461 encodes a predicted DNA methylase that is not
      associated with a cognate restriction endonuclease. We purified Cj1461 as a recombinant
      His-tagged protein and showed that Cj1461 can bind DNA and has DNA methyltransferase activity.
      We hypothesize that Cj1461 does not protect C. jejuni DNA from restriction endonucleases and
      may be involved in the regulation of genes important for the virulence of the bacterium. We
      inactivated the cj1461 ortholog in C. jejuni 81-176 to investigate its potential role in gene
      regulation. Proteome and DNA array results comparing 81-176 with its isogenic 81-176cj1461
      mutant indicated the deregulation of numerous genes, including many involved in
      virulence-associated pathways such as motility, flagellar glycosylation, chemotaxis, oxidative
      stress, iron uptake, and transformation competence. The 81-176cj1461 mutant was significantly
      less motile than C. jejuni 81-176, and was 30 times more adherent, but 800 times less invasive
      than wild-type in an in vitro INT407 tissue culture model. These results suggest that the
      regulation of multiple genes in C. jejuni 81-176, including some important for virulence, can
      be mediated in part by the DNA methyltransferase Cj1461.
AU  - Judge NA
AU  - Fields JA
AU  - Pajaniappan M
AU  - Newell DG
AU  - Manning J
AU  - Burns CM
AU  - Thompson SA
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 2005 105: 79.

PMID- Not included in PubMed...
VI  - 50
DP  - 1994
TI  - Differential expression of DNA methyltransferase in male germ cells.
PG  - 80
AB  - DNA methylation is involved in regulating gene expression and plays a critical role in normal
      development. Patterns of methylation are believed to be established during gametogenesis and
      early embryogenesis. To better understand how methylation patterns are established in the male
      mouse germ line we focused on the expression of the DNA methyltransferase (DNA MTase) which
      catalyzes the transfer of methyl groups from S-adenosyl-methionine to the 5' position of
      cytosine in DNA. Purified populations of premeiotic, meiotic and postmeiotic germ cells were
      isolated from adult and 17 day old mouse testis using cellular sedimentation at unit gravity
      on a Staput apparatus. Western analysis revealed abundant DNA MTase protein in postmitotic
      leptotene/zygotene spermatocyte and haploid round spermatid fractions but low levels in
      pachytene spermatocyte fractions. A 6.2kb DNA MTase transcript is specific to pachytene
      spermatocytes whereas in other cell types, a 5.2kb mRNA is present. These findings are
      supported by immunofluorescence studies where germ cells were stained for DNA MTase.
      Immunofluorescence further revealed DNA MTase staining patterns to vary within one isolated
      germ cell population suggesting differential expression and localization between the
      developmental steps in various cell types. We conclude that DNA MTase expression is regulated
      during spermatogenesis at a time when de novo methylation is known to occur. These studies
      contribute to our understanding of how methylation patterns are established in the male germ
      line and their importance during early development.
AU  - Jue K
AU  - Bestor T
AU  - Trasler JM
PT  - Journal Article
TA  - Biol. Reprod.
JT  - Biol. Reprod.
SO  - Biol. Reprod. 1994 50: 80.

PMID- 1979325
VI  - 172
DP  - 1990
TI  - Evidence for salt-associated restriction pattern modifications in the Archaeobacterium Haloferax mediterranei.
PG  - 7278-7281
AB  - DNA restriction pattern modifications were detected when Haloferax mediterranei
      was grown in low (10%) salt concentrations.  After cells were grown again in
      optimal (25%) salt concentrations, the original pattern was recovered.  These
      salt-associated DNA modifications were revealed with 5% of the 160 DNA
      fragments cloned and used as probes in hybridization experiments.  Patterns
      obtained when genomic DNA was digested with different restriction enzymes
      showed that these modifications are related not to insertions or deletions in
      the genome but to modifications of some specific sequences.
AU  - Juez G
AU  - Rodriguez-Valera F
AU  - Herrero N
AU  - Mojica FJM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1990 172: 7278-7281.

PMID- 10860721
VI  - 299
DP  - 2000
TI  - Genomic sequences of bacteriophages HK97 and HK022: pervasive genetic mosaicism in the lambdoid bacteriophages.
PG  - 27-51
AB  - We report the complete genome DNA sequences of HK97 (39,732 bp) and HK022
      (40,751 bp), double-stranded DNA bacteriophages of Escherichia coli and
      members of the lambdoid or lambda-like group of phages. We provide a
      comparative analysis of these sequences with each other and with two
      previously determined lambdoid family genome sequences, those of E. coli
      phage lambda and Salmonella typhimurium phage P22. The comparisons confirm
      that these phages are genetic mosaics, with mosaic segments separated by
      sharp transitions in the sequence. The mosaicism provides clear evidence
      that horizontal exchange of genetic material is a major component of
      evolution for these viruses. The data suggest a model for evolution in
      which diversity is generated by a combination of illegitimate and
      homologous recombination and mutational drift, and selection for function
      produces a population in which most of the surviving mosaic boundaries are
      located at gene boundaries or, in some cases, at protein domain boundaries
      within genes. Comparisons of these genomes highlight a number of
      differences that allow plausible inferences of specific evolutionary
      scenarios for some parts of the genome. The comparative analysis also
      allows some inferences about function of genes or other genetic elements.
      We give examples for the generalized recombination genes of HK97, HK022
      and P22, and for a putative headtail adaptor protein of HK97 and HK022. We
      also use the comparative approach to identify a new class of genetic
      elements, the morons, which consist of a protein-coding region flanked by
      a putative delta 70 promoter and a putative factor-independent
      transcription terminator, all located between two genes that may be
      adjacent in a different phage. We argue that morons are autonomous genetic
      modules that are expressed from the repressed prophage. Sequence
      composition of the morons implies that they have entered the phages'
      genomes by horizontal transfer in relatively recent evolutionary time.
AU  - Juhala RJ
AU  - Ford ME
AU  - Duda RL
AU  - Youlton A
AU  - Hatfull GF
AU  - Hendrix RW
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2000 299: 27-51.

PMID- 11705940
VI  - 69
DP  - 2001
TI  - DNA Adenine Methylase Is Essential for Viability and Plays a Role in the Pathogenesis of Yersinia pseudotuberculosis and Vibrio cholerae.
PG  - 7610-7615
AB  - Salmonella strains that lack or overproduce DNA adenine methylase (Dam) elicit a protective
      immune response to different Salmonella species. To generate vaccines against other bacterial
      pathogens, the dam genes of Yersinia pseudotuberculosis and Vibrio cholerae were disrupted but
      found to be essential for viability. Overproduction of Dam significantly attenuated the
      virulence of these two pathogens, leading to, in Yersinia, the ectopic secretion of virulence
      proteins (Yersinia outer proteins) and a fully protective immune response in vaccinated hosts.
      Dysregulation of Dam activity may provide a means for the development of vaccines against
      varied bacterial pathogens.
AU  - Julio SM
AU  - Heithoff DM
AU  - Provenzano D
AU  - Klose KE
AU  - Sinsheimer RL
AU  - Low DA
AU  - Mahan MJ
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2001 69: 7610-7615.

PMID- 11796641
VI  - 70
DP  - 2002
TI  - DNA adenine methylase overproduction in Yersinia pseudotuberculosis alters YopE expression and secretion and host immune responses to  infection.
PG  - 1006-1009
AB  - Yersinia pseudotuberculosis mutants that overproduce the DNA adenine methylase (Dam) are
      highly attenuated, confer fully protective immune
      responses, and secrete several Yersinia virulence proteins (Yersinia
      outer proteins [Yops]) under conditions that are nonpermissive for
      secretion in wild-type strains. We examined here the effects of Dam
      overproduction on Yersinia virulence determinant expression and
      secretion, as well as the host immune response to Yersinia antigens.
      Western blot analysis with convalescent antisera identified several
      low-calcium-responsive antigens whose synthesis was affected by Dam
      overproduction. One of these antigens was shown to be the type III
      secretion effector protein, YopE, a cytotoxin involved in
      antiphagocytosis. Dam overproduction disrupted both the thermal and
      calcium regulation of YopE synthesis and relaxed the thermal but not
      the calcium dependence of YopE secretion. Altered expression and/or
      secretion of Yersinia proteins in Dam-overproducing strains may
      contribute to the decreased virulence and heightened immunity observed
      in vaccinated hosts and may provide a means by which to deliver
      heterologous antigens and/or immune modulators of the inflammatory
      response.
AU  - Julio SM
AU  - Heithoff DM
AU  - Sinsheimer RL
AU  - Low DA
AU  - Mahan MJ
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2002 70: 1006-1009.

PMID- 22940470
VI  - 22
DP  - 2012
TI  - DNA methylation dynamics during sexual reproduction in Arabidopsis thaliana.
PG  - 1825-1830
AB  - DNA methylation maintains genome stability and regulates gene expression [1]. In  mammals, DNA
      methylation is reprogrammed in the germline from one generation to
      the next [2]. In plants, it was considered that patterns of DNA methylation are
      stably maintained through sexual reproduction [3-6]. However, a recent report
      showed discrete variations of DNA methylation profiles from mother to daughter
      plants [7]. The mechanisms that explain these variations have remained unknown.
      Here, we report that maintenance DNA methyltransferases are barely expressed
      during Arabidopsis female gametogenesis. In contrast, after fertilization both
      maintenance and de novo DNA methyltransferases are expressed strongly in the
      embryo. Embryogenesis is marked by increased de novo DNA methylation, reaching
      levels that are further maintained in the adult plant. The accumulation of these
      epigenetic marks after fertilization silences a methylation-sensitive fluorescent
      reporter. De novo DNA methylation in the embryo provides a mechanism that could
      account for the gradual remethylation of experimentally demethylated genomes [8,
      9]. In conclusion, we uncover that DNA methylation activity fluctuates during
      sexual reproduction. This cycle likely explains variations of genome-wide
      patterns of DNA methylation across generations in Arabidopsis [7, 10] and enables
      a limited degree of reprogramming of the epigenome.
AU  - Jullien PE
AU  - Susaki D
AU  - Yelagandula R
AU  - Higashiyama T
AU  - Berger F
PT  - Journal Article
TA  - Curr. Biol.
JT  - Curr. Biol.
SO  - Curr. Biol. 2012 22: 1825-1830.

PMID- Not carried by PubMed...
VI  - 25
DP  - 1987
TI  - Cloning and expression of the BdiI methylase gene in E. coli.
PG  - 40-45
AB  - The gene for the BdiI modification enzyme, which is one of BdiI
      restriction-modification system, from Brevibacterium divaricatum FERM 5948 was
      cloned and expressed in E. coli.  For cloning of the BdiI methylase gene, we
      have initially used three cloning site (EcoRI, BamHI and SalI) of plasmid
      vector pBR322 and adopted the retransformation method after BdiI restriction
      endonuclease cleavage.  Selection of transformants carrying the gene was based
      on the resistance of the modified plasmid encoding the enzyme to cleavage by
      BdiI restriction enzyme, and the recombinant plasmid pBDIM116 containing 5.6 kb
      EcoRI insert was proved to carry the gene.  Crude cell extracts prepared from
      strains carrying the plasmid pBDIM116 contained an
      S-adenosylmethionine-dependent methyltransferase activity specific for the BdiI
      recognition site, ATCGAT.  The restriction map was constructed with 11
      restriction enzyme, and the BdiI restriction-modification system was also
      discussed.
AU  - Jun HS
AU  - Kim YS
AU  - Choi KR
AU  - Rho HM
PT  - Journal Article
TA  - Korean J. Microbiol.
JT  - Korean J. Microbiol.
SO  - Korean J. Microbiol. 1987 25: 40-45.

PMID- 23405312
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Vibrio parahaemolyticus SNUVpS-1 Isolated from Korean Seafood.
PG  - e00132-12
AB  - Vibrio parahaemolyticus is the leading cause of food-borne diseases, and several  pathogenic
      strains cause global gastroenteritis outbreaks. Here, we report a
      draft genome sequence of V. parahaemolyticus SNUVpS-1, which was isolated from
      seafood in a fishery market in the Republic of Korea and contained TL, toxR, and
      toxRS(old) genes. The current draft genome sequence will contribute to the effort
      to monitor the spread of V. parahaemolyticus seafood isolates and clinical
      isolates.
AU  - Jun JW
AU  - Kim JH
AU  - Choresca CH
AU  - Shin SP
AU  - Han JE
AU  - Park SC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00132-12.

PMID- 21705594
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of the Obligate Piezophilic Hyperthermophilic Archaeon Pyrococcus yayanosii CH1.
PG  - 4297-4298
AB  - Pyrococcus yayanosii CH1 is the first obligate piezophilic hyperthermophilic archaeon isolated
      from the deep-sea hydrothermal site
      Ashadze on the mid-Atlantic ridge at a depth of 4,100 m. This organism
      grows within a temperature range of 80 to 108 degrees C and a hydrostatic
      pressure range of 20 to 120 MPa, with optima at 98 degrees C and 52 MPa,
      respectively. Here, we report the complete genome sequence (1,716,817 bp,
      with a G+C content of 51.6%) of the type strain P. yayanosii CH1(T) (= JCM
      16557). This genomic information reveals a systematic view of the
      piezoadaptation strategy and evolution scenario of metabolic pathways in
      Thermococcales.
AU  - Jun X
AU  - Lupeng L
AU  - Minjuan X
AU  - Oger P
AU  - Fengping W
AU  - Jebbar M
AU  - Xiang X
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4297-4298.

PMID- 20639327
VI  - 192
DP  - 2010
TI  - Complete genome sequence of the diesel-degrading Acinetobacter sp. strain DR1.
PG  - 4794-4795
AB  - The genus Acinetobacter is ubiquitous in soil, aquatic, and sediment environments and includes
      pathogenic strains, such as A. baumannii. Many
      Acinetobacter species isolated from various environments have
      biotechnological potential since they are capable of degrading a variety
      of pollutants. Acinetobacter sp. strain DR1 has been identified as a
      diesel degrader. Here we report the complete genome sequence of
      Acinetobacter sp. DR1 isolated from the soil of a rice paddy.
AU  - Jung J
AU  - Baek JH
AU  - Park W
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 4794-4795.

PMID- 22965096
VI  - 194
DP  - 2012
TI  - Genome Sequence of Pectin-Degrading Alishewanella aestuarii Strain B11T, Isolated from Tidal Flat Sediment.
PG  - 5476
AB  - We present the genome sequence of Alishewanella aestuarii B11(T) (=KCTC 22051(T)=DSM
      19476(T)). This species, isolated from tidal flat sediment, was
      reported to be a novel species. A. aestuarii is known to degrade pectin, an
      important component of plant cell wall. The presence of the genes related to
      pectin metabolism in this strain indicates its capability to utilize pectin.
AU  - Jung J
AU  - Choi S
AU  - Chun J
AU  - Park W
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5476.

PMID- 22461542
VI  - 194
DP  - 2012
TI  - Genome Sequence of Extracellular-Protease-Producing Alishewanella jeotgali Isolated from Traditional Korean Fermented Seafood.
PG  - 2097
AB  - Alishewanella jeotgali MS1(T) (= KCTC 22429(T) = JCM 15561(T)) was isolated from  a
      traditional Korean fermented seafood, gajami sikhae (jeotgal), and has been
      reported as a novel species. A. jeotgali was proven to have extracellular
      proteolytic activity, which may play an important role in the fermentation
      environment of food containing fish flesh. Here, we present the genome sequence
      of Alishewanella jeotgali MS1(T) as the first sequenced strain in the genus
      Alishewanella and its taxonomic relatives.
AU  - Jung J
AU  - Chun J
AU  - Park W
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2097.

PMID- 22887670
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of the Hyperthermophilic Archaeon Thermococcus sp. Strain CL1, Isolated from a Paralvinella sp. Polychaete Worm Collected from a  Hydrothermal Vent.
PG  - 4769-4770
AB  - Thermococcus sp. strain CL1 is a hyperthermophilic, anaerobic, and heterotrophic  archaeon
      isolated from a Paralvinella sp. polychaete worm living on an active
      deep-sea hydrothermal sulfide chimney on the Cleft Segment of the Juan de Fuca
      Ridge. To further understand the distinct characteristics of this archaeon at the
      genome level, its genome was completely sequenced and analyzed. Here, we announce
      the complete genome sequence (1,950,313 bp) of Thermococcus sp. strain CL1, with
      a focus on H(2)- and energy-producing capabilities and its amino acid
      biosynthesis and acquisition in an extreme habitat.
AU  - Jung JH
AU  - Holden JF
AU  - Seo DH
AU  - Park KH
AU  - Shin H
AU  - Ryu S
AU  - Lee JH
AU  - Park CS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4769-4770.

PMID- 30455841
VI  - 13
DP  - 2018
TI  - Complete genome sequence of Planococcus sp. PAMC21323 isolated from Antarctica and its metabolic potential to detoxify pollutants.
PG  - 31
AB  - The Planococcus sp. PAMC21323 is a yellow pigment-producing bacterium isolated from King
      George Island in Antarctica; it has a broad growth temperature range of
      5-40 degrees C. Herein, we describe the complete genome sequence information of
      the genus Planococcus with its annotated sequence, genetic features for
      bioremediation, and oxidative stress capacity. The Planococcus sp. PAMC21323
      possesses chromosomal DNA (3,196,500-bp) with plasmid DNA (3364-bp). The complete
      3,199,864-bp of the genome consists of 3171 genes including 60 transfer RNAs and
      24 ribosomal RNAs. Strain PAMC21323 encodes various genes associated with
      detoxification of heavy metal ions and aromatic hydrocarbons. Moreover, it is
      equipped with diverse stress response systems, which can be used to sense the
      internal and oxidative stresses caused by detoxification. This is the first
      report highlighting the genetic potential of Planococcus sp. PAMC21323 in
      bioremediation, suggesting application of this psychrotrophic strain in
      bioremediation in harsh environments.
AU  - Jung JH
AU  - Joe MH
AU  - Kim DH
AU  - Park H
AU  - Choi JI
AU  - Lim S
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2018 13: 31.

PMID- 22843576
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of the Hyperthermophilic Archaeon Pyrococcus sp. Strain  ST04, Isolated from a Deep-Sea Hydrothermal Sulfide Chimney on the Juan de Fuca  Ridge.
PG  - 4434-4435
AB  - Pyrococcus sp. strain ST04 is a hyperthermophilic, anaerobic, and heterotrophic archaeon
      isolated from a deep-sea hydrothermal sulfide chimney on the Endeavour
      Segment of the Juan de Fuca Ridge in the northeastern Pacific Ocean. To further
      understand the distinct characteristics of this archaeon at the genome level
      (polysaccharide utilization at high temperature and ATP generation by a Na(+)
      gradient), the genome of strain ST04 was completely sequenced and analyzed. Here,
      we present the complete genome sequence analysis results of Pyrococcus sp. ST04
      and report the major findings from the genome annotation, with a focus on its
      saccharolytic and metabolite production potential.
AU  - Jung JH
AU  - Lee JH
AU  - Holden JF
AU  - Seo DH
AU  - Shin H
AU  - Kim HY
AU  - Kim W
AU  - Ryu S
AU  - Park CS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4434-4435.

PMID- 28428315
VI  - 5
DP  - 2017
TI  - Improved High-Quality Draft Genome Sequence and Annotation of Burkholderia contaminans LMG 23361T.
PG  - e00245-17
AB  - Burkholderia contaminans LMG 23361 is the type strain of the species isolated from the milk of
      a dairy sheep with mastitis. Some pharmaceutical products
      contain disinfectants such as benzalkonium chloride (BZK) and previously we
      reported that B. contaminans LMG 23361T possesses the ability to inactivate BZK
      with high biodegradation rates. Here, we report an improved high-quality draft
      genome sequence of this strain.
AU  - Jung JY
AU  - Ahn Y
AU  - Kweon O
AU  - LiPuma JJ
AU  - Hussong D
AU  - Marasa BS
AU  - Cerniglia CE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00245-17.

PMID- 23144413
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Leuconostoc carnosum Strain JB16, Isolated from Kimchi.
PG  - 6672-6673
AB  - Leuconostoc carnosum strain JB16 was isolated from kimchi, the traditional Korean fermented
      food. Here, we report the complete genome sequence of L. carnosum
      strain JB16, consisting of a 1,645,096-bp circular chromosome with a G+C content
      of 37.24% and four plasmids.
AU  - Jung JY
AU  - Lee SH
AU  - Jeon CO
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6672-6673.

PMID- 23144409
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Leuconostoc gelidum Strain JB7, Isolated from Kimchi.
PG  - 6665
AB  - A strain of Leuconostoc gelidum, designated strain JB7, was isolated from kimchi, the
      representative Korean traditional fermented food. Here we announce the
      complete genome sequence of L. gelidum strain JB7, consisting of a 1,893,499-bp
      circular chromosome with a G+C content of 36.68%, and provide a description of
      its annotation.
AU  - Jung JY
AU  - Lee SH
AU  - Jeon CO
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6665.

PMID- 22247530
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Leuconostoc mesenteroides subsp. mesenteroides Strain J18, Isolated from Kimchi.
PG  - 730-731
AB  - Leuconostoc mesenteroides subsp. mesenteroides is one of the most predominant lactic acid
      bacterial groups during kimchi fermentation. Here,
      we report the complete genome sequence of L. mesenteroides subsp.
      mesenteroides J18, which was isolated from kimchi. The genome of the
      strain consists of a 1,896,561-bp chromosome and five plasmids.
AU  - Jung JY
AU  - Lee SH
AU  - Lee SH
AU  - Jeon CO
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 730-731.

PMID- 22038972
VI  - 193
DP  - 2011
TI  - Genome Sequence of Lentibacillus jeotgali GrbiT, Isolated from Traditional Korean Salt-Fermented Seafood.
PG  - 6414-6415
AB  - Lentibacillus jeotgali Grbi(T), isolated from a traditional Korean salt-fermented seafood, is
      a strictly aerobic, Gram-positive, nonmotile,
      endospore-forming, moderately halophilic bacterium belonging to the family
      Bacillaceae in the phylum Firmicutes. Here, the draft genome sequence of
      L. jeotgali Grbi(T) (3,775,822 bp with a G+C content of 42.5%) is
      reported. This is the first reported genome sequence from a Lentibacillus
      species.
AU  - Jung MJ
AU  - Roh SW
AU  - Kim MS
AU  - Whon TW
AU  - Bae JW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6414-6415.

PMID- 2172931
VI  - 18
DP  - 1990
TI  - Efficient cloning of PCR generated DNA containing terminal restriction endonuclease recognition sites.
PG  - 6156
AB  - None
AU  - Jung V
AU  - Pestka SB
AU  - Pestka S
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 6156.

PMID- 8389966
VI  - 218
DP  - 1993
TI  - Cloning of polymerase chain reaction-generated DNA containing terminal restriction endonuclease recognition sites.
PG  - 357-362
AB  - Using the polymerase chain reaction (PCR) to generate DNA containing terminal restriction
      endonuclease recognition sites to permit cloning usually relies on the use of unphosphorylated
      primers incorporating a restriction endonuclease recognition site of choice plus three or four
      extra 5' bases flanking that site. Various sites (e.g., NotI, XhoI, and XbaI) incorporated
      into the termini of PCR products have proved difficult to cut with their respective
      restriction endonucleases. There are several possible explanations for this difficulty; first,
      Taq polymersase might be inefficient for certain terminal sequences, producing frayed ends
      that cannot be cleaved by the restriction endonuclease. Alternatively, the "breathing" of
      terminal sequences might prevent the stable association of restriction endonucleases with
      terminal sites. Also, Taq polymerase or other contaminants might bind to the ends of the PCR
      products, blocking restriction endonuclease activity.
AU  - Jung V
AU  - Pestka SB
AU  - Pestka S
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1993 218: 357-362.

PMID- 26516406
VI  - 10
DP  - 2015
TI  - Draft genome sequence of a nitrate-reducing, o-phthalate degrading bacterium, Azoarcus sp. strain PA01(T).
PG  - 90
AB  - Azoarcus sp. strain PA01(T) belongs to the genus Azoarcus, of the family Rhodocyclaceae within
      the class Betaproteobacteria. It is a facultatively
      anaerobic, mesophilic, non-motile, Gram-stain negative, non-spore-forming, short
      rod-shaped bacterium that was isolated from a wastewater treatment plant in
      Constance, Germany. It is of interest because of its ability to degrade
      o-phthalate and a wide variety of aromatic compounds with nitrate as an electron
      acceptor. Elucidation of the o-phthalate degradation pathway may help to improve
      the treatment of phthalate-containing wastes in the future. Here, we describe the
      features of this organism, together with the draft genome sequence information
      and annotation. The draft genome consists of 4 contigs with 3,908,301 bp and an
      overall G + C content of 66.08 %. Out of 3,712 total genes predicted, 3,625 genes
      code for proteins and 87 genes for RNAs. The majority of the protein-encoding
      genes (83.51 %) were assigned a putative function while those remaining were
      annotated as hypothetical proteins.
AU  - Junghare M
AU  - Patil Y
AU  - Schink B
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 90.

PMID- 12595545
VI  - 31
DP  - 2003
TI  - De novo cytosine methylation in the differentiating macronucleus of the stichotrichous ciliate Stylonychia lemnae.
PG  - 1387-1391
AB  - Dramatic DNA reorganization and elimination processes occur during macronuclear
      differentiation in ciliates. In this study we analyzed
      whether cytosine methylation of specific sequences plays a functional role
      during DNA rearrangement. Three classes of sequences,
      macronuclear-destined sequences (MDSs, pCE7), members from a large family
      of transposon-like elements and micronuclear-specific sequences (pLJ01),
      differing in their structure and future destiny during nuclear
      differentiation, were studied in the micronucleus, the developing
      macronucleus and, when present, in the mature macronucleus. While the MDSs
      become processed to a 1.1 and 1.3 kb gene-sized macronuclear DNA molecule,
      the family of transposon-like elements represented by MaA81 becomes
      removed late in the course of polytene chromosome formation. The
      micronuclear-specific sequence pLJ01 is eliminated together with bulk
      micronuclear DNA during degradation of polytene chromosomes. No methylated
      cytosine could be detected in the vegetative macronucleus and no
      difference in methylation pattern was observed either between micronucleus
      and developing macronucleus in MDSs or in a micronuclear-specific
      sequence. However, a significant percentage of the cytosines contained in
      the transposon-like element becomes methylated de novo in the course of
      macronuclear differentiation. This is the first demonstration that
      cytosine methylation in specific sequences occurs during macronuclear
      differentiation and may provide a first step towards understanding
      epigenetic factors involved in DNA processing.
AU  - Juranek S
AU  - Wieden H-J
AU  - Lipps HJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2003 31: 1387-1391.

PMID- 
VI  - 
DP  - 2008
TI  - Engineering of bifunctional restriction endonucleases with novel specificities.
PG  - 1-46
AB  - CONCLUSIONS 1. The BseMII restriction-modification system is composed of two enzymes, a DNA
      methlytransferase and a restriction endonuclease, which are encoded by two convergently
      transcribed genes. The PpiI and TstI R-M systems are each composed of a single enzyme. 2.
      Regions predicted to participate in DNA target hydrolysis, methylation and recognition were
      identified in the polypeptide of BseMII restriction endonuclease. From the viewpoint of the
      structure-function organization, the BseMII REase is a suitable object for experiments aimed
      at changing specificity. 3. The structure-function organization of PpiI and TstI resemble that
      of AloI. Regions responsible for DNA target hydrolysis, methylation and recognition were
      identified in polypeptides of these enzymes. 4. The construction of active hybrids between
      AloI and PpiI has demonstrated that C-terminal regions of type IIB REases are involved in DNA
      target recognition and revealed that proximal target recognition domains are independent
      interchangeable modules. 5. Active hybrids recognizing novel DNA targets GAGN5GTG were
      generated by swapping of proximal and distal target recognition domains between PpiI and TstI.
      These results have demonstrated that novel type IIB REases can be engineered by recombination
      of their TRDs. 6. The increase in the Tst-PpiTRD1 activity resulting from a single amino acid
      substitution Gly1006Leu demonstrates that properties of hybrid REases can be improved by
      rational mutagenesis. 7. Hybrid type IIB enzymes similarly to progenitor restriction
      endonucleases cleave DNA on both sides of recognition sequences and display cleavage site
      variability: at some positions enzymes hydrolyze DNA at two points differing from each other
      by one nucleotide.
AU  - Jurenaite-Urbanaviciene S
PT  - Journal Article
TA  - Ph.D. Thesis, Vilnius University
JT  - Ph.D. Thesis, Vilnius University
SO  - Ph.D. Thesis, Vilnius University 2008 : 1-46.

PMID- 11160921
VI  - 29
DP  - 2001
TI  - Characterization of BseMII, a new type IV restriction-modification system, which recognizes the pentanucleotide sequence 5'-CTCAG(N)10/8.
PG  - 895-903
AB  - We report the properties of the new BseMII restriction and modification enzymes from Bacillus
      stearothermophilus Isl 15-111, which recognize the sequence 5'-CTCAG, and the nucleotide
      sequence of the genes encoding them. The restriction endonuclease R.BseMII makes a staggered
      cut at the tenth base pair downstream of the recognition sequence on the upper strand,
      producing a two base 3'-protruding end.  Magnesium ions and S-adenosyl-L-methionine (AdoMet)
      are required for cleavage.  S-adenosylhomocysteine and sinefungin can replace AdoMet in the
      cleavage reaction. The BseMII methyltransferase modifies unique adenine residues in both
      strands of the target sequence 5'-CTCAG-3'/5'-CTGAG-3'. Monomeric R.BseMII in addition to
      endonucleolytic activity also possesses methyltransferase activity that modifies the A base
      only within the 5'-CTCAG strand of the target duplex. The deduced amino acid sequence of the
      restriction endonuclease contains conserved motifs of DNA N6-adenine methylases involved in
      S-adenosyl-L-methionine binding and catalysis. According to its structure and enzymatic
      properties, R.BseMII may be regarded as a representative of the type IV restriction
      endonucleases.
AU  - Jurenaite-Urbanaviciene S
AU  - Kazlauskiene R
AU  - Urbelyte V
AU  - Maneliene Z
AU  - Petrusyte M
AU  - Lubys A
AU  - Janulaitis A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2001 29: 895-903.

PMID- 17553965
VI  - 104
DP  - 2007
TI  - Generation of DNA cleavage specificities of type II restriction endonucleases by reassortment of target recognition domains.
PG  - 10358-10363
AB  - Type II restriction endonucleases (REases) cleave double-stranded DNA at specific sites within
      or close to their recognition sequences. Shortly
      after their discovery in 1970, REases have become one of the primary tools
      in molecular biology. However, the list of available specificities of type
      II REases is relatively short despite the extensive search for them in
      natural sources and multiple attempts to artificially change their
      specificity. In this study, we examined the possibility of generating
      cleavage specificities of REases by swapping putative target recognition
      domains (TRDs) between the type IIB enzymes AloI, PpiI, and TstI. Our
      results demonstrate that individual TRDs recognize distinct parts of the
      bipartite DNA targets of these enzymes and are interchangeable. Based on
      these properties, we engineered a functional type IIB REase having
      previously undescribed DNA specificity. Our study suggests that the
      TRD-swapping approach may be used as a general technique for the
      generation of type II enzymes with predetermined specificities.
AU  - Jurenaite-Urbanaviciene S
AU  - Serksnaite J
AU  - Kriukiene E
AU  - Giedriene J
AU  - Venclovas C
AU  - Lubys A
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2007 104: 10358-10363.

PMID- 3382434
VI  - 14
DP  - 1988
TI  - The effects of N4-methylcytosine and 5-methylcytosine on the thermal stability of DNA double helix.
PG  - 158-165
AB  - The thermodynamic parameters (DeltaH, DeltaS) of the helix-coil transition of
      self-complementary oligonucleotides d(CGCGCGCG), d(CG5mCGCGCG), d(CG4mCGCGCG),
      d(GGACCCGGGTCC), d(GGA5mCCCGGGTCC), and d(GGA4mCCCGGGTCC) were determined.  The
      substitution of 4mC for C was found to decrease the melting temperature of the
      oligonucleotides.  The destabilization effect of the two substitutions is
      equivalent to the change of an A.T for a G.C pair.  The free energy decrease of
      helix-coil transition due to the introduction of two 4mC into an octanucleotide
      was estimated to be 1.24 kcal/mol.
AU  - Jurgaitis AP
AU  - Butkus VV
AU  - Klimasauskas SJ
AU  - Janulaitis A
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1988 14: 158-165.

PMID- 
VI  - 
DP  - 1999
TI  - I. Structures of  intron encoded homing endonucleases and II. Allosteric regulation of pyruvate kinase.
PG  - 1-146
AB  - I.  Homing is the lateral transfer of an intervening genetic sequence,
      either an intron or an intein, to a cognate allele lacking the element resulting
      in the duplication of the intervening sequence.  The process of homing is
      initiated by site-specific endonucleases that are encoded by open reading frames
      within the mobile elements.  Several features of these proteins make them
      attractive subjects for structural studies.  First, these unique endonucleases
      may be contrasted with a variety of enzymes involved in nucleic acid strand
      breakage and rearrangement, particularly restriction endonucleases.  Second,
      because they are encoded within the intervening sequence, limitations in the
      length of the open reading frames that encode them are also imposed on the
      folded protein structures.  Third, these enzymes display a unique strategy of
      flexible recognition of very long DNA target sites.  This strategy allows the
      enzymes to minimize non-specific cleavage within the host genome, while
      maximizing their ability to cleave closely related variants of the homing
      recognition site.  The structural studies of homing endonucleases presented here
      provide insight to their unique mechanisms of recognition and cleavage of DNA.
      II.  The activation of regulated isozymes of pyruvate kinase (PK) by fructose-
      1,6-bis-phosphate (FBP) directly influences cytosolic levels of ATP and GTP and
      the flux of glycolytic carbon into fermentation pathways and the Krebs cycle.
      This pattern of regulation may be important to cell proliferation, as
      demonstrated by the re-expression of an allosterically regulated, fetal isozyme
      of PK in tumor cells.  The structure of allosterically regulated pyruvate kinase
      from Saccharomyces cerevisiae complexed with phosphoglycolate (a substrate
      analogue), Mn2+, and K+ in the presence and absence of FBP was solved to
      identify the allosteric binding site.  The location, structure, and interactions
      within the allosteric site are in agreement with the pattern of alternate
      genetic splicing that leads to regulated forms of the enzyme in humans.
      Deregulating the allosteric control of PK in yeast by either site-directed
      mutation or expression of non-regulated isozymes has profound effects on cell
      growth and cell-cycle profiles.
AU  - Jurica MS
PT  - Journal Article
TA  - Ph.D. Thesis, University of Washington
JT  - Ph.D. Thesis, University of Washington
SO  - Ph.D. Thesis, University of Washington 1999 : 1-146.

PMID- 9809068
VI  - 2
DP  - 1998
TI  - DNA recognition and cleavage by the LAGLIDADG homing endonuclease I-CreI.
PG  - 469-476
AB  - The structure of the LAGLIDADG intron-encoded homing endonuclease I-CreI bound to homing site
      DNA has been determined. The interface is formed by an extended, concave beta sheet from each
      enzyme monomer that contacts each DNA half-site, resulting in direct side-chain contacts to 18
      of the 24 base pairs across the full-length homing site. The structure indicates that I-CreI
      is optimized to its role in genetic transposition by exhibiting long site-recognition while
      being able to cleave many closely related target sequences. DNA cleavage is mediated by a
      compact pair of active sites in the I-CreI homodimer, each of which contains a separate bound
      divalent cation.
AU  - Jurica MS
AU  - Monnat RJ Jr
AU  - Stoddard BL
PT  - Journal Article
TA  - Mol. Cell
JT  - Mol. Cell
SO  - Mol. Cell 1998 2: 469-476.

PMID- 10487208
VI  - 55
DP  - 1999
TI  - Homing endonucleases: structure, function and evolution.
PG  - 1304-1326
AB  - 'Homing' is the lateral transfer of an intervening genetic sequence, either an intron or an
      intein, to a cognate allele that lacks that element. The end result of homing is the
      duplication of the intervening sequence. The process is initiated by site-specific
      endonucleases that are encoded by open reading frames within the mobile elements. Several
      features of these proteins make them attractive subjects for structural and functional
      studies. First, these endonucleases, while unique, may be contrasted with a variety of enzymes
      involved in nucleic acid strand breakage and rearrangement, particularly restriction
      endonucleases. Second, because they are encoded within the intervening sequence, there are
      interesting limitations on the position and length of their open reading frames, and therefore
      on their structures. Third, these enzymes display a unique strategy of flexible recognition of
      very long DNA target sites. This strategy allows these sequences to minimize nonspecific
      cleavage within the host genome, while maximizing the ability of the endonuclease to cleave
      closely related variants of the homing site. Recent studies explain a great deal about the
      biochemical and genetic mechanisms of homing, and also about the structure and function of
      several representative members of the homing endonuclease families.
AU  - Jurica MS
AU  - Stoddard BL
PT  - Journal Article
TA  - Cell. Mol. Life Sci.
JT  - Cell. Mol. Life Sci.
SO  - Cell. Mol. Life Sci. 1999 55: 1304-1326.

PMID- 18945701
VI  - 36
DP  - 2008
TI  - Formation of nucleoprotein filaments by mammalian DNA methyltransferase Dnmt3a in complex with regulator Dnmt3L.
PG  - 6656-6663
AB  - The C-terminal domains of Dnmt3a and Dnmt3L form elongated heterotetramers (3L-3a-3a-3L).
      Analytical ultracentrifugation confirmed the Dnmt3a-C/3L-C
      complex exists as a 2:2 heterotetramer in solution. The 3a-3a interface is
      the DNA-binding site, while both interfaces are essential for AdoMet
      binding and catalytic activity. Hairpin bisulfite analysis shows
      correlated methylation of two CG sites in a distance of approximately 8-10
      bp in the opposite DNA strands, which corresponds to the geometry of the
      two active sites in one Dnmt3a-C/3L-C tetramer. Correlated methylation was
      also observed for two CG sites at similar distances in the same DNA
      strand, which can be attributed to the binding of two tetramers next to
      each other. DNA-binding experiments show that Dnmt3a-C/3L-C complexes
      multimerize on the DNA. Scanning force microscopy demonstrates filament
      formation rather than binding of single tetramers and shows that
      protein-DNA filament formation leads to a 1.5-fold shortening of the DNA
      length.
AU  - Jurkowska RZ
AU  - Anspach N
AU  - Urbanke C
AU  - Jia D
AU  - Reinhardt R
AU  - Nellen W
AU  - Cheng X
AU  - Jeltsch A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2008 36: 6656-6663.

PMID- 21913079
VI  - 791
DP  - 2011
TI  - DNA Methyltransferase Assays.
PG  - 157-177
AB  - DNA methyltransferases are important enzymes and their inhibition has many potential
      applications. The investigation of DNA methyltransferases as well as screening for potential
      inhibitors requires specialized enzyme assays. In this chapter, we describe three DNA
      methyltransferase assays, each of them based on a different method: (1) An assay using
      radioactively labeled Ado Met and biotinylated DNA substrates that is ideal for enzymatic
      characterization of these enzymes. (2) An assay using bisulfite conversion of in vitro
      methylated DNA that is ideal to determine details of the methylation pattern introduced by
      DNA-(cytosine C5)-methyltransferases. (3) A novel fluorescence-coupled, restriction-based
      assay suitable for high-throughput screening of DNA methyltransferase inhibitors.
AU  - Jurkowska RZ
AU  - Ceccaldi A
AU  - Zhang Y
AU  - Arimondo PB
AU  - Jeltsch A
PT  - Journal Article
TA  - Methods Mol. Biol.
JT  - Methods Mol. Biol.
SO  - Methods Mol. Biol. 2011 791: 157-177.

PMID- 21243710
VI  - 12
DP  - 2011
TI  - Structure and Function of Mammalian DNA Methyltransferases.
PG  - 206-222
AB  - DNA methylation plays an important role in epigenetic signalling, having an impact on gene
      regulation, chromatin structure, development
      and disease. Here, we review the structures and functions of the
      mammalian DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b, including
      their domain structures, catalytic mechanisms, localisation,
      regulation, post-translational modifications and interaction with
      chromatin and other proteins, summarising data obtained in genetic,
      cell biology and enzymatic studies. We focus on the question of how the
      molecular and enzymatic properties of these enzymes are connected to
      the dynamics of DNA methylation patterns and to the roles the enzymes
      play in the processes of de novo and maintenance DNA methylation.
      Recent enzymatic and genome-wide methylome data have led to a new model
      of genomic DNA methylation patterns based on the preservation of
      average levels of DNA methylation in certain regions, rather than the
      methylation states of individual CG sites.
AU  - Jurkowska RZ
AU  - Jurkowski TP
AU  - Jeltsch A
PT  - Journal Article
TA  - Chembiochem
JT  - Chembiochem
SO  - Chembiochem 2011 12: 206-222.

PMID- 21400651
VI  - 12
DP  - 2011
TI  - Approaches to Enzyme and Substrate Design of the Murine Dnmt3a DNA Methyltransferase.
PG  - 1589-1594
AB  - 
AU  - Jurkowska RZ
AU  - Siddique AN
AU  - Jurkowski TP
AU  - Jeltsch A
PT  - Journal Article
TA  - Chembiochem
JT  - Chembiochem
SO  - Chembiochem 2011 12: 1589-1594.

PMID- 17977824
VI  - 282
DP  - 2007
TI  - The M.EcoRV DNA-(adenine N-6)-methyltransferase uses DNA bending for recognition of an expanded EcoDam recognition site.
PG  - 36942-36952
AB  - The M. EcoRV DNA methyltransferase recognizes GATATC sites. It is related to EcoDam, which
      methylates GATC sites. The DNA binding domain
      of M. EcoRV is similar to that of EcoDam suggesting a similar mechanism
      of DNA recognition. We show that amino acid residue Lys(11) of M. EcoRV
      is involved in recognition of Gua(1) and Arg(128) contacts the Gua in
      base pair 6. These residues correspond to Lys(9) and Arg(124) in
      EcoDam, which recognize the Gua residues in both strands of the Dam
      recognition sequence, indicating that M. EcoRV and EcoDam make similar
      contacts to outermost base pairs of their recognition sequences and M.
      EcoRV recognizes its target site as an expanded GATC site. In contrast
      to EcoDam, M. EcoRV considerably bends the DNA (59 +/- 4 degrees)
      suggesting indirect readout of the AT-rich inner sequence. Recognition
      of an expanded target site by DNA bending is a new principle for
      changing DNA recognition specificity of proteins during molecular
      evolution. R128A is inefficient in DNA bending and binding, whereas
      K11A bends DNA with relaxed sequence specificity. These results suggest
      a temporal order of the formation of protein-DNA contacts in which the
      Gua(6)-Arg(128) contact forms early followed by DNA bending and,
      finally, the formation of the Lys(11)-Gua(1) contact.
AU  - Jurkowski TP
AU  - Anspach N
AU  - Kulishova L
AU  - Nellen W
AU  - Jeltsch A
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2007 282: 36942-36952.

PMID- 22140515
VI  - 6
DP  - 2011
TI  - On the Evolutionary Origin of Eukaryotic DNA Methyltransferases and Dnmt2.
PG  - e28104
AB  - The Dnmt2 enzymes show strong amino acid sequence similarity with eukaryotic and prokaryotic
      DNA-(cytosine C5)-methyltransferases. Yet,
      Dnmt2 enzymes from several species were shown to methylate tRNA-Asp and
      had been proposed that eukaryotic DNA methyltransferases evolved from a
      Dnmt2-like tRNA methyltransferase ancestor [Goll et al., 2006, Science,
      311, 395-8]. It was the aim of this study to investigate if this
      hypothesis could be supported by evidence from sequence alignments. We
      present phylogenetic analyses based on sequence alignments of the
      methyltransferase catalytic domains of more than 2300 eukaryotic and
      prokaryotic DNA-(cytosine C5)-methyltransferases and analyzed the
      distribution of DNA methyltransferases in eukaryotic species. The Dnmt2
      homologues were reliably identified by an additional conserved CFT
      motif next to motif IX. All DNA methyltransferases and Dnmt2 enzymes
      were clearly separated from other RNA-(cytosine-C5)-methyltransferases.
      Our sequence alignments and phylogenetic analyses indicate that the
      last universal eukaryotic ancestor contained at least one member of the
      Dnmt1, Dnmt2 and Dnmt3 families of enzymes and additional RNA
      methyltransferases. The similarity of Dnmt2 enzymes with DNA
      methyltransferases and absence of similarity with RNA
      methyltransferases combined with their strong RNA methylation activity
      suggest that the ancestor of Dnmt2 was a DNA methyltransferase and an
      early Dnmt2 enzyme changed its substrate preference to tRNA. There is
      no phylogenetic evidence that Dnmt2 was the precursor of eukaryotic
      Dnmts. Most likely, the eukaryotic Dnmt1 and Dnmt3 families of DNA
      methyltransferases had an independent origin in the prokaryotic DNA
      methyltransferase sequence space.
AU  - Jurkowski TP
AU  - Jeltsch A
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2011 6: e28104.

PMID- 21357458
VI  - 62
DP  - 2012
TI  - Characterization of Tetragenococcus strains from sugar thick juice reveals a novel species, Tetragenococcus osmophilus sp. nov., and divides Tetragenococcus halophilus into two subspecies, halophilus subsp. nov. and flandriensis subsp. nov.
PG  - 129-137
AB  - Most bacteria recovered so far from sugar thick juice during storage represent
      strains of the species Tetragenococcus halophilus. Recently, several
      Gram-positive, non-motile, non-spore-forming cocci with other physiological and
      genetic traits were isolated from sugar thick juice samples from different
      origins. In this study, representative isolates were investigated using a
      polyphasic taxonomic approach. The 16S rRNA gene sequence similarity between
      these isolates and their closest relative, Tetragenococcus muriaticus, was 97.4%.
      The level of DNA-DNA relatedness between isolate T1(T), representing the newly
      found Tetragenococcus isolates, and T. muriaticus was 57%. Isolate T1(T) had a
      DNA G+C content of 36.7 mol%. Phylogenetic data and genomic and phenotypic
      features demonstrated that the isolates represent a novel species, for which the
      name Tetragenococcus osmophilus sp. nov. is proposed with T1(T) as the type
      strain (=LMG 26041(T) =DSM 23765(T)). Additionally, T. halophilus isolates from
      high-salt and high-sugar environments showed clear differences in several
      physiological and genetic characteristics like RAPD fingerprints and 16S rRNA
      gene sequences. DNA-DNA hybridizations, however, showed 79 to 80% relatedness
      between osmophilic and halophilic T. halophilus isolates, demonstrating that the
      different strains belong to the same species. Based on the phenotypic and
      genotypic differences observed, as well as the different origins of the strains
      and the industrial relevance of thick juice degradation, two subspecies of T.
      halophilus are described in this manuscript: T. halophilus subsp. halophilus
      subsp. nov. for the strains isolated from salt media and T. halophilus subsp.
      flandriensis subsp. nov. for the strains isolated from sugar-rich environments,
      which were first isolated in Flanders, Belgium. The type strains for the
      subspecies are IAM 1676(T) (=LMG 11490(T) =DSM 20339(T)) and T5(T) (=LMG 26042(T)
      =DSM 23766(T)), respectively.
AU  - Juste A
AU  - Van Trappen S
AU  - Verreth C
AU  - Cleenwerck I
AU  - De Vos P
AU  - Lievens B
AU  - Willems KA
PT  - Journal Article
TA  - Int. J. Syst. Evol. Microbiol.
JT  - Int. J. Syst. Evol. Microbiol.
SO  - Int. J. Syst. Evol. Microbiol. 2012 62: 129-137.

PMID- 7527544
VI  - 91
DP  - 1994
TI  - Toxicity of 5-aza-2'-deoxycytidine to mammalian cells is mediated primarily by covalent trapping of DNA methyltransferase rather than DNA demethylation.
PG  - 11797-11801
AB  - The deoxycytidine analog 5-aza-2'-deoxycytidine (5-azadCyd) has been widely used as a DNA
      methylation inhibitor to experimentally induce gene expression and cellular differentiation.
      Prior to the availability of mutant mice with altered DNA methyltransferase levels, treatment
      of cells with drugs has been the only means to experimentally manipulate the level of genomic
      DNA methylation in mammalian cells. Substitution of DNA with 5-azadCyd leads to covalent
      trapping of the enzyme, thereby depleting the cells of enzyme activity and resulting in DNA
      demethylation. 5-AzadCyd or 5-azacytidine treatment causes multiple changes in treated cells,
      including activation of silent genes, decondensation of chromatin, and induction of cellular
      differentiation, all of which are believed to be consequences of drug-induced demethylation.
      5-AzadCyd is highly toxic in cultured cells and animals and is utilized as a potent antitumor
      agent for treatment of certain human cancers. It has been postulated that the toxicity of the
      drug in mammalian cells is also due to its inhibition of DNA methylation. The chemistry of the
      methylation reaction is consistent, however, with an alternative mechanism: the cyto-toxic
      effect of 5-azadCyd may be directly mediated through the covalent binding of DNA
      methyltransferase to 5-azadCyd-substituted DNA. We have tested this possibility by using
      embryonic stem cells and mice with reduced levels of DNA methyltransferase due to a targeted
      mutation of the gene. When exposed to 5-azadCyd mutant embryonic stem cells or embryos were
      significantly more resistant to the toxic effects of the drug than wild-type cells and
      embryos, respectively. These results strongly suggest that the cellular DNA methyltransferase
      itself, rather than the secondary demethylation of genomic DNA, is the primary mediator of
      5-azadCyd cytotoxicity. In light of our results, some conclusions from previous studies using
      5-azad-Cyd in order to experimentally manipulate cellular methylation levels may have to be
      reassessed. Also, our data make clear predictions for cancer treatment: tumor cells with
      elevated DNA methyltransferase levels would be expected to be susceptible to treatment with
      5-azadCyd, whereas tumors with reduced levels of the enzyme would be resistant.
AU  - Juttermann R
AU  - Li E
AU  - Jaenisch R
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1994 91: 11797-11801.

PMID- 15293790
VI  - 31
DP  - 2004
TI  - Bsu2413I and Bfi2411I, two new thermophilic type II restriction endonucleases from Bacillus subtilis and Bacillus firmus: isolation and  partial purification. Thermophilic endonucleases from two Bacillus  species.
PG  - 139-142
AB  - Two new thermophilic type II restriction endonucleases, which we designated as Bsu2413I and
      Bfi2411I, have been isolated from gram-positive thermophilic bacteria Bacillus subtilis strain
      2413 and Bacillus firmus strain 2411 respectively and partially purified.  The restriction
      endonucleases were extracted from cell extracts and purified using single step purification
      through phosphocellulose column chromatography, SDS-PAGE profile showed denatured molecular
      weights of 33 and 67 kDa for the Bsu2413I and 39 and 67 kDa for the Bfi2411I.  The partially
      purified Bsu2413I enzyme restricted pBR322 DNA into two fragments of 3250 and 1100 bp whereas
      Bfi2411I enzyme restricted pBR322 DNA into two fragments of 3500 and 800 bp.  The activity of
      both endonucleases was assayed at 55oC and they required Mg+2 as cofactor like other type II
      restriction endonucleases.
AU  - Jutur PP
AU  - Hoti SL
AU  - Reddy AR
PT  - Journal Article
TA  - Mol. Biol. Rep.
JT  - Mol. Biol. Rep.
SO  - Mol. Biol. Rep. 2004 31: 139-142.

PMID- 16644193
VI  - 162
DP  - 2007
TI  - Isolation, purification and properties of new restriction endonucleases from Bacillus badius and Bacillus lentus.
PG  - 378-383
AB  - We tentatively named two enzymes as Bbal and Blel, which were isolated and purified from
      Gram-positive mesophilic bacteria Bacillus badius
      1458 and Bacillus lentus 1689 respectively, by ammonium sulphate
      precipitation, phosphocellulose and heparin-sepharose column
      chromatography. SDS-PAGE protein profiles for Bbal and Blel showed
      denatured molecular weights of 52 and 48 kDa, respectively. Bbal
      hydrolyzed pUC18 DNA into 1900 and 700 bp, pBR322 DNA into two
      fragments of 2800 and 1500 bp and Phi x 174 DNA into 3800 and 1600 bp.
      Blel hydrolyzed pUC18 DNA into 1800 and 800 bp, pBR322 DNA into two
      fragments of 2700 and 1600 bp and Phi x 174 DNA into 3700 and 1700 bp.
      The effects of temperature, ionic strength, pH and Mg2+ ion
      concentrations were studied to demonstrate some biochemical properties
      of Bbal and Blel. Maximum activities of these enzymes were observed at
      37 degrees C (pH 8.0) with 100 mM NaCl and 10 mM Mg2+ concentrations.
AU  - Jutur PP
AU  - Reddy AR
PT  - Journal Article
TA  - Microbiol. Res.
JT  - Microbiol. Res.
SO  - Microbiol. Res. 2007 162: 378-383.

PMID- 15269543
VI  - 26
DP  - 2004
TI  - BpaI and BpnI: novel type II restriction endonucleases from Bacillus pasteurii and Bacillus pantothenticus.
PG  - 929-932
AB  - Two novel type II restriction endonucleases, designated as BpaI and BpnI, were isolated from
      Bacillus pasteurii strain 1761 and Bacillus
      pantothenticus strain 1639, respectively. They were partially purified
      and SDS-PAGE indicated Mr values of 28 and 67 kDa for BpaI, 28 and 48
      kDa for BpnI. The partially purified endonucleases hydrolyzed DNA into
      discrete fragments: pUC18 (2.6 kb for BpaI; 1.8 and 0.8 kb for BpnI),
      pBR322 (2.5 and 1.8 kb for BpaI; 2.6 and 1.7 kb for BpnI) and Phix174
      DNA (3.2 and 2.1 kb for BpaI; 4 and 1.3 kb for BpnI).
AU  - Jutur PP
AU  - Reddy AR
PT  - Journal Article
TA  - Biotechnol. Lett.
JT  - Biotechnol. Lett.
SO  - Biotechnol. Lett. 2004 26: 929-932.

PMID- 12549825
VI  - 29
DP  - 2002
TI  - Isolation and partial purification of a novel type II restriction endonuclease Bsu121 I, from Bacillus subtilis - Bsu121 I, a type II  restriction endonuclease from Bacillus subtilis.
PG  - 383-385
AB  - A new type II restriction endonuclease which we designated as Bsu121I has been isolated from
      the
      gram-positive bacterium Bacillus subtilis strain
      121 and partially purified. The restriction endonuclease was isolated
      from cell extracts using step-wise purification through ammonium
      sulfate precipitation, followed by phosphocellulose column
      chromatography. SDS-PAGE profile showed denatured molecular weights (23
      and 67 kDa) of the endonuclease. The partially purified enzyme
      restricted pBR322 DNA into two fragments of 3200 and 1700 bp. The
      endonuclease activity required Mg+2 as cofactor like other type II
      endonucleases.
AU  - Jutur PP
AU  - Reddy AR
PT  - Journal Article
TA  - Mol. Biol. Rep.
JT  - Mol. Biol. Rep.
SO  - Mol. Biol. Rep. 2002 29: 383-385.

PMID- 28428290
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Acinetobacter johnsonii C6, an Environmental Isolate Engaging in Interspecific Metabolic Interactions.
PG  - e00155-17
AB  - Acinetobacter johnsonii C6 originates from creosote-polluted groundwater and performs
      ecological and evolutionary interactions with Pseudomonas putida in
      biofilms. The draft genome of A. johnsonii C6 is 3.7 Mbp and was shaped by mobile
      genetic elements. It reveals genes facilitating the biodegradation of aromatic
      hydrocarbons and resistance to antimicrobials and metals.
AU  - Kaas RS
AU  - Mordhorst H
AU  - Leekitcharoenphon P
AU  - Dyring JJ
AU  - Haagensen JAJ
AU  - Molin S
AU  - Pamp SJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00155-17.

PMID- 22789474
VI  - 163
DP  - 2013
TI  - Characterization and optimization of Bacillus subtilis ATCC 6051 as an expression host.
PG  - 97-104
AB  - The genome sequence of Bacillus subtilis ATCC 6051 and its suitability as an
      expression host for recombinant protein production was determined. The comparison
      of this undomesticated wild type with the widely used laboratory strain B.
      subtilis 168 reveals a high degree of congruency between the two strains.
      Differences could only be detected on the level of point mutations or small
      insertions. B. subtilis ATCC 6051 shows none of the auxotrophies known for B.
      subtilis 168 and is able to produce polyketides. It exhibits better use of
      complex media and higher genomic stability through reduced natural competence.
      Consequently, B. subtilis ATCC 6051 was genetically modified to yield an
      optimized strain for the production of heterologously expressed proteins under
      control of an acetoin-inducible promoter.
AU  - Kabisch J
AU  - Thurmer A
AU  - Hubel T
AU  - Popper L
AU  - Daniel R
AU  - Schweder T
PT  - Journal Article
TA  - J. Biotechnol.
JT  - J. Biotechnol.
SO  - J. Biotechnol. 2013 163: 97-104.

PMID- 16511177
VI  - 61
DP  - 2005
TI  - Crystallization and preliminary crystallographic analysis of the (cytosine-5)-DNA methyltransferase NlaX from Neisseria lactamica.
PG  - 852-854
AB  - Crystals of the (cytosine-5)-DNA methyltransferase NlaX from Neisseria lactamica (molecular
      weight 36.5 kDa) have been grown at 291 K using 2.5 M NaCl as precipitant.  The crystals
      diffract to 3.0 A resolution at 100 K.  The crystals belong to space group P321, with
      unit-cell parameters a = 121.98, b = 121.98, c = 56.71 A.  There is one molecule in the
      asymmetric unit and the solvent content is estimated to be 62.1% by volume.
AU  - Kachalova GS
AU  - Artyukh RI
AU  - Lavrova NV
AU  - Ryazanova EM
AU  - Karyagina AS
AU  - Kubareva EA
AU  - Bartunik HD
PT  - Journal Article
TA  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
JT  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
SO  - Acta Crystallogr. F Struct. Biol. Cryst. Commun. 2005 61: 852-854.

PMID- 16511033
VI  - 61
DP  - 2005
TI  - Crystallization and preliminary crystallographic analysis of the site-specific DNA nickase Nb.BspD6I.
PG  - 332-334
AB  - Crystals of site-specific DNA nickase Nb.BspD6I (of molecular weight 70.8 kDa) have been grown
      at 291 K using PEG 8000 as precipitant. The
      diffraction pattern of the crystal extends to 3.3 A resolution at 100 K.
      The crystal belongs to space group P2(1), with unit-cell parameters a =
      57.76, b = 90.67, c = 71.71, beta = 110.1 degrees. There is one molecule
      in the asymmetric unit and the solvent content is estimated to be 53% by
      volume.
AU  - Kachalova GS
AU  - Rogulin EA
AU  - Artyukh RI
AU  - Perevyazova TA
AU  - Zheleznaya LA
AU  - Matvienko NI
AU  - Bartunik HD
PT  - Journal Article
TA  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
JT  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
SO  - Acta Crystallogr. F Struct. Biol. Cryst. Commun. 2005 61: 332-334.

PMID- 18835275
VI  - 384
DP  - 2008
TI  - Structural Analysis of the Heterodimeric Type IIS Restriction Endonuclease R.BspD6I Acting as a Complex between a Monomeric Site-specific Nickase and  a Catalytic Subunit.
PG  - 489-502
AB  - The heterodimeric restriction endonuclease R.BspD6I from Bacillus species D6 recognizes a
      pseudosymmetric sequence and cuts both DNA strands outside the recognition sequence. The large
      subunit, Nt.BspD6I, acts as a type IIS site-specific monomeric nicking endonuclease. The
      isolated small subunit, ss.BspD6I, does not bind DNA and is not catalytically active. We
      solved the crystal structures of Nt.BspD6I and ss.BspD6I at high resolution. Nt.BspD6I
      consists of three domains, two of which exhibit structural similarity to the recognition and
      cleavage domains of FokI. ss.BspD6I has a fold similar to that of the cleavage domain of
      Nt.BspD6I, each containing a PD-(D/E)XK motif and a histidine as an additional putative
      catalytic residue. In contrast to the DNA-bound FokI structure, in which the cleavage domain
      is rotated away from the DNA, the crystal structure of Nt.BspD6I shows the recognition and
      cleavage domains in favorable orientations for interactions with DNA. Docking models of
      complexes of Nt.BspD6I and R.BspD6I with cognate DNA were constructed on the basis of
      structural similarity to individual domains of FokI, R.BpuJI and HindIII. A three-helix bundle
      forming an interdomain linker in Nt.BspD6I acts as a rigid spacer adjusting the orientations
      of the spatially separated domains to match the distance between the recognition and cleavage
      sites accurately.
AU  - Kachalova GS
AU  - Rogulin EA
AU  - Yunusova AK
AU  - Artyukh RI
AU  - Perevyazova TA
AU  - Matvienko NI
AU  - Zheleznaya LA
AU  - Bartunik HD
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2008 384: 489-502.

PMID- 17768358
VI  - 63
DP  - 2007
TI  - Crystallization and preliminary x-ray diffraction analysis of the small subunit of the heterodimeric restriction endonuclease R.BspD6I.
PG  - 795-797
AB  - The heterodimeric restriction endonuclease R.BspD6I is composed of a small subunit with a
      cleavage site and a large subunit, containing a recognition domain and a cleavage domain, that
      may function separately as a monomeric nicking endonuclease.  Here, the crystallization of the
      small subunit and diffraction data collection to 1.5 A resolution are reported.
AU  - Kachalova GS
AU  - Yunusova AK
AU  - Artyukh RI
AU  - Rogulin EA
AU  - Perevyazova TA
AU  - Zheleznaya LA
AU  - Matvienko NI
AU  - Bartunik HD
PT  - Journal Article
TA  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
JT  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
SO  - Acta Crystallogr. F Struct. Biol. Cryst. Commun. 2007 63: 795-797.

PMID- 10934517
VI  - 13
DP  - 1999
TI  - The FokI methyltransferase from Flavobacterium okeanokoites - Purification and characterization of the enzyme and its truncated derivatives.
PG  - 1-15
AB  - The gene encoding the FokI methyltransferase from Flavobacterium okeanokoites was cloned into
      an Escherichia coli vector. The
      transcriptional start sites were mapped as well as putative -10 and -35
      regions of the fokIM promoter. Enzyme overproduction was ensured by
      cloning the fokIM gene under the phi 10 promoter of phage T7. M.FokI
      was purified using a two-step chromatography procedure. M.FokI is a
      monomeric protein with an Mr = 76,000 +/- 1,500 under denaturing
      conditions. It contains 21 Arg residues, at least one of which is
      required for activity as shown by inhibition using 2,3-butanedione.
      Deletion mutants in the N- and C-terminus of M.FokI were isolated and
      characterized. The N-terminal derivative (M.FokIN) methylates the
      adenine residue within the sequence 5'-GGATG-3', whereas the C-terminal
      derivative (M.FokIC) modifies the adenine residue within the sequence
      5'-CATCC-3'. Substrate-protection studies, utilizing chemical
      modification combined with data on the effect of divalent cations and
      pH on methylation activity, proved the existence of two catalytic
      centers within the FokI methyltransferase molecule. M.FokI and its
      truncated derivatives require S-adenosyl-L-methionine as the
      methyl-group donor, and they are strongly inhibited by divalent cations
      (Mg2+, Ca2+, Ba2+, Mn2+ and Zn2+) and S-adenosyl-L-homocysteine. The
      Km values for the methyl donor, S-adenosyl-L-methionine are 0.6 microM
      (M.FokI), 0.3 microM (M.FokIN), and 0.9 microM (M.FokIC) while the Km
      values for substrate lambda DNA are 1.2 nM (M.FokI): 1.4 nM (M.FokIN),
      and 1.3 nM (M.FokIC).
AU  - Kaczorowski T
AU  - Sektas M
AU  - Skowron P
AU  - Podhajska AJ
PT  - Journal Article
TA  - Mol. Biotechnol.
JT  - Mol. Biotechnol.
SO  - Mol. Biotechnol. 1999 13: 1-15.

PMID- 2583511
VI  - 80
DP  - 1989
TI  - Purification and characterization of the FokI restriction endonuclease.
PG  - 209-216
AB  - The restriction endonuclease FokI from Flavobacterium okeanokoites was purified
      to homogeneity.  Based on gel filtration, sedimentation and sodium dodecyl
      sulfate-polyacrylamide-gel electrophoresis, the following properties of the
      enzyme were determined:  FokI exists in one active monomeric form, and has an
      Mr of 64,000-65,400.  FokI is a strongly basic protein with an isoelectric
      point of 9.4.  The enzyme exhibits restriction activity in the pH range 5.0 to
      10.5 (maximum level at pH 7.0-8.5) and its divalent cation requirement is
      satisfied not only by Mg2+, but also by Co2+, Mn2+, Ni2+, Cd2+, Zn2+ and Fe2+.
AU  - Kaczorowski T
AU  - Skowron P
AU  - Podhajska AJ
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1989 80: 209-216.

PMID- 2999112
VI  - 260
DP  - 1985
TI  - Catalytic properties of the HhaII restriction endonuclease.
PG  - 15345-15351
AB  - The catalytic properties of the HhaII restriction endonuclease were studied
      using plasmid pSK11 DNA containing a single 5'-G-A-N-T-C HhaII cleavage site as
      substrate.  Reactions were followed by two methods: 1) gel electrophoretic
      analysis of nicked circular and linear DNA products, or 2) release of
      32P-labeled inorganic phosphate from specifically labeled HhaII sites in a
      reaction coupled with bacterial alkaline phosphatase.  The enzyme is optimally
      active at 37C in 10 mM Tris-HCl (pH 9.1) and 4-10 mM MgCl2 without added NaCl.
      Activity is stabilized by the presence of 2-mercaptoethanol and 0.2% Triton
      X-100 or 50 lg/ml bovine serum albumin.  At enzyme concentrations below 10 nM
      and using pSK11 as substrate, initial kinetic rates were dependent on the order
      of mixing of reactants.  A lag of 3-4 min was observed if enzyme or substrate
      was added last.  Preincubation of substrate and enzyme followed by initiation
      of the reaction with MgCl2 or preincubation of the enzyme with nonspecific DNA
      followed by initiation with substrate eliminated or reduced the lag,
      respectively, and speeded up the reactions.  Under a wide range of reaction
      conditions, nicked pSK11 DNA accumulated early, while linear molecules appeared
      later, suggesting that HhaII cleaves one strand at a time in separate binding
      events.  The apparent Km for covalently closed pSK11 DNA molecules was
      approximately 17 nM, and the turnover number for the conversion of covalent to
      nicked sites was 1.1 single strand scissions/min.  Pre-steady state kinetic
      analysis indicated that cleavage of the first phosphodiester bond in a site is
      first order with a rate constant of about 0.8 min-1, while cleavage of the
      second phosphodiester bond is first order with a rate constant of about 0.2
      min-1.
AU  - Kaddurah-Daouk R
AU  - Cho P
AU  - Smith HO
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1985 260: 15345-15351.

PMID- 25035330
VI  - 2
DP  - 2014
TI  - Whole-Genome Sequence of Brucella canis Strain SVA13, Isolated from an Infected Dog.
PG  - e00700-14
AB  - An outbreak of canine brucellosis in Sweden was confirmed by the National Veterinary Institute
      (SVA) in August 2013. The whole genome of the causative
      agent was sequenced, assembled, and analyzed.
AU  - Kaden R
AU  - Agren J
AU  - Ferrari S
AU  - Lindberg M
AU  - Backman S
AU  - Wahab T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00700-14.

PMID- 8992297
VI  - 30
DP  - 1996
TI  - SegE endonuclease from phage T4. I. Cloning, expression and biochemical characteristics of endonuclease activity.
PG  - 1096-1106
AB  - 
AU  - Kadyrov FA
AU  - Kaliman AV
AU  - Kriukov VM
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1996 30: 1096-1106.

PMID- 7858519
VI  - 339
DP  - 1994
TI  - SegE-a new site-specific endodeoxyribonuclease from bacteriophage T4.
PG  - 404-406
AB  - 
AU  - Kadyrov FA
AU  - Kriukov VM
AU  - Shliapnikov MG
AU  - Baev AA
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1994 339: 404-406.

PMID- Not included in PubMed...
VI  - 339
DP  - 1994
TI  - SegE--a new site-specific endodeoxyribonuclease of bacteriophage T4.
PG  - 145-147
AB  - Introns of group I were found in nuclear DNA of Tetrahymena, mitochondrial genomes of fungi,
      genomes of cyanobacteria, archaebacteria and bacteriophages, particularly in the genome of
      bacteriophage T4.  Most of these introns code for specific endonucleases that provide the
      transfer of intron DNA into genes lacking introns by introducing double-strand breaks at the
      sites of intron insertion.  Earlier, we determined the DNA nucleotide sequence of the region
      of phage T4 hoc and uvsW genes containing an open reading frame (ORF205) designated as hoc2
      gene.  The amino acid sequence of the product of this gene was shown to share a high degree of
      homology with a site-specific endodeoxyribonuclease, SegA.  Subsequently, the gene was
      classified with phage T4 genes coding for proteins, similar to endonucleases of group I
      introns (seg), and termed segE.  The five members of the group (segA, segB, segC, segD, and
      segE) are homologous to each other.
AU  - Kadyrov FA
AU  - Kryukov VM
AU  - Shlyapnikov MG
AU  - Baev AA
PT  - Journal Article
TA  - Dokl. Biochem.
JT  - Dokl. Biochem.
SO  - Dokl. Biochem. 1994 339: 145-147.

PMID- 9326373
VI  - 415
DP  - 1997
TI  - A phage T4 site-specific endonuclease, SegE, is responsible for a non-reciprocal genetic exchange between T-even-related phages.
PG  - 75-80
AB  - The bacteriophage T4 segE gene encoding site-specific endonuclease lies between the hoc.1 and
      uvsW genes.  The similar region of T-even-related phage RB30 lacks the segE gene.  Here we
      demonstrate that the phage T4 segE gene is inherited preferably by progeny of mixed infection
      with RB30.  The preferred inheritance of the segE gene depends on its own expression and is
      based on a non-reciprocal homologous recombination event providing the transfer of the gene
      from the segE-containing to the segE-lacking allele.  The SegE endonuclease cleaves DNA in a
      site located at the 5' end of the uvsW gene in the RB30 genome.  The T4 DNA is also cleaved
      by the enzyme, but less efficiently.  The cleavage at the RB30 site appears to initiate the
      observed conversion, which is stimulated by DNA homology and accompanied by co-conversion of
      flanking markers.  Our findings provide a novel example of endonuclease-dependent generation
      of genetic variation in prokaryotes.
AU  - Kadyrov FA
AU  - Shlyapnikov MG
AU  - Kryukov VM
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1997 415: 75-80.

PMID- 28729269
VI  - 5
DP  - 2017
TI  - Multiple Genome Sequences of Lactobacillus plantarum Strains.
PG  - e00654-17
AB  - We report here the genome sequences of four Lactobacillus plantarum strains which vary in
      surface hydrophobicity. Bioinformatic analysis, using additional genomes
      of Lactobacillus plantarum strains, revealed a possible correlation between the
      cell wall teichoic acid-type and cell surface hydrophobicity and provide the
      basis for consecutive analyses.
AU  - Kafka TA
AU  - Geissler AJ
AU  - Vogel RF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00654-17.

PMID- 8332512
VI  - 21
DP  - 1993
TI  - Probing CpG methylation at CACGTG with BbrPI restriction enzyme.
PG  - 2950
AB  - The sequence CACGTG is known to be a recognition site for basic helix-loop-helix binding
      proteins such as Max and Myc. This site is a common element which is present in the upstream
      region of a variety of genes that participate in developmental processes. Being a
      CpG-containing sequence, it is prone to methylation in vertebrates. It is therefore of
      importance to probe for the status of methylation of this site since CpG modification
      frequently affects protein binding. The restriction enzyme BbrPI has been shown to be
      sensitive to cytosine methylation at this site. However, since the substrate used for BbrPI
      digestion has been prepared by PCR with 5-methyldCTP replacing dCTP, it was impossible to
      conclude whether methylation of the outer cytosine, the inner cytosine or both is required to
      inhibit digestion by BbrPI. We, therefore, use here lambda DNA methylated in vitro by M.SssI
      as substrate for BbrPI digestion. The Spiroplasma methylase, M.SssI, is known to methylate
      exclusively CpG sequences. Therefore, only the inner cytosine residue in CACGTG is expected to
      be methylated by M.SssI. The results shown in Figure 1 clearly indicate that methylation of
      the inner cytosine residue in CACGTG is sufficient to inhibit digestion by BbrPI. It is
      therefore possible to probe the status of methylation of this site in mammalian genomic DNA by
      BbrPI digestion followed by Southern blotting. Such an analysis with digested DNA from various
      tissues of the mouse revealed that a BbrPI site in the mouse homeobox gene HoxA5 is methylated
      in a tissue-specific manner.
AU  - Kafri T
AU  - Hershko A
AU  - Razin A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 2950.

PMID- 11325934
VI  - 183
DP  - 2001
TI  - The CcrM DNA methyltransferase of Agrobacterium tumefaciens is essential, and its activity is cell cycle regulated.
PG  - 3065-3075
AB  - DNA methylation is now recognized as a regulator of multiple bacterial cellular processes.
      CcrM is a DNA adenine methyltransferase found in
      the alpha subdivision of the proteobacteria. Like the Dam enzyme, which
      is found primarily in Escherichia coli and other gamma proteobacteria,
      it does not appear to be part of a DNA restriction-modification system.
      The CcrM homolog of Agrobacterium tumefaciens was found to be essential
      for viability. Overexpression of CcrM is associated with significant
      abnormalities of cell morphology and DNA ploidy. Mapping of the
      transcriptional start site revealed a conserved binding motif for the
      global response regulator CtrA at the -35 position; this motif was
      footprinted by purified Caulobacter crescentus CtrA protein in its
      phosphorylated state. We have succeeded in isolating synchronized
      populations of Agrobacterium cells and analyzing their progression
      through the cell cycle. We demonstrate that DNA replication and cell
      division can be followed in an orderly manner and that flagellin
      expression is cyclic, consistent with our observation that motility
      varies during the cell cycle. Using these synchronized populations, we
      show that CcrM methylation of the chromosome is restricted to the late
      S phase of the cell cycle. Thus, within the alpha subdivision, there is
      a conserved cell cycle dependence and regulatory mechanism controlling
      ccrM expression.
AU  - Kahng LS
AU  - Shapiro L
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2001 183: 3065-3075.

PMID- 22673913
VI  - 3
DP  - 2012
TI  - Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription.
PG  - 886
AB  - DNA cytosine methylation regulates gene expression in mammals. In bacteria, its role in gene
      expression and genome architecture is less
      understood. Here we perform high-throughput sequencing of
      bisulfite-treated genomic DNA from Escherichia coli K12 to describe,
      for the first time, the extent of cytosine methylation of bacterial DNA
      at single-base resolution. Whereas most target sites (C(m)CWGG) are
      fully methylated in stationary phase cells, many sites with an extended
      CC(m)CWGG motif are only partially methylated in exponentially growing
      cells. We speculate that these partially methylated sites may be
      selected, as these are slightly correlated with the risk of
      spontaneous, non-synonymous conversion of methylated cytosines to
      thymines. Microarray analysis in a cytosine methylation-deficient
      mutant of E. coli shows increased expression of the stress response
      sigma factor RpoS and many of its targets in stationary phase. Thus,
      DNA cytosine methylation is a regulator of stationary phase gene
      expression in E. coli.
AU  - Kahramanoglou C
AU  - Prieto AI
AU  - Khedkar S
AU  - Haase B
AU  - Gupta A
AU  - Benes V
AU  - Fraser GM
AU  - Luscombe NM
AU  - Seshasayee ASN
PT  - Journal Article
TA  - Nat. Commun.
JT  - Nat. Commun.
SO  - Nat. Commun. 2012 3: 886.

PMID- 25977436
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Two Clinical Isolates of Mycobacterium tuberculosis from Sputum of Kazakh Patients.
PG  - e00466-15
AB  - Here, we report the draft genome sequences of two clinical isolates of Mycobacterium
      tuberculosis (MTB-476 and MTB-489) isolated from sputum of Kazakh
      patients.
AU  - Kairov U
AU  - Kozhamkulov U
AU  - Molkenov A
AU  - Rakhimova S
AU  - Askapuli A
AU  - Zhabagin M
AU  - Akhmetova A
AU  - Yerezhepov D
AU  - Abilova Z
AU  - Abilmazhinova A
AU  - Bismilda V
AU  - Chingisova L
AU  - Zhumadilov Z
AU  - Akilzhanova A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00466-15.

PMID- 25359916
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Rhizobium rhizogenes Strain ATCC 15834.
PG  - e01108-14
AB  - Here, we present the draft genome of Rhizobium rhizogenes strain ATCC 15834. The  genome
      contains 7,070,307 bp in 43 scaffolds. R. rhizogenes, also known as
      Agrobacterium rhizogenes, is a plant pathogen that causes hairy root disease.
      This hairy root induction has been used in biotechnology for the generation of
      transgenic root cultures.
AU  - Kajala K
AU  - Coil DA
AU  - Brady SM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01108-14.

PMID- 1368599
VI  - 54
DP  - 1990
TI  - Isolation of restriction-reduced mutants from Streptomyces.
PG  - 2611-2617
AB  - Restriction-reduced mutants were isolated from Streptomyces rosa subsp.
      notoensis KA301 and S. tanashiensis strain Kala which produce the
      benzoisochromanequinone antibiotics nanaomycin and kalafungin, respectively.
      The mutants of S. rosa, which can be transformed with a multi-copy plasmid and
      in which the actinophage Pa16 can propagate, were selected.  They were
      transformed with a single-copy plasmid propagated in S. lividans TK24, and with
      its modified plasmid propagated in the mutant at higher efficiency.  The
      mutants of S. tanashiensis were selected by their capability to be transformed
      with a multi-copy plasmid.  The efficiency of transformation with a single-copy
      plasmid propagated in S. lividans TK24 was low, but was much increased by
      heating the protoplasts at 42C for 15 min prior to the transformation.  These
      mutants derived from both strains probably lack at least one of their
      restriction systems.
AU  - Kakinuma S
AU  - Ikeda H
AU  - Tanaka H
AU  - Omura S
PT  - Journal Article
TA  - Agric. Biol. Chem.
JT  - Agric. Biol. Chem.
SO  - Agric. Biol. Chem. 1990 54: 2611-2617.

PMID- 25291766
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of 'Candidatus Phytoplasma asteris' Strain OY-V, an Unculturable Plant-Pathogenic Bacterium.
PG  - e00944-14
AB  - Phytoplasmas are unculturable plant-pathogenic bacteria causing devastating damage to
      agricultural production worldwide. Here, we report the draft genome
      sequence of 'Candidatus Phytoplasma asteris' strain OY-V. Most of the known
      virulence factors and host-interacting proteins were conserved in OY-V. This
      genome furthers our understanding of genetic diversity and pathogenicity of
      phytoplasmas.
AU  - Kakizawa S
AU  - Makino A
AU  - Ishii Y
AU  - Tamaki H
AU  - Kamagata Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00944-14.

PMID- 7870578
VI  - 23
DP  - 1995
TI  - Characterization of an Arabidopsis thaliana DNA hypomethylation mutant.
PG  - 130-137
AB  - We have recently isolated two Arabidopsis thaliana DNA hypomethylation mutations, identifying
      the DDM1 locus, that cause a 70% reduction in genomic 5-methylcytosine levels. Here we
      describe further phenotypic and biochemical characterization of the ddm1 mutants. ddm1/ddm1
      homozygotes exhibited altered leaf shape, increased cauline leaf number, and a delay in the
      onset of flowering when compared to non-mutant siblings in a segregating population. Our
      biochemical characterization investigated two possible mechanisms for DNA hypomethylation. In
      order to see if ddm1 mutations affect DNA methyltransferase function, we compared DNA
      methyltransferase activities in extracts from wild-type for both the CpI and CpNpG substrates
      suggesting that the DDM1 locus does not encode a DNA methyltransferase. Moreover, the ddm1
      mutations did not affect the intracellular level of S-adenosylmethionine, the methyl group
      donor for DNA methylation. The possibility that the DDM1 gene product functions as a modifier
      of DNA methylation is discussed.
AU  - Kakutani T
AU  - Jeddeloh JA
AU  - Richards EJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1995 23: 130-137.

PMID- 21685297
VI  - 193
DP  - 2011
TI  - Draft Genome Sequence of the Thermoalkaliphilic Caldalkalibacillus thermarum Strain TA2.A1.
PG  - 4290-4291
AB  - The genes and molecular machines that allow for a thermoalkaliphilic lifestyle have not been
      defined. To address this goal, we report on the
      improved high-quality draft genome sequence of Caldalkalibacillus
      thermarum strain TA2.A1, an obligately aerobic bacterium that grows
      optimally at pH 9.5 and 65 to 70 degrees C on a wide variety of carbon and
      energy sources.
AU  - Kalamorz F et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4290-4291.

PMID- 24625868
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Vibrio parahaemolyticus Environmental Strain UCM-V493.
PG  - e00159-14
AB  - Vibrio parahaemolyticus is the leading bacterial cause of seafood-related gastroenteritis in
      the world. Here, we report the complete genome sequence and
      annotation of an environmental strain of V. parahaemolyticus, UCM-V493, with the
      aim of understanding the differences between the clinical and environmental
      isolates of the bacteria. We also make some preliminary sequence comparisons with
      the clinical strain RIMD2210633.
AU  - Kalburge SS
AU  - Polson SW
AU  - Boyd CK
AU  - Katz L
AU  - Turnsek M
AU  - Tarr CL
AU  - Martinez-Urtaza J
AU  - Boyd EF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00159-14.

PMID- 28963220
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Salmonella enterica Isolates Containing Incompatibility Group I1 Plasmids from Swine, Poultry, and Human Sources.
PG  - e01056-17
AB  - The draft genome sequences of eight Salmonella enterica isolates from various sources were
      evaluated for the influence of incompatibility group I1 (IncI1)
      plasmids on virulence. Strains SE142, SE143, SE144, and SE146 originated from
      swine, SE36N and SE89N from poultry-related sources, and SE991 and SE1148 from
      human patients.
AU  - Kaldhone PR
AU  - Khajanchi BK
AU  - Han J
AU  - Nayak R
AU  - Ricke SC
AU  - Foley SL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01056-17.

PMID- 19880644
VI  - 76
DP  - 2010
TI  - Crucial Role for Insertion Sequence Elements in Lactobacillus helveticus Evolution as Revealed by Interstrain Genomic Comparison.
PG  - 212-220
AB  - Lactobacillus helveticus is a versatile dairy bacterium found to possess heterogeneous
      genotypes depending on the ecosystem from which
      it was isolated. The recently published genome sequence showed the
      remarkable flexibility of its structure, demonstrated by a substantial
      level of insertion sequence (IS) element expansion in association with
      massive gene decay. To assess this diversity and examine the level of
      genome plasticity within the L. helveticus species, an array-based
      comparative genome hybridization (aCGH) experiment was designed in
      which 10 strains were analyzed. The aCGH experiment revealed 16
      clusters of open reading frames (ORFs) flanked by IS elements. Four of
      these ORFs are associated with restriction/modification which may have
      played a role in accelerated evolution of strains in a commercially
      intensive ecosystem undoubtedly challenged through successive phage
      attack. Furthermore, analysis of the IS-flanked clusters demonstrated
      that the most frequently encountered ISs were also those most abundant
      in the genome (IS1201, ISL2, ISLhe1, ISLhe2, ISLhe65, and ISLhe63).
      These findings contribute to the overall viewpoint of the versatile
      character of IS elements and the role they may play in bacterial genome
      plasticity.
AU  - Kaleta P
AU  - O'Callaghan J
AU  - Fitzgerald GF
AU  - Beresford TP
AU  - Ross RP
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2010 76: 212-220.

PMID- 21693016
VI  - 12
DP  - 2011
TI  - Comparative genome analysis and genome-guided physiological analysis of Roseobacter litoralis.
PG  - 324
AB  - ABSTRACT: BACKGROUND: Roseobacter litoralis OCh149, the type species of
      the genus, and Roseobacter denitrificans OCh114 were the first described
      organisms of the Roseobacter clade, an ecologically important group of
      marine bacteria. Both species were isolated from seaweed and are able to
      perform aerobic anoxygenic photosynthesis. RESULTS: The genome of R.
      litoralis OCh149 contains one circular chromosome of 4,505,211 bp and
      three plasmids of 93,578 bp (pRLO149_94), 83,129 bp (pRLO149_83) and
      63,532 bp (pRLO149_63). Of the 4537 genes predicted for R. litoralis, 1122
      (24.7%) are not present in the genome of R. denitrificans. Many of the
      unique genes of R. litoralis are located in genomic islands and on
      plasmids. On pRLO149_83 several potential heavy metal resistance genes are
      encoded which are not present in the genome of R. denitrificans. The
      comparison of the heavy metal tolerance of the two organisms showed an
      increased zinc tolerance of R. litoralis. In contrast to R. denitrificans,
      the photosynthesis genes of R. litoralis are plasmid encoded. The activity
      of the photosynthetic apparatus was confirmed by respiration rate
      measurements, indicating a growth-phase dependent response to light.
      Comparative genomics with other members of the Roseobacter clade revealed
      several genomic regions that were only conserved in the two Roseobacter
      species. One of those regions encodes a variety of genes that might play a
      role in host association of the organisms. The catabolism of different
      carbon and nitrogen sources was predicted from the genome and combined
      with experimental data. In several cases, e.g. the degradation of some
      algal osmolytes and sugars, the genome-derived predictions of the
      metabolic pathways in R. litoralis differed from the phenotype.
      CONCLUSIONS: The genomic differences between the two Roseobacter species
      are mainly due to lateral gene transfer and genomic rearrangements.
      Plasmid pRLO149_83 contains predominantly recently acquired genetic
      material whereas pRLO149_94 was probably translocated from the chromosome.
      Plasmid pRLO149_63 and one plasmid of R. denitrifcans (pTB2) seem to have
      a common ancestor and are important for cell envelope biosynthesis.
      Several new mechanisms of substrate degradation were indicated from the
      combination of experimental and genomic data. The photosynthetic activity
      of R. litoralis is probably regulated by nutrient availability.
AU  - Kalhoefer D
AU  - Thole S
AU  - Voget S
AU  - Lehmann R
AU  - Liesegang H
AU  - Wollher A
AU  - Daniel R
AU  - Simon M
AU  - Brinkhoff T
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2011 12: 324.

PMID- 3250843
VI  - 303
DP  - 1988
TI  - Cloning and study of the structural organization of the region of inh(lip)-hoc genes of T4 bacteriophage.
PG  - 1486-1489
AB  - The cells infected with T-even bacteriophages have been demonstrated to carry early and late
      phage-specific mRNA.  It has been established that the early genes are transcribed from the
      l-strand of DNA in anticlockwise direction, whereas the late genes are transcribed clockwise
      in the r-strand of DNA in the genetic map of T4 phage.  A major part of late T4 phage genes is
      located between genes 2 and 54, but the chromosomal segment between genes 24 and 25 contains,
      besides the late genes inh and hoc, early (medium) genes uvsY and uvsW(dar).  The inh(lip)
      codes for the inhibitor of proteinase, the product of gene 21.  This inhibitor, either in its
      natural form or after modification with the help of genetic engineering techniques, is
      particularly interesting for studying the mechanism of protein processing and for its possible
      use in biotechnology analogous to the product of pin gene of T4 phage.  Gene hoc is promising
      for making highly antigenic proteinous structures, which would be discussed below.
AU  - Kaliman AV
AU  - Khasanova MA
AU  - Kryukov VM
AU  - Tanyashin VI
AU  - Baev AA
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1988 303: 1486-1489.

PMID- 2377482
VI  - 18
DP  - 1990
TI  - The  nucleotide sequence of the region of bacteriophage T4 inh(lip)-hoc genes.
PG  - 4277
AB  - 
AU  - Kaliman AV
AU  - Khasanova MA
AU  - Kryukov VM
AU  - Tanyashin VI
AU  - Bayev AA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 4277.

PMID- 28475781
VI  - 64
DP  - 2017
TI  - 2015 Epidemic of Severe Streptococcus agalactiae Sequence Type 283 Infections in Singapore Associated With the Consumption of Raw Freshwater Fish: A Detailed Analysis of Clinical, Epidemiological, and Bacterial Sequencing Data.
PG  - S145-S152
AB  - Background: Streptococcus agalactiae (group B Streptococcus [GBS]) has not been
      described as a foodborne pathogen. However, in 2015, a large outbreak of severe
      invasive sequence type (ST) 283 GBS infections in adults epidemiologically linked
      to the consumption of raw freshwater fish occurred in Singapore. We attempted to
      determine the scale of the outbreak, define the clinical spectrum of disease, and
      link the outbreak to contaminated fish. Methods: Time-series analysis was
      performed on microbiology laboratory data. Food handlers and fishmongers were
      screened for enteric carriage of GBS. A retrospective cohort study was conducted
      to assess differences in demographic and clinical characteristics of patients
      with invasive ST283 and non-ST283 infections. Whole-genome sequencing was
      performed on human and fish ST283 isolates from Singapore, Thailand, and Hong
      Kong. Results: The outbreak was estimated to have started in late January 2015.
      Within the study cohort of 408 patients, ST283 accounted for 35.8% of cases.
      Patients with ST283 infection were younger and had fewer comorbidities but were
      more likely to develop meningoencephalitis, septic arthritis, and spinal
      infection. Of 82 food handlers and fishmongers screened, none carried ST283.
      Culture of 43 fish samples yielded 13 ST283-positive samples. Phylogenomic
      analysis of 161 ST283 isolates from humans and fish revealed they formed a tight
      clade distinguished by 93 single-nucleotide polymorphisms. Conclusions: ST283 is
      a zoonotic GBS clone associated with farmed freshwater fish, capable of causing
      severe disease in humans. It caused a large foodborne outbreak in Singapore and
      poses both a regional and potentially more widespread threat.
AU  - Kalimuddin S
AU  - Chen SL
AU  - Lim CTK
AU  - Koh TH
AU  - Tan TY
AU  - Kam M
AU  - Wong CW
AU  - Mehershahi KS
AU  - Chau ML
AU  - Ng LC
AU  - Tang WY
AU  - Badaruddin H
AU  - Teo J
AU  - Apisarnthanarak A
AU  - Suwantarat N
AU  - Ip M
AU  - Holden MTG
AU  - Hsu LY
AU  - Barkham T
PT  - Journal Article
TA  - Clin. Infect. Dis.
JT  - Clin. Infect. Dis.
SO  - Clin. Infect. Dis. 2017 64: S145-S152.

PMID- 3025698
VI  - 0
DP  - 1986
TI  - Isolation of HindIII isoschizomeric restriction endonuclease from Bordetella bronchiseptica.
PG  - 16-19
AB  - Site-specific restriction endonuclease BbrI has been found in bacteriophage resistant strain
      B. bronchioseptica 4994.  The technique was elaborated for purification of BbrI to the stage
      free of nuclease and phosphatase contamination.  The yield of purified enzyme is 6000-20,000
      units per 10 g of biomass.  BbrI recognises and cleaves the same DNA sequence as HindIII with
      the formation of four-nucleotide cohesive ends.  The simplicity of cultivation, security for
      human, presence of the single restriction endonuclease and the high level of tis production
      make B. bronchioseptica 4994 a promising producer of BbrI restriction endonuclease,
      isoschizomeric to HindIII, for use in experimental practice and in industry.
AU  - Kalinin VN
AU  - Lapaeva IA
AU  - Lunin VG
AU  - Skripkin EA
AU  - Smirnov VD
AU  - Tikchonenko TI
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1986 0: 16-19.

PMID- 12948626
VI  - 104
DP  - 2003
TI  - The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins.
PG  - 5-25
AB  - The complete genomic sequence of Corynebacterium glutamicum ATCC 13032, well-known in industry
      for the production of amino acids, e.g. of
      L-glutamate and L-lysine was determined. The C. glutamicum genome was
      found to consist of a single circular chromosome comprising 3282708 base
      pairs. Several DNA regions of unusual composition were identified that
      were potentially acquired by horizontal gene transfer, e.g. a segment of
      DNA from C. diphtheriae and a prophage-containing region. After automated
      and manual annotation, 3002 protein-coding genes have been identified, and
      to 2489 of these, functions were assigned by homologies to known proteins.
      These analyses confirm the taxonomic position of C. glutamicum as related
      to Mycobacteria and show a broad metabolic diversity as expected for a
      bacterium living in the soil. As an example for biotechnological
      application the complete genome sequence was used to reconstruct the
      metabolic flow of carbon into a number of industrially important products
      derived from the amino acid L-aspartate.
AU  - Kalinowski J et al
PT  - Journal Article
TA  - J. Biotechnol.
JT  - J. Biotechnol.
SO  - J. Biotechnol. 2003 104: 5-25.

PMID- 26272557
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Phytopathogenic Pectobacterium atrosepticum Bacteriophage Peat1.
PG  - e00760-15
AB  - Pectobacterium atrosepticum is a common phytopathogen causing significant economic losses
      worldwide. To develop a biocontrol strategy for this blackleg
      pathogen of solanaceous plants, P. atrosepticum bacteriophage Peat1 was isolated
      and its genome completely sequenced. Interestingly, morphological and sequence
      analyses of the 45,633-bp genome revealed that phage Peat1 is a member of the
      family Podoviridae and most closely resembles the Klebsiella pneumoniae
      bacteriophage KP34. This is the first published complete genome sequence of a
      phytopathogenic P. atrosepticum bacteriophage, and details provide important
      information for the development of biocontrol by advancing our understanding of
      phage-phytopathogen interactions.
AU  - Kalischuk M
AU  - Hachey J
AU  - Kawchuk L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00760-15.

PMID- 21677849
VI  - 4
DP  - 2011
TI  - Complete genome sequence of Arthrobacter phenanthrenivorans type strain (Sphe3).
PG  - 123-130
AB  - Arthrobacter phenanthrenivorans is the type species of the genus, and is able to  metabolize
      phenanthrene as a sole source of carbon and energy. A.
      phenanthrenivorans is an aerobic, non-motile, and Gram-positive bacterium,
      exhibiting a rod-coccus growth cycle which was originally isolated from a
      creosote polluted site in Epirus, Greece. Here we describe the features of this
      organism, together with the complete genome sequence, and annotation.
AU  - Kallimanis A et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 4: 123-130.

PMID- 22180818
VI  - 5
DP  - 2011
TI  - Complete genome sequence of Mycobacterium sp. strain (Spyr1) and reclassification to Mycobacterium gilvum Spyr1.
PG  - 144-153
AB  - Mycobacterium sp.Spyr1 is a newly isolated strain that occurs in a creosote contaminated site
      in Greece. It was isolated by an enrichment method using pyrene
      as sole carbon and energy source and is capable of degrading a wide range of PAH
      substrates including pyrene, fluoranthene, fluorene, anthracene and acenapthene.
      Here we describe the genomic features of this organism, together with the
      complete sequence and annotation. The genome consists of a 5,547,747 bp
      chromosome and two plasmids, a larger and a smaller one with sizes of 211,864 and
      23,681 bp, respectively. In total, 5,588 genes were predicted and annotated.
AU  - Kallimanis A
AU  - Karabika E
AU  - Mavromatis K
AU  - Lapidus A
AU  - Labutti KM
AU  - Liolios K
AU  - Ivanova N
AU  - Goodwin L
AU  - Woyke T
AU  - Velentzas AD
AU  - Perisynakis A
AU  - Ouzounis CC
AU  - Kyrpides NC
AU  - Koukkou AI
AU  - Drainas C
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 5: 144-153.

PMID- 10192388
VI  - 21
DP  - 1999
TI  - Comparative genomes of Chlamydia pneumoniae and C. trachomatis.
PG  - 385-389
AB  - Chlamydia are obligate intracellular eubacteria that are phylogenetically separated from other
      bacterial divisions. C. trachomatis and C. pneumoniae are both pathogens of humans but differ
      in their tissue tropism and spectrum of diseases. C. pneumoniae is a newly recognized species
      of Chlamydia that is a natural pathogen of humans, and causes pneumonia and bronchitis. In the
      United States, approximately 10% of pneumonia cases and 5% of bronchitis cases are attributed
      to C. pneumoniae infection. Chronic disease may result following respiratory-acquired
      infection, such as reactive airway disease, adult-onset asthma and potentially lung cancer. In
      addition, C. pneumoniae infection has been associated with atherosclerosis. C. trachomatis
      infection causes trachoma, an ocular infection that leads to blindness, and sexually
      transmitted diseases such as pelvic inflammatory disease, chronic pelvic pain, ectopic
      pregnancy and epididymitis.  Although relatively little is known about C. trachomatis biology,
      even less is known concerning C. pneumoniae. Comparison of the C. pneumoniae genome with the
      C. trachomatis genome will provide an understanding of the common biological processes
      required for infection and survival in mammalian cells.  Genomic differences are implicated in
      the unique properties that differentiate the two species in disease spectrum. Analysis of the
      1,230,230-nt C. pneumoniae genome revealed 214 protein-coding sequences not found in C.
      trachomatis, most without homologues to other known sequences. Prominent comparative findings
      include  expansion of a novel family of 21 sequence-variant outer-membrane proteins,
      conservation of a type-III secretion virulence system, three serine/threonine protein kinases
      and a pair of  parologous phospholipase-D-like proteins, additional purine and biotin
      biosynthetic capability, a homologue for aromatic amino acid (tryptophan) hydroxylase and the
      loss of tryptophan biosynthesis genes.
AU  - Kalman S
AU  - Mitchell W
AU  - Marathe R
AU  - Lammel C
AU  - Fan J
AU  - Hyman RW
AU  - Olinger L
AU  - Grimwood J
AU  - Davis RW
AU  - Stephens RS
PT  - Journal Article
TA  - Nat. Genet.
JT  - Nat. Genet.
SO  - Nat. Genet. 1999 21: 385-389.

PMID- 5557802
VI  - 10
DP  - 1971
TI  - Glutathione-catalyzed hydrogen isotope exchange at position 5 of uridine.  A model for enzymic carbon alkylation reactions of pyrimidines.
PG  - 2567-2573
AB  - The effect of glutathione on the exchange of hydrogen to deuterium at
      position 5 of uridine
      was studied by using proton magnetic resonance spectroscopy.  It was found that in D2O
      solutions, at
      80o, the rate of H-isotope exchange was enhanced in the presence of GSH and that the
      enhancement of
      the pseudo-first-order rate of exchange was proportional to the GSH concentration.  The
      results obtained
      with GSH derivatives indicated the requirement of a free SH group for catalysis.  The
      GSH-catalyzed H-
      isotope exchange showed a bell-shaped dependence on the OD- ion concentration,
      suggesting that in
      the rate-determining step the ionized SH group of GSH reacts with the nonionized species
      of Urd.
      Ionization of Urd causes a substantial shielding of the proton at position 6, indicating the
      increased
      electron density of the 5,6-double bond, which may account for the lack of reactivity
      observed at high pD
      values.  The results are consistent with a catalytic mechanism of H-isotope exchange
      involving the
      reversible addition elimination of the SH group of GSH across the 5,6-double bond of
      Urd.  The
      relevance of these findings to the mechanism of enzyme-catalyzed C-alkylation reactions of
      pyrimidine
      nucleotides is discussed.
AU  - Kalman TI
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1971 10: 2567-2573.

PMID- 1727392
VI  - 6
DP  - 1992
TI  - Characterization of overexpressed BamHII methylase.
PG  - A217
AB  - Both M.BamHI and M.BamHII recognize the palindromic sequence, 5'-GGATCC-3', and
      catalyze the transfer of a methyl group from S-adenosylmethionine to the
      internal cytosine within the recognition sequence.  Both enzymes have been
      cloned, sequenced and expressed in E. coli.  These two methylases utilize an
      unusual UUG initiation codon and are expressed at limited levels.  We wish to
      report increased expression by changing the initiation codon to AUG using the
      site-directed mutagenesis.  Mutants were subcloned into various expression
      vectors (pSP64, pKK223-3, pPL-Lambda and Pet-11) and sequenced via double
      stranded dideoxy sequencing.  These constructs were transformed into the
      appropriate host and protein production was assayed by SDS-PAGE.  Constructs
      yielding the highest amount of intact protein were selected for subsequent
      purification procedures.  M.BamHI (in pSP64) was purified to apparent
      homogeneity from SURE cells by sequential chromatography using
      Phosphocellulose, Phenyl Sepharose and G-150 as previously cited, (Vanek, P.G.,
      Ph.D. Thesis, Georgetown University, 1991).  M.BamHII (in Pet-11) was purified
      to apparent homogeneity from BL21DE3(pLysS) by sequential chromatography using
      Phosphocellulose, Heparin Sepharose, Blue Sepharose and G-50.  The BamHII
      methylase has an approximate Mw of 32 Kd as predicted from sequence analysis
      and confirmed by SDS-PAGE analysis of the purified protein.  This low Mw
      confers a unique advantage for further biochemical and structural studies.  To
      date, the BamHII methylase has been partially characterized and further
      biochemical and biophysical studies, including crystallization, are in
      progress.
AU  - Kaloss WD
AU  - Connaughton JF
AU  - Vanek PG
AU  - Chirikijan JG
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1992 6: A217.

PMID- Not included in PubMed...
VI  - 61
DP  - 1992
TI  - Characterization of overexpressed BamHII methylase.
PG  - A217
AB  - Both M.BamHI and M.BamHII recognize the palindromic sequence, 5'-GGATCC-3', and
      catalyze the transfer of a methyl group from S-adenosylmethionine to the
      internal cytosine within the recognition sequence.  Both enzymes have been
      cloned, sequenced and expressed in E. coli.  These two methylases utilize an
      unusual UUG initiation codon and are expressed at limited levels.  We wish to
      report increased expression by changing the initiation codon to AUG using the
      site-directed mutagenesis.  Mutants were subcloned into various expression
      vectors (pSP64, pKK223-3, pPL-Lambda and Pet-11) and sequenced via double
      stranded dideoxy sequencing.  These constructs were transformed into the
      appropriate host and protein production was assayed by SDS-PAGE.  Constructs
      yielding the highest amount of intact protein were selected for subsequent
      purification procedures.  M.BamHI (in pSP64) was purified to apparent
      homogeneity from SURE cells by sequential chromatography using
      Phosphocellulose, Phenyl Sepharose and G-150 as previously cited, (Vanek, P.G.,
      Ph.D. Thesis, Georgetown University, 1991).  M.BamHII (in Pet-11) was purified
      to apparent homogeneity from BL21DE3(pLysS) by sequential chromatography using
      Phosphocellulose, Heparin Sepharose, Blue Sepharose and G-50.  The BamHII
      methylase has an approximate Mw of 32 kd as predicted from sequence analysis
      and confirmed by SDS-PAGE analysis of the purified protein.  This low Mw
      confers a unique advantage for further biochemical and structural studies.  To
      date, the BamHII methylase has been partially characterized and further
      biochemical and biophysical studies, including crystallization, are in
      progress.
AU  - Kaloss WD
AU  - Connaughton JF
AU  - Vanek PG
AU  - Chirikjian JC
PT  - Journal Article
TA  - Biophys. J.
JT  - Biophys. J.
SO  - Biophys. J. 1992 61: A217.

PMID- 8651960
VI  - 22
DP  - 1996
TI  - Bsp153AI and BspM39I - New isoschizomers of restriction endonuclease PvuII.
PG  - 108-110
AB  - New restriction endonucleases, Bsp153AI and BspM39I, were isolated from
      Bacillus species strains 153A and M39, respectively.  The enzymes recognize and cleave the
      nucleotide sequence (5')CAG|CTG / (3')GTC|GAC and are true isoschizomers of restriction
      endonuclease PvuII.
AU  - Kalugin AA
AU  - Rina M
AU  - Eldarov MA
AU  - Markaki M
AU  - Korolev SV
AU  - Samko OT
AU  - Khoroshutina EB
AU  - Sikolov NN
AU  - Bouriotis V
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1996 22: 108-110.

PMID- 25767239
VI  - 3
DP  - 2015
TI  - Draft genome sequences of gammaproteobacterial methanotrophs isolated from lake washington sediment.
PG  - e00103-15
AB  - The genomes of Methylosarcina lacus LW14(T) (=ATCC BAA-1047(T) = JCM 13284(T)), Methylobacter
      sp. strain 21/22, Methylobacter sp. strain 31/32, Methylomonas sp.
      strain LW13, Methylomonas sp. strain MK1, and Methylomonas sp. strain 11b were
      sequenced and are reported here. All the strains are obligately methanotrophic
      bacteria isolated from the sediment of Lake Washington.
AU  - Kalyuzhnaya MG
AU  - Lamb AE
AU  - McTaggart TL
AU  - Oshkin IY
AU  - Shapiro N
AU  - Woyke T
AU  - Chistoserdova L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00103-15.

PMID- 17159199
VI  - 152
DP  - 2006
TI  - Plasmid pBP136 from Bordetella pertussis represents an ancestral form of IncP-1beta plasmids without accessory mobile elements.
PG  - 3477-3484
AB  - The complete 41 268 bp nucleotide sequence of the IncP-1beta plasmid pBP136 from the human
      pathogen Bordetella pertussis, the primary aetiological agent of whooping cough, was
      determined and analysed. This plasmid carried a total of 46 ORFs: 44 ORFs corresponding to the
      genes in the conserved IncP-1beta backbone, and 2 ORFs similar to the XF1596 and XF1597 genes
      with unknown function of the plant pathogen Xylella fastidiosa. Interestingly, pBP136 had no
      accessory genes carrying genetic traits such as antibiotic or mercury resistance and/or
      xenobiotic degradation. Moreover, pBP136 had only two of the kle genes (kleAE) that have been
      reported to be important for the stability of IncP-1 plasmid in Pseudomonas aeruginosa.
      Phylogenetic analysis of the Kle proteins revealed that the KleA and KleE of pBP136 were
      phylogenetically distant from those of the present IncP-1 plasmids. In contrast, IncC1 and
      KorC, encoded upstream and downstream of the kle genes respectively, and the
      replication-initiation protein, TrfA, were closely related to those of the IncP-1beta 'R751
      group'. These results suggest that (i) pBP136 without any apparent accessory genes diverged
      early from an ancestor of the present IncP-1beta plasmids, especially those of the R751 group,
      and (ii) the kle genes might be incorporated independently into the backbone region of the
      IncP-1 plasmids for their stable maintenance in various host cells.
AU  - Kamachi K
AU  - Sota M
AU  - Tamai Y
AU  - Nagata N
AU  - Konda T
AU  - Inoue T
AU  - Top EM
AU  - Arakawa Y
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2006 152: 3477-3484.

PMID- 25908147
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Erythromycin-Resistant Streptococcus gallolyticus subsp. gallolyticus NTS 31106099 Isolated from a Patient with Infective Endocarditis and  Colorectal Cancer.
PG  - e00370-15
AB  - Streptococcus gallolyticus subsp. gallolyticus is known for its close association with
      infective endocarditis and colorectal cancer in humans. Here, we report the
      draft genome sequence of highly erythromycin-resistant strain NTS 31106099
      isolated from a patient with infective endocarditis and colorectal cancer.
AU  - Kambarev S
AU  - Cate C
AU  - Corvec S
AU  - Pecorari F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00370-15.

PMID- 28450515
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Mycobacterium ulcerans S4018 Isolated from a Patient with an Active Buruli Ulcer in Benin, Africa.
PG  - e00248-17
AB  - Currently, there are only two publicly available genomes of Mycobacterium ulcerans-the
      causative agent of the neglected, but devastating, tropical disease
      Buruli ulcer. Here, we report the draft genome sequence of isolate S4018,
      recovered from an active cutaneous lesion of a patient with Buruli ulcer in
      Benin, Africa.
AU  - Kambarev S
AU  - Corvec S
AU  - Chauty A
AU  - Marion E
AU  - Marsollier L
AU  - Pecorari F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00248-17.

PMID- 28428309
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Two Highly Erythromycin-Resistant Streptococcus gallolyticus subsp. gallolyticus Isolates Containing a Novel Tn916-Like Element,   Tn6331.
PG  - e00226-17
AB  - Recently, we reported the draft genome sequence of Streptococcus gallolyticus NTS31106099. It
      was found to contain a previously unknown putative Tn916-like
      conjugative transposon, Tn6263 Here, we report the draft genome sequences of two
      other clinical isolates, NTS31301958 and NTS31307655. Both of them contain
      another novel element, Tn6331, which is highly similar to Tn6263.
AU  - Kambarev S
AU  - Pecorari F
AU  - Corvec S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00226-17.

PMID- 18977197
VI  - 377
DP  - 2008
TI  - Cyclin-dependent kinase-like 5 binds and phosphorylates DNA methyltransferase 1.
PG  - 1162-1167
AB  - DNA methyltransferase 1 (Dnmt1) is an enzyme that recognizes and methylates hemimethylated CpG
      after DNA replication to maintain methylation patterns. Although the N-terminal region of
      Dnmt1 isknown to interact with various proteins, such as methyl-CpG-binding protein 2 (MeCP2),
      the associationsof protein kinases with this region have not been reported. In the present
      study, we found that a 110-kDaprotein kinase in mouse brain could bind to the N-terminal
      domain of Dnmt1. This 110-kDa kinase was
      identified as cyclin-dependent kinase-like 5 (CDKL5) by LC-MS/MS analysis. CDKL5 and Dnmt1
      werefound to colocalize in nuclei and appeared to interact with each other. Catalytically
      active CDKL5,CDKL5(1-352), phosphorylated the N-terminal region of Dnmt1 in the presence of
      DNA. Considering thatdefects in the MeCP2 or CDKL5 genes cause Rett syndrome, we propose that
      the interaction betweenDnmt1 and CDKL5 may contribute to the pathogenic processes of Rett
      syndrome.
AU  - Kameshita I
AU  - Sekiguchi M
AU  - Hamasaki D
AU  - Sugiyama Y
AU  - Hatano N
AU  - Suetake I
AU  - Tajima S
AU  - Sueyoshi N
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 2008 377: 1162-1167.

PMID- 29439054
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Acidithiobacillus sp. Strain SH, a Marine Acidophilic Sulfur-Oxidizing Bacterium.
PG  - e01603-17
AB  - We announce here the genome sequence of a marine acidophilic sulfur-oxidizing bacterium,
      Acidithiobacillus sp. strain SH. The bacterium has potential for use
      in bioleaching of sulfide ores from seawater and contains a noble gene for
      thiosulfate quinone oxidoreductase in addition to specific genes for the
      oxidation of reduced inorganic sulfur compounds.
AU  - Kamimura K
AU  - Sharmin S
AU  - Yoshino E
AU  - Tokuhisa M
AU  - Kanao T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01603-17.

PMID- 19014591
VI  - 8
DP  - 2008
TI  - Type II restriction endonuclease R.Hpy188I belongs to the GIY-YIG nuclease superfamily, but exhibits an unusual active site.
PG  - 48
AB  - Background: Catalytic domains of Type II restriction endonucleases (REases) belong to a few
      unrelated three-dimensional folds. While the
      PD-(D/E)XK fold is most common among these enzymes, crystal structures
      have been also determined for single representatives of two other
      folds: PLD (R. Bfil) and half-pipe (R. Pabl). Bioinformatics analyses
      supported by mutagenesis experiments suggested that some REases belong
      to the HNH fold (e. g. R. KpnI), and that a small group represented by
      R. Eco29kl belongs to the GIY-YIG fold. However, for a large fraction
      of REases with known sequences, the three-dimensional fold and the
      architecture of the active site remain unknown, mostly due to extreme
      sequence divergence that hampers detection of homology to enzymes with
      known folds.
      Results: R.Hpy188I is a Type II REase with unknown structure.
      PSI-BLAST searches of the non-redundant protein sequence database
      reveal only 1 homolog (R. HpyF17I, with nearly identical amino acid
      sequence and the same DNA sequence specificity). Standard application
      of state-of-the-art protein fold-recognition methods failed to predict
      the relationship of R. Hpy188I to proteins with known structure or to
      other protein families. In order to increase the amount of evolutionary
      information in the multiple sequence alignment, we have expanded our
      sequence database searches to include sequences from metagenomics
      projects. This search resulted in identification of 23 further members
      of R. Hpy188I family, both from metagenomics and the non-redundant
      database. Moreover, fold-recognition analysis of the extended R.
      Hpy188I family revealed its relationship to the GIY-YIG domain and
      allowed for computational modeling of the R. Hpy188I structure.
      Analysis of the R. Hpy188I model in the light of sequence conservation
      among its homologs revealed an unusual variant of the active site, in
      which the typical Tyr residue of the YIG half-motif had been
      substituted by a Lys residue. Moreover, some of its homologs have the
      otherwise invariant Arg residue in a non-homologous position in
      sequence that nonetheless allows for spatial conservation of the
      guanidino group potentially involved in phosphate binding.
      Conclusion: The present study eliminates a significant "white spot"
      on the structural map of REases. It also provides important insight
      into sequence-structure-function relationships in the GIY-YIG nuclease
      superfamily. Our results reveal that in the case of proteins with no or
      few detectable homologs in the standard "non-redundant" database, it is
      useful to expand this database by adding the metagenomic sequences,
      which may provide evolutionary linkage to detect more remote homologs.
AU  - Kaminska KH
AU  - Kawai M
AU  - Boniecki M
AU  - Kobayashi I
AU  - Bujnicki JM
PT  - Journal Article
TA  - BMC Struct. Biol.
JT  - BMC Struct. Biol.
SO  - BMC Struct. Biol. 2008 8: 48.

PMID- 28883138
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Type Strain Sphingopyxis witflariensis DSM 14551.
PG  - e00924-17
AB  - Here, we present the draft genome sequence of Sphingopyxis witflariensis strain DSM 14551. The
      assembly consists of 38 contigs and contains 4,306,761 bp, with a
      GC content of 63.3%.
AU  - Kaminski MA
AU  - Furmanczyk EM
AU  - Dziembowski A
AU  - Sobczak A
AU  - Lipinski L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00924-17.

PMID- 28912333
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Type Strain Sphingopyxis bauzanensis DSM 22271.
PG  - e01014-17
AB  - We present here the draft genome sequence of Sphingopyxis bauzanensis DSM 22271.  The assembly
      contains 4,258,005 bp in 28 scaffolds and has a GC content of 63.3%.
      A series of specific genes involved in the catabolism or transport of aromatic
      compounds was identified.
AU  - Kaminski MA
AU  - Furmanczyk EM
AU  - Dziembowski A
AU  - Sobczak A
AU  - Lipinski L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01014-17.

PMID- 23605040
VI  - 41
DP  - 2013
TI  - Massively parallel characterization of restriction endonucleases.
PG  - e119
AB  - Restriction endonucleases are highly specific in recognizing the particular DNA sequence they
      act on. However, their activity is affected by sequence context, enzyme concentration and
      buffer composition. Changes in these factors may lead to either ineffective cleavage at the
      cognate restriction site or relaxed specificity allowing cleavage of degenerate 'star'
      sites. Additionally, uncharacterized restriction endonucleases and engineered variants present
      novel activities. Traditionally, restriction endonuclease activity is assayed on simple
      substrates such as plasmids and synthesized oligonucleotides. We present and use
      high-throughput Illumina sequencing-based strategies to assay the sequence specificity and
      flanking sequence preference of restriction endonucleases. The techniques use fragmented DNA
      from sequenced genomes to quantify restriction endonuclease cleavage on a complex genomic DNA
      substrate in a single reaction. By mapping millions of restriction site-flanking reads back to
      the Escherichia coli and Drosophila melanogaster genomes we were able to quantitatively
      characterize the cognate and star site activity of EcoRI and MfeI and demonstrate genome-wide
      decreases in star activity with engineered high-fidelity variants EcoRI-HF and MfeI-HF, as
      well as quantify the influence on MfeI cleavage conferred by flanking nucleotides. The methods
      presented are readily applicable to all type II restriction endonucleases that cleave both
      strands of double-stranded DNA.
AU  - Kamps-Hughes N
AU  - Quimby A
AU  - Zhu Z
AU  - Johnson EA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2013 41: e119.

PMID- 381674
VI  - 130
DP  - 1979
TI  - The nucleotide sequence recognized by the Escherichia coli K12 restriction and modification enzymes.
PG  - 191-209
AB  - The sites recognized by the Escherichia coli K1 restriction endonuclease were
      localized to defined regions on the genomes of phage PhiXsK1, PhiXsK2, and G4
      by the marker rescue technique.  Methyl groups placed on the genome of plasmid
      pBR322 by the E.coli K12 modification methylase were mapped in HinfI fragments
      1 and 3, and HaeIII fragments 1 and 3.  A homology of seven nucleotides in the
      configuration: 5'-A-A-C . . 6N . . G-T-G-C-3', where 6N represents six
      unspecified nucleotides, was found among the DNA sequences containing the five
      EcoK sites of PhiXsK1, PhiXsK2, G4, and pBR322.  Three lines of evidence
      indicate that this sequence constitutes the recognition site of the E.coli K12
      restriction enzyme.  This sequence does not occur on PhiXam3cs70, simian virus
      40 (SV40), and fd DNAs which do not possess EcoK sites, and occurs only once on
      PhiXsK1, PhiXsK2, and G4 DNAs, and twice on pBR322 DNA.  In order to prove that
      all seven conserved nucleotides are essential for the recognition by the E.coli
      K12 restriction enzyme, the nucleotide sequences of PhiX174, G4, SV40, fd, and
      pBR322 were searched for sequences differing from the sequence 5'-A-A-C . . 6N
      . . G-T-G-C-3' at only one of the specified positions.  It was found that
      sequences differing at each of the specified positions occur on DNA sequences
      that do not contain the EcoK sites.  Thus, the recognition site of the E.coli
      K12 restriction enzyme has the same basic structure as that of the EcoB site
      (Lautenberger et al., 1978).  In each case there are two domains, one
      containing three and the other four specific nucleotides, separated by a
      sequence of unspecified bases.  However, the unspecified sequence in the EcoK
      site must be precisely six bases instead of the eight found in the EcoB site.
      Alignment of the EcoK and EcoB sites suggests that four of the seven specified
      nucleotides are conserved between the sequences recognized by these two allelic
      restriction and modification systems.
AU  - Kan NC
AU  - Lautenberger JA
AU  - Edgell MH
AU  - Hutchison CA III
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1979 130: 191-209.

PMID- Not included in PubMed...
VI  - 37
DP  - 1978
TI  - Recognition site of the Escherichia coli K restriction enzyme.
PG  - 1499
AB  - Two mutations of PhiX174 which confer sensitivity to restriction by E. coli K12
      have been localized on the DNA sequence using the marker rescue technique.  The
      sKI site lies between positions 817 and 953 while  sK2 lies between positions
      1780 and 1900 (as numbered by Sanger et al., 1977).  The sKI mutation results
      in the loss of the HhaI site between fragments 11 and 14, while the sK2
      mutation leads to loss of the HhaI site between fragments 9a and 8a.  Sequence
      analysis of these two mutant DNAs compared with the PhiX174am3cs70 sequence
      verifies this and shows a C5T change at position 874 on the + strand of sK1
      DNA, and a G5A change at position 1867 on the + strand of sK2 DNA.  The
      following alignment gives the most homology between these sites: 5'
      TAAAAAACGTTCTGGTGCTCGC 3' (+ strand of sK1) 3' CGGAAAACGAACAAGTGCAAGA 3' (-
      strand of sK2) Since GTGC occurs 24 times in the sequence of PhiX174am3cs70 RF
      DNA, some other nucleotides must be involved in the recognition site, which is
      most likely to be an interrupted sequence.  The EcoK site on G4 RF DNA is being
      mapped.  Comparison between the G4 DNA sequence in this region and the two
      sites on PhiX174 should further define the sequence recognized by the EcoK
      restriction enzyme.
AU  - Kan NC
AU  - Lautenberger JA
AU  - Edgell MH
AU  - Hutchison CA III
PT  - Journal Article
TA  - Fed. Proc.
JT  - Fed. Proc.
SO  - Fed. Proc. 1978 37: 1499.

PMID- 1427082
VI  - 121
DP  - 1992
TI  - Cloning, sequencing, overproduction, and purification of M.CviBI (GANTC) methyltransferase from Chlorella virus NC-1A.
PG  - 1-7
AB  - We have cloned and sequenced the cvibIM gene from Chlorella virus NC-1A by selecting for the
      modification phenotype. The modification gene was cloned on a 7-kb BamHI fragment inserted
      into the BamHI site of the pUC13 plasmid. The cvibIM gene was localized at the 3' end of this
      fragment. Sequencing of this region revealed a large open reading frame that codes for
      methyltransferase (MTase: symbol M) (predicting 260 amino acids). M.CviBI (GANTC) aa sequence
      is homologous to M.dam (GATC), M.DpnII (GATC) and M.T4 (GATC), and not so to M.HinfI (GANTC),
      M.HhaII (GANTC), and M.DpnA (GATC). We also describe the use of the polymerase chain reaction
      technique to alter transcriptonal and translational signals surrounding this gene so as to
      achieve overexpression in Escherichia coli. This construct yields M.CviBI at 2-3% of the total
      cellular protein. The MTase was purified by phosphocellulose, DEAE, and gel filtration
      chromatography. Its size by SDS-PAGE is approximately 28 kDa, in good agreement with that
      predicted from the nucleotide sequence.
AU  - Kan TN
AU  - Lin L
AU  - Chandrasegaran S
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1992 121: 1-7.

PMID- 28369487
VI  - 162
DP  - 2017
TI  - Conserved threonine 1505 in the catalytic domain stabilizes mouse DNA methyltransferase 1.
PG  - 271-278
AB  - In mammals, DNA methyltransferase 1 (DNMT1) is responsible for propagating the DNA methylation
      pattern into the next generation through selective methylation of hemi-methylated CpG that
      emerges just after replication, a process known as maintenance methylation. The T1505, which
      is conserved among DNMT1s of vertebrates, in the catalytic domain of mouse DNMT1 forms the
      hydrogen bond with the W1512, which is also conserved among vertebrates and one of the
      essential residues in recognition of the 5-methylcytosine in hemi-methylated CpGs. However,
      importance of the hydrogen bond between T1505 and W1512 is unknown. In this study, we
      determined the crystal structure of mouse DNMT1(291-1620) that replaced T1505 with alanine
      (DNMT1(291-1620)T1505A) and examined its DNA methylation activity in vitro. Although the
      mutation lost the hydrogen bond between T1505 and W1512, the overall structure of
      DNMT1(291-1620)T1505A remained almost identical with that of the wild type. Structural
      stability and DNA methylation activity of DNMT1(291-1620)T1505A under physiological
      temperature were lower than those of DNMT1(291-1620). T1505 is crucial on the DNA methylation
      activity of DNMT1 through stabilizing its structure during ongoing round of DNA methylation.
AU  - Kanada K
AU  - Takeshita K
AU  - Suetake I
AU  - Tajima S
AU  - Nakagawa A
PT  - Journal Article
TA  - J. Biochem. (Tokyo)
JT  - J. Biochem. (Tokyo)
SO  - J. Biochem. (Tokyo) 2017 162: 271-278.

PMID- 17294471
VI  - 3
DP  - 2007
TI  - Site-specific ligation of DNA-modified gold nanoparticles activated by the restriction enzyme StyI.
PG  - 67-70
AB  - 
AU  - Kanaras AG
AU  - Wang ZX
AU  - Hussain I
AU  - Brust M
AU  - Cosstick R
AU  - Bates AD
PT  - Journal Article
TA  - Small
JT  - Small
SO  - Small 2007 3: 67-70.

PMID- 26139717
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Bacillus thuringiensis Serovar Tolworthi Strain Pasteur Institute Standard.
PG  - e00710-15
AB  - The genome sequence of Bacillus thuringiensis serovar tolworthi strain Pasteur Institute
      Standard was determined. The genome consists of a 5.9-Mb chromosome and
      eight plasmids, one of which is linear. The second largest plasmid (293 kb)
      carries the genes encoding insecticidal proteins.
AU  - Kanda K
AU  - Nakashima K
AU  - Nagano Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00710-15.

PMID- 
VI  - 14
DP  - 2004
TI  - Engineering and applications of chimeric nucleases.
PG  - 413-434
AB  - Each human cell contains about 3x10^9 base pairs within its genome.  With the first sequence
      of the human genome now available, biologists estimate that there are about 30,000-40,000
      different genes within the genome.  This is fewer than originally anticipated, but still a
      huge number.  These genes code for all of the human body's proteins.  Simple mutations within
      the coding region of critical genes can lead to the formation of abnormal proteins, resulting
      in disease phenotypes, premature death, or failure of an embryo to develop.  Furthermore,
      mutations that affect the regulatory region of genes can result in aberrant gene expression
      within cells, and give rise to cancer phenotypes.  The Holy Grail of the Human Genome Project
      is Gene Therapy, that is, how genes might someday be used, modified, or even changed to
      correct human disease.
AU  - Kandavelou K
AU  - Mani M
AU  - Durai S
AU  - Chandrasegaran S
PT  - Journal Article
TA  - Nucleic Acids Mol. Biol.
JT  - Nucleic Acids Mol. Biol.
SO  - Nucleic Acids Mol. Biol. 2004 14: 413-434.

PMID- 11425474
VI  - 200
DP  - 2001
TI  - Restriction enzyme BstZ17I is sensitive to cytosine methylation.
PG  - 191-193
AB  - The cleavage patterns of a subset of restriction enzymes are blocked or impaired when a
      methylated CpG is overlapped with either the 5' or 3' end of the canonical restriction site.
      BstZ17I restriction endonuclease is a blunt-end cutter, which recognises the hexanucleotide
      sequence GTA^TAC. In this report, I show that the BstZ17I restriction enzyme is sensitive to
      cytosine methylation. Using both in vitro-methylated episomal plasmids and lambda DNA, I
      demonstrate that the BstZ17I restriction enzyme is sensitive to cytosine methylation that
      occurs 3' and/or 5' of the canonical recognition sequence.
AU  - Kanduri C
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2001 200: 191-193.

PMID- 2146742
VI  - 250
DP  - 1990
TI  - Protein splicing converts the yeast TFP1 gene product to the 69-kD subunit of the vacuolar H+-adenosine triphosphatase.
PG  - 651-657
AB  - The TFP1 gene of the yeast Saccharomyces cerevisiae encodes two proteins: the 69-kilodalton
      (kD) catalytic subunit of the vacuolar proton-translocating adenosine triphosphatase
      (H+-ATPase) and a 50-kD protein. The 60-kD subunit is encoded by the 5' and 3' thirds of the
      TFP1 coding region, whereas the 50-kD protein is encoded by the central third. Evidence is
      presented that both the 60-kD and 50-kD proteins are obtained from a single translation
      product that is cleaved to release the 50-kD protein and spliced to form the 69-kD subunit.
AU  - Kane PM
AU  - Yamashiro CT
AU  - Wolczyk DF
AU  - Neff N
AU  - Goebl M
AU  - Stevens TH
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1990 250: 651-657.

PMID- 17158667
VI  - 189
DP  - 2007
TI  - Whole-Genome Analysis of the Methyl tert-Butyl Ether-Degrading Beta-Proteobacterium Methylibium petroleiphilum PM1.
PG  - 1931-1945
AB  - Methylibium petroleiphilum PM1 is a methylotroph distinguished by its ability to completely
      metabolize the fuel oxygenate methyl tert-butyl
      ether (MTBE). Strain PM1 also degrades aromatic (benzene, toluene, and
      xylene) and straight-chain (C(5) to C(12)) hydrocarbons present in
      petroleum products. Whole-genome analysis of PM1 revealed an approximately
      4-Mb circular chromosome and an approximately 600-kb megaplasmid,
      containing 3,831 and 646 genes, respectively. Aromatic hydrocarbon and
      alkane degradation, metal resistance, and methylotrophy are encoded on the
      chromosome. The megaplasmid contains an unusual t-RNA island, numerous
      insertion sequences, and large repeated elements, including a 40-kb region
      also present on the chromosome and a 29-kb tandem repeat encoding
      phosphonate transport and cobalamin biosynthesis. The megaplasmid also
      codes for alkane degradation and was shown to play an essential role in
      MTBE degradation through plasmid-curing experiments. Discrepancies between
      the insertion sequence element distribution patterns, the distributions of
      best BLASTP hits among major phylogenetic groups, and the G+C contents of
      the chromosome (69.2%) and plasmid (66%), together with comparative genome
      hybridization experiments, suggest that the plasmid was recently acquired
      and apparently carries the genetic information responsible for PM1's
      ability to degrade MTBE. Comparative genomic hybridization analysis with
      two PM1-like MTBE-degrading environmental isolates ( approximately 99%
      identical 16S rRNA gene sequences) showed that the plasmid was highly
      conserved (ca. 99% identical), whereas the chromosomes were too diverse to
      conduct resequencing analysis. PM1's genome sequence provides a foundation
      for investigating MTBE biodegradation and exploring the genetic regulation
      of multiple biodegradation pathways in M. petroleiphilum and other
      MTBE-degrading beta-proteobacteria.
AU  - Kane SR
AU  - Chakicherla AY
AU  - Chain PS
AU  - Schmidt R
AU  - Shin MW
AU  - Legler TC
AU  - Scow KM
AU  - Larimer FW
AU  - Lucas SM
AU  - Richardson PM
AU  - Hristova KR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2007 189: 1931-1945.

PMID- 15215868
VI  - 429
DP  - 2004
TI  - Essential role for de novo DNA methyltransferase Dnmt3a in paternal and maternal imprinting.
PG  - 900-903
AB  - Imprinted genes are epigenetically marked during gametogenesis so that they are exclusively
      expressed from either the paternal or the maternal
      allele in offspring. Imprinting prevents parthenogenesis in mammals and is
      often disrupted in congenital malformation syndromes, tumours and cloned
      animals. Although de novo DNA methyltransferases of the Dnmt3 family are
      implicated in maternal imprinting, the lethality of Dnmt3a and Dnmt3b
      knockout mice has precluded further studies. We here report the disruption
      of Dnmt3a and Dnmt3b in germ cells, with their preservation in somatic
      cells, by conditional knockout technology. Offspring from Dnmt3a
      conditional mutant females die in utero and lack methylation and
      allele-specific expression at all maternally imprinted loci examined.
      Dnmt3a conditional mutant males show impaired spermatogenesis and lack
      methylation at two of three paternally imprinted loci examined in
      spermatogonia. By contrast, Dnmt3b conditional mutants and their offspring
      show no apparent phenotype. The phenotype of Dnmt3a conditional mutants is
      indistinguishable from that of Dnmt3L knockout mice, except for the
      discrepancy in methylation at one locus. These results indicate that both
      Dnmt3a and Dnmt3L are required for methylation of most imprinted loci in
      germ cells, but also suggest the involvement of other factors.
AU  - Kaneda M
AU  - Okano M
AU  - Hata K
AU  - Sado T
AU  - Tsujimoto N
AU  - Li E
AU  - Sasaki H
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2004 429: 900-903.

PMID- 28183772
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Bradyrhizobium japonicum J5, Isolated from a Soybean  Nodule in Hokkaido, Japan.
PG  - e01619-16
AB  - Soybean bradyrhizobia form root nodules on soybean plants and symbiotically fix N2 Strain J5
      is phylogenetically far from well-known representatives within the
      Bradyrhizobium japonicum linage. The complete genome showed the largest single
      chromosomal (10.1 Mb) and symbiosis island (998 kb) among complete genomes of
      soybean bradyrhizobia.
AU  - Kanehara K
AU  - Minamisawa K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01619-16.

PMID- 26564049
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Halostagnicola sp. A56, an Extremely Halophilic Archaeon Isolated from the Andaman Islands.
PG  - e01332-15
AB  - The first draft genome of Halostagnicola sp. A56, isolated from the Andaman Islands is
      reported here. The A56 genome comprises 3,178,490 bp in 26 contigs
      with a G+C content of 60.8%. The genome annotation revealed that A56 could have
      potential applications for the production of polyhydroxyalkanoate or bioplastics.
AU  - Kanekar SP
AU  - Saxena N
AU  - Pore SD
AU  - Arora P
AU  - Kanekar PP
AU  - Dhakephalkar PK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01332-15.

PMID- Not included in PubMed...
VI  - 64
DP  - 1987
TI  - The action of endonucleases and methylases:  Electrophoretic analysis of DNA restriction fragments.
PG  - 274-278
AB  - The restriction endonucleases have played an essential role in the development
      of the field of recombinant DNA technology.  These enzymes catalyze the
      hydrolysis of double-stranded DNA with a high level of specificity to generate
      a well-defined series of polynucleotides called restriction fragments.  The
      sequence specificity has been employed to generate fragments for the
      construction of recombinant DNA molecules and for DNA sequence analysis.  This
      paper presents the procedures used in endonuclease digestion and the
      electrophoretic analysis of the restriction fragments.  In fact, two related
      experiments are outlined.  One involves the use of a restriction endonuclease
      to generate a set of well-defined fragments which then may be used as molecular
      weight standards for gel electrophoresis.  With this as an aid, the cleavage
      pattern of the DNA with other endonucleases can be analyzed.  The second
      experiment employs endonucleases to monitor the protection afforded the DNA
      upon methylation and illustrates the differences obtained upon in vitro and in
      vivo methylation.
AU  - Kaneko KJ
AU  - Burke JM
AU  - Kaplan LJ
PT  - Journal Article
TA  - J. Chem. Educ.
JT  - J. Chem. Educ.
SO  - J. Chem. Educ. 1987 64: 274-278.

PMID- 27932653
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Two Fabibacter sp. Strains Isolated from Coastal Surface Water of Aburatsubo Inlet, Japan.
PG  - e01360-16
AB  - Here, we report the draft genome sequences of Fabibacter sp. strain 4D4 and F. misakiensis
      strain SK-8T, isolated from surface seawater of a semienclosed inlet.
AU  - Kaneko R
AU  - Wong SK
AU  - Ogura Y
AU  - Hayashi T
AU  - Yoshizawa S
AU  - Hamasaki K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01360-16.

PMID- 11759840
VI  - 8
DP  - 2001
TI  - Complete genomic sequence of the filamentous nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120.
PG  - 205-213
AB  - The nucleotide sequence of the entire genome of a filamentous cyanobacterium, Anabaena sp.
      strain PCC 7120, was determined. The genome of Anabaena consisted of a single chromosome
      (6,413,771 bp) and six plasmids, designated pCC7120alpha (408,101 bp), pCC7120beta (186,614
      bp), pCC7120gamma (101,965 bp), pCC7120delta (55,414 bp), pCC7120epsilon (40,340 bp), and
      pCC7120zeta (5,584 bp). The chromosome bears 5368 potential protein-encoding genes, four sets
      of rRNA genes, 48 tRNA genes representing 42 tRNA species, and 4 genes for small structural
      RNAs. The predicted products of 45% of the potential protein-encoding genes showed sequence
      similarity to known and predicted proteins of known function, and 27% to translated products
      of hypothetical genes. The remaining 28% lacked significant similarity to genes for known and
      predicted proteins in the public DNA databases. More than 60 genes involved in various
      processes of heterocyst formation and nitrogen fixation were assigned to the chromosome based
      on their similarity to the reported genes. One hundred and ninety-five genes coding for
      components of two-component signal transduction systems, nearly 2.5 times as many as those in
      Synechocystis sp. PCC 6803, were identified on the chromosome. Only 37% of the Anabaena genes
      showed significant sequence similarity to those of Synechocystis, indicating a high degree of
      divergence of the gene information between the two cyanobacterial strains.
AU  - Kaneko T et al
PT  - Journal Article
TA  - DNA Res.
JT  - DNA Res.
SO  - DNA Res. 2001 8: 205-213.

PMID- 8905238
VI  - 3
DP  - 1996
TI  - Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803.  II.  Sequence determination of the entire genome and assignment of poential protein-coding regions (supplement).
PG  - 185-209
AB  - none
AU  - Kaneko T et al
PT  - Journal Article
TA  - DNA Res.
JT  - DNA Res.
SO  - DNA Res. 1996 3: 185-209.

PMID- 8905231
VI  - 3
DP  - 1996
TI  - Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. Strain PCC6803.  II.  Sequence determination of the entire genome and assignment of potential protein-coding regions.
PG  - 109-136
AB  - The sequence determination of the entire genome of the Synechocystis sp. strain PCC6803 was
      completed.  The total length of the genome finally confirmed was 3,573,470 bp, including the
      previously reported sequence of 1,003,450 bp from map position 64% to 92% of the genome.  The
      entire sequence was assembled from the sequences of the physical map-based contigs of cosmid
      clones and of lambda clones and long PCR products which were used for gap-filling.  The
      accuracy of the sequence was guaranteed by analysis of both strands of DNA through the entire
      genome.  The authenticity of the assembled sequence wqs supported by restriction analysis of
      long PCR products, which were directly amplified from the genomic DNA using the assembled
      sequence data.  To predict the potential protein-coding regions, analysis of open reading
      frames (ORFs), analysis by the GeneMark program and similarity search to databases were
      performed.  As a result, a total of 3,168 potential protein genes were assigned on the genome,
      in which 145 (4.6%) were identical to reported genes and 1,257 (39.6%) and 340 (10.8%) showed
      similarity to reported and hypothetical genes, respectively.  The remaining 1,426 (45.0%) had
      no apparent similarity to any genes in databases.  Among the potential protein genes assigned,
      128 were related to the genes participating in photosynthetic reactions.  The sum of the
      sequences coding for potential protein genes occupies 87% of the genome length.  By adding
      rRNA and tRNA genes, therefore, the genome has a very compact arrangement of protein- and
      RNA-coding regions.  A notable feature on the gene organization of the genome was that 99
      ORFs, which showed similarity to transposase genes and could be classified into 6 groups, were
      found spread all over the genome, and at least 26 of them appeared to remain intact.  The
      result implies that rearrangement of the genome occurred frequently during and after
      establishment of this species.
AU  - Kaneko T et al
PT  - Journal Article
TA  - DNA Res.
JT  - DNA Res.
SO  - DNA Res. 1996 3: 109-136.

PMID- 11214968
VI  - 7
DP  - 2000
TI  - Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti.
PG  - 331-338
AB  - The complete nucleotide sequence of the genome of a symbiotic bacterium Mesorhizobium loti
      strain MAFF303099 was determined. The genome of M. loti consisted of a single chromosome
      (7,036,071 bp) and two plasmids, designated as pMLa (351,911 bp) and pMLb (208, 315 bp). The
      chromosome comprises 6752 potential protein-coding genes, two sets of rRNA genes and 50 tRNA
      genes representing 47 tRNA species. Fifty-four percent of the potential protein genes showed
      sequence similarity to genes of known function, 21% to hypothetical genes, and the remaining
      25% had no apparent similarity to reported genes. A 611-kb DNA segment, a highly probable
      candidate of a symbiotic island, was identified, and 30 genes for nitrogen fixation and 24
      genes for nodulation were assigned in this region.  Codon usage analysis suggested that the
      symbiotic island as well as the plasmids originated and were transmitted from other genetic
      systems. The genomes of two plasmids, pMLa and pMLb, contained 320 and 209 potential
      protein-coding genes, respectively, for a variety of biological functions. These include genes
      for the ABC-transporter system, phosphate assimilation, two-component system, DNA replication
      and conjugation, but only one gene for nodulation was identified.
AU  - Kaneko T et al
PT  - Journal Article
TA  - DNA Res.
JT  - DNA Res.
SO  - DNA Res. 2000 7: 331-338.

PMID- 11214974
VI  - 7
DP  - 2000
TI  - Complete genome structure of the Nitrogen-fixing symbiotic bacterium Mesorhizobium loti (Supplement).
PG  - 381-406
AB  - none
AU  - Kaneko T et al
PT  - Journal Article
TA  - DNA Res.
JT  - DNA Res.
SO  - DNA Res. 2000 7: 381-406.

PMID- 18192279
VI  - 14
DP  - 2007
TI  - Complete Genomic Structure of the Bloom-forming Toxic Cyanobacterium Microcystis aeruginosa NIES-843.
PG  - 247-256
AB  - The nucleotide sequence of the complete genome of a cyanobacterium, Microcystis aeruginosa
      NIES-843, was determined. The genome of M.
      aeruginosa is a single, circular chromosome of 5 842 795 base pairs (bp)
      in length, with an average GC content of 42.3%. The chromosome comprises
      6312 putative protein-encoding genes, two sets of rRNA genes, 42 tRNA
      genes representing 41 tRNA species, and genes for tmRNA, the B subunit of
      RNase P, SRP RNA, and 6Sa RNA. Forty-five percent of the putative
      protein-encoding sequences showed sequence similarity to genes of known
      function, 32% were similar to hypothetical genes, and the remaining 23%
      had no apparent similarity to reported genes. A total of 688 kb of the
      genome, equivalent to 11.8% of the entire genome, were composed of both
      insertion sequences and miniature inverted-repeat transposable elements.
      This is indicative of a plasticity of the M. aeruginosa genome, through a
      mechanism that involves homologous recombination mediated by repetitive
      DNA elements. In addition to known gene clusters related to the synthesis
      of microcystin and cyanopeptolin, novel gene clusters that may be involved
      in the synthesis and modification of toxic small polypeptides were
      identified. Compared with other cyanobacteria, a relatively small number
      of genes for two component systems and a large number of genes for
      restriction-modification systems were notable characteristics of the M.
      aeruginosa genome.
AU  - Kaneko T et al
PT  - Journal Article
TA  - DNA Res.
JT  - DNA Res.
SO  - DNA Res. 2007 14: 247-256.

PMID- 24710291
VI  - 2
DP  - 2011
TI  - Complete Genome Sequence of the Soybean Symbiont Bradyrhizobium japonicum Strain USDA6T.
PG  - 763-787
AB  - The complete nucleotide sequence of the genome of the soybean symbiont Bradyrhizobium
      japonicum strain USDA6T was determined. The genome of USDA6T is a single circular chromosome
      of 9,207,384 bp. The genome size is similar to that of the genome of another soybean symbiont,
      B. japonicum USDA110 (9,105,828 bp).  Comparison of the whole-genome sequences of USDA6T and
      USDA110 showed colinearity of major regions in the two genomes, although a large inversion
      exists between them. A significantly high level of sequence conservation was detected in three
      regions on each genome. The gene constitution and nucleotide sequence features in these three
      regions indicate that they may have been derived from a symbiosis island. An ancestral, large
      symbiosis island, approximately 860 kb in total size, appears to have been split into these
      three regions by unknown large-scale genome rearrangements. The two integration events
      responsible for this appear to have taken place independently, but through comparable
      mechanisms, in both genomes.
AU  - Kaneko T
AU  - Maita S
AU  - Hirakawa H
AU  - Uchiike N
AU  - Minamisawa K
AU  - Watanabe A
AU  - Sato S
PT  - Journal Article
TA  - Genes
JT  - Genes
SO  - Genes 2011 2: 763-787.

PMID- 14686584
VI  - 10
DP  - 2003
TI  - Structural analysis of four large plasmids harboring in a unicellular cyanobacterium, Synechocystis sp. PCC 6803.
PG  - 221-228
AB  - The genome of the unicellular cyanobacterium Synechocystis sp. PCC 6803 consists of a single
      chromosome and several plasmids of different sizes,
      and the nucleotide sequences of the chromosome and three small plasmids
      (5.2 kb, 2.4 kb, and 2.3 kb) have already been sequenced. We newly
      determined the nucleotide sequences of four large plasmids, which have
      been identified in our laboratory (pSYSM:120 kb, pSYSX:106 kb, pSYSA:103
      kb, and pSYSG:44 kb). Computer-aided analysis was performed to explore the
      genetic information carried by these plasmids. A total of 397 potential
      protein-encoding genes were predicted, but little information was obtained
      about the functional relationship of plasmids to host cell, as a large
      portion of the predicted genes (77%) were of unknown function. The
      occurrence of the potential genes on plasmids was divergent, and parA was
      the only gene common to all four large plasmids. The distribution data of
      a Cyanobacterium-specific sequence (HIP1: 5'-GCGATCGC-3') suggested that
      respective plasmids could have originated from different cyanobacterial
      strains.
AU  - Kaneko T
AU  - Nakamura Y
AU  - Sasamoto S
AU  - Watanabe A
AU  - Kohara M
AU  - Matsumoto M
AU  - Shimpo S
AU  - Yamada M
AU  - Tabata S
PT  - Journal Article
TA  - DNA Res.
JT  - DNA Res.
SO  - DNA Res. 2003 10: 221-228.

PMID- 12597275
VI  - 9
DP  - 2002
TI  - Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110.
PG  - 189-197
AB  - The complete nucleotide sequence of the genome of a symbiotic bacterium
      Bradyrhizobium japonicum USDA110 was determined. The genome of B. japonicum was a
      single circular chromosome 9,105,828 bp in length with an average GC content of
      64.1%. No plasmid was detected. The chromosome comprises 8317 potential
      protein-coding genes, one set of rRNA genes and 50 tRNA genes. Fifty-two percent
      of the potential protein genes showed sequence similarity to genes of known
      function and 30% to hypothetical genes. The remaining 18% had no apparent
      similarity to reported genes. Thirty-four percent of the B. japonicum genes
      showed significant sequence similarity to those of both Mesorhizobium loti and
      Sinorhizobium meliloti, while 23% were unique to this species. A presumptive
      symbiosis island 681 kb in length, which includes a 410-kb symbiotic region
      previously reported by Gottfert et al., was identified. Six hundred fifty-five
      putative protein-coding genes were assigned in this region, and the functions of
      301 genes, including those related to symbiotic nitrogen fixation and DNA
      transmission, were deduced. A total of 167 genes for transposases/104 copies of
      insertion sequences were identified in the genome. It was remarkable that 100 out
      of 167 transposase genes are located in the presumptive symbiotic island. DNA
      segments of 4 to 97 kb inserted into tRNA genes were found at 14 locations in the
      genome, which generates partial duplication of the target tRNA genes. These
      observations suggest plasticity of the B. japonicum genome, which is probably due
      to complex genome rearrangements such as horizontal transfer and insertion of
      various DNA elements, and to homologous recombination.
AU  - Kaneko T
AU  - Nakamura Y
AU  - Sato S
AU  - Minamisawa K
AU  - Uchiumi T
AU  - Sasamoto S
AU  - Watanabe A
AU  - Idesawa K
AU  - Iriguchi M
AU  - Kawashima K
AU  - Kohara M
AU  - Matsumoto M
AU  - Shimpo S
AU  - Tsuruoka H
AU  - Wada T
AU  - Yamada M
AU  - Tabata S
PT  - Journal Article
TA  - DNA Res.
JT  - DNA Res.
SO  - DNA Res. 2002 9: 189-197.

PMID- 29449379
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of the Nitrogen-Fixing and Hormogonia-Inducing Cyanobacterium Nostoc cycadae Strain WK-1, Isolated from the Coralloid Roots of  Cycas revoluta.
PG  - e00021-18
AB  - We report here the whole-genome sequence of Nostoc cycadae strain WK-1, which was isolated
      from cyanobacterial colonies growing in the coralloid roots of the
      gymnosperm Cycas revoluta It can provide valuable resources to study the
      mutualistic relationships and the syntrophic metabolisms between the
      cyanobacterial symbiont and the host plant, C. revoluta.
AU  - Kanesaki Y
AU  - Hirose M
AU  - Hirose Y
AU  - Fujisawa T
AU  - Nakamura Y
AU  - Watanabe S
AU  - Matsunaga S
AU  - Uchida H
AU  - Murakami A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00021-18.

PMID- 28385845
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequences of Two Closely Related Bacteria, Actinomyces sp. Strain Chiba101 and Actinomyces denticolens DSM 20671T.
PG  - e00126-17
AB  - Actinomyces sp. strain Chiba101, isolated from an arthritic leg joint of a pig raised in
      Japan, is a bacterium closely related to Actinomyces denticolens Here,
      we deciphered the complete genome sequence of Actinomyces sp. Chiba101 and the
      high-quality draft genome sequence of A. denticolens DSM 20671T.
AU  - Kanesaki Y
AU  - Ishige T
AU  - Sekigawa Y
AU  - Kobayashi T
AU  - Torii Y
AU  - Yokoyama E
AU  - Ishiwata H
AU  - Hamada M
AU  - Tamura T
AU  - Azuma R
AU  - Murakami S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00126-17.

PMID- 29519830
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Bacillus licheniformis Heshi-B2, Isolated from Fermented Rice Bran in a Japanese Fermented Seafood Dish.
PG  - e00118-18
AB  - Bacillus licheniformis Heshi-B2 was isolated from fermented rice bran in Heshiko, a food
      produced by aging salted mackerel with fresh rice bran. Here, we report
      the draft genome sequence of B. licheniformis Heshi-B2, originating from a
      Heshiko sample from Fukui Prefecture, Japan.
AU  - Kanesaki Y
AU  - Kubota E
AU  - Ohtake R
AU  - Higashi Y
AU  - Nagaoka J
AU  - Suzuki T
AU  - Akuzawa S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00118-18.

PMID- 25523770
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Bifidobacterium longum 105-A, a Strain with High Transformation Efficiency.
PG  - e01311-14
AB  - Bifidobacterium longum 105-A shows high transformation efficiency and allows for  the
      generation of gene knockout mutants through homologous recombination. Here,
      we report the complete genome sequence of strain 105-A. Genes encoding at least
      four putative restriction-modification systems were found in this genome, which
      might contribute to its transformation efficiency.
AU  - Kanesaki Y
AU  - Masutani H
AU  - Sakanaka M
AU  - Shiwa Y
AU  - Fujisawa T
AU  - Nakamura Y
AU  - Yokota A
AU  - Fukiya S
AU  - Suzuki T
AU  - Yoshikawa H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01311-14.

PMID- 3031593
VI  - 15
DP  - 1987
TI  - Studies on SP6 promoter using a new plasmid vector that allows gene insertion at the transcription initiation site.
PG  - 2279-2294
AB  - This paper documents the cleavage by HphI at a site 9 bases away from the
      recognition sequence, with the production of a single base extension.  This is
      in contrast to the usual 8 bases.
AU  - Kang C
AU  - Wu C-W
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1987 15: 2279-2294.

PMID- 11735126
VI  - 289
DP  - 2001
TI  - Dnmt3b, de novo DNA methyltransferase, interacts with SUMO-1 and Ubc9 through its N-terminal region and is subject to modification by SUMO-1.
PG  - 862-868
AB  - Dnmt3b, a DNA methyltransferase, is essential for mammalian development potentially through
      its transcription repression activity. To
      comprehend the underlying regulatory mechanism of Dnmt3b, we isolated
      small ubiquitin-like modifier 1 (SUMO-1) and Ubc9 as Dnmt3b-interacting
      proteins using yeast two-hybrid screens. Deletion analysis and
      colocalization experiment demonstrated that Dnmt3b interacts with
      SUMO-1 and Ubc9 at its N-terminal region. We also confirmed the
      modification of Dnmt3b by SUMO-1 in vivo. These results suggest that
      sumoylation may constitute a regulation mechanism of Dnmt3b in vivo.
AU  - Kang ES
AU  - Park CW
AU  - Chung JH
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 2001 289: 862-868.

PMID- 
VI  - 103
DP  - 2003
TI  - Distribution of Helicobacter pylori 51-specific genes on other Korean isolates of Helicobacter pylori.
PG  - D-069
AB  - Background: Many disease-related genes of H. pylori such as cagA, vacA, ure and sod were
      identified and well-studied. Entire genome of H.
      pylori strain 51, a Korean isolate, has been sequenced. It had 1,454
      orfs. We searched disease-specific genes on Korean H. pylori isolates.
      Method: The nucleotide sequences of open reading frames of three H.
      pylori strains (26685, J99, 51) were compared one another and searched
      the strain-specific orf. Five type strains of H. pylori and 80 Korean
      isolates were screened with strain 51-specific orfs by overgo
      hybridization. Result: Ninteen Korean strain 51-specific orfs were
      identified. They included restriction endonuclease S subunits (hsdD,
      khp538), ATPase involved in conjugal plasmid transfer (traG, khp924),
      ATPase involved in pili and flagella biosynthesis (virB11, khp925),
      VirB10 component of type IV secretion system (virB10, khp926),
      Adenine-specific DNA methylase (khp1073), site-specific
      integrase-resolvase (khp1371), transposase (khp1372), restriction
      endonuclease S subunits (hsdS, khp1385), amino acid transporters (lysP,
      khp1391), site-specific DNA methylase (dcm, khp1406),
      membrane-associated metal-dependent hydrolase (khp1425) and seven
      putative ORFs. To investigate distribution of the genes, four type
      strains and 80 Korean H. pylori isolates that were isolated from
      gastric cancer, gastric ulcer, duodenal ulcer and gastritis were
      screened. Four orfs (khp594, khp900, khp1251, khp1391) were revealed to
      be abundant in most Korean isolates. Conclusion: We found 19 Korean
      strain 51-specific orfs by the comparison of the nucleotide sequence of
      orfs of three sequenced H. pylori strains. But none of them seemed to
      be disease-specific. But at least four orfs seemed to be specific in
      korean isolates. We are expecting that we can find more reasonable
      result by screening more Korean isolates.
AU  - Kang HL
AU  - Park YH
AU  - Lee EJ
AU  - Kim MH
AU  - Kim JS
AU  - Park SG
AU  - Song JY
AU  - Park JU
AU  - Baik SC
AU  - Ko GH
AU  - Youn HS
AU  - Lee WK
AU  - Cho MJ
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 2003 103: D-069.

PMID- 21602327
VI  - 193
DP  - 2011
TI  - Genome sequence of strain IMCC2047, a novel marine member of the Gammaproteobacteria.
PG  - 3688-3689
AB  - Strain IMCC2047 was isolated from the Yellow Sea using dilution-to-extinction culturing. The
      strain was shown to occupy a
      distinct phylogenetic position within the Gammaproteobacteria. Here we
      present the genome sequence of strain IMCC2047 that harbors genes for
      various metabolic pathways including proteorhodopsin and ribulose
      bisphosphate carboxylase.
AU  - Kang I
AU  - Kang D
AU  - Oh HM
AU  - Kim H
AU  - Kim HJ
AU  - Kang TW
AU  - Kim SY
AU  - Cho JC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3688-3689.

PMID- 28186143
VI  - 7
DP  - 2017
TI  - The first complete genome sequences of the acI lineage, the most abundant freshwater Actinobacteria, obtained by whole-genome-amplification of dilution-to-extinction cultures.
PG  - 42252
AB  - The acI lineage of the phylum Actinobacteria is the most abundant bacterial group
      in most freshwater lakes. However, due to difficulties in laboratory cultivation,
      only two mixed cultures and some incomplete single-amplified or
      metagenome-derived genomes have been reported for the lineage. Here, we report
      the initial cultivation and complete genome sequences of four novel strains of
      the acI lineage from the tribes acI-A1, -A4, -A7, and -C1. The acI strains,
      initially isolated by dilution-to-extinction culturing, eventually failed to be
      maintained as axenic cultures. However, the first complete genomes of the acI
      lineage were successfully obtained from these initial cultures through whole
      genome amplification applied to more than hundreds of cultured acI cells. The
      genome sequences exhibited features of genome streamlining and showed that the
      strains are aerobic chemoheterotrophs sharing central metabolic pathways, with
      some differences among tribes that may underlie niche diversification within the
      acI lineage. Actinorhodopsin was found in all strains, but retinal biosynthesis
      was complete in only A1 and A4 tribes.
AU  - Kang I
AU  - Kim S
AU  - Islam MR
AU  - Cho JC
PT  - Journal Article
TA  - Sci. Rep.
JT  - Sci. Rep.
SO  - Sci. Rep. 2017 7: 42252.

PMID- 22689238
VI  - 194
DP  - 2012
TI  - Genome Sequence of 'Candidatus Aquiluna' sp. Strain IMCC13023, a Marine Member of the Actinobacteria Isolated from an Arctic Fjord.
PG  - 3550-3551
AB  - We report the genome sequence of actinobacterial strain IMCC13023, isolated from  arctic fjord
      seawater. Phylogenetic analysis of 16S rRNA gene showed that the
      strain is related to 'Candidatus Aquiluna rubra.' The genome information suggests
      that strain IMCC13023 is a photoheterotroph carrying actinorhodopsin, with the
      smallest genome ever reported for a free-living member of the Actinobacteria.
AU  - Kang I
AU  - Lee K
AU  - Yang SJ
AU  - Choi A
AU  - Kang D
AU  - Lee YK
AU  - Cho JC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3550-3551.

PMID- 20639329
VI  - 192
DP  - 2010
TI  - Genome sequence of Fulvimarina pelagi HTCC2506T, a Mn(II)-oxidizing alphaproteobacterium possessing an aerobic anoxygenic photosynthetic gene  cluster and Xanthorhodopsin.
PG  - 4798-4799
AB  - Fulvimarina pelagi is a Mn(II)-oxidizing marine heterotrophic bacterium in the order
      Rhizobiales. Here we announce the draft genome sequence of F.
      pelagi HTCC2506(T), which was isolated from the Sargasso Sea by using
      dilution-to-extinction culturing. The genome sequence contained a
      xanthorhodopsin gene as well as a photosynthetic gene cluster, which
      suggests the coexistence of two different phototrophic mechanisms in a
      single microorganism.
AU  - Kang I
AU  - Oh HM
AU  - Lim SI
AU  - Ferriera S
AU  - Giovannoni SJ
AU  - Cho JC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 4798-4799.

PMID- 20889754
VI  - 192
DP  - 2010
TI  - Genome Sequence of the Marine Alphaproteobacterium HTCC2150, Assigned to the Roseobacter Clade.
PG  - 6315-6316
AB  - Here we announce the genome sequence of a marine bacterium, HTCC2150, that was isolated off
      the Oregon coast using dilution-to-extinction culturing
      and that is affiliated with the Roseobacter clade. The 16S rRNA phylogeny
      showed that the strain was closely related to members of the RCA clade.
      The genome sequence suggests that strain HTCC2150 is an organoheterotroph
      carrying diverse metabolic potential, including a close relationship with
      phytoplankton.
AU  - Kang I
AU  - Oh HM
AU  - Vergin KL
AU  - Giovannoni SJ
AU  - Cho JC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 6315-6316.

PMID- 21036993
VI  - 193
DP  - 2010
TI  - Genome Sequence of strain HTCC2083, a Novel Member of the Marine Roseobacter Clade.
PG  - 319-320
AB  - Strain HTCC2083 was isolated from Oregon seawater using dilution-to-extinction culturing and
      represents a novel member of the Roseobacter clade. The draft genome sequence of HTCC2083 is
      presented here. The genome is predicted to contain genes for aerobic anoxygenic phototrophy,
      sulfite-oxidizing chemolithotrophy, anapleurotic CO2 fixation, carbon monoxide oxidation, and
      dimethylsulphoniopropionate (DMSP) utilization.
AU  - Kang I
AU  - Vergin KL
AU  - Oh HM
AU  - Choi A
AU  - Giovannoni SJ
AU  - Cho JC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 193: 319-320.

PMID- 28702200
VI  - 19
DP  - 2017
TI  - Complete genome sequence of the Bifidobacterium animalis subspecies lactis BL3, preventive probiotics for acute colitis and colon cancer.
PG  - 34-37
AB  - We report the genome sequence of Bifidobacterium animalis subspecies lactis BL3,
      which has preventive properties on acute colitis and colon cancer. The genome of
      BL3, which was isolated from Korean faeces, consisted of a 1 944 323 bp size
      single chromosome, and its G+C content was 60.5%. Genome comparison against the
      closest Bifidobacterium animalis strain revealed that BL3 had particularly
      different regions of four areas encoding flavin-nucleotide-binding protein,
      transposase, multidrug ABC transporter and ATP binding protein.
AU  - Kang J
AU  - Chung WH
AU  - Lim TJ
AU  - Lim S
AU  - Nam YD
PT  - Journal Article
TA  - New Microbes New Infect.
JT  - New Microbes New Infect.
SO  - New Microbes New Infect. 2017 19: 34-37.

PMID- 28439274
VI  - 8
DP  - 2017
TI  - Complete Genome Sequence of Lactobacillus casei LC5, a Potential Probiotics for Atopic Dermatitis.
PG  - 413
AB  - 
AU  - Kang J
AU  - Chung WH
AU  - Lim TJ
AU  - Whon TW
AU  - Lim S
AU  - Nam YD
PT  - Journal Article
TA  - Front. Immunol.
JT  - Front. Immunol.
SO  - Front. Immunol. 2017 8: 413.

PMID- 24502234
VI  - 136
DP  - 2014
TI  - Design of Sequence-Specific DNA Binding Molecules for DNA Methyltransferase Inhibition.
PG  - 3687-3694
AB  - The CpG dyad, an important genomic feature in DNA methylation and transcriptional regulation,
      is an attractive target for small molecules. To assess the utility of minor groove binding
      oligomers for CpG recognition, we screened a small library of hairpin pyrrole-imidazole
      polyamides targeting the sequence 5'-CGCG-3' and assessed their sequence specificity using
      an unbiased next-generation sequencing assay. Our findings indicate that hairpin polyamide of
      sequence PyIm beta Im-gamma-PyIm beta Im (1), previously identified as a high affinity
      5'-CGCG-3' binder, favors 5'-GCGC-3' in an unanticipated reverse binding orientation.
      Replacement of one beta alanine with Py to afford PyImPyIm-gamma-PyIm beta Im (3) restores the
      preference for 5'-CGCG-3' binding in a forward orientation. The minor groove binding hairpin
      3 inhibits DNA methyltransferase activity in the major groove at its target site more
      effectively than 1, providing a molecular basis for design of sequence-specific antagonists of
      CpG methylation.
AU  - Kang JJS
AU  - Meier JL
AU  - Dervan PB
PT  - Journal Article
TA  - J. Am. Chem. Soc.
JT  - J. Am. Chem. Soc.
SO  - J. Am. Chem. Soc. 2014 136: 3687-3694.

PMID- 16946611
VI  - 40
DP  - 2006
TI  - Effect of Weissella cibaria isolates on the formation of Streptococcus mutans biofilm.
PG  - 418-425
AB  - The objective of this study was to isolate and identify lactic acid bacteria able
      to inhibit the in vitro formation of Streptococcus mutans biofilm as well as the
      in vivo formation of oral biofilm. Two strains, CMS1 and CMS3, exhibiting
      profound inhibitory effects on the formation of S. mutans biofilm and the
      proliferation of S. mutans, were isolated from children's saliva and identified
      as Weissella cibaria by 16S rDNA sequencing. The water-soluble polymers produced
      from sucrose by the W. cibaria isolates also inhibited the formation of S. mutans
      biofilm. According to the results of thin-layer chromatographic analysis, the
      hydrolysates of water-soluble polymers produced by the isolates were identical to
      those of dextran, forming mostly alpha-(1-6) glucose linkages. In the clinical
      study, the subjects mouthrinsed with a solution containing W. cibaria CMS1
      evidenced plaque index reduction of approximately 20.7% (p < 0.001). These
      results indicate that the W. cibaria isolates possess the ability to inhibit
      biofilm formation, both in vitro and in vivo.
AU  - Kang MS
AU  - Chung J
AU  - Kim SM
AU  - Yang KH
AU  - Oh JS
PT  - Journal Article
TA  - Caries Res.
JT  - Caries Res.
SO  - Caries Res. 2006 40: 418-425.

PMID- 28983008
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of Weissella cibaria Strains CMU, CMS1, CMS2, and CMS3  Isolated from Infant Saliva in South Korea.
PG  - e01103-17
AB  - Weissella cibaria strain CMU is used as a commercial oral care probiotic in South Korea. Here,
      we present the complete genome sequences of four W. cibaria strains
      (CMU, CMS1, CMS2, and CMS3) isolated from the saliva of an infant living in
      Gwangju, South Korea.
AU  - Kang MS
AU  - Yeu JE
AU  - Oh JS
AU  - Shin BA
AU  - Kim JH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01103-17.

PMID- 10206949
VI  - 274
DP  - 1999
TI  - Interaction of SeqA and Dam methylase on the hemimethylated origin of Escherichia coli chromosomal DNA replication.
PG  - 11463-11468
AB  - Preferential binding of SeqA protein to hemimethylated oriC, the origin of Escherichia coli
      chromosomal replication, delays methylation by Dam methylase.  Because the SeqA-oriC
      interaction appears to be essential in timing of chromosomal replication initiation, the
      biochemical functions of SeqA protein and Dam methylase at the 13-mer L, M., and R region
      containing 4 GATC sequences at the left end of oriC were examined.  We found that SeqA protein
      preferentially bound hemimethylated 13-mers but not fully nor unmethylated 13-mers.
      Regardless of strand methylation, the binding of SeqA protein to the hemimethylated GATC
      sequence of 13-mer L was followed by additional binding to other hemimethylated GATC sequences
      of 13-mer M and R.  On the other hand, Dam methylase did not discriminate binding of 13-mers
      in different methylation patterns and was not specific to GATC sequences.  The binding
      specificity and higher affinity of SeqA protein over Dam methylase to the hemimethylated
      13-mers along with the reported cellular abundance of this protein explains the dominant
      action of SeqA protein over Dam methylase to the newly replicated oriC for the sequestration
      of chromosomal replication.  Furthermore, SeqA protein bound to hemimethylated 13-mers was not
      dissociated by Dam methylase, and most SeqA protein spontaneously dissociated 10 min after
      binding.  Also, SeqA protein delayed the in vitro methylation of hemimethylated 13-mers by Dam
      methylase.  These in vitro results suggest that the intrinsic binding instability of SeqA
      protein results in release of sequestrated hemimethylated oriC.
AU  - Kang S
AU  - Lee H
AU  - Han JS
AU  - Hwang DS
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1999 274: 11463-11468.

PMID- 3036132
VI  - 145
DP  - 1987
TI  - The effects of DNA methylation by HhaI methylase on the cleavage reactions by HaeII, AhaII and BanI endonuclease.
PG  - 482-487
AB  - The DNA methylated by HhaI methylase was resistant against cleavage of HaeII or
      AhaII endonuclease indicating that the methyl group of the C5 position of the
      innermost cytosine nucleotide interferes with the interaction between the
      enzyme and hexameric recognition sequence.  Considering that HaeII or AhaII
      methylase has not been isolated yet, the result explained above is a useful
      information for protecting a double stranded DNA from being cleaved by HaeII or
      AhaII endonuclease. In contrast to HaeII or AhaII endonuclease, BanI
      endonuclease which also has HhaI sequence as its tetrameric core was able to
      cleave the same DNA normally.  This result suggests that the C5 position of the
      inmost pyrimidine nucleotide is not an important contact point between BanI
      endonuclease and its hexameric recognition sequence.
AU  - Kang SC
AU  - Choi WS
AU  - Yoo OJ
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1987 145: 482-487.

PMID- Not carried by PubMed...
VI  - 23
DP  - 1985
TI  - Purification and characterization of AccI endonuclease.
PG  - 13-19
AB  - AccI endonuclease has been isolated from 300g (wet weight) cells of
      Acinetobacter calcoaceticus.  The cells were broken by using French press at
      20,000 p.s.i.  After ammonium sulfate fractionation, the enzyme was further
      purified by heparin agarose, DEAE-sephadex, Affi-gel Blue, phosphocellulose,
      and hydroxylapatite column chromatography.  The purified AccI endonuclease has
      a single polypeptide species and its subunit molecular weight was 45,000 +/-
      1,000 daltons as judged by 10% SDS-polyacrylamide gel electrophoresis.  The
      isolated enzyme was essentially free of contaminating nucleases as judged by
      homochromatography by using a 32P-labeled oligonucleotide.  The enzyme showed
      maximum activity at pH values between 8.0 and 11.0, and in the presence of
      MgCl2.  AccI endonuclease was maximally active in the absence of NaCl and was
      completely inhibited at 200 mM NaCl.
AU  - Kang SC
AU  - Yoo OJ
PT  - Journal Article
TA  - Korean J. Microbiol.
JT  - Korean J. Microbiol.
SO  - Korean J. Microbiol. 1985 23: 13-19.

PMID- Not carried by PubMed...
VI  - 19
DP  - 1986
TI  - DNA protection by methylation with AluI methylase against cleavages of HindIII, SstI, PvuII and SacI endonucleases.
PG  - 41-46
AB  - The cleavage reactions of HindIII, SstI, PvuII and SacI endonucleases were inhibited by the
      methylation of AluI methylase.  To analyze the cleavage reactions quantitatively, tritium
      labeled pBR322 and pPG3282 plasmid DNAs (pBR322 DNA contains HindIII and PvuII sites, while
      pPG3282 DNA which is a hog gastrin cDNA clone contains SstI and SacI sites) were used, and the
      degree of the inhibition against cleavages by the four kinds of endonucleases was measured.
      The results imply that we can predict the specificities of the related hexameric restriction
      methylases which have not been isolated yet.  And the predictions are the followings:  (1) The
      methylation sites of SstI methylase is not identical with AluI methylase since SstI
      endonuclease slowly cut the sequences methylated by AluI methylase.  (2)  The methylation
      sites of PvuII and SacI methylases could be identical with AluI methylase since PvuII and SacI
      endonucleases could not cut the sequences methylated by AluI methylase.
AU  - Kang SC
AU  - Yoon H
AU  - Yoo OJ
PT  - Journal Article
TA  - Korean Biochem. J.
JT  - Korean Biochem. J.
SO  - Korean Biochem. J. 1986 19: 41-46.

PMID- 19594434
VI  - 17
DP  - 2010
TI  - Stationary Phase Expression, Purification, and Characterization of XorKI, a Restriction Endonuclease from Xanthomonas oryzae pv. oryzae.
PG  - 381-385
AB  - An endonuclease from Xanthomonas oryzae pathovar oryzae KACC 10331, XorKI, was heterologously
      produced in Escherichia coli by applying the
      stationary state induction method. The yield was 5.4 mg of XorKI per
      liter of LB medium. XorKI existed in multiple oligomeric forms as
      evidenced by gel filtration chromatography. The specific activity of
      purified XorKI was 323000 units per mg.
AU  - Kang WY et al
PT  - Journal Article
TA  - Protein Pept. Lett.
JT  - Protein Pept. Lett.
SO  - Protein Pept. Lett. 2010 17: 381-385.

PMID- 22843572
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Streptococcus thermophilus Strain MN-ZLW-002.
PG  - 4428-4429
AB  - Streptococcus thermophilus MN-ZLW-002 was originally isolated from traditionally  fermented
      Chinese dairy products. One of the strain-dependent characteristics of
      this bacterium is its ability to produce exopolysaccharides (EPSs). This study
      determined and analyzed the genome sequence of MN-ZLW-002. Its complete genome
      comprised 2,046 genes and 1,848,520 nucleotides with an average GC content of
      39%. The EPS cluster of MN-ZLW-002 includes 25 open reading frames (ORFs), and
      some results indicate a horizontal gene transfer between MN-ZLW-002 and other
      lactic acid bacteria (LAB).
AU  - Kang X
AU  - Ling N
AU  - Sun G
AU  - Zhou Q
AU  - Zhang L
AU  - Sheng Q
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4428-4429.

PMID- 25614565
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Bacillus pumilus Strain WP8, an Efficient Plant Growth-Promoting Rhizobacterium.
PG  - e01452-14
AB  - Bacillus pumilus strain WP8 is an efficient plant growth-promoting rhizobacterium. Here, we
      present the complete genome of WP8 and its genes
      involved in plant growth promotion and biocontrol.
AU  - Kang Y
AU  - Shen M
AU  - Wang H
AU  - Zhao Q
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01452-14.

PMID- 7832816
VI  - 206
DP  - 1995
TI  - Different effects of base analog substitutions in BamHI restriction site on recognition by BamHI endonuclease and BamHI methylase.
PG  - 997-1002
AB  - BamHI endonuclease and BamHI methylase were used to investigate their specific interaction
      with the common recognition sequence, GGATCC. Five derivatives of the oligonucleotide,
      GACGGATCCGTC, containing a variety of single-base analog substitutions within the hexameric
      recognition core were synthesized. Steady-state kinetics for the reaction of the endonuclease
      and the methylase showed that both enzymes recognize the sequences by contacting with
      functional groups exposed in both major and minor grooves of the site but in different ways.
      Removal or substitution of the 5-methyl group in thymidine blocked the endonuclease reaction
      completely but still allowed the methylase reaction with less efficiency. The data also showed
      that the methylase made a critical minor groove contact with the 2-amino group of the first G
      but the endonuclease did with that of the second G.
AU  - Kang YK
AU  - Lee HB
AU  - Noh MJ
AU  - Cho N-Y
AU  - Yoo OJ
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1995 206: 997-1002.

PMID- 8508139
VI  - 29
DP  - 1993
TI  - Effects of modified bases in sequence recognition by ClaI endonuclease and ClaI methylase.
PG  - 859-865
AB  - To understand the functional groups required for sequence recognition, dodecanucleotides
      containing the ClaI sequence with the middle positions containing modified bases were
      synthesized and used as substrates for ClaI endonuclease and ClaI methylase reactions. For the
      modification, dU, 5-bromo-dU, and dI were used. Km values of these two enzymes were determined
      for normal and modified oligonucleotides. Our data showed that 5-CH3 groups of the first and
      second T residues of the hexanucleotide sequence were essential contact points for ClaI
      methylase. However, ClaI endonuclease was still active without either one of those methyl
      groups with elevated Km values. Bromine could compensate significantly for the loss of 5-CH3
      groups at both positions. On the other hand, the 2-amino group of the G residue appeared to be
      an essential contact point for both enzymes. It has been concluded that ClaI enconuclease and
      ClaI methylase recognize the sequence in different ways.
AU  - Kang YK
AU  - Ryu J
AU  - Yoo OJ
PT  - Journal Article
TA  - Biochem. Mol. Biol. Int.
JT  - Biochem. Mol. Biol. Int.
SO  - Biochem. Mol. Biol. Int. 1993 29: 859-865.

PMID- 786629
VI  - 67
DP  - 1976
TI  - Use of a Sequence-Specific DNA-Binding Ligand to probe the Environments of EcoRI Restriction Endonuclease Cleavage Sites.
PG  - 367-371
AB  - The DNAs of bacteriophage lambda and adenovirus were incubated with the
      sequence-specific DNA-binding ligand 6,4'-diamidino-2-phenylindole.  Digestion
      of the ligant - DNA complexes with EcoRI nuclease and subsequent agarose gel
      electrophoresis demonstrated that the ligand inhibited nuclease activity at
      some sites, but not at others.  The results suggest that
      diamidino-2-phenylindole can be used to probe the immediate environments of the
      EcoRI cleavage sites.
AU  - Kania J
AU  - Fanning TG
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1976 67: 367-371.

PMID- 12663548
VI  - 163
DP  - 2003
TI  - Arabidopsis MET1 cytosine methyltransferase mutants.
PG  - 1109-1122
AB  - We describe the isolation and characterization of two missense mutations in the
      cytosine-DNA-methyltransferase gene, MET1, from the flowering plant
      Arabidopsis thaliana. Both missense mutations, which affect the catalytic
      domain of the protein, led to a global reduction of cytosine methylation
      throughout the genome. Surprisingly, the met1-2 allele, with the weaker
      DNA hypomethylation phenotype, alters a well-conserved residue in
      methyltransferase signature motif I. The stronger met1-1 allele caused
      late flowering and a heterochronic delay in the juvenile-to-adult rosette
      leaf transition. The distribution of late-flowering phenotypes in a
      mapping population segregating met1-1 indicates that the flowering-time
      phenotype is caused by the accumulation of inherited defects at loci
      unlinked to the met1 mutation. The delay in flowering time is due in part
      to the formation and inheritance of hypomethylated fwa epialleles, but
      inherited defects at other loci are likely to contribute as well.
      Centromeric repeat arrays hypomethylated in met1-1 mutants are partially
      remethylated when introduced into a wild-type background, in contrast to
      genomic sequences hypomethylated in ddm1 mutants. ddm1 met1 double mutants
      were constructed to further our understanding of the mechanism of DDM1
      action and the interaction between two major genetic loci affecting global
      cytosine methylation levels in Arabidopsis.
AU  - Kankel MW
AU  - Ramsey DE
AU  - Stokes TL
AU  - Flowers SK
AU  - Haag JR
AU  - Jeddeloh JA
AU  - Riddle NC
AU  - Verbsky ML
AU  - Richards EJ
PT  - Journal Article
TA  - Genetics
JT  - Genetics
SO  - Genetics 2003 163: 1109-1122.

PMID- 17071965
VI  - 34
DP  - 2006
TI  - A real-time assay for monitoring nucleic acid cleavage by quadruplex formation.
PG  - e141
AB  - Direct and straightforward methods to follow nucleic acid cleavage are needed. A
      spectrophotometric quadruplex formation assay (QFA) was
      developed, which allows real-time monitoring of site-specific cleavage of
      nucleic acids. QFA was applied to study both protein and nucleic acid
      restriction enzymes, and was demonstrated to accurately determine
      Michaelis-Menten parameters for the cleavage reaction catalyzed by EcoRI.
      QFA can be used to study the mechanisms of protein-nucleic acid
      recognition. QFA is also a useful tool for dissecting individual nicking
      rates of a double-stranded cleavage.
AU  - Kankia BI
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2006 34: e141.

PMID- 2585490
VI  - 209
DP  - 1989
TI  - Conservation of organization in the specificity polypeptides of two families of Type I restriction enzymes.
PG  - 335-344
AB  - We have identified the recognition sequence for the Citrobacter freundii
      restriction endonuclease CfrA, a member of the A-family of type I R-M enzymes.
      This bipartite target sequence differs in both its components from those of
      other type I enzymes.  We determined the nucleotide sequence of its specificity
      gene (hsdS) and a comparison of this with its relative EcoA identifies two
      extensive variable regions, an organization analogous to that found in the
      K-family of type I R-M enzymes.  The specificity polypeptides of the A-family,
      unlike those of K, have an N-terminal conserved region, and this includes a
      sequence repeated within the central conserved region.  A second repeat
      sequence, identified at the amino acid level, coincides with the only sequence
      similarity common to all type I S polypeptides.  Sequences immediately
      downstream from the hsdS genes of EcoA, CfrA, EcoK, B and D are almost
      identical, consistent with an allelic chromosomal location.
AU  - Kannan P
AU  - Cowan GM
AU  - Daniel AS
AU  - Gann AAF
AU  - Murray NE
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1989 209: 335-344.

PMID- 3323824
VI  - 208
DP  - 1987
TI  - Restriction alleviation and enchancement of mutagenesis of the bacteriophage T4 chromosome in recBCsbcA strains of Escherichia coli.
PG  - 413-418
AB  - The restriction of non glucosylated phage T4 DNA is reduced significantly in
      host bacterial strains carrying recBCsbcA mutations even in the presence of a
      functional rgl gene.  In recBCsbcA hosts a high frequency of phage mutations
      are observed both in the glucosyl transferase genes and in the DNA sequences
      recognised by the rgl restriction enzymes.  This hypermutagenic property of the
      recBCsbcA strains is not dependent on the glucosylation of the phage DNA, and
      the mutagenesis is localized to certain regions of the T4 chromosome.  However,
      alleviation of rgl restriction in recBCsbcA strains is due neither to the
      increased mutagenesis, nor to the absence of a functional rgl system, since
      second site mutations (rra) restore rgl restriction without affecting
      hypermutagenesis.
AU  - Kannan PR
AU  - Dharmalingam K
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1987 208: 413-418.

PMID- 29903815
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of a Novel Mutant Strain of Vibrio parahaemolyticus from Pacific White Shrimp (Penaeus vannamei).
PG  - e00497-18
AB  - The acute hepatopancreatic necrosis disease (AHPND) of Penaeus vannamei shrimp is caused by
      Vibrio parahaemolyticus carrying toxin genes, pirA and pirB We report
      the complete genome sequence of the novel V. parahaemolyticus strain R14, which
      did not display AHPND symptoms in P. vannamei despite containing the binary toxin
      genes.
AU  - Kanrar S
AU  - Dhar AK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00497-18.

PMID- 29930055
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of a Deletion Mutant of Vibrio parahaemolyticus from Pacific White Shrimp (Penaeus vannamei).
PG  - e00544-18
AB  - Vibrio parahaemolyticus carrying the toxin genes pirA and pirB causes acute hepatopancreatic
      necrosis disease in shrimp. A genome sequence of V.
      parahaemolyticus strain R13 was determined that showed deletions of the entire
      pirA gene and the 5' end of the pirB gene and does not cause the disease in
      experimental challenge.
AU  - Kanrar S
AU  - Dhar AK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00544-18.

PMID- 1348102
VI  - 36
DP  - 1992
TI  - DNA restriction enzymes and RFLPs in medicine.
PG  - 129-140
AB  - *

          1 Restriction Enzymes (Endonucleases)

        1.1 General information

        1.2 Restriction enzymes and molecular cloning

        1.3 Restriction enzymes, chromosomal mapping, and gene expression

        1.4 Technical notes

          2 Restriction fragment-length polymorphisms

        2.1 RFLPs defined

        2.2 RFLPs and alleles in human genetic disorders

      2.2.1 Linkage of RFLPs to genetic diseases

      2.2.2 Restriction enzymes to detect disease-causing mutations

      2.2.3 Haplotypes and linkage disequilibrium

        2.3 RFLPs in neoplasia and cancer

      2.3.1 Loss of RFLP heterozygosity and tumor suppressor genes

      2.3.2 Clonality analysis of hematolymphoid neoplasms

      2.3.3 Consistent chromosomal translocations

      2.3.4 Clonality studies of nonhematolymphoid tumors

        2.4 Infectious diseases

          3 Overview

      

AU  - Kant JA
PT  - Journal Article
TA  - Methods Biochem. Anal.
JT  - Methods Biochem. Anal.
SO  - Methods Biochem. Anal. 1992 36: 129-140.

PMID- 21460084
VI  - 193
DP  - 2011
TI  - Genome Sequence of 'Pedosphaera parvula' Ellin514, an Aerobic Verrucomicrobial Isolate from Pasture Soil.
PG  - 2900-2901
AB  - "Pedosphaera parvula" Ellin514 is an aerobically grown verrucomicrobial
      isolate from pasture soil. It is one of the few cultured representatives
      of subdivision 3 of the phylum Verrucomicrobia. Members of this group are
      widespread in terrestrial environments.
AU  - Kant R et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 2900-2901.

PMID- 21478337
VI  - 193
DP  - 2011
TI  - Genome sequence of Lactobacillus amylovorus GRL1118, isolated from the pig ileum.
PG  - 3147-3148
AB  - Lactobacillus amylovorus is a common member of the beneficial microbiota present in the pig
      gastrointestinal tract (GIT). Here, we report the genome sequence of surface layer (S-layer)
      protein carrying, and potential probiotic L. amylovorus GRL1118, that was isolated from
      porcine ileum and showed strong adherence to the pig intestinal epithelial cells.
AU  - Kant R
AU  - Paulin L
AU  - Alatalo E
AU  - de Vos WM
AU  - Palva A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3147-3148.

PMID- 21131492
VI  - 193
DP  - 2010
TI  - Genome Sequence of Lactobacillus amylovorus GRL1112.
PG  - 789-790
AB  - Lactobacillus amylovorus is a common member of the normal gastrointestinal tract (GIT)
      microbiota in pigs. Here, we report the genome sequence of L.
      amylovorus GRL1112, a porcine faeces isolate displaying strong adherence
      to the pig intestinal epithelial cells. The strain is of interest as it is
      a potential probiotic bacterium.
AU  - Kant R
AU  - Paulin L
AU  - Alatalo E
AU  - de Vos WM
AU  - Palva A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 193: 789-790.

PMID- 25838483
VI  - 3
DP  - 2015
TI  - Genome Sequence of the Butyrate-Producing Anaerobic Bacterium Anaerostipes hadrus PEL 85.
PG  - e00224-15
AB  - Anaerostipes hadrus PEL 85, which was isolated from human feces, is a Gram-positive rod-shaped
      bacterium. The species may play an important role in gut
      health, as it was previously reported to produce butyric acid. Here, we present
      the genome assembly of PEL 85, a novel strain of A. hadrus.
AU  - Kant R
AU  - Rasinkangas P
AU  - Satokari R
AU  - Pietila TE
AU  - Palva A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00224-15.

PMID- 25908141
VI  - 3
DP  - 2015
TI  - Genome Sequences of Four Staphylococcus aureus Strains Isolated from Bovine Mastitis.
PG  - e00334-15
AB  - Staphylococcus aureus is a major causative agent of mastitis in dairy cows. The pathogenicity
      of S. aureus may vary; it is able to cause severe clinical
      mastitis, but most often it is associated with chronic subclinical mastitis.
      Here, we present the genome assemblies of four S. aureus strains from bovine
      mastitis.
AU  - Kant R
AU  - Taponen S
AU  - Koort J
AU  - Paulin L
AU  - Avall-Jaaskelainen S
AU  - Palva A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00334-15.

PMID- 27056237
VI  - 4
DP  - 2016
TI  - Genome Sequence of Lactobacillus brevis Strain D6, Isolated from Smoked Fresh Cheese.
PG  - e00264-16
AB  - The autochthonousLactobacillus brevisstrain D6, isolated from smoked fresh cheese, carries a
      45-kDa S-layer protein. Strain D6 has shown adhesion to
      extracellular matrix proteins and to Caco-2 intestinal epithelial cells, as well
      as immunomodulatory potential and beneficial milk technological properties.
      Hence, it could be used as a potential probiotic starter culture for cheese
      production.
AU  - Kant R
AU  - Uroic K
AU  - Hynonen U
AU  - Kos B
AU  - Suskovic J
AU  - Palva A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00264-16.

PMID- 27042262
VI  - 11
DP  - 2016
TI  - Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment.
PG  - 25
AB  - Shimia strain SK013 is an aerobic, Gram-negative, rod shaped alphaproteobacterium affiliated
      with the Roseobacter group within the family Rhodobacteraceae. The
      strain was isolated from surface sediment (0-1 cm) of the Skagerrak at 114 m
      below sea level. The 4,049,808 bp genome of Shimia str. SK013 comprises 3,981
      protein-coding genes and 47 RNA genes. It contains one chromosome and no
      extrachromosomal elements. The genome analysis revealed the presence of genes for
      a dimethylsulfoniopropionate lyase, demethylase and the trimethylamine
      methyltransferase (mttB) as well as genes for nitrate, nitrite and dimethyl
      sulfoxide reduction. This indicates that Shimia str. SK013 is able to switch from
      aerobic to anaerobic metabolism and thus is capable of aerobic and anaerobic
      sulfur cycling at the seafloor. Among the ability to convert other sulfur
      compounds it has the genetic capacity to produce climatically active dimethyl
      sulfide. Growth on glutamate as a sole carbon source results in formation of
      cell-connecting filaments, a putative phenotypic adaptation of the
      surface-associated strain to the environmental conditions at the seafloor. Genome
      analysis revealed the presence of a flagellum (fla1) and a type IV pilus
      biogenesis, which is speculated to be a prerequisite for biofilm formation. This
      is also related to genes responsible for signalling such as N-acyl homoserine
      lactones, as well as quip-genes responsible for quorum quenching and antibiotic
      biosynthesis. Pairwise similarities of 16S rRNA genes (98.56 % sequence
      similarity to the next relative S. haliotis) and the in silico DNA-DNA
      hybridization (21.20 % sequence similarity to S. haliotis) indicated Shimia str.
      SK013 to be considered as a new species. The genome analysis of Shimia str. SK013
      offered first insights into specific physiological and phenotypic adaptation
      mechanisms of Roseobacter-affiliated bacteria to the benthic environment.
AU  - Kanukollu S
AU  - Voget S
AU  - Pohlner M
AU  - Vandieken V
AU  - Petersen J
AU  - Kyrpides NC
AU  - Woyke T
AU  - Shapiro N
AU  - Goker M
AU  - Klenk HP
AU  - Cypionka H
AU  - Engelen B
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 25.

PMID- 25700392
VI  - 3
DP  - 2015
TI  - Genome Sequence and Annotation of Helicobacter pylori Strain Hp238, Isolated from a Taiwanese Patient with Mucosa-Associated Lymphoid Tissue Lymphoma.
PG  - e00006-15
AB  - We present the complete genome sequence of Helicobacter pylori strain Hp238, isolated from a
      Taiwanese patient with gastric mucosa-associated lymphoid tissue  lymphoma. Importantly, H.
      pylori strain Hp238 can multiply in THP-1 cells after internalization through the induction of
      autophagosome formation. These genome data will help to identify genes associated with H.
      pylori intracellular multiplication and pathogenesis.
AU  - Kao CY
AU  - Chen JW
AU  - Huang YT
AU  - Sheu SM
AU  - Sheu BS
AU  - Wu JJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00006-15.

PMID- 28360152
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Carbapenem-Resistant Klebsiella pneumoniae Strain 1756, Isolated from a Pus Specimen.
PG  - e00066-17
AB  - Carbapenem-resistant Klebsiella pneumoniae strain 1756 was isolated from a pus specimen from a
      Taiwanese patient. Here, the complete genome sequence of strain
      1756 is presented.
AU  - Kao CY
AU  - Yan JJ
AU  - Lin YC
AU  - Zheng PX
AU  - Wu JJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00066-17.

PMID- 11889109
VI  - 184
DP  - 2002
TI  - Genome sequence and analysis of the oral bacterium Fusobacterium nucleatum strain ATCC 25586.
PG  - 2005-2018
AB  - We present a complete DNA sequence and metabolic analysis of the dominant oral bacterium
      Fusobacterium nucleatum. Although not considered a major dental pathogen on its own, this
      anaerobe facilitates the aggregation and establishment of several other species including the
      dental pathogens Porphyromonas gingivalis and Bacteroides forsythus. The F. nucleatum strain
      ATCC 25586 genome was assembled from shotgun sequences and analyzed using the ERGO
      bioinformatics suite (http://www.integratedgenomics.com). The genome contains 2.17 Mb encoding
      2,067 open reading frames, organized on a single circular chromosome with 27% GC content.
      Despite its taxonomic position among the gram-negative bacteria, several features of its core
      metabolism are similar to that of gram-positive Clostridium spp., Enterococcus spp., and
      Lactococcus spp. The genome analysis has revealed several key aspects of the pathways of
      organic acid, amino acid, carbohydrate, and lipid metabolism. Nine very-high-molecular-weight
      outer membrane proteins are predicted from the sequence, none of which has been reported in
      the literature. More than 137 transporters for the uptake of a variety of substrates such as
      peptides, sugars, metal ions, and cofactors have been identified. Biosynthetic pathways exist
      for only three amino acids: glutamate, aspartate, and asparagine. The remaining amino acids
      are imported as such or as di- or oligopeptides that are subsequently degraded in the
      cytoplasm. A principal source of energy appears to be the fermentation of glutamate to
      butyrate. Additionally, desulfuration of cysteine and methionine yields ammonia, H2S, methyl
      mercaptan, and butyrate, which are capable of arresting fibroblast growth, thus preventing
      wound healing and aiding penetration of the gingival epithelium. The metabolic capabilities of
      F. nucleatum revealed by its genome are therefore consistent with its specialized niche in the
      mouth.
AU  - Kapatral V et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2002 184: 2005-2018.

PMID- 12799352
VI  - 13
DP  - 2003
TI  - Genome Analysis of F. nucleatum sub spp vincentii and Its Comparison With the Genome of F. nucleatum ATCC 25586.
PG  - 1180-1189
AB  - We present the draft genome sequence and its analysis for Fusobacterium nucleatum sub spp.
      vincentii (FNV), and compare that genome with F.
      nucleatum ATCC 25586 (FN). A total of 441 FNV open reading frames (ORFs)
      with no orthologs in FN have been identified. Of these, 118 ORFs have no
      known function and are unique to FNV, whereas 323 ORFs have functional
      orthologs in other organisms. In addition to the excretion of butyrate,
      H2S and ammonia-like FN, FNV has the additional capability to excrete
      lactate and aminobutyrate. Unlike FN, FNV is likely to incorporate
      galactopyranose, galacturonate, and sialic acid into its O-antigen. It
      appears to transport ferrous iron by an anaerobic ferrous transporter.
      Genes for eukaryotic type serine/threonine kinase and phosphatase,
      transpeptidase E-transglycosylase Pbp1A are found in FNV but not in FN.
      Unique ABC transporters, cryptic phages, and three types of
      restriction-modification systems have been identified in FNV. ORFs for
      ethanolamine utilization, thermostable carboxypeptidase, gamma
      glutamyl-transpeptidase, and deblocking aminopeptidases are absent from
      FNV. FNV, like FN, lacks the classical catalase-peroxidase system, but
      thioredoxin/glutaredoxin enzymes might alleviate oxidative stress. Genes
      for resistance to antibiotics such as acriflavin, bacitracin, bleomycin,
      daunorubicin, florfenicol, and other general multidrug resistance are
      present. These capabilities allow Fusobacteria to survive in a mixed
      culture in the mouth.
AU  - Kapatral V
AU  - Ivanova N
AU  - Anderson I
AU  - Reznik G
AU  - Bhattacharyya A
AU  - Gardner WL
AU  - Mikhailova N
AU  - Lapidus A
AU  - Larsen N
AU  - D'Souza M
AU  - Walunas T
AU  - Haselkorn R
AU  - Overbeek R
AU  - Kyrpides N
PT  - Journal Article
TA  - Genome Res.
JT  - Genome Res.
SO  - Genome Res. 2003 13: 1180-1189.

PMID- 17183163
VI  - 63
DP  - 2007
TI  - Purification, crystallization and preliminary X-ray analysis of the BseCI DNA methyltransferase from Bacillus stearothermophilus in complex with its cognate DNA.
PG  - 12-14
AB  - The DNA methyltransferase M. BseCI from Bacillus stearothermophilus (EC 2.1.1.72), a
      579-amino-acid enzyme, methylates the N6 atom of the 30
      adenine in the sequence 50-ATCGAT-3'. M.BseCI was crystallized in
      complex with its cognate DNA. The crystals were found to belong to the
      hexagonal space group P6, with unit-cell parameters a = b = 87.0, c =
      156.1 angstrom, beta = 120.0 degrees and one molecule in the asymmetric
      unit. Two complete data sets were collected at wavelengths of 1.1 and
      2.0 angstrom to 2.5 and 2.8 angstrom resolution, respectively, using
      synchrotron radiation at 100 K.
AU  - Kapetaniou EG
AU  - Kotsifaki D
AU  - Providaki M
AU  - Rina M
AU  - Bouriotis V
AU  - Kokkinidis M
PT  - Journal Article
TA  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
JT  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
SO  - Acta Crystallogr. F Struct. Biol. Cryst. Commun. 2007 63: 12-14.

PMID- 1721700
VI  - 19
DP  - 1991
TI  - Cloning, characterization and evolution of the BsuFI restriction endonuclease gene of Bacillus subtilis and purification of the enzyme.
PG  - 6457-6463
AB  - The restriction endonuclease (R.BsuFI) of Bacillus subtilis recognizes the target DNA sequence
      5' CCGG. The R.BsuFI gene was found in close proximity to the cognate M.BsuFI gene, which had
      previously been characterized. Cloning of the R.BsuFI gene in E. coli was only possible with
      the M.BsuFI Mtase gene present on a compatible plasmid. The cloned R.BsuFI gene was expressed
      in E. coli and restriction activity was observed in vivo and in vitro. The R.BsuFI gene
      consists of 1185 bp, coding for a protein of 395 amino acids with a calculated molecular
      weight of 45.6 kD. The R.BsuFI enzyme was purified to homogeneity following overexpression. It
      presumably works as a dimer and cleaves the 5' CCGG target sequence between the two cytosines
      to produce sticky ends with 5' CG overhangs, like the isoschizomers R.MspI and R.HpaII. The
      relatedness between R.BsuFI and R.MspI is reflected by significant similarities of the amino
      acid sequences of both enzymes. This is the first case where such similarities have been
      observed between isoschizomeric restriction endonucleases which belong to 5mC specific R/M
      systems. This observation suggests that R.BsuFI and R.MspI genes derive from a common
      ancestor. In spite of such functional and evolutionary relatedness, the R/M systems differ in
      the arrangement of their R and M genes. In the BsuFI system transcription of the two genes is
      convergent, whereas divergent transcription occurs in the MspI system.
AU  - Kapfer W
AU  - Walter J
AU  - Trautner TA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 6457-6463.

PMID- 12426348
VI  - 184
DP  - 2002
TI  - Vibrio cholerae phage K139: complete genome sequence and comparative genomics of related phages.
PG  - 6592-6601
AB  - In this report, we characterize the complete genome sequence of the
      temperate phage K139, which morphologically belongs to the Myoviridae
      phage family (P2 and 186). The prophage genome consists of 33,106 bp, and
      the overall GC content is 48.9%. Forty-four open reading frames were
      identified. Homology analysis and motif search were used to assign
      possible functions for the genes, revealing a close relationship to
      P2-like phages. By Southern blot screening of a Vibrio cholerae strain
      collection, two highly K139-related phage sequences were detected in
      non-O1, non-O139 strains. Combinatorial PCR analysis revealed almost
      identical genome organizations. One region of variable gene content was
      identified and sequenced. Additionally, the tail fiber genes were
      analyzed, leading to the identification of putative host-specific sequence
      variations. Furthermore, a K139-encoded Dam methyltransferase was
      characterized.
AU  - Kapfhammer D
AU  - Blass J
AU  - Evers S
AU  - Reidl J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2002 184: 6592-6601.

PMID- 1090619
VI  - 250
DP  - 1975
TI  - Cleavage of nonglucosylated bacteriophage T4 deoxyribonucleic acid by restriction endonuclease EcoRI.
PG  - 2395-2397
AB  - DNAs lacking the glucosyl modification (Glc-) and additionally lacking the
      6-methylaminopurine (N6-methyladenine) modification (Glc-, MeAde-) were
      prepared from appropriate T4 mutants.  These DNAs were cleaved by the purified
      restriction endonuclease EcoRI from Escherichia coli.  Normally modified DNA
      (Glc+, MeAde+) was not attacked.  The EcoRII and the Hemophilus enzymes HindII
      and HindIII do not attack Glc-, MeAde- T4 DNA, possibly due to the presence of
      6-hydroxymethylcytosine.  EcoRI produces approximately 40 specific fragments
      from Glc- DNA ranging in molecular weights from 0.3 to 10.5x10/6.
AU  - Kaplan DA
AU  - Nierlich DP
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1975 250: 2395-2397.

PMID- 6297483
VI  - 109
DP  - 1982
TI  - Variation in the inhibition of restriction enzyme cleavage of lambda phage DNA produced by two covalent binding antitumor agents:  Anthramycin and Mitomycin C.
PG  - 639-648
AB  - DNA-drug complexes containing various levels of covalently bound mitomycin C
      (MC) or anthramycin were subjected to the actions of a number of restriction
      enzymes.  While MC presented only a partial block to the actions of a number of
      these enzymes, anthramycin, at high binding ratios, blocked enzymatic activity
      very well.  The contrast seen in the restriction cleavage of these DNA-drug
      complexes may be related to the different points of attachement in DNA (minor
      groove vs. major groove) for these drugs.  Although similarities in
      electrophoretic band patterns exist for both drug complexes, certain
      differences indicative of preferences in binding sequences do not necessarily
      lie immediately within the restriction cut sites but may effect the cutting of
      these sites from a distance.  The results also further support anthramycin's
      potential usage as a selective/reversible blocking agent for recombinant
      research.
AU  - Kaplan DJ
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1982 109: 639-648.

PMID- 22582375
VI  - 194
DP  - 2012
TI  - Genome Sequence of Kingella kingae Septic Arthritis Isolate PYKK081.
PG  - 3017
AB  - Kingella kingae is a human oral bacterium that can cause infections of the skeletal system in
      children. The bacterium is also a cardiovascular pathogen
      causing infective endocarditis in children and adults. We report herein the draft
      genome sequence of septic arthritis K. kingae strain PYKK081.
AU  - Kaplan JB
AU  - Lo C
AU  - Xie G
AU  - Johnson SL
AU  - Chain PS
AU  - Donnelly R
AU  - Kachlany SC
AU  - Balashova NV
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3017.

PMID- 23469352
VI  - 1
DP  - 2013
TI  - Genome Sequence of Alcaligenes sp. Strain HPC1271.
PG  - e00235-12
AB  - We report a draft genome sequence of sp. strain HPC1271, which demonstrates antimicrobial
      activity against multidrug-resistant bacteria. Antibiotic
      production by has not been frequently reported, and hence, the availability of
      the genome sequence should enable us to explore new antibiotic-producing gene
      clusters.
AU  - Kapley A
AU  - Sagarkar S
AU  - Tanksale H
AU  - Sharma N
AU  - Qureshi A
AU  - Khardenavis A
AU  - Purohit HJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00235-12.

PMID- 7628716
VI  - 160
DP  - 1995
TI  - SgfI, a new type-II restriction endonuclease that recognizes the octanucleotide sequence 5'-GCGAT/CGC-3'.
PG  - 55-58
AB  - A new restriction endonuclease (ENase), SgfI, has been isolated from the bacterium
      Streptomyces sp. SgfI recognizes the 8-bp palindrome 5'-GCGATCGC-3' and cleaves
      double-stranded DNA after the T in this sequence, producing a two-base 3' overhang compatible
      with PvuI termini.  SgfI is a rare-cutting ENase and should be useful for megabase mapping
      experiments.
AU  - Kappelman JR
AU  - Brady M
AU  - Knoche K
AU  - Murray E
AU  - Schoenfeld T
AU  - Williams R
AU  - Vesselinova N
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 160: 55-58.

PMID- 23450099
VI  - 7
DP  - 2012
TI  - Complete genome sequence of the facultatively chemolithoautotrophic and methylotrophic alpha Proteobacterium Starkeya novella type strain (ATCC 8093(T)).
PG  - 44-58
AB  - (Starkey 1934) Kelly . 2000 is a member of the family in the order , which is thus far poorly
      characterized at the genome level. Cultures from this species are
      most interesting due to their facultatively chemolithoautotrophic lifestyle,
      which allows them to both consume carbon dioxide and to produce it. This feature
      makes an interesting model organism for studying the genomic basis of regulatory
      networks required for the switch between consumption and production of carbon
      dioxide, a key component of the global carbon cycle. In addition, is of interest
      for its ability to grow on various inorganic sulfur compounds and several
      C1-compounds such as methanol. Besides , is only the second species in the family
      with a completely sequenced genome of a type strain. The current taxonomic
      classification of this group is in significant conflict with the 16S rRNA data.
      The genomic data indicate that the physiological capabilities of the organism
      might have been underestimated. The 4,765,023 bp long chromosome with its 4,511
      protein-coding and 52 RNA genes was sequenced as part of the DOE Joint Genome
      Institute Community Sequencing Program (CSP) 2008.
AU  - Kappler U et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 7: 44-58.

PMID- 27274784
VI  - 11
DP  - 2016
TI  - Complete genome sequence of the haloalkaliphilic, obligately chemolithoautotrophic thiosulfate and sulfide-oxidizing gamma-proteobacterium  Thioalkalimicrobium cyclicum type strain ALM 1 (DSM 14477(T)).
PG  - 38
AB  - Thioalkalimicrobium cyclicum Sorokin et al. 2002 is a member of the family Piscirickettsiaceae
      in the order Thiotrichales. The gamma-proteobacterium belongs
      to the colourless sulfur-oxidizing bacteria isolated from saline soda lakes with
      stable alkaline pH, such as Lake Mono (California) and Soap Lake (Washington
      State). Strain ALM 1(T) is characterized by its adaptation to life in the
      oxic/anoxic interface towards the less saline aerobic waters (mixolimnion) of the
      stable stratified alkaline salt lakes. Strain ALM 1(T) is the first
      representative of the genus Thioalkalimicrobium whose genome sequence has been
      deciphered and the fourth genome sequence of a type strain of the
      Piscirickettsiaceae to be published. The 1,932,455 bp long chromosome with its
      1,684 protein-coding and 50 RNA genes was sequenced as part of the DOE Joint
      Genome Institute Community Sequencing Program (CSP) 2008.
AU  - Kappler U
AU  - Davenport K
AU  - Beatson S
AU  - Lapidus A
AU  - Pan C
AU  - Han C
AU  - Montero-Calasanz MC
AU  - Land M
AU  - Hauser L
AU  - Rohde M
AU  - Goker M
AU  - Ivanova N
AU  - Woyke T
AU  - Klenk HP
AU  - Kyrpides NC
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 38.

PMID- 28336588
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Three Nontypeable Strains of Haemophilus influenzae, C188, R535, and 1200, Isolated from Different Types of Disease.
PG  - e00035-17
AB  - Nontypeable Haemophilus influenzae is a persistent human respiratory pathogen known to be
      involved in a range of acute and chronic respiratory diseases. Here,
      we report the genome sequences of three H. influenzae strains isolated from
      sputum, otitis media, and blood. Comparative analyses revealed significant
      differences in the gene contents including the presence of genes mediating
      antibiotic resistance.
AU  - Kappler U
AU  - Dhouib R
AU  - Nair RP
AU  - McEwan AG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00035-17.

PMID- 28408670
VI  - 5
DP  - 2017
TI  - Insights into the Psychrophilic and Sea Ice-Specific Lifestyle of Marinobacter sp. Strain AC-23: a Genomic Approach.
PG  - e00134-17
AB  - Marinobacter sp. strain AC-23 was isolated from Kongsfjorden in the Arctic. Here, we report
      the first draft genome sequence of a putative novel species of the
      genus Marinobacter comprising 4,149,715 bp, with a mean G+C content of 54.4%. The
      draft genome sequence will aid in understanding the psychrophilic and sea
      ice-specific lifestyle.
AU  - Kapse N
AU  - Singh P
AU  - Roy U
AU  - Singh SM
AU  - Dhakephalkar PK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00134-17.

PMID- 523319
VI  - 7
DP  - 1979
TI  - Methylation of somatic vs germ cell DNAs analyzed by restriction endonuclease digestions.
PG  - 2303-2322
AB  - Bacterial restriction endonucleases containing the dinucleotide CpG in their
      cleavage sequences were used to compare the methylation patterns of primarily
      repeated DNA sequences in (1) bovine somatic cell native DNAs vs bovine sperm
      cell native DNA and (2) native vs renatured bovine liver and sperm cell DNAs.
      The restriction patterns of sperm native DNA differ markedly from those of
      somatic cell native DNAs when using HpaII, HhaI, and AvaI but not when using
      the enzymes EcoRI and MspI.  Digestion patterns of germ cell renatured DNA
      differed significantly from those of germ cell native DNA when using HpaII but
      not when using MspI or EcoRI.  The results may not be due to artifacts of
      renaturation of the DNAs.  The results are consistent with the concept that
      germ cell DNA may be strand asymmetrically hemimethylated.  The data also
      suggest that methylation of the 5'-cytosine in the sequence CCGG renders this
      site insensitive to cleavage by MspI.
AU  - Kaput J
AU  - Sneider TW
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1979 7: 2303-2322.

PMID- Not included in PubMed...
VI  - 6
DP  - 1970
TI  - Susceptibility of the bacteriophage T5 to host-controlled restriction and modification in the Salmonella derby strain 456.
PG  - 121-128
AB  - It was shown that wild type of bacteriophage T5 (T5h+) was not susceptible to
      host-controlled variation in a bacterial host control system, consisting of E.
      coli strains B, K-12 or BB and Salmonella derby 456 strain.  The h-mutants of
      T5 phage, obtained on B/1,5 strain of E. coli, became susceptible to
      restriction and modification on s. derby 456.  The phage T5h, grown on E. coli
      B, K-12 or BB cells showed an efficiency of plating (eop) on S. derby 456 about
      10/7 - 10/9.  a small number of plaques formed by these mutants on S. derby
      456, contained only modified phage T5h 456 possessing eop equal to 1.0 when
      grown on E. coli strains or on S. derby 456.  Acquirement of susceptibility to
      host-controlled variation by phage T5 was due to host range mutation, which
      indicates that the susceptibility of the phages to this variation is an
      inheritant character of phage DNA, and is subjected to genetic changes and
      selection.  The data obtained allow a suggestion concerning phage genome
      contribution to the processes of the host controlled restriction and
      modification.  The rate of restriction of phage T5h, observed in S. derby 456
      host, after maintaining on E. coli strains and T5h+ phage non-susceptibility to
      the observed effect, indicate that this system of HCV (host-controlled
      variation) might be used as a new experimental model for investigating
      processes of mutational changes of susceptibility of DNA molecule to the
      restricting and modifying mechanisms of host cells.
AU  - Karabecov BP
AU  - Oganesian MG
AU  - Airumian BA
PT  - Journal Article
TA  - Genetika
JT  - Genetika
SO  - Genetika 1970 6: 121-128.

PMID- 329915
VI  - 84
DP  - 1977
TI  - Transformation of EcoRI restriction endonuclease substrate specificity under the influence of glycerol.
PG  - 46-48
AB  - The restriction endonuclease EcoRI hydrolyzes DNA to a greater number of fragments in the
      presence of glycerol than under normal conditions.  This enzyme begins to work by the
      so-called EcoRI*-type of restriction when glycerol concentration reaches 50%.  The EcoRI*
      activity appeared in experiments only when the ionic strength of the solution was decreased
      and pH of the solution was increased.  However, under such extreme conditions the enzyme was
      quickly inactivated and it was difficult to obtain reproducible results especially for
      hydrolysis of the high-molecular DNA.  The suggested conditions for the EcoRI* activity permit
      to obtain reproducible results, this being practically equivalent to discovery of the new
      restriction endonuclease.
AU  - Karamov EV
AU  - Naroditsky BS
AU  - Zavizion BA
AU  - Tikhonenko TI
PT  - Journal Article
TA  - Biull. Eksp. Biol. Med.
JT  - Biull. Eksp. Biol. Med.
SO  - Biull. Eksp. Biol. Med. 1977 84: 46-48.

PMID- 23542886
VI  - 10
DP  - 2013
TI  - Direct transfer of whole genomes from bacteria to yeast.
PG  - 410-412
AB  - Transfer of genomes into yeast facilitates genome engineering for genetically intractable
      organisms, but this process has been hampered by the need for cumbersome isolation of intact
      genomes before transfer. Here we demonstrate direct cell-to-cell transfer of bacterial genomes
      as large as 1.8 megabases (Mb)into yeast under conditions that promote cell fusion. Moreover,
      we discovered that removal of restriction endonucleases from donor bacteria resulted in the
      enhancement of genome transfer.
AU  - Karas BJ
AU  - Jablanovic J
AU  - Sun L
AU  - Ma L
AU  - Goldgof GM
AU  - Stam J
AU  - Ramon A
AU  - Manary MJ
AU  - Winzeler EA
AU  - Venter JC
AU  - Weyman PD
AU  - Gibson DG
AU  - Glass JI
AU  - Hutchison CAIII
AU  - Smith HO
AU  - Suzuki Y
PT  - Journal Article
TA  - Nat. Methods
JT  - Nat. Methods
SO  - Nat. Methods 2013 10: 410-412.

PMID- 26823581
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Probiotic Enterococcus faecium Strain L-3.
PG  - e01622-15
AB  - We report here the draft genome sequence of the bacteriocin producer Enterococcus faecium
      strain L-3, isolated from a probiotic preparation, Laminolact, which is
      widely used in the Russian Federation. The draft genome sequence is composed of
      74 contigs for a total of 2,643,001 bp, with 2,646 coding genes. Five clusters
      for bacteriocin production were found.
AU  - Karaseva A
AU  - Tsapieva A
AU  - Pachebat J
AU  - Suvorov A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01622-15.

PMID- 22328766
VI  - 194
DP  - 2012
TI  - Genome Sequence of Aggregatibacter actinomycetemcomitans RHAA1, Isolated from a Rhesus Macaque, an Old World Primate.
PG  - 1275-1276
AB  - Aggregatibacter actinomycetemcomitans is implicated in localized aggressive periodontitis. We
      report the first genome sequence of an A. actinomycetemcomitans
      strain isolated from an Old World primate.
AU  - Karched M
AU  - Furgang D
AU  - Planet PJ
AU  - Desalle R
AU  - Fine DH
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1275-1276.

PMID- 27034490
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Flavobacterium sp. 316, a Baltic Sea Isolate Exhibiting  a High Level of Resistance to Marine Stress Conditions.
PG  - e00180-16
AB  - Here, we present the draft genome sequence ofFlavobacteriumsp. 316, isolated from brackish
      water of the Gulf of Gdansk, southern Baltic Sea. The assembly contains
      3,971,755 bp in 17 scaffolds. The sequence will facilitate postgenomic studies on
      bacterial stress responses in the challenging habitat of the Baltic Sea.
AU  - Karczewska-Golec J
AU  - Kochanowska-Lyzen M
AU  - Olszewski P
AU  - Balut M
AU  - Moskot M
AU  - Piotrowski A
AU  - Golec P
AU  - Szalewska-Palasz A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00180-16.

PMID- 27340075
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Shewanella baltica M1 Isolated from Brackish Surface Water of the Gulf of Gdansk.
PG  - e00611-16
AB  - Here, we present the 5.168-Mbp draft genome sequence of Shewanella baltica M1, the first
      Shewanella strain from the Gulf of Gdansk to have its genome sequenced
      and annotated. The availability of the genome sequence of strain M1 will promote
      further global analyses of bacterial stress responses in the unique Gulf of
      Gdansk ecosystem.
AU  - Karczewska-Golec J
AU  - Strapagiel D
AU  - Sadowska M
AU  - Szalewska-Palasz A
AU  - Golec P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00611-16.

PMID- 24386888
VI  - 352
DP  - 2014
TI  - Complete nucleotide sequence of a conjugative IncF plasmid from an Escherichia coli isolate of equine origin containing blaCMY-2 within a novel genetic context.
PG  - 123-127
AB  - A blaCMY-2 -containing conjugative IncF plasmid denoted as pEQ011, previously
      identified in a multidrug-resistant Escherichia coli isolate of equine origin,
      was characterized. The plasmid consisted of 85 507 bp, with 118 predicted open
      reading frames. This is the first known report demonstrating the association of a
      blaCMY-2 gene with an IncF incompatibility-type plasmid backbone. A novel genetic
      arrangement was identified wherein the blaCMY-2 resistance gene was proximally
      flanked by IS1294 along with a partial blc gene located distally and within a
      yacABC operon.
AU  - Karczmarczyk M
AU  - Wang J
AU  - Leonard N
AU  - Fanning S
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2014 352: 123-127.

PMID- 28104653
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Microbacterium sp. Strain Alg239_V18, an Actinobacterium Retrieved from the Marine Sponge Spongia sp.
PG  - e01457-16
AB  - Here, we describe the draft genome sequence of Microbacterium sp. strain Alg239_V18, an
      actinobacterium retrieved from the marine sponge Spongia sp.
      Genome annotation revealed a vast gene repertoire involved in antibiotic and
      heavy metal-resistance, and a versatile carbohydrate assimilation metabolism with
      potential for chitin utilization.
AU  - Karimi E
AU  - Goncalves JM
AU  - Reis M
AU  - Costa R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01457-16.

PMID- 28546497
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of the Autotrophic Acetogen Clostridium formicaceticum DSM 92T Using Nanopore and Illumina Sequencing Data.
PG  - e00423-17
AB  - Here, we report the closed genome sequence of Clostridium formicaceticum, an Rnf- and
      cytochrome-containing autotrophic acetogen that is able to convert carbon
      monoxide to acetate using the Wood-Ljungdahl pathway. The genome consists of a
      circular chromosome (4.59 Mb).
AU  - Karl MM
AU  - Poehlein A
AU  - Bengelsdorf FR
AU  - Daniel R
AU  - Durre P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00423-17.

PMID- 1313968
VI  - 20
DP  - 1992
TI  - Statistical analyses of counts and distributions of restriction sites in DNA sequences.
PG  - 1363-1370
AB  - Counts and spacings of all 4- and 6-bp palindromes in DNA sequences from a
      broad range of organisms were investigated.  Both 4- and 6-bp average
      palindrome counts were significantly low in all bacteriophages except one,
      probably as a means of avoiding restriction enzyme cleavage.  The exception, T4
      of normal 4- and 6-palindrome counts, putatively derives protection from
      modification of cytosine to hydroxymethylcytosine plus glycosylation.  The
      counts and distributions of 4-bp and of 6-bp restriction sites in bacterial
      species are variable.  Bacterial cells with multiple restriction systems for
      4-bp or 6-bp target specificities are low in aggregate 4- or 6-bp palindrome
      counts/kb, respectively, but bacterial cells lacking exact 4-cutter enzymes
      generally show normal or high counts of 4-bp palindromes when compared with
      random control sequences of comparable nucleotide frequencies.  For example, E.
      coli, apparently without an exact 4-bp target restriction endonuclease (see
      text), contains normal aggregate 4-palindrome counts/kb, while B. subtilis,
      which abounds with 4-bp restriction system, shows a significant
      under-representation of 4-palindrome counts.  Both E. coli and B. subtilis have
      many 6-bp restriction enzymes and concomitantly diminished aggregate
      6-palindrome counts/kb.  Eukaryote, viral, and organelle sequences generally
      have aggregate 4- and 6-palindromic counts/kb in the normal range.
      Interpretations of these results are given in terms of restriction/methylation
      regimes, recombination and transcription processes, and possible structural and
      regulatory roles of 4- and 6-bp palindromes.
AU  - Karlin S
AU  - Burge C
AU  - Campbell AM
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 1363-1370.

PMID- 2848159
VI  - 132
DP  - 1988
TI  - Mutual competitive inhibition between target sites during the restriction endonuclease digestion of DNA.
PG  - 1-6
AB  - The reaction rate of restriction endonuclease was evaluated theoretically, considering the
      competition between target sites and a nonspecific DNA.  An equation for the initial cleavage
      rate at a single site for a DNA substrate containing more than one recognition site was
      derived.  The consequences for the study of preferential cleavage were discussed.
AU  - Karlovsky P
PT  - Journal Article
TA  - J. Theor. Biol.
JT  - J. Theor. Biol.
SO  - J. Theor. Biol. 1988 132: 1-6.

PMID- 2848160
VI  - 132
DP  - 1988
TI  - Calculation of individual cleavage rates from partial digests in restriction endonuclease kinetics.
PG  - 7-14
AB  - A correction for results obtained by an analysis of DNA molecules partially
      cleaved with restriction endonuclease was suggested.  The correction was proved
      on model data.  Applications to (i) electron-microscopic analysis of singly
      cleaved molecules, (ii) partial digestion of a circular molecule followed by
      complete digestion with a second enzyme, (iii) systems with great cleavage
      differences, and (iv) partial cleavage of end-labelled molecules were
      discussed.
AU  - Karlovsky P
PT  - Journal Article
TA  - J. Theor. Biol.
JT  - J. Theor. Biol.
SO  - J. Theor. Biol. 1988 132: 7-14.

PMID- 3028020
VI  - 35
DP  - 1986
TI  - Kinetics of circular DNA molecule digestion by restriction endonuclease A: Computation of kinetic constants from time dependence of fragment concentrations.
PG  - 279-292
AB  - A model for kinetics of circular substrate cleavage by restriction endonuclease
      was formulated.  The aim of the analysis of the model was to extract kinetic
      constants for all target sites from time-dependence of fragment concentration
      in reaction products.  That was proved to be possible for molecules with an odd
      number of fragments only.  A symmetry of the molecules with an even number of
      fragment is the cause.  A solution for molecules witih an odd number of
      fragments was found and methods for dealing with the other moleculars were
      suggested.
AU  - Karlovsky P
PT  - Journal Article
TA  - Acta Biotheor.
JT  - Acta Biotheor.
SO  - Acta Biotheor. 1986 35: 279-292.

PMID- 3017308
VI  - 235
DP  - 1986
TI  - A re-evaluation of evidence attributing the difference in cleavage rates of restriction endonuclease at different sites in the substrate to differences in KM values.
PG  - 611-612
AB  - The only result supporting the hypothesis that the differences in restriction
      endonuclease cleavage rates at various target sites are caused by differences
      in KM values was reported by Forsblom, Rigler, Ehrenberg, Petterson & Philipson
      [(1976) Nucl. Acids Res. 3, 3255-3269].  The present work shows that the
      kinetic analysis in that paper is based on incorrect derivation and in fact
      provides no support for the hypothesis mentioned.
AU  - Karlovsky P
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 1986 235: 611-612.

PMID- 24407651
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Lactobacillus plantarum 2165.
PG  - e01179-13
AB  - This report describes a draft genome sequence of Lactobacillus plantarum 2165. The data
      demonstrate the presence of a large number of genes responsible for
      sugar metabolism and the fermentation activity of this bacterium. Different cell
      surface proteins, including fibronectin and mucus-binding adhesins, may
      contribute to the beneficial probiotic properties of this strain.
AU  - Karlyshev AV
AU  - Abramov VM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01179-13.

PMID- 26744375
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Lactobacillus plantarum 2025.
PG  - e01532-15
AB  - A draft genome sequence of Lactobacillus plantarum 2025 was derived using Ion Torrent
      sequencing technology. The total size of the assembly (3.33 Mb) was in
      agreement with the genome sizes of other strains of this species. The data will
      assist in revealing the genes responsible for the specific properties of this
      strain.
AU  - Karlyshev AV
AU  - Khlebnikov VC
AU  - Kosarev IV
AU  - Abramov VM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01532-15.

PMID- 26769947
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of 'Cohnella kolymensis' B-2846.
PG  - e01587-15
AB  - A draft genome sequence of 'Cohnella kolymensis' strain B-2846 was derived using  IonTorrent
      sequencing technology. The size of the assembly and G+C content were
      in agreement with those of other species of this genus. Characterization of the
      genome of a novel species of Cohnella will assist in bacterial systematics.
AU  - Karlyshev AV
AU  - Kudryashova EB
AU  - Ariskina EV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01587-15.

PMID- 24201200
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Corynebacterium pseudodiphtheriticum Strain 090104 'Sokolov'.
PG  - e00921-13
AB  - This report describes the first draft genome sequence of a Corynebacterium
      pseudodiphtheriticum strain. The information on the genome organization and
      putative gene products will assist in better understanding of the molecular
      mechanisms involved in the beneficial probiotic effects of this bacterium.
AU  - Karlyshev AV
AU  - Melnikov VG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00921-13.

PMID- 24948771
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Bacillus subtilis strain KATMIRA1933.
PG  - e00619-14
AB  - In this report, we present a draft sequence of Bacillus subtilis KATMIRA1933. Previous studies
      demonstrated probiotic properties of this strain partially
      attributed to production of an antibacterial compound, subtilosin. Comparative
      analysis of this strain's genome with that of a commercial probiotic strain, B.
      subtilis Natto, is presented.
AU  - Karlyshev AV
AU  - Melnikov VG
AU  - Chikindas ML
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00619-14.

PMID- 24948774
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Bacillus amyloliquefaciens B-1895.
PG  - e00633-14
AB  - In this report, we present a draft genome sequence of Bacillus amyloliquefaciens  strain
      B-1895. Comparison with the genome of a reference strain demonstrated
      similar overall organization, as well as differences involving large gene
      clusters.
AU  - Karlyshev AV
AU  - Melnikov VG
AU  - Chistyakov VA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00633-14.

PMID- 24558253
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Lactobacillus crispatus 2029.
PG  - e01221-13
AB  - This report describes a draft genome sequence of Lactobacillus crispatus 2029. The reads
      generated by the Ion Torrent PGM were assembled into contigs with a
      total size of 2.2 Mb. The data were annotated using the NCBI GenBank and RAST
      servers. A comparison with the reference strain revealed specific features of the
      genome.
AU  - Karlyshev AV
AU  - Melnikov VG
AU  - Khlebnikov VC
AU  - Abramov VM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01221-13.

PMID- 24558254
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Lactobacillus rhamnosus 2166.
PG  - e01222-13
AB  - In this report, we present a draft sequence of the genome of Lactobacillus rhamnosus strain
      2166, a potential novel probiotic. Genome annotation and read
      mapping onto a reference genome of L. rhamnosus strain GG allowed for the
      identification of the differences and similarities in the genomic contents and
      gene arrangements of these strains.
AU  - Karlyshev AV
AU  - Melnikov VG
AU  - Kosarev IV
AU  - Abramov VM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01222-13.

PMID- 23969051
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Lactobacillus gasseri Strain 2016.
PG  - e00624-13
AB  - Different common factors contribute to the antagonistic properties of Lactobacillus gasseri
      toward various pathogens. However, there is
      strain-to-strain variation in the probiotic properties of this bacterium. The
      draft genome sequence of L. gasseri strain 2016 determined in this study will
      assist in understanding the genetic basis for such variation.
AU  - Karlyshev AV
AU  - Melnikov VG
AU  - Kosarev IV
AU  - Khlebnikov VC
AU  - Sukhikh GT
AU  - Abramov VM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00624-13.

PMID- 24285651
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Lactobacillus jensenii Strain MD IIE-70(2).
PG  - e01005-13
AB  - A draft genome sequence of Lactobacillus jensenii strain MD IIE-70(2) was determined using Ion
      PGM technology. The reads were mapped to a reference strain
      and assembled using a combination of tools. The genetic features revealed in this
      study will assist in understanding the probiotic properties of Lactobacillus
      bacteria.
AU  - Karlyshev AV
AU  - Nadarajah S
AU  - Abramov VM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01005-13.

PMID- 24285652
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Lactobacillus fermentum Strain 3872.
PG  - e01006-13
AB  - This report describes a draft genome sequence of Lactobacillus fermentum strain 3872. The data
      revealed remarkable similarity to and dissimilarity with the
      published genome sequences of other strains of the species. The absence of and
      variation in structures of some adhesins and the presence of an additional
      adhesin may reflect adaptation of the bacterium to different host systems and may
      contribute to specific properties of this strain as a new probiotic.
AU  - Karlyshev AV
AU  - Raju K
AU  - Abramov VM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01006-13.

PMID- 24948775
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Enterococcus faecalis MB5259.
PG  - e00634-14
AB  - In this study, we present a draft genome sequence of Enterococcus faecalis MB5259, a promising
      probiotic strain. The identified differences and common
      features between this strain and reference strains will assist in better
      understanding the mechanism of antibacterial action and in developing novel
      probiotics.
AU  - Karlyshev AV
AU  - Robyn J
AU  - Rasschaert G
AU  - Heyndrickx M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00634-14.

PMID- 26659681
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of a Probiotic Strain, Lactobacillus fermentum UCO-979C.
PG  - e01439-15
AB  - This report describes a draft genome sequence of Lactobacillus fermentum strain UCO-979C. The
      reads generated by a Ion Torrent PGM were assembled into contigs,
      with a total size of 2.01 Mb. The data were annotated using the NCBI GenBank and
      RAST servers. Specific features of the genome are highlighted.
AU  - Karlyshev AV
AU  - Villena J
AU  - Gonzalez C
AU  - Albarracin L
AU  - Barros J
AU  - Garcia A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01439-15.

PMID- 26941150
VI  - 4
DP  - 2016
TI  - Genome Sequence of a Virulent Pseudomonas aeruginosa Strain, 12-4-4(59), Isolated from the Blood Culture of a Burn Patient.
PG  - e00079-16
AB  - Pseudomonas aeruginosa is an opportunistic pathogen that frequently infects wounds,
      significantly impairs wound healing, and causes morbidity and mortality
      in burn patients. Here, we report the genome sequence of a virulent strain of P.
      aeruginosa, 12-4-4(59), isolated from the blood culture of a burn patient.
AU  - Karna SL
AU  - Chen T
AU  - Chen P
AU  - Peacock TJ
AU  - Abercrombie JJ
AU  - Leung KP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00079-16.

PMID- 7720955
VI  - 9
DP  - 1995
TI  - Peculiarity of the recognition and cleavage by restriction endonuclease EcoRII.
PG  - A1400
AB  - The restriction endonuclease EcoRII binds with high affinity to the duplex DNA 5' CC(A/T)GG
      3' and specifically cleaves it at the 5' end of the site as indicated by the arrow. It has
      been shown that EcoRII requires an auxiliary site for activation, and the formation of a
      four-strand supersite was suggested. To understand the enzymatic mechanism and the interaction
      of EcoRII with two recognition sites, we have studied binding and cleavage of DNA duplexes
      containing canonical or modified EcoRII sites by EcoRII. The reactions were analyzed by
      polyacrylamide gel electrophoresis under non-denaturing conditions. We have shown, that (T to
      5-fluorodeoxyuridine) or (A to N6-methyldeoxyadenosine) substitutions in the central base pair
      do not affect DNA recognition, but they have a dramatic influence on cleavage. At the same
      time modification or substitution of C or G nucleotides in the recognition sequence affects
      both recognition and rate of cleavage of DNA. These data suggests that specific interaction
      with the central base pair (A/T) contributes to the catalytic activity of the enzyme. Based on
      these data we present a model for four-strand supersite formation of the enzyme-substrate
      complex.
AU  - Karpova E
AU  - Kubareva E
AU  - Petrauskene O
AU  - Joschimiak A
AU  - Van Kley H
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1995 9: A1400.

PMID- 1470181
VI  - 26
DP  - 1992
TI  - Formation of two types of enzyme-substrate complexes at the interaction of EcoRII restriction endonuclese with synthetic DNA duplexes.
PG  - 993-998
AB  - Binding of EcoRII restriction endonuclease to synthetic oligodeoxyribonucleotide substrates of
      11-30 base pairs long was investigated by polyacrylamide gel electrophoresis under
      nondenaturing conditions in the absence of Mg2+ ions. Irrespective of the length of a
      substrate, two types of specific DNA-protein complexes were shown to be formed. Their mobility
      in gels was close to that of the monomer (45 kDa) and dimer (90 kDa) of marker protein
      ovalbumin. The ratio of these complexes in solution depended on that of the molar
      concentrations of EcoRII restriction endonuclease and DNA duplexes. The possible structure of
      the complexes is discussed.
AU  - Karpova EA
AU  - Kubareva EA
AU  - Buryanov YI
AU  - Gromova ES
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1992 26: 993-998.

PMID- 8490558
VI  - 29
DP  - 1993
TI  - Peculiaritites of the binding of restriction endonuclease EcoRII to synthetic DNA duplexes.
PG  - 113-121
AB  - The binding of restriction endonuclease EcoRII to synthetic oligodeoxyribonucleotide
      substrates 11 to 30 bp long was investigated by gradient polyacrylamide gel electrophoresis
      under nondenaturing conditions in the absence of Mg2+ ions. Irrespective of the substrate's
      length, two types of specific DNA-protein complexes were shown to be formed. Their mobility in
      gels was close to that of the monomer and the dimer of the marker ovalbumin. The number of
      such complexes in solution depended on the ratio of the molar concentrations of restriction
      endonuclease EcoRII and the DNA duplex. The possible structure of the complexes is discussed.
AU  - Karpova EA
AU  - Kubareva EA
AU  - Gromova ES
AU  - Buryanov YI
PT  - Journal Article
TA  - Biochem. Mol. Biol. Int.
JT  - Biochem. Mol. Biol. Int.
SO  - Biochem. Mol. Biol. Int. 1993 29: 113-121.

PMID- 10791921
VI  - 48
DP  - 1999
TI  - A model of EcoRII restriction endonuclease action: The active complex is most likely formed by one protein subunit and one DNA recognition site.
PG  - 91-98
AB  - To elucidate the mechanism of interaction of restriction endonuclease EcoRII with DNA, we
      studied by native gel electrophoresis the binding of this endonuclease to a set of synthetic
      DNA-duplexes containing the modified or canonical recognition sequence 5'-d(CCA/TGG)-3'.
      All binding substrates or substrate analogues tested could be divided into two major groups:
      (I) duplexes that, at the interaction with endonuclease EcoRII, form two types of stable
      complexes on native gel in the absence of Mg2+ cofactor; (ii) duplexes that form only one type
      of complex, observed both in the presence and absence of Mg2+.  Unlike the latter, duplexes
      under the first group can be hydrolyzed by endonuclease.  Data obtained suggest that the
      active complex is most likely formed by one protein subunit and one DNA recognition sequence.
      A model of EcoRII endonuclease action is presented.
AU  - Karpova EA
AU  - Kubareva EA
AU  - Shabarova ZA
PT  - Journal Article
TA  - Life
JT  - Life
SO  - Life 1999 48: 91-98.

PMID- 10489460
VI  - 55
DP  - 1999
TI  - Crystallization and preliminary x-ray diffraction analysis of restriction endonuclease EcoRII.
PG  - 1604-1605
AB  - Crystals of the restriction endonuclease EcoRII have been obtained by the vapor-diffusion
      technique in the presence of ammonium sulfate or polyethylene glycol. The best crystals were
      grown with ammonium sulfate as a precipitant. Crystals with dimensions of up to 0.6 x 0. 6 x
      0.6 mm have been observed. The crystals diffract to about 4.0 A resolution at a
      cryo-temperature of 100 K using a rotating-anode X-ray source and a Rigaku R-AXIS IV
      imaging-plate detector. The space group has been determined to be either I23 or I2(1)3, with
      unit-cell parameters a = b = c = 160.3 A, alpha = beta = gamma = 90 degrees. The crystal
      asymmetric unit contains two protein molecules, and self-rotation function analysis shows a
      pseudo-twofold symmetry relating the two monomers. Attempts to improve the resolution of
      crystal diffraction and to search for heavy-atom derivatives are under way.
AU  - Karpova EA
AU  - Meehan E
AU  - Pusey ML
AU  - Chen L
PT  - Journal Article
TA  - Acta Crystallogr. D Biol. Crystallogr.
JT  - Acta Crystallogr. D Biol. Crystallogr.
SO  - Acta Crystallogr. D Biol. Crystallogr. 1999 55: 1604-1605.

PMID- 
VI  - 
DP  - 1988
TI  - The genes for two procaryotic DNA modification methylases.
PG  - 1-95
AB  - None
AU  - Karreman C
PT  - Journal Article
TA  - Ph.D. Thesis, State University of Leiden, Holland
JT  - Ph.D. Thesis, State University of Leiden, Holland
SO  - Ph.D. Thesis, State University of Leiden, Holland 1988 : 1-95.

PMID- 2836360
VI  - 170
DP  - 1988
TI  - Isolation and characterization of the modification methylase M.SinI.
PG  - 2533-2536
AB  - A sequence-specific modification methylase (M.SinI) was isolated and purified from Escherichia
      coli harboring a derivative of recombinant plasmid pSI4 (see accompanying manuscript: C.
      Karreman and A. de Waard, J. Bacteriol. 170:2527-2532, 1988), which contains a Salmonella
      infantis DNA insert. The enzyme uniquely methylates the internal deoxycytidylate residue in
      the nucleotide sequence GG(A/T)MeCC, thereby protecting DNA completely against cleavage by
      restriction endonuclease R.SinI or R.AvaII [GG(A/T)CC], and in part against cleavage by
      R.Sau96I (GGNCC).
AU  - Karreman C
AU  - de Waard A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1988 170: 2533-2536.

PMID- 2104605
VI  - 172
DP  - 1990
TI  - Agmenellum quadruplicatum M.AquI, a novel modification methylase.
PG  - 266-272
AB  - The complete type II modification methylase of Agmenellum quadruplicatum was cloned in
      Escherichia coli as an R.Sau3A fragment of approximately 4.5 kilobases. The coding sequence
      was contained in a stretch of 1,156 base pairs which was organized into two parallel, partly
      overlapping open reading frames of 248 and 139 codons. In vivo complementation experiments
      showed that the synthesis of both predicted peptides was required for full methylase activity.
      The amino acid sequences were considerably similar to regions of other deoxycytidylate
      methylases.
AU  - Karreman C
AU  - de Waard A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1990 172: 266-272.

PMID- 2836359
VI  - 170
DP  - 1988
TI  - Cloning and complete nucleotide sequences of the TypeII restriction-modification genes of Salmonella infantis.
PG  - 2527-2532
AB  - The complete typeII restriction-modification system of Salmonella infantis was
      cloned in Escherichia coli as an R.Sau3AI fragment of 3,430 base pairs.  The
      clone was shown to express the restriction endonuclease as well as the
      modification methylase.  The nucleotide sequence of the above fragment showed
      two open reading frames of 461 and 230 codons in tail-to-tail orientation.
      These were shown to represent the modification methylase M.SinI and the
      restriction endonuclease R.SinI, respectively.  The methylase M.SinI amino acid
      sequence revealed a considerable similarity to those of other deoxycytidylate
      methylases.  In contrast, endonuclease R.SinI did not exhibit such a similarity
      to other restriction enzymes.
AU  - Karreman C
AU  - de Waard A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1988 170: 2527-2532.

PMID- 3016641
VI  - 14
DP  - 1986
TI  - Isolation of a deoxycytidylate methyl transferase capable of protecting DNA uniquely against cleavage by endonuclease R. AquI (isoschizomer of AvaI).
PG  - 5199-5205
AB  - A sequence-specific modification methylase (M.AquI) was isolated and purified
      from Agmenellum quadruplicatum (Synechococcus PCC 7002).  This enzyme uniquely
      methylates the deoxycytidylate residue in the sequence *CYCGRG indicated by the
      asterisk.  It was shown to protect DNA against cleavage by restriction
      endonucleases AvaI, SmaI and XhoI, which recognize the sequences CYCGRG,
      CCCGGG, and CTCGAG, respectively.
AU  - Karreman C
AU  - Tandeau de Marsac N
AU  - de Waard A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1986 14: 5199-5205.

PMID- 11884634
VI  - 30
DP  - 2002
TI  - Methylation of adenine in the nuclear DNA of Tetrahymena is internucleosomal and independent of histone H1.
PG  - 1364-1370
AB  - There are about 50 copies of each chromosome in the somatic macronucleus of the ciliated
      protozoan Tetrahymena. Approximately 0.8% of the adenine residues in the macronuclear DNA of
      Tetrahymena are methylated to N6-methyladenine. The degree of methylation varies between sites
      from a very low percentage to >90%. In this study a correlation was found between nucleosome
      positioning and DNA methylation. Eight GATC sites with different levels of methylation were
      examined. There was a direct correlation between the degree of methylation and proximity to
      linker DNA at these sites. Although methylation occurs preferentially in linker DNA, the
      patterns and extent of methylation in a histone H1 knockout strain were virtually
      indistinguishable from those in wild-type cells.
AU  - Karrer KM
AU  - VanNuland TA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2002 30: 1364-1370.

PMID- 9753722
VI  - 26
DP  - 1998
TI  - Position effect takes precedence over target sequence in determination of adenine methylation patterns in the nuclear genome of a eukaryote, Tetrahymena thermophila.
PG  - 4566-4573
AB  - Approximately 0.8% of the adenine residues in the macronuclear DNA of the ciliated protozoan
      Tetrahymena thermophila are modified to N6-methyladenine.  DNA methylation is site specific
      and the pattern of methylation is constant between clonal cell lines.  In vivo, modification
      of adenine residues appears to occur exclusively in the sequence 5'-NAT-3', but no consensus
      sequence for modified sites has been found.  In this study, DNA fragments containing a site
      that is uniformly methylated on the 50 copies of the macronuclear chromosome were cloned into
      the extrachromosomal rDNA.  In the novel location on the rDNA minichromosome, the site was
      unmethylated.  The result was the same whether the sequences were introduced in a methylated
      or unmethylated state and regardless of the orientation of the sequence with respect to the
      origin of DNA replication.  The data show that sequence is insufficient to account for
      site-specific methylation in Tetrahymena and argue that other factors determine the pattern of
      DNA methylation.
AU  - Karrer KM
AU  - VanNuland TA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1998 26: 4566-4573.

PMID- 
VI  - 0
DP  - 1999
TI  - Detection and purification of a new restriction endonuclease, LlaMI, from Lactococcus lactis subsp. lactis M19.
PG  - F17
AB  - One of the multiple phage defense systems present in bacteria is the Restriction/modification
      system.  Type II restriction endonucleases recognize specific nucleotide sequences in invading
      phage DNA and cleave the DNA at these sites.  We describe a new restriction activity, LlaMI,
      present in cell extracts of Lactococcus lactis subsp. lactis M19, a variant isolated from a
      commercially available industrial starter culture.  We have characterized the strain M19 by
      molecular typing using AP-PCR fingerprinting and plasmid profile analysis.  During the
      purification of LlaMI, non-specific nuclease activity was detected.  The nuclease activity
      could be separated from the LlaMI activity using low-pressure anion exchange and affinity
      chromatography.  Partially-purified cell extracts were tested for restriction activity on the
      following substrates: DNA of phages lambda, PhiX174 and T7 and plasmids pBR322 and Litmus 29.
      The LlaMI DNA cleavage patterns closely resemble those of restriction enzyme ScrFI, produced
      by Lactococcus lactis subsp. cremoris UC503.
AU  - Karska-Wysocki B
AU  - Hua NM
AU  - Vzdornov D
AU  - Szatmari G
AU  - Mamet-Bratley MD
PT  - Journal Article
TA  - Sixth Symposium on Lactic Acid Bacteria Genetics, Metabolism and Applications
JT  - Sixth Symposium on Lactic Acid Bacteria Genetics, Metabolism and Applications
SO  - Sixth Symposium on Lactic Acid Bacteria Genetics, Metabolism and Applications 1999 0: F17.

PMID- 
VI  - 0
DP  - 1996
TI  - Characterization of a new restriction endonuclease, LlaGI, produced  by Lactococcus lactis subsp. cremoris G2.
PG  - P088
AB  - A new sequence-specific endonuclease from Lactococcus lactis
      subsp. cremoris G2 was identified, by restriction maping, as the first
      reported isoschizomer of NheI.  We have confirmed this identification with
      a cloning test and have named this new Type II restriction endonuclease
      LlaGI.  We have characterized the enzyme-producing strain G2 by molecular
      typing using AP-PCR fingerprinting and plasmid profile analysis.  These
      tests demonstrated the presence of amplicons of 200 to 900 bp and the
      presence of five plasmid bands at appropriate size positions of 7 to 25
      kbp.  Extracts containing LlaGI nuclease did not digest DNA from the
      producing strain, suggesting that a modification activity is also present
      in this strain.  Specific endonuclease digestion of phage DNA was detected
      in diluted crude extracts corresponding to 0.9 ug (wet-weight) G2
      cells/ml.  During purification of LlaGI from crude extracts, non-specific
      nuclease activity was detected in fractions containing the restriction
      enzyme.  This contamination could be effectively separated from LlaGI
      activity using low-pressure anion exchange chromatography and elution with
      a gradient of NaCl or KCl.  We are currently developing a purification
      protocol for potential commercial production of this new restriction
      endonuclease.
AU  - Karska-Wysocki B
AU  - Szatmari G
AU  - Barrette B
AU  - Mamet-Bratley MD
PT  - Journal Article
TA  - Life Sc. Confer. Ottawa
JT  - Life Sc. Confer. Ottawa
SO  - Life Sc. Confer. Ottawa 1996 0: P088.

PMID- 
VI  - 0
DP  - 1995
TI  - A new restriction endonuclease activity found in Lactococcus  cremoris G2.
PG  - D2-D9
AB  - Only a few strains of Lactococcus species have been demonstrated
      to have type II restriction endonuclease activity.  These enzymes recognize
      specific nucleotide sequence and cleave DNA at these sites.  Here we
      describe a novel restriction enzyme activity present in cell extracts of a
      Lactococcus cremoris G2 strain isolated from a commercial mixed-starter
      culture used in the manufacture of Cheddar cheese.  Cell crude extracts
      were obtained by sonification of stationary phase cultures grown in M17, or
      in whey medium.  The cell extracts were tested for DNA restriction activity
      on lambda, PhiX174 and pBR322 DNA substrates.  Electrophoretic analysis of
      restriction digests revealed the presence of only one cleavage site in
      lambda and pBR322 DNA, and the absence of cleavage of PhiX174 DNA.  The
      enzymatic activity of the extract was shown to be greater than 13,000 units
      per gram (wet weight) of cells.  The electrophoretic patterns of this
      restriction enzyme activity was compared with known restriction
      enzymes.  This analysis clearly demonstrated that this new restriction
      enzyme activity is identical to that of the restriction enzyme
      NheI.  Indicating that the new restriction enzyme activity is the first
      known isoschizomer of NheI.  The determination of the cleavage site of this
      new enzyme is currently in progress.  We propose that this non-pathogenic
      food-grade microorganism will be a better source for the NheI enzyme, which
      is currently isolated from a Neisseria mucosa species originally isolated
      from the human pharynx.
AU  - Karska-Wysocki B
AU  - Szatmari G
AU  - Beauregard G
AU  - Mamet-Bratley MD
PT  - Journal Article
TA  - Life Sc. Confer. Ottawa
JT  - Life Sc. Confer. Ottawa
SO  - Life Sc. Confer. Ottawa 1995 0: D2-D9.

PMID- 3025703
VI  - 4
DP  - 1985
TI  - Separation of enzymes for modification methylases and restrictases from Shigella sonnei 47.
PG  - 31-35
AB  - Two systems for DNA host specificity have been demonstrated for Shigella sonnei cells, SsoI
      and SsoII.  The aim of the present work was to separate the modifying methylases and
      restriction endonucleases from Shigella sonnei and to study the modifying functions of
      methylases M.SsoI and M.SsoII.  The possibilities to separate the methylation and restriction
      enzymes by column chromatography on affinity, ion exchange and hydrophobic sorbents were
      analyzed.  The scheme for separation of methylases and restriction endonucleases of Shigella
      sonnei was elaborated, consisting of the fractioning of total preparation on phenylsepharose
      and subsequent isoelectrofocusing on ampholines.  The modification functions of M.SsoI and
      M.SsoII methylases obtained by this technique and devoid of concomitant restriction
      endonucleases were studied.  The in vitro experiments have shown the acceptor DNA methylated
      by M.SsoI or M.SsoII to be resistant to R.SsoI or R.SsoII.
AU  - Kartashova IM
AU  - Nikolskaya II
AU  - Debov SS
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1985 4: 31-35.

PMID- 29449387
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Escherichia coli Isolates from India.
PG  - e00047-18
AB  - Escherichia coli causes diarrhea and extraintestinal infections in humans and animals. Here,
      we report the draft genome sequences of Escherichia coli strains
      360/16 and 646, isolated from neonatal calves.
AU  - Karunakaran AC
AU  - Milton AAP
AU  - Rajendrakumar AM
AU  - Sahu AR
AU  - Pandey A
AU  - Ghatak S
AU  - Abhishek NVK
AU  - Gandham R
AU  - Agarwal RK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00047-18.

PMID- 24201204
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of an Extensively Drug-Resistant Mycobacterium tuberculosis Clinical Isolate of the Ural Strain OSDD493.
PG  - e00928-13
AB  - We describe the genome sequencing and analysis of a clinical isolate of Mycobacterium
      tuberculosis belonging to the Ural strain OSDD493 from India.
AU  - Karuthedath VS
AU  - Vir SA
AU  - Kumar SP
AU  - Garg P
AU  - Mohan KV
AU  - Katoch K
AU  - Chauhan DS
AU  - Scaria V
AU  - Sivasubbu S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00928-13.

PMID- 23908284
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of a Clinical Isolate of Multidrug-Resistant Mycobacterium  tuberculosis East African Indian Strain OSDD271.
PG  - e00541-13
AB  - We describe the genome sequencing and analysis of a clinical isolate of Mycobacterium
      tuberculosis East African Indian (EAI) strain OSDD271 from India.
AU  - Karuthedath-Vellarikkal S
AU  - Patowary A
AU  - Singh M
AU  - Periwal V
AU  - Singh AV
AU  - Singh PK
AU  - Garg P
AU  - Mohan KV
AU  - Katoch K
AU  - Jangir PK
AU  - Sharma R
AU  - Chauhan DS
AU  - Scaria V
AU  - Sivasubbu S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00541-13.

PMID- 9153310
VI  - 25
DP  - 1997
TI  - Specific binding of SsoII DNA methyltransferase to its promoter region provides the regulation of SsoII restriction-modification gene expression.
PG  - 2114-2120
AB  - The regulation of the SsoII restriction-modification system from Shigella sonnei was studied
      in vivo and in vitro.  In lacZ fusion experiments, SsoII methyltransferase (M.SsoII) was found
      to repress its own synthesis but stimulate expression of the cognate restriction endonuclease.
      The N-terminal 72 amino acids of M.SsoII, predicted to form a helix-turn-helix motif, was
      found to be responsible for the specific DNA-binding and regulatory function of M.SsoII.
      Similar HTH motifs are predicted in the N-terminus of a number of 5-methylcytosine
      methyltransferases, particularly M.EcoRII, M.dcm and M.MspI, of which the ability to regulate
      autogenously has been proposed.  In vitro, the binding of M.SsoII to its target DNA was
      investigated using a mobility shift assay.  M.SsoII forms a specific and stable complex with a
      140 bp DNA fragment containing the promoter region of SsoII R-M system.  The dissociation
      constant (Kd) was determined to be 1.5 x 10^-8 M.  DNaseI footprinting experiments
      demonstrated that M.SsoII protects a 48-52 bp region immediately upstream of the M.SsoII
      coding sequence which includes the predicted -10 promoter sequence of M.SsoII and the -10 and
      -35 sequences of R.SsoII.
AU  - Karyagina A
AU  - Shilov I
AU  - Tashlitskii V
AU  - Khodoun M
AU  - Vasilev S
AU  - Lau PCK
AU  - Nikolskaya I
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1997 25: 2114-2120.

PMID- 2215521
VI  - 7
DP  - 1990
TI  - Genetic determinants for the enzymes of bacterial restriction-modification systems.
PG  - 3-11
AB  - Recent data on the molecular arrangement and functioning of the genetic
      determinants for the enzymes of restriction-modification systems are discussed.
      The problems of restriction endonuclease and methylase gene localization, the
      regulation of the activity of the genes for Type II restriction-modification
      systems, the characteristics of the primary structure of the genes and
      phylogeny of restriction endonucleases and methylases are reviewed.
AU  - Karyagina AS
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1990 7: 3-11.

PMID- 8364113
VI  - 58
DP  - 1993
TI  - A new method for isolation and purification of restriction endonuclease SsoII.
PG  - 908-912
AB  - A new method for isolation and purification of restriction endonuclease SsoII which results in
      a homogeneous preparation suitable for all types of fine physico-chemical assays has been
      elaborated. The procedure includes four chromatographic steps: fractionation on
      butyl-Toyopearl, combined chromatography on SP-Toyopearl and phosphocellulose PII, and
      chromatography on DEAE-Toyopearl and on QAE-Toyopearl. The use of fast flow sorbents
      (Toyopearl) makes it possible to reduce the time needed for the separation of proteins and to
      optimize the fractionation conditions, thus avoiding the dialysis between the chromatographic
      steps which significantly decreased the enzyme activity yields in previous purification
      schemes. The isolation of restriction endonuclease SsoII by the new method usually takes four
      days.
AU  - Karyagina AS
AU  - Levchenko IY
AU  - Nikolskaya II
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1993 58: 908-912.

PMID- 7916706
VI  - 124
DP  - 1993
TI  - Analysis of the nucleotide and derived amino acid sequences of the SsoII restriction endonuclease and methyltransferase.
PG  - 13-19
AB  - A 2648-bp fragment from the P4 plasmid of Shigella sonnei strain 47 coding for the SsoII
      restriction endonuclease (ENase) and methyltransferase (MTase) (recognition sequence
      5'-CCNGG) was sequenced. Two divergently arranged open reading frames of 905 bp for the SsoII
      ENase (R.SsoII) and 1137 bp for the MTase (M.SsoII were identified. The coding regions are
      separated by 110 bp. The calculated Mr of R.SsoII (35937) and M.SsoII (42887) are in good
      agreement with values previously obtained by in vitro transcription-translation experiments,
      i.e., 35 and 43 kDa for the ENase and MTase, respectively. The M.SsoII amino acid (aa)
      sequence revealed a considerable similarity to m5C-MTases recognizing the related sequences -
      M.EcoRII, M.dcm, M.MspI, M.BsuFI, M.HpaII, and M.HhaI. Surprisingly, the greatest degree of
      homology has been observed between the aa sequences of M.SsoII and M.NlaX, with an
      unidentified recognition sequence. The multiple alignment of aa sequences helps to identify
      the blocks of conserved aa in variable regions of MTases. These conserved aa can play a key
      role in target recognition. Some aspects of evolution of m5C-MTases are discussed.
AU  - Karyagina AS
AU  - Lunin VG
AU  - Degtyarenko KN
AU  - Uvarov VY
AU  - Nikolskaya II
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1993 124: 13-19.

PMID- 2833695
VI  - 12
DP  - 1987
TI  - Activity of the restriction endonuclease SsoII in Escherichia coli cells transformed by Shigella sonnei 47 plasmids.
PG  - 26-29
AB  - The inverse dependence of activity of restriction endonuclease SsoII
      preparations on the number of low molecular mass plasmids of Shigella sonnei
      transforming Escherichia coli recipient cells producing the enzyme has been
      shown.  An Escherichia coli strain efficiently producing one of two Shigella
      sonnei 47 restriction endonucleases, SsoII, has been isolated.  The producer
      strain harbours two of the nine Shigella sonnei 47 plasmids.  One of them, P4,
      codes for the SsoII+ phenotype while another, P9, determines the plasmids
      conjugation transfer.  Biochemical and physiological characteristics of the
      producer strain XS13 are identical to the ones of the recipient Escherichia
      coli strain PS200.  XS13 is unable to induce keratoconjunctivitis in guinea
      pigs in pathogenicity test.
AU  - Karyagina AS
AU  - Lunin VG
AU  - Gruber IM
AU  - Polyachenko VM
AU  - Nikolskaya II
AU  - Debov SS
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1987 12: 26-29.

PMID- 7607533
VI  - 157
DP  - 1995
TI  - The SsoII and NlaX DNA methyltransferases: overproduction and functional analysis.
PG  - 93-96
AB  - Overproduction of the NlaX DNA methyltransferase (M.NlaX) in an Escherichia coli host
      conferred resistance to SsoII restriction endonuclease (R.SsoII) digestion.  This suggested an
      overlap of sequence specificity between M.NlaX and M.SsoII, the latter of which modifies the
      internal cytosine of the target sequence 5'-CCNGG-3'.  A variant of M.NlaX (M.Sso/Nla),
      containing an N-terminal extension from M.SsoII, was also enzymatically active.  Using
      deletion analysis, the N-terminal 71 amino-acid residues of M.SsoII were shown to be essential
      for modification activity.
AU  - Karyagina AS
AU  - Lunin VG
AU  - Levtchenko IY
AU  - Labbe D
AU  - Brousseau R
AU  - Lau PCK
AU  - Nikolskaya II
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 93-96.

PMID- 3540633
VI  - 10
DP  - 1986
TI  - Functional characteristics of plasmids of Shigella sonnei 47 strains.
PG  - 16-21
AB  - The phenotypic characteristics of Shigella sonnei strain 47 containing 7 plasmids of low
      molecular weight and 2 plasmids 60-100 Md large have been studied.  The strains of Escherichia
      coli containing the single plasmids or plasmid groups from Shigella sonnei have been obtained
      by transformation and conjugation.  The comparison of phenotypes of the strains obtained has
      helped to find the plasmid location of the determinants for streptomycin resistance (P7),
      genes for colicinogenicity abd colicin immunity (P5), the enzymes of host cell specificty
      system Sso47I (P6), Sso47II (P4) and the genes for the conjugative DNA transfer (P9).
      Escherichia coli strains producing individual restriction enzymes SsoI and SsoII have been
      isolated.
AU  - Karyagina AS
AU  - Lunin VG
AU  - Nikolskaia II
AU  - Debov SS
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1986 10: 16-21.

PMID- 2185134
VI  - 87
DP  - 1990
TI  - Characterization of the genetic determinants of SsoII-restriction endonuclease and modification methyltransferase.
PG  - 113-118
AB  - The genes encoding SsoI and SsoII restriction endonuclease (ENase) and
      methyltransferase (MTase) are located on the small plasmids P6 and P4,
      respectively, of Shigella sonnei strain 47.  Functions provided by plasmids P5,
      P7 and P9, which include colicinogenicity and immunity to colicin E1,
      resistance to streptomycin (Sm), and conjugative DNA transfer, respectively,
      have also been identified.  The genes of the SsoII restriction-modification
      (R-M) system have been cloned into Escherichia coli expressing the
      35-kDa(ENase) and 43-kDa(MTase) products.  A restriction map of the P4 plasmid
      DNA was determined, and the approximate location of the genes encoding SsoII
      ENase and MTase (ssoIIR and ssoIIM) on that have been established.  SsoI is an
      isoschisomer of EcoRI and SsoII cleaves the recognition sequence 5'-CCNGG
      producing 5'-protruding 5-nt long cohesive ends.
AU  - Karyagina AS
AU  - Lunin VG
AU  - Nikolskaya II
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1990 87: 113-118.

PMID- 2657413
VI  - 3
DP  - 1989
TI  - Localization of SsoII restriction endonuclease and methylase genes on the physical map of plasmid P4.
PG  - 16-20
AB  - A restriction map of naturally occuring plasmid P4 from Shigella sonnei 47
      strain coding for the SsoII restriction endonuclease and methylase genes has
      been made.  Using the genetic engineering approach the locations of the SsoII
      host cell specificity system enzyme genes have been determined.
AU  - Karyagina AS
AU  - Lunin VG
AU  - Nikolskaya II
AU  - Debov SS
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1989 3: 16-20.

PMID- 8381347
VI  - 12
DP  - 1993
TI  - A model for chromatin opening: stimulation of topoisomerase II and restriction enzyme cleavage of chromatin by distamycin.
PG  - 115-126
AB  - Histone H1 preferentially and cooperatively binds scaffold-associated regions (SARS) in vitro
      via specific interactions with the numerous short A+T-rich tracts (A-tracts) contained in
      these sequences. Selective titration of A-tracts by the oligopeptide distamycin abolishes this
      interaction and results in a redistribution of H1. Similarly, treatment of intact cells and
      isolated nuclei with distamycin specifically enhances cleavage of internucleosomal linkers of
      SARs by topoisomerase II and restriction enzymes. The increased accessibility of these linkers
      is thought to result from the unfolding (or opening) of the chromatin fiber and to be due to a
      reduced occupancy by histone H1. Chromatin extraction and H1 assembly experiments support this
      view. We discuss a model whereby open, H1-depleted chromatin regions may be generated by
      titration of A-tracts by putative distamycin analogues; this local opening may spread to
      adjacent regions assuming highly cooperative H1-H1 interactions in chromatin.
AU  - Kas E
AU  - Poljak L
AU  - Adachi Y
AU  - Laemmli K
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1993 12: 115-126.

PMID- 9455482
VI  - 4
DP  - 1997
TI  - Sequence analysis of the groESL-cotA region of the Bacillus subtilis genome, containing the restriction/modification system genes.
PG  - 335-339
AB  - We have determined a 35-kb sequence of the groESL-gutR-cotA (45o-52o) region of the Bacillus
      subtilis genome.  In addition to the groESL, gutRB and cotA genes reported previously, we have
      newly identified 24 ORFs including gutA and fruC genes, encoding glucitol permease and
      fructokinase, respectively.  The inherent restriction/modification system genes, hsdMR and
      hsdMM, were mapped between groESL and gutRB, and we have identified two open reading frames
      (ORFs) encoding 5-methylcytosine forming DNA methyltransferase and an operon probably encoding
      a restriction enzyme complex.  The unusual genome structure of few ORFs and lower GC content
      around the restriction/modification genes strongly suggests that the region originated from a
      bacteriophage integrated during evolution.
AU  - Kasahara Y
AU  - Nakai S
AU  - Ogasawara N
AU  - Yata K
AU  - Sadaie Y
PT  - Journal Article
TA  - DNA Res.
JT  - DNA Res.
SO  - DNA Res. 1997 4: 335-339.

PMID- 
VI  - 100
DP  - 2000
TI  - Use of plasmid transformation to find new restriction enzymes.
PG  - 371
AB  - Recent genome projects have revealed many restriction enzymes and their corresponding
      methylases, specifically of type I and III.  Traditionally, restriction enzymes have been
      discovered by classical restriction and modification phenomenon of bacteriophages (type I, II,
      and III) or direct enzyme assay (most type II enzymes).  Once genes are cloned, DNA
      hybridization is also used to discover other enzymes with similar DNA sequences.  To avoid the
      traditional limitation of using bacteriophages or biochemical assays, we have designed a
      feasibility study using plasmid transformation to detect the restriction activities of the
      cell.  Plasmids were made by subcloning six BamHI fragments from bacteriophage lambda DNA into
      a pUC derivative plasmid, pMECA.  These plasmids were transformed into E. coli strains
      representing each type of restriction system (type I: EcoKI, EcoAI, Eco124I; type II: HindIII;
      type III: EcoPI).  As a control, plasmids were also transformed into E. coli C, which does not
      contain a restriction system and efficiency of transformation values were obtained by
      comparison.  Reduction of relative EOT values (10^-1 - 10^-3) were observed in each BamHI
      subclone containing the corresponding recognition sites.  These results suggest that the
      presence of restriction enzymes can be predicted using this plasmid transformation method as
      an alternative to phage experiments or biochemical studies.  Accumulation of DNA sequence data
      also makes it possible to predict the recognition sequence of a restriction enzyme with the
      use of computer analysis.
AU  - Kasarjian J
AU  - Kawai S
AU  - Ryu J
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 2000 100: 371.

PMID- 
VI  - 102
DP  - 2002
TI  - Determination of the methylation sites of the type I restriction enzymes, KpnAI and KpnBI of Klebsiella species.
PG  - 236
AB  - Type I restriction endonucleases have been identified widely in bacteria since the completion
      of the first genome sequence project of
      Haemophilus influenzae in 1995. The enzymes recognize non-palindromic
      bipartite DNA sequences made up of a 3-4 base pair (bp) 5' region, a
      6-8 bp nonspecific spacer, and a 4-5 bp 3' region. The corresponding
      adenine N6-methyltransferase modifies a specific adenine in each strand
      within the recognition sequence to protect DNA from cleavage.
      Traditionally, type I enzymes in enteric bacteria are classified into
      distinguished families: IA, IB, IC and ID. Two type I restriction and
      modification systems, KpnAI (type ID) and KpnBI (new family), have been
      identified in Klebsiella oxytoca M5a1 (originally classified as K.
      pneumoniae), and Klebsiella pneumoniae GM236, respectively. We have
      previously developed a simple transformation method to identify their
      recognition sequence. Using a series of plasmids with known DNA
      sequence and a computer program, the recognition sequence of KpnAI and
      KpnBI were determined to be GAA(N6)TGCC and CAAA(N6) RTCA,
      respectively. In this study the sensitivity of the type II restriction
      endonuclease, HindIII, to site-specific modification at 6-methyladenine
      is used to determine the methylation sites of KpnAI and KpnBI. We
      designed several synthetic DNA oligonucleotides containing a HindIII
      recognition site overlapping with either a KpnAI or KpnBI site. The
      oligonucleotide was then cloned into plasmid pMECA and transferred into
      a KpnAI or KpnBI containing strain, M5a1 or GM236, respectively for
      modification. Methylated plasmids were subjected to HindIII digestion.
      When the methylated adenine (A*) of the synthetic recognition sequence
      overlapped with the methylated adenine in the HindIII sequence
      (A*AGCTT), the plasmids were protected from cleavage HindIII. The
      methylation of the opposite strand KpnBI recognition sequence was
      determined using the in vivo activity of dam+ and dam- strains.
AU  - Kasarjian J
AU  - Valinluck V
AU  - Ryu J
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 2002 102: 236.

PMID- 
VI  - 101
DP  - 2001
TI  - Identification of the recognition sequence of KpnAI, a type ID restriction enzyme, in Klebsiella pneumoniae M5a1.
PG  - 403
AB  - Type II restriction enzymes have been studied extensively due to their usefulness in genetic
      engineering, while our knowledge of type I and
      III systems remains limited. Recent bacterial genome sequencing
      projects suggest an abundance of all three types of
      restriction-modification (R-M) systems. Finding new type I and III
      restriction systems and identifying their recognition sites is
      difficult, leaving many recognition sites still unknown. KpnAI, an R-M
      system from Klebsiella pneumoniae, has previously been cloned and
      sequenced in our laboratory. Analysis of both DNA and protein sequences
      identified this system as a new member of the type ID family. Here we
      have determined the recognition sequence for KpnAI using a simple in
      vivo plasmid transformation method, specifically developed in our lab,
      which can also be used as a tool to identify new R-M systems. Two sets
      of plasmids were made by subcloning DNA fragments from bacteriophage
      lambda and Escherichia coli. Each set of 30 plasmids was then
      transformed into M5a1 using the restriction-minus mutant, M5a1R as a
      control. Only when the plasmid contained a restriction site, a
      reduction (10-2) in transformation frequency was observed when compared
      to the control. These results identified the presence of a recognition
      site in 24 plasmids and absence of a site in 32 plasmids. A computer
      program was developed to search for a common sequence that exists in
      all positive plasmids but is not found in any negative plasmids. One
      unique recognition sequence was identified and a 19 base synthetic
      oligonucleotide containing this sequence was cloned into pMECA.
      Transformation into strain M5a1 resulted in a significant reduction in
      transformation frequency confirming the recognition sequence of KpnAI
      to be GAA(6N)TGCC. This model system can be extended to many bacterial
      species to search for new restriction enzymes and their recognition
      sequences.
AU  - Kasarjian JKA
AU  - Burnett AS
AU  - Ryu J
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 2001 101: 403.

PMID- 11217142
VI  - 49
DP  - 2001
TI  - Use of plasmid transformation to find new restriction enzymes and their recognition sequences.
PG  - 12A
AB  - Restriction-modification systems are widespread in bacteria and consist of both a restriction
      endonuclease and a corresponding methylase.  Bacterial genome sequencing projects, however,
      suggest that many restriction enzymes have yet to be discovered.  Restriction enzymes are
      classified into three types (I, II, III) and type II restriction enzymes are useful in genetic
      engineering.  Traditionally, restriction enzymes have been discovered by classical restriction
      and modification tests, requiring bacteriophages or direct enzyme assay.  DNA hybridization
      can find new homologous sequences, but unique DNA sequences will be overlooked and the high
      cost of bacterial genome projects may limit its usefulness.  We have established a new
      quantitative R-M test based on plasmid transformation efficiency using DNA fragments derived
      from E. coli phage lambda.  This test is similar to traditional "efficiency of plating" assays
      but measures "efficiency of transformation".  Plasmids were made by subcloning six BamHI
      fragments from lambda into pMECA, a pUC derivative plasmid.  These six plasmids were each
      transformed into bacterial strains representing each type of restriction system (type I;
      EcoAI, EcoRI, Eco124I; type II: HindIII; type III: EcoPI).  Reduction of relative EOT values
      (10-1-10-3) were observed in each BamHI subclone containing the corresponding recognition
      sites.  These results confirm the effectiveness of this new method.  This method was also used
      to predict the recognition sequence of KpnAI, a type I R-M system from Klebsiella pneumoniae,
      M5a1.  A total of 29 lambda subclones were constructed and transformed into M5a1 to determine
      the presence (+) or absence (-) of a recognition site.  DNA sequence information was then
      compared using the newly developed computer program, Seth Analyzer.  Transformation of a
      synthetic oligonucleotide containing the predicted recognition sequence confirmed the
      recognition sequence of KpnAI to be GAA(6N)TGCC.  Because plasmid transformation methods are
      available for many bacteria, this model system can be extended to many bacterial species to
      search for new restriction enzymes and their recognition sequences.
AU  - Kasarjian JKA
AU  - Burnett AS
AU  - Ryu J
PT  - Journal Article
TA  - J. Invest. Med.
JT  - J. Invest. Med.
SO  - J. Invest. Med. 2001 49: 12A.

PMID- 15199175
VI  - 32
DP  - 2004
TI  - The recognition and modification sites for the bacterial type I restriction systems KpnAI, StySEAI, StySENI and StySGI.
PG  - e82
AB  - Using an in vivo plasmid transformation method, we have determined the DNA sequences
      recognized by the KpnAI, StySEAI, StySENI and StySGI R-M systems from Klebsiella oxytoca
      strain M5a1, Salmonella eastbourne, Salmonella enteritidis and Salmonella gelsenkirchen,
      respectively. These type I restriction-modification systems were originally identified using
      traditional phage assay, and described here is the plasmid transformation test and computer
      program used to determine their DNA recognition sequences. For this test, we constructed two
      sets of plasmids, pL and pE, that contain phage lambda and Escherichia coli K-12 chromosomal
      DNA fragments, respectively. Further, using the methylation sensitivities of various known
      type II restriction enzymes, we identified the target adenines for methylation (listed in bold
      italics below as A or T in case of the complementary strand). The recognition sequence and
      methylation sites are GAA(6N)TGCC (KpnAI), ACA(6N)TYCA (StySEAI), CGA(6N)TACC (StySENI) and
      TAAC(7N)RTCG (StySGI). These DNA recognition sequences all have a typical type I bipartite
      pattern and represent three novel specificities and one isoschizomer (StySENI). For
      confirmation, oligonucleotides containing each of the predicted sequences were synthesized,
      cloned into plasmid pMECA and transformed into each strain, resulting in a large reduction in
      efficiency of transformation (EOT).
AU  - Kasarjian JKA
AU  - Hidaka M
AU  - Horiuchi T
AU  - Iida M
AU  - Ryu J
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2004 32: e82.

PMID- 12595571
VI  - 31
DP  - 2003
TI  - New restriction enzymes discovered from Escherichia coli clinical strains using a plasmid transformation method.
PG  - e22
AB  - The presence of restriction enzymes in bacterial cells has been predicted by either classical
      phage restriction-modification (R-M) tests, direct in
      vitro enzyme assays or more recently from bacterial genome sequence
      analysis. We have applied phage R-M test principles to the transformation
      of plasmid DNA and established a plasmid R-M test. To validate this test,
      six plasmids that contain BamHI fragments of phage lambda DNA were
      constructed and transformed into Escherichia coli strains containing known
      R-M systems including: type I (EcoBI, EcoAI, Eco124I), type II (HindIII)
      and type III (EcoP1I). Plasmid DNA with a single recognition site showed a
      reduction of relative efficiency of transformation (EOT = 10(-1)-10(-2)).
      When multiple recognition sites were present, greater reductions in EOT
      values were observed. Once established in the cell, the plasmids were
      subjected to modification (EOT = 1.0). We applied this test to screen
      E.coli clinical strains and detected the presence of restriction enzymes
      in 93% (14/15) of cells. Using additional subclones and the computer
      program, RM Search, we identified four new restriction enzymes, Eco377I,
      Eco585I, Eco646I and Eco777I, along with their recognition sequences,
      GGA(8N)ATGC, GCC(6N)TGCG, CCA(7N)CTTC, and GGA(6N)TATC, respectively.
      Eco1158I, an isoschizomer of EcoBI, was also found in this study.
AU  - Kasarjian JKA
AU  - Iida M
AU  - Ryu J
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2003 31: e22.

PMID- 16040596
VI  - 33
DP  - 2005
TI  - Four new type I restriction enzymes identified in Escherichia coli clinical isolates.
PG  - e114
AB  - Using a plasmid transformation method and the RM search computer program, four type I
      restriction enzymes with new recognition sites and two isoschizomers (EcoBI and Eco377I) were
      identified in a collection of clinical Escherichia coli isolates. These new enzymes were
      designated Eco394I, Eco826I, Eco851I and Eco912I. Their recognition sequences were determined
      to be GAC(5N)RTAAY, GCA(6N)CTGA, GTCA(6N)TGAY and CAC(5N)TGGC, respectively. A methylation
      sensitivity assay, using various synthetic oligonucleotides, was used to identify the adenines
      that prevent cleavage when methylated (underlined). These results suggest that type I enzymes
      are abundant in E.coli and many other bacteria, as has been inferred from bacterial genome
      sequencing projects.
AU  - Kasarjian JKA
AU  - Kodama Y
AU  - Iida M
AU  - Matsuda K
AU  - Ryu J
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2005 33: e114.

PMID- 25146143
VI  - 2
DP  - 2014
TI  - Genome Sequence of Mycobacterium tuberculosis C2, a Cerebrospinal Fluid Clinical  Isolate from Central India.
PG  - e00842-14
AB  - We report the annotated genome sequence of a Mycobacterium tuberculosis clinical  isolate from
      the cerebrospinal fluid of a tuberculous meningitis patient admitted
      to the Central India Institute of Medical Sciences, Nagpur, India.
AU  - Kashyap RS
AU  - Bhullar SS
AU  - More RP
AU  - Puranik S
AU  - Purohit HJ
AU  - Taori GM
AU  - Daginawala HF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00842-14.

PMID- Not carried by PubMed...
VI  - 52
DP  - 1991
TI  - Studies of a DNA modification methyltransferase from Rhodobacter sphaeroides.
PG  - 1407B
AB  - The DNA methyltransferases represent an interesting class of enzymes for the
      study of protein-DNA interactions due to their high specificity, structural
      simplicity, and biological importance.  RsrI methyltransferase (M.RsrI) from
      Rhodobacter sphaeroides recognizes duplex d(GAATTC) and deposits methyl groups
      at the N6 position of the central adenine.  M.RsrI was purified to homogeneity
      from R. sphaeroides, and its gene cloned and sequenced.  The purification used
      four chromatography columns, and yielded up to 100 micrograms of enzyme.
      M.RsrI was overexpressed in E. coli and the yield of the purification improved
      by about 100-fold with respect to that from R. sphaeroides.  Several physical
      and biochemical properties of the RsrI methyltransferase were determined:
      molecular weight under denaturing and nondenaturing conditions, isoelectric
      point, optimal reaction conditions, the mode of methyl group transfer, and the
      enzyme-DNA binding.  M.RsrI was compared to a functionally identical enzyme
      from E. coli, EcoRI methyltransferase (M.EcoRI).  M.RsrI and M.EcoRI differ in
      their physical properties, including a striking lack of similarity in their
      deduced amino acid sequences.  The two methyltransferases might recognize the
      cognate DNA sequence differently, because they do not bind to DNA with equal
      efficiencies under the same conditions.  However, M.RsrI and M.EcoRI share
      identical catalytic properties.  Both transfer one methyl group to the
      recognition sequence per binding event.  M.RsrI and M.EcoRI represent an
      opportunity to elucidate the mode of action of two structurally different but
      functionally identical enzymes.  It is possible that these enzymes retain
      functional similarity by having essentially the same three dimensional
      configuration.  Alternatively, they might have dissimilar structures as well as
      mechanistic differences.
AU  - Kaszubska W
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1991 52: 1407B.

PMID- 2690017
VI  - 17
DP  - 1989
TI  - Purification, cloning and sequence analysis of RsrI DNA methyltransferase: lack of homology between two enzymes, RsrI and EcoRI, that methylate the same nucleotide in identical recognition sequences.
PG  - 10403-10425
AB  - RsrI DNA methyltransferase (M.RsrI) from Rhodobacter sphaeroides has been
      purified to homogeneity, and its gene cloned and sequenced.  This enzyme
      catalyzes methylation of the same central adenine residue in the duplex
      recognition sequence d(GAATTC) as does M.EcoRI.  The reduced and denatured
      molecular weight of the RsrI methyltransferase (MTase) is 33,600 Da.  A
      fragment of R. sphaeroides chromosomal DNA exhibited M.RsrI activity in E. coli
      and was used to sequence the rsrIM gene.  The deduced amino acid sequence of
      M.RsrI shows partial homology to those of the type II adenine MTases HinfI and
      DpnA and N4-cytosine MTases BamHI and PvuII, and to the type III adenine MTases
      EcoP1 and EcoP15.  In contrast to their corresponding isoschizomeric
      endonucleases, the deduced amino acid sequences of the RsrI and EcoRI MTases
      show very little homology.  Either the EcoRI and RsrI restriction modification
      systems assembled independently from closely related endonuclease and more
      distantly related MTase genes, or the MTase genes diverged more than their
      partner endonuclease genes.  The rsrIM gene sequence has also been determined
      by Stephenson and Greene (Nucl. Acids Res. (1989) 17, this issue).
AU  - Kaszubska W
AU  - Aiken C
AU  - O'Connor CD
AU  - Gumport RI
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 10403-10425.

PMID- 3266862
VI  - 74
DP  - 1988
TI  - RsrI restriction-modification enzymes from Rhodobacter sphaeroides.
PG  - 83-84
AB  - Meeting Abstract
AU  - Kaszubska W
AU  - Aiken CR
AU  - Gumport RI
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 83-84.

PMID- 1511884
VI  - 118
DP  - 1992
TI  - Purification and characterization of the M.RsrI DNA methyltransferase from Escherichia coli.
PG  - 5-11
AB  - The gene (rsrIM) encoding the RsrI DNA methyltransferase (M.RsrI) from Rhodobacter sphaeroides
      was cloned and expressed in Escherichia coli. Under the control of a bacteriophage T7
      promotor, 2% of the total protein in a crude extract was M.RsrI. This level of expression
      represents an approximately 50-fold increase over that present in the natural host.
      Chromatography using DNA cellulose and the S-adenosylmethionine analogue, sinefungin, was
      useful in purifying the enzyme to homogeneity. The purification yielded 100 times more enzyme
      than was obtained from the same quantity of R.sphaeroides cell paste. M.RsrI deposits one
      methyl group per productive DNA-binding event, as does its functional but
      sequence-nonhomologous analogue, M.EcoRI. Unlike M.EcoRI, the R. sphaeroides enzyme is a dimer
      at micromolar concentrations.
AU  - Kaszubska W
AU  - Webb HK
AU  - Gumport R
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1992 118: 5-11.

PMID- 19346307
VI  - 191
DP  - 2009
TI  - Genome Sequence of the Anaerobic, Thermophilic and Cellulolytic Bacterium Anaerocellum thermophilum DSM 6725.
PG  - 3760-3761
AB  - Anaerocellum thermophilum DSM 6725 is a strictly anaerobic bacterium that grows optimally at
      75 degrees C. It uses a variety of polysaccharides, including crystalline cellulose and
      untreated plant biomass, and has potential utility in biomass conversion. Here we report its
      complete genome sequence of 2.97 Mb, which is contained within one chromosome and two plasmids
      (of 8.3 and 3.6 kb). The genome encodes a broad set of cellulolytic enzymes, transporters and
      pathways for sugar utilization and compared to those of other saccharolytic, anaerobic
      thermophiles is most similar to that of Caldicellulosiruptor saccharolyticus DSM 8903.
AU  - Kataeva IA
AU  - Yang SJ
AU  - Dam P
AU  - Poole FLII
AU  - Yin Y
AU  - Zhou F
AU  - Chou WC
AU  - Xu Y
AU  - Goodwin L
AU  - Sims DR
AU  - Detter JC
AU  - Hauser LG
AU  - Westpheling J
AU  - Adams MW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2009 191: 3760-3761.

PMID- 27231354
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Five Rapidly Growing Mycobacterium Species, M. thermoresistibile, M. fortuitum subsp. acetamidolyticum, M. canariasense, M.  brisbanense, and M. novocastrense.
PG  - e00322-16
AB  - We report here the draft genome sequences of five rapidly growing Mycobacterium (RGM) species
      potentially pathogenic to humans, M. thermoresistibile, M.
      fortuitum subsp. acetamidolyticum, M. canariasense, M. brisbanense, and M.
      novocastrense As the clinical importance of RGMs is increasingly being recognized
      worldwide, these sequences would contribute to further advances in RGM research.
AU  - Katahira K
AU  - Ogura Y
AU  - Gotoh Y
AU  - Hayashi T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00322-16.

PMID- 25792068
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of SS52, a Strain of Escherichia coli O157:H7 Recovered  from Supershedder Cattle.
PG  - e01569-14
AB  - Shiga toxin-producing Escherichia coli O157:H7 causes foodborne infections, and cattle are the
      primary reservoir. Some animals, known as supershedders, excrete
      orders of magnitude more E. coli O157:H7 in the feces than normal. Here, we
      report the complete genome sequence of the SS52 supershedder strain of E. coli
      O157:H7.
AU  - Katani R
AU  - Cote R
AU  - Raygoza GJA
AU  - Li L
AU  - Arthur TM
AU  - DebRoy C
AU  - Mwangi MM
AU  - Kapur V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01569-14.

PMID- 23408234
VI  - 6
DP  - 2012
TI  - Complete genome sequence of Oscillibacter valericigenes Sjm18-20(T) (=NBRC 101213(T)).
PG  - 406-414
AB  - Oscillibacter valericigenes is a mesophilic, strictly anaerobic bacterium belonging to the
      clostridial cluster IV. Strain Sjm18-20(T) (=NBRC 101213(T) =DSM
      18026(T)) is the type strain of the species and represents the genus
      Oscillibacter Iino et al. 2007. It was isolated from the alimentary canal of a
      Japanese corbicula clam (Corbicula japonica) collected on a seacoast in Shimane
      Prefecture in Japan. Phylogenetically, strain Sjm18-20(T) is closest to
      uncultured bacteria in digestive tracts, including the enriched cells thought to
      represent Oscillospira guilliermondii Chatton and Perard 1913. The isolated
      phylogenetic position and some distinct characteristics prompted us to determine
      the complete genome sequence. The 4,410,036 bp chromosome and the 60,586 bp
      plasmid were predicted to encode a total of 4,723 protein-coding genes.
AU  - Katano Y
AU  - Fujinami S
AU  - Kawakoshi A
AU  - Nakazawa H
AU  - Oji S
AU  - Iino T
AU  - Oguchi A
AU  - Ankai A
AU  - Fukui S
AU  - Terui Y
AU  - Kamata S
AU  - Harada T
AU  - Tanikawa S
AU  - Suzuki K
AU  - Fujita N
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 6: 406-414.

PMID- 12770909
VI  - 84
DP  - 2003
TI  - Single molecule detection of DNA looping by NgoMIV restriction endonuclease.
PG  - 4053-4061
AB  - Single molecule fluorescence resonance energy transfer (FRET) and fluorescence correlation
      spectroscopy were used to investigate DNA looping
      by NgoMIV restriction endonuclease. Using a linear double-stranded DNA
      (dsDNA) molecule labeled with a fluorescence donor molecule, Cy3, and
      fluorescence acceptor molecule, Cy5, and by varying the concentration of
      NgoMIV endonuclease from 0 to 3 x 10(-6) M, it was possible to detect and
      determine diffusion properties of looped DNA/protein complexes. FRET
      efficiency distributions revealed a subpopulation of complexes with an
      energy transfer efficiency of 30%, which appeared upon addition of enzyme
      in the picomolar to nanomolar concentration range (using 10(-11) M dsDNA).
      The concentration dependence, fluorescence burst size analysis, and
      fluorescence correlation analysis were all consistent with this
      subpopulation arising from a sequence specific interaction between an
      individual enzyme and a DNA molecule. A 30% FRET efficiency corresponds to
      a distance of approximately 65 A, which correlates well with the distance
      between the ends of the dsDNA molecule when bound to NgoMIV according to
      the crystal structure of this complex. Formation of the looped complexes
      was also evident in measurements of the diffusion times of freely
      diffusing DNA molecules with and without NgoMIV. At very high protein
      concentrations compared to the DNA concentration, FRET and fluorescence
      correlation spectroscopy results revealed the formation of larger
      DNA/protein complexes.
AU  - Katiliene Z
AU  - Katilius E
AU  - Woodbury NW
PT  - Journal Article
TA  - Biophys. J.
JT  - Biophys. J.
SO  - Biophys. J. 2003 84: 4053-4061.

PMID- 20134230
VI  - 20
DP  - 2010
TI  - Unbalanced Restriction Impairs SOS-induced DNA Repair Effects.
PG  - 30-38
AB  - The contribution of a type II restriction-modification system (R-M system) to genome integrity
      and cell viability was investigated. We
      established experimental conditions that enabled the achievement of
      hemimethylated and unmethylated states for the specific bases of the
      recognition sequences of the host's DNA. To achieve this, we
      constructed the MboII R-M system containing only one (i.e., M2.MboII)
      out of two functional MboII methyltransferases found in Moraxella
      bovis. Using the incomplete R-M system, we were able to perturb the
      balance between methylation and restriction in an inducible manner. We
      demonstrate that upon the SOS-induced DNA repair in mitomycin C treated
      cells, restriction significantly reduces cell viability. Similar
      results for the well-studied wild-type EcoRI R-M system, expressed
      constitutively in Escherichia coli, were obtained. Our data provide
      further insights into the benefits and disadvantages of maintaining of
      a type II R-M system, highlighting its impact on host cell fitness.
AU  - Katna A
AU  - Boratynski R
AU  - Furmanek-Blaszk B
AU  - Zolcinska N
AU  - Sektas M
PT  - Journal Article
TA  - J. Microbiol. Biotechnol.
JT  - J. Microbiol. Biotechnol.
SO  - J. Microbiol. Biotechnol. 2010 20: 30-38.

PMID- Not carried by PubMed...
VI  - 51
DP  - 1989
TI  - Isolation and characterization of restriction endonuclease from amino acid- or nucleic acid-producing bacteria.
PG  - 3-9
AB  - Restriction enzymes are endonucleases that recognize specific nucleotide
      sequences in double stranded DNA and cleave both strands of the duplex.  In the
      cell of origin each restriction enzyme is part of a restriction-modification
      system, consisting of the restriction endonuclease and a matched modification
      enzyme which recognizes and modifies the same nucleotide sequence in the DNA
      strand.  Modification thus protects cellular DNA from restriction, however,
      foreign DNA cleaved by the restriction endonuclease and further degraded by
      other enzymes.  Such restriction modification systems, first detected by phage
      restriction and modification, are widespread in bacteria and are thought to
      play a role in eliminating foreign DNA that gains entrance to the cell via
      viruses or as naked DNA.  The discovery of the first Class II endonuclease was
      reported by Smith and Wilcox (1970).  Since that time, the number of Class II
      restriction endonucleases available in purified form has been increasing at a
      remarkable pace, and it is now very often possible to find one or several
      restriction endonucleases having the specificity one desires.  This review is
      mainly concerned with general properties and applications of Class II
      restriction endonucleases including some properties of the restriction
      endonucleases isolated from amino acid- or nucleic acid-producing bacteria and
      related species in our laboratory.
AU  - Kato F
PT  - Journal Article
TA  - Dojin News
JT  - Dojin News
SO  - Dojin News 1989 51: 3-9.

PMID- 26184940
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of a Phenanthrene Degrader, Mycobacterium sp. Strain EPa45, Isolated from a Phenanthrene-Degrading Consortium.
PG  - e00782-15
AB  - Many polycyclic aromatic hydrocarbons (PAHs) are serious environmental pollutants, and their
      toxicity threatens human and wildlife health (1, 2). Microbial biodegradation of PAHs has thus
      drawn considerable attention, and various PAHdegrading bacterial strains have been isolated
      (3).
AU  - Kato H
AU  - Ogawa N
AU  - Ohtsubo Y
AU  - Ohshima K
AU  - Toyoda A
AU  - Yamazoe A
AU  - Mori H
AU  - Maruyama F
AU  - Nagata Y
AU  - Hattori M
AU  - Fujiyama A
AU  - Kurokawa K
AU  - Tsuda M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00782-15.

PMID- 22461545
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Lactococcus lactis IO-1, a Lactic Acid Bacterium That Utilizes Xylose and Produces High Levels of L-Lactic Acid.
PG  - 2102-2103
AB  - We report the complete genome sequence of Lactococcus lactis IO-1 (= JCM7638). It is a
      nondairy lactic acid bacterium, produces nisin Z, ferments xylose, and
      produces predominantly l-lactic acid at high xylose concentrations. From ortholog
      analysis with other five L. lactis strains, IO-1 was identified as L. lactis
      subsp. lactis.
AU  - Kato H
AU  - Shiwa Y
AU  - Oshima K
AU  - Machii M
AU  - Araya-Kojima T
AU  - Zendo T
AU  - Shimizu-Kadota M
AU  - Hattori M
AU  - Sonomoto K
AU  - Yoshikawa H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2102-2103.

PMID- Not carried by PubMed...
VI  - 47
DP  - 1990
TI  - Inhibition of restriction endonucleases by hot water extracts of spices.
PG  - 84-87
AB  - Forty samples of spices were investigated for their inhibitory activities to
      the cleavage of lambda DNA by restriction endonucleases.  Bayberry, clove
      eucalyptus, melissa, nutmeg, oregano, peppermint and savory showed complete
      inhibition to HindIII, under the condition employed.  Hot water extract of
      clove showed marked inhibitory activity (MIC 2 micrograms/ml) and that of
      oregano and peppermint showed potent inhibition (MIC 20 micrograms/ml).  MIC of
      clove extract for five restriction endonucleases were determined.  MIC for
      EcoRI and HindIII was 0.8 micrograms/ml, and 12.5 micrograms/ml for BamHI, 50
      micrograms/ml for BglII and PstI.  Specificity of inhibition for restriction
      endonucleases by hot water extract of clove was found.
AU  - Kato J
AU  - Endo T
AU  - Kawamura H
AU  - Nakashima Y
AU  - Furukoshi K
AU  - Oishi K
PT  - Journal Article
TA  - Bull. Coll. Agr. Vet. Med.
JT  - Bull. Coll. Agr. Vet. Med.
SO  - Bull. Coll. Agr. Vet. Med. 1990 47: 84-87.

PMID- 24504001
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Lactobacillus namurensis Chizuka 01, Isolated from Nukadoko, a Pickling Bed of Fermented Rice Bran.
PG  - e01263-13
AB  - Lactobacillus namurensis Chizuka 01 was isolated from nukadoko, which is a fermented rice bran
      bed traditionally used in Japan for pickling vegetables.
      Here, we report the first draft of an annotated genome sequence of this organism.
      This paper is the first published report of the genomic sequence of L.
      namurensis.
AU  - Kato K
AU  - Toh H
AU  - Sakamoto N
AU  - Mori K
AU  - Tashiro K
AU  - Hibi N
AU  - Sonomoto K
AU  - Nakayama J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01263-13.

PMID- 28818888
VI  - 5
DP  - 2017
TI  - Genome Sequence of Lactobacillus sakei LK-145 Isolated from a Japanese Sake Cellar as a High Producer of d-Amino Acids.
PG  - e00656-17
AB  - This announcement reports the complete genome sequence of strain LK-145 of Lactobacillus sakei
      isolated from a Japanese sake cellar as a potent strain for
      the production of large amounts of d-amino acids. Three putative genes encoding
      an amino acid racemase were identified.
AU  - Kato S
AU  - Oikawa T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00656-17.

PMID- 28774971
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequence of Leuconostoc mesenteroides LT-38, a Non-Spore-Forming Gram-Positive Lactic Acid Bacterium.
PG  - e00670-17
AB  - The present study reports the complete genome sequence of Leuconostoc mesenteroides strain
      LT-38, which is a non-spore-forming Gram-positive lactic
      acid bacterium. The genome is composed of a 2,022,184-bp circular chromosome and
      contains 2,005 putative protein-coding genes.
AU  - Kato S
AU  - Oikawa T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00670-17.

PMID- 28774969
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequence of Lactobacillus sakei LT-13 Isolated from Moto Starter of  Sake.
PG  - e00651-17
AB  - Lactobacillus sakei strain LT-13 is a lactic acid bacterium isolated from moto starter of
      Japanese sake. This genome analysis revealed that the genome is
      composed of a circular chromosome and one plasmid, which contain 1,938 and 8
      putative protein-coding genes, respectively.
AU  - Kato S
AU  - Oikawa T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00651-17.

PMID- 28751393
VI  - 5
DP  - 2017
TI  - Genome Sequence of Leuconostoc mesenteroides LK-151 Isolated from a Japanese Sake Cellar as a High Producer of d-Amino Acids.
PG  - e00661-17
AB  - Here, we report the complete genome sequence of strain LK-151 of Leuconostoc mesenteroides,
      which was isolated from a Japanese sake cellar and has the
      potential to produce large amounts of d-amino acids, namely, d-Ala and d-Glu. The
      genome contains 4 genes related to d-amino acid production.
AU  - Kato S
AU  - Oikawa T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00661-17.

PMID- 25180586
VI  - 9
DP  - 2014
TI  - Unique features of a Japanese 'Candidatus Liberibacter asiaticus' strain revealed by whole genome sequencing.
PG  - e106109
AB  - Citrus greening (huanglongbing) is the most destructive disease of citrus worldwide.  It is
      spread by citrus psyllids and is associated with phloem-limited bacteria of three species of
      a-Proteobacteria, namely, 'Candidatus Liberibacter asiaticus', 'Ca.  L. americanus', and
      'Ca. L. africanus'.  Recent findings suggested that some Japanese strains lack the
      bacteriophage-type DNA polymerase region (DNA pol), in contrast to the Floridian psy62 strain.
      The whole genome sequence of the pol-negative 'Ca. L. asiaticus' Japanese isolate lshi-1 was
      determined by metagenomic analysis of DNA extracted from 'Ca. L. asiaticus'-infected
      psyllids and leaf midribs.  The 1.19-Mb genome has an average 36.32% GC content.  Annotation
      revealed 13 operons encoding rRNA and 44 tRNA genes, but no typical bacterial
      pathogenesis-related genes were located within the genome, similar to the Floridian psy62 and
      Chinese gxpsy.  In contrast to other 'Ca. L. asiaticus' strains, the genome of the Japanese
      Ishi-1 strain lacks a prophage-related region.
AU  - Katoh H
AU  - Miyata S
AU  - Inoue H
AU  - Iwanami T
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2014 9: e106109.

PMID- 28814130
VI  - 81
DP  - 2017
TI  - Identification and characterization of a sulfoglycosidase from Bifidobacterium bifidum implicated in mucin glycan utilization.
PG  - 2018-2027
AB  - Human gut symbiont bifidobacteria possess carbohydrate-degrading enzymes that act on the
      O-linked glycans of intestinal mucins to utilize those carbohydrates as carbon sources.
      However, our knowledge about mucin type O-glycan degradation by bifidobacteria remains
      fragmentary, especially regarding how they decompose sulfated glycans, which are abundantly
      found in mucin sugar-chains. Here, we examined the abilities of several Bifidobacterium
      strains to degrade a sulfated glycan substrate and identified a
      6-sulfo-beta-d-N-acetylglucosaminidase, also termed sulfoglycosidase, encoded by bbhII from
      Bifidobacterium bifidum JCM 7004. A recombinant BbhII protein showed a substrate preference
      toward 6-sulfated and 3,4-disulfated N-acetylglucosamines over non-sulfated and 3-sulfated
      N-acetylglucosamines. The purified BbhII directly released 6-sulfated N-acetylglucosamine from
      porcine gastric mucin and the expression of bbhII was moderately induced in the presence of
      mucin. This de-capping activity may promote utilization of sulfated glycans of mucin by other
      bacteria including bifidobacteria, thereby establishing the symbiotic relationship between
      human and gut microbes.
AU  - Katoh T
AU  - Maeshibu T
AU  - Kikkawa K
AU  - Gotoh A
AU  - Tomabechi Y
AU  - Nakamura M
AU  - Liao W-H
AU  - Yamaguchi M
AU  - Ashida H
AU  - Yamamoto K
AU  - Katayama T
PT  - Journal Article
TA  - Biosci. Biotechnol. Biochem.
JT  - Biosci. Biotechnol. Biochem.
SO  - Biosci. Biotechnol. Biochem. 2017 81: 2018-2027.

PMID- 16233708
VI  - 98
DP  - 2004
TI  - Activation of restriction enzyme by electrochemically released magnesium ion.
PG  - 293-297
AB  - Observation and cutting of DNA molecules at intended positions permit several new experimental
      methods that are completely different from
      conventional molecular biology methods; therefore several cutting
      methods have been proposed and studied. In this paper. a new cutting
      method for a DNA molecule by localizing the activity of a restriction
      enzyme is presented. Since most restriction enzymes require magnesium
      ions for their activation, local restriction enzyme activity can be
      controlled by the local concentration of magnesium ions. Applying a
      direct current (dc) voltage to a needle electrode of metallic magnesium
      made it possible to control the local magnesium ion concentration at
      the tip of the needle. The restriction enzyme was activated only, when
      magnesium ions were electrochemically supplied.
AU  - Katsura S
AU  - Harada N
AU  - Maeda Y
AU  - Komatsu J
AU  - Matsuura S
AU  - Takashima K
AU  - Mizuno A
PT  - Journal Article
TA  - J. Biosci. Bioeng.
JT  - J. Biosci. Bioeng.
SO  - J. Biosci. Bioeng. 2004 98: 293-297.

PMID- 28254969
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Desulfuromonas acetexigens Strain 2873, a Novel Anode-Respiring Bacterium.
PG  - e01522-16
AB  - Here, we report the draft genome sequence of Desulfuromonas acetexigens strain 2873, which was
      originally isolated from digester sludge from a sewage treatment
      plant in Germany. This bacterium is capable of anode respiration with high
      electrochemical activity in microbial electrochemical systems. The draft genome
      contains 3,376 predicted protein-coding genes and putative multiheme c-type
      cytochromes.
AU  - Katuri KP
AU  - Albertsen M
AU  - Saikaly PE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01522-16.

PMID- 12872006
VI  - 2
DP  - 2003
TI  - Automated identification of putative methyltransferases from genomic open reading frames.
PG  - 525-540
AB  - We have analyzed existing methodologies and created novel methodologies for the automatic
      assignment of S-adenosylmethionine (AdoMet)-dependent
      methyltransferase functionality to genomic open reading frames based on
      predicted protein sequences. A large class of the AdoMet-dependent
      methyltransferases shares a common binding motif for the AdoMet cofactor
      in the form of a seven-strand twisted beta-sheet; this structural
      similarity is mirrored in a degenerate sequence similarity that we refer
      to as methyltransferase signature motifs. These motifs are the basis of
      our assignments. We find that simple pattern matching based on the motif
      sequence is of limited utility and that a new method of "sensitized
      matrices for scoring methyltransferases" (SM(2)) produced with modified
      versions of the MEME and MAST tools gives greatly improved results for the
      Saccharomyces cerevisiae yeast genome. From our analysis, we conclude that
      this class of methyltransferases makes up approximately 0.6-1.6% of the
      genes in the yeast, human, mouse, Drosophila melanogaster, Caenorhabditis
      elegans, Arabidopsis thaliana, and Escherichia coli genomes. We provide
      lists of unidentified genes that we consider to have a high probability of
      being methyltransferases for future biochemical analyses.
AU  - Katz JE
AU  - Dlakic M
AU  - Clarke S
PT  - Journal Article
TA  - Mol. Cell. Proteomics
JT  - Mol. Cell. Proteomics
SO  - Mol. Cell. Proteomics 2003 2: 525-540.

PMID- 25013135
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Environmental Vibrio cholerae 2012EL-1759 with Similarities to the V. cholerae O1 Classical Biotype.
PG  - e00617-14
AB  - Vibrio cholerae 2012EL-1759 is an environmental isolate from Haiti that was recovered in 2012
      during a cholera outbreak. The genomic backbone is similar to
      that of the prototypical V. cholerae O1 classical biotype strain O395, and it
      carries the Vibrio pathogenicity islands (VPI-1 and VPI-2) and a cholera toxin
      (CTX) prephage.
AU  - Katz LS
AU  - Turnsek M
AU  - Kahler A
AU  - Hill VR
AU  - Boyd EF
AU  - Tarr CL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00617-14.

PMID- 2436455
VI  - 35
DP  - 1986
TI  - Identification of a new restriction endonuclease, EagI, from Enterobacter agglomerans.
PG  - 317-320
AB  - The preliminary studies presented in this communication indicate that EndoR.
      EagI and the restriction endonuclease EcoRII as well as EndoR. BstNI recognize
      identical palindromic sites on the DNA substrate i.e. they are isoschizomers.
      Since EndoR. EcoRII and EndoR. BstNI recognize the sequence CC(A/T)GG. EndoR.
      EagI should recognize the same nucleotide sequence.
AU  - Kauc L
AU  - Leszczynska K
PT  - Journal Article
TA  - Acta Microbiol. Pol.
JT  - Acta Microbiol. Pol.
SO  - Acta Microbiol. Pol. 1986 35: 317-320.

PMID- 
VI  - 0
DP  - 1976
TI  - Degradation of Transforming Deoxyribonucleic Acid by the ATP Dependent Restriction Endonuclease Isolated from Haemophilus Influenzae Rf.
PG  - 257-262
AB  - The deoxyribonucleic acid of different serological types of Haemophilus
      influenzae was shown to be degraded by the ATP dependent restriction
      endonuclease isolated from H.influenzae Rf.
AU  - Kauc L
AU  - Piekarowicz A
PT  - Journal Article
TA  - Modern Trends in Bacterial Transformation and Transfection.
JT  - Modern Trends in Bacterial Transformation and Transfection.
SO  - Modern Trends in Bacterial Transformation and Transfection. 1976 0: 257-262.

PMID- 33045
VI  - 92
DP  - 1978
TI  - Purification and properties of a new restriction endonuclease from Haemophilus influenzae Rf.
PG  - 417-426
AB  - Haemophilus influenzae Rf 232, showing the phenomena of restriction and
      modification, contains an endonuclease that inactivates in vitro the biological
      activity of DNAs lacking the strain-specific modification.  This specific
      restriction endonuclease has been purified to near homogeneity by a procedure
      that includes DNA-agarose chromatography.  This highly purified enzyme requires
      ATP and Mg2+ for activity and is stimulated by S-adenosylmethionine.  The
      enzyme seems to cleave DNA at well-defined sites, since it produces a specific
      pattern of bands upon agarose gel electrophoresis.  The enzyme has no ATPase
      activity.  A methylase activity is observed in the course of the
      endonucleolytic reaction, which probably protects some of the DNA sites from
      cleavage.
AU  - Kauc L
AU  - Piekarowicz A
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1978 92: 417-426.

PMID- 67762
VI  - 26
DP  - 1977
TI  - Degradation of transforming and transfecting DNA by the restriction endonucleases of Type I and Type II isolated from Haemophilus influenzae.
PG  - 137-148
AB  - The restriction endonucleases of type I and II from Haemophilus influenzae were studied for
      their activity on transforming and transfecting DNA.  Type I restriction enzyme from
      Haemophilus influenzae Rf, which requires adenosine 5'-triphosphate, reduced the size of
      unmodified bacterial DNA from 66 x 106 daltons to approximately 18 x 106 daltons and did not
      attack modified DNA.  The action of this enzyme gives only a low level of inactivation of
      single and linked markers in the transforming DNA.  In contrast the HP1c1 phage DNA was
      drastically inactivated by this enzyme.  The endoR.Hind III degrades the unmodified bacterial
      DNA but the segments generated by this enzyme are still capable of being integrated in
      transformation.  The enzyme has no activity on HP1c1 phage DNA.
AU  - Kauc L
AU  - Piekarowicz A
PT  - Journal Article
TA  - Acta Microbiol. Pol.
JT  - Acta Microbiol. Pol.
SO  - Acta Microbiol. Pol. 1977 26: 137-148.

PMID- 2171587
VI  - 9
DP  - 1990
TI  - Restriction endonuclease cleavage at the termini of PCR products.
PG  - 304-305
AB  - None
AU  - Kaufman DL
AU  - Evans GA
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 1990 9: 304-305.

PMID- 10664586
VI  - 25
DP  - 2000
TI  - Anticodon nucleases.
PG  - 70-74
AB  - A tRNALys-specific anticodon nuclease is kept in a latent form in a rare Escherichia coli
      strain, complexed with a DNA restriction enzyme. A phage T4 inhibitor of DNA restriction
      activates anticodon nuclease, but other T4 proteins restore tRNALys. Detection of a homologous
      system in Neisseria and a different anticodon nuclease in colicin E5 suggest ubiquity and
      diversity of such tRNA toxins. Analysis of these systems could reveal novel RNA recognition
      and cleavage mechanisms.
AU  - Kaufmann G
PT  - Journal Article
TA  - Trends Biochem. Sci.
JT  - Trends Biochem. Sci.
SO  - Trends Biochem. Sci. 2000 25: 70-74.

PMID- 8095080
VI  - 17C
DP  - 1993
TI  - In vivo reconstitution of latent anticodon nuclease: A tRNA restriction enzyme masked by hsd restriction-modification proteins.
PG  - 174
AB  - E. coli prr+ strains encode a latent form of phage T4-induced, tRNA Lys-specific anticodon
      nuclease. The latent enzyme comprises a core factor encoded by prrC and cognate masking
      elements encoded by flanking, hsd type Ic restriction modification genes. We have
      reconstituted latent anticodon nuclease from separate, core and masking components in vivo by
      complementing a prr cosmid carrying a null prrC mutation with PrrC provided in trans.
      Expression of prrC from a low copy plasmid, insufficient to elicit detectable core activity by
      itself, yielded in the presence of the hsd masking factors a full-fledged latent anticodon
      nuclease phenotype. The data indicate that the Hsd proteins not only mask PrrC's activity but
      also stabilize it maintaining the RNA restriction enzyme as an antiviral contingency.
AU  - Kaufmann G
AU  - Amitsur M
AU  - Chapman-Shimshoni D
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1993 17C: 174.

PMID- 27795271
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Two Geobacillus Species Strains, Isolated from Oil Wells and Surface Soil above Oil Pools.
PG  - e01129-16
AB  - Here, we present the draft genome sequences of two Geobacillus species strains isolated from
      oil wells and surface soil above oil pools in Lithuania.
AU  - Kaunietis A
AU  - de Jong A
AU  - Pranckute R
AU  - Buivydas A
AU  - Kuipers OP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01129-16.

PMID- 27540068
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Phosphate-Solubilizing Bacterium Paraburkholderia tropica Strain P-31 Isolated from Pomegranate (Punica granatum) Rhizosphere.
PG  - e00844-16
AB  - We report the 8.9 Mb draft genome sequence of phosphate-solubilizing bacterium
      Paraburkholderia tropica strain P-31, isolated from pomegranate (Punica granatum)
      rhizosphere. The draft genome sequence of Paraburkholderia tropica strain P-31
      consists of 8,881,246 bp with a G+C content of 64.7%, 8,039 protein-coding genes,
      and 49 RNAs.
AU  - Kaur C
AU  - Selvakumar G
AU  - Ganeshamurthy AN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00844-16.

PMID- 24051322
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of a Hexachlorocyclohexane-Degrading Bacterium, Sphingobium baderi Strain LL03T.
PG  - e00751-13
AB  - Sphingobium baderi strain LL03(T) was isolated from hexachlorocyclohexane (HCH)-contaminated
      soil from Spolana, Czech Republic. Strain LL03(T) is a mutant
      that is deficient in linB and linC (genes that encode hexachlorocyclohexane
      haloalkane dehalogenase and dehydrogenase, respectively). The draft genome
      sequence of LL03(T) (~4.85 Mb) consists of 92 contigs and 4,914 coding sequences,
      with a G+C content of 63.5%.
AU  - Kaur J
AU  - Verma H
AU  - Tripathi C
AU  - Khurana JP
AU  - Lal R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00751-13.

PMID- 7636474
VI  - 76
DP  - 1995
TI  - Identification and characterization of the frog virus 3 DNA methyltransferase gene.
PG  - 1937-1943
AB  - Cytosine DNA methyltransferases (MTases) first recognize specific nucleotide sequences and
      then transfer a methyl group from S-adenosylmethionine to cytosine.  This division of function
      is reflected in five highly conserved motifs shared by cytosine Mtases.  The region containing
      the first four motifs is responsible for the catalytic function whereas the region containing
      the fifth motif V provides specificity of binding to DNA.  In at least one case, two separate
      proteins, one containing the first four motifs and the second containing the last motif
      combine to provide full functional activity.  In the frog virus 3 (FV3) genome we have
      identified an open reading frame (ORF) whose deduced amino acid (aa) sequence contains motifs
      characteristic of prokaryotic as well as eukaryotic MTases.  The ORF consists of 642 bp which
      codes for a protein of 214 aa with a predicted molecular mass of 24.8 kDa.  This ORF contains
      the first four highly conserved motifs of cytosine MTases but the fifth motif, responsible for
      DNA binding specificity, is missing.  Presumably, FV3 MTase is composed of two subunits.
      Northern blot analysis showed that the putative MTase ORF is transcribed into two transcripts
      belonging to the delayed-early class of FV3 messages.  These two transcripts appear to be
      initiated at two different start sites but terminate in the same 3' region of the gene.  The
      transcription start sites are not preceded by any known promoter sequences, but two regions of
      hyphenated dyad symmetry are present at the 3' end of the message.  A protein with a
      molecular mass of ~28 kDa was synthesized by a rabbit reticulocyte lysate programmed with
      capped runoff transcripts from the cloned gene, suggesting that the ORF can be transcribed
      into a message coding for a viral protein.  Overall, our results suggest that we have
      identified a gene for a subunit of MTase in the FV3 genome.
AU  - Kaur K
AU  - Rohozinski J
AU  - Goorha R
PT  - Journal Article
TA  - J. Gen. Virol.
JT  - J. Gen. Virol.
SO  - J. Gen. Virol. 1995 76: 1937-1943.

PMID- 23558534
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Amycolatopsis decaplanina Strain DSM 44594T.
PG  - e0013813
AB  - We report the 8.5-Mb genome sequence of Amycolatopsis decaplanina strain DSM 44594(T),
      isolated from a soil sample from India. The draft genome of strain DSM
      44594(T) consists of 8,533,276 bp with a 68.6% G+C content, 7,899 protein-coding
      genes, and 57 RNAs.
AU  - Kaur N
AU  - Kumar S
AU  - Bala M
AU  - Raghava GP
AU  - Mayilraj S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0013813.

PMID- 17344322
VI  - 35
DP  - 2007
TI  - Restriction endonuclease MvaI is a monomer that recognizes its target sequence asymmetrically.
PG  - 2035-2046
AB  - Restriction endonuclease MvaI recognizes the sequence CC/WGG (W stands for A or T, '/'
      designates the cleavage site) and generates products with single nucleotide 5'-overhangs. The
      enzyme has been noted for its tolerance towards DNA modifications. Here, we report a
      biochemical characterization and crystal structures of MvaI in an apo-form and in a complex
      with target DNA at 1.5 A resolution. Our results show that MvaI is a monomer and recognizes
      its pseudosymmetric target sequence asymmetrically. The enzyme consists of two lobes. The
      catalytic lobe anchors the active site residues Glu36, Asp50, Glu55 and Lys57 and contacts the
      bases from the minor grove side. The recognition lobe mediates all major grove interactions
      with the bases. The enzyme in the crystal is bound to the strand with T at the center of the
      recognition sequence. The crystal structure with calcium ions and DNA mimics the prereactive
      state. MvaI shows structural similarities to BcnI, which cleaves the related sequence CC/SGG
      and to MutH enzyme, which is a component of the DNA repair machinery, and nicks one DNA strand
      instead of making a double-strand break.
AU  - Kaus-Drobek M
AU  - Czapinska H
AU  - Sokolowska M
AU  - Tamulaitis G
AU  - Szczepanowski RH
AU  - Urbanke C
AU  - Siksnys V
AU  - Bochtler M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2007 35: 2035-2046.

PMID- 23105048
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Psychrophilic Deep-Sea Bacterium Moritella marina MP-1 (ATCC 15381).
PG  - 6296-6297
AB  - Moritella marina MP-1 is a bacterial species known for its production of docosahexaenoic acid.
      We present the draft genome sequence of the type strain
      Moritella marina MP-1 (ATCC 15381), having 4,636,778 bp with a G+C content of
      40.5% and consisting of 83 contigs.
AU  - Kautharapu KB
AU  - Jarboe LR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6296-6297.

PMID- 28153893
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Plant Growth-Promoting Drought-Tolerant Bacillus sp. Strain CMAA 1363 Isolated from the Brazilian Caatinga Biome.
PG  - e01534-16
AB  - The strain of Bacillus sp. CMAA 1363 was isolated from the Brazilian Caatinga biome and showed
      plant growth-promoting traits and ability to promote maize
      growth under drought stress. Sequencing revealed genes involved in stress
      response and plant growth promotion. These genomic features might aid in the
      protection of plants against the negative effects imposed by drought.
AU  - Kavamura VN
AU  - Santos SN
AU  - Taketani RG
AU  - Vasconcellos RL
AU  - Melo IS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01534-16.

PMID- 26941132
VI  - 4
DP  - 2016
TI  - First High-Quality Draft Genome Sequence of Pasteurella multocida Sequence Type 128 Isolated from Infected Bone.
PG  - e00023-16
AB  - We report here the first high-quality draft genome sequence of Pasteurella multocida sequence
      type 128, which was isolated from the infected finger bone of
      an adult female who was bitten by a domestic dog. The draft genome will be a
      valuable addition to the scarce genomic resources available for P. multocida.
AU  - Kavousi N
AU  - Eng WW
AU  - Lee YP
AU  - Tan LH
AU  - Thuraisingham R
AU  - Yule CM
AU  - Gan HM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00023-16.

PMID- 21092102
VI  - 11
DP  - 2010
TI  - Translational independence between overlapping genes for a restriction endonuclease and its transcriptional regulator.
PG  - 87
AB  - Background: Most type II restriction-modification (RM) systems have two independent enzymes
      that act on the same DNA sequence: a modification
      methyltransferase that protects target sites, and a restriction
      endonuclease that cleaves unmethylated target sites. When RM genes
      enter a new cell, methylation must occur before restriction activity
      appears, or the host's chromosome is digested. Transcriptional
      mechanisms that delay endonuclease expression have been identified in
      some RM systems. A substantial subset of those systems is controlled by
      a family of small transcription activators called C proteins. In the
      PvuII system, C. PvuII activates transcription of its own gene, along
      with that of the downstream endonuclease gene. This regulation results
      in very low R. PvuII mRNA levels early after gene entry, followed by
      rapid increase due to positive feedback. However, given the lethal
      consequences of premature REase accumulation, transcriptional control
      alone might be insufficient. In C-controlled RM systems, there is a +/-
      20 nt overlap between the C termination codon and the R (endonuclease)
      initiation codon, suggesting possible translational coupling, and in
      many cases predicted RNA hairpins could occlude the ribosome binding
      site for the endonuclease gene.Results: Expression levels of lacZ
      translational fusions to pvuIIR or pvuIIC were determined, with the
      native pvuII promoter having been replaced by one not controlled by C.
      PvuII. In-frame pvuIIC insertions did not substantially decrease either
      pvuIIC-lacZ or pvuIIR-lacZ expression (with or without C. PvuII
      provided in trans). In contrast, a frameshift mutation in pvuIIC
      decreased expression markedly in both fusions, but mRNA measurements
      indicated that this decrease could be explained by transcriptional
      polarity. Expression of pvuIIR-lacZ was unaffected when the pvuIIC stop
      codon was moved 21 nt downstream from its WT location, or 25 or 40 bp
      upstream of the pvuIIR initiation codon. Disrupting the putative
      hairpins had no significant effects.Conclusions: The initiation of
      translation of pvuIIR appears to be independent of that for pvuIIC.
      Direct tests failed to detect regulatory rules for either gene overlap
      or the putative hairpins. Thus, at least during balanced growth,
      transcriptional control appears to be sufficiently robust for proper
      regulation of this RM system.
AU  - Kaw MK
AU  - Blumenthal RM
PT  - Journal Article
TA  - BMC Mol. Biol.
JT  - BMC Mol. Biol.
SO  - BMC Mol. Biol. 2010 11: 87.

PMID- 15557639
VI  - 72
DP  - 2004
TI  - BBE02 disruption mutants of Borrelia burgdorferi B31 have a highly transformable, infectious phenotype.
PG  - 7147-7154
AB  - We constructed highly transformable and infectious Borrelia burgdorferi B31 by inactivating
      BBE02, a putative restriction-modification gene on
      the linear plasmid lp25. The low-passage-number B31 clones 5A4
      (containing all plasmids) and 5A18 (lp28-4(-) lp56(-)) were used for
      this study, and BBE02 was disrupted by homologous recombination. The
      transformation efficiency with the shuttle vector pBSV2C03::gntDeltakan
      was increased from <1 to similar to10 colonies per mug of DNA for 5A4
      and 5A4 BBE02::Kan(r) and from 14 to approximately 600 colonies per mug
      of DNA for 5A18 and 5A18 BBE02::Kanr. lp25, which is required for
      infectivity in mice, was retained in BBE02 mutants transformed with
      pBSV2C03::gntDeltakan, but lp25 was not detected in transformants of
      the parental clones 5A4 and 5A18. BBE02 disruptants and
      pBSV2C03::gntDeltakan transformants of these clones remained infectious
      in C3H/HeN mice, and the 50% infective doses of the BBE02 disruptants
      were <10(2) organisms per mouse. The inactivation of BBE02 thus
      eliminates a transformation barrier for infectious B. burgdorferi B31
      and will provide a valuable tool for studying the virulence factors of
      Lyme disease.
AU  - Kawabata H
AU  - Norris SJ
AU  - Watanabe H
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2004 72: 7147-7154.

PMID- 26358298
VI  - 22
DP  - 2015
TI  - Complete genome and gene expression analyses of Asaia bogorensis reveal unique responses to culture with mammalian cells as a potential opportunistic human pathogen.
PG  - 357-366
AB  - Asaia bogorensis, a member of acetic acid bacteria (AAB), is an aerobic bacterium
      isolated from flowers and fruits, as well as an opportunistic pathogen that
      causes human peritonitis and bacteraemia. Here, we determined the complete
      genomic sequence of the As. bogorensis type strain NBRC 16594, and conducted
      comparative analyses of gene expression under different conditions of co-culture
      with mammalian cells and standard AAB culture. The genome of As. bogorensis
      contained 2,758 protein-coding genes within a circular chromosome of 3,198,265
      bp. There were two complete operons encoding cytochrome bo3-type ubiquinol
      terminal oxidases: cyoABCD-1 and cyoABCD-2. The cyoABCD-1 operon was
      phylogenetically common to AAB genomes, whereas the cyoABCD-2 operon belonged to
      a lineage distinctive from the cyoABCD-1 operon. Interestingly, cyoABCD-1 was
      less expressed under co-culture conditions than under the AAB culture conditions,
      whereas the converse was true for cyoABCD-2. Asaia bogorensis shared
      pathogenesis-related genes with another pathogenic AAB, Granulibacter
      bethesdensis, including a gene coding pathogen-specific large bacterial adhesin
      and additional genes for the inhibition of oxidation and antibiotic resistance.
      Expression alteration of the respiratory chain and unique hypothetical genes may
      be key traits that enable the bacterium to survive under the co-culture
      conditions.
AU  - Kawai M
AU  - Higashiura N
AU  - Hayasaki K
AU  - Okamoto N
AU  - Takami A
AU  - Hirakawa H
AU  - Matsushita K
AU  - Azuma Y
PT  - Journal Article
TA  - DNA Res.
JT  - DNA Res.
SO  - DNA Res. 2015 22: 357-366.

PMID- 26430053
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of a Heterotrophic Facultative Anaerobic Thermophilic Bacterium, Ardenticatena maritima Strain 110ST.
PG  - e01145-15
AB  - Ardenticatena maritima strain 110S(T) is a filamentous bacterium isolated from an iron-rich
      coastal hydrothermal field, and it is a unique isolate capable of dissimilatory iron or
      nitrate reduction among the members of the bacterial phylum Chloroflexi. Here, we report the
      draft genome sequence comprising 3,569,367 bp, containing 3,355 predicted coding sequences
      (CDSs).
AU  - Kawaichi S
AU  - Yoshida T
AU  - Sako Y
AU  - Nakamura R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01145-15.

PMID- 
VI  - 
DP  - 1991
TI  - Application of recombinant DNA technique to the production of N-acetylneuraminate lyase and restriction enzymes.
PG  - 1-102
AB  - Chapter I. N-Acetylneuraminate lyase Chapter II. 1) Cloning of BamHI RM system in B. subtilis
      2) Cloning and sequencing of the AccI RM system 3) Cloning and expression of the BanI and
      BanIII RM systems from Bacillus aneurinolyticus 4) Nucleotide sequence of the BanI RM genes 5)
      Nucleotide sequence of the BanIII M gene.
AU  - Kawakami B
PT  - Journal Article
TA  - Ph.D. Thesis, University of Kyoto University
JT  - Ph.D. Thesis, University of Kyoto University
SO  - Ph.D. Thesis, University of Kyoto University 1991 : 1-102.

PMID- 1368703
VI  - 55
DP  - 1991
TI  - Cloning and nucleotide sequences of the AccI restriction-modification genes in Acinetobacter calcoaceticus.
PG  - 1553-1559
AB  - The genes of the AccI restriction-modification system specific for
      GT(A/C)(G/T)AC were cloned from the chromosomal DNA of Acinetobacter
      calcoaceticus, and their nucleotides sequenced.  The restriction and
      modification genes coded for polypeptides with calculated molecular weights of
      42,494 and 63,078, respectively.  Both the enzymes were coded by the same DNA
      strand and the restriction gene was upstream of the methylase gene, separated
      by 2 bp.  The restriction gene was significantly expressed in E. coli cells, so
      that the AccI restriction endonuclease could be purified to homogeneity.
      Analysis by sodium dodecyl sulfate-polyacrylamide  gel electrophoresis and gel
      filtration indicated that the catalytically active form of the endonuclease was
      tetrameric.  Sequence comparison with related enzymes indicated that AccI
      methylase contained a segment of tetra-amino acids, NPPY, characteristic of
      N6-adenine methylases.  In addition, some homologous regions were found in the
      sequence of HincII methylase specific for GT(C/T) (A/G)AC.
AU  - Kawakami B
AU  - Hilzheber C
AU  - Nagatomo M
AU  - Oka M
PT  - Journal Article
TA  - Agric. Biol. Chem.
JT  - Agric. Biol. Chem.
SO  - Agric. Biol. Chem. 1991 55: 1553-1559.

PMID- Not included in PubMed...
VI  - 70
DP  - 1990
TI  - Cloning and expression of the BamHI restriction-modification system in Bacillus subtilis.
PG  - 211-214
AB  - The genes of the GGATCC-specific BamHI restriction-modification system of
      Bacillus amyloliquefaciens H have been cloned and expressed in Bacillus
      subtilis MT-2.  B. subtilis MT-2 carrying the recombinant plasmid (pBamHIRM22)
      produced about 10-fold more BamHI restriction endonuclease and BamHI methylase
      than B. amyloliquefaciens H did.  B. subtilis MT-2(pBamHIRM22) restricted
      unmodified phage.  Restriction and modification genes were stably maintained in
      B. subtilis MT-2 on one plasmid and the produced BamHI endonuclease remained
      stable even in the stationary phase of the culture.  BamHI endonuclease from B.
      subtilis MT-2 (pBamHIRM22) had the same molecular weight and N-terminal amino
      acid sequence as that from B. amyloliquefaciens H.
AU  - Kawakami B
AU  - Katsuragi N
AU  - Maekawa Y
AU  - Imanaka T
PT  - Journal Article
TA  - J. Ferment. Bioeng.
JT  - J. Ferment. Bioeng.
SO  - J. Ferment. Bioeng. 1990 70: 211-214.

PMID- 1368640
VI  - 54
DP  - 1990
TI  - Nucleotide sequence of the gene coding for the BanIII DNA methyltransferase in Bacillus aneurinolyticus.
PG  - 3227-3233
AB  - The gene coding for the ATCGAT specific BanIII DNA methyltransferase (M.BanIII)
      of Bacillus aneurinolyticus was cloned and its nucleotides sequenced.  The
      coding region was assigned on the nucleotide sequence on the basis of the
      N-terminal amino acid sequence and molecular weight of the enzyme.  The
      M.BanIII gene coded for a protein of 580 amino acid residues (MW 66,344).
      Comparison with other methylases indicated that the M.BanIII sequence contained
      a segment of tetra-amino acids, NPPY, characteristic of N6-adenine methylases.
      In addition, some homologous regions were found in the sequences of type II
      adenine methylases PaeR7I(CTCGAG), TaqI(TCGA) and PstI(CTGCAG), containing TCGA
      within the recognition sequences.
AU  - Kawakami B
AU  - Sasaki A
AU  - Oka M
AU  - Maekawa Y
PT  - Journal Article
TA  - Agric. Biol. Chem.
JT  - Agric. Biol. Chem.
SO  - Agric. Biol. Chem. 1990 54: 3227-3233.

PMID- 9584868
VI  - 44
DP  - 1997
TI  - A novel restriction endonuclease UnbI, a neoschizomer of Sau96I from an unidentified psychrofilic bacterium from Antarctica is inhibited by phosphate ions.
PG  - 849-852
AB  - A novel type II restriction endonuclease UnbI was isolated from an unidentified psychrofilic
      bacterial strain from Antarctica.  UnbI recognizes and cleaves the sequence 5'-GGNCC-3',
      producing 5 nucleotide long sticky ends.  In this respect it differs from its neoschizomer
      Sau96I and all other restriction enzymes recognizing this sequence.  UnbI has a relatively low
      temperature optimum of 15 C to 20 C and its activity is completely inhibited by inorganic
      phosphate.
AU  - Kawalec M
AU  - Borsuk P
AU  - Piechula S
AU  - Stepien PP
PT  - Journal Article
TA  - Acta Biochim. Pol.
JT  - Acta Biochim. Pol.
SO  - Acta Biochim. Pol. 1997 44: 849-852.

PMID- 3008081
VI  - 14
DP  - 1986
TI  - A new restriction endonuclease from Spirulina platensis.
PG  - 1985-1989
AB  - Three restriction endonucleases, SplI, SplII and SplIII have been purified partially from
      Spirulina platensis subspecies siamese and named.  SplI cleaves bacteriophage lambda DNA at
      one site, phi X 174 RF DNA at two sites, but does not cleave pBR322 DNA.  This enzyme
      recognizes the sequence 5'CGTACG3'3'GCATCG5'and cuts the site indicated by the arrows.
      SplIII is an isoschizomer of HaeIII.
AU  - Kawamura M
AU  - Sakakibara M
AU  - Watanabe T
AU  - Kita K
AU  - Hiraoka N
AU  - Obayashi A
AU  - Takagi M
AU  - Yano K
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1986 14: 1985-1989.

PMID- 9679203
VI  - 5
DP  - 1998
TI  - Complete sequence and gene organization of the genome of a hyper-thermophilic Archaebacterium, Pyrococcus horikoshii OT3 (Supplement).
PG  - 147-155
AB  - The circular genome of Pyrococcus horikoshii OT3, (1,738,505 bp long), was opened at the
      junction of Srf I-C and Srf I-E fragments, and is represented by a linear map starting from
      this site.  The nucleotide positions are indicated on the linear map by numerals in kb.  Above
      and below the physical maps, the potential protein-coding regions assigned are indicated by
      boxes with arrowheads, indicating the direction of transcription.  The detailed assignment
      procedures are described in the main article in this issue.  The results of ORF similarity and
      motif searches are shown using the following color codes: red, similarities to reported genes
      with known functions; blue, similarities to hypothetical genes; green, some motifs but without
      significant similarity to the registered sequences; and no color, no apparent similarity to
      any reported genes and no significant protein motifs.  The ORF names defined in the main
      article are given to each ORF, and the positions of the rRNA and tRNA genes are indicated by
      closed box and vertical bars with a "T", respectively.  The sequence data reported here have
      been deposited in DDBJ/Genbank/EMBL databases under accession numbers AP000001 (nucleotide
      positions 1-287,000), AP000002 (287,001-544,000), AP000003 (544,001-777,000), AP000004
      (777,001-994,000), AP000005 (994,001-1,166,000), AP000006 (1,166,001-1,485,000), and AP000007
      (1,485,001-1,738,505).
AU  - Kawarabayasi Y et al
PT  - Journal Article
TA  - DNA Res.
JT  - DNA Res.
SO  - DNA Res. 1998 5: 147-155.

PMID- 9679194
VI  - 5
DP  - 1998
TI  - Complete sequence and gene organization of the genome of a hyper-thermophilic Archaebacterium, Pyrococcus horikoshii OT3.
PG  - 55-76
AB  - The complete sequence of the genome of a hyper-thermophilic Archaebacterium, Pyrococcus
      horikoshii OT3, has been determined by assembling the sequences of the physical map-based
      contigs of fosmid clones and of long polymerase chain reaction products which were used for
      gap-filling.  The entire length of the genome was 1,738,505 bp.  The authenticity of the
      entire genome sequence was supported by restriction analysis of long PCR products, which were
      directly amplified from the genomic DNA.  As the potential protein-coding regions, a total of
      2061 open reading frames were assigned, and by similarity search against public databases, 406
      (19.7%) were related to genes with putative function and 453 (22.0%) to the sequences
      registered but with unknown function.  The remaining 1202 ORFs (58.3%) did not show any
      significant similarity to the sequences in the databases.  Sequence comparison among the
      assigned ORFs in the genome provided evidence that a considerable number of ORFs were
      generated by sequence duplication.  By similarity search, 11 ORFs were assumed to contain
      intein elements.  The RNA genes identified were a single 16S-23S rRNA operon, two 5S rRNA
      genes and 46 tRNA genes including two with the intron structure.  All the assigned ORFs and
      RNA coding regions occupied 91.25% of the whole genome.  The data presented in this paper are
      available on the internet at http://www.nite.go.jp.
AU  - Kawarabayasi Y et al
PT  - Journal Article
TA  - DNA Res.
JT  - DNA Res.
SO  - DNA Res. 1998 5: 55-76.

PMID- 11572479
VI  - 8
DP  - 2001
TI  - Complete genome sequence of an aerobic thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain7.
PG  - 123-140
AB  - The complete genomic sequence of an aerobic thermoacidophilic crenarchaeon, Sulfolobus
      tokodaii strain7 which optimally grows at 80 degrees C, at low pH, and under aerobic
      conditions, has been determined by the whole genome shotgun method with slight modifications.
      The genomic size was 2,694,756 bp long and the G + C content was 32.8%. The following
      RNA-coding genes were identified: a single 16S-23S rRNA cluster, one 5S rRNA gene and 46 tRNA
      genes (including 24 intron-containing tRNA genes). The repetitive sequences identified were
      SR-type repetitive sequences, long dispersed-type repetitive sequences and Tn-like repetitive
      elements. The genome contained 2826 potential protein-coding regions (open reading frames,
      ORFs). By similarity search against public databases, 911 (32.2%) ORFs were related to
      functional assigned genes, 921 (32.6%) were related to conserved ORFs of unknown function, 145
      (5.1%) contained some motifs, and the remaining 849 (30.0%) did not show any significant
      similarity to the registered sequences. The ORFs with functional assignments included the
      candidate genes involved in sulfide metabolism, the TCA cycle and the respiratory chain.
      Sequence comparison provided evidence suggesting the integration of plasmid, rearrangement of
      genomic structure, and duplication of genomic regions that may be responsible for the larger
      genomic size of the S. tokodaii strain7 genome. The genome contained eukaryote-type genes
      which were not identified in other archaea and lacked the CCA sequence in the tRNA genes. The
      result suggests that this strain is closer to eukaryotes among the archaea strains so far
      sequenced. The data presented in this paper are also available on the internet homepage
      (http://www.bio.nite.go.jp/E-home/genome_list-e.html).
AU  - Kawarabayasi Y et al
PT  - Journal Article
TA  - DNA Res.
JT  - DNA Res.
SO  - DNA Res. 2001 8: 123-140.

PMID- 10382966
VI  - 6
DP  - 1999
TI  - Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1.
PG  - 83-101
AB  - The complete sequence of the genome of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum
      pernix K1, which optimally grows at 95 degrees C, has been determined by the whole genome
      shotgun method with some modifications. The entire length of the genome was 1,669,695 bp. The
      authenticity of the entire sequence was supported by restriction analysis of long PCR
      products, which were directly amplified from the genomic DNA. As the potential protein-coding
      regions, a total of 2,694 open reading frames (ORFs) were assigned. By similarity search
      against public databases, 633 (23.5%) of the ORFs were related to genes with putative function
      and 523 (19.4%) to the sequences registered but with unknown function. All the genes in the
      TCA cycle except for that of alpha-ketoglutarate dehydrogenase were included, and instead of
      the alpha-ketoglutarate dehydrogenase gene, the genes coding for the two subunits of
      2-oxoacid:ferredoxin oxidoreductase were identified. The remaining 1,538 ORFs (57.1%) did not
      show any significant similarity to the sequences in the databases. Sequence comparison among
      the assigned ORFs suggested that a considerable member of ORFs were generated by sequence
      duplication. The RNA genes identified were a single 16S-23S rRNA operon, two 5S rRNA genes and
      47 tRNA genes including 14 genes with intron structures. All the assigned ORFs and RNA coding
      regions occupied 89.12% of the whole genome. The data presented in this paper are available on
      the internet homepage (http://www.mild.nite.go.jp).
AU  - Kawarabayasi Y et al
PT  - Journal Article
TA  - DNA Res.
JT  - DNA Res.
SO  - DNA Res. 1999 6: 83-101.

PMID- 8595248
VI  - 6
DP  - 1995
TI  - Mitochondrial HSP70 as a subunit of eukaryotic multi-site-specific endonuclease, Endo.SceI; auto-phosphorylation and heat stability.
PG  - 135a
AB  - A eukaryotic site-specific endonuclease, Endo.SceI, that cuts DNA at multiple sites, is an
      initiator of homologous gene conversion in yeast mitochondria.  The active form of Endo.SceI
      is a heterodimer of a 75 kDa-subunit and a 50 kDa-subunit.  The 75 kDa-subunit is a
      mitochondrial 70 kDa heat shock protein (HSP70) and encoded by a nuclear gene, ENS1 (identical
      to SSC1).  HSP70 protein has ATP-related activities; such as ATP binding, an ATPase, and a
      protein kinase.  We investigated ATP-related activities of HSP70 protein in Endo.SceI.  We
      found that the 75 kDa-subunit of Endo.SceI exhibits a protein kinase activity.  The kinase
      activity specifically phosphorylated the 75 kDa-subunit, but not the 50 kDa-subunit or other
      proteins tested.  The phosphorylating activity requires Ca2+ and an acidic pH, and is greatly
      stimulated by the presence of the 50 kDa-subunit.  Ca2+ increased the electrophoretic mobility
      of Endo.SceI.  The auto-phosphorylation of the 75 kDa-subunit, by itself, does not have a
      direct effect on DNase, but the phosphorylation condition stabilizes DNase activity of
      Endo.SceI against heat-inactivation.  This stabilization was dependent upon Ca2+ and ATP, as
      well as ATP-gamma-S or ADP.  In addition, ATP-gamma-S and ADP inhibited the
      auto-phosphorylation of the 75 kDa-subunit.  These findings suggest that Ca2+ ions induced the
      conformational change of Endo.SceI in which the binding of nucleotides, such as ATP and ADP,
      regulated the heat-stability and autophosphorylation of Endo.SceI.
AU  - Kawasaki K
AU  - Shibata T
PT  - Journal Article
TA  - Mol. Biol. Cell
JT  - Mol. Biol. Cell
SO  - Mol. Biol. Cell 1995 6: 135a.

PMID- 15618627
VI  - 68
DP  - 2004
TI  - Roles of the HSP70-Subunit in a eukaryotic multi-site-specific endonuclease, Endo.SceI: Autophosphorylation and heat stability.
PG  - 2557-2564
AB  - The 70 kDa heat shock proteins (HSP70) are a family of molecular chaperones that bind
      transiently to unfolded proteins in an ATP/ADP
      dependent manner. Endo.SceI comprises a unique example for mitochondria. HSP70, which exists
      in a stable complex with a nucleolytic subunit as a multi-site specific DNase. The
      HSP70-subunit in Endo.SceI was autophosphorylated by ATP in vitro. The
      autophosphorylation was higher in the Endo.SceI complex form than in
      the free form. Although the autophosphorylation had no significant
      effect on the endonucleolytic activity of Endo.SceI, the factors
      favoring autophosphorylation protected the endonucleolytic activity of
      Endo.SceI against heat inactivation. ATP, adenosine
      5'-O-(3-thiotriphosphate) (ATP-gamma-S), and ADP not only protected the
      endonucleolytic activity against heat inactivation in the presence of
      Ca2+ ions, but also reduced the labeling of the HSP70-subunit by
      [gamma-P-32]ATP in Endo.SceI. These findings suggest that the
      HSP70-subunit shields Endo.SceI from heat inactivation through ATP/ADP
      binding.
AU  - Kawasaki K
AU  - Shibata T
AU  - Ito F
PT  - Journal Article
TA  - Biosci. Biotechnol. Biochem.
JT  - Biosci. Biotechnol. Biochem.
SO  - Biosci. Biotechnol. Biochem. 2004 68: 2557-2564.

PMID- 1761062
VI  - 202
DP  - 1991
TI  - Sequence-specific complex formation of DNA and a eukaryotic sequence-specific endonuclease, SceI.
PG  - 665-671
AB  - Endo.SceI is a eukaryotic sequence-specific endonuclease of 120 kDa that causes
      sequence-specific double-stranded scission of DNA.  Unlike results with restriction enzymes,
      we found a consensus sequence around the cleavage sites for Endo.SceI instead of a common
      sequence.  We searched for conditions for studying the binding of Endo.SceI to DNA other than
      cutting.  Under optimized conditions including gel mobility shift assay, Endo.SceI exhibited
      sequence-specific binding to a short double-stranded DNA (41 base pairs) containing a cleavage
      site and the DNA reisolated from the protein-DNA complex was not cleaved.  The analysis of the
      complex of Endo.SceI and DNA isolated by the gel mobility shift experiments showed that the
      DNA-binding entity in the Endo.SceI preparation does have Endo.SceI activity and consists of
      an equal amount of 75-kDa and 50-kDa polypeptides.  Based on this observation from previous
      studies, we conclude that Endo.SceI is a heterodimer of the 75-kDa and 50-kDa subunits.  Under
      the present assay conditions, Endo.SceI did not show binding to single-stranded DNA having the
      same sequence of either plus or minus strand of the double-stranded DNA containing the
      cleavage site (the 41-bp DNA).  Endo.SceI showed significantly higher affinity for the
      consensus sequence than the major cleavage site in pBR322 DNA.  Unlike the cleavage of DNA by
      Endo.SceI which requires Mg2+, this sequence-specific binding is independent of but stimulated
      by Mg2+.
AU  - Kawasaki K
AU  - Takahashi M
AU  - Ando T
AU  - Shibata T
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1991 202: 665-671.

PMID- 2002067
VI  - 266
DP  - 1991
TI  - DNA sequence recognition by a eukaryotic sequence-specific endonuclease, Endo.SceI, from Saccharomyces cerevisiae.
PG  - 5342-5347
AB  - A eukaryotic sequence-specific endonuclease, Endo.SceI, causes
      sequence-specific double-stranded scission of double-stranded DNA to produce
      cohesive ends with four bases protruding at the 3' termini.  Unlike the case of
      restriction enzymes, an asymmetric 26-base pair consensus sequence was found
      around the cleavage site for Endo.SceI instead of a common sequence.  We
      analyzed the base pairs that interacted with Endo.SceI on the recognition of
      its cleavage sites.  A region comprising -10 through +16 base pairs from the
      center of the cleavage site was shown to be essential and sufficient for the
      sequence-specific cutting with Endo.SceI by experiments involving synthesized
      DNAs.  Methylation interference experiments indicate that bases in the region
      comprising the +7 through +14 base pairs are involved in close contact with
      Endo.SceI in its recognition of the cleavage site.  This +7 through +14-base
      pair region overlaps the most stringently conserved sequence in the consensus
      sequence for the cleavage site, suggesting that this region constitutes the
      core for the recognition by Endo.SceI.
AU  - Kawasaki K
AU  - Takahashi M
AU  - Natori M
AU  - Shibata T
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1991 266: 5342-5347.

PMID- 29915111
VI  - 0
DP  - 2018
TI  - Microevolution of aquatic Streptococcus agalactiae ST-261 from Australia indicates dissemination via imported tilapia and ongoing adaptation to marine hosts or environment.
PG  - AEM.00859-18
AB  - Streptococcus agalactiae (GBS) causes disease in a wide range of animals. The serotype Ib
      lineage is highly adapted to aquatic hosts, exhibiting substantial
      genome reduction compared with terrestrial conspecifics. Here we sequence genomes
      from 40 GBS isolates including 25 from wild fish and captive stingrays in
      Australia, six local veterinary or human clinical isolates, and nine isolates
      from farmed tilapia in Honduras and compare with 42 genomes from public
      databases. Phylogenetic analysis based on non-recombinant core genome SNPs
      indicated that aquatic serotype Ib isolates from Queensland were distantly
      related to local veterinary and human clinical isolates. In contrast, Australian
      aquatic isolates are most closely related to a tilapia isolate from Israel,
      differing by only 63 core-genome SNPs. A consensus minimum spanning tree based on
      core genome SNPs indicates dissemination of ST-261 from an ancestral tilapia
      strain, which is congruent with several introductions of tilapia into Australia
      from Israel during the 1970s and 1980s. Pan-genome analysis identified 1,440
      genes as core with the majority being dispensable or strain-specific with
      non-protein-coding intergenic regions (IGRs) divided amongst core and
      strain-specific genes. Aquatic serotype Ib strains have lost many virulence
      factors during adaptation, but six adhesins were well conserved across the
      aquatic isolates and might be critical for virulence in fish and targets for
      vaccine development. The close relationship amongst recent ST-261 isolates from
      Ghana, USA and China with the Israeli tilapia isolate from 1988 implicates the
      global trade in tilapia seed for aquaculture in the widespread dissemination of
      serotype Ib fish-adapted GBS.ImportanceStreptococcus agalactiae (GBS) is a
      significant pathogen of humans and animals. Some lineages have become adapted to
      particular hosts and serotype Ib is highly specialized to fish. Here we show that
      this lineage is likely to have been distributed widely by the global trade in
      tilapia for aquaculture, with probable introduction into Australia in the 1970s
      and subsequent dissemination in wild fish populations. We report variability in
      the polysaccharide capsule amongst this lineage, but identify a cohort of common
      surface proteins that may be a focus of future vaccine development to reduce the
      biosecurity risk in international fish trade.
AU  - Kawasaki M
AU  - Delamare-Deboutteville J
AU  - Bowater RO
AU  - Walker MJ
AU  - Beatson S
AU  - Ben Zakour NL
AU  - Barnes AC
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2018 0: AEM.00859-18.

PMID- 8651930
VI  - 222
DP  - 1996
TI  - Folding-dependent in vitro protein splicing of the Saccharomyces cerevisiae VMA1 protozyme.
PG  - 827-832
AB  - VMA1 translational product undergoes excision of a 50-kDa intervening segment (VDE:
      VMAI-derived endonuclease) and religation of the flanking regions to create a 69-kDa catalytic
      subunit of vacuolar membrane H+-ATPase.  VDEs conjugated with polypeptides at both N- and
      C-terminal ends were expressed in Escherichia coli and examined for their ability to catalyze
      self-splicing.  Processed VDE was found in soluble pools, while unspliced precursors
      accumulated in insoluble pools, forming inclusion bodies.  We demonstrate in vitro protein
      splicing by refolding of the denatured precursor molecules.  The processing reaction
      efficiently occurs with the purified precursor peptide.  VDE bracketed by only 6 proximal and
      4 distal amino acids is autocatalytically processed.
AU  - Kawasaki M
AU  - Makino S-I
AU  - Matsuzawa H
AU  - Satow Y
AU  - Ohya Y
AU  - Anraku Y
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1996 222: 827-832.

PMID- 11121031
VI  - 97
DP  - 2000
TI  - Archaeal adaptation to higher temperatures revealed by genomic sequence of Thermoplasma volcanium.
PG  - 14257-14262
AB  - The complete genomic sequence of the archaeon Thermoplasma volcanium, possessing optimum
      growth temperature (OGT) of 60 degrees C, is reported. By systematically comparing this
      genomic sequence with the other known genomic sequences of archaea, all possessing higher OGT,
      a number of strong correlations have been identified between characteristics of genomic
      organization and the OGT. With increasing OGT, in the genomic DNA, frequency of clustering
      purines and pyrimidines into separate dinucleotides rises (e.g., by often forming AA and TT,
      whereas avoiding TA and AT). Proteins coded in a genome are divided into two distinct
      subpopulations possessing isoelectric points in different ranges (i.e., acidic and basic), and
      with increasing OGT the size of the basic subpopulation becomes larger. At the metabolic
      level, genes coding for enzymes mediating pathways for synthesizing some coenzymes, such as
      heme, start missing. These findings provide insights into the design of individual genomic
      components, as well as principles for coordinating changes in these designs for the adaptation
      to new environments. Full author list: Kawashima, T., Amano, N., Koike, H., Makino, S.-i.,
      Higuchi, S., Kawashima-Ohya, Y., Watanabe, K., Yamazaki, M., Kanehori, K., Kawamoto, T.,
      Nunoshiba, T., Yamamoto, Y., Aramaki, H., Makino, K., Suzuki, M.
AU  - Kawashima T
AU  - Amano N
AU  - Koike H
AU  - Makino S-i
AU  - Higuchi S
AU  - Kawashima-Ohya Y
AU  - Watanabe K
AU  - Yamazaki M
AU  - Kanehori K
AU  - Kawamoto T
AU  - Nunoshiba T
AU  - Yamamoto Y
AU  - Aramaki H
AU  - Makino K
AU  - Suzuki M
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2000 97: 14257-14262.

PMID- 
VI  - 75
DP  - 1999
TI  - Determination of the complete genomic DNA sequence of Thermoplasma volcanium GSS1.
PG  - 213-218
AB  - The complete genomic DNA sequence of the aero/anaero-facultative archaebacterium, Thermoplasma
      volcanium GSS1, has been determined.  A number of DNA fragments were cloned by using the
      phage, cosmid, and BAC systems, and sequenced.  The remaining 30 gaps were bridged by DNA
      fragments constructed using the polymerase chain reaction.  The repetition in sequencing the
      same base positions was 13.1 +/- 7.5 fold.  The alignment of the DNA fragments and the
      completeness of the genomic sequence were confirmed by the consistency of the genomic sequence
      with the lengths and partial sequences of a second set of DNA fragments that altogether
      covered 88% of the genome.  The number of bases found in the genomic sequence is 1,584,799,
      with a G/C content of 39.9%.  The combination of the four types of bases in the new genomic
      sequence is compared with those in known genomic sequences of similar sizes.
AU  - Kawashima T
AU  - Yamamoto Y
AU  - Aramaki H
AU  - Nunoshiba T
AU  - Kawamoto T
AU  - Watanabe K
AU  - Yamazaki M
AU  - Kanehori K
AU  - Amano N
AU  - Ohya Y
AU  - Makino K
AU  - Suzuki M
PT  - Journal Article
TA  - Proc. Jpn. Acad.
JT  - Proc. Jpn. Acad.
SO  - Proc. Jpn. Acad. 1999 75: 213-218.

PMID- 22535927
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Halomonas sp. Strain KM-1, a Moderately Halophilic Bacterium That Produces the Bioplastic Poly(3-Hydroxybutyrate).
PG  - 2738-2739
AB  - We report the draft genome sequence of Halomonas sp. strain KM-1, which was isolated in Ikeda
      City, Osaka, Japan, and which produces the bioplastic
      poly(3-hydroxybutyrate). The total length of the assembled genome is 4,992,811
      bp, and 4,220 coding sequences were predicted within the genome. Genes encoding
      proteins that are involved in the production and depolymerization of
      poly(3-hydroxybutyrate) were identified. The identification of these genes might
      be of use in the production of the bioplastic poly(3-hydroxybutyrate) and its
      monomer 3-hydroxybutyrate.
AU  - Kawata Y
AU  - Kawasaki K
AU  - Shigeri Y
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2738-2739.

PMID- 29545299
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Vibrio penaeicida Strain TUMSAT-NU1, Isolated from Diseased Shrimp in Japan.
PG  - e00153-18
AB  - Vibrio penaeicida is a bacterial pathogen of cultured shrimp. The draft genome sequence of V.
      penaeicida strain TUMSAT-NU1 consists of 100 scaffolds with a
      total of 6.41 Mbp. We identified possible virulence factors, and we found that V.
      penaeicida and Vibrio nigripulchritudo are closely related.
AU  - Kawato S
AU  - Nozaki R
AU  - Kondo H
AU  - Hirono I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00153-18.

PMID- 
VI  - 81
DP  - 2015
TI  - Complete Genome Sequence Analysis of Two Pseudomonas plecoglossicida Phages, Potential Therapeutic Agents.
PG  - 874-881
AB  - 
AU  - Kawato Y
AU  - Yasuike M
AU  - Nakamura Y
AU  - Shigenobu Y
AU  - Fujiwara A
AU  - Sano M
AU  - Nakai T
PT  - Journal Article
TA  - J. Appl. Environ. Microbiol.
JT  - J. Appl. Environ. Microbiol.
SO  - J. Appl. Environ. Microbiol. 2015 81: 874-881.

PMID- 14506783
VI  - 293
DP  - 2003
TI  - Identification of genetic differences between strains of Campylobacter jejuni using differential genomic hybridisation and comparative  genomics.
PG  - 130-131
AB  - Campylobacter jejuni is the most frequently identified bacterial causative agent of diarrhoeal
      disease in humans worldwide.  Strain diversity and variable host response lead to a spectrum
      of outcomes from infection ranging from asymptomatic to severe inflammatory diarrhoea.  The
      mode of transmission to humans is unclear but strains have been isolated from a variety of
      environmental sources including poultry and water.  It is hypothesised that novel genes within
      different strains may relate to different clinical outcomes for ability to survive in varied
      environmental niches.  In order to test this hypothesis DNA from the sequenced strain
      NCTC11168 was hybridised to whole genome macro-arrays of different strains of C. jejuni with
      different characteristics to identify regions of DNA not presnt in the sequenced strain.  The
      strain specific DNA was further characterized by sequencing, analysis and comparison to the
      sequenced 11168 genome.  Preliminary hybridisation results using strain 81-176 show that this
      method of differential hybridisation can be used to detect variable regions of DNA as well as
      strain-specific DNA.  To date, 271 sequences unique to 81-176 have been assembled into 58
      clusters.  These clusters contain predicted coding sequences with similarity to transporters
      and a -glutamyltranspeptidase as well as several with no database similarities.  In addition,
      genes with similarity to proteins that are suface associated, proteins involved in the
      respiratory chain and restriction modification enzymes were shown to differ between 81-176 and
      11168; these are all known to be highly variable between Campylobacter strains.
AU  - Kay E
AU  - Wren BW
AU  - Parkhill J
PT  - Journal Article
TA  - Int. J. Med. Microbiol.
JT  - Int. J. Med. Microbiol.
SO  - Int. J. Med. Microbiol. 2003 293: 130-131.

PMID- 25502682
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Streptococcus agalactiae Strains Isolated from Nile Tilapia (Oreochromis niloticus) Farms in Thailand.
PG  - e01300-14
AB  - During 2009-2011, two clinical and one environmental strains of Streptococcus agalactiae were
      isolated from Nile tilapia (Oreochromis niloticus) farms in
      Thailand. Draft genome sequences of two clinical isolates comprise 2,048,343 and
      2,105,006 bp, while environmental isolates comprise 2,097,115 bp, having 1,573 to
      1,578 coding sequences, respectively.
AU  - Kayansamruaj P
AU  - Pirarat N
AU  - Kondo H
AU  - Hirono I
AU  - Rodkhum C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01300-14.

PMID- 6287768
VI  - 0
DP  - 1982
TI  - Isolation and purification of Bordetella pertussis restriction endonuclease BpeI.
PG  - 56-57
AB  - New restriction endonuclease has been isolated from Bordetella pertussis
      vaccine strain 305 and purified in 1 stage on Sepharose covalently bound with
      blue dextran.  The isolated restrictase has been found capable of breaking down
      lambda-phage DNA into 7 fragments.  According to its specificity, BpeI is the
      isoschizomer of HindIII obtained from Haemophilus influenzae strain Rd.
AU  - Kazennova EV
AU  - Tarasov AP
AU  - Mileikovskaya MM
AU  - Semina IE
AU  - Tsvetkova NV
PT  - Journal Article
TA  - Zh. Mikrobiol. Epidemiol. Immunobiol.
JT  - Zh. Mikrobiol. Epidemiol. Immunobiol.
SO  - Zh. Mikrobiol. Epidemiol. Immunobiol. 1982 0: 56-57.

PMID- 3022754
VI  - 12
DP  - 1986
TI  - A new specific endodeoxyribonuclease from Escherichia coli RFL 72.
PG  - 836-838
AB  - A restriction endonuclease Eco72I with a novel substrate specificity has been isolated from
      Escherichia coli strain RFL 72.  The enzyme recognizes 5'CAG^GTG 3' 3'GTG^CAC 5'
      hexanucleotide palindromic sequence and cleaves it, as indicated by the arrows, to produce
      blunt ended fragments.
AU  - Kazlauskiene R
AU  - Maneliene Z
AU  - Butkus V
AU  - Petrusyte M
AU  - Janulaitis A
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1986 12: 836-838.

PMID- 28751402
VI  - 5
DP  - 2017
TI  - Whole-Genome Shotgun Sequences of Salmonella enterica Serovar Typhimurium Lilleengen Type Strains LT1, LT18, LT19, LT20, LT21, and LT22.
PG  - e00720-17
AB  - The Lilleengen type (LT) collection of Salmonella enterica serovar Typhimurium strains has
      served the scientific community as a group of model organisms for
      basic genetic and biochemical pathway research. Here, we report the whole-genome
      shotgun sequences of Salmonella enterica serovar Typhimurium strains LT1, LT18,
      LT19, LT20, LT21, and LT22.
AU  - Kazmierczak RA
AU  - Best AA
AU  - Nguyen D
AU  - Eisenstark A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00720-17.

PMID- 28126948
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of the Dairy Isolate Lactobacillus acidipiscis ACA-DC 1533.
PG  - e01533-16
AB  - Lactobacillus acidipiscis is a Gram-positive lactic acid bacterium belonging to the
      Lactobacillus salivarius clade. Here, we present the first complete genome
      sequence of L. acidipiscis isolated from traditional Greek Kopanisti cheese.
      Strain ACA-DC 1533 may play a key role in the strong organoleptic characteristics
      of Kopanisti cheese.
AU  - Kazou M
AU  - Alexandraki V
AU  - Pot B
AU  - Tsakalidou E
AU  - Papadimitriou K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01533-16.

PMID- 28751400
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of the Sourdough Isolate Lactobacillus zymae ACA-DC 3411.
PG  - e00699-17
AB  - Lactobacillus zymae is a Gram-positive lactic acid bacterium belonging to the Lactobacillus
      brevis clade. Here, we report the first complete genome sequence of
      L. zymae ACA-DC 3411, which was isolated from traditional Greek wheat sourdough.
      Whole-genome analysis may reveal adaptive traits of strain ACA-DC 3411 in the
      sourdough ecosystem.
AU  - Kazou M
AU  - Alexandraki V
AU  - Pot B
AU  - Tsakalidou E
AU  - Papadimitriou K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00699-17.

PMID- 28153908
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequence of the Cheese Isolate Lactobacillus rennini ACA-DC 565.
PG  - e01579-16
AB  - In this study, we present the first complete genome sequence of Lactobacillus rennini ACA-DC
      565, a strain isolated from a traditional Greek overripened
      Kopanisti cheese called Mana. Although the species has been associated with
      cheese spoilage, the strain ACA-DC 565 may contribute to the intense organoleptic
      characteristics of Mana cheese.
AU  - Kazou M
AU  - Alexandraki V
AU  - Pot B
AU  - Tsakalidou E
AU  - Papadimitriou K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01579-16.

PMID- 24634440
VI  - 42
DP  - 2014
TI  - Crystal structure of the 5hmC specific endonuclease PvuRts1I.
PG  - 5929-5936
AB  - PvuRts1I is a prototype for a larger family of restriction endonucleases that cleave DNA
      containing 5-hydroxymethylcytosine (5hmC) or 5-glucosylhydroxymethylcytosine (5ghmC), but not
      5-methylcytosine (5mC) or cytosine. Here, we report a crystal structure of the enzyme at 2.35
      A resolution. Although the protein has been crystallized in the absence of DNA, the structure
      is very informative. It shows that PvuRts1I consists of an N-terminal, atypical PD-(D/E)XK
      catalytic domain and a C-terminal SRA domain that might accommodate a flipped 5hmC or 5ghmC
      base. Changes to predicted catalytic residues of the PD-(D/E)XK domain or to the putative
      pocket for a flipped base abolish catalytic activity. Surprisingly, fluorescence changes
      indicative of base flipping are not observed when PvuRts1I is added to DNA substrates
      containing pyrrolocytosine in place of 5hmC (5ghmC). Despite this caveat, the structure
      suggests a model for PvuRts1I activity and presents opportunities for protein engineering to
      alter the enzyme properties for biotechnological applications.
AU  - Kazrani AA
AU  - Kowalska M
AU  - Czapinska H
AU  - Bochtler M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2014 42: 5929-5936.

PMID- 28839012
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Magnetospirillum sp. ME-1, a Novel Magnetotactic Bacterium Isolated from East Lake, Wuhan, China.
PG  - e00485-17
AB  - A novel spiral magnetotactic bacterium, Magnetospirillum sp. ME-1, was isolated from East Lake
      in China. Here we report the complete genome of ME-1, which
      contains a 4,551,873-bp circular chromosome and a 5,222-bp circular plasmid. The
      magnetosome biogenesis-specific genes are located in a 97,664-bp magnetosome
      genomic island.
AU  - Ke L
AU  - Liu P
AU  - Liu S
AU  - Gao M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00485-17.

PMID- 23209218
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Brucella suis Field Strain BCB025 of Sequence Type ST22.
PG  - 6959
AB  - Brucella is a genus of relatively conservative pathogenic bacteria. Brucella suis is the most
      diversified Brucella species. Strains of B. suis belong to different
      sequence types. Here, we report the genome sequence of B. suis strain BCB025, one
      isolate of the sequence type 22 epidemic in China.
AU  - Ke Y
AU  - Wang Y
AU  - Yuan X
AU  - Xu J
AU  - Zhen Q
AU  - Wang Z
AU  - Li T
AU  - Wang D
AU  - Huang L
AU  - Song H
AU  - Chen Z
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6959.

PMID- 22965104
VI  - 194
DP  - 2012
TI  - Genome Sequences of Brucella melitensis 16M and Its Two Derivatives 16M1w and 16M13w, Which Evolved In Vivo.
PG  - 5489
AB  - Brucella melitensis is an intracellular pathogen that induces chronic infection in humans.
      Here, we report the genome sequences of 16M and its two derivatives,
      16M1w and 16M13w, which were allowed to adapt in vivo for 1 and 13 weeks,
      respectively. Our findings contribute to the investigation of adaptive mutations
      and mechanisms of chronic infection by B. melitensis.
AU  - Ke Y
AU  - Yuan X
AU  - Wang Y
AU  - Bai Y
AU  - Xu J
AU  - Song H
AU  - Huang L
AU  - Chen Z
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5489.

PMID- 22965081
VI  - 194
DP  - 2012
TI  - Genome Sequence of Brucella melitensis S66, an Isolate of Sequence Type 8, Prevalent in China.
PG  - 5451
AB  - Brucella melitensis is the most-represented Brucella species causing human brucellosis in
      China. Here we report the complete genome sequence of B.
      melitensis strain S66, a representative strain of sequence type 8 (ST8), which is
      prevalent in China, making it possible to compare the genome sequences of
      isolates from different countries.
AU  - Ke Y
AU  - Yuan X
AU  - Zhen Q
AU  - Wang Y
AU  - Li T
AU  - Sun Y
AU  - Song H
AU  - Huang L
AU  - Wang D
AU  - Cui B
AU  - Mao K
AU  - Chen Z
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5451.

PMID- 23209199
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Brucella melitensis 133, an Isolate of Biovar 1 of Sequence Type 32.
PG  - 6932
AB  - Brucellosis is highly epidemic in China. Of the six classical species, Brucella melitensis and
      biovar 1 are the most represented species and biovar that cause
      human brucellosis in China. Here, we report the genome sequence of Brucella
      melitensis strain 133, a strain of biovar 1 of sequence type 32.
AU  - Ke Y
AU  - Zhen Q
AU  - Li T
AU  - Wang Y
AU  - Yuan X
AU  - Xu J
AU  - Huang L
AU  - Wang D
AU  - Song H
AU  - Chen Z
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6932.

PMID- 16299353
VI  - 33
DP  - 2005
TI  - StpA protein from Escherichia coli condenses supercoiled DNA in preference to linear DNA and protects it from digestion by DNase I and EcoKI.
PG  - 6540-6546
AB  - The nucleoid-associated protein, StpA, of Escherichia coli binds non-specifically to
      double-stranded DNA (dsDNA) and apparently forms
      bridges between adjacent segments of the DNA. Such a coating of protein on
      the DNA would be expected to hinder the action of nucleases. We
      demonstrate that StpA binding hinders dsDNA cleavage by both the
      non-specific endonuclease, DNase I, and by the site-specific type I
      restriction endonuclease, EcoKI. It requires approximately one StpA
      molecule per 250-300 bp of supercoiled DNA and approximately one StpA
      molecule per 60-100 bp on linear DNA for strong inhibition of the
      nucleases. These results support the role of StpA as a
      nucleoid-structuring protein which binds DNA segments together. The
      inhibition of EcoKI, which cleaves DNA at a site remote from its initial
      target sequence after extensive DNA translocation driven by ATP
      hydrolysis, suggests that these enzymes would be unable to function on
      chromosomal DNA even during times of DNA damage when potentially lethal,
      unmodified target sites occur on the chromosome. This supports a role for
      nucleoid-associated proteins in restriction alleviation during times of
      cell stress.
AU  - Keatch SA
AU  - Leonard PG
AU  - Ladbury JE
AU  - Dryden DT
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2005 33: 6540-6546.

PMID- 15520467
VI  - 32
DP  - 2004
TI  - Alleviation of restriction by DNA condensation and non-specific DNA binding ligands.
PG  - 5841-5850
AB  - During conditions of cell stress, the type I restriction and modification enzymes of bacteria
      show reduced, but not zero, levels of restriction of
      unmethylated foreign DNA. In such conditions, chemically identical
      unmethylated recognition sequences also occur on the chromosome of the
      host but restriction alleviation prevents the enzymes from destroying the
      host DNA. How is this distinction between chemically identical DNA
      molecules achieved? For some, but not all, type I restriction enzymes,
      alleviation is partially due to proteolytic degradation of a subunit of
      the enzyme. We identify that the additional alleviation factor is
      attributable to the structural difference between foreign DNA entering the
      cell as a random coil and host DNA, which exists in a condensed nucleoid
      structure coated with many non-specific ligands. The type I restriction
      enzyme is able to destroy the 'naked' DNA using a complex reaction linked
      to DNA translocation, but this essential translocation process is
      inhibited by DNA condensation and the presence of non-specific ligands
      bound along the DNA.
AU  - Keatch SA
AU  - Su TJ
AU  - Dryden DT
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2004 32: 5841-5850.

PMID- 29853498
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Pseudomonas stutzeri Type Strain SGAir0442, Isolated  from Singapore Air Samples.
PG  - e00424-18
AB  - Pseudomonas stutzeri strain SGAir0442 was isolated from tropical air samples collected in
      Singapore. It is a Gram-negative denitrifying bacterium and an
      opportunistic human pathogen. Its complete genome consists of one chromosome of
      4.52 Mb, containing 4,129 protein-coding genes, 12 rRNA subunits, and 62 tRNAs.
AU  - Kee C et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00424-18.

PMID- 29954893
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Acinetobacter schindleri SGAir0122 Isolated from Singapore Air.
PG  - e00567-18
AB  - Acinetobacter schindleri strain SGAir0122 was isolated from tropical air samples  collected in
      Singapore. The prevalence of nosocomial infection caused by this
      Gram-negative bacterium indicates its clinical significance as an opportunistic
      human pathogen. Its complete genome consists of one chromosome of 3.105 Mb and a
      plasmid of 181 kb.
AU  - Kee C et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00567-18.

PMID- 
VI  - 16
DP  - 2005
TI  - HNH Endonucleases.
PG  - 49-65
AB  - HNH endonucleases cleave phosphodiester bonds in many biological contexts, including intron
      homing, degradation of genomic DNA, repair of genomic DNA, and restriction of viral DNA.  In
      the 10 years since the HNH motif was first reported, around 500 members have been identified,
      which have the following database identifiers: cd00085, SM00507 and pfam01844.  HNH enzymes
      are found in all biological kingdoms, encoded by group I and group II introns, inteins, as
      well as free-standing open reading frames.  In the first part of this chapter, we describe the
      consensus sequence subsets that are associated with HNH enzymes and the proteins that
      accommodate them.  We then present the biochemical properties of HNH enzymes and the proteins
      that accommodate them.  We then present the biochemical properties of HNH enzymes as a group,
      and finally describe recent structural data on HNH enzymes bound to DNA highlighting plausible
      cleavage mechanisms.  Throughout, we describe how HNH enzymes are part of a wider group of
      enzymes generally referred to as beta beta alpha-Me or His-Me endonucleases that also includes
      His-Cys homing endonucleases and the eukaryotic apoptotic enzyme caspase-activated DNase.
AU  - Keeble AH
AU  - Mate MJ
AU  - Kleanthous C
PT  - Journal Article
TA  - Nucleic Acids Mol. Biol.
JT  - Nucleic Acids Mol. Biol.
SO  - Nucleic Acids Mol. Biol. 2005 16: 49-65.

PMID- 7753189
VI  - 375
DP  - 1995
TI  - The selfish pursuit of sex.
PG  - 283
AB  - A letter arguing that inteins are selfish elements relevant to the evolution of sex.
AU  - Keeling PJ
AU  - Roger AJ
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1995 375: 283.

PMID- 29146837
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Naturally Competent Bacillus simplex Strain WY10.
PG  - e01295-17
AB  - We sequenced a naturally competent bacterial isolate, WY10, cultured from a Wyoming soil
      sample. Sequence analysis revealed that WY10 is a novel strain of
      Bacillus simplex To our knowledge, WY10 is the first B. simplex strain to be
      characterized as naturally competent for DNA uptake by transformation.
AU  - Keen EC
AU  - Bliskovsky VV
AU  - Adhya SL
AU  - Dantas G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01295-17.

PMID- 29025954
VI  - 5
DP  - 2017
TI  - Three Draft Genome Sequences of Vibrio coralliilyticus Strains Isolated from Bivalve Hatcheries.
PG  - e01162-17
AB  - Reported here are the genome sequences of three Vibrio coralliilyticus isolates RE87, AIC-7,
      and 080116A. Each strain was isolated in association with oyster
      larvae in commercial aquaculture systems. These draft genomes will be useful for
      further studies in understanding the genomic features contributing to V.
      coralliilyticus pathogenicity.
AU  - Kehlet-Delgado H
AU  - Richards GP
AU  - Hase C
AU  - Mueller RS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01162-17.

PMID- 
VI  - 134
DP  - 2008
TI  - Dam methylation is essential in vibrio vulnificus and influences its interactions with host cells.
PG  - A713
AB  - DNA methylation is an important epigenetic regulator in bacteria, and several pathogens
      display altered virulence when their methylating
      enzymes are knocked out or overexpressed. We hypothesized that
      methylation by the Dam (DNA adenine methylase) enzyme plays key roles
      in Vibrio vulnificus, a leading cause of lethal seafood-borne
      infections. Our arms were to determine the consequences of altered Dam
      levels on V. vulnificus gene expression and its interactions with host
      cells, specifically its effects on infection-induced barrier function
      alteration and inflammation. We sought to knock out Dam, but
      chromosomal dam could only be disrupted in the presence of a
      plasmid-borne copy of the gene. Thus, dam is essential for the survival
      of this pathogen and so we overexpressed it using the arabinose
      promoter. We then performed 2-D gel analysis of lysates and culture
      supernatants, and found that a discrete subset of proteins was indeed
      up- or downregulated under conditions of dam overexpression. To
      determine whether these changes in protein levels resulted in altered
      bacterial interactions with host cells, we assayed epithelial barrier
      function and the inflammatory response. To study barrier function, we
      characterized the effects of V. vulnificus on the transepithelial
      electrical resistance (TER) of Caco-2 cell monolayers. Wild-type V.
      vulnificus were applied to the apical surface of Caco-2 cells grown on
      permeable filters, using plain medium as a negative control. We
      observed a reproducible drop in TER of the infected monolayer, with a
      decline of 53+/-6% after two hours, when lactate dehydrogenase assays
      determined that cytotoxicity was not significantly different from
      control. TER did not drop when supernatants were used or bacteria were
      treated with chloramphenicol; thus, impairment of barrier function by
      V. vulnificus requires new bacterial protein synthesis. We then studied
      the effects of dam-overexpressing and control strains on TER, after
      confirming that they grew at the same rate. The dam-overexpressing
      strain yielded a delayed decrease in TER (decline of 15 +/- 3% at 2 h
      and 52 +/- 5% at four hours) compared to the control strain. To study
      the inflammatory response to V. vulnificus, we assayed secretion of the
      pro-inflammatory cytokine, IL-8, by Caco-2 cells. incubation of
      wild-type bacteria with the cells led to a reproducible, time-dependent
      induction of IL-8 that was not dependent on flagella and was
      consistently increased by 50% under conditions of dam overexpression.
      In summary, we are the first to demonstrate that dam methylation is not
      only essential for the viability of V. vulnificus but may influence its
      interactions with host cells.
AU  - Kehrl JH
AU  - Patel KB
AU  - Kahng LS
PT  - Journal Article
TA  - Gastroenterology
JT  - Gastroenterology
SO  - Gastroenterology 2008 134: A713.

PMID- 24501648
VI  - 9
DP  - 2013
TI  - Non-contiguous finished genome sequence and description of Bacillus massiliogorillae sp. nov.
PG  - 93-105
AB  - Strain G2(T) sp. nov. is the type strain of B. massiliogorillae, a proposed new species within
      the genus Bacillus. This strain, whose genome is described here,
      was isolated in France from the fecal sample of a wild western lowland gorilla
      from Cameroon. B. massiliogorillae is a facultative anaerobic, Gram-variable,
      rod-shaped bacterium. Here we describe the features of this organism, together
      with the complete genome sequence and annotation. The 5,431,633 bp long genome (1
      chromosome but no plasmid) contains 5,179 protein-coding and 98 RNA genes,
      including 91 tRNA genes.
AU  - Keita MB
AU  - Diene SM
AU  - Robert C
AU  - Raoult D
AU  - Fournier PE
AU  - Bittar F
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 9: 93-105.

PMID- 25197465
VI  - 9
DP  - 2014
TI  - Non-contiguous finished genome sequence and description of Gorillibacterium massiliense gen. nov, sp. nov., a new member of the family Paenibacillaceae.
PG  - 807-820
AB  - Strain G5(T) gen. nov., sp. nov. is the type strain of Gorillibacterium massiliense, a newly
      proposed genus within the family Paenibacillaceae. This
      strain, whose genome is described here, was isolated in France from a stool
      sample of a wild Gorilla gorilla subsp. gorilla from Cameroon. G. massiliense is
      a facultatively anaerobic, Gram negative rod. Here we describe the features of
      this bacterium, together with the complete genome sequence and annotation. The
      5,546,433 bp long genome (1 chromosome but no plasmid) contains 5,145
      protein-coding and 76 RNA genes, including 69 tRNA genes.
AU  - Keita MB
AU  - Padhmanabhan R
AU  - Caputo A
AU  - Robert C
AU  - Delaporte E
AU  - Raoult D
AU  - Fournier PE
AU  - Bittar F
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 807-820.

PMID- 25197481
VI  - 9
DP  - 2014
TI  - Non-contiguous finished genome sequence and description of Paenibacillus gorillae sp. nov.
PG  - 1031-1045
AB  - Strain G1(T) sp. nov. is the type strain of Paenibacillus gorillae a newly proposed species
      within the genus Paenibacillus. This strain, whose genome is
      described here, was isolated in France from the fecal sample of a wild western
      lowland gorilla from Cameroon. P. gorillae is a facultative anaerobic,
      Gram-negative, rod-shaped bacterium. Here we describe the features of this
      organism, together with the complete genome sequence and annotation. The
      6,257,967 bp long genome (one chromosome but no plasmid) contains 5,856
      protein-coding and 62 RNAs genes, including 60 tRNA genes.
AU  - Keita MB
AU  - Padhmananabhan R
AU  - Caputo A
AU  - Robert C
AU  - Delaporte E
AU  - Raoult D
AU  - Fournier PE
AU  - Bittar F
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 1031-1045.

PMID- 15225994
VI  - 34
DP  - 2004
TI  - Factors influencing resistance of UV-irradiated DNA to the restriction endonuclease cleavage.
PG  - 213-222
AB  - DNA molecules of pUC19, pBR322 and PhiX174 were irradiated by various doses of UV light and
      the irradiated molecules were cleaved by about
      two dozen type II restrictases. The irradiation generally blocked the
      cleavage in a dose-dependent way. In accordance with previous studies,
      the (A + T)-richness and the (PyPy) dimer content of the restriction
      site belongs among the factors that on average, cause an increase in
      the resistance of UV damaged DNA to the restrictase cleavage. However,
      we observed strong effects of UV irradiation even with (G + C)-rich and
      (PyPy)-poor sites. In addition, sequences flanking the restriction site
      influenced the protection in some cases (e.g. HindIII), but not in
      others (e.g. SalI), whereas neoschizomer couples SmaI and AvaI, or SacI
      and Ecl136II, cleaved the UV-irradiated DNA similarly. Hence the
      intrastrand thymine dimers located in the recognition site are not the
      only photoproduct blocking the restrictases. UV irradiation of the
      A-form generally made the irradiated DNA less resistant to restrictase
      cleavage than irradiation in the B-form and in some cases, the A-form
      completely protected the UV-irradiated DNA against the damage
      recognized by the restrictases. The present results also demonstrate
      that the UV irradiation approach used to generate partial digests in
      genomic DNA studies, can be extended to the (G + C)-rich and
      (PyPy)-poor restriction sites. The present extensive and quantitative
      data can be used in genomic applications of UV damage probing by
      restrictases.
AU  - Kejnovsky E
AU  - Nejedly K
AU  - Kypr J
PT  - Journal Article
TA  - Int. J. Biol. Macromol.
JT  - Int. J. Biol. Macromol.
SO  - Int. J. Biol. Macromol. 2004 34: 213-222.

PMID- 
VI  - 
DP  - 1990
TI  - Defining domains of the EcoK methylase by mutational analyses and DNA sequence comparisons.
PG  - 1-207
AB  - EcoK is a type I restriction and modification enzyme. It recognizes a defined DNA sequence and
      may methylate specific adenine residues within this target site, on each stand of the DNA.
      EcoK is composed of three different subunits encoded by the hsdR, M and S genes of E. coli
      K-12. The S subunit dictates the recognition specificity and together with M forms the
      methylase. All three enzyme subunits are necessary to form the restriction complex. Although
      this is also capable of DNA modification its activity is selected in reponse to the presence
      or absence of target site methylation. The methylase too is sensitive to the methylation state
      of the target site. Efficient modification requires the imprint of a methyl group in the
      complementary strand of the recognition sequence, whilst unmodified DNA, the normal substrate
      for restriction, is only methylated inefficiently. (Suri et al., 1984). The experiments
      described aim to identify functional domains of the EcoK methylase, from either the
      comparative analyses of polypeptide sequences, or the phenotypes of mutations. Related type I
      enzymes can interchange their subunits; unrelated enzymes cannot, and no general similarities
      are detected when unrelated polypeptides are compared (see Bickle, 1987). Nevertheless, the
      subunits of unrelated enzymes are presumed to be functionally analogous and sequence motifs
      common to all type I enzymes, may identify polypeptide domains involved in common activities.
      Mutational analyses have been limited to mutant derivatives of the EcoK methylase specifically
      defective in only a particular aspect of their activity, and have focused on mutations that
      apparently alter the substrate specificity of EcoK. The phenotypes of the new mutations
      identified are consistent with enzymes that fail to differentiate between hemimethylated and
      unmethylated target sites. These mutations cluster in a region of the hsdM gene, and may
      identify a polypeptide domain responsible for recognition of target site methylation.
AU  - Kelleher JE
PT  - Journal Article
TA  - Ph.D. Thesis, University of Edinburgh
JT  - Ph.D. Thesis, University of Edinburgh
SO  - Ph.D. Thesis, University of Edinburgh 1990 : 1-207.

PMID- 1833555
VI  - 221
DP  - 1991
TI  - Mutations that confer de novo activity upon a maintenance methyltransferase.
PG  - 431-440
AB  - DNA methyltransferases are not only sequence specific in their action, but they
      also differentiate between the alternative methylation states of a target site.
      Some methyltransferases are equally active on either unmethylated or
      hemimethylated DNA and consequently function as de novo methyltransferases.
      Others are specific for hemimethylated target sequences, consistent with the
      postulated role of a maintenance methyltransferase in perpetuating a pattern of
      DNA modification.  The molecular basis for the difference between de novo and
      maintenance methyltransferase activity is unknown, yet fundamental to cellular
      activities that are affected by different methylation states of the genome.
      The methyltransferase activity of the type I restriction and modification
      system, EcoK, is the only known prokaryotic methyltransferase shown to be
      specific for hemimethylated target sequences.  We have isolated mutants of
      Escherichia coli K-12 which are able to modify unmethylated target sequences
      efficiently in a manner indicative of de novo methyltransferase activity.
      Consistent with this change in specificity, some mutations shift the balance
      between DNA restriction and modification as if both activities now compete at
      unmethylated targets.  Two genes encode the methyltransferase and all the
      mutations are loosely clustered within one of them.
AU  - Kelleher JE
AU  - Daniel AS
AU  - Murray NE
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1991 221: 431-440.

PMID- 1830580
VI  - 173
DP  - 1991
TI  - A novel activity in Escherichia coli K-12 that directs restriction of DNA modified at CG dinucleotides.
PG  - 5220-5223
AB  - The restriction systems McrA and McrB of Escherichia coli K-12 are known to
      attack DNA containing modified cytosine.  In strains lacking both activities,
      however, we observed that DNA methylated at CG dinucleotides (as is mammalian
      DNA) was still significantly restricted.  We show that this substantial barrier
      to the acceptance of 5-methylcytosine-containing DNA is attributable to a
      hitherto unknown activity of the Mrr restriction system.  Strikingly, the
      multiple systems used by the gut inhabitant to determine the fate of invading
      DNA will all limit genetic exchange with its mammalian host(s), reinforcing the
      idea that one role of DNA methylation is to serve as a molecular passport (E.A.
      Raleigh, R. Trimarchi, and H. Revel, Genetics 122:279-296, 1989).
AU  - Kelleher JE
AU  - Raleigh EA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1991 173: 5220-5223.

PMID- 7607496
VI  - 157
DP  - 1995
TI  - On the regulation and diversity of restriction in Escherichia coli.
PG  - 229-230
AB  - The effect of UV irradiation on restriction mediated by four endogenous restriction systems of
      E. coli K-12 was investigated using a uniform testing method.  Restriction by all four
      systems was reduced when treated cells were separately challenged with lambda phage carrying
      modification patterns that elicit restriction by each system.  The response of each system was
      genetically and physiologically distinct.
AU  - Kelleher JE
AU  - Raleigh EA
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 229-230.

PMID- 7928948
VI  - 176
DP  - 1994
TI  - Response to UV damage by four Escherichia coli K-12 restriction systems.
PG  - 5888-5896
AB  - To understand the role of restriction in regulating gene flow in bacterial populations, we
      would like to understand the regulation of restriction enzyme activity. Several
      antirestriction (restriction alleviation) systems are known that reduce the activity of type I
      restriction enzymes like EcoKI in vivo. Most of these do not act on type II or type III
      enzymes, but little information is available for the unclassified modification-dependent
      systems, of which there are three in E. coli K-12. Of particular interest are two
      physiological controls on type I enzymes: EcoKI restriction is reduced 2 to 3 orders of
      magnitude following DNA damage, and a similar effect is seen constitutively in Dam- cells. We
      used the behavior of EcoKI as a control for testing the response to UV treatment of the three
      endogenous modification-dependent restriction systems of K-12, McrA, McrBC, and Mrr. Two of
      these were also tested for response to Dam status. We find that all four resident restriction
      systems show reduced activity following UV treatment, but not in a unified fashion; each
      response was genetically and physiologically distinct. Possible mechanisms are discussed.
AU  - Kelleher JE
AU  - Raleigh EA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1994 176: 5888-5896.

PMID- 28356072
VI  - 18
DP  - 2017
TI  - Comparative and functional genomics of the Lactococcus lactis taxon; insights into evolution and niche adaptation.
PG  - 267
AB  - BACKGROUND: Lactococcus lactis is among the most widely studied lactic acid
      bacterial species due to its long history of safe use and economic importance to
      the dairy industry, where it is exploited as a starter culture in cheese
      production. RESULTS: In the current study, we report on the complete sequencing
      of 16 L. lactis subsp. lactis and L. lactis subsp. cremoris genomes. The
      chromosomal features of these 16 L. lactis strains in conjunction with 14
      completely sequenced, publicly available lactococcal chromosomes were assessed
      with particular emphasis on discerning the L. lactis subspecies division,
      evolution and niche adaptation. The deduced pan-genome of L. lactis was found to
      be closed, indicating that the representative data sets employed for this
      analysis are sufficient to fully describe the genetic diversity of the taxon.
      CONCLUSIONS: Niche adaptation appears to play a significant role in governing the
      genetic content of each L. lactis subspecies, while (differential) genome decay
      and redundancy in the dairy niche is also highlighted.
AU  - Kelleher P
AU  - Bottacini F
AU  - Mahony J
AU  - Kilcawley KN
AU  - van Sinderen D
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2017 18: 267.

PMID- 4863697
VI  - 98
DP  - 1966
TI  - Host specificity of DNA produced by Escherichia coli.  8.Its acquisition by phage lambda and its persistence through consecutive growth cycles.
PG  - 247-256
AB  - Earlier papers in this series have demonstrated that host-controlled modification of
      bacteriophage lambda consists of the donation of a specific label to the phage DNA by the
      bacterial host cells.  The experiments to be described in this paper were originally designed
      to extend these observations to other types of host specificity, in particular to that
      produced by E. coli B.  Technically, such experiments were facilitated by the availability of
      restrictionless (r-) bacterial mutants which still provide full modification (m+): Density
      labelled lambda K was grown in normal medium for one cycle on a Br-m+ strain and the progeny
      phages analyzes for their parental DNA content by density gradient centrifugation.  The
      density fractions were then tested for both K and B host specificities.  Phage particles with
      fully heavy, hence conserved, DNA molecules had both K- and B-specificity.  The fractions of
      phages with densities corresponding to particles with halfheavy, supposedly semiconserved DNA
      molecules also plated on both K and B indicator.  But a more careful analysis revealed that
      only about half of such phages still grew on K, whereas the other half was degraded upon
      infection of K bacteria.  Repeated consecutive growth cycles were also performed and allowed
      firstly to confirm the findings of Arber, Hattman and Dussoix (1963) that under normal
      conditions both strands of lambda DNA are carrying host specificity, and secondly to conclude
      that the reduced probability of acceptance by strain K of lambda.K.B phage with semiconserved
      DNA cannot find its explanation in the physico-chemical plarity of the K-modified strand.
AU  - Kellenberger G
AU  - Symonds N
AU  - Arber W
PT  - Journal Article
TA  - Z. Vererbungsl.
JT  - Z. Vererbungsl.
SO  - Z. Vererbungsl. 1966 98: 247-256.

PMID- 
VI  - 109
DP  - 2009
TI  - A New Counterselectable Marker for Desulfovibrio vulgaris, the upp gene, Allowed for the Construction of a Marker less Deletion of a Type 1 Restriction Enzyme that Exhibits Increased Transformation Efficiency.
PG  - 0
AB  - In recent years, the genetic manipulation of the sulfate-reducing bacterium Desulfovibrio
      vulgaris Hildenborough has seen enormous progress; however, the current method of deletion
      construction via marker exchange mutagenesis does not allow for easy selection of multiple
      sequential gene deletions because of the need for multiple selectable markers. To broaden the
      repertoire of genetic tools for manipulation of D. vulgaris, an in-frame markerless deletion
      system has been developed based on the upp-encoded uracil phosphoribosyltransferase as an
      element for a counterselection strategy. In wild-type D. vulgaris, growth is inhibited by the
      toxic pyrimidine analog 5-fluorouracil (5-FU), whereas a mutant bearing a deletion of the upp
      gene, strain JW710, is resistant to 5-FU. The introduction of a plasmid containing the
      wild-type upp gene expressed constitutively from the aph(5')-III promoter (the promoter for
      the kanamycin resistance gene in Tn5) into JW710 restored sensitivity to 5-FU to wild-type
      levels. This observation is the basis for the establishment of a two-step integration and
      excision strategy for deleting genes of interest. Since this in-frame deletion does not leave
      behind an antibiotic cassette, multiple gene deletions can be generated in a single strain.
      With this method, a markerless deletion of the R-subunit (DVU1703) of a type I
      restriction-modification system (hsdR), strain JW7035, was constructed. The transformation
      efficiency of the JW7035 strain is greater (an approximate 2-log increase in transformants)
      compared to wild-type DvH when transforming stable plasmids via electroporation.
AU  - Keller KL
AU  - Bender KS
AU  - Wall JD
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 2009 109: 0.

PMID- 19837844
VI  - 75
DP  - 2009
TI  - Development of a markerless genetic exchange system for Desulfovibrio vulgaris Hildenborough and its use in generating a strain with increased  transformation efficiency.
PG  - 7682-7691
AB  - In recent years, the genetic manipulation of the sulfate-reducing bacterium Desulfovibrio
      vulgaris Hildenborough has seen enormous progress.
      In spite of this progress, the current marker exchange deletion method
      does not allow for easy selection of multiple sequential gene deletions in
      a single strain because of the limited number of selectable markers
      available in D. vulgaris. To broaden the repertoire of genetic tools for
      manipulation, an in-frame, markerless deletion system has been developed.
      The counterselectable marker that makes this deletion system possible is
      the pyrimidine salvage enzyme, uracil phosphoribosyltransferase, encoded
      by upp. In wild-type D. vulgaris, growth was shown to be inhibited by the
      toxic pyrimidine analog 5-fluorouracil (5-FU), whereas a mutant bearing a
      deletion of the upp gene was resistant to 5-FU. When a plasmid containing
      the wild-type upp gene expressed constitutively from the aph(3')-II
      promoter (promoter for the kanamycin resistance gene in Tn5) was
      introduced into the upp deletion strain, sensitivity to 5-FU was restored.
      This observation allowed us to develop a two-step integration and excision
      strategy for the deletion of genes of interest. Since this in-frame
      deletion strategy does not retain an antibiotic cassette, multiple
      deletions can be generated in a single strain without the accumulation of
      genes conferring antibiotic resistances. We used this strategy to generate
      a deletion strain lacking the endonuclease (hsdR, DVU1703) of a type I
      restriction-modification system that we designated JW7035. The
      transformation efficiency of the JW7035 strain was found to be 100 to
      1,000 times greater than that of the wild-type strain when stable plasmids
      were introduced via electroporation.
AU  - Keller KL
AU  - Bender KS
AU  - Wall JD
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2009 75: 7682-7691.

PMID- 23887920
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences of Five Multilocus Sequence Types of Nonencapsulated Streptococcus pneumoniae.
PG  - e00520-13
AB  - Nonencapsulated Streptococcus pneumoniae can colonize the human nasopharynx and cause
      conjunctivitis and otitis media. Different deletions in the capsular
      polysaccharide biosynthesis locus and different multilocus sequence types have
      been described for nonencapsulated strains. Draft genome sequences were generated
      to provide insight into the genomic diversity of these strains.
AU  - Keller LE
AU  - Thomas JC
AU  - Luo X
AU  - Nahm MH
AU  - McDaniel LS
AU  - Robinson DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00520-13.

PMID- 27540075
VI  - 4
DP  - 2016
TI  - Genomic Insights into Aquimarina sp. Strain EL33, a Bacterial Symbiont of the Gorgonian Coral Eunicella labiata.
PG  - e00855-16
AB  - To address the metabolic potential of symbiotic Aquimarina spp., we report here the genome
      sequence of Aquimarina sp. strain EL33, a bacterium isolated from the
      gorgonian coral Eunicella labiata This first-described (to our knowledge)
      animal-associated Aquimarina genome possesses a sophisticated repertoire of genes
      involved in drug/antibiotic resistance and biosynthesis.
AU  - Keller-Costa T
AU  - Silva R
AU  - Lago-Leston A
AU  - Costa R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00855-16.

PMID- 25780500
VI  - 9
DP  - 2014
TI  - Genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain NZP2037.
PG  - 7
AB  - Mesorhizobium loti strain NZP2037 was isolated in 1961 in Palmerston North, New Zealand from a
      Lotus divaricatus root nodule. Compared to most other M. loti
      strains, it has a broad host range and is one of very few M. loti strains able to
      form effective nodules on the agriculturally important legume Lotus pedunculatus.
      NZP2037 is an aerobic, Gram negative, non-spore-forming rod. This report reveals
      that the genome of M. loti strain NZP2037 does not harbor any plasmids and
      contains a single scaffold of size 7,462,792 bp which encodes 7,318
      protein-coding genes and 70 RNA-only encoding genes. This rhizobial genome is one
      of 100 sequenced as part of the DOE Joint Genome Institute 2010 Genomic
      Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.
AU  - Kelly S et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 7.

PMID- 2999111
VI  - 260
DP  - 1985
TI  - Purification of the HhaII restriction endonuclease from an overproducer Escherichia coli clone.
PG  - 15339-15344
AB  - An Escherichia coli K12 strain carrying the HhaII methylase and restriction
      genes on two separate compatible plasmids, pSK5 and pSK7, is used to
      overproduce the restriction endonuclease.  Plasmid pSK5 expresses the methylase
      gene constitutively from its chloramphenicol resistance gene promoter, and
      plasmid pSK7 expresses the restriction endonuclease under control of the lacUV5
      promoter.  Induction of the two-plasmid clone with 1 mM
      isopropyl-1-thio-b-D-galactopyranoside results in a 15-fold increase in HhaII
      endonuclease activity.  The enzyme has been purified to apparent homogeneity.
      It migrates as a 23-kilodalton polypeptide on denaturing sodium dodecyl
      sulfate-polyacrylamide electrophoretic gels and as a 51-kilodalton native
      protein dimer on a high pressure liquid chromatogrpahy sizing column.
AU  - Kelly S
AU  - Kaddurah-Daouk R
AU  - Smith HO
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1985 260: 15339-15344.

PMID- 25780499
VI  - 9
DP  - 2014
TI  - Genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain R7A.
PG  - 6
AB  - Mesorhizobium loti strain R7A was isolated in 1993 in Lammermoor, Otago, New Zealand from a
      Lotus corniculatus root nodule and is a reisolate of the inoculant
      strain ICMP3153 (NZP2238) used at the site. R7A is an aerobic, Gram-negative,
      non-spore-forming rod. The symbiotic genes in the strain are carried on a 502-kb
      integrative and conjugative element known as the symbiosis island or
      ICEMlSym(R7A). M. loti is the microsymbiont of the model legume Lotus japonicus
      and strain R7A has been used extensively in studies of the plant-microbe
      interaction. This report reveals that the genome of M. loti strain R7A does not
      harbor any plasmids and contains a single scaffold of size 6,529,530 bp which
      encodes 6,323 protein-coding genes and 75 RNA-only encoding genes. This rhizobial
      genome is one of 100 sequenced as part of the DOE Joint Genome Institute 2010
      Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB)
      project.
AU  - Kelly S
AU  - Sullivan J
AU  - Ronson C
AU  - Tian R
AU  - Brau L
AU  - Munk C
AU  - Goodwin L
AU  - Han C
AU  - Woyke T
AU  - Reddy T
AU  - Huntemann M
AU  - Pati A
AU  - Mavromatis K
AU  - Markowitz V
AU  - Ivanova N
AU  - Kyrpides N
AU  - Reeve W
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 6.

PMID- 30533900
VI  - 7
DP  - 2018
TI  - Draft Genome Sequence of Salinisphaera sp. Strain KSM-18, an Obligately Halophilic Bacterium Isolated from a Triassic Salt Mine.
PG  - e00897-18
AB  - Here, we report the draft genome sequence of Salinisphaera sp. strain KSM-18. This obligately
      halophilic bacterium was isolated from a brine sample obtained
      from a Triassic salt mine.
AU  - Kelly SA
AU  - Megaw J
AU  - Gilmore BF
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e00897-18.

PMID- 5312501
VI  - 51
DP  - 1970
TI  - A restriction enzyme from Hemophilus influenzae II.  Base sequence of the recognition site.
PG  - 393-409
AB  - Hemophilus influenzae strain Rd contains an enzyme, endonuclease R, which
      specifically degrades foreign DNA.  With phage T7 DNA as substrate the
      endonuclease introduces a limited number (about 40) double-strand breaks
      (5'-phosphoryl, 3'-hydroxyl).  The limit product has an average length of about
      1000 nucleotide pairs and contains no single-strand breaks.  We have explored
      the nucleotide sequences at the 5'-ends of the limit product by labeling the
      5'-phosphoryl groups (using polynucleotide kinase) and characterizing the
      labeled fragments released by various nucleases.  Two classes of 5'-terminal
      sequences were obtained: pApApCpNp...(60%) and pGpApCpNp...(40%), where N
      indicates that the base in the 4th position is not unique.  The dinucleoside
      monophosphates at the 3'-ends were isolated after micrococcal nuclease
      digestion of the limit product and identified as TpT(60%) and TpC(40%).  We
      conclude that endonuclease R of H. influenzae recognizes the following specific
      nucleotide sequence: 5' . . . pGpTpPy^pPupApCp . . . 3' 3' . . .
      pCpApPup^PypTpGp . . . 5' The implications of the twofold rotational symmetry
      of this sequence are discussed.
AU  - Kelly TJ Jr
AU  - Smith HO
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1970 51: 393-409.

PMID- Not included in PubMed...
VI  - 29
DP  - 1970
TI  - The nucleotide sequence of the recognition site for a restriction enzyme from H. influenzae.
PG  - 405
AB  - H. influenzae strain Rd contains an endonuclease which specifically degrades
      foreign DNA (Smith & Wilcox, Fed. Proc. 28:465, 1969).  With T7 DNA as
      substrate the endonuclease introduces a limited number (about 40) of
      double-strand breaks (5'-phosphoryl, 3'-hydroxyl).  The limit product has an
      average length of about 1000 nucleotide pairs and contains no single-strand
      breaks.  We have explored the nucleotide sequences at the 5'-ends of the limit
      product by labeling the 5'-phosphoryl groups (using polynucleotide kinase) and
      characterising the labeled fragments released by various nucleases.  Two
      classes of 5'-sequences were obtained:  pApApCpXp...(60%) and
      pGpApCpXp...(40%), where X indicates that the base in the 4th position is not
      unique.  The dinucleoside monophosphates at the 3'-ends were isolated after
      micrococcal nuclease digestion of the limit product and identified as TpT (60%)
      and TpC (40%).  We conclude that the H. influenzae endonuclease recognizes the
      following specific nucleotide sequence: 5' ...pGpTpPy^pPupApCp... 3'     ^break
      3' ...pCpApPup^PypTpGp... 5' The two-fold rotational symmetry of this sequence
      has interesting implications concerning the mechanism of action of the H.
      influenzae endonuclease.
AU  - Kelly TJ
AU  - Smith HO
PT  - Journal Article
TA  - Fed. Proc.
JT  - Fed. Proc.
SO  - Fed. Proc. 1970 29: 405.

PMID- 24009606
VI  - 4
DP  - 2013
TI  - Interaction between the genomes of Lactococcus lactis and phages of the P335 species.
PG  - 257
AB  - Phages of the P335 species infect Lactococcus lactis and have been particularly
      studied because of their association with strains of L. lactis subsp. cremoris
      used as dairy starter cultures. Unlike other lactococcal phages, those of the
      P335 species may have a temperate or lytic lifestyle, and are believed to
      originate from the starter cultures themselves. We have sequenced the genome of
      L. lactis subsp. cremoris KW2 isolated from fermented corn and found that it
      contains an integrated P335 species prophage. This 41 kb prophage (Phi KW2) has a
      mosaic structure with functional modules that are highly similar to several other
      phages of the P335 species associated with dairy starter cultures. Comparison of
      the genomes of 26 phages of the P335 species, with either a lytic or temperate
      lifestyle, shows that they can be divided into three groups and that the
      morphogenesis gene region is the most conserved. Analysis of these phage genomes
      in conjunction with the genomes of several L. lactis strains shows that prophage
      insertion is site specific and occurs at seven different chromosomal locations.
      Exactly how induced or lytic phages of the P335 species interact with
      carbohydrate cell surface receptors in the host cell envelope remains to be
      determined. Genes for the biosynthesis of a variable cell surface polysaccharide
      and for lipoteichoic acids (LTAs) are found in L. lactis and are the main
      candidates for phage receptors, as the genes for other cell surface carbohydrates
      have been lost from dairy starter strains. Overall, phages of the P335 species
      appear to have had only a minor role in the adaptation of L. lactis subsp.
      cremoris strains to the dairy environment, and instead they appear to be an
      integral part of the L. lactis chromosome. There remains a great deal to be
      discovered about their role, and their contribution to the evolution of the
      bacterial genome.
AU  - Kelly WJ
AU  - Altermann E
AU  - Lambie SC
AU  - Leahy SC
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2013 4: 257.

PMID- 26981167
VI  - 11
DP  - 2016
TI  - The complete genome sequence of Eubacterium limosum SA11, a metabolically versatile rumen acetogen.
PG  - 26
AB  - Acetogens are a specialized group of anaerobic bacteria able to produce acetate from CO2 and
      H2 via the Wood-Ljungdahl pathway. In some gut environments
      acetogens can compete with methanogens for H2, and as a result rumen acetogens
      are of interest in the development of microbial approaches for methane
      mitigation. The acetogen Eubacterium limosum SA11 was isolated from the rumen of
      a New Zealand sheep and its genome has been sequenced to examine its potential
      application in methane mitigation strategies, particularly in situations where
      hydrogenotrophic methanogens are inhibited resulting in increased H2 levels in
      the rumen. The 4.15 Mb chromosome of SA11 has an average G + C content of 47 %,
      and encodes 3805 protein-coding genes. There is a single prophage inserted in the
      chromosome, and several other gene clusters appear to have been acquired by
      horizontal transfer. These include genes for cell wall glycopolymers, a type VII
      secretion system, cell surface proteins and chemotaxis. SA11 is able to use a
      variety of organic substrates in addition to H2/CO2, with acetate and butyrate as
      the principal fermentation end-products, and genes involved in these metabolic
      pathways have been identified. An unusual feature is the presence of 39 genes
      encoding trimethylamine methyltransferase family proteins, more than any other
      bacterial genome. Overall, SA11 is a metabolically versatile organism, but its
      ability to grow on such a wide range of substrates suggests it may not be a
      suitable candidate to take the place of hydrogen-utilizing methanogens in the
      rumen.
AU  - Kelly WJ
AU  - Henderson G
AU  - Pacheco DM
AU  - Li D
AU  - Reilly K
AU  - Naylor GE
AU  - Janssen PH
AU  - Attwood GT
AU  - Altermann E
AU  - Leahy SC
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 26.

PMID- 20689770
VI  - 5
DP  - 2010
TI  - The Glycobiome of the Rumen Bacterium Butyrivibrio proteoclasticus B316 Highlights Adaptation to a Polysaccharide-Rich Environment.
PG  - E11942
AB  - Determining the role of rumen microbes and their enzymes in plant
      polysaccharide breakdown is fundamental to understanding digestion and
      maximising productivity in ruminant animals. Butyrivibrio proteoclasticus
      B316(T) is a Gram-positive, butyrate-forming rumen bacterium with a key
      role in plant polysaccharide degradation. The 4.4Mb genome consists of 4
      replicons; a chromosome, a chromid and two megaplasmids. The chromid is
      the smallest reported for all bacteria, and the first identified from the
      phylum Firmicutes. B316 devotes a large proportion of its genome to the
      breakdown and reassembly of complex polysaccharides and has a highly
      developed glycobiome when compared to other sequenced bacteria. The
      secretion of a range of polysaccharide-degrading enzymes which initiate
      the breakdown of pectin, starch and xylan, a subtilisin family protease
      active against plant proteins, and diverse intracellular enzymes to break
      down oligosaccharides constitute the degradative capability of this
      organism. A prominent feature of the genome is the presence of multiple
      gene clusters predicted to be involved in polysaccharide biosynthesis.
      Metabolic reconstruction reveals the absence of an identifiable gene for
      enolase, a conserved enzyme of the glycolytic pathway. To our knowledge
      this is the first report of an organism lacking an enolase. Our analysis
      of the B316 genome shows how one organism can contribute to the
      multi-organism complex that rapidly breaks down plant material in the
      rumen. It can be concluded that B316, and similar organisms with broad
      polysaccharide-degrading capability, are well suited to being early
      colonizers and degraders of plant polysaccharides in the rumen
      environment.
AU  - Kelly WJ
AU  - Leahy SC
AU  - Altermann E
AU  - Yeoman CJ
AU  - Dunne JC
AU  - Kong Z
AU  - Pacheco DM
AU  - Li D
AU  - Noel SJ
AU  - Moon CD
AU  - Cookson AL
AU  - Attwood GT
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2010 5: E11942.

PMID- 25780506
VI  - 9
DP  - 2014
TI  - The complete genome sequence of the rumen methanogen Methanobacterium formicicum  BRM9.
PG  - 15
AB  - Methanobacterium formicicum BRM9 was isolated from the rumen of a New Zealand Friesan cow
      grazing a ryegrass/clover pasture, and its genome has been sequenced
      to provide information on the phylogenetic diversity of rumen methanogens with a
      view to developing technologies for methane mitigation. The 2.45 Mb BRM9
      chromosome has an average G + C content of 41%, and encodes 2,352 protein-coding
      genes. The genes involved in methanogenesis are comparable to those found in
      other members of the Methanobacteriaceae with the exception that there is no
      [Fe]-hydrogenase dehydrogenase (Hmd) which links the methenyl-H4MPT reduction
      directly with the oxidation of H2. Compared to the rumen Methanobrevibacter
      strains, BRM9 has a much larger complement of genes involved in determining
      oxidative stress response, signal transduction and nitrogen fixation. BRM9 also
      has genes for the biosynthesis of the compatible solute ectoine that has not been
      reported to be produced by methanogens. The BRM9 genome has a prophage and two
      CRISPR repeat regions. Comparison to the genomes of other Methanobacterium
      strains shows a core genome of ~1,350 coding sequences and 190 strain-specific
      genes in BRM9, most of which are hypothetical proteins or prophage related.
AU  - Kelly WJ
AU  - Leahy SC
AU  - Li D
AU  - Perry R
AU  - Lambie SC
AU  - Attwood GT
AU  - Altermann E
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 15.

PMID- 27056228
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the Rumen Methanogen Methanobrevibacter olleyae YLM1.
PG  - e00232-16
AB  - Methanobrevibacter olleyaeYLM1 is a hydrogenotrophic methanogen, isolated from the rumen of a
      lamb. Its genome has been sequenced to provide information on the
      genomic diversity of rumen methanogens and support the development of approaches
      to reduce methane formation by ruminants.
AU  - Kelly WJ
AU  - Li D
AU  - Lambie SC
AU  - Cox F
AU  - Attwood GT
AU  - Altermann E
AU  - Leahy SC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00232-16.

PMID- 27056226
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Methanogenic Archaeon ISO4-G1, a Member of the Methanomassiliicoccales, Isolated from a Sheep Rumen.
PG  - e00221-16
AB  - Methanogenic archaeon ISO4-G1 is a methylotrophic methanogen belonging to the
      orderMethanomassiliicoccalesthat was isolated from a sheep rumen. Its genome has
      been sequenced to provide information on the genetic diversity of rumen
      methanogens in order to develop technologies for ruminant methane mitigation.
AU  - Kelly WJ
AU  - Li D
AU  - Lambie SC
AU  - Jeyanathan J
AU  - Cox F
AU  - Li Y
AU  - Attwood GT
AU  - Altermann E
AU  - Leahy SC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00221-16.

PMID- 27536339
VI  - 11
DP  - 2016
TI  - The complete genome sequence of the rumen methanogen Methanobrevibacter millerae  SM9.
PG  - 49
AB  - Methanobrevibacter millerae SM9 was isolated from the rumen of a sheep maintained on a fresh
      forage diet, and its genome has been sequenced to provide information
      on the phylogenetic diversity of rumen methanogens with a view to developing
      technologies for methane mitigation. It is the first rumen isolate from the
      Methanobrevibacter gottschalkii clade to have its genome sequence completed. The
      2.54 Mb SM9 chromosome has an average G + C content of 31.8 %, encodes 2269
      protein-coding genes, and harbors a single prophage. The overall gene content is
      comparable to that of Methanobrevibacter ruminantium M1 and the type strain of M.
      millerae (ZA-10(T)) suggesting that the basic metabolism of these two
      hydrogenotrophic rumen methanogen species is similar. However, M. millerae has a
      larger complement of genes involved in methanogenesis including genes for methyl
      coenzyme M reductase II (mrtAGDB) which are not found in M1. Unusual features of
      the M. millerae genomes include the presence of a tannase gene which shows high
      sequence similarity with the tannase from Lactobacillus plantarum, and large
      non-ribosomal peptide synthase genes. The M. millerae sequences indicate that
      methane mitigation strategies based on the M. ruminantium M1 genome sequence are
      also likely to be applicable to members of the M. gottschalkii clade.
AU  - Kelly WJ
AU  - Pacheco DM
AU  - Li D
AU  - Attwood GT
AU  - Altermann E
AU  - Leahy SC
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 49.

PMID- 25858841
VI  - 3
DP  - 2015
TI  - Genome Sequences of Two Bovine Mastitis-Causing Escherichia coli Strains.
PG  - e00259-15
AB  - Escherichia coli is one of the main pathogenic agents causing inflammatory infections in the
      bovine udder. Here, we report the draft genome sequences of two
      strains isolated from different cases of clinical mastitis.
AU  - Kempf F
AU  - Loux V
AU  - Germon P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00259-15.

PMID- 29505558
VI  - 14
DP  - 2018
TI  - Synchronous termination of replication of the two chromosomes is an evolutionary selected feature in Vibrionaceae.
PG  - e1007251
AB  - Vibrio cholerae, the causative agent of the cholera disease, is commonly used as
      a model organism for the study of bacteria with multipartite genomes. Its two
      chromosomes of different sizes initiate their DNA replication at distinct time
      points in the cell cycle and terminate in synchrony. In this study, the
      time-delayed start of Chr2 was verified in a synchronized cell population. This
      replication pattern suggests two possible regulation mechanisms for other Vibrio
      species with different sized secondary chromosomes: Either all Chr2 start DNA
      replication with a fixed delay after Chr1 initiation, or the timepoint at which
      Chr2 initiates varies such that termination of chromosomal replication occurs in
      synchrony. We investigated these two models and revealed that the two chromosomes
      of various Vibrionaceae species terminate in synchrony while Chr2-initiation
      timing relative to Chr1 is variable. Moreover, the sequence and function of the
      Chr2-triggering crtS site recently discovered in V. cholerae were found to be
      conserved, explaining the observed timing mechanism. Our results suggest that it
      is beneficial for bacterial cells with multiple chromosomes to synchronize their
      replication termination, potentially to optimize chromosome related processes as
      dimer resolution or segregation.
AU  - Kemter FS
AU  - Messerschmidt SJ
AU  - Schallopp N
AU  - Sobetzko P
AU  - Lang E
AU  - Bunk B
AU  - Sproer C
AU  - Teschler JK
AU  - Yildiz FH
AU  - Overmann J
AU  - Waldminghaus T
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2018 14: e1007251.

PMID- 27034491
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Streptococcus pneumoniae with High-Level Resistance to  Respiratory Fluoroquinolones.
PG  - e00181-16
AB  - Streptococcus pneumoniaeis the leading cause of community-acquired pneumonia. Levofloxacin is
      a fluoroquinolone used for treatment of severe community-acquired
      pneumonia. Here, we describe the draft genome sequences ofS. pneumoniaewith
      emerging resistance to levofloxacin, resulting in failure of treatment of
      pneumococcal pneumonia.
AU  - Keness Y
AU  - Bisharat N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00181-16.

PMID- 19074193
VI  - 37
DP  - 2009
TI  - The structure of M.EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein.
PG  - 762-770
AB  - Type-I DNA restriction-modification (R/M) systems are important agents in limiting the
      transmission of mobile genetic elements responsible for
      spreading bacterial resistance to antibiotics. EcoKI, a Type I R/M enzyme
      from Escherichia coli, acts by methylation- and sequence-specific
      recognition, leading to either methylation of DNA or translocation and
      cutting at a random site, often hundreds of base pairs away. Consisting of
      one specificity subunit, two modification subunits, and two DNA
      translocase/endonuclease subunits, EcoKI is inhibited by the T7 phage
      antirestriction protein ocr, a DNA mimic. We present a 3D density map
      generated by negative-stain electron microscopy and single particle
      analysis of the central core of the restriction complex, the M.EcoKI
      M(2)S(1) methyltransferase, bound to ocr. We also present complete atomic
      models of M.EcoKI in complex with ocr and its cognate DNA giving a clear
      picture of the overall clamp-like operation of the enzyme. The model is
      consistent with a large body of experimental data on EcoKI published over
      40 years.
AU  - Kennaway CK
AU  - Obarska-Kosinska A
AU  - White JH
AU  - Tuszynska I
AU  - Cooper LP
AU  - Bujnicki JM
AU  - Trinick J
AU  - Dryden DT
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: 762-770.

PMID- 22215814
VI  - 26
DP  - 2012
TI  - Structure and operation of the DNA-translocating type I DNA restriction enzymes.
PG  - 92-104
AB  - Type I DNA restriction/modification (RM) enzymes are molecular machines found in the majority
      of bacterial species. Their early discovery paved
      the way for the development of genetic engineering. They control
      (restrict) the influx of foreign DNA via horizontal gene transfer into
      the bacterium while maintaining sequence-specific methylation
      (modification) of host DNA. The endonuclease reaction of these enzymes
      on unmethylated DNA is preceded by bidirectional translocation of
      thousands of base pairs of DNA toward the enzyme. We present the
      structures of two type I RM enzymes, EcoKI and EcoR124I, derived using
      electron microscopy (EM), small-angle scattering (neutron and X-ray),
      and detailed molecular modeling. DNA binding triggers a large
      contraction of the open form of the enzyme to a compact form. The path
      followed by DNA through the complexes is revealed by using a DNA mimic
      anti-restriction protein. The structures reveal an evolutionary link
      between type I RM enzymes and type II RM enzymes.
AU  - Kennaway CK
AU  - Taylor JE
AU  - Song CF
AU  - Potrzebowski W
AU  - Nicholson W
AU  - White JH
AU  - Swiderska A
AU  - Obarska-Kosinska A
AU  - Callow P
AU  - Cooper LP
AU  - Roberts GA
AU  - Artero JB
AU  - Bujnicki JM
AU  - Trinick J
AU  - Kneale GG
AU  - Dryden DTF
PT  - Journal Article
TA  - Genes Dev.
JT  - Genes Dev.
SO  - Genes Dev. 2012 26: 92-104.

PMID- 27587809
VI  - 4
DP  - 2016
TI  - Genome Sequences of Three Spore-Forming Bacteria Isolated from the Feces of Organically Raised Chickens.
PG  - e00880-16
AB  - Antibiotic feed supplements have been implicated in the rise of multidrug-resistant bacteria.
      An alternative to antibiotics is probiotics. Here,
      we report the genome sequences of two Bacillus and one Solibacillus species, all
      spore-forming, Gram-positive bacteria, isolated from the feces organically raised
      chicken feces, with potential to serve as probiotics.
AU  - Kennedy V
AU  - Van Laar TA
AU  - Aleru O
AU  - Thomas M
AU  - Ganci M
AU  - Rawat M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00880-16.

PMID- 7681727
VI  - 73
DP  - 1993
TI  - Reverse transcriptase activity associated with maturase-encoding group II introns in yeast mitochondria.
PG  - 133-146
AB  - Group II introns ai1 and ai2 of the yeast mtDNA cox1 gene encode reverse transcriptase-like
      proteins that function in RNA splicing and may play a role in intron mobility and excision. We
      find that ribonucleoprotein particles from yeast mitochondria contain a reverse transcriptase
      activity that is likely encoded by ai1 and ai2 and is highly specific for the introns and
      their flanking exons.  Using a mutant strain with elevated activity, we show that the reverse
      transcriptase uses either excised intron RNA or cox1 pre-mRNA as template and initiates cDNA
      synthesis near the 3' end of ai2 and immediately downstream in E3.  Our results suggest that
      introns ai1 and ai2 are retroelements, which encode reverse transcriptases that have adapted
      to function in RNA splicing.
AU  - Kennell JC
AU  - Moran JV
AU  - Perlman PS
AU  - Butow RA
AU  - Lambowitz AM
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1993 73: 133-146.

PMID- 22328753
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Mycoplasma pneumoniae Type 2a Strain 309, Isolated in Japan.
PG  - 1253-1254
AB  - Mycoplasma pneumoniae strain 309, a type 2a (subtype 2 variant) strain of this bacterium, has
      variations in the P1 protein, which is responsible for attachment
      of the bacterium to host cells. Here, we report the complete genome sequence of
      M. pneumoniae strain 309 isolated from a pneumonia patient in Japan.
AU  - Kenri T
AU  - Horino A
AU  - Matsui M
AU  - Sasaki Y
AU  - Suzuki S
AU  - Narita M
AU  - Ohya H
AU  - Okazaki N
AU  - Shibayama K
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1253-1254.

PMID- 28619800
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of the p1 Gene Type 2b and 2c Strains Mycoplasma pneumoniae KCH-402 and KCH-405.
PG  - e00513-17
AB  - Here, we present the complete genome sequences of Mycoplasma pneumoniae KCH-402 and KCH-405,
      which are p1 gene type 2b and 2c strains, respectively. These
      strains harbor variations in the orf6 gene, which encodes the
      cytadherence-related proteins P40 and P90.
AU  - Kenri T
AU  - Suzuki M
AU  - Horino A
AU  - Sekizuka T
AU  - Kuroda M
AU  - Fujii H
AU  - Hashimoto T
AU  - Nakajima H
AU  - Ohya H
AU  - Shibayama K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00513-17.

PMID- 25587021
VI  - 7
DP  - 2015
TI  - Habitat visualization and genomic analysis of 'Candidatus Pantoea carbekii,' the primary symbiont of the brown marmorated stink bug.
PG  - 620-635
AB  - Phytophagous pentatomid insects can negatively impact agricultural productivity
      and the brown marmorated stink bug (Halyomorpha halys) is an emerging invasive
      pest responsible for damage to many fruit crops and ornamental plants in North
      America. Many phytophagous stink bugs, including H. halys, harbor
      gammaproteobacterial symbionts that likely contribute to host development, and
      characterization of symbiont transmission/acquisition and their contribution to
      host fitness may offer alternative strategies for managing pest species.
      "Candidatus Pantoea carbekii" is the primary occupant of gastric ceca lumina
      flanking the distal midgut of H. halys insects and it is acquired each generation
      when nymphs feed on maternal extrachorion secretions following hatching. Insects
      prevented from symbiont uptake exhibit developmental delays and aberrant
      behaviors. To infer contributions of Ca. P. carbekii to H. halys, the complete
      genome was sequenced and annotated from a North American H. halys population.
      Overall, the Ca. P. carbekii genome is nearly one-fourth (1.2 Mb) that of
      free-living congenerics, and retains genes encoding many functions that are
      potentially host-supportive. Gene content reflects patterns of gene
      loss/retention typical of intracellular mutualists of plant-feeding insects.
      Electron and fluorescence in situ microscopic imaging of H. halys egg surfaces
      revealed that maternal extrachorion secretions were populated with Ca. P.
      carbekii cells. The reported findings detail a transgenerational mode of symbiont
      transmission distinct from that observed for intracellular insect mutualists and
      illustrate the potential additive functions contributed by the bacterial symbiont
      to this important agricultural pest.
AU  - Kenyon LJ
AU  - Meulia T
AU  - Sabree ZL
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2015 7: 620-635.

PMID- 28705986
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Multidrug-Resistant Cellulosimicrobium sp. Strain KWT-B, Isolated from Feces of Hirundo rustica.
PG  - e00641-17
AB  - Migratory birds have been postulated as potential spreaders of antibiotic resistance.
      Multidrug-resistant Cellulosimicrobium sp. strain KWT-B was isolated
      from the feces of Hirundo rustica A draft genome sequence indicated that the
      strain harbors multidrug-resistant transporters, multidrug efflux pumps, a
      vancomycin-resistant protein, and metallo-beta-lactamases.
AU  - Kenzaka T
AU  - Ishimoto Y
AU  - Tani K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00641-17.

PMID- 25359918
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Amoeba-Resistant Aeromonas spp. Isolated from Aquatic Environments.
PG  - e01115-14
AB  - Amoeba-resistant Aeromonas veronii ARB3 and Aeromonas media ARB13 and ARB20, which may be
      important intracellular pathogens of eukaryotic hosts, were isolated
      from pond and river waters. The draft genome sequences indicate that the strains
      harbor multiple protein secretion systems and toxins that induce disruption of
      the actin cytoskeleton.
AU  - Kenzaka T
AU  - Nakahara M
AU  - Higuchi S
AU  - Maeda K
AU  - Tani K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01115-14.

PMID- 29567744
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Multidrug-Resistant Stenotrophomonas pavanii BWK1, Isolated from Mareca penelope Feces.
PG  - e00187-18
AB  - Migratory birds serve as vectors by transmitting antibiotic-resistant bacteria across large
      distances. Here, we isolated a multidrug-resistant Stenotrophomonas
      pavanii strain, BWK1, from Mareca penelope feces. Analysis of the draft genome
      sequence of the isolated strain indicated that BWK1 harbors a class A
      beta-lactamase, metallo-beta-lactamase, and several multidrug efflux pumps.
AU  - Kenzaka T
AU  - Tani K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00187-18.

PMID- 29567743
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Carbapenem-Resistant Pseudomonas fluorescens Strain BWKM6, Isolated from Feces of Mareca penelope.
PG  - e00186-18
AB  - Migratory birds are potential vehicles of antibiotic-resistant bacteria. Here, we isolated the
      multidrug-resistant Pseudomonas fluorescens strain BWKM6 from the
      feces of Mareca penelope The strain's draft genome sequence indicates that it
      harbors a metallo-beta-lactamase, a class C beta-lactamase, and several multidrug
      efflux pumps.
AU  - Kenzaka T
AU  - Tani K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00186-18.

PMID- 28983007
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Extended-Spectrum Beta-Lactamase-Producing Serratia fonticola BWK15 Isolated from Feces of Anas penelope.
PG  - e01102-17
AB  - Migratory birds have been postulated as potential vehicles of antibiotic resistance. Here we
      isolated the extended-spectrum beta-lactamase
      (ESBL)-producing Serratia fonticola strain BWK15 from the feces of Anas penelope
      The strain's draft genome sequence indicated that it harbors class A ESBL, class
      C beta-lactamase, and many multidrug efflux pumps.
AU  - Kenzaka T
AU  - Tani K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01102-17.

PMID- 24831148
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of an Antifungal Bacterium Isolated from the Breeding Environment of Dorcus hopei binodulosus.
PG  - e00424-14
AB  - Burkholderia sp. strain A1 was isolated from a decaying log present in the breeding
      environment of a stag beetle. The draft genome sequence indicates that
      strain A1 harbors many biosynthesis molecules, which have antimicrobial
      properties, and thus potentially eliminates the fungi by producing antifungal
      compounds, such as siderophores.
AU  - Kenzaka T
AU  - Yamada Y
AU  - Tani K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00424-14.

PMID- 27417843
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Sphingobium sp. Strain TCM1 and Sphingomonas sp. Strain TDK1, Haloalkyl Phosphate Flame Retardant- and Plasticizer-Degrading Bacteria.
PG  - e00668-16
AB  - Sphingobium sp. strain TCM1 and Sphingomonas sp. strain TDK1 are haloalkyl phosphate flame
      retardant- and plasticizer-degrading bacteria. We report here the
      draft genome sequences of these strains to provide insights into the molecular
      mechanism underlying their degradation ability.
AU  - Kera Y
AU  - Abe K
AU  - Kasai D
AU  - Fukuda M
AU  - Takahashi S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00668-16.

PMID- 22582370
VI  - 194
DP  - 2012
TI  - Genome Sequence of Lactobacillus salivarius SMXD51, a Potential Probiotic Strain  Isolated from Chicken Cecum, Showing Anti-Campylobacter Activity.
PG  - 3008-3009
AB  - We report the draft genome sequence of Lactobacillus salivarius SMXD51, isolated  from the
      cecum of healthy chickens showing an activity against Campylobacter-the
      food-borne pathogen that is the most common cause of gastroenteritis in the
      European Union (EU)-and potentially interesting features for a probiotic strain,
      explaining our interest in it.
AU  - Kergourlay G
AU  - Messaoudi S
AU  - Dousset X
AU  - Prevost H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3008-3009.

PMID- 26763977
VI  - 66
DP  - 2016
TI  - Methanosarcina flavescens sp. nov., a methanogenic archaeon isolated from a full-scale anaerobic digester.
PG  - 1533-1538
AB  - A novel, strictly anaerobic, methanogenic archaeon, strain E03.2(T), was isolated
      from a full-scale biogas plant in Germany. Cells were non-motile sarcina-like
      cocci, occurring in aggregates. Strain E03.2(T) grew autotrophically on H2 plus
      CO2, and additionally cells could utilize acetate, methanol, moni-, di- and
      trimethylamine as carbon and energy sources; however, growth or methanogenesis on
      formate was not observed. Yeast extract and vitamins stimulated growth but were
      not mandatory. The optimal growth temperature of strain E03.2(T) was
      approximately 45 degrees C; maximal growth rates were obtained at about pH 7.0 in
      the presence of approximately 6.8 mM NaCl. The DNA G+C content of strain E03.2(T)
      was 41.3 mol%. Phylogenetic analyses based on 16S rRNA gene and mcrA sequences
      placed strain E03.2(T) within the genus Methanosarcina. Based on 16S rRNA gene
      sequence similarity strain E03.2(T) was related to seven different species of the
      genus Methanosarcina, but most closely related to Methanosarcina thermophila
      TM-1(T). Phenotypic, physiological and genomic characteristics indicated that
      strain E03.2(T) represents a novel species of the genus Methanosarcina, for which
      the name Methanosarcina flavescens sp. nov. is proposed. The type strain is
      E03.2(T) ( = DSM 100822(T) = JCM 30921(T)).
AU  - Kern T
AU  - Fischer MA
AU  - Deppenmeier U
AU  - Schmitz RA
AU  - Rother M
PT  - Journal Article
TA  - Int. J. Syst. Evol. Microbiol.
JT  - Int. J. Syst. Evol. Microbiol.
SO  - Int. J. Syst. Evol. Microbiol. 2016 66: 1533-1538.

PMID- 26227607
VI  - 3
DP  - 2015
TI  - First Complete Genome Sequence of a Salmonella enterica subsp. enterica Serovar Derby Strain Associated with Pork in France.
PG  - e00853-15
AB  - In France, Salmonella enterica subsp. enterica serovar Derby is one of the most often isolated
      serovars in pigs. Here, we describe the draft genome sequence of a
      strain isolated from a pig. This strain had the most frequent pulsed-field gel
      electrophoresis (PFGE) and antimicrobial patterns (S, SSU, T) usually observed in
      pig production in France. Those patterns have been also highlighted in human
      isolates.
AU  - Kerouanton A
AU  - Hirchaud E
AU  - Rose V
AU  - Esnault E
AU  - Naquin D
AU  - Denis M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00853-15.

PMID- 20957358
VI  - 89
DP  - 2011
TI  - DNA restriction-modification systems in the ethanologen, Zymomonas mobilis ZM4.
PG  - 761-769
AB  - To better understand the DNA restriction-modification (R-M) systems for more amenable strain
      development of the alternative industrial
      ethanologen, Zymomonas mobilis, three gene knockout mutants were
      constructed. The gene knockout mutants were tested for their DNA
      restriction activities by the determination of transformation
      efficiency using methylated and unmethylated foreign plasmid DNAs.
      Inactivation of a putative mrr gene encoded by ZMO0028 (zmrr) resulted
      in a 60-fold increase in the transformation efficiency when
      unmethylated plasmid DNA was used. This indicated that the putative mrr
      gene may serve as a type IV restriction-modification system in Z.
      mobilis ZM4. To assign the function of a putative type I DNA
      methyltransferase encoded by ZMO1933 (putative S subunit) and ZMO1934
      (putative M subunit), the putative S subunit was inactivated. The gene
      inactivation of ZMO1933 resulted in a 30-fold increase in the
      transformation efficiency when methylated plasmid DNA was introduced,
      indicating that the putative S subunit possibly serves as a part of
      functional type I R-M system(s). Growth studies performed on the mutant
      strains indicate inactivation of the type I S subunit resulted in a
      lower maximum specific glucose consumption rate and biomass yield,
      while inactivation of the type IV Zmrr had the opposite effect, with an
      increase in the maximum specific growth rate and biomass yield.
AU  - Kerr AL
AU  - Jeon YJ
AU  - Svenson CJ
AU  - Rogers PL
AU  - Neilan BA
PT  - Journal Article
TA  - Appl. Microbiol. Biotechnol.
JT  - Appl. Microbiol. Biotechnol.
SO  - Appl. Microbiol. Biotechnol. 2011 89: 761-769.

PMID- 25883278
VI  - 3
DP  - 2015
TI  - Complete Genome Sequences of Two Helicobacter pylori Strains from a Canadian Arctic Aboriginal Community.
PG  - e00209-15
AB  - We report here the complete genome sequences of two Amerind Helicobacter pylori strains from
      Aklavik, Northwest Territories, Canada. One strain contains extra
      iron-cofactored urease genes and ~140 rearrangements in its chromosome relative
      to other described strains (typically differing from one another by <10
      rearrangements), suggesting that it represents a novel lineage of H. pylori.
AU  - Kersulyte D
AU  - Bertoli MT
AU  - Tamma S
AU  - Keelan M
AU  - Munday R
AU  - Geary J
AU  - Veldhuyzen-van-Zanten S
AU  - Goodman KJ
AU  - Berg DE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00209-15.

PMID- 10986230
VI  - 182
DP  - 2000
TI  - Functional organization and insertion specificity of IS607, a chimeric element of Helicobacter pylori.
PG  - 5300-5308
AB  - A search by subtractive hybridization for sequences present in only
      certain strains of Helicobacter pylori led to the discovery of a 2-kb
      transposable element to be called IS607, which further PCR and
      hybridization tests indicated was present in about one-fifth of H. pylori
      strains worldwide. IS607 contained two open reading frames (ORFs) of
      possibly different phylogenetic origin. One ORF (orfB) exhibited
      protein-level homology to one of two putative transposase genes found in
      several other chimeric elements including IS605 (also of H. pylori) and
      IS1535 (of Mycobacterium tuberculosis). The second IS607 gene (orfA) was
      unrelated to the second gene of IS605 and might possibly be chimeric
      itself: it exhibited protein-level homology to merR bacterial regulatory
      genes in the first approximately 50 codons and homology to the second gene
      of IS1535 (annotated as "resolvase," apparently due to a weak short
      recombinase motif) in the remaining three-fourths of its length. IS607 was
      found to transpose in Escherichia coli, and analyses of sequences of
      IS607-target DNA junctions in H. pylori and E. coli indicated that it
      inserted either next to or between adjacent GG nucleotides, and generated
      either a 2-bp or a 0-bp target sequence duplication, respectively.
      Mutational tests showed that its transposition in E. coli required orfA
      but not orfB, suggesting that OrfA protein may represent a new, previously
      unrecognized, family of bacterial transposases.
AU  - Kersulyte D
AU  - Mukhopadhyay AK
AU  - Shirai M
AU  - Nakazawa T
AU  - Berg DE
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2000 182: 5300-5308.

PMID- 4866792
VI  - 1
DP  - 1967
TI  - The restriction of bacteriophage lambda in Escherichia coli strain W.
PG  - 333-347
AB  - Escherichia coli strain w adsorbs phage lambda very efficiently but the phage does not form
      plaques on this strain.  In a very small fraction (10^-4) of the infected cells the phage
      grows and produces small bursts of progeny phage also unable to form plaques on strain w.  E.
      coli strain w is lysogenic for a temperate phage, wPhi, related to phage P2.  Non-restricting
      hosts for phage lambda became restricting hosts when made lysogenic for wPhi.  When
      32P-labelled lambda adsorbed to restricting wPhi lysogenic hosts, >20% of the 32P become
      acid-soluble shortly after infection.  No wPhi specific modification was carried by the small
      number of lambda phages which escaped this restriction process.  It is concluded that wPhi
      controls a host-restriction mechanism but not a host-modification process, and in parallel
      with other examples of host-controlled restriction and modification can be represented as r+m-
      or r+mo.  LambdaW mutants have been isolated which escape this restriction and which form
      plaques on strain w and wPhi lysogenic strains with an efficiency of I.0.  With these mutants
      a w-specific host modification controlled by the genome of strain w was demonstrated.  Mixed
      infection experiments with restricted lambda and unrestricted lambda w showed that that
      restricted phage did not block the growth of the unrestricted mutant nor did the mutant permit
      the restricted phage to grow.  In addition it was shown that lambda obtained from bacteria
      mixedly infected with lambda and lambdaW was still unable to grow in restricting hosts and
      lambda w similarly obtained from mixedly infected bacteria still retained its ability to grow
      on restricting hosts.  It is concluded that there is a nucleotide sequence in the DNA of phage
      lambda which, when lambda infects a restricting host, is specifically recognized by the
      restriction mechanism controlled by the wPhi.  The mutation to lambda w involves an alteration
      to this sequence such that it is no longer recognized by the restriction mechanism of the
      wPhi.  Mutants of wPhi were isolated not restrictive for phage lambda.
AU  - Kerszman G
AU  - Glover SW
AU  - Aronovitch J
PT  - Journal Article
TA  - J. Gen. Virol.
JT  - J. Gen. Virol.
SO  - J. Gen. Virol. 1967 1: 333-347.

PMID- Not included in PubMed...
VI  - 62
DP  - 1997
TI  - Site-specific endonuclease from thermophilic Bacillus species MK strain is isoschizomer of SalI.
PG  - 1029-1036
AB  - Screening of thermophilic bacterial strains revealed a strain containing site-specific
      endonuclease BspMKI.  Endonuclease was purified to functional homogeneity during sequential
      chromatographic steps.  The enzyme recognizes sequences 5'-G/TCGAC-3' on DNA molecule and
      its isoschizomer of endonuclease SalI.  The molecular mass of BspMKI is about 45 kD.  The
      enzyme is maximally active at 55oC and MRB (50 mM NaCl, 10 mM Tris-HCl, pH 7.4, 10 mM MgCl2, 1
      mM dithiothreitol) is the optimal buffer.  The enzyme is highly stable and retains its
      activity during two weeks at room temperature.
AU  - Kerzhner MA
AU  - Shiryaev SA
AU  - Zheleznaya LA
AU  - Matvienko NI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1997 62: 1029-1036.

PMID- 25502661
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Biofilm-Producing Bacillus subtilis Strain B-1, Isolated from an Oil Field.
PG  - e01163-14
AB  - We report here the draft genome sequence of the Bacillus subtilis strain B-1, a strain known
      to form biofilms. The biofilm matrix mainly consists of the
      biopolymer gamma-polyglutamate (gamma-PGA). The sequence of the genome of this
      strain allows the study of specific genes involved in biofilm formation.
AU  - Kesel S
AU  - Moormann F
AU  - Gumperlein I
AU  - Mader A
AU  - Morikawa M
AU  - Lieleg O
AU  - Opitz M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01163-14.

PMID- 6190136
VI  - 11
DP  - 1983
TI  - Effect of CpG methylation on MspI.
PG  - 3571-3580
AB  - The restriction enzyme MspI is inhibited by the presence of a methyl moiety at
      the external cytosine of the sequence CCGG, but is generally unaffected by
      methylation at the internal cytosine.  At specific subsets of this sequence
      such as the hexanucleotide CCGGCC, however, methylation of the internal
      cytosine strongly inhibits MspI digestion, leading to artifacts in the
      interpretation of DNA methylation analyses.  Our results show, for instance,
      that the CCGG site at the 5' end of the human gamma globin gene, which was
      thought to be methylated at both the internal and external cytosines, is
      actually methylated only at the internal CpG residue.
AU  - Keshet E
AU  - Cedar H
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1983 11: 3571-3580.

PMID- 11812857
VI  - 29
DP  - 2001
TI  - FspAI, a unique type II restriction endonuclease that recognizes the octanucleotide sequence 5'-RTGC^GCAY-3'.
PG  - e120
AB  - A new type II restriction endonuclease designated FspAI has been partially purified from a
      Flexibacter species Tv-m21K. FspAI recognizes the octanucleotide sequence
      5'-RTGCdecreaseGCAY-3' and cleaves it in the center generating blunt-ended DNA fragments.
AU  - Kesminiene A
AU  - Maneliene Z
AU  - Vitkute J
AU  - Petrusyte M
AU  - Janulaitis A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2001 29: e120.

PMID- Not included in PubMed...
VI  - 0
DP  - 1987
TI  - Class II restriction endonucleases.
PG  - 225-279
AB  - The availability of a large variety of class II restriction endonucleases with
      different site specificities is the basis of recombinant DNA technology and
      numerous analytical applications.  The importance of this enzyme class is
      demonstrated by recent findings in the detailed analysis of gene structure and
      the rapid succession of spectacular advances in genetic engineering (Malcolm
      1981; O'Connor et al. 1984).
AU  - Kessler C
PT  - Journal Article
TA  - Cytogenetics
JT  - Cytogenetics
SO  - Cytogenetics 1987 0: 225-279.

PMID- Not carried by PubMed...
VI  - 22
DP  - 1988
TI  - Restriction enzymes.
PG  - 37-49
AB  - None
AU  - Kessler C
PT  - Journal Article
TA  - Chemie in unserer Zeit
JT  - Chemie in unserer Zeit
SO  - Chemie in unserer Zeit 1988 22: 37-49.

PMID- 3458013
VI  - 10D
DP  - 1986
TI  - Screening for novel Type II restriction endonucleases.
PG  - 101
AB  - Besides various species of lactic acid bacteria (Lactobacillus, Pediococcus and
      Leuconostoc) we have screened 252 different non-pathogenic species of the
      genera Achromobacter, Acinetobacter, Alcaligenes, Brevibacterium, Enterobacter,
      Flavobacterium and Herpetosiphon for the presence of potentially new type II
      restriction endonucleases.  Among the above lactic acid bacteria screened, we
      could not detect any specific activities, whereas in all the other genera we
      found a high number of species producing different type II restriction
      endonucleases.
AU  - Kessler C
AU  - Bolton BJ
AU  - Comer MJ
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1986 10D: 101.

PMID- 3030890
VI  - 47
DP  - 1986
TI  - Specificity of restriction endonucleases and methylases - a review (Edition 2).
PG  - 1-153
AB  - The properties and sources of all known restriction endonucleases and
      methylases are listed.  The enzymes are cross-indexed (Table I), classified
      according to their recognition sequence homologies (Table II), and
      characterized within Table II by the cleavage and methylation positions, the
      number of recognition sites on the double-stranded DNA of the bacteriophages
      lambda, phiX174 and M13mp7, the viruses Ad2 and SV40, the plasmids pBR322 and
      pBR328, and the microorganisms from which they originate.  Other tabulated
      properties of the restriction endonucleases included relaxed specificities
      (integrated into Table II), the structure of the generated fragment ends (Table
      III), and the sensitivity to different kinds of DNA methylation (Table V).  In
      Table IV the conversion of two-and four-base 5'-protruding ends into new
      recognition sequences is compiled which is obtained by the fill-in reaction
      with Klenow fragment of the Escherichia coli DNA polymerase I or additional
      nuclease S1 treatment followed by ligation of the modified fragment termini.
      Interconversion of restriction sites generates novel cloning sites without the
      need of linkers.  This should improve the flexibility of genetic engineering
      experiments.  Table VI classifies the restriction methylases according to the
      nature of the methylated base(s) within their recognition sequences.  This
      table also comprises restriction endonucleases which are known to be inhibited
      or activated by the modified nucleotides.  The detailed sequences of those
      overlapping restriction sites are also included which become resistant to
      cleavage after the sequential action of corresponding restriction methylases
      and endonuclease.  By this approach large DNA fragments can be generated which
      is helpful in the construction of genomic libraries.  The data given in both
      Table IV and VI allow the design of novel sequence specificities.  These
      procedures complement the creation of universal cleavage specificities applying
      class IIS enzymes and bivalent DNA adapter molecules.
AU  - Kessler C
AU  - Holtke HJ
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1986 47: 1-153.

PMID- 2172084
VI  - 92
DP  - 1990
TI  - Specificity of restriction endonucleases and DNA modification methyltransferases - a review (Edition 3) .
PG  - 1-248
AB  - The properties and sources of all known class-I, class-II and class-III
      restriction endonucleases (ENases) and DNA modification methyltransferases
      (MTases) are listed and newly subclassified according to their sequence
      specificity.  In addition, the enzymes are distinguished in a novel manner
      according to sequence specificity, cleavage position and methylation
      sensitivity.  Furthermore, new nomenclature rules are proposed for
      unambiguously defined enzyme names.  In the various Tables, the enzymes are
      cross-indexed alphabetically according to their names (Table I), classified
      according to their recognition sequence homologies (Table II), and
      characterized within Table II by the cleavage and methylation positions, the
      number of recognition sites on the DNA of the bacteriophages lambda, PhiX174,
      and M13mp7, the viruses Ad2 and SV40, the plasmids pBR322 and pBR328, and the
      microorganisms from which they originate.  Other tabulated properties of the
      ENases include relaxed specificities (integrated within Table II), the
      structure of the generated fragment ends (Table III), interconversion of
      restriction sites (Table IV) and the sensitivity to different kinds of DNA
      methylation (Table V).  Table VI shows the influence of class-II MTases on the
      activity of class-II ENases with at least partially overlapping recognition
      sequences.  Table VII lists all class-II restriction endonucleases and MTases
      which are commercially available.
AU  - Kessler C
AU  - Manta V
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1990 92: 1-248.

PMID- 6282698
VI  - 16
DP  - 1981
TI  - SphI restriction map of bacteriophage lambda DNA.
PG  - 321-323
AB  - Upon reinvestigation, the number of cleavage sites for site-specific
      endonuclease SphI on lambda DNA was found to be six.  The SphI restriction map
      of the lambda cI857Sam7 genome was determined.
AU  - Kessler C
AU  - Nesch G
AU  - Brack R
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1981 16: 321-323.

PMID- 2985469
VI  - 33
DP  - 1985
TI  - Recognition sequences of restriction endonucleases and methylases - a review.
PG  - 1-102
AB  - The properties and sources of all known endonucleases and methylases acting site-specifically
      on DNA are listed. The enzymes are crossindexed (Table I), classified according to homologies
      within their recognition sequences (Table II), and characterized within Table II by the
      cleavage and methylation positions, the number of recognition sites on the DNA of the
      bacteriophages lambda, PhiX174 and M13mp7, the viruses Ad2 and SV40, the plasmids pBR322 and
      pBR328 and the microorganims from which they originate. Other tabulated properties of the
      restriction endonucleases include relaxed specificites (Table III), the structure of the
      restriction fragment ends (Table IV), and the sensitivity to different kinds of DNA
      methylation (Table V). Table VI classifies the methylases according to the nature of the
      methylated base(s) within their recognition sequences. This table also comprises those
      restriction endonucleases, which are known to be inhibited by the modified nucleotides.
      Furthermore, this review includes a restriction map of bacteriophage lambda DNA based on
      sequence data. Table VII lists the exact nucleotide positions of the cleavage sites, the
      length of the generated fragments ordered according to size, and the effects of the
      Escherichia coli dam- and dcm-coded methylases M Eco dam and M Eco dcmI on the particular
      recognition sites.
AU  - Kessler C
AU  - Neumaier PS
AU  - Wolf W
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1985 33: 1-102.

PMID- 26988054
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Aliiroseovarius crassostreae CV919-312, the Causative Agent of Roseovarius Oyster Disease (Formerly Juvenile Oyster Disease).
PG  - e00148-16
AB  - Aliiroseovarius crassostreae CV919-312 is a marine alphaproteobacterium and the causative
      agent of Roseovarius oyster disease. We announce here the draft genome
      sequence of A. crassostreae CV919-312 and identify potential virulence genes
      involved in pathogenicity.
AU  - Kessner L
AU  - Spinard E
AU  - Gomez-Chiarri M
AU  - Rowley DC
AU  - Nelson DR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00148-16.

PMID- 24503987
VI  - 2
DP  - 2014
TI  - Genome Sequences of Four Acinetobacter baumannii-A. calcoaceticus Complex Isolates from Combat-Related Infections Sustained in the Middle East.
PG  - e00026-14
AB  - Acinetobacter baumannii is among the most prevalent bacterial causes of combat-related
      infections on the battlefield. Antibiotic resistance and a poor
      understanding of the protective host immune responses make treatment difficult.
      Here, we report the genome sequences of four clinical Acinetobacter baumannii-A.
      calcoaceticus complex isolates exhibiting significant differences in virulence in
      a mouse sepsis model.
AU  - Ketter P
AU  - Guentzel MN
AU  - Chambers JP
AU  - Jorgensen J
AU  - Murray CK
AU  - Cap AP
AU  - Yu JJ
AU  - Eppinger M
AU  - Arulanandam BP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00026-14.

PMID- 18159947
VI  - 3
DP  - 2007
TI  - Patterns and implications of gene gain and loss in the evolution of Prochlorococcus.
PG  - E231
AB  - Prochlorococcus is a marine cyanobacterium that numerically dominates the
      mid-latitude oceans and is the smallest known oxygenic phototroph.
      Numerous isolates from diverse areas of the world's oceans have been
      studied and shown to be physiologically and genetically distinct. All
      isolates described thus far can be assigned to either a tightly clustered
      high-light (HL)-adapted clade, or a more divergent low-light (LL)-adapted
      group. The 16S rRNA sequences of the entire Prochlorococcus group differ
      by at most 3%, and the four initially published genomes revealed patterns
      of genetic differentiation that help explain physiological differences
      among the isolates. Here we describe the genomes of eight newly sequenced
      isolates and combine them with the first four genomes for a comprehensive
      analysis of the core (shared by all isolates) and flexible genes of the
      Prochlorococcus group, and the patterns of loss and gain of the flexible
      genes over the course of evolution. There are 1,273 genes that represent
      the core shared by all 12 genomes. They are apparently sufficient,
      according to metabolic reconstruction, to encode a functional cell. We
      describe a phylogeny for all 12 isolates by subjecting their complete
      proteomes to three different phylogenetic analyses. For each non-core
      gene, we used a maximum parsimony method to estimate which ancestor likely
      first acquired or lost each gene. Many of the genetic differences among
      isolates, especially for genes involved in outer membrane synthesis and
      nutrient transport, are found within the same clade. Nevertheless, we
      identified some genes defining HL and LL ecotypes, and clades within these
      broad ecotypes, helping to demonstrate the basis of HL and LL adaptations
      in Prochlorococcus. Furthermore, our estimates of gene gain events allow
      us to identify highly variable genomic islands that are not apparent
      through simple pairwise comparisons. These results emphasize the
      functional roles, especially those connected to outer membrane synthesis
      and transport that dominate the flexible genome and set it apart from the
      core. Besides identifying islands and demonstrating their role throughout
      the history of Prochlorococcus, reconstruction of past gene gains and
      losses shows that much of the variability exists at the "leaves of the
      tree," between the most closely related strains. Finally, the
      identification of core and flexible genes from this 12-genome comparison
      is largely consistent with the relative frequency of Prochlorococcus genes
      found in global ocean metagenomic databases, further closing the gap
      between our understanding of these organisms in the lab and the wild.
AU  - Kettler GC
AU  - Martiny AC
AU  - Huang K
AU  - Zucker J
AU  - Coleman ML
AU  - Rodrigue S
AU  - Chen F
AU  - Lapidus A
AU  - Ferriera S
AU  - Johnson J
AU  - Steglich C
AU  - Church GM
AU  - Richardson P
AU  - Chisholm SW
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2007 3: E231.

PMID- 9465029
VI  - 95
DP  - 1998
TI  - Real-time enzyme kinetics monitored by dual-color fluorescence cross-correlation spectroscopy.
PG  - 1416-1420
AB  - A method for sensitively monitoring enzyme kinetics and activities by using dual-color
      fluorescence cross-correlation spectroscopy is described.  This universal method enables the
      development of highly sensitive and precise assays for real-time kinetic analyses of any
      catalyzed cleavage or addition reaction, where a chemical linkage is formed or cleaved through
      an enzyme's action between two fluorophores that can be discriminated spectrally.  In this
      work, a homogeneous assay with restriction endonuclease EcoRI and a 66-bp double-stranded DNA
      containing the GAATTC recognition site and fluorophores at each 5' end is described.  The
      enzyme activity can be quantified down to the low picomolar range (>1.6 pM) where the rate
      constants are linearly dependent on the enzyme concentrations over two orders of magnitude.
      Furthermore, the reactions were monitored online at various initial substrate concentrations
      in the nanomolar range, and the reaction rates were clearly represented by the
      Michaelis-Menten equation with a KM of 14+/- 1 nM and a kcat of 4.6 +/- 0.2 min-1.  In
      addition to kinetic studies and activity determinations, it is proposed that enzyme assays
      based on the dual-color fluorescence cross-correlation spectroscopy will be very useful for
      high-throughput screening and evolutionary biotechnology.
AU  - Kettling U
AU  - Koltermann A
AU  - Schwille P
AU  - Eigen M
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1998 95: 1416-1420.

PMID- Not carried by PubMed...
VI  - 78
DP  - 1970
TI  - Host-controlled modification and restriction of foreign chromosomal and plasmid DNA in Shigella flexneri strains.
PG  - 51-58
AB  - The hsp gene (the genetic determinant for host-controlled restriction and
      modification) was transferred from an E. coli K12 strain into a S. flexneri
      strain, and in reverse the same gene from a Shigella strain was introduced into
      E. coli K12.  The presence of the heterologous hsp gene was tested by phage T5.
      It was demonstrated in interrupted mating experiments with the hybrids as
      recipients that the hsp hybrids had acquired changed recipient characters
      resembling those of the strains from which the hsp originated.
AU  - Ketyi J
AU  - Orskov F
PT  - Journal Article
TA  - Acta Path. Microbiol. Scand.
JT  - Acta Path. Microbiol. Scand.
SO  - Acta Path. Microbiol. Scand. 1970 78: 51-58.

PMID- 27340512
VI  - 11
DP  - 2016
TI  - Genome sequence of the organohalide-respiring Dehalogenimonas alkenigignens type  strain (IP3-3(T)).
PG  - 44
AB  - Dehalogenimonas alkenigignens IP3-3(T) is a strictly anaerobic, mesophilic, Gram  negative
      staining bacterium that grows by organohalide respiration, coupling the
      oxidation of H2 to the reductive dehalogenation of polychlorinated alkanes.
      Growth has not been observed with any non-polyhalogenated alkane electron
      acceptors. Here we describe the features of strain IP3-3(T) together with genome
      sequence information and its annotation. The 1,849,792 bp high-quality-draft
      genome contains 1936 predicted protein coding genes, 47 tRNA genes, a single
      large subunit rRNA (23S-5S) locus, and a single, orphan, small unit rRNA (16S)
      locus. The genome contains 29 predicted reductive dehalogenase genes, a large
      majority of which lack cognate genes encoding membrane anchoring proteins.
AU  - Key TA
AU  - Richmond DP
AU  - Bowman KS
AU  - Cho YJ
AU  - Chun J
AU  - da Costa MS
AU  - Rainey FA
AU  - Moe WM
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 44.

PMID- 22740660
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of the Volcano-Inhabiting Thermoacidophilic Methanotroph Methylacidiphilum fumariolicum Strain SolV.
PG  - 3729-3730
AB  - The draft genome of Methylacidiphilum fumariolicum SolV, a thermoacidophilic methanotroph of
      the phylum Verrucomicrobia, is presented. Annotation revealed
      pathways for one-carbon, nitrogen, and hydrogen catabolism and respiration
      together with central metabolic pathways. The genome encodes three orthologues of
      particulate methane monooxygenases. Sequencing of this genome will help in the
      understanding of methane cycling in volcanic environments.
AU  - Khadem AF et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3729-3730.

PMID- 27738037
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Four Salmonella enterica Strains Isolated from Turkey-Associated Sources.
PG  - e01122-16
AB  - We report the draft genomes of four Salmonella enterica isolates evaluated for the
      contribution of plasmids to virulence. Strains SE163A, SE696A, and SE710A
      carry plasmids demonstrated to facilitate plasmid-associated virulence, while
      SE819 is less virulent and has been used as a recipient for conjugation
      experiments to assess plasmid-encoded virulence mechanisms.
AU  - Khajanchi BK
AU  - Han J
AU  - Gokulan K
AU  - Zhao S
AU  - Gies A
AU  - Foley SL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01122-16.

PMID- 28104654
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Acidophilic, Halotolerant, and Iron/Sulfur-Oxidizing Acidihalobacter prosperus DSM 14174 (Strain V6).
PG  - e01469-16
AB  - The principal genomic features of Acidihalobacter prosperus DSM 14174 (strain V6) are
      presented here. This is a mesophilic, halotolerant, and iron/sulfur-oxidizing
      acidophile that was isolated from seawater at Vulcano, Italy. It has potential
      for use in biomining applications in regions where high salinity exists in the
      source water and ores.
AU  - Khaleque HN
AU  - Ramsay JP
AU  - Murphy RJ
AU  - Kaksonen AH
AU  - Boxall NJ
AU  - Watkin EL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01469-16.

PMID- 28546494
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Acidihalobacter ferrooxidans DSM 14175 (Strain V8), a New Iron- and Sulfur-Oxidizing, Halotolerant, Acidophilic Species.
PG  - e00413-17
AB  - The use of halotolerant acidophiles for bioleaching provides a biotechnical approach for the
      extraction of metals from regions where high salinity exists in
      the ores and source water. Here, we describe the first draft genome of a new
      species of a halotolerant and iron- and sulfur-oxidizing acidophile,
      Acidihalobacter ferrooxidans DSM 14175 (strain V8).
AU  - Khaleque HN
AU  - Ramsay JP
AU  - Murphy RJT
AU  - Kaksonen AH
AU  - Boxall NJ
AU  - Watkin ELJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00413-17.

PMID- 23792750
VI  - 1
DP  - 2013
TI  - Genome Sequence of Proteus mirabilis Strain PR03, Isolated from a Local Hospital  in Malaysia.
PG  - e00327-13
AB  - Proteus mirabilis is one of the pathogenic agents that commonly causes urinary tract
      infections among elderly individuals and long-term catheterized patients.
      Here, we report a draft genome sequence of Proteus mirabilis strain PR03
      (3,932,623 bp, with a G+C content of 38.6%) isolated from a local hospital in
      Malaysia.
AU  - Khalid MI
AU  - Teh LK
AU  - Lee LS
AU  - Zakaria ZA
AU  - Salleh MZ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00327-13.

PMID- 26044438
VI  - 3
DP  - 2015
TI  - Genome Sequence of Anoxybacillus flavithermus Strain AK1, a Thermophile Isolated  from a Hot Spring in Saudi Arabia.
PG  - e00604-15
AB  - Anoxybacillus flavithermus strain AK1 was isolated from Al-Ain Alhara, a thermal  hot spring
      located 50 km southeast of the city of Gazan, Saudi Arabia (16 degrees
      56'N, 43 degrees 15'E). The sequenced and annotated genome is 2,630,664 bp and
      encodes 2,799 genes.
AU  - Khalil A
AU  - Sivakumar N
AU  - Qarawi S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00604-15.

PMID- 25953177
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Martelella endophytica YC6887, Which Has Antifungal Activity Associated with a Halophyte.
PG  - e00366-15
AB  - Martelella endophytica YC6887, which produces antifungal compounds against fungal and oomycete
      pathogens, was isolated from the root of a halophyte, Rosa rugosa,
      collected at a tidal flat in South Korea. Its full-genome sequence shows that it
      is a circular DNA, without a plasmid, of about 4.8 Mb in size.
AU  - Khan A
AU  - Khan H
AU  - Chung EJ
AU  - Hossain MT
AU  - Chung YR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00366-15.

PMID- 29122873
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Ciprofloxacin-Resistant Salmonella enterica Strains with Multiple-Antibiotic Resistance, Isolated from Imported Foods.
PG  - e01222-17
AB  - We report here the draft genome sequences of 15 ciprofloxacin-resistant Salmonella enterica
      strains with resistance to multiple other antibiotics,
      including aminoglycosides, beta-lactams, sulfonamides, tetracycline, and
      trimethoprim, isolated from different imported foods. Three strains (NCTR75,
      NCTR281, and NCTR350) showed a high level of ciprofloxacin resistance compared to
      that of the other isolates. The whole-genome sequencing data provide a better
      understanding of the antibiotic resistance mechanisms and virulence properties of
      these isolates.
AU  - Khan AA
AU  - Khajanchi BK
AU  - Khan SA
AU  - Elkins CA
AU  - Foley SL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01222-17.

PMID- 29242224
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the First NDM-4-Producing Escherichia coli Strain (AK1), Isolated from Sewage Water of a North Indian Hospital.
PG  - e01366-17
AB  - We report here the draft genome sequence of the first isolated NDM-4-producing Escherichia
      coli strain, isolated from sewage water at a North Indian hospital.
      The genome has an assembly size of 5,076,053 bp, arranged in 129 contigs, with
      5,271 genes and a G+C content of 50.47%.
AU  - Khan AU
AU  - Beg AZ
AU  - Verma PK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01366-17.

PMID- 20071747
VI  - 38
DP  - 2010
TI  - A putative mobile genetic element carrying a novel type IIF restriction-modification system (PluTI).
PG  - 3019-3030
AB  - Genome comparison and genome context analysis were used to find a putative mobile element in
      the genome of Photorhabdus luminescens, an
      entomopathogenic bacterium. The element is composed of 16-bp direct
      repeats in the terminal regions, which are identical to a part of
      insertion sequences (ISs), a DNA methyltransferase gene homolog, two genes
      of unknown functions and an open reading frame (ORF) (plu0599) encoding a
      protein with no detectable sequence similarity to any known protein. The
      ORF (plu0599) product showed DNA endonuclease activity, when expressed in
      a cell-free expression system. Subsequently, the protein, named R.PluTI,
      was expressed in vivo, purified and found to be a novel type IIF
      restriction enzyme that recognizes 5'-GGCGC/C-3' (/ indicates position of
      cleavage). R.PluTI cleaves a two-site supercoiled substrate at both the
      sites faster than a one-site supercoiled substrate. The modification
      enzyme homolog encoded by plu0600, named M.PluTI, was expressed in
      Escherichia coli and shown to protect DNA from R.PluTI cleavage in vitro,
      and to suppress the lethal effects of R.PluTI expression in vivo. These
      results suggested that they constitute a restriction-modification system,
      present on the putative mobile element. Our approach thus allowed
      detection of a previously uncharacterized family of DNA-interacting
      proteins.
AU  - Khan F
AU  - Furuta Y
AU  - Kawai M
AU  - Kaminska KH
AU  - Ishikawa K
AU  - Bujnicki JM
AU  - Kobayashi I
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2010 38: 3019-3030.

PMID- 12065479
VI  - 70
DP  - 2002
TI  - Identification of Escherichia coli genes that are specifically expressed in a murine model of septicemic infection.
PG  - 3404-3412
AB  - Identification and characterization of bacterial genes that are induced during the disease
      process are important in understanding the molecular
      mechanism of disease and can be useful in designing antimicrobial drugs to
      control the disease. The identification of in vivo induced (ivi) genes of
      an Escherichia coli septicemia strain by using antibiotic-based in vivo
      expression technology is described. Bacterial clones resistant to
      chloramphenicol in vivo were recovered from the livers of infected mice.
      Most of the ivi clones were sensitive to chloramphenicol when grown in
      vitro. Using reverse transcription-PCR, it was demonstrated that selected
      ivi clones expressed cat in the livers of infected mice but not during in
      vitro growth. A total of 750 colonies were recovered after three
      successive rounds of in vivo selection, and 168 isolated ivi clones were
      sequenced. The sequence analysis revealed that 37 clones encoded
      hypothetical proteins found in E. coli K-12, whereas 10 clones contained
      genes that had no significant homology to DNA sequences in GenBank. Two
      clones were found to contain transposon-related functions. Other clones
      contained genes required for amino acid metabolism, anaerobic respiration,
      DNA repair, the heat shock response, and the cellular repressor of the SOS
      response. In addition, one clone contained the aerobactin biosynthesis
      gene iucA. Mutations were introduced in to seven of the identified ivi
      genes. An in vivo mouse challenge-competition assay was used to determine
      if the mutants were attenuated. The results suggested that these ivi genes
      were important for survival in vivo, and three of the seven mutant ivi
      clones were required for successful infection of mice.
AU  - Khan MA
AU  - Isaacson RE
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2002 70: 3404-3412.

PMID- 27811090
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Five Clinical Strains of Brucella melitensis Isolated from Patients Residing in Kuwait.
PG  - e01144-16
AB  - Human brucellosis is a neglected and underrecognized infection of widespread geographic
      distribution. Brucellosis is present on all inhabited continents and
      endemic in many areas of the world, including Kuwait and the Middle East. Here,
      we present draft genome assemblies of five Brucella melitensis strains isolated
      from brucellosis patients in Kuwait.
AU  - Khan MW
AU  - Habibi N
AU  - Shaheed F
AU  - Mustafa AS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01144-16.

PMID- 26868381
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Two Methicillin-Resistant Clinical Staphylococcus aureus Isolates.
PG  - e01396-15
AB  - Here, we report the draft genome sequences of two methicillin-resistant Staphylococcus aureus
      (MRSA) clinical isolates, hospital-associated perirectal
      isolate 32S (ST 239) from a colitis tracheostomy patient and community-associated
      MRSA isolate 42S (ST 772) from a hepatic-splenomegaly patient in Rawalpindi,
      Pakistan.
AU  - Khan S
AU  - Sung K
AU  - Iram S
AU  - Nawaz M
AU  - Xu J
AU  - Marasa B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01396-15.

PMID- 26272564
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Multidrug-Resistant Enterococcus faecium Clinical Isolate VRE3, with a Sequence Type 16 Pattern and Novel Structural Arrangement of  Tn1546.
PG  - e00871-15
AB  - Multidrug-resistant Enterococcus faecium has emerged as a nosocomial pathogen that may infect
      the body at various sites, including the gastrointestinal tract,
      and has serious implications in human health and disease. Here, we present the
      draft genome sequence of clinical strain VRE3, which exhibited a sequence type 16
      (ST16) pattern and carried truncated Tn1546, a mobile genetic element encoding a
      high level of vancomycin resistance.
AU  - Khan S
AU  - Sung K
AU  - Marasa B
AU  - Min S
AU  - Kweon O
AU  - Nawaz M
AU  - Cerniglia C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00871-15.

PMID- 24976892
VI  - 9
DP  - 2013
TI  - Complete genome sequence of Enterobacter sp. IIT-BT 08: A potential microbial strain for high rate hydrogen production.
PG  - 359-369
AB  - Enterobacter sp. IIT-BT 08 belongs to Phylum: Proteobacteria, Class: Gammaproteobacteria,
      Order: Enterobacteriales, Family: Enterobacteriaceae. The
      organism was isolated from the leaves of a local plant near the Kharagpur railway
      station, Kharagpur, West Bengal, India. It has been extensively studied for
      fermentative hydrogen production because of its high hydrogen yield. For further
      enhancement of hydrogen production by strain development, complete genome
      sequence analysis was carried out. Sequence analysis revealed that the genome was
      linear, 4.67 Mbp long and had a GC content of 56.01%. The genome properties
      encode 4,393 protein-coding and 179 RNA genes. Additionally, a putative pathway
      of hydrogen production was suggested based on the presence of formate hydrogen
      lyase complex and other related genes identified in the genome. Thus, in the
      present study we describe the specific properties of the organism and the
      generation, annotation and analysis of its genome sequence as well as discuss the
      putative pathway of hydrogen production by this organism.
AU  - Khanna N et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 9: 359-369.

PMID- 23405333
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Opportunistic Human Pathogen Morganella morganii SC01.
PG  - e00051-12
AB  - We report the 4.1-Mb draft genome sequence of Morganella morganii SC01, a
      gammaproteobacterium, isolated from an Indian human fecal sample.
AU  - Khatri I
AU  - Dureja C
AU  - Raychaudhuri S
AU  - Subramanian S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00051-12.

PMID- 24309733
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Plant Growth-Promoting Rhizobacterium Pantoea sp. Strain AS-PWVM4.
PG  - e00947-13
AB  - Nonpathogenic Pantoea spp. have been shown to confer biofertilizer and biocontrol activities,
      indicating their potential for increasing crop yield. Herein, we
      provide the high-quality genome sequence of Pantoea sp. strain AS-PWVM4, a
      Gram-negative motile plant growth-promoting rhizobacterium isolated from a
      pomegranate plant. The 4.9-Mb genome contains genes related to plant growth
      promotion and the synthesis of siderophores.
AU  - Khatri I
AU  - Kaur S
AU  - Devi U
AU  - Kumar N
AU  - Sharma D
AU  - Subramanian S
AU  - Saini AK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00947-13.

PMID- 23105089
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Rhodovulum sp. Strain PH10, a Phototrophic Alphaproteobacterium Isolated from a Soil Sample of Mangrove of Namkhana, India.
PG  - 6363
AB  - We report the 4.8-Mb draft genome of Rhodovulum sp. strain PH10, a phototrophic bacterium
      belonging to class Alphaproteobacteria, isolated from a soil sample
      collected from the mangrove forest of Namkhana in India. This genome is the first
      from the genus Rhodovulum and will lead to a better understanding of the
      genes/pathways involved in activities like phototrophic growth and nitrogen
      fixation in this group of bacteria.
AU  - Khatri I
AU  - Nupur KS
AU  - Subramanian S
AU  - Pinnaka AK
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6363.

PMID- 23409257
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of an Alphaproteobacterium, Caenispirillum salinarum AK4(T), Isolated from a Solar Saltern.
PG  - e00199-12
AB  - We report the 4.9-Mb genome sequence of Caenispirillum salinarum AK4(T) isolated  from a
      sediment sample collected from a solar saltern at Kakinada, Andhra
      Pradesh, India.
AU  - Khatri I
AU  - Singh A
AU  - Korpole S
AU  - Pinnaka AK
AU  - Subramanian S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00199-12.

PMID- 29700139
VI  - 6
DP  - 2018
TI  - Complete Chromosome and Plasmid Sequences of Two Plant Pathogens, Dickeya solani  Strains D s0432-1 and PPO 9019.
PG  - e00233-18
AB  - Dickeya solani species are emerging bacterial pathogens of Solanum tuberosum Here, we announce
      the complete genome sequences of two strains, Dickeya solani D
      s0432-1 and PPO 9019. Strain PPO 9019 represents the first described member of
      the genus Dickeya with an extrachromosomal genetic element.
AU  - Khayi S
AU  - Blin P
AU  - Chong TM
AU  - Chan KG
AU  - Faure D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00233-18.

PMID- 27942352
VI  - 11
DP  - 2016
TI  - Complete genome anatomy of the emerging potato pathogen Dickeya solani type strain IPO 2222T.
PG  - 87
AB  - Several species of the genus Dickeya provoke soft rot and blackleg diseases on a  wide range
      of plants and crops. Dickeya solani has been identified as the
      causative agent of diseases outbreaks on potato culture in Europe for the last
      decade. Here, we report the complete genome of the D. solani IPO 2222T. Using
      PacBio and Illumina technologies, a unique circular chromosome of 4,919,833 bp
      was assembled. The G + C content reaches 56% and the genomic sequence contains
      4,059 predicted proteins. The ANI values calculated for D. solani IPO 2222T vs.
      other available D. solani genomes was over 99.9% indicating a high genetic
      homogeneity within D. solani species.
AU  - Khayi S
AU  - Blin P
AU  - Chong TM
AU  - Chan KG
AU  - Faure D
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 87.

PMID- 29371347
VI  - 6
DP  - 2018
TI  - Complete Genome Sequences of the Plant Pathogens Dickeya solani RNS 08.23.3.1.A and Dickeya dianthicola RNS04.9.
PG  - e01447-17
AB  - Dickeya spp. are bacterial pathogens causing soft-rot and blackleg diseases on a  wide range
      of ornamental plants and crops. In this paper, we announce the PacBio
      complete genome sequences of the plant pathogens Dickeya solani RNS 08.23.3.1.A
      (PRI3337) and Dickeya dianthicola RNS04.9.
AU  - Khayi S
AU  - Blin P
AU  - Chong TM
AU  - Robic K
AU  - Chan KG
AU  - Faure D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01447-17.

PMID- 24482527
VI  - 2
DP  - 2014
TI  - Genome Sequence of the Emerging Plant Pathogen Dickeya solani Strain RNS 08.23.3.1A.
PG  - e01270-13
AB  - Here we present the genome sequence of Dickeya solani strain RNS 08.23.3.1A (PRI3337),
      isolated from Solanum tuberosum. Dickeya solani, recently described on
      potato cultures in Europe, is a proposed new taxon closely related to the Dickeya
      dianthicola and Dickeya dadantii species.
AU  - Khayi S
AU  - Mondy S
AU  - Beury-Cirou A
AU  - Moumni M
AU  - Helias V
AU  - Faure D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01270-13.

PMID- 25635020
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of the Three Pectobacterium-Antagonistic Bacteria Pseudomonas brassicacearum PP1-210F and PA1G7 and Bacillus simplex BA2H3.
PG  - e01497-14
AB  - Pectobacterium spp. are bacterial pathogens causing soft rot diseases on a wide range of
      plants and crops. We present in this paper the draft genome sequences of
      three bacterial strains, Pseudomonas brassicacearum PP1-210F and PA1G7 and
      Bacillus simplex BA2H3, which exhibit antagonistic activities against the
      Pectobacterium plant pathogens.
AU  - Khayi S
AU  - Raoul-des-Essarts Y
AU  - Mondy S
AU  - Moumni M
AU  - Helias V
AU  - Beury-Cirou A
AU  - Faure D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01497-14.

PMID- 25297844
VI  - 143
DP  - 2015
TI  - Genomic overview of the phytopathogen Pectobacterium wasabiae strain RNS 08.42.1A suggests horizontal acquisition of quorum-sensing genes.
PG  - 241-252
AB  - The blackleg and soft-rot diseases caused by pectinolytic enterobacteria such as
      Pectobacterium and Dickeya are major causes of losses affecting potato crop in the field and
      upon storage. In this work, we report the isolation, characterization and genome analysis of
      the Pectobacterium wasabiae (formerly identified as Pectobacterium carotovorum subsp.
      carotovorum) strain RNS 08.42.1A, that has been isolated from a Solanum tuberosum host plant
      in France. Comparative genomics with 3 other P. wasabiae strains isolated from potato plants
      in different areas in North America and Europe, highlighted both a strong similarity at the
      whole genome level (ANI > 99 %) and a conserved synteny of the virulence genes. In addition,
      our analyses evidenced a robust separation between these four P. wasabiae strains and the type
      strain P. wasabiae CFBP 3304(T), isolated from horseradish in Japan. In P. wasabiae RNS
      08.42.1A, the expI and expR nucleotidic sequences are more related to those of some
      Pectobacterium atrosepticum and P.
      carotovorum strains (90 % of identity) than to those of the other potato P.
      wasabiae strains (70 to 74 % of identity). This could suggest a recruitment of these genes in
      the P. wasabiae strain RNS 08.42.1A by an horizontal transfer between pathogens infecting the
      same potato host plant.
AU  - Khayi S
AU  - Raoul-des-Essarts Y
AU  - Quetu-Laurent A
AU  - Moumni M
AU  - Helias V
AU  - Faure D
PT  - Journal Article
TA  - Genetica
JT  - Genetica
SO  - Genetica 2015 143: 241-252.

PMID- 23209210
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Staphylococcus aureus ST672, an Emerging Disease Clone from India.
PG  - 6946-6947
AB  - We report the draft genome sequence of methicillin-resistant Staphylococcus aureus (MRSA)
      strain ST672, an emerging disease clone in India, from a septicemia
      patient. The genome size is about 2.82 Mb with 2,485 open reading frames (ORFs).
      The staphylococcal cassette chromosome mec (SCCmec) element (type V) and immune
      evasion cluster appear to be different from those of strain ST772 on preliminary
      examination.
AU  - Khedkar S
AU  - Prabhakara S
AU  - Loganathan RM
AU  - Chandana S
AU  - Gowda M
AU  - Arakere G
AU  - Seshasayee ASN
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6946-6947.

PMID- 24558239
VI  - 2
DP  - 2014
TI  - Draft Genome Sequencing of Methanobrevibacter oralis Strain JMR01, Isolated from  the Human Intestinal Microbiota.
PG  - e00073-14
AB  - Methanobrevibacter oralis, an anaerobic methanogenic archaeon, has been previously isolated
      from the human oral cavity. Here, sequencing a stool isolate
      (strain JMR01) yielded a 2.065-Mb genome with a 27.78% G+C content containing a
      total of 2,042 open reading frames and 3 clusters of regularly interspaced short
      palindromic repeat (CRISPR) loci with associated Cas proteins.
AU  - Khelaifia S
AU  - Garibal M
AU  - Robert C
AU  - Raoult D
AU  - Drancourt M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00073-14.

PMID- 24459264
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of a Human-Associated Isolate of Methanobrevibacter arboriphilicus, the Lowest-G+C-Content Archaeon.
PG  - e01181-13
AB  - We report the draft genome sequence of Methanobrevibacter arboriphilicus strain ANOR1,
      isolated from the human gut. Its 2.21-Mb genome exhibits a 25.46% G+C
      content, the lowest value among archaea. The genome of M. arboriphilicus contains
      a total of 2,111 open reading frames and three clusters of regularly interspaced
      short palindromic repeat (CRISPR) loci with associated Cas proteins.
AU  - Khelaifia S
AU  - Garibal M
AU  - Robert C
AU  - Raoult D
AU  - Drancourt M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01181-13.

PMID- 22307287
VI  - 78
DP  - 2012
TI  - Complete Genome Sequence of Virulence-Enhancing Siphophage VHS1 from Vibrio harveyi.
PG  - 2790-2796
AB  - Vibrio harveyi siphophage 1 (VHS1) is a tailed phage with an icosahedral head of
      approximately 66 nm in diameter and an unornamented, flexible tail of
      approximately 153 nm in length. When Vibrio harveyi 1114GL is lysogenized with
      VHS1, its virulence for the black tiger shrimp (Penaeus monodon) increases by
      more than 100 times, and this coincides with production of a toxin(s) associated
      with shrimp hemocyte agglutination. Curiously, the lysogen does not show
      increased virulence for the whiteleg shrimp (Penaeus [Litopenaeus] vannamei).
      Here we present and annotate the complete, circular genome of VHS1 (81,509 kbp;
      GenBank accession number JF713456). By software analysis, the genome contains 125
      putative open reading frames (ORFs), all of which appear to be located on the
      same DNA strand, similar to the case for many other bacteriophages. Most of the
      putative ORFs show no significant homology to known sequences in GenBank. Notable
      exceptions are ORFs for a putative DNA polymerase and putative phage structural
      proteins, including a portal protein, a phage tail tape measure protein, and a
      phage head protein. The last protein was identified as a component of the
      species-specific toxin mixture described above as being associated with
      agglutination of hemocytes from P. monodon.
AU  - Khemayan K
AU  - Prachumwat A
AU  - Sonthayanon B
AU  - Intaraprasong A
AU  - Sriurairatana S
AU  - Flegel TW
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2012 78: 2790-2796.

PMID- 4876102
VI  - 31
DP  - 1966
TI  - The specificity of DNA-methylase in T2-phage infected E. coli B cells.
PG  - 405-415
AB  - Activity of the enzymatic system responsible for DNA methylation considerably increases after
      infection of E. coli B cells with T2 phage.  The increase is inhibited by chloramphenicol.
      The non-infected cells contain no inhibitor of DNA methylation, and the infected ones - no
      activator of this reaction.  Hence, there is T2 phage induced production of phage DNA
      methylase along with the synthesis of other enzymes.  Enzymatic preparations from the
      non-infected and infected bacteria are capable of methylating heterologous (thymus, M.
      lysodeikticus etc.) DNA but do not react with DNA from non-infected E. coli and from T2 and T4
      phages.  However, both the enzymes methylate DNA of E. coli and T2 phage if it was
      incompletely methylated in intact cells prior to isolation.  Partially methylated DNA loses
      its methyl-acceptor ability with respect to the enzyme of non-infected cells after incubation
      in vitro with the enzymatic system from infected cells.  Hence, the non-infected and the
      infected cell methylases both react with the same combinations of nucleotides in E. coli and
      T2 phage DNA, i.e., have the same specificity.  It is proposed, that methylated nucleotides in
      DNA have something to do with the interaction with RNA-polymerase.  RNA prior to, as well as
      after infection with T2 phage being synthesized with the same RNA-polymerase, bacterial as
      well as phage DNA ought to contain the same sequences of methylated nucleotides.  This
      explains the observed identity of specificities of the T2-phage induced methylase and of that
      existing prior to infection.
AU  - Khesin RB
AU  - Bogdanova ES
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1966 31: 405-415.

PMID- 28428314
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of the Original Escherichia coli Isolate, Strain NCTC86.
PG  - e00243-17
AB  - Escherichia coli is the most well-studied bacterium and a common colonizer of the lower
      mammalian gastrointestinal tract. We report here the complete genome
      sequence of the original Escherichia coli isolate, strain NCTC86, which was
      described by Theodor Escherich, for whom the genus is named.
AU  - Khetrapal V
AU  - Mehershahi KS
AU  - Chen SL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00243-17.

PMID- 28495766
VI  - 5
DP  - 2017
TI  - Ten Genome Sequences of Human and Livestock Isolates of Bacillus anthracis from the Country of Georgia.
PG  - e00256-17
AB  - Bacillus anthracis causes the acute fatal disease anthrax, is a proven biological weapon, and
      is endemic in Georgia, where human and animal cases are reported
      annually. Here, we present whole-genome sequences of 10 historical B. anthracis
      strains from Georgia.
AU  - Khmaladze E
AU  - Dzavashvili G
AU  - Chanturia G
AU  - Nikolich MP
AU  - Chain PSG
AU  - Johnson SL
AU  - Imnadze P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00256-17.

PMID- 23814105
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Methylomicrobium buryatense Strain 5G, a Haloalkaline-Tolerant Methanotrophic Bacterium.
PG  - e00053-13
AB  - Robust growth of the gammaproteobacterium Methylomicrobium buryatense strain 5G on methane
      makes it an attractive system for CH4-based biocatalysis. Here we
      present a draft genome sequence of the strain that will provide a valuable
      framework for metabolic engineering of the core pathways for the production of
      valuable chemicals from methane.
AU  - Khmelenina VN et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00053-13.

PMID- 9451440
VI  - 275
DP  - 1998
TI  - Stalling of human DNA (cytosine-5) methyltransferase at single-strand conformers from a site of dynamic mutation.
PG  - 67-79
AB  - Single-strand conformers from the C-rich strand of the triplet repeat at the FMR-1 locus are
      rapidly and selectively methylated by the human DNA (cytosine-5) methyltransferase.  The
      apparent affinity of the enzyme for the FMR-1 SSC is about tenfold higher than it is for a
      control Watson-Crick paired duplex.  The de novo methylation rate for the SSC is over 150-fold
      higher than the de novo rate for the control duplex.  Methylation of what is generally called
      a hemi-methylated duplex occurs with a rate enhancement of over 100-fold, while methylation of
      what can be viewed as a hemi-methylated FMR-1 SSC is actually slower than the de novo rate.
      The pronounced inhibition of the methyltransferase by the methylated SSC sugggests that the
      enzyme has a higher affinity for the methylated product of its reaction with the SSC than it
      has for the unmethylated SSC substrate.  Gel retardation studies show that the
      methyltransferase binds selectively to SSCs from the C-rich strand of the FMR-1 triplet
      repeat.  This suggests a two-step stalling process in which the human methyltransferase first
      selectively methylates and subsequently stalls at the C-rich strand SSC.  Stalling may reflect
      the inability of the enzyme to release a DNA product that is fixed in a conformation
      resembling its transition state by the unusual structure of the substrate.  In particular, the
      data suggest that DNA methyltransferase may physically participate in biological processes
      that lead to dynamic mutation at FMR-1.  In general, the data raise the possibility that a
      two-step stalling process occurs at secondary structures associated with chromosome
      instability, chromosome remodelling, viral replication or viral integration and may account
      for the local hypermethylation and global hypomethylation associated with viral and non-viral
      tumorigenesis.
AU  - Kho MR
AU  - Baker DJ
AU  - Laayoun A
AU  - Smith SS
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1998 275: 67-79.

PMID- 3029578
VI  - 0
DP  - 1986
TI  - Purification and properties of two restriction endonucleases from Bacillus subtilis.
PG  - 23-25
AB  - Two restriction endonucleases, Bsu1532I and Bsu1854I, have been isolated from
      Bac. subtilis 1532 and 1854 cells and characterized.  The first of them,
      Bsu1532I, recognizes and digests the tetranucleotide palindrome sequence GC^GC,
      while Bsu1854I recognizes and digests the degenerate hexanucleotide sequence
      GPuGCPy^C.  The optimum conditions were determined for both enzymes, and the
      influence of various cofactors on the reactions catalyzed by them were studied.
AU  - Kholmina GV
AU  - Rebentish BA
AU  - Kozlovskii Y-E
AU  - Sorokin AV
AU  - Goldenberg DS
AU  - Prozorov AA
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1986 0: 23-25.

PMID- 6253247
VI  - 253
DP  - 1980
TI  - Isolation and characterization of a new site-specific endonuclease, EcoRV.
PG  - 495-497
AB  - None
AU  - Kholmina GV
AU  - Rebentish BA
AU  - Skoblov YS
AU  - Mironov AA
AU  - Yankovskii NK
AU  - Kozlov YI
AU  - Glatmann LI
AU  - Moroz AF
AU  - Debabov VG
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1980 253: 495-497.

PMID- 11376944
VI  - 269
DP  - 2001
TI  - The shuffling function of resolvases.
PG  - 121-130
AB  - Redistribution (shuffling) of genetic material between replicons requires
      consecutive recombination at four points, two of which (X, X') are
      involved in the replicon fusion and the other two (Y, Y'), in the
      cointegrate resolution. The fusion of replicons by bacterial resolvases
      makes the second recombination round at sites Y and Y' problematic because
      of the high probability of the reverse reaction. Structural differences of
      the res sites recognized by resolvase could delay the reverse reaction,
      thus enhancing the probability of recombination at sites Y, Y', but the
      direct reaction ensuring it (i.e. the fusion of replicons via different
      res sites) has not been described yet. Here, a genetic system to test
      intermolecular recombination at heterogeneous res sites has been
      developed. The system was based on the res site (RS2) of the novel
      resolution system, cinH-RS2, encoded by pKLH2, pKLH204 and pKLH205. As its
      partner, the res site of RP4 located in the par locus, the res site of
      transposon gammadelta or Tn1721, the incomplete site RS1 consisting only
      of the (crossover) subsite resI also found in pKLH2/204/205 and others
      were used. Except for the pairing of RS2 x gammadelta res, recombination
      was observed in each case even when the homology shared by partners did
      not exceed 35% (as in RS2 x par). In the latter case, the presence in cis
      of an additional, enhancer-like-acting element was required. Pairing of
      crossover subsites during site-specific recombination occurred in either
      orientation, depending on the structure of res partners and the kind of
      resolvase acting on the sites. With the complete res sites, the
      antiparallel alignment resulted in the production of an unusual res having
      the accessory subsites II and III at both sides of I, and a res lacking II
      and III. The wide range of frequencies was observed not only in the fusion
      formation but also in the dissociation of the resulting cointegrates.
      Hence, the resolvase-mediated interreplicon exchange of the DNA segments
      by fusion via an inefficient reaction (at sites X, X') and dissociation
      via an efficient one (at sites Y, Y') become possible.
AU  - Kholodii G
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 2001 269: 121-130.

PMID- 27494913
VI  - 71
DP  - 2016
TI  - Tracking inter-institutional spread of NDM and identification of a novel NDM-positive plasmid, pSg1-NDM, using next-generation sequencing approaches.
PG  - 3081-3089
AB  - OBJECTIVES: Owing to gene transposition and plasmid conjugation, New Delhi
      metallo-beta-lactamase (NDM) is typically identified among varied
      Enterobacteriaceae species and STs. We used WGS to characterize the chromosomal
      and plasmid molecular epidemiology of NDM transmission involving four
      institutions in Singapore. METHODS: Thirty-three Enterobacteriaceae isolates
      (collection years 2010-14) were sequenced using short-read
      sequencing-by-synthesis and analysed. Long-read single molecule, real-time
      sequencing (SMRTS) was used to characterize genetically a novel plasmid pSg1-NDM
      carried on Klebsiella pneumoniae ST147. RESULTS: In 20 (61%) isolates, blaNDM was
      located on the pNDM-ECS01 plasmid in the background of multiple bacterial STs,
      including eight K. pneumoniae STs and five Escherichia coli STs. In six (18%)
      isolates, a novel blaNDM-positive plasmid, pSg1-NDM, was found only in K.
      pneumoniae ST147. The pSg1-NDM-K. pneumoniae ST147 clone (Sg1-NDM) was fully
      sequenced using SMRTS. pSg1-NDM, a 90 103 bp IncR plasmid, carried genes
      responsible for resistance to six classes of antimicrobials. A large portion of
      pSg1-NDM had no significant homology to any known plasmids in GenBank. pSg1-NDM
      had no conjugative transfer region. Combined chromosomal-plasmid phylogenetic
      analysis revealed five clusters of clonal bacterial NDM-positive plasmid
      transmission, of which two were inter-institution clusters. The largest
      inter-institution cluster involved six K. pneumoniae ST147-pSg1-NDM isolates.
      Fifteen patients were involved in transmission clusters, of which four had ward
      contact, six had hospital contact and five had an unknown transmission link.
      CONCLUSIONS: A combined sequencing-by-synthesis and SMRTS approach can determine
      effectively the transmission clusters of blaNDM and genetically characterize
      novel plasmids. Plasmid molecular epidemiology is important to understanding NDM
      spread as blaNDM-positive plasmids can conjugate extensively across species and
      STs.
AU  - Khong WX et al
PT  - Journal Article
TA  - J. Antimicrob. Chemother.
JT  - J. Antimicrob. Chemother.
SO  - J. Antimicrob. Chemother. 2016 71: 3081-3089.

PMID- Not included in PubMed...
VI  - 177
DP  - 1984
TI  - Restriction endonucleases from Bifidobacterium bifidum.
PG  - 57-60
AB  - Three restriction endonucleases, BbiI, BbiII and BbiIII, have been isolated
      from Bifidobacterium bifidum.  The recognition and cleavage specificity of
      BbiII was determined to be 5'-GR^CGYC-3', identical to that of AcyI isolated
      from a cyanobacterium Anabaena cylindrica.  The other two enzymes, BbiI and
      BbiIII, were found to be isoschizomers of PstI and XhoI, respectively.
AU  - Khosaka T
AU  - Kiwaki M
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1984 177: 57-60.

PMID- 6098530
VI  - 31
DP  - 1984
TI  - BinI: A new site-specific endonuclease from Bifidobacterium infantis.
PG  - 251-255
AB  - A new restriction endonuclease, BinI, from Bifidobacterium infantis 659 has
      been isolated.  By mapping and sequencing of the cleavage sites on SV40 DNA, it
      was deduced that BinI recognizes the asymmetric pentanucleotide sequence
      5'-GGATCNNNN^-3'3'-CCTAGNNNNN^5'and cleaves at the sites indicated by the
      arrows, generating mononucleotide 5'-terminal extensions.  BinI is a member of
      a unique class of Type-II restriction endonucleases which recognize a specific
      but asymmetric sequence and cleave at a site several bases away.
AU  - Khosaka T
AU  - Kiwaki M
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1984 31: 251-255.

PMID- 6315484
VI  - 163
DP  - 1983
TI  - Two site-specific endonucleases BinSI and BinSII from Bifidobacterium infantis.
PG  - 170-174
AB  - Two site-specific endonucleases, BinSI and BinSII, were isolated from
      Bifidobacterium infantis S76e.  BinSI was found to be an isoschizomer of EcoRII, while
      BinSII was shown to have the same sequence and cutting specificity as BbeI, 5'-
      GGCGCC-3'.  Both BinSII- and BbeI-generated DNA fragments could be ligated with
      HaeII-generated DNA fragments.
AU  - Khosaka T
AU  - Kiwaki M
AU  - Rak B
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1983 163: 170-174.

PMID- 6282709
VI  - 17
DP  - 1982
TI  - A new site-specific endonuclease BbeI from Bifidobacterium breve.
PG  - 117-122
AB  - A new site-specific endonuclease, BbeI, has been partially purified from the
      anerobic bacterium, Bifidobacterium breve.  BbeI recognizes the hexanucleotide
      sequence5'-GGCGC^C-3' 3'-C^CGCGG-5'and cleaves it at the sites indicated by the
      arrows, producing 3'-cohesive termini four bases long.
AU  - Khosaka T
AU  - Sakurai T
AU  - Takahashi H
AU  - Saito H
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1982 17: 117-122.

PMID- 23957912
VI  - 5
DP  - 2013
TI  - Comparing the genomes of Helicobacter pylori clinical strain UM032 and Mice-adapted derivatives.
PG  - 25
AB  - Background: Helicobacter pylori is a Gram-negative bacterium that persistently infects the
      human stomach inducing chronic inflammation.
      The exact mechanisms of pathogenesis are still not completely
      understood. Although not a natural host for H. pylori, mouse infection
      models play an important role in establishing the immunology and
      pathogenicity of H. pylori. In this study, for the first time, the
      genome sequences of clinical H. pylori strain UM032 and mice-adapted
      derivatives, 298 and 299, were sequenced using the PacBio Single
      Molecule, Real-Time (SMRT) technology.
      Result: Here, we described the single contig which was achieved for
      UM032 (1,599,441 bp), 298 (1,604,216 bp) and 299 (1,601,149 bp).
      Preliminary analysis suggested that methylation of H. pylori genome
      through its restriction modification system may be determinative of its
      host specificity and adaptation.
      Conclusion: Availability of these genomic sequences will aid in
      enhancing our current level of understanding the host specificity of H.
      pylori.
AU  - Khosravi Y
AU  - Rehvathy V
AU  - Wee WY
AU  - Wang S
AU  - Baybayan P
AU  - Singh S
AU  - Ashby M
AU  - Ong J
AU  - Amoyo AA
AU  - Seow SW
AU  - Choo SW
AU  - Perkins T
AU  - Chua EG
AU  - Tay A
AU  - Marshall BJ
AU  - Loke MF
AU  - Goh KL
AU  - Pettersson S
AU  - Vadivelu J
PT  - Journal Article
TA  - Gut Pathog.
JT  - Gut Pathog.
SO  - Gut Pathog. 2013 5: 25.

PMID- 404125
VI  - 232
DP  - 1977
TI  - 2,6-Diaminopurine - a new adenine-replacing base in the DNA of cyanophage S-2.
PG  - 965-968
AB  - By now only some of the physicochemical properties of extremely few viruses of
      blue-green algae-cyanophages-have been studied.  Unfortunately, the information
      on the nucleotide composition of the DNA of cyanophages is based only on a
      determination of the GC content according to the melting point and buoyant
      density.  However, this does not permit a correct determination even of the
      composition, if the DNA contains unusual and minor bases.  Unusual bases, which
      can entirely replace cytosine or thymine residues, have been found in the DNA
      of many bacterial phages.  The DNAs of cyanophages have not been studied at all
      in this respect.  Moreover, it is unknown whether these DNAs contain the
      modified residues of the usual bases, characterisitic of many prokaryotes and
      responsible for host modification and restriction.  It is also unclear whether
      host restriction and modification analogous to that in bacteria exist in
      blue-green algae and cyanophages.  Therefore, a study of the intrinsic nature
      of the bases in the DNA of cyanophages is of special interest.  In this work we
      studied the composition and some physicochemical properties of the DNA of a new
      cyanophage S-2, which lyses the blue-green alga Synechococcus sp. 698 (from the
      collection of the Biological Institute of Leningrad University).  We isolated
      this cyanophage from aquatic samples, taken in the environs of Leningrad.  It
      consists of an icosahedral head 56 nm in diameter and a flexible,
      noncontractile tail process 120 nm long.  The phage was concentrated by
      chromatography on DEAE-cellulose (Whatman DE32) and purified by centrifuging in
      a CsCl gradient.  The cyanophage DNA was isolated by a phenol method.
AU  - Khudyakov IY
AU  - Kirnos MD
AU  - Aleksandrushkina NI
AU  - Vanyushin BF
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1977 232: 965-968.

PMID- 676082
VI  - 88
DP  - 1978
TI  - Cyanophage S-2L contains DNA with 2,6-diaminopurine substituted for adenine.
PG  - 8-18
AB  - Cyanophage S-2L, which lyses some strains of unicellular cyanobacteria of the
      genus Synechococcus, has a polyhedral head 56 nm in diameter and a flexible
      noncontractile tail 120 nm in length.  In S-2L phage DNA, 2,6-diaminopurine is
      completely substituted for adenine.  This base and the corresponding
      deoxyribonucleoside have been isolated from acid and enzymatic hydrolyzates of
      the phage DNA, respectively, and have been identified according to optical and
      chromatographic behavior.  S-2L phage DNA is linear and double-stranded and has
      a molecular weight of 26 to 28,000000.  The buoyant density of this DNA is CsCl
      is 1.731 g/cm3.  2,6-Diaminopurine stabilizes the secondary structure of phage
      DNA, i.e., the melting temperature of the latter (Tm is 85.6 degrees in
      0.1xSSC) is 3.6 degrees higher than that of the usual adenine-containing DNA of
      equivalent base composition.
AU  - Khudyakov IY
AU  - Kirnos MD
AU  - Alexandrushkina NI
AU  - Vanyushin BF
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1978 88: 8-18.

PMID- 16233156
VI  - 93
DP  - 2002
TI  - Genetic manipulation system in propionibacteria.
PG  - 1-8
AB  - Members of the genus Propionibacterium are widely used in the production of vitamin B12'
      tetrapyrrole compounds, and propionic acid
      as well as in the probiotic and cheese industries. Shuttle vectors were
      developed in propionibacteria using replicons from endogenous plasmids
      in Propionibacterium and Escherichia coli and an appropriate selection
      marker. Efficient transformation was achieved using the shuttle
      vector prepared from Propionibacterium freudenreichii to overcome the
      high restriction modification system in propionibacteria. Expression
      vectors with native promoters for use in propionibacteria were also
      developed. Using this system, cholesterol oxidase, which is used as a
      diagnostic enzyme, was produced in P freudenreichii. Genes involved in
      5-aminolevulinic acid (ALA) and vitamin 13, biosynthesis in
      propionibacteria were isolated. ALA in propionibacteria could be
      synthesized via both the C4 pathway (condensation of glycine and
      succinyl CoA) and the C5 pathway (from glutamate). The hemA gene
      encoding ALA synthase from Rhodobacter spheroides, was overexpressed
      and ALA accumulated in P. freudenreichii. Thus, the genetic manipulation
      systems in propionibacteria will facilitate genetic studies of
      probioties and the vitamin B-12 biosynthetic pathway.
AU  - Kiatpapan P
AU  - Murooka Y
PT  - Journal Article
TA  - J. Biosci. Bioeng.
JT  - J. Biosci. Bioeng.
SO  - J. Biosci. Bioeng. 2002 93: 1-8.

PMID- 29946312
VI  - 9
DP  - 2018
TI  - Streptomyces spp. From Ethiopia Producing Antimicrobial Compounds: Characterization via Bioassays, Genome Analyses, and Mass Spectrometry.
PG  - 1270
AB  - A total of 416 actinomycete cultures were isolated from various unique
      environments in Ethiopia and tested for bioactivity. Six isolates with pronounced
      antimicrobial activity were chosen for taxonomic identification and further
      investigation. Morphological and cultural properties of the isolates were found
      to be consistent with those of the genus Streptomyces, which was further
      confirmed by phylogenetic analysis based on 16S rRNA gene sequences. One of the
      isolates, designated Streptomyces sp. Go-475, which displayed potent activity
      against both pathogenic yeasts and Gram-positive bacteria, was chosen for further
      investigation. Metabolite profiles and bioactivity of Go-475 incubated on wheat
      bran-based solid and soya flour-based liquid media were compared using
      high-resolution LC-MS. This allowed identification of several known compounds,
      and suggested the ability of Go-475 to produce new secondary metabolites. Major
      anti-bacterial compounds were purified from liquid cultures of Go-475, and their
      structures elucidated by NMR and HRMS as 8-O-methyltetrangomycin and
      8-O-methyltetrangulol. In addition, many potentially novel metabolites were
      detected, the majority of which were produced in solid media-based fermentation.
      The genome sequence of Streptomyces sp. Go-475 was obtained using a hybrid
      assembly approach of high quality Illumina short read and low quality Oxford
      Nanopore long read data. The complete linear chromosome of 8,570,609 bp,
      featuring a G+C content of 71.96%, contains 7,571 predicted coding sequences, 83
      t(m)RNA genes, and six rrn operons. Analysis of the genome for secondary
      metabolite biosynthesis gene clusters further confirmed potential of this isolate
      to synthesize chemically diverse natural products, and allowed to connect certain
      clusters with experimentally confirmed molecules.
AU  - Kibret M
AU  - Guerrero-Garzon JF
AU  - Urban E
AU  - Zehl M
AU  - Wronski VK
AU  - Ruckert C
AU  - Busche T
AU  - Kalinowski J
AU  - Rollinger JM
AU  - Abate D
AU  - Zotchev SB
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2018 9: 1270.

PMID- 28473387
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Gardnerella vaginalis Strain ATCC 49145 Associated with  Bacterial Vaginosis.
PG  - e00286-17
AB  - Gardnerella vaginalis is a Gram-variable bacterium associated with bacterial vaginosis, a
      common vaginal inflammation in women of reproductive age. This study
      reports the whole-genome sequencing for the clinical isolate strain ATCC 49145.
      The draft genome is composed of 21 contigs containing 1,325 protein-coding
      sequences, 45 tRNAs and a single tmRNA (SsrA).
AU  - Kidane DT
AU  - Arivett BA
AU  - Crigler J
AU  - Vick EJ
AU  - Farone AL
AU  - Farone MB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00286-17.

PMID- 25858825
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Mannheimia haemolytica Strain Mh10517, Isolated from  Sheep in South Africa.
PG  - e00129-15
AB  - Respiratory disease caused by Mannheimia haemolytica is a major concern in the cattle and
      small stock industry worldwide. This problem arises due to the
      interaction of numerous contributing factors, including physical stresses
      associated with weaning, shipment, inclement weather, and overcrowding coupled
      with viral and bacterial infections. The whole genome of M. haemolytica strain
      Mh10517 was analyzed using an Illumina MiSeq high-throughput sequencing platform.
      The genome size is 2.67 Mb with 2,879 predicted gene sequences. The availability
      of this genome sequence will advance studies on various aspects of the biology of
      M. haemolytica in Africa and the world at large.
AU  - Kidanemariam GA
AU  - Bihon W
AU  - Faranani R
AU  - Mafofo J
AU  - Rees J
AU  - Madoroba E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00129-15.

PMID- 24416416
VI  - 9
DP  - 2014
TI  - Comparative Genome Analysis of Campylobacter fetus Subspecies Revealed Horizontally Acquired Genetic Elements Important for Virulence and Niche Specificity.
PG  - E85491
AB  - Campylobacter fetus are important animal and human pathogens and the two major
      subspecies differ strikingly in pathogenicity. C. fetus subsp. venerealis is
      highly niche-adapted, mainly infecting the genital tract of cattle. C. fetus
      subsp. fetus has a wider host-range, colonizing the genital- and intestinal-tract
      of animals and humans. We report the complete genomic sequence of C. fetus subsp.
      venerealis 84-112 and comparisons to the genome of C. fetus subsp. fetus 82-40.
      Functional analysis of genes predicted to be involved in C. fetus virulence was
      performed. The two subspecies are highly syntenic with 92% sequence identity but
      C. fetus subsp. venerealis has a larger genome and an extra-chromosomal element.
      Aside from apparent gene transfer agents and hypothetical proteins, the unique
      genes in both subspecies comprise two known functional groups: lipopolysaccharide
      production, and type IV secretion machineries. Analyses of
      lipopolysaccharide-biosynthesis genes in C. fetus isolates showed linkage to
      particular pathotypes, and mutational inactivation demonstrated their roles in
      regulating virulence and host range. The comparative analysis presented here
      broadens knowledge of the genomic basis of C. fetus pathogenesis and host
      specificity. It further highlights the importance of surface-exposed structures
      to C. fetus pathogenicity and demonstrates how evolutionary forces optimize the
      fitness and host-adaptation of these pathogens.
AU  - Kienesberger S
AU  - Sprenger H
AU  - Wolfgruber S
AU  - Halwachs B
AU  - Thallinger GG
AU  - Perez-Perez GI
AU  - Blaser MJ
AU  - Zechner EL
AU  - Gorkiewicz G
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2014 9: E85491.

PMID- 1943784
VI  - 204
DP  - 1991
TI  - Genetic manipulation of Streptomyces: integrating vectors and gene replacement.
PG  - 430-458
AB  - The Streptomyces chromosome is a circle of about 72% G + C DNA at
      least 1.5 times the size of the Escherichia coli chromosome.~ Streptomyces
      coelicolor A3(2) is genetically by far the most studied streptomycete, with
      a detailed chromosomal linkage map 2 and a combined physical/genetic
      map based on pulsed-field gel analysis of large fragments generated by
      enzymes that recognize permutations of the sequence A3T3 such as AseI,
      DraI, and SspI. 3 In S. coelicolor fundamental studies of differentiation,
      antibiotic production, and many other aspects of cell and molecular biology are being made by
      a combination of in vivo and in vitro genetics.4,5 As
      well as being amenable to a wide range of in vivo genetic procedures, the
      A3(2) strain is an excellent host for the homologous cloned DNA required
      for many of these studies. However, S. coelicolor shows very strong
      restriction against DNA from E. coli, so the closely related Streptomyces
      lividans 66 has been used for most heterologous cloning. 6-8 Streptomyces
      lividans is largely nonrestricting and has the added advantage that it can
      be used as an intermediate host for cloned DNA manipulated in E. coli
      and destined for S. coelicolor A3(2). [Streptomyces coelicolor A3(2) has a
      methylation-dependent restriction system. Bifunctional plasmids isolated
      from a completely nonmethylating (Dam- Dcm- HsdS-) strain of E. coli
      transform S. coelicolor. 9 This approach first succeeded for Streptomyces
      avermitilis, which has methylation-dependent restriction systems. ~o]
      Whether the recently discovered ability of some E. coli plasmids to promote
      conjugation with Streptomyces, leading to plasmid transfer, u will
      alleviate restriction barriers remains to be seen, but it clearly has some
      other interesting practical implications. Differences between S. coelicolor
      and S. lividans are listed in Table I.
AU  - Kieser T
AU  - Hopwood DA
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1991 204: 430-458.

PMID- 17309843
VI  - 41
DP  - 2007
TI  - Single-molecule and population probing of chromatin structure using DNA methyltransferases.
PG  - 320-332
AB  - Probing chromatin structure with DNA methyltransferases offers advantages over more commonly
      used nuclease-based and chromatin
      immunoprecipitation methods for detection of nucleosomes and
      non-histone protein DNA interactions. Here, we describe two related
      methods in which the readout of MTase accessibility is obtained by
      assaying 5-methylcytosine in DNA through the PCR-based technique of
      bisulfite genomic sequencing. The methyltransferase accessibility
      protocol (MAP) determines the relative frequency at which the enzyme
      accesses each of its target sites over an entire population of PCR
      amplified product. While MAP yields much quantitative information about
      relative accessibility of a region of chromatin, a complementary
      single-molecule view of methyltransferase accessibility, termed MAP for
      individual templates (MAP-IT), is provided by analysis of cloned PCR
      products. Absolute rather than relative methylation frequencies in a
      region are obtained by summing the methylation status at each site over
      a cohort of clones. Moreover, as the integrity of individual molecules
      is maintained in MAP-IT, unique information about the distribution of
      multiple footprints along continuous regions is gleaned. In principle,
      the population MAP and single-molecule MAP-IT strategies can be used to
      analyze chromatin structure in a variety of model systems. Here, we
      describe the application of MAP in living Saccharomyces cerevisiae
      cells and MAP-IT in the analysis of a mammalian tumor suppressor gene
      in nuclei. This application of MAP-IT provides the first means to
      simultaneously determine CpG methylation of mammalian genes and their
      overlying chromatin structure in the same single DNA molecule.
AU  - Kilgore JA
AU  - Hoose SA
AU  - Gustafson TL
AU  - Porter W
AU  - Kladde MP
PT  - Journal Article
TA  - Methods
JT  - Methods
SO  - Methods 2007 41: 320-332.

PMID- 29853510
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of the Virulent Aeromonas salmonicida subsp. masoucida Strain RFAS1.
PG  - e00470-18
AB  - Here, we report the complete genome sequence of the pathogenic Aeromonas salmonicida subsp.
      masoucida strain RFAS1, isolated from black rockfish and
      showing signs of furunculosis. Sequencing with the PacBio platform yielded a
      circular chromosome of 4,783,004 bp and two plasmids (70,968 bp and 63,563 bp)
      harboring 4,411, 67, and 71 protein-coding genes, respectively.
AU  - Kim A
AU  - Nguyen TL
AU  - Kim DH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00470-18.

PMID- 26941142
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Toluene-Resistant Staphylococcus epidermidis SNUT.
PG  - e00057-16
AB  - Here, we report draft sequence of the Gram-positive toluene-resistant bacterium Staphylococcus
      epidermidis SNUT. The draft genome sequence is 2,511,658 bases,
      with 2,346 protein-coding genes, 57 tRNA-coding genes, and 8 rRNA genes.
AU  - Kim B
AU  - Kim J
AU  - Park H
AU  - Park J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00057-16.

PMID- 22535933
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Mycobacterium intracellulare Strain ATCC 13950T.
PG  - 2750
AB  - Here we report the first complete genome sequence of Mycobacterium intracellulare ATCC
      13950(T), a Mycobacterium avium complex (MAC) strain. This genome sequence will serve as a
      valuable reference for understanding the epidemiologic, biological, and pathogenic aspects of
      the disparity between MAC members.
AU  - Kim B-J
AU  - Choi BS
AU  - Lim JS
AU  - Choi IY
AU  - Lee JH
AU  - Chun J
AU  - Kook YH
AU  - Kim BJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2750.

PMID- 29449383
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Methanobrevibacter smithii Strain KB11, Isolated from a Korean Fecal Sample.
PG  - e00038-18
AB  - The archaeon Methanobrevibacter smithii is a major colonizer of the human gut.
      Methanobrevibacter smithii strain KB11 was newly isolated from a Korean fecal
      sample. Here, we present the complete genome sequence of strain KB11 and a brief
      comparison with that of M. smithii type strain ATCC 35061(T).
AU  - Kim BC
AU  - Jeong H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00038-18.

PMID- 22815454
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Mycobacterium intracellulare Clinical Strain MOTT-36Y, Belonging to the INT5 Genotype.
PG  - 4141-4142
AB  - Here we report the complete genome sequence of the Mycobacterium intracellulare clinical
      strain MOTT-36Y, previously grouped into the INT5 genotype among the 5
      genotypes of M. intracellulare. This genome sequence will serve as a valuable
      reference for understanding the disparity in virulence and epidemiologic traits
      between M. intracellulare-related strains.
AU  - Kim BJ
AU  - Choi BS
AU  - Choi IY
AU  - Lee JH
AU  - Chun J
AU  - Hong SH
AU  - Kook YH
AU  - Kim BJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4141-4142.

PMID- 22628501
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Mycobacterium intracellulare Clinical Strain MOTT-64, Belonging to the INT1 Genotype.
PG  - 3268
AB  - Here, we report the complete genome sequence of the Mycobacterium intracellulare  clinical
      strain MOTT-64, previously grouped into the INT1 genotype among five
      genotypes of M. intracellulare. This genome sequence will serve as a valuable
      reference for understanding the disparity in the virulence and epidemiologic
      traits among M. intracellulare genotypes.
AU  - Kim BJ
AU  - Choi BS
AU  - Lim JS
AU  - Choi IY
AU  - Kook YH
AU  - Kim BJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3268.

PMID- 22535946
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Mycobacterium intracellulare Clinical Strain MOTT-02.
PG  - 2771
AB  - Here, we report the first complete genome sequence of the Mycobacterium intracellulare
      clinical strain MOTT-02, which was previously grouped in the INT2
      genotype of M. intracellulare. This genome sequence will serve as a valuable
      reference for improving the understanding of the disparity in the virulence and
      epidemiologic traits between M. intracellulare genotypes.
AU  - Kim BJ
AU  - Choi BS
AU  - Lim JS
AU  - Choi IY
AU  - Lee JH
AU  - Chun J
AU  - Kook YH
AU  - Kim BJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2771.

PMID- 23833135
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Mycobacterium massiliense Clinical Strain Asan 50594, Belonging to the Type II Genotype.
PG  - e00429-13
AB  - We report the complete genome sequence of the Mycobacterium massiliense clinical  strain Asan
      50594, which was grouped into the M. massiliense type II genotype,
      isolated from a Korean patient. This genome sequence will serve as a valuable
      reference for understanding the disparity in virulence and epidemiological traits
      between strains belonging to the Mycobacterium abscessus complex.
AU  - Kim BJ
AU  - Kim BR
AU  - Hong SH
AU  - Seok SH
AU  - Kook YH
AU  - Kim BJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00429-13.

PMID- 23929490
VI  - 1
DP  - 2013
TI  - Whole-Genome Sequence of a Novel Species, Mycobacterium yongonense DSM 45126T.
PG  - e00604-13
AB  - Here, we report the complete genome sequence of Mycobacterium yongonense DSM 45126(T),
      genetically closely related to the INT5 genotype of M. intracellulare.
AU  - Kim BJ
AU  - Kim BR
AU  - Lee SY
AU  - Seok SH
AU  - Kook YH
AU  - Kim BJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00604-13.

PMID- 22740678
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Leaf-Colonizing Bacterium Bacillus sp. Strain 5B6, Isolated from a Cherry Tree.
PG  - 3758-3759
AB  - Plant growth-promoting bacteria colonize various habitats, including the phyllosphere. Here,
      we present the high-quality draft genome sequence of Bacillus
      sp. strain 5B6, which was isolated from the leaf of a cherry tree. The 3.9-Mb
      genome uncovers its potential for understanding the nature of leaf colonization
      as well as antibiosis against plant pathogens.
AU  - Kim BK
AU  - Chung JH
AU  - Kim SY
AU  - Jeong H
AU  - Kang SG
AU  - Kwon SK
AU  - Lee CH
AU  - Song JY
AU  - Yu DS
AU  - Ryu CM
AU  - Kim JF
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3758-3759.

PMID- 21914867
VI  - 193
DP  - 2011
TI  - Genome Sequence of an Ammonia-Oxidizing Soil Archaeon, 'Candidatus Nitrosoarchaeum koreensis' MY1.
PG  - 5539-5540
AB  - Ammonia-oxidizing archaea are ubiquitous microorganisms which play important
      roles in global nitrogen and carbon cycle on earth. Here we present the
      high-quality draft genome sequence of an ammonia-oxidizing archaeon, "Candidatus
      Nitrosopumilus koreensis" MY1, that dominated an enrichment culture of a soil
      sample from the rhizosphere. Its genome contains genes for survival in the
      rhizosphere environment as well as those for carbon fixation and ammonium
      oxidation to nitrite.
AU  - Kim BK
AU  - Jung MY
AU  - Yu DS
AU  - Park SJ
AU  - Oh TK
AU  - Rhee SK
AU  - Kim JF
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5539-5540.

PMID- 22740682
VI  - 194
DP  - 2012
TI  - Genome Sequence of an Oligohaline Hyperthermophilic Archaeon, Thermococcus zilligii AN1, Isolated from a Terrestrial Geothermal Freshwater Spring.
PG  - 3765-3766
AB  - Thermococcus zilligii, a thermophilic anaerobe in freshwater, is useful for physiological
      research and biotechnological applications. Here we report the
      high-quality draft genome sequence of T. zilligii AN1(T). The genome contains a
      number of genes for an immune system and adaptation to a microbial biomass-rich
      environment as well as hydrogenase genes.
AU  - Kim BK
AU  - Lee SH
AU  - Kim SY
AU  - Jeong H
AU  - Kwon SK
AU  - Lee CH
AU  - Song JY
AU  - Yu DS
AU  - Kang SG
AU  - Kim JF
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3765-3766.

PMID- 22740674
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Shiga Toxin-Producing Escherichia coli Strain NCCP15657.
PG  - 3751-3752
AB  - Shiga toxin-producing Escherichia coli causes bloody diarrhea and hemolytic-uremic syndrome
      and serious outbreaks worldwide. Here, we report the
      draft genome sequence of E. coli NCCP15657 isolated from a patient. The genome
      has virulence genes, many in the locus of enterocyte effacement (LEE) island,
      encoding a metalloprotease, the Shiga toxin, and constituents of type III
      secretion.
AU  - Kim BK
AU  - Song GC
AU  - Hong GH
AU  - Seong WK
AU  - Kim SY
AU  - Jeong H
AU  - Kang SG
AU  - Kwon SK
AU  - Lee CH
AU  - Song JY
AU  - Yu DS
AU  - Park MS
AU  - Cho SH
AU  - Kim JF
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3751-3752.

PMID- 22843581
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Staphylococcus saprophyticus subsp. saprophyticus M1-1,  Isolated from the Gills of a Korean Rockfish, Sebastes schlegeli Hilgendorf,  after High Hydrostatic Pressure Processing.
PG  - 4441-4442
AB  - A bacterium designated M1-1 was isolated from the gills of a Korean rockfish, Sebastes
      schlegeli Hilgendorf, after high hydrostatic pressure processing.
      Studies of 16S rRNA phylogeny and comparative genomics demonstrated that the
      isolate belongs to Staphylococcus saprophyticus subsp. saprophyticus. Here, we
      report the draft genome sequence of S. saprophyticus subsp. saprophyticus M1-1
      (KACC 16562).
AU  - Kim BS
AU  - Kim CT
AU  - Park BH
AU  - Kwon S
AU  - Cho YJ
AU  - Kim N
AU  - Kim CJ
AU  - Chun J
AU  - Kwak J
AU  - Maeng JS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4441-4442.

PMID- 14769331
VI  - 326
DP  - 2004
TI  - A column method for determination of DNA cytosine-C-5-methyltransferase activity.
PG  - 21-24
AB  - DNA methylation at the 5th position of cytosine has been found to be correlated with
      tumorigenesis. An inhibitor of DNA methylase could,
      therefore, be used as an anticancer drug. However, only a few
      inhibitory compounds have been discovered due to the limitations for
      assaying the DNA methylation. In this study, we describe a modification
      of DNA cytosine-C5-methyltransferase assay system utilizing
      [H-3]-labeled S-adenosyl-methionine (SAM) and Sephadex G-25 column.
      Pre-treatment of either lambda DNA or the promoter region of human
      telomerase (hTERT) with HaeIII methylase greatly reduced the digestion
      of the DNAs with the corresponding restriction enzyme HaeIII
      endonuclease (over 100-fold), and the result was further confirmed by
      agarose gel electrophoresis. Application of this column method to
      another modification/restriction system, EcoRI methylase/endonuclease,
      gave rise to the similar results. Our data suggest that the newly
      developed column method could be effective for rapid screening of large
      number of cytosine methylase inhibitors and could also be applicable to
      other DNA methylases.
AU  - Kim BY
AU  - Kwon OS
AU  - Joo SA
AU  - Park JA
AU  - Heo KY
AU  - Kim MS
AU  - Ahn JS
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 2004 326: 21-24.

PMID- 25573933
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Bacillus amyloliquefaciens subsp. plantarum CC178, a  Phyllosphere Bacterium Antagonistic to Plant Pathogenic Fungi.
PG  - e01368-14
AB  - Bacillus amyloliquefaciens subsp. plantarum strain CC178 is a phyllosphere bacterium with
      antagonistic activity against a wide range of plant fungal
      pathogens. The genome of strain CC178 is 3,916,828 bp in size and harbors 3,972
      genes. Six giant gene clusters are dedicated to the nonribosomal synthesis of
      antimicrobial polypeptides and polyketides.
AU  - Kim BY
AU  - Lee SY
AU  - Ahn JH
AU  - Song J
AU  - Kim WG
AU  - Weon HY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01368-14.

PMID- 23209247
VI  - 194
DP  - 2012
TI  - Draft Genome Sequencing of Bacillus sp. Strain M2-6, Isolated from the Roots of Korean Ginseng, Panax ginseng C. A. Meyer, after High-Hydrostatic-Pressure  Processing.
PG  - 7003-7004
AB  - A bacterium, designated M2-6, was isolated from Korean ginseng, Panax ginseng C.  A. Meyer,
      roots after high-hydrostatic-pressure processing. On the basis of 16
      rRNA gene phylogeny, the isolate was presumptively identified as a Bacillus sp.
      Here we report the draft genome sequence of Bacillus sp. strain M2-6 (= KACC
      16563).
AU  - Kim CT
AU  - Kim BS
AU  - Kim MJ
AU  - Park BH
AU  - Kwon S
AU  - Maeng HY
AU  - Kwak J
AU  - Chun J
AU  - Cho YJ
AU  - Kim N
AU  - Kim CJ
AU  - Maeng JS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 7003-7004.

PMID- 22535938
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Anaerobic Bacterium Clostridium arbusti SL206T.
PG  - 2758
AB  - A new Clostridium species has been isolated from pear orchard soil in Daejeon, Republic of
      Korea. The isolate, Clostridium arbusti SL206(T) (KCTC 5449(T)), showed a nitrogenase activity
      as well as an organic acid production. Here we first report the draft genome sequence of a
      novel species in the genus Clostridium within the largest Gram-positive group.
AU  - Kim D-S
AU  - Jung MY
AU  - Sin Y
AU  - Kim DW
AU  - Paek J
AU  - Kim RN
AU  - Park IS
AU  - Kook JK
AU  - Nam SH
AU  - Kim A
AU  - Kang A
AU  - Park HS
AU  - Choi SH
AU  - Chang YH
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2758.

PMID- 21868804
VI  - 193
DP  - 2011
TI  - Draft Genome Sequence of Shewanella sp. Strain HN-41, Which Produces Arsenic-Sulfide Nanotubes.
PG  - 5039-5040
AB  - The dissimilatory metal reducing bacterium Shewanella sp. strain HN-41 was first reported to
      produce novel photoactive As-S nanotubes via reduction
      of As(V) and S(2)O(3)(2-) under anaerobic conditions. Here we report the
      draft genome sequence and annotation of strain HN-41.
AU  - Kim DH
AU  - Jiang S
AU  - Lee JH
AU  - Cho YJ
AU  - Chun J
AU  - Choi SH
AU  - Park HS
AU  - Hur HG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5039-5040.

PMID- 21742864
VI  - 193
DP  - 2011
TI  - Genome Sequence of Lactobacillus cypricasei KCTC 13900.
PG  - 5053-5054
AB  - Lactobacillus cypricasei KCTC 13900 is important in the generation of particular flavours and
      in other ripening processes associated with
      specific cheeses. Here we announce the draft genome sequence of
      Lactobacillus cypricasei KCTC 13900, isolated from cheeses and describe
      major findings from its annotation.
AU  - Kim DS
AU  - Choi SH
AU  - Kim DW
AU  - Kim RN
AU  - Nam SH
AU  - Kang A
AU  - Kim A
AU  - Park HS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5053-5054.

PMID- 21131494
VI  - 193
DP  - 2010
TI  - Genome Sequence of Leuconostoc gelidum KCTC 3527 Isolated from Kimchi.
PG  - 799-800
AB  - Leuconostoc gelidum KCTC 3527 is found mainly in vegetables and plays an important role in
      vegetable fermentation, including that of Korean traditional kimchi. Here we announce the
      draft genome sequence of Leuconostoc gelidum KCTC 3527, isolated from Korean traditional
      kimchi and describe major findings from its annotation.
AU  - Kim DS
AU  - Choi SH
AU  - Kim DW
AU  - Kim RN
AU  - Nam SH
AU  - Kang A
AU  - Kim A
AU  - Park HS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 193: 799-800.

PMID- 21914893
VI  - 193
DP  - 2011
TI  - Genome Sequence of Lactobacillus versmoldensis KCTC 3814.
PG  - 5589-5590
AB  - Lactobacillus versmoldensis KCTC 3814 was isolated from raw fermented poultry salami. The
      species was present in high numbers and frequently
      dominated the lactic acid bacteria (LAB) populations of the products.
      Here, we announce the draft genome sequence of Lactobacillus versmoldensis
      KCTC 3814, isolated from poultry salami, and describe major findings from
      its annotation.
AU  - Kim DS
AU  - Choi SH
AU  - Kim DW
AU  - Kim RN
AU  - Nam SH
AU  - Kang A
AU  - Kim A
AU  - Park HS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5589-5590.

PMID- 21183671
VI  - 193
DP  - 2010
TI  - Genome Sequence of Leuconostoc inhae KCTC 3774 Isolated from Kimchi.
PG  - 1278-1279
AB  - The Leuconostoc inhae KCTC 3774 strain is a gram-positive, non-spore-forming,
      heterofermentative, spherical or lenticular lactic acid bacteria. Here we announce the draft
      genome sequence of Leuconostoc inhae KCTC 3774, isolated from traditional Korean kimchi and
      describe major findings from its annotation.
AU  - Kim DS
AU  - Choi SH
AU  - Kim DW
AU  - Kim RN
AU  - Nam SH
AU  - Kang A
AU  - Kim A
AU  - Park HS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 193: 1278-1279.

PMID- 21097615
VI  - 193
DP  - 2010
TI  - Genome Sequence of Weissella cibaria KACC 11862.
PG  - 797-798
AB  - The Weissella cibaria KACC 11862 is Gram-positive heterofermentative Leuconostoc-like lactic
      acid bacteria and it is widely distributed in
      Korean traditional foods such as kimchi. Here we report the draft genome
      sequence of the type strain Weissella cibaria KACC 11862 (1,599 known
      gene, 80 RNA), which consists of 72 large contigs (>100 bp in size).
AU  - Kim DS
AU  - Choi SH
AU  - Kim DW
AU  - Nam SH
AU  - Kim RN
AU  - Kang A
AU  - Kim A
AU  - Park HS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 193: 797-798.

PMID- 22493209
VI  - 194
DP  - 2012
TI  - Genome Sequence of Peptoniphilus rhinitidis 1-13T, an Anaerobic Coccus Strain Isolated from Clinical Specimens.
PG  - 2405-2406
AB  - A new Peptoniphilus species has been isolated from samples from a patient who was scheduled
      for endoscopic sinus surgery for chronic rhinosinusitis. The isolate,
      Peptoniphilus rhinitidis 1-13(T) (KCTC 5985(T)), can use peptone as a sole carbon
      source and produce butyrate as a metabolic end product. This is the first report
      of the draft genome sequence of a novel species in the genus Peptoniphilus within
      the group of Gram-positive anaerobic cocci.
AU  - Kim DS
AU  - Jung MY
AU  - Kang A
AU  - Cho J
AU  - Sin Y
AU  - Paek J
AU  - Kim DW
AU  - Kim RN
AU  - Nam SH
AU  - Kim A
AU  - Park HS
AU  - Choi SH
AU  - Chang YH
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2405-2406.

PMID- 7518278
VI  - 32
DP  - 1994
TI  - Effects of base analog substitutions in the sequence, CCGG, on the cleavage and methylation reactions of HpaII and MspI endonucleases and their cognate methylases.
PG  - 507-514
AB  - HpaII endonuclease, HpaII methylase, MspI endonuclease, and MspI methylase were used to
      investigate their specific interactions with the common recognition sequence, CCGG. Six
      derivatives of the oligonucleotide, AGCCCGGGCT, containing a variety of single base analog
      substitutions within the tetrameric recognition core were synthesized. Steady state kinetic
      values for the reactions of all 4 enzymes with these oligonucleotide substrates were obtained.
      Our data suggest that there are close contacts between the C5 positions of both cytosine
      residues and the enzymes except that MspI endonuclease can accommodate a methyl group at the
      C5 position of the second cytosine residue. The data also showed that minor groove
      interactions between the 2-amino group of both G residues and the HpaII or MspI endonuclease
      were essential for activity. However, these interactions were not essential for methylase
      activity except that the oliogonucleotide substituted with inosine nucleotide at the first G
      position did not react with MspI methylase.
AU  - Kim DS
AU  - Kang YK
AU  - Yoo OJ
PT  - Journal Article
TA  - Biochem. Mol. Biol. Int.
JT  - Biochem. Mol. Biol. Int.
SO  - Biochem. Mol. Biol. Int. 1994 32: 507-514.

PMID- 22535932
VI  - 194
DP  - 2012
TI  - Genome Sequence of Myroides injenensis M09-0166T, Isolated from Clinical Specimens.
PG  - 2748-2749
AB  - A new Myroides species has been isolated from the urine of a patient with fever in spite of
      multiple antibiotic treatments who had undergone a radical
      hysterectomy for cervical cancer and percutaneous nephrostomies for
      hydronephrosis in the past. The isolate, Myroides injenensis M09-0166(T) (KCTC
      23367(T)), showed a high level of resistance to multiple antibiotic agents. Here
      we provide the first report of the draft genome sequence of a novel species in
      the genus Myroides within the nonfermenting Gram-negative group.
AU  - Kim DS
AU  - Paek J
AU  - Shin JH
AU  - Kim DW
AU  - Jung MY
AU  - Kim RN
AU  - Sin Y
AU  - Kook JK
AU  - Nam SH
AU  - Kim A
AU  - Kang A
AU  - Park HS
AU  - Choi SH
AU  - Chang YH
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2748-2749.

PMID- 22582374
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Probiotic Bacterium Sporolactobacillus vineae SL153T.
PG  - 3015-3016
AB  - The novel Sporolactobacillus vineae SL153(T) strain has excellent intestinal adherence and
      growth inhibitory effect on pathogenic microorganisms, including
      Vibrio genus microorganisms, and therefore can be effectively used for the
      prevention and treatment of disease caused by pathogenic microorganisms. Here, we
      first report the draft genome sequence of a novel species in the genus
      Sporolactobacillus.
AU  - Kim DS
AU  - Sin Y
AU  - Kim DW
AU  - Paek J
AU  - Kim RN
AU  - Jung MY
AU  - Park IS
AU  - Kim A
AU  - Kang A
AU  - Park HS
AU  - Choi SH
AU  - Chang YH
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3015-3016.

PMID- 21742889
VI  - 193
DP  - 2011
TI  - Draft Genome Sequence of Lactobacillus mali KCTC 3596.
PG  - 5037
AB  - We announce the draft genome sequence of the type strain Lactobacillus mali KCTC 3596
      (2,652,969 bp, with a G+C content of 36.0%) that one of the
      most prevalent lactic acid bacteria present during the manufacturing
      process of Apple juice, which consists of 122 large contigs (>100 bp in
      size). All of the contigs were assembled by Newbler Assembler 2.3 (454
      Life Science).
AU  - Kim DW
AU  - Choi SH
AU  - Kang A
AU  - Nam SH
AU  - Kim DS
AU  - Kim RN
AU  - Kim A
AU  - Park HS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5037.

PMID- 21868802
VI  - 193
DP  - 2011
TI  - Draft Genome Sequence of Lactobacillus zeae KCTC 3804.
PG  - 5023
AB  - We announce the draft genome sequence of the type strain Lactobacillus zeae KCTC 3804
      (3,110,326 bp, with a G+C content of 47.8%), which is one
      of the most prevalent lactic acid bacteria present during the processing
      of raw cow's milk. The genome consists of 113 large contigs (>100 bp). All
      of the contigs were assembled by Newbler Assembler 2.3 (454 Life Science).
AU  - Kim DW
AU  - Choi SH
AU  - Kang A
AU  - Nam SH
AU  - Kim DS
AU  - Kim RN
AU  - Kim A
AU  - Park HS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5023.

PMID- 21914865
VI  - 193
DP  - 2011
TI  - Draft Genome Sequence of Lactobacillus malefermentans KCTC 3548.
PG  - 5537
AB  - We announce the draft genome sequence of the type strain Lactobacillus malefermentans KCTC
      3548 (2,003,922 bp, with a G+C content of 41.1%),
      which is one of the most prevalent lactic acid bacteria present during the
      manufacturing process of beer; the genome consists of 172 large contigs
      (>100 bp in size). All of the contigs were assembled by using Newbler
      Assembler 2.3 (454 Life Science).
AU  - Kim DW
AU  - Choi SH
AU  - Kang A
AU  - Nam SH
AU  - Kim DS
AU  - Kim RN
AU  - Kim A
AU  - Park HS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5537.

PMID- 21705609
VI  - 193
DP  - 2011
TI  - Genome Sequence of Leuconostoc pseudomesenteroides KCTC 3652.
PG  - 4299
AB  - We announce the genome sequence of one of the most prevalent lactic acid bacteria present
      during the manufacturing process of cane juice, the type
      strain Leuconostoc pseudomesenteroides KCTC 3652 (3,244,985 bp, with a G+C
      content of 38.3%), which consists of 1,160 large contigs (>100 bp in
      size). All of the contigs were assembled by the Newbler Assembler 2.3
      software program (454 Life Sciences).
AU  - Kim DW
AU  - Choi SH
AU  - Kang A
AU  - Nam SH
AU  - Kim RN
AU  - Kim A
AU  - Kim DS
AU  - Park HS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4299.

PMID- 28473394
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Pediococcus pentosaceus Strain FBL2, a Probiotic Bacterium Isolated from Jogaejeot, a Salted Fermented Food, in the Republic of  Korea.
PG  - e00303-17
AB  - Pediococcus pentosaceus strain FBL2 is a lactic acid bacterium isolated in the Republic of
      Korea from jogaejeot, a salted fermented food made with shellfish. P.
      pentosaceus strain FBL2 comprised 54 contigs (>/=1 kb) and had a total draft
      genome size of 1,934,229 bp with a G+C content of 37.2%.
AU  - Kim E
AU  - Kim JH
AU  - Park SB
AU  - Kim MJ
AU  - Kim HJ
AU  - Kim CG
AU  - Choo DW
AU  - Kim HY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00303-17.

PMID- 28473395
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Tetragenococcus halophilus Strain FBL3, a Probiotic Bacterium Isolated from Galchijeot, a Salted Fermented Food, in the Republic of  Korea.
PG  - e00304-17
AB  - Tetragenococcus halophilus strain FBL3 is a lactic acid bacterium isolated from galchijeot, a
      fermented food made from the salted guts of the hairtail fish, in
      the Republic of Korea. The draft genome of T. halophilus strain FBL3 comprised 87
      contigs (>/=1 kb) with a total size of 2,420,904 bp and a G+C content of 38.5%.
AU  - Kim E
AU  - Kim JH
AU  - Yang SM
AU  - Suh SM
AU  - Kim HJ
AU  - Kim CG
AU  - Choo DW
AU  - Kim HY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00304-17.

PMID- 26450744
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Lactobacillus plantarum Strain SNU.Lp177 from Pig Feces  in South Korea.
PG  - e01184-15
AB  - Herein we report a draft genome sequence for Lactobacillus plantarum SNU.Lp177, which was
      isolated from animal gut pig feces in South Korea. The draft genome of  L. plantarum SNU.Lp177
      contains 3,204,772 bp with a G+C content of 44.98% in 101  contigs (N50 = 116,595 bp).
AU  - Kim EB
AU  - Jin GD
AU  - Lee JY
AU  - Choi YJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01184-15.

PMID- 23405360
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Fructophilic Lactobacillus florum.
PG  - e00025-12
AB  - Herein we report the first genome sequence for Lactobacillus florum. L. florum 2F was isolated
      from Valencia orange leaves and is fructophilic, like other strains of this species. The draft
      genome of L. florum 2F contains 1,261,842 bp with a G+C content of 41.5% in 46 contigs (>/=500
      bp).
AU  - Kim EB
AU  - Tyler CA
AU  - Kopit LM
AU  - Marco ML
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00025-12.

PMID- 22328748
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Gluconobacter morbifer G707T, a Pathogenic Gut Bacterium Isolated from Drosophila melanogaster Intestine.
PG  - 1245
AB  - Gluconobacter morbifer G707(T), a minor member of gut microbiota, was isolated from fruit fly
      (Drosophila melanogaster). Here, the draft genome sequence of
      Gluconobacter morbifer G707(T) is reported.
AU  - Kim EK
AU  - Kim SH
AU  - Nam HJ
AU  - Choi MK
AU  - Lee KA
AU  - Choi SH
AU  - Seo YY
AU  - You H
AU  - Kim B
AU  - Lee WJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1245.

PMID- 22328749
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Commensalibacter intestini A911T, a Symbiotic Bacterium  Isolated from Drosophila melanogaster Intestine.
PG  - 1246
AB  - Commensalibacter intestini A911(T), a predominant symbiotic bacterium capable of  stably
      colonizing gut epithelia, was isolated from the fruit fly, Drosophila
      melanogaster. Here we report the draft genome sequence of Commensalibacter
      intestini A911(T).
AU  - Kim EK
AU  - Kim SH
AU  - Nam HJ
AU  - Choi MK
AU  - Lee KA
AU  - Choi SH
AU  - Seo YY
AU  - You H
AU  - Kim B
AU  - Lee WJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1246.

PMID- 24265491
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Lactobacillus plantarum Strain WJL, a Drosophila Gut Symbiont.
PG  - e00937-13
AB  - Lactobacillus plantarum strain WJL, a member of the symbiotic gut bacteria, was isolated from
      the intestine of the fruit fly, Drosophila melanogaster. Here, we
      report the draft genome sequence of L. plantarum WJL.
AU  - Kim EK
AU  - Park YM
AU  - Lee OY
AU  - Lee WJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00937-13.

PMID- Not carried by PubMed...
VI  - 5
DP  - 1989
TI  - Some differences between BamHI and BnaI, the restrictases with the same specificity.
PG  - 86-89
AB  - The restriction endonuclease BnaI, being a BamHI true isoschizomer, is isolated from B. natto
      B3364 strain. Its molecular weight, stability and optimal reaction conditions are studied.
      Comparative investigations have shown that according to these physicochemical characteristics
      the BamHI and BnaI enzymes differ from each other in spite of their analogous specificity.
AU  - Kim EL
AU  - Makhovich OP
AU  - Maliuta SS
PT  - Journal Article
TA  - Biopol. Kletka
JT  - Biopol. Kletka
SO  - Biopol. Kletka 1989 5: 86-89.

PMID- 2583516
VI  - 80
DP  - 1989
TI  - A new isoschizomer, BnaI, of the BamHI restriction endonuclease.
PG  - 363-368
AB  - By assaying the yield of phage SPO1 we have identified a new
      restriction-modification activity in the Bacillus natto B3364 strain.  A class
      II restriction endonuclease, BnaI, isolated from the crude extract of B3364
      cells was shown to be a true isoschizomer of the BamHI endonuclease.  The Mr,
      stability and optimal conditions required for DNA digestion were determined for
      BnaI.  Although both enzymes show the same specificity, BnaI and BamHI differ
      from each other in all the properties specified above.
AU  - Kim EL
AU  - Maliuta SS
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1989 80: 363-368.

PMID- 2551737
VI  - 255
DP  - 1989
TI  - Purification of a DNA methyltransferase from Bacillus natto B3364.
PG  - 361-364
AB  - An S-adenosyl-L-methionine: DNA-methyltransferase, termed M.BnaI, was purified from Bacillus
      natto B3364 strain by successive column chromatography. The molecular weight determined by gel
      filtration was 37 kDa for M.BnaI. Analysis of methyltransferase by sodium dodecyl
      sulfate-polyacrylamide gel electrophoresis showed correspondence of the M.BnaI activity with
      one protein band at a molecular weight of 35 kDa. Sequencing of pUC19 DNA methylated with
      M.BnaI showed the cytosine-5 methylation in the BnaI recognition sequence GGAT^CC at the
      position indicated by the arrow.
AU  - Kim EL
AU  - Maliuta SS
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1989 255: 361-364.

PMID- Not carried by PubMed...
VI  - 4
DP  - 1986
TI  - BnaI a new isoshisomer of the restrictase BamHI.
PG  - 24-27
AB  - Studies of restricted reproduction of phage SPO1 have disclosed a restriction-modification
      system in the strain Bacillus natto B3364. Restriction endonuclease BnaI of class II has been
      isolated and purified. BnaI has been shown to be a true isoschizomer of the restrictase BamHI.
AU  - Kim EL
AU  - Malyuta SS
PT  - Journal Article
TA  - Biotekhnologiya
JT  - Biotekhnologiya
SO  - Biotekhnologiya 1986 4: 24-27.

PMID- 29326213
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Chryseobacterium camelliae Dolsongi-HT1, a Green Tea  Isolate with Keratinolytic Activity.
PG  - e01421-17
AB  - The complete genome sequence of Chryseobacterium camelliae Dolsongi-HT1 is reported here. C.
      camelliae Dolsongi-HT1, having keratinolytic activity, was
      isolated from green tea leaves in the Dolsongi tea garden in Jeju, South Korea.
      The strain Dolsongi-HT1 has 28 candidate protease genes, which may be utilized in
      further studies and industrial applications of keratinase.
AU  - Kim EM
AU  - Hwang KH
AU  - Park JS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01421-17.

PMID- 12145218
VI  - 21
DP  - 2002
TI  - Co-operation and communication between the human maintenance and de novo DNA (cytosine-5) methyltransferases.
PG  - 4183-4195
AB  - Three different families of DNA (cytosine-5) methyltransferases, DNMT1, DNMT3a and DNMT3b,
      participate in establishing and maintaining genomic methylation patterns during mammalian
      development. These enzymes have a large N-terminal domain fused to a catalytic domain. The
      catalytic domain is homologous to prokaryotic (cytosine-5) methyltransferases and contains the
      catalytic PC dipeptide, while the N-terminus acts as a transcriptional repressor by recruiting
      several chromatin remodeling proteins. Here, we show that the human de novo enzymes hDNMT3a
      and hDNMT3b form complexes with the major maintenance enzyme hDNMT1. Antibodies against hDNMT1
      pull down both the de novo enzymes. Furthermore, the N-termini of the enzymes are involved in
      protein-protein interactions. Immunocytochemical staining revealed mostly nuclear
      co-localization of the fusion proteins, with the exception of hDNMT3a, which is found either
      exclusively in cytoplasm or in both nucleus and cytoplasm. Pre-methylated substrate DNAs
      exhibited differential methylation by de novo and maintenance enzymes. In vivo co-expression
      of hDNMT1 and hDNMT3a or hDNMT3b leads to methylation spreading in the genome, suggesting
      co-operation between de novo and maintenance enzymes during DNA methylation.
AU  - Kim G-D
AU  - Ni J
AU  - Kelesoglu N
AU  - Roberts RJ
AU  - Pradhan S
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 2002 21: 4183-4195.

PMID- 22965076
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Brucella abortus A13334, a New Strain Isolated from the Fetal Gastric Fluid of Dairy Cattle.
PG  - 5444
AB  - Brucella abortus is a major pathogen that infects livestock and humans. A new strain of B.
      abortus (A13334) was isolated from the fetal gastric fluid of a
      dairy cow, with the aim of using it to compare genetic properties, analyze
      virulence factor, and survey the epidemiological relationship to other Brucella
      species. Here, we report the complete and annotated genome sequence of B. abortus
      A13334.
AU  - Kim H
AU  - Jeong W
AU  - Jeoung HY
AU  - Song JY
AU  - Kim JS
AU  - Beak JH
AU  - Parisutham V
AU  - Lee SK
AU  - Kim JW
AU  - Kim JY
AU  - Jung SC
AU  - Her M
AU  - An DJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5444.

PMID- 16095917
VI  - 44
DP  - 2005
TI  - Expression, purification, and biochemical characterization of the intron-encoded endonuclease, I-CreII.
PG  - 162-172
AB  - The ORF of the Cr.psbA4 intron of Chlamydomonas reinhardtii mediates efficient intron homing,
      and contains an H-N-H and possibly a GIY-YIG
      motif. The ORF was over-expressed in Escherichia coli without
      non-native amino acids, but was mostly insoluble. However,
      co-over-expression of E coli chaperonins GroEL/GroES solubilized
      similar to 50% of the protein, which was purified by ion-exchange and
      heparin-affinity chromatography. Biochemical characterization showed
      that the protein is a double-strand-specific endonuclease that cleaves
      fused psbA exon 4-exon 5 DNA, and was named I-CreII. I-CreII has a
      relatively relaxed divalent metal ion requirement (Mg2+, Mn2+, Ca2+,
      and Fe2+ supported cleavage), is insensitive to salt < 350 mM, and is
      stabilized by DNA. Cleavage of target DNA occurs close (4 nt on the top
      strand) to the intron-insertion site, and leaves 2-nt 3'-OH overhangs,
      similar to GIY-YIG endonucleases. The boundaries of the recognition
      sequence span similar to 30 bp, and encompass the cleavage and
      intron-insertion sites. Cleavage of heterologous psbA DNAs indicates
      the enzyme can tolerate multiple, but not all, substitutions in the
      recognition site. This work will facilitate further study of this novel
      endonuclease, which may also find use in site-specific manipulation of
      chloroplast DNA.
AU  - Kim HH
AU  - Corina LE
AU  - Suh JK
AU  - Herrin DL
PT  - Journal Article
TA  - Protein Expr. Purif.
JT  - Protein Expr. Purif.
SO  - Protein Expr. Purif. 2005 44: 162-172.

PMID- 25336658
VI  - 289
DP  - 2014
TI  - A single module type I polyketide synthase directs de novo macrolactone biogenesis during galbonolide biosynthesis in Streptomyces galbus.
PG  - 34557-34568
AB  - Galbonolide (GAL) A and B are antifungal macrolactone polyketides produced by
      Streptomyces galbus. During their polyketide chain assembly, GAL-A and -B
      incorporate methoxymalonate and methylmalonate, respectively, in the fourth chain
      extension step. The methoxymalonyl-acyl carrier protein biosynthesis locus (galG
      to K) is specifically involved in GAL-A biosynthesis, and this locus is
      neighbored by a gene cluster composed of galA-E. GalA-C constitute a single
      module, highly reducing type I polyketide synthase (PKS). GalD and GalE are
      cytochrome P450 and Rieske domain protein, respectively. Gene knock-out
      experiments verified that galB, -C, and -D are essential for GAL biosynthesis. A
      galD mutant accumulated a GAL-C that lacked two hydroxyl groups and a double bond
      when compared with GAL-B. A [U-(13)C]propionate feeding experiment indicated that
      no rare precursor other than methoxymalonate was incorporated during GAL
      biogenesis. A search of the S. galbus genome for a modular type I PKS system, the
      type that was expected to direct GAL biosynthesis, resulted in the identification
      of only one modular type I PKS gene cluster. Homology analysis indicated that
      this PKS gene cluster is the locus for vicenistatin biosynthesis. This cluster
      was previously reported in Streptomyces halstedii. A gene deletion of the vinP2
      ortholog clearly demonstrated that this modular type I PKS system is not involved
      in GAL biosynthesis. Therefore, we propose that GalA-C direct macrolactone
      polyketide formation for GAL. Our studies provide a glimpse into a novel
      biochemical strategy used for polyketide synthesis; that is, the iterative
      assembly of propionates with highly programmed beta-keto group modifications.
AU  - Kim HJ
AU  - Karki S
AU  - Kwon SY
AU  - Park SH
AU  - Nahm BH
AU  - Kim YK
AU  - Kwon HJ
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2014 289: 34557-34568.

PMID- 28596395
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Vibrio coralliilyticus 58, Isolated from Pacific Oyster (Crassostrea gigas) Larvae.
PG  - e00437-17
AB  - We report here the complete genome of Vibrio coralliilyticus strain 58, which was originally
      isolated from inactive Pacific oyster (Crassostrea gigas) larvae in
      Japan. The assembled genome consisted of two chromosomes and one plasmid. These
      data will provide valuable information and important insights into the
      biodiversity of this organism.
AU  - Kim HJ
AU  - Kim JH
AU  - Jun JW
AU  - Giri SS
AU  - Chi C
AU  - Yun S
AU  - Kim SG
AU  - Kim SW
AU  - Kang JW
AU  - Jeong DG
AU  - Park SC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00437-17.

PMID- 22247529
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Pantoea ananatis B1-9, a Nonpathogenic Plant Growth-Promoting Bacterium.
PG  - 729
AB  - Pantoea ananatis B1-9 is an endophytic Gram-negative rhizobacterium that was isolated for its
      ability to promote plant growth and improve crop
      yield in the field. Here we report the draft genome sequence of P.
      ananatis B1-9. Comparison of this sequence to the sequenced genome of a
      plant-pathogenic P. ananatis strain, LMG20103, indicated that the
      pathogenesis-related genes were absent, but a subset of gene functions
      that may be related to its plant growth promotion were present.
AU  - Kim HJ
AU  - Lee JH
AU  - Kang BR
AU  - Rong X
AU  - McSpadden GBB
AU  - Ji HJ
AU  - Park CS
AU  - Kim YC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 729.

PMID- 22072653
VI  - 193
DP  - 2011
TI  - Draft Genome Sequence of the Biocontrol Bacterium Chromobacterium sp. Strain C-61.
PG  - 6803-6804
AB  - Chromobacterium sp. strain C-61 is a plant-associated bacterium with proven capacities to
      suppress plant diseases. Here, we report the draft
      genome sequence and automatic annotation of strain C-61. A comparison of
      this sequence to the sequenced genome of Chromobacterium violaceum ATCC
      12472 indicates the novelty of C-61 and a subset of gene functions that
      may be related to its biocontrol activities.
AU  - Kim HJ
AU  - Park JY
AU  - Han SH
AU  - Lee JH
AU  - Rong X
AU  - McSpadden GBB
AU  - Park SK
AU  - Kim YC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6803-6804.

PMID- 17337479
VI  - 99
DP  - 2007
TI  - Properties of a tobacco DNA methyltransferase, NtMET1 and its involvement in chromatin movement during cell division.
PG  - 845-856
AB  - Background and Aims Plants possess three types of DNA methyltransferase, among which
      methyltransferase type 1 (MET1) is
      considered to play a major role by maintaining the CpG methylation
      patterns. However, little information is available as to its enzymatic
      activity, interacting proteins and spatial and temporal behaviours
      during DNA replication. In the present study, one example, NtMET1 from
      tobacco plants, was selected and an analysis was made of its
      biochemical properties and cellular localization.
      Methods NtMET1 was expressed in Sf9 insect cells, and a purified
      sample was subjected to a standard in vitro methylation assay.
      Intramolecular interaction was examined by the yeast two-hybrid and
      pull-down assays. Transgenic tobacco plants (Nicotiana tabacum)
      over-expressing NtMET1 were constructed via Agrobacterium-mediated
      transformation. Cellular localization was examined by fluorescence
      protein fusion, which was expressed in tobacco bright yellow 2 cells.
      Key Results In vitro assays showed no detectable methylation
      activity when both hemimethylated and unmethylated DNA samples were
      used as the substrate. In planta assays with over-expressing transgenic
      lines showed no hypermethylation but rather hypomethylation of genomc
      DNA. The inability of methylation was conceivably due to a tight
      intramolecular interaction between the N- and C-terminal regions with
      the catalytic domain residing on the C-terminus being completely
      masked. Cellular localization analyses indicated that NtMET1 localized
      to the nucleus in the resting stage and migrates to the cytoplasm
      during mitosis, particularly at metaphase. The pattern observed
      resembled that of Ran GTPase, and in vitro pull-down assays showed a
      clear interaction between NtMET1 and AtRAN3, an Arabidopsis orthologue
      of tobacco Ran GTPase, NtRan-A1.
      Conclusions The results suggest that enzymatic activity of NtMET1
      is well adjusted by its own intra/intermolecular interaction and
      perhaps by interactions with other proteins, one of which was found to
      be Ran GTPase. Results also revealed that NtMET1 becomes localized to
      the vicinity of chromatin with the aid of Ran GTPase during cell
      division, and may play an important role in progress through mitosis
      independently of methylation activity.
AU  - Kim HJ
AU  - Yano A
AU  - Wada Y
AU  - Sano H
PT  - Journal Article
TA  - Ann. Bot.
JT  - Ann. Bot.
SO  - Ann. Bot. 2007 99: 845-856.

PMID- 29122863
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Indigo-Producing Bacterium Celeribacter sp. Strain TSPH2.
PG  - e01124-17
AB  - Celeribacter sp. strain TSPH2, a novel producer of indigo, was isolated from oil-contaminated
      sediment. We present here its genome sequence consisting of one
      circular chromosome (4 Mb) and one plasmid (0.15 Mb), with an overall G+C content
      of 60.9%. This strain contains oxygenase genes involved in indigo synthesis, such
      as flavin-containing monooxygenase.
AU  - Kim HS
AU  - Cha SH
AU  - Suk HY
AU  - Kwon TH
AU  - Woo JH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01124-17.

PMID- 29348337
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Sphingorhabdus sp. YGSMI21, Exhibiting High Enantioselective Epoxide Hydrolase Activity.
PG  - e01441-17
AB  - Sphingorhabdus sp. YGSMI21 is a novel strain exhibiting high enantioselective hydrolysis
      activity for styrene oxide. Here, we present its complete genome
      sequence, consisting of one circular chromosome (3.86 Mb) and one plasmid (0.196
      Mb).
AU  - Kim HS
AU  - Cha SH
AU  - Suk HY
AU  - Park NH
AU  - Woo JH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01441-17.

PMID- 22933763
VI  - 194
DP  - 2012
TI  - Genome Sequence of Pectin-Degrading Alishewanella agri, Isolated from Landfill Soil.
PG  - 5135-5136
AB  - Alishewanella agri BL06(T) (= KCTC 22400(T) = JCM 15597(T)) was isolated from landfill soil in
      Pohang, South Korea. A. agri showed the ability to degrade
      pectin, a structural heteropolysaccharide present in the cell wall of plants.
      Here we report the genome sequence of Alishewanella agri BL06(T), the second
      sequenced strain in the genus Alishewanella.
AU  - Kim J
AU  - Jung J
AU  - Sung JS
AU  - Chun J
AU  - Park W
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5135-5136.

PMID- 25477411
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Sphingopyxis sp. Strain MWB1, a Crude-Oil-Degrading Marine Bacterium.
PG  - e01256-14
AB  - Sphingopyxis sp. strain MWB1, which is capable of degrading crude oil, diesel, and kerosene,
      was isolated from crude oil-contaminated seashore in Tae-an, South
      Korea. Here, we report the draft genome sequence of this strain, which comprises
      3,118,428 bp with a G+C content of 62.85 mol%.
AU  - Kim J
AU  - Kim SJ
AU  - Kim SH
AU  - Kim SI
AU  - Moon YJ
AU  - Park SJ
AU  - Kahng HY
AU  - Chung YH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01256-14.

PMID- 25700396
VI  - 3
DP  - 2015
TI  - Genome Sequence of Arthrobacter sp. MWB30, Isolated from a Crude Oil-Contaminated Seashore.
PG  - e00013-15
AB  - We report here the draft genome sequence of Arthrobacter sp. MWB30 strain, isolated from a
      crude oil-contaminated seashore in Tae-an, South Korea, which is  able to degrade the crude
      oil and its derivatives. The draft genome sequence of 4,647,008 bp provides a resource for the
      identification of crude oil-degrading mechanisms in strain MWB30.
AU  - Kim J
AU  - Kim SJ
AU  - Kim SH
AU  - Moon YJ
AU  - Park SJ
AU  - Kim SI
AU  - Kahng HY
AU  - Chung YH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00013-15.

PMID- 28336585
VI  - 5
DP  - 2017
TI  - Genome Sequence of Deinococcus marmoris PAMC 26562 Isolated from Antarctic Lichen.
PG  - e00013-17
AB  - Deinococcus marmoris strain PAMC 26562 was isolated from Usnea sp., a lichen collected from
      King George Island, Antarctica. We report here the draft genome
      sequence of strain PAMC 26562, which has xanthorhodopsin and carbon monoxide
      dehydrogenase genes in addition to major metabolic pathways presented in
      deinococcal genomes.
AU  - Kim J
AU  - Kwon KK
AU  - Kim BK
AU  - Hong SG
AU  - Oh HM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00013-17.

PMID- 29650580
VI  - 6
DP  - 2018
TI  - High-Quality Whole-Genome Sequences for 59 Historical Shigella Strains Generated  with PacBio Sequencing.
PG  - e00282-18
AB  - Shigella spp. are enteric pathogens that cause shigellosis. We report here the high-quality
      whole-genome sequences of 59 historical Shigella strains that
      represent the four species and a variety of serotypes.
AU  - Kim J
AU  - Lindsey RL
AU  - Garcia-Toledo L
AU  - Loparev VN
AU  - Rowe LA
AU  - Batra D
AU  - Juieng P
AU  - Stoneburg D
AU  - Martin H
AU  - Knipe K
AU  - Smith P
AU  - Strockbine N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00282-18.

PMID- 22072646
VI  - 193
DP  - 2011
TI  - Draft Genome Sequence of Dietzia alimentaria 72T, Belonging to the Family Dietziaceae, Isolated from a Traditional Korean Food.
PG  - 6791
AB  - Actinobacterial strain 72(T), named Dietzia alimentaria, which belongs to the family
      Dietziaceae, was isolated from a traditional Korean food made
      from clams. The draft genome sequence of D. alimentaria 72(T) contains
      3,352,817 bp, with a G+C content of 67.34%.
AU  - Kim J
AU  - Roh SW
AU  - Bae JW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6791.

PMID- Not carried by PubMed...
VI  - 212
DP  - 1996
TI  - Footprinting of cytosine-5--methyltransferase by Pt2(pop)44-.
PG  - A290
AB  - The photoreagent Pt2(pop)44- (1, pop = P2O5H22-) cleaves DNA upon visible irradiation via
      abstraction of the 4' and 5' hydrogens, which provide a sequence-neutral cleavage ladder.
      The development of 1 for use as an anionic DNA photocleavage agent has prompted us to apply it
      to obtaining the footprint of the M.HhaI (cytosine-5) methyltransferase.  The binding of
      M.HhaI to its DNA substrate causes large conformational changes with an extensive contact with
      DNA around the active site.  A comparison of photocleavage with data from the crystal
      structure of a reaction intermediate between the M.HhaI methyltransferase and a DNA
      oligonucleotide shows a correlation between cleavage by 1 and the effects of electrostatic
      forces in the binding of protein to nucleic acids.  Also underway is an anlaysis of the
      photocleavage products to provide additional quantitation of the cleavage pathways.
AU  - Kim J
AU  - Thorp HH
PT  - Journal Article
TA  - ACS Abstracts
JT  - ACS Abstracts
SO  - ACS Abstracts 1996 212: A290.

PMID- 15728358
VI  - 102
DP  - 2005
TI  - Crystal structure of DNA sequence specificity subunit of a type I restriction-modification enzyme and its functional implications.
PG  - 3248-3253
AB  - Type I restriction-modification enzymes are differentiated from type II and type III enzymes
      by their recognition of two specific dsDNA sequences separated by a given spacer and cleaving
      DNA randomly away from the recognition sites. They are oligomeric proteins formed by three
      subunits: a specificity subunit, a methylation subunit, and a restriction subunit. We solved
      the crystal structure of a specificity subunit from Methanococcus jannaschii at 2.4 Angstroms
      resolution. Two highly conserved regions (CRs) in the middle and at the C terminus form a
      coiled-coil of long antiparallel alpha-helices. Two target recognition domains form globular
      structures with almost identical topologies and two separate DNA binding clefts with a modeled
      DNA helix axis positioned across the CR helices. The structure suggests that the coiled-coil
      CRs act as a molecular ruler for the separation between two recognized DNA sequences.
      Furthermore, the relative orientation of the two DNA binding clefts suggests kinking of bound
      dsDNA and exposing of target adenines from the recognized DNA sequences.
AU  - Kim J-S
AU  - DeGiovanni A
AU  - Jancarik J
AU  - Adams PD
AU  - Yokota H
AU  - Kim R
AU  - Kim S-H
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2005 102: 3248-3253.

PMID- 18281406
VI  - 190
DP  - 2008
TI  - The Complete Genome Sequence of Leuconostoc citreum KM20.
PG  - 3093-3094
AB  - Leuconostoc citreum is one of the most prevalent lactic acid bacteria during the manufacturing
      process of kimchi, the best-known Korean
      traditional dish. Here we present the complete genome sequence of L.
      citreum KM20. It consists of a 1.80-Mb chromosome and four circular
      plasmids, and reveals genes likely involved in kimchi fermentation and its
      probiotic effects.
AU  - Kim JF
AU  - Jeong H
AU  - Lee JS
AU  - Choi SH
AU  - Ha M
AU  - Hur CG
AU  - Kim JS
AU  - Lee S
AU  - Park HS
AU  - Park YH
AU  - Oh TK
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2008 190: 3093-3094.

PMID- 20851896
VI  - 192
DP  - 2010
TI  - Genome Sequence of the Polymyxin-Producing Plant-Probiotic Rhizobacterium Paenibacillus polymyxa E681.
PG  - 6103-6104
AB  - Paenibacillus polymyxa E681, a spore-forming, low-G+C, Gram-positive bacterium isolated from
      the rhizosphere of winter barley grown in South
      Korea, has great potential for agricultural applications due to its
      ability to promote plant growth and suppress plant diseases. Here we
      present the complete genome sequence of P. polymyxa E681. Its 5.4-Mb
      genome encodes functions specialized to the plant-associated lifestyle and
      characteristics that are beneficial to plants, such as the production of a
      plant growth hormone, antibiotics, and hydrolytic enzymes.
AU  - Kim JF
AU  - Jeong H
AU  - Park SY
AU  - Kim SB
AU  - Park YK
AU  - Choi SK
AU  - Ryu CM
AU  - Hur CG
AU  - Ghim SY
AU  - Oh TK
AU  - Kim JJ
AU  - Park CS
AU  - Park SH
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 6103-6104.

PMID- 19011029
VI  - 191
DP  - 2009
TI  - Genome sequence of the probiotic bacterium Bifidobacterium animalis subsp. lactis AD011.
PG  - 678-679
AB  - Bifidobacterium animalis subsp. lactis is a probiotic bacterium that naturally inhabits the
      guts of most mammals, including humans. Here we
      report the complete genome sequence of B. animalis subsp. lactis AD011
      that was isolated from an infant fecal sample. Biological functions
      encoded in a single circular chromosome of 1,933,695 bp, smallest among
      the completely sequenced bifidobacterial genomes, are suggestive of their
      probiotic functions, such as utilization of bifidogenic factors and a
      variety of glycosidic enzymes and biosynthesis of polysaccharides.
AU  - Kim JF
AU  - Jeong H
AU  - Yu DS
AU  - Choi SH
AU  - Hur CG
AU  - Park MS
AU  - Yoon SH
AU  - Kim DW
AU  - Ji GE
AU  - Park HS
AU  - Oh TK
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2009 191: 678-679.

PMID- Not carried by PubMed...
VI  - 17
DP  - 1985
TI  - Preparation of restriction endonuclease-AluI from Arthrobacter Luteus.
PG  - 149-154
AB  - Extraction and purification of the restriction endonuclease, Alu-I, were
      performed from Arthrobacter luteus.  The harvested cells were disrupted by the
      treament of lysozyme and sonification, and the uspernant was precipitated with
      70% saturation of ammonium sulfate.  The protein sediment was dissolved in
      buffer solution and dialysed to the same buffer solution.  This solution was
      successively applied to phosphocellulose, heparin-agarose, and Ultrogel AcA34
      (LKB) column chromatography for the purification procedure.  The purified AluI
      enzyme was revealed the singel band on SDS-polyacrylamide gel electrophoresis
      and the molecular weight was shown 52 Kdal, attaining its specific activity to
      312.5 units/mg or protein.  No difference was observed between our enzyme
      preparation and commerical AluI (BRL) on agarose gel electropherogram.  The
      enzyme sample after treatment with heparin-agarose also had multiprotein bands,
      indicating the protein contaminant, however, all bands but a single band of
      AluI enzyme disappeared by the subsequent column chromatography of Ultrogel
      AcA34.
AU  - Kim JH
AU  - Boo YB
AU  - Lee KY
PT  - Journal Article
TA  - Korean J. Biochem.
JT  - Korean J. Biochem.
SO  - Korean J. Biochem. 1985 17: 149-154.

PMID- 27635005
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Leptolyngbya sp. KIOST-1, a Filamentous Cyanobacterium with Biotechnological Potential for Alimentary Purposes.
PG  - e00984-16
AB  - Here, we report the draft genome of cyanobacterium Leptolyngbya sp. KIOST-1 isolated from a
      microalgal culture pond in South Korea. The genome consists of 13
      contigs containing 6,320,172 bp, and a total of 5,327 coding sequences were
      predicted. This genomic information will allow further exploitation of its
      biotechnological potential for alimentary purposes.
AU  - Kim JH
AU  - Kang DH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00984-16.

PMID- 26044414
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Human-Pathogenic Lactococcus garvieae LG-ilsanpaik-gs201105 That Caused Acute Acalculous Cholecystitis.
PG  - e00464-15
AB  - Lactococcus garvieae, which is generally known as a marine and freshwater fish pathogen, is
      now considered to be an emerging zoonotic pathogen in both human and
      veterinary medicine. In recent years, we have reported the infection of L.
      garvieae LG-ilsanpaik-gs201105 in the gallbladder of an old fisherman. In this
      study, we present the draft genome sequence of L. garvieae LG-ilsanpaik-gs201105,
      with a total genome size of 1,960,261 bp in 53 contigs and a 38.1% average G+C
      content. Interestingly, the capsule gene cluster, which was known as one of the
      crucial virulence factors in L. garvieae, was not detected in our isolate. This
      is the first genome sequence of human-pathogenic L. garvieae, which caused acute
      acalculous cholecystitis.
AU  - Kim JH
AU  - Kang DH
AU  - Park SC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00464-15.

PMID- 27174278
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Lactobacillus sakei Strain FBL1, a Probiotic Bacterium Isolated from Mukeunji, a Long-Fermented Kimchi, in South Korea.
PG  - e00365-16
AB  - This report describes the 2,032,158-bp draft genome sequence of Lactobacillus sakei (L. sakei)
      strain FBL1, isolated from mukeunji purchased at the Gwangju
      World Kimchi Culture Festival in 2012, South Korea. The total draft genome size
      was 2,032,158 bp with a G+C content of 41.2%.
AU  - Kim JH
AU  - Kim E
AU  - Kim CG
AU  - Choo DW
AU  - Kim HY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00365-16.

PMID- 
VI  - 31
DP  - 1998
TI  - Mode of action on EcoRI restriction endonuclease: EcoRI and EcoRI variant N199H have active monomeric forms.
PG  - 149-155
AB  - The N199H variant of the EcoRI endonuclease has about twice the catalytic activity of the
      wild-type.  A comparison of their biochemical characteristics, using synthetic
      oligonucleotides 5'-dAAAACTTAAGAAAAAAAAAAA-3' (KA) and 5'-dTTTTTGAATTCTTTTTTTTTT-3' (KT),
      helps to define the cleavage reaction pathway of these enzymes.  Both EcoRI and EcoRI variant
      N199H were found to cleave single-stranded KA or KT about three times faster than the
      double-stranded forms, although the KT oligonucleotide was more susceptible.  Using the ssDNA
      substrate in kinetic analyses, lower Km values were obtained for the N199H variant than for
      the wild-type at low (50 mM), as well as high (200 mM), sodium chloride concentrations.  This
      difference between the endonucleases is attributed to a greater accessibility for the
      substrate by the variant, and also a higher affinity for the DNA backbone.  It also appears
      that the relative activities of the two enzymes, particularly at high ionic strength, are
      proportional to their populations in the monomeric enzyme form.  That is, according to gel
      filtration data, half of the N199H molecules exist as monomers in 200 mM NaCl, whereas those
      of the wild-type are mainly dimeric.  Consequently, the Asp199 residue of the EcoRI
      endonuclease may be implicated in the protein-protein interaction leading to dimerization, as
      well as in coupling to DNA substrates.  In summary, it is proposed that active monomeric
      endonuclease molecules, derived from the dimeric enzyme, recognize and form a complex with a
      single stranded form of the DNA substrate, which then undergoes nucleophilic substitution and
      cleavage.
AU  - Kim JJ
AU  - Koh S
AU  - Kim JS
AU  - Lee D-S
PT  - Journal Article
TA  - J. Biochem. Mol. Biol.
JT  - J. Biochem. Mol. Biol.
SO  - J. Biochem. Mol. Biol. 1998 31: 149-155.

PMID- 8675021
VI  - 171
DP  - 1996
TI  - EcoRI variant N199H has enhanced specific activity.
PG  - 129-130
AB  - The Asn199 residue of the EcoRI restriction endonuclease has been replaced with
      other amino acids to investigate whether it mediates nucleotide recognition or catalytic
      activity.
      Cassette mutagenesis gave variants of EcoRI: N199D, N199H, N199L, N199R, N199S and
      N199V.  Their relative cleavage rates were found to be in the following order: N199H>EcoRI
      (wild type; wt)>N199L>N199V>N199S>N199R>N199D.  In particular, EcoRI variant N199H
      showed about a two-fold higher specific activity than that of the wt enzyme.
AU  - Kim JJ
AU  - Min KT
AU  - Kim MH
AU  - Augh SJ
AU  - Kim B-D
AU  - Lee D-S
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1996 171: 129-130.

PMID- 18985277
VI  - 66
DP  - 2009
TI  - Epigenetic mechanisms in mammals.
PG  - 596-612
AB  - DNA and histone methylation are linked and subjected to mitotic inheritance in mammals. Yet
      how methylation is propagated and maintained between successive cell divisions is not fully
      understood. A series of enzyme families that can add methylation marks to cytosine
      nucleobases, and lysine and arginine amino acid residues has been discovered. Apart from
      methyltransferases, there are also histone modification enzymes and accessory proteins, which
      can facilitate and/or target epigenetic marks. Several lysine and arginine demethylases have
      been discovered recently, and the presence of an active DNA demethylase is speculated in
      mammalian cells. A mammalian methyl DNA binding protein MBD2 and de novo DNA methyltransferase
      DNMT3A and DNMT3B are shown experimentally to possess DNA demethylase activity. Thus, complex
      mammalian epigenetic mechanisms appear to be dynamic yet reversible along with a
      well-choreographed set of events that take place during mammalian development.
AU  - Kim JK
AU  - Samaranayake M
AU  - Pradhan S
PT  - Journal Article
TA  - Cell. Mol. Life Sci.
JT  - Cell. Mol. Life Sci.
SO  - Cell. Mol. Life Sci. 2009 66: 596-612.

PMID- 22933762
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Brucella canis Strain HSK A52141, Isolated from the Blood of an Infected Dog.
PG  - 5134
AB  - Brucella canis infection can be clinically inapparent in dogs, and when infection goes
      unnoticed, there is a chance for dog-to-human transmission. A new strain of
      B. canis was isolated from the blood of an infected dog in order to analyze the
      pathogenic mechanism, compare genetic properties, and develop new genetic tools
      for early diagnosis of canine brucellosis. Herein, we report the complete genome
      sequence of the strain B. canis HSK A52141. This is the second complete genome
      sequence and biological annotation available for a member of B. canis.
AU  - Kim JS
AU  - Jeong W
AU  - Jeoung HY
AU  - Song JY
AU  - Kim H
AU  - Beak JH
AU  - Parisutham V
AU  - Lee SK
AU  - Kim JW
AU  - Kim JY
AU  - Jung SC
AU  - Her M
AU  - An DJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5134.

PMID- 25446906
VI  - 44
DP  - 2014
TI  - Complete nucleotide sequence of the IncI1 plasmid pSH4469 encoding CTX-M-15 extended-spectrum beta-lactamase in a clinical isolate of Shigella sonnei from an outbreak in the Republic of Korea.
PG  - 533-537
AB  - An outbreak of extended-spectrum B-lactamase (ESBL)-producing Shigella sonnei infections
      occurred in a school for disabled children in Gyeongbuk Province, Republic of Korea, in 2008.
      Five students were affected. Pulsed-field gel electrophoresis (PFGE) analysis revealed that
      all of the ESBL-producing S. sonnei isolates belonged to the same clone, and nucleotide
      sequence analysis of ESBL genes revealed that they harboured blaCTX-M-15. This is the first
      identification of blaCTX-M-15 in Shigella spp. in South Korea. In this study, a plasmid
      carrying the blaCTX-M-15 gene, designated pSH4469, recovered from a S. sonnei isolate
      responsible for the outbreak was characterised. Replicon typing and plasmid multilocus
      sequence typing (pMLST) analysis of plasmids in the outbreak strain identified that the
      blaCTX-M-15 gene was located on an IncI1 incompatibility group plasmid of sequence type 16
      (ST16). The complete nucleotide sequence of pSH4469 revealed that this plasmid is 91109 bp and
      harbours 119 putative genes, including another antibiotic resistance gene (blaTEM-1b) that is
      often associated with the ISEcp1-blaCTX-M-15-orf477delta transposable unit. The plasmid
      consists of a large backbone with considerable homology to the pEK204 plasmid isolated from
      Escherichia coli in the UK, except for insertion of an IS66 element found in pEK204. These
      data demonstrate that IncI1 plasmids are used as a successful platform for efficient
      horizontal gene transfer, thereby resulting in the dissemination of CTX-M-type B-lactamases
      among Enterobacteriaceae.
AU  - Kim JS
AU  - Kim J
AU  - Jeon S-E
AU  - Kim S-J
AU  - Kim N-O
AU  - Hong S
AU  - Kang Y-H
AU  - Han S
AU  - Chung GT
PT  - Journal Article
TA  - Int. J. Antimicrob. Agents
JT  - Int. J. Antimicrob. Agents
SO  - Int. J. Antimicrob. Agents 2014 44: 533-537.

PMID- 17456140
VI  - 54
DP  - 2007
TI  - Cj1461 DNA methyltransferase in Campylobacter jejuni 81-176 is involved in the regulation of virulence characteristics and bacterial cellular functions.
PG  - 103
AB  - DNA methylases such as Dam can regulate transcription of virulence-associated genes in
      bacteria.  Cj1461 is a DNA methyltransferase conserved in Campylobacter species.  A
      cj1461-insertional mutant of C. jejuni 81-176 had significantly reduced motility at 37C, and
      the reduced motility was partially but significantly recovered in a strain complemented with
      native cj1461 (P<0.05).  A Cj1461-overexpression strain of 81-176 was constructed by
      expressing an inducible cj1461 gene on the shuttle vector pRY111.  cj1461 and cj1462 (flgI)
      were about 1.5- and 1.8-fold overexpressed, respectively, in the Cj1461-overexpression strain
      based on real-time PCR analysis.  In addition, the overexpression strain showed significantly
      increased motility (P<0.05) compared to 81-176 containing pRY111 alone.  Proteome analysis of
      the Cj1461-overexpression strain showed the altered expression of more than 20 proteins
      including PEB1a, PEB3, PEB4, major outer membrane protein, gamma-glutamyl transpeptidase,
      thiol peroxidase, alkyl hydroperoxide reductase, trigger factor and several TCA cycle enzymes.
      These data, along with the altered regulation of numerous C. jejuni genes in the cj1461
      mutant, suggest that Cj1461 DNA methyltransferase is involved in regulating virulence
      characteristics such as motility and other bacterial cellular processes in C. jejuni 81-176.
AU  - Kim JS
AU  - Li J
AU  - Barnes IHA
AU  - Thompson SA
PT  - Journal Article
TA  - Zoonoses Public Health
JT  - Zoonoses Public Health
SO  - Zoonoses Public Health 2007 54: 103.

PMID- 18689478
VI  - 190
DP  - 2008
TI  - Role of the Campylobacter jejuni cj1461 DNA methyltransferase in regulating virulence characteristics.
PG  - 6524-6529
AB  - Mutation of the cj1461 predicted methyltransferase gene reduced the motility of Campylobacter
      jejuni 81-176. Electron microscopy revealed
      that the mutant strain had flagella but with aberrant structure. The
      Delta cj1461 mutant was sevenfold more adherent to but 50-fold less
      invasive of INT-407 human epithelial cells than the wild type.
AU  - Kim JS
AU  - Li JQ
AU  - Barnes IHA
AU  - Baltzegar DA
AU  - Pajaniappan M
AU  - Cullen TW
AU  - Trent MS
AU  - Burns CM
AU  - Thompson SA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2008 190: 6524-6529.

PMID- 22247158
VI  - 78
DP  - 2012
TI  - A Novel Restriction-Modification System Is Responsible for Temperature-Dependent Phage Resistance in Listeria monocytogenes ECII.
PG  - 1995-2004
AB  - Listeria monocytogenes epidemic clone II (ECII) strains are unusual in being completely
      resistant to phage when grown at low temperatures (<=
      30 degrees C). In the current study we constructed and characterized a
      mariner-based mutant (J46C) of the ECII strain H7550-Cd-S that lacked
      temperature-dependent resistance to phage. The transposon was localized
      in LMOh7858 2753 (open reading frame [ORF] 2753), a member of a 12-ORF
      genomic island unique to ECII strains. ORF 2753 and ORF 2754 exhibited
      homologies to restriction endonucleases and methyltransferases
      associated with type II restriction-modification (RM) systems. In
      silico-based predictions of the recognition site for this putative RM
      system were supported by resistance of DNA from ECII strains to
      digestion by BfuI, a type II restriction enzyme specific for GTATCC
      (N6/5). Similarly to J46C, a mutant harboring an in-frame deletion of
      ORF 2753 was susceptible to phage regardless of temperature of growth
      (25 C or 37 degrees C). Genetic complementation restored phage
      resistance in 25 degrees C-grown cells of ORF 2753 mutants. Reverse
      transcription (RT) and quantitative real-time PCR data suggested
      enhanced transcription of ORF 2753 at low temperatures (<= 25 degrees
      C) compared to 37 degrees C. In contrast, available transcriptional
      data suggested that the putative methyltransferase (ORF 2754) was
      constitutively expressed at all tested temperatures (4 to 37 degrees
      C). Thus, temperature-dependent resistance of L. monocytogenes ECII to
      phage is mediated by temperature-dependent expression of the
      restriction endonuclease associated with a novel RM system (LmoH7)
      unique to this epidemic clone.
AU  - Kim JW
AU  - Dutta V
AU  - Elhanafi D
AU  - Lee S
AU  - Osborne JA
AU  - Kathariou S
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2012 78: 1995-2004.

PMID- 27313284
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Vancomycin-Intermediate Staphylococcus aureus Strains in South Korea.
PG  - e00027-16
AB  - We report here the draft genome sequences of four vancomycin-intermediate Staphylococcus
      aureus (VISA) strains from South Korean hospitals participating in
      a nationwide laboratory surveillance program for vancomycin-intermediate and
      vancomycin-resistant Staphylococcus aureus All strains harbor mutations in the
      walKR, graSR, and/or rpoB genes that are known frequently mutated determinants of
      VISA.
AU  - Kim JW
AU  - Yoo JI
AU  - Kang GS
AU  - Lee YS
AU  - Yu JY
AU  - Park C
AU  - Kim IH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00027-16.

PMID- 20622503
VI  - 20
DP  - 2010
TI  - Improvement of Transformation Efficiency Through In Vitro Methylation and SacII Site Mutation of Plasmid Vector in Bifidobacterium longum MG1.
PG  - 1022-1026
AB  - The different cleavage patterns of pYBamy59 plasmid isolated from E. coli DH5 alpha and B.
      longum MG1 by the cell extract of B. longum MG1
      suggested that the main reason for its low transformation efficiency
      was related to the restriction modification (R-M) system. To confirm
      the correlation between the R-M system and transformation efficiency,
      in vitro methylation and site-directed mutagenesis were performed in
      pYBamy59. Sequence analysis of pYBamy59 fragments digested by the cell
      extract of B. longum MG1 revealed that all fragments were generated by
      restriction of the sequence recognized by SacII endonuclease. When
      pYBamy59 from E. coli was methylated in vitro by CpG or GpC
      methyltransferase, it was protected from SacII digestion. Site-directed
      mutagenesis, which removed SacII sites from pYBamy59, or in vitro
      methylation of pYBamy59 showed 8- to 15-fold increases in the
      transformation efficiency over intact pYBamy59. Modification of the
      Sad-related R-M system in B. longum MG1 and in vitro methylation in
      pYBamy 59 can improve the transformation efficiency in this strain. The
      results showed that the R-M system is a factor to limit introduction of
      exogenous DNA, and in vitro modification is a convenient method to
      overcome the barrier of the R-M system for transformation.
AU  - Kim JY
AU  - Wang Y
AU  - Park MS
AU  - Ji GE
PT  - Journal Article
TA  - J. Microbiol. Biotechnol.
JT  - J. Microbiol. Biotechnol.
SO  - J. Microbiol. Biotechnol. 2010 20: 1022-1026.

PMID- 27491981
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of the Proteorhodopsin-Containing Marine Flavobacterium  Dokdonia donghaensis DSW-1T, Isolated from Seawater off Dokdo in the East Sea  (Sea of Korea).
PG  - e00804-16
AB  - Dokdonia spp. have been used for investigating the lifestyles of proteorhodopsin-containing
      photoheterotrophs and for understanding marine
      photobiology. Here, we report the complete genome sequence of Dokdonia
      donghaensis DSW-1(T) using the PacBio sequencing platform. It should provide a
      valuable resource for comparative genomic studies of marine life harboring
      microbial rhodopsins among others.
AU  - Kim K
AU  - Kwon SK
AU  - Yoon JH
AU  - Kim JF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00804-16.

PMID- 22933767
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of the Human Pathogen Halomonas stevensii S18214T.
PG  - 5143
AB  - Halomonas stevensii is a Gram-negative, moderately halophilic bacterium causing environmental
      contamination and infections in a dialysis center. Here we present
      the 3.7-Mb draft genome sequence of the type strain (S18214(T)) of H. stevensii,
      which will give insight into the pathogenic potential of H. stevensii.
AU  - Kim KK
AU  - Lee KC
AU  - Jeong H
AU  - Stevens DA
AU  - Lee JS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5143.

PMID- 23144405
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of the Extremely Halophilic Archaeon Halogranum salarium B-1T.
PG  - 6659
AB  - Halogranum salarium is an extremely halophilic archaeon isolated from evaporitic  salt
      crystals and belongs to the family Halobacteriaceae. Here, we present the
      4.5-Mb draft genome sequence of the type strain (B-1(T)) of H. salarium. This is
      the first report of the draft genome sequence of a haloarchaeon in the genus
      Halogranum.
AU  - Kim KK
AU  - Lee KC
AU  - Lee JS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6659.

PMID- 22966187
VI  - 86
DP  - 2012
TI  - Complete Genome Sequence of Bacteriophage SSU5 Specific for Salmonella enterica serovar Typhimurium Rough Strains.
PG  - 10894
AB  - Salmonella enterica serovar Typhimurium rough strain-specific phage SSU5 was
      isolated, and its whole genome was sequenced. The 103,229-bp-long double-stranded
      DNA genome of SSU5 encodes 130 open reading frames with one tRNA for asparagine.
      Genomic analysis revealed that SSU5 might be the phylogenetic origin of cryptic
      plasmid pHCM2 harbored by Salmonella Typhi CT18.
AU  - Kim M
AU  - Kim S
AU  - Ryu S
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 2012 86: 10894.

PMID- 23986584
VI  - 87
DP  - 2013
TI  - Antirepression System Associated with the Life Cycle Switch in the Temperate Podoviridae Phage SPC32H.
PG  - 11775-11786
AB  - Prophages switch from lysogenic to lytic mode in response to the host SOS response. The
      primary factor that governs this switch is a phage repressor, which is typically a host
      RecA-dependent autocleavable protein. Here, in an effort to reveal the mechanism underlying
      the phenotypic differences between the Salmonella temperate phages SPC32H and SPC32N, whose
      genome sequences differ by only two nucleotides, we identified a new class of Podoviridae
      phage lytic switch antirepressor that is structurally distinct from the previously reported
      Sipho- and Myoviridae phage antirepressors. The SPC32H repressor (Rep) is not cleaved by the
      SOS response but instead is inactivated by a small antirepressor (Ant), the expression of
      which is negatively controlled by host LexA. A single nucleotide mutation in the consensus
      sequence of the LexA-binding site, which overlaps with the ant promoter, results in
      constitutive Ant synthesis and consequently induces SPC32N to enter the lytic cycle. Numerous
      potential Ant homologues were identified in a variety of putative prophages and temperate
      Podoviridae phages, indicating that antirepressors may be widespread among temperate phages in
      the order Caudovirales to mediate a prudent prophage induction.
AU  - Kim M
AU  - Ryu S
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 2013 87: 11775-11786.

PMID- 22933771
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Escherichia coli W26, an Enteric Strain Isolated from Cow Feces.
PG  - 5149-5150
AB  - An enteric bacterium, Escherichia coli W26 (KACC 16630), was isolated from feces  from a
      healthy cow in South Korea. Here, we report the draft genome sequence of
      the isolate, which is closely affiliated with commensal strains belonging to E.
      coli phylogroup B1.
AU  - Kim M
AU  - Yi H
AU  - Cho YJ
AU  - Jang J
AU  - Hur HG
AU  - Chun J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5149-5150.

PMID- 29747442
VI  - 19
DP  - 2018
TI  - Safety Evaluations of Bifidobacterium bifidum BGN4 and Bifidobacterium longum BORI.
PG  - E1422
AB  - Over the past decade, a variety of lactic acid bacteria have been commercially
      available to and steadily used by consumers. However, recent studies have shown
      that some lactic acid bacteria produce toxic substances and display properties of
      virulence. To establish safety guidelines for lactic acid bacteria, the Food and
      Agriculture Organization of the United Nations (FAO)/World Health Organization
      (WHO) has suggested that lactic acid bacteria be characterized and proven safe
      for consumers and rsquo; health via multiple experiments (e.g., antibiotic
      resistance, metabolic activity, toxin production, hemolytic activity, infectivity
      in immune-compromised animal species, human side effects, and adverse-outcome
      analyses). Among the lactic acid bacteria, Bifidobacterium and Lactobacillus
      species are probiotic strains that are most commonly commercially produced and
      actively studied. Bifidobacterium bifidum BGN4 and Bifidobacterium longum BORI
      have been used in global functional food markets (e.g., China, Germany, Jordan,
      Korea, Lithuania, New Zealand, Poland, Singapore, Thailand, Turkey, and Vietnam)
      as nutraceutical ingredients for decades, without any adverse events. However,
      given that the safety of some newly screened probiotic species has recently been
      debated, it is crucial that the consumer safety of each commercially utilized
      strain be confirmed. Accordingly, this paper details a safety assessment of B.
      bifidum BGN4 and B. longum BORI via the assessment of ammonia production,
      hemolysis of blood cells, biogenic amine production, antimicrobial susceptibility
      pattern, antibiotic resistance gene transferability, PCR data on antibiotic
      resistance genes, mucin degradation, genome stability, and possession of
      virulence factors. These probiotic strains showed neither hemolytic activity nor
      mucin degradation activity, and they did not produce ammonia or biogenic amines
      (i.e., cadaverine, histamine or tyramine). B. bifidum BGN4 and B. longum BORI
      produced a small amount of putrescine, commonly found in living cells, at levels
      similar to or lower than that found in other foods (e.g., spinach, ketchup, green
      pea, sauerkraut, and sausage). B. bifidum BGN4 showed higher resistance to
      gentamicin than the European Food Safety Authority (EFSA) cut-off. However, this
      paper shows the gentamicin resistance of B. bifidum BGN4 was not transferred via
      conjugation with L. acidophilus ATCC 4356, the latter of which is highly
      susceptible to gentamicin. The entire genomic sequence of B. bifidum BGN4 has
      been published in GenBank (accession no.: CP001361.1), documenting the lack of
      retention of plasmids capable of transferring an antibiotic-resistant gene.
      Moreover, there was little genetic mutation between the first and 25th
      generations of B. bifidum BGN4. Tetracycline-resistant genes are prevalent among
      B. longum strains; B. longum BORI has a tet(W) gene on its chromosome DNA and has
      also shown resistance to tetracycline. However, this research shows that its
      tetracycline resistance was not transferred via conjugation with L. fermentum
      AGBG1, the latter of which is highly sensitive to tetracycline. These findings
      support the continuous use of B. bifidum BGN4 and B. longum BORI as probiotics,
      both of which have been reported as safe by several clinical studies, and have
      been used in food supplements for many years.
AU  - Kim MJ
AU  - Ku S
AU  - Kim SY
AU  - Lee HH
AU  - Jin H
AU  - Kang S
AU  - Li R
AU  - Johnston TV
AU  - Park MS
AU  - Ji GE
PT  - Journal Article
TA  - Int. J. Mol. Sci.
JT  - Int. J. Mol. Sci.
SO  - Int. J. Mol. Sci. 2018 19: E1422.

PMID- 22072652
VI  - 193
DP  - 2011
TI  - Draft Genome Sequence of Bacteroides faecis MAJ27T, a Strain Isolated from Human Feces.
PG  - 6801-6802
AB  - Despite the ecological importance of the dominant gut bacteria Bacteroides, few genomes have
      been defined. The Gram-negative, strictly
      anaerobic intestinal bacterium Bacteroides faecis MAJ27(T) was isolated
      from the feces of a healthy adult. Here, the draft genome sequence of the
      type strain B. faecis MAJ27 (6.11 Mbp) is reported.
AU  - Kim MS
AU  - Whon TW
AU  - Roh SW
AU  - Shin NR
AU  - Bae JW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6801-6802.

PMID- 26430042
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Mycobacterium bovis Clinical Strain 1595, Isolated from the Laryngopharyngeal Lymph Node of South Korean Cattle.
PG  - e01124-15
AB  - Mycobacterium bovis strain 1595 was isolated from the lymph node of South Korean  native
      cattle. The complete genome sequence of strain 1595 was determined in 2 contigs and was found
      to be 4,351,712 bp in size, with a 65.64% G+C content and 4,358 predicted protein-coding
      genes.
AU  - Kim N
AU  - Jang Y
AU  - Kim JK
AU  - Ryoo S
AU  - Kwon KH
AU  - Kang SS
AU  - Byeon HS
AU  - Lee HS
AU  - Lim YH
AU  - Kim JM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01124-15.

PMID- 26659693
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequence of Mycobacterium bovis W-1171, Isolated from the Laryngopharyngeal Lymph Node of a Wild Boar in South Korea.
PG  - e01464-15
AB  - Mycobacterium bovis W-1171 was isolated from a wild boar living in a free-ranging field in
      Gyeonggido, South Korea. The whole-genome sequence of this strain was
      determined in 50 contigs, which was 4,304,865 bp with a 65.57% G+C content. In
      total 3,945 protein-coding genes were predicted from this assembly.
AU  - Kim N
AU  - Jang Y
AU  - Park SY
AU  - Song WS
AU  - Kim JT
AU  - Lee HS
AU  - Lim YH
AU  - Kim JM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01464-15.

PMID- 6093038
VI  - 12
DP  - 1984
TI  - Interactive recognition in EcoRI restriction enzyme-DNA complex.
PG  - 7285-7292
AB  - A solution study of interaction between DNA and EcoRI restriction enzyme shows
      that there is a definite distortion of DNA in the specific recognition
      complexes but no measurable DNA distortion in the non-specific interaction.
AU  - Kim R
AU  - Modrich P
AU  - Kim S-H
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1984 12: 7285-7292.

PMID- 2833816
VI  - 240
DP  - 1988
TI  - Cleaving DNA at any predetermined site with adapter-primers and class-IIS restriction enzymes.
PG  - 504-506
AB  - A four-component system has been designed that makes it possible to prepare a
      double-stranded (ds) DNA fragment; one fragment end is predesigned (by the use
      of a class-IIS restriction enzyme and adapter-primer), and the other end
      corresponds to any normal restriction cut.  The system is composed of the phage
      M13mp7 single stranded (ss) target DNA; the Fok I restriction enzyme; an
      oligodeoxynucleotide adapter-primer, which permits one to introduce Fok I cuts
      at any specified site in the target DNA; and DNA polymerase, which converts the
      ss target into a ds form ready for cloning.  In this system, the
      oligodeoxynucleotide adapter-primer serves several purposes.  The 5' hairpin ds
      domain of the adapter-primer  contains a Fok I recognition site.  Its 3' ss
      domain selects a complementary site on the target ss DNA, hybridizes with it to
      form the ds cleavage site, and serves as a primer to convert the ss M13mp7
      target to ds DNA.
AU  - Kim SC
AU  - Podhajska AJ
AU  - Szybalski W
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1988 240: 504-506.

PMID- 1647357
VI  - 100
DP  - 1991
TI  - A novel gene-fusing vector: construction of a 5'-GGmCC-specific chimeric methyltransferase, M.BspRI/M.BsuRI.
PG  - 45-50
AB  - A vector was designed to allow predetermined and precise fusion between two
      genes by constructing a cassette with two unique class-IIS restriction sites,
      5'-ACCTGC3' (BspMI) and 5'-CCGGATG-3' (FokI overlapping with MspI), arranged
      back-to-back in a divergent manner and inserted at the HincII site of a
      multiple cloning site (MCS) in plasmid pUC18 or analogous vehicle.  Two DNA
      fragments or genes to be precisely fused are cloned into the MCS parts located
      on each side of the cassette containing the two unique class-IIS restriction
      sites.  The BspMI and MspI/FokI sites are used to generate unidirectional
      deletions of the genes as previously described (Hasan et al., Gene 50(1986)
      55-62; Posfai and Szybalski, Nucleic Acids Res. 16(1988)6245).  The precisely
      trimmed genes are ligated after the cassette containing the unique class-IIS
      restriction sites are excised with BspMI + FokI and the termini were blunted
      with mung-bean nuclease.  This method was used to construct a hybrid
      methyltransferase (MTase) from the M.BspRI and M.BsuRI MTases, which share a
      high degree of overall homology (about 65%) and have the identical sequence
      specificity (5'-GGmCC-3').  A hybrid MTase composed of the N-terminal part of
      M.BspRI and the C-terminal part of M.BsuRI was constructed and found to be
      fully functional.
AU  - Kim SC
AU  - Posfai G
AU  - Szybalski W
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1991 100: 45-50.

PMID- 8636998
VI  - 258
DP  - 1996
TI  - Structural requirements for FokI-DNA interaction and oligodeoxyribonucleotide- instructed cleavage.
PG  - 638-649
AB  - The FokI restriction endonuclease recognizes the double-stranded (ds) 5'-GGATG-3'
      site and cuts at the 9th and 13th nucleotides downstream from the 5'-3' and 3'-5'
      strands, respectively.  To elucidate the interaction between FokI and DNA, and the effect of
      Mg2+
      on this interaction, we used FokI with various combinations of dsDNA, single-stranded (ss) DNA
      and oligodeoxyribonucleotides (oligos) containing a double-stranded hairpin carrying the FokI
      recognition site.  Oligo- and dsDNA-FokI interactions showed that for fully effective
      recognition,
      two or more base-pairs were required outside the 5'-GGATG-3' site.  When using FokI with
      ssDNA and oligos, precise cutting with no observable byproducts was observed at the 9th or
      13th
      nucleotide.  This was independent of whether the region between the recognition and cut sites
      was
      perfectly complementary or whether there were up to four mismatches in this region, or a
      single
      mismatch within the cut site.  Moreover, FokI cleavage, when followed by step-wise filling-in
      of
      FokI cohesive ends in the dsDNA, allowed FokI to recleave such sites when two or more
      nucleotides were added, releasing 2-mer, 3-mer, or 4-mer single-stranded chains.
      Electrophoretic
      mobility shift assays showed that the DNA helix was bent when complexed with FokI (without
      Mg2+).  Such a complex, when formed in the absence of Mg2+, did not accept the subsequently
      added Mg2+ for several minutes.  This suggests a tight, diffusion-resistant contact between
      the
      enzyme and the cognate DNA sequence.  In the presence of Mg2+, the half-life of the complex
      FokI and dsDNA was 12 minutes at 22oC.  In the absence of Mg2+, such a complex, possessing a
      terminally located 5'-GGATG-3' site, had a half-life of 1.5 to 2 minutes.  However, if
      magnesium
      ions were present, this complex had a stability similar to that of a complex formed with dsDNA
      containing a centrally located 5'-GGATG-3' site.
AU  - Kim SC
AU  - Skowron PM
AU  - Szybalski W
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1996 258: 638-649.

PMID- 30533919
VI  - 7
DP  - 2018
TI  - Draft Genome Sequence of 'Candidatus Izimaplasma sp.' Strain ZiA1, Obtained from  a Toluene-Degrading and Iron-Reducing Enrichment Culture.
PG  - e00861-18
AB  - Here, we report the draft genome sequence of 'Candidatus Izimaplasma sp.' strain  ZiA1 (1.88
      Mb and 29.6% G+C content). Strain ZiA1 was cocultured with
      iron-reducing and toluene-degrading bacteria in an enrichment culture from tidal
      flat sediment. Like the genomes of other strains of 'Ca. Izimaplasma,' the ZiA1
      genome contained genes required for anaerobic fermentation.
AU  - Kim SJ
AU  - Park SJ
AU  - Kim JG
AU  - Jung MY
AU  - Gwak JH
AU  - Rhee SK
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e00861-18.

PMID- 22493207
VI  - 194
DP  - 2012
TI  - Genome sequence of a novel member of the genus psychrobacter isolated from antarctic soil.
PG  - 2403
AB  - Psychrobacter spp. have shown characteristics indicating remarkable capabilities  at subzero
      temperatures that identify them as potential model organisms for the
      study of low-temperature adaptations. Here we present the draft genome sequence
      of Psychrobacter sp. PAMC 21119, which was isolated from permafrost soil of
      Antarctica; this information could provide insight into adaptation and evolution
      strategies under extreme environmental conditions.
AU  - Kim SJ
AU  - Shin SC
AU  - Hong SG
AU  - Lee YM
AU  - Choi IG
AU  - Park H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2403.

PMID- 22461541
VI  - 194
DP  - 2012
TI  - Genome Sequence of Janthinobacterium sp. Strain PAMC 25724, Isolated from Alpine  Glacier Cryoconite.
PG  - 2096
AB  - The draft genome of Janthinobacterium sp. strain PAMC 25724, which is a violacein-producing
      psychrotolerant bacterium, was determined. The strain was
      isolated from glacier cryoconite of the Alps mountain permafrost region. The
      sequence will allow identification and characterization of the genetic
      determination of its cold-adaptive properties.
AU  - Kim SJ
AU  - Shin SC
AU  - Hong SG
AU  - Lee YM
AU  - Lee H
AU  - Lee J
AU  - Choi IG
AU  - Park H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2096.

PMID- 25103761
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Bacillus anthracis HYU01, Isolated from Soil Samples  in the Korean Peninsula.
PG  - e00769-14
AB  - Bacillus anthracis is a Gram-positive endospore-forming bacterium that causes the zoonotic
      disease anthrax. We report a complete genome sequence of B. anthracis
      strain HYU01, isolated from Changnyung, which belongs to the B branch (B.Br.)
      001/002 canonical single nucleotide polymorphism (canSNP) group.
AU  - Kim SK
AU  - Chung WH
AU  - Kim SH
AU  - Jung KH
AU  - Kim N
AU  - Chai YG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00769-14.

PMID- 22740675
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Unclassified Marine Gammaproteobacterium BDW918.
PG  - 3753-3754
AB  - The unclassified marine gammaproteobacterium BDW918, which utilizes volatile fatty acids but
      not most common carbohydrates and amino acids, was isolated from
      Dokdo seawater in South Korea. Here we present a draft genome of the strain
      BDW918, which encodes many putative genes related to fatty acid metabolism and
      aromatic hydrocarbon degradation.
AU  - Kim SM
AU  - Cho SJ
AU  - Lee SB
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3753-3754.

PMID- 28302786
VI  - 5
DP  - 2017
TI  - Genome Sequences of Four Nonhuman/Nonclinical Salmonella enterica Serovar Kentucky ST198 Isolates Recovered between 1972 and 1973.
PG  - e01699-16
AB  - Salmonella enterica serovar Kentucky is a polyphyletic member of S. enterica subclade A1 with
      multiple sequence types that often colonize the same hosts but
      in different frequencies on different continents. To evaluate the genomic
      features involved in S Kentucky host specificity, we sequenced the genomes of
      four isolates recovered in the 1970s.
AU  - Kim SW
AU  - Haley BJ
AU  - Roberson D
AU  - Allard M
AU  - Hammack TS
AU  - Brown EW
AU  - Van Kessel JA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01699-16.

PMID- 28860238
VI  - 5
DP  - 2017
TI  - Genome Sequences of 30 Escherichia coli O157:H7 Isolates Recovered from a Single  Dairy Farm and Its Associated Off-Site Heifer-Raising Facility.
PG  - e00814-17
AB  - Cattle are the primary reservoir of Escherichia coli O157:H7, the most frequently isolated
      serotype of enterohemorrhagic E. coli infections among humans in North
      America. To evaluate the diversity of E. coli O157:H7 isolates within a single
      dairy herd, the genomes of 30 isolates collected over a 7-year period were
      sequenced.
AU  - Kim SW
AU  - Karns JS
AU  - Van Kessel JAS
AU  - Haley BJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00814-17.

PMID- 28818889
VI  - 5
DP  - 2017
TI  - Genome Sequences of Five Multidrug-Resistant Escherichia coli Sequence Type 117 Isolates Recovered from Dairy Calves.
PG  - e00732-17
AB  - Escherichia coli sequence type 117 (ST117) strains have been recovered from poultry with
      colibacillosis, as well as from urinary tract infections and fatal
      septic infections in humans. To further investigate ST117 isolates recovered from
      nonpoultry food animals, we sequenced the genomes of five ST117 isolates from
      dairy calves in Pennsylvania.
AU  - Kim SW
AU  - Karns JS
AU  - Van Kessel JAS
AU  - Haley BJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00732-17.

PMID- 
VI  - 40
DP  - 2010
TI  - Correlation between Sau1 restriction and modification complex type and coagulase serotype or SCCmec type of Staphylococcus aureus.
PG  - 163-170
AB  - Staphylococcus aureus coagulase serotype I to VIII isolated from clinical samples could be
      classified into two groups,
      methicillin-sensitive S. aurues (MSSA) and methicilln-resistant S. aurues (MRSA), by
      antibiotics susceptibility and
      existence of mecA which is a gene related with methicillin resistance. Coagulase serotype I,
      VI, and VIII were MSSA
      which showed different antimicrobial susceptibility. Coagluase serotype II-V and VII are MRSA
      in which mecA and
      SCCmec are detected. To analyze Sau1 restriction and modification (R-M) complex types by
      coagulase type and
      SCCmec type, sau1hsdR, sau1hsdM and sau1hsdS genes involved in Sau1 R-M complex were detected
      by PCR, we
      found five complex types such as M1, R2M2, R2M2, R2M2S1, and R2M2S2. Coagulase serotype I, VI,
      and VIII of
      MSSA were M1, R2M2 and R2M2, respectively. SCCmec type II and coagulase serotype II, SCCmec
      type III and
      coagulase serotype III, SCCmec type IV and coagulase serotype V, and SCCmec type IV and
      coagulase serotype IV,
      VII of MRSA were Sau1 R-M complex type R2M2S1, R2M2, R2M2, and R2M2S2, respectively. Taken
      together,
      correlation between Sau1 R-M complex types and coagulase or SCCmec types of S. aureus was
      found.
AU  - Kim SY
AU  - Hwang SM
AU  - Chang KS
PT  - Journal Article
TA  - J. Bacteriol. Virol.
JT  - J. Bacteriol. Virol.
SO  - J. Bacteriol. Virol. 2010 40: 163-170.

PMID- 
VI  - 97
DP  - 2008
TI  - Optimal culture condition of restriction endonuclease Bci528I producing strain by QE method.
PG  - 42-43
AB  - In this paper we determine optimal culture condition of Bacillus circulans 528 on production
      of a new restriction endonuclease Bci528I by QE method.
AU  - Kim UY
AU  - Jon SC
AU  - Ra SR
PT  - Journal Article
TA  - Choson Minjujuui Inmin Konghwaguk Kwahagwon Tongbo
JT  - Choson Minjujuui Inmin Konghwaguk Kwahagwon Tongbo
SO  - Choson Minjujuui Inmin Konghwaguk Kwahagwon Tongbo 2008 97: 42-43.

PMID- 24092779
VI  - 1
DP  - 2013
TI  - Genome Sequence of Marine Bacterium Idiomarina sp. Strain 28-8, Isolated from Korean Ark Shells.
PG  - e00772-13
AB  - Idiomarina sp. strain 28-8 is an aerobic, Gram-negative, flagellar bacterium isolated from the
      bodies of ark shells (Scapharca broughtonii) collected from
      underwater sediments in Gangjin Bay, South Korea. Here, we present the draft
      genome sequence of Idiomarina sp. 28-8 (2,971,606 bp, with a G+C content of
      46.9%), containing 2,795 putative coding sequences.
AU  - Kim WJ
AU  - Kim YO
AU  - Kim DG
AU  - Nam BH
AU  - Kong HJ
AU  - Jung H
AU  - Lee SJ
AU  - Kim DW
AU  - Kim DS
AU  - Chae SH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00772-13.

PMID- 21685281
VI  - 193
DP  - 2011
TI  - Draft Genome Sequence of Kocuria rhizophila P7-4.
PG  - 4286-4287
AB  - We report the draft genome sequence of Kocuria rhizophila P7-4, which was isolated from the
      intestine of Siganus doliatus caught in the Pacific
      Ocean. The 2.83-Mb genome sequence consists of 75 large contigs (>100 bp
      in size) and contains 2,462 predicted protein-coding genes.
AU  - Kim WJ
AU  - Kim YO
AU  - Kim DS
AU  - Choi SH
AU  - Kim DW
AU  - Lee JS
AU  - Kong HJ
AU  - Nam BH
AU  - Kim BS
AU  - Lee SJ
AU  - Park HS
AU  - Chae SH
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4286-4287.

PMID- 28963201
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Three Novel Low-Abundance Species Strains Isolated from Kefir Grain.
PG  - e00869-17
AB  - We report here the genome sequences of three novel bacterial species strains-Bacillus
      kefirresidentii Opo, Rothia kefirresidentii KRP, and
      Streptococcus kefirresidentii YK-isolated from kefir grains collected in Germany.
      The draft genomes of these isolates were remarkably dissimilar (average
      nucleotide identities, 77.80%, 89.01%, and 92.10%, respectively) to those of the
      previously sequenced strains.
AU  - Kim Y
AU  - Blasche S
AU  - Patil KR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00869-17.

PMID- 7905633
VI  - 91
DP  - 1994
TI  - Chimeric restriction endonuclease.
PG  - 883-887
AB  - Fok I restriction endonuclease recognizes the nonpalindromic pentadeoxyribonucleotide
      5'-GGATG-3'-5'-CATCC-3' in duplex DNA and cleaves 9 and 13 nt away from the recognition
      site. Recently, we reported the presence of two distinct and separable domains within this
      enzyme: one for the sequence-specific recognition of DNA (the DNA-binding domain) and the
      other for the endonuclease activity (the cleavage domain). Here, we report the construction of
      a chimeric restriction endonuclease by linking the Drosphila Ultrabithorax homeodomain to the
      cleavage domain (F/N) of Fok I restriction endonuclease. The hybrid enzyme, Ubx-F/N, was
      purified, and its cleavage properties were characterized. The hybrid enzyme show the same DNA
      sequence-binding preference as that of Ubx; as expected, it cleaves the DNA away from the
      recognition site. On the 5'-TTAATGGTT-3' strand the hybrid enzyme cleaves 3 nt away from the
      recognition site, whereas it cuts the complementary 5'-AACCATTAA-3' strand 8, 9, or 10 nt
      away from the binding site. Similarly engineered hybrid enzymes could be valuable tools in
      physical mapping and sequencing of large eukaryotic genomes.
AU  - Kim Y
AU  - Chandrasegaran S
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1994 91: 883-887.

PMID- 
VI  - 0
DP  - 1994
TI  - Studies on the canonical DNA-EcoRI endonuclease complex and the EcoRI kink.
PG  - 225-246
AB  - The crystal structure of the complex between EcoRI endonuclease and the cognate
      oligonucleotide TCGCGAATTCGCG was determined to 2.7 A resolution by multiple isomorphous
      derivatives and refined to an R-factor of 0.21.  The complex includes two protein subunits
      related by a two-fold axis of rotational symmetry; they have alpha/beta architecture with the
      cleavage site at a "switch point" of the beta sheet.  Sequence specificity is mediated by
      eighteen hydrogen bonds and numerous Van der Walls contacts between the protein and the DNA
      bases.  The DNA is distorted in the complex; the "EcoRI kink" is characterized by unusual
      roll, increased rise, underwinding, a "kink" or "jog" in the backbone at the ApA step and
      widening of both the major and minor grooves.
AU  - Kim Y
AU  - Choi J
AU  - Grable JC
AU  - Greene P
AU  - Hager P
AU  - Rosenberg JM
PT  - Journal Article
TA  - Structural Biology: The State of the Art.
JT  - Structural Biology: The State of the Art.
SO  - Structural Biology: The State of the Art. 1994 0: 225-246.

PMID- 2399465
VI  - 249
DP  - 1990
TI  - Refinement of EcoRI endonuclease crystal structure: A revised protein chain tracing.
PG  - 1307-1309
AB  - None
AU  - Kim Y
AU  - Grable JC
AU  - Love R
AU  - Greene PJ
AU  - Rosenberg JM
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1990 249: 1307-1309.

PMID- 8577732
VI  - 93
DP  - 1996
TI  - Hybrid restriction enzymes: Zinc finger fusions to FokI cleavage domain.
PG  - 1156-1160
AB  - A long-term goal in the field of restriction-modification enzymes has been to generate
      restriction endonucleases with novel sequence specificities by mutating or engineering
      existing enzymes.  This will avoid the increasingly arduous task of extensive screening of
      bacteria and other microorganisms for new enzymes.  Here, we report the deliberate creation of
      novel site-specific endonucleases by linking two different zinc finger proteins to the
      cleavage domain of FokI endonuclease.  Both fusion proteins are active and under optimal
      conditions cleave DNA in a sequence-specific manner.  Thus, the modular structure of FokI
      endonuclease and the zinc finger motifs makes it possible to create "artificial" nucleases
      that will cut DNA near a predetermined site.  This opens the way to generate many new enzymes
      with tailor-made sequence specifities desirable for various applications.
AU  - Kim Y-G
AU  - Cha J
AU  - Chandrasegaran S
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1996 93: 1156-1160.

PMID- 9371768
VI  - 94
DP  - 1997
TI  - Construction of a Z-DNA-specific restriction endonuclease.
PG  - 12875-12879
AB  - Novel restriction enzymes can be created by fusing the nuclease domain of FokI endonuclease
      with defined DNA binding domains.  Recently, we have characterized a domain (Za) from the
      N-terminal region of human double-stranded RNA adenosine deaminase, which binds the
      Z-conformation with high specificity.  Here we report creation of a conformation-specific
      endonuclease, Za nuclease, which is a chimera of Za and FokI nuclease.  Purified Za nuclease
      cleaves negatively supercoiled plasmids only when they contain a Z-DNA forming insert, such as
      (dC-dG)13.  The precise location of the cleavage sites was determined by primer extension.
      Cutting has been mapped to the edge of the B-Z junction, suggesting that Za nuclease binds
      within the Z-DNA insert, but cleaves in the nearby B-DNA, by using a mechanism similar to type
      IIs restriction enzymes.  These data show that Za binds Z-DNA in an environment similar to
      that in a cell.  Za nuclease, a structure-specific restriction enzyme, may be a useful tool
      for further study of the biological role of Z-DNA.
AU  - Kim Y-G
AU  - Kim PS
AU  - Herbert A
AU  - Rich A
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1997 94: 12875-12879.

PMID- 7989374
VI  - 269
DP  - 1994
TI  - Insertion and deletion mutants of FokI restriction endonuclease.
PG  - 31978-31982
AB  - FokI restriction endonuclease recognizes the nonpalindromic pentadeoxyribonucleotide,
      5'-GGATG-3':5'-CATCC-3' in duplex DNA and cleaves 9 and 13 nucleotides away from the
      recognition site. We have reported the presence of two distinct and separable protein domains
      within this enzyme: one for the sequence-specific recognition of DNA (the DNA binding domain)
      and the other for the endonuclease's activity (the cleavage domain). Our studies have
      suggested that the two domains are connected by a linker region, which appears to be amenable
      for repositioning of the DNA-sequence recognition domain with respect to the catalytic domain.
      Here, we report the construction of several insertion (4-, 8-, 12-, 18-, 19-, or 23-amino acid
      residues) and deletion (4- or 7-amino acid residues) mutants of the linker region of FokI
      endonuclease. The mutant enzymes were purified, and their cleavage properties were
      characterized. The mutants have the same DNA sequence specificity as the wild-type enzyme.
      However, compared with the wild-type enzyme, the insertion mutants cleave predominantly one
      nucleotide further away from the recognition site on both strands of the DNA substrate. The
      four-codon deletion mutant shows relaxed specificity at the cut site while the seven-codon
      deletion appears to inactivate the enzyme. The DNA binding and cleavage domains of FokI appear
      to be linked by a relatively malleable linker. No simple linear relationship exists between
      the linker length and the distance of the cut site from the recognition site. Furthermore, the
      four-codon insertion mutants cleave DNA substrates containing hemi-methylated FokI sites; they
      do not cleave fully methylated substrates. These results are best explained as a consequence
      of protein-protein interactions between the domains.
AU  - Kim Y-G
AU  - Li L
AU  - Chandrasegaran S
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1994 269: 31978-31982.

PMID- 9426005
VI  - 203
DP  - 1997
TI  - Site-specific cleavage of DNA-RNA hybrids by zinc finger/FokI cleavage domain fusions.
PG  - 43-49
AB  - Zinc-finger proteins of the Cys2His2 type bind DNA-RNA hybrids with affinities comparable to
      those for DNA duplexes.  Such zinc-finger proteins were converted into site-specific cleaving
      enzymes by fusing them to the FokI cleavage domain.  The  proteins are active and under
      optimal conditions cleave DNA duplexes in a sequence-specific manner.  These fusions also
      exhibit site-specific cleavage of the DNA strand within DNA-RNA hybrids albeit at a lower
      efficiency (~/-50-fold) compared to the cleavage of the DNA duplexes.  These engineered
      endonucleases represent the first of their kind in terms of their DNA-RNA cleavage properties,
      and they may have important biological applications.
AU  - Kim Y-G
AU  - Shi Y
AU  - Berg M
AU  - Chandrasegaran S
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1997 203: 43-49.

PMID- 9628342
VI  - 379
DP  - 1998
TI  - Chimeric restriction enzyme: Gal4 fusion to FokI cleavage domain.
PG  - 489-495
AB  - Gal4, a yeast protein, activates transcription of genes required for metabolism of galactose
      and melibiose.  It binds as a dimer to a consensus palindromic 17-base pair DNA sequence.  It
      is a member of the third family of proteins that contain zinc-mediated peptide loops that
      interact specifically with nucleic acids.  Gal4 has a very distinctive zinc coordination
      profile and mode of DNA-binding.  Here, we report the creation of a novel site-specific
      endonuclease by linking the N-terminal 147 amino acids of Gal4 to the cleavage domain of FokI
      endonuclease.  The fusion protein is active and under optimal conditions, binds to a 17 bp
      consensus DNA site and cleaves near this site.  As expected, the cleavage occurs on either
      side of the consensus binding site(s).
AU  - Kim Y-G
AU  - Smith J
AU  - Durgesha M
AU  - Chandrasegaran S
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1998 379: 489-495.

PMID- 29046742
VI  - 12
DP  - 2017
TI  - Complete genome sequence of Paenibacillus yonginensis DCY84T, a novel plant Symbiont that promotes growth via induced systemic resistance.
PG  - 63
AB  - This article reports the full genome sequence of Paenibacillus yonginensis DCY84T (KCTC33428,
      JCM19885), which is a Gram-positive rod-shaped bacterium isolated
      from humus soil of Yongin Forest in Gyeonggi Province, South Korea. The genome
      sequence of strain DCY84T provides greater understanding of the Paenibacillus
      species for practical use. This bacterium displays plant growth promotion via
      induced systemic resistance of abiotic stresses.
AU  - Kim YJ
AU  - Sukweenadhi J
AU  - Seok JW
AU  - Kang CH
AU  - Choi ES
AU  - Subramaniyam S
AU  - Yang DC
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 63.

PMID- 21685286
VI  - 193
DP  - 2011
TI  - Genome Sequence of Acinetobacter sp. Strain P8-3-8, Isolated from Fistularia commersonii in Vietnam.
PG  - 4288-4289
AB  - Acinetobacter sp. strain P8-3-8 is an aerobic, Gram-negative marine bacterium isolated from
      the intestine of the bluespotted cornetfish
      (Fistularia commersonii). Here, we present the draft genome sequence of
      Acinetobacter sp. P8-3-8 (3,905,565 bp, with a G+C content of 37.6%)
      containing 3,621 putative coding sequences. The genome data reveal a high
      density of genes encoding transcriptional regulators involved in anaerobic
      respiration.
AU  - Kim YO
AU  - Kim WJ
AU  - Choi SH
AU  - Kim DS
AU  - Kim DW
AU  - Lee JS
AU  - Kong HJ
AU  - Nam BH
AU  - Kim BS
AU  - Lee SJ
AU  - Park HS
AU  - Chae SH
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4288-4289.

PMID- 26112795
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Streptacidiphilus oryzae TH49T, an Acidophilic Actinobacterium Isolated from Soil.
PG  - e00703-15
AB  - The draft genome sequence of Streptacidiphilus oryzae strain TH49(T), an acidophilic
      actinobacterium, was obtained. The draft is composed of six scaffolds
      totaling 7.8 Mbp, and it contains 6,829 protein-coding genes and 91 RNA genes.
      Genes related to respiratory nitrate reduction, siderophore production, and
      biosynthesis of other secondary metabolites were identified.
AU  - Kim YR
AU  - Park S
AU  - Kim TS
AU  - Kim MK
AU  - Han JH
AU  - Joung Y
AU  - Kim SB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00703-15.

PMID- 
VI  - 48
DP  - 2012
TI  - Antimicrobial and Biogenic Amine-Degrading Activity of.
PG  - 163-170
AB  - In order to inhibit the growth of pathogens and degrade biogenic amines during the
      fermentation of soybean products, an isolate with antimicrobial activity against pathogens and
      biogenic amine-degrading property was obtained from 83 traditionally fermented soybean
      products. The morphological and biochemical tests and the phylogenetic relationship among 16S
      rRNA gene sequences indicated that the isolate named as the strain SCK B11 was most closely
      related to Bacillus licheniformis. The cell-free supernatant of two day cultures was active
      against several pathogens including Enterococcus faecalis, Listeria monocytosis, Micrococcus
      luteus, Pseudomonas aeruginosa, Bacillus cereus, and Staphylococcus aureus. PCR analysis was
      conducted to determine relatedness to antimicrobial lantibiotics and biosurfactants produced
      by Bacillus spp., but showed negative for the genes encoding surfactin, lichenysin, and
      lichenicidine. Electron microscopic observation indicated that the antimicrobial agent seemed
      to attack the membrane of the pathogens, leaving the ghost or shrunken cells. The strain was
      found to degrade histamine by 72% and tyramine by 66% in the cooked soybean containing 5.3% of
      biogenic amine over 10 days of fermentation time. The use of selected strain would be a
      potential control measure in manufacturing traditionally fermented soybean products that are
      difficult to control pathogens and biogenic amine levels.
AU  - Kim YS
AU  - Jeong JO
AU  - Cho SH
AU  - Jeong DY
AU  - Uhm T-B
PT  - Journal Article
TA  - Misaengmul Hakhoe Chi
JT  - Misaengmul Hakhoe Chi
SO  - Misaengmul Hakhoe Chi 2012 48: 163-170.

PMID- Not carried by PubMed...
VI  - 24
DP  - 1986
TI  - Characterization of the restriction endonuclease BdiI from Brevibacterium divaricatum.
PG  - 18-23
AB  - A new type II restriction endonuclease, BdiI, has been isolated from Brevibacterium
      divaricatum FERM 5948 by procedures of ammonium sulfate fractionation, DEAE-cellulose
      chromatography and heparin agarose chromatography. The purified BdiI restriction endonuclease
      had the same cleavage patterns as ClaI whose recognition sequence is 5'ATCGAT3'. From the
      result that lambda-ClaI DNA fragment could be cloned in pBR322 digested with BdiI, it has been
      proven that BdiI cuts between T and C (R'AT/CGAT3') within the recognition sequence and
      produces 5'pCG cohesive end. The optimal temperature for the BdiI restriction endonuclease
      activity was 37C, and optimal salt (NaCl) concentration was 50-100 mM.
AU  - Kim YS
AU  - Rho HM
PT  - Journal Article
TA  - Korean J. Microbiol.
JT  - Korean J. Microbiol.
SO  - Korean J. Microbiol. 1986 24: 18-23.

PMID- Not carried by PubMed...
VI  - 17
DP  - 1984
TI  - Purification and Characterization of PstI Methylase from Providencia stuartii 164.
PG  - 107-119
AB  - In this report, we described the purification and characterization of PstI
      methylase from Providencia stuartii 164.  PstI methylase was a site-specific
      methylase and has been found to have methylation activity on single-stranded
      PhiX174 DNA.  This purified PstI methylase will be valuable for the study of
      the structure and expression of PstI restriction-modification gene.
AU  - Kim YS
AU  - Rho HM
PT  - Journal Article
TA  - Korean Biochem. J.
JT  - Korean Biochem. J.
SO  - Korean Biochem. J. 1984 17: 107-119.

PMID- 766758
VI  - 68
DP  - 1976
TI  - The release of oligonucleotides by the Escherichia coli B restriction endonuclease.
PG  - 585-591
AB  - The Escherichia coli B (Eco B) restriction endonuclease releases approximately
      75 nucleotides as acid-soluable oligonucleotides for each single-strand
      endonucleolytic scission that it catalyzes.  This reaction, like the
      endonucleolytic cleavage, requires ATP, Mg++, S-adenosylmethionine, and
      unmodified DNA containing appropriate specificity sites.  Like the endonuclease
      reaction, the release of oligonucleotides terminates after roughly 5 minutes.
      The acid-soluable oligonucleotides have an average chain length of roughly 7,
      and an apparently random base composition.
AU  - Kimball M
AU  - Linn S
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1976 68: 585-591.

PMID- 23833136
VI  - 1
DP  - 2013
TI  - The Draft Genome Sequence of Nocardioides sp. Strain CF8 Reveals the Scope of Its Metabolic Capabilities.
PG  - e00439-13
AB  - Nocardioides sp. strain CF8 was isolated from a soil sample collected at the Hanford
      Department of Energy site, Richland, WA. The strain was identified in
      microcosms based on its ability to grow on butane and has been characterized for
      its potential applications in the biodegradation of halogenated hydrocarbons.
      Here, the draft genome sequence is reported.
AU  - Kimbrel JA
AU  - Chang J
AU  - Arp DJ
AU  - Sayavedra-Soto LA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00439-13.

PMID- 22300632
VI  - 22
DP  - 2012
TI  - A vast collection of microbial genes that are toxic to bacteria.
PG  - 802-809
AB  - In the process of clone-based genome sequencing, initial assemblies frequently
      contain cloning gaps that can be resolved using cloning-independent methods, but
      the reason for their occurrence is largely unknown. By analyzing 9,328,693
      sequencing clones from 393 microbial genomes, we systematically mapped more than
      15,000 genes residing in cloning gaps and experimentally showed that their
      expression products are toxic to the Escherichia coli host. A subset of these
      toxic sequences was further evaluated through a series of functional assays
      exploring the mechanisms of their toxicity. Among these genes, our assays
      revealed novel toxins and restriction enzymes, and new classes of small,
      non-coding toxic RNAs that reproducibly inhibit E. coli growth. Further analyses
      also revealed abundant, short, toxic DNA fragments that were predicted to
      suppress E. coli growth by interacting with the replication initiator DnaA. Our
      results show that cloning gaps, once considered the result of technical problems,
      actually serve as a rich source for the discovery of biotechnologically valuable
      functions, and suggest new modes of antimicrobial interventions.
AU  - Kimelman A
AU  - Levy A
AU  - Sberro H
AU  - Kidron S
AU  - Leavitt A
AU  - Amitai G
AU  - Yoder-Himes D
AU  - Wurtzel O
AU  - Zhu Y
AU  - Rubin E
AU  - Sorek R
PT  - Journal Article
TA  - Genome Res.
JT  - Genome Res.
SO  - Genome Res. 2012 22: 802-809.

PMID- 19302297
VI  - 107
DP  - 2009
TI  - Induction of the histidine decarboxylase genes of Photobacterium damselae subsp. damselae (formally P. histaminum) at low pH.
PG  - 485-497
AB  - AIMS: To elucidate the detailed mechanism of histamine production by Photobacterium damselae
      subsp. damselae. METHODS AND RESULTS: Histidine decarboxylase and related genes of P. damselae
      subsp. damselae were cloned, and three open reading frames named as hdcT, hdcA and hisRS were
      identified. The hdcA gene encodes a polypeptide of 377 amino acids and is considered to be the
      pyridoxal-P dependent histidine decarboxylase. The hdcT gene is assumed to be a
      histidine/histamine antiporter, and the hisRS gene is considered to be a histidyl-tRNA
      synthetase. Recombinant Escherichia coli strains harbouring plasmids carrying the P. damselae
      hdc genes were shown to over-excrete histamine extracellularly. Northern blot analysis and
      quantitative RT-PCR revealed high levels of mono- and bi-cistronic transcripts of hdcA, hdcT
      and hisRS genes under conditions of low pH and histidine excess. CONCLUSIONS: The hdcA gene of
      P. damselae was constructed as an operon with putative histidine/histamine antiporter and
      histidyl-tRNA synthetase. Mono- and poly-cistronic transcripts and acid induction were
      detected. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first report of cloning the
      histidine decarboxylase gene cluster in gram-negative bacteria. Also, these genes were induced
      under acidic conditions and in the presence of excess histidine.
AU  - Kimura B
AU  - Takahashi H
AU  - Hokimoto S
AU  - Tanaka Y
AU  - Fujii T
PT  - Journal Article
TA  - J. Appl. Microbiol.
JT  - J. Appl. Microbiol.
SO  - J. Appl. Microbiol. 2009 107: 485-497.

PMID- 9010768
VI  - 120
DP  - 1996
TI  - Isolation and expression of a Xenopus laevis DNA methyltransferase cDNA.
PG  - 1182-1189
AB  - A Xenopus DNA methyltransferase cDNA was isolated from a Xenopus oocyte cDNA library by
      screening with the mouse DNA methyltransferase cDNA as a probe.  The elucidated nucleotide
      sequence gave a 4,470 nucleotide open reading frame, and the predicted protein was composed of
      1,490 amino acid residues, showing high homology to animal DNA methyltransferases, especially
      in the catalytic domain in the carboxyl-terminal region.  The cysteine-rich region and the
      Lys-Gly repeat which were first found in the mouse sequence were conserved in Xenopus.
      However, 200 amino acid residues at the amino-terminus of Xenopus DNA methyltransferase were
      quite different from those of mouse and human, but showed 70% homology with those of chicken.
      The cloned Xenopus DNA methyltransferase cDNA expressed in COS1 cells showed a significant DNA
      methyltransferase activity.  The size of the translation product of Xenopus DNA
      methyltransferase cDNA expressed in COS1 cells was identical with that of the endogenous DNA
      methyltransferase in Xenopus A6 cells and also with the size of newly synthesized DNA
      methyltransferase in Xenopus oocytes.  However, a slightly larger immunoreactive band of about
      205 kDa, and a small immunoreactive band of about 100 kDa, which were poorly labeled by short
      incubation with radiolabeled amino acids, were the main bands in stage I-III and stage IV-VI
      oocytes, respectively.
AU  - Kimura H
AU  - Ishihara G
AU  - Tajima S
PT  - Journal Article
TA  - J. Biochem. (Tokyo)
JT  - J. Biochem. (Tokyo)
SO  - J. Biochem. (Tokyo) 1996 120: 1182-1189.

PMID- 12799438
VI  - 31
DP  - 2003
TI  - Transcription of mouse DNA methyltransferase 1 (Dnmt1) is regulated by both E2F-Rb-HDAC-dependent and -independent pathways.
PG  - 3101-3113
AB  - Abnormal expression of Dnmt1 in vivo induces cellular alterations such as transformation, and
      an increase in Dnmt1 mRNA plays a causal role in
      c-fos-, ras- and SV40 large T antigen-induced transformation of
      fibroblasts in vitro. Here, we have investigated the regulation of Dnmt1
      transcription. We identified the promoter region and major transcription
      start sites of mouse Dnmt1 and found two important cis-elements within the
      core promoter region. One is an E2F binding site, and the other is a
      binding site for an as yet unidentified factor. Point mutations in the two
      cis-elements decreased promoter activity in both non-transformed and
      transformed cells. Thus, both sites play a critical role in regulation of
      Dnmt1 transcription in proliferating cells. Treatment with trichostatin A,
      a specific inhibitor of histone deacetylase, increased Dnmt1 promoter
      activity in G0/G1-arrested NIH 3T3 cells. Furthermore, the decrease in
      promoter activity induced by expression of E2F-1 and Rb was reversed by
      trichostatin A treatment of Saos-2 cells. Taken together, these data
      indicate that transcription of Dnmt1 is regulated in a complex fashion by
      E2F and other transcription factors through E2F-Rb-HDAC-dependent and
      -independent pathways. These findings suggest that Dnmt1 is a target gene
      of these pathways in cell proliferation, cell transformation and
      tumorigenesis.
AU  - Kimura H
AU  - Nakamura T
AU  - Ogawa T
AU  - Tanaka S
AU  - Shiota K
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2003 31: 3101-3113.

PMID- 12473678
VI  - 278
DP  - 2003
TI  - Methyl-CpG-binding Protein, MeCP2, Is a Target Molecule for Maintenance DNA Methyltransferase, Dnmt1.
PG  - 4806-4812
AB  - During mammalian cell division, DNA methylation patterns are transferred accurately to the
      newly synthesized DNA strand. This depends on
      maintenance DNA methyltransferase activity. DNA methylation can affect
      chromatin organization and gene expression by recruitment of histone
      deacetylases (HDACs). Here we show that the methyl-CpG binding protein,
      MeCP2, interacts directly with the maintenance DNA methyltransferase,
      Dnmt1. The region of MeCP2 that interacts with Dnmt1 corresponds to the
      transcription repressor domain which can also recruit HDACs via a
      corepressor, mSin3A. Dnmt1 can form complexes with HDACs as well as MeCP2.
      Surprisingly, the MeCP2-Dnmt1 complex does not contain the histone
      deacetylase, HDAC1. Thus, Dnmt1 takes the place of the mSin3A-HDAC1
      complex, indicating that the MeCP2-interacting Dnmt1 does not bind to
      HDAC1. Further, we demonstrate that MeCP2 can form a complex with
      hemimethylated as well as fully methylated DNA. Immunoprecipitated MeCP2
      complexes show DNA methyltransferase activity to hemimethylated DNA. These
      results suggest that Dnmt1 associates with MeCP2 in order to perform
      maintenance methylation in vivo. We propose that genome-wide and/or
      -specific local DNA methylation may be maintained by the Dnmt1-MeCP2
      complexes, bound to hemimethylated DNA. Dnmt1 may be recruited to targeted
      regions via multiple steps that may or may not involve histone
      deacetylases.
AU  - Kimura H
AU  - Shiota K
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2003 278: 4806-4812.

PMID- 10348922
VI  - 125
DP  - 1999
TI  - Xenopus maintenance-type DNA methyltransferase is accumulated and translocated into germinal vesicles of oocytes.
PG  - 1175-1182
AB  - In vertebrates, DNA methylation plays an important role in the regulation of gene expression
      and embryogenesis. DNA methyltransferase, which catalyzes the introduction of a methyl group
      at the 5th position of cytosine in the CpG sequence, is highly accumulated in mouse oocytes
      and is excluded from nuclei [Carlson et al. (1992) Genes Dev. 6, 2536-2541]. In this study, we
      examined the expression level and localization of Xenopus DNA methyltransferase in oocytes
      during oogenesis. The DNA methyltransferase protein was detectable in stage III oocytes and
      increased thereafter, until the oocytes had matured. The rate of DNA methyltransferase
      synthesis rapidly increased after stage IV oocytes. Different from in mouse oocytes, DNA
      methyltransferase was equally distributed in the nuclear and post-nuclear fractions, in stage
      VI oocytes. DNA methyltransferase translocated into nuclei was uniformly localized in the
      nuclear matrix, and the accumulated DNA methyltransferase in stage VI nuclei had DNA
      methylation activity.
AU  - Kimura H
AU  - Suetake I
AU  - Tajima S
PT  - Journal Article
TA  - J. Biochem. (Tokyo)
JT  - J. Biochem. (Tokyo)
SO  - J. Biochem. (Tokyo) 1999 125: 1175-1182.

PMID- 9878564
VI  - 253
DP  - 1998
TI  - Expression of rat DNA (cytosine-5) methyltransferase (DNA MTase) in rodent trophoblast giant cells: Molecular cloning and characterization of rat DNA MTase.
PG  - 495-501
AB  - Methylation of genomic DNA is involved in the basic mechanism of gene inactivation, chromatin
      organization, X chromosome inactivation and genomic imprinting.  A pattern of DNA methylation
      is maintained in mitotic cells by DNA (cytosine-5) methyltransferase (DNA MTase).  The DNA
      MTase has been shown to be also expressed in postmitotic cells such as neurons.  In the
      present report, as an approach to analyzing mechanisms underlying regulation of DNA MTase
      expression, we first isolated rat DNA MTase cDNA.  The isolated cDNA encoded a protein of
      1,622 amino acid residues showing 88.3% and 64.2% homology with mouse and human DNA MTase,
      respectively.  Northern blot analysis showed that DNA MTase mRNA was highly expressed in
      placenta during mid- to late-pregnancy.  We then analyzed the expression of DNA MTase in
      Rcho-1 cells, a rat choriocarcinoma-derived cell line, which cease cell division but keep
      replicating genomic DNA when differentiated in vitro.  We found that the expression of DNA
      MTase protein was decreased in terminally differentiated Rcho-1 cells whereas DNA MTase mRNA
      was consistently expressed.  This result suggested posttranscriptional regulation of DNA MTase
      activity in Rcho-1 cells.  The Rcho-1 cells would be a valuable model for studying the
      regulation of gene expression and function of DNA MTase in postmitotic, differentiated cells.
AU  - Kimura H
AU  - Takeda T
AU  - Tanaka S
AU  - Ogawa T
AU  - Shiota K
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1998 253: 495-501.

PMID- 25792041
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Pseudomonas abietaniphila KF717 (NBRC 110669), Isolated  from Biphenyl-Contaminated Soil in Japan.
PG  - e00059-15
AB  - Pseudomonas abietaniphila KF717 utilizes biphenyl as a sole source of carbon and  energy and
      degrades polychlorinated biphenyls (PCBs). We report here the
      6,930,016-bp genome sequence of this strain, which contains 6,323 predicted
      coding sequences (CDSs), including the biphenyl-utilizing bph gene cluster.
AU  - Kimura N
AU  - Yamazoe A
AU  - Hosoyama A
AU  - Hirose J
AU  - Watanabe T
AU  - Suenaga H
AU  - Fujihara H
AU  - Futagami T
AU  - Goto M
AU  - Furukawa K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00059-15.

PMID- 15972856
VI  - 33
DP  - 2005
TI  - Identification of novel restriction endonuclease-like fold families among hypothetical proteins.
PG  - 3598-3605
AB  - Restriction endonucleases and other nucleic acid cleaving enzymes form a large and extremely
      diverse superfamily that display little sequence similarity despite retaining a common core
      fold responsible for cleavage. The lack of significant sequence similarity between protein
      families makes homology inference a challenging task and hinders new family identification
      with traditional sequence-based approaches. Using the consensus fold recognition method
      Meta-BASIC that combines sequence profiles with predicted protein secondary structure, we
      identify nine new restriction endonuclease-like fold families among previously uncharacterized
      proteins and predict these proteins to cleave nucleic acid substrates. Application of
      transitive searches combined with gene neighborhood analysis allow us to confidently link
      these unknown families to a number of known restriction endonuclease-like structures and thus
      assign folds to the uncharacterized proteins. Finally, our method identifies a novel
      restriction endonuclease-like domain in the C-terminus of RecC that is not detected with
      structure-based searches of the existing PDB database.
AU  - Kinch LN
AU  - Ginalski K
AU  - Rychlewski L
AU  - Grishin NV
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2005 33: 3598-3605.

PMID- 28183767
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Arthrobacter sp. Strain UCD-GKA (Phylum Actinobacteria).
PG  - e01599-16
AB  - Here we present the draft genome of Arthrobacter sp. strain UCD-GKA. The assembly contains
      4,930,274 bp in 33 contigs. This strain was isolated from the handle of
      a weight bar in the UC Davis Activities and Recreation Center.
AU  - Kincheloe GN
AU  - Eisen JA
AU  - Coil DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01599-16.

PMID- 8294016
VI  - 136
DP  - 1993
TI  - Cloning of the YenI restriction endonuclease and methyltransferase from Yersinia enterocolitica serotype O8 and construction of a transformable R-M+ mutant.
PG  - 271-275
AB  - Two different clonal groups of pathogenic Yersinia enterocolitica strains, American and
      non-American, have been recognized. These are distinguished by a number of criteria, including
      their virulence in a murine model of infection. However, genetic analysis of virulence in
      American strains has been hampered due to the severe restriction of transformed of
      electroporated DNA. Thus, we cloned the yenIMR locus from American serotype strain 8081c,
      which encodes YenI, an isoschizomer pf PstI. This clone encodes both the restriction
      endonuclease and methyltransferase. The location of the genes on the clone was determined and
      this information was used to construct a small deletion (400 bp) that results in an R-M+
      phenotype. This mutation was recombined onto the Y. enterocolitica chromosome to give an R-M+
      mutant which showed at least a 1000-fold increase in electroporation frequency compared to the
      wild-type strain. Southern analysis using a probe derived from yenIMR indicated that American
      serotype strains have this locus whereas non-American serotype strains do not.
AU  - Kinder SA
AU  - Badger JL
AU  - Bryant GO
AU  - Pepe JC
AU  - Miller VL
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1993 136: 271-275.

PMID- 7476171
VI  - 16
DP  - 1995
TI  - Restriction alleviation and modification enhancement by the Rac prophage of Escherichia coli K-12.
PG  - 769-777
AB  - Bacteriophage lambda encodes an antirestriction function, Ral, which is able to modulate the
      activity of the Escherichia coli K-12 restriction and modification system, EcoKI. Here we
      report the characterization of an analogous function, Lar, expressed by E. coli sbcA mutants
      and the hybrid phage lambda reverse. E. coli sbcA mutants and lambda reverse both express
      genes of the Rac prophage, and we have located the lar gene immediately downstream of recT in
      this element. The lar gene has been cloned in an expression plasmid, and a combination of
      site-directed mutagenesis and labelling of plasmid-encoded proteins has enabled us to identify
      a number of translational products of lar, the smallest of which is sufficient for restriction
      alleviation. Lar, like Ral, is able both to alleviate restriction and to enhance modification
      by EcoKI. Lar, therefore, is functionally similar to Ral and the nucleotide sequences of their
      genes share 47% identity, indicating a common origin. A comparison of the predicted amino acid
      sequences of Lar and Ral shows only a 25% identity, but a few short regions do align and may
      indicate residues important for structure and/or function.
AU  - King G
AU  - Murray NE
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1995 16: 769-777.

PMID- 7607494
VI  - 157
DP  - 1995
TI  - Modification enhancement and restriction alleviation by bacteriophage lambda.
PG  - 225
AB  - The activity of EcoKI, and related restriction and modification (R-M) systems, is modulated by
      the bacteriophage lambda ral gene product.  We have identified the coding sequence for an
      analogous function in the Rac prophage of E. coli K-12.
AU  - King G
AU  - Murray NE
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 225.

PMID- 7889321
VI  - 2
DP  - 1994
TI  - Restriction enzymes in cells, not eppendorfs.
PG  - 465-469
AB  - Restriction enzymes are essential reagents to molecular biologists, but their relevance to
      bacterial populations is less obvious. Most bacteria encode restriction and modification
      systems and these are commonly considered to be a barrier to phage infection. Current evidence
      also supports a more general role for them in genetic recombination.
AU  - King G
AU  - Murray NE
PT  - Journal Article
TA  - Trends Microbiol.
JT  - Trends Microbiol.
SO  - Trends Microbiol. 1994 2: 465-469.

PMID- 
VI  - 100
DP  - 2000
TI  - Complementation of type ID restriction-modification systems between KpnAI and StySBLI.
PG  - 371
AB  - Type I restriction-modification systems are the most complex R-M systems in bacteria and
      consist of three different subunits, encoded by the hsdR (restriction/cleavage of DNA), hsdM
      (modification/methylation of DNA), and hsdS (recognition of DNA sequence) genes.  KpnAI, a
      restriction system from Klebsiella pneumoniae strain M5a1, is a member of the Type ID family.
      The predicted peptide sequences of KpnAI have a high degree of similarity with the StySBLI
      system, a prototype of type ID, from Salmonella blegdam, showing 95% and 98% homology in the
      HsdR and hsdM peptide sequences, respectively.  Differences in the hsdS genes (44% homology)
      however, suggest that each system has its own distinct DNA recognition sequence.  A series of
      complementation tests were conducted to test whether the two systems are functionally
      homologous.  Classical complementation tests were conducted using chromosomal mutants for
      StySBLI and plasmids containing KpnAI, and then conversely chromosomal mutants for KpnAI and
      plasmids containing StySBLI.  A new complementation method was also conducted by transforming
      two plasmids, containing genes from the KpnAI and StySBLI respectively, into E. coli C.  The
      results were obtained using a classical R-M test with lambda and SBS bacteriophages and
      determining the efficiency of plating (EOP).  The degree of restriction for the StySBLI and
      KpnAI mutants was 10-5 and 10-3, respectively, and 10-3 for the two plasmid complementation.
      The results show that the two different systems are functionally homologous and
      complementable.
AU  - King J
AU  - Umezu K
AU  - Ryu J
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 2000 100: 371.

PMID- 15222766
VI  - 43
DP  - 2004
TI  - Binding and conformational analysis of phosphoramidate restriction enzyme interactions.
PG  - 8551-8559
AB  - Phosphoramidates are modified deoxyoligonucleotides that feature nitrogen in place of the
      3'-oxygen of a phosphodiester linkage. Noted
      for stability against nuclease activity, these linkages are of both
      mechanistic and therapeutic interest. While a number of studies
      characterizing the properties of oligonucleotides composed entirely of
      phosphoramidate linkages have been published, little is known about how
      singly substituted phosphoramidate substitutions affect the
      thermodynamics and structure of protein-oligonucleotide interactions.
      We chose to investigate these interactions with PvuII endonuclease, the
      DNA binding behavior of which is well-characterized. Oligonucleotide
      duplexes containing a phosphoramidate substitution at the scissile
      phosphates were resistant to cleavage by the enzyme, even after
      extended incubations. However, the enzyme was able to cleave the native
      strand in a native: phosphoramidate heteroduplex at a rate comparable
      to that observed with the native substrate. Ca(II)-stimulated PvuII
      binding for a phosphoramidate-substituted oligonucleotide is comparable
      to that of the native duplex (K-d approximate to 200 pM). K-d values
      obtained in the presence of Mg(II) are somewhat weaker (K-d approximate
      to 10 nM). Under metal-free conditions, the enzyme exhibited a
      remarkable approximate to50-fold greater affinity for the modified
      oligonucleotide relative to the native substrate (5 vs 240 nM). While
      P-31 NMR spectra indicate increased chemical shift dispersion in the
      free phosphoramidate duplex, the spectrum of the enzyme-bound duplex is
      similar to that of the native duplex. H-1-N-15 HSQC analysis indicates
      that enzyme conformations in the presence of these oligonucleotides are
      also comparable. The tight binding of the phosphoramidate duplex under
      metal-free conditions and its resistance to cleavage are attributed to
      local conformational adjustments propagating from the O-N substitution.
AU  - King JB
AU  - Bowen LM
AU  - Dupureur CM
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2004 43: 8551-8559.

PMID- 8464692
VI  - 21
DP  - 1993
TI  - Noncomplementary DNA double-strand-break rejoining in bacterial and human cells.
PG  - 1055-1059
AB  - We examined the rejoining of noncomplementary restriction enzyme-produced DNA double-strand
      breaks in Escherichia coli and in cultured human cells. The enzymes used in this study, ClaI,
      BamHI and SalI, produce double-strand breaks with 5' protruding single strands. The joining
      of a ClaI-produced DNA end to a BamHI-produced end or to a SalI-produced end was examined at
      the DNA sequence level. End rejoining in E.coli was studied by transforming cultures with
      linear plasmid DNA that was gel purified from restriction digests, and end rejoining in
      cultured human cells was studied by introducing enzymes into the cells by electroporation. The
      human cells used contain an Epstein-Barr virus (EBV)-based shuttle vector, pHAZE, that was
      recovered and introduced into E.coli for further analysis. The major products of DNA
      end-joining processes observed in linear plasmid-transformed E.coli and in the human cells
      exposed to restriction enzymes were identical. Furthermore, the deletions observed in both
      systems and in the spontaneous mutant plasmid in untreated human cells had a common underlying
      feature: short stretches of directly repeated DNA at the junction sites.
AU  - King JS
AU  - Valcarcel ER
AU  - Rufer JT
AU  - Phillps JW
AU  - Morgan WF
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 1055-1059.

PMID- 2745417
VI  - 264
DP  - 1989
TI  - Glu-111 is required for activation of the DNA cleavage center of EcoRI endonuclease.
PG  - 11807-11815
AB  - Gap repair in the presence of 2'-deoxycytosine 5'-O-(1-thiotriphosphate) has
      been utilized to mutagenize the amino-terminal one-half of the structural gene
      for EcoRI endonuclease.  This approach has led to identification of over 200
      mutants defective in endonuclease function.  One mutant protein, which binds to
      the EcoRI sequence but displays greatly reduced cleavage activity, is the
      consequence of a Glu to Gly change at position 111.  This protein has been
      purified to homogeneity and characterized in detail.  Subunit interactions
      governing the tetramer to dimer transition of the mutant endonuclease are near
      normal as are parameters governing its interaction with specific and
      nonspecific DNA sequences.  However, the rate constants for first and second
      strand cleavage steps are reduced by 60,000- and 30,000-fold, respectively, as
      a consequence of the Glu->Gly change.  The defect in chemical cleavage steps
      can be partially overcome by elevating the pH of the reaction buffer from 7.6
      to 8.5, conditions which enhance the rate of EcoRI strand cleavage by wild type
      enzyme to a similar degree.  We suggest that the Glu-111 mutation affects an
      interface between recognition and cleavage functions of the enzyme, an idea
      consistent with the suggestion that the cleavage center of the endonuclease is
      subject to activation upon specific recognition of the EcoRI sequence.
AU  - King K
AU  - Benkovic SJ
AU  - Modrich P
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1989 264: 11807-11815.

PMID- 3956763
VI  - 45
DP  - 1986
TI  - Mutationally altered forms of EcoRI endonuclease selectively defective in DNA cleavage.
PG  - 1913
AB  - Gap repair in the presence of dNTP[alpha-S] has been utilized to mutagenize
      regions of the structural gene for EcoRI endonuclease.  This approach has led
      to identification of several mutant enzymes which retain specific affinity for
      the EcoRI sequence, but display greatly reduced cleavage activity.  One such
      protein, involving a Glu to Gly change at position 111 (BG111), has been
      purified to homogeneity and characterized in detail.  Thermodynamic and kinetic
      parameters governing interaction of the mutant protein with the EcoRI sequence
      are comparable to values for the wild type enzyme.  subunit interactions
      governing the tetramer to dimer transition are also normal.  However, the first
      order rate constants for first and second strand cleavage steps are reduced by
      a factor of at least 10,000-fold relative to wild type endonuclease.  We
      suggest that this mutation affects the interface between recognition and
      cleavage domains of the enzyme.
AU  - King K
AU  - Wright D
AU  - Modrich P
PT  - Journal Article
TA  - Fed. Proc.
JT  - Fed. Proc.
SO  - Fed. Proc. 1986 45: 1913.

PMID- Not carried by PubMed...
VI  - 8
DP  - 1988
TI  - Glutamate 111 of EcoRI endonuclease is required for DNA cleavage activation.
PG  - 79
AB  - The EcoRI restriction endonuclease is a well-characterized model system for
      studying the interaction of enzymes with specific DNA sequences.  X-ray
      crystallography has revealed major features of the interaction of this enzyme
      with DNA, but has not answered important questions about the mechanism of DNA
      cleavage.  We have used the cloned EcoRI endonuclease gene as a target for
      site-directed mutagenesis to probe the functional role of various amino acid
      residues in the enzyme.  Our studies demonstrate that glutamate 111 plays a
      critical role in activation of the cleavage function of the enzyme.
AU  - King K
AU  - Wright DJ
AU  - Modrich P
PT  - Journal Article
TA  - Miami BioTechnology Winter Symposium
JT  - Miami BioTechnology Winter Symposium
SO  - Miami BioTechnology Winter Symposium 1988 8: 79.

PMID- 8058824
VI  - 31
DP  - 1994
TI  - Transformation of Mycoplasma capricolum and examination of DNA restriction modification in M. capricolum and Mycroplasma mycoides subsp. mycoides.
PG  - 308-311
AB  - Plasmids pIKD and pIKD-erm have recently been developed as mycoplasmal cloning vectors. In
      this report, we demonstrate that these plasmids can replicate in Mycoplasma capricolum, a
      mycoplasmal species for which transformation had not previously been characterized. Both
      plasmids are stably maintained at a higher copy number than in their parental species,
      Mycoplasma mycoides subsp. mycoides. We have also examined the possibility of one or more
      restriction-modification systems affecting transformation frequencies in both species.
AU  - King KW
AU  - Dybvig K
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 1994 31: 308-311.

PMID- 29122861
VI  - 5
DP  - 2017
TI  - Genome Sequences of Subcluster K5 Mycobacteriophages AlleyCat, Edugator, and Guillsminger.
PG  - e01122-17
AB  - Bacteriophages AlleyCat, Edugator, and Guillsminger were isolated on Mycobacterium smegmatis
      mc(2)155 from enriched soil samples. All are members of
      mycobacteriophage subcluster K5, with genomes of 62,112 to 63,344 bp. Each genome
      contains 92 to 99 predicted protein-coding genes and one tRNA. Guillsminger is
      the first mycobacteriophage to carry an IS1380 family transposon.
AU  - King RA et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01122-17.

PMID- 28030649
VI  - 11
DP  - 2016
TI  - Whole Genome Sequence and Comparative Genomics of the Novel Lyme Borreliosis Causing Pathogen, Borrelia mayonii.
PG  - E0168994
AB  - Borrelia mayonii, a Borrelia burgdorferi sensu lato (Bbsl) genospecies, was
      recently identified as a cause of Lyme borreliosis (LB) among patients from the
      upper midwestern United States. By microscopy and PCR, spirochete/genome loads in
      infected patients were estimated at 105 to 106 per milliliter of blood. Here, we
      present the full chromosome and plasmid sequences of two B. mayonii isolates,
      MN14-1420 and MN14-1539, cultured from blood of two of these patients. Whole
      genome sequencing and assembly was conducted using PacBio long read sequencing
      (Pacific Biosciences RSII instrument) followed by hierarchical genome-assembly
      process (HGAP). The B. mayonii genome is ~1.31 Mbp in size (26.9% average GC
      content) and is comprised of a linear chromosome, 8 linear and 7 circular
      plasmids. Consistent with its taxonomic designation as a new Bbsl genospecies,
      the B. mayonii linear chromosome shares only 93.83% average nucleotide identity
      with other genospecies. Both B. mayonii genomes contain plasmids similar to B.
      burgdorferi sensu stricto lp54, lp36, lp28-3, lp28-4, lp25, lp17, lp5, 5 cp32s,
      cp26, and cp9. The vls locus present on lp28-10 of B. mayonii MN14-1420 is
      remarkably long, being comprised of 24 silent vls cassettes. Genetic differences
      between the two B. mayonii genomes are limited and include 15 single nucleotide
      variations as well as 7 fewer silent vls cassettes and a lack of the lp5 plasmid
      in MN14-1539. Notably, 68 homologs to proteins present in B. burgdorferi sensu
      stricto appear to be lacking from the B. mayonii genomes. These include the
      complement inhibitor, CspZ (BB_H06), the fibronectin binding protein, BB_K32, as
      well as multiple lipoproteins and proteins of unknown function. This study shows
      the utility of long read sequencing for full genome assembly of Bbsl genomes,
      identifies putative genome regions of B. mayonii that may be linked to clinical
      manifestation or tissue tropism, and provides a valuable resource for
      pathogenicity, diagnostic and vaccine studies.
AU  - Kingry LC
AU  - Batra D
AU  - Replogle A
AU  - Rowe LA
AU  - Pritt BS
AU  - Petersen JM
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2016 11: E0168994.

PMID- 27417836
VI  - 4
DP  - 2016
TI  - Chromosome and Linear Plasmid Sequences of a 2015 Human Isolate of the Tick-Borne Relapsing Fever Spirochete, Borrelia turicatae.
PG  - e00655-16
AB  - The sequences of the complete linear chromosome and 7 linear plasmids of the relapsing fever
      spirochete Borrelia turicatae are presented in this report. The
      925,547 bp of chromosome and 380,211 bp of plasmid sequence were predicted to
      contain a total of 1,131 open reading frames, with an average G+C content of
      29.7%.
AU  - Kingry LC
AU  - Batra D
AU  - Replogle A
AU  - Sexton C
AU  - Rowe L
AU  - Stermole BM
AU  - Christensen AM
AU  - Schriefer ME
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00655-16.

PMID- 28153903
VI  - 5
DP  - 2017
TI  - Toward a Complete North American Borrelia miyamotoi Genome.
PG  - e01557-16
AB  - Borrelia miyamotoi, of the relapsing-fever spirochete group, is an emerging tick-borne
      pathogen causing human illness in the northern hemisphere. Here, we
      present the chromosome, eight extrachromosomal linear plasmids, and a draft
      sequence for five circular and one linear plasmid of a Borrelia miyamotoi strain
      isolated from an Ixodes sp. tick from Connecticut, USA.
AU  - Kingry LC
AU  - Replogle A
AU  - Batra D
AU  - Rowe LA
AU  - Sexton C
AU  - Dolan M
AU  - Connally N
AU  - Petersen JM
AU  - Schriefer ME
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01557-16.

PMID- 28912318
VI  - 5
DP  - 2017
TI  - Chromosome and Large Linear Plasmid Sequences of a Borrelia miyamotoi Strain Isolated from Ixodes pacificus Ticks from California.
PG  - e00960-17
AB  - Borrelia miyamotoi, a relapsing fever group spirochete, is an emerging tick-borne pathogen. It
      has been identified in ixodid ticks across the Northern Hemisphere,
      including the West Coast of the United States. We describe the chromosome and
      large linear plasmid sequence of a B. miyamotoi isolate cultured from a
      California field-collected Ixodes pacificus tick.
AU  - Kingry LC
AU  - Replogle A
AU  - Dolan M
AU  - Sexton C
AU  - Padgett KA
AU  - Schriefer ME
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00960-17.

PMID- 12954757
VI  - 31
DP  - 2003
TI  - DNA supercoiling enables the Type IIS restriction enzyme BspMI to recognize the relative orientation of two DNA sequences.
PG  - 5221-5228
AB  - Many proteins can sense the relative orientations of two sequences at distant locations in
      DNA: some require sites in inverted (head-to-head)
      orientation, others in repeat (head-to-tail) orientation. Like many
      restriction enzymes, the BspMI endonuclease binds two copies of its target
      site before cleaving DNA. Its target is an asymmetric sequence so two
      sites in repeat orientation differ from sites in inverted orientation.
      When tested against supercoiled plasmids with two sites 700 bp apart in
      either repeated or inverted orientations, BspMI had a higher affinity for
      the plasmid with repeated sites than the plasmid with inverted sites. In
      contrast, on linear DNA or on supercoiled DNA with sites 1605 bp apart,
      BspMI interacted equally with repeated or inverted sites. The ability of
      BspMI to detect the relative orientation of two DNA sequences thus depends
      on both the topology and the length of the intervening DNA. Supercoiling
      may restrain the juxtaposition of sites 700 bp apart to a particular
      alignment across the superhelical axis, but the juxtaposition of sites in
      linear DNA or far apart in supercoiled DNA may occur without restraint.
      BspMI can therefore act as a sensor of the conformational dynamics of
      supercoiled DNA.
AU  - Kingston IJ
AU  - Gormley NA
AU  - Halford SE
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2003 31: 5221-5228.

PMID- 9657874
VI  - 260
DP  - 1998
TI  - Single-molecule analysis of restriction DNA fragments using fluorescence correlation spectroscopy.
PG  - 166-172
AB  - The cleavage of fluorescence-labeled M13DNA (7250 bp) using HaeIII, HgaI, BsmAI, and BspMI was
      analyzed by fluorescence correlation spectroscopy in a small volume (1.5 x 10^-15 liters).
      The digestion process can be monitored by the decrease in amplitude of the fluorescence
      correlation function while the original DNA molecule is divided into several fragments by the
      enzymes.  To analyze this reaction by FCS, we derived a practical equation for estimating the
      number of molecules in the FCS measurements.  Under standard enzymatic conditions, HaeIII and
      BsmAI digested fluorescence-labeled DNA to completion in the range of 8 h, whereas HgaI and
      BspMI digested the DNA after 40 h.  The comparison of recognition sequences suggested that
      some tagged nucleotides could be inserted between the recognition site and the cleavage site
      of the slow enzyme group.  The decrease in amplitude in the fluorescence correlation function
      quantitatively monitors the hydrolysis of DNA during the digestion process.
AU  - Kinjo M
AU  - Nishimura G
AU  - Koyama T
AU  - Mets U
AU  - Rigler R
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 1998 260: 166-172.

PMID- 29860278
VI  - 10
DP  - 2018
TI  - Parallel and Gradual Genome Erosion in the Blattabacterium Endosymbionts of Mastotermes darwiniensis and Cryptocercus Wood Roaches.
PG  - 1622-1630
AB  - Almost all examined cockroaches harbor an obligate intracellular endosymbiont, Blattabacterium
      cuenoti. On the basis of genome content, Blattabacterium has been
      inferred to recycle nitrogen wastes and provide amino acids and cofactors for its
      hosts. Most Blattabacterium strains sequenced to date harbor a genome of
      approximately 630 kbp, with the exception of the termite Mastotermes darwiniensis
      ( approximately 590 kbp) and Cryptocercus punctulatus ( approximately 614 kbp), a
      representative of the sister group of termites. Such genome reduction may have
      led to the ultimate loss of Blattabacterium in all termites other than
      Mastotermes. In this study, we sequenced 11 new Blattabacterium genomes from
      three species of Cryptocercus in order to shed light on the genomic evolution of
      Blattabacterium in termites and Cryptocercus. All genomes of Cryptocercus-derived
      Blattabacterium genomes were reduced ( approximately 614 kbp), except for that
      associated with Cryptocercus kyebangensis, which comprised 637 kbp. Phylogenetic
      analysis of these genomes and their content indicates that Blattabacterium
      experienced parallel genome reduction in Mastotermes and Cryptocercus, possibly
      due to similar selective forces. We found evidence of ongoing genome reduction in
      Blattabacterium from three lineages of the C. punctulatus species complex, which
      independently lost one cysteine biosynthetic gene. We also sequenced the genome
      of the Blattabacterium associated with Salganea taiwanensis, a subsocial
      xylophagous cockroach that does not vertically transmit gut symbionts via
      proctodeal trophallaxis. This genome was 632 kbp, typical of that of nonsubsocial
      cockroaches. Overall, our results show that genome reduction occurred on multiple
      occasions in Blattabacterium, and is still ongoing, possibly because of new
      associations with gut symbionts in some lineages.
AU  - Kinjo Y
AU  - Bourguignon T
AU  - Tong KJ
AU  - Kuwahara H
AU  - Lim SJ
AU  - Yoon KB
AU  - Shigenobu S
AU  - Park YC
AU  - Nalepa CA
AU  - Hongoh Y
AU  - Ohkuma M
AU  - Lo N
AU  - Tokuda G
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2018 10: 1622-1630.

PMID- 21507356
VI  - 101
DP  - 2011
TI  - Regulation of Expression and Activity of DNA (Cytosine-5) Methyltransferases in Mammalian Cells.
PG  - 311-333
AB  - Three active DNA methyltransferases have been identified in mammalian cells, Dnmt1, Dnmt3a,
      and Dnmt3b.  DNMT1 is primarily a maintenance methyltransferase, as it prefers to methylate
      hemi-methylated DNA during DNA replication and in vitro.  DNMT3A and DNMT3B are de novo
      methyltransferases and show similar activity on unmethylated and hemimethylated DNA. DNMT3L,
      which lacks the catalytic domain, binds to DNMT3A and DNMT3B variants and facilitates their
      chromatin targeting, presumably for de novo methylation.  There are several mechanisms by
      which mammalian cells regulate DNMT levels, including varied transcriptional activation of the
      respective genes and posttranslational modifications of the enzymes that can affect catalytic
      activity, targeting, and enzyme degradation.  In addition, binding of miRNAs or RNA-binding
      proteins can also alter the expression of DNMTs.  These regulatory processes can be disrupted
      in disease or by environmental factors, resulting in altered DNMT expression and aberrant DNA
      methylation patterns.
AU  - Kinney SRM
AU  - Pradhan S
PT  - Journal Article
TA  - Prog. Mol. Biol. Transl. Sci.
JT  - Prog. Mol. Biol. Transl. Sci.
SO  - Prog. Mol. Biol. Transl. Sci. 2011 101: 311-333.

PMID- 
VI  - 19
DP  - 2007
TI  - Ligation of Nanoparticle Coated DNA Cleaved with Restriction Enzymes.
PG  - 3586-3588
AB  - Material synthesis at the nanoscale frequently relies on biological molecules for inspiration,
      selectivity, and specificity.  Molecular templates using biomolecules have been used to
      fabricate structures with specific sizes and shapes.  Often times, the biological function of
      the template molecule is utilized to connect nanoscale structures, site-specifically catalyze
      reactions, or enzymatically modify templated segments.  The specificity of these biomolecular
      interactions can often lead to straightforward fabrication methods of materials that are
      difficult to synthesize by conventional means.  One of the simplest and most easily adapted
      forms of such interactions is that involving the hybridization of single-stranded DNA to its
      double-helix form.  This interaction has been used to drive the formation of complex
      structures, nanoparticle conjugates, and DNA-based electronics.  More recently, the
      introduction of DNA-manipulating enzymes has been investigated.  We have previously
      demonstrated the ability of restriction endonucleases, which cut DNA at specific sequences, to
      fragment phage DNA templated with magnetic nanoparticles.  DNA ligases, which oppose the
      function of restriction enzymes by repairing cleaved DNA molecules, have recently been used to
      generate specific connectivity between DNA-modified nanoparticles.
AU  - Kinsella JM
AU  - Shalaev MV
AU  - Ivanisevic A
PT  - Journal Article
TA  - Chem. Mater.
JT  - Chem. Mater.
SO  - Chem. Mater. 2007 19: 3586-3588.

PMID- 25908143
VI  - 3
DP  - 2015
TI  - Complete Genome Sequencing of Protease-Producing Novel Arthrobacter sp. Strain IHBB 11108 Using PacBio Single-Molecule Real-Time Sequencing Technology.
PG  - e00346-15
AB  - A previously uncharacterized species of the genus Arthrobacter, strain IHBB 11108 (MCC 2780),
      is a Gram-positive, strictly aerobic, nonmotile, cold-adapted, and
      protease-producing alkaliphilic actinobacterium, isolated from shallow
      undersurface water from Chandra Tal Lake, Lahaul-Spiti, India. The complete
      genome of the strain is 3.6 Mb in size with an average 58.97% G+C content.
AU  - Kiran S
AU  - Swarnkar MK
AU  - Pal M
AU  - Thakur R
AU  - Tewari R
AU  - Singh AK
AU  - Gulati A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00346-15.

PMID- 22689234
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of the Human Pathogen Streptomyces somaliensis, a Significant Cause of Actinomycetoma.
PG  - 3544-3545
AB  - We report the draft genome sequence of the human pathogen Streptomyces somaliensis (DSM
      40738), a pathogen within a genus of largely saprophytic
      organisms. S. somaliensis causes severe and debilitating deep tissue and bone
      infections. The genome sequence is deposited in DDBJ/EMBL/GenBank with the
      accession number AJJM01000000.
AU  - Kirby R
AU  - Sangal V
AU  - Tucker NP
AU  - Zakrzewska-Czerwinska J
AU  - Wierzbicka K
AU  - Herron PR
AU  - Chu CJ
AU  - Chandra G
AU  - Fahal AH
AU  - Goodfellow M
AU  - Hoskisson PA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3544-3545.

PMID- 15193127
VI  - 69
DP  - 2004
TI  - Significance of codon usage and irregularities of rare codon distribution in genes for expression of BspLU11III methyltransferases.
PG  - 647-657
AB  - Genes of adenine-specific DNA-methyltransferase M.BspLU11IIIa and cytosine-specific
      DNA-methyltransferase M.BspLU11IIIb of the type IIG BspLU11III restriction-modification system
      from the thermophilic strain Bacillus sp. LU11 were expressed in E. coli. They contain a large
      number of codons that are rare in E. coli and are characterized by equal values of codon
      adaptation index (CAI) and expression level measure (E(g)). Rare codons are either diffused
      (M.BspLU11IIIa) or located in clusters (M.BspLU11IIIb). The expression level of the
      cytosine-specific DNA-methyltransferase was increased by a factor of 7.3 and that of
      adenine-specific DNA only by a factor of 1.25 after introduction of the plasmid pRARE
      supplying tRNA genes for six rare codons in E. coli. It can be assumed that the plasmid
      supplying minor tRNAs can strongly increase the expression level of only genes with cluster
      distribution of rare codons. Using heparin-Sepharose and phosphocellulose chromatography and
      gel filtration on Sephadex G-75 both DNA-methyltransferases were isolated as
      electrophoretically homogeneous proteins (according to the results of SDS-PAGE).
AU  - Kirienko NV
AU  - Lepikhov KA
AU  - Zheleznaya LA
AU  - Matvienko NI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 2004 69: 647-657.

PMID- 2168869
VI  - 107
DP  - 1990
TI  - Effect of unusual polyamines on cleavage of DNA by restriction enzymes.
PG  - 661-665
AB  - The effect of unusual polyamines, such as thermine, caldopentamine,
      caldohexamine, tris(3-aminopropyl)amine, or tetrakis(3-aminopropyl)ammonium, on
      the activities of various restriction endonucleases was investigated by using
      an Escherichia coli plasmid as a substrate, which contains a high GC content
      fragment from an extreme thermophile.  Restriction enzymes used were SmaI,
      BanII, NaeI, RsaI, and TaqI.  Most of the polyamines tested were inhibitory to
      the enzyme activities.  The larger and more branched a polyamine was, the more
      the activities of nucleases were inhibited.  The inhibition was positively
      correlated with the polyamine concentration.  The sites protected by a
      polyamine were identical to those protected by other polyamines, and also
      identical to those which were less sensitive to the restriction enzyme in the
      absence of polyamines.  No sequence specificity was seen among these sites.
AU  - Kirino H
AU  - Kuwahara R
AU  - Hamasaki N
AU  - Oshima T
PT  - Journal Article
TA  - J. Biochem. (Tokyo)
JT  - J. Biochem. (Tokyo)
SO  - J. Biochem. (Tokyo) 1990 107: 661-665.

PMID- 29954913
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of a Potentially Novel Streptococcus Species Belonging to the Streptococcus mitis Group.
PG  - e00620-18
AB  - We report here the draft genome sequence of a Streptococcus species belonging to  the S. mitis
      group. While a clear species identification cannot be made for the
      isolate, it appears that its most recent common ancestor is the species S.
      pseudopneumoniae.
AU  - Kirkeleite IO
AU  - Bohlin J
AU  - Scheffer L
AU  - Weme ET
AU  - Vestrheim DF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00620-18.

PMID- 15554190
VI  - 38
DP  - 2004
TI  - Type IIE and IIF restriction endonucleases interacting with two recognition sites on DNA.
PG  - 886-900
AB  - Recent studies have shown that restriction endonucleases (REs), which are broadly used in
      genetic engineering and molecular biology, vary not
      only in nucleotide sequence of the recognition site, but also in the
      mechanism of their interaction with DNA. This review focuses on type
      IIF and HE REs, which require simultaneous interaction with two
      nucleotide sequences for efficient DNA cleavage. Crystal structures of
      these REs and their complexes with DNA, stepwise interactions with DNA,
      catalytic mechanisms of DNA hydrolysis, and DNA looping are considered.
      Type HE REs have provided an example of a new type of DNA-protein
      recognition: two copies of one recognition sequence interact
      specifically with two different amino acid sequences and two different
      structural motifs of one polypeptide chain.
AU  - Kirsanova OV
AU  - Baskunov VB
AU  - Gromova ES
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2004 38: 886-900.

PMID- 19916931
VI  - 74
DP  - 2009
TI  - Inhibition of C5-cytosine-DNA-methyltransferases.
PG  - 1175-1186
AB  - Changes in the methylation pattern of genomic DNA, particularly hypermethylation of tumor
      suppressor genes, occur at early stages of tumor development. Errors in DNA methylation
      contribute to both initiation and progression of various cancers. This stimulates significant
      interest in searching for inhibitors of C5-DNA-methyltransferases (MTases). Here we review the
      known nucleoside mechanism-based reversible and irreversible inhibitors of the MTases, as well
      as non-nucleoside ones, and discuss their inhibitory mechanisms and application for MTase
      investigations and cancer therapy.
AU  - Kirsanova OV
AU  - Cherepanova NA
AU  - Gromova ES
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2009 74: 1175-1186.

PMID- 26586877
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Amantichitinum ursilacus IGB-41, a New Chitin-Degrading  Bacterium.
PG  - e01309-15
AB  - Amantichitinum ursilacus IGB-41 is a new species of chitin-degrading bacterium isolated from
      soil, which secretes potential industrial enzymes. The genome of A.
      ursilacus was sequenced, and the gene set encoding chitinases was identified.
      Here, we present the draft genome of 4.9 Mb, comprising 38 contigs, and the
      corresponding annotation.
AU  - Kirstahler P
AU  - Gunther M
AU  - Grumaz C
AU  - Lindemann E
AU  - Rupp S
AU  - Zibek S
AU  - Sohn K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01309-15.

PMID- 25977412
VI  - 3
DP  - 2015
TI  - Genome Sequence of the Electrogenic Petroleum-Degrading Thalassospira sp. Strain  HJ.
PG  - e00483-15
AB  - We present the draft genome of the petroleum-degrading Thalassospira sp. strain HJ, isolated
      from tidal marine sediment. Knowledge of this genomic information
      will inform studies on electrogenesis and means to degrade environmental organic
      contaminants, including compounds found in petroleum.
AU  - Kiseleva L
AU  - Garushyants SK
AU  - Briliute J
AU  - Simpson DJ
AU  - Cohen MF
AU  - Goryanin I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00483-15.

PMID- 28104646
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of a Chitinophaga Strain Isolated from a Lignocellulose Biomass-Degrading Consortium.
PG  - e01056-16
AB  - Chitinophaga comprises microorganisms capable of degrading plant-derived carbohydrates,
      serving as a source of new tools for the characterization and
      degradation of plant biomass. Here, we report the draft genome assembly of a
      Chitinophaga strain with 8.2 Mbp and 7,173 open reading frames (ORFs), isolated
      from a bacterial consortium that is able to degrade lignocellulose.
AU  - Kishi LT
AU  - Lopes EM
AU  - Fernandes CC
AU  - Fernandes GC
AU  - Sacco LP
AU  - Carareto ALM
AU  - Lemos EG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01056-16.

PMID- 11442057
VI  - 46
DP  - 2001
TI  - Site specificity of the Arabidopsis METI DNA methyltransferase demonstrated through hypermethylation of the superman locus.
PG  - 171-183
AB  - Plants with low levels of DNA methylation show a range of developmental abnormalities
      including homeotic transformation of floral organs. Two independent DNA methyltransferase I
      (METI) antisense transformants with low levels of DNA methylation had flowers with increased
      numbers of stamens which resembled flowers seen on the loss-of-function superman (sup) mutant
      plants and on transgenic plants that ectopically express APETALA3 (AP3). These METI antisense
      plants have both increased and decreased methylation in and around the sup gene, compared with
      untransformed controls. DNA from the antisense plants was demethylated at least 4 kb upstream
      of the sup gene, while there was dense methylation around the start of transcription and
      within the coding region of this gene; these regions were unmethylated in control DNA.
      Methylation within the sup gene was correlated with an absence of SUP transcripts. The pattern
      and density of methylation was heterogeneous among different DNA molecules from the same
      plant, with some molecules being completely unmethylated. Methylcytosine occurred in
      asymmetric sites and in symmetric CpA/TpG but rarely in CpG dinucleotides in the antisense
      plants. In contrast, segregants lacking the METI antisense construct and epimutants with a
      hypermethylated allele of sup (clark kent 3), both of which have active METI genes, showed a
      higher frequency of methylation of CpG dinucleotides and of asymmetric cytosines. We conclude
      that METI is the predominant CpG methyltransferase and directly or indirectly affects
      asymmetric methylation.
AU  - Kishimoto N
AU  - Sakai H
AU  - Jackson J
AU  - Jacobsen SE
AU  - Meyerowitz EM
AU  - Dennis ES
AU  - Finnegan EJ
PT  - Journal Article
TA  - Plant Mol. Biol.
JT  - Plant Mol. Biol.
SO  - Plant Mol. Biol. 2001 46: 171-183.

PMID- 29449397
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Listeria monocytogenes Strain CIIMS-PH-1, a Serovar 4b Isolate from Infant Septicemia.
PG  - e01320-17
AB  - We report here the draft genome sequence of Listeria monocytogenes CIIMS-PH-1, an isolate
      obtained from a 16-day-old infant with septicemia. The draft genome of
      CIIMS-PH-1 consisted of 2,939,183 bp and is a member of sequence type 308, clonal
      complex 1, and lineage I.
AU  - Kishnani PM
AU  - Tiwari AA
AU  - Gautam V
AU  - Sharma M
AU  - Barbuddhe SB
AU  - Doijad SP
AU  - Chakraborty T
AU  - Nayak AR
AU  - Bhartiya NM
AU  - Daginawala HF
AU  - Singh LR
AU  - Kashyap RS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01320-17.

PMID- 29519823
VI  - 6
DP  - 2018
TI  - Whole-Genome Sequence of Brucella melitensis CIIMS-BH-2, a Biovar 2 Strain Isolated from Human Blood.
PG  - e00079-18
AB  - Brucella species are the etiological agent of brucellosis in humans and animals.  Here, we
      report the whole-genome sequence of Brucella melitensis strain
      CIIMS-BH-2, belonging to biovar 2. The draft assembly of CIIMS-BH-2 is 3.31 Mb in
      size, with 57.2% G+C content.
AU  - Kishnani PM
AU  - Tiwari AA
AU  - Mangalgi SS
AU  - Barbuddhe SB
AU  - Daginawala HF
AU  - Singh LR
AU  - Kashyap RS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00079-18.

PMID- 30202937
VI  - 46
DP  - 2018
TI  - Crystal structure of the modification-dependent SRA-HNH endonuclease TagI.
PG  - 10489-10503
AB  - TagI belongs to the recently characterized SRA-HNH family of modification-dependent
      restriction endonucleases (REases) that also includes
      ScoA3IV (Sco5333) and TbiR51I (Tbis1). Here, we present a crystal structure of
      dimeric TagI, which exhibits a DNA binding site formed jointly by the nuclease
      domains, and separate binding sites for modified DNA bases in the two protomers.
      The nuclease domains have characteristic features of HNH/betabetaalpha-Me REases,
      and catalyze nicks or double strand breaks, with preference for /RY and RYN/RY
      sites, respectively. The SRA domains have the canonical fold. Their pockets for
      the flipped bases are spacious enough to accommodate 5-methylcytosine (5mC) or
      5-hydroxymethylcytosine (5hmC), but not glucosyl-5-hydroxymethylcytosine (g5hmC).
      Such preference is in agreement with the biochemical determination of the TagI
      modification dependence and the results of phage restriction assays. The ability
      of TagI to digest plasmids methylated by Dcm (C5mCWGG), M.Fnu4HI (G5mCNGC) or
      M.HpyCH4IV (A5mCGT) suggests that the SRA domains of the enzyme are tolerant to
      different sequence contexts of the modified base.
AU  - Kisiala M
AU  - Copelas A
AU  - Czapinska H
AU  - Xu SY
AU  - Bochtler M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2018 46: 10489-10503.

PMID- 26634751
VI  - 3
DP  - 2015
TI  - Nineteen Whole-Genome Assemblies of Yersinia pestis subsp. microtus, Including Representatives of Biovars caucasica, talassica, hissarica, altaica,  xilingolensis, and ulegeica.
PG  - e01342-15
AB  - The etiologic agent of plague, Yersinia pestis, includes two subspecies, of which Y. pestis
      subsp. microtus contains the strains that cause only occasional
      diseases in humans that are not accompanied by human-to-human transmission. Here,
      we report the draft genome sequences of 19 Y. pestis strains (across 6 biovars of
      Y. pestis subsp. microtus).
AU  - Kislichkina AA
AU  - Bogun AG
AU  - Kadnikova LA
AU  - Maiskaya NV
AU  - Platonov ME
AU  - Anisimov NV
AU  - Galkina EV
AU  - Dentovskaya SV
AU  - Anisimov AP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01342-15.

PMID- 29348336
VI  - 6
DP  - 2018
TI  - Nine Whole-Genome Assemblies of Yersinia pestis subsp. microtus bv. Altaica Strains Isolated from the Altai Mountain Natural Plague Focus (No. 36) in Russia.
PG  - e01440-17
AB  - We report here the draft genome sequences of nine Yersinia pestis subsp. microtus bv. Altaica
      strains isolated from the Altai Mountain plague focus (no. 36), which
      represent the 0.PE4 phylogroup circulating in populations of Mongolian pika
      (Ochotona pallasi).
AU  - Kislichkina AA
AU  - Bogun AG
AU  - Kadnikova LA
AU  - Maiskaya NV
AU  - Solomentsev VI
AU  - Dentovskaya SV
AU  - Balakhonov SV
AU  - Anisimov AP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01440-17.

PMID- 28839028
VI  - 5
DP  - 2017
TI  - Eight Whole-Genome Assemblies of Yersinia pestis subsp. microtus bv. caucasica Isolated from the Common Vole (Microtus arvalis) Plague Focus in Dagestan,  Russia.
PG  - e00847-17
AB  - We here report the draft genome sequences of 8 Yersinia pestis subsp. microtus bv. caucasica
      strains isolated from the East Caucasian (previous name, Dagestan)
      mountain focus (no. 39), representing the most ancient branch of the 0.PE2
      phylogroup circulating in populations of common voles (Microtus arvalis).
AU  - Kislichkina AA
AU  - Bogun AG
AU  - Kadnikova LA
AU  - Maiskaya NV
AU  - Solomentsev VI
AU  - Platonov ME
AU  - Dentovskaya SV
AU  - Anisimov AP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00847-17.

PMID- 29930050
VI  - 6
DP  - 2018
TI  - Six Whole-Genome Assemblies of Yersinia pestis subsp. microtus bv. ulegeica (Phylogroup 0.PE5) Strains Isolated from Mongolian Natural Plague Foci.
PG  - e00536-18
AB  - Here, we report the draft genome sequences of six Yersinia pestis subsp. microtus bv. ulegeica
      strains isolated from the territory of Mongolia and representing the
      0.PE5 phylogroup circulating in populations of voles and picas.
AU  - Kislichkina AA
AU  - Bogun AG
AU  - Kadnikova LA
AU  - Maiskaya NV
AU  - Solomentsev VI
AU  - Sizova AA
AU  - Dentovskaya SV
AU  - Balakhonov SV
AU  - Anisimov AP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00536-18.

PMID- 6301941
VI  - 21
DP  - 1983
TI  - Molecular cloning and expression in Escherichia coli of two modification methylase genes of Bacillus subtilis.
PG  - 111-119
AB  - Two modification methylase genes of Bacillus subtilis R were cloned in
      Escherichia coli by using a selection procedure which is based on the
      expression of these genes.  Both genes code for DNA-methyl-transferases which
      render the DNA of the cloning host E. coli HB101 insensitive to the BspRI
      (5'-GGCC) endonuclease of Bacillus sphaericus R.  One of the cloned genes is
      part of the restriction-modification (RM) system BsuRI of B. subtilis R with
      specificity for 5'-GGCC.  The other one is associated with the lysogenizing
      phage SPbeta and produces the methylase M.BsuSPbetaI with specificity for
      5'-GGCC.  The fragment carrying the SPbeta-derived gene also directs the
      synthesis in E. coli of a third methylase activity (M.BsuSPbetaII), which
      protects the host DNA against HpaII and MspI cleavage within the sequence
      5'-CCGG.  Indirect evidence suggests that the two SPbeta modification
      activities are encoded by the same gene.  No cross-hybridization was detected
      either between the M.BsuRI and M.BsuSPbeta genes or between these and the
      modification methylase gene of B. sphaericus R, which codes for the enzyme
      M.BspRI with 5'-GGCC specificity.
AU  - Kiss A
AU  - Baldauf F
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1983 21: 111-119.

PMID- 2062664
VI  - 19
DP  - 1991
TI  - M.KpnI is an adenine-methyltransferase.
PG  - 3460
AB  - The recognition sequence of the KpnI restriction-modification system is GGTACC.
      There are conflicting reports in the literature concerning the nucleotide
      methylated by the KpnI methyltransferase.  In one paper it was suggested that
      M.KpnI produces m4-cytosine.  Other investigators obtained indirect evidence
      suggesting but not proving that it methylates the adenine in the recognition
      sequence.  Here we present direct evidence showing that M.KpnI is an
      adenine-methyltransferase.
AU  - Kiss A
AU  - Finta C
AU  - Venetianer P
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 3460.

PMID- 2997708
VI  - 13
DP  - 1985
TI  - Nucleotide sequence of the BsuRI restriction-modification system.
PG  - 6403-6420
AB  - The genes of the 5'-GGCC specific BsuRI restriction-modification system of
      Bacillus subtillis have been cloned and expressed in E. coli and their
      nucleotide sequence has been determined.  The restriction and modification
      genes code for polypeptides with calculated molecular weights of 66,314 and
      49,642, respectively.  Both enzymes are coded by the same DNA strand.  The
      restriction gene is upstream of the methylase gene and the coding regions are
      separated by 780 bp.  Analysis of the RNA transcripts by S1-nuclease mapping
      indicates that the restriction and modification genes are transcribed from
      different promoters.  Comparison of the amino acid sequences revealed no
      homology between the BsuRI restriction and modification enzymes.  There are,
      however, regions of homology between the BsuRI methylase and two other GGCC
      specific modification enzymes, the BspRI and SPR methylases.
AU  - Kiss A
AU  - Posfai G
AU  - Keller CC
AU  - Venetianer P
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1985 13: 6403-6420.

PMID- 11470876
VI  - 29
DP  - 2001
TI  - Role of DNA minor groove interactions in substrate recognition by the M.SinI and M.EcoRII DNA (cytosine-5) methyltransferases.
PG  - 3188-3194
AB  - The SinI and EcoRII DNA methyltransferases recognize sequences (GG(A)/(T)CC and CC(A)/(T)GG,
      respectively), which are characterized by an (A)/(T) ambiguity. Recognition of the A.T and T.A
      base pair was studied by in vitro methyltransferase assays using oligonucleotide substrates
      containing a hypoxanthine.C base pair in the central position of the recognition sequence.
      Both enzymes methylated the substituted oligonucleotide with an efficiency that was comparable
      to methylation of the canonical substrate. These observations indicate that M.SinI and
      M.EcoRII discriminate between their canonical recognition site and the site containing a G.C
      or a C.G base pair in the center of the recognition sequence (GG(G)/(C)CC and CC(G)/(C)GG,
      respectively) by interaction(s) in the DNA minor groove. M.SinI mutants displaying a decreased
      capacity to discriminate between the GG(A)/(T)CC and GG(G)/(C)CC sequences were isolated by
      random mutagenesis and selection for the relaxed specificity phenotype. These mutations led to
      amino acid substitutions outside the variable region, previously thought to be the sole
      determinant of sequence specificity. These observations indicate that (A)/(T) versus (G)/(C)
      discrimination is mediated by interactions between the large domain of the methyltransferase
      and the minor groove surface of the DNA.
AU  - Kiss A
AU  - Posfai G
AU  - Zsurka G
AU  - Rasko T
AU  - Venetianer P
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2001 29: 3188-3194.

PMID- 590742
VI  - 1
DP  - 1977
TI  - A new sequence-specific endonuclease (Bsp) from Bacillus sphaericus.
PG  - 323-329
AB  - A new restriction endonuclease has been isolated from Bacillus sphaericus R.
      The purification procedure includes Bio-Gel filtration (NH4)2SO4 fractionation
      and phosphocellulose chromatography.  After the phosphocellulose step the
      enzyme preparation is free of non-specific nucleases.  Bsp cleaves
      double-stranded DNA with the same specificity as Bacillus subtilis (Bsu) and
      Haemophilus aegyptius (HaeIII) restriction endonucleases, as concluded from
      digests and double-digests of PhiX174 replicative form DNA with Bsu and Bsp.
      The 5'-terminal nucleotide of the cleavage products was shown to be C.
      Bacillus sphaericus R produces Bsp in extremely large quantities and the enzyme
      can be easily purified in high yield.
AU  - Kiss A
AU  - Sain B
AU  - Csordas-Toth E
AU  - Venetianer P
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1977 1: 323-329.

PMID- 18189249
VI  - 9
DP  - 2008
TI  - Functional reassembly of split enzymes on-site: a novel approach for highly sequence-specific targeted DNA methylation.
PG  - 351-353
AB  - In mammalian genomes, a significant fraction of the cytosine residues is methylated at the
      5-position, and this modified nucleobase is found in 5'CG-3' sequences.  The methylation
      patterns of the genome changes during ontogenesis, depends on the tissue and can substantially
      differ in several diseases, notably cancer.  We are only at the beginning of understanding the
      biological role of DNA methylation in higher organisms, but the emerging view is that
      methylation of the promoter region of a substantial fraction of genes leads to transcriptional
      inactivation (gene silencing).
AU  - Kiss A
AU  - Weinhold E
PT  - Journal Article
TA  - Chembiochem
JT  - Chembiochem
SO  - Chembiochem 2008 9: 351-353.

PMID- 21304745
VI  - 3
DP  - 2010
TI  - Complete genome sequence of 'Thermobaculum terrenum' type strain (YNP1).
PG  - 153-162
AB  - 'Thermobaculum terrenum' Botero et al. 2004 is the sole species within the proposed genus
      'Thermobaculum'. Strain YNP1(T) is the only cultivated member of
      an acid tolerant, extremely thermophilic species belonging to a phylogenetically
      isolated environmental clone group within the phylum Chloroflexi. At present, the
      name 'Thermobaculum terrenum' is not yet validly published as it contravenes Rule
      30 (3a) of the Bacteriological Code. The bacterium was isolated from a slightly
      acidic extreme thermal soil in Yellowstone National Park, Wyoming (USA).
      Depending on its final taxonomic allocation, this is likely to be the third
      completed genome sequence of a member of the class Thermomicrobia and the seventh
      type strain genome from the phylum Chloroflexi. The 3,101,581 bp long genome with
      its 2,872 protein-coding and 58 RNA genes is a part of the Genomic Encyclopedia
      of Bacteria and Archaea project.
AU  - Kiss H et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 3: 153-162.

PMID- 22675585
VI  - 5
DP  - 2011
TI  - Complete genome sequence of the filamentous gliding predatory bacterium Herpetosiphon aurantiacus type strain (114-95).
PG  - 356-370
AB  - Herpetosiphon aurantiacus Holt and Lewin 1968 is the type species of the genus Herpetosiphon,
      which in turn is the type genus of the family Herpetosiphonaceae, type family of the order
      Herpe-tosiphonales in the phylum Chloroflexi. H. aurantiacus cells are organized in filaments
      which can rapidly glide. The species is of interest not only because of its rather isolated
      position in the tree of life, but also because Herpetosiphon ssp. were identified as predators
      capable of facultative pre-dation by a wolf pack strategy and of degrading the prey organisms
      by excreted hydrolytic en-zymes. The genome of H. aurantiacus strain 114-95T is the first
      completely sequenced genome of a member of the family Herpetosiphonaceae. The 6,346,587 bp
      long chromosome and the two 339,639 bp and 99,204 bp long plasmids with a total of 5,577
      protein-coding and 77 RNA genes was sequenced as part of the DOE Joint Genome Institute
      Program DOEM 2005.
AU  - Kiss H et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 5: 356-370.

PMID- 21304711
VI  - 2
DP  - 2010
TI  - Complete genome sequence of Denitrovibrio acetiphilus type strain (N2460).
PG  - 270-279
AB  - Denitrovibrio acetiphilus Myhr and Torsvik 2000 is the type species of the genus
      Denitrovibrio in the bacterial family Deferribacteraceae. It is of phylogenetic
      interest because there are only six genera described in the family
      Deferribacteraceae. D. acetiphilus was isolated as a representative of a
      population reducing nitrate to ammonia in a laboratory column simulating the
      conditions in off-shore oil recovery fields. When nitrate was added to this
      column undesirable hydrogen sulfide production was stopped because the sulfate
      reducing populations were superseded by these nitrate reducing bacteria. Here we
      describe the features of this marine, mesophilic, obligately anaerobic organism
      respiring by nitrate reduction, together with the complete genome sequence, and
      annotation. This is the second complete genome sequence of the order
      Deferribacterales and the class Deferribacteres, which is the sole class in the
      phylum Deferribacteres. The 3,222,077 bp genome with its 3,034 protein-coding and
      51 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Kiss H et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 2: 270-279.

PMID- 23177215
VI  - 115
DP  - 2013
TI  - Development of genetic transformation and heterologous expression system in carboxydotrophic thermophilic acetogen Moorella thermoacetica.
PG  - 347-352
AB  - To develop a microbial production platform based on hydrogen and carbon dioxide, a genetic
      transformation system for the thermophilic acetogen
      Moorella thermoacetica ATCC39073 was developed. The uracil auxotrophic
      strain dpyrF was constructed by disrupting pyrF for orotate
      monophosphate decarboxylase. The transformation plasmids were
      methylated by restriction methylases of M. thermoacetica to avoid the
      decomposition of introduced plasmids by restriction-modification
      system. Reintroduction of native pyrF into the mutant by homologous
      recombination ensured recovery from uracil auxotrophy. To test
      heterologous gene expression in dpyrF, the lactate dehydrogenase (LDH)
      gene (T-ldh) from Thermoanaerobacter pseudethanolicus ATCC33223 was
      electroporated into dpyrF with a promoter of the
      glyceraldehyde-3-phosphate dehydrogenase (G3PD) gene of M.
      thermoacetica ATCC39073. The resulting transformant (C31) successfully
      transcribed T-ldh and exhibited higher LDH activity than ATCC39073 and
      dpyrF, yielding 6.8 mM of lactate from fructose, whereas ATCC39073 did
      not produce lactate.
AU  - Kita A
AU  - Iwasaki Y
AU  - Sakai S
AU  - Okuto S
AU  - Takaoka K
AU  - Suzuki T
AU  - Yano S
AU  - Sawayama S
AU  - Tajima T
AU  - Kato J
AU  - Nishio N
AU  - Murakami K
AU  - Nakashimada Y
PT  - Journal Article
TA  - J. Biosci. Bioeng.
JT  - J. Biosci. Bioeng.
SO  - J. Biosci. Bioeng. 2013 115: 347-352.

PMID- 
VI  - 67
DP  - 2009
TI  - Molecular evolution of restriction endonucleases.
PG  - 254-257
AB  - 
AU  - Kita K
PT  - Journal Article
TA  - Baiosaiensu to Indasutori
JT  - Baiosaiensu to Indasutori
SO  - Baiosaiensu to Indasutori 2009 67: 254-257.

PMID- 
VI  - 41
DP  - 2003
TI  - Type II restriction-modification gene coded by the E. coli genome. Vestiges of horizontal transfer via phages.
PG  - 348-350
AB  - 
AU  - Kita K
PT  - Journal Article
TA  - Kagaku To Seibutsu
JT  - Kagaku To Seibutsu
SO  - Kagaku To Seibutsu 2003 41: 348-350.

PMID- Not included in PubMed...
VI  - 48
DP  - 1984
TI  - Determination of the cleavage site of restriction enzyme, AccII, using synthetic oligonucleotide.
PG  - 531-532
AB  - None
AU  - Kita K
AU  - Hiraoka N
AU  - Kimizuka F
AU  - Obayashi A
PT  - Journal Article
TA  - Agric. Biol. Chem.
JT  - Agric. Biol. Chem.
SO  - Agric. Biol. Chem. 1984 48: 531-532.

PMID- 2997733
VI  - 13
DP  - 1985
TI  - Interaction of the restriction endonuclease ScaI with its substrates.
PG  - 7015-7024
AB  - The kinetic constants of the site-specific endonuclease, ScaI, for various
      substrates were determined.  We estimated Vmax and Km for octa-, deca-,
      dodeca-, and hexadecanucleotides and for plasmid pBR322 DNA.  Vmax for these
      substrates were close, but Km were quite different (in decreasing order, octa-
      > deca-, dodeca-, hexadeca- > pBR322).  The results were discussed with respect
      to the tertiary structure of substrate.
AU  - Kita K
AU  - Hiraoka N
AU  - Kimizuka F
AU  - Obayashi A
AU  - Kojima H
AU  - Takahashi H
AU  - Saito H
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1985 13: 7015-7024.

PMID- 3001647
VI  - 13
DP  - 1985
TI  - AccIII, a new restriction endonuclease from Acinetobacter calcoaceticus.
PG  - 8685-8694
AB  - A new site-spectific restriction endonuclease, AccIII, was isolated from Acinetobacter
      calcoaceticus. AccIII recognizes T^CCGGA and cleaves at the position shown by the arrow.
      AccIII activity was inhibited by adenine methylation at the overlapping dam methylase
      recognition sequence.
AU  - Kita K
AU  - Hiraoka N
AU  - Oshima A
AU  - Kadonishi S
AU  - Obayashi A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1985 13: 8685-8694.

PMID- 12644501
VI  - 185
DP  - 2003
TI  - Evidence for horizontal transfer of the EcoT38I restriction-modification gene to chromosomal DNA by the P2 phage and diversity of defective P2 prophages in Escherichia coli TH38 strains.
PG  - 2296-2305
AB  - A DNA fragment carrying the genes coding for a novel EcoT38I restriction endonuclease
      (R.EcoT38I) and EcoT38I methyltransferase (M.EcoT38I), which
      recognize G(A/G)GC(C/T)C, was cloned from the chromosomal DNA of
      Escherichia coli TH38. The endonuclease and methyltransferase genes were
      in a head-to-head orientation and were separated by a 330-nucleotide
      intergenic region. A third gene, the C.EcoT38I gene, was found in the
      intergenic region, partially overlapping the R.EcoT38I gene. The gene
      product, C.EcoT38I, acted as both a positive regulator of R.EcoT38I gene
      expression and a negative regulator of M.EcoT38I gene expression.
      M.EcoT38I purified from recombinant E. coli cells was shown to be a
      monomeric protein and to methylate the inner cytosines in the recognition
      sequence. R.EcoT38I was purified from E. coli HB101 expressing M.EcoT38I
      and formed a homodimer. The EcoT38I restriction (R)-modification (M)
      system (R-M system) was found to be inserted between the A and Q genes of
      defective bacteriophage P2, which was lysogenized in the chromosome at
      locI, one of the P2 phage attachment sites observed in both E. coli K-12
      MG1655 and TH38 chromosomal DNAs. Ten strains of E. coli TH38 were
      examined for the presence of the EcoT38I R-M gene on the P2 prophage.
      Conventional PCR analysis and assaying of R activity demonstrated that all
      strains carried a single copy of the EcoT38I R-M gene and expressed R
      activity but that diversity of excision in the ogr, D, H, I, and J genes
      in the defective P2 prophage had arisen.
AU  - Kita K
AU  - Kawakami H
AU  - Tanaka H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2003 185: 2296-2305.

PMID- 2685747
VI  - 17
DP  - 1989
TI  - Overproduction and crystallization of FokI restriction endonuclease.
PG  - 8741-8753
AB  - To overproduce FokI endonuclease (R. FokI) in an Escherichia coli system, the coding region of
      R.FokI predicted from the nucleotide sequence was generated from the FokI operon and joined to
      the tac promoter of an expression vector, pKK223-3.  By introduction of the plasmid into E.
      coli UT481 cells expressing the FokI methylase gene, the R.FokI activity was overproduced
      about 30-fold, from which R. FokI was purified in amounts sufficient for crystallization.  The
      removal of a stem-loop structure immediately upstream of the R. FokI coding region was
      essential for overproduction.
AU  - Kita K
AU  - Kotani H
AU  - Hiraoka N
AU  - Nakamura T
AU  - Yonaha K
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 8741-8753.

PMID- 1741303
VI  - 20
DP  - 1992
TI  - StsI, a new FokI isoschizomer from Streptococcus sanguis 54, cleaves 5' GGATG(N)10/14 3'.
PG  - 618
AB  - StsI, an isoschizomer of FokI has been isolated from Streptococcus sanguis 54.
      StsI recognizes the non-palindromic sequence 5'-GGATG-3'.  Unlike its
      isoschizomer, StsI cleaves DNA 10 nucleotides to the right from the noted
      recognition sequence and 14 nucleotides to the right on the opposite strand.
      StsI was purified from the cell extracts by combined chromatographies on
      phosphocellulose, DEAE-cellulose, heparin-Sepharose, hydroxylapatite, and
      Affi-Gel Blue agarose.  The purified enzyme was homogeneous on
      SDS-polyacrylamide gel electrophoresis.  The molecular mass of the enzyme was
      estimated at 70 kDa.  The StsI activity was eluted at 70 kDa from a gel
      filtration column.  These results indicated that the active form of StsI was a
      monomer.
AU  - Kita K
AU  - Kotani H
AU  - Ohta H
AU  - Yanase H
AU  - Kato N
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 618.

PMID- 2784436
VI  - 264
DP  - 1989
TI  - The FokI restriction-modification system  I. Organization and nucleotide sequences of the restriction and modification genes.
PG  - 5751-5756
AB  - A DNA fragment that carried the genes coding for FokI endonuclease and
      methylase was cloned from the chromosomal DNA of Flavobacterium okeanokoites,
      and the coding regions were assigned to the nucleotide sequence by deletion
      analysis.  The methylase gene was 1941 base pairs (bp) long, corresponding to a
      protein of 647 amino acid residues (Mr=75622), and the endonuclease gene was
      1749 bp long, corresponding to a protein of 583 amino acid residues (Mr=66216).
      The assignment of the methylase gene was further confirmed by analysis of the
      N-terminal amino acid sequence.  The endonuclease gene was downstream from the
      methylase gene in the same orientation, separated by 69 bp.  The promoter site,
      which could be recognized by Escherichia coli RNA polymerase, was upstream from
      the methylase gene, and the sequences adhering to the ribosome-binding sequence
      were identified in front of the respective genes.  Analysis of the gene
      products expressed in E. coli cells by gel filtration and sodium dodecyl
      sulfate-polyacrylamide gel electrophoresis indicated that the molecular weights
      of both enzymes coincided well with the values estimated from the nucleotide
      sequences, and that the monomeric forms were catalytically active.  No
      significant similarity was found between the sequences of the two enzymes.
      Sequence comparison with other related enzymes indicated that FokI methylase
      contained two copies of a segment of tetra-amino acids which is characteristic
      of adenine-specific methylase.
AU  - Kita K
AU  - Kotani H
AU  - Sugisaki H
AU  - Takanami M
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1989 264: 5751-5756.

PMID- 1387204
VI  - 20
DP  - 1992
TI  - Cloning and sequence analysis of the StsI restriction-modification gene: presence of homology to FokI restriction-modification enzymes.
PG  - 4167-4172
AB  - StsI endonuclease (R.StsI), a type IIs restriction endonuclease found in Streptococcus sanguis
      54, recognizes the same sequence as FokI but cleaves at different positions. A DNA fragment
      that carried the genes for R.StsI and StsI methylase (M.StsI) was cloned from the chromosomal
      DNA of S. sanguis 54, and its nucleotide sequence was analyzed. The endonuclease gene was
      1,806 bp long, corresponding to a protein of 602 amino acid residues (Mr=68,388), and the
      methylase gene was 1,959 bp long, corresponding to a protein of 653 amino acids residues (Mr
      =76,064). The assignment of the endonuclease gene was confirmed by analysis of the N-terminal
      amino acid sequence. Genes for the two proteins were in a tail-to-tail orientation, separated
      by a 131-nucleotide intercistronic region. The predicted amino acid sequences between the StsI
      system and the FokI system showed a 49% identity between the methylases and a 30% identity
      between the endonucleases. The sequence comparison of M.StsI with various methylases showed
      that the N-terminal half of M.StsI matches M.NlaII, and the C-terminal half matches adenine
      methylases that recognize GATC and GATATC.
AU  - Kita K
AU  - Suisha M
AU  - Kotani H
AU  - Yanase H
AU  - Kato N
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 4167-4172.

PMID- 8635752
VI  - 169
DP  - 1996
TI  - Overproduction and characterization of the StsI restriction endonuclease.
PG  - 69-73
AB  - The StsI restriction endonuclease (R.StsI), a class-IIS restriction endonuclease, found in
      Streptococcus sanguis 54, is a heteroschizomer of R.FokI, which recognizes 5M-U-GGATG-3M-U.
      To overproduce R.StsI in Escherichia coli, the coding region of R.StsI was joined to the tac
      promoter of an expression vector, pKK223-3.  By introduction of the plasmid into E. coli UT481
      cells expressing the fokIM gene, R.StsI activity was overproduced, from which R.StsI was
      purified homogeneously.  We compared the properties of R.StsI with those of R.FokI.  The
      optimum reaction conditions for R.StsI were quite different from those for R.FokI.  R.StsI is
      an acidic protein (pI 6.3).  Anti-R.StsI serum did not cross-react with R.FokI, indicating
      three-dimensional structural dissimilarity.  The domain structure of R.StsI was elucidated by
      digestion with trypsin.  In the presence of substrate DNA, R.StsI was digested to yield 45-kDa
      N-terminal and 23-kDa C-terminal fragments.  The amino-acid sequences around the trypsin
      cleavage sites of R.StsI and R.FokI were quite homologous.
AU  - Kita K
AU  - Suisha M
AU  - Shintoh M
AU  - Yanase H
AU  - Kato N
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1996 169: 69-73.

PMID- 7963862
VI  - 66
DP  - 1994
TI  - Enzymology of restriction enzymes.
PG  - 1237-1245
AB  - A review
AU  - Kita K
AU  - Takasaki Y
PT  - Journal Article
TA  - Seikagaku
JT  - Seikagaku
SO  - Seikagaku 1994 66: 1237-1245.

PMID- 10542186
VI  - 181
DP  - 1999
TI  - Evidence of horizontal transfer of the EcoO109I restriction-modification gene to Escherichia coli chromosomal DNA.
PG  - 6822-6827
AB  - A DNA fragment carrying the genes coding for EcoO109I endonuclease and EcoO109I methylase,
      which recognize the nucleotide sequence 5'-(A/G) GGNCC(C/T)-3', was cloned from the
      chromosomal DNA of Escherichia coli H709c.  The EcoO109I restriction-modification system was
      found to be inserted between the int and psu genes from satellite bacteriophage P4, which were
      lysogenized in the chromosome at the P4 phage attachment site of the corresponding leuX gene
      observed in E. coli K-12 chromosomal DNA.  The sid gene of the prophage was inactivated by
      insertion of one copy of IS21.  These findings may shed light on the horizontal transfer and
      stable maintenance of the R-M system.
AU  - Kita K
AU  - Tsuda J
AU  - Kato T
AU  - Okamoto K
AU  - Yanase H
AU  - Tanaka M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1999 181: 6822-6827.

PMID- 12177297
VI  - 30
DP  - 2002
TI  - C.EcoO109I, a regulatory protein for production of EcoO109I restriction endonuclease, specifically binds to and bends DNA upstream of its translational start site.
PG  - 3558-3565
AB  - The EcoO109I restriction-modification system, which recognizes 5'-(A/G)GGNCC(C/T)-3', has
      been cloned, and contains convergently transcribed endonuclease and methylase. The role and
      action mechanism of the gene product, C.EcoO109I, of a small open reading frame located
      upstream of ecoO109IR were investigated in vivo and in vitro.  The results of deletion
      analysis suggested that C.EcoO109I acts as a positive regulator of ecoO109IR expression but
      has little effect on ecoO109IM expression. Assaying of promoter activity showed that the
      expression of ecoO109IC was regulated by its own gene product, C.EcoO109I. C.EcoO109I was
      overproduced as a His-tag fusion protein in recombinant Escherichia coli HB101 and purified to
      homogeneity. C.EcoO109I exists as a homodimer, and recognizes and binds to the DNA sequence
      5'-CTAAG(N)(5)CTTAG-3' upstream of the ecoO109IC translational start site. It was also shown
      that C.EcoO109I bent the target DNA by 54 +/- 4 degrees.
AU  - Kita K
AU  - Tsuda J
AU  - Nakai S-y
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2002 30: 3558-3565.

PMID- 11791726
VI  - 65
DP  - 2001
TI  - Characterization and overproduction of EcoO109I methyltransferase.
PG  - 2512-2518
AB  - In order to characterize EcoO109I methyltransferase, a recombinant Escherichia coli clone that
      overproduces the enzyme was constructed.
      The coding region of M.EcoO109I was joined to the lac promoter of an
      expression vector, pUC118, and the resulting plasmid was introduced
      into E. coli HB101. M.EcoO109I was purified homogeneously from
      IPTG-induced cells, and was found to consist of a monomer subunit.
      M.EcoO109I uniquely methylates the inner deoxycytidylate residue in the
      sequence 5'-(A/G)GGNCC(C/T)-3' to produce 5-methylcytosine. The enzyme
      was most active at pH 8.0-8.5 and 50 C. The enzyme activity was
      not affected by the addition of Mg2+ or EDTA.
AU  - Kita K
AU  - Tsuda J
AU  - Nishigaki R
PT  - Journal Article
TA  - Biosci. Biotechnol. Biochem.
JT  - Biosci. Biotechnol. Biochem.
SO  - Biosci. Biotechnol. Biochem. 2001 65: 2512-2518.

PMID- 25301659
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Rhodococcus erythropolis JCM 6824, an Aurachin RE Antibiotic Producer.
PG  - e01026-14
AB  - Rhodococcus erythropolis JCM 6824 is the producer of the quinoline antibiotic aurachin RE.
      This bacterium also degrades and utilizes some aromatic compounds,
      such as biphenyl and benzoate. Here, we report the draft genome sequence of this
      strain.
AU  - Kitagawa W
AU  - Hata M
AU  - Sekizuka T
AU  - Kuroda M
AU  - Ishikawa J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01026-14.

PMID- 29880592
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Klebsiella quasipneumoniae Strain S05, a Fouling-Causing Bacterium Isolated from a Membrane Bioreactor.
PG  - e00471-18
AB  - We report here the complete genome sequence of Klebsiella quasipneumoniae strain  S05, a
      bacterium capable of producing membrane fouling-causing soluble substances
      and capable of respiring on oxygen, nitrate, and an anodic electrode. The genomic
      information of strain S05 should help predict metabolic pathways associated with
      these unique biological properties of this bacterium.
AU  - Kitajima M
AU  - Ishizaki S
AU  - Jang J
AU  - Ishii S
AU  - Okabe S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00471-18.

PMID- 23580712
VI  - 1
DP  - 2013
TI  - Genome Sequence of the Obligate Gammaproteobacterial Methanotroph Methylomicrobium album Strain BG8.
PG  - e00170-13
AB  - The complete genome sequence of Methylomicrobium album strain BG8, a methane-oxidizing
      gammaproteobacterium isolated from freshwater, is reported.
      Aside from a conserved inventory of genes for growth on single-carbon compounds,
      M. album BG8 carries a range of gene inventories for additional carbon and
      nitrogen transformations but no genes for growth on multicarbon substrates or for
      N fixation.
AU  - Kits KD et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00170-13.

PMID- 21725020
VI  - 193
DP  - 2011
TI  - Genome Sequence of Methyloversatilis universalis FAM5T, a Methylotrophic Representative of the Order Rhodocyclales.
PG  - 4541
AB  - Rhodocyclales are representative of versatile bacteria that are able to utilize a wide variety
      of organic compounds for growth, but only few
      strains have been isolated in pure culture thus far. Here we present the
      genome sequence of Methyloversatilis universalis FAM5(T), the first
      cultivable methylotrophic member of the order.
AU  - Kittichotirat W
AU  - Good NM
AU  - Hall R
AU  - Bringel F
AU  - Lajus A
AU  - Medigue C
AU  - Smalley NE
AU  - Beck D
AU  - Bumgarner R
AU  - Vuilleumier S
AU  - Kalyuzhnaya MG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4541.

PMID- 8896748
VI  - 40
DP  - 1996
TI  - Inhibition of restriction endonucleases by DNA sequence-reading ligands.
PG  - 263-272
AB  - DNA sequence-reading bisquaternary ammonium heterocycles SN 6570, SN 6999, SN 6053, SN 6132,
      SN 6131, SN 18071 and the non-specific binders SN 6113, SN 5754, SN 6324, and SN 4094
      influence the enzymatic activity of restriction endonucleases in different manners.  A
      prerequisite for sequence-specific ligand interaction is a dAdT run of at least four base
      pairs.  The sequence-specific binders inhibit the cleavage activity of restriction
      endonucleases EcoRI, SspI, and DraI with four and six dAdT base pairs in their restriction
      sites, while the activity of SalI and BamHI with less than four dAdT base pairs in their
      recognition motifs remains unaffected.  On the contrary, the non-specific binding DNA ligands
      are incapable of suppressing the digestion for restriction nucleases under research.  These
      results are in line with our footprint data.  The inhibitory effect is independent of the
      number of cleavage sites in DNA and of whether the macromolecule exists in the ccc or lds
      conformation.  Sequence specific binding of the ligand SN 6043 in close vicinity to the
      cleavage sites of restriction endonuclease DraI also interferes with enzyme inhibition.
AU  - Kittler L
AU  - Bell A
AU  - Baguley BC
AU  - Lober G
PT  - Journal Article
TA  - Biochem. Mol. Biol. Int.
JT  - Biochem. Mol. Biol. Int.
SO  - Biochem. Mol. Biol. Int. 1996 40: 263-272.

PMID- 9628346
VI  - 379
DP  - 1998
TI  - Sequence specific modulation of DNA restriction enzyme cleavage by minor groove binders.
PG  - 519-525
AB  - The inhibition of restriction endonuclease cleavage by a series of bisquaternary ammonium
      derivatives which bind to the minor groove of DNA has been studied.  The derivatives
      considered included six sequence-selective binders (SN 6570, SN 6999, SN 6050, SN 6132, SN
      6131 and SN 18071) and four non-specific binders (SN 6113, SN 5754, SN 6324 and SN 4094) and
      can be distinguished by their activity on restriction endonucleases.  Digestion experiments
      with pUC19 DNA were monitored electrophoretically using the transition of the covalently
      closed circular DNA into the linear double stranded one.  Only the sequence-specific binders
      inhibit the cleavage activity of restriction endonucleases EcoRI, SspI and DraI with four and
      six dAdT-base pairs within their restriction sites, while the activity of SalI and BamHI with
      less than four dAdT-sequences was unaffected.  In contrast, the non-specific binding ligands
      were incapable of suppressing enzyme digestion.  The inhibition of the restriction
      endonuclease PvuII indicates that ligand binding in close vicinity to the cleavage sites is
      also involved in the enzyme inhibition.  The dAdT-content in proximity to the palindromic
      sequences of three DraI cutting sites in pUC19DNA explains why the derivative SN 6053 protects
      these sequences in different manners.  Gel shift experiments indicated that BQA-derivatives
      inhibit the DNA-enzyme complex formation if the ligand was added to the DNA before the enzyme.
      In contrast, complex formation between DNA and enzyme remained unchanged when the enzyme was
      added first.
AU  - Kittler L
AU  - Bell A
AU  - Baguley BC
AU  - Loeber G
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1998 379: 519-525.

PMID- 23640197
VI  - 1
DP  - 2013
TI  - Genome Sequence of Halanaerobium saccharolyticum subsp. saccharolyticum Strain DSM 6643T, a Halophilic Hydrogen-Producing Bacterium.
PG  - e00187-13
AB  - Halanaerobium saccharolyticum is a halophilic anaerobic fermentative bacterium capable of
      producing hydrogen, a potential future energy carrier molecule. The
      high-quality draft genome of H. saccharolyticum subsp. saccharolyticum strain DSM
      6643(T) consists of 24 contigs for 2,873,865 bp with a G+C content of 32.3%.
AU  - Kivisto A
AU  - Larjo A
AU  - Ciranna A
AU  - Santala V
AU  - Roos C
AU  - Karp M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00187-13.

PMID- 25193305
VI  - 6
DP  - 2014
TI  - Evolution and Comparative Genomics of Campylobacter jejuni ST-677 Clonal Complex.
PG  - 2424-2438
AB  - Campylobacter is the most common bacterial cause of gastroenteritis in the European Union with
      over 200,000 laboratory-confirmed cases reported annually. This is the first study to describe
      findings related to comparative genomics analyses of the sequence type (ST)-677 clonal complex
      (CC), a Campylobacter jejuni lineage associated with bacteremia cases in humans. We performed
      whole-genome sequencing, using Illumina HiSeq sequencing technology, on five related ST-677 CC
      isolates from two chicken farms to identify microevolution taking place at the farms. Our
      further aim was to identify novel putative virulence determinants from the ST-677 CC genomes.
      For this purpose, clinical isolates of the same CC were included in comparative genomic
      analyses against well-known reference strains of C. jejuni. Overall, the ST-677 CC was
      recognized as a highly clonal lineage with relatively small differences between the genomes.
      Among the farm isolates differences were identified mainly in the lengths of the homopolymeric
      tracts in genes related to the capsule, lipo-oligosaccharide, and flagella. We identified
      genomic features shared with C. jejuni subsp. doylei, which has also been shown to be
      associated with bacteremia in humans. These included the degradation of the cytolethal
      distending toxin operon and similarities between the capsular polysaccharide biosynthesis
      loci. The phase-variable GDP-mannose 4,6-dehydratase (EC 4.2.1.47) (wcbK, CAMP1649),
      associated with the capsular polysaccharide biosynthesis locus, may play a central role in
      ST-677 CC conferring acid and serum resistance during different stages of infection.
      Homology-based searches revealed several additional novel features and characteristics,
      including two putative type Vb secretion systems and a novel restriction
      modification/methyltransferase gene cluster, putatively associated with pathogenesis and niche
      adaptation.
AU  - Kivisto RI
AU  - Kovanen S
AU  - Skarp-de-Haan A
AU  - Schott T
AU  - Rahkio M
AU  - Rossi M
AU  - Hanninen M-L
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2014 6: 2424-2438.

PMID- 
VI  - 0
DP  - 2009
TI  - Restriction enzymes.
PG  - 118-122
AB  - 
AU  - Kiwaki M
PT  - Journal Article
TA  - Bifizusukin Yakurutokabu
JT  - Bifizusukin Yakurutokabu
SO  - Bifizusukin Yakurutokabu 2009 0: 118-122.

PMID- 23991468
VI  - 318
DP  - 1985
TI  - An intron in the 23S ribosomal RNA gene of the archaebacterium Desulfurococcus mobilis.
PG  - 675-677
AB  - The archaebacteria have been defined, at a molecular level, as constituting a third primary
      kingdom consisting of the methanogens, the extreme halophiles, and the sulphur-dependent
      extreme thermophiles. In reaching this conclusion, Woese and colleagues used the 16S ribosomal
      RNA as an approximate chronometer for evolutionary time and demonstrated that, at a nucleotide
      sequence level, the archaebacteria are as different from the eubacteria and eukaryotes as the
      latter kingdoms are from one another. Current research on archaebacteria is yielding valuable
      insights into the evolutionary relationships between archaebacteria, eubacteria and
      eukaryotes, and into the early forms of cellular life. Here, we extend this knowledge by
      providing the first evidence for the occurrence of an intron within any prokaryotic ribosomal
      RNA. The intron was found within the 23S rRNA gene of the sulphur-dependent and anaerobic
      Thermoproteale Desulfurococcus mobilis, which was isolated from hot acidic springs in Iceland
      at temperatures up to 97oC. The intron contains 622 base pairs (bp); it is very A+T-rich (65%)
      compared with the 23S rRNA gene (34%), and it exhibits a large open reading frame. The
      splicing site occurs in domain IV of the 23S RNA at a position close to that of an intron of
      the lower eukaryote Physarum polycephalum; the intron does not readily fall into one of the
      three classes of eukaryotic nuclear introns because it has features in common with those of
      classes I (rRNA) and III (transfer RNA).
AU  - Kjems J
AU  - Garrett RA
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1985 318: 675-677.

PMID- 9469849
VI  - 26
DP  - 1998
TI  - Rapid detection of functional expression of C-5-DNA methytransferases in yeast.
PG  - 1354-1355
AB  - We have previously employed the cytosine-5-DNA methyltransferase, M.SssI, as a probe for
      chromatin architecture in intact cells.  Although M.SssI offers the highest resolution of any
      currently available MTase, the difficulty in establishing stable, methylation-positive strains
      poses a barrier to its general utility as a chromatin probe.  We describe a single screen for
      M.SssI-expressing strains that eliminates the purification of PCR products amplified from
      bisulfite-treated DNA, use of radioisotopes, polyacrylamide sequencing gel electrophoresis,
      and autoradiography.  The high throughput of the method now makes it feasible to introduce
      M.SssI into a vareity of wild-type and mutant genetic backgrounds.
AU  - Kladde MP
AU  - Simpson RT
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1998 26: 1354-1355.

PMID- 8902807
VI  - 274
DP  - 1996
TI  - Chromatin structure mapping in vivo using methyltransferases.
PG  - 214-233
AB  - Realization of the role of chromatin structure in the function of RNA polymerases in
      eukaryotic cells has grown rapidly in the past decade.  Effects of the nucleosomal
      organization of DNA on transcriptional initiation have been documented both in vivo and in
      vitro.  Several studies have addressed the mechanical difficulties faced by RNA polymerase
      encountering a nucleosome during transcriptional elongation, offering varying possible
      resolutions to this problem.   Above the local difficulties which polymerases must face in the
      basic nucleosomal organization of chromatin, there are higher order structures, including
      chromatin domains, which have been implicated in more global silencing, such as position
      effect variegation, X-chromosome inactivation, epigenetic inheritance, and centromeric and
      telomeric repression.  All these considerations make methods for assessment of chromatin
      structure of importance to those scientists interested in transcriptional mechanisms in
      eukaryotic cells.  Historically, chromatin structure investigations have relied on enzymatic
      (micrococcal nuclease or DNase I) or chemical (hydroxyl radical, methidium propyl-EDTA-iron,
      cooper-phenanthroline) probes to degrade DNA; proteins, either histones or non-histone
      regulatory proteins, left a footprint on DNA by blocking the access of the reagent to the
      nucleic acid, enabling deductions about potential structures of the nucleoprotein complex.  In
      general, isolation of nuclei is required prior to analysis of chromatin.  This makes the
      detection of the labile chromatin constituents problematic, limiting conclusions about the
      structure of transcribed or repressed genes.
AU  - Kladde MP
AU  - Simpson RT
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1996 274: 214-233.

PMID- 10372375
VI  - 304
DP  - 1999
TI  - DNA methyltransferases as probes of chromatin structure in vivo.
PG  - 431-447
AB  - A complementary strategy to conventional methods for probing chromatin organization utilizes
      the expression of foreign DNA methyltransferases in intact Saccharomyces cerevisiae.  At
      current levels of expression of several foreign methyltransferases in yeast, no deleterious
      effects to cellular metabolism have been detected.  The innocuousness of methyltransferase
      expression and the absence of endogenous adenine or cytosine methylation in the yeast genome
      allow detection of de novo DNA modification in DNA that is directly isolated from engineered,
      methylation-proficient cells.  The ability to bypass the isolation of nuclei, thereby avoiding
      loss of labile constituents or possible reorganization of chromosome structure, has provided
      the motivation for developing methyltransferase probing strategies.
AU  - Kladde MP
AU  - Xu M
AU  - Simpson RT
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1999 304: 431-447.

PMID- Not carried by PubMed...
VI  - 19
DP  - 1991
TI  - Development of bacteriophage-resistant strains of lactic acid bacteria.
PG  - 675-682
AB  - One exciting area that has emerged through genetic analysis of the lactococci is the
      definition and practical application of gene systems that provide phage resistance to these
      industrially important bacteria.  Naturally occurring phage-insensitive strains have been
      characterized and found to harbor multiple defense systems which can act at different points
      of the lytic cycle to prevent the successful adsorption, infection, or replication of virulent
      phages.  Although phage attack on lactococcal starter cultures is still a major problem for
      the cultured dairy products industries, this can now be successfully addressed using genetic
      approaches to construct strains which are resistant to the phages often encountered in the
      industry.  In this paper I will describe the various phage defense systems that are naturally
      present in lactococci, their individual and combined effects, and the genetic strategies which
      are currently available to construct phage-insensitive strains for dairy fermentations.  In
      addition, I will discuss the molecular responses of virulent phages which have appeared in the
      industry following the introduction and use of specialized starter cultures carrying defined
      mechanisms of phage resistance.  The genetic routes whereby industrial phages elicit
      counter-defenses against lactococcal resistance mechanism provide new and important
      information that will facilitate the development of improved starter culture systems and
      phage-resistant lactic acid bacteria.
AU  - Klaenhammer TR
PT  - Journal Article
TA  - Food Biotech.
JT  - Food Biotech.
SO  - Food Biotech. 1991 19: 675-682.

PMID- Not included in PubMed...
VI  - 46
DP  - 1987
TI  - Plasmid-directed mechanisms for bacteriophage defense in lactic streptococci.
PG  - 313-325
AB  - Genetic studies with lactic streptococci have identified a variety of plasmids
      coding for systems that interfere with phage adsorption, direct restriction and
      modification activities, and disrupt various stages in the phage lytic cycle.
      This review describes mechanisms of phage defense that are plasmid-directed in
      lactic streptococci, examines the physical and genetic properties of the
      plasmids involved, and discusses genetic strategies for construction of
      phage-insensitive starter cultures for dairy fermentations.
AU  - Klaenhammer TR
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1987 46: 313-325.

PMID- Not included in PubMed...
VI  - 72
DP  - 1989
TI  - Genetic characterization of multiple mechanisms of phage defense from a prototype phage-insensitive strain, Lactococcus lactis ME2.
PG  - 3429-3443
AB  - Lactococci used as starter cultures in dairy fermentations are highly
      susceptible to attack by bacteriophage.  Genetic studies with Lactococcus
      lactis ME2, a prototype phage-insensitive strain, have identified
      plasmid-encoded defenses, which interfere with phage adsorption, restrict and
      modify phages, or abort lytic phage infection.  Restriction and modification
      and abortion of phage infection were localized on two distinct
      self-transmissible plasmids, pTN20 and pTR2030, respectively, orginating from
      L. lactis ME2.  A comparison of the physical and genetic characteristics of
      these two conjugative plasmids is presented.  Conjugation and cloning
      strategies employed to assemble these complementary mechanisms of phage
      resistance will be discussed.  The collective expression of different defense
      systems provided a greater phage resistance to dairy lactococci.  Starter
      cultures that are recalcitrant to phage attack can be constructed from existing
      strains through application of genetic technologies, which assemble
      complementary mechanisms of phage defense.
AU  - Klaenhammer TR
PT  - Journal Article
TA  - J. Dairy Sci.
JT  - J. Dairy Sci.
SO  - J. Dairy Sci. 1989 72: 3429-3443.

PMID- 
VI  - 0
DP  - 1994
TI  - Bacteriophages and bacteriophage resistance.
PG  - 106-168
AB  - Food and dairy fermentations rely on the growth and acid
      producing ability of the lactic acid bacteria.  Many of these have
      remained as traditional fermentations, where the process is driven by
      the natural microflora associated with the raw material.  Increasing
      consistency, improved quality and processing efficiencies have followed
      the development of controlled fermentations.  These rely on the activity
      of a starter culture which is intentionally inoculated in order to drive
      the primary fermentation.  However, with the increased control granted
      through the repeated use of a defined starter culture comes the potential
      for disruption of the fermentation by bacteriophage.
AU  - Klaenhammer TR
AU  - Fitzgerald GF
PT  - Journal Article
TA  - Genetics and Biotechnology of Lactic Acid Bacteria.
JT  - Genetics and Biotechnology of Lactic Acid Bacteria.
SO  - Genetics and Biotechnology of Lactic Acid Bacteria. 1994 0: 106-168.

PMID- 
VI  - 8
DP  - 1991
TI  - Molecular analysis of pTR2030 gene systems that confer bacteriophage resistance to Lactococci.
PG  - 124-130
AB  - None
AU  - Klaenhammer TR
AU  - Romero D
AU  - Sing W
AU  - Hill C
PT  - Journal Article
TA  - Genetics and Molecular Biology of Streptococci, Lactococci, and Enterococci
JT  - Genetics and Molecular Biology of Streptococci, Lactococci, and Enterococci
SO  - Genetics and Molecular Biology of Streptococci, Lactococci, and Enterococci 1991 8: 124-130.

PMID- 11536742
VI  - 45
DP  - 1996
TI  - Restriction endonuclease activity in Clostridium thermocellum and Clostridium thermosaccharolyticum.
PG  - 127-131
AB  - Clostridium thermocellum cell extracts exhibit specific endonuclease activity with
      very little non-specific exonuclease activity at 55oC.  The Dam methylation system of
      Escherichia
      coli offers complete protection from digestion by C. thermocellum ATCC 27405 cell extracts for
      all
      DNA tested (totaling >100kb, insuring that most potential restriction sequences have been
      exposed).  Based on both the Dam recognition sequence and the similarity of cell extract and
      MboI
      DNA digests, the C. thermocellum restriction enzyme recognition sequence appears to be
      5' GATC 3'.  Cell extracts made from a second thermophile, C. thermosaccarolyticum ATCC
      31960 do not exhibit specific endonuclease activity under the conditions tested.  Genomic DNA
      from C. thermocellum exhibits a Dam+ phenotype while genomic DNA from C.
      thermosaccarolyticum exhibits a Dam- phenotype.
AU  - Klapatch TR
AU  - Demain AL
AU  - Lynd LR
PT  - Journal Article
TA  - Appl. Microbiol. Biotechnol.
JT  - Appl. Microbiol. Biotechnol.
SO  - Appl. Microbiol. Biotechnol. 1996 45: 127-131.

PMID- 22123757
VI  - 193
DP  - 2011
TI  - Draft Genome Sequence of Streptomyces sp. Strain Wigar10, Isolated from a Surface-Sterilized Garlic Bulb.
PG  - 6999-7000
AB  - Streptomyces sp. strain Wigar10 was isolated from a surface-sterilized garlic bulb (Allium
      sativum var. Purple Stripe). Its genome encodes
      several novel secondary metabolite biosynthetic gene clusters and provides
      a genetic basis for further investigation of this strain's chemical
      biology and potential for interaction with its garlic host.
AU  - Klassen JL
AU  - Adams SM
AU  - Bramhacharya S
AU  - Giles SS
AU  - Goodwin LA
AU  - Woyke T
AU  - Currie CR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6999-7000.

PMID- 26659670
VI  - 3
DP  - 2015
TI  - Genome Sequences of Three Pseudoalteromonas Strains (P1-8, P1-11, and P1-30), Isolated from the Marine Hydroid Hydractinia echinata.
PG  - e01380-15
AB  - The genomes of three Pseudoalteromonas strains (P1-8, P1-11, and P1-30) were sequenced and
      assembled. These genomes will inform future study of the genes
      responsible for the production of biologically active compounds responsible for
      these strains' antimicrobial, biofouling, and algicidal activities.
AU  - Klassen JL
AU  - Rischer M
AU  - Wolf T
AU  - Guo H
AU  - Shelest E
AU  - Clardy J
AU  - Beemelmanns C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01380-15.

PMID- 26679587
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Six Pseudoalteromonas Strains, P1-7a, P1-9, P1-13-1a, P1-16-1b, P1-25, and P1-26, Which Induce Larval Settlement and Metamorphosis in  Hydractinia echinata.
PG  - e01477-15
AB  - To gain a broader understanding of the importance of a surface-associated lifestyle and
      morphogenic capability, we have assembled and annotated the genome
      sequences of Pseudoalteromonas strains P1-7a, P1-9, P1-13-1a, P1-16-1b, P1-25,
      and P1-26, isolated from Hydractinia echinata. These genomes will allow detailed
      studies on bacterial factors mediating interkingdom communication.
AU  - Klassen JL
AU  - Wolf T
AU  - Rischer M
AU  - Guo H
AU  - Shelest E
AU  - Clardy J
AU  - Beemelmanns C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01477-15.

PMID- 19307581
VI  - 106
DP  - 2009
TI  - The mosaic genome structure of the Wolbachia wRi strain infecting Drosophila simulans.
PG  - 5725-5730
AB  - The obligate intracellular bacterium Wolbachia pipientis infects around 20% of all insect
      species. It is maternally inherited and induces
      reproductive alterations of insect populations by male killing,
      feminization, parthenogenesis, or cytoplasmic incompatibility. Here, we
      present the 1,445,873-bp genome of W. pipientis strain wRi that induces
      very strong cytoplasmic incompatibility in its natural host Drosophila
      simulans. A comparison with the previously sequenced genome of W.
      pipientis strain wMel from Drosophila melanogaster identified 35
      breakpoints associated with mobile elements and repeated sequences that
      are stable in Drosophila lines transinfected with wRi. Additionally, 450
      genes with orthologs in wRi and wMel were sequenced from the W. pipientis
      strain wUni, responsible for the induction of parthenogenesis in the
      parasitoid wasp Muscidifurax uniraptor. The comparison of these A-group
      Wolbachia strains uncovered the most highly recombining intracellular
      bacterial genomes known to date. This was manifested in a 500-fold
      variation in sequence divergences at synonymous sites, with different
      genes and gene segments supporting different strain relationships. The
      substitution-frequency profile resembled that of Neisseria meningitidis,
      which is characterized by rampant intraspecies recombination, rather than
      that of Rickettsia, where genes mostly diverge by nucleotide
      substitutions. The data further revealed diversification of ankyrin repeat
      genes by short tandem duplications and provided examples of horizontal
      gene transfer across A- and B-group strains that infect D. simulans. These
      results suggest that the transmission dynamics of Wolbachia and the
      opportunity for coinfections have created a freely recombining
      intracellular bacterial community with mosaic genomes.
AU  - Klasson L
AU  - Westberg J
AU  - Sapountzis P
AU  - Naslund K
AU  - Lutnaes Y
AU  - Darby AC
AU  - Veneti Z
AU  - Chen L
AU  - Braig HR
AU  - Garrett R
AU  - Bourtzis K
AU  - Andersson SG
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2009 106: 5725-5730.

PMID- 6276697
VI  - 184
DP  - 1981
TI  - Restriction of Streptomyces phage SH5 by endonuclease ShyI from Streptomyces hygroscopicus 0477.
PG  - 286-288
AB  - DNA of the temperate Streptomyces phage SH5 (DNA molecular weight 27 x 106) is
      subject to restriction-modification mediated by S. hygroscopicus 0477.  S.
      levoris 1331 and 2340.  The restriction endonuclease ShyI (isoschizomeric with
      SacII) isolated from S. hygroscopicus 0477 is involved in restriction of
      SH5-1331 and SH5-2340 DNAs in S. hygroscopicus 0477.
AU  - Klaus S
AU  - Hartmann M
AU  - Krugel H
AU  - Roth M
AU  - Walter F
AU  - Rautenstein YI
AU  - Solovyeva NY
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1981 184: 286-288.

PMID- 10722605
VI  - 68
DP  - 2000
TI  - Molecular and biological analysis of eight genetic islands that distinguish Neisseria meningitidis from the closely related pathogen   Neisseria gonorrhoeae.
PG  - 2082-2095
AB  - The pathogenic species Neisseria meningitidis and Neisseria gonorrhoeae cause dramatically
      different diseases despite strong relatedness at the
      genetic and biochemical levels. N. meningitidis can cross the blood-brain
      barrier to cause meningitis and has a propensity for toxic septicemia
      unlike N. gonorrhoeae. We previously used subtractive hybridization to
      identify DNA sequences which might encode functions specific to bacteremia
      and invasion of the meninges because they are specific to N. meningitidis
      and absent from N. gonorrhoeae. In this report we show that these
      sequences mark eight genetic islands that range in size from 1.8 to 40 kb
      and whose chromosomal location is constant. Five of these genetic islands
      were conserved within a representative set of strains and/or carried genes
      with homologies to known virulence factors in other species. These were
      deleted, and the mutants were tested for correlates of virulence in vitro
      and in vivo. This strategy identified one island, region 8, which is
      needed to induce bacteremia in an infant rat model of meningococcal
      infection. Region 8 encodes a putative siderophore receptor and a
      disulfide oxidoreductase. None of the deleted mutants was modified in its
      resistance to the bactericidal effect of serum. Neither were the mutant
      strains altered in their ability to interact with endothelial cells,
      suggesting that such interactions are not encoded by large genetic islands
      in N. meningitidis.
AU  - Klee SR
AU  - Nassif X
AU  - Kusecek B
AU  - Merker P
AU  - Beretti JL
AU  - Achtman M
AU  - Tinsley CR
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2000 68: 2082-2095.

PMID- 12566566
VI  - 100
DP  - 2003
TI  - Complete genome sequence of Lactobacillus plantarum WCFS1.
PG  - 1990-1995
AB  - The 3,308,274-bp sequence of the chromosome of Lactobacillus plantarum strain WCFS1, a single
      colony isolate of strain NCIMB8826 that was
      originally isolated from human saliva, has been determined, and contains
      3,052 predicted protein-encoding genes. Putative biological functions
      could be assigned to 2,120 (70%) of the predicted proteins. Consistent
      with the classification of L. plantarum as a facultative
      heterofermentative lactic acid bacterium, the genome encodes all enzymes
      required for the glycolysis and phosphoketolase pathways, all of which
      appear to belong to the class of potentially highly expressed genes in
      this organism, as was evident from the codon-adaptation index of
      individual genes. Moreover, L. plantarum encodes a large
      pyruvate-dissipating potential, leading to various end-products of
      fermentation. L. plantarum is a species that is encountered in many
      different environmental niches, and this flexible and adaptive behavior is
      reflected by the relatively large number of regulatory and transport
      functions, including 25 complete PTS sugar transport systems. Moreover,
      the chromosome encodes >200 extracellular proteins, many of which are
      predicted to be bound to the cell envelope. A large proportion of the
      genes encoding sugar transport and utilization, as well as genes encoding
      extracellular functions, appear to be clustered in a 600-kb region near
      the origin of replication. Many of these genes display deviation of
      nucleotide composition, consistent with a foreign origin. These findings
      suggest that these genes, which provide an important part of the
      interaction of L. plantarum with its environment, form a lifestyle
      adaptation region in the chromosome.
AU  - Kleerebezem M et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2003 100: 1990-1995.

PMID- 1061131
VI  - 73
DP  - 1976
TI  - Novel properties of a restriction endonuclease isolated from Haemophilus parahaemolyticus.
PG  - 293-297
AB  - The sequences in lambda DNA in and around six sites cut by HphI, a restriction
      enzyme isolated from Haemophilus parahaemolyticus, are compared.  The enzyme
      produces a staggered cut around an AT or TA base pair, but the sequences
      immediately surrounding the cleavage sites bear no obvious relation to one
      another.  Eight (in some cases nine) base pairs to one side of each cleavage
      site is the common sequence TCACCAGTGC.  Two lines of evidence indicate that
      these bases constitute part or all of the Hph recognition site.  First,
      mutations in this sequence prevent HphI cutting.  Second,
      dimethylsulfate-mediated methylation of Gs and As in this site prevent cutting,
      whereas methylation of purines in the region between this sequence and the
      cleavage sites has no such effect.  There is discernible 2-fold rotational
      symmetry neither in the common sequence nor around the cleavage sites.
AU  - Kleid D
AU  - Humayun Z
AU  - Jeffrey A
AU  - Ptashne M
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1976 73: 293-297.

PMID- 6246336
VI  - 65
DP  - 1980
TI  - Purification and properties of the HphI endonuclease.
PG  - 163-166
AB  - 5' CGGTGATACTGAGCA^CATCAG   3' GCCACTATGACTCG^TGTAGTC The nucleotide
      sequence-specific endonuclease from Haemophilus parahaemolyticus has properties
      that differ from the majority of type II restriction endonuclease.  This enzyme
      recognizes an unsymmetric nucleotide sequence and cleaves the DNA at a site
      approximately one turn of the helix from the center of the recognition
      sequence.  The recognition sequence has been demonstrated to be a five base
      pair sequence 5' GGTGA   3' CCACT.
AU  - Kleid DG
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1980 65: 163-166.

PMID- 5327303
VI  - 96
DP  - 1965
TI  - Mechanisms of host-controlled modification of phage T1.
PG  - 346-363
AB  - Complementation tests using T1 amber-mutants show that all genes of restricted
      phage so far investigated are able to function in the restricting host.  This
      ability is quickly lost when m-RNA synthesis is blocked.  The ability of
      functioning of restricted phage genes depends on their location on the phage
      genome.  A model is discussed explaining this polarization in terms of directed
      transcription of T1 DNA.  As in host cells lysogenic for P1 restricted T1 DNA
      is destroyed after infection of strains THU or BG43, which also act on T1 by
      HCM.  T1 phages which do not bear P1 specific modification may in rare cases
      escape from restriction in host cells lysogenic for P1 - either by infecting a
      nonrestricting exceptional cell or when they are very quickly protected against
      destruction, probably by rapid modification.  Multiple infection does not
      increase this low probability of survival of the single phage.  T1 DNA contains
      5-methylcytosine and 6-methylaminopurine.  The amount of these bases in the DNA
      is independent of the host specificity controlled by P1.  However, coinfection
      of P1 lysogenic cells with T1 and T3 simultaneously prevents T1 DNA from being
      methylated and modified.  It may therefore be concluded that the mechanisms of
      modifying T1 in this host strain consists in methylating T1 DNA in a specific
      pattern.  T2gt, a mutant of T2 containing nonglucosylated DNA, is restricted by
      cells lysogenic for P1 while it cannot be modified by the same host.  The
      question is discussed, whether this result has some implication concerning the
      role of 5 MC in the postulated HCM pattern since 5 MC cannot be formed in T2gt
      DNA.
AU  - Klein A
PT  - Journal Article
TA  - Z. Vererbungsl.
JT  - Z. Vererbungsl.
SO  - Z. Vererbungsl. 1965 96: 346-363.

PMID- 5327302
VI  - 96
DP  - 1965
TI  - Host-controlled modification.
PG  - 324-345
AB  - The phenomena and effects of host-controlled modification (HCM) as described in
      the literature are comprehensively discussed.  The review includes the
      occurrence of HCM, the restriction and modification caused by CM, its influence
      on bacterial and phage crosses, and the function of restricted genes.  Besides,
      genetic control of HCM and mutation effects of HCM and UV-irradiation are
      reviewed.
AU  - Klein A
PT  - Journal Article
TA  - Z. Vererbungsl.
JT  - Z. Vererbungsl.
SO  - Z. Vererbungsl. 1965 96: 324-345.

PMID- 14300763
VI  - 18
DP  - 1965
TI  - Role of methylation in host controlled modification of phage T1.
PG  - 440-445
AB  - Non-mutational changes upon growth on certain bacterial host strains concerning
      host range properties have been found in many bacteriophages.  This phenomenon
      is known as host controlled modification (HCM).  Phage particles thus carry a
      host specificity determined by the bacterial strain on which they were
      produced.  Upon infection of a different bacterial strain the phage may be
      either accepted or rejected on the basis of its specificity.  If accepted, it
      multiplies in the new host cell and acquires a new specificity.  Arber and
      Dussoix (1962) and Dussoix and Arber (1962) showed that host specificity of
      phage lambda is carried by the phage DNA.  The chemical basis of HCM in lambda
      is unknown.  It was suggested by in vitro experiments of Gold and Hurwitz
      (1963) that different methylation of lambda DNA by different host cells might
      confer different host specificity to the phage.  Ledinko (1964), however, found
      equal amounts of 5-methylcytosine (5-MC) in DNA extracted from phage lambda
      carrying the host specificities derived from the strains Escherichia coli
      C,B,K, or K(P1).  Evidence will be presented here that (1) T1-DNA may in some
      cases be methylated to different extents depending on its host specificity and
      (2) that methylation is the chemical basis or at least an absolute requirement
      for HCM of phage T1 by bacterial host cells lysogenic for P1.  In addition a
      new system of HCM acting on T1 will be described which does not overlap with
      the P1 system.
AU  - Klein A
AU  - Sauerbier W
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1965 18: 440-445.

PMID- 27795241
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Curtobacterium sp. Strain UCD-KPL2560 (Phylum Actinobacteria).
PG  - e01040-16
AB  - Here, we present the draft genome sequence of the actinobacterium Curtobacterium  sp. strain
      UCD-KPL2560, which was isolated from the running surface of an indoor
      track field house in Medford, MA, USA (42.409716 degrees N, -71.115169 degrees
      W). The genome assembly contains 3,480,487 bp in 156 contigs.
AU  - Klein BA
AU  - Lemon KP
AU  - Faller LL
AU  - Jospin G
AU  - Eisen JA
AU  - Coil DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01040-16.

PMID- 28232444
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Dermacoccus nishinomiyaensis Strains UCD-KPL2534 and UCD-KPL2528 Isolated from an Indoor Track Facility.
PG  - e01652-16
AB  - We present here the draft genome sequences of Dermacoccus nishinomiyaensis strains UCD-KPL2534
      and UCD-KPL2528, which were isolated at an indoor track
      facility in Medford, MA, USA (42.409716, -71.115169) from an exit door handle and
      settle dust, respectively. The genome assemblies contain 3,088,111 bp in 58
      contigs and 3,162,381 bp in 100 contigs, respectively.
AU  - Klein BA
AU  - Lemon KP
AU  - Gajare P
AU  - Jospin G
AU  - Eisen JA
AU  - Coil DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01652-16.

PMID- 23469357
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Uropathogenic Escherichia coli Strain J96.
PG  - e00245-12
AB  - J96 (O4:K6) was isolated from a human pyelonephritis patient. Here, we report the draft genome
      sequence of J96, which contains virulence genes, including adhesion
      factors, alpha-hemolysins, and cytotoxic necrotizing factor. J96 infects the
      kidney and bladder, making it an important tool for studying pathogenesis.
AU  - Klein EA
AU  - Gitai Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00245-12.

PMID- 26430039
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Erwinia billingiae OSU19-1, Isolated from a Pear Tree Canker.
PG  - e01119-15
AB  - Plant-associated Erwinia include pathogenic and nonpathogenic species. We report  the 5.6-Mb
      genome sequence of Erwinia billingiae OSU19-1, isolated from a canker  on a pear tree
      inoculated with Erwinia amylovora. OSU19-1 and a closely related European isolate, E.
      billingiae Eb661(T), share many similarities including 40 kb of plasmid sequence.
AU  - Klein JM
AU  - Bennett RW
AU  - MacFarland L
AU  - Abranches DaSME
AU  - Meza-Turner BM
AU  - Dark PM
AU  - Frey ME
AU  - Wellappili DP
AU  - Beugli AD
AU  - Jue HJ
AU  - Mellander JM
AU  - Wei W
AU  - Ream W
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01119-15.

PMID- 12139629
VI  - 45
DP  - 2002
TI  - Natrialba magadii virus phiCh1: first complete nucleotide sequence and functional organization of a virus infecting a haloalkaliphilic archaeon.
PG  - 851-863
AB  - The double-stranded (ds)DNA virus phiCh1 infects the haloalkaliphilic
      archaeon Natrialba magadii. The complete DNA sequence of 58 498 bp of the
      temperate virus was established, and the probable functions of 21 of 98
      phiCh1-encoded open reading frames (ORFs) have been assigned. This
      knowledge has been used to propose functional modules each required for
      specific functions during virus development. The phiCh1 DNA is terminally
      redundant and circularly permuted and therefore appears to be packaged by
      the so-called headful mechanism. The presence of ORFs encoding homologues
      of proteins involved in plasmid replication as well as experimental
      evidence indicate a plasmid-mediated replication strategy of the virus.
      Results from nanosequencing of virion components suggest covalent
      cross-linking of monomers of at least one of the structural proteins
      during virus maturation. A comparison of the phiCh1 genome with the partly
      sequenced genome of Halobacterium salinarum virus phiH revealed a close
      relationship between the two viruses, although their host organisms live
      in distinct environments with respect to the different pH values required
      for growth.
AU  - Klein R
AU  - Baranyi U
AU  - Rossler N
AU  - Greineder B
AU  - Scholz H
AU  - Witte A
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2002 45: 851-863.

PMID- 26941136
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a Strictly Anaerobic Dichloromethane-Degrading Bacterium.
PG  - e00037-16
AB  - An anaerobic, dichloromethane-degrading bacterium affiliated with novel Peptococcaceae was
      maintained in a microbial consortium. The organism originated
      from pristine freshwater sediment collected from Rio Mameyes in Luquillo, Puerto
      Rico, in October 2009 (latitude 18 degrees 21'43.9', longitude -65 degrees
      46'8.4'). The draft genome sequence is 2.1 Mb and has a G+C content of 43.5%.
AU  - Kleindienst S
AU  - Higgins SA
AU  - Tsementzi D
AU  - Konstantinidis KT
AU  - Mack EE
AU  - Loffler FE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00037-16.

PMID- 27103723
VI  - 4
DP  - 2016
TI  - Complete Draft Genome Sequence of Escherichia coli JF733.
PG  - e00298-16
AB  - ITALIC! Escherichia coliJF733 is a strain with a long history in research on membrane proteins
      and processes. However, tracing back the strain development
      raises some questions concerning the correct genotype of JF733. Here, we present
      the complete draft genome of ITALIC! E. coliJF733 in order to resolve any
      remaining uncertainties.
AU  - Kleiner GR
AU  - Wibberg D
AU  - Winkler A
AU  - Kalinowski J
AU  - Wertz JE
AU  - Friehs K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00298-16.

PMID- 28963204
VI  - 5
DP  - 2017
TI  - Complete Draft Genome Sequence of Escherichia coli K802.
PG  - e00934-17
AB  - Escherichia coli K802 is an old strain used for cloning experiments, as well as for the
      production of recombinant proteins. To understand the genomic background
      of E. coli K802 better, we present here its complete draft genome sequence.
AU  - Kleiner-Grote GRM
AU  - Wibberg D
AU  - Winkler A
AU  - Kalinowski J
AU  - Friehs K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00934-17.

PMID- 27609917
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Three Northern German Epidemic Staphylococcus aureus (ST247) Strains Containing Multiple Copies of IS256.
PG  - e00936-16
AB  - We report the draft genome sequences of three multiresistant Staphylococcus aureus strains of
      sequence type 247 (ST247). The methicillin-resistant S. aureus
      (MRSA) SA1450/94 is vancomycin susceptible, while the clinical MRSA isolate S.
      aureus SA137/93A and its spontaneous laboratory mutant SA137/93G are
      characterized by intermediate vancomycin susceptibility.
AU  - Kleinert F
AU  - Kallies R
AU  - Zweynert A
AU  - Bierbaum G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00936-16.

PMID- 21887323
VI  - 6
DP  - 2011
TI  - Divalent Metal Ion Differentially Regulates the Sequential Nicking Reactions of the GIY-YIG Homing Endonuclease I-BmoI.
PG  - e23804
AB  - Homing endonucleases are site-specific DNA endonucleases that function as mobile genetic
      elements by introducing double-strand breaks or nicks
      at defined locations. Of the major families of homing endonucleases,
      the modular GIY-YIG endonucleases are least understood in terms of
      mechanism. The GIY-YIG homing endonuclease I-BmoI generates a
      double-strand break by sequential nicking reactions during which the
      single active site of the GIY-YIG nuclease domain must undergo a
      substantial reorganization. Here, we show that divalent metal ion plays
      a significant role in regulating the two independent nicking reactions
      by I-BmoI. Rate constant determination for each nicking reaction
      revealed that limiting divalent metal ion has a greater impact on the
      second strand than the first strand nicking reaction. We also show that
      substrate mutations within the I-BmoI cleavage site can modulate the
      first strand nicking reaction over a 314-fold range. Additionally,
      in-gel DNA footprinting with mutant substrates and modeling of an
      I-BmoI-substrate complex suggest that amino acid contacts to a critical
      GC-2 base pair are required to induce a bottom-strand distortion that
      likely directs conformational changes for reaction progress.
      Collectively, our data implies mechanistic roles for divalent metal ion
      and substrate bases, suggesting that divalent metal ion facilitates the
      re-positioning of the GIY-YIG nuclease domain between sequential
      nicking reactions.
AU  - Kleinstiver BP
AU  - Berube-Janzen W
AU  - Fernandes AD
AU  - Edgell DR
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2011 6: e23804.

PMID- 20061372
VI  - 38
DP  - 2010
TI  - A unified genetic, computational and experimental framework identifies functionally relevant residues of the homing endonuclease I-BmoI.
PG  - 2411-2427
AB  - Insight into protein structure and function is best obtained through a synthesis of
      experimental, structural and bioinformatic data. Here, we
      outline a framework that we call MUSE (mutual information, unigenic
      evolution and structure-guided elucidation), which facilitated the
      identification of previously unknown residues that are relevant for
      function of the GIY-YIG homing endonuclease I-BmoI. Our approach
      synthesizes three types of data: mutual information analyses that identify
      co-evolving residues within the GIY-YIG catalytic domain; a unigenic
      evolution strategy that identifies hyper- and hypo-mutable residues of
      I-BmoI; and interpretation of the unigenic and co-evolution data using a
      homology model. In particular, we identify novel positions within the
      GIY-YIG domain as functionally important. Proof-of-principle experiments
      implicate the non-conserved I71 as functionally relevant, with an I71N
      mutant accumulating a nicked cleavage intermediate. Moreover, many
      additional positions within the catalytic, linker and C-terminal domains
      of I-BmoI were implicated as important for function. Our results represent
      a platform on which to pursue future studies of I-BmoI and other
      GIY-YIG-containing proteins, and demonstrate that MUSE can successfully
      identify novel functionally critical residues that would be ignored in a
      traditional structure-function analysis within an extensively studied
      small domain of approximately 90 amino acids.
AU  - Kleinstiver BP
AU  - Fernandes AD
AU  - Gloor GB
AU  - Edgell DR
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2010 38: 2411-2427.

PMID- 23558745
VI  - 41
DP  - 2013
TI  - The monomeric GIY-YIG homing endonuclease I-BmoI uses a molecular anchor and a flexible tether to sequentially nick DNA.
PG  - 5413-5427
AB  - The GIY-YIG nuclease domain is found within protein scaffolds that participate in diverse
      cellular pathways and contains a single active site that hydrolyzes DNA
      by a one-metal ion mechanism. GIY-YIG homing endonucleases (GIY-HEs) are
      two-domain proteins with N-terminal GIY-YIG nuclease domains connected to
      C-terminal DNA-binding and they are thought to function as monomers. Using I-BmoI
      as a model GIY-HE, we test mechanisms by which the single active site is used to
      generate a double-strand break. We show that I-BmoI is partially disordered in
      the absence of substrate, and that the GIY-YIG domain alone has weak affinity for
      DNA. Significantly, we show that I-BmoI functions as a monomer at all steps of
      the reaction pathway and does not transiently dimerize or use sequential
      transesterification reactions to cleave substrate. Our results are consistent
      with the I-BmoI DNA-binding domain acting as a molecular anchor to tether the
      GIY-YIG domain to substrate, permitting rotation of the GIY-YIG domain to
      sequentially nick each DNA strand. These data highlight the mechanistic
      differences between monomeric GIY-HEs and dimeric or tetrameric GIY-YIG
      restriction enzymes, and they have implications for the use of the GIY-YIG domain
      in genome-editing applications.
AU  - Kleinstiver BP
AU  - Wolfs JM
AU  - Edgell DR
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2013 41: 5413-5427.

PMID- 22566637
VI  - 109
DP  - 2012
TI  - Monomeric site-specific nucleases for genome editing.
PG  - 8061-8066
AB  - Targeted manipulation of complex genomes often requires the introduction of a double-strand
      break at defined locations by
      site-specific DNA endonucleases. Here, we describe a monomeric nuclease
      domain derived from GIY-YIG homing endonucleases for genome-editing
      applications. Fusion of the GIY-YIG nuclease domain to three-member
      zinc-finger DNA binding domains generated chimeric GIY-zinc finger
      endonucleases (GIY-ZFEs). Significantly, the I-TevI-derived fusions
      (Tev-ZFEs) function in vitro as monomers to introduce a double-strand
      break, and discriminate in vitro and in bacterial and yeast assays
      against substrates lacking a preferred 5'-CNNNG-3' cleavage motif. The
      Tev-ZFEs function to induce recombination in a yeast-based assay with
      activity on par with a homodimeric Zif268 zinc-finger nuclease. We also
      fused the I-TevI nuclease domain to a catalytically inactive LADGLIDADG
      homing endonuclease (LHE) scaffold. The monomeric Tev-LHEs are active
      in vivo and similarly discriminate against substrates lacking the
      5'-CNNNG-3' motif. The monomeric Tev-ZFEs and Tev-LHEs are distinct
      from the FokI-derived zinc-finger nuclease and TAL effector nuclease
      platforms as the GIY-YIG domain alleviates the requirement to design
      two nuclease fusions to target a given sequence, highlighting the
      diversity of nuclease domains with distinctive biochemical properties
      suitable for genome-editing applications.
AU  - Kleinstiver BP
AU  - Wolfs JM
AU  - Kolaczyk T
AU  - Roberts AK
AU  - Hu SX
AU  - Edgell DR
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2012 109: 8061-8066.

PMID- 23144383
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of the Methane-Oxidizing Bacterium Methylococcus capsulatus (Texas).
PG  - 6626
AB  - Methanotrophic bacteria perform major roles in global carbon cycles via their unique enzymatic
      activities that enable the oxidation of one-carbon compounds,
      most notably methane. Here we describe the annotated draft genome sequence of the
      aerobic methanotroph Methylococcus capsulatus (Texas), a type strain originally
      isolated from sewer sludge.
AU  - Kleiveland CR
AU  - Hult LT
AU  - Kuczkowska K
AU  - Jacobsen M
AU  - Lea T
AU  - Pope PB
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6626.

PMID- 9389475
VI  - 390
DP  - 1997
TI  - The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus.
PG  - 364-370
AB  - Archaeoglobus fulgidus is the first sulphur-metabolizing organism to have its genome sequence
      determined.  Its genome of 2,178,400 base pairs contains 2,436 open reading frames.  The
      information processing systems and the biosynthetic pathways for essential components
      (nucleotides, amino acids and cofactors) have extensive correlation with their counterparts in
      the archaeon Methanococcus jannaschii.  The genomes of these two Archaea indicate dramatic
      differences in the way these organisms sense their environment, perform regulatory and
      transport functions, and gain energy.  In contrast to M. jannaschii, A. fulgidus has fewer
      restriction-modification systems, and none of its genes appears to contain inteins.  A quarter
      (651 ORFs) of the A. fulgidus genome encodes functionally uncharacterized yet conserved
      proteins, two-thirds of which are shared with M. jannaschii (428 ORFs).  Another quarter of
      the genome encodes new proteins indicating substantial archaeal gene diversity.
AU  - Klenk H-P et al
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1997 390: 364-370.

PMID- 22180816
VI  - 5
DP  - 2011
TI  - Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2) and reclassification in the new genus, Kyrpidia gen. nov. as  Kyrpidia tusciae comb. nov. and emendation of the family Alicyclobacillaceae da  Costa and Ra.
PG  - 121-134
AB  - Bacillus tusciae Bonjour and Aragno 1994 is a hydrogen-oxidizing, thermoacidophilic spore
      former that lives as a facultative chemolithoautotroph in solfataras. Although 16S rRNA gene
      sequencing was well established at the time of the initial description of the organism, 16S
      sequence data were not available and the strain was placed into the genus Bacillus based on
      limited chemotaxonomic information. Despite the now obvious misplacement of strain T2 as a
      member of the genus Bacillus in 16S rRNA-based phylogenetic trees, the misclassification
      remained uncorrected for many years, which was likely due to the extremely difficult,
      analysis-hampering cultivation conditions and poor growth rate of the strain. Here we provide
      a taxonomic re-evaluation of strain T2T (= DSM 2912 = NBRC 15312) and propose its
      reclassification as the type strain of a new species, Kyrpidia tusciae, and the type species
      of the new genus Kyrpidia, which is a sister-group of Alicyclobacillus. The family
      Alicyclobacillaceae da Costa and Rainey, 2010 is emended. The 3,384,766 bp genome with its
      3,323 protein-coding and 78 RNA genes is part of the Genomic Encyclopedia of Bacteria and
      Archaea project.
AU  - Klenk HP et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 5: 121-134.

PMID- 22768365
VI  - 6
DP  - 2012
TI  - Genome sequence of the soil bacterium Saccharomonospora azurea type strain (NA-128(T)).
PG  - 220-229
AB  - Saccharomonospora azurea Runmao et al. 1987 is a member of the genus Saccharomonospora, which
      is in the family Pseudonocardiaceae and thus far poorly
      characterized genomically. Members of the genus Saccharomonospora are of interest
      because they originate from diverse habitats, such as leaf litter, manure,
      compost, the surface of peat, and moist and over-heated grain, and may play a
      role in the primary degradation of plant material by attacking hemicellulose.
      Next to S. viridis, S. azurea is only the second member in the genus
      Saccharomonospora for which a completely sequenced type strain genome will be
      published. Here we describe the features of this organism, together with the
      complete genome sequence with project status 'Improved high quality draft', and
      the annotation. The 4,763,832 bp long chromosome with its 4,472 protein-coding
      and 58 RNA genes was sequenced as part of the DOE funded Community Sequencing
      Program (CSP) 2010 at the Joint Genome Institute (JGI).
AU  - Klenk HP
AU  - Held B
AU  - Lucas S
AU  - Lapidus A
AU  - Copeland A
AU  - Hammon N
AU  - Pitluck S
AU  - Goodwin LA
AU  - Han C
AU  - Tapia R
AU  - Brambilla EM
AU  - Potter G
AU  - Land M
AU  - Ivanova N
AU  - Rohde M
AU  - Goker M
AU  - Detter JC
AU  - Kyrpides NC
AU  - Woyke T
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 6: 220-229.

PMID- 22768369
VI  - 6
DP  - 2012
TI  - Genome sequence of the ocean sediment bacterium Saccharomonospora marina type strain (XMU15(T)).
PG  - 265-275
AB  - Saccharomonospora marina Liu et al. 2010 is a member of the genus Saccharomonospora, in the
      family Pseudonocardiaceae that is poorly characterized
      at the genome level thus far. Members of the genus Saccharomonospora are of
      interest because they originate from diverse habitats, such as leaf litter,
      manure, compost, surface of peat, moist, over-heated grain, and ocean sediment,
      where they might play a role in the primary degradation of plant material by
      attacking hemicellulose. Organisms belonging to the genus are usually
      Gram-positive staining, non-acid fast, and classify among the actinomycetes. Here
      we describe the features of this organism, together with the complete genome
      sequence (permanent draft status), and annotation. The 5,965,593 bp long
      chromosome with its 5,727 protein-coding and 57 RNA genes was sequenced as part
      of the DOE funded Community Sequencing Program (CSP) 2010 at the Joint Genome
      Institute (JGI).
AU  - Klenk HP
AU  - Lu M
AU  - Lucas S
AU  - Lapidus A
AU  - Copeland A
AU  - Pitluck S
AU  - Goodwin LA
AU  - Han C
AU  - Tapia R
AU  - Brambilla EM
AU  - Potter G
AU  - Land M
AU  - Ivanova N
AU  - Rohde M
AU  - Goker M
AU  - Detter JC
AU  - Li WJ
AU  - Kyrpides NC
AU  - Woyke T
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 6: 265-275.

PMID- 23558528
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of a Mannheimia haemolytica Serotype 6 Isolate Collected from the Nasopharynx of a Beef Calf with Bovine Respiratory Disease.
PG  - e0005113
AB  - The draft genome of a Mannheimia haemolytica serotype 6 isolate obtained from the nasopharynx
      of a feedlot calf with bovine respiratory disease is described.
AU  - Klima CL
AU  - Cook SR
AU  - Hahn KR
AU  - Amoako KK
AU  - Alexander TW
AU  - Hendrick S
AU  - McAllister TA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0005113.

PMID- 3574306
VI  - 21
DP  - 1987
TI  - Investigation of specificity of DNA-methylases BcnI, CfrI and Cfr10I.
PG  - 87-92
AB  - The site specificity of three DNA methylases BcnI, CfrI and Cfr10I was
      determined to be 5'Cm4C(C/G)GG, 5'PyGGm5CCPu and 5'Pum5CCGGPy, respectively.
      Using the modification methylases under investigation with known restriction
      endonucleases, fourteen new DNA cleavage specificities can be created.  Some
      aspects of the use of restriction endonucleases in DNA methylation analysis are
      discussed.
AU  - Klimasauskas S
AU  - Butkus V
AU  - Janulaitis A
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1987 21: 87-92.

PMID- 8293469
VI  - 76
DP  - 1994
TI  - Hhal methyltransferase flips its target base out of the DNA helix.
PG  - 357-369
AB  - The crystal structure has been determined at 2.8 A resolution for a chemically-trapped
      covalent reaction intermediate between the Hhal DNA cytosine-5-methyltransferase,
      S-adenosyl-L-homocysteine, and a duplex 13-mer DNA oligonucleotide containing methylated
      5-fluorocytosine at its target. The DNA is located in a cleft between the two domains of the
      protein and has the characteristic conformation of B-form DNA, except for a disrupted G-C base
      pair that contains the target cytosine. The cytosine residue has swung completely out of the
      DNA helix and is positioned in the active site, which itself has undergone a large
      conformational change. The DNA is contacted from both the major and the minor grooves, but
      almost all base-specific interactions between the enzyme and the recognition bases occur in
      the major groove, through two glycine-rich loops from the small domain. The structure suggests
      how the active nucleophile reaches its target, directly supports the proposed mechanism for
      cytosine-5 DNA methylation, and illustrates a novel mode of sequence-specific DNA regonition.
AU  - Klimasauskas S
AU  - Kumar S
AU  - Roberts RJ
AU  - Cheng X
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1994 76: 357-369.

PMID- 1659688
VI  - 19
DP  - 1991
TI  - The sequence specificity domain of cytosine-C5 methylases.
PG  - 6183-6190
AB  - Prokaryotic DNA[cytosine-C5] methyltransferases (m5C-methylases) share a common
      architectural arrangement of ten conserved sequence motifs.  A series of eleven
      hybrids have been constructed between the HpaII (recognition sequence: Cm5CGG)
      and HhaI (recognition sequence: Gm5CGC) DNA-methylases.  The hybrids were
      over-expressed in E. coli and their in vivo methylation phenotypes
      investigated.  Six were inactive by our assay while five of them retained
      partial methylation activity and full specificity.  In all five cases the
      specificity matched that of the parent methylase which contributed the
      so-called variable region, located between conserved motifs VIII and IX.  This
      was the only sequence held in common between the active hybrids and for the
      first time provides unequivocal evidence that the specificity determinants of
      the mono-specific m5C-methylases are located within the variable region.
      Correlation of the hybrid methylase structure with the efficiency of
      methylation suggests that conserved motif IX may interact with the variable
      region whereas motif X most probably interacts with the N-terminal half of the
      molecule.
AU  - Klimasauskas S
AU  - Nelson JL
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 6183-6190.

PMID- 7753630
VI  - 23
DP  - 1995
TI  - M.HhaI binds tightly to substrates containing mismatches at the target base.
PG  - 1388-1395
AB  - The (cytosine-5) DNA methyltransferase M.HhaI causes its target cytosine base to be flipped
      completely out of the DAN helix upon binding. We have investigated the effects of replacing
      the target cytosine by other, mismatched bases, including adenine, guanine, thymine and
      uracil. We find that M.HhaI binds more tightly to such mismatched substrates and can even
      transfer a methyl group to uracil if a G:U mismatch is present. Other mismatched substrates in
      which the orphan guanine is changed exhibit similar behavior. Overall, the affinity of DNA
      binding correlates inversely with the stability of the target base pair, while the nature of
      the target base appears irrelevant for complex formation. The presence of a cofactor analog,
      S-adenosyl-L-homocysteine, greatly enhances the selectivity of the methyltransferase for
      cytosine at the target site. We propose that the DNA methyltransferases have evolved from
      mismatch binding proteins and that base flipping was, and still is, a key element in many
      DNA-enzyme interactions.
AU  - Klimasauskas S
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1995 23: 1388-1395.

PMID- 7607483
VI  - 157
DP  - 1995
TI  - Disruption of the target G-C base-pair by the HhaI methyltransferase.
PG  - 163-164
AB  - HhaI MTase binds DNA duplexes containing mismatches at the target base position with higher
      affinity than that observed for the canonical substrate.  The stability of these MTase-DNA
      complexes inversely correlates with the strength of the base pair that is disrupted upon
      interaction.  This finding may offer a general tool to detect other enzymes that flip bases
      out of the DNA helix.
AU  - Klimasauskas S
AU  - Roberts RJ
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 163-164.

PMID- 2251121
VI  - 18
DP  - 1990
TI  - M.SmaI is an N4-methylcytosine specific DNA-methylase.
PG  - 6607-6609
AB  - An enzymatic activity rendering DNA immune to the action of the SmaI restriction endonuclease
      in the presence of S-adenosyl-L-methionine has been detected in Serratia marcescens Sb. This
      methylase, M.SmaI, modifies the second cytosine residue of the substrate sequence CCCGGG
      yielding N4-methylcytosine.
AU  - Klimasauskas S
AU  - Steponaviciene D
AU  - Maneliene Z
AU  - Petrusyte M
AU  - Butkus V
AU  - Janulaitis A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 6607-6609.

PMID- 9427765
VI  - 17
DP  - 1998
TI  - Dynamic modes of the flipped-out cytosine during HhaI methyltransferase-DNA interactions in solution.
PG  - 317-324
AB  - Flipping of a nucleotide out of a B-DNA helix into the active site of an enzyme has been
      observed for the HhaI and HaeIII cytosine-5 methyltransferases (M.HhaI and M.HaeIII) and for
      numerous DNA repair enzymes.  Here we studied the base flipping motions in the binary
      M.HhaI-DNA and the ternary M.HhaI-DNA-cofactor systems in solution.  Two 5-fluorocytosines
      were introduced into the DNA in the places of the target cytosine and, as an internal control,
      a cytosine positioned two nucleotides upstream of the recognition sequence 5'-GCGC-3'.  The
      19F NMR spectra combined with gel mobility data show that interaction with the enzyme induces
      partition of the target base among three states, i.e. stacked in the B-DNA, an ensemble of
      flipped-out forms and the flipped-out form locked in the enzyme active site.  Addition of the
      cofactor analogue S-adenosyl-L-homocysteine greatly enhances the trapping of the target
      cytosine in the catalytic site.  Distinct dynamic modes of the target cytosine have thus been
      identified along the reaction pathway, which includes novel base-flipping intermediates that
      were not observed in previous X-ray structures.  The new data indicate that flipping of the
      target base out of the DNA helix is not dependent on binding of the cytosine in the catalytic
      pocket of M.HhaI, and suggest an active role in the enzyme in the opening of the DNA duplex.
AU  - Klimasauskas S
AU  - Szyperski T
AU  - Serva S
AU  - Wuthrich K
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1998 17: 317-324.

PMID- 2690010
VI  - 17
DP  - 1989
TI  - Sequence motifs characteristic of DNA[cytosine-N4]methylases:  similarity to adenine and cytosine-C5 DNA-methylases.
PG  - 9823-9832
AB  - The sequences coding for DNA[cytosine-N4]methyltransferases MvaI (from
      Micrococcus varians RFL19) and Cfr9I (from Citrobacter freundii RFL9) have been
      determined.  The predicted methylases are proteins of 454 and 300 amino acids,
      respectively.  Primary structure comparison of M.Cfr9I and another m4C-forming
      methylase, M.PvuII, revealed extended regions of homology.  The sequence
      comparison of the three DNA[cytosine-N4]-methylases using originally developed
      software revealed two conserved patterns, DPF-GSGT and TSPPY, which were found
      similar also to those of adenine and DNA[cytosine-C5]-methylases.  These data
      provided a basis for global alignment and classification of DNA-methylase
      sequences.  Structural considerations led us to suggest that the first region
      could be the binding site of AdoMet, while the second is thought to be directly
      involved in the modification of the exocyclic amino group.
AU  - Klimasauskas S
AU  - Timinskas A
AU  - Menkevicius S
AU  - Butkiene D
AU  - Butkus V
AU  - Janulaitis A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 9823-9832.

PMID- Not carried by PubMed...
VI  - 0
DP  - 1990
TI  - Sequence motifs characteristic of DNA-cytosine-N4-methyltransferases:  The two domains of global similarity within DNA-methylases.
PG  - 4-12
AB  - Sequences coding for DNA [cytosine-N4] methyltransferases MvaI (from Micrococcus varians
      RFL19) and Cfr91 (from Citrobacter freundii RFL9) have been determined.  The methylases
      predicted are proteins of 454 and 300 amino acids, respectively.  Primary structure comparison
      to other m4C-forming methylases, M. PvuII and M. SmaI, revealed two conserved patterns
      DPF-GSGTTGV and TSPPY---R; these patterns were found to have analogues within all adenine and
      DNA[cytosine-C5]-methylase sequences known ever since.  The presence of the two homology
      domains in all known DNA-methylases provided a basis for their global alignment and
      classification.  DNA-methylases can be divided into four groups (S,D,N,G) on the basis of
      substrate-structural peculiarities or into two families (S,D and N,G) based on the relative
      positioning of these domains within sequences.  A subset of SD family sequences differing from
      the others in reversed MTase domain configuration 21 (instead of the usual 12) forms a
      structurally very compact subfamily of proteins.
AU  - Klimasauskas S
AU  - Timinskas A
AU  - Menkevicius S
AU  - Butkiene D
AU  - Butkus V
AU  - Janulaitis A
PT  - Journal Article
TA  - Eksp. Biol.
JT  - Eksp. Biol.
SO  - Eksp. Biol. 1990 0: 4-12.

PMID- 17254657
VI  - 25
DP  - 2007
TI  - A new tool for biotechnology: AdoMet-dependent methyltransferases.
PG  - 99-104
AB  - AdoMet-dependent methyltransferases catalyze highly specific methyl group transfers from the
      ubiquitous cofactor S-adenosyl-L-methionine to a multitude of biological targets in the cell.
      Recently, DNA methyltransferases have been used for the sequence-specific, covalent attachment
      of larger chemical groups to plasmid and bacteriophage DNA using two classes of synthetic
      Ado-Met analogs.  These synthetic cofactors, in combination with the myriad AdoMet-dependent
      methyltransferases available in nature, provide new molecular tools for precise, targeted
      functionalization and labeling of large natural DNAs and, in all likelihood, RNAs and
      proteins.  This paves the way for numerous novel applications in the functional analysis of
      biological methylation, biotechnology and medical diagnostics.
AU  - Klimasauskas S
AU  - Weinhold E
PT  - Journal Article
TA  - Trends Biotechnol.
JT  - Trends Biotechnol.
SO  - Trends Biotechnol. 2007 25: 99-104.

PMID- 
VI  - 33
DP  - 2000
TI  - 'Restriction-PCR' - a superior replacement for restriction endonucleases in DNA cloning applications.
PG  - 162-165
AB  - Polymerase chain reaction (PCR) is well established as an indispensable tool of molecular
      biology; and yet a limitation for cloning
      applications continues to be that products often require subsequent
      restriction digests, blunt-end ligation, or the use of special linear
      vectors, Here a rapid, PCR-based system is described for the simple,
      restriction enzyme-free generation of synthetic, 'restriction-like' DNA
      fragments with staggered ends. Any 3'- or 5'-protruding terminus, but
      also non-palindromic overhangs with an unrestricted single strand
      length are specifically created. With longer overhangs,
      'Restriction-PCR' does not even require a ligation step prior to
      transformation. Thereby the technique presents a powerful tool e.g. for
      a successive, authentic reconstitution of sub-fragments of long genes
      with no need to manipulate the sequence or to introduce restriction
      sites. Since restriction enzyme-free and thereby devoid of the limitations
      of partial DNA digests, 'Restriction-PCR' allows a straight one-step
      generation and cloning of difficult DNA fragments that internally carry
      additional sites for those endonucleases involved in the cloning. Small
      site-specific sequence insertions or deletions can be precisely
      engineered into genes of interest. With these properties
      'Restriction-PCR' has the potential to add significant speed and
      versatility to a wide variety of DNA cloning applications.
AU  - Klimkait T
PT  - Journal Article
TA  - J. Biochem. Mol. Biol.
JT  - J. Biochem. Mol. Biol.
SO  - J. Biochem. Mol. Biol. 2000 33: 162-165.

PMID- 30295835
VI  - 46
DP  - 2018
TI  - Controller protein of restriction-modification system Kpn2I affects transcription of its gene by acting as a transcription elongation roadblock.
PG  - 10810-10826
AB  - C-proteins control restriction-modification (R-M) systems' genes transcription to ensure
      sufficient levels of restriction endonuclease to allow protection from
      foreign DNA while avoiding its modification by excess methyltransferase. Here, we
      characterize transcription regulation in C-protein dependent R-M system Kpn2I.
      The Kpn2I restriction endonuclease gene is transcribed from a constitutive, weak
      promoter, which, atypically, is C-protein independent. Kpn2I C-protein (C.Kpn2I)
      binds upstream of the strong methyltransferase gene promoter and inhibits it,
      likely by preventing the interaction of the RNA polymerase sigma subunit with the
      -35 consensus element. Diminished transcription from the methyltransferase
      promoter increases transcription from overlapping divergent C-protein gene
      promoters. All known C-proteins affect transcription initiation from R-M genes
      promoters. Uniquely, the C.Kpn2I binding site is located within the coding region
      of its gene. C.Kpn2I acts as a roadblock stalling elongating RNA polymerase and
      decreasing production of full-length C.Kpn2I mRNA. Mathematical modeling shows
      that this unusual mode of regulation leads to the same dynamics of accumulation
      of R-M gene transcripts as observed in systems where C-proteins act at
      transcription initiation stage only. Bioinformatics analyses suggest that
      transcription regulation through binding of C.Kpn2I-like proteins within the
      coding regions of their genes may be widespread.
AU  - Klimuk E
AU  - Bogdanova E
AU  - Nagornykh M
AU  - Rodic A
AU  - Djordjevic M
AU  - Medvedeva S
AU  - Pavlova O
AU  - Severinov K
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2018 46: 10810-10826.

PMID- 26564053
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Four Streptomyces Isolates from the Populus trichocarpa Root Endosphere and Rhizosphere.
PG  - e01344-15
AB  - Draft genome sequences for four Actinobacteria from the genus Streptomyces are presented.
      Streptomyces is a metabolically diverse genus that is abundant in
      soils and has been reported in association with plants. The strains described in
      this study were isolated from the Populus trichocarpa endosphere and rhizosphere.
AU  - Klingeman DM
AU  - Utturkar S
AU  - Lu TY
AU  - Schadt CW
AU  - Pelletier DA
AU  - Brown SD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01344-15.

PMID- 22207747
VI  - 194
DP  - 2012
TI  - Shotgun Genome Sequence of a Yersinia enterocolitica Isolate from the Philippines.
PG  - 542-543
AB  - The first shotgun genome sequence of a microbial pathogen from the Philippines is reported.
      Yersinia enterocolitica subsp. palearctica strain
      PhRBD_Ye1 is the first Y. enterocolitica strain sequenced from an animal
      source, swine, which is a natural source of yersiniosis. The closest
      phylogenetic match is a human clinical isolate from Germany.
AU  - Klinzing DC
AU  - Matias RR
AU  - Skowronski E
AU  - Alvarez M
AU  - Liles V
AU  - Dimamay MP
AU  - Natividad FF
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 542-543.

PMID- 21705587
VI  - 193
DP  - 2011
TI  - Complete genome sequence of the marine cellulose- and xylan-degrading bacterium Glaciecola sp. strain 4H-3-7+YE-5.
PG  - 4547-4548
AB  - Glaciecola sp. 4H-3-7+YE-5 was isolated from subseafloor sediments at Suruga Bay in Japan and
      is capable of efficiently hydrolyzing cellulose
      and xylan. The complete genome sequence of Glaciecola sp. 4H-3-7+YE-5
      revealed several genes encoding putatively novel glycoside hydrolases
      offering a high potential for plant biomass degradation.
AU  - Klippel B et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4547-4548.

PMID- 21725025
VI  - 193
DP  - 2011
TI  - Complete Genome Sequences of Krokinobacter sp. strain 4H-3-7-5 and Lacinutrix sp. strain 5H-3-7-4, polysaccharide-degrading members of the family  Flavobacteriaceae.
PG  - 4545-4546
AB  - Two members of the family Flavobacteriaceae were isolated from subseafloor sediments using
      artificial seawater with cellulose, xylan and chitin as
      sole carbon and energy sources. Here, we present the complete genome
      sequences of Krokinobacter sp. 4H-3-7-5 and Lacinutrix sp. 5H-3-7-4 which
      both encode for putatively novel enzymes involved in cellulose,
      hemicellulose and chitin metabolism.
AU  - Klippel B et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4545-4546.

PMID- 14702321
VI  - 186
DP  - 2004
TI  - Sequence Analysis of the Mobile Genome Island pKLC102 of Pseudomonas aeruginosa C.
PG  - 518-534
AB  - The Pseudomonas aeruginosa plasmid pKLC102 coexists as a plasmid and a
      genome island in clone C strains. Whereas the related plasmid pKLK106
      reversibly recombines with P. aeruginosa clone K chromosomes at one of the
      two tRNA(Lys) genes, pKLC102 is incorporated into the tRNA(Lys) gene only
      close to the pilA locus. Targeting of the other tRNA(Lys) copy in the
      chromosome is blocked by a 23,395-bp mosaic of truncated PAO open reading
      frames, transposons, and pKLC102 homologs. Annotation and phylogenetic
      analysis of the large 103,532-bp pKLC102 sequence revealed that pKLC102 is
      a hybrid of plasmid and phage origin. The plasmid lineage conferred oriV
      and genes for replication, partitioning, and conjugation, including a pil
      cluster encoding type IV thin sex pili and an 8,524-bp chvB glucan
      synthetase gene that is known to be a major determinant for host tropism
      and virulence. The phage lineage conferred integrase, att, and a syntenic
      set of conserved hypothetical genes also observed in the
      tRNA(Gly)-associated genome islands of P. aeruginosa clone C chromosomes.
      In subgroup C isolates from patients with cystic fibrosis, pKLC102 was
      irreversibly fixed into the chromosome by the insertion of the large
      23,061-bp class I transposon TNCP23, which is a composite of plasmid,
      integron, and IS6100 elements. Intramolecular transposition of a copy of
      IS6100 led to chromosomal inversions and disruption of plasmid synteny.
      The case of pKLC102 in P. aeruginosa clone C documents the intraclonal
      evolution of a genome island from a mobile ancestor via a reversibly
      integrated state to irreversible incorporation and dissipation in the
      chromosome.
AU  - Klockgether J
AU  - Reva O
AU  - Larbig K
AU  - Tummler B
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2004 186: 518-534.

PMID- 28116041
VI  - 12
DP  - 2017
TI  - High-quality draft genome sequence of Rhizobium mesoamericanum strain STM6155, a  Mimosa pudica microsymbiont from New Caledonia.
PG  - 7
AB  - Rhizobium mesoamericanum STM6155 (INSCD = ATYY01000000) is an aerobic, motile, Gram-negative,
      non-spore-forming rod that can exist as a soil saprophyte or as an
      effective nitrogen fixing microsymbiont of the legume Mimosa pudica L.. STM6155
      was isolated in 2009 from a nodule of the trap host M. pudica grown in
      nickel-rich soil collected near Mont Dore, New Caledonia. R. mesoamericanum
      STM6155 was selected as part of the DOE Joint Genome Institute 2010 Genomic
      Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) genome
      sequencing project. Here we describe the symbiotic properties of R.
      mesoamericanum STM6155, together with its genome sequence information and
      annotation. The 6,927,906 bp high-quality draft genome is arranged into 147
      scaffolds of 152 contigs containing 6855 protein-coding genes and 71 RNA-only
      encoding genes. Strain STM6155 forms an ANI clique (ID 2435) with the sequenced
      R. mesoamericanum strain STM3625, and the nodulation genes are highly conserved
      in these strains and the type strain of Rhizobium grahamii CCGE501T. Within the
      STM6155 genome, we have identified a chr chromate efflux gene cluster of six
      genes arranged into two putative operons and we postulate that this cluster is
      important for the survival of STM6155 in ultramafic soils containing high
      concentrations of chromate.
AU  - Klonowska A
AU  - Lopez-Lopez A
AU  - Moulin L
AU  - Ardley J
AU  - Gollagher M
AU  - Marinova D
AU  - Tian R
AU  - Huntemann M
AU  - Reddy TB
AU  - Varghese N
AU  - Woyke T
AU  - Markowitz V
AU  - Ivanova N
AU  - Seshadri R
AU  - Baeshen MN
AU  - Baeshen NA
AU  - Kyrpides N
AU  - Reeve W
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 7.

PMID- 2825826
VI  - 21
DP  - 1987
TI  - Codification and evolution of experimentally observed specific recognition sites for restriction enzymes on DNA.
PG  - 33-49
AB  - The list of published restriction endonucleases along with their substrates
      provides an excellent data base for the evaluation of the evolution and
      codification of the key elements for specific recognition sites on the DNA.  In
      this paper the considerations will be limited to palindromic tetramer-,
      pentamer-, and hexamer-sequences.  It is basically assumed that each base pair
      within these sequences has to be recognized by directionally unique bidentate
      hydrogen bonds either within the plane of the base pair or by bridging the
      appropriate H-bond donor/acceptor groups of the neighbouring bases of the same
      strand.  Thus sequence specificity is mediated by twelve (eight) H-bonds,
      originating from the protein recognition modules.  Besides a pronounced
      preference for GC base pairs expressed by their high frequency in the most
      abundant sequences, serving the need of maximal thermodynamic stability of the
      double helical substrates, it can also be shown that the stacking of
      consecutive bases within the recognition site sequences plays a major role in
      shaping the particular DNA/protein interface.  Finally it will be demonstrated
      that the full set of sequences discussed in this paper can readily be derived
      by stepwise expanding the vocabulary of three simple tetrameric sequences by
      inserting single base pairs into the centre of a minimal sequence, thus
      creating all the published pentameric restriction sites, or by inserting/adding
      two GC base pairs in a palindromic way, thus creating the known multiplicity of
      hexameric sites.
AU  - Klump H
PT  - Journal Article
TA  - Biosystems
JT  - Biosystems
SO  - Biosystems 1987 21: 33-49.

PMID- 24786957
VI  - 2
DP  - 2014
TI  - Genome Sequences of Three Frequently Used Listeria monocytogenes and Listeria ivanovii Strains.
PG  - e00404-14
AB  - We present the complete de novo assembled genome sequences of Listeria monocytogenes strains
      WSLC 1001 (ATCC 19112) and WSLC 1042 (ATCC 23074) and
      Listeria ivanovii WSLC 3009, three strains frequently used for the propagation
      and study of bacteriophages because they are presumed to be free of inducible
      prophages.
AU  - Klumpp J
AU  - Staubli T
AU  - Schmitter S
AU  - Hupfeld M
AU  - Fouts DE
AU  - Loessner MJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00404-14.

PMID- 6308270
VI  - 168
DP  - 1983
TI  - Effects of 5 cytosine methylation on the B-Z transition in DNA restriction fragments and recombinant plasmids.
PG  - 51-71
AB  - Alternating (dC-dG)n regions in DNA restriction fragments and recombinant
      plasmids were methylated at the 5 position of the cytosine residues by the HhaI
      methylase.  Methylation lowers the concentration of NaCl or MgCl2 necessary to
      cause the B-Z conformational transition in these sequences.  Ionic strengths
      higher than physiological conditions are required to form the Z conformation
      when the methylated (dC-dG)n tract is contiguous with regions that do not form
      Z structures, in contrast to the results with the DNA polymer
      poly(m5dC-dG).poly(m5dC-dG).  In supercoiled plasmids containing (dC-dG)n
      sequences, methylation reduces the number of negative supercoils necessary to
      stabilize the Z conformation.  Calculations of the observed free energy
      contributions of the B-Z junction and cytosine methylation suggest that two
      junctions offset the favorable effect of methylation on the Z conformation in
      (dC-dG)n sequences (about 29 base-pairs in length).  Studies with individual
      methylated topoisomers demonstrate that increasing Na+ concentration up to
      approximately 0.2M inhibits the formation of the Z conformation in the
      (m5dC-dG)n region of supercoiled plasmids.  The results suggest that
      methylation may serve as a triggering mechanism for Z DNA formation in
      supercoiled DNAs.
AU  - Klysik J
AU  - Stirdivant SM
AU  - Singleton CK
AU  - Zacharias W
AU  - Wells RD
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1983 168: 51-71.

PMID- 7932730
VI  - 243
DP  - 1994
TI  - A symmetrical model for the domain structure of Type I DNA methyltransferases.
PG  - 1-5
AB  - Type I DNA methyltransferases are complex multisubunit enzymes that methylate a specific base
      in each half of an asymmetric bipartite DNA recognition sequence. The specificity (S) subunit
      contains two corresponding DNA sequence recognition domains, plus a number of conserved
      regions which interact with two modification (M) subunits to form a trimeric enzyme of the
      form M2S. The way in which the subunits interact with DNA in a pseudo-symmetric fashion has
      long been unclear. Analysis of internal sequence repeats in the S-subunit shows the occurrence
      of significant homologies between the central conserved domain and sequences near the N and C
      termini. On the basis of this "split repeat", a "circular" organization of the domains of this
      subunit is proposed that provides the required symmetry for interacting with the M-subunits
      and with the target DNA sequence. In the proposed model, one M-subunit interacts with the N-
      and C-terminal conserved regions of the S-subunit, which are thereby brought into close
      proximity. The second M-subunit makes equivalent contacts with repeated sequences in the
      central conserved domain. The model suggests a more general scheme for the imposition of
      pseudo-dyad symmetry on protein subunits that have internal repeats by making equivalent
      contacts with additional subunits.
AU  - Kneale GG
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1994 243: 1-5.

PMID- 3198418
VI  - 61
DP  - 1988
TI  - Plasmid mediated restricted and modification in Acinetobacter sp.
PG  - 284-285
AB  - Evidence will be presented for a novel plasmid mediated restriction and
      modification system active on broad host range plasmids in an alkane utilising
      Acinetobacter sp.  Genetic studies using the transmissable R-factor pAV1 have
      demonstrated that this system is distinct from the previously described system
      specified by pAV2 in Acinetobacter sp. EBF65/65.  Evidence will also be
      presented indicating that pAV1 is able to escape plasmid mediated restriction
      by the mobilisation of cryptic plasmids.
AU  - Knight AI
AU  - Lilley RJ
AU  - Buckland RM
AU  - Warner PJ
PT  - Journal Article
TA  - Heredity
JT  - Heredity
SO  - Heredity 1988 61: 284-285.

PMID- 17584917
VI  - 7
DP  - 2007
TI  - Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches.
PG  - 40
AB  - BACKGROUND: PD-(D/E)XK nucleases constitute a large and highly diverse superfamily of enzymes
      that display little sequence similarity despite
      retaining a common core fold and a few critical active site residues. This
      makes identification of new PD-(D/E)XK nuclease families a challenging
      task as they usually escape detection with standard sequence-based
      methods. We developed a modified transitive meta profile search approach
      and to consider the structural diversity of PD-(D/E)XK nuclease fold more
      thoroughly we analyzed also lower than threshold Meta-BASIC hits to select
      potentially correct predictions placed among unreliable or incorrect ones.
      RESULTS: Application of a modified transitive Meta-BASIC searches on
      updated PFAM families and PDB structures resulted in detection of five new
      PD-(D/E)XK nuclease families encompassing hundreds of so far
      uncharacterized and poorly annotated proteins. These include four families
      catalogued in PFAM database as domains of unknown function (DUF506,
      DUF524, DUF1626 and DUF1703) and YhgA-like family of putative
      transposases. Three of these families represent extremely distant homologs
      (DUF506, DUF524, and YhgA-like), while two are newly defined in updated
      database (DUF1626 and DUF1703). In addition, we also confidently
      identified an extended AAA-ATPase domain in the N-terminal region of
      DUF1703 family proteins. CONCLUSION: Obtained results suggest that
      detailed analysis of below threshold Meta-BASIC hits may push limits
      further for distant homology detection in the 'midnight zone' of homology.
      All identified families conserve the core evolutionary fold, secondary
      structure and hydrophobic patterns common to existing PD-(D/E)XK nucleases
      and maintain critical active site motifs that contribute to nucleic acid
      cleavage. Further experimental investigations should address the predicted
      activity and clarify potential substrates providing further insight into
      detailed biological role of these newly detected nucleases.
AU  - Knizewski L
AU  - Kinch LN
AU  - Grishin NV
AU  - Rychlewski L
AU  - Ginalski K
PT  - Journal Article
TA  - BMC Struct. Biol.
JT  - BMC Struct. Biol.
SO  - BMC Struct. Biol. 2007 7: 40.

PMID- 1594458
VI  - 20
DP  - 1992
TI  - Ssp5230I, a novel isoschizomer of AatII from Streptomyces recognizing 5'-GACGT/C-3'.
PG  - 2378
AB  - We have isolated Ssp5230I, a novel class-II restriction endonuclease from Streptomyces species
      recognizing the palindromic sequence 5'-GACGT/C-3' generating 3'-protruding
      ACGT-tetranucleotides. With respect to its isoschizomer AatII it can be isolated in higher
      purity and stability. From the mapping and sequencing data the specificity of Ssp5230I is
      concluded as 5'-GACGT/C-3' 3'-C/TGCAG-5'.
AU  - Knoblich IM
AU  - Sellmann E
AU  - Kaluza K
AU  - Frey B
AU  - Auer J
AU  - Schmitz GG
AU  - Westermann P
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 2378.

PMID- 15629920
VI  - 187
DP  - 2005
TI  - Nature of the Promoter Activated by C.PvuII, an Unusual Regulatory Protein Conserved among Restriction-Modification Systems.
PG  - 488-497
AB  - A widely distributed family of small regulators, called C proteins, controls a subset of
      restriction-modification systems. The C proteins
      studied to date activate transcription of their own genes and that of
      downstream endonuclease genes; this arrangement appears to delay
      endonuclease expression relative to that of the protective
      methyltransferase when the genes enter a new cell. C proteins bind to
      conserved sequences called C boxes. In the PvuII system, the C boxes have
      been reported to extend from -23 to +3 relative to the transcription start
      for the gene for the C protein, an unexpected starting position relative
      to a bound activator. This study suggests that transcript initiation
      within the C boxes represents initial, C-independent transcription of
      pvuIICR. The major C protein-dependent transcript appears to be a
      leaderless mRNA starting farther downstream, at the initiation codon for
      the pvuIIC gene. This conclusion is based on nuclease S1 transcript
      mapping and the effects of a series of nested deletions in the promoter
      region. Furthermore, replacing the region upstream of the pvuIIC
      initiation codon with a library of random oligonucleotides, followed by
      selection for C-dependent transcription, yielded clones having sequences
      that resemble -10 promoter hexamers. The -35 hexamer of this promoter
      would lie within the C boxes. However, the spacing between C boxes/-35 and
      the apparent -10 hexamer can be varied by +/-4 bp with little effect. This
      suggests that, like some other activator-dependent promoters, PpvuIICR may
      not require a -35 hexamer. Features of this transcription activation
      system suggest explanations for its broad host range.
AU  - Knowle D
AU  - Lintner RE
AU  - Touma YM
AU  - Blumenthal RM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2005 187: 488-497.

PMID- 10849434
VI  - 275
DP  - 2000
TI  - Inhibition of DNA methyltransferase inhibits DNA replication.
PG  - 17986-17990
AB  - Ectopic expression of DNA methyltransferase transforms vertebrate cells, and inhibition of DNA
      methyltransferase reverses the transformed phenotype by an unknown mechanism. We tested the
      hypothesis that the presence of an active DNA methyltransferase is required for DNA
      replication in human non-small cell lung carcinoma A549 cells. We show that the inhibition of
      DNA methyltransferase by two novel mechanisms negatively affects DNA synthesis and progression
      through the cell cycle. Competitive polymerase chain reaction of newly synthesized DNA shows
      decreased origin activity at three previously characterized origins of replication following
      DNA methyltransferase inhibition. We suggest that the requirement of an active DNA
      methyltransferase for the functioning of the replication machinery has evolved to coordinate
      DNA replication and inheritance of the DNA methylation pattern.
AU  - Knox JD
AU  - Araujo FD
AU  - Bigey P
AU  - Slack AD
AU  - Price GB
AU  - Zannis-Hadjopoulos M
AU  - Szyf M
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2000 275: 17986-17990.

PMID- 28280014
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of a Novel Coriobacteriaceae sp. Strain, EMTCatB1, Reconstructed from the Metagenome of a Thermophilic Electromethanogenic  Biocathode.
PG  - e00022-17
AB  - A draft genome of Coriobacteriaceae sp. strain EMTCatB1 was determined through taxonomic
      binning of a metagenome of a thermophilic biocathode actively
      catalyzing electromethanogenesis. This genome will provide information about the
      biocathode ecosystem, as well as the natural diversity of the Coriobacteriaceae
      family.
AU  - Kobayashi H
AU  - Fu Q
AU  - Maeda H
AU  - Sato K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00022-17.

PMID- 21470838
VI  - 167
DP  - 2011
TI  - Symbiont of the stink bug Plautia stali synthesizes rough-type lipopolysaccharide.
PG  - 48-54
AB  - The structures and biosynthesis of lipopolysaccharide (LPS), a major component of
      the outer membrane of Gram-negative bacteria, have been studied extensively in
      cultured bacteria such as Escherichia coli. In contrast, little is known about
      the structures and biosynthesis of the LPS of unculturable bacteria, including
      insect symbionts, many of which are Gram-negative bacteria. A brown-winged green
      bug, Plautia stali, is known to harbor a single species of gamma-proteobacterium
      in the posterior mid-gut caeca. To characterize the features of its LPS, we
      analyzed the genome sequence of the symbiont, and identified the putative genes
      involved in LPS synthesis. Genes involved in the synthesis of lipid A and the
      core oligosaccharide were found in the genome, but waaL, which encodes the
      O-antigen ligase, was not. Furthermore, we characterized the LPS of this symbiont
      using SDS-polyacrylamide gel electrophoresis (SDS-PAGE) and Toll-like receptor 4
      (TLR4) stimulation assays. Consistent with the genomic analysis, the SDS-PAGE
      analysis suggested that the symbiont had rough-type LPS, which lacked the
      O-antigen. The TLR4 stimulation assay demonstrated that LPS purified from the
      symbionts activated NF-kappaB-dependent reporter expression, indicating the
      existence of a bioactive lipid A portion in the LPS. These results suggest that
      the P. stali symbiont produces rough-type LPS.
AU  - Kobayashi H
AU  - Kawasaki K
AU  - Takeishi K
AU  - Noda H
PT  - Journal Article
TA  - Microbiol. Res.
JT  - Microbiol. Res.
SO  - Microbiol. Res. 2011 167: 48-54.

PMID- 28860250
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Methanothermobacter sp. Strain EMTCatA1, Reconstructed from the Metagenome of a Thermophilic Electromethanogenesis-Catalyzing  Biocathode.
PG  - e00892-17
AB  - A draft genome of Methanothermobacter sp. strain EMTCatA1 was reconstructed from  a metagenome
      of a thermophilic electromethanogenic biocathode. This genome will
      provide information about methanogens catalyzing methanogenesis at the
      biocathodes.
AU  - Kobayashi H
AU  - Sun X
AU  - Fu Q
AU  - Maeda H
AU  - Sato K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00892-17.

PMID- 
VI  - 0
DP  - 1996
TI  - DNA modification and restriction: Selfish behavior of an epigenetic system.
PG  - 155-172
AB  - Type II restriction endonucleases are known to make double-strand breaks within or near
      specific recognition sequences on duplex DNA.  Cognate modification enzymes can methylate
      these sequences and protect them from cleavage.  The tight association of a cognate
      restriction enzyme gene with a modification gene has been termed the (type II)
      restriction-modification system.  Although the RM systems that have been described are
      individually highly specific for one or a few recognition sequences, collectively the
      sequences recognized are quite diverse.  Type II RM systems are ubiquitous in prokaryotes and
      in archaebacteria but are absent from eukaryotes.  Type II restriction enzymes cleave foreign
      DNA such as viral and plasmid DNA when this DNA has not been modified by the appropriate
      modification enzyme.  In this way, cells are protected from invasion by foreign DNA.  Thus, it
      has been widely believed that the evolution and maintenance of type II restriction
      modification systems have been driven by the cell's need to protect itself from infection by
      foreign DNA (the cellular defense hypothesis).  However, there are several unresolved issues
      that cannot be explained satisfactorily by this cellular defense hypothesis.  Here, I present
      experimental evidence and theoretical arguments for an alternative hypothesis (the selfish
      gene hypothesis) that the evolution of at least some RM gene pairs is driven by their
      "selfishness" in the genetic and evolutionary sense of the term.
AU  - Kobayashi I
PT  - Journal Article
TA  - Epigenetic Mechanisms of Gene Regulation
JT  - Epigenetic Mechanisms of Gene Regulation
SO  - Epigenetic Mechanisms of Gene Regulation 1996 0: 155-172.

PMID- 
VI  - 14
DP  - 2004
TI  - Restriction-modification systems as minimal forms of life.
PG  - 19-62
AB  - A restriction endonuclease recognizes a specific DNA sequence and introduces a double-strand
      break.  A cognate modification enzyme methylates the same sequence and thereby protects it
      from cleavage.  Together, these two enzymes form a restriction-modification system.  The genes
      encoding the restriction endonuclease and the cognate modification enzyme are often tightly
      linked and can be termed a restriction-modification gene complex.  Restriction enzymes will
      cleave incoming DNA if it has not been modified by a cognate or another appropriate
      methyltransferase.  Consequently, it is widely believed that restriction-modification systems
      have been maintained by bacteria because they serve to defend the cells from infection by
      viral, plasmid, and other foreign DNAs (cellular defense hypothesis).
AU  - Kobayashi I
PT  - Journal Article
TA  - Nucleic Acids Mol. Biol.
JT  - Nucleic Acids Mol. Biol.
SO  - Nucleic Acids Mol. Biol. 2004 14: 19-62.

PMID- 
VI  - 
DP  - 2004
TI  - Genetic addiction: A principle of gene symbiosis in a genome.
PG  - 105-144
AB  - One of the surprising aspects of the genome that became clear during its decoding is the
      fluidity of the genes.  Genomes are full of mobile symbiotic or parasitic genetic elements.
      Moreover, evolutionary analyses have suggested that many genes have joined genomes relatively
      recently from distantly related organisms.  This is particularly true for the bacterial and
      archaeal genomes, which contain genes that even come from eukaryotes.  In addition,
      comparisons of closely related genome sequences have revealed that genomes experience frequent
      rearrangements during their evolution.  These observations suggest that, rather than being a
      well-designed blueprint, the genome is a community of genes that essentially act selfishly and
      potentially do not have the overall order of the genome as their primary interest.
AU  - Kobayashi I
PT  - Journal Article
TA  - Plasmid Biology
JT  - Plasmid Biology
SO  - Plasmid Biology 2004 : 105-144.

PMID- 
VI  - 
DP  - 1999
TI  - Homologous recombination and sex as a strategy against selfish genes attacking the genome.
PG  - 354-356
AB  - An important issue in current biology is our failure to adequately explain the forces
      underlying the evolution and maintenance of sex.  Here we refer to sex broadly as the
      interaction that occurs between homologous chromosomes of often different clonal original
      (outcrossing), an event that leads to recombination, frequently between distantly located
      genes (crossing-over).  We propose that sex is maintained to combat the existence of
      ever-changing molecular parasites that attack the organism's genome.
AU  - Kobayashi I
PT  - Journal Article
TA  - Molecular Strategies in Biological Evolution
JT  - Molecular Strategies in Biological Evolution
SO  - Molecular Strategies in Biological Evolution 1999 : 354-356.

PMID- 
VI  - 48
DP  - 2002
TI  - Restriction modification systems as selfish mobile genetic elements maintaining and rearranging the genome.
PG  - 260-261
AB  - A restriction enzyme gene is often linked to a modification methylase gene whose role is to
      protect the recognition site from breakage by the restriction enzyme.  Attempts to eliminate
      some of these restriction-modification gene complexes from bacterial cells lead to cell death
      through restriction breakage in the genome.  Such post-segregational cell killing was observed
      when a restriction -modification gene complex was challenged by a competitor genetic element
      and likely has competitive advantage.  Comparison of closely related bacterial genomes
      revealed linkage of genome polymorphisms, such as insertion and inversion, with
      restriction-modification gene complexes.  Restriction site avoidance in bacterial genomes and
      other observations provide further support for our hypothesis that some
      restriction-modification gene complexes behave as selfish mobile elements that have attacked
      and shaped the genomes.  Indeed our attempts to eliminate a restriction-modification gene
      complex from a cell led to various genome rearrangements in the laboratory - genome-wide
      duplication and inversion events, intra-genomic movement of a restriction-modification gene
      complex, and tandem amplification of a restriction-modification gene complex.  These genome
      rearrangements are likely caused and selected by the restriction attacks.
AU  - Kobayashi I
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 2002 48: 260-261.

PMID- 
VI  - 18
DP  - 1999
TI  - Reshaping the genome: DNA restriction-modification systems as mobile genetic elements.
PG  - 1846-1857
AB  - 
AU  - Kobayashi I
PT  - Journal Article
TA  - Saibo Kogaku
JT  - Saibo Kogaku
SO  - Saibo Kogaku 1999 18: 1846-1857.

PMID- 
VI  - 1246
DP  - 2002
TI  - Life cycle of restriction-modification gene complexes, powers in genome evolution.
PG  - 191-200
AB  - Increasing lines of evidence suggest that gene complexes encoding restriction modification
      enzymes may behave as selfish mobile genetic elements affecting genome stability and genome
      evolution.  I here compare their hypothetical life cycles with those of temperate
      bacteriophage DNAs and other mobile elements.  The restriciton modification gene complexes may
      establish themselves in a new host avoiding cell killing.  Upon some environmental signals,
      they would be induced to multiply.  The multiplied RM gene complex may be released to the
      environment and taken up by other cells in naturally competent bacteria.  In some aspects,
      they could be regarded as DNA viruses without a capsid, or DNA viroids.  They may play the
      role of power giving order to the community of genes called the genome.
AU  - Kobayashi I
PT  - Journal Article
TA  - Int. Congr. Ser.
JT  - Int. Congr. Ser.
SO  - Int. Congr. Ser. 2002 1246: 191-200.

PMID- 
VI  - 45
DP  - 2001
TI  - Evolution and Diversity.
PG  - 162-163
AB  - A type II restriction enzyme gene is often linked to a modification methylase gene whose role
      is to protect the recognition site from breakage in the genome.  This postsegregational
      killing or postdisturbance killing can be very severe.  Block to replication of a ts plasmid
      carrying an EcoRII RM gene complex leads to immediate loss of viability by several orders of
      magnitude.  The cell killing was observed when an RM plasmid was challenged by an incompatible
      plasmid.  Similar resistance was observed when chromosomally located RM was threatened by a
      homologous stretch of DNA in E. coli.  Many of the progeny carried the donor gene as well as
      the recipient gene and lost the donor gene in the absence of its selection.  Each of these
      unstable diploids have experienced megabase-size genome rearrangements that include
      duplication of the RM locus in question and inversion.  Precise homologous recombination at
      ectopic IS3 was shown to be involved in these rearrangements.  Comparisons of closely related
      bacterial genomes revealed that restriction-modification gene complexes are often linked with
      gross genome polymorphism.  One comparison suggests insertion of restriction modification gene
      complexes into a genome with a long (ca. 100 bp) target duplication.  Comparison of two
      complete genome sequences of Pyrococcus suggested transposition of restriction modification
      gene complexes with linked genes.  We hypothesize that the rearrangements in the laboratory
      and in the natural environments have resulted from attack of restriction enzymes on the
      chromosome.  Only those genomes that have incorporated RM genes in question and allowed their
      expression would survive.  Their behavior as selfish mobile elements may explain their
      competition - specificity of sequence recognition and mutual exclusion (superinfection
      exclusion) - and clarify certain aspects of bacterial recombination repair.  The killing is
      severe in mutants defective in XerCD-mediated site-specific recombination at dif site in E.
      coli chromosome.  This result provides support to the hypothesis that this site-specific
      recombination system is important in DNA damage repair.  Strong postdisturbance killing by
      EcoRII RM is suppressed by Dcm, an orphan methylase.  This vaccine effect may explain why Dcm
      is present at all.  The selfish self-maintenance of the restriction modification genes also
      provides a unique opportunity for stable maintenance and table expression of useful genes in
      bacteria.
AU  - Kobayashi I
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 2001 45: 162-163.

PMID- 11557807
VI  - 29
DP  - 2001
TI  - Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution.
PG  - 3742-3756
AB  - Restriction-modification (RM) systems are composed of genes that encode a restriction enzyme
      and a modification methylase. RM systems sometimes behave as discrete units of life, like
      viruses and transposons. RM complexes attack invading DNA that has not been properly modified
      and thus may serve as a tool of defense for bacterial cells. However, any threat to their
      maintenance, such as a challenge by a competing genetic element (an incompatible plasmid or an
      allelic homologous stretch of DNA, for example) can lead to cell death through restriction
      breakage in the genome. This post-segregational or post-disturbance cell killing may provide
      the RM complexes (and any DNA linked with them) with a competitive advantage. There is
      evidence that they have undergone extensive horizontal transfer between genomes, as inferred
      from their sequence homology, codon usage bias and GC content difference. They are often
      linked with mobile genetic elements such as plasmids, viruses, transposons and integrons. The
      comparison of closely related bacterial genomes also suggests that, at times, RM genes
      themselves behave as mobile elements and cause genome rearrangements. Indeed some bacterial
      genomes that survived post-disturbance attack by an RM gene complex in the laboratory have
      experienced genome rearrangements. The avoidance of some restriction sites by bacterial
      genomes may result from selection by past restriction attacks. Both bacteriophages and
      bacteria also appear to use homologous recombination to cope with the selfish behavior of RM
      systems. RM systems compete with each other in several ways. One is competition for
      recognition sequences in post-segregational killing. Another is super-infection exclusion,
      that is, the killing of the cell carrying an RM system when it is infected with another RM
      system of the same regulatory specificity but of a different sequence specificity. The
      capacity of RM systems to act as selfish, mobile genetic elements may underlie the structure
      and function of RM enzymes.
AU  - Kobayashi I
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2001 29: 3742-3756.

PMID- 11802400
VI  - 46
DP  - 2001
TI  - Genome comparison: involvement of restriction modification genes in genome rearrangements.
PG  - 2393-2399
AB  - 
AU  - Kobayashi I
PT  - Journal Article
TA  - Tanpakushitsu Kakusan Koso
JT  - Tanpakushitsu Kakusan Koso
SO  - Tanpakushitsu Kakusan Koso 2001 46: 2393-2399.

PMID- Not carried by PubMed...
VI  - 14
DP  - 1995
TI  - Selfish genes for restriction-modification systems.
PG  - 1015-1023
AB  - 
AU  - Kobayashi I
PT  - Journal Article
TA  - Saibo Kogaku
JT  - Saibo Kogaku
SO  - Saibo Kogaku 1995 14: 1015-1023.

PMID- 9769733
VI  - 14
DP  - 1998
TI  - Selfishness and death: raison d'etre of restriction, recombination and mitochondria.
PG  - 368-374
AB  - Type II restriction-modification gene complexes, such as the EcoRI system, are not easily lost
      from their host cell.  The descendants of cells that lose a restriction-modification gene
      complex are unable to modify a sufficient number of recognition sites in their chromosomes to
      protect them from lethal attack by the remaining molecules of the restriction enzyme.  This
      capacity to act as a selfish genetic element is likely to have contributed to the spread and
      maintenance of restriction-modification systems.  Homologous recombination machineries of
      cells and viruses appear to be well adapted to cope with these elements.  By extrapolation,
      the capacity of mitochondria to kill their host eukaryotic cell might have stabilized their
      initial symbiosis.
AU  - Kobayashi I
PT  - Journal Article
TA  - Trends Genet.
JT  - Trends Genet.
SO  - Trends Genet. 1998 14: 368-374.

PMID- Not included in PubMed...
VI  - 19
DP  - 1994
TI  - Why are there restriction enzymes and genetic recombination?
PG  - 464
AB  - If self-replication of genetic information is the essential feature of life process, why has

      the process of homologous recombination, which generates variation, evolved at all? The

      double-strand break repair model of homologous recombination (for which we have evidence)

      proposes that generation of double-strand break on otherwise intact DNA initiates homologous

      recombination. Might this be too destructive as a means of generating recombinant progeny? We

      obtained several experimental results that suggest a feature of homologous interaction, a

      feature that enabled evolution of homologous recombination, is destruction of genetic

      information.

      

      Why are there restriction enzymes?

      

      Double-strand break of DNA plays an important role in homologous recombination in vivo. It

      is believed that restriction/modification system serves for destruction of foreign DNA such as

      viral DNA. But this theory cannot explain easily presence of rare cutters and other phenomena.

      We found that restriction enzyme gene and modification methylase gene on a plasmid stabilize

      it. Our results support the following post-segregational killing mechanism: When a cell that

      has lost the plasmid continues dividing, the modification enzymes become dilute and cannot

      modify all of the thousands of recognition sites on the chromosome. The remaining restriction

      enzymes will cleave the chromosome and kill the host cells. As a result, most viable cells in

      a population carry the plasmid. In brief, turning off of a pair of genes, a killer and an

      anti-killer, will program cell lineage for death. A restriction modification system is a

      parasite or a selfish element such as a transposon. Its benfit to the host is protection

      against foreign DNA. Thus it can be called a symbiont.

      

AU  - Kobayashi I
PT  - Journal Article
TA  - Cell Struct. Funct.
JT  - Cell Struct. Funct.
SO  - Cell Struct. Funct. 1994 19: 464.

PMID- 10607611
VI  - 9
DP  - 1999
TI  - Shaping the genome--restriction-modification systems as mobile genetic elements.
PG  - 649-656
AB  - A restriction enzyme gene is often linked to a modification methylase gene the role of which
      is to protect a recognition site on DNA from breakage by the former. Loss of some
      restriction-modification gene complexes leads to cell death through restriction breakage in
      the genome. Their behavior as genomic parasites/symbionts may explain the distribution of
      restriction sites and clarify certain aspects of bacterial recombination repair and
      mutagenesis. A comparison of bacterial genomes supports the hypothesis that
      restriction-modification gene complexes are mobile elements involved in various genome
      rearrangements and evolution.
AU  - Kobayashi I
AU  - Nobusato A
AU  - Kobayashi-Takahashi N
AU  - Uchiyama I
PT  - Journal Article
TA  - Curr. Opin. Genet. Dev.
JT  - Curr. Opin. Genet. Dev.
SO  - Curr. Opin. Genet. Dev. 1999 9: 649-656.

PMID- 
VI  - 37
DP  - 2003
TI  - Molecular characterization of a lactococcal plasmid reducing the growth rate of host cells.
PG  - 53-57
AB  - Lactococcus lactis subsp. lactis biovar. diacetylactis DRC1 carries more than 6 plasmids,
      including a 7.4 kb cryptic plasmid, which was
      designated as pDR1-1. The pDR1-1 plasmid was found to significantly
      affect the maximum specific growth rate (mu(max)) of the host cells
      because of its limiting effect on growth. To investigate the properties
      of the limiting effect, the entire nucleotide sequence of pDR1-1 was
      determined. It consisted of 7412 bp, and 6 open reading frames (ORFs)
      were identified. The first ORF showed a high degree of similarity to a
      family of replication genes (rep) that are commonly found in
      lactococcal strains. The rep gene in pDR1-1 was followed by a second
      ORF of unknown function. Directly downstream of the second ORF, a third
      ORF was found, that showed homology to the S subunit from type I
      restriction/modification systems. No significant similarity to the
      contents of the database was found for the other ORFs. PCR analysis was
      carried out in order to detect pDR1-1 in the other L. lactis strains.
      The mu(max) of the pDR1-1-positive strain was the same as that of DRC1.
      These results suggest that the load of pDR1-1 (or pDR1-1-like plasmid)
      is a major factor influencing the mu(max) of DRC1 because of its
      limiting effect on growth, an effect which is much more pronounced than
      that produced by the overall load of other coexisting plasmids.
AU  - Kobayashi M
AU  - Nomura M
AU  - Fujita Y
AU  - Ohmomo S
AU  - Okamoto T
PT  - Journal Article
TA  - Japan Agricultural Research Quarterly
JT  - Japan Agricultural Research Quarterly
SO  - Japan Agricultural Research Quarterly 2003 37: 53-57.

PMID- 12390490
VI  - 35
DP  - 2002
TI  - Influence of lactococcal plasmid on the specific growth rate of host cells.
PG  - 403-408
AB  - Aims: To investigate a lactococcal plasmid responsible for a reduction in growth rate of its
      host cell.  Methods and Results: Lactococcus lactis subsp. lactis biovar. diacetylactis DRC1
      carries a high number of plasmids.  The DRC1 wild-type strain was found to grow more slowly
      than a plasmid-free derivative of DRC1.  The plasmids extracted from DRC1 together with an
      indicator plasmid were cotransformed into the plasmid-free strain DRC1021.  A 7.4-kb cryptic
      plasmid, designated pDR1-1, was found to significantly affect the maximum specific growth rate
      (umax) of the host cell.  Polymerase chain reaction (PCR) analysis was carried out in order to
      detect the presence of pDR1-1 in the other L. lactis strains.  The umax of the single
      pDR1-1-positive strain was determined to be the same as that of DRC1.  Significance and Impact
      of the Study: These results suggest that pDR1-1 (or a pDR1-1-like plasmid) is a critical
      factor in the reduction of the umax of DRC1, and that its effect on the umax is significantly
      greater than that of any other coexisting plasmid.
AU  - Kobayashi M
AU  - Nomura M
AU  - Fujita Y
AU  - Okamoto T
AU  - Ohmomo S
PT  - Journal Article
TA  - Lett. Appl. Microbiol.
JT  - Lett. Appl. Microbiol.
SO  - Lett. Appl. Microbiol. 2002 35: 403-408.

PMID- 17986766
VI  - 71
DP  - 2007
TI  - Manipulation for Plasmid Elimination by Transforming Synthetic Competitors Diversifies Lactococcus lactis Starters Applicable to Food Products.
PG  - 2647-2654
AB  - This study was designed selectively to eliminate a theta-plasmid from
      Lactococcus lactis strains by transforming synthetic competitors. A
      shuttle vector for Escherichia coli and L. lactis, pDB1, was constructed
      by ligating a partial replicon of pDR1-1B, which is a 7.3 kb theta-plasmid
      in L. lactis DRC1, with an erythromycin resistance gene into pBluescript
      II KS(+). This versatile vector was used to construct competitors to
      common lactococcal theta-plasmids. pDB1 contains the 5' half of the
      replication origin and the 3' region of repB of pDR1-1B, but lacks the
      1.1-kb region normally found between these two segments. A set of primers,
      Pv3 and Pv4, was designed to amplify the 1.1-kb middle parts of the
      general theta-replicons of lactococcal plasmids. When the PCR products
      were cloned into the Nru I and Xho I sites of pDB1, synthetic replicons
      were constructed and replication activity was restored. A number of
      theta-plasmids in L. lactis ssp. lactis and cremoris were eliminated
      selectively by transforming the synthetic competitors. These competitors
      were easily eliminated by subculture for a short time in the absence of
      selection. The resulting variants contained no exogenous DNA and are
      suitable for food products, since part of the phenotype was altered
      without altering other plasmids indispensable for fermentation.
AU  - Kobayashi M
AU  - Nomura M
AU  - Kimoto H
PT  - Journal Article
TA  - Biosci. Biotechnol. Biochem.
JT  - Biosci. Biotechnol. Biochem.
SO  - Biosci. Biotechnol. Biochem. 2007 71: 2647-2654.

PMID- 26251493
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Paenibacillus polymyxa Strain Mc5Re-14, an Antagonistic  Root Endophyte of Matricaria chamomilla.
PG  - e00861-15
AB  - Paenibacillus polymyxa strain Mc5Re-14 was isolated from the inner root tissue of Matricaria
      chamomilla (German chamomile). Mc5Re-14 revealed promising in vitro
      antagonistic activity against plant and opportunistic human pathogens. The 6.0-Mb
      draft genome reveals genes putatively involved in pathogen suppression and direct
      and indirect plant growth promotion.
AU  - Koberl M
AU  - White RAIII
AU  - Erschen S
AU  - El-Arabi TF
AU  - Jansson JK
AU  - Berg G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00861-15.

PMID- 26251492
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Streptomyces sp. Strain Wb2n-11, a Desert Isolate with Broad-Spectrum Antagonism against Soilborne Phytopathogens.
PG  - e00860-15
AB  - Streptomyces sp. strain Wb2n-11, isolated from native desert soil, exhibited broad-spectrum
      antagonism against plant pathogenic fungi, bacteria, and
      nematodes. The 8.2-Mb draft genome reveals genes putatively responsible for its
      promising biocontrol activity and genes which enable the soil bacterium to
      directly interact beneficially with plants.
AU  - Koberl M
AU  - White RAIII
AU  - Erschen S
AU  - El-Arabi TF
AU  - Jansson JK
AU  - Berg G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00860-15.

PMID- 26272562
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Bacillus amyloliquefaciens Strain Co1-6, a Plant Growth-Promoting Rhizobacterium of Calendula officinalis.
PG  - e00862-15
AB  - The genome sequence of Bacillus amyloliquefaciens strain Co1-6, a plant growth-promoting
      rhizobacterium (PGPR) with broad-spectrum antagonistic activity
      against plant-pathogenic fungi, bacteria, and nematodes, consists of a single
      3.9-Mb circular chromosome. The genome reveals genes putatively responsible for
      its promising biocontrol and PGP properties.
AU  - Koberl M
AU  - White RAIII
AU  - Erschen S
AU  - Spanberger N
AU  - El-Arabi TF
AU  - Jansson JK
AU  - Berg G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00862-15.

PMID- 21952547
VI  - 193
DP  - 2011
TI  - Genome Sequence of the Marine Photoheterotrophic Bacterium Erythrobacter sp. Strain NAP1.
PG  - 5881-5882
AB  - Here we report the full genome sequence of marine phototrophic bacterium Erythrobacter sp.
      strain NAP1. The 3.3-Mb genome contains a full set of
      photosynthetic genes organized in one 38.9-kb cluster; however, it does
      not contain genes for CO(2) or N(2) fixation, thereby confirming that the
      organism is a photoheterotroph.
AU  - Koblizek M
AU  - Janouskovec J
AU  - Obornik M
AU  - Johnson JH
AU  - Ferriera S
AU  - Falkowski PG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5881-5882.

PMID- 26305944
VI  - 112
DP  - 2015
TI  - Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira.
PG  - 11371-11376
AB  - Nitrospira are a diverse group of nitrite-oxidizing bacteria and among the environmentally
      most widespread nitrifiers. However, they remain scarcely studied
      and mostly uncultured. Based on genomic and experimental data from Nitrospira
      moscoviensis representing the ubiquitous Nitrospira lineage II, we identified
      ecophysiological traits that contribute to the ecological success of Nitrospira.
      Unexpectedly, N. moscoviensis possesses genes coding for a urease and cleaves
      urea to ammonia and CO2. Ureolysis was not observed yet in nitrite oxidizers and
      enables N. moscoviensis to supply ammonia oxidizers lacking urease with ammonia
      from urea, which is fully nitrified by this consortium through reciprocal
      feeding. The presence of highly similar urease genes in Nitrospira lenta from
      activated sludge, in metagenomes from soils and freshwater habitats, and of other
      ureases in marine nitrite oxidizers, suggests a wide distribution of this
      extended interaction between ammonia and nitrite oxidizers, which enables
      nitrite-oxidizing bacteria to indirectly use urea as a source of energy. A
      soluble formate dehydrogenase lends additional ecophysiological flexibility and
      allows N. moscoviensis to use formate, with or without concomitant nitrite
      oxidation, using oxygen, nitrate, or both compounds as terminal electron
      acceptors. Compared with Nitrospira defluvii from lineage I, N. moscoviensis
      shares the Nitrospira core metabolism but shows substantial genomic dissimilarity
      including genes for adaptations to elevated oxygen concentrations. Reciprocal
      feeding and metabolic versatility, including the participation in different
      nitrogen cycling processes, likely are key factors for the niche partitioning,
      the ubiquity, and the high diversity of Nitrospira in natural and engineered
      ecosystems.
AU  - Koch H
AU  - Lucker S
AU  - Albertsen M
AU  - Kitzinger K
AU  - Herbold C
AU  - Spieck E
AU  - Nielsen PH
AU  - Wagner M
AU  - Daims H
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2015 112: 11371-11376.

PMID- 8506131
VI  - 21
DP  - 1993
TI  - Probing DNA-protein interactions in vitro with the CpG DNA methyltransferase.
PG  - 2339-2342
AB  - A sensitive method was devised to monitor the in vitro binding of nuclear proteins from HeLa
      cells presumably to the major groove of DNA. Upon the incubation of DNA with nuclear extracts,
      the complexed DNA was incubated with the CpG DNA methyltransferase from Spiroplasma species.
      Subsequently, the DNA was repurified, and the location of the methylated cytidine residues was
      determined by the hydrazine reaction of the DNA sequencing method. By using as DNA substrate
      the VAI (virus associated) region of human adenovirus type 2 (Ad2) DNA or specific Alu
      sequences associated with a number of human genes, it was documented that those segments of
      DNA that were protected by bound proteins against the reaction with DNaseI also escaped in
      vitro methylation by the CpG DNA methyltransferase. This new footprinting method provides a
      sensitive indicator for in vitro DNA-protein interactions which are specific for the major
      groove of DNA.
AU  - Kochanek S
AU  - Renz D
AU  - Doerfler W
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 2339-2342.

PMID- 9073065
VI  - 187
DP  - 1997
TI  - Genome structure of the Lactobacillus temperate phage Phi g1e: the whole genome sequence and the putative promoter/repressor system.
PG  - 45-53
AB  - The complete genome sequence of a Lactobacillus temperate phage phi g1e was established. The
      double-stranded DNA is composed of 42,259 bp, and encodes for sixty-two possible open reading
      frames (ORF) as well as several potential regulatory sequences. Based on comparative analysis
      with other related proteins of the Lactobacillus and Lactococcus phages as well as the
      Escherichia coli phages (such as lambda), functions were putatively assigned to several phi
      g1e ORFs: cng and cpg (encoding for repressors), hel (helicase), ntp (NTPase), and several
      ORFs (e.g., minor capsid proteins). An about 1000-bp DNA region of phi g1e containing cpg and
      cng was inferred to function as a promoter/repressor system for the phi g1e lysogenic and
      lytic pathway.
AU  - Kodaira KI
AU  - Oki M
AU  - Kakikawa M
AU  - Watanabe N
AU  - Hirakawa M
AU  - Yamada K
AU  - Taketo A
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1997 187: 45-53.

PMID- 24115546
VI  - 1
DP  - 2013
TI  - Genome Sequence of Halomonas sp. Strain A3H3, Isolated from Arsenic-Rich Marine Sediments.
PG  - e00819-13
AB  - We report the genome sequence of Halomonas sp. strain A3H3, a bacterium with a high tolerance
      to arsenite, isolated from multicontaminated sediments of the
      l'Estaque harbor in Marseille, France. The genome is composed of a 5,489,893-bp
      chromosome and a 157,085-bp plasmid.
AU  - Koechler S
AU  - Plewniak F
AU  - Barbe V
AU  - Battaglia-Brunet F
AU  - Jost B
AU  - Joulian C
AU  - Philipps M
AU  - Vicaire S
AU  - Vincent S
AU  - Ye T
AU  - Bertin PN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00819-13.

PMID- 27445379
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Herbinix luporum SD1D, a New Cellulose-Degrading Bacterium Isolated from a Thermophilic Biogas Reactor.
PG  - e00687-16
AB  - A novel cellulolytic bacterial strain was isolated from an industrial-scale biogas plant. The
      16S rRNA gene sequence of the strain SD1D showed 96.4%
      similarity to Herbinix hemicellulosilytica T3/55(T), indicating a novel species
      within the genus Herbinix (family Lachnospiraceae). Here, the complete genome
      sequence of Herbinix luporum SD1D is reported.
AU  - Koeck DE
AU  - Maus I
AU  - Wibberg D
AU  - Winkler A
AU  - Zverlov VV
AU  - Liebl W
AU  - Puhler A
AU  - Schwarz WH
AU  - Schluter A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00687-16.

PMID- 27340074
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Propionispora sp. Strain 2/2-37, a New Xylan-Degrading Bacterium Isolated from a Mesophilic Biogas Reactor.
PG  - e00609-16
AB  - The novel mesophilic bacterial strain Propionispora sp. 2/2-37 was isolated from  an
      industrial-scale biogas plant. Comparative 16S rRNA gene sequencing revealed
      that the isolate constitutes a new subcluster within the order Selenomonadales
      The 2/2-37 draft genome sequence was established and provides the genetic basis
      for application of this microorganism in degradation of biomass for bio-fuel
      production.
AU  - Koeck DE
AU  - Maus I
AU  - Wibberg D
AU  - Winkler A
AU  - Zverlov VV
AU  - Liebl W
AU  - Puhler A
AU  - Schwarz WH
AU  - Schluter A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00609-16.

PMID- 27738036
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Gordonia sp. Strain UCD-TK1 (Phylum Actinobacteria).
PG  - e01121-16
AB  - Here, we present the draft genome of Gordonia sp. strain UCD-TK1. The assembly contains
      5,470,576 bp in 98 contigs. This strain was isolated from a disinfected
      ambulatory surgery center.
AU  - Koenigsaecker TM
AU  - Eisen JA
AU  - Coil DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01121-16.

PMID- 12074151
VI  - 32
DP  - 2002
TI  - Improved blunt-end cloning by replacing EcoRV with Eco32I.
PG  - 1244-1246
AB  - The restriction endonuclease EcoRV, which recognizes and cleaves DNA containing 5'-GATATC-3'
      sequences, is among the best characterized and most frequently used blunt-end cutting
      restriction enzymes.  Its recognition site is present in many cloning vectors currently in
      use.  Compared with that of cohesive ends, blunt-end ligation is generally more difficult
      because a higher number of background colonies is formed that result from self-ligation of
      vector  molecules.  We (and others) have found that when using EcoRV even "white color"
      selection often fails so that one ends up with a large number of apparently positive (white)
      colonies.  Here we demonstrate that this problem can be reduced if one uses Eco32I, an
      isoschizomer of EcoRV, instead.
AU  - Koesters R
AU  - von Knebel-Doeberitz M
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 2002 32: 1244-1246.

PMID- 24009125
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Pseudomonas pelagia CL-AP6, a Psychrotolerant Bacterium  Isolated from Culture of Antarctic Green Alga Pyramimonas gelidicola.
PG  - e00699-13
AB  - Pseudomonas pelagia CL-AP6, isolated from a culture of the Antarctic green alga Pyramimonas
      gelidicola, is a psychrotolerant bacterium. Here, we report the draft
      genome sequence of this strain, which may provide insights into the mutualistic
      interaction between microalgae and bacteria in sea ice, as well as the cold
      adaptation mechanisms of bacteria.
AU  - Koh HY
AU  - Jung W
AU  - Do H
AU  - Lee JH
AU  - Kim HJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00699-13.

PMID- 23144403
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Paenisporosarcina sp. Strain TG-14, a Psychrophilic Bacterium Isolated from Sediment-Laden Stratified Basal Ice from Taylor Glacier,    McMurdo Dry Valleys, Antarctica.
PG  - 6656-6657
AB  - The psychrophilic bacterium Paenisporosarcina sp. TG-14 was isolated from sediment-laden
      stratified basal ice from Taylor Glacier, McMurdo Dry Valleys,
      Antarctica. Here we report the draft genome sequence of this strain, which may
      provide useful information on the cold adaptation mechanism in extremely variable
      environments.
AU  - Koh HY
AU  - Lee SG
AU  - Lee JH
AU  - Doyle S
AU  - Christner BC
AU  - Kim HJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6656-6657.

PMID- 29301903
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Singapore Klebsiella pneumoniae subsp. pneumoniae Isolate DS32358_14, Which Contains the Carbapenemase Gene blaVIM-1.
PG  - e01377-17
AB  - We sequenced the first blaVIM-1-positive Klebsiella pneumoniae strain isolated in Singapore.
      The isolate belongs to multilocus sequence type 2542 (ST2542), and blaVIM-1 was the first gene
      in an integron that also contained aacA4, aphA15, aadA1, catB2, qacEdelta1, and sul1.
AU  - Koh TH
AU  - Abdul-Rahman NB
AU  - Teo JWP
AU  - La MV
AU  - Periaswamy B
AU  - Chen SL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01377-17.

PMID- 24233594
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Sphingobium ummariense Strain RL-3, a Hexachlorocyclohexane-Degrading Bacterium.
PG  - e00956-13
AB  - Here, we report the draft genome sequence of the hexachlorocyclohexane (HCH)-degrading
      bacterium Sphingobium ummariense strain RL-3, which was isolated
      from the HCH dumpsite located in Lucknow, India (27 degrees 00'N and 81 degrees
      09'E). The annotated draft genome sequence (4.75 Mb) of strain RL-3 consisted of
      139 contigs, 4,645 coding sequences, and 65% G+C content.
AU  - Kohli P
AU  - Dua A
AU  - Sangwan N
AU  - Oldach P
AU  - Khurana JP
AU  - Lal R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00956-13.

PMID- 25700416
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Hafnia paralvei Strain GTA-HAF03.
PG  - e01592-14
AB  - Hafnia paralvei is a Gram-negative member of the Enterobacteriaceae family, closely related to
      the opportunistic pathogen Hafnia alvei. We report here the first draft genome sequence of H.
      paralvei, from the beef trim isolate GTA-HAF03, consisting of a 5.0-Mbp assembly encoding
      4,382 proteins and 90 predicted RNAs.
AU  - Kohlman ME
AU  - Carrillo CD
AU  - Wong A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01592-14.

PMID- 26227594
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Bacteriocin-Producing Bradyrhizobium japonicum Strain FN1.
PG  - e00812-15
AB  - Bradyrhizobium japonicum strain FN1 was found to produce bacteriocin-like zones of clearing
      when tested against other strains of bradyrhizbia. The genome was
      sequenced, and several putative bacteriocin-producing genes, in addition to the
      expected genes involved in nodulation and nitrogen fixation, were identified.
AU  - Kohlmeier MG
AU  - Yudistira H
AU  - Zhang XL
AU  - Fristensky B
AU  - Levin DB
AU  - Sparling R
AU  - Oresnik IJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00812-15.

PMID- 28066393
VI  - 7
DP  - 2016
TI  - Fuerstia marisgermanicae gen. nov., sp. nov., an Unusual Member of the Phylum Planctomycetes from the German Wadden Sea.
PG  - 2079
AB  - Members of the phylum Planctomycetes are ubiquitous bacteria that dwell in
      aquatic and terrestrial habitats. While planctomycetal species are important
      players in the global carbon and nitrogen cycle, this phylum is still
      undersampled and only few genome sequences are available. Here we describe strain
      NH11T, a novel planctomycete obtained from a crustacean shell (Wadden Sea,
      Germany). The phylogenetically closest related cultivated species is Gimesia
      maris, sharing only 87% 16S rRNA sequence identity. Previous isolation attempts
      have mostly yielded members of the genus Rhodopirellula from water of the German
      North Sea. On the other hand, only one axenic culture of the genus Pirellula was
      obtained from a crustacean thus far. However, the 16S rRNA gene sequence of
      strain NH11T shares only 80% sequence identity with the closest relative of both
      genera, Rhodopirellula and Pirellula. Thus, strain NH11T is unique in terms of
      origin and phylogeny. While the pear to ovoid shaped cells of strain NH11T are
      typical planctomycetal, light-, and electron microscopic observations point
      toward an unusual variation of cell division through budding: during the division
      process daughter- and mother cells are connected by an unseen thin tubular-like
      structure. Furthermore, the periplasmic space of strain NH11T was unusually
      enlarged and differed from previously known planctomycetes. The complete genome
      of strain NH11T, with almost 9 Mb in size, is among the largest planctomycetal
      genomes sequenced thus far, but harbors only 6645 protein-coding genes. The
      acquisition of genomic components by horizontal gene transfer is indicated by the
      presence of numerous putative genomic islands. Strikingly, 45 "giant genes" were
      found within the genome of NH11T. Subsequent analysis of all available
      planctomycetal genomes revealed that Planctomycetes as such are especially rich
      in "giant genes". Furthermore, Multilocus Sequence Analysis (MLSA) tree
      reconstruction support the phylogenetic distance of strain NH11T from other
      cultivated Planctomycetes of the same phylogenetic cluster. Thus, based on our
      findings, we propose to classify strain NH11T as Fuerstia marisgermanicae gen.
      nov., sp. nov., with the type strain NH11T, within the phylum Planctomycetes.
AU  - Kohn T
AU  - Heuer A
AU  - Jogler M
AU  - Vollmers J
AU  - Boedeker C
AU  - Bunk B
AU  - Rast P
AU  - Borchert D
AU  - Glockner I
AU  - Freese HM
AU  - Klenk HP
AU  - Overmann J
AU  - Kaster AK
AU  - Rohde M
AU  - Wiegand S
AU  - Jogler C
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2016 7: 2079.

PMID- 3034675
VI  - 216
DP  - 1987
TI  - In situ distribution of EcoRI methylase and restriction endonuclease in cells of Escherichia coli Bs5.
PG  - 207-210
AB  - Specific IgG antibodies were raised in rabbits against purified EcoRI methylase
      and restriction endonuclease.  Post embedding labeling experiments, using the
      protein A-gold technique, were made with paraformaldehyde-glutaraldehyde fixed
      cells, embedded in Lowicryl K4M resin at low temperatures.  Labeling with
      methylase-specific antibodies showed 60-70% of gold particles in the cytoplasm
      and 30-40% at the cell envelope, whereas the use of restriction enzyme-specific
      antibodies led to a distribution of 10-30% in the cytoplasm and 70-90% in the
      cell envelope.  The results coincide with the proposed function of the enzymes:
      in the cytoplasm methylase protects the cells' own DNA from self-destruction,
      and the restriction endonuclease cuts foreign DNA when entering the cell.
AU  - Kohring GW
AU  - Mayer F
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1987 216: 207-210.

PMID- 2992974
VI  - 37
DP  - 1985
TI  - Immunoelectron microscopic localization of the restriction endonuclease EcoRI in Escherichia coli BS5.
PG  - 1-6
AB  - Purified restriction endonuclease EcoRI isolated fom Escherichia coli BS5 was
      used for the production of enzyme-specific IgG antibodies in rabbits.  For
      enzyme localization experiments, paraformaldehyde-glutaraldehyde-fixed cells
      were embedded and polymerized by a low-temperature procedure using Lowicryl
      K4M.  the immuno electron microscopic protein A-gold technique and an
      immuno-gold method revealed that 70% of the enzyme-specific labeling were
      located in the cell envelope whereas 30% were found in the cytoplasm.  In
      metal-shadowed preparations, no indications for the presence of the enzme could
      be found on the cell surface; however, on the surface of cell protoplasts
      enzyme specific labeling could be detected.  The results indicate the presence
      of major amount of EcoRI in the periplasmic space of the cell where it might be
      loosely bound or even freely diffusible.
AU  - Kohring GW
AU  - Mayer F
PT  - Journal Article
TA  - Eur. J. Cell Biol.
JT  - Eur. J. Cell Biol.
SO  - Eur. J. Cell Biol. 1985 37: 1-6.

PMID- 25523780
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Acetobacter tropicalis Type Strain NBRC16470, a Producer of Optically Pure d-Glyceric Acid.
PG  - e01329-14
AB  - Here we report the 3.7-Mb draft genome sequence of Acetobacter tropicalis NBRC16470(T), which
      can produce optically pure d-glyceric acid (d-GA; 99%
      enantiomeric excess) from raw glycerol feedstock derived from biodiesel fuel
      production processes.
AU  - Koike H
AU  - Sato S
AU  - Morita T
AU  - Fukuoka T
AU  - Habe H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01329-14.

PMID- 
VI  - 81
DP  - 2005
TI  - GATC Methylation by Dam methylase in archaea: its roles and possible transcription regulation by an FFRP.
PG  - 278-290
AB  - Methylation of pairs of adenines at their N6 positions in GATC sites (GATC methylation) in
      archaeal genomic DNAs has been studied. Genomic DNAs in cells of three archaeal species were
      found as fully methylated, while those of four other archaeal species were free of such
      methylation. Consistently with this pattern of the presence or absence of GATC methylation,
      homologues of E. coli Dam methylase was found present or absent, but various other types of
      DNA methylases were not. A Dam homologue from Pyrococcus sp. OT3 was expressed and its
      expected function of methylating GATC was confirmed. By methylation of each adenine the DNA
      duplex was destabilized by 0.56 +/- 0.10 Kcal/mol, and this effect was additive. For some
      archaea, transcription regulation of Dam methylase gene appears to be needed upon cell
      replication, and in regions upstream of three Dam methylase genes, nucleotide sequences close
      to TTTTCTTTGAAAA were present. This arrangement, five bases each at the ends, which are
      complementary to each other, sandwiching three T bases at the center, fits into a pattern the
      same as those recognized by dimers of transcription factors, feast/famine regulatory proteins
      (FFRPs).
AU  - Koike H
AU  - Yokoyama K
AU  - Kawashima T
AU  - Yamasaki T
AU  - Makino S
AU  - Clowney L
AU  - Suzuki M
PT  - Journal Article
TA  - Proc. Jpn. Acad., B, Phys. Biol. Sci.
JT  - Proc. Jpn. Acad., B, Phys. Biol. Sci.
SO  - Proc. Jpn. Acad., B, Phys. Biol. Sci. 2005 81: 278-290.

PMID- 27604221
VI  - 33
DP  - 2016
TI  - Population Evolution of Helicobacter pylori through Diversification in DNA Methylation and Interstrain Sequence Homogenization.
PG  - 2848-2859
AB  - Decoding of closely related genomes is now revealing the process of population evolution. In
      bacteria, population divergence appears associated with a unique
      set of sequence-specific epigenetic DNA methylation systems, often within
      restriction-modification (RM) systems. They might define a unique gene expression
      pattern and limit genetic flux between lineages in population divergence. We
      addressed the contribution of methylation systems to population diversification
      in panmictic bacterial species, Helicobacter pylori, which shows an
      interconnected population structure through frequent mutual recombination. We
      analyzed complete genome sequences of 28 strains collected in Fukui, Japan. Their
      nucleotide sequences are closely related although fine-scale analyses revealed
      two subgroups likely reflecting human subpopulations. Their sequences are tightly
      connected by homologous recombination. Our extensive analysis of RM systems
      revealed an extreme variability in DNA methyltransferases, especially in their
      target recognition domains. Their diversity was, however, not immediately related
      to the genome sequence diversity, except for very closely related strains. An
      interesting exception is a hybrid strain, which likely has conserved the
      methylation gene repertoire from one parent but diversified in sequence by
      massive acquisition of fragmentary DNA sequences from the other parent. Our
      results demonstrate how a bacterial population can be extremely divergent in
      epigenetics and yet homogenized in sequence.
AU  - Kojima KK
AU  - Furuta Y
AU  - Yahara K
AU  - Fukuyo M
AU  - Shiwa Y
AU  - Nishiumi S
AU  - Yoshida M
AU  - Azuma T
AU  - Yoshikawa H
AU  - Kobayashi I
PT  - Journal Article
TA  - Mol. Biol. Evol.
JT  - Mol. Biol. Evol.
SO  - Mol. Biol. Evol. 2016 33: 2848-2859.

PMID- 23408487
VI  - 6
DP  - 2012
TI  - Non contiguous-finished genome sequence and description of Bacillus timonensis sp. nov.
PG  - 346-355
AB  - Bacillus timonensis strain MM10403188(T) sp. nov. is the type strain of a proposed new species
      within the genus Bacillus. This strain, whose genome is
      described here, was isolated from the fecal flora of a healthy patient. B.
      timonensis is an aerobic Gram-negative rod shaped bacterium. Here we describe the
      features of this organism, together with the complete genome sequence and
      annotation. The 4,632,049 bp long genome (1 chromosome but no plasmid) contains
      4,610 protein-coding and 74 RNA genes, including 5 rRNA genes.
AU  - Kokcha S
AU  - Mishra AK
AU  - Lagier JC
AU  - Million M
AU  - Leroy Q
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 6: 346-355.

PMID- 23408786
VI  - 7
DP  - 2012
TI  - Non-contiguous finished genome sequence and description of Brevibacterium senegalense sp. nov.
PG  - 233-245
AB  - Brevibacterium senegalense strain JC43(T) sp. nov. is the type strain of Brevibacterium
      senegalense sp. nov., a new species within the Brevibacterium
      genus. This strain, whose genome is described here, was isolated from the fecal
      flora of a healthy Senegalese patient. B. senegalense is an aerobic rod-shaped
      Gram-positive bacterium. Here we describe the features of this organism, together
      with the complete genome sequence and annotation. The 3,425,960 bp long genome (1
      chromosome but no plasmid) contains 3,064 protein-coding and 49 RNA genes.
AU  - Kokcha S
AU  - Ramasamy D
AU  - Lagier JC
AU  - Robert C
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 7: 233-245.

PMID- 24652980
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Clostridium pasteurianum NRRL B-598, a Potential Butanol or Hydrogen Producer.
PG  - e00192-14
AB  - We present a draft genome sequence of Clostridium pasteurianum NRRL B-598. This strain
      ferments saccharides by two-stage acetone-butanol (AB) fermentation, is
      oxygen tolerant, and has high hydrogen yields.
AU  - Kolek J
AU  - Sedlar K
AU  - Provaznik I
AU  - Patakova P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00192-14.

PMID- 6271579
VI  - 132
DP  - 1981
TI  - Relaxed specificity of endonuclease BamHI as determined by identification of recognition sites in SV40 and pBR322 DNAs.
PG  - 101-104
AB  - The specificity of restriction nucleases, which is very high under conventional
      conditions, may become 'relaxed' in certain media (e.g., at decreased ionic
      strength, in the presence of organic solvents).  The 'condition-relaxed'
      recognition sites usually correspond to shortened or degenerate sequences
      derived from the 'canonic' ones.  The reasons for relaxation are unclear,
      although they are of great interest for understanding the mechanism of
      restriction nuclease action in general.  Up to now, the structure of 'relaxed'
      sites has been determined for only 3 endonucleases: EcoRI, Bsu1, BstI.  This
      communication is concerned with the determination of the structure of 'relaxed'
      restriction sites for the endonuclease BamHI.  These sites in SV40 and pBR322
      DNAs appeared to be GGATC and GPuATCC (cf. canonic site GGATCC).
AU  - Kolesnikov VA
AU  - Zinovev VV
AU  - Yashina LN
AU  - Karginov VA
AU  - Baclanov MM
AU  - Malygin EG
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1981 132: 101-104.

PMID- 9929881
VI  - 32
DP  - 1998
TI  - Interaction of endonuclease EcoRI with short specific and nonspecific oligonucleotides.
PG  - 1025-1033
AB  - 
AU  - Kolocheva TI
AU  - Demidov SA
AU  - Maksakova GA
AU  - Nevinskii GA
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1998 32: 1025-1033.

PMID- 11547921
VI  - 51
DP  - 2001
TI  - Interaction of endonuclease EcoRI with short specific and nonspecific oligonucleotides.
PG  - 189-195
AB  - The interaction of EcoRI with different oligodeoxyribonucleotides (ODNs) was analyzed using
      the method of the slow step-by-step simplification in their complexity. Orthophosphate (KI =
      31 mM), 2-deoxyribose 5-phosphate (KI = 4.6 mM) and different dNMPs (KI = 2.1-2.5 mM) were
      shown to be the minimal ligands of the enzyme. The lengthening of a nonspecific d(pN)n (n =
      1-6) by one nucleotide unit resulted in the increase of their affinity by a factor of
      approximately 2.0. Weak nonspecific electrostatic contacts of EcoRI with internucleotide
      phosphate groups of ODNs can account for about 5 orders of magnitude in the ligand affinity,
      whereas the contribution of specific interactions between EcoRI and d(pN)n is no more than 2
      orders of magnitude of a total ODN's affinity.
AU  - Kolocheva TI
AU  - Maksakova GA
AU  - Bugreev DD
AU  - Nevinsky GA
PT  - Journal Article
TA  - Life
JT  - Life
SO  - Life 2001 51: 189-195.

PMID- 22965088
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Flavobacterium sp. Strain F52, Isolated from the Rhizosphere of Bell Pepper (Capsicum annuum L. cv. Maccabi).
PG  - 5462-5463
AB  - Here we report the draft genome sequence of Flavobacterium sp. strain F52, isolated from the
      rhizosphere of bell pepper (Capsicum annuum L. cv. Maccabi).
      Flavobacterium spp. are ubiquitous in the rhizospheres of agricultural crops;
      however, little is known about their physiology. To our knowledge, this is the
      first published genome of a root-associated Flavobacterium strain.
AU  - Kolton M
AU  - Green SJ
AU  - Harel YM
AU  - Sela N
AU  - Elad Y
AU  - Cytryn E
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5462-5463.

PMID- Not carried by PubMed...
VI  - 19
DP  - 1991
TI  - Determination of substrate specificity of restriction endonuclease Vha464I.
PG  - 60-61
AB  - The recognition sequence and cleavage point of restriction endonuclease Vha464I have been
      determined as 5'C^TTAAG.
AU  - Kolykhalov AA
AU  - Repin VE
AU  - Fish AM
AU  - Rechkunova NI
AU  - Degtyarev SK
PT  - Journal Article
TA  - Sib. Biol. J.
JT  - Sib. Biol. J.
SO  - Sib. Biol. J. 1991 19: 60-61.

PMID- 27738042
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Marine-Derived Bacillus subtilis TP-B0611, a Producer of Bacilosarcins and Amicoumacins.
PG  - e01134-16
AB  - Here, we report the draft genome sequence of Bacillus subtilis TP-B0611, which produces the
      isocoumarin-type compounds bacilosarcin and amicoumacin. The genome
      encodes three nonribosomal peptide synthetase (NRPS) gene clusters and one hybrid
      polyketide synthase (PKS)/NRPS gene cluster. The hybrid PKS/NRPS gene cluster was
      identified to be responsible for the biosynthesis of bacilosarcins and
      amicoumacins.
AU  - Komaki H
AU  - Hosoyama A
AU  - Ichikawa N
AU  - Igarashi Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01134-16.

PMID- 27795278
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Streptomyces sp. TP-A0874, a Catechoserine Producer.
PG  - e01163-16
AB  - We report the draft genome sequence of Streptomyces sp. TP-A0874 isolated from compost. This
      strain produces catechoserine, a new catecholate-type inhibitor of
      tumor cell invasion. The genome harbors at least six gene clusters for polyketide
      and nonribosomal peptide biosyntheses. The biosynthetic gene cluster for
      catechoserines was identified by bioinformatic analysis.
AU  - Komaki H
AU  - Hosoyama A
AU  - Ichikawa N
AU  - Igarashi Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01163-16.

PMID- 27738040
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Streptomyces sp. SPMA113, a Prajinamide Producer.
PG  - e01126-16
AB  - We report here the draft genome sequence of Streptomyces sp. SPMA113 isolated from soil in
      Thailand. This strain produces a new modified peptide, prajinamide,
      which has adipocyte differentiation activity. The genome harbors at least 30 gene
      clusters for synthases of polyketide and nonribosomal peptide, suggesting its
      potential to produce diverse secondary metabolites.
AU  - Komaki H
AU  - Hosoyama A
AU  - Ichikawa N
AU  - Panbangred W
AU  - Igarashi Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01126-16.

PMID- 28082502
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of an Anicemycin Producer, Streptomyces sp. TP-A0648.
PG  - e01468-16
AB  - We report the draft genome sequence of Streptomyces sp. TP-A0648 isolated from a  leaf of
      Aucuba japonica This strain produces a new tumor cell growth inhibitor
      designated anicemycin. The genome harbors at least 12 biosynthetic gene clusters
      for polyketides and nonribosomal peptides, suggesting the potential to produce
      diverse secondary metabolites.
AU  - Komaki H
AU  - Hosoyama A
AU  - Kimura A
AU  - Ichikawa N
AU  - Igarashi Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01468-16.

PMID- 27738048
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Thermogemmatispora onikobensis NBRC 111776T, an Aerial Mycelium- and Spore-Forming Thermophilic Bacterium Belonging to the Class  Ktedonobacteria.
PG  - e01156-16
AB  - Here, we report the draft genome sequence of Thermogemmatispora onikobensis NBRC  111776T, an
      aerial mycelium- and spore-forming thermophilic bacterium belonging
      to the class Ktedonobacteria The genome contains five biosynthetic gene clusters
      coding for secondary metabolites, such as terpene, thiopeptide, lantipeptide,
      nonribosomal peptide, and lassopeptide, suggesting the potential to produce
      secondary metabolites.
AU  - Komaki H
AU  - Hosoyama A
AU  - Yabe S
AU  - Yokota A
AU  - Uchino Y
AU  - Takano H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01156-16.

PMID- 26450726
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of an Anthracimycin Producer, Streptomyces sp. TP-A0875.
PG  - e01149-15
AB  - Here, we report the draft genome sequence of an anthracimycin producer, Streptomyces sp.
      TP-A0875. The genome contains at least two type I polyketide synthase (PKS) gene clusters, two
      type II PKS gene clusters, and three nonribosomal peptide synthetase gene clusters. The gene
      cluster for anthracimycin biosynthesis was identified based on the PKS domain organization.
AU  - Komaki H
AU  - Ichikawa N
AU  - Hosoyama A
AU  - Fujita N
AU  - Harunari E
AU  - Igarashi Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01149-15.

PMID- 25700394
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Marine-Derived Streptomyces sp. TP-A0873, a Producer of a Pyrrolizidine Alkaloid Bohemamine.
PG  - e00008-15
AB  - Streptomyces sp. TP-A0873, isolated from deep-sea water, produces three different classes of
      secondary metabolites: antimycin, bohemamine, and alkylated butenolides. In order to assess
      the biosynthetic potential of this strain, draft  genome sequencing was carried out. The
      genome contained at least 14 gene clusters for polyketide synthase (PKS) and nonribosomal
      peptide synthetase (NRPS).
AU  - Komaki H
AU  - Ichikawa N
AU  - Hosoyama A
AU  - Fujita N
AU  - Igarashi Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00008-15.

PMID- 26380643
VI  - 10
DP  - 2015
TI  - Draft genome sequence of marine-derived Streptomyces sp. TP-A0598, a producer of  anti-MRSA antibiotic lydicamycins.
PG  - 58
AB  - Streptomyces sp. TP-A0598, isolated from seawater, produces lydicamycin, structurally unique
      type I polyketide bearing two nitrogen-containing five-membered rings, and four congeners
      TPU-0037-A, -B, -C, and -D. We herein report the 8 Mb draft genome sequence of this strain,
      together with classification and features of the organism and generation, annotation and
      analysis of the genome sequence. The genome encodes 7,240 putative ORFs, of which 4,450 ORFs
      were assigned with COG categories. Also, 66 tRNA genes and one rRNA operon were identified.
      The genome contains eight gene clusters involved in the production of polyketides and
      nonribosomal peptides. Among them, a PKS/NRPS gene  cluster was assigned to be responsible for
      lydicamycin biosynthesis and a plausible biosynthetic pathway was proposed on the basis of
      gene function prediction. This genome sequence data will facilitate to probe the potential of
      secondary metabolism in marine-derived Streptomyces.
AU  - Komaki H
AU  - Ichikawa N
AU  - Hosoyama A
AU  - Fujita N
AU  - Igarashi Y
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 58.

PMID- 25013138
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Marine-Derived Actinomycete Nocardiopsis sp. Strain TP-A0876, a Producer of Polyketide Pyrones.
PG  - e00665-14
AB  - Here we report the draft genome sequence of Nocardiopsis sp. strain TP-A0876, isolated from
      marine sediment, which produces polyketide-derived pyrones called
      nocapyrones. The genome contains three polyketide synthase (PKS) gene clusters,
      one of which was proposed to be responsible for nocapyrone biosynthesis. This
      genome sequence will facilitate the study of the potential for secondary
      metabolism in Nocardiopsis strains.
AU  - Komaki H
AU  - Ichikawa N
AU  - Hosoyama A
AU  - Fujita N
AU  - Igarashi Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00665-14.

PMID- 26659684
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Streptomyces sp. TP-A0356, a Producer of Yatakemycin.
PG  - e01446-15
AB  - Here, we report the draft genome sequence of Streptomyces sp. TP-A0356, a producer of a potent
      antitumor antibiotic, yatakemycin, to evaluate potential for
      secondary metabolite production. The genome sequence data suggest the presence of
      at least nine gene clusters for polyketide synthases and nonribosomal peptide
      synthetases in this strain.
AU  - Komaki H
AU  - Ichikawa N
AU  - Hosoyama A
AU  - Fujita N
AU  - Igarashi Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01446-15.

PMID- 26659677
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Nonomuraea sp. TP-A0861, a Producer of Myxochelin A.
PG  - e01430-15
AB  - Nonomuraea sp. TP-A0861 produces the nonribosomal peptide myxochelin A, which is  known as a
      microbial siderophore. Here, we report its draft genome sequence. The
      genome contains at least three nonribosomal peptide synthetase gene clusters, one
      of which is proposed to be responsible for the biosynthesis of myxochelin A.
AU  - Komaki H
AU  - Ichikawa N
AU  - Hosoyama A
AU  - Fujita N
AU  - Igarashi Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01430-15.

PMID- 26659676
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Streptomyces sp. TP-A0871, a Producer of Heronamide C.
PG  - e01429-15
AB  - Streptomyces sp. TP-A0871 produces the polyene macrolactam heronamide C. Here, we report its
      draft genome sequence to get insight into heronamide biosynthesis and
      genome-mining for novel secondary metabolites of polyketide and nonribosomal
      peptide classes. The genome encodes over nine orphan gene clusters for polyketide
      and/or nonribosomal peptide syntheses.
AU  - Komaki H
AU  - Ichikawa N
AU  - Hosoyama A
AU  - Fujita N
AU  - Igarashi Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01429-15.

PMID- 26472848
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Streptomyces sp. TP-A0890, a Producer of FR-900452 and A-74863a.
PG  - e01212-15
AB  - Here, we report the draft genome sequence of Streptomyces sp. TP-A0890, a producer of
      FR-900452 and A-74863a. The genome was found to contain at least eight polyketide synthase and
      nonribosomal peptide synthetase gene clusters. A prediction of gene functions based on the
      sequence similarity allowed us to assign the biosynthetic gene clusters for FR-900452 and
      A-74863a.
AU  - Komaki H
AU  - Ichikawa N
AU  - Hosoyama A
AU  - Fujita N
AU  - Igarashi Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01212-15.

PMID- 26659694
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Linfuranone Producer Microbispora sp. GMKU 363.
PG  - e01471-15
AB  - Here, we report the draft genome sequence of Microbispora sp. GMKU 363, a plant-derived
      actinomycete that produces linfuranone A, a linear polyketide
      modified with a furanone ring possessing adipocyte differentiation inducing
      activity. The biosynthetic gene cluster for linfuranone was identified by
      analyzing polyketide synthase genes in the genome.
AU  - Komaki H
AU  - Ichikawa N
AU  - Hosoyama A
AU  - Fujita N
AU  - Thamchaipenet A
AU  - Igarashi Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01471-15.

PMID- 27795808
VI  - 11
DP  - 2016
TI  - Draft genome sequence of Micromonospora sp. DSW705 and distribution of biosynthetic gene clusters for depsipeptides bearing 4-amino-2,4-pentadienoate in  actinomycetes.
PG  - 84
AB  - Here, we report the draft genome sequence of Micromonospora sp. DSW705 (=NBRC 110037), a
      producer of antitumor cyclic depsipeptides rakicidins A and B,
      together with the features of this strain and generation, annotation, and
      analysis of the genome sequence. The 6.8 Mb genome of Micromonospora sp. DSW705
      encodes 6,219 putative ORFs, of which 4,846 are assigned with COG categories. The
      genome harbors at least three type I polyketide synthase (PKS) gene clusters, one
      nonribosomal peptide synthetase (NRPS) gene clusters, and three hybrid PKS/NRPS
      gene clusters. A hybrid PKS/NRPS gene cluster encoded in scaffold 2 is
      responsible for rakicidin synthesis. DNA database search indicated that the
      biosynthetic gene clusters for depsipeptides bearing 4-amino-2,4-pentadienoate
      are widely present in taxonomically diverse actinomycetes.
AU  - Komaki H
AU  - Ichikawa N
AU  - Hosoyama A
AU  - Hamada M
AU  - Harunari E
AU  - Ishikawa A
AU  - Igarashi Y
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 84.

PMID- 27800124
VI  - 11
DP  - 2016
TI  - Draft genome sequence of Streptomyces sp. TP-A0867, an alchivemycin producer.
PG  - 85
AB  - Streptomyces sp. TP-A0867 (=NBRC 109436) produces structurally complex polyketides designated
      alchivemycins A and B. Here, we report the draft genome
      sequence of this strain together with features of the organism and assembly,
      annotation, and analysis of the genome sequence. The 9.9 Mb genome of
      Streptomyces sp. TP-A0867 encodes 8,385 putative ORFs, of which 7,232 were
      assigned with COG categories. We successfully identified a hybrid polyketide
      synthase (PKS)/ nonribosomal peptide synthetase (NRPS) gene cluster that could be
      responsible for alchivemycin biosynthesis, and propose the biosynthetic pathway.
      The alchivemycin biosynthetic gene cluster is also present in Streptomyces
      rapamycinicus NRRL 5491T, Streptomyces hygroscopicus subsp. hygroscopicus NBRC
      16556, and Streptomyces ascomycinicus NBRC 13981T, which are taxonomically highly
      close to strain TP-A0867. This study shows a representative example that
      distribution of secondary metabolite genes is correlated with evolution within
      the genus Streptomyces.
AU  - Komaki H
AU  - Ichikawa N
AU  - Oguchi A
AU  - Hamada M
AU  - Harunari E
AU  - Kodani S
AU  - Fujita N
AU  - Igarashi Y
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 85.

PMID- 25657283
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Streptomyces albus Strain NBRC 13014T, the Type Species  of the Genus Streptomyces.
PG  - e01527-14
AB  - Streptomyces albus is the type species of the genus Streptomyces. Here, we report the draft
      genome sequence of S. albus strain NBRC 13014(T). The genome contains
      at least seven orphan polyketide synthase and nonribosomal peptide synthetase
      gene clusters. The genome sequence will also serve as a valuable reference for
      Streptomyces taxonomy.
AU  - Komaki H
AU  - Ichikawa N
AU  - Oguchi A
AU  - Hamada M
AU  - Tamura T
AU  - Fujita N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01527-14.

PMID- 25573937
VI  - 3
DP  - 2015
TI  - Draft genome sequences of six type strains of the genus streptacidiphilus.
PG  - e01387-14
AB  - Members of the genus Streptacidiphilus are acidophilic actinomycetes with streptomycete-like
      features. Here, we report the draft genome sequences of the
      type strains of Streptacidiphilus albus, Streptacidiphilus anmyonensis,
      Streptacidiphilus carbonis, Streptacidiphilus jiangxiensis, Streptacidiphilus
      melanogenes, and Streptacidiphilus neutrinimicus. These genome sequences will
      serve as valuable references for understanding their taxonomic relationships,
      genetic characteristics, and potentials for industry.
AU  - Komaki H
AU  - Ichikawa N
AU  - Oguchi A
AU  - Hamada M
AU  - Tamura T
AU  - Fujita N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01387-14.

PMID- 27198007
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Streptomyces hygroscopicus subsp. hygroscopicus NBRC 16556.
PG  - e00139-16
AB  - Here, we report the draft genome sequence of strain NBRC 16556, deposited as Streptomyces
      hygroscopicus subsp. hygroscopicus into the NBRC culture collection.
      An average nucleotide identity analysis confirmed that the taxonomic
      identification is correct. The genome sequence will serve as a valuable reference
      for genome mining to search new secondary metabolites.
AU  - Komaki H
AU  - Ichikawa N
AU  - Oguchi A
AU  - Hamada M
AU  - Tamura T
AU  - Suzuki K
AU  - Fujita N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00139-16.

PMID- 27785333
VI  - 11
DP  - 2016
TI  - Draft genome sequence of Streptomyces sp. MWW064 for elucidating the rakicidin biosynthetic pathway.
PG  - 83
AB  - Streptomyces sp. MWW064 (=NBRC 110611) produces an antitumor cyclic depsipeptide  rakicidin D.
      Here, we report the draft genome sequence of this strain together
      with features of the organism and generation, annotation and analysis of the
      genome sequence. The 7.9 Mb genome of Streptomyces sp. MWW064 encoded 7,135
      putative ORFs, of which 6,044 were assigned with COG categories. The genome
      harbored at least three type I polyketide synthase (PKS) gene clusters, seven
      nonribosomal peptide synthetase (NRPS) gene clusters, and four hybrid PKS/NRPS
      gene clusters, from which a hybrid PKS/NRPS gene cluster responsible for
      rakicidin synthesis was successfully identified. We propose the biosynthetic
      pathway based on bioinformatic analysis, and experimentally proved that the
      pentadienoyl unit in rakicidins is derived from serine and malonate.
AU  - Komaki H
AU  - Ishikawa A
AU  - Ichikawa N
AU  - Hosoyama A
AU  - Hamada M
AU  - Harunari E
AU  - Nihira T
AU  - Panbangred W
AU  - Igarashi Y
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 83.

PMID- 28912306
VI  - 5
DP  - 2017
TI  - Complete Nucleotide Sequence of Klebsiella pneumoniae Bacteriophage vB_KpnM_KpV477.
PG  - e00694-17
AB  - The double-stranded DNA (dsDNA) bacteriophage vB_KpnM_KpV477, with a broad spectrum of lytic
      activity against Klebsiella pneumoniae, including strains of
      capsular serotypes K1, K2, and K57, was isolated from a clinical sample. The
      phage genome comprises 168,272 bp, with a G+C content of 39.3%, and it contains
      275 putative coding sequences (CDSs) and 17 tRNAs.
AU  - Komisarova EV
AU  - Kislichkina AA
AU  - Krasilnikova VM
AU  - Bogun AG
AU  - Fursova NK
AU  - Volozhantsev NV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00694-17.

PMID- 10518607
VI  - 27
DP  - 1999
TI  - PI-PfuI and PI-PfuII, intein-coded homing endonucleases from Pyrococcus furiosus.  I. Purification and identification of the homing-type endonuclease activities.
PG  - 4167-4174
AB  - We screened for proteins with specific binding activity to Holliday junction DNA from the
      hyperthermophilic archaeon Pyrococcus furiosus and found a protein that has specific affinity
      for DNA with a branched structure, like a three-way or four-way junction. The protein was
      identified as one of the two inteins encoded in the gene for ribonucleotide reductase (RNR) by
      gene cloning. These two inteins were spliced out from the precursor protein as polypeptides
      with molecular weights of 53.078 and 43.976 kDa, respectively. The amino acid sequences of
      these inteins have two copies of the LAGLIDADG motif, which is found in the site-specific DNA
      endonucleases. The purified proteins actually cleaved double-stranded DNA with the sequence of
      the intein(-)allele, and, therefore, they were designated PI-PfuI and PI-PfuII. They generate
      a 4 bp 3'-OH overhang with a 5'-phosphate, like other known homing endonucleases originating
      from inteins. The optimal conditions of the DNA cleavage reaction, including temperature, pH,
      and concentrations of KCl and MgCl(2), have been determined. The high affinity for junction
      DNA of PI-PfuI was confirmed using the purified protein.
AU  - Komori K
AU  - Fujita N
AU  - Ichiyanagi K
AU  - Shinagawa H
AU  - Morikawa K
AU  - Ishino Y
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1999 27: 4167-4174.

PMID- 10518608
VI  - 27
DP  - 1999
TI  - PI-PfuI and PI-PfuII, intein-coded homing endonucleases from Pyrococcus furiosus.  II. Characterization of the binding and cleavage abilities by site-directed mutagenesis.
PG  - 4175-4182
AB  - PI-PfuI and PI-PfuII from Pyrococcus furiosus are homing endonucleases, as shown in the
      accompanying paper. These two endonucleases are produced by protein splicing from the
      precursor protein including ribonucleotide reductase (RNR).  We show here that both enzymes
      specifically interact with their substrate DNA and distort the DNA strands by 73 degrees and
      67 degrees, respectively. They have two copies of the amino acid sequence motif LAGLIDADG,
      which is present in the majority of homing endonucleases and provides some of the catalytic
      residues necessary for DNA cleavage activity.  Site-specific mutagenesis studies showed that
      two acidic residues in the motifs, Asp149 and Glu250 in PI-PfuI, and Asp156 and Asp249 in
      PI-PfuII, were critical for catalysis. The third residues of the active site triads, as
      predicted from the structure of PI-SceI, were Asn225 in PI-PfuI and Lys224 in PI-PfuII.
      Substitution of Asn225 in PI-PfuI by Ala did not affect catalysis. The cleavage activity of
      PI-PfuII was 50-fold decreased by the substitution of Ala for Lys224.  The binding affinity of
      the mutant protein for the substrate DNA also decreased 6-fold. The Lys in PI-PfuII may play a
      direct or indirect role in catalysis of the endonuclease activity.
AU  - Komori K
AU  - Ichiyanagi K
AU  - Morikawa K
AU  - Ishino Y
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1999 27: 4175-4182.

PMID- 24710319
VI  - 9
DP  - 2014
TI  - Flexibility of the Linker between the Domains of DNA Methyltransferase SsoII Revealed by Small-Angle X-Ray Scattering: Implications for Transcription Regulation in SsoII Restriction-Modification System.
PG  - e93453
AB  - Cytosine-5)-DNA methyltransferase SsoII (M. SsoII) consists of a methyltransferase domain
      (residues 72-379) and an N-terminal region (residues 1-71) which regulates transcription in
      SsoII restriction-modification system. Small-angle X-ray scattering (SAXS) is employed here to
      study the low resolution structure of M.SsoII and its complex with DNA containing the
      methylation site. The shapes reconstructed ab initio from the SAXS data reveal two distinct
      protein domains of unequal size. The larger domain matches the crystallographic structure of a
      homologous DNA methyltransferase HhaI (M.HhaI), and the cleft in this domain is occupied by
      DNA in the model of the complex reconstructed from the SAXS data. This larger domain can thus
      be identified as the methyltransferase domain whereas the other domain represents the
      N-terminal region. Homology modeling of the M.SsoII structure is performed by using the model
      of M.HhaI for the methyltransferase domain and representing the N-terminal region either as a
      flexible chain of dummy residues or as a rigid structure of a homologous protein (phage 434
      repressor) connected to the methyltransferase domain by a short flexible linker. Both models
      are compatible with the SAXS data and demonstrate high mobility of the N-terminal region. The
      linker flexibility might play an important role in the function of M.SsoII as a transcription
      factor.
AU  - Konarev PV
AU  - Kachalova GS
AU  - Ryazanova AY
AU  - Kubareva EA
AU  - Karyagina AS
AU  - Bartunik HD
AU  - Svergun DI
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2014 9: e93453.

PMID- 710408
VI  - 89
DP  - 1978
TI  - Biochemical characterization of the restriction-modification system of Bacillus sphaericus.
PG  - 523-529
AB  - A type II restriction endonuclease (endo R-Bsp) has been purified from Bacillus
      sphaericus to electrophoretic homogeneity.  The enzyme appears to be a single
      polypeptide chain with a molecular weight of 35000.  Its pH optimum is around
      8.2, it requires 20 mM Mg2+ for optimal activity and it is inhibited by Zn2+.
      The yield of the enzyme is higher than that of any type I restriction
      endonuclease so far reported.  The enzyme also cleaves single-stranded DNA,
      albeit at a slower rate.  It seems likely that single-stranded DNA is cleaved
      at the same sequences as double-stranded DNA.  Bacillus sphaericus also
      contains a modification methylase (meth M-Bsp) which completely protects the
      cell's own DNA against cleavage by its restriction endonuclease.  The methylase
      activity has been partially purified, it copurifies with the nuclease until the
      next to the last step.  The enzyme does not require ATP or Mg2+, it transfers
      the methyl group of S-adenosyl-methionine to cytosine residues of DNA.  As the
      action of this methylase completely protects any DNA from endo R-Bsp cleavage,
      it seems likely that the methylase recognizes and methylates the same sequence
      (dG-dG-dC-dC) as the nuclease.
AU  - Koncz C
AU  - Kiss A
AU  - Venetianer P
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1978 89: 523-529.

PMID- 24723705
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Six Strains of Vibrio parahaemolyticus Isolated from Early Mortality Syndrome/Acute Hepatopancreatic Necrosis Disease Shrimp in Thailand.
PG  - e00221-14
AB  - Some strains of Vibrio parahaemolyticus cause acute hepatopancreatic necrosis disease (AHPND)
      in shrimp. We sequenced 3 AHPND and 3 non-AHPND strains and found that all of them lacked the
      pathogenicity island relevant to human infection. A unique sequence encoding a type IV
      pilus/type IV secretion system was found in 3 AHPND strains.
AU  - Kondo H
AU  - Tinwongger S
AU  - Proespraiwong P
AU  - Mavichak R
AU  - Unajak S
AU  - Nozaki R
AU  - Hirono I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00221-14.

PMID- 26383659
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Non-Vibrio parahaemolyticus Acute Hepatopancreatic Necrosis Disease Strain KC13.17.5, Isolated from Diseased Shrimp in Vietnam.
PG  - e00978-15
AB  - A strain of Vibrio (KC13.17.5) causing acute hepatopancreatic necrosis disease (AHPND) in
      shrimp in northern Vietnam was isolated. Normally, AHPND is caused by  Vibrio
      parahaemolyticus, but the genomic sequence of the strain indicated that it belonged to Vibrio
      harveyi. The sequence data included plasmid-like sequences and putative virulence genes.
AU  - Kondo H
AU  - Van PT
AU  - Dang LT
AU  - Hirono I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00978-15.

PMID- 28818910
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of a Clinical Isolate of Streptococcus mutans Strain HM.
PG  - e00826-17
AB  - We report the draft genome sequence of Streptococcus mutans strain HM isolated from a
      4-year-old girl with infective endocarditis. The genomics information will
      provide information on the genetic diversity and virulence potential of S. mutans
      strain HM.
AU  - Kondo Y
AU  - Nishimata H
AU  - Hidaka K
AU  - Hasuwa T
AU  - Moriuchi H
AU  - Fujiwara T
AU  - Hoshino T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00826-17.

PMID- 28007849
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Streptococcus sp. Strain NPS 308.
PG  - e01349-16
AB  - Streptococcus sp. strain NPS 308, isolated from an 8-year-old girl diagnosed with infective
      endocarditis, likely presents a novel species of Streptococcus Here, we present a complete
      genome sequence of this species, which will contribute to better understanding of the
      pathogenesis of infective endocarditis.
AU  - Kondo Y
AU  - Ogura Y
AU  - Sato K
AU  - Imamura K
AU  - Hoshino T
AU  - Nishiguchi M
AU  - Hasuwa T
AU  - Moriuchi H
AU  - Hayashi T
AU  - Fujiwara T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01349-16.

PMID- 10655607
VI  - 7
DP  - 2000
TI  - The servant with the scissors.
PG  - 99-100
AB  - In 1978, Werner Arber, (Biozentrum der Universitat, Basel, Switzerland), Dan Nathans and
      Hamilton Smith (both at Johns Hopkins University School of Medicine, Baltimore, Maryland, USA)
      were awarded the Nobel Prize in Physiology or Medicine for the discovery of "restriction
      enzymes and their application to problems of molecular genetics".  Almost immediately, the
      application of these enzymes to genetics led to "new and far reaching results".  In fact, it
      is hard to imagine what the biological sciences would look like today without restriction
      maps, cloning and the ability to alter genes at will, to name just a few everyday tools of the
      trade.  But how did this crucial discovery come about?
AU  - Konforti B
PT  - Journal Article
TA  - Nat. Struct. Biol.
JT  - Nat. Struct. Biol.
SO  - Nat. Struct. Biol. 2000 7: 99-100.

PMID- 24265495
VI  - 1
DP  - 2013
TI  - Genome Sequence of Dyella ginsengisoli Strain LA-4, an Efficient Degrader of Aromatic Compounds.
PG  - e00961-13
AB  - Dyella ginsengisoli strain LA-4 can efficiently degrade environmental pollutants  such as
      biphenyl and azo dyes. Here, we present a 4.55-Mb draft genome sequence
      of strain LA-4, which may provide further insights into the molecular mechanism
      in environmental pollution remediation.
AU  - Kong C
AU  - Wang L
AU  - Li P
AU  - Qu Y
AU  - Tang H
AU  - Wang J
AU  - Zhou H
AU  - Ma Q
AU  - Zhou J
AU  - Xu P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00961-13.

PMID- 
VI  - 
DP  - 1998
TI  - Characterization of a new restriction-modification system, the BcgI system of Bacillus coagulans.
PG  - 1-130
AB  - The BcgI and other BcgI-like restriction endonucleases differ from other types of
      endonucleases in that they cleave double-stranded DNA on both sides of their recognition
      sequences to excise a short fragment in the presence of Mg++ and S-adenosylmethionine.  To
      understand the relationship between BcgI-like enzymes and the classic types of enzymes, the
      functional organization and enzymatic properties of BcgI of Bacillus coagulans were analyzed.
      The BcgI restriction-modification system is a bifunctional protein complex which can cleave or
      methylate DNA.  The dual cleavage/methylation activities are dependent on the methylation
      state of its DNA substrate.  BcgI cleaves unmethylated DNA only; however, it methylates
      hemimethylated DNA preferentially.  The 71.6-kDa A subunit of BcgI contains two conserved
      m6A-methyltransferase motifs, which form a hydrophobic pocket for AdoMet.  AdoMet serves as
      allosteric activator for both cleavage and methylation reactions.  By mutational analysis, the
      endonuclease activity of BcgI has been assigned to the amino-terminal half of the A subunit,
      and a putative endonuclease motif, PE...EXK, has also been identified.  Substitutions in the
      endonuclease motif of conserved charged residues by Ala completely abolish DNA cleavage
      activity of BcgI, but have no effect on DNA methylation activity, suggesting this motif is
      most likely the endonuclease active site of BcgI.  While the A subunit serves as the
      restriction/methylation subunit, the 39.2-kDa B subunit is likely to be the specificity
      subunit.  This suggestion is based on the required participation of the B subunit in the
      methyltransferase and endonuclease reactions and its structural similarity with the S subunit
      of type I R-M systems.  The stoichiometry of BcgI R-M system is one S subunit, which
      determines the recognition sequence of substrate DNA, and two RM subunits which cleave (or
      methylate) its substrate bilaterally.  BcgI forms a hexamer of (RM)4S2 in solution.  The
      hexamer contains two functional trimer units of (RM)2S1, and may be capable of interacting
      with two recognition sequences.  Indeed, the BcgI enzyme cleaves DNA substrates containing two
      recognition sequences much more efficiently than substrates containing a single sequence.
AU  - Kong H
PT  - Journal Article
TA  - Ph.D. Thesis, Boston University
JT  - Ph.D. Thesis, Boston University
SO  - Ph.D. Thesis, Boston University 1998 : 1-130.

PMID- 9642063
VI  - 279
DP  - 1998
TI  - Analyzing the functional organization of a novel restriction modification system, the BcgI system.
PG  - 823-832
AB  - BcgI is a novel, multi-subunit, restriction-modification system that differs from all the
      other types of R-M system in its genetic and functional organization.  The holoenzyme contains
      two diferent subunits, BcgI A and BcgI B.  Both are required for endonuclease and
      methyltransferase activities.  Here, we show that the endonuclease activity is mediated by the
      N-terminal portion of the A subunit.  We made this assignment by mutational analysis.  The
      analytic strategy involved three steps.  First, the methyltransferase activity was inactivated
      by site-directed mutagenesis of a conserved methyltransferase motif also found in the A
      subunit.  One of the R+M- mutants could not methylate DNA but was still able to cleave it,
      therefore expression of this mutant gene was lethal to the host.  This lethal phenotype
      allowed the selective isolation of cleavage-deficient mutations in a second round of random
      mutagenesis in this mutant background.  The R- mutations were all located in the N-terminal
      portion of the A subunit.  There are five potential endonuclease motifs within this region.
      Conserved acidic residues in each of these motifs were substituted with alanine by
      site-directed mutagenesis of the wild-type A gene.  The results identified one motif,
      P52E53-(X)12-E66D67K68, as the probable endonuclease active-site.  Further support for this
      assignment was obtained by another round of site-directed mutagenesis directed to residues
      surrounding this motif.  The results showed that DNA cleavage activity was mediated by the
      predicted, conserved residues, and not any of the surrounding non-conserved residues.  One
      mutant protein, BcgI-E53A, with a single amino acid substitution decreased the DNA cleavage
      activity at least 700-fold.  Our present model for the functional organization of BcgI locates
      both endonuclease and methyltransferase domains in the A subunit, with the target recognition
      domain located in the B subunit.
AU  - Kong H
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1998 279: 823-832.

PMID- 2821503
VI  - 15
DP  - 1987
TI  - Isolation and identification of restriction endonuclease BstFI.
PG  - 7205
AB  - BstFI, an isoschizomer of HindIII, has been purified from Bacillus stearothermophilus FH58
      isolated from the soil of the campus of Fudan University. Sequencing data show that the
      cleavage site of BstFI is A/AGCTT, the same as HindIII. 10,000 units BstFI can be obtained
      from each gram wet w. of cells. BstFI is active over a temperature range from 37C to 65C.  The
      optimal temperature for its action is 55C. The optimal pH and ionic concentration of the assay
      buffer for the optimum activity of BstFI is 7.0 -7.5 and 50-100 mM NaCl, respectively.  BstFI
      is very stable during incubation at 45C for as long as 10 hrs., but loses its activity easily
      at 50C.
AU  - Kong H
AU  - Chen Z
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1987 15: 7205.

PMID- 10954588
VI  - 28
DP  - 2000
TI  - Functional analysis of putative restriction-modification system genes in the Helicobacter pylori J99 genome.
PG  - 3216-3223
AB  - Helicobacter pylori is a gram-negative bacterium, which colonizes the gastric mucosa of
      humans and is implicated in a wide range of gastroduodenal diseases. The genomic sequences of
      two H. pylori strains, 26695 and J99, have been published recently. About two dozen potential
      restriction-modification (R-M) systems have been annotated in both genomes, which is far above
      the average number of R-M systems in other sequenced genomes. Here we describe a functional
      analysis of the 16 putative Type II R-M systems in the H. pylori J99 genome. To express
      potentially toxic endonuclease genes, a unique vector was constructed, which features
      repression and antisense transcription as dual control elements. To determine the methylation
      activities of putative DNA methyltransferases, we developed polyclonal antibodies able to
      detect DNA containing N6-methyladenine or N4-methylcytosine. We found that <30% of the
      potential Type II R-M systems in H. pylori J99 strain were fully functional, displaying both
      endonuclease and methyltransferase activities. Helicobacter pylori may maintain a variety of
      functional R-M systems, which are believed to be a primitive bacterial 'immune' system, by
      alternatively turning on/off a subset of numerous R-M systems.
AU  - Kong H
AU  - Lin LF
AU  - Porter N
AU  - Stickel S
AU  - Byrd D
AU  - Posfai J
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2000 28: 3216-3223.

PMID- 2308865
VI  - 18
DP  - 1990
TI  - A new type II restriction endonuclease, BsmAI, from Bacillus stearothermophilus.
PG  - 686
AB  - None
AU  - Kong H
AU  - Morgan RD
AU  - Chen Z
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 686.

PMID- 2339077
VI  - 18
DP  - 1990
TI  - Identification of a new type II restriction endonuclease BsaAI.
PG  - 2832
AB  - None
AU  - Kong H
AU  - Morgan RD
AU  - Chen Z
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 2832.

PMID- 8451198
VI  - 21
DP  - 1993
TI  - A unique restriction endonuclease, BcgI, from Bacillus coagulans.
PG  - 987-991
AB  - We have purified and characterized a new restriction endonuclease, BcgI, which has properties
      unlike those of the three recognized classes of restriction enzymes. BcgI was isolated from
      Bacillus coagulans, and it recognizes the sequence CGAN6TGC. BcgI cleaves double stranded DNA
      on both strands upstream and downstream of the recognition sequence, so that the recognition
      sequence is released as a 34-base pair fragment with 2-base 3'-extensions. Mg++ and
      S-adenosylmethionine are required for cleavage. Sinefungin, a structural analogue of AdoMet
      which generally inhibits methylase activity, can replace AdoMet in the cleavage reaction. The
      apparent binding constant Kapp for AdoMet is about 100 nM, while the Kapp for sinefungin is
      about 500 nM.
AU  - Kong H
AU  - Morgan RD
AU  - Maunus RE
AU  - Schildkraut I
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 987-991.

PMID- 8276869
VI  - 269
DP  - 1994
TI  - Characterization of BcgI, a new kind of restriction-modification system.
PG  - 683-690
AB  - The BcgI restriction enzyme from Bacillus coagulans is unusual in that it cleaves on both
      sides of its recognition site, CGAN6TGC, releasing a fragment that includes the site and
      several bases on each side. We report the organization and nucleotide sequences of the genes
      for the BcgI restriction-modification system and the properties of the proteins that they
      encode. The system comprises two adjacent, similarly oriented genes. The proximal gene, bcgIA,
      codes for a 637-amino acid protein (molecular mass = 71.6 kDa) that resembles certain m6
      A-specific DNA-methyltransferases, particularly those that constitute the modification subunit
      of type I restriction-modification systems. The distal gene bcgIB, codes for a 341-amino acid
      protein (molecular mass = 39.2 kDa) that resembles none of the sequences in the sequence data
      bases. The two genes overlap by several nucleotides. Alone, neither protein restricts or
      modifies DNA, but, together, they form a complex in the proportion A2B that does both. DNA
      binding assays showed that the DNA-protein complex can be formed only in the presence of both
      subunits, suggesting that the association of inactive subunits generates the active BcgI
      enzyme that can bind DNA and then either cleaves or methylates at target site.
AU  - Kong H
AU  - Roemer SE
AU  - Waite-Rees PA
AU  - Benner JS
AU  - Wilson GG
AU  - Nwankwo DO
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1994 269: 683-690.

PMID- 9628365
VI  - 379
DP  - 1998
TI  - Does BcgI, a unique restriction endonuclease, require two recognition sites for cleavage?
PG  - 605-609
AB  - BcgI is a multi-subunit restriction-modification complex.  BcgI prefers pBR322 DNA over pUC19
      in a DNA cleavage reaction. Linearized pBR322 contains two BcgI recognition sites and pUC19
      has only one site.  To test whether two target sites are required for BcgI cleavage, one of
      the two sites in pBR322 was deleted, and as a result pBR322-1 became a poor substrate for
      BcgI.  Conversely, adding a BcgI site to pUC19 makes it a much better substrate for BcgI
      cleavage.  In addition, the BcgI (R-M) complex forms a heterohexamer in solution that is
      capable of interacting with two recognition sites.  Our results suggest that BcgI requires two
      recognition sites for cleavage.
AU  - Kong H
AU  - Smith CL
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1998 379: 605-609.

PMID- 9278491
VI  - 25
DP  - 1997
TI  - Substrate DNA and cofactor regulate the activities of a multi-functional restriction-modification enzyme, BcgI.
PG  - 3687-3692
AB  - The BcgI restriction-modification system consists of two subunits, A and B.  It is a
      bifunctional protein complex which can cleave or methylate DNA.  The regulation of these
      competing activities is determined by the DNA substrates and cofactors.  BcgI is an active
      endonuclease and a poor methyltransferase on unmodified DNA substrates.  In contrast, BcgI is
      an active methyltransferase and an inactive endonuclease on hemimethylated DNA substrates.
      The cleavage and methylation reactions share cofactors.  While BcgI requires Mg2+ and
      S-adenosyl methionine (AdoMet) for DNA cleavage, its methylation reaction requires only AdoMet
      and yet is significantly stimulated by Mg2+.  Site-directed mutagenesis was carried out to
      investigate the relationship between AdoMet binding and BcgI DNA cleavage/methylation
      activities.  Most substitutions of conserved residues forming the AdoMet binding pocket in the
      A subunit abolished both methylation and cleavage activities, indicating that AdoMet binding
      is an early common step required for both cleavage and methylation.  However, one mutation
      (Y439A) abolished only the methylation activity, not the DNA cleavage activity.  This mutant
      protein was purified and its methylation, cleavage and AdoMet binding activities were tested
      in vitro.  BcgI-Y439A had no detectable methylation activity, but it retained 40% of the
      AdoMet binding and DNA cleavage activities.
AU  - Kong H
AU  - Smith CL
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1997 25: 3687-3692.

PMID- 12552800
VI  - 41
DP  - 2001
TI  - The characterization of pJW566 from L. lactis subsp. cremoris W56.
PG  - 542-547
AB  - The plasmid pJW566 was isolated from L. lactis subsp. cremoris W56, one strain for Danish
      chadder mixed starter cultures. The strain containing
      plasmid pJW566 showed resistance against three common phages species
      936, c2 and P335 worldwide. It was found that pJW566 encoded for an
      restriction and modification system, and showed strong resistance to
      phage CHCP412 when it was introduced into the industrial strain L.
      lactis CHCC2281 in milk medium. The endonuclease activity analysis
      indicated that the endonuclease required Mg2+, ATP, and was stimulated
      by AdoMet.
AU  - Kong J
AU  - Gu X
AU  - Ma G
PT  - Journal Article
TA  - Wei Sheng Wu Xue Bao
JT  - Wei Sheng Wu Xue Bao
SO  - Wei Sheng Wu Xue Bao 2001 41: 542-547.

PMID- 26941133
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Pseudomonas syringae pv. lapsa Strain ATCC 10859, Isolated from Infected Wheat.
PG  - e00024-16
AB  - Pseudomonas syringae pv. lapsa is a pathovar of Pseudomonas syringae that can infect wheat.
      The complete genome of P. syringae pv. lapsa strain ATCC 10859
      contains a 5,918,899-bp circular chromosome with 4,973 coding sequences, 16
      rRNAs, 69 tRNAs, and an average GC content of 59.13%. The analysis of this genome
      revealed several gene clusters that are related to pathogenesis and virulence.
AU  - Kong J
AU  - Jiang H
AU  - Li B
AU  - Zhao W
AU  - Li Z
AU  - Zhu S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00024-16.

PMID- 11940153
VI  - 34
DP  - 2002
TI  - The ability of the plasmid-encoded restriction and modification system LlaBIII to protect Lactococcus lactis against bacteriophages.
PG  - 249-253
AB  - Aims: To investigate the potential of the plasmid-encoded restriction and modification (R/M)
      system LlaBIII to protect Lactococcus lactis
      against bacteriophages during milk fermentations.
      Methods and Results: The R/M system LlaBIII on plasmid pJW566 was
      cloned with a chloramphenicol cassette, resulting in plasmid pJK1. When
      introduced into L. lactis strains, pJK1 conferred increased phage
      resistance against the three most common lactococcal phage species 936,
      c2, and P335 and three unclassified industrial phages. The growth of
      the strains in RSM was not affected by the presence of plasmid pJK1.
      Conclusions: The plasmid-encoded R/M system LlaBIII has great
      ability to protect L. lactis strains against bacteriophages in milk
      fermentations.
      Significance and Impact of the Study: This study evaluates the
      ability of the LlaBIII R/M system to function as a phage defence
      mechanism which is an essential step prior to considering utilizing it
      for improving starter cultures.
AU  - Kong J
AU  - Josephsen J
PT  - Journal Article
TA  - Lett. Appl. Microbiol.
JT  - Lett. Appl. Microbiol.
SO  - Lett. Appl. Microbiol. 2002 34: 249-253.

PMID- 12557405
VI  - 42
DP  - 2002
TI  - The resistance conferred by the R/M system LlaBIII against bacteriophages.
PG  - 246-250
AB  - LlaBIII, isolated from the naturally occurring plasmid pJW566 from Lactococcus lactis subsp.
      cremoris W56, encoded a restriction and modification (R/M) system. The plasmid pJK1 carrying
      the R/M system LlaBIII was transformed into L. lactis IL1403 with type I R/M system located on
      chromosome and the strain MG1614(pAW601) with AbiS gene on plasmid pAW601, respectively. The
      transformants obtained showed stacking resistance against bacteriophages. The plasmid pJK1 was
      transformed into industrial strains L. lactis SMQ86 and CHCC2281, the transformants showed the
      EOP of the bacteriophages decreased by 10-3 and 10-5, respectively. The results indicated that
      the R/M system LlaBIII could protect strains from bacteriophages in dairy fermentation.
AU  - Kong J
AU  - Josephsen J
AU  - Ma G-R
PT  - Journal Article
TA  - Wei Sheng Wu Xue Bao
JT  - Wei Sheng Wu Xue Bao
SO  - Wei Sheng Wu Xue Bao 2002 42: 246-250.

PMID- 11910761
VI  - 17
DP  - 2001
TI  - Cloning and structure analysis of a restriction and modification system, LlaBIII from Lactococcus lactis subsp. cremoris W56.
PG  - 663-668
AB  - A 22.4 kb naturally occurring plasmid pJW566, isolated from L. lactis W56, was found to encode
      an R/M system named LlaBIII. The LlaBIII R/M system was isolated on a chloramphenicol
      resistant derivative of plasmid pJW566, resulting in a plasmid pJK1. Subcloning analysis
      showed that the LlaBIII determinant was located on a 5 kb HindIII-Sph I fragment. The fragment
      was sequenced. It contained a single open reading frame (ORF), corresponding to a protein of
      1584 or 1576 aa. In the deduced amino acid sequence seven helicase motifs characteristic of
      endonuclease type I and type III and a conserved catalysis motif X in the R subunits of type I
      R/M systems were located in the N-terminus, followed by four conserved motifs found in DNA
      N6-adenine methyltransferases. The C-terminus of the deduced amino acid sequence showed no
      homology to known R/M systems. Therefore, this polypeptide encoded by LlaBIII is a
      multifunctional protein possessing putative DNA recognition, methylation and restriction
      activities.
AU  - Kong J
AU  - Josephsen J
AU  - Ma GR
PT  - Journal Article
TA  - Sheng Wu Gong Cheng Xue Bao
JT  - Sheng Wu Gong Cheng Xue Bao
SO  - Sheng Wu Gong Cheng Xue Bao 2001 17: 663-668.

PMID- 28705963
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of 1,183 Salmonella Strains from the 100K Pathogen Genome  Project.
PG  - e00518-17
AB  - Salmonella is a common food-associated bacterium that has substantial impact on worldwide
      human health and the global economy. This is the public release of
      1,183 Salmonella draft genome sequences as part of the 100K Pathogen Genome
      Project. These isolates represent global genomic diversity in the Salmonella
      genus.
AU  - Kong N
AU  - Davis M
AU  - Arabyan N
AU  - Huang BC
AU  - Weis AM
AU  - Chen P
AU  - Thao K
AU  - Ng W
AU  - Chin N
AU  - Foutouhi S
AU  - Foutouhi A
AU  - Kaufman J
AU  - Xie Y
AU  - Storey DB
AU  - Weimer BC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00518-17.

PMID- 22952751
VI  - 7
DP  - 2012
TI  - I-PfoP3I: A Novel Nicking HNH Homing Endonuclease Encoded in the Group I Intron of the DNA Polymerase Gene in Phormidium foveolarum Phage Pf-WMP3.
PG  - e43738
AB  - Homing endonucleases encoded in a group I self-splicing intron in a protein-coding gene in
      cyanophage genomes have not been reported, apart
      from some free-standing homing edonucleases. In this study, a nicking
      DNA endonuclease, I-PfoP3I, encoded in a group IA2 intron in the DNA
      polymerase gene of a T7-like cyanophage Pf-WMP3, which infects the
      freshwater cyanobacterium Phormidium foveolarum is described. The
      Pf-WMP3 intron splices efficiently in vivo and self-splices in vitro
      simultaneously during transcription. I-PfoP3I belongs to the HNH family
      with an unconventional C-terminal HNH motif. I-PfoP3I nicks the
      intron-minus Pf-WMP3 DNA polymerase gene more efficiently than the
      Pf-WMP4 DNA polymerase gene that lacks any intervening sequence in
      vitro, indicating the variable capacity of I-PfoP3I. I-PfoP3I cleaves 4
      nt upstream of the intron insertion site on the coding strand of EXON 1
      on both intron-minus Pf-WMP3 and Pf-WMP4 DNA polymerase genes. Using an
      in vitro cleavage assay and scanning deletion mutants of the intronless
      target site, the minimal recognition site was determined to be a 14 bp
      region downstream of the cut site. I-PfoP3I requires Mg2+, Ca2+ or Mn2+
      for nicking activity. Phylogenetic analysis suggests that the intron
      and homing endonuclease gene elements might be inserted in Pf-WMP3
      genome individually after differentiation from Pf-WMP4. To our
      knowledge, this is the first report of the presence of a group I
      self-splicing intron encoding a functional homing endonuclease in a
      protein-coding gene in a cyanophage genome.
AU  - Kong SL
AU  - Liu XY
AU  - Fu LW
AU  - Yu XC
AU  - An CC
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2012 7: e43738.

PMID- 29798912
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Bacillus velezensis PEBA20, a Strain with a Plant Growth-Promoting Effect and Biocontrol Potential.
PG  - e00286-18
AB  - Bacillus velezensis PEBA20 is a poplar endophyte with biocontrol activities and plant
      growth-promoting effects. The genome of B. velezensis PEBA20 was sequenced
      and the draft genome assembled, with a length of 4,249,176 bp and 4,487 genes.
AU  - Kong WJ
AU  - Yan YC
AU  - Li XY
AU  - Liu ZY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00286-18.

PMID- 28729264
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Burkholderia stabilis FERMP-21014.
PG  - e00636-17
AB  - Cholesterol esterase (EC 3.1.1.13) was identified in a bacterium, Burkholderia stabilis strain
      FERMP-21014. Here, we report the complete genome sequence of B.
      stabilis FERMP-21014, which has been used in the commercial production of
      cholesterol esterase. The genome sequence information may be useful for improving
      production levels of cholesterol esterase.
AU  - Konishi K
AU  - Kumagai T
AU  - Sakasegawa SI
AU  - Tamura T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00636-17.

PMID- 18580971
VI  - 2
DP  - 2008
TI  - Genomic patterns of recombination, clonal divergence and environment in marine microbial populations.
PG  - 1052-1065
AB  - Microorganisms represent the largest reservoir of biodiversity on Earth,
      both in numbers and total genetic diversity, but it remains unclear
      whether this biodiversity is organized in discrete units that correspond
      to ecologically coherent species. To further explore this question, we
      examined patterns of genomic diversity in sympatric microbial populations.
      Analyses of a total of approximately 200 Mb of microbial community genomic
      DNA sequence recovered from 4000 m depth in the Pacific Ocean revealed
      discrete sequence-defined populations of Bacteria and Archaea, with
      intrapopulation genomic sequence divergence ranging from approximately 1%
      to approximately 6%. The populations appeared to be maintained, at least
      in part, by intrapopulation genetic exchange (homologous recombination),
      although the frequency of recombination was estimated to be about three
      times lower than that observed previously in thermoacidophilic archaeal
      biofilm populations. Furthermore, the genotypes of a given population were
      clearly distinguishable from their closest co-occurring relatives based on
      their relative abundance in situ. The genetic distinctiveness and the
      matching sympatric abundances imply that these genotypes share similar
      ecophysiological properties, and therefore may represent fundamental units
      of microbial diversity in the deep sea. Comparisons to surface-dwelling
      relatives of the Sargasso Sea revealed that distinct sequence-based
      clusters were not always detectable, presumably due to environmental
      variations, further underscoring the important relationship between
      environmental contexts and genetic mechanisms, which together shape and
      sustain microbial population structure.
AU  - Konstantinidis KT
AU  - DeLong EF
PT  - Journal Article
TA  - ISME J.
JT  - ISME J.
SO  - ISME J. 2008 2: 1052-1065.

PMID- 23209255
VI  - 194
DP  - 2012
TI  - Revised Sequence and Annotation of the Rhodobacter sphaeroides 2.4.1 Genome.
PG  - 7016-7017
AB  - The DNA sequences of chromosomes I and II of Rhodobacter sphaeroides strain 2.4.1 have been
      revised, and the annotation of the entire genomic sequence, including
      both chromosomes and the five plasmids, has been updated. Errors in the
      originally published sequence have been corrected, and approximately 11% of the
      coding regions in the original sequence have been affected by the revised
      annotation.
AU  - Kontur WS
AU  - Schackwitz WS
AU  - Ivanova N
AU  - Martin J
AU  - Labutti K
AU  - Deshpande S
AU  - Tice HN
AU  - Pennacchio C
AU  - Sodergren E
AU  - Weinstock GM
AU  - Noguera DR
AU  - Donohue TJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 7016-7017.

PMID- 24903870
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Pseudomonas sp. Strain Ant30-3, a Psychrotolerant Bacterium with Biodegradative Attribute Isolated from Antarctica.
PG  - e00522-14
AB  - Pseudomonas sp. strain Ant30-3, isolated from fuel-contaminated Antarctic soil, exhibited
      distinctive psychrotolerant attributes and the potential for degrading
      aromatic hydrocarbon compounds at cold temperatures. We report here the 6.14-Mb
      draft genome of Ant30-3, which will provide insights into the genomic basis for
      the psychrotolerant and biodegradative properties of this bacterium.
AU  - Koo H
AU  - Basu MK
AU  - Crowley M
AU  - Aislabie J
AU  - Bej AK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00522-14.

PMID- 25103756
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Hymenobacter sp. Strain IS2118, Isolated from a Freshwater Lake in Schirmacher Oasis, Antarctica, Reveals Diverse Genes for  Adaptation to Cold Ecosystems.
PG  - e00739-14
AB  - Hymenobacter sp. IS2118, isolated from a freshwater lake in Schirmacher Oasis, Antarctica,
      produces extracellular polymeric substance (EPS) and manifests
      tolerance to cold, UV radiation (UVR), and oxidative stress. We report the
      5.26-Mb draft genome of strain IS2118, which will help us to understand its
      adaptation and survival mechanisms in Antarctic extreme ecosystems.
AU  - Koo H
AU  - Ptacek T
AU  - Crowley M
AU  - Swain AK
AU  - Osborne JD
AU  - Bej AK
AU  - Andersen DT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00739-14.

PMID- 26798103
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Janthinobacterium sp. Ant5-2-1, Isolated from Proglacial Lake Podprudnoye in the Schirmacher Oasis of East Antarctica.
PG  - e01600-15
AB  - Janthinobacterium sp. Ant5-2-1, isolated from the Schirmacher Oasis of East Antarctica,
      produces a purple-violet pigment, manifests diverse energy metabolism
      abilities, and tolerates cold, ultraviolet radiation, and other environmental
      stressors. We report here the 6.19-Mb draft genome of strain Ant5-2-1, which will
      help understand its survival mechanisms in extreme Antarctic ecosystems.
AU  - Koo H
AU  - Strope BM
AU  - Kim EH
AU  - Shabani AM
AU  - Kumar R
AU  - Crowley MR
AU  - Andersen DT
AU  - Bej AK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01600-15.

PMID- 1336096
VI  - 216
DP  - 1992
TI  - Conferring new cleavage specificities of restriction endonucleses.
PG  - 321-329
AB  - Detailed protocols for Achilles Heel cleavage are presented.
AU  - Koob M
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1992 216: 321-329.

PMID- 1454542
VI  - 20
DP  - 1992
TI  - RecA-AC: single-site cleavage of plasmids and chromosomes at any predetermined restriction site.
PG  - 5831-5836
AB  - We have developed a novel version of the Achilles' Cleavage (AC) reaction in which virtually
      any restriction site on DNA of any size can be converted to a unique cleavage site. We first
      polymerized RecA protein on a synthetic oligodeoxyribonucleotide (oligo) in the presence of a
      nonhydrolyzable ATP analogue to generate oligo:RecA nucleoprotein filaments. These filaments
      were then incubated with plasmid or intact chromosomal DNA from Saccharomyces cerevisiae to
      form stable complexes in the yeast LEU2 gene at the target sequence identical (or
      complementary) to that of the oligo. When HhaII (HinfI) methyltransferase (M.HhaII) was added,
      all of the recognition sites for HhaII with the exception of the one protected by the RecA
      filament were methylated and thus no longer cleaved by the cognate restriction endonuclease
      (HinfI). After inactivation of the RecA and the M.HhaII, HinfI was used to efficiently cleave
      the plasmid or chromosome specifically at the targeted restriction site. Since oligos specific
      for any sequence can be easily synthesized and the other reagents necessary to perform
      RecA-mediated AC (RecA-AC) reactions on both plasmids and intact chromosomes are readily
      available, this procedure can be applied immediately to the precise dissection and analysis of
      genomic DNA from any source and to any other research problem requiring efficient, highly
      specific cleavage of DNA at predetermined sites.
AU  - Koob M
AU  - Burkiewicz A
AU  - Kur J
AU  - Szybalski W
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 5831-5836.

PMID- 2842862
VI  - 241
DP  - 1988
TI  - Conferring operator specificity on restriction endonucleases.
PG  - 1084-1086
AB  - Mapping and manipulation of very large genomes, including the human genome,
      would be facilitated by the availability of a DNA cleavage method with very
      high site specificity.  Therefore, a general method was devised that extends
      the effective recognition sequences well beyond the present 8-base pair limit
      by combining the specificity of the restriction endonuclease with that of
      another sequence-specific protein that binds tightly to DNA.  It was shown that
      the tightly binding lac or lamba repressor protects a restriction site within
      the operator from specific modification methylases, M.HhaI or M.HphI, while all
      other similar sites are methylated and thus rendered uncleavable.  A plasmid
      containing a symmetric lac operator was specifically cleaved by HhaI, only at
      the site within the operator, after M.HhaI methylation in the presence of the
      lac repressor, whereas the remaining 31 HhaI sites on this plasmid were
      methylated and thus not cleaved.  Analogous results were obtained with the
      HaeII site within the lac operator which was similarly protected by the lac
      repressor, and with the HphI site within the phage lambda OL operator, which
      was protected by lambda repressor from M.HphI methylation.
AU  - Koob M
AU  - Grimes E
AU  - Szybalski W
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1988 241: 1084-1086.

PMID- 2854805
VI  - 74
DP  - 1988
TI  - Conferring new specificity upon restriction endonucleases by combining repressor-operator interaction and methylation.
PG  - 165-167
AB  - Meeting Abstract
AU  - Koob M
AU  - Grimes E
AU  - Szybalski W
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 165-167.

PMID- Not carried by PubMed...
VI  - 51
DP  - 1991
TI  - Achilles' cleavage:  A general approach for conferring expanded specificities on restriction endonucleases.
PG  - 5161B
AB  - Mapping and manipulation of very large genomes would be facilitated by the
      availability of a DNA cleavage method with a very high site specificity.  I
      have devised a general method for efficiently extending the effective
      recognition sequence of a restriction endonuclease well beyond its natural
      limits.  The key to this process, which I call Achilles' Cleavage (AC), is
      methylation of the DNA substrate in the presence of a DNA-binding molecule that
      forms sequence-specific complexes capable of excluding the methyltransferase
      (MTase).  Cleavable restriction sites remain only at those sites where the
      recognition sites for the cognate restriction enzyme and the DNA-binding
      molecule overlap.  The lac repressor and its ideal, symmetric binding site
      (lacOs), which contains the recognition sites for both HaeII (5'-AGCGCT) and
      HhaI (5'-GCGC), were used as a model system for the development of this
      approach.  Plasmid DNA containing lacOs was methylated by HhaI MTase (M-HhaI)
      in the presence of LacI.  After inactivation of M.HhaI and lacI, HhaI and HaeII
      were used to completely and specifically cleave the plasmid at the lacOs
      sequence.  LacI-mediated AC of a lambda genome containing lacOs produced
      similar results.  In order to test this approach on the large genomes for which
      it was designed, protocols were developed for the efficient methylation and
      digestion of intact chromosomal DNA embedded in agarose microbeads.  Model
      genomes were generated by introducing lacOs into the 4.7-Mb circular genome of
      Escherichia coli and into one of the 16 chromosomes in the 15-Mb genome of
      Saccharomyces cerevisiae.  Subsequent treatment with the AC protocol resulted
      in complete cleavage of these genomes exclusively at the inserted lacOs.  These
      experiments demonstrate the feasibility of using the AC approach to efficiently
      extend the specificity of restriction enzymes and create new tools for the
      mapping precise molecular dissection of multimegabase genomes.
AU  - Koob MD
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1991 51: 5161B.

PMID- 7770912
VI  - 20
DP  - 1995
TI  - A protein splice-junction motif in hedgehog family proteins.
PG  - 141-142
AB  - Protein splicing is a recently discovered, complex post-translational
      modification that includes two concerted proteolytic cleavages and one ligation reaction,
      and produces two distinct, functional proteins from a single polypeptide.  By analogy with
      introns and exons in RNA precursors, the internal protein that is excised from the
      translation product is called an intein, whereas the two terminal portions, when ligated,
      form a fusion protein called extein.  So far, the intein-extein organization has been
      observed in about ten proteins from yeast, bacteria and Archaea; in most of these cases, the
      inteins are inserted within or near nucleotide-binding domains.  Protein splicing is thought
      to be an autocatalytic process, since it can occur in heterologous systems; for example,
      intein-containing proteins from Mycobacterium and Thermococcus have been synthesized
      in Escherichia coli, and protein splicing has been demonstrated with the purified intein-
      containing DNA polymerase from Pyrococcus.
AU  - Koonin EV
PT  - Journal Article
TA  - Trends Biochem. Sci.
JT  - Trends Biochem. Sci.
SO  - Trends Biochem. Sci. 1995 20: 141-142.

PMID- 166680
VI  - 391
DP  - 1975
TI  - A rapid purification method of restriction endonucleases from Haemophilus strains.
PG  - 109-120
AB  - A simple and rapid method of purification of restriction endonucleases from
      different Haemophilus strains is presented.  By this method highly purified and
      stable enzymes can be obtained.  Separation of different restriction activities
      present in the same strain is possible.  This method was so far successfully
      used with Haemophilus influenzae, Haemophilus parainfluenzae and Haemophilus
      aegyptius strains.  The main advantages over previously published procedures
      reside in the simplification of certain purification steps (for instance the
      BioGel A 0.5 M filtration is replaced by a hydroxyapatite batch step),
      elimination of exonuclease activity by fractionation with (NH4)2SO4, separation
      of different restriction activities by phosphocellulose chromatography,
      application of this method to various strains and high purification degree of
      enzymes.
AU  - Kopecka H
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1975 391: 109-120.

PMID- 25502665
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Pseudoalteromonas sp. Strain PLSV, an Ulvan-Degrading Bacterium.
PG  - e01257-14
AB  - We present the draft genome sequence of Pseudoalteromonas sp. strain PLSV, isolated from the
      feces of an Aplysia sea slug. The addition of the PLSV genome
      to the existing genomes of three other ulvan-degrading bacterial species will
      enhance our understanding of ulvan utilization.
AU  - Kopel M
AU  - Helbert W
AU  - Henrissat B
AU  - Doniger T
AU  - Banin E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01257-14.

PMID- 25125644
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Nonlabens ulvanivorans, an Ulvan-Degrading Bacterium.
PG  - e00793-14
AB  - Here we report the draft genome sequence of the bacterium Nonlabens ulvanivorans, which was
      recently isolated. To our knowledge, this is the first published genome
      of a characterized ulvan-degrading bacterium. Revealing the ulvan utilization
      pathways may provide access to a vast marine biomass source that has yet to be
      exploited.
AU  - Kopel M
AU  - Helbert W
AU  - Henrissat B
AU  - Doniger T
AU  - Banin E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00793-14.

PMID- 25342689
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Two Ulvan-Degrading Isolates, Strains LTR and LOR, That Belong to the Alteromonas Genus.
PG  - e01081-14
AB  - Here, we report the draft genome sequence of two ulvan-degrading Alteromonas spp. isolated
      from the feces of the sea slug, Aplysia. These sequenced genomes display
      a unique ulvan degradation machinery compared with ulvanolytic enzymes previously
      identified in Nonlabens ulvanivorans.
AU  - Kopel M
AU  - Helbert W
AU  - Henrissat B
AU  - Doniger T
AU  - Banin E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01081-14.

PMID- 25081267
VI  - 2
DP  - 2014
TI  - Finished Genome Sequence of the Unicellular Cyanobacterium Synechocystis sp. Strain PCC 6714.
PG  - e00757-14
AB  - Synechocystis sp. strain PCC 6714 is a unicellular cyanobacterium closely related to the
      popular model organism Synechocystis sp. strain PCC 6803. A combination of
      PacBio SMRT and Illumina GAIIx data results in a highly accurate finished genome
      sequence that provides a reliable resource for further comparative analyses.
AU  - Kopf M
AU  - Klahn S
AU  - Voss B
AU  - Stuber K
AU  - Huettel B
AU  - Reinhardt R
AU  - Hess WR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00757-14.

PMID- 20616070
VI  - 107
DP  - 2010
TI  - Clostridium ljungdahlii represents a microbial production platform based on syngas.
PG  - 13087-13092
AB  - Clostridium ljungdahlii is an anaerobic homoacetogen, able to ferment
      sugars, other organic compounds, or CO(2)/H(2) and synthesis gas
      (CO/H(2)). The latter feature makes it an interesting microbe for the
      biotech industry, as important bulk chemicals and proteins can be produced
      at the expense of CO(2), thus combining industrial needs with sustained
      reduction of CO and CO(2) in the atmosphere. Sequencing the complete
      genome of C. ljungdahlii revealed that it comprises 4,630,065 bp and is
      one of the largest clostridial genomes known to date. Experimental data
      and in silico comparisons revealed a third mode of anaerobic
      homoacetogenic metabolism. Unlike other organisms such as Moorella
      thermoacetica or Acetobacterium woodii, neither cytochromes nor sodium
      ions are involved in energy generation. Instead, an Rnf system is present,
      by which proton translocation can be performed. An electroporation
      procedure has been developed to transform the organism with plasmids
      bearing heterologous genes for butanol production. Successful expression
      of these genes could be demonstrated, leading to formation of the biofuel.
      Thus, C. ljungdahlii can be used as a unique microbial production platform
      based on synthesis gas and carbon dioxide/hydrogen mixtures.
AU  - Kopke M
AU  - Held C
AU  - Hujer S
AU  - Liesegang H
AU  - Wiezer A
AU  - Wollherr A
AU  - Ehrenreich A
AU  - Liebl W
AU  - Gottschalk G
AU  - Durre P
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2010 107: 13087-13092.

PMID- 6280874
VI  - 28
DP  - 1982
TI  - Partially deficient methylation of cytosine in DNA at CCA/TGG sites stimulates genetic recombination of bacteriophage lambda.
PG  - 531-541
AB  - Lambda bacteriophages grown on arl mutants of Escherichia coli display
      intermediate levels
      of cytosine methylation: less 5-methylcytosine than phages grown on wild-type bacteria but
      more than
      phages grown on dcm mutants, and thus lacking the methylated sequences (Cm5CA/TGG)
      characteristic of E.
      coli K-12 bacteria.  Arl- phages are one twelfth as resistant to EcoRII restriction
      (recognition site CCA/TGG)
      as Arl+ phages, but 40-fold more resistant than Dcm- phages.  Chromatographic analyses
      show the 5-
      methylcytosine content of Arl- DNA to be one third that of Arl+ DNA.  Altered cytosine
      methylation
      frequency correlates with two previously described properties of Arl- phages, increased
      genetic
      recombination and unusual sensitivity of phage DNA to endonuclease S1, which are absent
      in phages grown
      on dcm or dcm arl bacteria.  Methylated/unmethylated heteroduplex DNA prepared in vitro
      (one strand from
      Eco RII-modified phages/one from Dcm- phages) is highly recombinogenic but not S1-
      sensitive.  We
      hypothesize that hemimethylated CCA/TGG sites in Arl- DNA are necessary and sufficient
      for enhanced
      recombination, and necessary but not sufficient for S1 sensitivity.
AU  - Korba BE
AU  - Hays JB
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1982 28: 531-541.

PMID- 3033600
VI  - 15
DP  - 1987
TI  - Cross index for improving cloning selectivity by partially filling in 5'-extensions of DNA produced by type II restriction endonucleases.
PG  - 3199-3220
AB  - A cross index is presented for using the improved selectivity offered by the
      Hung and Wensink (Nucl. Acids Res. 12, 1863-1874, 1984) method of partially
      filling in 5'-extensions produced by type II restriction endonucleases.   After
      this treatment, DNA fragments which normally cannot be ligated to one another,
      can be joined providing that complementary cohesive ends have been generated.
      The uses of this technique, which include the prevention of DNA fragments (both
      vector and insert) auto-annealing, are discussed.
AU  - Korch C
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1987 15: 3199-3220.

PMID- 3024974
VI  - 161
DP  - 1986
TI  - In-vivo-modified gonococcal plasmid pJD1: A model system for analysis of restriction enzyme sensitivity to DNA modifications.
PG  - 519-524
AB  - The 4207-bp cryptic plasmid (pJD1) of Neisseria gonorrhoeae has 5-methylcytosine bases present
      at several positions in the DNA sequence. Fortuitously, these modified bases lie in the
      recognition sequences of many restriction enzymes.  This feature makes the cryptic plasmid a
      model system for assaying the effect of these modified cytosines on the activities of the
      following restriction endonucleases and their isoschizomers: R.AvaII, R.BamHI, R.BglI,
      R.Fnu4HI, R.HaeII, R.HaeIII, R.HhaI, R.HpaII, R.KpnI, R.MspI, R.NaeI, R.NarI, R.NciI, R.NgoI,
      R.NgoII, and R.Sau96I.  Of particular interest was the finding that methylation of one of the
      external cytosines of the palindrome 5'-CCGG-3' prevented its cleavage by R.MspI, but not by
      R.HpaII as had been suggested by Walder et al. [J. Biol. Chem. (1983) 158,1235-1241]. Shows
      HhaI cleaves hemimethylated GCGm5C and BglI cannot cleave 5'GCCNNNNNGGm5C/3'CGGNNNNNCm5CG.
AU  - Korch C
AU  - Hagblom P
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1986 161: 519-524.

PMID- 3918988
VI  - 161
DP  - 1985
TI  - Type III 5-methylcytosine modification of DNA in Neisseria gonorrhoeae.
PG  - 1236-1237
AB  - We present here the first report of a type III methyltransferase that modifies a cytosine,
      Neisseria gonorrhoeae 82409/55(pJD1) modifies the first cytosine on only one strand from the
      5' end of the nonpalindromic sequence: 5'-GGTGA-3' 3'-CCACT-5' m.  We have called this
      modifying activity M.NgoVIII.
      [ The enzyme called NgoVIII in this abstract has been renamed NgoHVIII, Jan/1998. ]
AU  - Korch C
AU  - Hagblom P
AU  - Normark S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1985 161: 1236-1237.

PMID- 6411687
VI  - 155
DP  - 1983
TI  - Sequence-specific DNA modification in Neisseria gonorrhoeae.
PG  - 1324-1332
AB  - Neisseria gonorrhoaea 82409/55(pJD1) is postulated to possess six DNA sequence-specific
      cytosine methyltransferases and one DNA sequence-specific N6-adenine methyltransferase.  From
      the DNA sequencing of the plasmid pJD1 (manuscript in preparation) by a modification of the
      Maxam and Gilbert chemical cleavage procedure, the cytosine methylation specificities were
      demonstrated. Five of these methylating enzymes and their respective specificities are M.NgoI
      (5'-PuGmCGCPy-3'), M.NgoII (5'-GGmCC-3'), M.NgoIV (5'-GmCCGGC-3'), M.NgoV
      (5'-GGNNmCC-3'), and M.NgoVII (5'-GmC(C/G)GC-3').  M.NgoVI (5'-GATC-3') does not
      methylate the cytosine of its recognition sequence, in agreement with a detected adenine
      modification.  A biological implication of these different DNA methylating activities is
      discussed.
      [ The enzyme called M.NgoI in this abstract has been renamed M.NgoHIP, Jan/1998. ]
      [ The enzyme called M.NgoII in this abstract has been renamed M.NgoHIIP, Jan/1998. ]
      [ The enzyme called M.NgoIV in this abstract has been renamed M.NgoHIVP, Jan/1998. ]
      [ The enzyme called M.NgoV in this abstract has been renamed M.NgoHVP, Jan/1998. ]
      [ The enzyme called M.NgoVI in this abstract has been renamed M.NgoHVIP, Jan/1998. ]
      [ The enzyme called M.NgoVII in this abstract has been renamed M.NgoHVIIP, Jan/1998. ]
AU  - Korch C
AU  - Hagblom P
AU  - Normark S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1983 155: 1324-1332.

PMID- 24034426
VI  - 14
DP  - 2013
TI  - Reducing assembly complexity of microbial genomes with single-molecule sequencing.
PG  - R101
AB  - BACKGROUND: The short reads output by first- and second-generation DNA sequencing instruments
      cannot completely reconstruct microbial chromosomes. Therefore, most
      genomes have been left unfinished due to the significant resources required to
      manually close gaps in draft assemblies. Third-generation, single-molecule
      sequencing addresses this problem by greatly increasing sequencing read length,
      which simplifies the assembly problem. RESULTS: To measure the benefit of
      single-molecule sequencing on microbial genome assembly, we sequenced and
      assembled the genomes of six bacteria and analyzed the repeat complexity of 2,267
      complete bacteria and archaea. Our results indicate that the majority of known
      bacterial and archaeal genomes can be assembled without gaps, at finished-grade
      quality, using a single PacBio RS sequencing library. These single-library
      assemblies are also more accurate than typical short-read assemblies and hybrid
      assemblies of short and long reads. CONCLUSIONS: Automated assembly of long,
      single-molecule sequencing data reduces the cost of microbial finishing to $1,000
      for most genomes, and future advances in this technology are expected to drive
      the cost lower. This is expected to increase the number of completed genomes,
      improve the quality of microbial genome databases, and enable high-fidelity,
      population-scale studies of pan-genomes and chromosomal organization.
AU  - Koren S
AU  - Harhay GP
AU  - Smith TP
AU  - Bono JL
AU  - Harhay DM
AU  - McVey SD
AU  - Radune D
AU  - Bergman NH
AU  - Phillippy AM
PT  - Journal Article
TA  - Genome Biol.
JT  - Genome Biol.
SO  - Genome Biol. 2013 14: R101.

PMID- 22575758
VI  - 22
DP  - 2012
TI  - Going beyond five bases in DNA sequencing.
PG  - 251-261
AB  - DNA sequencing has provided a wealth of information about biological systems, but thus far has
      focused on the four canonical bases, and 5-methylcytosine through
      comparison of the genomic DNA sequence to a transformed four-base sequence
      obtained after treatment with bisulfite. However, numerous other chemical
      modifications to the nucleotides are known to control fundamental life functions,
      influence virulence of pathogens, and are associated with many diseases. These
      modifications cannot be accessed with traditional sequencing methods. In this
      opinion, we highlight several emerging single-molecule sequencing techniques that
      have the potential to directly detect many types of DNA modifications as an
      integral part of the sequencing protocol.
AU  - Korlach J
AU  - Turner SW
PT  - Journal Article
TA  - Curr. Opin. Struct. Biol.
JT  - Curr. Opin. Struct. Biol.
SO  - Curr. Opin. Struct. Biol. 2012 22: 251-261.

PMID- 21705582
VI  - 193
DP  - 2011
TI  - Genome analysis of a Mycoplasma hyorhinis strain derived from a primary human melanoma cell line.
PG  - 4543-4544
AB  - The complete genome of Mycoplasma hyorhinis strain MCLD has been sequenced and annotated. This
      genome differs by inversion of a 14.4kb and 3.7kb
      fragments and a deletion of a 9.9kb fragment from M. hyorhinis strain
      HUB-1, isolated from swine respiratory tract. The genome revealed 778 CDSs
      with a limited number of vlp genes encoding for variable surface
      lipoproteins.
AU  - Kornspan JD
AU  - Lysnyansky I
AU  - Kahan T
AU  - Herrmann R
AU  - Rottem S
AU  - Nir-Paz R
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4543-4544.

PMID- 8992958
VI  - 22
DP  - 1996
TI  - Site-specific endonuclease BcuAI from Bacillus cereus A.
PG  - 528-531
AB  - A new restriction endonuclease was isolated from Bacillus cereus BKM B-814 by means of the
      cell disruption with ultrasonication, ammonium sulfate fractionation of the cell-free extract,
      and chromatography on DEAE-Sepharose to give about 1400 U of the enzyme per gram of cells.
      The enzyme revealed the maximum activity at 30-37oC, pH 7.6-8.2, and 5-10 mM MgCl2 under a
      high ionic strength (50mM Tris-HCl, 100mM NaCl).  The site-specific endonuclease BcuAI was
      found to recognize the 5' G/G(A/T)CC sequence in double-stranded DNA and cleave it as shown
      with the arrow, thus being a true isoschisomer of the AvaII restriction endonuclease.
AU  - Korolev SV
AU  - Samko OT
AU  - Eldarov MA
AU  - Kalugin AA
AU  - Khoroshutina EB
AU  - Omelyanyuk NM
AU  - Sokolov NN
AU  - Skryabin KG
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1996 22: 528-531.

PMID- 9611760
VI  - 0
DP  - 1998
TI  - Isolation and characterization of the specificity of new restriction endonucleases Bsp4009I and AsiI - isoschizomers of BamHI.
PG  - 32-35
AB  - New type II restriction endonucleases AsiI and Bsp4009I are detected in Azotobacter species
      N55 and Bacillus species 4009, respectively.  Purified preparations of the restriction enzymes
      free from interfering nucleases and phosphatases were obtained by column chromatography on
      phosphocellulose and heparin-sepharose (AsiI) and phosphocellulose and DEAE-cellulose
      (Bsp4009I).  The yield of purified AsiI and Bsp4009I was 16 x 10^3 and 8 x 10^3 units per g of
      wet cells, respectively.  The above restriction endonucleases recognize the 5'-G/GATCC-3'
      sequence on double-stranded DNA and cleave it as shown, thus being true isoschizomers of BamHI
      restriction endonuclease.
AU  - Korolev SV
AU  - Sokolov NN
AU  - Rina M
AU  - Eldarov MA
AU  - Omelyanyuk NM
AU  - Markaki M
AU  - Skryabin KG
AU  - Bouriotis V
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1998 0: 32-35.

PMID- 8360620
VI  - 139
DP  - 1993
TI  - Sensitivity of naturally occurring coliphages to type I and type II restriction and modification.
PG  - 1283-1290
AB  - Protection against lethal infections by bacteriophage may seem the most likely role of
      restriction-modification (R-M) systems in bacteria and the reason for their evolution. There
      are, however, phenomena which question this phage-mediated selection hypothesis for the
      maintenance of extant R-M systems. Most prominent among these are the mechanisms phage have to
      avoid or otherwise limit the effects of the restriction endonucleases produced by their host
      bacteria. To evaluate the importance of these antirestriction mechanisms in Escherichia coli,
      we have examined the sensitivity of coliphage from natural and laboratory sources to a series
      of type I and II R-M systems. The results of our study indicate that, in vivo, restriction
      endonucleases have no effect on a substantial fraction of naturally occurring coliphage. The
      absence of restriction sites appears to be the most common reason why these phage are
      unaffected by type II restriction endonucleases, but other antirestriction mechanisms also
      operate. On the other hand, the frequency of naturally occurring coliphage sensitive to
      restriction appears sufficiently great for phage-mediated selection to be a viable hypothesis
      for the maintenance R-M in E. coli and its accessory elements.
AU  - Korona R
AU  - Korona B
AU  - Levin BR
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1993 139: 1283-1290.

PMID- Not included in PubMed...
VI  - 47
DP  - 1993
TI  - Phage-mediated selection and the evolution and maintenance of restriction-modification.
PG  - 556-575
AB  - Restriction-modification (R-M) was discovered because it provides bacteria with immunity to
      phage infection. But, is phage-mediated selection the sole mechanism responsible for the
      evolution and maintenance of these ubiquitous and multiply evolved systems? In an effort to
      answer this question, we have performed experiments with laboratory populations of E. coli and
      phage and computer simulations. We consider two ecological situations whereby phage-mediated
      selection could favor R-M immunity; i) when bacteria with a novel R-M system invade
      communities of phage-sensitive bacteria in which there are one or more species of phage, and
      ii) when bacteria colonize bacterial-free habitats in which phage are present. The results of
      our experiments indicate that in established communities of bacteria and phage, the advantage
      R-M provides an invading population of bacteria is ephemeral. Within short order, mutants
      resistant (refractory) to the phage evolve in the dominant population and subsequently in the
      invading population. The outcome of competition then depends on the relative fitness of the
      resistant states of these bacterial clones, rather than R-M. As a consequence of sequential
      selection for independent mutants, this rapid evolution of resistance occurs even when two and
      three species of phage are present. While in our experiments resistance also evolved when
      bacteria colonized new habitats in which phage were present, a novel R-M system greatly
      augmented the likelihood of their becoming established. We interpret the results of this study
      as support for the hypothesis that the latter, colonization selection, may play an important
      role in the evolution and maintenance of restriction-modification. However, we also see these
      results and other observations we discuss as questioning whether protection against phage is
      the unique biological role of restriction-modification.
AU  - Korona R
AU  - Levin BR
PT  - Journal Article
TA  - Evolution
JT  - Evolution
SO  - Evolution 1993 47: 556-575.

PMID- 24072862
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of the Probiotic Strain Lactobacillus casei (Formerly Lactobacillus paracasei) LOCK919.
PG  - e00758-13
AB  - Lactobacillus casei is usually regarded as a bacterium that lives naturally in the human
      intestinal tract, where it can contribute to host health and
      well-being. We describe here the complete genome sequence of L. casei LOCK919, a
      strain with probiotic properties isolated from child feces. The genome consists
      of a 3.11-Mb chromosome and a 29,768-bp plasmid.
AU  - Koryszewska-Baginska A
AU  - Aleksandrzak-Piekarczyk T
AU  - Bardowski J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00758-13.

PMID- 24558250
VI  - 2
DP  - 2014
TI  - Genome Sequence of the Probiotic Strain Lactobacillus rhamnosus (Formerly Lactobacillus casei) LOCK908.
PG  - e00120-14
AB  - Lactobacillus rhamnosus LOCK908, a patented probiotic strain (Polish patent no. 209987), was
      isolated from the feces of a healthy 6-year-old girl. Here, we
      present the complete genome sequence of LOCK908 and identify genes likely to be
      involved in the biosynthesis of exopolysaccharides (EPSs).
AU  - Koryszewska-Baginska A
AU  - Bardowski J
AU  - Aleksandrzak-Piekarczyk T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00120-14.

PMID- 8983190
VI  - 39
DP  - 1996
TI  - Chromosomal location of three wheat sequences with homology to pollen allergen encoding, DNA replication regulating, and DNA (cytosine-5)-methyltransferase genes in wheat and rye.
PG  - 1213-1215
AB  - Three wheat sequences, shown to be homologous to pollen allergen encoding, DNA replication
      regulating, and DNA (cytosine-5)-methyltransferase genes were localized on chromosomes using
      nullisomic-tetrasomic wheat ('Chinese Spring') and wheat-rye ('Chinese
      Spring'/'Imperial') addition lines.  Whereas the loci for the pollen allergen encoding
      sequence (Tri a III) were shown to be located on homoeologous group 4, the DNA replication
      regulating (Rep) and DNA (cytosine-5)-methyltransferase (Mtase) genes were located to
      homoeologous groups 1 and 7, respectively, of Triticeae.  Chromosomal rearrangements in wheat
      and rye relative to each other are discussed.
AU  - Korzun V
AU  - Balzer HJ
AU  - Balzer A
AU  - Baumlein H
AU  - Borner A
PT  - Journal Article
TA  - Genome
JT  - Genome
SO  - Genome 1996 39: 1213-1215.

PMID- 25367914
VI  - 59
DP  - 2014
TI  - The resistome of Pseudomonas aeruginosa in relationship to phenotypic susceptibility.
PG  - 427-436
AB  - Many clinical isolates of Pseudomonas aeruginosa cause infections that are
      difficult to eradicate due to their resistance to a wide variety of antibiotics.
      Key genetic determinants of resistance were identified through genome sequences
      of 390 clinical isolates of P. aeruginosa, obtained from diverse geographic
      locations collected between 2003 and 2012 and were related to microbiological
      susceptibility data for meropenem, levofloxacin, and amikacin. beta-Lactamases
      and integron cassette arrangements were enriched in the established
      multidrug-resistant lineages of sequence types ST111 (predominantly O12) and
      ST235 (O11). This study demonstrates the utility of next-generation sequencing
      (NGS) in defining relevant resistance elements and highlights the diversity of
      resistance determinants within P. aeruginosa. This information is valuable in
      furthering the design of diagnostics and therapeutics for the treatment of P.
      aeruginosa infections.
AU  - Kos VN
AU  - Deraspe M
AU  - McLaughlin RE
AU  - Whiteaker JD
AU  - Roy PH
AU  - Alm RA
AU  - Corbeil J
AU  - Gardner H
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2014 59: 427-436.

PMID- 23990577
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of a Thermophilic Hydrogenotrophic Methanogen, Methanothermobacter sp. Strain CaT2.
PG  - e00672-13
AB  - We isolated a thermophilic hydrogenotrophic methanogen, Methanothermobacter sp. strain CaT2,
      which is able to aggregate and utilize formate. Here, we report the
      complete genome sequence of this organism.
AU  - Kosaka T
AU  - Toh H
AU  - Toyoda A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00672-13.

PMID- 16352836
VI  - 188
DP  - 2006
TI  - Reconstruction and regulation of the central catabolic pathway in the thermophilic propionate-oxidizing syntroph Pelotomaculum  thermopropionicum.
PG  - 202-210
AB  - Obligate anaerobic bacteria fermenting volatile fatty acids in syntrophic association with
      methanogenic archaea share the intermediate bottleneck
      step in organic-matter decomposition. These organisms (called syntrophs)
      are biologically significant in terms of their growth at the thermodynamic
      limit and are considered to be the ideal model to address bioenergetic
      concepts. We conducted genomic and proteomic analyses of the thermophilic
      propionate-oxidizing syntroph Pelotomaculum thermopropionicum to obtain
      the genetic basis for its central catabolic pathway. Draft sequencing and
      subsequent targeted gap closing identified all genes necessary for
      reconstructing its propionate-oxidizing pathway (i.e., methylmalonyl
      coenzyme A pathway). Characteristics of this pathway include the
      following. (i) The initial two steps are linked to later steps via
      transferases. (ii) Each of the last three steps can be catalyzed by two
      different types of enzymes. It was also revealed that many genes for the
      propionate-oxidizing pathway, except for those for propionate coenzyme A
      transferase and succinate dehydrogenase, were present in an operon-like
      cluster and accompanied by multiple promoter sequences and a putative gene
      for a transcriptional regulator. Proteomic analysis showed that enzymes in
      this pathway were up-regulated when grown on propionate; of these enzymes,
      regulation of fumarase was the most stringent. We discuss this tendency of
      expression regulation based on the genetic organization of the open
      reading frame cluster. Results suggest that fumarase is the central
      metabolic switch controlling the metabolic flow and energy conservation in
      this syntroph.
AU  - Kosaka T
AU  - Uchiyama T
AU  - Ishii S
AU  - Enoki M
AU  - Imachi H
AU  - Kamagata Y
AU  - Ohashi A
AU  - Harada H
AU  - Ikenaga H
AU  - Watanabe K
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2006 188: 202-210.

PMID- 17407166
VI  - 68
DP  - 2007
TI  - A model of restriction endonuclease MvaI in complex with DNA: A template for interpretation of experimental data and a guide for specificity engineering.
PG  - 324-336
AB  - R.MvaI is a Type II restriction enzyme (REase), which specifically recognizes the
      pentanucleotide DNA sequence 5'-CCWGG-3' (W indicates A
      or T). It belongs to a family of enzymes, which recognize related
      sequences, including 5'-CCSGG-3'(S indicates G or C) in the case of
      R.BcnI, or 5'-CCNGG-3' (where N indicates any nucleoside) in the case
      of R.ScrFI. REases from this family hydrolyze the phosphodiester bond
      in the DNA between the 2nd and 3rd base in both strands, thereby
      generating a double strand break with 5'-protruding single nucleotides.
      So far, no crystal structures of REases with similar cleavage patterns
      have been solved. Characterization of sequence-structure-function
      relationships in this family would facilitate understanding of
      evolution of sequence specificity among REases and could aid in
      engineering of enzymes with new specificities. However, sequences of
      R.MvaI or its homologs show no significant similarity to any proteins
      with known structures, thus precluding straightforward comparative
      modeling. We used a fold recognition approach to identify a remote
      relationship between R.MvaI and the structure of DNA repair enzyme
      MutH, which belongs to the PD-(D/E)XK superfamily together with many
      other REases. We constructed a homology model of R.MvaI and used it to
      predict functionally important amino acid residues and the mode of
      interaction with the DNA. In particular, we predict that only one
      active site of R.MvaI interacts with the DNA target at a time, and the
      cleavage of both strands (5'-CCAGG-3' and 5'-CCTGG-3') is achieved by
      two independent catalytic events. The model is in good agreement with
      the available experimental data and will serve as a template for
      further analyses of R.MvaI, R.BcnI, R.ScrFI and other related enzymes.
AU  - Kosinski J
AU  - Kubareva E
AU  - Bujnicki JM
PT  - Journal Article
TA  - Proteins
JT  - Proteins
SO  - Proteins 2007 68: 324-336.

PMID- 23045508
VI  - 194
DP  - 2012
TI  - Genome Sequence of Pectobacterium sp. Strain SCC3193.
PG  - 6004
AB  - We report the complete and annotated genome sequence of the plant-pathogenic enterobacterium
      Pectobacterium sp. strain SCC3193, a model strain isolated from
      potato in Finland. The Pectobacterium sp. SCC3193 genome consists of a 516,411-bp
      chromosome, with no plasmids.
AU  - Koskinen JP
AU  - Laine P
AU  - Niemi O
AU  - Nykyri J
AU  - Harjunpaa H
AU  - Auvinen P
AU  - Paulin L
AU  - Pirhonen M
AU  - Palva T
AU  - Holm L
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6004.

PMID- 26500719
VI  - 10
DP  - 2015
TI  - Complete genome sequence of Propionibacterium freudenreichii DSM 20271(T).
PG  - 83
AB  - Propionibacterium freudenreichii subsp. freudenreichii DSM 20271(T) is the type strain of
      species Propionibacterium freudenreichii that has a long history of
      safe use in the production dairy products and B12 vitamin. P. freudenreichii is
      the type species of the genus Propionibacterium which contains Gram-positive,
      non-motile and non-sporeforming bacteria with a high G + C content. We describe
      the genome of P. freudenreichii subsp. freudenreichii DSM 20271(T) consisting of
      a 2,649,166 bp chromosome containing 2320 protein-coding genes and 50 RNA-only
      encoding genes.
AU  - Koskinen P
AU  - Deptula P
AU  - Smolander OP
AU  - Tamene F
AU  - Kammonen J
AU  - Savijoki K
AU  - Paulin L
AU  - Piironen V
AU  - Auvinen P
AU  - Varmanen P
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 83.

PMID- 2597679
VI  - 1009
DP  - 1989
TI  - Nucleotide sequence of the EcoRII restriction endonuclease gene.
PG  - 290-292
AB  - The nucleotide sequence of a 1394 basepair (bp) DNA fragment containing the EcoRII restriction
      endonuclease (R.EcoRII) gene was determined.  The endonuclease gene is 1206 bp in length
      (predicted 402 amino acids (aa) and Mr=45,178) and is separated by 33 bp from the EcoRII
      modification methylase (M.EcoRII) gene.  The EcoRII restriction-modification system has a
      tail-to-tail organization of the two genes.
AU  - Kossykh V
AU  - Repyk A
AU  - Kaliman A
AU  - Buryanov Y
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1989 1009: 290-292.

PMID- 15028690
VI  - 186
DP  - 2004
TI  - A DNA Adenine Methyltransferase of Escherichia coli That Is Cell Cycle Regulated and Essential for Viability.
PG  - 2061-2067
AB  - DNA sequence analysis revealed that the putative yhdJ DNA methyltransferase gene of
      Escherichia coli is 55% identical to the Nostoc
      sp. strain PCC7120 gene encoding DNA methyltransferase AvaIII, which
      methylates adenine in the recognition sequence, ATGCAT. The yhdJ gene was
      cloned, and the enzyme was overexpressed and purified. Methylation and
      restriction analysis showed that the DNA methyltransferase methylates the
      first adenine in the sequence ATGCAT. This DNA methylation was found to be
      regulated during the cell cycle, and the DNA adenine methyltransferase was
      designated M.EcoKCcrM (for "cell cycle-regulated methyltransferase"). The
      CcrM DNA adenine methyltransferase is required for viability in E. coli,
      as a strain lacking a functional genomic copy of ccrM can be isolated only
      in the presence of an additional copy of ccrM supplied in trans. The cells
      of such a knockout strain stopped growing when expression of the inducible
      plasmid ccrM gene was shut off. Overexpression of M.EcoKCcrM slowed
      bacterial growth, and the ATGCAT sites became fully methylated throughout
      the cell cycle; a high proportion of cells with an anomalous size
      distribution and DNA content was found in this population. Thus, the
      temporal control of this methyltransferase may contribute to accurate cell
      cycle control of cell division and cellular morphology. Homologs of
      M.EcoKCcrM are present in other bacteria belonging to the gamma
      subdivision of the class Proteobacteria, suggesting that methylation at
      ATGCAT sites may have similar functions in other members of this group.
AU  - Kossykh VG
AU  - Lloyd RS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2004 186: 2061-2067.

PMID- 8449414
VI  - 125
DP  - 1993
TI  - Sequence motifs common to the EcoRII restriction endonuclease and the proposed sequence specificity domain of three DNA-[cytosine-C5] methyltransferases.
PG  - 65-68
AB  - We have compared the deduced amino acids (aa) sequences of the EcoRII restriction endonuclease
      (R.EcoRII) and the proposed specificity (target recognition) domains of three
      DNA-[cytosine-C5] methyltransferases (MTases). M.EcoRII, M.Dcm, and M.SPR, each of which
      recognizes the same nucleotide sequence, CCWGG (where W is A or T). We have identified a
      region containing sequence motifs that are partially conserved in the MTases and R.EcoRII.
      This may be the first example of aa sequence homology between a MTase specificity (target
      recognition) domain and its cognate restriction endonuclease (ENase). It suggests that this
      region is important for DNA recognition by R.EcoRII and that the EcoRII ENase and MTase genes
      may have evolved from a common progenitor.
AU  - Kossykh VG
AU  - Repyk AV
AU  - Hattman S
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1993 125: 65-68.

PMID- 7649307
VI  - 370
DP  - 1995
TI  - Function of Pro-185 in the ProCys of conserved motif IV in the EcoRII [cytosine-C5]-DNA methyltransferase.
PG  - 75-77
AB  - ProCys in the conserved sequence motif IV of [cytosine-C5]-DNA methyltransferases is known to
      be part of the catalytic site.  The Cys residue is directly involved in forming a covalent
      bond with the C6 of the target cytosine.  We have found that substitution of Pro-185 with
      either Ala or Ser resulted in a reduced rate of methyl group transfer by the EcoRII DNA
      methyltransferase.  In addition, we observed an increase in the Km for substrate
      S-adenosyl-L-methionine (AdoMet), but a decrease in the Km for substrate DNA.  This is
      reflected in minor changes in kcat/Km for DNA, but in 10- to 100-fold reductions in kcat/Km
      for AdoMet.  This suggests that Pro-185 is important to properly orient the activated cytosine
      and AdoMet for methyl group transfer by direct interaction with AdoMet and indirectly via the
      Cys interaction with cytosine.
AU  - Kossykh VG
AU  - Schlagman SL
AU  - Hattman S
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1995 370: 75-77.

PMID- 16617501
VI  - 21
DP  - 1993
TI  - Conserved sequence motif DPPY in region IV of the phage T4 Dam DNA-[N6-adenine]-methyltransferase is important for S-adenosyl-L-methionine binding.
PG  - 3563-3566
AB  - Comparison of the deduced amino acid sequences of DNA-[N6-adenine]-methyltransferases has
      revealed several conserved regions. All of these enzymes contain a DPPY-motif, or a variant of
      it. By site-directed mutagenesis of a cloned T4 dam gene, we have altered the first proline
      residue in this motif (located in conserved region IV of the T4 Dam-MTase) to alanine or
      threonine. The mutant enzymic forms, P172A and P172T, were overproduced and purified. Kinetic
      studies showed that compared to the wild-type (wt) the two mutant enzymic forms had:(i) an
      increased (6 and 23-fold, respectively) Km for substrate, S-adenosylmethionine (AdoMet) and an
      increased (6 and 23-fold) Ki for product, S-adenosyl-homocysteine (AdoHcy); (ii) a slightly
      reduced (1.5 and 3-fold lower) kcat; (iii) a strongly reduced kcat/Km AdoMet (10 and 80-fold);
      and (iv) the same Km for substrate DNA. Equilibrium dialysis studies showed that the mutant
      enzymes had a reduced (3 and 7-fold lower) Ka for AdoMet; all forms bound two molecules of
      AdoMet. Taken together these data indicate that the P172A and P172T alterations resulted
      primarily in a reduced affinity for AdoMet. This suggests that the DPPY-motif is important for
      AdoMet-binding, and that region IV contains an AdoMet-binding site.
AU  - Kossykh VG
AU  - Schlagman SL
AU  - Hattman S
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 3563-3566.

PMID- 7782299
VI  - 270
DP  - 1995
TI  - Phage T4 DNA [N6-adenine]Methyltransferase.
PG  - 14389-14393
AB  - The bacteriophage T4 dam gene, encoding the Dam DNA [N6-adenine]methyltransferase (MTase), has
      been subcloned into the plasmid expression vector, pJW2. In this construct, designated
      pINT4dam, transcription is from the regulatable phage lambda PR and PL promoters, arranged in
      tandem. A two-step purification scheme using DEAE-cellulose and phosphocellulose columns in
      series, followed by hydroxyapatite chromatography, was developed to purify the enzyme to near
      homogeneity. The yield of purified protein was 2 mg/g of cell paste. The MTase has an s20,w of
      3.0 S and a Stokes radius of 23 Angstroms and exists in solution as a monomer. The Km for the
      methyl donor, S-adenosylmethionine, is 0.1 x 10-6M, and the Km for substrate nonglucosylated,
      unmethylated T4 gt-dam- DNA is 1.1 x 10/-12M. The products of DNA methylation,
      S-adenosyl-L-homocysteine and methylated DNA, are competitive inhibitors of the reaction; Ki
      values of 2.4 x 10/-6M and 4.6 x 10/-12 M, respectively, were observed. T4 Dam methylates the
      palindromic tetranucleotide, GATC, designated the canonical sequence. However, at high
      MTase:DNA ratios, T4 Dam can methylate some noncanonical sequences belonging to GAY (where Y
      represents cytosine or thymine).
AU  - Kossykh VG
AU  - Schlagman SL
AU  - Hattman S
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1995 270: 14389-14393.

PMID- 8233814
VI  - 21
DP  - 1993
TI  - Conserved sequence motif DPPY in region IV of the phage T4 Dam DNA-[N6-adenine]-methyltransferase is important for S-adenosyl-L-methionine binding.
PG  - 4659-4662
AB  - Comparison of the deduced amino acid sequences of DNA-[N6-adenine]-methyltransferases has
      revealed several conserved regions. All of these enzymes contain a DPPY [or closely related]
      motif. By site-directed mutagenesis of a cloned T4 dam gene, we have altered the first proline
      residue in this motif [located in conserved region IV of the T4 Dam-MTase] to alanine or
      threonine. The mutant enzymic forms, P172A and P172T, were overproduced and purified. Kinetic
      studies showed that compared to the wild-type [wt] the two mutant enzymic forms had: (i) an
      increased [5 and 20-fold, respectively] Km for substrate, S-adenosyl-methionine [AdoMet]; (ii)
      a slightly reduced [2 and 4-fold lower] kcat; (iii) a strongly reduced kcat/Km AdoMet [10 and
      100-fold]; and (iv) almost the same Km for substrate DNA. Equilibrium dialysis studies showed
      that the mutant enzymes had a reduced [4 and 9-fold lower] Ka for AdoMet. Taken together these
      data indicate that the p172A and P172T alterations resulted primarily in a reduced affinity
      for AdoMet. This suggests that the DPPY-motif is important for AdoMet-binding, and that region
      IV contains or is part of an AdoMet-binding site.
AU  - Kossykh VG
AU  - Schlagman SL
AU  - Hattman S
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 4659-4662.

PMID- 7607473
VI  - 157
DP  - 1995
TI  - Studies on the function of conserved sequence motifs in the T4 Dam-[N6-adenine] and EcoRII [C5-cytosine] DNA methyltransferases.
PG  - 125-126
AB  - We used site-directed oligodeoxyribonucleotide-mediated mutagenesis and kinetic studies with
      purified wild-type (wt) and mutant proteins to evaluate the role of the conserved sequence
      motifs in two prokaryotic DNA MTases.  We suggest that: (i) the main role of Pro in the
      M.EcoRII PC-motif is to restrict the conformational freedom of Cys and orient it in a manner
      essential for catalysis; (ii) in both M.EcoRII and T4 Dam the FXGXG-motif positions AdoMet
      with respect to the catalytic site; (iii) the DPPY-motif in T4 Dam (region IV) is important
      for AdoMet-binding and may be part of the binding site; and (iv) the RXNXKXXFXXPFK-motif in T4
      Dam (region III) is part of the DNA binding/recognition domain.
AU  - Kossykh VG
AU  - Schlagman SL
AU  - Hattman S
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 125-126.

PMID- 9150219
VI  - 179
DP  - 1997
TI  - Comparative studies of the phage T2 and T4 DNA (N6-adenine) methyltransferases: Amino acid changes that affect catalytic activity.
PG  - 3239-3243
AB  - The bacteriophage T2 and T4 dam genes code for a DNA (N6-adenine) methyltransferase (Mtase).
      Nonglucosylated, hydroxymethylcytosine-containing T2gt- virion DNA has a higher level of
      methylation than T4gt- virion DNA does.  To investigate the basis for this difference, we
      compared the intracellular enzyme levels following phage infection as well as the in vitro
      intrinsic methylation capabilities of purified T2 and T4 Dam Mtases.  Results from Western
      blotting (immunoblotting) showed that the same amounts of MTase protein were produced after
      infection with T2 and T4.  Kinetic analyses with purified homogeneous enzymes showed that the
      two MTases had similar Km values for the methyl donor, S-adenosyl-L-methionine, and for
      substrate DNA.  In contrast, they had different kcat values (two-fold higher for T2 Dam
      MTase).  We suggest that this difference can account for the ability of T2 Dam to methylate
      viral DNA in vivo to a higher level than does T4 Dam.  Since the T2 and T4 MTases differ at
      only three amino acid residues (at positions 20 [T4, Ser; T2, Pro], 26 [T4, Asn; T2, Asp], and
      188 [T4, Asp; T2, Glu]), we have produced hybrid proteins to determine which residue(s) is
      responsible for increased catalytic activity.  The results of these analyses showed that the
      residues at positions 20 and 26 are responsible for the different kcat values of the two
      MTases for both canonical and noncanonical sites.  Moreover, a single substitution of either
      residue 20 or 26 was sufficient to increase the kcat of T4 Dam.
AU  - Kossykh VG
AU  - Schlagman SL
AU  - Hattman S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1997 179: 3239-3243.

PMID- 28453854
VI  - 45
DP  - 2017
TI  - The dynamics of the monomeric restriction endonuclease BcnI during its interaction with DNA.
PG  - 5968-5979
AB  - Endonucleases that generate DNA double strand breaks often employ two independent subunits
      such that the active site from each subunit cuts either DNA strand.
      Restriction enzyme BcnI is a remarkable exception. It binds to the 5-CC/SGG-3
      (where S = C or G, '/' designates the cleavage position) target as a monomer
      forming an asymmetric complex, where a single catalytic center approaches the
      scissile phosphodiester bond in one of DNA strands. Bulk kinetic measurements
      have previously shown that the same BcnI molecule cuts both DNA strands at the
      target site without dissociation from the DNA. Here, we analyse the BcnI DNA
      binding and target recognition steps at the single molecule level. We find, using
      FRET, that BcnI adopts either 'open' or 'closed' conformation in solution. Next,
      we directly demonstrate that BcnI slides over long distances on DNA using 1D
      diffusion and show that sliding is accompanied by occasional jumping events,
      where the enzyme leaves the DNA and rebinds immediately at a distant site.
      Furthermore, we quantify the dynamics of the BcnI interactions with cognate and
      non-cognate DNA, and determine the preferred binding orientation of BcnI to the
      target site. These results provide new insights into the intricate dynamics of
      BcnI-DNA interactions.
AU  - Kostiuk G
AU  - Dikic J
AU  - Schwarz FW
AU  - Sasnauskas G
AU  - Seidel R
AU  - Siksnys V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2017 45: 5968-5979.

PMID- 21227928
VI  - 39
DP  - 2011
TI  - Degenerate sequence recognition by the monomeric restriction enzyme: single mutation converts BcnI into a strand-specific nicking endonuclease.
PG  - 3744-3753
AB  - Unlike orthodox Type II restriction endonucleases that are homodimers and interact with the
      palindromic 4-8-bp DNA sequences, BcnI is a monomer which has a single active site but cuts
      both DNA strands within the 5'-CC downward arrowCGG-3'/3'-GGG downward arrowCC-5' target
      site (' downward arrow' designates the cleavage position). Therefore, after cutting the
      first strand, the BcnI monomer must re-bind to the target site in the opposite orientation;
      but in this case, it runs into a different central base because of the broken symmetry of the
      recognition site. Crystal-structure analysis shows that to accept both the C:G and G:C base
      pairs at the center of its target site, BcnI employs two symmetrically positioned histidines
      H77 and H219 that presumably change their protonation state depending on the binding mode. We
      show here that a single mutation of BcnI H77 or H219 residues restricts the cleavage activity
      of the enzyme to either the 5'-CCCGG-3' or the 5'-CCGGG-3' strand, thereby converting BcnI
      into a strand-specific nicking endonuclease. This is a novel approach for engineering of
      monomeric restriction enzymes into strand-specific nucleases.
AU  - Kostiuk G
AU  - Sasnauskas G
AU  - Tamulaitiene G
AU  - Siksnys V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2011 39: 3744-3753.

PMID- 22843592
VI  - 194
DP  - 2012
TI  - Genome sequences for six rhodanobacter strains, isolated from soils and the terrestrial subsurface, with variable denitrification capabilities.
PG  - 4461-4462
AB  - We report the first genome sequences for six strains of Rhodanobacter species isolated from a
      variety of soil and subsurface environments. Three of these
      strains are capable of complete denitrification and three others are not.
      However, all six strains contain most of the genes required for the respiration
      of nitrate to gaseous nitrogen. The nondenitrifying members of the genus lack
      only the gene for nitrate reduction, the first step in the full denitrification
      pathway. The data suggest that the environmental role of bacteria from the genus
      Rhodanobacter should be reevaluated.
AU  - Kostka JE
AU  - Green SJ
AU  - Rishishwar L
AU  - Prakash O
AU  - Katz LS
AU  - Marino-Ramirez L
AU  - Jordan IK
AU  - Munk C
AU  - Ivanova N
AU  - Mikhailova N
AU  - Watson DB
AU  - Brown SD
AU  - Palumbo AV
AU  - Brooks SC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4461-4462.

PMID- 7819264
VI  - 34
DP  - 1995
TI  - Mg2+ binding to the active site of EcoRV endonuclease: A crystallographic study of complexes with substrate and product DNA at 2 Angstrom resolution.
PG  - 683-696
AB  - The type II restriction endonuclease EcoRV was crystallized as a complex with the substrate
      DNA undecamer AAAGATATCTT. These crystals diffract to much better resolution (2 Angstrom) than
      was the case for the previously reported complex with the decamer GGGATATCCC. The crystal
      structure contains one dimer complex in the asymmetric unit and was solved by molecular
      replacement. The same kinked DNA conformation characteristic for enzyme-bound cognate DNA is
      observed. Crystals, soaked with Mg2+, show the essential cofactor bound at only one active
      site of the dimer, and the DNA is not cleaved. The Mg2+ has one oxygen from the scissile
      phosphodiester group and two carboxylate oxygens, one from Asp74 and one from Asp90, in its
      octahedral ligand sphere. The scissile phosphodiester group is pulled by 1 Angstrom toward the
      Mg2+. After substrate cleavage in solution, isomorphous crystals containing the
      enzyme--product--Mg2+ complex were obtained. In this structure, each of the 5'-phosphate
      groups is bound to two Mg2+. The kinked DNA conformation is essentially maintained, but the
      two central adenines, 3' to the cleavage sites, form an unusual cross-strand base stacking.
      The structures have been refined to R factors of 0.16 at 2.1-2.0 Angstrom resolution
      maintaining very good stereochemistry. On the basis of these structures and inspired by recent
      kinetic data, we have constructed a transition state model with two metals bound to the
      scissile phosphorane group.
AU  - Kostrewa D
AU  - Winkler FK
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1995 34: 683-696.

PMID- 6313222
VI  - 35
DP  - 1983
TI  - A site-specific endonuclease essential for mating-type switching in Saccharomyces cerevisiae.
PG  - 167-174
AB  - We have detected two site-specific endonucleases in strains of Saccharomyces cerevisiae. One
      endonuclease, which we call YZ endo, is present only in yeast strains that are undergoing
      mating-type interconversion. The site at which YZ endo cleaves corresponds to the in vivo
      double-strand break occuring at the mating-type locus in yeast undergoing mating-type
      interconversion. YZ endo generates a site-specific double-strand break having 4-base 3'
      extensions terminating in 3' hydroxyl groups. The site of cleavage occurs in the Z1 region
      near the YZ junction of the mating-type locus. Mutant mating-type loci known to decrease the
      frequency of mating-type interconversion are correspondingly poor substrates for YZ endo in
      vitro. In vitro analysis of a number of such altered recognition sites has delimited the
      sequences required for cleavage. The molecular genetics of mating-type interconversion is
      discussed in the context of this endonucleolytic activity. The second endonuclease, which we
      refer to as SceII, is present in all strains of S. cerevisiae we have examined. The cleavage
      site of SceII has been determined and proves to be unrelated to the cleavage site of YZ endo.
AU  - Kostriken R
AU  - Strathern JN
AU  - Klar AJS
AU  - Hicks JB
AU  - Heffron F
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1983 35: 167-174.

PMID- 344017
VI  - 238
DP  - 1978
TI  - Escherichia coli K-12 plasmid R245 controlling EcoRII restriction and DNA modification.
PG  - 1227-1230
AB  - 
AU  - Kosykh VG
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1978 238: 1227-1230.

PMID- 385263
VI  - 247
DP  - 1979
TI  - Cloning the genes of EcoRII restrictase and methylase.
PG  - 1269-1271
AB  - 
AU  - Kosykh VG
AU  - Buryanov YI
AU  - Baev AA
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1979 247: 1269-1271.

PMID- 6248737
VI  - 178
DP  - 1980
TI  - Molecular Cloning of EcoRII Endonuclease and Methylase Genes.
PG  - 717-718
AB  - The genes for restriction-modification system EcoRII have been cloned from
      plasmid N3 DNA using RSF2124 as a vector plasmid.  The hybrid plasmids
      designated pFK321 and pFK322 contained a 5.8 megadaltons EcoRI - fragment
      derived from N3 DNA including the genes for restriction-modification system
      EcoRII and a gene for resistance to sulfanilamide.
AU  - Kosykh VG
AU  - Buryanov YI
AU  - Bayev AA
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1980 178: 717-718.

PMID- 6288334
VI  - 265
DP  - 1982
TI  - Mapping the EcoRII restrictase and methylase genes on recombinant plasmids.
PG  - 727-730
AB  - None
AU  - Kosykh VG
AU  - Glinskaite IV
AU  - Buryanov JI
AU  - Baev AA
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1982 265: 727-730.

PMID- 3060197
VI  - 53
DP  - 1988
TI  - Purification of the restriction endonuclease EcoRII using monoclonal antibodies.
PG  - 1474-1478
AB  - Hybridomas producing monoclonal antibodies to the restriction endonuclease
      EcoRII were produced after immunization of two BALB/c mice with a preparation
      of the homogeneous enzyme.  The IgG were obtained from ascites fluid, purified,
      and covalently bonded to CNBr-activated Sepharose 4B.  The immunosorbent
      obtained was used for the isolation of the restriction endonuclease EcoRII.
      The isolated restriction endonuclease EcoRII gave one band in polyacrylamide
      gel electrophoresis with sodium sulfate.  The enzyme was obtained in a good
      yield with high specific activity.
AU  - Kosykh VG
AU  - Mantsygin YA
AU  - Svyatukhina NV
AU  - Vitenene IV
AU  - Buryanov YI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1988 53: 1474-1478.

PMID- 6282342
VI  - 47
DP  - 1982
TI  - Isolation, purification and properties of restriction endonuclease EcoRII.
PG  - 619-625
AB  - The restriction endonuclease EcoRII was isolated and purified to homogeneity.  The isolation
      procedure involved the use of the E. coli strain B834/pSK323, containing the recombinant
      plasmid pSK323 which provides for the overproduction of EcoRII enzymes.  Data from gel
      filtration and SDS electrophoresis suggest that the restriction endonuclease EcoRII is a
      protein made up of two subunits, each with molecular weight of 44000.
AU  - Kosykh VG
AU  - Puntezhis SA
AU  - Buryanov YI
AU  - Baev AA
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1982 47: 619-625.

PMID- 2612358
VI  - 308
DP  - 1989
TI  - Primary structure of the restriction endonuclease EcoRII gene.
PG  - 1497-1499
AB  - None
AU  - Kosykh VG
AU  - Repik AV
AU  - Kaliman AV
AU  - Buryanov YI
AU  - Baev AA
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1989 308: 1497-1499.

PMID- 6266480
VI  - 655
DP  - 1981
TI  - Overproduction of the EcoRII endonuclease and methylase by Escherichia coli strains carrying recombinant plasmids constructed in vitro.
PG  - 102-106
AB  - Recombinant DNA molecules were constructed from the plasmid pIL203 and the
      EcoRI-fragment of N3 plasmid containing EcoRII endonuclease and methylase genes
      and also a gene for resistance to sulfanilamide.  The pIL203 plasmid, used as a
      vector, consisted of the BamHI-EcoRI-fragment of the plasmid pBR322 conferring
      resistance to ampicillin and the BamHI-EcoRI-fragment of lambda phage
      containing promoters, a thermosensitive mutation in the cI gene and a
      suppressible amber mutation in the cro gene.
      Ampicillin-sulfanilamide-resistant clones were selected and tested for their
      restriction and modification phenotype.  The recombinant plasmid DNA, isolated
      from ApRSuR-resistant clones, which restricted and modified phage lambda imm21
      with EcoRII specificity, had the EcoRI-fragment with EcoRII genes in a single
      orientation.  The recombinant plasmid pSK323 was transferred into E. coli
      strains with su-, su1, su2 or su3 phenotypes.  The synthesis of products of
      EcoRII genes by these strains grown at 37C is increased by 10-50-fold.
AU  - Kosykh VG
AU  - Solonin AS
AU  - Buryanov YI
AU  - Bayev AA
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1981 655: 102-106.

PMID- 25744998
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of the Opitutaceae Bacterium Strain TAV5, a Potential Facultative Methylotroph of the Wood-Feeding Termite Reticulitermes flavipes.
PG  - e00060-15
AB  - The Opitutaceae bacterium strain TAV5, a member of the phylum Verrucomicrobia, was isolated
      from the wood-feeding termite hindgut. We report here its complete
      genome sequence, which contains a chromosome and a plasmid of 7,317,842 bp and
      99,831 bp, respectively. The genomic analysis reveals genes for methylotrophy,
      lignocellulose degradation, and ammonia and sulfate assimilation.
AU  - Kotak M
AU  - Isanapong J
AU  - Goodwin L
AU  - Bruce D
AU  - Chen A
AU  - Han CS
AU  - Huntemann M
AU  - Ivanova N
AU  - Land ML
AU  - Nolan M
AU  - Pati A
AU  - Woyke T
AU  - Rodrigues JL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00060-15.

PMID- 2170941
VI  - 18
DP  - 1990
TI  - Sse8387I, a new type-II restriction endonuclease that recognizes the octanucleotide sequence 5'-CCTGCAGG-3'.
PG  - 5637-5640
AB  - A type II restriction endonuclease designated Sse8387I was partially purified
      from Streptomyces sp. 8387.  This enzyme cleaved adenovirus 2 DNA at three
      sites, lambda phage DNA at five sites, and pUC18 and M13mp18 RF DNA at one site
      each, but did not cleave the DNAs from pBR322, SV40, or PhiX174.  Sse8387I
      recognized the octanucleotide sequence 5'-CCTGCA^GG-3', cleaving where shown by
      the arrow.  Sse8387I is the first restriction endonuclease to be reported that
      recognizes an octanucleotide sequence consisting of all four nucleotides,
      G,A,T, and C.  The frequency of occurrence of Sse83787I sites within sequenced
      regions of primate genomes was 2.4 times that of NotI sites.
AU  - Kotani H
AU  - Nomura Y
AU  - Kawashima Y
AU  - Sagawa H
AU  - Takagi M
AU  - Kita A
AU  - Ito H
AU  - Kato I
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 5637-5640.

PMID- 24744343
VI  - 2
DP  - 2014
TI  - Genome Sequence of Salt-Tolerant Bacillus safensis Strain VK, Isolated from Saline Desert Area of Gujarat, India.
PG  - e00337-14
AB  - 
AU  - Kothari VV
AU  - Kothari RK
AU  - Kothari CR
AU  - Bhatt VD
AU  - Nathani NM
AU  - Koringa PG
AU  - Joshi CG
AU  - Vyas BR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00337-14.

PMID- 24009116
VI  - 1
DP  - 2013
TI  - Genome Sequence of Salt-Tolerant Bacillus safensis Strain VK, Isolated from Saline Desert Area of Gujarat, India.
PG  - e00671-13
AB  - Bacillus safensis strain VK was isolated from the rhizosphere of a cumin plant growing in the
      saline desert of Radhanpar, Gujarat, India. Here, we provide the
      3.68-Mb draft genome sequence of B. safensis VK, which might provide information
      about the salt tolerance and genes encoding enzymes for the strain's plant
      growth-promoting potential.
AU  - Kothari VV
AU  - Kothari RK
AU  - Kothari CR
AU  - Bhatt VD
AU  - Nathani NM
AU  - Koringa PG
AU  - Joshi CG
AU  - Vyas BR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00671-13.

PMID- 29192080
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Heavy Metal-Resistant Soil Bacterium Serratia marcescens S2I7, Which Has the Ability To Degrade Polyaromatic Hydrocarbons.
PG  - e01338-17
AB  - Serratia marcescens S2I7 is a heavy metal-resistant, polyaromatic hydrocarbon-degrading
      bacterium isolated from petroleum-contaminated sites. The
      genome contains one circular chromosome (5,241,555 bp; GC content 60.1%) with
      4,533 coding sequences. The draft genome sequence includes specific genetic
      elements for degradation of hydrocarbons and for heavy metal resistance.
AU  - Kotoky R
AU  - Singha LP
AU  - Pandey P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01338-17.

PMID- 25428972
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Fish Pathogenic Vibrio vulnificus Biotype 2.
PG  - e01224-14
AB  - Vibrio vulnificus is a marine pathogen capable of causing severe soft tissue infections and
      septicemia in humans. V. vulnificus biotype 2 is the etiological
      agent of fish vibriosis. We describe here the first draft genome sequence of V.
      vulnificus biotype 2, strain ES-7601, isolated from an infected eel in Japan.
AU  - Koton Y
AU  - Eghbaria S
AU  - Gordon M
AU  - Chalifa-Caspi V
AU  - Bisharat N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01224-14.

PMID- 28596403
VI  - 5
DP  - 2017
TI  - Three Draft Genome Sequences of the Bacterial Plant Pathogen Ralstonia solanacearum, Isolated in Georgia.
PG  - e00480-17
AB  - Ralstonia solanacearum, the causative agent of bacterial wilt, is a devastating bacterial
      plant pathogen with a wide range of hosts. We report here the first
      draft genome sequences for three strains of Ralstonia solanacearum isolated from
      infected potato, tomato, and pepper plants in Georgia.
AU  - Kotorashvili A
AU  - Meparishvili G
AU  - Gogoladze G
AU  - Kotaria N
AU  - Muradashvili M
AU  - Zarandia M
AU  - Tsaguria D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00480-17.

PMID- 2836721
VI  - 22
DP  - 1988
TI  - Weakening of the type-I restriction in the presence of plasmids of the incI group. General characteristics and molecular cloning of ard gene.
PG  - 270-276
AB  - Plasmids of the incI group possess the ability to weaken the effect of type-I
      restrictases on unmodified DNA.  The ard locus, which is responsible for weakening of
      type I restriction, is located in plasmid ColIb-P9(incIa) in the region of the Sal GI-C
      fragment.  Cloning was conducted of the ard locus in multicopy vector pBR322.  The ard
      gene specifically weakens type-I restriction (EcoK, EcoB, EcoA, EcoD) and does not
      influence restrictase systems of type II (EcoRI) and III (EcoPI).  Activity of the ard gene
      does not depend on bacterial genes recA, lexA, recBC, recF.  Product of the ard gene does
      not influence the process of methylation of DNA by type-I fragments and is not a specific
      methylase.
AU  - Kotova VY
AU  - Zavilgelskii GB
AU  - Belogurov AA
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1988 22: 270-276.

PMID- 
VI  - 41
DP  - 2007
TI  - Probing of contacts between EcoRII DNA methyltransferase and DNA with the use of substrate analogs and molecular modeling.
PG  - 806-819
AB  - The molecular mechanisms of DNA recognition and modification by EcoRII DNA methyltransferase
      (M.EcoRII) were studied using 14-mer substrate
      analogs containing 2-aminopurine or 1',2'-dideoxy-D-ribofuranose in the
      M.EcoRII recognition site. The efficiency of DNA binding and
      methylation depended on the position of a modified nucleoside residue
      in the recognition site. A structural model of M.EcoRII in complex with
      substrate DNA and the cofactor analog S-adenosyl-L-homocysteine
      (AdoHcy) was constructed using the available crystal structures of
      M.Hha and M.HaeIII and the recent Frankenstein's monster approach. The
      amino acid residues interacting with DNA were predicted based on the
      model. In addition, theoretical and experimental findings made it
      possible to predict the groups of atoms of the heterocyclic bases of
      the M.EcoRII recognition site that are presumably involved in the
      interactions with the enzyme.
AU  - Koudan EV
AU  - Brevnov MG
AU  - Subach OM
AU  - Rechkoblit OA
AU  - Bujnicki JM
AU  - Gromova ES
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2007 41: 806-819.

PMID- 15473707
VI  - 22
DP  - 2004
TI  - Homology modeling of the CG-specific DNA methyltransferase SssI and its complexes with DNA and AdoHcy.
PG  - 339-345
AB  - Prokaryotic DNA methyltransferase M.SssI recognizes and methylates C5 position of the cytosine
      residue within the CG dinucleotides in DNA. It
      is an excellent model for studying the mechanism of interaction between
      CG-specific eukaryotic methyltransferases and DNA. We have built a
      structural model of M.SssI in complex with the substrate DNA and its
      analogues as well as the cofactor analogue S-adenosyl-L-homocysteine
      (AdoHcy) using the previously solved structures of M.HhaI and M.HaeIII
      as templates. The model was constructed according to the recently
      developed "FRankenstein's monster" approach. Based on the model, amino
      acid residues taking part in cofactor binding, target recognition and
      catalysis were predicted. We also modeled covalent modification of the
      DNA substrate and studied its influence on protein-DNA interactions.
AU  - Koudan EV
AU  - Bujnicki JM
AU  - Gromova ES
PT  - Journal Article
TA  - J. Biomol. Struct. Dyn.
JT  - J. Biomol. Struct. Dyn.
SO  - J. Biomol. Struct. Dyn. 2004 22: 339-345.

PMID- 12437380
VI  - 20
DP  - 2002
TI  - DNA duplexes containing photoactive derivatives of 2'-deoxyuridine as photocrosslinking probes for EcoRII DNA methyltransferase-substrate interaction.
PG  - 421-428
AB  - EcoRII DNA methyltransferase (M.EcoRII) recognizes the DNA sequence 5'.CC*T/AGG.3' and
      catalyzes the transfer of the methyl group from S-adenosyl-L-methionine to the C5 position of
      the inner cytosine residue (C*). We obtained several DNA duplexes containing photoactive
      5-iodo-2'-deoxyuridine (i(5)dU) or
      5-[4-(3-(trifluoromethyl)-3H-diazirin-3-yl)phenyl]-2'-deoxyuridine (Tfmdp-dU) to characterize
      regions of M.EcoRII involved in DNA binding and to investigate the DNA double helix
      conformational changes that take place during methylation. The efficiencies of methylation,
      DNA binding affinities and M.EcoRII-DNA photocrosslinking yields strongly depend on the type
      of modification and its location within the EcoRII recognition site. The data obtained agree
      with the flipping of the target cytosine out of the DNA double helix for catalysis. To probe
      regions of M.EcoRII involved in DNA binding, covalent conjugates M.EcoRII-DNA were cleaved by
      cyanogen bromide followed by analysis of the oligonucleotide-peptides obtained. DNA duplexes
      containing i(5)dU or Tfmdp-dU at the central position of the recognition site, or instead of
      the target cytosine were crosslinked to the Gly(268)-Met(391) region of the EcoRII methylase.
      Amino acid residues from this region may take part both in substrate recognition and
      stabilization of the extrahelical target cytosine residue.
AU  - Koudan EV
AU  - Subach OM
AU  - Korshunova GA
AU  - Romanova EA
AU  - Eritja R
AU  - Gromova ES
PT  - Journal Article
TA  - J. Biomol. Struct. Dyn.
JT  - J. Biomol. Struct. Dyn.
SO  - J. Biomol. Struct. Dyn. 2002 20: 421-428.

PMID- 15843599
VI  - 22
DP  - 2005
TI  - Degeneration and domestication of a selfish gene in yeast: Molecular evolution versus site-directed mutagenesis.
PG  - 1535-1538
AB  - VDE is a homing endonuclease gene in yeasts with an unusual evolutionary history including
      horizontal transmission, degeneration, and domestication into the mating-type switching locus
      HO. We investigate here the effects of these features on its molecular evolution. In addition,
      we correlate rates of evolution with results from site-directed mutagenesis studies.
      Functional elements have lower rates of evolution than degenerate ones and higher conservation
      at functionally important sites. However, functionally important and unimportant sites are
      equally likely to have been involved in the evolution of new function during the domestication
      of VDE into HO. The domestication event also indicates that VDE has been lost in some species
      and that VDE has been present in yeasts for more than 50 Myr.
AU  - Koufopanou V
AU  - Burt A
PT  - Journal Article
TA  - Mol. Biol. Evol.
JT  - Mol. Biol. Evol.
SO  - Mol. Biol. Evol. 2005 22: 1535-1538.

PMID- 11861883
VI  - 19
DP  - 2002
TI  - Adaptation for horizontal transfer in a homing endonuclease.
PG  - 239-246
AB  - Selfish genes of no function other than self-propagation are susceptible to degeneration if
      they become fixed in a population, and regular transfer to new species may be the only means
      for their long-term persistence. To test this idea we surveyed 24 species of yeast for VDE, a
      nuclear, intein-associated homing endonuclease gene (HEG) originally discovered in
      Saccharomyces cerevisiae. Phylogenetic analyses show that horizontal transmission has been a
      regular occurrence in its evolutionary history. Moreover, VDE appears to be specifically
      adapted for horizontal transmission. Its 31-bp recognition sequence is an unusually
      well-conserved region in an unusually well-conserved gene. In addition, the nine nucleotide
      sites most critical for homing are also unusually well conserved. Such adaptation for
      horizontal transmission presumably arose as a consequence of selection, both among HEGs at
      different locations in the genome and among variants at the same location. The frequency of
      horizontal transmission must therefore be a key feature constraining the distribution and
      abundance of these genes.
AU  - Koufopanou V
AU  - Goddard MR
AU  - Burt A
PT  - Journal Article
TA  - Mol. Biol. Evol.
JT  - Mol. Biol. Evol.
SO  - Mol. Biol. Evol. 2002 19: 239-246.

PMID- 3156795
VI  - 30
DP  - 1985
TI  - Protection of nonmodified phage lambda against EcoK restriction mediated by recA protein.
PG  - 17-24
AB  - A study was conducted to establish whether the EcoK-specific restriction, which is alleviated
      in E. coli cells after UV induction of the SOS response (Day 1977), is also alleviated under
      the influence of an increased level of recA protein without induction of other SOS functions.
      The host cells used were E. coli K-12, strain AB2497, and its derivatives; the nonmodified
      phage lambda was a mutant b2b5(vir).  An increase of the recA protein level was induced using
      the plasmid pX02, which is a recombinant of pBR322 carrying the recA gene of E. coli.
      AB2497(pX02) cells were found to exhibit a lower level of restriction than those without
      plasmid.  The results indicate that the recA protein protects phage DNA during the process of
      restriction.  A further factor affecting restriction is the growth phase of the culture of the
      restricting host: cells in the late stationary phase exhibit lower restriction than those in
      the exponential phase of growth.  By a combination of these two factors (presence of plasmid
      pX02 and stationary growth phase) one can reduce the restriction of nonmodified phage about
      300 times.
AU  - Koukalova B
AU  - Kuhrova V
AU  - Reich J
PT  - Journal Article
TA  - Folia Microbiol. (Praha)
JT  - Folia Microbiol. (Praha)
SO  - Folia Microbiol. (Praha) 1985 30: 17-24.

PMID- 21742897
VI  - 193
DP  - 2011
TI  - Genome sequence of the ethanol-producing Zymomonas mobilis subsp. pomaceae lectotype strain ATCC 29192.
PG  - 5049-5050
AB  - Zymomonas mobilis is an alphaproteobacterium studied for bioethanol production. Different
      strains of this organism have been hitherto
      sequenced; they all belong to the Z. mobilis subsp. mobilis taxon. Here we
      report the finished and annotated genome sequence of strain ATCC 29192, a
      cider spoiling agent isolated in the United Kingdom. ATCC 29192 is the
      lectotype of the second best characterized subspecies of Z. mobilis, Z.
      mobilis subsp. pomaceae. The nucleotide sequence of ATCC 29192 is more
      deviant from that of mobilis representatives, which justifies its distinct
      taxonomic positioning and proves particularly useful for comparative and
      functional genomics analyses.
AU  - Kouvelis VN
AU  - Davenport KW
AU  - Brettin TS
AU  - Bruce D
AU  - Detter C
AU  - Han C
AU  - Nolan M
AU  - Tapia R
AU  - Damoulaki A
AU  - Kyrpides NC
AU  - Typas MA
AU  - Pappas KM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5049-5050.

PMID- 19767433
VI  - 191
DP  - 2009
TI  - Complete genome sequence of ethanol producer Zymomonas mobilis NCIMB 11163.
PG  - 7140-7141
AB  - Zymomonas mobilis is an ethanol producing alpha-proteobacterium currently considered as major
      candidate organism for bioethanol production. Here we report the finished and annotated genome
      sequence of the Z. mobilis subsp. mobilis strain NCIMB 11163, a British ale infecting isolate.
      This is the first Z. mobilis strain whose genome, chromosomal and plasmid, is presented in its
      entirety.
AU  - Kouvelis VN
AU  - Saunders E
AU  - Brettin TS
AU  - Bruce D
AU  - Detter C
AU  - Han C
AU  - Typas MA
AU  - Pappas KM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2009 191: 7140-7141.

PMID- 24407627
VI  - 2
DP  - 2014
TI  - Finished Genome of Zymomonas mobilis subsp. mobilis Strain CP4, an Applied Ethanol Producer.
PG  - e00845-13
AB  - Zymomonas mobilis subsp. mobilis is one of the most rigorous ethanol-producing organisms known
      to date, considered by many to be the prokaryotic alternative to
      yeast. The two most applied Z. mobilis subsp. mobilis strains, ZM4 and CP4,
      derive from Recife, Brazil, and have been isolated from sugarcane fermentations.
      Of these, ZM4 was the first Z. mobilis representative strain to be sequenced and
      analyzed. Here, we report the finishing of the genome sequence of strain CP4,
      which is highly similar but not identical to that of ZM4.
AU  - Kouvelis VN
AU  - Teshima H
AU  - Bruce D
AU  - Detter C
AU  - Tapia R
AU  - Han C
AU  - Tampakopoulou VO
AU  - Goodwin L
AU  - Woyke T
AU  - Kyrpides NC
AU  - Typas MA
AU  - Pappas KM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00845-13.

PMID- 11483533
VI  - 20
DP  - 2001
TI  - dim-2 encodes a DNA methyltransferase responsible for all known cytosine methylation in Neurospora.
PG  - 4309-4323
AB  - To understand better the control of DNA methylation, we cloned and characterized the dim-2
      gene of Neurospora crassa, the only eukaryotic gene currently known in which mutations appear
      to eliminate DNA methylation. The dim-2 gene is responsible for methylation in both
      symmetrical and asymmetrical sites. We mapped dim-2 between wc-1 and un-10 on linkage group
      (LG) VIIR and identified the gene by RFLP mapping and genetic complementation. Dim-2 encodes a
      1454 amino acid protein including a C-terminal domain homologous to known DNA
      methyltransferases (MTases) and a novel N-terminal domain. Neither a deletion that removed the
      first 186 amino acids of the protein nor a mutation in a putative nucleotide binding site
      abolished function, but a single amino acid substitution in the predicted catalytic site did.
      Tests for repeat-induced point mutation (RIP) indicated that dim-2 does not play a role in
      this process, i.e. duplicated sequences are mutated in dim-2 strains, as usual, but the
      mutated sequences are not methylated, unlike the situation in dim-2(+) strains. We conclude
      that dim-2 encodes an MTase that is responsible for all DNA methylation in vegetative tissues
      of Neurospora.
AU  - Kouzminova E
AU  - Selker EU
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 2001 20: 4309-4323.

PMID- 2848191
VI  - 0
DP  - 1988
TI  - On the restriction endonucleases immobilization.
PG  - 13-15
AB  - The search for optimal variants of restriction endonuclease immobilization was
      begun recently.  For some enzymes immobilization was successful due to the
      presence of covalent bonds on CNBr-sepharose (EcoRI, BamHI, HindIII, TagI,
      PaeI, SalI, PvuII).  For the enzymes EcoRI, BamHI and HindIII it was due to
      hydrophobic interaction with triethyl-agarose (triethyl-triphenylmethane).  The
      high yield (up to 80%) of enzymatic activity has been obtained for small number
      of restriction endonucleases.  In the experiments of several aminoacid residues
      modification and immobilization of restriction endonucleases the participation
      of lysine, arginine, glutamic acid and SH- or S-S-groups in the catalysis and
      (or) binding of these enzymes with DNA has been shown.  The restriction
      endonuclease immobilization experiments and research into the enzyme's active
      centre enrich each other and are very interesting for their use in molecular
      biology and deepening our knowledge of protein-nucleic interactions.
AU  - Kovalenko NA
AU  - Sokolov NN
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1988 0: 13-15.

PMID- 1534987
VI  - 18
DP  - 1992
TI  - Immobilization of restriction endonucleases EcoRI, PaeI and LplI.
PG  - 210-216
AB  - In search for sorbents (silica gels, styrene-divinylbenzene copolymers),for immobilization of
      some restriction endonucleases, derivatives of trityl-containing silochroms are shown to bind
      EcoRI, Pae I and LplI endonuclease with the retention of 10-20, 60-70 and 40-60% activity,
      respectively. The immobilized restriction endonucleases have unchanged substrate specificity,
      can be used several times and are stable during storage. Tritylaminopropylsilochrom is
      suggested to be the sorbent of choice.
AU  - Kovalenko NA
AU  - Sokolov NN
AU  - Chercasova TA
AU  - Vonsky VE
AU  - Leikin YA
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1992 18: 210-216.

PMID- 8350878
VI  - 3
DP  - 1993
TI  - Isolation and properties of the restriction endonuclease BstBSI from the thermophilic soil bacterium Bacillus stearothermophilus BS.
PG  - 22-25
AB  - The discovery at the beginning of the 1970s of site-specific endodeoxyribonucleases, known
      under the name of "restriction endonucleases", which cleave DNA into strictly determined
      fragments, served as the basis for the creation of a number of fundamentally new approaches to
      the analysis of nucleic acid structure and was one of the decisive prerequisites for the birth
      of genetic engineering. These enzymes, which interact highly specifically with DNA, are also
      of great interest in the study of the mechanisms of DNA-protein interactions. At present,
      despite the large assortment of site-specific endonucleases already available, the search for
      them is continuing. The main stimulus for continuing investigations, as before, is the effort
      to supplement the arsenal with enzymes with various substrate specificities and thereby to
      expand the possibilities for experimenters.  In the course of the study of the distribution of
      restriction-modification enzymes in various taxonomic groups of microorganisms, we discovered
      several thermophilic strains of the genus Bacillus that produce specific endonucleases. In
      particular, we reported on a new site-specific endonuclease BstBSI from a soil isolate of B.
      stearothermophilus BS. This work presents data on the purification and characterization of the
      endonuclease BstBSI.
AU  - Kovalevskaya NP
AU  - Ivanov LY
AU  - Zheleznaya A
AU  - Matvienko NI
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1993 3: 22-25.

PMID- 1831259
VI  - 19
DP  - 1991
TI  - BstBSI, a restriction endonuclease from Bacillus stearothermophilus BS which recognizes 5'GTATAC3'.
PG  - 4296
AB  - BstBSI, a type II restriction endonuclease, has been isolated from Bacillus stearothermophilus
      BS.  BstBSI, an isoschizomer of SnaI, recognizes the six base palindromic sequence and cleaves
      it as indicated by arrows:
      5'GTA^TAC3'
      3'CAT^ATG5'.
      BstBSI recognizes three sites on lambda DNA.  Double digestion mapping with BstBSI and EcoRI,
      SmaI, KpnI, MluI and PvuII showed that BstBSI sites were roughly localized to the genome map
      positions 15200, 18900, 19500.  Examination of the sequences of the lambda DNA showed that the
      sequence GTATAC was present in all of these positions.  The cleavage of the T7 DNA results in
      7 visible fragments of more than 1 kb length (upper band is a doublet) of expected molecular
      weights.  To identify the cleavage site within the recognition sequence, the recombinant phage
      M13tg130 with KpnI-SmaI fragment with coordinates 18556-19397 of lambda DNA was constructed.
      It has the BstBSI recognition site nearby the KpnI site.  The cleavage site was determined by
      cleavage of a primed-synthesis reaction.  Cleavage product resulted in a single band
      comigrated with A in the middle of the recognition sequence.  An addition of T4 DNA polymerase
      did not change the position of the band.  These results indicate that the BstBSI cleaves the
      recognition sequence in the middle and produces blunt end fragments.  The molecular weight of
      the native enzyme determined by gel filtration method is approximately 80000.  The crude
      extract contained more than 50000 units per gram of wet cells.
AU  - Kovalevskaya NP
AU  - Ivanov LY
AU  - Zheleznaya LA
AU  - Matvienko NI
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 4296.

PMID- 8285920
VI  - 19
DP  - 1993
TI  - Isolation and properties of the site-specific endonuclease BspTS514I from thermophilic bacterium Bacillus species TS514.
PG  - 1073-1076
AB  - New site-specific endonucleases BspBS31I, BstBS32I, BspIS4I, BstTS5I, BspTS514I were isolated
      from five thermophilic soil bacteria Bacillus sp. BS31, B. stearothermophilus BS32, Bacillus
      sp. IS4, B. stearothermophilus TS5, Bacillus sp. TS514. The enzymes are isoschizomers of the
      restriction endonuclease BbvII. Endonuclease BspTS514I was obtained pure from interfering
      contaminations by two consecutive chromatographies on blue agarose and hydroxyapatite. The
      enzyme exhibits a maximal activity at 55oC in 10 mM tris-HCl (pH 9.2), 10 mM MgCl2 and 50 mM
      NaCl.
AU  - Kovalevskaya NP
AU  - Zelinskaya NV
AU  - Zheleznaya LA
AU  - Matvienko NI
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1993 19: 1073-1076.

PMID- 8022326
VI  - 63
DP  - 1994
TI  - A new thermophilic strain Bacillus coagulans, producing the site-specific endonuclease BcoKI.
PG  - 235-238
AB  - The strain, producing the new site-specific endonuclease BcoKI has been found during the
      screening of thermophilic bacteria isolated from tobacco. A phenotype characteristic of the
      strain is given. It has been identified as a new strain Bacillus coagulans. BcoKI, a class-IIS
      restriction endonuclease has been obtained by three consecutive chromatographies on blue
      agarose, hydroxyapatite and heparin-Sepharose. BcoKI, an isoschizomer of Ksp6321, recognizes
      the six base non-palindromic sequence 5'CTCTTC3' and cleaves one nucleotide 3' of the 3'
      cytosine on this strand and four nucleotides 5' of the 5' guanine on the opposite strand to
      generate a three base 5' overhang.
AU  - Kovalevskaya NP
AU  - Zhelenznaya LA
AU  - Zelinskaya NV
AU  - Matvienko NI
PT  - Journal Article
TA  - Mikrobiologiia
JT  - Mikrobiologiia
SO  - Mikrobiologiia 1994 63: 235-238.

PMID- 1300999
VI  - 18
DP  - 1992
TI  - BspLS21, a new site-specific endonuclease from thermophilic bacterium Bacillus species LS2.
PG  - 1473-1477
AB  - A new restriction endonuclease BspLS2I was isolated from the thermophilic bacterium Bacillus
      species LS2 and purified by blue sepharose and hydroxyapatite chromatographies. The enzyme is
      an isoschizomer of SduI from Streptococcus durans. BspLS2I recognizes the sequence
      5'G(G/A/T)GC(C/T/A)^C3' on double-stranded DNA and cleaves it is indicated by the arrow to
      yield sticky-ended DNA fragments. Maximum catalytic activity of the endonuclease was found in
      10 mM Tris-HCl (pH7.9) in the presence of 15-30 mM MgCl2 at 50oC. The phage T4 glucosylated
      DNA is not cleaved by the enzyme.
AU  - Kovalevskaya NP
AU  - Zheleznaya LA
AU  - Matvienko NI
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1992 18: 1473-1477.

PMID- 10508668
VI  - 3
DP  - 1999
TI  - Type II restriction endonucleases: structural, functional and evolutionary relationships.
PG  - 578-583
AB  - Type II restriction endonucleases are a paradigm for site-specific cleavage of DNA. Recent
      structural analyses, in particular in the presence of various divalent metals, have shed new
      insight into the mechanisms of catalysis. In addition, during this past year the crystal
      structure determinations of MutH, lambda-exonuclease and FokI have revealed that these
      proteins are also members of the same family.
AU  - Kovall RA
AU  - Matthews BW
PT  - Journal Article
TA  - Curr. Opin. Chem. Biol.
JT  - Curr. Opin. Chem. Biol.
SO  - Curr. Opin. Chem. Biol. 1999 3: 578-583.

PMID- 9653111
VI  - 95
DP  - 1998
TI  - Structural, functional, and evolutionary relationships between lambda-exonuclease and the type II restriction endonucleases.
PG  - 7893-7897
AB  - Lambda-exonuclease participates in DNA recombination and repair.  It binds a free end of
      double-stranded DNA and degrades one stand in the 5' to 3' direction.  The primary sequence
      does not appear to be related to any other protein, but the crystal structure shows part of
      lambda-exonuclease to be similar to the type II restriction endonucleases PvuII and EcoRV.
      There is also a weaker correspondence with EcoRI, BamHI, and Cfr10I.  The structure
      comparisons not only suggest that these enzymes all share a similar catalytic mechanism and a
      common structural ancestor but also provide strong evidence that the toroidal structure of
      lambda-exonuclease encircles its DNA substrate during hydrolysis.
AU  - Kovall RA
AU  - Matthews BW
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1998 95: 7893-7897.

PMID- 
VI  - 17
DP  - 2000
TI  - Inhibition of tobacco DNA methyltransferase in vivo causes unequal hypomethylation of DNA repeated sequences.
PG  - 1144-1145
AB  - DNA repetitive sequences are characterized with a high content of methylated cytosine
      (5-methylcytosine, 5-mC).  In tobacco genomic DNA about 30% of all cytosine residues are
      methylated.  However, in our previous study it was found that two families of 5S rDNA
      reiterated sequence have more than 50% of all cytosine residues methylated suggesting that
      differences in DNA methylation levels between DNA repeated sequences may exist.  The aim of
      this study was to compare the methylation patterns in several repetitive DNA sequences of
      Nicotiana tabacum nuclear genome as well as their susceptibility to the effect of a
      hypomethylating drug dihydroxypropyladenine.  This drug is thought to reduce DNA
      methyltransferase activity by increasing S-adenosylhomocysteine levels.  To detect methylation
      state in CG and CCG sites in DNA loci studied, methylation-sensitive restriction enzymes
      (MspI, HapII, Sau3A1 and BamHI) were used.
AU  - Kovarik A
AU  - Koukalova B
AU  - Lim LZ
AU  - Matyasek R
AU  - Lichtenstein CP
AU  - Leitch AR
AU  - Bezdek M
PT  - Journal Article
TA  - J. Biomol. Struct. Dyn.
JT  - J. Biomol. Struct. Dyn.
SO  - J. Biomol. Struct. Dyn. 2000 17: 1144-1145.

PMID- 10219084
VI  - 27
DP  - 1999
TI  - Configuration of the catalytic GIY-YIG domain of intron endonuclease I-TevI: coincidence of computational and molecular findings.
PG  - 2115-2125
AB  - I-TevI is a member of the GIY-YIG family of homing endonucleases.  It is folded into two
      structural and functional domains, an N-terminal catalytic domain and a C-terminal DNA-binding
      domain, separated by a flexible linker.  In this study we have used genetic anlayses,
      computational sequence analysis and NMR spectroscopy to define the configuration of the
      N-terminal domain and its relationship to the flexible linker.  The catalytic domain is an
      alpha/beta structure contained within the first 92 amino acids of the 245-amino acid protein
      followed by an unstructured linker.  Remarkably, this structured domain corresponds precisely
      to the GIY-YIG module defined by sequence comparisons of 57 proteins including more than 30
      newly reported members of the family.  Although much of the unstructured linker is not
      essential for activity, residues 93-116 are required, raising the possibility that this region
      may adopt an alternate conformation upon DNA binding.  Two invariant residues of the GIY-YIG
      module, Arg27 and Glu75, located in alpha-helices, have properties of catalytic residues.
      Furthermore, the GIY-YIG sequence elements for which the module is named form part of a
      three-stranded antiparallel beta-sheet that is important for I-TevI structure and function.
AU  - Kowalski JC
AU  - Belfort M
AU  - Stapleton MA
AU  - Holpert M
AU  - Dansereau JT
AU  - Pietrokovski S
AU  - Baxter SM
AU  - Derbyshire V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1999 27: 2115-2125.

PMID- 12431440
VI  - 28
DP  - 2002
TI  - Characterization of homing endonucleases.
PG  - 365-373
AB  - Homing endonucleases are a class of site-specific DNA endonucleases encoded by open reading
      frames within introns and inteins. They initiate the mobility of their host element by
      recognizing intronless or inteinless alleles of their host gene and making a double-strand
      break. The homing endonucleases are notable for their long target sites and a tolerance for
      sequence polymorphisms in their substrates. The methods used to study homing endonucleases are
      similar to those used to study protein-DNA interactions in general. However, some variations
      and specialized techniques are useful in characterizing homing endonucleases and these methods
      are discussed.
AU  - Kowalski JC
AU  - Derbyshire V
PT  - Journal Article
TA  - Methods
JT  - Methods
SO  - Methods 2002 28: 365-373.

PMID- 20008069
VI  - 192
DP  - 2010
TI  - Virulence factors encoded by Legionella longbeachae identified on the basis of the genome sequence analysis of clinical isolate D-4968.
PG  - 1030-1044
AB  - Legionella longbeachae causes most cases of legionellosis in Australia and may be
      underreported worldwide due to the lack of L. longbeachae-specific diagnostic tests. L.
      longbeachae displays distinctive differences in intracellular trafficking, caspase 1
      activation, and infection in mouse models compared to Legionella pneumophila, yet these two
      species have indistinguishable clinical presentations in humans. Unlike other legionellae,
      which inhabit freshwater systems, L. longbeachae is found predominantly in moist soil. In this
      study, we sequenced and annotated the genome of an L. longbeachae clinical isolate from
      Oregon, isolate D-4968, and compared it to the previously published genomes of L.
      pneumophila. The results revealed that the D-4968 genome is larger than the L.
      pneumophila genome and has a gene order that is different from that of the L.
      pneumophila genome. Genes encoding structural components of type II, type IV Lvh, and type IV
      Icm/Dot secretion systems are conserved. In contrast, only 42/140 homologs of genes encoding
      L. pneumophila Icm/Dot substrates have been found in the D-4968 genome. L. longbeachae encodes
      numerous proteins with eukaryotic motifs and eukaryote-like proteins unique to this species,
      including 16 ankyrin repeat-containing proteins and a novel U-box protein. We predict that
      these proteins are secreted by the L. longbeachae Icm/Dot secretion system. In contrast to the
      L. pneumophila genome, the L. longbeachae D-4968 genome does not contain flagellar
      biosynthesis genes, yet it contains a chemotaxis operon. The lack of a flagellum explains the
      failure of L. longbeachae to activate caspase 1 and trigger pyroptosis in murine macrophages.
      These unique features of L. longbeachae may reflect adaptation of this species to life in
      soil.
AU  - Kozak NA
AU  - Buss M
AU  - Lucas CE
AU  - Frace M
AU  - Govil D
AU  - Travis T
AU  - Olsen-Rasmussen M
AU  - Benson RF
AU  - Fields BS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 1030-1044.

PMID- 29427765
VI  - 59
DP  - 2018
TI  - Comparative genome analysis reveals a complex population structure of Legionella pneumophila subspecies.
PG  - 172-185
AB  - The majority of Legionnaires' disease (LD) cases are caused by Legionella
      pneumophila, a genetically heterogeneous species composed of at least 17
      serogroups. Previously, it was demonstrated that L. pneumophila consists of three
      subspecies: pneumophila, fraseri and pascullei. During an LD outbreak
      investigation in 2012, we detected that representatives of both subspecies
      fraseri and pascullei colonized the same water system and that the
      outbreak-causing strain was a new member of the least represented subspecies
      pascullei. We used partial sequence based typing consensus patterns to mine an
      international database for additional representatives of fraseri and pascullei
      subspecies. As a result, we identified 46 sequence types (STs) belonging to
      subspecies fraseri and two STs belonging to subspecies pascullei. Moreover, a
      recent retrospective whole genome sequencing analysis of isolates from New York
      State LD clusters revealed the presence of a fourth L. pneumophila subspecies
      that we have termed raphaeli. This subspecies consists of 15 STs. Comparative
      analysis was conducted using the genomes of multiple members of all four L.
      pneumophila subspecies. Whereas each subspecies forms a distinct phylogenetic
      clade within the L. pneumophila species, they share more average nucleotide
      identity with each other than with other Legionella species. Unique genes for
      each subspecies were identified and could be used for rapid subspecies detection.
      Improved taxonomic classification of L. pneumophila strains may help identify
      environmental niches and virulence attributes associated with these genetically
      distinct subspecies.
AU  - Kozak-Muiznieks NA
AU  - Morrison SS
AU  - Mercante JW
AU  - Ishaq MK
AU  - Johnson T
AU  - Caravas J
AU  - Lucas CE
AU  - Brown E
AU  - Raphael BH
AU  - Winchell JM
PT  - Journal Article
TA  - Infect. Genet. Evol.
JT  - Infect. Genet. Evol.
SO  - Infect. Genet. Evol. 2018 59: 172-185.

PMID- 27151801
VI  - 4
DP  - 2016
TI  - Three Genome Sequences of Legionella pneumophila subsp. pascullei Associated with Colonization of a Health Care Facility.
PG  - e00335-16
AB  - Here, we report the complete genome sequences of three Legionella pneumophila subsp. pascullei
      strains (including both serogroup 1 and 5 strains) that were
      found in the same health care facility in 1982 and 2012.
AU  - Kozak-Muiznieks NA
AU  - Morrison SS
AU  - Sammons S
AU  - Rowe LA
AU  - Sheth M
AU  - Frace M
AU  - Lucas CE
AU  - Loparev VN
AU  - Raphael BH
AU  - Winchell JM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00335-16.

PMID- 15663787
VI  - 5
DP  - 2005
TI  - Natural history of S-adenosylmethionine-binding proteins.
PG  - 19
AB  - Background.  S-adenosylmethionine is a source of diverse chemical groups used in biosynthesis
      and modification of virtually every class of biomolecules. The most notable reaction requiring
      S-adenosylmethionine, transfer of methyl group, is performed by a large class of enzymes,
      S-adenosylmethionine-dependent methyltransferases, which have been the focus of considerable
      structure-function studies. Evolutionary trajectories of these enzymes, and especially of
      other classes of S-adenosylmethionine-binding proteins, nevertheless, remain poorly
      understood. We addressed this issue by computational comparison of sequences and structures of
      various S-adenosylmethionine-binding proteins.  Results.  Two widespread folds, Rossmann fold
      and TIM barrel, have been repeatedly used in evolution for diverse types of
      S-adenosylmethionine conversion. There were also cases of recruitment of other relatively
      common folds for S-adenosylmethionine binding. Several classes of proteins have unique
      unrelated folds, specialized for just one type of chemistry and unified by the theme of
      internal domain duplications. In several cases, functional divergence is evident, when
      evolutionarily related enzymes have changed the mode of binding and the type of chemical
      transformation of S-adenosylmethionine. There are also instances of functional convergence,
      when biochemically similar processes are performed by drastically different classes of
      S-adenosylmethionine-binding proteins.  Comparison of remote sequence similarities and
      analysis of phyletic patterns suggests that the last universal common ancestor of cellular
      life had between 10 and 20 S-adenosylmethionine-binding proteins from at least 5 fold classes,
      providing for S-adenosylmethionine formation, polyamine biosynthesis, and methylation of
      several substrates, including nucleic acids and peptide chain release factor.  Conclusion.  We
      have observed several novel relationships between families that were not known to be related
      before, and defined 15 large superfamilies of SAM-binding proteins, at least 5 of which may
      have been represented in the last common ancestor.
AU  - Kozbial PZ
AU  - Mushegian AR
PT  - Journal Article
TA  - BMC Struct. Biol.
JT  - BMC Struct. Biol.
SO  - BMC Struct. Biol. 2005 5: 19.

PMID- 24218615
VI  - 110
DP  - 2013
TI  - Global methylation state at base-pair resolution of the Caulobacter genome throughout the cell cycle.
PG  - E4658-E4667
AB  - The Caulobacter DNA methyltransferase CcrM is one of five master cell-cycle regulators. CcrM
      is transiently present near the end of DNA replication when it
      rapidly methylates the adenine in hemimethylated GANTC sequences. The timing of
      transcription of two master regulator genes and two cell division genes is
      controlled by the methylation state of GANTC sites in their promoters. To explore
      the global extent of this regulatory mechanism, we determined the methylation
      state of the entire chromosome at every base pair at five time points in the cell
      cycle using single-molecule, real-time sequencing. The methylation state of 4,515
      GANTC sites, preferentially positioned in intergenic regions, changed
      progressively from full to hemimethylation as the replication forks advanced.
      However, 27 GANTC sites remained unmethylated throughout the cell cycle,
      suggesting that these protected sites could participate in epigenetic regulatory
      functions. An analysis of the time of activation of every cell-cycle regulatory
      transcription start site, coupled to both the position of a GANTC site in their
      promoter regions and the time in the cell cycle when the GANTC site transitions
      from full to hemimethylation, allowed the identification of 59 genes as
      candidates for epigenetic regulation. In addition, we identified two previously
      unidentified N6-methyladenine motifs and showed that they maintained a constant
      methylation state throughout the cell cycle. The cognate methyltransferase was
      identified for one of these motifs as well as for one of two 5-methylcytosine
      motifs.
AU  - Kozdon JB
AU  - Melfi MD
AU  - Luong K
AU  - Clark TA
AU  - Boitano M
AU  - Wang S
AU  - Zhou B
AU  - Gonzalez D
AU  - Collier J
AU  - Turner SW
AU  - Korlach J
AU  - Shapiro L
AU  - McAdams HH
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2013 110: E4658-E4667.

PMID- 25977410
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Lactobacillus rhamnosus CLS17.
PG  - e00478-15
AB  - We announce the draft genome sequence of the type strain Lactobacillus rhamnosus  CLS17
      (2,889,314 nt, with a GC content of 46.8%), which is one of the most
      prevalent lactic acid bacteria present during the manufacturing process of dairy
      products; the genome consists of 71 large contigs (>100 bp in size). It contains
      2,643 protein-coding sequences, single predicted copies of the 5S, 16S, and 23S
      rRNA genes, and 51 predicted tRNAs.
AU  - Kozhakhmetov SS
AU  - Kushugulova AR
AU  - Saduakhasova SA
AU  - Shakhabayeva GS
AU  - Khassenbekova ZR
AU  - Molkenov AB
AU  - Kairov UE
AU  - Issayeva RB
AU  - Nurgozhin TS
AU  - Zhumadilov ZS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00478-15.

PMID- 27516508
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Two Magnetotactic Bacteria, Magnetospirillum moscoviense BB-1 and Magnetospirillum marisnigri SP-1.
PG  - e00814-16
AB  - We report here the draft genome sequences of two recently isolated magnetotactic  species,
      Magnetospirillum moscoviense BB-1 and Magnetospirillum marisnigri SP-1.
      The genome of M. moscoviense BB-1 has 4,164,497 bp, 65.2% G+C content, and
      comprises 207 contigs. The genome of M. marisnigri SP-1 consists of 131 contigs
      and has a length of 4,619,819 bp and 64.7% G+C content.
AU  - Koziaeva VV
AU  - Dziuba MV
AU  - Ivanov TM
AU  - Kuznetsov BB
AU  - Skryabin KG
AU  - Grouzdev DS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00814-16.

PMID- 24744327
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Campylobacter corcagiensis Strain CIT045T, a Representative of a Novel Campylobacter Species Isolated from Lion-Tailed Macaques (Macaca silenus).
PG  - e00248-14
AB  - Campylobacter corcagiensis CIT045(T) (=CCUG 64942(T), LMG 27932(T)), a new member of the
      Campylobacter genus, has recently been isolated from lion-tailed macaques in Cork, Ireland. To
      further characterize this new species and its potential pathogenicity, the genome sequence of
      C. corcagiensis was determined and is presented here.
AU  - Koziel M
AU  - Lucid A
AU  - Bullman S
AU  - Corcoran GD
AU  - Lucey B
AU  - Sleator RD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00248-14.

PMID- 1896406
VI  - 37
DP  - 1991
TI  - Interactions between EcoRI restriction endonuclease and DNA.
PG  - 23-32
AB  - *

      A review in Polish arranged as:

         I. Specific interactions between proteins and DNA

        II. EcoRI endonuclease

      II-1. EcoRI activity

      II-2. Contact-points between EcoRI protein and DNA

      II-3. Application of synthetic oligonucleotides in the studies on the mechanism of EcoRI

            endonuclease action

      II-4. X-Ray studies on the EcoRI endonuclease - DNA complex

      

AU  - Koziolkiewicz M
PT  - Journal Article
TA  - Postepy Biochem.
JT  - Postepy Biochem.
SO  - Postepy Biochem. 1991 37: 23-32.

PMID- 1390728
VI  - 31
DP  - 1992
TI  - Application of phosphate-backbone-modified oligonucleotides in the studies on EcoRI endonuclease mechanism of action.
PG  - 9460-9466
AB  - Chemical synthesis of oligodeoxyribonucleotides modified at a preselected internucleotide bond
      by the replacement of one of the two nonbridging oxygens by a sulfur atom or an ethoxy group
      yields model substrates for studies on DNA-protein interactions. Chromatographic (RP-HPLC)
      separaton of the diastereomers of oligonucleotides containing EcoRI canonical sequence
      together with the assignment of the substituent of orientation in the DNA molecule allowed
      study of the stereochemical aspects of DNA-EcoRI endonuclease interaction. The DNA segment
      involved in interactions between EcoRI protein and phosphate groups appeared to be larger than
      its canonical sequence,...GAATTC...,and was extended to the nonamer. The modification of
      certain internucleotide bonds within this nonamer caused significant or complete protection
      against the nucleolytic action of EcoRI and, in some cases, manifested the
      diastereoselectivity of the enzyme. On the basis of the results of EcoRI-catalyzed hydrolysis
      of stereodefined phosphorothioate and phosphotriester substrates, we propose a model to
      explain this phenomenon at the molecular level.
AU  - Koziolkiewicz M
AU  - Stec WJ
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1992 31: 9460-9466.

PMID- 26769932
VI  - 4
DP  - 2016
TI  - Genome Sequence of Nitrosomonas communis Strain Nm2, a Mesophilic Ammonia-Oxidizing Bacterium Isolated from Mediterranean Soil.
PG  - e01541-15
AB  - The complete genome sequence of Nitrosomonas communis strain Nm2, a mesophilic
      betaproteobacterial ammonia oxidizer isolated from Mediterranean soils in Corfu,
      Greece, is reported here. This is the first genome to describe a cluster 8
      Nitrosomonas species and represents an ammonia-oxidizing bacterium commonly found
      in terrestrial ecosystems.
AU  - Kozlowski JA
AU  - Kits KD
AU  - Stein LY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01541-15.

PMID- 26966201
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Nitrosomonas ureae Strain Nm10, an Oligotrophic Group 6a Nitrosomonad.
PG  - e00094-16
AB  - The complete genome of Nitrosomonas ureae strain Nm10, a mesophilic betaproteobacterial
      ammonia oxidizer isolated from Mediterranean soils in
      Sardinia, Italy, is reported here. This genome represents a cluster 6a
      nitrosomonad.
AU  - Kozlowski JA
AU  - Kits KD
AU  - Stein LY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00094-16.

PMID- 1744134
VI  - 266
DP  - 1991
TI  - Squence and structure of endonuclease II-dependent cleavage sites in bacteriophage T4 DNA.
PG  - 23407-23415
AB  - Endonuclease II of bacteriophage T4 is required for in vivo restriction of
      cytosine-containing DNA from its host, Escherichia coli, (as well as from phage
      mutants lacking cytosine modification), normally the first step in the
      reutilization of host DNA nucleotides for synthesis of phage DNA in infected
      cells.  The phage cytosine-DNA is fragmented incompletely to yield genetically
      defined fragments.  This restriction is different from that of type I, II, or
      III restriction enzymes.  We have located seven major endonuclease II-dependent
      restriction sites in the T4 genome, of which three were analyzed in detail; in
      addition, abundant sites were cleaved in <5% of all molecules.  Sites I, II,
      and III shared the sequence 5'-CCGNNTTGGC-3' and were cleaved in about 25% (I
      and III) and 65% (II) of all molecules, predominantly staggered around the
      first or second of the central unspecified base pairs to yield fragments with
      one 5' base.  The less frequently cleaved sites I and III deviated from site II
      in predicted helical structure when viewed from the consensus strand, and in
      sequence when viewed from the opposite strand.  Thus, interaction with a
      particular helical structure as well as recognition of the bases in DNA appears
      important for efficient cleavage.
AU  - Krabbe M
AU  - Carlson K
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1991 266: 23407-23415.

PMID- 2984549
VI  - 19
DP  - 1985
TI  - The EcoRV restriction-modification system:  genes, enzymes, synthetic substrates.
PG  - 278-284
AB  - By a combination of deletion mutagenesis induced by nuclease, followed by
      determination of the DNA nucleotide sequence, the organization of the genes of
      the EcoRV restriction-modification system, encoded by plasmid, was established.
      The genes of the restriction endonuclease (a protein with a size of 29,000)
      and methylase (a protein with a size of 35,000) are read in opposite directions
      from an intergene region with a size of 310 nucleotides, containing two
      promoter regions.  No homology of the primary structures of the restriction
      endonuclease EcoRV and the restriction endonuclease EcoRI, which recognizes a
      similar nucleotide sequence and is also encoded by a plasmid, was detected.
      The interaction of restriction endonuclease EcoRV with synthetic
      deoxyoligonucleotides containing a phosphoamide bond in the site of the
      presumed action of the restriction endonuclease was investigated.  It was shown
      that this analog, in contrast to the synthetic dodecamer of the same structure,
      but not containing phosphoamide bonds, is not split out by the restriction
      endonuclease; in the control experiment it was found that under the action of
      the restriction endonuclease EcoRV, blunt ends (GAT^ATC), rather than sticky
      ends (GATAT^C) are formed, as was shown earlier.
AU  - Kraev AS
AU  - Kravets AN
AU  - Chernov BK
AU  - Skryabin KG
AU  - Baev AA
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1985 19: 278-284.

PMID- 6617459
VI  - 270
DP  - 1983
TI  - The DNA ligase gene of bacteriophage T4.
PG  - 1495-1500
AB  - note: This paper shows that GAGCT^C is a site for SduI.  This is the missing
      sequence from the earlier paper in FEBS Lett.
AU  - Kraev AS
AU  - Zimin AA
AU  - Mironova MV
AU  - Janulaitis A
AU  - Tanyashin VI
AU  - Skryabin KG
AU  - Bayev AA
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1983 270: 1495-1500.

PMID- 16352841
VI  - 188
DP  - 2006
TI  - Genomic Changes during Chronic Helicobacter pylori Infection.
PG  - 249-254
AB  - The gastric pathogen Helicobacter pylori shows tremendous genetic variability within human
      populations, both in gene content and at the
      sequence level. We investigated how this variability arises by comparing
      the genome content of 21 closely related pairs of isolates taken from the
      same patient at different time points. The comparisons were performed by
      hybridization with whole-genome DNA microarrays. All loci where
      microarrays indicated a genomic change were sequenced to confirm the
      events. The number of genomic changes was compared to the number of
      homologous replacement events without loss or gain of genes that we had
      previously determined by multilocus sequence analysis and mathematical
      modeling based on the sequence data. Our analysis showed that the great
      majority of genetic changes were due to homologous recombination, with
      1/650 events leading to a net gain or loss of genes. These results suggest
      that adaptation of H. pylori to the host individual may principally occur
      through sequence changes rather than loss or gain of genes.
AU  - Kraft C
AU  - Stack A
AU  - Josenhans C
AU  - Niehus E
AU  - Dietrich G
AU  - Correa P
AU  - Fox JG
AU  - Falush D
AU  - Suerbaum S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2006 188: 249-254.

PMID- 26358593
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of the Clinical Strain Acinetobacter baumannii R2090 Carrying the Chromosomally Encoded Metallo-beta-Lactamase Gene blaNDM-1.
PG  - e01008-15
AB  - Acinetobacter baumannii is an emerging human pathogen causing nosocomial and
      community-acquired infections. Here, we present the complete genome sequence of the clinical
      A. baumannii strain R2090 carrying the metallo-beta-lactamase gene blaNDM-1 in its chromosome
      within the transposon Tn125.
AU  - Krahn T
AU  - Wibberg D
AU  - Maus I
AU  - Winkler A
AU  - Nordmann P
AU  - Puhler A
AU  - Poirel L
AU  - Schluter A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01008-15.

PMID- 26227605
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Acinetobacter baumannii CIP 70.10, a Susceptible Reference Strain for Comparative Genome Analyses.
PG  - e00850-15
AB  - The complete genome sequence for the reference strain Acinetobacter baumannii CIP 70.10 (ATCC
      15151) was established. The strain was isolated in France in 1970, is
      susceptible to most antimicrobial compounds, and is therefore of importance for
      comparative genome analyses with clinical multidrug-resistant (MDR) A. baumannii
      strains to study resistance development and acquisition in this emerging human
      pathogen.
AU  - Krahn T
AU  - Wibberg D
AU  - Maus I
AU  - Winkler A
AU  - Puhler A
AU  - Poirel L
AU  - Schluter A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00850-15.

PMID- 2847759
VI  - 14
DP  - 1988
TI  - A new type of cleavage of the recognition sequence by a site-specific endonuclease Bst4.4I from Bacillus stearothermophilus 4.4.
PG  - 916-920
AB  - A site-specific endonuclease Bst4.4I was isolated from the cell extract of
      Bacillus stearothermophilus 4.4 and partially purified by chromatography on
      Ultragel AcA-44 and heparin-Sepharose.  It was shown that the endonuclease
      cleaves lambda and M13 DNA yielding distinct fragments just as endonucleases of
      Types II and III but, in contrast to them, can produce two two-strand cuts
      separated with 30 to 32 nucleotides in the region of the recognition site.
AU  - Kramarov VM
AU  - Fomenkov AI
AU  - Matvienko NI
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1988 14: 916-920.

PMID- 2823833
VI  - 13
DP  - 1987
TI  - A new sequence-specific endonuclease CauB3I from Chloroflexus aurantiacus B3.
PG  - 773-776
AB  - A sequence-specific endonuclease CauB3I has been isolated from cell extracts of
      Chloroflexus aurantiacus and partially purified by chromatography on
      heparin-sepharose; the yield was 3000 units per 1 g of cells.  The final
      preparation is free of non-specific nucleases.  It is shown that endonuclease
      CauB3I recognizes 5' T^CCGGA 3' sequence in double-stranded DNA and cleaves it
      as shown.  Methylation of adenine in the recognition sequence makes it
      resistant to CauB3I.
AU  - Kramarov VM
AU  - Fomenkov AI
AU  - Matvienko NI
AU  - Ubieta RH
AU  - Smolianinov VV
AU  - Gorlenko VM
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1987 13: 773-776.

PMID- Not included in PubMed...
VI  - 10
DP  - 1984
TI  - Another site-specific endonuclease from Rhodopseudomonas sphaeroides.
PG  - 46-49
AB  - A site-specific endonuclease RshII has been purified by chromatography on
      Ultro-gel AcA-44, aminohexyl-Sepharose 4B and heparin-Sepharose 6B.  The final
      preparation did not contain nonspecific nucleases or endonuclease RshI.  The
      RshII endonuclease has been shown to recognize in double-stranded DNA the
      following nucleotide sequence:  5'-C'C (C) GG-3'/3'-GG (G) CC-5'.
AU  - Kramarov VM
AU  - Mazanov AL
AU  - Pachkunov DM
AU  - Smolyaninov VV
AU  - Matvienko NI
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1984 10: 46-49.

PMID- Not included in PubMed...
VI  - 8
DP  - 1982
TI  - Isolation of a second site-specific endonuclease from Xanthomonas holcicola and its characterization.
PG  - 220-223
AB  - A method is proposed for purifying the site-specific endonuclease XhoII by
      chromatography on phosphocellulose and aminohexyl-Sepharose.  The final product
      contains no nonspecific nucleases as impurities nor the endonuclease XhoI.  It
      has been shown that the endonuclease recognizes and hydrolyzes DNA in the
      nucleotide sequence 5'R-G-A-T-C-Y3'.  According to the results of gel
      filtration, the molecular weight of the endonuclease is 40,000 +/- 2000.  In
      the hydrolysis of DNA by the endonuclease, Mg2+ can be replaced by Mn2+.
AU  - Kramarov VM
AU  - Mazanov AL
AU  - Smolyaninov VV
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1982 8: 220-223.

PMID- 
VI  - 0
DP  - 1983
TI  - Site-specific endonucleases BmeI and RshII.
PG  - 22-26
AB  - None
AU  - Kramarov VM
AU  - Pachkunov DM
AU  - Matvienko NI
PT  - Journal Article
TA  - Nek. Aspekty Fiziol. Mikroorg. Akad. Nauk. SSR.
JT  - Nek. Aspekty Fiziol. Mikroorg. Akad. Nauk. SSR.
SO  - Nek. Aspekty Fiziol. Mikroorg. Akad. Nauk. SSR. 1983 0: 22-26.

PMID- 2554130
VI  - 0
DP  - 1989
TI  - New site-specific endonuclease producer strains of Bacillus genera.
PG  - 42-45
AB  - 52 Bacillus strains have been tested for their production of site-specific
      endonucleases.  The sequence recognized by the enzymes was determined for 23
      enzymes, the cleavage site inside the sequence was determined for 5 enzymes.
      All the enzymes under study were found to be isoschizomers of known enzymes.
      The selected strains are unusual for their high level of site-specific
      endonucleases content and may be used as producers of the enzymes.
AU  - Kramarov VM
AU  - Skrypina NA
AU  - Smolyaninov VV
AU  - Smirnov VV
AU  - Resnik SR
AU  - Sorokulova IB
AU  - Matvienko NI
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1989 0: 42-45.

PMID- 6268201
VI  - 46
DP  - 1981
TI  - DNA methylase from Arthrobacter luteus screens DNA from the action of site-specific endonuclease AluI.
PG  - 1526-1529
AB  - DNA-methylase was isolated from a cell extract of A. luteus and partially
      purified by chromatography on phosphocellulose.  The purified enzyme methylates
      DNA of phage lambda and plasmids pBR322, thus making them resistant to a
      subsequent action of endonuclease AluI.  It has been shown that cytosine is the
      object of methylation within DNA.  This modification does not screen DNA from
      the action of site-specific endonucleases SalI, Bam HI, EcoRI, EcoRII, XhoI and
      XhoII  It has been experimentally demonstrated that the isolated methylase is
      site-specific and identifies in the DNA the nucleotide sequence 5'-AGCT-3', by
      methylating cytosine in the DNA.
AU  - Kramarov VM
AU  - Smolyaninov VV
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1981 46: 1526-1529.

PMID- 8590870
VI  - 344
DP  - 1995
TI  - Use of specific binding of peptide nucleic acids to DNA in the "Achilles heel" method.
PG  - 552-555
AB  - 
AU  - Krasilnikova MM
AU  - Izvolskii KI
AU  - Krupnik OV
AU  - Lazurkin YS
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1995 344: 552-555.

PMID- 17125791
VI  - 365
DP  - 2006
TI  - Probing Interactions within the Synaptic DNA-SfiI Complex by AFM Force Spectroscopy.
PG  - 1407-1416
AB  - SfiI belongs to a family of restriction enzymes that function as tetramers, binding two
      recognition regions for the DNA cleavage reaction.
      The SfiI protein is an attractive and convenient model for studying
      synaptic complexes between DNA and proteins capable of site-specific
      binding. The enzymatic action of SfiI has been very well characterized.
      However, the properties of the complex before the cleavage reaction are
      not clear. We used single-molecule force spectroscopy to analyze the
      strength of interactions within the SfiI-DNA complex. In these
      experiments, the stability of the synaptic complex formed by the enzyme
      and two DNA duplexes was probed in a series of approach-retraction cycles.
      In order to do this, one duplex was tethered to the surface and the other
      was tethered to the probe. The complex was formed by the protein present
      in the solution. An alternative setup, in which the protein was anchored
      to the surface, allowed us to probe the stability of the complex formed
      with only one duplex in the approach-retraction experiments, with the
      duplex immobilized at the probe tip. Both types of complexes are
      characterized by similar rupture forces. The stability of the complex was
      determined by measuring the dependence of rupture forces on force loading
      rates (dynamic force spectroscopy) and the results suggest that the
      dissociation reaction of the SfiI-DNA complex has a single energy barrier
      along the dissociation path. Dynamic force spectroscopy was instrumental
      in revealing the role of the 5 bp spacer region within the palindromic
      recognition site on DNA-SfiI in the stability of the complex. The data
      show that, although the change of non-specific sequence does not alter the
      position of the activation barrier, it changes values of the off rates
      significantly.
AU  - Krasnoslobodtsev AV
AU  - Shlyakhtenko LS
AU  - Lyubchenko YL
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2006 365: 1407-1416.

PMID- 17057704
VI  - 24
DP  - 2006
TI  - Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72.
PG  - 1385-1391
AB  - Azoarcus sp. strain BH72, a mutualistic endophyte of rice and other
      grasses, is of agrobiotechnological interest because it supplies
      biologically fixed nitrogen to its host and colonizes plants in remarkably
      high numbers without eliciting disease symptoms. The complete genome
      sequence is 4,376,040-bp long and contains 3,992 predicted protein-coding
      sequences. Genome comparison with the Azoarcus-related soil bacterium
      strain EbN1 revealed a surprisingly low degree of synteny. Coding
      sequences involved in the synthesis of surface components potentially
      important for plant-microbe interactions were more closely related to
      those of plant-associated bacteria. Strain BH72 appears to be 'disarmed'
      compared to plant pathogens, having only a few enzymes that degrade plant
      cell walls; it lacks type III and IV secretion systems, related toxins and
      an N-acyl homoserine lactones-based communication system. The genome
      contains remarkably few mobile elements, indicating a low rate of recent
      gene transfer that is presumably due to adaptation to a stable, low-stress
      microenvironment.
AU  - Krause A et al
PT  - Journal Article
TA  - Nat. Biotechnol.
JT  - Nat. Biotechnol.
SO  - Nat. Biotechnol. 2006 24: 1385-1391.

PMID- 21075930
VI  - 193
DP  - 2010
TI  - Complete genome sequence of adherent invasive Escherichia coli UM146 isolated from ileal Crohn's disease biopsy tissue.
PG  - 583
AB  - Escherichia coli UM146 was isolated from the ileum of a Crohn's disease patient. It adheres
      to and invades enterocytes and can replicate inside
      macrophages. Its complete genome sequence reveals that it is most closely
      related to the human urinary tract pathogen E. coli CFT073, but it has a
      host of genes that are novel and for which function has not been ascribed.
AU  - Krause DO
AU  - Little AC
AU  - Dowd SE
AU  - Bernstein CN
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 193: 583.

PMID- 
VI  - 827
DP  - 2002
TI  - A new engine for cleaving nucleic acid.
PG  - 270-293
AB  - Rapid and accurate cleavage of nucleic acid material, such as DNA and RNA, is a fundamentally
      important biochemical process in all living
      organisms carried out by enzymes called nucleases. We present here a
      discussion and comparison of two nucleases of widely disparate
      properties but who share a newly described nuclease active site
      geometry. Serratia marcescens, a pathogenic Gram negative bacterium
      produces an enzyme that presents a new paradigm in nucleases. Its fold
      is new, it is capable of very rapid, and relatively non sequence
      dependent cleavage of several types of DNA and RNA. On the other hand,
      I-PpoI is a homing endonuclease which is encoded by a group I intron in
      the rRNA genes of Physarum polycephalum (1). It also possesses a new
      fold, but it only slowly cleaves DNA at a very specific 15 by site.
      Both enzymes possess the same active site geometry, but no other
      structural homology. The structural basis for their different
      properties is due to two main factors, the nature of their interaction
      with substrate and the presence of a mobile metal in I-Ppol
      endonuclease that must migrate into position prior to catalysis.
AU  - Krause KL
AU  - Miller MD
PT  - Journal Article
TA  - ACS Symp. Ser.
JT  - ACS Symp. Ser.
SO  - ACS Symp. Ser. 2002 827: 270-293.

PMID- 9819822
VI  - 3
DP  - 1998
TI  - High homology of plasmids carrying class II restriction modification systems, EcoRV isoschizomers, and their prevalence in natural Escherichia coli strains.
PG  - 20-22
AB  - Screening of 660 clinical Enterobacteriaceae strains from the collection of L.V. Gromashevsky,
      Kiev Institute of Epidemiology and Infectious Diseases, for specific endonuclease activity
      revealed site-specific endonucleases, EcoRV isoschizomers, in 6 E. coli strains.  Genes coding
      for endonucleases and methyltransferases were localized on small (6.2 kb) multicopy Hsd+
      plasmids.  All plasmids were successfully transferred in laboratory strain E. coli K802.
      Restriction analysis and subcloning showed no differences in the structural and functional
      organization of the plasmids studied and a previously revealed pLB1 plasmid, thus reflecting
      their high homology, if not identity.  These data allow us to propose effective horizontal
      transfer of EcoRV plasmids among natural E. coli isolates in the region studied.
AU  - Kravets AN
AU  - Pertsev AV
AU  - Tarutina ZE
AU  - Solonin AS
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1998 3: 20-22.

PMID- 9611755
VI  - 0
DP  - 1998
TI  - New isoschizomers of restriction endonucleases in Pseudomonas aeruginosa strains.
PG  - 14-17
AB  - Testing of Pseudomonas aeruginosa strains from the collection of the L.V. Gromashevsky
      Institute of Epidemiology and Infectious Diseases (Kiev) for specific endonucleases resulted
      in the isolation of five class II restriction endonucleases, which were partially purified and
      their recognition targets were determined.  Two of these endonucleases, Pae2kI and Pae18kI,
      are isoschizomers of BglII (5'-AGACTC-3').  Pae5kI and Pae14kI, recognize the
      5'-CCGC/GG-3' sequence and are therefore true isoschizomers of SacII.  Hence, Pae17kI is an
      isoschizomer of PvuII and cleaves the DNA within the recognition sequence 5'-CAG/CTG-3'.
      BglII and PvuII are for the first time detected in Pseudomonas aeruginosa.
AU  - Kravets AN
AU  - Pertsev AV
AU  - Tarutina ZY
AU  - Krendelev YD
AU  - Zakharova MV
AU  - Beletskaya IV
AU  - Solonin AS
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1998 0: 14-17.

PMID- 1338550
VI  - 7
DP  - 1992
TI  - Plasmid localization and cloning of restriction-modification genes from Citrobacter freundii 4111 strain.
PG  - 4-7
AB  - Over 60 producing strains of restriction endonucleases type II have been found among 500
      different strains, mostly Enterobacteriaceae. The strain Citrobacter freundii 4111 produces
      restriction endonuclease CfrBI, a new isoschizomer of StyI. The genes of the
      restriction-modification system CfrBI were located on the multicopy plasmid pZE8 containing
      the ColE1-type replicon and cloned into E. coli K802. The deletion variant of 3.2-kb pZE8
      which contains intact restriction-modification and a DNA fragement responsible for autonomous
      plasmid replication was selected among the recombinant plasmids. The strain with higher R.
      CfrBI production (at least 10,000,000 U/g cells, which is 500-fold higher than the wild
      strain) was constructed.
AU  - Kravets AN
AU  - Solonin AS
AU  - Zakharova MV
AU  - Tarutina ZE
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1992 7: 4-7.

PMID- 2194115
VI  - 24
DP  - 1990
TI  - Cloning of genes of the EcoRV restriction-modification system and regulation of their expression.
PG  - 438-447
AB  - A number of recombinant plasmids bearing genes of the EcoRV
      restriction-modification system were constructed.  The individual genes were
      inserted into plasmids belonging to different incompatibility groups.  The
      regulatory regions of the genes coding for the methylase and restriction
      endonuclease were cloned and studied.  It was shown using the specialized
      vector pVE8 that the promoter region determining transcription of the
      restriction endonuclease was comparable in terms of efficiency with the early
      promoters of phage lambda and equaled approximately 70% of the efficiency of
      the left-oriented promoter PL.  The promoter region of the methylase gene
      provided about one half as efficient transcription as did the promoter region
      of the restriction-endonuclease gene.  A recombinant plasmid was obtained in
      which the EcoRV restriction-endonuclease gene found itself under the control of
      the complementary regulated promoter of phage lambda, PR, and provided
      30-40-fold enhancement of biosynthesis of the restriction endonuclease, given
      inactivation of the phage-lambda-c1857 temperature-sensitive repressor.  Under
      inducing conditions, the amount of EcoRV restriction endonuclease in the
      superproducer strain amounted to approximately 10% of the total cell protein.
      The factors conducive to the level of EcoRV restriction endonuclease induction
      attained are discussed.
AU  - Kravets AN
AU  - Zakharova MV
AU  - Solonin AS
AU  - Kuzmin NP
AU  - Tanyushin VI
AU  - Glatman LI
AU  - Moroz AF
AU  - Baev AA
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1990 24: 438-447.

PMID- 1909787
VI  - 19
DP  - 1991
TI  - Two novel restriction endonucleases from Pseudomonas aeruginosa.
PG  - 4781
AB  - PaePI and PaeHI, type II restriction endonucleases have been isolated from
      clinical strain Pseudomonas aeruginosa 4148.  The enzymes were separated and
      purified by chromatography on DEAE-cellulose DE52, hydroxylapatite and mono Q
      column (FPLC system, Pharmacia Ltd).
AU  - Kravetz AN
AU  - Tarutina ZE
AU  - Solonin AS
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 4781.

PMID- 8335254
VI  - 129
DP  - 1993
TI  - The cleavage sites and localization of genes encoding the restriction endonuclease Eco1831I and EcoHI.
PG  - 153-154
AB  - The restriction endonucleases Eco1831I and EcoHI cleave before the first 5'-cytosine in the
      recognition sequence 5'CCSGG 3'/3' GGSCC 5' (where S=G or C), generate 5-base 5' cohesive
      ends and are encoded by homologous plasmids that are restricted in McrA+ hosts. Thus, they
      differ in their cleavage specificity from that of the BcnI isoschizomer, which cleaves after
      the second 5' cytosine.
AU  - Kravetz AN
AU  - Zakharova MV
AU  - Beletskaya IV
AU  - Sineva EV
AU  - Denjmuchametov MM
AU  - Petrov SI
AU  - Glatman LI
AU  - Solonin AS
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1993 129: 153-154.

PMID- 8385321
VI  - 21
DP  - 1993
TI  - Two novel restriction endonucleases from Klebsiella pneumoniae.
PG  - 1501
AB  - Kpn49kI and Kpn49kII, type II restriction endonucleases have been isolated from the clinical
      strain Klebsiella pneumoniae 49k.
AU  - Kravetz AN
AU  - Zakharova MV
AU  - Beljetzkaja IV
AU  - Pertzev AV
AU  - Spivak OI
AU  - Solonin AS
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 1501.

PMID- 25814599
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Four Bacillus thermoamylovorans Strains Isolated from Milk and Acacia Gum, a Food Ingredient.
PG  - e00165-15
AB  - The thermophilic bacterium Bacillus thermoamylovorans produces highly heat-resistant spores
      that can contaminate food products, leading to their
      spoilage. Here, we present the whole-genome sequences of four B.
      thermoamylovorans strains, isolated from milk and acacia gum.
AU  - Krawczyk AO
AU  - Berendsen EM
AU  - Eijlander RT
AU  - de Jong A
AU  - Wells-Bennik MH
AU  - Kuipers OP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00165-15.

PMID- 26679589
VI  - 3
DP  - 2015
TI  - Next-Generation Whole-Genome Sequencing of Eight Strains of Bacillus cereus, Isolated from Food.
PG  - e01480-15
AB  - Bacillus cereus can contaminate food and cause emetic and diarrheal foodborne illness. Here,
      we report whole-genome sequences of eight strains of B. cereus,
      isolated from different food sources.
AU  - Krawczyk AO
AU  - de Jong A
AU  - Eijlander RT
AU  - Berendsen EM
AU  - Holsappel S
AU  - Wells-Bennik MH
AU  - Kuipers OP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01480-15.

PMID- 27174261
VI  - 4
DP  - 2016
TI  - Genome Sequences of 12 Spore-Forming Bacillus Species, Comprising Bacillus coagulans, Bacillus licheniformis, Bacillus amyloliquefaciens, Bacillus  sporothermodurans, and Bacillus vallismortis, Isolated from Foods.
PG  - e00103-16
AB  - Here, we report the draft genomes of twelve isolates of five different Bacillus species, all
      spore-forming, Gram-positive bacteria.
AU  - Krawczyk AO
AU  - de Jong A
AU  - Holsappel S
AU  - Eijlander RT
AU  - van Heel A
AU  - Berendsen EM
AU  - Wells-Bennik MH
AU  - Kuipers OP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00103-16.

PMID- 24302578
VI  - 42
DP  - 2014
TI  - The complex methylome of the human gastric pathogen Helicobacter pylori.
PG  - 2415-2432
AB  - The genome of Helicobacter pylori is remarkable for its large number of
      restriction-modification (R-M) systems, and strain-specific diversity in R-M systems has been
      suggested to limit natural transformation, the major driving force of genetic diversification
      in H. pylori. We have determined the comprehensive methylomes of two H. pylori strains at
      single base resolution, using Single Molecule Real-Time (SMRT) sequencing. For strains 26695
      and J99-R3, 17 and 22 methylated sequence motifs were identified, respectively. For most
      motifs, almost all sites occurring in the genome were detected as methylated. Twelve novel
      methylation patterns corresponding to nine recognition sequences were detected (26695, 3;
      J99-R3, 6). Functional inactivation, correction of frameshifts as well as cloning and
      expression of candidate methyltransferases (MTases) permitted not only the functional
      characterization of multiple, yet undescribed, MTases, but also revealed novel features of
      both Type I and Type II R-M systems, including frameshift-mediated changes of sequence
      specificity and the interaction of one MTase with two alternative specificity subunits
      resulting in different methylation patterns. The methylomes of these well-characterized H.
      pylori strains will provide a valuable resource for future studies investigating the role of
      H. pylori R-M systems in limiting transformation as well as in gene regulation and host
      interaction.
AU  - Krebes J
AU  - Morgan RD
AU  - Bunk B
AU  - Sproeer C
AU  - Luong K
AU  - Parusel R
AU  - Anton BP
AU  - Koenig C
AU  - Josenhans C
AU  - Overmann J
AU  - Roberts RJ
AU  - Korlach J
AU  - Suerbaum S
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2014 42: 2415-2432.

PMID- 25486633
VI  - 194
DP  - 2015
TI  - Two-stage gene assembly/cloning of a member of the TspDTI subfamily of bifunctional restriction endonucleases, TthHB27I.
PG  - 67-80
AB  - The Therms sp. family of bifunctional type IIS/IIG/IIC restriction endonucleases
      (REase)-methyltransferases (MTase) comprises thermo-stable TaqII, TspGWI, TspDTI, TsoI,
      Tth111II/TthHB27I enzymes as well as a number of putative enzymes/open reading frames (ORFs).
      All of the family members share properties including a large protein size (ca. 120 kDa), amino
      acid (aa) sequence homologies, enzymatic activity modulation by S-adenosylmethionine (SAM),
      recognition of similar asymmetric cognate DNA sites and cleavage at a distance of 1119 nt.
      Analysis of the enzyme aa sequences and domain/motif organisation led to further Therms sp.
      family division into the TspDTI and TspGWI subfamilies. The latter exhibits an unprecedented
      phenomenon of DNA recognition change upon substitution of SAM by its analogue, sinefungin
      (SIN), towards a very frequent DNA cleavage. We report cloning in Escherichia coli (E. coli),
      using a two-stage procedure and a putative tthHB27IRM gene, detected by bioinformatics
      analysis of the Therms thermophilus HB27 (T. thermophilus) genome. The functionality of a 3366
      base pair (bp)-/1121 aa-long, high GC content ORF was validated experimentally through the
      expression in E. coli. Protein features corroborated with the reclassification of TthHB27I
      into the TspDTI subfamily, which manifested in terms of aa-sequence/motif homologies and
      insensitivity to SIN-induced specificity shift. However, both SAM and SIN stimulated the REase
      DNA cleavage activity by at least 16-32 times; the highest was observed for the Therms sp.
      family. The availability of TthHB27I and the need to include SAM or SIN in the reaction in
      order to convert the enzyme from 'hibernation' status to efficient DNA cleavage is of
      practical significance in molecular biotechnology, extending the palette of available REase
      specificities.
AU  - Krefft D
AU  - Zylicz-Stachula A
AU  - Mulkiewicz E
AU  - Papkov A
AU  - Jezewska-Frackowiak J
AU  - Skowron PM
PT  - Journal Article
TA  - J. Biotechnol.
JT  - J. Biotechnol.
SO  - J. Biotechnol. 2015 194: 67-80.

PMID- 26272577
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Leptospira santarosai Strains U160, U164, and U233, Isolated from Asymptomatic Cattle.
PG  - e00910-15
AB  - In the present work, we announce the draft genomes for three new strains (U160, U164, and
      U233) of Leptospira santarosai, isolated from urine samples from
      asymptomatic cattle in Rio de Janeiro, Brazil.
AU  - Kremer FS
AU  - Eslabao MR
AU  - Provisor M
AU  - Woloski RD
AU  - Ramires OV
AU  - Moreno LZ
AU  - Moreno AM
AU  - Hamond C
AU  - Lilenbaum W
AU  - Dellagostin OA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00910-15.

PMID- 25414488
VI  - 2
DP  - 2014
TI  - Finished Genome Sequence of the Laboratory Strain Escherichia coli K-12 RV308 (ATCC 31608).
PG  - e00971-14
AB  - Escherichia coli strain K-12 substrain RV308 is an engineered descendant of the K-12 wild-type
      strain. Like its ancestor, it is an important organism in
      biotechnological research and is heavily used for the expression of single-chain
      variable fragments. Here, we report the complete genome sequence of E. coli K-12
      RV308 (ATCC 31608).
AU  - Krempl PM
AU  - Mairhofer J
AU  - Striedner G
AU  - Thallinger GG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00971-14.

PMID- 21491685
VI  - 285
DP  - 2010
TI  - The Characterization of Restriction Endonucleases: the Work of Hamilton Smith.
PG  - e2-3
AB  - Hamilton Othanel Smith was born in 1931 in New York City.  In 1937, he and his family moved to
      Champaign-Urbana, Illinois, because his father had joined the faculty of the department of
      education at the University of Illinois.  As a boy, Smith was interested in chemistry,
      electricity, and electronics, and he spent many hours with his brother in their basement
      laboratory, which was stocked with supplies purchased from their paper route earnings.  Smith
      attended a small college preparatory school called the University Laboratory High School and
      graduated in 3 years largely tue to this science teacher who allowed him to complete chemistry
      and physics during the summer.
AU  - Kresge N
AU  - Simoni RD
AU  - Hill RL
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2010 285: e2-3.

PMID- Not carried by PubMed...
VI  - 31
DP  - 1986
TI  - Interaction of caffeine with DNA:  an evaluation with restriction endonucleases.
PG  - 31-38
AB  - The endonucleolytic action of several restriction enzymes on the lambda, pBR322
      and PhiX174 (RF I, RF II and single-stranded virion DNA) were tested in the
      presence of caffeine.  No aberrant restriction cleavage pattern was observed by
      adding caffeine directly to the restriction reaction mixture.  DNA pretreated
      with caffeine also exhibited similar results.  Ligation of DNA fragments,
      havaing either protruding single-strand or flush ends, is not affected by
      caffeine.  These results strongly argue against the possible interaction of
      caffeine with DNA.
AU  - Kretchmar SA
AU  - Chiu HS
AU  - Srinivasan A
PT  - Journal Article
TA  - Microbios Lett.
JT  - Microbios Lett.
SO  - Microbios Lett. 1986 31: 31-38.

PMID- 1649819
VI  - 173
DP  - 1991
TI  - Identification and characterization of a gene responsible for inhibiting propagation of methylated DNA sequences in mcrA mcrB1 Escherichia coli strains.
PG  - 4707-4716
AB  - Identifying and eliminating endogenous bacterial enzyme systems can
      significantly increase the efficiency of propagation of eukaryotic DNA in
      Escherichia coli.  We have recently examined one such system which inhibits the
      propagation of lambda DNA rescued from transgenic mouse tissues.  This rescue
      procedure utilizes lambda packaging extracts for excision of the lambda DNA
      from the transgenic mouse genome, as well as E. coli cells for subsequent
      infection and propagation.  This assay, in combination with conjugal mating, P1
      transduction, and gene cloning, was used to identify and characterize the E.
      coli locus responsible for this difference in efficiency.  It was determined
      that the E. coli K-12 mcrB gene when expressed on a high-copy-number plasmid
      can cause a decrease in rescue efficiency despite the presence of the mcrB1
      mutation, which inactivates the classic McrB restriction activity.  (This
      mutation was verified by sequence analysis.)  However, this McrB1 activity is
      not observed when the cloned mcrB1 gene is inserted into the E. coli genome at
      one copy per chromosome.  A second locus was identified which causes a decrease
      in rescue efficiency both when expressed on a high-copy-number plasmid and when
      inserted into the genome.  The data presented here suggest that this locus is
      mrr and that the mrr gene product can recognize and restrict
      cytosine-methylated sequences.  Removal of this DNA region including the mrr
      gene from E. coli K-12 strains allows high rescue efficiencies equal to those
      of E. coli C strains.  These modified E. coli K-12 plating strains and lambda
      packaging extract strains should also allow a significant improvement in the
      efficiency and representation of eukaryotic genomic and cDNA libraries.
AU  - Kretz PL
AU  - Kohler SW
AU  - Short JM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1991 173: 4707-4716.

PMID- 2548161
VI  - 17
DP  - 1989
TI  - Effect of lambda packaging extract mcr restriction activity on DNA cloning.
PG  - 5409
AB  - The negative effect of bacterial mcrA and mcrB restriction activity on the cloning of
      methylated DNA has recently been demonstrated. In order to determine the effect of these
      restriction systems on lambda and cosmid packaging, an mcrA-, B-, hsd-, mrr- packaging extract
      strain was constructed by P1 transduction. The extract prepared from this strain, Gigapack II,
      was tested against the restriction positive (mcrA+,B-) extract, Gigapack I, by comparing
      efficiencies in constructing a cosmid library. The results indicate that these restriction
      enzymes are active in lambda packaging extracts and can affect cloning efficiencies. The
      elimination of mcrA,B restriction activity from Gigapack II allowed a 2-3 fold increase in the
      number of cosmid clones obtained. Similar effects have been observed with lambda libraries.
      This effect has also been shown to increase as the extent of DNA methylation increases. The
      results demonstrate the importance of utilizing restriction deficient lambda packaging
      extracts for improved cloning efficiency and possibly genomic representation. Optimal results
      are obtained when both mcrA-,B- packaging extracts and plating strains are used.
AU  - Kretz PL
AU  - Reid CH
AU  - Greener A
AU  - Short JM
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 5409.

PMID- 3549359
VI  - 213
DP  - 1987
TI  - dam methylase from E. coli: Circular dichroism investigations of the secondary structure and influence of S-adenosylmethionine.
PG  - 297-300
AB  - The enzyme dam methylase which recognizes and methylates the adenine in the palindromic
      sequence GATC in DNA was isolated and the secondary structure was determined by CD
      spectroscopy and various predicting methods from the amino acid sequence. The interaction of
      dam methylase with S-adenosylmethionine was studied by CD spectroscopy indicating a decrease
      of the percentage of alpha-helix as the amount of S-adenosylmethionine bound to the enzyme was
      increased.
AU  - Kriebardis A
AU  - Guschlbauer W
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1987 213: 297-300.

PMID- 20543037
VI  - 76
DP  - 2010
TI  - Targeted Chromosomal Knockouts in Mycoplasma pneumoniae.
PG  - 5297-5299
AB  - Most gene knockouts in mycoplasmas are achieved through labor-intensive
      transposon mutagenesis. Here, we describe a method for making targeted
      deletions in Mycoplasma pneumoniae by use of homologous recombination. In
      this method, M. pneumoniae is transformed with a plasmid carrying an
      antibiotic resistance marker flanked by 1-kb regions surrounding the
      target gene. Following selection for the antibiotic resistance, colonies
      are screened for double crossovers which indicate complete deletion of the
      target open reading frame.
AU  - Krishnakumar R
AU  - Assad-Garcia N
AU  - Benders GA
AU  - Phan Q
AU  - Montague MG
AU  - Glass JI
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2010 76: 5297-5299.

PMID- 8038713
VI  - 32
DP  - 1994
TI  - Interaction of EcoPI modification methylase with S-adenosyl-L-methionine: a UV-crosslinking study.
PG  - 623-632
AB  - EcoPI modification methylase was radioactively labeled when incubated with
      S-adenosyl-L-[methyl-3H]methionine in the presence of ultraviolet light. Crosslinking of the
      enzyme as detected by electrophoresis on sodium dodecyl sulfate - polyacrylamide gel followed
      by fluorography and autoradiography, was shown to be specific by a number of criteria. More
      importantly, EcoPI modification methylase was also radioactively labeled with
      S-adenosyl-L-[carboxyl-14C]methionine demonstrating that labeling involved binding of the
      entire AdoMet molecule rather than methylation of the protein. Further, c2 EcoPI mutant DNA
      modification methylases which show negligible or very little methylation activity,
      correspondingly formed a weak or no adduct upon crosslinking. These results suggest that
      photolabeling of EcoPI DNA modification methylase occurs at the AdoMet binding site.
AU  - Krishnamurthy V
AU  - Rao DN
PT  - Journal Article
TA  - Biochem. Mol. Biol. Int.
JT  - Biochem. Mol. Biol. Int.
SO  - Biochem. Mol. Biol. Int. 1994 32: 623-632.

PMID- 11341931
VI  - 1544
DP  - 2001
TI  - Structure-based sequence alignment of type-II restriction endonucleases.
PG  - 217-228
AB  - The type-II restriction endonucleases generally do not share appreciable amino acid sequence
      homology. The crystal structures of restriction endonucleases EcoRI and BamHI have shown these
      enzymes to possess striking 3D-structural resemblance, i.e., they have a similar overall fold
      and similar active sites, though they possess <23% sequence identity. Structural
      superimposition of EcoRI, BamHI, EcoRV, and PvuII based on active site residues led to
      sequence alignments which showed nine possible sequence motifs. EcoRV and PvuII show a more
      similar pattern than EcoRI and BamHI suggesting that they belong to a different subgroup. The
      motifs are characterized by charged and/or hydrophobic residues. From other studies on the
      structure of these endonucleases, three of the motifs could be implicated in DNA binding,
      three in forming the active site and one in dimer formation. However, the motifs were not
      identifiable by regular sequence alignment methods. It is found that motif IX in BamHI is
      formed by reverse sequence order and the motif IX in PvuII is formed from the symmetry related
      monomer of the dimer. The inter-motif distance is also quite different in these cases. Of the
      nine motifs, motif III has been earlier identified as containing the PD motif involving one of
      the active site residues. These motifs were used in a modified profile analysis procedure to
      identify similar regions in eight other endonuclease sequences for which structures are not
      known.
AU  - Krishnaswamy TDS
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 2001 1544: 217-228.

PMID- 1972980
VI  - 18
DP  - 1990
TI  - Digestion conditions resulting in altered cut site specificity for HinfI.
PG  - 3665
AB  - None
AU  - Kriss J
AU  - Herrin G
AU  - Forman L
AU  - Cotton R
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 3665.

PMID- 25189588
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Actinobaculum schaalii Strain CCUG 27420.
PG  - e00880-14
AB  - Complete genome sequencing of the emerging uropathogen Actinobaculum schaalii indicates that
      an important mechanism of its virulence is attachment pili, which
      allow the organism to adhere to the surface of animal cells, greatly enhancing
      the ability of this organism to colonize the urinary tract.
AU  - Kristiansen R
AU  - Dueholm MS
AU  - Bank S
AU  - Nielsen PH
AU  - Karst SM
AU  - Cattoir V
AU  - Lienhard R
AU  - Grisold AJ
AU  - Olsen AB
AU  - Reinhard M
AU  - Soby KM
AU  - Christensen JJ
AU  - Prag J
AU  - Thomsen TR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00880-14.

PMID- 22328750
VI  - 194
DP  - 2012
TI  - De Novo Genome Project for the Aromatic Degrader Rhodococcus pyridinivorans Strain AK37.
PG  - 1247-1248
AB  - Here, we present the complete genome sequence of Rhodococcus pyridinivorans AK37  strain NCAIM
      PB1376, which was isolated from an oil-polluted site in Hungary. R.
      pyridinivorans AK37 is an aerobic, nonsporulating, nonmotile, Gram-positive
      bacterium with remarkable aromatic-decomposing activity.
AU  - Kriszt B
AU  - Tancsics A
AU  - Cserhati M
AU  - Toth A
AU  - Nagy I
AU  - Horvath B
AU  - Nagy I
AU  - Tamura T
AU  - Kukolya J
AU  - Szoboszlay S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1247-1248.

PMID- 
VI  - 
DP  - 2007
TI  - Restriction endonuclease MnlI - A member of the HNH family of endonucleases.
PG  - 1-45
AB  - CONCLUSIONS
      1. The Type IIS restriction-modification system MnlI is composed of N6-methyladenine and
      C5-methylcytosine methyltransferases and a restriction enzyme. The methyltransferases modify
      cytosine and adenine on the opposite strands of the recognition sequence, resulting in
      5'-m5CCTC-3'/5'-Gm6AGG-3'. The MnlI restriction endonuclease cleaves both DNA strands 7/6
      nucleotides downstream of the recognition site.
      2. The active site of MnlI REase resembles those of the bacterial colicin DNases ColE7 and
      ColE9, which belong to the HNH superfamily of nucleases. The motif 306Rx3ExHHx14Nx8H located
      in the C-terminal part of the protein comprises the active site of MnlI.
      3. MnlI is a homodimeric protein capable of binding two copies of its recognition sequence.
      Simultaneous binding of two DNA target sites stimulates DNA cleavage by MnlI.
      4. A two-domain structure of the Type IIS restriction endonuclease MnlI has been identified by
      limited proteolysis. An N-terminal domain of the enzyme mediates the sequence-specific
      interaction with DNA and in part the dimerization of MnlI. It binds the recognition sequence
      as a monomer, though it displays an ability to interact with two copies of the recognition
      sequence as a dimer. A C-terminal domain of MnlI is determined to be monomeric in solution.
      5. The C-terminal domain of MnlI REase resembles bacterial colicin nucleases in its oligomeric
      state and requirement for alkaline earth as well as transition metal ions for double- and
      single-stranded DNA cleavage activities.
      6. The fusion of the non-specific HNH-type nuclease to the DNA binding domain had transformed
      MnlI into a Mg2+-, Ni2+-, Co2+-, Mn2+-, Zn2+-, Ca2+-dependent sequence-specific enzyme.
      Nevertheless, MnlI retains a residual single-stranded DNA cleavage activity controlled by its
      C-terminal colicin-like nuclease domain. The cleavage of ds- and ssDNA by MnlI with a wide
      range of divalent metal ions is unparalleled among restriction endonucleases characterized to
      date.
AU  - Kriukiene E
PT  - Journal Article
TA  - Ph.D. Thesis, Vilnius University
JT  - Ph.D. Thesis, Vilnius University
SO  - Ph.D. Thesis, Vilnius University 2007 : 1-45.

PMID- 17055493
VI  - 580
DP  - 2006
TI  - Domain organization and metal ion requirement of the Type IIS restriction endonuclease MnlI.
PG  - 6115-6122
AB  - A two-domain structure of the Type US restriction endonuclease Mull has been identified by
      limited proteolysis. An N-terminal domain of the
      enzyme mediates the sequence-specific interaction with DNA, whereas a
      monomeric C-terminal domain resembles bacterial colicin nucleases in
      its requirement for alkaline earth as well as transition metal ions for
      double- and single-stranded DNA cleavage activities. The results
      indicate that the fusion of the non-specific HNH-type nuclease to the
      DNA binding domain had transformed Mull into a Mg2+-, Ni2+-, Co2+-,
      Mn2+-, Zn2+-, Ca2+-dependent sequence-specific enzyme. Nevertheless,
      Mull retains a residual single-stranded DNA cleavage activity
      controlled by its C-terminal colicin-like nuclease domain.
AU  - Kriukiene E
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 2006 580: 6115-6122.

PMID- 16024301
VI  - 1751
DP  - 2005
TI  - MnlI - The member of H-N-H subtype of Type IIS restriction endonucleases.
PG  - 194-204
AB  - The Type IIS restriction endonuclease MnlI recognizes the non-palindromic nucleotide sequence
      5'-CCTC(N)7/6 down arrow and
      cleaves DNA strands as indicated by the arrow. The genes encoding MnlI
      restriction-modification system were cloned and sequenced. It comprises
      N6-methyladenine and C5-methylcytosine methyltransferases and the
      restriction endonuclease. Biochemical studies revealed that MnlI
      restriction endonuclease cleaves double- and single-stranded DNA, and
      that it prefers different metal ions for hydrolysis of these
      substrates. Mg2+ ions were shown to be required for the specific
      cleavage of double-stranded DNA, whereas Ni2+ and some other transition
      metal ions were preferred for nonspecific cleavage of single-stranded
      DNA. The C-terminal part of MnlI restriction endonuclease revealed an
      intriguing similarity with the H-N-H type nucleolytic domain of
      bacterial toxins, Colicin E7 and Colicin E9. Alanine replacements in
      the conserved sequence motif 306Rx(3)ExHHx(14)Nx(8)H greatly reduced
      specific activity of MnlI, and some mutations even completely
      inactivated the enzyme. However, none of these mutations had effect on
      MnlI binding to the specific DNA, and on its oligomerisation state as
      well. We interpret the presented experimental evidence as a suggestion
      that the motif 306Rx(3)ExHHx(14)Nx(8)H represents the active site of
      Mnll. Consequentially, MnlI seems to be the member of Type IIS with the
      active site of the H-N-H type.
AU  - Kriukiene E
AU  - Lubiene J
AU  - Lagunavicius A
AU  - Lubys A
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 2005 1751: 194-204.

PMID- 
VI  - 2
DP  - 1998
TI  - Cloning and analysis of DNA regions adjacent to methyltransferase Lsp1109I of restriction-modification system Lsp1109I, type IIs.
PG  - 62-65
AB  - DNA regions flanking genes lsp11091R? were cloned and sequenced.  Two open reading frames
      transcribed in the same polarity as the lsp1109IMR? were found.  One of them, lsp-inv, encodes
      a protein which has 41-46% of amino acids identical with proteins belonging to the family of
      Din invertases.  This suggests that lsp-inv is possibly the gene of invertase Listeria sp.
      Translation product of the second ORF (lsp-tnp), shares 23-26% homology with transposases of
      various mobile DNA elements.  Possible function of these genes is discussed.  Analysis of
      complementary DNA strand revealed four additional ORFs whose products possess no homology with
      any aa sequence from EMBL data bank.
AU  - Kriukiene E
AU  - Lubys A
PT  - Journal Article
TA  - Biologija
JT  - Biologija
SO  - Biologija 1998 2: 62-65.

PMID- 
VI  - 1
DP  - 1998
TI  - Comparison of two restriction-modification systems recognizing the same GGATCC sequence.
PG  - 55-59
AB  - Restriction-modification system Bsp98I from Bacillus species RFL98 recognizing the sequence
      GGATCC has been cloned and sequenced.  The determined sequence predicts a methyltransferase of
      388 amino acids, Mr 45 kDa, and a restriction endonuclease of 199 aa, Mr 22.5 kDa.
      Comparisons of the predicted aa sequences indicated that Bsp98I and isoschizomeric BamHI
      restriction endonucleases share 28% identity, whereas the corresponding methyltransferases
      share 42% identity.  This observation suggests that Bsp98I and BamHI genes derive from a
      common ancestor.  Regardless of such evolutionary relatedness, the Bsp98I R-M system has no
      equivalent of the bamHIC gene which is involved in regulation of expression of BamHI R-M
      genes.  This clearly indicates that the regulation of Bsp98I R-M genes is different.  Despite
      the marginal similarity among R.BamHI and R.Bsp98I, the aa residues of catalytic/Mg2+ binding
      center as well as the ones making the major groove contacts in R.BamHI can be found in
      appropriate positions of the aligned aa sequence of R.Bsp98I.  In contrast, some amino acids
      of R.BamHI that make contacts in the minor groove are absent in R.Bsp98I.
AU  - Kriukiene E
AU  - Lubys A
PT  - Journal Article
TA  - Biologija
JT  - Biologija
SO  - Biologija 1998 1: 55-59.

PMID- 24092796
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences of Two Salmonella Strains from the SARA Collection, SARA64 (Muenchen) and SARA33 (Heidelberg), Provide Insight into Their Antibiotic  Resistance.
PG  - e00806-13
AB  - The Salmonella enterica strains that are representatives of the S. enterica serovar
      Typhimurium complex in reference collection A (SARA) are closely related
      but exhibit differences in antibiotic resistance, which could have public health
      consequences. To better understand the mechanisms behind these resistances, we
      sequenced the genomes of two multidrug-resistant strains: SARA64 (Muenchen) and
      SARA33 (Heidelberg).
AU  - Kroft BS
AU  - Brown EW
AU  - Meng J
AU  - Gonzalez-Escalona N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00806-13.

PMID- 7607523
VI  - 157
DP  - 1995
TI  - Organization and gene expression within restriction-modification systems of Herpetosiphon giganteus.
PG  - 43-47
AB  - We have characterized a family of related restriction-modification (R-M) systems from the soil
      bacterium Herpetosiphon giganteus (Hgi).  A comparison of their genetic organization reveals
      two types of regulatory proteins, called controlling ORF C.  While one of these small reading
      frames derived from RM.HgiCI seems to be an enhancer of its own promoter, evidence is provided
      for a silencer function of the other ORF C derived from the closely related AvaII-type
      systems RM.HgiBI/CII/EI.  The respective silencer function is detected during our various
      attempts to clone three isoschizomers with unusually high differences in their specific
      activity.  Sequencing and site-directed mutagenesis revealed just two amino acids as being
      responsible for a massive increase in specific activity of these endonucleases.
AU  - Kroger M
AU  - Blum E
AU  - Deppe E
AU  - Dusterhoft A
AU  - Erdmann D
AU  - Kilz S
AU  - Meyer-Rogge S
AU  - Mostl D
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 43-47.

PMID- 2828870
VI  - 155
DP  - 1987
TI  - Restriction enzyme HgiCI characterization of the 6-nucleotide staggered cut sequence and its application in mismatch cloning.
PG  - 3-10
AB  - The gliding bacterium Herpetosiphon giganteus became one of the most
      intensively screened groups of organisms in the search for new restriction
      enzymes.  Among the 10 strains tested, 17 enzymes could be found with seven
      different but related recognition sequences.  This led to a hypothesis
      regarding the evolutionary relationship among these enzymes and could be a
      basis for a better understanding of the biochemical mechanism of restriction
      enzymes-DNA target interaction.  Among these enzymes HgiCI is remarkably
      different from all other previously described endonucleases, since it produces
      5'-hexanucleotide protruding ends.  Combined with the fact that HgiCI
      recognizes a degenerate sequence, specific applications of this enzymatic
      activity in gene technology are possible.  Usually, for specific base pairing
      within 5'- or 3'- protruding ends, a match of 2 bp is fair, while four matching
      base pairs lead to highly efficient ligase reactions.  Since a perfect match of
      6 bp may not be required, we used HgiCI-restricted DNA fragments in order to
      test whether DNA ligase reactions among hexanucleotide protruding ends could
      proceed in spite of some mismatch positions.  Our results presented here allow
      the conclusion that is is possible to obtain mismatched ligase reaction
      products in considerable fractions.  A wider application of this observation
      seems possible, since an isoschizomer of HgiCI BanI, is available commercially
      and is obtained from an unrelated strain Bacillus aneurinolyticus (IAM 1077).
      In contrast to the data given in the literature, we have determined via
      cross-ligation that BanI also produces 5'-hexanucleotide protruding DNA
      fragments.  In this article we intend to focus on the methodology used to
      characterize recognition sequences and on the application of HgiCI (BanI)
      fragment ends in mismatch cloning rather than on enzyme purification
      procedures.
AU  - Kroger M
AU  - Hobom G
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1987 155: 3-10.

PMID- 6320124
VI  - 12
DP  - 1984
TI  - The nucleotide sequence recognized by the Escherichia coli A restriction and modification enzyme.
PG  - 887-899
AB  - The nucleotide recognition sequence for the restriction-modification enzyme of
      Escherichia coli A (EcoA) has been determined to be GAG-7N-GTCA.  This sequence
      is fairly similar, but distinctly different from the two other type I
      restriction enzyme recognition sites known for E. coli B and E. coli K12,
      respectively.  N6-adenosine methylation has been observed at nucleotide
      positions 2 and 12 within that sequence after modification by EcoA.  As a
      reference point for mapping the single EcoA site in lambda, the position of
      lambda point mutation Oam29 has been determined also.
AU  - Kroger M
AU  - Hobom G
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1984 12: 887-899.

PMID- 6326052
VI  - 12
DP  - 1984
TI  - Eight new restriction endonucleases from Herpetosiphon giganteus - divergent evolution in a family of enzymes.
PG  - 3127-3141
AB  - Characterization of eight restriction endonucleases isolated from five strains
      of Herpetosiphon giganteus is described.  HgiCI from strain Hpg9 recognizes and
      cleaves the degenerate sequence: 7GGPyPuCC, producing 5'-hexanucleotide
      protruding ends.  Endonucleases HgiBI, HgiCII and HgiEI are isoschizomers of
      AvaII; HgiCIII and HgiDII are isoschizomers of SalI; and HgiDI and HgiGI are
      isoschizomers of AcyI.  Based upon their closely related and in part
      overlapping recognition specificities a close evolutionary relationship is
      proposed for all known Hgi restriction endonucleases.
AU  - Kroger M
AU  - Hobom G
AU  - Schutte H
AU  - Mayer H
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1984 12: 3127-3141.

PMID- 26294633
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Parabacteroides goldsteinii with Putative Novel Metallo-beta-Lactamases Isolated from a Blood Culture from a Human Patient.
PG  - e00937-15
AB  - Parabacteroides goldsteinii was isolated from a blood culture. Genomic DNA was sequenced using
      a MiSeq sequencer and assembled using the SPAdes genome
      assembler. The draft genome sequence was 6,851,868 bp, spanning 282 contigs of
      5,253 coding sequences, 66 tRNAs, and 5 rRNAs. Several putative novel
      metallo-beta-lactamases were discovered.
AU  - Krogh TJ
AU  - Agergaard CN
AU  - Moller-Jensen J
AU  - Justesen US
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00937-15.

PMID- 318859
VI  - 474
DP  - 1977
TI  - The restriction endonuclease cleavage map of rat liver mitochondrial DNA.
PG  - 61-68
AB  - Mitochondrial DNA from rat liver contains six sites for cleavage by the
      restriction endonucleases HindIII and EcoRI.  A large stretch of DNA,
      comprising about 40% of the mitochondrial genome is not cleaved by either of
      the enzymes; eight cleavage sites are located on a DNA stretch of 35% of the
      genome length suggestive of an unequal distribution of the A-T basepairs over
      the molecule.  The number of HindIII and EcoRI fragments is much higher than
      reported for other mammalian mitochondrial DNAs up to now.
AU  - Kroon AM
AU  - Bakker H
AU  - Holtrop M
AU  - Terpstra P
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1977 474: 61-68.

PMID- 21965409
VI  - 77
DP  - 2011
TI  - Genome and Proteome of Campylobacter jejuni Bacteriophage NCTC 12673.
PG  - 8265-8271
AB  - Campylobacter jejuni continues to be the leading cause of bacterial food-borne illness
      worldwide, so improvements to current methods used
      for bacterial detection and disease prevention are needed. We describe
      here the genome and proteome of C. jejuni bacteriophage NCTC 12673 and
      the exploitation of its receptor-binding protein for specific bacterial
      detection. Remarkably, the 135-kb Myoviridae genome of NCTC 12673
      differs greatly from any other proteobacterial phage genome described
      (including C. jejuni phages CP220 and CPt10) and instead shows closest
      homology to the cyanobacterial T4-related myophages. The phage genome
      contains 172 putative open reading frames, including 12 homing
      endonucleases, no visible means of packaging, and a putative
      trans-splicing intein. The phage DNA appears to be strongly associated
      with a protein that interfered with PCR amplification and estimation of
      the phage genome mass by pulsed-field gel electrophoresis.
      Identification and analyses of the receptor-binding protein (Gp48)
      revealed features common to the Salmonella enterica P22 phage tailspike
      protein, including the ability to specifically recognize a host
      organism. Bacteriophage receptor-binding proteins may offer promising
      alternatives for use in pathogen detection platforms.
AU  - Kropinski AM
AU  - Arutyunov D
AU  - Foss M
AU  - Cunningham A
AU  - Ding W
AU  - Singh A
AU  - Pavlov AR
AU  - Henry M
AU  - Evoy S
AU  - Kelly J
AU  - Szymanski CM
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2011 77: 8265-8271.

PMID- 17825342
VI  - 369
DP  - 2007
TI  - The genome of epsilon 15, a serotype-converting, group E1 Salmonella enterica-specific bacteriophage.
PG  - 234-244
AB  - The genome sequence of the Salmonella enterica serovar Anatum-specific, serotype-converting
      bacteriophage 05 has been completed. The
      nonredundant genome contains 39,671 bp and 51 putative genes. It most
      closely resembles the genome of phi V10, an Escherichia coli O157:H7
      specific temperate phage, with which it shares 36 related genes. More
      distant relatives include the Burkholderia cepacia-specific phage,
      BccpC6B (8 similar genes), the Bordetella bronchiseptica-specific
      phage, BPP-1 (8 similar genes) and the Photobacterium profundum
      prophage, P P phi pr1 (6 similar genes).
      epsilon 15 gene identifications based on homologies with known gene
      families include the terminase small and large subunits, integrase,
      endolysin, two holins, two DNA methylase enzymes (one adenine-specific
      and one cytosine-specific) and a RecT-like enzyme. Genes identified
      experimentally include those coding for the serotype conversion
      proteins, the tail fiber, the major capsid protein and the major
      repressor. epsilon 15's attP site and the Salmonella attB site with
      which it interacts during lysogenization have also been determined.
AU  - Kropinski AM
AU  - Kovalyova IV
AU  - Billington SJ
AU  - Patrick AN
AU  - Butts BD
AU  - Guichard JA
AU  - Pitcher TJ
AU  - Guthrie CC
AU  - Sydlaske AD
AU  - Barnhill LM
AU  - Havens KA
AU  - Day KR
AU  - Falk DR
AU  - McConnell MR
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 2007 369: 234-244.

PMID- 25212627
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of a Serratia marcescens Strain Isolated from a Preterm Neonatal Blood Sepsis Patient at the Royal Infirmary, Edinburgh, Scotland, United  Kingdom.
PG  - e00908-14
AB  - Herein, we report the draft genome sequence for isolate ED-NGS-1015 of Serratia marcescens,
      cultivated from a blood sample obtained from a neonatal sepsis
      patient at the Royal Infirmary in Edinburgh, Scotland, United Kingdom.
AU  - Kropp KA
AU  - Lucid A
AU  - Carroll J
AU  - Belgrudov V
AU  - Walsh P
AU  - Kelly B
AU  - Smith C
AU  - Dickinson P
AU  - O'Driscoll A
AU  - Templeton K
AU  - Ghazal P
AU  - Sleator RD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00908-14.

PMID- 25212626
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of an Enterococcus faecalis Strain Isolated from a Neonatal Blood Sepsis Patient.
PG  - e00907-14
AB  - Herein, we report the draft genome sequence of Enterococcus faecalis ED-NGS-1009, cultivated
      from a blood sample taken from a neonatal sepsis patient at the Royal
      Infirmary in Edinburgh, Scotland, United Kingdom.
AU  - Kropp KA
AU  - Lucid A
AU  - Carroll J
AU  - Belgrudov V
AU  - Walsh P
AU  - Kelly B
AU  - Smith C
AU  - Dickinson P
AU  - O'Driscoll A
AU  - Templeton K
AU  - Ghazal P
AU  - Sleator RD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00907-14.

PMID- 25189586
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of a Staphylococcus warneri Strain Isolated from a Preterm  Neonate Blood Sepsis Patient at the Royal Infirmary, Edinburgh, Scotland.
PG  - e00877-14
AB  - Herein, we report the draft genome sequence of Staphylococcus warneri ED-NGS-1001, cultivated
      from a blood sample taken from a preterm neonate blood
      sepsis patient at the Royal Infirmary, Edinburgh, Scotland, United Kingdom.
AU  - Kropp KA
AU  - Lucid A
AU  - Carroll J
AU  - Belgrudov V
AU  - Walsh P
AU  - Kelly B
AU  - Smith C
AU  - Dickinson P
AU  - O'Driscoll A
AU  - Templeton K
AU  - Ghazal P
AU  - Sleator RD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00877-14.

PMID- 25189584
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of a Streptococcus agalactiae Strain Isolated from a Preterm Neonate Blood Sepsis Patient at the Royal Infirmary, Edinburgh, Scotland.
PG  - e00875-14
AB  - Herein, we report the draft genome sequence of Streptococcus agalactiae ED-NGS-1000,
      cultivated from a blood sample taken from a preterm neonate blood
      sepsis patient at the Royal Infirmary, Edinburgh, Scotland, United Kingdom.
AU  - Kropp KA
AU  - Lucid A
AU  - Carroll J
AU  - Belgrudov V
AU  - Walsh P
AU  - Kelly B
AU  - Smith C
AU  - Dickinson P
AU  - O'Driscoll A
AU  - Templeton K
AU  - Ghazal P
AU  - Sleator RD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00875-14.

PMID- 25212625
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of a Staphylococcus aureus Isolate Taken from the Blood of  a Preterm Neonatal Blood Sepsis Patient.
PG  - e00906-14
AB  - Herein, we report the draft genome sequence of Staphylococcus aureus ED-NGS-1006, cultivated
      from a blood sample taken from a neonatal sepsis patient at the Royal
      Infirmary in Edinburgh, Scotland, United Kingdom.
AU  - Kropp KA
AU  - Lucid A
AU  - Carroll J
AU  - Belgrudov V
AU  - Walsh P
AU  - Kelly B
AU  - Templeton K
AU  - Smith C
AU  - Dickinson P
AU  - O'Driscoll A
AU  - Ghazal P
AU  - Sleator RD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00906-14.

PMID- 25212624
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of a Pantoea sp. Isolated from a Preterm Neonatal Blood Sepsis Patient.
PG  - e00904-14
AB  - Herein, we report the draft genome sequence of Pantoea sp. ED-NGS-1003, cultivated from a
      blood sample taken from a neonatal sepsis patient at the Royal
      Infirmary, Edinburgh, Scotland, United Kingdom.
AU  - Kropp KA
AU  - Lucid A
AU  - Carroll J
AU  - Belgrudov V
AU  - Walsh P
AU  - Kelly B
AU  - Templeton K
AU  - Smith C
AU  - Dickinson P
AU  - O'Driscoll A
AU  - Ghazal P
AU  - Sleator RD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00904-14.

PMID- 28729268
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Root-Associated Sugarcane Growth-Promoting Microbispora  sp. Strain GKU 823.
PG  - e00647-17
AB  - The endophytic plant growth-promoting Microbispora sp. strain GKU 823 was isolated from the
      roots of sugarcane cultivated in Thailand. It has an estimated
      9.4-Mbp genome and a G+C content of 71.3%. The genome sequence reveals several
      genes associated with plant growth-promoting traits and extensive specialized
      metabolite biosynthesis.
AU  - Kruasuwan W
AU  - Hoskisson PA
AU  - Thamchaipenet A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00647-17.

PMID- 28495785
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Plant Growth-Promoting Endophytic Streptomyces sp. GKU 895 Isolated from the Roots of Sugarcane.
PG  - e00358-17
AB  - Streptomyces sp. GKU 895 is an endophytic actinomycete isolated from the roots of sugarcane.
      GKU 895 has a genome of 8.3 Mbp and the genome exhibits adaptations
      related to plant growth-promoting activity. It also has extensive specialized
      metabolite biosynthetic gene clusters apparent in its genome.
AU  - Kruasuwan W
AU  - Salih TS
AU  - Brozio S
AU  - Hoskisson PA
AU  - Thamchaipenet A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00358-17.

PMID- 7669344
VI  - 17
DP  - 1995
TI  - The significance of distance and orientation of restriction endonuclease recognition sites in viral DNA genomes.
PG  - 177-184
AB  - Studies on phage T3 and T7 have shown that these viruses avoid restriction not only by the
      phage-coded Ocr (and S-adenosylmethionine hydrolase) protein functions or by the complete loss
      of specific recognition sites for certain restriction endonucleases from their genomes, but
      also that there are two additional modes: resistance towards EcoP15 (which recognizes a non-
      symmetrical sequence) is achieved by an identical orientation of all the recognition sites in
      the virus genome (strand bias) and in the case of EcoRII by the extreme reduction in number
      and thereby greater distance between recognition sites in the genome.  These observations led
      to the discovery that certain restriction endonucleases require the simultaneous cooperation
      with two DNA sites for their function, as well as to the ongoing elucidation of the molecular
      modes of action of these enzymes.  Type II and type III enzymes display fundamentally
      different mechanisms of protein- DNA interaction.  For EcoRII we favor a model of simultaneous
      binding of two DNA sites to a dimeric enzyme molecule (neighboring sites of the same, looping,
      DNA molecule or sites located on different DNA molecules), while the action of EcoP15 seems to
      conform with a tracking- collision model of two enzyme molecules bound to inversely oriented
      recognition sites.  In addition to podoviruses T3 and T7, strand bias of recognition sequences
      for different type III DNA modification-restriction enzymes is also observed in the inoviruses
      M13, IKE and PF3.
AU  - Krueger DH
AU  - Kupper D
AU  - Meisel A
AU  - Reuter M
AU  - Schroeder C
PT  - Journal Article
TA  - FEMS Microbiol. Rev.
JT  - FEMS Microbiol. Rev.
SO  - FEMS Microbiol. Rev. 1995 17: 177-184.

PMID- 7607484
VI  - 157
DP  - 1995
TI  - Restriction endonucleases functionally interacting with two DNA sites.
PG  - 165
AB  - Simultaneous interaction with two recognition sites was found to be a precondition for DNA
      cleavage by certain type-II and type-III restriction endonucleases.  Nevertheless, the
      molecular mechanisms of the protein-DNA interaction are different between members of both
      classes of enzymes.
AU  - Krueger DH
AU  - Kupper D
AU  - Meisel A
AU  - Tierlich M
AU  - Reuter M
AU  - Schroeder C
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 165.

PMID- 1097737
VI  - 16
DP  - 1975
TI  - Biological functions of the bacteriophage T3 SAMase gene.
PG  - 453-455
AB  - Certain differences between phage T3 on the one hand and T3sam and T7 on the other hand
      indicate that the T3-coded SAMase function is responsible (i) for the development of the
      pseudolysogenic state by preventing T3 DNA methylation, and (ii) for the partial protection of
      the phage DNA against restriction by the P system.
AU  - Krueger DH
AU  - Presber W
AU  - Hansen S
AU  - Rosenthal HA
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1975 16: 453-455.

PMID- 16018543
VI  - 38
DP  - 2005
TI  - Reliable detection of DNA cytosine methylation at CpNpG sites using the engineered restriction enzyme EcoRII-C.
PG  - 855-856
AB  - Methylation of cytosine to 5-methylcytosine (mC) is the most important epigenetic DNA
      alteration in eukaryotes.  Cytosine methylation is involved in establishing a silenced
      chromatin stage through interaction with DNA-binding proteins and recruitment of histone
      deacetylases and other histone-modifying enzymes leading to chromatin remodeling.  In this
      fashion, DNA methylation is connected with processes of normal and pathological gene
      regulation, DNA replication, virus latency, parental imprinting embryonic development,
      carcinogenesis, and genetic diseases in higher organisms.  Analogous to the terms
      transcriptome and proteome, the neologism methylome has been proposed to describe the complete
      set of DNA methylation in a cell, which carries information in addition to the naked DNA
      sequence.  The methylome changes over time and, depending on its alterations, is linked to
      aging, cancer, and polymorphic variation in populations.
AU  - Krueger DH
AU  - Reuter M
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 2005 38: 855-856.

PMID- 14685246
VI  - 426
DP  - 2003
TI  - A conspicuous nickel protein in microbial mats that oxidize methane anaerobically.
PG  - 878-881
AB  - Anaerobic oxidation of methane (AOM) in marine sediments is an important microbial process in
      the global carbon cycle and in control of greenhouse
      gas emission. The responsible organisms supposedly reverse the reactions
      of methanogenesis, but cultures providing biochemical proof of this have
      not been isolated. Here we searched for AOM-associated cell components in
      microbial mats from anoxic methane seeps in the Black Sea. These mats
      catalyse AOM rather than carry out methanogenesis. We extracted a
      prominent nickel compound displaying the same absorption spectrum as the
      nickel cofactor F430 of methyl-coenzyme M reductase, the terminal enzyme
      of methanogenesis; however, the nickel compound exhibited a higher
      molecular mass than F430. The apparent variant of F(430) was part of an
      abundant protein that was purified from the mat and that consists of three
      different subunits. Determined amino-terminal amino acid sequences matched
      a gene locus cloned from the mat. Sequence analyses revealed similarities
      to methyl-coenzyme M reductase from methanogenic archaea. The abundance of
      the nickel protein (7% of extracted proteins) in the mat suggests an
      important role in AOM.
AU  - Krueger M
AU  - Meyerdierks A
AU  - Gloeckner FO
AU  - Amann R
AU  - Widdel F
AU  - Kube M
AU  - Reinhardt R
AU  - Kahnt J
AU  - Boecher R
AU  - Thauer RK
AU  - Shima S
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2003 426: 878-881.

PMID- 
VI  - 0
DP  - 1994
TI  - Host-controlled modification and restriction.
PG  - 669-674
AB  - The application of restriction endonucleases has revolutionized molecular biological research.

      As so often was the case, studies on bacterial viruses led to the discovery of this class of

      enzyme. At the beginning of the fifties, the observation was noted that phages 'remember'

      the last host strain in which they reproduced. Depending on the host, the virus carries a

      specific modification which usually improves its ability to grow on the same host in

      subsequent rounds of infection, while impairing its growth in others. Host-controlled

      modification results in a reversible phenotype, clearly distinguishable from irreversible

      mutational changes in host range.

      

      The molecular explanation of these phenomena (first demonstrated for phage lambda and P2)

      was elaborated in the 60s and 70s by groups of W. Arber, H.O. Smith, M. Meselson and others.

      Host-controlled modification consists of a specific DNA methylation at a defined recognition

      sequence of 4-8 bp. Restriction is caused by DNA cleavage occurring at an unmethylated

      recognition site. Pairs of corresponding DNA methylases and restriction endonucleases (i.e.

      recognizing the same site) coded by hsd genes (host specificity of DNA) in bacterial cells are

      responsible for these activities. During DNA replication, recognition sequences in nascent

      daughter strands are transiently unmethylated. Such hemimethylated sites are preferential

      substrates for DNA methylases, while sites unmethylated in both strands are primary targets of

      restriction endonucleases and are very rarely methylated.

      

      DNA modification consists of a C-5 or N-4 methylation of cytosine or an N-6 methylation of

      adenine in the recognition sequence. S-Adenosylmethionine (AdoMet) functions as the methyl

      donor. DNA restriction results in fragments with cohesive or blunt ends which are further

      degraded intracellularly by other nucleases, in particular by the recBCD=exoV enzyme.

      

      DNA modification/restriction (M/R) systems ae ubiquitous in the procaryote world but there

      is no unequivocal evidence of their existence in higher eucaryotes.

      

AU  - Kruger DH
PT  - Journal Article
TA  - Encyclop. Virol.
JT  - Encyclop. Virol.
SO  - Encyclop. Virol. 1994 0: 669-674.

PMID- Not carried by PubMed...
VI  - 37
DP  - 1987
TI  - Methylases as regulators of gene activity.
PG  - 268-270
AB  - None
AU  - Kruger DH
PT  - Journal Article
TA  - Wiss. Fortsch.
JT  - Wiss. Fortsch.
SO  - Wiss. Fortsch. 1987 37: 268-270.

PMID- Not carried by PubMed...
VI  - 107
DP  - 1988
TI  - Methylation of DNA as a molecular biological regulatory signal.
PG  - 257-266
AB  - Methylation of adenine or cytosine adds information to the DNA double strand
      which can influence the interactions between DNA and proteins.  Besides the
      protection of DNA against corresponding restriction endonucleases in
      prokaryotic cells, a number of new functions of DNA methylation in prokaryotic
      and eukaryotic cells have been demonstrated.  These observations are mainly
      related to the regulation of gene expression.  In gene technology in vitro,
      artificial DNA methylation is exploited to change the number of sensitive
      recognition sites for certain restriction endonucleases.  Finally, the
      properties of the first natural inhibitory protein (Ocr) against DNA
      methylation and the possible significance of cellular effector molecules
      specifically blocking or enhancing DNA methylation are discussed.
AU  - Kruger DH
PT  - Journal Article
TA  - Biol. Zentralbl.
JT  - Biol. Zentralbl.
SO  - Biol. Zentralbl. 1988 107: 257-266.

PMID- 2836807
VI  - 16
DP  - 1988
TI  - EcoRII can be activated to cleave refractory DNA recognition sites.
PG  - 3997-4008
AB  - EcoRII restriction sites [5'-CC(A/T)GG] in phage T3 and T7 DNA are refractory
      to cleavage by EcoRII, but become sensitive to cleavage in the presence of DNAs
      which contain an abundance of EcoRII sensitive sites (e.g. pBR322 or lambda
      DNA).  Studies using fragments of pBR322 containing different numbers of EcoRII
      sites show that the susceptibility to EcoRII cleavage is proportional to the
      number of sites in the individual fragment.  We postulate that EcoRII is the
      prototype of restriction endonucleases which require at least 2 simultaneously
      bound substrate sites for their activation.  EcoRII sites are refractory when
      they occur at relatively low frequency in the DNA.  The restriction enzyme can
      be activated by DNA with a higher frequency of sites.
AU  - Kruger DH
AU  - Barcak GJ
AU  - Reuter M
AU  - Smith HO
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1988 16: 3997-4008.

PMID- 2839163
VI  - 47
DP  - 1988
TI  - Abolition of DNA recognition site resistance to the restriction endonuclease EcoRII.
PG  - K1-K5
AB  - The EcoRII recognition sites 5'-CC(A/T)GG-3' which occur three times in T3 DNA
      are refractory to this restriction endonuclease.  However, these sites are
      specifically cleaved by EcoRII when a second, susceptible DNA species (pBR322,
      phage lambda) is present.
AU  - Kruger DH
AU  - Barcak GJ
AU  - Smith HO
PT  - Journal Article
TA  - Biomed. Biochim. Acta
JT  - Biomed. Biochim. Acta
SO  - Biomed. Biochim. Acta 1988 47: K1-K5.

PMID- 6314109
VI  - 47
DP  - 1983
TI  - Bacteriophage Survival:  Multiple mechanisms for avoiding the deoxyribonucleic acid restriction systems of their hosts.
PG  - 345-360
AB  - None
AU  - Kruger DH
AU  - Bickle TA
PT  - Journal Article
TA  - Microbiol. Rev.
JT  - Microbiol. Rev.
SO  - Microbiol. Rev. 1983 47: 345-360.

PMID- Not carried by PubMed...
VI  - 0
DP  - 1990
TI  - DNA methylation and restriction processes in Escherichia coli: Insights by use of bacterial viruses T3 and T7.
PG  - 113-124
AB  - DNA modification-restriction enzymes of Escherichia coli cells can be grouped into 3 families,
      called type I, II, and III. The ocr+ gene of T7 encodes the first known inhibitor protein
      specifically blocking a group of methylases and endonucleases which, in particular, belong to
      the type I (EcoB, EcoK) enzymes. The appearance of recognition sites for type II enzymes
      (e.g., EcoRII, methylases EcoDam and EcoDcm) is strongly counterselected in the T7 genome,
      furthermore, there are additional mechanisms preventing the enzymes from acting on the
      remaining sites. For instance, EcoRII is a restriction enzyme which requires the coordinated
      presence of at least 2 recognition sites in the substrate DNA for its activity. Sites which do
      not fulfill this requirement are refractory to EcoRII but can be cleaved by this enzyme in the
      presence of a second, susceptible DNA species or oligonucleotides. The resistance of T7 DNA
      towards the type III enzyme EcoP15 is explained by the absolute strand bias of the
      non-symmetric sites (in which only 1 strand can be methylated) in the DNA molecule. These data
      allow some understanding of how the endogenous DNA in EcoP15-encoding cells could be protected
      against self-restriction during replication. The frequency and polarity of recognition sites
      in the DNA molecula may play a critical role in the function of certain restriction
      endonucleases and methylases.
AU  - Kruger DH
AU  - Bickle TA
AU  - Reuter M
AU  - Pein C-D
AU  - Schroeder C
PT  - Journal Article
TA  - Nucleic Acid Methylation
JT  - Nucleic Acid Methylation
SO  - Nucleic Acid Methylation 1990 0: 113-124.

PMID- 2467142
VI  - 13D
DP  - 1989
TI  - Studies on DNA methylation and restriction processes by use of bacterial virus T7.
PG  - 200
AB  - DNA modification-restriction enzymes of Escherichia coli cells can be grouped into 3 families,
      called type I,II, and III. The ocr+ gene of T7 encodes the first known inhibitor protein
      specifically blocking a group of methylases and endonucleases which, in particular, belong to
      the type I (EcoB, EcoK) enzymes. The appearance of recognition sites for type II enzymes
      (e.g., EcoRII, methylases EcoDam and EcoDcm) is strongly counterselected in the T7 genome,
      futhermore, there are additional mechanisms preventing the enzymes from acting on the
      remaining sites. For instance, EcoRII is a restriction enzyme which requires the coordinated
      presence of at least 2 recognition sites in the substrate DNA for its activity. Sites which do
      not fulfill this requirement are refractory to EcoRII but can be cleaved by this enzyme in the
      presence of a second, susceptible DNA species or oligonucleotides (CDP et al., submitted). The
      resistance of T7 DNA towards the type III enzyme EcoP15 is explained by the absolute strand
      bias of the non-symmetric sites (in which only one strand can be methylated) in the DNA
      molecule (4; CS et al., in prep.). These data allow some understanding of how the endogenous
      DNA in EcoP15-encoding cells could be protected against self-restriction during replication.
      The frequency and polarity of recognition sites in the DNA molecule may play a critical role
      the function of certain restriction endonucleases and methylases.
AU  - Kruger DH
AU  - Bickle TA
AU  - Reuter M
AU  - Pein CD
AU  - Schroeder C
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1989 13D: 200.

PMID- 345078
VI  - 159
DP  - 1978
TI  - Protection of foreign DNA against host-controlled restriction in bacterial cells.
PG  - 107-110
AB  - Foreign F'lac plasmid DNA which is introduced into potentially restricting E.
      coli recipient cells can be protected from restriction by preinfecting the
      recipient cells with UV-inactivated T3 or T7 bacteriophages which express the
      ocr gene function.  The recipient cells survive and are able to replicate
      themselves as well as the newly acquired plasmid.
AU  - Kruger DH
AU  - Chernin LS
AU  - Hansen S
AU  - Rosenthal HA
AU  - Goldfarb DM
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1978 159: 107-110.

PMID- 702116
VI  - 41
DP  - 1978
TI  - The ocr gene function of bacterial viruses T3 and T7 prevents host-controlled modification.
PG  - 189-192
AB  - On pre-infection of the host Escherichia coli B with u.v.-inactivated T3 or T7
      phage able to express their early genes (like 0.3), B-specific modification of
      super-infecting, successfully multiplying viruses does not take place.  the ocr
      gene function (gene 0.3) of T3 and T7 not only prevents host-specific DNA
      restriction but also modification, probably by inhibiting the same late step in
      the interaction between the restriction enzyme and DNA.
AU  - Kruger DH
AU  - Gola G
AU  - Weisshuhn I
AU  - Hansen S
PT  - Journal Article
TA  - J. Gen. Virol.
JT  - J. Gen. Virol.
SO  - J. Gen. Virol. 1978 41: 189-192.

PMID- 788357
VI  - 16
DP  - 1976
TI  - Host-controlled modification and restriction of bacteriophage T7 by various Escherichia coli B strains in vivo.
PG  - 73-76
AB  - It is known for more than 20 years that phages possess a "memory" for the host strain on which
      they grew last.  For instance, lambda phages grown on E. coli K are restricted in E. coli B
      cells, i.e. their efficiency of plating on E. coli B cells is several orders of magnitude
      below their e.o.p. on E. coli K host cells.  This effect is reversible, phages grown on E.
      coli B are restricted by E. coli K but grow well on E. coli B.  Therefore, the phage DNA is
      not mutated but rather modified or - in absence of the right modification - restricted by the
      host.  For phage lambda the molecular basis of this modification/restriction consists in a
      host-specific methylation or an endonucleolytic DNA degradation at specific recognition sites
      of the phage DNA.  Meanwhile, the M/R of DNA (not only of phage DNA!) has been recognized as a
      general principle in molecular genetics with wide practical applications.
AU  - Kruger DH
AU  - Hansen S
AU  - Presber W
PT  - Journal Article
TA  - Z. Allg. Mikrobiol.
JT  - Z. Allg. Mikrobiol.
SO  - Z. Allg. Mikrobiol. 1976 16: 73-76.

PMID- 6300450
VI  - 45
DP  - 1983
TI  - The ocr+ gene function of bacteriophages T3 and T7 counteracts the Salmonella typhimurium DNA restriction systems SA and SB.
PG  - 1147-1149
AB  - In host cells containing the Salmonella typhimurium DNA
      restriction-modification systems SA+ and SB+, replication of the ocr+
      bacteriophages T3 and T7 is not impaired.  However, ocr(gene 0.3) mutants of
      these phages are susceptible to DNA restriction and modification by the SA+ and
      SB+ systems.
AU  - Kruger DH
AU  - Hansen S
AU  - Reuter M
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1983 45: 1147-1149.

PMID- 345634
VI  - 17
DP  - 1977
TI  - Different restriction of bacteriophages T3 and T7 by P1-lysogenic cells and the role of the T3-coded SAMase.
PG  - 581-591
AB  - The intracellular growth of the phages T3 and T7 is restricted in the
      presence of the Escherichia coli prophage P1.  Phage T3 has a higher ability to express its
      genome and to damage the host cell than T7.  This partial protection of T3 against P1
      restriction is due to the T3-coded SAMase, an enzyme which degrades S-
      adenosylmethionine, the cofactor of the P1 restriction endonuclease.  Since we did not
      observe DNA cleavage in vivo, we conclude that the in vivo action of the P1 nuclease is
      limited to a SAM-dependent repressor-like binding to T3 and T7 DNA, while further
      reactions with the DNA (modification vs cleavage) are blocked.
AU  - Kruger DH
AU  - Presber W
AU  - Hansen S
AU  - Rosenthal HA
PT  - Journal Article
TA  - Z. Allg. Mikrobiol.
JT  - Z. Allg. Mikrobiol.
SO  - Z. Allg. Mikrobiol. 1977 17: 581-591.

PMID- 2086761
VI  - 9
DP  - 1990
TI  - Cloning of the resistant EcoRII recognition site of phage T7 into an EcoRII-sensitive plasmid makes the site susceptible to the restriction enzyme.
PG  - 679-683
AB  - The recognition sequence 5'-CC(A/T)GG for EcoRII in the bacteriophage T7 genome
      is refractory to this restriction endonuclease, despite not bearing the
      specific (protective) methylation.  Following the integration of this site as
      part of a 219 bp fragment (in which the recognition sequence is flanked by
      about 100 bp of T7 origin) into the EcoRII-sensitive vector pUC18, the T7 site
      becomes susceptible to cleavage, too.  The same is true of recombinant pBR322
      plasmids containing the T7-derived recognition site.  The results show that the
      flanking sequences are not immediately responsible for the refractory behaviour
      of EcoRII sites and are in agreement with data according to which EcoRII
      requires the coordinated presence of at least two recognition sites in its DNA
      substrate.
AU  - Kruger DH
AU  - Prosch S
AU  - Reuter M
AU  - Goebel W
PT  - Journal Article
TA  - J. Basic Microbiol.
JT  - J. Basic Microbiol.
SO  - J. Basic Microbiol. 1990 9: 679-683.

PMID- 6285143
VI  - 185
DP  - 1982
TI  - Influence of phage T3 and T7 gene functions on a Type III (EcoP1) DNA restriction-modification system in vivo.
PG  - 457-461
AB  - The ocr+ gene function (gp 0.3) of bacteriophages T3 and T7 not only
      counteracts type I (EcoB, EcoK) but also type III restriction endonucleases
      (EcoP1).  Despite the presence of recognition sites, phage DNA as well as
      simultaneously introduced plasmid DNA are protected by ocr+ expression against
      both the endonucleolytic and the methylating activities of the EcoP1 enzyme.
      Nevertheless, the EcoP1 protein causes the exclusion of T3 and T7 in
      P1-lysogenic cells, apparently by exerting a repressor-like effect on phage
      gene expression.  T3 which induces an S-adenosylmethionine hydrolase is less
      susceptible to the repressor effect of the SAM-stimulated EcoP1 enzyme.  The
      abundance of EcoP1 recognition sites in the T7 genome is explained by their
      near identity with the T7 DNA primase recognition site.
AU  - Kruger DH
AU  - Reuter M
AU  - Hansen S
AU  - Schroeder C
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1982 185: 457-461.

PMID- 6308393
VI  - 190
DP  - 1983
TI  - Restriction of bacteriophage T3 and T7 ocr+ strains by the type II restriction endonuclease EcoRV.
PG  - 349-351
AB  - When E. coli cells carrying the plasmid pLG13 coding for the newly discovered
      type II restriction endonuclease EcoRV are infected with phage T3 or T7, only
      T7 is able to replicate normally. T3 wild-type as well as its mutants are
      subject to DNA restriction in vivo and in vitro.  The EcoRV enzyme cuts T3 DNA
      at 5 sites.  T7 and its ocr- mutants have no EcoRV sites in their DNA.  In
      contrast to the anti-restriction acitivity of the T3 and T7 ocr+ gene functon
      against type I and III restriction enzymes, the ocr+ protein is unable to
      inactivate the type II restriction endonuclease EcoRV.
AU  - Kruger DH
AU  - Reuter M
AU  - Schroeder C
AU  - Glatman LI
AU  - Chernin LS
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1983 190: 349-351.

PMID- 329108
VI  - 153
DP  - 1977
TI  - Active protection by bacteriophages T3 and T7 against E. coli B- and K-specific restriction of their DNA.
PG  - 99-106
AB  - The bacteriophages T3 and T7 are not modified and restricted by E. coli
      strains with different host specificity (E. coli B, K, 0) in vivo.  The phages code for a gene
      product with the ability to overcome classical restriction (ocr): ocr- mutants are subject to
      modification and restriction via DNA methylation vs cleavage.  The T3 genome possesses
      recognition sites for the restriction endonuclease R.EcoB which, unless the DNA is B-
      specifically modified, trigger 5-7 DNA cleavages.  The ocr gene function of T3 and T7 is
      located within the gene 0.3 region of these phages and is not identical with the sam
      (SAMase) function of T3.  The mechanism of ocr protection remains unclear, while it is
      certain that this protection by the gene 0.3 protein is exerted in the infected cell and not
      through "over-all" modification in the preceding growth cycle of the phage.
AU  - Kruger DH
AU  - Schroeder C
AU  - Hansen S
AU  - Rosenthal HA
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1977 153: 99-106.

PMID- 3266863
VI  - 74
DP  - 1988
TI  - Use of bacterial virus T7 as a tool for the study of DNA methylation.
PG  - 85-87
AB  - Meeting Abstract
AU  - Kruger DH
AU  - Schroeder C
AU  - Reuter M
AU  - Bickle TA
AU  - Bogdarina IG
AU  - Buryanov YI
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 85-87.

PMID- 3894024
VI  - 150
DP  - 1985
TI  - DNA methylation of bacterial viruses T3 and T7 by different DNA methylases in Escherichia coli K12 cells.
PG  - 323-330
AB  - We have investigated the susceptibility of the genomes of the related bacteriophages T3 and T7
      to the three major DNA methyltransferases (EcoK, dam, dcm) of their host, Escherichia coli
      K12. In vivo the EcoK host specificity enzyme only methylates the DNA of ocr phages. This is
      due to an inhibition of the enzyme by the phage ocr gene product, which had previously been
      shown to be an inhibitor of the restriction endonuclease. EcoK-specific DNA methylation
      protects the ocr viruses after one growth cycle on these host cells against the action of
      corresponding restriction endonuclease EcoK. Owing to the unique S-adenosyl-L-methionine
      hydrolase (sam) activity of the T3-coded ocr protein, the T3 DNA is absolutely devoid of the
      methylated bases 6-methylaminopurine and 5-methylcytosine. In contrast to this, T7 derivatives
      and sam- derivatives of T3 carry a small number of about 2-4 molecules 6-methylaminopurine and
      5-methylcytosine per genome. The presence of 6-methylaminopurine is due to dam methylation,
      though the majority of dam sites remain unmethylated. In vivo as well as in vitro the ocr
      protein has no influence on the activities of the dam and dcm methylase. The experiments gave
      some evidence for the existence of a second cytosine methylase in E. coli K12. Besides dam and
      dcm recognition sites being undermethylated, their absolute number in T3 and T7 DNAs is far
      below the expected value. Moreover, one of the two dcm sites present in T7 (Studier strain) is
      missing in our T7 strain owing to a 1300-base-pair deletion in gene 0.7.
AU  - Kruger DH
AU  - Schroeder C
AU  - Reuter M
AU  - Bogdarina IG
AU  - Buryanov YI
AU  - Bickle TA
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1985 150: 323-330.

PMID- 2476230
VI  - 15
DP  - 1989
TI  - Avoidance of DNA methylation:  A virus-encoded methylase inhibitor and evidence for counterselection of methylase recognition sites in viral genomes.
PG  - 87-95
AB  - The ocr+ gene of bacterial virus T7 codes for the first protein recognized to
      inhibit a specific group of DNA methylases.  The recognition sequences of
      several other DNA methylases, not susceptible to Ocr inhibition, are
      significantly suppressed in the virus genome.  The bacterial virus T3 encodes
      an Ado-Met hydrolase, destroying the methyl donor and causing T3 DNA to be
      totally unmethylated.  These observations could stimulate analogous
      investigations into the regulation of DNA methylation patterns of eukaryotic
      viruses and cells.  For instance, an underrepresentation of methylation sites
      (5'-CG) is also true for animal DNA viruses.  Moreover, we were able to
      disclose some novel properties of DNA restriction-modification enzymes
      concerning the protection of DNA recognition sequences in which only one strand
      can be methylated (e.g., type III enzyme EcoP15) and the primary resistance of
      (unmethylated) DNA recognition sites towards type II restriction endonuclease
      EcoRII.
AU  - Kruger DH
AU  - Schroeder C
AU  - Santibanez-Koref M
AU  - Reuter M
PT  - Journal Article
TA  - Cell Biophys.
JT  - Cell Biophys.
SO  - Cell Biophys. 1989 15: 87-95.

PMID- Not included in PubMed...
VI  - 373
DP  - 1992
TI  - A nuclear protein from HeLa cells containing a methyltransferase specific domain binds to an intragenic region of the adenovirus 12 CS-1 E1A oncogene.
PG  - 789
AB  - We identified a binding motif (CAGCTGC) for bHLH (basic region Helix Loop Helix) proteins in
      the coding part of the Adenovirus 12 E1a gene. The growth enhanced but transformation
      defective Vero-cell host range mutant CS-1 of Adenovirus 12 has a 69 bp deletion in E1a
      adjacent to this binding site. We examined the intragenic site in the E1a-gene for binding of
      HeLa and Vero nuclear proteins using gel shift assays. We obtained comparable patterns of 3-4
      retarded bands for wild type and mutant E1a sequences using DNA fragments and mutant
      oligonucleotides (Cdel). Oligonucleotides bearing motifs for the transcription factors AP-4
      and/or AP-1 significantly affected the binding of nuclear proteins to the E1a probes, whereas
      motifs for E2F, ATF, fac-b, and NF1 had little or no effect. SDS-PAGE analysis of Cdel binding
      protein, purified by different methods, revealed average molecular weights of 70 kDa and 84
      kDa. Constructs containing the intragenic DNA fragments of Ad12 wild type and CS-1 mutant E1a,
      the SV40 promotor, and the CAT gene did not cause any enhanced or decreased CAT-activity after
      transfection of HeLa cells compared to pCAT-promotor construct alone. Screening of a HeLa
      lambda-gt11 expression library for Cdel-binding proteins resulted in five identical
      cDNA-clones containing a 450 bp open reading frame. We identified a 25 amino acid long domain
      that has 80% homology to the conserved region X of (cytidine-5)-DNA-methyltransferases. We
      currently investigate the function of the purified protein.
AU  - Kruger H
AU  - Kirch H
PT  - Journal Article
TA  - Biol. Chem. Hoppe Seyler
JT  - Biol. Chem. Hoppe Seyler
SO  - Biol. Chem. Hoppe Seyler 1992 373: 789.

PMID- 1316864
VI  - 114
DP  - 1992
TI  - Characterization of the mcrBC region of Escherichia coli K-12 wild-type and mutant strains.
PG  - 1-12
AB  - We have carried out an analysis of the Escherichia coli K-12 mcrBC locus in order to (1)
      elucidate its genetic organization, (2) to identify the proteins encoded by this region, and
      (3) to characterize their involvement in the restriction of DNA containing methylated cytosine
      residues. In vitro expression of recombinant plasmids carrying all or portions of the mcrBC
      region revealed that the mcrB and mcrC genes are organized as an operon. The mcrBC operon
      specifies five proteins, as evident from parallel in vitro and in in vivo expression studies.
      Three proteins of 53,35 and 34 kDa originate from mcrB expression, while two proteins of 37
      and 16 kDa arise from mcrC expression. Products of both the mcrB and mcrC genes are required
      to restrict the methylated substrate DNA used in this study. We also determined the nature of
      mutant mcrBC loci in comparison to the E. coli K-12 wild-type mcrBC locus. A major goal of
      these studies was to clarify the nature of the mcrB-1 mutation, which is carried by some
      strains employed in previous analyses of the E. coli K-12 McrBC system. Based on our analyses
      the mutant strains investigated could be divided into different complementation groups. The
      mcrB-1 mutation is a nonsense or frameshift mutation located within mcrB. It causes premature
      termination of mcrB gene product synthesis and reduces the level of mcrC gene expression. This
      finding helps to understand an existing conflict in the literature. We also describe
      temperature-sensitive McrA activity in some of the strains analysed and its relationship to
      the previously defined differences in the tolerance levels of E. coli K-12 mcrBC mutants to
      cytosine methylation.
AU  - Kruger T
AU  - Grund C
AU  - Wild C
AU  - Noyer-Weidner M
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1992 114: 1-12.

PMID- 7781618
VI  - 14
DP  - 1995
TI  - McrB: a prokaryotic protein specifically recognizing DNA containing modified cytosine residues.
PG  - 2661-2669
AB  - Restriction of DNA by the Escherichia coli K-12 McrBC restriction endonuclease, which consists
      of the two subunits McrB and McrC, depends on the presence of modified cytosine residues in a
      special constellation. From previous work by others it was known that restriction of
      5-methylcytosine-containing DNA requires two methylated 5'-PuC sites separated by about 40-80
      non-defined base pairs. Here we show that binding of the McrBC nuclease is mediated
      exclusively by the McrB subunit. McrB has a low affinity for non-methylated DNA, with which it
      forms low molecular weight complexes. The affinity for DNA is significantly increased, with
      variations depending on the sequence context, by hemi- or fully methylated 5'-PuC sites.
      Binding to such substrates yields high molecular weight complexes, presumably involving
      several McrB molecules. Methylation at unique 5'-PuC sites can be sufficient to stimulate DNA
      binding by McrB. As such substrates are not cleaved by the nuclease, restriction apparently
      requires the coordinated interaction of molecules bound to neighboring 5'-PumC sites. The
      binding properties of McrB exhibit some similarities to recently identified eukaryotic
      proteins interacting in a non-sequence-specific manner with DNA containing methylated 5'-CpG
      sequences and might point to a common molecular origin of these proteins. In addition to DNA,
      McrB also binds GTP, an essential cofactor in DNA restriction by McrBC. McrC neither binds to
      DNA nor modulates the DNA binding potential of McrB. As McrC is essential for restriction it
      appears to predominantly function in catalysis.
AU  - Kruger T
AU  - Wild C
AU  - Noyer-Weidner M
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1995 14: 2661-2669.

PMID- Not carried by PubMed...
VI  - 109
DP  - 1990
TI  - Biological functions of restriction endonucleases.
PG  - 257-266
AB  - The biological function of restriction endonucleases in bacterial cells is
      reviewed (in german).  A description of the different classes of restriction
      endonucleases is followed by a discussion of their evolutionary significance in
      maintaining the compromise between genetic stabilility and variability of
      microorganisms.  Restriction enzymes have a role in the defence against lethal
      phage infection as well as in genetic recombination.  Two groups of enzymes in
      Salmonella and Escherichia strains are presented as examples of restriction
      enzyme evolution.  Certain bacterial cells express defence systems which attack
      methylated DNA.  These enzymes complicate the cloning of methylated eukaryotic
      DNA.
AU  - Kruger VDH
AU  - Reuter M
AU  - Chernin LS
AU  - Gachechiladze KK
AU  - Chanishvili TG
AU  - Schroeder C
PT  - Journal Article
TA  - Biol. Zentralbl.
JT  - Biol. Zentralbl.
SO  - Biol. Zentralbl. 1990 109: 257-266.

PMID- 9026721
VI  - 30
DP  - 1996
TI  - Endonuclease SegE phage T4.  II. Determination and characterization of recognition site.
PG  - 1307-1315
AB  - 
AU  - Krukov VM
AU  - Shlyapnikov MG
AU  - Kadyrov FA
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1996 30: 1307-1315.

PMID- 24501624
VI  - 8
DP  - 2013
TI  - Complete genome sequence of Dehalobacter restrictus PER-K23(T.).
PG  - 375-388
AB  - Dehalobacter restrictus strain PER-K23 (DSM 9455) is the type strain of the species
      Dehalobacter restrictus. D. restrictus strain PER-K23 grows by
      organohalide respiration, coupling the oxidation of H2 to the reductive
      dechlorination of tetra- or trichloroethene. Growth has not been observed with
      any other electron donor or acceptor, nor has fermentative growth been shown.
      Here we introduce the first full genome of a pure culture within the genus
      Dehalobacter. The 2,943,336 bp long genome contains 2,826 protein coding and 82
      RNA genes, including 5 16S rRNA genes. Interestingly, the genome contains 25
      predicted reductive dehalogenase genes, the majority of which appear to be full
      length. The reductive dehalogenase genes are mainly located in two clusters,
      suggesting a much larger potential for organohalide respiration than previously
      anticipated.
AU  - Kruse T et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 375-388.

PMID- 332589
VI  - 13
DP  - 1977
TI  - Discovery of new type of restriction and modification in enterobacteriaceae.
PG  - 1079-1088
AB  - The adsorption of 23 new lamboid bacteriophages to 547 strains which were isolated from a
      natural population of Enterobacteriaceae was studied.  The frequency of positive combinations
      of phage-bacterium with adsorption is not more than 2%.  A study of possible causes of limited
      growth of lambdoid phages in the bacterial strains revealed that neither homoimmune prophage
      nor prophage P2 are single factors of the growth limitation.  It is found that in natural
      populations a selection of bacterial strains with the least limitation of phage takes place.
      Three cases of killing bacteria after infection with high multiplicity are found.  The reason
      of the killing effect is manifestation of some functions by infecting phages.  A new
      restriction-modification system is found which differs from restriction-modification system A,
      B, K, 15, P1, EcoRI, EcoRII.  Most strains, which adsorb phages but do not support their
      growth, are supposed to possess several mechanisms of restriction.  Thus, the search for new
      restriction systems in Escherichia coli is worthwhile.
AU  - Krylov VN
AU  - Karapetian AT
PT  - Journal Article
TA  - Genetika
JT  - Genetika
SO  - Genetika 1977 13: 1079-1088.

PMID- 
VI  - 63
DP  - 1998
TI  - Transition-metal complexes as inhibitors of proteins recognizing double-stranded fragments of nucleic acids.
PG  - 1251-1257
AB  - A 30-membered DNA duplex containing the recognition site of restriction endonuclease SsoII and
      a 30-membered RNA-DNA hybrid duplex, a substrate of E. coli RNase H, were synthesized.  The
      cleavage of the 30-membered fragments of nucleic acids catalyzed by endonucleases in the
      presence of Co-phthalocyanine complex [CoPc(COONa)8 containing eight carboxyl groups at the
      periphery of the ligand was studied.  It was shown that the efficiency of enzyme catalysis
      decreases in the presence of the metal complex for both endonucleases.  By addition of a
      100-fold excess of Co-phthalocyanine complex with respect to DNA duplex the initial rate of
      substrate hydrolysis by restriction endonuclease SsoII is observed to decrease twice.  An
      equimolar ratio of the metal complex and hybrid duplex leads to essentially complete
      inhibition of RNA cleavage by RNase H from E. coli.  The inhibition of catalytic activity of
      enzymes recognizing the double-stranded nucleic acids in the presence of Co-phthalocyanine
      complex is assumed to be caused by the ability of the latter to interact with DNA, RNA, and
      DNA-RNA duplexes.
AU  - Krynetskaya NF
AU  - Kubareva EA
AU  - Timchenko MA
AU  - Belkov VM
AU  - Shabarova ZA
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1998 63: 1251-1257.

PMID- 23682145
VI  - 1
DP  - 2013
TI  - Genome Sequence of Bacillus subtilis MB73/2, a Soil Isolate Inhibiting the Growth of Plant Pathogens Dickeya spp. and Rhizoctonia solani.
PG  - e00238-13
AB  - Bacillus subilis MB73/2 is a Gram-positive bacterium isolated in Poland from a meadow soil
      sample. When tested in vitro, the strain shows strong antagonism
      toward plant pathogens-the soft rot-causing bacteria Dickeya spp. and the crown
      rot fungus Rhizoctonia solani. Here, we present the genome sequence of MB73/2.
AU  - Krzyzanowska DM
AU  - Iwanicki A
AU  - Ossowicki A
AU  - Obuchowski M
AU  - Jafra S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00238-13.

PMID- 28878862
VI  - 12
DP  - 2017
TI  - Permanent draft genome sequence of Frankia sp. NRRL B-16219 reveals the presence  of canonical nod genes, which are highly homologous to those detected in  Candidatus Frankia Dg1 genome.
PG  - 51
AB  - Frankia sp. NRRL B-16219 was directly isolated from a soil sample obtained from the
      rhizosphere of Ceanothus jepsonii growing in the USA. Its host plant range
      includes members of Elaeagnaceae species. Phylogenetically, strain NRRL B-16219
      is closely related to 'Frankia discariae' with a 16S rRNA gene similarity of
      99.78%. Because of the lack of genetic tools for Frankia, our understanding of
      the bacterial signals involved during the plant infection process and the
      development of actinorhizal root nodules is very limited. Since the first three
      Frankia genomes were sequenced, additional genome sequences covering more diverse
      strains have helped provide insight into the depth of the pangenome and attempts
      to identify bacterial signaling molecules like the rhizobial canonical nod genes.
      The genome sequence of Frankia sp. strain NRRL B-16219 was generated and
      assembled into 289 contigs containing 8,032,739 bp with 71.7% GC content.
      Annotation of the genome identified 6211 protein-coding genes, 561 pseudogenes,
      1758 hypothetical proteins and 53 RNA genes including 4 rRNA genes. The NRRL
      B-16219 draft genome contained genes homologous to the rhizobial common
      nodulation genes clustered in two areas. The first cluster contains nodACIJH
      genes whereas the second has nodAB and nodH genes in the upstream region.
      Phylogenetic analysis shows that Frankia nod genes are more deeply rooted than
      their sister groups from rhizobia. PCR-sequencing suggested the widespread
      occurrence of highly homologous nodA and nodB genes in microsymbionts of field
      collected Ceanothus americanus.
AU  - Ktari A
AU  - Nouioui I
AU  - Furnholm T
AU  - Swanson E
AU  - Ghodhbane-Gtari F
AU  - Tisa LS
AU  - Gtari M
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 51.

PMID- 24407648
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Spiroplasma apis B31T (ATCC 33834), a Bacterium Associated with May Disease of Honeybees (Apis mellifera).
PG  - e01151-13
AB  - Spiroplasma apis B31(T) (ATCC 33834) is a wall-less bacterium in the class Mollicutes that has
      been linked to May disease of honeybees (Apis mellifera).
      Here, we report the complete genome sequence of this bacterium to facilitate the
      investigation of its virulence factors.
AU  - Ku C
AU  - Lo WS
AU  - Chen LL
AU  - Kuo CH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01151-13.

PMID- 23711669
VI  - 5
DP  - 2013
TI  - Complete genomes of two dipteran-associated spiroplasmas provided insights into the origin, dynamics, and impacts of viral invasion in Spiroplasma.
PG  - 1151-1164
AB  - Spiroplasma is a genus of wall-less, low-GC, Gram-positive bacteria with helical morphology.
      As commensals or pathogens of plants, insects, ticks, or crustaceans, they are closely related
      with mycoplasmas and form a monophyletic group (Spiroplasma-
      Entomoplasmataceae-Mycoides) with Mycoplasma mycoides and its relatives. In this study, we
      report the complete genome sequences of S. chrysopicola and S. syrphidicola from the
      Chrysopicola clade. These species form the sister group to the Citri clade, which includes
      several well-known pathogenic spiroplasmas. Surprisingly, these two newly available genomes
      from the Chrysopicola clade contain no plectroviral genes, which were found to be
      highly repetitive in the previously sequenced genomes from the Citri clade. Based on the
      genome alignment and patterns of GC-skew, these two Chrysopicola genomes appear to be
      relatively stable, rather than being highly rearranged as those from the Citri clade.
      Phylogenetic analyses suggest that the susceptibility to plectroviral invasion probably
      originated in the common ancestor of the Citri clade or one of its subclades. This
      susceptibility may be attributed to the absence of antiviral systems found in the Chrysopicola
      clade. Using the virus-free genomes of the Chrysopicola clade as references, we inferred the
      putative viral integration sites in the Citri genomes. Comparisons of syntenic regions suggest
      that the extensive viral invasion in the Citri clade promoted genome rearrangements and
      expansions. More importantly, the viral invasion may have facilitated horizontal gene
      transfers that contributed to adaptation in the Citri clade.
AU  - Ku C
AU  - Lo WS
AU  - Chen LL
AU  - Kuo CH
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2013 5: 1151-1164.

PMID- 2827692
VI  - 13
DP  - 1987
TI  - Interaction of EcoRII restriction and modification enzymes with synthetic DNA fragments.  X. Hydrolysis of substrates with structural anomalies.
PG  - 1205-1211
AB  - Interaction of the EcoRII restriction endonuclease with a set of 30-membered
      substrates having structural anomalies in the recognition site (^CCT/AGG) and
      in adjacent sequences has been studied.  A nick in the centre of the EcoRII
      recognition site between dC and dA residues slows down hydrolysis of the
      nonmodified strand, whereas the modified one is not cleaved.  Removal of the
      phosphate group from the nick in this substrate does not alter the rate of the
      cleavage.  The absence of one of the phosphate groups in the flanking sequence
      at a twobase-pair distance from the recognition site slows down the enzymatic
      hydrolysis.  Removal of dA or dT out of the EcoRII recognition site blocks the
      enzymatic reaction.  It appears that EcoRII does not interact with the
      phosphate group between dC and dA residues in the recognition site.
      Suggestions are made concerning possible contacts of the EcoRII restriction
      endonuclease with dA- and dT-residues of the recognition site and with the
      sugar-phosphate backbone of the adjacent nucleotide sequences.
AU  - Kubareva EA
AU  - Gromova ES
AU  - Ortskaya TS
AU  - Shabarova ZA
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1987 13: 1205-1211.

PMID- 2015301
VI  - 1088
DP  - 1991
TI  - Oligonucleotide cleavage by restriction endonucleases MvaI and EcoRII: a comprehensive study on the influence of structural parameters on the enzyme-substrate interaction.
PG  - 395-400
AB  - To elucidate the mechanism of action of restriction endonucleases -
      isoschizomers EcoRII and MvaI - a study was made of their interaction with a
      set of synthetic oligonucleotide duplexes containing a single 5'-d(CCA/TGG)-3'
      EcoRII (MvaI) recognition site.  The substrates had varying length and
      structure of the nucleotide sequences flanking the recognition site.  The
      structure of the flanking sequence is important for the cleavage by EcoRII and
      MvaI enzymes; there is a structure which was found to speed up the EcoRII and
      MvaI action.  The cleavage of oligonucleotide duplexes by EcoRII enzyme does
      not go to completion.  EcoRII endonuclease cleaved extended substrates less
      efficiently than short ones.  Extension of the flanking sequences, with the
      same nucleotide surrounding of the recognition site, substantially altered the
      whole kinetic pattern of MvaI hydrolysis.  This was not observed with EcoRII
      enzyme.  The restriction endonuclease MvaI distinguished between dA and dT
      residues in the recognition site, which was reflected in the higher rate of
      hydrolysis of the dA-containing strand of the quasipalindromic DNA duplex.
AU  - Kubareva EA
AU  - Gromova ES
AU  - Pein C-D
AU  - Krug A
AU  - Oretskaya TS
AU  - Cech D
AU  - Shabarova ZA
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1991 1088: 395-400.

PMID- 2375778
VI  - 16
DP  - 1990
TI  - Cleavage of substrates containing modified amino groups in heterocyclic bases by MvaI and EcoRII restriction endonucleases.
PG  - 501-506
AB  - 14-membered DNA-duplexes containing modified nucleoside residues, viz 4-N-methyldeoxycytidine
      (m4dC), 6-N-methyldeoxyadenosine (m6dA) or deoxyinosine (dI), in only one strand of the
      recognition site (CCA/TGG) of MvaI and EcoRII endonucleases were synthesized.  It was shown
      that MvaI and EcoRII endonucleases interact with the exocyclic amino groups of the external dC
      residues and of the central dA residue of the recognition site exposed into the DNA major
      groove.  These endonucleases which are isoschizomers were found to possess different
      mechanisms of substrate cleavage.  The ability of MvaI endonuclease to hydrolyze only the
      unmodified strand of methylated duplexes allows one to make site-directed single-strand nicks
      in double-stranded DNA. Elimination of the 2-NH2-group located in the minor groove of DNA by
      substituting dI for dG had little, if any, effect on the hydrolytic activity of EcoRII and
      MvaI endonucleases.
AU  - Kubareva EA
AU  - Gromova ES
AU  - Romanova EA
AU  - Oretskaya TS
AU  - Shabarova ZA
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1990 16: 501-506.

PMID- 9279140
VI  - 11
DP  - 1997
TI  - DNA dumbbells as substrates for studying restriction-modification and repair enzymes.
PG  - A1309
AB  - The use of the DNA dumbbells (duplexes covalently closed on both ends by single stranded
      loops) for investigation of restriction-modification and repair enzymes has been demonstrated.
      Their substrate properties in comparison with DNA hairpins have been analysed in the reactions
      with type II restriction endonucleases (R): MvaI, EcoRII, SsoII and
      DNA-(5-methylcytosine)methyltransferase (M): SsoII.  The hairpin and dumbbell, containing dU
      instead of dT in the center of the restriction-modification enzyme's recognition site
      (5'CCWGG3'), have been used to evaluate the uracil removal from ds DNA with high duplex
      stability by uracil-DNA glycosylase.  R.EcoRII, R.MvaI and R.SsoII interact more efficiently
      with more stable hairpin-like substrate than with equivalent linear DNA duplex.  Less
      efficiency is observed for dumbbell cleavage by restriction endonucleases as compared with
      hairpin-like duplex.  The decreased conformational mobility of the strands in the dumbbell
      might affect adversely on the substrate hydrolysis by the restriction endonucleases.  Addition
      of the 14-membered DNA substrate accelerates the cleavage of the dumbbell by R.EcoRII.
      M.SsoII and UDG reveal 1.5-2.5-fold preference for dsDNA duplex over hairpin-like DNA, which
      is 30 C more stable.  The most stable dumbbell is also a poor substrate for M.SsoII and
      especially for UDG.  The M.SsoII or UDG functioning is more effective when the double helix is
      less stable.
AU  - Kubareva EA
AU  - Kuznetsova SA
AU  - Kanevsky IA
AU  - Karyagina AS
AU  - Nikolskaya II
AU  - Shabarova ZA
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1997 11: A1309.

PMID- 2842156
VI  - 175
DP  - 1988
TI  - The role of modifications in oligonucleotides in sequence recognition by MvaI restriction endonuclease.
PG  - 615-618
AB  - The interaction of MvaI restriction endonuclease with 14-membered
      deoxyribonucleotide duplexes containing modifications within the recognition
      site (CC[A/T]GG) has been studied.  Substitution of m5dC for the internal dC
      residue, as well as substitution of fl5dU or rU for dT did not influence the
      initial rate of hydrolysis (Vo) of modified strands, whereas the hydrolysis of
      unmodified strands was inhibited in some cases.  Furthermore, the substitution
      of a pyrophosphate bond for a scissile phosphodiester bond in one strand
      completely inhibited digestion in this strand without any decrease of the rate
      of hydrolysis of the unmodified strand.  In contrast to EcoRI endonuclease,
      which recognizes the same DNA sequence, in the case of MvaI endonuclease
      substrate recognition is possible in a wide range of conformational, electronic
      and hydrophobic alterations within the recognition site.
AU  - Kubareva EA
AU  - Pein C-D
AU  - Gromova ES
AU  - Kuznezova SA
AU  - Tashlitzki VN
AU  - Chech D
AU  - Shabarova ZA
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1988 175: 615-618.

PMID- 1668695
VI  - 24
DP  - 1991
TI  - DNA duplexes with non-nucleotide inserts: interaction with restriction endonucleases.
PG  - 308
AB  - Modified DNA duplexes with trimethylene bridges or 1,2-dideoxy-D-ribofuranose instead of one
      of the nucleoside residues are of interest as DNA analogs with the sugar-phosphate backbone
      partially or completely preserved but with the heterocyclic base removed.  Another type of
      non-nucleotide insert - 9[1'-hydroxy-2'- (hydroxymethyl)ethoxy]methylguanine (acyclic dG) -
      leads to distortion of the sugar moiety of nucleoside residue while the base is preserved.
      14-membered DNA duplexes have been constructed containing single non-nucleotide inserts in the
      recognition sites (5'-CC(A/T)GG-3' and 5'-CCNGG-3') of a number of restriction
      endonucleases (R).dG residues or one of the nucleosides of the central base-pair of the
      recognition site have been modified.  It has been shown by UV spectroscopy and CD that
      non-nucleotide inserts bring about some destabilization of the double helix without essential
      distortion of its geometry.  Substrate properties of DNA duplexes with non-nucleotide inserts
      have been studied.  R. ScrFI and R.SsoII recognize the CCNGG sequence.  R.ScrFI cleaves all
      the modified duplexes, but with reduced efficiency.  Introduction of trimethylene bridge or
      1,2-dideoxy-D-ribofuranose into the recognition site induces an increase in the cleavage
      efficiency of modified substrates and change of specificity of their hydrolysis by R.SsoII.
      Restoration of R.SsoII specificity is observed in the case of acyclic dG-containing substrate
      when guanine base is returned.  To preserve canonical R.SsoII specificity the enzyme should be
      able to form discrimination contacts with internal and external dG and central nucleoside
      residues of the recognition site.  DNA duplexes with non-nucleotide inserts in the CC(A/T)GG
      recognition sequence (with the exception of acyclic dG insert) are resistant to R.MvaI,
      R.BstNI and R.EcoRII.  Probably, these enzymes interact specifically with each base of the
      central A.T pair and with both dG residues.  A comparative analysis of the functioning of
      restriction enodnucleases - isoschizomers - has been done on the basis of these data.
AU  - Kubareva EA
AU  - Petrauskene OV
AU  - Karyagina AS
AU  - Nikolskaya II
AU  - Gromova ES
PT  - Journal Article
TA  - Nucleic Acids Symp. Ser.
JT  - Nucleic Acids Symp. Ser.
SO  - Nucleic Acids Symp. Ser. 1991 24: 308.

PMID- 1445438
VI  - 18
DP  - 1992
TI  - Change of cleavage site of synthetic substrates by SsoII restriction endonuclease due to non-nucleotide inserts into the recognition sequence.
PG  - 1131-1134
AB  - The cleavage of synthetic DNA duplexes containing 1,3-propanediol, 1,2-dideoxy-D-ribofuranose
      or 9-[1'-hydroxy-2'-(hydroxymethyl)ethoxy]methylguanine (glG) residues instead of one of the
      dG residues or one of the nucleosides of the central base pair of the recognition site by
      SsoII restriction endonuclease (CCNGG) has been studied. It is found that the non-nucleotide
      insertions (except for glG) result in a change of the SsoII cleavage site and an increase of
      the efficiency of the cleavage. The novel noncanonical cleavage occurs at the phosphodiester
      bond adjoining the non-nucleotide insert from the 5'-end.
AU  - Kubareva EA
AU  - Petrauskene OV
AU  - Karyagina AS
AU  - Nikolskaya II
AU  - Gromova ES
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1992 18: 1131-1134.

PMID- 1408753
VI  - 20
DP  - 1992
TI  - Cleavage of synthetic substrates containing non-nucleotide inserts by restriction endonucleases. Change in the cleavage specificity of endonuclease SsoII.
PG  - 4533-4538
AB  - A study was made of the interaction between restriction endonucleases recognizing CCNGG (SsoII
      and ScrFI) or CCA/TGG (MvaI and EcoRII) DNA sequences and a set of synthetic substrates
      containing 1,3-propanediol,1,2-dideoxy-D-ribofuranose or
      9-[1'-hydroxy-2'-(hydroxymethyl)ethoxy] methylguanine (glG) residues replacing either one of
      the central nucleosides or dG residues in the recognition site. The non-nucleotide inserts
      (except for glG) introduced into the recognition site both increase the efficiency of SsoII
      and change its specificity. A cleavage at the noncanonical position takes place, in some cases
      in addition to the correct ones. Noncanonical hydrolysis by SsoII occurs at the phosphodiester
      bond adjacent to the point of modification towards the 5'-end. With the guanine base returned
      (the substrate with glG), the correct cleavage position is restored. ScrFI specifically
      cleaves all the modified substrates. DNA duplexes with non-nucleotide inserts (except for the
      glG-containing duplex) are resistant to hydrolysis by MvaI and EcoRII. Prompted by the data
      obtained we discuss the peculiarities of recognition by restriction endonucleases of
      5-membered DNA sequences which have completely or partially degenerate central base pairs. It
      is sugegested that SsoII forms a complex with DNA in an "open" form.
AU  - Kubareva EA
AU  - Petrauskiene OV
AU  - Karyagina AS
AU  - Tashlitsky VN
AU  - Nikolskaya II
AU  - Gromova ES
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 4533-4538.

PMID- 10666447
VI  - 28
DP  - 2000
TI  - Identification of a base-specific contact between the restriction endonuclease SsoII and its recognition sequence by photocross-linking.
PG  - 1085-1091
AB  - A target sequence-specific DNA binding region of the restriction endonuclease Sso II was
      identified by photocross-linking with an oligodeoxynucleotide duplex which was substituted
      with 5-iododeoxyuridine (5-IdU) at the central position of the Sso II recognition site
      (CCNGG). For this purpose the Sso II-DNA complex was irradiated with a helium/cadmium laser
      (325 nm). The cross-linking yield obtained was approximately 50%. In the presence of excess
      unmodified oligodeoxynucleotide or with oligodeoxynucleotides substituted with 5-IdU
      elsewhere, no cross-linking was observed, indicating the specificity of the cross-linking
      reaction. The cross-linked Sso II-oligodeoxynucleotide complex was digested with chymotrypsin,
      a cross-linked peptide- oligodeoxynucleotide complex isolated and the site of cross-linking
      identified by Edman sequencing to be Trp61. In line with this identification is the finding
      that the W61A variant cannot be cross-linked with the IdU-substituted oligodeoxynucleotide,
      shows a decrease in affinity towards DNA and is inactive in cleavage. It is concluded that the
      region around Trp61 is involved in specific binding of Sso II to its DNA substrate.
AU  - Kubareva EA
AU  - Thole H
AU  - Karyagina AS
AU  - Oretskaya TS
AU  - Pingoud A
AU  - Pingoud V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2000 28: 1085-1091.

PMID- 12238762
VI  - 33
DP  - 2002
TI  - Determination of methylation site of DNA-methyltransferase NlaX by a hybrid method.
PG  - 526-531
AB  - Using a new method based on a combination of bisulfite reaction, the repair enzyme uracil-DNA
      glycosylase, and synthetic oligodeoxyribonucleotides, the methylation site of
      DNA-methyltransferase NlaX (M.NlaX) from Neisseria lactamica was established to be the inner
      cytosine in the double-stranded pentanucleotide recognition sequence 5'-CCNGG-3' (where N =
      any nucleoside). 5-Methylcytosine (m5C) type modification by M-N1aX was confirmed by the use
      of oligonucleotide substrates that contain 5-fluoro-2'-deoxycytidine.
AU  - Kubareva EA
AU  - Walter J
AU  - Karyagina AS
AU  - Vorobeva OV
AU  - Lau PC
AU  - Trautner T
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 2002 33: 526-531.

PMID- 11812241
VI  - 66
DP  - 2001
TI  - Determination of a non-methylated deoxycytidine desidue in the decognition site of DNA-methyltransferases.
PG  - 1356-1360
AB  - A method for determination of a non-methylated deoxycytidine (dC) residue in the recognition
      site of 5-cytosine DNA-methyltransferases is suggested. The method is based on treatment of
      methylated DNA by sodium bisulfite and successive reaction of the thus modified DNA with a
      repair enzyme, uracil-DNA glycosylase. This method was successfully applied to identify NlaX
      methyltransferase specificity.
AU  - Kubareva EA
AU  - Walter J
AU  - Vorobeva OV
AU  - Razumikhin MV
AU  - Karyagina AS
AU  - Lau PCK
AU  - Trautner T
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 2001 66: 1356-1360.

PMID- 16116419
VI  - 23
DP  - 2005
TI  - Genome sequence of the chlorinated compound-respiring bacterium Dehalococcoides species strain CBDB1.
PG  - 1269-1273
AB  - Dehalococcoides species are strictly anaerobic bacteria, which catabolize many of the most
      toxic and persistent chlorinated aromatics and aliphatics
      by reductive dechlorination and are used for in situ bioremediation of
      contaminated sites. Our sequencing of the complete 1,395,502 base pair
      genome of Dehalococcoides strain CBDB1 has revealed the presence of 32
      reductive-dehalogenase-homologous (rdh) genes, possibly conferring on the
      bacteria an immense dehalogenating potential. Most rdh genes were
      associated with genes encoding transcription regulators such as
      two-component regulatory systems or transcription regulators of the
      MarR-type. Four new paralog groups of rdh-associated genes without known
      function were detected. Comparison with the recently sequenced genome of
      Dehalococcoides ethenogenes strain 195 reveals a high degree of gene
      context conservation (synteny) but exceptionally high plasticity in all
      regions containing rdh genes, suggesting that these regions are under
      intense evolutionary pressure.
AU  - Kube M
AU  - Beck A
AU  - Zinder SH
AU  - Kuhl H
AU  - Reinhardt R
AU  - Adrian L
PT  - Journal Article
TA  - Nat. Biotechnol.
JT  - Nat. Biotechnol.
SO  - Nat. Biotechnol. 2005 23: 1269-1273.

PMID- 20565991
VI  - 11
DP  - 2010
TI  - Genome comparison of the epiphytic bacteria Erwinia billingiae and E. tasmaniensis with the pear pathogen E. pyrifoliae.
PG  - 393
AB  - ABSTRACT: BACKGROUND: The genus Erwinia includes plant-associated
      pathogenic and non-pathogenic Enterobacteria. Important pathogens such as
      Erwinia amylovora, the causative agent of fire blight and E. pyrifoliae
      causing bacterial shoot blight of pear in Asia belong to this genus. The
      species E. tasmaniensis and E. billingiae are epiphytic bacteria and may
      represent antagonists for biocontrol of fire blight. The presence of genes
      putative involved in virulence in E. amylovora and E. pyrifoliae is of
      special interest for these species in consequence. RESULTS: Here we
      provide the complete genome sequences of the pathogenic E. pyrifoliae
      strain Ep1/96 with a size of 4.1 Mb and of the non-pathogenic species E.
      billingiae strain Eb661 with a size of 5.4 Mb, de novo determined by
      conventional Sanger sequencing and next generation sequencing techniques.
      Genome comparison reveals large inversions resulting from homologous
      recombination events. Furthermore, comparison of deduced proteins
      highlights a relation of E. billingiae strain Eb661 to E. tasmaniensis
      strain Et1/99 and a distance to E. pyrifoliae for the overall gene content
      as well as for the presence of encoded proteins representing virulence
      factors for the pathogenic species. Pathogenicity of E. pyrifoliae is
      supposed to have evolved by accumulation of potential virulence factors.
      E. pyrifoliae carries factors for type III secretion and cell invasion.
      Other genes described as virulence factors for E. amylovora are involved
      in the production of exopolysaccharides, the utilization of plant
      metabolites such as sorbitol and sucrose. Some virulence-associated genes
      of the pathogenic species are present in E. tasmaniensis but mostly absent
      in E. billingiae. CONCLUSION: The data of the genome analyses correspond
      to the pathogenic lifestyle of E. pyrifoliae and underlines the epiphytic
      localization of E. tasmaniensis and E. billingiae as a saprophyte.
AU  - Kube M
AU  - Migdoll AM
AU  - Gehring I
AU  - Heitmann K
AU  - Mayer Y
AU  - Kuhl H
AU  - Knaust F
AU  - Geider K
AU  - Reinhardt R
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2010 11: 393.

PMID- 18582369
VI  - 9
DP  - 2008
TI  - The linear chromosome of the plant-pathogenic mycoplasma 'Candidatus Phytoplasma mali'.
PG  - 306
AB  - BACKGROUND: Phytoplasmas are insect-transmitted, uncultivable bacterial plant pathogens that
      cause diseases in hundreds of economically important
      plants. They represent a monophyletic group within the class Mollicutes
      (trivial name mycoplasmas) and are characterized by a small genome with a
      low GC content, and the lack of a firm cell wall. All mycoplasmas,
      including strains of 'Candidatus (Ca.) Phytoplasma asteris' and 'Ca. P.
      australiense', examined so far have circular chromosomes, as is the case
      for almost all walled bacteria. RESULTS: Our work has shown that 'Ca.
      Phytoplasma mali', the causative agent of apple proliferation disease, has
      a linear chromosome. Linear chromosomes were also identified in the
      closely related provisional species 'Ca. P. pyri' and 'Ca. P. prunorum'.
      The chromosome of 'Ca. P. mali' strain AT is 601,943 bp in size and has a
      GC content of 21.4%. The chromosome is further characterized by large
      terminal inverted repeats and covalently closed hairpin ends. Analysis of
      the protein-coding genes revealed that glycolysis, the major
      energy-yielding pathway supposed for 'Ca. P. asteris', is incomplete in
      'Ca. P. mali'. Due to the apparent lack of other metabolic pathways
      present in mycoplasmas, it is proposed that maltose and malate are
      utilized as carbon and energy sources. However, complete ATP-yielding
      pathways were not identified. 'Ca. P. mali' also differs from 'Ca. P.
      asteris' by a smaller genome, a lower GC content, a lower number of
      paralogous genes, fewer insertions of potential mobile DNA elements, and a
      strongly reduced number of ABC transporters for amino acids. In contrast,
      'Ca. P. mali' has an extended set of genes for homologous recombination,
      excision repair and SOS response than 'Ca. P. asteris'. CONCLUSION: The
      small linear chromosome with large terminal inverted repeats and
      covalently closed hairpin ends, the extremely low GC content and the
      limited metabolic capabilities reflect unique features of 'Ca. P. mali',
      not only within phytoplasmas, but all mycoplasmas. It is expected that the
      genome information obtained here will contribute to a better understanding
      of the reduced metabolism of phytoplasmas, their fastidious nutrition
      requirements that prevented axenic cultivation, and the mechanisms
      involved in pathogenicity.
AU  - Kube M
AU  - Schneider B
AU  - Kuhl H
AU  - Dandekar T
AU  - Heitmann K
AU  - Migdoll AM
AU  - Reinhardt R
AU  - Seemuller E
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2008 9: 306.

PMID- 24158107
VI  - 24
DP  - 2013
TI  - Analysis of the Complete Genomes of Acholeplasma brassicae, A. palmae and A. laidlawii and Their Comparison to the Obligate Parasites from ' Candidatus Phytoplasma'.
PG  - 19-36
AB  - Analysis of the completely determined genomes of the plant-derived Acholeplasma
      brassicae strain O502 and A. palmae strain J233 revealed that the circular
      chromosomes are 1,877,792 and 1,554,229 bp in size, have a G + C content of 36
      and 29%, and encode 1,690 and 1,439 proteins, respectively. Comparative analysis
      of these sequences and previously published genomes of A. laidlawii strain PG-8,
      'Candidatus Phytoplasma asteris' strains, 'Ca. P. australiense' and 'Ca. P. mali'
      show a limited shared basic genetic repertoire. The acholeplasma genomes are
      characterized by a low number of rearrangements, duplication and integration
      events. Exceptions are the unusual duplication of rRNA operons in A. brassicae
      and an independently introduced second gene for a single-stranded binding protein
      in both genera. In contrast to phytoplasmas, the acholeplasma genomes differ by
      encoding the cell division protein FtsZ, a wide variety of ABC transporters, the
      F0F1 ATP synthase, the Rnf-complex, SecG of the Sec-dependent secretion system, a
      richly equipped repertoire for carbohydrate metabolism, fatty acid, isoprenoid
      and partial amino acid metabolism. Conserved metabolic proteins encoded in
      phytoplasma genomes such as the malate dehydrogenase SfcA, several transporters
      and proteins involved in host-interaction, and virulence-associated effectors
      were not predicted for the acholeplasmas. (c) 2013 S. Karger AG, Basel.
AU  - Kube M
AU  - Siewert C
AU  - Migdoll AM
AU  - Duduk B
AU  - Holz S
AU  - Rabus R
AU  - Seemuller E
AU  - Mitrovic J
AU  - Muller I
AU  - Buttner C
AU  - Reinhardt R
PT  - Journal Article
TA  - J. Mol. Microbiol. Biotechnol.
JT  - J. Mol. Microbiol. Biotechnol.
SO  - J. Mol. Microbiol. Biotechnol. 2013 24: 19-36.

PMID- 26294634
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of the Nonpathogenic Soil-Dwelling Bacterium Clostridium sporogenes Strain NCIMB 10696.
PG  - e00942-15
AB  - Clostridium sporogenes is a harmless spore-forming anaerobe that is widely distributed in
      soil/water and in the intestines of humans and animals. It is
      extensively used as a safe model to test the suitability of new preservative
      methods by the food industry and has potential to deliver therapeutic agents to
      tumors.
AU  - Kubiak AM
AU  - Poehlein A
AU  - Budd P
AU  - Kuehne SA
AU  - Winzer K
AU  - Theys J
AU  - Lambin P
AU  - Daniel R
AU  - Minton NP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00942-15.

PMID- 24508035
VI  - 32
DP  - 2014
TI  - Immunization with a DNA adenine methylase over-producing Yersinia pseudotuberculosis vaccine confers robust cross-protection against heterologous pathogenic serotypes.
PG  - 1451-1459
AB  - Yersinia pseudotuberculosis is a foodborne pathogen that can cause serious human illness.
      Although the source and route of transmission often remain obscure, livestock have been
      implicated in some cases. The diversity of yersiniae present on farms and their widespread
      distribution in animal and environmental reservoirs necessitates the use of broad prophylactic
      strategies that are efficacious against many serotypes simultaneously. Herein, immunization of
      mice with a modified, live attenuated Y. pseudotuberculosis vaccine that overproduces the DNA
      adenine methylase (Dam P) conferred robust protection against virulent challenge (150-fold
      LD50) with homologous and heterologous serotypes that have been associated with human disease
      (O:1, O:1a, O:3). Further, the dam gene was shown to be essential for cell viability in all (7
      of 7) Y. pseudotuberculosis strains tested. Direct selection for the inheritance of dam mutant
      alleles in Y. pseudotuberculosis resulted in dam strain variants that contained compensatory
      (second-site suppressor) mutations in genes encoding methyl-directed mismatch repair proteins
      (mutHLS) that are involved in suppression of the non-viable cell phenotype in all (19/19)
      strains tested. Such dam mutH variants exhibited a significant increase in virulence and
      spontaneous mutation frequency relative to that of a Dam P vaccine strain. These studies
      indicate that Y. pseudotuberculosis Dam P strains conferred potent cross-protective efficacy
      as well as decreased virulence and spontaneous mutation frequency relative to those that lack
      Dam, which have compensatory mutations in mutHLS loci. These data suggest that development of
      yersiniae livestock vaccines based on Dam overproduction is a viable mitigation strategy to
      reduce these potential foodborne contaminants. (C) 2014 Elsevier Ltd. All rights reserved.
AU  - Kubicek-Sutherland JZ
AU  - Heithoff DM
AU  - Ersoy SC
AU  - Shimp WR
AU  - Mahan MJ
PT  - Journal Article
TA  - Vaccine
JT  - Vaccine
SO  - Vaccine 2014 32: 1451-1459.

PMID- 
VI  - 56
DP  - 2005
TI  - DNA methylase 3B (DNMT3B).
PG  - 378-379
AB  - 
AU  - Kubota T
PT  - Journal Article
TA  - Seitai Kagaku
JT  - Seitai Kagaku
SO  - Seitai Kagaku 2005 56: 378-379.

PMID- 18203234
VI  - 47
DP  - 2008
TI  - Synthesis of DNA dumbbell based inhibitors for the human DNA methyltransferase Dnmt1.
PG  - 1515-1518
AB  - DNA methyltransferases convert deoxycytidine nucleobases in DNA into 5-methyldeoxycytidines
      using the cofactor S-adenosylmethionine as the methyl group donor.  Methylation of the
      canonical dC base, particularly in gene promoter regions, induces complex processes, which
      finally lead to the silencing of the corresponding gene.  This epigenetic gene silencing is of
      paramount importance for cellular differentiation.  Altered methylation patterns and
      corresponding changes in gene expression are found in practically all tumor cells.  The major
      DNA methyltransferase Dnmt1 is a 183-kDa-large protein that preferentially methylates dC bases
      in hemimethylated d(cpG) sequences after DNA replication.
AU  - Kuch D
AU  - Schermelleh L
AU  - Manetto S
AU  - Leonhardt H
AU  - Carell T
PT  - Journal Article
TA  - Angew. Chem. Int. Ed. Engl.
JT  - Angew. Chem. Int. Ed. Engl.
SO  - Angew. Chem. Int. Ed. Engl. 2008 47: 1515-1518.

PMID- 20006515
VI  - 18
DP  - 2010
TI  - Novel and selective DNA methyltransferase inhibitors: Docking-based virtual screening and experimental evaluation.
PG  - 822-829
AB  - The DNA methyltransferase (DNMT) enzyme family consists of four members with diverse functions
      and represents one of the most promising targets
      for the development of novel anticancer drugs. However, the standard
      drugs for DNMT inhibition are non-selective cytosine analogues with
      considerable cytotoxic side-effects that have been developed several
      decades ago. In this work, we conducted a virtual screening of more
      than 65,000 lead-like compounds selected from the National Cancer
      Institute collection using a multistep docking approach with a
      previously validated homology model of the catalytic domain of human
      DNMT1. Experimental evaluation of top-ranked molecules led to the
      discovery of novel small molecule DNMT1 inhibitors. Virtual screening
      hits were further evaluated for DNMT3B inhibition revealing several
      compounds with selectivity towards DNMT1. These are the first small
      molecules reported with biochemical selectivity towards an individual
      DNMT enzyme capable of binding in the same pocket as the native
      substrate cytosine, and are promising candidates for further rational
      optimization and development as anticancer drugs. The availability of
      enzyme-selective inhibitors will also be of great significance for
      understanding the role of individual DNMT enzymes in epigenetic
      regulation.
AU  - Kuck D
AU  - Singh N
AU  - Lyko F
AU  - Medina-Franco JL
PT  - Journal Article
TA  - Bioorg. Med. Chem.
JT  - Bioorg. Med. Chem.
SO  - Bioorg. Med. Chem. 2010 18: 822-829.

PMID- 24115542
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Gallibacterium anatis bv. haemolytica 12656-12 Liver, an Isolate Obtained from the Liver of a Septicemic Chicken.
PG  - e00810-13
AB  - We report the draft genome sequence of Gallibacterium anatis bv. haemolytica strain 12656-12
      Liver. This strain was isolated from the liver of a septicemic
      layer chicken in Denmark in 1981. The strain has been used extensively for
      experimental purposes.
AU  - Kudirkiene E
AU  - Christensen H
AU  - Bojesen AM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00810-13.

PMID- 25523777
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Chelonobacter oris Strain 1662T, Associated with Respiratory Disease in Hermann's Tortoises.
PG  - e01322-14
AB  - Chelonobacter oris 1662(T) is a type strain of the recently described species of  the
      Pasteurellaceae family. The strain was isolated from the choanae of a captive
      tortoise with signs of respiratory tract infection. The genome reported here is
      approximately 2.6 Mb in size and has a G+C content of 47.1%.
AU  - Kudirkiene E
AU  - Hansen MJ
AU  - Bojesen AM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01322-14.

PMID- 24699965
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Psychrobacter Strains JCM 18900, JCM 18901, JCM 18902,  and JCM 18903, Isolated Preferentially from Frozen Aquatic Organisms.
PG  - e00280-14
AB  - Four Psychrobacter strains, JCM 18900, JCM 18901, JCM 18902, and JCM 18903, related to either
      Psychrobacter nivimaris or Psychrobacter cibarius, were isolated from frozen marine animals.
      The genome information of these four strains will be useful for studies of their physiology
      and adaptation properties to frozen conditions.
AU  - Kudo T et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00280-14.

PMID- 24948773
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Vibrio sp. Strains Isolated from Tetrodotoxin-Bearing Scavenging Gastropod.
PG  - e00623-14
AB  - Vibrio sp. strains JCM 18905 and JCM 19053 were isolated from a tetrodotoxin (TTX)-bearing
      scavenging gastropod, and Vibrio sp. strain JCM 18904 was isolated
      from a sea cucumber. All these are closely related to Vibrio alginolyticus. Their
      comparative genome information is useful for studies of TTX production in
      bacteria.
AU  - Kudo T
AU  - Kawauchi A
AU  - Nakahara T
AU  - Zhang X
AU  - Taniyama S
AU  - Takatani T
AU  - Arakawa O
AU  - Oshima K
AU  - Suda W
AU  - Kitamura K
AU  - Iida T
AU  - Iino T
AU  - Inoue T
AU  - Hongoh Y
AU  - Hattori M
AU  - Ohkuma M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00623-14.

PMID- 24948772
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Geomicrobium sp. Strains JCM 19037, JCM 19038, JCM 19039, and JCM 19055, Isolated from Aquatic Samples.
PG  - e00622-14
AB  - Haloalkaliphilic strains JCM 19037, JCM 19038, JCM 19039, and JCM 19055, closely  related to
      Geomicrobium sediminis, were isolated from aquatic samples, and their
      draft genome sequences were determined. The genome information of these four
      strains will be useful for studies of their physiology and ecology.
AU  - Kudo T
AU  - Nakahara T
AU  - Zhang X
AU  - Taniyama S
AU  - Arakawa O
AU  - Murase S
AU  - Nakata H
AU  - Oshima K
AU  - Suda W
AU  - Kitamura K
AU  - Iida T
AU  - Oshida Y
AU  - Inoue T
AU  - Hongoh Y
AU  - Hattori M
AU  - Ohkuma M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00622-14.

PMID- 24652985
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Cyclodextrin-Producing Alkaliphilic Bacillus Strains JCM 19045, JCM 19046, and JCM 19047.
PG  - e00211-14
AB  - Bacillus strains JCM 19045, JCM 19046, and JCM 19047 are alkaliphiles that produce
      beta-cyclodextrin from starch. They are related to Bacillus xiaoxiensis
      and Bacillus lehensis. The genome information for these three strains will be
      useful for studies of the physiological role of cyclodextrin and cyclodextrin
      production.
AU  - Kudo T
AU  - Sakamoto K
AU  - Akinaga M
AU  - Kawauchi A
AU  - Nakahara T
AU  - Zhang X
AU  - Yamada A
AU  - Oshima K
AU  - Suda W
AU  - Kuwahara H
AU  - Nakamura N
AU  - Nogi Y
AU  - Kitamura K
AU  - Yuki M
AU  - Iida T
AU  - Moriya S
AU  - Inoue T
AU  - Hongoh Y
AU  - Hattori M
AU  - Ohkuma M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00211-14.

PMID- 33837
VI  - 38
DP  - 1979
TI  - A New Restriction Endonuclease from Streptomyces Stanford.
PG  - 780
AB  - A new site-specific endonuclease activity distinguishable from Sst I, II and
      III was isolated from Streptomyces stanford. This enzyme, designated Sst IV,
      cleaved SV40 DNA once, adeno-virus type-2 DNA four times, and lambda(wt) DNA
      several times (incompletely), but did not cleave PhiX174 RF or pBR322 DNA.  Sst
      IV was active in 15 mM Tris-HCL (pH 7.5, mM MgCl2, 90 mM NaCl and 6mM
      2-mercaptoethanol at 37C.  The enzyme was purified free of specific and
      non-specific nucleases by column chromatography which included
      phosphocellulose, DEAE cellulose, hydroxylapatite and Blue-CNBr agarose.  The
      amount of Sst IV recovered was about 2% of that for Sst II.  The number and
      sizes of fragments actually generated by co-digestion of pBR322, PhiX174 RF or
      SV40 DNA with Sst IV and other known restriction endonucleases were compared
      with a computer generated table of predicted fragmentation patterns of these
      DNAs (R. Blakesley, BRL FOCUS 1, NO. 4 (1978)) To tentatively identify the
      recognition sequence of SstIV as 5'-TGATCA-3'.  Thus, SstIV has a specificity
      similar to that of AtuCI, BclI and CpeI.  The recognition sequence is being
      confirmed by direct sequence analysis.
AU  - Kuebbing D
AU  - Blakesley RJ
PT  - Journal Article
TA  - Fed. Proc.
JT  - Fed. Proc.
SO  - Fed. Proc. 1979 38: 780.

PMID- 24051319
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences for 10 Isolates of the Swine Pathogen Haemophilus parasuis.
PG  - e00739-13
AB  - Haemophilus parasuis colonizes the upper respiratory tract of swine and can cause a severe
      systemic disease known as Glasser's disease. We report here the draft
      genome sequences of 10 isolates from geographically diverse locations
      representing the full virulence spectrum of the microorganism, which will aid in
      understanding the pathobiology of H. parasuis.
AU  - Kuehn JS
AU  - Register KB
AU  - Phillips GJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00739-13.

PMID- Not included in PubMed...
VI  - 376
DP  - 1995
TI  - Mutational analysis of the function of Ile197 in the EcoRI restriction endonuclease.
PG  - S122
AB  - The endonuclease EcoRI is one of the best studied type II restriction enzymes.  It recognizes
      and cleaves the double stranded DNA sequence GAATTC in both single strands between G and A
      with high specificity.  Based on the X-ray structure Ile197 has been proposed to form a van
      der Waals contact with cytosine of this recognition sequence.  We have exchanged Ile197 for
      Ala, Arg and Met by site directed mutagenesis and analysed the purified mutant proteins
      (I197A, M and R) biochemically and physicochemically.  Secondary structure composition
      measured by CD-spectroscopy was unchanged for all mutants.  They cleave DNA with approximately
      the same specific activity as the wild type enzyme.  For the I197A and the I197M mutants pH
      optimum is shifted to alkaline conditions resulting in a 5-10 fold higher enzymatic activity
      at pH 8.8.  Furthermore, the I197M mutant shows slight changes in its dependence on sequence
      flanking the recognition sequence.  We assume that a hydrophobic contact of Ile197 to cytosine
      is not important for activity of the EcoRI endonuclease.  But changes at this position
      influence the conformation of the enzyme leading to a higher activity at alkaline pH on
      substrates with a specific sequence surrounding.
AU  - Kuester W
AU  - Alves J
PT  - Journal Article
TA  - Biol. Chem. Hoppe Seyler
JT  - Biol. Chem. Hoppe Seyler
SO  - Biol. Chem. Hoppe Seyler 1995 376: S122.

PMID- 25197466
VI  - 9
DP  - 2014
TI  - Genome analysis of Desulfotomaculum gibsoniae strain Groll(T) a highly versatile  Gram-positive sulfate-reducing bacterium.
PG  - 821-839
AB  - Desulfotomaculum gibsoniae is a mesophilic member of the polyphyletic spore-forming genus
      Desulfotomaculum within the family Peptococcaceae. This
      bacterium was isolated from a freshwater ditch and is of interest because it can
      grow with a large variety of organic substrates, in particular several aromatic
      compounds, short-chain and medium-chain fatty acids, which are degraded
      completely to carbon dioxide coupled to the reduction of sulfate. It can grow
      autotrophically with H2 + CO2 and sulfate and slowly acetogenically with H2 +
      CO2, formate or methoxylated aromatic compounds in the absence of sulfate. It
      does not require any vitamins for growth. Here, we describe the features of D.
      gibsoniae strain Groll(T) together with the genome sequence and annotation. The
      chromosome has 4,855,529 bp organized in one circular contig and is the largest
      genome of all sequenced Desulfotomaculum spp. to date. A total of 4,666 candidate
      protein-encoding genes and 96 RNA genes were identified. Genes of the acetyl-CoA
      pathway, possibly involved in heterotrophic growth and in CO2 fixation during
      autotrophic growth, are present. The genome contains a large set of genes for the
      anaerobic transformation and degradation of aromatic compounds, which are lacking
      in the other sequenced Desulfotomaculum genomes.
AU  - Kuever J et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 821-839.

PMID- 27445392
VI  - 4
DP  - 2016
TI  - Genome Sequence of Bibersteinia trehalosi Strain Y31 Isolated from the Pneumonic  Lung of a Bighorn Sheep.
PG  - e00722-16
AB  - Here, we report the genome sequence for Bibersteinia trehalosi strain Y31, isolated from the
      lungs of a bighorn sheep (Ovis canadensis) that had succumbed
      to pneumonia, which exhibits proximity-dependent inhibition (PDI) of Mannheimia
      haemolytica The sequence will be used to understand the mechanism of PDI for
      these organisms.
AU  - Kugadas A
AU  - Humann JL
AU  - Pierle SA
AU  - Srikumaran S
AU  - Brayton KA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00722-16.

PMID- 10601625
VI  - 463
DP  - 1999
TI  - Structural parsimony in endonuclease active sites: should the number of homing endonuclease families be redefined?
PG  - 1-2
AB  - Homing endonucleases are classified into four families based on active site sequence motifs.
      Through structural comparisons we have found structural similarities between the endonuclease
      domain of colicin E9, an H-N-H motif-containing enzyme, and both the non-specific nuclease
      from Serratia and I-PpoI, a His-Cys box-containing homing endonuclease. Our comparison
      identifies conservation at the heart of all three enzyme active sites and so argues for a
      re-classification of H-N-H and His-Cys box homing endonucleases as a single family. We suggest
      the 'betabetaalpha-Me family' of homing enzymes to reflect the three elements of secondary
      structure and the metal ion that define the motif.
AU  - Kuhlmann UC
AU  - Moore GR
AU  - James R
AU  - Kleanthous C
AU  - Hemmings AM
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1999 463: 1-2.

PMID- 
VI  - 20
DP  - 2003
TI  - Site-specific nicking of duplex DNA using PNAs and restriction endonucleases.
PG  - 916-917
AB  - A variety of research procedures in molecular biology and biochemistry include as a
      fundamental step the selective cleavage of a designated sequence in only one strand of
      double-stranded DNA (DNA nicking).  To achieve the goal, restriction endonuclease-like nicking
      enzymes can be employed.  However, very few nicking enzymes (nickases) are available and they
      recognize short sequences of less than or equal to 7 bp.  It is therefore highly desirable to
      develop new nicking systems with much higher sequence selectivity.  We design such systems
      using homopyrimidine peptide nucleic acids (PNAs).  In our design we take advantage of the
      ability of homopyrimidine PNAs to sequence-specifically invade duplex DNA.  When such PNAs are
      targeted to two short homopurine stretches on the same strand of duplex DNA, the opposite DNA
      strand becomes accessible for hybridization with an oligonucleotide.  We demonstrate that the
      thus formed secondary DNA duplex can serve as a substrate for a restriction endonuclease,
      provided that it contains the recognition sequence of the enzyme.  As a result, only one
      strand of the parent DNA is cleaved leading to nicked duplex DNA after removal of PNAs.  All
      restriction endonucleases tested by us (AluI, BbsI, BglII, KpnI, SbfI, and SphI), have worked
      well in our design leading to quantitative yield of the nicked product.  Together with the
      fact that the typical target site in our protocol spans about 20-25 bp, our results indicate
      that a vast class of semi-synthetic rare-cleaving DNA nickases has been generated.
AU  - Kuhn H
AU  - Frank-Kamenetskii MD
AU  - Demidov VV
PT  - Journal Article
TA  - J. Biomol. Struct. Dyn.
JT  - J. Biomol. Struct. Dyn.
SO  - J. Biomol. Struct. Dyn. 2003 20: 916-917.

PMID- 12718541
VI  - 42
DP  - 2003
TI  - Artificial site-specific DNA-nicking system based on common restriction enzymes assisted by PNA openers.
PG  - 4985-4992
AB  - We report on the peptide nucleic acid (PNA)-directed design of a DNA-nicking system that
      enables selective and quantitative cleavage of one
      strand of duplex DNA at a designated site, thus mimicking natural nickases
      and significantly extending their potential. This system exploits the
      ability of pyrimidine PNAs to serve as openers for specific DNA sites by
      invading the DNA duplex and exposing one DNA strand for oligonucleotide
      hybridization. The resultant secondary duplex can act as a substrate for a
      restriction enzyme, which ultimately creates a nick in the parent DNA. We
      demonstrate that several restriction enzymes of different types could be
      successfully used in the PNA-assisted system we developed. Importantly,
      the enzyme cleavage efficiency is basically not impaired on such
      artificially generated substrates, compared with the efficiency on regular
      DNA duplexes. Our design originates a vast class of semisynthetic
      rare-cleaving DNA nickases, which are essentially absent at present. In
      addition, we show that the site-specific PNA-assisted nicking of duplex
      DNA can be engaged in a rolling-circle DNA amplification (RCA) reaction.
      This new RCA format demonstrates the practical potential of the novel
      biomolecular tool we propose for DNA technology and DNA diagnostics.
AU  - Kuhn H
AU  - Hu Y
AU  - Frank-Kamenetskii MD
AU  - Demidov VV
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2003 42: 4985-4992.

PMID- 3015739
VI  - 42
DP  - 1986
TI  - Positive-selection vectors utilizing lethality of the EcoRI endonuclease.
PG  - 253-263
AB  - The construction and use of a series of positive-selection vectors are
      described.  These plasmids encode EcoRI endonuclease, the synthesis of which is
      under the control of the lacUV5 promoter.  The pKG2 plasmid encodes a wild-type
      EcoRI endonuclease.  In the absence of EcoRI methylase, the endonuclease is
      lethal.  Cloning into any of the unique restriction sites within the
      endonuclease-coding gene allows survival of the transformed
      EcoRI-methylase-less host.  The pKGW and pKGS plasmids encode an altered EcoRI
      endonuclease which, when repressed in the lacIQ host, allows survival in the
      absence of the methylase.  Induction with IPTG, however, results in cell death
      as a result of high-level EcoRI synthesis.  Cloning into any of the unique
      restriction sites within the EcoRI gene of pKGW or pKGS allows survival of
      derepressed transformed cells.  These vectors strongly select for cloning
      events which inactivate the endonuclease gene.
AU  - Kuhn I
AU  - Stephenson F
AU  - Boyer H
AU  - Greene P
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1986 42: 253-263.

PMID- 4552763
VI  - 63
DP  - 1972
TI  - Host specificity of DNA produced by Escherichia coli. XV.  The role of nucleotide methylation in in vitro B-specific modification.
PG  - 9-19
AB  - It is shown that in vitro Escherichia coli strain B-specific modification of
      the replicative form of bacteriophage fd DNA is accompanied by the methylation
      of certain adenine moieties to form N-6-methyladenine.  The reaction follows
      first order kinetics and saturation is reached when about four adenines are
      methylated per replicative form.  No methyl groups are transferred to
      B-modified DNA.  The replicative form of a one step mutant of fd, which has a
      reduced sensitivity towards B-specific restriction, has lost two of the four
      methyl acceptor sites.  The replicative form of a second step mutant, which is
      not subject to B-specific restriction, is completely refractory to methylation
      by the modification enzyme.  It is therefore concluded that the B-modification
      and the B-restriction enzyme react with the same sites on the substrate DNA and
      that the replicative form of wild type fd has two such sites.  The number of
      N-6-methyladenines per B-specificity site of fully modified double-stranded DNA
      is two.
AU  - Kuhnlein U
AU  - Arber W
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1972 63: 9-19.

PMID- 4895540
VI  - 63
DP  - 1969
TI  - Host specificity of DNA produced by Escherichia coli, XI.  In vitro modification of phage fd replicative form.
PG  - 556-562
AB  - An enzymatic activity, having the properties expected by a B-specific
      host-controlled modification enzyme, has been purified from an extract of
      Escherichia coli strain B.  This activity renders the unmodified replicative
      form of phage fd resistant to B-specific restriction and is only present in
      strains carrying intact genes for type B modification.  In phosphate buffer,
      the enzyme acts optimally at pH 6 and is dependent upon a single cofactor,
      S-adenosylmethionine.
AU  - Kuhnlein U
AU  - Linn S
AU  - Arber W
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1969 63: 556-562.

PMID- 4908449
VI  - 34
DP  - 1969
TI  - In vitro modifikation der replikativen form des bakteriophagen fd.
PG  - 136
AB  - None
AU  - Kuhnlein U
AU  - Linn S
AU  - Arber W
PT  - Journal Article
TA  - Pathol. Microbiol. (Basel)
JT  - Pathol. Microbiol. (Basel)
SO  - Pathol. Microbiol. (Basel) 1969 34: 136.

PMID- 7514149
VI  - 142
DP  - 1994
TI  - Organization and sequence of the HpaII restriction-modification system and adjacent genes.
PG  - 9-15
AB  - We report the organization of the HpaII restriction and modification (R-M) system from
      Haemophilus parainfluenzae (recognition sequence: 5'...CCGG...3'), the sequence of the gene
      coding for the HpaII restriction endonuclease, and the sequence of the upstream flanking DNA.
      The HpaII system comprises two genes, hpaIIM, coding for the methyltransferase (MTase; 358
      amino acids (aa), 40.4 kDa: product, Cm5CGG), and hpaIIR, coding for the restriction
      endonuclease (ENase: 358aa, 40.9 kDa: product, C'CGG). The genes are adjacent, they have the
      same orientation, and they occur in the order hpaIIM then hpaIIR. The ENase bears little aa
      sequence similarity to the isoschizomeric R.BsuFI and R.MspI ENases. Upstream of, and partly
      overlapping hpaIIM is the coding sequence for a 141-aa protein that resembles the
      very-short-patch-repair endonuclease (Vsr) of Escherichia coli. Upstream of that is the coding
      sequence for a protein that resembles valyl-tRNA synthetase (ValS).
AU  - Kulakauskas S
AU  - Barsomian JM
AU  - Lubys A
AU  - Roberts RJ
AU  - Wilson GG
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1994 142: 9-15.

PMID- 7768854
VI  - 177
DP  - 1995
TI  - DNA restriction-modification systems mediate plasmid maintenance.
PG  - 3451-3454
AB  - Two plasmid-carried restriction-modification (R-M) systems, EcoRI (from pMB1 of Escherichia
      coli) and Bsp6I (from pXH13 of Bacillus sp. strain RFL6), enhance plasmid segregational
      stability in E. coli and Bacillus subtilis, respectively. Inactivation of the endonuclease or
      the presence of the methylase in trans abolish the stabilizing activity of the R-M systems. We
      propose that R-M systems mediate plasmid segregational stability by postsegregational killing
      of plasmid-free cells. Plasmid-encoded methyltransferase modifies host DNA and thus prevents
      its digestion by the restriction endonuclease. Plasmid loss entails degradation and/or
      dilution of the methylase during cell growth and appearance of unmethylated sites in the
      chromosome. Double-strand breaks, introduced at these sites by the endonuclease, eventually
      cause the death of the plasmid-free cells. Contribution to plasmid stability is a previously
      unrecognized biological role of the R-M systems.
AU  - Kulakauskas S
AU  - Lubys A
AU  - Ehrlich SD
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1995 177: 3451-3454.

PMID- 25395642
VI  - 2
DP  - 2014
TI  - Whole-Genome Sequencing and Mutation Analysis of Two Extensively Drug-Resistant Sputum Isolates of Mycobacterium tuberculosis (VRFCWCF XDRTB 232 and VRFCWCF  XDRTB 1028) from Chennai, India.
PG  - e01173-14
AB  - We announce the draft genome sequence of two extensively drug-resistant Mycobacterium
      tuberculosis strains, VRFCWCF XDRTB 232 and VRFCWCF XDRTB 1028,
      isolated from the sputum samples of a patient clinically suspected to have
      tuberculosis, and we also report novel mutations that confer drug resistance.
AU  - Kulandai LT
AU  - Lakshmipathy D
AU  - Ramasubban G
AU  - Vetrivel U
AU  - Rao MH
AU  - Rathinam S
AU  - Narasimhan M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01173-14.

PMID- 19564389
VI  - 77
DP  - 2009
TI  - Analysis of the genome of the Escherichia coli O157:H7 2006 spinach-associated outbreak isolate indicates candidate genes that may enhance virulence.
PG  - 3713-3721
AB  - In addition to causing diarrhea, Escherichia coli O157:H7 infection can
      lead to hemolytic uremic syndrome (HUS), a severe disease characterized by
      hemolysis and renal failure. Differences in HUS frequency among E. coli
      O157:H7 outbreaks have been noted, but there is incomplete understanding
      of bacterial factors that promote HUS. In 2006, an outbreak of E. coli
      O157:H7, caused by consumption of contaminated spinach, occurred with a
      notably high frequency of HUS. We sequenced the genome of this strain
      (TW14359) with the goal of identifying candidate genetic factors that
      contribute to an enhanced ability to cause HUS. The TW14359 genome
      contains 70-kb of DNA segments not present in either of the two reference
      O157:H7 genomes. We identified seven putative virulence determinants,
      including two putative Type III secretion system effector proteins,
      candidate genes that could result in increased pathogenicity or,
      alternatively, adaptation to plants, and an intact anaerobic nitric oxide
      reductase gene, norV. We surveyed one hundred O157:H7 isolates for the
      presence of these putative virulence determinants. A norV deletion was
      found in over half of strains surveyed and correlates strikingly with the
      absence of stx1. The other putative virulence factors were found in eight
      to thirty-five percent of O157:H7 isolates surveyed and their presence
      also correlates with the presence of norV and absence of stx1 indicating
      the presence of norV may serve as a marker of greater propensity for HUS
      similar to the correlation between the absence of stx1 and HUS propensity.
AU  - Kulasekara BR et al
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2009 77: 3713-3721.

PMID- Not included in PubMed...
VI  - 21
DP  - 1987
TI  - New type-II restrictase from cells of Erwinia herbicola.
PG  - 250-254
AB  - Forty strains of the bacterial genus Erwinia were tested for the presence of
      restrictases.  Type-II restrictases identical in properties were isolated and
      partially purified from cells of Erw. herbicola strains 9/5 and 8608.  It was
      established that restrictase EheI recognizes the sequence of nucleotides
      5'-GGCGCC-3' and is a false isoschizomer of enzymes NarI, NdaI, NunII, and
      BbeI, since EheI cleaves the sequence in the middle, forming blunt ends, as
      opposed to the enzymes listed, which form sticky 5'- or 3'-ends when cleaving
      DNA.  Optimal conditions of cleavage of DNA by EheI restrictase are determined.
AU  - Kulba AM
AU  - Abdel-Sabur MS
AU  - Butkus VV
AU  - Janulaitis A
AU  - Fomichev YK
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1987 21: 250-254.

PMID- Not carried by PubMed...
VI  - 2
DP  - 1997
TI  - Detection of restriction endonucleases in Aeromonas bacteria.
PG  - 47-49
AB  - 
AU  - Kulba AM
AU  - Elgammudi AA
PT  - Journal Article
TA  - Vestn. Beloruss. Gos. Univ.
JT  - Vestn. Beloruss. Gos. Univ.
SO  - Vestn. Beloruss. Gos. Univ. 1997 2: 47-49.

PMID- 29301891
VI  - 6
DP  - 2018
TI  - Whole-Genome Sequencing of Six Borrelia miyamotoi Clinical Strains Isolated in Russia.
PG  - e01424-17
AB  - Here, we report the whole-genome sequence of six clinical Borrelia miyamotoi isolates from the
      Russian Federation. Using two independent next-generation
      sequencing platforms, we determined the complete sequence of the chromosome and
      several plasmids. All strains have an Asian genotype with 99.8% chromosome
      nucleotide similarity with B. miyamotoi strain FR64b.
AU  - Kuleshov KV
AU  - Koetsveld J
AU  - Goptar IA
AU  - Markelov ML
AU  - Kolyasnikova NM
AU  - Sarksyan DS
AU  - Toporkova MG
AU  - Kirdyashkina NP
AU  - Shipulin GA
AU  - Hovius JW
AU  - Platonov AE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01424-17.

PMID- 25035324
VI  - 2
DP  - 2014
TI  - Draft Genome Sequencing of Vibrio cholerae O1 El Tor Isolates Collected in the Russian Federation from Imported Cholera Cases.
PG  - e00624-14
AB  - We report the draft genome sequencing of five Vibrio cholerae O1 El Tor clinical  isolates
      collected in the Russian Federation from imported cholera cases in 2006,
      2010, and 2012. In the initial phylogenetic analysis, one isolate clustered with
      the Haiti/Nepal-4 group.
AU  - Kuleshov KV
AU  - Vodop'ianov SO
AU  - Dedkov VG
AU  - Markelov ML
AU  - Kermanov AV
AU  - Kruglikov VD
AU  - Vodop'ianov AS
AU  - Pisanov RV
AU  - Chemisova OS
AU  - Mazrukho AB
AU  - Titova SV
AU  - Shipulin GA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00624-14.

PMID- 23969060
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences of Vibrio cholerae O1 ElTor Strains 2011EL-301 and P-18785, Isolated in Russia.
PG  - e00659-13
AB  - We report the draft whole-genome sequences of two Vibrio cholerae O1 strains, the
      environmental toxigenic strain 2011EL-301 and the clinical nontoxigenic strain
      P-18785, both isolated in Russia. Some basic data comparing the two against the
      GenBank repository are provided.
AU  - Kuleshov KV
AU  - Vodop'ianov SO
AU  - Markelov ML
AU  - Dedkov VG
AU  - Kermanov AV
AU  - Kruglikov VD
AU  - Vodop'ianov AS
AU  - Pisanov RV
AU  - Mazrukho AB
AU  - Shipulin GA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00659-13.

PMID- 28848533
VI  - 8
DP  - 2017
TI  - Genome Plasticity and Polymorphisms in Critical Genes Correlate with Increased Virulence of Dutch Outbreak-Related Coxiella burnetii Strains.
PG  - 1526
AB  - Coxiella burnetii is an obligate intracellular bacterium and the etiological
      agent of Q fever. During 2007-2010 the largest Q fever outbreak ever reported
      occurred in The Netherlands. It is anticipated that strains from this outbreak
      demonstrated an increased zoonotic potential as more than 40,000 individuals were
      assumed to be infected. The acquisition of novel genetic factors by these C.
      burnetii outbreak strains, such as virulence-related genes, has frequently been
      proposed and discussed, but is not proved yet. In the present study, the whole
      genome sequence of several Dutch strains (CbNL01 and CbNL12 genotypes), a few
      additionally selected strains from different geographical locations and publicly
      available genome sequences were used for a comparative bioinformatics approach.
      The study focuses on the identification of specific genetic differences in the
      outbreak related CbNL01 strains compared to other C. burnetii strains. In this
      approach we investigated the phylogenetic relationship and genomic aspects of
      virulence and host-specificity. Phylogenetic clustering of whole genome sequences
      showed a genotype-specific clustering that correlated with the clustering
      observed using Multiple Locus Variable-number Tandem Repeat Analysis (MLVA).
      Ortholog analysis on predicted genes and single nucleotide polymorphism (SNP)
      analysis of complete genome sequences demonstrated the presence of
      genotype-specific gene contents and SNP variations in C. burnetii strains. It
      also demonstrated that the currently used MLVA genotyping methods are highly
      discriminatory for the investigated outbreak strains. In the fully reconstructed
      genome sequence of the Dutch outbreak NL3262 strain of the CbNL01 genotype, a
      relatively large number of transposon-linked genes were identified as compared to
      the other published complete genome sequences of C. burnetii. Additionally, large
      numbers of SNPs in its membrane proteins and predicted virulence-associated genes
      were identified in all Dutch outbreak strains compared to the NM reference strain
      and other strains of the CbNL12 genotype. The presence of large numbers of
      transposable elements and mutated genes, thereof most likely resulted in high
      level of genome rearrangements and genotype-specific pathogenicity of outbreak
      strains. Thus, the epidemic potential of Dutch outbreak strains could be linked
      to increased genome plasticity and mutations in critical genes involved in
      virulence and the evasion of the host immune system.
AU  - Kuley R
AU  - Kuijt E
AU  - Smits MA
AU  - Roest HIJ
AU  - Smith HE
AU  - Bossers A
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2017 8: 1526.

PMID- 9000619
VI  - 264
DP  - 1996
TI  - Regulation of the activity of the type IC EcoR124I restriction enzyme.
PG  - 891-906
AB  - Restriction-modification systems must regulate the expression of their genes so that the
      chromosomal genome is modified at all times by the methyltransferase to protect the host cell
      from the potential lethal action of the cognate restriction endonuclease.  Since type I R-M
      systems can be transferred to non-modified Escherichia coli cells by conjugation or
      transformation without killing the recipient, they must have some means to regulate their
      restriction activity upon entering a new host cell to avoid restriction of unprotected host
      DNA and cell death.  This is especially true for EcoR124I, a type IC family member, which is
      coded for by a conjugative plasmid.  Control of EcoR124I restriction activity is most likely
      at the post-translational level as the transfer of the EcoR124I system into a recipient cell
      that already expressed the HsdR subunit of this system was not a lethal event.  Additionally,
      the kinetics of restriction activity upon transfer of the genes coding for the EcoR124I RM
      system to a recipient cell are the same, irrespective of the modification state of the
      recipient cell or the presence or absence of the EcoR124I HsdR subunit in the new host cells.
      The mechanism controlling the restriction activity of a type IC R-M system upon transfer to a
      new host cell is different from that controlling the chromosomally coded type IA and IB R-M
      systems.  The previously discovered hsdC mutant, which affects the establishment of the type
      IA system EcoKI, was shown to affect the establishment of the type IB system EcoAI, but to
      have no influence on EcoR124I.
AU  - Kulik EM
AU  - Bickle TA
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1996 264: 891-906.

PMID- 26975655
VI  - 44
DP  - 2016
TI  - Structural insights into DNA sequence recognition by Type ISP restriction-modification enzymes.
PG  - 4396-4408
AB  - Engineering restriction enzymes with new sequence specificity has been an unaccomplished
      challenge, presumably because of the complexity of target
      recognition. Here we report detailed analyses of target recognition by Type ISP
      restriction-modification enzymes. We determined the structure of the Type ISP
      enzyme LlaGI bound to its target and compared it with the previously reported
      structure of a close homologue that binds to a distinct target, LlaBIII. The
      comparison revealed that, although the two enzymes use almost a similar set of
      structural elements for target recognition, the residues that read the bases
      vary. Change in specificity resulted not only from appropriate substitution of
      amino acids that contacted the bases but also from new contacts made by
      positionally distinct residues directly or through a water bridge. Sequence
      analyses of 552 Type ISP enzymes showed that the structural elements involved in
      target recognition of LlaGI and LlaBIII were structurally well-conserved but
      sequentially less-conserved. In addition, the residue positions within these
      structural elements were under strong evolutionary constraint, highlighting the
      functional importance of these regions. The comparative study helped decipher a
      partial consensus code for target recognition by Type ISP enzymes.
AU  - Kulkarni M
AU  - Nirwan N
AU  - van Aelst K
AU  - Szczelkun MD
AU  - Saikrishnan K
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2016 44: 4396-4408.

PMID- 29097479
VI  - 5
DP  - 2017
TI  - Complete and Draft Genome Sequences of Eight Oceanic Pseudomonas aeruginosa Strains.
PG  - e01255-17
AB  - Pseudomonas aeruginosa is one of the most common model bacterial species, and genomes of
      hundreds of strains of this species have been sequenced to date.
      However, currently there is only one available genome of an oceanic isolate.
      Here, we report two complete and six draft genome sequences of P. aeruginosa
      isolates from the open ocean.
AU  - Kumagai Y
AU  - Yoshizawa S
AU  - Nakamura K
AU  - Ogura Y
AU  - Hayashi T
AU  - Kogure K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01255-17.

PMID- 24874677
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Winogradskyella sp. Strain PG-2, a Proteorhodopsin-Containing Marine Flavobacterium.
PG  - e00490-14
AB  - Winogradskyella sp. strain PG-2 is a marine flavobacterium isolated from surface  seawater.
      This organism contains proteorhodopsin, which can convert light energy
      into available forms of biochemical energy. Here, we present its complete genome
      sequence and annotation, which provide further insights into the life strategy of
      proteorhodopsin-mediated phototrophy in the ocean.
AU  - Kumagai Y
AU  - Yoshizawa S
AU  - Oshima K
AU  - Hattori M
AU  - Iwasaki W
AU  - Kogure K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00490-14.

PMID- Not carried by PubMed...
VI  - 46
DP  - 1988
TI  - Recombination of DNA in blue-green algae - restriction enzyme systems and transfection vectors.
PG  - 38-41
AB  - One table describes the presence of a number of new restriction enzymes in
      seven strains of blue-green algae.  It is concluded that African and American
      strains of Spirulina can be clearly distinguished from one another on the basis
      of restriction enzyme content.
AU  - Kumano M
AU  - Sakakibara M
PT  - Journal Article
TA  - Baiosaiensu to Indasutori
JT  - Baiosaiensu to Indasutori
SO  - Baiosaiensu to Indasutori 1988 46: 38-41.

PMID- 
VI  - 0
DP  - 2005
TI  - Restriction endonucleases.
PG  - 55-74
AB  - Restriction endonucleases bind specifically to and cleave the sugar phosphate backbone (bond
      between deoxyribose and phosphate groups) in double stranded DNA at specific sites within or
      adjacent to a particular sequence known as recognition sequence.  Restriction endonucleases
      are of three types: Type I, Type II and Type III.  Types I and III restriction endonucleases
      carry modification (like methylation) and ATP dependent cleavage activities in the same
      protein.  Type III restriction endonucleases cleave the DNA at the recognition site and then
      dissociate from the substrate.  However, type I restriction endonucleases bind to the
      recognition sequence but cleave at random sites when the DNA loops back to the bound enzyme.
      Neither type I nor type III restriction endonucleases are widely used in genetic engineering.
      Type II restriction endonucleases are commonly used in genetic engineering.  They are the
      invaluable molecular scissors.  These restriction endonucleases cut both strands of duplex DNA
      with in a stretch of just a few bases.  Therefore, only type II restriction enonucleases are
      described in this chapter.  Nomenclature of the restriction endonucleases is based on the
      source of their isolation from an organism.  In case of restriction endonucleases, enzyme
      activity is described in units considering one unit of the restriction endonuclease as the
      amount of the enzyme required to hydrolyze one microgram of lambda DNA to completion in one
      hour at the optimum temperature in a total volume of 50 ul of the assay mixture.  The lambda
      DNA, due to its large size (approximately 50 Kb), is considered to have recognition sites
      almost for all the restriction endonucleases.
AU  - Kumar A
AU  - Garg N
PT  - Journal Article
TA  - Genet. Eng. (N Y)
JT  - Genet. Eng. (N Y)
SO  - Genet. Eng. (N Y) 2005 0: 55-74.

PMID- 28057749
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Highly Virulent Race 4/Biovar 3 of Ralstonia solanacearum CaRs_Mep Causing Bacterial Wilt in Zingiberaceae Plants in India.
PG  - e01420-16
AB  - The genome of Ralstonia solanacearum CaRs_Mep, a race 4/biovar 3/phylotype I bacterium causing
      wilt in small cardamom and other Zingiberaceae plants, was
      sequenced. Analysis of the 5.7-Mb genome sequence will aid in better
      understanding of the genetic determinants of host range, host jump, survival,
      pathogenicity, and virulence of race 4 of R. solanacearum.
AU  - Kumar A
AU  - Munjal V
AU  - Sheoran N
AU  - Prameela TP
AU  - Suseelabhai R
AU  - Aggarwal R
AU  - Jain RK
AU  - Eapen SJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01420-16.

PMID- 24970827
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of trh+ Vibrio parahaemolyticus VP-49, Isolated from Seafood Harvested along the Mangalore Coast, India.
PG  - e00607-14
AB  - Vibrio parahaemolyticus is a seafood-borne pathogen autochthonous to the marine and estuarine
      ecosystem, which is responsible for gastroenteritis due to the
      consumption of contaminated raw seafood. Here, we report the draft genome
      sequence of V. parahaemolyticus VP-49, isolated from seafood, to identify the
      different virulence attributes and to study the mechanisms that enhance its
      environmental fitness.
AU  - Kumar BK
AU  - Deekshit VK
AU  - Rai P
AU  - Gurtler V
AU  - Karunasagar I
AU  - Karunasagar I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00607-14.

PMID- 27811115
VI  - 4
DP  - 2016
TI  - Genome Sequence of Pandoraea sp. ISTKB, a Lignin-Degrading Betaproteobacterium, Isolated from Rhizospheric Soil.
PG  - e01240-16
AB  - We report here the genome sequence of Pandoraea sp. ISTKB, a betaproteobacterium  isolated
      from rhizospheric soil in the backwaters of Alappuzha, Kerala, India.
      The strain is alkalotolerant and grows on medium containing lignin as a sole
      carbon source. Genes and pathways related to lignin degradation were complemented
      by genomic analysis.
AU  - Kumar M
AU  - Gazara RK
AU  - Verma S
AU  - Kumar M
AU  - Verma PK
AU  - Thakur IS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01240-16.

PMID- 27795274
VI  - 4
DP  - 2016
TI  - Genome Sequence of Carbon Dioxide-Sequestering Serratia sp. Strain ISTD04 Isolated from Marble Mining Rocks.
PG  - e01141-16
AB  - The Serratia sp. strain ISTD04 has been identified as a carbon dioxide (CO2)-sequestering
      bacterium isolated from marble mining rocks in the Umra area,
      Rajasthan, India. This strain grows chemolithotrophically on media that contain
      sodium bicarbonate (NaHCO3) as the sole carbon source. Here, we report the genome
      sequence of 5.07 Mb Serratia sp. ISTD04.
AU  - Kumar M
AU  - Gazara RK
AU  - Verma S
AU  - Kumar M
AU  - Verma PK
AU  - Thakur IS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01141-16.

PMID- 19796097
VI  - 108
DP  - 2010
TI  - Diversity of 16S rRNA and dioxygenase genes detected in coal-tar-contaminated site undergoing active bioremediation.
PG  - 1252-1262
AB  - AIMS: In order to develop effective bioremediation strategies for
      polyaromatic hydrocarbons (PAHs) degradation, the composition and
      metabolic potential of microbial communities need to be better understood,
      especially in highly PAH contaminated sites in which little information on
      the cultivation-independent communities is available. METHODS AND RESULTS:
      Coal-tar-contaminated soil was collected, which consisted of 122.5 mg
      g(-1) total extractable PAH compounds. Biodegradation studies with this
      soil indicated the presence of microbial community that is capable of
      degrading the model PAH compounds viz naphthalene, phenanthrene and pyrene
      at 50 ppm each. PCR clone libraries were established from the DNA of the
      coal-tar-contaminated soil, targeting the 16S rRNA to characterize (i) the
      microbial communities, (ii) partial gene fragment encoding the Rieske iron
      sulfur center (alpha-subunit) common to all PAH dioxygenase enzymes and
      (iii) beta-subunit of dioxygenase. Phylotypes related to Proteobacteria
      (Alpha-, Epsilon- and Gammaproteobacteria), Acidobacteria, Actinobacteria,
      Firmicutes, Gemmatimonadetes and Deinococci were detected in 16S rRNA
      derived clone libraries. Many of the gene fragment sequences of
      alpha-subunit and beta-subunit of dioxygenase obtained from the respective
      clone libraries fell into clades that are distinct from the reference
      dioxygenase gene sequences. Presence of consensus sequence of the Rieske
      type [2Fe-2S] cluster binding site suggested that these gene fragments
      encode for alpha-subunit of dioxygenase gene. CONCLUSIONS: Sequencing of
      the cloned libraries representing alpha-subunit gene fragments (Rf1) and
      beta-subunit of dioxygenase showed the presence of hitherto unidentified
      dioxygenase in coal-tar-contaminated soil. SIGNIFICANCE AND IMPACT OF THE
      STUDY: The combination of the Rieske primers and bacterial community
      profiling represents a powerful tool for both assessing bioremediation
      potential and the exploration of novel dioxygenase genes in a contaminated
      environment.
AU  - Kumar M
AU  - Khanna S
PT  - Journal Article
TA  - J. Appl. Microbiol.
JT  - J. Appl. Microbiol.
SO  - J. Appl. Microbiol. 2010 108: 1252-1262.

PMID- 3004561
VI  - 24
DP  - 1985
TI  - Resonance assignment of the 500-MHz proton NMR spectrum of self-complementary dodecanucleotide d-GGATCCGGATCC:  altered conformations at BamHI cleavage sites.
PG  - 7703-7711
AB  - Resonance assignments of nonexchangeable base and sugar protons of the
      self-complementary dodecanucleotide d-GGATCCGGATCC have been obtained by
      two-dimensional NMR methods and strategies derived from interproton distance
      calculations on different secondary structures of nucleic acids.
      Conformational details about the glycosidic dihedral angle and sugar pucker
      have been derived from the relative intensities of cross peaks in the
      two-dimensional J-correlated and nuclear Overhauser enhancement correlated
      spectra in D2O solution.  It is observed that d-GGATCCGGATCC assumes a
      predominantly B-type conformation with sequence-dependent changes along the
      chain.  The recognition site of BamHI shows a distinctly different geometrical
      environment.  The sugar rings of G1 and G7 assume a C3'-endo geometry while the
      rest of the sugars possess C2'-endo geometry.
AU  - Kumar MR
AU  - Hosur RV
AU  - Roy KB
AU  - Miles HT
AU  - Govil G
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1985 24: 7703-7711.

PMID- 23045484
VI  - 194
DP  - 2012
TI  - Next-Generation Sequencing and De Novo Assembly, Genome Organization, and Comparative Genomic Analyses of the Genomes of Two Helicobacter pylori Isolates  from Duodenal Ulcer Patients in India.
PG  - 5963-5964
AB  - The prevalence of different H. pylori genotypes in various geographical regions indicates
      region-specific adaptations during the course of evolution. Complete
      genomes of H. pylori from countries with high infection burdens, such as India,
      have not yet been described. Herein we present genome sequences of two H. pylori
      strains, NAB47 and NAD1, from India. In this report, we briefly mention the
      sequencing and finishing approaches, genome assembly with downstream statistics,
      and important features of the two draft genomes, including their phylogenetic
      status. We believe that these genome sequences and the comparative genomics
      emanating thereupon will help us to clearly understand the ancestry and biology
      of the Indian H. pylori genotypes, and this will be helpful in solving the
      so-called Indian enigma, by which high infection rates do not corroborate the
      minuscule number of serious outcomes observed, including gastric cancer.
AU  - Kumar N
AU  - Mukhopadhyay AK
AU  - Patra R
AU  - De R
AU  - Baddam R
AU  - Shaik S
AU  - Alam J
AU  - Tiruvayipati S
AU  - Ahmed N
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5963-5964.

PMID- 29721151
VI  - 13
DP  - 2018
TI  - Strategies for high-altitude adaptation revealed from high-quality draft genome of non-violacein producing Janthinobacterium lividum ERGS5:01.
PG  - 11
AB  - A light pink coloured bacterial strain ERGS5:01 isolated from glacial stream water of Sikkim
      Himalaya was affiliated to Janthinobacterium lividum based on 16S
      rRNA gene sequence identity and phylogenetic clustering. Whole genome sequencing
      was performed for the strain to confirm its taxonomy as it lacked the typical
      violet pigmentation of the genus and also to decipher its survival strategy at
      the aquatic ecosystem of high elevation. The PacBio RSII sequencing generated
      genome of 5,168,928 bp with 4575 protein-coding genes and 118 RNA genes. Whole
      genome-based multilocus sequence analysis clustering, in silico DDH similarity
      value of 95.1% and, the ANI value of 99.25% established the identity of the
      strain ERGS5:01 (MCC 2953) as a non-violacein producing J. lividum. The genome
      comparisons across genus Janthinobacterium revealed an open pan-genome with the
      scope of the addition of new orthologous cluster to complete the genomic
      inventory. The genomic insight provided the genetic basis of freezing and
      frequent freeze-thaw cycle tolerance and, for industrially important enzymes.
      Extended insight into the genome provided clues of crucial genes associated with
      adaptation in the harsh aquatic ecosystem of high altitude.
AU  - Kumar R
AU  - Acharya V
AU  - Singh D
AU  - Kumar S
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2018 13: 11.

PMID- 29348345
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Vibrio parahaemolyticus Strain M1-1, Which Causes Acute  Hepatopancreatic Necrosis Disease in Shrimp in Vietnam.
PG  - e01468-17
AB  - We report here the genome sequence of Vibrio parahaemolyticus strain M1-1, which  causes a
      mild form of shrimp acute hepatopancreatic necrosis disease (AHPND).
      Compared to other virulent strains, the M1-1 genome appeared to express several
      additional genes, while some genes were missing. These instabilities may be
      related to the reduced virulence of M1-1.
AU  - Kumar R
AU  - Chang CC
AU  - Ng TH
AU  - Ding JY
AU  - Tseng TC
AU  - Lo CF
AU  - Wang HC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01468-17.

PMID- 24051323
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Sphingobium lactosutens Strain DS20T, Isolated from a Hexachlorocyclohexane Dumpsite.
PG  - e00753-13
AB  - Sphingobium lactosutens DS20(T) has been isolated from the hexachlorocyclohexane  (HCH)
      dumpsite in Lucknow, India, but does not degrade any of the HCH isomers.
      Here, we present the ~5.36-Mb draft genome sequence of strain DS20(T), which
      consists of 110 contigs and 5,288 coding sequences, with a G+C content of 63.1%.
AU  - Kumar R
AU  - Dwivedi V
AU  - Negi V
AU  - Khurana JP
AU  - Lal R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00753-13.

PMID- 22879937
VI  - 7
DP  - 2012
TI  - Comparative Transcriptomics of H. pylori Strains AM5, SS1 and Their hpyAVIBM Deletion Mutants: Possible Roles of Cytosine Methylation.
PG  - e42303
AB  - Helicobacter pylori is an important human pathogen and one of the most successful chronic
      colonizers of the human body. H. pylori uses diverse
      mechanisms to modulate its interaction with the host in order to
      promote chronic infection and overcome host immune response.
      Restriction-modification genes are a major part of strain-specific
      genes present in H. pylori. The role of N-6 -adenine methylation in
      bacterial gene regulation and virulence is well established but not
      much is known about the effect of C-5 -cytosine methylation on gene
      expression in prokaryotes. In this study, it was observed by microarray
      analysis and RT-PCR, that deletion of an orphan C-5 -cytosine
      methyltransferase, hpyAVIBM in H. pylori strains AM5and SS1 has a
      significant effect on the expression of number of genes belonging to
      motility, adhesion and virulence. AM Delta DhpyAVIBM mutant strain has
      a different LPS profile and is able to induce high IL-8 production
      compared to wild-type. hpyAVIBM from strain 26695 is able to complement
      mutant SS1 and AM5 strains. This study highlights a possible
      significance of cytosine methylation in the physiology of H. pylori.
AU  - Kumar R
AU  - Mukhopadhyay AK
AU  - Ghosh P
AU  - Rao DN
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2012 7: e42303.

PMID- 20180846
VI  - 277
DP  - 2010
TI  - Characterization of an N6 adenine methyltransferase from Helicobacter pylori strain 26695 which methylates adjacent adenines on the same strand.
PG  - 1666-1683
AB  - Genomic sequences of Helicobacter pylori strains 26695, J99, HPAGI and G27 have revealed an
      abundance of restriction and modification genes.
      hp0050, which encodes an N6 adenine DNA methyltransferase, was cloned,
      overexpressed and purified to near homogeneity. It recognizes the
      sequence 5'-GRRG-3' (where R is A or G) and, most intriguingly,
      methylates both adenines when R is A (5'-GAAG-3'). Kinetic analysis
      suggests a nonprocessive (repeated-hit) mechanism of methylation in
      which HP0050 methyltransferase methylates one adenine at a time in the
      sequence 5'-GAAG-3'. This is the first report of an N6 adenine DNA
      methyltransferase that methylates two adjacent residues on the same
      strand. Interestingly, HP0050 homologs from two clinical strains of H.
      pylori (PG227 and 128) methylate only 5'-GAGG-3' compared with
      5'-GRRG-3' in strain 26695. HP0050 methyltransferase is highly
      conserved as it is present in more than 90% of H. pylori strains.
      Inactivation of hp0050 in strain PG227 resulted in poor growth,
      suggesting its role in the biology of H. pylori. Collectively, these
      findings provide impetus for exploring the role(s) of this conserved
      DNA methyltransferase in the cellular processes of H. pylori.
AU  - Kumar R
AU  - Mukhopadhyay AK
AU  - Rao DN
PT  - Journal Article
TA  - FEBS J.
JT  - FEBS J.
SO  - FEBS J. 2010 277: 1666-1683.

PMID- 
VI  - 19
DP  - 2014
TI  - Helicobacter pylori Restriction Modification systems: Role beyond genome protection.
PG  - 0
AB  - 
AU  - Kumar R
AU  - Prasad Y
AU  - Rao DN
PT  - Journal Article
TA  - Helicobacter
JT  - Helicobacter
SO  - Helicobacter 2014 19: 0.

PMID- 21110832
VI  - 433
DP  - 2011
TI  - A nucleotide insertion between two adjacent methyltransferases in Helicobacter pylori results in a bifunctional DNA methyltransferase.
PG  - 487-495
AB  - Helicobacter pylori has a dynamic R-M (restriction-modification) system. It is capable of
      acquiring new R-M systems from the environment
      in the form of DNA released from other bacteria or other H. pylon
      strains. Random mutations in RM genes can result in non-functional R-M
      systems or R-M systems with new properties. hpyAVIAM and hpyAVIBM are
      two solitary DNA MTase (methyltransferase) genes adjacent to each other
      and lacking a cognate restriction enzyme gene in H. pylori strain
      26695. Interestingly, in an Indian strain D27, hpyAVIAM hpyAVIBM
      encodes a single bifunctional polypeptide clue to insertion of a
      nucleotide just before the stop codon of hpyAVIBM and, when a similar
      mutation was made in hpyAVIAM hpyAVIBM from strain 26695, a functional
      MTase with an N-terminal C-5-cytosine MTase domain and a C-terminal
      N-6-adenine MTase domain was constructed. Mutations in the AdoMet
      (S-adenosylmethionine)-binding motif or in the catalytic motif of
      M.HpyAVIA or M.HpyAVIB selectively abrogated the C-5-cytosine or
      N-6-adenine methylation activity of M.HpyAVIA-M.HpyAVIB fusion protein.
      The present study highlights the ability of H. pylori to evolve genes
      with unique functions and thus generate variability. For organisms such
      as H. pylori, which have a small genome, these adaptations could be
      important for their survival in the hostile host environment.
AU  - Kumar R
AU  - Rao DN
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 2011 433: 487-495.

PMID- 23150247
VI  - 61
DP  - 2012
TI  - Role of DNA methyltransferases in epigenetic regulation in bacteria.
PG  - 81-102
AB  - In prokaryotes, alteration in gene expression was observed with the modification  of DNA,
      especially DNA methylation. Such changes are inherited from generation to
      generation with no alterations in the DNA sequence and represent the epigenetic
      signal in prokaryotes. DNA methyltransferases are enzymes involved in DNA
      modification and thus in epigenetic regulation of gene expression. DNA
      methylation not only affects the thermodynamic stability of DNA, but also changes
      its curvature. Methylation of specific residues on DNA can affect the protein-DNA
      interactions. DNA methylation in prokaryotes regulates a number of physiological
      processes in the bacterial cell including transcription, DNA mismatch repair and
      replication initiation. Significantly, many reports have suggested a role of DNA
      methylation in regulating the expression of a number of genes in virulence and
      pathogenesis thus, making DNA methlytransferases novel targets for the designing
      of therapeutics. Here, we summarize the current knowledge about the influence of
      DNA methylation on gene regulation in different bacteria, and on bacterial
      virulence.
AU  - Kumar R
AU  - Rao DN
PT  - Journal Article
TA  - Subcell. Biochem.
JT  - Subcell. Biochem.
SO  - Subcell. Biochem. 2012 61: 81-102.

PMID- 22269034
VI  - 279
DP  - 2012
TI  - Mutations in hpyAVIBM, C5 cytosine DNA methyltransferase from Helicobacter pylori result in relaxed specificity.
PG  - 1080-1092
AB  - The genome of Helicobacter pylori is rich in restrictionmodification (RM) systems.
      Approximately 4% of the genome codes for components of RM
      systems. hpyAVIBM, which codes for a phase-variable C5 cytosine
      methyltransferase (MTase) from H. pylori, lacks a cognate restriction
      enzyme. Over-expression of M.HpyAVIB in Escherichia coli enhances the
      rate of mutations. However, when the catalytically inactive F9N or C82W
      mutants of M.HpyAVIB were expressed in E. coli, mutations were not
      observed. The M.HpyAVIB gene itself was mutated to give rise to
      different variants of the MTase. M.HpyAVIB variants were purified and
      differences in kinetic properties and specificity were observed.
      Intriguingly, purified MTase variants showed relaxed substrate
      specificity. Homologues of hpyAVIBM homologues amplified and sequenced
      from different clinical isolates showed similar variations in sequence.
      Thus, hpyAVIBM presents an interesting example of allelic variations in
      H. pylori where changes in the nucleotide sequence result in proteins
      with new properties.
AU  - Kumar R
AU  - Sabareesh V
AU  - Mukhopadhyay AK
AU  - Rao DN
PT  - Journal Article
TA  - FEBS J.
JT  - FEBS J.
SO  - FEBS J. 2012 279: 1080-1092.

PMID- 26543128
VI  - 3
DP  - 2015
TI  - Genome Assembly of Chryseobacterium polytrichastri ERMR1:04, a Psychrotolerant Bacterium with Cold Active Proteases, Isolated from East Rathong Glacier in  India.
PG  - e01305-15
AB  - We report here the genome assembly of a psychrotolerant bacterium, Chryseobacterium
      polytrichastri ERMR1:04, which secretes cold-active proteases.
      The bacterium was isolated from a pristine location, the East Rathong Glacier in
      the Sikkim Himalaya. The 5.53-Mb genome provides insight into the cold-active
      industrial enzyme and adaptation in the cold environment.
AU  - Kumar R
AU  - Singh D
AU  - Swarnkar MK
AU  - Singh AK
AU  - Kumar S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01305-15.

PMID- 18083524
VI  - 16
DP  - 2008
TI  - Activation and inhibition of DNA methyltransferases by S-adenosyl-L-homocysteine analogues.
PG  - 2276-2285
AB  - The inhibition of methyltransferases is currently of high interest, particularly in the areas
      of microbial infection and cell
      proliferation, as there have been serious attempts to develop novel
      anti-microbial agents. In the present investigation, a series of
      11S-adenosyl-L-homocysteine analogues have been synthesized and effect
      of these analogues on DNA methylation catalyzed by DNA
      methyltransferases was studied. It was found that, while
      5'-S-(propionic acid) 5-deoxy-9-(1'-beta-D-ribofuranosyl) 1,
      3-dideazaadenine was an activator of EcoP15I and HhaI DNA
      methyltransferases, 5'-S-(propionic acid)
      5'-deoxy-9-(1'-beta-dribofuran osyl)adenine inhibited the
      methyltransferases in a non-competitive manner. An understanding of the
      binding of analogues to DNA methyltransferases will greatly assist the
      design of novel anti-microbial compounds.
AU  - Kumar R
AU  - Srivastava R
AU  - Singh RK
AU  - Surolia A
AU  - Rao DN
PT  - Journal Article
TA  - Bioorg. Med. Chem.
JT  - Bioorg. Med. Chem.
SO  - Bioorg. Med. Chem. 2008 16: 2276-2285.

PMID- 8639660
VI  - 35
DP  - 1996
TI  - Functional characterization of the precursor and spliced forms of RecA protein of Mycobacterium tuberculosis.
PG  - 1793-1802
AB  - The recA locus of pathogenic mycobacteria differs from that of
      nonpathogenic species because it contains large intervening sequences nested in the RecA
      homology region that are excised by an unusual protein-splicing reaction.  In vivo assays
      indicated that Mycobacterium tuberculosis recA partially complemented Escherichia coli
      recA mutants for recombination and mutagenesis.  Further, splicing of the 85 kDa
      precursor to 38 kDa MtRecA protein was necessary for the display of its activity, in vivo.
      To gain insights into the molecular basis for partial and lack of complementation by
      MtRecA and 85 kDa proteins, respectively, we purified both of them to homogeneity.
      MtRecA protein, but not the 85 kDa form, bound stoichiometrically to single-stranded
      DNA in the presence of ATP.  MtRecA protein was cross-linked to 8-azidoadenosine 5'-
      triphosphate with reduced efficiency, and kinetic analysis of ATPase activity suggested that
      it is due to decreased affinity for ATP.  In contrast, the 85 kDa form was unable to bind
      ATP, in the presence or absence of ssDNA and, consequently, was entirely devoid of
      ATPase activity.  Molecular modeling studies suggested that the decreased affinity of
      MtRecA protein for ATP and the reduced efficiency of its hydrolysis might be due to the
      widening of the cleft which alters the hydrogen bonds and the contact area between the
      enzyme and the substrate and changes in the disposition of the amino acid residues around
      the magnesium ion and the gamma-phosphate.  The formation of joint molecules promoted
      by MtRecA protein was stimulated by SSB when the former was added first.  The
      probability of an association between the lack and partial levels of biological activity of
      RecA protein(s) to that of illegitimate recombination in pathogenic mycobacteria is
      considered.
AU  - Kumar RA
AU  - Vaze MB
AU  - Chandra NR
AU  - Vijayan M
AU  - Muniyappa K
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1996 35: 1793-1802.

PMID- 23538907
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Rhodococcus triatomae Strain BKS 15-14.
PG  - e0012913
AB  - We report the 5.8-Mb genome sequence of Rhodococcus triatomae BKS 15-14, isolated from an ant
      hill soil sample, collected from Bhitarkanika Mangrove Reserve
      Forest, Odisha, India. The draft genome of strain BKS 15-14 consists of 5,824,349
      bp, with a G+C content of 69%, 5,387 protein-coding genes, and 57 RNAs.
AU  - Kumar S
AU  - Bala M
AU  - Raghava GP
AU  - Mayilraj S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0012913.

PMID- 8127644
VI  - 22
DP  - 1994
TI  - The DNA (cytosine-5) methyltransferases.
PG  - 1-10
AB  - A review of the m5C-methyltransferases relating sequence to structure and function.
AU  - Kumar S
AU  - Cheng X
AU  - Klimasauskas S
AU  - Sha M
AU  - Posfai J
AU  - Roberts RJ
AU  - Wilson GG
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1994 22: 1-10.

PMID- 1390649
VI  - 31
DP  - 1992
TI  - Purification, crystallization, and preliminary X-ray diffraction analysis of an M.HhaI-AdoMet complex.
PG  - 8648-8653
AB  - The type-II DNA-(cytosine-5)-methyltransferase M.HhaI was overexpressed in Escherichia coli
      and purified to apparent homogeneity. The purification scheme exploits a unique high salt
      back-extraction step to solubilize M.HhaI selectively, followed by FPLC chromatography. The
      yield of purified protein was 0.75-1.0 mg per gram of bacterial paste. M.HhaI could be
      isolated in two forms: bound with its cofactor S-adenosylmethionine (AdoMet) or devoid of the
      cofactor. The AdoMet-bound form was capable of methylating DNA in vitro in the absence of
      exogenous AdoMet. From kinetic studies of the purified enzyme, values for KmAdoMet(60 nM),
      KiAdoHyc(0.4 nM), and Kcat (0.22s-1) were determined. The purified enzyme bound with its
      cofactor was crystallized by the hanging drop vapor diffusion technique. Crystals were of
      monoclinic space group P21 and had unit-cell dimensions of a = 55.3 A, b = 72.7 A, c = 91.0 A,
      and B=102.5o, with two molecules of M.HhaI in each of the two asymmetric units. The crystals
      diffract beyond 2.5 A and are suitable for structure determination.
AU  - Kumar S
AU  - Cheng X
AU  - Pflugrath JW
AU  - Roberts RJ
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1992 31: 8648-8653.

PMID- 9207024
VI  - 25
DP  - 1997
TI  - DNA containing 4'-thio-2'-deoxycytidine inhibits methylation by HhaI methyltransferase.
PG  - 2773-2783
AB  - 4'-Thio-2'-deoxycytidine was synthesized as a 5'-protected phosphoramidite compatible with
      solid phase DNA synthesis.  When incorporated as the target cytosine (C*) in the GC*GC
      recognition sequence for the DNA methyltransferase M.HhaI, methyl transfer was strongly
      inhibited.  In contrast, these same oligonucleotides were normal substrates for the cognate
      restriction endonuclease R.HhaI and its isoschizomer R.HindP1I.  M.HhaI was able to bind both
      4'-thio-modified DNA and unmodified DNA to equivalent extents under equilibrium conditions.
      However, the presence of 4'-thio-2'-deoxycytidine decreased the half-life of the complex by
      >10-fold.  The crystal stucture of a ternary complex of M.HhaI, AdoMet and DNA containing
      4'-thio-2'-deoxycytidine was solved at 2.05 A resolution with a crystallographic R-factor of
      0.186 and R-free of 0.231.  The structure is not grossly different from previously solved
      ternary complexes containing M.HhaI, DNA and AdoHcy.  The difference electron density suggests
      partial methylation at C5 of the flipped target 4'-thio-2'-deoxycytidine.  The inhibitory
      effect of the 4' sulfur atom on enzymatic activity may be traced to perturbation of a step in
      the methylation reaction after DNA binding but prior to methyl transfer.  This inhibitory
      effect can be partially overcome after a considerably long time in the crystal environment
      where the packing prevents complex dissociation and the target is accurately positioned within
      the active site.
AU  - Kumar S
AU  - Horton JR
AU  - Jones GD
AU  - Walker RT
AU  - Roberts RJ
AU  - Cheng X
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1997 25: 2773-2783.

PMID- 28522707
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Luminescent Strain Vibrio campbellii LB102, Isolated from a Black Tiger Shrimp (Penaeus monodon) Broodstock Rearing System.
PG  - e00342-17
AB  - We report here the genome sequence of Vibrio campbellii LB102, isolated from the  broodstock
      rearing system of a shrimp hatchery in India. Sequence analysis
      revealed the presence of effector toxins of the type III (YopT, sharing 39%
      identity with Yersinia pestis) and type VI (VgrG-3 and hemolysin coregulated
      protein of V. cholerae) secretion systems.
AU  - Kumar S
AU  - Jangam AK
AU  - Akhil V
AU  - Rajendran V
AU  - Katneni VK
AU  - Sahaya RJJ
AU  - Grover M
AU  - Nagaleekar VK
AU  - Alavandi SV
AU  - Vijayan KK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00342-17.

PMID- 8448145
VI  - 32
DP  - 1993
TI  - Orientation isomers of the mitomycin C interstrand cross-link in non-self-complementary DNA. Differential effect of the two isomers on restriction endonuclease cleavage at a nearby site.
PG  - 1364-1372
AB  - Reductively activated mitomycin C (MC) forms DNA interstrand cross-links between two guanines
      at CG.CG sequences. It is predictable that such cross-links should occur in two isomeric
      strand orientations in duplex DNA (except when located in the center of a self-complementary
      duplex). This was verified by the isolation and characterization of a pair of two isomeric
      oligonucleotides in each case of five non-self-complementary duplexes of 8-bp length,
      cross-linked by MC. Isomer separation was accomplished by reverse-phase HPLC. The isomers in a
      pair were formed in approximately 1:1 proportion.Their structures were rigorously
      characterized by a two-step cross-linking procedure: first 1-monoalkylation of each strand,
      followed by conversion to a cross-linked duplex by annealing the monoalkylated strand to its
      complement in the presence of a reducing agent. The resulting individual authentic orientation
      isomers were used as standards for identification of the two isomers formed in the original
      (one-step) cross-linking reactions. A 16-bp duplex oligonucleotide was synthesized featuring
      the AluI cognate sequence, separated from a MC cross-link site by only 1 bp. Its two MC
      cross-linked isomers were prepared separately, and their rate of cleavage by AluI was
      determined using HPLC. Cleavage of both the unmodified and cross-linked duplexes was
      nonsymmetrical. The isomer in which the 2-NH3+ of MC is oriented toward the AluI site was
      cleaved essentially at the same rate as the control duplex, while cleavage of the isomer with
      the MC indoloquinone group oriented toward the AluI site was inhibited 2-fold at the
      faster-cleaved strand. This difference demonstrates that the two orientations of the MC
      cross-link can exert differential effects on protein-DNA interactions. The modest inhibition
      of AluI cleavage relative to that by CC-1065 [Hurley,L.H., Needham-VanDevanter,D.R., and
      Lee,C.(1987)Proc. Natl. Acad. Sci. U.S.A. 84, 6412-6416] may indicate relatively low
      distortion of DNA by the MC cross-link. This notion is supported by a comparison with psoralen
      cross-links.
AU  - Kumar S
AU  - Johnson WS
AU  - Tomasz M
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1993 32: 1364-1372.

PMID- 29538771
VI  - 46
DP  - 2018
TI  - N4-cytosine DNA methylation regulates transcription and pathogenesis in Helicobacter pylori.
PG  - 3429-3445
AB  - Many bacterial genomes exclusively display an N4-
      methyl cytosine base (m4C), whose physiological
      significance is not yet clear. Helicobacter pylori is
      a carcinogenic bacterium and the leading cause of
      gastric cancer in humans. Helicobacter pylori strain
      26695 harbors a single m4C cytosine methyltransferase,
      M2.HpyAII which recognizes 5 TCTTC 3 sequence
      and methylates the first cytosine residue. To
      understand the role of m4C modification, M2.hpyAII
      deletion strain was constructed. Deletion strain displayed
      lower adherence to host AGS cells and reduced
      potential to induce inflammation and apoptosis.
      M2.hpyAII gene deletion strain exhibited reduced
      capacity for natural transformation, which was
      rescued in the complemented strain carrying an active
      copy of M2.hpyAII gene in the genome. Genomewide
      gene expression and proteomic analysis were
      carried out to discern the possible reasons behind
      the altered phenotype of the M2.hpyAII gene deletion
      strain. Upon the loss of m4C modification a total
      of 102 genes belonging to virulence, ribosome assembly
      and cellular components were differentially
      expressed. The present study adds a functional role
      for the presence of m4C modification in H. pylori and
      provides the first evidence that m4C signal acts as a
      global epigenetic regulator in H. pylori.
AU  - Kumar S
AU  - Karmakar BC
AU  - Nagarajan D
AU  - Mukhopadhyay AK
AU  - Morgan RD
AU  - Rao DN
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2018 46: 3429-3445.

PMID- 23405287
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Type Species of the Genus Citrobacter, Citrobacter freundii MTCC 1658.
PG  - e00120-12
AB  - We report the 5.0-Mb genome sequence of the type species of the genus Citrobacter, Citrobacter
      freundii strain MTCC 1658, isolated from canal water. This draft genome sequence of C.
      freundii strain MTCC 1658(T) consists of 5,001,265 bp with a G+C content of 51.61%, 4,691
      protein-coding genes, 70 tRNAs, and 10 rRNAs.
AU  - Kumar S
AU  - Kaur C
AU  - Kimura K
AU  - Takeo M
AU  - Raghava GP
AU  - Mayilraj S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00120-12.

PMID- 23599292
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Streptomyces gancidicus Strain BKS 13-15.
PG  - e00150-13
AB  - We report the 7.3-Mbp genome sequence of Streptomyces gancidicus strain BKS 13-15, isolated
      from mangrove sediment samples collected from the Bhitar Kanika
      Mangrove Reserve Forest, Odissha, India. The draft genome of strain Streptomyces
      gancidicus strain BKS 13-15 consists of 7,300,479 bp with 72.6% G+C content,
      6,631 protein-coding genes, and 71 RNAs.
AU  - Kumar S
AU  - Kaur N
AU  - Singh NK
AU  - Raghava GP
AU  - Mayilraj S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00150-13.

PMID- 23409261
VI  - 1
DP  - 2013
TI  - Genome Sequence of Non-O1 Vibrio cholerae PS15.
PG  - e00227-12
AB  - The draft genome sequence of a non-O1 Vibrio cholerae strain, PS15, organized into 3,512 open
      reading frames within a 3.9-Mb genome, was determined. The PS15
      genome sequence will allow for the study of the evolution of virulence and
      environmental adaptation in V. cholerae.
AU  - Kumar S
AU  - Lindquist IE
AU  - Sundararajan A
AU  - Rajanna C
AU  - Floyd JT
AU  - Smith KP
AU  - Andersen JL
AU  - He G
AU  - Ayers RM
AU  - Johnson JA
AU  - Werdann JJ
AU  - Sandoval AA
AU  - Mojica NM
AU  - Schilkey FD
AU  - Mudge J
AU  - Varela MF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00227-12.

PMID- 26543133
VI  - 3
DP  - 2015
TI  - Genome Sequence of Acinetobacter baumannii Strain 10441_14 Belonging to ST451, Isolated from India.
PG  - e01322-15
AB  - Acinetobacter baumannii resistance to carbapenems is of global concern. Here, we  report the
      3.9 Mb draft genome of a cerebrospinal fluid isolate of A. baumannii
      strain 10441_14 which is carbapenem resistant and belongs to ST451. This genome
      will further help in the understanding of the drug resistance mechanism,
      epidemiology, and pathology of this bacterium.
AU  - Kumar S
AU  - Patil PP
AU  - Midha S
AU  - Ray P
AU  - Patil PB
AU  - Gautam V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01322-15.

PMID- 26472849
VI  - 3
DP  - 2015
TI  - Genome Sequence of Acinetobacter baumannii Strain 5021_13, Isolated from Cerebrospinal Fluid.
PG  - e01213-15
AB  - We report here the 4.1-Mb draft genome sequence of Acinetobacter baumannii strain 5021_13, a
      cerebrospinal fluid isolate from northern India. This genome information will help studies
      toward understanding the epidemiology and pathogenicity of this important nosocomial pathogen.
AU  - Kumar S
AU  - Patil PP
AU  - Midha S
AU  - Ray P
AU  - Patil PB
AU  - Gautam V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01213-15.

PMID- 22740671
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Marine Bacterium Marinilabilia salmonicolor JCM 21150T.
PG  - 3746
AB  - We report the 4.98-Mb genome sequence of Marinilabilia salmonicolor JCM 21150(T), which was
      isolated from marine mud in the year 1961. The draft genome of strain
      Marinilabilia salmonicolor JCM 21150(T) contains 4,982,627 bp with a G+C content
      of 41.92% and 4,227 protein coding genes, 52 tRNAs, and 3 rRNAs.
AU  - Kumar S
AU  - Subramanian S
AU  - Raghava GP
AU  - Pinnaka AK
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3746.

PMID- 22628512
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Nitroaromatic Compound-Degrading Bacterium Burkholderia sp. Strain SJ98.
PG  - 3286
AB  - We report the 7.85-Mb genome sequence of Burkholderia sp. strain SJ98, isolated from
      agricultural fields of Assam, India. The draft genome of this strain will be
      helpful in studying the genetic pathways involved in the degradation of aromatic
      compounds.
AU  - Kumar S
AU  - Vikram S
AU  - Raghava GP
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3286.

PMID- 22740661
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Halotolerant Bacterium Imtechella halotolerans K1T.
PG  - 3731
AB  - We report the 3.087-Mb genome sequence of Imtechella halotolerans K1(T), isolated from an
      estuarine water sample collected from Kochi, Kerala, India. Strain K1 was
      recently reported as a novel genus of the family Flavobacteriaceae.
AU  - Kumar S
AU  - Vikram S
AU  - Subramanian S
AU  - Raghava GP
AU  - Pinnaka AK
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3731.

PMID- 23950132
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Winogradskyella psychrotolerans RS-3T, Isolated from the Marine Transect of Kongsfjorden, Ny-Alesund, Svalbard, Arctic Ocean.
PG  - e00630-13
AB  - The 4.3-Mb genome of Winogradskyella psychrotolerans strain RS-3(T), isolated from a sediment
      sample of a marine transect of Kongsfjorden, Ny-Alesund, Svalbard, Arctic Ocean, is reported.
AU  - Kumar-Pinnaka PA
AU  - Ara S
AU  - Singh A
AU  - Shivaji S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00630-13.

PMID- 23950134
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Leifsonia rubra Strain CMS 76RT, Isolated from a Cyanobacterial Mat Sample from a Pond in Wright Valley, McMurdo, Antarctica.
PG  - e00633-13
AB  - The 2.7-Mb draft genome sequence of Leifsonia rubra strain CMS 76R(T), isolated from a
      cyanobacterial mat sample from a pond in Wright Valley, McMurdo, Antarctica, is reported.
AU  - Kumar-Pinnaka PA
AU  - Singh A
AU  - Ara S
AU  - Begum Z
AU  - Reddy GS
AU  - Shivaji S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00633-13.

PMID- 29496824
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Plant Growth-Promoting and Drought-Tolerant Bacillus altitudinis FD48, Isolated from Rice Phylloplane.
PG  - e00019-18
AB  - The genome sequence of a temperature-tolerant strain, Bacillus altitudinis FD48,  is described
      here. The reads were assembled into contigs with a total size of 3.7
      Mb. The genome information will aid in understanding its role in alleviating
      stress in crop plants as a potential bioinoculant for agricultural applications.
AU  - Kumaravel S
AU  - Thankappan S
AU  - Raghupathi S
AU  - Uthandi S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00019-18.

PMID- 26586870
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Facultative Methylotrophs, Gemmobacter sp. Strain LW1 and Mesorhizobium sp. Strain 1M-11, Isolated from Movile Cave, Romania.
PG  - e01266-15
AB  - Facultative methylotrophs belonging to the genera Gemmobacter and Mesorhizobium were isolated
      from microbial mat and cave water samples obtained from the Movile
      Cave ecosystem. Both bacteria can utilize methylated amines as their sole carbon
      and nitrogen source. Here, we report the draft genome sequences of Gemmobacter
      sp. strain LW1 and Mesorhizobium sp. strain IM1.
AU  - Kumaresan D
AU  - Wischer D
AU  - Hillebrand-Voiculescu AM
AU  - Murrell JC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01266-15.

PMID- 26586884
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Potential Probiotic Lactobacillus sp. HFC8, Isolated  from Human Gut Using PacBio SMRT Sequencing.
PG  - e01337-15
AB  - We report a 3.07-Mb complete genome sequence of a lactic acid bacterium, Lactobacillus sp.
      HFC8. The gene-coding clusters are predicated for probiotic
      characteristics, like bacteriocin production, cell adhesion, bile salt
      hydrolysis, lactose metabolism, autoaggregation, and tolerance to oxidative
      stress.
AU  - Kumari M
AU  - Swarnkar MK
AU  - Kumar S
AU  - Singh AK
AU  - Gupta M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01337-15.

PMID- 26543124
VI  - 3
DP  - 2015
TI  - Genome Sequence of a Potential Probiotic Strain, Lactobacillus fermentum HFB3, Isolated from a Human Gut.
PG  - e01296-15
AB  - A draft genome sequence of 2.04 Mb is reported for Lactobacillus fermentum HFB3,  which is a
      lactic acid bacterium with probiotic properties. The gene-coding
      clusters also predicted the presence of genes responsible for probiotic
      characteristics.
AU  - Kumari M
AU  - Swarnkar MK
AU  - Kumar S
AU  - Singh AK
AU  - Gupta M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01296-15.

PMID- 29519829
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Marinomonas fungiae Strain AN44(T) (JCM 18476(T)), Isolated from the Coral Fungia echinata from the Andaman Sea.
PG  - e00112-18
AB  - Marinomonas fungiae strain AN44(T) was isolated from mucus of the coral Fungia echinata
      Optimum growth occurs at 3 to 5% NaCl. The draft genome is 4.2 Mb, with
      3,776 protein-coding genes. It harbors genes for the degradation of aromatic
      compounds, such as quinate, ferulate, p-coumarate, protocatechuate, and
      p-hydroxyphenylacetate.
AU  - Kumari P
AU  - Badhai J
AU  - Das SK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00112-18.

PMID- 29903823
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Fish Pathogen Aeromonas bestiarum GA97-22.
PG  - e00524-18
AB  - Aeromonas bestiarum is a Gram-negative mesophilic motile bacterium causing acute  hemorrhagic
      septicemia or chronic skin ulcers in fish. Here, we report the draft
      genome sequence of A. bestiarum strain GA97-22, which was isolated from rainbow
      trout in 1997. This genome sequence will improve our understanding of the complex
      taxonomy of motile aeromonads.
AU  - Kumru S
AU  - Tekedar HC
AU  - Griffin MJ
AU  - Waldbieser GC
AU  - Liles MR
AU  - Sonstegard T
AU  - Schroeder SG
AU  - Lawrence ML
AU  - Karsi A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00524-18.

PMID- 27231366
VI  - 4
DP  - 2016
TI  - Genome Sequence of the Fish Pathogen Flavobacterium columnare Genomovar II Strain 94-081.
PG  - e00430-16
AB  - Flavobacterium columnare causes columnaris disease in fresh and brackish water worldwide. F.
      columnare strain 94-081 was isolated from a diseased channel
      catfish in 1994; its genome sequence is the first completed genomovar II
      sequence.
AU  - Kumru S
AU  - Tekedar HC
AU  - Waldbieser GC
AU  - Karsi A
AU  - Lawrence ML
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00430-16.

PMID- 26966205
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Commercial Textile Dye-Decolorizing and -Degrading Bacillus subtilis Strain C3 Isolated in India.
PG  - e00104-16
AB  - Bacillus subtilis C3, a commercial textile dye-decolorizing and -degrading bacterium, was
      isolated from the common effluent treatment plant (CEPT) of the
      Jetpur textile dyeing and printing industrial sector situated in the district of
      Rajkot, Gujarat, India. Here, we present the annotated 4.18-Mb draft genome
      sequence of B. subtilis C3, providing information about the metabolic pathways
      involved in decolorization and degradation of several commercial textile azo
      dyes. Thus, we confirm B. subtilis C3 as a potential candidate for bioremediation
      of textile effluents.
AU  - Kunadia K
AU  - Nathani NM
AU  - Kothari V
AU  - Kotadia RJ
AU  - Kothari CR
AU  - Joshi A
AU  - Rank JK
AU  - Faldu PR
AU  - Shekar MC
AU  - Viroja MJ
AU  - Patel PA
AU  - Jadeja D
AU  - Reddy B
AU  - Pal SR
AU  - Koringa PG
AU  - Joshi CG
AU  - Kothari RK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00104-16.

PMID- 
VI  - 
DP  - 2005
TI  - Identification and characterization of IPOD, a novel interaction partner of the DNA methyltransferase Dnmt2 from Drosophila melanogaster.
PG  - 1-142
AB  - 
AU  - Kunert N
PT  - Journal Article
TA  - Ph.D. Thesis, Germany
JT  - Ph.D. Thesis, Germany
SO  - Ph.D. Thesis, Germany 2005 : 1-142.

PMID- 159959
VI  - 132
DP  - 1979
TI  - A third restriction endonuclease from Xanthomonas malvacearum.
PG  - 133-139
AB  - An additional sequence-specific endonuclease, XmaIII, has been partially
      purified from Xanthomonas malvacearum.  XmaIII recognizes ten cleavage sites in
      adenovirus 2 DNA, two sites in bacteriophage lambda and no site in either
      simian virus 40 DNA or PhiX174 DNA.  It recognizes the sequence 5' C-^G-G-C-C-G
      3' 3' G-C-C-G-G^-C 5' and cleaves at the sites indicated by the arrows.  No
      other endonuclease with this particular nucleotide sequence specificity has
      been reported.
AU  - Kunkel LM
AU  - Silberklang M
AU  - McCarthy BJ
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1979 132: 133-139.

PMID- 22207742
VI  - 194
DP  - 2012
TI  - Complete Sequences of Plasmids from the Hemolytic-Uremic Syndrome-Associated Escherichia coli Strain HUSEC41.
PG  - 532-533
AB  - The complete and annotated sequences of four plasmids from a historical enteroaggregative
      Shiga toxin-producing Escherichia coli (HUSEC) serotype
      O104:H4 strain, HUSEC41/01-09591, isolated in 2001 in Germany are
      reported.
AU  - Kunne C
AU  - Billion A
AU  - Mshana SE
AU  - Schmiedel J
AU  - Domann E
AU  - Hossain H
AU  - Hain T
AU  - Imirzalioglu C
AU  - Chakraborty T
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 532-533.

PMID- 9384377
VI  - 390
DP  - 1997
TI  - The complete genome sequence of the Gram-positive bacterium Bacillus subtilis.
PG  - 249-256
AB  - Bacillus subtilis is the best-characterized member of the Gram-positive bacteria.  Its genome
      of 4,214,810 base pairs comprises 4,100 protein-coding genes.  Of these protein-coding genes,
      53% are represented once, while a quarter of the genome corresponds to several gene families
      that have been greatly expanded by gene duplication, the largest family containing 77 putative
      ATP-binding transport proeins.  In addition, a large proportion of the genetic capacity is
      devoted to the utilization of a variety of carbon sources, including many plant-derived
      molecules.  The identification of five signal peptidase genes, as well as several genes for
      components of the secretion apparatus, is important given the capacity of Bacillus strains to
      secrete large amounts of industrially important enzymes.  Many of the genes are involved in
      the synthesis of secondary metabolites, including antibiotics, that are more typically
      associated with Streptomyces species.  The genome contains at least ten prophages or remnants
      of prophages, indicating that bacteriophage infection has played an important evolutionary
      role in horizontal gene transfer, in particular in the propagation of bacterial pathogenesis.
AU  - Kunst F et al
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1997 390: 249-256.

PMID- 28408682
VI  - 5
DP  - 2017
TI  - Draft Whole-Genome Sequence of 'Candidatus Liberibacter asiaticus' Strain TX2351  Isolated from Asian Citrus Psyllids in Texas, USA.
PG  - e00170-17
AB  - We report here the draft genome sequence of 'Candidatus Liberibacter asiaticus' strain
      TX2351, collected from Asian citrus psyllids in south Texas, USA. The
      TX2351 genome has a size of 1,252,043 bp, a G+C content of 36.5%, 1,184 predicted
      open reading frames, and 52 RNA genes.
AU  - Kunta M
AU  - Zheng Z
AU  - Wu F
AU  - da Graca JV
AU  - Park JW
AU  - Deng X
AU  - Chen J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00170-17.

PMID- 9628367
VI  - 379
DP  - 1998
TI  - Mutual activation of two restriction endonucleases: interaction of EcoPI and EcoP15.
PG  - 617-620
AB  - Type III restriction endonucleases recognize nonsymmetric nucleotide sequences.  A necessary
      condition for DNA cleavage is the presence of two unmethylated recognition sites which are
      inversely ('head-to-head') oriented in the DNA double strand.  A DNA substrate possessing
      one EcoP1 and one EcoP15 site in the head-to-head configuration could not be cleaved by the
      individual enzymes, however, it was specifically digested in the simultaneous presence of both
      enzymes.  In agreement with the tracking-collision model for the DNA interaction of type III
      enzymes cleavage could be abolished by Lac repressor bound between the two sites.  We conclude
      that two different type III enzymes can functionally cooperate in the cleavage of DNA.
AU  - Kunz A
AU  - Mackeldanz P
AU  - Mucke M
AU  - Meisel A
AU  - Reuter M
AU  - Schroeder C
AU  - Kruger DH
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1998 379: 617-620.

PMID- 9628354
VI  - 379
DP  - 1998
TI  - An experimental selection system to identify bacterial cells exhibiting a new DNA host specificity.
PG  - 563-566
AB  - Restriction-modification enzymes interact with DNA sequences in a highly specific manner.
      Mutations within the DNA binding region of the enzymes could be expected to produce enzyme
      variants with changed DNA sequence specificities.  We developed an efficient in vivo selection
      system that enabled us to detect one cell coding for a restriction-modification system with a
      new DNA sequence specificity in a background of more than 10^6 cells with the original DNA
      sequence specificity.
AU  - Kunz A
AU  - Meisel A
AU  - Mackeldanz P
AU  - Reuter M
AU  - Kruger DH
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1998 379: 563-566.

PMID- 28798170
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequence of the Soil Bacterium Micrococcus sp. KBS0714.<jour_book>Genome Announc.
PG  - e00697-17
AB  - We present here a draft genome assembly of Micrococcus sp. KBS0714, which was isolated from
      agricultural soil. The genome provides insight into the strategies
      that Micrococcus spp. use to contend with environmental stressors such as
      desiccation and starvation in environmental and host-associated ecosystems.
AU  - Kuo V
AU  - Shoemaker WR
AU  - Muscarella ME
AU  - Lennon JT
PT  - Journal Article
TA  - 
JT  - 
SO  -  2017 5: e00697-17.

PMID- 2981177
VI  - 179
DP  - 1985
TI  - Inhibition of the activity of restriction endonucleases by spermidine and spermine.
PG  - 17-20
AB  - Physiological concentrations (0.5-2.0 mM) of spermidine and spermine were
      observed to inhibit the digestion in vitro of plasmid pJDB 207 by the
      restriction endonucleases BamHI (EC 3.1.23.6), EcoRI (EC3.2.23.13), HindIII
      (EC3.1.23.20), HpaI (EC3.1.23.23) and PstI (EC3.1.23.31).  The polyamines
      protected all the tested restriction sequences of DNA, since the activity of
      all endonucleases used was strongly inhibited.  These results show the need for
      caution when using polyamines as experimental tools for recombinant DNA
      chemistry.
AU  - Kuosmanen M
AU  - Poso H
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1985 179: 17-20.

PMID- 10415100
VI  - 272
DP  - 1999
TI  - Oligonucleotide stimulators allow complete cleavage of agarose-embedded DNA by particular type II restriction endonucleases.
PG  - 275-277
AB  - In previous work we and others discovered several restriction endonucleases requiring the
      simultaneous interaction with two copies of their respective recognition sequence for enzyme
      activity.  EcoRII was the first restriction enzyme for which this special property has been
      described, and the mechanism underlying the cooperative interaction with two sites in the
      substrate DNA was studied in more detail.  Complete cleavage of a resistant DNA site (present
      alone or at a great distance to a second site in a DNA molecule) can be achieved by providing
      the required second copy of the recognition site on short synthetic oligonucleotide duplexes.
      This principle has been verified for at least 12 restriction endonucleases so far (e.g.,
      EcoRII, HpaII, NaeI, NarI, SfiI, and others).  In addition, the practical importance of
      restriction enzyme stimulation by specific oligo duplexes for the reliable detection of
      prokaryotic Dcm methylation by comparative DNA digestion with EcoRII/BstNI and of eukaryotic
      CpG methylation with HpaII/MspI has been demonstrated.  Now we wanted to verify that the
      technique of oligo duplex-based stimulation of those restriction endonucleases is also
      applicable for digesting DNA being embedded in agarose as necessary for the handling of larger
      genomic DNA.
AU  - Kupper D
AU  - Moncke-Buchner E
AU  - Reuter M
AU  - Kruger DH
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 1999 272: 275-277.

PMID- 7607534
VI  - 157
DP  - 1995
TI  - Overproduction of His-tagged EcoRII restriction endonuclease and terminally deleted mutant proteins.
PG  - 97-98
AB  - EcoRII was the first restriction endonuclease (ENase) reported requiring the cooperative
      interaction with at least two DNA sites for activity.  Using two different expression systems
      the enzyme could be purified and its special substrate requirements were further analyzed.  At
      the present state of knowledge we suggest a model of simultaneous binding of two DNA sites to
      one dimeric enzyme molecule.
AU  - Kupper D
AU  - Reuter M
AU  - Kruger DH
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 97-98.

PMID- 7756833
VI  - 6
DP  - 1995
TI  - Hyperexpressed EcoRII renatured from inclusion bodies and native enzyme both exhibit essential cooperativity with two DNA sites.
PG  - 1-9
AB  - EcoRII was the first restriction endonuclease (ENase) reported needing the cooperative
      interaction with at least two DNA sites for activity. We constructed an EcoRII-overproducing
      strain of Escherichia coli by placing the coding sequence under control of the T7 gene 10
      regulatory elements. The yield of EcoRII expression could be increased to about 10% of total
      soluble cellular protein. Inclusion bodies are formed that mainly consist of insoluble EcoRII
      molecules. After solubilization by 6M guanidine hydrochloride refolding of the enzyme was
      achieved by dilution into appropriate buffer. The endonuclease was purified to homogeneity
      from both the soluble protein fraction and the protein renatured from inclusion bodies. Their
      identity was proven by circular dichroism and analysis of enzyme activity with respect to the
      special substrate requirements of EcoRII. It is shown that EcoRII cleavage of
      oligodeoxyribonucleotide duplexes (oligo duplexes) with only one recognition site follows a
      sigmoidal concentration dependence, i.e., they cannot be cleaved below a distinct low DNA
      concentration where simultaneous interaction with two substrate molecules is no longer
      possible. We demonstrate that the restriction of oligo duplexes containing two recognition
      sites does not show this concentration dependence, confirming an intramolecular site
      cooperativity.
AU  - Kupper D
AU  - Reuter M
AU  - Mackeldanz P
AU  - Meisel A
AU  - Alves J
AU  - Schroeder C
AU  - Kruger DH
PT  - Journal Article
TA  - Protein Expr. Purif.
JT  - Protein Expr. Purif.
SO  - Protein Expr. Purif. 1995 6: 1-9.

PMID- 9383549
VI  - 23
DP  - 1997
TI  - Reliable detection of DNA CpG methylation profiles by the isoschizomers MspI/HpaII using oligonucleotide stimulators.
PG  - 843-846
AB  - The increasing interest in methylation patterns of mammalian DNA demands a simple and reliable
      method to clearly differentiate between cytosine and 5-methylcytosine within a specific DNA
      region.  The simplest and most commonly used approach is the analysis with restriction
      endonucleases exhibiting different methylation sensitivities, like the MspI/HpaII pair of
      isoschizomeric enzymes.  Whereas MspI cleaves the recognition sequence 5'-CCGG independently
      of the methylation state of the internal C, cleavage by HpaII is blocked by the presence of
      5-MeC at this site.  The method is compromised by the fact that methylation can be detected
      only in those CpGs that are located within the tetranucleotide recognition sequence.
AU  - Kupper D
AU  - Reuter M
AU  - Meisel A
AU  - Kruger DH
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 1997 23: 843-846.

PMID- 3248715
VI  - 74
DP  - 1988
TI  - Cloning and structure of the M.BepI modification methyltransferase.
PG  - 33
AB  - Meeting abstract
AU  - Kupper D
AU  - Zhou J-G
AU  - Kiss A
AU  - Venetianer P
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 33.

PMID- 2784204
VI  - 17
DP  - 1989
TI  - Cloning and structure of the BepI modification methylase.
PG  - 1077-1088
AB  - The gene coding for a CGCG specific DNA methylase has been cloned in E. coli from
      Brevibacterium epidermidis.  The enzyme, named BepI methylase, is probably the cognate
      methylase of the FnuDII isoschizomer BepI endonuclease isolated from this strain.  The
      expression of BepI methylase in E. coli is dependent on the orientation of the cloned fragment
      suggesting that the gene is transcribed from a promoter on the plasmid vector.  No BepI
      endonuclease could be detected in the clones producing BepI methylase.  The nucleotide
      sequence of the BepI methylase gene has been determined, it predicts a protein of 403 amino
      acids (M:45,447).  Analysis of the amino acid sequence deduced from the nucleotide sequence
      revealed similarities between the BepI methylase and other cytosine methylases.  M.BepI
      methylates the external cytosine in its recognition sequence.
AU  - Kupper D
AU  - Zhou J-G
AU  - Venetianer P
AU  - Kiss A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 1077-1088.

PMID- 10903888
VI  - 274
DP  - 2000
TI  - Preferential cleavage sites for Sau3A restriction endonuclease in human ribosomal DNA.
PG  - 11-15
AB  - Previous studies of cloned ribosomal DNA (rDNA) variants isolated from the cosmid library of
      human chromosome 13 have revealed some disproportion in representativity of different rDNA
      regions (N. S. Kupriyanova, K. K. Netchvolodov, P. M. Kirilenko, B. I. Kapanadze, N. K.
      Yankovsky, and A. P. Ryskov, Mol. Biol. 30, 51-60, 1996). Here we show nonrandom cleavage of
      human rDNA with Sau3A or its isoschizomer MboI under mild hydrolysis conditions. The
      hypersensitive cleavage sites were found to be located in the ribosomal intergenic spacer
      (rIGS), especially in the regions of about 5-5.5 and 11 kb upstream of the rRNA transcription
      start point. This finding is based on sequence mapping of the rDNA insert ends in randomly
      selected cosmid clones of human chromosome 13 and on the data of digestion kinetics of cloned
      and noncloned human genomic rDNA with Sau3A and MboI. The results show that the methylation
      status and superhelicity state of the rIGS have no effect on cleavage site sensitivity. It is
      interesting that all primary cleavage sites are adjacent to or entering into Alu or Psi cdc 27
      retroposons of the rIGS suggesting a possible role of neighboring sequences in nuclease
      accessibility. The results explain nonequal representation of rDNA sequences in the human
      genomic DNA library used for this study.
AU  - Kupriyanova NS
AU  - Kirilenko PM
AU  - Netchvolodov KK
AU  - Ryskov AP
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 2000 274: 11-15.

PMID- 7509559
VI  - 42
DP  - 1993
TI  - Integration host factor (IHF) applied for partial digestion by restriction endonucleases in large DNA molecules (IARC procedure).
PG  - 145-150
AB  - The IHF protein of Escherichia coli was successfully used in IHF-mediated Achilles' Heel
      Cleavage (IHF-AC) technique and leads to the generation of very rare restriction sites in
      large DNA molecules. The first step of this procedure is methylation of DNA in the presence of
      IHF, when the overlapping ihf/restriction sites are protected from methylation, and in the
      second step the DNA is cut by the cognate restriction enzyme. The aim of the present study is
      to develop a very exact and reproducible procedure to obtain only a few well-defined cuts with
      the IHF-pre-treated DNA, depending on the variety of all parameters. This technique (IARC,
      i.e., IHF-assisted rare cutters) employs the restriction enzyme and only one auxiliary protein
      (IHF). The advantage of the IARC procedure is that no methylation is required (as opposed to
      the IHF-AC method). Using the IARC approach, the effects of various IHF concentrations were
      evaluated on the cleavage activity of the DraI, PacI, PmeI, and SwaI enzymes using DNA of
      phage lambda or the entire genomic 4.7-Mb DNA of E. coli. At low IHF concentrations only a few
      cut sites were eliminated by IHF binding, but a high IHF concentration, enzymes were able to
      cut in only one or several specific sites.
AU  - Kur J
PT  - Journal Article
TA  - Acta Microbiol. Pol.
JT  - Acta Microbiol. Pol.
SO  - Acta Microbiol. Pol. 1993 42: 145-150.

PMID- 7509558
VI  - 42
DP  - 1993
TI  - Use of IHF mediated achilles' heel cleavage (IHF-AC) method for mapping ihf sites.
PG  - 137-144
AB  - We have shown that Integration Host Factor of E. coli can successfully be used in the
      IHF-mediated Achilles' Heel Cleavage (IHF-AC), for generating rare natural cleavage sites.
      The first step of this procedure is methylation of DNA in the presence of IHF, when the
      overlapping ihf/restriction sites are protected from methylation, and in the second step the
      DNA is cut by the cognate restriction enzyme. The extent of cleavage could be controlled by
      varying the IHF:DNA ratio and temperature. The aim of the present study is to demonstrate that
      IHF-AC procedure might serve as a useful tool for finding new protein-binding sites which
      overlap known restriction sites. I have used this approach in conjunction with several MTases
      to find several other unknown IHF-binding sites.
AU  - Kur J
PT  - Journal Article
TA  - Acta Microbiol. Pol.
JT  - Acta Microbiol. Pol.
SO  - Acta Microbiol. Pol. 1993 42: 137-144.

PMID- 1531969
VI  - 110
DP  - 1992
TI  - A novel method for converting common restriction enzymes into rare cutters:  integration host factor-mediated Achilles' cleavage (IHF-AC).
PG  - 1-7
AB  - Integration host factor (IHF)-mediated protection against enzymatic methylation at
      ihf-overlapping sites provides the basis for this novel application of the Achilles' cleavage
      (AC) technique [Koob et al., Science 241 (1988) 1084-1086] for generating rare natural
      cleavage sites. When applying IHF-AC to plasmid, phage lambda, Escherichia coli and yeast
      genomes, only a few of the EcoRI, HinfI, and MboI sites (which overlapped the ihf sites)
      remained cleavable after prior methylation with the cognate M.EcoRI, M.HinfI, or Dam
      methyltransferases in the presence of IHF. Thus, IHF-AC essentially converted these enzymes
      into very rare cutters. The extent of cleavage could be controlled by varying the IHF:DNA
      ratio and temperature. Moreover, the method permits the genomic location and strength of the
      ihf sites to be determined.
AU  - Kur J
AU  - Koob M
AU  - Burkiewicz A
AU  - Szybalski W
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1992 110: 1-7.

PMID- Not carried by PubMed...
VI  - 22
DP  - 1991
TI  - BspRI methyltransferase as a marker for electron microscopic physical mapping.
PG  - 213-221
AB  - An approach is described in this paper for direct physical mapping of DNA by
      electron microscopy.  It implies visualization of specific
      DNA-methyltransferase complexes followed by computer analysis of electron
      micrographs.  The BspRI methylase (recognition site GGCC) was used as a marker
      owing to the large difference (at least three orders of magnitude) between its
      specific and non-specific interaction with DNA, as revealed by the gel
      retardation technique.  For electron microscopic mapping the optimum conditions
      were established in order to produce the maps practically without non-specific
      noise.  The approach was tested with well-characterized plasmid DNAs-pA03,
      pUC19 and pBR322 carrying 4,11 and 22 GGCC sites respectively. The results were
      analyzed and the applications of the method are discussed.
AU  - Kurakin AV
AU  - Zaritskaya LS
AU  - Metliskaya AZ
AU  - Volodin AA
AU  - Cherny DI
PT  - Journal Article
TA  - Micron and Microscopica Acta
JT  - Micron and Microscopica Acta
SO  - Micron and Microscopica Acta 1991 22: 213-221.

PMID- 25323721
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Ionic Liquid-Tolerant Bacterium Bacillus amyloliquefaciens CMW1.
PG  - e01051-14
AB  - Here, we report the draft genome sequence of an ionic liquid-tolerant bacterium,  Bacillus
      amyloliquefaciens CMW1, which is newly isolated from a Japanese
      fermented soybean paste. The genome sequence will allow for a characterization of
      the molecular mechanism of its ionic liquid tolerance.
AU  - Kurata A
AU  - Hirose Y
AU  - Misawa N
AU  - Hurunaka K
AU  - Kishimoto N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01051-14.

PMID- 25278530
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of a Deep-Sea Bacterium, Bacillus niacini Strain JAM F8, Involved in the Degradation of Glycosaminoglycans.
PG  - e00983-14
AB  - Here, we report the draft genome sequence of Bacillus niacini JAM F8, which was newly isolated
      from deep-sea sediment at a depth of 2,759 m from the
      Izu-Ogasawara Trench. An array of genes related to degradation of
      glycosaminoglycans in this bacterium was identified by whole-genome analysis.
AU  - Kurata A
AU  - Nishimura M
AU  - Kishimoto N
AU  - Kobayashi T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00983-14.

PMID- 25540343
VI  - 2
DP  - 2014
TI  - Complete Genome Sequencing of Borrelia valaisiana and Borrelia afzelii Isolated from Ixodes persulcatus Ticks in Western Siberia.
PG  - e01315-14
AB  - Lyme disease, caused by bacteria of the Borrelia burgdorferi sensu lato complex,  is the most
      frequent tick-borne infection in Eurasia. Here, we report the
      complete genome sequence of the Borrelia valaisiana Tom 4006 and Borrelia afzelii
      Tom 3107 strains isolated from Ixodes persulcatus ticks in western Siberia.
AU  - Kurilshikov AM
AU  - Fomenko NV
AU  - Stronin OV
AU  - Tikunov AY
AU  - Kabilov MR
AU  - Tupikin AE
AU  - Tikunova NV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01315-14.

PMID- 29371342
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of a Leptospira interrogans Strain Isolated from the Urine  of an Asymptomatic Dog in Thailand.
PG  - e01140-17
AB  - In 2014, Leptospira interrogans strain CUDO8 was isolated from the urine of an asymptomatic
      dog in Thailand. Here we report the draft genome sequence of this
      pathogenic bacterium.
AU  - Kurilung A
AU  - Keeratipusana C
AU  - Suriyaphol P
AU  - Prapasarakul N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01140-17.

PMID- 11418146
VI  - 357
DP  - 2001
TI  - Whole genome sequencing of meticillin-resistant Staphylococcus aureus.
PG  - 1225-1240
AB  - Staphylococcus aureus is one of the major causes of community-acquired and hospital-acquired
      infections.  It produces numerous toxins including superantigens that cause unique disease
      entities such as toxic-shock syndrome and staphylococcal scarlet fever, and has acquired
      resistance to practically all antibiotics.  Whole genome analysis is a necessary step towards
      future development of countermeasures against this organism.
AU  - Kuroda M et al
PT  - Journal Article
TA  - Lancet
JT  - Lancet
SO  - Lancet 2001 357: 1225-1240.

PMID- 25614571
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Bacillus selenatarsenatis SF-1T, a Promising Agent for Bioremediation of Environments Contaminated with Selenium and Arsenic.
PG  - e01466-14
AB  - Bacillus selenatarsenatis sp. nov. strain SF-1(T) is a promising agent for bioremediation of
      environments contaminated with selenium and arsenic. Here, we
      report the draft genome sequence of this strain.
AU  - Kuroda M
AU  - Ayano H
AU  - Sei K
AU  - Yamashita M
AU  - Ike M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01466-14.

PMID- 29167253
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Sphingobium fuliginis OMI, a Bacterium That Degrades Alkylphenols and Bisphenols.
PG  - e01323-17
AB  - Sphingobium fuliginis OMI is a bacterium that can degrade a variety of recalcitrant
      alkylphenols and bisphenols. This study reports the draft genome
      sequence of S. fuliginis OMI.
AU  - Kuroda M
AU  - Ogata Y
AU  - Yahara T
AU  - Yokoyama T
AU  - Ishizawa H
AU  - Takada K
AU  - Inoue D
AU  - Sei K
AU  - Ike M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01323-17.

PMID- 16135568
VI  - 102
DP  - 2005
TI  - Whole genome sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection.
PG  - 13272-13277
AB  - Staphylococcus saprophyticus is a uropathogenic Staphylococcus frequently isolated from young
      female outpatients presenting with uncomplicated
      urinary tract infections. We sequenced the whole genome of S.
      saprophyticus type strain ATCC 15305, which harbors a circular chromosome
      of 2,516,575 bp with 2,446 ORFs and two plasmids. Comparative genomic
      analyses with the strains of two other species, Staphylococcus aureus and
      Staphylococcus epidermidis, as well as experimental data, revealed the
      following characteristics of the S. saprophyticus genome. S. saprophyticus
      does not possess any virulence factors found in S. aureus, such as
      coagulase, enterotoxins, exoenzymes, and extracellular matrix-binding
      proteins, although it does have a remarkable paralog expansion of
      transport systems related to highly variable ion contents in the urinary
      environment. A further unique feature is that only a single ORF is
      predictable as a cell wall-anchored protein, and it shows positive
      hemagglutination and adherence to human bladder cell associated with
      initial colonization in the urinary tract. It also shows significantly
      high urease activity in S. saprophyticus. The uropathogenicity of S.
      saprophyticus can be attributed to its genome that is needed for its
      survival in the human urinary tract by means of novel cell wall-anchored
      adhesin and redundant uro-adaptive transport systems, together with
      urease.
AU  - Kuroda M
AU  - Yamashita A
AU  - Hirakawa H
AU  - Kumano M
AU  - Morikawa K
AU  - Higashide M
AU  - Maruyama A
AU  - Inose Y
AU  - Matoba K
AU  - Toh H
AU  - Kuhara S
AU  - Hattori M
AU  - Ohta T
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2005 102: 13272-13277.

PMID- 15885098
VI  - 272
DP  - 2005
TI  - Adaptation of intronic homing endonuclease for successful horizontal transmission.
PG  - 2487-2496
AB  - Group I introns are thought to be self-propagating mobile elements, and are distributed over a
      wide range of organisms through horizontal
      transmission. Intron invasion is initiated through cleavage of a target
      DNA by a homing endonuclease encoded in an open reading frame (ORF)
      found within the intron. The intron is likely of no benefit to the host
      cell and is not maintained over time, leading to the accumulation of
      mutations after intron invasion. Therefore, regular invasional
      transmission of the intron to a new species at least once before its
      degeneration is likely essential for its evolutionary long-term
      existence. In many cases, the target is in a protein-coding region
      which is well conserved among organisms, but contains ambiguity at the
      third nucleotide position of the codon. Consequently, the homing
      endonuclease might be adapted to overcome sequence polymorphisms at the
      target site. To address whether codon degeneracy affects horizontal
      transmission, we investigated the recognition properties of a homing
      enzyme, I-CsmI, that is encoded in the intronic ORF of a group I intron
      located in the mitochondrial COB gene of the unicellular green alga
      Chlamydomonas smithii. We successfully expressed and purified three
      types of N-terminally truncated I-CsmI polypeptides, and assayed the
      efficiency of cleavage for 81 substrates containing single nucleotide
      substitutions. We found a slight but significant tendency that I-CsmI
      cleaves substrates containing a silent or tolerated amino acid change
      more efficiently than nonsilent or nontolerated ones. The published
      recognition properties of I-SpomI, I-ScaI, and I-SceII were
      reconsidered from this point of view, and we detected proficient
      adaptation of I-SpomI, I-ScaI, and I-SceII for target site sequence
      degeneracy. Based on the results described above, we propose that
      intronic homing enzymes are adapted to cleave sequences that might
      appear at the target region in various species, however, such
      adaptation becomes less prominent in proportion to the time elapsed
      after intron invasion into a new host.
AU  - Kurokawa S
AU  - Bessho Y
AU  - Higashijima K
AU  - Shirouzu M
AU  - Yokoyama S
AU  - Watanabe KI
AU  - Ohama T
PT  - Journal Article
TA  - FEBS J.
JT  - FEBS J.
SO  - FEBS J. 2005 272: 2487-2496.

PMID- 23929466
VI  - 1
DP  - 2013
TI  - Whole-Genome Sequence of Fish-Pathogenic Mycobacterium sp. Strain 012931, Isolated from Yellowtail (Seriola quinqueradiata).
PG  - e00534-13
AB  - The genus Mycobacterium comprises a large number of well-characterized species, several of
      which are human and animal pathogens. Here, we report the whole-genome
      sequence of Mycobacterium sp. strain 012931, a fish pathogen responsible for huge
      losses in aquaculture farms in Japan. The strain was isolated from a marine fish,
      yellowtail (Seriola quinqueradiata).
AU  - Kurokawa S
AU  - Kabayama J
AU  - Nho SW
AU  - Hwang SD
AU  - Hikima J
AU  - Jung TS
AU  - Kondo H
AU  - Hirono I
AU  - Takeyama H
AU  - Aoki T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00534-13.

PMID- 590744
VI  - 1
DP  - 1977
TI  - Distamycin A and its analogs as agents for blocking of endo R. EcoRI activity.
PG  - 389-395
AB  - Distamycin A (Dst) and its analogs protect the lambda phage DNA from cleavage
      with endoR. EcoRI and show selective affinity for different recognition sites
      of endoR. EcoRI on this DNA producing enlarged DNA fragments of various
      composition and length.  The affinity of the antibiotic for DNA is influenced
      by the number of pyrrol carboxamide units in Dst molecule and does not strongly
      depend on the substitution of the N-methyl group by the N-propyl one.  Since in
      the complex with DNA the antibiotics of the Dst type are localized in its minor
      groove a conclusion can be made that the minor groove of DNA is needed for the
      interaction of the restriction endonuclease with DNA.
AU  - Kuroyedov AA
AU  - Grokhovsky SL
AU  - Zhuze AL
AU  - Nosikov VV
AU  - Polyanovsky OL
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1977 1: 389-395.

PMID- 15458627
VI  - 12
DP  - 2004
TI  - Mechanisms of Coupling between DNA Recognition Specificity and Catalysis in EcoRI Endonuclease.
PG  - 1775-1788
AB  - Proteins that bind to specific sites on DNA often do so in order to carry out catalysis or
      specific protein-protein interaction while bound to the
      recognition site. Functional specificity is enhanced if this second
      function is coupled to correct DNA site recognition. To analyze the
      structural and energetic basis of coupling between recognition and
      catalysis in EcoRI endonuclease, we have studied stereospecific
      phosphorothioate (P(S)) or methylphosphonate (P(Me)) substitutions at the
      scissile phosphate GpAATTC or at the adjacent phosphate GApATTC in
      combination with molecular-dynamics simulations of the catalytic center
      with bound Mg(2+). The results show the roles in catalysis of individual
      phosphoryl oxygens and of DNA distortion and suggest that a "crosstalk
      ring" in the complex couples recognition to catalysis and couples the two
      catalytic sites to each other.
AU  - Kurpiewski MR
AU  - Engler LE
AU  - Wozniak LA
AU  - Kobylanska A
AU  - Koziolkiewicz M
AU  - Stec WJ
AU  - Jen-Jacobson L
PT  - Journal Article
TA  - Structure
JT  - Structure
SO  - Structure 2004 12: 1775-1788.

PMID- 8688420
VI  - 35
DP  - 1996
TI  - Chiral phosphorothioates as probes of protein interactions with individual DNA phosphoryl oxygens:  Essential interactions of EcoRI endonuclease with the phosphate at pGAATTC.
PG  - 8846-8854
AB  - The contact between EcoRI endonuclease and the "primary clamp" phosphate of its recognition
      site pGAATTC is absolutely required for recognition of the canonical and all variant DNA
      sites.  We have probed this contact using oligonucleotides containing the single
      stereospecific (Rp)- or (Sp)- phosphorothioates.  At the GAApTTC position, where the
      endonuclease interacts with only one phosphoryl oxygen at the central DNA kink, Rp-Ps inhibits
      and Sp-Ps stimulates binding and cleavage; in contrast, at the pGAATTC position both
      diastereomers inhibit binding.  For single-strand substitution, the penalty in binding free
      energy (delta delta Go bind) is slightly greater for Sp-Ps (+0.9 kcal/mol) than for Rp-Ps
      (+0.7 kcal/mol).  Binding penalties are approximately additive for double-strand substitution
      (Rp,Rp-Ps or Sp,Sp-Ps).  Neither Ps diastereomer in one DNA strand affects the first-order
      rate constants for cleavage in the unmodified DNA strand, and only Sp-Ps inhibits the cleavage
      rate constant (3-fold) in the modified DNA strand.  Thus, the second-order cleavage rate
      (including binding and catalysis) is inhibited 14-fold by Sp-Ps and 45-fold by Sp,Sp-Ps.  In
      the canonical complex, the phosphate at pGAATTC is completely surrounded by protein and each
      nonbridging phosphoryl oxygen receives two hydrogen bonds from the endonuclease, such that in
      either orientation the increased bond length of P-S- inhibits binding.  However, the pro-Sp
      oxygen interacts with residues that are connected (by proximity or inter-side-chain hydrogen
      bonding) to side chains with essential roles in catalysis, so cleavage is preferentially
      inhibited when these side chains are slightly displaced by the Sp-Ps diastereomer.
AU  - Kurpiewski MR
AU  - Koziolkiewicz M
AU  - Wilk A
AU  - Stec WJ
AU  - Jen-Jacobson L
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1996 35: 8846-8854.

PMID- 27340069
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Achromobacter sp. Strain AR476-2, Isolated from a Cellulolytic Consortium.
PG  - e00587-16
AB  - Achromobacter sp. AR476-2 is a noncellulolytic strain previously isolated from a  cellulolytic
      consortium selected from samples of insect gut. Its genome sequence
      could contribute to the unraveling of the complex interaction of microorganisms
      and enzymes involved in the biodegradation of lignocellulosic biomass in nature.
AU  - Kurth D
AU  - Romero CM
AU  - Fernandez PM
AU  - Ferrero MA
AU  - Martinez MA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00587-16.

PMID- 26802429
VI  - 8
DP  - 2016
TI  - Genome sequence and analysis of Escherichia coli MRE600, a colicinogenic, nonmotile strain that lacks RNase I and the type I methyltransferase, EcoKI.
PG  - 742-752
AB  - Escherichia coli strain MRE600 was originally identified for its low RNase I
      activity and has therefore been widely adopted by the biomedical research
      community as a preferred source for the expression and purification of transfer
      RNAs and ribosomes. Despite its widespread use, surprisingly little information
      about its genome or genetic content exists. Here, we present the first de novo
      assembly and description of the MRE600 genome and epigenome. To provide context
      to these studies of MRE600, we include comparative analyses with E. coli K-12
      MG1655 (K12). Pacific Biosciences Single Molecule, Real-Time (SMRT) sequence
      reads were assembled into one large chromosome (4.83 Mb) and three smaller
      plasmids (89.1 kb, 56.9 kb, and 7.1 kb). Interestingly, the 7.1 kb plasmid
      possesses genes encoding a colicin E1 protein and its associated immunity
      protein. The MRE600 genome has a G+C content of 50.8% and contains a total of
      5181 genes, including 4913 protein-encoding genes and 268 RNA genes. We
      identified 41,469 modified DNA bases (0.83% of total) and found that MRE600 lacks
      the gene for type I methyltransferase, EcoKI. Phylogenetic, taxonomic, and
      genetic analyses demonstrate that MRE600 is a divergent E. coli strain that
      shares features of the closely related genus, Shigella. Nevertheless, comparative
      analyses between MRE600 and E. coli K12 show that these two strains exhibit
      nearly identical ribosomal proteins, ribosomal RNAs, and highly homologous tRNA
      species. Substantiating prior suggestions that MRE600 lacks RNase I activity, the
      RNase I-encoding gene, rna, contains a single premature stop codon early in its
      open reading frame.
AU  - Kurylo CM
AU  - Alexander N
AU  - Dass RA
AU  - Parks MM
AU  - Altman RA
AU  - Vincent CT
AU  - Mason CE
AU  - Blanchard SC
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2016 8: 742-752.

PMID- 14597009
VI  - 50
DP  - 2003
TI  - Type I restriction enzyme with RecA protein promotes illegitimate recombination.
PG  - 202-212
AB  - Illegitimate (non-homologous) recombination requires little or no sequence homology between
      recombining DNAs and has been regarded as being a process
      distinct from homologous recombination, which requires a long stretch of
      homology between recombining DNAs. However, we have found a type of
      illegitimate recombination that requires an interaction between long
      homologous DNA sequences. It was detected when a plasmid that carried
      2-kb-long inverted repeats was subjected to type I (EcoKI) restriction in
      vivo within a special mutant strain of Escherichia coli. In the present
      work, we analyzed genetic requirements for this type of illegitimate
      recombination in well-defined genetic backgrounds. Our analysis
      demonstrated dependence on RecA function and on the presence of two EcoKI
      sites on the substrate DNA. These results are in harmony with a model in
      which EcoKI restriction enzyme attacks an intermediate of homologous
      recombination to divert it to illegitimate recombination.
AU  - Kusano K
AU  - Asami Y
AU  - Fujita A
AU  - Tanokura M
AU  - Kobayashi I
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 2003 50: 202-212.

PMID- 7479944
VI  - 92
DP  - 1995
TI  - Restriction-modification systems as genomic parasites in competition for specific sequences.
PG  - 11095-11099
AB  - Restriction-modification (RM) systems are believed to have evolved to protect cells from
      foreign DNA.  However, this hypothesis may not be sufficient to explain the diversity and
      specificity in sequence recognition, as well as other properties, of these systems.  We report
      that the EcoRI restriction endonuclease-modification methylase (rm) gene pair stabilizes
      plasmids that carry it and that this stabilization is blocked by an RM of the same sequence
      specificity (EcoRI or its isoschizomer, RsrI) but not by an RM of a different specificity
      (PaeR7I) on another plasmid.  The PaeR7I rm likewise stabilizes plasmids, unless an rm gene
      pair with identical sequence specificity is present.  Our analysis supports the following
      model for stabilization and incompatibility: the descendants of cells that have lost an rm
      gene pair expose the recognition sites in their chromosomes to lethal attack by any remaining
      restriction enzymes unless modification by another RM system of the same specificity protects
      these sites.  Competition for specific sequences among these selfish genes may have generated
      the great diversity and specificity in sequence recognition among RM systems.  Such altruistic
      suicide strategies, similar to those found in virus-infected cells, may have allowed selfish
      RM systems to spread by effectively competing with other selfish genes.
AU  - Kusano K
AU  - Naito T
AU  - Handa N
AU  - Kobayashi I
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1995 92: 11095-11099.

PMID- 9286991
VI  - 179
DP  - 1997
TI  - A new type of illegitimate recombination is dependent on restriction and homologous interaction.
PG  - 5380-5390
AB  - Illegitimate (nonhomologous) recombination requires little or no sequence homology between
      recombining DNAs and has been regarded as being a process distinct from homologous
      recombination, which requires a long stretch of homology between recombining DNAs.  Under
      special conditions in Escherichia coli, we have found a new type of illegitimate recombination
      that requires an interaction between homologous DNA sequences.  It was detected when a plasmid
      that carried 2-kb-long inverted repeats was subjected to type II restriction in vitro and type
      I (EcoKI) restriction in vivo within a delta-rac recBC recG ruvC strain.  Removal of one of
      the repeats or its replacement with heterologous DNA resulted in a reduction in the level of
      recombination.  The recombining sites themselves shared, at most a few base pairs of homology.
      Many of the recombination events joined a site in one of the repeats with a site in another
      repeat.  In two of the products, one of the recombining sites was at the end of one of the
      repeats.  Removal of one of the EcoKI sites resulted in decreased recombination.  We discuss
      the possibility that some structure made by homologous interaction between the long repeats is
      used by the EcoKI restriction enzyme to promote illegitimate recombination.  The possible
      roles and consequences of this type of homologous interaction are discussed.
AU  - Kusano K
AU  - Sakagami K
AU  - Yokochi T
AU  - Naito T
AU  - Tokinaga Y
AU  - Euda E
AU  - Kobayashi I
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1997 179: 5380-5390.

PMID- 1453962
VI  - 6
DP  - 1992
TI  - The HsdS polypeptide of the Type IC restriction enzyme EcoR124 is a sequence-specific DNA-binding protein.
PG  - 3251-3256
AB  - The HsdS and HsdM polypeptides of the type IC restriction enzyme EcoR124 have been purified
      independently and used in a set of gel retardation experiments to determine the minimum
      requirements for sequence-specific recognition of DNA by this enzyme. The HsdS polypeptide
      alone is able to bind to DNA in a sequence-specific manner. In addition, whilst the presence
      of the HsdM polypeptide gives rise to a stimulation of DNA binding by the HsdS subunit it is
      not clear whether, under the conditions of the experiments reported here, the HsdS subunit
      maintains the same interactions with the HsdM subunits observed in the absence of DNA.
AU  - Kusiak M
AU  - Price C
AU  - Rice D
AU  - Hornby DP
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1992 6: 3251-3256.

PMID- 1326764
VI  - 89
DP  - 1992
TI  - Tagging developmental genes in Dictyostelium by restriction enzyme-mediated integration of plasmid DNA.
PG  - 8803-8807
AB  - Introduction of restriction enzyme along with linearized plasmid results in integration of
      plasmid DNA at genomic restriction sites in a high proportion of the resulting transformants.
      We have found that electroporating BamHI or EcoRI together with pyr5-6 plasmids cut with the
      same enzyme stimulates the efficiency of transformation in Dictyostelium discoideum more than
      20-fold over the rate seen when plasmid DNA alone is introduced. Restriction enzyme-mediated
      integration generates insertions into genomic restriction sites in an apparently random
      manner, some of which cause mutations. About 1 in 400 of the Dictyostelium transformants
      displayed arrested or aberrant development. The integrated plasmid, along with flanking
      genomic DNA, was excised from some of these mutants, cloned in Escherichia coli, and used to
      transform other Dictyostelium cells. Homologous recombination within the flanking sequences
      resulted in the same phenotypes displayed by the original mutants, directly demonstrating that
      the affected genes were responsible for the specific morphological phenotypes. This method of
      insertional mutagenesis should be useful for tagging, and subsequent cloning, of many
      developmentally important genes that can be identified by their mutant phenotypes.
AU  - Kuspa A
AU  - Loomis WF
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1992 89: 8803-8807.

PMID- 24334665
VI  - 80
DP  - 2014
TI  - The lineage-specific distribution of IS-excision enhancer in enterotoxigenic Escherichia coli isolated from swine.
PG  - 1394-1402
AB  - Insertion sequences (ISs) are the simplest transposable elements and are widely distributed in
      bacteria; however, they also play important roles in genome evolution. We recently identified
      a protein called IS-excision enhancer (IEE) in enterohemorrhagic Escherichia coli (EHEC) O157.
      IEE promotes the excision of IS elements belonging to the IS3 family, such as IS629, as well
      as several other families. IEE-mediated IS excision
      generates various genomic deletions that lead to the diversification of the bacterial genome.
      IEE has been found in a broad range of bacterial species; however, among sequenced E. coli
      strains, IEE is primarily found in EHEC isolates. In this study, we investigated non-EHEC
      pathogenic E. coli strains isolated from domestic animals and found that IEE is distributed in
      specific lineages of enterotoxigenic E. coli (ETEC) strains of serotypes O139
      or O149 isolated from swine. The iee gene is located within integrative elements that are
      similar to SpLE1 of EHEC O157. All iee-positive ETEC lineages also contained multiple copies
      of IS629, a preferred substrate of IEE, and their genomic locations varied significantly
      between strains, as observed in O157. These data suggest that IEE may have been transferred
      among EHEC and ETEC in swine via SpLE1 or SpLE1-like integrative
      elements. In addition, IS629 is actively moving in the ETEC O139 and O149 genomes, and as in
      EHEC O157, is promoting the diversification of these genomes in combination with IEE.
AU  - Kusumoto M
AU  - Fukamizu D
AU  - Ogura Y
AU  - Yoshida E
AU  - Yamamoto F
AU  - Iwata T
AU  - Ooka T
AU  - Akiba M
AU  - Hayashi T
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2014 80: 1394-1402.

PMID- 8806566
VI  - 223
DP  - 1996
TI  - Analysis of 76 kb of the Chlorella virus PBCV-1 330-kb genome: Map positions 182 to 258.
PG  - 303-317
AB  - Analysis of 76 kb of newly sequencing DNA, located between map positions 182 and 258 kb in the
      330-kb chlorella virus PBCV-1 genome, revealed 175 open reading frames of 65 codons or longer.
      One hundred and five of these 175 ORFs were considered major ORFs.  Twenty-one of the 105
      major ORFs resembled proteins in databases including ribonucleotide reductase small subunit,
      RNase III, thioredoxin, glutaredoxin, protein disulfide isomerase, deoxynucleoside kinase,
      frog virus 3 ATPase, Acetobacter cellulose synthase, a bacteriophage encoded endonuclease, and
      two C-5 cytosine DNA methyltransferases.  One of the ORFs was the PBCV-1 major capsid protein.
      The 105 major ORFs were evenly distributed along the genome.  One set of ORFs was separated by
      543 nucleotides whereas 75 of the ORFs were separated by fewer than 100 nucleotides.  Nineteen
      of the 175 ORFs resembled other PBCV-1 ORFs, suggesting that they represent either gene
      duplications or gene families.
AU  - Kutish GF
AU  - Li Y
AU  - Lu Z
AU  - Furuta M
AU  - Rock DL
AU  - Van Etten JL
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1996 223: 303-317.

PMID- 
VI  - 0
DP  - 1983
TI  - Structure, organization, and manipulation of the genome.
PG  - 277-290
AB  - Recent analysis of T4 transcription patterns, gene sequences, origins of replication, and
      related data have taken advantage of the extensive restriction mapping of T4 and its
      correlation with the genetic map.  Here we summarize the current data, including the locations
      of those genes and specific transcripts that have now been mapped to within a few hundred base
      pairs.  This is a continuing project; therefore, any additional sequence data, clone analyses,
      and promoter mapping data will be greatly appreciated by the authors.  Sequence data should
      also be submitted to the T4 sequence bank being maintained by Larry Gold, University of
      Colorado, Boulder, Colo. 80309.
AU  - Kutter E
AU  - Rueger W
PT  - Journal Article
TA  - Bacteriophage T4
JT  - Bacteriophage T4
SO  - Bacteriophage T4 1983 0: 277-290.

PMID- 
VI  - 0
DP  - 1994
TI  - Genomic map of bacteriophage T4.
PG  - 491-519
AB  - The map presented here is based on the T4 DNA sequence, integrated with information from
      genetic analysis.  In general, the results agree well with those initially determined by
      restriction analysis and the genetic map of Wood and Revel.
AU  - Kutter E
AU  - Stidham T
AU  - Guttman B
AU  - Kutter E
AU  - Batts D
AU  - Peterson S
AU  - Javakhishvili TD
AU  - Arisaka F
AU  - Mesyanzhinov V
AU  - Rueger W
AU  - Mosig G
PT  - Journal Article
TA  - Molecular Biology of Bacteriophage T4
JT  - Molecular Biology of Bacteriophage T4
SO  - Molecular Biology of Bacteriophage T4 1994 0: 491-519.

PMID- 8896756
VI  - 40
DP  - 1996
TI  - The methylation pattern of a cytosine DNA-methyltransferase gene in Arabidopsis thaliana plants.
PG  - 347-353
AB  - Using a PCR-amplified 5'-end proximal 600-bp fragment and two cDNA clones of cytosine
      DNA-methyltransferase gene of Arabidopsis thaliana as specific probes in hybridization with
      plant DNA samples, hydrolyzed by methylation-sensitive restriction endonucleases HpaII and
      MspI, it has been established that CCGG sites located in the 5'-end proximal part of cytosine
      DNA-methyltransferase gene are highly methylated at internal C and less but detectably
      methylated at external C residues.  On the contrary, all CCGG sites in 3'-terminal half of
      the coding region were found to be unmethylated at both external and internal C residues.  No
      significant differences between methylation patterns of cytosine DNA-methyltransferase gene in
      various organs (leaf, stem, flower) of the Arabidopsis thaliana plant were detected.
AU  - Kutueva LI
AU  - Ashapkin VV
AU  - Vanyushin BF
PT  - Journal Article
TA  - Biochem. Mol. Biol. Int.
JT  - Biochem. Mol. Biol. Int.
SO  - Biochem. Mol. Biol. Int. 1996 40: 347-353.

PMID- 24874672
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of blaNDM-1-Positive Escherichia coli O25b-ST131 Clone Isolated from an Environmental Sample.
PG  - e00462-14
AB  - A multidrug-resistant NDM-1 carbapenamase-producing Escherichia coli sequence type 131 (ST131)
      organism was obtained from vacuum cleaner dust collected from
      the home of a case patient. Here, we report the assembly and annotation of its
      genome.
AU  - Kutumbaka KK
AU  - Han S
AU  - Mategko J
AU  - Nadala C
AU  - Buser GL
AU  - Cassidy MP
AU  - Beldavs ZG
AU  - Weissman SJ
AU  - Morey KE
AU  - Vega R
AU  - Samadpour M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00462-14.

PMID- 26358606
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Beer Spoilage Bacterium Megasphaera cerevisiae Strain PAT 1T.
PG  - e01045-15
AB  - The genus Megasphaera harbors important spoilage organisms that cause beer spoilage by
      producing off flavors, undesirable aroma, and turbidity. Megasphaera  cerevisiae is mainly
      found in nonpasteurized low-alcohol beer. In this study, we  report the draft genome of the
      type strain of the genus, M. cerevisiae strain PAT 1(T).
AU  - Kutumbaka KK
AU  - Pasmowitz J
AU  - Mategko J
AU  - Reyes D
AU  - Friedrich A
AU  - Han S
AU  - Martens-Habbena W
AU  - Neal-McKinney J
AU  - Janagama HK
AU  - Nadala C
AU  - Samadpour M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01045-15.

PMID- 27801909
VI  - 11
DP  - 2017
TI  - Genome of 'Ca. Desulfovibrio trichonymphae', an H2-oxidizing bacterium in a tripartite symbiotic system within a protist cell in the termite gut.
PG  - 766-776
AB  - The cellulolytic protist Trichonympha agilis in the termite gut permanently hosts
      two symbiotic bacteria, 'Candidatus Endomicrobium trichonymphae' and 'Candidatus
      Desulfovibrio trichonymphae'. The former is an intracellular symbiont, and the
      latter is almost intracellular but still connected to the outside via a small
      pore. The complete genome of 'Ca. Endomicrobium trichonymphae' has previously
      been reported, and we here present the complete genome of 'Ca. Desulfovibrio
      trichonymphae'. The genome is small (1 410 056 bp), has many pseudogenes, and
      retains biosynthetic pathways for various amino acids and cofactors, which are
      partially complementary to those of 'Ca. Endomicrobium trichonymphae'. An amino
      acid permease gene has apparently been transferred between the ancestors of these
      two symbionts; a lateral gene transfer has affected their metabolic capacity.
      Notably, 'Ca. Desulfovibrio trichonymphae' retains the complex system to oxidize
      hydrogen by sulfate and/or fumarate, while genes for utilizing other substrates
      common in desulfovibrios are pseudogenized or missing. Thus, 'Ca. Desulfovibrio
      trichonymphae' is specialized to consume hydrogen that may otherwise inhibit
      fermentation processes in both T. agilis and 'Ca. Endomicrobium trichonymphae'.
      The small pore may be necessary to take up sulfate. This study depicts a
      genome-based model of a multipartite symbiotic system within a cellulolytic
      protist cell in the termite gut.The ISME Journal advance online publication, 1
      November 2016; doi:10.1038/ismej.2016.143.
AU  - Kuwahara H
AU  - Yuki M
AU  - Izawa K
AU  - Ohkuma M
AU  - Hongoh Y
PT  - Journal Article
TA  - ISME J.
JT  - ISME J.
SO  - ISME J. 2017 11: 766-776.

PMID- 21791478
VI  - 18
DP  - 2011
TI  - The lifestyle of the segmented filamentous bacterium: a non-culturable gut-associated immunostimulating microbe inferred by whole-genome sequencing.
PG  - 291-303
AB  - Numerous microbes inhabit the mammalian intestinal track and strongly impact host
      physiology; however, our understanding of this ecosystem remains limited owing to
      the high complexity of the microbial community and the presence of numerous
      non-culturable microbes. Segmented filamentous bacteria (SFBs), which are
      clostridia-related Gram-positive bacteria, are among such non-culturable
      populations and are well known for their unique morphology and tight attachment
      to intestinal epithelial cells. Recent studies have revealed that SFBs play
      crucial roles in the post-natal maturation of gut immune function, especially the
      induction of Th17 lymphocytes. Here, we report the complete genome sequence of
      mouse SFBs. The genome, which comprises a single circular chromosome of 1 620 005
      bp, lacks genes for the biosynthesis of almost all amino acids,
      vitamins/cofactors and nucleotides, but contains a full set of genes for
      sporulation/germination and, unexpectedly, for chemotaxis/flagella-based
      motility. These findings suggest a triphasic lifestyle of the SFB, which
      comprises two types of vegetative (swimming and epicellular parasitic) phases and
      a dormant (spore) phase. Furthermore, SFBs encode four types of flagellin, three
      of which are recognized by Toll-like receptor 5 and could elicit the innate
      immune response. Our results reveal the non-culturability, lifestyle and
      immunostimulation mechanisms of SFBs and provide a genetic basis for the future
      development of the SFB cultivation and gene-manipulation techniques.
AU  - Kuwahara T
AU  - Ogura Y
AU  - Oshima K
AU  - Kurokawa K
AU  - Ooka T
AU  - Hirakawa H
AU  - Itoh T
AU  - Nakayama-Imaohji H
AU  - Ichimura M
AU  - Itoh K
AU  - Ishifune C
AU  - Maekawa Y
AU  - Yasutomo K
AU  - Hattori M
AU  - Hayashi T
PT  - Journal Article
TA  - DNA Res.
JT  - DNA Res.
SO  - DNA Res. 2011 18: 291-303.

PMID- 15466707
VI  - 101
DP  - 2004
TI  - Genomic analysis of Bacteroides fragilis reveals extensive DNA inversions regulating cell surface adaptation.
PG  - 14919-14924
AB  - Bacteroides are predominant human colonic commensals, but the principal pathogenic species,
      Bacteroides fragilis (BF), lives closely associated
      with the mucosal surface, whereas a second major species, Bacteroides
      thetaiotaomicron (BT), concentrates within the colon. We find
      corresponding differences in their genomes, based on determination of the
      genome sequence of BF and comparative analysis with BT. Both species have
      acquired two mechanisms that contribute to their dominance among the
      colonic microbiota: an exceptional capability to use a wide range of
      dietary polysaccharides by gene amplification and the capacity to create
      variable surface antigenicities by multiple DNA inversion systems.
      However, the gene amplification for polysaccharide assimilation is more
      developed in BT, in keeping with its internal localization. In contrast,
      external antigenic structures can be changed more systematically in BF.
      Thereby, at the mucosal surface, where microbes encounter continuous
      attack by host defenses, BF evasion of the immune system is favored, and
      its colonization and infectious potential are increased.
AU  - Kuwahara T
AU  - Yamashita A
AU  - Hirakawa H
AU  - Nakayama H
AU  - Toh H
AU  - Okada N
AU  - Kuhara S
AU  - Hattori M
AU  - Hayashi T
AU  - Ohnishi Y
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2004 101: 14919-14924.

PMID- 2787475
VI  - 0
DP  - 1989
TI  - Site specific restriction endonuclease BtcI from Bacillus thuringiensis var. canadensis.
PG  - 36-39
AB  - Efficiency of bacteriophage Tp4 plating on Bacillus thuringiensis var.
      canadensis H5 (Can) is decreased 10^7-fold as compared with the efficiency of
      plating on Bacillus thuringiensis var. galleriae H5 (Gal).  Bacteriophage Tp4
      having propagated for one cycle in Can cells can be further grown in this
      strain without restriction.  The site specific restriction endonuclease BtcI
      isolated from Bacillus thuringiensis var. canadensis recognises the same
      nucleotide sequence GATC in DNA as recognised by restriction endonuclease
      Sau3AI.
AU  - Kuzin AI
AU  - Bolesnin MI
AU  - Smolyaninov VV
AU  - Azizbekyan RR
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1989 0: 36-39.

PMID- 25908139
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Agrobacterium nepotum Strain 39/7T and Agrobacterium sp. Strain KFB 330.
PG  - e00331-15
AB  - Tumorigenic strains of Agrobacterium spp. are responsible for crown gall disease  of numerous
      plant species. We present here draft genome sequences of
      nonpathogenic Agrobacterium nepotum strain 39/7(T) (CFBP 7436(T), LMG 26435(T)),
      isolated from crown gall tumor on Prunus cerasifera, and tumorigenic
      Agrobacterium sp. strain KFB 330 (CFBP 8308, LMG 28674), isolated from galls on
      raspberry.
AU  - Kuzmanovic N
AU  - Pulawska J
AU  - Prokic A
AU  - Ivanovic M
AU  - Zlatkovic N
AU  - Gasic K
AU  - Obradovic A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00331-15.

PMID- 199404
VI  - 236
DP  - 1977
TI  - A specific endonuclease in Klebsiella pneumoniae OK8.
PG  - 477-480
AB  - None
AU  - Kuzmin NP
AU  - Fodor I
AU  - Baev AA
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1977 236: 477-480.

PMID- 6200765
VI  - 18
DP  - 1984
TI  - Physical and catalytic properties of homogeneous restriction endonuclease EcoRV.
PG  - 166-173
AB  - The characteristics of restriction endonuclease EcoRV, puried earlier to a homogeneous state
      from a superproductive strain constructed in vitro, were determined by gel filtration and
      electrophoresis in polyacrylamide gel under denaturing conditions.  The enzyme has a molecular
      weight of 25,000. Restriction endonuclease EcoRV differs immunologically from the enzymes
      EcoRI and EcoRII.  The catalytic properties of restriction endonuclease EcoRV were determined:
      the dependence of the enzymatic activity on the pH of the medium, the ionic strength of the
      solution, the temperature, and the presence of divalent metal cations (Mn2+, Mg2+, Co2+, Zn2+,
      Ni2+, Cd2+), and organic solvents (glycerol, dimethylsulfoxide, ethanol).  It was found that
      the specificity of EcoRV decreases when divalent magnesium ions are replaced by manganese or
      when organic solvents are added.  The enzyme is capable of digesting "protected" DNAs of
      T-even bacteriophages:  glycosylated and containing 5-hydroxmethylcytosine.  Methylated EcoRV
      DNA of bacteriophage lambda, grown on a strain of E. coli containing an EcoRV
      restriction-modification system, is cleaved by EcoRV on noncanonical cleavage sites under
      conditions of a decrease in the specificity of the enzyme.  The DNA fragments formed upon
      cleavage by EcoRV on noncanonical sites are inserted into canonical EcoRV site of cleavage of
      the vector plasmid pBR322 DNA molecule.
AU  - Kuzmin NP
AU  - Loseva SP
AU  - Belyaeva RK
AU  - Kravets AN
AU  - Solonin AS
AU  - Tanyashin VI
AU  - Baev AA
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1984 18: 166-173.

PMID- 21037015
VI  - 193
DP  - 2010
TI  - Draft genome sequence of the anoxygenic filamentous phototrophic bacterium Oscillochloris trichoides ssp. DG-6.
PG  - 321-322
AB  - Oscillillochloris trichoides is a mesophilic filamentous photoautotrophic non-sulfur
      diazotrophic bacterium which is capable for carbon dioxide fixation via the reductive pentose
      phosphate cycle and possesses no assimilative sulfate reduction. Here we present the draft
      genome sequence of Oscillillochloris trichoides ssp.DG6, the type strain of the specie, which
      has permitted the prediction of genes for carbon and nitrogen metabolism and light harvesting
      apparatus.
AU  - Kuznetsov BB
AU  - Ivanovsky RN
AU  - Keppen OI
AU  - Sukhacheva MV
AU  - Bumazhkin BK
AU  - Patutina EO
AU  - Beletsky AV
AU  - Mardanov AV
AU  - Baslerov RV
AU  - Panteleeva AN
AU  - Kolganova TV
AU  - Ravin NV
AU  - Skryabin KG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 193: 321-322.

PMID- Not carried by PubMed...
VI  - 3
DP  - 1987
TI  - Interaction between EcoRII restriction/modification enzymes and synthetic DNA fragments. Synthesis of substrates containing a single recognition site.
PG  - 283-289
AB  - 9-16 membered oligodeoxyribonucleotides forming DNA-duplexes with one EcoRII
      site (native or modified) were synthesized by the block triester method.  The
      modifications involved the replacement of one (or two) cytidine or thymidine
      moieties in duplexes for m5dC or f5dU, respectively.  30-membered DNA-duplex
      was obtained by enzymatic ligation of five overlapping oligonucleotides.  The
      substitutions introduced neither result in any significant destabilization nor
      distort the double helix geometry as is evidenced by the UV- and
      CD-spectroscopy methods.
AU  - Kuznetsova SA
AU  - Kubareva EA
AU  - Oretskaya TS
AU  - Dolinnaya NG
AU  - Krynetskaya NF
AU  - Gromova ES
AU  - Shabarova ZA
AU  - Cech D
PT  - Journal Article
TA  - Biopol. Kletka
JT  - Biopol. Kletka
SO  - Biopol. Kletka 1987 3: 283-289.

PMID- 2984842
VI  - 31
DP  - 1985
TI  - Identification of the system modification-restriction in Staphylococci.
PG  - 121-125
AB  - A new system of host specificity of DNA, called Sau67 according to the available nomenclature,
      was identified in Staphylococcus aureus 6782 strain by means of cross titration with
      staphylophage 729 considering that the phage exhibited the highly effective absorption
      properties.  A total preparation of Sau67 methylases was isolated using ammonium sulfate
      fractionation.  The enzyme preparation contained methylases of cytosine and adenine, where the
      activity of adenine methylases constituted only 5% of the total methylase activity.  As shown
      by kinetics of methylation a low content of unspecific cellular nucleases was found in the St.
      aureus 6782 strain; these reasons are important for isolation of restricting endonucleases
      containing in the strain.  100 microg of protein of the total enzymatic fraction enabled the
      methylation of the acceptor DNA at a maximal rate within 1.5 hr of incubation in phosphate
      buffer, pH 7.9.  The fraction of cytosine methylases free of adenine methylating activity was
      obtained after chromatography on Sepharose blue with NaCl concentration stepwise gradient.
AU  - Kvachadze LI
AU  - Andriashvili IA
AU  - Chanishvili TG
AU  - Arutyunyan EE
AU  - Nikolskaia II
AU  - Debov SS
PT  - Journal Article
TA  - Vopr. Med. Khim.
JT  - Vopr. Med. Khim.
SO  - Vopr. Med. Khim. 1985 31: 121-125.

PMID- 12007812
VI  - 209
DP  - 2002
TI  - Transformation using in vivo and in vitro methylation in Streptomyces griseus.
PG  - 243-248
AB  - Streptomyces griseus does not readily take up foreign DNA isolated from other Streptomyces
      species or Escherichia coli, presumably due to its
      unique restriction-modification systems that function as a barrier for
      interspecific DNA transfer. To efficiently transform S. griseus by
      avoiding the restriction barriers, we methylated incoming DNA in vivo
      and in vitro and treated protoplasts with heat prior to transformation.
      Whereas heat treatment of protoplasts or methylation of the E.
      coli-Streptomyces shuttle vectors (pXE4 and pKK1443) did not
      prominently improve the transformation efficiency, HpaII methylation of
      the vectors from any E. coli strains tested in this study highly
      increased the transformation efficiency. The highest transformation
      efficiency was observed when the shuttle vectors were isolated from the
      dam, hsd strain of E. coli (GM161) and methylated by AluI and HpaII
      methyltransferases, and the efficiency was approximately the same as
      that of the vectors from S. griseus. We identified several
      restriction-modification systems that decrease the transformation
      efficiency. This research also led us to understand methylation
      profiles and restriction-modification systems in S. griseus.
AU  - Kwak J
AU  - Jiang H
AU  - Kendrick KE
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2002 209: 243-248.

PMID- 25211235
VI  - 9
DP  - 2014
TI  - Genome Information of Methylobacterium oryzae, a Plant-Probiotic Methylotroph in the Phyllosphere.
PG  - E106704
AB  - Pink-pigmented facultative methylotrophs in the Rhizobiales are widespread in the
      environment, and many Methylobacterium species associated with plants produce
      plant growth-promoting substances. To gain insights into the life style at the
      phyllosphere and the genetic bases of plant growth promotion, we determined and
      analyzed the complete genome sequence of Methylobacterium oryzae CBMB20T, a
      strain isolated from rice stem. The genome consists of a 6.29-Mb chromosome and
      four plasmids, designated as pMOC1 to pMOC4. Among the 6,274 coding sequences in
      the chromosome, the bacterium has, besides most of the genes for the central
      metabolism, all of the essential genes for the assimilation and dissimilation of
      methanol that are either located in methylotrophy islands or dispersed. M. oryzae
      is equipped with several kinds of genes for adaptation to plant surfaces such as
      defense against UV radiation, oxidative stress, desiccation, or nutrient
      deficiency, as well as high proportion of genes related to motility and
      signaling. Moreover, it has an array of genes involved in metabolic pathways that
      may contribute to promotion of plant growth; they include auxin biosynthesis,
      cytokine biosynthesis, vitamin B12 biosynthesis, urea metabolism, biosorption of
      heavy metals or decrease of metal toxicity, pyrroloquinoline quinone
      biosynthesis, 1-aminocyclopropane-1-carboxylate deamination, phosphate
      solubilization, and thiosulfate oxidation. Through the genome analysis of M.
      oryzae, we provide information on the full gene complement of M. oryzae that
      resides in the aerial parts of plants and enhances plant growth. The
      plant-associated lifestyle of M. oryzae pertaining to methylotrophy and plant
      growth promotion, and its potential as a candidate for a bioinoculant targeted to
      the phyllosphere and focused on phytostimulation are illuminated.
AU  - Kwak MJ
AU  - Jeong H
AU  - Madhaiyan M
AU  - Lee Y
AU  - Sa TM
AU  - Oh TK
AU  - Kim JF
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2014 9: E106704.

PMID- 28770029
VI  - 12
DP  - 2017
TI  - Complete genome sequence of the sand-sediment actinobacterium Nocardioides dokdonensis FR1436T.
PG  - 44
AB  - Nocardioides dokdonensis, belonging to the class Actinobacteria, was first isolated from sand
      sediment of a beach in Dokdo, Korea, in 2005. In this study,
      we determined the genome sequence of FR1436, the type strain of N. dokdonensis,
      and analyzed its gene contents. The genome sequence is the second complete one in
      the genus Nocardioides after that of Nocardioides sp. JS614. It is composed of a
      4,376,707-bp chromosome with a G + C content of 72.26%. From the genome sequence,
      4,104 CDSs, three rRNA operons, 51 tRNAs, and one tmRNA were predicted, and
      71.38% of the genes were assigned putative functions. Through the sequence
      analysis, dozens of genes involved in steroid metabolism, especially its
      degradation, were detected. Most of the identified genes were located in large
      gene clusters, which showed high similarities with the gene clusters in
      Pimelobacter simplex VKM Ac-2033D. Genomic features of N. dokdonensis associated
      with steroid catabolism indicate that it could be used for research and
      application of steroids in science and industry.
AU  - Kwak MJ
AU  - Kwon SK
AU  - Kim JF
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 44.

PMID- 26664701
VI  - 10
DP  - 2015
TI  - Genome sequence of Lysobacter dokdonensis DS-58(T), a gliding bacterium isolated  from soil in Dokdo, Korea.
PG  - 123
AB  - Lysobacter dokdonensis DS-58, belonging to the family Xanthomonadaceae, was isolated from a
      soil sample in Dokdo, Korea in 2011. Strain DS-58 is the type
      strain of L. dokdonensis. In this study, we determined the genome sequence to
      describe the genomic features including annotation information and COG functional
      categorization. The draft genome sequence consists of 25 contigs totaling
      3,274,406 bp (67.24 % G + C) and contains 3,155 protein coding genes, 2 copies of
      ribosomal RNA operons, and 48 transfer RNA genes. Among the protein coding genes,
      75.91 % of the genes were annotated with a putative function and 87.39 % of the
      genes were assigned to the COG category. In the genome of L. dokdonensis, a large
      number of genes associated with protein degradation and antibiotic resistance
      were detected.
AU  - Kwak MJ
AU  - Kwon SK
AU  - Yoon JH
AU  - Kim JF
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 123.

PMID- 22843575
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of the Endophytic Bacterium Burkholderia sp. Strain KJ006.
PG  - 4432-4433
AB  - Endophytes live inside plant tissues without causing any harm and may even benefit plants.
      Here, we provide the high-quality genome sequence of Burkholderia
      sp. strain KJ006, an endophytic bacterium of rice with antifungal activity. The
      6.6-Mb genome, consisting of three chromosomes and a single plasmid, contains
      genes related to plant growth promotion or degradation of aromatic compounds.
AU  - Kwak MJ
AU  - Song JY
AU  - Kim SY
AU  - Jeong H
AU  - Kang SG
AU  - Kim BK
AU  - Kwon SK
AU  - Lee CH
AU  - Yu DS
AU  - Park SH
AU  - Kim JF
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4432-4433.

PMID- 27486485
VI  - 11
DP  - 2016
TI  - Draft genome sequence of Mycobacterium rufum JS14(T), a polycyclic-aromatic-hydrocarbon-degrading bacterium from petroleum-contaminated  soil in Hawaii.
PG  - 47
AB  - Mycobacterium rufum JS14(T) (=ATCC BAA-1377(T), CIP 109273(T), JCM 16372(T), DSM  45406(T)), a
      type strain of the species Mycobacterium rufum sp. . belonging to
      the family Mycobacteriaceae, was isolated from polycyclic aromatic hydrocarbon
      (PAH)-contaminated soil in Hilo (HI, USA) because it harbors the capability of
      degrading PAH. Here, we describe the first genome sequence of strain JS14(T),
      with brief phenotypic characteristics. The genome is composed of 6,176,413 bp
      with 69.25 % G + C content and contains 5810 protein-coding genes with 54 RNA
      genes. The genome information on M. rufum JS14(T) will provide a better
      understanding of the complexity of bacterial catabolic pathways for degradation
      of specific chemicals.
AU  - Kwak Y
AU  - Li QX
AU  - Shin JH
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 47.

PMID- 27555890
VI  - 11
DP  - 2016
TI  - High quality draft genome sequence of the type strain of Pseudomonas lutea OK2(T), a phosphate-solubilizing rhizospheric bacterium.
PG  - 51
AB  - Pseudomonas lutea OK2(T) (=LMG 21974(T), CECT 5822(T)) is the type strain of the  species and
      was isolated from the rhizosphere of grass growing in Spain in 2003
      based on its phosphate-solubilizing capacity. In order to identify the functional
      significance of phosphate solubilization in Pseudomonas Plant growth promoting
      rhizobacteria, we describe here the phenotypic characteristics of strain OK2(T)
      along with its high-quality draft genome sequence, its annotation, and analysis.
      The genome is comprised of 5,647,497 bp with 60.15 % G + C content. The sequence
      includes 4,846 protein-coding genes and 95 RNA genes.
AU  - Kwak Y
AU  - Park GS
AU  - Shin JH
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 51.

PMID- 15788529
VI  - 102
DP  - 2005
TI  - The complete genomes and proteomes of 27 Staphylococcus aureus bacteriophages.
PG  - 5174-5179
AB  - Bacteriophages are the most abundant life forms in the biosphere. They
      play important roles in bacterial ecology, evolution, adaptation to new
      environments, and pathogenesis of human bacterial infections. Here, we
      report the complete genomic sequences, and predicted proteins of 27
      bacteriophages of the Gram-positive bacterium Staphylococcus aureus.
      Comparative nucleotide and protein sequence analysis indicates that these
      phages are a remarkable source of untapped genetic diversity, encoding
      2,170 predicted protein-encoding ORFs, of which 1,402 cannot be annotated
      for structure or function, and 522 are proteins with no similarity to
      other phage or bacterial sequences. Based on their genome size,
      organization of their gene map and comparative nucleotide and protein
      sequence analysis, the S. aureus phages can be organized into three
      groups. Comparison of their gene maps reveals extensive genome mosaicism,
      hinting to a large reservoir of unidentified S. aureus phage genes. Among
      the phages in the largest size class (178-214 kbp) that we characterized
      is phage Twort, the first discovered bacteriophage (responsible for the
      Twort-D'Herelle effect). These phage genomes offer an exciting opportunity
      to discern molecular mechanisms of phage evolution and diversity.
AU  - Kwan T
AU  - Liu J
AU  - Dubow M
AU  - Gros P
AU  - Pelletier J
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2005 102: 5174-5179.

PMID- 24675862
VI  - 2
DP  - 2014
TI  - Genome Sequence of the Quorum-Quenching Rhodococcus erythropolis Strain R138.
PG  - e00224-14
AB  - Rhodococcus erythropolis strain R138 was isolated from the rhizosphere of Solanum tuberosum
      and selected for its capacity to degrade N-acyl-homoserine lactones,
      quorum-sensing signals used as communication molecules by the potato pathogens
      Pectobacterium and Dickeya. Here, we report the genome sequence of Rhodococcus
      erythropolis strain R138.
AU  - Kwasiborski A
AU  - Mondy S
AU  - Beury-Cirou A
AU  - Faure D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00224-14.

PMID- 23788545
VI  - 1
DP  - 2013
TI  - Genome Sequence of the Pectobacterium atrosepticum Strain CFBP6276, Causing Blackleg and Soft Rot Diseases on Potato Plants and Tubers.
PG  - e00374-13
AB  - Pectobacterium atrosepticum strain CFBP6276 is a pectinolytic enterobacterium causing blackleg
      and soft rot of the stem and tuber of Solanum tuberosum. Its
      virulence is under the control of quorum sensing, with N-acylhomoserine lactones
      as communication signals. Here, we report the genome sequence of P. atrosepticum
      strain CFBP6276.
AU  - Kwasiborski A
AU  - Mondy S
AU  - Beury-Cirou A
AU  - Faure D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00374-13.

PMID- 25566225
VI  - 5
DP  - 2014
TI  - The dam replacing gene product enhances Neisseria gonorrhoeae FA1090 viability and biofilm formation.
PG  - 712
AB  - Many Neisseriaceae do not exhibit Dam methyltransferase activity and, instead of the dam gene,
      possess drg (dam replacing gene) inserted in the leuS/dam locus. The drg locus in Neisseria
      gonorrhoeae FA1090 has a lower GC-pairs content (40.5%) compared to the whole genome of N.
      gonorrhoeae FA1090 (52%). The gonococcal drg gene encodes a DNA endonuclease Drg, with GmeATC
      specificity. Disruption of drg or insertion of the dam gene in gonococcal genome changes the
      level of expression of genes as shown by transcriptome analysis. For the drg-deficient N.
      gonorrhoeae mutant, a total of 195 (8.94% of the total gene pool) genes exhibited an altered
      expression compared to the wt strain by at least 1.5 fold. In dam-expressing N. gonorrhoeae
      mutant, the expression of 240 genes (11% of total genes) was deregulated. Most of these
      deregulated genes were involved in translation, DNA repair, membrane biogenesis and energy
      production as shown by cluster of orthologous group analysis. In vivo, the inactivation of drg
      gene causes the decrease of the number of live neisserial cells and long lag phase of growth.
      The insertion of dam gene instead of drg locus restores cell viability. We have also shown
      that presence of the drg gene product is important for N. gonorrhoeae FA1090 in adhesion,
      including human epithelial cells, and biofilm formation. Biofilm produced by drg-deficient
      strain is formed by more dispersed cells, compared to this one formed by parental strain as
      shown by scanning electron and confocal microscopy. Also adherence assays show a significantly
      smaller biomass of formed biofilm (OD570 = 0.242 +/- 0.038) for drg-deficient strain, compared
      to wild-type strain (OD570 = 0.378 +/- 0.057). Dam-expressing gonococcal cells produce
      slightly weaker biofilm with cells embedded in an extracellular matrix. This strain has also a
      five times reduced ability for adhesion to human epithelial cells. In this context, the
      presence of Drg is more advantageous for N. gonorrhoeae biology than Dam presence.
AU  - Kwiatek A
AU  - Bacal P
AU  - Wasiluk A
AU  - Trybunko A
AU  - Adamczyk-Poplawska M
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2014 5: 712.

PMID- 15184558
VI  - 150
DP  - 2004
TI  - DNA methyltransferases from Neisseria meningitidis and Neisseria gonorrhoeae FA1090 associated with mismatch nicking endonucleases.
PG  - 1713-1722
AB  - The genes encoding the DNA methyltransferases M.NmeDI and M.NmeAl from Neisseria meningitidis
      associated with the genes encoding putative Vsr
      endonucleases were overexpressed in Escherichia coli. The enzymes were
      purified to apparent homogeneity on Ni-NTA agarose columns, yielding
      proteins of 49  1 kDa and 39.6  1 kDa, respectively, under
      denaturing conditions. M.NmeDI recognizes the degenerate sequence
      5'-RCCGGB-3'. It methylates the first 5' cytosine residue on both
      strands within the core sequence CCGG. The enzyme shows higher affinity
      with the hemimethylated degenerate sequence than with the unmethylated
      degenerate sequence. Comparison of the amino acid sequence of the
      target-recognizing domain of M.NmeDI with the closest neighbours
      recognizing the sequence 5'-RCCGGY-3' showed the presence of the
      homologous domain and an additional domain that may be responsible for
      recognizing the degenerate sequence. M.NmeAl recognizes the sequence
      5'-CCGG-3' and methylates the second 5' cytosine residue on both DNA
      strands. In Neisseria gonorrhoeae strain FA1090 the homologues of these
      ORFs are truncated due to a variety of mutations.
AU  - Kwiatek A
AU  - Kobes M
AU  - Olejnik K
AU  - Piekarowicz A
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2004 150: 1713-1722.

PMID- 20511499
VI  - 192
DP  - 2010
TI  - Neisseria gonorrhoeae FA1090 encodes two classes of Vsr endonucleases.
PG  - 3951-3960
AB  - Very Short Patch repair systems prevent mutations resulting from deamination of
      5-methylcytosine to thymine. The Vsr endonuclease is the key enzyme of this system, providing
      sequence specificity. We identified two genes encoding Vsr endonucleases from Neisseria
      gonorrhoeae FA1090, V.NgoAXIII and V.NgoAXIV, based on DNA sequence similarity to genes
      encoding Vsr endonucleases from other bacteria. After expression of the gonococcal genes in
      Escherichia coli, the proteins were biochemically characterized and the endonucleolytic
      activity and specificity of V.NgoAXIII and V.NgoAXIV were determined. V.NgoAXIII was found to
      be multispecific and recognizes T:G mismatches in every tested nucleotide context whereas
      V.NgoAXIV recognizes T:G mismatches in the following sequences: GTGG, CTGG, GTGC, ATGC or
      CTGC. Alanine mutagenesis of conserved residues showed that Asp50 and His68 of V.NgoAXIII and
      Asp51 and His69 of V.NgoAXIV are essential for hydrolytic activity. Glu25, His64 and Asp97 of
      V.NgoAXIV and Glu24, Asp63 and Asp97 of V.NgoAXIII are important but not crucial for activity
      V.NgoAXIII and V.NgoAXIV. However, Glu24 and Asp63 are also important for the specificity of
      V.NgoAXIII. On the basis of our results, concerning features of Vsr endonucleases encoded by
      N. gonorrhoeae FA1090, we postulate that at least two types of Vsr endonucleases can be
      distinguished.
AU  - Kwiatek A
AU  - Luczkiewicz M
AU  - Bandyra K
AU  - Stein DC
AU  - Piekarowicz A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 3951-3960.

PMID- 17897964
VI  - 35
DP  - 2007
TI  - The restriction endonuclease R.NmeDI from Neisseria meningitidis that recognizes a palindromic sequence and cuts the DNA on both sides of the  recognition sequence.
PG  - 6539-6546
AB  - The restriction endonuclease Type II R.NmeDI from Neisseria meningitidis 2120 (serogroup C,
      ST-11 complex) was characterized. The cloned nmeDIR
      gene was expressed in Escherichia coli cells, and the endonucleolytic and
      restriction activities of R.NmeDI were then observed in vitro and in vivo.
      The nmeDIR gene consists of 1056 bp coding 351 aa protein with a
      calculated molecular weight of M((r)) = 39 000 +/- 1000 Da. The R.NmeDI
      enzyme was purified to apparent homogeneity following overexpression,
      using metal affinity chromatography. This enzyme recognizes a palindrome
      sequence and cleaves double-stranded DNA upstream and downstream of its
      recognition sequence (12/7) RCCGGY (7/12) (R = A/G, Y = C/T) cutting out a
      25-bp fragment. R.NmeDI cleaves in two steps. The enzyme cleaves the first
      strand randomly on either side of the recognition sequence generating an
      intermediate, and the second cleavage occurs more slowly and results in
      the production of a final reaction product. The R.NmeDI endonuclease
      requires two recognition sequences for effective cleavage. The tetramer is
      an active form of the R.NmeDI enzyme.
AU  - Kwiatek A
AU  - Piekarowicz A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2007 35: 6539-6546.

PMID- 6401818
VI  - 45
DP  - 1983
TI  - Substrate specificity of two bacteriophage-associated endo-N-acetylneuraminidases.
PG  - 367-374
AB  - For Escherichia coli Bos12 (O16:K92:H-), a bacteriophage (phi 92) has been
      isolated which carries a depolymerase active on the K92 capsular polysaccharide.
      As seen under the electron microscope, phi 92 belongs to Bradley's morphology
      group A and is different from the phage phi 1.2 previously described (Kwiatkowski
      et al., J. Virol. 43:697-704, 1982), which grows on E. coli K235 (O1:K1:H-),
      depolymerizes colominic acid, and belongs to morphology group C. The specificity
      of the phi 1.2- and phi 92-associated endo-N-acetylneuraminidases has been
      studied with respect to the following substrates (all alkali treated, and where
      NeuNAc represents N-acetylneuraminic acid): (i) [-alpha-NeuNAc-(2 leads to 8)-]n
      (colominic acid), (ii) [-alpha-NeuNAc-(2 leads to 8)-alpha-NeuNAc-(2 leads to
      9)-]n (E. coli K92 polysaccharide), and (iii) [-alpha-NeuNAc-(2 leads to 9)-]n
      (Neisseria meningitidis type C capsular polysaccharide). The increase in
      periodate consumption of these glycans upon incubation with purified phi 1.2 or
      phi 92 particles was measured, and the split products obtained from all
      substrates after exhaustive degradation were analyzed by gel chromatography. It
      was found that the Neisseria polysaccharide is not appreciably affected by either
      virus enzyme and that phi 1.2 only depolymerizes a small fraction of the K92
      glycan. Colominic acid, however, is completely degraded by both agents, phi 92
      yielding smaller fragments (one to six NeuNAc residues) than phi 1.2 (two to
      seven). Phage phi 92 additionally depolymerizes the K92 glycan, essentially to
      oligosaccharides of two, four, and six residues. The size distribution of these
      K92 oligosaccharides indicates that the phi 92 enzyme predominantly cleaves the
      alpha(2 leads to 8) linkages in this polymer.
AU  - Kwiatkowski B
AU  - Boschek B
AU  - Thiele H
AU  - Stirm S
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1983 45: 367-374.

PMID- 3463994
VI  - 83
DP  - 1986
TI  - Introduction and expression of the bacterial PaeR7 methylase gene in mammalian cells.
PG  - 7713-7717
AB  - An approach is devised for studying the role of DNA methylation in eukaryotic
      gene expression.  The approach is based on the expression of site-specific
      bacterial methylase genes in animal cells.  A model system using the cloned
      PaeR7 (an isoschizomer of XhoI) methylase gene was constructed to test the
      feasibility of this approach.  Expression plasmids for the PaeR7 methylase gene
      were introduced into mouse Ltk- cells by cotransfection with the cloned chicken
      thymidine kinase (tk) gene.  Several of the cell strains derived from Tk+
      colonies were found to express the PaeR7 gene as judged by four criteria:  the
      cellular DNA of these strains showed increased resistance to cleavage by XhoI;
      these strains contained cellular proteins that comigrated with pure PaeR7
      methylase protein, as visualized by immunoblotting; PaeR7 methylase activity
      was found in vitro in crude extracts of total cellular protein from these
      strains; and murine adenovirus genomes grown on cells expressing PaeR7
      methylase showed resistance to cleavage to PaeR7 endonuclease.  The potential
      applications of this approach for the study of cellular and viral gene
      regulation, DNA repair, and restriction modification are discussed.
AU  - Kwoh TJ
AU  - Kwoh DY
AU  - McCue AW
AU  - Davis GR
AU  - Patrick D
AU  - Gingeras TR
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1986 83: 7713-7717.

PMID- 2850539
VI  - 16
DP  - 1988
TI  - Introduction and expression of the bacterial PaeR7I restriction endonuclease gene in mouse cells containing the PaeR7I methylase.
PG  - 11489-11506
AB  - To study the factors essential for a functional restriction system, the PaeR7I
      restriction-modification system has been introduced and expressed in murine
      cells.  Transfer of this system was accomplished in two steps.  First, cells
      containing sufficient PaeR7I methylase to completely methylate the mouse genome
      were constructed.  In the second step, the mouse metallothionein
      promoter-regulated, endonuclease expression vector linked to the hygromycin B
      resistance selection marker was used to transfect the high methylase-expressing
      cells.  Sixty percent of the clones isolated contained PaeR7I endonuclease
      enzymatic activity.  Transfected cells expressing both methylase and
      endonuclease were incapable of blocking infection by DNA viruses, and possible
      explanations are discussed.
AU  - Kwoh TJ
AU  - Obermiller PS
AU  - McCue AW
AU  - Kwoh DY
AU  - Sullivan SA
AU  - Gingeras TR
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1988 16: 11489-11506.

PMID- 25540356
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Clostridium butyricum Strain NOR 33234, Isolated from an Elderly Patient with Diarrhea.
PG  - e01356-14
AB  - Clostridium butyricum is one of the species frequently present in patients' stool samples.
      However, the identification of this species is sometimes difficult.
      Here, we present the draft genome of Clostridium butyricum NOR 33234, which was
      isolated from a patient with suspected Clostridium difficile infection-associated
      diarrhea and resembles Clostridium clostridioforme in biochemical tests.
AU  - Kwok JS
AU  - Ip M
AU  - Chan TF
AU  - Lam WY
AU  - Tsui SK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01356-14.

PMID- 23292138
VI  - 5
DP  - 2013
TI  - Genomic makeup of the marine flavobacterium Nonlabens (Donghaeana) dokdonensis DSW-6 and identification of a novel class of rhodopsins.
PG  - 187-199
AB  - Rhodopsin-containing marine microbes such as those in the class Flavobacteria
      play a pivotal role in the biogeochemical cycle of the euphotic zone .
      Deciphering the genome information of flavobacteria and accessing the diversity
      and ecological impact of microbial rhodopsins is important in understanding and
      preserving the global ecosystems. The genome sequence of the orange-pigmented
      marine flavobacterium Nonlabens dokdonensis (basonym: Donghaeana dokdonensis)
      DSW-6 was determined. As a marine photoheterotroph, DSW-6 has written in its
      genome physiological features that allow survival in marine oligotrophic
      environments. The sequence analysis also uncovered a gene encoding an unexpected
      type of microbial rhodopsin containing a unique motif in addition to a
      proteorhodopsin gene and a number of photolyase or cryptochrome genes. Homologs
      of the novel rhodopsin gene were found in other flavobacteria,
      alphaproteobacteria, a species of cytophaga, a deinococcus, and even a eukaryote
      diatom. They all contain the characteristic NQ motif and form a phylogenetically
      distinct group. Expression analysis of this rhodopsin gene in DSW-6 indicated
      that it is induced at high NaCl concentrations, as well as in the presence of
      light and the absence of nutrients. Genomic and metagenomic surveys demonstrate
      the diversity of the NQ rhodopsins in nature and the prevalent occurrence of the
      encoding genes among microbial communities inhabiting hypersaline niches,
      suggesting its involvement in sodium metabolism and the sodium-adapted lifestyle.
AU  - Kwon SK
AU  - Kim BK
AU  - Song JY
AU  - Kwak MJ
AU  - Lee CH
AU  - Yoon JH
AU  - Oh TK
AU  - Kim JF
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2013 5: 187-199.

PMID- 26021919
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Enterohemorrhagic Escherichia coli O157 NCCP15739, Isolated in the Republic of Korea.
PG  - e00522-15
AB  - Enterohemorrhagic Escherichia coli (EHEC) is the main cause of the recent outbreaks of
      diarrhea, hemolytic-uremic syndrome (HUS), and hemorrhagic colitis
      worldwide. Herein, we present the draft genome sequence of the NCCP15739 isolate
      from a patient in the Republic of Korea.
AU  - Kwon T
AU  - Cho SH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00522-15.

PMID- 26893431
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Mycobacterium tuberculosis KT-0184, Isolated in South Korea.
PG  - e01755-15
AB  - Here, we describe the draft genome sequence of Mycobacterium tuberculosis KT-0184, from the
      Beijing family. This genome will provide insight into the
      evolution and adaptation of M. tuberculosis KT-0184 in human hosts.
AU  - Kwon T
AU  - Han SJ
AU  - Yoo WG
AU  - Yun MR
AU  - Lee S
AU  - Lee JS
AU  - Kim DW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01755-15.

PMID- 26868407
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Mycobacterium tuberculosis KT-0133, Isolated in South Korea.
PG  - e01731-15
AB  - Here, we present the draft genome sequence of Mycobacterium tuberculosis KT-0133, which
      belongs to the Korean-Beijing family. This sequence will provide a new
      perspective on the evolution and accommodation of M. tuberculosis KT-0133 in
      human hosts.
AU  - Kwon T
AU  - Han SJ
AU  - Yoo WG
AU  - Yun MR
AU  - Lee S
AU  - Lee JS
AU  - Kim DW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01731-15.

PMID- 26769936
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Klebsiella pneumoniae subsp. pneumoniae KP617, Coproducing OXA-232 and NDM-1 Carbapenemases, Isolated in South Korea.
PG  - e01550-15
AB  - The prevalence of Klebsiella pneumoniae coproducing carbapenemase metallo-beta-lactamase 1
      (NDM-1) and OXA-48 has been increasing globally since
      2013. The complete genome of KP617 was sequenced and assembled into a circular
      chromosome and two plasmids. This sequence provides the genetic background for
      understanding the evolution of carbapenemase genes in K. pneumoniae KP617.
AU  - Kwon T
AU  - Yang JW
AU  - Lee S
AU  - Yun MR
AU  - Yoo WG
AU  - Kim HS
AU  - Cha JO
AU  - Kim DW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01550-15.

PMID- 23105065
VI  - 194
DP  - 2012
TI  - Draft genome sequence of the xylan-degrading marine bacterium strain s124, representing a novel species of the genus oceanicola.
PG  - 6325
AB  - We isolated a xylan-degrading bacterium from seawater of Micronesia and identified it as
      Oceanicola sp. strain S124. We sequenced the Oceanicola sp. S124
      genome using GSFLX 454 pyrosequencing and predicted 4,433 open reading frames
      (ORFs) including putative saccharification and phage-related genes.
AU  - Kwon YK
AU  - Kim JJ
AU  - Kim JH
AU  - Jeon SM
AU  - Ye BR
AU  - Jang J
AU  - Heo SJ
AU  - Park SC
AU  - Kang DH
AU  - Oh C
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6325.

PMID- 26823585
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of the Proteorhodopsin-Containing Marine Bacterium Sediminicola sp. YIK13.
PG  - e01635-15
AB  - Sediminicola sp. YIK13 is a marine flavobacterium, isolated from tidal flat sediment. Here, we
      present the first complete genome sequence of this genus,
      which consists of 3,569,807 bp with 39.4% GC content. This strain contains
      proteorhodopsin, as well as retinal biosynthesis genes, allowing it to utilize
      sunlight as an energy source.
AU  - Kwon YM
AU  - Kim SJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01635-15.

PMID- Not carried by PubMed...
VI  - 26
DP  - 1988
TI  - Characterization of BmaI methylase from Bacillus macerans.
PG  - 88-92
AB  - The isolation and characterization of a new type II methylase, BmaI methylase,
      from Bacillus macerans ATCC 8244 were described.  BmaI methylase was isolated
      by procedures of ammonium sulfate fractionation, DEAE-cellulose chromatography
      and phosphocellulose chromatography.  Two types of methylases were present in
      this strain and only one of the two was a site specific BmaI methylase.  The
      pBR322 DNA methylated by BmaI methylase was not cleaved by BmaI endonuclease,
      and pBR322 DNA cleaved by BmaI endonuclease was not methylated by BmaI
      methylase.  The optimal pH for the BmaI methylase activity was 7.5, and optimal
      NaCl concentration was about 50 mM.  BmaI methylase could methylate
      single-stranded M13mp18 DNA.
AU  - Kwon YT
AU  - Jun HS
AU  - Rho HM
PT  - Journal Article
TA  - Korean J. Microbiol.
JT  - Korean J. Microbiol.
SO  - Korean J. Microbiol. 1988 26: 88-92.

PMID- Not carried by PubMed...
VI  - 26
DP  - 1988
TI  - Characterization of BmaI endonuclease from Bacillus macerans ATCC 8244.
PG  - 1-5
AB  - The isolation and characterization of a new type II restriction endonuclease,
      BmaI, from Bacillus macerans ATCC 8244 were described.  BmaI endonuclease was
      partially purified by procedures of ammonium sulfate fractionation,
      DEAE-cellulose and phosphocellulose chromatographies.  This enzyme recognized
      one site on pBR322 DNA, two sites on Bluescribe DNA, three sites on lambda DNA
      and no site on SV40 DNA.  The same cleavage patterns for various DNAs as PvuI
      indicated that BmaI is an isoschizomer of PvuI whose recognition sequence is
      5'-CGATCG-3'.  The optimal pH for the BmaI endonuclease activity was about 7.0
      and optimal NaCl concentration was about 100 mM.  Manganese ion could partially
      replace magnesium as a cofactor, but calcium could not at all.
AU  - Kwon YT
AU  - Jun HS
AU  - Rho HM
PT  - Journal Article
TA  - Korean J. Microbiol.
JT  - Korean J. Microbiol.
SO  - Korean J. Microbiol. 1988 26: 1-5.

PMID- 10613866
VI  - 182
DP  - 2000
TI  - Characterization of the endogenous plasmid from Pseudomonas alcaligenes NCIB 9867: DNA sequence and mechanism of transfer.
PG  - 81-90
AB  - The endogenous plasmid pRA2 from Pseudomonas alcaligenes NCIB 9867 was determined to have
      32,743 bp with a G+C content of 59.8%, Sequence
      analysis predicted a total of 29 open reading frames, with
      approximately half of them contributing towards the functions of
      plasmid replication, mobilization, and stability. The Pac25I
      restriction-modification system and two mobile elements, Tn5563 and
      IS1633, were physically localized. An additional eight open reading
      frames with unknown functions were also detected. pRA2 was genetically
      tagged with the Omega Str(r)/Spc(r) gene cassette by homologous
      recombination, Intrastrain transfer of pRA2-encoded genetic markers
      between isogenic mutants of P. alcaligenes NCIB 9867,were observed at
      high frequencies (2.4 x 10(-4) per donor). This transfer aas determined
      to be mediated by a natural transformation process that required
      cell-cell contact and was completely sensitive to DNase I (1 mg/ml),
      Efficient transformation was also observed when pRA2 DNA was applied
      directly onto the cells, while transformation with foreign plasmid DNAs
      was not observed. pRA2 could be conjugally transferred into Pseudomonas
      putida RA713 and KT2440 recipients only when plasmid RK2/RP4 transfer
      functions were provided in trams, Plasmid stability analysis
      demonstrated that pRA2 could be stably maintained in its original host,
      P. alcaligenes NCIB 9867, as well as in P. putida RA713 after 100
      generations of nonselective growth. Disruption of the pRA2 pac25I
      restriction endonuclease gene did not alter plasmid stability, while
      the pRA2 minireplicon exhibited only partial stability, This indicates
      that other pRA2-encoded determinants could have significant roles in
      influencing plasmid stability.
AU  - Kwong SM
AU  - Yeo CC
AU  - Suwanto A
AU  - Poh CL
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2000 182: 81-90.

PMID- 25053814
VI  - 111
DP  - 2014
TI  - Genomics and host specialization of honey bee and bumble bee gut symbionts.
PG  - 11509-11514
AB  - Gilliamella apicola and Snodgrassella alvi are dominant members of the honey bee  (Apis spp.)
      and bumble bee (Bombus spp.) gut microbiota. We generated complete
      genomes of the type strains G. apicola wkB1(T) and S. alvi wkB2(T) (isolated from
      Apis), as well as draft genomes for four other strains from Bombus. G. apicola
      and S. alvi were found to occupy very different metabolic niches: The former is a
      saccharolytic fermenter, whereas the latter is an oxidizer of carboxylic acids.
      Together, they may form a syntrophic network for partitioning of metabolic
      resources. Both species possessed numerous genes [type 6 secretion systems,
      repeats in toxin (RTX) toxins, RHS proteins, adhesins, and type IV pili] that
      likely mediate cell-cell interactions and gut colonization. Variation in these
      genes could account for the host fidelity of strains observed in previous
      phylogenetic studies. Here, we also show the first experimental evidence, to our
      knowledge, for this specificity in vivo: Strains of S. alvi were able to colonize
      their native bee host but not bees of another genus. Consistent with specific,
      long-term host association, comparative genomic analysis revealed a deep
      divergence and little or no gene flow between Apis and Bombus gut symbionts.
      However, within a host type (Apis or Bombus), we detected signs of horizontal
      gene transfer between G. apicola and S. alvi, demonstrating the importance of the
      broader gut community in shaping the evolution of any one member. Our results
      show that host specificity is likely driven by multiple factors, including direct
      host-microbe interactions, microbe-microbe interactions, and social transmission.
AU  - Kwong WK
AU  - Engel P
AU  - Koch H
AU  - Moran NA
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2014 111: 11509-11514.

PMID- 25395644
VI  - 2
DP  - 2014
TI  - Genome Sequences of Lactobacillus sp. Strains wkB8 and wkB10, Members of the Firm-5 Clade, from Honey Bee Guts.
PG  - e01176-14
AB  - We sequenced two strains from the Lactobacillus Firm-5 clade, a dominant group of symbionts in
      the guts of honey bees and other social bees. The genome of strain
      wkB8, comprising a 1.93-Mb chromosome and a 6.4-kb plasmid, was fully closed,
      while strain wkB10 was assembled into 32 contigs. These genomes will provide
      insights into how gut symbionts evolve and interact with their host species.
AU  - Kwong WK
AU  - Mancenido AL
AU  - Moran NA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01176-14.

PMID- 25359910
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Ristocetin-Producing Strain Amycolatopsis sp. Strain MJM2582 Isolated in South Korea.
PG  - e01091-14
AB  - The draft genome sequence of a ristocetin-producing Amycolatopsis strain (sp. MJM2582)
      isolated in South Korea is reported here. This strain has a genome of
      approximately 8.9 Mb containing 7,933 predicted genes, including the ristocetin
      cluster and 32 additional predicted secondary metabolite biosynthesis clusters.
AU  - Kwun MJ
AU  - Cheng J
AU  - Yang SH
AU  - Lee DR
AU  - Suh JW
AU  - Hong HJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01091-14.

PMID- 25323720
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Amycolatopsis lurida NRRL 2430, Producer of the Glycopeptide Family Antibiotic Ristocetin.
PG  - e01050-14
AB  - We report here the first draft genome sequence for Amycolatopsis lurida NRRL 2430, the
      producer of the glycopeptide antibiotic ristocetin. The 9-Mbp genome is
      predicted to harbor 8,143 genes, including those belonging to the ristocetin
      biosynthesis cluster and 31 additional predicted secondary metabolite gene
      clusters.
AU  - Kwun MJ
AU  - Hong HJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01050-14.

PMID- 25081262
VI  - 2
DP  - 2014
TI  - Genome Sequence of Streptomyces toyocaensis NRRL 15009, Producer of the Glycopeptide Antibiotic A47934.
PG  - e00749-14
AB  - Here we report the draft genome sequence of Streptomyces toyocaensis strain NRRL  15009 which
      is the producer of the glycopeptide antibiotic A47934. The genome
      sequence is predicted to harbor a total of 26 secondary metabolite biosynthetic
      gene clusters including the A47934 cluster.
AU  - Kwun MJ
AU  - Hong HJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00749-14.

PMID- 22328665
VI  - 194
DP  - 2012
TI  - Escherichia coli Serotype O55:H7 Diversity Supports Parallel Acquisition of Bacteriophage at Shiga Toxin Phage Insertion Sites during Evolution of the O157:H7 Lineage.
PG  - 1885-1896
AB  - Enteropathogenic Escherichia coli (EPEC) continues to be a leading cause of
      mortality and morbidity in children around the world. Two EPEC genomes have been
      fully sequenced: those of EPEC O127:H6 strain E2348/69 (United Kingdom, 1969) and
      EPEC O55:H7 strain CB9615 (Germany, 2003). The O55:H7 serotype is a recent
      precursor to the virulent enterohemorrhagic E. coli O157:H7. To explore the
      diversity of O55:H7 and better understand the clonal evolution of O157:H7, we
      fully sequenced EPEC O55:H7 strain RM12579 (California, 1974), which was
      collected 1 year before the first U.S. isolate of O157:H7 was identified in
      California. Phage-related sequences accounted for nearly all differences between
      the two O55:H7 strains. Additionally, O55:H7 and O157:H7 strains were tested for
      the presence and insertion sites of Shiga toxin gene (stx)-containing
      bacteriophages. Analysis of non-phage-associated genes supported core elements of
      previous O157:H7 stepwise evolutionary models, whereas phage composition and
      insertion analyses suggested a key refinement. Specifically, the placement and
      presence of lambda-like bacteriophages (including those containing stx) should
      not be considered stable evolutionary markers or be required in placing O55:H7
      and O157:H7 strains within the stepwise evolutionary models. Additionally, we
      suggest that a 10.9-kb region (block 172) previously believed unique to O55:H7
      strains can be used to identify early O157:H7 strains. Finally, we defined two
      subsets of O55:H7 strains that share an as-yet-unobserved or extinct common
      ancestor with O157:H7 strains. Exploration of O55:H7 diversity improved our
      understanding of the evolution of E. coli O157:H7 and suggested a key revision to
      accommodate existing and future configurations of stx-containing bacteriophages
      into current models.
AU  - Kyle JL
AU  - Cummings CA
AU  - Parker CT
AU  - Quinones B
AU  - Vatta P
AU  - Newton E
AU  - Huynh S
AU  - Swimley M
AU  - Degoricija L
AU  - Barker M
AU  - Fontanoz S
AU  - Nguyen K
AU  - Patel R
AU  - Fang R
AU  - Tebbs R
AU  - Petrauskene O
AU  - Furtado M
AU  - Mandrell RE
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1885-1896.

PMID- 22403614
VI  - 7
DP  - 2012
TI  - The Highly Virulent 2006 Norwegian EHEC O103:H25 Outbreak Strain Is Related to the 2011 German O104:H4 Outbreak Strain.
PG  - E31413
AB  - In 2006, a severe foodborne EHEC outbreak occured in Norway. Seventeen cases were
      recorded and the HUS frequency was 60%. The causative strain, Esherichia coli
      O103:H25, is considered to be particularly virulent. Sequencing of the outbreak
      strain revealed resemblance to the 2011 German outbreak strain E. coli O104:H4,
      both in genome and Shiga toxin 2-encoding (Stx2) phage sequence. The nucleotide
      identity between the Stx2 phages from the Norwegian and German outbreak strains
      was 90%. During the 2006 outbreak, stx(2)-positive O103:H25 E. coli was isolated
      from two patients. All the other outbreak associated isolates, including all food
      isolates, were stx-negative, and carried a different phage replacing the Stx2
      phage. This phage was of similar size to the Stx2 phage, but had a distinctive
      early phage region and no stx gene. The sequence of the early region of this
      phage was not retrieved from the bacterial host genome, and the origin of the
      phage is unknown. The contaminated food most likely contained a mixture of E.
      coli O103:H25 cells with either one of the phages.
AU  - L'abee-Lund TM
AU  - Jorgensen HJ
AU  - O'Sullivan K
AU  - Bohlin J
AU  - Ligard G
AU  - Granum PE
AU  - Lindback T
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2012 7: E31413.

PMID- 29348351
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of the Halophilic Methylotrophic Methanogen Archaeon Methanohalophilus portucalensis Strain FDF-1(T).
PG  - e01482-17
AB  - We report here the complete genome sequence (2.08 Mb) of Methanohalophilus portucalensis
      strain FDF-1(T), a halophilic methylotrophic methanogen isolated
      from the sediment of a saltern in Figeria da Foz, Portugal. The average
      nucleotide identity and DNA-DNA hybridization analyses show that
      Methanohalophilus mahii, M. halophilus, and M. portucalensis are three different
      species within the Methanosarcinaceae family.
AU  - L'Haridon S
AU  - Corre E
AU  - Guan Y
AU  - Vinu M
AU  - La Cono V
AU  - Yakimov M
AU  - Stingl U
AU  - Toffin L
AU  - Jebbar M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01482-17.

PMID- 28209822
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Methanohalophilus halophilus DSM 3094T, Isolated from a Cyanobacterial Mat and Bottom Deposits at Hamelin Pool, Shark Bay, Northwestern  Australia.
PG  - e01604-16
AB  - The complete genome sequence of Methanohalophilus halophilus DSM 3094T, a member  of the
      Methanosarcinaceae family and the Methanosarcianales order, consists of
      2,022,959 bp in one contig and contains 2,137 predicted genes. The genome is
      consistent with a halophilic methylotrophic anaerobic lifestyle, including the
      methylotrophic and CO2-H2 methanogensis pathways.
AU  - L'Haridon S
AU  - Corre E
AU  - Guan Y
AU  - Vinu M
AU  - La Cono V
AU  - Yakimov M
AU  - Stingl U
AU  - Toffin L
AU  - Jebbar M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01604-16.

PMID- 27081128
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Clostridium sporogenes Strain UC9000 Isolated from Raw Milk.
PG  - e00244-16
AB  - Clostridium sporogenesis a causative agent of food spoilage and is often used as  the
      nontoxigenic surrogate forClostridium botulinum Here, we described the draft
      genome sequence and annotation ofC. sporogenesstrain UC9000 isolated from raw
      milk.
AU  - La Torre A
AU  - Bassi D
AU  - Zotta T
AU  - Orru L
AU  - Lamontanara A
AU  - Cocconcelli PS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00244-16.

PMID- 7959052
VI  - 150
DP  - 1994
TI  - The response of M.HpaII to heteroduplexes.
PG  - 195-196
AB  - Synthetic oligodeoxyribonucleotide duplexes have been used to study the methylation
      specificity of M.HpaII, a bacterial DNA methyltransferase. Substrates of four types were
      compared. A 30-mer containing a Watson-Crick paired CCGG recognition sequence was rapidly
      methylated at the central cytosine on each strand in the recognition sequence. A 30-mer
      containing an asymmetrically methylated recognition sequence, of the type transiently produced
      by DNA replication, was rapidly methylated at the central cytosine on the unmethylated strand.
      A heteroduplex containing an A.C mispair in the recognition sequence (CCGG/CCAG) was rapidly
      methylated at the cytosine in the mispair. A heteroduplex containing an A.C and an adjacent
      C.C mispair in the recognition sequence (CCGG/CCCA) was not methylated at a significant rate.
      The results show that M.HpaII can tolerate a single mispair at its recognition site in a
      heteroduplex without loss of activity or specificity.
AU  - Laayoun A
AU  - Baker DJ
AU  - Riley J
AU  - Smith SS
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1994 150: 195-196.

PMID- 7784214
VI  - 23
DP  - 1995
TI  - Methylation of slipped duplexes, snapbacks and cruciforms by human DNA(cytosine-5)methyltransferase.
PG  - 1584-1589
AB  - When human DNA(cytosine-5)methyltransferase was used to methylate a series of snapback
      oligodeoxynucleotides of differing stem lengths, each containing a centrally located CG
      dinucleotide recognition site, the enzyme required a minimum of 22 base pairs in the stem for
      maximum activity. Extrahelical cytosines in slipped duplexes that were 30 base pairs in length
      acted as effective methyl acceptors and were more rapidly methylated than cytosines that were
      Watson-Crick paired. Duplexes containing hairpins of CCG repeats in cruciform structures in
      which the enzyme recognition sequence was disrupted by a C.C mispair were also more rapidly
      methylated than control Watson-Crick-paired duplexes. Since enzymes have higher affinities for
      their transition states than for their substrates, the results with extrahelical and mispaired
      cytosines suggest that these structures can be viewed as analogs of the transition state
      intermediates produced during catalysis by methyltransferases.
AU  - Laayoun A
AU  - Smith SS
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1995 23: 1584-1589.

PMID- 7971991
VI  - 91
DP  - 1994
TI  - Three-dimensional structure of the adenine-specific DNA methyltransferase M.TaqI in complex with the cofactor S-adenosylmethionine.
PG  - 10957-10961
AB  - The Thermus aquaticus DNA methyltransferase M.TaqI (EC 2.1.1.72) methylates N6 of adenine in
      the specific double-helical DNA sequence TCGA by transfer of -CH3 from the cofactor
      S-adenosyl-L-methionine. The x-ray crystal structure at 2.4 Angstrom resolution of this enzyme
      in complex with S-adenosylmethionine shows alpha/beta folding of the polypeptide into two
      domains of about equal size. They are arranged in the form of a C with a wide cleft suitable
      to accommodate the DNA substrate. The N-terminal domain is dominated by a nine-stranded
      beta-sheet; it contains the two conserved segments typical for N-methyltranferases which form
      a pocket for cofactor binding. The C-terminal domain is formed by four small beta-sheets and
      alpha-helices. The three-dimensional folding of M.TaqI is similar to that of the
      cytosine-specific HhaI methyltransferase, where the large Beta-sheet in the N-terminal domain
      contains all conserved segments and the enzymatically functional parts, and the smaller
      C-terminal domain is less structured.
AU  - Labahn J
AU  - Granzin J
AU  - Schluckebier G
AU  - Robinson DP
AU  - Jack WE
AU  - Schildkraut I
AU  - Saenger W
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1994 91: 10957-10961.

PMID- 2277628
VI  - 224
DP  - 1990
TI  - Cloning and characterization of two tandemly arranged DNA methyltransferase genes of Neisseria lactamica: An adenine-specific M.NlaIII and a cytosine-type methylase.
PG  - 101-110
AB  - The gene encoding the Neisseria lactamica III DNA methyltransferase (M.NlaIII) which
      recognizes the sequence CATG has been cloned and expressed in Escherichia coli. DNA sequencing
      of a 3.125 kb EcoRI-PstI fragment localizes the M.NlaIII gene to a 334 codon open reading
      frame (ORF) and identifies, 468 bp downstream, a second ORF of 313 amino acids, which is
      referred to as M.NlaX. Both proteins are detectable in the E. coli coupled in vitro
      transcription-translation system; they are apparently expressed from separate N. lactamica
      promoters. The N-terminal half of the previously characterized M.FokI, which methylates
      adenine in one of the DNA strands with its asymmetric recognition sequence (GGATG), is found
      to have 41% sequence identity and a further 11.7% sequence similarity with M.NlaIII. Among the
      conserved amino acids is the well known DPPY sequence motif. With one exception, analysis of
      the nucleotides coding for the DP dipeptide in all known DPPY sequences shows the presence of
      an inherent DNA adenine methylation (dam) recognition site of GATC. A low level of expression
      of M.NlaX in E. coli prevents the elucidation of its sequence recognition specificity.
      Sequence analysis of M.NlaX shows that it is closely related to the group of monospecific
      5-methylcytosine DNA methyltransferases (M.EcoRII, Dcm, M.HpaII and M.HhaI) which all have a
      modified cytosine at the second position of the recognition sequences. Both M.EcoRII and Dcm
      amino acid sequences are about 50% identical with M.NlaX; a considerable degree of sequence
      identity is found in the so-called variable region which is believed to be responsible for
      sequence recognition specificity. M.NlaX is probably the counterpart to the E. coli Dcm in N.
      lactamica.
AU  - Labbe D
AU  - Holtke HJ
AU  - Lau PCK
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1990 224: 101-110.

PMID- 26769926
VI  - 4
DP  - 2016
TI  - Complete Genome and Plasmid Sequences of Three Canadian Isolates of Salmonella enterica subsp. enterica Serovar Heidelberg from Human and Food Sources.
PG  - e01526-15
AB  - Isolates of Salmonella enterica subsp. enterica serovar Heidelberg are often associated with
      poultry products and may cause severe human illness. Here, we
      report the fully assembled genome and plasmid sequences of three S. Heidelberg
      strains with phage types 9, 29, and 41.
AU  - Labbe G
AU  - Edirmanasinghe R
AU  - Ziebell K
AU  - Nash JH
AU  - Bekal S
AU  - Parmley EJ
AU  - Mulvey MR
AU  - Johnson RP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01526-15.

PMID- 27635008
VI  - 4
DP  - 2016
TI  - Complete Genome Sequences of 17 Canadian Isolates of Salmonella enterica subsp. enterica Serovar Heidelberg from Human, Animal, and Food Sources.
PG  - e00990-16
AB  - Salmonella enterica subsp. enterica serovar Heidelberg is a highly clonal serovar frequently
      associated with foodborne illness. To facilitate subtyping efforts, we
      report fully assembled genome sequences of 17 Canadian S Heidelberg isolates
      including six pairs of epidemiologically related strains. The plasmid sequences
      of eight isolates contain several drug resistance genes.
AU  - Labbe G
AU  - Ziebell K
AU  - Bekal S
AU  - Macdonald KA
AU  - Parmley EJ
AU  - Agunos A
AU  - Desruisseau A
AU  - Daignault D
AU  - Slavic D
AU  - Hoang L
AU  - Ramsay D
AU  - Pollari F
AU  - Robertson J
AU  - Nash JH
AU  - Johnson RP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00990-16.

PMID- 2841649
VI  - 16
DP  - 1988
TI  - BspMII and AccIII are an isoschizomer pair which differ in their sensitivity to cytosine methylation.
PG  - 7184
AB  - The latest tabulation of restriction endonuclease sensitivities to
      site-specific DNA methylation has shown that BspMII is able to cut the
      methylated sequence TCCGGmA while AccIII is not.  We found that cellular DNA
      from Acinetobacter calcoaceticus showed complete resistance to the action of
      restriction endonuclease AccIII but sensitivity to the action of restriction
      endonuclease BspMII, an isoschizomer of AccIII (results not shown).  This
      experiment indicates that the methylation sensitivity of restriction enzymes
      AccIII and BspMII are not the same.  We then tested both enzymes (AccIII and
      BspMII) for sensitivity to cytosine methylation within their recognition sites
      by using M.MspI (mCCGG) and M.HpaII (CmCGG) methylases on various DNA
      substrates.  Adenovirus 2 DNA was used for this experiment (Fig. 1) and
      additional tests were done with lambda DNA and pLQ61 DNA (which has 2 AccIII
      sites and is derived from pBR328) (results not shown).  We conclude that BspMII
      does not cleave the modified sequences TmCCGGA and TCmCGGA, and that
      restriction by AccIII is not affected by methylation of either cytosine in the
      same recognization sequence.  Thus, we suggest that the enzyme M.BspMII is a
      DNA-cytosine-methyltransferase while M.AccIII is a
      DNA-adenine-methyltransferase.
AU  - Labbe S
AU  - Xia Y
AU  - Roy PH
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1988 16: 7184.

PMID- Not carried by PubMed...
VI  - 53
DP  - 1993
TI  - Structure and function of DNA phosphotriester substrates of the restriction endonuclease AluI.
PG  - 2842
AB  - The duplex d(GGAAGCTAGG).d(CCTAGCTTCC) is a substrate for AluI, which cleaves at the center of
      the AGCT recognition sequence when magnesium ion is present. Large scale synthesis of the
      2,2,2-trichloro-1,1-dimethylethyl phosphotriester derivative d(GGAAGp(TCDME)CTAGG) was done
      using phosphite chemistry. The two diastereomers were separated on a large scale by HPLC. Both
      diastereomers formed a stable heteroduplex with a complementary unmodified strand in the
      hydrolysis buffer. Both modified duplexes bound to AluI with affinity similar to that of the
      natural duplex, as determined by gel shift assays. When incubated with AluI under identical
      conditions, one diastereomeric heteroduplex remained intact, while the other was hydrolyzed at
      G-C in the unmodified strand. No cleavage of the modified strand was observed in either case,
      nor was any hydrolysis detected when the single-stranded unmodified complement was treated.
      The configuration at the phosphotriester sites was assigned from 2D NMR spectral data.
      Resonance assignments for most nonexchangeable protons were made using DQF-COSY and NOESY.
      Most resonances fell within expected ranges; however the central dG H3' and dC H5'{5'}
      residues in the modified strands were shifted significantly downfield. The diastereomer
      exhibiting NOE cross-relaxation between the methyl protons in the TCDME modification and the
      C6 H6, C6 H4', C6 H5' H5{'}, G5 H3', and G5 H4' in the modified strand was assigned the
      Rp configuration. The diastereomer showing cross-relaxation between the methyl protons of the
      TCDME modification and the C6 H5'H5{'}, G5 H3', and G5 H4' in the modified strand was
      assigned the Sp configuration. This assignment agrees with one based on chemical degradation
      of the oligomers. The 3D structuers of the heteroduplexes were determined by integrating
      resolved NOE cross-peaks and converting the volumes into distances for each mixing time. The
      derived distances were applied to models and subjected to refinement. The refined structures
      correspond to B-form DNA but with distortions in the region of the modified site. The triester
      group of the Sp duplex projects out from the double helix into the aqueous environment,
      whereas that of the Rp isomer points into the major groove.
AU  - Labeots LA
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1993 53: 2842.

PMID- 25059859
VI  - 2
DP  - 2014
TI  - Genome Sequence of Bacillus safensis CFA06, Isolated from Biodegraded Petroleum in Brazil.
PG  - e00642-14
AB  - Bacillus safensis is a microorganism recognized for its biotechnological and industrial
      potential due to its interesting enzymatic portfolio. Here, as a means
      of gathering information about the importance of this species in oil
      biodegradation, we report a draft genome sequence of a strain isolated from
      petroleum.
AU  - Laborda PR
AU  - Fonseca FS
AU  - Angolini CF
AU  - Oliveira VM
AU  - Souza AP
AU  - Marsaioli AJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00642-14.

PMID- 27034482
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Seven Multidrug-Resistant Acinetobacter baumannii Strains, Isolated from Respiratory Samples in Spain.
PG  - e00083-16
AB  - The draft genome sequences of seven multidrug-resistantAcinetobacter baumanniiclinical strains
      belonging to sequence types ST-208 and ST-218 are
      reported in this study. They were isolated from tracheobronchial aspirate of
      mechanically ventilated adult patients admitted to the intensive care unit of a
      Spanish tertiary hospital during 2010 to 2011.
AU  - Labrador-Herrera G
AU  - Alvarez R
AU  - Lopez-Rojas R
AU  - Smani Y
AU  - Cebrero-Cangueiro T
AU  - Rueda A
AU  - Perez FJ
AU  - Pachon J
AU  - Pachon-Ibanez ME
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00083-16.

PMID- 25013142
VI  - 2
DP  - 2014
TI  - First Complete Genome Sequence of Staphylococcus xylosus, a Meat Starter Culture  and a Host to Propagate Staphylococcus aureus Phages.
PG  - e00671-14
AB  - Staphylococcus xylosus is a bacterial species used in meat fermentation and a commensal
      microorganism found on animals. We present the first complete circular
      genome from this species. The genome is composed of 2,757,557 bp, with a G+C
      content of 32.9%, and contains 2,514 genes and 79 structural RNAs.
AU  - Labrie SJ
AU  - El Haddad L
AU  - Tremblay DM
AU  - Plante PL
AU  - Wasserscheid J
AU  - Dumaresq J
AU  - Dewar K
AU  - Corbeil J
AU  - Moineau S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00671-14.

PMID- 20348932
VI  - 8
DP  - 2010
TI  - Bacteriophage resistance mechanisms.
PG  - 317-327
AB  - Phages are now acknowledged as the most abundant microorganisms on the planet and are also
      possibly the most diversified. This diversity is mostly driven by their dynamic adaptation
      when facing selective pressure such as phage resistance mechanisms, which are widespread in
      bacterial hosts. When infecting bacterial cells, phages face a range of antiviral mechanisms,
      and they have evolved multiple tactics to avoid, circumvent or subvert these mechanisms in
      order to thrive in most environments. In this Review, we highlight the most important
      antiviral mechanisms of bacteria as well as the counter-attacks used by phages to evade these
      systems.
AU  - Labrie SJ
AU  - Samson JE
AU  - Moineau S
PT  - Journal Article
TA  - Nat. Rev. Microbiol.
JT  - Nat. Rev. Microbiol.
SO  - Nat. Rev. Microbiol. 2010 8: 317-327.

PMID- 25999573
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Streptococcus thermophilus SMQ-301, a Model Strain for Phage-Host Interactions.
PG  - e00480-15
AB  - Streptococcus thermophilus is used by the dairy industry to manufacture yogurt and several
      cheeses. Using PacBio and Illumina platforms, we sequenced the genome
      of S. thermophilus SMQ-301, the host of several virulent phages. The genome is
      composed of 1,861,792 bp and contains 2,037 genes, 67 tRNAs, and 18 rRNAs.
AU  - Labrie SJ
AU  - Tremblay DM
AU  - Plante PL
AU  - Wasserscheid J
AU  - Dewar K
AU  - Corbeil J
AU  - Moineau S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00480-15.

PMID- 29122855
VI  - 5
DP  - 2017
TI  - Complete Annotated Genome Sequences of Four Klebsiella pneumoniae Phages Isolated from Sewage in Poland.
PG  - e00919-17
AB  - Four lytic phages, vB_KpnP_BIS33, vB_KpnP_IL33, and vB_KpnP_PRA33 of the Podoviridae family
      and vB_KpnM_BIS47 of the Myoviridae family, which act against
      animal-pathogenic Klebsiella pneumoniae strains, were isolated from sewage plants
      in Poland. They possess double-stranded DNA genomes of 41,697 bp, 41,335 bp,
      40,605 bp, and 147,443 bp, respectively.
AU  - Labudda L
AU  - Strapagiel D
AU  - Karczewska-Golec J
AU  - Golec P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00919-17.

PMID- 21304652
VI  - 1
DP  - 2009
TI  - Complete genome sequence of Anaerococcus prevotii type strain (PC1).
PG  - 159-165
AB  - Anaerococcus prevotii (Foubert and Douglas 1948) Ezaki et al. 2001 is the type species of the
      genus, and is of phylogenetic interest because of its arguable
      assignment to the provisionally arranged family 'Peptostreptococcaceae'. A.
      prevotii is an obligate anaerobic coccus, usually arranged in clumps or tetrads.
      The strain, whose genome is described here, was originally isolated from human
      plasma; other strains of the species were also isolated from clinical specimen.
      Here we describe the features of this organism, together with the complete genome
      sequence and annotation. This is the first completed genome sequence of a member
      of the genus. Next to Finegoldia magna, A. prevotii is only the second species
      from the family 'Peptostreptococcaceae' for which a complete genome sequence is
      described. The 1,998,633 bp long genome (chromosome and one plasmid) with its
      1852 protein-coding and 61 RNA genes is a part of the Genomic Encyclopedia of
      Bacteria and Archaea project.
AU  - Labutti K et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2009 1: 159-165.

PMID- 21304695
VI  - 3
DP  - 2010
TI  - Permanent draft genome sequence of Dethiosulfovibrio peptidovorans type strain (SEBR 4207).
PG  - 85-92
AB  - Dethiosulfovibrio peptidovorans Magot et al. 1997 is the type species of the genus
      Dethiosulfovibrio of the family Synergistaceae in the recently created
      phylum Synergistetes. The strictly anaerobic, vibriod, thiosulfate-reducing
      bacterium utilizes peptides and amino acids, but neither sugars nor fatty acids.
      It was isolated from an offshore oil well where it was been reported to be
      involved in pitting corrosion of mild steel. Initially, this bacterium was
      described as a distant relative of the genus Thermoanaerobacter, but was not
      assigned to a genus, it was subsequently placed into the novel phylum
      Synergistetes. A large number of repeats in the genome sequence prevented an
      economically justifiable closure of the last gaps. This is only the third
      published genome from a member of the phylum Synergistetes. The 2,576,359 bp long
      genome consists of three contigs with 2,458 protein-coding and 59 RNA genes and
      is part of the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Labutti K et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 3: 85-92.

PMID- 21304691
VI  - 3
DP  - 2010
TI  - Complete genome sequence of Planctomyces limnophilus type strain (Mu 290).
PG  - 47-56
AB  - Planctomyces limnophilus Hirsch and Muller 1986 belongs to the order Planctomycetales, which
      differs from other bacterial taxa by several distinctive
      features such as internal cell compartmentalization, multiplication by forming
      buds directly from the spherical, ovoid or pear-shaped mother cell and a cell
      wall which is stabilized by a proteinaceous layer rather than a peptidoglycan
      layer. Besides Pirellula staleyi, this is the second completed genome sequence of
      the family Planctomycetaceae. P. limnophilus is of interest because it differs
      from Pirellula by the presence of a stalk and its structure of fibril bundles,
      its cell shape and size, the formation of multicellular rosettes, low salt
      tolerance and red pigmented colonies. The 5,460,085 bp long genome with its 4,304
      protein-coding and 66 RNA genes is a part of the Genomic Encyclopedia of Bacteria
      and Archaea project.
AU  - Labutti K et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 3: 47-56.

PMID- 25342686
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of the Oral Spirochete Bacterium Treponema putidum Strain OMZ 758T (ATCC 700334T).
PG  - e01076-14
AB  - The oral spirochete bacterium Treponema putidum inhabits human periodontal niches. The
      complete genome sequence of the OMZ 758(T) (ATCC 700334(T)) strain of
      this species was determined, revealing a 2,796,913-bp chromosome, with a G+C
      content of 37.30% and a single plasmid (pTPu1; 3,649 bp) identical to pTS1 from
      Treponema denticola.
AU  - Lacap-Bugler DC
AU  - Jiang J
AU  - Huo YB
AU  - Chan Y
AU  - Leung FC
AU  - Watt RM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01076-14.

PMID- 29788909
VI  - 19
DP  - 2018
TI  - Whole genome analysis reveals the diversity and evolutionary relationships between necrotic enteritis-causing strains of Clostridium perfringens.
PG  - 379
AB  - BACKGROUND: Clostridium perfringens causes a range of diseases in animals and
      humans including necrotic enteritis in chickens and food poisoning and gas
      gangrene in humans. Necrotic enteritis is of concern in commercial chicken
      production due to the cost of the implementation of infection control measures
      and to productivity losses. This study has focused on the genomic analysis of a
      range of chicken-derived C. perfringens isolates, from around the world and from
      different years. The genomes were sequenced and compared with 20 genomes
      available from public databases, which were from a diverse collection of isolates
      from chickens, other animals, and humans. We used a distance based phylogeny that
      was constructed based on gene content rather than sequence identity. Similarity
      between strains was defined as the number of genes that they have in common
      divided by their total number of genes. In this type of phylogenetic analysis,
      evolutionary distance can be interpreted in terms of evolutionary events such as
      acquisition and loss of genes, whereas the underlying properties (the gene
      content) can be interpreted in terms of function. We also compared these methods
      to the sequence-based phylogeny of the core genome. RESULTS: Distinct pathogenic
      clades of necrotic enteritis-causing C. perfringens were identified. They were
      characterised by variable regions encoded on the chromosome, with predicted roles
      in capsule production, adhesion, inhibition of related strains, phage
      integration, and metabolism. Some strains have almost identical genomes, even
      though they were isolated from different geographic regions at various times,
      while other highly distant genomes appear to result in similar outcomes with
      regard to virulence and pathogenesis. CONCLUSIONS: The high level of diversity in
      chicken isolates suggests there is no reliable factor that defines a chicken
      strain of C. perfringens, however, disease-causing strains can be defined by the
      presence of netB-encoding plasmids. This study reveals that horizontal gene
      transfer appears to play a significant role in genetic variation of the C.
      perfringens chromosome as well as the plasmid content within strains.
AU  - Lacey JA
AU  - Allnutt TR
AU  - Vezina B
AU  - Van TT
AU  - Stent T
AU  - Han X
AU  - Rood JI
AU  - Wade B
AU  - Keyburn AL
AU  - Seemann T
AU  - Chen H
AU  - Haring V
AU  - Johanesen PA
AU  - Lyras D
AU  - Moore RJ
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2018 19: 379.

PMID- 21131495
VI  - 193
DP  - 2010
TI  - Complete Genome Sequence of Burkholderia rhizoxinica, the Endosymbiont of Rhizopus microsporus.
PG  - 783-784
AB  - Burkholderia rhizoxinica is an intracellular symbiont of the phytopathogenic fungus Rhizopus
      microsporus. The vertically transmitted
      endosymbiont not only delivers the antimitotic macrolide rhizoxin to its
      host, but is also essential for vegetative spore formation of the fungus.
      To shed light on the genetic equipment of this model organism, we
      sequenced the whole genome of B. rhizoxinica HKI 0454, thus providing the
      first genomic insight into of an intracellular mutualist of a fungal
      species. The 3.75 Mb genome consists of a chromosome and two
      strain-specific plasmids. Primary metabolism appears to be specialized for
      the uptake of fungal metabolites. Besides the rhizoxin biosynthesis gene
      cluster, there are 14 loci coding for nonribosomal peptide synthetase
      (NRPS) assembly lines, which represent novel targets for genomic mining of
      cryptic natural products. Furthermore, the endosymbionts are equipped with
      a repertoire of virulence-related factors, which can now be studied to
      elucidate molecular mechanisms underlying bacterial-fungal interaction.
AU  - Lackner G
AU  - Moebius N
AU  - Partida-Martinez L
AU  - Hertweck C
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 193: 783-784.

PMID- 236309
VI  - 250
DP  - 1975
TI  - A deoxyribonuclease of Diplococcus pneumoniae specific for methylated DNA.
PG  - 4060-4066
AB  - A deoxyribonuclease specific for methylated DNA was isolated from Diplococcus
      pneumoniae.  The enzyme, an endonuclease, degrades DNA from Escherichia coli to
      fragments of average molecular weight about half a million; it forms discrete
      fragments from phage lambda DNA.  Methyl-deficient E. coli DNA is not attacked,
      neither is DNA from Micrococcus radiodurans, which contains no methylated
      adenine or cytosine.  Nor is DNA from D. pneumoniae or phage T7 attacked.
      However, DNA from M. radiodurans, D. pneumoniae, and T7 is attacked after
      methylation with an E. coli extract.  Methylated T7 DNA is degraded to discrete
      fragments.  Although the genetic transforming activity of normal DNA from D.
      pneumoniae is not affected by the enzyme, transforming activity of methylated
      DNA is destroyed.  The enzyme is designated endonuclease R.DpnI.  Under certain
      conditions another enzyme of complementary specificity can be isolated.  This
      enzyme, designated endonuclease R.DpnII, produces a similar pattern of
      fragments from the DNA of T7 without prior methylation of the DNA.  It also
      degrades normal DNA from D. pneumoniae.  It is suggested that this pair of
      enzymes plays a role in some unknown control process, which would involve a
      large fraction of the specific base sequences that are methylated in E. coli
      DNA and are present but not methylated in DNA from other sources.
AU  - Lacks S
AU  - Greenberg B
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1975 250: 4060-4066.

PMID- 20509
VI  - 114
DP  - 1977
TI  - Complementary specificity of restriction endonucleases of Diplococcus pneumoniae with respect to DNA methylation.
PG  - 153-168
AB  - Restriction endonucleases DpnI and DpnII are produced by two distinct strains of Diplococcus
      pneumoniae. The two enzymes show complementary specificity with respect to methylation of
      sites in DNA. From the identity of its cleavage site with that of MboI, it appears that DpnII
      cleaves at the unmodified sequence 5'-G-A-T-C-3'. DpnI cleaves at the same sequence when the
      adenine residue is methylated. Both enzymes produce only double-stranded breaks in susceptible
      DNA. Their susceptibility to DpnI and not DpnII shows that essentially all the G-A-T-C
      sequences are methylated in DNA from the pneumococcal strain that produces DpnII as well as in
      DNA from Hemophilus influenzae and Escherichia coli. In the dam-3 mutant of E. coli none of
      these sequences appear to be methylated. Residual adenine methylation in the dam-3 mutant DNA
      most likely occurs at different sites. Different but characteristic degrees of methylation at
      G-A-T-C sites are found in the DNA of bacterial viruses grown in E. coli. DNAs from mammalian
      cells and viruses are not methylated at this sequence. Mitochondrial DNA from Paramecium
      aurelia is not methylated, but a small proportion of G-A-T-C sequences in the macronuclear DNA
      of this eukaryote appear to be methylated. Possible roles of sequence-specific methylation in
      the accommodation of plasmids, in the replication of DNA, in the regulation of gene function
      and in the restriction of viral infection are discussed.
AU  - Lacks S
AU  - Greenberg B
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1977 114: 153-168.

PMID- 366
VI  - 124
DP  - 1975
TI  - Membrane location of a deoxyribonuclease implicated in the genetic transformation of Diplococcus pneumoniae.
PG  - 1321-1329
AB  - The cellular localization of enzymes in Diplococcus pneumoniae was examined by
      fractionation of spheroplasts.  A deoxyribonuclease implicated in the entry of
      deoxyribonucleic acid (DNA) into the cell during genetic transformation was
      located in the cell membrane.  This enzyme, the major endonuclease of the cell
      (endonuclease I), which is necessary for the conversion of donor DNA to single
      strands inside the cell and oligonucleotides outside, thus could act at the
      cell surface.  Another enzyme, the cell wall lysin (autolysin), was also found
      in the membrane fraction.  Other enzymes, including amylomaltase, two
      exonucleases, an adenosine triphosphate-dependent deoxyribonuclease, and a
      restriction type endonuclease, were predominantly periplasmic in location.
      Spheroplasts were obtained spontaneously on incubation of pneumococcal cells in
      concentrated sugar solutions.  The autolytic enzyme appears to be involved in
      this process.  Cells that were physiologically competent to take up DNA formed
      osmotically sensitive spheroplasts two to three times faster than cells that
      were not in the competent state.  Although some genetically incompetent mutants
      also formed spheroplasts more slowly, other such mutants formed them at the
      faster rate.
AU  - Lacks S
AU  - Neuberger M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1975 124: 1321-1329.

PMID- 6246334
VI  - 65
DP  - 1980
TI  - Purification and properties of the complementary endonucleases DpnI and DpnII.
PG  - 138-146
AB  - None
AU  - Lacks SA
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1980 65: 138-146.

PMID- 10712690
VI  - 35
DP  - 2000
TI  - Regulation of competence for genetic transformation in Streptococcus pneumoniae: expression of dpnA, a late competence gene encoding a DNA methyltransferase of the DpnII restriction system.
PG  - 1089-1098
AB  - The chromosomal DpnII gene cassette of Streptococcus pneumoniae encodes two methyltransferases
      and an endonuclease. One methyltransferase acts on double-stranded and the other on
      single-stranded DNA. Two mRNAs are transcribed from the cassette. One, a SigA promoter
      transcript, includes all three genes; the other includes a truncated form of the second
      methyltransferase gene (dpnA) and the endonuclease gene. The truncated dpnA, which is
      translated from the second start codon in the full gene, was shown to produce active enzyme. A
      promoter reporter plasmid for S. pneumoniae was devised to characterize the promoter for the
      second mRNA. This transcript was found to depend on a promoter that responded to the induction
      of competence for genetic transformation. The promoter contains the combox sequence recognized
      by a SigH-containing RNA polymerase. As part of the competence regulon, the dpnA gene makes a
      product able to methylate incoming plasmid strands to protect them from the endonuclease and
      allow plasmid establishment. Its function differs from most genes in the regulon, which are
      involved in DNA uptake. Comparison of R6 and Rx strains of S. pneumoniae showed the
      temperature dependence of transformation in R6 to result from temperature sensitivity of the
      uptake apparatus and not the development of competence.
AU  - Lacks SA
AU  - Ayalew S
AU  - de la Campa AG
AU  - Greenberg B
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2000 35: 1089-1098.

PMID- 6297760
VI  - 31
DP  - 1982
TI  - Identification of base mismatches recognized by the heteroduplex-DNA-repair system of Streptococcus pneumoniae.
PG  - 327-336
AB  - The susceptibility to repair of particular base mismatches by the hex system of
      Streptococcus pneumoniae was examined by comparison of the nucleotide sequence
      of the wild-type and eight mutant alleles of the malM gene.  A detailed
      restriction map was constructed for pLS70, and the nucleotide sequence was
      determined for its 3475 bp chromosomal insert, which contains the entire malM
      gene (encoding amylomaltase), portions of malX and malP (encoding a membrane
      protein and a phosphorylase, respectively) and a control region.  Transition
      mismatches were highly susceptible to repair; transversion mismatches, much
      less so.  A mismatch caused by a single-nucleotide deletion was reparable, but
      mismatches with longer deletions were not.  The hex system also reduced
      spontaneous reversion of mutations corresponding to transitions.  It is
      suggested that recognition of donor or nascent DNA strands by the hex system
      depends on single-strand breaks in the target strand, and that the role of DNA
      methylation in mismatch repair of Escherichia coli can be accommodated to this
      model.
AU  - Lacks SA
AU  - Dunn JJ
AU  - Greenberg B
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1982 31: 327-336.

PMID- 8467964
VI  - 7
DP  - 1993
TI  - Atypical ribosome binding sites and regulation of gene expression in the DpnII restriction enzyme system of S. pneumoniae.
PG  - A1082
AB  - Strains of Streptococcus pneumoniae express either the DpnI or DpnII restriction systems,
      which are complementary in that DpnI cleaves methylated GATC sites, whereas DpnII cleaves
      unmethylated GATC. The genes for each system are contained in a cassette located at one
      particular position in the chromosome. The DpnII cassette contains three genes in an operon
      that specifies two methylases, DpnM and DpnA, and the DpnII endonuclease. Translation of DpnM
      and DpnA appears to depend on atypical ribosome binding sites, containing 5'-ATTTC-(5 or
      6n)-TATA-3' sequences located upstream of the start codon, rather than Shine-Dalgarno
      sequences. Changes within this atypical sequence, but not outside it, block translation.
      Proteins appear to be synthesized from atypical sites equally well in S. pneumoniae and E.
      coli. The atypical sequence, also, is complementary to an unpaired region of 16S rRNA. These
      unusual ribosome binding sites may play a role in the selective translation of methylases
      prior to the endonuclease when the DpnII cassette is introduced into a cell.
AU  - Lacks SA
AU  - Greenberg B
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1993 7: A1082.

PMID- 7541761
VI  - 157
DP  - 1995
TI  - Possible regulation of DNA methyltransferase expression by RNA processing in Streptococcus pneumoniae.
PG  - 209-212
AB  - Atypical ribosome-binding sites lacking Shine-Dalgarno sequences appear to be used for
      translation of the DpnM and DpnA DNA methyltransferases of the DpnII restriction system.
      Preliminary results indicate that the 5'-endpoints of DpnII system mRNAs result from
      degradation of the original transcript.  These tentative findings serve as the basis for a
      possible regulatory model that would accommodate the DpnII cassette either as a single copy in
      the chromosome or on a multicopy plasmid.
AU  - Lacks SA
AU  - Greenberg B
AU  - Sabelnikov AG
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 209-212.

PMID- 3019562
VI  - 46
DP  - 1986
TI  - Genetic basis of the complementary DpnI and DpnII restriction systems of S. pneumoniae:  An intercellular cassette mechanism.
PG  - 993-1000
AB  - Cells of S. pneumoniae contain either DpnI, a restriction endonuclease that
      cleaves only the methylated DNA sequence 5'-GmeATC-3', or DpnII, which cleaves
      the same sequence when not methylated.  A chromosomal DNA segment containing
      DpnII genes was cloned in S. pneumoniae.  Nucleotide sequencing of this segment
      revealed genes encoding the methylase and endonuclease and a third protein of
      unknown function.  When the plasmid was introduced into DpnI cells,
      recombination during chromosomal facilitation of its establishment substituted
      genes encoding the DpnI endonuclease and another protein in place of the DpnII
      genes.  DNA hybridization and sequencing showed that the DpnI and DpnII
      segments share homology on either side but not between themselves or with other
      regions of the chromosome.  Thus, the complementary restriction systems are
      found on nonhomologous and mutally exclusive cassettes that can be inserted
      into a particular point in the chromosome of S. pneumoniae on the basis of
      neighboring homology.
AU  - Lacks SA
AU  - Mannarelli BM
AU  - Springhorn SS
AU  - Greenberg B
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1986 46: 993-1000.

PMID- 
VI  - 0
DP  - 1987
TI  - Genetics of the complementary restriction systems DpnI and DpnII revealed by cloning and recombination in Streptococcus pneumoniae.
PG  - 31-41
AB  - Restriction enzymes, because they are able to recognize and cleave specific
      sequences in DNA, have had an enormous impact on genetic analysis and
      engineering.  This review is concerned with some unusual restriction enzyme
      systems found in Streptococcus pneumonia.
AU  - Lacks SA
AU  - Mannarelli BM
AU  - Springhorn SS
AU  - Greenberg B
AU  - de la Campa A
PT  - Journal Article
TA  - Streptococcal Genetics
JT  - Streptococcal Genetics
SO  - Streptococcal Genetics 1987 0: 31-41.

PMID- 
VI  - 0
DP  - 1993
TI  - Gene expression in the DpnI and DpnII restriction enzyme systems of Streptococcus pneumoniae.
PG  - 169-178
AB  - Although a number of bacterial species are naturally transformable, that is, their cells are
      able to take up external DNA in substantial amounts and integrate it into the chromosome
      without artificial manipulation of the cell surface, Streptococcus pneumoniae, the first
      species in which this phenomenon was detected, remains a prototype of such transformation.
      This is partly because these bacteria do not appear to use other forms of genetic exchange for
      transfer of chromosomal genes, such as conjugation and transduction, but rely solely on
      DNA-mediated transformation.  Cells of S. pneumoniae also contain potent restriction
      endonucleases able to severely restrict DNA introduced during viral infection.  Therefore, it
      should be interesting to examine the effects of the restriction enzyme systems on transforming
      DNA.  Our current understanding of the genetic basis of the complementary DpnI and DpnII
      restriction systems and of the biochemistry of their component enzymes will be briefly
      reviewed.  The manner in which these enzymes impinge on the transfer of chromosomal genes and
      of plasmids will be examined in detail.  It will be seen that far from acting against
      "foreign" DNA in general, the restriction systems seem to be designed to exclude only
      infecting viral DNA.  The presence of complementary restriction systems in different cells of
      S. pneumoniae enhances their effectiveness in blocking viral infection and promoting species
      survival.  This enhanced effectiveness requires the expression of alternative restriction
      systems.  Therefore, the ability of the cells to transfer the restriction enzyme genes and to
      regulate their expression are important for survival of the species.  The final part of this
      paper will present currently available information on this topic.  In particular, the
      localization of the restriction genes in cassettes, their transcription products, and the role
      of a possibly new class of ribosome binding sites will be examined in relation to the
      regulation of restriction gene expression.
AU  - Lacks SA
AU  - Sabelnikov AG
AU  - Chen J-D
AU  - Greenberg B
PT  - Journal Article
TA  - DNA Transfer and Gene Expression in Microorganisms
JT  - DNA Transfer and Gene Expression in Microorganisms
SO  - DNA Transfer and Gene Expression in Microorganisms 1993 0: 169-178.

PMID- 6327647
VI  - 158
DP  - 1984
TI  - Transfer of recombinant plasmids containing the gene for DpnII DNA methylase into strains of Streptococcus pneumoniae that produce DpnI or DpnII restriction endonucleases.
PG  - 905-909
AB  - Plasmid transfer via the transformation pathway of Streptococcus pneumoniae was
      weakly restricted by the DpnI or DpnII restriction endonuclease, either of
      which gave a reduction only to 0.4, compared with phage infection, which was
      restricted to 10^-5.  The greater sensitivity of plasmid transfer compared with
      chromosomal transformation, which was not at all restricted, can be attributed
      to partially double-stranded intermediates formed from two complementary donor
      fragments.  However, clustering of potential restriction sites in the plasmids
      increased the probability of escape from restriction.  The recombinant plasmid
      pMP10, in which the gene for the DpnII DNA methylase was cloned, can be
      transferred to strains that contain neither restriction enzyme or that contain
      DpnII as readily as can the vector pMP5.  Introduction of pMP10 raised the
      level of methylase by five times the level normally present in DpnII strains.
      Transfer of pMP10 to DpnI-containing strains was infrequent, presumably owing
      to the suicidal methylation of DNA which rendered it susceptible to the host
      endonuclease.  The few clones in which pMP10 was established had lost DpnI.
      Loss of the plasmid after curing of the cell eliminated the methylase but did
      not restore DpnI.  Although this loss of DpnI could result from spontaneous
      mutation, its relatively high frequency, 0.1% suggested that the loss was due
      to a regulatory shift.
AU  - Lacks SA
AU  - Springhorn SS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1984 158: 905-909.

PMID- 6321445
VI  - 157
DP  - 1984
TI  - Cloning in Streptococcus pneumoniae of the gene for DpnII DNA methylase.
PG  - 934-936
AB  - The gene coding for the pneumococcal DNA adenine methylase that recognizes the
      sequence 5'-GATC-3' was cloned in a strain of Streptococcus pneumoniae that
      lacked both restriction endonucleases DpnI and DpnII.  The gene was cloned as a
      3.7-kilobase fragment of chromosomal DNA from a DpnII-containing strain
      inserted in both possible orientations in the multicopy plasmid vector pMP5 to
      give recombinant plasmids pMP8 and pMP10.  Recombinant plasmids were selected
      by their resistance to DpnII cleavage.  Cells carrying the recombinant plasmids
      modified phage in vivo so that it was restricted by DpnI-but not
      DpnII-containing hosts.  They also showed levels of DNA methylase activity five
      times higher than that in cells of the original DpnII strain.  No DpnII
      activity was observed in the clones; therefore, it was concluded that the
      insert did not contain an intact DpnII endonuclease gene and that methylation
      of host DNA did not turn on a latent form of the gene.
AU  - Lacks SA
AU  - Springhorn SS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1984 157: 934-936.

PMID- 
VI  - 8
DP  - 1991
TI  - Restriction/Modification systems of Pneumococci:  Why two methylases in the DpnII system?
PG  - 71-76
AB  - None
AU  - Lacks SA
AU  - Springhorn SS
AU  - Cerritelli S
PT  - Journal Article
TA  - Genetics and Molecular Biology of Streptococci, Lactococci, and Enterococci
JT  - Genetics and Molecular Biology of Streptococci, Lactococci, and Enterococci
SO  - Genetics and Molecular Biology of Streptococci, Lactococci, and Enterococci 1991 8: 71-76.

PMID- 23887921
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Lactobacillus plantarum Strain IPLA 88.
PG  - e00524-13
AB  - Here, we report a 3.2-Mbp draft assembly for the genome of Lactobacillus plantarum IPLA 88.
      The sequence of this sourdough isolate provides insight into
      the adaptation of this versatile species to different environments.
AU  - Ladero V
AU  - Alvarez-Sieiro P
AU  - Redruello B
AU  - Del Rio B
AU  - Linares DM
AU  - Martin MC
AU  - Fernandez M
AU  - Alvarez MA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00524-13.

PMID- 26089428
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Putrescine-Producing Strain Lactococcus lactis subsp. lactis 1AA59.
PG  - e00669-15
AB  - We report here the 2,576,542-bp genome annotated draft assembly sequence of Lactococcus lactis
      subsp. lactis 1AA59. This strain-isolated from a traditional
      cheese-produces putrescine, one of the most frequently biogenic amines found in
      dairy products.
AU  - Ladero V
AU  - Del Rio B
AU  - Linares DM
AU  - Fernandez M
AU  - Mayo B
AU  - Martin MC
AU  - Alvarez MA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00669-15.

PMID- 25342694
VI  - 2
DP  - 2014
TI  - Genome Sequence Analysis of the Biogenic Amine-Producing Strain Lactococcus lactis subsp. cremoris CECT 8666 (Formerly GE2-14).
PG  - e01088-14
AB  - We here report a 2,801,031-bp annotated draft assembly for the Lactococcus lactis subsp.
      cremoris GE2-14 genome. This dairy strain produces the biogenic amine
      putrescine. This sequence may help identify the mechanisms regulating putrescine
      biosynthesis and throw light on ways to reduce its presence in fermented foods.
AU  - Ladero V
AU  - Del Rio B
AU  - Linares DM
AU  - Fernandez M
AU  - Mayo B
AU  - Martin MC
AU  - Alvarez MA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01088-14.

PMID- 24435875
VI  - 2
DP  - 2014
TI  - Genome Sequence Analysis of the Biogenic Amine-Degrading Strain Lactobacillus casei 5b.
PG  - e01199-13
AB  - We here report a 3.02-Mbp annotated draft assembly of the Lactobacillus casei 5b  genome. The
      sequence of this biogenic amine-degrading dairy isolate may help
      identify the mechanisms involved in the catabolism of biogenic amines and perhaps
      shed light on ways to reduce the presence of these toxic compounds in food.
AU  - Ladero V
AU  - Herrero-Fresno A
AU  - Martinez N
AU  - Del Rio B
AU  - Linares DM
AU  - Fernandez M
AU  - Martin MC
AU  - Alvarez MA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01199-13.

PMID- 23682153
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Tyramine Producer Enterococcus durans Strain IPLA 655.
PG  - e00265-13
AB  - We here report a 3.059-Mbp draft assembly for the genome of Enterococcus durans strain IPLA
      655. This dairy isolate provides a model for studying the regulation
      of the biosynthesis of tyramine (a toxic compound). These results should aid our
      understanding of tyramine production and allow tyramine accumulation in food to
      be reduced.
AU  - Ladero V
AU  - Linares DM
AU  - Del Rio B
AU  - Fernandez M
AU  - Martin MC
AU  - Alvarez MA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00265-13.

PMID- 23409274
VI  - 1
DP  - 2013
TI  - Genome Sequence of Weissella ceti NC36, an Emerging Pathogen of Farmed Rainbow Trout in the United States.
PG  - e00187-12
AB  - Novel Weissella sp. bacteria have recently been reported to be associated with disease
      outbreaks in cultured rainbow trout (Oncorhynchus mykiss) at commercial
      farms in China, Brazil, and the United States. Here we present the first genome
      sequence of this novel Weissella species, isolated from the southeastern United
      States.
AU  - Ladner JT
AU  - Welch TJ
AU  - Whitehouse CA
AU  - Palacios GF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00187-12.

PMID- 23409273
VI  - 1
DP  - 2013
TI  - Genome Sequence of Moraxella macacae 0408225, a Novel Bacterial Species Isolated  from a Cynomolgus Macaque with Epistaxis.
PG  - e00188-12
AB  - Moraxella macacae is a recently described bacterial species that has been associated with at
      least two outbreaks of epistaxis in macaques. Here we present
      the first genome sequence of this novel species, isolated from a symptomatic
      cynomolgus macaque at the U.S. Army Medical Research Institute of Infectious
      Diseases.
AU  - Ladner JT
AU  - Whitehouse CA
AU  - Koroleva GI
AU  - Palacios GF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00188-12.

PMID- 28254978
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Plant Growth-Promoting Rhizobacterium Acinetobacter  radioresistens Strain SA188 Isolated from the Desert Plant Indigofera argentea.
PG  - e01708-16
AB  - Acinetobacter radioresistens strain SA188 is a plant endophytic bacterium, isolated from root
      nodules of the desert plants Indigofera spp., collected in
      Jizan, Saudi Arabia. Here, we report the 3.2-Mb draft genome sequence of strain
      SA188, highlighting characteristic pathways for plant growth-promoting activity
      and environmental adaptation.
AU  - Lafi FF
AU  - Alam I
AU  - Bisseling T
AU  - Geurts R
AU  - Bajic VB
AU  - Hirt H
AU  - Saad MM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01708-16.

PMID- 28007863
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the Phosphate-Solubilizing Bacterium Pseudomonas argentinensis Strain SA190 Isolated from the Desert Plant Indigofera argentea.
PG  - e01431-16
AB  - Pseudomonas argentinensis strain SA190 is a plant endophytic-inhabiting bacterium that was
      isolated from root nodules of the desert plant Indigofera argentea collected from the Jizan
      region of Saudi Arabia. Here, we report the genome sequence of SA190, highlighting several
      functional genes related to plant growth-promoting activity, environment adaption, and
      antifungal activity.
AU  - Lafi FF
AU  - Alam I
AU  - Geurts R
AU  - Bisseling T
AU  - Bajic VB
AU  - Hirt H
AU  - Saad MM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01431-16.

PMID- 28254977
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Ochrobactrum intermedium Strain SA148, a Plant Growth-Promoting Desert Rhizobacterium.
PG  - e01707-16
AB  - Ochrobactrum intermedium strain SA148 is a plant growth-promoting bacterium isolated from
      sandy soil in the Jizan area of Saudi Arabia. Here, we report the
      4.9-Mb draft genome sequence of this strain, highlighting different pathways
      characteristic of plant growth promotion activity and environmental adaptation of
      SA148.
AU  - Lafi FF
AU  - Alam I
AU  - Geurts R
AU  - Bisseling T
AU  - Bajic VB
AU  - Hirt H
AU  - Saad MM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01707-16.

PMID- 28209831
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Enterobacter sp. Sa187, an Endophytic Bacterium Isolated from the Desert Plant Indigofera argentea.
PG  - e01638-16
AB  - Enterobacter sp. Sa187 is a plant endophytic bacterium, isolated from root nodules of the
      desert plant Indigofera argentea, collected from the Jizan region
      of Saudi Arabia. Here, we report the genome sequence of Sa187, highlighting
      several genes involved in plant growth-promoting activity and environmental
      adaption.
AU  - Lafi FF
AU  - Alam I
AU  - Geurts R
AU  - Bisseling T
AU  - Bajic VB
AU  - Hirt H
AU  - Saad MM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01638-16.

PMID- 28082490
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Plant Growth-Promoting Pseudomonas punonensis Strain D1-6 Isolated from the Desert Plant Erodium hirtum in Jordan.
PG  - e01437-16
AB  - Pseudomonas punonensis strain D1-6 was isolated from roots of the desert plant Erodium hirtum,
      near the Dead Sea in Jordan. The genome of strain D1-6 reveals
      several key plant growth-promoting and herbicide-resistance genes, indicating a
      possible specialized role for this endophyte.
AU  - Lafi FF
AU  - AlBladi ML
AU  - Salem NM
AU  - Al-Banna L
AU  - Alam I
AU  - Bajic VB
AU  - Hirt H
AU  - Saad MM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01437-16.

PMID- 27469951
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the Plant Growth-Promoting Cupriavidus gilardii Strain JZ4 Isolated from the Desert Plant Tribulus terrestris.
PG  - e00678-16
AB  - We isolated the plant endophytic bacterium Cupriavidus gilardii strain JZ4 from the roots of
      the desert plant Tribulus terrestris, collected from the Jizan
      region, Saudi Arabia. We report here the draft genome sequence of JZ4, together
      with several enzymes related to plant growth-promoting activity, environmental
      adaption, and antifungal activity.
AU  - Lafi FF
AU  - Bokhari A
AU  - Alam I
AU  - Bajic VB
AU  - Hirt H
AU  - Saad MM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00678-16.

PMID- 27811099
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Halomonas elongata Strain K4, an Endophytic Growth-Promoting Bacterium Enhancing Salinity Tolerance In Planta.
PG  - e01214-16
AB  - Halomonas elongata strain K4 is an endophytic bacterial strain that was isolated  from roots
      of Cyperus conglomeratus collected at the Red Sea coast in Thuwal,
      Saudi Arabia. Here, we present a draft genome sequence of this strain,
      highlighting a number of pathways involved in plant growth promotion under salt
      stress.
AU  - Lafi FF
AU  - Ramirez-Prado JS
AU  - Alam I
AU  - Bajic VB
AU  - Hirt H
AU  - Saad MM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01214-16.

PMID- 28126944
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Plant Growth-Promoting Micrococcus luteus Strain K39 Isolated from Cyperus conglomeratus in Saudi Arabia.
PG  - e01520-16
AB  - Micrococcus luteus strain K39 is an endophyte bacterium isolated from roots of the desert
      plant Cyperus conglomeratus collected from the Red Sea shore, Thuwal,
      Saudi Arabia. The draft genome sequence of strain K39 revealed a number of
      enzymes involved in salinity and oxidative stress tolerance or having
      herbicide-resistance activity.
AU  - Lafi FF
AU  - Ramirez-Prado JS
AU  - Alam I
AU  - Bajic VB
AU  - Hirt H
AU  - Saad MM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01520-16.

PMID- 25676769
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Cellulophaga sp. E6, a Marine Algal Epibiont That Produces a Quorum-Sensing Inhibitory Compound Active against Pseudomonas  aeruginosa.
PG  - e01565-14
AB  - The genus Cellulophaga is composed of obligate aerobic Gram-negative bacteria commonly found
      in association with marine algae. We report the approximately
      4.42-Mbp draft genome sequence of Cellulophaga sp. E6, which inhibits
      N-(3-oxododecanoyl)-l-homoserine lactone (3-oxo-C12-HSL)-mediated quorum sensing
      (QS), lasB transcription, and biofilm formation by Pseudomonas aeruginosa.
AU  - Lafleur JE
AU  - Costa SK
AU  - Bitzer AS
AU  - Silby MW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01565-14.

PMID- 20961958
VI  - 39
DP  - 2011
TI  - Identification of new homologs of PD-(D/E)XK nucleases by support vector machines trained on data derived from profile-profile alignments.
PG  - 1187-1196
AB  - PD-(D/E)XK nucleases, initially represented by only Type II restriction enzymes, now comprise
      a large and extremely diverse superfamily of
      proteins. They participate in many different nucleic acids transactions
      including DNA degradation, recombination, repair and RNA processing.
      Different PD-(D/E)XK families, although sharing a structurally conserved
      core, typically display little or no detectable sequence similarity except
      for the active site motifs. This makes the identification of new
      superfamily members using standard homology search techniques challenging.
      To tackle this problem, we developed a method for the detection of
      PD-(D/E)XK families based on the binary classification of profile-profile
      alignments using support vector machines (SVMs). Using a number of both
      superfamily-specific and general features, SVMs were trained to identify
      true positive alignments of PD-(D/E)XK representatives. With this method
      we identified several PFAM families of uncharacterized proteins as
      putative new members of the PD-(D/E)XK superfamily. In addition, we
      assigned several unclassified restriction enzymes to the PD-(D/E)XK type.
      Results show that the new method is able to make confident assignments
      even for alignments that have statistically insignificant scores. We also
      implemented the method as a freely accessible web server at
      http://www.ibt.lt/bioinformatics/software/pdexk/.
AU  - Laganeckas M
AU  - Margelevicius M
AU  - Venclovas C
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2011 39: 1187-1196.

PMID- 23408657
VI  - 6
DP  - 2012
TI  - Non-contiguous finished genome sequence and description of Alistipes timonensis sp. nov.
PG  - 315-324
AB  - Alistipes timonensis strain JC136(T) sp. nov. is the type strain of A. timonensis sp. nov., a
      new species within the genus Alistipes. This strain, whose genome is
      described here, was isolated from the fecal flora of a healthy patient. A.
      timonensis is an obligate anaerobic rod. Here we describe the features of this
      organism, together with the complete genome sequence and annotation. The
      3,497,779 bp long genome (one chromosome but no plasmid) contains 2,742
      protein-coding and 50 RNA genes, including three rRNA genes.
AU  - Lagier JC
AU  - Armougom F
AU  - Mishra AK
AU  - Nguyen TT
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 6: 315-324.

PMID- 25197479
VI  - 9
DP  - 2014
TI  - Non contiguous-finished genome sequence and description of Clostridium jeddahense sp. nov.
PG  - 1003-1019
AB  - Clostridium jeddahense strain JCD(T) (= CSUR P693 = DSM 27834) is the type strain of C.
      jeddahense sp. nov. This strain, whose genome is described here, was
      isolated from the fecal flora of an obese 24 year-old Saudian male (BMI=52
      kg/m(2)). Clostridium jeddahense strain JCD(T) is an obligate Gram-positive
      bacillus. Here we describe the features of this organism, together with the
      complete genome sequence and annotation. The 3,613,503 bp long genome (1
      chromosome, no plasmid) exhibits a G+C content of 51.95% and contains 3,462
      protein-coding and 53 RNA genes, including 4 rRNA genes.
AU  - Lagier JC
AU  - Bibi F
AU  - Ramasamy D
AU  - Azhar EI
AU  - Robert C
AU  - Yasir M
AU  - Jiman-Fatani AA
AU  - Alshali KZ
AU  - Fournier PE
AU  - Raoult D
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 1003-1019.

PMID- 24019988
VI  - 7
DP  - 2013
TI  - Non contiguous-finished genome sequence and description of Enterobacter massiliensis sp. nov.
PG  - 399-412
AB  - Enterobacter massiliensis strain JC163(T) sp. nov. is the type strain of E. massiliensis sp.
      nov., a new species within the genus Enterobacter. This strain,
      whose genome is described here, was isolated from the fecal flora of a healthy
      Senegalese patient. E. massiliensis is an aerobic rod. Here we describe the
      features of this organism, together with the complete genome sequence and
      annotation. The 4,922,247 bp long genome (1 chromosome but no plasmid) exhibits a
      G+C content of 55.1% and contains 4,644 protein-coding and 80 RNA genes,
      including 5 rRNA genes.
AU  - Lagier JC
AU  - El Karkouri K
AU  - Mishra AK
AU  - Robert C
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 7: 399-412.

PMID- 22675604
VI  - 6
DP  - 2012
TI  - Non-contiguous finished genome sequence and description of Anaerococcus senegalensis sp. nov.
PG  - 116-125
AB  - Anaerococcus senegalensis strain JC48T sp. nov. is the type strain of A. senegalensis sp.
      nov., a new species within the genus Anaerococcus. This strain, whose genome is described
      here, was isolated from the fecal flora of a healthy patient. A. senegalensis is an obligate
      anaerobic coccus. Here we describe the features of this organism, together with the complete
      genome sequence and annotation. The 1,790,835 bp long genome (1 chromosome but no plasmid)
      contains 1,721 protein-coding and 53 RNA genes, including 5 rRNA genes.
AU  - Lagier JC
AU  - El Karkouri K
AU  - Nguyen TT
AU  - Armougom F
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 6: 116-125.

PMID- 24019984
VI  - 7
DP  - 2013
TI  - Non contiguous-finished genome sequence and description of Senegalemassilia anaerobia gen. nov., sp. nov.
PG  - 343-356
AB  - Senegalemassilia anaerobia strain JC110(T) sp.nov. is the type strain of Senegalemassilia
      anaerobia gen. nov., sp. nov., the type species of a new genus
      within the Coriobacteriaceae family, Senegalemassilia gen. nov. This strain,
      whose genome is described here, was isolated from the fecal flora of a healthy
      Senegalese patient. S. anaerobia is a Gram-positive anaerobic coccobacillus. Here
      we describe the features of this organism, together with the complete genome
      sequence and annotation. The 2,383,131 bp long genome contains 1,932
      protein-coding and 58 RNA genes.
AU  - Lagier JC
AU  - Elkarkouri K
AU  - Rivet R
AU  - Couderc C
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 7: 343-356.

PMID- 23407294
VI  - 7
DP  - 2012
TI  - Non-contiguous finished genome sequence and description of Herbaspirillum massiliense sp. nov.
PG  - 200-209
AB  - Herbaspirillum massiliense strain JC206(T) sp. nov. is the type strain of H. massiliense sp.
      nov., a new species within the genus Herbaspirillum. This strain,
      whose genome is described here, was isolated from the fecal flora of a healthy
      Senegalese patient. H. massiliense is an aerobic rod. Here we describe the
      features of this organism, together with the complete genome sequence and
      annotation. The 4,186,486 bp long genome (one chromosome but no plasmid) contains
      3,847 protein-coding and 54 RNA genes, including 3 rRNA genes.
AU  - Lagier JC
AU  - Gimenez G
AU  - Robert C
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 7: 200-209.

PMID- 26523201
VI  - 10
DP  - 2015
TI  - Genome sequence of Oceanobacillus picturae strain S1, an halophilic bacterium first isolated in human gut.
PG  - 91
AB  - Oceanobacillus picturae is a strain of a moderately halophilic bacterium, first isolated from
      a mural painting. We demonstrate, for the first time, the culture
      of human Oceanobacillus picturae, strain S1(T), whose genome is described here,
      from a stool sample collected from a 25-year-old Saoudian healthy individual. We
      used a slightly modified standard culture medium adding 100 g/L of NaCl. We
      provide a short description of this strain including its MALDI-TOF spectrum, the
      main identification tool currently used in clinical microbiology. The 3,675,175
      bp long genome exhibits a G + C content of 39.15 % and contains 3666
      protein-coding and 157 RNA genes. The draft genome sequence of Oceanobacillus
      picturae has a similar size to the Oceanobacillus kimchii (respectively 3.67 Mb
      versus 3.83 Mb). The G + C content was higher compared with Oceanobacillus
      kimchii (respectively 39.15 % and 35.2 %). Oceanobacillus picturae shared almost
      identical number of genes (3823 genes versus 3879 genes), with a similar ratio of
      genes per Mb (1041 genes/Mb versus 1012 genes/Mb). The genome sequencing of
      Oceanobacillus picturae strain S1 isolated for the first time in a human, will be
      added to the 778 genome projects from the gastrointestinal tract listed by the
      international consortium Human Microbiome Project.
AU  - Lagier JC
AU  - Khelaifia S
AU  - Azhar EI
AU  - Croce O
AU  - Bibi F
AU  - Jiman-Fatani AA
AU  - Yasir M
AU  - Helaby HB
AU  - Robert C
AU  - Fournier PE
AU  - Raoult D
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 91.

PMID- 23408774
VI  - 7
DP  - 2012
TI  - Non contiguous-finished genome sequence and description of Cellulomonas massiliensis sp. nov.
PG  - 258-270
AB  - Cellulomonas massiliensis strain JC225(T) sp. nov. is the type strain of Cellulomonas
      massiliensis sp., a new species within the genus Cellulomonas. This
      strain, whose genome is described here, was isolated from the fecal flora of a
      healthy Senegalese patient. C. massiliensis is an aerobic rod-shaped bacterium.
      Here we describe the features of this organism, together with the complete genome
      sequence and annotation. The 3,407,283 bp long genome contains 3,083
      protein-coding and 48 RNA genes.
AU  - Lagier JC
AU  - Ramasamy D
AU  - Rivet R
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 7: 258-270.

PMID- 12655008
VI  - 31
DP  - 2003
TI  - Repair of hydrolytic DNA deamination damage in thermophilic bacteria: cloning and characterization of a Vsr endonuclease homolog from Bacillus stearothermophilus.
PG  - 1913-1920
AB  - Hydrolytic deamination of 5-methyl cytosine in double stranded DNA results in formation of a
      T/G mismatch that-if left unrepaired-leads to a C-->T
      transition mutation in half of the progeny. In addition to several
      mismatch-specific glycosylases that have been found in both pro- and
      eukaryotes to channel this lesion into base excision repair by removing
      the T from the mismatch, Vsr endonuclease from Escherichia coli has been
      described which initiates repair by an endonucleolytic strand incision 5'
      to the mismatched T. We have isolated a gene coding for a homolog of
      E.coli Vsr endonuclease from the thermophilic bacterium Bacillus
      stearothermophilus H3 (Vsr.Bst) using a method that allows PCR
      amplification with degenerated primers of gene segments which code for
      only one highly conserved amino acid region. Vsr.Bst was produced
      heterologously in E.coli and purified to apparent homogeneity. Vsr.Bst
      specifically incises heteroduplex DNA with a preference for T/G
      mismatches. The selectivity of Vsr.Bst for the sequence context of the T/G
      mismatch appears less pronounced than for Vsr.Eco.
AU  - Laging M
AU  - Lindner E
AU  - Fritz H-J
AU  - Kramer W
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2003 31: 1913-1920.

PMID- 
VI  - 156
DP  - 2008
TI  - First Report of Erwinia amylovora Fire Blight in Belarus.
PG  - 638-640
AB  - 
AU  - Lagonenko AL
AU  - Komardina VS
AU  - Nikolaichik YA
AU  - Evtushenkov AN
PT  - Journal Article
TA  - J. Phytopathol.
JT  - J. Phytopathol.
SO  - J. Phytopathol. 2008 156: 638-640.

PMID- 22374948
VI  - 194
DP  - 2012
TI  - Genome Sequences of Three Leuconostoc citreum Strains, LBAE C10, LBAE C11, and LBAE E16, Isolated from Wheat Sourdoughs.
PG  - 1610-1611
AB  - Leuconostoc citreum is a key microorganism in fermented foods of plant origin. Here we report
      the draft genome sequence for three strains of Leuconostoc
      citreum, LBAE C10, LBAE C11, and LBAE E16, which have been isolated from
      traditional French wheat sourdoughs.
AU  - Laguerre S
AU  - Amari M
AU  - Vuillemin M
AU  - Robert H
AU  - Loux V
AU  - Klopp C
AU  - Morel S
AU  - Gabriel B
AU  - Remaud-Simeon M
AU  - Gabriel V
AU  - Moulis C
AU  - Fontagne-Faucher C
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1610-1611.

PMID- Not carried by PubMed...
VI  - 1
DP  - 1997
TI  - DNA binding by MunI restriction endonuclease.
PG  - 13-20
AB  - Investigation of DNA binding properties by gel shift assay indicated that in the absence of
      cofactor at pH 8.0, WT MunI binds to DNA containing or lacking the recognition sequence with
      similar affinity and only at a high excess of protein.  Contrary to the WT enzyme, E98A and
      D83A mutants under the same conditions bound DNA containing the recognition sequence with high
      affinity.  With noncognate DNA the latter mutants exhibited only a weak binding characteristic
      of the WT MunI.  The increased affinity of the mutants to the cognate DNA suggest that E98A
      and D83A replacements can mimic the effect of Mg2+ ion during the development of the
      specificity of MunI restriction enzyme at the catalytic step.  An increased affinity of the WT
      MunI to the cognate DNA was observed also at low pH or in the presence Ca2+ ions.  Indeed, in
      contrast to the binding experiments at pH 8.0, gel-shift analysis at pH 6.5 indicated a tight
      sequence-specific binding of WT MunI to the cognate DNA suggesting that the protonation of the
      active site carboxylate residue(s) with anomalous high pKa value control the binding
      specificity.  Interestingly, Ca2+ ions that did not support DNA cleavage by MunI were able to
      induce DNA binding specificity of WT MunI at pH 8.0 and probably mimic the role of Mg2+ ions
      in the development of sequence specific binding.  The relief of unfavorable repulsive
      constraints either by replacement of carboxylate(s) lowering the pH or metal ion binding leads
      to the manifestation of binding specificity by MunI.
AU  - Lagunavicius A
PT  - Journal Article
TA  - Biologija
JT  - Biologija
SO  - Biologija 1997 1: 13-20.

PMID- 9287152
VI  - 36
DP  - 1997
TI  - DNA binding specificity of MunI restriction endonuclease is controlled by pH and calcium ions: Involvement of active site carboxylate residues.
PG  - 11093-11099
AB  - Gel shift analysis reveals that at pH 8.3 in the absence of Mg2+, MunI restriction
      endonuclease exhibits little DNA binding specificity, as compared with the D83A and E98A
      mutants of MunI.  This suggests that charged carboxylate residue(s) influence the DNA binding
      specificity of MunI.  In our efforts to establish the determinants of MunI binding
      specificity, we investigated the possible role of the ionic milieu, and we found that lowering
      pH or elevating Ca2+ levels per se induces specific DNA recognition by WT MunI.  In contrast
      to the binding experiments at pH 8.3, gel shift analysis at pH 6.5 indicated tight
      sequence-specific binding of WT MunI in the absence of Mg2+, suggesting that protonation of
      active site carboxylate residue(s) which manifest anomalously high pKa value(s) control
      binding specificity.  Interestingly, Ca2+ ion concentrations, which did not support DNA
      cleavage by MunI also induced DNA binding specificity in WT MunI at pH 8.3.  To explore
      possible structural changes upon DNA binding, we then used a limited proteolysis technique.
      Trypsin cleavage of MunI--DNA complexes indicated that in the presence of cognate DNA the MunI
      restriction endonuclease became resistant to proteolytic cleavage, suggesting that binding of
      specific DNA induced a structural change.  CD measurements confirmed this observation,
      suggesting minor secondary structural differences between complexes of MunI with cognate and
      noncognate DNA. These results therefore suggest that binding of MunI to its recognition
      sequence triggers a conformational transition that correctly juxtaposes active site
      carboxylate residues, which then chelate Mg2+ ions.  In the absence of Mg2+ ions, at pH 8.3,
      conditions in which carboxylate groups would be expected to be completely ionized,
      electrostatic repulsion between charged carboxylates and phosphate oxygens is enhanced such as
      to interfere with specific DNA binding.  Elimination of such repulsive constraints by
      replacement of carboxylate residues, by lowering pH, or by metal ion binding, then promotes
      MunI binding specificity.
AU  - Lagunavicius A
AU  - Grazulis S
AU  - Balciunaite E
AU  - Vainius D
AU  - Siksnys V
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1997 36: 11093-11099.

PMID- 12589753
VI  - 326
DP  - 2003
TI  - The metal-independent type IIS restriction enzyme BfiI is a dimer that binds two DNA sites but has only one catalytic centre.
PG  - 1051-1064
AB  - BfiI is a novel type IIs restriction endonuclease that, unlike all other restriction enzymes
      characterised to date, cleaves DNA in the absence of
      Mg(2+). The amino acid sequence of the N-terminal part of BfiI has some
      similarities to Nuc of Salmonella typhimurium, an EDTA-resistant nuclease
      akin to phospholipase D. The dimeric form of Nuc contains a single active
      site composed of residues from both subunits. To examine the roles of the
      amino acid residues of BfiI that align with the catalytic residues in Nuc,
      a set of alanine replacement mutants was generated by site-directed
      mutagenesis. The mutationally altered forms of BfiI were all catalytically
      inactive but were still able to bind DNA specifically. The active site of
      BfiI is thus likely to be similar to that of Nuc. BfiI was also found by
      gel-filtration to be a dimer in solution. Both gel-shift and pull-down
      assays indicated that the dimeric form of BfiI binds two copies of its
      recognition sequence. In reactions on plasmids with either one or two
      copies of its recognition sequence, BfiI cleaved the DNA with two sites
      more rapidly than that with one site. Yet, when bound to two copies of its
      recognition sequence, the BfiI dimer cleaved only one phosphodiester bond
      at a time. The dimer thus seems to contain two DNA-binding domains but
      only one active site.
AU  - Lagunavicius A
AU  - Sasnauskas G
AU  - Halford SE
AU  - Siksnys V
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2003 326: 1051-1064.

PMID- Not carried by PubMed...
VI  - 0
DP  - 1996
TI  - Mutational analysis of MunI restriction endonuclease.
PG  - 35-38
AB  - Mapping of the conserved sequence regions between MunI and EcoRI restriction endonucleases to
      the known X-ray structure of the EcoRI restriction enzyme allowed us to identify a sequence
      motif 82PDX14EXK as a putative catalytic site of MunI.  Site-directed mutagenesis was used to
      test whether amino acids P82, D83, E98 and K100 were important for catalytic activity of MunI.
      A set of MunI mutants (P82A, D83A, E98Q, E98Q, E98A, K100E, K100A) altered at the putative
      catalytic site was obtained using site-directed mutagenesis, and the catalytic properties of
      the mutants were studied in vivo and in vitro.  The phenotypes observed in vivo and in vitro
      for the mutants of putative catalytic site residues of MunI were consistent with the proposed
      active site function.  Investigation of the cleavage properties of these mutants revealed that
      E98Q replacement in MunI resulted in alteration of metal ion binding.  Contrary to the wild
      type enzyme, this mutant was activated by Mn2+ ions more effectively than by Mg2+ ions.
AU  - Lagunavicius A
AU  - Siksnys V
PT  - Journal Article
TA  - Biologija
JT  - Biologija
SO  - Biologija 1996 0: 35-38.

PMID- 9287151
VI  - 36
DP  - 1997
TI  - Site-directed mutagenesis of putative active site residues of MunI restriction endonuclease: replacement of catalytically essential carboxylate residues triggers DNA binding specificity.
PG  - 11086-11092
AB  - Mapping of the conserved sequence regions in the restriction endonucleases MunI (C/AATTG) and
      EcoRI (G/AATTC) to the known X-ray structure of EcoRI allowed us to identify the sequence
      motif 82PDX14EXK as the putative catalytic/Mg2+ ion binding site of MunI.  Site-directed
      mutagenesis was then used to test whether amino acids P82, D83, E98, and K100 were important
      for the catalytic activity of MunI.  Mutation P82A generated only a marginal effect on the
      cleavage properties of the enzyme.  Investigation of the cleavage properties of the D83, E98,
      and K100 substitution mutants, however, in vivo and in vitro, revealed either an absence of
      catalytic activity or markedly reduced catalytic activity.  Interestingly, the deleterious
      effect of the E98Q replacement in vitro was partially overcome by replacement of the metal
      cofactor used.  Though the catalytic activity of the E98Q mutant was only 0.4% of WT under
      standard conditions (in the presence of Mg2+ ions), the mutant exhibited 40% of WT catalytic
      activity in buffer supplemented with Mn2+ ions.  Further, the DNA binding properties of these
      substitution mutants were analyzed using the gel shift assay technique.  In the absence of
      Mg2+ ions, WT MunI bound both cognate DNA and noncognate sequences with similar low
      affinities.  The D83A and E98A mutants, in contrast, in the absence of Mg2+ ions, exhibited
      significant specificity of binding to cognate DNA, suggesting that the substitutions made can
      simulate the effect of the Mg2+ ion in conferring specificity to the MunI restriction enzyme.
AU  - Lagunavicius A
AU  - Siksnys V
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1997 36: 11086-11092.

PMID- 27445378
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a Dyella-Like Bacterium from the Planthopper Hyalesthes  obsoletus.
PG  - e00686-16
AB  - We report here the draft genome sequence of a Dyella-like bacterium (DLB) isolated from
      Hyalesthes obsoletus, the insect vector of the uncultivable
      mollicute bacterium 'Candidatus Phytoplasma.' This isolate inhibits Spiroplasma
      melliferum, a cultivable mollicute. The draft genome of DLB consists of 4,196,214
      bp, with a 68.6% G+C content, and 3,757 genes were predicted.
AU  - Lahav T
AU  - Zchori-Fein E
AU  - Naor V
AU  - Freilich S
AU  - Iasur-Kruh L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00686-16.

PMID- 28254964
VI  - 5
DP  - 2017
TI  - Annotated Whole-Genome Shotgun Sequence of Multidrug-Resistant Mycobacterium tuberculosis MTB13_M Isolated from Morocco.
PG  - e01756-16
AB  - Here, we describe the annotated genome sequence of Mycobacterium tuberculosis MTB13_M. The
      organism was isolated from a sputum sample in Morocco.
AU  - Lahlou L
AU  - El Mrimar N
AU  - Alouane T
AU  - Laamarti M
AU  - Karti S
AU  - Benhrif O
AU  - El Mesbahi H
AU  - Lemriss H
AU  - Bssaibis F
AU  - Maleb A
AU  - El Rarit S
AU  - Zegmout A
AU  - El Jaoudi R
AU  - Frikh M
AU  - Lemnouar A
AU  - Dakka T
AU  - Elouennass M
AU  - Ibrahimi A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01756-16.

PMID- 29146858
VI  - 5
DP  - 2017
TI  - Whole-Genome Shotgun Sequences of Three Multidrug-Resistant Mycobacterium tuberculosis Strains Isolated from Morocco.
PG  - e01275-17
AB  - Tuberculosis is a contagious disease that usually attacks the lungs but sometimes attacks
      other parts of the body, such as the kidneys, glands, and bones. It is an
      endemic and major public health problem in Morocco. Tuberculosis is transmitted
      through the airways via the inhalation of microdroplets containing Mycobacterium
      tuberculosis We present here the whole-genome shotgun sequences of three
      multidrug-resistant M. tuberculosis strains isolated from Morocco.
AU  - Lahlou L
AU  - El Mrimar N
AU  - Laamarti M
AU  - Alouane T
AU  - Bendahou MA
AU  - Bssaibis F
AU  - Ben Lahlou Y
AU  - Zegmout A
AU  - El Hafidi N
AU  - ElJaoudi R
AU  - Frikh M
AU  - Lemnouar A
AU  - Elouennass M
AU  - Ibrahimi A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01275-17.

PMID- 25269084
VI  - 9
DP  - 2014
TI  - In Vivo Mutational Characterization of DndE Involved in DNA Phosphorothioate Modification.
PG  - e107981
AB  - DNA phosphorothioate (PT) modification is a recently identified epigenetic modification that
      occurs in the sugar-phosphate backbone of prokaryotic DNA. Previous studies have demonstrated
      that DNA PT modification is governed by the five DndABCDE proteins in a sequence-selective and
      R-P stereo-specific manner. Bacteria may have acquired this physiological modification along
      with dndFGH as a restriction-modification system. However, little is known about the
      biological function of Dnd proteins, especially the smallest protein, DndE, in the PT
      modification pathway. DndE was reported to be a DNA-binding protein with a preference for
      nicked dsDNA in vitro; the binding of DndE to DNA occurs via six positively charged lysine
      residues on its surface. The substitution of these key lysine residues significantly decreased
      the DNA binding affinities of DndE proteins to undetectable levels. In this study, we
      conducted site-directed mutagenesis of dndE on a plasmid and measured DNA PT modifications
      under physiological conditions by mass spectrometry. We observed distinctive differences from
      the in vitro binding assays. Several mutants with lysine residues mutated to alanine decreased
      the total frequency of PT modifications, but none of the mutants completely eliminated PT
      modification. Our results suggest that the nicked dsDNA-binding capacity of DndE may not be
      crucial for PT modification and/or that DndE may have other biological functions in addition
      to binding to dsDNA.
AU  - Lai C
AU  - Wu X
AU  - Chen C
AU  - Huang T
AU  - Xiong X
AU  - Wu S
AU  - Gu M
AU  - Deng Z
AU  - Chen Xi
AU  - Chen S
AU  - Wang L
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2014 9: e107981.

PMID- 24812229
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Escherichia coli E1728 Isolated from Marine Sediment in  Hong Kong.
PG  - e00430-14
AB  - Recent findings of Escherichia coli persisting autochthonously in environmental matrices
      outside animal bodies have revealed largely unknown facets of the
      lifestyle and ecophysiology of the species that have yet to be explored. Here, we
      report the draft genome sequence of E. coli E1728 isolated from marine sediment.
AU  - Lai JY
AU  - Zhang H
AU  - Chiang MH
AU  - Yu M
AU  - Zhang R
AU  - Lau SC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00430-14.

PMID- 25291771
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Three Escherichia coli Strains Investigated for the Effects of Lysogeny on Niche Diversification.
PG  - e00955-14
AB  - During the course of investigating the effects of lysogeny on niche diversification of
      Escherichia coli, we used the temperate phages induced from
      one E. coli strain to infect another and created an isogenic lysogen of the
      latter. The draft genome sequences of the three E. coli strains are reported
      herein.
AU  - Lai JY
AU  - Zhang H
AU  - Chiang MH
AU  - Yu M
AU  - Zhang R
AU  - Lau SC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00955-14.

PMID- 25256706
VI  - 64
DP  - 2014
TI  - Celeribacter indicus sp. nov. a polycyclic aromatic hydrocarbon-degrading bacterium from deep-sea sediment and reclassification of Huaishuia halophila as Celeribacter halophilus comb. nov.
PG  - 4160-4167
AB  - A taxonomic study was carried out on strain P73(T), which was isolated from
      deep-sea sediment of the Indian Ocean by enrichment of polycyclic aromatic
      hydrocarbons. The strain was able to degrade biphenyl, naphthalene,
      2-methylnaphthalene, 2,6-dimethylnaphthalene, acenaphthene, anthracene,
      phenanthrene, dibenzothiophene, dibenzofuran, fluorene, 4-methyldibenzothiophene
      and fluoranthene, but not pyrene or chrysene. Phylogenetic analysis based on 16S
      rRNA gene sequences showed that strain P73(T) formed a clade with the genera
      Celeribacter and Huaishuia within the family Rhodobacteraceae, with highest
      sequence similarity of 96.98 % to Celeribacter neptunius H 14(T), followed by
      Huaishuia halophila ZXM137(T) (96.42 %). The bacterium was Gram-stain-negative,
      oxidase- and catalase-positive, rod-shaped and non-motile. Growth was observed at
      salinities from 0.5 to 12 % and at temperatures from 10 to 41 degrees C. The
      principal fatty acids (>10 %) of strain P73(T) were summed feature 8 (C18 :
      1omega7c/omega6c) and C19 : 0omega8c cyclo. The sole respiratory quinone was
      Q-10. The major lipids were phosphatidylglycerol, one unknown aminolipid, one
      unknown phospholipid and one unknown lipid; a second unknown phospholipid and one
      unknown glycolipid were present as minor components. The G+C content of the
      chromosomal DNA was 66.0 mol%. The combined genotypic and phenotypic data show
      that strain P73(T) represents a novel species of the genus Celeribacter, for
      which the name Celeribacter indicus sp. nov. is proposed. The type strain is
      P73(T) ( = MCCC 1A01112(T) = LMG 27600(T) = DSM 27257(T)). Phylogenetic study and
      existing phenotypic information also show that Huaishuia halophila should be
      transferred to the genus Celeribacter as Celeribacter halophilus comb. nov. (type
      strain ZXM137(T) = MCCC 1A06432(T) = CGMCC 1.8891(T) = LMG 24854(T)).
AU  - Lai Q
AU  - Cao J
AU  - Yuan J
AU  - Li F
AU  - Shao Z
PT  - Journal Article
TA  - Int. J. Syst. Evol. Microbiol.
JT  - Int. J. Syst. Evol. Microbiol.
SO  - Int. J. Syst. Evol. Microbiol. 2014 64: 4160-4167.

PMID- 23209227
VI  - 194
DP  - 2012
TI  - Genome Sequence of Galbibacter marinum Type Strain ck-I2-15.
PG  - 6973
AB  - Galbibacter marinum strain ck-I2-15(T) was isolated from an arsenite-resistant consortium
      enriched from the deep sea sediment of a hydrothermal vent field on
      the Southwest Indian Ocean Ridge. Here, we present the draft genome of strain
      ck-I2-15(T), which contains 3,572,447 bp with a G+C content of 37.04% and
      contains 3,099 protein-coding genes and 38 tRNA genes.
AU  - Lai Q
AU  - Li C
AU  - Shao Z
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6973.

PMID- 23209217
VI  - 194
DP  - 2012
TI  - Genome Sequence of Nitratireductor pacificus Type Strain pht-3B.
PG  - 6958
AB  - Nitratireductor pacificus strain pht-3B(T) was isolated from a pyrene-degrading consortium
      enriched from the deep sea sediment of the Pacific Ocean. Here, we
      present the draft genome of strain pht-3B(T), which contains 4,466,205 bp with a
      G+C content of 65.51% and contains 4,197 protein-coding genes and 46 tRNA genes.
AU  - Lai Q
AU  - Li G
AU  - Shao Z
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6958.

PMID- 23209238
VI  - 194
DP  - 2012
TI  - Genome Sequence of Nitratireductor indicus Type Strain C115.
PG  - 6990
AB  - Nitratireductor indicus strain C115(T) was isolated from a crude-oil-degrading consortium
      enriched from deep seawater of the Indian Ocean. Here, we present the
      draft genome of strain C115(T), which contains 4,992,479 bp with a G+C content of
      60.8% and contains 4,825 protein-coding genes and 45 tRNA genes.
AU  - Lai Q
AU  - Li G
AU  - Yu Z
AU  - Shao Z
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6990.

PMID- 23144414
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Alcanivorax dieselolei Type Strain B5.
PG  - 6674
AB  - Alcanivorax dieselolei B5(T) was isolated from oil-contaminated surface water of  the Bohai
      Sea of China and characterized by the efficient degradation of alkane
      (C(5)-C(36)). Here we report the complete genome of B5(T) and genes associated
      with alkane degradation.
AU  - Lai Q
AU  - Li W
AU  - Shao Z
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6674.

PMID- 23144416
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of the Pyrene-Degrading Bacterium Cycloclasticus sp. Strain P1.
PG  - 6677
AB  - Cycloclasticus sp. strain P1 was isolated from deep-sea sediments of the Pacific  Ocean and
      characterized as a unique bacterium in the degradation of pyrene, a
      four-ring polycyclic aromatic hydrocarbon (PAH). Here we report the complete
      genome of P1 and genes associated with PAH degradation.
AU  - Lai Q
AU  - Li W
AU  - Wang B
AU  - Yu Z
AU  - Shao Z
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6677.

PMID- 23209239
VI  - 194
DP  - 2012
TI  - Genome Sequence of Bacillus sp. Strain HYC-10, Isolated from Intestinal Tract Contents from a Marine Fish (Mugil cephalus).
PG  - 6991
AB  - Bacillus sp. strain HYC-10 was isolated with intestinal tract content of a fish,  Mugil
      cephalus, captured from the sea close to Xiamen Island, China. Here, we
      present the draft genome of strain HYC-10, which contains 3,611,918 bp with a G+C
      content of 41.30% and contains 3,687 protein-coding genes and 33 tRNA genes.
AU  - Lai Q
AU  - Liu Y
AU  - Shao Z
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6991.

PMID- 23209202
VI  - 194
DP  - 2012
TI  - Genome Sequence of an Alkane-Degrading Bacterium, Alcanivorax pacificus Type Strain W11-5, Isolated from Deep Sea Sediment.
PG  - 6936
AB  - Alcanivorax pacificus W11-5(T) was isolated from a pyrene-degrading consortium, enriched from
      the deep sea sediment of the Pacific Ocean. Strain W11-5(T) can
      degrade various n-alkanes. Here we report the draft genome of W11-5(T) and genes
      associated with alkane degradation.
AU  - Lai Q
AU  - Shao Z
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6936.

PMID- 23209207
VI  - 194
DP  - 2012
TI  - Genome Sequence of Oceanibaculum indicum Type Strain P24.
PG  - 6942
AB  - Oceanibaculum indicum type strain P24 was isolated from a
      polycyclic-aromatic-hydrocarbon-degrading consortium enriched from a
      deep-seawater sample collected from the Indian Ocean. Here we present the draft
      genome of strain P24(T), which contains 3,952,792 bp with a G+C content of 65.5%
      and contains 3,755 protein-coding genes and 45 tRNAs.
AU  - Lai Q
AU  - Shao Z
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6942.

PMID- 23209215
VI  - 194
DP  - 2012
TI  - Genome Sequence of Thalassospira profundimaris Type Strain WP0211.
PG  - 6956
AB  - Thalassospira profundimaris WP0211(T) was isolated from a pyrene-degrading consortium,
      enriched from deep-sea sediment collected from the West Pacific
      Ocean. Here, we present the draft genome of strain WP0211(T), which contains
      4,380,232 bp with a G+C content of 55.19% and contains 4,040 protein-coding genes
      and 45 tRNAs.
AU  - Lai Q
AU  - Shao Z
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6956.

PMID- 23209216
VI  - 194
DP  - 2012
TI  - Genome Sequence of Thalassospira xiamenensis Type Strain M-5.
PG  - 6957
AB  - Thalassospira xiamenensis M-5(T) was isolated from the surface water of a waste oil pool at
      the oil storage dock in the city of Xiamen, Fujian Province, China.
      Here, we present the draft genome of strain M-5(T), which contains 4,705,237 bp
      with a G+C content of 54.65% and contains 4,343 protein-coding genes and 46 tRNA
      genes.
AU  - Lai Q
AU  - Shao Z
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6957.

PMID- 23209226
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Alkane-Degrading Bacterium Alcanivorax hongdengensis Type  Strain A-11-3.
PG  - 6972
AB  - Alcanivorax hongdengensis A-11-3(T) was isolated from an oil-enriched consortium  enriched
      from the surface seawater of Hong-Deng dock in the Straits of Malacca
      and Singapore. Strain A-11-3(T) can degrade n-alkane and produce a lipopeptide
      biosurfactant. Here we report the genome of A-11-3(T) and the genes associated
      with alkane degradation.
AU  - Lai Q
AU  - Shao Z
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6972.

PMID- 23209203
VI  - 194
DP  - 2012
TI  - Genome Sequence of Gallaecimonas xiamenensis Type Strain 3-C-1.
PG  - 6937
AB  - Gallaecimonas xiamenensis 3-C-1(T) was isolated from a crude-oil-degrading consortium enriched
      from the surface seawater around Xiamen Island. Here, we
      present the draft genome of strain 3-C-1(T), which contains 4,062,282 bp with a
      G+C content of 60.58% and contains 3,798 protein-coding genes and 65 tRNAs.
AU  - Lai Q
AU  - Wang L
AU  - Wang W
AU  - Shao Z
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6937.

PMID- 23209204
VI  - 194
DP  - 2012
TI  - Genome Sequence of Idiomarina xiamenensis Type Strain 10-D-4.
PG  - 6938
AB  - Idiomarina xiamenensis strain 10-D-4(T) was isolated from an oil-degrading consortium enriched
      from surface seawater around the Xiamen island. Here, we
      present the draft genome of strain 10-D-4(T), which contains 2,899,282 bp with a
      G+C content of 49.48% and contains 2,673 protein-coding genes and 43 tRNA genes.
AU  - Lai Q
AU  - Wang L
AU  - Wang W
AU  - Shao Z
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6938.

PMID- 26847900
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequencing Reveals a New Genospecies of Methylobacterium sp. GXS13,  Isolated from Vitis vinifera L. Xylem Sap.
PG  - e01695-15
AB  - The whole-genome sequence of a new genospecies of Methylobacterium sp., named GXS13 and
      isolated from grapevine xylem sap, is reported and demonstrates
      potential for methylotrophy, cytokinin synthesis, and cell wall modification. In
      addition, biosynthetic gene clusters were identified for cupriachelin,
      carotenoid, and acyl-homoserine lactone using the antiSMASH server.
AU  - Lai WX
AU  - Gan HM
AU  - Hudson AO
AU  - Savka MA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01695-15.

PMID- 11083844
VI  - 68
DP  - 2000
TI  - Identification of genes present specifically in a virulent strain of Klebsiella pneumoniae.
PG  - 7149-7151
AB  - Klebsiella pneumoniae is a common cause of septicemia and urinary tract infections. The
      PCR-supported genomic subtractive hybridization was
      employed to identify genes specifically present in a virulent strain of K.
      pneumoniae. Analysis of 25 subtracted DNA clones has revealed 19 distinct
      nucleotide sequences. Two of the sequences were found to be the genes
      encoding the transposase of Tn3926 and a capsule polysaccharide exporting
      enzyme. Three sequences displayed moderate homology with bvgAS, which
      encodes a two-component signal transduction system in Bordetella
      pertussis. The rest of the sequences did not exhibit homology with any
      known genes. The distribution of these novel sequences varied greatly in
      K. pneumoniae clinical isolates, reflecting the heterogeneous nature of
      the K. pneumoniae population.
AU  - Lai YC
AU  - Yang SL
AU  - Peng HL
AU  - Chang HY
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2000 68: 7149-7151.

PMID- 8675039
VI  - 171
DP  - 1996
TI  - The unique organization of the rpoB region of Spiroplasma citri: a restriction and modification system gene is adjacent to rpoB.
PG  - 95-98
AB  - A 6.5-kb DNA fragment containing the gene (rpoB) encoding the RNA polymerase (RNAP) beta
      subunit, from the mollicute Spiroplasma citri (Sc), was cloned and sequenced.  The classical
      eubacterial organization, with the genes (rplK, A, J and L) encoding ribosomal proteins L11,
      L1, L10 and L12 located immediately upstream from rpoB, was not found in the Sc DNA.  Instead,
      an open reading frame (hsdS) potentially encoding a component of a type I restriction and
      modification system was identified upstream from rpoB, and sequences showing similarities with
      insertion elements were found between hsdS and rpoB.
AU  - Laigret F
AU  - Gaurivaud P
AU  - Bove J-M
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1996 171: 95-98.

PMID- 21304700
VI  - 2
DP  - 2010
TI  - Complete genome sequence of Spirosoma linguale type strain (1).
PG  - 176-185
AB  - Spirosoma linguale Migula 1894 is the type species of the genus. S. linguale is a free-living
      and non-pathogenic organism, known for its peculiar ringlike and
      horseshoe-shaped cell morphology. Here we describe the features of this organism,
      together with the complete genome sequence and annotation. This is only the third
      completed genome sequence of a member of the family Cytophagaceae. The 8,491,258
      bp long genome with its eight plasmids, 7,069 protein-coding and 60 RNA genes is
      part of the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Lail K et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 2: 176-185.

PMID- 26112792
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus CRL871, a Folate-Producing Strain Isolated from a Northwestern Argentinian Yogurt.
PG  - e00693-15
AB  - Lactobacillus delbrueckii subsp. bulgaricus CRL871 is the first strain of L. delbrueckii
      subsp. bulgaricus reported as a folate-producing strain. We report
      the draft genome sequence of L. delbrueckii subsp. bulgaricus CRL871 (2,063,981
      bp, G+C content of 49.1%). This strain is of great biotechnological importance to
      the dairy industry because it constitutes an alternative to folic acid
      fortification.
AU  - Laino JE
AU  - Hebert EM
AU  - Savoy-de-Giori G
AU  - LeBlanc JG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00693-15.

PMID- 24115540
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences of Strains of Pasteurella multocida Isolated from the United Kingdom and the United States.
PG  - e00773-13
AB  - Pasteurella multocida is a major pathogen of farm animals and has worldwide distribution. Here
      we report the draft genome sequences of four strains that were
      isolated from animals in the United Kingdom and the United States and represent
      pathogenic and commensal presentation of the bacterium.
AU  - Lainson FA
AU  - Dagleish MP
AU  - Fontaine M
AU  - Bayne C
AU  - Hodgson JC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00773-13.

PMID- 24092794
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Pasteurella multocida A:3 Strain 671/90.
PG  - e00803-13
AB  - Pasteurella multocida serogroup A is commonly isolated from nasal swabs of clinically healthy
      calves and also from diseased lung tissue in bovine pneumonia.
      Here, we report the draft genome sequence of the virulent strain P. multocida
      671/90, which has been characterized previously in experimental infections of
      calves and mice.
AU  - Lainson FA
AU  - Dagleish MP
AU  - Fontaine MC
AU  - Bayne C
AU  - Hodgson JC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00803-13.

PMID- 7537636
VI  - 81
DP  - 1995
TI  - Suppression of intestinal neoplasia by DNA hypomethylation.
PG  - 197-205
AB  - We have used a combination of genetics and pharmacology to assess the effects of reduced DNA
      methyltransferase activity on ApcMin-induced intestinal neoplasia in mice. A reduction in the
      DNA methyltransferase activity in Min mice due to heterozygosity of the DNA methyltransferase
      gene, in conjunction with a weekly dose of the DNA methyltransferase inhibitor
      5-aza-deoxycytidine, reduced the average number of intestinal adenomas from 113 in the control
      mice to only 2 polyps in the treated heterozygotes. Hence, DNA methyl-transferase activity
      contributes substantially to tumor developments in this mouse model of intestinal neoplasia.
      Our results argue against an oncogenic effect of DNA hypomethylation. Moreover, they are
      consistent with a role for DNA methyltransferase in the generation of the C to T transitions
      seen at high frequency in human colorectal tumors.
AU  - Laird PW
AU  - Jackson-Grusby L
AU  - Fazeli A
AU  - Dickinson SL
AU  - Jung WE
AU  - Li E
AU  - Weinberg RA
AU  - Jaenisch R
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1995 81: 197-205.

PMID- 8982461
VI  - 30
DP  - 1996
TI  - The role of DNA methylation in cancer genetics and epigenetics.
PG  - 441-464
AB  - The past few years have seen a wider acceptance of a role for DNA methylation in cancer.  This
      can be attributed to three developments.  First, the documentation of the over-representation
      of mutations at CpG dinucleotides has convincingly implicated DNA methylation in the
      generation of oncogenic point mutations.  The second important advance has been the
      demonstration of epigenetic silencing of tumor suppressor genes by DNA methylation.  The third
      development has been the utilization of experimental methods to manipulate DNA methylation
      levels.  These studies demonstrate that DNA methylation changes in cancer cells are not mere
      by-products of malignant transformation, but can play an instrumental role in the cancer
      process.  It seems clear that DNA methylation plays a variety of roles in different cancer
      types and probably at different stages of oncogenesis.  DNA methylation is intricately
      involved in a wide diversity of cellular processes.  Likewise, it appears to exert its
      influence on the cancer process through a diverse array of mechanisms.  It is our task not
      only to identify these mechanisms, but to determine their relative importance for each state
      and type of cancer.  Our hope then will be to translate that knowledge into clinical
      applications.
AU  - Laird PW
AU  - Jaenisch R
PT  - Journal Article
TA  - Annu. Rev. Genet.
JT  - Annu. Rev. Genet.
SO  - Annu. Rev. Genet. 1996 30: 441-464.

PMID- 8446035
VI  - 7
DP  - 1993
TI  - Genetic analysis of the phi C31-specific phage growth limitation (Pgl) system of  Streptomyces coelicolor A3(2).
PG  - 329-336
AB  - The phage growth limitation (Pgl) system of Streptomyces coelicolor A3(2) was shown to be
      specific to phi C31 homo-immune phages, and to be absent from the
      closely related strain Streptomyces lividans. A 16 kb fragment of S. coelicolor
      A3(2) DNA was isolated which complemented the Pgl- phenotype of J1501, a pgl
      mutant derivative of the Pglts S. coelicolor strain M130. The cloned DNA
      complemented only half of the available pgl mutants, which therefore represented
      at least two groups, designated Pgl class A and class B strains. It follows that
      more than one kind of high-frequency genetic event can lead to the Pgl-
      phenotype. Crosses between class A and class B strains yielded high frequencies
      of Pgl+ recombinants. Crosses between strains of the same class gave no Pgl+
      recombinants. The cloned DNA was altered by deletion or apparent point mutation
      upon passage through the two class B strains tested, such that it was no longer
      capable of complementing class A strains. This accumulation of mutations might
      suggest that the expression of the cloned DNA is toxic to at least some class B
      strains. The nature of the genetic instability associated with the Pgl system was
      not detectable by Southern blot analysis.
AU  - Laity C
AU  - Chater KF
AU  - Lewis CG
AU  - Buttner MJ
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1993 7: 329-336.

PMID- 24136966
VI  - 342
DP  - 2013
TI  - Genomically Recoded Organisms Expand Biological Functions.
PG  - 357-360
AB  - We describe the construction and characterization of a genomically recoded organism (GRO). We
      replaced all known UAG stop codons in Escherichia coli MG1655 with synonymous UAA codons,
      which permitted the deletion of release factor 1 and reassignment of UAG translation function.
      This
      GRO exhibited improved properties for incorporation of nonstandard amino acids that expand the
      chemical diversity of proteins in vivo. The GRO also exhibited increased resistance to T7
      bacteriophage, demonstrating that new genetic codes could enable increased viral resistance.
AU  - Lajoie MJ
AU  - Rovner AJ
AU  - Goodman DB
AU  - Aerni H-R
AU  - Haimovich AD
AU  - Kuznetsov G
AU  - Mercer JA
AU  - Wang HH
AU  - Carr PA
AU  - Mosberg JA
AU  - Rohland N
AU  - Schultz PG
AU  - Jacobson JM
AU  - Rinehart J
AU  - Church GM
AU  - Isaacs FJ
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2013 342: 357-360.

PMID- 24136844
VI  - 1
DP  - 2013
TI  - Genome Sequences of Listeria monocytogenes Serotype 4b Variant Strains Isolated from Clinical and Environmental Sources.
PG  - e00771-13
AB  - Listeria monocytogenes strains that show a novel PCR serotyping profile (IVb-v1)  have been
      reported recently. Here, we announce the draft genome sequences of five
      L. monocytogenes IVb-v1 strains isolated from the United States and Australia
      that harbor a 6.3-kb DNA cassette characteristic of serotype 1/2a strains.
AU  - Laksanalamai P
AU  - Steyert SR
AU  - Burall LS
AU  - Datta AR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00771-13.

PMID- 24855307
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Multidrug-Resistant Mycobacterium tuberculosis Strain CWCFVRF MDRTB 670, Isolated from the Sputum of a Patient from Chennai, India,  with Clinically Suspected Tuberculosis.
PG  - e00475-14
AB  - We announce the draft genome sequence of a multidrug-resistant Mycobacterium tuberculosis
      strain (CWCFVRF MDRTB 670) isolated from sputum from a patient with
      clinically suspected tuberculosis.
AU  - Lakshmipathy D
AU  - Vetrivel U
AU  - Irudayam LT
AU  - Ramasubban G
AU  - Madhavan HN
AU  - Sridhar R
AU  - Meenakshi N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00475-14.

PMID- 25035331
VI  - 2
DP  - 2014
TI  - Whole Genome Sequence of Polyresistant Mycobacterium tuberculosis CWCFVRF PRTB 19 Sputum Isolate from Chennai, India, Closely Clustering with East African Indian 5  Genogroup.
PG  - e00702-14
AB  - We announce the draft genome sequence of a polyresistant Mycobacterium tuberculosis strain
      (CWCFVRF PRTB 19) isolated from the sputum of a clinically
      suspected tuberculosis patient, and it closely clusters to the East African
      Indian 5 (EAI5) lineage.
AU  - Lakshmipathy D
AU  - Vetrivel U
AU  - Ramasubban G
AU  - Kulandai LT
AU  - Madhavan HN
AU  - Sridhar R
AU  - Meenakshi N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00702-14.

PMID- 23704187
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Cellulolytic, Mesophilic, Anaerobic Bacterium Clostridium termitidis Strain CT1112 (DSM 5398).
PG  - e00281-13
AB  - Here, we report the draft genome sequence of Clostridium termitidis strain CT1112 (DSM 5398),
      a mesophilic, cellulolytic bacterium that can utilize a variety of
      sugars, as well as pure cellulose, as a sole carbon source; it also synthesizes
      fermentation end products with potential industrial applications.
AU  - Lal S
AU  - Ramachandran U
AU  - Zhang X
AU  - Munir R
AU  - Sparling R
AU  - Levin DB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00281-13.

PMID- 24136853
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Hydrogen- and Ethanol-Producing Bacterium Clostridium intestinale Strain URNW.
PG  - e00871-13
AB  - Here, we report the draft genome sequence of Clostridium intestinale strain URNW, which can
      convert biomass to useful products such as biofuels (hydrogen or
      ethanol) and other soluble end products.
AU  - Lal S
AU  - Ramachandran U
AU  - Zhang X
AU  - Sparling R
AU  - Levin DB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00871-13.

PMID- 29074669
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Rhodococcus enclensis 23b-28, a Model Strain Isolated from Cloud Water.
PG  - e01199-17
AB  - The whole genome of Rhodococcus enclensis 23b-28, a bacterial strain isolated from cloud
      water, was sequenced. This microorganism is equipped with genes able
      to degrade aromatic compounds and could thus play a role in complex organic
      matter decomposition in cloud water.
AU  - Lallement A
AU  - Besaury L
AU  - Eyheraguibel B
AU  - Amato P
AU  - Sancelme M
AU  - Mailhot G
AU  - Delort AM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01199-17.

PMID- 22366422
VI  - 194
DP  - 2012
TI  - Comparative Analysis of the First Complete Enterococcus faecium Genome.
PG  - 2334
AB  - Vancomycin-resistant enterococci (VRE) are one of the leading causes of nosocomial infections
      in healthcare facilities around the globe. In particular, infections caused by
      vancomycin-resistant Enterococcus faecium are becoming increasingly common. Comparative and
      functional genomic studies of E. faecium isolates have so far been limited owing to the lack
      of a fully assembled E. faecium genome sequence. Here we address this issue and report the
      complete 3.0 Mb genome sequence of the multi-locus sequence type 17 vancomycin-resistant
      Enterococcus faecium strain Aus0004, isolated from the bloodstream of a patient in Melbourne,
      Australia in 1998. The genome comprises a 2.9 Mb circular chromosome and three circular
      plasmids. The chromosome harbours putative E. faecium virulence factors such as enterococcal
      surface protein, hemolysin and collagen-binding adhesion. Aus0004 has a very large accessory
      genome (38%) that includes, three prophage and two genomic islands absent among 22 other E.
      faecium genomes. One of the prophage was present as inverted 50kb repeats that appear to have
      facilitated a 683 kb chromosomal inversion across the replication terminus, resulting in a
      striking replichore imbalance. Other distinctive features include 95 insertion sequence
      elements and a single chromosomal copy of Tn1549 containing the vanB vancomycin-resistance
      element. A complete E. faecium genome will be a useful resource to assist our understanding of
      this emerging nosocomial pathogen.
AU  - Lam MC
AU  - Seemann T
AU  - Bulach DM
AU  - Gladman SL
AU  - Chen H
AU  - Haring V
AU  - Moore RJ
AU  - Ballard S
AU  - Grayson ML
AU  - Johnson PD
AU  - Howden BP
AU  - Stinear TP
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2334.

PMID- 1420162
VI  - 31
DP  - 1992
TI  - Spectroscopic studies of arsenic(III) binding to Escherichia coli RI methyltransferase and to two mutants, C223S and W183F.
PG  - 10438-10442
AB  - The interactions of an arsenic(III) reagent, (CH3)2AsSCH2CONH2, with two Escherichia coli RI
      methyltransferase mutants, W183F and C223S, have been studied by phosphorescence, optically
      detected magnetic resonance, and fluorescence spectroscopy. The phosphorescence specrum of the
      W183F mutant containing only one tryptophan at position 225 reveals a single 0,0-band that is
      red-shifted by 9.8 nm upon binding of As(III). Fluorescence titration of W183F with
      (CH3)2AsSCH2CONH2 produces a large tryptophan fluorescence quenching. Analysis of the
      quenching data points to a single high-affinity As(III) binding site that is associated with
      the fluorescence quenching. Triplet-state kinetic measurements performed on the perturbed
      tryptophan show large reductions in the lifetimes of the triplet sublevels, especially that of
      the Tx sublevel. As(III) binding to the enzymes at a site very close to the Trp225 residue
      induces an external heavy-atom effect, showing that the perturber atom is in van der Waals
      contact with the indole chromophore. In the case of the C223S mutant, a single tryptophan
      0,0-band also is observed in the phosphorescence spectrum but no change occurs upon addition
      of the As(III) reagent. Fluorescence titration of C223S with As(III) shows essentially no
      quenching of tryptophan fluorescence, in contrast with W183F. These results along with
      previous triplet-state and biochemical studies on the wild-type enzyme [Tsao,D.H>H., & Maki,
      A.H. (1991) Biochemistry 30, 4565-4572], show that As(III) binds with high affinity to the
      Cys223 residue and that the Trp225 side chain is located close enough to that of Cys223 to
      produce a heavy-atom perturbation when As(III) is bound.
AU  - Lam WC
AU  - Tsao DHH
AU  - Maki AH
AU  - Maegley KA
AU  - Reich NO
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1992 31: 10438-10442.

PMID- 27133026
VI  - 24
DP  - 2016
TI  - Indirect DNA Sequence Recognition and Its Impact on Nuclease Cleavage Activity.
PG  - 862-873
AB  - LAGLIDADG meganucleases are DNA cleaving enzymes used for genome engineering. While their
      cleavage specificity can be altered using several protein engineering
      and selection strategies, their overall targetability is limited by highly
      specific indirect recognition of the central four base pairs within their
      recognition sites. In order to examine the physical basis of indirect sequence
      recognition and to expand the number of such nucleases available for genome
      engineering, we have determined the target sites, DNA-bound structures, and
      central four cleavage fidelities of nine related enzymes. Subsequent
      crystallographic analyses of a meganuclease bound to two noncleavable target
      sites, each containing a single inactivating base pair substitution at its
      center, indicates that a localized slip of the mutated base pair causes a small
      change in the DNA backbone conformation that results in a loss of metal occupancy
      at one binding site, eliminating cleavage activity.
AU  - Lambert AR
AU  - Hallinan JP
AU  - Shen BW
AU  - Chik JK
AU  - Bolduc JM
AU  - Kulshina N
AU  - Robins LI
AU  - Kaiser BK
AU  - Jarjour J
AU  - Havens K
AU  - Scharenberg AM
AU  - Stoddard BL
PT  - Journal Article
TA  - Structure
JT  - Structure
SO  - Structure 2016 24: 862-873.

PMID- 18400177
VI  - 16
DP  - 2008
TI  - Structures of the Rare-Cutting Restriction Endonuclease NotI Reveal a Unique Metal Binding Fold Involved in DNA Binding.
PG  - 558-569
AB  - The structure of the rare-cutting restriction endonuclease NotI, which recognizes the 8 bp
      target 5'-GCGGCCGC-3', has been solved with and
      without bound DNA. Because of its specificity (recognizing a site that
      occurs once per 65 kb), NotI is used to generate large genomic fragments
      and to map DNA methylation status. NotI contains a unique metal binding
      fold, found in a variety of putative endonucleases, occupied by an iron
      atom coordinated within a tetrahedral Cys4 motif. This domain positions
      nearby protein elements for DNA recognition, and serves a structural role.
      While recognition of the central six base pairs of the target is
      accomplished via a saturated hydrogen bond network typical of restriction
      enzymes, the most peripheral base pairs are engaged in a single direct
      contact in the major groove, reflecting reduced pressure to recognize
      those positions. NotI may represent an evolutionary intermediate between
      mobile endonucleases (which recognize longer target sites) and canonical
      restriction endonucleases.
AU  - Lambert AR
AU  - Sussman D
AU  - Shen B
AU  - Maunus R
AU  - Nix J
AU  - Samuelson J
AU  - Xu SY
AU  - Stoddard BL
PT  - Journal Article
TA  - Structure
JT  - Structure
SO  - Structure 2008 16: 558-569.

PMID- 6320895
VI  - 781
DP  - 1984
TI  - Resistance of DNA from filamentous and unicellular cyanobacteria to restriction endonuclease cleavage.
PG  - 45-55
AB  - Chromosomal DNA from nine species of filamentous cyanobacteria as
      diverse as Nostoc, Gloeotrichia and Plectonema is suggested to be extensively modified
      (methylated) by its resistance to cleavage by a number of restriction endonucleases.  A
      remarkably similar pattern of DNA modification in these species contrasts with the known
      heterogeneity of their type II restriction endonuclease content.  In particular, Nostoc PCC
      73102, which lacks detectable sequence-specific endonucleases, is shown to possess
      extensive DNA modification.  The use of isoschizomers demonstrates the presence of a
      methylase in the filamentous strains analogous to the dam enzyme of Escherichia coli.  As a
      preliminary to assessing the significance of the DNA modification, a study of susceptibility
      to restriction endonuclease cleavage of the genomes of five unicellular cyanobacteria
      revealed considerable variation between the different strains.  The significance of the DNA
      modification patterns elucidated is discussed in terms of the restriction endonuclease
      content and cellular differentiation of the relevant cyanobacterial strains.
AU  - Lambert GR
AU  - Carr NG
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1984 781: 45-55.

PMID- Not carried by PubMed...
VI  - 49
DP  - 1996
TI  - The chemistry of biology: Molecular evolution, the total synthesis of proteins, and DNA restriction and modification.
PG  - 1179-1196
AB  - Three topics of current interest in modern biological organic chemistry are presented:
      molecular evolution, the total synthesis of proteins, and the study of DNA restriction and
      modification systems.  These topics are used to illustrate the application of chemical
      understanding to the study of chemistry in a biological context.
AU  - Lambert JN
PT  - Journal Article
TA  - Aust. J. Chem.
JT  - Aust. J. Chem.
SO  - Aust. J. Chem. 1996 49: 1179-1196.

PMID- 24604643
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Lactococcus lactis subsp. cremoris HPT, the First Defined-Strain Dairy Starter Culture Bacterium.
PG  - e00107-14
AB  - Lactococcus lactis subsp. cremoris HP(T) has been widely used in studies of the metabolism of
      lactococcal dairy starter cultures. A comparison of the draft HP(T)
      genome with those from other strains of L. lactis subsp. cremoris will aid our
      understanding of the domestication and evolution of these important industrial
      cultures.
AU  - Lambie SC
AU  - Altermann E
AU  - Leahy SC
AU  - Kelly WJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00107-14.

PMID- 26413197
VI  - 10
DP  - 2015
TI  - The complete genome sequence of the rumen methanogen Methanosarcina barkeri CM1.
PG  - 57
AB  - Methanosarcina species are the most metabolically versatile of the methanogenic Archaea and
      can obtain energy for growth by producing methane via the
      hydrogenotrophic, acetoclastic or methylotrophic pathways. Methanosarcina barkeri
      CM1 was isolated from the rumen of a New Zealand Friesian cow grazing a
      ryegrass/clover pasture, and its genome has been sequenced to provide information
      on the phylogenetic diversity of rumen methanogens with a view to developing
      technologies for methane mitigation. The 4.5 Mb chromosome has an average G + C
      content of 39 %, and encodes 3523 protein-coding genes, but has no plasmid or
      prophage sequences. The gene content is very similar to that of M. barkeri Fusaro
      which was isolated from freshwater sediment. CM1 has a full complement of genes
      for all three methanogenesis pathways, but its genome shows many differences from
      those of other sequenced rumen methanogens. Consequently strategies to mitigate
      ruminant methane need to include information on the different methanogens that
      occur in the rumen.
AU  - Lambie SC
AU  - Kelly WJ
AU  - Leahy SC
AU  - Li D
AU  - Reilly K
AU  - McAllister TA
AU  - Valle ER
AU  - Attwood GT
AU  - Altermann E
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 57.

PMID- 2536590
VI  - 56
DP  - 1989
TI  - Infectious introns.
PG  - 323-326
AB  - Among the most vigorously debated questions in modern biology is whether introns were present
      in primordial genes and subsequently lost from most present-day prokaryotes or whether they
      are more recent additions to eukaryotic genes. While it is not necessarily true that all
      introns originated in the same way from a common ancestor, recent studies, represented by four
      papers in this issue of Cell, provide definitive evidence that a number of group I introns can
      propagate themselves by insertion of group II introns and for relationships between these
      introns and autonomous elements.
AU  - Lambowitz AM
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1989 56: 323-326.

PMID- 8352597
VI  - 62
DP  - 1993
TI  - Introns as mobile genetic elements.
PG  - 587-622
AB  - *

      Introduction

      Intron Structure and Splicing Pathway

      Group I introns

      Group II introns

      Archaeal introns

      Intron Mobility

      Intron distribution

      Intron-encoded proteins

      Intron acquisition or loss

      Autonomous introns and intronlike elements

      An autonomous Group II intron -- a-senDNA

      Mitochondrial plasmids of neurospora

      Intron evaluation

      Introns early and late

      ORF acquisition and evolution of group I intron mobility

      Acquisition of group II intron ORFs

      Regulation of intron mobility

      Horizontal transmission?

      Concluding remarks

      

AU  - Lambowitz AM
AU  - Belfort M
PT  - Journal Article
TA  - Annu. Rev. Biochem.
JT  - Annu. Rev. Biochem.
SO  - Annu. Rev. Biochem. 1993 62: 587-622.

PMID- 
VI  - 
DP  - 1999
TI  - Group I and Group II ribozymes as RNPs: Clues to the past and guides to the future.
PG  - 451-485
AB  - Group I and group II introns are not only catalytic RNAs, but also mobile genetic elements.
      The success of these introns as mobile elements almost certainly relates to their innate
      self-splicing capability, which enables them to propagate by inserting into host genes while
      only minimally impairing gene expression.  Nevertheless, both types of introns have become
      dependent on proteins for efficient splicing in vivo to help fold the intron RNA into the
      catalytically active structure.  A review.
AU  - Lambowitz AM
AU  - Caprara MG
AU  - Zimmerly S
AU  - Perlman PS
PT  - Journal Article
TA  - The RNA World
JT  - The RNA World
SO  - The RNA World 1999 : 451-485.

PMID- 
VI  - 16
DP  - 2005
TI  - Group II intron homing endonucleases: ribonucleoprotein complexes with programmable target specificity.
PG  - 121-145
AB  - Group II intron homing endonucleases are ribonucleoproteins consisting of a catalytically
      active intron RNA and an intron-encoded protein, with reverse transcriptase and/or DNA
      endonuclease activity.  The RNP is formed when the IEP binds to the intron in unspliced RNA
      and promotes its splicing by stabilizing the catalytically active RNA structure.  Afterwards,
      the IEP remains tightly bound to the excised intron RNA to constitute the homing endonuclease.
      The homing endonuclease promotes intron mobility by a remarkable mechanism in which the intron
      RNA reverse splices directly into a target DNA and is then reverse-transcribed by the IEP.
      Importantly, the target site for intron insertion is determined mainly by base pairing between
      short sequence elements in the intron RNA and target DNA, making it straightforward to change
      the target specificity of the homing endonuclease simply by modifying the intron RNA.  This
      feature combined with their very high specificity and insertion frequencies have made it
      possible to develop mobile group II introns into gene targeting vectors, called "targetrons",
      with programmable target specificity.
AU  - Lambowitz AM
AU  - Mohr G
AU  - Zimmerly S
PT  - Journal Article
TA  - Nucleic Acids Mol. Biol.
JT  - Nucleic Acids Mol. Biol.
SO  - Nucleic Acids Mol. Biol. 2005 16: 121-145.

PMID- 25767234
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Lactobacillus plantarum Lp90 Isolated from Wine.
PG  - e00097-15
AB  - Here, we describe the draft genome sequence and annotation of Lactobacillus plantarum strain
      Lp90, the first sequenced genome of a L. plantarum strain
      isolated from wine. This strain has a noticeable ropy phenotype and showed
      potential probiotic properties. The genome consists of 3,324,076 bp (33 contigs)
      and contains 3,155 protein coding genes, 34 pseudogenes, and 84 RNA genes.
AU  - Lamontanara A
AU  - Caggianiello G
AU  - Orru L
AU  - Capozzi V
AU  - Michelotti V
AU  - Bayjanov JR
AU  - Renckens B
AU  - van Hijum SA
AU  - Cattivelli L
AU  - Spano G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00097-15.

PMID- 24994801
VI  - 2
DP  - 2014
TI  - Genome Sequence of Oenococcus oeni OM27, the First Fully Assembled Genome of a Strain Isolated from an Italian Wine.
PG  - e00658-14
AB  - Oenococcus oeni OM27 is a strain selected from 'Nero di Troia' wine undergoing spontaneous
      malolactic fermentation. 'Nero di Troia' is a wine made from 'Uva di
      Troia' grapes, an autochthonous black grape variety from the Apulian region
      (south of Italy). In this paper we present a 1.78-Mb assembly of the O. oeni OM27
      genome, the first fully assembled genome of an O. oeni strain from an Italian
      wine.
AU  - Lamontanara A
AU  - Orru L
AU  - Cattivelli L
AU  - Russo P
AU  - Spano G
AU  - Capozzi V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00658-14.

PMID- 28280034
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Enterobacter sp. Strain ODB01, a Bacterium That Degrades Crude Oil.
PG  - e01763-16
AB  - Enterobacter sp. strain ODB01, which was isolated from the Changqing oil field, can degrade
      crude oil efficiently and use crude oil as its sole source of carbon
      and energy. We report the complete genome sequence of ODB01. The results promote
      its application in the remediation of petroleum contaminants.
AU  - Lan H
AU  - Yang H
AU  - Li P
AU  - Wang C
AU  - Zhou H
AU  - Zhou H
AU  - Pan H
AU  - Yu Y
AU  - Lu X
AU  - Tian Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01763-16.

PMID- 20383462
VI  - 42
DP  - 2010
TI  - DNA methyltransferases and methyl-binding proteins of mammals.
PG  - 243-252
AB  - In mammals, DNA methylation, characterized by the transfer of the methyl group from
      S-adenosylmethionines to a base (mainly referred to cytosine), acts as a major epigenetic
      modification. In parallel to DNA sequences arrangement, modification of methylation to DNA
      sequences has far-reaching influence on biological functions and activities, for it involves
      controlling gene transcription, regulating chromatin structure, sustaining genome stability
      and integrity, maintaining parental imprinting and X-chromosome inactivation, suppressing
      homologous recombination as well as limiting transposable elements, during which DNA
      methyltransferases (DNMTs) and methyl-binding proteins play important roles. Their aberrance
      can give rise to dysregulation of gene expression, cell maltransformation and so on. Hence, it
      is necessary to gain a good understanding of these two important kinds of proteins, which will
      help to better investigate the epigenetic mechanisms and manipulate the modifications
      according to our will based on its reversibility. Here we briefly review our current
      understanding of DNMTs and methyl-binding proteins in mammals.
AU  - Lan J
AU  - Hua S
AU  - He XN
AU  - Zhang Y
PT  - Journal Article
TA  - Acta Biochim. Biophys. Sin.
JT  - Acta Biochim. Biophys. Sin.
SO  - Acta Biochim. Biophys. Sin. 2010 42: 243-252.

PMID- 
VI  - 9
DP  - 2010
TI  - cDNA Cloning of Goat DNA Methyltransferase 1, Screening of shRNA Vectors and Influences to Development of Nuclear Transfer Embryos.
PG  - 1035-1040
AB  - This study was designed to clone cDNA of goat DNA methyltransferase 1 (DNMT1) gene, to screen
      an effective shRNA-producing vector targeting
      goat DNA methyltransferase 1 and to improve the developmental
      competence of goat nuclear transfer embryos by decreasing the DNMT1
      expression in donor cells. In this study, PCR primers were designed
      against regions of high homology between bovine and sheep sequences and
      then used to amplify the larger portions of the coding regions. Next, 3
      RNAi oligonucleotides were designed based on the cloned sequences and
      inserted into pRNAT-U6.1/Neo vector, acquiring 3 new vectors,
      respectively termed pRNAD1, pRNAD2 and pRNAD3. Then the positive cells
      were sorted by flow cytometry after transfection and detected by
      real-time PCR analysis and sodium bisulfite genomic sequencing.
      Finally, the developmental rates of nuclear transfer (NT) embryos
      generated using donor cells with and without the effective shRNA vector
      respectively, as well as in vitro fertilization (IVF) embryos were
      observed and recorded. The results showed that the coding regions of
      goat DNA methyltransferase 1 gene was successfully cloned (GenBank no.
      FJ617538). Furthermore, an effective interfering shRNA (pRNAD2) was
      obtained, with its interference effect being 47.88%. Finally, NT
      embryos with shRNA vector harbored better developmental competence
      during morula and blastocyst stage compared to controls (P<0.05),
      reaching the similar rates to IVF embryos (P>0.05). In conclusion, goat
      DNA methyltransferase 1 gene cDNA was cloned and sequenced, an
      effective shRNA vector responsible for inhibiting DNA methyltransferase
      1 expression was developed and the developmental competence of goat
      nuclear transfer morulae and blastcysts was significantly improved,
      which provided a feasible pathway for improving goat nuclear transfer
      embryo development competence by decreasing the methylation level in
      donor cells through RNAi-mediated manner.
AU  - Lan J
AU  - Hua S
AU  - Liu J
AU  - Zhang Y
PT  - Journal Article
TA  - Agric. Sci. China
JT  - Agric. Sci. China
SO  - Agric. Sci. China 2010 9: 1035-1040.

PMID- 19286788
VI  - 75
DP  - 2009
TI  - Characterization of a New Plasmid-Like Prophage in a Pandemic Vibrio parahaemolyticus O3:K6 Strain.
PG  - 2659-2667
AB  - Vibrio parahaemolyticus is a common food-borne pathogen that is normally associated with
      seafood. In 1996, a pandemic O3:K6 strain
      abruptly appeared and caused the first pandemic of this pathogen to
      spread throughout many Asian countries, America, Europe, and Africa.
      The role of temperate bacteriophages in the evolution of this pathogen
      is of great interest. In this work, a new temperate phage, VP882, from
      a pandemic O3: K6 strain of V. parahaemolyticus was purified and
      characterized after mitomycin C induction. VP882 was a Myoviridae
      bacteriophage with a polyhedral head and a long rigid tail with a
      sheath-like structure. It infected and lysed high proportions of V.
      parahaemolyticus, Vibrio vulnificus, and Vibrio cholerae strains. The
      genome of phage VP882 was sequenced and was 38,197 bp long, and 71
      putative open reading frames were identified, of which 27 were putative
      functional phage or bacterial genes. VP882 had a linear plasmid-like
      genome with a putative protelomerase gene and cohesive ends. The genome
      does not integrate into the host chromosome but was maintained as a
      plasmid in the lysogen. Analysis of the reaction sites of the
      protelomerases in different plasmid-like phages revealed that VP882 and
      Phi HAP-1 were highly similar, while N15, Phi KO2, and PY54 made up
      another closely related group. The presence of DNA adenine methylase
      and quorum-sensing transcriptional regulators in VP882 may play a
      specific role in this phage or regulate physiological or
      virulence-associated traits of the hosts. These genes may also be
      remnants from the bacterial chromosome following transduction.
AU  - Lan SF
AU  - Huang CH
AU  - Chang CH
AU  - Liao WC
AU  - Lin IH
AU  - Jian WN
AU  - Wu YG
AU  - Chen SY
AU  - Wong HC
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2009 75: 2659-2667.

PMID- 27151784
VI  - 4
DP  - 2016
TI  - Near-Complete Genome Sequence of Clostridium paradoxum Strain JW-YL-7.
PG  - e00229-16
AB  - Clostridium paradoxum strain JW-YL-7 is a moderately thermophilic anaerobic alkaliphile
      isolated from the municipal sewage treatment plant in Athens, GA. We
      report the near-complete genome sequence of C. paradoxum strain JW-YL-7 obtained
      by using PacBio DNA sequencing and Pilon for sequence assembly refinement with
      Illumina data.
AU  - Lancaster WA
AU  - Utturkar SM
AU  - Poole FL
AU  - Klingeman DM
AU  - Elias DA
AU  - Adams MW
AU  - Brown SD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00229-16.

PMID- 27811109
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Strain LSUCC0135, an Early Diverging Member of the Order Methylophilales in the Phylum Betaproteobacteria.
PG  - e01231-16
AB  - We present the draft genome of Methylophilales sp. strain LSUCC0135, isolated using
      high-throughput dilution-to-extinction culturing methods from the coast of
      Freshwater City, Louisiana, USA. The genome indicates metabolic flexibility for
      differing oxygen concentrations and electron donors.
AU  - Lanclos VC
AU  - Henson MW
AU  - Pitre DM
AU  - Thrash JC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01231-16.

PMID- 21304633
VI  - 1
DP  - 2009
TI  - Complete genome sequence of Beutenbergia cavernae type strain (HKI 0122).
PG  - 21-28
AB  - Beutenbergia cavernae (Groth et al. 1999) is the type species of the genus and is of
      phylogenetic interest because of its isolated location in the actinobacterial
      suborder Micrococcineae. B. cavernae HKI 0122(T) is a Gram-positive, non-motile,
      non-spore-forming bacterium isolated from a cave in Guangxi (China). B. cavernae
      grows best under aerobic conditions and shows a rod-coccus growth cycle. Its cell
      wall peptidoglycan contains the diagnostic L-lysine <-- L-glutamate interpeptide
      bridge. Here we describe the features of this organism, together with the
      complete genome sequence, and annotation. This is the first completed genome
      sequence from the poorly populated micrococcineal family Beutenbergiaceae, and
      this 4,669,183 bp long single replicon genome with its 4225 protein-coding and 53
      RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Land M et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2009 1: 21-28.

PMID- 21304636
VI  - 1
DP  - 2009
TI  - Complete genome sequence of Actinosynnema mirum type strain (101).
PG  - 46-53
AB  - Actinosynnema mirum Hasegawa et al. 1978 is the type species of the genus, and is of
      phylogenetic interest because of its central phylogenetic location in the
      Actino-synnemataceae, a rapidly growing family within the actinobacterial
      suborder Pseudo-nocardineae. A. mirum is characterized by its motile spores borne
      on synnemata and as a producer of nocardicin antibiotics. It is capable of
      growing aerobically and under a moderate CO(2) atmosphere. The strain is a
      Gram-positive, aerial and substrate mycelium producing bacterium, originally
      isolated from a grass blade collected from the Raritan River, New Jersey. Here we
      describe the features of this organism, together with the complete genome
      sequence and annotation. This is the first complete genome sequence of a member
      of the family Actinosynnemataceae, and only the second sequence from the
      actinobacterial suborder Pseudonocardineae. The 8,248,144 bp long single replicon
      genome with its 7100 protein-coding and 77 RNA genes is part of the Genomic
      Encyclopedia of Bacteria and Archaea project.
AU  - Land M et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2009 1: 46-53.

PMID- 21677860
VI  - 4
DP  - 2011
TI  - Non-contiguous finished genome sequence of Bacteroides coprosuis type strain (PC139).
PG  - 233-243
AB  - Bacteroides coprosuis Whitehead et al. 2005 belongs to the genus Bacteroides, which is a
      member of the family Bacteroidaceae. Members of the genus Bacteroides
      in general are known as beneficial protectors of animal guts against pathogenic
      microorganisms, and as contributors to the degradation of complex molecules such
      as polysaccharides. B. coprosuis itself was isolated from a manure storage pit of
      a swine facility, but has not yet been found in an animal host. The species is of
      interest solely because of its isolated phylogenetic location. The genome of B.
      coprosuis is already the 5(th) sequenced type strain genome from the genus
      Bacteroides. The 2,991,798 bp long genome with its 2,461 protein-coding and 78
      RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea
      project.
AU  - Land M et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 4: 233-243.

PMID- 1479902
VI  - 216
DP  - 1992
TI  - Characterization of Type II DNA-Methyltransferases.
PG  - 244-259
AB  - 
AU  - Landry D
AU  - Barsomian JM
AU  - Feehery GR
AU  - Wilson GG
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1992 216: 244-259.

PMID- 2744483
VI  - 77
DP  - 1989
TI  - M.FokI methylates adenine in both strands of its asymmetric recognition sequence.
PG  - 1-10
AB  - M.FokI, a type-IIS modification enzyme from Flavobacterium okeanokoites, was purified, and its
      activity was characterized in vitro.  The enzyme was found to be a DNA-adenine
      methyltransferase and to methylate both strands of the asymmetric FokI recognition sequence:
      M.FokI
      5'-GGATG / CCTAC-5' M.FokI-> 5'-GGm6ATG/CCTm6AC-5.  M.FokI does not methylate
      single-stranded DNA, nor does it methylate double-stranded DNA at sequences other than FokI
      sites.
AU  - Landry D
AU  - Looney MC
AU  - Feehery GR
AU  - Slatko BE
AU  - Jack WE
AU  - Schildkraut I
AU  - Wilson GG
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1989 77: 1-10.

PMID- 11972330
VI  - 30
DP  - 2002
TI  - Two self-splicing group I introns in the ribonucleotide reductase large subunit gene of Staphylococcus aureus phage Twort.
PG  - 1935-1943
AB  - We have recently described three group I introns inserted into a single gene, orf142, of the
      staphylococcal bacteriophage Twort and suggested the presence of at least two additional
      self-splicing introns in this phage genome. Here we report that two previously uncharacterized
      introns, 429 and 1087 nt in length, interrupt the Twort gene coding for the large subunit of
      ribonucleotide reductase (nrdE). Reverse transcription-polymerase chain reaction (RT-PCR) of
      RNA isolated from Staphylococcus aureus after phage infection indicates that the introns are
      removed from the primary transcript in vivo. Both nrdE introns show sequence similarity to the
      Twort orf142 introns I2 and I3, suggesting either a common origin of these introns or
      shuffling of intron structural elements. Intron 2 encodes a DNA endonuclease, I-TwoI, with
      similarity to homing endonucleases of the HNH family. Like I-HmuI and I-HmuII, intron-encoded
      HNH endonucleases in Bacillus subtilis phages SPO1 and SP82, I-TwoI nicks only one strand of
      its DNA recognition sequence. However, whereas I-HmuI and I-HmuII cleave the template strand
      in exon 2, I-TwoI cleaves the coding strand in exon 1. In each case, the 3' OH created on the
      cut strand is positioned to prime DNA synthesis towards the intron, suggesting that this
      reaction contributes to the mechanism of intron homing. Both nrdE introns are inserted in
      highly conserved regions of the ribonucleotide reductase gene, next to codons for functionally
      important residues.
AU  - Landthaler M
AU  - Begley U
AU  - Lau NC
AU  - Shub DA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2002 30: 1935-1943.

PMID- 15205433
VI  - 186
DP  - 2004
TI  - Group I intron homing in Bacillus phages SPO1 and SP82: A gene conversion event initiated by a nicking homing endonuclease.
PG  - 4307-4314
AB  - Many group I introns encode endonucleases that promote intron homing by initiating a
      double-stranded break-mediated homologous recombination event. In this work we describe intron
      homing in Bacillus subtilis phages SPO1 and SP82. The introns encode the DNA endonucleases
      I-HmuI and I-HmuII, respectively, which belong to the H-N-H endonuclease family and possess
      nicking activity in vitro. Coinfections of B. subtilis with intron-minus and intron-plus
      phages indicate that I-HmuI and I-HmuII are required for homing of the SPO1 and SP82 introns,
      respectively. The homing process is a gene conversion event that does not require the major B.
      subtilis recombination pathways, suggesting that the necessary functions are provided by
      phage-encoded factors. Our results provide the first examples of H-N-H endonuclease-mediated
      intron homing and the first demonstration of intron homing initiated by a nicking
      endonuclease.
AU  - Landthaler M
AU  - Lau NC
AU  - Shub DA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2004 186: 4307-4314.

PMID- 16569414
VI  - 358
DP  - 2006
TI  - I-Basl and I-Hmul: Two phage intron-encoded endonucleases with homologous DNA recognition sequences but distinct DNA Specificities.
PG  - 1137-1151
AB  - I-HmuI and I-BasI are two highly similar nicking DNA endonucleases, which are each encoded by
      a group I intron inserted into homologous sites within
      the DNA polymerase genes of Bacillus phages SPO1 and Bastille,
      respectively. Here, we present a comparison of the DNA specificities and
      cleavage activities of these enconucleases with homologous target sites.
      I-BasI has properties that are typical of homing endonucleases, nicking
      the intron-minus polymerase genes in either host genome, three nucleotides
      downstream of the intron insertion site. In contrast, I-HmuI nicks both
      the intron-plus and intron-minus site in its own host genome, but does not
      act on the target from Bastille phage. Although the enzymes have distinct
      DNA substrate specificities, both bind to an identical 25bp region of
      their respective intron-minus DNA polymerase genes surrounding the intron
      insertion site. The endonucleases appear to interact with the DNA
      substrates in the downstream exon 2 in a similar manner. However, whereas
      I-HmuI is known to make its only base-specific contacts within this exon
      region, structural modeling analyses predict that I-BasI might make
      specific base contacts both upstream and downstream of the site of intron
      insertion. The predicted requirement for base-specific contacts in exon 1
      for cleavage by I-BasI was confirmed experimentally. This explains the
      difference in substrate specificities between the two enzymes, including
      the observation that the former enzyme is relatively insensitive to the
      presence of an intron upstream of exon 2. These differences are likely a
      consequence of divergent evolutionary constraints.
AU  - Landthaler M
AU  - Shen BW
AU  - Stoddard BL
AU  - Shub DA
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2006 358: 1137-1151.

PMID- 12799434
VI  - 31
DP  - 2003
TI  - The nicking homing endonuclease I-BasI is encoded by a group I intron in the DNA polymerase gene of the Bacillus thuringiensis phage Bastille.
PG  - 3071-3077
AB  - Here we describe the discovery of a group I intron in the DNA polymerase gene of Bacillus
      thuringiensis phage Bastille. Although the intron
      insertion site is identical to that of the Bacillus subtilis phages SPO1
      and SP82 introns, the Bastille intron differs from them substantially in
      primary and secondary structure. Like the SPO1 and SP82 introns, the
      Bastille intron encodes a nicking DNA endonuclease of the H-N-H family,
      I-BasI, with a cleavage site identical to that of the SPO1-encoded enzyme
      I-HmuI. Unlike I-HmuI, which nicks both intron-minus and intron-plus DNA,
      I-BasI cleaves only intron-minus alleles, which is a characteristic of
      typical homing endonucleases. Interestingly, the C-terminal portions of
      these H-N-H phage endonucleases contain a conserved sequence motif, the
      intron-encoded endonuclease repeat motif (IENR1) that also has been found
      in endonucleases of the GIY-YIG family, and which likely comprises a small
      DNA-binding module with a globular betabetaalphaalphabeta fold, suggestive
      of module shuffling between different homing endonuclease families.
AU  - Landthaler M
AU  - Shub DA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2003 31: 3071-3077.

PMID- 4545997
VI  - 249
DP  - 1974
TI  - DNA fragments carrying genes for tRNATyrI.
PG  - 738-742
AB  - The duplicated genes coding for tRNA TyrI have been isolated using
      site-specific nucleases and gel electrophoresis.  An unduplicated sequence of
      4-120 base pairs separates the two genes.  Specific DNA fragments can be
      obtained in sizes appropriate for both functional and structural analysis of
      the tRNA TyrI region.
AU  - Landy A
AU  - Foeller C
AU  - Ross W
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1974 249: 738-742.

PMID- 4437524
VI  - 133
DP  - 1974
TI  - Isolation of a functional lac regulatory region.
PG  - 273-281
AB  - A DNA fragment containing the lac regulatory region has been isolated by
      digestion of lambda plac 5 DNA with restriction endonuclease from Hemophilus
      influenzae Rd followed by gel electrophoresis.  This DNA fragment, which is
      approximately 660 base pairs, is identified by its ability to bind purified lac
      repressor, and has been shown to be functional in a coupled
      transcription-translation system.  A smaller repressor binding fragment of
      approximately 174 base pairs has been derived from the larger fragment
      utilizing a secondary digestion with restriction endonuclease from Hemophilus
      aegyptius.
AU  - Landy A
AU  - Olchowski E
AU  - Ross W
AU  - Reiness G
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1974 133: 273-281.

PMID- 4545267
VI  - 13
DP  - 1974
TI  - Digestion of deoxyribonucleic acids from bacteriophage T7, lambda, and Phi80h with site-specific nucleases from Hemophilus influenzae strain Rc and strain Rd.
PG  - 2134-2142
AB  - The digestion profiles of DNA from bacteriophage T7, lambda, and Phi80h by the
      site-specific nucleases from Hemophilus influenzae strain Rc and strain Rd have
      been analyzed.  The DNA fragments range in molecular weight from approximately
      0.02 to 3 Md and are resolved by polyacrylamide-agarose gel electrophoresis.
      The digestion profiles thus produced are unique and characteristic for both the
      DNA and the nuclease.  The T7 DNA digestion products produced by the Rc and Rd
      nucleases are identical.  With Phi80h and lambda DNAs only 87 and 71%
      respectively, of the total number of fragments produced by the Rd nuclease are
      common to both nuclease digestions, the remaining DNA fragments being unique to
      either the Rc or the Rd digestions.  Strain Rc possesses a site-specific
      nuclease activity which is identical to an activity found in strain Rd.  In
      addition strain Rd carries a second activity which is not found in strain Rc
      and which elutes at slightly higher salt on phosphocellulose.  Protection
      experiments with individual modification methylases of strain Rd (Roy, P.H. and
      Smith, H.O. (1973), J. Mol. Biol. 81: 427) establish that the nuclease which is
      common to both Rd and Rc is associated with methylase II.  This nuclease in
      strain Rd is called HindII and in strain Rc is called HincII according to the
      nomenclature proposed by Smith and Nathans (Smith, H.O., and Nathans, D.
      (1973), J. Mol. Biol. 81: 419-423.  The additional activity which elutes second
      from phosphocellulose is HindIII.  The HincII-HindII activity (i.e., HincII or
      HindII) is best prepared from strain Rc.  It makes 34 cuts in lambda DNA, 43
      cuts in Phi80h DNA, and 51 cuts in T7 DNA.  The HindIII nuclease makes no cuts
      in T7 DNA and 6 and 4 cuts in lambda and Phi80h DNA, respectively.  A
      nomenclature system for the DNA digestion products is proposed and all the DNA
      fragments produced by Rc and Rd digestions of the three related phages, Phi80h
      ambl, Phi80h psuIII+-, and Phi80h psuIII+ are identified and their molecular
      weights are presented.
AU  - Landy A
AU  - Ruedisueli E
AU  - Robinson L
AU  - Foeller C
AU  - Ross W
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1974 13: 2134-2142.

PMID- 21304649
VI  - 1
DP  - 2009
TI  - Complete genome sequence of Dyadobacter fermentans type strain (NS114).
PG  - 133-140
AB  - Dyadobacter fermentans (Chelius and Triplett, 2000) is the type species of the genus
      Dyadobacter. It is of phylogenetic interest because of its location in the
      Cytophagaceae, a very diverse family within the order 'Sphingobacteriales'. D.
      fermentans has a mainly respiratory metabolism, stains Gram-negative, is
      non-motile and oxidase and catalase positive. It is characterized by the
      production of cell filaments in aging cultures, a flexirubin-like pigment and its
      ability to ferment glucose, which is almost unique in the aerobically living
      members of this taxonomically difficult family. Here we describe the features of
      this organism, together with the complete genome sequence, and its annotation.
      This is the first complete genome sequence of the sphingobacterial genus
      Dyadobacter, and this 6,967,790 bp long single replicon genome with its 5804
      protein-coding and 50 RNA genes is part of the Genomic Encyclopedia of Bacteria
      and Archaea project.
AU  - Lang E et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2009 1: 133-140.

PMID- 21475590
VI  - 4
DP  - 2011
TI  - Complete genome sequence of Weeksella virosa type strain (9751).
PG  - 81-90
AB  - Weeksella virosa Holmes et al. 1987 is the sole member and type species of the genus Weeksella
      which belongs to the family Flavobacteriaceae of the phylum
      Bacteroidetes. Twenty-nine isolates, collected from clinical specimens provided
      the basis for the taxon description. While the species seems to be a saprophyte
      of the mucous membranes of healthy man and warm-blooded animals a causal
      relationship with disease has been reported in a few instances. Except for the
      ability to produce indole and to hydrolyze Tween and proteins such as casein and
      gelatin, this aerobic, non-motile, non-pigmented bacterial species is
      metabolically inert in most traditional biochemical tests. The 2,272,954 bp long
      genome with its 2,105 protein-coding and 76 RNA genes consists of one circular
      chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea
      project.
AU  - Lang E et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 4: 81-90.

PMID- 1865925
VI  - 352
DP  - 1991
TI  - Pseudo domains in phage-encoded DNA methyltransferases.
PG  - 645-648
AB  - 5-Cytosine-DNA-methyltransferases, which are found in many organisms ranging
      from bacteriophages to mammals, transfer a methyl group from
      S-adenosylmethionine to the carbon-5 of a cytosine residue in specific DNA
      target sequences.  Some phage-encoded methyltransferases methylate more than
      one sequence:  these enzymes contain several independent target-recognizing
      domains each responsible for recognizing a different site.  The amino-acid
      sequences of these multispecific methyltransferases reveal that some enzymes in
      addition carry domains that do not contribute to the enzymes' methylation
      potential, but strongly resemble previously identified target-recognizing
      domains.  Here we show that introducing defined amino-acid alterations into
      these inactive domains endows these enzymes with additional methylation
      specificities.  Gel retardation analysis demonstrates that these novel
      methylation specificities correlate with the acquisition of additional
      DNA-binding potential of the proteins.
AU  - Lange C
AU  - Jugel A
AU  - Walter J
AU  - Noyer-Weidner M
AU  - Trautner TA
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1991 352: 645-648.

PMID- 2055471
VI  - 100
DP  - 1991
TI  - M.H2I, a multispecific 5C-DNA methyltransferase encoded by Bacillus amyloliquefaciens phage H2.
PG  - 213-218
AB  - Bacillus amyloliquefaciens phage H2 codes for a multispecific
      cytosine-5-DNA-methyltransferase (MTase), M.H2I, which methylates GGCC, GCNGC
      and G(A/G/T)GC(T/C/A)C target sequences.  The gene coding for M.H2I was cloned
      in Escherichia coli and its nucleotide (nt) sequence was determined.  It
      consists of 1509 bp, corresponding to a protein of 503 amino acids (aa) with a
      calculated Mr of 57,166.  A comparison of the aa sequence of M.H2I with those
      of the multispecific MTases encoded by Bacillus subtilis phages SPR, Phi3T and
      Rho11S, revealed that M.H2I is closely related to these enzymes.  A very high
      degree of homology was observed between M.H2I and M.Rho11S, with 96.2% aa
      identity and 97.8% nt identity of the corresponding genes.
AU  - Lange C
AU  - Noyer-Weidner M
AU  - Trautner TA
AU  - Weiner M
AU  - Zahler SA
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1991 100: 213-218.

PMID- 7607474
VI  - 157
DP  - 1995
TI  - Altered sequence recognition specificity of a C5-DNA methyltransferase carrying a chimeric 'target recognizing domain'.
PG  - 127-128
AB  - A MTase with a chimeric TRD with the N-terminal half derived from a TRD recognizing GCNGC, the
      C-terminal half from one with CCWGG recognition, was constructed.  Its target specificity is
      reported (hemimethylation of the first C in GCTGGC).
AU  - Lange C
AU  - Wild C
AU  - Trautner TA
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 127-128.

PMID- 8635477
VI  - 15
DP  - 1996
TI  - Identification of a subdomain within DNA-(cytosine-C5)-methyltransferases responsible for the recognition of the 5' part of their DNA target.
PG  - 1443-1450
AB  - In previous work on DNA-(cytosine-C5)-methyltransferases (C5-MTases), domains had been
      identified which are responsible for the sequence specificity of the different enzymes
      (target-recognizing domains, TRDs).  Here we have analyzed the DNA methylation patterns of two
      C5-MTases containing reciprocal chimeric TRDs, consisting of the N- and C-terminal parts
      derived from two different parental TRDs specifying the recognition of 5'-CC(A/T)GG-3' and
      5'-GCNGC-3'.  Sequences recognized by these engineered MTases were non-symmetrical and
      degenerate, but contained at their 5' part a consensus sequence which was very similar to the
      5' part of the target recognized by the parental TRD which contributed the N-terminal moiety
      of the chimeric TRD.  The results are discussed in connection with the present understanding
      of the mechanism of DNA target recognition of C5-MTases.  They demonstrate the possibility of
      designing C5-MTases with novel DNA methylation specificities.
AU  - Lange C
AU  - Wild C
AU  - Trautner TA
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1996 15: 1443-1450.

PMID- 7720955
VI  - 9
DP  - 1995
TI  - Colinearity between amino acids of the target recognizing domains of a C5-DNA-methyltransferase and the nucleotide sequence of its target.
PG  - A1391
AB  - Cytosine (C5)-DNA methyltransferases (C5-MTases) are composed of several highly conserved
      domains involved in general steps of the methylation reaction and one variable target
      recognizing domain (TRD), which is responsible for the recognition of the enzymes' specific
      DNA targets.  TRDs have between about 30 and 50 amino acids of different composition.  We have
      constructed two MTases with recombinant TRDs combining the amino- and carboxy terminal halves
      of two (parental) TRDs, which recognize the pentameric sequences 5'-GCNGC (I) and
      5'-CC(A/T)GG (II).  DNA methylated by the recombinant enzymes was treated with bisulfite to
      distinguish cytosines from methyl-cytosines and then sequenced.  We observe that the TRD whose
      amino terminus was derived from enzyme (I) recognized hexameric, non-symmetrical sequences
      with the consensus 5'-GCTGGC.  The reciprocal TRD was inactive, but could be activated by
      site specific mutagenesis to recognize the target 5'-PyNCCPyPy.  Neither of the enzymes
      methylated the parental sequence.  The results are compatible with the three dimensional
      structure of M.HhaI complexed with its DNA target, where two sequential recognition loops of
      the TRD interact with contiguous parts of the DNA target.
AU  - Lange C
AU  - Wild C
AU  - Trautner TA
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1995 9: A1391.

PMID- Not included in PubMed...
VI  - 59
DP  - 1989
TI  - Effect of restriction-modification systems on transfer of foreign DNA into Lactococcus lactis subsp. lactis.
PG  - 301-306
AB  - The efficiency of transfer of plasmid pIP501 DNA into Restriction/Modification
      (R/M) proficient strains of Lactococcus lactis subsp. lactis strongly depends
      on the mode of transfer.  In two strains, each one containing a different R/M
      system, the efficiency of protoplast transformation with unmodified pIP501 DNA
      was restriction by more than 3 orders of magnitude when compared to pIP501
      carrying the host modification.  By contrast, no difference was observed when
      modified or unmodified DNA was introduced into the same hosts by
      electroporation.  The pIP501 conjugation frequency between a R-/M- donor an an
      isogenic recipient were also unaffected whether the recipient possesses a R/M
      system or not.
AU  - Langella P
AU  - Chopin A
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1989 59: 301-306.

PMID- 18541926
VI  - 11
DP  - 2008
TI  - Cleavage of mispaired heteroduplex DNA substrates by numerous restriction enzymes.
PG  - 1-12
AB  - The utility of restriction endonucleases as a tool in molecular biology is in large part due
      to the high degree of specificity with which they
      cleave well-characterized DNA recognition sequences. The specificity of
      restriction endonucleases is not absolute, yet many commonly used
      assays of biological phenomena and contemporary molecular biology
      techniques rely on the premise that restriction enzymes will cleave
      only perfect cognate recognition sites. In vitro, mispaired
      heteroduplex DNAs are commonly formed, especially subsequent to
      polymerase chain reaction amplification. We investigated a panel of
      restriction endonucleases to determine their ability to cleave
      mispaired heteroduplex DNA substrates. Two straightforward,
      non-radioactive assays are used to evaluate mispaired heteroduplex DNA
      cleavage: a PCR amplification method and an oligonucleotide-based
      assay. These assays demonstrated that most restriction endonucleases
      are capable of site-specific double-strand cleavage with heteroduplex
      mispaired DNA substrates, however, certain mispaired substrates do
      effectively abrogate cleavage to undetectable levels. These data are
      consistent with mispaired substrate cleavage previously reported for
      Eco RI and, importantly, extend our knowledge of mispaired heteroduplex
      substrate cleavage to 13 additional enzymes.
AU  - Langhans MT
AU  - Palladino MJ
PT  - Journal Article
TA  - Curr. Issues Mol. Biol.
JT  - Curr. Issues Mol. Biol.
SO  - Curr. Issues Mol. Biol. 2008 11: 1-12.

PMID- 6298727
VI  - 11
DP  - 1983
TI  - Does the specific recognition of DNA by the restriction endonuclease EcoRI involve a linear diffusion step?  Investigation of the processivity of the EcoRI endonuclease.
PG  - 501-513
AB  - The time course of the EcoRI endonuclease catalysed cleavage of three
      substrates, two plasmid DNAs and one oligonucleotide, each with two EcoRI
      sites, was measured.  The two plasmid DNAs with the EcoRI sites 318 and 96 base
      pairs apart are cut in a distributive fashion, while the oligonucleotide with
      the EcoRI sites 8 base pairs apart is cut in a partially processive manner.  It
      is concluded that a linear diffusion of the EcoRI endonuclease on its substrate
      across long stretches of DNA is not likely to be operative during the
      recognition process.  Microscopic dissociation-reassociation processes,
      however, increase the probability of the enzyme to attack further sites located
      in the immediate vicinity of a given site.
AU  - Langowski J
AU  - Alves J
AU  - Pingoud A
AU  - Maass G
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1983 11: 501-513.

PMID- 6255431
VI  - 8
DP  - 1980
TI  - Inhibition of EcoRI action by polynucleotides.  A characterization of the non-specific binding of the enzyme to DNA.
PG  - 4727-4736
AB  - The cleavage of the plasmid pBR322 by the restriction endonuclease EcoRI has
      been studied in the presence of various polynucleotides and the double stranded
      octanucleotide d-(GGAATTCC) in order to clarify whether there is a preferential
      interation of EcoRI with DNA sequences other than -GAATTC-.  The steady state
      kinetic analysis shows that all polynucleotides investigated with the possible
      exception of poly-dG.poly-dC inhibit the cleavage competitively with Ki values
      in the range of 10-4 to 10-5 [M nucleotides].  The Ki of d-(GGAATTCC) is
      1.5.10-6 [M nucleotides], indicating that the specific binding is approx. 2
      orders of magnitude stronger than non-specific binding.
AU  - Langowski J
AU  - Pingoud A
AU  - Goppelt M
AU  - Maass G
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1980 8: 4727-4736.

PMID- 6269084
VI  - 9
DP  - 1981
TI  - Transient cleavage kinetics of the EcoRI restriction endonuclease measured in a pulsed quench-flow apparatus:  enzyme concentration-dependent activity change.
PG  - 3483-3490
AB  - We report measurements of the cleavage rate of pBR322 plasmid DNA by
      restriction endonuclease EcoRI as a function of enzyme and DNA concentration.
      The reaction, which at high excess of enzyme over DNA occurs between 0.2 and 5
      seconds, was studied by the means of a microprocessor controlled pulsed
      quench-flow apparatus.  Enzyme concentrations were between 1 and 100 nM with
      DNA concentrations being 3 to 6 nM (specific EcoRI sites).  The catalytic
      constants for cleavage of the first and second phosphodiester bonds as measured
      at high enzyme concentration both have the same value of 0.35 sec-1 at 21C.  At
      enzyme concentrations comparable to or less than DNA concentration, the rate of
      the first cleavage is proportional to enzyme concentration, while the second
      step is independent of concentration.  At approx. 10 nM EcoRI endonuclease
      concentration, a rate increase shows up in both the first and the second
      cleavage.  We suggest that this increase is due to the tetramerization reported
      by Modrich & Zabel, which occurs in this concentration range.
AU  - Langowski J
AU  - Urbanke C
AU  - Pingoud A
AU  - Maass G
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1981 9: 3483-3490.

PMID- 17041037
VI  - 189
DP  - 2007
TI  - Genome Sequence of Avery's Virulent Serotype 2 Strain D39 of Streptococcus pneumoniae and Comparison with That of Unencapsulated Laboratory Strain  R6.
PG  - 38-51
AB  - Streptococcus pneumoniae (pneumococcus) is a leading human respiratory pathogen that causes a
      variety of serious mucosal and invasive diseases.
      D39 is an historically important serotype 2 strain that was used in
      experiments by Avery and coworkers to demonstrate that DNA is the genetic
      material. Although isolated nearly a century ago, D39 remains extremely
      virulent in murine infection models and is perhaps the strain used most
      frequently in current studies of pneumococcal pathogenesis. To date, the
      complete genome sequences have been reported for only two S. pneumoniae
      strains: TIGR4, a recent serotype 4 clinical isolate, and laboratory
      strain R6, an avirulent, unencapsulated derivative of strain D39. We
      report here the genome sequences and new annotation of two different
      isolates of strain D39 and the corrected sequence of strain R6.
      Comparisons of these three related sequences allowed deduction of the
      likely sequence of the D39 progenitor and mutations that arose in each
      isolate. Despite its numerous repeated sequences and IS elements, the
      serotype 2 genome has remained remarkably stable during cultivation, and
      one of the D39 isolates contains only five relatively minor mutations
      compared to the deduced D39 progenitor. In contrast, laboratory strain R6
      contains 71 single-base-pair changes, six deletions, and four insertions
      and has lost the cryptic pDP1 plasmid compared to the D39 progenitor
      strain. Many of these mutations are in or affect the expression of genes
      that play important roles in regulation, metabolism, and virulence. The
      nature of the mutations that arose spontaneously in these three strains,
      the relative global transcription patterns determined by microarray
      analyses, and the implications of the D39 genome sequences to studies of
      pneumococcal physiology and pathogenesis are presented and discussed.
AU  - Lanie JA
AU  - Ng WL
AU  - Kazmierczak KM
AU  - Andrzejewski TM
AU  - Davidsen TM
AU  - Wayne KJ
AU  - Tettelin H
AU  - Glass JI
AU  - Winkler ME
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2007 189: 38-51.

PMID- 9863048
VI  - 25
DP  - 1998
TI  - PCR-based random mutagenesis method using spiked oligonucleotides to randomize selected parts of a gene without any wild-type background.
PG  - 958-965
AB  - Site-directed mutagenesis is a common tool to analyze protein structure and function.  In
      polymerase chain reaction (PCR)-based SDM methods, the mutation is introduced by a PCR primer.
      Also, a restriction-enzyme-marker site is often introduced to allow fast and convenient
      screening for the presence of the mutation.  Usually, each primer encodes only one particular
      amino acid exchange.  In principle then, it is sufficient to identify one marker-positive
      clone.  Under these circumstances, the level of background of nonmutated genes is not
      important considering that more than approximately 20% of the clones carry the mutation.  If
      only 20% of the transformants contained a mutated gene, then screening 10-20 of the clones
      would be sufficient to identify at least one mutant, with a probability of 90%-99%.  However,
      the approach of introducing nucleotide exchanges into a gene by a PCR primer can be easily
      extended to randomize larger parts of the gene if spiked oligonucleotides, which contain some
      degree of a mixture of all 4 nucleotides, are used.  Then, one usually intends to isolate as
      many mutant clones as possible to obtain as large a library of mutated genes as possible.
      Because it is impossible with respect to time and cost to screen more than a few hundred
      clones, a method for mutagenesis that excludes the wild-type genes from the transformants with
      high confidence is required.
AU  - Lanio T
AU  - Jeltsch A
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 1998 25: 958-965.

PMID- 10948435
VI  - 29
DP  - 2000
TI  - Automated purification of His6-tagged proteins allows exhaustive screening of libraries generated by random mutagenesis.
PG  - 338-342
AB  - In the course of site-directed mutagenesis or directed evolution
      experiments, large numbers of
      protein variants are often generated. To characterize functional properties of
      individual
      mutant proteins in vitro, a rapid and reliable protein purification system is
      required. We
      have developed an automated method for the parallel purification of 96 different
      protein
      variants that takes about two hours. Using a 96-well format, the whole process
      can be
      performed automatically by a pipetting robot. Coupled with a suitable assay,
      again using a
      96-well format, all variants can be functionally characterized within a few
      hours. The protein
      purification procedure described here is based on the interaction between His6-
      tagged proteins
      and Ni-NTA-coated microplates. Typical yields are 3-8 pmol purified
      protein/well, which is
      sufficient to analyze most enzymatic activities. Using this procedure, we have
      purified and
      characterized variants of the restriction endonuclease EcoRV, which were
      produced in an effort
      to enhance the selectivity of this enzyme. For this purpose, three amino acid
      residues were
      randomized in a region known from the co-crystal structure to be located at the
      protein-DNA
      interface. From a library of about 1200 variants, predominantly single and
      double mutants,
      more than 1000 variants were purified and characterized in parallel, which
      corresponds to an
      almost complete screening of the library.
AU  - Lanio T
AU  - Jeltsch A
AU  - Pingoud A
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 2000 29: 338-342.

PMID- 10810159
VI  - 13
DP  - 2000
TI  - On the possibilities and limitations of rational protein design to expand the specificity of restriction enzymes: a case study employing EcoRV as the target.
PG  - 275-281
AB  - The restriction endonuclease EcoRV has been characterized in structural and functional terms
      in great detail. Based on this detailed information we employed a structure-guided approach to
      engineer variants of EcoRV that should be able to discriminate between differently flanked
      EcoRV recognition sites. In crystal structures of EcoRV complexed with d(CGGGATATCCC)(2) and
      d(AAAGATATCTT)(2), Lys104 and Ala181 closely approach the two base pairs flanking the GATATC
      recognition site and thus were proposed to be a reasonable starting point for the rational
      extension of site specificity in EcoRV [Horton,N.C. and Perona,J.J. (1998) J. Biol. Chem.,
      273, 21721-21729]. To test this proposal, several single (K104R, A181E, A181K) and double
      mutants of EcoRV (K104R/A181E, K104R/A181K) were generated. A detailed characterization of all
      variants examined shows that only the substitution of Ala181 by Glu leads to a considerably
      altered selectivity with both oligodeoxynucleotide and macromolecular DNA substrates, but not
      the predicted one, as these variants prefer cleavage of a TA flanked site over all other
      sites, under all conditions tested. The substitution of Lys104 by Arg, in contrast, which
      appeared to be very promising on the basis of the crystallographic analysis, does not lead to
      variants which differ very much from the EcoRV wild-type enzyme with respect to the flanking
      sequence preferences. The K104R/A181E and K104R/A181K double mutants show nearly the same
      preferences as the A181E and A181K single mutants. We conclude that even for the very well
      characterized restriction enzyme EcoRV, properties that determine specificity and selectivity
      are difficult to model on the basis of the available structural information.
AU  - Lanio T
AU  - Jeltsch A
AU  - Pingoud A
PT  - Journal Article
TA  - Protein Eng.
JT  - Protein Eng.
SO  - Protein Eng. 2000 13: 275-281.

PMID- 9761673
VI  - 283
DP  - 1998
TI  - Towards the design of rare cutting restriction endonucleases: using directed evolution to generate variants of EcoRV differing in their substrate specificity by two orders of magnitude.
PG  - 59-69
AB  - The restriction endonuclease EcoRV cleaves DNA highly specifically within GATATC sequences. In
      order to create EcoRV variants that have an extended recognition site we have employed a
      semi-rational random mutagenesis/selection procedure. Twenty-two amino acid residues were
      subjected to random mutagenesis and about 500 EcoRV variants representing three generations of
      mutants were screened. Among these some highly active variants that strongly prefer AT-flanked
      cleavage sites (e.g. S183A/Q224R, T93S/I103F/S183A/T222S or N97T/S183A/T222S) and others that
      prefer GC flanks (e.g. K104N/A181T) were identified. As wild-type EcoRV does not discriminate
      between these cleavage sites, the generation of these variants represents a significant first
      step towards redesigning EcoRV to become an 8 or 10 bp cutter. Such enzymes, only very rarely
      found in nature, could be extremely helpful for the manipulation of large DNA fragments.
AU  - Lanio T
AU  - Jeltsch A
AU  - Pingoud A
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1998 283: 59-69.

PMID- 8961353
VI  - 9
DP  - 1996
TI  - EcoRV-T94V: a mutant restriction endonucleaase with an altered substrate specificity towards modified oligodeoxynucleotides.
PG  - 1005-1010
AB  - Synthetic oligodeoxynucleotides with single methyl phosphonate substitutions were used for an
      analysis of the contribution of phosphate contacts to the recognition of the cleavage site by
      the restriction endonuclease EcoRV.  Only in the last position within the recognition
      sequence, is the methyl phosphonate substitution tolerated by the enzyme.  The wild type
      enzyme cleaves the SP diastereomer of the oligodeoxynucleotide GACGATATmpCGTC and the
      unmodified sequence with equal rates, whereas the RP diastereomer is cleaved much more slowly.
      Inspection of the crystal structure of an EcoRV-DNA complex revealed that the non-bridging
      oxygen atoms of the phosphodiester bond between the T and C bases are in hydrogen bonding
      distance of the hydroxyl group of the amino acid Thr94.  We therefore tried to engineer a
      variant of EcoRV that would prefer a methyl phosphonate linkage over a normal phophodiester
      bond and produced mutants with amino acid exchanges at position 94.  One of them, Thr94Val,
      shows a dramatically reduced activity towards the unmodified DNA and does not accept the RP
      diastereomer, but cleaves the SP diastereomer with the same rate as wild type EcoRV.  Its
      selectivity, i.e. the ratio of cleavage rates determined for the unmodified and modified
      substrates, differs by three orders of magnitude from that of the wild type enzyme.
AU  - Lanio T
AU  - Selent U
AU  - Wenz C
AU  - Wende W
AU  - Schulz A
AU  - Adiraj M
AU  - Katti SB
AU  - Pingoud A
PT  - Journal Article
TA  - Protein Eng.
JT  - Protein Eng.
SO  - Protein Eng. 1996 9: 1005-1010.

PMID- 2995029
VI  - 152
DP  - 1985
TI  - Cloning of DNA segments of phage 2C, which allows autonomous plasmid replication in Bacillus subtilis.
PG  - 137-142
AB  - The chromosome of Bacillus subtilis phage 2C is a 100-MDa double-stranded DNA molecule,
      containing hydroxymethyluracil in place of thymine and carrying redundant ends each
      encompassing 10% of the genome. 2C DNA was cleaved with EcoRI and HindIII, and cloned in the
      shuttle plasmids pSC 540 and pCP 115, both containing segments originating from B. subtilis
      and Escherichia coli plasmids. These chimaerical plasmids, carrying the chloramphenicol
      resistance gene, were unable to replicate in B. subtilis; this ability was restored, however,
      after the insertion of viral DNA segments. Physical maps of the recombinant plasmids were
      made; a large deletion of the E. coli-derived segment of pSC 540 was observed (which
      paralleled a loss of replication in this host), whereas addition of 2C DNA segments in pCP 115
      was not accompanied by deletion (replication in E. coli was conserved in this case). Cloned
      viral segments mapped mostly, but not exclusively, within the redundant ends of 2C DNA. It is
      suggested that the thirteen recombinant clones carried the replication origin region of phage
      2C DNA, and that these sequences originated within or close to the redundant extremities of
      the viral chromosome.
AU  - Lannoy NN
AU  - Hoet PP
AU  - Cocito CG
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1985 152: 137-142.

PMID- 23788541
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence and Annotation of the Entomopathogenic Bacterium Xenorhabdus nematophila Strain F1.
PG  - e00342-13
AB  - We report the 4.3-Mb genome sequence of Xenorhabdus nematophila strain F1, a Gram-negative
      bacterium that is a symbiont of the entomopathogenic nematode
      Steinernema carpocapsae and pathogenic by direct injection for a wide variety of
      insects.
AU  - Lanois A
AU  - Ogier JC
AU  - Gouzy J
AU  - Laroui C
AU  - Rouy Z
AU  - Givaudan A
AU  - Gaudriault S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00342-13.

PMID- 22072650
VI  - 193
DP  - 2011
TI  - Draft Genome Sequence of Bizionia argentinensis, Isolated from Antarctic Surface Water.
PG  - 6797-6798
AB  - A psychrotolerant marine bacterial strain, designated JUB59(T), was isolated from Antarctic
      surface seawater and classified as a new species
      of the genus Bizionia. Here, we present the first draft genome sequence
      for this genus, which suggests interesting features such as UV resistance,
      hydrolytic exoenzymes, and nitrogen metabolism.
AU  - Lanzarotti E
AU  - Pellizza L
AU  - Bercovich A
AU  - Foti M
AU  - Coria SH
AU  - Vazquez SC
AU  - Ruberto L
AU  - Hernandez EA
AU  - Dias RL
AU  - Mac CWP
AU  - Cicero DO
AU  - Smal C
AU  - Nicolas MF
AU  - Vasconcelos AT
AU  - Marti MA
AU  - Turjanski AG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6797-6798.

PMID- 3033822
VI  - 29
DP  - 1986
TI  - HsaI:  A restriction enzyme from human being.
PG  - 947-953
AB  - The HsaI restriction enzyme from the embryos of human, Homo sapiens, has been
      isolated with both the tissue extract and nuclear extract.  It proves to be an
      unusual enzyme, clearly related functionally to Type II endonuclease.  HsaI
      seems to be an isoschizomer of EcoRI, but it has a distinctive property of
      elution, differing from EcoRI.  Upon SDS-polyacrylamide gel electrophoresis,
      the enzyme preparation showed Coomassie blue staining bands, having the
      molecular weight of 65,000 and 22,000 daltons in size, respectively.
AU  - Lao W
AU  - Chen S
PT  - Journal Article
TA  - Sci. Sin.
JT  - Sci. Sin.
SO  - Sci. Sin. 1986 29: 947-953.

PMID- 22180813
VI  - 5
DP  - 2011
TI  - Genome sequence of the moderately thermophilic halophile Flexistipes sinusarabici strain (MAS10).
PG  - 86-96
AB  - Flexistipes sinusarabici Fiala et al. 2000 is the type species of the genus Flexistipes in the
      family Deferribacteraceae. The species is of interest because
      of its isolated phylogenetic location in a genomically under-characterized region
      of the tree of life, and because of its origin from a multiply extreme
      environment; the Atlantis Deep brines of the Red Sea, where it had to struggle
      with high temperatures, high salinity, and a high concentrations of heavy metals.
      This is the fourth completed genome sequence to be published of a type strain of
      the family Deferribacteraceae. The 2,526,590 bp long genome with its 2,346
      protein-coding and 53 RNA genes is a part of the Genomic Encyclopedia of Bacteria
      and Archaea project.
AU  - Lapidus A et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 5: 86-96.

PMID- 21304631
VI  - 1
DP  - 2009
TI  - Complete genome sequence of Brachybacterium faecium type strain (Schefferle 6-10).
PG  - 3-11
AB  - Brachybacterium faecium Collins et al. 1988 is the type species of the genus, and is of
      phylogenetic interest because of its location in the Dermabacteraceae, a
      rather isolated family within the actinobacterial suborder Micrococcineae. B.
      faecium is known for its rod-coccus growth cycle and the ability to degrade uric
      acid. It grows aerobically or weakly anaerobically. The strain described in this
      report is a free-living, nonmotile, Gram-positive bacterium, originally isolated
      from poultry deep litter. Here we describe the features of this organism,
      together with the complete genome sequence, and annotation. This is the first
      complete genome sequence of a member of the actinobacterial family
      Dermabacteraceae, and the 3,614,992 bp long single replicon genome with its 3129
      protein-coding and 69 RNA genes is part of the Genomic Encyclopedia of Bacteria
      and Archaea project.
AU  - Lapidus A et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2009 1: 3-11.

PMID- 22675589
VI  - 5
DP  - 2011
TI  - Genome sequence of the filamentous, gliding Thiothrix nivea neotype strain (JP2(T)).
PG  - 398-406
AB  - Thiothrix nivea (Rabenhorst 1865) Winogradsky 1888 (Approved Lists 1980) emend. Larkin and
      Shinabarger 1983 is the type species of the genus Thiothrix in the
      family Thiotrichaceae. The species is of interest not only because of its
      isolated location in the yet to be genomically characterized region of the tree
      of life, but also because of its life-style with gliding gonidia, the multilayer
      sheath, rosettes, and the embedded sulfur granules. Strain JP2(T) is the neotype
      strain of the species which was first observed by Rabenhorst in 1865 and later
      reclassified by Winogradsky in 1888 into the then novel genus Thiothrix. This is
      the first completed (improved-high-quality-draft) genome sequence to be published
      of a member of the family Thiotrichaceae. The genome in its current assembly
      consists of 15 contigs in four scaffolds with a total of 4,691,711 bp bearing
      4,542 protein-coding and 52 RNA genes and is a part of the Genomic Encyclopedia
      of Bacteria and Archaea project.
AU  - Lapidus A et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 5: 398-406.

PMID- 21622745
VI  - 193
DP  - 2011
TI  - Genomes of three methylotrophs from a single niche reveal the genetic and metabolic divergence of the Methylophilaceae.
PG  - 3757-3764
AB  - The genomes of three representatives of the family Methylophilaceae, Methylotenera mobilis
      JLW8, Methylotenera versatilis 301 and Methylovorus glucosetrophus SIP3-4, all isolated from a
      single study site, Lake Washington in Seattle, were completely sequenced. These were compared
      to each other and to the previously published genomes of Methylobacillus flagellatus KT and an
      unclassified Methylophilales strain HTCC2181. Comparative analysis revealed that the core
      genome of Methylophilaceae may be as small as approximately 600 genes while the pangenome may
      be as large as approximately 6000 genes. Significant divergence between the genomes was
      uncovered in terms of both gene content and gene and protein conservation, including varied
      presence of certain genes involved in methylotrophy. Overall, our data demonstrate that
      metabolic potentials can vary significantly between different species of Methylophilaceae,
      including organisms inhabiting the very same environment. These data suggest that genetic
      divergence among the members of this family may be responsible for their specialized and
      non-redundant functions in C1 cycling and in turn suggest means for their successful
      co-existence in their specific ecological niches.
AU  - Lapidus A
AU  - Clum A
AU  - Labutti K
AU  - Kaluzhnaya MG
AU  - Lim S
AU  - Beck DA
AU  - Glavina del Rio T
AU  - Nolan M
AU  - Mavromatis K
AU  - Huntemann M
AU  - Lucas S
AU  - Lidstrom ME
AU  - Ivanova N
AU  - Chistoserdova L
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3757-3764.

PMID- 27174280
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Branchiibius sp. NY16-3462-2, Isolated from a Mixed Clinical Sample.
PG  - e00368-16
AB  - Here, we report the release of a draft genome assembly of a Gram-positive cocci Branchiibius
      sp. NY16-3462-2 with a high-GC content, sequenced from a mixed
      clinical sample containing Mycobacterium tuberculosis This genome is the first
      publicly available sequence from a representative of the genus Branchiibius.
AU  - Lapierre P
AU  - Halse TA
AU  - Shea J
AU  - Escuyer VE
AU  - Musser KA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00368-16.

PMID- 19079266
VI  - 16
DP  - 2009
TI  - Structure of the motor subunit of type I restriction-modification complex EcoR124I.
PG  - 94-95
AB  - Type I restriction-modification enzymes act as conventional adenine methylases on
      hemimethylated DNAs, but unmethylated recognition targets
      induce them to translocate thousands of base pairs before cleaving
      distant sites nonspecifically. The first crystal structure of a type I
      motor subunit responsible for translocation and cleavage suggests how
      the pentameric translocating complex is assembled and provides a
      structural framework for translocation of duplex DNA by RecA-like
      ATPase motors.
AU  - Lapkouski M
AU  - Panjikar S
AU  - Janscak P
AU  - Smatanova IK
AU  - Carey J
AU  - Ettrich R
AU  - Csefalvay E
PT  - Journal Article
TA  - Nat. Struct. Mol. Biol.
JT  - Nat. Struct. Mol. Biol.
SO  - Nat. Struct. Mol. Biol. 2009 16: 94-95.

PMID- 17620716
VI  - 63
DP  - 2007
TI  - Purification, crystallization and preliminary X-ray analysis of the HsdR subunit of the EcoR124I endonuclease from Escherichia coli.
PG  - 582-585
AB  - EcoR124I is a multicomplex enzyme belonging to the type I restriction-modification system from
      Escherichia coli. Although
      EcoR124I has been extensively characterized biochemically, there is no
      direct structural information available about particular subunits. HsdR
      is a motor subunit that is responsible for ATP hydrolysis, DNA
      translocation and cleavage of the DNA substrate recognized by the
      complex. Recombinant HsdR subunit was crystallized using the
      sitting-drop vapour-diffusion method. Crystals belong to the primitive
      monoclinic space group, with unit-cell parameters a = 85.75, b =
      124.71, c = 128.37 angstrom, beta = 108.14 degrees. Native data were
      collected to 2.6 angstrom resolution at the X12 beamline of EMBL
      Hamburg.
AU  - Lapkouski M
AU  - Panjikar S
AU  - Smatanova IK
AU  - Csefalvay E
PT  - Journal Article
TA  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
JT  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
SO  - Acta Crystallogr. F Struct. Biol. Cryst. Commun. 2007 63: 582-585.

PMID- 29622614
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Bowmanella denitrificans JL63, a Bacterium Isolated from Whiteleg Shrimp (Litopenaeus vannamei) That Can Inhibit the Growth of Vibrio  parahaemolyticus.
PG  - e00215-18
AB  - Bowmanella denitrificans strain JL63 was isolated from a whiteleg shrimp (Litopenaeus
      vannamei) and was determined to have antibacterial activity against
      an acute hepatopancreatic necrosis disease (AHPND) strain of Vibrio
      parahaemolyticus Here, we report the draft genome sequence of this strain and
      identify genes that are potentially involved in its antibacterial activity.
AU  - LaPorte JP
AU  - Spinard EJ
AU  - Gomez-Chiarri M
AU  - Rowley DC
AU  - Mekalanos JJ
AU  - Nelson DR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00215-18.

PMID- 12601140
VI  - 15
DP  - 2002
TI  - Structural basis of ICF-causing mutations in the methyltransferase domain of DNMT3B.
PG  - 1005-1014
AB  - Mutations in the gene encoding for a de novo methyltransferase, DNMT3B, lead to an autosomal
      recessive Immunodeficiency, Centromeric instability and Facial anomalies (ICF) syndrome. To
      analyse the protein structure and consequences of ICF-causing mutations, we modelled the
      structure of the DNMT3B methyltransferase domain based on Haemophilus haemolyticus protein in
      complex with the cofactor AdoMet and the target DNA sequence. The structural model has a
      two-subdomain fold where the DNA-binding region is situated between the subdomains on a
      surface cleft having positive electrostatic potential. The smaller subdomains of the
      methyltransferases differ in length and sequences and therefore only the target recognition
      domain loop was modelled to show the location of an ICF-causing mutation. Based on the model,
      the DNMT3B recognizes the GC sequence and flips the cytosine from the double-stranded DNA to
      the catalytic pocket. The amino acids in the cofactor and target cytosine binding sites and
      also the electrostatic properties of the binding pockets are conserved. In addition, a
      registry of all known ICF-causing mutations, DNMT3Bbase, was constructed. The structural
      principles of the pathogenic mutations based on the modelled structure and the analysis of chi
      angle rotation changes of mutated side chains are discussed.
AU  - Lappalainen I
AU  - Vihinen M
PT  - Journal Article
TA  - Protein Eng.
JT  - Protein Eng.
SO  - Protein Eng. 2002 15: 1005-1014.

PMID- 28209814
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Axenic Strain Phormidesmispriestleyi ULC007, a Cyanobacterium Isolated from Lake Bruehwiler (Larsemann Hills, Antarctica).
PG  - e01546-16
AB  - Phormidesmis priestleyi ULC007 is an Antarctic freshwater cyanobacterium. Its draft genome is
      5,684,389 bp long. It contains a total of 5,604 protein-encoding
      genes, of which 22.2% have no clear homologues in known genomes. To date, this
      draft genome is the first one ever determined for an axenic cyanobacterium from
      Antarctica.
AU  - Lara Y
AU  - Durieu B
AU  - Cornet L
AU  - Verlaine O
AU  - Rippka R
AU  - Pessi IS
AU  - Misztak A
AU  - Joris B
AU  - Javaux EJ
AU  - Baurain D
AU  - Wilmotte A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01546-16.

PMID- 1328335
VI  - 59
DP  - 1992
TI  - Different bacteriophage resistance mechanisms in Streptococcus salivarius subsp. thermophilus.
PG  - 349-357
AB  - Streptococcus salivarius subsp. thermophilus strain NST5 exhibited a temperature-dependent
      defence mechanism against the virulent bacteriophages phiB1.2 and phiA1.1. It was active at 42
      degrees C but not at 30 degrees C as demonstrated by a significant increase of both plaque
      size and efficiency of plaquing. This defence mechanism did not affect host-dependent phage
      replication and did not interfere with phage adsorption to NST5. These results suggest that it
      interfered with phage development. The phages phiT33, phiT58, phiD1, phiT21 and phiT9,
      belonging to the same phage type as phiB1.2, were examined for their ability to infect NST3
      and NST5. Restriction modification systems of different specificity were detected in NST3 and
      NST5; host-dependent phage replication was detected at 30 and 42 degrees C; an abortive
      defence mechanism was detected in NST5 which was active at 42 degrees C, but not 30 degreesC,
      and was independent of restriction modification action or interference with phage adsorption.
      Our investigations of phage-host interactions showed that the two Str. salivarius subsp.
      thermophilus strains studied avoided attack by related bacteriophages by evolving at least
      three different resistance systems.
AU  - Larbi D
AU  - Decaris B
AU  - Simonet JM
PT  - Journal Article
TA  - J. Dairy Res.
JT  - J. Dairy Res.
SO  - J. Dairy Res. 1992 59: 349-357.

PMID- 2825126
VI  - 15
DP  - 1987
TI  - Cleavage by ApaI is inhibited by overlapping dcm methylation.
PG  - 9087
AB  - 
AU  - Larimer FW
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1987 15: 9087.

PMID- 4922217
VI  - 52
DP  - 1970
TI  - Host specificity of DNA produced by Escherichia coli.  XIII.  Breakdown of cellular DNA upon growth in ethionine of strains with r15+, r+P1 or r+N3 restriction phenotypes.
PG  - 337-348
AB  - All methionine-requiring strains of Escherichia coli which have been tested show a two-fold
      increase in DNA content when grown in the presence of ethionine or norleucine. In addition, E.
      coli strains with the restriction phenotype r15+, rP1+ or rN3+ will degrade their
      intracellular DNA when these methionine analogs are substituted for required methionine in the
      growth medium. Degradation does not occur in restriction-deficient mutants and in strains
      carrying the rK+, rA+ or rB+ phenotypes alone. Breakdown of DNA appears to be a characteristic
      of the restriction gene products rather than of the location of these genes on plasmid or
      chromosomal DNA molecules.
AU  - Lark C
AU  - Arber W
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1970 52: 337-348.

PMID- 23792746
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Staphylococcus aureus Strain M1, a Unique t024-ST8-IVa Danish Methicillin-Resistant S. aureus Clone.
PG  - e00336-13
AB  - We report the genome sequence, in five contigs, of a methicillin-resistant Staphylococcus
      aureus isolate designated M1. This clinical isolate was from the
      index patient of a methicillin-resistant Staphylococcus aureus (MRSA) outbreak in
      Copenhagen, Denmark, that started in 2003. This strain is sequence type 8 (ST8),
      spa type t024, and staphylococcal cassette chromosome mec element (SCCmec) type
      IVa.
AU  - Larner-Svensson H
AU  - Worning P
AU  - Bartels MD
AU  - Hestbjerg HL
AU  - Boye K
AU  - Westh H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00336-13.

PMID- 25918839
VI  - 10
DP  - 2015
TI  - Francisella tularensis Subtype A.II Genomic Plasticity in Comparison with Subtype A.I.
PG  - E0124906
AB  - Although Francisella tularensis is considered a monomorphic intracellular
      pathogen, molecular genotyping and virulence studies have demonstrated important
      differences within the tularensis subspecies (type A). To evaluate genetic
      variation within type A strains, sequencing and assembly of a new subtype A.II
      genome was achieved for comparison to other completed F. tularensis type A
      genomes. In contrast with the F. tularensis A.I strains (SCHU S4, FSC198,
      NE061598, and TI0902), substantial genomic variation was observed between the
      newly sequenced F. tularensis A.II strain (WY-00W4114) and the only other
      publically available A.II strain (WY96-3418). Genome differences between
      WY-00W4114 and WY96-3418 included three major chromosomal translocations, 1580
      indels, and 286 nucleotide substitutions of which 159 were observed in predicted
      open reading frames and 127 were located in intergenic regions. The majority of
      WY-00W4114 nucleotide deletions occurred in intergenic regions, whereas most of
      the insertions and substitutions occurred in predicted genes. Of the nucleotide
      substitutions, 48 (30%) were synonymous and 111 (70%) were nonsynonymous.
      WY-00W4114 and WY96-3418 nucleotide polymorphisms were predominantly G/C to A/T
      allelic mutations, with WY-00W4114 having more A+T enrichment. In addition, the
      A.II genomes contained a considerably higher number of intact genes and longer
      repetitive sequences, including transposon remnants than the A.I genomes.
      Together these findings support the premise that F. tularensis A.II may have a
      fitness advantage compared to the A.I subtype due to the higher abundance of
      functional genes and repeated chromosomal sequences. A better understanding of
      the selective forces driving F. tularensis genetic diversity and plasticity is
      needed.
AU  - Larson MA
AU  - Nalbantoglu U
AU  - Sayood K
AU  - Zentz EB
AU  - Bartling AM
AU  - Francesconi SC
AU  - Fey PD
AU  - Dempsey MP
AU  - Hinrichs SH
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2015 10: E0124906.

PMID- 19521508
VI  - 5
DP  - 2009
TI  - Molecular evolutionary consequences of niche restriction in Francisella tularensis, a facultative intracellular pathogen.
PG  - e1000472
AB  - Francisella tularensis is a potent mammalian pathogen well adapted to intracellular habitats,
      whereas F. novicida and F. philomiragia are less virulent
      in mammals and appear to have less specialized lifecycles. We explored
      adaptations within the genus that may be linked to increased host association, as
      follows. First, we determined the genome sequence of F. tularensis subsp.
      mediasiatica, the only subspecies that had not been previously sequenced. This
      genome, and those of 12 other F. tularensis isolates, were then compared to the
      genomes of F. novicida (three isolates) and F. philomiragia (one isolate). Signs
      of homologous recombination were found in approximately 19.2% of F. novicida and
      F. philomiragia genes, but none among F. tularensis genomes. In addition, random
      insertions of insertion sequence elements appear to have provided raw materials
      for secondary adaptive mutations in F. tularensis, e.g. for duplication of the
      Francisella Pathogenicity Island and multiplication of a putative glycosyl
      transferase gene. Further, the five major genetic branches of F. tularensis seem
      to have converged along independent routes towards a common gene set via
      independent losses of gene functions. Our observations suggest that despite an
      average nucleotide identity of >97%, F. tularensis and F. novicida have evolved
      as two distinct population lineages, the former characterized by clonal structure
      with weak purifying selection, the latter by more frequent recombination and
      strong purifying selection. F. tularensis and F. novicida could be considered the
      same bacterial species, given their high similarity, but based on the
      evolutionary analyses described in this work we propose retaining separate
      species names.
AU  - Larsson P
AU  - Elfsmark D
AU  - Svensson K
AU  - Wikstrom P
AU  - Forsman M
AU  - Brettin T
AU  - Keim P
AU  - Johansson A
PT  - Journal Article
TA  - PLoS Pathog.
JT  - PLoS Pathog.
SO  - PLoS Pathog. 2009 5: e1000472.

PMID- 19696314
VI  - 325
DP  - 2009
TI  - Creating bacterial strains from genomes that have been cloned and engineered in yeast.
PG  - 1693-1696
AB  - We recently reported the chemical synthesis, assembly, and cloning of a bacterial genome in
      yeast. To produce a synthetic cell, the genome must be transferred from yeast to a receptive
      cytoplasm. Here we describe methods to accomplish this. We cloned a Mycoplasma mycoides genome
      as a yeast centromeric plasmid and then transplanted it into Mycoplasma capricolum to produce
      a viable M. mycoides cell. While in yeast, the genome was altered by using yeast genetic
      systems and then transplanted to produce a new strain of M. mycoides. These methods allow the
      construction of strains that could not be produced with genetic tools available for this
      bacterium.
AU  - Lartigue C
AU  - Vashee S
AU  - Algire MA
AU  - Chuang RY
AU  - Benders GA
AU  - Ma L
AU  - Noskov VN
AU  - Denisova EA
AU  - Gibson DG
AU  - Assad-Garcia N
AU  - Alperovich N
AU  - Thomas DW
AU  - Merryman C
AU  - Hutchison CAIII
AU  - Smith HO
AU  - Venter JC
AU  - Glass JI
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2009 325: 1693-1696.

PMID- 27034502
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Vibrio toranzoniae Strain CECT 7225T.
PG  - e00212-16
AB  - Vibrio toranzoniae(CECT 7225(T)) was isolated from healthy reared carpet shell clams in
      Galicia (Northwest Spain). In addition, this species has been recently
      identified as a potential pathogen of red conger eel in Chile. The draft genome
      sequence has 4.5 Mbp, a G+C content of 43.9%, and >3,800 protein-coding genes.
AU  - Lasa A
AU  - Gibas CJ
AU  - Romalde JL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00212-16.

PMID- 22392282
VI  - 16
DP  - 2012
TI  - Plasmid pP62BP1 isolated from an Arctic Psychrobacter sp. strain carries two highly homologous type II restriction-modification systems and a putative organic sulfate metabolism operon.
PG  - 363-376
AB  - The complete nucleotide sequence of plasmid pP62BP1 (34,467 bp), isolated from Arctic sp. DAB
      AL62B, was determined and annotated. The
      conserved plasmid backbone is composed of several genetic modules,
      including a replication system (REP) with similarities to the REP
      region of the iteron-containing plasmid pPS10 of . The additional
      genetic load of pP62BP1 includes two highly related type II
      restriction-modification systems and a set of genes () encoding enzymes
      engaged in the metabolism of organic sulfates, plus a putative
      transcriptional regulator (SlfR) of the AraC family. The pP62BP1 has a
      compact and unique structure. It is predicted that the enzymes SlfC,
      SlfH, SlfS and SlfL carry out a chain of reactions leading to the
      transformation of alkyl sulfates into acyl-CoA, with dodecyl sulfate
      (SDS) as a possible starting substrate. Comparative analysis of the
      nucleotide sequences of pP62BP1 and other spp. plasmids revealed their
      structural diversity. However, the presence of a few highly conserved
      DNA segments in pP62BP1, plasmid 1 of K5 and pRWF-101 of sp. PRwf-1 is
      indicative of recombinational shuffling of genetic information, and is
      evidence of lateral gene transfer in the Arctic environment.
AU  - Lasek R
AU  - Dziewit L
AU  - Bartosik D
PT  - Journal Article
TA  - Extremophiles
JT  - Extremophiles
SO  - Extremophiles 2012 16: 363-376.

PMID- 3300770
VI  - 26
DP  - 1987
TI  - A probe for the mutagenic activity of the carcinogen 4-aminobiphenyl:  synthesis and characterization of an M13mp10 genome containing the major carcinogen-DNA adduct at a unique site.
PG  - 3072-3081
AB  - The duplex genome of Escherichia coli virus M13mp10 was modified at a unique
      site to contain N-(deoxyguanosin-8-yl)-4-aminobiphenyl (dG8-ABP), the major
      carcinogen-DNA adduct of the human bladder carcinogen 4-aminobiphenyl.  A
      tetradeoxynucleotide containing a single dG8-ABP residue was synthesized by
      reacting 5'-d(TpGpCpA)-3' with N-acetoxy-N-(trifluoroacetyl)-4-aminobiphenyl,
      followed by high-performance liquid chromatography purification of the
      principal reaction product 5'-d(TpG8-ABPpCpA)-3' (yield 15-30%).
      Characterization by fast atom bombardment mass spectrometry confirmed the
      structure as an intact 4-aminobiphenyl-modified tetranucleotide, while 1H
      nuclear magnetic resonance spectroscopy established the site of substitution
      and the existence of ring stacking between the carcinogen residue and DNA
      bases.  Both 5'-d(TpG8-ABPpCpA)-3' and 5'-d(TpGpCpA)-3' were 5'-phosphorylated
      by use of bacteriophage T4 polynucleotide kinase and were incorporated into a
      four-base gap uniquely positioned in the center of the recognition site for the
      restriction endonuclease PstI, in an otherwise duplex genome of M13mp10.  In
      the case of the adducted tetranucleotide, dG8-ABP was located in the minus
      strand at genome position 6270.  Experiments in which the tetranucleotides were
      5' end labeled with [32P] phosphate revealed the following: (i) the adducted
      oligomer, when incubated in a 1000-fold molar excess in the presence of T4 DNA
      ligase and ATP, was found to be incorporated into the gapped DNA molecules with
      an efficiency of approximately 30%, as compared to the unadducted d(pTpGpCpA),
      which was incorporated with 60% ligation efficiency; (ii) radioactivity from
      the 5' end of each tetranucleotide was physically mapped to a restriction
      fragment that contained the PstI site and represented 0.2% of the genome; (iii)
      the presence of the lesion within the PstI recognition site inhibited the
      ability of PstI to cleave the genome at this site; (iv) in genomes in which
      ligation occurred, T4 DNA ligase was capable of covalently joining both
      modified and unmodified tetranucleotides to the gapped structures on both the
      5' and the 3' ends with at least 90% efficiency.  Evidence also is presented
      showing that the dG8-ABP-modified tetranucleotide was stable to the conditions
      of the recombinant DNA techniques used to insert it into the viral genome.  On
      the basis of these and other data, the dG8-ABP-modified genome was judged to be
      a useful probe for investigation of site-specific mutagenesis in E. coli.
AU  - Lasko DD
AU  - Basu AK
AU  - Kadlubar FF
AU  - Evans FE
AU  - Lay JO
AU  - Essigmann JM
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1987 26: 3072-3081.

PMID- 28280007
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of a Staphylococcus epidermidis Strain with Exceptional  Antimicrobial Activity.
PG  - e00004-17
AB  - Staphylococcus epidermidis is a Gram-positive bacterium that is prevalent on human skin. The
      species is associated with skin health, as well as with
      opportunistic infections. Here, we report the complete genome sequence of S.
      epidermidis 14.1.R1, isolated from human skin. In bacterial interference assays,
      the strain showed exceptional antimicrobial activity.
AU  - Lassen SB
AU  - Lomholt HB
AU  - Bruggemann H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00004-17.

PMID- 26543108
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequences of Mycobacterium bovis Strain MbURU-001, Isolated from Fresh Bovine Infected Samples.
PG  - e01237-15
AB  - Bovine tuberculosis in cattle has a high incidence in Uruguay, where it is considered a
      disease of national importance. We present the genome sequence of
      Mycobacterium bovis strain MbURU-001, isolated from pectoral lymph nodes of a
      bovine host from a cattle farm.
AU  - Lasserre M
AU  - Berna L
AU  - Greif G
AU  - Diaz-Viraque F
AU  - Iraola G
AU  - Naya H
AU  - Castro-Ramos M
AU  - Juambeltz A
AU  - Robello C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01237-15.

PMID- 798471
VI  - 23
DP  - 1976
TI  - Restriction and modification of Shigella flexneri phages by R factors.
PG  - 259-270
AB  - Out of 420 R factors derived from Shigella flexneri strains, 50.8% restricted Escherichia coli
      and S. flexneri phages.  Phage restriction was produced both by fi- and fi+ R factors.  The R
      factors were divided into nine groups on the basis of the efficiency of plating of S. flexneri
      phages.  Changes of phage types were produced by transferring R factors of different
      restrictive types.  The changes offered some information concerning the evolution of phage
      types.  Studies on phage modification supported the grouping of R factors determined on the
      basis of restriction.  R factors of different restrictive types were type-specific except for
      types VIII and IX.  Modified phages proved to be highly practical for epidemiological
      purposes.  The use of modified phages, as an additional phage-set besides the basic phage-set,
      was suggested to trace the source of strains which changed their phage types as an effect of R
      factors.
AU  - Laszlo VG
AU  - Rimanoczy I
PT  - Journal Article
TA  - Acta Microbiol. Acad. Sci. Hung.
JT  - Acta Microbiol. Acad. Sci. Hung.
SO  - Acta Microbiol. Acad. Sci. Hung. 1976 23: 259-270.

PMID- 28619792
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequence of Bacillus stratosphericus Strain 5Co, Isolated from Lichen Usnea florida in Central Florida, United States, with High Tolerance to  Salt and Heavy Metal.
PG  - e00500-17
AB  - Bacillus stratosphericus strain 5Co was isolated from lichen Usnea florida in central Florida,
      United States. Here, we report a draft genome sequence of this
      strain, which consists of 159 contigs spanning 3,628,496 bp, with a G+C content
      of 41.3% and comprises 3,729 predicted coding sequences.
AU  - Lata P
AU  - Govindarajan SS
AU  - Qi F
AU  - Li JL
AU  - Maurya SK
AU  - Sahoo MK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00500-17.

PMID- 28619802
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Extended-Spectrum-Beta-Lactamase-Producing Morganella morganii Strains AA1 and AV1, Isolated from a Freshwater Lake and  Eicchorniacrassipes Roots.
PG  - e00527-17
AB  - Two strains of Morganella morganii, AA1 and AV1, were isolated from freshwater and Eicchornia
      crassipes roots, respectively. Here, we report their draft genome
      sequences, which are ~3.6 Mb and have 51% G+C content. The predicted coding
      sequences (3,259 for strain AA1 and 3,345 for strain AV1) encode beta-lactamases,
      transpeptidases, and penicillin-binding proteins.
AU  - Lata P
AU  - Govindarajan SS
AU  - Qi F
AU  - Li JL
AU  - Maurya SK
AU  - Sahoo MK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00527-17.

PMID- 29146861
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequence of Pantoea americana Strain VS1, an Extended-Spectrum beta-Lactamase-Producing Epibiont Isolated from Magnolia grandiflora.
PG  - e01285-17
AB  - Pantoea americana strain VS1, an extended-spectrum beta-lactamase-producing epibiont, was
      isolated from Magnolia grandiflora in central Florida, USA. Here,
      we report the de novo whole-genome sequence of this strain, which consists of a
      total of 191 contigs spanning 5,412,831 bp, with a GC content of 57.3% and
      comprising 4,836 predicted coding sequences.
AU  - Lata P
AU  - Govindarajan SS
AU  - Qi F
AU  - Li JL
AU  - Maurya SK
AU  - Sahoo MK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01285-17.

PMID- 28705985
VI  - 5
DP  - 2017
TI  - De Novo Whole-Genome Sequence of Pantoea latae Strain AS1, Isolated from Zamia floridana Rhizosphere in Central Florida, USA.
PG  - e00640-17
AB  - Pantoea latae strain AS1 was isolated from the rhizophere of a cycad, Zamia floridana, in
      central Florida, USA. Here, we report the de novo whole-genome
      sequence of this strain, which consists of a total of 83 contigs spanning
      4,960,415 bp, with a G+C content of 59.6%, and comprising 4,527 predicted coding
      sequences.
AU  - Lata P
AU  - Govindarajan SS
AU  - Qi F
AU  - Li JL
AU  - Maurya SK
AU  - Sahoo MK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00640-17.

PMID- 28153888
VI  - 5
DP  - 2017
TI  - Deep Sequencing-Identified Kanamycin-Resistant Paenibacillus sp. Strain KS1 Isolated from Epiphyte Tillandsia usneoides (Spanish Moss) in Central Florida,  USA.
PG  - e01523-16
AB  - Paenibacillus sp. strain KS1 was isolated from an epiphyte, Tillandsia usneoides  (Spanish
      moss), in central Florida, USA. Here, we report a draft genome sequence
      of this strain, which consists of a total of 398 contigs spanning 6,508,195 bp,
      with a G+C content of 46.5% and comprising 5,401 predicted coding sequences.
AU  - Lata P
AU  - Govindarajan SS
AU  - Qi F
AU  - Li JL
AU  - Sahoo MK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01523-16.

PMID- 23637642
VI  - 9
DP  - 2013
TI  - The Genome Organization of Thermotoga maritima Reflects Its Lifestyle.
PG  - E1003485
AB  - The generation of genome-scale data is becoming more routine, yet the subsequent
      analysis of omics data remains a significant challenge. Here, an approach that
      integrates multiple omics datasets with bioinformatics tools was developed that
      produces a detailed annotation of several microbial genomic features. This
      methodology was used to characterize the genome of Thermotoga maritima-a
      phylogenetically deep-branching, hyperthermophilic bacterium. Experimental data
      were generated for whole-genome resequencing, transcription start site (TSS)
      determination, transcriptome profiling, and proteome profiling. These datasets,
      analyzed in combination with bioinformatics tools, served as a basis for the
      improvement of gene annotation, the elucidation of transcription units (TUs), the
      identification of putative non-coding RNAs (ncRNAs), and the determination of
      promoters and ribosome binding sites. This revealed many distinctive properties
      of the T. maritima genome organization relative to other bacteria. This genome
      has a high number of genes per TU (3.3), a paucity of putative ncRNAs (12), and
      few TUs with multiple TSSs (3.7%). Quantitative analysis of promoters and
      ribosome binding sites showed increased sequence conservation relative to other
      bacteria. The 5'UTRs follow an atypical bimodal length distribution comprised of
      "Short" 5'UTRs (11-17 nt) and "Common" 5'UTRs (26-32 nt). Transcriptional
      regulation is limited by a lack of intergenic space for the majority of TUs.
      Lastly, a high fraction of annotated genes are expressed independent of growth
      state and a linear correlation of mRNA/protein is observed (Pearson r = 0.63,
      p<2.2x10(-16) t-test). These distinctive properties are hypothesized to be a
      reflection of this organism's hyperthermophilic lifestyle and could yield novel
      insights into the evolutionary trajectory of microbial life on earth.
AU  - Latif H
AU  - Lerman JA
AU  - Portnoy VA
AU  - Tarasova Y
AU  - Nagarajan H
AU  - Schrimpe-Rutledge AC
AU  - Smith RD
AU  - Adkins JN
AU  - Lee DH
AU  - Qiu Y
AU  - Zengler K
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2013 9: E1003485.

PMID- 25125650
VI  - 2
DP  - 2014
TI  - A Gapless, Unambiguous Genome Sequence of the Enterohemorrhagic Escherichia coli  O157:H7 Strain EDL933.
PG  - e00821-14
AB  - Escherichia coli EDL933 is the prototypic strain for enterohemorrhagic E. coli serotype
      O157:H7, associated with deadly food-borne outbreaks. Because the
      publicly available sequence of the EDL933 genome has gaps and >6,000 ambiguous
      base calls, we here present an updated high-quality, unambiguous genome sequence
      with no assembly gaps.
AU  - Latif H
AU  - Li HJ
AU  - Charusanti P
AU  - Palsson BO
AU  - Aziz RK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00821-14.

PMID- 10512711
VI  - 293
DP  - 1999
TI  - Active site dynamics of the HhaI methyltransferase: Insights from computer simulation.
PG  - 9-18
AB  - A molecular dynamics study was performed on the DNA methyltransferase M.HhaI in a ternary
      complex with DNA and AdoMet in solution. Methylation involves addition of the Cys81 sulfhydryl
      anion to the 6-position of Cyt18, followed by a nucleophilic attack of the resultant carbanion
      at C5 on the AdoMet methyl group. It was found in this simulation that the distances between
      the sulfhydryl group (SG) of Cys81 to the C6 of Cyt18 (SG-C6) and methyl carbon (CH3) of
      AdoMet to the C5 of cytosine (CH3-C5) are dependent on the dihedral angle chi
      (O4'-C1'-N1-C2) of the nucleotide. When the chi angle of Cyt18 is low (<-80 degrees ), the
      SG-C6 and CH3-C5 distances are large. A high chi angle (>-80 degrees ) for the target cytosine
      residue reduces the distances for both SG-C6 and CH3-C5, and the angles formed between the
      cytosine ring and AdoMet correspond well to values for the transition state structures formed
      during methylation of cytosine from ab initio calculations. Two possible proton sources for
      protonation of N3 of the cytosine residue upon formation of the covalent intermediate were
      found in the simulation. The protonated amine group of AdoMet could provide a proton via a
      water bridge, or Arg163 could also be the source of the proton for N3 via a water bridge. The
      simulation provides insights into how the H5 of cytosine could go from the active site into
      solvent. Conserved residues Asn304 and Gln82 stabilize a water network within the active site
      of M.HhaI which provides a route for H5 to diffuse into bulk solvent. An initially distant
      water molecule was able to diffuse into the active site of the enzyme and replace a position
      of a crystallographic water molecule in close proximity to the C5 of cytosine. The movement of
      this water molecule showed that a channel exists between Gln82 and the AdoMet in M.HhaI which
      allows both water and protons to easily gain access to the active site of the enzyme.
AU  - Lau EY
AU  - Bruice TC
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1999 293: 9-18.

PMID- 28138356
VI  - 12
DP  - 2017
TI  - Genome features of moderately halophilic polyhydroxyalkanoate-producing Yangia sp. CCB-MM3.
PG  - 12
AB  - Yangia sp. CCB-MM3 was one of several halophilic bacteria isolated from soil sediment in the
      estuarine Matang Mangrove, Malaysia. So far, no member from the
      genus Yangia, a member of the Rhodobacteraceae family, has been reported
      sequenced. In the current study, we present the first complete genome sequence of
      Yangia sp. strain CCB-MM3. The genome includes two chromosomes and five plasmids
      with a total length of 5,522,061 bp and an average GC content of 65%. Since a
      different strain of Yangia sp. (ND199) was reported to produce a
      polyhydroxyalkanoate copolymer, the ability for this production was tested in
      vitro and confirmed for strain CCB-MM3. Analysis of its genome sequence confirmed
      presence of a pathway for production of propionyl-CoA and gene cluster for PHA
      production in the sequenced strain. The genome sequence described will be a
      useful resource for understanding the physiology and metabolic potential of
      Yangia as well as for comparative genomic analysis with other Rhodobacteraceae.
AU  - Lau NS
AU  - Sam KK
AU  - Amirul AA
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 12.

PMID- 8190068
VI  - 243
DP  - 1994
TI  - The NlaIV restriction and modification genes of Neisseria lactamica are flanked by leucine biosynthesis genes.
PG  - 24-31
AB  - The genes encoding the Neisseria lactamica restriction endonuclease IV (R.NlaIV) and its
      cognate DNA methyltransferase (M.NlaIV), both of which recognize the sequence GGNNCC, have
      been cloned in Escherichia coli and overexpressed using the T7 polymerase/promoter system.
      Analysis of a sequenced 3.58kb fragment established the gene order, leuD-M.NlaIV-R.NlaIV-leuB.
      The predicted primary sequence of M.NlaIV (423 amino acids) shows the highest degree of
      identity to a pair of cytosine-specific methyltransferases, M.BanI (44.9%) and M.HgiCI
      (44.3%), which recognize the sequence GGYRCC (Y, pyrimidines; R, purines). In contrast, the
      R.NlaIV protein sequence (243 amino acids) is unique in the existing database, a situation
      that holds for most endonucleases. Flanking the NlaIV modification and restriction genes are
      homologues of the leuD and leuB genes of enteric bacteria, which code for enzymes in the
      leucine biosynthesis pathway. This gene context implies a possible new mode of gene regulation
      for the RM.NlaIV system, which would involve a mechanism similar to the recently discovered
      leucine/Lrp regulon in E. coli.
AU  - Lau PCK
AU  - Forghani F
AU  - Labbe D
AU  - Bergeron H
AU  - Brousseau R
AU  - Holtke HJ
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1994 243: 24-31.

PMID- 6257544
VI  - 121
DP  - 1980
TI  - AquI: a more easily purified isoschizomer of AvaI.
PG  - 200-202
AB  - Since its first description by Murray and coworkers the restriction
      endonuclease AvaI, which recognizes and cleaves at the sequence C^PyCGPuG, has
      found wide use in DNA sequence studies.  There are, however, three difficulties
      associated with preparation of this enzyme from its usual source, Anabaena
      variabilis (Kutzing).  This sheathed filamentous cyanobacterium does not
      readily yield single colonies on agar plates and is thus not easily rid of
      contaminating bacteria.  It grows slowly (generation times of the order of
      24h).  Furthermore, it contains two additional restriction endonucleases, AvaII
      and AvaIII.  We frequently find commercial preparations of AvaI to be
      contaminated with one of these additional enzymes, and Roizes et al. were
      unable to separate AvaI and AvaIII.  We report here that Agmenellum
      quadruplicatum (strain PR-6) produces an isoschizomer of AvaI (AquI).  This
      unicellular cyanobacterium is readily maintained in axenic condition, grows
      rapidly (4-5h generation time at 37C) and contains only this single restriction
      endonuclease activity.
AU  - Lau RH
AU  - Doolittle WF
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1980 121: 200-202.

PMID- Not included in PubMed...
VI  - 179
DP  - 1985
TI  - Site-specific restriction endonuclease from the filamentous cyanobacterium Nostoc sp. MAC PCC 8009.
PG  - 129-132
AB  - We report here the presence of a type-II restriction endonuclease in the
      filamentous cyanobacterium Nostoc sp. MAC PCC 8009.  This restriction enzyme,
      Nsp MACI, is the first reported isoschizomer of BglII and is very readily
      purified from non-specific deoxyribonuclease activity in the crude lysate by
      one round of phosphocellulose column chromatography.
AU  - Lau RH
AU  - Visentin LP
AU  - Martin SM
AU  - Hofman JD
AU  - Doolittle WF
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1985 179: 129-132.

PMID- 26380639
VI  - 10
DP  - 2015
TI  - Genome sequence of the pink-pigmented marine bacterium Loktanella hongkongensis type strain (UST950701-009P(T)), a representative of the Roseobacter group.
PG  - 51
AB  - Loktanella hongkongensis UST950701-009P(T) is a Gram-negative, non-motile and rod-shaped
      bacterium isolated from a marine biofilm in the subtropical seawater of Hong Kong. When
      growing as a monospecies biofilm on polystyrene surfaces, this bacterium is able to induce
      larval settlement and metamorphosis of a ubiquitous polychaete tubeworm Hydroides elegans. The
      inductive cues are low-molecular weight compounds bound to the exopolymeric matrix of the
      bacterial cells. In the  present study we describe the features of L. hongkongensis strain DSM
      17492(T) together with its genome sequence and annotation and novel aspects of its phenotype.
      The 3,198,444 bp long genome sequence encodes 3104 protein-coding genes and 57 RNA genes. The
      two unambiguously identified extrachromosomal replicons contain replication modules of the
      RepB and the Rhodobacteraceae-specific DnaA-like type, respectively.
AU  - Lau SC
AU  - Riedel T
AU  - Fiebig A
AU  - Han J
AU  - Huntemann M
AU  - Petersen J
AU  - Ivanova NN
AU  - Markowitz V
AU  - Woyke T
AU  - Goker M
AU  - Kyrpides NC
AU  - Klenk HP
AU  - Qian PY
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 51.

PMID- 25999561
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Catabacter hongkongensis Type Strain HKU16T, Isolated from a Patient with Bacteremia and Intestinal Obstruction.
PG  - e00531-15
AB  - We report the draft genome sequence of Catabacter hongkongensis, a catalase-positive bacterium
      which causes bacteremia with high mortality. The
      3.2-Mb genome contains 3,161 protein coding sequences, including putative
      catalase and motility-related proteins, and antibiotic resistance genes, which
      could be important for its virulence and adaptation to diverse environments.
AU  - Lau SK
AU  - Teng JL
AU  - Huang Y
AU  - Curreem SO
AU  - Tsui SK
AU  - Woo PC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00531-15.

PMID- 2162523
VI  - 18
DP  - 1990
TI  - The selective inhibitory effect of netropsin on relaxation of sequence specificity of restriction endonuclease SgrAI recognizing 5'-CR^CCGGYG-3'.
PG  - 3421
AB  - None
AU  - Laue F
AU  - Ankenbauer W
AU  - Schmitz GG
AU  - Kessler C
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 3421.

PMID- 1899848
VI  - 97
DP  - 1991
TI  - A complex family of class-II restriction endonucleases, DsaI-VI, in Dactylococcopsis salina.
PG  - 87-95
AB  - A series of class-II restriction endonucleases (ENases) was discovered in the halophilic,
      phototrophic, gas-vacuolated cyanobacterium Dactylococcopsis salina sp. nov. The six novel
      enzymes are characterized by the following recognition sequences and cut positions: 5'
      -C^CRYGG-3' (DsaI); 5' -GG^CC-3' (DsaII); 5' -R^GATCY-3' (DsaIII); 5' -G^GWCC-3'
      (DsaIV); 5' -^CCNGG-3' (DsaV); and 5' -GTMKAC-3' (DsaVI), where W = A or T, M = A or C, K
      = G or T, and N = A, G, C or T. In addition, traces of further possible activity were
      detected. DsaI has a novel sequence specificity and DsaV is an isoschizomer of ScrFI, but with
      a novel cut specificity. A purification procedure was established to separate all six ENases,
      resulting in their isolation free of contaminating nuclease activities. DsaI cleavage is
      influenced by N6-methyladenine residues [derived from the Escherichia coli-encoded DNA
      methyltransferase (MTase) M.Eco damI] within the overlapping sequence 5'-CCRYM/GGATC-3';
      DsaV hydrolysis is inhibited by a C-5 methylcytosine residue in its recognition sequence
      (5'-CM/CNGG-3'), generated in some DsaV sites by the E. coli-encoded MTase, M.Eco dcmI.
AU  - Laue F
AU  - Evans LR
AU  - Jarsch M
AU  - Brown NL
AU  - Kessler C
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1991 97: 87-95.

PMID- 27979941
VI  - 4
DP  - 2016
TI  - Complete Genome Sequences of Enterococcus rotai LMG 26678T and Enterococcus silesiacus LMG 23085T.
PG  - e01387-16
AB  - The inclusion of molecular methods in the characterization of the novel species Enterococcus
      horridus necessitated the sequencing and assembly of the genomes of
      the closely related Enterococcus rotai and Enterococcus silesiacus Sequencing
      using Illumina technology in combination with optical mapping led to the
      generation of closed genomes for both isolates.
AU  - Lauer AC
AU  - Humrighouse BW
AU  - Loparev V
AU  - Shewmaker PL
AU  - Whitney AM
AU  - McQuiston JR
AU  - McLaughlin RW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01387-16.

PMID- 26679585
VI  - 3
DP  - 2015
TI  - Genome Sequences of Oblitimonas alkaliphila gen. nov. sp. nov. (Proposed), a Novel Bacterium of the Pseudomonadaceae Family.
PG  - e01474-15
AB  - Results obtained through 16S rRNA gene sequencing and phenotypic testing of eight related, but
      unidentified, isolates located in a historical collection at the
      Centers for Disease Control and Prevention suggested that these isolates belong
      to a novel genera of bacteria. The genomes of the bacteria, to be named
      Oblitimonas alkaphilia gen. nov. sp. nov., were sequenced using Illumina
      technology. Closed genomes were produced for all eight isolates.
AU  - Lauer AC
AU  - Nicholson AC
AU  - Humrighouse BW
AU  - Emery B
AU  - Drobish A
AU  - Juieng P
AU  - Loparev V
AU  - McQuiston JR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01474-15.

PMID- 28572330
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Clover (Trifolium repens L.) Root Endophyte Paraburkholderia sp. Strain A27.
PG  - e00466-17
AB  - Paraburkholderia sp. strain A27, isolated from the root material of white clover, has plant
      growth-promoting activity on a range of agriculturally important
      plants. The draft genome of this bacterium is 7,393,089 bp and harbors a range of
      genes putatively involved in host colonization.
AU  - Laugraud A
AU  - Young S
AU  - Gerard E
AU  - O'Callaghan M
AU  - Wakelin S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00466-17.

PMID- 28408678
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of a Kale (Brassica oleracea L.) Root Endophyte, Pseudomonas sp. Strain C9.
PG  - e00163-17
AB  - Pseudomonas sp. strain C9 is a plant growth-promoting bacterium isolated from the root tissue
      of Brassica oleracea L. grown in soil from Marlborough, New Zealand.
      Its draft genome of 6,350,161 bp contains genes associated with plant growth
      promotion and biological control.
AU  - Laugraud A
AU  - Young S
AU  - Gerard E
AU  - O'Callaghan M
AU  - Wakelin S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00163-17.

PMID- 19586932
VI  - 37
DP  - 2009
TI  - Dissecting protein-induced DNA looping dynamics in real time.
PG  - 5454-5464
AB  - Many proteins that interact with DNA perform or enhance their specific functions by binding
      simultaneously to multiple target sites, thereby
      inducing a loop in the DNA. The dynamics and energies involved in this
      loop formation influence the reaction mechanism. Tethered particle motion
      has proven a powerful technique to study in real time protein-induced DNA
      looping dynamics while minimally perturbing the DNA-protein interactions.
      In addition, it permits many single-molecule experiments to be performed
      in parallel. Using as a model system the tetrameric Type II restriction
      enzyme SfiI, that binds two copies of its recognition site, we show here
      that we can determine the DNA-protein association and dissociation steps
      as well as the actual process of protein-induced loop capture and release
      on a single DNA molecule. The result of these experiments is a
      quantitative reaction scheme for DNA looping by SfiI that is rigorously
      compared to detailed biochemical studies of SfiI looping dynamics. We also
      present novel methods for data analysis and compare and discuss these with
      existing methods. The general applicability of the introduced techniques
      will further enhance tethered particle motion as a tool to follow
      DNA-protein dynamics in real time.
AU  - Laurens N
AU  - Bellamy SR
AU  - Harms AF
AU  - Kovacheva YS
AU  - Halford SE
AU  - Wuite GJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: 5454-5464.

PMID- 22373924
VI  - 40
DP  - 2012
TI  - DNA looping by FokI: the impact of twisting and bending rigidity on protein-induced looping dynamics.
PG  - 4988-4997
AB  - Protein-induced DNA looping is crucial for many genetic processes such as transcription, gene
      regulation and DNA replication. Here, we use
      tethered-particle motion to examine the impact of DNA bending and twisting
      rigidity on loop capture and release, using the restriction endonuclease FokI as
      a test system. To cleave DNA efficiently, FokI bridges two copies of an
      asymmetric sequence, invariably aligning the sites in parallel. On account of the
      fixed alignment, the topology of the DNA loop is set by the orientation of the
      sites along the DNA. We show that both the separation of the FokI sites and their
      orientation, altering, respectively, the twisting and the bending of the DNA
      needed to juxtapose the sites, have profound effects on the dynamics of the
      looping interaction. Surprisingly, the presence of a nick within the loop does
      not affect the observed rigidity of the DNA. In contrast, the introduction of a
      4-nt gap fully relaxes all of the torque present in the system but does not
      necessarily enhance loop stability. FokI therefore employs torque to stabilise
      its DNA-looping interaction by acting as a 'torsional' catch bond.
AU  - Laurens N
AU  - Rusling DA
AU  - Pernstich C
AU  - Brouwer I
AU  - Halford SE
AU  - Wuite GJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: 4988-4997.

PMID- 12234687
VI  - 294
DP  - 2002
TI  - Characterization of IS999, an unstable genetic element in Mycobacterium avium.
PG  - 249-257
AB  - An IS3-family insertion element, IS999, was identified in the opportunistic pathogen
      Mycobacterium avium. The 1347 bp element has 29 bp
      inverted repeats and two overlapping open reading frames coding for
      putative transposases. It was detected in the genomes of ten of 12 M.
      avium isolates examined. Copy numbers ranged from four to 16. IS999 is
      less stable than IS1245, the most commonly-used marker for typing M. avium
      isolates. Among 60 colonies picked from a single patient isolate, there
      were two distinct IS1245 restriction fragment length polymorphism banding
      patterns compared to eight distinct IS999 patterns (five in one IS1245
      group and three in the other). In view of its instability, we asked
      whether transposition of IS999 might have phenotypic consequences.
      Nucleotide sequence analysis of insertion sites in four isolates revealed
      16 putative structural genes that were variably disrupted by IS999.
      Insertions into hdhA, a gene that codes for a putative short chain alcohol
      dehydrogenase, were distributed non-randomly between colony type variants,
      consistent with phenotypic consequences that exert selective pressure.
      These observations illustrate the genetic heterogeneity that can exist
      within populations of M. avium that appear to be homogeneous by IS1245
      analysis. IS999 may be a useful marker for tracking, at the sub-strain
      level, the rapid genetic drift that M. avium isolates undergo in nature
      and in the laboratory.
AU  - Laurent JP
AU  - Faske S
AU  - Cangelosi GA
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 2002 294: 249-257.

PMID- 
VI  - 280
DP  - 2013
TI  - Engineering DNA methyltransferases for a novel cofactor.
PG  - 173-174
AB  - Cofactors are metals, or organic compounds, which play fundamental roles in enzymes.  Cofactor
      engineering has only been partially pursued and rarely have natural cofactors been substituted
      with synthetic organic molecules.  Herein, we have designed a synthetic compound presenting in
      its structure few key modifications that, in turn, an engineered enzyme can exploit to achieve
      cofactor specificity, tight binding and orthogonal recognition of it instead of the natural
      cofactor.  The cofactor was designed considering aspects like cell permeability, which allows
      extracellular administration of the cofactor, and the possibility to track the enzyme's
      product.  The key candidate of our investigation is DNA methyltransferases, that use
      S-adenosyl methionine as methyl donor to methylate specific DNA target sequences.  Although
      these enzymes are key epigenetic mediators, their genomic targets are often unknown and their
      cellular remain poorly understood.  To remodel the catalytic site for the new cofactor, a
      protein engineering study ahs been carried out, using computational design as well as directed
      evolution.  We believe that the evolved mammalian DNA methylases which will have acquired
      orthogonality for the synthetic cofactor, as well as the ability to modify DNA with tractable
      groups, will provide new insights regarding the role of this enzyme in epigentics, including
      in dictating the genomic methylation patterns in cancer.
AU  - Laurino P
AU  - Tawfik D
PT  - Journal Article
TA  - FEBS J.
JT  - FEBS J.
SO  - FEBS J. 2013 280: 173-174.

PMID- 23723392
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Deep-Sea Bacterium Shewanella benthica Strain KT99.
PG  - e00210-13
AB  - We report the draft genome sequence of the obligately piezophilic Shewanella benthica strain
      KT99 isolated from the abyssal South Pacific Ocean. Strain KT99
      is the first piezophilic isolate from the Tonga-Kermadec trench, and its genome
      provides many clues on high-pressure adaptation and the evolution of deep-sea
      piezophilic bacteria.
AU  - Lauro FM
AU  - Chastain RA
AU  - Ferriera S
AU  - Johnson J
AU  - Yayanos AA
AU  - Bartlett DH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00210-13.

PMID- 23723403
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of the Deep-Sea Bacterium Psychromonas Strain CNPT3.
PG  - e00304-13
AB  - Members of the genus Psychromonas are commonly found in polar and deep-sea environments. Here
      we present the genome of Psychromonas strain CNPT3.
      Historically, it was the first bacterium shown to piezoregulate the composition
      of its membrane lipids and to have a higher growth rate at 57 megapascals (MPa)
      than at 0.1 MPa.
AU  - Lauro FM
AU  - Stratton TK
AU  - Chastain RA
AU  - Ferriera S
AU  - Johnson J
AU  - Goldberg SM
AU  - Yayanos AA
AU  - Bartlett DH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00304-13.

PMID- 3248727
VI  - 74
DP  - 1988
TI  - Duplication and variation as a phylogenetic principle of Type II DNA methyltransferases.
PG  - 243
AB  - Meeting Abstract
AU  - Lauster R
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 243.

PMID- 2541254
VI  - 206
DP  - 1989
TI  - Evolution of type II DNA methyltransferases:  A gene duplication model.
PG  - 313-321
AB  - On the basis of consensus sequences, which had previously been defined for two
      groups of closely related cytosine-specific and adenine-specific DNA
      methyltransferases, homologies can be detected that indicate a common origin
      for these proteins.  Intramolecular comparisons of several of these enzymes
      reveal homology relationships, which suggests that gene duplication is a
      phylogenetic principle in the evolution of the Mtases.  One or two duplications
      of an ancestral gene encoding a 12,000 to 16,000 Mr protein, followed by
      divergent evolution, may have led to very different protein structures and
      could explain the differences in amino acid sequences, molecular weights and
      biochemical properties.  Intermolecular and intramolecular homologies were also
      recognized in type II restriction endonucleases, suggesting a very similar
      evolutionary pathway.
AU  - Lauster R
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1989 206: 313-321.

PMID- 2787021
VI  - 17
DP  - 1989
TI  - Close relationship between the HinfI and DpnA DNA-methyltransferase.
PG  - 4402
AB  - None
AU  - Lauster R
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 4402.

PMID- 3609310
VI  - 220
DP  - 1987
TI  - The GATATC-modification enzyme EcoRV is closely related to the GATC-recognizing methyltransferases DpnII and dam from E. coli and phage T4.
PG  - 167-176
AB  - The amino acid sequence of EcoRV DNA methyltransferase which methylates the amino group of the
      5'-adenine residue of the target sequence GATATC has been found to be closely related to that
      of three other adenine methyltransferases, DpnII, dam and damT4, the target sequence of which
      is GATC. Despite large differences on the DNA level, the four sequences show four blocks of
      homologies. One of these blocks has the sequence DVYXDPPY and is found with little
      modification in numerous other DNA methyltransferases. It is speculated that it could be the
      binding site of the methyl donor, S-adenosylmethionine. On the other hand, the identification
      of a DNA-binding region is more tenuous. As expected, no analogies with (dimeric) repressors
      and cro proteins which have the characteristic helix-turn-helix motif have been observed.
AU  - Lauster R
AU  - Kriebardis A
AU  - Guschlbauer W
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1987 220: 167-176.

PMID- 2716049
VI  - 206
DP  - 1989
TI  - Cytosine-specific type II DNA methyltransferases:  A conserved enzyme core with variable target-recognizing domains.
PG  - 305-312
AB  - Comparisons of the amino acid sequences of m5C DNA methyltransferases (Mtases)
      from 11 prokaryotes and one eukaryote reveal a very similar organization.
      Among all the enzymes one can distinguish highly conserved core sequences and
      variable regions.  The core sequences apparently mediate steps of the
      methylation reaction that are common to all the enzymes.  The major variable
      region has been shown in our previous studies on multispecific phage Mtases to
      contain the target-recognizing domains (TRDs) of these enzymes.  Here we have
      compared the amino acid sequences of various TRDs from phage Mtases.  This has
      revealed the presence of both highly conserved and variable amino acids.  We
      postulate that the conserved residues represent a consensus sequence defining a
      TRD, whereas the specificity of the TRD is determined by the variable residues.
      We have observed similarity between this consensus sequence and sequences in
      the variable region of the monospecific Mtases.  We predict that the regions
      thus identified represent part of the TRDs of monospecific Mtases.
AU  - Lauster R
AU  - Trautner TA
AU  - Noyer-Weidner M
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1989 206: 305-312.

PMID- Not included in PubMed...
VI  - 31
DP  - 1972
TI  - The DNA modification methylase and restriction endonuclease of Escherichia coli B.
PG  - 474
AB  - The modification and restriction enzymes from E. coli B have been extensively
      purified.  As judged by SDS gel electrophoresis, the methylase contains two
      subunits, beta and gamma, of molecular weights 60,000 and 55,000, respectively.
      The endonuclease contains beta, gamma and a third subunit, alpha, of molecular
      weight 135,000.  These results are consistent with the observations of Hubacek
      and Glover [J. Mol. Biol. 50, 11, 1970] showing that the hss and hsm genes are
      required for both activities, and in addition, the hsr gene is required for
      restriction.  The methylase is isolated in an active 6S form, beta 1 gamma 1,
      but it is able to disproportionate into an active 11S form, beta 3 gamma 1.
      The endonuclease activity sediments in a broad peak around 15S and contains
      alpha, beta, and gamma in the approximate ratio 2.5:2.5:1.  This material is a
      mixture of active enzyme species, each containing the three subunits, but in
      different proportions.  The methylase forms 6-methylaminopurine using
      S-adenosylmethionine (SAM) as the methyl donor.  It acts optimally at pH 5.8,
      and is stimulated 3- to 5-fold by Mg++, Mn++, or Ca++, and 30% by ATP.  The
      endonuclease requires Mg++, SAM, and ATP, and unlike the methylase, it degrades
      massive amounts of ATP to ADP and Pi during its action on DNA.  Both enzymes
      are inhibited by S-adenosylethionine or 5'-methylthioadenosine, but not by
      S-adenosylhomocysteine.
AU  - Lautenberger J
AU  - Eskin B
AU  - Linn S
PT  - Journal Article
TA  - Fed. Proc.
JT  - Fed. Proc.
SO  - Fed. Proc. 1972 31: 474.

PMID- 6260588
VI  - 12
DP  - 1980
TI  - The nucleotide sequence recognized by the BstEII restriction endonuclease.
PG  - 171-174
AB  - The restriction site for the BstEII endonuclease is characterized by the
      heptamer sequence: 5'-G-^G-T-N-A-C-C-3' 3'-C-C-A-N-T-G-^G-5' with five
      nucleotide long cohesive termini.
AU  - Lautenberger JA
AU  - Edgell MH
AU  - Hutchison CA III
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1980 12: 171-174.

PMID- 390163
VI  - 131
DP  - 1979
TI  - The DNA sequence on bacteriophage G4 recognized by the Escherichia coli B restriction enzyme.
PG  - 871-875
AB  - Bacteriophage G4 possesses a single EcoB site located in the overlap between restriction
      fragments HinfI-12 and HaeIII-6.  The sequence 5'-T-G-A...8N...T-G-C-T occurs once in this
      segment and nowhere else in the DNA sequence of G4.  Four independent G4 mutants that were not
      restricted by Escherichia coli B possessed the sequence 5'-T-G-A...8N...T-G-C-C.  The common
      sequence shared by the previously mapped EcoB sites on PhiXsB1, simian virus 40, f1, and fd
      DNAs is 5'-T-G-A...8N...T-G-C-T...9N...T.  However, the sequence in the region of the G4 EcoB
      site contains an A instead of the final T conserved in these other examples.  When the G4 EcoB
      site is aligned with the other EcoB sites, there are no conserved residues within 50 bases of
      the common sequence, 5'-T-G-A...8N....T-G-C-T, except for those seven residues.  The analysis
      of the EcoB site on G4 provides further evidence that only those seven bases are recognized by
      the E. coli B restriction enzyme.
AU  - Lautenberger JA
AU  - Edgell MH
AU  - Hutchison CA III
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1979 131: 871-875.

PMID- 209460
VI  - 75
DP  - 1978
TI  - Recognition site of Escherichia coli B restriction enzyme on PhiXsB1 and simian virus 40 DNAs: An interrupted sequence.
PG  - 2271-2275
AB  - Methyl groups placed on PhiXsB1 replicative form DNA by the Escherichia coli B
      modification enzyme are located in the overlap between fragments MboII-3 and
      AluI-2, a 61-base-pair DNA segment.  Mutations that led to loss of
      susceptibility to restriction by E. coli B occurred within this segment at
      three positions spanning 14 nucleotides.  A sequence difference between PhiXsB1
      and PhiXam3cs70, a PhiX174 strain not restricted by E. coli B, occurs at one of
      these positions.  The site on simian virus 40 DNA methylated by the
      modification enzyme is located in the 115-base-pair overlap between fragments
      HaeIII-I and AluI-G.  The sequences of these segments of PhiXsB1 and simian
      virus 40 DNA and two regions of phage f1 DNA recognized by the E. coli B
      restriction enzyme [Ravetch, J.V., Horiuchi, K. & Zinder, N.D. (1978) Proc.
      Natl. Acad. Sci. USA 75, 2266-2270] contain a homology of nine bases in the
      configuration:  5'-T-G-A...8N...T-G-C-G...9N...T-N-N-T-3'. The sequence
      5'-T-G-A...8N...T-G-C-T-3' may constitute the restriction enzyme recognition
      site since it does not occur in PhiXam3cs70 DNA and occurs only once in simian
      virus 40 DNA, and since all observed mutations leading to loss of the site
      occur at one of the bases specified by this sequence.  Analysis of the sequence
      of PhiXam3cs70 showed that if no other residues are recognizd, all seven of
      these bases are essential for recognition and the interval between the two
      groups of specified bases must be precisely eight.
AU  - Lautenberger JA
AU  - Kan NC
AU  - Lackey D
AU  - Linn S
AU  - Edgell MH
AU  - Hutchison CA III
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1978 75: 2271-2275.

PMID- 4568606
VI  - 247
DP  - 1972
TI  - The deoxyribonucleic acid modification and restriction enzymes of Escherichia coli B. I. Purification, subunit structure, and catalytic properties of the modification methylase.
PG  - 6176-6182
AB  - The modification methylase of Escherichia coli B has been purified to apparent
      homogeneity.  The enzyme can exist in several forms, each possessing two
      nonidentical polypeptides, b and c, of molecular weights of 60,000 and 55,000,
      respectively.  Freshly isolated enzyme has the structure b1c1, but upon storage
      at neutral pH and low salt, it disproportionates, producing another form, b3c1.
      Treatment at pH 5 converts the mixture of b3c1 and b1c1 to a mixture of b1c1
      and another form b2c1, whereas exposure to high salt breaks down the b3c1
      structure.  The enzyme is inhibited by S-adenosylethionine and
      5'-methylthioadenosine, but not by S-adenosylhomocysteine.  None of these
      compounds can replace the required cofactor, S-adenosylmethionine.  The enzyme
      can methylate a wide variety of DNAs, but not DNA produced by E. coli B.
AU  - Lautenberger JA
AU  - Linn S
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1972 247: 6176-6182.

PMID- 6248428
VI  - 9
DP  - 1980
TI  - The recognition site of Type II restriction enzyme BglI is interrupted.
PG  - 213-231
AB  - The Type II restriction endonuclease BglI recognizes the interrupted DNA
      sequence 5'-G-C-C-N-N-N-N-N-G-G-C-.  This sequence occurs at all locations in
      over 33,000 base pairs of DNA sequence where the enzyme was found to cut DNA
      and nowhere else.  All six of the specified bases are essential parts of the
      site since all groups of five of the six bases occur in the DNA sequences
      tested and none of them are cut by BglI.  The length of the block of
      intervening unspecified positions must be exactly five since all other sizes
      between zero and 15 occur in the DNA sequences searched and none are cut by
      BglI.  The 5'-terminal nucleotides of BglI cleaved phage G4 replicative form
      DNA and plasmid pER18 DNA were compared with the DNA sequences near the BglI
      sites on these DNAs.  These results indicated that BglI cuts within the
      intervening unspecified region and produces single-stranded 3' termini that are
      three bases long.  The BglI recognition site and cleavage points can thus be
      represented as follows: 5'-G-C-C-N-N-N-N-^-N-G-G-C-3'   This study of the BglI
      recognition site was facilitated by the use of inexpensive microcomputers.  A
      system of programs was developed that allowed analysis of over 33 kb of DNA
      sequences stored on flexible magnetic disks or audio cassettes.  While these
      programs were generally written in the higher level language BASIC, some
      assembly language subroutines were utilized to reduce executive time.
AU  - Lautenberger JA
AU  - White CT
AU  - Haigwood NL
AU  - Edgell MH
AU  - Hutchison CA
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1980 9: 213-231.

PMID- 20951641
VI  - 301
DP  - 2011
TI  - A multiresistance megaplasmid pLG1 bearing a hylEfm genomic island in hospital Enterococcus faecium isolates.
PG  - 165-175
AB  - Enterococcus faecium is considered to be a nosocomial pathogen with
      increasing medical importance. The putative virulence factor, hyl(Efm),
      encoding a putative hyaluronidase, is enriched among the
      hospital-associated polyclonal subpopulation of E. faecium.. The hyl(Efm)
      gene is described to be part of a genomic island and was recently
      identified to be plasmid-located. Here, we present a description of the
      structure, localization, and distribution of the putative pathogenicity
      factor hyl(Efm) and its putative island among 39 clinical isolates and
      elucidate the composition and host range of pLG1, a hyl(Efm)
      multiresistance plasmid of approximately 281.02kb. The hyl(Efm) gene was
      located within a 17,824-bp element highly similar to the putative genomic
      island (GI) structure that had been previously described. This genomic
      region was conserved among 39 hyl(Efm)-positive strains with variation in
      a specific region downstream of hyl(Efm) in 18 strains. The putative
      hyl(Efm) was located on large plasmids (150-350kb) in 37 strains. pLG1
      could be horizontally transferred into four different E. faecium recipient
      strains (n=4) but not into E. faecalis (n=3). Sequencing of pLG1 resolved
      putative plasmid replication, conjugation, and maintenance determinants as
      well as a pilin gene cluster, carbon uptake and utilization genes, heavy
      metal and antibiotic resistance clusters. The hyl(Efm) transferable
      plasmid pLG1 bears additional putative pathogenicity factors and
      antibiotic resistance genes. These findings suggest horizontal gene
      transfer of virulence factors and antibiotic resistance gene clusters by a
      single genetic event (conjugative transfer) which might be triggered by
      heavy antibiotic use common in health care units where E. faecium is
      increasingly prevalent.
AU  - Laverde-Gomez JA
AU  - van Schaik W
AU  - Freitas AR
AU  - Coque TM
AU  - Weaver KE
AU  - Francia MV
AU  - Witte W
AU  - Werner G
PT  - Journal Article
TA  - Int. J. Med. Microbiol.
JT  - Int. J. Med. Microbiol.
SO  - Int. J. Med. Microbiol. 2011 301: 165-175.

PMID- 20675487
VI  - 192
DP  - 2010
TI  - Draft genome sequences of two Neisseria meningitidis serogroup C clinical isolates.
PG  - 5270-5271
AB  - Neisseria meningitidis is a human-specific pathogen known for its capability to cause sepsis
      and meningitis. Here we report the availability
      of 2 draft genome sequences obtained from patients infected during the
      same epidemic outbreak. Both bacterial isolates belong to serogroup C, but
      their genome sequences show local and remarkable differences compared with
      each other or with the reference genome of strain FAM18.
AU  - Lavezzo E
AU  - Toppo S
AU  - Barzon L
AU  - Cobelli C
AU  - Di Camillo B
AU  - Finotello F
AU  - Franchin E
AU  - Peruzzo D
AU  - Toffolo GM
AU  - Trevisan M
AU  - Palu G
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 5270-5271.

PMID- 26203333
VI  - 10
DP  - 2015
TI  - High quality draft genome sequence of Leucobacter chironomi strain MM2LB(T) (DSM  19883(T)) isolated from a Chironomus sp. egg mass.
PG  - 21
AB  - Leucobacter chironomi strain MM2LB(T) (Halpern et al., Int J Syst Evol Microbiol  59:665-70
      2009) is a Gram-positive, rod shaped, non-motile, aerobic,
      chemoorganotroph bacterium. L. chironomi belongs to the family Microbacteriaceae,
      a family within the class Actinobacteria. Strain MM2LB(T) was isolated from a
      chironomid (Diptera; Chironomidae) egg mass that was sampled from a waste
      stabilization pond in northern Israel. In a phylogenetic tree based on 16S rRNA
      gene sequences, strain MM2LB(T) formed a distinct branch within the radiation
      encompassing the genus Leucobacter. Here we describe the features of this
      organism, together with the complete genome sequence and annotation. The DNA GC
      content is 69.90%. The chromosome length is 2,964,712 bp. It encodes 2,690
      proteins and 61 RNA genes. L. chironomi genome is part of the Genomic
      Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG)
      project.
AU  - Laviad S
AU  - Lapidus A
AU  - Copeland A
AU  - Reddy T
AU  - Huntemann M
AU  - Pati A
AU  - Ivanova NN
AU  - Markowitz VM
AU  - Pukall R
AU  - Klenk HP
AU  - Woyke T
AU  - Kyrpides NC
AU  - Halpern M
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 21.

PMID- 26203340
VI  - 10
DP  - 2015
TI  - High quality draft genome sequence of Brachymonas chironomi AIMA4(T) (DSM 19884(T)) isolated from a Chironomus sp. egg mass.
PG  - 29
AB  - Brachymonas chironomi strain AIMA4(T) (Halpern et al., 2009) is a Gram-negative,  non-motile,
      aerobic, chemoorganotroph bacterium. B. chironomi is a member of the
      Comamonadaceae, a family within the class Betaproteobacteria. This species was
      isolated from a chironomid (Diptera; Chironomidae) egg mass, sampled from a waste
      stabilization pond in northern Israel. Phylogenetic analysis based on the 16S
      rRNA gene sequences placed strain AIMA4(T) in the genus Brachymonas. Here we
      describe the features of this organism, together with the complete genome
      sequence and annotation. The DNA GC content is 63.5%. The chromosome length is
      2,509,395 bp. It encodes 2,382 proteins and 68 RNA genes. Brachymonas chironomi
      genome is part of the Genomic Encyclopedia of Type Strains, Phase I: the one
      thousand microbial genomes (KMG) project.
AU  - Laviad S
AU  - Lapidus A
AU  - Han J
AU  - Haynes M
AU  - Reddy T
AU  - Huntemann M
AU  - Pati A
AU  - Ivanova NN
AU  - Mavromatis K
AU  - Lang E
AU  - Rohde M
AU  - Markowitz V
AU  - Woyke T
AU  - Klenk HP
AU  - Kyrpides NC
AU  - Halpern M
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 29.

PMID- 28491240
VI  - 12
DP  - 2017
TI  - High quality permanent draft genome sequence of Chryseobacterium bovis DSM 19482T, isolated from raw cow milk.
PG  - 31
AB  - Chryseobacterium bovis DSM 19482T (Hantsis-Zacharov et al., Int J Syst Evol Microbiol
      58:1024-1028, 2008) is a Gram-negative, rod shaped, non-motile,
      facultative anaerobe, chemoorganotroph bacterium. C. bovis is a member of the
      Flavobacteriaceae, a family within the phylum Bacteroidetes. It was isolated when
      psychrotolerant bacterial communities in raw milk and their proteolytic and
      lipolytic traits were studied. Here we describe the features of this organism,
      together with the draft genome sequence and annotation. The DNA G + C content is
      38.19%. The chromosome length is 3,346,045 bp. It encodes 3236 proteins and 105
      RNA genes. The C. bovis genome is part of the Genomic Encyclopedia of Type
      Strains, Phase I: the one thousand microbial genomes study.
AU  - Laviad-Shitrit S et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 31.

PMID- 20142834
VI  - 11
DP  - 2010
TI  - Establishing, maintaining and modifying DNA methylation patterns in plants and animals.
PG  - 204-220
AB  - Cytosine DNA methylation is a stable epigenetic mark that is crucial for diverse  biological
      processes, including gene and transposon silencing, imprinting and X chromosome inactivation.
      Recent findings in plants and animals have greatly increased our understanding of the pathways
      used to accurately target, maintain and modify patterns of DNA methylation and have revealed
      unanticipated mechanistic similarities between these organisms. Key roles have emerged for
      small RNAs, proteins with domains that bind methylated DNA and DNA glycosylases in these
      processes. Drawing on insights from both plants and animals should deepen our understanding of
      the regulation and biological significance of DNA methylation.
AU  - Law JA
AU  - Jacobsen SE
PT  - Journal Article
TA  - Nat. Rev. Genet.
JT  - Nat. Rev. Genet.
SO  - Nat. Rev. Genet. 2010 11: 204-220.

PMID- 24675846
VI  - 2
DP  - 2014
TI  - Genome Sequence of a Presumptive Mannheimia haemolytica Strain with an A1/A6-Cross-Reactive Serotype from a White-Tailed Deer (Odocoileus virginianus).
PG  - e00114-14
AB  - Mannheimia haemolytica is a Gram-negative bacterium and the principal etiological agent
      associated mostly with bovine respiratory disease complex. However, we
      report here the sequence of a strain with the novel A1/A6-cross-reactive
      serotype, strain PKL10, isolated from white-tailed deer. PKL10 was isolated from
      the spleen of farmed white-tailed deer showing clinical signs of pneumonia. The
      genome structure of PKL10 is dramatically different from that of previously
      sequenced isolates, which was demonstrated by genome alignments. In addition, the
      coding sequences in PKL10 share approximately 86% sequence identity with the
      coding sequences in other fully sequenced M. haemolytica strains. This suggests
      that PKL10 is a novel Mannheimia species.
AU  - Lawrence PK
AU  - Bey RF
AU  - Wiener B
AU  - Kittichotirat W
AU  - Bumgarner RE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00114-14.

PMID- 19966002
VI  - 192
DP  - 2010
TI  - Genome sequences of Mannheimia haemolytica serotype A2: ovine and bovine isolates.
PG  - 1167-1168
AB  - This report describes the genome sequences of Mannheimia haemolytica serotype A2
      isolated from pneumonic lungs of two different ruminant species, one from Ovis
      aries, designated ovine (O), and the other from Bos taurus, designated bovine
      (B).
AU  - Lawrence PK
AU  - Kittichotirat W
AU  - Bumgarner RE
AU  - McDermott JE
AU  - Herndon DR
AU  - Knowles DP
AU  - Srikumaran S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 1167-1168.

PMID- 25189591
VI  - 2
DP  - 2014
TI  - Genome-Wide Association Studies of Virulent and Avirulent Haemophilus parasuis Serotype 4 Strains.
PG  - e00884-14
AB  - Haemophilus parasuis is a normal commensal of the upper respiratory tract of healthy pigs.
      However, in conjunction with stress and/or viral infections, or in
      immunocompromised animals, H. parasuis can transform into a pathogen causing
      Glasser's disease, which is typically characterized by fibrinous polyserositis,
      polyarthritis, meningitis, and sometimes acute pneumonia and septicemia. H.
      parasuis serotype 5 is highly virulent and more frequently isolated from
      respiratory and systemic infection in pigs. Recently Newport Laboratories
      isolated highly virulent H. parasuis serotype 4 strains from the tissues of
      diseased pigs. This study was undertaken to identify the genes responsible for H.
      parasuis serotype 4 virulence. To achieve this objective we performed genome-wide
      association studies (GWAS) across two virulent and three avirulent H. parasuis
      serotype 4 strains.
AU  - Lawrence PK
AU  - Wiener BL
AU  - Kolander-Bremer T
AU  - Bey RF
AU  - Stine DL
AU  - Kittichotirat W
AU  - Bumgarner RE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00884-14.

PMID- 
VI  - 102
DP  - 2002
TI  - Plasmid content determines the ability to transform Borrelia burgdorferi.
PG  - 179
AB  - The progress of research on Borrelia burgdorferi, the causative agent of Lyme disease, has
      been hampered by the lack of genetic techniques that can
      be used in the laboratory. Recent advancements in this field have included
      the development of a reliable selection marker and the creation of both
      stable shuttle vectors and a suicide vector to truncate linear plasmids.
      To date, many researchers have published successful genetic manipulation
      of high passage isolates of B. burgdorferi, but only very limited success
      has been reported with low passage clones. Along with increased
      transformation efficiency, high passage clones have also lost the ability
      to infect the mammalian host, due to loss of plasmids during in vitro
      passage. In this study, we have utilized the pBSV2 shuttle vector to
      transform a library of low passage clones of B. burgdorferi B31 to
      determine if the increased transformation efficiency seen in high passage
      clones can be attributed to loss of one of the plasmids. Three
      transformation phenotypes were identified that correlate with the presence
      or absence of lp25 and/or lp56. Clones that lacked both plasmids yielded
      greater than 1000 transformants per mug of DNA, whereas isolates that
      possessed both plasmids yielded 0 to 5 transformants per mug of DNA. B.
      burgdorferi that lacked either lp25 or lp56 had an intermediate
      transformation efficiency. To date, all transformants isolated from
      lp25-positive clones electroporated with pBSV2 lack lp25, consistent with
      selective transformation of individual cells in which lp25 was missing.
      This information indicates that lp25 and lp56 represent important barriers
      against successful B. burgdorferi transformation, which may be related to
      plasmid-encoded restriction modification systems.
AU  - Lawrenz MB
AU  - Kawabata H
AU  - Norris SJ
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 2002 102: 179.

PMID- 12183522
VI  - 70
DP  - 2002
TI  - Decreased electroporation efficiency in Borrelia burgdorferi containing linear plasmids lp25 and lp56: impact on transformation of infectious  B. burgdorferi.
PG  - 4798-4804
AB  - The presence of the linear plasmids lp25 and lp56 of Borrelia burgdorferi B31 was found to
      dramatically decrease the rate of transformation by electroporation with the shuttle vector
      pBSV2, an autonomously replicating plasmid that confers kanamycin resistance (P. E. Stewart,
      R. Thalken, J. L. Bono, and P. Rosa, Mol. Microbiol. 39:714-721, 2001). B. burgdorferi B31
      clones had transformation efficiencies that were either low, intermediate, or high, and this
      phenotype correlated with the presence or absence of lp25 and lp56. Under the conditions
      utilized in this study, no transformants were detected in clones that contained both lp25 and
      lp56; the few kanamycin-resistant colonies isolated did not contain pBSV2, indicating that the
      resistance was due to mutation. Intermediate electroporation rates (10 to 200 colonies per
      micro g of DNA) were obtained with B31 clones that were either lp25(-) and lp56(+) or lp25(+)
      and lp56(-). Clones in this group that initially contained lp25 lacked this plasmid in pBSV2
      transformants, a finding consistent with selective transformation of lp25(-) variants. High
      transformation rates (>1,000 colonies per micro g of DNA) occurred in clones that lacked both
      lp25 and lp56. Sequence analysis indicated that lp25 and lp56 contain genes that may encode
      restriction and/or modification systems that could result in the low transformation rates
      obtained with strains containing these plasmids. The previously reported correlation between
      lp25 and infectivity in mice, coupled with the barrier lp25 presents to transformation, may
      explain the difficulty in obtaining virulent transformants of B. burgdorferi.
AU  - Lawrenz MB
AU  - Kawabata H
AU  - Purser JE
AU  - Norris SJ
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2002 70: 4798-4804.

PMID- 21784942
VI  - 193
DP  - 2011
TI  - Complete Genome and Proteome of Acholeplasma laidlawii.
PG  - 4943-4953
AB  - We present the complete genome sequence and proteogenomic map for Acholeplasma laidlawii
      PG-8A: class Mollicutes, order Acholeplasmatales,
      family Acholeplasmataceae. The genome of A. laidlawii is represented by a
      single 1 496 992 b.p. circular chromosome with the average G+C content of
      31 mol%. This is the longest genome among the Mollicutes with a known
      nucleotide sequence. It contains genes of polymerase type I, SOS-response,
      and signal transduction systems, as well as RNA regulatory elements,
      riboswitches and T-boxes. This demonstrates a significant capability for
      the regulation of gene expression and mutagenic response to stress.
      Acholeplasma laidlawii and phytoplasmas are the only Mollicutes known to
      use the universal genetic code, in which UGA is a stop codon. Within the
      Mollicutes group, only the sterol-nonrequiring Acholeplasma has the
      capacity to synthesize saturated fatty acids de novo. Proteomic data was
      used in the primary annotation of the genome, validating expression of
      many predicted proteins. We also detected post-translational modifications
      of A.laidlawii proteins: phosphorylation and acylation. Seventy four
      candidate phosphorylated proteins were found: sixteen candidates are
      proteins unique to A. laidlawii, and eleven of them are surface-anchored
      or integral membrane proteins, which implies the presence of active
      signaling pathways. Among twenty acylated proteins, fourteen contained
      palmitic chains, and six, stearic chains. No residue of linoleic or oleic
      acid was observed. Acylated proteins were mainly components of sugar and
      inorganic ion transport systems, and were surface-anchored proteins with
      unknown functions.
AU  - Lazarev VN et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4943-4953.

PMID- 10376821
VI  - 145
DP  - 1999
TI  - Nucleotide sequence of the Bacillus subtilis temperate bacteriophage SPbetaetac2.
PG  - 1055-1067
AB  - The Bacillus subtilis 168 chromosomal region extending from 184 degrees to 195 degrees,
      corresponding to prophage SPbeta, has been completely sequenced using DNA of the
      thermoinducible SPbetac2 mutant.  This 134416 bp segment comprises 187 putative ORFs which,
      according to their orientation, were grouped into three clusters.  Compared to its host,
      SPbetac2 is characterized by a lower G&C content, shorter mean ORF length, as well as a
      different usage of start codons.  Nearly 75% of predicted ORFs do not share significant
      homologies to sequences in available databases.  The only highly similar proteins to
      SPbetac2-encoded ones are host paralogues.  SPbetac2 promoter regions contain SOS box
      consensus sequences and a repeated motif, designated SPbeta repeated element, that is absent
      from the host genome.  Gene sspC, encoding the small acid-soluble protein C, that has been
      previously sequenced and mapped to the vicinity of the SPbeta region, was found to be part of
      the prophage.
AU  - Lazarevic V
AU  - Dusterhoft A
AU  - Soldo B
AU  - Hilbert H
AU  - Mauel C
AU  - Karamata D
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 1999 145: 1055-1067.

PMID- 9465078
VI  - 95
DP  - 1998
TI  - Introns and intein coding sequence in the ribonucleotide reductase genes of Bacillus subtilis temperate bacteriophage SPbeta.
PG  - 1692-1697
AB  - The two putative ribonucleotide reductase subunits of the Bacillus subtilis bacteriophage
      SPbeta are encoded by the bnrdE and bnrdF genes that are highly similar to corresponding host
      paralogs, located on the opposite replication arm.  In contrast to their bacterial
      counterparts, bnrdE and bnrdF each are interrupted by a group I intron, efficiently removed in
      vivo by mRNA processing.  The bnrdF intron contains an ORF encoding a polypeptide similar to
      homing endonucleases responsible for intron mobility, whereas the bnrdE intron has no obvious
      trace of coding sequence.  The downstream bnrdE exon harbors an intervening sequence not
      excised at the level of the primary transcript, which encodes an in-frame polypeptide
      displaying all the features of an intein.  Presently, this is the only intein identified in
      bacteriophages.  In addition, bnrdE provides an example of a group I intron and an intein
      coding sequence within the same gene.
AU  - Lazarevic V
AU  - Soldo B
AU  - Dusterhoft A
AU  - Hilbert H
AU  - Mauel C
AU  - Karamata D
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1998 95: 1692-1697.

PMID- 2173603
VI  - 16
DP  - 1990
TI  - Isolation and characteristics of new restriction endonucleases from Haemophilus influenzae.
PG  - 889-897
AB  - Various strains of Haemophilus influenzae have been examined for the presence
      of site-specific endonuclease activities, and eleven restriction endonucleases
      have been isolated from seven strains.  For all the endonucleases recognition
      sequences were determined, for three of them cleavage sites being identified.
      The enzymes proved to be isoschizomers of known endonucleases, viz. Hin1I,
      Hin8I - AcyI; Hin1II, Hin8II-NlaIII; Hin2I, Hin5I-HpaII; Hin3I-CauII;
      Hin5II-AsuI; Hin5III-HindIII; Hin6I, Hin7I-HhaI.  Restriction endonucleases
      Hin1I, Hin1II and Hin6I recognize nucleotide sequences 5'GR^CGYC, 5'CATG^,
      5'G^CGC, respectively, and cleave them as indicated by the arrows.
AU  - Lazareviciute L
AU  - Maneliene Z
AU  - Padegimiene A
AU  - Kiuduliene L
AU  - Laucys V
AU  - Bitinaite J
AU  - Gruber IM
AU  - Polyachenko VM
AU  - Butkus V
AU  - Janulaitus A
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1990 16: 889-897.

PMID- 26021922
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequence of Serratia liquefaciens HUMV-21, a Cytotoxic, Quorum-Sensing, and Biofilm-Producing Clinical Isolate.
PG  - e00533-15
AB  - A clinical isolate of Serratia liquefaciens (strain HUMV-21) was obtained from a  skin ulcer
      of an adult patient. We report here its complete genome assembly using
      PacBio single-molecule real-time (SMRT) sequencing, which resulted in a single
      circular chromosome with 5.3 Mb. About 5,844 protein-coding genes are predicted
      from this assembly.
AU  - Lazaro-Diez M
AU  - Acosta F
AU  - Remuzgo-Martinez S
AU  - Ocampo-Sosa A
AU  - Ocejo-Vinyals JG
AU  - Bravo J
AU  - El Aamri F
AU  - Escuela O
AU  - Martinez-Martinez L
AU  - Ramos-Vivas J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00533-15.

PMID- 27313299
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequence of Hafnia alvei HUMV-5920, a Human Isolate.
PG  - e00556-16
AB  - A clinical isolate of Hafnia alvei (strain HUMV-5920) was obtained from a urine sample from an
      adult patient. We report here its complete genome assembly using
      PacBio single-molecule real-time (SMRT) sequencing, which resulted in a
      chromosome with 4.5 Mb and a circular contig of 87 kb. About 4,146 protein-coding
      genes are predicted from this assembly.
AU  - Lazaro-Diez M
AU  - Redondo-Salvo S
AU  - Arboleya-Agudo A
AU  - Ocejo-Vinyals JG
AU  - Chapartegui-Gonzalez I
AU  - Ocampo-Sosa AA
AU  - Acosta F
AU  - Martinez-Martinez L
AU  - Ramos-Vivas J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00556-16.

PMID- 30144503
VI  - 52
DP  - 2018
TI  - Genomic path to panresistance in a clinical isolate of Klebsiella pneumoniae.
PG  - 713-718
AB  - Carbapenem-resistant Klebsiella pneumoniae (CRKP) have spread globally through
      tertiary hospitals. Many CRKP clinical isolates are multi-drug resistant and may
      become eventually pan-drug resistant (PDR). We present the closed genome of a
      pan-drug resistant VIM-1-producer K. pneumoniae strain (KP1050) obtained in a
      tertiary hospital . The isolate belonged to ST54 and had five extrachromosomal
      elements, four plasmids and a circular phage genome. Most resistance genes were
      located in two clusters borne by two of the plasmids, a class 1 integron that
      contained up to fourteen genes, including a VIM-1 metallo-beta-lactamase gene,
      and an IS26 transposon that contained a mobile element from A. baumannii encoding
      the amikacin resistance gene aac(6')-Ian. A multi-drug resistant isolate obtained
      six years before was identified retrospectively and sequenced. Comparison of the
      two genomes showed that chromosomal mutations in outer membrane porins, ramR and
      phoQ genes contributed to increase the resistance spectrum.
AU  - Lazaro-Perona F
AU  - Sotillo A
AU  - Troyano-Hernaez P
AU  - Gomez-Gil R
AU  - Vega-Bueno A
AU  - Mingorance J
PT  - Journal Article
TA  - Int. J. Antimicrob. Agents
JT  - Int. J. Antimicrob. Agents
SO  - Int. J. Antimicrob. Agents 2018 52: 713-718.

PMID- 30285095
VI  - 10
DP  - 2018
TI  - Bacillus wiedmannii biovar thuringiensis: A Specialized Mosquitocidal Pathogen with Plasmids from Diverse Origins.
PG  - 2823-2833
AB  - Bacillus cereus sensu lato also known as B. cereus group is composed of an
      ecologically diverse bacterial group with an increasing number of related
      species, some of which are medically or agriculturally important. Numerous e ff
      orts have been undertaken to allow presumptive di ff erentiation of B. cereus
      group species from one another. FCC41 is a Bacillus sp. strain toxic against
      mosquito species like Aedes aegypti, Aedes (Ochlerotatus) albifasciatus, Culex
      pipiens, Culex quinquefasciatus, and Culex apicinus, some of them responsible for
      the transmission of vector-borne diseases. Here, we report the complete genome
      sequence of FCC41 strain, which consists of one circular chromosome and eight
      circular plasmids ranging in size from 8 to 490 kb. This strain harbors six
      crystal protein genes, including cry24Ca, two cry4-like and two cry52-like, a
      cry41-like parasporin gene and multiple virulence factors. The phylogenetic
      analysis of the whole-genome sequence of this strain with molecular approaches
      places this strain into the Bacillus wiedmannii cluster. However, according with
      phenotypical characteristics such as the mosquitocidal activity due to the
      presence of Cry proteins found in the parasporal body and cry genes encoded in
      plasmids of different sizes, indicate that this strain could be renamed as B.
      wiedmannii biovar thuringiensis strain FCC41.
AU  - Lazarte JN
AU  - Lopez RP
AU  - Ghiringhelli PD
AU  - Beron CM
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2018 10: 2823-2833.

PMID- 15917582
VI  - 125
DP  - 2005
TI  - Eco1524I, a type II restriction endonuclease - Isolation, partial purification, and characterization.
PG  - 189-199
AB  - Various strains of Escherichia coli, isolated from different patients, were screened for type
      II restriction endonuclease activity. In 1 out
      of 23 patients, a type II restriction endonuclease activity was found.
      The restriction endonuclease designated Eco1524I was purified to near
      homogeneity, based on hydroxyapatite and heparin sepharose
      chromatography. Eco1524I exhibited endonuclease restriction activity in
      the pH range from 6.0 to 10.0 (maximum level at pH 8.0) and required
      Mg2+ as divalent cation. The enzyme was stable till temperature 55
      degrees C and pH range from 6.0 to 10.0. Eco1524I recognized the
      sequence 6-bp palindromic 5'AGG|CCT 3', producing blunt end
      and is found to be an isoschizomer of StuI.
AU  - Lazim H
AU  - Josephsen J
AU  - Ben Hassen A
AU  - Belhadj O
AU  - Limam R
PT  - Journal Article
TA  - Appl. Biochem. Biotechnol.
JT  - Appl. Biochem. Biotechnol.
SO  - Appl. Biochem. Biotechnol. 2005 125: 189-199.

PMID- 7525273
VI  - 13
DP  - 1994
TI  - Homing of a group II intron in yeast mitochondrial DNA is accompanied by unidirectional co-conversion of upstream-located markers.
PG  - 4963-4972
AB  - Group II introns ai1 and ai2 of the Saccharomyces cerevisiae mitochondrial COX1 gene encode
      proteins having a dual function (maturase and reverse transcriptase) and are mobile genetic
      elements.  By construction of adequate donor genomes, we demonstrate that each of them is
      self-sufficient and practices homing in the absence of homing-type endonucleases encoded by
      either group I introns or the ENS2 gene.  Each of the S. cerevisiae group II self-mobile
      introns was tested for its ability to invade mitochondrial DNA (mtDNA) from two related
      Saccharomyces species.  Surprisingly, only ai2 was observed to integrate into both genomes.
      The non-mobility of ai1 was clearly correlated with some polymorphic changes occurring in
      sequences flanking its insertion sites in the recipient mtDNAs.  Importantly, studies of the
      behavior of these introns in interspecific crosses demonstrate that flanking marker
      co-conversion accompanying group II intron homing is unidirectional and efficient only in the
      3' to 5' direction towards the upstream exon.  Thus, the polar co-conversion and dependence
      of the splicing proficiency of the intron reported previously by us are hallmarks of group II
      intron homing, which significantly distinguish it from the strictly DNA-based group I intron
      homing and strictly RNA-based group II intron transposition.
AU  - Lazowska J
AU  - Meunier B
AU  - Macadre C
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1994 13: 4963-4972.

PMID- 1330224
VI  - 315
DP  - 1992
TI  - Two homologous mitochondrial introns from closely related Saccharomyces species differ by only a few amino acid replacements in their open reading frames: one is mobile, the other is not.
PG  - 37-41
AB  - We have undertaken a comprehensive study of the gene conversion of all the mitochondrial
      introns of Saccharomyces capensis.  The approach used involved the measurement of intron
      transmission amongst the progeny of crosses between a recipient strain (Saccharomyces
      cerevisiae intronless mitochondria) and various donor strains (Saccharomyces capensis, with
      various combinations of mitochondrial introns).  We have shown that the S. capensis second
      intron (bi2 of cytochrome b gene) is extremely active as a donor in gene conversion whereas
      its homologous S. cerevisiae intron is not.  Determination of the sequence of the S. capensis
      intron demonstrates that it differs from that of the homologous S. cerevisiae intron (bi2) by
      a very small number of nucleotide substitutions.
AU  - Lazowska J
AU  - Szczepanek T
AU  - Macadre C
AU  - Dakova M
PT  - Journal Article
TA  - C.R. Acad. Sci. III
JT  - C.R. Acad. Sci. III
SO  - C.R. Acad. Sci. III 1992 315: 37-41.

PMID- 22689230
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of the Strong Mutator Salmonella enterica subsp. enterica Serotype Heidelberg Strain B182.
PG  - 3537-3538
AB  - In bacteria, normal mutation frequencies are mostly around 10(-10) per base pair. However,
      there exists natural isolates, called 'mutators,' that exhibit permanent
      mutation occurrences up to 1,000-fold greater than usual. As mutations play
      essential roles, particularly in the evolution of antibiotic resistance, bacteria
      showing elevated mutation rates could have an important responsibility in the
      emergence of antibiotic resistance, especially in the clinical background. In
      this announcement, we report the first complete genome sequence of the Salmonella
      enterica subsp. enterica serotype Heidelberg B182 mutator strain, isolated from
      bovine feces (France), which consists of a 4,750,465-bp circular chromosome
      (cB182_4750; GC, 52.2%) and one circular plasmid of 37,581 bp (pB182_37; GC,
      42.8%).
AU  - Le Bars H
AU  - Bousarghin L
AU  - Bonnaure-Mallet M
AU  - Jolivet-Gougeon A
AU  - Barloy-Hubler F
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3537-3538.

PMID- 16807237
VI  - 281
DP  - 2006
TI  - DNA damage-induced down-regulation of human Cdc25C and Cdc2 is mediated by cooperation between p53 and maintenance DNA (Cytosine-5) methyltransferase 1.
PG  - 24161-24170
AB  - The Cdc25C phosphatase mediates cellular entry into mitosis in mammalian cells. Cdc25C
      activates Cdc2 for entry into mitosis by dephosphorylating Thr and Tyr at the site of
      inhibitory phosphorylation. The Cdc25C gene contains tumor suppressor p53 binding sites and is
      demonstrated to contribute to the p53-dependent cell cycle arrest upon DNA damage. Here we
      show that both Cdc25C and Cdc2 were down-regulated in wild-type HCT116 cells but not in
      p53-null, DNMT1-null or DNMT1and DNMT3b-null cells, upon p53 stabilization following
      doxorubicin-mediated DNA damage. Furthermore, zebularine, a drug that selectively traps and
      depletes nuclear DNMT1 and DNMT3b, relieved p53-mediated repression of endogenous Cdc25C and
      Cdc2. Methylation analysis of the Cdc25C and Cdc2 promoter displayed internal CG methylation
      proximal to the p53 binding site upon DNA damage in a p53-dependent manner. Chromatin
      immunoprecipitation of doxorubicin treated wild-type HCT116 cells showed the presence of
      DNMT1, p53, H3K9me2, and the transcriptional repressor HDAC1 on the Cdc25C and Cdc2 promoters,
      suggesting their involvement as repressive complexes in Cdc25C and Cdc2 gene silencing. Thus,
      the general mechanism of p53-mediated gene repression may involve recruitment of other
      repressive factors.
AU  - Le Gac G
AU  - Esteve P-O
AU  - Ferec C
AU  - Pradhan S
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2006 281: 24161-24170.

PMID- 10220893
VI  - 173
DP  - 1999
TI  - Functional analaysis of the hemK gene product involvement in protoporphyrinogen oxidase activity in yeast.
PG  - 175-182
AB  - The Escherichia coli hemK gene has been described as being involved in protoporphyrinogen
      oxidase activity; however, there is no biochemical evidence for this. In the context of
      characterizing the mechanisms of protoporphyrinogen oxidation in the yeast Saccharomyces
      cerevisiae, we investigated the yeast homolog of HemK, which is encoded by the ORF YNL063w, to
      find out whether it has any protoporphyrinogen oxidase activity and/or whether it modulates
      protoporphyrinogen oxidase activity. Phenotype analysis and enzyme activity measurements
      indicated that the yeast HemK homolog is not involved in protoporphyrinogen oxidase activity.
      Complementation assays in which the yeast HemK homolog is overproduced do not restore
      wild-type phenotypes in a yeast strain with deficient protoporphyrinogen oxidase activity.
      Protein sequence analysis of HemK-related proteins revealed consensus motif for
      S-adenosyl-methionine-dependent methyltransferase.
AU  - Le Guen L
AU  - Santos R
AU  - Camadro J-M
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1999 173: 175-182.

PMID- 30533912
VI  - 7
DP  - 2018
TI  - Draft Genome Sequences of Two Carbapenemase-Producing Klebsiella pneumoniae Strains Isolated from Blood Cultures.
PG  - e01057-18
AB  - Carbapenemase-producing Klebsiella pneumoniae represents an emerging public health issue.
      Here, we present the draft whole-genome sequences of K. pneumoniae
      clinical strains KPL0.1 (OXA-48 carbapenemase) and KPL0.2 (NDM-1 carbapenemase).
      These genome sequences should help in investigating pathophysiological mechanisms
      of digestive colonization or infection with these highly resistant bacteria.
AU  - Le Guern R
AU  - Grandjean T
AU  - Faure K
AU  - Bauduin M
AU  - Kipnis E
AU  - Dessein R
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e01057-18.

PMID- 21398544
VI  - 193
DP  - 2011
TI  - Genome Sequence of two Staphylococcus aureus ovine strains that induce severe (strain O11) and mild (strain O46) mastitis.
PG  - 2353-2354
AB  - Staphylococcus aureus is a major etiological agent of mastitis in ruminants. We report here
      the genome sequences of two ovine strains that were isolated from gangrenous (strain O11) and
      subclinical (strain O46) ewe mastitis. Both strains belong to the same clonal complex. Despite
      this close genotypic relationship, the two isolates were shown to reproducibly induce highly
      divergent type of infections, either severe (O11) or mild (O46) mastitis in experimental ewe
      model.
AU  - Le Marechal C
AU  - Hernandez D
AU  - Schrenzel J
AU  - Even S
AU  - Berkova N
AU  - Thiery R
AU  - Vautor E
AU  - Fitzgerald JR
AU  - Francois P
AU  - Le Loir Y
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 2353-2354.

PMID- 23516184
VI  - 1
DP  - 2013
TI  - Genome Sequence of Vibrio cholerae G4222, a South African Clinical Isolate.
PG  - e0004013
AB  - Vibrio cholerae, a Gram-negative pathogen autochthonous to the aquatic environment, is the
      causative agent of cholera. Here, we report the complete
      genome sequence of V. cholerae G4222, a clinical isolate from South Africa.
AU  - le Roux WJ
AU  - Chan WY
AU  - De Maayer P
AU  - Venter SN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0004013.

PMID- Not carried by PubMed...
VI  - 10
DP  - 1988
TI  - Purification of restriction endonuclease MspI.
PG  - 35-37
AB  - A new procedure has been developed for the purification of restriction
      endonuclease Msp I.  The procedure uses Sephadex G-200 gel filtration,
      chromatography on phosphocellulose and heparin sepharose, and gives product
      with sufficient purity to permit its use in genetic engineering.
AU  - Le Y
AU  - Zhu S
PT  - Journal Article
TA  - Huaxue Shiji
JT  - Huaxue Shiji
SO  - Huaxue Shiji 1988 10: 35-37.

PMID- 20126622
VI  - 5
DP  - 2010
TI  - The genome sequence of the rumen methanogen Methanobrevibacter ruminantium M1.
PG  - e8926
AB  - Background: Methane (CH4) is a potent greenhouse gas (GHG), having a global warming potential
      21 times that of carbon dioxide (CO2). Methane emissions from agriculture represent around 40%
      of the emissions produced by human-related activities, the single largest source being enteric
      fermentation, mainly in ruminant livestock. Technologies to reduce these emissions are
      lacking. Ruminant methane is formed by the action of methanogenic archaea typified by
      Methanobrevibacter ruminantium, which is present in ruminants fed a wide variety of diets
      worldwide. To gain more insight into the lifestyle of a rumen methanogen, and to identify
      genes and proteins that can be targeted to reduce methane production, we have
      sequenced the 2.93 Mb genome of M. ruminantium M1, the first rumen methanogen genome to be
      completed.  Methodology/Principal Findings: The M1 genome was sequenced, annotated and
      subjected to comparative genomic and
      metabolic pathway analyses. Conserved and methanogen-specific gene sets suitable as targets
      for vaccine development or chemogenomic-based inhibition of rumen methanogens were identified.
      The feasibility of using a synthetic peptidedirected vaccinology approach to target epitopes
      of methanogen surface proteins was demonstrated. A prophage genome was described and its lytic
      enzyme, endoisopeptidase PeiR, was shown to lyse M1 cells in pure culture. A predicted
      stimulation of M1 growth by alcohols was demonstrated and microarray analyses indicated
      up-regulation of methanogenesis genes during co-culture with a hydrogen (H2) producing rumen
      bacterium. We also report the discovery of non-ribosomal peptide synthetases in M. ruminantium
      M1, the first reported in archaeal species.  Conclusions/Significance: The M1 genome sequence
      provides new insights into the lifestyle and cellular processes of this important rumen
      methanogen. It also defines vaccine and chemogenomic targets for broad inhibition of rumen
      methanogens and represents a significant contribution to worldwide efforts to mitigate
      ruminant methane emissions and reduce production of anthropogenic greenhouse gases.
AU  - Leahy SC
AU  - Kelly WJ
AU  - Altermann E
AU  - Ronimus RS
AU  - Yeoman CJ
AU  - Pacheco DM
AU  - Li D
AU  - Kong Z
AU  - McTavish S
AU  - Sang C
AU  - Lambie SC
AU  - Janssen PH
AU  - Attwood GT
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2010 5: e8926.

PMID- 23991254
VI  - 8
DP  - 2013
TI  - The Complete genome sequence of Methanobrevibacter sp. AbM4.
PG  - 215-227
AB  - Methanobrevibacter sp. AbM4 was originally isolated from the abomasal contents of a sheep and
      was chosen as a representative of the
      Methanobrevibacter wolinii clade for genome sequencing. The AbM4 genome
      is smaller than that of the rumen methanogen M. ruminantium M1 (2.0 Mb
      versus 2.93 Mb), encodes fewer open reading frames (ORFs) (1,671 versus
      2,217) and has a lower G+C percentage (29% versus 33%). Overall, the
      composition of the AbM4 genome is very similar to that of M1 suggesting
      that the methanogenesis pathway and central metabolism of these strains
      are highly similar, and both organisms are likely to be amenable to
      inhibition by small molecule inhibitors and vaccine-based methane
      mitigation technologies targeting these conserved features. The main
      differences compared to M1 are that AbM4 has a complete coenzyme M
      biosynthesis pathway and does not contain a prophage or non-ribosomal
      peptide synthase genes. However, AbM4 has a large CRISPR region and
      several type I and type II restriction-modification system components.
      Unusually, DNA-directed RNA polymerase beta' and beta ' subunits of
      AbM4 are joined, a feature only previously observed in some
      thermophilic archaea. AbM4 has a much reduced complement of genes
      encoding adhesin-like proteins which suggests it occupies a ruminal
      niche different from that of M1.
AU  - Leahy SC
AU  - Kelly WJ
AU  - Li D
AU  - Li Y
AU  - Altermann E
AU  - Lambie SC
AU  - Cox F
AU  - Attwood GT
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 215-227.

PMID- 26779129
VI  - 6
DP  - 2015
TI  - Comparative Genomics of Two ST 195 Carbapenem-Resistant Acinetobacter baumannii with Different Susceptibility to Polymyxin Revealed Underlying Resistance  Mechanism.
PG  - 1445
AB  - Acinetobacter baumannii is a Gram-negative nosocomial pathogen of importance due  to its
      uncanny ability to acquire resistance to most antimicrobials. These
      include carbapenems, which are the drugs of choice for treating A. baumannii
      infections, and polymyxins, the drugs of last resort. Whole genome sequencing was
      performed on two clinical carbapenem-resistant A. baumannii AC29 and AC30 strains
      which had an indistinguishable ApaI pulsotype but different susceptibilities to
      polymyxin. Both genomes consisted of an approximately 3.8 Mbp circular chromosome
      each and several plasmids. AC29 (susceptible to polymyxin) and AC30 (resistant to
      polymyxin) belonged to the ST195 lineage and are phylogenetically clustered under
      the International Clone II (IC-II) group. An AbaR4-type resistance island (RI)
      interrupted the comM gene in the chromosomes of both strains and contained the
      bla OXA-23 carbapenemase gene and determinants for tetracycline and streptomycin
      resistance. AC29 harbored another copy of bla OXA-23 in a large (~74 kb)
      conjugative plasmid, pAC29b, but this gene was absent in a similar plasmid
      (pAC30c) found in AC30. A 7 kb Tn1548::armA RI which encodes determinants for
      aminoglycoside and macrolide resistance, is chromosomally-located in AC29 but
      found in a 16 kb plasmid in AC30, pAC30b. Analysis of known determinants for
      polymyxin resistance in AC30 showed mutations in the pmrA gene encoding the
      response regulator of the two-component pmrAB signal transduction system as well
      as in the lpxD, lpxC, and lpsB genes that encode enzymes involved in the
      biosynthesis of lipopolysaccharide (LPS). Experimental evidence indicated that
      impairment of LPS along with overexpression of pmrAB may have contributed to the
      development of polymyxin resistance in AC30. Cloning of a novel variant of the
      bla AmpC gene from AC29 and AC30, and its subsequent expression in E. coli also
      indicated its likely function as an extended-spectrum cephalosporinase.
AU  - Lean SS
AU  - Yeo CC
AU  - Suhaili Z
AU  - Thong KL
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2015 6: 1445.

PMID- 28450513
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Tessaracoccus sp. Strain T2.5-30 Isolated from 139.5  Meters Deep on the Subsurface of the Iberian Pyritic Belt.
PG  - e00238-17
AB  - Here, we report the complete genome sequence of Tessaracoccus sp. strain T2.5-30, which
      consists of a chromosome with 3.2 Mbp, 70.4% G+C content, and 3,005 coding
      DNA sequences. The strain was isolated from a rock core retrieved at a depth of
      139.5 m in the subsurface of the Iberian Pyritic Belt (Spain).
AU  - Leandro T
AU  - da Costa MS
AU  - Sanz JL
AU  - Amils R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00238-17.

PMID- 24201191
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Mycobacterium abscessus subsp. bolletii INCQS 00594.
PG  - e00896-13
AB  - An epidemic of surgical-site infections by a single strain of Mycobacterium abscessus subsp.
      bolletii affected >1,700 patients in Brazil from 2004 to 2008.
      The genome of the epidemic prototype strain M. abscessus subsp. bolletii INCQS
      00594, deposited in the collection of the National Institute for Health Quality
      Control (INCQS), was sequenced.
AU  - Leao SC
AU  - Matsumoto CK
AU  - Viana-Niero C
AU  - Ramos RT
AU  - Carneiro AR
AU  - Barbosa MS
AU  - Lima KV
AU  - Lopes ML
AU  - Azevedo V
AU  - Silva A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00896-13.

PMID- 27034496
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the N2-Fixing Cyanobacterium Nostoc piscinale CENA21, Isolated from the Brazilian Amazon Floodplain.
PG  - e00189-16
AB  - We announce here the draft genome sequence ofNostoc piscinaleCENA21, a diazotrophic
      heterocyst-forming cyanobacterium isolated from the Solimoes River,
      Amazon Basin, Brazil. It consists of one circular chromosome scaffold with 11
      contigs and total size of 7,094,556 bp. Secondary metabolite annotations indicate
      a good source for the discovery of novel natural products.
AU  - Leao T
AU  - Guimaraes PI
AU  - de Melo AG
AU  - Ramos RT
AU  - Leao PN
AU  - Silva A
AU  - Fiore MF
AU  - Schneider MP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00189-16.

PMID- 1830740
VI  - 17
DP  - 1991
TI  - Determination of substrate specificity of a site-specific deoxyribonuclease RtrI.
PG  - 277-279
AB  - A new site-specific deoxyribonuclease RtrI from Rhizobium trifolii has been
      shown to recognize the sequence 5'-G^TCGAC-3' in double-stranded DNA and to
      cleave it at the point indicated by an arrow.  Therefore the enzyme is a true
      isoschizomer of the restriction endonuclease SalI.
AU  - Lebedev LR
AU  - Afinogenova GN
AU  - Andreeva IS
AU  - Pustoshilova NM
AU  - Pozdnyakov SG
AU  - Chizhikov VE
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1991 17: 277-279.

PMID- Not included in PubMed...
VI  - 27
DP  - 1991
TI  - Isolation of restriction endonuclease RsaI from Rhodopseudomonas sphaeroides and study of its properties.
PG  - 330-337
AB  - A technique is proposed for the isolation of the restrictase RsaI from
      Rhodopseudomonas sphaeroides, which involves cultivation of the bacteria under
      aerobic conditions, ultrasonic disruption of the cells, fractionation in the
      PEG-dextran two-phase system, chromatography on phosphocellulose P-11 and
      heparin-sepharose.  The enzyme yield from 1 g of wet cells is 35000 U.
      Gel-filtration through Sephadex G-200 and electrophoresis in polyacrylamide gel
      under denaturing conditions showed that RsaI in solution was a monomer with a
      molecular weight of 24000 +/- 2000.  The optimal conditions for the highest
      enzymatic activity are the following: NaCl concentration 0-20 mM; Mg2+
      concentration 10-12 mM, pH 8.0-8.5; 37-50C.  Mg2+ ions cannot be replaced with
      Mn2+, Zn2+, Ca2+ and Cu2+ ions.  Glycerol and ethanol at concentrations up to
      10%, and p-chloromercuric benzoate at concentrations up to 0.3 mM have no
      inhibitory effect.
AU  - Lebedev LR
AU  - Pustoshilova NM
AU  - Repin VE
AU  - Degtyarev SK
PT  - Journal Article
TA  - Prikl. Biokhim. Mikrobiol.
JT  - Prikl. Biokhim. Mikrobiol.
SO  - Prikl. Biokhim. Mikrobiol. 1991 27: 330-337.

PMID- 11766257
VI  - 47
DP  - 2001
TI  - The sensitivity of E. coli and C. freundii strains to 5-azacytidine.
PG  - 477-482
AB  - The sensitivity of E. coli and C. freundii strains to 5-azacytidine and restrictase activity
      of partially purified cell-free extracts were investigated.  Restrictase activity was found
      only in 5-azacytidine-sensitive strains.  In the 5-azacytidine-resistant strains restrictase
      activity was not detected.
AU  - Lebenka AI
AU  - Melvidas VI
PT  - Journal Article
TA  - Vopr. Med. Khim.
JT  - Vopr. Med. Khim.
SO  - Vopr. Med. Khim. 2001 47: 477-482.

PMID- Not included in PubMed...
VI  - 53
DP  - 1988
TI  - Enzymes of DNA restriction-modification from Caulobacter fusiformis BC-25.
PG  - 1895-1899
AB  - The CfuII system of restriction-modification enzymes, as well as the methylase
      CfuIII, was detected in cells of Caulobacter fusiformis BC-25.  R.CfuII
      recognizes and cleaves the sequence 5'-CTGCA^G-3' (PstI).  This system has the
      corresponding methylase CfuII, which protects the host DNA.  The manifestation
      of R.CfuII activity requires Mg2+ or Mn2+.  M.CfuIII protects DNA from cleavage
      by the restriction endonuclease EcoRI.  Modification of DNA by a Cfu of type
      III is a generic characteristic of Caulobacter.
AU  - Lebenka AY
AU  - Chitavichyus DB
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1988 53: 1895-1899.

PMID- 7032611
VI  - 46
DP  - 1981
TI  - DNA methylation in the cells of Escherichia coli MRE 600 in the presence of S-methylmethionine.
PG  - 2160-2163
AB  - The effect of S-methylmethionine, a methyl group donor, on enzymatic methylation of DNA in E.
      coli MRE 600 cells was studied.  It was found that SMM can be used as a donor of methyl groups
      during bacterial DNA methylation in vivo without changing the specificity of DNA methylation.
AU  - Lebenka AY
AU  - Kanopkaite SI
AU  - Buryanov YI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1981 46: 2160-2163.

PMID- 2790075
VI  - 54
DP  - 1989
TI  - DNA methylase Sau3AI:  isolation and properties.
PG  - 1009-1014
AB  - DNA-methylase Sau3AI has been isolated for the first time from Staphylococcus aureus 3A cells
      and purified by column chromatography on phosphocellulose PII, heparin-Sepharose and blue
      Sepharose. The purified enzyme methylates the GATC sequence with the formation of GATm5C as
      can be evidenced from the protection of DNA from digestion with restrictases Sau3AI and BamHI,
      the lack of the C3H3-group incorporation into Sau3AI DNA-restricts and the formation of a
      single methylated base m5C. Sau3AI methylase modifies only double-stranded (but not
      single-stranded) DNA. Thus, methylase Sau3AI modifies both DNA chains in the recognition site
      during a single binding act. The 5-azacytidine-containing DNA inhibits by 95% the activity of
      methylase Sau3AI. Ado-met is the single methyl group donor for methylase Sau3AI. The presence
      of m6A in the recognition site does not affect the activity of methylase Sau3AI. The practical
      recommendations for the use of M.Sau3AI, alongside with M.Eco dam, for the study of dam
      methylation by additional methylation of the DNA in vitro in the presence of
      [methyl-3H]-S-adenosyl-methionine are given.
AU  - Lebenka AY
AU  - Rackus YA
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1989 54: 1009-1014.

PMID- 28963224
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Xenophilus sp., a Novel Bacterium Isolated from the Skin of a Southern Leopard Frog (Rana sphenocephala) in Florida, USA.
PG  - e01067-17
AB  - We report here the draft genome sequence of a novel Xenophilus species cultured from the skin
      of a southern leopard frog (Rana sphenocephala). Compared to
      previously sequenced bacterial genomes, our novel isolate showed the most
      significant homology with Xenophilus azovorans The assembled genome is 3,978,285
      bp, with 3,704 predicted genes and one predicted plasmid.
AU  - Lebert BM
AU  - Sanford SA
AU  - Reisinger LM
AU  - Forsman AM
AU  - Savage AE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01067-17.

PMID- 
VI  - 53
DP  - 2007
TI  - The ability of bacterial DNA methyltransferases to use methylcobalamine as a cofactor in DNA methylation reactions.
PG  - 159-163
AB  - The ability of bacterial DNA methyltransferases Alu I, Cfr I, Cfr 6, Cfr 10, Eco RI, Eco RII,
      Msp I, Mva I, Pvu I, Pvu II, and Sau 3A to use
      methyl-cobalamine and methyl-methionine as cofactors of DNA methylation
      in vitro. These bacterial DNA methyl transferase used
      methyl-cobalamine, but not methylmethionine for DNA methylation.
AU  - Lebionka AY
AU  - Melvidas VI
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 2007 53: 159-163.

PMID- 212732
VI  - 75
DP  - 1978
TI  - DNA modifying enzymes of Agrobacterium tumefaciens: Effect of DNA topoisomerase, restriction endonuclease, and unique DNA endonuclease on plasmid and plant DNA.
PG  - 4097-4101
AB  - Extracts from Agrobacterium tumefaciens strain 1D135 contain three enzymes that
      have been characterized and partially purified.  The first enzyme, a DNA
      topoisomerase, appeared to relax only negatively twisted DNA.  The second
      enzyme, AtuI, a type II restriction endonuclease, generated the identical DNA
      digestion pattern as EcoRII when several DNAs were used.  The third enzyme,
      endonuclease A, showed a preference for superhelical DNAs as substrates.  When
      plasmid pCK135DNA, obtained from the virulent strain 1D135 of A. tumefaciens,
      or plant DNA was exposed to the three enzymes, changes in DNA patterns were
      observed due to either conformational changes or digestion of the DNAs.  These
      enzymes may function in vivo in the processing and incorporation of bacterial
      DNA in plant cells.
AU  - LeBon JM
AU  - Kado CI
AU  - Rosenthal LJ
AU  - Chirikjian JG
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1978 75: 4097-4101.

PMID- 24371201
VI  - 1
DP  - 2013
TI  - High-Quality Draft Genome Sequence of Vagococcus lutrae Strain LBD1, Isolated from the Largemouth Bass Micropterus salmoides.
PG  - e01087-13
AB  - Vagococci are usually isolated from marine hosts and occasionally from endodontic infections.
      Using 16S rRNA gene comparison, the closest relatives are members of
      the genera Enterococcus and Carnobacterium. A draft sequence of Vagococcus lutrae
      was generated to clarify the relationship of Vagococcus to these and other
      related low-G+C Gram-positive bacteria.
AU  - Lebreton F
AU  - Valentino MD
AU  - Duncan LB
AU  - Zeng Q
AU  - Manson McGA
AU  - Earl AM
AU  - Gilmore MS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01087-13.

PMID- 23963180
VI  - 4
DP  - 2013
TI  - Emergence of epidemic multidrug-resistant Enterococcus faecium from animal and commensal strains.
PG  - e00534-13
AB  - UNLABELLED: Enterococcus faecium, natively a gut commensal organism, emerged as a leading
      cause of multidrug-resistant hospital-acquired infection in the 1980s. As
      the living record of its adaptation to changes in habitat, we sequenced the
      genomes of 51 strains, isolated from various ecological environments, to
      understand how E. faecium emerged as a leading hospital pathogen. Because of the
      scale and diversity of the sampled strains, we were able to resolve the lineage
      responsible for epidemic, multidrug-resistant human infection from other strains
      and to measure the evolutionary distances between groups. We found that the
      epidemic hospital-adapted lineage is rapidly evolving and emerged approximately
      75 years ago, concomitant with the introduction of antibiotics, from a population
      that included the majority of animal strains, and not from human commensal lines.
      We further found that the lineage that included most strains of animal origin
      diverged from the main human commensal line approximately 3,000 years ago, a time
      that corresponds to increasing urbanization of humans, development of hygienic
      practices, and domestication of animals, which we speculate contributed to their
      ecological separation. Each bifurcation was accompanied by the acquisition of new
      metabolic capabilities and colonization traits on mobile elements and the loss of
      function and genome remodeling associated with mobile element insertion and
      movement. As a result, diversity within the species, in terms of sequence
      divergence as well as gene content, spans a range usually associated with
      speciation. IMPORTANCE: Enterococci, in particular vancomycin-resistant
      Enterococcus faecium, recently emerged as a leading cause of hospital-acquired
      infection worldwide. In this study, we examined genome sequence data to
      understand the bacterial adaptations that accompanied this transformation from
      microbes that existed for eons as members of host microbiota. We observed changes
      in the genomes that paralleled changes in human behavior. An initial bifurcation
      within the species appears to have occurred at a time that corresponds to the
      urbanization of humans and domestication of animals, and a more recent
      bifurcation parallels the introduction of antibiotics in medicine and
      agriculture. In response to the opportunity to fill niches associated with
      changes in human activity, a rapidly evolving lineage emerged, a lineage
      responsible for the vast majority of multidrug-resistant E. faecium infections.
AU  - Lebreton F
AU  - van Schaik W
AU  - McGuire AM
AU  - Godfrey P
AU  - Griggs A
AU  - Mazumdar V
AU  - Corander J
AU  - Cheng L
AU  - Saif S
AU  - Young S
AU  - Zeng Q
AU  - Wortman J
AU  - Birren B
AU  - Willems RJ
AU  - Earl AM
AU  - Gilmore MS
PT  - Journal Article
TA  - MBio
JT  - MBio
SO  - MBio 2013 4: e00534-13.

PMID- Not carried by PubMed...
VI  - 343
DP  - 1992
TI  - SwaI, a unique restriction endonuclease from Staphylococcus warneri, which recognizes 5'-ATTTAAAT-3'.
PG  - 121-122
AB  - Restriction endonucleases with low cutting frequencies are important tools in molecular
      genetics. Analysis of complex DNA molecules e.g. chromosomes requires cutting of DNA into
      fragments of megabase size range. Nucleases with low cutting frequencies either recognize
      sequences which are under represented in chromosomal DNA or are characterized by recognition
      sequences of more than six base pairs. We discovered and isolated SwaI a novel class-II
      restriction endonuclease from Staphylococcus warneri whose recognition specificity requires
      eight nucleotides.
AU  - Lechner M
AU  - Frey B
AU  - Laue F
AU  - Ankenbauer W
AU  - Schmitz G
PT  - Journal Article
TA  - Fresenius Z. Anal. Chem.
JT  - Fresenius Z. Anal. Chem.
SO  - Fresenius Z. Anal. Chem. 1992 343: 121-122.

PMID- 1594448
VI  - 20
DP  - 1992
TI  - SwaI, a unique restriction endonuclease from Staphylococcus warneri, which recognizes 5'-ATTTAAAT-3'.
PG  - 2293-2296
AB  - A novel class-II restriction endonuclease designated SwaI was purified from Staphyloccus
      warneri. This enzyme cleaves adenovirus 2 DNA, SV40 DNA and M13mp7 at one site each, but does
      not cleave lambda, PhiX174, pBR322 or pBR328 DNA. SwaI recognizes the octanucleotide sequence
      5'-ATTTAAAT-3', cleaving in the center of the recognition sequence creating blunt ended DNA
      fragments. SwaI was used to digest chromosomal DNA from various microorganisms and human
      cells.
AU  - Lechner M
AU  - Frey B
AU  - Laue F
AU  - Anton-Botella J
AU  - Smith CL
AU  - Ankenbauer W
AU  - Schmitz GG
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 2293-2296.

PMID- 24482531
VI  - 6
DP  - 2014
TI  - Phylogenomics of 'Candidatus Hepatoplasma crinochetorum,' a Lineage of Mollicutes Associated with Noninsect Arthropods.
PG  - 407-415
AB  - Bacterial gut communities of arthropods are highly diverse and tightly related to
      host feeding habits. However, our understanding of the origin and role of the
      symbionts is often hindered by the lack of genetic information. "Candidatus
      Hepatoplasma crinochetorum" is a Mollicutes symbiont found in the midgut glands
      of terrestrial isopods. The only available nucleotide sequence for this symbiont
      is a partial 16S rRNA gene sequence. Here, we present the 657,101 bp assembled
      genome of Candidatus Hepatoplasma crinochetorum isolated from the terrestrial
      isopod Armadillidium vulgare. While previous 16S rRNA gene-based analyses have
      provided inconclusive results regarding the phylogenetic position of Candidatus
      Hepatoplasma crinochetorum within Mollicutes, we performed a phylogenomic
      analysis of 127 Mollicutes orthologous genes which confidently branches the
      species as a sister group to the Hominis group of Mycoplasma. Several genome
      properties of Candidatus Hepatoplasma crinochetorum are also highlighted compared
      with other Mollicutes genomes, including adjacent tryptophan tRNA genes, which
      further our understanding of the evolutionary dynamics of these genes in
      Mollicutes, and the presence of a probably inactivated CRISPR/Cas system, which
      constitutes a testimony of past interactions between Candidatus Hepatoplasma
      crinochetorum and mobile genetic elements, despite their current lack in this
      streamlined genome. Overall, the availability of the complete genome sequence of
      Candidatus Hepatoplasma crinochetorum paves the way for further investigation of
      its ecology and evolution.
AU  - Leclercq S
AU  - Dittmer J
AU  - Bouchon D
AU  - Cordaux R
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2014 6: 407-415.

PMID- 5326091
VI  - 91
DP  - 1966
TI  - Genetics of host-controlled restriction anad modification of deoxyribonucleic acid in Escherichia coli.
PG  - 1029-1036
AB  - The locus for the host specific restriction and modification of
      deoxyribonucleic acid in Escherichia coli has been mapped by matings between
      mutants for these characters in strains K-12, C600, and B. Linkage analysis and
      kinetics of marker transfer indicate that a single or closely linked multiple
      chromosomal site located about 4 min counterclockwise to leucine is responsible
      for these activities.  Secondary factors which affect the quantitative level of
      restriction also were detected.  Wild-type recombinants were isolated in
      crosses between rm- (restriction or modification, or both) mutants.  The
      expression in zygotes of the restrictionless character of a rm- donor is masked
      by a separate, physiological impairment of restriction, which results from
      mating and is independent of the modification state of the donor.  The
      relevance of the restriction character to mating incompatibilities in these and
      other bacterial strains is considered.
AU  - Lederberg S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1966 91: 1029-1036.

PMID- 5321954
VI  - 27
DP  - 1965
TI  - Host-controlled restriction and modification of deoxyribonucleic acid in Eschericia coli.
PG  - 378-387
AB  - In Escherichia coli strain C600 (which has the host specificity of K12),
      restrictions against infection by phage lambda of host specificities B and C
      have the same sensitivity to heat inactivation.  Likewise, in strain B,
      restrictions against phage lambda of host specificities C600 and C have an
      identical heat sensitivity.  Strain C600(P1) has a heat sensitivity for loss of
      its P1-directed restriction different from that of its C600-controlled
      restriction.  Mutants of K12-type strains and of B which are impaired in their
      restriction and modification activities have been isolated.  In K12 strains,
      restrictions toward phage lambda of host specificities C and B are impaired by
      the same mutation.  In B, restrictions toward phage lambda of host
      specificities C and C600 also are lost simultaneously by mutation.  The
      coordinate changes in restriction by heat treatment and by mutation indicate
      that a common mechanism for restriction of lambda of host specificities C and B
      operates in K12 strains, and that a single mechanism for restriction of phage
      lambda of host specificities C and K12 occurs in strain B.  Restrictionless
      mutants of B, unlike their parent, act as fertile F- in crosses with K12 Hfr
      strains.  Modificationless mutants of K12 Hfr, unlike their parent, are no
      longer fertile with restricting C600 strains.  Thus, the same mutations affect
      the modification and/or restriction of the DNA of bacteria as well as phage.
      Models are proposed for host restriction and modfication.  The models visualize
      restriction as either a screening of new DNA by a DNA-site specific degrading
      activity-successful passage permitting the DNA to operate in that cell-or a
      seavenging of new DNA by a nonspecific degrading activity when such DNA fails
      to be complexed with a site-specific protecting agent.
AU  - Lederberg S
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1965 27: 378-387.

PMID- 25342680
VI  - 2
DP  - 2014
TI  - Genome Sequences of Brucella abortus and Brucella suis Strains Isolated from Bovine in Zimbabwe.
PG  - e01063-14
AB  - This is a report of whole-genome sequences of a Brucella abortus strain and two Brucella suis
      strains isolated from bovine in Zimbabwe. These strains were
      selected based on their origin and data obtained when using multiplex PCR assays,
      then sequenced using next-generation sequencing technologies.
AU  - Ledwaba B
AU  - Mafofo J
AU  - van Heerden H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01063-14.

PMID- 4527604
VI  - 71
DP  - 1974
TI  - A cleavage map of bacteriophage PhiX174 genome.
PG  - 2882-2886
AB  - Restriction endonucleases isolated from Hemophilus influenzae, Hemophilus
      parainfluenzae, and Hemophilus aegyptius were used to cleave PhiX174
      replicative form DNA into three sets of specific DNA fragments.  The order of
      these fragments in the PhiX replicative form molecule was determined by (1)
      analysis of partial digest products, (2) analysis of overlapping sets of
      fragments produced by two different restrictive enzymes.  On the basis of these
      results, a detailed physical map of the PhiX174 genome has been constructed
      with respect to the cleavage sites of all three enzymes.
AU  - Lee AS
AU  - Sinsheimer RL
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1974 71: 2882-2886.

PMID- 19450230
VI  - 421
DP  - 2009
TI  - SUMOylation enhances DNA methyltransferase 1 activity.
PG  - 449-461
AB  - DNA methylation regulates gene expression through Complex network of protein-protein and
      protein-DNA interactions in chromatin. The
      maintenance methylase, DNMT1 (DNA methyltransferase 1), is a prominent
      enzyme in the process that is linked to DNA replication and drives the
      heritable nature of epigenetic modifications. The mechanistic details
      that explain how DNMT1 catalytic action is directed and regulated in
      chromatin are important ill our overall understanding of gene control.
      In this work, we show that DNMT1 is modified by SUMOylation and we have
      mapped these SUMOylation sites by defined mutations. SUMOylated DNMT1
      is catalytically active on genomic DNA in vivo and we find that
      SUMOylation significantly enhances the methylase activity of DNMT1 both
      in vitro and in chromatin. These data suggest that SUMOylation
      modulates the endogenous activity of a prominent epigenetic maintenance
      pathway in somatic cells.
AU  - Lee B
AU  - Muller MT
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 2009 421: 449-461.

PMID- 16230360
VI  - 280
DP  - 2005
TI  - Procainamide is a specific inhibitor of DNA methyltransferase 1.
PG  - 40749-40756
AB  - CpG island hypermethylation occurs in most cases of cancer, typically resulting in the
      transcriptional silencing of critical cancer genes.
      Procainamide has been shown to inhibit DNA methyltransferase activity
      and reactivate silenced gene expression in cancer cells by reversing
      CpG island hypermethylation. We report here that procainamide
      specifically inhibits the hemimethylase activity of DNA
      methyltransferase 1 (DNMT1), the mammalian enzyme thought to be
      responsible for maintaining DNA methylation patterns during
      replication. At micromolar concentrations, procainamide was found to be
      a partial competitive inhibitor of DNMT1, reducing the affinity of the
      enzyme for its two substrates, hemimethylated DNA and
      S-adenosyl-L-methionine. By doing so, procainamide significantly
      decreased the processivity of DNMT1 on hemimethylated DNA. Procainamide
      was not a potent inhibitor of the de novo methyltransferases DNMT3a and
      DNMT3b2. As further evidence of the specificity of procainamide for
      DNMT1, procainamide failed to lower genomic 5-methyl-2'-deoxycytidine
      levels in HCT116 colorectal cancer cells when DNMT1 was genetically
      deleted but significantly reduced genomic 5-methyl-2'-deoxycytidine
      content in parental HCT116 cells and in HCT116 cells where DNMT3b was
      genetically deleted. Because many reports have strongly linked DNMT1
      with epigenetic alterations in carcinogenesis, procainamide may be a
      useful drug in the prevention of cancer.
AU  - Lee BH
AU  - Yegnasubramanian S
AU  - Lin XH
AU  - Nelson WG
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2005 280: 40749-40756.

PMID- 15673718
VI  - 33
DP  - 2005
TI  - The genome sequence of Xanthomonas oryzae pathovar oryzae KACC10331, the bacterial blight pathogen of rice.
PG  - 577-586
AB  - The nucleotide sequence was determined for the genome of Xanthomonas oryzae pathovar oryzae
      (Xoo) KACC10331, a bacterium that causes bacterial
      blight in rice (Oryza sativa L.). The genome is comprised of a single, 4
      941 439 bp, circular chromosome that is G + C rich (63.7%). The genome
      includes 4637 open reading frames (ORFs) of which 3340 (72.0%) could be
      assigned putative function. Orthologs for 80% of the predicted Xoo genes
      were found in the previously reported X.axonopodis pv. citri (Xac) and
      X.campestris pv. campestris (Xcc) genomes, but 245 genes apparently
      specific to Xoo were identified. Xoo genes likely to be associated with
      pathogenesis include eight with similarity to Xanthomonas avirulence (avr)
      genes, a set of hypersensitive reaction and pathogenicity (hrp) genes,
      genes for exopolysaccharide production, and genes encoding extracellular
      plant cell wall-degrading enzymes. The presence of these genes provides
      insights into the interactions of this pathogen with its gramineous host.
AU  - Lee BM
AU  - Park YJ
AU  - Park DS
AU  - Kang HW
AU  - Kim JG
AU  - Song ES
AU  - Park IC
AU  - Yoon UH
AU  - Hahn JH
AU  - Koo BS
AU  - Lee GB
AU  - Kim H
AU  - Park HS
AU  - Yoon KO
AU  - Kim JH
AU  - Jung CH
AU  - Koh NH
AU  - Seo JS
AU  - Go SJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2005 33: 577-586.

PMID- 24652978
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Pseudomonas aeruginosa SG17M, an Environmental Isolate Belonging to Clone C, Prevalent in Patients and Aquatic Habitats.
PG  - e00186-14
AB  - Pseudomonas aeruginosa SG17M is an environmental isolate recovered from river water in the
      city of Mulheim, Germany. SG17M belongs to clone C, which is
      distributed worldwide. This is the first clone C strain whose genome sequence has
      been determined.
AU  - Lee C
AU  - Peters V
AU  - Melefors O
AU  - Romling U
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00186-14.

PMID- 29167249
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Tepidibacter mesophilus Strain JCM 16806T Isolated from  Soil Polluted by Crude Oil in China.
PG  - e01308-17
AB  - Here, we report the draft genome sequence of Tepidibacter mesophilus strain JCM 16806T, which
      was isolated from an oil field. It is composed of 3,310,272 bp and
      contains 3,160 protein-coding genes, 8 5S rRNAs, 3 16S rRNAs, and 69 tRNAs.
AU  - Lee CG
AU  - Yuki M
AU  - Iida T
AU  - Nakaho K
AU  - Ohkuma M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01308-17.

PMID- 26450743
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Elizabethkingia sp. BM10, a Symbiotic Bacterium of the Wood-Feeding Termite Reticulitermes speratus KMT1.
PG  - e01181-15
AB  - Elizabethkingia sp. BM10 was isolated from the hindgut of the wood-feeding termite
      Reticulitermes speratus KMT1. It had cellobiohydrolase and beta-glucosidase activities but not
      endo-beta-glucanase activity. The complete sequence of its genome, which has a total size of
      4,242,519 bases, is reported here. The genomic analysis identified six beta-glucosidase
      candidate genes and three beta-glucanase candidate genes.
AU  - Lee D
AU  - Kim YK
AU  - Kim YS
AU  - Kim TJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01181-15.

PMID- 19129632
VI  - 73
DP  - 2009
TI  - WeGAS: a web-based microbial genome annotation system.
PG  - 213-216
AB  - We have developed WeGAS, a Web based microbial Genome
      Annotation System, which provides features that include gene prediction,
      homology search, promoter/motif analysis, genome browsing, gene ontology
      analysis based on the COGs and GO, and metabolic pathway analysis with
      web-based interfaces. Most raw data and intermediate data from genome
      projects can be managed with the WeGAS database system, and analysis
      results, including information on each gene and final genome maps, are
      provided by its visualization modules. Especially, a pie-view browser
      displaying circular maps of contigs and a COG-GO combination browser are
      very helpful for an overview of projects. Major public microbial genome
      databases can be imported, searched, and browsed through the WeGAS
      modules. WeGAS is freely accessible via web site
      http://ns.smallsoft.co.kr:8051.
AU  - Lee D
AU  - Seo H
AU  - Park C
AU  - Park K
PT  - Journal Article
TA  - Biosci. Biotechnol. Biochem.
JT  - Biosci. Biotechnol. Biochem.
SO  - Biosci. Biotechnol. Biochem. 2009 73: 213-216.

PMID- 17038190
VI  - 7
DP  - 2006
TI  - Genomic analysis reveals that Pseudomonas aeruginosa virulence is combinatorial.
PG  - R90
AB  - ABSTRACT: BACKGROUND: Pseudomonas aeruginosa is a ubiquitous environmental bacterium and an
      important opportunistic human pathogen. Generally, the
      acquisition of genes in the form of pathogenicity islands distinguishes
      pathogenic isolates from non-pathogens. We therefore sequenced a highly
      virulent strain of P. aeruginosa, PA14, and compared it to a previously
      sequenced (and less pathogenic) strain, PAO1, to identify novel virulence
      genes. RESULTS: The PA14 and PAO1 genomes are remarkably similar, although
      PA14 has a slightly larger genome (6.5 MB) than PAO1 (6.3 MB). We
      identified 58 PA14 gene clusters that are absent in PAO1 to determine
      which of these genes, if any, contribute to its enhanced virulence in a
      Caenorhabditis elegans pathogenicity model. First, we tested 18 additional
      diverse strains in the C. elegans model and observed a wide range of
      pathogenic potential; however, genotyping these strains using a custom
      microarray showed that the presence of PA14 genes absent in PAO1 did not
      correlate with the virulence of these strains. Second we utilized a
      full-genome non-redundant mutant library of PA14 to identify five genes
      (absent in PAO1) required for C. elegans killing. Surprisingly, although
      these five genes are present in many other P. aeruginosa strains, they do
      not correlate with virulence in C. elegans. CONCLUSIONS: Genes required
      for pathogenicity in one strain of P. aeruginosa are neither required for
      nor predictive of virulence in other strains. We therefore propose that
      virulence in this organism is multifactorial and combinatorial, the result
      of a pool of pathogenicity-related genes that interact in various
      combinations in different genetic backgrounds.
AU  - Lee DG
AU  - Urbach JM
AU  - Wu G
AU  - Liberati NT
AU  - Feinbaum RL
AU  - Miyata S
AU  - Diggins LT
AU  - He J
AU  - Saucier M
AU  - Deziel E
AU  - Friedman L
AU  - Li L
AU  - Grills G
AU  - Montgomery K
AU  - Kucherlapati R
AU  - Rahme LG
AU  - Ausubel FM
PT  - Journal Article
TA  - Genome Biol.
JT  - Genome Biol.
SO  - Genome Biol. 2006 7: R90.

PMID- 16174769
VI  - 280
DP  - 2005
TI  - Repair of methylation damage in DNA and RNA by mammalian AlkB homologues.
PG  - 39448-39459
AB  - Human and Escherichia coli derivatives of AlkB enzymes remove methyl groups from
      1-methyladenine and 3-methylcytosine in nucleic acids via an
      oxidative mechanism that releases the methyl group as formaldehyde. In
      this report, we demonstrate that the mouse homologues of the
      alpha-ketoglutarate Fe(II) oxygen-dependent enzymes mAbh2 and Abh3 have
      activities comparable to those of their human counterparts. The mAbh2 and
      mAbh3 release modified bases from both DNA and RNA. Comparison of the
      activities of the homogenous ABH2 and ABH3 enzymes demonstrate that these
      activities are shared by both sets of enzymes. An assay for the detection
      of alpha-ketoglutarate Fe(II) dioxygenase activity using an
      oligodeoxyribonucleotide with a unique modification shows activity for all
      four enzymes studied and a loss of activity for eight mutant proteins.
      Steady-state kinetics for removal of methyl groups from DNA substrates
      indicates that the reactions of the proteins are close to the diffusion
      limit. Moreover, mAbh2 or mAbh3 activity increases survival in a strain
      defective in alkB. The mRNAs of AHB2 and ABH3 are expressed most in testis
      for ABH2 and ABH3, whereas expression of the homologous mouse genes is
      different. The mAbh3 is strongly expressed in testis, whereas highest
      expression of mAbh2 is in heart. Other purified human AlkB homologue
      proteins ABH4, ABH6, and ABH7 do not manifest activity. The demonstration
      of mAbh2 and mAbh3 activities and their distributions provide data on
      these mammalian homologues of AlkB that can be used in animal studies.
AU  - Lee DH
AU  - Jin SG
AU  - Cai S
AU  - Chen Y
AU  - Pfeifer GP
AU  - O'Connor TR
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2005 280: 39448-39459.

PMID- 26566422
VI  - 10
DP  - 2015
TI  - Complete genome sequence of Bacillus cereus FORC_005, a food-borne pathogen from  the soy sauce braised fish-cake with quail-egg.
PG  - 97
AB  - Due to abundant contamination in various foods, the pathogenesis of Bacillus cereus has been
      widely studied in physiological and molecular level. B. cereus
      FORC_005 was isolated from a Korean side dish, soy sauce braised fish-cake with
      quail-egg in South Korea. While 21 complete genome sequences of B. cereus has
      been announced to date, this strain was completely sequenced, analyzed, and
      compared with other complete genome sequences of B. cereus to elucidate the
      distinct pathogenic features of a strain isolated in South Korea. The genomic DNA
      containing a circular chromosome consists of 5,349,617-bp with a GC content of
      35.29 %. It was predicted to have 5170 open reading frames, 106 tRNA genes, and
      42 rRNA genes. Among the predicted ORFs, 3892 ORFs were annotated to encode
      functional proteins (75.28 %) and 1278 ORFs were predicted to encode hypothetical
      proteins (748 conserved and 530 non-conserved hypothetical proteins). This genome
      information of B. cereus FORC_005 would extend our understanding of its
      pathogenesis in genomic level for efficient control of its contamination in foods
      and further food poisoning.
AU  - Lee DH
AU  - Kim HR
AU  - Chung HY
AU  - Lim JG
AU  - Kim S
AU  - Kim SK
AU  - Ku HJ
AU  - Kim H
AU  - Ryu S
AU  - Choi SH
AU  - Lee JH
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 97.

PMID- 23105088
VI  - 194
DP  - 2012
TI  - Genome Sequence of Oscillibacter ruminantium Strain GH1, Isolated from Rumen of Korean Native Cattle.
PG  - 6362
AB  - Oscillibacter ruminantium strain GH1 was isolated from the rumen of Korean native cattle
      (HanWoo; Bos taurus coreanae). Here, we present the 3.07-Mb draft genome
      of this strain, which could reveal the presence of certain fiber-specific
      glycoside hydrolases and butyric acid-producing genes.
AU  - Lee GH
AU  - Kumar S
AU  - Lee JH
AU  - Chang DH
AU  - Kim DS
AU  - Choi SH
AU  - Rhee MS
AU  - Lee DW
AU  - Yoon MH
AU  - Kim BC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6362.

PMID- 22815460
VI  - 194
DP  - 2012
TI  - Genome Sequence of Herbaspirillum sp. Strain GW103, a Plant Growth-Promoting Bacterium.
PG  - 4150
AB  - Herbaspirillum sp. strain GW103 was isolated from rhizosphere soil of the reed Phragmites
      australis on reclaimed land. Here we report the 5.05-Mb draft genome
      sequence of the strain, providing bioinformation about the agronomic benefits of
      this strain, such as multiple traits relevant to plant root colonization and
      plant growth promotion.
AU  - Lee GW
AU  - Lee KJ
AU  - Chae JC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4150.

PMID- 
VI  - 2
DP  - 1998
TI  - Identification of hemimethylated DNA binding activity in the seqA mutant.
PG  - 351-353
AB  - A 245 bp segment of E. coli chromosomal replication origin, oriC, contains 11 repeats of the
      GATC sequence in which adenine is methylated by Dam methylase.  Newly replicated oriC is
      hemimethylated.  The parental strand of the newly replicated oriC is methylated, but the
      nascent strand is not yet methylated until methylated by Dam methylase.  The hemimethylated
      oriC plays an important role in the regulation of chromosomal replication.  Activity in the
      seqA mutant was identified to bind preferentially to hemimethylated DNA, but not to
      fully-methylated DNA.  This activity may participate in the sequestration of initiation of
      chromosomal replication.
AU  - Lee H
AU  - Kang S
AU  - Yim J-B
AU  - Hwang DS
PT  - Journal Article
TA  - Korean J. Biol. Sci.
JT  - Korean J. Biol. Sci.
SO  - Korean J. Biol. Sci. 1998 2: 351-353.

PMID- 23472222
VI  - 1
DP  - 2013
TI  - Whole-Genome Sequence of Mycobacterium intracellulare Clinical Strain MOTT-H4Y, Belonging to INT5 Genotype.
PG  - e00006-13
AB  - Here, we report the draft genome sequence of the clinical strain MOTT-H4Y, grouped previously
      into the INT5 genotype of the 5 genotypes of .
AU  - Lee H
AU  - Kim BJ
AU  - Kim K
AU  - Hong SH
AU  - Kook YH
AU  - Kim BJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00006-13.

PMID- 22582384
VI  - 194
DP  - 2012
TI  - Genome Sequence of Sphingomonas sp. Strain PAMC 26621, an Arctic-Lichen-Associated Bacterium Isolated from a Cetraria sp.
PG  - 3030
AB  - The lichen-associated bacterial strain Sphingomonas sp. PAMC 26621 was isolated from an Arctic
      lichen Cetraria sp. on Svalbard Islands. Here we report the draft genome sequence of this
      strain, which could provide novel insights into the molecular principles of lichen-microbe
      interactions.
AU  - Lee H
AU  - Shin SC
AU  - Lee J
AU  - Kim SJ
AU  - Kim BK
AU  - Hong SG
AU  - Kim EH
AU  - Park H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3030.

PMID- 29192082
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Bacillus velezensis YJ11-1-4, a Strain with Broad-Spectrum Antimicrobial Activity, Isolated from Traditional Korean Fermented  Soybean Paste.
PG  - e01352-17
AB  - Bacillus velezensis YJ11-1-4 is a strain that exhibits broad-spectrum antimicrobial activity
      against various pathogens. It was isolated from doenjang,
      a traditional Korean fermented soybean paste. The genome comprises a single
      circular chromosome of 4,006,637 bp with 46.42% G+C content without plasmids.
AU  - Lee HJ
AU  - Chun BH
AU  - Jeon HH
AU  - Kim YB
AU  - Lee SH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01352-17.

PMID- 24425747
VI  - 64
DP  - 2014
TI  - Ramlibacter solisilvae sp. nov., isolated from forest soil, and emended description of the genus Ramlibacter.
PG  - 1317-1322
AB  - A Gram-staining-negative, strictly aerobic, white-colony-forming bacterium, designated strain
      5-10(T), was isolated from forest soil of Bac Kan Province in Vietnam. Cells were non-motile
      rods or coccoids, showing oxidase- and catalase-positive reactions. Growth was observed at
      10-37 degrees C (optimum, 30 degrees C), at pH 5.0-9.0 (optimum, pH 7.0) and in the presence
      of 0-1.0 % (w/v) NaCl (optimum, 0-0.5 %). The major cellular fatty acids were summed feature 3
      (comprising C16 : 1omega6c and/or C16 : 1omega7c), C16 : 0, C10 : 0 3-OH and summed feature 8
      (comprising C18 : 1omega6c and/or C18 : 1omega7c). The G+C content of the genomic DNA was 69.9
      mol% and the only respiratory quinone detected was ubiquinone 8 (Q-8). Phylogenetic analysis
      based on 16S rRNA gene sequences showed that strain 5-10(T) formed a tight phyletic lineage
      with members of the genus Ramlibacter. Strain 5-10(T) was most closely related to Ramlibacter
      tataouinensis TTB310(T) (97.3 %), but the DNA-DNA relatedness level between the two strains
      was 38.2+/-1.8 %. Based on phenotypic, chemotaxonomic and molecular features, strain 5-10(T)
      was shown to represent a novel species of the genus Ramlibacter, for which the name
      Ramlibacter solisilvae sp. nov. is proposed. The type strain is 5-10(T) ( = KACC 17567(T) =
      JCM 19319(T)). An emended description of the genus Ramlibacter is also proposed.
AU  - Lee HJ
AU  - Lee SH
AU  - Lee SS
AU  - Lee JS
AU  - Kim Y
AU  - Kim SC
AU  - Jeon CO
PT  - Journal Article
TA  - Int. J. Syst. Evol. Microbiol.
JT  - Int. J. Syst. Evol. Microbiol.
SO  - Int. J. Syst. Evol. Microbiol. 2014 64: 1317-1322.

PMID- 20054126
VI  - 65
DP  - 2009
TI  - Expression, crystallization and preliminary X-ray diffraction analysis of a modification subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016.
PG  - 1271-1273
AB  - Modification (HsdM) and specificity (HsdS) subunits are constituents of an active
      methyltransferase (MTase) of multifunctional type I
      restriction enzymes. To provide a molecular background on HsdM, a
      putative hsdM gene from Vibrio vulnificus YJ016 (HsdM Vv) was cloned
      and the expressed protein was purified and crystallized from 22%(w/v)
      polyethylene glycol 8000, 0.02 M imidazole pH 7.5 and 5 mM
      beta-mercaptoethanol. Diffraction data were collected to 1.86 angstrom
      resolution using synchrotron radiation. The crystal belonged to the
      tetragonal space group P4(1)2(1)2 or P4(3)2(1)2, with unit-cell
      parameters a = b = 78.9, c = 165.8 angstrom. With one molecule in the
      asymmetric unit, the crystal volume per unit protein weight was 2.12
      angstrom(3) Da(-1), with a solvent content of 42%.
AU  - Lee HJ
AU  - Nishi K
AU  - Song JM
AU  - Kim JS
PT  - Journal Article
TA  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
JT  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
SO  - Acta Crystallogr. F Struct. Biol. Cryst. Commun. 2009 65: 1271-1273.

PMID- 21602357
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Hyperthermophilic Pyrococcus sp. Strain NA2, Isolated from Deep-Sea Hydrothermal Vent Area.
PG  - 3666-3667
AB  - Pyrococcus sp. NA2, isolated from a deep-sea hydrothermal vent sample, is a novel marine
      hyperthermophilic archaeon to grow optimally at 93 degrees C. The complete genome sequence of
      the strain contains all genes for
      tricarboxylic acid cycle except for succinate dehydrogease/fumarate reductase, but it doesn't
      encode proteins involved in polysaccharide utilization.
AU  - Lee HS
AU  - Bae SS
AU  - Kim MS
AU  - Kwon KK
AU  - Kang SG
AU  - Lee JH
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3666-3667.

PMID- 18790866
VI  - 190
DP  - 2008
TI  - The complete genome sequence of Thermococcus onnurineus NA1 reveals a mixed heterotrophic and carboxydotrophic metabolism.
PG  - 7491-7499
AB  - Members of the genus Thermococcus, sulfur-reducing
      hyperthermophilic archaea, are ubiquitously present in various deep-sea hydrothermal vent
      systems and are considered to play a significant role in the microbial consortia. We present
      the complete genome sequence and feature analysis of Thermococcus onnurineus NA1 isolated from
      a deep-sea hydrothermal vent area, which reveal clues to its physiology. Based on results of
      genomic analysis, T. onnurineus NA1 possesses the metabolic pathways for organotrophic growth
      on peptides, amino acids, or sugars. More interesting was the discovery that the genome
      encoded unique proteins that are involved in carboxydotrophy to generate energy by oxidation
      of CO to CO(2), thereby providing a mechanistic basis for growth with CO as a substrate. This
      lithotrophic feature in combination with carbon fixation via RuBisCO (ribulose
      1,5-bisphosphate carboxylase/oxygenase) introduces a new strategy with a complementing energy
      supply for T. onnurineus NA1 potentially allowing it to cope with nutrient stress in the
      surrounding of hydrothermal vents, providing the first genomic evidence for the
      carboxydotrophy in Thermococcus.
AU  - Lee HS
AU  - Kang SG
AU  - Bae SS
AU  - Lim JK
AU  - Cho Y
AU  - Kim YJ
AU  - Jeon JH
AU  - Cha SS
AU  - Kwon KK
AU  - Kim HT
AU  - Park CJ
AU  - Lee HW
AU  - Kim SI
AU  - Chun J
AU  - Colwell RR
AU  - Kim SJ
AU  - Lee JH
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2008 190: 7491-7499.

PMID- 21622754
VI  - 193
DP  - 2011
TI  - Genome Sequence of the Algicidal Bacterium Kordia algicida OT-1.
PG  - 4031-4032
AB  - Kordia algicida OT-1 is an algicidal bacterium against the bloom-forming microalgae. The
      genome sequence of K. algicida revealed a number of
      interesting features, including degradation of macromolecules, the
      biosynthesis of carotenoid pigment and secondary metabolites, and the
      capacity for gliding motility, which might facilitate the understanding of
      algicidal mechanisms.
AU  - Lee HS
AU  - Kang SG
AU  - Kwon KK
AU  - Lee JH
AU  - Kim SJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4031-4032.

PMID- 26380039
VI  - 10
DP  - 2015
TI  - Draft genome sequence of the extremely halophilic archaeon Haladaptatus cibarius  type strain D43(T) isolated from fermented seafood.
PG  - 53
AB  - An extremely halophilic archaeon, Haladaptatus cibarius D43(T), was isolated from traditional
      Korean salt-rich fermented seafood. Strain D43(T) shows the highest 16S rRNA gene sequence
      similarity (98.7 %) with Haladaptatus litoreus RO1-28(T),  is Gram-negative staining, motile,
      and extremely halophilic. Despite potential industrial applications of extremely halophilic
      archaea, their genome characteristics remain obscure. Here, we describe the whole genome
      sequence and annotated features of strain D43(T). The 3,926,724 bp genome includes 4,092
      protein-coding and 57 RNA genes (including 6 rRNA and 49 tRNA genes) with an average G + C
      content of 57.76 %.
AU  - Lee HW
AU  - Kim DW
AU  - Lee MH
AU  - Kim BY
AU  - Cho YJ
AU  - Yim KJ
AU  - Song HS
AU  - Rhee JK
AU  - Seo MJ
AU  - Choi HJ
AU  - Choi JS
AU  - Lee DG
AU  - Yoon C
AU  - Nam YD
AU  - Roh SW
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 53.

PMID- 26472824
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of 'Candidatus Phytoplasma pruni' Strain CX, a Plant-Pathogenic Bacterium.
PG  - e01117-15
AB  - 'Candidatus Phytoplasma pruni' strain CX, belonging to subgroup 16SrIII-A, is a
      plant-pathogenic bacterium causing economically important diseases in many fruit  crops. Here,
      we report the draft genome sequence, which consists of 598,508 bases, with a G+C content of
      27.21 mol%.
AU  - Lee IM
AU  - Shao J
AU  - Bottner-Parker KD
AU  - Gundersen-Rindal DE
AU  - Zhao Y
AU  - Davis RE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01117-15.

PMID- 27587812
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Cryobacterium arcticum Strain PAMC 27867, Isolated from a Sedimentary Rock Sample in Northern Victoria Land, Antarctica.
PG  - e00885-16
AB  - Cryobacterium arcticum PAMC 27867, a psychrotolerant, Gram-positive bacterium, was isolated
      from a sedimentary rock sample collected at Eureka Spurs in northern
      Victoria Land, Antarctica. Here, we report the genome sequence of C. arcticum
      PAMC 27867.
AU  - Lee J
AU  - Cho A
AU  - Yang JY
AU  - Woo J
AU  - Lee HK
AU  - Hong SG
AU  - Kim OS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00885-16.

PMID- 27302759
VI  - 7
DP  - 2016
TI  - Deciphering Clostridium tyrobutyricum metabolism based on the whole genome sequence and proteome analyses.
PG  - e00743-16
AB  - Clostridium tyrobutyricum is a Gram-positive anaerobic bacterium that efficiently produces
      butyric acid and is considered
      a promising host for anaerobic production of bulk chemicals. Due to limited knowledge on the
      genetic and metabolic
      characteristics of this strain, however, little progress has been made in metabolic
      engineering of this strain. Here we report
      the complete genome sequence of C. tyrobutyricum KCTC 5387 (ATCC 25755), which consists of a
      3.07-Mbp chromosome
      and a 63-kbp plasmid. The results of genomic analyses suggested that C. tyrobutyricum produces
      butyrate from butyrylcoenzyme
      A (butyryl-CoA) through acetate reassimilation by CoA transferase, differently from
      Clostridium acetobutylicum,
      which uses the phosphotransbutyrylase-butyrate kinase pathway; this was validated by reverse
      transcription-PCR
      (RT-PCR) of related genes, protein expression levels, in vitro CoA transferase assay, and
      fed-batch fermentation. In addition,
      the changes in protein expression levels during the course of batch fermentations on glucose
      were examined by shotgun
      proteomics. Unlike C. acetobutylicum, the expression levels of proteins involved in glycolytic
      and fermentative pathways
      in C. tyrobutyricum did not decrease even at the stationary phase. Proteins related to energy
      conservation
      mechanisms, including Rnf complex, NfnAB, and pyruvate-phosphate dikinase that are absent in
      C. acetobutylicum, were
      identified. Such features explain why this organism can produce butyric acid to a much higher
      titer and better tolerate
      toxic metabolites. This study presenting the complete genome sequence, global protein
      expression profiles, and genomebased
      metabolic characteristics during the batch fermentation of C. tyrobutyricum will be valuable
      in designing strategies
      for metabolic engineering of this strain.
      IMPORTANCE Bio-based production of chemicals from renewable biomass has become increasingly
      important due to our concerns
      on climate change and other environmental problems. C. tyrobutyricum has been used for
      efficient butyric acid production.
      In order to further increase the performance and expand the capabilities of this strain toward
      production of other chemicals,
      metabolic engineering needs to be performed. For this, better understanding on the metabolic
      and physiological
      characteristics of this bacterium at the genome level is needed. This work reporting the
      results of complete genomic and proteomic
      analyses together with new insights on butyric acid biosynthetic pathway and energy
      conservation will allow development
      of strategies for metabolic engineering of C. tyrobutyricum for the bio-based production of
      various chemicals in addition
      to butyric acid.
AU  - Lee J
AU  - Jang Y-S
AU  - Han M-J
AU  - Kim JY
AU  - Lee SY
PT  - Journal Article
TA  - MBio
JT  - MBio
SO  - MBio 2016 7: e00743-16.

PMID- 27445386
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Psychrobacter alimentarius PAMC 27889, a Psychrophile Isolated from an Antarctic Rock Sample.
PG  - e00704-16
AB  - Psychrobacter alimentarius PAMC 27889, a Gram-negative, psychrophilic bacterium,  was isolated
      from an Antarctic rock sample. Here, we report the complete genome
      of P. alimentarius PAMC 27889, which has the nonmevalonate methylerythritol
      phosphate pathway of terpenoid biosynthesis and a complete gene cluster for
      benzoate degradation.
AU  - Lee J
AU  - Kwon M
AU  - Yang JY
AU  - Woo J
AU  - Lee HK
AU  - Hong SG
AU  - Kim OS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00704-16.

PMID- 21551304
VI  - 193
DP  - 2011
TI  - Genome Sequence of Strain TW15, a Novel Member of the Genus Ruegeria Belonging to the Marine Roseobacter Clade.
PG  - 3401-3402
AB  - Ruegeria sp. TW15, which belongs to the family Rhodobacteraceae, was isolated from an ark clam
      in the South Sea of Korea. Here is presented the
      draft genome sequence of Ruegeria sp. TW15 (4,490,771 bp, with a G+C
      content of 55.7%), a member of the marine Roseobacter clade, which
      comprises up to 20% of bacterioplankton in the coastal and oceanic mixed
      layer.
AU  - Lee J
AU  - Roh SW
AU  - Whon TW
AU  - Shin NR
AU  - Kim YO
AU  - Bae JW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3401-3402.

PMID- 22582371
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of a Sphingomonas sp., an Endosymbiotic Bacterium Isolated  from an Arctic Lichen Umbilicaria sp.
PG  - 3010-3011
AB  - Sphingomonas sp. strain PAMC 26617 has been isolated from an Arctic lichen Umbilicaria sp. on
      the Svalbard Islands. Here we present the draft genome
      sequence of this strain, which represents a valuable resource for understanding
      the symbiotic mechanisms between endosymbiotic bacteria and lichens surviving in
      extreme environments.
AU  - Lee J
AU  - Shin SC
AU  - Kim SJ
AU  - Kim BK
AU  - Hong SG
AU  - Kim EH
AU  - Park H
AU  - Lee H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3010-3011.

PMID- 22106383
VI  - 85
DP  - 2011
TI  - Complete Genome Sequence of Salmonella Bacteriophage SPN3US.
PG  - 13470-13471
AB  - Salmonella bacteriophage SPN3US was isolated from a chicken fecal sample. It is a virulent
      phage belonging
      to the Myoviridae family and showing effective inhibition of Salmonella enterica and a few
      Escherichia coli
      O157:H7 strains. Here we announce the completely sequenced first genome of a Salmonella phage
      using flagella
      as receptors. It is the largest genome among Salmonella phages sequenced to date, and major
      findings from its
      annotation are described.
AU  - Lee J-H
AU  - Shin H
AU  - Kim H
AU  - Ryu S
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 2011 85: 13470-13471.

PMID- Not carried by PubMed...
VI  - 17
DP  - 1984
TI  - The purification and characterization of PvuII, restriction endonuclease.
PG  - 357-364
AB  - Restriction endonuclease PvuII has been purified from Proteus vulgaris, aerobic
      bacterium, by streptomycin sulfate fractionation, (NH4)SO4 precipitation, gel
      filtration on Sephadex G-150, Phosphocellulose (P11) chromatography, and
      DEAE-cellulose chromatography.
AU  - Lee J-I
AU  - Yang C-H
PT  - Journal Article
TA  - Korean Biochem. J.
JT  - Korean Biochem. J.
SO  - Korean Biochem. J. 1984 17: 357-364.

PMID- Not carried by PubMed...
VI  - 32
DP  - 1994
TI  - Characterization of a restriction endonuclease AspJI from Alcaligenes sp. J-482.
PG  - 285-290
AB  - About 500 bacterial and fungal strains from a wide variety of natural habitats were screened
      for a new type II restriction endonuclease.  Among the 500 species, we selected one species
      that produced a new restriction endonuclease.  This strain has an optimum temperature of 30oC
      for growth.  Morphological, cultural, and physiological characteristics were examined for
      identification of the isolated strain J-482.  This strain was found to belong to the genus
      Alcaligenes.  The restriction endonuclease was named as AspJI and partially purified from
      Alcaligenes sp. J-482 by DEAE-Sephadex A-50 column chromatography and gel filtration.  Most of
      other nucleases were removed by the purification steps.  The AspJI has a substrate
      specificity to lambda DNA, pBR322 and Adenovirus-2 DNA.  For its maximal activity, the
      isolated enzyme requires MgCl2, which should be at least 12.5  mM and it does not need any
      other cofactors.  It is maximally active in the absence of NaCl and is completely inactivated
      at 100 mM NaCl.  The pH and temperature optima for activity were pH 7.5 and 37oC,
      respectively.  The DNA fragments generated by digesting lambda DNA, pBR322, and Adenovirus-2
      DNA with AspJI were the same as that produced by AatII.  This suggests that AspJI is an
      isoschizomer of AatII.
AU  - Lee J-T
AU  - Cho T-J
AU  - Lim J-Y
PT  - Journal Article
TA  - Korean J. Microbiol.
JT  - Korean J. Microbiol.
SO  - Korean J. Microbiol. 1994 32: 285-290.

PMID- 19851738
VI  - 47
DP  - 2009
TI  - Prediction of bacterial proteins carrying a nuclear localization signal and nuclear targeting of HsdM from Klebsiella pneumoniae.
PG  - 641-645
AB  - Nuclear targeting of bacterial proteins is an emerging pathogenic mechanism whereby bacterial
      proteins can interact with nuclear
      molecules and alter the physiology of host cells. The fully sequenced
      bacterial genome can predict proteins that target the nuclei of host
      cells based on the presence of nuclear localization signal (NLS). In
      the present study, we predicted bacterial proteins with the NLS
      sequences from Klebsiella pneumoniae by bioinformatic analysis, and 13
      proteins were identified as carrying putative NLS sequences. Among
      them, HsdM, a subunit of KpnAl that is a type I
      restriction-modification system found in K. pneumoniae, was selected
      for the experimental proof of nuclear targeting in host cells. HsdM
      carried the NLS sequences, (7)KKAKAKK(13), in the N-terminus. A
      transient expression of HsdM-EGFP in COS-1 cells exhibited exclusively
      a nuclear localization of the fusion proteins, whereas the fusion
      proteins of HsdM with substitutions in residues lysine to alanine in
      the NLS sequences, (7)AAAKAAA(13), were localized in the cytoplasm.
      HsdM was co-localized with importin o in the nuclei of host cells.
      Recombinant HsdM alone methylated the eukaryotic DNA in vitro assay.
      Although HsdM tested in this study has not been considered to be a
      virulence factor, the prediction of NLS motifs from the full sequenced
      genome of bacteria extends our knowledge of functional genomics to
      understand subcellular targeting of bacterial proteins.
AU  - Lee JC
AU  - Kim DS
AU  - Moon DC
AU  - Lee JH
AU  - Kim MJ
AU  - Lee SM
AU  - Lee YS
AU  - Kang SW
AU  - Lee EJ
AU  - Kang SS
AU  - Lee E
AU  - Hyun SH
PT  - Journal Article
TA  - J. Microbiol.
JT  - J. Microbiol.
SO  - J. Microbiol. 2009 47: 641-645.

PMID- 23012287
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Weissella koreensis KCTC 3621T.
PG  - 5711-5712
AB  - Weissella koreensis is a Gram-positive, rod-shaped, nonmotile, and facultative anaerobic
      species belonging to the lactic acid bacteria (LAB). The members of
      this species have been repeatedly isolated from kimchi (a traditional Korean
      fermented food) and are known for their beneficial effects on human and animal
      intestinal microflora through producing various clinically important amino acids
      such as gamma-aminobutyric acid and ornithine. Here we report the genome sequence
      of the type strain of W. koreensis (KCTC 3621(T)) to provide taxonomic and
      functional insights into the species.
AU  - Lee JH
AU  - Bae JW
AU  - Chun J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5711-5712.

PMID- 21742886
VI  - 193
DP  - 2011
TI  - Genome Sequence of Lactobacillus johnsonii PF01, Isolated from Piglet Feces.
PG  - 5030-5031
AB  - Lactobacillus johnsonii PF01, an autochthonous bacterium of the gastrointestinal tract, was
      isolated from a fecal sample of piglet. The
      strain adhered specifically to the duodenal and jejunal epithelial cells
      of the piglet and had high bile resistance activity. Here, we report a
      genomic sequence of L. johnsonii PF01.
AU  - Lee JH
AU  - Chae JP
AU  - Lee JY
AU  - Lim JS
AU  - Kim GB
AU  - Ham JS
AU  - Chun J
AU  - Kang DK
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5030-5031.

PMID- 23012294
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Klebsiella pneumoniae subsp. pneumoniae DSM 30104T.
PG  - 5722-5723
AB  - Klebsiella pneumoniae is a Gram-negative, rod-shaped, nonmotile, and opportunistic pathogenic
      species with clinical importance. It is a part of
      natural flora of humans and animals. Here we report the draft genome sequence of
      the type strain of Klebsiella pneumoniae subsp. pneumoniae (DSM 30104(T)) to
      provide taxonomic and functional insights into the species.
AU  - Lee JH
AU  - Cheon IS
AU  - Shim BS
AU  - Kim DW
AU  - Kim SW
AU  - Chun J
AU  - Song M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5722-5723.

PMID- 22733879
VI  - 86
DP  - 2012
TI  - Complete Genome Sequence of Cronobacter sakazakii Temperate Bacteriophage phiES15.
PG  - 7713-7714
AB  - While most phage genome studies have been focused on the virulent phages, the
      inducible temperate bacteriophage genome study provides more detailed information
      about the interaction between the host strain and the phage. To study this
      interaction in detail, UV-induced phiES15 bacteriophage was isolated from the
      host strain Cronobacter sakazakii ES15 and its genome was completely sequenced.
      Here we announce the genome sequence of phiES15 and report major findings from
      the annotation.
AU  - Lee JH
AU  - Choi Y
AU  - Shin H
AU  - Lee J
AU  - Ryu S
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 2012 86: 7713-7714.

PMID- 18505588
VI  - 9
DP  - 2008
TI  - Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth.
PG  - 247
AB  - BACKGROUND: Bifidobacteria are frequently proposed to be associated with good intestinal
      health primarily because of their overriding dominance in
      the feces of breast fed infants. However, clinical feeding studies with
      exogenous bifidobacteria show they don't remain in the intestine,
      suggesting they may lose competitive fitness when grown outside the gut.
      RESULTS: To further the understanding of genetic attenuation that may be
      occurring in bifidobacteria cultures, we obtained the complete genome
      sequence of an intestinal isolate, Bifidobacterium longum DJO10A that was
      minimally cultured in the laboratory, and compared it to that of a culture
      collection strain, B. longum NCC2705. This comparison revealed colinear
      genomes that exhibited high sequence identity, except for the presence of
      17 unique DNA regions in strain DJO10A and six in strain NCC2705. While
      the majority of these unique regions encoded proteins of diverse function,
      eight from the DJO10A genome and one from NCC2705, encoded gene clusters
      predicted to be involved in diverse traits pertinent to the human
      intestinal environment, specifically oligosaccharide and polyol
      utilization, arsenic resistance and lantibiotic production. Seven of these
      unique regions were suggested by a base deviation index analysis to have
      been precisely deleted from strain NCC2705 and this is substantiated by a
      DNA remnant from within one of the regions still remaining in the genome
      of NCC2705 at the same locus. This targeted loss of genomic regions was
      experimentally validated when growth of the intestinal B. longum in the
      laboratory for 1,000 generations resulted in two large deletions, one in a
      lantibiotic encoding region, analogous to a predicted deletion event for
      NCC2705. A simulated fecal growth study showed a significant reduced
      competitive ability of this deletion strain against Clostridium difficile
      and E. coli. The deleted region was between two IS30 elements which were
      experimentally demonstrated to be hyperactive within the genome. The other
      deleted region bordered a novel class of mobile elements, termed mobile
      integrase cassettes (MIC) substantiating the likely role of these elements
      in genome deletion events. CONCLUSION: Deletion of genomic regions, often
      facilitated by mobile elements, allows bifidobacteria to adapt to
      fermentation environments in a very rapid manner (2 genome deletions per
      1,000 generations) and the concomitant loss of possible competitive
      abilities in the gut.
AU  - Lee JH
AU  - Karamychev VN
AU  - Kozyavkin SA
AU  - Mills D
AU  - Pavlov AR
AU  - Pavlova NV
AU  - Polouchine NN
AU  - Richardson PM
AU  - Shakhova VV
AU  - Slesarev AI
AU  - Weimer B
AU  - O'Sullivan DJ
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2008 9: 247.

PMID- 23144390
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Paenisporosarcina sp. Strain TG-20, a Psychrophilic Bacterium Isolated from the Basal Ice of Taylor Glacier.
PG  - 6636
AB  - We report the draft genome sequence of Paenisporosarcina sp. strain TG-20, which  is 4.12 Mb
      in size and consists of 4,071 protein-coding genes and 76 RNA genes.
      The genome sequence of Paenisporosarcina sp. TG-20 may provide useful information
      about molecular adaptations that enhance survival in icy subsurface environments.
AU  - Lee JH
AU  - Koh HY
AU  - Lee SG
AU  - Doyle S
AU  - Christner BC
AU  - Kim HJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6636.

PMID- 23469331
VI  - 1
DP  - 2013
TI  - Genome Sequence of Methanobrevibacter sp. Strain JH1, Isolated from Rumen of Korean Native Cattle.
PG  - e00002-13
AB  - The sp. strain JH1 was isolated from the rumen of Korean native cattle (HanWoo; ). Here, we
      provide a 2.06-Mb draft genome sequence of strain JH1 that might
      provide more information about the lifestyle of rumen methanogens and about the
      genes and proteins that can be targeted to curb methane emissions.
AU  - Lee JH
AU  - Rhee MS
AU  - Kumar S
AU  - Lee GH
AU  - Chang DH
AU  - Kim DS
AU  - Choi SH
AU  - Lee DW
AU  - Yoon MH
AU  - Kim BC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00002-13.

PMID- 23605589
VI  - 158
DP  - 2013
TI  - Complete genome sequence analysis of bacterial-flagellum-targeting bacteriophage chi.
PG  - 2179-2183
AB  - Bacteriophage chi is a well-known phage that infects pathogens such as E. coli,
      Salmonella, and Serratia via bacterial flagella. To further understand its
      host-phage interaction and infection mechanism via host flagella, the genome was
      completely sequenced and analyzed. The phage genome contains 59,407-bp-length DNA
      with a GC content of 56.51 %, containing 75 open reading frames (ORFs) with no
      tRNA genes. Its annotation and functional analysis revealed that chi is
      evolutionarily very closely related to Enterobacter phage Enc34 and Providencia
      phage Redjac. However, most of the annotated genes encode hypothetical proteins,
      indicating that further genomic study of phage chi is required to elucidate the
      bacterial-flagellum-targeting infection mechanism of phage chi.
AU  - Lee JH
AU  - Shin H
AU  - Choi Y
AU  - Ryu S
PT  - Journal Article
TA  - Arch. Virol.
JT  - Arch. Virol.
SO  - Arch. Virol. 2013 158: 2179-2183.

PMID- 22887668
VI  - 194
DP  - 2012
TI  - Genome Sequence of Lactobacillus mucosae LM1, Isolated from Piglet Feces.
PG  - 4766
AB  - Lactobacillus mucosae LM1, isolated from stool samples of a healthy piglet, displays good in
      vitro mucin adhesion and antimicrobial activity against
      pathogenic bacteria. To elucidate its antimicrobial effects and to find its
      epithelial cell and mucin adhesion genes, the genomic sequence of L. mucosae LM1
      was investigated.
AU  - Lee JH
AU  - Valeriano VD
AU  - Shin YR
AU  - Chae JP
AU  - Kim GB
AU  - Ham JS
AU  - Chun J
AU  - Kang DK
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4766.

PMID- 24748440
VI  - 69
DP  - 2014
TI  - Spirosoma radiotolerans sp. nov., a gamma-radiation-resistant bacterium isolated from gamma ray-irradiated soil.
PG  - 286-291
AB  - A Gram-negative, short-rod-shaped bacterial strain with gliding motility,
      designated as DG5A(T), was isolated from a rice field soil in South Korea.
      Phylogenic analysis using 16S rRNA gene sequence of the new isolate showed that
      strain DG5A(T) belong to the genus Spirosoma in the family Spirosomaceae, and the
      highest sequence similarities were 95.5 % with Spirosoma linguale DSM 74(T), 93.4
      % with Spirosoma rigui WPCB118(T), 92.8 % with Spirosoma luteum SPM-10(T), 92.7 %
      with Spirosoma spitsbergense SPM-9(T), and 91.9 % with Spirosoma panaciterrae
      Gsoil 1519(T). Strain DG5A(T) revealed resistance to gamma and UV radiation.
      Chemotaxonomic data showed that the most abundant fatty acids were summed feature
      C(16:1) omega7c/C(16:1) omega6c (36.90 %), C(16:1) omega5c (29.55 %), and
      iso-C(15:0) (14.78 %), and the major polar lipid was phosphatidylethanolamine
      (PE). The DNA G+C content of strain DG5A(T) was 49.1 mol%. Together, the
      phenotypic, phylogenetic, and chemotaxonomic data supported that strain DG5A(T)
      presents a novel species of the genus Spirosoma, for which the name Spirosoma
      radiotolerans sp. nov., is proposed. The type strain is DG5A(T) (=KCTC 32455(T) =
      JCM19447(T)).
AU  - Lee JJ
AU  - Srinivasan S
AU  - Lim S
AU  - Joe M
AU  - Im S
AU  - Bae SI
AU  - Park KR
AU  - Han JH
AU  - Park SH
AU  - Joo BM
AU  - Park SJ
AU  - Kim MK
PT  - Journal Article
TA  - Curr. Microbiol.
JT  - Curr. Microbiol.
SO  - Curr. Microbiol. 2014 69: 286-291.

PMID- 28785416
VI  - 2
DP  - 2016
TI  - Functional analysis of the first complete genome sequence of a multidrug resistant sequence type 2 Staphylococcus epidermidis.
PG  - e000077
AB  - Staphylococcus epidermidis is a significant opportunistic pathogen of humans. The ST2 lineage
      is frequently multidrug-resistant and accounts for most of the
      clinical disease worldwide. However, there are no publically available, closed
      ST2 genomes and pathogenesis studies have not focused on these strains. We report
      the complete genome and methylome of BPH0662, a multidrug-resistant,
      hospital-adapted, ST2 S. epidermidis, and describe the correlation between
      resistome and phenotype, as well as demonstrate its relationship to publically
      available, international ST2 isolates. Furthermore, we delineate the methylome
      determined by the two type I restriction modification systems present in BPH0662
      through heterologous expression in Escherichia coli, allowing the assignment of
      each system to its corresponding target recognition motif. As the first, to our
      knowledge, complete ST2 S. epidermidis genome, BPH0662 provides a valuable
      reference for future genomic studies of this clinically relevant lineage.
      Defining the methylome and the construction of these E. coli hosts provides the
      foundation for the development of molecular tools to bypass restriction
      modification systems in this lineage that has hitherto proven intractable.
AU  - Lee JYH
AU  - Monk IR
AU  - Pidot SJ
AU  - Singh S
AU  - Chua KYL
AU  - Seemann T
AU  - Stinear TP
AU  - Howden BP
PT  - Journal Article
TA  - Microbial Genomics
JT  - Microbial Genomics
SO  - Microbial Genomics 2016 2: e000077.

PMID- 23144394
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Escherichia coli AI27, a Porcine Isolate Belonging to Phylogenetic Group B1.
PG  - 6640-6641
AB  - Escherichia coli AI27 is a putatively commensal strain isolated from feces of a pig. Here we
      report the draft genome sequence of E. coli AI27. This is the first
      porcine strain in the phylogenetic group B1 whose genome sequence has been
      determined.
AU  - Lee K
AU  - Yi H
AU  - Cho YJ
AU  - Jang J
AU  - Hur HG
AU  - Chun J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6640-6641.

PMID- 7870574
VI  - 23
DP  - 1995
TI  - A bacterial methyltransferase M.EcoHK31I requires two proteins for in vitro methylation.
PG  - 103-108
AB  - The genes encoding the EcoHK31I restriction-modification (R-M) system were isolated from a
      clinically-isolated Escherichia coli strain HK31. The entire R-M system of EcoHK31I is located
      in a 2.1 kb fragment. R.EcoHK31I is an isoschizomer of EaeI which recognizes and cleaves
      Y/GGCCR. M.EcoHK31I consists of two polypeptides alpha and beta with sizes 309 and 176 aa,
      respectively. Polypeptide beta is encoded within an alternative reading frame of polypeptide
      alpha. All the conserved motifs in mC5-MTases can be found in polypeptide alpha except motif
      IX which is present in polypeptide beta. Polypeptides alpha and beta were separately
      synthesized in a T7 promoter controlled over-expression system and in vitro methylation
      occurred only when the two extracts were mixed and thus confirms that two polypeptides are
      required for methylation.
AU  - Lee K-F
AU  - Kam K-M
AU  - Shaw P-C
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1995 23: 103-108.

PMID- 8660301
VI  - 314
DP  - 1996
TI  - Overproduction, purification and characterization of M.EcoHK31I, a bacterial methyltransferase with two polypeptides.
PG  - 321-326
AB  - The two overlapping genes coding for EcoHK31I methyltransferase have previously been cloned,
      sequenced and expressed.  Here we describe protocols developed to purify polypeptides alpha
      and beta together or separately, to apparent homogeneity by various chromatographic media.
      M.EcoHK31I is a heterodimer with a native molecular mass of 61 kDa.  Its specific activity
      towards non-methylated lambda DNA was 3.0 x 105 units per mg of protein.  The respective
      denatured molecular masses of polypeptides alpha and beta were 38 and 23 kDa, and their pI
      values were 8.7 and 6.8.  Initial rate kinetic parameters of the native enzyme were 2.0 nM,
      0.58 uM and 3 min-1 for Km DNA, Km AdoMet and kcat, respectively, where AdoMet stands for
      S-adenosyl-L-methionine.  Fully active enzyme was reconstituted by co-purifying the two
      separately synthesized polypeptides, and activity assays confirmed our previous finding that
      two polypeptides were needed to methylate substrate DNA.
AU  - Lee K-F
AU  - Liaw Y-C
AU  - Shaw P-C
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 1996 314: 321-326.

PMID- 9628335
VI  - 379
DP  - 1998
TI  - Sequence comparison of the EcoHK31I and EaeI restriction-modification systems suggests an intergenic transfer of genetic material.
PG  - 437-441
AB  - The genes coding for the EcoHK31I and EaeI restriction-modification systems from Escherichia
      coli strain HK31 and Enterobacter aerogenes, respectively, have been cloned and sequenced.
      Both ENases recognize and cleave Y/GGCCR leaving 4 nucleotide 5'-protruding ends, while the
      MTases modify the internal cytosine.  The systems were isolated on a 2.3 kb AseI fragment for
      EcoHK31I, and a 4.6 kb HindIII fragment for EaeI.  The R and M genes of both systems converge
      and overlap by 14 nucleotides.  Previously, we found that M.EcoHK31I consisted of two
      subunits, (alpha and beta), with the beta subunit being translated from an alternative open
      reading frame within the gene encoding the alpha subunit.  Sequence comparison between the
      EcoHK31I and EaeI systems reveals striking similarity.  The aeaIM gene also encodes alpha and
      beta polypeptides of 309 and 176 amino acids which share 95% and 97% identity, respectively,
      with those of ecoHK31IM.  eCoHK31IR and aeaIR encode proteins of 318 and 315 aa, respectively,
      which share 92% identity but are otherwise unique in the GenBank database.  The EaeI and the
      EcoHK31I R-M systems were found to be flanked by genes coding for integrases.  It is possible
      that these integrases have facilitated the transfer of this system among different bacterial
      species.
AU  - Lee K-F
AU  - Shaw P-C
AU  - Picone SJ
AU  - Wilson GG
AU  - Lunnen KD
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1998 379: 437-441.

PMID- 1542588
VI  - 20
DP  - 1992
TI  - Restriction endonuclease from thermophilic bacterial species III.  Isolation and characterization of BsiHKAI.
PG  - 921
AB  - BsiHKAI is a type II restriction endonuclease from a Bacillus
      stearothermophilus strain isolated from soil.  BsiHKAI in 1l culture (4.7 g wet
      cells) was purified by a DEAE-sephacel column (30 ml bed volume).  Enzyme
      eluted at about 0.3 M NaCl was dialysed against buffer A (1) and loaded onto a
      heparin column (8 ml bed volume).  Enzyme eluted at 0.4 - 0.5 M NaCl was
      dialysed against buffer B (1) and loaded onto an FPLC Mono Q anion exchange
      column.  Enzyme was eluted at 0.3 - 0.4 M NaCl. The purified enzyme was used to
      digest various DNA with known sequences (Fig. 1).  The sizes and numbers of
      fragments produced are identical to those cleaved by mesophilic enzyme HgiAI
      which recognizes 5'G(AT)GC(AT)C3' (2).  The cleavage site of BsiHKA I was
      determined according to (3) using pUC18 DNA as the template and a 17 mer
      oligonucleotide with sequence 5'CAGCACTGACCCTTTTG 3' as the primer.  The primer
      was annealed to position 359-375 of the denatured pUC18 DNA and was extended
      through the BsiHKAI site at position 444.  Figure 2 shows that the cleavage
      product of reaction I comigrates with the band corresponding to nucleotide T in
      the sequence GAGCTC and reaction II comigrates with the band corresponding to
      the first G nucleotide.  Therefore, BsiHKAI recognizes and cleaves
      5'G(AT)GC(AT)!C3'.  The optimal buffer for this enzyme was medium salt (4) and
      optimal reaction temperature 60C.
AU  - Lee K-F
AU  - Shi S-D
AU  - Kam K-M
AU  - Shaw P-C
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 921.

PMID- 26568784
VI  - 10
DP  - 2015
TI  - Complete genome sequence of the thermophilic Acidobacteria, Pyrinomonas methylaliphatogenes type strain K22(T).
PG  - 101
AB  - Strain K22(T) is the type species of the recently- described genus Pyrinomonas, in subdivision
      4 of the phylum Acidobacteria (Int J Syst Evol Micr. 2014;
      64(1):220-7). It was isolated from geothermally-heated soil from Mt. Ngauruhoe,
      New Zealand, using low-nutrient medium. P. methylaliphatogenes K22(T) has a
      chemoheterotrophic metabolism; it can hydrolyze a limited range of simple
      carbohydrates and polypeptides. Its cell membrane is dominated by iso-branching
      fatty acids, and up to 40 % of its lipid content is membrane-spanning and ether
      lipids. It is obligately aerobic, thermophilic, moderately acidophilic, and
      non-spore-forming. The 3,788,560 bp genome of P. methylaliphatogenes K22(T) has a
      G + C content of 59.36 % and contains 3,189 protein-encoding and 55 non-coding
      RNA genes. Genomic analysis was consistent with nutritional requirements; in
      particular, the identified transporter classes reflect the oligotrophic nature of
      this strain.
AU  - Lee KC
AU  - Morgan XC
AU  - Power JF
AU  - Dunfield PF
AU  - Huttenhower C
AU  - Stott MB
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 101.

PMID- 9368536
VI  - 46
DP  - 1997
TI  - Restriction endonucleases in clinical isolates of Shigella spp.
PG  - 949-952
AB  - Thirteen restriction endonuclease-containing strains were isolated from a collection of 186
      clinical isolates of Shigella spp.  Among these, eight and five isolates carried isoschizomers
      of EcoRII and NciI, respectively.  The former restriction-modification system was homologous
      to that of EcoRII and was located on plasmids with sizes of 46.6 or 55.6 kb.  Isolates
      producing NciI isoschizomers contained a 5.7-kb nontransferable plasmid.  Together with
      antimicrobial susceptibility tests and plasmid profile studies, it is concluded that these two
      R-M systems are not widely spread but confined to strains with similar antibiotic resistance
      and plasmid profile.
AU  - Lee KF
AU  - Ling JM-L
AU  - Kam K-M
AU  - Clark DR
AU  - Shaw P-C
PT  - Journal Article
TA  - J. Med. Microbiol.
JT  - J. Med. Microbiol.
SO  - J. Med. Microbiol. 1997 46: 949-952.

PMID- Not carried by PubMed...
VI  - 7
DP  - 1991
TI  - Cytotoxicity of patulin and its effect on lambda DNA cleavage by restriction endonuclease.
PG  - 157-163
AB  - The effect of patulin, a mycotoxin, on the growth of Escherichia coli cells was investigated.
      E. coli cell elongation usually shown during SOS-response for DNA repair was induced by 20 ug
      of patulin per ml. After staining the E. coli chromosome with a fluorescent dye (DAPI, 4',
      6-diamino-2-phenyl-indole), chromosomal DNA partitioning was not affected by patulin. This
      observation indicates that patulin acts as a DNA damaging agent which is effective for E. coli
      cell elongation introduced by the inhibition of septum formation. Moreover, patulin inhibits
      the cleavage reaction of some restriction endonucleases (StyI, AsnI, BamHI, HindIII) on lambda
      phage DNA. The restriction endonucleolytic fragments of lambda phage DNA preincubated with
      patulin were larger than standard digestion products. The lambda DNA recognition site
      (cleavage site) for StyI (C^CAAGG) was very sensitive to patulin, while the site for AsnI had
      a very low reactivity with patulin. It seems likely that the cytosine of StyI recognition
      sequences in lambda phage DNA would be a highly possible target nucleotide for patulin.
AU  - Lee KS
PT  - Journal Article
TA  - Korean J. Toxicol.
JT  - Korean J. Toxicol.
SO  - Korean J. Toxicol. 1991 7: 157-163.

PMID- Not carried by PubMed...
VI  - 15
DP  - 1982
TI  - Cloning and Expression of the Pst I Restriction Endonuclease Gene.
PG  - 315-329
AB  - We report the cloning of the PstI restriction-modification system of
      Providencia stuartii 164.  The DNA isolated from the native PstI producing
      strain, P. stuartii 164, was completely digested with HindIII and inserted into
      the HindIII target site of pBR322.  The cloned strain of E. coli was selected
      on the basis of acquired resistance to bacteriophage Phi80 infection and PstI
      endonuclease productivity.  Plasmid and host DNA from the cloned E. coli were
      not digested by PstI, and the strain produced PstI restriction endonuclease.
      These results indicated that both the restriction enzyme and modification
      (methylase) genes had been cloned and were being expressed.  The plasmid (pRL
      829) isolated from the cloned strain contains an insert of approximately 3,700
      base pairs.  The cloned E. coli produces approximately 15 times more PstI
      endonuclease activity than does the native strain under similar conditions of
      culture.
AU  - Lee KS
AU  - Seo SY
AU  - Lee SW
AU  - Rho HM
PT  - Journal Article
TA  - Korean Biochem. J.
JT  - Korean Biochem. J.
SO  - Korean Biochem. J. 1982 15: 315-329.

PMID- 24356844
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Klebsiella pneumoniae Strain KP-1.
PG  - e01082-13
AB  - Klebsiella pneumoniae is ubiquitous in the environment and is a member of a three-species
      biofilm model. We compared the genome sequence of an environmental
      isolate, K. pneumoniae strain KP-1, to those of two clinical strains (NTUH-K2044
      and MGH 78578). KP-1 possesses strain-specific prophage sequences that
      distinguish it from the clinical strains.
AU  - Lee KW
AU  - Arumugam K
AU  - Purbojati RW
AU  - Tay QX
AU  - Williams RB
AU  - Kjelleberg S
AU  - Rice SA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01082-13.

PMID- 25197474
VI  - 9
DP  - 2014
TI  - The Genome Sequence of a Type ST239 Methicillin-Resistant Staphylococcus aureus Isolate from a Malaysian Hospital.
PG  - 933-939
AB  - We report the genome sequence of a healthcare-associated MRSA type ST239 clone isolated from a
      patient with septicemia in Malaysia. This clone typifies the
      characteristics of ST239 lineage, including resistance to multiple antibiotics
      and antiseptics.
AU  - Lee L
AU  - Teh L
AU  - Zainuddin Z
AU  - Salleh M
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 933-939.

PMID- 25977428
VI  - 3
DP  - 2015
TI  - Complete Genome Sequences of Caldicellulosiruptor sp. Strain Rt8.B8, Caldicellulosiruptor sp. Strain Wai35.B1, and 'Thermoanaerobacter  cellulolyticus'.
PG  - e00440-15
AB  - The genus Caldicellulosiruptor contains extremely thermophilic, cellulolytic bacteria capable
      of lignocellulose deconstruction. Currently, complete genome
      sequences for eleven Caldicellulosiruptor species are available. Here, we report
      genome sequences for three additional Caldicellulosiruptor species: Rt8.B8 DSM
      8990 (New Zealand), Wai35.B1 DSM 8977 (New Zealand), and 'Thermoanaerobacter
      cellulolyticus' strain NA10 DSM 8991 (Japan).
AU  - Lee LL et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00440-15.

PMID- 22740666
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Pedobacter agri PB92T, Which Belongs to the Family Sphingobacteriaceae.
PG  - 3738
AB  - Strain PB92(T) of Pedobacter agri, which belongs to the family Sphingobacteriaceae, was
      isolated from soil in the Republic of Korea. The draft
      genome of strain PB92(T) contains 5,141,552 bp, with a G+C content of 38.0%. This
      is the third genome sequencing project of the type strains among the Pedobacter
      species.
AU  - Lee M
AU  - Roh SW
AU  - Lee HW
AU  - Yim KJ
AU  - Kim KN
AU  - Bae JW
AU  - Choi KS
AU  - Jeon YJ
AU  - Jung WK
AU  - Kang H
AU  - Hyun CG
AU  - Kim D
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3738.

PMID- Not carried by PubMed...
VI  - 93
DP  - 1993
TI  - Cloning and mapping of the hsdR genes of KpnAI and KpnBI restriction-modification systems of Klebsiella pneumoniae.
PG  - 199
AB  - Two possible type I restriction-modification systems, KpnAI and KpnBI have been identified in

      K. pneumoniae strains M5a1 and GM236 respectively (ASM Abstracts 1989, p180). The hsdR genes

      from Sau3AI partially digested chromosomes of both strains were cloned into the BamHI site of

      either pBR322 or pUC18. The clones expressing an r+ phenotype in r-m- recipients were

      identified among the transformants resistant to non-modified phage SBS. A total of four clones

      (8.8 to 14.8 kb) of KpnAI and two (5.8 and 6.2 kb) of KpnBI were obtained. The common portion

      of these clones, which supposedly code for hsdR genes, were inferred as a 3.3 kb HindIII

      fragment of KpnAI and a 3.9 kb EcoRI fragment for KpnBI respectively. Complementation results

      with r-m- mutants suggest that the 6.2 kb fragment of the KpnBI clone contains a second gene

      (either hsdM or hsdS) as well.

      

      Clones of each type were hybridized to a membrane which contains pulsed-field gel

      electrophoresed fragments of the chromosome of the corresponding strain. The KpnAI clone was

      mapped on a 19 Kb XbaI fragment, located at about 40 min on the recently constructed physical

      map of the M5a1 chromosome (ASM Abstracts 1992, p212). Similarly, the KpnBI clone was mapped

      on a 40 kb XbaI fragment of the GM236 chromosome.

      

AU  - Lee N
AU  - Valinluck B
AU  - Randriamahefa A
AU  - Rutebuka O
AU  - Ryu J
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1993 93: 199.

PMID- 9268663
VI  - 271
DP  - 1997
TI  - KpnAI, a new type I restriction-modification system in Klebsiella pneumoniae.
PG  - 342-348
AB  - The KpnAI restriction-modification system has been identified in Klebsiella pneumoniae strain
      M5a1.  The restriction gene of KpnAI was first cloned into pBR322 using an r-m+ M5a1
      derivative and phage SBS for screening.  Subsequently, an adjacent DNA fragment showing
      modification activity was cloned into pUC19.  A total of 7.2 kb DNA sequencing data revealed
      three open reading frames, corresponding to hsdR, hsdM and hsdS genes of type I R-M systems.
      The predicted hsdR, hsdM and hsdS-coded peptides shared 95%, 98% and 44% identity,
      respectively, with the corresponding peptides of the recently identified StySBLI system, a
      prototype of the type ID family.  This high homology suggests that KpnAI is also a member of
      the type ID family.  The KpnAI system seems to be the first type I system identified in
      Klebsiella species.
AU  - Lee NS
AU  - Rutebuka O
AU  - Arakawa T
AU  - Bickle TA
AU  - Ryu J
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1997 271: 342-348.

PMID- Not carried by PubMed...
VI  - 94
DP  - 1994
TI  - DNA sequence of the hsdR region of KpnBI R-M system of Klebsiella pneumoniae GM236.
PG  - 237
AB  - The hsdR gene of the KpnBI restriction-modification (R-M) system of Klebsiella pneumoniae

      GM236 was cloned (ASM Abstracts 1993, p199). The DNA sequence of a 3.5 kb BamHI-EcoRI fragment

      that includes the hsdR gene was determined by the Sanger's dideoxy method. An open reading

      frame (ORF) of 3,039 bp (nucleotides 219 to 3,257) is the coding region for the HsdR

      polypeptide. The 1,013 amino acid product deduced from the nucleotide sequence would have a

      molecular weight of 116,312 daltons, in excellent agreement with the 116 kD size estimated

      from the electrophoretic mobility of the putative HsdR protein in SDS polyacrylamide gels.

      

      The nucleotide sequence of the hsdR gene showed no significant similarity to any other

      sequence in the GenBank database. However, the amino acid sequence scored highly with

      EcoR124/3I, a type I restriction enzyme. After alignment of the two proteins, two conserved

      domains, an ATP binding and a DNA binding domain, were found.

      

      Seven small ORFs were identified within a few kb on either side of the hsdR gene. When

      subcloned, none of these ORFs showed any modification activity. This suggests that the KpnBI

      system differs from other R-M systems where the hsdR and hsdM genes are adjacent. However,

      complementation with an r-KpnBIm-KpnBI mutant suggests that one downstream ORF is a positive

      effector for expression of the KpnBI modification activity. Therefore, a control gene for the

      KpnBI modification genes may be located next to the hsdR gene.

      

AU  - Lee NS
AU  - Ryu J
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1994 94: 237.

PMID- 25035337
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Endosymbiont 'Candidatus Ruthia magnifica' UCD-CM (Phylum Proteobacteria).
PG  - e00717-14
AB  - Here, we present the draft genome of the endosymbiont 'Candidatus Ruthia magnifica' UCD-CM,
      a member of the phylum Proteobacteria, found from the gills of
      a deep-sea giant clam, Calyptogena magnifica. The assembly consists of 1,160,249
      bp contained in 18 contigs.
AU  - Lee RD
AU  - Jospin G
AU  - Coil DA
AU  - Eisen JA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00717-14.

PMID- 26543114
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Pseudoalteromonas tetraodonis Strain UCD-SED8 (Phylum Gammaproteobacteria).
PG  - e01276-15
AB  - Here, we present the draft genome sequence of Pseudoalteromonas tetraodonis UCD-SED8, a marine
      bacterium normally associated with the production of
      tetrodotoxin in pufferfish. This strain was isolated from sediment samples
      surrounding Zostera marina roots collected from Bodega Marine, California. The
      assembly consists of 4,017,727 bp contained in 35 contigs.
AU  - Lee RD
AU  - Jospin G
AU  - Lang JM
AU  - Eisen JA
AU  - Coil DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01276-15.

PMID- 26988038
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Two Pseudoalteromonas porphyrae Strains Isolated from Seagrass Sediment.
PG  - e00092-16
AB  - Here, we present the draft genome sequences of Pseudoalteromonas porphyrae UCD-SED9 and
      UCD-SED14 (phylum Proteobacteria). These strains were isolated from
      sediment surrounding the roots of the seagrass, Zostera marina, collected near
      the UC, Davis Bodega Marine Laboratory (Bodega Bay, California). The assemblies
      contain 4,847,456 bp and 4,817,752 bp, respectively.
AU  - Lee RD
AU  - Jospin G
AU  - Lang JM
AU  - Eisen JA
AU  - Coil DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00092-16.

PMID- 26893436
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Two Vibrio splendidus Strains, Isolated from Seagrass Sediment.
PG  - e01769-15
AB  - Here, we present the draft genome sequences of Vibrio splendidus UCD-SED7 and UCD-SED10
      (phylum Proteobacteria). These strains were isolated from sediment
      surrounding Zostera marina roots near the UC Davis Bodega Marine Laboratory
      (Bodega, Bay, California). These assemblies contain 5,334,236 bp and 5,904,824
      bp, respectively.
AU  - Lee RD
AU  - Jospin G
AU  - Lang JM
AU  - Eisen JA
AU  - Coil DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01769-15.

PMID- 26586901
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Bacillus vietnamensis Strain UCD-SED5 (Phylum Firmicutes).
PG  - e01376-15
AB  - Here, we present the draft genome sequence of Bacillus vietnamensis UCD-SED5 (phylum
      Firmicutes). This strain was isolated from sediment surrounding Zostera
      marina roots near the UC Davis Bodega Marine Laboratory (Bodega Bay, California)
      and represents the second genome of this species. The assembly consists of
      4,325,707 bp, in 108 contigs.
AU  - Lee RD
AU  - Jospin G
AU  - Lang JM
AU  - Eisen JA
AU  - Coil DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01376-15.

PMID- 21742873
VI  - 193
DP  - 2011
TI  - Genomic sequence of Lactobacillus ruminis SPM0211, isolated from a fecal sample from a healthy Korean.
PG  - 5034
AB  - Lactobacillus ruminis SPM0211 is a potential probiotic strain that shows antimicrobial
      activity against emerging pathogens. Here, we present the
      draft genomic sequence of L. ruminis SPM0211, isolated from a fecal sample
      from a healthy Korean, and we describe both the common and unique features
      of this strain.
AU  - Lee S
AU  - Cho YJ
AU  - Lee AH
AU  - Chun J
AU  - Ha NJ
AU  - Ko G
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5034.

PMID- 26798104
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Mycobacterium tuberculosis KT-0192, Isolated in South Korea.
PG  - e01601-15
AB  - We report the draft genome sequence of totally drug-resistant (XDR) Mycobacterium tuberculosis
      KT-0192. This sequence will provide new insights into the main cause
      and evolution of drug resistance in M. tuberculosis KT-0192.
AU  - Lee S
AU  - Han SJ
AU  - Kwon T
AU  - Yoo WG
AU  - Yun MR
AU  - Lee JS
AU  - Kim DW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01601-15.

PMID- 22327591
VI  - 78
DP  - 2012
TI  - Two Novel Type II Restriction-Modification Systems Occupying Genomically Equivalent Locations on the Chromosomes of Listeria monocytogenes Strains.
PG  - 2623-2630
AB  - Listeria monocytogenes is responsible for the potentially life-threatening food-borne disease
      listeriosis. One
      epidemic-associated clonal group of L. monocytogenes, epidemic clone I
      (ECI), harbors a Sau3AI-like restriction-modification (RM) system also
      present in the same genomic region in certain strains of other
      lineages. In this study, we identified and characterized two other,
      novel type II RM systems, LmoJ2 and LmoJ3, at this same locus. LmoJ2
      and LmoJ3 appeared to recognize GCWGC (W = A or T) and GCNGC,
      respectively. Both RM systems consisted of genes with GC content below
      the genome average and were in the same genomic region in strains of
      different serotypes and lineages, suggesting site-specific horizontal
      gene transfer. Genomic DNA from the LmoJ2 and LmoJ3 strains grown at
      various temperatures (4 to 42 degrees C) was resistant to digestion
      with restriction enzymes recognizing GCWGC or GCNGC, indicating that
      the methyltransferases were expressed under these conditions. Phages
      propagated in an LmoJ2-harboring strain exhibited moderately increased
      infectivity for this strain at 4 and 8 degrees C but not at higher
      temperatures, while phages propagated in an LmoJ3 strain had
      dramatically increased infectivity for this strain at all temperatures.
      Among the sequenced Listeria phages, lytic phages possessed
      significantly fewer recognition sites for these RM systems than
      lysogenic phages, suggesting that in lytic phages sequence content
      evolved toward reduced susceptibility to such RM systems. The ability
      of LmoJ2 and LmoJ3 to protect against phages may affect the efficiency
      of phages as biocontrol agents for L. monocytogenes strains harboring
      these RM systems.
AU  - Lee S
AU  - Ward TJ
AU  - Siletzky RM
AU  - Kathariou S
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2012 78: 2623-2630.

PMID- 28336593
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of the Plasmid-Bearing Lactobacillus fermentum Strain SNUV175, a Probiotic for Women's Health Isolated from the Vagina of a Healthy  South Korean Woman.
PG  - e00045-17
AB  - Lactobacillus fermentum SNUV175 has been identified as a probiotic strain that inhibits
      pathogenic microorganisms related to women's health. We present the
      complete genomic sequence of the strain L. fermentum SNUV175 isolated from the
      vagina of a South Korean woman. This genomic information may provide insight into
      the functional activity of this strain.
AU  - Lee S
AU  - You HJ
AU  - Kwon B
AU  - Ko G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00045-17.

PMID- 28280032
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Lactobacillus jensenii Strain SNUV360, a Probiotic for Treatment of Bacterial Vaginosis Isolated from the Vagina of a Healthy Korean  Woman.
PG  - e01757-16
AB  - Lactobacillus jensenii SNUV360 is a potential probiotic strain that shows antimicrobial
      activity for the treatment of bacterial vaginosis. Here, we present
      the complete genomic sequence of L. jensenii SNUV360, isolated from a vaginal
      sample from a healthy Korean woman. Analysis of the sequence may provide insight
      into its functional activity.
AU  - Lee S
AU  - You HJ
AU  - Kwon B
AU  - Ko G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01757-16.

PMID- 1644754
VI  - 174
DP  - 1992
TI  - Type II DNA restriction-modification system and an endonuclease from the ruminal bacterium Fibrobacter succinogenes S85.
PG  - 5275-5283
AB  - Fibrobacter succinogenes is an important cellulolytic bacterium found in the rumen and cecum
      of herbivores.  Numerous attempts to introduce foreign DNA into F. succinogenes S85 have
      failed, suggesting the presence of genetic barriers in this organism.  Results from this study
      clearly demonstrate that F. succinogenes S85 possesses a type II restriction endonuclease,
      FsuI, which recognizes the sequence 5'-GG(A/T)CC-3'.  Analysis of the restriction products
      on sequencing gels showed that FsuI cleaves between the two deoxyguanosine residues, yielding
      a 3-base 5' protruding end.  These data demonstrate that FsuI is an isoschizomer of AvaII.  A
      methyltransferase activity has been identified in the cell extract of F. succinogenes S85.
      This activity modified DNA in vitro and protected the DNA from restriction by FsuI and AvaII.
      DNA modified in vivo by a cloned methylase gene, which codes for M.Eco47II, also protected the
      DNA from restriction by FsuI, suggesting that FsuI is inhibited by methylation at one or both
      deoxycytosine residues of the recognition sequence.  The methyltransferase activity in F.
      succinogenes S85 is likely modifying the same deoxycytosine residues, but the exact site(s) is
      unknown.  A highly active DNase (DNase A) was also isolated from the cell extract of this
      organism.  DNase A is an endonuclease which showed high activity to all forms of DNA
      (single-stranded, double-stranded, linear, and circular) but no activity on RNA.  In vitro,
      the DNase A hydrolyzed F. succinogenes S85 DNA extensively, indicating the lack of protection
      against hydrolysis by this enzyme.  In the presence of Mg2+, DNA was hydrolyzed to fragments
      of 8 to 10 nucleotides in length.  The presence of DNase A and the type II
      restriction-modification system of F. succinogenes S85 may be the barriers preventing the
      introduction of foreign DNA into this bacterium.  Author agreed to change name to FssI to
      avoid confusion with previous enzyme named FsuI.
AU  - Lee SF
AU  - Forsberg CW
AU  - Gibbins AM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1992 174: 5275-5283.

PMID- 22965082
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Moritella dasanensis Strain ArB 0140, a Psychrophilic Bacterium Isolated from the Arctic Ocean.
PG  - 5452-5453
AB  - The psychrophilic bacterium Moritella dasanensis strain ArB 0140 was isolated near a glacier
      in Kongsfjorden, Svalbard Archipelago, Norway. Here we report a
      4.89-Mb draft genome sequence of Moritella dasanensis ArB 0140, which could
      provide comprehensive information on a psychrophilic mechanism in extreme
      environments.
AU  - Lee SG
AU  - Koh HY
AU  - Lee JH
AU  - Kang SH
AU  - Kim HJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5452-5453.

PMID- 27932655
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Nitrilotriacetate-Degrading Aminobacter aminovorans KCTC 2477T.
PG  - e01363-16
AB  - Aminobacter aminovorans is a Gram-negative, pleomorphic rod-shaped, flagellated,  and
      obligately aerobic bacterium that was isolated from soil. Here, we report the
      complete genome sequence of A. aminovorans KCTC 2477T, which degrades
      nitrilotriacetate-metal complexes and iminodiacetate, a metabolic intermediate of
      nitrilotriacetate.
AU  - Lee SH
AU  - Choe H
AU  - Nasir A
AU  - Park DS
AU  - Kim KM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01363-16.

PMID- 22207748
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of the BTEX-Degrading Bacterium Pseudoxanthomonas spadix BD-a59.
PG  - 544
AB  - Pseudoxanthomonas spadix BD-a59, able to metabolize all six BTEX (benzene, toluene,
      ethylbenzene, and o-, m-, and p-xylene) compounds, was isolated
      from gasoline-contaminated sediment. Here, we report the complete 3.45-Mb
      genome sequence and annotation of strain BD-a59. These advance the
      understanding of strain BD-a59's genomic properties and pollutant
      metabolic versatility.
AU  - Lee SH
AU  - Jin HM
AU  - Lee HJ
AU  - Kim JM
AU  - Jeon CO
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 544.

PMID- 23144427
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Salimicrobium sp. Strain MJ3, Isolated from Myulchi-Jeot, Korean Fermented Seafood.
PG  - 6695
AB  - Salimicrobium sp. strain MJ3 was isolated from myulchi-jeot, traditional fermented seafood
      made from anchovy in South Korea. Here we announce the draft
      genome sequence of Salimicrobium sp. MJ3 with 2,717,782 bp, which consists of 45
      contigs (>500 bp in size), and provide a description of their annotation.
AU  - Lee SH
AU  - Jung JY
AU  - Jeon CO
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6695.

PMID- 21914872
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Leuconostoc kimchii Strain C2, Isolated from Kimchi.
PG  - 5548
AB  - Leuconostoc kimchii strain C2 was isolated from fermented kimchi in Korea. Here we announce
      the complete genome sequence of Leuconostoc kimchii
      strain C2, consisting of a 1,877,174-bp chromosome with a G+C content of
      37.9% and no plasmid and describe major findings from its annotation.
AU  - Lee SH
AU  - Jung JY
AU  - Lee SH
AU  - Jeon CO
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5548.

PMID- 27834699
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Pediococcus pentosaceus Strain wikim 20, Isolated from Korean Kimchi.
PG  - e01233-16
AB  - Pediococcus pentosaceus strain wikim 20 is a lactic acid bacterium that was isolated from
      kimchi, a representative traditional Korean fermented food. Here,
      we announce the complete genome sequence of P. pentosaceus strain wikim 20
      consisting of a 1,830,629-bp chromosome and provide a description of its
      annotation.
AU  - Lee SH
AU  - Jung MY
AU  - Park B
AU  - Sung-Oh S
AU  - Park HW
AU  - Choi HJ
AU  - Lee JH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01233-16.

PMID- 28473381
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Lactobacillus curvatus Strain WiKim38 Isolated from Kimchi.
PG  - e00273-17
AB  - Lactobacillus curvatus WiKim38 is a potential probiotic strain isolated from kimchi, a
      traditional Korean fermented food. The complete genome of the WiKim38
      strain consisted of a circular chromosome of 1,940,170 bp in length with a G+C
      content of 41.93%.
AU  - Lee SH
AU  - Jung MY
AU  - Song JH
AU  - Lee M
AU  - Chang JY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00273-17.

PMID- Not carried by PubMed...
VI  - 7
DP  - 1985
TI  - Cloning of PstI methylase gene.
PG  - 42-48
AB  - The clonings of PstI restriction-modification system were reported in two cases.  One was by
      Walder et al. (1981) and the other was by Lee et al. (1982). pRL829 constructed by Lee et al.
      was a recombinant plasmid containing 3.7kb insert fragment at HindIII site of pBR322, which
      encoded whole PstI restriction-modification system.  In this research, a new recombinant
      plasmid, pRL830, containing only PstI methylase gene was constructed from pRL829 by partial
      digestion with HincII.  pRL830 contained 2.2kb insert DNA out of 3.7kb insert of pRL829.  The
      host DNA and plasmid from the cells transformed with pRL830 were not cleaved by PstI,
      suggesting that PstI methylase gene was cloned and expressed in the cells.  However, E. coli
      transformed with pRL830 was easily infected and lysed by bacteriophage Phi80, indicating that
      PstI endonuclease gene was at least inactivated or removed from pRL830.  Soluble fractions
      from the E. coli containing pRL830 were passed through the DEAE-cellulose and phosphocellulose
      columns.  Eluted enzyme fraction with salt gradient were assayed for the PstI endonuclease and
      methylase activities. Results showed that PstI methylase activity was detected, whereas PstI
      endonuclease activity was not.  It was convinced pRL830 encoded PstI methylase gene, but not
      endonuclease gene.
AU  - Lee SH
AU  - Rho HM
PT  - Journal Article
TA  - Korean J. Genet.
JT  - Korean J. Genet.
SO  - Korean J. Genet. 1985 7: 42-48.

PMID- 23105070
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Virgibacillus halodenitrificans 1806.
PG  - 6332-6333
AB  - Virgibacillus halodenitrificans 1806 is an endospore-forming halophilic bacterium isolated
      from salterns in Korea. Here, we report the draft genome sequence of V.
      halodenitrificans 1806, which may reveal the molecular basis of osmoadaptation
      and insights into carbon and anaerobic metabolism in moderate halophiles.
AU  - Lee SJ
AU  - Lee YJ
AU  - Jeong H
AU  - Lee SJ
AU  - Lee HS
AU  - Pan JG
AU  - Kim BC
AU  - Lee DW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6332-6333.

PMID- 24201201
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of an Anaerobic and Extremophilic Bacterium, Caldanaerobacter yonseiensis, Isolated from a Geothermal Hot Stream.
PG  - e00923-13
AB  - Caldanaerobacter yonseiensis is a strictly anaerobic, thermophilic, spore-forming bacterium,
      which was isolated from a geothermal hot stream in Indonesia. This
      bacterium utilizes xylose and produces a variety of proteases. Here, we report
      the draft genome sequence of C. yonseiensis, which reveals insights into the
      pentose phosphate pathway and protein degradation metabolism in thermophilic
      microorganisms.
AU  - Lee SJ
AU  - Lee YJ
AU  - Park GS
AU  - Kim BC
AU  - Lee SJ
AU  - Shin JH
AU  - Lee DW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00923-13.

PMID- 23144421
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of the Thermophilic Bacterium Anoxybacillus kamchatkensis G10.
PG  - 6684-6685
AB  - Anoxybacillus kamchatkensis G10 is a spore-forming thermophilic bacterium isolated from a hot
      spring in Indonesia. Here, we report the draft genome
      sequence of A. kamchatkensis G10 that may reveal insights into aerobic/anaerobic
      metabolisms and carbon utilization in moderate thermophiles.
AU  - Lee SJ
AU  - Lee YJ
AU  - Ryu N
AU  - Park S
AU  - Jeong H
AU  - Lee SJ
AU  - Kim BC
AU  - Lee DW
AU  - Lee HS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6684-6685.

PMID- 7978282
VI  - 220
DP  - 1994
TI  - A fluorometric assay for DNA cleavage reactions characterized with BamHI restriction endonuclease.
PG  - 377-383
AB  - Fluorescently labeled oligonucleotides and DNA fragments have promise in nucleic acid research
      with applications that include DNA hybridization, automated DNA sequencing, fluorescence
      anisotropy, and resonance energy transfer studies. Past concerns with fluorescent-labeled DNA
      arose from interactions between fluorophores and DNA that result in quenched fluorescence.
      This quenching phenomenon is most problematic in fluorescence resonance energy transfer
      studies because quenching of the donor fluorescence could result from either resonance energy
      transfer or nontransfer effects. In the present study, relief of nontransfer quenching of a
      14-mer fluorescein 5-isothiocyanate (FITC)-labeled oliognucleotide containing the BamHI
      restriction site was characterized with both steady-state and time-resolved fluorescence
      techniques. The FITC-labeled single strand was best fit by a triexponential decay with
      lifetimes of 0.5, 2.7, and 4.2 ns. The 4.2-ns component was found to contribute more than 80%
      of the total steady-state intensity. Upon annealing with an unmodified complementary strand,
      the contribution from the 4.2-ns component was significantly decreased, resulting in twofold
      quenching of total fluorescence. We reasoned that this quenching phenomenon should be a
      reversible process and could be employed to study strand separation processes in molecular
      biology. Hence, cleavage of the fluorescently labeled substrate was examined using DNase I and
      BamHI restriction endonuclease. Our results show that the quenched fluorescence is totally
      recovered upon cleavage (compared to that of the single strand). The extent of cleavage
      measured by fluorescence was confirmed by nondenaturing polyacrylamide gel electrophoresis
      analysis. We believe this fluorescence dequenching technique may be used to quantify the
      kinetics of other DNA strand separation and cleavage processes in molecular biology.
AU  - Lee SP
AU  - Porter D
AU  - Chirikjian JG
AU  - Knutson JR
AU  - Han MK
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 1994 220: 377-383.

PMID- 8298050
VI  - 66
DP  - 1994
TI  - The development of a fluorescence assay for the BamHI restriction endonuclease utilizing modified oligonucleotides.
PG  - A163
AB  - Fluorescent labeled oigonucleotides and DNA fragments have promise in nucleic acid research
      including DNA hybridization, automated DNA sequencing, and fluorescence anisotropy or
      resonance energy transfer studies. One concern with fluorescent-labeled DNA is that the
      interactions between fluorophores and DNA may result in quenching of the probe fluorescence.
      This quenching phenomenon is most problematic in fluorescence enegy transfer studies because
      donor quenching can occur as a result of both resonance transfer and these non-transfer
      effects. In the present studies, the nontransfer quenching of a 14-mer FITC-labeled
      oligonucleotide with the BamHI restriction site was characterized with both steady-state and
      time-resolved fluoescence techniques. The FITC-labeled single strand was best fit by
      triexponential decay with lifetimes of 0.5, 2.7, and 4.2 ns. The 4.2 ns component was found to
      contribute more than 80% of total steady-state intensity. Upon annealing with an unmodified
      complementary strand, the 4.2 ns component was significantly decreased, resulting in 2-fold
      quenching of total fluorescence. We examined the reversible quenching process and applied our
      findings to quantify DNA strand separation and cleavage processes. Utilizing this information,
      we developed a continuous fluorescence assay for the restriction endonucleases reaction for
      BamHI.
AU  - Lee SP
AU  - Porter DK
AU  - Chirikjian JG
AU  - Knutson JR
AU  - Han MK
PT  - Journal Article
TA  - Biophys. J.
JT  - Biophys. J.
SO  - Biophys. J. 1994 66: A163.

PMID- 26251490
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Bacillus megaterium Siphophage Stills.
PG  - e00855-15
AB  - Bacillus megaterium is a soil-dwelling bacterium frequently used in research as a model
      organism and in industry in protein production applications. Bacteriophages
      may be used to enhance the use of this bacterium. Here, we describe the complete
      genome of B. megaterium siphophage Stills and its core features.
AU  - Lee SS
AU  - Kongari RR
AU  - Hernandez AC
AU  - Kuty EGF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00855-15.

PMID- 23209201
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of the Biocontrol Bacterium Bacillus amyloliquefaciens Strain M27.
PG  - 6934-6935
AB  - Bacillus amyloliquefaciens strain M27 is a biocontrol agent with antagonistic activities
      against a wide range of fungal pathogens. Here we present the 3.86-Mb
      draft genome sequence of the bacterium with the aims of providing insights into
      the genomic basis of its antifungal mechanism and facilitating its application in
      the biocontrol of plant diseases.
AU  - Lee SY
AU  - Kim BY
AU  - Ahn JH
AU  - Song J
AU  - Seol YJ
AU  - Kim WG
AU  - Weon HY
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6934-6935.

PMID- 24407626
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Petroleum Oil-Degrading Marine Bacterium Pseudomonas taeanensis Strain MS-3, Isolated from a Crude Oil-Contaminated Seashore.
PG  - e00818-13
AB  - Pseudomonas taeanensis MS-3(T), isolated from a crude oil-contaminated seashore in South
      Korea, is capable of degrading petroleum oils, such as gasoline, diesel,
      and kerosene. Here, we report the draft genome sequence of this strain, which
      consists of 5,477,045 bp, with a G+C content of 60.72%.
AU  - Lee SY
AU  - Kim SH
AU  - Lee DG
AU  - Shin S
AU  - Yun SH
AU  - Choi CW
AU  - Chung YH
AU  - Choi JS
AU  - Kahng HY
AU  - Kim SI
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00818-13.

PMID- 1416617
VI  - 665
DP  - 1992
TI  - Vector construction, transformation, and gene amplification in Clostridium acetobutylicum ATCC 824.
PG  - 39-51
AB  - The acetone-butanol-ethanol fermentation by the gram-positive, endo-
      spore-forming, obligate
      anaerobe Clostridium acetobutylicum has received renewed interest because recombinant
      DNA technology
      offers the possibility of creating genetically engineered strains as potential producers of
      these solvents from
      renewable biomass.  The ability to express homologous and heterologous genes in C.
      acetobutylicum and
      alter the cellular metabolism in a beneficial way is critical to the creation of overproducing
      strains for
      industrial applications.  It is also necessary to understand the molecular mechanisms
      involved in metabolic
      regulation in order to rationally manipulate metabolic pathways using recDNA technology.
AU  - Lee SY
AU  - Mermelstein LD
AU  - Bennett GN
AU  - Papoutsakis ET
PT  - Journal Article
TA  - Ann. NY Acad. Sci.
JT  - Ann. NY Acad. Sci.
SO  - Ann. NY Acad. Sci. 1992 665: 39-51.

PMID- 25477408
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of an Aniline-Degrading Bacterium, Burkholderia sp. K24.
PG  - e01250-14
AB  - Burkholderia sp. K24 is an aniline-degrading soil bacterium that utilizes aniline and its
      analogues as sole carbon and nitrogen sources. Here, we report the draft
      genome sequence of this strain that consists of 8,344,181 bp, with a G+C content
      of 61.7%.
AU  - Lee SY
AU  - Yun SH
AU  - Choi CW
AU  - Lee DG
AU  - Choi JS
AU  - Kahng HY
AU  - Kim SI
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01250-14.

PMID- 9406406
VI  - 63
DP  - 1997
TI  - Construction of a Helicobacter pylori-Escherichia coli shuttle vector for gene transfer in Helicobacter pylori.
PG  - 4866-4871
AB  - In this study, a Helicobacter pylori-Escherichia coli shuttle vector was constructed for
      transferring DNA into H. pylori.  The smallest cryptic plasmid (1.2 kb), pHP489, among those
      harbored by 77 H. pylori isolates was selected as a base replicon for constructing vectors.
      HindIII-digested pHP-489 was ligated with a kanamycin resistance gene [aph(3')-III], which
      originated from Campylobacter jejuni, to produce the recombinant plasmid pHP489K.  pHP489K was
      efficiently transformed into and stably maintained in H. pylori strains.  The shuttle vector
      pBHP489K (3.6kb) was constructed by the recombination of pHP489, ColE1, and aph(3')-III
      sequences.  PBHP489K was reciprocally transformed into and maintained in both H. pylori and E.
      coli.  Introduction of the shuttle vector clone DNA (pBHP489K/AB; 6.7 kb), containing the ureA
      and ureB genes of H. pylori, into urease-negative mutants of H. pylori led to the restoration
      of their urease activity.  The transformants were confirmed to contain the incoming plasmid
      DNA.  PBHP489K satisfied the requirements for an H. pylori-E. coli shuttle vector, implying
      that it might be a useful vector for investigating pathogenicity and restriction-modification
      systems of H. pylori.
AU  - Lee W-K
AU  - An Y-S
AU  - Kim K-H
AU  - Kim S-H
AU  - Song J-Y
AU  - Ryu B-D
AU  - Choi Y-J
AU  - Yoon Y-H
AU  - Baik S-C
AU  - Rhee K-H
AU  - Cho M-J
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1997 63: 4866-4871.

PMID- 26031894
VI  - 16
DP  - 2015
TI  - The complete methylome of Helicobacter pylori UM032.
PG  - 424
AB  - BACKGROUND: The genome of the human gastric pathogen Helicobacter pylori encodes  a large
      number of DNA methyltransferases (MTases), some of which are shared among
      many strains, and others of which are unique to a given strain. The MTases have
      potential roles in the survival of the bacterium. In this study, we sequenced a
      Malaysian H. pylori clinical strain, designated UM032, by using a combination of
      PacBio Single Molecule, Real-Time (SMRT) and Illumina MiSeq next generation
      sequencing platforms, and used the SMRT data to characterize the set of
      methylated bases (the methylome). RESULTS: The N4-methylcytosine and
      N6-methyladenine modifications detected at single-base resolution using SMRT
      technology revealed 17 methylated sequence motifs corresponding to one Type I and
      16 Type II restriction-modification (R-M) systems. Previously unassigned
      methylation motifs were now assigned to their respective MTases-coding genes.
      Furthermore, one gene that appears to be inactive in the H. pylori UM032 genome
      during normal growth was characterized by cloning. CONCLUSION: Consistent with
      previously-studied H. pylori strains, we show that strain UM032 contains a
      relatively large number of R-M systems, including some MTase activities with
      novel specificities. Additional studies are underway to further elucidating the
      biological significance of the R-M systems in the physiology and pathogenesis of
      H. pylori.
AU  - Lee WC
AU  - Anton BP
AU  - Wang S
AU  - Baybayan P
AU  - Singh S
AU  - Ashby M
AU  - Chua EG
AU  - Tay CY
AU  - Thirriot F
AU  - Loke MF
AU  - Goh KL
AU  - Marshall BJ
AU  - Roberts RJ
AU  - Vadivelu J
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2015 16: 424.

PMID- 27139604
VI  - 36
DP  - 2016
TI  - Prediction of putative resistance islands in a carbapenem-resistant Acinetobacter baumannii global clone 2 clinical isolate.
PG  - 320-324
AB  - Background: We investigated the whole genome sequence (WGS) of a carbapenem-resistant
      Acinetobacter baumannii isolate belonging to the global clone 2 (GC2) and predicted resistance
      islands using a software tool.
      Methods: A. baumannii strain YU-R612 was isolated from the sputum of a 61-yr-old man with
      sepsis. The WGS of the YU-R612 strain was obtained by using the PacBio RS II Sequencing System
      (Pacific Biosciences Inc., USA). Antimicrobial resistance genes and resistance islands were
      analyzed by using ResFinder and Genomic Island Prediction software (GIPSy), respectively.
      Results: The YU-R612 genome consisted of a circular chromosome (ca. 4,075 kb) and two plasmids
      (ca. 74 kb and 5 kb). Its sequence type (ST) under the Oxford scheme was ST191, consistent
      with assignment to GC2. ResFinder analysis showed that YU-R612 possessed the following
      resistance genes: four -lactamase genes blaADC-30, blaOXA-66, blaOXA-23, and blaTEM-1; armA,
      aadA1, and aacA4 as aminoglycoside resistance-encoding genes; aac(6)Ib-cr for fluoroquinolone
      resistance; msr(E) for macrolide, lincosamide, and streptogramin B resistance; catB8 for
      phenicol resistance; and sul1 for sulfonamide resistance. By GIPSy analysis, six putative
      resistant islands (PRIs) were determined on the YU-R612 chromosome. Among them, PRI1 possessed
      two copies of Tn2009 carrying blaOXA-23, and PRI5 carried two copies of a class I integron
      carrying sul1 and armA genes.
      Conclusions: By prediction of resistance islands in the carbapenem-resistant A. baumannii
      YU-R612 GC2 strain isolated in Korea, PRIs were detected on the chromosome that possessed
      Tn2009 and class I integrons. The prediction of resistance islands using software tools was
      useful for analysis of the WGS.
AU  - Lee Y
PT  - Journal Article
TA  - Ann. Lab. Med.
JT  - Ann. Lab. Med.
SO  - Ann. Lab. Med. 2016 36: 320-324.

PMID- 27688336
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the Environmentally Isolated Acinetobacter pittii Strain IPK_TSA6.1.
PG  - e01028-16
AB  - Acinetobacter pittii is an opportunistic pathogen frequently isolated from Acinetobacter
      infections other than those from Acinetobacter baumannii Multidrug
      resistance in A. pittii, including resistance to carbapenems, has been
      increasingly reported worldwide. Here, we report the 4.14-Mbp draft genome
      sequence of A. pittii IPK_TSA6.1 that was isolated from a nonhospital setting.
AU  - Lee Y
AU  - Jang S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01028-16.

PMID- 29700142
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Multiple-Antibiotic-Resistant Streptococcus parauberis Strain SPOF3K, Isolated from Diseased Olive Flounder (Paralichthys  olivaceus).
PG  - e00248-18
AB  - Here, we report the complete genome sequence of multiple-antibiotic-resistant Streptococcus
      parauberis strain SPOF3K, isolated from the kidney of a diseased
      olive flounder in South Korea in 2013. Sequencing using a PacBio platform yielded
      a circular chromosome of 2,128,740 bp and a plasmid of 23,538 bp, harboring 2,123
      and 24 protein-coding genes, respectively.
AU  - Lee Y
AU  - Nguyen TL
AU  - Kim A
AU  - Kim N
AU  - Roh HJ
AU  - Han HJ
AU  - Jung SH
AU  - Cho MY
AU  - Kang HY
AU  - Kim DH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00248-18.

PMID- 12433997
VI  - 30
DP  - 2002
TI  - Investigating the target recognition of DNA cytosine-5 methyltransferase HhaI by library selection using in vitro compartmentalization.
PG  - 4937-4944
AB  - In vitro compartmentalisation (IVC), a technique for selecting genes encoding enzymes based on
      compartmentalising gene translation and enzymatic reactions in emulsions, was used to
      investigate the interaction of the DNA cytosine-5 methyltransferase M.HhaI with its target DNA
      (5'-GCGC-3'). Crystallography shows that the active site loop from the large domain of
      M.HhaI interacts with a flipped-out cytosine (the target for methylation) and two target
      recognition loops (loops I and II) from the small domain make almost all the other
      base-specific interactions. A library of M.HhaI genes was created by randomising all the loop
      II residues thought to make base-specific interactions and directly determine target
      specificity. The library was selected for 5'-GCGC-3' methylation. Interestingly, in 11
      selected active clones, 10 different sequences were found and none were wild-type. At two of
      the positions mutated (Ser252 and Tyr254) a number of different amino acids could be
      tolerated. At the third position, however, all active mutants had a glycine, as in wild-type
      M.HhaI, suggesting that Gly257 is crucial for DNA recognition and enzyme activity. Our results
      suggest that recognition of base pairs 3 and 4 of the target site either relies entirely on
      main chain interactions or that different residues from those identified in the crystal
      structure contribute to DNA recognition.
AU  - Lee Y-F
AU  - Tawfik DS
AU  - Griffiths AD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2002 30: 4937-4944.

PMID- 347400
VI  - 5
DP  - 1978
TI  - Preparation and properties of insolubilized restriction endonucleases.
PG  - 679-689
AB  - Type II restriction endonucleases BamHI and EcoRI were covalently coupled to
      Sepharose.  These insolubilized enzymes generated fragment patterns for several
      viral DNAs identical to those produced by the respective free enzymes.
      Conditions for optimal activity were similar for both bound and unbound form of
      the enzymes.  Insolubilization improved thermal stability of BamHI and EcoRI.
      The bound enzyme can be recovered from reaction mixtures and reused several
      times.  Upon storage at 4C, coupled endonucleases remained stable for several
      months.
AU  - Lee Y-H
AU  - Blakesley RW
AU  - Smith LA
AU  - Chirikjian JG
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1978 5: 679-689.

PMID- 9714811
VI  - 415
DP  - 1998
TI  - Effects of nickel on DNA methyltransferase activity and genomic DNA methylation levels.
PG  - 213-218
AB  - Methylation of DNA plays an important role in organizing the genome into transcriptionally
      active and inactive zones.  Nickel compounds cause chromatin condensation and DNA methylation
      in the transgenic gpt+ Chinese hamster cell line (G12).  Here we show that nickel is an
      inhibitor of cytosine 5-methyltransferase activity in vivo and in vitro.  In living cells,
      this inhibition is transient and following a recovery period after nickel treatment, Mtase
      activity slightly rebounds.  Genomic DNA methylation levels are also somewhat decreased
      following nickel treatment, but with time, there is an elevation of total DNA methylation
      above basal levels and before any rebound of methyltransferase activity.  These results
      suggest that nickel exposure can elevate total genomic DNA methylation levels even when DNA
      methyltransferase activity is depressed.  These findings may explain the hypermethylation of
      senescence and tumor suppressor genes found during nickel carcinogenesis and support the model
      of a direct effect of Ni2+ on chromatin leading to de novo DNA methylation.
AU  - Lee Y-W
AU  - Broday L
AU  - Costa M
PT  - Journal Article
TA  - Mutat. Res.
JT  - Mutat. Res.
SO  - Mutat. Res. 1998 415: 213-218.

PMID- 21311921
VI  - 156
DP  - 2011
TI  - Complete genomic sequence of virulent Cronobacter sakazakii phage ESSI-2 isolated from swine feces.
PG  - 721-724
AB  - A newly identified virulent Cronobacter sakazakii phage, ESSI-2, was
      isolated from fecal samples from swine. The morphological characteristics
      evident under a transmission electron microscope indicated that phage
      ESSI-2 belonged to the family Myoviridae. The genome of phage ESSI-2
      comprised a double-stranded DNA of 28,765 bp with a G+C content of 55.17%.
      Bioinformatic analysis of the phage genome identified 36 putative open
      reading frames (ORFs). The genome of phage ESSI-2 was not significantly
      similar to that of a previously reported bacteriophage of the members of
      Enterobacteriaceae. A lysogeny module was found within the genome of this
      virulent phage.
AU  - Lee YD
AU  - Chang HI
AU  - Park JH
PT  - Journal Article
TA  - Arch. Virol.
JT  - Arch. Virol.
SO  - Arch. Virol. 2011 156: 721-724.

PMID- 6246339
VI  - 65
DP  - 1980
TI  - Preparation and properties of immobilized sequence specific endonucleases.
PG  - 173-182
AB  - The type II restriction endonucleases have become valuable reagents for research in molecular
      biology.  This is primarily due to their unique property of cleaving DNAs at a limited number
      of specific sites.  These enzymes have been employed for use in physical DNA mapping, plasmid
      construction, and gene cloning.  Most of these enzymes recognize and cleave DNA at specific
      sequences, which are usually in the form of a palindrome.  Since there is evidence implying
      that these endonucleases are membrane bound, one approach to studying them is to determine
      what effect insolubilization (i.e., mimicking membrane binding) has on their activity.
AU  - Lee YH
AU  - Blakesley R
AU  - Smith LA
AU  - Chirikjian G
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1980 65: 173-182.

PMID- 457653
VI  - 254
DP  - 1979
TI  - Sequence-specific endonuclease BglI.
PG  - 6838-6841
AB  - The sequence-specific endonuclease BglI from Bacillus globigii (RUB561) has
      been purified to homogeneity as determined by denaturing polyacrylamide gel
      analysis.  The active form of the enzyme is a single polypeptide with a
      molecular weight of 32,000.  The enzyme requires Mg2+ in the reaction mixture
      and displays a broad pH and monovalent cation requirement.  BglI is not
      sensitive to sulfhydryl reagents but was affected by reagents that modify
      lysine and arginine residues.  When lysine residues were modified by pyridoxal
      5'-phosphate, both binding and catalysis were diminished while modification of
      arginine residues by 2,3-butanedione inhibited the enzyme activity but had no
      effect on its binding properties.
AU  - Lee YH
AU  - Chirikjian JG
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1979 254: 6838-6841.

PMID- Not included in PubMed...
VI  - 37
DP  - 1978
TI  - Preparation and properties of matrix-bound restriction endonucleases.
PG  - 1414
AB  - Properties of these specific endonucleases have made them valuable reagents for
      several areas of research.  These enzymes are present in bacterial cells
      although functions for most such enzymes are not known.  In as much as several
      restriction endonucleases are potentially membrane bound, we have undertaken to
      investigate the effect of insolubilization on their stability and reaction
      characteristics.  Using cyanogen bromide activated sepharose we have covalently
      coupled several enzymes including the widely used BamHI, EcoRI and HindIII.
      Matrix bound ezymes digest DNAs, generating an identical pattern to those
      produced by the respective free enzyme, indicating no change in specificity.
      Specific activities for bound enzymes were 100-4000 units/ml of sepharose,
      where a unit digests 1 microgram DNA at 37C in 1 hr.  Coupled enzymes display
      high thermal stability making them useful in probing DNA structure at high
      temperatures.  Coupled enzymes are reusable, can be removed rapidly from
      reaction mixtures, and adapted to a flow-through system.
AU  - Lee YH
AU  - Smith LA
AU  - Blakesley RW
PT  - Journal Article
TA  - Fed. Proc.
JT  - Fed. Proc.
SO  - Fed. Proc. 1978 37: 1414.

PMID- 26421103
VI  - 10
DP  - 2015
TI  - Genome sequence of a native-feather degrading extremely thermophilic Eubacterium, Fervidobacterium islandicum AW-1.
PG  - 71
AB  - Fervidobacterium islandicum AW-1 (KCTC 4680) is an extremely thermophilic anaerobe isolated
      from a hot spring in Indonesia. This bacterium could degrade
      native chicken feathers completely at 70 degrees C within 48 h, which is of
      potential importance on the basis of relevant environmental and agricultural
      issues in bioremediation and development of eco-friendly bioprocesses for the
      treatment of native feathers. However, its genomic and phylogenetic analysis
      remains unclear. Here, we report the high-quality draft genome sequence of an
      extremely thermophilic anaerobe, F. islandicum AW-1. The genome consists of
      2,359,755 bp, which encodes 2,184 protein-coding genes and 64 RNA-encoding genes.
      This may reveal insights into anaerobic metabolism for keratin degradation and
      also provide a biological option for poultry waste treatments.
AU  - Lee YJ
AU  - Jeong H
AU  - Park GS
AU  - Kwak Y
AU  - Lee SJ
AU  - Lee SJ
AU  - Park MK
AU  - Kim JY
AU  - Kang HK
AU  - Shin JH
AU  - Lee DW
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 71.

PMID- 23105082
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Bacillus oceanisediminis 2691.
PG  - 6351-6352
AB  - Bacillus oceanisediminis 2691 is an aerobic, Gram-positive, spore-forming, and moderately
      halophilic bacterium that was isolated from marine sediment of the
      Yellow Sea coast of South Korea. Here, we report the draft genome sequence of B.
      oceanisediminis 2691 that may have an important role in the bioremediation of
      marine sediment.
AU  - Lee YJ
AU  - Lee SJ
AU  - Jeong H
AU  - Kim HJ
AU  - Ryu N
AU  - Kim BC
AU  - Lee HS
AU  - Lee DW
AU  - Lee SJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6351-6352.

PMID- 23012284
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Bacillus endophyticus 2102.
PG  - 5705-5706
AB  - Bacillus endophyticus 2102 is an endospore-forming, plant growth-promoting rhizobacterium
      isolated from a hypersaline pond in South Korea. Here we present
      the draft sequence of B. endophyticus 2102, which is of interest because of its
      potential use in the industrial production of algaecides and bioplastics and for
      the treatment of industrial textile effluents.
AU  - Lee YJ
AU  - Lee SJ
AU  - Kim SH
AU  - Lee SJ
AU  - Kim BC
AU  - Lee HS
AU  - Jeong H
AU  - Lee DW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5705-5706.

PMID- 33837
VI  - 38
DP  - 1979
TI  - Subpalindromic sequences as inhibitors for restriction endonucleases.
PG  - 294
AB  - BglI from B. globigii was purified to homogeneity using several chromatographic
      steps including phenyl-sepharose.  The enzyme is a single polypeptide chain of
      32,000 daltons as determined by calibrated techniques.  BglI activity required
      Mg++ and was stimulated by NaCl.  When Mn++ replaced Mg++ in the reaction
      mixture, no change in specificity was observed.  Arg, and lys, but not
      sulfhydryl groups were necessary for activity.  The effect of subpalindromic
      sequences to inhibit restriction endonuclease activity was examined using
      purified BglI and BamHI.  The degree of inhibition on the BamHI (G7GATCC) was
      found to be d(pG)2>d(pC)2>d(pApT) while d(pA)2, d(pGpA) and d(pCpT)2 had no
      effect.  In addition, d(pTpC) > d(pG)2=d(pC)2 inhibited BglI GGCCG
      AGGCGGCCCT^CGGCC CCGGC^TCCGCCCGGA GCCGG Application of this method in studies
      on the mechanism of binding and catalysis for BamHI, BglI and other restriction
      endonucleases as well as cognate methylases will be presented.
AU  - Lee YW
AU  - Clanton D
AU  - Chirikjian JG
PT  - Journal Article
TA  - Fed. Proc.
JT  - Fed. Proc.
SO  - Fed. Proc. 1979 38: 294.

PMID- 25639682
VI  - 13
DP  - 2015
TI  - R-M systems go on the offensive.
PG  - 131
AB  - Restriction-modification (R-M) systems protect bacteria against the integration of foreign DNA
      from, for example, phages.  These systems rely on restriction enzymes that cleave foreign
      unmethylated DNA at specific short sequence motifs; methylation of 'self' DNA protects the
      bacterial genome from
      its own restriction enzymes. Importantly, high frequency inversions in genes coding for R-M
      systems in Bacteroides fragilis have been shown to affect the cleavage specificity of these
      systems1. Now, Croucher et al.2
      and Manso et al.3 describe a similar strategy in Streptococcus pneumoniae, and show that these
      R-M systems are not limited to the defence against phages but can also regulate the expression
      of genes involved in bacterial virulence.
AU  - Lees J
AU  - Gladstone RA
PT  - Journal Article
TA  - Nat. Rev. Microbiol.
JT  - Nat. Rev. Microbiol.
SO  - Nat. Rev. Microbiol. 2015 13: 131.

PMID- 4700514
VI  - 11
DP  - 1973
TI  - Restriction and modification of bacteriophage in Bacillus stearothermophilus.
PG  - 606-609
AB  - Host-controlled restriction and modification of TP-1C phage and infectious
      phage DNA occurs in Bacillus stearothermophilus and is subject to control by
      TP-8 or TP-12 prophage.
AU  - Lees ND
AU  - Welker NE
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1973 11: 606-609.

PMID- 15203217
VI  - 84
DP  - 2004
TI  - Identification of 11 pseudogenes in the DNA methyltransferase gene family in rodents and humans and implications for the functional loci.
PG  - 193-204
AB  - DNA (cytosine-5-)-methyltransferase genes are important for normal development in mice and
      humans. We describe here 11 pseudogenes spread
      among human, mouse, and rat belonging to this gene family, ranging from
      1 pseudogene in humans to 7 in rat, all belonging to the Dnmt3
      subfamily. All except 1 rat Dnmt3b pseudogene appear to be
      transcriptionally silent. Dnmt3a2, a transcript variant of Dnmt3a
      starting at an alternative promoter, had the highest number of
      processed pseudogenes, while none were found for the canonical Dnmt3a,
      suggesting the former transcript is more highly expressed in germ
      cells. Comparison of human, mouse, and rat Dnmt3a2 sequences also
      suggests that human exon 8 is a recent acquisition. Alignment of the
      3'UTR of Dnmt3a2 among the functional genes and the processed
      pseudogenes suggested that a second polyadenylation site downstream of
      the RefSeq poly(A) was being used in mice, resulting in a longer 3'UTR,
      a finding confirmed by RT-PCR in mouse tissues. We also found conserved
      cytoplasmic polyadenylation elements, usually implicated in regulating
      translation in oocytes, in Dnmt3b and Dnmt1. Expression of DNMT3B in
      the mouse oocyte was confirmed by immunocytochemistry. These results
      clarify the structure of a number of loci in the three species examined
      and provide some useful insights into the structure and evolution of
      this gene family.
AU  - Lees-Murdock DJ
AU  - McLoughlin GA
AU  - McDaid JR
AU  - Quinn LM
AU  - O'Doherty A
AU  - Hiripi L
AU  - Hack CJ
AU  - Walsh CP
PT  - Journal Article
TA  - Genomics
JT  - Genomics
SO  - Genomics 2004 84: 193-204.

PMID- 22666370
VI  - 7
DP  - 2012
TI  - Gene Repertoire Evolution of Streptococcus pyogenes Inferred from Phylogenomic Analysis with Streptococcus canis and Streptococcus dysgalactiae.
PG  - E37607
AB  - Streptococcus pyogenes, is an important human pathogen classified within the
      pyogenic group of streptococci, exclusively adapted to the human host. Our goal
      was to employ a comparative evolutionary approach to better understand the
      genomic events concomitant with S. pyogenes human adaptation. As part of
      ascertaining these events, we sequenced the genome of one of the potential sister
      species, the agricultural pathogen S. canis, and combined it in a comparative
      genomics reconciliation analysis with two other closely related species,
      Streptococcus dysgalactiae and Streptococcus equi, to determine the genes that
      were gained and lost during S. pyogenes evolution. Genome wide phylogenetic
      analyses involving 15 Streptococcus species provided convincing support for a
      clade of S. equi, S. pyogenes, S. dysgalactiae, and S. canis and suggested that
      the most likely S. pyogenes sister species was S. dysgalactiae. The
      reconciliation analysis identified 113 genes that were gained on the lineage
      leading to S. pyogenes. Almost half (46%) of these gained genes were phage
      associated and 14 showed significant matches to experimentally verified bacteria
      virulence factors. Subsequent to the origin of S. pyogenes, over half of the
      phage associated genes were involved in 90 different LGT events, mostly involving
      different strains of S. pyogenes, but with a high proportion involving the horse
      specific pathogen S. equi subsp. equi, with the directionality almost exclusively
      (86%) in the S. pyogenes to S. equi direction. Streptococcus agalactiae appears
      to have played an important role in the evolution of S. pyogenes with a high
      proportion of LGTs originating from this species. Overall the analysis suggests
      that S. pyogenes adaptation to the human host was achieved in part by (i) the
      integration of new virulence factors (e.g. speB, and the sal locus) and (ii) the
      construction of new regulation networks (e.g. rgg, and to some extent speB).
AU  - Lefebure T
AU  - Richards VP
AU  - Lang P
AU  - Pavinski-Bitar P
AU  - Stanhope MJ
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2012 7: E37607.

PMID- 25103760
VI  - 2
DP  - 2014
TI  - Whole-Genome Shotgun Sequence of Arthrospira platensis Strain Paraca, a Cultivated and Edible Cyanobacterium.
PG  - e00751-14
AB  - Here we report the whole-genome shotgun sequence of a Peruvian strain of Arthrospira platensis
      (Paraca), a cultivated and edible haloalkaliphilic
      cyanobacterium of great scientific, technical, and economic potential.
AU  - Lefort F
AU  - Calmin G
AU  - Crovadore J
AU  - Falquet J
AU  - Hurni JP
AU  - Osteras M
AU  - Haldemann F
AU  - Farinelli L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00751-14.

PMID- 23405356
VI  - 1
DP  - 2013
TI  - Whole-Genome Shotgun Sequence of Pseudomonas viridiflava, a Bacterium Species Pathogenic to Ararabidopsis thaliana.
PG  - e00116-12
AB  - We report here the first whole-genome shotgun sequence of Pseudomonas viridiflava strain
      UASWS38, a bacterium species pathogenic to the biological model plant Ararabidopsis thaliana
      but also usable as a biological control agent and thus of great scientific interest for
      understanding the genetics of plant-microbe interactions.
AU  - Lefort F
AU  - Calmin G
AU  - Crovadore J
AU  - Osteras M
AU  - Farinelli L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00116-12.

PMID- 24503983
VI  - 2
DP  - 2014
TI  - Whole-Genome Shotgun Sequence of Bacillus amyloliquefaciens Strain UASWS BA1, a Bacterium Antagonistic to Plant Pathogenic Fungi.
PG  - e00016-14
AB  - We report here the whole-genome shotgun sequence of Bacillus amyloliquefaciens strain UASWS
      BA1, isolated from inner wood tissues of a decaying Platanus x
      acerifolia tree. This strain proved to be antagonistic to several plant
      pathogenic fungi and oomycetes and can be developed as a biological control agent
      in agriculture.
AU  - Lefort F
AU  - Calmin G
AU  - Pelleteret P
AU  - Farinelli L
AU  - Osteras M
AU  - Crovadore J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00016-14.

PMID- 9109100
VI  - 3
DP  - 1997
TI  - Electrotransformation of Streptococcus pneumoniae: Evidence for restriction of the DNA on entry.
PG  - 101-104
AB  - Electrotransformation is a method generally used in biotechnology to introduce recombinant DNA
      into a wide range of bacteria.  However the mechanism of DNA entry is poorly understood.  We
      report that in Streptococcus pneumoniae, a naturally transformable species,
      electrotransformation efficiently introduces a plasmid replicon.  DNA is strongly restricted
      by the restriction-modification systems DpnI and DpnII which degrade methylated and
      nonmethylated DNA respectively at GATC sequences.  This suggests that in electrotransformation
      double-strand DNA penetrates into these bacteria without a single-strand step in contrast to
      natural transformation.  Single-strand DNA by itself is able to electrotransform very weakly
      and linearized double-stranded plasmid DNA yields barely detectable levels of transformants.
AU  - LeFrancois J
AU  - Gasc A-M
AU  - Sicard M
PT  - Journal Article
TA  - Microb. Drug Resist.
JT  - Microb. Drug Resist.
SO  - Microb. Drug Resist. 1997 3: 101-104.

PMID- 9043128
VI  - 143
DP  - 1997
TI  - Electrotransformation of Streptococcus pneumoniae: evidence for restriction of DNA on entry.
PG  - 523-526
AB  - Electrotransformation is a method generally used in biotechnology to introduce recombinant DNA
      into a wide range of bacteria.  However, the mechanism of DNA entry is poorly understood.  We
      report that in Streptococcus pneumoniae, a naturally transformable species,
      electrotransformation efficiently introduces a plasmid replicon.  DNA is strongly restricted
      by the restriction-modification systems DpnI and DpnII which degrade methylated and
      non-methylated DNA, respectively, at GATC sequences.  This suggests that in
      electrotransformation double-stranded DNA penetrates into these bacteria without a
      single-stranded DNA step in contrast to natural transformation.  Single-stranded DNA by itself
      is able to electrotransform very weakly and linearized double-stranded plasmid DNA yields
      barely detectable levels of transformants.
AU  - Lefrancois J
AU  - Sicard AM
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 1997 143: 523-526.

PMID- 29167247
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Burkholderia puraquae Type Strain CAMPA 1040, Isolated from Hospital Settings in Cordoba, Argentina.
PG  - e01302-17
AB  - We report here the draft genome sequence of Burkholderia puraquae type strain CAMPA 1040, a
      member of the Burkholderia cepacia complex. This strain, isolated
      from a hemodialysis water reservoir, harbors several stress tolerance genes, such
      as the systems for low oxygen survival, for copper tolerance, and for osmotic
      stress resistance.
AU  - Leguizamon M
AU  - Draghi WO
AU  - Montanaro P
AU  - Schneider A
AU  - Prieto CI
AU  - Martina P
AU  - Lagares A
AU  - Lasch P
AU  - Bosch A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01302-17.

PMID- 
VI  - 24
DP  - 2004
TI  - Identification of a new restriction modification system in Helicobacter pylori.
PG  - S211
AB  - Restriction modification systems are among the largest categories of specific genes in
      Helicobacter pylori.  In an H. pylori strain isolated from a patient with gastric MALT
      lymphoma, a new RMS was identified by subtractive hydridisation and chromosome walking.  This
      RMS is present in a highly conserved area of the H. pylori genome of J99 and 26,695 reference
      strains, but harbouring an ORF with unknown function and without homologies to a methylase or
      an endonuclease.  This RMS was also described in parallel by Taiwanese researchers and named
      HpyCII.  Its restriction site is identical to BccI (RMS type 1 of Bacteroides cacae).  Our
      goal was to study the prevalence and the genetic evolution of this RMS in H. pylori.  The
      prevalence of this new RMS was tested by PCR and dot blot hybridisation on a collection of
      62II.pylori strains isolated from patients with gastric MALT lymphoma.  The restriciton
      profiles obtained with BccI on the chromosomal DNA of these strains were then compared to the
      amplicon size obtained with primers designed on the ORF flanking HpyCII.  The prevalence of
      HpyCII in our collection of H. pylori strains from gastric MALT lymphoma, was 66.1% (41/62).
      For 35 strains (85.4%) the amplicons obtained had the expected size of 3831 bp indicating that
      the RMS was complete.  In 30 out of 35 of these strains (85.7%), the DNA obtained was
      protected from digestion by BccI as expected while in five cases a digestion was observed.
      For six additional strains, a 1636 bp amplicon was obtained indicating that probably a
      truncated RMS was prsent.  DNA from these six strains were digested by BccI.  For most H.
      pylori strains harbouring HpyCII, this RMS is present in an active form.  The genetic
      evolution from an active to an inactive form, then to its complete deletion as in reference
      strains, remains to be determined.  To further investigate the question, amplicons from
      strains with discrepant results will be sequenced.
AU  - Lehours P
AU  - Chaineux J
AU  - Dupouy S
AU  - Menard A
AU  - Morgner A
AU  - Megraud F
PT  - Journal Article
TA  - Int. J. Antimicrob. Agents
JT  - Int. J. Antimicrob. Agents
SO  - Int. J. Antimicrob. Agents 2004 24: S211.

PMID- 17346936
VI  - 158
DP  - 2007
TI  - Genetic diversity of the HpyC1I restriction modification system in Helicobacter pylori.
PG  - 265-271
AB  - Helicobacter pylori is unique because of the unusually high number and diversity of its
      restriction modification (R-M) systems. HpyC1I R-M was
      recently characterized and contains an endonuclease which is an
      isoschizomer of the endonuclease BccI. This R-M is involved in
      adherence to gastric epithelial cells, a crucial step in bacterial
      pathogenesis. This observation illustrates the fact that R-M systems
      have other putative biological functions in addition to protecting the
      bacterial genome from external DNA. The genomic diversity of HpyC1I R-M
      was evaluated more precisely on a large collection of H. pylori strains
      by PCR, susceptibility to BccI digestion and sequencing. The results
      obtained support the mechanism of gain and loss of this R-M system in
      the H. pylori genome, and suggest that it is an ancestral system which
      gradually disappears during H. pylori evolution, following successive
      steps: (1) inactivation of the endonuclease gene, followed or
      accompanied by: (2) inactivation of the methyltransferase genes, and
      then: (3) definitive loss, leaving only short endonuclease remnant
      sequences.
AU  - Lehours P
AU  - Dupouy S
AU  - Chaineux J
AU  - Ruskone-Fourmestraux A
AU  - Delchier JC
AU  - Morgner A
AU  - Megraud F
AU  - Menard A
PT  - Journal Article
TA  - Res. Microbiol.
JT  - Res. Microbiol.
SO  - Res. Microbiol. 2007 158: 265-271.

PMID- 22086490
VI  - 2
DP  - 2011
TI  - Genome sequencing reveals a phage in Helicobacter pylori.
PG  - e00239-11
AB  - Helicobacter pylori chronically infects the gastric mucosa in more than half of the human
      population; in a subset of this population, its presence
      is associated with development of severe disease, such as gastric cancer.
      Genomic analysis of several strains has revealed an extensive H. pylori
      pan-genome, likely to grow as more genomes are sampled. Here we describe
      the draft genome sequence (63 contigs; 26x mean coverage) of H. pylori
      strain B45, isolated from a patient with gastric mucosa-associated
      lymphoid tissue (MALT) lymphoma. The major finding was a 24.6-kb prophage
      integrated in the bacterial genome. The prophage shares most of its genes
      (22/27) with prophage region II of Helicobacter acinonychis strain Sheeba.
      After UV treatment of liquid cultures, circular DNA carrying the prophage
      integrase gene could be detected, and intracellular tailed phage-like
      particles were observed in H. pylori cells by transmission electron
      microscopy, indicating that phage production can be induced from the
      prophage. PCR amplification and sequencing of the integrase gene from 341
      H. pylori strains from different geographic regions revealed a high
      prevalence of the prophage (21.4%). Phylogenetic reconstruction showed
      four distinct clusters in the integrase gene, three of which tended to be
      specific for geographic regions. Our study implies that phages may play
      important roles in the ecology and evolution of H. pylori. IMPORTANCE:
      Helicobacter pylori chronically infects the gastric mucosa in more than
      half of the human population, and while most of the infected individuals
      do not develop disease, H. pylori infection doubles the risk of developing
      gastric cancer. An abundance and diversity of viruses (phages) infect
      microbial populations in most environments and are important mediators of
      microbial diversity. Our finding of a 24.6-kb prophage integrated inside
      an H. pylori genome and the observation of circular integrase
      gene-containing DNA and phage-like particles inside cells upon UV
      treatment demonstrate that we have discovered a viable H. pylori phage.
      The additional finding of integrase genes in a large proportion of
      screened isolates of diverse geographic origins indicates that the
      prevalence of prophages may have been underestimated in H. pylori. Since
      phages are important drivers of microbial evolution, the discovery should
      be important for understanding and predicting genetic diversity in H.
      pylori.
AU  - Lehours P
AU  - Vale FF
AU  - Bjursell MK
AU  - Melefors O
AU  - Advani R
AU  - Glavas S
AU  - Guegueniat J
AU  - Gontier E
AU  - Lacomme S
AU  - Alves MA
AU  - Menard A
AU  - Megraud F
AU  - Engstrand L
AU  - Andersson AF
PT  - Journal Article
TA  - MBio
JT  - MBio
SO  - MBio 2011 2: e00239-11.

PMID- 28163828
VI  - 12
DP  - 2017
TI  - Potential probiotic-associated traits revealed from completed high quality genome sequence of Lactobacillus fermentum 3872.
PG  - 19
AB  - The article provides an overview of the genomic features of Lactobacillus fermentum strain
      3872. The genomic sequence reported here is one of three L.
      fermentum genome sequences completed to date. Comparative genomic analysis
      allowed the identification of genes that may be contributing to enhanced
      probiotic properties of this strain. In particular, the genes encoding putative
      mucus binding proteins, collagen-binding proteins, class III bacteriocin, as well
      as exopolysaccharide and prophage-related genes were identified. Genes related to
      bacterial aggregation and survival under harsh conditions in the gastrointestinal
      tract, along with the genes required for vitamin production were also found.
AU  - Lehri B
AU  - Seddon AM
AU  - Karlyshev AV
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 19.

PMID- 8898232
VI  - 122
DP  - 1996
TI  - De novo DNA cytosine methyltransferase activities in mouse embryonic stem cells.
PG  - 3195-3205
AB  - It has been a controversial issue as to how many DNA cytosine methyltransferase mammalian
      cells have and whether de novo methylation and maintenance methylation activities are encoded
      by a single gene or two different genes.  To address these questions, we have generated a null
      mutation of the only known mammalian DNA methyltransferase gene through homologous
      recombination in mouse embryonic stem cells and found that the development of the homozygous
      embryos is arrested prior to the 8-somite stage.  Surprisingly, the null mutant embryonic stem
      cells are viable and contain low but stable levels of methyl cytosine and methyltransferase
      activity, suggesting the existence of a second DNA methyltransferase in mammalian cells.
      Further studies indicate that de novo methylation activity is not impaired by the mutation as
      integrated provirus DNA in MoMuLV-infected homozygous embryonic stem cells become methylated
      at a similar rate as in wild-type cells.  Differentiation of mutant cells results in further
      reduction of methyl cytosine levels, consistent with the de novo methylation activity being
      down regulated in differentiated cells.  These results provide the first evidence that an
      independently encoded DNA methyltransferase is present in mammalian cells which is capable of
      de novo methylating cellular and viral DNA in vivo.
AU  - Lei H
AU  - Oh SP
AU  - Okano M
AU  - Juttermann R
AU  - Goss KA
AU  - Jaenisch R
AU  - Li E
PT  - Journal Article
TA  - Development
JT  - Development
SO  - Development 1996 122: 3195-3205.

PMID- 25883277
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Paenibacillus polymyxa CF05, a Strain of Plant Growth-Promoting Rhizobacterium with Elicitation of Induced Systemic Resistance.
PG  - e00198-15
AB  - Paenibacillus polymyxa CF05 is a Gram-positive rod-shaped bacterium isolated from the interior
      of an ancient tree, Cryptomeria fortunei, in China. This bacterium
      displays potent biocontrol effects against certain soil-borne diseases and the
      elicitation of induced systemic resistance in tomatoes. Here, we report the
      complete genome sequence of P. polymyxa CF05.
AU  - Lei M
AU  - Lu P
AU  - Jin L
AU  - Wang Y
AU  - Qin J
AU  - Xu X
AU  - Zhang L
AU  - Wang Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00198-15.

PMID- 25977416
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Norvancomycin-Producing Strain Amycolatopsis orientalis  CPCC200066.
PG  - e00296-15
AB  - Amycolatopsis orientalis CPCC200066 is an actinomycete that can produce the glycopeptide
      antibiotic norvancomycin, which has significant inhibitory activity
      against Gram-positive cocci and bacilli. Here, we report the draft genome
      sequence of A. orientalis CPCC200066 and identified the genes involved in
      norvancomycin biosynthesis.
AU  - Lei X
AU  - Yuan F
AU  - Shi Y
AU  - Li X
AU  - Wang L
AU  - Hong B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00296-15.

PMID- 22543635
VI  - 157
DP  - 2012
TI  - Sequencing and analysis of the complete genome of Rana grylio virus (RGV).
PG  - 1559-1564
AB  - Infection with Rana grylio virus (RGV), an iridovirus isolated in China in 1995,
      resulted in a high mortality rate in frogs. The complete genome sequence of RGV
      was determined and analyzed. The genomic DNA was 105,791 bp long, with 106 open
      reading frames (ORFs). Dot plot analysis showed that the gene order of RGV shared
      colinearity with three completely sequenced ranaviruses. A phylogenetic tree was
      constructed based on concatenated sequences of iridovirus 26 core-gene-encoded
      proteins, and the result showed high bootstrap support for RGV being a member of
      the genus Ranavirus and that iridoviruses of other genera also clustered closely.
      A microRNA (miRNA) prediction revealed that RGV could encode 18 mature miRNAs,
      many of which were located near genes associated with virus replication.
      Thirty-three repeated sequences were found in the RGV genome. These results
      provide insight into the genetic nature of RGV and are useful for laboratory
      diagnosis for vertebrate iridoviruses.
AU  - Lei XY
AU  - Ou T
AU  - Zhu RL
AU  - Zhang QY
PT  - Journal Article
TA  - Arch. Virol.
JT  - Arch. Virol.
SO  - Arch. Virol. 2012 157: 1559-1564.

PMID- 25814601
VI  - 3
DP  - 2015
TI  - Complete Genome Sequences of Escherichia coli Strains 1303 and ECC-1470 Isolated  from Bovine Mastitis.
PG  - e00182-15
AB  - Escherichia coli is the leading causative agent of acute bovine mastitis. Here, we report the
      complete genome sequence of E. coli O70:H32 strain 1303, isolated
      from an acute case of bovine mastitis, and E. coli Ont:Hnt strain ECC-1470,
      isolated from a persistent infection.
AU  - Leimbach A
AU  - Poehlein A
AU  - Witten A
AU  - Scheutz F
AU  - Schukken Y
AU  - Daniel R
AU  - Dobrindt U
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00182-15.

PMID- 27469942
VI  - 4
DP  - 2016
TI  - Whole-Genome Draft Sequences of Six Commensal Fecal and Six Mastitis-Associated Escherichia coli Strains of Bovine Origin.
PG  - e00753-16
AB  - The bovine gastrointestinal tract is a natural reservoir for commensal and pathogenic
      Escherichia coli strains with the ability to cause mastitis. Here, we
      report the whole-genome sequences of six E. coli isolates from acute mastitis
      cases and six E. coli isolates from the feces of udder-healthy cows.
AU  - Leimbach A
AU  - Poehlein A
AU  - Witten A
AU  - Wellnitz O
AU  - Shpigel N
AU  - Petzl W
AU  - Zerbe H
AU  - Daniel R
AU  - Dobrindt U
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00753-16.

PMID- 9490066
VI  - 251
DP  - 1998
TI  - The Flavobacterium okeanokoites adenine-N6-specific DNA-methyltransferase M.FokI is a tandem enzyme of two independent domains with very different kinetic properties.
PG  - 899-906
AB  - The Flavobacterium okeanokoites adenine-N6-specific DNA-methyltransferase, M.FokI, modifies
      both adenine residues within its asymmetric recognition sequence 5'-GGATG/CATCC-3'.  It is a
      fusion protein comprising two independent enzymes.  We have cloned, overexpressed and purified
      full-length M.FokI as well as both individual domains and analyzed their kinetics of DNA
      methylation using unmethylated and hemimethylated oligodeoxynucleotide substrates.  Our data
      show that both domains of M.FokI methylate DNA independently of each other but cooperate in
      DNA binding.  In agreement to former studies, the N-terminal domain of M.FokI modifies the
      upper strand of the recognition sequence (GGATG).  It strongly prefers hemimethylated
      (5'-GGATG/CmATCC-3'; mA=N6-methyladenosine) over unmethylated substrates.  In contrast, the
      terminal domain prefers unmethylated DNA substrates.  Surprisingly, in addition to methylating
      the lower strand of the recognition sequence (CATCC), M.FokI-(355-647) also modifies the upper
      strand (GGATG), albeit with a lower activity.  In addition methylation was detected at CACCC
      sites, but not at sites in which a central AT dinucleotide is flanked by at least one A.T or
      T.A base pair.  These results suggests that M.FokI-(335-647) either has a very degenerate
      specificity for (G/C)AT(G/C) and sites similar to CATCC or GGATG or, alternatively, that it
      has a dual specificity for CATCC and GGATG.
AU  - Leismann O
AU  - Roth M
AU  - Friedrich T
AU  - Wende W
AU  - Jeltsch A
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1998 251: 899-906.

PMID- 27284140
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Hydrotalea flava Strain CCUG 51397T.
PG  - e00527-16
AB  - We report the draft genome sequence of Hydrotalea flava CCUG 51397(T), the type strain of the
      genus Hydrotalea (family Chitinophagaceae), isolated from water
      samples in southern Sweden.
AU  - Leite LR
AU  - Medeiros JD
AU  - Fernandes GR
AU  - Araujo F
AU  - Pylro VS
AU  - Salim AC
AU  - Volpini A
AU  - Oliveira G
AU  - Cuadros-Orellana S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00527-16.

PMID- 26586878
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Two South African Bacillus anthracis Strains.
PG  - e01313-15
AB  - Bacillus anthracis is a Gram-positive bacterium that causes anthrax, mainly in herbivores
      through exotoxins and capsule produced on plasmids, pXO1 and pXO2.
      This paper compares the whole-genome sequences of two B. anthracis strains from
      an endemic region and a sporadic outbreak in South Africa. Sequencing was done
      using next-generation sequencing technologies.
AU  - Lekota KE
AU  - Mafofo J
AU  - Madoroba E
AU  - Rees J
AU  - van Heerden H
AU  - Muchadeyi FC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01313-15.

PMID- 16593855
VI  - 84
DP  - 1987
TI  - Nonreciprocal recombination between alleles of the chloroplast 23S rRNA gene in interspecific Chlamydomonas crosses.
PG  - 4166-4170
AB  - The inheritance of six polymorphic loci mapping in the rRNA-encoding (rDNA) region of the
      inverted repeat sequence of chloroplast DNA (cpDNA) was scored in hybrid subclones derived
      from reciprocal interspecific crosses between the green algae Chlamydomonas eugametos and
      Chlamydomonas moewusii. In order to enhance the detection of cells that had undergone
      recombination between parental cpDNAs, hybrids were selected that inherited a chloroplast
      antiboiotic-resistance marker contributed by the mating-type-minus (mt-) parent, the parent
      that normally contributes fewer cpDNA molecules. The major findings of this study can be
      summarized as follows. (i) The majority of the hybrids (14/17) were recombinant for cpDNA
      markers in the 10-kilobase-pair rDNA region under study. (ii) Only one allele of each
      polymorphic cpDNA locus was ever detected in the hybrids, thus suggesting that newly
      recombined rDNA sequences in one copy of the inverted repeat are rapidly spread to the other
      by a copy-correction mechanism. (iii) Chloroplast streptomycin-resistance (sr-2) and
      erythromycin-resistance (er-nM1) loci, although showing litle or no genetic linkage, were
      mapped to the 16S and 23S rRNA gene regions of the cpDNA, respectively, by virtue of their
      perfect coinheritance with polymorphic markers within these genes. (iv) cpDNA markers
      associated with a putative intron of the C. eugametos 23S rRNA gene were inherited by all 17
      hybrids. Such a result is similar to that observed for certain alleles of the large rRNA gene
      of yeast mitochrondria in crosses between Omega+ and Omega- strains.
AU  - Lemieux C
AU  - Lee RW
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1987 84: 4166-4170.

PMID- 27284154
VI  - 4
DP  - 2016
TI  - Genome Sequences of Multiresistant Staphylococcus capitis Pulsotype NRCS-A and Methicillin-Susceptible S. capitis Pulsotype NRCS-C.
PG  - e00541-16
AB  - Here, we report the draft genome sequences of methicillin-susceptible Staphylococcus captis
      pulsotype NCRS-C (CR02 strain) and multiresistant
      Staphylococcus captis pulsotype NCRS-A (CR07 strain).
AU  - Lemriss H
AU  - Dumont Y
AU  - Lemriss S
AU  - Martins-Simoes P
AU  - Butin M
AU  - Lahlou L
AU  - Rasigade JP
AU  - El Kabbaj S
AU  - Laurent F
AU  - Ibrahimi A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00541-16.

PMID- 25197487
VI  - 9
DP  - 2014
TI  - Non-contiguous finished genome sequence of Staphylococcus capitis CR01 (pulsetype NRCS-A).
PG  - 1118-1127
AB  - Staphylococcus capitis is a coagulase-negative staphylococcus (CoNS) commonly found in the
      human microflora. Recently, a clonal population of Staphylococcus
      capitis (denominated NRCS-A) was found to be a major cause of late-onset sepsis
      (LOS) in several neonatal intensive care units in France. Here, we report the
      complete genome sequence and annotation of the prototype Staphylococcus capitis
      NCRS-A strain CR01. The 2,504,472 bp long genome (1 chromosome and no plasmids)
      exhibits a G+C content of 32.81%, and contains 2,468 protein-coding and 59 tRNA
      genes and 4 rRNA genes.
AU  - Lemriss H
AU  - Lemriss S
AU  - Butin M
AU  - Ibrahimi A
AU  - El Kabbaj S
AU  - Rasigade J
AU  - Laurent F
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 1118-1127.

PMID- 26251481
VI  - 3
DP  - 2015
TI  - Genome Sequences of Four Staphylococcus capitis NRCS-A Isolates from Geographically Distant Neonatal Intensive Care Units.
PG  - e00501-15
AB  - Staphylococcus capitis pulsotype NRCS-A was previously reported as a frequent cause of
      late-onset sepsis in neonatal intensive care units (NICUs) worldwide.
      Here, we report the whole-genome shotgun sequences of four S. capitis pulsotype
      NCRS-A strains, CR03, CR04, CR05, and CR09, isolated from Belgium, Australia, the
      United Kingdom, and France, respectively.
AU  - Lemriss H
AU  - Lemriss S
AU  - Martins-Simoes P
AU  - Butin M
AU  - Lahlou L
AU  - Rasigade JP
AU  - Kearns A
AU  - Denis O
AU  - Deighton M
AU  - Ibrahimi A
AU  - Laurent F
AU  - El Kabbaj S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00501-15.

PMID- 25035334
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of the Alga-Degrading Bacteria Aeromonas hydrophila Strain AD9 and Pseudomonas pseudoalcaligenes Strain AD6.
PG  - e00709-14
AB  - Aeromonas hydrophila AD9 and Pseudomonas pseudoalcaligenes AD6 have been linked to algal cell
      degradation. Here we report the draft genomes of A. hydrophila AD9
      and P. pseudoalcaligenes AD6 for the investigation of causative agents for algal
      cell degradation.
AU  - Lenneman EM
AU  - Barney BM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00709-14.

PMID- 26496947
VI  - 44
DP  - 2016
TI  - Transient overexpression of DNA adenine methylase enables efficient and mobile genome engineering with reduced off-target effects.
PG  - e36
AB  - Homologous recombination of single-stranded oligonucleotides is a highly efficient process for
      introducing precise mutations into the genome of E. coli
      and other organisms when mismatch repair (MMR) is disabled. This can result in
      the rapid accumulation of off-target mutations that can mask desired phenotypes,
      especially when selections need to be employed following the generation of
      combinatorial libraries. While the use of inducible mutator phenotypes or other
      MMR evasion tactics have proven useful, reported methods either require
      non-mobile genetic modifications or costly oligonucleotides that also result in
      reduced efficiencies of replacement. Therefore a new system was developed,
      Transient Mutator Multiplex Automated Genome Engineering (TM-MAGE), that solves
      problems encountered in other methods for oligonucleotide-mediated recombination.
      TM-MAGE enables nearly equivalent efficiencies of allelic replacement to the use
      of strains with fully disabled MMR and with an approximately 12- to 33-fold lower
      off-target mutation rate. Furthermore, growth temperatures are not restricted and
      a version of the plasmid can be readily removed by sucrose counterselection.
      TM-MAGE was used to combinatorially reconstruct mutations found in evolved
      salt-tolerant strains, enabling the identification of causative mutations and
      isolation of strains with up to 75% increases in growth rate and greatly reduced
      lag times in 0.6 M NaCl.
AU  - Lennen RM
AU  - Nilsson WAI
AU  - Pedersen M
AU  - Bonde M
AU  - Luo H
AU  - Herrgard MJ
AU  - Sommer MO
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2016 44: e36.

PMID- 29941872
VI  - 15
DP  - 2018
TI  - A reassessment of DNA-immunoprecipitation-based genomic profiling.
PG  - 499-504
AB  - DNA immunoprecipitation followed by sequencing (DIP-seq) is a common enrichment method for
      profiling DNA modifications in mammalian genomes. However, the results
      of independent DIP-seq studies often show considerable variation between profiles
      of the same genome and between profiles obtained by alternative methods. Here we
      show that these differences are primarily due to the intrinsic affinity of IgG
      for short unmodified DNA repeats. This pervasive experimental error accounts for
      50-99% of regions identified as 'enriched' for DNA modifications in DIP-seq data.
      Correction of this error profoundly altered DNA-modification profiles for
      numerous cell types, including mouse embryonic stem cells, and subsequently
      revealed novel associations among DNA modifications, chromatin modifications and
      biological processes. We conclude that both matched input and IgG controls are
      essential in order for the results of DIP-based assays to be interpreted
      correctly, and that complementary, non-antibody-based techniques should be used
      to validate DIP-based findings to avoid further misinterpretation of genome-wide
      profiling data.
AU  - Lentini A
AU  - Lagerwall C
AU  - Vikingsson S
AU  - Mjoseng HK
AU  - Douvlataniotis K
AU  - Vogt H
AU  - Green H
AU  - Meehan RR
AU  - Benson M
AU  - Nestor CE
PT  - Journal Article
TA  - Nat. Methods
JT  - Nat. Methods
SO  - Nat. Methods 2018 15: 499-504.

PMID- 25953159
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Citrobacter rodentium DBS100 (ATCC 51459), a Primary Model of Enterohemorrhagic Escherichia coli Virulence.
PG  - e00415-15
AB  - Citrobacter rodentium is a Gram-negative bacterium which causes transmissible murine colonic
      hyperplasia and models the virulence of enterohemorrhagic
      Escherichia coli in vivo. Thus, C. rodentium is used to study human
      gastrointestinal disease. We present the draft genome sequence of C. rodentium
      strain ATCC 51459, also known as DBS100.
AU  - Lenz A
AU  - Tomkins J
AU  - Fabich AJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00415-15.

PMID- 17455934
VI  - 129
DP  - 2007
TI  - 2-Aminopurine Flipped into the Active Site of the Adenine-Specific DNA Methyltransferase M.TaqI: Crystal Structures and Time-Resolved Fluorescence.
PG  - 6240-6248
AB  - We report the crystal structure of the DNA adenine-N6 methyltransferase, M.TaqI, complexed
      with DNA, showing the fluorescent adenine analog, 2-aminopurine, flipped out of the DNA helix
      and occupying virtually the same position in the active site as the natural target adenine.
      Time-resolved fluorescence spectroscopy of the crystalline complex faithfully reports this
      state: base flipping is accompanied by the loss of the very short ( approximately 50 ps)
      lifetime component associated with fully base-stacked 2-aminopurine in DNA, and 2-aminopurine
      is subject to considerable quenching by pi-stacking interactions with Tyr108 in the catalytic
      motif IV (NPPY). This proves 2-aminopurine to be an excellent probe for studying base flipping
      by M.TaqI and suggests similar quenching in the active sites of DNA and RNA adenine-N6 as well
      as DNA cytosine-N4 methyltransferases sharing the conserved motif IV. In solution, the same
      distinctive fluorescence response confirms complete destacking from DNA and is also observed
      when the proposed key residue for base flipping by M.TaqI, the target base partner thymine, is
      substituted by an abasic site analog. The corresponding cocrystal structure shows
      2-aminopurine in the active site of M.TaqI, demonstrating that the partner thymine is not
      essential for base flipping. However, in this structure, a shift of the 3' neighbor of the
      target base into the vacancy left after base flipping is observed, apparently replicating a
      stabilizing role of the missing partner thymine. Time-resolved fluorescence and acrylamide
      quenching measurements of M.TaqI complexes in solution provide evidence for an alternative
      binding site for the extra-helical target base within M.TaqI and suggest that the partner
      thymine assists in delivering the target base into the active site.
AU  - Lenz T
AU  - Bonnist EYM
AU  - Pljevaljcic G
AU  - Neely RK
AU  - Dryden DTF
AU  - Scheidig AJ
AU  - Jones AC
AU  - Weinhold E
PT  - Journal Article
TA  - J. Am. Chem. Soc.
JT  - J. Am. Chem. Soc.
SO  - J. Am. Chem. Soc. 2007 129: 6240-6248.

PMID- 23409269
VI  - 1
DP  - 2013
TI  - Draft Genome of Spiribacter salinus M19-40, an Abundant Gammaproteobacterium in Aquatic Hypersaline Environments.
PG  - e00179-12
AB  - We have previously used a de novo metagenomic assembly approach to describe the presence of an
      abundant gammaproteobacterium comprising nearly 15% of the
      microbial community in an intermediate salinity solar saltern pond. We have
      obtained this microbe in pure culture and describe the genome sequencing of the
      halophilic photoheterotrophic microbe, Spiribacter salinus M19-40.
AU  - Leon MJ
AU  - Ghai R
AU  - Fernandez AB
AU  - Sanchez-Porro C
AU  - Rodriguez-Valera F
AU  - Ventosa A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00179-12.

PMID- 25101067
VI  - 5
DP  - 2014
TI  - The methylome of the gut microbiome: disparate Dam methylation patterns in intestinal Bacteroides dorei.
PG  - 361
AB  - Despite the large interest in the human microbiome in recent years, there are no reports of
      bacterial DNA methylation in the microbiome.  Here metagenomic sequencing using the Pacific
      Biosciences platform allowed for rapid identification of bacterial GATC methylation status of
      a bacterial species in human stool samples.  For this work, two stool samples were chosen that
      were dominated by a single species, Bacteroides dorei.  Based on 16S rRNA analysis, this
      species represented over 45% of the bacteria present in these two samples.  The B. dorei
      genome sequence from these samples was determined and the GATC methylation sites mapped.  The
      Bacteroides dorei genome from one subject lacked any GATC methylation and lacked the DNA
      adenine methyltransferase genes.  In contrast, B. dorei from another subject contained 20,551
      methylated GATC sites.  Of the 4970 open reading frames identified in the GATC methylated B.
      dorei genome, 3184 genes were methylated as well as 1735 GATC methylations in intergenic
      regions.  These results suggest that DNA methylation patterns are important to consider in
      multi-omic analyses of microbiome samples seeking to discover the diversity of bacterial
      functions and may differ between disease states.
AU  - Leonard MT
AU  - Davis-Richardson AG
AU  - Ardissone AN
AU  - Kemppainen KM
AU  - Drew JC
AU  - Ilonen J
AU  - Knip M
AU  - Simell O
AU  - Toppari J
AU  - Veijola R
AU  - Hyoty H
AU  - Triplett EW
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2014 5: 361.

PMID- 23408754
VI  - 7
DP  - 2012
TI  - Complete genome sequence of Liberibacter crescens BT-1.
PG  - 271-283
AB  - 
AU  - Leonard MT
AU  - Fagen JR
AU  - Davis-Richardson AG
AU  - Davis MJ
AU  - Triplett EW
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 7: 271-283.

PMID- 24285647
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Carnobacterium gilichinskyi Strain WN1359T (DSM 27470T).
PG  - e00985-13
AB  - We report the complete genome sequence of Carnobacterium gilichinskyi strain WN1359,
      previously isolated from Siberian permafrost and capable of growth under
      cold (0 degrees C), anoxic, CO2-dominated, low-pressure (0.7-kPa) conditions in a
      simulation of the Mars atmosphere.
AU  - Leonard MT
AU  - Panayotova N
AU  - Farmerie WG
AU  - Triplett EW
AU  - Nicholson WL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00985-13.

PMID- 24812223
VI  - 2
DP  - 2014
TI  - Complete Genome Sequences of Lactobacillus johnsonii Strain N6.2 and Lactobacillus reuteri Strain TD1.
PG  - e00397-14
AB  - We report here the complete genome sequences of Lactobacillus johnsonii strain N6.2, a
      homofermentative lactic acid intestinal bacterium, and Lactobacillus
      reuteri strain TD1, a heterofermentative lactic acid intestinal bacterium, both
      isolated from a type 1 diabetes-resistant rat model.
AU  - Leonard MT
AU  - Valladares RB
AU  - Ardissone A
AU  - Gonzalez CF
AU  - Lorca GL
AU  - Triplett EW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00397-14.

PMID- 24699962
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Multidrug-Resistant Escherichia coli Strain LR09, Isolated from a Wastewater Treatment Plant.
PG  - e00272-14
AB  - We report the draft genome sequence of Escherichia coli O1:H6 strain LR09, which  was isolated
      from a wastewater treatment plant and displays high resistance to five fluoroquinolone
      antimicrobials. The assembled data determine that the strain clusters with E. coli phylogroup
      F and harbors a plasmid conferring resistance to a broad spectrum of antibiotics.
AU  - Leonard SR
AU  - Lacher DW
AU  - Elkins CA
AU  - Jung CM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00272-14.

PMID- 25657266
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of the Enteroinvasive Escherichia coli Strains M4163 and 4608-58.
PG  - e01395-14
AB  - We report here the draft genome sequences of enteroinvasive Escherichia coli (EIEC) O124:H30
      strain M4163 isolated from imported French cheese and EIEC
      O143:H26 strain 4608-58. The assembled data determined that both strains contain
      multiple copies of the ipaH gene, as well as the pINV A form of the invasion
      plasmid.
AU  - Leonard SR
AU  - Lacher DW
AU  - Lampel KA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01395-14.

PMID- 29773638
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of New Vancomycin-Resistant Enterococcus faecium Sequence Type 1421.
PG  - e00438-18
AB  - The spread of vancomycin-resistant Enterococcus faecium (VREfm) has become a challenge to
      health care infection control worldwide. In 2015, a marked increase
      in VREfm isolation was detected in acute public hospitals in Tasmania. We report
      here the draft whole-genome sequence of a newly designated VREfm sequence type,
      sequence type 1421 (ST1421).
AU  - Leong KWC
AU  - Cooley LA
AU  - O'Toole RF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00438-18.

PMID- 28818892
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Two Enterobacter cloacae subsp. cloacae Strains Isolated from Australian Hematology Patients with Bacteremia.
PG  - e00756-17
AB  - Enterobacter cloacae is a common member of the gut microbiota in healthy individuals. However,
      it is also an opportunistic pathogen, capable of causing
      bacteremia. We report the draft genomes of two Enterobacter cloacae subspecies
      cloacae strains isolated from hematology patients with bacteremia. Both isolates
      carry genes encoding extended-spectrum beta-lactamases.
AU  - Leong LEX
AU  - Shaw D
AU  - Papanicolas L
AU  - Lagana D
AU  - Bastian I
AU  - Rogers GB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00756-17.

PMID- 1423634
VI  - 71
DP  - 1992
TI  - A targeting sequence directs DNA methyltransferase to sites of DNA replication in mammalian nuclei.
PG  - 865-873
AB  - Tissue-specific patterns of methylated deoxycytidine residues in the mammalian genome are
      preserved by postreplicative methylation of newly synthesized DNA. DNA methyltransferase
      (MTase) is here shown to associate with replication foci during S phase but to display a
      difuse nucleoplasmic distribution in non-S phase cells. Analysis of DNA MTase-B-galactosidase
      fusion proteins has shown that association with replication foci is mediated by a novel
      targeting sequence located near the N-terminus of DNA MTase. This sequence has the properties
      expected of a targeting sequence in that it is not required for enzymatic activity, prevents
      proper targeting when deleted and, when fused to B-galactosidase, causes the fusion protein to
      associate with replication foci in a cell cycle-dependent manner.
AU  - Leonhardt H
AU  - Page AW
AU  - Weier HU
AU  - Bestor TH
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1992 71: 865-873.

PMID- 19439656
VI  - 106
DP  - 2009
TI  - A precise reconstruction of the emergence and constrained radiations of Escherichia coli O157 portrayed by backbone concatenomic analysis.
PG  - 8713-8718
AB  - Single nucleotide polymorphisms (SNPs) in stable genome regions provide
      durable measurements of species evolution. We systematically identified
      each SNP in concatenations of all backbone ORFs in 7 newly or previously
      sequenced evolutionarily instructive pathogenic Escherichia coli O157:H7,
      O157:H(-), and O55:H7. The 1,113 synonymous SNPs demonstrate emergence of
      the largest cluster of this pathogen only in the last millennium.
      Unexpectedly, shared SNPs within circumscribed clusters of organisms
      suggest severely restricted survival and limited effective population
      sizes of pathogenic O157:H7, tenuous survival of these organisms in
      nature, source-sink evolutionary dynamics, or, possibly, a limited number
      of mutations that confer selective advantage. A single large segment
      spanning the rfb-gnd gene cluster is the only backbone region convincingly
      acquired by recombination as O157 emerged from O55. This concatenomic
      analysis also supports using SNPs to differentiate closely related
      pathogens for infection control and forensic purposes. However,
      constrained radiations raise the possibility of making false associations
      between isolates.
AU  - Leopold SR
AU  - Magrini V
AU  - Holt NJ
AU  - Shaikh N
AU  - Mardis ER
AU  - Cagno J
AU  - Ogura Y
AU  - Iguchi A
AU  - Hayashi T
AU  - Mellmann A
AU  - Karch H
AU  - Besser TE
AU  - Sawyer SA
AU  - Whittam TS
AU  - Tarr PI
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2009 106: 8713-8718.

PMID- 27516518
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Idiomarina woesei Strain W11T (DSM 27808T) Isolated from the Andaman Sea.
PG  - e00831-16
AB  - Idiomarina woesei strain W11(T) was isolated from the Andaman Sea. Heterotrophic  growth was
      observed at 30 to 37 degrees C and pH 7 to 9. It grows in the presence
      of 0.5 to 12% (wt/vol) NaCl, and optimum growth occurred at 5 to 6% NaCl. The
      estimated genome is 2.4 Mb and encodes 2,305 proteins.
AU  - Lepcha RT
AU  - Poddar A
AU  - Whitman WB
AU  - Das SK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00831-16.

PMID- 26159531
VI  - 3
DP  - 2015
TI  - Draft Whole-Genome Sequence of Serratia sp. Strain TEL, Associated with Oscheius  sp. TEL-2014 (Nematoda: Rhabditidae) Isolated from a Grassland in South Africa.
PG  - e00747-15
AB  - Here, we report on the draft genome sequence of Serratia sp. strain TEL, associated with
      Oscheius sp. TEL-2014 (Nematoda: Rhabditidae, KM492926) isolated
      from a grassland in Suikerbosrand Nature Reserve near Johannesburg in South
      Africa. Serratia sp. strain TEL has a genome size of 5,000,541 bp with 4,647
      genes and a G+C content of 59.1%.
AU  - Lephoto TE
AU  - Featherston J
AU  - Gray VM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00747-15.

PMID- 11713319
VI  - 29
DP  - 2001
TI  - Characterization of the type IV restriction modification system BspLU11III from Bacillus sp. LU11.
PG  - 4691-4698
AB  - We report the characterization and cloning of the genes for an unusual type IV
      restriction-modification system, BspLU11III, from Bacillus sp. LU11. The system consists of
      two methyltransferases and one endonuclease, which also possesses methyltransferase activity.
      The three genes of the restriction-modification system, bsplu11IIIMa, bsplu11IIIMb and
      bsplu11IIIR, are closely linked and tandemly arranged. The corresponding enzymes recognize the
      dsDNA sequence 5'-GGGAC-3'/5'-GTCCC-3', with M.BspLU11IIIa modifying the A (underlined) of
      one strand and M.BspLU11IIIb the inner C (underlined) of the other strand. R.BspLU11III has
      both endonuclease and adenine-specific methyltransferase activities and is able to protect the
      DNA against cleavage by itself. In contrast to all type IV restriction-modification systems
      described so far, which have only one adenine-specific methyltransferase, BspLU11III is the
      first type IV restriction-modification system that includes two methyltransferases, one of
      them being cytosine specific.
AU  - Lepikhov K
AU  - Tchernov A
AU  - Zheleznaja L
AU  - Matvienko N
AU  - Walter J
AU  - Trautner TA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2001 29: 4691-4698.

PMID- 20532244
VI  - 5
DP  - 2010
TI  - Identification of novel pathogenicity loci in Clostridium perfringens strains that cause avian necrotic enteritis.
PG  - E10795
AB  - Type A Clostridium perfringens causes poultry necrotic enteritis (NE), an
      enteric disease of considerable economic importance, yet can also exist as
      a member of the normal intestinal microbiota. A recently discovered
      pore-forming toxin, NetB, is associated with pathogenesis in most, but not
      all, NE isolates. This finding suggested that NE-causing strains may
      possess other virulence gene(s) not present in commensal type A isolates.
      We used high-throughput sequencing (HTS) technologies to generate draft
      genome sequences of seven unrelated C. perfringens poultry NE isolates and
      one isolate from a healthy bird, and identified additional novel
      NE-associated genes by comparison with nine publicly available reference
      genomes. Thirty-one open reading frames (ORFs) were unique to all NE
      strains and formed the basis for three highly conserved NE-associated loci
      that we designated NELoc-1 (42 kb), NELoc-2 (11.2 kb) and NELoc-3 (5.6
      kb). The largest locus, NELoc-1, consisted of netB and 36 additional
      genes, including those predicted to encode two leukocidins, an
      internalin-like protein and a ricin-domain protein. Pulsed-field gel
      electrophoresis (PFGE) and Southern blotting revealed that the NE strains
      each carried 2 to 5 large plasmids, and that NELoc-1 and -3 were localized
      on distinct plasmids of sizes approximately 85 and approximately 70 kb,
      respectively. Sequencing of the regions flanking these loci revealed
      similarity to previously characterized conjugative plasmids of C.
      perfringens. These results provide significant insight into the
      pathogenetic basis of poultry NE and are the first to demonstrate that
      netB resides in a large, plasmid-encoded locus. Our findings strongly
      suggest that poultry NE is caused by several novel virulence factors,
      whose genes are clustered on discrete pathogenicity loci, some of which
      are plasmid-borne.
AU  - Lepp D
AU  - Roxas B
AU  - Parreira VR
AU  - Marri PR
AU  - Rosey EL
AU  - Gong J
AU  - Songer JG
AU  - Vedantam G
AU  - Prescott JF
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2010 5: E10795.

PMID- 29051260
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of a Community-Acquired Methicillin-Resistant Staphylococcus aureus USA300 Isolate from a River Sample.
PG  - e01166-17
AB  - The increasing emergence of multiresistant bacteria in health care settings in the community
      and in the environment represents a major health threat worldwide.
      Here, we report the draft genome sequence of a community-acquired
      methicillin-resistant Staphylococcus aureus (CA-MRSA) USA300 isolate (W1) from a
      small river in southern Austria.
AU  - Lepuschitz S
AU  - Mach R
AU  - Springer B
AU  - Allerberger F
AU  - Ruppitsch W
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01166-17.

PMID- 29724848
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of the First Documented Clinical Siccibacter turicensis Isolate in Austria.
PG  - e00380-18
AB  - The nonpathogenic species Siccibacter turicensis is closely related to members of the
      food-associated pathogenic genus Cronobacter and has been detected in fruit
      powders, formula, spices, and herbs. Here, we report on the first clinical
      isolate of S. turicensis, recovered from the labial angle of a patient with
      angular cheilitis.
AU  - Lepuschitz S
AU  - Pekard-Amenitsch S
AU  - Haunold R
AU  - Schill S
AU  - Schriebl A
AU  - Mach R
AU  - Allerberger F
AU  - Ruppitsch W
AU  - Forsythe SJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00380-18.

PMID- 29146834
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Carbapenemase-Producing Serratia marcescens Isolated from a Patient with Chronic Obstructive Pulmonary Disease.
PG  - e01288-17
AB  - The occurrence of multidrug-resistant Serratia marcescens strains producing
      metallo-beta-lactamases or extended-spectrum beta-lactamases represents a serious
      public health threat. Here, we report the draft genome sequence of a
      multidrug-resistant carbapenemase-producing Serratia marcescens isolate recovered
      from the bronchoalveolar lavage specimen of a patient suffering from chronic
      obstructive pulmonary disease (COPD).
AU  - Lepuschitz S
AU  - Sorschag S
AU  - Springer B
AU  - Allerberger F
AU  - Ruppitsch W
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01288-17.

PMID- 18218029
VI  - 10
DP  - 2008
TI  - Elevated atmospheric CO2 affects soil microbial diversity associated with trembling aspen.
PG  - 926-941
AB  - The effects of elevated atmospheric CO(2) (560 p.p.m.) and subsequent
      plant responses on the soil microbial community composition associated
      with trembling aspen was assessed through the classification of 6996
      complete ribosomal DNA sequences amplified from the Rhinelander WI
      free-air CO(2) and O(3) enrichment (FACE) experiments microbial community
      metagenome. This in-depth comparative analysis provides an unprecedented,
      detailed and deep branching profile of population changes incurred as a
      response to this environmental perturbation. Total bacterial and
      eukaryotic abundance does not change; however, an increase in
      heterotrophic decomposers and ectomycorrhizal fungi is observed. Nitrate
      reducers of the domain bacteria and archaea, of the phylum Crenarchaea,
      potentially implicated in ammonium oxidation, significantly decreased with
      elevated CO(2). These changes in soil biota are evidence for altered
      interactions between trembling aspen and the microorganisms in its
      surrounding soil, and support the theory that greater plant detritus
      production under elevated CO(2) significantly alters soil microbial
      community composition.
AU  - Lesaulnier C
AU  - Papamichail D
AU  - McCorkle S
AU  - Ollivier B
AU  - Skiena S
AU  - Taghavi S
AU  - Zak D
AU  - van der Lelie D
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2008 10: 926-941.

PMID- 18787695
VI  - 4
DP  - 2008
TI  - The genome of Borrelia recurrentis, the agent of deadly louse-borne relapsing fever, is a degraded subset of tick-borne Borrelia duttonii.
PG  - e1000185
AB  - In an effort to understand how a tick-borne pathogen adapts to the body louse, we sequenced
      and compared the genomes of the recurrent fever agents
      Borrelia recurrentis and B. duttonii. The 1,242,163-1,574,910-bp
      fragmented genomes of B. recurrentis and B. duttonii contain a unique
      23-kb linear plasmid. This linear plasmid exhibits a large polyT track
      within the promoter region of an intact variable large protein gene and a
      telomere resolvase that is unique to Borrelia. The genome content is
      characterized by several repeat families, including antigenic
      lipoproteins. B. recurrentis exhibited a 20.4% genome size reduction and
      appeared to be a strain of B. duttonii, with a decaying genome, possibly
      due to the accumulation of genomic errors induced by the loss of recA and
      mutS. Accompanying this were increases in the number of impaired genes and
      a reduction in coding capacity, including surface-exposed lipoproteins and
      putative virulence factors. Analysis of the reconstructed ancestral
      sequence compared to B. duttonii and B. recurrentis was consistent with
      the accelerated evolution observed in B. recurrentis. Vector
      specialization of louse-borne pathogens responsible for major epidemics
      was associated with rapid genome reduction. The correlation between gene
      loss and increased virulence of B. recurrentis parallels that of
      Rickettsia prowazekii, with both species being genomic subsets of
      less-virulent strains.
AU  - Lescot M
AU  - Audic S
AU  - Robert C
AU  - Nguyen TT
AU  - Blanc G
AU  - Cutler SJ
AU  - Wincker P
AU  - Couloux A
AU  - Claverie JM
AU  - Raoult D
AU  - Drancourt M
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2008 4: e1000185.

PMID- 25087740
VI  - 188
DP  - 2014
TI  - Development of an in vivo methylation system for the solventogen Clostridium saccharobutylicum NCP 262 and analysis of two endonuclease mutants.
PG  - 97-99
AB  - The genome of the biotechnologically important solventogenic Clostridium saccharobutylicum NCP
      262 contains two operons coding for genes of presumed type I RM systems belonging to the
      families A and C. They represent a limiting factor for the development of transformation and
      conjugation protocols. We established an efficient triparental mating system to transfer DNA
      to C. saccharobutylicum by conjugation, which includes an in vivo methylation of the donor
      DNA. Furthermore we describe increased rates of conjugation in knock-out mutants of the
      restrictase subunits of both RM systems.
AU  - Lesiak JM
AU  - Liebl W
AU  - Ehrenreich A
PT  - Journal Article
TA  - J. Biotechnol.
JT  - J. Biotechnol.
SO  - J. Biotechnol. 2014 188: 97-99.

PMID- 27811104
VI  - 4
DP  - 2016
TI  - Finished Genome Sequence of the Highly Multidrug-Resistant Human Urine Isolate Citrobacter freundii Strain SL151.
PG  - e01225-16
AB  - Citrobacter freundii is a Gram-negative opportunistic pathogen that is increasingly being
      recognized as a causative agent of hospital-acquired urinary
      tract infections and an important reservoir of antimicrobial resistance
      determinants. In this report, we describe the finished genome sequence of C.
      freundii strain SL151, a highly multidrug-resistant human urine isolate.
AU  - Leski TA
AU  - Taitt CR
AU  - Bangura U
AU  - Ansumana R
AU  - Stenger DA
AU  - Wang Z
AU  - Vora GJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01225-16.

PMID- 1849100
VI  - 280
DP  - 1991
TI  - The inhibition of restriction endonucleases due to Z-DNA in negatively supercoiled plasmids.
PG  - 91-93
AB  - Plasmid pGC20 containing the (dGC) insert in the SmaI recognition site has been
      used to study the inhibition of cleavage by different restriction endonucleases
      due to Z-DNA formation in the (dCG) sequence of the negatively supercoiled
      plasmid.  Data obtained indicate the different sensitivity of restriction
      endonucleases to DNA conformational perturbations resulted from Z-DNA
      formation.  Therefore, the inhibition of DNA cleavage by a particular
      restriction endonuclease cannot serve as a criterion for the estimation of the
      length of B-Z junctions in circular supercoiled DNAs.
AU  - Lesnik EA
AU  - Beschetnikova ZA
AU  - Maslova RN
AU  - Varshavsky JM
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1991 280: 91-93.

PMID- 1892579
VI  - 8
DP  - 1991
TI  - The influence of Z-DNA formation on the activity of restriction endonucleases.
PG  - A118
AB  - Plasmid pGC20 containing the (dGC)9 insert in SmaI recognition site has been
      used to study the inhibition of cleavage by six different restriction
      endonucleases due to Z-DNA formation in negatively supercoiled plasmid.  The
      recognition sites of the KpnI, SacI and EcoRI were located correspondingly at
      0, 6 and 12 b.p. away from Z-DNA.  The recognition sites of the BamHI, XbaI and
      SalI were 1, 7 and 13 b.p. away from Z-DNA on the other side of it.  Formation
      of Z-DNA in the (CG)10 sequence inhibited cleavage by restriction endonucleases
      to different extents.  In the KpnI, SacI and EcoRI series the degree of enzyme
      inhibition decreased as the distance between their recognition sites and the
      insert increased.  Such a correlation was not observed in the BamHI, XbaI and
      SalI series.  All three endonucleases were rather strongly inhibited.  These
      data indicate on the different sensitivity of restriction endonucleases to DNA
      conformational perturbations resulted from Z-DNA formation in the negatively
      supercoiled plasmid.  Therefore, the inhibition of DNA cleavage by a particular
      restriction endonuclease cannot serve as a criterion for the estimation of the
      length of B-Z junctions in circular supercoiled DNAs.
AU  - Lesnik EA
AU  - Beschetnikova ZA
AU  - Maslova RN
AU  - Varshavsky JM
PT  - Journal Article
TA  - J. Biomol. Struct. Dyn.
JT  - J. Biomol. Struct. Dyn.
SO  - J. Biomol. Struct. Dyn. 1991 8: A118.

PMID- 2561178
VI  - 23
DP  - 1989
TI  - The influence of Z-conformation of the enzyme activity of restriction endonucleases.
PG  - 1638-1644
AB  - Recombinant plasmid pGC20 containing (GC)9-insert into the SmaI site of pUC19
      has been used to study the inhibition of cleavage by six restriction
      endonucleases; KpnI, SacI, EcoRI and also BamHI, XbaI and SalI, due to Z-DNA
      formation in negatively supercoiled plasmids.  The recognition sites of these
      enzymes were located at different distances on both side of the (CG)
      10-sequence.  It was shown that the inhibition of cleavage by KpnI, SacI and
      EcoRI decreased in this series as fast as the distance between recognition site
      and B-Z junction was increased, and no inhibition of cleavage by EcoRI was
      found.  However, such a correlation was not found in the series of BamHI, XbaI
      and SalI.  In contrast with EcoRI the cleavage by SalI was inhibited
      completely.  These results indicate the difference in sensitivity of
      restriction endonucleases to the structural perturbations of DNA associated
      with B-Z junctions.  It seems to depend on features of the enzyme-substrate
      interaction mechanisms and also on recognition and flanking sequences of DNA.
      Consequently, experiments with the inhibition of the cleavage by any enzyme
      cannot help to determine the dimension of the region of DNA with altered
      structure.
AU  - Lesnik EA
AU  - Khalimullina ZA
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1989 23: 1638-1644.

PMID- 1447218
VI  - 267
DP  - 1992
TI  - Steroselective interaction with chiral phosphorothioates at the central DNA kink of the EcoRI endonuclease-GAATTC Complex.
PG  - 24810-24818
AB  - We have probed the contacts between EcoRI endonuclease and the central phosphate of its
      recognition site GAApTTC, using synthetic oligonucleotides containing single sterospecific Rp-
      or Sp-phosphorothioates (ps). These substitutions produce subtle sterospecific effects on
      EcoRI endonuclease binding and cleavage. An Sp-Ps substitution in one strand of the DNA duplex
      improves binding free energy by -1.5 kcal/mol, whereas the Rp-Ps substitution has an
      unfavorable effect (+0.3 kcal/mol) on binding free energy. These effects derive principally
      from changes in the first order rate constants for dissociation of the enzyme-DNA commplexes.
      The first order rate constants for strand scission are also affected, in that a strand
      containing Sp-Ps substitution is cleaved 2 to 3 times more rapidly than a strand containing a
      normal prochiral phosphate, whereas a strand containing Rp-Ps substitution is cleaved about 3
      times slower than normal. As a result, single-strand substitutions produce pronounced
      asymmetry in the rates of cleavage of the two DNA strands, and this effect is exaggerated in
      an Rp,Sp-heteroduplex. Ethylation-interference foot-printing indicates that none of the Ps
      substitutions cause any major change in contacts between endonuclease and DNA phosphates. When
      an Sp-Ps localizes P=O in the DNA major groove, a hydrogen -bonding interaction with the
      backbone amide-NH of Gly116 of the endonuclease is improved relative to that with a prochiral
      phosphate having intermediate P-O bond order and delocalized charge.
AU  - Lesser DR
AU  - Grajkowski A
AU  - Kurpiewski MR
AU  - Koziolkiewicz M
AU  - Stec WJ
AU  - Jacobson LJ
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1992 267: 24810-24818.

PMID- 2237428
VI  - 250
DP  - 1990
TI  - The energetic basis of specificity in the EcoRI endonuclease-DNA interaction.
PG  - 776-786
AB  - High sequence selectivity in DNA-protein interactions was analyzed by measuring
      discrimination by EcoRI endonuclease between the recognition site GAATTC and
      systematically altered DNA sites.  Base analogue substitutions that preserve
      the sequence-dependent conformational motif of the GAATTC site permit deletion
      of single sites of protein-base contact at a cost of +1 to +2 kcal/mol.
      However, the introduction of any one incorrect natural base pair costs +6 to
      +13 kcal/mol in transition state interaction energy, the resultant of the
      following interdependent factors:  deletion of one or two hydrogen bonds
      between the protein and a purine base; unfavorable steric apposition between a
      group on the protein and an incorrectly placed functional group on a base;
      disruption of a pyrimidine contact with the protein; loss of some crucial
      interactions between protein and DNA phosphates; and an increased energetic
      cost of attaining the required DNA conformation in the transition state
      complex.  EcoRI endonuclease thus achieves stringent discrimination by both
      direct readout (protein-base contacts) and indirect readout (protein-phosphate
      contacts and DNA conformation) of the DNA sequence.
AU  - Lesser DR
AU  - Kurpiewski MR
AU  - Jen-Jacobson L
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1990 250: 776-786.

PMID- 8356054
VI  - 90
DP  - 1993
TI  - Facilitated distortion of the DNA site enhances EcoRI endonuclease-DNA recognition.
PG  - 7548-7552
AB  - We have measured the binding of EcoRI endonuclease to a complete set of purine-base analogue
      sites, each of which deletes one functional group that forms a hydrogen bond with the
      endonuclease in the canonical GAATTC complex. For five of six functional group deletions, the
      observed penalty in binding free energy is +1.3 to +1.7 kcal/mol. For two of these cases
      (replacement of adenine N7 with carbon) a single protein-base hydrogen bond is removed without
      deleting an interstrand Watson-Crick hydrogen bond or causing structural adaptation in the
      complex. This observation establishes that the incremental energetic contribution of one
      protein-base hydrogen bond is about -1.5 kcal.mol. By contrast, deletion of the N6-amino group
      of the inner adenine in the site improves binding by -1.0 kcal/mol because the penalty for
      deleting a protein-base hydrogen bond is outweighed by facilitation of the required DNA
      distortion (kinking) in the complex. This result provides direct evidence that the energetic
      cost of distorting a DNA site can make an unfavorable contribution to protein-DNA binding.
AU  - Lesser DR
AU  - Kurpiewski MR
AU  - Waters T
AU  - Connolly BA
AU  - Jen-Jacobson L
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1993 90: 7548-7552.

PMID- 20941392
VI  - 6
DP  - 2010
TI  - The genome of a pathogenic rhodococcus: cooptive virulence underpinned by key gene acquisitions.
PG  - e1001145
AB  - We report the genome of the facultative intracellular parasite Rhodococcus equi, the only
      animal pathogen within the biotechnologically important actinobacterial genus Rhodococcus. The
      5.0-Mb R. equi 103S genome is significantly smaller than those of environmental rhodococci.
      This is due to genome expansion in nonpathogenic species, via a linear gain of paralogous
      genes and an accelerated genetic flux, rather than reductive evolution in R. equi. The 103S
      genome lacks the extensive catabolic and secondary metabolic complement of environmental
      rhodococci, and it displays unique adaptations for host colonization and competition in the
      short-chain fatty acid-rich intestine and manure of herbivores--two main R. equi reservoirs.
      Except for a few horizontally acquired (HGT) pathogenicity loci, including a cytoadhesive
      pilus determinant (rpl) and the virulence plasmid vap pathogenicity island (PAI) required for
      intramacrophage survival, most of the potential virulence-associated genes identified in R.
      equi are conserved in environmental rhodococci or have homologs in nonpathogenic
      Actinobacteria. This suggests a mechanism of virulence evolution based on the cooption of
      existing core actinobacterial traits, triggered by key host niche-adaptive HGT events. We
      tested this hypothesis by investigating R. equi virulence plasmid-chromosome crosstalk, by
      global transcription profiling and expression network analysis. Two chromosomal genes
      conserved in environmental rhodococci, encoding putative chorismate mutase and anthranilate
      synthase enzymes involved in aromatic amino acid biosynthesis, were strongly coregulated with
      vap PAI virulence genes and required for optimal proliferation in macrophages. The regulatory
      integration of chromosomal metabolic genes under the control of the HGT-acquired plasmid PAI
      is thus an important element in the cooptive virulence of R. equi.
AU  - Letek M et al
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2010 6: e1001145.

PMID- 424288
VI  - 6
DP  - 1979
TI  - A restriction enzyme from Fusobacterium nucleatum 4H which recognizes GCNGC.
PG  - 17-25
AB  - A site-specific restriction endonuclease Fnu4HI isolated from Fusobacterium
      nucleatum 4H recognizes the DNA nucleotide sequence 5'-G C^N G C-3' 3'-C G N^C
      G-5' and cleaves as indicated by the arrows.
AU  - Leung DW
AU  - Lui ACP
AU  - Merilees H
AU  - McBride BC
AU  - Smith M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1979 6: 17-25.

PMID- 29188195
VI  - 7
DP  - 2017
TI  - Comparative Genomic Analysis of Two Clonally Related Multidrug Resistant Mycobacterium tuberculosis by Single Molecule Real Time Sequencing.
PG  - 478
AB  - Background: Multidrug-resistant tuberculosis (MDR-TB) is posing a major threat to
      global TB control. In this study, we focused on two consecutive MDR-TB isolated
      from the same patient before and after the initiation of anti-TB treatment. To
      better understand the genomic characteristics of MDR-TB, Single Molecule
      Real-Time (SMRT) Sequencing and comparative genomic analyses was performed to
      identify mutations that contributed to the stepwise development of drug
      resistance and growth fitness in MDR-TB under in vivo challenge of anti-TB drugs.
      Result: Both pre-treatment and post-treatment strain demonstrated concordant
      phenotypic and genotypic susceptibility profiles toward rifampicin, pyrazinamide,
      streptomycin, fluoroquinolones, aminoglycosides, cycloserine, ethionamide, and
      para-aminosalicylic acid. However, although both strains carried identical
      missense mutations at rpoB S531L, inhA C-15T, and embB M306V, MYCOTB Sensititre
      assay showed that the post-treatment strain had 16-, 8-, and 4-fold elevation in
      the minimum inhibitory concentrations (MICs) toward rifabutin, isoniazid, and
      ethambutol respectively. The results have indicated the presence of additional
      resistant-related mutations governing the stepwise development of MDR-TB. Further
      comparative genomic analyses have identified three additional polymorphisms
      between the clinical isolates. These include a single nucleotide deletion at
      nucleotide position 360 of rv0888 in pre-treatment strain, and a missense
      mutation at rv3303c (lpdA) V44I and a 6-bp inframe deletion at codon 67-68 in
      rv2071c (cobM) in the post-treatment strain. Multiple sequence alignment showed
      that these mutations were occurring at highly conserved regions among pathogenic
      mycobacteria. Using structural-based and sequence-based algorithms, we further
      predicted that the mutations potentially have deleterious effect on protein
      function. Conclusion: This is the first study that compared the full genomes of
      two clonally-related MDR-TB clinical isolates during the course of anti-TB
      treatment. Our work has demonstrated the robustness of SMRT Sequencing in
      identifying mutations among MDR-TB clinical isolates. Comparative genome analysis
      also suggested novel mutations at rv0888, lpdA, and cobM that might explain the
      difference in antibiotic resistance and growth pattern between the two MDR-TB
      strains.
AU  - Leung KS
AU  - Siu GK
AU  - Tam KK
AU  - To SW
AU  - Rajwani R
AU  - Ho PL
AU  - Wong SS
AU  - Zhao WW
AU  - Ma OC
AU  - Yam WC
PT  - Journal Article
TA  - Front Cell Infect Microbiol
JT  - Front Cell Infect Microbiol
SO  - Front Cell Infect Microbiol 2017 7: 478.

PMID- 2557583
VI  - 17
DP  - 1989
TI  - Screening and characterization of restriction endonucleases from a bacterial culture collection in Hong Kong.
PG  - 10133
AB  - None
AU  - Leung SM
AU  - Chan KY
AU  - Suen YK
AU  - Shaw PC
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 10133.

PMID- Not included in PubMed...
VI  - 66
DP  - 1990
TI  - Purification and characterization of restriction endonuclease BcoI from a soil isolate of Bacillus coagulans.
PG  - 153-156
AB  - A soil isolate identified as Bacillus coagulans is found to produce BcoI, an
      isoschizomer of AvaI and with the same cleavage site.  This thermostable
      enzyme, BcoI, is produced at high level and can be isolated by passing the
      crude bacterial lysate through a DEAE-cellulose column.
AU  - Leung SM
AU  - Kam KM
AU  - Chan KY
AU  - Shaw PC
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1990 66: 153-156.

PMID- 27231376
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Mycobacterium interjectum Strain ATCC 51457T.
PG  - e00452-16
AB  - Mycobacterium interjectum is a nontuberculosis species rarely responsible for human infection.
      The draft genome of M. interjectum ATCC 51457(T) comprises
      5,927,979 bp, exhibiting 67.91% G+C content, 5,314 protein-coding genes, and 51
      predicted RNA genes.
AU  - Levasseur A
AU  - Asmar S
AU  - Robert C
AU  - Drancourt M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00452-16.

PMID- 27231371
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Mycobacterium houstonense Strain ATCC 49403T.
PG  - e00443-16
AB  - Mycobacterium houstonense is a nontuberculous species rarely responsible for human infection.
      The draft genome of M. houstonense ATCC 49403(T) comprises
      6,451,020 bp, exhibiting a 66.96% G+C content, 5,881 protein-coding genes, and 65
      predicted RNA genes.
AU  - Levasseur A
AU  - Asmar S
AU  - Robert C
AU  - Drancourt M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00443-16.

PMID- 15305924
VI  - 6
DP  - 2004
TI  - Phylogeny-function analysis of (meta)genomic libraries: screening for expression of ribosomal RNA genes by large-insert library fluorescent in situ hybridization (LIL-FISH).
PG  - 990-998
AB  - We assessed the utility of fluorescent in situ hybridization (FISH) in the
      screening of clone libraries of (meta)genomic or environmental DNA for the
      presence and expression of bacterial ribosomal RNA (rRNA) genes. To
      establish proof-of-principle, we constructed a fosmid-based library in
      Escherichia coli of large-sized genomic DNA fragments of the mycophagous
      soil bacterium Collimonas fungivorans, and hybridized 768 library clones
      with the Collimonas-specific fluorescent probe CTE998-1015. Critical to
      the success of this approach (which we refer to as large-insert library
      FISH or LIL-FISH) was the ability to induce fosmid copy number, the
      exponential growth status of library clones in the FISH assay and the use
      of a simple pooling strategy to reduce the number of hybridizations.
      Twelve out of 768 E. coli clones were suspected to harbour and express
      Collimonas 16S rRNA genes based on their hybridization to CTE998-1015.
      This was confirmed by the finding that all 12 clones were also identified
      in an independent polymerase chain reaction-based screening of the same
      768 clones using a primer set for the specific detection of Collimonas 16S
      ribosomal DNA (rDNA). Fosmids isolated from these clones were grouped by
      restriction analysis into two distinct contigs, confirming that C.
      fungivorans harbours at least two 16S rRNA genes. For one contig,
      representing 1-2% of the genome, the nucleotide sequence was determined,
      providing us with a narrow but informative view of Collimonas genome
      structure and content.
AU  - Leveau JH
AU  - Gerards S
AU  - de Boer W
AU  - van Veen JA
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2004 6: 990-998.

PMID- 
VI  - 0
DP  - 1986
TI  - Restriction-modification immunity and the maintenance of genetic diversity in bacterial populations.
PG  - 669-688
AB  - A simple model is presented of the population dynamics of phage and bacteria
      with restriction-modification immunity.  The analysis of this model suggests
      that: i) in phage-limited communities of bacteria, there are broad conditions
      under which this type of immune system will maintain clonal diversity via
      frequency-dependent selection that favors rare restriction-modification types;
      and ii) when phage-resistant bacteria are present and the community is limited
      by resources, the conditions for this mechanism to maintain clonal diversity
      are much narrower.  Reviewing that which is known about the genetic structure
      of natural populations of E. coli and the population biology of bacteriophage,
      the proposition is evaluated that this type of phage-mediated,
      frequency-dependent selection is responsible for maintaining the considerable
      chromosomal gene and plasmid diversity found in this bacterial species.
      Finally, the analogy is considered between this type of phage-mediated
      selection on restriction-modification diversity and that postulated earlier for
      parasite-mediated, frequency-dependent selection maintaining antigenic
      diversity in vertebrates.
AU  - Levin BR
PT  - Journal Article
TA  - Evolutionary Processes and Theory
JT  - Evolutionary Processes and Theory
SO  - Evolutionary Processes and Theory 1986 0: 669-688.

PMID- Not included in PubMed...
VI  - 7
DP  - 1989
TI  - Low frequency restriction enzymes in pulsed field electrophoresis.
PG  - 1033-1036
AB  - None
AU  - Levine JD
AU  - Cech CL
PT  - Journal Article
TA  - Biotechnology
JT  - Biotechnology
SO  - Biotechnology 1989 7: 1033-1036.

PMID- 17567566
VI  - 21
DP  - 2007
TI  - Plastic cells and populations: DNA substrate characteristics in Helicobacter pylori transformation define a flexible but conservative system for genomic variation.
PG  - 3458-3467
AB  - Helicobacter pylori, bacteria that colonize the human gastric mucosa, are naturally competent
      for transformation by exogenous DNA, and show a
      panmictic population structure. To understand the mechanisms involved
      in its horizontal gene transfer, we sought to define the interval
      required from exposure to substrate DNA until DNA uptake and expression
      of a selectable phenotype, as well as the relationship of transforming
      fragment length, concentration, homology, symmetry, and strandedness,
      to the transformation frequency. We provide evidence that natural
      transformation in H. pylori differs in efficiency among wild-type
      strains but is saturable and varies with substrate DNA length,
      symmetry, strandedness, and species origin. We show that H. pylori
      cells can be transformed within one minute of contact with DNA, by DNA
      fragments as small as 50 bp, and as few as 5 bp on one flank of a
      selectable single nucleotide mutation is sufficient substrate for
      recombination of a transforming fragment, and that double-stranded DNA
      is the preferred (1000-fold > single-stranded) substrate. The high
      efficiency of double-stranded DNA as transformation substrate, in
      conjunction with strain-specific restriction endonucleases suggests a
      model of short-fragment recombination favoring closest relatives,
      consistent with the observed H. pylori population biology.
AU  - Levine SM
AU  - Lin EA
AU  - Emara W
AU  - Kang J
AU  - DiBenedetto M
AU  - Ando T
AU  - Falush D
AU  - Blaser MJ
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 2007 21: 3458-3467.

PMID- 1691706
VI  - 9
DP  - 1990
TI  - The optional E. coli prr locus encodes a latent form of phage T4-induced anticodon nuclease.
PG  - 1383-1389
AB  - The optional Escherichia coli prr locus restricts phage T4 mutants lacking polynucleotide
      kinase or RNA ligase.  Underlying this restriction is the specific manifestation of the
      T4-induced anticodon nuclease, an enzyme which triggers the cleavage-ligation of the host
      tRNALys.  We report here the molecular cloning, nucleotide sequence and mutational analysis of
      prr-associated DNA.  The results indicate that prr encodes a latent form of anticodon nuclease
      consisting of a core enzyme and cognate masking agents.  They suggest that the T4-encoded
      factors of anticodon nuclease counteract the prr-encoded masking agents, thus activating the
      latent enzyme.  The encoding of a tRNA cleavage-ligation pathway by two separate genetic
      systems which cohabitate E. coli may provide a clue to the evolution of RNA splicing
      mechanisms mediated by proteins.
AU  - Levitz R
AU  - Chapman D
AU  - Amitsur M
AU  - Green R
AU  - Snyder L
AU  - Kaufmann G
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1990 9: 1383-1389.

PMID- 7225321
VI  - 20
DP  - 1981
TI  - Deoxyribonucleic acid modification methylase from Bacillus stearothermophilus.
PG  - 1120-1127
AB  - A modification methylase was isolated from Bacillus stearothermophilus 1503-4R
      (Bst153I) and purified to homogeneity.  The enzyme is an acidic protein and
      composed of a subunit with a molecular weight of 105000, and only the
      tetrameric form was detected in solution.  The methylase exhibited maximal
      activity between 54 and 61C and between pH 8.1 and 9.3.  In contrast to
      Bst1503I endonuclease [Catterall, J.F., & Welker, N.E. (1977) J. Bacteriol.
      129: 1110-1120], the methylase is completely inactivated when exposed to
      temperatures near the optimal growth temperature (63-67C).  The methylase was
      also inactivated when exposed to temperatures below the minimal growth
      temperature (48-53C).  The thermostability of the methylase is significantly
      enhanced by Na+, K+, or NH4+.  Membrane-bound methylase is resistant to heat
      inactivation at temperatures near the maximum growth temperature (73-75C).  The
      methylase functions as a tetramer.  The initial rates of methyl transfer are
      first order in methylase concentration, and the enzyme obeys Michaelis-Menten
      kinetics with respect to DNA but not to S-adenosyl-L-methionine.
AU  - Levy WP
AU  - Welker NE
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1981 20: 1120-1127.

PMID- Not included in PubMed...
VI  - 37
DP  - 1978
TI  - Purification and properties of a modification methylase from Bacillus stearothermophilus (Meth M.Bst 1503).
PG  - 1414
AB  - A modification methylase has been isolated from B. stearothermophilus 1503-4R
      Res+Mod+ (Math M.Bst 1503) and purified 500 fold from sonicated protoplasts
      using ammonium sulfate fractionation, Bio Gel A5m gel filtration and
      DEAE-cellulose ion exhange column chromatography.  Incurbation of Meth M.Pst
      1503 with various DNA substrates in the presence of S-adenosyl methionine
      protects these substrates from the action of Endo R.Bst 1503.  Meth M.Bst 1503
      has an apparent molecular weight between 400,000-450,000 daltons.  A single
      protein staining band with a molecular weight of between 90,000-100,000 daltons
      is obtained when the enzyme is analyzed by SDS polyacrylamide gel
      electrohoresis.  Meth M.Bst 1503 does not exhibit restriction endonuclease
      activity.  The enzyme in 50% glycerol can be stored at -25C for at least 3
      weeks with no detectable loss of activity.  Data are presented which indicate
      that Endo R.Bst 1503 and Meth M.Bst 1503 do not share a common polypeptide.
      Temperature and pH profiles of enzymatic activity were determined.
AU  - Levy WP
AU  - Welker NE
PT  - Journal Article
TA  - Fed. Proc.
JT  - Fed. Proc.
SO  - Fed. Proc. 1978 37: 1414.

PMID- 27688328
VI  - 4
DP  - 2016
TI  - Genome Sequences of 11 Human Vaginal Actinobacteria Strains.
PG  - e00887-16
AB  - The composition of the vaginal microbiota is an important health determinant. Several members
      of the phylum Actinobacteria have been implicated in bacterial
      vaginosis, a condition associated with many negative health outcomes. Here, we
      present 11 strains of vaginal Actinobacteria (now available through BEI
      Resources) along with draft genome sequences.
AU  - Lewis AL
AU  - Deitzler GE
AU  - Ruiz MJ
AU  - Weimer C
AU  - Park S
AU  - Robinson LS
AU  - Hallsworth-Pepin K
AU  - Wollam A
AU  - Mitreva M
AU  - Lewis WG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00887-16.

PMID- 16289630
VI  - 363
DP  - 2005
TI  - Use of a restriction endonuclease cytotoxicity assay to identify inducible GAL1 promoter variants with reduced basal activity - for use  in fucntional genomics.
PG  - 183-192
AB  - Inducible promoter fusions are commonly employed to study the biological functions of genes as
      well as to investigate mechanisms of transcription regulation. A concern for many studies of
      heterologous gene expression is that steady state transcription may be too high under
      non-inducing conditions, producing undesired phenotypes prior to induction. Fusions containing
      the galactose-inducible GAL1 promoter joined to PvuII, a bacterial DNA endonuclease gene, are
      toxic to yeast cells even under non-inducing conditions, i.e., in glucose media. This toxicity
      was utilized in conjunction with PCR-based mutagenesis of the GAL1 regulatory region to
      isolate mutant promoters that retained high inducibility but exhibited reduced basal level
      expression. The Mig1 repressor binding and putative TATA box regions were unchanged among four
      mutant promoters examined in detail. However, each promoter contained one or more mutations
      within previously identified binding sites for the Gal4 activator protein. Genetic assays
      developed to monitor GAL1p::I-SceI endonuclease-induced recombination demonstrated that basal
      expression from two of the new promoters (designated GAL1-V4 and GAL1-V10) was strongly
      reduced. These experiments and additional quantitative luciferase reporter gene assays
      demonstrate the utility of the approach for identifying promoters that permit more tightly
      controlled gene expression.
AU  - Lewis LK
AU  - Lobachev K
AU  - Westmoreland JW
AU  - Karthikeyan G
AU  - Williamson KMJJJ
AU  - Resnick MA
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 2005 363: 183-192.

PMID- 21079689
VI  - 6
DP  - 2010
TI  - DNA Methylation and Normal Chromosome Behavior in Neurospora Depend on Five Components of a Histone Methyltransferase Complex, DCDC.
PG  - e1001196
AB  - Methylation of DNA and of Lysine 9 on histone H3 (H3K9) is associated with gene silencing in
      many animals, plants, and fungi. In Neurospora
      crassa, methylation of H3K9 by DIM-5 directs cytosine methylation by
      recruiting a complex containing Heterochromatin Protein-1 (HP1) and the
      DIM-2 DNA methyltransferase. We report genetic, proteomic, and
      biochemical investigations into how DIM-5 is controlled. These studies
      revealed DCDC, a previously unknown protein complex including DIM-5,
      DIM-7, DIM-9, CUL4, and DDB1. Components of DCDC are required for
      H3K9me3, proper chromosome segregation, and DNA methylation.
      DCDC-defective strains, but not HP1-defective strains, are
      hypersensitive to MMS, revealing an HP1-independent function of H3K9
      methylation. In addition to DDB1, DIM-7, and the WD40 domain protein
      DIM-9, other presumptive DCAFs (DDB1/CUL4 associated factors)
      co-purified with CUL4, suggesting that CUL4/DDB1 forms multiple
      complexes with distinct functions. This conclusion was supported by
      results of drug sensitivity tests. CUL4, DDB1, and DIM-9 are not
      required for localization of DIM-5 to incipient heterochromatin
      domains, indicating that recruitment of DIM-5 to chromatin is not
      sufficient to direct H3K9me3. DIM-7 is required for DIM-5 localization
      and mediates interaction of DIM-5 with DDB1/CUL4 through DIM-9. These
      data support a two-step mechanism for H3K9 methylation in Neurospora.
AU  - Lewis ZA
AU  - Adhvaryu KK
AU  - Honda S
AU  - Shiver AL
AU  - Knip M
AU  - Sack R
AU  - Selker EU
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2010 6: e1001196.

PMID- 23012292
VI  - 194
DP  - 2012
TI  - Genome Sequence of a Highly Efficient Aerobic Denitrifying Bacterium, Pseudomonas stutzeri T13.
PG  - 5720
AB  - Pseudomonas stutzeri T13 is a highly efficient aerobic denitrifying bacterium. Information
      about the genome of this aerobic denitrifying bacterium has been
      limited until now. We present the draft genome of P. stutzeri T13. The results
      could provide further insight into the aerobic denitrification mechanism in
      strain T13.
AU  - Li A
AU  - Gai Z
AU  - Cui D
AU  - Ma F
AU  - Yang J
AU  - Zhang X
AU  - Sun Y
AU  - Ren N
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5720.

PMID- 21914861
VI  - 193
DP  - 2011
TI  - Genome Sequence of Agrobacterium tumefaciens Strain F2, a Bioflocculant-Producing Bacterium.
PG  - 5531
AB  - Agrobacterium tumefaciens F2 is an efficient bioflocculant-producing bacterium. But the genes
      related to the metabolic pathway of bioflocculant
      biosynthesis in strain F2 are unknown. We present the draft genome of A.
      tumefaciens F2. It could provide further insight into the biosynthetic
      mechanism of polysaccharide-like bioflocculant in strain F2.
AU  - Li A
AU  - Geng J
AU  - Cui D
AU  - Shu C
AU  - Zhang S
AU  - Yang J
AU  - Xing J
AU  - Wang J
AU  - Ma F
AU  - Hu S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5531.

PMID- 28495782
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Staphylococcus fleurettii Strain MBTS-1 Isolated from Cucumber.
PG  - e00335-17
AB  - The draft genome of Staphylococcus fleurettii MBTS-1, isolated from cucumber in northern
      Germany, was sequenced. Analysis showed that the assembled genome had a
      size of 2,582,128 bp with a predicted total of 2,491 protein-encoding genes, 9
      rRNAs, 5 ncRNAs, and 44 tRNAs. This strain did not contain plasmid DNA.
AU  - Li B
AU  - Brinks E
AU  - Franz CMAP
AU  - Cho GS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00335-17.

PMID- 21914875
VI  - 193
DP  - 2011
TI  - Complete Genome Analysis of Sulfobacillus acidophilus Strain TPY, Isolated from a Hydrothermal Vent in the Pacific Ocean.
PG  - 5555-5556
AB  - Sulfobacillus acidophilus strain TPY is a moderately thermoacidophilic bacterium originally
      isolated from a hydrothermal vent in the Pacific
      Ocean. Ferrous iron and sulfur oxidation in acidic environments in strain
      TPY have been confirmed. Here we report the genome sequence and annotation
      of the strain TPY, which is the first complete genome of Sulfobacillus
      acidophilus.
AU  - Li B
AU  - Chen Y
AU  - Liu Q
AU  - Hu S
AU  - Chen X
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5555-5556.

PMID- 22843587
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Rice Pathogen Dickeya zeae Strain ZJU1202.
PG  - 4452-4453
AB  - Dickeya zeae is a phytopathogenic bacterium causing soft rot diseases in a wide range of
      economically important crops. Here we present the draft genome sequence
      of strain ZJU1202, which is the causal agent of rice foot rot in China. The draft
      genome will contribute to epidemiological and comparative genomic studies and the
      quarantine of this devastating phytopathogen.
AU  - Li B
AU  - Shi Y
AU  - Ibrahim M
AU  - Liu H
AU  - Shan C
AU  - Wang Y
AU  - Kube M
AU  - Xie GL
AU  - Sun G
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4452-4453.

PMID- 29712658
VI  - 0
DP  - 2018
TI  - Determination of MIC Distribution and Mechanisms of Decreased Susceptibility to Bedaquiline Among Clinical Isolates of Mycobacterium abscessus.
PG  - AAC.00175-18
AB  - Chemotherapeutic options are very limited against Mycobacterium abscessus infections.
      Bedaquiline, a new anti-tuberculosis drug, is effective for the
      treatment of multidrug-resistant TB. However, little data is available on
      bedaquiline in treating M. abscessus infections. In this study, we reported the
      in vitro susceptibility profile of M. abscessus clinical isolates to bedaquiline
      and investigated the potential molecular mechanisms of decreased susceptibility.
      A total of 197 M. abscessus clinical isolates were collected from sputum and
      bronchoalveolar fluid of patients with lung infections. Standard broth
      microdilution test revealed that bedaquiline exhibited high in vitro killing
      activity against M. abscessus isolates, with MIC50 of 0.062 and MIC90 of 0.125
      mg/L. Whole genome sequencing data showed that no nonsynonymous mutation occurred
      in atpE, the gene encoding the bedaquiline targeted protein. However, of 6
      strains with decreased susceptibility of bedaquiline (MIC=0.5-1 mg/L), 3 strains
      had nonsynonymous mutations in mab_4384, the gene encoding the repressor of
      efflux pump MmpS5/MmpL5. qRT-PCR analysis showed that the expression of
      MmpS5/MmpL5 in the group with decreased susceptibility to bedaquiline were
      significantly higher than those with medium MIC (MIC=0.125-0.5 mg/L) or low MIC
      group (MIC</= 0.062 mg/L). Two isolates with increased MIC didn't show
      overexpression of MmpS5/MmpL5, which couldn't be explained by known molecular
      mechanisms. This is the first report showing the association of MmpS5/MmpL5 with
      decreased bedaquiline susceptibility in M. abscessus clinical isolates, and
      suggesting the presence of other yet-to-be identified mechanisms for decreased
      bedaquiline susceptibility in M. abscessus.
AU  - Li B
AU  - Ye M
AU  - Guo Q
AU  - Zhang Z
AU  - Yang S
AU  - Ma W
AU  - Yu F
AU  - Chu H
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2018 0: AAC.00175-18.

PMID- 19747395
VI  - 10
DP  - 2009
TI  - ICRPfinder: a fast pattern design algorithm for coding sequences and its application in finding potential restriction enzyme recognition sites.
PG  - 286
AB  - Background: Restriction enzymes can produce easily definable segments from DNA sequences by
      using a variety of cut patterns. There are,
      however, no software tools that can aid in gene building - that is,
      modifying wild-type DNA sequences to express the same wild-type amino
      acid sequences but with enhanced codons, specific cut sites, unique
      post-translational modifications, and other engineered-in components
      for recombinant applications. A fast DNA pattern design algorithm,
      ICRPfinder, is provided in this paper and applied to find or create
      potential recognition sites in target coding sequences.
      Results: ICRPfinder is applied to find or create restriction enzyme
      recognition sites by introducing silent mutations. The algorithm is
      shown capable of mapping existing cut-sites but importantly it also can
      generate specified new unique cut-sites within a specified region that
      are guaranteed not to be present elsewhere in the DNA sequence.
      Conclusion: ICRPfinder is a powerful tool for finding or creating
      specific DNA patterns in a given target coding sequence. ICRPfinder
      finds or creates patterns, which can include restriction enzyme
      recognition sites, without changing the translated protein sequence.
      ICRPfinder is a browser-based JavaScript application and it can run on
      any platform, in on-line or off-line mode.
AU  - Li C
AU  - Li YH
AU  - Zhang XM
AU  - Stafford P
AU  - Dinu V
PT  - Journal Article
TA  - BMC Bioinformatics
JT  - BMC Bioinformatics
SO  - BMC Bioinformatics 2009 10: 286.

PMID- 29097469
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Clostridium perfringens LLY_N11, a Necrotic Enteritis-Inducing Strain Isolated from a Healthy Chicken Intestine.
PG  - e01225-17
AB  - Clostridium perfringens strain LLY_N11, a commensal bacterium, which previously induced
      necrotic enteritis in an experimental study, was isolated from the
      intestine of a young healthy chicken. Here, we present the complete genome
      sequence of this strain, which may provide a better understanding of the
      molecular mechanisms involved in necrotic enteritis pathogenesis.
AU  - Li C
AU  - Yan X
AU  - Lillehoj HS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01225-17.

PMID- 24029756
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Thermoanaerobacter sp. Strain A7A, Reconstructed from a  Metagenome Obtained from a High-Temperature Hydrocarbon Reservoir in the Bass  Strait, Australia.
PG  - e00701-13
AB  - The draft genome sequence of Thermoanaerobacter sp. strain A7A was reconstructed  from a
      metagenome of a microbial consortium obtained from the Tuna oil field in
      the Gippsland Basin, Australia. The organism is a strict anaerobe that is
      predicted to ferment a range of simple sugars and undertake sulfur reduction.
AU  - Li D
AU  - Greenfield P
AU  - Rosewarne CP
AU  - Midgley DJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00701-13.

PMID- 8247133
VI  - 366
DP  - 1993
TI  - Role for DNA methylation in genomic imprinting.
PG  - 362-366
AB  - The paternal and maternal genomes are not equivalent and both are required for mammalian
      development. The difference between the parental genomes is believed to be due to
      gametespecific differential modification, a process known as genomic imprinting. The study of
      transgene methylation has shown that methylation patterns can be inherited in a
      parent-of-origin-specific manner, suggesting that DNA mthylation may play a role in genomic
      imprinting. The functional significance of DNA methylation in genomic imprinting was
      strengthened by the recent finding that CpG islands (or sites) in three imprinted genes, H19,
      insulin-like growth factor 2 (Igf-2), and Igf-2 receptor (Igf-2r), are differentially
      methylated depending on their parental origin. We have examined the expression of these three
      imprinted genes in mutant mice that are deficient in DNA methyltransferase activity. We report
      here that expression of all three genes was affected in mutant embryos: the normally silent
      paternal allele of the H19 gene was activated, whereas the normally active paternal allele of
      the Igf-2 gene and the active maternal allele of the Igf-2r gene were repressed. Our results
      demonstrate that a normal level of DNA methylation is required for controlling differential
      expression of the paternal and maternal alleles of imprinted genes.
AU  - Li E
AU  - Beard C
AU  - Jaenisch R
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1993 366: 362-366.

PMID- 1606615
VI  - 69
DP  - 1992
TI  - Targeted mutation of the DNA methyltransferase gene results in embryonic lethality.
PG  - 915-926
AB  - Gene targeting in embryonic stem (ES) cells has been used to mutate the murine DNA
      methyltransferase gene. ES cell lines homozygous for the mutation were generated by
      consecutive targeting of both wild-type alleles; the mutant cells were viable and showed no
      obvious abnormalities with respect to growth rate or morphology, and had only trace levels of
      DNA methyltransferase activity. A quantitative end-labeling assay showed that the level of m5C
      in the DNA of homozygous mutant cells was about one-third that of wild-type cells, and
      Southern blot analysis after cleavage of the DNA with a methylation-sensitive restriction
      endonuclease revealed substantial demethylation of endogenous retroviral DNA. The mutation was
      introduced into the germline of mice and found to cause a recessive lethal phenotype.
      Homozygous embryos were stunted, delayed in development, and did not survive past
      mid-gestation. The DNA of homozygous embryos showed a reduction of the level of m5C similar to
      that of homozygous ES cells. These results indicate that while a 3-fold reduction in levels of
      genomic m5C has no detectable effect on the viability or proliferation of ES cells in culture,
      a similar reduction of DNA methylation in embryos causes abnormal development and embryonic
      lethality.
AU  - Li E
AU  - Bestor TH
AU  - Jaenisch R
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1992 69: 915-926.

PMID- 21551298
VI  - 193
DP  - 2011
TI  - Draft Genome Sequence of Marine bacterium Streptomyces griseoaurantiacus M045, which produces Novel Manumycin-type Antibiotics with a pABA Core Component.
PG  - 3417-3418
AB  - Streptomyces griseoaurantiacus M045 isolated from marine sediment produces manumycin and
      chinikomycin antibiotics. Here we present a high-quality
      draft genome sequence of S. griseoaurantiacus M045, the first marine
      Streptomyces species to be sequenced and annotated. The genome encodes
      several gene clusters for biosynthesis of secondary metabolites and has
      provided insight into genomic islands linking secondary metabolism to
      functional adaptation in marine S. griseoaurantiacus M045.
AU  - Li F
AU  - Jiang P
AU  - Zheng H
AU  - Wang S
AU  - Zhao G
AU  - Qin S
AU  - Liu Z
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3417-3418.

PMID- 17151075
VI  - 35
DP  - 2007
TI  - Chimeric DNA methyltransferases target DNA methylation to specific DNA sequences and repress expression of target genes.
PG  - 100-112
AB  - Gene silencing by targeted DNA methylation has potential applications in basic research and
      therapy. To establish targeted methylation in human
      cell lines, the catalytic domains (CDs) of mouse Dnmt3a and Dnmt3b DNA
      methyltransferases (MTases) were fused to different DNA binding domains
      (DBD) of GAL4 and an engineered Cys2His2 zinc finger domain. We
      demonstrated that (i) Dense DNA methylation can be targeted to specific
      regions in gene promoters using chimeric DNA MTases. (ii) Site-specific
      methylation leads to repression of genes controlled by various cellular or
      viral promoters. (iii) Mutations affecting any of the DBD, MTase or target
      DNA sequences reduce targeted methylation and gene silencing. (iv)
      Targeted DNA methylation is effective in repressing Herpes Simplex Virus
      type 1 (HSV-1) infection in cell culture with the viral titer reduced by
      at least 18-fold in the presence of an MTase fused to an engineered zinc
      finger DBD, which binds a single site in the promoter of HSV-1 gene
      IE175k. In short, we show here that it is possible to direct DNA MTase
      activity to predetermined sites in DNA, achieve targeted gene silencing in
      mammalian cell lines and interfere with HSV-1 propagation.
AU  - Li F
AU  - Papworth M
AU  - Minczuk M
AU  - Rohde C
AU  - Zhang Y
AU  - Ragozin S
AU  - Jeltsch A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2007 35: 100-112.

PMID- 22628517
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Streptococcus pneumoniae Strain ST556, a Multidrug-Resistant Isolate from an Otitis Media Patient.
PG  - 3294-3295
AB  - Streptococcus pneumoniae is a major pathogen causing bacterial infection in the middle ear of
      humans. We previously used S. pneumoniae strain ST556, a
      low-passage 19F isolate from an otitis media patient, to perform a whole-genome
      screen for ear infection-associated genes in a chinchilla model. This report
      presents the complete genome sequence of ST556. The genome sequence will provide
      information complementary to the experimental data from our genetic study of this
      strain.
AU  - Li G
AU  - Hu FZ
AU  - Yang X
AU  - Cui Y
AU  - Yang J
AU  - Qu F
AU  - Gao GF
AU  - Zhang JR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3294-3295.

PMID- 26893434
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Pseudomonas aeruginosa Phage-Resistant Variant PA1RG.
PG  - e01761-15
AB  - Bacteria have evolved several defense systems against phage predation. Here, we report the
      6,500,439-bp complete genome sequence of the Pseudomonas aeruginosa
      phage-resistant variant PA1RG. Single-molecule real-time (SMRT) sequencing and de
      novo assembly revealed a single contig with 320-fold sequence coverage.
AU  - Li G
AU  - Lu S
AU  - Shen M
AU  - Le S
AU  - Tan Y
AU  - Li M
AU  - Zhao X
AU  - Wang J
AU  - Shen W
AU  - Guo K
AU  - Yang Y
AU  - Zhu H
AU  - Li S
AU  - Zhu J
AU  - Rao X
AU  - Hu F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01761-15.

PMID- 24072867
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Vibrio anguillarum M3, a Serotype O1 Strain Isolated  from Japanese Flounder in China.
PG  - e00769-13
AB  - Vibrio anguillarum is an important bacterial pathogen that causes vibriosis in marine fish. We
      present the complete genome sequence of V. anguillarum M3, a
      serotype O1 clinical strain isolated from Japanese flounder (Paralichthys
      olivaceus) in Shandong, China.
AU  - Li G
AU  - Mo Z
AU  - Li J
AU  - Xiao P
AU  - Hao B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00769-13.

PMID- 23144372
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Actinobacillus pleuropneumoniae Serotype 7 Strain S-8.
PG  - 6606-6607
AB  - The Gram-negative bacterium Actinobacillus pleuropneumoniae is the etiological agent of
      porcine pleuropneumonia, a respiratory disease that leads to severe
      economic losses in the swine industry. For years, scientists working with it have
      lacked a reliable genome sequence for comparison with other Actinobacillus
      species. Here, we report the draft genome sequence of A. pleuropneumoniae
      serotype 7 (strain S-8), isolated from swine lung in China in 1992.
AU  - Li G
AU  - Xie F
AU  - Zhang Y
AU  - Wang C
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6606-6607.

PMID- 26868397
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Sphingomonas sp. WG, a Welan Gum-Producing Strain.
PG  - e01709-15
AB  - We report the draft genome sequence of Sphingomonas sp. WG, a high welan gum-producing strain
      with a yield of 33 g/L. The core of wel cluster for welan
      gum biosynthesis contained 24 coding sequences in the genome, which will provide
      the genetic information on welan gum production.
AU  - Li H
AU  - Feng ZM
AU  - Sun YJ
AU  - Zhou WL
AU  - Jiao X
AU  - Zhu H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01709-15.

PMID- 19153140
VI  - 37
DP  - 2009
TI  - Generation of single-chain LAGLIDADG homing endonucleases from native homodimeric precursor proteins.
PG  - 1650-1662
AB  - Homing endonucleases (HEs) cut long DNA target sites with high specificity to initiate and
      target the lateral transfer of mobile introns or inteins.
      This high site specificity of HEs makes them attractive reagents for gene
      targeting to promote DNA modification or repair. We have generated several
      hundred catalytically active, monomerized versions of the
      well-characterized homodimeric I-CreI and I-MsoI LAGLIDADG family homing
      endonuclease (LHE) proteins. Representative monomerized I-CreI and I-MsoI
      proteins (collectively termed mCreIs or mMsoIs) were characterized in
      detail by using a combination of biochemical, biophysical and structural
      approaches. We also demonstrated that both mCreI and mMsoI proteins can
      promote cleavage-dependent recombination in human cells. The use of single
      chain LHEs should simplify gene modification and targeting by requiring
      the expression of a single small protein in cells, rather than the
      coordinate expression of two separate protein coding genes as is required
      when using engineered heterodimeric zinc finger or homing endonuclease
      proteins.
AU  - Li H
AU  - Pellenz S
AU  - Ulge U
AU  - Stoddard BL
AU  - Monnat RJ Jr
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: 1650-1662.

PMID- 23105078
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Bartonella quintana, a Bacterium Isolated from Rhesus Macaques.
PG  - 6347
AB  - Bartonella quintana is a re-emerging pathogen and the causative agent of a broad  spectrum of
      disease manifestations in humans. The present study reports the
      complete genome of B. quintana strain RM_11, which was isolated from rhesus
      macaques.
AU  - Li H
AU  - Tong Y
AU  - Huang Y
AU  - Bai J
AU  - Yang H
AU  - Liu W
AU  - Cao W
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6347.

PMID- 22121229
VI  - 40
DP  - 2012
TI  - Comprehensive homing endonuclease target site specificity profiling reveals evolutionary constraints and enables genome engineering applications.
PG  - 2587-2598
AB  - Homing endonucleases (HEs) promote the evolutionary persistence of selfish DNA elements by
      catalyzing element lateral transfer into new host organisms. The high
      site specificity of this lateral transfer reaction, termed homing, reflects both
      the length (14-40 bp) and the limited tolerance of target or homing sites for
      base pair changes. In order to better understand molecular determinants of
      homing, we systematically determined the binding and cleavage properties of all
      single base pair variant target sites of the canonical LAGLIDADG homing
      endonucleases I-CreI and I-MsoI. These Chlorophyta algal HEs have very similar
      three-dimensional folds and recognize nearly identical 22 bp target sites, but
      use substantially different sets of DNA-protein contacts to mediate site-specific
      recognition and cleavage. The site specificity differences between I-CreI and
      I-MsoI suggest different evolutionary strategies for HE persistence. These
      differences also provide practical guidance in target site finding, and in the
      generation of HE variants with high site specificity and cleavage activity, to
      enable genome engineering applications.
AU  - Li H
AU  - Ulge UY
AU  - Hovde BT
AU  - Doyle LA
AU  - Monnat RJ Jr
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: 2587-2598.

PMID- 25523768
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of New Bacillus cereus Strain tsu1.
PG  - e01294-14
AB  - This paper reports the draft genome sequence of new Bacillus cereus strain tsu1,  isolated on
      an agar-cellulose plate. The draft genome sequence is 5.81 Mb,
      revealing 5,673 coding sequences. It contains genes for cellulose-degradation and
      biosynthesis pathways of polyhydroxybutyrate (PHB) and 8 rRNA genes (5S, 16S, and
      23S).
AU  - Li H
AU  - Zhou S
AU  - Johnson T
AU  - Vercruysse K
AU  - Ropelewski AJ
AU  - Thannhauser TW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01294-14.

PMID- 28729260
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Polysaccharide-Degrading Marine Bacterium Pseudoalteromonas sp. Strain A601.
PG  - e00590-17
AB  - Pseudoalteromonas sp. strain A601 is a marine bacterium with excellent
      polysaccharide-degrading capabilities. Here, we present a high-quality draft
      genome sequence of strain A601 with a size of approximately 4.89 Mb and a mean
      G+C content of 40.0%. Various putative polysaccharide-degrading genes were found
      in the draft genome.
AU  - Li J
AU  - Cheng Y
AU  - Wang D
AU  - Li J
AU  - Wang Y
AU  - Han W
AU  - Li F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00590-17.

PMID- 29046739
VI  - 12
DP  - 2017
TI  - High-quality-draft genomic sequence of Paenibacillus ferrarius CY1T with the potential to bioremediate Cd, Cr and Se contamination.
PG  - 60
AB  - Paenibacillus ferrarius CY1T (= KCTC 33419T = CCTCC AB2013369T) is a Gram-positive, aerobic,
      endospore-forming, motile and rod-shaped bacterium
      isolated from iron mineral soil. This bacterium reduces sulfate (SO42-) to S2-,
      which reacts with Cd(II) to generate precipitated CdS. It also reduces the toxic
      chromate [Cr(VI)] and selenite [Se(VI)] to the less bioavailable chromite
      [Cr(III)] and selenium (Se0), respectively. Thus, strain CY1T has the potential
      to bioremediate Cd, Cr and Se contamination, which is the main reason for the
      interest in sequencing its genome. Here we describe the features of strain CY1T,
      together with the draft genome sequence and its annotation. The 9,184,169 bp long
      genome exhibits a G + C content of 45.6%, 7909 protein-coding genes and 81 RNA
      genes. Nine putative Se(IV)-reducing genes, five putative Cr(VI) reductase and
      nine putative sulfate-reducing genes were identified in the genome.
AU  - Li J
AU  - Guo W
AU  - Shi M
AU  - Cao Y
AU  - Wang G
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 60.

PMID- 24594606
VI  - 9
DP  - 2014
TI  - Sequential Isolation in a Patient of Raoultella planticola and Escherichia coli Bearing a Novel ISCR1 Element Carrying blaNDM-1.
PG  - E89893
AB  - BACKGROUND: The gene for New Delhi metallo-beta-lactamase 1 (NDM-1) has been
      reported to be transmitted via plasmids which are easily transferable and capable
      of wide distribution. We report the isolation of two NDM-1 producing strains and
      possible in vivo transfer of blaNDM-1 in a patient. METHODS: Clinical samples
      were collected for bacterial culture and antibiotic susceptibility testing from a
      patient during a 34-day hospitalization. The presence of blaNDM-1 was detected by
      PCR and sequencing. Plasmids of interest were sequenced. Medical records were
      reviewed for evidence of association between the administration of antibiotics
      and the acquisition of the NDM-1 resistance. RESULTS: A NDM-1 positive Raoultella
      planticola was isolated from blood on the ninth day of hospitalization without
      administration of any carbapenem antibiotics and a NDM-1 positive Escherichia
      coli was isolated from feces on the 29th day of hospitalization and eight days
      after imipenem administration. The blaNDM-1 was carried by a 280 kb plasmid
      pRpNDM1-1 in R. planticola and a 58 kb plasmid pEcNDM1-4 in E. coli. The two
      plasmids shared a 4812 bp NDM-1-ISCR1 element which was found to be excisable
      from the plasmid as a free form and transferrable in vitro to a NDM-1 negative
      plasmid from E. coli. CONCLUSION: blaNDM-1 was embedded in an ISCR1 complex class
      1 integron as a novel 4812 bp NDM-1-ISCR1 element. The element was found to be
      able to self excise to become a free form, which may provide a new vehicle for
      NDM-1 dissemination. This mechanism could greatly accelerate the spread of NDM-1
      mediated broad spectrum beta-lactam resistance.
AU  - Li J
AU  - Lan R
AU  - Xiong Y
AU  - Ye C
AU  - Yuan M
AU  - Liu X
AU  - Chen X
AU  - Yu D
AU  - Liu B
AU  - Lin W
AU  - Bai X
AU  - Wang Y
AU  - Sun Q
AU  - Wang Y
AU  - Zhao H
AU  - Meng Q
AU  - Chen Q
AU  - Zhao A
AU  - Xu J
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2014 9: E89893.

PMID- 27427949
VI  - 12
DP  - 2016
TI  - Epigenetic Switch Driven by DNA Inversions Dictates Phase Variation in Streptococcus pneumoniae.
PG  - e1005762
AB  - DNA methylation is an important epigenetic mechanism for phenotypic diversification in all
      forms of life. We previously described remarkable
      cell-to-cell heterogeneity in epigenetic pattern within a clonal population of
      Streptococcus pneumoniae, a leading human pathogen. We here report that the
      epigenetic diversity is caused by extensive DNA inversions among hsdSA, hsdSB,
      and hsdSC, three methyltransferase hsdS genes in the Spn556II type-I restriction
      modification (R-M) locus. Because hsdSA encodes the sequence recognition subunit
      of this type-I R-M DNA methyltransferase, these site-specific recombinations
      generate pneumococcal cells with variable HsdSA alleles and thereby diverse
      genome methylation patterns. Most importantly, the DNA methylation pattern
      specified by the HsdSA1 allele leads to the formation of opaque colonies, whereas
      the pneumococci lacking HsdSA1 produce transparent colonies. Furthermore, this
      HsdSA1-dependent phase variation requires intact DNA methylase activity encoded
      by hsdM in the Spn556II (renamed colony opacity determinant or cod) locus. Thus,
      the DNA inversion-driven ON/OFF switch of the hsdSA1 allele in the cod locus and
      resulting epigenetic switch dictate the phase variation between the opaque and
      transparent phenotypes. Phase variation has been well documented for its
      importance in pneumococcal carriage and invasive infection, but its molecular
      basis remains unclear. Our work has discovered a novel epigenetic cause for this
      significant pathobiology phenomenon in S. pneumoniae. Lastly, our findings
      broadly represents a significant advancement in our understanding of bacterial
      R-M systems and their potential in shaping epigenetic and phenotypic diversity of
      the prokaryotic organisms because similar site-specific recombination systems
      widely exist in many archaeal and bacterial species.
AU  - Li J
AU  - Li JW
AU  - Feng Z
AU  - Wang J
AU  - An H
AU  - Liu Y
AU  - Wang Y
AU  - Wang K
AU  - Zhang X
AU  - Miao Z
AU  - Liang W
AU  - Sebra R
AU  - Wang G
AU  - Wang WC
AU  - Zhang JR
PT  - Journal Article
TA  - PLoS Pathog.
JT  - PLoS Pathog.
SO  - PLoS Pathog. 2016 12: e1005762.

PMID- 23704176
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Haemophilus parasuis gx033, a Serotype 4 Strain Isolated from the Swine Lower Respiratory Tract.
PG  - e00224-13
AB  - Haemophilus parasuis serotype 4 is a Gram-negative pathogen that is the most prevalent H.
      parasuis serovar in the world, but its genome sequence information
      has not yet been reported. Thus, we determined the genome of H. parasuis strain
      gx033, a serovar 4 strain isolated from a lung specimen of a diseased piglet in
      southwestern China. Here, we present the first draft genome sequence of this
      species.
AU  - Li J
AU  - Peng H
AU  - Xu LG
AU  - Xie YZ
AU  - Xuan XB
AU  - Ma CX
AU  - Hu S
AU  - Chen ZX
AU  - Yang W
AU  - Xie YP
AU  - Pan Y
AU  - Tao L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00224-13.

PMID- 17263334
VI  - 79
DP  - 2007
TI  - Hairpin fluorescence DNA probe for real-time monitoring of DNA methylation.
PG  - 1050-1056
AB  - DNA methylation catalyzed by methylase plays an important role in many biological events.
      However, traditional methods of methylase activity
      analysis by gel electrophoresis were laborious and discontinuous. In
      this paper, we report a new strategy to study methylase activity using
      fluorescent probes coupled with enzyme-linkage reactions. A hairpin DNA
      probe is prepared with a fluorophore and a quencher linked at the 5'-
      and 3'-terminus of the probe. A disturbance of the stem sequence by DNA
      methylation would cause the separation of the fluorophore and the
      quencher, resulting in the restoration of the fluorescence. We used DNA
      adenine methylation (Dam) methyltransferase (MTase) and Dpn I
      endonuclease, both having a 5'-G-A-T-C-3' recognition sequence. Dam
      MTase catalyzed the methylation of the sequence of 5'-GATC-3', and Dpn
      I cut the sequence of 5'-G-Am-T-C-3'. The fluorescence of the hairpin
      probe was restored when it was cleaved by Dpn I endonuclease during the
      course of methylation. Unlike traditional methods, this assay was done
      in real time and could be used to monitor the dynamic process of
      methylation. Our method is easy, simple, and nonradioactive, yet as
      efficient as gel electrophoresis in detecting the activity of
      methylase. It also had the potential to screen suitable inhibitor drugs
      for Dam methylase.
AU  - Li J
AU  - Yan HF
AU  - Wang KM
AU  - Tan WH
AU  - Zhou XW
PT  - Journal Article
TA  - Anal. Chem.
JT  - Anal. Chem.
SO  - Anal. Chem. 2007 79: 1050-1056.

PMID- 1909785
VI  - 19
DP  - 1991
TI  - Ssp RFI, a novel class-II restriction endonuclease from Synechococcus RF-1 recognizing 5'TT/CGAA-3' .
PG  - 4770
AB  - A novel class II restriction endonuclease has been isolated from a
      cyanobacterium Synechococcus RF-1, which shows a circadian rhythm in its
      nitrogen fixation activity, and designated as SspRFI.  The enzyme recognizes
      the palindrome 5'-TT/CGAA-3' and generates 5'-protruding CG-dinucleotides.  Its
      isoschizomers have also been isolated from Streptomyces, Bacillus,
      Lactobacillus and other cyanobacteria.  SspRFI favors low salt conditions and
      can be inhibited by a methylation of the intter adenine residue.
AU  - Li J-K
AU  - Tu J
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 4770.

PMID- 17938196
VI  - 27
DP  - 2007
TI  - Synergistic function of DNA Methyltransferases dnmt3a and dnrnt3b in the methylation of Oct4 and Nanog.
PG  - 8748-8759
AB  - DNA methylation plays an important role in gene silencing in mammals. Two de novo
      methyltransferases, Dnmt3a and Dnmt3b, are required for the
      establishment of genomic methylation patterns in development. However,
      little is known about their coordinate function in the silencing of
      genes critical for embryonic development and how their activity is
      regulated. Here we show that Dnmt3a and Dnmt3b are the major components
      of a native complex purified from embryonic stem cells. The two enzymes
      directly interact and mutually stimulate each other both in vitro and
      in vivo. The stimulatory effect is independent of the catalytic
      activity of the enzyme. In differentiating embryonic carcinoma or
      embryonic stem cells and mouse postimplantation embryos, they function
      synergistically to methylate the promoters of the Oct4 and Nanog genes.
      Inadequate methylation caused by ablating Dnmt3a and Dnmt3b is
      associated with dysregulated expression of Oct4 and Nanog during the
      differentiation of pluripotent cells and mouse embryonic development.
      These results suggest that Dnmt3a and Dnmt3b form a complex through
      direct contact in living cells and cooperate in the methylation of the
      promoters of Oct4 and Nanog during cell differentiation. The physical
      and functional interaction between Dnmt3a and Dnmt3b represents a novel
      regulatory mechanism to ensure the proper establishment of genomic
      methylation patterns for gene silencing in development.
AU  - Li JY
AU  - Pu MT
AU  - Hirasawa R
AU  - Li BZ
AU  - Huang YN
AU  - Zeng R
AU  - Jing NH
AU  - Chen T
AU  - Li E
AU  - Sasaki H
AU  - Xu GL
PT  - Journal Article
TA  - Mol. Cell. Biol.
JT  - Mol. Cell. Biol.
SO  - Mol. Cell. Biol. 2007 27: 8748-8759.

PMID- 21257769
VI  - 193
DP  - 2011
TI  - Genome Sequence of Paracoccus sp.TRP, a Chlorpyrifos Biodegrader.
PG  - 1786-1787
AB  - A Paracoccus sp. strain TRP, isolated from activated sludge, could completely biodegrade
      chlorpyrifos and 3,5,6-trichloro-2-pyridinol. Here, we report the draft genome sequence of
      Paracoccus sp.strain TRP which could be used to predict genes for xenobiotics biodegradation
      and metabolism.
AU  - Li K
AU  - Wang S
AU  - Shi Y
AU  - Qu J
AU  - Zhai Y
AU  - Xu L
AU  - Xu Y
AU  - Song J
AU  - Liu L
AU  - Rahman MA
AU  - Yan Y
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 1786-1787.

PMID- Not carried by PubMed...
VI  - 55
DP  - 1994
TI  - Studies on FokI (a type IIS) restriction endonuclease.
PG  - 877B-878B
AB  - FokI restriction endonuclease recognizes the nonpalindromic pentadeoxyribonucleotide
      5'-GGATG-3'/5'-CATCC-3' in duplex DNA and cleaves 9 and 13 nucleotides away from the
      recognition site. This implies that this enzyme has separate domains for DNA recognition and
      cleavage. The fokIM and fokIR were subcloned into Escherichia coli. FokI endonuclease was
      overexpressed and purified to homogeneity. The recognition and cleavage domains of FokI were
      analyzed by trypsin digestion. FokI in the presence of a DNA substrate is cleaved into a 41
      kDa amino-terminal fragment and a 25 kDA carboxyl-terminal fragment. Gel-mobility-shift assays
      indicate that all the protein contacts necessary for the sequence-specific recognition of DNA
      substrates are encoded within the 41 kDa fragment. On further digestion, the 41 kDa fragment
      degrades into 30 kDa amino-terminal and 11 kDa carboxyl-terminal fragments which together bind
      DNA substrates. Thus, the 41 kDa amino-terminal fragment constitutes the FokI recognition
      domain. This was confirmed by the characterization of two carboxyl-terminal deletion mutant
      proteins (41 kDa and 30 kDa, respectively) of FokI. The 41 kDa mutant protein binds the DNA
      sequence 5'-GGATG-3':5' - CATCC-3' specifically like the wild-type FokI. The 30 kDa mutant
      protein does not bind DNA. Addition of the HPLC-purified 11 kDa fragment to the 30 kDa mutant
      protein restores its sequence specific DNA-binding property. The affinity of the 41 kDa mutant
      protein for the DNA substrate is comparable to that of the wild-type FokI. The 41 kDa mutant
      protein interacts with its substrate in a similar way compared to the wild-type enzyme as
      revealed by hydroxyl radical footprinting experiments. The 25 kDa carboxyl-terminal fragment
      of FokI cleaves DNA substrates non-specifically in the presence of MgCl2. Thus, the 25 kDa
      fragment constitutes the FokI cleavage domain. Additional amino acids have been introduced
      between the two domains of FokI by insertion mutagenesis. The mutant enzymes have the same DNA
      sequence specificity as the wild-type FokI. However, compared with the wild-type enzyme, they
      cleave one nucleotide further away from the recognition site on both strands of the DNA
      substrates. Thus, it is possible to alter the cleavage distance of FokI by protein
      engineering.
AU  - Li L
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1994 55: 877B-878B.

PMID- 16116077
VI  - 102
DP  - 2005
TI  - The complete genome sequence of Mycobacterium avium subspecies paratuberculosis.
PG  - 12344-12349
AB  - We describe here the complete genome sequence of a common clone of Mycobacterium avium
      subspecies paratuberculosis (Map) strain K-10, the
      causative agent of Johne's disease in cattle and other ruminants. The K-10
      genome is a single circular chromosome of 4,829,781 base pairs and encodes
      4,350 predicted ORFs, 45 tRNAs, and one rRNA operon. In silico analysis
      identified >3,000 genes with homologs to the human pathogen, M.
      tuberculosis (Mtb), and 161 unique genomic regions that encode 39
      previously unknown Map genes. Analysis of nucleotide substitution rates
      with Mtb homologs suggest overall strong selection for a vast majority of
      these shared mycobacterial genes, with only 68 ORFs with a synonymous to
      nonsynonymous substitution ratio of >2. Comparative sequence analysis
      reveals several noteworthy features of the K-10 genome including: a
      relative paucity of the PE/PPE family of sequences that are implicated as
      virulence factors and known to be immunostimulatory during Mtb infection;
      truncation in the EntE domain of a salicyl-AMP ligase (MbtA), the first
      gene in the mycobactin biosynthesis gene cluster, providing a possible
      explanation for mycobactin dependence of Map; and Map-specific sequences
      that are likely to serve as potential targets for sensitive and specific
      molecular and immunologic diagnostic tests. Taken together, the
      availability of the complete genome sequence offers a foundation for the
      study of the genetic basis for virulence and physiology in Map and enables
      the development of new generations of diagnostic tests for bovine Johne's
      disease.
AU  - Li L
AU  - Bannantine JP
AU  - Zhang Q
AU  - Amonsin A
AU  - May BJ
AU  - Alt D
AU  - Banerji N
AU  - Kanjilal S
AU  - Kapur V
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2005 102: 12344-12349.

PMID- 8464886
VI  - 90
DP  - 1993
TI  - Alteration of the cleavage distance of Fok I restriction endonuclease by insertion mutagenesis.
PG  - 2764-2768
AB  - FokI restriction endonuclease recognizes the nonpalindromic pentadeoxyribonucleotide
      5'-GGATC-3'-5'CATCC-3' in duplex DNA and cleaves 9 and 13 nucleotides away from the
      recognition site. Recently, we reported the presence of two distinct and separable protein
      domains within this enzyme-one for the sequence-specific recognition and the other for
      endonuclease activity. Here, we report the construction of two insertion mutants of FokI
      endonuclease. The mutant enzymes were purified, and their cleavage properties were
      characterized. The mutants have the same DNA sequence specificity as the wild-type enzyme.
      However compared with the wild-type enzyme, they cleave one nucleotide further away from the
      recognition site on both strands of the DNA substrates. Thus, it is possible to alter the
      cleavage distance of FokI by protein engineering.
AU  - Li L
AU  - Chandrasegaran S
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1993 90: 2764-2768.

PMID- 23105062
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Salmonella enterica Serovar Typhimurium ST1660/06, a Multidrug-Resistant Clinical Strain Isolated from a Diarrheic Patient.
PG  - 6319-6320
AB  - Salmonella enterica serovar Typhimurium is one of the most prevalent serovars of  Salmonella
      that causes human gastroenteritis. Here, we report the draft genome
      sequence of the S. Typhimurium multidrug-resistant strain ST1660/06. Comparative
      genomic analysis unveiled three strain-specific genomic islands that potentially
      confer the multidrug resistance and virulence of the strain.
AU  - Li L
AU  - Cheng CK
AU  - Cheung MK
AU  - Law PT
AU  - Ling JM
AU  - Kam KM
AU  - Cheung WM
AU  - Kwan HS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6319-6320.

PMID- 22815449
VI  - 194
DP  - 2012
TI  - Genome Sequences of Two Thermophilic Bacillus licheniformis Strains, Efficient Producers of Platform Chemical 2,3-Butanediol.
PG  - 4133-4134
AB  - Both Bacillus licheniformis strains 10-1-A and 5-2-D are efficient producers of
      2,3-butanediol. Here we present 4.3-Mb and 4.2-Mb assemblies of their genomes.
      The key genes for the regulation and metabolism of 2,3-butanediol production were
      annotated, which may provide further insights into the molecular mechanism for
      the production of 2,3-butanediol with high yield and productivity.
AU  - Li L
AU  - Su F
AU  - Wang Y
AU  - Zhang L
AU  - Liu C
AU  - Li J
AU  - Ma C
AU  - Xu P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4133-4134.

PMID- 24948764
VI  - 2
DP  - 2014
TI  - Genome Sequence of meso-2,3-Butanediol-Producing Strain Serratia marcescens ATCC  14041.
PG  - e00590-14
AB  - Serratia marcescens strain ATCC 14041 was found to be an efficient meso-2,3-butanediol
      (meso-2,3-BD) producer from glucose and sucrose. Here we
      present a 5.0-Mb assembly of its genome. We have annotated 4 coding sequences
      (CDSs) for meso-2,3-BD fermentation and 2 complete operons including 6 CDSs for
      sucrose utilization.
AU  - Li L
AU  - Wang Y
AU  - Li K
AU  - Su F
AU  - Ma C
AU  - Xu P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00590-14.

PMID- 24970831
VI  - 2
DP  - 2014
TI  - Genome Sequence of Thermophilic Bacillus licheniformis Strain 3F-3, an Efficient  Pentose-Utilizing Producer of 2,3-Butanediol.
PG  - e00615-14
AB  - Bacillus licheniformis strain 3F-3 is an efficient pentose-utilizing producer of  platform
      chemical, 2,3-butanediol. Here we present a 4.1-Mb assembly of its
      genome. The key genes for pentose utilization, regulation, and metabolism of
      2,3-butanediol were annotated, which may provide further insights into the
      molecular mechanism of 2,3-butanediol production from biomass pentose.
AU  - Li L
AU  - Wang Y
AU  - Wang K
AU  - Li K
AU  - Ma C
AU  - Xu P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00615-14.

PMID- 1584761
VI  - 89
DP  - 1992
TI  - Functional domains in FokI restriction endonuclease.
PG  - 4275-4279
AB  - The PCR was used to alter transcriptional and translational signals surround the
      Flavobacterium okeanokoites restriction endonuclease (fokIR) gene, so as to achieve high
      expression in Escherichia coli. By changing the ribosome-binding site sequence preceding the
      fokIR gene to match the consensus E. coli signal and by placing a positive retroregulator
      stem-loop sequence downstream of the gene, FokI yield was increased to 5-8% of total cellular
      protein. FokI was purified to homogeneity with phosphocellulose, DEAE-Sephadex, and gel
      chromatography, yielding 50 mg of pure FokI endonuclease per liter of culture medium. The
      recognition and cleavage domains of FokI were analyzed by trypsin digestion. FokI in the
      absence of a DNA substrate cleaves into a 58-kDa carboxyl-terminal and 8-kDa amino-terminal
      fragment. The 58-kDa fragment does not bind the DNA substrate. FokI in the presence of a DNA
      substrate cleaves into a 41-kDa amino-terminal fragment and a 25-kDa carboxyl-terminal
      fragment. On further digestion, the 41-kDa fragment degrades into 30-kDa amino terminal and
      11-kDa carboxyl-terminal fragments. The cleaved fragments both bind DNA substrates, as does
      the 41-kDa fragment. Gel-mobility-shift assays indicate that all the protein contacts
      necessary for the sequence-specific recognition of DNA substrates are encoded within the
      41-kDa fragment. Thus, the 41-kDa amino-terminal fragment constitutes the FokI recognition
      domain. The 25-kDa fragment purified by using a DEAE-Sephadex column, cleaves nonspecifically
      both methylated (pACYCfokIM) and nonmethylated (pTZ19R) DNA substrates in the presence of
      MgCl2. Thus, the 25-kDa carboxyl-terminal fragment constitutes the FokI cleavage domain.
AU  - Li L
AU  - Wu LP
AU  - Chandrasegaran S
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1992 89: 4275-4279.

PMID- 8224897
VI  - 133
DP  - 1993
TI  - C-terminal deletion mutants of the FokI restriction endonuclease.
PG  - 79-84
AB  - *

      We have constructed two C-terminal deletion mutants of the FokI restriction endonuclease by

      using the polymerase-chain-reaction technique and expressed them in Escherichia coli. The two

      mutant proteins (MP) of 41 and 30 kDa, were purified to homogeneity and their DNA-binding

      properties were characterized. The 41-kDa MP specifically binds the DNA sequence:

      

         5'GGATG

         3'CCTAC

      

      like the wild-type (wt) FokI, but does not cleave DNA. The 30-kDa MP does not bind DNA. The

      affinity of the 41-kDa MP for the DNA substrate is comparable to that of wt FokI. The 41-kDa

      MP interacts with its substrate like the wt FokI, as revealed by hydroxyl radical footprinting

      experiments. In the presence of a DNA substrate, the 41-kDa MP is cleaved by trypsin into a

      30-kDa N-terminal fragment and an 11-kDa C-terminal fragment. Addition of the HPLC-purified

      11-kDa C-terminal fragment to the 30-kDa MP restores its sequence-specific DNA binding
      property.

      These results confirm that the N-terminal 41-kDa fragment of the FokI ENase constitutes the

      DNA recognition domain of the ENase.

      

AU  - Li L
AU  - Wu LP
AU  - Clarke R
AU  - Chandrasegaran S
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1993 133: 79-84.

PMID- 23409271
VI  - 1
DP  - 2013
TI  - Genome of Cupriavidus sp. HMR-1, a Heavy Metal-Resistant Bacterium.
PG  - e00202-12
AB  - Cupriavidus sp. HMR-1 was isolated from a heavy metal-enriched culture of activated sludge
      from a wastewater treatment plant in Hong Kong. Here, we release
      the HMR-1 genome to provide basic genetic characteristics for a better
      understanding of its multiple heavy metal resistance properties.
AU  - Li LG
AU  - Cai L
AU  - Zhang T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00202-12.

PMID- 1201711
VI  - 223
DP  - 1975
TI  - Production of Specific Fragments of T4 DNA by Endonuclease EcoRI.
PG  - 1262-1265
AB  - Restriction enzyme EcoRI was used to cleave nonglucosylated bacteriophage T4
      DNA in a minimum 41 fragments, which were separated on agarose gels.  The
      fragments were estimated to fall within the size range of 8.2-0.38 Mdalton. It
      was shown that either alpha- or beta-glucosylation protects fully T4 DNA
      against EcoRI function. Recombinant cells E. coli K12 r 2,4-, r 6-(RI)/6
      harbouring the RI plasmid were isolated.  The efficiency of plating of
      different T4 mutants with nonglucosylated and partly glucosylated DNA on them
      was not lower then on the strain E. coli K 12 r 2,4-,r6-.
AU  - Li LI
AU  - Tanyashin VI
AU  - Matvienko NI
AU  - Bayev AA
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1975 223: 1262-1265.

PMID- 23209234
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Clostridium sp. Strain BNL1100, a Cellulolytic Mesophile Isolated from Corn Stover.
PG  - 6982-6983
AB  - We present the full genome sequence of Clostridium sp. strain BNL1100, a Gram-positive,
      endospore-forming, lignocellulolytic bacterium isolated from a
      corn stover enrichment culture. The 4,613,747-bp genome of strain BNL1100
      contains 4,025 putative protein-coding genes, of which 103 are glycoside
      hydrolases, the highest detected number in cluster III clostridia.
AU  - Li LL
AU  - Taghavi S
AU  - Izquierdo JA
AU  - van der Lelie D
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6982-6983.

PMID- 28254975
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Thalassospira xiamenensis Strain MCCC 1A03042T.
PG  - e01702-16
AB  - Thalassospira xiamenensis strain MCCC 1A03042T was isolated from deep-sea sediment of the
      Indian Ocean, and it was characterized with heavy-metal arsenic
      tolerance. Here, we present the draft genome of strain MCCC 1A03042T, which
      contains 4,786,207 bp with a G+C content of 52.6% and 4,359 protein-coding genes.
AU  - Li M
AU  - Yang S
AU  - Lai Q
AU  - Shao Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01702-16.

PMID- 15731760
VI  - 37
DP  - 2005
TI  - MAGIC, an in vivo genetic method for the rapid construction of recombinant DNA molecules.
PG  - 311-319
AB  - We describe a highly engineered in vivo cloning method, mating-assisted genetically integrated
      cloning (MAGIC), that facilitates the rapid
      construction of recombinant DNA molecules. MAGIC uses bacterial mating, in
      vivo site-specific endonuclease cleavage and homologous recombination to
      catalyze the transfer of a DNA fragment between a donor vector in one
      bacterial strain and a recipient plasmid in a separate bacterial strain.
      Recombination events are genetically selected and result in placement of
      the gene of interest under the control of new regulatory elements with
      high efficiency. MAGIC eliminates the need for restriction enzymes, DNA
      ligases, preparation of DNA and all in vitro manipulations required for
      subcloning and allows the rapid construction of multiple constructs with
      minimal effort. We show that MAGIC can generate constructs for expression
      in multiple organisms. As this new method requires only the simple mixing
      of bacterial strains, it represents a substantial advance in
      high-throughput recombinant DNA production that will save time, effort and
      expense in functional genomics studies.
AU  - Li MZ
AU  - Elledge SJ
PT  - Journal Article
TA  - Nat. Genet.
JT  - Nat. Genet.
SO  - Nat. Genet. 2005 37: 311-319.

PMID- 20102440
VI  - 33
DP  - 2010
TI  - Difference in genes between a high virulence strain G4 and a low virulence strain G18 of Flavobacterium columnare by using suppression subtractive hybridization.
PG  - 403-412
AB  - Flavobacterium columnare is the causative agent of columnaris disease. Different genetic
      groups of F. columnare show to some extent different degrees of virulence. To identify genetic
      differences between
      the high virulence strain G4 and the low virulence strain G18 of F. columnare, suppression
      subtractive hybridization was used. A total of 46 genes were identified from the virulent
      strain G4, 35 of which
      showed some degree of homology with known proteins and can be classified into 11 categories:
      DNA replication or recombination proteins, inorganic
      ion transport proteins, outer membrane proteins, enterotoxin, binding proteins, YD repeat
      proteins, transposase, chaperon, signal transduction-
      related proteins, regulatory proteins, metabolism-
      related proteins. Several putative virulence factors identified in other bacteria could also
      be identified in the virulent strain G4, such as ferrous
      iron transport protein, TonB-dependent receptor, transposases, as well as ABC transporter
      permease protein. The flanking region of a putative transposase ISFclI was analysed, and a
      putative Rhs element was located at the downstream of the putative transposase. The analysis
      of isfcl I gene in
      24 strains of F. columnare isolated in China revealed that 11 strains have isfcl I, and all
      the strains from Zhaoqing, Anhui and Qingjiang have
      isfclI.
AU  - Li N
AU  - Zhang J
AU  - Zhang LQ
AU  - Nie P
PT  - Journal Article
TA  - J. Fish Dis.
JT  - J. Fish Dis.
SO  - J. Fish Dis. 2010 33: 403-412.

PMID- 22655971
VI  - 160
DP  - 2012
TI  - Type I restriction-modification system and its resistance in electroporation efficiency in Flavobacterium columnare.
PG  - 61-68
AB  - Flavobacterium columnare, the causative agent of columnaris disease, infects freshwater fish
      worldwide. However, the pathogenicity of this
      bacterium is poorly understood due possibly to the lack of an efficient
      in-frame knockout technique. In order to improve electroporation
      efficiency, the type I restriction-modification system (R-M system) was
      cloned and its role in electroporation was examined in F. columnare
      G(4) strain. The complete sequence of type I R-M system in the
      bacterium, designated as Fcl, contains all three subunits of type I R-M
      system, named as fclM, fclS, fclR, respectively, with the
      identification of a hypothetical gene, fclX. Constitutive transcription
      of the three genes was observed in F. columnare G(4) by RT-PCR. The ORF
      of fclM and fclS was cloned into the plasmid pACYC184 and transformed
      into Escherichia colt TOP10. The resultant E. coli strain, designated
      as E. coli TOPmt, was transformed with the integrative plasmid pGL006
      constructed for F. columnare G(4). The integrative plasmid was
      re-isolated from TOPmt and incubated with the lysate of F. columnare
      G(4). The re-isolated integrative plasmid, designated as pGL006',
      showed higher resistance than pGL006. With pGL006', the electroporation
      efficiency of the strain G(4) increased 2.6 times, while that of F.
      columnare G(18) was not obviously improved. Furthermore, a method to
      improve the electroporation efficiency of F. columnare G(4) was
      developed using the integrative plasmid methylated by E. coil TOPmt
      which contains the fclM and fclS gene of F. columnare G(4). Further
      analyses showed that the fcl gene cluster may be a unique type I R-M
      system in F. columnare G(4). It will be of significant interest to
      examine the composition and diversity of R-M systems in strains of F.
      columnare in order to set up a suitable genetic manipulation system for
      the bacterium.
AU  - Li N
AU  - Zhang LQ
AU  - Zhang J
AU  - Liu ZX
AU  - Huang B
AU  - Zhang SH
AU  - Nie P
PT  - Journal Article
TA  - Vet. Microbiol.
JT  - Vet. Microbiol.
SO  - Vet. Microbiol. 2012 160: 61-68.

PMID- 22461553
VI  - 194
DP  - 2012
TI  - Genome Sequence of Paenibacillus sp. Strain Aloe-11, an Endophytic Bacterium with Broad Antimicrobial Activity and Intestinal Colonization Ability.
PG  - 2117-2118
AB  - Paenibacillus sp. strain Aloe-11, a Gram-positive, spore-forming, facultatively anaerobic
      bacterium isolated from the root of Aloe chinensis in the southwest
      region of China, has excellent antibiotic activity and intestine colonization
      ability. Here, we present the 5.8-Mb draft genome sequence of Paenibacillus sp.
      strain Aloe-11.
AU  - Li NZ
AU  - Xia T
AU  - Xu YL
AU  - Qiu RR
AU  - Xiang H
AU  - He D
AU  - Peng YY
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2117-2118.

PMID- 25035336
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of a New Shigella flexneri Subserotype, 4S BJ10610.
PG  - e00715-14
AB  - Shigella flexneri is of great concern in the prevalence of shigellosis and resistance to many
      antibiotics in developing countries. Here, we report the draft
      genome sequence of a new S. flexneri subserotype, 4S BJ10610, isolated from the
      stool specimens of a patient in Beijing, China.
AU  - Li P
AU  - Yang C
AU  - Wang J
AU  - Yi S
AU  - Li H
AU  - Wang Y
AU  - Qiu S
AU  - Song H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00715-14.

PMID- 22117845
VI  - 14
DP  - 2012
TI  - Genetic structure of three fosmid-fragments encoding 16S rRNA genes of the Miscellaneous Crenarchaeotic Group (MCG): implications for physiology and evolution of marine sedimentary archaea.
PG  - 467-479
AB  - Archaea of the Miscellaneous Crenarchaeotic Group (MCG) exist widely in soil,
      freshwater and marine sediments of both surface and subsurface. However, current
      knowledge about this group is limited to its phylogenetic diversity. An archaeal
      16S library was constructed from a sediment sample from the South China Sea,
      which was dominated by MCG and Marine Group I (MG-I). A metagenomic library was
      constructed from the same sediment sample, and three MCG fosmids (E6-3G, E37-7F
      and E48-1C) containing 16S rRNA genes were screened. Annotation showed that the
      three genomic fragments encode a variety of open reading frames (ORFs) that are
      potentially homologous to important functional genes related to lipid
      biosynthesis, energy metabolism, and resistance to oxidants. No colinear regions
      were found between MCG fosmids and reported archaeal genomic fragments or
      genomes, suggesting that the MCG archaea are quite different from the sequenced
      archaea in gene arrangement. Analyses of both the phylogenies of 16S rRNA genes
      and several informational processing genes and nucleotide frequencies showed that
      MCG archaea are distinct from MG-I plus relatives. In addition, tetranucleotide
      frequency analysis in combination with phylogenetic analysis suggested that some
      fragments in the MCG fosmids are probably derived from non-MCG or non-archaeal
      genomes.
AU  - Li PY
AU  - Xie BB
AU  - Zhang XY
AU  - Qin QL
AU  - Dang HY
AU  - Wang XM
AU  - Chen XL
AU  - Yu J
AU  - Zhang YZ
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2012 14: 467-479.

PMID- 25301657
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Salmonella enterica Serovar Choleraesuis Vaccine Strain C500 Attenuated by Chemical Mutation.
PG  - e01022-14
AB  - Salmonella enterica serovar Choleraesuis strain C500 is a live vaccine attenuated by chemical
      methods. Here, we report the complete genome sequence of the strain,
      which may be helpful for elucidating the attenuation mechanism of the vaccine
      strain.
AU  - Li Q
AU  - Hu Y
AU  - Xu L
AU  - Xie X
AU  - Tao M
AU  - Jiao X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01022-14.

PMID- 28883127
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Lactobacillus brevis Strain 3M004, a Probiotic with Potential Quorum-Sensing Regulation.
PG  - e00675-17
AB  - We present here the draft genome sequence of Lactobacillus brevis strain 3M004, a probiotic
      that has potential for regulating quorum sensing. The strain was
      obtained from a type of aquafeed. The assembly consists of 2,459,326 bp and
      contains 33 contigs, with a G+C content of 45.10%.
AU  - Li Q
AU  - Pan Y
AU  - Ding L
AU  - Hong H
AU  - Yan S
AU  - Wu B
AU  - Liang Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00675-17.

PMID- 26380647
VI  - 10
DP  - 2015
TI  - Complete genome sequence of Bacillus thuringiensis strain HD521.
PG  - 62
AB  - Bacillus thuringiensis is the most widely used biological pesticide in the world. It belongs
      to the Bacillus cereus sensu lato group, which contains six species. Among these six species,
      B. thuringiensis, B. anthracis, and B. cereus have a low genetic diversity. B. thuringiensis
      strain HD521 shows maroon colony which is different from most of the B. thuringiensis strains.
      Strain HD521 also displays an ability to inhibit plant sheath blight disease pathogen
      (Rhizoctonia solani AG1 IB) growth and can form bipyramidal parasporal crystals consisting of
      three cry7 genes. These crystals have an insecticidal activity against Henosepilachna
      vigintioctomaculata larva (Coleoptera). Here we report the complete genome sequence of strain
      HD521, which has one chromosome and six circular plasmids.
AU  - Li Q
AU  - Xu LZ
AU  - Zou T
AU  - Ai P
AU  - Huang GH
AU  - Li P
AU  - Zheng AP
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 62.

PMID- 26988036
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequencing of Macrolide-Resistant Mycoplasma pneumoniae Strain S355, Isolated in China.
PG  - e00087-16
AB  - Macrolide-resistant Mycoplasma pneumoniae plays an important role in refractory M. pneumoniae
      pneumonia. Here, we present the whole-genome sequencing of the
      macrolide-resistant M. pneumoniae strain S355. The annotated full-genome sequence
      might provide a new insight into drug resistance in M. pneumoniae and can help
      pediatricians recognize the disease earlier.
AU  - Li S
AU  - Liu F
AU  - Sun H
AU  - Zhu B
AU  - Lv N
AU  - Xue G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00087-16.

PMID- 21422209
VI  - 55
DP  - 2011
TI  - Novel types of staphylococcal cassette chromosome mec elements identified in clonal complex 398 methicillin-resistant Staphylococcus aureus strains.
PG  - 3046-3050
AB  - The structures of staphylococcal cassette chromosome mec (SCCmec) elements
      carried by 31 clonal complex 398 (CC398) methicillin-resistant
      Staphylococcus aureus (MRSA) strains isolated from the participants at a
      conference were analyzed. The SCCmecs were classified into novel types,
      namely, IX, X, V(5C2&5) subtype c, and IVa. Type V(5C2&5) subtype c, IX,
      and X SCCmecs carried genes conferring resistance to metals. The
      structures of SCCmecs from CC398 strains were distinct from those normally
      found in humans, adding to the evidence that humans are not the original
      host for CC398.
AU  - Li S
AU  - Skov RL
AU  - Han X
AU  - Larsen AR
AU  - Larsen J
AU  - Sorum M
AU  - Wulf M
AU  - Voss A
AU  - Hiramatsu K
AU  - Ito T
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2011 55: 3046-3050.

PMID- 27056229
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of the Macrolide-Resistant Mycoplasma pneumoniae Strain  C267 in China.
PG  - e00236-16
AB  - Macrolide-resistantMycoplasma pneumoniaestrains can cause severeM. pneumoniaepneumonia in
      children. Here, we report the complete genome sequence of
      the macrolide-resistantM. pneumoniaestrain C267, deposited in GenBank under
      accession number CP014267, which provides new insights for other potential
      macrolide-resistant mechanisms inM. pneumoniaeclinical isolates in China.
AU  - Li S
AU  - Sun H
AU  - Liu F
AU  - Zhao H
AU  - Zhu B
AU  - Lv N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00236-16.

PMID- 24723719
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Paenibacillus polymyxa SQR-21, a Plant Growth-Promoting Rhizobacterium with Antifungal Activity and Rhizosphere Colonization Ability.
PG  - e00281-14
AB  - Here we report the complete genome sequence of a plant growth-promoting
      rhizobacterium (PGPR), Paenibacillus polymyxa SQR-21, which consists of one
      circular chromosome of 5,828,438 bp with 5,024 coding sequences (CDS). The data
      presented highlight multiple sets of functional genes associated with its
      plant-beneficial characteristics.
AU  - Li S
AU  - Yang D
AU  - Qiu M
AU  - Shao J
AU  - Guo R
AU  - Shen B
AU  - Yin X
AU  - Zhang R
AU  - Zhang N
AU  - Shen Q
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00281-14.

PMID- 22933774
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of the Naphthalene-Degrading Pseudomonas putida Strain ND6.
PG  - 5154-5155
AB  - Pseudomonas putida strain ND6 is an efficient naphthalene-degrading bacterium. The complete
      genome of strain ND6 was sequenced and annotated. The genes encoding
      the enzymes involved in catechol degradation by the ortho-cleavage pathway were
      found in the chromosomal sequence, which indicated that strain ND6 is able to
      metabolize naphthalene by the catechol meta- and ortho-cleavage pathways.
AU  - Li S
AU  - Zhao H
AU  - Li Y
AU  - Niu S
AU  - Cai B
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5154-5155.

PMID- 23469355
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Escherichia coli Strain LCT-EC59.
PG  - e00242-12
AB  - The space environment is a very special condition under which many organisms change many
      features. is employed widely as a prokaryotic model organism in the
      fields of biotechnology and microbiology. Here, we present the draft genome
      sequence of strain LCT-EC59 exposed to space conditions.
AU  - Li T
AU  - Chen J
AU  - Chang D
AU  - Fang X
AU  - Wang J
AU  - Guo Y
AU  - Su L
AU  - Xu G
AU  - Wang Y
AU  - Chen Z
AU  - Liu C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00242-12.

PMID- 20699274
VI  - 39
DP  - 2010
TI  - TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain.
PG  - 359-372
AB  - DNA double-strand breaks enhance homologous recombination in cells and have been exploited for
      targeted genome editing through use of engineered
      endonucleases. Here we report the creation and initial characterization of
      a group of rare-cutting, site-specific DNA nucleases produced by fusion of
      the restriction enzyme FokI endonuclease domain (FN) with the
      high-specificity DNA-binding domains of AvrXa7 and PthXo1. AvrXa7 and
      PthXo1 are members of the transcription activator-like (TAL) effector
      family whose central repeat units dictate target DNA recognition and can
      be modularly constructed to create novel DNA specificity. The hybrid
      FN-AvrXa7, AvrXa7-FN and PthXo1-FN proteins retain both recognition
      specificity for their target DNA (a 26 bp sequence for AvrXa7 and 24 bp
      for PthXo1) and the double-stranded DNA cleaving activity of FokI and,
      thus, are called TAL nucleases (TALNs). With all three TALNs, DNA is
      cleaved adjacent to the TAL-binding site under optimal conditions in
      vitro. When expressed in yeast, the TALNs promote DNA homologous
      recombination of a LacZ gene containing paired AvrXa7 or asymmetric
      AvrXa7/PthXo1 target sequences. Our results demonstrate the feasibility of
      creating a tool box of novel TALNs with potential for targeted genome
      modification in organisms lacking facile mechanisms for targeted gene
      knockout and homologous recombination.
AU  - Li T
AU  - Huang S
AU  - Jiang WZ
AU  - Wright D
AU  - Spalding MH
AU  - Weeks DP
AU  - Yang B
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2010 39: 359-372.

PMID- 22843582
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Escherichia coli LCT-EC106.
PG  - 4443-4444
AB  - Escherichia coli is a Gram-negative, rod-shaped bacterium that is commonly found  in the
      intestine of warm-blooded organisms. Most E. coli strains are harmless,
      but some serotypes can cause serious food poisoning in humans. Here, we present
      the complete genome sequence of Escherichia coli LCT-EC106, which was isolated
      from CGMCC 1.2385.
AU  - Li T
AU  - Pu F
AU  - Yang R
AU  - Fang X
AU  - Wang J
AU  - Guo Y
AU  - Chang D
AU  - Su L
AU  - Guo N
AU  - Jiang X
AU  - Zhao J
AU  - Liu C
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4443-4444.

PMID- 20554247
VI  - 300
DP  - 2010
TI  - Identification of Streptococcus suis serotype 2 genes preferentially expressed in the natural host.
PG  - 482-488
AB  - Streptococcus suis serotype 2 (SS2) is an important zoonotic pathogen for swine
      and humans. Previous research about the mechanism of SS2 infection was largely
      established on in vitro or ex vivo models. In this study, we focused on the
      identification of SS2 genes preferentially expressed in vivo during natural
      infection in pigs. Eighty SS2 genes were identified to be up-regulated in the
      porcine brains and lungs by selective capture of transcribed sequences (SCOTS)
      and comparative dot blot analysis, followed by quantitative RT-PCR validation.
      These genes could be classified into 5 functional categories: metabolism, cell
      wall associated proteins, transporters, cell replication, and function unknown.
      Some of these genes may contribute to the survival and pathogenesis of SS2 in the
      host via the following strategies. First, SS2 evades the host innate immune
      clearance through modifying its metabolism and cell wall composition as indicated
      by the up-regulation of the corresponding gene ldh and pbp2A, respectively.
      Secondly, SS2 adapts to the in vivo conditions by inducing the expression of the
      two-component signal transduction system VicKR which may function on the target
      genes such as pcsB involved in stress response and cell wall biosynthesis.
      Thirdly, SS2 enhances its virulence in vivo by up-regulating the virulence genes,
      such as sly, pdgA, ssp, gidA, gcp and hp1311. Further study of these in vivo
      up-regulated genes will contribute to understanding the in vivo survival
      mechanism and pathogenesis of SS2.
AU  - Li W
AU  - Liu L
AU  - Qiu D
AU  - Chen H
AU  - Zhou R
PT  - Journal Article
TA  - Int. J. Med. Microbiol.
JT  - Int. J. Med. Microbiol.
SO  - Int. J. Med. Microbiol. 2010 300: 482-488.

PMID- 15246534
VI  - 336
DP  - 2004
TI  - Complete nucleotide sequence and organization of the naphthalene catabolic plasmid pND6-1 from Pseudomonas sp. strain ND6.
PG  - 231-240
AB  - Pseudomonas sp. strain ND6, which was isolated from industrial wastewater in
      Tianjin, China, was capable of dissimilating naphthalene as sole carbon and
      energy sources. We identified one plasmid, pND6-1, which was associated with the
      metabolism of naphthalene and determined the complete nucleotide sequence of
      pND6-1 (101,858 bp) using a whole-genome-shotgun approach. Computational analyses
      indicated that the naphthalene metabolism of the strain ND6 is associated with
      this plasmid. This is the first report of a complete sequence of naphthalene
      catabolic plasmid. pND6-1 encodes 102 putative coding sequences (CDSs). Among
      them, 23 CDSs were predicted to be involved in naphthalene catabolism, 14 were
      predicted to be involved in transposition and integration, 2 encoded putative
      transporters, 3 were putative transcriptional regulators, and 9 were proteins
      necessary for plasmid replication and partitioning. Most of the naphthalene
      catabolic genes of pND6-1 have 99-100% identity in amino acid sequences
      homologous to their nearest counterparts found in plasmid pDTG1, NAH7 and in a
      chromosome region in Pseudomonas stutzeri AN10 except for two duplicated genes
      (ND013 and ND016). Results of this study indicated that globally distributed
      naphthalene catabolic genes are highly conserved among different bacterial
      species.
AU  - Li W
AU  - Shi J
AU  - Wang X
AU  - Han Y
AU  - Tong W
AU  - Ma L
AU  - Liu B
AU  - Cai B
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 2004 336: 231-240.

PMID- 22882077
VI  - 84
DP  - 2012
TI  - Signal Amplification of Graphene Oxide Combining with Restriction Endonuclease for Site-Specific Determination of DNA Methylation and Assay of Methyltransferase Activity.
PG  - 7583-7590
AB  - Site-specific identification of DNA methylation and assay of MTase activity are important in
      determining specific cancer types, providing
      insights into the mechanism of gene repression, and developing novel
      drugs to treat methylation-related diseases. This work reports an
      electrochemical method for gene-specific methylation detection and
      MTase activity assay using HpaII endonuclease to improve selectivity
      and employing signal amplification of graphene oxide (GO) to enhance
      the assay sensitivity. The method was developed by designing a probe
      DNA, which was immobilized on electrode surface, to hybridize with
      target DNA (one 137 mer DNA from exon 8 promoter region of the Homo
      sapiens p53 gene, was extracted from HCT116 cells). The assay is based
      on the electrochemical responses of the reporter (thionine), which was
      conjugated to 3'-terminus of the probe DNA via GO, after the DNA hybrid
      was methylated (under catalysis of M.SssI MTase) and cleaved by HpaII
      endonuclease (a site-specific endonuclease recognizing the duplex
      symmetrical sequence of 5'-CCGG-3' and catalyzing cleavage between the
      cytosines). This model can determine DNA methylation at the site of CpG
      and has an ability to discriminate the target DNA sequence from even
      single-base mismatched sequence. The electrochemical signal has a
      linear relationship with M.SssI activities ranging from 0.1 to 450 U/mL
      with a detection limit of similar to(0.05 +/- 0.02) U/mL at a
      signal/noise of 3. The advantages of this assay are ease of performance
      having a good specificity and selectivity. In addition, we also
      demonstrate the method can be used for rapid evaluation and screening
      of the inhibitors of MTase and has a potential application in discovery
      of new anticancer drugs.
AU  - Li W
AU  - Wu P
AU  - Zhang H
AU  - Cai CX
PT  - Journal Article
TA  - Anal. Chem.
JT  - Anal. Chem.
SO  - Anal. Chem. 2012 84: 7583-7590.

PMID- 22843599
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Moderately Halotolerant, Arsenite-Oxidizing Bacterium Pseudomonas stutzeri TS44.
PG  - 4473-4474
AB  - We present the draft genome sequence of Pseudomonas stutzeri TS44, a moderately halotolerant,
      arsenite-oxidizing bacterium isolated from arsenic-contaminated
      soil. The genome contains genes for arsenite oxidation, arsenic resistance, and
      ectoine/hydroxyectoine biosynthesis. The genome information will be useful for
      exploring adaptation of P. stutzeri TS44 to an arsenic-contaminated environment.
AU  - Li X
AU  - Gong J
AU  - Hu Y
AU  - Cai L
AU  - Johnstone L
AU  - Grass G
AU  - Rensing C
AU  - Wang G
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4473-4474.

PMID- 23516215
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of the Probiotic Lactobacillus plantarum Strain ZJ316.
PG  - e0009413
AB  - Lactobacillus plantarum strain ZJ316, a probiotic strain with several functions,  was isolated
      from healthy newborn infant fecal samples. Here we report the
      finished and annotated genome sequence of this organism.
AU  - Li X
AU  - Gu Q
AU  - Lou X
AU  - Zhang X
AU  - Song D
AU  - Shen L
AU  - Zhao Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0009413.

PMID- 26950328
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Olsenella scatoligenes SK9K4T, a Producer of 3-Methylindole (Skatole) and 4-Methylphenol (p-Cresol), Isolated from Pig Feces.
PG  - e00042-16
AB  - Olsenella scatoligenes SK9K4(T) is a strictly anaerobic bacterium isolated from pig feces that
      produces the malodorous compounds 3-methylindole (skatole) and
      4-methylphenol (p-cresol). Here, we report the 2.47 Mbp draft genome sequence of
      SK9K4(T), exploring pathways for the synthesis of skatole and p-cresol from the
      amino acids tryptophan and tyrosine, respectively.
AU  - Li X
AU  - Hojberg O
AU  - Noel SJ
AU  - Canibe N
AU  - Jensen BB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00042-16.

PMID- 22328747
VI  - 194
DP  - 2012
TI  - Genome sequence of the highly efficient arsenite-oxidizing bacterium Achromobacter arsenitoxydans SY8.
PG  - 1243-1244
AB  - We report the draft genome sequence of Achromobacter arsenitoxydans SY8, the first reported
      arsenite-oxidizing bacterium belonging to the genus Achromobacter and containing a genomic
      arsenic island, an intact type III secretion system, and multiple metal(loid) transporters.
      The genome may be helpful to explore the mechanisms intertwining metal(loid) resistance and
      pathogenicity.
AU  - Li X
AU  - Hu Y
AU  - Gong J
AU  - Lin Y
AU  - Johnstone L
AU  - Rensiing C
AU  - Wang G
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1243-1244.

PMID- 22328747
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Highly Efficient Arsenite-Oxidizing Bacterium Achromobacter arsenitoxydans SY8.
PG  - 1243-1244
AB  - We report the draft genome sequence of Achromobacter arsenitoxydans SY8, the first reported
      arsenite-oxidizing bacterium belonging to the genus Achromobacter
      and containing a genomic arsenic island, an intact type III secretion system, and
      multiple metal(loid) transporters. The genome may be helpful to explore the
      mechanisms intertwining metal(loid) resistance and pathogenicity.
AU  - Li X
AU  - Hu Y
AU  - Gong J
AU  - Lin Y
AU  - Johnstone L
AU  - Rensing C
AU  - Wang G
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1243-1244.

PMID- 23516203
VI  - 1
DP  - 2013
TI  - Whole-Genome Sequence of a Freshwater Aerobic Anoxygenic Phototroph, Porphyrobacter sp. Strain AAP82, Isolated from the Huguangyan Maar Lake in  Southern China.
PG  - e0007213
AB  - The Porphyrobacter genus (of the class Alphaproteobacteria) contains aerobic anoxygenic
      phototrophic species. Here we report a draft genome sequence of a
      freshwater bacterium, Porphyrobacter sp. strain AAP82. It contains a 38-kb-long
      photosynthesis gene cluster, but carbon-fixation genes are absent. The presence
      of respiratory enzymes, tricarboxylic acid (TCA) cycle, and the Entner-Doudoroff
      pathway demonstrates its aerobic photoorganotrophic character.
AU  - Li X
AU  - Koblizek M
AU  - Feng F
AU  - Li Y
AU  - Jian J
AU  - Zeng Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0007213.

PMID- 25953191
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Se(IV)-Reducing Bacterium Pseudomonas migulae ES3-33.
PG  - e00406-15
AB  - Pseudomonas migulae ES3-33 is a Gram-negative strain that strongly reduces Se(IV) and was
      isolated from a selenium mining area in Enshi, southwest China. Here we
      present the draft genome of this strain containing potential genes involved in
      selenite reduction and a large number of genes encoding resistances to copper and
      antibiotics.
AU  - Li X
AU  - Kot W
AU  - Wang D
AU  - Zheng S
AU  - Wang G
AU  - Hansen LH
AU  - Rensing C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00406-15.

PMID- 24558240
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of mc251, a Highly Hydrogen Peroxide-Resistant Mycobacterium smegmatis Mutant Strain.
PG  - e00092-14
AB  - Here, we report the draft genome sequence of the Mycobacterium tuberculosis-like
      Mycobacterium smegmatis mutant strain, mc(2)51, compared to that of wild-type
      strain M. smegmatis mc(2)155. The draft genome sequence comprises 6,823,739 bp,
      revealing 6,569 coding DNA sequences (CDSs) and 50 RNA genes (4 rRNA genes and 46
      tRNA genes).
AU  - Li X
AU  - Liu F
AU  - Hu Y
AU  - Mi K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00092-14.

PMID- 26950318
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Megasphaera sp. Strain DJF_B143, an Isolate from Pig Hindgut Unable to Produce Skatole.
PG  - e00007-16
AB  - The butyrate-producing Megasphaera spp. predominate in the pig hindgut and may play important
      roles in gut health. Moreover, one Megasphaera isolate has been
      reported to produce the boar taint compound, skatole. Here, we provide a 2.58-Mbp
      draft genome of a pig hindgut isolate, Megasphaera sp. DJF_B143, unable to
      produce skatole.
AU  - Li X
AU  - Marshall IP
AU  - Schreiber L
AU  - Hojberg O
AU  - Canibe N
AU  - Jensen BB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00007-16.

PMID- 18611388
VI  - 381
DP  - 2008
TI  - Continuous monitoring of restriction endonuclease cleavage activity by universal molecular beacon light quenching coupled with real-time polymerase chain reaction.
PG  - 1-7
AB  - We describe a method for sensitive monitoring of restriction endonuclease kinetics and
      activity by use of a universal molecular beacon (U-MB) coupled with real-time polymerase chain
      reaction (PCR). The method is used to monitor the progress of DNA cleavage in a sealed
      reaction tube and offers more accurate and high-throughput detection. The template has a
      universal tail hybridized with the U-MB and the remaining sequence is complementary to one of
      the restriction endonuclease digestion products. The U-MB is replaced by the extension of
      digested product and the fluorescence quenches. With this concept, one universal fluorescence
      probe can be used in different enzyme analytical systems. In the work described here,
      homogenous assays were performed with the restriction endonucleases AluI, EcoRI, XhoI, and
      SacI at smoothly controlled temperature. Cleavage efficiencies were determined, and the
      potential applications of this method were discussed. Furthermore, the AluI and EcoRI cleavage
      reactions were monitored online at varying substrate concentrations at the molecular level,
      and K(m), V(max), and K(cat) values were calculated. The results suggest that U-MB monitoring
      of restriction endonuclease assays based on real-time PCR will be very useful for
      high-throughput, sensitive, and precise assays for enzyme activity screening and evolutionary
      biotechnology analysis.
AU  - Li X
AU  - Song C
AU  - Zhao M
AU  - Li Y
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 2008 381: 1-7.

PMID- 23908294
VI  - 1
DP  - 2013
TI  - Genome Sequence of the Polyphosphate-Accumulating Organism Arthrobacter sp. Strain PAO19 Isolated from Maize Rhizosphere Soil.
PG  - e00566-13
AB  - Arthrobacter sp. strain PAO19 is a polyphosphate-accumulating organism isolated from maize
      rhizosphere soil. Here we report its genome sequence, which may shed
      light on its role in phosphate removal from water bodies. To our knowledge, this
      is the first genome announcement of a polyphosphate-accumulating strain of the
      genus Arthrobacter.
AU  - Li X
AU  - Yuan H
AU  - Yang J
AU  - Li B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00566-13.

PMID- 25428967
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Probiotic Lactobacillus plantarum Strain FMNP01, Isolated from Mango Fruit.
PG  - e01207-14
AB  - Lactobacillus plantarum strain FMNP01 is a new strain with probiotic properties that was
      isolated from fresh mango from Guangzhou, China. Here, we report the
      complete genome of this organism.
AU  - Li XF
AU  - Liao XY
AU  - Liu YF
AU  - Guo LQ
AU  - Ye ZW
AU  - Lin JF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01207-14.

PMID- 24115537
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Lactobacillus plantarum Strain AY01, Isolated from the Raw Material of Fermented Goat Milk Cheese.
PG  - e00737-13
AB  - Lactobacillus plantarum is an important probiotic that is isolated mostly from fermented
      foods. Here, we report the first draft genome sequence of L. plantarum
      strain AY01, isolated from the raw material of fermented goat milk cheese. This
      bacterium, with optimum growth at 30 degrees C, has a G+C content of 43.68%.
AU  - Li XR
AU  - Gong FM
AU  - Zheng HJ
AU  - Zhang ZH
AU  - Luo YY
AU  - Liu CJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00737-13.

PMID- 25858837
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences for Canadian Isolates of Pectobacterium carotovorum subsp. brasiliense with Weak Virulence on Potato.
PG  - e00240-15
AB  - Pectobacterium carotovurum subsp. brasiliense causes soft rot and blackleg diseases on potato.
      Here, we report the draft genome sequences of three weakly
      virulent P. carotovurum subsp. brasiliense strains isolated in Canada. Analysis
      of these genome sequences will help to pinpoint differences in virulence among P.
      carotovurum subsp. brasiliense strains from tropical/subtropical and temperate
      regions, such as Canada and United States. A small number of key factors for
      adaptation to this bacterium's specific environmental niche were also evaluated.
AU  - Li XS
AU  - Yuan KX
AU  - Cullis J
AU  - Levesque CA
AU  - Chen W
AU  - Lewis CT
AU  - De Boer SH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00240-15.

PMID- 28935724
VI  - 5
DP  - 2017
TI  - Genome Sequences for Multiple Clavibacter Strains from Different Subspecies.
PG  - e00721-17
AB  - The Gram-positive genus Clavibacter harbors economically important plant pathogens infecting a
      variety of agricultural crops, such as potato, tomato,
      corn, barley, etc. Here, we report five new genome sequences, those of strains
      CFIA-Cs3N, CFIA-CsR14, LMG 3663T, LMG 7333T, and ATCC 33566T, from different
      subspecies of Clavibacter michiganensis All these genomic data will be used for
      reclassification and niche-adapted feature comparisons.
AU  - Li XS
AU  - Yuan XK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00721-17.

PMID- 21551295
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Staphylococcus aureus T0131, an ST239-MRSA-SCCmec type III Clone isolated in China.
PG  - 3411-3412
AB  - We report here the complete genome sequence of Staphylococcus aureu T0131, which is a
      multi-resistant clinical isolate recovered in China and the
      first sequenced epidemic ST239-MRSA-SCCmec type III strain obtained in
      Asia. Comparison with two published genomes of ST239 reveals the
      polymorphism among strains of this type from different continents.
AU  - Li Y
AU  - Cao B
AU  - Zhang Y
AU  - Zhou J
AU  - Yang B
AU  - Wang L
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3411-3412.

PMID- Not carried by PubMed...
VI  - 6
DP  - 1990
TI  - Study on a type II restriction endonuclease NcrI.
PG  - 309-313
AB  - NcrI isolated from Nocardia carnea C-212 strain is a type II restriction endonuclease.  By
      comparing the NcrI digests of lambda DNA with that of the BglII and characterization of the
      recognition specificity and its cleavage site, NcrI is identified as an isoschizomer of BglII,
      with cleavage site the same as that of BglII at:
      5'...A^GATCT...3'
      3'...TCTAG^A...5'.
AU  - Li Y
AU  - Fu P
AU  - Shi L-Y
PT  - Journal Article
TA  - Chinese Biochem. J.
JT  - Chinese Biochem. J.
SO  - Chinese Biochem. J. 1990 6: 309-313.

PMID- 30505389
VI  - 13
DP  - 2018
TI  - Complete genome sequence of Arcticibacterium luteifluviistationis SM1504(T), a cytophagaceae bacterium isolated from Arctic surface seawater.
PG  - 33
AB  - Arcticibacterium luteifluviistationis SM1504(T) was isolated from Arctic surface  seawater and
      classified as a novel genus of the phylum Bacteroides. To date, no
      Arcticibacterium genomes have been reported, their genomic compositions and
      metabolic features are still unknown. Here, we reported the complete genome
      sequence of A. luteifluviistationis SM1504(T), which comprises 5,379,839 bp with
      an average GC content of 37.20%. Genes related to various stress (such as
      radiation, osmosis and antibiotics) resistance and gene clusters coding for
      carotenoid and flexirubin biosynthesis were detected in the genome. Moreover, the
      genome contained a 245-kb genomic island and a 15-kb incomplete prophage region.
      A great percentage of proteins belonging to carbohydrate metabolism especially in
      regard to polysaccharides utilization were found. These related genes and
      metabolic characteristics revealed genetic basis for adapting to the diverse
      extreme Arctic environments. The genome sequence of A. luteifluviistationis
      SM1504(T) also implied that the genus Arcticibacterium may act as a vital organic
      carbon matter decomposer in the Arctic seawater ecosystem.
AU  - Li Y
AU  - Guo XH
AU  - Dang YR
AU  - Sun LL
AU  - Zhang XY
AU  - Chen XL
AU  - Qin QL
AU  - Wang P
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2018 13: 33.

PMID- 22633940
VI  - 38
DP  - 2012
TI  - Electrogenerated chemiluminescence biosensing method for the detection of DNA methylation and assay of the methyltransferase activity.
PG  - 407-410
AB  - A novel electrogenerated chemiluminescence (ECL) biosensing method for highly sensitive
      detection of DNA methylation and assay of the CpG
      methyltransferase (M. Sssl) activity was developed on basis of
      enzyme-linkage reactions and ruthenium complex served as an ECL tag.
      The ECL biosensing electrode was fabricated by self-assembling 5'-thiol
      modified 32-mer single-strand DNA (ss-DNA)-tagged with ruthenium bis
      (2,2'-bipyridine) (2,2'-bipyridine-4,4'-dicarboxylic
      acid)-ethylenediamine on the surface of a gold electrode, and then
      hybridized with complementary ss-DNA to form duplex DNA (ds-DNA). When
      M. Sssl and S-adenosylmethionine were introduced, all cytosine residues
      within 5'-CG-3' of ds-DNA on the biosensing electrode were methylated.
      After the methylated biosensing electrode was treated by HpaII
      endonuclease, the un-methylated cytosines were cleaved, thus led to
      decrease ECL signal. The ECL intensity of ECL biosensing electrode is
      related to the methylation level and M. Sssl activity in a fixed
      concentration HpaII endonuclease. The increased ECL intensity was
      direct proportion to M. Sssl activity in the range from 0.05 to 100
      U/mL with a detection limit of 0.02 U/mL. This work demonstrates that
      the combination of the enzyme-linkage reactions with a highly sensitive
      ECL technique is a great promising approach for the detection of DNA
      methylation level, assay of the activity of MTase, and evaluation of
      the capability of inhibitors for the methyltransferase.
AU  - Li Y
AU  - Huang CC
AU  - Zheng JB
AU  - Qi HL
PT  - Journal Article
TA  - Biosensors and Bioelectronics
JT  - Biosensors and Bioelectronics
SO  - Biosensors and Bioelectronics 2012 38: 407-410.

PMID- 27602181
VI  - 11
DP  - 2016
TI  - The complete genome sequence of the methanogenic archaeon ISO4-H5 provides insights into the methylotrophic lifestyle of a ruminal representative of the  Methanomassiliicoccales.
PG  - 59
AB  - Methane emissions from agriculture represent around 9 % of global anthropogenic greenhouse
      emissions. The single largest source of this methane is animal enteric
      fermentation, predominantly from ruminant livestock where it is produced mainly
      in their fermentative forestomach (or reticulo-rumen) by a group of archaea known
      as methanogens. In order to reduce methane emissions from ruminants, it is
      necessary to understand the role of methanogenic archaea in the rumen, and to
      identify their distinguishing characteristics that can be used to develop methane
      mitigation technologies. To gain insights into the role of methylotrophic
      methanogens in the rumen environment, the genome of a methanogenic archaeon has
      been sequenced. This isolate, strain ISO4-H5, was isolated from the ovine rumen
      and belongs to the order Methanomassiliicoccales. Genomic analysis suggests
      ISO4-H5 is an obligate hydrogen-dependent methylotrophic methanogen, able to use
      methanol and methylamines as substrates for methanogenesis. Like other organisms
      within this order, ISO4-H5 does not possess genes required for the first six
      steps of hydrogenotrophic methanogenesis. Comparison between the genomes of
      different members of the order Methanomassiliicoccales revealed strong
      conservation in energy metabolism, particularly in genes of the methylotrophic
      methanogenesis pathway, as well as in the biosynthesis and use of pyrrolysine.
      Unlike members of Methanomassiliicoccales from human sources, ISO4-H5 does not
      contain the genes required for production of coenzyme M, and so likely requires
      external coenzyme M to survive.
AU  - Li Y
AU  - Leahy SC
AU  - Jeyanathan J
AU  - Henderson G
AU  - Cox F
AU  - Altermann E
AU  - Kelly WJ
AU  - Lambie SC
AU  - Janssen PH
AU  - Rakonjac J
AU  - Attwood GT
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 59.

PMID- 27491987
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Paenibacillus polymyxa KF-1, an Excellent Producer of Microbicides.
PG  - e00727-16
AB  - We report here the draft genome sequence of Paenibacillus polymyxa KF-1, which exhibits
      excellent antimicrobial activity. It encodes the synthase of bacitracin,
      kalimantacin, bacillomycin, iturin, fusaricidin, tridecaptin, and pelgipeptin and
      biosynthetic pathways of antiviral curldan and levan polysaccharides. Also, a
      novel prophage is involved in this genome that contains endolysin-encoding genes.
AU  - Li Y
AU  - Li Q
AU  - Li Y
AU  - Gao J
AU  - Fan X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00727-16.

PMID- 28428833
VI  - 12
DP  - 2017
TI  - Complete genome sequence of Kosakonia oryzae type strain Ola 51T.
PG  - 28
AB  - Strain Ola 51T (=LMG 24251T = CGMCC 1.7012T) is the type strain of the species Kosakonia
      oryzae and was isolated from surface-sterilized roots of the wild rice
      species Oryza latifolia grown in Guangdong, China. Here we summarize the features
      of the strain Ola 51T and describe its complete genome sequence. The genome
      contains one circular chromosome of 5,303,342 nucleotides with 54.01% GC content,
      4773 protein-coding genes, 16 rRNA genes, 76 tRNA genes, 13 ncRNA genes, 48
      pseudo genes, and 1 CRISPR array.
AU  - Li Y
AU  - Li S
AU  - Chen M
AU  - Peng G
AU  - Tan Z
AU  - An Q
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 28.

PMID- 26514405
VI  - 1857
DP  - 2016
TI  - Characterization of red-shifted phycobilisomes isolated from the chlorophyll f-containing cyanobacterium Halomicronema hongdechloris.
PG  - 107-114
AB  - Phycobilisomes are the main light-harvesting protein complexes in cyanobacteria
      and some algae. It is commonly accepted that these complexes only absorb green
      and orange light, complementing chlorophyll absorbance. Here, we present a new
      phycobilisome derived complex that consists only of allophycocyanin core
      subunits, having red-shifted absorption peaks of 653 and 712 nm. These
      red-shifted phycobiliprotein complexes were isolated from the chlorophyll
      f-containing cyanobacterium, Halomicronema hongdechloris, grown under
      monochromatic 730 nm-wavelength (far-red) light. The 3D model obtained from
      single particle analysis reveals a double disk assembly of 120-145 A with two
      alpha/beta allophycocyanin trimers fitting into the two separated disks. They are
      significantly smaller than typical phycobilisomes formed from allophycocyanin
      subunits and core-membrane linker proteins, which fit well with a reduced
      distance between thylakoid membranes observed from cells grown under far-red
      light. Spectral analysis of the dissociated and denatured phycobiliprotein
      complexes grown under both these light conditions shows that the same bilin
      chromophore, phycocyanobilin, is exclusively used. Our findings show that
      red-shifted phycobilisomes are required for assisting efficient far-red light
      harvesting. Their discovery provides new insights into the molecular mechanisms
      of light harvesting under extreme conditions for photosynthesis, as well as the
      strategies involved in flexible chromatic acclimation to diverse light
      conditions.
AU  - Li Y
AU  - Lin Y
AU  - Garvey CJ
AU  - Birch D
AU  - Corkery RW
AU  - Loughlin PC
AU  - Scheer H
AU  - Willows RD
AU  - Chen M
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 2016 1857: 107-114.

PMID- 21551296
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Aeromonas Veronii Strain B565.
PG  - 3389-3390
AB  - Aeromonas veronii strain B565 was isolated from aquaculture pond sediment in China. We present
      here the complete genome sequence of B565 and compare
      it with 2 published genome sequences of pathogenic strains in Aeromonas
      genus. The result represents an independent step-wise acquisition of
      virulence factors of pathogenic strains in this genus.
AU  - Li Y
AU  - Liu Y
AU  - Zhou Z
AU  - Huang H
AU  - Ren Y
AU  - Zhang Y
AU  - Li G
AU  - Zhou Z
AU  - Wang L
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3389-3390.

PMID- 9356347
VI  - 237
DP  - 1997
TI  - Analysis of 74 kb of DNA located at the right end of the 330-kb chlorella virus PBCV-1 genome.
PG  - 360-377
AB  - This report completes a preliminary analysis of the sequence of the 330,740-bp chlorella virus
      PBCV-1 genome, the largest virus genome to be sequenced to date.  The PBCV-1 genome is 57% the
      size of the genome from the smallest self-replicating organism, Mycoplasma genitalium,
      Analysis of 74 kb of newly sequenced DNA, from the right terminus of the PBCV-1 genome,
      revealed 153 open reading frames of 65 codons or longer.  Eighty-five of these ORFs, which are
      evenly distributed on both strands of the DNA, were considered major ORFs.  Fifty-nine of the
      major ORFs were separated by less than 100 bp.  The largest intergenic distance was 729 bp,
      which occurred between two ORFs located in the 2.2-kb inverted terminal repeat region of the
      PBCV-1 genome.  Twenty-seven of the 85 major ORFs resemble proteins in databases, including
      the large subunit of ribonucleotide diphosphate reductase, ATP-dependent DNA ligase, type II
      DNA topoisomerase, a helicase, histidine decarboxylase, dCMP deaminase, dUTP pyrophosphatase,
      proliferating cell nuclear antigen, a transposase, fungal translation elongation factor 3, UDP
      glucose dehydrogenase, a protein kinase, and an adeneine DNA methyltransferase and its
      corresponding DNA site-specific endonuclease.  Seventeen of the 153 ORFs resembled other
      PBCV-1 ORFs, suggesting that they represent either gene duplications or gene families.
AU  - Li Y
AU  - Lu Z
AU  - Sun L
AU  - Ropp S
AU  - Kutish GF
AU  - Rock DL
AU  - Van Etten JL
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1997 237: 360-377.

PMID- 25103755
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Dye-Decolorizing and Nanowire-Producing Bacterium Shewanella xiamenensis BC01.
PG  - e00721-14
AB  - Shewanella xiamenensis BC01 is an important biodecolorizing and nanowire-producing bacterium
      which was found in Xiamen, China. Here, we present
      the draft genome sequence consisting of 4,677,169 bp (GC content, 46.21%) and
      3,999 coded proteins. This information boosts insight into and understanding of
      the genetic evolution of Shewanella species.
AU  - Li Y
AU  - Ng IS
AU  - Zhang X
AU  - Wang N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00721-14.

PMID- 26750304
VI  - 6
DP  - 2016
TI  - Changes in pathogenicity and immunogenicity of Mycoplasma mycoides subsp. mycoides strains revealed by comparative genomics analysis.
PG  - 19081
AB  - Mycoplasma mycoides subsp. mycoides is the causative agent of contagious bovine
      pleuropneumonia. A pathogenic strain BEN-1 was isolated from bovine lung and
      underwent continuous passages in rabbits for 468 generations. During this
      process, the strain's strong virulence became weak and, gradually, it lost the
      ability to confer protective immunity in cattle but developed virulence in
      rabbits. In order to gain insight into the mechanisms behind the reduction in
      virulence and the loss of immunogenicity, we sequenced five representative
      strains of the BEN series, including the original strain (BEN-1), the strain
      generation that first acquired virulence in rabbits (BEN-50), the two vaccine
      strain generations (BEN-181 and BEN-326), and the strain generation showing the
      greatest loss of immunogenicity (BEN-468). The gene mutation rate in the four
      different propagation stages varied greatly, and over half of variations observed
      in each generation were removed during the propagation process. However, the
      variation maintained in the BEN-468 generation might contribute to its changes in
      virulence and immunogenicity. We thus identified 18 genes associated with host
      adaptation, six genes contributing to virulence in cattle, and 35 genes
      participating in conferring immunity in cattle. These findings might help us
      optimize the vaccine to obtain more effective immunization results.
AU  - Li Y
AU  - Wang Y
AU  - Wang R
AU  - Zhu Y
AU  - Liu S
AU  - Wang Q
AU  - Shao J
AU  - Chen Y
AU  - Gao L
AU  - Zhou C
AU  - Liu H
AU  - Wang X
AU  - Zheng H
AU  - Xin J
PT  - Journal Article
TA  - Sci. Rep.
JT  - Sci. Rep.
SO  - Sci. Rep. 2016 6: 19081.

PMID- 
VI  - 137
DP  - 2014
TI  - Label-free and amplified electrogenerated chemiluminescence biosensing method for the determination of DNA methyltransferase activity using signal reagent-assembled graphene oxide.
PG  - 454-461
AB  - A novel label-free electrogenerated chemiluminescence (ECL) biosensing method for the
      determination of DNA methyltransferase (MTase) activity was developed on base of
      enzyme-linkage reactions and tris(1, 10-phenanthroline) ruthenium-assembled graphene oxide
      (GO) served as an ECL signal compound. The ECL biosensing electrode was fabricated by
      self-assembling 5'-thiol modified hairpin-capture DNA probe containing methylation
      recognition site 5'-GATC-3' on the surface of a gold electrode. When DNA adenine methylation
      (Dam) MTase and S-adenosyl-L-methionine were introduced, all adenine residues within
      5'-GATC-3' of hairpin-capture DNA probe on the biosensing electrode were methylated. After
      the methylated biosensing electrode was treated by the methylation-sensitive restriction
      endonuclease Dpn I, the methylated adenines were cleaved, methylation-induced scission of
      hairpin-capture DNA probe would displace the hairpin section and remain the 'capture DNA
      probe' section on the gold electrode, then a long ssDNA was immobilized via the partial
      hybridization reaction between long ssDNA and hairpin-capture DNA probe remained section, the
      more binding site allow tris(1, 10-phenanthroline) ruthenium-assembled GO to be more bound to
      the long ssDNA on the electrode surface through both hydrophobic and pi-pi stacking
      interaction, in conjunction with the generation of a increased ECL signal. The ECL intensity
      versus the concentration of Dam MTase was linear in the range from 0.02 unit/mL to 10 unit/mL.
      The detection limit was 0.01 unit/mL. This work demonstrates that using the different
      affinities of GO for ssDNA and dsDNA for the fabrication of the label-free ECL biosensing
      method for DNA MTase activity is promising approach.
AU  - Li Y
AU  - Yan Z
AU  - Zheng J
AU  - Qi H
PT  - Journal Article
TA  - Electrochim. Acta.
JT  - Electrochim. Acta.
SO  - Electrochim. Acta. 2014 137: 454-461.

PMID- 29963027
VI  - 9
DP  - 2018
TI  - Genome Sequencing of Streptomyces atratus SCSIOZH16 and Activation Production of Nocardamine via Metabolic Engineering.
PG  - 1269
AB  - The Actinomycetes are metabolically flexible microorganisms capable of producing
      a wide range of interesting compounds, including but by no means limited to,
      siderophores which have high affinity for ferric iron. In this study, we report
      the complete genome sequence of marine-derived Streptomyces atratus ZH16 and the
      activation of an embedded siderophore gene cluster via the application of
      metabolic engineering methods. The S. atratus ZH16 genome reveals that this
      strain has the potential to produce 26 categories of natural products (NPs)
      barring the ilamycins. Our activation studies revealed S. atratus SCSIO ZH16 to
      be a promising source of the production of nocardamine-type (desferrioxamine)
      compounds which are important in treating acute iron intoxication and performing
      ecological remediation. We conclude that metabolic engineering provides a highly
      effective strategy by which to discover drug-like compounds and new NPs in the
      genomic era.
AU  - Li Y
AU  - Zhang C
AU  - Liu C
AU  - Ju J
AU  - Ma J
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2018 9: 1269.

PMID- 21731639
VI  - 6
DP  - 2011
TI  - The Complete Genome Sequence of Mycoplasma bovis Strain Hubei-1.
PG  - e20999
AB  - Infection by Mycoplasma bovis (M. bovis) can induce diseases, such as pneumonia and otitis
      media in young calves and
      mastitis and arthritis in older animals. Here, we report the finished and annotated genome
      sequence of M. bovis strain
      Hubei-1, a strain isolated in 2008 that caused calf pneumonia on a Chinese farm. The genome of
      M. bovis strain Hubei-1
      contains a single circular chromosome of 953,114 bp with a 29.37% GC content. We identified
      803 open reading frames
      (ORFs) that occupy 89.5% of the genome. While 34 ORFs were Hubei-1 specific, 662 ORFs had
      orthologs in the M. bovis type
      strain PG45 genome. Genome analysis validated lateral gene transfer between M. bovis and the
      Mycoplasma mycoides
      subspecies mycoides, while phylogenetic analysis found that the closest M. bovis neighbor is
      Mycoplasma agalactiae.
      Glycerol may be the main carbon and energy source of M. bovis, and most of the biosynthesis
      pathways were incomplete.
      We report that 47 lipoproteins, 12 extracellular proteins and 18 transmembrane proteins are
      phase-variable and may help M.
      bovis escape the immune response. Besides lipoproteins and phase-variable proteins, genomic
      analysis found two possible
      pathogenicity islands, which consist of four genes and 11 genes each, and several other
      virulence factors including
      hemolysin, lipoate protein ligase, dihydrolipoamide dehydrogenase, extracellular cysteine
      protease and 59-nucleotidase.
AU  - Li Y
AU  - Zheng H
AU  - Liu Y
AU  - Jiang Y
AU  - Xin J
AU  - Chen W
AU  - Song Z
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2011 6: e20999.

PMID- 25428978
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Algicidal Bacterium Mangrovimonas yunxiaonensis Strain LY01.
PG  - e01234-14
AB  - Mangrovimonas yunxiaonensis LY01, a novel bacterium isolated from mangrove sediment, showed
      high algicidal effects on harmful algal blooms of Alexandrium
      tamarense. Here, we present the first draft genome sequence of this strain to
      further understanding of the functional genes related to algicidal activity.
AU  - Li Y
AU  - Zhu H
AU  - Li C
AU  - Zhang H
AU  - Chen Z
AU  - Zheng W
AU  - Xu H
AU  - Zheng T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01234-14.

PMID- 17175537
VI  - 35
DP  - 2007
TI  - Association of Dnmt3a and thymine DNA glycosylase links DNA methylation with base-excision repair.
PG  - 390-400
AB  - While methylcytosines serve as the fifth base encoding epigenetic information, they are also a
      dangerous endogenous mutagen due to their
      intrinsic instability. Methylcytosine undergoes spontaneous deamination,
      at a rate much higher than cytosine, to generate thymine. In mammals, two
      repair enzymes, thymine DNA glycosylase (TDG) and methyl-CpG binding
      domain 4 (MBD4), have evolved to counteract the mutagenic effect of
      methylcytosines. Both recognize G/T mismatches arising from methylcytosine
      deamination and initiate base-excision repair that corrects them to G/C
      pairs. However, the mechanism by which the methylation status of the
      repaired cytosines is restored has remained unknown. We show here that the
      DNA methyltransferase Dnmt3a interacts with TDG. Both the PWWP domain and
      the catalytic domain of Dnmt3a are able to mediate the interaction with
      TDG at its N-terminus. The interaction affects the enzymatic activity of
      both proteins: Dnmt3a positively regulates the glycosylase activity of
      TDG, while TDG inhibits the methylation activity of Dnmt3a in vitro. These
      data suggest a mechanistic link between DNA repair and remethylation at
      sites affected by methylcytosine deamination.
AU  - Li YQ
AU  - Zhou PZ
AU  - Zheng XD
AU  - Walsh CP
AU  - Xu GL
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2007 35: 390-400.

PMID- 28860251
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequence of Chlamydia abortus Strain GN6 Isolated from Aborted Yak Fetus.
PG  - e00893-17
AB  - The obligate intracellular Gram-negative bacterium Chlamydia abortus is one of the causative
      agents of abortion and fetal loss in sheep, goats, and cattle in
      many countries. It also affects the reproductivity of yaks (Bos grunniens). This
      study reports the whole-genome sequence of Chlamydia abortus strain GN6, which
      was isolated from aborted yak fetus in Qinghai-Tibetan Plateau, China.
AU  - Li Z
AU  - Cai J
AU  - Cao X
AU  - Lou Z
AU  - Chao Y
AU  - Kan W
AU  - Zhou J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00893-17.

PMID- 23209214
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Human-Pathogenic Bacterium Vibrio vulnificus Type Strain ATCC 27562.
PG  - 6954-6955
AB  - Vibrio vulnificus, which is the causative agent of cholera, is a Gram-negative, curved,
      motile, and rod-shaped bacterium. Here, we present the draft genome
      sequence of the type strain, ATCC 27562, which was the first isolated Vibrio
      vulnificus strain.
AU  - Li Z
AU  - Chen H
AU  - Chen X
AU  - Zhou T
AU  - Zhao L
AU  - Zhang C
AU  - Jin W
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6954-6955.

PMID- 29567737
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Bacillus velezensis Lzh-a42, a Plant Growth-Promoting Rhizobacterium Isolated from Tomato Rhizosphere.
PG  - e00161-18
AB  - The plant growth-promoting rhizobacterium Bacillus velezensis strain Lzh-a42, which has
      antimicrobial activity, was isolated from tomato rhizosphere. Here, we
      report its genome sequence, which includes several predicted functional genes
      related to secondary metabolite biosynthesis, antimicrobial activity, and biofilm
      synthesis.
AU  - Li Z
AU  - Chen M
AU  - Ran K
AU  - Wang J
AU  - Zeng Q
AU  - Song F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00161-18.

PMID- 29724833
VI  - 6
DP  - 2018
TI  - Genome Sequence of Pseudomonas chlororaphis Lzh-T5, a Plant Growth-Promoting Rhizobacterium with Antimicrobial Activity.
PG  - e00328-18
AB  - Pseudomonas chlororaphis Lzh-T5 is a plant growth-promoting rhizobacterium (PGPR) with
      antimicrobial activity isolated from tomato rhizosphere in the city of
      Dezhou, Shandong Province, China. Here, the draft genome sequence of P.
      chlororaphis Lzh-T5 is reported, and several functional genes related to
      antifungal antibiotics and siderophore biosynthesis have been found in the
      genome.
AU  - Li Z
AU  - Li X
AU  - Zeng Q
AU  - Chen M
AU  - Liu D
AU  - Wang J
AU  - Shen L
AU  - Song F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00328-18.

PMID- 22328762
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Sinorhizobium meliloti CCNWSX0020, a Nitrogen-Fixing Symbiont with Copper Tolerance Capability Isolated from Lead-Zinc Mine Tailings.
PG  - 1267-1268
AB  - Sinorhizobium meliloti CCNWSX0020 was isolated from Medicago lupulina plants growing in
      lead-zinc mine tailings, which can establish a symbiotic relationship
      with Medicago species. Also, the genome of this bacterium contains a number of
      protein-coding sequences related to metal tolerance. We anticipate that the
      genomic sequence provides valuable information to explore environmental
      bioremediation.
AU  - Li Z
AU  - Ma Z
AU  - Hao X
AU  - Wei G
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1267-1268.

PMID- 28883140
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Listeria monocytogenes Strains from Listeriosis Outbreaks Linked to Soft Cheese in Washington State.
PG  - e00936-17
AB  - Listeria monocytogenes has caused listeriosis outbreaks linked to soft cheese. Here, we report
      the draft genome sequences of seven L. monocytogenes isolates
      from two possibly related outbreaks caused by soft cheese products in Washington
      State.
AU  - Li Z
AU  - Marsland PA
AU  - Meek RT
AU  - Eckmann K
AU  - Allard MW
AU  - Perez-Osorio AC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00936-17.

PMID- 29472333
VI  - 6
DP  - 2018
TI  - Complete Genome Sequences of Two Porcine Enterotoxigenic Escherichia coli Strains.
PG  - e00059-18
AB  - Enterotoxigenic Escherichia coli (ETEC) is one of the main causes of illness and  death in
      neonatal and recently weaned pigs. Here, we sequenced the genomes of two
      ETEC strains that were previously used as inactivated vaccines in China.
AU  - Li Z
AU  - Song N
AU  - Li W
AU  - Hardwidge PR
AU  - Bu Z
AU  - Liu S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00059-18.

PMID- 21994922
VI  - 193
DP  - 2011
TI  - Genome Sequence of the Tobacco Bacterial Wilt Pathogen Ralstonia solanacearum.
PG  - 6088-6089
AB  - Ralstonia solanacearum is a causal agent of plant bacterial wilt with thousands of distinct
      strains in a heterogeneous species complex. Here we
      report the genome sequence of a phylotype IB strain, Y45, isolated from
      tobacco (Nicotiana tabacum) in China. Compared with the published genomes
      of eight strains which were isolated from other hosts and habitats, 794
      specific genes and many rearrangements/inversion events were identified in
      the tobacco strain, demonstrating that this strain represents an important
      node within the R. solanacearum complex.
AU  - Li Z
AU  - Wu S
AU  - Bai X
AU  - Liu Y
AU  - Lu J
AU  - Liu Y
AU  - Xiao B
AU  - Lu X
AU  - Fan L
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6088-6089.

PMID- 21868801
VI  - 193
DP  - 2011
TI  - Genome Sequence of the Halotolerant Marine Bacterium Myxococcus fulvus HW-1.
PG  - 5015-5016
AB  - Myxococcus fulvus HW-1 (ATCC BAA-855) is a halotolerant marine myxobacterium. This strain
      exhibits complex social behaviors in the
      presence of low concentrations of seawater but adopts an asocial living
      pattern under oceanic conditions. The whole genome of M. fulvus HW-1 will
      enable us to further investigate the details of its evolution.
AU  - Li ZF
AU  - Li X
AU  - Liu H
AU  - Liu X
AU  - Han K
AU  - Wu ZH
AU  - Hu W
AU  - Li FF
AU  - Li YZ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5015-5016.

PMID- 28336597
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Providencia stuartii PS71, a Multidrug-Resistant Strain  Associated with Nosocomial Infections in Greece.
PG  - e00056-17
AB  - Providencia stuartii is frequently associated with nosocomial outbreaks and displays intrinsic
      resistance to many commonly used antimicrobials. We report
      here the draft genome sequence of a P. stuartii strain carrying acquired
      resistance genes conferring panresistance to cephalosporins (blaSHV-5 and
      blaVEB-1), carbapenems (blaVIM-1), and aminoglycosides (rmtB) involved in an
      outbreak in Greek hospitals.
AU  - Liakopoulos A
AU  - Oikonomou O
AU  - Wareham DW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00056-17.

PMID- 11756544
VI  - 22
DP  - 2002
TI  - Cooperativity between DNA methyltransferases in the maintenance methylation of repetitive elements.
PG  - 480-491
AB  - We used mouse embryonic stem (ES) cells with systematic gene knockouts for DNA
      methyltransferases to delineate the roles of DNA methyltransferase 1 (Dnmt1) and Dnmt3a and
      Dnmt3b in maintaining methylation patterns in the mouse genome. Dnmt1 alone was able to
      maintain
      methylation of most CpG-poor regions analyzed. In contrast, both Dnmt1 and Dnmt3a and/or
      Dnmt3b were required for methylation of a select class of sequences which included abundant
      murine LINE-1 promoters. We used a novel hemimethylation assay to show that even in wild-type
      cells these sequences contain high levels of hemimethylated DNA, suggestive of poor
      maintenance methylation. We showed that Dnmt3a and/or -3b could restore methylation of these
      sequences to pretreatment levels following transient exposure of cells to 5-aza-CdR, whereas
      Dnmt1 by itself could not. We conclude that ongoing de novo methylation by Dnmt3a and/or
      Dnmt3b compensates for inefficient maintenance methylation by Dnmt1 of these endogenous
      repetitive sequences. Our results reveal a previously unrecognized degree of cooperativity
      among mammalian DNA methyltransferases in ES cells.
AU  - Liang G
AU  - Chan MF
AU  - Tomigahara Y
AU  - Tsai YC
AU  - Gonzales FA
AU  - Li E
AU  - Laird PW
AU  - Jones PA
PT  - Journal Article
TA  - Mol. Cell. Biol.
JT  - Mol. Cell. Biol.
SO  - Mol. Cell. Biol. 2002 22: 480-491.

PMID- 24083337
VI  - 13
DP  - 2013
TI  - Naturally-occurring, dually-functional fusions between restriction endonucleases  and regulatory proteins.
PG  - 218
AB  - Background: Restriction-modification (RM) systems appear to play key roles in modulating gene
      flow among bacteria and archaea. Because the restriction
      endonuclease (REase) is potentially lethal to unmethylated new host cells,
      regulation to ensure pre-expression of the protective DNA methyltransferase
      (MTase) is essential to the spread of RM genes. This is particularly true for
      Type IIP RM systems, in which the REase and MTase are separate,
      independently-active proteins. A substantial subset of Type IIP RM systems are
      controlled by an activator-repressor called C protein. In these systems, C
      controls the promoter for its own gene, and for the downstream REase gene that
      lacks its own promoter. Thus MTase is expressed immediately after the RM genes
      enter a new cell, while expression of REase is delayed until sufficient C protein
      accumulates. To study the variation in and evolution of this regulatory
      mechanism, we searched for RM systems closely related to the well-studied C
      protein-dependent PvuII RM system. Unexpectedly, among those found were several
      in which the C protein and REase genes were fused. Results: The gene for
      CR.NsoJS138I fusion protein (nsoJS138ICR, from the bacterium Niabella soli) was
      cloned, and the fusion protein produced and partially purified. Western blots
      provided no evidence that, under the conditions tested, anything other than
      full-length fusion protein is produced. This protein had REase activity in vitro
      and, as expected from the sequence similarity, its specificity was
      indistinguishable from that for PvuII REase, though the optimal reaction
      conditions were different. Furthermore, the fusion was active as a C protein, as
      revealed by in vivo activation of a lacZ reporter fusion to the promoter region
      for the nsoJS138ICR gene. Conclusions: Fusions between C proteins and REases have
      not previously been characterized, though other fusions have (such as between
      REases and MTases). These results reinforce the evidence for impressive
      modularity among RM system proteins, and raise important questions about the
      implications of the C-REase fusions on expression kinetics of these RM systems.
AU  - Liang J
AU  - Blumenthal RM
PT  - Journal Article
TA  - BMC Evol. Biol.
JT  - BMC Evol. Biol.
SO  - BMC Evol. Biol. 2013 13: 218.

PMID- 30534351
VI  - 13
DP  - 2018
TI  - Complete genome of Rhizobium leguminosarum Norway, an ineffective Lotus micro-symbiont.
PG  - 36
AB  - Rhizobia bacteria engage in nitrogen-fixing root nodule symbiosis, a mutualistic  interaction
      with legume plants in which a bidirectional nutrient exchange takes
      place. Occasionally, this interaction is suboptimal resulting in the formation of
      ineffective nodules in which little or no atmospheric nitrogen fixation occurs.
      Rhizobium leguminosarum Norway induces ineffective nodules in a wide range of
      Lotus hosts. To investigate the basis of this phenotype, we sequenced the
      complete genome of Rl Norway and compared it to the genome of the closely related
      strain R. leguminosarum bv. viciae 3841. The genome comprises 7,788,085 bp,
      distributed on a circular chromosome containing 63% of the genomic information
      and five large circular plasmids. The functionally classified bacterial gene set
      is distributed evenly among all replicons. All symbiotic genes (nod, fix, nif)
      are located on the pRLN3 plasmid. Whole genome comparisons revealed differences
      in the metabolic repertoire and in protein secretion systems, but not in
      classical symbiotic genes.
AU  - Liang J
AU  - Hoffrichter A
AU  - Brachmann A
AU  - Marin M
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2018 13: 36.

PMID- 17439960
VI  - 35
DP  - 2007
TI  - DNA modification by sulfur: analysis of the sequence recognition specificity surrounding the modification sites.
PG  - 2944-2954
AB  - The Dnd (DNA degradation) phenotype, reflecting a novel DNA modification by sulfur in
      Streptomyces lividans 1326, was strongly aggravated when one (dndB) of
      the five genes (dndABCDE) controlling it was mutated. Electrophoretic banding
      patterns of a plasmid (pHZ209), reflecting DNA degradation, displayed a clear
      change from a preferential modification site in strain 1326 to more random
      modifications in the mutant. Fourteen randomly modifiable sites on pHZ209 were
      localized, and each seemed to be able to be modified only once. Residues in a
      region (5'-c-cGGCCgccg-3') including a highly conserved 4-bp central core
      (5'-GGCC-3') in a well-documented preferential modification site were assessed
      for their necessity by site-directed mutagenesis. While the central core (GGCC)
      was found to be stringently required in 1326 and in the mutant, 'gccg' flanking
      its right could either abolish or reduce the modification frequency only in the
      mutant, and two separate nucleotides to the left had no dramatic effect. The lack
      of essentiality of DndB for S-modification suggests that it might only be
      required for enhancing or stabilizing the activity of a protein complex at the
      required preferential modification site, or resolving secondary structures
      flanking the modifiable site(s), known to constitute an obstacle for efficient
      modification.
AU  - Liang J
AU  - Wang Z
AU  - He X
AU  - Li J
AU  - Zhou X
AU  - Deng Z
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2007 35: 2944-2954.

PMID- 
VI  - 13
DP  - 2013
TI  - Naturally-occurring, dually-functional fusions between restriction endonucleases and regulatory proteins.
PG  - 0
AB  - Background: Restriction-modification (RM) systems appear to play key roles in modulating gene
      flow among bacteria and archaea. Because the
      restriction endonuclease (REase) is potentially lethal to unmethylated
      new host cells, regulation to ensure pre-expression of the protective
      DNA methyltransferase (MTase) is essential to the spread of RM genes.
      This is particularly true for Type IIP RM systems, in which the REase
      and MTase are separate, independently-active proteins. A substantial
      subset of Type IIP RM systems are controlled by an activator-repressor
      called C protein. In these systems, C controls the promoter for its own
      gene, and for the downstream REase gene that lacks its own promoter.
      Thus MTase is expressed immediately after the RM genes enter a new
      cell, while expression of REase is delayed until sufficient C protein
      accumulates. To study the variation in and evolution of this regulatory
      mechanism, we searched for RM systems closely related to the
      well-studied C protein-dependent PvuII RM system. Unexpectedly, among
      those found were several in which the C protein and REase genes were
      fused.
      Results: The gene for CR. NsoJS138I fusion protein (nsoJS138ICR,
      from the bacterium Niabella soli) was cloned, and the fusion protein
      produced and partially purified. Western blots provided no evidence
      that, under the conditions tested, anything other than full-length
      fusion protein is produced. This protein had REase activity in vitro
      and, as expected from the sequence similarity, its specificity was
      indistinguishable from that for PvuII REase, though the optimal
      reaction conditions were different. Furthermore, the fusion was active
      as a C protein, as revealed by in vivo activation of a lacZ reporter
      fusion to the promoter region for the nsoJS138ICR gene.
      Conclusions: Fusions between C proteins and REases have not
      previously been characterized, though other fusions have (such as
      between REases and MTases). These results reinforce the evidence for
      impressive modularity among RM system proteins, and raise important
      questions about the implications of the C-REase fusions on expression
      kinetics of these RM systems.
AU  - Liang JX
AU  - Blumenthal RM
PT  - Journal Article
TA  - BMC Evol. Biol.
JT  - BMC Evol. Biol.
SO  - BMC Evol. Biol. 2013 13: 0.

PMID- 28860256
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Vibrio sp. Strain 2521-89, a Close Relative of Vibrio cholerae Isolated from Lake Water in New Mexico, USA.
PG  - e00905-17
AB  - Vibrio sp. strain 2521-89 is an environmental isolate from lake water in New Mexico, USA.
      Average nucleotide identity, in silico DNA-DNA hybridization, and
      core genome single-nucleotide polymorphism (SNP)-based phylogenetic analysis
      suggest that this may be a potentially novel species that is closely related to
      Vibrio cholerae.
AU  - Liang K
AU  - Orata FD
AU  - Winkjer NS
AU  - Rowe LA
AU  - Tarr CL
AU  - Boucher Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00905-17.

PMID- 22887678
VI  - 194
DP  - 2012
TI  - Genome Sequence of Pseudomonas putida Strain SJTE-1, a Bacterium Capable of Degrading Estrogens and Persistent Organic Pollutants.
PG  - 4781-4782
AB  - Pseudomonas putida strain SJTE-1 can utilize 17beta-estradiol and other environmental
      estrogens/toxicants, such as estrone, and naphthalene as sole
      carbon sources. We report the draft genome sequence of strain SJTE-1 (5,551,505
      bp, with a GC content of 62.25%) and major findings from its annotation, which
      could provide insights into its biodegradation mechanisms.
AU  - Liang R
AU  - Liu H
AU  - Tao F
AU  - Liu Y
AU  - Ma C
AU  - Liu X
AU  - Liu J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4781-4782.

PMID- 25953158
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Paenibacillus polymyxa EBL06, a Plant Growth-Promoting Bacterium Isolated from Wheat Phyllosphere.
PG  - e00414-15
AB  - Paenibacillus polymyxa strain EBL06 is a plant growth-promoting bacterium with high antifungal
      activity. The estimated genome of this strain is 5.68 Mb in size
      and harbors 4,792 coding sequences (CDSs).
AU  - Liang S
AU  - Jin D
AU  - Wang X
AU  - Fan H
AU  - Bai Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00414-15.

PMID- 
VI  - 22
DP  - 2005
TI  - Acceleration of de novo DNA synthesis by restriction enzymes.
PG  - 766-767
AB  - We have found that in the presence of a restriction endonuclease, DNA polymerase efficiently
      synthesizes and amplifies DNA in the absence of any added template and primer nucleic acid
      under isothermal conditions.  In the presence of restriction endonuclease Tsp509I (recognition
      sequence /AATT) or TspRI (recognition sequence: NNCAG(C)TGNN/), more than 90% of the available
      dNTPs can be consumed by Vent (exo-) DNA polymerase in 1 h at 70oC.  The synthesized DNA has a
      highly repetitive palindromic sequence containing recognition sites for the restriction
      enzyme, e.g. (AAAAATTTTT)n and (ATACACTGTATATACAGTG-TAT)n.  Our data show that the high
      efficiency of the restriction-endonuclease-DNA-polymerase (RE-pol) DNA synthesis results from
      an efficient exponential amplification involving digestion-elongation cycles.
AU  - Liang X
AU  - Jensen K
AU  - Frank-Kamenetskii MD
PT  - Journal Article
TA  - J. Biomol. Struct. Dyn.
JT  - J. Biomol. Struct. Dyn.
SO  - J. Biomol. Struct. Dyn. 2005 22: 766-767.

PMID- 15491153
VI  - 43
DP  - 2004
TI  - Very efficient template/primer-independent DNA synthesis by thermophilic DNA polymerase in the presence of a thermophilic  restriction endonuclease.
PG  - 13459-13466
AB  - We have found that, in the presence of a thermophilic restriction endonuclease, thermophilic
      DNA polymerase efficiently synthesizes and
      amplifies DNA in the absence of any added template and primer nucleic
      acid under isothermal conditions. More than 10 micrograms of DNA can be
      synthesized by 1 unit of DNA polymerase in 1 h, and the reaction
      proceeds until available dNTPs are consumed. We used mostly the Tsp509I
      restriction endonuclease (recognition sequence: ^AATT), the
      TspRI restriction endonuclease (recognition sequence: NNCA(G/C)TGNN^), and Vent (exo(-)) and
      Vent DNA polymerase. The synthesized
      double-stranded DNA has a highly repetitive palindromic sequence, e.g.
      (AAAAATTTTT)(n) and (ATACACTGTATATACAGTGTAT)(n). In every repeating
      unit, there are one or two recognition sites for the restriction
      enzyme. Our data show that the high efficiency of the
      restriction-endonuclease-DNA-polymerase (RE-pol) DNA synthesis results
      from an efficient exponential amplification involving
      digestion-elongation cycles: a longer DNA with numerous recognition
      sites for the restriction enzyme is digested to short fragments, and
      the short fragments are used as seeds for elongation to synthesize
      longer DNA. A possible role of RE-pol DNA synthesis in the evolutionary
      development of genetic materials is briefly discussed.
AU  - Liang XG
AU  - Jensen K
AU  - Frank-Kamenetskii MD
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2004 43: 13459-13466.

PMID- 27257197
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Bacillus sp. GZT, a 2,4,6-Tribromophenol-Degrading Strain Isolated from the River Sludge of an Electronic Waste-Dismantling Region.
PG  - e00474-16
AB  - Here, we report the draft genome sequence of Bacillus sp. strain GZT, a 2,4,6-tribromophenol
      (TBP)-degrading bacterium previously isolated from an
      electronic waste-dismantling region. The draft genome sequence is 5.18 Mb and has
      a G+C content of 35.1%. This is the first genome report of a brominated flame
      retardant-degrading strain.
AU  - Liang Z
AU  - Li G
AU  - An T
AU  - Das R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00474-16.

PMID- 27445374
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a Tetrabromobisphenol A-Degrading Strain, Ochrobactrum sp. T, Isolated from an Electronic Waste Recycling Site.
PG  - e00680-16
AB  - Ochrobactrum sp. T was previously isolated from a sludge sample collected from an electronic
      waste recycling site and characterized as a unique tetrabromobisphenol
      A (TBBPA)-degrading bacterium. Here, the draft genome sequence (3.9 Mb) of
      Ochrobactrum sp. T is reported to provide insights into its diversity and its
      TBBPA biodegradation mechanism in polluted environments.
AU  - Liang Z
AU  - Li G
AU  - An T
AU  - Zhang G
AU  - Das R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00680-16.

PMID- 29954901
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Six Skin Isolates of Streptococcus pyogenes.
PG  - e00592-18
AB  - Whole-genome shotgun sequences and bottom-up assembly of contigs of six skin isolates of
      Streptococcus pyogenes, viz, NS88.3 (emm98.1), NS223 (emm91), NS455
      (emm52), SS1448 (emm86.2), SS1572 (emm223), and SS1574 (emm224), are presented
      here. All contigs were annotated, and the gene arrangements and the inferred
      proteins were consistent with a pattern D classification.
AU  - Liang Z
AU  - Stephens M
AU  - Ploplis VA
AU  - Lee SW
AU  - Castellino FJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00592-18.

PMID- 27540052
VI  - 4
DP  - 2016
TI  - Genomic Sequencing of Orientia tsutsugamushi Strain Karp, an Assembly Comparable  to the Genome Size of the Strain Ikeda.
PG  - e00702-16
AB  - Orientia tsutsugamushi, an intracellular bacterium, belongs to the family Rickettsiaceae This
      study presents the draft genome sequence of strain Karp, with
      2.0 Mb as the size of the completed genome. This nearly finished draft genome
      sequence was annotated with the RAST server and the contents compared to those of
      the other strains.
AU  - Liao HM
AU  - Chao CC
AU  - Lei H
AU  - Li B
AU  - Tsai S
AU  - Hung GC
AU  - Ching WM
AU  - Lo SC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00702-16.

PMID- 25822089
VI  - 47
DP  - 2015
TI  - Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells.
PG  - 469-478
AB  - DNA methylation is a key epigenetic modification involved in regulating gene expression and
      maintaining genomic integrity. Here we inactivated all three
      catalytically active DNA methyltransferases (DNMTs) in human embryonic stem cells
      (ESCs) using CRISPR/Cas9 genome editing to further investigate the roles and
      genomic targets of these enzymes. Disruption of DNMT3A or DNMT3B individually as
      well as of both enzymes in tandem results in viable, pluripotent cell lines with
      distinct effects on the DNA methylation landscape, as assessed by whole-genome
      bisulfite sequencing. Surprisingly, in contrast to findings in mouse, deletion of
      DNMT1 resulted in rapid cell death in human ESCs. To overcome this immediate
      lethality, we generated a doxycycline-responsive tTA-DNMT1* rescue line and
      readily obtained homozygous DNMT1-mutant lines. However, doxycycline-mediated
      repression of exogenous DNMT1* initiates rapid, global loss of DNA methylation,
      followed by extensive cell death. Our data provide a comprehensive
      characterization of DNMT-mutant ESCs, including single-base genome-wide maps of
      the targets of these enzymes.
AU  - Liao J
AU  - Karnik R
AU  - Gu H
AU  - Ziller MJ
AU  - Clement K
AU  - Tsankov AM
AU  - Akopian V
AU  - Gifford CA
AU  - Donaghey J
AU  - Galonska C
AU  - Pop R
AU  - Reyon D
AU  - Tsai SQ
AU  - Mallard W
AU  - Joung JK
AU  - Rinn JL
AU  - Gnirke A
AU  - Meissner A
PT  - Journal Article
TA  - Nat. Genet.
JT  - Nat. Genet.
SO  - Nat. Genet. 2015 47: 469-478.

PMID- 22965083
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Klebsiella oxytoca E718, a New Delhi Metallo-beta-Lactamase-1-Producing Nosocomial Strain.
PG  - 5454
AB  - We report the complete genome sequence of Klebsiella oxytoca E718, a New Delhi
      metallo-beta-lactamase-1 (NDM-1)-producing strain isolated from a renal
      transplant patient. The genome contains a 6,097,032-bp chromosome and two
      multidrug resistance plasmids with sizes of 324,906 bp and 110,781 bp.
AU  - Liao TL
AU  - Lin AC
AU  - Chen E
AU  - Huang TW
AU  - Liu YM
AU  - Chang YH
AU  - Lai JF
AU  - Lauderdale TL
AU  - Wang JT
AU  - Chang SC
AU  - Tsai SF
AU  - Chen YT
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5454.

PMID- 24356835
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of NDM-1-Producing Klebsiella pneumoniae Clinical Isolate 303K.
PG  - e01069-13
AB  - Multidrug-resistant New Delhi metallo-beta-lactamase 1 (NDM-1)-producing bacteria have spread
      globally and become a major clinical and public health threat. We
      report here the draft genome sequence of the Klebsiella pneumoniae clinical
      isolate 303K, harboring an NDM-1 coding sequence.
AU  - Liao YC
AU  - Chen YH
AU  - Lin HH
AU  - Mu JJ
AU  - Wu HS
AU  - Chen FC
AU  - Hsiung CA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01069-13.

PMID- 25189576
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of the Mycobacterium tuberculosis Clinical Strains A2 and  A4, Isolated from a Relapse Patient in Taiwan.
PG  - e00672-14
AB  - The recurrence rate of Mycobacterium tuberculosis in Taiwan is 3%. Here, we present the draft
      genome sequences of M. tuberculosis strains A2 and A4 from a
      relapse patient. The draft genome sequences comprise 4,443,031 bp and 4,487,096
      bp, revealing 4,220 and 4,143 coding sequences for A2 and A4, respectively, as
      well as 49 tRNA genes for the both isolates.
AU  - Liao YC
AU  - Chen YY
AU  - Lin HH
AU  - Chang JR
AU  - Su IJ
AU  - Huang TS
AU  - Dou HY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00672-14.

PMID- 24903871
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Mycobacterium tuberculosis Clinical Isolate C2, Belonging to the Latin American-Mediterranean Family.
PG  - e00536-14
AB  - Tuberculosis remains a major infectious disease in Taiwan. Here we present the draft genome
      sequence of the Mycobacterium tuberculosis C2 strain, belonging to
      the Latin American-Mediterranean lineage. The draft genome sequence comprises
      4,453,307 bp with a G+C content of 65.6%, revealing 4,390 coding genes and 45
      tRNA genes.
AU  - Liao YC
AU  - Chen YY
AU  - Lin HH
AU  - Chang JR
AU  - Su IJ
AU  - Huang TS
AU  - Dou HY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00536-14.

PMID- 26659689
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Mycobacterium tuberculosis Clinical Strain W06, a Prevalent Beijing Genotype Isolated in Taiwan.
PG  - e01460-15
AB  - Mycobacterium tuberculosis strain W06, analyzed by molecular methods, was classified as a
      modern Beijing M. tuberculosis strain, the most predominant
      strain in Taiwan. To our knowledge, this is the first draft genome announcement
      of a Beijing M. tuberculosis strain in Taiwan.
AU  - Liao YC
AU  - Liu TT
AU  - Chang JR
AU  - Chen YY
AU  - Lin HH
AU  - Hsu CH
AU  - Lin CY
AU  - Lo YC
AU  - Dou HY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01460-15.

PMID- 29853504
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Bacillus urumqiensis BZ-SZ-XJ18(T), a Moderately Haloalkaliphilic Bacterium Isolated from a Saline-Alkaline Lake.
PG  - e00460-18
AB  - The moderately haloalkaliphilic bacterium Bacillus urumqiensis BZ-SZ-XJ18(T) was  isolated
      from a saline-alkaline lake located in the Xinjiang Uyghur Autonomous
      Region of China. Optimum growth occurred at the total Na(+) concentration of 1.08
      M, with a broad optimum pH of 8.5 to 9.5. The draft genome consists of
      approximately 3.28 Mb and contains 3,228 predicted genes. A number of genes
      associated with adaptation strategies for osmotic balance and alkaline pH
      homeostasis were identified, providing pertinent insight into specific
      adaptations to the double-extreme environment.
AU  - Liao Z
AU  - Ren C
AU  - Guo X
AU  - Yan Y
AU  - Li J
AU  - Zhao B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00460-18.

PMID- 29748400
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Two Salmonella Strains Isolated from Wild Animals on the Eastern Shore of Virginia.
PG  - e00329-18
AB  - Antimicrobial-resistant (AMR) Salmonella infections pose a significant public health threat.
      Here, we announce two draft genomes of Salmonella strains isolated
      from wildlife harboring an alarming array of antibiotic resistance genes.
      Continued investigations of these genomes will provide insight into the possible
      attribution of AMR Salmonella infection of wild animals.
AU  - Libuit KG
AU  - Turner L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00329-18.

PMID- 25540338
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Pseudomonas mediterranea Strain CFBP 5447T, a Producer of Filmable Medium-Chain-Length Polyhydroxyalkanoates.
PG  - e01260-14
AB  - Pseudomonas mediterranea strain CFBP 5447(T) is a phytopathogenic bacterium isolated from
      tomato plants affected by pith necrosis disease. Moreover, its
      ability to produce medium-chain-length polyhydroxyalkanoates (mcl-PHAs) in
      culture from different carbon sources and valuable microbial products, such as
      cyclic lipopeptides, has been well documented. Here, we report the first draft
      genome sequence of this species.
AU  - Licciardello G
AU  - Bella P
AU  - Devescovi G
AU  - Strano CP
AU  - Sarris PF
AU  - Catara AF
AU  - Venturi V
AU  - Catara V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01260-14.

PMID- 2959653
VI  - 169
DP  - 1987
TI  - Bacterial genes mutL, mutS, and dcm participate in repair of mismatches at 5-methylcytosine sites.
PG  - 5241-5246
AB  - Certain amber mutationsn in the cI gene of bacteriophage lambda appear to recombine very
      frequently with nearby mutations. The aberrant mutations included C-to-T transitiions at the
      second cytosine in 5'CC(A/T)GG sequences (which are subject to methylation by bacterial
      cytosine methylase) and in 5'CCAG and 5'CAGG sequences. Excess cI+ recombinants arising in
      crosses that utilize these mutations are attributable to the correction of mismatches by a
      bacterial very-short-patch (VSP) mismatch repair system. In the present study I found that two
      genes required for methyladenine-directed (long-patch) mismatch repair, mutL and mutS, also
      functioned in VSP mismatch repair; mutH and mutU (uvrD) were dispensable. VSP mismatch repair
      was greatly reduced in a dcm Escherichia coli mutant, in which 5-methylcytosine was not
      methylated. However, mismatches in heterduplexes prepared from lambda DNA lacking
      5-methylcytosine were repaired in dcm+ bacteria. These results indicate that the product of
      gene dcm has a repair function in addition to its methylase activity.
AU  - Lieb M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1987 169: 5241-5246.

PMID- 6225003
VI  - 191
DP  - 1983
TI  - Specific mismatch correction in bacteriophage lambda crosses by very short patch repair.
PG  - 118-125
AB  - In crosses under rec+, red+, gam+ conditions, mutation am6 in the cI
      (repressor) gene of bacteriophage lambda recombines with other cI mutations
      much more frequently than predicted by the physical distances involved.  In
      four-factor crosses of am6 with mutations located 22-60 base pairs to the left,
      cI+ recombinants that are expected to require three crossovers (triple
      recombinants) are more frequent than recombinants that require only one
      crossover.  However, when am6 is crossed with large insertions in cI, which may
      be expected to interfere with the formation of heteroduplexes by branch
      migration, the frequency of cI+ triple recombinants is very low.  In addition,
      cI+ recombinants in crosses between am6 and adjacent mutations have a high
      probability of retaining the flanking markers of the am6 parent.  These
      findings suggest that am6 is particularly susceptible to mismatch repair in
      heteroduplexes spanning cI.  A large fraction of such heteroduplexes are
      presumed to be the result of branch migration from crossovers occuring at some
      distance from am6.  The absence of co-repair when am6 is crossed with adjacent
      cI mutations indicates that most repair tracts extend no farther than about 20
      bp to either side of the mismatch.  The am6 mutation arose in the glutamine
      codon in a CCAGG sequence, in which the central cytosines are methylated in K12
      strains.  Their location in methylated sequences may make certain amber
      mutations susceptible to a specific very short patch (VSP) repair.
AU  - Lieb M
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1983 191: 118-125.

PMID- 1829427
VI  - 128
DP  - 1991
TI  - Spontaneous Mutation at a 5-methylcytosine hotspot is prevented by very short patch (VSP) mismatch repair.
PG  - 23-27
AB  - In many strains of Escherichia coli, the product of gene dcm methylates the internal cytosines
      in the sequence 5'CC(A or T)GG. Spontaneous deamination of 5-methylcytosine produces thymine
      which, if not corrected, can result in a transition mutation. 5-Methylcytosines in the lacI
      gene are hotspots for spontaneous C to T mutations. dcm is linked to vsr, a gene required for
      very short patch (VSP) repair. VSP respir corrects T.G mispairs in the following contexts:
      CTAGG/GGTCC, CTTGG/GGACC, TAGG/GTCC and CTAG/GGTC. I have investigated the relationships
      between cytosine methylation, mutation, and VSP repair. Spontaneous mutations in the repressor
      (cI) gene of lambda prophage were isolated in wild-type and mutant lysogens. A hotspot for
      spontaneous mutation that corresponds with a 5-methylcytosine was observed in wild-type
      lysogens but was not present in bacteria lacking both methylase and VSP repair activity.
      Introduction of a plasmid containg dcm+ and vsr+ restored the mutation hotspot. If the added
      plasmid carried only dcm+, the frequency of spontaneous mutations at the 5-methylcytosine was
      over 10-fold higher than in Dcm+Vsr+ lysogens. The addition of vsr on a plasmid to a wild-type
      lysogen resulted in a 4-fold reduciton in mutation at the hotspot. These findings support the
      previously untested hypothesis that VSP repair prevents mutations resulting from deamination
      of 5-methylcytosine.
AU  - Lieb M
PT  - Journal Article
TA  - Genetics
JT  - Genetics
SO  - Genetics 1991 128: 23-27.

PMID- 2948873
VI  - 114
DP  - 1986
TI  - Very short patch mismatch repair in phage lambda: repair sites and length of repair tracts.
PG  - 1041-1060
AB  - Five amber mutations in the repressor (cI) gene of bacteriophage lambda recombine anomalously
      with nearby cI mutations.  When any of these markers is used in four-factor crosses, cI+
      recombinants that are expected to require three crossovers occur at high frequencies.  These
      recombinants are attributable to very-short-patch (VSP) repair of specific mismatches in DNA
      heteroduplexes formed during recombination between the markers flanking cI.  The sites of the
      repair-prone mutations and the lengths of repair tracts have now been determined.  Amber
      mutations subject to VSP repair are C to T transitions in 5'CCA/TGG, the sequence methylated
      by the product of gene dcm, and also in the related 5'CAGG or 5'CCAG sequences.  Ambers
      arising in CAG sequences found in other contexts, or in codons other than CAG, were not
      subject to VSP repair.  Rapair tracts rarely, if ever, exceed ten nucleotides in length, and
      can be as short as two nucleotides.  A repair-prone mutation does not stimulate recombination
      between flanking cI markers.
AU  - Lieb M
AU  - Allen E
AU  - Read D
PT  - Journal Article
TA  - Genetics
JT  - Genetics
SO  - Genetics 1986 114: 1041-1060.

PMID- 8736526
VI  - 20
DP  - 1996
TI  - Very short patch repair: reducing the cost of cytosine methylation.
PG  - 467-473
AB  - In Escherichia coli and related bacteria, the product of gene dcm methylates the second
      cytosine of 5'-CCWGG sequences (where W is A or T).  Deamination of 5-methylcytosine results
      in C to T mutations.  The mutagenic potential of 5meC is reduced by a system called very short
      patch repair, which replaces T with C.  T:G and U:G mispairs in the methylatable sequence and
      in related sequences are recognized by the product of vsr, a gene adjacent to dcm.  Vsr
      creates a nick just 5' of the mispaired pyrimidine to initiate the repair.  Additional
      products known to be required for VSP repair are DNA polymerase I and DNA ligase.  MutS and
      MutL have a stimulatory role but are not required.  The ability of Vsr to recognize T:G
      mispairs in sequences related to CCWGG is probably responsible for over- and
      under-representation of certain tetranucleotides in the E. coli genome.  Although VSP repair
      reduces spontaneous mutations at 5meCs in replicating bacteria, mutation hot-spots persist at
      these sites. Under conditions that more accurately mimic the natural environment of E. coli,
      VSP repair appears to be effective in preventing mutation at 5meC.
AU  - Lieb M
AU  - Bhagwat AS
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1996 20: 467-473.

PMID- 3049557
VI  - 170
DP  - 1988
TI  - Very short patch mismatch repair activity associated with gene dcm is not conferred by a plasmid coding for EcoRII methylase.
PG  - 4967-4968
AB  - The only cytosine methylase in Escherichia coli K-12 methylates the second cytosine in the
      sequence CC(A/T)GG and is encoded by gene dcm. Methylation and very short patch mismatch
      repair activities lacking in a dcm mutant of E. coli were restored by a plasmid containing the
      cloned dcm gene. In contrast, plasmids with the gene for EcoRII methylase, which is a homolog
      of dcm, restored only cytosine methylase activity and not mismatch repair.
AU  - Lieb M
AU  - Bhagwat AS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1988 170: 4967-4968.

PMID- 9023361
VI  - 94
DP  - 1997
TI  - 5-Methylcytosine is not a mutation hot spot in nondividing Escherichia coli.
PG  - 940-945
AB  - Spontaneous deamination of 5-methylcytosine (5meC) causes hot spots of C.G-T.A mutations in
      Escherichia coli and in human cells.  In E. coli, the resulting T.G mispairs can be corrected
      to C.G by very short patch (VSP) repair, which requires the product of gene vsr.  Mutation hot
      spots in genes of replicating vsr+ bacteria are attributable to low Vsr activity.  To
      determine the rate of deamination of 5meC and the efficiency of VSP repair in nondividing
      bacteria, we used kanamycin-sensitive (KanS) lysogens containing a lambda kan- prophage.
      Deamination of a 5meC in the kan- gene resulted in mutation to kanamycin resistance (KanR).
      Lysogens containing a single lambda kan- prophage per bacterial genome were grown in synthetic
      medium with limiting amino acids and stored at 15oC or 37oC.  In the absence of VSP repair,
      KanR mutants accumulated at the rate of approximately 1.3 x 10^-7 per bacterium per day at
      37oC.  This is similar to the 5meC--T mutation rate reported for DNA in solution.  In vsr+
      bacteria, the KanR accumulation rate was 3 x 10^-9 per bacterium per day, which is not
      significantly higher than the rate observed when the target cytosine was unmethylated.  The
      increase in KanR mutants was barely detectable in vsr+ cultures stored at 15oC for 4 months.
      It is likely that mutation hot spots at 5meC in rapidly dividing cells are attributable to
      insufficient time for T.G correction in the interval between deamination of 5meC and
      subsequent DNA replication.  DNA synthesis occurred in bacteria starved for amino acids and
      this synthesis was not highly mutagenic.
AU  - Lieb M
AU  - Rehmat S
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1997 94: 940-945.

PMID- 7836300
VI  - 177
DP  - 1995
TI  - Very short patch repair of T:G mismatches in vivo: importance of context and accessory proteins.
PG  - 660-666
AB  - In Escherichia coli, T:G mismatches in specific contexts are corrected by a very short patch
      (VSP) repair system. Previous studies have shown that the product of gene vsr mediates
      correction of T:G to C:G in the 5'CTAGG/3'GGTCC context and in some related contexts. Amber
      mutations that arose in CAG sequences in gene cI of bacteriophage lambda were used to
      determine the effect of flanking bases on the repair of T:G mispairs arising during phage
      recombination. The experimental findings were combined with published data on mismatch repair
      of mutations in lambda gene P and E. coli gene lacI. While VSP repair was most efficient in
      the context 5'CTAGG, there was very significant correction when either the 5' C or the 3' G
      was replaced by another base. Some mismatch repair of TAG to CAG occurred in all contexts
      tested. Reduction in VSP repair caused by the lack of MutL or MutS was fully complemented by
      the addition of vsr+ plasmids when the T:G mispair was in the 5'CTAGG/3'GGTCC context. VSP
      repair was decreased in bacteria containing mutS+ on a multicopy plasmid. It is suggested that
      VSP repair maintains sequences such as the repetitive extragenic palindromic (REP) and Chi
      sequences, which have important roles in E. coli and closely related bacteria.
AU  - Lieb M
AU  - Rehmat S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1995 177: 660-666.

PMID- 11591694
VI  - 183
DP  - 2001
TI  - Interaction of MutS and Vsr: Some Dominant-Negative mutS Mutations That Disable Methyladenine-Directed Mismatch Repair Are Active in Very-Short-Patch Repair.
PG  - 6487-6490
AB  - In Escherichia coli and related bacteria, the very-short-patch (VSP) repair pathway uses an
      endonuclease, Vsr, to correct T.G mismatches that result from the deamination of
      5-methylcytosines in DNA to C.G. The products of mutS and mutL, which are required for
      adenine methylation-directed mismatch repair (MMR), enhance VSP repair. Multicopy plasmids
      carrying mutS alleles that are dominant negative for MMR were tested for their effects on VSP
      repair. Some mutS mutations (class I) did not lower VSP repair in a mutS(+) background, and
      most class I mutations increased VSP repair in mutS cells more than plasmids containing
      mutS(+). Other plasmid-borne mutS mutations (class II) and mutS(+) decreased VSP repair in the
      mutS(+) background. Thus, MutS protein lacking functions required for MMR can still
      participate in VSP repair, and our results are consistent with a model in which MutS binds
      transiently to the mispair and then translocates away from the mispair to create a specialized
      structure that enhances the binding of Vsr.
AU  - Lieb M
AU  - Rehmat S
AU  - Bhagwat AS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2001 183: 6487-6490.

PMID- 15276835
VI  - 341
DP  - 2004
TI  - Stopped-flow and mutational analysis of base flipping by the Escherichia coli dam DNA-(adenine-N6)-methyltransferase.
PG  - 443-454
AB  - By stopped-flow kinetics using 2-aminopurine as a probe to detect base flipping, we show here
      that base flipping by the Escherichia coli Dam
      DNA-(adenine-N6)-methyltransferase (MTase) is a biphasic process:
      target base flipping is very fast (k(flip) > 240 s(-1)), but binding of
      the flipped base into the active site pocket of the enzyme is slow (k =
      0.1-2 s(-1)). Whereas base flipping occurs in the absence of
      S-adenosyl-L-methionine (AdoMet), binding of the target base in the
      active site pocket requires AdoMet. Our data suggest that the tyrosine
      residue in the DPPY motif conserved in the active site of
      DNA-(adenine-N6)-MTases stacks to the flipped target base. Substitution
      of the aspartic acid residue of the DPPY motif by alanine abolished
      base flipping, suggesting that this residue contacts and stabilizes the
      flipped base. The exchange of Ser188 located in a loop next to the
      active center by alanine led to a seven- to eightfold reduction of
      k(flip), which was also reduced with substrates having altered GATC
      recognition sites and in the absence of AdoMet. These findings provide
      evidence that the enzyme actively initiates base flipping by
      stabilizing the transition state of the process. Reduced rates of base
      flipping in substrates containing the target base in a non-canonical
      sequence demonstrate that DNA recognition by the MTase starts before
      base flipping. DNA recognition, cofactor binding and base flipping are
      correlated and efficient base flipping takes place only if the enzyme
      has bound to a cognate target site and AdoMet is available.
AU  - Liebert K
AU  - Hermann A
AU  - Schlickenrieder M
AU  - Jeltsch A
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2004 341: 443-454.

PMID- 17545164
VI  - 282
DP  - 2007
TI  - Two alternative conformations of S-Adenosyl-L-homocysteine bound to Escherichia coli DNA adenine methyltransferase and the implication of conformational changes in regulating the catalytic cycle.
PG  - 22848-22855
AB  - The crystal structure of the Escherichia coli DNA adenine methyltransferase( EcoDam) in a
      binary complex with the cofactor
      product S-adenosyl-L-homocysteine ( AdoHcy) unexpectedly showed the
      bound AdoHcy in two alternative conformations, extended or folded. The
      extended conformation represents the catalytically competent
      conformation, identical to that of EcoDam-DNA-AdoHcy ternary complex.
      The folded conformation prevents catalysis, because the homocysteine
      moiety occupies the target Ade binding pocket. The largest difference
      between the binary and ternary structures is in the conformation of the
      N-terminal hexapeptide ( (9)KWAGGK(14)). Cofactor binding leads to a
      strong change in the fluorescence of Trp(10), whose indole ring
      approaches the cofactor by 3.3 angstrom. Stopped-flow kinetics
      andAdoMetcross-linking studies indicate that the cofactor prefers
      binding to the enzyme after preincubation with DNA. In the presence of
      DNA, AdoMet binding is similar to 2-fold stronger than AdoHcy binding.
      In the binary complex the side chain of Lys(14) is disordered, whereas
      Lys(14) stabilizes the active site in the ternary complex. Fluorescence
      stopped-flow experiments indicate that Lys(14) is important for EcoDam
      binding of the extrahelical target base into the active site pocket.
      This suggests that the hexapeptide couples specific DNA binding
      (Lys(9)), AdoMet binding (Trp(10)), and insertion of the flipped target
      base into the active site pocket (Lys(14)).
AU  - Liebert K
AU  - Horton JR
AU  - Chahar S
AU  - Orwick M
AU  - Cheng XD
AU  - Jeltsch A
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2007 282: 22848-22855.

PMID- 21345093
VI  - 364
DP  - 2011
TI  - Identification of a salmonellosis outbreak by means of molecular sequencing.
PG  - 981-982
AB  - 
AU  - Lienau EK
AU  - Strain E
AU  - Wang C
AU  - Zheng J
AU  - Ottesen AR
AU  - Keys CE
AU  - Hammack TS
AU  - Musser SM
AU  - Brown EW
AU  - Allard MW
AU  - Cao G
AU  - Meng J
AU  - Stones R
PT  - Journal Article
TA  - N. Engl. J. Med.
JT  - N. Engl. J. Med.
SO  - N. Engl. J. Med. 2011 364: 981-982.

PMID- 20802048
VI  - 192
DP  - 2010
TI  - Complete Genome Sequence of Methanothermobacter marburgensis, a Methanoarchaeon Model Organism.
PG  - 5850-5851
AB  - The circular genome sequence of the chemolithoautotrophic euryarchaeon Methanothermobacter
      marburgensis, with 1,639,135 bp, was determined and
      compared with that of Methanothermobacter thermautotrophicus. The genomes
      of the two model methanogens differ substantially in protein coding
      sequences, in insertion sequence (IS)-like elements, and in clustered
      regularly interspaced short palindromic repeats (CRISPR) loci.
AU  - Liesegang H
AU  - Kaster AK
AU  - Wiezer A
AU  - Goenrich M
AU  - Wollherr A
AU  - Seedorf H
AU  - Gottschalk G
AU  - Thauer RK
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 5850-5851.

PMID- 21705598
VI  - 193
DP  - 2011
TI  - Draft Genome of the Psychrotolerant Acidophile Acidithiobacillus ferrivorans SS3.
PG  - 4304-4305
AB  - Acidithiobacillus ferrivorans SS3 is a psychrotolerant acidophile capable of growth in the
      range of 5 degrees  to 30 degrees C (optimum,
      approximately 25 degrees C). It gains energy from the oxidation of ferrous
      iron and inorganic sulfur compounds and obtains organic carbon from carbon
      dioxide. Here, we present the draft genome sequence of A. ferrivorans SS3
      that will permit investigation of genes involved in growth in acidic
      environments at low temperatures.
AU  - Liljeqvist M
AU  - Valdes J
AU  - Holmes DS
AU  - Dopson M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4304-4305.

PMID- Not carried by PubMed...
VI  - 1
DP  - 1996
TI  - Cisplatin adducts in DNA: distortion and recognition.
PG  - 189-191
AB  - cis-Diamminedichloroplatinum (II) (cisplatin) and derivatives are very successful anticancer
      chemotherapeutic agents.  They crosslink cellular DNA, forming bifunctional adducts with the
      N7 of guanine bases.  In this review, recent structures of cisplatin adducts are summarized,
      and the significance for the recognition of DNA structure by proteins is discussed.  Two new
      structures of intrastrand GpG adducts have been presented, showing a significant kinking of
      the helix axis and a novel hybrid A-B helical geometry.  The relevance of this structure to
      the recognition of HMG-box and related proteins is discussed.  A new structure of a
      cross-strand cisplatin adduct reveals a major disruption of the local DNA structure.  The
      basepairs containing the modified guanine bases are broken, with extrusion of the cytosine
      bases into the solvent.  The backbone reverses direction locally, with the result that the
      platinum adduct is located in what is the minor groove of the DNA overall.  The extrusion of
      single bases out of the helix is strongly reminiscent of the effect of certain methylases on
      their DNA targets.
AU  - Lilley DMJ
PT  - Journal Article
TA  - J. Biol. Inorg. Chem.
JT  - J. Biol. Inorg. Chem.
SO  - J. Biol. Inorg. Chem. 1996 1: 189-191.

PMID- 25502679
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Lactobacillus sakei Strain wikim 22, Isolated from Kimchi in Chungcheong Province, South Korea.
PG  - e01296-14
AB  - We report the draft genome sequence of Lactobacillus sakei strain wikim 22, a Lactobacillus
      species isolated from kimchi in North Chungcheong Province, South
      Korea, having 155 contigs with 2,447 genes and an average G+C content of 40.61%.
AU  - Lim HI
AU  - Lee J
AU  - Jang JY
AU  - Park HW
AU  - Choi HJ
AU  - Kim TW
AU  - Kang MR
AU  - Lee JH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01296-14.

PMID- 19329631
VI  - 191
DP  - 2009
TI  - Complete Genome Sequence of Burkholderia glumae BGR1.
PG  - 3758-3759
AB  - Burkholderia glumae is the causative agent of grain and seedling rot in rice and of bacterial
      wilt in many field crops. Here, we report the complete genome sequence of B. glumae BGR1
      isolated from a diseased rice panicle in Korea.
AU  - Lim J
AU  - Lee TH
AU  - Nahm BH
AU  - Choi YD
AU  - Kim M
AU  - Hwang I
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2009 191: 3758-3759.

PMID- 22275096
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of the Fenitrothion-Degrading Burkholderia sp. Strain YI23.
PG  - 896
AB  - Burkholderia species are ubiquitous in soil environments. Many Burkholderia species isolated
      from various environments have the potential
      to biodegrade man-made chemicals. Burkholderia sp. strain YI23 was
      isolated from a golf course soil and identified as a
      fenitrothion-degrading bacterium. In this study, we report the complete
      genome sequence of Burkholderia sp. strain YI23.
AU  - Lim JS
AU  - Choi BS
AU  - Choi AY
AU  - Kim KD
AU  - Kim DI
AU  - Choi IY
AU  - Ka JO
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 896.

PMID- 29348360
VI  - 6
DP  - 2018
TI  - Complete Genome Sequences of Three Moraxella osloensis Strains Isolated from Human Skin.
PG  - e01509-17
AB  - Here, we present the complete whole-genome sequences of three Moraxella osloensis strains with
      octylphenol polyethoxylate-degrading abilities. These strains were
      isolated from human skin.
AU  - Lim JY
AU  - Hwang I
AU  - Ganzorig M
AU  - Huang SL
AU  - Cho GS
AU  - Franz CMAP
AU  - Lee K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01509-17.

PMID- 29348361
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Paracoccus yeei TT13, Isolated from Human Skin.
PG  - e01514-17
AB  - Paracoccus yeei TT13 was isolated from human skin because of its ability to degrade propylene
      glycol. Here, we present the whole-genome sequence of this
      strain; it possesses one 3.58-Mb chromosome and six plasmids. TT13 genome
      analysis indicated that this bacterium has denitrification potential.
AU  - Lim JY
AU  - Hwang I
AU  - Ganzorig M
AU  - Pokhriyal S
AU  - Singh R
AU  - Lee K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01514-17.

PMID- 26877770
VI  - 8
DP  - 2016
TI  - Whole genome sequencing of 'Faecalibaculum rodentium' ALO17, isolated from C57BL/6J laboratory mouse feces.
PG  - 3
AB  - BACKGROUND: Intestinal microorganisms affect host physiology, including ageing.
      Given the difficulty in controlling for human studies of the gut microbiome, mouse models
      provide an alternative avenue to study such relationships. In this study, we report on the
      complete genome of "Faecalibaculum rodentium" ALO17, a bacterium that was isolated from the
      faeces of a 9-month-old female C57BL/6J mouse. This strain will be utilized in future in vivo
      studies detailing the relationships between the gut microbiome and ageing. RESULTS: The whole
      genome sequence of "F. rodentium" ALO17 was obtained using single-molecule, real-time
      (SMRT) technique on a PacBio instrument. The assembled genome consisted of
      2,542,486 base pairs of double-stranded DNA with a GC content of 54.0 % and no plasmids. The
      genome was predicted to contain 2794 open reading frames, 55 tRNA genes, and 38 rRNA genes.
      The 16S rRNA gene of ALO17 was 86.9 % similar to that of Allobaculum stercoricanis DSM
      13633(T), and the average overall nucleotide identity between strains ALO17 and DSM 13633(T)
      was 66.8 %. After confirming the phylogenetic relationship between "F. rodentium" ALO17 and A.
      stercoricanis DSM 13633(T), their whole genome sequences were compared, revealing that "F.
      rodentium" ALO17 contains more fermentation-related genes than A. stercoricanis DSM 13633(T).
      Furthermore, "F. rodentium" ALO17 produces higher levels of lactic acid than A. stercoricanis
      DSM 13633(T) as determined by high-performance liquid chromatography. CONCLUSION: The
      availability of the "F. rodentium" ALO17 whole genome sequence will enhance studies concerning
      the gut microbiota and host physiology, especially when investigating the molecular
      relationships between gut microbiota and ageing.
AU  - Lim S
AU  - Chang DH
AU  - Ahn S
AU  - Kim BC
PT  - Journal Article
TA  - Gut Pathog.
JT  - Gut Pathog.
SO  - Gut Pathog. 2016 8: 3.

PMID- 29976613
VI  - 6
DP  - 2018
TI  - Genome Sequence of Bacillus velezensis SGAir0473, Isolated from Tropical Air Collected in Singapore.
PG  - e00642-18
AB  - Bacillus velezensis strain SGAir0473 (Firmicutes) was isolated from tropical air  collected in
      Singapore. Its genome was assembled using short reads and
      single-molecule real-time sequencing and comprises one chromosome with 4.18 Mb.
      The genome consists of 3,937 protein-coding genes, 86 tRNAs, and 27 rRNAs.
AU  - Lim SBY et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00642-18.

PMID- 19028901
VI  - 191
DP  - 2009
TI  - Complete genome sequence of Rhodobacter sphaeroides KD131.
PG  - 1118-1119
AB  - Rhodobacter sphaeroides is a purple nonsulfur photosynthetic bacterium that is considered a
      possible source of H(2) production. R. sphaeroides
      KD131, which was isolated from sea mud in South Korea, was found to
      produce high levels of H(2). Here we report the complete and annotated
      genome sequence of R. sphaeroides KD131.
AU  - Lim SK
AU  - Kim SJ
AU  - Cha SH
AU  - Oh YK
AU  - Rhee HJ
AU  - Kim MS
AU  - Lee JK
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2009 191: 1118-1119.

PMID- 29348352
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Lacinutrix venerupis DOK2-8 Isolated from Marine Sediment from the East Sea, Republic of Korea.
PG  - e01485-17
AB  - Lacinutrix venerupis has recently been considered a potential fish pathogen. Here, we report
      the complete genome sequence of L. venerupis DOK2-8, which
      possesses several virulence-related genes. This strain may be potentially
      virulent to other marine organisms, and its genomic information will provide
      important insights into the biodiversity of the genus Lacinutrix.
AU  - Lim SR
AU  - Jeong DG
AU  - Chi WJ
AU  - Kim JH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01485-17.

PMID- 26903988
VI  - 7
DP  - 2016
TI  - Complete Genome Sequence Analysis of Pandoraea pnomenusa Type Strain DSM 16536T Isolated from a Cystic Fibrosis Patient.
PG  - 109
AB  - The genus of Pandoraea was first proposed in 2000 following the isolation from the sputum of
      cystic fibrosis patients (Coenye et al., 2000). Five species were initially assigned to the
      novel genus namely Pandoraea apista, Pandoraea pulmonicola, Pandoraea pnomenusa, Pandoraea
      sputorum, and Pandoraea norimbergensis but the description of four new species and another
      four genomospecies in the subsequent years led to a total of nine species and four
      genomospecies within the genus of Pandoraea (Daneshvar et al., 2001; Anandham et al., 2010;
      Sahin et al., 2011). The isolation of Pandoraea spp. from various environmental samples such
      as water, sludge, and soils have been reported, but to date, only P. pnomenusa, P. apista, P.
      pulmonicola, and P. sputorum were isolated from clinical specimens such as blood, sputum and
      bronchial fluid of patients with cystic fibrosis or chronic lung diseases (Coenye et al.,
      2000; Daneshvar et al., 2001; Stryjewski et al., 2003; Han-Jen et al., 2013). Members of
      Pandoraea tend to exhibit broad resistance to ampicillin, extended-spectrum cephalosporins,
      aztreonam, aminoglycosides, and meropenem but they are sensitive to imipenem (Daneshvar et
      al., 2001; Stryjewski et al., 2003). However, the clinical significance and prevalence of
      these multi-drug resistant bacteria among patients with cystic fibrosis or respiratory
      diseases remained unknown since Pandoraea spp. are usually misidentified as Burkholderia
      cepacia complex, Ralstonia pickettii, or Ralstonia paucula (Segonds et al., 2003). Ambiguity
      in differentiating between B. cepacia complex, Ralstonia spp. and Pandoraea spp. can be
      resolved by 16S ribosomal DNA-PCR (Coenye et al., 2001) and gyrB gene restriction fragment
      length polymorphism (Coenye and LiPuma, 2002) but the limited use of molecular typing methods
      in routine clinical microbiological laboratory has resulted in the underreporting of Pandoraea
      spp. in clinical cases.
AU  - Lim YL
AU  - Ee R
AU  - Yong D
AU  - Yu CY
AU  - Ang GY
AU  - Tee KK
AU  - Yin WF
AU  - Chan KG
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2016 7: 109.

PMID- 26941143
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence and Methylome Analysis of Aeromonas hydrophila Strain YL17, Isolated from a Compost Pile.
PG  - e00060-16
AB  - In this report, we announce the complete genome sequence of Aeromonas hydrophila  strain YL17.
      Single-molecule real-time (SMRT) DNA sequencing was used to generate
      the complete genome sequence and the genome-wide DNA methylation profile of this
      environmental isolate. A total of five unique DNA methyltransferase recognition
      motifs were reported here.
AU  - Lim YL
AU  - Roberts RJ
AU  - Ee R
AU  - Yin WF
AU  - Chan KG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00060-16.

PMID- 28360158
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Corynebacterium pseudotuberculosis Strain PA05 Isolated  from an Ovine Host in Para State, Brazil.
PG  - e00082-17
AB  - We report here the draft genome sequence of Corynebacterium pseudotuberculosis PA05, isolated
      from an ovine host in Para State, Brazil. C. pseudotuberculosis is
      an etiological agent of diseases with veterinary and medical importance. The
      genome contains 2,435,137 bp, a G+C content of 52.2%, 2,295 coding sequences,
      five pseudogenes, 53 tRNAs, and six rRNAs.
AU  - Lima AC
AU  - de Moura VA
AU  - Pinheiro KD
AU  - Paixao CT
AU  - da Costa WL
AU  - Folador AR
AU  - Guaraldi AL
AU  - Ramos RT
AU  - Silva A
AU  - Marques JM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00082-17.

PMID- 23640380
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Bacillus stratosphericus LAMA 585, Isolated from the Atlantic Deep Sea.
PG  - e00204-13
AB  - Bacillus stratosphericus LAMA 585 was isolated from the Mid-Atlantic-Ridge seafloor (5,500-m
      depth). This bacterium presents the capacity for cellulase,
      xylanase, and lipase production when growing aerobically in marine-broth media.
      Genes involved in the tolerance of oligotrophic and extreme conditions and
      prospection of biotechnological products were annotated in the draft genome (3.7
      Mb).
AU  - Lima AO
AU  - Cabral A
AU  - Andreote FD
AU  - Cavalett A
AU  - Pessatti ML
AU  - Dini-Andreote F
AU  - da Silva MA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00204-13.

PMID- 24435858
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Rhodobacter sp. Strain CACIA 14H1, a Heterotrophic Bacterium Obtained from a Nonaxenic Culture of a Cyanobium Species.
PG  - e01116-13
AB  - Despite their prominent importance, few efforts have been paid to the genomic analysis of
      heterotrophic bacteria associated with cyanobacteria. Thus, this work
      presents the draft genome sequence (~3.9 Mbp) of a heterotrophic bacterium
      (Rhodobacter sp. strain CACIA 14H1) recovered from a nonaxenic culture of a
      Cyanobium species.
AU  - Lima AR
AU  - Siqueira AS
AU  - Dos Santos BG
AU  - da Silva FD
AU  - Inada DT
AU  - Lima CP
AU  - Cardoso JF
AU  - Vianez-Junior JL
AU  - Nunes MR
AU  - Goncalves EC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01116-13.

PMID- 25013140
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Brazilian Cyanobium sp. Strain CACIAM 14.
PG  - e00669-14
AB  - Given the scarcity of data pertaining to whole-genome sequences of cyanobacterial strains
      isolated in Brazil, we hereby present the draft genome sequence of the
      Cyanobium sp. strain CACIAM 14, isolated in southeastern Amazonia.
AU  - Lima AR
AU  - Siqueira AS
AU  - Dos Santos BG
AU  - da Silva FD
AU  - Lima CP
AU  - Cardoso JF
AU  - Vianez JJL
AU  - Dall'Agnol LT
AU  - McCulloch JA
AU  - Nunes MR
AU  - Goncalves EC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00669-14.

PMID- 24435876
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Blastomonas sp. Strain CACIA 14H2, a Heterotrophic Bacterium Associated with Cyanobacteria.
PG  - e01200-13
AB  - With the new methods for assembling sequence data from metagenomic samples, the genomic study
      of heterotrophic bacterium-cyanobacterium associations can now be
      improved. In this work, the draft genome sequence of Blastomonas sp. strain CACIA
      14H2, obtained from a nonaxenic culture of a Cyanobium sp., is presented.
AU  - Lima AR
AU  - Siqueira AS
AU  - Dos Santos BG
AU  - da Silva FD
AU  - Lima CP
AU  - Cardoso JF
AU  - Vianez-Junior JL
AU  - Nunes MR
AU  - Goncalves EC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01200-13.

PMID- 28705982
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Alkalinema sp. Strain CACIAM 70d, a Cyanobacterium Isolated from an Amazonian Freshwater Environment.
PG  - e00635-17
AB  - In order to increase the genomic data of cyanobacterial strains isolated in Brazil, we hereby
      present the draft genome sequence of the Alkalinema sp. strain
      CACIAM 70d, isolated from an Amazonian freshwater environment. This report
      describes the first genome available for this genus.
AU  - Lima ARJ
AU  - Castro WO
AU  - Moraes PHG
AU  - Siqueira AS
AU  - Aguiar DCF
AU  - de Lima CPS
AU  - Vianez-Junior JLSG
AU  - Nunes MRT
AU  - Dall'Agnol LT
AU  - Goncalves EC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00635-17.

PMID- 29146856
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Xanthomonas campestris pv. viticola Strain CCRMXCV 80 from Brazil.
PG  - e01263-17
AB  - Here, we report the complete 5.3-Mb genome sequence of Xanthomonas campestris pv. viticola
      (CCRMXCV 80), which causes grapevine (Vitis vinifera L.) bacterial
      canker. Genome data will improve our understanding of the strain's comparative
      genomics and epidemiology, and help to further define plant protection and
      quarantine procedures.
AU  - Lima NB
AU  - Gama MAS
AU  - Mariano RLR
AU  - Silva WJ Jr
AU  - Farias ARG
AU  - Falcao RM
AU  - Sousa-Paula LC
AU  - Benko-Iseppon AM
AU  - Paiva SSL Jr
AU  - Balbino VQ
AU  - Souza EB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01263-17.

PMID- Not carried by PubMed...
VI  - 13
DP  - 1978
TI  - Heterogeneity among strains of lactic streptococci.
PG  - 1-8
AB  - Heterogeneity within lactic streptococcal cultures was studied with respect to
      acid production and phage sensitivity.  All strains were found to accumulate
      slow coagulating variants at different rates, depending upon the growth media
      used.  Maintenance of cultures in M17 broth resulted in a significant
      accumulation of slow coagulating variants for most strains studied.  In all but
      one strain investigated, variants were detected which exhibited different phage
      sensitivies.  When isolates from these cultures were examined four phenotypes
      were observed:  1) Variants exhibiting host modification and restriction of
      phages; 2) Variants which adsorbed but did not form plaques (with one or more
      particular phages); 3) Variants resistant against one or more particular
      phages; 4) Variants sensitive to different phages.  Generally only one or two
      of these four phenotypes were recovered from any one strain but a detailed
      investigation of strain 108 showed that all four phenotypes were present.  The
      appearance of these variants was dependent upon the nature of subculturing
      medium, being much more rapid in M17 broth than in autoclaved reconstituted
      skim milk.  The commercial importance of these findings is discussed.
AU  - Limsowtin GKY
AU  - Heap HA
AU  - Lawrence RC
PT  - Journal Article
TA  - New Zealand J. Dairy Sci. Techn.
JT  - New Zealand J. Dairy Sci. Techn.
SO  - New Zealand J. Dairy Sci. Techn. 1978 13: 1-8.

PMID- 23105059
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Klebsiella pneumoniae 1084, a Hypermucoviscosity-Negative K1 Clinical Strain.
PG  - 6316
AB  - We report the complete genome sequence of Klebsiella pneumoniae 1084, a
      hypermucoviscosity-negative K1 clinical strain. Sequencing and annotation
      revealed a 5,386,705-bp circular chromosome (57.4% G+C content), which contains
      4,962 protein-coding genes, 80 tRNA genes, and 25 rRNA genes.
AU  - Lin AC
AU  - Liao TL
AU  - Lin YC
AU  - Lai YC
AU  - Lu MC
AU  - Chen YT
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6316.

PMID- 22535944
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of the Novel Agarolytic Bacterium Aquimarina agarilytica ZC1.
PG  - 2769
AB  - The marine bacterium ZC1 is the type strain of the recently identified novel species
      Aquimarina agarilytica. It can produce multiple agarases. Here we report
      the draft genome sequence of strain ZC1 (4,253,672 bp, with a GC content of
      32.8%) and major findings from its annotation. It is the first reported genome in
      the genus Aquimarina.
AU  - Lin B
AU  - Lu G
AU  - Li S
AU  - Hu Z
AU  - Chen H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2769.

PMID- 6258165
VI  - 8
DP  - 1980
TI  - A sequence-specific endonuclease (XmnI) from Xanthomonas manihotis.
PG  - 6189-6198
AB  - A type II restriction endonuclease XmnI with a novel site specificity has been
      isolated from Xanthomonas manihotis.  XmnI does not cleave SV40 DNA, but
      cleaves PhiX174 DNA into three fragments, which constitute 76.61%, 18.08% and
      5.31% of the total length of 5386 base pairs, and cleaves pBR322 DNA into two
      fragments of 55.71% and 44.29% of the entire 4362 base pairs.  The nucleotide
      sequences around the cleavage sites made by XmnI are not exactly homologous,
      but they have a common sequence of 5' GAANNNNTTC 3' according to a simple
      computer program analysis on nucleotide sequences of PhiX174 DNA, pBR322 DNA
      and SV40 DNA. The results suggest that the cleavage site of XmnI is located
      within its recognition sequence of 5' GAANNNNTTC 3'.
AU  - Lin B-C
AU  - Chien M-C
AU  - Lou S-Y
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1980 8: 6189-6198.

PMID- 23469345
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of the Porcine Strain Brachyspira pilosicoli P43/6/78(T.).
PG  - e00215-12
AB  - Reported herein is the complete genome sequence of strain P43/6/78, isolated from a pig with
      clinical disease. This sequence will aid in the study of genome-wide
      comparison among species.
AU  - Lin C
AU  - den Bakker HC
AU  - Suzuki H
AU  - Lefebure T
AU  - Ponnala L
AU  - Sun Q
AU  - Stanhope MJ
AU  - Wiedmann M
AU  - Duhamel GE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00215-12.

PMID- 25103766
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Linezolid-Resistant Enterococcus faecalis Clinical Isolate HS0914.
PG  - e00782-14
AB  - We report the draft genome sequence of linezolid-resistant Enterococcus faecalis  strain
      HS-0914 isolated from a teaching hospital in Shanghai, China. The draft
      genome sequence is composed of 61 contigs for 2,816,079 bp. Ribosomal RNA
      mutations and cfr, which mediates linezolid resistance, are not present.
AU  - Lin D
AU  - Guo Y
AU  - Chen C
AU  - Fuzhu Y
AU  - Xiao S
AU  - Zhu D
AU  - Wang M
AU  - Xu X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00782-14.

PMID- 23704186
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of 'Candidatus Liberibacter americanus' Bacterium Associated with Citrus Huanglongbing in Brazil.
PG  - e00275-13
AB  - We report here the draft genome sequence of 'Candidatus Liberibacter americanus'  strain
      PW_SP. The 1,176,071-bp genome, with 31.6% G+C content, comprises 948 open
      reading frames, 38 tRNAs, and three complete rRNAs.
AU  - Lin H
AU  - Coletta-Filho HD
AU  - Han CS
AU  - Lou B
AU  - Civerolo EL
AU  - Machado MA
AU  - Gupta G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00275-13.

PMID- 23640196
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of a Chinese Strain of 'Candidatus Liberibacter asiaticus'.
PG  - e00184-13
AB  - We report here the complete genome sequence of 'Candidatus Liberibacter asiaticus' (strain
      Guangxi-1). The 1,268,237-bp genome with a 36.5% G+C content
      comprises 1,141 open reading frames, 44 tRNAs, and 3 complete rRNAs in a circular
      chromosome.
AU  - Lin H
AU  - Han CS
AU  - Liu B
AU  - Lou B
AU  - Bai X
AU  - Deng C
AU  - Civerolo EL
AU  - Gupta G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00184-13.

PMID- 26184931
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of 'Candidatus Liberibacter africanus,' a Bacterium Associated with Citrus Huanglongbing.
PG  - e00733-15
AB  - We report here the complete genome sequence of 'Candidatus Liberibacter africanus' strain
      PTSAPSY. The 1,192,232-bp genome with 34.5% G+C content
      comprises 1,017 open reading frames, 44 tRNAs, and three complete rRNAs in a
      circular chromosome.
AU  - Lin H
AU  - Pietersen G
AU  - Han C
AU  - Read DA
AU  - Lou B
AU  - Gupta G
AU  - Civerolo EL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00733-15.

PMID- 27795261
VI  - 4
DP  - 2016
TI  - Two Genome Sequences of Klebsiella pneumoniae Strains with Sequence Type 23 and Capsular Serotype K1.
PG  - e01097-16
AB  - Here, we report the whole-genome sequences of Klebsiella pneumoniae ED2 and ED23, isolated,
      respectively, from bacteremic patients with liver abscesses (ED2) and
      patients with primary liver abscess and metastatic meningitis (ED23). Both
      strains were of multilocus sequence type 23 with capsule serotype K1.
AU  - Lin HH
AU  - Chen YS
AU  - Hsiao HW
AU  - Hsueh PT
AU  - Ni WF
AU  - Chen YL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01097-16.

PMID- 21633709
VI  - 6
DP  - 2011
TI  - Sequencing and Comparative Genome Analysis of Two Pathogenic Streptococcus gallolyticus Subspecies: Genome Plasticity, Adaptation and Virulence.
PG  - e20519
AB  - Streptococcus gallolyticus infections in humans are often associated with bacteremia,
      infective endocarditis and colon cancers. The disease manifestations are different depending
      on the subspecies of S. gallolyticus causing the infection. Here, we present the complete
      genomes of S. gallolyticus ATCC 43143 (biotype I) and S. pasteurianus ATCC 43144 (biotype
      II.2).  The genomic differences between the two biotypes were characterized with comparative
      genomic analyses. The chromosome of ATCC 43143 and ATCC 43144 are 2,36 and 2,10 Mb in length
      and encode 2246 and 1869 CDS respectively.  The organization and genomic contents of both
      genomes were most similar to the recently published S. gallolyticus UCN34, where 2073 (92%)
      and 1607 (86%) of the ATCC 43143 and ATCC 43144 CDS were conserved in UCN34 respectively.
      There are around 600 CDS conserved in all Streptococcus genomes, indicating the Streptococcus
      genus has a small core-genome (constitute around 30% of total CDS) and substantial
      evolutionary plasticity. We identified eight and five regions of genome plasticity in ATCC
      43143 and ATCC 43144 respectively. Within these regions, several proteins were recognized to
      contribute to the fitness and virulence of each of the two subspecies. We have also predicted
      putative cell-surface associated proteins that could play a role in adherence to host tissues,
      leading to persistent infections causing sub-acute and chronic diseases in
      humans. This study showed evidence that the S. gallolyticus still possesses genes making it
      suitable in a rumen environment, whereas the ability for S. pasteurianus to live in rumen is
      reduced. The genome heterogeneity and genetic diversity among the two biotypes, especially
      membrane and lipoproteins, most likely contribute to the differences in the pathogenesis of
      the two S. gallolyticus biotypes and the type of disease an infected patient eventually
      develops.
AU  - Lin I-H
AU  - Liu T-T
AU  - Teng Y-T
AU  - Wu H-L
AU  - Liu Y-M
AU  - Wu K-M
AU  - Chang C-H
AU  - Hsu M-T
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2011 6: e20519.

PMID- 11784849
VI  - 22
DP  - 2002
TI  - Murine de novo methyltransferase Dnmt3a demonstrates strand asymmetry and site preference in the methylation of DNA in vitro.
PG  - 704-723
AB  - CpG methylation is involved in a wide range of biological processes in vertebrates as well as
      in plants and fungi. To date, three enzymes, Dnmt1, Dnmt3a, and Dnmt3b, are known to have DNA
      methyltransferase activity in mouse and human. It has been proposed that de novo methylation
      observed in early embryos is predominantly carried out by the Dnmt3a and Dnmt3b
      methyltransferases, while Dntm1 is believed to be responsible for maintaining the established
      methylation patterns upon replication. Analysis of the sites methylated in vivo using the
      bisulfite genomic sequencing method confirms the previous finding that some regions of the
      plasmid are much more methylated by Dnmt3a than other regions on the same plasmid. However,
      the preferred targets of the enzyme cannot be determined due to the presence of other
      methylases, DNA binding proteins, and chromatin structure. To discern the DNA targets of
      Dnmt3a without these compounding factors, sites methylated by Dnmt3a in vitro were analyzed.
      These analyses revealed that the two cDNA strands have distinctly different methylation
      patterns. Dnmt3a prefers CpG sites on a strand in which it is flanked by pyrimidines over CpG
      sites flanked by purines in vitro. These findings indicate that, unlike Dnmt1, Dnmt3a most
      likely methylates one strand of DNA without concurrent methylation of the CpG site on the
      complementary strand. These findings also indicate that Dnmt3a may methylate some CpG sites
      more frequently than others, depending on the sequence context. Methylation of each DNA strand
      independently and with possible sequence preference is a novel feature among the known DNA
      methyltransferases.
AU  - Lin IG
AU  - Han L
AU  - Taghva A
AU  - O'Brien LE
AU  - Hsieh CL
PT  - Journal Article
TA  - Mol. Cell. Biol.
JT  - Mol. Cell. Biol.
SO  - Mol. Cell. Biol. 2002 22: 704-723.

PMID- 9742098
VI  - 18
DP  - 1998
TI  - I-PpoI, the endonuclease encoded by the group I intron PpLSU3, is expressed from an RNA polymerase I transcript.
PG  - 5809-5817
AB  - PpLSU3, a mobile group I intron in the rRNA genes of Physarum polycephalum, also can home into
      yeast chromosomal ribosomal DNA (rDNA). By integrating PpLSU3 into the rDNA copies of a yeast
      strain temperature sensitive for RNA polymerase I, we have shown that the I-PpoI homing
      endonuclease encoded by PpLSU3 is expressed from an RNA polymerase I transcript. We have also
      developed a method to integrate mutant forms of PpLSU3 as well as the Tetrahymena intron
      TtLSU1 into rDNA, by expressing I-PpoI in trans. Analysis of I-PpoI expression levels in these
      mutants, along with subcellular fractionation of intron RNA, strongly suggests that the
      full-length excised intron RNA, but not RNAs that are further cleaved, serves as or gives rise
      to the mRNA.
AU  - Lin J
AU  - Vogt VM
PT  - Journal Article
TA  - Mol. Cell. Biol.
JT  - Mol. Cell. Biol.
SO  - Mol. Cell. Biol. 1998 18: 5809-5817.

PMID- 28385849
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of a High-Level Colistin-Resistant Clinical Strain of the Enterobacter cloacae Complex.
PG  - e00131-17
AB  - Strain WCHECl-C4 of the Enterobacter cloacae complex, recovered from the blood of a patient
      with peritonitis, was high-level resistant to colistin. Here, we report
      its 5.1-Mb draft genome sequence, comprising 92 contigs with an average 55.74%
      G+C content. The genome contained 4,783 coding sequences and 68 tRNA genes.
AU  - Lin J
AU  - Zhao F
AU  - Feng Y
AU  - Zong Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00131-17.

PMID- 29301886
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Elizabethkingia miricola Strain EM798-26 Isolated from the Blood of a Cancer Patient.
PG  - e01408-17
AB  - Elizabethkingia miricola EM798-26 was isolated from the blood of a patient with diffuse large
      B-cell lymphoma in Taiwan. We report here the complete genome
      sequence of EM798-26, which contains a G+C content of 35.7% and 3,877 candidate
      protein-coding genes.
AU  - Lin JN
AU  - Lai CH
AU  - Yang CH
AU  - Huang YH
AU  - Lin HH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01408-17.

PMID- 27789647
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Elizabethkingia anophelis Strain EM361-97 Isolated from  the Blood of a Cancer Patient.
PG  - e01215-16
AB  - Elizabethkingia anophelis EM361-97 was isolated from the blood of a patient with
      nasopharyngeal carcinoma and lung cancer. We report the draft genome sequence of
      EM361-97, which contains a G+C content of 35.7% and 3,611 candidate
      protein-encoding genes.
AU  - Lin JN
AU  - Yang CH
AU  - Lai CH
AU  - Huang YH
AU  - Lin HH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01215-16.

PMID- 26203334
VI  - 10
DP  - 2015
TI  - Complete genome sequence of endophytic nitrogen-fixing Klebsiella variicola strain DX120E.
PG  - 22
AB  - Klebsiella variicola strain DX120E (=CGMCC 1.14935) is an endophytic nitrogen-fixing bacterium
      isolated from sugarcane crops grown in Guangxi, China
      and promotes sugarcane growth. Here we summarize the features of the strain
      DX120E and describe its complete genome sequence. The genome contains one
      circular chromosome and two plasmids, and contains 5,718,434 nucleotides with
      57.1% GC content, 5,172 protein-coding genes, 25 rRNA genes, 87 tRNA genes, 7
      ncRNA genes, 25 pseudo genes, and 2 CRISPR repeats.
AU  - Lin L
AU  - Wei C
AU  - Chen M
AU  - Wang H
AU  - Li Y
AU  - Li Y
AU  - Yang L
AU  - An Q
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 22.

PMID- 12903440
VI  - 22
DP  - 2000
TI  - Alternative splicing of de novo methyltransferase gene 3b in adult and newborn mice.
PG  - 312-316
AB  - Objective. To unravel the biological significance of the alternative splicing of de novo
      methyltransferase 3b, expression of the Dnmt3b gene in various tissues and developmental
      stages was investigated in postnatal mice.  Methods. RT-PCR and capillary electrophoresis were
      employed to analyze the alternative splicing pattern of Dnmt3b in tissues of newborn and adult
      mice.  The results had been further reaffirmed by repeating and statistics analysis.
      Bioinformatics tools were used to predict the structure and hydrophobicity of the Dnmt3b
      exon10 coding sequence.  Results. The isoform with Dnmt3b exon10 was the abundant form in the
      lung of newborn mice and in the liver of both newborn and adult mice, while in other tissues
      of newborn and adult mice, the spliced isoform was present as the predominant one.  The
      peptide encoded by Dnmt3b exon10 was mainly random coil on the surface of Dnmt3b protein.
      Conclusions. The data demonstrate that the specific expression of Dnmt3b exists in tissues and
      developmental stages of postnatal mice.  The alternative splicing of the exon 10 of Dnmt3b is
      possibly involved in the regulation of Dnmt3b's catalytic function.  These results provide an
      insight into the developmental regulation and physiological function of the alternative
      splicing of the Dnmt3b gene.
AU  - Lin L
AU  - Xu Q
AU  - Zhang Y
AU  - Yin B
AU  - Fan Y
AU  - Luo Y
AU  - Han S
AU  - Zhang Z
AU  - Wu G
AU  - Shen Y
PT  - Journal Article
TA  - Zhongguo Yixue Kexueyuan Xuebao
JT  - Zhongguo Yixue Kexueyuan Xuebao
SO  - Zhongguo Yixue Kexueyuan Xuebao 2000 22: 312-316.

PMID- 25593265
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Vibrio owensii GRA50-12, Isolated from Green Algae in the Intertidal Zone of Eastern Taiwan.
PG  - e01438-14
AB  - Vibrio owensii GRA50-12 was isolated from symbiotic green algae of coral. The genome contains
      genes encoding toxin production, virulence regulation, stress
      response proteins, types II, IV, and VI secretion systems, and proteins for the
      metabolism of aromatic compounds, which reflects its pathogenic potential and its
      ecological roles in the ocean.
AU  - Lin LC
AU  - Lin GH
AU  - Tseng YH
AU  - Yu MS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01438-14.

PMID- 11226310
VI  - 98
DP  - 2001
TI  - Comparative genomics of the restriction-modification systems in Helicobacter pylori.
PG  - 2740-2745
AB  - Helicpbacter pylori is a Gram-negative bacterial pathogen with a small genome of 1.64-1.67 Mb.
      More than 20 putative DNA
      restriction-modification (R-M) systems, comprising more than 4% of the
      total genome, have been identified in the two completely sequenced H.
      pylori strains, 26695 and J99, based on sequence similarities. In this
      study, we have investigated the biochemical activities of 14 Type II
      R-M systems in H. pylori 26695. Less than 30% of the Type II R-M
      systems in 26695 are fully functional, similar to the results obtained
      from strain J99. Although nearly 90% of the R-M genes are shared by the
      two H. pylori strains, different sets of these R-M genes are
      functionally active in each strain. Interestingly, all strain-specific
      R-M genes are active, whereas most shared genes are inactive. This
      agrees with the notion that strain-specific genes have been acquired
      more recently through horizontal transfer from other bacteria and
      selected far function. Thus, they are less likely to he impaired by
      random mutations. Our results also show that H. pylori has extremely
      diversified R-M systems in different strains, and that the diversity
      may be maintained by constantly acquiring new R-M systems and by
      inactivating and deleting the old ones.
AU  - Lin LF
AU  - Posfai J
AU  - Roberts RJ
AU  - Kong HM
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2001 98: 2740-2745.

PMID- 10708765
VI  - 469
DP  - 2000
TI  - One-codon alternative splicing of the CpG MTase dnmt1 transcript in mouse somatic cells.
PG  - 101-104
AB  - The genomic methylation patterns in the mammalian somatic cells are presumably maintained by a
      single enzyme, dnmt1. In mouse, this DNA
      (cytosine-5)-methyltransferase, or CpG MTase, is encoded by the Dnmt1 gene. We now present
      evidence that in different tissues and cell types, the primary transcript of
      mouse dnmt1 is alternatively spliced to generate two poly-(A) RNAs of approximately similar
      abundance. This alternative splicing most likely originates from the existence
      of two tandemly arranged acceptor sites separated by only 3 nt. The two Dnmt1 mRNAs thus
      encode two CpG MTases differing by two amino acids. We discuss the
      implications of the discovery of two dnmt1 isozymes, instead of one enzyme as previously
      thought, in the somatic cells of both mouse and human.
AU  - Lin MJ
AU  - Lee TL
AU  - Hsu DW
AU  - Shen CK
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 2000 469: 101-104.

PMID- 15533947
VI  - 280
DP  - 2005
TI  - DNA methyltransferase gene dDnmt2 and longevity of Drosophila.
PG  - 861-864
AB  - The DNA methylation program of the fruit fly Drosophila melanogaster is carried out by the
      single DNA methyltransferase gene dDnmt2, the
      function of which is unknown before. We present evidence that
      intactness of the gene is required for maintenance of the normal life
      span of the fruit flies. In contrast, overexpression of dDnmt2 could
      extend Drosophila life span. The study links the Drosophila DNA
      methylation program with the small heatshock proteins and longevity/
      aging and has interesting implication on the eukaryotic DNA methylation
      programs in general.
AU  - Lin MJ
AU  - Tang LY
AU  - Reddy MN
AU  - Shen CKJ
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2005 280: 861-864.

PMID- 23965132
VI  - 347
DP  - 2013
TI  - Draft Genome Sequences of Two Super-XDR Isolates of M. tuberculosis from China.
PG  - 93-96
AB  - The prevalence of drug-resistance in Mycobacterium tuberculosis is already having a negative
      impact on the control of TB. We report the draft genome sequences of
      two super-extensively drug-resistant (S-XDR) Mycobacterium tuberculosis isolates
      from China, FJ05194 (lineage 2) and GuangZ0019 (lineage 4), and compare them to
      the H37Rv reference strain to identify possible sources of genetic variation
      associated with their extensive drug resistance. Our results suggest that their
      extensive drug resistance most likely results from the stepwise accumulation of
      resistances to individual drugs. This article is protected by copyright. All
      rights reserved.
AU  - Lin N
AU  - Liu Z
AU  - Zhou J
AU  - Wang S
AU  - Fleming J
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2013 347: 93-96.

PMID- 2471145
VI  - 17
DP  - 1989
TI  - Cloning and characterization of the genes encoding the MspI restriction modification system.
PG  - 3001-3011
AB  - The genes encoding the MspI restriction modification system, which recognizes
      the sequence 5' CCGG, have been cloned into pUC9.  Selection was based on
      expression of the cloned methylase gene which renders plasmid DNA insensitive
      to MspI cleavage in vitro.  Initially, an insert of 15 kb was obtained which,
      upon subcloning, yielded a 3 kb EcoRI to HindIII insert, carrying the genes for
      both the methylase and the restriction enzyme.  This insert has been sequenced.
      Based upon the sequence, together with appropriate subclones, it is shown that
      the two genes are transcribed divergently with the methylase gene encoding a
      polypeptide of 418 amino acids, while the restriction enzyme is composed of 262
      amino acids.  Comparison of the sequence of the MspI methylase with other
      cytosine methylases shows a striking degree of similarity.  Especially
      noteworthy is the high degree of similarity with the HhaI and EcoRII
      methylases.
AU  - Lin PM
AU  - Lee CH
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 3001-3011.

PMID- 23405302
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Simiduia agarivorans SA1(T), a Marine Bacterium Able  To Degrade a Variety of Polysaccharides.
PG  - e00039-12
AB  - Simiduia agarivorans strain SA1(T) is able to degrade a variety of polysaccharides found in
      marine algae, plants, and animals. The genome of S. agarivorans SA1(T) consists of a single
      chromosome (4,309,711 bp), and its information may provide insights into the
      polysaccharide-degrading capability, cell division, flagellar motility, and chemotaxis of this
      bacterium.
AU  - Lin SY
AU  - Shieh WY
AU  - Chen JS
AU  - Tang SL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00039-12.

PMID- 14711809
VI  - 279
DP  - 2004
TI  - Isolation and characterization of a HpyC1I restriction-modification system in Helicobacter pylori.
PG  - 11156-11162
AB  - Using transposon shuttle mutagenesis, we identified six Helicobacter pylori mutants from the
      NTUH-C1 strain that exhibited decreased adherence and cell elongation. Inverse polymerase
      chain reaction and DNA sequencing revealed that the same locus was interrupted in these six
      mutants. Nucleotide and amino acid sequences showed no homologies with H. pylori 26695 and J99
      strains. This novel open reading frame contained 1617 base pairs. The amino acid sequence
      shared 24% identity with a putative nicking enzyme in Bacillus halodurans and 23 and 20%
      identity with type IIS restriction endonucleases PleI and MlyI, respectively. The purified
      protein, HpyC1I, showed endonuclease activity with the recognition and cleavage site
      5'-CCATC( 4/5)-3'. Two open reading frames were located upstream of the gene encoding
      HpyC1I. Together, HpyC1I and these two putative methyltransferases (M1.HpyC1I and M2.HpyC1I)
      function as a restriction-modification (R-M) system. The HpyC1I R-M genes were found in 9 of
      the 15 H. pylori strains tested. When compared with the full genome, significantly lower G + C
      content of HpyC1I R-M genes implied that these genes might have been acquired by horizontal
      gene transfer. Plasmid DNA transformation efficiencies and chromosomal DNA digestion assays
      demonstrated protection from HpyC1I digestion by the R-M system. In conclusion, we have
      identified a novel R-M system present in similar to 60% of H. pylori strains. Disruption of
      this R-M system results in cell elongation and susceptibility to HpyC1I digestion.
AU  - Lin TL
AU  - Shun CT
AU  - Chang KC
AU  - Wang JT
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2004 279: 11156-11162.

PMID- 27979951
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Community-Acquired Klebsiella pneumoniae KP36, a Strain Isolated from a Patient with an Upper Urinary Tract Infection.
PG  - e01403-16
AB  - Here, we announce the complete genome sequence of Klebsiella pneumoniae KP36, a strain
      isolated from a patient with a severe community-acquired urinary tract
      infection. This genome provides insights into the pathogenesis of a pandemic K.
      pneumoniae strain from a community-acquired urinary tract infection.
AU  - Lin WH
AU  - Zheng PX
AU  - Liu T
AU  - Tseng CC
AU  - Chen WC
AU  - Wang MC
AU  - Wu JJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01403-16.

PMID- 25212616
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Pseudoalteromonas sp. Strain A2, an Isolate with High Antioxidative Activity from Arctic Seawater.
PG  - e00885-14
AB  - Here we report the draft genome sequence of Pseudoalteromonas strain A2, isolated from Arctic
      seawater in the pack-ice zone, which has high antioxidative activity
      against H2O2. The genomics information of this strain will facilitate the study
      of antioxidative mechanisms, cold adaptation properties, and evolution of this
      genus.
AU  - Lin X
AU  - Wang Z
AU  - Li Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00885-14.

PMID- 
VI  - 194
DP  - 2011
TI  - Draft genome sequence of Halomonas sp. Strain HAL1, a moderately halophilic arsenite-oxidizing bacterium isolated from gold-mine soil.
PG  - 199-200
AB  - We report the draft genome sequence of arsenite-oxidizing Halomonas sp. strain HAL1, isolated
      from the soil of a gold mine. Genes encoding proteins involved in arsenic resistance and
      transformation, phosphate utilization and uptake, and betaine biosynthesis were identified.
      Their identification might help in understanding how arsenic and phosphate metabolism are
      intertwined.
AU  - Lin Y
AU  - Fan H
AU  - Hao X
AU  - Johnstone L
AU  - Hu Y
AU  - Wei G
AU  - Alwathnani HA
AU  - Wang G
AU  - Rensing C
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 194: 199-200.

PMID- 22038968
VI  - 193
DP  - 2011
TI  - Draft Genome of Streptomyces zinciresistens K42, a Novel Metal-Resistant Species Isolated from Copper-Zinc Mine Tailings.
PG  - 6408-6409
AB  - A draft genome sequence of Streptomyces zinciresistens K42, a novel Streptomyces species
      displaying a high level of resistance to zinc and
      cadmium, is presented here. The genome contains a large number of genes
      encoding proteins predicted to be involved in conferring metal resistance.
      Many of these genes appear to have been acquired through horizontal gene
      transfer.
AU  - Lin Y
AU  - Hao X
AU  - Johnstone L
AU  - Miller SJ
AU  - Baltrus DA
AU  - Rensing C
AU  - Wei G
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6408-6409.

PMID- 24277045
VI  - 58
DP  - 2014
TI  - A Novel Staphylococcal Cassette Chromosomal Element, SCCfusC, Carrying fusC and speG in Fusidic Acid-Resistant Methicillin-Resistant Staphylococcus aureus.
PG  - 1224-1227
AB  - A high prevalence of fusC (16/46, 59%) was found in fusidic acid-resistant
      methicillin-resistant Staphylococcus aureus isolates collected from 2008 to 2010.
      Nucleotide sequencing of fusC and flanking regions revealed a novel
      staphylococcal cassette chromosome (SCC) structure, SCCfusC, which was integrated
      into rlmH and located upstream from SCCmec. The SCCfusC element contained speG,
      which may contribute to the polyamine resistance.
AU  - Lin YT
AU  - Tsai JC
AU  - Chen HJ
AU  - Hung WC
AU  - Hsueh PR
AU  - Teng LJ
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2014 58: 1224-1227.

PMID- 24265500
VI  - 1
DP  - 2013
TI  - Whole-Genome Sequencing of Lactobacillus shenzhenensis Strain LY-73T.
PG  - e00972-13
AB  - Lactobacillus shenzhenensis strain LY-73T is a novel species which was first isolated from
      fermented goods. Here, we report the draft genome sequence of
      Lactobacillus shenzhenensis LY-73T.
AU  - Lin Z
AU  - Liu Z
AU  - Yang R
AU  - Zou Y
AU  - Wan D
AU  - Chen J
AU  - Guo M
AU  - Zhao J
AU  - Fang C
AU  - Yang R
AU  - Liu F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00972-13.

PMID- 28450504
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of the Gamma-Aminobutyric Acid-Producing Strain Streptococcus thermophilus APC151.
PG  - e00205-17
AB  - Here is presented the whole-genome sequence of Streptococcus thermophilus APC151, isolated
      from a marine fish. This bacterium produces gamma-aminobutyric acid
      (GABA) in high yields and is biotechnologically suitable to produce naturally
      GABA-enriched biofunctional yogurt. Its complete genome comprises 2,097 genes and
      1,839,134 nucleotides, with an average G+C content of 39.1%.
AU  - Linares DM
AU  - Arboleya S
AU  - Ross RP
AU  - Stanton C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00205-17.

PMID- 20639323
VI  - 192
DP  - 2010
TI  - Genome Sequences of Lactococcus lactis MG1363 (Revised) and NZ9000 and Comparative Physiological Studies.
PG  - 5806-5812
AB  - Lactococcus lactis NZ9000 and its parent MG1363 are the most commonly used lactic acid
      bacteria for expression and physiological studies. We noted
      unexpected but significant differences in the growth behaviors of both
      strains. We sequenced the entire genomes of the original NZ9000 and MG1363
      strains using an ultradeep sequencing strategy. The analysis of the L.
      lactis NZ9000 genome yielded 79 differences, mostly point mutations, with
      the annotated genome sequence of L. lactis MG1363. Resequencing of the
      MG1363 strain revealed that 73 out of the 79 differences were due to
      errors in the published sequence. Comparative transcriptomic studies
      revealed several differences in the regulation of genes involved in sugar
      fermentation, which can be explained by two specific mutations in a region
      of the ptcC promoter with a key role in the regulation of cellobiose and
      glucose uptake.
AU  - Linares DM
AU  - Kok J
AU  - Poolman B
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 5806-5812.

PMID- 25858843
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Piezotolerant and Crude Oil-Degrading Bacterium Rhodococcus qingshengii Strain TUHH-12.
PG  - e00268-15
AB  - We report here the draft genome sequence of Rhodococcus qingshengii strain TUHH-12. The
      ability of this piezotolerant bacterium to grow on crude oil and
      tetracosane as sole carbon sources at 150 x 10(5) Pa makes it useful in studies
      of hydrocarbon degradation under simulated deep-sea conditions.
AU  - Lincoln SA
AU  - Hamilton TL
AU  - Valladares JAG
AU  - Schedler M
AU  - Macalady JL
AU  - Muller R
AU  - Freeman KH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00268-15.

PMID- 9628327
VI  - 379
DP  - 1998
TI  - Enzymatic methylation of DNA - Roles and prospects.
PG  - 375-376
AB  - The occurrence of a fifth base in the DNA of mammalian cells and plant cells has been known
      for close to fifty years.  However, the difficulties in relating 5-methylcytosine residues to
      specific functional roles, and the apparent absence of such DNA residues in the intensely
      studied eukaryotes Drosophila melanogaster and Saccharomyces cerevisiae, meant there were
      relatively few investigations carried out on DNA methylation until recently.  New data on DNA
      methylation as a mechanism for silencing of gene expression and its involvement in other
      aspects of epigenetic control in mammalian cells, as well as the embryonic lethal phenotype of
      gene knockout mouse constructs lacking the methyltransferase required for maintenance
      methylation, have greatly increased the amount of activity in the field.  Nevertheless,
      several potentially important aspects, such as the complicated perturbations of DNA
      methylation patterns in cancer cells involving both hypermethylation and hypomethylation, and
      the mechanisms of de novo methylation and demethylation, are still at very early stages of
      investigation.  The merging data on eukaryotes may be contrasted with the, by now, well
      established roles of DNA methylation in bacteria.  This occurs at DNA adenine as well as
      cytosine residues, and serves to protect the genome from endogenous restriction endonucleases
      as well as providing a strategy for strand discrimination in mismatch repair immediately after
      DNA replication.
AU  - Lindahl T
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1998 379: 375-376.

PMID- 2263494
VI  - 18
DP  - 1990
TI  - An anticodon nuclease gene inserted into a hsd region encoding a type I DNA restriction system.
PG  - 7170
AB  - None
AU  - Linder P
AU  - Doelz R
AU  - Gubler M
AU  - Bickle TA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 7170.

PMID- 9826348
VI  - 66
DP  - 1998
TI  - Complete DNA sequence and detailed analysis of the Yersinia pestis KIM5 plasmid encoding murine toxin and capsular antigen.
PG  - 5731-5742
AB  - Yersinia pestis, the causative agent of plague, harbors at least three plasmids necessary for
      full virulence of the organism, two of which are
      species specific. One of the Y. pestis-specific plasmids, pMT1, is thought
      to promote deep tissue invasion, resulting in more acute onset of symptoms
      and death. We determined the entire nucleotide sequence of Y. pestis KIM5
      pMT1 and identified potential open reading frames (ORFs) encoded by the
      100,990-bp molecule. Based on codon usage for known yersinial genes,
      homology with known proteins in the databases, and potential ribosome
      binding sites, we determined that 115 of the potential ORFs which we
      considered could encode polypeptides in Y. pestis. Five of these ORFs were
      genes previously identified as being necessary for production of the
      classic virulence factors, murine toxin (MT), and the fraction 1 (F1)
      capsule antigen. The regions of pMT1 encoding MT and F1 were surrounded by
      remnants of multiple transposition events and bacteriophage, respectively,
      suggesting horizontal gene transfer of these virulence factors. We
      identified seven new potential virulence factors that might interact with
      the mammalian host or flea vector. Forty-three of the remaining 115
      putative ORFs did not display any significant homology with proteins in
      the current databases. Furthermore, DNA sequence analysis allowed the
      determination of the putative replication and partitioning regions of
      pMT1. We identified a single 2,450-bp region within pMT1 that could
      function as the origin of replication, including a RepA-like protein
      similar to RepFIB, RepHI1B, and P1 and P7 replicons. Plasmid partitioning
      function was located ca. 36 kb from the putative origin of replication and
      was most similar to the parABS bacteriophage P1 and P7 system. Y. pestis
      pMT1 encoded potential genes with a high degree of similarity to a wide
      variety of organisms, plasmids, and bacteriophage. Accordingly, our
      analysis of the pMT1 DNA sequence emphasized the mosaic nature of this
      large bacterial virulence plasmid and provided implications as to its
      evolution.
AU  - Lindler LE
AU  - Plano GV
AU  - Burland V
AU  - Mayhew GF
AU  - Blattner FR
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 1998 66: 5731-5742.

PMID- 11349138
VI  - 292
DP  - 2001
TI  - Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation.
PG  - 2077-2080
AB  - Epigenetic silenced alleles of the Arabidopsis SUPERMAN locus (the clark kent alleles) are
      associated with dense hypermethylation at noncanonical cytosines (CpXpG and asymmetric sites,
      where X = A, T, C, or G). A genetic screen for suppressors of a hypermethylated clark kent
      mutant identified nine loss-of-function alleles of CHROMOMETHYLASE3 (CMT3), a novel cytosine
      methyltransferase homolog. These cmt3 mutants display a wild-type morphology but exhibit
      decreased CpXpG methylation of the SUP gene and of other sequences throughout the genome. They
      also show reactivated expression of endogenous retrotransposon sequences. These results show
      that a non-CpG DNA methyltransferase is responsible for maintaining epigenetic gene silencing.
AU  - Lindroth AM
AU  - Cao X
AU  - Jackson JP
AU  - Zilberman D
AU  - McCallum CM
AU  - Henikoff S
AU  - Jacobsen SE
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2001 292: 2077-2080.

PMID- 19811948
VI  - 300
DP  - 2010
TI  - Genomic variation and evolution of Staphylococcus aureus.
PG  - 98-103
AB  - The evolution of new human and animal pathogenic strains of Staphylococcus aureus has been due
      to the accumulation of mobile genetic elements (MGE) encoding methicillin resistance and
      virulence factors into successful lineages. These include epidemic methicillin-resistant S.
      aureus in hospitals (EMRSA), community-associated MRSA (CA-MRSA), fully vancomycin-resistant
      MRSA (VRSA) and livestock-associated MRSA (LA-MRSA). The S. aureus population in humans is
      dominated by about ten S. aureus lineages while animals generally have different lineages.
      Individual isolates within each lineage have unique combination of MGE often encoding
      virulence and resistance genes. S. aureus evolves due to point mutation and selection, but
      also dramatically due to the horizontal transfer of these MGE between strains or from other
      species or genera. Horizontal transfer, by conjugation or transduction, can be blocked by S.
      aureus restriction modification systems which are lineage specific. Because of the mobility of
      MGE, there are prospects for increasingly Virulent and resistant Strains to emerge that could
      severely affect healthcare and agriculture more effectively than the current pathogens.
AU  - Lindsay JA
PT  - Journal Article
TA  - Int. J. Med. Microbiol.
JT  - Int. J. Med. Microbiol.
SO  - Int. J. Med. Microbiol. 2010 300: 98-103.

PMID- 24439196
VI  - 304
DP  - 2014
TI  - Staphylococcus aureus genomics and the impact of horizontal gene transfer.
PG  - 103-109
AB  - Whole genome sequencing and microarrays have revealed the population structure of
      Staphylococcus aureus, and identified epidemiological shifts, transmission routes, and
      adaptation of major clones. S. aureus genomes are highly diverse. This is partly due to a
      population structure of conserved lineages, each with unique combinations of genes encoding
      surface proteins, regulators, immune evasion and virulence pathways. Even more variable are
      the mobile genetic elements (MGE), which encode key proteins for antibiotic resistance,
      virulence and host-adaptation. MGEs can transfer at high frequency between isolates of the
      same lineage by horizontal gene transfer (HGT). There is increasing evidence that HGT is key
      to bacterial adaptation and success. Recent studies have shed light on new mechanisms of DNA
      transfer such as transformation, the identification of receptors for transduction, on
      integration of DNA pathways, mechanisms blocking transfer including CRISPR and new restriction
      systems, strategies for evasion of restriction barriers, as well as factors influencing MGE
      selection and stability. These studies have also lead to new tools enabling construction of
      genetically modified clinical S. aureus isolates. This review will focus on HGT mechanisms and
      their importance in shaping the evolution of new clones adapted to antibiotic resistance,
      healthcare, communities and livestock.
AU  - Lindsay JA
PT  - Journal Article
TA  - Int. J. Med. Microbiol.
JT  - Int. J. Med. Microbiol.
SO  - Int. J. Med. Microbiol. 2014 304: 103-109.

PMID- 28860257
VI  - 5
DP  - 2017
TI  - High-Quality Draft Genome Sequences for Four Drug-Resistant or Outbreak-Associated Shigella sonnei Strains Generated with PacBio Sequencing and   Whole-Genome Maps.
PG  - e00906-17
AB  - Drug-resistant Shigella sonnei poses a clinical and public health challenge. We report here
      the high-quality draft whole-genome sequences of four
      outbreak-associated S. sonnei isolates; three were resistant to two or more
      antibiotics, and one was resistant to streptomycin only.
AU  - Lindsey RL
AU  - Batra D
AU  - Rowe L
AU  - Loparev VN
AU  - Juieng P
AU  - Garcia-Toledo L
AU  - Bicknese A
AU  - Stripling D
AU  - Martin H
AU  - Chen J
AU  - Strockbine N
AU  - Trees E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00906-17.

PMID- 28302788
VI  - 5
DP  - 2017
TI  - High-Quality Genome Sequence of an Escherichia coli O157 Strain Carrying an mcr-1 Resistance Gene Isolated from a Patient in the United States.
PG  - e01725-16
AB  - Enterobacteriaceae carrying plasmid-mediated colistin resistance have been found  around the
      world. We report here the high-quality whole-genome sequence of an
      Escherichia coli O157:H48 isolate (2016C-3936C1) from Connecticut that carried
      the mcr-1 resistance gene on an IncX4-type plasmid.
AU  - Lindsey RL
AU  - Batra D
AU  - Rowe L
AU  - Loparev VN
AU  - Stripling D
AU  - Garcia-Toledo L
AU  - Knipe K
AU  - Juieng P
AU  - Sheth M
AU  - Martin H
AU  - Laufer HA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01725-16.

PMID- 30393782
VI  - 7
DP  - 2018
TI  - PacBio Genome Sequences of Escherichia coli Serotype O157:H7, Diffusely Adherent  E. coli, and Salmonella enterica Strains, All Carrying Plasmids with an mcr-1 Resistance Gene.
PG  - e01025-18
AB  - We report here Illumina-corrected PacBio whole-genome sequences of an Escherichia coli
      serotype O157:H7 strain (2017C-4109), an E. coli serotype O[undetermined]:H2
      strain (2017C-4173W12), and a Salmonella enterica subsp. enterica serovar
      Enteritidis strain (2017K-0021), all of which carried the mcr-1 resistance gene
      on an IncI2 or IncX4 plasmid. We also determined that pMCR-1-CTSe is identical to
      a previously published plasmid, pMCR-1-CT.
AU  - Lindsey RL
AU  - Batra D
AU  - Smith P
AU  - Patel PN
AU  - Tagg KA
AU  - Garcia-Toledo L
AU  - Loparev VN
AU  - Juieng P
AU  - Sheth M
AU  - Joung YJ
AU  - Rowe LA
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e01025-18.

PMID- 26679598
VI  - 3
DP  - 2015
TI  - Complete Genome Sequences of Two Shiga Toxin-Producing Escherichia coli Strains from Serotypes O119:H4 and O165:H25.
PG  - e01496-15
AB  - Shiga toxin-producing Escherichia coli (STEC) is an important foodborne pathogen. Here, we
      report complete whole-genome sequences for two STEC strains of serotypes
      O119:H4 and O165:H25 isolated from clinical cases in the United States.
AU  - Lindsey RL
AU  - Knipe K
AU  - Rowe L
AU  - Garcia-Toledo L
AU  - Loparev V
AU  - Juieng P
AU  - Trees E
AU  - Strockbine N
AU  - Stripling D
AU  - Gerner-Smidt P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01496-15.

PMID- 27365352
VI  - 4
DP  - 2016
TI  - High-Quality Draft Genome Sequences for Five Non-O157 Shiga Toxin-Producing Escherichia coli Strains Generated with PacBio Sequencing and Optical Maps.
PG  - e00626-16
AB  - Shiga toxin-producing Escherichia coli (STEC) is a foodborne pathogen. We report  here the
      high-quality draft whole-genome sequences of five STEC strains isolated  from clinical cases
      in the United States. This report is for STEC of serotypes O55:H7, O79:H7, O91:H14, O153:H2,
      and O156:H25.
AU  - Lindsey RL
AU  - Rowe L
AU  - Garcia-Toledo L
AU  - Loparev V
AU  - Knipe K
AU  - Stripling D
AU  - Martin H
AU  - Trees E
AU  - Juieng P
AU  - Batra D
AU  - Strockbine N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00626-16.

PMID- 25013133
VI  - 2
DP  - 2014
TI  - Draft Whole-Genome Sequences of Nine Non-O157 Shiga Toxin-Producing Escherichia coli Strains.
PG  - e00501-14
AB  - Shiga toxin-producing Escherichia coli (STEC) is an important food-borne pathogen. Here, we
      report the draft whole-genome sequences of nine STEC strains
      isolated from clinical cases in the United States. This is the first report of
      such information for STEC of serotypes O69, H11, O145:H25, O118:H16, O91:H21,
      O146:H21, O45:H2, O128:H2, and O121:H19.
AU  - Lindsey RL
AU  - Trees E
AU  - Sammons S
AU  - Loparev V
AU  - Frace M
AU  - Strockbine N
AU  - Sabol AL
AU  - Sowers E
AU  - Stripling D
AU  - Martin H
AU  - Knipe K
AU  - Rowe L
AU  - Gerner-Smidt P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00501-14.

PMID- 
VI  - 
DP  - 2000
TI  - The enzymology of bacterial dna methyltransferases.
PG  - 109
AB  - DNA methyltransferases are excellent prototypes for investigating DNA distortion and enzymne
      specificity because catalysis requires the extrahelical stabilization of the target base
      within the enzyme active site.  Equilibrium dissociation constants were determined for the
      binding of the DNA (adenine-N6-)-methyltransferase M.EcoRI to DNA containing abasic sites and
      base analogs incorporated at the target base.  Tighter binding to oligonucleotides containing
      destabilized target base pairs was observed, corroborating spectroscopic evidence for
      nucleoside flipping by that enzyme.
AU  - Lindstrom WM Jr
PT  - Journal Article
TA  - Ph.D. Thesis, Univ. of California, Santa Barbara
JT  - Ph.D. Thesis, Univ. of California, Santa Barbara
SO  - Ph.D. Thesis, Univ. of California, Santa Barbara 2000 : 109.

PMID- 
VI  - 13
DP  - 1999
TI  - HhaI DNA cytosine-C5 methyltransferase: Reconciling function and structure.
PG  - A1443
AB  - HhaI DNA methyltransferase utilizes S-adenosyl-L-methionine to modify the 5-carbon of the
      inner cytosine in the cognate sequence 5'-GCGC-3'.  We directly demonstrate the catalytic
      competence of the enzyme-DNA complex, and the catalytic incompetence of the enzyme-AdoMet
      complex.  Formation of the dead-end enzyme-AdoMet complex is consistent with the AdoMet
      binding observed by x-ray crystallographic analysis of the binary complex.  The enzyme has a
      two-fold preference for unmethylated over hemimethylated DNA based on kcat/KmDNA.  The methyl
      transfer step contributes little to this discrimination, in contrast to the mammalian DNA
      cytosine methyltransferase.  Surprisingly, in the absence of any cofactor, the enzyme binds
      hemimethylated DNA seven-fold more tightly than unmethylated DNA.  This overall DNA binding
      affinity is increased 10,000-fold and the preference for hemimethylated DNA is enhanced to
      greater than 140-fold in the ternary enzyme-DNA-cofactor complex.  The differential binding
      affinities of hemi- and unmethylated substrates directly alter how the enzyme processes its
      substrate during the catalytic cycle.  Our functional characterization is presented in the
      context of the available co-crystal structures of the enzyme-hemimethylated DNA-cofactor,
      enzyme-unmethylated DNA-cofactor, and enzyme-AdoMet complexes.  The combined functional and
      structural analyses provide insight into the discrimination of hemi- and unmethylated DNA, and
      the methyl transfer step, and comparisons with the mammalian DNA methyltransferase.
AU  - Lindstrom WM Jr
AU  - Flynn J
AU  - Reich NO
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1999 13: A1443.

PMID- 12507474
VI  - 325
DP  - 2003
TI  - Functional analysis of BamHI DNA cytosine-N4 methyltransferase.
PG  - 711-720
AB  - We show that the kinetic mechanism of the DNA (cytosine-N(4)-)-methyltransferase M.BamHI,
      which modifies the underlined
      cytosine (GGATCC), differs from cytosine C(5) methyltransferases, and is
      similar to that observed with adenine N(6) methyltransferases. This
      suggests that the obligate order of ternary complex assembly and
      disassembly depends on the type of methylation reaction. In contrast, the
      single-turnover rate of catalysis for M.BamHI (0.10s(-1)) is closer to the
      DNA (cytosine-C(5)-)-methyltransferases (0.14s(-1)) than the DNA
      (adenine-N(6)-)-methyltransferases (>200s(-1)). The nucleotide flipping
      transition dominates the single-turnover constant for adenine N(6)
      methyltransferases, and, since the disruption of the guanine-cytosine
      base-pair is essential for both types of cytosine DNA methyltransferases,
      this transition may be a common, rate-limiting step for methylation for
      these two enzyme subclasses. The similar overall rate of catalysis by
      M.BamHI and other DNA methyltransferases is consistent with a common
      rate-limiting catalytic step of product dissociation. Our analyses of
      M.BamHI provide functional insights into the relationship between the
      three different classes of DNA methyltransferases that complement both
      prior structural and evolutionary insights.
AU  - Lindstrom WM Jr
AU  - Malygin EG
AU  - Ovechkina LG
AU  - Zinoviv VV
AU  - Reich NO
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2003 325: 711-720.

PMID- 10671528
VI  - 275
DP  - 2000
TI  - Reconciling structure and function in HhaI DNA cytosine-C-5 methyltransferase.
PG  - 4912-4919
AB  - Pre-steady state partitioning analysis of the HhaI DNA methyltransferase directly demonstrates
      the catalytic competence of the
      enzyme DNA complex and the lack of catalytic competence of the
      enzyme-S-adenosyl-L-methionine (AdoMet) complex. The enzyme.AdoMet
      complex does form, albeit with a 50-fold decrease in affinity compared
      with the ternary enzyme.AdoMet.DNA complex. These findings reconcile
      the distinct binding orientations previously observed within the binary
      enzyme.AdoMet and ternary enzyme.S-adenosyl-L-homocysteine.DNA crystal
      structures. The affinity of the enzyme for DNA is increased 900-fold in
      the presence of its cofactor, and the preference for hemimethylated DNA
      is increased to 12-fold over unmethylated DNA We suggest that this
      preference is partially due to the energetic cost of retaining a cavity
      in place of the B-methyl moiety in the ternary complex with the
      unmethylated DNA, as revealed by the corresponding crystal structures.
      The hemi- and unmethylated substrates alter the fates and lifetimes of
      discrete enzyme substrate intermediates during the catalytic cycle.
      Hemimethylated substrates partition toward product formation versus
      dissociation significantly more than unmethylated substrates. The
      mammalian DNA cytosine-C-5 methyltransferase Dnmt1 shows an even more
      pronounced partitioning toward product formation.
AU  - Lindstrom WM
AU  - Flynn J
AU  - Reich NO
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2000 275: 4912-4919.

PMID- 28232431
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Marinobacter hydrocarbonoclasticus Strain STW2, a Polycyclic Aromatic Hydrocarbon-Degrading and Denitrifying Bacterium from the  Rhizosphere of Seagrass Enhalus acodoides.
PG  - e01412-16
AB  - Here, we report the draft genome sequence of Marinobacter hydrocarbonoclasticus strain STW2,
      which was isolated from the rhizosphere of seagrass Enhalus
      acodoides This study will facilitate future studies on the genetic pathways of
      marine microbes capable of both polycyclic aromatic hydrocarbon degradation and
      nitrate reduction.
AU  - Ling J
AU  - Lin L
AU  - Zhang Y
AU  - Lin X
AU  - Ahamad M
AU  - Zhou W
AU  - Dong J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01412-16.

PMID- 14752048
VI  - 32
DP  - 2004
TI  - Modification of de novo DNA methyltransferase 3a (Dnmt3a) by SUMO-1 modulates its interaction with histone deacetylases (HDACs) and its capacity to repress transcription.
PG  - 598-610
AB  - The de novo DNA methyltransferase Dnmt3a is one of three mammalian DNA methyltransferases that
      has been shown to play crucial roles in embryonic development, genomic imprinting and
      transcriptional silencing. Despite its importance, very little is known about how the
      enzymatic activity and transcriptional repression functions of Dnmt3a are regulated. Here we
      show that Dnmt3a interacts with multiple components of the sumoylation machinery, namely the
      E2 sumo conjugating enzyme Ubc9 and the E3 sumo ligases PIAS1 and PIASx , all of which are
      involved in conjugating the small ubiquitin-like modifier polypeptide, SUMO-1, to its target
      proteins. Dnmt3a is modified by SUMO-1 in vivo and in vitro and the region of Dnmt3a
      responsible for interaction maps to the N-terminal regulatory domain. Functionally,
      sumoylation of Dnmt3a disrupts its ability to interact with histone deacetylases (HDAC1/2),
      but not with another interaction partner, Dnmt3b. Conditions that enhance the sumoylation of
      Dnmt3a in vivo abolish its capacity to repress transcription. These studies reveal a new level
      of regulation governing Dnmt3a whereby a post-translational modification can dramatically
      regulate its interaction with specific protein partners and alter its ability to repress
      transcription.
AU  - Ling Y
AU  - Sankpal UT
AU  - Robertson AK
AU  - McNally JG
AU  - Karpova T
AU  - Robertson KD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2004 32: 598-610.

PMID- Not carried by PubMed...
VI  - 33
DP  - 1992
TI  - 6-Thioguanine substituted DNA as a substrate for restriction endonucleases and ligases.
PG  - 543
AB  - 
AU  - Ling YH
AU  - Nelson JA
AU  - Chan JY
AU  - Beattie KL
PT  - Journal Article
TA  - Proc. Amer. Assoc. Cancer Res.
JT  - Proc. Amer. Assoc. Cancer Res.
SO  - Proc. Amer. Assoc. Cancer Res. 1992 33: 543.

PMID- 362532
VI  - 202
DP  - 1978
TI  - The 1978 Nobel prize in physiology or medicine.
PG  - 1069-1071
AB  - The 1978 Nobel Prize in Physiology or Medicine was awarded to Werner Arber, 49, of the
      Biozentrum in Basel, Switzerland; Hamilton O. Smith, 47 of Johns Hopkins University; and to
      Daniel Nathans, 50, also of Johns Hopkins University.  The awards recognize the development of
      restriction endonucleases, enzymes that can be used to study genetic organization and to
      manipulate DNA for "genetic engineering".  Arber is credited with having first predicted the
      existence of the enzymes, Smith with having isolated the first such enzyme and describing its
      specific reaction, and Nathans with having first applied these enzymes to the study of gene
      organization and regulation.
AU  - Linn S
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1978 202: 1069-1071.

PMID- 4870862
VI  - 59
DP  - 1968
TI  - Host specificity of DNA produced by Escherichia coli, X.  In vitro restriction of phage fd replicative form.
PG  - 1300-1306
AB  - An activity has been found in fractionated extracts from Escherichia coli which
      reduces the infectivity of the replicative form of phage fd DNA.  It is
      correlated with the in vivo restriction phenomenon by (1) its presence only in
      fractions from restricting strains of bacteria and (2) its specificity for
      nonmodified DNA.  The inactivation requires S-adenosylmethionine, ATP, Mg++,
      and the products of at least two gene functions; it seems to be accompanied by
      double-strand cleavage of the DNA.
AU  - Linn S
AU  - Arber W
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1968 59: 1300-1306.

PMID- 4599006
VI  - 33
DP  - 1974
TI  - Host-controlled restriction and modification enzymes of Escherichia coli B1,2.
PG  - 1128-1134
AB  - The Escherichia coli B modification methylase transfers a methyl group from
      S-adenosylmethionine to DNA in a reaction wherein the enzyme may not turn over.
      The corresponding restriction endonuclease puts one nick into the DNA, or
      converts a previously placed restriction nick into a double-strand break in a
      reaction which requires ATP and S-adenosylmethionine.  The DNA is not cleaved
      at the specific recognition site, as demonstrated by centrifugational and
      electrophoretic analyses and the fact that restricted DNA can be methylated by
      the modification enzyme.  After the DNase event, the enzyme no longer cleaves
      DNA, but forms a complex with S-adenosylmethionine and the DNA molecule which
      it has restricted.  This complex actively hydrolyzes ATP to ADP and Pi.  The
      modification enzyme exists in several forms, each having in some ratio the
      polypeptides b and c, and a (molecular weight, 135,000).  In vitro
      complementation analyses demonstrate that b and c from modification enzyme are
      active in a restriction reaction when mixed with a factor that appears to be
      the alpha-subunit.  These results are compatible with the genetic analysis of
      the system.  The nature of the recognition site and the complexity of the
      restriction reaction are discussed.
AU  - Linn S
AU  - Lautenberger JA
AU  - Eskin B
AU  - Lackey D
PT  - Journal Article
TA  - Fed. Proc.
JT  - Fed. Proc.
SO  - Fed. Proc. 1974 33: 1128-1134.

PMID- 24340004
VI  - 8
DP  - 2013
TI  - Helicobacter pylori genomic microevolution during naturally occurring transmission between adults.
PG  - e82187
AB  - The human gastric pathogen Helicobacter pylori is usually acquired during childhood and, in
      the absence of treatment, chronic infection persists through most of the host's life.
      However, the frequency and importance of H. pylori transmission between adults is
      underestimated. Here we sequenced the complete genomes of H. pylori strains
      that were transmitted between spouses and analysed the genomic changes. Similar to H. pylori
      from chronic infection, a significantly high proportion of the determined 31 SNPs and 10
      recombinant DNA fragments affected
      genes of the hop family of outer membrane proteins, some of which are known to be adhesins. In
      addition, changes in a fucosyltransferase gene modified the LPS component of the bacterial
      cell surface, suggesting strong diversifying selection. In contrast, virulence factor genes
      were not affected by the genomic changes. We propose a model of the genomic changes that are
      associated with the transmission and adaptation of H. pylori to a new human host.
AU  - Linz B
AU  - Windsor HM
AU  - Gajewski JP
AU  - Hake CM
AU  - Drautz DI
AU  - Schuster SC
AU  - Marshall BJ
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2013 8: e82187.

PMID- 24924186
VI  - 5
DP  - 2014
TI  - A mutation burst during the acute phase of Helicobacter pylori infection in humans and rhesus macaques.
PG  - 4165
AB  - The evolution rate and genetic changes that occur during chronic infection with Helicobacter
      pylori have been analysed, but little is known about the genomic changes during the initial,
      acute bacterial infection phase.  Here we analyse the rate and pattern of genome evolution in
      H. pylori from the genomes of two input strains isolated from human volunteers with
      asymptomatic infection, and the genomes of two output strains collected 20 and 44 days after
      re-infection.  Similarly, we analyse genome evolution in bacteria from the genome sequences of
      input and output strains sequentially taken after experimental infection of a rhesus macaque.
      The estimated mutation rate reveals a mutation burst during the acute infection phase that is
      over 10 times faster than the mutation rate during chronic infection, and orders of magnitude
      faster than mutation rates in any other bacteria.  The elevated frequency of mutations in
      outer membrane protein genes suggests that the mutation burst facilitates rapid host
      adaptation of the bacteria.
AU  - Linz B
AU  - Windsor HM
AU  - McGraw JJ
AU  - Hansen LM
AU  - Gajewski JP
AU  - Tomsho LP
AU  - Hake CM
AU  - Solnick JV
AU  - Schuster SC
AU  - Marshall BJ
PT  - Journal Article
TA  - Nat. Commun.
JT  - Nat. Commun.
SO  - Nat. Commun. 2014 5: 4165.

PMID- 11120683
VI  - 16
DP  - 2000
TI  - Finding pathogenicity islands and gene transfer events in genome data.
PG  - 932-940
AB  - Motivation: There is a growing literature on wavelet theory and wavelet methods showing
      improvements on more classical techniques, especially in the contexts of smoothing and
      extraction of fundamental components of signals. G+C patterns occur at different lengths
      (scales) and, for this reason, G+C plots are usually difficult to interpret. Current methods
      for genome analysis choose a window size and compute a Chi-squared statistics of the average
      value for each window with respect to the whole genome. Results: Firstly, wavelets are used to
      smooth G+C profiles to locate characteristic patterns in genome sequences. The method we use
      is based on performing a Chi-squared statistics on the wavelet coefficients of a profile; thus
      we do not need to choose a fixed window size, in that the smoothing occurs at a set of
      different scales. Secondly, a wavelet scalogram is used as a measure for sequence profile
      comparison; this tool is very general and can be applied to other sequence profiles commonly
      used in genome analysis. We show applications to the analysis of Deinococcus radiodurans
      chromosome I, of two strains of Helicobacter pylori (26695, J99) and two of Neisseria
      meningitidis (serogroup B strain MC58 and serogroup A strain Z2491).  We report a list of loci
      that have different G+C content with respect to the nearby regions; the analysis of N.
      meningitidis serogroup B shows two new large regions with low G+C content that are putative
      pathogenicity islands. Availability: Software and numerical results (profiles, scalograms,
      high and low frequency components) for all the genome sequences analyzed are available upon
      request from the authors.
AU  - Lio P
AU  - Vannucci M
PT  - Journal Article
TA  - Bioinformatics
JT  - Bioinformatics
SO  - Bioinformatics 2000 16: 932-940.

PMID- 22180808
VI  - 5
DP  - 2011
TI  - Complete genome sequence of the gliding, heparinolytic Pedobacter saltans type strain (113).
PG  - 30-40
AB  - Pedobacter saltans Steyn et al. 1998 is one of currently 32 species in the genus  Pedobacter
      within the family Sphingobacteriaceae. The species is of interest for
      its isolated location in the tree of life. Like other members of the genus P.
      saltans is heparinolytic. Cells of P. saltans show a peculiar gliding, dancing
      motility and can be distinguished from other Pedobacter strains by their ability
      to utilize glycerol and the inability to assimilate D-cellobiose. The genome
      presented here is only the second completed genome sequence of a type strain from
      a member of the family Sphingobacteriaceae to be published. The 4,635,236 bp long
      genome with its 3,854 protein-coding and 67 RNA genes consists of one chromosome,
      and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Liolios K et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 5: 30-40.

PMID- 21304716
VI  - 2
DP  - 2010
TI  - Complete genome sequence of Thermobispora bispora type strain (R51).
PG  - 318-326
AB  - Thermobispora bispora (Henssen 1957) Wang et al. 1996 is the type species of the  genus
      Thermobispora. This genus is of great interest because it is strictly
      thermophilic and because it has been shown for several of its members that the
      genome contains substantially distinct (6.4% sequence difference) and
      transcriptionally active 16S rRNA genes. Here we describe the features of this
      organism, together with the complete genome sequence and annotation. This is the
      second completed genome sequence of a member from the suborder
      Streptosporangineae and the first genome sequence of a member of the genus
      Thermobispora. The 4,189,976 bp long genome with its 3,596 protein-coding and 63
      RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Liolios K et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 2: 318-326.

PMID- 23991249
VI  - 8
DP  - 2013
TI  - Complete genome sequence of the halophilic bacterium Spirochaeta africana type strain (Z-7692(T)) from the alkaline Lake Magadi in the East African Rift.
PG  - 165-176
AB  - Spirochaeta africana Zhilina et al. 1996 is an anaerobic, aerotolerant, spiral-shaped
      bacterium that is motile via periplasmic flagella. The type strain
      of the species, Z-7692(T), was isolated in 1993 or earlier from a bacterial bloom
      in the brine under the trona layer in a shallow lagoon of the alkaline equatorial
      Lake Magadi in Kenya. Here we describe the features of this organism, together
      with the complete genome sequence, and annotation. Considering the pending
      reclassification of S. caldaria to the genus Treponema, S. africana is only the
      second 'true' member of the genus Spirochaeta with a genome-sequenced type strain
      to be published. The 3,285,855 bp long genome of strain Z-7692(T) with its 2,817
      protein-coding and 57 RNA genes is a part of the G enomic E ncyclopedia of B
      acteria and A rchaea project.
AU  - Liolos K et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 165-176.

PMID- 23209228
VI  - 194
DP  - 2012
TI  - Genome Sequence of Acinetobacter baumannii TYTH-1.
PG  - 6974
AB  - Acinetobacter baumannii has emerged recently as a major cause of health care-associated
      infections due to the extent of its antimicrobial resistance and
      its propensity to cause large nosocomial outbreaks. Here we report the genome
      sequence of Acinetobacter baumannii TYTH-1 isolated in Taiwan during 2008.
AU  - Liou ML
AU  - Liu CC
AU  - Lu CW
AU  - Hsieh MF
AU  - Chang KC
AU  - Kuo HY
AU  - Lee CC
AU  - Chang CT
AU  - Yang CY
AU  - Tang CY
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6974.

PMID- 
VI  - 81
DP  - 2002
TI  - Directed mutagenesis of the DNA-adenine-methyltransferase (DAM) gene in Actinobacillus actinomycetemcomitans (Aa) by conjugation.
PG  - A-145
AB  - Actinobacillus actinomycetemcomitans (Aa) is a slow growing, fastidious, Gram-negative,
      capnophillic bacterium.  Of the over 500 different organisms in the oral cavity, Aa is one
      which has been strongly implicated in juvenile and adult periodontis.  Aa manifests disease by
      its ability to produce toxins, adhere to and invade epithelial cells.
      DNA-adenine-methyltransferase (DAM) is generally associated with DNA modification, but it may
      also act as a global regulator of gene expression in many organisms.  By adding methyl groups
      to various sites along the genome, DAM alters the interactions of regulatory proteins with
      their target genes.  Recently, virulence genes in Salmonella strains have been shown to be
      modulated by DAM methylation.  Objectives:  To create a DAM minus strain of Aa SUNY465 for use
      in evaluating the role of DAM in Aa virulence.  Methods: The dam gene was cloned and
      sequenced.  The PCR-amplified gene was disrupted by insertion of an antibiotic cassette into a
      unique blunt ended restriction site.  The disrupted gene was cloned into a conjugative plasmid
      and transferred from E. coli SM10(lpir) to Aa.  Results: The insertional mutation resulted in
      the loss of Dam methylation of the Aa genome as shown by restriction analysis using DpnI &
      DpnII endonucleases, which cleave DNA at methylated and non-methylated sites, respectively.
      Confirmation of the genetic mutation was confirmed by colony PCR and Southern blot analysis.
      Conclusion: The chromosomal gene coding for DNA-adenine-methyltransferase of A.
      actinomycetemcomitans has been cloned, sequenced, and disrupted.
AU  - Lippmann JE
AU  - Wu H
AU  - Fives-Taylor PM
PT  - Journal Article
TA  - J. Dent. Res.
JT  - J. Dent. Res.
SO  - J. Dent. Res. 2002 81: A-145.

PMID- 
VI  - 236
DP  - 2008
TI  - BIOT 7-Creation of a type IIS restriction endonuclease with a long recognition sequence.
PG  - 0
AB  - We have engineered a novel family of type IIS restriction endonucleases that combines the high
      specificity of the homing endonuclease I-SceI with the type-IIS cleavage of FokI. Our hybrid
      endonucleases feature a non-cleaving mutant of I-SceI linked to the catalytic domain of FokI
      through a series of peptide linkers. We find that length and composition of the linker affect
      the cleavage specificity of the hybrid enzymes. The endonucleases containing the FokI native
      linker or a 20-residue synthetic linker are the most specific, cutting double-stranded DNA
      exactly two and seven nucleotides from the recognition sequence to generate homogeneous, 5',
      five-base overhangs. These two hybrid endonucleases generate DNA cleavage products that can be
      ligated with greater than 80% fidelity.
      We anticipate that these novel enzymes will be particularly useful for manipulating or
      assembling kilobase and longer DNA fragments, which are likely to contain recognition sites
      for all natural type IIS restriction endonucleases.
AU  - Lippow SM
AU  - Aha PM
AU  - Parker MH
AU  - Blake WJ
AU  - Baynes BM
AU  - Lipovsek D
PT  - Journal Article
TA  - ACS Abstracts
JT  - ACS Abstracts
SO  - ACS Abstracts 2008 236: 0.

PMID- 19304757
VI  - 37
DP  - 2009
TI  - Creation of a type IIS restriction endonuclease with a long recognition sequence.
PG  - 3061-3073
AB  - Type IIS restriction endonucleases cleave DNA outside their recognition sequences, and are
      therefore particularly useful in the assembly of DNA
      from smaller fragments. A limitation of type IIS restriction endonucleases
      in assembly of long DNA sequences is the relative abundance of their
      target sites. To facilitate ligation-based assembly of extremely long
      pieces of DNA, we have engineered a new type IIS restriction endonuclease
      that combines the specificity of the homing endonuclease I-SceI with the
      type IIS cleavage pattern of FokI. We linked a non-cleaving mutant of
      I-SceI, which conveys to the chimeric enzyme its specificity for an 18-bp
      DNA sequence, to the catalytic domain of FokI, which cuts DNA at a defined
      site outside the target site. Whereas previously described chimeric
      endonucleases do not produce type IIS-like precise DNA overhangs suitable
      for ligation, our chimeric endonuclease cleaves double-stranded DNA
      exactly 2 and 6 nt from the target site to generate homogeneous, 5',
      four-base overhangs, which can be ligated with 90% fidelity. We anticipate
      that these enzymes will be particularly useful in manipulation of DNA
      fragments larger than a thousand bases, which are very likely to contain
      target sites for all natural type IIS restriction endonucleases.
AU  - Lippow SM
AU  - Aha PM
AU  - Parker MH
AU  - Blake WJ
AU  - Baynes BM
AU  - Lipovsek D
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: 3061-3073.

PMID- 28302780
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Pseudomonas sp. BDAL1 Reconstructed from a Bakken Shale  Hydraulic Fracturing-Produced Water Storage Tank Metagenome.
PG  - e00033-17
AB  - We report the 5,425,832 bp draft genome of Pseudomonas sp. strain BDAL1, recovered from a
      Bakken shale hydraulic fracturing-produced water tank
      metagenome. Genome annotation revealed several key biofilm formation genes and
      osmotic stress response mechanisms necessary for survival in hydraulic
      fracturing-produced water.
AU  - Lipus D
AU  - Ross D
AU  - Bibby K
AU  - Gulliver D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00033-17.

PMID- 27587817
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Methanohalophilus mahii Strain DAL1 Reconstructed from a Hydraulic Fracturing-Produced Water Metagenome.
PG  - e00899-16
AB  - We report here the 1,882,100-bp draft genome sequence of Methanohalophilus mahii  strain DAL1,
      recovered from Marcellus Shale hydraulic fracturing-produced water
      using metagenomic contig binning. Genome annotation revealed several key
      methanogenesis genes and provides valuable information on archaeal activity
      associated with hydraulic fracturing-produced water environments.
AU  - Lipus D
AU  - Vikram A
AU  - Ross DE
AU  - Bibby K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00899-16.

PMID- 28619787
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Four Pseudomonas aeruginosa Isolates Obtained from Patients with Chronic Obstructive Pulmonary Disease.
PG  - e00147-17
AB  - Patients suffering chronic obstructive pulmonary disease are frequently infected  by
      Pseudomonas aeruginosa Nevertheless, the number of sequenced isolates causing
      this type of infection is low. Here, we present the draft genomes of four P.
      aeruginosa isolates obtained from patients presenting chronic obstructive
      pulmonary disease.
AU  - Lira F
AU  - Garcia-Leon G
AU  - Oliver A
AU  - Martinez JL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00147-17.

PMID- 22689246
VI  - 194
DP  - 2012
TI  - Whole-Genome Sequence of Stenotrophomonas maltophilia D457, a Clinical Isolate and a Model Strain.
PG  - 3563-3564
AB  - Stenotrophomonas maltophilia is an opportunistic pathogen with an environmental origin, and it
      is an increasingly relevant cause of nosocomial infections. Here
      we present the whole-genome sequence of S. maltophilia strain D457, a clinical
      isolate that is being used as a model for studying antibiotic resistance in this
      bacterial species.
AU  - Lira F
AU  - Hernandez A
AU  - Belda E
AU  - Sanchez MB
AU  - Moya A
AU  - Silva FJ
AU  - Martinez JL
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3563-3564.

PMID- 
VI  - 1
DP  - 2000
TI  - Phage T4-ancoded Stp alleviates the DNA restriction activity of EcoR124I endonuclease by affecting a critical step in the subunit assembly pathway.
PG  - 57-64
AB  - The tRNA(Lys)-specific anticodon nuclease is kept latent by virtue of a physical
      association with the type IC DNA
      restriction-modification enzyme EcoprrI. Previous work in vivo has
      indicated that the phage T4-encoded polypeptide Stp inhibits EcoprrI
      DNA restriction and activates anticodon nuclease. These studies also
      suggested that EcoprrI is the immediate target of Stp. The presumptive
      interaction was investigated here in vitro using the synthetic Stp-like
      polypeptide Stp sub(2-26). Stp sub(2-26) inhibited the DNA restriction
      activity of both EcoprrI and the related type IC DNA restriction enzyme
      EcoR124I in crude cell extracts more effectively than with purified
      EcoR124I. However, complementation with an EcoR124I-free crude extract
      fully restored Stp function, suggesting the existence of any
      co-operating host factor(s). Stp sub(2-26) also enhanced limited
      proteolysis of the purified EcoR124I holoenzyme (HsdR sub(2)M sub(2)S),
      but not the HsdM sub(2)S subassembly indicating that the R subunit is
      important for the interaction and, perhaps, serves as the immediate
      target of Stp. Stp sub(2-26) also produced a subtle shift of the
      equilibrium between the Hsd R2 M2 S1 and Hsd R1 M2
      S1 subassembly towards the latter form. Since only the
      holoenzyme is active as a restriction endonuclease, this effect can
      account for the ability of Stp to inhibit the DNA restriction enzyme
      and activate the appended anticodon nuclease.
AU  - Lisle W
AU  - Dutta CF
AU  - Penner M
AU  - Amitsur M
AU  - Kaufmann G
AU  - Firman K
PT  - Journal Article
TA  - Mol. Biol. Today
JT  - Mol. Biol. Today
SO  - Mol. Biol. Today 2000 1: 57-64.

PMID- 19081059
VI  - 16
DP  - 2008
TI  - Early interrogation and recognition of DNA sequence by indirect readout.
PG  - 1828-1837
AB  - Control of replication, transcription, recombination and repair requires proteins capable of
      finding particular DNA sequences in a background of a large excess of nonspecific sequences.
      Such recognition can involve direct readout, with direct contacts to the bases of DNA, or in
      some cases through the less well characterized indirect readout mechanisms. In order to
      measure the relative contributions of direct and indirect readout by a sequence specific
      endonuclease,  HincII, a mutant enzyme deficient in a direct contact, was characterized, and
      surprisingly showed no loss of sequence specificity. The three dimensional crystal structure
      shows the loss of most of the direct readout contacts to the DNA, possibly capturing an
      early stage in target site recognition using predominately indirect readout to prescreen sites
      before full sequence interrogation.
AU  - Little EJ
AU  - Babic AC
AU  - Horton NC
PT  - Journal Article
TA  - Structure
JT  - Structure
SO  - Structure 2008 16: 1828-1837.

PMID- 15993893
VI  - 351
DP  - 2005
TI  - DNA-induced conformational changes in type II restriction endonucleases: The structure of unliganded HincII.
PG  - 76-88
AB  - The 2.1 angstrom crystal structure of the unliganded type II restriction endonuclease, HincII,
      is described. Although the asymmetric
      unit contains only a single monomer, crystal lattice contacts bring two
      monomers together to form a dimer very similar to that found in the DNA
      bound form. Comparison with the published DNA bound structure reveals
      that the DNA binding pocket is expanded in the unliganded structure.
      Comparison of the unliganded and DNA liganded structures reveals a
      simple rotation of subunits by 11 degrees each, or 22 degrees total, to
      a more closed structure around the bound DNA. Comparison of this
      conformational change to that observed in the other type II restriction
      endonucleases where DNA bound and unliganded forms have both been
      characterized, shows considerable variation in the types of
      conformational changes that can occur. The conformational changes in
      three can be described by a simple rotation of subunits, while in two
      others both rotation and translation of subunits relative to one
      another occurs. In addition, the endonucleases having subunits that
      undergo the greatest amount of rotation upon DNA binding are found to
      be those that distort the bound DNA the least, suggesting that DNA
      bending may be less facile in dimers possessing greater flexibility (c)
      2005 Elsevier Ltd. All rights reserved.
AU  - Little EJ
AU  - Horton NC
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2005 351: 76-88.

PMID- 25792046
VI  - 3
DP  - 2015
TI  - Genome Sequence of the Solvent-Producing Clostridium beijerinckii Strain 59B, Isolated from Staffordshire Garden Soil.
PG  - e00108-15
AB  - The genome sequence of the solvent-producing, spore-forming, saccharolytic, mesophilic
      bacterium Clostridium beijerinckii strain 59B, isolated from
      Staffordshire garden soil, was obtained via a combination of sequencing with the
      454 and Illumina platforms. This information will allow for metabolic engineering
      of a potentially industrially useful strain.
AU  - Little GT
AU  - Winzer K
AU  - Minton NP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00108-15.

PMID- 6099315
VI  - 32
DP  - 1984
TI  - Creating new restriction sites by silent changes in coding sequences.
PG  - 67-73
AB  - We present methods for identifying a useful type of DNA site - one that can be
      mutated to create a new restriction site within a coding region without
      changing the amino acid sequence.  These "latent sites" are abundant - silent
      mutations creating one of 44 different 6-bp or 8-bp recognition sites were
      found at relatively high density, roughly one latent site per 9 bp, in the
      eleven genes tested.  Our analysis suggests that site-directed mutagenesis can
      be used to refashion coding sequences at will for flexible analysis.
AU  - Little JW
AU  - Mount DW
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1984 32: 67-73.

PMID- 27198018
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of a Marine Bacterium, Pseudomonas pseudoalcaligenes Strain S1, with High Mercury Resistance and Bioaccumulation Capacity.
PG  - e00381-16
AB  - Pseudomonas pseudoalcaligenes S1, a marine bacterium, exhibited strong resistance to a high
      concentration of Hg(2+) and remarkable Hg(2+) bioaccumulation capacity.
      Here, we report the 6.9-Mb genome sequence of P. pseudoalcaligenes S1, which may
      help clarify its phylogenetic status and provide further understanding of the
      mechanisms of mercury bioremediation in a marine environment.
AU  - Liu B
AU  - Bian C
AU  - Huang H
AU  - Yin Z
AU  - Shi Q
AU  - Deng X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00381-16.

PMID- 23405361
VI  - 1
DP  - 2013
TI  - Draft genome sequences of five strains in the genus thauera.
PG  - e00052-12
AB  - Thauera species are members of the betaproteobacteria and are most noted for their ability to
      metabolize aromatic compounds under anoxic conditions. Here, we
      announce the draft genome sequences of five Thauera strains in an effort to
      provide further genetic information as a resource for understanding the
      ecological function of this environmentally important genus.
AU  - Liu B
AU  - Frostegard A
AU  - Shapleigh JP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00052-12.

PMID- 29348340
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Bacillus methylotrophicus Strain NKG-1, Isolated from the Changbai Mountains, China.
PG  - e01454-17
AB  - We report here the complete genome sequence of Bacillus methylotrophicus NKG-1, isolated from
      rare dormant volcanic soils on the Changbai Mountains in China. The
      4.20-Mb genome contains 4,432 genes and has a G+C content of 47.06%.
AU  - Liu B
AU  - Ge B
AU  - Azhar N
AU  - Zhao W
AU  - Cui H
AU  - Zhang K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01454-17.

PMID- 22287625
VI  - 40
DP  - 2012
TI  - A novel non-homologous recombination-mediated mechanism for Escherichia coli unilateral flagellar phase variation.
PG  - 4530-4538
AB  - Flagella contribute to the virulence of bacteria through chemotaxis, adhesion to
      and invasion of host surfaces. Flagellar phase variation is believed to
      facilitate bacterial evasion of the host immune response. In this study, the flnA
      gene that encodes Escherichia coli H17 flagellin was examined by whole genome
      sequencing and genetic deletion analysis. Unilateral flagellar phase variation
      has been reported in E. coli H3, H47 and H17 strains, although the mechanism for
      phase variation in the H17 strain has not been previously understood. Analysis of
      phase variants indicated that the flagellar phase variation in the H17 strain was
      caused by the deletion of an approximately 35 kb DNA region containing the flnA
      gene from diverse excision sites. The presence of covalently closed
      extrachromosomal circular forms of this excised 35 kb region was confirmed by the
      two-step polymerase chain reaction. The deletion and complementation test
      revealed that the Int1157 integrase, a tyrosine recombinase, mediates the
      excision of this region. Unlike most tyrosine recombinases, Int1157 is suggested
      to recognize diverse sites and mediate recombination between non-homologous DNA
      sequences. This is the first report of non-homologous recombination mediating
      flagellar phase variation.
AU  - Liu B
AU  - Hu B
AU  - Zhou Z
AU  - Guo D
AU  - Guo X
AU  - Ding P
AU  - Feng L
AU  - Wang L
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: 4530-4538.

PMID- 26530456
VI  - 66
DP  - 2016
TI  - Bacillus gobiensis sp. nov., isolated from a soil sample.
PG  - 379-384
AB  - A Gram-stain-positive, rod-shaped, endospore-forming, aerobic bacterium
      designated FJAT-4402T, was isolated from the weed rhizosphere soil of the Gobi
      desert in the Xinjiang Autonomous Region in the north-west of China. Isolate
      FJAT-4402T grew at 15-40 degrees C (optimum 30 degrees C), pH 5-10 (optimum pH 7)
      and in 0-3 % (w/v) NaCl (optimum 0 %). Phylogenetic analyses, based on 16S rRNA
      gene sequences, showed that isolate FJAT-4402T was a member of the genus Bacillus
      and was most closely related to Bacillus licheniformis DSM 13T (96.2 %). The
      isolate showed 33.3 % DNA-DNA relatedness to the closest reference isolate, B.
      licheniformis DSM 13T. The diagnostic diamino acid of the peptidoglycan of
      isolate FJAT-4402T was meso-diaminopimelic acid and the predominant isoprenoid
      quinone was MK-7. The major cellular fatty acids were anteiso-C15 : 0 (28.5 %),
      iso-C15 : 0 (20.1 %), anteiso-C17 : 0 (14.3 %), iso-C16 : 0 (9.6 %), C16 : 0 (8.4
      %), iso-C17 : 0 (6.2 %) and iso-C14 : 0 (4.7 %) and the DNA G+C content was 42.0
      mol%. The phenotypic, chemotaxonomic and genotypic properties indicated that
      strain FJAT-4402T represents a novel species within the genus Bacillus, for which
      the name Bacillus gobiensis sp. nov. is proposed. The type strain is FJAT-4402T (
      = DSM 29500T = CGMCC 1.12902T).
AU  - Liu B
AU  - Liu GH
AU  - Cetin S
AU  - Schumann P
AU  - Pan ZZ
AU  - Chen QQ
PT  - Journal Article
TA  - Int. J. Syst. Evol. Microbiol.
JT  - Int. J. Syst. Evol. Microbiol.
SO  - Int. J. Syst. Evol. Microbiol. 2016 66: 379-384.

PMID- 27979958
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Type Strains Bacillus drentensis DSM 15600T and Bacillus novalis DSM 15603T.
PG  - e01423-16
AB  - Here, we report the draft genome sequences of Bacillus drentensis DSM 15600T and  Bacillus
      novalis DSM 15603T with 5,305,306 bp and 5,667,584 bp, respectively,
      which will provide useful information for the functional gene mining and
      application of these two species. The average DNA G+C contents were 38.91% and
      40.01%, respectively.
AU  - Liu B
AU  - Liu GH
AU  - Zhu YJ
AU  - Wang JP
AU  - Che JM
AU  - Chen QQ
AU  - Chen Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01423-16.

PMID- 24407638
VI  - 2
DP  - 2014
TI  - Genome Sequence of Pseudomonas aeruginosa Strain LCT-PA41, with Changed Metabolism after Space Flight.
PG  - e01124-13
AB  - To explore the effects of space flight on microorganisms, Pseudomonas aeruginosa  ATCC 27853
      was sent into orbit for 398 h on the spacecraft ShenZhou VIII. Here,
      we present the draft genome sequence of the P. aeruginosa strain LCT-PA41,
      determined after space flight.
AU  - Liu C
AU  - Hu J
AU  - Fang X
AU  - Zhang D
AU  - Chang D
AU  - Wang J
AU  - Li T
AU  - Guo Y
AU  - Dai W
AU  - Liu C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01124-13.

PMID- 26391348
VI  - 16
DP  - 2015
TI  - Genome analysis and in vivo virulence of porcine extraintestinal pathogenic Escherichia coli strain PCN033.
PG  - 717
AB  - BACKGROUND: Strains of extraintestinal pathogenic Escherichia coli (ExPEC) can
      invade and colonize extraintestinal sites and cause a wide range of infections.
      Genomic analysis of ExPEC has mainly focused on isolates of human and avian
      origins, with porcine ExPEC isolates yet to be sequenced. To better understand
      the genomic attributes underlying the pathogenicity of porcine ExPEC, we isolated
      two E. coli strains PCN033 and PCN061 from pigs, assessed their in vivo
      virulence, and completed and compared their genomes. RESULTS: Animal experiments
      demonstrated that strain PCN033, but not PCN061, was pathogenic in a pig model.
      The chromosome of PCN033 was 384 kb larger than that of PCN061. Among the
      PCN033-specific sequences, genes encoding adhesins, unique lipopolysaccharide,
      unique capsular polysaccharide, iron acquisition and transport systems, and
      metabolism were identified. Additionally, a large plasmid PCN033p3 harboring many
      typical ExPEC virulence factors was identified in PCN033. Based on the genetic
      variation between PCN033 and PCN061, corresponding phenotypic differences in
      flagellum-dependent swarming motility and metabolism were verified. Furthermore,
      the comparative genomic analyses showed that the PCN033 genome shared many
      similarities with genomic sequences of human ExPEC strains. Additionally,
      comparison of PCN033 genome with other nine characteristic E. coli genomes
      revealed 425 PCN033-special coding sequences. Genes of this subset included those
      encoding type I restriction-modification (R-M) system, type VI secretion system
      (T6SS) and membrane-associated proteins. CONCLUSIONS: The genetic and phenotypic
      differences between PCN033 and PCN061 could partially explain their differences
      in virulence, and also provide insight towards the molecular mechanisms of
      porcine ExPEC infections. Additionally, the similarities between the genomes of
      PCN033 and human ExPEC strains suggest that some connections between porcine and
      human ExPEC strains exist. The first completed genomic sequence for porcine ExPEC
      and the genomic differences identified by comparative analyses provide a baseline
      understanding of porcine ExPEC genetics and lay the foundation for their further
      study.
AU  - Liu C
AU  - Zheng H
AU  - Yang M
AU  - Xu Z
AU  - Wang X
AU  - Wei L
AU  - Tang B
AU  - Liu F
AU  - Zhang Y
AU  - Ding Y
AU  - Tang X
AU  - Wu B
AU  - Johnson TJ
AU  - Chen H
AU  - Tan C
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2015 16: 717.

PMID- 24385574
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Porphyromonas gingivalis Strain SJD2, Isolated from the  Periodontal Pocket of a Patient with Periodontitis in China.
PG  - e01091-13
AB  - Porphyromonas gingivalis strain SJD2 was isolated from subgingival plaque of a patient in
      China with chronic periodontitis. Here, we report the draft genome of
      this strain, with a size of 2,328,850 bp, average G+C content of 48.3%, and 2,020
      predicted protein-coding sequences.
AU  - Liu D
AU  - Zhou Y
AU  - Naito M
AU  - Yumoto H
AU  - Li Q
AU  - Miyake Y
AU  - Liang J
AU  - Shu R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01091-13.

PMID- 27013049
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Streptomyces canus ATCC 12647, a Producer of Telomycin.
PG  - e00173-16
AB  - We present here the genome sequence ofStreptomyces canusATCC 12647, a producer of the
      antibiotic telomycin, noted for its unique antibacterial activity against
      cardiolipin. Genomic analysis using the bioinformatics tool PRISM revealed the
      presence of multiple biosynthetic gene clusters, including those for telomycin
      and other natural products of potential pharmacological interest.
AU  - Liu DY
AU  - Li Y
AU  - Magarvey NA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00173-16.

PMID- 28183779
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of 'Candidatus Synechococcus spongiarum' m9, Binned from a  Metagenome of South China Sea Sponge Theonella swinhoei.
PG  - e01307-16
AB  - 'Candidatus Synechococcus spongiarum' represents the widespread cyanobacterial symbionts
      found in marine sponges with relatively high genomic variability and
      likely important ecological roles. We present here the draft genome sequence of
      'Candidatus Synechococcus spongiarum' m9, which was assembled from a metagenome
      of Theonella swinhoei sampled in the South China Sea.
AU  - Liu F
AU  - Li J
AU  - Li Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01307-16.

PMID- 29636463
VI  - 7
DP  - 2018
TI  - Genomic analysis of oral Campylobacter concisus strains identified a potential bacterial molecular marker associated with active Crohn's disease.
PG  - 64
AB  - Campylobacter concisus is an oral bacterium that is associated with inflammatory
      bowel disease (IBD) including Crohn's disease (CD) and ulcerative colitis (UC).
      C. concisus consists of two genomospecies (GS) and diverse strains. This study
      aimed to identify molecular markers to differentiate commensal and IBD-associated
      C. concisus strains. The genomes of 63 oral C. concisus strains isolated from
      patients with IBD and healthy controls were examined, of which 38 genomes were
      sequenced in this study. We identified a novel secreted enterotoxin B homologue,
      Csep1. The csep1 gene was found in 56% of GS2 C. concisus strains, presented in
      the plasmid pICON or the chromosome. A six-nucleotide insertion at the position
      654-659 bp in csep1 (csep1-6bpi) was found. The presence of csep1-6bpi in oral C.
      concisus strains isolated from patients with active CD (47%, 7/15) was
      significantly higher than that in strains from healthy controls (0/29, P =
      0.0002), and the prevalence of csep1-6bpi positive C. concisus strains was
      significantly higher in patients with active CD (67%, 4/6) as compared to healthy
      controls (0/23, P = 0.0006). Proteomics analysis detected the Csep1 protein. A
      csep1 gene hot spot in the chromosome of different C. concisus strains was found.
      The pICON plasmid was only found in GS2 strains isolated from the two relapsed CD
      patients with small bowel complications. This study reports a C. concisus
      molecular marker (csep1-6bpi) that is associated with active CD.
AU  - Liu F
AU  - Ma R
AU  - Tay CYA
AU  - Octavia S
AU  - Lan R
AU  - Chung HKL
AU  - Riordan SM
AU  - Grimm MC
AU  - Leong RW
AU  - Tanaka MM
AU  - Connor S
AU  - Zhang L
PT  - Journal Article
TA  - Emerg. Microbes Infect.
JT  - Emerg. Microbes Infect.
SO  - Emerg. Microbes Infect. 2018 7: 64.

PMID- 27284137
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of a Clinical Isolate of Enterobacter asburiae.
PG  - e00523-16
AB  - We report here the complete genome sequence of Enterobacter asburiae strain ENIPBJ-CG1,
      isolated from a bone marrow transplant patient. The size of the
      genome sequence is approximately 4.65 Mb, with a G+C content of 55.76%, and it is
      predicted to contain 4,790 protein-coding genes.
AU  - Liu F
AU  - Yang J
AU  - Xiao Y
AU  - Li L
AU  - Yang F
AU  - Jin Q
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00523-16.

PMID- 24874686
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Bacillus thuringiensis Strain LM1212, Isolated from the  Cadaver of an Oryctes gigas Larva in Madagascar.
PG  - e00516-14
AB  - We report the draft genome sequence of Bacillus thuringiensis strain LM1212, which
      differentiates into crystal producers or spore formers during the
      stationary phase. Availability of this genome sequence will facilitate the study
      of spore formation, crystal formation, cell differentiation, and evolution of B.
      thuringiensis.
AU  - Liu G
AU  - Deng C
AU  - Song L
AU  - Peng Q
AU  - Zhang J
AU  - Lereclus D
AU  - Song F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00516-14.

PMID- 23144388
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Aerobic Bacterium Bacillus sp. Strain FJAT-13831.
PG  - 6633
AB  - Bacillus sp. strain FJAT-13831 was isolated from the no. 1 pit soil of Emperor Qin's
      Terracotta Warriors in Xi'an City, People's Republic of China. The isolate
      showed a close relationship to the Bacillus cereus group. The draft genome
      sequence of Bacillus sp. FJAT-13831 was 4,425,198 bp in size and consisted of
      5,567 genes (protein-coding sequences [CDS]) with an average length of 782 bp and
      a G+C value of 36.36%.
AU  - Liu G
AU  - Liu B
AU  - Lin N
AU  - Tang W
AU  - Tang J
AU  - Lin Y
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6633.

PMID- 24459256
VI  - 2
DP  - 2014
TI  - Genome Sequence of Bacillus sp. Strain FJAT-14515.
PG  - e01123-13
AB  - We report the draft genome sequence of Bacillus sp. strain FJAT-14515. The genome is 5.44 Mb
      in length. It covers 5,263 genes with an average length of 791 bp, has
      a G+C value of 37.06%, and contains 67 tRNAs, 31 small RNAs, and 5 rRNA loci.
AU  - Liu G
AU  - Liu B
AU  - Tang W
AU  - Che J
AU  - Lin Y
AU  - Zhu Y
AU  - Su M
AU  - Tang J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01123-13.

PMID- 21203499
VI  - 6
DP  - 2010
TI  - Cleavage of Phosphorothioated DNA and Methylated DNA by the Type IV Restriction Endonuclease ScoMcrA.
PG  - e1001253
AB  - Many taxonomically diverse prokaryotes enzymatically modify their DNA by replacing a
      non-bridging oxygen with a sulfur atom at specific sequences.
      The biological implications of this DNA S-modification
      (phosphorothioation) were unknown. We observed that simultaneous
      expression of the dndA-E gene cluster from Streptomyces lividans 66, which
      is responsible for the DNA S-modification, and the putative Streptomyces
      coelicolor A(3)2 Type IV methyl-dependent restriction endonuclease
      ScoA3McrA (Sco4631) leads to cell death in the same host. A His-tagged
      derivative of ScoA3McrA cleaved S-modified DNA and also Dcm-methylated DNA
      in vitro near the respective modification sites. Double-strand cleavage
      occurred 16-28 nucleotides away from the phosphorothioate links. DNase I
      footprinting demonstrated binding of ScoA3McrA to the Dcm methylation
      site, but no clear binding could be detected at the S-modified site under
      cleavage conditions. This is the first report of in vitro endonuclease
      activity of a McrA homologue and also the first demonstration of an enzyme
      that specifically cleaves S-modified DNA.
AU  - Liu G
AU  - Ou HY
AU  - Wang T
AU  - Li L
AU  - Tan H
AU  - Zhou X
AU  - Rajakumar K
AU  - Deng Z
AU  - He X
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2010 6: e1001253.

PMID- 23516207
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Bacillus thuringiensis subsp. kurstaki Strain HD73.
PG  - e0008013
AB  - Bacillus thuringiensis is a Gram-positive bacterium that produces intracellular protein
      crystals toxic to a wide variety of insect larvae. We report the complete
      genome sequence of Bacillus thuringiensis subsp. kurstaki strain HD73 from the
      Centre OILB (Institut Pasteur, France), which belongs to serotype 3ab and is
      toxic to lepidopteran larvae.
AU  - Liu G
AU  - Song L
AU  - Shu C
AU  - Wang P
AU  - Deng C
AU  - Peng Q
AU  - Lereclus D
AU  - Wang X
AU  - Huang D
AU  - Zhang J
AU  - Song F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0008013.

PMID- 23144401
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Streptococcus agalactiae GD201008-001, Isolated in China from Tilapia with Meningoencephalitis.
PG  - 6653
AB  - This work describes a whole-genome sequence of Streptococcus agalactiae strain GD201008-001, a
      pathogen causing meningoencephalitis in cultural tilapia in
      China. The genome sequence provides opportunities to understand the piscine GBS
      pathogenicity and its genetic basis associated with host tropism.
AU  - Liu G
AU  - Zhang W
AU  - Lu C
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6653.

PMID- 25377706
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Bacillus fengqiuensis FJAT-14578, Isolated from a Soil Sample in China.
PG  - e01126-14
AB  - Here, we report the first high-quality draft genome sequence of Bacillus fengqiuensis
      FJAT-14578, isolated from a soil sample collected from China. The
      genome size was 5,569,389 bp, with a 40.93 mol% G+C content. The number of tRNAs
      was 69 and of rRNAs was 10 (5S, 16S, and 23S).
AU  - Liu GH
AU  - Liu B
AU  - Tang JY
AU  - Che JM
AU  - Zhu YJ
AU  - Su MX
AU  - Wang JP
AU  - Chen QQ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01126-14.

PMID- 28104649
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of a Potential Novel Bacillus sp. Strain, FJAT-18017, Isolated from a Potato Field.
PG  - e01424-16
AB  - Bacillus sp. strain FJAT-18017 was isolated from a potato field in Xinjiang, China. This paper
      is the first report, to our knowledge, to demonstrate the fully
      sequenced and completely annotated genome of Bacillus sp. FJAT-18017. The genome
      size is 5,265,521 bp. The average G+C content was 42.42%.
AU  - Liu GH
AU  - Liu B
AU  - Wang JP
AU  - Che JM
AU  - Chen QQ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01424-16.

PMID- 26251494
VI  - 3
DP  - 2015
TI  - High-Quality Genome Sequence of Bacillus vireti DSM 15602T for Setting Up Phylogenomics for the Genomic Taxonomy of Bacillus-Like Bacteria.
PG  - e00864-15
AB  - Bacillus vireti DSM 15602(T) is a Gram-negative, spore-forming, and facultatively anaerobic
      bacterium. Here, we report the 5.309-Mb draft genome sequence of B.
      vireti DSM 15602(T), which will provide useful information for setting up
      phylogenomics for the genomic taxonomy of Bacillus-like bacteria, as well as for
      the functional gene mining and application of B. vireti.
AU  - Liu GH
AU  - Liu B
AU  - Wang JP
AU  - Che JM
AU  - Chen QQ
AU  - Chen Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00864-15.

PMID- 27340061
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Bacillus simplex DSM 1321 for Setting Up Phylogenomics in Genomic Taxonomy of the Bacillus-Like Bacteria.
PG  - e00574-16
AB  - Bacillus simplex DSM 1321 is a Gram-positive, spore-forming, and aerobic bacterium. Here, we
      report the draft genome sequence of B. simplex DSM 1321, with
      6,494,937 bp, which will provide useful information for setting up phylogenomics
      in genomic taxonomy of the Bacillus-like bacteria as well as for the functional
      gene mining and application of B. simplex DSM 1321.
AU  - Liu GH
AU  - Liu B
AU  - Wang JP
AU  - Che JM
AU  - Chen QQ
AU  - Chen Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00574-16.

PMID- 26543111
VI  - 3
DP  - 2015
TI  - Genome Sequence of Type Strain Lysinibacillus macroides DSM 54T.
PG  - e01271-15
AB  - Lysinibacillus macroides DSM 54(T) is a Gram-positive, spore-forming bacterium. Here, we
      report the 4,866,035-bp genome sequence of Lysinibacillus macroides DSM
      54(T), which will accelerate the application of degrading xylan and provide
      useful information for genomic taxonomy and phylogenomics of Bacillus-like
      bacteria.
AU  - Liu GH
AU  - Liu B
AU  - Wang JP
AU  - Che JM
AU  - Chen QQ
AU  - Chen Z
AU  - Ge CB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01271-15.

PMID- 26404591
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Bacillus sp. FJAT-27238 for Setting up Phylogenomic Analysis of Genomic Taxonomy of Bacillus-Like Bacteria.
PG  - e00985-15
AB  - Bacillus sp. FJAT-27238 is a Gram-positive, spore-forming, and aerobic bacterium. Here, we
      report the draft genome sequence of Bacillus sp. FJAT-27238, with 6,134,829 bp, which will
      provide useful information for setting up phylogenomic analysis of the genomic taxonomy of
      Bacillus-like bacteria as well as for the functional gene mining and application of strain
      FJAT-27238. The genomic DNA G+C  content was 47.37%.
AU  - Liu GH
AU  - Liu B
AU  - Wang JP
AU  - Che JM
AU  - Chen QQ
AU  - Zhu YJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00985-15.

PMID- 26358604
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Type Strain Lysinibacillus xylanilyticus DSM 23493T.
PG  - e01037-15
AB  - Lysinibacillus xylanilyticus DSM 23493(T) is a Gram-positive, spore-forming bacterium. Here,
      we report the 5.22-Mb genome sequence of Lysinibacillus xylanilyticus DSM 23493(T), which will
      accelerate the application of degrading xylan and provide useful information for genomic
      taxonomy and phylogenomics of Bacillus-like bacteria.
AU  - Liu GH
AU  - Liu B
AU  - Wang JP
AU  - Che JM
AU  - Zheng XF
AU  - Chen QQ
AU  - Ge CB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01037-15.

PMID- 26494657
VI  - 3
DP  - 2015
TI  - Genome Sequence of Paenibacillus sp. Strain FJAT-28004 for the Genome Sequencing  Project for Genomic Taxonomy and Phylogenomics of Bacillus-Like Bacteria.
PG  - e00863-15
AB  - Paenibacillus sp. strain FJAT-28004 is a spore forming and strictly aerobic bacterium. Here,
      we report the draft 7,479,858-bp genome sequence of Paenibacillus sp. FJAT-28004, which will
      provide useful information for genomic taxonomy and phylogenomics of the genus Paenibacillus,
      as well as for the functional gene mining and application of Paenibacillus sp. FJAT-28004.
AU  - Liu GH
AU  - Liu B
AU  - Wang JP
AU  - Che JM
AU  - Zhu YJ
AU  - Chen QQ
AU  - Ruan CQ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00863-15.

PMID- 26494684
VI  - 3
DP  - 2015
TI  - Genome Sequence of Type Strain Bacillus decisifrondis E5HC-32T (DSM 11725T), Isolated from Soil Underlying the Decaying Leaf Litter of a Slash Pine Forest.
PG  - e01249-15
AB  - Bacillus decisifrondis E5HC-32(T) (DSM 11725(T)) is a Gram-positive, subterminal  spherical
      spore-forming, strictly aerobic bacterium. Here, we report the 5,613,728-bp genome sequence of
      B. decisifrondis E5HC-32(T), which is the first genome information of this species and will
      provide useful information for genomic taxonomy and phylogenomics of Bacillus-like bacteria.
AU  - Liu GH
AU  - Liu B
AU  - Wang JP
AU  - Chen QQ
AU  - Che JM
AU  - Zheng XF
AU  - Ge CB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01249-15.

PMID- 27313309
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Bacillus mesonae FJAT-13985T (=DSM 25968T) for Setting Up Phylogenomics in Genomic Taxonomy of the Bacillus-Like Bacteria.
PG  - e00575-16
AB  - Bacillus mesonae FJAT-13985(T) is a Gram-positive, spore-forming, and aerobic bacterium. Here,
      we report the draft genome sequence of B. mesonae FJAT-13985(T)
      with 5,807,726 bp, which will provide useful information for setting up
      phylogenomics in the genomic taxonomy of the Bacillus-like bacteria, as well as
      for the functional gene mining and application of B. mesonae FJAT-13985(T).
AU  - Liu GH
AU  - Liu B
AU  - Zhu YJ
AU  - Wang JP
AU  - Che JM
AU  - Chen QQ
AU  - Chen Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00575-16.

PMID- 28729276
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Paenibacillus sp. Strain MY03, a Terrestrial Bacterium Capable of Degrading Multiple Marine-Derived Polysaccharides.
PG  - e00678-17
AB  - The bacterium Paenibacillus sp. strain MY03, isolated from the root soil of cypress, can
      effectively degrade marine-derived polysaccharides such as agar,
      alginate, and chitin. Here, we present the draft genome sequence of MY03.
      Putative enzymes, including 3 agarases, 1 alginate lyase, and 1 chitinase, were
      found.
AU  - Liu H
AU  - Cheng Y
AU  - Gu J
AU  - Wang Y
AU  - Li J
AU  - Li F
AU  - Han W
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00678-17.

PMID- 28183774
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Paenibacillus polymyxa YC0136, a Plant Growth-Promoting Rhizobacterium Isolated from Tobacco Rhizosphere.
PG  - e01635-16
AB  - Paenibacillus polymyxa strain YC0136 is a plant growth-promoting rhizobacterium with
      antimicrobial activity, which was isolated from tobacco rhizosphere. Here,
      we report the complete genome sequence of P. polymyxa YC0136. Several genes with
      antifungal and antibacterial activity were discovered.
AU  - Liu H
AU  - Liu K
AU  - Li Y
AU  - Wang C
AU  - Hou Q
AU  - Xu W
AU  - Fan L
AU  - Zhao J
AU  - Gou J
AU  - Du B
AU  - Ding Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01635-16.

PMID- 23012277
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Plant Pathogen Pseudomonas syringae pv. panici LMG 2367.
PG  - 5693-5694
AB  - Pseudomonas syringae pv. panici is a phytopathogenic bacterium causing brown stripe disease in
      economically important crops worldwide. Here, we announce the
      draft genome sequence of Pseudomonas syringae pv. panici LMG2367 to provide
      further valuable insights for comparison of the pathovars among species
      Pseudomonas syringae.
AU  - Liu H
AU  - Qiu H
AU  - Zhao W
AU  - Cui Z
AU  - Ibrahim M
AU  - Jin G
AU  - Li B
AU  - Zhu B
AU  - Xie GL
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5693-5694.

PMID- 28912334
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Paenibacillus sp. XY044, a Potential Plant Growth Promoter Isolated from a Tea Plant.
PG  - e01016-17
AB  - Paenibacillus sp. XY044 is an endophytic bacterium isolated from the stem of a tea plant
      (Camellia sinensis cv. Maoxie). Here, we present the draft genome
      sequence of XY044, which includes genes encoding features related to plant growth
      promotion and biocontrol.
AU  - Liu H
AU  - Shan W
AU  - Zhou Y
AU  - Yu X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01016-17.

PMID- 26966199
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Escherichia coli Strain SEC470, Isolated from a Piglet Experiencing Diarrhea.
PG  - e00088-16
AB  - Escherichia coli strain SEC470 is a diarrhea-causing strain, isolated from a piglet
      experiencing serious diarrhea in Jingxi Province, China. Here, we present
      the draft genome of this strain, which provides the genetic basis for exploring
      the mechanism of enterotoxigenic E. coli infections.
AU  - Liu H
AU  - Song L
AU  - Cai Y
AU  - Wang Y
AU  - Yu L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00088-16.

PMID- 28183775
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Paenibacillus polymyxa YC0573, a Plant Growth-Promoting Rhizobacterium with Antimicrobial Activity.
PG  - e01636-16
AB  - Paenibacillus polymyxa strain YC0573 is a plant growth-promoting rhizobacterium with
      antimicrobial activity, which was isolated from tobacco rhizosphere. Here,
      we report the complete genome sequence of P. polymyxa YC0573. Antifungal and
      antibacterial genes were discovered.
AU  - Liu H
AU  - Wang C
AU  - Li Y
AU  - Liu K
AU  - Hou Q
AU  - Xu W
AU  - Fan L
AU  - Zhao J
AU  - Gou J
AU  - Du B
AU  - Ding Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01636-16.

PMID- 21994921
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Haloarcula hispanica, a Model Haloarchaeon for Studying Genetics, Metabolism, and Virus-Host Interaction.
PG  - 6086-6087
AB  - Haloarcula hispanica is an extremely halophilic archaeon that has an unusually low restriction
      barrier and is therefore significant for
      studying archaeal genetics, metabolism, and virus-host interactions. Here
      we report the complete genome sequence (3,890,005 bp) of H. hispanica
      strain CGMCC 1.2049, consisting of two chromosomes and one megaplasmid.
AU  - Liu H
AU  - Wu Z
AU  - Li M
AU  - Zhang F
AU  - Zheng H
AU  - Han J
AU  - Liu J
AU  - Zhou J
AU  - Wang S
AU  - Xiang H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6086-6087.

PMID- 25125638
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Propionibacterium acnes Type Strain ATCC6919 and Antibiotic-Resistant Strain HL411PA1.
PG  - e00740-14
AB  - Propionibacterium acnes is a major skin commensal and is associated with acne vulgaris, the
      most common skin disease. Here we report the draft genome sequences
      of two P. acnes strains, the type strain ATCC6919 and an antibiotic-resistant
      strain, HL411PA1.
AU  - Liu J
AU  - Cheng A
AU  - Bangayan NJ
AU  - Barnard E
AU  - Curd E
AU  - Craft N
AU  - Li H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00740-14.

PMID- 28479507
VI  - 108
DP  - 2017
TI  - Complete genome sequence and bioinformatics analyses of Bacillus thuringiensis strain BM-BT15426.
PG  - 55-60
AB  - OBJECTIVES: This study aimed to investigate the genetic characteristics of
      Bacillus thuringiensis strain BM-BT15426. METHODS: B. thuringiensis strain was
      identified by sequencing the PCR product (amplifying 16S rRNA gene) using ABI
      Prism 377 DNA Sequencer. The genome was sequenced using PacBio RS II sequencers
      and assembled de novo using HGAP. Also, further genome annotation was performed.
      RESULTS: The genome of B. thuringiensis strain BM-BT15426 has a length of
      5,246,329 bp and contains 5409 predicted genes with an average G + C content of
      35.40%. Three genes were involved in the "Infectious diseases: Amoebiasis"
      pathway. A total of 21 virulence factors and 9 antibiotic resistant genes were
      identified. CONCLUSIONS: The major pathogenic factors of B. thuringiensis strain
      BM-BT15426 were identified through complete genome sequencing and bioinformatics
      analyses which contributes to further study on pathogenic mechanism and phenotype
      of B. thuringiensis.
AU  - Liu J
AU  - Li L
AU  - Peters BM
AU  - Li B
AU  - Chen D
AU  - Xu Z
AU  - Shirtliff ME
PT  - Journal Article
TA  - Microb. Pathog.
JT  - Microb. Pathog.
SO  - Microb. Pathog. 2017 108: 55-60.

PMID- 12555536
VI  - 39
DP  - 1999
TI  - Expression detection and location analysis of BstNI isoschizomer restriction-modification system gene.
PG  - 209-214
AB  - Some genetic markers of E. coli HB101 and JM110 were identified, two bacterial strains were
      used as recipients respectively to detect the expression of a restriction endonuclease gene
      and a methylase gene of BstNI isoschizomer restriction-modification system.  DNA fragment
      containing the R-M genes was deleted unidirectionally with exoIII and 23 deletion subclones
      were obtained.  According to the enzyme activity of each subclone, R and M gene were located
      respectively at the regions of 0.2 to 1.4 kb and 1.5 to 3.3 kb from cloning site PstI.
      Analysis showed that the R-M system belongs to type II, two genes are controlled by the
      different promoters; the recognition sequence of this system is the same as that of
      DNA-cytosine methyltransferase (Dcm), the latter's methylation function can resist the R
      enzyme.  It was interesting that the recombinant plasmid with an R+M- genotype appeared to be
      lethal to dcm+ hosts yet.  This indicated that the M gene closely linking to R gene is of
      critical importance for the existence of the R-M system in process of evolution.
AU  - Liu J
AU  - Xue Y
AU  - Meng Y
AU  - Zhao X
AU  - Cai Y
PT  - Journal Article
TA  - Wei Sheng Wu Xue Bao
JT  - Wei Sheng Wu Xue Bao
SO  - Wei Sheng Wu Xue Bao 1999 39: 209-214.

PMID- 12903509
VI  - 22
DP  - 2000
TI  - Expression and deletion analysis of EcoRII endonuclease and methylase gene.
PG  - 111-114
AB  - Objective. To clone the complete EcoRII restriction endonuclease gene (ecoRIIR) and
      methyltransferase (ecoRIIM) gene into one vector and to analyze the expression of the whole
      system.  Methods. Unidirectional deletion subclones, constructed with ExoIII, of the ecoRIIR/M
      genes were preliminarily located in the cloned fragments according to the enzyme activities of
      each subclone, exact deletion sites were determined by sequencing, and transcriptional start
      sites were mapped by S1 mapping.  Results.  The DNA fragment which was cloned into pBluescript
      SK+ contained the complete ecoRIIR gene and ecoRIIM gene, there are two transcriptional start
      sites in the ecoRIIR gene, 132 bp to 458 bp from 3' end of the ecoRIIR gene are indispensable
      to enzyme activities and deletion of 202 bp from the 3' end of the ecoRIIM gene made it lose
      the capability to resist specific cleavage by EcoRIIR enzyme, deletion of coding region and
      flanking sequence of one gene did not affect the expression of the other gene, the recombinant
      only containing ecoRIIR gene appeared to be lethal to dcm+ host.  Conclusions. ecoRIIM gene
      closely linked to the ecoRIIR gene was very important for the existence of the R-M system in
      the process of evolution, but the key to make sure that the EcoRIIR enzyme is produced later
      than the EcoRIIM enzyme does not exist at the transcriptional level.
AU  - Liu J
AU  - Zhao X
AU  - Meng Y
AU  - Shen J
AU  - Xue Y
AU  - Shi S
AU  - Cai Y
PT  - Journal Article
TA  - Zhongguo Yi Xue Ke Xue Yuan Xue Bao
JT  - Zhongguo Yi Xue Ke Xue Yuan Xue Bao
SO  - Zhongguo Yi Xue Ke Xue Yuan Xue Bao 2000 22: 111-114.

PMID- 12903755
VI  - 16
DP  - 2001
TI  - Expression and deletion analysis of EcoRII endonuclease and methylase gene.
PG  - 200-203
AB  - Objective. To clone complete EcoRII restriction endonuclease gene (ecoRIIR) and
      methyltransferase gene (ecoRIIM) in one vector and to analyze the coordinated expression of
      this whole R-M system.  Methods. Unidirectional deletion subclones were constructed with
      ExoIII. ecoRIIR/M genes were preliminarily located in the cloned fragment according to the
      enzyme activities of subclones.  Exact deletion sites were determined by sequencing, and
      transcriptional start sites were determined by S1 mapping.  Results. The DNA fragment which
      was cloned into pBluescript SK + contained intact ecoRIIR gene and ecoRIIM gene, and two
      transcriptional start sites of ecoRIIIR gene were determined.  132bp to 458bp from 3' end of
      ecoRIIR gene are indispensable to enzyme activities and deletion of 202bp from 3' end of
      ecoRIIM gene made enzyme lose the capability in DNA protection to resist specific cut with
      EcoRII endonuclease (EcoRII.R).  Deletion of the coding and flanking sequences of one gene did
      not affect the expression of the other gene, and the recombinants only containing ecoRIIR gene
      appeared to be lethal to dcm+ host.  Conclusion. ecoRIIIM gene linking closely to ecoRIIR gene
      is very important for the existence of the R-M system in process of evolution, but the key to
      control EcoRII R-M order may not exist in transcriptional level.
AU  - Liu J
AU  - Zhao X
AU  - Meng Y
AU  - Shen J
AU  - Xue Y
AU  - Shi S
AU  - Cai Y
PT  - Journal Article
TA  - Chin. Med. Sci. J.
JT  - Chin. Med. Sci. J.
SO  - Chin. Med. Sci. J. 2001 16: 200-203.

PMID- 23144410
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Biocontrol Agent Microbacterium barkeri Strain 2011-R4.
PG  - 6666-6667
AB  - Microbacterium barkeri strain 2011-R4 is a Gram-positive epiphyte which has been  confirmed as
      a biocontrol agent against several plant pathogens in our previous
      studies. Here, we present the draft genome sequence of this strain, which was
      isolated from the rice rhizosphere in Tonglu city, Zhejiang province, China.
AU  - Liu J
AU  - Zhou Q
AU  - Ibrahim M
AU  - Liu H
AU  - Jin G
AU  - Zhu B
AU  - Xie G
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6666-6667.

PMID- 
VI  - 16
DP  - 2000
TI  - High expression and purification of EcoRII restriction endonuclease.
PG  - 417-420
AB  - EcoRII was the first restriction endonuclease ever found
      requiring the cooperative interaction with the least two DNA sites for
      digestion activity.  To study the specific activity, EcoRII was purified
      from hyperexpression engineering bacteria in which the specific
      expression products increased to about 20% of total cellular protein.
      By using chromatography on DEAE-cellulose column, phosphocellulose
      column and FPLC of Resource Q, the enzyme was purified from soluble
      protein fraction.  The inclusion bodies were solved and renatured, and
      the enzyme was purified from this part of protein with higher specific
      activity by using FPLC of Resource Q.  Detection showed that the enzyme
      was purified to homogeneity and was free of detectable contamination by
      other DNase (exo and endo).
AU  - Liu J-Y
AU  - Zhao X-J
AU  - Cai YY
AU  - Shen J
AU  - Meng Y
PT  - Journal Article
TA  - Chin. J. Biochem. Mol. Biol.
JT  - Chin. J. Biochem. Mol. Biol.
SO  - Chin. J. Biochem. Mol. Biol. 2000 16: 417-420.

PMID- 12665573
VI  - 23
DP  - 2003
TI  - Endogenous assays of DNA methyltransferases: Evidence for differential activities of DNMT1, DNMT2, and DNMT3 in mammalian cells in vivo.
PG  - 2709-2719
AB  - While CpG methylation can be readily analyzed at the DNA sequence level in wild-type and
      mutant cells, the actual DNA (cytosine-5) methyltransferases
      (DNMTs) responsible for in vivo methylation on genomic DNA are less
      tractable. We used an antibody-based method to identify specific
      endogenous DNMTs (DNMT1, DNMT1b, DNMT2, DNMT3a, and DNMT3b) that stably
      and selectively bind to genomic DNA containing 5-aza-2'-deoxycytidine
      (aza-dC) in vivo. Selective binding to aza-dC-containing DNA suggests that
      the engaged DNMT is catalytically active in the cell. DNMT1b is a splice
      variant of the predominant maintenance activity DNMT1, while DNMT2 is a
      well-conserved protein with homologs in plants, yeast, Drosophila, humans,
      and mice. Despite the presence of motifs essential for transmethylation
      activity, catalytic activity of DNMT2 has never been reported. The data
      here suggest that DNMT2 is active in vivo when the endogenous genome is
      the target, both in human and mouse cell lines. We quantified relative
      global genomic activity of DNMT1, -2, -3a, and -3b in a mouse
      teratocarcinoma cell line. DNMT1 and -3b displayed the greatest in vivo
      binding avidity for aza-dC-containing genomic DNA in these cells. This
      study demonstrates that individual DNMTs can be tracked and that their
      binding to genomic DNA can be quantified in mammalian cells in vivo. The
      different DNMTs display a wide spectrum of genomic DNA-directed activity.
      The use of an antibody-based tracking method will allow specific DNMTs and
      their DNA targets to be recovered and analyzed in a physiological setting
      in chromatin.
AU  - Liu K
AU  - Wang YF
AU  - Cantemir C
AU  - Muller MT
PT  - Journal Article
TA  - Mol. Cell. Biol.
JT  - Mol. Cell. Biol.
SO  - Mol. Cell. Biol. 2003 23: 2709-2719.

PMID- 25414493
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Cellulose-Digesting Bacterium Sporocytophaga myxococcoides PG-01.
PG  - e01154-14
AB  - Sporocytophaga myxococcoides, a Gram-negative bacterium isolated from soil, is an efficient
      hydrolyzer of crystalline cellulose. Here, we report its draft genome
      sequence, which may provide important genetic information regarding the
      cellulolytic and hemicellulolytic enzymes that contribute to the
      cellulose-degrading abilities of this bacterium.
AU  - Liu L
AU  - Gao P
AU  - Chen G
AU  - Wang L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01154-14.

PMID- 26893413
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of the Type Strain of Aeromonas schubertii, ATCC 43700.
PG  - e00012-16
AB  - We sequenced the complete genome of the type strain of Aeromonas schubertii, ATCC 43700. The
      full genome sequence of A. schubertii ATCC 43700 is 4,356,858 bp,
      which encodes 3,842 proteins and contains 110 predicted RNA genes.
AU  - Liu L
AU  - Li N
AU  - Zhang D
AU  - Fu X
AU  - Shi C
AU  - Lin Q
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00012-16.

PMID- 26798095
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of the Highly Virulent Aeromonas schubertii Strain WL1483, Isolated from Diseased Snakehead Fish (Channa argus) in China.
PG  - e01567-15
AB  - We sequenced the complete genome of the highly virulent Aeromonas schubertii strain WL1483,
      which was isolated from diseased snakehead fish (Channa argus) in
      China. The full genome sequence of A. schubertii WL1483 is 4,400,034 bp, which
      encodes 4,376 proteins and contains 195 predicted RNA genes.
AU  - Liu L
AU  - Li N
AU  - Zhang D
AU  - Fu X
AU  - Shi C
AU  - Lin Q
AU  - Hao G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01567-15.

PMID- 21994934
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of the Industrial Strain Ketogulonicigenium vulgare WSH-001.
PG  - 6108-6109
AB  - Ketogulonicigenium vulgare is an industrial organism commonly used in the vitamin C industry.
      Here, we report the finished, annotated, and compared
      3.28-Mbp high-quality genome sequence of Ketogulonicigenium vulgare
      WSH-001, a 2-keto-l-gulonic acid-producing industrial strain stocked in
      our laboratory.
AU  - Liu L
AU  - Li Y
AU  - Zhang J
AU  - Zhou Z
AU  - Liu J
AU  - Li X
AU  - Zhou J
AU  - Du G
AU  - Wang L
AU  - Chen J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6108-6109.

PMID- 22038958
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of the Industrial Strain Bacillus megaterium WSH-002.
PG  - 6389-6390
AB  - Bacillus megaterium, an industrial strain, has been widely used in protein production and the
      vitamin C industry. Here we reported a finished,
      annotated, and compared 4.14-Mbp high-quality genome sequence of B.
      megaterium WSH-002, which is the companion strain for Ketogulonicigenium
      vulgare in the vitamin C industry and is stocked in our laboratory.
AU  - Liu L
AU  - Li Y
AU  - Zhang J
AU  - Zou W
AU  - Zhou Z
AU  - Liu J
AU  - Li X
AU  - Wang L
AU  - Chen J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6389-6390.

PMID- 1606134
VI  - 31
DP  - 1992
TI  - Mutation of asparagine 229 to aspartate in thymidylate synthase converts the enzyme to a deoxycytidylate methylase.
PG  - 5100-5104
AB  - The conserved Asn 229 of thymidylate synthase (TS) forms a cyclic hydrogen bond network with
      the 3-NH and 4-O of the nucleotide substrate dUMP. The Asn 229 to Asp mutant of Lactobacillus
      casei thymidylate synthase (TS N229D) has been prepared, purified, and investigated.
      Steady-state kinetic parameters of TS N229D show 3.5- and 10-fold increases in the Km values
      of CH2H4 folate and dUMP, respectively, and a 1000-fold decrease in kcat. Most important, the
      Asp 229 mutation changes the substrate specificity of TS to an enzyme which recognizes and
      methylates dCMP in preference to dUMP. With TS N229D the Km for dCMP is about 3-fold higher
      than for dUMP, and the Km for CH2H4 folate is increased about 5-fold; however, the kcat for
      dCMP methylation is 120-fold higher than that for dUMP methylation. Specificity for dCMP
      versus dUMP, as measured by Kcat/Km, changes from negligible with wild-type TS to about a
      40-fold increase with TS N229D. TS N229D reacts with CH2H4 folate and FdUMP or FdCMP to form
      ternary complexes which are analogous to the TS-FdUMP-CH2H4 folate complex. From what is known
      of the mechanism and structure of TS, the dramatic change in substrate specificity of TS N229D
      is proposed to involve a hydrogen bond network between Asp 229 and the 3-N and 4-NH2 of the
      cytosine mechanism is proposed for related enzymes which catalyze one-carbone transfers to
      cytosine heterocycles.
AU  - Liu L
AU  - Santi DV
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1992 31: 5100-5104.

PMID- 26634753
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Vibrio owensii Strain SH-14, Which Causes Shrimp Acute Hepatopancreatic Necrosis Disease.
PG  - e01395-15
AB  - We sequenced Vibrio owensii strain SH-14, which causes serious acute hepatopancreatic necrosis
      disease (AHPND) in shrimp. Sequence analysis showed a
      large extrachromosomal plasmid, which encoded pir toxin genes and shared highly
      sequence similarity with the one observed in AHPND-causing Vibrio
      parahaemolyticus strains. The results suggest that this plasmid appears to play
      an important role in shrimp AHPND.
AU  - Liu L
AU  - Xiao J
AU  - Xia X
AU  - Pan Y
AU  - Yan S
AU  - Wang Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01395-15.

PMID- 28082485
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequence of Streptococcus parauberis Strain SP-llh, Isolated from Cows with Mastitis in Western China.
PG  - e01389-16
AB  - Streptococcus parauberis strain SP-llh was isolated from cows with mastitis in western China
      in 2015. The 2,522,235-bp genome sequence consists of 46 large
      contigs in 14 scaffolds and contains 2,620 predicted protein-coding genes, with a
      G+C content of 35.3%.
AU  - Liu L
AU  - Yang F
AU  - Li X
AU  - Luo J
AU  - Zhang Z
AU  - Li H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01389-16.

PMID- 26516404
VI  - 10
DP  - 2015
TI  - Genomic information of the arsenic-resistant bacterium Lysobacter arseniciresistens type strain ZS79(T) and comparison of Lysobacter draft genomes.
PG  - 88
AB  - Lysobacter arseniciresistens ZS79(T) is a highly arsenic-resistant,rod-shaped, motile,
      non-spore-forming, aerobic, Gram-negative bacterium. In this study, four
      Lysobacter type strains were sequenced and the genomic information of L.
      arseniciresistens ZS79(T) and the comparative genomics results of the Lysobacter
      strains were described. The draft genome sequence of the strain ZS79(T) consists
      of 3,086,721 bp and is distributed in 109 contigs. It has a G+C content of 69.5 %
      and contains 2,363 protein-coding genes including eight arsenic resistant genes.
AU  - Liu L
AU  - Zhang S
AU  - Luo M
AU  - Wang G
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 88.

PMID- 21551305
VI  - 193
DP  - 2011
TI  - Complete genome sequence of Metallosphaera cuprina, a metal sulfide-oxidizing archaeon from hot spring.
PG  - 3387-3388
AB  - The genome of metal sulfide oxidizing, thermoacidiphilic Metallosphaera cuprina Ar-4 has been
      completely sequenced and annotated. Originally
      isolated from a sulfuric hotspring, strain Ar-4 grows optimally at 65
      degrees C and pH of 3.5. The M. cuprina genome has a 1,840,348 bp circular
      chromosome (2029 ORFs) and is 16% smaller than the previously sequenced
      Metallosphaera sedula genome. Compared to the M. sedula genome, there are
      no counterpart genes in the M. cuprina genome for about 480 ORFs in the M.
      sedula genome, of which 243 ORFs are annotated as hypothetical proteins.
      Still, there are 235 ORFs uniquely occurring in M. cuprina. Genome
      annotation supports that M. cuprina lives a facultative life on CO(2) and
      organics, and obtains energy from oxidation of sulfidic ores and reduced
      inorganic sulfuric compounds.
AU  - Liu LJ
AU  - You XY
AU  - Zheng HJ
AU  - Wang SY
AU  - Jiang CY
AU  - Liu SJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3387-3388.

PMID- 26798090
VI  - 4
DP  - 2016
TI  - Revised Genome Sequence of the Purple Photosynthetic Bacterium Blastochloris viridis.
PG  - e01520-15
AB  - Blastochloris viridis is a unique anaerobic, phototrophic purple bacterium that produces
      bacteriochlorophyll b. Here we report an improved genome sequence of
      Blastochloris viridis DSM133, which is instrumental to the studies of
      photosynthesis, metabolic versatility, and genetic engineering of this
      microorganism.
AU  - Liu LN
AU  - Faulkner M
AU  - Liu X
AU  - Huang F
AU  - Darby AC
AU  - Hall N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01520-15.

PMID- 23788537
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Vibrio parahaemolyticus V110, Isolated from Shrimp in Hong Kong.
PG  - e00300-13
AB  - We report the whole-genome sequence of a tdh- and trh-negative Vibrio parahaemolyticus strain,
      V110, from shrimp. The major difference of V110 from
      clinical strains was its lack of the type III secretion system T3SS2, a key
      component of virulence. Further sequence comparison can shed light on the
      pathogenesis of V. parahaemolyticus.
AU  - Liu M
AU  - Chen S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00300-13.

PMID- 14973019
VI  - 186
DP  - 2004
TI  - Genomic and genetic analysis of Bordetella bacteriophages encoding reverse transcriptase-mediated tropism-switching cassettes.
PG  - 1503-1517
AB  - Liu et al. recently described a group of related temperate bacteriophages that infect
      Bordetella subspecies and undergo a unique
      template-dependent, reverse transcriptase-mediated tropism switching
      phenomenon (Liu et al., Science 295:2091-2094, 2002). Tropism switching
      results from the introduction of single nucleotide substitutions at
      defined locations in the VR1 (variable region 1) segment of the mtd
      (major tropism determinant) gene, which determines specificity for
      receptors on host bacteria. In this report, we describe the complete
      nucleotide sequences of the 42.5- to 42.7-kb double-stranded DNA
      genomes of three related phage isolates and characterize two additional
      regions of variability. Forty-nine coding sequences were identified. Of
      these coding sequences, bbp36 contained VR2 (variable region 2), which
      is highly dynamic and consists of a variable number of identical 19-bp
      repeats separated by one of three 5-bp spacers, and bpm encodes a DNA
      adenine methylase with unusual site specificity and a homopolymer tract
      that functions as a hotspot for frameshift mutations. Morphological and
      sequence analysis suggests that these Bordetella phage are genetic
      hybrids of P22 and T7 family genomes, lending further support to the
      idea that regions encoding protein domains, single genes, or blocks of
      genes are readily exchanged between bacterial and phage genomes.
      Bordetella bacteriophages are capable of transducing genetic markers in
      vitro, and by using animal models, we demonstrated that lysogenic
      conversion can take place in the mouse respiratory tract during
      infection.
AU  - Liu MS
AU  - Gingery M
AU  - Doulatov SR
AU  - Liu YC
AU  - Hodes A
AU  - Baker S
AU  - Davis P
AU  - Simmonds M
AU  - Churcher C
AU  - Mungall K
AU  - Quail MA
AU  - Preston A
AU  - Harvill ET
AU  - Maskell DJ
AU  - Eiserling FA
AU  - Parkhill J
AU  - Miller JF
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2004 186: 1503-1517.

PMID- 22408243
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Klebsiella pneumoniae subsp. pneumoniae HS11286, a Multidrug-Resistant Strain Isolated from Human Sputum.
PG  - 1841-1842
AB  - Klebsiella pneumoniae is an important pathogen commonly associated with opportunistic
      infections. Here we report the genome sequence of a strain,
      HS11286, isolated from human sputum in 2011 in Shanghai, China. It contains one
      chromosome (5.3 Mb), three multidrug resistance plasmids ( approximately 110 kb),
      including a carbapenemase producer, and three small plasmids ( approximately 3
      kb).
AU  - Liu P
AU  - Li P
AU  - Jiang X
AU  - Bi D
AU  - Xie Y
AU  - Tai C
AU  - Deng Z
AU  - Rajakumar K
AU  - Ou HY
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1841-1842.

PMID- 
VI  - 25
DP  - 2014
TI  - Sensitive detection of DNA methyltransferase activity based on rolling circle amplification technology.
PG  - 1047-1051
AB  - This work develops a fluorescence approach for sensitive detection of DNA methyltransferase
      activity based on endonuclease and rolling circle amplification (RCA) technique. In the
      presence of DNA adenine methylation (Dam) MTase, the methylation-responsive sequence of
      hairpin probe is methylated and cleaved by the methylation-sensitive restriction endonuclease
      Dpn I. The products cleaved by restriction endonuclease Dpn I then function as a signal primer
      to initiate RCA reaction by hybridizing with the circular DNA template. Each RCA product
      containing thousands of repeated sequences might hybridize with a large number of molecular
      beacons (detection probes), resulting in an enhanced fluorescence signal. In the absence of
      Dam MTase, neither methylation/cleavage nor RCA reaction can be initiated and no fluorescence
      signal is observed. The proposed method exhibits a dynamic range from 0.5 U/mL to 30 U/mL and
      a detection limit of 0.18 U/mL. This method can be used for the screening of antimicrobial
      drugs and has a great potential to be further applied in early clinical diagnosis.
AU  - Liu P
AU  - Yang X-Hai
AU  - Wang Q
AU  - Huang J
AU  - Liu J-Bo
AU  - Zhu Y
AU  - He L-L
AU  - Wang Ke-Min
PT  - Journal Article
TA  - Chin. Chem. Lett.
JT  - Chin. Chem. Lett.
SO  - Chin. Chem. Lett. 2014 25: 1047-1051.

PMID- 28217108
VI  - 8
DP  - 2017
TI  - Chemotaxis without Conventional Two-Component System, Based on Cell Polarity and Aerobic Conditions in Helicity-Switching Swimming of Spiroplasma eriocheiris.
PG  - 58
AB  - Spiroplasma eriocheiris is a pathogen that causes mass mortality in Chinese
      mitten crab, Eriocheir sinensis. S. eriocheiris causes tremor disease and infects
      almost all of the artificial breeding crustaceans, resulting in disastrous
      effects on the aquaculture economy in China. S. eriocheiris is a wall-less
      helical bacterium, measuring 2.0 to 10.0 mum long, and can swim up to 5 mum per
      second in a viscous medium without flagella by switching the cell helicity at a
      kink traveling from the front to the tail. In this study, we showed that S.
      eriocheiris performs chemotaxis without the conventional two-component system, a
      system commonly found in bacterial chemotaxis. The chemotaxis of S. eriocheiris
      was observed more clearly when the cells were cultivated under anaerobic
      conditions. The cells were polarized as evidenced by a tip structure, swimming in
      the direction of the tip, and were shown to reverse their swimming direction in
      response to attractants. Triton X-100 treatment revealed the internal structure,
      a dumbbell-shaped core in the tip that is connected by a flat ribbon, which
      traces the shortest line in the helical cell shape from the tip to the other
      pole. Sixteen proteins were identified as the components of the internal
      structure by mass spectrometry, including Fibril protein and four types of MreB
      proteins.
AU  - Liu P
AU  - Zheng H
AU  - Meng Q
AU  - Terahara N
AU  - Gu W
AU  - Wang S
AU  - Zhao G
AU  - Nakane D
AU  - Wang W
AU  - Miyata M
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2017 8: 58.

PMID- 26988061
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of an NDM-5-Producing Klebsiella pneumoniae Sequence Type 14 Strain of Serotype K2.
PG  - e01610-15
AB  - We report here the draft genome sequence of uropathogenic Klebsiella pneumoniae sequence type
      14 strain of serotype K2 possessing blaNDM-5, isolated from a
      65-year-old male in China without a history of travel abroad.
AU  - Liu PP
AU  - Liu Y
AU  - Wang LH
AU  - Wei DD
AU  - Wan LG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01610-15.

PMID- 23682149
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Serratia marcescens Strain VGH107, a Taiwanese Clinical Isolate.
PG  - e00249-13
AB  - Serratia marcescens, a member of the family Enterobacteriaceae, is the causative  agent of
      various types of wound infections. We report a high-quality draft genome
      sequence of S. marcescens strain VGH107, which was isolated from a patient with
      an infection from a snakebite wound.
AU  - Liu PY
AU  - Huang YT
AU  - Lin SY
AU  - Chang GC
AU  - Chen JW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00249-13.

PMID- 1314209
VI  - 113
DP  - 1992
TI  - The effect of methylation outside the recognition sequence of restriction endonuclease PvuII on its cleavage efficiency.
PG  - 89-93
AB  - This study is to extend our earlier observation that Dam and Dcm methylation outside the PvuII
      recognition sequence inhibited PvuII cleavage in one of the three PvuII sites of pGEM4Z-ras
      DNA. In this paper, a new recombinant plasmid DNA, pGEM4-SV40ori-anti-ras, was constructed
      which has only two PvuII sites, I and II. The Dam and Dcm-methylated and unmethylated DNAs
      were produced in Escherichia coli and linearized by ScaI. The DNA molecules were digested with
      different amounts of PvuII. The results show that by comparing the DNA fragment number and
      intensity of the partial and final products in agarose gels, PvuII site I on the methylated
      DNA molecule was digested four- to eight-fold more slowly than site II. In the unmethylated
      plasmid DNA, the two PvuII sites were cleaved at about the same rate. The difference was
      caused only by methylation of Dam and Dcm sites outside the PvuII recognition sequence. A
      methylated Dam site immediately adjacent to the less efficiently cut PvuII site I may be
      responsible for the inhibitory effect. We suggest that a new parameter, involving methylation
      of sites outside the recognition sequence, be considered in kinetic experiments on cleavage.
AU  - Liu Q
AU  - Chen X
AU  - Zhao X
AU  - Chen Y
AU  - Chen D
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1992 113: 89-93.

PMID- 16582101
VI  - 34
DP  - 2006
TI  - Distance determination by GIY-YIG intron endonucleases: Discrimination between repression and cleavage functions.
PG  - 1755
AB  - GIY-YIG homing endonucleases are modular proteins, with conserved N-terminal catalytic domains
      connected by linkers to C-terminal DNA-binding domains. I-TevI, the T4 phage GIY-YIG intron
      endonuclease, functions both in promoting td intron homing, and in acting as a transcriptional
      autorepressor. Repression is achieved by binding to an operator, which is cleaved at 100-fold
      reduced efficiency relative to the intronless homing site. The linker includes a zinc finger,
      which functions in distance determination, to constrain the catalytic domain to cleave the
      homing site at a fixed position. Here we show that I-BmoI, a related GIY-YIG endonuclease
      lacking a zinc finger, also possesses some cleavage distance discrimination. Furthermore,
      hybrid endonucleases constructed by swapping the domains of I-BmoI and I-TevI are active,
      precise and demonstrate that features other than the zinc finger facilitate distance
      determination. Most importantly, I-TevI zinc finger mutants cleave the operator more
      efficiently than the homing site, the converse of wild-type protein. These results are
      consistent with the zinc finger acting as a measuring device, directing efficient cleavage of
      the homing site to promote intron mobility, while reducing cleavage at the operator to ensure
      transcriptional autorepression and phage viability.
AU  - Liu Q
AU  - Derbyshire V
AU  - Balfort M
AU  - Edgell DR
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2006 34: 1755.

PMID- 28496940
VI  - 12
DP  - 2017
TI  - Complete genome sequence of bacteriochlorophyll-synthesizing bacterium Porphyrobacter neustonensis DSM 9434.
PG  - 32
AB  - The genus Porphyrobacter belongs to aerobic anoxygenic phototrophic bacteria cluster.
      Porphyrobacter neustonensis DSM 9434 was isolated from a eutrophic
      freshwater pond in Australia, and is able to synthesize Bacteriochlorophyll a as
      well as grow under aerobic conditions. It is the type species of the genus
      Porphyrobacter. Here we describe the characteristics of the strain DSM 9434,
      including the genome sequence and annotation, synthesis of BChl a, and metabolic
      pathways of the organism. The genome of strain DSM 9434 comprises 3,090,363 bp
      and contains 2,902 protein-coding genes, 47 tRNA genes and 6 rRNA genes. Strain
      DSM 9434 encodes 46 genes which participate in BChl a synthesis and this
      investigation shed light on the evolution and functional implications regarding
      bacteriochlorophyll synthesis.
AU  - Liu Q
AU  - Wu YH
AU  - Cheng H
AU  - Xu L
AU  - Wang CS
AU  - Xu XW
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 32.

PMID- 18499124
VI  - 379
DP  - 2008
TI  - Role of the interdomain linker in distance determination for remote cleavage by homing endonuclease I-TevI.
PG  - 1094-1106
AB  - I-TevI is a modular intron-encoded endonuclease, consisting of an N-terminal catalytic domain
      and a C-terminal DNA-binding domain, joined
      by a 75 amino acid linker. This linker can be divided into three
      regions, starting at the N terminus: the deletion-intolerant (DI)
      region; the deletion-tolerant (DT) region; and a zinc finger, which
      acts as a distance determinant for cleavage. To further explore linker
      function, we generated deletion and substitution mutants that were
      tested for their preference to cleave at a particular distance or at
      the correct sequence. Our results demonstrate that the I-TevI linker is
      multi-functional, a property that sets it apart from junction sequences
      in most other proteins. First, the linker DI region has a role in
      I-TevI cleavage activity. Second, the DT linker region participates in
      distance determination, as evident from DT mutants that display a
      phenotype similar to that of the zinc-finger mutants in their selection
      of a cleavage site. Finally, NMR analysis of a freestanding 56 residue
      linker segment showed an unstructured stretch corresponding to the DI
      region and a portion of the DT region, followed by a beta-strand
      corresponding to the remainder of the DT region and containing a key
      distance-determining arginine, R129. Mutation of this arginine to
      alanine abolished distance determination and disrupted the beta-strand,
      indicating that the structure of the DT linker region has a role in
      cleavage at a fixed distance.
AU  - Liu QQ
AU  - Dansereau JT
AU  - Puttamadappa SS
AU  - Shekhtman A
AU  - Derbyshire V
AU  - Belfort M
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2008 379: 1094-1106.

PMID- 23045506
VI  - 194
DP  - 2012
TI  - Genome Sequence of an OXA23-Producing, Carbapenem-Resistant Acinetobacter baumannii Strain of Sequence Type ST75.
PG  - 6000-6001
AB  - The increase of Acinetobacter baumannii resistance to carbapenems is of great concern. OXA23
      is one of the most prevalent carbapenemases of A. baumannii that
      causes outbreaks. Here, we announce the genome sequence of an OXA23-producing A.
      baumannii strain assigned ST75, a newly emerged sequence type harboring
      carbapenemase.
AU  - Liu S
AU  - Wang Y
AU  - Xu J
AU  - Li Y
AU  - Guo J
AU  - Ke Y
AU  - Yuan X
AU  - Wang L
AU  - Du X
AU  - Wang Z
AU  - Huang L
AU  - Zhang N
AU  - Chen Z
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6000-6001.

PMID- 8341713
VI  - 90
DP  - 1993
TI  - Genomic mapping with I-CeuI, an intron-encoded endonuclease specific for genes for ribosomal RNA, in Salmonella ssp., Escherichia coli, and other bacteria.
PG  - 6874-6878
AB  - Construction of physical maps of genomes by pulsed-field gel electrophoresis requires enxymes
      which cut the genome into an analyzable number of fragments; most produce too many fragments.
      The enzyme I-CeuI, encoded by a mobile intron in the chloroplast 23S ribosomal RNA (rrl) gene
      of Chlamydomonas eugametos, cuts a 26-bp site in the rrl gene. This enzyme digests DNA of
      Salmonella typhimurium at seven sites, each corresponding to one of the rrl genes of the rrn
      operons, but at no other site. These seven fragments were located on the previously determined
      XbaI physical map, and the I-CeuI sites, and thus the rrn genes of S. typhimurium, were mapped
      on the 4800-kb chromosome. Escherichia coli K-12 also yields seven fragments of sizes similar
      to those of S. typhimurium, indicating conservation of rrn genes and their location, and a
      chromosome size of 4600 kb. The sizes of the E. coli fragments are close to the size predicted
      from restriction maps and nucleotide sequence. The I-CeuI maps of Salmonella typhi were
      deduced after digesting genomic DNA with I-CeuI and probing with DNA of S. typhimurium; the
      data indicated strong conservation of rrn gene number and position and genome sizes up to 4950
      kb. Digestion of DNA of other bacteria (species of Haemophilus, Neisseria, Proteus, and
      Pasteurella) suggested that only rrn genes are cut in all these species. I-CeuI digestion
      followed by pulsed-field gel electrophoresis is a powerful tool for determining genome
      structure and evolution.
AU  - Liu SL
AU  - Hessel A
AU  - Sanderson KE
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1993 90: 6874-6878.

PMID- 29146839
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Myroides sp. N17-2, a Multidrug-Resistant Bacterium Isolated from Radiation-Polluted Soils.
PG  - e01301-17
AB  - We report here the 4.29-Mb draft genome sequence of Myroides sp. N17-2, a new bacterium
      isolated from radiation-polluted soils in Xinjiang, Uyghur Autonomous
      Region, China. The acquisition of its genome will provide valuable information to
      reveal the relationship between radiation and multidrug resistance.
AU  - Liu T
AU  - Zhu L
AU  - Zhang Z
AU  - Jiang L
AU  - Huang H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01301-17.

PMID- 
VI  - 55
DP  - 2012
TI  - Cloning and expression profiling of the DNA methyltransferase Dnmt3 gene in the Chinese honeybee, Apis cerana cerana (Hymenoptera: Apidae).
PG  - 284-290
AB  - To explore the pattern of methylation in the Chinese honeybee, Apis cerana cerana, the DNA
      methyltransferase 3 (Dnmt3) gene in A. cerana
      cerana was cloned by using RT-PCR, and the quantitative analysis of the
      expression level of Dnmt3 mRNA in different developmental stages of
      worker (4 d-old pupa, 1, 7 and 30 d-old workers, and laying worker) and
      queen (4 d-old pupa, 1 d-old queen and laying queen) were conducted
      using real-time qPCR. The full-length cDNA of Dnmt3 gene (GenBank
      accession no. JQ740768) is 2 277 bp, encoding 758 amino acids, and the
      predicted MW and pI are 88. 24 kD and 7. 85, respectively. Based on the
      comparison of the domain and the phylogenetic tree of the amino acids
      of Dnmt3 in A. cerana cerana and other species, the sequence obtained
      has up to 99% identity with that of A. mellifera. The Dnmt3 transcript
      was clearly detected in different developmental stages of worker and
      queen, and it was expressed significantly higher in 30 d-old worker
      than in 1 d- and 7 d-old worker (P < 0.05), while no difference existed
      between 1 d- and 7 d-old worker (P > 0. 05). The Dnmt3 transcript was
      expressed higher in queen pupae than in worker pupae (P < 0.05), and
      was higher in 1 d-old queen than in 1 d-old worker (P <0. 05). The
      expression level of Dnmt3 gene between laying worker and laying queen
      had no significant difference. The results suggested that Dnmt3 may be
      involved in the division of labor in workers and ovary development in
      honeybees.
AU  - Liu T-T
AU  - Liu J-F
AU  - Wang W-X
AU  - Wang H
AU  - Wang Z-L
AU  - Zeng Z-J
AU  - Yan W-Y
PT  - Journal Article
TA  - Acta Entomologica Sinica
JT  - Acta Entomologica Sinica
SO  - Acta Entomologica Sinica 2012 55: 284-290.

PMID- Not carried by PubMed...
VI  - 58
DP  - 1997
TI  - Fluorescence studies of EcoRI restriction endonuclease structure and dynamics.
PG  - 681
AB  - Sequence specific protein-DNA interaction involves changes in protein conformation and
      dynamics.  Research work involved in this thesis is the study of structure and dynamics of
      EcoRI restriction endonuclease N-termini.  The N-termini of EcoRI endonuclease has been shown
      to be essential for DNA cleavage and also stabilize EcoRI-DNA complex.  But they are not
      resolved in the X-ray crystal structure.  An Asn3Cys mutation was made at the N-termini by
      site-directed mutagenesis and the mutant was subjected to cysteine crosslinking, pyrene
      labeling and fluorescence studies.  Chemical crosslinking of Asn3Cys mutant and steady-state
      fluorescence studies of pyrene-labeled mutant indicated that the N-termini are in close
      proximity and probably involved in the dimer interface.  Time resolved fluorescence
      measurements revealed dynamics of the N-termini by examining the dissociation and reformation
      of pyrene excimers as well as the monomer spectral shifts caused by N-terminal segment
      movements.  Fluorescence anisotropy decay analysis indicated the N-termini are on the protein
      surface and not totally disoriented in solution.  Substrate DNA binding, however, causes the
      N-termini to be more mobile without affecting the proximity relationship.  Fluorescence energy
      transfer experiments were carried out using a double-mutant Asn3Cys,Trp104Tyr.  The through
      space distance between the fluorescent labels, MIANS or 1,5 -IAEDANS, and Trp246 is around 30
      Angstroms.  Substrate DNA binding decreased the distance to 26 Angstroms but cofactor Mg2+ ion
      did not cause any distance change.  Single Trp246 fluorescence in the double mutant also
      revealed possible conformational changes upon substrate DNA or cofactor binding.  Experimental
      evidence indicates that the N-termini are located at the dimer interface but distal to the DNA
      binding site.  The findings provide further insight into the function of the N-termini of
      EcoRI endonuclease.
AU  - Liu W
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1997 58: 681.

PMID- 9799508
VI  - 37
DP  - 1998
TI  - N-termini of EcoRI restriction endonuclease dimer are in close proximity on the protein surface.
PG  - 15457-15465
AB  - The N-terminal region of EcoRI endonuclease is essential for cleavage yet is invisible in the
      2.5 A crystal structure of endonuclease-DNA. We used site-directed fluorescence spectroscopy
      and chemical cross-linking to locate the N-terminal region and assess its flexibility in the
      absence and presence of DNA substrate. The second amino acid in each subunit of the homodimer
      was replaced with cysteine and labeled with pyrene or reacted with bifunctional cross-linkers.
      The broad absorption spectra and characteristic excimer emission bands of pyrene-labeled
      muteins indicated stacking of the two pyrene rings in the homodimer. Proximity of N-terminal
      cysteines was confirmed by disulfide bond formation and chemical cross-linking. The dynamics
      of the N-terminal region were determined from time-resolved emission anisotropy measurements.
      The anisotropy decay had two components: a fast component with rotational correlation time of
      0.3-3 ns representing probe internal motions and a slow component with 50-100 ns correlation
      time representing overall tumbling of the protein conjugate. We conclude that the N-termini
      are close together at the dimer interface with limited flexibility. Binding of Mg2+ cofactor
      or DNA substrate did not affect the location or flexibility of the N-terminal region as sensed
      by pyrene fluorescence and cross-linking, indicating that substrate binding is not accompanied
      by folding or unfolding of the N-terminus.
AU  - Liu W
AU  - Chen Y
AU  - Watrob H
AU  - Bartlett SG
AU  - Jen-Jacobson L
AU  - Barkley MD
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1998 37: 15457-15465.

PMID- 20802032
VI  - 192
DP  - 2010
TI  - Complete Genome Sequence of Mycoplasma hyorhinis Strain HUB-1.
PG  - 5844-5845
AB  - Mycoplasma hyorhinis is generally considered a swine pathogen yet is most commonly found
      infecting laboratory cell lines. An increasing body of
      evidence suggests that chronic infections with M. hyorhinis may cause
      oncogenic transformation. Here, we announce the complete genome sequence
      of M. hyorhinis strain HUB-1.
AU  - Liu W
AU  - Fang L
AU  - Li S
AU  - Li Q
AU  - Zhou Z
AU  - Feng Z
AU  - Luo R
AU  - Shao G
AU  - Wang L
AU  - Chen H
AU  - Xiao S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 5844-5845.

PMID- 21148737
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Mycoplasma hyopneumoniae Strain 168.
PG  - 1016-1017
AB  - Mycoplasma hyopneumoniae strain 168, a pathogenic strain prevalent in China, was isolated in
      1974. Although this strain has been widespread for
      a long time, the genome sequence had not been determined. Here, we
      announce the complete genome sequence of M. hyopneumoniae strain 168.
AU  - Liu W
AU  - Feng Z
AU  - Fang L
AU  - Zhou Z
AU  - Li Q
AU  - Li S
AU  - Luo R
AU  - Wang L
AU  - Chen H
AU  - Shao G
AU  - Xiao S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 1016-1017.

PMID- 23105063
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Brucella melitensis Biovar 3 Strain NI, Isolated from an Aborted Bovine Fetus.
PG  - 6321
AB  - From an aborted bovine fetus in China, a bacterial strain named NI was isolated and identified
      as Brucella melitensis by a PCR assay. Strain NI was further
      characterized as B. melitensis biovar 3 using biochemical assays. Here we report
      the complete genome sequence of strain NI.
AU  - Liu W
AU  - Jing Z
AU  - Ou Q
AU  - Cui B
AU  - He Y
AU  - Wu Q
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6321.

PMID- 28935746
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of a Novel Bioflocculant-Producing Strain, Microbacterium paludicola CC3.
PG  - e01008-17
AB  - Microbacterium paludicola CC3 exhibits the capability to produce polysaccharide
      bioflocculants. Here, we report the whole-genome sequence of M. paludicola CC3,
      which may be helpful in understanding the genetic basis of the biosynthesis of
      polysaccharide bioflocculants as well as in promoting its production and
      application in industrial fields.
AU  - Liu W
AU  - Liu C
AU  - Sun D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01008-17.

PMID- 23384176
VI  - 14
DP  - 2013
TI  - Comparative genomic analyses of Mycoplasma hyopneumoniae pathogenic 168 strain and its high-passaged attenuated strain.
PG  - 80
AB  - BACKGROUND: Mycoplasma hyopneumoniae is the causative agent of porcine enzootic
      pneumonia (EP), a mild, chronic pneumonia of swine. Despite presenting with low
      direct mortality, EP is responsible for major economic losses in the pig
      industry. To identify the virulence-associated determinants of M. hyopneumoniae,
      we determined the whole genome sequence of M. hyopneumoniae strain 168 and its
      attenuated high-passage strain 168-L and carried out comparative genomic
      analyses. RESULTS: We performed the first comprehensive analysis of M.
      hyopneumoniae strain 168 and its attenuated strain and made a preliminary survey
      of coding sequences (CDSs) that may be related to virulence. The 168-L genome has
      a highly similar gene content and order to that of 168, but is 4,483 bp smaller
      because there are 60 insertions and 43 deletions in 168-L. Besides these indels,
      227 single nucleotide variations (SNVs) were identified. We further investigated
      the variants that affected CDSs, and compared them to reported virulence
      determinants. Notably, almost all of the reported virulence determinants are
      included in these variants affected CDSs. In addition to variations previously
      described in mycoplasma adhesins (P97, P102, P146, P159, P216, and LppT), cell
      envelope proteins (P95), cell surface antigens (P36), secreted proteins and
      chaperone protein (DnaK), mutations in genes related to metabolism and growth may
      also contribute to the attenuated virulence in 168-L. Furthermore, many mutations
      were located in the previously described repeat motif, which may be of primary
      importance for virulence. CONCLUSIONS: We studied the virulence attenuation
      mechanism of M. hyopneumoniae by comparative genomic analysis of virulent strain
      168 and its attenuated high-passage strain 168-L. Our findings provide a
      preliminary survey of CDSs that may be related to virulence. While these include
      reported virulence-related genes, other novel virulence determinants were also
      detected. This new information will form the foundation of future investigations
      into the pathogenesis of M. hyopneumoniae and facilitate the design of new
      vaccines.
AU  - Liu W
AU  - Xiao S
AU  - Li M
AU  - Guo S
AU  - Li S
AU  - Luo R
AU  - Feng Z
AU  - Li B
AU  - Zhou Z
AU  - Shao G
AU  - Chen H
AU  - Fang L
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2013 14: 80.

PMID- 22628516
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Pasteurella multocida HN06, a Toxigenic Strain of Serogroup D.
PG  - 3292-3293
AB  - Pasteurella multocida is an important etiological agent that can cause many economically
      important diseases in a wide range of mammals and birds. Here, we
      report the complete genome sequence of P. multocida HN06, a toxigenic serogroup D
      strain isolated from a diseased pig in China.
AU  - Liu W
AU  - Yang M
AU  - Xu Z
AU  - Zheng H
AU  - Liang W
AU  - Zhou R
AU  - Wu B
AU  - Chen H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3292-3293.

PMID- 24051314
VI  - 1
DP  - 2013
TI  - Genome Sequence of Saccharopolyspora erythraea D, a Hyperproducer of Erythromycin.
PG  - e00718-13
AB  - Saccharopolyspora erythraea is a Gram-positive bacterium that can produce antibiotics.
      However, this microorganism must often be genetically improved for
      higher production before it can be used in an industrial setting. Here, we report
      the whole-genome sequence of the industrial hyperproducer strong mutator
      Saccharopolyspora erythraea strain D.
AU  - Liu WB
AU  - Yu WB
AU  - Gao SH
AU  - Ye BC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00718-13.

PMID- 19229335
VI  - 4
DP  - 2009
TI  - Salmonella paratyphi C: genetic divergence from Salmonella choleraesuis and pathogenic convergence with Salmonella typhi.
PG  - E4510
AB  - BACKGROUND: Although over 1400 Salmonella serovars cause usually
      self-limited gastroenteritis in humans, a few, e.g., Salmonella typhi and
      S. paratyphi C, cause typhoid, a potentially fatal systemic infection. It
      is not known whether the typhoid agents have evolved from a common
      ancestor (by divergent processes) or acquired similar pathogenic traits
      independently (by convergent processes). Comparison of different typhoid
      agents with non-typhoidal Salmonella lineages will provide excellent
      models for studies on how similar pathogens might have evolved.
      METHODOLOGIES/PRINCIPAL FINDINGS: We sequenced a strain of S. paratyphi C,
      RKS4594, and compared it with previously sequenced Salmonella strains.
      RKS4594 contains a chromosome of 4,833,080 bp and a plasmid of 55,414 bp.
      We predicted 4,640 intact coding sequences (4,578 in the chromosome and 62
      in the plasmid) and 152 pseudogenes (149 in the chromosome and 3 in the
      plasmid). RKS4594 shares as many as 4346 of the 4,640 genes with a strain
      of S. choleraesuis, which is primarily a swine pathogen, but only 4008
      genes with another human-adapted typhoid agent, S. typhi. Comparison of
      3691 genes shared by all six sequenced Salmonella strains placed S.
      paratyphi C and S. choleraesuis together at one end, and S. typhi at the
      opposite end, of the phylogenetic tree, demonstrating separate ancestries
      of the human-adapted typhoid agents. S. paratyphi C seemed to have
      suffered enormous selection pressures during its adaptation to man as
      suggested by the differential nucleotide substitutions and different sets
      of pseudogenes, between S. paratyphi C and S. choleraesuis. CONCLUSIONS:
      S. paratyphi C does not share a common ancestor with other human-adapted
      typhoid agents, supporting the convergent evolution model of the typhoid
      agents. S. paratyphi C has diverged from a common ancestor with S.
      choleraesuis by accumulating genomic novelty during adaptation to man.
AU  - Liu WQ
AU  - Feng Y
AU  - Wang Y
AU  - Zou QH
AU  - Chen F
AU  - Guo JT
AU  - Peng YH
AU  - Jin Y
AU  - Li YG
AU  - Hu SN
AU  - Johnston RN
AU  - Liu GR
AU  - Liu SL
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2009 4: E4510.

PMID- 23045485
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of the Endophytic Enterobacter cloacae subsp. cloacae Strain ENHKU01.
PG  - 5965
AB  - Enterobacter cloacae subsp. cloacae strain ENHKU01 is a Gram-negative endophyte isolated from
      a diseased pepper (Capsicum annuum) plant in Hong Kong. This is the
      first complete genome sequence report of a plant-endophytic strain of E. cloacae
      subsp. cloacae.
AU  - Liu WY
AU  - Chung KM
AU  - Wong CF
AU  - Jiang JW
AU  - Hui RK
AU  - Leung FC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5965.

PMID- 29748410
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of a 'Candidatus Brocadia' Bacterium Enriched from Activated Sludge Collected in a Tropical Climate.
PG  - e00406-18
AB  - Here, we present the draft genome sequence of an anaerobic ammonium-oxidizing bacterium
      (AnAOB), 'Candidatus Brocadia,' which was enriched in an anammox
      reactor. A 3.2-Mb genome sequence comprising 168 contigs was assembled, in which
      2,765 protein-coding genes, 47 tRNAs, and one each of 5S, 16S, and 23S rRNAs were
      annotated. No evidence for the presence of a nitric oxide-forming nitrite
      reductase was found.
AU  - Liu X
AU  - Arumugam K
AU  - Natarajan G
AU  - Seviour TW
AU  - Drautz-Moses DI
AU  - Wuertz S
AU  - Law Y
AU  - Williams RBH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00406-18.

PMID- 23012282
VI  - 194
DP  - 2012
TI  - Genome Sequences of Pseudomonas luteola XLDN4-9 and Pseudomonas stutzeri XLDN-R,  Two Efficient Carbazole-Degrading Strains.
PG  - 5701-5702
AB  - Pseudomonas luteola XLDN4-9 and Pseudomonas stutzeri XLDN-R are two efficient
      carbazole-degrading pseudomonad strains. Here we present 4.63- and 4.70-Mb
      assemblies of their genomes. Their annotated key genes for carbazole catabolism
      are similar, which may provide further insights into the molecular mechanism of
      carbazole degradation in Pseudomonas.
AU  - Liu X
AU  - Gai Z
AU  - Tao F
AU  - Yu H
AU  - Tang H
AU  - Xu P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5701-5702.

PMID- 27056227
VI  - 4
DP  - 2016
TI  - The Genome Sequence of Alcaligenes faecalis NBIB-017 Contains Genes with Potentially High Activities against Erwinia carotovora.
PG  - e00222-16
AB  - Alcaligenes faecalisNBIB-017, a Gram-negative bacterium, was isolated from soil in China.
      Here, we provide the complete genome sequence of this bacterium, which
      possesses a high number of genes encoding antibacterial factors, including
      proteins and small molecular peptides.
AU  - Liu X
AU  - Huang D
AU  - Wu J
AU  - Yu C
AU  - Zhou R
AU  - Liu C
AU  - Zhang W
AU  - Yao J
AU  - Cheng M
AU  - Guo S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00222-16.

PMID- 26893430
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Multidrug-Resistant Citrobacter freundii Strain P10159, Isolated from Urine Samples from a Patient with Esophageal Carcinoma.
PG  - e01754-15
AB  - Citrobacter freundii is an opportunistic pathogen that can cause diarrhea, septicemia,
      meningitis, and urinary tract infections. We report here the complete
      genome sequence of C. freundii strain P10159, isolated from urine samples from a
      patient in China with esophageal carcinoma. The genome has 5,080,321 bp and 4,768
      coding sequences, with a G+C content of 51.7%.
AU  - Liu X
AU  - Huang Y
AU  - Xu X
AU  - Zhao Y
AU  - Sun Q
AU  - Zhang Z
AU  - Zhang X
AU  - Wu Y
AU  - Wang J
AU  - Zhou D
AU  - An X
AU  - Pei G
AU  - Wang Y
AU  - Mi Z
AU  - Yin Z
AU  - Tong Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01754-15.

PMID- 29192077
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Bacillus vallismortis NBIF-001, a Novel Strain from Shangri-La, China, That Has High Activity against Fusarium oxysporum.
PG  - e01305-17
AB  - Bacillus vallismortis NBIF-001, a Gram-positive bacterium, was isolated from soil in
      Shangri-La, China. Here, we provide the complete genome sequence of this
      bacterium, which has a 3,929,787-bp-long genome, including 4,030 protein-coding
      genes and 195 RNA genes. This strain possesses a number of genes encoding
      virulence factors of pathogens.
AU  - Liu X
AU  - Min Y
AU  - Huang D
AU  - Zhou R
AU  - Fang W
AU  - Liu C
AU  - Rao B
AU  - Zhang G
AU  - Wang K
AU  - Yang Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01305-17.

PMID- 24855295
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Bacillus thuringiensis NBIN-866 with High Nematocidal Activity.
PG  - e00429-14
AB  - Bacillus thuringiensis NBIN-866, a Gram-positive bacterium, was isolated from soil in China.
      We announce here the draft genome sequence of strain B.
      thuringiensis NBIN-866, which possesses highly nematocidal factors, such as
      proteins and small molecular peptides.
AU  - Liu X
AU  - Zhou R
AU  - Fu G
AU  - Zhang W
AU  - Min Y
AU  - Tian Y
AU  - Huang D
AU  - Wang K
AU  - Wan Z
AU  - Yao J
AU  - Yang Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00429-14.

PMID- 11092822
VI  - 34
DP  - 2000
TI  - Protein-splicing intein: Genetic mobility, origin, and evolution.
PG  - 61-76
AB  - Intein is the protein equivalent of intron and has been discovered in increasing numbers of
      organisms and host proteins.  A self-splicing intein catalyzes its own removal from the host
      protein through a posttranslational process of protein splicing.  A mobile intein displays a
      site-specific endonuclease activity that confers genetic mobility to the intein through intein
      homing.  Recent findings of intein structure and the mechanism of protein splicing illuminated
      how inteins work and yielded clues regarding intein's origin, spread, and evolution.  Inteins
      can evolve into new structures and new functions, such as split inteins that do
      trans-splicing.  The structural basis of intein function needs to be identified for a full
      understanding of the origin and evolution of this marvelous genetic element.
AU  - Liu X-Q
PT  - Journal Article
TA  - Annu. Rev. Genet.
JT  - Annu. Rev. Genet.
SO  - Annu. Rev. Genet. 2000 34: 61-76.

PMID- 9223276
VI  - 94
DP  - 1997
TI  - A DnaB intein in Rhodothermus marinus: Indication of recent intein homing across remotely related organisms.
PG  - 7851-7856
AB  - A dnaB gene encoding a homologue of the Escherichia coli DNA helicase DnaB was cloned and
      sequenced in the thermophilic eubacterium Rhodothermus marinus, predicting a DnaB protein that
      harbors an intein.  This DnaB intein is 428 amino acid residues long, has several putative
      intein sequence motifs (including two putative endonuclease motifs), and is capable of protein
      splicing when produced in E. coli cells.  The R. marinus DnaB intein is a close homologue of a
      DnaB intein in the cyanobacterium Synechocystis sp. strain PCC6803.  The two inteins are
      positioned identically in their respective DnaB proteins.  They also share a 54% sequence
      identity (74% sequence similarity) that is markedly higher than the 37% sequence identity
      shared by the extein sequences of the two DnaB proteins.  Horizontal intein transfer (homing)
      is therefore invoked to relate these two DnaB inteins.  The codon usage of R. marinus DnaB
      intein coding sequence differs markedly from the codon usage of its flanking extein coding
      sequences and other genes in the same genome, suggesting more recent acquisition of the DnaB
      intein in this organism.
AU  - Liu X-Q
AU  - Hu Z
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1997 94: 7851-7856.

PMID- 25635021
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Vibrio alginolyticus ATCC 17749T.
PG  - e01500-14
AB  - Vibrio alginolyticus is a Gram-negative halophilic bacterium and has been recognized as an
      opportunistic pathogen in both humans and marine animals. It is
      the causative agent of food-borne diseases, such as gastroenteritis, and it
      invades through wounds in predisposed individuals. In this study, we present the
      completed genome of V. alginolyticus ATCC 17749(T) through high-throughput
      sequencing.
AU  - Liu XF
AU  - Cao Y
AU  - Zhang HL
AU  - Chen YJ
AU  - Hu CJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01500-14.

PMID- 24855293
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Burkholderia sp. Strain MP-1, a Methyl Parathion (MP)-Degrading Bacterium from MP-Contaminated Soil.
PG  - e00344-14
AB  - Burkholderia sp. strain MP-1 was isolated from pesticide-contaminated soil. Herein, we report
      the draft genome sequence of strain MP-1, which contains 168
      contigs of 8,611,053 bp, with a G+C content of 62.55% and 7,631 protein-coding
      genes.
AU  - Liu XY
AU  - Luo XJ
AU  - Li CX
AU  - Lai QL
AU  - Xu JH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00344-14.

PMID- 25197462
VI  - 9
DP  - 2014
TI  - Draft genome sequence of Bacillus amyloliquefaciens HB-26.
PG  - 775-782
AB  - Bacillus amyloliquefaciens HB-26, a Gram-positive bacterium was isolated from soil in China.
      SDS-PAGE analysis showed this strain secreted six major protein
      bands of 65, 60, 55, 34, 25 and 20 kDa. A bioassay of this strain reveals that it
      shows specific activity against P. brassicae and nematode. Here we describe the
      features of this organism, together with the draft genome sequence and
      annotation. The 3,989,358 bp long genome (39 contigs) contains 4,001
      protein-coding genes and 80 RNA genes.
AU  - Liu XY
AU  - Min Y
AU  - Wang KM
AU  - Wan ZY
AU  - Zhang ZG
AU  - Cao CX
AU  - Zhou RH
AU  - Jiang AB
AU  - Liu CJ
AU  - Zhang GY
AU  - Cheng XL
AU  - Zhang W
AU  - Yang ZW
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 775-782.

PMID- 25197470
VI  - 9
DP  - 2014
TI  - Draft genome sequence of Dyadobacter tibetensis type strain (Y620-1) isolated from glacial ice.
PG  - 883-892
AB  - Dyadobacter tibetensis Y620-1 is the type strain of the species Dyadobacter tibetensis,
      isolated from ice at a depth of 59 m from a high altitude glacier in
      China (5670 m above sea level). It is psychrotolerant with growth temperature
      ranges of 4 to 35 degrees C. Here we describe the features of this organism,
      together with the draft genome sequence and annotation. The 5,313,963 bp long
      genome contains 4,828 protein-coding genes and 39 RNA genes. To the best of our
      knowledge, this is the first Dyadobacter strain that was isolated from glacial
      ice. This study provides genetic information of this organism to identify the
      genes linked to its specific mechanisms for adaption to extreme glacial
      environment.
AU  - Liu Y
AU  - Hu A
AU  - Shen L
AU  - Yao T
AU  - Jiao N
AU  - Wang N
AU  - Xu B
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 883-892.

PMID- 17618069
VI  - 400
DP  - 2007
TI  - Regulation of the EcoRI restriction-modification system: Identification of ecoRIM gene promoters and their upstream negative regulators in the ecoRIR gene.
PG  - 140-149
AB  - Type II restriction-modification (R-M) systems are composed of linked restriction endonuclease
      and modification methyltransferase genes and serve as barriers to horizontal gene transfer
      even though they are mobile in themselves.  Their products kill host bacterial cells that have
      lost the R-M genes, a process that helps to maintain the frequency of the R-M systems in the
      viable cell population.  Their establishment and maintenance in a bacterial host are expected
      to involve fine regulation of their gene expression.  In the present study, we analyzed
      transcription of the modification gene and its regulation within the EcoRI R-M system.
      Northern blotting revealed that the downstream ecoRIM gene is transcribed as a monocistronic
      mRNA and as part of a larger bicistronic mRNA together with the upstream ecoRIR gene.  Primer
      extension, RNase protection, and mutational analysis using lacZ gene fusions identified two
      overlapping promoters for ecoRIM gene transcription within the ecoRIR gene.  Further
      mutational analysis revealed that two upstream AT-rich elements within the ecoRIR gene,
      "AATAAA" and "ATTATAAATATA", function as negative regulators of these promoters.  Simultaneous
      substitution of these two elements resulted in a four-fold increase in beta-galactosidase
      activity and a five-fold increase in transcript levels as measured by RNase protection assay.
      RNA measurements of the ecoRIM transcript suggested that these elements decreased ecoRIM
      expression by interfering with transcription initiation of the ecoRIM promoters.  Possible
      roles for these ecoRIM promoters and their negative regulators in the EcoRI R-M system are
      discussed.
AU  - Liu Y
AU  - Ichige A
AU  - Kobayashi I
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 2007 400: 140-149.

PMID- 24482513
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Pseudomonas chlororaphis YL-1, a Biocontrol Strain Suppressing Plant Microbial Pathogens.
PG  - e01225-13
AB  - Pseudomonas chlororaphis YL-1 was isolated from soybean root tips and showed a broad range of
      antagonistic activities to microbial plant pathogens. Here, we
      report the high-quality draft genome sequence of YL-1, which consists of a
      chromosome with an estimated size of 6.8 Mb with a G+C value of 63.09%.
AU  - Liu Y
AU  - Lu SE
AU  - Baird SM
AU  - Qiao J
AU  - Du Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01225-13.

PMID- 9461465
VI  - 26
DP  - 1998
TI  - Multiple domains are involved in the targeting of the mouse DNA methyltransferase to the DNA replication foci.
PG  - 1038-1045
AB  - It has been shown that, during the S-phase of the cell cycle, the mouse DNA methyltransferase
      is targeted to sites of DNA replication by an amino acid sequence (aa 207-455) lying in the
      N-terminal domain of the enzyme.  In this paper it is shown, by using enhanced green
      fluorescent protein fusions, that peptide sequences of DNA MTase are also involved in this
      targeting.  The work focuses on a sequence, downstream of the reported targeting sequence,
      which is homologous to the Polybromo-1 protein.  This motif (designated as PBHD) is separated
      from the reported targeting sequence by a zinc-binding motif.  Primed in situ extension using
      centromeric-specific primers was used to show that both the host DNA MTase and EGFP fusion
      proteins containing the targeting sequences were localized to centromeric, but not telomeric,
      regions during late S-phase and mitosis.  Also found was that, in ~10% of the S-phase cells,
      the EGFP fusions did not co-localize with the centromeric regions.  Mutants containing either,
      or both, of these targeting sequences could act as dominant negative mutants against the host
      DNA MTase.  EGFP fusion proteins, containing the reported TS (aa 207-455), were targeted to
      centromeric regions throughout the mitotic stage which lead to the discovery of similar
      behavior of the endogenous DNA MTase although the host MTase showed much less intense staining
      than in S-phase cells.  The biological role of the centromeric localization of DNA MTase
      during mitosis is currently unknown.
AU  - Liu Y
AU  - Oakeley EJ
AU  - Sun L
AU  - Jost J-P
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1998 26: 1038-1045.

PMID- 10899996
VI  - 97
DP  - 2000
TI  - m5C RNA and m5C DNA methyl transferases use different cysteine residues as catalysts.
PG  - 8263-8265
AB  - A family of RNA m(5)C methyl transferases (MTases) containing over 55 members in eight
      subfamilies has been identified recently by an iterative search of the genomic sequence
      databases by using the known 16S rRNA m(5)C 967 MTase, Fmu, as an initial probe. The RNA m(5)C
      MTase family contained sequence motifs that were highly homologous to motifs in the DNA m(5)C
      MTases, including the ProCys sequence that contains the essential Cys catalyst of the
      functionally similar DNA-modifying enzymes; it was reasonable to assign the Cys nucleophile to
      be that in the conserved ProCys. The family also contained an additional conserved Cys residue
      that aligns with the nucleophilic catalyst in m(5)U54 tRNA MTase. Surprisingly, the mutant of
      the putative Cys catalyst in the ProCys sequence was active and formed a covalent complex with
      5-fluorocytosine-containing RNA, whereas the mutant at the other conserved Cys was inactive
      and unable to form the complex. Thus, notwithstanding the highly homologous sequences and
      similar functions, the RNA m(5)C MTase uses a different Cys as a catalytic nucleophile than
      the DNA m(5)C MTases. The catalytic Cys seems to be determined, not by the target base that is
      modified, but by whether the substrate is DNA or RNA. The function of the conserved ProCys
      sequence in the RNA m(5)C MTases remains unknown.
AU  - Liu Y
AU  - Santi DV
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2000 97: 8263-8265.

PMID- 
VI  - 11
DP  - 2009
TI  - Cloning, expression and nucleotide sequence analysis of gene encoding for BamHI methyltransferase from Bacillus amyloliquefaciens CICIM B2125.
PG  - 65-68
AB  - A gene encoding for BamHI methyltransferase was cloned from Bacillus amyloliquefaciens CICIM
      B2125.  The bamHIM was expressed under its own promoter in E. coli JM109.  The gene contained
      an open reading frame of 1,271 bp, which encoded for 423 amino acid residues.  The molecular
      weight of mature protein was 49 kD.  The BamHI site could be methylased by the enzyme M.BamHI.
      The amino acid sequence analysis revealed that the enzyme contained a domain of Rossmann-fold
      (NAD(P)(+)-binding proteins.
AU  - Liu Y
AU  - Shen W
AU  - Shi G
AU  - Wang Z
PT  - Journal Article
TA  - Shengwu Jishu Tongbao
JT  - Shengwu Jishu Tongbao
SO  - Shengwu Jishu Tongbao 2009 11: 65-68.

PMID- 8759002
VI  - 24
DP  - 1996
TI  - In differentiating mouse myoblasts DNA methyltransferase is posttranscriptionally and posttranslationally regulated.
PG  - 2718-2722
AB  - Upon the onset of mouse myoblast differentiation there is a rapid drop in DNA
      methyltransferase activity followed by a genome wide demethylation.  Here we show by using
      specific antibodies directed against DNA methyltransferase that upon differentiation there was
      a rapid drop in nuclear DNA methyltransferase whilst the internal control histone H1 remained
      constant.  The loss of nuclear methyltransferase was not due to a translocation of the enzyme
      from the nucleus to the cytoplasm where there was an increase in creatine phosphokinase
      protein.  In vitro run on experiments carried out with growing and differentiating myoblast
      nuclei showed no difference in the rate of DNA methyltransferase mRNA synthesis.  As measured
      by Northern blot hybridization the relative half life of DNA methyltransferase mRNA in growing
      and differentiating cells in the presence of Actinomycin D was 5h and 1h 30min, respectively,
      whereas in the same cells the half life of histone H4 mRNA was in both cases 80 min.  As
      measured by a combination of pulse chase experiments with labeled leucine and
      immunoprecipitation, the relative half-life of DNA methyltransferase in growing and
      differentiating cells was ~18h and 4h 30min, respectively.
AU  - Liu Y
AU  - Sun L
AU  - Jost J-P
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1996 24: 2718-2722.

PMID- 9033675
VI  - 7
DP  - 1996
TI  - In differentiating mouse myoblasts DNA methyltransferase is posttranscriptionally and posttranslationally regulated.
PG  - 8a
AB  - Upon the onset of mouse myoblast differentiation there is a rapid drop in DNA
      methyltransferase activity followed by a genome wide demethylation.  Here we show by using
      specific antibodies directed against DNA methyltransferase that upon differentiation there was
      a rapid drop in nuclear DNA methyltransferase whilst the internal control Histone H1 remained
      constant.  The loss of nuclear methyltransferase was not due to a translocation of the enzyme
      from the nucleus to the cytoplasm where there was an increase in creatine phosphokinase
      protein.  In vitro run on experiments carried out with growing and differentiating myoblast
      nuclei showed no difference in the rate of DNA methyltransferase mRNA synthesis.  As measured
      by Northern blot hybridization the relative half life of DNA methyltransferase mRNA in growing
      and differentiating cells in the presence of Actinomycin D was 5 h and 1 h 30 min
      respectively, whereas in the same cells the half life of Histone H4 mRNA was in both cases 80
      minutes.  As measured by a combination of pulse chase experiments with labeled leucine and
      immunoprecipitation, the relative half life of DNA methyltransferase in growing and
      differentiating cells was approximately 18 h and 4 h 30 min respectively.
AU  - Liu Y
AU  - Sun L
AU  - Jost J-P
PT  - Journal Article
TA  - Mol. Biol. Cell
JT  - Mol. Biol. Cell
SO  - Mol. Biol. Cell 1996 7: 8a.

PMID- 24272266
VI  - 69
DP  - 2014
TI  - Investigation of a multiresistance gene cfr that fails to mediate resistance to phenicols and oxazolidinones in Enterococcus faecalis.
PG  - 892-898
AB  - OBJECTIVES: To investigate the basis of susceptibility to phenicols and
      oxazolidinones of the porcine Enterococcus faecalis CPPF5 despite the presence of
      the multiresistance gene cfr. METHODS: Southern blotting, conjugation and
      transformation analyses were conducted to confirm the plasmid location and
      transferability of cfr in CPPF5. The genetic environment of cfr was determined by
      sequence analysis. Transcription and translation of cfr were examined by RT-PCR
      and western blotting, respectively, and modifications at A2503 within the 23S
      rRNA sequence were identified by primer extension. RESULTS: Electrotransformation
      and Southern blotting indicated that CPPF5 and its transformant 5B2-3 contained
      two cfr-carrying plasmids approximately 50 and approximately 12 kb in size. The
      complete 12,270 bp sequence of the smaller plasmid, pCPPF5, was determined and
      shared 99.9% (12,269/12,270 bp) identity with the corresponding region of the
      cfr-carrying plasmid pEF-01 in E. faecalis of cattle origin. Moreover, the
      genetic environment of cfr in the approximately 50 kb plasmid was the same as
      that in pCPPF5 according to sequencing results. Although cfr mRNA, Cfr protein
      and a modification at the A2503 site were detected, the cfr-carrying transformant
      5B2-3 did not have elevated MICs of chloramphenicol, florfenicol and linezolid,
      indicating that cfr fails to mediate resistance to the respective antibiotics in
      E. faecalis. CONCLUSIONS: This is the first report of the cfr gene failing to
      elevate MICs of the corresponding antibiotics. Although the genetic basis for the
      apparent 'no resistance' phenotype remains to be determined, this finding may
      have implications for surveillance studies that target the cfr gene.
AU  - Liu Y
AU  - Wang Y
AU  - Schwarz S
AU  - Wang S
AU  - Chen L
AU  - Wu C
AU  - Shen J
PT  - Journal Article
TA  - J. Antimicrob. Chemother.
JT  - J. Antimicrob. Chemother.
SO  - J. Antimicrob. Chemother. 2014 69: 892-898.

PMID- 24604652
VI  - 2
DP  - 2014
TI  - Genome Sequence of Luteimonas huabeiensis HB-2, a Novel Species of Luteimonas with High Oil Displacement Efficiency.
PG  - e00152-14
AB  - Luteimonas huabeiensis HB-2 is a novel and newly isolated strain, which shows a superior
      property of oil displacement. Here, we present a 4.3-Mb assembly of its
      genome. The key genes for phospholipid and fatty acid metabolism were annotated,
      which are crucial for crude oil emulsification and recovery.
AU  - Liu Y
AU  - Yao S
AU  - Liu Y
AU  - Xu Y
AU  - Cheng C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00152-14.

PMID- 25197449
VI  - 9
DP  - 2014
TI  - High-quality draft genome sequence of nematocidal Bacillus thuringiensis Sbt003.
PG  - 624-631
AB  - Bacillus thuringiensis represents one of the six species of 'Bacillus cereus group' in the
      genus Bacillus within the family Bacillaceae. Strain Sbt003 was
      isolated from soil and identified as B. thuringiensis. It harbors at least seven
      plasmids and produces three shapes of parasporal crystals including oval,
      bipyramidal and rice. SDS-PAGE analysis of spore-crystal suspension of this
      strain reveals six major protein bands, which implies the presence of multiple
      parasporal crystal genes. Bioassay of this strain reveals that it shows specific
      activity against nematodes and human cancer cells. In this study, we report the
      whole genomic shotgun sequences of Sbt003. The high-quality draft of the genome
      is 6,175,670 bp long (including chromosome and plasmids) with 6,372
      protein-coding and 80 RNA genes.
AU  - Liu Y
AU  - Ye W
AU  - Zheng J
AU  - Fang L
AU  - Peng D
AU  - Ruan L
AU  - Sun M
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 624-631.

PMID- 25081255
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of a Symbiotic Bacterium, Rhizobium vignae CCBAU 05176T.
PG  - e00657-14
AB  - The Rhizobium vignae strain CCBAU 05176(T) was isolated from a root nodule of Astragalus
      dahuricus grown in Hebei Province, China. It grows on yeast mannitol
      agar (YMA) supplemented with 0 to 2% (wt/vol) NaCl. We report the annotated
      genome sequence of this strain in a 6.34-Mb scaffold.
AU  - Liu Y
AU  - Yi Z
AU  - Zeng R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00657-14.

PMID- 26744370
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Streptococcus sp. X13SY08, Isolated from Murray Cod (Maccullochella peelii peelii).
PG  - e01470-15
AB  - Streptococcus sp. X13SY08, isolated from freshwater Murray cod fi sh, likely presents a novel
      species of Streptococcus. Here, we present an annotated draft
      genome sequence of this species, which will improve our understanding of its
      physiology and pathogenesis.
AU  - Liu Y
AU  - Zeng R
AU  - Weng B
AU  - Luo T
AU  - Luo Q
AU  - Xu L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01470-15.

PMID- 24771061
VI  - 57
DP  - 2014
TI  - Establishment of an efficient transformation protocol and its application in marine-derived Bacillus strain.
PG  - 627-635
AB  - Marine-derived Bacillus strains have been proved to be a very promising source for natural
      product leads. However, transformation of environmental strains is much more difficult than
      that of domesticated strains. Here, we report the development of an efficient and robust
      electroporation-based transformation system for marine-derived Bacillus marinus B-9987, which
      is a macrolactin antibiotics producer and a very promising biological control agent against
      fungal plant diseases. The transformation efficiency was greatly enhanced 10(3)-fold by using
      unmethylated plasmid to bypass modification-restriction barrier, and using glycine betaine to
      protect cells from electrical damages during electroporation. Addition of HEPES and 2 mmol L-1
      MgCl2 further improved the efficiency by additional 2-fold, with a maximum value of 7.1x10(4)
      cfu/mu g pHT3101. To demonstrate the feasibility and efficiency of the protocol, a green
      fluorescent protein reporter system was constructed; furthermore, phosphopantetheinyl
      transferase gene sfp, which is essential to the biosynthesis of polyketides and nonribosomal
      peptides, was overexpressed in B-9987, leading to increased production of macrolactin A by
      about 1.6-fold. In addition, this protocol is also applicable to marine-derived Bacillus
      licheniforms EI-34-6, indicating it could be a reference for other undomesticated Bacillus
      strains. To our knowledge, this is the first report regarding the transformation of
      marine-derived Bacillus strain.
AU  - Liu Y
AU  - Zheng H
AU  - Zhan GH
AU  - Qin W
AU  - Tian L
AU  - Li WL
PT  - Journal Article
TA  - Sci. China C Life Sci.
JT  - Sci. China C Life Sci.
SO  - Sci. China C Life Sci. 2014 57: 627-635.

PMID- 26679582
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Xanthomonas campestris pv. campestris Strain 17 from  Taiwan.
PG  - e01466-15
AB  - Xanthomonas campestris pv. campestris 17 is a Gram-negative bacterium that is phytopathogenic
      to cruciferous plants in Taiwan. The 4,994,426-bp-long genome
      consists of 24 contigs with 4,050 protein-coding genes, 1 noncoding RNA (ncRNA)
      gene, 6 rRNA genes, and 55 tRNA genes.
AU  - Liu YC
AU  - Wang SC
AU  - Yu YJ
AU  - Fung KM
AU  - Yang MT
AU  - Tseng YH
AU  - Tsai SF
AU  - Sun HS
AU  - Lyu PC
AU  - Chou SH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01466-15.

PMID- 17616602
VI  - 189
DP  - 2007
TI  - Negative regulation of the EcoRI restriction enzyme gene is associated with intragenic reverse promoters.
PG  - 6928-6935
AB  - Type 11 restriction-modification systems are expected to possess mechanisms for tight
      regulation of their expression to suppress the
      potential of lethal attack on their host bacteria when they establish
      and maintain themselves within them. Although the EcoRI restriction
      enzyme has been well characterized, regulation of its expression is
      still poorly understood. In this study, mutational analysis with lacZ
      gene fusion and primer extension assay identified a promoter for the
      transcription of the ecoRIR gene. Further analyses revealed that an
      intragenic region containing two overlapping reverse promoter-like
      elements acted as a negative regulator for ecoRIR gene expression. The
      activity of these putative reverse promoters was verified by
      transcriptional gene fusion, primer extension and in vitro
      transcription. Mutations in these reverse promoters resulted in
      increased gene expression in both translational and transcriptional
      gene fusions. An RNase protection assay revealed that the transcript
      level of the wild type relative to that of the reverse promoter mutant
      at the downstream regions was much lower than the level at the upstream
      regions. This suggests that these reverse promoter-like elements affect
      their downstream transcript level. The possible mechanisms of this kind
      of negative regulation, in addition to their possible biological roles,
      are discussed.
AU  - Liu YP
AU  - Kobayashi I
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2007 189: 6928-6935.

PMID- 28973912
VI  - 114
DP  - 2017
TI  - Structural basis underlying complex assembly and conformational transition of the type I R-M system.
PG  - 11151-11156
AB  - Type I restriction-modification (R-M) systems are multisubunit enzymes with separate
      DNA-recognition (S), methylation (M), and restriction (R) subunits. Despite extensive studies
      spanning five decades, the detailed molecular mechanisms underlying subunit assembly and
      conformational transition are still unclear due to the lack of high-resolution structural
      information. Here, we report the atomic structure of a type I MTase complex (2M+1S) bound to
      DNA and cofactor S-adenosyl methionine in the 'open' form. The intermolecular interactions
      between M and S subunits are mediated by a four-helix bundle motif, which also determines the
      specificity of the interaction. Structural comparison between open and previously reported
      low-resolution 'closed' structures identifies the huge conformational changes within the
      MTase complex. Furthermore, biochemical results show that R subunits prefer to load onto the
      closed form MTase. Based on our results, we proposed an updated model for the complex
      assembly. The work reported here provides guidelines for future applications in molecular
      biology.
AU  - Liu YP
AU  - Tang Q
AU  - Zhang JZ
AU  - Tian LF
AU  - Gao P
AU  - Yan XX
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2017 114: 11151-11156.

PMID- 24267588
VI  - 14
DP  - 2013
TI  - Genomic analysis reveals key aspects of prokaryotic symbiosis in the phototrophic consortium 'Chlorochromatium aggregatum'.
PG  - R127
AB  - BACKGROUND: 'Chlorochromatium aggregatum' is a phototrophic consortium, a
      symbiosis that may represent the highest degree of mutual interdependence between
      two unrelated bacteria not associated with a eukaryotic host. 'Chlorochromatium
      aggregatum' is a motile, barrel-shaped aggregate formed from a single cell of
      'Candidatus Symbiobacter mobilis", a polarly flagellated, non-pigmented,
      heterotrophic bacterium, which is surrounded by approximately 15 epibiont cells
      of Chlorobium chlorochromatii, a non-motile photolithoautotrophic green sulfur
      bacterium. RESULTS: We analyzed the complete genome sequences of both organisms
      to understand the basis for this symbiosis. Chl. chlorochromatii has acquired
      relatively few symbiosis-specific genes; most acquired genes are predicted to
      modify the cell wall or function in cell-cell adhesion. In striking contrast,
      'Ca. S. mobilis' appears to have undergone massive gene loss, is probably no
      longer capable of independent growth, and thus may only reproduce when consortia
      divide. A detailed model for the energetic and metabolic bases of the dependency
      of 'Ca. S. mobilis' on Chl. chlorochromatii is described. CONCLUSIONS: Genomic
      analyses suggest that three types of interactions lead to a highly sophisticated
      relationship between these two organisms. Firstly, extensive metabolic exchange,
      involving carbon, nitrogen, and sulfur sources as well as vitamins, occurs from
      the epibiont to the central bacterium. Secondly, 'Ca. S. mobilis' can sense and
      move towards light and sulfide, resources that only directly benefit the
      epibiont. Thirdly, electron cycling mechanisms, particularly those mediated by
      quinones and potentially involving shared protonmotive force, could provide an
      important basis for energy exchange in this and other symbiotic relationships.
AU  - Liu Z
AU  - Muller J
AU  - Li T
AU  - Alvey RM
AU  - Vogl K
AU  - Frigaard NU
AU  - Rockwell NC
AU  - Boyd ES
AU  - Tomsho LP
AU  - Schuster SC
AU  - Henke P
AU  - Rohde M
AU  - Overmann J
AU  - Bryant DA
PT  - Journal Article
TA  - Genome Biol.
JT  - Genome Biol.
SO  - Genome Biol. 2013 14: R127.

PMID- 21344558
VI  - 50
DP  - 2011
TI  - Methyltransferase-Directed Derivatization of 5-Hydroxymethylcytosine in DNA.
PG  - 2090-2093
AB  - The modification of cytosine by S-adenosylmethionine-dependent DNA methyltransferases is part
      of an intricate epigenetic regulation mechanism in vertebrates.  DNA cytosine-5
      methyltransferases (catalyze the transfer of a methyl group from S-adenosyl-L-methionine to
      the cytosine residue in CpG dinucleotides.  Recent studies of genomic DNA from mouse embryonic
      stem cells, neurons, and the brain found that a substantial fraction of 5-methylcytosine in CG
      sequences is converted into 5-hydroxymethylcytosine by the action of 2-oxoglutarate- and
      Fe2+-dependent oxygenases of the TET family.  As interactions of the 5-methyl- and
      5-hydroxymethyl groups with cellular proteins in DNA are distinct, hmC residues may play an
      independent role in yet unknown epigenetic pathways during embryonic development, brain
      functioning, and cancer progression.  However, further studies of these intriguing phenomena
      are hampered by the lack of efficient analytical techniques for mapping hmC residues in the
      genome.  Herein we show that C5-MTases can direct the condensation of exogenous thiols and
      selenols with hmC in DNA to yield the corresponding 5-chalcogenomethyl derivatives.  These
      transformations open new possibilities for the sequence-specific derivatization and analysis
      of this newly discovered epigenetic mark in mammalian DNA.
AU  - Liutkeviciute Z
AU  - Kriukiene E
AU  - Grigaityte I
AU  - Masevicius V
AU  - Klimasauskas S
PT  - Journal Article
TA  - Angew. Chem. Int. Ed. Engl.
JT  - Angew. Chem. Int. Ed. Engl.
SO  - Angew. Chem. Int. Ed. Engl. 2011 50: 2090-2093.

PMID- 
VI  - 279
DP  - 2012
TI  - Catalytic versatility of DNA cytosine-5 methyltransferases: reactions involving non-cofactor-like substrates.
PG  - 540
AB  - DNA cytosine-5 methyltransferases catalyze site-specific transfers of a methyl group from the
      cofactor S-adenosyl-L-methionine (SAM) onto the 5-position of their target cytosine residues
      in DNA.  Recently we have shown that, in the absence of SAM, methyltranferases are able to add
      formaldehyde to their target cytosines yielding 5-hydroxymethylcytosine.  This reaction can be
      reversed yielding unmodified cytosine, or can be further extended by condensation with thiols
      or selenols.  Lately hmC was discovered in mammals DNA but the biological role of this new
      base is unclear because further studies are restricted by the lack of efficient analytical
      techniques for mapping hmC residues in the genome.  These atypical reactions of DNA cytosine-5
      methyltransferase open new ways for analysis of hnmC in genomic DNA and provide inroads into
      active demethylation of 5-methylcytosine residues in the genome.
AU  - Liutkeviciute Z
AU  - Kriukiene E
AU  - Grigaityte I
AU  - Vainorius G
AU  - Masevicius V
AU  - Klimasauskas S
PT  - Journal Article
TA  - FEBS J.
JT  - FEBS J.
SO  - FEBS J. 2012 279: 540.

PMID- 19430486
VI  - 5
DP  - 2009
TI  - Cytosine-5-methyltransferases add aldehydes to DNA.
PG  - 400-402
AB  - Targeted methylation of cytosine residues by S-adenosylmethionine-dependent DNA
      methyltransferases modulates gene
      expression in vertebrates. Here we show that
      cytosine-5-methyltransferases catalyze reversible covalent addition of
      exogenous aliphatic aldehydes to their target residues in DNA, thus
      yielding corresponding 5-alpha-hydroxyalkylcytosines. Such atypical
      enzymatic reactions with non-cofactor-like substrates open new ways for
      sequence-specific derivatization of DNA and demonstrate enzymatic
      exchange of 5-hydroxymethyl groups on cytosine in support of an
      oxidative mechanism of DNA demethylation.
AU  - Liutkeviciute Z
AU  - Lukinavicius G
AU  - Masevicius V
AU  - Daujotyte D
AU  - Klimasauskas S
PT  - Journal Article
TA  - Nat. Chem. Biol.
JT  - Nat. Chem. Biol.
SO  - Nat. Chem. Biol. 2009 5: 400-402.

PMID- 25125648
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Burkholderia sordidicola S170, a Potential Plant Growth  Promoter Isolated from Coniferous Forest Soil in the Czech Republic.
PG  - e00810-14
AB  - Burkholderia species are key players in the accumulation of carbon from cellulose
      decomposition in coniferous forest ecosystems. We report here the draft genome of
      Burkholderia sordidicola strain S170, containing features associated with known
      genes involved in plant growth promotion, the biological control of plant
      diseases, and green remediation technologies.
AU  - Llado S
AU  - Xu Z
AU  - Sorensen SJ
AU  - Baldrian P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00810-14.

PMID- 23535597
VI  - 496
DP  - 2013
TI  - Predominant archaea in marine sediments degrade detrital proteins.
PG  - 215-218
AB  - Half of the microbial cells in the Earth's oceans are found in sediments. Many of these cells
      are members of the Archaea, single-celled prokaryotes in a domain of
      life separate from Bacteria and Eukaryota. However, most of these archaea lack
      cultured representatives, leaving their physiologies and placement on the tree of
      life uncertain. Here we show that the uncultured miscellaneous crenarchaeotal
      group (MCG) and marine benthic group-D (MBG-D) are among the most numerous
      archaea in the marine sub-sea floor. Single-cell genomic sequencing of one cell
      of MCG and three cells of MBG-D indicated that they form new branches basal to
      the archaeal phyla Thaumarchaeota and Aigarchaeota, for MCG, and the order
      Thermoplasmatales, for MBG-D. All four cells encoded extracellular
      protein-degrading enzymes such as gingipain and clostripain that are known to be
      effective in environments chemically similar to marine sediments. Furthermore, we
      found these two types of peptidase to be abundant and active in marine sediments,
      indicating that uncultured archaea may have a previously undiscovered role in
      protein remineralization in anoxic marine sediments.
AU  - Lloyd KG
AU  - Schreiber L
AU  - Petersen DG
AU  - Kjeldsen KU
AU  - Lever MA
AU  - Steen AD
AU  - Stepanauskas R
AU  - Richter M
AU  - Kleindienst S
AU  - Lenk S
AU  - Schramm A
AU  - Jorgensen BB
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2013 496: 215-218.

PMID- 9354758
VI  - 44
DP  - 1997
TI  - Mechanistic link between DNA methyltransferases and DNA repair enzymes by base flipping.
PG  - 139-151
AB  - Rotation of a DNA nucleotide out of the double helix and into a protein binding pocket ("base
      flipping") was first observed in the structure of a DNA methyltransferase.  There is now
      evidence that a variety of proteins, particularly DNA repair enzymes, use base flipping in
      their interactions with DNA.  Though the mechanisms for base movement into extrahelical
      positions are still unclear, the focus of this review is how base recognition is modulated by
      the stringency of binding to the extrahelical base(s) or sugar moiety.
AU  - Lloyd RS
AU  - Cheng X
PT  - Journal Article
TA  - Biopolymers
JT  - Biopolymers
SO  - Biopolymers 1997 44: 139-151.

PMID- 23300489
VI  - 9
DP  - 2013
TI  - Comprehensive Methylome Characterization of Mycoplasma genitalium and Mycoplasma  pneumoniae at Single-Base Resolution.
PG  - e1003191
AB  - In the bacterial world, methylation is most commonly associated with restriction-modification
      systems that provide a defense mechanism against
      invading foreign genomes. In addition, it is known that methylation plays
      functionally important roles, including timing of DNA replication, chromosome
      partitioning, DNA repair, and regulation of gene expression. However, full DNA
      methylome analyses are scarce due to a lack of a simple methodology for rapid and
      sensitive detection of common epigenetic marks (ie N(6)-methyladenine (6 mA) and
      N(4)-methylcytosine (4 mC)), in these organisms. Here, we use Single-Molecule
      Real-Time (SMRT) sequencing to determine the methylomes of two related human
      pathogen species, Mycoplasma genitalium G-37 and Mycoplasma pneumoniae M129, with
      single-base resolution. Our analysis identified two new methylation motifs not
      previously described in bacteria: a widespread 6 mA methylation motif common to
      both bacteria (5'-CTAT-3'), as well as a more complex Type I m6A sequence motif
      in M. pneumoniae (5'-GAN(7)TAY-3'/3'-CTN(7)ATR-5'). We identify the
      methyltransferase responsible for the common motif and suggest the one involved
      in M. pneumoniae only. Analysis of the distribution of methylation sites across
      the genome of M. pneumoniae suggests a potential role for methylation in
      regulating the cell cycle, as well as in regulation of gene expression. To our
      knowledge, this is one of the first direct methylome profiling studies with
      single-base resolution from a bacterial organism.
AU  - Lluch-Senar M
AU  - Luong K
AU  - Llorens-Rico V
AU  - Delgado J
AU  - Fang G
AU  - Spittle K
AU  - Clark TA
AU  - Schadt E
AU  - Turner SW
AU  - Korlach J
AU  - Serrano L
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2013 9: e1003191.

PMID- 26564036
VI  - 3
DP  - 2015
TI  - A Novel Member of Chitinophagaceae Isolated from a Human Peritoneal Tumor.
PG  - e01297-15
AB  - Peritoneal tumors from a rare malignancy, pseudomyxoma peritonei, frequently contain bacteria.
      Evidence suggests that tumor-associated bacteria contribute to
      pseudomyxoma peritonei development and/or progression. One unique isolate
      (PMP191F) was characterized via whole-genome sequencing using the Illumina MiSeq
      platform. PMP191F shows similarities to the Chitinophaga, Niastella, and
      Flavitalea genera.
AU  - Lo AS
AU  - Merrell DS
AU  - Lei H
AU  - Sardi A
AU  - McAvoy T
AU  - Testerman TL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01297-15.

PMID- 24501642
VI  - 9
DP  - 2013
TI  - Non-contiguous finished genome sequence and description of Clostridium dakarense  sp. nov.
PG  - 14-27
AB  - Clostridium dakarense strain FF1(T), is the type strain of Clostridium dakarense  sp. nov., a
      new species within the genus Clostridium. This strain, whose genome
      is described here, was isolated from the fecal flora of a 4-month-old Senegalese
      child suffering from gastroenteritis. C. dakarense sp. nov. strain FF1(T) is an
      obligate anaerobic Gram-positive bacillus. Here we describe the features of this
      organism, together with the complete genome sequence and annotation. The
      3,735,762 bp long genome (1 chromosome but no plasmid) exhibits a G+C content of
      27.98% and contains 3,843 protein-coding and 73 RNA genes, including 8 rRNA
      genes.
AU  - Lo CI
AU  - Mishra AK
AU  - Padhmanabhan R
AU  - Samb B
AU  - Sow AG
AU  - Robert C
AU  - Couderc C
AU  - Faye N
AU  - Raoult D
AU  - Fournier PE
AU  - Fenollar F
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 9: 14-27.

PMID- 26568786
VI  - 10
DP  - 2015
TI  - Genome sequence and description of Pantoea septica strain FF5.
PG  - 103
AB  - Strain FF5 was isolated from the skin flora of a healthy Senegalese 35-year-old woman. This
      strain was identified as belonging to the species Pantoea septica
      based on rpoB sequence identity of 99.7 % with Pantoea septica strain LMG 5345(T)
      and a highest MALDI-TOF-MS score of 2.3 with Pantoea septica. Like P. septica,
      this FF5 strain is a Gram-negative, aerobic, motile, and rod-shaped bacterium.
      Currently, 17 genomes have been sequenced within the genus Pantoea but none for
      Pantoea septica. Herein, we compared the genomic properties of strain FF5 to
      those of other species within the genus Pantoea. The genome of this strain is
      4,548,444 bp in length (1 chromosome, no plasmid) with a G + C content of 59.1 %
      containing 4125 protein-coding and 68 RNA genes (including 2 rRNA operons). We
      also performed an extensive phenotypic analysis showing new phenotypic
      characteristics such as the production of alkaline phosphatase, acid phosphatase
      and naphthol-AS-BI-phosphohydrolase.
AU  - Lo CI
AU  - Padhmanabhan R
AU  - Mediannikov O
AU  - Nguyen TT
AU  - Raoult D
AU  - Fournier PE
AU  - Fenollar F
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 103.

PMID- 26221422
VI  - 10
DP  - 2015
TI  - High-quality genome sequence and description of Bacillus dielmoensis strain FF4(T) sp. nov.
PG  - 41
AB  - Strain FF4(T) was isolated from the skin flora of a 16-year-old healthy Senegalese female.
      This strain exhibited a 16S rRNA sequence similarity of 97.5 %
      with Bacillus fumarioli, the phylogenetically closest species with standing in
      nomenclature and a poor MALDI-TOF-MS score (1.1 to 1.3) that does not allow any
      identification. Using a polyphasic study consisting of phenotypic and genomic
      analyses, strain FF4(T) was Gram-positive, aerobic, rod-shaped, and exhibited a
      genome of 4,563,381 bp (1 chromosome but no plasmid) with a G + C content of 40.8
      % that coded 4,308 protein-coding and 157 RNA genes (including 5 rRNA operons).
      On the basis of these data, we propose the creation of Bacillus dielmoensis sp.
      nov.
AU  - Lo CI
AU  - Padhmanabhan R
AU  - Mediannikov O
AU  - Terras J
AU  - Robert C
AU  - Faye N
AU  - Raoult D
AU  - Fournier PE
AU  - Fenollar F
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 41.

PMID- 27081435
VI  - 11
DP  - 2016
TI  - High-quality draft genome sequence and description of Haemophilus massiliensis sp. nov.
PG  - 31
AB  - Strain FF7(T) was isolated from the peritoneal fluid of a 44-year-old woman who suffered from
      pelvic peritonitis. This strain exhibited a 16S rRNA sequence
      similarity of 94.8 % 16S rRNA sequence identity with Haemophilus parasuis, the
      phylogenetically closest species with a name with standing in nomenclature and a
      poor MALDI-TOF MS score (1.32 to 1.56) that does not allow any reliable
      identification. Using a polyphasic study made of phenotypic and genomic analyses,
      strain FF7(T) was a Gram-negative, facultatively anaerobic rod and member of the
      family Pasteurellaceae. It exhibited a genome of 2,442,548 bp long genome (one
      chromosome but no plasmid) contains 2,319 protein-coding and 67 RNA genes,
      including 6 rRNA operons. On the basis of these data, we propose the creation of
      Haemophilus massiliensis sp. nov. with strain FF7(T) (= CSUR P859 = DSM 28247) as
      the type strain.
AU  - Lo CI
AU  - Sankar SA
AU  - Fall B
AU  - Sambe-Ba B
AU  - Diawara S
AU  - Gueye MW
AU  - Mediannikov O
AU  - Blanc-Tailleur C
AU  - Wade B
AU  - Raoult D
AU  - Fournier PE
AU  - Fenollar F
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 31.

PMID- 17344860
VI  - 446
DP  - 2007
TI  - Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria.
PG  - 537-541
AB  - Microbes comprise the majority of extant organisms, yet much remains to be
      learned about the nature and driving forces of microbial diversification.
      Our understanding of how microorganisms adapt and evolve can be advanced
      by genome-wide documentation of the patterns of genetic exchange,
      particularly if analyses target coexisting members of natural communities.
      Here we use community genomic data sets to identify, with strain
      specificity, expressed proteins from the dominant member of a genomically
      uncharacterized, natural, acidophilic biofilm. Proteomics results reveal a
      genome shaped by recombination involving chromosomal regions of tens to
      hundreds of kilobases long that are derived from two closely related
      bacterial populations. Inter-population genetic exchange was confirmed by
      multilocus sequence typing of isolates and of uncultivated natural
      consortia. The findings suggest that exchange of large blocks of gene
      variants is crucial for the adaptation to specific ecological niches
      within the very acidic, metal-rich environment. Mass-spectrometry-based
      discrimination of expressed protein products that differ by as little as a
      single amino acid enables us to distinguish the behaviour of closely
      related coexisting organisms. This is important, given that microorganisms
      grouped together as a single species may have quite distinct roles in
      natural systems and their interactions might be key to ecosystem
      optimization. Because proteomic data simultaneously convey information
      about genome type and activity, strain-resolved community proteomics is an
      important complement to cultivation-independent genomic (metagenomic)
      analysis of microorganisms in the natural environment.
AU  - Lo I
AU  - Denef VJ
AU  - Verberkmoes NC
AU  - Shah MB
AU  - Goltsman D
AU  - Dibartolo G
AU  - Tyson GW
AU  - Allen EE
AU  - Ram RJ
AU  - Detter JC
AU  - Richardson P
AU  - Thelen MP
AU  - Hettich RL
AU  - Banfield JF
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2007 446: 537-541.

PMID- 23516213
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of an Actinobacterium, Brachybacterium muris Strain UCD-AY4.
PG  - e0008613
AB  - Here we present the draft genome of an actinobacterium, Brachybacterium muris UCD-AY4. The
      assembly contains 3,257,338 bp and has a GC content of 70%. This
      strain was isolated from a residential bath towel and has a 16S rRNA gene 99.7%
      identical to that of the original B. muris strain, C3H-21.
AU  - Lo JR
AU  - Lang JM
AU  - Darling AE
AU  - Eisen JA
AU  - Coil DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0008613.

PMID- 25792057
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Pseudomonas fluorescens SRM1, an Isolate from Spoiled Raw Milk.
PG  - e00138-15
AB  - Pseudomonas fluorescens is considered a major milk spoilage organism due to its psychrotrophic
      nature and ability to produce heat-stable proteases and lipases.
      Here, we report the draft genome and annotation of P. fluorescens SRM1 isolated
      from spoiled raw milk and the presence of an operon encoding spoilage enzymes.
AU  - Lo R
AU  - Stanton-Cook MJ
AU  - Beatson SA
AU  - Turner MS
AU  - Bansal N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00138-15.

PMID- 23873917
VI  - 5
DP  - 2013
TI  - Comparison of metabolic capacities and inference of gene content evolution in mosquito-associated Spiroplasma diminutum and S. taiwanense.
PG  - 1512-1523
AB  - Mosquitoes are hosts of several Spiroplasma species that belong to different serogroups. To
      investigate the genetic mechanisms that may be involved in the utilization of similar hosts in
      these phylogenetically distinct bacteria, we determined the complete genome sequences of S.
      diminutum and S. taiwanense for comparative analysis. The genome alignment indicates that
      their chromosomal organization is highly conserved,
      which is in sharp contrast to the elevated genome instabilities observed in other Spiroplasma
      lineages. Examination of the substrate utilization strategies revealed that S. diminutum can
      use a wide range of carbohydrates, suggesting that it is well suited to living in the gut (and
      possibly the circulatory system) of its mosquito hosts. In comparison, S. taiwanense has lost
      several carbohydrate utilization genes and acquired additional sets of oligopeptide
      transporter genes through tandem duplications, suggesting
      that proteins from digested blood meal or lysed host cells may be an important nutrient
      source. Moreover, one glycerol-3-phosphate oxidase gene (glpO) was found in S. taiwanense but
      not S. diminutum. This gene is linked to the production of reactive oxygen species and has
      been shown to be a major virulence factor in Mycoplasma mycoides. This finding may explain the
      pathogenicity of S. taiwanense observed in previous artificial infection experiments, while no
      apparent effect was found for S. diminutum. To infer the gene content evolution at deeper
      divergence levels, we incorporated other Mollicutes genomes for comparative analyses. The
      results suggest that the losses of biosynthetic pathways are a recurrent theme in these
      host-associated bacteria.
AU  - Lo W-S
AU  - Ku C
AU  - Chen L-L
AU  - Chang T-H
AU  - Kuo C-H
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2013 5: 1512-1523.

PMID- 25278541
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Vibrio vulnificus 93U204, a Bacterium Isolated from Diseased Tilapia in Taiwan.
PG  - e01005-14
AB  - Vibrio vulnificus 93U204 is a bacterium isolated from a moribund tilapia collected in
      Kaohsiung, Taiwan. Here, we report the complete genome sequence of
      this bacterium to facilitate the investigation of its pathogenicity and for
      comparative analyses with human-pathogenic strains within the same species.
AU  - Lo WS
AU  - Chen H
AU  - Chen CY
AU  - Kuo CH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01005-14.

PMID- 27660788
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Spiroplasma turonicum Tab4cT, a Bacterium Isolated from Horse Flies (Haematopota sp.).
PG  - e01010-16
AB  - Spiroplasma turonicum Tab4c(T) was isolated from a horse fly (Haematopota sp.; probably
      Haematopota pluvialis) collected at Champchevrier, Indre-et-Loire,
      Touraine, France, in 1991. Here, we report the complete genome sequence of this
      bacterium to facilitate the investigation of its biology and the comparative
      genomics among Spiroplasma spp.
AU  - Lo WS
AU  - Gasparich GE
AU  - Kuo CH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01010-16.

PMID- 28082500
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Spiroplasma sp. TU-14.
PG  - e01465-16
AB  - Spiroplasma sp. TU-14 was isolated from a contaminated sample of Entomoplasma lucivorax
      PIPN-2T obtained from the International Organization for Mycoplasmology
      collection. Here, we report the complete genome sequence of this bacterium to
      facilitate the investigation of its biology and the comparative genomics among
      Spiroplasma spp.
AU  - Lo WS
AU  - Haryono M
AU  - Gasparich GE
AU  - Kuo CH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01465-16.

PMID- 26430038
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Spiroplasma litorale TN-1T (DSM 21781), a Bacterium Isolated from a Green-Eyed Horsefly (Tabanus nigrovittatus).
PG  - e01116-15
AB  - Spiroplasma litorale TN-1(T) (DSM 21781) was isolated from the gut of a green-eyed horsefly
      (Tabanus nigrovittatus), collected at Ocracoke Island in North Carolina in 1983. Here, we
      report the complete genome sequence of this bacterium to facilitate the investigation of its
      biology.
AU  - Lo WS
AU  - Lai YC
AU  - Lien YW
AU  - Wang TH
AU  - Kuo CH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01116-15.

PMID- 26494686
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Spiroplasma cantharicola CC-1T (DSM 21588), a Bacterium Isolated from Soldier Beetle (Cantharis carolinus).
PG  - e01253-15
AB  - Spiroplasma cantharicola CC-1(T) (DSM 21588) was isolated from the gut of a soldier beetle
      (Cantharis carolinus) collected in Maryland, USA. Here, we report  the complete genome
      sequence of this bacterium to facilitate the investigation of its biology.
AU  - Lo WS
AU  - Liu PY
AU  - Kuo CH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01253-15.

PMID- 1630320
VI  - 6
DP  - 1992
TI  - Expression of the Escherichia coli dam gene.
PG  - 1841-1851
AB  - The Escherichia coli dam gene and upstream sequences were cloned from the Kohara phage 4D4.
      Five promoters were found to contribute to dam gene transcription.  P1 and P2 (the major
      promoter) were situated approximately 3.5 kb upstream of the structural gene, P3 was within
      the aroB gene, P4 was within the urf74.3 gene, and P5 was in the urf74.3-dam intergenic
      region.  The nucleotide sequence of 2280 bp of DNA containing P1 and P2 was determined and
      shown to have the potential to encode a protein of approximately 16 kDa between P1, P2 and the
      aroB gene.  This 16 kDa open reading frame has been identified as aroK, the gene for shikimic
      acid kinase I.  Thus the dam gene is part of an operon containing aroK, aroB, urf74.3, and
      dam.  The transcriptional start points of the promoters were determined.  A comparison of
      their nucleotide sequences suggested that P1-P4 were all recognized by the sigma 70 subunit of
      the RNA polymerase.
AU  - Lobner-Olesen A
AU  - Boye E
AU  - Marinus MG
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1992 6: 1841-1851.

PMID- 15802246
VI  - 8
DP  - 2005
TI  - Dam methylation: coordinating cellular processes.
PG  - 154-160
AB  - GATC sequences in Escherichia coli DNA are methylated at the adenine residue by DNA adenine
      methyltransferase (DamMT). These methylated
      residues and/or the level of DamMT can influence cellular functions
      such as gene transcription, DNA mismatch repair, initiation of
      chromosome replication and nucleoid structure. In certain bacteria,
      unlike E coli, DamMT is essential for viability perhaps owing to its
      role in chromosome replication. DamMT has also been implicated as a
      virulence factor in bacterial pathogenesis. The origin and phylogeny of
      DamMT, based on sequenced genomes, has been deduced.
AU  - Lobner-Olesen A
AU  - Skovgaard O
AU  - Marinus MG
PT  - Journal Article
TA  - Curr. Opin. Microbiol.
JT  - Curr. Opin. Microbiol.
SO  - Curr. Opin. Microbiol. 2005 8: 154-160.

PMID- 8918477
VI  - 15
DP  - 1996
TI  - Chromosomal replication incompatibility in Dam methyltransferase deficient Escherichia coli cells.
PG  - 5999-6008
AB  - Dam methyltransferase deficient Escherichia coli cells containing minichromosomes were
      constructed.  Free plasmid DNA could not be detected in these cells and the minichromosomes
      were found to be integrated in multiple copies in the origin of replication (oriC) region of
      the host chromosome.  The absence of the initiation cascade in Dam- cells is proposed to
      account for this observation of apparent incompatibility between plasmid and chromosomal
      copies of oriC.  Studies using oriC-pBR322 chimeric plasmids and their deletion derivatives
      indicated that the incompatibility determinant is an intact and functional oriC sequence.  The
      seqA2 mutation was found to overcome the incompatibility phenotype by increasing the cellular
      oriC copy number 3-fold thereby allowing minichromosomes to coexist with the chromosome.  The
      replication pattern of a wild-type strain with multiple integrated minichromosomes in the oriC
      region of the chromosome, led to the conclusion that initiation of DNA replication commences
      at a fixed cell mass, irrespective of the number of origins contained on the chromosome.
AU  - Lobner-Olesen A
AU  - von Freiesleben U
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1996 15: 5999-6008.

PMID- 15489417
VI  - 186
DP  - 2004
TI  - Genome of bacteriophage P1.
PG  - 7032-7068
AB  - P1 is a bacteriophage of Escherichia coli and other enteric bacteria.
      It lysogenizes its hosts as a circular, low-copy-number plasmid. We have
      determined the complete nucleotide sequences of two strains of a P1
      thermoinducible mutant, P1 c1-100. The P1 genome (93,601 bp) contains at
      least 117 genes, of which almost two-thirds had not been sequenced
      previously and 49 have no homologs in other organisms. Protein-coding
      genes occupy 92% of the genome and are organized in 45 operons, of which
      four are decisive for the choice between lysis and lysogeny. Four others
      ensure plasmid maintenance. The majority of the remaining 37 operons are
      involved in lytic development. Seventeen operons are transcribed from
      sigma(70) promoters directly controlled by the master phage repressor C1.
      Late operons are transcribed from promoters recognized by the E. coli RNA
      polymerase holoenzyme in the presence of the Lpa protein, the product of a
      C1-controlled P1 gene. Three species of P1-encoded tRNAs provide
      differential controls of translation, and a P1-encoded DNA
      methyltransferase with putative bifunctionality influences transcription,
      replication, and DNA packaging. The genome is particularly rich in Chi
      recombinogenic sites. The base content and distribution in P1 DNA indicate
      that replication of P1 from its plasmid origin had more impact on the base
      compositional asymmetries of the P1 genome than replication from the lytic
      origin of replication.
AU  - Lobocka MB
AU  - Rose DJ
AU  - Rusin M
AU  - Plunkett G III
AU  - Samojedny A
AU  - Lehnherr H
AU  - Yarmolinsky MB
AU  - Blattner FR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2004 186: 7032-7068.

PMID- 8424953
VI  - 1171
DP  - 1993
TI  - Purification and characterisation of BstLVI restriction endonuclease, a thermostable isoschizomer of ClaI from Bacillus stearothermophilus LV.
PG  - 295-298
AB  - This work describes the purification and biochemical characterization of BstLVI restriction
      endonuclease, a thermostable isoschizomer of ClaI, from Bacillus stearothermophilus LV. The
      enzyme was purified by successive DEAE-cellulose, Affi-Gel Blue and Heparin-Sepharose CL-6B
      column chromatography. A molecular weight of 37000 was determined for BstLVI by gel
      filtration. As expected for thermophilic proteins, the enzyme showed a high stability towards
      heat and also to other known protein-denaturing agents.
AU  - Lobos C
AU  - Vasquez C
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1993 1171: 295-298.

PMID- 3114425
VI  - 132
DP  - 1986
TI  - dam Methylation in the archaebacteria.
PG  - 3055-3059
AB  - The DNA of certain species of halophilic and methanogenic archaebacteria is dam methylated, as
      shown by restriction endonuclease sensitivities. The Dam+ phenotype appears to be confined to
      particular taxonomic groupings defined by DNA:rRNA hybridization or 16S RNA oligonucleotide
      cataloging.
AU  - Lodwick D
AU  - Ross HNM
AU  - Harris JE
AU  - Almond JW
AU  - Grant WD
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1986 132: 3055-3059.

PMID- 16861634
VI  - 74
DP  - 2006
TI  - Lysogeny of Streptococcus pneumoniae with MM1 Phage: Improved Adherence and Other Phenotypic Changes.
PG  - 4486-4495
AB  - Pneumococcal prophages are extremely frequent, but no role in pathogenesis has so far been
      attributed to them. We isolated a variant of phage MM1, named MM1-1998, from a serotype 24
      strain of Streptococcus pneumoniae. We created three isogenic strain pairs (serotypes 3, 4,
      and 24) that differed only by the lysogenic presence of the MM1-1998 phage and did a
      phenotypic comparison. Lysogeny led to improved adherence to inert surfaces and pharyngeal
      cells compared to that with the cured variants of the strains. We found that lysogeny with
      MM1-1998 coincided with a more transparent phenotype and phage curing with more opaque
      colonies in all strain pairs, and we discovered that transparency was associated with more
      successful and stable lysogeny. Since transparency alone was possibly responsible for the
      adherence difference, we further compared the TIGR4 lysogen with an equally transparent
      variant of TIGR4 in order to reassess the role of phage or transparency separately. The
      results revealed that improved adherence was independently associated with lysogeny with the
      MM1-1998 phage. Other phenotypic differences such as faster growth, increased autolysis, and
      decreased intracellular hemolytic activity were more likely due to transparency. By improving
      the adherence of pneumococci, this prophage may contribute to their fitness and possibly to
      their persistence in humans.
AU  - Loeffler JM
AU  - Fischetti VA
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2006 74: 4486-4495.

PMID- 3023633
VI  - 190
DP  - 1986
TI  - Modification Enhancement by Restriction Alleviation Protein (Ral) of Bacteriophage lambda.
PG  - 11-22
AB  - The product of the lambda ral gene alleviates restriction and enhances
      modification by the Escherichia coli K-12 restriction and modification system.
      An open reading frame (orf) located between genes N and Ealpha10 has been
      assigned to the ral gene.  We have cloned this orf in a plasmid where its
      transcription is controlled by a thermolabile lambda repressor.  Inactivation
      of the lambda repressor caused a 1000-fold reduction in K-specific restriction
      of unmodified lambda phage and a 100-fold increase in modification.  In
      minicells transformed with ral+ plasmids, derepression resulted in the
      appearance of a polypeptide with a lower mobility than that predicted for a
      protein encoded by the orf attributed to ral; in a transcription and
      translation system in vitro DNA from a ral+ plasmid encoded a polypeptide with
      the same mobility.  This polypeptide was absent when the plasmid DNA carried a
      mutant ral gene.  The nucleotide sequence of this mutant gene defined two base
      changes, one of which inactivates the initiation codon of the orf.  The K
      restriction endonuclease, which is also a K-specific methylase, is encoded by
      three genes designated hsdR, hsdM and hsdS, although the hsdR polypeptide is
      not essential for the methylase activity.  We show that Ral enchances
      modification in a host strain lacking the entire hsdR gene, and lambda phages
      carrying the hsdM and S genes modify their their own DNA inefficiently in the
      absence of Ral, despite the fact that derivatives of these phages provide
      efficient amplification of the K-specific methylase.  Our data support a model
      in which, as a consequence of the interaction of Ral with either the hsdM or
      the hsdS polypeptide, the conformation of the enzyme is changed and the
      efficiency of methylation of unmodified target sites is enhanced.  It has been
      postulated that Ral counteracts Rho, but in our experiments Ral did not relieve
      transcriptional polarity.
AU  - Loenen W
AU  - Murray N
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1986 190: 11-22.

PMID- 24068554
VI  - 42
DP  - 2014
TI  - Type I restriction enzymes and their relatives.
PG  - 20-44
AB  - Type I restriction enzymes (REases) are large pentameric proteins with separate restriction
      (R), methylation (M) and DNA sequence-recognition (S) subunits. They were the first REases to
      be discovered and purified, but unlike the enormously useful Type II REases, they have yet to
      find a place in the enzymatic toolbox of molecular biologists. Type I enzymes have been
      difficult to characterize, but this is changing as genome analysis reveals their genes, and
      methylome analysis reveals their recognition sequences. Several Type I REases have been
      studied in detail and what has been learned about them invites greater attention. In this
      article, we discuss aspects of the biochemistry, biology and regulation of Type I REases, and
      of the mechanisms that bacteriophages and plasmids have evolved to evade them. Type I REases
      have a remarkable ability to change sequence specificity by domain shuffling and
      rearrangements. We summarize the classic experiments and observations that led to this
      discovery, and we discuss how this ability depends on the modular organizations of the enzymes
      and of their S subunits. Finally, we describe examples of Type II restriction-modification
      systems that have features in common with Type I enzymes, with emphasis on the varied Type IIG
      enzymes.
AU  - Loenen WA
AU  - Dryden DT
AU  - Raleigh EA
AU  - Wilson GG
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2014 42: 20-44.

PMID- 24141096
VI  - 42
DP  - 2014
TI  - Highlights of the DNA cutters: a short history of the restriction enzymes.
PG  - 3-19
AB  - In the early 1950's, 'host-controlled variation in bacterial viruses' was reported as a
      non-hereditary phenomenon: one cycle of viral growth on certain bacterial hosts affected the
      ability of progeny virus to grow on other hosts by either restricting or enlarging their host
      range. Unlike mutation, this change was reversible, and one cycle of growth in the previous
      host returned the virus to its original form. These simple observations heralded the discovery
      of the endonuclease and methyltransferase activities of what are now termed Type I, II, III
      and IV DNA restriction-modification systems. The Type II restriction enzymes (e.g. EcoRI) gave
      rise to recombinant DNA technology that has transformed molecular biology and medicine. This
      review traces the discovery of restriction enzymes and their continuing impact on molecular
      biology and medicine.
AU  - Loenen WA
AU  - Dryden DT
AU  - Raleigh EA
AU  - Wilson GG
AU  - Murray NE
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2014 42: 3-19.

PMID- 23990325
VI  - 42
DP  - 2014
TI  - The other face of restriction: modification-dependent enzymes.
PG  - 56-69
AB  - The 1952 observation of host-induced non-hereditary variation in bacteriophages by Salvador
      Luria and Mary Human led to the discovery in the 1960s of modifying enzymes that glucosylate
      hydroxymethylcytosine in T-even phages and of genes encoding corresponding host activities
      that restrict non-glucosylated phage DNA: rglA and rglB (restricts glucoseless phage). In the
      1980's, appreciation of the biological scope of these activities was dramatically expanded
      with the demonstration that plant and animal DNA was also sensitive to restriction in cloning
      experiments. The rgl genes were renamed mcrA and mcrBC (modified cytosine restriction). The
      new class of modification-dependent restriction enzymes was named Type IV, as distinct from
      the familiar modification-blocked Types I-III. A third Escherichia coli enzyme, mrr (modified
      DNA rejection and restriction) recognizes both methylcytosine and methyladenine. In recent
      years, the universe of modification-dependent enzymes has expanded greatly. Technical advances
      allow use of Type IV enzymes to study epigenetic mechanisms in mammals and plants. Type IV
      enzymes recognize modified DNA with low sequence selectivity and have emerged many times
      independently during evolution. Here, we review biochemical and structural data on these
      proteins, the resurgent interest in Type IV enzymes as tools for epigenetic research and the
      evolutionary pressures on these systems.
AU  - Loenen WA
AU  - Raleigh EA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2014 42: 56-69.

PMID- 14654681
VI  - 31
DP  - 2003
TI  - Tracking EcoKI and DNA fifty years on: a golden story full of surprises.
PG  - 7059-7069
AB  - 1953 was a historical year for biology, as it marked the birth of the DNA helix, but also a
      report by Bertani and Weigle on 'a barrier to infection'
      of bacteriophage lambda in its natural host, Escherichia coli K-12, that
      could be lifted by 'host-controlled variation' of the virus. This paper
      lay dormant till Nobel laureate Arber and PhD student Dussoix showed that
      the lambda DNA was rejected and degraded upon infection of different
      bacterial hosts, unless it carried host-specific modification of that DNA,
      thus laying the foundations for the phenomenon of restriction and
      modification (R-M). The restriction enzyme of E.coli K-12, EcoKI, was
      purified in 1968 and required S-adenosylmethionine (AdoMet) and ATP as
      cofactors. By the end of the decade there was substantial evidence for a
      chromosomal locus hsdK with three genes encoding restriction (R),
      modification (M) and specificity (S) subunits that assembled into a large
      complex of >400 kDa. The 1970s brought the message that EcoKI cut away
      from its DNA recognition target, to which site the enzyme remained bound
      while translocating the DNA past itself, with concomitant ATP hydrolysis
      and subsequent double-strand nicks. This translocation event created
      clearly visible DNA loops in the electron microscope. EcoKI became the
      archetypal Type I R-M enzyme with curious DNA translocating properties
      reminiscent of helicases, recognizing the bipartite asymmetric site
      AAC(N6)GTGC. Cloning of the hsdK locus in 1976 facilitated molecular
      understanding of this sophisticated R-M complex and in an elegant 'pas de
      deux' Murray and Dryden constructed the present model based on a large
      body of experimental data plus bioinformatics. This review celebrates the
      golden anniversary of EcoKI and ends with the exciting progress on the
      vital issue of restriction alleviation after DNA damage, also first
      reported in 1953, which involves intricate control of R subunit activity
      by the bacterial proteasome ClpXP, important results that will keep
      scientists on the EcoKI track for another 50 years to come.
AU  - Loenen WAM
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2003 31: 7059-7069.

PMID- 3323532
VI  - 198
DP  - 1987
TI  - Organization and sequence of the hsd genes of Escherichia coli K12.
PG  - 159-170
AB  - The nucleotide sequence of the hsdR and M genes, together with that for hsdS
      comprises an 8400 base segment spanning the entire hsd region of Escherichia
      coli K-12.  The three hsd genes are transcribed in the same direction, but from
      two promoters.  hsdR and hsdM are separated by 492 base-pairs, whereas the
      termination codon of hsdM overlaps the initiation codon of hsdS.  pres precedes
      hsdR, and our data indicate a transcription termination signal in the interval
      between hsdR and -mod, as expected if transcription of hsdM and S is dependent
      on pmod.  Transcription from pres is not influenced by the products of the hsdM
      and S genes, and the mechanism whereby restriction is prevented when the hsd
      region is transferred to a modification-deficient cell remains to be
      elucidated.  A segment of the predicted amino acid sequence of the M
      polypeptide shares homology with a variety of adenine methylases and may
      identify part of the active site for methylation of specific adenine residues.
      The R polypeptide shows homology with a variety of ATPases, and pronounced
      regions of alpha-helical structure are predicted, one of which is amphipathic.
AU  - Loenen WAM
AU  - Daniel AS
AU  - Braymer HD
AU  - Murray NE
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1987 198: 159-170.

PMID- 8577256
VI  - 16
DP  - 1995
TI  - Heterogeneous endolysins in Listeria monocytogenes bacteriophages: a new class of enzymes and evidence for conserved holin genes within the siphoviral lysis cassettes.
PG  - 1231-1241
AB  - Listeria monocytogenes bacteriophages A118, A500 and A511 are members of three distinct phage
      groups with characteristic host ranges. Their endolysin (ply) genes were cloned and expressed
      in Escherichia coli as demonstrated by the conferred lytic phenotype when colonies of
      recombinant cells were overlaid with a lawn of Listeria cells. The nucleotide sequences of the
      cloned DNA fragments were determined and the individual enzymes (PLY118, 30.8 kDa; PLY500,
      33.4 kDa; PLY511, 36.5 kDa) were shown to have varying degrees of homology within their
      N-terminal or C-terminal domains. Transcriptional analysis revealed them to be 'late' genes
      with transcription beginning 15-20 min post-infection. The enzymes were overexpressed and
      partially purified and their individual specificities examined. When applied exogenously, the
      lysins induced rapid lysis of Listeria strains from all species but generally did not affect
      other bacteria. Using hydrolysis of purified listerial cell walls, PLY511 was characterized as
      an N-acetylmuramoyl-L-alanine amidase (EC 3.5.1.28) and shows homology in its N-terminal
      domain to other enzymes of this type. In contrast, PLY118 and PLY500 were shown to represent a
      new class of cell wall lytic enzymes which cleave between the L-alanine and D-glutamate
      residues of listerial peptidoglycan; these were designated as L-alanoyl-D-glutamate
      peptidases. These two enzymes share homology in the N-terminal domain which we propose
      determines hydrolytic specificity. Highly conserved holin (hol) gene sequences are present
      upstream of ply118 and ply500. They encode proteins of structural similarity to the product of
      phage lambda gene S, and are predicted to be membrane proteins which form pores to allow
      access of the lysins to their peptidoglycan substrates. This arrangement of conserved holin
      genes with downstream lysin genes among the siphoviral lysis cassettes explains why the
      cytoplasmic endolysins alone are not lethal, since they require a specific transport function
      across the cell membrane.
AU  - Loessner MJ
AU  - Wendlinger G
AU  - Scherer S
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1995 16: 1231-1241.

PMID- 25323714
VI  - 2
DP  - 2014
TI  - Genome Sequence of a Tigecycline-Resistant Clinical Isolate of Acinetobacter baumannii Strain AB031 Obtained from a Bloodstream Infection.
PG  - e01036-14
AB  - We report here the 3.8-Mbp genome sequence of a blood isolate of Acinetobacter baumannii
      strain AB031.
AU  - Loewen PC
AU  - Alsaadi Y
AU  - Fernando D
AU  - Kumar A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01036-14.

PMID- 25323713
VI  - 2
DP  - 2014
TI  - Genome Sequence of an Extremely Drug-Resistant Clinical Isolate of Acinetobacter  baumannii Strain AB030.
PG  - e01035-14
AB  - We report the 4.3-Mbp genome sequence of a blood isolate of Acinetobacter baumannii strain
      AB030.
AU  - Loewen PC
AU  - Alsaadi Y
AU  - Fernando D
AU  - Kumar A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01035-14.

PMID- 24812222
VI  - 2
DP  - 2014
TI  - Genome Sequence of Pseudomonas brassicacearum DF41.
PG  - e00390-14
AB  - Pseudomonas brassicacearum DF41, a Gram-negative soil bacterium, is able to suppress the
      fungal pathogen Sclerotinia sclerotiorum through a process known as
      biological control. Here, we present a 6.8-Mb assembly of its genome, which is
      the second fully assembled genome of a P. brassicacearum strain.
AU  - Loewen PC
AU  - Switala J
AU  - Fernando WG
AU  - de Kievit T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00390-14.

PMID- 25035328
VI  - 2
DP  - 2014
TI  - Genome Sequence of Pseudomonas chlororaphis Strain PA23.
PG  - e00689-14
AB  - Pseudomonas chlororaphis strain PA23 is a plant-beneficial bacterium that is able to suppress
      disease caused by the fungal pathogen Sclerotinia sclerotiorum
      through a process known as biological control. Here we present a 7.1-Mb assembly
      of the PA23 genome.
AU  - Loewen PC
AU  - Villenueva J
AU  - Fernando WG
AU  - de Kievit T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00689-14.

PMID- 25838493
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Pseudomonas sp. nov. H2.
PG  - e00241-15
AB  - We report the draft genome sequence of Pseudomonas sp. nov. H2, isolated from creek sediment
      in Moscow, ID, USA. The strain is most closely related to
      Pseudomonas putida. However, it has a slightly smaller genome that appears to
      have been impacted by horizontal gene transfer and poorly maintains IncP-1
      plasmids.
AU  - Loftie-Eaton W
AU  - Suzuki H
AU  - Bashford K
AU  - Heuer H
AU  - Stragier P
AU  - De Vos P
AU  - Settles ML
AU  - Top EM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00241-15.

PMID- 15729342
VI  - 433
DP  - 2005
TI  - The genome of the protist parasite Entamoeba histolytica.
PG  - 865-868
AB  - Entamoeba histolytica is an intestinal parasite and the causative agent of amoebiasis, which
      is a significant source of morbidity and mortality in developing countries. Here we present
      the genome of E. histolytica, which reveals a variety of metabolic adaptations shared with two
      other amitochondrial protist pathogens: Giardia lamblia and Trichomonas vaginalis. These
      adaptations include reduction or elimination of most mitochondrial metabolic pathways and the
      use of oxidative stress enzymes generally associated with anaerobic prokaryotes. Phylogenomic
      analysis identifies evidence for lateral gene transfer of bacterial genes into the E.
      histolytica genome, the effects of which centre on expanding aspects of E. histolytica's
      metabolic repertoire. The presence of these genes and the potential for novel metabolic
      pathways in E. histolytica may allow for the development of new chemotherapeutic agents. The
      genome encodes a large number of novel receptor kinases and contains expansions of a variety
      of gene families, including those associated with virulence. Additional genome features
      include an abundance of tandemly repeated transfer-RNA-containing arrays, which may have a
      structural function in the genome. Analysis of the genome provides new insights into the
      workings and genome evolution of a major human pathogen.
AU  - Loftus B et al
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2005 433: 865-868.

PMID- 8568886
VI  - 255
DP  - 1996
TI  - Intron-encoded endonuclease I-TevII binds across the minor groove and induces two distinct conformational changes in its DNA substrate.
PG  - 412-424
AB  - I-TevII is the homing endonuclease encoded by the sunY intron of bacteriophage T4.  The enzyme
      cleaves an intronless sunY gene near the exon I-exon II junction, thereby initiating intron
      homing into its cognate intronless allele.  Specifically, I-TevII cleaves its DNA target 13 to
      15 nucleotides downstream of the sunY intron insertion site, generating 2-nt 3'-OH
      extensions.  Here, we present evidence that I-TevII makes predominantly minor groove contacts
      in two regions of its recognition sequence, as does I-TevI, the other homing endonuclease
      encoded by phage T4.  Following cleavage, I-TevII was shown to remain bound to one of its DNA
      products, suggesting possible additional roles for the endonuclease in the mobility process.
      Interestingly, two distinct conformational changes were detected by gel analysis in the DNA
      substrate following binding by I-TevII, one occurring in the absence of Mg2+, the second being
      dependent on the presence of Mg2+.  The Mg2+-induced distortion accompanies a nick in one
      strand, and may serve to bring the cleavage site on the other strand into proximity with the
      catalytic domain of the protein.
AU  - Loizos N
AU  - Silva GH
AU  - Belfort M
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1996 255: 412-424.

PMID- 7991569
VI  - 91
DP  - 1994
TI  - Evolution of mobile group I introns: recognition of intron sequences by an intron-encoded endonuclease.
PG  - 11983-11987
AB  - Mobile group I introns are hypothesized to have arisen after invasion by endonuclease-encoding
      open reading frames (ORFs) which mediate their mobility. Consistent with an endonuclease-ORF
      invasion event, we report similarity between exon junction sequences (the recognition site for
      the mobility endonuclease) and intron sequences flanking the endonuclease ORF in the sunY gene
      of phage T4. Furthermore, we have demonstrated the ability of the intron-encoded endonuclease
      to recognize and cleave these intron sequences when present in fused form in synthetic
      constructs. These observations and accompanying splicing data are consistent with models in
      which the invading endonuclease ORF is provided safe haven within a splicing element. In turn
      the intron is afforded immunity to the endonuclease product, which imparts mobility to the
      intron.
AU  - Loizos N
AU  - Tillier ERM
AU  - Belfort M
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1994 91: 11983-11987.

PMID- 19542273
VI  - 191
DP  - 2009
TI  - Genome sequence of the emerging pathogen Helicobacter canadensis.
PG  - 5566-5567
AB  - We determined the genome sequence of the type strain of Helicobacter
      canadensis, an emerging human pathogen with diverse animal reservoirs.
      Potential virulence determinants carried by the genome include systems for
      N-linked glycosylation and capsular export. A protein-based phylogenetic
      analysis places H. canadensis close to Wolinella succinogenes.
AU  - Loman NJ
AU  - Snyder LA
AU  - Linton JD
AU  - Langdon R
AU  - Lawson AJ
AU  - Weinstock GM
AU  - Wren BW
AU  - Pallen MJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2009 191: 5566-5567.

PMID- 29348329
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of 510 Listeria monocytogenes Strains from Food Isolates and Human Listeriosis Cases from Northern Italy.
PG  - e01276-17
AB  - Listeriosis outbreaks are frequently multistate/multicountry outbreaks, underlining the
      importance of molecular typing data for several diverse and
      well-characterized isolates. Large-scale whole-genome sequencing studies on
      Listeria monocytogenes isolates from non-U.S. locations have been limited.
      Herein, we describe the draft genome sequences of 510 L. monocytogenes isolates
      from northern Italy from different sources.
AU  - Lomonaco S
AU  - Gallina S
AU  - Filipello V
AU  - Sanchez LM
AU  - Kastanis GJ
AU  - Allard M
AU  - Brown E
AU  - Amato E
AU  - Pontello M
AU  - Decastelli L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01276-17.

PMID- 6247632
VI  - 44
DP  - 1980
TI  - Genetics and Molecular Biology of Streptomyces Bacteriophages.
PG  - 206-229
AB  - The streptomycetes are genetically among the most tractable of bacteria.  In
      the best-studied strain, Streptomyces coelicolor A3, chromosome mapping is
      straightforward, and a single circular linkage map of more than 100 markers has
      been established.  Extremely efficient protoplast fusion can be induced by
      polyethylene glycol.  Plasmids have been demonstrated both physically and
      genetically, and some of them are self-transmissible sex factors having a
      variety of interactions with the host chromosome.  Reintroduction
      (transformation) of isolated plasmid deoxyribonucleic acid (DNA) into
      protoplasts occurs at high frequency in the presence of polyethylene glycol.
      These features are important in the study of several special characteristics of
      streptomycetes, in particular, their remarkable status as antibiotic producers
      and their morphological complexity.  Much greater progress will be possible in
      these investigations when the techniques already available are supplemented by
      gene cloning and transposon genetics and by systems for fine-structure mapping.
      Among the important requirements for the development and optimum exploitation
      of such techniques is an understanding of Streptomyces phages, particularly of
      their genetics and DNA. About a decade ago it was possible for major reviews of
      S. coelicolor genetics and Streptomyces phages to be completely independent of
      each other; the potential benefits of using a genetically studied host in phage
      studies, and vice versa, were unfulfilled.  More recently, considerable
      advances have been made in the genetic and physical analysis of these phages
      and their interactions with their hosts.  Thus, when temperate phages acting on
      S. coelicolor A3 were isolated, it became possible to initiate studies of such
      problems as the relationship between phages and differentiated bacteria,
      comparison with model eubacterial phage-host systems, the genetic basis of
      lysogenization in streptomycetes, the structure and function of the genomes of
      Streptomyces phages, and the development of Streptomyces phages as DNA-cloning
      vectors.  Both temperate and virulent phages have been instrumental in
      understanding Streptomyces host-controlled restriction and modification (RM)
      systems, and they have also helped in various aspects of the genetic analysis
      of streptomycetes. The most extensive studies have been of the temperate phage
      UC31, and we will focus on this phage as a main theme, with occasional
      variations provided by observations on some other phages.  We shall then
      consider these and other results in the context of the use of phages as vectors
      for the introduction of particular DNA segments into streptomycetes, and
      finally review interactions between the phages and host-controlled RM systems.
AU  - Lomovskaya ND
AU  - Chater KF
AU  - Mkrtumian NM
PT  - Journal Article
TA  - Microbiol. Rev.
JT  - Microbiol. Rev.
SO  - Microbiol. Rev. 1980 44: 206-229.

PMID- 21622746
VI  - 193
DP  - 2011
TI  - Genome sequence of Pseudomonas sp. S9, an extracellular arylsulfatase producing bacterium isolated from the mangrove soil.
PG  - 4041
AB  - Pseudomonas sp. S9 was originally isolated from the mangrove soil in Xiamen, China. It is an
      aerobic bacterium which shows extracellular
      arylsulfatase activity. Here, we describe the 4.8 Mb draft genome sequence
      of Pseudomonas sp. S9 which exhibits novel cysteine-type sulfatases.
AU  - Long M
AU  - Ruan L
AU  - Yu Z
AU  - Xu X
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4041.

PMID- 29122881
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequencing of a Human Clinical Isolate of emm28 Streptococcus pyogenes Causing Necrotizing Fasciitis Acquired Contemporaneously with Hurricane   Harvey.
PG  - e01269-17
AB  - We discovered an emm28 Streptococcus pyogenes isolate causing necrotizing fasciitis in a
      patient exposed to the floodwaters of Hurricane Harvey in the
      Houston, TX, metropolitan area in August 2017. The Oxford Nanopore MinION
      instrument provided sufficient genome sequence data within 1 h of beginning
      sequencing to close the genome.
AU  - Long SW
AU  - Kachroo P
AU  - Musser JM
AU  - Olsen RJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01269-17.

PMID- 29051239
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequencing of a Human Clinical Isolate of the Novel Species Klebsiella quasivariicola sp. nov.
PG  - e01057-17
AB  - In a study of 1,777 Klebsiella strains, we discovered KPN1705, which was distinct from all
      recognized Klebsiella spp. We closed the genome of strain KPN1705 using
      a hybrid of Illumina short-read and Oxford Nanopore long-read technologies. For
      this novel species, we propose the name Klebsiella quasivariicola sp. nov.
AU  - Long SW
AU  - Linson SE
AU  - Ojeda SM
AU  - Cantu C
AU  - Davis JJ
AU  - Brettin T
AU  - Olsen RJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01057-17.

PMID- 28512093
VI  - 8
DP  - 2017
TI  - Population Genomic Analysis of 1,777 Extended-Spectrum Beta-Lactamase-Producing Klebsiella pneumoniae Isolates, Houston, Texas: Unexpected Abundance of Clonal Group 307.
PG  - e00489-17
AB  - Klebsiella pneumoniae is a major human pathogen responsible for high morbidity and mortality
      rates. The emergence and spread of strains resistant to multiple
      antimicrobial agents and documented large nosocomial outbreaks are especially
      concerning. To develop new therapeutic strategies for K. pneumoniae, it is
      imperative to understand the population genomic structure of strains causing
      human infections. To address this knowledge gap, we sequenced the genomes of
      1,777 extended-spectrum beta-lactamase-producing K. pneumoniae strains cultured
      from patients in the 2,000-bed Houston Methodist Hospital system between
      September 2011 and May 2015, representing a comprehensive, population-based
      strain sample. Strains of largely uncharacterized clonal group 307 (CG307) caused
      more infections than those of well-studied epidemic CG258. Strains varied
      markedly in gene content and had an extensive array of small and very large
      plasmids, often containing antimicrobial resistance genes. Some patients with
      multiple strains cultured over time were infected with genetically distinct
      clones. We identified 15 strains expressing the New Delhi metallo-beta-lactamase
      1 (NDM-1) enzyme that confers broad resistance to nearly all beta-lactam
      antibiotics. Transcriptome sequencing analysis of 10 phylogenetically diverse
      strains showed that the global transcriptome of each strain was unique and highly
      variable. Experimental mouse infection provided new information about
      immunological parameters of host-pathogen interaction. We exploited the large
      data set to develop whole-genome sequence-based classifiers that accurately
      predict clinical antimicrobial resistance for 12 of the 16 antibiotics tested. We
      conclude that analysis of large, comprehensive, population-based strain samples
      can assist understanding of the molecular diversity of these organisms and
      contribute to enhanced translational research.IMPORTANCEKlebsiella pneumoniae
      causes human infections that are increasingly difficult to treat because many
      strains are resistant to multiple antibiotics. Clonal group 258 (CG258) organisms
      have caused outbreaks in health care settings worldwide. Using a comprehensive
      population-based sample of extended-spectrum beta-lactamase (ESBL)-producing K.
      pneumoniae strains, we show that a relatively uncommon clonal type, CG307, caused
      the plurality of ESBL-producing K. pneumoniae infections in our patients. We
      discovered that CG307 strains have been abundant in Houston for many years. As
      assessed by experimental mouse infection, CG307 strains were as virulent as
      pandemic CG258 strains. Our results may portend the emergence of an especially
      successful clonal group of antibiotic-resistant K. pneumoniae.
AU  - Long SW
AU  - Olsen RJ
AU  - Eagar TN
AU  - Beres SB
AU  - Zhao P
AU  - Davis JJ
AU  - Brettin T
AU  - Xia F
AU  - Musser JM
PT  - Journal Article
TA  - MBio
JT  - MBio
SO  - MBio 2017 8: e00489-17.

PMID- 2001353
VI  - 30
DP  - 1991
TI  - Characterization of DNA metabolizing enzymes in situ following polyacrylamide gel electrophoresis.
PG  - 2655-2664
AB  - We have detected the in situ activities of DNA glycosylase, endonuclease, DNA
      polymerase, and DNA ligase using a novel polyacrylamide activity gel
      electrophoresis procedure.  DNA metabolizing enzymes were resolved through
      either native or SDS-polyacrylamide gels containing defined 32P-labeled
      oligonucleotides annealed to M13 DNA.  After electrophoresis, these enzymes
      catalyzed in situ reactions and their [32P]DNA products were resolved from the
      gel by a second dimension of electrophoresis through a denaturing DNA
      sequencing gel.  Detection of modified (degraded or elongated) oligonucleotide
      chains was used to locate various enzyme activities.  The catalytic and
      physical properties of Novikoff hepatoma DNA polymerase beta were found to be
      similar under both in vitro and in situ conditions.  With 3'-terminally matched
      and mismatched [32P]DNA substrates in the same activity gel, DNA polymerase
      and/or 3' to 5' exonuclease activities of Escherichia coli DNA polymerase I
      (large fragment), DNA polymerase III (holoenzyme), and exonuclease III were
      detected and characterized.  In addition, use of matched and mismatched DNA
      primers permitted the uncoupling of mismatch excision and chain extension
      steps.  Activities first detected in nondenaturing activity gels as either
      multifunctional or multimeric enzymes were also identified in denaturing
      activity gels, and assignment of activities to specific polypeptides suggested
      subunit composition.  Furthermore, DNA substrates cast within polyacrylamide
      gels were successfully modified by the exogenous enzymes polynucleotide kinase
      and alkaline phosphatase before and after in situ detection of E. coli DNA
      ligase activity, respectively.  Several restriction endonucleases and the
      tripeptide (Lys-Trp-Lys), which acts as an apurinic/apyrimidinic endonuclease,
      were able to diffuse into gels and modify DNA.  This ability to create
      intermediate substrates within activity gels could prove extremely useful in
      delineating the steps of DNA replication and repair pathways.
AU  - Longley MJ
AU  - Mosbaugh DW
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1991 30: 2655-2664.

PMID- 26184934
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Streptococcus pyogenes emm28 Clinical Isolate M28PF1, Responsible for a Puerperal Fever.
PG  - e00750-15
AB  - We report the sequence of the Streptococcus pyogenes emm28 strain M28PF1, isolated from a
      patient with postpartum endometritis. The M28 protein is smaller
      than that of MGAS6180 (NC_007296.1). Furthermore, the 1,896,976-bp-long
      chromosome presents, compared to that of MGAS6180, an inversion between the two
      comX genes.
AU  - Longo M
AU  - De Jode M
AU  - Plainvert C
AU  - Weckel A
AU  - Hua A
AU  - Chateau A
AU  - Glaser P
AU  - Poyart C
AU  - Fouet A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00750-15.

PMID- 26450725
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Coriobacteriaceae Strain 68-1-3, a Novel Mucus-Degrading Isolate from the Swine Intestinal Tract.
PG  - e01143-15
AB  - A novel Coriobacteriaceae bacterium (strain 68-1-3) was isolated from the ileum of the swine
      intestinal tract using a selective mucus-based medium. Here we present the finished genome
      sequence for the swine commensal, totaling 1.97 Mb in size.
AU  - Looft T
AU  - Bayles DO
AU  - Alt DP
AU  - Stanton TB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01143-15.

PMID- 2684765
VI  - 80
DP  - 1989
TI  - Nucleotide sequence of the FokI restriction-modification system:  separate strand-specificity domains in the methyltransferase.
PG  - 193-208
AB  - The genes for FokI, a type-IIS restriction-modification system from
      Flavobacterium okeanokoites (asymmetric recognition sequence:
      5'-GGATG/3'-CCTAC), were cloned into Escherichia coli.  Recombinants carrying
      the fokIR and fokIM genes were found to modify their DNA completely, and to
      restrict lambdoid phages weakly.  The nucleotide sequences of the genes were
      determined, and the probable start codons were confirmed by amino acid
      sequencing.  The FokI endonuclease (R.FokI) and methyltransferase (M.FokI) are
      encoded by single, adjacent genes, aligned in the same orientation, in the
      order M then R.  The genes are large by the standards of type-II systems, 1.9
      kb for the M gene, and 1.7 kb for the R gene.  Preceding each gene is a pair of
      FokI recognition sites; it is conceivable that interactions between the sites
      and the FokI proteins could regulate expression of the genes.
AU  - Looney MC
AU  - Moran LS
AU  - Jack WE
AU  - Feehery GR
AU  - Benner JS
AU  - Slatko BE
AU  - Wilson GG
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1989 80: 193-208.

PMID- 11787061
VI  - 84
DP  - 2002
TI  - Differential maintenance and de novo methylating activity by three DNA methyltransferases in aging and immortalized fibroblasts.
PG  - 324-334
AB  - Genomic methylation, which influences many cellular processes such as gene expression and
      chromatin organization, generally declines with
      cellular senescence although some genes undergo paradoxical
      hypermethylation during cellular aging and immortalization. To explore
      potential mechanisms for this process, we analyzed the methylating
      activity of three DNA methyltransferases (Dnmts) in aging and
      immortalized WI-38 fibroblasts. Overall maintenance methylating
      activity by the Dnmts greatly decreased during cellular senescence. In
      immortalized WI-38 cells, maintenance methylating activity was similar
      to that of normal young cells. Combined de novo methylation activity of
      the Dnmts initially decreased but later increased as WI-38 cells aged
      and was strikingly elevated in immortalized cells. To further elucidate
      the mechanisms for changes in DNA methylation in aging and immortalized
      cells, the individual Dnmts were separated and individually assessed
      for maintenance and de novo methylating activity. We resolved three
      Dnmt fractions, one of which was the major maintenance
      methyltransferase, Dnmt1, which declined steadily in activity with
      cellular senescence and immortalization. However, a more basic Dnmt,
      which has significant de novo methylating activity, increased markedly
      in activity in aging and immortalized cells. We have identified this
      methyltransferase as Dnmt3b which has an important role in neoplastic
      transformation but its role in cellular senescence and immortalization
      has not previously been reported. An acidic Dnmt we isolated also had
      increased de novo methylating activity in senescent and immortalized
      WI-38 cells. These studies indicate that reduced genome-wide
      methylation in aging cells may be attributed to attenuated Dnmt1
      activity but that regional or gene-localized hypermethylation in aging
      and immortalized cells may be linked to increased de novo methylation
      by Dnmts other than the maintenance methyltransferase.
AU  - Lopatina N
AU  - Haskell JF
AU  - Andrews LG
AU  - Poole JC
AU  - Saldanha S
AU  - Tollefsbol T
PT  - Journal Article
TA  - J. Cell. Biochem.
JT  - J. Cell. Biochem.
SO  - J. Cell. Biochem. 2002 84: 324-334.

PMID- 3888295
VI  - 50
DP  - 1985
TI  - Determination of the recognition site for adenine-specific methylase of Shigella sonnei 47 by hydrazinolysis of DNA, followed by separation of the purine oligonucleotides by thin-layer chromatography on DEAE-cellulose.
PG  - 495-502
AB  - A method has been developed for the separation of oligopurine units according
      to length and composition by two-dimensional thin-layer chromatography on
      plates with DEAE-cellulose, permitting a comparative analysis of the content of
      various purine isopliths in DNA of different origin.  In the case of the
      analysis of methylated DNA, the method permits a comparison of the substrate
      specificity of various enzymes of methylation of the adenine residues in DNA.
      In conjunction with enzymatic treatment of labeled methylated isopliths, the
      method permits determination of the methylatable sequence and in a number of
      cases an ascertainment of the recognition site for adenine-specific methylase
      as a whole.  The proposed method was used to establish the fact that the
      methylase SsoI recognizes the sequence 5' ...G-*A-A-T-T-C...3' and methylates
      the adenine residue closest to its 5'-end.
AU  - Lopatina NG
AU  - Kirnos MD
AU  - Suchkov SV
AU  - Vanyushin BF
AU  - Nikolskaya II
AU  - Debov SS
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1985 50: 495-502.

PMID- 3056530
VI  - 53
DP  - 1988
TI  - Cytosine DNA-methylase SsoII from Shigella sonnei 47 cells.
PG  - 1265-1269
AB  - Shigella sonnei 47 cells were found to contain DNA-methylase SsoII which is a
      modifying component of the system of host specificity of SsoII.  The
      recognition sequence (RS) of methylase SsoII is represented by a five-member
      palindromic structure -5'...CCNGG...3'- with a degenerate central nucleotide.
      Modification of SsoII affords protection of acceptor DNA not only from SsoII
      type restriction, but also from other restrictases, e.g., EcoRII having an
      analogous RS but with a less degenerate central nucleotide pair.  A simple and
      rapid procedure for isolation and purification of DNA-methylase SsoII, which
      employs hydrophobic chromatography on phenyl-Sepharose, has been developed.
      The enzyme preparation does not contain trace amounts of specific and
      nonspecific endonucleases and keeps stable on storage in 30% glycerol over a
      period of one year.
AU  - Lopatina NG
AU  - Lopareva EN
AU  - Posypanova AM
AU  - Nikolskaya A
AU  - Debov SS
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1988 53: 1265-1269.

PMID- 354911
VI  - 240
DP  - 1978
TI  - Presence of 2 DNA-methylases of cytosine in Escherichia coli CK cells.
PG  - 1475-1477
AB  - 
AU  - Lopatina NG
AU  - Nikolskaya II
AU  - Buryanov YI
AU  - Debov SS
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1978 240: 1475-1477.

PMID- 7025443
VI  - 27
DP  - 1981
TI  - Determination of the recognition sites of adenine DNA-methylases from Escherichia coli CK.
PG  - 220-223
AB  - DNA-methylases from a strain of E. coli CK were studied.  Three adenine methylases were found
      in the strain studied, which were eluted by 0.16M, 0.23M and 0.7M NaCl in phosphocellulose
      P-11 chromatography.  According to this, the enzymes were designated as DM-A16, DM-A23 and
      DM-A-70.  Indirect data on the presence of adenine specific methylases dissimilar in their
      recognition sites in cells of E. coli CK were obtained using the test of additional
      methylation modified by I.I. Nikolskaya.  These conclusions were confirmed, when the
      dinucleotide sequence was determined in the recognition site using DM-A23 and DM-A70.  The
      methylase DM-A23 was shown to recognize the dinucleotide sequence 5'...A-G...3'.
AU  - Lopatina NG
AU  - Nikolskaya II
AU  - Sverdiov ED
AU  - Debov SS
PT  - Journal Article
TA  - Vopr. Med. Khim.
JT  - Vopr. Med. Khim.
SO  - Vopr. Med. Khim. 1981 27: 220-223.

PMID- 3907723
VI  - 50
DP  - 1985
TI  - Site-specificity of DNA methylases from Shigella sonnei 47 cells.
PG  - 1694-1701
AB  - A complex approach involving isoplith analysis, enzymatic treatment of methylated isopliths
      and computer analysis of experimental data has been used to determine site specificity of six
      methylases from Shigella sonnei 47 cells termed according to their base specificity and pI as
      MC4.2, MC5.3, MC6.2, MC7.4, MC8.4 and MA9.5.  It has been found that the recognition site of
      MA9.5 is a palindrome of the 5' ...GAATTC...3' type and that this enzyme is an isomethylomer
      of M.EcoRI.  It has been demonstrated for the first time for methylases that the recognition
      site of MC4.2 is represented by a non-symmetrical four-member sequence, 5'...NCCCCN...3'
      characterized by unique blocking of cytosines.  MC8.4 possesses a broad specificity of
      substrate recognition and methylates the cytosine residue within the non-symmetrical unique
      sequence 5'...N(C/Pu) CCN...3', whose 5'-terminal base is depleted in three nucleotides.
      MC5.3 methylates the 3'-terminal cytosine residue within the composition of the
      pentanucleotide palindrome recognition site, 5'...CCNGG...3' MC6.2 and MC7.4 possess
      identical pentanucleotide recognition sites, 5'...(Py)CNG(Pu)...3', but are distinguished by
      pI.  The latter finding has been shown for the first time for different methylases within one
      strain.
AU  - Lopatina NG
AU  - Suchkov SV
AU  - Kulikov SM
AU  - Nikolskaya II
AU  - Debov SS
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1985 50: 1694-1701.

PMID- 22792073
VI  - 8
DP  - 2012
TI  - Comparative Genomics of Plant-Associated Pseudomonas spp.: Insights into Diversity and Inheritance of Traits Involved in Multitrophic Interactions.
PG  - E1002784
AB  - We provide here a comparative genome analysis of ten strains within the
      Pseudomonas fluorescens group including seven new genomic sequences. These
      strains exhibit a diverse spectrum of traits involved in biological control and
      other multitrophic interactions with plants, microbes, and insects. Multilocus
      sequence analysis placed the strains in three sub-clades, which was reinforced by
      high levels of synteny, size of core genomes, and relatedness of orthologous
      genes between strains within a sub-clade. The heterogeneity of the P. fluorescens
      group was reflected in the large size of its pan-genome, which makes up
      approximately 54% of the pan-genome of the genus as a whole, and a core genome
      representing only 45-52% of the genome of any individual strain. We discovered
      genes for traits that were not known previously in the strains, including genes
      for the biosynthesis of the siderophores achromobactin and pseudomonine and the
      antibiotic 2-hexyl-5-propyl-alkylresorcinol; novel bacteriocins; type II, III,
      and VI secretion systems; and insect toxins. Certain gene clusters, such as those
      for two type III secretion systems, are present only in specific sub-clades,
      suggesting vertical inheritance. Almost all of the genes associated with
      multitrophic interactions map to genomic regions present in only a subset of the
      strains or unique to a specific strain. To explore the evolutionary origin of
      these genes, we mapped their distributions relative to the locations of mobile
      genetic elements and repetitive extragenic palindromic (REP) elements in each
      genome. The mobile genetic elements and many strain-specific genes fall into
      regions devoid of REP elements (i.e., REP deserts) and regions displaying
      atypical tri-nucleotide composition, possibly indicating relatively recent
      acquisition of these loci. Collectively, the results of this study highlight the
      enormous heterogeneity of the P. fluorescens group and the importance of the
      variable genome in tailoring individual strains to their specific lifestyles and
      functional repertoire.
AU  - Loper JE et al
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2012 8: E1002784.

PMID- 29674552
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Burkholderia gladioli Coa14, a Bacterium with Petroleum  Bioremediation Potential Isolated from Coari Lake, Amazonas, Brazil.
PG  - e00301-18
AB  - Burkholderia gladioli Coa14 is a bacterium isolated from water collected from Coari Lake
      (Amazonas, Brazil) that shows a capacity for survival in a medium
      containing only oil as a carbon source. Here, we report its draft genome
      sequence, highlighting some genes involved with petroleum derivative degradation.
AU  - Lopes EF
AU  - Da Costa JG
AU  - Wolf IR
AU  - Lima JPA
AU  - Astolfi-Filho S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00301-18.

PMID- 28232432
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Bradyrhizobium elkanii TnphoA 33, a Producer of Polyhydroxyalkanoates.
PG  - e01502-16
AB  - The genus Bradyrhizobium comprises bacteria with the ability to form nitrogen-fixing symbioses
      with legumes. They are of great interest in
      agriculture, as well as for the production of biopolymers such as
      polyhydroxyalkanoates. Here, we report the draft genome assembly of
      Bradyrhizobium elkanii TnphoA 33 comprising 9 Mb, 1,124 contigs, and 9,418 open
      reading frames.
AU  - Lopes EM
AU  - Kishi LT
AU  - Fernandes CC
AU  - Paganelli FL
AU  - Alves LM
AU  - Lemos EG
AU  - de Souza JA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01502-16.

PMID- 22689248
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Corynebacterium pseudotuberculosis Strain Cp267, Isolated from a Llama.
PG  - 3567-3568
AB  - In this work we report the genome of Corynebacterium pseudotuberculosis strain 267, isolated
      from a llama. This pathogen is of great veterinary and economic
      importance, as it is the cause of caseous lymphadenitis in several livestock
      species around the world and causes significant losses due to the high cost of
      treatment.
AU  - Lopes T et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3567-3568.

PMID- 25977431
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Burkholderia andropogonis Type Strain ICMP2807, Isolated from Sorghum bicolor.
PG  - e00455-15
AB  - Here, we report the draft genome sequence of Burkholderia andropogonis ICMP2807,  a
      phytopathogenic bacterium isolated from Sorghum bicolor plants in the United
      States.
AU  - Lopes-Santos L
AU  - Castro DB
AU  - Ottoboni LM
AU  - Park D
AU  - Weir BS
AU  - Destefano SA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00455-15.

PMID- 29255573
VI  - 12
DP  - 2017
TI  - Draft genome sequence of Pseudomonas extremaustralis strain USBA-GBX 515 isolated from Superparamo soil samples in Colombian Andes.
PG  - 78
AB  - Here we present the physiological features of Pseudomonas extremaustralis strain  USBA-GBX-515
      (CMPUJU 515), isolated from soils in Superparamo ecosystems, > 4000
      m.a.s.l, in the northern Andes of South America, as well as the thorough analysis
      of the draft genome. Strain USBA-GBX-515 is a Gram-negative rod shaped bacterium
      of 1.0-3.0 mum x 0.5-1 mum, motile and unable to form spores, it grows
      aerobically and cells show one single flagellum. Several genetic indices, the
      phylogenetic analysis of the 16S rRNA gene sequence and the phenotypic
      characterization confirmed that USBA-GBX-515 is a member of Pseudomonas genus
      and, the similarity of the 16S rDNA sequence was 100% with P. extremaustralis
      strain CT14-3(T). The draft genome of P. extremaustralis strain USBA-GBX-515
      consisted of 6,143,638 Mb with a G + C content of 60.9 mol%. A total of 5665
      genes were predicted and of those, 5544 were protein coding genes and 121 were
      RNA genes. The distribution of genes into COG functional categories showed that
      most genes were classified in the category of amino acid transport and metabolism
      (10.5%) followed by transcription (8.4%) and signal transduction mechanisms
      (7.3%). We performed experimental analyses of the lipolytic activity and results
      showed activity mainly on short chain fatty acids. The genome analysis
      demonstrated the existence of two genes, lip515A and est515A, related to a
      triacylglycerol lipase and carboxylesterase, respectively. Ammonification genes
      were also observed, mainly nitrate reductase genes. Genes related with synthesis
      of poly-hydroxyalkanoates (PHAs), especially poly-hydroxybutyrates (PHBs), were
      detected. The phaABC and phbABC operons also appeared complete in the genome. P.
      extremaustralis strain USBA-GBX-515 conserves the same gene organization of the
      type strain CT14-3(T). We also thoroughly analyzed the potential for production
      of secondary metabolites finding close to 400 genes in 32 biosynthetic gene
      clusters involved in their production.
AU  - Lopez G
AU  - Diaz-Cardenas C
AU  - Shapiro N
AU  - Woyke T
AU  - Kyrpides NC
AU  - David AJ
AU  - Gonzalez LN
AU  - Restrepo S
AU  - Baena S
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 78.

PMID- 26966211
VI  - 4
DP  - 2016
TI  - Genome Sequences of Five Clinical Isolates of Klebsiella pneumoniae.
PG  - e00040-16
AB  - Klebsiella pneumoniae is a nosocomial pathogen of emerging importance and displays resistance
      to broad-spectrum antibiotics, such as carbapenems. Here, we
      report the genome sequences of five clinical K. pneumoniae isolates, four of
      which are carbapenem resistant. Carbapenem resistance is conferred by hydrolyzing
      class A beta-lactamases found adjacent to transposases.
AU  - Lopez LL
AU  - Rusconi B
AU  - Gildersleeve H
AU  - Qi C
AU  - McLaughlin M
AU  - Scheetz MH
AU  - Seshu J
AU  - Eppinger M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00040-16.

PMID- 27609928
VI  - 4
DP  - 2016
TI  - Genome Sequence of a Clinical Strain of Acinetobacter baumannii Belonging to the  ST79/PFGE-HUI-1 Clone Lacking the AdeABC (Resistance-Nodulation-Cell  Division-Type) Efflux Pump.
PG  - e00962-16
AB  - Increased expression of chromosomal genes for resistance-nodulation-cell division-type efflux
      systems plays a major role in the multidrug resistance of
      Acinetobacter baumannii Little is known about the genetic characteristics of
      clinical strains of Acinetobacter baumannii lacking the AdeABC pump. In this
      study, we sequenced the genome of clinical strain Ab421 GEIH-2010 (belonging to
      clone ST79/PFGE-HUI-1 from the GEIH-REIPI Ab. 2010 project) which lacks this
      efflux pump.
AU  - Lopez M
AU  - Alvarez-Fraga L
AU  - Gato E
AU  - Blasco L
AU  - Poza M
AU  - Fernandez-Garcia L
AU  - Bou G
AU  - Tomas M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00962-16.

PMID- 27795287
VI  - 4
DP  - 2016
TI  - Genomic Evolution of Two Acinetobacter baumannii Clinical Strains from ST-2 Clones Isolated in 2000 and 2010 (ST-2_clon_2000 and ST-2_clon_2010).
PG  - e01182-16
AB  - Acinetobacter baumannii is a successful nosocomial pathogen due to its ability to persist in
      hospital environments by acquiring mobile elements such as
      transposons, plasmids, and phages. In this study, we compared two genomes of A.
      baumannii clinical strains isolated in 2000 (ST-2_clon_2000) and 2010
      (ST-2_clon_2010) from GenBank project PRJNA308422.
AU  - Lopez M
AU  - Rueda A
AU  - Florido JP
AU  - Blasco L
AU  - Gato E
AU  - Fernandez-Garcia L
AU  - Martinez-Martinez L
AU  - Fernandez-Cuenca F
AU  - Pachon J
AU  - Cisneros JM
AU  - Garnacho-Montero J
AU  - Vila J
AU  - Rodriguez-Bano J
AU  - Pascual A
AU  - Bou G
AU  - Tomas M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01182-16.

PMID- 12680604
VI  - 24
DP  - 2003
TI  - Genotyping of DNA using sequence-specific methyltransferases followed by immunochemical detection.
PG  - 11-28
AB  - Modern molecular genetics relies on the ability to map the positions of genes on chromosomes,
      relative to known DNA markers. The first such DNA
      markers described were Restriction Fragment Length Polymorphisms, but any
      restriction endonuclease used for RFLP mapping is just one member of a
      restriction-modification pair. For each restriction endonuclease, there is
      a companion methyltransferase (MTase) that has the same DNA sequence
      specificity. Therefore, in principle, it should be possible to use MTases
      rather than restriction enzymes to detect polymorphic sites in DNA. We
      have used sequence-specific DNA MTases to detect polym orphisms in closely
      related viral pathogens. If at least one MTase recognition site is present
      in PCR-amplified DNA, then methyl groups are incorporated; if no MTase
      site is present, then methyl groups are not incorporated. When several
      different sequence-specific DNA MTase reactions are carried out, the
      pattern of methyl incorporation defines a DNA MTase genotype. DNA MTase
      Genotyping (DMG) can be used to rapidly diagnose heritable or infectious
      diseases, to immunochemically detect DNA at defined 2 to 8 base pair
      sites, or to characterize the amplicons by constructing ordered maps.
AU  - Lopez OJ
AU  - Quintanar A
AU  - Padhye NV
AU  - Nelson M
PT  - Journal Article
TA  - J. Immunoassay Immunochem.
JT  - J. Immunoassay Immunochem.
SO  - J. Immunoassay Immunochem. 2003 24: 11-28.

PMID- 25745005
VI  - 3
DP  - 2015
TI  - Genome Sequences of Five Disinfectant-Resistant Listeria monocytogenes Strains from Two Iberian Pork-Processing Plants.
PG  - e00077-15
AB  - We announce the draft genome sequences of five Listeria monocytogenes strains from two Iberian
      pork-processing plants located in Spain that were distinguished
      by their resistance to benzalkonium chloride. These strains seem highly adapted
      to the meat-processing environment according to their persistence and
      transmission capabilities.
AU  - Lopez-Alonso V
AU  - Ortiz S
AU  - Martinez-Suarez JV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00077-15.

PMID- 20008574
VI  - 184
DP  - 2010
TI  - Regulation of Salmonella enterica Pathogenicity Island 1 by DNA Adenine Methylation.
PG  - 637-649
AB  - DNA adenine methylase (Dam ) mutants of Salmonella enterica are attenuated in the mouse model
      and present multiple virulence-related
      defects. Impaired interaction of Salmonella Dam mutants with the
      intestinal epithelium has been tentatively correlated with reduced
      secretion of pathogenicity island 1 (SPI-1) effectors. In this study,
      we show that S. enterica Dam mutants contain lowered levels of the
      SPI-1 transcriptional regulators HilA, HilC, HilD, and InvF. Epistasis
      analysis indicates that Dam-dependent regulation of SPI-1 requires
      HilD, while HilA, HilC, and InvF are dispensable. A transcriptional
      hilD::lac fusion is expressed at similar levels in Dam(+) and Dam
      hosts. However, lower levels of hilD mRNA are found in a Dam
      background, thus providing unsuspected evidence that Dam methylation
      might exert post-transcriptional regulation of hilD expression. This
      hypothesis is supported by the following lines of evidence: (i) lowered
      levels of hilD mRNA are found in Salmonella Dam mutants when hilD is
      transcribed from a heterologous promoter; (ii) increased hilD mRNA
      turnover is observed in Dam mutants; (iii) lack of the Hfq RNA
      chaperone enhances hilD mRNA instability in Dam mutants; and (iv) lack
      of the RNA degradosome components polynucleotide phosphorylase and
      ribonuclease E suppresses hilD mRNA instability in a Dam background.
      Our report of Dam-dependent control of hilD mRNA stability suggests
      that DNA adenine methylation plays hitherto unknown roles in
      post-transcriptional control of gene expression.
AU  - Lopez-Garrido J
AU  - Casadesus J
PT  - Journal Article
TA  - Genetics
JT  - Genetics
SO  - Genetics 2010 184: 637-649.

PMID- 28684561
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Salinivibrio proteolyticus, Salinivibrio sharmensis, Salinivibrio siamensis, Salinivibrio costicola subsp. alcaliphilus, Salinivibrio costicola subsp. vallismortis, and 29 New Isolates Belonging to the Genus Salinivibrio.
PG  - e00244-17
AB  - The draft genome sequences of 5 type strains of species of the halophilic genus Salinivibrio
      and 29 new isolates from different hypersaline habitats belonging to
      the genus Salinivibrio have been determined. The genomes have 3,123,148 to
      3,641,359 bp, a G+C content of 49.2 to 50.9%, and 2,898 to 3,404 open reading
      frames (ORFs).
AU  - Lopez-Hermoso C
AU  - de la Haba RR
AU  - Sanchez-Porro C
AU  - Bayliss SC
AU  - Feil EJ
AU  - Ventosa A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00244-17.

PMID- 23352736
VI  - 36
DP  - 2013
TI  - New insights into the archaeal diversity of a hypersaline microbial mat obtained by a metagenomic approach.
PG  - 205-214
AB  - A metagenomic approach was carried out in order to study the genetic pool of a
      hypersaline microbial mat, paying more attention to the archaeal community and,
      specifically, to the putatively methanogenic members. The main aim of the work
      was to expand the knowledge of a likely ecologically important archaeal lineage,
      candidate division MSBL1, which is probably involved in methanogenesis at very
      high salinities. The results obtained in this study were in accordance with our
      previous report on the bacterial diversity encountered by using a number of
      molecular techniques, but remarkable differences were found in the archaeal
      diversity retrieval by each of the procedures used (metagenomics and 16S
      rRNA-based methods). The lack of synteny for most of the metagenomic fragments
      with known genomes, together with the low degree of similarity of the annotated
      open reading frames (ORFs) with the sequences in the databases, reflected the
      high degree of novelty in the mat community studied. Linking the sequenced clones
      with representatives of division MSBL1 was not possible because of the lack of
      additional information concerning this archaeal group in the public gene
      repositories. However, given the high abundance of representatives of this
      division in the 16S rRNA clone libraries and the low identity of the archaeal
      clones with known genomes, it was hypothesized that some of them could arise from
      MSBL1 genomes. In addition, other prokaryotic groups known to be relevant in
      organic matter mineralization at high salinities were detected.
AU  - Lopez-Lopez A
AU  - Richter M
AU  - Pena A
AU  - Tamames J
AU  - Rossello-Mora R
PT  - Journal Article
TA  - Syst. Appl. Microbiol.
JT  - Syst. Appl. Microbiol.
SO  - Syst. Appl. Microbiol. 2013 36: 205-214.

PMID- 23729633
VI  - 5
DP  - 2013
TI  - Genomic Diversity of 'Deep Ecotype' Alteromonas macleodii Isolates: Evidence for Pan-Mediterranean Clonal Frames.
PG  - 1220-1232
AB  - We have compared genomes of Alteromonas macleodii "deep ecotype" isolates from
      two deep Mediterranean sites and two surface samples from the Aegean and the
      English Channel. A total of nine different genomes were analyzed. They belong to
      five clonal frames (CFs) that differ among them by approximately 30,000
      single-nucleotide polymorphisms (SNPs) over their core genomes. Two of the CFs
      contain three strains each with nearly identical genomes ( approximately 100 SNPs
      over the core genome). One of the CFs had representatives that were isolated from
      samples taken more than 1,000 km away, 2,500 m deeper, and 5 years apart. These
      data mark the longest proven persistence of a CF in nature (outside of clinical
      settings). We have found evidence for frequent recombination events between or
      within CFs and even with the distantly related A. macleodii surface ecotype. The
      different CFs had different flexible genomic islands. They can be classified into
      two groups; one type is additive, that is, containing different numbers of gene
      cassettes, and is very variable in short time periods (they often varied even
      within a single CF). The other type was more stable and produced the complete
      replacement of a genomic fragment by another with different genes. Although this
      type was more conserved within each CF, we found examples of recombination among
      distantly related CFs including English Channel and Mediterranean isolates.
AU  - Lopez-Perez M
AU  - Gonzaga A
AU  - Rodriguez-Valera F
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2013 5: 1220-1232.

PMID- 25395631
VI  - 2
DP  - 2014
TI  - Genome Sequence of 'Thalassospira australica' NP3b2T Isolated from St. Kilda Beach, Tasman Sea.
PG  - e01139-14
AB  - Here, we present the draft genome of 'Thalassospira australica' NP3b2(T), a potential
      poly(ethylene terephthalate) (PET) plastic biodegrader. This genomic
      information will enhance information on the genetic basis of metabolic pathways
      for the degradation of PET plastic.
AU  - Lopez-Perez M
AU  - Rodriguez-Valera F
AU  - Webb HK
AU  - Crawford RJ
AU  - Ivanova EP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01139-14.

PMID- 27587806
VI  - 4
DP  - 2016
TI  - Complete Genome Sequences of Four Enterohemolysin-Positive (ehxA) Enterocyte Effacement-Negative Shiga Toxin-Producing Escherichia coli Strains.
PG  - e00846-16
AB  - Shiga toxin-producing Escherichia coli (STEC) strains are important foodborne pathogens
      associated with human disease. Most disease-associated STEC strains
      carry the locus of enterocyte effacement (LEE); however, regularly LEE-negative
      STEC strains are recovered from ill patients. Few reference sequences are
      available for these isolate types. Here, we report here the complete genome
      sequences for four LEE-negative STEC strains.
AU  - Lorenz SC
AU  - Kotewicz ML
AU  - Hoffmann M
AU  - Gonzalez-Escalona N
AU  - Fischer M
AU  - Kase JA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00846-16.

PMID- 27151783
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Cylindrospermopsis raciborskii (Cyanobacteria) Strain ITEP-A1 Isolated from a Brazilian Semiarid Freshwater Body: Evidence of Saxitoxin  and Cylindrospermopsin Synthetase Genes.
PG  - e00228-16
AB  - Cylindrospermopsis raciborskii ITEP-A1 is a saxitoxin-producing cyanobacterium. We report the
      draft genome sequence of ITEP-A1, which comprised 195 contigs that
      were assembled with SPAdes and annotated with Rapid Annotation using Subsystem
      Technology. The identified genome sequence had 3,605,836 bp, 40.1% G+C, and
      predicted 3,553 coding sequences (including the synthetase genes).
AU  - Lorenzi AS
AU  - Silva GG
AU  - Lopes FA
AU  - Chia MA
AU  - Edwards RA
AU  - Bittencourt-Oliveira MC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00228-16.

PMID- 11526227
VI  - 98
DP  - 2001
TI  - CmC(a/t)GG methylation: a new epigenetic mark in mammalian DNA?
PG  - 10034-10036
AB  - Twenty-five years ago, based on the knowledge of cytosine methylation in higher organisms and
      the newly discovered bacterial adenine methyltransferase, Riggs and Holliday and Pugh
      independently proposed that the covalent modification of DNA by methylation might serve as a
      means to propagate heritable expression states in eukaryotes.  In the years since, the
      association between cytosine methylation and transcriptional silencing in mammalian cells has
      become well established, and a number of proteins that catalyze the transfer of a methyl group
      to the 5-carbon of the cytosine pyrimidine ring have been cloned and characterized.  These DNA
      methyltransferases (m5C-MTases) are encoded by a diverse family of genes found in prokaryotes
      as well as all four groups of eukaryotes.
AU  - Lorincz MC
AU  - Groudine M
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2001 98: 10034-10036.

PMID- 12370304
VI  - 22
DP  - 2002
TI  - DNA methylation density influences the stability of an epigenetic imprint and Dnmt3a/b-independent de novo methylation.
PG  - 7572-7580
AB  - DNA methylation plays an important role in transcriptional repression. To gain insight into
      the dynamics of demethylation and de novo methylation, we introduced a proviral reporter,
      premethylated at different densities, into a defined chromosomal site in murine
      erythroleukemia cells and monitored the stability of the introduced methylation and reporter
      gene expression. A high density of methylation was faithfully propagated in vivo. In contrast,
      a low level of methylation was not stable, with complete demethylation and associated
      transcriptional activation or maintenance-coupled de novo methylation and associated silencing
      occurring with equal probability. Deletion of the proviral enhancer increased the probability
      of maintenance-coupled de novo methylation, suggesting that this enhancer functions in part to
      antagonize such methylation. The DNA methyltransferases (MTases) Dnmt3a and Dnmt3b are thought
      to be the sole de novo MTases in the mammalian genome. To determine whether these enzymes are
      responsible for maintenance-coupled de novo methylation, the unmethylated or premethylated
      proviral reporter was introduced into DNA MTase-deficient embryonic stem cells. These studies
      revealed the presence of a Dnmt3a/Dnmt3b-independent de novo methyltransferase activity that
      is stimulated by the presence of preexisting methylation.
AU  - Lorincz MC
AU  - Schubeler D
AU  - Hutchinson SR
AU  - Dickerson DR
AU  - Groudine M
PT  - Journal Article
TA  - Mol. Cell. Biol.
JT  - Mol. Cell. Biol.
SO  - Mol. Cell. Biol. 2002 22: 7572-7580.

PMID- 27881544
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Lysinibacillus xylanilyticus SR-86.
PG  - e01317-16
AB  - Lysinibacillus xylanilyticus belongs to the family Bacillaceae and was first described in 2010
      with the type strain L. xylanilyticus XDB9. It is able to both
      degrade xylan and use it as the sole carbon source. Here, we describe the 4.8-Mb
      genome of the strain L. xylanilyticus SR-86, which was isolated from organic
      waste.
AU  - Loscar ME
AU  - Huptas C
AU  - Wenning M
AU  - Sieber V
AU  - Schmid J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01317-16.

PMID- 
VI  - 36
DP  - 1997
TI  - Isolation of thermostable restriction endonuclease from thermophilic Synechococcus elongatus T3.
PG  - 272-275
AB  - A restriction endonuclease was isolated from thermophilic cyanobacterium Synechococcus
      elongatus T3, which was named SelI.  This restriction endonuclease was characterized as an
      isoschizomer of Sau96I, its recognition sequences is GGNCC.  Bu the reaction conditions of
      SelI are different from that of Sau96I.  SalI is a thermostable restriction endonuclease with
      optimal reaction temperature 50-70oC.
AU  - Lou S
AU  - Wu L
PT  - Journal Article
TA  - J. Xiamen Univ.
JT  - J. Xiamen Univ.
SO  - J. Xiamen Univ. 1997 36: 272-275.

PMID- 28360168
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Streptomyces specialis Type Strain GW41-1564 (DSM 41924).
PG  - e00101-17
AB  - Here, we report the draft genome sequence of Streptomyces specialis type strain GW41-1564,
      which was isolated from soil. This 5.87-Mb genome exhibits a high G+C
      content of 72.72% and contains 5,486 protein-coding genes.
AU  - Loucif L
AU  - Michelle C
AU  - Terras J
AU  - Rolain JM
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00101-17.

PMID- 27721915
VI  - 11
DP  - 2016
TI  - High-quality draft genome sequence of Sedimenticola selenatireducens strain AK4OH1T, a gammaproteobacterium isolated from estuarine sediment.
PG  - 66
AB  - Sedimenticola selenatireducens strain AK4OH1T (= DSM 17993T = ATCC BAA-1233T) is  a
      microaerophilic bacterium isolated from sediment from the Arthur Kill
      intertidal strait between New Jersey and Staten Island, NY. S. selenatireducens
      is Gram-negative and belongs to the Gammaproteobacteria. Strain AK4OH1T was the
      first representative of its genus to be isolated for its unique coupling of the
      oxidation of aromatic acids to the respiration of selenate. It is a versatile
      heterotroph and can use a variety of carbon compounds, but can also grow
      lithoautotrophically under hypoxic and anaerobic conditions. The draft genome
      comprises 4,588,530 bp and 4276 predicted protein-coding genes including genes
      for the anaerobic degradation of 4-hydroxybenzoate and benzoate. Here we report
      the main features of the genome of S. selenatireducens strain AK4OH1T.
AU  - Louie TS
AU  - Giovannelli D
AU  - Yee N
AU  - Narasingarao P
AU  - Starovoytov V
AU  - Goker M
AU  - Klenk HP
AU  - Lang E
AU  - Kyrpides NC
AU  - Woyke T
AU  - Bini E
AU  - Haggblom MM
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 66.

PMID- 26823597
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Corynebacterium pseudotuberculosis Viscerotropic Strain N1.
PG  - e01673-15
AB  - We present the complete genome sequence of Corynebacterium pseudotuberculosis strain N1. The
      sequencing was performed with the Ion Torrent Personal Genome
      Machine system. The genome is a circular chromosome with 2,337,845 bp, a G+C
      content of 52.85%, and a total of 2,045 coding sequences, 12 rRNAs, 49 tRNAs, and
      58 pseudogenes.
AU  - Loureiro D
AU  - Portela RW
AU  - Sousa TJ
AU  - Rocha F
AU  - Pereira FL
AU  - Dorella FA
AU  - Carvalho AF
AU  - Menezes N
AU  - Macedo ES
AU  - Moura-Costa LF
AU  - Meyer R
AU  - Leal CA
AU  - Figueiredo HC
AU  - Azevedo V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01673-15.

PMID- 29674528
VI  - 6
DP  - 2018
TI  - Complete and Draft Genome Sequences of Nine Lactobacillus sakei Strains Selected  from the Three Known Phylogenetic Lineages and Their Main Clonal Complexes.
PG  - e00082-18
AB  - We present here the complete and draft genome sequences of nine Lactobacillus sakei strains,
      selected from the entire range of clonal complexes from the three
      known lineages of the species. The strains were chosen to provide a wide view of
      pangenomic and plasmidic diversity for this important foodborne species.
AU  - Loux V
AU  - Coeuret G
AU  - Zagorec M
AU  - Champomier VMC
AU  - Chaillou S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00082-18.

PMID- 25886522
VI  - 16
DP  - 2015
TI  - Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii.
PG  - 296
AB  - BACKGROUND: Propionibacterium freudenreichii (PF) is an actinobacterium used in cheese
      technology and for its probiotic properties. PF is also extremely
      adaptable to several ecological niches and can grow on a variety of carbon and
      nitrogen sources. The aim of this work was to discover the genetic basis for
      strain-dependent traits related to its ability to use specific carbon sources.
      High-throughput sequencing technologies were ideal for this purpose as they have
      the potential to decipher genomic diversity at a moderate cost. RESULTS: 21
      strains of PF were sequenced and the genomes were assembled de novo. Scaffolds
      were ordered by comparison with the complete reference genome CIRM-BIA1, obtained
      previously using traditional Sanger sequencing. Automatic functional annotation
      and manual curation were performed. Each gene was attributed to either the core
      genome or an accessory genome. The ability of the 21 strains to degrade 50
      different sugars was evaluated. Thirty-three sugars were degraded by none of the
      sequenced strains whereas eight sugars were degraded by all of them. The
      corresponding genes were present in the core genome. Lactose, melibiose and
      xylitol were only used by some strains. In this case, the presence/absence of
      genes responsible for carbon uptake and degradation correlated well with the
      phenotypes, with the exception of xylitol. Furthermore, the simultaneous presence
      of these genes was in line the metabolic pathways described previously in other
      species. We also considered the genetic origin (transduction, rearrangement) of
      the corresponding genomic islands. Ribose and gluconate were degraded to a
      greater or lesser extent (quantitative phenotype) by some strains. For these
      sugars, the phenotypes could not be explained by the presence/absence of a gene
      but correlated with the premature appearance of a stop codon interrupting protein
      synthesis and preventing the catabolism of corresponding carbon sources.
      CONCLUSION: These results illustrate (i) the power of correlation studies to
      discover the genetic basis of binary strain-dependent traits, and (ii) the
      plasticity of PF chromosomes, probably resulting from horizontal transfers,
      duplications, transpositions and an accumulation of mutations. Knowledge of the
      genetic basis of nitrogen and sugar degradation opens up new strategies for the
      screening of PF strain collections to enable optimum cheese starter, probiotic
      and white biotechnology applications.
AU  - Loux V
AU  - Mariadassou M
AU  - Almeida S
AU  - Chiapello H
AU  - Hammani A
AU  - Buratti J
AU  - Gendrault A
AU  - Barbe V
AU  - Aury JM
AU  - Deutsch SM
AU  - Parayre S
AU  - Madec MN
AU  - Chuat V
AU  - Jan G
AU  - Peterlongo P
AU  - Azevedo V
AU  - Le Loir Y
AU  - Falentin H
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2015 16: 296.

PMID- 27789646
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Pigmentation-Negative Yersinia pestis Strain Cadman.
PG  - e01207-16
AB  - Here, we report the genome sequence of Yersinia pestis strain Cadman, an attenuated strain
      lacking the pgm locus. Y. pestis is the causative agent of
      plague and generally must be worked with under biosafety level 3 (BSL-3)
      conditions. However, strains lacking the pgm locus are considered safe to work
      with under BSL-2 conditions.
AU  - Lovett S
AU  - Chase K
AU  - Koroleva G
AU  - Palacios G
AU  - Rozak D
AU  - Ladner JT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01207-16.

PMID- 18396448
VI  - 11
DP  - 2008
TI  - Clocks and switches: bacterial gene regulation by DNA adenine methylation.
PG  - 106-112
AB  - N(6) methylation in adenosine moieties causes changes in DNA structure and can modulate
      DNA-protein interactions. In both alpha-Proteobacteria and gamma-Proteobacteria,
      postreplicative formation of N(6)-methyl-adenine regulates transcription of specific genes and
      provides two general types of controls: (i) clock-like controls that permit transient gene
      transcription during a specific stage of DNA replication; (ii) switch-like controls in which
      transcription is regulated by a DNA methylation pattern. DNA adenine methylation may also
      regulate gene expression by affecting nucleoid topology. Recent transcriptomic studies have
      unveiled novel cases of genes regulated by DNA adenine methylation, including virulence genes
      of bacterial pathogens.
AU  - Low DA
AU  - Casadesus J
PT  - Journal Article
TA  - Curr. Opin. Microbiol.
JT  - Curr. Opin. Microbiol.
SO  - Curr. Opin. Microbiol. 2008 11: 106-112.

PMID- 11705888
VI  - 69
DP  - 2001
TI  - Roles of DNA adenine methylation in regulating bacterial gene expression and virulence.
PG  - 7197-7204
AB  - DNA methylation provides a mechanism by which additional information is imparted to DNA, and
      such epigenetic information can alter the timing and targeting of cellular events.  DNA
      methylation occurs throughout the living world, including bacteria, plants, and mammals. Until
      recently, methylated DNA sequences were not detected in the fruit fly, in brewer's yeast, or
      in the nematode.  However, analysis by Lyko and colleagues showed that Drosophila melanogaster
      does contain methylated DNA, and thus it is possible that yeast and worms may also have it.
      In this review, we focus our attention on the roles of DNA methylation in regulating bacterial
      gene expression and virulence.  Although some background information about DNA methylation is
      presented, we refer the reader to excellent reviews on the subject.  DNA methylation occurs at
      the C-5 or N-4 positions of cytosine and at the N-6 position of adenine and is catalyzed by
      enzymes known as DNA methyltransferases (Mtases).  All MTases use S-adenosyl methionine as a
      methyl donor.  DNA methylation has historically been associated with DNA
      restriction-modification systems thought to be important in protecting cells from foreign DNAs
      such as transposons and viral DNAs.  Restriction-modification systems contain a DNA methylase
      that protects host DNA sequences from restriction with their cognate restriction enzymes,
      which digest unmodified foreign DNAs.  Certain MTases, including DNA cytosine MTase (Dcm),
      which methylates the C-5 position of cytosine in CC(A/T)GG sequences, DNA adenine methylase
      (Dam), which methylates N-6 of adenine in GATC sequences, and cell cycle-regulated methylase
      (CcrM), which methylates the N-6 adenine of GAnTC, do not have cognate restriction enzymes
      associated with them.  These methylases participate in cellular regulatory events, including
      those that control bacterial virulence, which are the primary focus of this review.
AU  - Low DA
AU  - Weyand NJ
AU  - Mahan MJ
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2001 69: 7197-7204.

PMID- 30533917
VI  - 7
DP  - 2018
TI  - Complete Genome Sequence of Moraxella bovis Strain Epp-63 (300), an Etiologic Agent of Infectious Bovine Keratoconjunctivitis.
PG  - e01004-18
AB  - We report here the complete closed genome sequence of Moraxella bovis strain Epp-63 (300)
      (Epp63). This strain was isolated from an infectious bovine
      keratoconjunctivitis (IBK) case in 1963. Since then, Epp63 has been used
      extensively for IBK research. Consequently, the genome sequence of Epp63 should
      help elucidate IBK host-pathogen interactions.
AU  - Loy JD
AU  - Dickey AM
AU  - Clawson ML
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e01004-18.

PMID- 10385008
VI  - 81
DP  - 1999
TI  - The amino acidic substitution of cysteine 167 by serine (C167S) in BstVI restriction endonuclease of Bacillus stearothermophilus V affects its conformation and thermostability.
PG  - 261-266
AB  - The restriction endonuclease BstVI from Bacillus stearothermophilus V contains three cysteine
      residues at positions 134, 167 and 180. Titration of Cys residues with DTNB showed that none
      of them are involved in disulphide bond formation. Cysteine triplets 134 and 167 were modified
      by recombinant PCR to introduce a serine residue in each case. The mutated genes were cloned
      into pGEM-T vector and transformed into E. coli JM109. Even though pGEM-T is not designed for
      expression, the mutant proteins were efficiently expressed in E. coli. The endonuclease
      carrying the mutation C134S was purified to homogeneity but appeared to be very unstable. In
      contrast, the C167S mutant enzyme was stable when pure and was studied biochemically. This
      mutant enzyme was as stable and resistant to protein-denaturing agents as the wild type
      enzyme. The activity of both enzymes was not affected by preincubations of 2 h at 80 degrees
      C. A short preincubation at 95 degrees C caused a complete inactivation of the mutant enzyme
      while the wild type endonuclease retained 30% of its activity. Moreover, the C167S BstVI was
      more susceptible to be hydrolyzed by proteinase K and trypsin compared to the wild type
      endonuclease. These results show that the substitution Cys --> Ser at position 167 affects the
      configuration and thermostability of BstVI restriction endonuclease.
AU  - Loyola C
AU  - Saavedra C
AU  - Gomez I
AU  - Vasquez C
PT  - Journal Article
TA  - Biochimie
JT  - Biochimie
SO  - Biochimie 1999 81: 261-266.

PMID- 28663293
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Pseudomonas koreensis CI12, a Bacillus cereus 'Hitchhiker' from the Soybean Rhizosphere.
PG  - e00570-17
AB  - Pseudomonas koreensis CI12 was coisolated with Bacillus cereus from a root of a soybean plant
      grown in a field in Arlington, WI. Here, we report the draft genome
      sequence of P. koreensis CI12 obtained by Illumina sequencing.
AU  - Lozano GL
AU  - Bravo JI
AU  - Handelsman J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00570-17.

PMID- 27587823
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Biocontrol Agent Bacillus cereus UW85.
PG  - e00910-16
AB  - Bacillus cereus UW85 was isolated from a root of a field-grown alfalfa plant from Arlington,
      WI, and identified for its ability to suppress damping off, a disease
      caused by Phytophthora megasperma f. sp. medicaginis on alfalfa. Here, we report
      the draft genome sequence of B. cereus UW85, obtained by a combination of Sanger
      and Illumina sequencing.
AU  - Lozano GL
AU  - Holt J
AU  - Ravel J
AU  - Rasko DA
AU  - Thomas MG
AU  - Handelsman J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00910-16.

PMID- 6273420
VI  - 256
DP  - 1981
TI  - DNA determinants important in sequence recognition by EcoRI endonuclease.
PG  - 13200-13206
AB  - Alkylation interference and protection methods (Siebenlist, U., and Gilbert,
      W., (1980) Proc. Natl. Acad. Sci. USA 77, 122-126) have been utilized to deduce
      potential DNA contracts involved in specific complex formation between EcoRI
      endonuclease and its recognition sequence.  The endonuclease protected the N7
      position (major groove) of the dG and the N3 position (minor groove) of both dA
      residues within the EcoRI sequence against alkylation by dimethylsulfate,
      d(7Gp7Ap7ApTpTpC), suggesting the presence of polypeptide in both grooves in
      the vicinity of affected nitrogens.  Results of methylation interference
      analysis suggest that the N7 of the EcoRI site dG and the N3 of the central dA,
      d(7GpAp7ApTpTpC), are utilized as contacts by the enzyme.  The failure to
      observe interference upon methylation of the 5'-penultimate dA within the
      sequence implies that the endonuclease does not bond to the N3 of this residue,
      despite the fact that it is protected against alkylation by the protein.
      Ethylation interference patterns suggest four major phosphate contacts between
      endonuclease and each DNA strand.  Two of these phosphates are 5'-external to
      the EcoRI sequence, d(7pN7pG7pApA7pTpTpC), suggesting involvement of outside
      phosphates in electrostatic interactions.  Moreover, alkylation protection and
      interference effects on the two DNA strands display perfect 2-fold symmetry.
      Thus, the endonuclease interacts with a minimum of 10 nucleotide pairs to yield
      a DNA-protein complex characterized by elements of symmetry.  In contrast,
      specific alkylation effects were not observed in comparable experiments with
      the endonuclease and a DNA which had been previously methylated by the EcoRI
      modification enzyme.
AU  - Lu A-L
AU  - Jack WE
AU  - Modrich P
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1981 256: 13200-13206.

PMID- 7056404
VI  - 41
DP  - 1982
TI  - DNA contacts and mechanism of specific site location of EcoRI endonuclease, and effects of modification methylation on DNA helix conformation.
PG  - 1199
AB  - Alkylation interference and protection methods have been utilized to deduce
      potential DNA contacts involved in specific complex formation between EcoRI
      endonuclease and its recognition sequence.  The endonuclease interacts
      symmetrically with a minimum of 10 nucleotide pairs, including nitrogens in
      both major and minor grooves and phosphate groups along the DNA backbone.
      Dissociation and association rates for site-specific EcoRI endonuclease-DNA
      complexes increase with increasing DNA chain length up to a plateau.  Since
      intrinsic EcoRI site Keq are identical for the different length DNA fragments,
      outside DNA sequences must form the basis for observed kinetic differences.
      Thus, outside DNA sequences lie on the major kinetic pathway by which EcoRI
      endonuclease locates and leaves its recognition site.  Conformational changes
      associated with DNA biological methylation was investigated (using the
      electrophoresis band shift method).  The DNA helix was found to be unwound
      about 0.5 degree for each methyl group introduced to the N6 position of
      adenine.  No detectable effect (< 0.2 degree) was observed when methyl group
      was introduced to DNA on C5 of cytosine.
AU  - Lu AL
AU  - Cheng SC
AU  - Jack WE
AU  - Modrich P
PT  - Journal Article
TA  - Fed. Proc.
JT  - Fed. Proc.
SO  - Fed. Proc. 1982 41: 1199.

PMID- 28729255
VI  - 5
DP  - 2017
TI  - Genome Sequences of Two Listeria monocytogenes Strains from Nectarines Associated with Listeriosis in 2014.
PG  - e00389-17
AB  - Listeria monocytogenes is an important foodborne pathogen. Here, we present the annotated
      whole genome of Listeria monocytogenes strains F14M01297-C2 and
      F14M01297-C4, isolated from nectarines distributed by a packing facility in
      California during an investigation of listeriosis associated with stone fruit in
      2014.
AU  - Lu C
AU  - Marjanovic O
AU  - Morales C
AU  - Kiang D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00389-17.

PMID- 12512062
VI  - 124
DP  - 2003
TI  - Relationship between Helicobacter pylori restriction endonuclease-replacing gene, Hrga and clinical outcome.
PG  - A270
AB  - Background: Recently, polymorphisms in the hpyIII locus in Helicobacter pylori have been
      identified and the presence of a new gene, hrgA, that had replaced hpyIIIR, was reported to be
      related to gastric cancer in Asian strains.  However, this relation was data-derived and the
      hypothesis has not yet been confirmed.  Aims: To confirm the relationship between hrgA allelic
      type and clinical outcome in strains from both Asian and Western countries.  Methods: We
      examined H. pylori strains from Asia (Korea, Hong Kong, Thailand, Taiwan, and Vietnam) and
      Western countries (Columbia, Canada, France, and Italy).  hrgA and hpyIIIR status were
      determined by polymerase chain reaction.  Results: There were 332 strains including as 172
      Asian (49 cancer, 123 non-cancer) and 160 Western strains (50 gastric cancer, 90 non-cancer).
      The prevalence of hrgA gene was significantly higher in Western strains 46.8% than Asian
      strains (33.7%) irrespective of the clinical outcome (P = 0.01).  In Asian, the prevalence of
      hrgA gene was 34.78% in strains from cancer and 33.3% from non-cancer.  In western countries,
      the prevalence of hrgA gene was 50% in strains from cancer and 45% from non-cancer.
      Discussion: We were unable to confirm the hypothesis that the hrgA gene was related to gastric
      cancer.  We found no relationship between the prevalence of the hrgA gene and clinical outcome
      in either Asian or Western countries.  The prevalence of hrgA gene was higher in Western
      strains compared with Asian strains which are the opposite of other important putative
      virulence factors such as cag pathogenicity island, vacA s1 genotype, babA2 genotypes and oipA
      "on" types.
AU  - Lu H
AU  - Graham D
AU  - Xiao SD
AU  - Gutierrez O
AU  - Yamaoka Y
PT  - Journal Article
TA  - Gastroenterology
JT  - Gastroenterology
SO  - Gastroenterology 2003 124: A270.

PMID- 24158556
VI  - 1
DP  - 2013
TI  - Genome Sequence of Growth-Improving Paenibacillus mucilaginosus Strain KNP414.
PG  - e00881-13
AB  - Paenibacillus mucilaginosus is a critical growth-improving silicate bacterium. Here, we report
      the complete genome sequence of P. mucilaginosus strain KNP414.
      This information will provide us with the opportunity to understand its molecular
      mechanisms and develop more effective utilization of the strain.
AU  - Lu JJ
AU  - Wang JF
AU  - Hu XF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00881-13.

PMID- 12188183
VI  - 33
DP  - 2002
TI  - Optimizing DpnI digestion conditions to detect replicated DNA.
PG  - 316-318
AB  - In vitro replication systems are powerful tools for studying DNA replication and repair.
      Replication competent cellular extracts can be used with reporter plasmids that contain the
      simian virus 40 (SV40) DNA replication origin.  Replication is initiated by the addition of
      the large T antigen.  By using plasmid DNA prepared in bacteria expressing adenosine methylase
      as substrate, processive eukaryotic replication involving polymerase alpha, beta and epsilon
      can be distinguished from gap-filling reactions mediated by other DNA polymerases such as
      polymerase beta by the methylation status of the resulting DNA (Figure 1).  The bacterially
      derived plasmid will contain methyladenosine at the DpnI restriction site, GATC, making the
      plasmid susceptible to DpnI cleavage.  The complete absence of methylation profoundly
      suppresses DNA cleavage by DpnI.  However, after a single round of semi-conservative
      replication, the DNA is only hemimethylated.  The susceptibility of hemimethylated DNA has not
      been well studied, though previous work suggests that replicated DNA also may be susceptible
      to cleavage.  We demonstrate that under conditions of enzyme excess, long duration digestion,
      or small DNA amounts, the hemimethylated DNA is susceptible to DpnI cleavage.  Other
      investigators have identified that DpnI digestions can be difficult to interpret. For the
      analysis of DNA replication, we optimized the digestion conditions so that only fully
      methylated DNA would be digested, preserving hemimethylated DNA for analyses.
AU  - Lu L
AU  - Patel H
AU  - Bissler JJ
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 2002 33: 316-318.

PMID- 15964605
VI  - 339
DP  - 2005
TI  - Complete genome sequence analysis of an iridovirus isolated from the orange-spotted grouper, Epinephelus coioides.
PG  - 81-100
AB  - Orange-spotted grouper iridovirus (OSGIV) was the causative agent of
      serious systemic diseases with high mortality in the cultured
      orange-spotted grouper, Epinephelus coioides. Here we report the complete
      genome sequence of OSGIV. The OSGIV genome consists of 112,636 bp with a
      G+C content of 54%. 121 putative open reading frames (ORF) were identified
      with coding capacities for polypeptides varying from 40 to 1168 amino
      acids. The majority of OSGIV shared homologies to other iridovirus genes.
      Phylogenetic analysis of the major capsid protein, ATPase, cytosine DNA
      methyl transferase and DNA polymerase indicated that OSGIV was closely
      related to infectious spleen and kidney necrosis virus (ISKNV) and rock
      bream iridovirus (RBIV), but differed from lymphocytisvirus and ranavirus.
      The determination of the genome of OSGIV will facilitate a better
      understanding of the molecular mechanism underlying the pathogenesis of
      the OSGIV and may provide useful information to develop diagnosis method
      and strategies to control outbreak of OSGIV.
AU  - Lu L
AU  - Zhou SY
AU  - Chen C
AU  - Weng SP
AU  - Chan SM
AU  - He JG
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 2005 339: 81-100.

PMID- 26472841
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Klebsiella variicola Strain HKUOPLA, a Cellulose-Degrading Bacterium Isolated from Giant Panda Feces.
PG  - e01200-15
AB  - We report here the complete genome sequence of Klebsiella variicola strain HKUOPLA, isolated
      from a giant panda feces sample collected from Ocean Park, Hong Kong. The complete genome of
      this bacterium may contribute toward the discovery of efficient cellulose-degrading pathways.
AU  - Lu MG
AU  - Jiang J
AU  - Liu L
AU  - Ma AP
AU  - Leung FC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01200-15.

PMID- 26564041
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Klebsiella pneumoniae Strain HKUOPLC, a Cellulose-Degrading Bacterium Isolated from Giant Panda Feces.
PG  - e01318-15
AB  - We report here the complete genome sequence of Klebsiella pneumoniae strain HKUOPLC, isolated
      from a giant panda fecal sample collected from Ocean Park, Hong
      Kong. The complete genome of this bacterium may contribute to the discovery of
      efficient cellulose-degrading pathways.
AU  - Lu MG
AU  - Jiang J
AU  - Liu L
AU  - Ma AP
AU  - Leung FC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01318-15.

PMID- 25792050
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Terribacillus aidingensis Strain MP602, a Moderately  Halophilic Bacterium Isolated from Cryptomeria fortunei in Tianmu Mountain in  China.
PG  - e00126-15
AB  - Terribacillus aidingensis strain MP602, which was isolated from an ancient tree (Cryptomeria
      forunei) in Tianmu Mountain in China, has antagonistic activity
      against several certain phytopathogenic fungi. Here, we report the genome
      sequence of this strain. This is the first complete genome report of the
      Terribacillus genus.
AU  - Lu P
AU  - Lei M
AU  - Xiao F
AU  - Zhang L
AU  - Wang Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00126-15.

PMID- 26659688
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Pseudomonas aeruginosa PA1, Isolated from a Patient with a Respiratory Tract Infection.
PG  - e01453-15
AB  - We report the 6,498,072-bp complete genome sequence of Pseudomonas aeruginosa PA1, which was
      isolated from a patient with a respiratory tract infection in
      Chongqing, People's Republic of China. Whole-genome sequencing was performed
      using single-molecule real-time (SMRT) technology, and de novo assembly revealed
      a single contig with 396-fold sequence coverage.
AU  - Lu S
AU  - Le S
AU  - Li G
AU  - Shen M
AU  - Tan Y
AU  - Zhao X
AU  - Wang J
AU  - Shen W
AU  - Guo K
AU  - Yang Y
AU  - Zhu H
AU  - Li S
AU  - Li M
AU  - Zhu J
AU  - Rao X
AU  - Hu F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01453-15.

PMID- 22123760
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of the Neonatal-Meningitis-Associated Escherichia coli Strain CE10.
PG  - 7005
AB  - Neonatal bacterial meningitis continues to be an important cause of mortality and morbidity
      worldwide. Escherichia coli possessing the K1
      capsular polysaccharide is the most common Gram-negative pathogen causing
      neonatal meningitis. Here we present the complete genome sequence of
      neonatal meningitis-associated E. coli strain CE10, a unique K1 strain
      with a functional type III secretion system. Functional analysis of the
      genome should enhance our knowledge of the pathogenesis of neonatal E.
      coli K1 meningitis.
AU  - Lu S
AU  - Zhang X
AU  - Zhu Y
AU  - Kim KS
AU  - Yang J
AU  - Jin Q
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 7005.

PMID- 24375107
VI  - 196
DP  - 2013
TI  - Comparative analysis of the full genome of the Helicobacter pylori isolate, Sahul64, identifies genes of high divergence.
PG  - 1073-1083
AB  - Isolates of Helicobacter pylori can be classified phylogeographically. High genetic diversity
      and rapid microevolution are a hallmark of H. pylori genomes, a phenomenon that is proposed to
      play a functional role in persistence and colonisation of diverse human populations. To
      provide further genomic evidence in the lineage of H. pylori and to further characterise
      diverse strains of this pathogen in different human populations, we report the finished genome
      sequence of Sahul64, an H. pylori strain isolated from an Indigenous Australian. Our analysis
      identified highly divergent genes, when compared to the 38 publically available genomes, which
      include genes involved in the biosynthesis and modification of lipopolysaccharide, putative
      prophage genes, restriction modification components and hypothetical genes. Furthermore, the
      virulence associated vacA locus is a pseudogene and the cagPAI is not present. However, the
      genome does contain a gene cluster associated with pathogenicity including dupA. Our analysis
      found that with the addition of Sahul64 to the 38 genomes, the core genome content of H.
      pylori is reduced by approximately 14% ( approximately 170 genes) and the pan-genome has
      expanded from 2070 to 2238 genes. We have identified three putative horizontally acquired
      regions, including one that is likely to have been acquired prior to speciation from the
      closely related Helicobacter cetorum. Our results suggest that Sahul64, with the absence of
      cagPAI, highly divergent cell envelope proteins and a predicted non-transportable VacA, could
      be more highly adapted to ancient indigenous Australian people but with lower virulence
      potential compared to other sequenced and cagPAI positive H. pylori strains.
AU  - Lu W
AU  - Wise MJ
AU  - Tay CY
AU  - Windsor HM
AU  - Marshall BJ
AU  - Peacock C
AU  - Perkins T
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2013 196: 1073-1083.

PMID- 24092780
VI  - 1
DP  - 2013
TI  - Genome Sequence of the Fructan-Degrading Organism Marinimicrobium sp. Strain LS-A18, Isolated from a Marine Solar Saltern.
PG  - e00776-13
AB  - Marinimicrobium sp. strain LS-A18 is a fructan-degrading organism isolated from a brine sample
      from a marine solar saltern in Jiaozhou Bay, China. The draft genome
      sequence of this bacterium is 3,815,107 bp in length, with a G+C content of
      59.03%. To our knowledge, this is the first genome announcement of a
      fructan-degrading strain of the genus Marinimicrobium.
AU  - Lu WD
AU  - Pang HQ
AU  - Guo LZ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00776-13.

PMID- 25953184
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Clavibacter michiganensis subsp. insidiosus R1-1 Using PacBio Single-Molecule Real-Time Technology.
PG  - e00396-15
AB  - We report here the complete genome sequence of Clavibacter michiganensis subsp. insidiosus
      R1-1, isolated in Minnesota, USA. The R1-1 genome, generated by a de
      novo assembly of PacBio sequencing data, is the first complete genome sequence
      available for this subspecies.
AU  - Lu Y
AU  - Samac DA
AU  - Glazebrook J
AU  - Ishimaru CA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00396-15.

PMID- 8614977
VI  - 216
DP  - 1996
TI  - Analysis of 94 kb of the chlorella virus PBCV-1 330-kb genome: Map positions 88 to 182.
PG  - 102-123
AB  - Analysis of 94 kb of DNA, located between map positions 88 and 182 kb in the 330-kb chlorella
      virus PBCV-1 genome, revealed 195 open reading frames 65 codons or longer.  One hundred and
      five of the 195 ORFs were considered major ORFs.  Twenty-six of the 105 major ORFs resembled
      genes in the databases including three chitinases, a chitosanase, three serine/threonine
      protein kinases, two additional protein kinases, a tyrosine protein phosphatase, two ankyrins,
      an ornithine decarboxylase, a copper/zinc-superoxide dismutase, a proliferating cell nuclear
      antigen, a DNA polymerase, a fibronectin-binding protein, the yeast Ski2 protein, an adenine
      DNA methyltransferase and its corresponding DNA site-specific endonuclease, and an amidase.
      The genes for the 105 major ORFs were evenly distributed along the genome and, except for one
      noncoding 1788-nucleotide stretch, the genes were close together.  Unexpectedly, a 900-bp
      region in the 1788-bp noncoding sequence resembled a CpG island.
AU  - Lu Z
AU  - Li Y
AU  - Que Q
AU  - Kutish GF
AU  - Rock DL
AU  - Van Etten JL
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1996 216: 102-123.

PMID- 22493204
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of a Thermophilic Methanogen, Methanocella conradii HZ254, Isolated from Chinese Rice Field Soil.
PG  - 2398-2399
AB  - Members of the order Methanocellales play a key role in methane emissions in paddy fields.
      Because of their slow growth and fastidious culture conditions,
      pure cultures are difficult to isolate and have been unavailable until recently.
      Here we report the complete genome sequence of a novel isolate in this group,
      Methanocella conradii strain HZ254.
AU  - Lu Z
AU  - Lu Y
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2398-2399.

PMID- 25502673
VI  - 2
DP  - 2014
TI  - Genome Sequence of the Petroleum Hydrocarbon-Degrading Bacterium Alcanivorax sp.  Strain 97CO-5.
PG  - e01277-14
AB  - Alcanivorax sp. strain 97CO-5 was isolated from a crude-oil-degrading consortium, enriched
      from Yellow Sea sediment of China. Here, we present the draft genome of
      strain 97CO-5, which comprises 3,251,558 bp with a G+C content of 54.54% and
      contains 2,962 protein-coding genes and 42 tRNAs.
AU  - Luan X
AU  - Cui Z
AU  - Gao W
AU  - Li Q
AU  - Yin X
AU  - Zheng L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01277-14.

PMID- 7607501
VI  - 157
DP  - 1995
TI  - Cloning and analysis of the plasmid-borne genes encoding the Bsp6I restriction and modification enzymes.
PG  - 25-29
AB  - The Bsp6I restriction and modification (R-M) system has been localized on the plasmid pXH13,
      naturally occurring in the Bacillus sp. strain RFL6.  The genes coding for the Bsp6I-R-M
      system, an Fnu4HI isoschizomer recognizing the sequence GCNGC, have been cloned in Escherichia
      coli by two steps.  The nucleotide sequence of a 2126-bp region containing the genes for
      restriction endonuclease (ENase; bsp6IR) and DNA methyltransferase (MTase; bsp6IM) has been
      determined.  The genes are separated by 99 bp and are arranged tandemly with bsp6IR preceding
      bsp6IM.  The DNA sequence predicts an ENase of 174 amino acids (19.9 kDa) and a MTase of 315
      aa (36.3 kDa).  M.Bsp6I contains all the conserved aa sequence motifs characteristic for
      m5C-MTases.  In addition, its variable region exhibits a slight similarity to the
      5'-GCNGC-3'-specific target-recognition domain from M.Phi3T.  No aa sequence similarity was
      found between R.Bsp6I and M.Bsp6I, nor among R.Bsp6I and other known ENases.  We have tested
      recombinant plasmids carrying the complete R-M system for their ability to transform native
      and pre-methylated Escherichia coli hosts.  The results indicate that pre-methylation
      increases the efficiency of establishment of the complete R-M system.  In addition, we have
      obtained orientation-dependent differences in transformation efficiency.
AU  - Lubys A
AU  - Janulaitis A
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 25-29.

PMID- 10518615
VI  - 27
DP  - 1999
TI  - Structural organization and regulation of the plasmid-borne type II restriction-modification system Kpn21 from Klebsiella pneumoniae RFL2.
PG  - 4228-4234
AB  - Kpn2I enzymes of a type II restriction-modification (R-M) system from the bacterium Klebsiella
      pneumoniae strain RFL2 recognize the sequence 5'-TCCGGA-3'. The Kpn2I R-M genes have been
      cloned and expressed in Escherichia coli. DNA sequence analysis revealed the presence of two
      convergently transcribed open reading frames (ORFs) coding for a restriction endonuclease
      (Enase) of 301 amino acids (34.8 kDa) and methyltransferase (Mtase) of 375 amino acids (42.1
      kDa). The 3'-terminal ends of these genes ( kpn2IR and kpn2IM, respectively) overlap by 11
      bp. In addition, a small ORF (gene kpn2IC ) capable of coding for a protein of 96 amino acids
      in length (10.6 kDa) was found upstream of kpn2IM. The direction of kpn2IC transcription is
      opposite to that of kpn2IM. The predicted amino acid sequence of this ORF includes a probable
      helix-turn-helix motif. We show that the product of kpn2IC represses expression of the Kpn2I
      Mtase but has no influence on expression of the Enase gene. Such a mode of regulation is
      unique among R-M systems analyzed so far. The Kpn2I R-M is located on the K.pneumoniae RFL2
      plasmid pKp4.3, which is able to replicate in E.coli cells.
AU  - Lubys A
AU  - Jurenaite S
AU  - Janulaitis A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1999 27: 4228-4234.

PMID- Not carried by PubMed...
VI  - 0
DP  - 1996
TI  - Cloning of the genes encoding type IIS restriction-modification system HphI from Haemophilus parahaemolyticus.
PG  - 39-41
AB  - The restriction-modification system HphI from Haemophilus parahaemolyticus was cloned into E.
      coli and sequenced.  Five open reading frames aligned in the same orientation were found.  The
      first ORF, orfX, is incomplete and encodes an unknown protein.  The next is the gene for
      C5-methylcytosine forming HphI methylase (hphIMC).  The third gene codes for the
      N6-methyladenine forming HphI methylase (hphIMA).  The fourth gene encodes HphI restriction
      endonuclease.  The expression of hphIR was obtained only after the subcloning of this gene
      under the control of T7 RNA polymerase promoter.  The last gene, menB, codes for the
      dihydroxynaphthoate synthase.
AU  - Lubys A
AU  - Lubiene J
PT  - Journal Article
TA  - Biologija
JT  - Biologija
SO  - Biologija 1996 0: 39-41.

PMID- 8759008
VI  - 24
DP  - 1996
TI  - Cloning and analysis of the genes encoding the type IIS restriction-modification system HphI from Haemophilus parahaemolyticus.
PG  - 2760-2766
AB  - The genomic region encoding the type IIS restriction-modification (R-M) system HphI (enzymes
      recognizing the asymmetric sequence 5'-GGTGA-3'/5'-TCACC-3') from Haemophilus
      parahaemolyticus were cloned into Escherichia coli and sequenced.  Sequence analysis of the
      R-M HphI system revealed three adjacent genes aligned in the same orientation: a cytosine 5
      methyltransferase (gene hphIMC), an adenine N6 methyltransferase (hphIMA) and the HphI
      restriction endonuclease (gene hphIR).  Either methyltransferase is capable of protecting
      plasmid DNA in vivo against the action of the cognate restriction endonuclease.  hphIMA
      methylation renders plasmid DNA resistant to R.HindIII at overlapping sites, suggesting that
      the adenine methyltransferase modifies the 3'-terminal A residue on the GGTGA strand.  Strong
      homology was found between the N-terminal part of the m6A methyltransferase and an
      unidentified reading frame interrupted by an incomplete galE gene of Neisseria meningitidis.
      The HphI R-M genes are flanked by a copy of a 56 bp direct nucleotide repeat on each side.
      Similar sequences have also been identified in the non-coding regions of H.influenzae Rd DNA.
      Possible involvement of the repeat sequences in the mobility of the HphI R-M system is
      discussed.
AU  - Lubys A
AU  - Lubiene J
AU  - Kulakauskas S
AU  - Stankevicius K
AU  - Timinskas A
AU  - Janulaitis A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1996 24: 2760-2766.

PMID- 8163180
VI  - 141
DP  - 1994
TI  - Cloning and analysis of translational control for genes encoding the Cfr9I restriction-modification system.
PG  - 85-89
AB  - The complete type-II Cfr9I restriction-modification (R-M) system of Citrobacter freundii
      strain RFL9, recognizing the DNA sequence CCCGGG, has been cloned and expressed, and
      functionally active enzymes have been produced in Escherichia coli. Both the methyltransferase
      (MTase; M.Cfr9I) and restriction endonuclease (ENase; R.Cfr9I) were found to be encoded on a
      2.3-kb cloned fragment in the same transcriptional orientation, but differing in translational
      phases. The last codon (underlined) (ATGA) of the MTase-encoding gene (Cf9IM) overlaps with
      the start codon for the ENase-encoding gene (overlined) Cfr9IR). A nucleotide sequence
      complementary to a predicted Shine-Dalgarno sequence preceeding cfr9IR is within this gene.
      Predicted free energy (deltaG) for formation of the mRNA secondary structure involving these
      complementary sequences was found to be - 16.1 kcal mol. Amino-acid sequence homology of 80%
      was found between R.Cfr9I and R.XcyI.
AU  - Lubys A
AU  - Menkevicius S
AU  - Timinskas A
AU  - Butkus V
AU  - Janulaitis A
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1994 141: 85-89.

PMID- 30269783
VI  - 224
DP  - 2018
TI  - Characterization of plasmids harboring blaCTX-M genes in Escherichia coli from French pigs.
PG  - 100-106
AB  - Resistance to extended-spectrum cephalosporins is prevalent in French pig E. coli
      isolates. The aim of this study was to characterize the plasmids and genes
      present in pathogenic and commensal extended-spectrum cephalosporins -resistant
      isolates. The resistance plasmids of 26 strains were sequenced and then analyzed
      to identify resistance and virulence genes. Results showed that resistance to
      extended-spectrum cephalosporins in French pig E. coli isolates is-as in other
      food animals in France-mainly carried by highly similar blaCTX-M-1 IncI1/ST3
      plasmids. These plasmids very often bear other resistance genes such as
      resistance to sulphonamides (sul2), trimethoprim (dfrA17) and aminoglycosides
      (aadA5), and occasionally to tetracycline (tet(A)), macrolides (mph(A) and erm
      genes), phenicols (floR) or streptomycin (strA, strB). Few virulence genes were
      detected, including colicins, heat-stable enterotoxins, adhesins or
      temperature-sensitive hemagglutinins. The other cefotaximases detected were
      blaCTX-M-27 and blaCTX-M-14, the latter being on an IncF plasmid which showed
      very close identity to a human epidemic plasmid. Importantly, resistance genes
      for quinolones or polymyxins were never detected on the extended-spectrum
      cephalosporins resistance plasmids. These results are helpful to evidence the
      risk of co-selecting cephalosporins -resistance using antibiotics outside this
      group. They also highlight the occasional presence in pigs of human epidemic
      plasmids.
AU  - Lucas P
AU  - Jouy E
AU  - Le Devendec L
AU  - de Boisseson C
AU  - Perrin-Guyomard A
AU  - Jove T
AU  - Blanchard Y
AU  - Touzain F
AU  - Kempf I
PT  - Journal Article
TA  - Vet. Microbiol.
JT  - Vet. Microbiol.
SO  - Vet. Microbiol. 2018 224: 100-106.

PMID- 11160929
VI  - 29
DP  - 2001
TI  - Rapid evolution of the DNA-binding site in LAGLIDADG homing endonucleases.
PG  - 960-969
AB  - Sequence analysis of chloroplast and mitochondrial large subunit rRNA genes from over 75 green
      algae disclosed 28 new group I intron-encoded proteins carrying a single LAGLIDADG motif.
      These putative homing endonucleases form four subfamilies of homologous enzymes, with the
      members of each subfamily being encoded by introns sharing the same insertion site. We showed
      that four divergent endonucleases from the I-CreI subfamily cleave the same DNA substrates.
      Mapping of the 66 amino acids that are conserved among the members of this subfamily on the
      3-dimensional structure of I-CreI bound to its recognition sequence revealed that these
      residues participate in protein folding, homodimerization, DNA recognition and catalysis.
      Surprisingly, only seven of the 21 I-CreI amino acids interacting with DNA are conserved,
      suggesting that I-CreI and its homologs use different subsets of residues to recognize the
      same DNA sequence. Our sequence comparison of all 45 single-LAGLIDADG proteins identified so
      far suggests that these proteins share related structures and that there is a weak pressure in
      each subfamily to maintain identical protein-DNA contacts. The high sequence variability we
      observed in the DNA-binding site of homologous LAGLIDADG endonucleases provides insight into
      how these proteins evolve new DNA specificity.
AU  - Lucas P
AU  - Otis C
AU  - Mercier J-P
AU  - Turmel M
AU  - Lemieux C
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2001 29: 960-969.

PMID- 23045491
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of the Thermophilic, Piezophilic, Heterotrophic Bacterium Marinitoga piezophila KA3.
PG  - 5974-5975
AB  - Marinitoga piezophila KA3 is a thermophilic, anaerobic, chemoorganotrophic, sulfur-reducing
      bacterium isolated from the Grandbonum deep-sea hydrothermal vent
      site at the East Pacific Rise (13 degrees N, 2,630-m depth). The genome of M.
      piezophila KA3 comprises a 2,231,407-bp circular chromosome and a 13,386-bp
      circular plasmid. This genome was sequenced within Department of Energy Joint
      Genome Institute CSP 2010.
AU  - Lucas S et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5974-5975.

PMID- 23458837
VI  - 7
DP  - 2012
TI  - Complete genome sequence of Marinomonas posidonica type strain (IVIA-Po-181(T)).
PG  - 31-43
AB  - IVIA-Po-181 Lucas-Elio 2011 belongs to the family within the phylum . Different species of the
      genus can be readily isolated from the seagrass . is among the
      most abundant species of the genus detected in the cultured microbiota of
      suggesting a close relationship with this plant, which has a great ecological
      value in the Mediterranean Sea, covering an estimated surface of 38,000 Km. Here
      we describe the genomic features of . The 3,899,940 bp long genome harbors 3,544
      protein-coding genes and 107 RNA genes and is a part of the project.
AU  - Lucas-Elio P
AU  - Goodwin L
AU  - Woyke T
AU  - Pitluck S
AU  - Nolan M
AU  - Kyrpides NC
AU  - Detter JC
AU  - Copeland A
AU  - Lu M
AU  - Bruce D
AU  - Detter C
AU  - Tapia R
AU  - Han S
AU  - Land ML
AU  - Ivanova N
AU  - Mikhailova N
AU  - Johnston AW
AU  - Sanchez-Amat A
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 7: 31-43.

PMID- 22675599
VI  - 6
DP  - 2012
TI  - Complete genome sequence of the melanogenic marine bacterium Marinomonas mediterranea type strain (MMB-1(T)).
PG  - 63-73
AB  - Marinomonas mediterranea MMB-1(T) Solano & Sanchez-Amat 1999 belongs to the family
      Oceanospirillaceae within the phylum Proteobacteria. This species is of
      interest because it is the only species described in the genus Marinomonas to
      date that can synthesize melanin pigments, which is mediated by the activity of a
      tyrosinase. M. mediterranea expresses other oxidases of biotechnological
      interest, such as a multicopper oxidase with laccase activity and a novel
      L-lysine-epsilon-oxidase. The 4,684,316 bp long genome harbors 4,228
      protein-coding genes and 98 RNA genes and is a part of the Genomic Encyclopedia
      of Bacteria and Archaea project.
AU  - Lucas-Elio P
AU  - Goodwin L
AU  - Woyke T
AU  - Pitluck S
AU  - Nolan M
AU  - Kyrpides NC
AU  - Detter JC
AU  - Copeland A
AU  - Teshima H
AU  - Bruce D
AU  - Detter C
AU  - Tapia R
AU  - Han S
AU  - Land ML
AU  - Ivanova N
AU  - Mikhailova N
AU  - Johnston AW
AU  - Sanchez-Amat A
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 6: 63-73.

PMID- 
VI  - 5
DP  - 2012
TI  - Complete genome sequence of the melanogenic marine bacterium Marinomonas mediterranea type strain (MMB-1T).
PG  - 63-73
AB  - 
AU  - Lucas-Elio P
AU  - Goodwin L
AU  - Woyke T
AU  - Pitluck S
AU  - Nolan M
AU  - Kyrpides NC
AU  - Detter JC
AU  - Copeland A
AU  - Teshima H
AU  - Bruce D
AU  - Detter C
AU  - Tapia R
AU  - Han S
AU  - Land ML
AU  - Ivanova N
AU  - Mikhailova N
AU  - Johnston AWB
AU  - Sanchez-Amat A
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 5: 63-73.

PMID- 10998327
VI  - 275
DP  - 2000
TI  - Broad-range bacteriophage resistance in Streptococcus thermophilus by insertional mutagenesis.
PG  - 267-277
AB  - Streptococcus thermophilus is a lactic acid bacterium used in industrial milk fermentation. To
      obtain phage-resistant starters, S. thermophilus strain Sfi1 was submitted to mutagenesis with
      the thermolabile insertional vector pG(+)host9:ISS1 followed by a challenge with the lytic S.
      thermophilus phage Sfi19.  Vector insertions into four distinct sites led to a
      phage-resistance phenotype. Three mutants were characterized further. They were protected
      against the homologous challenging phage and 14 heterologous phages. All three mutants
      adsorbed phages. No intracellular phage DNA synthesis was observed in mutants R7 and R71,
      while mutant R24 showed a delayed and diminished phage DNA synthesis compared to the parental
      Sfi1 strain. In mutant R7 a short deletion occurred next to the insertion site which removed
      the upstream sequences and the 15 initial codons from orf 394, encoding a likely transmembrane
      protein.  Analogy with other phage systems suggests an involvement of this protein in the
      phage DNA injection process. In mutant R24 the vector was inserted into orf 269 predicting an
      oxido-reductase. When the vector sequence was removed via homologous recombination across the
      duplicated insertion elements, mutant R24 returned to the phage susceptibility of the parental
      strain. This observation suggested that inactivation of orf  269 was not crucial for the
      resistance phenotype. A gene encoding a likely restriction subunit of a type I
      restriction-modification system was located directly downstream of the insertion site in
      mutant R24. HsdM and hsdS genes encoding the modification and specificity subunits of a type I
      R-M system and biological evidence for an active R-M system were detected in strain Sfi1,
      suggesting involvement of a type I R-M system in the resistance phenotype of R24.
AU  - Lucchini S
AU  - Sidoti J
AU  - Brussow H
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 2000 275: 267-277.

PMID- 24723712
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Campylobacter ureolyticus Strain CIT007, the First Whole-Genome Sequence of a Clinical Isolate.
PG  - e00262-14
AB  - Herein, we present the draft genome sequence of Campylobacter ureolyticus. Strain CIT007 was
      isolated from a stool sample from an elderly female presenting with diarrheal illness and
      end-stage chronic renal disease.
AU  - Lucid A
AU  - Bullman S
AU  - Koziel M
AU  - Corcoran GD
AU  - Cotter PD
AU  - Sleator RD
AU  - Lucey B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00262-14.

PMID- 20624973
VI  - 107
DP  - 2010
TI  - A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria.
PG  - 13479-13484
AB  - Nitrospira are barely studied and mostly uncultured nitrite-oxidizing bacteria, which are,
      according to molecular data, among the most diverse
      and widespread nitrifiers in natural ecosystems and biological wastewater
      treatment. Here, environmental genomics was used to reconstruct the
      complete genome of 'Candidatus Nitrospira defluvii' from an activated
      sludge enrichment culture. On the basis of this first-deciphered
      Nitrospira genome and of experimental data, we show that Ca. N. defluvii
      differs dramatically from other known nitrite oxidizers in the key enzyme
      nitrite oxidoreductase (NXR), in the composition of the respiratory chain,
      and in the pathway used for autotrophic carbon fixation, suggesting
      multiple independent evolution of chemolithoautotrophic nitrite oxidation.
      Adaptations of Ca. N. defluvii to substrate-limited conditions include an
      unusual periplasmic NXR, which is constitutively expressed, and pathways
      for the transport, oxidation, and assimilation of simple organic compounds
      that allow a mixotrophic lifestyle. The reverse tricarboxylic acid cycle
      as the pathway for CO(2) fixation and the lack of most classical defense
      mechanisms against oxidative stress suggest that Nitrospira evolved from
      microaerophilic or even anaerobic ancestors. Unexpectedly, comparative
      genomic analyses indicate functionally significant lateral gene-transfer
      events between the genus Nitrospira and anaerobic ammonium-oxidizing
      planctomycetes, which share highly similar forms of NXR and other proteins
      reflecting that two key processes of the nitrogen cycle are evolutionarily
      connected.
AU  - Lucker S
AU  - Wagner M
AU  - Maixner F
AU  - Pelletier E
AU  - Koch H
AU  - Vacherie B
AU  - Rattei T
AU  - Damste JS
AU  - Spieck E
AU  - Le Paslier D
AU  - Daims H
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2010 107: 13479-13484.

PMID- 22582376
VI  - 194
DP  - 2012
TI  - Genome Sequences of the Ethanol-Tolerant Lactobacillus vini Strains LMG 23202T and JP7.8.9.
PG  - 3018
AB  - We report on the genome sequences of Lactobacillus vini type strain LMG 23202(T)(DSM
      20605)isolated from fermenting grape musts in Spain) and the industrial strain L. vini JP7.8.9
      (isolated from a bioethanol plant in northeast Brazil.  All contigs were assembled using
      gsAssembler, and genes were predicted and annotated using Rapid Annotation using Subsystem
      Technology (RAST). The identified genome sequence of LMG 23202(T) had 2.201.333 bp, 37.6% G+C,
      and 1,833 genes, whereas the identified genome sequence of JP7.8.9 had 2.301.037 bp, 37.8%
      G+C, and 1,739 genes. The gene repertoire of the species L. vini offers promising
      opportunities for biotechnological applications.
AU  - Luckwu-de-Lucena BT
AU  - Silva GG
AU  - Manoel-Dos-Santos B
AU  - Dias GM
AU  - Amaral GR
AU  - Moreira AP
AU  - de Morais JMA
AU  - Dutilh BE
AU  - Edwards RA
AU  - Balbino V
AU  - Thompson CC
AU  - Thompson FL
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3018.

PMID- 26564042
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequence of Mycobacterium bovis BCG-1 (Russia).
PG  - e01320-15
AB  - BCG vaccine (Mycobacterium bovis BCG-1 [Russia]) is the most important component  of
      tuberculosis prophylaxis in Russia. This study represents the complete genome
      sequence and genetic characteristics of M. bovis BCG-1 (Russia), which has been
      used to manufacture BCG vaccine in Russia and in some other countries.
AU  - Ludannyy R
AU  - Alvarez FM
AU  - Levi D
AU  - Markelov M
AU  - Dedkov V
AU  - Aleksandrova N
AU  - Shipulin G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01320-15.

PMID- 25814612
VI  - 3
DP  - 2015
TI  - Complete Genome Sequences of a Clinical Isolate and an Environmental Isolate of Vibrio parahaemolyticus.
PG  - e00216-15
AB  - Vibrio parahaemolyticus is the leading cause of seafood-borne infections in the United States.
      We report complete genome sequences for two V. parahaemolyticus
      strains isolated in 2007, CDC_K4557 and FDA_R31 of clinical and oyster origin,
      respectively. These two sequences might assist in the investigation of
      differential virulence of this organism.
AU  - Ludeke CH
AU  - Kong N
AU  - Weimer BC
AU  - Fischer M
AU  - Jones JL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00216-15.

PMID- 29774086
VI  - 13
DP  - 2018
TI  - Complete genome sequence of 'Thiodictyon syntrophicum' sp. nov. strain Cad16(T),  a photolithoautotrophic purple sulfur bacterium isolated from the alpine meromictic Lake Cadagno.
PG  - 14
AB  - 'Thiodictyon syntrophicum' sp. nov. strain Cad16(T) is a photoautotrophic purple  sulfur
      bacterium belonging to the family of Chromatiaceae in the class of
      Gammaproteobacteria. The type strain Cad16(T) was isolated from the chemocline of
      the alpine meromictic Lake Cadagno in Switzerland. Strain Cad16(T) represents a
      key species within this sulfur-driven bacterial ecosystem with respect to carbon
      fixation. The 7.74-Mbp genome of strain Cad16(T) has been sequenced and
      annotated. It encodes 6237 predicted protein sequences and 59 RNA sequences.
      Phylogenetic comparison based on 16S rRNA revealed that Thiodictyon elegans
      strain DSM 232(T) the most closely related species. Genes involved in sulfur
      oxidation, central carbon metabolism and transmembrane transport were found.
      Noteworthy, clusters of genes encoding the photosynthetic machinery and pigment
      biosynthesis are found on the 0.48 Mb plasmid pTs485. We provide a detailed
      insight into the Cad16(T) genome and analyze it in the context of the microbial
      ecosystem of Lake Cadagno.
AU  - Luedin SM
AU  - Pothier JF
AU  - Danza F
AU  - Storelli N
AU  - Frigaard NU
AU  - Wittwer M
AU  - Tonolla M
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2018 13: 14.

PMID- 24558236
VI  - 2
DP  - 2014
TI  - The Genome Sequence of Bifidobacterium moukalabense DSM 27321 Highlights the Close Phylogenetic Relatedness with the Bifidobacterium dentium Taxon.
PG  - e00048-14
AB  - Bifidobacterium moukalabense DSM 27321 is the reference strain for a recently described new
      bifidobacterial species that has been isolated from a wild west
      lowland gorilla. Here, we report the whole-genome sequence of DSM 27321, which
      supports very close phylogenetic relatedness with members of the Bifidobacterium
      adolescentis phylogenetic group and, in particular, the Bifidobacterium dentium
      taxon.
AU  - Lugli GA
AU  - Duranti S
AU  - Milani C
AU  - Turroni F
AU  - Viappiani A
AU  - Mangifesta M
AU  - van Sinderen D
AU  - Ventura M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00048-14.

PMID- 24297705
VI  - 18
DP  - 2014
TI  - Isolation and characterization of phage-host systems from the Baltic Sea ice.
PG  - 121-130
AB  - In search for sea ice bacteria and their phages from the Baltic Sea ice, two ice
      samples were collected from land-fast ice in a south-west Finland coastal site in
      February and March 2011. Bacteria were isolated from the melted sea ice samples
      and phages were screened from the same samples for 43 purified isolates.
      Plaque-producing phages were found for 15 bacterial isolates at 3 degrees C. Ten
      phage isolates were successfully plaque purified and eight of them were chosen
      for particle purification to analyze their morphology and structural proteins.
      Phage 1/32 infecting an isolate affiliated to phylum Bacteroidetes
      (Flavobacterium sp.) is a siphovirus and six phages infecting isolates affiliated
      to gamma-Proteobacteria (Shewanella sp.) hosts were myoviruses. Cross titrations
      between the hosts showed that all studied phages are host specific. Phage
      solutions, host growth and phage infection were tested in different temperatures
      revealing phage temperature tolerance up to 45 degrees C, whereas phage infection
      was in most of the cases retarded above 15 degrees C. This study is the first to
      report isolation and cultivation of ice bacteria and cold-active phages from the
      Baltic Sea ice.
AU  - Luhtanen AM
AU  - Eronen-Rasimus E
AU  - Kaartokallio H
AU  - Rintala JM
AU  - Autio R
AU  - Roine E
PT  - Journal Article
TA  - Extremophiles
JT  - Extremophiles
SO  - Extremophiles 2014 18: 121-130.

PMID- 29976614
VI  - 6
DP  - 2018
TI  - Genome Sequence of Pantoea ananatis SGAir0210, Isolated from Outdoor Air in Singapore.
PG  - e00643-18
AB  - Pantoea ananatis SGAir0210 was isolated from outdoor air collected in Singapore.  The genome
      was assembled from long reads generated by single-molecule real-time
      sequencing complemented with short reads. The genome size was approximately 4.81
      Mb, with 4,303 protein-coding genes, 80 tRNAs, and 22 rRNAs identified.
AU  - Luhung I et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00643-18.

PMID- 424284
VI  - 6
DP  - 1979
TI  - Site specific endonuclease from Fusobacterium nucleatum.
PG  - 1-15
AB  - Four different isolates of Fusobacterium nucleatum (A,C,D and E) contain
      restriction endonucleases of differing specificity.  Whilst many of the
      endonucleases are isochizomers of known enzymes, two novel activities are Fnu
      DII which recognizes and cleaves the sequence 5'-CG^CG-3' 3'-GC^GC-5' and Fnu
      EI which recognizes and cleaves the sequence 5'-^GATC-3' 3'-CTAG^-5'
      irrespective of the extent of methylation of the adenine residues.
AU  - Lui ACP
AU  - McBride BC
AU  - Vovis GF
AU  - Smith M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1979 6: 1-15.

PMID- 28082504
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Pseudomonas aeruginosa Strain Hex1T Isolated from Soils  Contaminated with Used Lubricating Oil in Argentina.
PG  - e01473-16
AB  - Pseudomonas aeruginosa Hex1T was isolated from soils contaminated with used lubricating oil
      from a garage in Cordoba, Argentina. This strain is capable of
      utilizing this pollutant as the sole carbon and energy source. Here, we present
      the 6.9-Mb draft genome sequence of Hex1T, which contains many heavy
      metal-resistance genes.
AU  - Lujan AM
AU  - Feliziani S
AU  - Smania AM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01473-16.

PMID- 27738035
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Tenacibaculum soleae UCD-KL19.
PG  - e01120-16
AB  - Here, we present the draft genome sequence of Tenacibaculum soleae strain UCD-KL19. The
      assembly contains 3,012,701 bp in 46 contigs. This strain was
      isolated from a seagrass leaf (Zostera marina) collected from Bodega Bay, CA, as
      a part of an undergraduate student research project on isolating bacteria from
      seagrass.
AU  - Lujan KM
AU  - Eisen JA
AU  - Coil DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01120-16.

PMID- 28360178
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Pseudomonas moraviensis UCD-KL30, Vibrio ostreicida UCD-KL16, Colwellia sp. Strain UCD-KL20, Shewanella sp. Strain UCD-KL12, and  Shewanella sp. Strain UCD-KL21, Isolated from Seagrass.
PG  - e00023-17
AB  - Here, we present the draft genome sequences for five bacterial strains. These strains were all
      isolated from seagrass (Zostera marina) collected from Bodega
      Bay, CA, as a part of an undergraduate research project focused on
      seagrass-associated microbes.
AU  - Lujan KM
AU  - Eisen JA
AU  - Coil DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00023-17.

PMID- 11179886
VI  - 11
DP  - 2001
TI  - BglII and MunI: what a difference a base makes.
PG  - 14-18
AB  - Restriction endonucleases are resilient to alterations in their DNA-binding specificities.
      Structures of the BglII and MunI endonucleases bound to their palindromic DNA sites, which
      differ by only their outer base pairs from the recognition sequences of BamHI and EcoRI,
      respectively, have recently been determined. A comparison of these complexes reveals
      surprising differences and similarities in structure, and provides a basis for understanding
      the immutability of restriction endonucleases.
AU  - Lukacs CM
AU  - Aggarwal AK
PT  - Journal Article
TA  - Curr. Opin. Struct. Biol.
JT  - Curr. Opin. Struct. Biol.
SO  - Curr. Opin. Struct. Biol. 2001 11: 14-18.

PMID- 10655616
VI  - 7
DP  - 2000
TI  - Understanding the immutability of restriction enzymes: crystal structure of BglII and its DNA substrate at 1.5A resolution.
PG  - 134-140
AB  - Restriction endonucleases are remarkably resilient to alterations in their DNA binding
      specificity. To understand the basis of this immutability, we have determined the crystal
      structure of endonuclease BglII bound to its recognition sequence (AGATCT), at 1. 5 A
      resolution. We compare the structure of BglII to endonuclease BamHI, which recognizes a
      closely related DNA site (GGATCC). We show that both enzymes share a similar alpha/beta core,
      but in BglII, the core is augmented by a beta-sandwich domain that encircles the DNA to
      provide extra specificity.  Remarkably, the DNA is contorted differently in the two
      structures, leading to different protein-DNA contacts for even the common base pairs.
      Furthermore, the BglII active site contains  a glutamine in place of the glutamate at the
      general base position in BamHI, and only a single metal is found coordinated to the putative
      nucleophilic water and the phosphate oxygens. This surprising diversity in structures shows
      that different strategies can be successful in achieving site-specific recognition and
      catalysis in restriction endonucleases.
AU  - Lukacs CM
AU  - Kucera R
AU  - Schildkraut I
AU  - Aggarwal AK
PT  - Journal Article
TA  - Nat. Struct. Biol.
JT  - Nat. Struct. Biol.
SO  - Nat. Struct. Biol. 2000 7: 134-140.

PMID- Not included in PubMed...
VI  - 14
DP  - 1986
TI  - Fluorescent labelling of EcoRI and EcoRV.
PG  - 259-260
AB  - Fluorescent chromophores, covalently attached to proteins, have been widely used as reporter
      groups to monitor associations of proteins with ligands, either by observing perturbations to
      fluorescence spectra or by fluorescence polarization methods.  In the latter, given excitation
      with light polarized in the vertical plane and measurements of emission in both horizontal and
      vertical planes, the binding of a ligand that increases the rotational correlation time of the
      protein (relative to the excited state lifetime of the fluorophore) may reduce the H/V ratio.
AU  - Luke PA
AU  - Halford SE
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 1986 14: 259-260.

PMID- 2996987
VI  - 37
DP  - 1985
TI  - Solubility of the EcoRI restriction endonuclease and its purification from an over-producing strain.
PG  - 241-246
AB  - The solubility of the EcoRI restriction endonuclease was measured in solutions
      of varying NaCl concentrations, at different temperatures and in the presence
      of DNA.  The precipitation of the protein was enhanced by low NaCl
      concentrations, by elevated temperatures, and by the addition of DNA.  These
      observations are discussed in relationship to the interaction of this protein
      with DNA.  The purification of the EcoRI restriction enzyme from a strain of
      Escherichia coli that over-produces this enzyme was hampered by the
      insolubility of the protein, and hence the purification procedure was modified
      to optimize the recovery of active enzyme.
AU  - Luke PA
AU  - Halford SE
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1985 37: 241-246.

PMID- 3333365
VI  - 5
DP  - 1987
TI  - The EcoRV restriction endonuclease.
PG  - 185-207
AB  - Type II restriction endonucleases have attracted attention for two main
      reasons:  firstly, their many applications in the dissection of DNA and in the
      construction of novel DNA molecules; secondly, as systems for studying the
      interactions of proteins with specific DNA sequences.  With respect to the
      latter, the EcoRI restriction endonuclease has been examined in greater depth
      than any other type II enzyme.  However, the EcoRI enzyme has a major
      disadvantage as a system for studying DNA-protein interactions:  the protein
      has a remarkably low solubility.  The solutions in which EcoRI shows maximal
      activity, and also affinity for its recognition site, are saturated at less
      than 0.5 microM of this protein.  Consequently, many techniques that have been
      developed to study protein-ligand interactions but which require high
      concentrations of the protein in solution, such as NMR spectroscopy, cannot be
      used on EcoRI.  But this drawback does not apply to all type II restriction
      enzymes.  A different enzyme, the EcoRV restriction endonuclease, has special
      advantages as a system for studying DNA-protein interactions.  In particular,
      this is the only type II restriction enzyme (apart from EcoRI) for which
      crystals of the protein have been reported.
AU  - Luke PA
AU  - McCallum SA
AU  - Halford SE
PT  - Journal Article
TA  - Gene Amplif. Anal.
JT  - Gene Amplif. Anal.
SO  - Gene Amplif. Anal. 1987 5: 185-207.

PMID- 
VI  - 273
DP  - 2006
TI  - Conversion of DNA methyltransferases to alkyltransferases via cofactor engineering.
PG  - 336-337
AB  - S-Adenosyl-L-methionine (AdoMet) is a biological sulfonium compound known as the major methyl
      donor in the cell.  AdoMet-dependent methyltransferases (MTases) catalyze the transfer of the
      methyl group from the cofactor S-adenosyl-L-methionine (AdoMet) to defined positions within
      various substrates like DNA, RNA, proteins and other biomolecules.  A series of new AdoMet
      analogs with extended linear carbon chains replacing the methyl group was obtained by chemical
      synthesis.  Remarkably, we find that extended groups containing a double or triple
      carbon-carbon bond one unit away from the sulfonium center, was opposed to saturated carbon
      chains, are readily transferred onto DNA owing to conjugative stabilization of the SN2-like
      transition state.  The MTase-assisted transalkylations of DNA are truly catalytic, efficient
      and proceed in a sequence-specific manner yielding corresponding adenine-N-6, cytosine-N4 or
      cytosine-5 derivatives.
AU  - Lukinavicius G
AU  - Klimasauskas S
AU  - Dalhoff C
AU  - Weinhold E
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 2006 273: 336-337.

PMID- 17309265
VI  - 129
DP  - 2007
TI  - Targeted labeling of DNA by methyltransferase-directed transfer of activated groups (mTAG).
PG  - 2758-2759
AB  - Methyltransferases catalyze highly specific transfers of methyl groups from the ubiquitous
      cofactor S-adenosyl-L-methionine (AdoMet) to
      various biopolymers like DNA, RNA, and proteins. Here we describe the
      first synthetic analogue of AdoMet with an activated side chain
      carrying a primary amino group that permits efficient
      methyltransferase-directed functionalization of DNA and subsequent
      amine-specific chemoligations with various reporter groups. The
      demonstrated two-step sequence-specific labeling of natural DNA offers
      a facile way to query the methylation status of the target sites and
      envisions numerous applications in functional studies and medical
      diagnostics.
AU  - Lukinavicius G
AU  - Lapiene V
AU  - Stasevskij Z
AU  - Dalhoff C
AU  - Weinhold E
AU  - Klimasauskas S
PT  - Journal Article
TA  - J. Am. Chem. Soc.
JT  - J. Am. Chem. Soc.
SO  - J. Am. Chem. Soc. 2007 129: 2758-2759.

PMID- 23042683
VI  - 40
DP  - 2012
TI  - Engineering the DNA cytosine-5 methyltransferase reaction for sequence-specific labeling of DNA.
PG  - 11594-11602
AB  - DNA methyltransferases catalyse the transfer of a methyl group from the ubiquitous cofactor
      S-adenosyl-L-methionine (AdoMet) onto specific target sites
      on DNA and play important roles in organisms from bacteria to humans. AdoMet
      analogs with extended propargylic side chains have been chemically produced for
      methyltransferase-directed transfer of activated groups (mTAG) onto DNA, although
      the efficiency of reactions with synthetic analogs remained low. We performed
      steric engineering of the cofactor pocket in a model DNA cytosine-5
      methyltransferase (C5-MTase), M.HhaI, by systematic replacement of three
      non-essential positions, located in two conserved sequence motifs and in a
      variable region, with smaller residues. We found that double and triple
      replacements lead to a substantial improvement of the transalkylation activity,
      which manifests itself in a mild increase of cofactor binding affinity and a
      larger increase of the rate of alkyl transfer. These effects are accompanied with
      reduction of both the stability of the product DNA-M.HhaI-AdoHcy complex and the
      rate of methylation, permitting competitive mTAG labeling in the presence of
      AdoMet. Analogous replacements of two conserved residues in M.HpaII and M2.Eco31I
      also resulted in improved transalkylation activity attesting a general
      applicability of the homology-guided engineering to the C5-MTase family and
      expanding the repertoire of sequence-specific tools for covalent in vitro and ex
      vivo labeling of DNA.
AU  - Lukinavicius G
AU  - Lapinaite A
AU  - Urbanaviciute G
AU  - Gerasimaite R
AU  - Klimasauskas S
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: 11594-11602.

PMID- 23557731
VI  - 8
DP  - 2013
TI  - Enhanced Chemical Stability of AdoMet Analogues for Improved Methyltransferase-Directed Labeling of DNA.
PG  - 1134-1139
AB  - Methyltransferases catalyze specific transfers of methyl groups from the ubiquitous cofactor
      S-adenosyl-L-methionine (AdoMet) to various
      nucleophilic positions in biopolymers like DNA, RNA, and proteins. We
      had previously described synthesis and application of AdoMet analogues
      carrying sulfonium-bound 4-substituted but-2-ynyl side chains for
      transfer by methyltransferases. Although useful in certain
      applications, these cofactor analogues exhibited short lifetimes in
      physiological buffers. Examination of the reaction kinetics and
      products showed that their fast inactivation followed a different
      pathway than observed for AdoMet and rather involved a pH-dependent
      addition of a water molecule to the side chain. This side reaction was
      eradicated by synthesis of a series of cofactor analogues in which the
      separation between an electronegative group and the triple bond was
      increased from one to three carbon units. The designed hex-2-ynyl
      moiety-based cofactor analogues with terminal amino, azide, or alkyne
      groups showed a markedly improved enzymatic transalkylation activity
      and proved well suitable for methyltransferase-directed
      sequence-specific labeling of DNA in vitro and in bacterial cell
      lysates.
AU  - Lukinavicius G
AU  - Tomkuviene M
AU  - Masevicius V
AU  - Klimasauskas S
PT  - Journal Article
TA  - ACS Chem. Biol.
JT  - ACS Chem. Biol.
SO  - ACS Chem. Biol. 2013 8: 1134-1139.

PMID- 
VI  - 28
DP  - 2000
TI  - Restriction endonucleases of type II from two endophytic strains of Bacillus.
PG  - A181
AB  - Restriction modification systems were found in more than 3000 bacterial species.  It is
      generally accepted that their primary role is to protect host bacteria against phage
      infection.  We used a simple technique proposed by Belavin with our modification, for
      detection of bacterial restriction endonucleases.  Endonucleases activity of 24 Bacillus
      strains isolated from inner tissues of cotton plants was tested by this method.  Enzyme of
      Bacillus licheniformis IMB B-55O8B (Bli55O8B) cuts DNA of lambda phage at 2 sites and DNA of
      T7 phage at 29 sites.  We found that computer calculated numbers of DNAs fragments and their
      molecular sizes that would be generated at the sequence GGTCTC, correlated with the observed
      cleavage frequency of the both mentioned substrates.  We suppose a new isoschisomer of type II
      endonuclease of restriction Eco31I was isolated from Bacillus licheniformis IMB B-55O8B.  A
      restriction endonuclease of Bacillus subtilis IMB 5044B (Bsu5044B) cut DNA at M13mp18 at four
      sites, DNA of pUC19 at six sites and DNA of pBR322 at fifteen sites.  We found that computer
      calculated number of fragments that would be generated the sequence 5'-GGNCC-3' correlated
      with the observed cleavage frequency of the above mentioned substrates.  Recently this
      sequence was determined for restrictase Asu1.  Similarity of digestion profiles of gel
      electrophoresis of T7 and lambda DNA fragments obtained after treating by Cfr13I (isoschizomer
      of AsuI) and Bsu5O44B was evidence of Bsu5044B could be new isoschizomer of AsuI.  Thus two
      endophytic strains of Bacillus were found to produce endonucleases of restriction.  Found
      enzymes were isoschizomers of well known enzymes AsuI and EcoR31I.
AU  - Lukyanchuk V
AU  - Reva O
AU  - Polishchuk L
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 2000 28: A181.

PMID- 10330874
VI  - 61
DP  - 1999
TI  - Determination of site-specificity of the II type restriction endonuclease in Streptomyces sp. 48.
PG  - 80-83
AB  - The activity of a restriction endonuclease which splits DNA of lambda and T7 phages into 8
      fragments has been detected in the mycelium lysates of the 2-days culture of Streptomyces sp.
      48.  The fragments dimensions according to the data of agarose gel electrophoresis, coincide
      with those of AsuII fragments of DNA of lambda and T7 phages.  This allows the studied Ssp48
      restrictase to be considered the isoschizomer of AsuII restriction endonuclease.
AU  - Lukyanchuk VV
AU  - Polishchuk LV
AU  - Strizhkova GM
AU  - Kopieiko OP
AU  - Matselyukh BP
PT  - Journal Article
TA  - Mikrobiol. Zh.
JT  - Mikrobiol. Zh.
SO  - Mikrobiol. Zh. 1999 61: 80-83.

PMID- 10565148
VI  - 61
DP  - 1999
TI  - Type-II site-specific restriction endonucleases in endophytic strains of the genus Bacillus.
PG  - 28-30
AB  - Using a modified Belavin's method the site-specific II type restriction endonucleases were
      determined for two endophytic strains of the Bacillus genus from the inner tissues of cotton
      plants.
AU  - Lukyanchuk VV
AU  - Reva OM
AU  - Polishchuk LV
PT  - Journal Article
TA  - Mikrobiol. Zh.
JT  - Mikrobiol. Zh.
SO  - Mikrobiol. Zh. 1999 61: 28-30.

PMID- 12244718
VI  - 71
DP  - 2002
TI  - Endophytic bacilli producing type II restriction endonucleases.
PG  - 491-493
AB  - Two of thirteen bacillar strains isolated from the inner tissues of cotton plants were found
      to produce type II restriction endonucleases. The investigation of the site specificity of
      these enzymes showed that they are AsuI and Eco31I isoschizomers.
AU  - Lukyanchuk VV
AU  - Reva ON
AU  - Polishchuk LV
PT  - Journal Article
TA  - Mikrobiologiia
JT  - Mikrobiologiia
SO  - Mikrobiologiia 2002 71: 491-493.

PMID- 9859640
VI  - 60
DP  - 1998
TI  - Search for site-specific endonucleases of the II type restriction among Streptomycetes.
PG  - 33-35
AB  - Three Streptomycetes strains producing endonucleases of restriction of II type have been found
      using the modified method of Belavin.
AU  - Lukyanchuk VV
AU  - Strizhkova GM
AU  - Polishchuk LV
AU  - Kopeyko OP
AU  - Matselyukh BP
PT  - Journal Article
TA  - Mikrobiol. Zh.
JT  - Mikrobiol. Zh.
SO  - Mikrobiol. Zh. 1998 60: 33-35.

PMID- 
VI  - 16
DP  - 2000
TI  - Isolation of site-specific endonuclease of Streptomyces sp. 48.
PG  - 559-561
AB  - A method of isolation and purification of site-specific endonuclease of the II type S. sp. 48
      has been worked out.  It has been determined that the S. sp. 48 lysate contains only one
      enzyme with site-specific activity.  Maximum elution of the endonuclease was made by buffer
      with ionic strength of 350 mM NaCl.  This method provides sufficient purification and
      concentration of this enzyme with preservation of its specific activity.
AU  - Lukyanchuk VV
AU  - Suchanoff SM
AU  - Polishchuk LV
AU  - Matselyukh BP
PT  - Journal Article
TA  - Biopol. Kletka
JT  - Biopol. Kletka
SO  - Biopol. Kletka 2000 16: 559-561.

PMID- 23663295
VI  - 13
DP  - 2013
TI  - ST9 MRSA strains carrying a variant of type IX SCCmec identified in the Thai community.
PG  - 214
AB  - BACKGROUND: Infections caused by methicillin-resistant Staphylococcus aureus
      (MRSA) in Thailand occur most frequently in healthcare facilities. However,
      reports of community-associated MRSA are limited. METHODS: We characterized 14
      MRSA isolates from outpatients (O-1 to O-14) by phenotypic and genotypic methods
      and compared them with 5 isolates from inpatients (I-1 to I-5). Thai MRSA
      isolates from a healthcare worker (N-1) and a pig (P-1) were also included as ST9
      MRSA strains from other sources. RESULTS: All MRSA isolates from the outpatients
      and inpatients were multidrug-resistant (resistant to >/=3 classes of
      antimicrobials). All of them except strains O-2 and I-3 carried type III SCCmec
      and belonged to agrI, coagulase IV, spa type t037 or t233, which related to
      ST239. The strain O-2 (JCSC6690) carried type IX SCCmec and belonged to agrII,
      coagulaseXIc, spa type t337 and ST9, whereas the strain I-3 carried a type III
      SCCmec and belonged to ST1429. Nucleotide sequence determination revealed that
      the type IX SCCmec element in strain O-2 was distinct from that in a Thai ST398
      strain (JCSC6943) previously identified in 2011; nucleotide identities of ccrA
      and ccrB were 93 and 91%, respectively and several open reading frames (ORFs) at
      the joining regions were different. PCR experiments suggested that strain O-2 and
      N-1 carried similar SCCmec element, whereas that of strain P-1 was different,
      suggesting that distinct ST9-MRSA-IX clones might be spreading in this province.
      CONCLUSIONS: The SCCmecIX-ST9 MRSA clones of distinct SCCmec subtypes might have
      emerged in the Thai community and might also have disseminated into the hospital.
AU  - Lulitanond A
AU  - Ito T
AU  - Li S
AU  - Han X
AU  - Ma XX
AU  - Engchanil C
AU  - Chanawong A
AU  - Wilailuckana C
AU  - Jiwakanon N
AU  - Hiramatsu K
PT  - Journal Article
TA  - BMC Infect. Dis.
JT  - BMC Infect. Dis.
SO  - BMC Infect. Dis. 2013 13: 214.

PMID- 28546498
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Microbacterium foliorum Strain 122 Isolated from a Plant Growing in a Chronically Hydrocarbon-Contaminated Site.
PG  - e00434-17
AB  - Microbacterium foliorum strain 122 is a bacterial endophyte isolated from a Dactylis glomerata
      plant growing in a natural oil seep soil located in Oil
      Springs, Ontario, Canada. We present here a draft genome sequence of an
      endophytic strain that has promising potential in hydrocarbon degradation and
      plant growth promotion.
AU  - Lumactud R
AU  - Fulthorpe R
AU  - Sentchilo V
AU  - van der Meer JR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00434-17.

PMID- 28450526
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Plantibacterflavus Strain 251 Isolated from a Plant Growing in a Chronically Hydrocarbon-Contaminated Site.
PG  - e00276-17
AB  - Plantibacter flavus isolate 251 is a bacterial endophyte isolated from an Achillea millefolium
      plant growing in a natural oil seep soil located in Oil
      Springs, Ontario, Canada. We present here a draft genome sequence of an
      infrequently reported genus Plantibacter, highlighting an endophytic lifestyle
      and biotechnological potential.
AU  - Lumactud R
AU  - Fulthorpe R
AU  - Sentchilo V
AU  - van der Meer JR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00276-17.

PMID- 27198010
VI  - 4
DP  - 2016
TI  - Genome Sequence of Propionibacterium acidipropionici ATCC 55737.
PG  - e00248-16
AB  - Propionibacterium acidipropionici produces propionic acid as its main fermentation product.
      Traditionally derived from fossil fuels, environmental and
      sustainable issues have revived the interest in producing propionic acid using
      biological resources. Here, we present the closed sequence of Propionibacterium
      acidipropionici ATCC 55737, an efficient propionic acid producer.
AU  - Luna-Flores CH
AU  - Nielsen LK
AU  - Marcellin E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00248-16.

PMID- 27676587
VI  - 12
DP  - 2017
TI  - Improved production of propionic acid using genome shuffling.
PG  - 0
AB  - Traditionally derived from fossil fuels, biological production of propionic acid
      has recently gained interest. Propionibacterium species produce propionic acid as
      their main fermentation product. Production of other organic acids reduces
      propionic acid yield and productivity, pointing to by-products gene-knockout
      strategies as a logical solution to increase yield. However, removing by-product
      formation has seen limited success due to our inability to genetically engineer
      the best producing strains (i.e. Propionibacterium acidipropionici). To overcome
      this limitation, random mutagenesis continues to be the best path towards
      improving strains for biological propionic acid production. Recent advances in
      next generation sequencing opened new avenues to understand improved strains. In
      this work, we use genome shuffling on two wild type strains to generate a better
      propionic acid producing strain. Using next generation sequencing, we mapped the
      genomic changes leading to the improved phenotype. The best strain produced 25%
      more propionic acid than the wild type strain. Sequencing of the strains showed
      that genomic changes were restricted to single point mutations and gene
      duplications in well-conserved regions in the genomes. Such results confirm the
      involvement of gene conversion in genome shuffling as opposed to long genomic
      insertions.
AU  - Luna-Flores CH
AU  - Palfreyman RW
AU  - Kromer JO
AU  - Nielsen LK
AU  - Marcellin E
PT  - Journal Article
TA  - Biotechnol. J.
JT  - Biotechnol. J.
SO  - Biotechnol. J. 2017 12: 0.

PMID- 25744994
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of 'Terrisporobacter othiniensis' Isolated from a Blood Culture from a Human Patient.
PG  - e00042-15
AB  - 'Terrisporobacter othiniensis' (proposed species) was isolated from a blood culture. Genomic
      DNA was sequenced using a MiSeq benchtop sequencer (Illumina)
      and assembled using the SPAdes genome assembler. This resulted in a draft genome
      sequence comprising 3,980,019 bp in 167 contigs containing 3,449 coding
      sequences, 7 rRNAs, and 58 tRNAs.
AU  - Lund LC
AU  - Sydenham TV
AU  - Hogh SV
AU  - Skov M
AU  - Kemp M
AU  - Justesen US
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00042-15.

PMID- 16040995
VI  - 73
DP  - 2005
TI  - Slow genetic divergence of Helicobacter pylori strains during long-term colonization.
PG  - 4818-4822
AB  - The genetic variability of Helicobacter pylori is known to be high compared to that of many
      other bacterial species. H. pylori is adapted to
      the human stomach, where it persists for decades, and adaptation to each
      host results in every individual harboring a distinctive bacterial
      population. Although clonal variants may exist within such a population,
      all isolates are generally genetically related and thus derived from a
      common ancestor. We sought to determine the rate of genetic change of H.
      pylori over 9 years in two asymptomatic adult patients. Arbitrary primed
      PCR confirmed the relatedness of individual subclones within a patient.
      Furthermore, sequencing of 10 loci ( approximately 6,000 bp) in three
      subclones per time and patient revealed only two base pair changes among
      the subclones from patient I. All sequences were identical among the
      patient II subclones. However, PCR amplification of the highly divergent
      gene amiA revealed great variation in the size of the gene between the
      subclones within each patient. Thus, both patients harbored a single
      strain with clonal variants at both times. We also studied genetic changes
      in culture- and mouse-passaged strains, and under both conditions no
      genetic divergence was found. These results suggest that previous
      estimates of the rate of genetic change in H. pylori within an individual
      might be overestimates.
AU  - Lundin A
AU  - Bjorkholm B
AU  - Kupershmidt I
AU  - Unemo M
AU  - Nilsson P
AU  - Andersson DI
AU  - Engstrand L
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2005 73: 4818-4822.

PMID- 3074013
VI  - 74
DP  - 1988
TI  - Cloning Type II restriction and modification genes.
PG  - 25-32
AB  - We have cloned into Escherichia coli the genes for 38 type-II bacterial
      modification methyltransferases.  The clones were isolated by selecting in
      vitro for protectively modified recombinants.  Most of the clones modify their
      DNA fully but a substantial number modify only partially.  In approximately
      one-half of the clones, the genes for the corresponding endonucleases are also
      present.  Some of these clones restrict infecting phages and others do not.
      Clones carrying endonuclease genes but lacking methyltransferase genes have
      been found, in several instances, to be viable.
AU  - Lunnen KD
AU  - Barsomian JM
AU  - Camp RR
AU  - Card CO
AU  - Chen S-Z
AU  - Croft R
AU  - Looney MC
AU  - Meda MM
AU  - Moran LS
AU  - Nwankwo DO
AU  - Slatko BE
AU  - Van Cott EM
AU  - Wilson GG
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 25-32.

PMID- 2663652
VI  - 77
DP  - 1989
TI  - Characterization and cloning of MwoI (GCN7GC), a new type-II restriction-modification system from Methanobacterium wolfei.
PG  - 11-19
AB  - R.MwoI, a type-II restriction enzyme with the new specificity 5'-GCN7GC-3', was
      found in extracts of the thermophilic archaebacterium, Methanobacterium wolfei.
      R.MwoI cleaves duplex DNA producing fragments with 3-nt, 3'-terminal
      extensions, thus: GCN5/N2GC.  The genes coding for the MwoI restriction and
      modification enzymes were cloned into Escherichia coli on the plasmid vector
      pBR322.  The clones synthesize a low level of R.MwoI endonuclease.  The
      plasmids display incomplete MwoI-specific modification, suggesting that the
      clones synthesize a low level of the M.MwoI methyltransferases, too.
AU  - Lunnen KD
AU  - Morgan RD
AU  - Timan CJ
AU  - Krzycki JA
AU  - Reeve JN
AU  - Wilson GG
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1989 77: 11-19.

PMID- 21482770
VI  - 108
DP  - 2011
TI  - Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species.
PG  - 7200-7205
AB  - Defining bacterial species remains a challenging problem even for the model
      bacterium Escherichia coli and has major practical consequences for reliable
      diagnosis of infectious disease agents and regulations for transport and
      possession of organisms of economic importance. E. coli traditionally is thought
      to live within the gastrointestinal tract of humans and other warm-blooded
      animals and not to survive for extended periods outside its host; this
      understanding is the basis for its widespread use as a fecal contamination
      indicator. Here, we report the genome sequences of nine environmentally adapted
      strains that are phenotypically and taxonomically indistinguishable from typical
      E. coli (commensal or pathogenic). We find, however, that the commensal genomes
      encode for more functions that are important for fitness in the human gut, do not
      exchange genetic material with their environmental counterparts, and hence do not
      evolve according to the recently proposed fragmented speciation model. These
      findings are consistent with a more stringent and ecologic definition for
      bacterial species than the current definition and provide means to start
      replacing traditional approaches of defining distinctive phenotypes for new
      species with omics-based procedures. They also have important implications for
      reliable diagnosis and regulation of pathogenic E. coli and for the coliform
      cell-counting test.
AU  - Luo C
AU  - Walk ST
AU  - Gordon DM
AU  - Feldgarden M
AU  - Tiedje JM
AU  - Konstantinidis KT
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2011 108: 7200-7205.

PMID- 28572321
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Streptomyces sp. B9173, a Producer of Indole Diketopiperazine Maremycins.
PG  - e00447-17
AB  - Streptomyces sp. B9173 is a producer of maremycins, a group of naturally occurring
      2,5-diketopiperazines. Here, we report the draft genome sequence of
      Streptomyces sp. B9173, which comprises ~8.77 Mb, with a G+C content of 71.8%.
AU  - Luo F
AU  - Zou Y
AU  - Huang T
AU  - Lin S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00447-17.

PMID- 27079427
VI  - 7
DP  - 2016
TI  - Characterization of eukaryotic DNA N6-methyladenine by a highly sensitive restriction enzyme-assisted sequencing.
PG  - 11301
AB  - Although extensively studied in prokaryotes, the prevalence and significance of DNA
      N6-methyladenine (6mA or m6dA) in eukaryotes had been underappreciated until
      recent studies, which have demonstrated that 6mA regulates gene expression as a
      potential heritable mark. To interrogate 6mA sites at single-base resolution, we
      report DA-6mA-seq (DpnI-Assisted N6-methylAdenine sequencing), an approach that
      uses DpnI to cleave methylated adenine sites in duplex DNA. We find that DpnI
      cuts other sequence motifs besides the canonical GATC restriction sites, thereby
      expanding the utility of this method. DA-6mA-seq achieves higher sensitivity with
      nanograms of input DNA and lower sequencing depth than conventional approaches.
      We study 6mA at base resolution in the Chlamydomonas genome and apply the new
      method to two other eukaryotic organisms, Plasmodium and Penicillium. Combined
      with conventional approaches, our method further shows that most 6mA sites are
      fully methylated on both strands of DNA at various sequence contexts.
AU  - Luo GZ
AU  - Wang F
AU  - Weng X
AU  - Chen K
AU  - Hao Z
AU  - Yu M
AU  - Deng X
AU  - Liu J
AU  - He C
PT  - Journal Article
TA  - Nat. Commun.
JT  - Nat. Commun.
SO  - Nat. Commun. 2016 7: 11301.

PMID- 16236720
VI  - 102
DP  - 2005
TI  - Low-frequency normal mode in DNA HhaI methyltransferase and motions of residues involved in the base flipping.
PG  - 16194-16198
AB  - The results of normal-mode analyses are in accord with the proposal that a low-frequency
      motion of the HhaI methyltransferase enzyme is responsible for base flipping in bound DNA. The
      vectors of the low-frequency normal mode of residues Ser-85 and Ile-86 point directly to the
      phosphate and ribose moieties of the DNA backbone near the target base in position to rotate
      the dihedral angles and flip the base out of the DNA duplex. The vector of residue Gln-237 on
      the major groove is in the proper orientation to assist base separation. Our results favor the
      major groove pathway and the protein active process in base flipping.
AU  - Luo J
AU  - Bruice TC
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2005 102: 16194-16198.

PMID- 19054074
VI  - 290
DP  - 2009
TI  - Identification of an isoschizomer of the HhaI DNA methyltransferase in Mycoplasma arthritidis.
PG  - 195-198
AB  - The genome of Mycoplasma arthritidis strain 158 has modified cytosine residues at AGCT
      sequences that render the DNA resistant to digestion
      with the AluI restriction endonuclease. The DNA methyltransferase
      responsible for the base modification has previously been designated
      MarI. From the complete genome sequence of M. arthritidis, we identify
      Marth orf138 as a candidate marI gene. Marth orf138 was cloned in
      Escherichia coli and its TGA codons converted to TGG. DNA isolated from
      E. coli cells expressing the modified Marth orf138 gene was degraded by
      the AluI nuclease, indicating that Marth orf138 does not code for MarI.
      However, the DNA from E. coli was found to have acquired resistance to
      the restriction endonuclease HhaI. Genomic DNA from M. arthritidis was
      also found to be resistant to HhaI (recognizes GCGC). The M.
      arthritidis isoschizomer of the HhaI DNA methyltransferase, coded by
      Marth orf138, is designated MarII. Transformation of M. arthritidis was
      not significantly affected by modification of plasmid at HhaI sites,
      indicating that the mycoplasma lacks a restriction endonuclease that
      recognizes GCGC sites.
AU  - Luo WY
AU  - Tu AHT
AU  - Cao ZH
AU  - Yu HL
AU  - Dybvig K
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2009 290: 195-198.

PMID- 26679581
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Streptomyces mutabilis TRM45540, Isolated from a Hypersaline Soil Sample.
PG  - e01465-15
AB  - We report here the draft genome sequence of Streptomyces mutabilis TRM45540, a strain isolated
      from a soil sample from Xinjiang, China. Analysis of the genome
      using the bioinformatics tool antiSMASH showed the presence of many unique
      natural-product biosynthetic pathways.
AU  - Luo X
AU  - Wan C
AU  - Zhang L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01465-15.

PMID- 21622747
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of the Universal Killer, Salmonella enterica serovar Typhimurium UK-1 (ATCC 68169).
PG  - 4035-4036
AB  - The Salmonella enterica serovar Typhimurium strain UK-1 presents the highest invasion and
      virulence attributes among the most frequently
      studied strains. S. Typhimurium UK-1 has been used as the foundation for
      developing recombinant vaccines and been extensively used on virulence and
      colonization studies in chickens and mice. We describe here the complete
      genome sequence of S. Typhimurium UK-1. Comparative genomics of Salmonella
      Typhimurium will provide insight into factors that determine virulence and
      invasion.
AU  - Luo Y
AU  - Kong Q
AU  - Yang J
AU  - Golden G
AU  - Wanda SY
AU  - Jensen RV
AU  - Ernst PB
AU  - Curtiss RIII
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4035-4036.

PMID- 23990585
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences of Paenibacillus alvei A6-6i and TS-15.
PG  - e00673-13
AB  - Here, we report draft genomes of Paenibacillus alvei strains A6-6i and TS-15, which were
      isolated, respectively, from plant material and soil in the Virginia
      Eastern Shore (VES) tomato growing area. An array of genes related to
      antimicrobial biosynthetic pathways have been identified with whole-genome
      analyses of these strains.
AU  - Luo Y
AU  - Wang C
AU  - Allard S
AU  - Strain E
AU  - Allard MW
AU  - Brown EW
AU  - Zheng J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00673-13.

PMID- 18700039
VI  - 9
DP  - 2008
TI  - Complete genome of Phenylobacterium zucineum - a novel facultative intracellular bacterium isolated from human erythroleukemia cell line  K562.
PG  - 386
AB  - BACKGROUND: Phenylobacterium zucineum is a recently identified facultative intracellular
      species isolated from the human leukemia cell line K562.
      Unlike the known intracellular pathogens, P. zucineum maintains a stable
      association with its host cell without affecting the growth and morphology
      of the latter. RESULTS: Here, we report the whole genome sequence of the
      type strain HLK1T. The genome consists of a circular chromosome (3,996,255
      bp) and a circular plasmid (382,976 bp). It encodes 3,861 putative
      proteins, 42 tRNAs, and a 16S-23S-5S rRNA operon. Comparative genomic
      analysis revealed that it is phylogenetically closest to Caulobacter
      crescentus, a model species for cell cycle research. Notably, P. zucineum
      has a gene that is strikingly similar, both structurally and functionally,
      to the cell cycle master regulator CtrA of C. crescentus, and most of the
      genes directly regulated by CtrA in the latter have orthologs in the
      former. CONCLUSION: This work presents the first complete bacterial genome
      in the genus Phenylobacterium. Comparative genomic analysis indicated that
      the CtrA regulon is well conserved between C. crescentus and P. zucineum.
AU  - Luo Y
AU  - Xu X
AU  - Ding Z
AU  - Liu Z
AU  - Zhang B
AU  - Yan Z
AU  - Sun J
AU  - Hu S
AU  - Hu X
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2008 9: 386.

PMID- 22275104
VI  - 194
DP  - 2012
TI  - Genome Sequence of Benzo(a)pyrene-Degrading Bacterium Novosphingobium pentaromativorans US6-1.
PG  - 907
AB  - Novosphingobium pentaromativorans US6-1 showed a good ability to degrade high-molecular-weight
      polycyclic aromatic hydrocarbons. We report the
      draft genome sequence of strain US6-1, which contains a main chromosome
      (5,096,413 bp, G+C content of 63.1%) and two plasmids (188,476 and 60,085
      bp). The majority of the aromatic-hydrocarbon-degrading genes are encoded
      in the larger plasmid.
AU  - Luo YR
AU  - Kang SG
AU  - Kim SJ
AU  - Kim MR
AU  - Li N
AU  - Lee JH
AU  - Kwon KK
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 907.

PMID- 6269623
VI  - 654
DP  - 1981
TI  - Purification of the sequence-specific endonuclease SinI from Salmonella infantis.
PG  - 297-299
AB  - A sequence-specific endonuclease was isolated from a strain of Salmonella
      infantis.  Its recognition sequence proved to be identical to that of
      restriction endonuclease AvaII (an endonuclease from the blue-green alga
      Anabaena variabilis), G^G(A/T)CC.
AU  - Lupker HSC
AU  - Dekker BMM
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1981 654: 297-299.

PMID- 13168990
VI  - 18
DP  - 1953
TI  - Host-induced modifications of viruses.
PG  - 237-244
AB  - Viruses exhibit extensive adaptability to growth in various hosts or tissues.
      It was widely held in the past that virus adaptability reflected a peculiar
      plasticity of virus heredity, which allowed it to be directly influenced by its
      host cells.  The alternative interpretation of virus adaptation to new host
      cells as due to spontaneous mutations, which provide a range of genotypes for
      the new hosts to select from, always had authoritative proponents (see Findlay,
      1939).  This viewpoint finally gained wide recognition (see Burnet, 1946),
      partly as a consequence of the development of phage genetics and of the
      interpenetration of various branches of virology.  It is now recognized that
      most variation in virus properties is caused by viral mutations, and that virus
      plasticity results from the variety of genotypes present in the large viral
      populations.  It was, therefore, an unexpected development when a new type of
      virus variation was discovered in bacteriophages.  This has been called
      host-induced or host-controlled variation (Luria and Human, 1952; Ralston and
      Krueger, 1952; Anderson and Felix, 1952; Bertani and Weigle, 1953).  Its
      outstanding characteristics are that is is strictly phenotypic, non-hereditary,
      and that it is determined by the host cell in which a virus has been produced.
      In this paper, I shall summarize the features of this phenomenon; I shall
      compare it with other instances of nonhereditary phage variation; and I shall
      attempt to assess its possible bearing on certain problems in other areas of
      virology.
AU  - Luria SE
PT  - Journal Article
TA  - Cold Spring Harb. Symp. Quant. Biol.
JT  - Cold Spring Harb. Symp. Quant. Biol.
SO  - Cold Spring Harb. Symp. Quant. Biol. 1953 18: 237-244.

PMID- 4903120
VI  - 222
DP  - 1970
TI  - The recognition of DNA in Bacteria.
PG  - 88-102
AB  - Some bacteria have enzyme systems that scan invading DNA molecules injected by
      viruses and break them unless they are chemically marked at specific
      recognition sites.
AU  - Luria SE
PT  - Journal Article
TA  - Sci. Am.
JT  - Sci. Am.
SO  - Sci. Am. 1970 222: 88-102.

PMID- 12999684
VI  - 64
DP  - 1952
TI  - A nonhereditary, host-induced variation of bacterial viruses.
PG  - 557-569
AB  - One of virology's most generally valid rules is that the properties of virus particles are
      unaffected by the host in which they grow.  Host adaptation and tissue adaptation, the
      apparent exceptions, are explained today by selective reproduction of virus mutants in new
      hosts or in new tissues.  In analyzing the relation between certain phages and certain mutants
      of their bacterial hosts, we have encountered a novel situation: the genotype of the host in
      which a virus reproduces affects the phenotype of the new virus.  The phenotypic change
      suppresses the ability of the virus to reproduce in certain hosts but not in others.  It is a
      transient change, in the sense that one cycle of growth in a suitable host returns the virus
      to its original form.  Both the growth ability of the modified virus and, in some cases, its
      production from normal virus are controlled in part by the physiological state of the host
      cell.  The present paper describes these findings and discusses their general implications.
      Other instances of host-controlled phenotypic changes in bacteriophages have recently been
      discovered (Bertani and Weigle, 1952).
AU  - Luria SE
AU  - Human ML
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1952 64: 557-569.

PMID- 16388590
VI  - 45
DP  - 2006
TI  - DNA strand arrangement within the SfiI-DNA complex: atomic force microscopy analysis.
PG  - 152-158
AB  - The SfiI restriction enzyme binds to DNA as a tetramer holding two usually distant DNA
      recognition sites together before cleavage of the four DNA strands. To elucidate structural
      properties of the SfiI-DNA complex, atomic force microscopy (AFM) imaging of the complexes
      under noncleaving conditions (Ca2+ instead of Mg2+ in the reaction buffer) was performed.
      Intramolecular complexes formed by protein interaction between two binding sites in one DNA
      molecule (cis interaction) as well as complexes formed by the interaction of two sites in
      different molecules (trans interaction) were analyzed. Complexes were identified unambiguously
      by the presence of a tall spherical blob at the DNA intersections. To characterize the path of
      DNA within the complex, the angles between the DNA helices in the proximity of the complex
      were systematically analyzed. All the data show clear-cut bimodal distributions centered
      around peak values corresponding to 60 degrees and 120 degrees. To unambiguously distinguish
      between the crossed and bent models for the DNA orientation within the complex, DNA molecules
      with different arm lengths flanking the SfiI binding site were designed. The analysis of the
      AFM images for complexes of this type led to the conclusion that the DNA recognition sites
      within the complex are crossed. The angles of 60 degrees or 120 degrees between the DNA
      helices correspond to a complex in which one of the helices is flipped with respect to the
      orientation of the other. Complexes formed by five different recognition sequences
      (5'-GGCCNNNNNGGCC-3'), with different central base pairs, were also analyzed. Our results
      showed that complexes containing the two possible orientations of the helices were formed
      almost equally. This suggests no preferential orientation of the DNA cognate site within the
      complex, suggesting that the central part of the DNA binding site does not form strong
      sequence specific contacts with the protein.
AU  - Lushnikov AY
AU  - Potaman VN
AU  - Oussatcheva EA
AU  - Sinden RR
AU  - Lyubchenko YL
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2006 45: 152-158.

PMID- 26404602
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Gram-Positive Thermophilic Iron Reducer Thermincola  ferriacetica Strain Z-0001T.
PG  - e01072-15
AB  - A 3.19-Mbp draft genome of the Gram-positive thermophilic iron-reducing Firmicutes isolate
      from the Peptococcaceae family, Thermincola ferriacetica Z-0001, was assembled at ~100x
      coverage from 100-bp paired-end Illumina reads. The draft genome contains 3,274 predicted
      genes (3,187 protein coding genes) and  putative multiheme c-type cytochromes.
AU  - Lusk BG
AU  - Badalamenti JP
AU  - Parameswaran P
AU  - Bond DR
AU  - Torres CI
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01072-15.

PMID- 25540351
VI  - 2
DP  - 2014
TI  - Genome Sequences of Two Copper-Resistant Escherichia coli Strains Isolated from Copper-Fed Pigs.
PG  - e01341-14
AB  - The draft genome sequences of two copper-resistant Escherichia coli strains were  determined.
      These had been isolated from copper-fed pigs and contained additional
      putative operons conferring copper and other metal and metalloid resistances.
AU  - Luthje FL
AU  - Hasman H
AU  - Aarestrup FM
AU  - Alwathnani HA
AU  - Rensing C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01341-14.

PMID- 10425387
VI  - 437
DP  - 1999
TI  - Principal causes of hot spots for cytosine to thymine mutations at sites of cytosine methylation in growing cells.  A model, its experimental support and implications.
PG  - 11-20
AB  - In Escherichia coli and human cells, many sites of cytosine methylation in DNA are hot spots
      for C to T mutations. It is generally believed that T.G mismatches created by the hydrolytic
      deamination of 5-methylcytosines (5meC) are intermediates in the mutagenic pathway. A number
      of hypotheses have been proposed regarding the source of the mispaired thymine and how the
      cells deal with the mispairs. We have constructed a genetic reversion assay that utilizes a
      gene on a mini-F to compare the frequency of occurrence of C to T mutations in different
      genetic backgrounds in exponentially growing E. coli. The results identify at least two causes
      for the hot spot at a 5meC: (1) the higher rate of deamination of 5meC compared to C generates
      more T.G than uracil.G (U.G) mismatches, and (2) inefficient repair of T.G mismatches by the
      very short-patch (VSP) repair system compared to the repair of U. G mismatches by the
      uracil-DNA glycosylase (Ung). This combination of increased DNA damage when the cytosines are
      methylated coupled with the relative inefficiency in the post-replicative repair of T.G
      mismatches can be quantitatively modeled to explain the occurrence of the hot spot at 5meC.
      This model has implications for mutational hot and cold spots in all organisms.
AU  - Lutsenko E
AU  - Bhagwat AS
PT  - Journal Article
TA  - Mutat. Res.
JT  - Mutat. Res.
SO  - Mutat. Res. 1999 437: 11-20.

PMID- 25858840
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Shewanella sp. Strain CP20.
PG  - e00256-15
AB  - Shewanella sp. CP20 is a marine bacterium that survives ingestion by Tetrahymena  pyriformis
      and is expelled from the protozoan within membrane-bound vacuoles,
      where the bacterial cells show long-term survival. Here, we report the draft
      genome sequence of Shewanella sp. CP20 and discuss the potential mechanisms
      facilitating intraprotozoan survival.
AU  - Lutz C
AU  - Martin TQX
AU  - Sun S
AU  - McDougald D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00256-15.

PMID- 21217006
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of a Free-Living Vibrio furnissii sp. nov. Strain (NCTC 11218).
PG  - 1487-1488
AB  - The Vibrionales are widespread, free-living, Gram-negative proteobacteria that have been
      linked to pathogenicity in animals and gastroenteric infection in humans.  We report the
      annotated genome sequence of a free-living strain of Vibrio furnissii (NCTC 11218) harvested
      from an estuarine environment.  It consists of two circular chromosomes (3.2 Mb and 1.6 Mb)
      and reveals novel genes likely to be involved in pathogenicity.
AU  - Lux TM
AU  - Lee R
AU  - Love J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 1487-1488.

PMID- 27125485
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of 'Paramesorhizobium deserti' A-3-ET, a Strain Highly Resistant to Diverse beta-Lactam Antibiotics.
PG  - e00311-16
AB  - Here, we report the draft genome sequence of 'Paramesorhizobium deserti' A-3-E(T), a strain
      isolated from the Taklimakan Desert of Xinjiang, China, which
      is resistant to multiple beta-lactam antibiotics and other antibiotics
      (kanamycin, erythromycin, streptomycin, etc.) as well.
AU  - Lv R
AU  - Yang X
AU  - Fang N
AU  - Song Y
AU  - Luo X
AU  - Guo J
AU  - Peng F
AU  - Yang R
AU  - Cui Y
AU  - Fang C
AU  - Song Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00311-16.

PMID- 22247536
VI  - 194
DP  - 2012
TI  - Genome Sequence of Corynebacterium glutamicum ATCC 14067, Which Provides Insight into Amino Acid Biosynthesis in Coryneform Bacteria.
PG  - 742-743
AB  - We report the genome sequence of Corynebacterium glutamicum ATCC 14067 (once named
      Brevibacterium flavum), which is useful for taxonomy research
      and further molecular breeding in amino acid production. Preliminary
      comparison with those of the reported coryneform strains revealed some
      notable differences that might be related to the difficulties in molecular
      manipulation.
AU  - Lv Y
AU  - Liao J
AU  - Wu Z
AU  - Han S
AU  - Lin Y
AU  - Zheng S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 742-743.

PMID- 21994927
VI  - 193
DP  - 2011
TI  - Genome Sequence of Corynebacterium glutamicum S9114, a Strain for Industrial Production of Glutamate.
PG  - 6096-6097
AB  - Here we report the genome sequence of Corynebacterium glutamicum S9114, an industrial producer
      widely used in production of glutamate in China.
      Preliminary comparison with the sequences of the Corynebacterium
      glutamicum strains ATCC 13032 and R revealed some notable mutagenesis that
      might be related to the high yield of glutamate.
AU  - Lv Y
AU  - Wu Z
AU  - Han S
AU  - Lin Y
AU  - Zheng S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6096-6097.

PMID- 25814613
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Pseudomonas fluorescens Strains SF39a and SF4c, Potential Plant Growth Promotion and Biocontrol Agents.
PG  - e00219-15
AB  - Pseudomonas fluorescens SF4c and SF39a, strains isolated from wheat rhizosphere,  have
      potential applications in plant growth promotion and biocontrol of fungal
      diseases of crop plants. We report the draft genome sequences of SF4c and SF39a
      with estimated sizes of 6.5 Mb and 5.9 Mb, respectively.
AU  - Ly LK
AU  - Underwood GE
AU  - McCully LM
AU  - Bitzer AS
AU  - Godino A
AU  - Bucci V
AU  - Brigham CJ
AU  - Principe A
AU  - Fischer SE
AU  - Silby MW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00219-15.

PMID- 2825124
VI  - 15
DP  - 1987
TI  - Base pair opening dynamics of a 2-aminopurine substituted EcoRI restriction sequence and its unsubstituted counterpart in oligonucleotides.
PG  - 9011-9025
AB  - Studies of 1H NMR selective recovery were performed to determine the imino
      proton exchange with solvent water of the base pairs in the EcoRI endonuclease
      recognition sequence GAATTC, placed at the center of self-complementary decamer
      and dodecamer oligonucleotides.  In one oligonucleotide the innermost adenine
      was replaced by the fluorescent base analogue 2-aminopurine (2AP).  From the
      measurements at different concentrations of TRIS buffer acting as proton
      exchange catalyst, base pair lifetimes were evaluated.  The results at 25C show
      that the AT base pairs have lifetimes of the order of a few ms, whereas the
      surrounding GC base pairs in a dodecamer have lifetimes of about 100 ms.  The
      (2AP)T base pair has a shorter lifetime than the corresponding AT base pair.
      The temperature dependent optical absorption, and for the 2AP containing
      oligonucleotide fluorescence, were used to study the single strand-duplex
      equilibrium of the decamers.  The results indicate that NMR and the optical
      techniques, although applied at very different concentrations, monitor the same
      conformational transition of the oligonucleotide.
AU  - Lycksell PO
AU  - Graslund A
AU  - Claesens F
AU  - McLaughlin LW
AU  - Larsson U
AU  - Rigler R
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1987 15: 9011-9025.

PMID- 17209016
VI  - 189
DP  - 2007
TI  - Genome sequence and analysis of the soil cellulolytic actinomycete Thermobifida fusca YX.
PG  - 2477-2486
AB  - Thermobifida fusca is a moderately thermophilic soil bacterium that belongs to Actinobacteria.
      It is a major degrader of plant cell walls and
      has been used as a model organism for the study of secreted, thermostable
      cellulases. The complete genome sequence showed that T. fusca has a single
      circular chromosome of 3,642,249 bp predicted to encode 3,117 proteins and
      65 RNA species with a coding density of 85%. Genome analysis revealed the
      existence of 29 putative glycoside hydrolases in addition to the
      previously identified cellulases and xylanases. The glycosyl hydrolases
      include enzymes predicted to exhibit mainly dextran/starch- and
      xylan-degrading functions. T. fusca possesses two protein secretion
      systems: the sec general secretion system and the twin-arginine
      translocation system. Several of the secreted cellulases have sequence
      signatures indicating their secretion may be mediated by the twin-arginine
      translocation system. T. fusca has extensive transport systems for import
      of carbohydrates coupled to transcriptional regulators controlling the
      expression of the transporters and glycosylhydrolases. In addition to
      providing an overview of the physiology of a soil actinomycete, this study
      presents insights on the transcriptional regulation and secretion of
      cellulases which may facilitate the industrial exploitation of these
      systems.
AU  - Lykidis A
AU  - Mavromatis K
AU  - Ivanova N
AU  - Anderson I
AU  - Land M
AU  - DiBartolo G
AU  - Martinez M
AU  - Lapidus A
AU  - Lucas S
AU  - Copeland A
AU  - Richardson P
AU  - Wilson DB
AU  - Kyrpides N
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2007 189: 2477-2486.

PMID- 8918801
VI  - 24
DP  - 1996
TI  - Protein footprinting approach to mapping DNA binding sites of two archaeal homing enzymes: evidence for a two-domain protein structure.
PG  - 3982-3989
AB  - The archaeal intron-encoded homing enzymes I-PorI and I-DmoI belong to a family of
      endonucleases that contain two copies of a characteristic LAGLIDADG motif.  These
      endonucleases cleave their intron- or intein- alleles site-specifically, and thereby
      facilitate homing of the introns or inteins which encode them.  The protein structure and the
      mechanism of DNA recognition of these homing enzymes is largely unknown.  Therefore, we
      examined these properties of I-PorI and I-DmoI by protein footprinting.  Both proteins were
      susceptible to proteolytic cleavage within regions that are equidistant from each of the two
      LAGLIDADG motifs.  When complexed with their DNA substrates, a characteristic subset of the
      exposed sites, located in regions immediately after and 40-60 amino acids after each of the
      LAGLIDADG motifs, were protected.  Our data suggest that the enzymes are structured into two,
      tandemly repeated, domains, each containing both the LAGLIDADG motif and two putative DNA
      binding regions.  The latter contains a potentially novel DNA binding motif conserved in
      archaeal homing enzymes.  The results are consistent with a model where the LAGLIDADG
      endonucleases bind to their non-palindromic substrates as monomeric enzymes, with each of the
      two domains recognizing one half of the DNA substrate.
AU  - Lykke-Andersen J
AU  - Garrett RA
AU  - Kjems J
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1996 24: 3982-3989.

PMID- 9214642
VI  - 16
DP  - 1997
TI  - Mapping metal ions at the catalytic centres of two intron-encoded endonucleases.
PG  - 3272-3281
AB  - Divalent metal ions play a crucial role in forming the catalytic centres of DNA endonucleases.
      Substitution of Mg2+ ions by Fe2+ ions in two archaeal intron-encoded homing endonucleases,
      I-DmoI and I-PorI, yielded functional enzymes and enabled the generation of reactive hydroxyl
      radicals within the metal ion binding sites.  Specific hydroxyl radical-induced cleavage was
      observed within, and immediately after, two conserved LAGLIDADG motifs in both proteins and at
      sites at, and near, the scissile phosphates of the corresponding DNA substrates.  Titration of
      Fe2+-containing protein-DNA complexes with Ca2+ ions, which are unable to support
      endonucleolytic activity, was performed to distinguish between the individual metal ions in
      the complex.  Mutations of single amino acids in this region impaired catalytic activity and
      caused the preferential loss of a subset of hydroxyl radical cleavages in both the protein and
      the DNA substrate, suggesting an active role in metal ion coordination for these amino acids.
      The data indicate that the endonucleases cleave their DNA substrates as monomeric enzymes, and
      contain a minimum of four divalent metal ions located at or near the catalytic centres of each
      endonuclease.  The metal ions involved in cleaving the coding and the non-coding strand are
      positioned immediately after the N- and C-terminally located LAGLIDADG motifs, respectively.
      The dual protein/nucleic acid footprinting approach described here is generally applicable to
      other protein-nucleic acid complexes when the natural metal ion can be replaced by Fe2+.
AU  - Lykke-Andersen J
AU  - Garrett RA
AU  - Kjems J
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1997 16: 3272-3281.

PMID- 7984405
VI  - 22
DP  - 1994
TI  - DNA substrate specificity and cleavage kinetics of an archaeal homing-type endonuclease from Pyrobaculum organotrophum.
PG  - 4583-4590
AB  - The protein encoded by intron 1 of the single 23S rRNA gene of the archaeal hyperthermophile
      Pyrobaculum organotrophum was isolated and shown to constitute a homing-type DNA endonuclease,
      I-PorI. It cleaves the intron- 23S rDNA of the closely related organism Pyrobaculum islandicum
      near the site of intron insertion in Pb. organotrophum. In contrast, no endonuclease activity
      was detected for the protein product of intron 2 of the same gene of Pb. organotrophum which,
      like I-PorI, carries the LAGLI-DADG motif, common to group I intron-encoded homing enzymes.
      I-PorI cleaves optimally at 80oC, with kcat and km values of about 2 min-1 and 4 nM,
      respectively, and generates four nucleotide 3'-overhangs and 5'-phosphates. It can cleave a
      25 base pair DNA fragment encompassing the intron insertion site. A mutation-selection study
      established the base pair specificity of the endonuclease within a 17 bp region, from
      positions -6 to +11 with respect to the intron-insertion site. Four of the essential base
      pairs encode the sequence involved in the intron-exon interaction in the pre-rRNA that is
      required for recognition by the RNA splicing enzymes. Properties of the enzyme are compared
      and contrasted with those of eucaryotic homing endonucleases.
AU  - Lykke-Andersen J
AU  - Thi-Ngoc HP
AU  - Garrett RA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1994 22: 4583-4590.

PMID- 16234563
VI  - 97
DP  - 2005
TI  - DNA methyltransferase inhibitors and the development of epigenetic cancer therapies.
PG  - 1498-1506
AB  - Epimutations, such as the hypermethylation and epigenetic silencing of tumor suppressor genes,
      play a role in the etiology of human cancers.
      In contrast to DNA mutations, which are passively inherited through DNA
      replication, epimutations must be actively maintained because they are
      reversible. In fact, the reversibility of epimutations by
      small-molecule inhibitors provides the foundation for the use of such
      inhibitors in novel cancer therapy strategies. Among the compounds that
      inhibit epigenetic processes, the most extensively studied are DNA
      methyltransferase inhibitors. In this review, we examine the literature
      on DNA methyltransferase inhibitors and discuss the efficacy of such
      compounds as antitumor agents, as evaluated in phase I-III clinical
      trials. We also discuss future areas of research, including the
      development of nonnucleoside inhibitors, the application of novel
      bioanalytical tools for DNA methylation analysis (which will be
      important for the clinical application of these compounds by allowing
      rational approaches to trial design), the need to optimize treatment
      schedules for maximal biologic effectiveness, and the need to define
      molecular endpoints so that changes induced by demethylating drugs in
      patients can be monitored during treatment. Assays for genome-wide and
      tumor-specific DNA methylation also need to be further developed to
      establish the pharmacodynamic parameters of DNA methyltransferase
      inhibitors in patients and to provide rational approaches to maximizing
      the therapeutic efficacy of these compounds.
AU  - Lyko F
AU  - Brown R
PT  - Journal Article
TA  - J. Natl. Cancer Inst.
JT  - J. Natl. Cancer Inst.
SO  - J. Natl. Cancer Inst. 2005 97: 1498-1506.

PMID- 11117732
VI  - 408
DP  - 2000
TI  - DNA methylation in Drosophila melanogaster.
PG  - 538-540
AB  - Certain cytosine residues of eukaryotic DNA are methylated in inactive regions of the genome.
      For a long time the fruitfly Drosophila was thought to be an exception, but now the evidence
      points to the existence of a functional DNA-methylation system in Drosophila as well.  Here we
      show that DNA is methylated, but that Drosophila genomic methylation is restriction to the
      early stages of development.
AU  - Lyko F
AU  - Ramsahoye BH
AU  - Jaenisch R
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2000 408: 538-540.

PMID- 10545955
VI  - 23
DP  - 1999
TI  - Mammalian (cytosine-5) methyltransferases cause genomic DNA methylation and lethality in drosophila.
PG  - 363-366
AB  - CpG methylation is essential for mouse development as well as gene regulation and genome
      stability. Many features of mammalian DNA methylation are consistent with the action of a de
      novo methyltransferase that establishes methylation patterns during early development and the
      post-replicative maintenance of these patterns by a maintenance methyltransferase. The mouse
      methyltransferase Dnmt1 (encoded by Dnmt) shows a preference for hemimethylated substrates in
      vitro, making the enzyme a candidate for a maintenance methyltransferase. Dnmt1 also has de
      novo methylation activity in vitro, but the significance of this finding is unclear, because
      mouse embryonic stem (ES) cells contain a de novo methylating activity unrelated to Dnmt1
      (ref. 10). Recently, the Dnmt3 family of methyltransferases has been identified and shown in
      vitro to catalyse de novo methylation. To analyse the function of these enzymes, we expressed
      Dnmt and Dnmt3a in transgenic Drosophila melanogaster. The absence of endogenous methylation
      in Drosophila facilitates detection of experimentally induced methylation changes. In this
      system, Dnmt3a functioned as a de novo methyltransferase, whereas Dnmt1 had no detectable de
      novo methylation activity. When co-expressed, Dnmt1 and Dnmt3a cooperated to establish and
      maintain methylation patterns. Genomic DNA methylation impaired the viability of transgenic
      flies, suggesting that cytosine methylation has functional consequences for Drosophila
      development.
AU  - Lyko F
AU  - Ramsahoye BH
AU  - Kashevsky H
AU  - Tudor M
AU  - Mastrangelo MA
AU  - Orr-Weaver TL
AU  - Jaenisch R
PT  - Journal Article
TA  - Nat. Genet.
JT  - Nat. Genet.
SO  - Nat. Genet. 1999 23: 363-366.

PMID- 10906465
VI  - 95
DP  - 2000
TI  - The putative Drosophila methyltransferase gene dDnmt2 is contained in a transposon-like element and is expressed specifically in ovaries.
PG  - 215-217
AB  - Several organisms, including Drosophila melanogaster, are apparently devoid of DNA
      methylation. This might reflect a highly restricted activity of DNA methyltransferases, a loss
      of methyltransferase activity during evolution or the dispensability of DNA methylation due to
      an efficient substitute mechanism. Vestiges of a Drosophila DNA methylation system have been
      identified recently. We show here that the putative DNA methyltransferase gene, dDnmt2, is the
      component of a transposon-like element. This element also contains a second, novel open
      reading frame with homologies to a yeast protein involved in RNA processing. Both open reading
      frames are coordinately expressed and transcripts are present specifically in ovarian nurse
      cells as well as during early stages of embryonic development.
AU  - Lyko F
AU  - Whittaker AJ
AU  - Orr-Weaver TL
AU  - Jaenisch R
PT  - Journal Article
TA  - Mech. Dev.
JT  - Mech. Dev.
SO  - Mech. Dev. 2000 95: 215-217.

PMID- 26044431
VI  - 3
DP  - 2015
TI  - Draft genome sequences of two protease-producing strains of arsukibacterium, isolated from two cold and alkaline environments.
PG  - e00585-15
AB  - Arsukibacterium ikkense GCM72(T) and a close relative, Arsukibacterium sp. MJ3, were isolated
      from two cold and alkaline environments as producers of
      extracellular proteolytic enzymes active at high pH and low temperature. This
      report describes the two draft genome sequences, which may serve as sources of
      future industrial enzymes.
AU  - Lylloff JE
AU  - Hansen LB
AU  - Jepsen M
AU  - Hallin PF
AU  - Sorensen SJ
AU  - Stougaard P
AU  - Glaring MA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00585-15.

PMID- 28163826
VI  - 12
DP  - 2017
TI  - Draft genome sequences of eight bacteria isolated from the indoor environment: Staphylococcus capitis strain H36, S. capitis strain H65, S. cohnii strain H62,  S. hominis strain H69, Microbacterium sp. strain H83, Mycobacterium iranicum  strain H39, Plan.
PG  - 17
AB  - We report here the draft genome sequences of eight bacterial strains of the genera
      Staphylococcus, Microbacterium, Mycobacterium, Plantibacter, and
      Pseudomonas. These isolates were obtained from aerosol sampling of bathrooms of
      five residences in the San Francisco Bay area. Taxonomic classifications as well
      as the genome sequence and gene annotation of the isolates are described. As part
      of the 'Built Environment Reference Genome' project, these isolates and
      associated genome data provide valuable resources for studying the microbiology
      of the built environment.
AU  - Lymperopoulou DS
AU  - Coil DA
AU  - Schichnes D
AU  - Lindow SE
AU  - Jospin G
AU  - Eisen JA
AU  - Adams RI
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 17.

PMID- 20973964
VI  - 11
DP  - 2010
TI  - Genomic analysis and relatedness of P2-like phages of the Burkholderia cepacia complex.
PG  - 599
AB  - Background: The Burkholderia cepacia complex (BCC) is comprised of at least seventeen
      Gram-negative species that cause infections in cystic
      fibrosis patients. Because BCC bacteria are broadly antibiotic
      resistant, phage therapy is currently being investigated as a possible
      alternative treatment for these infections. The purpose of our study
      was to sequence and characterize three novel BCC-specific phages: KS5
      (vB BceM-KS5 or vB BmuZ-ATCC 17616), KS14 (vB BceM-KS14) and KL3 (vB
      BamM-KL3 or vB BceZ-CEP511).
      Results: KS5, KS14 and KL3 are myoviruses with the A1 morphotype.
      The genomes of these phages are between 32317 and 40555 base pairs in
      length and are predicted to encode between 44 and 52 proteins. These
      phages have over 50% of their proteins in common with enterobacteria
      phage P2 and so can be classified as members of the Peduovirinae
      subfamily and the 'P2-like viruses' genus. The BCC phage proteins
      similar to those encoded by P2 are predominantly structural components
      involved in virion morphogenesis. As prophages, KS5 and KL3 integrate
      into an AMP nucleosidase gene and a threonine tRNA gene, respectively.
      Unlike other P2-like viruses, the KS14 prophage is maintained as a
      plasmid. The P2 E+E' translational frameshift site is conserved among
      these three phages and so they are predicted to use frameshifting for
      expression of two of their tail proteins. The lysBC genes of KS14 and
      KL3 are similar to those of P2, but in KS5 the organization of these
      genes suggests that they may have been acquired via horizontal transfer
      from a phage similar to l. KS5 contains two sequence elements that are
      unique among these three phages: an ISBmu2-like insertion sequence and
      a reverse transcriptase gene. KL3 encodes an EcoRII-C
      endonuclease/methylase pair and Vsr endonuclease that are predicted to
      function during the lytic cycle to cleave non-self DNA, protect the
      phage genome and repair methylation-induced mutations.
      Conclusions: KS5, KS14 and KL3 are the first BCC-specific phages to
      be identified as P2-like. As KS14 has previously been shown to be
      active against Burkholderia cenocepacia in vivo, genomic
      characterization of these phages is a crucial first step in the
      development of these and similar phages for clinical use against the
      BCC.
AU  - Lynch KH
AU  - Stothard P
AU  - Dennis JJ
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2010 11: 599.

PMID- 22676492
VI  - 13
DP  - 2012
TI  - Comparative analysis of two phenotypically-similar but genomically-distinct Burkholderia cenocepacia-specific bacteriophages.
PG  - 223
AB  - ABSTRACT: BACKGROUND: Genomic analysis of bacteriophages infecting the
      Burkholderia cepacia complex (BCC) is an important preliminary step in the
      development of a phage therapy protocol for these opportunistic pathogens. The
      objective of this study was to characterize KL1 (vB_BceS_KL1) and AH2
      (vB_BceS_AH2), two novel Burkholderia cenocepacia-specific siphoviruses isolated
      from environmental samples. RESULTS: KL1 and AH2 exhibit several unique
      phenotypic similarities: they infect the same B. cenocepacia strains, they
      require prolonged incubation at 30degreesC for the formation of plaques at low
      titres, and they do not form plaques at similar titres following incubation at
      37degreesC. However, despite these similarities, we have determined using
      whole-genome pyrosequencing that these phages show minimal relatedness to one
      another. The KL1 genome is 42,832 base pairs (bp) in length and is most closely
      related to Pseudomonas phage 73 (PA73). In contrast, the AH2 genome is 58,065 bp
      in length and is most closely related to Burkholderia phage BcepNazgul. Using
      both BLASTP and HHpred analysis, we have identified and analyzed the putative
      virion morphogenesis, lysis, DNA binding, and MazG proteins of these two phages.
      Notably, MazG homologs identified in cyanophages have been predicted to
      facilitate infection of stationary phase cells and may contribute to the unique
      lysis phenotype of KL1 and AH2. CONCLUSIONS: The nearly indistinguishable
      phenotypes but distinct genomes of KL1 and AH2 provide further evidence of both
      vast diversity and convergent evolution in the BCC-specific phage population.
AU  - Lynch KH
AU  - Stothard P
AU  - Dennis JJ
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2012 13: 223.

PMID- 22139000
VI  - 78
DP  - 2012
TI  - Characterization of DC1, a broad-host-range Bcep22-like podovirus.
PG  - 889-891
AB  - Bcep22-like phages are a recently described group of podoviruses that infect
      strains of Burkholderia cenocepacia. We have isolated and characterized a novel
      member of this group named DC1. This podovirus shows many genomic similarities to
      BcepIL02 and Bcep22, but it infects strains belonging to multiple Burkholderia
      cepacia complex (BCC) species.
AU  - Lynch KH
AU  - Stothard P
AU  - Dennis JJ
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2012 78: 889-891.

PMID- 10878000
VI  - 275
DP  - 2000
TI  - Macromolecular Hydration Changes Associated with BamHI Binding and Catalysis.
PG  - 30561-30565
AB  - In this report, the effects of osmotic pressure on BamHI cognate binding and catalysis were
      investigated and compared with a previous study on EcoRI (Robinson, C. R. and Sligar, S. G.
      (1998) Proc. Natl. Acad. Sci. U.S.A. 95, 2186-2191). Our observation of the dependence of
      binding and catalytic parameters on osmotic pressure has allowed for the comparison of
      hydration changes associated with site-specific DNA recognition for both endonucleases. Over a
      large range of osmotic pressures (pi), the dependence of BamHI on osmotic stress during
      cognate binding and catalysis was very different from that of the related endonuclease EcoRI.
      The binding of EcoRI to cognate DNA was dominated by a dehydration of the endonuclease-DNA
      complex, whereas binding by BamHI to its cognate sequence was accompanied by a solvent release
      corresponding to some 125 fewer waters. Catalytic analysis at elevated osmotic pressures
      indicated that both endonucleases had undergone a net hydration of the complex with BamHI
      displaying a much greater dependence on osmotic stress than EcoRI. Although the enzymes shared
      core structural motifs, comparisons of high resolution x-ray structures revealed many
      different secondary structural features of the complexed endonucleases. The large difference
      in hydration changes by both BamHI and EcoRI could be attributed to these dissimilar secondary
      structural features, as well as the functional differences of the two endonucleases during
      site-specific DNA recognition.
AU  - Lynch TW
AU  - Sligar SG
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2000 275: 30561-30565.

PMID- 7603433
VI  - 247
DP  - 1995
TI  - Characterization of three genes in the dam-containing operon of Escherichia coli.
PG  - 546-554
AB  - The dam-containing operon in Escherichia coli is located at 74 min on the chromosomal map and
      contains the genes aroK, aroB, a gene called urf74.3,
      dam and trpS. We have determined the nucleotide sequence between the dam
      and trpS genes and show that it encodes two proteins with molecular
      weights of 24 and 27 kDa. Furthermore, we characterize the three genes
      urf74.3, 24kDa, 27kDa and the proteins they encode. The predicted amino
      acid sequences of the 24 and 27 kDa proteins are similar to those of the
      CbbE and CbbZ proteins, respectively, of the Alcaligenes eutrophus cbb
      operon, which encodes enzymes involved in the Calvin cycle. In separate
      experiments, we have shown that the 24 kDa protein has
      d-ribulose-5-phosphate epimerase activity (similar to CbbE), and we call
      the gene rpe. Similarly, the 27 kDa protein has 2-phosphoglycolate
      phosphatase activity (similar to CbbZ), and we name the gene gph. The
      Urf74.3 protein, with a predicted molecular weight of 46 kDa, migrated as
      a 70 kDa product under denaturing conditions. Overexpression of Urf74.3
      induced cell filamentation, indicating that Urf74.3 directly or indirectly
      interferes with cell division. We present evidence for translational
      coupling between aroB and urf74.3 and also between rpe and gph. Proteins
      encoded in the dam superoperon appear to be largely unrelated: Dam, and
      perhaps Urf74.3, are involved in cell cycle regulation, AroK, AroB, and
      TrpS function in aromatic amino acid biosynthesis, whereas Rpe and Gph are
      involved in carbohydrate metabolism.
AU  - Lyngstadaas A
AU  - Lobner-Olesen A
AU  - Boye E
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1995 247: 546-554.

PMID- 312287
VI  - 138
DP  - 1979
TI  - Characterization of a site-specific restriction endonuclease from Rhodopseudomonas sphaeroides.
PG  - 505-509
AB  - A type II restriction endonuclease, RshI, has been partially purified from
      photoheterotrophically grown Rhodopseudomonas sphaeroides strain 2.4.1.  The
      enzyme preparation, after a single DE-52 column fractionation, is free of 5'
      exonuclease and phospatase activities but contains a trace of 3' exonuclease
      activity.  Based upon deoxyribonucleic acid (DNA) sequencing data in the
      vicinity of the enzyme-promoted cleavage of pBR322 DNA, we have concluded that
      RshI probably recognizes the palinodromic hexanucleotide sequence 5'-CGATCG-3'
      and cleaves between the T and C.  Lambda cI857 DNA contains three RshI sites,
      two of which lie in the replaceable region.  The plasmid pBR322, which carries
      resistances to ampicillin and tetracycline, contains a single RshI site in the
      ampicillin resistance determinant.  Insertion of DNA into the RshI site of
      pBR322 results in loss of ampicillin resistance but retention of tetracycline
      resistance, thereby providing a convenient screening procedure for recombinant
      plasmids.
AU  - Lynn SP
AU  - Cohen LK
AU  - Gardner JF
AU  - Kaplan S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1979 138: 505-509.

PMID- 6247319
VI  - 142
DP  - 1980
TI  - RsaI: a new sequence-specific endonuclease activity from Rhodopseudomonas sphaeroides.
PG  - 380-383
AB  - A new type II sequence-specific endonuclease, RsaI, has been identified from
      Rhodopseudomonas sphaeroides strain 28/5.  An RsaI purification scheme that
      yields enzyme which is free of contaminating exonuclease and phosphatase
      activities after a single column fractionation has been developed.  The enzyme
      recognized the tetranucleotide sequence 5'-GTAC-3' and cleaved between the T
      and A, thereby generating flush ends.  RsaI should be extremely useful in
      deoxyribonucleic acid sequencing experiments.
AU  - Lynn SP
AU  - Cohen LK
AU  - Kaplan S
AU  - Gardner JF
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1980 142: 380-383.

PMID- 11123471
VI  - 89
DP  - 2000
TI  - Site-specific restriction endonucleases in cyanobacteria.
PG  - 979-991
AB  - Aim: Planktic cyanobacteria were screened for endodeoxyribonucleases. Principal component
      analysis (PCA) was employed to demonstrate a
      potential relationship between certain enzymes and a group of
      cyanobacteria. The data were obtained from a data bank and this study.
      Methods and Results: Enzymes were partially purified using column
      chromatography. Anabaena strains contained Asp83/1I(5'-TTCGAA-3'),
      Asp83/1II (5'-GGCC-3'), Asp90I (5'-ACRYGT-3') and five isoschizomeric
      enzymes (5'-ATCGAT-3'). Aphanizomenon and Microcystis strains contained
      ApcTR183I (5'-TGCGCA-3') and Msp199I (5'-CCGG-3'), respectively.
      Planktothrix strains possessed Psc2I (5'-GAANNNNTTC-3'), Psc27I and
      Psc28I (5'-TTCGAA-3'). PCA showed that the most common cyanobacterial
      endonuclease types were AvaII, AvaI and AsuII.
      Conclusions: All planktic cyanobacteria studied contained
      restriction endonucleases. The defined restriction endonucleases were
      isoschizomers of known enzymes. The Nostoc and the Spirulina genera had
      an association, while the majority of the genera had no association
      with certain endonuclease type(s).
      Significance and Impact of the Study: The defined enzymes in this
      study and the estimated trend in the endonuclease type distribution
      allow more efficient avoidance of cynobacterial restriction barriers.
AU  - Lyra C
AU  - Halme T
AU  - Torsti A-M
AU  - Tenkanen T
AU  - Sivonen K
PT  - Journal Article
TA  - J. Appl. Microbiol.
JT  - J. Appl. Microbiol.
SO  - J. Appl. Microbiol. 2000 89: 979-991.

PMID- 27688317
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Bacillus litoralis C44, Isolated from Chinese Scholar Tree (Sophora japonica) Forest Soil.
PG  - e01059-16
AB  - Bacillus litoralis C44 can hydrolyze rutin to produce isoquercetin by the enzyme
      alpha-l-rhamnosidase. We report here the genome sequence and annotation result of
      strain C44. The genomic information will serve as references to the physiology,
      genetics, and evolution of this species and further genetic engineering research
      in this species.
AU  - Lyu W
AU  - Wu Y
AU  - Liu Y
AU  - Lyu Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01059-16.

PMID- 24055317
VI  - 21
DP  - 2013
TI  - Allosteric Regulation of DNA Cleavage and Sequence-Specificity through Run-On Oligomerization.
PG  - 1848-1858
AB  - SgrAI is a sequence specific DNA endonuclease that functions through an unusual enzymatic
      mechanism that is allosterically activated 200- to 500-fold by effector
      DNA, with a concomitant expansion of its DNA sequence specificity. Using
      single-particle transmission electron microscopy to reconstruct distinct
      populations of SgrAI oligomers, we show that in the presence of allosteric,
      activating DNA, the enzyme forms regular, repeating helical structures
      characterized by the addition of DNA-binding dimeric SgrAI subunits in a run-on
      manner. We also present the structure of oligomeric SgrAI at 8.6 A resolution,
      demonstrating the conformational state of SgrAI in its activated form. Activated
      and oligomeric SgrAI displays key protein-protein interactions near the helix
      axis between its N termini, as well as allosteric protein-DNA interactions that
      are required for enzymatic activation. The hybrid approach reveals an unusual
      mechanism of enzyme activation that explains SgrAI's oligomerization and
      allosteric behavior.
AU  - Lyumkis D
AU  - Talley H
AU  - Stewart A
AU  - Shah S
AU  - Park CK
AU  - Tama F
AU  - Potter CS
AU  - Carragher B
AU  - Horton NC
PT  - Journal Article
TA  - Structure
JT  - Structure
SO  - Structure 2013 21: 1848-1858.

PMID- 11501397
VI  - 46
DP  - 2001
TI  - The restriction-modification system in Streptomyces flavopersicus.
PG  - 119-122
AB  - To clone bifunctional vectors in streptomycetes, it was necessary to define the
      restriction-modification system of Streptomyces
      flavopersicus. Plasmid DNA from bifunctional vectors pIJ699 and
      pXED3-13, isolated from E. coli strains with different methylation
      systems: E. coli DH5 alpha (dam(+) dcm(+)), E. coli MB5386 (dam dcm), E.
      coli CB51 (dam dcm(+)), E. coli NM544 (dam(+) dcm), was used for
      transformation of protoplasts from strain S. flavopersicus. Restriction
      of dcm-methylated DNA from S. flavopersicus was established. As a host
      in the intermediate cloning strain E.coli NM544 (dam(+) dcm) should be
      used, as the dcm-transmethylase-dependent strain S. flavopersicus does
      not process DNA from this strain.
AU  - Lyutzkanova D
AU  - Stoilova-Disheva M
AU  - Peltekova V
PT  - Journal Article
TA  - Folia Microbiol. (Praha)
JT  - Folia Microbiol. (Praha)
SO  - Folia Microbiol. (Praha) 2001 46: 119-122.

PMID- 25059860
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Staphylococcus xylosus HKUOPL8, a Potential Opportunistic Pathogen of Mammals.
PG  - e00653-14
AB  - We report here the first complete genome sequence of Staphylococcus xylosus strain HKUOPL8,
      isolated from giant panda feces. The whole genome sequence of
      this strain will provide an important framework for investigating the genes
      responsible for potential opportunistic infections with this species, as well as
      its survival in various environments.
AU  - Ma AP
AU  - Jiang J
AU  - Tun HM
AU  - Mauroo NF
AU  - Yuen CS
AU  - Leung FC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00653-14.

PMID- 27259995
VI  - 7
DP  - 2016
TI  - Biochemical and structural characterization of a DNA N6-adenine methyltransferase from Helicobacter pylori.
PG  - 40965-40977
AB  - DNA N6-methyladenine modification plays an important role in regulating a variety of
      biological functions in bacteria. However, the mechanism of sequence-specific
      recognition in N6-methyladenine modification remains elusive. M1.HpyAVI, a DNA
      N6-adenine methyltransferase from Helicobacter pylori, shows more promiscuous
      substrate specificity than other enzymes. Here, we present the crystal structures
      of cofactor-free and AdoMet-bound structures of this enzyme, which were
      determined at resolutions of 3.0 A and 3.1 A, respectively. The core structure of
      M1.HpyAVI resembles the canonical AdoMet-dependent MTase fold, while the putative
      DNA binding regions considerably differ from those of the other MTases, which may
      account for the substrate promiscuity of this enzyme. Site-directed mutagenesis
      experiments identified residues D29 and E216 as crucial amino acids for cofactor
      binding and the methyl transfer activity of the enzyme, while P41, located in a
      highly flexible loop, playing a determinant role for substrate specificity. Taken
      together, our data revealed the structural basis underlying DNA N6-adenine
      methyltransferase substrate promiscuity.
AU  - Ma B
AU  - Ma J
AU  - Liu D
AU  - Guo L
AU  - Chen H
AU  - Ding J
AU  - Liu W
AU  - Zhang H
PT  - Journal Article
TA  - Oncotarget
JT  - Oncotarget
SO  - Oncotarget 2016 7: 40965-40977.

PMID- 17004833
VI  - 110
DP  - 2006
TI  - Fluorescence study of DNA binding and bending by EcoRI DNA methyltransferase.
PG  - 19647-19651
AB  - We have applied fluorescence anisotropy and fluorescence resonance energy transfer (FRET)
      techniques to study the interaction between
      EcoRI DNA methyltransferase (M.EcoRI) and its target DNA in solution.
      Upon binding with M.EcoRI, the dsDNA containing GAATTC bends to flip
      out the second adenine for methylation. The binding affinity of M.
      EcoRI to two dsDNA fragments (20 and 38 bp) was studied with
      fluorescence anisotropy. Their binding constants at different
      temperatures from 20 to 40 degrees C were obtained, and the
      thermodynamic parameters of binding were derived. The results showed
      that M.EcoRI had a higher binding affinity to the short dsDNA strand
      than to the long one, and its binding to DNA was primarily
      entropy-driven. By labeling the 5' ends of the 20-bp dsDNA with two
      fluorescent dyes, fluorescein (FAM) and tetramethylrhodamine (TMR), we
      were able to monitor the enhanced TMR fluorescence in the presence of
      M.EcoRI. The end-to-end distance of the dsDNA determined from the FRET
      efficiency was changed from 72.4 to 63.4 angstrom, and the DNA bending
      angle was estimated as 57.8 degrees.
AU  - Ma BC
AU  - Wang J
AU  - Fang XH
PT  - Journal Article
TA  - J. Phys. Chem. B
JT  - J. Phys. Chem. B
SO  - J. Phys. Chem. B 2006 110: 19647-19651.

PMID- 17313935
VI  - 363
DP  - 2007
TI  - Real-time monitoring of restriction endonuclease activity using molecular beacon.
PG  - 294-296
AB  - Restriction endonucleases are one of the most important enzymes in molecular biology.  These
      enzymes are essential in recombinant technology, genotyping, mapping, and sequencing of large
      strands of DNA.  Because of the biological importance of restriction endonucleases and their
      wide use, restriction endonuclease activity assays are essential.  Traditional methods for
      assaying activity of restriciton endonucleases, such as gel electrophoresis, filter binding,
      high-performance liquid chromatography, and enzyme-linked immunosorbent assay, have been used.
      All of these methods, however, are discontinuous, time-consuming, and laborious, and they
      usually require isotope labeling.  Several spectroscopic methods using fluorescence
      measurements have been developed.  These assays are continuous.  However, up to now all of
      them have been designed only for doubly labeled DNA substrates with very large fluorophores
      that may interfere with recognition and reactivity with certain restriction endonucleases.
      Furthermore, the potential for achieving high sensitivity through fluorescent resonance energy
      transfer has not been fully realized.  Therefore, it is necessary to develop a sensitive,
      convenient, and non-isotope-labeled method for assaying restriction endonuclease activity.
AU  - Ma CB
AU  - Tang ZW
AU  - Wang KM
AU  - Tan WH
AU  - Yang XH
AU  - Li W
AU  - Li ZH
AU  - Lv XY
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 2007 363: 294-296.

PMID- 
VI  - 19
DP  - 2011
TI  - Sequence analysis of DNA methyltransferase gene from Largemouth bass ulcerative syndrome virus and its expression in prokaryote.
PG  - 342-349
AB  - In order to further reveal the characteristics of Largemouth bass ulcerative syndrome virus
      (LBUSV) isolated recently, a further study the group of LBUSV, DFV (Doctor fish virus) and
      LMBV (Largemouth bass virus), the full-length DNA methyltransferase (DNA MTase) gene was
      analyzed and expressed using prokaryotic system.  A about 200 bp core fragment was amplified
      and sequenced, and the full-length of DNA MTase was identified by genome walking.  The open
      reading frame (ORF) of DNA MTase gene was 663 bp encoding 220 amino acids (GenBank accession
      No. GU256634).  Motif analysis indicated that LBUSV DNA MTase protein contained blocks I, IV,
      VI and VIII, and cofactor binding sites, substrate interacting sites and DNA binding sites
      were also found in LBUSV DNA MTase, and the proline-proline-cysteine tripeptide was proposed
      catalytic site.  Additionally, the primers were designed according to DNA MTase ORF, and the
      PCR products were inserted in vector pBV220 and transformed to host Escherichia coli DH5a.
      After temperature inducement and SDS-PAGE analysis, the recombinant expression bacteria
      produced a special proein about 25 kD in molecular weight.  The analysis, the recombinant
      expression bacteria produced a special protein about 25 kD in molecular weight.  The
      proportion of recombinant protein in total bacterial protein was about 30%.  Characteristic
      analysis of DNA MTase gene showed that the predicted protein may play a role of DNA
      methyltransferase, and confirmed that the taxonomic status of LBUSV is genus Ranavirus of the
      family Iridoviridae.
AU  - Ma D
AU  - Bai J
AU  - Deng G
AU  - Li S
PT  - Journal Article
TA  - Nong Ye Sheng Wu Ji Shu Xue Bao
JT  - Nong Ye Sheng Wu Ji Shu Xue Bao
SO  - Nong Ye Sheng Wu Ji Shu Xue Bao 2011 19: 342-349.

PMID- 26769923
VI  - 4
DP  - 2016
TI  - Genome Sequence of a Typical Ultramicrobacterium, Curvibacter sp. Strain PAE-UM,  Capable of Phthalate Ester Degradation.
PG  - e01510-15
AB  - Curvibacter sp. strain PAE-UM, isolated from river sediment, is a typical ultramicrobacterium
      capable of phthalate ester degradation. The genome of
      Curvibacter sp. PAE-UM consists of 3,284,473 bp, and its information will provide
      insights into the molecular mechanisms underlying its degradation ability.
AU  - Ma D
AU  - Hao Z
AU  - Sun R
AU  - Bartlam M
AU  - Wang Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01510-15.

PMID- 1316190
VI  - 18
DP  - 1992
TI  - The group I intron of apocytochrome b gene from Chlamydomonas smithii encodes a site-specific endonuclease.
PG  - 1001-1004
AB  - The mitochondrial DNA molecules of two interfertile algal species, Chlamydomonas smithii and
      C. reinhardtii, are co-linear except for a 1075 bp intron (the alpha-insert) that is present
      in the cob gene of C. smithii. The alpha-insert, a group I intron (Cs cob.1) containing an
      open reading frame (ORF) which encodes a basic, hydrophilic protein of 237 amino acids, is
      unidirectionally transmitted to all diploid progeny during interspecific crosses. In this
      report, we show that the Cs cob.1-encoded protein is a site-specific endonuclease (I-Csm I)
      which could mediate intron transfer via the gene conversion mechanism. The Cs cob.1 ORF was
      cloned into the vector pMALcr1 and over-expressed as a hybrid protein fused to maltose-binding
      protein (MBP). This fusion protein exhibited an in vivo endonuclease activity which
      specifically cleaved the intron homing site within the intronless cob gene.
AU  - Ma DP
AU  - King YT
AU  - Kim Y
AU  - Luckett S
PT  - Journal Article
TA  - Plant Mol. Biol.
JT  - Plant Mol. Biol.
SO  - Plant Mol. Biol. 1992 18: 1001-1004.

PMID- 23792742
VI  - 1
DP  - 2013
TI  - Genome Sequence of an Environmental Isolate of the Bacterial Pathogen Legionella  pneumophila.
PG  - e00320-13
AB  - We report here the genomic sequence of Legionella pneumophila strain LPE509 from  the water
      distribution system of a hospital in Shanghai, China. This is the first
      complete genome sequence of an environmental L. pneumophila isolate. Genomic
      analyses identified approximately 600 genes unique to LPE509 compared to those of
      the 7 available L. pneumophila genomes.
AU  - Ma J
AU  - He Y
AU  - Hu B
AU  - Luo ZQ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00320-13.

PMID- 28860261
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Bacillus velezensis GQJK49, a Plant Growth-Promoting  Rhizobacterium with Antifungal Activity.
PG  - e00922-17
AB  - Bacillus velezensis GQJK49 is a plant growth-promoting rhizobacterium with antifungal
      activity, which was isolated from Lycium barbarum L. rhizosphere.
      Here, we report the complete genome sequence of B. velezensis GQJK49. Twelve gene
      clusters related to its biosynthesis of secondary metabolites, including
      antifungal and antibacterial antibiotics, were predicted.
AU  - Ma J
AU  - Liu H
AU  - Liu K
AU  - Wang C
AU  - Li Y
AU  - Hou Q
AU  - Yao L
AU  - Cui Y
AU  - Zhang T
AU  - Wang H
AU  - Wang B
AU  - Wang Y
AU  - Ge R
AU  - Xu B
AU  - Yao G
AU  - Xu W
AU  - Fan L
AU  - Ding Y
AU  - Du B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00922-17.

PMID- 28572331
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Bacillus subtilis GQJK2, a Plant Growth-Promoting Rhizobacterium with Antifungal Activity.
PG  - e00467-17
AB  - Bacillus subtilis GQJK2 is a plant growth-promoting rhizobacterium with antifungal activity
      which was isolated from Lycium barbarum L. rhizosphere. Here,
      we report the complete genome sequence of B. subtilis GQJK2. Ten gene clusters
      involved in the biosynthesis of antagonistic compounds were predicted.
AU  - Ma J
AU  - Liu H
AU  - Wang C
AU  - Xia Z
AU  - Liu K
AU  - Hou Q
AU  - Li Y
AU  - Zhang T
AU  - Wang H
AU  - Wang B
AU  - Wang Y
AU  - Ge R
AU  - Xu B
AU  - Yao G
AU  - Jiang Z
AU  - Hou W
AU  - Ding Y
AU  - Du B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00467-17.

PMID- 23525471
VI  - 41
DP  - 2013
TI  - Resriction endonuclease TseI cleaves A:A and T:T mismatches in CAG and CTG repeats.
PG  - 4999-5009
AB  - The type II restriction endonuclease TseI recognizes the DNA target sequence 5'-G^CWGC-3'
      (where W=A or T) and cleaves after the first G to produce fragments with three-base
      5'-overhangs.  We have determined that it is a dimeric protein capable of cleaving not only
      its target sequence but also one containing A:A or T:T mismatches at the central base pair in
      the target sequence.  The cleavage of targets containing these mismatches is as efficient as
      cleavage of the correct target sequence containing a central A:T base pair.  The cleavage
      mechanism does not apparently use a base flipping mechanism as found for some other type II
      restriction endonuclease recognizing similarly degenerate target sequences.  The ability of
      TseI to cleave targets with mismatches means that it can cleave the unusual DNA hairpin
      structures containing A:A or T:T mismatches formed by the repetitive DNA sequences associated
      with Huntington's disease (CAG repeats) and myotonic dystrophy type 1 (CTG repeats).
AU  - Ma L
AU  - Chen K
AU  - Clarke DJ
AU  - Nortcliffe CP
AU  - Wilson GG
AU  - Edwardson JM
AU  - Morton AJ
AU  - Jones AC
AU  - Dryden DTF
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2013 41: 4999-5009.

PMID- 24813995
VI  - 449
DP  - 2014
TI  - Time-resolved fluorescence of 2-aminopurine in DNA duplexes in the presence of the EcoP15I Type III restriction-modification enzyme.
PG  - 120-125
AB  - EcoP15I is a Type III DNA restriction and modification enzyme of Escherichia coli. We show
      that it contains two modification (Mod) subunits for sequence-specific methylation of DNA and
      one copy of a restriction endonuclease (Res) subunit for cleavage of DNA containing
      unmethylated target sequences. Previously the Mod(2) dimer in the presence of cofactors was
      shown to use nucleotide flipping to gain access to the adenine base targeted for methylation
      (Reddy and Rao, J. Mol. Biol. 298 (2000) 597-610.). Surprisingly the Mod(2) enzyme also
      appeared to flip a second adenine in the target sequence, one which was not subject to
      methylation. We show using fluorescence lifetime measurements of the adenine analogue,
      2-aminopurine, that only the methylatable adenine undergoes flipping by the complete
      Res(1)Mod(2) enzyme and that this occurs even in the absence of cofactors. We suggest that
      this is due to activation of the Mod(2) core by the Res subunit.
AU  - Ma L
AU  - Wu X
AU  - Wilson GG
AU  - Jones AC
AU  - Dryden DTF
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 2014 449: 120-125.

PMID- 24035855
VI  - 52
DP  - 2014
TI  - Assaying multiple restriction endonucleases functionalities and inhibitions on DNA microarray with multifunctional gold nanoparticle probes.
PG  - 118
AB  - Herein, a double-stranded (ds) DNA microarray-based resonance light scattering (RLS) assay
      with multifunctional gold nanoparticle (GNP) probes has been developed for studying
      restriction endonuclease functionality and inhibition. Because of decreasing significantly
      melting temperature, the enzyme-cleaved dsDNAs easily unwind to form single-stranded (ss)
      DNAs. The ssDNAs are hybridized with multiplex complementary ssDNAs functionalized GNP probes
      followed by silver enhancement and RLS detection. Thre restriction endonucleases (EcoRI, BamHI
      and EcoRV) and three potential inhibitors (doxorubicin hydrochloride (DOX), ethidium bromide
      (EB) and an EcoRI-derived helical peptide (alpha 4)) were selected to demonstrate capability
      of the assay. Enzyme activities of restriction endonucleases are detected simultaneously with
      high specificity down to the limits of 2.0 x 10(-2) U/mL for EcoRI, 1.1 x 10(-2) U/mL for
      BamHI and 1.6 x 10(-2) U/mL for EcoRV, respectively. More importantly, the inhibitory
      potencies of t hree inhibitors are showed quantitatively, indicating that our approach has
      great promise for high-throughput screening of restriction endonuclease inhibitors.
AU  - Ma L
AU  - Zhu Z
AU  - Li T
AU  - Wang Z
PT  - Journal Article
TA  - Biosensors and Bioelectronics
JT  - Biosensors and Bioelectronics
SO  - Biosensors and Bioelectronics 2014 52: 118.

PMID- 21037012
VI  - 193
DP  - 2010
TI  - Complete Genome Sequence of Paenibacillus polymyxa SC2, a Strain of Plant Growth Promoting Rhizobacteria with Broad-Spectrum Antimicrobial Activity.
PG  - 311-312
AB  - Paenibacillus polymyxa SC2 is an important plant growth promoting rhizobacterium (PGPR). Here
      we report the complete genome sequence of P. polymyxa SC2. Multiple sets of functional genes
      have been found in the genome. As far as we know, this is the first complete genome sequence
      of Paenibacillus polymyxa.
AU  - Ma M
AU  - Wang C
AU  - Ding Y
AU  - Li L
AU  - Shen D
AU  - Jiang X
AU  - Guan D
AU  - Cao F
AU  - Chen H
AU  - Feng R
AU  - Wang X
AU  - Ge Y
AU  - Yao L
AU  - Bing X
AU  - Yang X
AU  - Li J
AU  - Du B
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 193: 311-312.

PMID- 22843591
VI  - 194
DP  - 2012
TI  - Genome Sequence of a Novel Indigo-Producing Strain, Pseudomonas monteilii QM.
PG  - 4459-4460
AB  - Pseudomonas monteilii is a versatile bacterium found in various niches. A newly isolated
      strain, P. monteilii QM, can effectively produce indigoids from indoles.
      Here we present a 5.76-Mb assembly of the P. monteilii genome for the first time.
      It may provide abundant molecular information for the transformation of
      aromatics.
AU  - Ma Q
AU  - Qu Y
AU  - Tang H
AU  - Yu H
AU  - Ma F
AU  - Shi S
AU  - Zhang X
AU  - Zhou H
AU  - Zhou J
AU  - Xu P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4459-4460.

PMID- 25767238
VI  - 3
DP  - 2015
TI  - Genome Sequence of an Efficient Indole-Degrading Bacterium, Cupriavidus sp. Strain IDO, with Potential Polyhydroxyalkanoate Production Applications.
PG  - e00102-15
AB  - Cupriavidus sp. strain IDO has been shown to efficiently transform indole, and the genus of
      Cupriavidus has been described as a promising cell factory for
      polyhydroxyalkanoate synthesis from low-cost wastes. Here, we report the draft
      genome sequence of strain IDO, which may provide useful genetic information on
      indole metabolism and polyhydroxyalkanoate production.
AU  - Ma Q
AU  - Qu Y
AU  - Zhang Z
AU  - Li P
AU  - Tang H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00102-15.

PMID- 29242219
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Loktanella cinnabarina Strain XM1 Isolated from Coastal  Surface Water.
PG  - e01310-17
AB  - We report here the draft genome sequence of Loktanella cinnabarina strain XM1, which was
      isolated from coastal surface water and shared 99.43% 16S rRNA gene
      sequence identity with the deep-sea bacterium L. cinnabarina LL-001(T) The
      estimated genome size of strain XM1 is 3,782,785 bp, with a G+C content of 67.9%.
AU  - Ma R
AU  - Wang J
AU  - Wang Q
AU  - Ma Z
AU  - Li J
AU  - Chen L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01310-17.

PMID- 11897611
VI  - 46
DP  - 2002
TI  - Novel Type of Staphylococcal Cassette Chromosome mec Identified in Community-Acquired Methicillin-Resistant Staphylococcus aureus Strains.
PG  - 1147-1152
AB  - We identified a new type of staphylococcal cassette chromosome mec
      (SCCmec) from two community-acquired methicillin-resistant Staphylococcus
      aureus (MRSA) strains. The novel element, designated type IV SCCmec, had a
      unique combination of the class B mec gene complex and the type 2 ccr gene
      complex and was much smaller in size (21 to 24 kb) than previously
      identified SCCmec elements of hospital-acquired MRSA. Consistent with the
      strains' susceptibilities to various non-beta-lactam antibiotics, the type
      IV SCCmec was devoid of any antibiotic resistance genes other than the
      mecA gene.
AU  - Ma XX
AU  - Ito T
AU  - Tiensasitorn C
AU  - Jamklang M
AU  - Chongtrakool P
AU  - Boyle-Vavra S
AU  - Daum RS
AU  - Hiramatsu K
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2002 46: 1147-1152.

PMID- 19734336
VI  - 75
DP  - 2009
TI  - The Complete Genome of Comamonas testosteroni Reveals Its Genetic Adaptations to Changing Environments.
PG  - 6812-6819
AB  - Members of the gram-negative, strictly aerobic genus Comamonas occur in
      various environments. Here we report the complete genome of Comamonas
      testosteroni strain CNB-2. Strain CNB-2 has a circular chromosome that is
      5,373,643 bp long and has a G+C content of 61.4%. A total of 4,803 open
      reading frames (ORFs) were identified; 3,514 of these ORFs are
      functionally assigned to energy production, cell growth, signal
      transduction, or transportation, while 866 ORFs encode hypothetical
      proteins and 423 ORFs encode purely hypothetical proteins. The CNB-2
      genome has many genes for transportation (22%) and signal transduction
      (6%), which allows the cells to respond and adapt to changing
      environments. Strain CNB-2 does not assimilate carbohydrates due to the
      lack of genes encoding proteins involved in glycolysis and pentose
      phosphate pathways, and it contains many genes encoding proteins involved
      in degradation of aromatic compounds. We identified 66 Tct and nine TRAP-T
      systems and a complete tricarboxylic acid cycle, which may allow CNB-2 to
      take up and metabolize a range of carboxylic acids. This nutritional bias
      for carboxylic acids and aromatic compounds enables strain CNB-2 to occupy
      unique niches in environments. Four different sets of terminal oxidases
      for the respiratory system were identified, and they putatively functioned
      at different oxygen concentrations. This study conclusively revealed at
      the genomic level that the genetic versatility of C. testosteroni is vital
      for competition with other bacteria in its special niches.
AU  - Ma YF
AU  - Zhang Y
AU  - Zhang JY
AU  - Chen DW
AU  - Zhu Y
AU  - Zheng H
AU  - Wang SY
AU  - Jiang CY
AU  - Zhao GP
AU  - Liu SJ
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2009 75: 6812-6819.

PMID- 28642377
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of the Extremely Thermoacidophilic Archaeon Acidianus manzaensis YN-25.
PG  - e00438-17
AB  - The complete genome of Acidianus manzaensis YN-25 consists of a chromosome of 2,687,463 bp,
      with a G+C content of 30.62% and 2,746 coding DNA sequences. This
      archaeon contains a series of specific genes involved in the oxidation of
      elemental sulfur and reduced inorganic sulfur compounds.
AU  - Ma YL
AU  - Xia JL
AU  - Yang Y
AU  - Nie ZY
AU  - Liu HC
AU  - Liu LZ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00438-17.

PMID- 21914890
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Streptococcus equi subsp. zooepidemicus Strain ATCC 35246.
PG  - 5583-5584
AB  - Streptococcus equi subsp. zooepidemicus is an opportunistic pathogen. It has caused a very
      large economic loss in the swine industry of China and
      has become a threat to human health. We announce the complete genome
      sequence of S. equi subsp. zooepidemicus strain ATCC 35246, which provides
      opportunities to understand its pathogenesis mechanism and genetic basis.
AU  - Ma Z
AU  - Geng J
AU  - Zhang H
AU  - Yu H
AU  - Yi L
AU  - Lei M
AU  - Lu CP
AU  - Fan HJ
AU  - Hu S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5583-5584.

PMID- 23742619
VI  - 14
DP  - 2013
TI  - Insight into the specific virulence related genes and toxin-antitoxin virulent pathogenicity islands in swine streptococcosis pathogen Streptococcus equi ssp zooepidemicus strain ATCC35246.
PG  - 377
AB  - Background: Streptococcus equi ssp. zooepidemicus (S. zooepidemicus) is an important pathogen
      causing swine streptococcosis in China. Pathogenicity islands (PAIs) of S. zooepidemicus have
      been transferred among bacteria through horizontal gene transfer (HGT) and play important
      roles in the adaptation and increased virulence of S. zooepidemicus. The present study used
      comparative genomics to examine the different pathogenicities of S. zooepidemicus. Results:
      Genome of S. zooepidemicus ATCC35246 (Sz35246) comprises 2,167,264-bp of a single circular
      chromosome, with a GC content of 41.65%. Comparative genome analysis of Sz35246, S.
      zooepidemicus MGCS10565 (Sz10565), Streptococcus equi. ssp. equi. 4047 (Se4047) and S.
      zooepidemicus H70 (Sz70) identified 320 Sz35246-specific genes, clustered into three
      toxin-antitoxin (TA) systems PAIs and one restriction modification system (RM system) PAI.
      These four acquired PAIs encode proteins that may contribute to the overall pathogenic
      capacity and fitness of this bacterium to adapt to different hosts. Analysis of the in vivo
      and in vitro transcriptomes of this bacterium revealed differentially expressed PAI genes and
      non-PAI genes, suggesting that Sz35246 possess mechanisms for infecting animals and adapting
      to a wide range of host environments. Analysis of the genome identified potential Sz35246
      virulence genes. Genes of the Fim III operon were presumed to be involved in breaking the
      host-restriction of Sz35246. Conclusion: Genome wide comparisons of Sz35246 with three other
      strains and transcriptome analysis revealed novel genes related to bacterial virulence and
      breaking the host-restriction. Four specific PAIs, which were judged to have been transferred
      into Sz35246 genome through HGT, were identified for the first time. Further analysis of the
      TA and RM systems in the PAIs will improve our understanding of the pathogenicity of this
      bacterium and could lead to the development of diagnostics and vaccines.
AU  - Ma Z
AU  - Geng JN
AU  - Yi L
AU  - Xu B
AU  - Jia RY
AU  - Li Y
AU  - Meng QS
AU  - Fan HJ
AU  - Hu SN
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2013 14: 377.

PMID- 22689229
VI  - 194
DP  - 2012
TI  - Genome Sequence of Sphingomonas wittichii DP58, the First Reported Phenazine-1-Carboxylic Acid-Degrading Strain.
PG  - 3535-3536
AB  - Sphingomonas wittichii DP58 (CCTCC M 2012027), the first reported phenazine-1-carboxylic acid
      (PCA)-degrading strain, was isolated from pimiento
      rhizosphere soils. Here we present a 5.6-Mb assembly of its genome. This sequence
      would contribute to the elucidation of the molecular mechanism of PCA degradation
      to improve the antifungal's effectiveness or remove superfluous PCA.
AU  - Ma Z
AU  - Shen X
AU  - Hu H
AU  - Wang W
AU  - Peng H
AU  - Xu P
AU  - Zhang X
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3535-3536.

PMID- 29326224
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Megamonas funiformis Strain Marseille-P3344, Isolated from a Human Fecal Microbiota.
PG  - e01459-17
AB  - In this article, we present the draft genome sequence of Megamonas funiformis strain
      Marseille-P3344, isolated from a human fecal sample. The genome described
      here is composed of 2,464,704 nucleotides, with 2,230 protein-coding genes and 76
      RNA genes.
AU  - Maaloum M
AU  - Diop A
AU  - Ndongo S
AU  - Nguyen TT
AU  - Cadoret F
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01459-17.

PMID- 11439190
VI  - 105
DP  - 2001
TI  - Change in plasmid DNA structure, hypermethylation, and lon-proteolysis as steps in a replicative cascade.
PG  - 945-955
AB  - I have defined conditions under which RepFIC plasmid DNA can be maintained in a state of
      lowered helical density.  In exponentially growing cultures, the DNA of lowered helical
      density is present in small amounts but never totally absent, suggesting that it is a normal
      variant of plasmid maintenance.  It is fully methylated at frequent sites by
      dam-methyltransferase, some not previously recognized, further suggesting that the variant is
      a precursor of replication.  The low-helical density plasmid is present in dam hosts,
      indicating that methylation is not essential for the change in helical density.  The lowered
      helical density is stabilized in lon hosts, suggesting that Lon-protease may remove both the
      protein(s) that lower the helical density and the dam-methyltransferase after each round of
      replication.
AU  - Maas R
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 2001 105: 945-955.

PMID- Not carried by PubMed...
VI  - 137
DP  - 1987
TI  - Recognition of DNA sequences by restriction endonucleases.
PG  - 225-237
AB  - Type II restriction endonucleases recognize DNA sequences 4 or 6 base pairs
      long with very high specificity in a vast excess of non-specific DNA binding
      sites.  They cleave the DNA within or in the immediate vicinity of the
      recognition sequence.  Because of the immense importance of these enzymes in
      analysis, preparation and in vitro recombination of DNA many investigations
      have been carried out to understand the structural and mechanistic features
      underlying their mode of recognition.  Among approximately 500 type II
      restriction endonucleases described, EcoRI is the so far best studied enzyme.
      EcoRI is a dimeric protein with two identical subunits, the aminoacid sequence
      of which is known.  It recognizes the palindromic sequence -G^AATTC- -CTTAA^G-
      and cleaves the DNA double strand at the marked positions.  For its enzymatic
      activity it needs Mg2+ as a co-factor.  It was the first DNA-binding protein
      that was co-crystallized with its substrate TCGCGAATTCGCG by Frederick et al.
      in the absence of Mg2+.  The 3A X-ray analysis revealed a complementary
      interface between the enzyme and the major groove of the DNA.  The binding of
      the enzyme introduces distortions of the DNA, so called neo-kinks, and thereby
      widens the major groove.  In a more recent though preliminary presentation, a
      more detailed interpretation of the 3A-structure was given by J. Rosenberg, who
      suggested that EcoRI interacts with its canonical sequence via 12 hydrogen
      bonds between glutamic acid and arginine residues and the guanine and adenine
      residues of GAATTC.  However, the data available at present are not yet
      sufficient to understand the molecular basis of the EcoRI action.  A more
      detailed knowledge of the thermodynamic, kinetic and structural aspects of the
      EcoRI-DNA interaction is needed.  This contribution intends to present
      physicochemical studies on the binding and catalytic properties of EcoRI and to
      discuss structural aspects of the interaction.
AU  - Maass G
PT  - Journal Article
TA  - NATO ASI Ser.
JT  - NATO ASI Ser.
SO  - NATO ASI Ser. 1987 137: 225-237.

PMID- Not included in PubMed...
VI  - 367
DP  - 1986
TI  - Recognition of DNA-sequences by restriction endonucleases.
PG  - 47
AB  - Class II restriction endonucleases cleave DNA specifically at defined sites.
      EcoRI, e.g., which recognizes the sequence GAATTC, cleaves at sites differing
      in one base pair from this sequence by a factor of 103 to 105 more slowly than
      at its canonical site.  This specificity is a complex function of thermodynamic
      and kinetic parameters which govern the non-specific and specific binding of
      EcoRI to DNA, the linear diffusion of the protein along DNA and conformational
      changes of the enzyme and substrate.  We have been interested in the
      thermodynamics, kinetics as well as structural aspects of these processes in
      order to understand how DNA recognizing proteins interacting with DNA select
      their specific site in a huge excess of nonspecific sites.  The initial contact
      between EcoRI and its substrate is to nonspecific sites, binding to these sites
      in the presence of Mg2+ is by a least a factor of 100 weaker than to the
      specific site.  After nonspecific association EcoRI "slides" along the DNA in a
      random fashion:  at physiological Mg2+ concentrations EcoRI cleave several
      EcoRI sites in close proximity processively.  At high Mg2+ or at high ionic
      strength dissociation is favoured over linear diffusion, and consequently,
      processivity is suppressed.  Discrimination between specific and non-specific
      sites resides in several unique contacts that can only be formed in the
      specific complex.  Many studies have been carried out to define structural
      elements on the DNA important for recognition, few studies, however, were
      concerned with the identification of the regions of the protein important for
      specific binding.  Using bromodeoxyuridine containing oligodeoxynucleotides
      EcoRI was photo-crosslinked to its substrate via Met 157 demonstrating the
      involvement of this region in the recognition complex.  This identification was
      confirmed by the interference of antibodies against this region of EcoRI with
      the catalytic action of EcoRI.  Met 157 is at the end of a sequence which shows
      a striking homology to the sequence of the recognition helix of gene regulatory
      proteins.  We are currently probing the importance of individual amino acid
      residues for the catalytic action of EcoRI by site directed mutagenesis.
AU  - Maass G
AU  - Alves J
AU  - Fliess A
AU  - Pingoud A
AU  - Wolfes H
PT  - Journal Article
TA  - Hoppe Seylers Z. Physiol. Chem.
JT  - Hoppe Seylers Z. Physiol. Chem.
SO  - Hoppe Seylers Z. Physiol. Chem. 1986 367: 47.

PMID- 1892579
VI  - 8
DP  - 1991
TI  - Site-directed mutagenesis studies suggest that Asp91 is part of the catalytic center of the restriction endonuclease EcoRI.
PG  - A126
AB  - The comparison of the structures of EcoRI and EcoRV has revealed an interesting
      homology which presumably concerns the active center of the two enzymes:
      EcoRI:  90 - P D....... 111 E A K
      EcoRV:  73 - P D.......  90 D I K
      In the crystal structure of EcoRI Glu111 is near the bond cleaved.
AU  - Maass G
AU  - Ruter T
AU  - Oelgeschlager T
AU  - Alves J
AU  - Wolfes H
AU  - Pingoud A
PT  - Journal Article
TA  - J. Biomol. Struct. Dyn.
JT  - J. Biomol. Struct. Dyn.
SO  - J. Biomol. Struct. Dyn. 1991 8: A126.

PMID- 25999550
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of a Drug-Susceptible New Zealand Isolate of Mycobacterium  tuberculosis Lineage 3.
PG  - e00499-15
AB  - We report here the draft whole-genome sequence of a drug-susceptible lineage 3 (East-African
      Indian) isolate of Mycobacterium tuberculosis from New Zealand (NZ3DS1) and compare it to a
      multidrug-resistant lineage 3 isolate (NZ3MDR1) with an identical 24-locus mycobacterial
      interspersed repetitive-unit-variable-number tandem-repeat profile.
AU  - Mac Aogain M
AU  - Bower JE
AU  - Basu I
AU  - Freeman JT
AU  - O'Toole RF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00499-15.

PMID- 28596392
VI  - 5
DP  - 2017
TI  - Fourteen Draft Genome Sequences for the First Reported Cases of Azithromycin-Resistant Neisseria gonorrhoeae in Ireland.
PG  - e00403-17
AB  - Here, we report the draft genome assemblies of 14 azithromycin-resistant Neisseria gonorrhoeae
      clinical isolates, representing the first such strains
      identified in Ireland. Among these isolates are the first reported highly
      resistant strains (MIC >256 mg/liter), which both belonged to the ST1580 sequence
      type.
AU  - Mac Aogain M
AU  - Fennelly N
AU  - Walsh A
AU  - Lynagh Y
AU  - Bekaert M
AU  - Lawlor B
AU  - Walsh P
AU  - Kelly B
AU  - Rogers TR
AU  - Crowley B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00403-17.

PMID- 27389273
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a New Zealand Rangipo Strain of Mycobacterium tuberculosis.
PG  - e00657-16
AB  - The Rangipo genotype of the Mycobacterium tuberculosis complex has been associated with a
      number of tuberculosis (TB) outbreaks in New Zealand. We report
      here the draft whole-genome sequence of a representative isolate of this strain.
AU  - Mac Aogain M
AU  - Gautam SS
AU  - Bower JE
AU  - Basu I
AU  - O'Toole RF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00657-16.

PMID- 26634757
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Three Mycobacterium chimaera Respiratory Isolates.
PG  - e01409-15
AB  - Mycobacterium chimaera is an opportunistic human pathogen implicated in both pulmonary and
      cardiovascular infections. Here, we report the draft genome
      sequences of three strains isolated from human respiratory specimens.
AU  - Mac AM
AU  - Roycroft E
AU  - Raftery P
AU  - Mok S
AU  - Fitzgibbon M
AU  - Rogers TR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01409-15.

PMID- 1991728
VI  - 173
DP  - 1991
TI  - Efficient transformation of Bacillus thuringiensis requires nonmethylated plasmid DNA.
PG  - 1353-1356
AB  - The transformation efficiency of Bacillus thuringiensis depends upon the source of plasmid
      DNA. DNA isolated from B. thuringiensis, Bacillus megaterium, or a Dam-Dcm- Escherichia coli
      strain efficiently transformed several B. thuringiensis strains. B. thuringiensis strains were
      grouped according to which B. thuringiensis backgrounds were suitable sources of DNA for
      transformation of other B. thuringiensis strains, suggesting that B. thuringiensis strains
      differ in DNA modification and restriction. Efficient transformation allowed the demonstration
      of developmental regulation of cloned crystal protein genes in B. thuringiensis.
AU  - Macaluso A
AU  - Mettus A-M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1991 173: 1353-1356.

PMID- 25323711
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of a Multidrug-Resistant New Zealand Isolate of Mycobacterium tuberculosis Lineage 3.
PG  - e01017-14
AB  - Multidrug resistance constitutes a threat worldwide to the management of tuberculosis (TB). We
      report the draft whole-genome sequence of a lineage 3 (East-African Indian) isolate of
      Mycobacterium tuberculosis which presented as multidrug resistant in New Zealand, and describe
      a number of single-nucleotide polymorphisms in genes relating to drug resistance.
AU  - MacAogain M
AU  - Johari BM
AU  - Bower JE
AU  - O'Toole RF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01017-14.

PMID- 6098451
VI  - 3
DP  - 1984
TI  - Regulation of a new bacteriophage T4 gene, 69, that spans an origin of DNA replication.
PG  - 2863-2871
AB  - We have determined the DNA sequence and transcription patterns in a 3-kb segment (between 15
      and 18 kb on the standard phage T4 map) spanning an origin of DNA replication. A new gene, 69,
      spans this origin. Gene 69 codes for two overlapping proteins that share a common C-terminal
      segment. Defective DNA replication in an appropriate amber mutant shows that at least the
      larger of the two proteins is required for efficient T4 DNA replication. The two proteins
      coded by gene 69 are expressed from different transcripts that are under different regulation.
      The smaller protein, gp69*, can be expressed immediately from an Escherichia coli-like
      promoter, whereas expression of the larger protein, gp69, must be delayed since its middle
      promoter requires T4 coded proteins, most likely gp mot, for activation. We discuss the
      possible significance of two overlapping proteins in the assembly of replisomes. Gene 69 is
      bracketed by the nonessential early gene dam (DNA adenine methylase) and the late gene soc
      (small outer capsid protein). Transcripts through this region are interdigitated in a complex
      pattern, which reveals all elements that are thought to be important in regulation of
      pre-replicative and post-replicative T4 genes.
AU  - Macdonald PM
AU  - Mosig G
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1984 3: 2863-2871.

PMID- 28153902
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Campylobacter jejuni 11168H.
PG  - e01556-16
AB  - Campylobacter jejuni is the most prevalent cause of food-borne gastroenteritis in the
      developed world. The reference and original sequenced strain C. jejuni
      NCTC11168 has low levels of motility compared to clinical isolates. Here, we
      describe the draft genome of the laboratory derived hypermotile variant named
      11168H.
AU  - Macdonald SE
AU  - Gundogdu O
AU  - Dorrell N
AU  - Wren BW
AU  - Blake D
AU  - Stabler R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01556-16.

PMID- 30533926
VI  - 7
DP  - 2018
TI  - Draft Genome Sequences of Obligate Methylotrophs Methylovorus sp. Strain MM2 and  Methylobacillus sp. Strain MM3, Isolated from Grassland Soil.
PG  - e00824-18
AB  - Methylotrophs of the family Methylophilaceae were isolated from grassland soil. Here, we
      report the draft genome sequences of two obligate methylotrophs,
      Methylovorus sp. strain MM2 and Methylobacillus sp. strain MM3. These genome
      sequences provide further insights into the genetic and metabolic diversity of
      the Methylophilaceae.
AU  - Macey MC
AU  - Pratscher J
AU  - Crombie A
AU  - Murrell JC
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e00824-18.

PMID- 23220958
VI  - 79
DP  - 2013
TI  - Why Orange Guaymas Basin Beggiatoa spp. Are Orange: Single-Filament-Genome-Enabled Identification of an Abundant Octaheme Cytochrome    with Hydroxylamine Oxidase, Hydrazine Oxidase, and Nitrite Reductase Activities.
PG  - 1183-1190
AB  - Orange, white, and yellow vacuolated Beggiatoaceae filaments are visually dominant members of
      microbial mats found near sea floor hydrothermal vents and cold seeps, with orange filaments
      typically concentrated toward the mat centers. No marine vacuolate Beggiatoaceae are yet in
      pure culture, but evidence to date suggests they are nitrate-reducing, sulfide-oxidizing
      bacteria. The nearly complete genome sequence of a single orange Beggiatoa ("Candidatus
      Maribeggiatoa") filament from a microbial mat sample collected in 2008 at a hydrothermal site
      in Guaymas Basin (Gulf of California, Mexico) was recently obtained. From this sequence, the
      gene encoding an abundant soluble orange-pigmented protein in Guaymas Basin mat samples
      (collected in 2009) was identified by microcapillary reverse-phase high-performance liquid
      chromatography (HPLC) nano-electrospray tandem mass spectrometry (muLC-MS-MS) of a pigmented
      band excised from a denaturing polyacrylamide gel. The predicted protein sequence is related
      to a large group of octaheme cytochromes whose few characterized representatives are
      hydroxylamine or hydrazine oxidases. The protein was partially purified and shown by in vitro
      assays to have hydroxylamine oxidase, hydrazine oxidase, and nitrite reductase activities.
      From what is known of Beggiatoaceae physiology, nitrite reduction is the most likely in vivo
      role of the octaheme protein, but future experiments are required to confirm this tentative
      conclusion. Thus, while present-day genomic and proteomic techniques have allowed precise
      identification of an abundant mat protein, and its potential activities could be assayed,
      proof of its physiological role remains elusive in the absence of a pure culture that can be
      genetically manipulated.
AU  - MacGregor BJ
AU  - Biddle JF
AU  - Siebert JR
AU  - Staunton E
AU  - Hegg EL
AU  - Matthysse AG
AU  - Teske A
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2013 79: 1183-1190.

PMID- 23603674
VI  - 79
DP  - 2013
TI  - Mobile Elements in a Single-Filament Orange Guaymas Basin Beggiatoa ('Candidatus Maribeggiatoa') sp Draft Genome: Evidence for Genetic Exchange with Cyanobacteria.
PG  - 3974-3985
AB  - The draft genome sequence of a single orange Beggiatoa ('Candidatus Maribeggiatoa') filament
      collected from a microbial mat at a
      hydrothermal site in Guaymas Basin (Gulf of California, Mexico) shows
      evidence of extensive genetic exchange with cyanobacteria, in
      particular for sensory and signal transduction genes. A putative homing
      endonuclease gene and group I intron within the 23S rRNA gene; several
      group II catalytic introns; GyrB and DnaE inteins, also encoding homing
      endonucleases; multiple copies of sequences similar to the fdxN
      excision elements XisH and XisI (required for heterocyst
      differentiation in some cyanobacteria); and multiple sequences related
      to an open reading frame (ORF) (00024 0693) of unknown function all
      have close non-Beggiatoaceae matches with cyanobacterial sequences.
      Sequences similar to the uncharacterized ORF and Xis elements are found
      in other Beggiatoaceae genomes, a variety of cyanobacteria, and a few
      phylogenetically dispersed pleiomorphic or filamentous bacteria. We
      speculate that elements shared among filamentous bacterial species may
      have been exchanged in microbial mats and that some of them may be
      involved in cell differentiation.
AU  - MacGregor BJ
AU  - Biddle JF
AU  - Teske A
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2013 79: 3974-3985.

PMID- 2383267
VI  - 170
DP  - 1990
TI  - Reversible inhibition of EcoRI with elevated pressure.
PG  - 775-778
AB  - The endonuclease activity of EcoRI is completely inhibited at 200 MPa, 37C
      using the plasmid pBR322 as a substrate.  When assayed at 133 MPa approximately
      half the activity at atmospheric pressure was observed; from these data the
      standard molar volume change is estimated to be -80 cm3  mol-1.  Upon return to
      atmospheric pressure the enzyme reacted in a standard manner with its
      restriction site in pBR322.  Pressurization did not decrease the specificity of
      the endonuclease activity of the enzyme for its canonical site.  These results
      are discussed in terms of the role of ionic interactions in protein-DNA
      interactions.
AU  - Macgregor RB
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1990 170: 775-778.

PMID- 24926051
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Photobacterium halotolerans S2753, Producer of Bioactive Secondary Metabolites.
PG  - e00535-14
AB  - We report here the whole draft genome sequence of marine isolate Photobacterium halotolerans
      S2753, which produces the known antibiotic holomycin and also
      ngercheumicins and solonamides A and B, which interfere with virulence of
      methicillin-resistant Staphylococcus aureus strains by interacting with the
      quorum-sensing system.
AU  - Machado H
AU  - Mansson M
AU  - Gram L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00535-14.

PMID- 24786956
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Trueperella pyogenes, an Important Opportunistic Pathogen of Livestock.
PG  - e00400-14
AB  - Here, we report the complete genome sequence of Trueperella pyogenes TP6375, a strain isolated
      from the uterus of a dairy cow affected with metritis. The
      complete circular genome is 2,338,390 bp and contains several genes needed for
      pathogenicity.
AU  - Machado VS
AU  - Bicalho RC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00400-14.

PMID- 26493560
VI  - 16
DP  - 2015
TI  - Phylogenomics and sequence-structure-function relationships in the GmrSD family of Type IV restriction enzymes.
PG  - 336
AB  - BACKGROUND: GmrSD is a modification-dependent restriction endonuclease that specifically
      targets and cleaves glucosylated hydroxymethylcytosine (glc-HMC)
      modified DNA. It is encoded either as two separate single-domain GmrS and GmrD
      proteins or as a single protein carrying both domains. Previous studies suggested
      that GmrS acts as endonuclease and NTPase whereas GmrD binds DNA. METHODS: In
      this work we applied homology detection, sequence conservation analysis, fold
      recognition and homology modeling methods to study sequence-structure-function
      relationships in the GmrSD restriction endonucleases family. We also analyzed the
      phylogeny and genomic context of the family members. RESULTS: Results of our
      comparative genomics study show that GmrS exhibits similarity to proteins from
      the ParB/Srx fold which can have both NTPase and nuclease activity. In contrast
      to the previous studies though, we attribute the nuclease activity also to GmrD
      as we found it to contain the HNH endonuclease motif. We revealed residues
      potentially important for structure and function in both domains. Moreover, we
      found that GmrSD systems exist predominantly as a fused, double-domain form
      rather than as a heterodimer and that their homologs are often encoded in regions
      enriched in defense and gene mobility-related elements. Finally, phylogenetic
      reconstructions of GmrS and GmrD domains revealed that they coevolved and only
      few GmrSD systems appear to be assembled from distantly related GmrS and GmrD
      components. CONCLUSIONS: Our study provides insight into
      sequence-structure-function relationships in the yet poorly characterized family
      of Type IV restriction enzymes. Comparative genomics allowed to propose possible
      role of GmrD domain in the function of the GmrSD enzyme and possible active sites
      of both GmrS and GmrD domains. Presented results can guide further experimental
      characterization of these enzymes.
AU  - Machnicka MA
AU  - Kaminska KH
AU  - Dunin-Horkawicz S
AU  - Bujnicki JM
PT  - Journal Article
TA  - BMC Bioinformatics
JT  - BMC Bioinformatics
SO  - BMC Bioinformatics 2015 16: 336.

PMID- 19820117
VI  - 37
DP  - 2009
TI  - Cleavage of adenine-modified functionalized DNA by type II restriction endonucleases.
PG  - 7612-7622
AB  - A set of 6 base-modified 2'-deoxyadenosine derivatives was incorporated to diverse DNA
      sequences by primer extension using Vent (exo-) polymerase and
      the influence of the modification on cleavage by diverse restriction
      endonucleases was studied. While 8-substituted (Br or methyl) adenine
      derivatives were well tolerated by the restriction enzymes and the
      corresponding sequences were cleaved, the presence of 7-substituted
      7-deazaadenine in the recognition sequence resulted in blocking of
      cleavage by some enzymes depending on the nature and size of the
      7-substituent. All sequences with modifications outside of the recognition
      sequence were perfectly cleaved by all the restriction enzymes. The
      results are useful both for protection of some sequences from cleavage and
      for manipulation of functionalized DNA by restriction cleavage.
AU  - Macickova-Cahova H
AU  - Hocek M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: 7612-7622.

PMID- 21290545
VI  - 12
DP  - 2011
TI  - Cleavage of Functionalized DNA Containing 5-Modified Pyrimidines by Type II Restriction Endonucleases.
PG  - 431-438
AB  - A series of six pyrimidine-modified dNTPs-5-ethynyl-, 5-phenyl-, and
      5-(3-nitrophenyl)deoxycitidine and -deoxyuridine triphosphates-were
      prepared and incorporated by primer extension with Vent
      (exo-)polymerase to specific DNA sequences within or next to the
      recognition sequences of selected restriction endonucleases. The
      cleavage of these pyrimidine-modified DNA sequences by 13 restriction
      enzymes was then studied. Whereas the presence of any modified C within
      the target sequence completely prevented any restriction cleavage, most
      enzymes tolerated the presence of 5-ethynylU and two of them even the
      presence of 5-phenyl- and 5-(3-nitrophenyl)U. Modifications outside the
      recognition sequence were tolerated except in the case of phenyl
      derivatives with the PvuII enzyme. 5-EthynylC was used for protection
      of the recognition sequence from cleavage in the presence of the second
      unmodified copy of the same sequence that was cleaved.
AU  - Macickova-Cahova H
AU  - Pohl R
AU  - Hocek M
PT  - Journal Article
TA  - Chembiochem
JT  - Chembiochem
SO  - Chembiochem 2011 12: 431-438.

PMID- 23144422
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Actinobacillus suis H91-0380, a Virulent Serotype O2  Strain.
PG  - 6686-6687
AB  - Here, we report the first complete genome sequence of Actinobacillus suis, an important
      opportunistic pathogen of swine. By comparing the genome sequence of A.
      suis with those of other members of the family Pasteurellaceae, we hope to better
      understand the role of these organisms in health and disease in swine.
AU  - Macinnes JI
AU  - Mackinnon J
AU  - Bujold AR
AU  - Ziebell K
AU  - Kropinski AM
AU  - Nash JH
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6686-6687.

PMID- 11208790
VI  - 183
DP  - 2001
TI  - Lowering S-adenosylmethionine levels in Escherichia coli modulates C-to-T transition mutations.
PG  - 921-927
AB  - Deoxycytosine methylase (Dcm) enzyme activity causes mutagenesis in vitro either directly by
      enzyme-induced deamination of cytosine to uracil in the absence of the methyl donor,
      S-adenosylmethionine (SAM), or indirectly through spontaneous deamination of
      [5-methyl]cytosine to thymine. Using a Lac reversion assay, we investigated the contribution
      of the first mechanism to Dcm mutagenesis in vivo by lowering the levels of SAM. Escherichia
      coli SAM levels were lowered by reducing SAM synthetase activity via the introduction of a
      metK84 allele or by hydrolyzing SAM using the bacteriophage T3 SAM hydrolase.  The metK84
      strains exhibited increased C-to-T mutagenesis. Expression of the T3 SAM hydrolase gene, under
      the control of the arabinose-inducible P(BAD) promoter, effectively reduced Dcm-mediated
      genomic DNA methylation. However, increased mutagenesis was not observed until extremely high
      arabinose concentrations were used, and genome methylation at Dcm sites was negligible.
AU  - Macintyre G
AU  - Atwood CV
AU  - Cupples CG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2001 183: 921-927.

PMID- Not carried by PubMed...
VI  - 97
DP  - 1997
TI  - Analysis of the levels of Dcm and Vsr in E. coli.
PG  - 294
AB  - In Escherichia coli, T/G mismatches at C(T/G)WGG are cleaved by Vsr endonuclease, this is the
      initial step in the very short patch repair process which repairs the T/G mismatch to C/G.
      Since Dcm cytosine methylase methylates the second C in CCWGG, the function of VSP repair is
      probably the prevention of CG to TA mutations caused by deamination of 5-methylcytosine to
      thymine.  The dcm and vsr genes overlap, and are expressed from a single promoter situated
      upstream of dcm.  The cellular levels of Dcm and Vsr are unknown.  We are investigating the
      consequences of altering the levels of these two proteins.  Overexpression of Vsr in E. coli
      stimulates transition and frameshift mutations.  Overexpression of dcm does not stimulate
      mutations in cells with a functional vsr; in vsr-deleted cells, high levels of Dcm stimulate C
      to T transitions at 5-methylcytosines.  Thus the expression of a single copy of vsr on the
      chromosome is sufficient to counteract the mutagenic effect of even high levels of Dcm.  Since
      Vsr is mutagenic, the organization of these two genes may reflect the need to produce low
      levels of Vsr.  This would allow Vsr to counteract the mutagenic effects of Dcm, while
      minimizing the mutagenic effect of Vsr.  We have constructed plasmids which allow the
      purification of 6his-Dcm and 6his-Vsr.  The purified Dcm and Vsr will be used to produce
      antibodies, to analyse the relative levels of Dcm and Vsr in E. coli by Western blot analysis.
AU  - Macintyre G
AU  - Doiron K
AU  - Cupples G
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1997 97: 294.

PMID- 9324251
VI  - 179
DP  - 1997
TI  - The Vsr endonuclease of Escherichia coli: an efficient DNA repair enzyme and a potent mutagen.
PG  - 6048-6052
AB  - The Vsr endonuclease of Escherichia coli initiates the repair of T/G mismatches caused by
      deamination of 5-methylcytosine to thymine.  In this paper, we examine the capacity of Vsr to
      prevent CG-to-TA mutations in cells with increased transcription of the cytosine methylase
      gene (dcm).  We find that sufficient Vsr is produced by a single chromosomal copy of vsr to
      prevent mutagenesis.  We also investigate the cause of the transition and frameshift mutations
      in cells overproducing Vsr.  Neither the absence of the dcm methylase nor its overproduction
      affects Vsr-stimulated mutagenesis.  However, addition of mutS, mutL, or mutH on multicopy
      plasmids has a significant effect: mutL or mutH decreases the number of mutations, while mutS
      stimulates mutagenesis.  The mut-containing plasmids have the same effect in cells treated
      with 2-aminopurine and in cells made defective in DNA proofreading, two experimental
      situations known to cause transition and frameshift mutations by saturating mismatch repair.
AU  - Macintyre G
AU  - Doiron KMJ
AU  - Cupples CG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1997 179: 6048-6052.

PMID- 10400606
VI  - 181
DP  - 1999
TI  - Growth phase-dependent regulation of Vsr endonuclease may contribute to 5-methylcytosine mutational hot spots in Escherichia coli.
PG  - 4435-4436
AB  - Using rabbit polyclonal antibodies, we have shown that the Dcm cytosine methylase of
      Escherichia coli is maintained at a constant level during cell growth, while Vsr endonuclease
      levels are growth phase dependent. Decreased production of Vsr relative to Dcm during the log
      phase may contribute substantially to the mutability of 5-methylcytosine.
AU  - Macintyre G
AU  - Pitsikas P
AU  - Cupples CG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1999 181: 4435-4436.

PMID- 23220200
VI  - 95
DP  - 2013
TI  - Functional consequences of mutating conserved SF2 helicase motifs in the Type III restriction endonuclease EcoP15I translocase domain.
PG  - 817-823
AB  - For efficient DNA hydrolysis, Type III restriction endonuclease EcoP15I interacts with two
      inversely oriented recognition sites in an
      ATP-dependent process. EcoP15I consists of two methylation (Mod)
      subunits and a single restriction (Res) subunit yielding a
      multifunctional enzyme complex able to methylate or to hydrolyse DNA.
      Comprehensive sequence alignments, limited proteolysis and mass
      spectroscopy suggested that the Res subunit is a fusion of a motor or
      translocase (Tr) domain of superfamily II helicases and an endonuclease
      domain with a catalytic PD...EXK motif. In the Tr domain, seven
      predicted helicase motifs (I, la, II VI), a recently discovered Q-tip
      motif and three additional regions (Ilia, IVa, Va) conserved among Type
      III restriction enzymes have been identified that are predicted to be
      involved in DNA binding and ATP hydrolysis. Because DNA unwinding
      activity for EcoP15I (as for bona fide helicases) has never been found
      and EcoP15I ATPase rates are only low, the functional importance of the
      helicase motifs and regions was questionable and has never been probed
      systematically. Therefore, we mutated all helicase motifs and conserved
      regions predicted in Type III restriction enzyme EcoP15I and examined
      the functional consequences on EcoP15I enzyme activity and the
      structural integrity of the variants by CD spectroscopy. The resulting
      eleven enzyme variants all, except variant IVa, are properly folded
      showing the same secondary structure distribution as the wild-type
      enzyme. Classical helicase motifs I VI are important for ATP and DNA
      cleavage by EcoP15I and mutations therein led to complete loss of
      ATPase and cleavage activity. Among the catalytically inactive enzyme
      variants three preserved the ability to bind ATP. In contrast, newly
      assigned motifs Q-tip, Ia and Va are not essential for EcoP15I activity
      and the corresponding enzyme variants were still catalytically active.
      DNA binding was only marginally reduced (2-7 fold) in all enzyme
      variants tested.
AU  - Mackeldanz P
AU  - Alves J
AU  - Moncke-Buchner E
AU  - Wyszomirski KH
AU  - Kruger DH
AU  - Reuter M
PT  - Journal Article
TA  - Biochimie
JT  - Biochimie
SO  - Biochimie 2013 95: 817-823.

PMID- 24526652
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of a Novel Lactobacillus salivarius Strain Isolated from Piglet.
PG  - e01231-13
AB  - Lactobacillus salivarius is part of the vertebrate indigenous microbiota of the
      gastrointestinal tract, oral cavity, and milk. The properties associated with
      some L. salivarius strains have led to their use as probiotics. Here we describe
      the draft genome of the pig isolate L. salivarius cp400, providing insights into
      host-niche specialization.
AU  - Mackenzie DA
AU  - McLay K
AU  - Roos S
AU  - Walter J
AU  - Swarbreck D
AU  - Drou N
AU  - Crossman LC
AU  - Juge N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01231-13.

PMID- 21059957
VI  - 108
DP  - 2011
TI  - At the crossroads of vaginal health and disease, the genome sequence of Lactobacillus iners AB-1.
PG  - 4688-4695
AB  - Lactobacilli have long been regarded as important constituents of the healthy
      human vagina. Lactobacillus iners is the most frequently detected bacterial
      species in the vagina, but little is known about its characteristics. We report a
      description of the whole-genome sequence of L. iners AB-1 along with comparative
      analysis of published genomes of closely related strains of lactobacilli. The
      genome is the smallest Lactobacillus reported to date, with a 1.3-Mbp single
      chromosome. The genome seems to have undergone one or more rapid evolution events
      that resulted in large-scale gene loss and horizontal acquisition of a number of
      genes for survival in the vagina. L. iners may exhibit specialized adaptation
      mechanisms to the vaginal environment, such as an iron-sulfur cluster assembly
      system, and several unique sigma factors to regulate gene transcription in this
      fluctuating environment. A potentially highly expressed homolog of a
      cholesterol-binding lysin may also contribute to host cell adhesion or act as a
      defense mechanism against other microbes. Notably, there is a lack of apparent
      adhesion proteins, but several cell-anchor proteins were identified and may be
      important for interaction with the host mucosal tissues. L. iners is widely
      present in healthy females as well as those suffering from bacterial vaginosis or
      who have undergone antimicrobial therapy, suggesting that it is an important
      indigenous species of the vagina.
AU  - Macklaim JM
AU  - Gloor GB
AU  - Anukam KC
AU  - Cribby S
AU  - Reid G
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2011 108: 4688-4695.

PMID- 25179889
VI  - 15
DP  - 2014
TI  - Polymerase Synthesis of DNAs Bearing Vinyl Groups in the Major Groove and their Cleavage by Restriction Endonucleases.
PG  - 2306-2312
AB  - DNA molecules containing 5-vinyluracil, 5-vinylcytosine, or 7-deaza-7-vinyladenine were
      prepared by polymerase incorporation of the corresponding vinyl-modified 2-deoxyribonucleoside
      triphosphates, and the influence of the vinyl group in the major groove of DNA on the cleavage
      by diverse type II restriction endonucleases (REs) was studied. The presence of 5-vinyluracil
      was tolerated by most of the REs, whereas only some REs were able to cleave sequences
      containing 7-deaza-7-vinyladenine. The enzyme ScaI was found to cleave DNA containing
      5-vinylcytosine efficiently but not DNA containing the related 5-ethynylcytosine. All other
      REs failed to cleave sequences containing any cytosine modifications.
AU  - Mackova M
AU  - Pohl R
AU  - Hocek M
PT  - Journal Article
TA  - Chembiochem
JT  - Chembiochem
SO  - Chembiochem 2014 15: 2306-2312.

PMID- 28883148
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Staphylococcus epidermidis ATCC 12228 Chromosome and  Plasmids, Generated by Long-Read Sequencing.
PG  - e00954-17
AB  - Staphylococcus epidermidis ATCC 12228 was sequenced using a long-read method to generate a
      complete genome sequence, including some plasmid sequences. Some
      differences from the previously generated short-read sequence of this
      nonpathogenic and non-biofilm-forming strain were noted. The assembly size was
      2,570,371 bp with a total G+C% content of 32.08%.
AU  - MacLea KS
AU  - Trachtenberg AM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00954-17.

PMID- 7713905
VI  - 270
DP  - 1995
TI  - Expression of antisense to DNA methyltransferase mRNA induces DNA demethylation and inhibits tumorigenesis.
PG  - 8037-8043
AB  - Many tumor cell lines overexpress DNA methyltransferase (MeTase) activity; however it is still
      unclear whether this increase in DNA MeTase activity plays a casual role in naturally
      occurring tumors and cell lines, whether it is critical for the maintenance of transformed
      phenotypes, and whether inhibition of the DNA MeTase in tumor cells can reverse
      transformation. To address these basic questions, we transfected a murine adrenocortical tumor
      cell line Y1 with a chimeric construct expressing 600 base pairs from the 5' of the DNA
      MeTase cDNA in the antisense orientation. The antisense transfectants show DNA demethylation,
      distinct morphological alterations, are inhibited in their ability to grow in an
      anchorage-independent manner, and exhibit decreased tumorigenicity in syngeneic mice. Ex vivo,
      cells expressing the antisense construct show increased serum requirements, decreased rate of
      growth, and induction of an apoptotic death program upon serum deprivation.
      5-Azadeoxycytidine-treated cells exhibit a similar dose-dependent reversal of the transformed
      phenotype. These results support the hypothesis that the DNA MeTase is actively involved in
      oncogenic transformation.
AU  - MacLeod AR
AU  - Szyf M
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1995 270: 8037-8043.

PMID- Not included in PubMed...
VI  - 57
DP  - 1992
TI  - Synthesis of an oligonucleotide suicide substrate for DNA methyltransferases.
PG  - 2989-2991
AB  - The large-scale chemical synthesis of an oligodeoxynucleotide containing
      5-fluoro-2'-deoxycytidine (FdC)and its characterization are described. The FdC residue is
      introduced via the corresponding 4-O-(2,4,6-trimethylphenyl)-2'-deoxyuridine derivative,
      which undergoes clean conversion to FdC during removal of the oligonucleotide protecting
      groups with ammonia. A double-stranded oligodeoxynucleotide containing FdC inactivated the DNA
      methyltransferase enzyme M.HaeIII by irreversible formation of a covalent protein-DNA complex.
AU  - MacMillan AM
AU  - Chen L
AU  - Verdine GL
PT  - Journal Article
TA  - J. Org. Chem.
JT  - J. Org. Chem.
SO  - J. Org. Chem. 1992 57: 2989-2991.

PMID- Not carried by PubMed...
VI  - 88
DP  - 1988
TI  - Characterization of a unique methyl-specific restriction system in Streptomyces avermitilis.
PG  - 156
AB  - Streptomyces avermitilis contains a restriction system that restricts plasmid DNA containing
      N6-methyladenine or 5-methylcytosine. This system restricts DNA isolated from strains with DNA
      methylases. Shuttle vectors iolated from Escherichia coli, or plasmids isolated from
      modification proficient Streptomyces cannot be directly introduced into S. avermitilis. S.
      lividans appears to lack the ability to modify DNA. Plasmids isolated from S. lividans which
      have been modified in vitro with DNA methylases are restricted by S. avermitilis. The
      transformation frequency is reduced 1000-fold when plasmid DNA is modified by dam or TaqI
      methylases to contain N6-methyladenine, or by AluI, HhaI, or HphI methylases to contain
      5-methylcytosine. Methyl-specific restriction appears to be common in Streptomyces, since
      either N6-methyladenine-specific restriction, or 5-methylcytosine-specific restriction was
      observed in 7 of 9 strains tested. S. avermitilis is unique in that it restricts both
      N6-methyladenine and 5-methylcytosine containing DNA.
AU  - MacNeil D
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1988 88: 156.

PMID- 3056907
VI  - 170
DP  - 1988
TI  - Characterization of a unique methyl-specific restriction system in Streptomyces avermitilis.
PG  - 5607-5612
AB  - Streptomyces avermitilis contains a unique restriction system that restricts plasmid DNA
      containing N6-methyladenine or 5-methylcytosine. Shuttle vectors isolated from Escherichia
      coli RR1 or plasmids isolated from modification-proficient Streptomyces spp. cannot be
      directly introduced into S. avermitilis. This restriction barrier can be overcome by first
      transferring plasmids into Streptomyces lividans or a modification-deficient E. coli strain
      and then into S. avermitilis. The transformation frequency was reduced ->1,000-fold when
      plasmid DNA was modified by dam or TaqI methylases to contain N6-methyladenine or by AluI,
      HhaI, or HphI methylases to contain 5-methylcytosine. Methyl-specific restriction appears to
      be common in Streptomyces spp., since either N6-methyladenine-specific or
      5-methylcytosine-specific restriction was observed in seven of nine strains tested.
AU  - MacNeil DJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1988 170: 5607-5612.

PMID- 28408689
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Four Yersinia enterocolitica Strains, Isolated from Wild Ungulate Carcasses.
PG  - e00192-17
AB  - This study describes the draft genome sequences of four Yersinia enterocolitica strains,
      originally isolated from ungulate carcasses. These isolates were typed
      biochemically and two were determined to be highly virulent (biotype 1B). The
      draft genome sequences had a mean size of 4.77 Mb and a mean G+C content of
      47.1%.
AU  - Macori G
AU  - Romano A
AU  - Adriano D
AU  - Razzuoli E
AU  - Bianchi DM
AU  - Gallina S
AU  - Bellio A
AU  - Decastelli L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00192-17.

PMID- 3886164
VI  - 41
DP  - 1985
TI  - Transposition of an intron in yeast mitochondria requires a protein encoded by that intron.
PG  - 395-402
AB  - The optional 1143 bp intron in the yeast mitochondrial 21S rRNA gene (Omega+) is nearly
      quantitatively inserted in genetic crosses into 21S rRNA alleles that lack it (Omega-). The
      intron contains an open reading frame that can encode a protein of 235 amino acids, but no
      function has been ascribed to this sequence. We previously found an in vivo double-strand
      break in Omega- DNA at or close to the intron insertion site only in zygotes of Omega+ x
      Omega- crosses that appears with the same kinetics as intron insertion. We now show that
      mutations in the intron open reading frame that would alter the translation product
      simulataneously inhibit nonreciprocal Omega recombination and the in vivo double-strand break
      in Omega- DNA. These results provide evidence that the open reading frame encodes a protein
      required for intron transposition and support the role of the double strand break in the
      process.
AU  - Macreadie IG
AU  - Scott RM
AU  - Zinn AR
AU  - Butow RA
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1985 41: 395-402.

PMID- 7909343
VI  - 18C
DP  - 1994
TI  - Generation of a new type-I restriction-modification specificity by transposition.
PG  - 136
AB  - *

      We have characterised a novel mutant of EcoDXXI, a type IC DNA restriction and modification

      system, in which the specificity has been altered due to a Tn5 insertion into the middle of

      hsdS, the gene which codes the polypepide that confers DNA sequence specificity to both the

      restriction and modification reactions. With the type IR-M systems, both the DNA restriction

      and modification functions are carried out by a single enzyme composed of 3 subunits: hsdS

      (DNA binding specificity), hsdM (modification/methylation), and hsdR (restriction). A complex

      of only hsdS and hsdM can catalyse methylation but not restriction. Type I restriction of

      unmodified DNA occurs a great distance from the enzyme's recognition site and is accompanied

      by large amounts of ATP hydrolysis. It is proposed that the ATP hydrolysis fuels the "pumping"

      of the DNA past the bound enzyme to reach the cleavage site.

      

      Like other type I enzymes, the wild type EcoDXXI recognises a sequence composed of two

      asymmetrical half sites separated by a spacer region: TCA(N7)RTTC. Purification of the EcoDXXI

      mutant methylase and subsequent in vitro DNA methylation assays, identified the mutant

      recognition sequence as an interrupted palindrome. TCA(N8)TGA, in which the 5' half site of

      the wild type site is repeated in inverse orientation. The additional base pair in the

      non-specific spacer of the mutant recognition sequence maintains the proper spacing between

      the two methylatable adenine groups.

      

      Sequencing of both the wild type and mutant EcoDXXI hsdS genes showed that the Tn5 insertion

      occurred at nucleotide 673 of the 1221 bp gene. This effectively deletes the entire carboxyl

      DNA binding domain which recognises the 3' half of the EcoDXXI binding site. Subsequent

      deletion analysis demonstrated that the Tn5 element as well as the distal hsdS3' sequence are

      dispensible; an additional 65 bp of the hsdS sequence could also be removed without loss of

      methylation or restriction activity. The minimum characterised hsdS fragment encodes both the

      amino terminal DNA binding domain as well as the conserved repeated sequence that defines the

      length of the recognition site spacer region. The predicted 205 amino acid peptide must

      contain all the information necessary for DNA binding and subunit interactions. We propose

      that the EcoDXXI mutant methylase utilises two truncated hsdS subunits to recognise its

      binding site. The implications of this finding in terms of subunit interactions and the

      malleability of the type I R-M system will be discussed.

      

AU  - MacWilliams M
AU  - Meister J
AU  - Jutte H
AU  - Bickle T
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1994 18C: 136.

PMID- 8887569
VI  - 15
DP  - 1996
TI  - Generation of new DNA binding specificity by truncation of the type IC EcoDXXI hsdS gene.
PG  - 4775-4783
AB  - The hsdS subunit of a type IC restriction-modification enzyme is responsible for the enzyme's
      DNA binding specificity.  Type I recognition sites are characterized by two defined half-sites
      separated by a non-specific spacer of defined length.  The hsdS subunit contains two
      independent DNA binding domains, each targeted towards one DNA half-site.  We have shown
      previously that the 5' half of hsdS can code for a functional substitute of the full-length
      hsdS.  Here we demonstrate that the 3' half of the gene, when fused to the appropriate
      transcriptional and translational start signals, also codes for a peptide which imparts DNA
      binding specificity to the enzyme.  About half the natural hsdS size, the mutant peptide
      contains a single DNA recognition domain flanked by one copy of each internal repeat found in
      the full-length hsdS.  Deletion of either repeat sequence results in loss of activity.  Like
      the 5' hsdS mutant, the 3' mutant recognizes an interrupted palindrome, GAAYN5RTTC,
      suggesting that two truncated subunits participate in DNA recognition.  Coexpression of the
      5' hsdS mutant and the 3' hsdS mutant along with hsdM regenerates the wild-type methylation
      specificity.  Thus, there is a free assortment of subunits in the cell.
AU  - MacWilliams MP
AU  - Bickle TA
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1996 15: 4775-4783.

PMID- 29122856
VI  - 5
DP  - 2017
TI  - First Draft Genome Sequences of Three Strains of Francisella tularensis subsp. holarctica, Isolated from Hares and a Tick in France.
PG  - e00993-17
AB  - Here, we report the complete genome sequences of three strains of Francisella tularensis
      subsp. holarctica (11-789-5S, 11-935-13S, and 11-930-9S), isolated
      from brown hares and a tick during a tularemia outbreak in France, where
      tularemia is endemic.
AU  - Madani N
AU  - Giraud P
AU  - Mendy C
AU  - Colaneri C
AU  - Cherchame E
AU  - Cherfa MA
AU  - Richomme C
AU  - Decors A
AU  - Girault G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00993-17.

PMID- 25502683
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Methylobacterium sp. Strain L2-4, a Leaf-Associated Endophytic N-Fixing Bacterium Isolated from Jatropha curcas L.
PG  - e01306-14
AB  - Methylobacterium sp. strain L2-4 is an efficient nitrogen-fixing leaf colonizer of biofuel
      crop Jatropha curcas. This strain is able to greatly improve the
      growth and seed yield of Jatropha curcas and is the second reported genome
      sequence of plant growth-promoting bacteria isolated from Jatropha curcas.
AU  - Madhaiyan M
AU  - Chan KL
AU  - Ji L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01306-14.

PMID- 23908287
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Enterobacter sp. Strain R4-368, an Endophytic N-Fixing Gammaproteobacterium Isolated from Surface-Sterilized Roots of Jatropha   curcas L.
PG  - e00544-13
AB  - Enterobacter sp. strain R4-368 is one of the few characterized Jatropha endophytic
      diazotrophic bacteria and was isolated from surface-sterilized roots.
      This bacterium shows strong growth-promoting effects, being able to increase
      plant biomass and seed yields. Enterobacter sp. R4-368 is the second fully
      sequenced diazotrophic Enterobacter species. The sequence information shall
      facilitate the elucidation of the molecular mechanisms of plant growth promotion,
      nitrogen fixation in nonlegume plant species, and evolution of biological
      nitrogen fixation systems.
AU  - Madhaiyan M
AU  - Peng N
AU  - Ji L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00544-13.

PMID- 24723709
VI  - 2
DP  - 2014
TI  - Genome Sequence of Enterotoxigenic Escherichia coli Strain B2C.
PG  - e00247-14
AB  - Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrheal disease around the
      globe, causing an estimated 380,000 deaths annually. The disease is caused by a wide variety
      of strains. Here, we report the genome sequence of ETEC strain B2C, which was isolated from an
      American soldier in Vietnam.
AU  - Madhavan TP
AU  - Steen JA
AU  - Hugenholtz P
AU  - Sakellaris H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00247-14.

PMID- 22843573
VI  - 194
DP  - 2012
TI  - Whole-Genome Sequences of Two Clinical Isolates of Mycobacterium tuberculosis from Kerala, South India.
PG  - 4430
AB  - We report the annotated genome sequence of two clinical isolates of Mycobacterium tuberculosis
      isolated from Kerala, India.
AU  - Madhavilatha GK
AU  - Joseph BV
AU  - Paul LK
AU  - Kumar RA
AU  - Hariharan R
AU  - Mundayoor S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4430.

PMID- 21317317
VI  - 193
DP  - 2011
TI  - An Enterotoxin-Bearing Pathogenicity Island in Staphylococcus epidermidis.
PG  - 1854-1862
AB  - Cocolonization of human mucosal surfaces causes frequent encounters
      between various staphylococcal species, creating opportunities for the
      horizontal acquisition of mobile genetic elements. The majority of
      Staphylococcus aureus toxins and virulence factors are encoded on S.
      aureus pathogenicity islands (SaPIs). Horizontal movement of SaPIs between
      S. aureus strains plays a role in the evolution of virulent clinical
      isolates. Although there have been reports of the production of toxic
      shock syndrome toxin 1 (TSST-1), enterotoxin, and other superantigens by
      coagulase-negative staphylococci, no associated pathogenicity islands have
      been found in the genome of Staphylococcus epidermidis, a generally less
      virulent relative of S. aureus. We show here the first evidence of a
      composite S. epidermidis pathogenicity island (SePI), the product of
      multiple insertions in the genome of a clinical isolate. The taxonomic
      placement of S. epidermidis strain FRI909 was confirmed by a number of
      biochemical tests and multilocus sequence typing. The genome sequence of
      this strain was analyzed for other unique gene clusters and their
      locations. This pathogenicity island encodes and expresses staphylococcal
      enterotoxin C3 (SEC3) and staphylococcal enterotoxin-like toxin L (SElL),
      as confirmed by quantitative reverse transcription-PCR (qRT-PCR) and
      immunoblotting. We present here an initial characterization of this novel
      pathogenicity island, and we establish that it is stable, expresses
      enterotoxins, and is not obviously transmissible by phage transduction. We
      also describe the genome sequence, excision, replication, and packaging of
      a novel bacteriophage in S. epidermidis FRI909, as well as attempts to
      mobilize the SePI element by this phage.
AU  - Madhusoodanan J
AU  - Seo KS
AU  - Remortel B
AU  - Park JY
AU  - Hwang SY
AU  - Fox LK
AU  - Park YH
AU  - Deobald CF
AU  - Wang D
AU  - Liu S
AU  - Daugherty SC
AU  - Gill AL
AU  - Bohach GA
AU  - Gill SR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 1854-1862.

PMID- 20184512
VI  - 45
DP  - 2010
TI  - Diversity of DNA methyltransferases that recognize asymmetric target sequences.
PG  - 125-145
AB  - DNA methyltransferases (MTases) are a group of enzymes that catalyze the methyl group transfer
      from S-adenosyl-L-methionine in a sequence-specific manner. Orthodox Type II DNA MTases
      usually recognize palindromic DNA sequences and add a methyl group to the target base (either
      adenine or cytosine) on both strands. However, there are a number of MTases that recognize
      asymmetric target sequences and differ in their subunit organization. In a bacterial cell,
      after each round of replication, the substrate for any MTase is hemimethylated DNA, and it
      therefore needs only a single methylation event to restore the fully methylated state. This is
      in consistent with the fact that most of the DNA MTases studied exist as monomers in solution.
      Multiple lines of evidence suggest that some DNA MTases function as dimers. Further,
      functional analysis of many restriction-modification systems showed the presence of more than
      one or fused MTase genes. It was proposed that presence of two MTases responsible for the
      recognition and methylation of asymmetric sequences would protect the nascent strands
      generated during DNA replication from cognate restriction endonuclease. In this review, MTases
      recognizing asymmetric sequences have been grouped into different subgroups based on their
      unique properties. Detailed characterization of these unusual MTases would help in better
      understanding of their specific biological roles and mechanisms of action. The rapid progress
      made by the genome sequencing of bacteria and archaea may accelerate the identification and
      study of species- and strain-specific MTases of host-adapted bacteria and their roles in
      pathogenic mechanisms.</.
AU  - Madhusoodanan UK
AU  - Rao DN
PT  - Journal Article
TA  - Crit. Rev. Biochem. Mol. Biol.
JT  - Crit. Rev. Biochem. Mol. Biol.
SO  - Crit. Rev. Biochem. Mol. Biol. 2010 45: 125-145.

PMID- 11410355
VI  - 200
DP  - 2001
TI  - The LlaGI restriction and modification system of Lactococcus lactis W10 consists of only one single polypeptide.
PG  - 91-96
AB  - The naturally occurring 12.1-kb plasmid, pEW104, in Lactococcus lactis ssp. cremoris W10 was
      found to confer decreased bacteriophage sensitivity to its host. Plasmid pEW104 encodes a
      non-classic restriction and modification (R/M) system, named LlaGI, consisting of only one
      single polypeptide. Analysis of the amino acid sequence revealed the presence of a catalytic
      motif and seven helicase-like motifs (DEAD-box motifs) characteristic of type I and III
      endonucleases, followed by four conserved methylase motifs characteristic of
      adenine-methylases. A comparison between LlaGI and the very similar R/M system, LlaBIII,
      suggests that the C-terminal region of LlaGI, apparently containing no known motifs, could
      possibly specify target DNA recognition. Conceivably, the LlaGI gene is included in the operon
      of the plasmid replication machinery. Finally, it is proposed that LlaGI represents a variant
      of the type I R/M systems.
AU  - Madsen A
AU  - Josephsen J
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2001 200: 91-96.

PMID- 9628336
VI  - 379
DP  - 1998
TI  - Characterization of LlaCI, a new restriction-modification system from Lactococcus lactis subsp. cremoris W15.
PG  - 443-449
AB  - The genes encoding the restriction-modification system LlaCI have been found on the naturally
      occurring 7.0 kb plasmid pAW153 in L. lactis subsp. cremoris W15.  The R/M system was isolated
      on a chloramphenicol resistant derivative of the wild type plasmid (pAW153cat).  Plasmid
      pAW153cat and a 2.4 kb HincII-SphI fragment cloned into a high- and a low-copy vector
      conferred decreased sensitivity in L. lactis LM2301 and L. lactis SMQ86 against small
      isometric-headed phages of the 936 or P335 species, respectively.  Increased plasmid copy
      number enhanced the level of phage restriction.  Sequencing the 2.4 kb HincII-SphI fragment
      revealed two open reading frames arranged convergently with a 94 bp separation.  IIaCIM showed
      66% identity to hindIIIM, and IlaCIR showed 45% identity to hindIIIR.  The organization of the
      LlaCI operon differs from the HindIII operon, where the endonuclease and methylase genes
      overlap and are transcribed in the same direction.  The LlaCI methylase is predicted to be 296
      amino acids long, with 63% identity to the HindIII methylase, while the LlaCI endonuclease is
      predicted to consist of  324 or 332 amino acids, depending on the position of the start codon.
      It shows 24% identity to the HindIII endonuclease.
AU  - Madsen A
AU  - Josephsen J
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1998 379: 443-449.

PMID- 9647810
VI  - 64
DP  - 1998
TI  - Cloning and characterization of the lactococcal plasmid-encoded type II restriction/modification system, LlaDII.
PG  - 2424-2431
AB  - The LlaDII restriction/modification system was found on the naturally occurring 8.9-kb plasmid
      pHW393 in Lactococcus lactis subsp. cremoris W39.  A 2.4-kb PstI-EcoRI fragment inserted into
      the Escherichia coli-L.lactis shuttle vector pCI3340 conferred to L. lactis LM2301 and L.
      lactis SMQ86 resistance against representatives of the three most common lactococcal phage
      species: 936, P335, and c2.  The LlaDII endonuclease was partially purified and found to
      recognize and cleave the sequence 5'-GC/NGC-3', where the arrow indicates the cleavage site.
      It is thus an isoschizomer of the commercially available restriction endonuclease Fnu4HI.
      Sequencing of the 2.4-kb PstI-EcoRI fragment revealed two open reading frames-arranged
      tandemly and separated by a 105-bp intergenic region.  The endonuclease gene of 543 bp
      preceded the methylase gene of 954 bop.  The deduced amino acid sequence of the LlaDII R/M
      system showed high homology to that of its only sequence isoschizomer, Bsp6I from Bacillus sp.
      strain RFL6, with 41% identity between the endonucleases and 60% identity between the
      methylases.  The genetic organizations of the LlaDII and Bsp6I R/M systems are identical.
      Both methylases have two recognition sites (5'-GCGGC-3' and 5'-GCCGC-3') forming a
      putative stem-loop structure spanning part of the presumed -35 sequence and part of the
      intervening region between the -35 and -10 sequences.  Alignment of the LlaDII and Bsp6I
      methylases with other m5C methylases showed that the protein primary structures possessed the
      same organization.
AU  - Madsen A
AU  - Josephsen J
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1998 64: 2424-2431.

PMID- 
VI  - 11
DP  - 1997
TI  - The restriction and modification system LlaCI and its use in the development of phage resistant lactococcal starter cultures.
PG  - A1035
AB  - The mixed Cheddar starter culture, TK5, consisting of Lactococcus lactis strains, is highly
      bacteriophage resistant, and has been used for cheese production for 12 years.  One of the
      major problems encountered in the dairy industry is infection of the starter cultures by lytic
      phages.  It is possible to obtain plasmids encoding phage defense mechanisms from bacterial
      isolates of TK5.  The 7 kb plasmid, pAW153, from isolate W15, encodes the type II R/M system,
      LlaCI with recognition sequence AAGCTT, an isoschizomer of HindIII.  LlaCI restricts the small
      isometric headed lactococcal phage p2 with an EOP of 10^-2, this effect, together with other
      bacteriophage resistance mechanisms, will be utilized in experiments for the development of
      phage resistant starter cultures.  A 2.4 kb HincII-SphI fragment containing LlaCI was
      subcloned from pAW153 into pC13340 to generate pCAC1.  The nucleotide sequence of this
      fragment encoding the LlaCI activity has been determined.  Analysis of the DNA sequence
      predicts; A, a methylase of 296 amino acids showing 62% identity to M.HindIII, and B, an
      endonuclease of 332 amino acids showing 24% identity to R.HindIII.  The methylase is an
      adenine methylase containing the I-D-PY, LK, T-KP-L, and LD-F-GSGTT-A motifs characteristic of
      this class of adenine methylases.  Upstream of the two genes, putative ribosome binding sites
      and promoter regions are situated.
AU  - Madsen A
AU  - Nellemann LJ
AU  - Josephsen J
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1997 11: A1035.

PMID- 10964630
VI  - 44
DP  - 2000
TI  - Characterization of a novel plasmid-encoded HsdS subunit, S.LlaW12I, from Lactococcus lactis W12.
PG  - 196-200
AB  - A novel type I restriction-modification specificity subunit, S.LlaW12I, has been identified on
      the naturally occurring 8.0-kb plasmid pAW122 in the lactic acid bacterium Lactococcus lactis
      subsp. cremoris W12. Presence of the HsdS protein together with a complete type I
      restriction-modification system conferred increased phage restriction to the host, indicating
      exchange of specificity subunits. Sequence analysis showed that the S.LlaW12I subunit is most
      probably of type IC. Presumably, the hsdS gene is organized together with the repB gene on one
      transcriptional unit.
AU  - Madsen A
AU  - Westphal C
AU  - Josephsen J
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 2000 44: 196-200.

PMID- 27257204
VI  - 4
DP  - 2016
TI  - Draft Whole-Genome Sequence of Sphingobium sp. 22B, a Polycyclic Aromatic Hydrocarbon-Degrading Bacterium from Semiarid Patagonia, Argentina.
PG  - e00488-16
AB  - Sphingobium sp. 22B is a polycyclic aromatic hydrocarbon-degrading strain isolated from
      Patagonia, Argentina, with capabilities to withstand the
      environmental factors of that semiarid region. The draft genome shows the
      presence of genes related with responses to carbon starvation and drying
      environmental conditions.
AU  - Madueno L
AU  - Macchi M
AU  - Morelli IS
AU  - Coppotelli BM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00488-16.

PMID- 29567747
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Altererythrobacter sp. Strain B11, an Aromatic Monomer-Degrading Bacterium, Isolated from Deep-Sea Sediment under the Seabed off  Kashima, Japan.
PG  - e00200-18
AB  - Altererythrobacter sp. strain B11 is an aromatic monomer-degrading bacterium newly isolated
      from sediment under the seabed off Kashima, Japan, at a depth of
      2,100 m. Here, we report the complete nucleotide sequence of the genome of strain
      B11.
AU  - Maeda AH
AU  - Nishi S
AU  - Ishii S
AU  - Shimane Y
AU  - Kobayashi H
AU  - Ichikawa J
AU  - Kurosawa K
AU  - Arai W
AU  - Takami H
AU  - Ohta Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00200-18.

PMID- 24201196
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Sphingobium sp. Strain KK22, a High-Molecular-Weight Polycyclic Aromatic Hydrocarbon-Degrading Bacterium Isolated from Cattle Pasture   Soil.
PG  - e00911-13
AB  - Sphingobium sp. strain KK22 was isolated from a bacterial consortium that originated from
      cattle pasture soil from Texas. Strain KK22 grows on phenanthrene
      and has been shown to biotransform the high-molecular-weight (HMW) polycyclic
      aromatic hydrocarbon (PAH) benz[a]anthracene. The genome of strain KK22 was
      sequenced to investigate the genes involved in aromatic pollutant
      biotransformation.
AU  - Maeda AH
AU  - Nishi S
AU  - Ozeki Y
AU  - Ohta Y
AU  - Hatada Y
AU  - Kanaly RA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00911-13.

PMID- 16980466
VI  - 188
DP  - 2006
TI  - The Methanosarcina barkeri genome: comparative analysis with Methanosarcina acetivorans and Methanosarcina mazei reveals extensive  rearrangement within methanosarcinal genomes.
PG  - 7922-7931
AB  - We report here a comparative analysis of the genome sequence of Methanosarcina barkeri with
      those of Methanosarcina acetivorans and Methanosarcina mazei. The genome of M. barkeri is
      distinguished by having an organization that is well conserved with respect to the other
      Methanosarcina spp. in the region proximal to the origin of replication, with interspecies
      gene similarities as high as 95%. However, it is disordered and marked by increased
      transposase frequency and decreased gene synteny and gene density in the distal semigenome. Of
      the 3,680 open reading frames (ORFs) in M. barkeri, 746 had homologs with better than 80%
      identity to both M. acetivorans and M. mazei, while 128 nonhypothetical ORFs were unique
      (nonorthologous) among these species, including a complete formate dehydrogenase operon, genes
      required for N-acetylmuramic acid synthesis, a 14-gene gas vesicle cluster, and a
      bacterial-like P450-specific ferredoxin reductase cluster not previously observed or
      characterized for this genus. A cryptic 36-kbp plasmid sequence that contains an orc1 gene
      flanked by a presumptive origin of replication consisting of 38 tandem repeats of a
      143-nucleotide motif was detected in M. barkeri. Three-way comparison of these genomes reveals
      differing mechanisms for the accrual of changes. Elongation of the relatively large M.
      acetivorans genome is the result of uniformly distributed multiple gene scale insertions and
      duplications, while the M. barkeri genome is characterized by localized inversions associated
      with the loss of gene content. In contrast, the short M. mazei genome most closely
      approximates the putative ancestral organizational state of these species.
AU  - Maeder DL
AU  - Anderson I
AU  - Brettin TS
AU  - Bruce DC
AU  - Gilna P
AU  - Han CS
AU  - Lapidus A
AU  - Metcalf WW
AU  - Saunders E
AU  - Tapia R
AU  - Sowers KR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2006 188: 7922-7931.

PMID- 10430560
VI  - 152
DP  - 1999
TI  - Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P. horikoshii inferred from complete genomic sequences.
PG  - 1299-1305
AB  - Divergence of the hyperthermophilic Archaea, Pyrococcus furiosus and Pyrococcus horikoshii,
      was assessed by analysis of complete genomic sequences of both
      species. The average nucleotide identity between the genomic sequences is 70-75%
      within ORFs. The P. furiosus genome (1.908 mbp) is 170 kbp larger than the P.
      horikoshii genome (1.738 mbp) and the latter displays significant deletions in
      coding regions, including the trp, his, aro, leu-ile-val, arg, pro, cys, thr, and
      mal operons. P. horikoshii is auxotrophic for tryptophan and histidine and is
      unable to utilize maltose, unlike P. furiosus. In addition, the genomes differ
      considerably in gene order, displaying displacements and inversions. Six allelic
      intein sites are common to both Pyrococcus genomes, and two intein insertions
      occur in each species and not the other. The bacteria-like methylated chemotaxis
      proteins form a functional group in P. horikoshii, but are absent in P. furiosus.
      Two paralogous families of ferredoxin oxidoreductases provide evidence of gene
      duplication preceding the divergence of the Pyrococcus species.
AU  - Maeder DL
AU  - Weiss RB
AU  - Dunn DM
AU  - Cherry JL
AU  - Gonzalez JM
AU  - DiRuggiero J
AU  - Robb FT
PT  - Journal Article
TA  - Genetics
JT  - Genetics
SO  - Genetics 1999 152: 1299-1305.

PMID- 1727392
VI  - 6
DP  - 1992
TI  - Enhanced substrate specificity observed in EcoRI DNA methyltransferase upon mutagenesis of cysteine 223.
PG  - A61
AB  - The EcoRI DNA methyltransferase is part of a type II restriction modification
      system and methylates the second adenine in the recognition sequence GAATTC.
      Cys223 was implicated as a critical residue by our previous protein chemical
      data ((1990) J. Biol. Chem. 265,17713-17719) and by homology to other DNA
      methyltransferases.  Substitution of Cys223 with Ser, Ala, and Gly by site
      directed methods produced three mutant enzymes all with altered substrate
      specificity.  Kinetic analysis of the mutant enzymes yields kcat and kmDNA
      values for the canonical site, that do not significantly differ from those of
      the wild type enzyme.  However, a significant decrease in the methylation of
      non-canonical sequences is observed with the mutant enzymes both in vitro and
      in vivo.  Our results suggest that either Cys223 is near the DNA binding region
      or that flexibility in the region of Cys223 may be important for specificity.
AU  - Maegley K
AU  - Reich NO
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1992 6: A61.

PMID- Not included in PubMed...
VI  - 61
DP  - 1992
TI  - Enhanced substrate specificity observed in EcoRI DNA methyltransferase upon mutagenesis of cysteine 223.
PG  - A61
AB  - The EcoRI DNA methyltransferase is part of a type II restriction modification
      system and methylates the second adenine in the recognition sequence GAATTC.
      Cys223 was implicated as a critical residue by our previous protein chemical
      data [1990] J. Biol. Chem. 265, 17713-17719) and by homology to other DNA
      methyltransferases.  Substitution of Cys223 with Ser, Ala, and Gly by site
      directed methods produced three mutant enzymes all with altered substrate
      specificity.  Kinetic analysis of the mutant enzymes yields kcat and kmDNA
      values for the canonical site, that do not significantly differ from those of
      the wild type enzyme.  However, a significant decrease in the methylation of
      non-canonical sequences is observed with the mutant enzymes both in vitro and
      in vivo.  Our results suggest that either Cys223 is near the DNA binding region
      or that flexibility in the region of Cys223 may be important for specificity.
AU  - Maegley K
AU  - Reich NO
PT  - Journal Article
TA  - Biophys. J.
JT  - Biophys. J.
SO  - Biophys. J. 1992 61: A61.

PMID- Not included in PubMed...
VI  - 31
DP  - 1992
TI  - Enhanced substrate specificity observed in EcoRI DNA methyltransferase upon mutagenesis of cysteine 223.
PG  - 2197
AB  - The EcoRI DNA methyltransferase is part of a type-II restriction modification
      system and methylates the second adenine in the recognition sequence GAATTC.
      Cys223 was implicated as a critical residue by our previous protein chemical
      data [1990] J. Biol. Chem. 265, 17713-17719] and by homology to other DNA
      methyltransferases.  Substitution of Cys223 with Ser, Ala, and Gly by
      site-directed methods produced three mutant enzymes, all with altered substrate
      specificity.  Kinetic analysis of the mutant enzymes yields Kcat and KmDNA
      values for the canonical site that do not significantly differ from those of
      the wild type enzyme.  However, a significant decrease in the methylation of
      noncanonical sequences is observed with the mutant enzymes both in vitro and in
      vivo.  Our results suggest that either Cys223 is near the DNA binding region or
      that flexibility in the region of Cys223 may be important for specificity.
AU  - Maegley K
AU  - Reich NO
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1992 31: 2197.

PMID- Not carried by PubMed...
VI  - 203
DP  - 1992
TI  - Enhanced substrate specificity observed in EcoRI DNA methyltransferase upon mutagenesis of cysteine 223.
PG  - 57-BIOL
AB  - The EcoRI DNA methyltransferase is part of a type II restriction-modification system and
      methylates the second adenine in the recognition sequence GAATTC. Cys223 was implicated as a
      critical residue by our previous protein chemical data (JBC, 1990, 265: 17713-17719) and by
      homology to other DNA methyltransferases. Substitution of Cys223 with Ser, Ala and Gly by
      site-directed methods produced three mutant enzymes all with altered substrate specificity.
      Kinetic analysis of the mutant enzymes yields Kcat and KmDNA values for the cannonical site
      that do not significantly differ from those of the wild type enzyme. However, a significant
      decrease in the methylation of non-canonical sequences is observed with the mutant enzymes
      both in vitro and in vivo. Our results suggest that either Cys223 is near the DNA binding
      region or that flexibility in the region of Cys223 may be important for specificity.
AU  - Maegley K
AU  - Reich NO
PT  - Journal Article
TA  - ACS Abstracts
JT  - ACS Abstracts
SO  - ACS Abstracts 1992 203: 57-BIOL.

PMID- 8467964
VI  - 7
DP  - 1993
TI  - Enhanced substrate discriminiation and identification of an essential catalytic residue of the EcoRI DNA methyltransferase by site directed mutagenesis.
PG  - A1197
AB  - The EcoRI DNA methyltransferase (Mtase) is part of a type II restriction modification system
      and catalyzes the AdoMet dependent methylation of the ds-DNA sequence GAATTC. Cys223 was
      implicated as a critical functional residue by prevous protein chemical data [(1990) J. Biol.
      Chem. 265, 17713-17719] and by sequence homology. Substitution of Cys223 with Ser, Ala, and
      Gly by site directed mutagenesis produced three mutant Mtases with enhanced sequence
      specificity. Further characterization of the mutants has indicated possible mechanistic
      reasons for the enhanced specificity. Chemical modification with DEPC has identified one
      histidine residue with a pKa of approx 6, which is critical for catalysis. Site directed
      mutagenesis was used to identify which histidine is critical and to better understand the role
      of histidine in the chemical mechanism of the Mtase. Limited proteolysis of the Mtase in the
      presence of DNA and the AdoMet analog sinefungin produced a 26 kDa (p26) and a 12 kDa (p12)
      fragment [(1991) Biochemistry 30, 2940-2946]. Preliminary results suggested that the p26
      fragment retained significant activity. Therefore, p26 (aa's 105-end) was genetically
      produced, expressed and characterized.
AU  - Maegley K
AU  - Reich NO
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1993 7: A1197.

PMID- 2323503
VI  - 4
DP  - 1990
TI  - Limited proteolysis of EcoRI DNA methylase.
PG  - A1793
AB  - Limited proteolysis by soybean trpsin in the presence of various combinations
      of ligands was used to probe the domain structure of the EcoRI DNA methylase
      and its interactions with DNA, S-adenosyl methionine (AdoMet), S-Adenosyl
      homocysteine (AdoHcy) and sinefungin (an AdoMet analog).  Proteolysis at 37C
      initially results in cleavage at Lys-14 and Lys-16 followed by cleaving at
      Arg-217.  The resultant fragments (14,22,22.5 Kilodaltons) are relatively
      resistant to further cleavage.  This cleavage pattern was also found with
      proteases of different specificities.  This data suggests a tertiary structure
      consisting of two domains connected by a tether region.  In the presence of
      AdoMet, AdoHcy, or DNA the 22K and 14K fragments are formed, but the rate of
      proteolysis is slowed by as much as 100-fold.  Although AdoMet and sinefungin
      have comparable affinities for the methylase, sinefungin shows no ability to
      slow the rate of proteolysis.  Thus the methylase-sinefungin complex is
      conformationally distinct from the methylase-AdoMet complex.  In the presence
      of both DNA and sinefungin, proteolysis results in the cleavage of the first
      105 amino acids generating fragments of 12 and 26K.  These fragments show the
      greatest resistance to further proteolysis and initial results suggest that the
      26K fragment is active.
AU  - Maegley K
AU  - Shoemaker D
AU  - Everett B
AU  - Reich NO
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1990 4: A1793.

PMID- 2011036
VI  - 15G
DP  - 1991
TI  - Covalent intermediate in EcoRI DNA methyltransferase investigated by site directed mutagenesis.
PG  - 175
AB  - EcoRI DNA methyltransferase catalyses the methylation of the second adenine in
      the recognition sequence GAATTC, at the N6 position.  Our protein modification
      studies have implicated cysteine 223 as an important residue in the chemical
      mechanism of the methyltransferase (JBC 265, 17713-17719).  Cytosine N4 and
      adenine N6 methyltransferases are two unrelated classes of enzymes that
      catalyze similar reactions and our analyses show homology between both types of
      methyltransferases in the region of cysteine 223.  Based on these results and
      the fact that the N6 of adenine is a poor nucleophile, we have proposed a
      chemical mechanism involving a covalent enzyme-DNA intermediate.  Three mutants
      have been constructed to test the proposed mechanism; ser223, ala223 and
      gly223.  Characterization of these mutants will be described.
AU  - Maegley K
AU  - Shoemaker D
AU  - Reich NO
PT  - Journal Article
TA  - J. Cell. Biochem.
JT  - J. Cell. Biochem.
SO  - J. Cell. Biochem. 1991 15G: 175.

PMID- Not carried by PubMed...
VI  - 55
DP  - 1995
TI  - Structural and functional characterization of the EcoRI DNA methyltransferase.
PG  - 3293B
AB  - *

      This dissertation describes continued structural and functional characterization of the EcoRI

      DNA Methyltransferase (MTase). The MTase catalyzes the transfer of a methyl group from

      S-adenosyl-L-methionine (AdoMet) to the N6 position of the second adenine in the DNA sequence

      5' GAATTC 3'. Previously, little structural information was available on this MTase. Only

      recently has a crystal structure been solved for an AdoMet-dependent enzyme. Structural

      characterization of the MTase was performed using the techniques of limited proteolysis and

      fluorescence spectroscopy. Site-directed mutagenesis was used to investigate the role of

      Cys223 in the chemical mechanism of the MTase.

      

              Limited proteolysis of the MTase with trypsin suggests that the MTase is a two domain

      protein consisting of a large N-terminal domain connected to a smaller C-terminal domain by a

      flexible, solvent-exposed region. This "hinge" region contains part of the AdoMet binding site

      and is close to two residues discussed below, Trp225 and Cys223. Structural dynamics of the

      MTase were probed by performing proteolysis in the presence of the following ligands: AdoMet,

      S-adenosyl-L-homocysteine (AdoHcy), sinefungin (an AdoMet analog) and DNA. All of the ligands

      except sinefungin protected the Mtase from digestion, with AdoMet affording the greatest

      protection (approx. 1000-fold). These results imply that there are structural differences

      between the MTase-AdoMet, MTase-AdoHcy and MTase-sinefungin binary complexes.

      

              Fluorescence spectroscopy of the wild-type and tryptophan 183 to phenylalanine (WF183)

      mutant MTases suggests that the two tryptophans within the MTase (W183 and W225) are partially

      buried within the protein. Changes in the MTase emission spectrum upon AdoMet, AdoHcy,

      adenosine, or adenine binding are not consistent with a ligand induced conformational change.

      Therefore, the protection from proteolysis seen upon AdoMet binding is likely due to steric

      obstruction of the cleavage site by the bound cofactor or by increaased rigidity of the hinge

      region when AdoMet is bound.

      

              The fluorescence intensity of the wild-type MTase is substantially increased by the

      formation of the MTase-DNA complex, whereas the fluorescence intensity of the WF183 MTase-DNA

      complex decreases slightly upon DNA binding. This indicates that the fluorescence of

      tryptophan 225 is greatly enhanced upon DNA binding. DNA binding may cause a conformational

      change which results in the movement of tryptophan 225 away from a positively charged residue

      such as arginine or lysine. Alternatively, the negatively charged phosphate backbone of the

      DNA may form salt bridges with positively charged residues near tryptophan 225, thereby

      causing the fluorescence intensity to increase.

      

              Protein modification studies with the MTase implicated Cys223 as being critical for

      catalysis. Therefore, three mutant MTases were constructed, cysteine 223 to serine (CS223),

      alanine (CA223), and glycine (CG223). Kinetic analysis of the mutants indicates that their

      ability to methylate the canonical site remains unchanged, while their ability to methylate

      closely related non-canonical sites is significantly decreased. The mutant MTases are enhanced

      in their specificity. Detailed analysis of the CG223 mutant suggests that Cys223 does not

      directly contact the DNA. Initial velocity and single turnover kinetics showed that a

      significant portion of the enhanced specificity is due to a 5-fold decrease in the rate of

      methyl transfer (kmeth). For both the wild-type and CG223 MTases kmeth is substantially faster

      than kcat for canonical site methylation, whereas kmeth determines kcat for non-canonical

      methylation.

      

AU  - Maegley KA
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1995 55: 3293B.

PMID- 1526989
VI  - 267
DP  - 1992
TI  - Cofactor and DNA interactions in EcoRI DNA methyltransferase.
PG  - 18527-18532
AB  - EcoRI DNA methyltransferase contains tryptophans at positions 183 and 225. Tryptophan 225 is
      adjacent to residues previously implicated in S-adenosylmethionine (AdoMet) binding and to
      cysteine 223, previously shown to be the site of N-ethyl maleimide-mediated inactivation of
      the enyzme (Reich,N.O, and Everett,E. (1990) J. Biol Chem. 265, 8929-8934; Everett,E.A.,
      Falick, A.M., and Reich, N.O. (1990) J. Biol Chem 265, 17713-17719). The fluorescence spectra
      of the wild-type enzyme is centered at 338 nm indicating partial tryptophan solvent
      accessibility. Substitution of tryptophan 183 with phenylalanine results n a 45% drop in
      fluorescence intensity, but no shift in lambdamax. DNA binding to the wild-type
      methyltransferase caused an increase in the fluorescence intensity, while binding to the
      tryptophan 183 mutant had a quenching effect, suggesting that DNA binding induces a
      conformational change near both tryptophans. Binding of AdoMet and various AdoMet analogs to
      the wild-type methyltransferase results in no change in the fluorescence spectrum when
      excitation occurs at 295 nm, suggesting that no conformational change occurs, and AdoMet does
      not interact with either tryptophan. In contrast, quenching was observed when excitation
      occurred at 280 nm, suggesting that AdoMet and its analogs may be quenching tyrosine to
      tryptophan energy transfer. Protein-ligand complexes were titrated with acrylamide, and the
      data also implicate conformational changes upon DNA binding but not upon AdoMet binding,
      consistent with previous limited proteolysis results (Reich, N.O., Maegley, K.A., Shoemaker,
      D.D. and Everett, E. (1991) Biochemistry 30 2940-2946).
AU  - Maegley KA
AU  - Gonzalez L
AU  - Smith DW
AU  - Reich NO
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1992 267: 18527-18532.

PMID- 22092861
VI  - 325
DP  - 2011
TI  - Effect of Bacillus subtilis BsuM restriction-modification on plasmid transfer by polyethylene glycol-induced protoplast fusion.
PG  - 49-55
AB  - Polyethylene glycol (PEG)-induced cell fusion is a promising method to transfer larger DNA
      from one cell to another than conventional genetic
      DNA transfer systems. The laboratory strain Bacillus subtilis 168
      contains a restriction (R) and modification (M) system, BsuM, which
      recognizes the sequence 5'-CTCGAG-3'. To study whether the BsuM system
      affects DNA transfer by the PEG-induced cell fusion between R+M+ and
      R-M- strains, we examined transfer of plasmids pHV33 and pLS32neo
      carrying no and eight BsuM sites, respectively. It was shown that
      although the transfer of pLS32neo but not pHV33 from the R-M- to R+M+
      cells was severely restricted, significant levels of transfer of both
      plasmids from the R+M+ to R-M- cells were observed. The latter result
      shows that the chromosomal DNA in the R-M- cell used as the recipient
      partially survived restriction from the donor R+M+ cell, indicating
      that the BsuM R-M- strain is useful as a host for accepting DNA from
      cells carrying a restriction system(s). Two such examples were
      manifested for plasmid transfer from Bacillus circulans and Bacillus
      stearothermophilus strains to a BsuM-deficient mutant, B. subtilis
      RM125.
AU  - Maehara T
AU  - Itaya M
AU  - Ogura M
AU  - Tanaka T
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2011 325: 49-55.

PMID- Not included in PubMed...
VI  - 69
DP  - 1990
TI  - The relaxation of specificity of BanI restriction endonuclease from Bacillus aneurinolyticus IAM 1077.
PG  - 57-59
AB  - The restriction endonuclease BanI from Bacillus aneurinolyticus IAM 1077, which
      recognizes 5'-GGPyPuCC-3' and cleaves between G and G within this sequence, has
      decreased substrate specificity at high nuclease concentrations.  The
      relaxation of its specificity was enhanced during modified reactions:
      digestion of pBR322 DNA or lambda DNA in the presence of high glycerol and
      dimethyl-sulfoxide (DMSO) produced additional fragments in addition to the
      inherent fragments.  Therefore, it is required to check the reaction conditions
      carefully for generation of inherent fragments.
AU  - Maekawa Y
AU  - Kawakami B
PT  - Journal Article
TA  - J. Ferment. Bioeng.
JT  - J. Ferment. Bioeng.
SO  - J. Ferment. Bioeng. 1990 69: 57-59.

PMID- Not included in PubMed...
VI  - 69
DP  - 1990
TI  - Cloning and expression in Escherichia coli of the BanI and BanIII restriction-modification systems from Bacillus aneurinolyticus.
PG  - 195-198
AB  - The genes coding for the GGPyPuCC-specific (BanI) and ATCGAT-specific (BanIII)
      restriction-modification systems of Bacillus aneurinolyticus IAM1077 were
      cloned and expressed in Escherichia coli using pBR322 as a vector.  The
      plasmids carrying the BanI and BanIII restriction-modification genes were
      designated pBanIRM8 and pBanIIIRM12, respectively.  The restriction maps of
      these recombinant plasmids were constructed.  These two plasmids were stably
      maintained in E. coli HB101.  However, when E. coli JM109 was used as a host,
      pBanIIIRM12 was efficiently propagated but pBanIRM8 was not. The HB101 cells
      carrying only the restriction gene of BanIII were viable, but the BanI
      restriction gene carrier could not form colonies on agar plates.  The growth of
      bacteriophage lambda was strongly restricted only in the E. coli HB101 cells
      harboring pBanIRM8.  These facts indicate that the BanI restriction enzyme is
      expressed and functions more efficiently than BanI modification enzyme in E.
      coli.
AU  - Maekawa Y
AU  - Kawakami B
PT  - Journal Article
TA  - J. Ferment. Bioeng.
JT  - J. Ferment. Bioeng.
SO  - J. Ferment. Bioeng. 1990 69: 195-198.

PMID- 2358438
VI  - 107
DP  - 1990
TI  - Cloning and nucleotide sequences of the BanI restriction-modification genes in Bacillus aneurinolyticus.
PG  - 645-649
AB  - The genes of the BanI restriction-modification system specific for GGPyPuCC were cloned from
      the chromosomal DNA of Bacillus aneurinolyticus IAM107, and the coding regions were assigned
      on the nucleotide sequence on the basis of the N-terminal amino acid sequences and molecular
      weights of the enzymes. The restriction and modification genes coded for polypeptides with
      calculated molecular weights of 39,841 and 42,637, respectively. Both the enzymes were coded
      by the same DNA strand. The restriction gene was located upstream of the methylase gene,
      separated by 21 bp. The cloned genes were significantly expressed in E. coli cells, so that
      the respective enzymes could be purified to homogeneity. Analysis by sodium dodecyl sulfate
      polyacrylamide gel electrophoresis and gel filtration indicated that the catalytically active
      form of the endonuclease was dimeric and that of the methylase was monomeric. Comparison of
      the amino acid sequences revealed no significant homology between the endonuclease and
      methylase, though both enzymes recognize the same target sequence. Sequence comparison with
      other related enzymes indicated that BanI methylase contains sequences common to
      cytosine-specific methylases.
AU  - Maekawa Y
AU  - Yasukawa H
AU  - Kawakami B
PT  - Journal Article
TA  - J. Biochem. (Tokyo)
JT  - J. Biochem. (Tokyo)
SO  - J. Biochem. (Tokyo) 1990 107: 645-649.

PMID- 29437096
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Escherichia coli Strain M15-4, a Typical Enteropathogenic E. coli Strain Isolated in Mexico.
PG  - e01522-17
AB  - We present here the first draft genome sequence of a typical enteropathogenic Escherichia coli
      serotype O55:H51 strain, M15-4, isolated from a 2-month-old
      infant girl with acute diarrhea. The study of this Mexican isolate will provide
      insights to the virulence and drug resistance traits involved in its pathogenic
      potential.
AU  - Magana-Lizarraga JA
AU  - Ahumada-Santos YP
AU  - Parra-Unda JR
AU  - Uribe-Beltran MJ
AU  - Gomez-Gil B
AU  - Baez-Flores ME
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01522-17.

PMID- 29097472
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of a Mexican Community-Associated Methicillin-Resistant Staphylococcus epidermidis Strain.
PG  - e01236-17
AB  - We report here the first draft genome sequence of a Mexican communitarian
      methicillin-resistant Staphylococcus epidermidis (MRSE) strain whose genome
      harbors a wide variety of resistance determinants. The availability of this
      genome will allow the study of antibiotic resistance in Mexican staphylococci
      from a genomic perspective.
AU  - Magana-Lizarraga JA
AU  - Hernandez-Peinado JV
AU  - Ahumada-Santos YP
AU  - Parra-Unda JR
AU  - Uribe-Beltran MJ
AU  - Gomez-Gil B
AU  - Baez-Flores ME
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01236-17.

PMID- 28522712
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Pseudomonas sp. Strain Ep R1 Isolated from Echinacea purpurea Roots and Effective in the Growth Inhibition of Human Opportunistic  Pathogens Belonging to the Burkholderia cepacia Complex.
PG  - e00351-17
AB  - In this announcement, we detail the draft genome sequence of the Pseudomonas sp.  strain Ep
      R1, isolated from the roots of the medicinal plant Echinacea purpurea
      The elucidation of this genome sequence may allow the identification of genes
      associated with the production of antimicrobial compounds.
AU  - Maggini V
AU  - Presta L
AU  - Miceli E
AU  - Fondi M
AU  - Bosi E
AU  - Chiellini C
AU  - Fagorzi C
AU  - Bogani P
AU  - Di Pilato V
AU  - Rossolini GM
AU  - Mengoni A
AU  - Firenzuoli F
AU  - Perrin E
AU  - Fani R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00351-17.

PMID- 22207752
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Enterococcus mundtii CRL1656.
PG  - 550
AB  - We report the draft genome sequence of Enterococcus mundtii CRL1656, which was isolated from
      the stripping milk of a clinically healthy adult
      Holstein dairy cow from a dairy farm of the northwestern region of Tucuman
      (Argentina). The 3.10-Mb genome sequence consists of 450 large contigs and
      contains 2,741 predicted protein-coding genes.
AU  - Magni C
AU  - Espeche C
AU  - Repizo GD
AU  - Saavedra L
AU  - Suarez CA
AU  - Blancato VS
AU  - Espariz M
AU  - Esteban L
AU  - Raya RR
AU  - Font-de-Valdez G
AU  - Vignolo G
AU  - Mozzi F
AU  - Taranto MP
AU  - Hebert EM
AU  - Nader-Macias ME
AU  - Sesma F
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 550.

PMID- 26035127
VI  - 28
DP  - 2015
TI  - Comparative Genomics Within the Bacillus Genus Reveal the Singularities of Two Robust Bacillus amyloliquefaciens Biocontrol Strains.
PG  - 1102-1116
AB  - Bacillus amyloliquefaciens CECT 8237 and CECT 8238, formerly known as Bacillus
      subtilis UMAF6639 and UMAF6614, respectively, contribute to plant health by
      facing microbial pathogens or inducing the plant's defense mechanisms. We
      sequenced their genomes and developed a set of ad hoc scripts that allowed us to
      search for the features implicated in their beneficial interaction with plants.
      We define a core set of genes that should ideally be found in any beneficial
      Bacillus strain, including the production of secondary metabolites, volatile
      compounds, metabolic plasticity, cell-to-cell communication systems, and biofilm
      formation. We experimentally prove that some of these genetic elements are
      active, such as i) the production of known secondary metabolites or ii) acetoin
      and 2-3-butanediol, compounds that stimulate plant growth and host defense
      responses. A comparison with other Bacillus genomes permits us to find
      differences in the cell-to-cell communication system and biofilm formation and to
      hypothesize variations in their persistence and resistance ability in diverse
      environmental conditions. In addition, the major protection provided by CECT 8237
      and CECT 8238, which is different from other Bacillus strains against bacterial
      and fungal melon diseases, permits us to propose a correlation with their
      singular genetic background and determine the need to search for additional blind
      biocontrol-related features.
AU  - Magno-Perez-Bryan MC
AU  - Martinez-Garcia PM
AU  - Hierrezuelo J
AU  - Rodriguez-Palenzuela P
AU  - Arrebola E
AU  - Ramos C
AU  - de Vicente A
AU  - Perez-Garcia A
AU  - Romero D
PT  - Journal Article
TA  - Mol. Plant Microbe Interact.
JT  - Mol. Plant Microbe Interact.
SO  - Mol. Plant Microbe Interact. 2015 28: 1102-1116.

PMID- 9209041
VI  - 179
DP  - 1997
TI  - Temperate Myxococcus xanthus phage Mx8 encodes a DNA adenine methylase, Mox.
PG  - 4254-4263
AB  - Temperate bacteriophage Mx8 of Myxococcus xanthus encapsidates terminally repetitious DNA,
      packaged as circular permutations of its 49-kbp genome.  During both lytic and lysogenic
      development, Mx8 expresses a nonessential DNA methylase, Mox, which modifies adenine residues
      in occurrences of XhoI and PstI recognition sites, CTCGAG and CTGCAG, respectively, on both
      phage DNA and the host chromosome.  The mox gene is necessary for methylase activity in vivo,
      because an amber mutation in the mox gene abolishes activity.  The mox gene is the only phage
      gene required for methylase activity in vivo, because ectopic expression of mox as part of the
      M. xanthus mglBA operon results in partial methylation of the host chromosome.  The predicted
      amino acid sequence of Mox is related most closely to that of the methylase involved in the
      cell cycle control of Caulobacter crescentus.  We speculate that Mox acts to protect Mx8 phage
      DNA against restriction upon infection of a subset of natural M. xanthus hosts.  One natural
      isolate of M. xanthus, the lysogenic source of related phage Mx81, produces a restriction
      endonuclease with the cleavage specificity of endonuclease BstBI.
AU  - Magrini V
AU  - Salmi D
AU  - Thomas D
AU  - Herbert SK
AU  - Hartzell PL
AU  - Youderian P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1997 179: 4254-4263.

PMID- 27013044
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Two Extensively Drug-Resistant Acinetobacter baumannii  Strains Isolated from Pus Samples.
PG  - e00161-16
AB  - We report the draft genomes of two extensively drug-resistant (XDR)Acinetobacter
      baumanniistrains isolated from pus samples of two patients with surgical site
      infections at Sri Sathya Sai Institute of Higher Medical Sciences, Prasanthigram,
      India. The average genomic size and G+C content are 4 Mbp and 38.96% (AB28) and 4
      Mbp and 38.94% (AB30), respectively.
AU  - Mahalingam N
AU  - Manivannan B
AU  - Jadhao S
AU  - Mishra G
AU  - Nilawe P
AU  - Pradeep BE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00161-16.

PMID- 26798098
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Streptomyces vitaminophilus ATCC 31673, a Producer of Pyrrolomycin Antibiotics, Some of Which Contain a Nitro Group.
PG  - e01582-15
AB  - Streptomyces vitaminophilus produces pyrrolomycins, which are halogenated polyketide
      antibiotics. Some of the pyrrolomycins contain a rare nitro group
      located on the pyrrole ring. The 6.5-Mbp genome encodes 5,941 predicted
      protein-coding sequences in 39 contigs with a 71.9% G+C content.
AU  - Mahan KM
AU  - Klingeman DM
AU  - Hettich RL
AU  - Parry RJ
AU  - Graham DE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01582-15.

PMID- 
VI  - 67
DP  - 2001
TI  - DNA methylation regulates bacterial gene expression and virulence.
PG  - 356-361
AB  - DNA adenine methylase (Dam) plays a pivotal role in bacteria such as Escherichia coli and
      Salmonella - acting as a global regulator of gene expression and affecting a wide range of
      critical cellular functions, including DNA replication, DNA repair, transposition, and
      segregation of chromosomal DNA.  This extraordinary versatility stems from the inherent
      biochemical activity of Dam.  Thus, by adding methyl groups to various sites along the
      cellular DNA, Dam alters interactions of a variety of regulatory proteins with their
      designated gene targets and, in the process, effectively controls expression of those genes.
      In some cases, such changes modulate bacterial virulence and also serve to elicit protective
      immune responses in host organisms that Salmonella or other bacterial pathogens may infect.
AU  - Mahan MJ
AU  - Low DA
PT  - Journal Article
TA  - ASM News
JT  - ASM News
SO  - ASM News 2001 67: 356-361.

PMID- 25035332
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Deinococcus sp. Strain RL Isolated from Sediments of a Hot Water Spring.
PG  - e00703-14
AB  - Deinococcus sp. strain RL, a moderately thermophilic bacterium, was isolated from sediments of
      a hot water spring in Manikaran, India. Here, we report the draft
      genome (2.79 Mbp) of this strain, which contains 62 contigs and 2,614 coding DNA
      sequences, with an average G+C content of 69.4%.
AU  - Mahato NK
AU  - Tripathi C
AU  - Verma H
AU  - Singh N
AU  - Lal R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00703-14.

PMID- 1365896
VI  - 14
DP  - 1992
TI  - DNA triple-helix formation: an approach to artificial gene repressors?
PG  - 807-815
AB  - Certain sequences of double-helical DNA can be recognized and tightly bound by
      oligonucleotides. The effects of such triple-helical structures
      on DNA binding proteins have been studied. Stabilities of DNA
      triple-helices at or near physiological conditions are sufficient to
      inhibit DNA binding proteins directed to overlapping sites. Such proteins
      include restriction endonucleases, methylases, transcription factors, and
      RNA polymerases. These and other results suggest that
      oligonucleotide-directed triple-helix formation could provide the basis
      for designing artificial gene repressors. The general question of whether
      biological systems employ RNA molecules for recognition and regulation of
      double-helical DNA is discussed.
AU  - Maher LJ III
PT  - Journal Article
TA  - Bioessays
JT  - Bioessays
SO  - Bioessays 1992 14: 807-815.

PMID- 2549631
VI  - 245
DP  - 1989
TI  - Inhibition of DNA binding proteins by oligonucleotide-directed triple helix formation.
PG  - 725-733
AB  - Oligonucleotides that bind to duplex DNA in a sequence-specific manner by
      triple helix formation offer an approach to the experimental manipulation of
      sequence-specific protein binding.  Micromolar concentrations of pyrimidine
      oligodeoxyribonucleotides are shown to block recognition of double helical DNA
      by prokaryotic modifying enzymes and a eukaryotic transcription factor at a
      homopurine target site.  Inhibition is sequence-specific.  Oligonucleotides
      containing 5-methylcytosine provide substantially more efficient inhibition
      than oligonucleotides containing cytosine.  The results have implications for
      gene-specific repression by oligonucleotides or their analogs.
AU  - Maher LJ
AU  - Wold B
AU  - Dervan PB
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1989 245: 725-733.

PMID- 27587833
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Criibacterium bergeronii gen. nov., sp. nov., Strain CCRI-22567T, Isolated from a Vaginal Sample from a Woman with Bacterial  Vaginosis.
PG  - e00959-16
AB  - Criibacterium bergeronii gen. nov., sp. nov., CCRI-22567 is the type strain of the new genus
      Criibacterium The strain was isolated from a woman with bacterial
      vaginosis. The genome assembly comprised 2,384,460 bp, with 34.4% G+C content.
      This is the first genome announcement of a strain belonging to the genus
      Criibacterium.
AU  - Maheux AF
AU  - Berube E
AU  - Boudreau DK
AU  - Raymond F
AU  - Corbeil J
AU  - Roy PH
AU  - Boissinot M
AU  - Omar RF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00959-16.

PMID- 28982987
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Romboutsia weinsteinii sp. nov. Strain CCRI-19649T Isolated from Surface Water.
PG  - e00901-17
AB  - Romboutsia weinsteinii sp. nov. CCRI-19649T belongs to the genus Romboutsia The strain was
      isolated from a water sample harvested in Quebec City, Quebec, Canada.
      The genome assembly comprised 4,134,593 bp with a 29.3% GC content. This is the
      first documentation that reports the genome sequence of R. weinsteinii.
AU  - Maheux AF
AU  - Boudreau DK
AU  - Berube E
AU  - Boissinot M
AU  - Cantin P
AU  - Raymond F
AU  - Corbeil J
AU  - Omar RF
AU  - Bergeron MG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00901-17.

PMID- 29025937
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Romboutsia maritimum sp. nov. Strain CCRI-22766T, Isolated from Coastal Estuarine Mud.
PG  - e01044-17
AB  - The Romboutsia maritimum sp. nov. CCRI-22766T strain was isolated from coastal estuarine mud
      in New Zealand. The genome assembly comprised 2,854,352 bp, with
      27.1% G+C content. This is the first documentation that reports the genome
      sequence of R. maritimum.
AU  - Maheux AF
AU  - Boudreau DK
AU  - Berube E
AU  - Boissinot M
AU  - Raymond F
AU  - Brodeur S
AU  - Corbeil J
AU  - Brightwell G
AU  - Broda D
AU  - Omar RF
AU  - Bergeron MG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01044-17.

PMID- 29051240
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of a Sporulating and Motile Strain of Lachnotalea glycerini Isolated from Water in Quebec City, Canada.
PG  - e01059-17
AB  - Lachnotalea glycerini CCRI-19302 belongs to the genus Lachnotalea The strain was  isolated
      from a water sample harvested in Quebec City, Canada. The genome
      assembly comprised 4,694,231 bp, with 34.6% GC content. This is the first
      documentation to report the genome sequence of a sporulating and motile strain of
      L. glycerini.
AU  - Maheux AF
AU  - Boudreau DK
AU  - Berube E
AU  - Boissinot M
AU  - Raymond F
AU  - Brodeur S
AU  - Corbeil J
AU  - Isabel S
AU  - Omar RF
AU  - Bergeron MG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01059-17.

PMID- 25185514
VI  - 13
DP  - 2014
TI  - Progress in lactic acid bacterial phage research.
PG  - S1
AB  - Research on lactic acid bacteria (LAB) has advanced significantly over the past number of
      decades and these developments have been driven by the parallel advances in technologies such
      as genomics, bioinformatics, protein expression systems and structural biology, combined with
      the ever increasing commercial relevance of this group of microorganisms. Some of the more
      significant and impressive outputs have been in the domain of bacteriophage-host interactions
      which provides a prime example of the cutting-edge model systems represented by LAB research.
      Here, we present a retrospective overview of the key advances in LAB phage research including
      phage-host interactions and co-evolution. We describe how in many instances this knowledge can
      be pivotal in creating real improvements in the application of LAB cultures in commercial
      practice.
AU  - Mahony J
AU  - Bottacini F
AU  - van Sinderen D
AU  - Fitzgerald GF
PT  - Journal Article
TA  - Microb. Cell Fact.
JT  - Microb. Cell Fact.
SO  - Microb. Cell Fact. 2014 13: S1.

PMID- 19321416
VI  - 106
DP  - 2009
TI  - Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla.
PG  - 5859-5864
AB  - The adult human distal gut microbial community is typically dominated by 2
      bacterial phyla (divisions), the Firmicutes and the Bacteroidetes. Little
      is known about the factors that govern the interactions between their
      members. Here, we examine the niches of representatives of both phyla in
      vivo. Finished genome sequences were generated from Eubacterium rectale
      and E. eligens, which belong to Clostridium Cluster XIVa, one of the most
      common gut Firmicute clades. Comparison of these and 25 other gut
      Firmicutes and Bacteroidetes indicated that the Firmicutes possess smaller
      genomes and a disproportionately smaller number of glycan-degrading
      enzymes. Germ-free mice were then colonized with E. rectale and/or a
      prominent human gut Bacteroidetes, Bacteroides thetaiotaomicron, followed
      by whole-genome transcriptional profiling, high-resolution proteomic
      analysis, and biochemical assays of microbial-microbial and microbial-host
      interactions. B. thetaiotaomicron adapts to E. rectale by up-regulating
      expression of a variety of polysaccharide utilization loci encoding
      numerous glycoside hydrolases, and by signaling the host to produce
      mucosal glycans that it, but not E. rectale, can access. E. rectale adapts
      to B. thetaiotaomicron by decreasing production of its glycan-degrading
      enzymes, increasing expression of selected amino acid and sugar
      transporters, and facilitating glycolysis by reducing levels of NADH, in
      part via generation of butyrate from acetate, which in turn is used by the
      gut epithelium. This simplified model of the human gut microbiota
      illustrates niche specialization and functional redundancy within members
      of its major bacterial phyla, and the importance of host glycans as a
      nutrient foundation that ensures ecosystem stability.
AU  - Mahowald MA et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2009 106: 5859-5864.

PMID- 26514765
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Pseudomonas aeruginosa ATCC 9027 (DSM 1128), an Important Rhamnolipid Surfactant Producer and Sterility Testing Strain.
PG  - e01259-15
AB  - Pseudomonas aeruginosa ATCC 9027 (DSM1128) is often used as a quality-control strain for
      sterility and microbial contamination testing and is an important
      biosurfactant producer. Here, we present the 6.4-Mb draft genome sequence and
      highlight some genomic differences to its closest relative, P. aeruginosa strain
      PA7.
AU  - Mai-Prochnow A
AU  - Bradbury M
AU  - Murphy AB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01259-15.

PMID- 23969053
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Fast-Growing Bacterium Vibrio natriegens Strain DSMZ 759.
PG  - e00648-13
AB  - Vibrio natriegens is a Gram-negative bacterium known for its extremely short doubling time.
      Here we present the annotated draft genome sequence of Vibrio
      natriegens strain DSMZ 759, with the aim of providing insights about its high
      growth rate.
AU  - Maida I
AU  - Bosi E
AU  - Perrin E
AU  - Papaleo MC
AU  - Orlandini V
AU  - Fondi M
AU  - Fani R
AU  - Wiegel J
AU  - Bianconi G
AU  - Canganella F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00648-13.

PMID- 27491974
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Streptococcus agalactiae Strain S25 Isolated from Peritoneal Liquid of Nile Tilapia.
PG  - e00784-16
AB  - Streptococcus agalactiae (Lancefield group B; GBS) is one of the major pathogens  in fish
      production, especially in Nile tilapia (Oreochromis niloticus). The
      genomic characteristics of GBS isolated from fish must be more explored. Thus, we
      present here the genome of GBS S25, isolated from Nile tilapia from Brazil.
AU  - Mainardi RM
AU  - Lima JEA
AU  - Ribeiro JJC
AU  - Beloti V
AU  - Carmo AO
AU  - Kalapothakis E
AU  - Goncalves DD
AU  - Padua SB
AU  - Pereira UP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00784-16.

PMID- 25414489
VI  - 2
DP  - 2014
TI  - Finished Genome Sequence of Escherichia coli K-12 Strain HMS174 (ATCC 47011).
PG  - e00975-14
AB  - Escherichia coli strain K-12 substrain HMS174 is an engineered descendant of the  E. coli K-12
      wild-type strain. Like its ancestor, it is an important organism in
      biotechnological research and is used in fermentation processes for heterologous
      protein production. Here, we report the complete genome sequence of E. coli
      HMS174 (ATCC 47011).
AU  - Mairhofer J
AU  - Krempl PM
AU  - Thallinger GG
AU  - Striedner G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00975-14.

PMID- 27491976
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Legionella pneumophila JR32 and Lp01 Laboratory Strains Domesticated in Japan.
PG  - e00791-16
AB  - We report here the draft genome sequences of two Legionella pneumophila variant strains (JR32
      and Lp01_666) originally derived from a Philadelphia-1 clinical
      isolate, domesticated in Japan, with distinct susceptibility to amoebae. Detailed
      genomic analysis will allow us to better understand Legionella adaptation and
      survival mechanisms in host cells.
AU  - Maita C
AU  - Matushita M
AU  - Okubo T
AU  - Matsuo J
AU  - Miyake M
AU  - Nagai H
AU  - Yamaguchi H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00791-16.

PMID- 24482525
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Aquatic Phosphorus-Solubilizing and -Mineralizing Bacterium Bacillus sp. Strain CPSM8.
PG  - e01265-13
AB  - Bacillus sp. strain CPSM8 is an efficient solubilizer and mineralizer of phosphorus. Here, we
      present the 4.39-Mb draft genome sequence of the strain,
      providing insight into the phosphorus-releasing genes related to productivity in
      aquatic habitats.
AU  - Maitra N
AU  - Whitman WB
AU  - Ayyampalayam S
AU  - Samanta S
AU  - Sarkar K
AU  - Bandopadhyay C
AU  - Aftabuddin M
AU  - Sharma AP
AU  - Manna SK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01265-13.

PMID- 25883298
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Brevibacterium linens AE038-8, an Extremely Arsenic-Resistant Bacterium.
PG  - e00316-15
AB  - To understand the arsenic biogeocycles in the groundwaters at Tucuman, Argentina, we isolated
      Brevibacterium linens sp. strain AE38-8, obtained from
      arsenic-contaminated well water. This strain is extremely resistant to arsenicals
      and has arsenic resistance (ars) genes in its genome. Here, we report the draft
      genome sequence of B. linens AE38-8.
AU  - Maizel D
AU  - Utturkar SM
AU  - Brown SD
AU  - Ferrero MA
AU  - Rosen BP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00316-15.

PMID- 24652981
VI  - 2
DP  - 2014
TI  - Genomes of Two Clinical Isolates of Mycobacterium tuberculosis from Odisha, India.
PG  - e00199-14
AB  - We report whole-genome sequences of two clinical isolates of Mycobacterium tuberculosis
      isolated from patients in Odisha, India. The sequence analysis
      revealed that these isolates are of an ancestral type and might represent some of
      the 'pristine' isolates in India that have not admixed with other lineages.
AU  - Majid M
AU  - Kumar N
AU  - Qureshi A
AU  - Yerra P
AU  - Kumar A
AU  - Kumar MK
AU  - Tiruvayipati S
AU  - Baddam R
AU  - Shaik S
AU  - Srikantam A
AU  - Ahmed N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00199-14.

PMID- 2912512
VI  - 55
DP  - 1989
TI  - The importance of flanking sequences in the sequence specific cleavage by the restriction endonucleases RsaI, AluI and HaeIII.
PG  - 48a
AB  - Recent discoveries on the dependence in the sensitivity of some of restriction
      enzymes (REs) on conformational changes in DNA indicate a complex diversity in
      the nature of RE-DNA interaction.  Although the bases around these recognition
      sequences are believed to be of considerable importance, not much data is
      available in this regard.  We have studied the importance of flanking sequences
      in the sequence specific cleavage by the REs - RsaI, AluI and HaeIII.  The
      oligomers d(ACGTACGT), d(CGTACGTACG), poly d(ACGT), d(AGCTAGCT), poly d(AGCT),
      d(GGCC) and d(CCGGCCGG) were used as the substrates for the relevant enzymes.
      We have found that in the absence of the flanking bases the REs - RsaI, AluI
      and HaeIII fail to cleave the corresponding recognition sites.  The minimum
      number of such flanking bases (termed as flanking number or FN) has been found
      to be two (i.e., FN=2) for RsaI.  Preliminary indications showed that the
      flanking bases play an important role in the case of several other REs also.
      It appears to us that in the sequence specific cleavage of DNA by RE the
      flanking bases play two roles viz. (i) provide better binding and improved
      kinetic stability to the enzyme-DNA complex formed prior to cleavage and (ii)
      stabilization of the local active conformation by buffering out the
      neighbouring influences like fraying or altered structure.
AU  - Majumder K
PT  - Journal Article
TA  - Biophys. J.
JT  - Biophys. J.
SO  - Biophys. J. 1989 55: 48a.

PMID- 20800503
VI  - 18
DP  - 2010
TI  - Folding, DNA Recognition, and Function of GIY-YIG Endonucleases: Crystal Structures of R.Eco29kI.
PG  - 1321-1331
AB  - The GIY-YIG endonuclease family comprises hundreds of diverse proteins and a multitude of
      functions; none have been visualized bound to DNA. The
      structure of the GIY-YIG restriction endonuclease R.Eco29kI has been
      solved both alone and bound to its target site. The protein displays a
      domain-swapped homodimeric structure with several extended surface loops
      encircling the DNA. Only three side chains from each protein subunit
      contact DNA bases, two directly and one via a bridging solvent molecule.
      Both tyrosine residues within the GIY-YIG motif are positioned in the
      catalytic center near a putative nucleophilic water; the remainder of the
      active site resembles the HNH endonuclease family. The structure
      illustrates how the GIY-YIG scaffold has been adapted for the highly
      specific recognition of a DNA restriction site, in contrast to nonspecific
      DNA cleavage by GIY-YIG domains in homing endonucleases or
      structure-specific cleavage by DNA repair enzymes such as UvrC.
AU  - Mak AN
AU  - Lambert AR
AU  - Stoddard BL
PT  - Journal Article
TA  - Structure
JT  - Structure
SO  - Structure 2010 18: 1321-1331.

PMID- 17338633
VI  - 388
DP  - 2007
TI  - Characterization of the large subunit of EcoHK31I methyltransferase by structural modeling and mutagenesis.
PG  - 265-271
AB  - M.EcoHK31I is a naturally occurring mC5-methyltransferase with a large alpha polypeptide and a
      small beta polypeptide. Polypeptide alpha
      contains conserved motifs I-VIII and X, and polypeptide beta contains
      motif IX. To understand how polypeptide alpha carries out its function,
      a molecular model of the large domain of polypeptide a was generated
      using M.Hhal and M.Haelll as templates. The large domain is a mixed
      alpha/beta structure. Residues 15-19 in motif I (Phe-Naa-Gly-Naa) are
      conserved for cofactor binding. The key catalytic residue Cys-79 in
      motif IV is also conserved in comparison with other C-5 MTases.
      Comparing polypeptide a with M.Hhal and M.Haelll revealed a unique
      region upstream of motif X. To understand the role of this region, 14
      charged residues between R224 and E271 in the putative small domain
      were mutated. Activity assays indicated that most of these charges can
      be eliminated or changed conservatively. Among these charged residues,
      R224, E240, D245 and D251 may take part in proper interaction with DNA
      in the presence of polypeptide beta.
AU  - Mak ANS
AU  - Fung WT
AU  - Kong KPS
AU  - Poon AWS
AU  - Ngai SM
AU  - Shaw PC
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 2007 388: 265-271.

PMID- 24356837
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences of Two Strains of Propionibacterium acnes Isolated from Radical Prostatectomy Specimens.
PG  - e01071-13
AB  - Propionibacterium acnes is a Gram-positive bacterium that is closely associated with various
      parts of the human body, in particular with sebaceous follicles of
      the skin. It has also been frequently isolated from diseased human prostates.
      Here, we report draft genome sequences of two P. acnes strains, P6 and PA2,
      isolated from radical prostatectomy specimens.
AU  - Mak TN
AU  - Sfanos KS
AU  - Bruggemann H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01071-13.

PMID- 17030793
VI  - 103
DP  - 2006
TI  - Comparative genomics of the lactic acid bacteria.
PG  - 15611-15616
AB  - Lactic acid-producing bacteria are associated with various plant and animal niches and play a
      key role in the production of fermented foods and
      beverages. We report nine genome sequences representing the phylogenetic
      and functional diversity of these bacteria. The small genomes of lactic
      acid bacteria encode a broad repertoire of transporters for efficient
      carbon and nitrogen acquisition from the nutritionally rich environments
      they inhabit and reflect a limited range of biosynthetic capabilities that
      indicate both prototrophic and auxotrophic strains. Phylogenetic analyses,
      comparison of gene content across the group, and reconstruction of
      ancestral gene sets indicate a combination of extensive gene loss and key
      gene acquisitions via horizontal gene transfer during the coevolution of
      lactic acid bacteria with their habitats.
AU  - Makarova K et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2006 103: 15611-15616.

PMID- 23470997
VI  - 41
DP  - 2013
TI  - Comparative genomics of defense systems in archaea and bacteria.
PG  - 4360-4377
AB  - Our knowledge of prokaryotic defense systems has vastly expanded as the result of comparative
      genomic analysis, followed by experimental validation. This expansion is both quantitative,
      including the discovery of diverse new examples of known types of defense systems, such as
      restriction-modification or toxin-antitoxin systems, and qualitative, including the discovery
      of fundamentally new defense mechanisms, such as the CRISPR-Cas immunity system. Large-scale
      statistical analysis reveals that the distribution of different defense systems in bacterial
      and archaeal taxa is non-uniform, with four groups of organisms distinguishable with respect
      to the overall abundance and the balance between specific types of defense systems. The genes
      encoding defense system components in bacterial and archaea typically cluster in defense
      islands. In addition to genes encoding known defense systems, these islands contain numerous
      uncharacterized genes, which are candidates for new types of defense systems. The tight
      association of the genes encoding immunity systems and dormancy- or cell death-inducing
      defense systems in prokaryotic genomes suggests that these two major types of defense are
      functionally coupled, providing for effective protection at the population level.
AU  - Makarova KS
AU  - Wolf YI
AU  - Koonin EV
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2013 41: 4360-4377.

PMID- 21908672
VI  - 193
DP  - 2011
TI  - Defense islands in bacterial and archaeal genomes and prediction of novel defense systems.
PG  - 6039-6056
AB  - The arms race between cellular life forms and viruses is a major driving force of evolution. A
      substantial fraction of bacterial and archaeal
      genomes is dedicated to antivirus defense. We analyzed the distribution of
      defense genes and typical mobilome components (such as viral and
      transposon genes) in bacterial and archaeal genomes, and demonstrated
      statistically significant clustering of antivirus defense systems and
      mobile genes and elements in genomic islands. The defense islands are
      enriched in putative operons and contain numerous over-represented gene
      families. A detailed sequence analysis of the proteins encoded by genes in
      these families shows that many of them are diverged variants of known
      defense system components, whereas others show features, such as
      characteristic operonic organization, that are suggestive of novel defense
      systems. Thus, genomic islands provide abundant material for experimental
      study of bacterial and archaeal antivirus defense. Except for the
      CRISPR-Cas systems, different classes of defense systems, in particular
      toxin-antitoxin and restriction-modification systems, show non-random
      clustering in defense islands. It remains unclear to what extant these
      associations reflect functional cooperation between different defense
      systems and to what extent the islands are genomic 'sinks' that accumulate
      diverse non-essential genes, particularly those acquired via HGT. The
      characteristics of defense islands resemble those of mobilome islands.
      Defense and mobilome genes are non-randomly associated in islands,
      suggesting non-adaptive evolution of the islands via a preferential
      attachment-like mechanism underpinned by the addictive properties of
      defense systems such as toxins-antitoxins and an important role of
      horizontal mobility in the evolution of these islands.
AU  - Makarova KS
AU  - Wolf YI
AU  - Snir S
AU  - Koonin EV
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6039-6056.

PMID- 28495772
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of the Livestock-Associated Methicillin-Resistant Strain Staphylococcus aureus subsp. aureus 08S00974 (Sequence Type 398).
PG  - e00294-17
AB  - We report here the complete genome sequence of the livestock-associated methicillin-resistant
      Staphylococcus aureus strain 08S00974 from sequence type
      398 (ST398 LA-MRSA) isolated from a fatting pig at a farm in Germany.
AU  - Makarova O
AU  - Johnston P
AU  - Walther B
AU  - Rolff J
AU  - Roesler U
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00294-17.

PMID- 28495771
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of the Disinfectant Susceptibility Testing Reference Strain Staphylococcus aureus subsp. aureus ATCC 6538.
PG  - e00293-17
AB  - We report here the complete genome sequence of the methicillin-sensitive Staphylococcus aureus
      subsp. aureus strain ATCC 6538 (FDA 209, DSM 799, WDCM
      00032, and NCTC 10788).
AU  - Makarova O
AU  - Johnston P
AU  - Walther B
AU  - Rolff J
AU  - Roesler U
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00293-17.

PMID- 28104644
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Hydrogenibacillus schlegelii MA48, a Deep-Branching Member of the Bacilli Class of Firmicutes.
PG  - e00380-16
AB  - We report here the draft genome sequence of Hydrogenibacillus schlegelii MA48, a  thermophilic
      facultative anaerobe that can oxidize hydrogen aerobically. H.
      schlegelii MA48 belongs to a deep-branching clade of the Bacilli class and
      provides important insight into the acquisition of aerobic respiration within the
      Firmicutes phylum.
AU  - Maker A
AU  - Hemp J
AU  - Pace LA
AU  - Ward LM
AU  - Fischer WW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00380-16.

PMID- Not carried by PubMed...
VI  - 1432
DP  - 1991
TI  - Microwave-optical study of an As(III) derivative of EcoRI methylase.
PG  - 119-128
AB  - We report on the formation of an unusually stable As(III)-thiolate with a
      single high-affinity cysteine (Cys) of E. coli RI methylase, monitored via its
      influence on a neighboring tryptophan (Trp) residue in the enzyme structure.
      The binding was studied by Trp fluorescence quenching, low temperature
      phosphorescence and triplet state optically detected magnetic resonance (ODMR)
      of the intrinsic Trp residue(s).  The affected Trp is subject to an external
      heavy atom effect (HAE) from arsenic, quenching its fluorescence and reducing
      its phosphorescence lifetime from 6 sec to ca. 70 msec.  The enzyme high
      affinity binding site has at least 27 times the affinity for As(III) as does a
      typical sulfhydryl reagent, HSCH2CONH2.  The accessibility of the arsenical to
      this Cys site was reduced upon formation of the ternary complex
      methylase-DNA-sinefungin, suggesting a local conformational change in the
      enzyme when DNA is bound.  The enzymatic activity assay of methylase is not
      affected by the addition of a 1:1 molar ratio of the arsenical to the
      methylase, but incubation with an excess of As(III) causes complete loss of
      enzymatic activity.  This suggests that the high-affinity Cys residue is not a
      part of the active site of the enzyme, but the addition of a molar excess of
      arsenical to the enzyme derivatizes the Cys residue known to be located in the
      active site.
AU  - Maki AH
AU  - Tsao DHH
PT  - Journal Article
TA  - Biomol. Spectroscopy II
JT  - Biomol. Spectroscopy II
SO  - Biomol. Spectroscopy II 1991 1432: 119-128.

PMID- 9628576
VI  - 5
DP  - 1998
TI  - Complete nucleotide sequences of 93-kb and 3.3-kb plasmids of an enterohemorrhagic Escherichia coli O157:H7 derived from Sakai outbreak.
PG  - 1-9
AB  - Enterohemorrhagic Escherichia coli (EHEC) O157:H7, derived from an
      outbreak in Sakai city, Japan in 1996, possesses two kinds of plasmids: a
      93-kb plasmid termed pO157, found in clinical EHEC isolates world-wide and
      a 3.3-kb plasmid termed pOSAK1, prevalent in EHEC strains isolated in
      Japan. Complete nucleotide sequences of both plasmids have been
      determined, and the putative functions of the encoded proteins and the
      cis-acting DNA sequences have been analyzed. pO157 shares strikingly
      similar genes and DNA sequences with F-factor and the transmissible
      drug-resistant plasmid R100 for DNA replication, copy number control,
      plasmid segregation, conjugative functions and stable maintenance in the
      host, although it is defective in DNA transfer by conjugation due to the
      truncation and deletion of the required genes and DNA sequences. In
      addition, it encodes several proteins implicated in EHEC pathogenicity
      such as an EHEC hemolysin (HlyA), a catalase-peroxidase (KatP), a serine
      protease (EspP) and type II secretion system. pOSAK1 possesses a
      ColE1-like replication system, and the DNA sequence is extremely similar
      to that of a drug-resistant plasmid, NTP16, derived from Salmonella
      typhimurium except that it lacks drug resistance transposons.
AU  - Makino K
AU  - Ishii K
AU  - Yasunaga T
AU  - Hattori M
AU  - Yokoyama K
AU  - Yutsudo HC
AU  - Kubota Y
AU  - Yamaichi Y
AU  - Iida T
AU  - Yamamoto K
AU  - Honda T
AU  - Han CG
AU  - Ohtsubo E
AU  - Kasamatsu M
AU  - Hayashi T
AU  - Kuhara S
AU  - Shinagawa H
PT  - Journal Article
TA  - DNA Res.
JT  - DNA Res.
SO  - DNA Res. 1998 5: 1-9.

PMID- 12620739
VI  - 361
DP  - 2003
TI  - Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V cholerae.
PG  - 743-749
AB  - BACKGROUND: Vibrio parahaemolyticus, a gram-negative marine bacterium, is a worldwide cause of
      food-borne gastroenteritis. V parahaemolyticus
      strains of a few specific serotypes, probably derived from a common clonal
      ancestor, have lately caused a pandemic of gastroenteritis. The organism
      is phylogenetically close to V cholerae, the causative agent of cholera.
      METHODS: The whole genome sequence of a clinical V parahaemolyticus strain
      RIMD2210633 was established by shotgun sequencing. The coding sequences
      were identified by use of Gambler and Glimmer programs. Comparative
      analysis with the V cholerae genome was undertaken with MUMmer. FINDINGS:
      The genome consisted of two circular chromosomes of 3288558 bp and 1877212
      bp; it contained 4832 genes. Comparison of the V parahaemolyticus genome
      with that of V cholerae showed many rearrangements within and between the
      two chromosomes. Genes for the type III secretion system (TTSS) were
      identified in the genome of V parahaemolyticus; V cholerae does not have
      these genes. INTERPRETATION: The TTSS is a central virulence factor of
      diarrhoea-causing bacteria such as shigella, salmonella, and
      enteropathogenic Escherichia coli, which cause gastroenteritis by invading
      or intimately interacting with intestinal epithelial cells. Our results
      suggest that V parahaemolyticus and V cholerae use distinct mechanisms to
      establish infection. This finding explains clinical features of V
      parahaemolyticus infections, which commonly include inflammatory diarrhoea
      and in some cases systemic manifestations such as septicaemia, distinct
      from those of V cholerae infections, which are generally associated with
      non-inflammatory diarrhoea.
AU  - Makino K
AU  - Oshima K
AU  - Kurokawa K
AU  - Yokoyama K
AU  - Uda T
AU  - Tagomori K
AU  - Iijima Y
AU  - Najima M
AU  - Nakano M
AU  - Yamashita A
AU  - Kubota Y
AU  - Kimura S
AU  - Yasunaga T
AU  - Honda T
AU  - Shinagawa H
AU  - Hattori M
AU  - Iida T
PT  - Journal Article
TA  - Lancet
JT  - Lancet
SO  - Lancet 2003 361: 743-749.

PMID- 10734605
VI  - 74
DP  - 1999
TI  - Complete nucleotide sequence of the prophage VT2-Sakai carrying the verotoxin 2 genes of the enterohemorrhagic Escherichia coli O157:H7 derived from the Sakai outbreak.
PG  - 227-239
AB  - The enterohemorrhagic Escherichia coli (EHEC) O157:H7 strain RIMD 0509952, derived from an
      outbreak in Sakai city, Japan, in 1996, produces two kinds of verotoxins, VT1 and VT2, encoded
      by the stx1 and stx2 genes. In the EHEC strains, as well as in other VT-producing E. coli
      strains, the toxins are encoded by lysogenic bacteriophages. The EHEC O157:H7 strain RIMD
      0509952 did not produce plaque-forming phage particles upon inducing treatments. We have
      determined the complete nucleotide sequence of a prophage, VT2-Sakai, carrying the stx2A and
      stx2B genes on the chromosome, and presumed the putative functions of the encoded proteins and
      the cis-acting DNA elements based on sequence homology data. To our surprise, the sequences in
      the regions of VT2-Sakai corresponding to the early gene regulators and replication proteins,
      and the DNA sequences recognized by the regulators share very limited homology to those of the
      VT2-encoding 933W phage carried by the EHEC O157:H7 strain EDL933 reported by Plunkett et al.
      (J. Bacteriol., p1767-1778, 181, 1999), although the sequences corresponding to the structural
      components are almost identical. These data suggest that these two phages were derived from a
      common ancestral phage and that either or both of them underwent multiple genetic
      rearrangements. An IS629 insertion was found downstream of the stx2B gene and upstream of the
      lysis gene S, and this might be responsible for the absence of plaque-forming activity in the
      lysate obtained after inducing treatments.
AU  - Makino K
AU  - Yokoyama K
AU  - Kubota Y
AU  - Watanabe M
AU  - Kimura S
AU  - Yutsudo CH
AU  - Kurokawa K
AU  - Ishii K
AU  - Hattori M
AU  - Abe H
AU  - Yamamoto K
AU  - Hayashi T
AU  - Yasunaga T
AU  - Honda T
AU  - Sasakawa C
AU  - Shinagawa H
PT  - Journal Article
TA  - Genes Genet. Syst.
JT  - Genes Genet. Syst.
SO  - Genes Genet. Syst. 1999 74: 227-239.

PMID- 233262
VI  - 277
DP  - 1979
TI  - Inactivation of restriction endonuclease BamNx after infection with phage UNR2.
PG  - 64-65
AB  - A host-controlled restriction-modification system is a means of protection by a
      host against attacks of bacteriophages.  Recently, coliphage T3 and T7 have
      been found to overcome the host-controlled restriction-modification systems of
      their host strains Escherichia coli B and K, but details of the mechanism are
      not well understood at present.  We have found that a Bacillus subtilis phage
      UNR2rH, a mutant of UNR2, also has the ability to overcome the
      restriction-modification system of B. amyloliquefaciens strain N, and detected
      a BamNx inhibitor in cells infected with UNR2rH.
AU  - Makino O
AU  - Kawamura F
AU  - Saito H
AU  - Ikeda Y
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1979 277: 64-65.

PMID- 6255284
VI  - 179
DP  - 1980
TI  - Bacillus subtilis-Phage Phi1 overcomes host-controlled restriction by producing BamNx inhibitor protein.
PG  - 463-468
AB  - Bacillus amyloliquefaciens N produces two restriction enzymes, BamNI and BamNX.
      Subtilis-phage Phi1 is strongly restricted by BamNx.  We isolated Phi1rH, a
      mutant of phage Phi1, which overcame the BamNx-restriction by producing
      inhibitor.  This inhibitor inactivated BamNx specifically and reversibly.  The
      inhibitor directly interacted with BamNx and the inactivation might be the
      result of formation of a binary complex.  The inhibitory activity was sensitive
      to treatment with trypsin.  The molecular weight of the inhibitor protein was
      estimated to be approximately 20,000 daltons by gel filtration.
AU  - Makino O
AU  - Saito H
AU  - Ando T
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1980 179: 463-468.

PMID- 29773618
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Mariprofundus micogutta Strain ET2.
PG  - e00342-18
AB  - Mariprofundus micogutta strain ET2 was isolated in 2014 from a deep-sea hydrothermal field on
      the Bayonnaise Knoll of the Izu-Ogasawara arc. Here, we
      report its draft genome, which comprises 2,497,805 bp and contains 2,417
      predicted coding sequences.
AU  - Makita H
AU  - Nishi S
AU  - Takaki Y
AU  - Tanaka E
AU  - Nunoura T
AU  - Mitsunobu S
AU  - Takai K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00342-18.

PMID- 10449767
VI  - 96
DP  - 1999
TI  - Regulation of endonuclease activity by proteolysis prevents breakage of unmodified bacterial chromosomes by type I restriction enzymes.
PG  - 9757-9762
AB  - ClpXP-dependent proteolysis has been implicated in the delayed detection of restriction
      activity after the acquisition of the genes (hsdR, hsdM, and hsdS) that specify EcoKI and
      EcoAI, representatives of two families of type I restriction and modification (R-M) systems.
      Modification, once established, has been assumed to provide adequate protection against a
      resident restriction system. However, unmodified targets may be generated in the DNA of an
      hsd(+) bacterium as the result of replication errors or recombination-dependent repair. We
      show that ClpXP-dependent regulation of the endonuclease activity enables bacteria that
      acquire unmodified chromosomal target sequences to survive. In such bacteria, HsdR, the
      polypeptide of the R-M complex essential for restriction but not modification, is degraded in
      the presence of ClpXP. A mutation that blocks only the modification activity of EcoKI, leaving
      the cell with approximately 600 unmodified targets, is not lethal provided that ClpXP is
      present. Our data support a model in which the HsdR component of a type I restriction
      endonuclease becomes a substrate for proteolysis after the endonuclease has bound to
      unmodified target sequences, but before completion of the pathway that would result in DNA
      breakage.
AU  - Makovets S
AU  - Doronina VA
AU  - Murray NE
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1999 96: 9757-9762.

PMID- 14651617
VI  - 51
DP  - 2004
TI  - Is modification sufficient to protect a bacterial chromosome from a resident restriction endonuclease?
PG  - 135-147
AB  - It has been generally accepted that DNA modification protects the chromosome of a bacterium
      encoding a restriction and modification
      system. But, when target sequences within the chromosome of one such
      bacterium (Escherichia coli K-12) are unmodified, the cell does not
      destroy its own DNA; instead, ClpXP inactivates the nuclease, and
      restriction is said to be alleviated. Thus, the resident chromosome is
      recognized as 'self' rather than 'foreign' even in the absence of
      modification. We now provide evidence that restriction alleviation may
      be a characteristic of Type I restriction-modification systems, and
      that it can be achieved by different mechanisms. Our experiments
      support disassembly of active endonuclease complexes as a potential
      mechanism. We identify amino acid substitutions in a restriction
      endonuclease, which impair restriction alleviation in response to
      treatment with a mutagen, and demonstrate that restriction alleviation
      serves to protect the chromosome even in the absence of mutagenic
      treatment. In the absence of efficient restriction alleviation, a Type
      I restriction enzyme cleaves host DNA and, under these conditions,
      homologous recombination maintains the integrity of the bacterial
      chromosome.
AU  - Makovets S
AU  - Powell LM
AU  - Titheradge AJB
AU  - Blakely GW
AU  - Murray NE
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2004 51: 135-147.

PMID- 9593294
VI  - 28
DP  - 1998
TI  - ClpX and ClpP are essential for the efficient acquisition of genes specifying type IA and IB restriction systems.
PG  - 25-35
AB  - Efficient acquisition of genes that encode a restriction and modification system with
      specificities different from any already present in the recipient bacterium requires the
      sequential production of the new modification enzyme followed by the restriction activity in
      order that the chromosome of the recipient bacterium is protected against attack by the
      restriction endonuclease.  We show that ClpX and ClpP, the components of ClpXP protease, are
      necessary for the efficient transmission of the genes encoding EcoKI and EcoAI,
      representatives of two families of type I R-M systems, thus implicating ClpXP in the
      modulation of restriction activity.  Loss of ClpX imposed a bigger barrier than loss of ClpP,
      consistent with a dual role for ClpX, possibly as a chaperone and as a component of the ClpXP
      protease.  Transmission of genes specifying EcoKI was more dependent on ClpX and ClpP than
      transmission of the genes for EcoAI.  Sensitivity to absence of the protease was also
      influenced by the mode of gene transfer; conjugative transfer and transformation were more
      dependent on ClpXP than transduction.  In the absence of either ClpX or ClpP transfer of the
      EcoKI genes by P1-mediated transduction was impaired, transfer of the EcoAI genes was not.
AU  - Makovets S
AU  - Titheradge AJB
AU  - Murray NE
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1998 28: 25-35.

PMID- 9628369
VI  - 379
DP  - 1998
TI  - Restriction endonucleases can be used to confirm a structure of unusual DNA duplexes.
PG  - 625-630
AB  - Cyclic and polycyclic oligonucleotides were synthesized using chemical ligation.  Two types of
      catenanes with one and several intertwinings were produced.  The yield of these molecules
      depended on the ligation conditions and nucleotide sequence of the ligated oligonucleotide and
      its template.  Structure of ligation products was investigated and confirmed using restriction
      endonuclease MvaI.  Interaction of the synthesized molecules with restriction endonucleases
      SsoII, EcoRII and HindIII was also studied.
AU  - Maksimenko A
AU  - Gottikh MB
AU  - Kubareva EA
AU  - Fedorova OA
AU  - Shabarova ZA
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1998 379: 625-630.

PMID- 6255409
VI  - 8
DP  - 1980
TI  - A new restriction endonuclease from the anaerobic bacterium, Desulfovibrio desulfuricans, Norway.
PG  - 3125-3131
AB  - The purification and characterization of a new restriction endonuclease, DdeI,
      from a sulfate-reducing, anaerobic bacterium, Desulfovibrio desulfuricans,
      Norway, is reported.  The enzyme recognizes the sequence 5'-C-^T-N-A-G-3'
      3'-G-A-N-T-^C-5' and cleaves at the position indicated by the arrows.  The
      enzyme preparation obtained is suitable for restriction mapping and ligation.
AU  - Makula RA
AU  - Meagher RB
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1980 8: 3125-3131.

PMID- 9987133
VI  - 31
DP  - 1999
TI  - Masc2, a gene from Ascobolus encoding a protein with a DNA-methyltransferase activity in vitro, is dispensable for in vivo methylation.
PG  - 331-338
AB  - We have shown previously that masc1, a gene encoding a putative C5-DNA-methyltransferase, was
      necessary for the de novo 'Methylation Induced Premeiotically' (MIP) process and sexual
      reproduction in Ascobolus, whereas it was dispensable for maintenance methylation.  A second
      MTase gene from Asobolus, masc2, encodes a protein, Masc2, which possesses the large
      amino-terminal part characteristic of eukaryotic maintenance MTases.  In vitro assays have
      shown that Masc2 displays a methylation activity, suggesting that it might be the MTase
      responsible for maintenance methylation.  To check its function in vivo, we engineered a
      disruption of the masc2 gene.  The resulting mutant strains did not exhibit any particular
      phenotype during either vegetative growth or sexual reproduction.  Neither the masc2 mutation
      nor the double masc1 masc2 mutation had any detectable effect upon the maintenance of the
      pre-existing methylation of single gene copies previously subjected to MIP, natural
      retroelement-like repeats and tandemly repeated rDNA.  The masc2 mutation did not alter either
      MIP or the other de novo methylation process that operates in vegetative cells.  Nor did it
      impair the meiotic process of methylation transfer.  These results suggest that at least a
      third MTase gene responsible for maintenance and vegetative de novo methylation is present in
      Asobolus.
AU  - Malagnac F
AU  - Gregoire A
AU  - Goyon C
AU  - Rossignol J-L
AU  - Faugeron G
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1999 31: 331-338.

PMID- 9346245
VI  - 91
DP  - 1997
TI  - A gene essential for de novo methylation and development in Ascobolus reveals a novel type of eukaryotic DNA methyltransferase structure.
PG  - 281-290
AB  - Molecular mechanisms determining methylation patterns in eukaryotic genomes still remain
      unresolved.  We have characterized, in Ascobolus, a gene for de novo methylation.  This novel
      eukaryotic gene, masc1, encodes a protein that has all motifs of the catalytic domain of
      eukaryotic C5-DNA-methyltransferases but is unique in that it lacks a regulatory N-terminal
      domain.  The disruption of masc1 has no effect on viability or methylation maintenance but
      prevents the de novo methylation of DNA repeats, which takes place after fertilization,
      through the methylation induced premeiotically (MIP) process.  Crosses between parents
      harboring the masc1 disruption are arrested at an early stage of sexual reproduction,
      indicating that the activity of Masc1, the product of the gene, is crucial in this
      developmental process.
AU  - Malagnac F
AU  - Wendel B
AU  - Goyon C
AU  - Faugeron G
AU  - Zickler D
AU  - Rossignol J-L
AU  - Noyer-Weidner M
AU  - Vollmayr P
AU  - Trautner TA
AU  - Walter J
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1997 91: 281-290.

PMID- 23833134
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Multidrug-Resistant Pseudomonas aeruginosa Strain VRFPA02, Isolated from a Septicemic Patient in India.
PG  - e00425-13
AB  - Multidrug-resistant Pseudomonas aeruginosa strains, which are notable nosocomial  pathogens,
      have greatly increased the mortality rate of septicemic patients due
      to treatment failure. Here, we report the draft genome sequence of P. aeruginosa
      strain VRFPA02, a human bloodstream isolate that has phenotypically proven to be
      resistant to a broad spectrum of antibiotics.
AU  - Malathi J
AU  - Murugan N
AU  - Umashankar V
AU  - Bagyalakshmi R
AU  - Madhavan HN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00425-13.

PMID- 
VI  - 2
DP  - 1981
TI  - The use of restriction enzymes in genetic engineering.
PG  - 129-173
AB  - When the coliphage lambda is grown on E. coli strain C and then attempts are
      made to grow it in E. coli K12, it grows very poorly (Bertani and Weigle, 1953.
      It was shown that this was caused by a response of the host to the phage.
      Since the growth of the phage was restricted, the mechanism used by the E. coli
      was called a "restriction system".  Phage grown originally on K12 could be
      regrown efficiently on K12, and this implies that the host also possessed a
      means of protecting the phage from this restriction and the mechanism became a
      "restriction-modification system".  Meselson and Yuan (1968) incubated lambda
      DNA, which had been grown in E. coli K12, and lambda DNA from E. coli C with an
      extract from K12.  Analysis by sedimentation through a sucrose gradient showed
      that the k.K DNA was unaffected but that k.C DNA was degraded.  This
      degradation was limited in extent and suggested that the restriction system
      (enzyme) only hydrolysed the DNA at a small number of sites.  As it happens the
      restriction enzyme from E. coli K does not cut the DNA at specific sequences
      and hence has not been greatly exploited for genetic engineering. 	The first
      site specific restriction enzyme was discovered by Smith and Wilcox (1970)
      during their studies on recombination in Haemophilus influenzae.  They showed
      by viscometry that a Haemophilus cell extract degraded DNA from the
      bacteriophage P22 but had no effect on DNA from Haemophilus itself.  Using the
      purified enzyme Kelly and Smith (1970) showed that the breaks produced in T7
      DNA all occurred at the symmetrical sequence       5' ....G p T p Py^p Pu p A p
      C....3'	       3' ....C p A p Pu p^ Py p T p G...5' where the hydrolysis occurs
      at the phosphodiester bonds indicated by the arrows.  A catalogue of
      restriction endonucleases isolated since then now numbers over 250 examples,
      although it is not certain that all these are in fact different enzymes (Table
      1).  Excellent earlier reviews are by Roberts (1976) and Modrich (1979).
AU  - Malcolm ADB
PT  - Journal Article
TA  - Genet. Eng. (N Y)
JT  - Genet. Eng. (N Y)
SO  - Genet. Eng. (N Y) 1981 2: 129-173.

PMID- 3011543
VI  - 14
DP  - 1986
TI  - Binding sites of restriction endonucleases.
PG  - 202-204
AB  - There are now more than 600 known restriction endonucleases and these enzymes recognize more
      than 100 different base sequences in their DNA substrates.  When considering binding sites we
      must, of course, consider both the protein and the nucleic acid.  Many, but by no means all,
      of the nucleic acid sequences recognized show a two-fold rotational axis of symmetry, for
      example, BamHI recognizes GGATCCCCTAGG and HindIII cleaves at AAGCTTTTCGAA.   One might
      therefore expect this symmetry to be reflected in the protein's subunit structure and
      disposition of active sites.  While this probably holds in most cases, it is certainly not
      universally true because some of the nucleases are active as monomers (Koncz et al., 1978). 	
      Another feature worthy of comment is the predominance of G-C base-pairs in the recognition
      sites.  This can be illustrated by the fact that, although many enzymes (e.g. ApaI, SacII,
      BsePI, NarI, NaeI, SmaI) which recognize sequences composed entirely of GC's have been known
      for some time, the first all AT-recognizing enzyme (AhaIII) was only discovered very recently
      (Whitehead & Brown, 1982).  It is, of course, possible that the reasons for this bias are
      evolutionary rather then mechanistic, but to date there are no useful suggestions under either
      heading to account for this.
AU  - Malcolm ADB
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 1986 14: 202-204.

PMID- 6257569
VI  - 8
DP  - 1980
TI  - Measurement of differential reactivities at restriction endonuclease sites.
PG  - 734-735
AB  - Type II restriction endonucleases recognize and hydrolyse DNA at specific sites, often a
      symmetrical four- or six-base-pair sequence.  Although the presence of the unmethylated
      recognition sequence is both a necessary and sufficient condition for cleavage, it has been
      recognized for some time that the rate of cleavage is not constant and presumably depends on
      neighboring sequences.  Only a few attempts have so far been made to quantify these
      observations, but the methods used, involving either the use of deletion mutants or analysis
      of the data by a comparatively sophisticated computer analysis, may not be suitable for
      routine use.
AU  - Malcolm ADB
AU  - Mofatt JR
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 1980 8: 734-735.

PMID- 6269624
VI  - 655
DP  - 1981
TI  - Differential reactivities at restriction enzyme sites.
PG  - 128-135
AB  - A method has been developed to measure the rates of digestion by restriction
      enzymes at individual sites.  This involves a simple arithmetical treatment of
      the integrated areas from a densitometer scan of an ethidium bromide stained
      gel.  We have used this method to study the digestion by HpaI, HincII and SalI
      of pBR322 and PhiX174 DNA, and the effect of various DNA binding ligands.  One
      of the two HpaI sites in PhiX174 DNA is much more sensitive to inhibition by
      ligands such as netropsin, which display a preference for AT base pairs, than
      is the other site.  Inspection of the sequences flanking the restriction sites
      shows that the former contains a much higher proportion of AT base-pairs than
      does the latter.  The opposite phenomenon is observed with the two HincII sites
      in pBR322.  This illustrates the importance of neighbouring sequences in the
      interaction between restriction enzymes and their cleavage sites in DNA.
AU  - Malcolm ADB
AU  - Moffat JR
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1981 655: 128-135.

PMID- 6297562
VI  - 699
DP  - 1982
TI  - Differential inhibition of a restriction enzyme by quinoxaline antibiotics.
PG  - 211-216
AB  - The inhibition of cleavage by HpaI at two well-defined restriction sites in
      linearised PhiX174-RF DNA by quinoxaline antibiotics has been investigated.
      Echinomycin, which displays a certain preference for binding to GC basepairs,
      inhibits cleavage at one site much more than the other, whereas triostin A,
      which displays less pronounced sequence-selectivity, inhibits both sites about
      equally.  Other congeners inhibit reaction at the two sites with varying
      effectiveness.  The results demonstrate the usefulness of studying inhibition
      of cleavage at specific sites by restriction enzymes as a means of exploring
      the specificity of DNA-ligand interactions.
AU  - Malcolm ADB
AU  - Moffatt JR
AU  - Fox KR
AU  - Waring MJ
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1982 699: 211-216.

PMID- Not carried by PubMed...
VI  - 9
DP  - 1987
TI  - Restriction enzymes and DNA.
PG  - 193-222
AB  - The discovery of restriction and modification enzymes, which proved to be a
      major turning point in the progress of molecular biology, was a consequence of
      a bacteriological observation in the early 1950s (Luria and Human, 1952;
      Bertani and Weigle, 1953).  The two groups reported the curious behaviour of
      phage grown on two different strains of bacteria.  Phages propagated on one
      strain were found to grow poorly on the second and vice versa.  However, the
      few phages that escaped restriction could then grow well on the new host, thus
      being modifified in a way that afforded them protection from the restriction
      imposed by the host.
AU  - Malcolm ADB
AU  - Snounou G
PT  - Journal Article
TA  - Top. Mol. Struct. Biol.
JT  - Top. Mol. Struct. Biol.
SO  - Top. Mol. Struct. Biol. 1987 9: 193-222.

PMID- 21914902
VI  - 193
DP  - 2011
TI  - Genome Sequence of Lactobacillus pentosus IG1, a Strain Isolated from Spanish-Style Green Olive Fermentations.
PG  - 5605
AB  - Lactobacillus pentosus is the most prevalent lactic acid bacterium in Spanish-style green
      olive fermentations. Here we present the draft genome
      sequence of L. pentosus IG1, a bacteriocin-producing strain with
      biotechnological and probiotic properties isolated from this food
      fermentations.
AU  - Maldonado-Barragan A
AU  - Caballero-Guerrero B
AU  - Lucena-Padros H
AU  - Ruiz-Barba JL
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5605.

PMID- 23347599
VI  - 13
DP  - 2013
TI  - Phylogeographic evidence of cognate recognition site patterns and transformation efficiency differences in H. pylori: theory of strain dominance.
PG  - 14
AB  - Background: Helicobacter pylori has diverged in parallel to its human host, leading to
      distinct phylogeographic populations. Recent evidence suggests that in the current human
      mixing in Latin America, European H. pylori (hpEurope) are increasingly dominant at the
      expense of Amerindian haplotypes (hspAmerind). This phenomenon might occur via DNA
      recombination, modulated by restriction-modification systems (RMS), in which differences in
      cognate recognition sites (CRS) and in active methylases will det rmine direction and
      frequency of gene flow. We hypothesized that genomes from hspAmerind strains that evolved from
      a small founder population have lost CRS for RMS and active methylases, promoting hpEurope's
      DNA invasion. We determined the observed and expected frequencies of CRS for RMS in DNA from 7
      H. pylori whole genomes and 110 multilocus sequences. We also measured the number of active
      methylases by resistance to in vitro digestion by 16 restriction enzymes of genomic DNA from 9
      hpEurope and 9 hspAme rind strains, and determined the direction of DNA uptake in co-culture
      experiments of hspAmerind and hpEurope strains.Results: Most of the CRS were underrepresented
      with consistency between whole genomes and multilocus sequences. Although neither the
      frequency of CRS nor the number of active methylases differ among the bacterial populations
      (average 8.6 +/- 2.6), hspAmerind strains had a restriction profile distinct from that in
      hpEurope strains, with 15 recognition sites accounting for the differences. Am erindians
      strains also exhibited higher transformation rates than European strains, and were more
      susceptible to be subverted by larger DNA hpEurope-fragments than vice versa.Conclusions: The
      geographical variation in the pattern of CRS provides evidence for ancestral differences in
      RMS representation and function, and the transformation findings support the hypothesis of
      Europeanization of the Amerindian strains in Latin America via DNA recombination.
AU  - Maldonado-Contreras A
AU  - Mane SP
AU  - Zhang X-S
AU  - Pericchi L
AU  - Alarcon T
AU  - Contreras M
AU  - Linz B
AU  - Blaser MJ
AU  - Dominguez-Bello MG
PT  - Journal Article
TA  - BMC Microbiol.
JT  - BMC Microbiol.
SO  - BMC Microbiol. 2013 13: 14.

PMID- 
VI  - 107
DP  - 2007
TI  - Geographical differences in restriction-modification system cognate recognition sites in Helicobacter pylori.
PG  - 656
AB  - Restriction-modification systems provide a barrier to horizontal gene transfer. Restriction
      Endonucleases (RE) identify cognate DNA sequences and cleave the DNA, unless it is methylated.
      H. pylori, an obligate bacterium of the human stomach, is highly recombinant. But in which
      direction does recombination occurs? As human hosts mix, H. pylori strains (showing geographic
      clusters) also mix, but there seems to be a shift towards predominance of European alleles in
      cultured strains from Latin America. Why are Amerindian strains being lost? Are they being
      subverted by recombination? We hypothesize that European strains would have lower number of
      restriction sites than Amerindian strains, and an increased capability to subvert them. To
      test this hypothesis, we compared the number of cognate restriction sites in the DNA from H.
      pylori strains from Asian, European, African and Amerindian hosts. We analyzed in silico the
      restriction profiles of DNA sequences corresponding to 7 concatenated housekeeping gene
      sequences. DNA was digested in silico with 16 restriction enzymes (RE) previously reported to
      be present in H. pylori strains. Phylogenetic analysis showed 4 clusters by host origin, with
      Amerindian strains close to Asian strains. There was high variability in the number of cognate
      RE sites within and between the phylogroups. All strains had cognate sequences for at least 13
      of the 16 tested RE, and there were no significant differences in the number of cognate sites
      by phylogroup (p>0.05). The average number of restriction sites was 5.3 for European strains,
      5.2 for Amerindian, 5.5 for Asian and 4.9 for African strains. The results show little
      differences based in the number of cognate restriction sites between the phylogroups. However
      the possibility of RM differences among strain phylogroups given by the number of active
      methylases cannot be assessed in silico. In vitro assays need to be performed to test for the
      real susceptibility to RE digestion, which assesses the methylase functions.
AU  - Maldonado-Contreras AL
AU  - Olagibel L
AU  - Dominguez-Bello MG
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 2007 107: 656.

PMID- 21304651
VI  - 1
DP  - 2009
TI  - Complete genome sequence of Halogeometricum borinquense type strain (PR3).
PG  - 150-159
AB  - Halogeometricum borinquense Montalvo-Rodriguez et al. 1998 is the type species of the genus,
      and is of phylogenetic interest because of its distinct location
      between the halobacterial genera Haloquadratum and Halosarcina. H. borinquense
      requires extremely high salt (NaCl) concentrations for growth. It can not only
      grow aerobically but also anaerobically using nitrate as electron acceptor. The
      strain described in this report is a free-living, motile, pleomorphic,
      euryarchaeon, which was originally isolated from the solar salterns of Cabo Rojo,
      Puerto Rico. Here we describe the features of this organism, together with the
      complete genome sequence, and annotation. This is the first complete genome
      sequence of the halobacterial genus Halogeometricum, and this 3,944,467 bp long
      six replicon genome with its 3937 protein-coding and 57 RNA genes is part of the
      Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Malfatti S et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2009 1: 150-159.

PMID- 22933775
VI  - 194
DP  - 2012
TI  - Genome Sequence of Acinetobacter sp. Strain HA, Isolated from the Gut of the Polyphagous Insect Pest Helicoverpa armigera.
PG  - 5156
AB  - In this study, Acinetobacter sp. strain HA was isolated from the midgut of a fifth-instar
      larva of Helicoverpa armigera. Here, we report the draft genome
      sequence (3,125,085 bp) of this strain that consists of 102 contigs, 2,911
      predicted coding sequences, and a G+C content of 41%.
AU  - Malhotra J
AU  - Dua A
AU  - Saxena A
AU  - Sangwan N
AU  - Mukherjee U
AU  - Pandey N
AU  - Rajagopal R
AU  - Khurana P
AU  - Khurana JP
AU  - Lal R
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5156.

PMID- 22943564
VI  - 279
DP  - 2012
TI  - Role of DNA methylation in growth and differentiation in Physcomitrella patens and characterization of cytosine DNA methyltransferases.
PG  - 4081-4094
AB  - Epigenetic mechanisms such as DNA methylation are known to regulate important developmental
      processes in higher eukaryotes. However, little
      is known about the necessity and role of this process in early land
      plants. Using the methyltransferase (MTase) inhibitor zebularine
      (1-(beta-d-ribofuranosyl)-1,2-dihydropyrimidine-2-one), the impact of
      loss of genome-wide methylation on the overall development in
      Physcomitrellapatens was analyzed. It is observed that various aspects
      of growth and differentiation during gametophyte development become
      aberrant. A search for the core molecular components of methylation
      machinery, cytosine DNA MTases, revealed the presence of seven loci in
      the P.patens genome. Five of the loci code for MTases that are similar
      to corresponding proteins in higher plants, while two MTases appear
      specific to P.patens and are closely related to human DNMT3a and
      DNMT3b, respectively. These proteins possess all the conserved
      catalytic motifs characteristic of MTases and a domain of unknown
      function, DUF3444. Association of these highly conserved motifs with a
      DUF has not been reported in any of the MTases known so far. All the
      seven genes are differentially but ubiquitously expressed in
      gametophytes at low levels. Subcellular localization of GFP-fused
      proteins shows patterns of distribution that can be correlated with
      their putative cellular functions. This work bridges the knowledge of
      MTases in P.patens and makes this simple model plant accessible for
      studies on epigenetic aspects that remain intractable in higher plants.
AU  - Malik G
AU  - Dangwal M
AU  - Kapoor S
AU  - Kapoor M
PT  - Journal Article
TA  - FEBS J.
JT  - FEBS J.
SO  - FEBS J. 2012 279: 4081-4094.

PMID- 25395634
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Lactobacillus plantarum CMPG5300, a Human Vaginal Isolate.
PG  - e01149-14
AB  - The draft genome of a highly auto-aggregating Lactobacillus plantarum strain isolated from a
      human vagina is reported. The peculiar phenotype also provides an
      adhesive and co-aggregative potential with various pathogens, which could be of
      significance in the vaginal niche. Detailed genome analysis could aid in
      identifying the adhesins of the strain.
AU  - Malik S
AU  - Siezen RJ
AU  - Renckens B
AU  - Vaneechoutte M
AU  - Vanderleyden J
AU  - Lebeer S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01149-14.

PMID- 10066745
VI  - 274
DP  - 1999
TI  - Effect of tetrahydropyrimidine derivatives on protein-nucleic acids interaction.
PG  - 6920-6929
AB  - 2-Methyl-4-carboxy,5-hydroxy-3,4,5,5-tetrahydropyrimidine (THP(A) or hydroxyectoine) and
      2-methyl,4-carboxy-3,4,5,6-tetrahydropyrimidine (THP(B) or ectoine) are now recognized as
      ubiquitous bacterial osmoprotectants.  To evaluate the impact of tetrahydropyrimidine
      derivatives on protein-DNA interaction and on restriction-modification systems, we have
      examined their effect on the cleavage of plasmid DNA by 10 type II restriction endonucleases.
      THP(A) completely arrested the cleavage of plasmid and bacteriophage lambda DNA by EcoRI
      endonuclease at 0.4 mM and the oligonucleotide (d(CGCGAATTCGCG))2 at about 4.0 mM.  THP(B) was
      10-fold less effective than THP(A), whereas for betaine and proline, a notable inhibition was
      observed only at 100 mM.  Similar effects of THP(A) were observed for all tested restriction
      endonucleases, except for SmaI and PvuII, which were inhibited only partially at 50mM THP(A).
      No effect of THP(A) on the activity of DNase I, RNase A, and Taq DNA polymerase was noticed.
      Gel shift assays showed that THP(A) inhibited the EcoRI-(d-(CGCGAATTCGCG))2 complex formation,
      whereas facilitated diffusion of EcoRI along the DNA was not affected.  Methylation of the
      carboxy group significantly decreased the activity of THPs, suggesting that their zwitterionic
      character is essential for the inhibition effect.  Possible mechanisms of inhibition, role of
      THPs in the modulation of the protein-DNA interaction, and the in vivo relevance of the
      observed phenomena are discussed.
AU  - Malin G
AU  - Iakobashvili R
AU  - Lapidot A
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1999 274: 6920-6929.

PMID- 26941159
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Two Extensively Drug-Resistant Strains of Mycobacterium tuberculosis Belonging to the Euro-American S Lineage.
PG  - e01771-15
AB  - We report the whole-genome sequencing of two extensively drug-resistant tuberculosis strains
      belonging to the Euro-American S lineage. The RSA 114 strain
      showed single-nucleotide polymorphisms predicted to have drug efflux activity.
AU  - Malinga LA
AU  - Abeel T
AU  - Desjardins CA
AU  - Dlamini TC
AU  - Cassell G
AU  - Chapman SB
AU  - Birren BW
AU  - Earl AM
AU  - van der Walt M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01771-15.

PMID- 1329843
VI  - 10
DP  - 1992
TI  - Locating binding sites for the carcinogen N-acetoxy-N-acetyl-2-aminofluorene using restriction enzyme inhibition assays.
PG  - 83-96
AB  - Restriction enzyme inhibition studies have been employed to map the locations of high affinity
      binding sites of the carcinogen N-acetoxy-N-acetyl-2-aminofluorene (acetoxyAAF) on pBR322,
      phiX174 and SV40 DNAs. Bound carcinogen levels were kept low (less than 20 bound AAF moieties
      per DNA molecule) in order to observe only the binding to the high affinity sites. Inhibition
      of certain restriction enzymes was observed in a limited number of locations on these DNAs.
      Inhibition increased as bound AAF increased and the particular restriction enzymes inhibited
      varied with location. On all three DNAs, activities of these enzymes was not affected in other
      locations. Comparison of the sequences at the sites of inhibition on the three DNAs indicates
      that all sites have common sequence elements: the presence of either the sequence
      T(C/G)TT(G/C) or the sequence T(G/C)CTT(G/C).
AU  - Mallamaci MA
AU  - Bascoy ML
AU  - Brown J
AU  - Combates NJ
AU  - Winkle SA
PT  - Journal Article
TA  - J. Biomol. Struct. Dyn.
JT  - J. Biomol. Struct. Dyn.
SO  - J. Biomol. Struct. Dyn. 1992 10: 83-96.

PMID- 11504918
VI  - 98
DP  - 2001
TI  - CmC(A/T)GG DNA methylation in mature B cell lymphoma gene silencing.
PG  - 10404-10409
AB  - DNA methylation has been linked to gene silencing in cancer. Primary effusion lymphoma (PEL)
      and myeloma are lymphoid malignancies that arise
      from terminally differentiated B cells. Interestingly, PEL do not express
      immunoglobulins or most B lineage-specific genes. The B cell-specific B29
      (Igbeta/CD79b) gene is silenced in PEL and some myelomas but is expressed
      in other normal and malignant B cells. B29 expression was reactivated in
      PEL by demethylating and histone deacetylase inhibiting treatments.
      Bisulfite sequencing revealed two types of DNA methylation in silenced B29
      promoters: at conventional CpG and at CC(A/T)GG B29 promoter sites. The
      pattern of methylated CpG ((m)CpG) and C(m)C(A/T)GG B29 promoter
      methylation observed was similar to that recently reported for epigenetic
      silencing of an integrated retrovirus. Methylation of C(m)C(A/T)GG sites
      in the B29 promoter significantly repressed in vivo transcriptional
      activity. Also, methylation of a central conserved C(m)CTGG B29 promoter
      site blocked the binding of early B cell factor. This methylated motif
      formed DNA-protein complexes with nuclear extracts from all cell types
      examined. Therefore, C(m)C(A/T)GG methylation may represent an important
      type of epigenetic marker on mammalian DNA that impacts transcription by
      altering DNA-protein complex formation.
AU  - Malone CS
AU  - Miner MD
AU  - Doerr JR
AU  - Jackson JP
AU  - Jacobsen SE
AU  - Wall R
AU  - Teitell M
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2001 98: 10404-10409.

PMID- 28385856
VI  - 5
DP  - 2017
TI  - Updated Reference Genome Sequence and Annotation of Mycobacterium bovis AF2122/97.
PG  - e00157-17
AB  - We report here an update to the reference genome sequence of the bovine tuberculosis bacillus
      Mycobacterium bovis AF2122/97, generated using an
      integrative multiomics approach. The update includes 42 new coding sequences
      (CDSs), 14 modified annotations, 26 single-nucleotide polymorphism (SNP)
      corrections, and disclosure that the RD900 locus, previously described as absent
      from the genome, is in fact present.
AU  - Malone KM
AU  - Farrell D
AU  - Stuber TP
AU  - Schubert OT
AU  - Aebersold R
AU  - Robbe-Austerman S
AU  - Gordon SV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00157-17.

PMID- 7473738
VI  - 253
DP  - 1995
TI  - Structure-guided analysis reveals nine sequence motifs conserved among DNA amino-methyl-transferases, and suggests a catalytic mechanism for these enzymes.
PG  - 618-632
AB  - Previous X-ray crystallographic studies have revealed that the catalytic domain of a DNA
      methyltransferase (Mtase) generating C5-methylcytosine bears a striking structural similarity
      to that of a Mtase generating N6-methyladenine.  Guided by this common structure, we performed
      a multiple sequence alignment of 42 amino-Mtases (N6-adenine and N4-cytosine).  This
      comparison revealed nine conserved motifs, corresponding to the motifs I to VIII and X
      previously defined in C5-cytosine Mtases.  The amino and C5-cytosine Mtases thus appear to be
      more closely related than has been appreciated.  The amino Mtases could be divided into three
      groups, based on the sequential order of motifs, and this variation in order may explain why
      only two motifs were previously recognized in the amino Mtases.  The amino and C5-cytosine
      Mtases thus appear to be more closely related than has been appreciated.  The amino Mtases
      could be divided into three groups, based on the sequential order of motifs, and this
      variation in order may explain why only two motifs were previously recognized in the amino
      Mtases.  The Mtases grouped in this way show several other group-specific properties,
      including differences in amino acid sequence, molecular mass and DNA sequence specificity.
      Surprisingly, the N4-cytosine and N6-adenine Mtases do not form separate groups.  These
      results have implications for the catalytic mechanisms, evolution and diversification of ths
      family of enzymes.  Furthermore, a comparative analysis of the S-adenosyl-L-methionine and
      adenine/cytosine binding pockets suggests that, stucturally and functionally, they are
      remarkably similar to one another.
AU  - Malone T
AU  - Blumenthal RM
AU  - Cheng X
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1995 253: 618-632.

PMID- Not carried by PubMed...
VI  - 6
DP  - 1993
TI  - The target recognition domains from the methyltransferases of II class have common subdomains.
PG  - 46
AB  - The proteins of the class II restriction-modification systems are very interesting objects for
      biotechnology. Both endonuclease and methyltransferase enzymes recognize identical DNA target
      sites, but they are not significantly similar in their amino acid sequences. Recently,
      alignment for m5C-methyltransferases (m5C-Mets) was done and common domains (from 1 to 10) for
      these proteins were identified. The target recognition domain (TRDs) for BsuPhi3T and SprI
      m5C-Mets which recognize a specific DNA site were determined by site-directed mutagenesis. The
      location of TRDs is between domains 8 and 9, which were determined from the alignment of
      m5C-Met sequences. The size of TRDs varies from 86 to 274 amino acids. It was shown that some
      of the homologous sequences are within the TRD. We analyzed TRDs from 18 m5C-Met sequences for
      the presence of common subsequences and compared the subsequences with the restriction and
      methyltransferase enzyme sequences.
AU  - Maltchenko S
PT  - Journal Article
TA  - Protein Engineering Suppl.
JT  - Protein Engineering Suppl.
SO  - Protein Engineering Suppl. 1993 6: 46.

PMID- 19161295
VI  - 48
DP  - 2009
TI  - Impact of 7,8-Dihydro-8-oxoguanine on Methylation of the CpG Site by Dnmt3a (dagger).
PG  - 1361-1368
AB  - 7,8-Dihydro-8-oxoguanine (8-oxoG) is a ubiquitous oxidative DNA lesion resulting from injury
      to DNA via reactive oxygen species. 8-oxoG lesions
      may play a role in the formation of aberrant DNA methylation patterns
      during carcinogenesis. In this study, we assessed the effects of 8-oxoG on
      methylation and complex formation of nine 30-mer oligodeoxynucleotide
      duplexes by the catalytic domain of murine Dnmt3a DNA methyltransferase
      (Dnmt3a-CD). The effects of 8-oxoG on the methylation rate of
      hemimethylated duplexes varied from a 25-fold decrease to a 1.8-fold
      increase, depending on the position of the lesion relative to the
      Dnmt3a-CD recognition site (CpG) and target cytosine (C). The most
      significant effect was observed when 8-oxoG replaced guanine within the
      recognition site immediately downstream of the target cytosine.
      Fluorescence polarization experiments with fluorescein-labeled duplexes
      revealed that two molecules of Dnmt3a-CD bind per duplex, generating
      sigmoid binding curves. Duplexes exhibiting the highest apparent binding
      cooperativity formed the least stable 1:2 complexes with Dnmt3a-CD and
      were methylated at the lowest rate. Kinetic analyses disclosed the
      formation of very stable nonproductive enzyme-substrate complexes with
      hemimethylated duplexes that act as suicide substrates of Dnmt3a-CD. The
      presence of 8-oxoG within the CpG site downstream of the target cytosine
      markedly diminished productive versus nonproductive binding. We propose
      that 8-oxoG located adjacent to the target cytosine interferes with
      methylation by weakening the affinity of DNA for Dnmt3a-CD, thereby
      favoring a nonproductive binding mode.
AU  - Maltseva DV
AU  - Baykov AA
AU  - Jeltsch A
AU  - Gromova ES
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2009 48: 1361-1368.

PMID- 26823578
VI  - 4
DP  - 2016
TI  - Complete Genomic Sequence of an Avian Pathogenic Escherichia coli Strain of Serotype O7:HNT.
PG  - e01611-15
AB  - Avian pathogenic Escherichia coli (APEC) is associated with colibacillosis in poultry. Here,
      we present the first complete sequence of an APEC strain of the
      O7:HNT serotype and ST73 sequence type, isolated from a broiler with cellulitis.
      Complete genomes of APEC with distinct genetic backgrounds may be useful for
      comparative analysis.
AU  - Maluta RP
AU  - Nicholson B
AU  - Logue CM
AU  - Nolan LK
AU  - Rojas TC
AU  - Dias-da-Silveira W
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01611-15.

PMID- 19453271
VI  - 390
DP  - 2009
TI  - Dimeric/oligomeric DNA methyltransferases: an unfinished story.
PG  - 835-844
AB  - DNA methyltransferases (MTases) are enzymes that carry out post-replicative sequence-specific
      modifications. The initial
      experimental data on the structure and kinetic characteristics of the
      EcoRI MTase led to the paradigm that type II systems comprise dimeric
      endonucleases and monomeric MTases. In retrospect, this was logical
      because, while the biological substrate of the restriction endonuclease
      is two-fold symmetrical, the in vivo substrate for the MTase is
      generally hemi-methylated and, hence, inherently asymmetric. Thus, the
      paradigm was extended to include all DNA MTases except the more complex
      bifunctional type I and type III enzymes. Nevertheless, a gradual
      enlightenment grew over the last decade that has changed the accepted
      view on the structure of DNA MTases. These results necessitate a more
      complex view of the structure and function of these important enzymes.
AU  - Malygin EG
AU  - Evdokimov AA
AU  - Hattman S
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 2009 390: 835-844.

PMID- 11376154
VI  - 29
DP  - 2001
TI  - A dual role for substrate S-adenosyl-L-methionine in the methylation reaction with bacteriophage T4 Dam DNA-[N6-adenine]-methyltransferase.
PG  - 2361-2369
AB  - The fluorescence of 2-aminopurine (2A)-substituted duplexes (contained in the GATC target
      site) was investigated by titration with T4 Dam DNA-(N6-adenine)-methyltransferase. With an
      unmethylated target (2A/A duplex) or its methylated derivative (2A/mA duplex), T4 Dam produced
      up to a 50-fold increase in fluorescence, consistent with 2A being flipped out of the DNA
      helix. Though neither S-adenosyl-L-homocysteine nor sinefungin had any significant effect,
      addition of substrate S-adenosyl-L-methionine (AdoMet) sharply reduced the Dam-induced
      fluorescence with these complexes. In contrast, AdoMet had no effect on the fluorescence
      increase produced with an 2A/2A double-substituted duplex. Since the 2A/mA duplex cannot be
      methylated, the AdoMet-induced decrease in fluorescence cannot be due to methylation per se.
      We propose that T4 Dam alone randomly binds to the asymmetric 2A/A and 2A/mA duplexes, and
      that AdoMet induces an allosteric T4 Dam conformational change that promotes reorientation of
      the enzyme to the strand containing the native base. Thus, AdoMet increases enzyme
      binding-specificity, in addition to serving as the methyl donor. The results of
      pre-steady-state methylation kinetics are consistent with this model.
AU  - Malygin EG
AU  - Evdokimov AA
AU  - Zinoviev VV
AU  - Ovechkina LG
AU  - Lindstrom WM
AU  - Reich NO
AU  - Schlagman SL
AU  - Hattman S
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2001 29: 2361-2369.

PMID- 22260147
VI  - 47
DP  - 2012
TI  - DNA methyltransferases: Mechanistic models derived from kinetic analysis.
PG  - 97-193
AB  - The sequence-specific transfer of methyl groups from donor S-adenosyl-L-methionine (AdoMet) to
      certain positions of DNA-adenine or
      -cytosine residues by DNA methyltransferases (MTases) is a major form
      of epigenetic modification. It is virtually ubiquitous, except for some
      notable exceptions. Site-specific methylation can be regarded as a
      means to increase DNA information capacity and is involved in a large
      spectrum of biological processes. The importance of these functions
      necessitates a deeper understanding of the enzymatic mechanism(s) of
      DNA methylation. DNA MTases fall into one of two general classes; viz.
      amino-MTases and [C5-cytosine]-MTases. Amino-MTases, common in
      prokaryotes and lower eukaryotes, catalyze methylation of the exocyclic
      amino group of adenine ([N6-adenine]-MTase) or cytosine
      ([N4-cytosine]-MTase). In contrast, [C5-cytosine]-MTases methylate the
      cyclic carbon-5 atom of cytosine. Characteristics of DNA MTases are
      highly variable, differing in their affinity to their substrates or
      reaction products, their kinetic parameters, or other characteristics
      (order of substrate binding, rate limiting step in the overall
      reaction). It is not possible to present a unifying account of the
      published kinetic analyses of DNA methylation because different authors
      have used different substrate DNAs and/or reaction conditions.
      Nevertheless, it would be useful to describe those kinetic data and the
      mechanistic models that have been derived from them. Thus, this review
      considers in turn studies carried out with the most consistently and
      extensively investigated [N6-adenine]-, [N4-cytosine]- and
      [C5-cytosine]-DNA MTases.
AU  - Malygin EG
AU  - Hattman S
PT  - Journal Article
TA  - Crit. Rev. Biochem. Mol. Biol.
JT  - Crit. Rev. Biochem. Mol. Biol.
SO  - Crit. Rev. Biochem. Mol. Biol. 2012 47: 97-193.

PMID- 11058118
VI  - 28
DP  - 2000
TI  - Pre-steady state kinetics of bacteriophage T4 Dam DNA-[N6-adenine] methyltransferase: interaction with native (GATC) or modified sites.
PG  - 4207-4211
AB  - The DNA methyltransferase of bacteriophage T4 (T4 Dam MTase) recognizes the palindromic
      sequence GATC, and catalyzes transfer of the methyl group from S-adenosyl-L-methionine
      (AdoMet) to the N(6)-position of adenine [generating N(6)-methyladenine and
      S-adenosyl-L-homocysteine (AdoHcy)].  Pre-steady state kinetic analysis revealed that the
      methylation rate constant k(meth) for unmethylated and hemimethylated substrates (0.56 and
      0.47 s(-1), respectively) was at least 20-fold larger than the overall reaction rate constant
      k(cat) (0.023 s(-1)). This indicates that the release of products is the rate-limiting step in
      the reaction. Destabilization of the target-base pair did not alter the methylation rate,
      indicating that the rate of target nucleoside flipping does not limit k(meth). Preformed T4
      Dam MTase-DNA complexes are less efficient than preformed T4 Dam MTase-AdoMet complexes in the
      first round of catalysis. Thus, this data is consistent with a preferred route of reaction for
      T4 Dam MTase in which AdoMet is bound first; this preferred reaction route is not observed
      with the DNA-[C5-cytosine]-MTases.
AU  - Malygin EG
AU  - Lindstrom WM Jr
AU  - Schlagman SL
AU  - Hattman S
AU  - Reich NO
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2000 28: 4207-4211.

PMID- 12893823
VI  - 278
DP  - 2003
TI  - Bacteriophage T4Dam (DNA-(adenine-N6)-methyltransferase). Evidence for two distinct stages of methylation under single turnover conditions.
PG  - 41749-41755
AB  - We compared the (pre)steady-state and single turnover methylation kinetics of bacteriophage
      T4Dam (DNA-(adenine-N6)-methyltransferase)-mediated
      methyl group transfer from S-adenosyl-l-methionine (AdoMet) to
      oligodeoxynucleotide duplexes containing a single recognition site
      (palindrome 5'-GATC/5'-GATC) or some modified variant. T4Dam-AdoMet
      functions as a monomer under steady-state conditions (enzyme/DNA << 1),
      whereas under single turnover conditions (enzyme/DNA > 1), a catalytically
      active complex containing two Dam-AdoMet molecules is formed initially,
      and two methyl groups are transferred per duplex (to produce a methylated
      duplex and S-adenosyl-l-homocysteine (AdoHcy)). We propose that the single
      turnover reaction proceeds in two stages. First, two preformed
      T4Dam-AdoMet complexes bind opposite strands of the unmodified target
      site, and one enzyme molecule catalyzes the rapid transfer of the
      AdoMet-methyl group (kmeth1 = 0.21 s-1); this is 2.5-fold slower than the
      rate observed with monomeric T4Dam-AdoMet bound under pre-steady-state
      conditions for burst determination. In the second stage, methyl transfer
      to adenine in GATC on the complementary strand occurs at a rate that is 1
      order of magnitude slower (kmeth2 = 0.023 s-1). We suggest that under
      single turnover conditions, methylation of the second strand is
      rate-limited by Dam-AdoHcy dissociation or its clearance from the
      methylated complementary strand. The hemimethylated duplex 5'-GATC/5'-GMTC
      also interacts with T4Dam-AdoMet complexes in two stages under single
      turnover reaction conditions. The first stage (kmeth1) reflects
      methylation by dimeric T4Dam-AdoMet productively oriented to the strand
      with the adenine residue capable of methylation. The slower second stage
      (kmeth2) reflects methylation by enzyme molecules non-productively
      oriented to the GMTC chain, which then have to re-orient to the opposite
      productive chain. Substitutions of bases and deletions in the recognition
      site affect the kinetic parameters in different fashions. When the GAT
      portion of GATC was disrupted, the proportion of the initial productive
      enzyme-substrate complexes was sharply reduced.
AU  - Malygin EG
AU  - Lindstrom WM
AU  - Zinoviev VV
AU  - Evdokimov AA
AU  - Schlagman SL
AU  - Reich NO
AU  - Hattman S
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2003 278: 41749-41755.

PMID- 11234384
VI  - 35
DP  - 2001
TI  - Single turnover kinetics of methylation by T4 DNA-(N6-adenine)-methyltransferase.
PG  - 65-78
AB  - Interaction of T4 DNA-(N6-adenine)-methyltransferase was studied with a variety of synthetic
      oligonucleotide substrates containing the native
      recognition site GATC or its modified variants. The data obtained in
      the decisecond and second intervals of the reaction course allowed for
      the first time the substrate methylation rates to be compared with the
      parameters of the steady-state reaction. It was established that the
      substrate reaction proceeds in two stages. Because it is shown that in
      steady-state conditions T4 MTase forms a dimeric structure, the
      following sequence of events is assumed. Upon collision of a T4 MTase
      monomer with an oligonucleotide duplex, an asymmetrical complex forms
      in which the enzyme randomly oriented relative to one of the strands of
      the specific recognition site catalyzes a fast transfer of the methyl
      group from S-adenosylmethionine to the adenosine residue (k(1) = 0.21
      s(-1)). Simultaneously, a second T4 MTase subunit is added to the
      complex, providing for the continuation of the reaction. In the course
      of a second stage, which is by an order of magnitude slower (k(2) =
      0.023 s(-1) for duplex with the native site), the dimeric T4 MTase
      switches over to the second strand and the methylation of the second
      residue, target. The rate of the methyl group transfer from donor,
      S-adenosylmethionine, to DNA is much higher than the overall rate of
      the T4 MTase-catalyzed steady-state reaction, although this difference
      is considerably less than that shown for EcoRI MTase. Base
      substitutions and deletions in the recognition site affect the
      substrate parameters in different fashions. When the GAT sequence is
      disrupted, the proportion of the initial productive enzyme-substrate
      complexes is usually sharply reduced. The flipping of the adenosine
      residue to be modified in the recognition site upon interaction with
      the enzyme, revealed by fluorescence titration, supports the existing
      notions about the involvement of such a DNA deformation in reactions
      catalyzed by various DNA-MTases.
AU  - Malygin EG
AU  - Ovechkina LG
AU  - Evdokimov AA
AU  - Zinoviev VV
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2001 35: 65-78.

PMID- 11234382
VI  - 35
DP  - 2001
TI  - DNA-(N4-cytosine)-methyltransferase from Bacillus amyloliquefaciens: kinetic and substrate-binding properties.
PG  - 42-51
AB  - Interaction of DNA-(N4-cytosine)-methyltransferase from Bacillus amyloliquefaciens (BamHI
      MTase, 49 kDa) with a 20-mer duplex containing
      a palindromic recognition site GGATCC was studied by methods of
      steady-state and pre-steady-state kinetics of the methyl group
      transfer, gel retardation, and crosslinking of the enzyme subunits with
      glutaraldehyde. In steady-state conditions, BamHI MTase displays a
      simple kinetic behavior toward the 20-mer substrate. A linear
      dependence was observed for the reaction rate on the enzyme
      concentration and a Michaelis dependence of the reaction rate on the
      concentration of both substrates: S-adenosyl-L-methionine (SAM), the
      methyl group donor, and DNA, the methyl group acceptor. In independent
      experiments, the concentration of the 20-mer duplex or SAM was changed,
      the enzyme concentration being substantially lower than the
      concentrations of substrates. The k(cat) values determined in these
      conditions are in good agreement with one another and approximately
      equal to 0.05 s(-1). The K-M values for the duplex and SAM are 0.35 and
      1.6 nM, respectively. An analysis of single turnover kinetics (at
      limiting concentration of the 20-mer duplex) revealed the following
      characteristics of the BamHI MTase-dependent methylation of DNA. The
      value of the rate constant of the DNA methylation step at the enzyme
      saturating concentration is on average 0.085 s(-1), which is only 1.6
      times higher than the value determined in steady-state conditions. Only
      one of two target cytidine residues was methylated in a single turnover
      of the enzyme, which coincides with the earlier data on EcoRI MTase.
      Regardless of the order of enzyme preincubation with SAM and DNA, both
      curves for the single turnover methylation are comparable. These
      results are consistent with the model of the random order of the
      productive ternary enzyme-substrate complex formation. In contrast to
      the relatively simple kinetic behavior of BamHI MTase in the
      steady-state reaction are the data on the enzyme binding with DNA. In
      gel retardation experiments, there was no stoichiometrically simple
      complex with the oligonucleotide duplex even at low enzyme
      concentrations. The molecular mass of the complexes was so high that
      they did not enter 12% PAG. In experiments on crosslinking of the BamHI
      MTase subunits, it was shown that the enzyme in a free state exists as
      a dimer. Introduction of substoichiometric amounts of DNA into the
      reaction mixture results in pronounced multimerization of the enzyme.
      However, addition of SAM in saturating concentration at an excess of
      the oligonucleotide duplex over BamHI MTase converts most of the enzyme
      into a monomeric state.
AU  - Malygin EG
AU  - Ovechkina LG
AU  - Zinoviev VV
AU  - Linstrem UM
AU  - Reich NO
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2001 35: 42-51.

PMID- 9336474
VI  - 25
DP  - 1997
TI  - Interaction of the phage T4 Dam DNA-[N6-adenine] methyltransferase with oligonucleotides containing native or modified (defective) recognition sites.
PG  - 4393-4399
AB  - The DNA-[N6-adenine]-methyltransferase of phage T4 catalyzes methyl group transfer from
      S-adenosyl-L-methionine to the N6-position of adenine in the palindromic sequence, GATC.  We
      have used a gel shift assay to monitor complex formation between T4 Dam and various synthetic
      duplex oligonucleotides, either native or modified/defective.  The results are summarized as
      follows.  (i) T4 Dam bound with ~100-fold higher affinity to a 20mer specific
      (GATC-containing) duplex containing the canonical palindromic methylation sequence, GATC, than
      to a non-specific duplex containing another palindrome, GTAC.  (ii) Compared with the
      unmethylated duplex, the hemimethylated 20mer specific duplex had a slightly increased
      (~2-fold) ability to form complexes with T4 Dam.  (iii) No stable complex was formed with a
      synthetic 12mer specific (GATC-containing) duplex, although T4 Dam can methylate it.  This
      indicates that there is no relation between formation of a catalytically competent 12mer-Dam
      complex and one stable to gel electrophoresis.  (iv) Formation of a stable complex did not
      require that both strands be contiguous or completely complementary.  Absence of a single
      internucleotide phosphate strongly reduced complex formation only when missing between the T
      and C residues.  This suggests that if T4 Dam makes critical contact(s) with a backbone
      phosphate(s), then the one between T and C is the only likely candidate.  Having only one half
      of the recognition site intact on one strand was sufficient for stable complex formation
      provided that the 5' G.C base-pairs be present at both ends of the palindromic, GATC.  Since
      absence of either a G or C abolished T4 Dam binding, we conclude that both strands are
      recognized by T4 Dam.
AU  - Malygin EG
AU  - Petrov NA
AU  - Gorbunov YA
AU  - Kossykh VG
AU  - Hattman S
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1997 25: 4393-4399.

PMID- 15375160
VI  - 279
DP  - 2004
TI  - Bacteriophage T4Dam DNA-(adenine-N-6)-methyltransferase - Comparison of pre-steady state and single turnover methylation of 40-mer duplexes  containing two (un)modified target sites.
PG  - 50012-50018
AB  - We analyzed pre-steady state and single turnover kinetics of bacteriophage T4Dam
      DNA-(adenine-N-6)methyltransferase- mediated methyl
      group transfer from S-adenosyl-L-methionine ( AdoMet) to 40-mer
      duplexes containing native recognition sites (5'-GATC/5'- GATC) or some
      modified variant(s). The results extend a model from studies with
      single-site 20-mer duplexes. Under pre-steady state conditions,
      monomeric T4Dam methyltransferase- AdoMet complexes were capable of
      rapid methylation of adenine residues in 40-mer duplexes containing two
      sites. During processive movement of T4Dam to the next site, the
      rate-limiting step was the exchange of the product
      S-adenosyl-L-homocysteine ( AdoHcy) for AdoMet without T4Dam
      dissociating from the duplex. Consequently, instead of a single
      exponential rate dependence, complex methylation curves were obtained
      with at least two pre-steady state steps. With 40-mer duplexes
      containing a single target site, the kinetics were simpler, fitting a
      single exponential followed by a linear steady state phase. Single
      turnover methylation of 40-mer duplexes also proceeded in two stages.
      First, two dimeric T4Dam-AdoMet molecules bound, and each catalyzed a
      two-step methylation. Instead of processive movement of T4Dam, a
      conformational adaptation occurred. We propose that following methyl
      transfer to one strand, dimeric ( T4Dam-AdoMet)-(T4Dam-AdoHcy) was
      capable of rapidly reorienting itself and catalyzing methyl transfer to
      the target adenine on the complementary, unmethylated strand. This
      second stage methyl transfer occurred at a rate about 25-fold slower
      than in the first step; it was rate-limited by Dam-AdoHcy dissociation
      or its clearance from the methylated complementary strand. Under single
      turnover conditions, there was complete methylation of all target
      adenine residues with each of the two-site 40-mer duplexes.
AU  - Malygin EG
AU  - Sclavi B
AU  - Zinoviev VV
AU  - Evdokimov AA
AU  - Hattman S
AU  - Buckle M
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2004 279: 50012-50018.

PMID- Not carried by PubMed...
VI  - 9
DP  - 1989
TI  - Studies of the role of symmetry in the specific recognition of natural and synthetic DNA by type II restriction and modification enzymes.
PG  - 87-142
AB  - Type II restriction endonucleases and methylases are site-specific enzymes acting on synthetic
      and natural DNAs. In prokaryotic cells they make up a unique system of
      restriction-modification which destroys any foreign DNA penetrating the cell. The overwhelming
      majority of restrictases and methylases recognize palindromic sites with a second-order
      symmetry axis. Two alternative mechanisms for this recognition exist: (i) symmetric
      recognition by way of double-sided symmetrical contacts of the enzyme with non-overlapping
      nucleotide groups of the duplex site; (ii) asymmetric recognition is brought about through
      asymmetrical contact between the DNA chain and the enzyme molecule. The majority of
      restrictases have a subunit structure, the number of subunits being even. All type II
      methylases which have been isolated up to now consist of a single polypeptide chain, a monomer
      being their stable form in solution. A central theme that has emerged from the data is that
      multiple mechanisms exist for discrimination of base pairs. Hence, the elucidation of such
      enzyme-DNA binding schemes as may be employed in sequence discrimination requires the analysis
      of multiple systems. This review deals with our data on the interaction of restriction
      endonucleases and Ecodam methylase with various natural and synthetic substrates containing
      either completely symmetrical recognition sites or their asymmetrical variations. Our results
      concerning the properties of different substrates confirm a symetrical model of interaction
      between DNA and type II enzymes and demonstrate the probable interdependence of the active
      centers in the cases of the BamHI and Sau3AI endonuclease just as there is with Ecodam
      methylase. Dimerization of monomeric Ecodam methylase and endonuclease MvaI induced by the
      oligonucleotide substrate has been demonstrated by gel filtration, ultracentrifugation and
      small angle X-ray scattering methods. Thus, the catalytically active form of Ecodam methylase
      and other monomeric type II enzymes seems to be a dimer. In discussing the results, attention
      has mainly been paid to the significance of symmetry in the structures of both substrate DNs
      and type II enzymes with respect to providing a productive interaction.
AU  - Malygin EG
AU  - Zinovev VV
PT  - Journal Article
TA  - Sov. Sci. Rev. D. Physiochem. Biol.
JT  - Sov. Sci. Rev. D. Physiochem. Biol.
SO  - Sov. Sci. Rev. D. Physiochem. Biol. 1989 9: 87-142.

PMID- 3233224
VI  - 53
DP  - 1988
TI  - Influence of the structure of oligonucleotide substrates on the interaction with Eco dam methylase.
PG  - 1639-1647
AB  - The interaction of Eco dam methylase with synthetic substrates containing various damages in
      the recognition site of the enzyme was investigated. The imperfect oligonucleotide complexes
      contained a complete GATC recognition seuqence in one strand, but various defects in the
      complementary strand in the recognition site: omission of one or several nucleotides, the
      presence of an S-methylthiophosphate residue at the site of a break in the oligonucleotide
      strand. The presence of the S-methyl-thiophosphate residue has no significant effect on
      methylation in comparison with analogous substrates that did not contain an internucleotide
      phosphate. A productive enzyme-substrate interaction occurred only with oligonucleotide
      complexes containing both GA pairs in the recognition site of Eco dam methylase. The data
      obtained suggest that Eco dam methylase, like type II restriction endonucleases, can form a
      symmetrical structure in the enzyme-substrate complex.
AU  - Malygin EG
AU  - Zinovev VV
AU  - Gorbunov YA
AU  - Popov SG
AU  - Rechkunova NI
AU  - Buryanov YI
AU  - Nesternko VF
AU  - Baev AA
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1988 53: 1639-1647.

PMID- 12598537
VI  - 278
DP  - 2003
TI  - DNA (cytosine-N4-)- and -(adenine-N6-)-methyltransferases have different kinetic mechanisms but the same reaction route. A comparison of M.BamHI and T4 Dam.
PG  - 15713-15719
AB  - We studied the kinetics of methyl group transfer by the BamHI
      DNA-(cytosine-N(4)-)-methyltransferase (MTase) from Bacillus
      amyloliquefaciens to a 20-mer oligodeoxynucleotide duplex containing the
      palindromic recognition site GGATCC. Under steady state conditions the
      BamHI MTase displayed a simple kinetic behavior toward the 20-mer duplex.
      There was no apparent substrate inhibition at concentrations much higher
      than the K(m) for either DNA (100-fold higher) or S-adenosyl-l-methionine
      (AdoMet) (20-fold higher); this indicates that dead-end complexes did not
      form in the course of the methylation reaction. The DNA methylation rate
      was analyzed as a function of both substrate and product concentrations.
      It was found to exhibit product inhibition patterns consistent with a
      steady state random bi-bi mechanism in which the dominant order of
      substrate binding and product release (methylated DNA, DNA(Me), and
      S-adenosyl-l-homocysteine, AdoHcy) was Ado-Met DNA DNA(Me) AdoHcy. The
      M.BamHI kinetic scheme was compared with that for the T4 Dam
      (adenine-N(6)-)-MTase. The two differed with respect to an effector action
      of substrates and in the rate-limiting step of the reaction (product
      inhibition patterns are the same for the both MTases). From this we
      conclude that the common chemical step in the methylation reaction, methyl
      transfer from AdoMet to a free exocyclic amino group, is not sufficient to
      dictate a common kinetic scheme even though both MTases follow the same
      reaction route.
AU  - Malygin EG
AU  - Zinoviev VV
AU  - Evdokimov AA
AU  - Lindstrom WM Jr
AU  - Reich NO
AU  - Hattman S
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2003 278: 15713-15719.

PMID- 9927748
VI  - 27
DP  - 1999
TI  - Effect of base analog substitutions in the specific GATC site on binding and methylation of oligonucleotide duplexes by the bacteriophage T4 Dam DNA-[N6-adenine] methyltransferase.
PG  - 1135-1144
AB  - The interaction of the phage T4 Dam DNA-[N6-adenine] methyltransferase with 24mer synthetic
      oligonucleotide duplexes having different purine base substitutions in the palindromic
      recognition sequence, GATC, was investigated by means of gel shift and methyl transfer assays.
      The substitutions were introduced in either the upper or lower strand: guanine by
      7-deazaguanine (G-D) or 2-aminopurine (G-N) and target adenine by purine (A-P) or
      2-aminopurine (A-N).  The effects of each base modification on binding/methylation were
      approximately equivalent for both strands.  G-D and G-N substitutions resulted in a sharp
      decrease in binary complex formation.  This suggests that T4 Dam makes hydrogen bonds with
      either the N7- or O6-keto groups (or both) in forming the complex.  In contrast, A-P and A-N
      substitutions were much more tolerant for complex formation.  This confirms our earlier
      observations that the presence of intact 5'-G:C base pairs at both ends of the methylation
      site is critical, but that base substitutions within the central A:T base pairs show less
      inhibition of complex formation.  Addition of T4 Dam to a complete substrate mixture resulted
      in a burst of [3H]methylated product.  In all cases the substrate dependencies of bursts and
      methylation rates were proportional to each other.  For the perfect 24mer kcat=0.014/s and
      Km=7.7 nM was obtained.  In contrast to binary complex formation the two guanine substitutions
      exerted relatively minor effects on catalytic turnover (the kcat was reduced at most
      2.5-fold), while the two adenine substitutions showed stronger effects (5- to 15-fold
      reduction in kcat).  The effects of base analog substitutions on Km(DNA) were more variable:
      A-P (decreased); A-N and G-D (unchanged); G-N (increased).
AU  - Malygin EG
AU  - Zinoviev VV
AU  - Petrov NA
AU  - Evdokimov AA
AU  - Jen-Jacobson L
AU  - Kossykh VG
AU  - Hattman S
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1999 27: 1135-1144.

PMID- 6244210
VI  - 8
DP  - 1980
TI  - Alteration of the specificity of restriction endonucleases in the presence of organic solvents.
PG  - 163-177
AB  - The specificity of XbaI, SalI, HhaI, PstI, BamHI and SstI is relaxed in the
      presence of an organic solvent, such as 20% glycerol or 8% dimethylsulfoxide
      (DMSO).  This alteration, very pronounced in some cases, requires an excess of
      enzyme, varies from one kind of enzyme to another and is highly dependent on
      the pH, the ionic strength, the nature of the metallic cofactor and/or the
      presence of a second organic solvent.  Preliminary data concerning XbaI and
      BamHI used under conditions where the relaxation of specificity is moderate,
      suggest that some of the new ("pseudo") sites correspond to shortened sequences
      derived from the normal recognition sequence cleaved under the standard
      conditions of the reaction.
AU  - Malyguine E
AU  - Vannier P
AU  - Yot P
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1980 8: 163-177.

PMID- 4919756
VI  - 104
DP  - 1970
TI  - Genetic control of the secondary modification of deoxyribonucleic acid in Escherichia coli.
PG  - 57-62
AB  - The wild-type restriction and modification alleles of Escherichia coli K-12 and
      B were found to have no measurable effect on the patterns of methylated bases
      in the deoxyribonucleic acid (DNA) of these strains.  The genetic region
      controlling the methylation of cytosine in E. coli K-12 was mapped close to
      his, and the presence or absence of this gene in E. coli B or E. coli K had no
      effect on the restriction and modification properties of these strains.  Thus,
      only a few of the methylated bases in the DNA of these strains are involved in
      host modification, and the biological role of the remainder remains obscure.
AU  - Mamelak L
AU  - Boyer HW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1970 104: 57-62.

PMID- 3032685
VI  - 214
DP  - 1987
TI  - BliI, a restriction endonuclease from Bacillus licheniformis.
PG  - 305-307
AB  - From Bacillus licheniformis a site-specific restriction endonuclease, named
      BliI, has been purified and characterized.  BliI was able to digest lambda DNA
      at pH 9.1 over a wide temperature range (25-65C).  Digestion of lambda and
      PhiX174 DNAs with BliI produced banding patterns identical to those seen with
      HaeIII.  Therefore, BliI and HaeIII endonucleases are isoschizomers.
AU  - Manachini PL
AU  - Parini C
AU  - Fortina MG
AU  - Benazzi L
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1987 214: 305-307.

PMID- 27795239
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of an Escherichia coli Strain Isolated from a Gallus gallus Broiler Producing the Novel CTX-M-166 Variant.
PG  - e01029-16
AB  - We report here the draft genome sequence of the CTX-M-166-harboring O6:H16 sequence type 48
      (ST48)-fimH34 Escherichia coli strain recovered from a Gallus
      gallus broiler. Sequence analyses revealed the presence of an
      IncI1/ST103-ISEcp1-blaCTX-M-166-orf477 plasmid region and of diverse antibiotic
      resistance and virulence-acquired genes.
AU  - Manageiro V
AU  - Clemente L
AU  - Duarte S
AU  - Vieira L
AU  - Canica M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01029-16.

PMID- 26404603
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the First NDM-1-Producing Providencia stuartii Strain Isolated in Portugal.
PG  - e01077-15
AB  - We report here the draft genome sequence of the first NDM-1-producing Providencia stuartii
      strain isolated in Portugal. Sequence analyses revealed the presence of  an incompatibility
      group A/C2 (IncA/C2) plasmid and of diverse acquired genes conferring resistance to
      beta-lactams, aminoglycosides, tetracycline, macrolides, chloramphenicol, and sulfonamides.
      This sequence contributes to the evaluation of the spread of NDM-1 producers.
AU  - Manageiro V
AU  - Sampaio DA
AU  - Pereira P
AU  - Rodrigues P
AU  - Vieira L
AU  - Palos C
AU  - Canica M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01077-15.

PMID- 
VI  - 279
DP  - 2012
TI  - Structural mechanism of cognate DNA recognition by the BfiI restriction enzyme.
PG  - 446-447
AB  - Restriction endonuclease BfiI recognizes and cleaves the asymmetric DNA sequence
      5'-ACTGGG-3' downstream of the site independently of Mg-ions.  BfiI is evolved as a fusion
      of two domains: the C-terminal DNA binding domain similar to DNHA binding domans of EcoRII and
      B3 family of plant transcription factors, and the N-terminal catalytic domain, which is
      similar to the Nuc nuclease of S. thyphimurium.  We have solved the crystal structure of the
      BfiI DNA binding domjain in complex with the specific DNA to reveal the mechanism of the
      specific DNA recognition. Superposition of the apoBfiI structure with the DNA bound C-domain
      suggests that BfiI must change its conformation to accommopdate the scissile phosphate in the
      active site.  To get a glimpse on the structural changes occurring upon BfiI binding to
      cognate DNA we have performed the X-ray small angle scatterinhg measurements of apo and DNA
      bound BfiI.  Ab initio shape determination as well as rigid body modeling using the
      crystallographic data suggest that apo BfiI retains the similar conformation in the solution
      as in a crystal, whereas DNA bound BfiI shows a conformational flexibility.  The truncated
      heterodimar of BfiI which lacks one of the two DNHA-bidning domains was constructed in order
      to simplify the system for SAXS experiments.
AU  - Manakova E
AU  - Golovenko D
AU  - Grazulis S
AU  - Zaremba M
AU  - Siksnys V
PT  - Journal Article
TA  - FEBS J.
JT  - FEBS J.
SO  - FEBS J. 2012 279: 446-447.

PMID- 22495930
VI  - 40
DP  - 2012
TI  - Structural mechanisms of the degenerate sequence recognition by Bse634I restriction endonuclease.
PG  - 6741-6751
AB  - Restriction endonuclease Bse634I recognizes and cleaves the degenerate DNA sequence
      5'-R/CCGGY-3' (R stands for A or G; Y for T or C, '/' indicates a
      cleavage position). Here, we report the crystal structures of the Bse634I R226A
      mutant complexed with cognate oligoduplexes containing ACCGGT and GCCGGC sites,
      respectively. In the crystal, all potential H-bond donor and acceptor atoms on
      the base edges of the conserved CCGG core are engaged in the interactions with
      Bse634I amino acid residues located on the alpha6 helix. In contrast, direct
      contacts between the protein and outer base pairs are limited to van der Waals
      contact between the purine nucleobase and Pro203 residue in the major groove and
      a single H-bond between the O2 atom of the outer pyrimidine and the side chain of
      the Asn73 residue in the minor groove. Structural data coupled with biochemical
      experiments suggest that both van der Waals interactions and indirect readout
      contribute to the discrimination of the degenerate base pair by Bse634I.
      Structure comparison between related enzymes Bse634I (R/CCGGY), NgoMIV (G/CCGGC)
      and SgrAI (CR/CCGGYG) reveals how different specificities are achieved within a
      conserved structural core.
AU  - Manakova E
AU  - Grazulis S
AU  - Zaremba M
AU  - Tamulaitiene G
AU  - Golovenko D
AU  - Siksnys V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: 6741-6751.

PMID- 6090442
VI  - 259
DP  - 1984
TI  - Prediction of secondary structure for EcoRI endonuclease.
PG  - 11666-11667
AB  - The circular dichroism of EcoRI restriction endonuclease was measured to 178 nm
      and analyzed for secondary structure.  The results (33% alpha-helix, 25%
      beta-sheet, 17% turns, and 25% other structures) compare well with our joint
      prediction from sequence data.
AU  - Manavalan P
AU  - Johnson WC Jr
AU  - Modrich P
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1984 259: 11666-11667.

PMID- 22072648
VI  - 193
DP  - 2011
TI  - Genome Sequence of Desulfovibrio sp. A2, a Highly Copper Resistant, Sulfate-Reducing Bacterium Isolated from Effluents of a Zinc Smelter at  the Urals.
PG  - 6793-6794
AB  - Desulfovibrio sp. A2 is an anaerobic Gram-negative sulfate-reducing bacterium with remarkable
      tolerance to copper. It was isolated from
      wastewater effluents of a zinc smelter at the Urals. Here, we report the
      4.2-Mb draft genome sequence of Desulfovibrio sp. A2 and identify
      potential copper resistance mechanisms.
AU  - Mancini S
AU  - Abicht HK
AU  - Karnachuk OV
AU  - Solioz M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6793-6794.

PMID- 24558237
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Multidrug-Resistant Acinetobacter baumannii Strain MMC4, Isolated from a Patient in Tennessee.
PG  - e00051-14
AB  - Acinetobacter baumannii multidrug-resistant strain MMC4 was isolated from a bronchoalveolar
      lavage fluid sample from a patient in Nashville, TN, USA. Here,
      we report a draft genome sequence with a size of 3,985,367 bp, an average G+C
      content of 39.8%, and 3,863 predicted protein-coding sequences.
AU  - Mandape SN
AU  - Marshall DR
AU  - Dent LL
AU  - Pratap S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00051-14.

PMID- 25977443
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Thermophile Thermus filiformis ATCC 43280, Producer  of Carotenoid-(Di)glucoside-Branched Fatty Acid (Di)esters and Source of Hyperthermostable Enzymes of Biotechnological Interest.
PG  - e00475-15
AB  - Here, we present the draft genome sequence of Thermus fi liformis strain ATCC 43280, a
      thermophile bacterium capable of producing glycosylated carotenoids
      acylated with branched fatty acids and enzymes of biotechnological potential.
AU  - Mandelli F
AU  - Oliveira RB
AU  - Couger MB
AU  - Paixao DA
AU  - Camilo CM
AU  - Polikarpov I
AU  - Prade R
AU  - Riano-Pachon DM
AU  - Squina FM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00475-15.

PMID- 20400544
VI  - 192
DP  - 2010
TI  - Host-interactive genes in amerindian Helicobacter pylori diverge from their old world homologs and mediate inflammatory responses.
PG  - 3078-3092
AB  - Helicobacter pylori is the dominant member of the gastric microbiota and
      has been associated with an increased risk of gastric cancer and peptic
      ulcers in adults. H. pylori populations have migrated and diverged with
      human populations, and health effects vary. Here, we describe the whole
      genome of the cag-positive strain V225d, cultured from a Venezuelan Piaroa
      Amerindian subject. To gain insight into the evolution and host adaptation
      of this bacterium, we undertook comparative H. pylori genomic analyses. A
      robust multiprotein phylogenetic tree reflects the major human migration
      out of Africa, across Europe, through Asia, and into the New World,
      placing Amerindian H. pylori as a particularly close sister group to East
      Asian H. pylori. In contrast, phylogenetic analysis of the
      host-interactive genes vacA and cagA shows substantial divergence of
      Amerindian from Old World forms and indicates new genotypes (e.g., VacA
      m3) involving these loci. Despite deletions in CagA EPIYA and CRPIA
      domains, V225d stimulates interleukin-8 secretion and the hummingbird
      phenotype in AGS cells. However, following a 33-week passage in the mouse
      stomach, these phenotypes were lost in isolate V225-RE, which had a 15-kb
      deletion in the cag pathogenicity island that truncated CagA and
      eliminated some of the type IV secretion system genes. Thus, the unusual
      V225d cag architecture was fully functional via conserved elements, but
      the natural deletion of 13 cag pathogenicity island genes and the
      truncation of CagA impaired the ability to induce inflammation.
AU  - Mane SP et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 3078-3092.

PMID- 21914877
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of the Dog Commensal and Human Pathogen Capnocytophaga canimorsus Strain 5.
PG  - 5558-5559
AB  - Capnocytophaga canimorsus is a commensal Gram-negative bacterium, originally isolated from a
      dog's mouth, that causes septicemia in humans.
      C. canimorsus has the unusual ability to feed on host cells, including
      phagocytes. This capacity depends on surface-exposed glycan-foraging
      systems. Here we present the first complete genome sequence of a C.
      canimorsus strain (Cc5).
AU  - Manfredi P
AU  - Pagni M
AU  - Cornelis GR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5558-5559.

PMID- 26021913
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Three Capnocytophaga cynodegmi Strains Isolated from the Oral Cavity of Healthy Dogs.
PG  - e00200-15
AB  - Here, we present the draft genome sequences of three strains of Capnocytophaga cynodegmi. In
      contrast to the very close relationship among them, C. cynodegmi
      and Capnocytophaga canimorsus differ dramatically in terms of virulence in
      humans. Comparative genomics provided some understanding on how Capnocytophaga
      species may switch from being dog commensals to human pathogens.
AU  - Manfredi P
AU  - Renzi F
AU  - Cornelis GR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00200-15.

PMID- 26021912
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Three Capnocytophaga canimorsus Strains Isolated from Healthy Canine Oral Cavities.
PG  - e00199-15
AB  - Here, we present the draft genome sequences of three strains of Capnocytophaga canimorsus,
      each isolated from a different dog's mouth. Genome analysis provided
      evidence that these organisms may belong to a different nonpathogenic subtype of
      C. canimorsus.
AU  - Manfredi P
AU  - Renzi F
AU  - Cornelis GR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00199-15.

PMID- 26021910
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Three Capnocytophaga canimorsus Strains Isolated from Septic Patients.
PG  - e00193-15
AB  - Capnocytophaga canimorsus is a bacterium from the normal oral flora of dogs and cats that
      causes rare generalized infections in humans. In an attempt to
      determine whether infections could be caused by a subset of strains and to
      identify pathogenicity factors, we sequenced the genomes of three strains
      isolated from human infections.
AU  - Manfredi P
AU  - Renzi F
AU  - Cornelis GR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00193-15.

PMID- 23516182
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of the Avian Pathogenic Escherichia coli Strain APEC O78.
PG  - e0002613
AB  - Colibacillosis, caused by avian pathogenic Escherichia coli (APEC), is a significant disease,
      causing extensive animal and financial losses globally.
      Because of the significance of this disease, more knowledge is needed regarding
      APEC's mechanisms of virulence. Here, we present the fully closed genome sequence
      of a typical avian pathogenic E. coli strain belonging to the serogroup O78.
AU  - Mangiamele P
AU  - Nicholson B
AU  - Wannemuehler Y
AU  - Seemann T
AU  - Logue CM
AU  - Li G
AU  - Tivendale KA
AU  - Nolan LK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0002613.

PMID- 18682527
VI  - 36
DP  - 2008
TI  - A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library.
PG  - 5180-5188
AB  - The construction of metagenomic libraries has permitted the study of
      microorganisms resistant to isolation and the analysis of 16S rDNA
      sequences has been used for over two decades to examine bacterial
      biodiversity. Here, we show that the analysis of random sequence reads
      (RSRs) instead of 16S is a suitable shortcut to estimate the biodiversity
      of a bacterial community from metagenomic libraries. We generated 10,010
      RSRs from a metagenomic library of microorganisms found in human faecal
      samples. Then searched them using the program BLASTN against a prokaryotic
      sequence database to assign a taxon to each RSR. The results were compared
      with those obtained by screening and analysing the clones containing 16S
      rDNA sequences in the whole library. We found that the biodiversity
      observed by RSR analysis is consistent with that obtained by 16S rDNA. We
      also show that RSRs are suitable to compare the biodiversity between
      different metagenomic libraries. RSRs can thus provide a good estimate of
      the biodiversity of a metagenomic library and, as an alternative to 16S,
      this approach is both faster and cheaper.
AU  - Manichanh C
AU  - Chapple CE
AU  - Frangeul L
AU  - Gloux K
AU  - Guigo R
AU  - Dore J
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2008 36: 5180-5188.

PMID- 
VI  - 0
DP  - 1992
TI  - Mycoplasma DNA Restriction and Modification.
PG  - 325-330
AB  - *

      Mycoplasma DNA Restriction and Modification

      Introduction

      Restriction and Modification in Eubacteria

      Restriction-Modification Systems

      Restriction and Modification in Mycoplasmas

      Mycoplasma Restriction-modification systems

      A. laidlawii K2

      A. laidlawii JA1

      A. laidlawii JA1 Restriction and recA Mutants

      S. citri ASP2

      M. fermentans

      U. urealyticum 960

      Mycoplasma methylases

      Restriction-modification systems and Mycoplasma Evolution

      Acknowledgments

      References

      

AU  - Maniloff J
AU  - Dybvig K
AU  - Sladek TL
PT  - Journal Article
TA  - Mycoplasmas: Molecular Biology and Pathogenesis
JT  - Mycoplasmas: Molecular Biology and Pathogenesis
SO  - Mycoplasmas: Molecular Biology and Pathogenesis 1992 0: 325-330.

PMID- 27013045
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a Clinically Isolated Extensively Drug-Resistant Pseudomonas aeruginosa Strain.
PG  - e00162-16
AB  - We present the draft genome assembly of an extensively drug-resistant (XDR)Pseudomonas
      aeruginosastrain isolated from a patient with a history of
      genito urinary tuberculosis. The draft genome is 7,022,546 bp with a G+C content
      of 65.48%. It carries 7 phage genomes, genes for quorum sensing, biofilm
      formation, virulence, and antibiotic resistance.
AU  - Manivannan B
AU  - Mahalingam N
AU  - Jadhao S
AU  - Mishra A
AU  - Nilawe P
AU  - Pradeep BE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00162-16.

PMID- 11726692
VI  - 29
DP  - 2001
TI  - Restriction enzymes increase efficiencies of illegitimate DNA integration but decrease homologous integration in mammalian cells.
PG  - 4826-4833
AB  - Mammalian cells repair DNA double-strand breaks by illegitimate end-joining or by homologous
      recombination. We investigated the effects
      of restriction enzymes on illegitimate and homologous DNA integration
      in mammalian cells. A plasmid containing the neoR expression cassette,
      which confers G418 resistance, was used to select for illegitimate
      integration events in CHO wild-type and xrcc5 mutant cells.
      Co-transfection with the restriction enzymes BamHI, Bglll, EcoRI and
      Kpnl increased the efficiency of linearized plasmid integration up to
      5-fold in CHO cells. In contrast, the restriction enzymes did not
      increase the integration efficiency in xrcc5 mutant cells. Effects of
      restriction enzymes on illegitimate and homologous integration were
      also studied in mouse embryonic stem (ES) cells using a plasmid
      containing the neoR gene flanked by exon 3 of Hprt. The enzymes BamHI,
      Bglll and EcoRI increased the illegitimate integration efficiency of
      transforming DNA several-fold, similar to the results for CHO cells.
      However, all three enzymes decreased the absolute frequency of
      homologous integration apprx2-fold, and the percentage of homologous
      integration decreased >10-fold. This suggests that random DNA breaks
      attract illegitimate recombination (IR) events that compete with
      homology search.
AU  - Manivasakam P
AU  - Aubrecht J
AU  - Sidhom S
AU  - Schiestl RH
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2001 29: 4826-4833.

PMID- 9488490
VI  - 18
DP  - 1998
TI  - Nonhomologous end joining during restriction enzyme-mediated DNA integration in Saccharomyces cerevisiae.
PG  - 1736-1745
AB  - The BamHI restriction enzyme mediates integration of nonhomologous DNA into the Saccharomyces
      cerevisiae genome (R. H. Schiestl and T. D. Petes,
      Proc. Natl. Acad. Sci. USA 88:7585-7589, 1991). The present study
      investigates the mechanism of such events: in particular, the mediating
      activity of various restriction enzymes and the processing of resultant
      fragment ends. Our results show that in addition to BamHI, BglII and KpnI
      increase DNA integration efficiencies severalfold, while Asp718, HindIII,
      EcoRI, SalI, SmaI, HpaI, MscI, and SnaBI do not. Secondly, the three
      active enzymes stimulated integrations only of fragments containing 5' or
      3' overhangs but not of blunt-ended fragments. Thirdly, integrations
      mediated by one enzyme and utilizing a substrate created by another
      required at least 2 bp of homology. Furthermore, an Asp718 fragment
      possessing a 5' overhang integrated into a KpnI (isoschizomer) site
      possessing a 3' overhang, most likely by filling of the 5' overhang
      followed by 5' exonuclease digestion to produce a 3' end. We classified
      and analyzed the restriction enzyme-mediated integration events in the
      context of their genomic positions. The majority of events integrated into
      single sites. In the remaining 6 of 19 cases each end of the plasmid
      inserted into a different sequence, producing rearrangements such as
      duplications, deletions, and translocations.
AU  - Manivasakam P
AU  - Schiestl RH
PT  - Journal Article
TA  - Mol. Cell. Biol.
JT  - Mol. Cell. Biol.
SO  - Mol. Cell. Biol. 1998 18: 1736-1745.

PMID- 23995932
VI  - 79
DP  - 2013
TI  - The genome of the algae-associated marine flavobacterium Formosa agariphila KMM 3901T reveals a broad potential for the degradation of algal polysaccharides.
PG  - 6813
AB  - In recent years, representatives of the Bacteroidetes have been increasingly recognized as
      specialists for the degradation of macromolecules. Formosa constitutes a Bacteroidetes genus
      within the class Flavobacteria, whose members have been found in marine habitats with high
      levels of organic matter, such as an association with algae, invertebrates and fecal pellets.
      Here we report on the generation and analysis of the genome of the type strain of Formosa
      agariphila(KMM 3901T) - an isolate from the green algae Acrosiphonia sonderi.  F. agariphila
      is a facultative anaerobe with the capacity for mixed acid fermentation and denitrification.
      Its genome harbors 129 proteases and 88 glycoside hydrolases, indicating a pronounced
      specialization on the degradation of protein, polysaccharides and glycoproteins.  65 of the
      glycoside hydrolases are organized in at least 13 distinct polysaccharide utilization loci,
      where they are clustered with TonB-dependent receptors, SusD-like proteins,
      sensors/transcription factors, transporters and oftentimes sulfatases.  These loci play a
      pivotal role in bacteroidetal polysaccharide biodegradation, and in the case of F. agariphila
      revealed the capacity to degrade a wide range of algal polysaccharides from green, red and
      brown algae and thus a strong specialization of towards an algae-associated lifestyle.  This
      was corroborated by growth experiments, which confirmed usage of particularly those
      monosaccharides that constitute the building blocks of abundant agal polysaccharides as well
      as of distinct algal polysaccharides such as laminarins, xylans and k-carrageenans.
AU  - Mann AJ
AU  - Hahnke RL
AU  - Huang S
AU  - Werner J
AU  - Xing P
AU  - Barbeyron T
AU  - Huettel B
AU  - Stueber K
AU  - Reinhardt R
AU  - Harder J
AU  - Gloeckner FO
AU  - Amann RI
AU  - Teeling H
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2013 79: 6813.

PMID- 6765642
VI  - 1
DP  - 1981
TI  - The cloned HhaII restriction-modification system.
PG  - 229-237
AB  - I. Procedure for cloning restriction-modification (R-M) systems.  II. A clone that
      overproduces the HhaII R-M gene products.
      III. Biologic properties of the cloned HhaII R-M system.
      IV. The problem of site-specific DNA-protein interaction.
      V. HhaII*, a form of HhaII with grossly altered site specificity.
AU  - Mann MB
PT  - Journal Article
TA  - Gene Amplif. Anal.
JT  - Gene Amplif. Anal.
SO  - Gene Amplif. Anal. 1981 1: 229-237.

PMID- 350714
VI  - 3
DP  - 1978
TI  - Cloning of restriction and modification genes in E. coli: the HhaII system from Haemophilus haemolyticus.
PG  - 97-112
AB  - The genes for a Class II restriction-modification system (HhaII) from
      Haemophilus haemolyticus have been cloned in Escherichia coli.  The vector used
      for cloning was plasmid pBR322 which confers resistance to tetracycline and
      ampicillin and contains a single endonuclease R-PstI site,
      (5')C-T-G-C-A7-G(3'), in the ampicillin gene.  The procedure developed by
      Bolivar et al. (1977) was used to form DNA recombinants.  H. haemolyticus DNA
      was cleaved with PstI endonuclease and poly(dC) extensions were added to the
      3'-OH termini using terminal deoxynucleotidyl transferase.  Circular pBR322 DNA
      was cleaved to linear molecules with PstI endonuclease and poly(dG) extensions
      were added to the 3'-OH termini, thus regenerating the PstI cleavage site
      sequence.  Recombinant molecules, formed by annealing the two DNAs, were used
      to transfect a restriction and modification-deficient strain of E. coli (HB101
      r-m-recA).  Tetracycline-resistant clones were tested for acquisition of
      restriction phenotype (as measured by growth on plates seeded with phage
      lambdacI-0).  A single phage-resistant clone was found.  The recombinant
      plasmid, pDI10, isolated from this clone, had acquired 3 kilobases of
      additional DNA which could be excised with PstI endonuclease.  In addition to
      the restriction function, cells carrying the plasmid expressed the HhaII
      modification function.  Both activities have been partially purified by
      single-stranded DNA-agarose chromatography.  The cloned HhaII restriction
      activity yields cleavage patterns identical to HinfI. A restriction map of the
      cloned DNA segment is presented.
AU  - Mann MB
AU  - Rao RN
AU  - Smith HO
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1978 3: 97-112.

PMID- 
VI  - 0
DP  - 1979
TI  - Specificity of DNA Methylases from Haemophilus Sp.
PG  - 483-492
AB  - We have studied the specificity of three DNA cytosine methylases found in
      Haemophilus sp., which have the common property of acting at tetranucleotide
      sites containing cytosine and guanine residues.  The methylases belong to the
      three restriction and modification systems:  HhaI, HpaII, and HaeIII, for which
      the restriction endonuclease recognition sites are (5') pG-C-G-C, (5')
      pC-C-G-G, and (5') pG-G-C-C.  The sequence specificity and position of cytosine
      methylation within the recognition sequence for M.HpaII and M.HaeIII have been
      previously reported as (5') pC-CmC.1  Here we present comparable data for
      M.HhaI.  In addition, we determine the ability of each of the three methylases
      to utilize as substrates a variety of polymers containing base analogues.
      Judging from their behaviour on these substrates, we conclude that the
      mechanism for discriminating a given base pair varies from one enzyme to
      another.
AU  - Mann MB
AU  - Smith HO
PT  - Journal Article
TA  - Proceedings of the Conference on Transmethylation
JT  - Proceedings of the Conference on Transmethylation
SO  - Proceedings of the Conference on Transmethylation 1979 0: 483-492.

PMID- 
VI  - 0
DP  - 1977
TI  - Size of 5'-terminal fragments cleaved from poly(dG-dC) by EndoR.HhaI.
PG  - 269-271
AB  - None
AU  - Mann MB
AU  - Smith HO
PT  - Journal Article
TA  - Nucleic Acid - Protein Recognition
JT  - Nucleic Acid - Protein Recognition
SO  - Nucleic Acid - Protein Recognition 1977 0: 269-271.

PMID- 600794
VI  - 4
DP  - 1977
TI  - Specificity of HpaII and HaeIII DNA methylases.
PG  - 4211-4221
AB  - The methylases M HaeIII and M HpaII recognize the tetranucleotide sequences
      (5') G/C-G/C*-C*/G-C/G (5') and (5') C/G-C*/G-G/C*-G/C (5') respectively, in
      DNA, and transfer a methyl group from S-adenosylmethionine to the 5-position of
      cytosine on each strand as indicated by the asterisks.  Restriction
      endonuclease R HaeIII does not cleave the methylated sequence G/C-G/Cm-Cm/G-C/G
      but can cleave G/Cm-G/C-C/G-Cm/G in which methylation is introduced on the
      unnatural external cytosine positions.  Similarly, R HpaII does not cleave
      C/G-Cm/G-G/Cm-G/C but can cleave Cm/G-C/G-G/C-G/C.
AU  - Mann MB
AU  - Smith HO
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1977 4: 4211-4221.

PMID- 28232428
VI  - 5
DP  - 2017
TI  - Complete Genome and Plasmid Sequences of Staphylococcus aureus EDCC 5055 (DSM 28763), Used To Study Implant-Associated Infections.
PG  - e01698-16
AB  - Staphylococcus aureus EDCC 5055 (DSM 28763) is a human clinical wound isolate intensively used
      to study implant-associated infections in rabbit and rat
      infection models. Here, we report its complete genome sequence (2,794,437 bp)
      along with that of one plasmid (27,437 bp). This strain belongs to sequence type
      8 and contains a mecA gene.
AU  - Mannala GK
AU  - Hain T
AU  - Sproer C
AU  - Bunk B
AU  - Overmann J
AU  - Alt V
AU  - Domann E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01698-16.

PMID- 2989823
VI  - 82
DP  - 1985
TI  - Nucleotide sequence of the DpnII DNA methylase gene of Streptococcus pneumoniae and its relationship to the dam gene of Escherichia coli.
PG  - 4468-4472
AB  - The structural gene (dpnM) for the DpnII DNA methylase of Streptococcus pneumoniae, which is
      part of the DpnII restriction system and methylates adenine in the sequence 5'-G-A-T-C-3',
      was identified by subcloning fragments of a chromosomal segment from a DpnII-producing strain
      in an S. pneumoniae host/vector cloning system and demonstrating function of the gene also in
      Bacillus subtilis. Determination of the nucleotide sequence of the gene and adjacent DNA
      indicates that it encodes a polypeptide of 32,903 daltons. A putative promoter for
      transcription of the gene lies within a hundred nucleotides of the polypeptide start codon.
      Comparison of the coding sequence to that of the dam gene of Escherichia coli, which encodes a
      similar methylase, revealed 30% of the amino acid residues in the two enzymes to be identical.
      This homology presumably reflects a common origin of the two genes prior to the divergence of
      Gram-positive and Gram-negative bacteria. it is suggested that the restriction function of the
      gene is primitive, and that the homologous restriction system in E. coli has evolved to play
      an accessory role in heteroduplex DNA base mismatch repair.
AU  - Mannarelli BM
AU  - Balganesh TS
AU  - Greenberg B
AU  - Springhorn SS
AU  - Lacks SA
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1985 82: 4468-4472.

PMID- 27081122
VI  - 4
DP  - 2016
TI  - Draft Whole-Genome Sequences of Escherichia fergusonii Strains Isolated from Beef Trim (GTA-EF02), Ground Beef (GTA-EF03), and Chopped Kale (GTA-EF04).
PG  - e00185-16
AB  - Escherichia fergusoniiis a Gram-negative, rod-shaped, non-spore-forming member of
      theEnterobacteriaceaefamily and is a bacterium with both biotechnological
      applications and implication in human clinical disease. Here, we report the draft
      genome sequences of three isolates ofE. fergusoniifrom beef trim (GTA-EF02),
      ground beef (GTA-EF03), and chopped kale (GTA-EF04).
AU  - Manninger P
AU  - Koziol A
AU  - Carrillo CD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00185-16.

PMID- 10587440
VI  - 38
DP  - 1999
TI  - Chemical mechanism of DNA cleavage by the homing endonuclease I-PpoI.
PG  - 16178-16186
AB  - Homing endonucleases are distinguished by their ability to catalyze the cleavage of
      double-stranded DNA with extremely high specificity. I-PpoI endonuclease, a homing
      endonuclease from the slime mold Physarum polycephalum, is a small enzyme (2 x 20 kDa) of
      known three-dimensional structure that catalyzes the cleavage of a long target DNA sequence
      (15 base pairs). Here, a detailed chemical mechanism for catalysis of DNA cleavage by I-PpoI
      endonuclease is proposed and tested by creating six variants in which active-site residues are
      replaced with alanine. The side chains of three residues (Arg61, His98, and Asn119) are found
      to be important for efficient catalysis of DNA cleavage. This finding is consistent with the
      proposed mechanism in which His98 abstracts a proton from an attacking water molecule bound by
      an adjacent phosphoryl oxygen, Arg61 and Asn119 stabilize the pentavalent transition state,
      and Asn119 also binds to the essential divalent metal cation (e.g., Mg(2+) ion), which
      interacts with the 3'-oxygen leaving group. Because Mg(2+) is required for cleavage of a
      substrate with a good leaving group (p-nitrophenolate), Mg(2+) likely stabilizes the
      pentavalent transition state. The pH-dependence of k(cat) for catalysis by I-PpoI reveals a
      macroscopic pK(a) of 8.4 for titratable groups that modulate product release. I-PpoI appears
      to be unique among known restriction endonucleases and homing endonucleases in its use of a
      histidine residue to activate the attacking water molecule for in-line displacement of the
      3'-leaving group.
AU  - Mannino SJ
AU  - Jenkins CL
AU  - Raines RT
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1999 38: 16178-16186.

PMID- 27795251
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Five Novel Polyketide Synthetase-Containing Mouse Escherichia coli Strains.
PG  - e01082-16
AB  - We report herein the draft genomes of five novel Escherichia coli strains isolated from
      surveillance and experimental mice housed at MIT and the Whitehead
      Institute and describe their genomic characteristics in context with the
      polyketide synthetase (PKS)-containing pathogenic E. coli strains NC101, IHE3034,
      and A192PP.
AU  - Mannion A
AU  - Shen Z
AU  - Feng Y
AU  - Garcia A
AU  - Fox JG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01082-16.

PMID- 20093108
VI  - 79
DP  - 2010
TI  - Differential inhibition of restriction enzyme cleavage by chromophore-modified analogues of the antitumour antibiotics mithramycin and chromomycin reveals structure-activity relationships.
PG  - 1418-1427
AB  - Differential cleavage at three restriction enzyme sites was used to determine the specific
      binding to DNA of the antitumour antibiotics
      mithramycin A (MTA), chromomycin A(3) (CRO) and six
      chromophore-modified analogues bearing shorter side chains attached at
      C-3, instead of the pentyl chain All these antibiotics were obtained
      through combinatorial biosynthesis in the producer organisms. MTA, CRO
      and their six analogues showed differences in their capacity for
      inhibiting the rate of cleavage by restriction enzymes that recognize
      C/G-rich tracts. Changes in DNA melting temperature produced by these
      molecules were also analyzed, as well as their antiproliferative
      activities against a panel of colon, ovarian and prostate human
      carcinoma cell lines. Moreover, the cellular uptake of several
      analogues was examined to identify whether intracellular retention was
      related to cytotoxicity These experimental approaches provided mutually
      consistent evidence of a seeming correlation between the strength of
      binding to DNA and the antiproliferative activity of the
      chromophore-modified molecules Four of the analogues (mithramycin SK,
      mithramycin SDK, chromomycin SK and chromomycin SDK) showed promising
      biological profiles.
AU  - Mansilla S
AU  - Garcia-Ferrer I
AU  - Mendez C
AU  - Salas JA
AU  - Portugal J
PT  - Journal Article
TA  - Biochem. Pharmacol.
JT  - Biochem. Pharmacol.
SO  - Biochem. Pharmacol. 2010 79: 1418-1427.

PMID- 25268848
VI  - 5
DP  - 2014
TI  - A random six-phase switch regulates pneumococcal virulence via global epigenetic  changes.
PG  - 5055
AB  - Streptococcus pneumoniae (the pneumococcus) is the world's foremost bacterial pathogen in
      both morbidity and mortality. Switching between phenotypic forms (or
      'phases') that favour asymptomatic carriage or invasive disease was first
      reported in 1933. Here, we show that the underlying mechanism for such phase
      variation consists of genetic rearrangements in a Type I restriction-modification
      system (SpnD39III). The rearrangements generate six alternative specificities
      with distinct methylation patterns, as defined by single-molecule, real-time
      (SMRT) methylomics. The SpnD39III variants have distinct gene expression
      profiles. We demonstrate distinct virulence in experimental infection and in vivo
      selection for switching between SpnD39III variants. SpnD39III is ubiquitous in
      pneumococci, indicating an essential role in its biology. Future studies must
      recognize the potential for switching between these heretofore undetectable,
      differentiated pneumococcal subpopulations in vitro and in vivo. Similar systems
      exist in other bacterial genera, indicating the potential for broad exploitation
      of epigenetic gene regulation.
AU  - Manso AS
AU  - Chai MH
AU  - Atack JM
AU  - Furi L
AU  - De Ste CM
AU  - Haigh R
AU  - Trappetti C
AU  - Ogunniyi AD
AU  - Shewell LK
AU  - Boitano M
AU  - Clark TA
AU  - Korlach J
AU  - Blades M
AU  - Mirkes E
AU  - Gorban AN
AU  - Paton JC
AU  - Jennings MP
AU  - Oggioni MR
PT  - Journal Article
TA  - Nat. Commun.
JT  - Nat. Commun.
SO  - Nat. Commun. 2014 5: 5055.

PMID- 23766408
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences of Mycoplasma alkalescens, Mycoplasma arginini, and Mycoplasma bovigenitalium, Three Species with Equivocal Pathogenic Status for  Cattle.
PG  - e00348-13
AB  - We report here the draft genome sequences of Mycoplasma alkalescens, Mycoplasma arginini, and
      Mycoplasma bovigenitalium. These three species are regularly
      isolated from bovine clinical specimens, although their role in disease is
      unclear.
AU  - Manso-Silvan L et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00348-13.

PMID- 27174272
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Lampenflora Chlorobium limicola Strain Frasassi in a Sulfidic Cave System.
PG  - e00357-16
AB  - The draft genome sequence of Chlorobium limicola strain Frasassi was assembled from
      metagenomic sequencing of a green mat in an artificially lighted aquarium
      inside the Frasassi caves in Italy. The genome is 2.08 Mbp in size and contains
      the necessary genes for anoxygenic photosynthesis and CO2 fixation.
AU  - Mansor M
AU  - Macalady JL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00357-16.

PMID- 11585365
VI  - 485
DP  - 2001
TI  - Characterization of functional interactions among the Escherichia coli mismatch repair proteins using a bacterial two-hybrid assay.
PG  - 331-338
AB  - Vsr mediates very short patch repair in Escherichia coli, correcting T/G mismatches caused by
      deamination of 5-methylcytosine to thymine. MutS and
      MutL, part of the post-replication mismatch repair system, stimulate VSP
      repair. In this study, we use a bacterial two-hybrid assay to show that
      MutL interacts with Vsr. We also show that interaction between Vsr and
      MutL inhibits the ability of MutL to dimerize, to interact with MutS and
      MutH and to mediate a previously unknown interaction between MutS and
      MutH. This inhibition may explain why high levels of Vsr are mutagenic in
      vivo. In addition, we show that the Mut fusion proteins are repair
      proficient in the bacterial two-hybrid assay, making it possible to study
      their interactions in various genetic backgrounds, or in the presence of
      DNA damaging agents.
AU  - Mansour CA
AU  - Doiron KM
AU  - Cupples CG
PT  - Journal Article
TA  - Mutat. Res.
JT  - Mutat. Res.
SO  - Mutat. Res. 2001 485: 331-338.

PMID- 24435877
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Frankia sp. Strain CcI6, a Salt-Tolerant Nitrogen-Fixing Actinobacterium Isolated from the Root Nodule of Casuarina cunninghamiana.
PG  - e01205-13
AB  - Members of the actinomycete genus Frankia form a nitrogen-fixing symbiosis with 8 different
      families of actinorhizal plants. We report a 5.57-Mbp draft genome
      sequence for Frankia sp. strain CcI6, a salt-tolerant nitrogen-fixing
      actinobacterium isolated from root nodules of Casurina cunninghamiana grown in
      Egyptian soils.
AU  - Mansour SR
AU  - Oshone R
AU  - Hurst SGIV
AU  - Morris K
AU  - Thomas WK
AU  - Tisa LS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01205-13.

PMID- 10366527
VI  - 41
DP  - 1999
TI  - Nucleotide sequence of the F plasmid leading region.
PG  - 219-225
AB  - The entire nucleotide sequence of the first DNA segment of the conjugative
      F plasmid to enter the recipient cell, the leading region, is described.
      Analysis of the sequence provides further evidence that products encoded
      within the 13.2-kb leading region are likely to be expressed and perform
      functions associated with the transferred strand in the recipient cell.
AU  - Manwaring NP
AU  - Skurray RA
AU  - Firth N
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 1999 41: 219-225.

PMID- 26044434
VI  - 3
DP  - 2015
TI  - Genome Sequence of Rhodococcus sp. 4J2A2, a Desiccation-Tolerant Bacterium Involved in Biodegradation of Aromatic Hydrocarbons.
PG  - e00592-15
AB  - The genome sequence for Rhodococcus sp. 4J2A2, a newly described desiccation-tolerant strain
      that removes aromatic hydrocarbons, is reported here.
      The genome is estimated to be around 7.5 Mb in size, with an average G+C content
      of 60.77% and a predicted number of protein-coding sequences of 6,354.
AU  - Manzanera M
AU  - Garcia-Fontana C
AU  - Vilchez JI
AU  - Gonzalez-Lopez J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00592-15.

PMID- 26316631
VI  - 3
DP  - 2015
TI  - Genome Sequence of Microbacterium sp. Strain 3J1, a Highly Desiccation-Tolerant Bacterium That Promotes Plant Growth.
PG  - e00713-15
AB  - The genome sequence for Microbacterium sp. strain 3J1, a desiccation-tolerant organism
      isolated from the Nerium oleander rhizosphere, is reported here. The genome is estimated to be
      approximately 3.5 Mb in size, with an average G+C content of 67.7% and a predicted number of
      protein-coding sequences of 3,310.
AU  - Manzanera M
AU  - Garcia-Fontana C
AU  - Vilchez JI
AU  - Narvaez-Reinaldo JJ
AU  - Gonzalez-Lopez J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00713-15.

PMID- 26067978
VI  - 3
DP  - 2015
TI  - Genome Sequence of Arthrobacter koreensis 5J12A, a Plant Growth-Promoting and Desiccation-Tolerant Strain.
PG  - e00648-15
AB  - Arthrobacter koreensis 5J12A is a desiccation-tolerant organism isolated from the Nerium
      oleander rhizosphere. Here, we report its genome sequence, which may shed
      light on its role in plant growth promotion. This is believed to be the first
      published genome of a desiccation-tolerant plant growth promoter from the genus
      Arthrobacter.
AU  - Manzanera M
AU  - Narvaez-Reinaldo JJ
AU  - Garcia-Fontana C
AU  - Vilchez JI
AU  - Gonzalez-Lopez J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00648-15.

PMID- 24948757
VI  - 2
DP  - 2014
TI  - Genome Sequence of Arthrobacter siccitolerans 4J27, a Xeroprotectant-Producing Desiccation-Tolerant Microorganism.
PG  - e00526-14
AB  - We report the first genome sequence for Arthrobacter siccitolerans 4J27, a newly  described
      desiccation-tolerant species. The complete genome of A. siccitolerans
      4J27 has been sequenced and is estimated to be around 5.3 Mb in size, with an
      average GC content of 65.13%. We predict 4,480 protein-coding sequences (CDSs).
AU  - Manzanera M
AU  - Santa-Cruz-Calvo L
AU  - Vilchez JI
AU  - Garcia-Fontana C
AU  - Silva-Castro GA
AU  - Calvo C
AU  - Gonzalez-Lopez J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00526-14.

PMID- 25999566
VI  - 3
DP  - 2015
TI  - Genome Sequence of Leucobacter sp. 4J7B1, a Plant-Osmoprotectant Soil Microorganism.
PG  - e00398-15
AB  - We report the first genome sequence for Leucobacter sp. 4J7B1, a newly described
      desiccation-tolerant strain. The complete genome sequence of Leucobacter sp.
      4J7B1 has been sequenced and is estimated to be around 3.5 Mb in size, with an
      average GC content of 62.18%. We predict 2,953 protein-coding sequences.
AU  - Manzanera M
AU  - Vilchez JI
AU  - Garcia-Fontana C
AU  - Calvo C
AU  - Gonzalez-Lopez J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00398-15.

PMID- 24951564
VI  - 6
DP  - 2014
TI  - Settling down: the genome of Serratia symbiotica from the aphid Cinara tujafilina zooms in on the process of accommodation to a cooperative intracellular life.
PG  - 1683-1698
AB  - Particularly interesting cases of mutualistic endosymbioses come from the
      establishment of co-obligate associations of more than one species of
      endosymbiotic bacteria. Throughout symbiotic accommodation from a free-living
      bacterium, passing through a facultative stage and ending as an obligate
      intracellular one, the symbiont experiences massive genomic losses and phenotypic
      adjustments. Here, we scrutinized the changes in the coevolution of Serratia
      symbiotica and Buchnera aphidicola endosymbionts in aphids, paying particular
      attention to the transformations undergone by S. symbiotica to become an obligate
      endosymbiont. Although it is already known that S. symbiotica is facultative in
      Acyrthosiphon pisum, in Cinara cedri it has established a co-obligate
      endosymbiotic consortium along with B. aphidicola to fulfill the aphid's
      nutritional requirements. The state of this association in C. tujafilina, an
      aphid belonging to the same subfamily (Lachninae) that C. cedri, remained
      unknown. Here, we report the genome of S. symbiotica strain SCt-VLC from the
      aphid C. tujafilina. While being phylogenetically and genomically very closely
      related to the facultative endosymbiont S. symbiotica from the aphid A. pisum, it
      shows a variety of metabolic, genetic, and architectural features, which point
      toward this endosymbiont being one step closer to an obligate intracellular one.
      We also describe in depth the process of genome rearrangements suffered by S.
      symbiotica and the role mobile elements play in gene inactivations. Finally, we
      postulate the supply to the host of the essential riboflavin (vitamin B2) as key
      to the establishment of S. symbiotica as a co-obligate endosymbiont in the aphids
      belonging to the subfamily Lachninane.
AU  - Manzano-Marin A
AU  - Latorre A
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2014 6: 1683-1698.

PMID- 26457129
VI  - 10
DP  - 2015
TI  - The complete genome sequence and emendation of the hyperthermophilic, obligate iron-reducing archaeon 'Geoglobus ahangari' strain 234(T).
PG  - 77
AB  - 'Geoglobus ahangari' strain 234(T) is an obligate Fe(III)-reducing member of the
      Archaeoglobales, within the archaeal phylum Euryarchaeota, isolated from the
      Guaymas Basin hydrothermal system. It grows optimally at 88 degrees C by coupling
      the reduction of Fe(III) oxides to the oxidation of a wide range of compounds,
      including long-chain fatty acids, and also grows autotrophically with hydrogen
      and Fe(III). It is the first archaeon reported to use a direct contact mechanism
      for Fe(III) oxide reduction, relying on a single archaellum for locomotion,
      numerous curled extracellular appendages for attachment, and outer-surface
      heme-containing proteins for electron transfer to the insoluble Fe(III) oxides.
      Here we describe the annotation of the genome of 'G. ahangari' strain 234(T) and
      identify components critical to its versatility in electron donor utilization and
      obligate Fe(III) respiratory metabolism at high temperatures. The genome
      comprises a single, circular chromosome of 1,770,093 base pairs containing 2034
      protein-coding genes and 52 RNA genes. In addition, emended descriptions of the
      genus 'Geoglobus' and species 'G. ahangari' are described.
AU  - Manzella MP
AU  - Holmes DE
AU  - Rocheleau JM
AU  - Chung A
AU  - Reguera G
AU  - Kashefi K
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 77.

PMID- 23469343
VI  - 1
DP  - 2013
TI  - First Genome Sequence of a Syntrophic Acetate-Oxidizing Bacterium, Tepidanaerobacter acetatoxydans Strain Re1.
PG  - e00213-12
AB  - Syntrophic acetate-oxidizing bacteria (SAOB) have been identified as key organisms for
      efficient biogas production from protein-rich materials. is the
      first reported SAOB for which the genome has been sequenced. Genome analysis will
      aid us in understanding the mechanisms regulating syntrophy, particularly
      energy-conserving and electron transfer mechanisms.
AU  - Manzoor S
AU  - Bongcam-Rudloff E
AU  - Schnurer A
AU  - Muller B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00213-12.

PMID- 23538905
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Clostridium ultunense Strain Esp, a Syntrophic Acetate-Oxidizing Bacterium.
PG  - e0010713
AB  - Clostridium ultunense strain Esp belongs to the functional group of syntrophic
      acetate-oxidizing bacteria (SAOB), which have been identified as key organisms
      for efficient biogas production from protein-rich materials. Genome analysis and
      comparative genomics might aid us to define physiological features that are
      essential for maintaining this particular syntrophic lifestyle.
AU  - Manzoor S
AU  - Muller B
AU  - Niazi A
AU  - Bongcam-Rudloff E
AU  - Schnurer A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0010713.

PMID- 26566424
VI  - 10
DP  - 2015
TI  - Working draft genome sequence of the mesophilic acetate oxidizing bacterium Syntrophaceticus schinkii strain Sp3.
PG  - 99
AB  - Syntrophaceticus schinkii strain Sp3 is a mesophilic syntrophic acetate oxidizing bacterium,
      belonging to the Clostridia class within the phylum Firmicutes,
      originally isolated from a mesophilic methanogenic digester. It has been shown to
      oxidize acetate in co-cultivation with hydrogenotrophic methanogens forming
      methane. The draft genome shows a total size of 3,196,921 bp, encoding 3,688 open
      reading frames, which includes 3,445 predicted protein-encoding genes and 55 RNA
      genes. Here, we are presenting assembly and annotation features as well as basic
      genomic properties of the type strain Sp3.
AU  - Manzoor S
AU  - Muller B
AU  - Niazi A
AU  - Schnurer A
AU  - Bongcam-Rudloff E
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 99.

PMID- 23516223
VI  - 1
DP  - 2013
TI  - Genome Sequence of a Plant-Associated Bacterium, Bacillus amyloliquefaciens Strain UCMB5036.
PG  - e0011113
AB  - We announce here the genome sequence of Bacillus amyloliquefaciens strain UCMB5036, a plant
      growth-promoting bacterium isolated from a cotton plant. Its
      genome contains gene clusters involved in nonribosomal synthesis of secondary
      metabolites known for their antimicrobial activities. The availability of this
      genome will provide novel insights into plant-bacterium-associated activities.
AU  - Manzoor S
AU  - Niazi A
AU  - Bejai S
AU  - Meijer J
AU  - Bongcam-Rudloff E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0011113.

PMID- 27777650
VI  - 11
DP  - 2016
TI  - Complete genome sequence of Methanoculleus bourgensis strain MAB1, the syntrophic partner of mesophilic acetate-oxidising bacteria (SAOB).
PG  - 80
AB  - Methanoculleus bourgensis strain MAB1 has been identified as the hydrogenotrophic partner of
      mesophilic acetate-oxidising bacteria, a syntrophic relationship
      operating close to the thermodynamic equilibrium and of considerable importance
      in ammonia-rich engineered biogas processes. Methanoculleus bourgensis strain
      MAB1 belongs to the order Methanomicrobiales, family Methanomicrobiaceae, within
      the phylum Euryarchaeota. The genome shows a total size of 2,859,299 bp encoding
      3450 predicted protein-encoding genes, of which only 1472 (43 %) have been
      assigned tentative functions. The genome encodes further 44 tRNA genes and three
      rRNA genes (5S, 16S and 23S rRNA). This study presents assembling and annotation
      features as well as genomic traits related to ammonia tolerance and
      methanogenesis.
AU  - Manzoor S
AU  - Schnurer A
AU  - Bongcam-Rudloff E
AU  - Muller B
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 80.

PMID- 22418622
VI  - 6
DP  - 2012
TI  - Genomic evidence of rapid, global-scale gene flow in a Sulfolobus species.
PG  - 1613-1616
AB  - Local populations of Sulfolobus islandicus diverge genetically with geographical
      separation, and this has been attributed to restricted transfer of propagules
      imposed by the unfavorable spatial distribution of acidic geothermal habitat. We
      tested the generality of genetic divergence with distance in Sulfolobus species
      by analyzing genomes of Sulfolobus acidocaldarius drawn from three populations
      separated by more than 8000 km. In sharp contrast to S. islandicus, the
      geographically diverse S. acidocaldarius genomes proved to be nearly identical.
      We could not link the difference in genome conservation between the two species
      to a corresponding difference in genome stability or ecological factors affecting
      propagule dispersal. The results provide the first evidence that genetic
      isolation of local populations does not result primarily from properties
      intrinsic to Sulfolobus and the severe discontinuity of its geothermal habitat,
      but varies with species, and thus may reflect biotic interactions that act after
      propagule dispersal.
AU  - Mao D
AU  - Grogan D
PT  - Journal Article
TA  - ISME J.
JT  - ISME J.
SO  - ISME J. 2012 6: 1613-1616.

PMID- 28854637
VI  - 9
DP  - 2017
TI  - Comparative genomics of the dual-obligate symbionts from the treehopper, Entylia carinata (Hemiptera: Membracidae), provide insight into the origins and evolution of an ancient symbioses.
PG  - 1803-1815
AB  - 
AU  - Mao M
AU  - Yang X
AU  - Poff K
AU  - Bennett G
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2017 9: 1803-1815.

PMID- 
VI  - 5
DP  - 2013
TI  - Real Time in Vitro Regulation of DNA Methylation Using a 5-Fluorouracil Conjugated DNA-Based Stimuli-Responsive Platform.
PG  - 2604-2609
AB  - DNA methylation, catalyzed by methylases, plays a critical role in many biological processes,
      and many methylases have been regarded as
      promising targets for antimicrobial drugs. In this work, we report a
      stimulus responsive, self-regulating anticancer drug release platform,
      comprising a multifunctional DNA that upon methylation by
      methyltransferase (MTase) releases 5-fluorouracil (5-Fu) and in turn
      inhibits subsequent expression of MTase. The multifunctional DNA with
      anticancer drug are first methylated by DNA adenine methylation (DAM)
      methyltransferase (MTase) and then cut by the methylation-sensitive
      restriction endonuclease Dpn I. Removal of duplex from the functional
      DNA by the methylation/cleavage process will release the anticancer
      drug, resulting in inhibition of the activity of DAM in turn.
      Consequently, the enzyme activity of DAM MTase can be self-regulated.
      Furthermore, we found that the inhibition efficiency of 5-Fu
      significantly increase as it is functionalized with DNA.
AU  - Mao XH
AU  - Wei M
AU  - Zhu CF
AU  - Lu JX
AU  - Gao JM
AU  - Simon AJ
AU  - Shi JY
AU  - Huang Q
AU  - Fan CH
PT  - Journal Article
TA  - ACS Appl. Mater. Inter.
JT  - ACS Appl. Mater. Inter.
SO  - ACS Appl. Mater. Inter. 2013 5: 2604-2609.

PMID- 26227596
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Lactobacillus sp. Strain TCF032-E4, Isolated from Fermented Radish.
PG  - e00821-15
AB  - Here, we report the draft genome sequence of Lactobacillus sp. strain TCF032-E4 (= CCTCC
      AB2015090 = DSM 100358), isolated from a Chinese fermented radish. The
      total length of the 57 contigs is about 2.9 Mb, with a G+C content of 43.5 mol%
      and 2,797 predicted coding sequences (CDSs).
AU  - Mao Y
AU  - Chen M
AU  - Horvath P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00821-15.

PMID- 23929479
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Pseudomonas plecoglossicida Strain NB2011, the Causative Agent of White Nodules in Large Yellow Croaker (Larimichthys crocea).
PG  - e00586-13
AB  - We describe the draft genome sequence of Pseudomonas plecoglossicida strain NB2011, the
      causative agent of white nodules in cultured large yellow croaker
      (Larimichthys crocea) in China. The draft genome sequence of the bacterium
      consists of 5.41 million bp, with a G+C content of 62.8%. A total of 4,952 genes
      were identified.
AU  - Mao Z
AU  - Li M
AU  - Chen J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00586-13.

PMID- 22947175
VI  - 13
DP  - 2012
TI  - Comparative genomics of Brachyspira pilosicoli strains: genome rearrangements, reductions and correlation of genetic compliment with phenotypic diversity.
PG  - 454
AB  - ABSTRACT: BACKGROUND: The anaerobic spirochaete Brachyspira pilosicoli causes
      enteric disease in avian, porcine and human hosts, amongst others. To date, the
      only available genome sequence of B. pilosicoli is that of strain 95/1000, a
      porcine isolate. In the first intra-species genome comparison within the
      Brachyspira genus, we report the whole genome sequence of B. pilosicoli B2904, an
      avian isolate, the incomplete genome sequence of B. pilosicoli WesB, a human
      isolate, and the comparisons with B. pilosicoli 95/1000. We also draw on
      incomplete genome sequences from three other Brachyspira species. Finally we
      report the first application of the high-throughput Biolog phenotype screening
      tool on the B. pilosicoli strains for detailed comparisons between genotype and
      phenotype. RESULTS: Feature and sequence genome comparisons revealed a high
      degree of similarity between the three B. pilosicoli strains, although the
      genomes of B2904 and WesB were larger than that of 95/1000 (~2,765, 2.890 and
      2.596 Mb, respectively). Genome rearrangements were observed which correlated
      largely with the positions of mobile genetic elements. Through comparison of the
      B2904 and WesB genomes with the 95/1000 genome, features that we propose are
      non-essential due to their absence from 95/1000 include a peptidase, glycine
      reductase complex components and transposases. Novel bacteriophages were detected
      in the newly-sequenced genomes, which appeared to have involvement in intra- and
      inter-species horizontal gene transfer. Phenotypic differences predicted from
      genome analysis, such as the lack of genes for glucuronate catabolism in 95/1000,
      were confirmed by phenotyping. CONCLUSIONS: The availability of multiple B.
      pilosicoli genome sequences has allowed us to demonstrate the substantial genomic
      variation that exists between these strains, and provides an insight into genetic
      events that are shaping the species. In addition, phenotype screening allowed
      determination of how genotypic differences translated to phenotype. Further
      application of such comparisons will improve understanding of the metabolic
      capabilities of Brachyspira species.
AU  - Mappley LJ
AU  - Black ML
AU  - Abuoun M
AU  - Darby AC
AU  - Woodward MJ
AU  - Parkhill J
AU  - Turner AK
AU  - Bellgard MI
AU  - La T
AU  - Phillips ND
AU  - La Ragione RM
AU  - Hampson DJ
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2012 13: 454.

PMID- 26404598
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Methicillin-Resistant Clinical Staphylococcus aureus Isolate 51S (Sequence Type 291).
PG  - e01050-15
AB  - We report the draft genome sequence of a methicillin-resistant clinical Staphylococcus aureus
      isolate with a novel spa type and sequence type (ST291), isolated from a renal failure patient
      in Rawalpindi, Pakistan.
AU  - Marasa BS
AU  - Khan S
AU  - Iram S
AU  - Sung K
AU  - Xu J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01050-15.

PMID- 24604656
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of a Methicillin-Resistant Staphylococcus aureus ST1413 Strain for Studying Genetic Mechanisms of Antibiotic Resistance.
PG  - e00162-14
AB  - Here we report the whole draft genome sequence of a methicillin-resistant Staphylococcus
      aureus ST1413 strain. Determining the distribution and arrangement
      of various genes associated with drug resistance, toxicity, and diseases will
      enhance our understanding about its adaptability to thrive in different
      ecological niches and help in the development of effective treatments for
      enterotoxigenic staphylococcal infections.
AU  - Marasa BS
AU  - Revollo J
AU  - Iram S
AU  - Sung K
AU  - Xu J
AU  - Khan S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00162-14.

PMID- 26798111
VI  - 4
DP  - 2016
TI  - Complete Genome Sequences of Salmonella enterica Serovars Anatum and Anatum var.  15+, Isolated from Retail Ground Turkey.
PG  - e01619-15
AB  - The complete genome sequences of two isolates of Salmonella enterica serovars Anatum and
      Anatum var. 15+ revealed the presence of two plasmids of 112 kb and 3
      kb in size in each. The chromosome of Salmonella Anatum (4.83 Mb) was slightly
      smaller than that of Salmonella Anatum var. 15+ (4.88 Mb).
AU  - Marasini D
AU  - Abo-Shama UH
AU  - Fakhr MK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01619-15.

PMID- 26798110
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequencing of Salmonella enterica subsp. enterica Serovar Ouakam Isolated from Ground Turkey.
PG  - e01618-15
AB  - In this report, we announce the first whole-genome sequencing of Salmonella enterica subsp.
      enterica serovar Ouakam strain GNT-01, isolated from ground
      turkey retail meat. The strain has a chromosome of 5,088,451 bp long, with a G+C
      content of 52.3%, and a plasmid of 109,715 bp.
AU  - Marasini D
AU  - Abo-Shama UH
AU  - Fakhr MK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01618-15.

PMID- 29167261
VI  - 5
DP  - 2017
TI  - The Whole-Genome Sequence of Bacillus velezensis Strain SB1216 Isolated from the  Great Salt Plains of Oklahoma Reveals the Presence of a Novel Extracellular RNase  with Antitumor Activity.
PG  - e01343-17
AB  - The whole-genome sequence of Bacillus velezensis strain SB1216, isolated from the Great Salt
      Plains of Oklahoma, showed the presence of a 3,814,720-bp circular
      chromosome and no plasmids. The presence of a novel 870-bp extracellular RNase
      gene is predicted to be responsible for this strain's antitumor activity.
AU  - Marasini D
AU  - Cornell CR
AU  - Oyewole O
AU  - Sheaff RJ
AU  - Fakhr MK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01343-17.

PMID- 27635012
VI  - 4
DP  - 2016
TI  - Complete Genome Sequences of the Plasmid-Bearing Campylobacter coli Strains HC2-48, CF2-75, and CO2-160 Isolated from Retail Beef Liver.
PG  - e01004-16
AB  - The complete genome sequences of Campylobacter coli strains HC2-48, CF2-75, and CO2-160,
      isolated from retail beef liver, showed the presence of 1,663,782-,
      1,711,393-, and 1,683,224-bp circular chromosomes and 44,064-, 44,233-, and
      44,228-bp circular plasmids, respectively. This is the first reported
      Campylobacter coli genome sequence isolated from retail beef liver.
AU  - Marasini D
AU  - Fakhr MK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01004-16.

PMID- 29217797
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of Plasmid-Bearing Campylobacter coli and Campylobacter jejuni Strains Isolated from Retail Chicken Liver.
PG  - e01350-17
AB  - Complete genome sequences of Campylobacter coli strains WA333, YF2105, BG2108, MG1116, and
      BP3183 and Campylobacter jejuni strain IF1100 isolated from retail
      chicken liver showed the presence of 1,841,551-, 1,687,232-, 1,695,638-,
      1,665,146-, 1,695,360-, and 1,744,171-bp circular chromosomes, respectively.
      These isolates also contained plasmids ranging in size from 5,209 to 55,122 bp.
AU  - Marasini D
AU  - Fakhr MK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01350-17.

PMID- 27688318
VI  - 4
DP  - 2016
TI  - Complete Genome Sequences of Campylobacter jejuni Strains OD267 and WP2202 Isolated from Retail Chicken Livers and Gizzards Reveal the Presence of Novel  116-Kilobase and 119-Kilobase Megaplasmids with Type VI Secretion Systems.
PG  - e01060-16
AB  - Genome sequences of Campylobacter jejuni strains OD267 and WP2202, isolated from  chicken
      livers and gizzards, showed the presence of novel 116-kb and 119-kb
      megaplasmids, respectively. The two megaplasmids carry a type VI secretion system
      and tetracycline resistance genes. These are the largest sequenced Campylobacter
      plasmids to date.
AU  - Marasini D
AU  - Fakhr MK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01060-16.

PMID- 27231378
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequencing of a Campylobacter jejuni Strain Isolated from Retail Chicken Meat Reveals the Presence of a Megaplasmid with Mu-Like Prophage and  Multidrug Resistance Genes.
PG  - e00460-16
AB  - Genome sequencing of Campylobacter jejuni strain T1-21 isolated from retail chicken meat
      revealed the presence of a chromosome of 1,565,978 bp and a
      megaplasmid of 82,732 bp that contains Mu-like prophage and multidrug resistance
      genes. This is the first reported sequence of a Campylobacter megaplasmid >55 kb.
AU  - Marasini D
AU  - Fakhr MK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00460-16.

PMID- 29167266
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of Plasmid-Bearing Multidrug-Resistant Campylobacter jejuni and Campylobacter coli Strains with Type VI Secretion Systems, Isolated  from Retail Turkey and Pork.
PG  - e01360-17
AB  - We report the complete genome sequences of multidrug-resistant Campylobacter jejuni and
      Campylobacter coli isolated from retail turkey and pork, respectively.
      The chromosomes of these two isolates contained type VI secretion system genes.
      The two isolates also harbored large plasmids with antimicrobial resistance genes
      possibly contributing to their multidrug resistance.
AU  - Marasini D
AU  - Fakhr MK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01360-17.

PMID- 29167263
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of Campylobacter jejuni Strains Isolated from Retail Chicken and Chicken Gizzards.
PG  - e01351-17
AB  - Genome sequences of Campylobacter jejuni FJ3124 and ZP3204 isolated from retail chicken
      gizzards and Campylobacter jejuni TS1218 isolated from retail chicken
      showed the presence of 1,694,324-, 1,763,161-, and 1,762,596-bp circular
      chromosomes, respectively. Campylobacter jejuni ZP3204 and TS1218 harbored large
      tetracycline resistance plasmids with type IV secretion systems.
AU  - Marasini D
AU  - Fakhr MK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01351-17.

PMID- 19915993
VI  - 67
DP  - 2010
TI  - Homing endonucleases: from basics to therapeutic applications.
PG  - 727-748
AB  - Homing endonucleases (HE) are double-stranded DNAses that target large recognition sites
      (12-40 bp). HE-encoding sequences are usually embedded in either introns or inteins. Their
      recognition sites are extremely rare, with none or only a few of these sites present in a
      mammalian-sized genome. However, these enzymes, unlike standard restriction endonucleases,
      tolerate some sequence degeneracy within their recognition sequence. Several members of this
      enzyme family have been used as templates to engineer tools to cleave DNA sequences that
      differ from their original wild-type targets. These custom HEs can be used to stimulate
      double-strand break homologous recombination in cells, to induce the repair of defective genes
      with very low toxicity levels. The use of tailored HEs opens up new possibilities for gene
      therapy in patients with monogenic diseases that can be treated ex vivo. This review provides
      an overview of recent advances in this field.
AU  - Marcaida MJ et al
PT  - Journal Article
TA  - Cell. Mol. Life Sci.
JT  - Cell. Mol. Life Sci.
SO  - Cell. Mol. Life Sci. 2010 67: 727-748.

PMID- 18974222
VI  - 105
DP  - 2008
TI  - Crystal structure of I-DmoI in complex with its target DNA provides new insights into meganuclease engineering.
PG  - 16888-16893
AB  - Homing endonucleases, also known as meganucleases, are sequence-specific enzymes with large
      DNA recognition sites. These enzymes can be used to
      induce efficient homologous gene targeting in cells and plants, opening
      perspectives for genome engineering with applications in a wide series of
      fields, ranging from biotechnology to gene therapy. Here, we report the
      crystal structures at 2.0 and 2.1 A resolution of the I-DmoI meganuclease
      in complex with its substrate DNA before and after cleavage, providing
      snapshots of the catalytic process. Our study suggests that I-DmoI
      requires only 2 cations instead of 3 for DNA cleavage. The structure sheds
      light onto the basis of DNA binding, indicating key residues responsible
      for nonpalindromic target DNA recognition. In silico and in vivo analysis
      of the I-DmoI DNA cleavage specificity suggests that despite the
      relatively few protein-base contacts, I-DmoI is highly specific when
      compared with other meganucleases. Our data open the door toward the
      generation of custom endonucleases for targeted genome engineering using
      the monomeric I-DmoI scaffold.
AU  - Marcaida MJ
AU  - Prieto J
AU  - Redondo P
AU  - Nadra AD
AU  - Alibes A
AU  - Serrano L
AU  - Grizot S
AU  - Duchateau P
AU  - Paques F
AU  - Blanco FJ
AU  - Montoya G
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2008 105: 16888-16893.

PMID- 10700093
VI  - 18
DP  - 2000
TI  - Enzymes by post-restriction enzyme stability.
PG  - 243
AB  - The authors suggest that many restriction enzymes are sufficiently stable at room temperature
      that they could be transported abroad without expensive ice-packs or dry ice.
AU  - March JB
AU  - Clark J
PT  - Journal Article
TA  - Nat. Biotechnol.
JT  - Nat. Biotechnol.
SO  - Nat. Biotechnol. 2000 18: 243.

PMID- 28126939
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Lactococcus piscium CNCM I-4031, a Bioprotective Strain for Seafood Products.
PG  - e01510-16
AB  - Lactococcus piscium CNCM I-4031 is a psychotrophic foodborne lactic acid bacterium showing
      potential interest for the biopreservation of seafood products
      due to its inhibition properties toward pathogenic and spoilage bacteria. The
      analysis of its genome will provide a better understanding of the mechanisms of
      interaction between these bacteria.
AU  - Marche L
AU  - Saraoui T
AU  - Remenant B
AU  - Zagorec M
AU  - Prevost H
AU  - Delbarre-Ladrat C
AU  - Leroi F
AU  - Pilet MF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01510-16.

PMID- 721831
VI  - 253
DP  - 1978
TI  - Digestion of 5-bromodeoxyuridine-substituted lambda-DNA by restriction endonucleases.
PG  - 9075-9081
AB  - 5-bromodeoxyuridine (BrdUrd) DNA from bacteriophage lambda affects both the
      rates and sites of cleavage by Endo R.EcoRI, HindIII, and SmaI.  Endonucleases
      EcoRI and HindIII, both of which recognize nucleotide sequences that contain 4
      thymidine residues, cleaved fully substituted BrdUrd-DNA at the same sites as
      unsubstituted DNA.  However, when treated with limiting amounts of either of
      the two endonucleases, BrdUrd-DNA was digested more slowly than was the
      unsubstituted DNA.  Endo R.SmaI, which recognizes a nucleotide sequence that
      does not contain thymidine digested BrdUrd-DNA at approximately the same rate
      as unsubstituted DNA.  Surprisingly, one of the three SmaI sites in lambda-DNA
      (located at 0.656 on the genome's physical map) appeared to be highly resistant
      to cleavage by SmaI in substituted DNA.  Hence, cleavage of BrdUrd-DNA by SmaI
      generated three restriction products instead of the expected four products
      derived from unsubstituted DNA.  These BrdUrd-DNA products were identified as
      the characteristic SmaI.A and C fragments as well as an unusual, large product
      that contained the fused B and D fragments.  Therefore, the SmaI cleavage site
      at the junction of the B-D fragments appears to differ from the other two sites
      by aspects of DNA structure determined outside of the canonical SmaI
      recognition sequence.  This finding indicates that site-specific DNA enzymes
      can be influenced by DNA determinants that reside outside of the accepted
      recognition sequences of the enyzmes.
AU  - Marchionni MA
AU  - Roufa DJ
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1978 253: 9075-9081.

PMID- 28705981
VI  - 5
DP  - 2017
TI  - High-Quality Draft Genome Sequence of Lactobacillus casei Strain Z11, Isolated from a Human Adult Intestinal Biopsy Sample.
PG  - e00634-17
AB  - Several Lactobacillus casei strains are used as probiotics. L. casei strain Z11,  isolated
      from a human colon biopsy sample, has been suggested as a probiotic
      candidate based on promising properties in vitro Here, we present a 2.74-Mbp
      high-quality draft genome sequence for this strain.
AU  - Marcial-Coba MS
AU  - Marshall IPG
AU  - Schreiber L
AU  - Nielsen DS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00634-17.

PMID- 23661477
VI  - 1
DP  - 2013
TI  - Whole-Genome Sequence of the Microcin E492-Producing Strain Klebsiella pneumoniae RYC492.
PG  - e00178-13
AB  - Here, we report the draft genome sequence of the Gram-negative strain Klebsiella  pneumoniae
      RYC492, which produces the amyloid-forming and antibacterial peptide
      microcin E492. The sequenced genome consists of a 5,095,761-bp assembled open
      chromosome where the gene cluster for microcin production is located in a
      putative 31-kb genomic island flanked by sequence repeats and containing a
      putative integrase-coding gene.
AU  - Marcoleta A
AU  - Gutierrez-Cortez S
AU  - Maturana D
AU  - Monasterio O
AU  - Lagos R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00178-13.

PMID- 24482524
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Bacillus thuringiensis Strain BrMgv02-JM63, a Chitinolytic Bacterium Isolated from Oil-Contaminated Mangrove Soil in Brazil.
PG  - e01264-13
AB  - Here, we report the draft genome sequence and the automatic annotation of Bacillus
      thuringiensis strain BrMgv02-JM63. This genome comprises a set of genes
      involved in the metabolism of chitin and N-acetylglucosamine utilization, thus
      suggesting the possible role of this strain in the cycling of organic matter in
      mangrove soils.
AU  - Marcon J
AU  - Taketani RG
AU  - Dini-Andreote F
AU  - Mazzero GI
AU  - Soares FLJ
AU  - Melo IS
AU  - Azevedo JL
AU  - Andreote FD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01264-13.

PMID- 10094673
VI  - 181
DP  - 1999
TI  - Chromosome methylation and measurement of faithful, once and only once per cell cycle chromosome replication in Caulobacter crescentus.
PG  - 1984-1993
AB  - Caulobacter crescentus exhibits cell-type-specific control of chromosome replication and DNA
      methylation.  Asymmetric cell division yields a replicating stalked cell and a nonreplicating
      swarmer cell.  The motile swarmer cell must differentiate into a sessile stalked cell in order
      to replicate and execute asymmetric cell division.  This program of cell division implies that
      chromosome replication initiates in the stalked cell only once per cell cycle.  DNA
      methylation is restricted to the predivisional cell stage, and since DNA synthesis produces an
      unmethylated nascent strand, late DNA methylation also implies that DNA near the replication
      origin remains hemimethylated longer than DNA located further away.  In this report, both
      assumptions are tested with an engineered Tn5-based transposon, Tn5omega-MP.  This allows a
      sensitive Southern blot assay that measures fully methylated, hemimethylated, and unmethylated
      DNA duplexes.  Tn5omega-MP DNA near the replication origin remained hemimethylated longer than
      DNA located further away.  One Tn5omega-MP placed near the replication origin revealed small
      but detectable amounts of unmethylated duplex DNA in replicating stalked cells.  Extra DNA
      synthesis produces a second unmethylated nascent strand.  Therefore, measurement of
      unmethylated DNA is a critical test of the "once and only once per cell cycle" rule of
      chromosome replication in C. crescentus.  Fewer than 1 in 1,000 stalked cells prematurely
      initiate a second round of chromosome replication.  The implications for very precise negative
      control of chromosome replication are discussed with respect to the bacterial cell cycle.
AU  - Marczynski GT
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1999 181: 1984-1993.

PMID- 
VI  - 49
DP  - 2013
TI  - New low-copy plasmid in cyanobacterium Anabaena variabilis.
PG  - 798-805
AB  - Complete genome sequencing was performed for Anabaena variabilis ATCC 29413 from the
      collection of the Chair of Genetics, Department of
      Biology, Moscow State University, Russia. In addition to known plasmids
      A, B, and C, a new circular low-copy plasmid was detected and named D.
      It was also sequenced completely and found to have 27051 bp. The
      plasmid contained the parA and parB genes of the partition system, two
      genes that encode replication proteins, a gene for site-specific
      recombinase, a type-I restriction-modification system, and several
      genes with unknown functions. Analysis by PCR revealed the presence of
      plasmid D in two epiphytic strains from Vietnam, i.e., Anabaena sp. 182
      and Anabaena sp. 281, as well as in Anabaena sp. V5 and A. azollae
      (Newton's isolate).
AU  - Mardanov AV
AU  - Beletskii AV
AU  - Gumerov VM
AU  - Karbysheva EA
AU  - Mikheeva LE
PT  - Journal Article
TA  - Genetika
JT  - Genetika
SO  - Genetika 2013 49: 798-805.

PMID- 25414512
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Escherichia coli Strain VKPM B-10182, Producing the Enzyme for Synthesis of Cephalosporin Acids.
PG  - e01222-14
AB  - Escherichia coli strain VKPM B-10182, obtained by chemical mutagenesis from E. coli strain
      ATCC 9637, produces cephalosporin acid synthetase employed in the
      synthesis of beta-lactam antibiotics, such as cefazolin. The draft genome
      sequence of strain VKPM B-10182 revealed 32 indels and 1,780 point mutations that
      might account for the improvement in antibiotic synthesis that we observed.
AU  - Mardanov AV
AU  - Eldarov MA
AU  - Sklyarenko AV
AU  - Dumina MV
AU  - Beletsky AV
AU  - Yarotsky SV
AU  - Ravin NV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01222-14.

PMID- 21478349
VI  - 193
DP  - 2011
TI  - Complete genome sequence of the thermoacidophilic crenarchaeon Thermoproteus uzoniensis 768-20.
PG  - 3156-3157
AB  - Thermoproteus uzoniensis 768-20 is a thermoacidophilic anaerobic crenarchaeon isolated from a
      solfataric field in Kamchatka, Russia. The
      complete genome sequence reveals genes for protein and carbohydrate-active
      enzymes, beta-oxidation of fatty acids, the Embden-Meyerhof and
      Entner-Doudoroff pathways for glucose metabolism, the tricarboxylic acid
      cycle, the dicarboxylate/4-hydroxybutyrate cycle, hydrogenase and sulfur
      reductase.
AU  - Mardanov AV
AU  - Gumerov VM
AU  - Beletsky AV
AU  - Prokofeva MI
AU  - Bonch-Osmolovskaya EA
AU  - Ravin NV
AU  - Skryabin KG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3156-3157.

PMID- 22247528
VI  - 194
DP  - 2012
TI  - Complete genome sequence of strain 1860, a crenarchaeon of the genus pyrobaculum able to grow with various electron acceptors.
PG  - 727-728
AB  - Strain 1860, a novel member of the genus Pyrobaculum, is a hyperthermophilic organotrophic
      crenarchaeon growing anaerobically with
      various electron acceptors. The complete genome sequence reveals genes for
      several membrane-bound oxidoreductases, the Embden-Meyerhof and
      Entner-Doudoroff pathways for glucose metabolism, the tricarboxylic acid
      cycle, the glyoxylate cycle, and the dicarboxylate/4-hydroxybutyrate
      cycle.
AU  - Mardanov AV
AU  - Gumerov VM
AU  - Slobodkina GB
AU  - Beletsky AV
AU  - Bonch-Osmolovskaya EA
AU  - Ravin NV
AU  - Skryabin KG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 727-728.

PMID- 22843584
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of the Hyperthermophilic Cellulolytic Crenarchaeon 'Thermogladius cellulolyticus' 1633.
PG  - 4446-4447
AB  - Strain 1633, a novel member of the genus Thermogladius, isolated from a freshwater hot spring,
      is an anaerobic hyperthermophilic crenarchaeon capable of
      fermenting proteinaceous and cellulose substrates. The complete genome sequence
      reveals genes for protein and carbohydrate-active enzymes, the Embden-Meyerhof
      pathway for glucose metabolism, cytoplasmic NADP-dependent hydrogenase, and
      several energy-coupling membrane-bound oxidoreductases.
AU  - Mardanov AV
AU  - Kochetkova TV
AU  - Beletsky AV
AU  - Bonch-Osmolovskaya EA
AU  - Ravin NV
AU  - Skryabin KG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4446-4447.

PMID- 19447963
VI  - 75
DP  - 2009
TI  - Metabolic versatility and indigenous origin of the archaeon Thermococcus sibiricus, isolated from a siberian oil reservoir, as revealed by genome analysis.
PG  - 4580-4588
AB  - Thermococcus species are widely distributed in terrestrial and marine
      hydrothermal areas, as well as in deep subsurface oil reservoirs.
      Thermococcus sibiricus is a hyperthermophilic anaerobic archaeon isolated
      from a well of the never flooded oil-bearing Jurassic horizon of a
      high-temperature oil reservoir. To obtain insight into the genome of an
      archaeon inhabiting the oil reservoir, we have determined and annotated
      the complete 1,845,800-base genome of T. sibiricus. A total of 2,061
      protein-coding genes have been identified, 387 of which are absent in
      other members of the order Thermococcales. Physiological features and
      genomic data reveal numerous hydrolytic enzymes (e.g., cellulolytic
      enzymes, agarase, laminarinase, and lipases) and metabolic pathways,
      support the proposal of the indigenous origin of T. sibiricus in the oil
      reservoir, and explain its survival over geologic time and its
      proliferation in this habitat. Indeed, in addition to proteinaceous
      compounds known previously to be present in oil reservoirs at limiting
      concentrations, its growth was stimulated by cellulose, agarose, and
      triacylglycerides, as well as by alkanes. Two polysaccharide degradation
      loci were probably acquired by T. sibiricus from thermophilic bacteria
      following lateral gene transfer events. The first, a "saccharolytic gene
      island" absent in the genomes of other members of the order
      Thermococcales, contains the complete set of genes responsible for the
      hydrolysis of cellulose and beta-linked polysaccharides. The second
      harbors genes for maltose and trehalose degradation. Considering that
      agarose and laminarin are components of algae, the encoded enzymes and the
      substrate spectrum of T. sibiricus indicate the ability to metabolize the
      buried organic matter from the original oceanic sediment.
AU  - Mardanov AV
AU  - Ravin NV
AU  - Svetlitchnyi VA
AU  - Beletsky AV
AU  - Miroshnichenko ML
AU  - Bonch-Osmolovskaya EA
AU  - Skryabin KG
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2009 75: 4580-4588.

PMID- 25416759
VI  - 81
DP  - 2015
TI  - The genome of Geoglobus acetivorans: Fe(III) reduction, acetate utilization, autotrophic growth and degradation of aromatic compounds in a hyperthermophilic archaeon.
PG  - 1003-1012
AB  - Geoglobus acetivorans is a hyperthermophilic anaerobic euryarchaeon of the order
      Archaeoglobales isolated from deep-sea hydrothermal vents. A unique physiological
      feature of the members of the genus Geoglobus is their obligate dependence on
      Fe(III) reduction, which plays an important role in the geochemistry of
      hydrothermal systems. The features of this organism and its complete 1,860,815-bp
      genome sequence are described in this report. Genome analysis revealed pathways
      enabling oxidation of molecular hydrogen, proteinaceous substrates, fatty acids,
      aromatic compounds, n-alkanes and organic acids including acetate, through
      anaerobic respiration linked to Fe(III) reduction. Consistent with the inability
      of G. acetivorans to grow on carbohydrates, the modified Embden-Meyerhof pathway
      encoded by the genome is incomplete. Autotrophic CO2 fixation is enabled by the
      Wood-Ljungdahl pathway. Reduction of insoluble poorly crystalline Fe(III) oxide
      depends on the transfer of electrons from the quinone pool to multiheme c-type
      cytochromes exposed on the cell surface. Direct contact of the cells and Fe(III)
      oxide particles could be facilitated by pili-like appendages. Genome analysis
      indicated the presence of metabolic pathways for anaerobic degradation of
      aromatic compounds and n-alkanes, although the ability of G. acetivorans to grow
      on these substrates was not observed in laboratory experiments. Overall, our
      results suggest that Geoglobus species could play an important role in microbial
      communities of deep-sea hydrothermal vents as lithoautotrophic producers. An
      additional role as decomposers would close the biogeochemical cycle of carbon
      through complete mineralization of various organic compounds via Fe(III)
      respiration.
AU  - Mardanov AV
AU  - Slododkina GB
AU  - Slobodkin AI
AU  - Beletsky AV
AU  - Gavrilov SN
AU  - Kublanov IV
AU  - Bonch-Osmolovskaya EA
AU  - Skryabin KG
AU  - Ravin NV
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2015 81: 1003-1012.

PMID- 20581186
VI  - 76
DP  - 2010
TI  - The Genome Sequence of the Crenarchaeon Acidilobus saccharovorans Supports a New Order, Acidilobales, and Suggests an Important Ecological Role in Terrestrial Acidic Hot Springs.
PG  - 5652-5657
AB  - Acidilobus saccharovorans is an anaerobic, organotrophic,
      thermoacidophilic crenarchaeon isolated from a terrestrial hot spring. We
      report the complete genome sequence of A. saccharovorans, which has
      permitted the prediction of genes for Embden-Meyerhof and Entner-Doudoroff
      pathways and genes associated with the oxidative tricarboxylic acid cycle.
      The electron transfer chain is branched with two sites of proton
      translocation and is linked to the reduction of elemental sulfur and
      thiosulfate. The genomic data suggest an important role of the order
      Acidilobales in thermoacidophilic ecosystems whereby its members can
      perform a complete oxidation of organic substrates, closing the anaerobic
      carbon cycle.
AU  - Mardanov AV
AU  - Svetlitchnyi VA
AU  - Beletsky AV
AU  - Prokofeva MI
AU  - Bonch-Osmolovskaya EA
AU  - Ravin NV
AU  - Skryabin KG
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2010 76: 5652-5657.

PMID- 25237029
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Serratia grimesii Strain A2.
PG  - e00937-14
AB  - We report the first draft genome assembly of Serratia grimesii strain A2, previously
      identified as Escherichia coli strain A2, which produces protease
      ECP32 with a high specificity toward actin. S. grimesii strain A2 has multidrug
      resistance associated with a number of efflux pump genes.
AU  - Mardanova AM
AU  - Toymentseva AA
AU  - Gilyazeva AG
AU  - Kazakov SV
AU  - Shagimardanova EI
AU  - Khaitlina SY
AU  - Sharipova MR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00937-14.

PMID- 15699197
VI  - 151
DP  - 2005
TI  - Suppression subtractive hybridization as a basis to assess Mycoplasma agalactiae and Mycoplasma bovis genomic diversity and species-specific sequences.
PG  - 475-489
AB  - The phylogenically related Mycoplasma agalactiae and Mycoplasma bovis
      species are two ruminant pathogens difficult to differentiate and for
      which a limited amount of sequence data are available. To assess the
      degree of genomic diversity existing between and within these mycoplasma
      species, sets of DNA fragments specific for M. bovis type-strain PG45 or
      for M. agalactiae type-strain PG2 were isolated by suppression subtractive
      hybridization and used as probes on a panel of M. agalactiae and M. bovis
      field isolates. Results indicated that approximately 70 % of the DNA
      fragments specific to one or the other type strain are represented in all
      field isolates of the corresponding species. Only one M. bovis isolate,
      which was first classified as M. agalactiae, reacted with 15 % of the
      PG2-specific probes, while several M. agalactiae isolates reacted with 15
      % of the PG45-specific probes. Sequence analyses indicated that most of
      the genomic diversity observed within one species is related to ORFs with
      (i) no homologies to proteins recorded in the databases or (ii) homologies
      to proteins encoded by restriction modification systems. Reminiscent of
      gene transfer as a means for genomic diversity, a PG45-specific DNA
      fragment with significant homologies to a central protein of an
      integrative conjugative element of Mycoplasma fermentans (ICEF) was found
      in most M. bovis field isolates and in a few M. agalactiae isolates.
      Finally, sequences encoding part of DNA polymerase III were found in both
      sets of M. agalactiae- and M. bovis-specific DNA fragments and were used
      to design a species-specific PCR assay for the identification and
      differentiation of M. agalactiae and M. bovis.
AU  - Marenda MS
AU  - Sagne E
AU  - Poumarat F
AU  - Citti C
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2005 151: 475-489.

PMID- 28473372
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of the Aerobic Strains Lactobacillus gasseri AL3 and AL5.
PG  - e00213-17
AB  - Adaptation to the aerobic environment has been investigated in heterofermentative
      lactobacilli, while data on how homofermentative lactobacilli adapt to oxygen are
      limited. We report here the draft genome sequences of the aerobic strains
      Lactobacillus gasseri AL3 and AL5 that allow an in-depth investigation of the
      genes involved in oxidative metabolism and the stress response.
AU  - Maresca D
AU  - De Filippis F
AU  - Tytgat HLP
AU  - de Vos WM
AU  - Mauriello G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00213-17.

PMID- 22843594
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Antarctic Psychrophile Bacterium Planococcus antarcticus DSM 14505.
PG  - 4465
AB  - Planococcus antarcticus DSM 14505 is a psychrophile bacterium that was isolated from
      cyanobacterial mat samples, originally collected from ponds in McMurdo,
      Antarctica. This orange-pigmented bacterium grows at 4 degrees C and may possess
      interesting enzymatic activities at low temperatures. Here we report the first
      genomic sequence of P. antarcticus DSM 14505.
AU  - Margolles A
AU  - Gueimonde M
AU  - Sanchez B
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4465.

PMID- 28705983
VI  - 5
DP  - 2017
TI  - Completed Genome Sequences of Borrelia burgdorferi Sensu Stricto B31(NRZ) and Closely Related Patient Isolates from Europe.
PG  - e00637-17
AB  - Borrelia burgdorferi sensu stricto is a causative agent of human Lyme borreliosis in the
      United States and Europe. We report here the completed genome sequences of
      strain B31 isolated from a tick in the United States and two closely related
      strains from Europe, PAli and PAbe, which were isolated from patients with
      erythema migrans and neuroborreliosis, respectively.
AU  - Margos G
AU  - Hepner S
AU  - Mang C
AU  - Sing A
AU  - Liebl B
AU  - Fingerle V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00637-17.

PMID- 10715201
VI  - 297
DP  - 2000
TI  - Structure and Function of the Mouse DNA Methyltransferase Gene: Dnmt1 shows a Tripartite Structure.
PG  - 293-300
AB  - Dnmt1 is the predominant DNA methyltransferase (MTase) in mammals. The C-terminal domain of
      Dnmt1 clearly shares sequence similarity with many
      prokaryotic 5mC methyltransferases, and had been proposed to be sufficient for catalytic
      activity. We show here by deletion analysis that the C-terminal domain alone is not
      sufficient for methylating activity, but that a large part of the N-terminal domain is
      required in addition. Since this complex structure of Dnmt1 raises issues about its
      evolutionary origin, we have compared several eukaryotic MTases and have determined the
      genomic organization of the mouse Dnmt1 gene. The 5' most part of the
      N-terminal domain is dispensible for enzyme activity, includes the major nuclear import signal
      and comprises tissue-specific exons. Interestingly, the functional subdivision
      of Dnmt1 correlates well with the structure of the Dnmt1 gene in terms of intron/exon size
      distribution as well as sequence conservation. Our results, based on functional,
      structural and sequence comparison data, suggest that the gene has evolved from the fusion of
      at least three genes.
AU  - Margot JB
AU  - Aguirre-Arteta AM
AU  - Di Giacco BV
AU  - Pradhan S
AU  - Roberts RJ
AU  - Cardoso MC
AU  - Leonhardt H
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2000 297: 293-300.

PMID- 11596106
VI  - 83
DP  - 2001
TI  - Mammalian DNA methyltransferases show different subnuclear distributions.
PG  - 373-379
AB  - In mammalian cells, DNA methylation patterns are precisely maintained after DNA replication
      with defined changes occurring during development. The major DNA methyltransferase (Dnmt1) is
      associated with nuclear replication sites during S-phase, which is consistent with a role in
      maintenance methylation. The subcellular distribution of the recently discovered de novo DNA
      methyltransferases, Dnmt3a and Dnmt3b, was investigated by immunofluorescence and by epitope
      tagging. We now show that both Dnmt3a and Dnmt3b are distributed throughout the nucleoplasm
      but are not associated with nuclear DNA replication sites during S-phase. These results
      suggest that de novo methylation by Dnmt3a and Dnmt3b occurs independently of the replication
      process and might involve an alternative mechanism for accessing the target DNA. The different
      subcellular distribution of mammalian DNA methyltransferases might thus contribute to the
      regulation of DNA methylation.
AU  - Margot JB
AU  - Cardoso MC
AU  - Leonhardt H
PT  - Journal Article
TA  - J. Cell. Biochem.
JT  - J. Cell. Biochem.
SO  - J. Cell. Biochem. 2001 83: 373-379.

PMID- 12777184
VI  - 4
DP  - 2003
TI  - Interactions within the mammalian DNA methyltransferase family.
PG  - 7
AB  - BACKGROUND: In mammals, epigenetic information is established and maintained via the
      postreplicative methylation of cytosine residues by the
      DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b. Dnmt1 is required for
      maintenance methylation whereas Dnmt3a and Dnmt3b are responsible for de
      novo methylation. Contrary to Dnmt3a or Dnmt3b, the isolated C-terminal
      region of Dnmt1 is catalytically inactive, despite the presence of the
      sequence motifs typical of active DNA methyltransferases. Deletion
      analysis has revealed that a large part of the N-terminal domain is
      required for enzymatic activity. RESULTS: The role played by the
      N-terminal domain in this regulation has been investigated using the yeast
      two-hybrid system. We show here the presence of an intra-molecular
      interaction in Dnmt1 but not in Dnmt3a or Dnmt3b. This interaction was
      confirmed by immunoprecipitation and was localized by deletion mapping.
      Furthermore, a systematic analysis of interactions among the Dnmt family
      members has revealed that DNMT3L interacts with the C-terminal domain of
      Dnmt3a and Dnmt3b. CONCLUSIONS: The lack of methylating ability of the
      isolated C-terminal domain of Dnmt1 could be explained in part by a
      physical interaction between N- and C-terminal domains that apparently is
      required for activation of the catalytic domain. Our deletion analysis
      suggests that the tertiary structure of Dnmt1 is important in this process
      rather than a particular sequence motif. Furthermore, the interaction
      between DNMT3L and the C-terminal domains of Dnmt3a and Dnmt3b suggests a
      mechanism whereby the enzymatically inactive DNMT3L brings about the
      methylation of its substrate by recruiting an active methylase.
AU  - Margot JB
AU  - Ehrenhofer-Murray AE
AU  - Leonhardt H
PT  - Journal Article
TA  - BMC Mol. Biol.
JT  - BMC Mol. Biol.
SO  - BMC Mol. Biol. 2003 4: 7.

PMID- 16056220
VI  - 437
DP  - 2005
TI  - Genome sequencing in microfabricated high-density picolitre reactors.
PG  - 376-380
AB  - The proliferation of large-scale DNA-sequencing projects in recent years has
      driven a search for alternative methods to reduce time and cost. Here we describe
      a scalable, highly parallel sequencing system with raw throughput significantly
      greater than that of state-of-the-art capillary electrophoresis instruments. The
      apparatus uses a novel fibre-optic slide of individual wells and is able to
      sequence 25 million bases, at 99% or better accuracy, in one four-hour run. To
      achieve an approximately 100-fold increase in throughput over current Sanger
      sequencing technology, we have developed an emulsion method for DNA amplification
      and an instrument for sequencing by synthesis using a pyrosequencing protocol
      optimized for solid support and picolitre-scale volumes. Here we show the
      utility, throughput, accuracy and robustness of this system by shotgun sequencing
      and de novo assembly of the Mycoplasma genitalium genome with 96% coverage at
      99.96% accuracy in one run of the machine.
AU  - Margulies M et al
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2005 437: 376-380.

PMID- 26722012
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Streptomyces sp. Strain CCM_MD2014, Isolated from Topsoil in Woods Hole, Massachusetts.
PG  - e01506-15
AB  - Here, we present the complete genome sequence of Streptomyces sp. strain CCM_MD2014 (phylum
      Actinobacteria), isolated from surface soil in Woods Hole, MA.
      Its single linear chromosome of 8,274,043 bp in length has a 72.13% G+C content
      and contains 6,948 coding sequences.
AU  - Mariita RM
AU  - Bhatnagar S
AU  - Hanselmann K
AU  - Hossain MJ
AU  - Korlach J
AU  - Boitano M
AU  - Roberts RJ
AU  - Liles MR
AU  - Moss AG
AU  - Leadbetter JR
AU  - Newman DK
AU  - Dawson SC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01506-15.

PMID- 26722011
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Curtobacterium sp. Strain MR_MD2014, Isolated from Topsoil in Woods Hole, Massachusetts.
PG  - e01504-15
AB  - Here, we present the 3,443,800-bp complete genome sequence of Curtobacterium sp.  strain
      MR_MD2014 (phylum Actinobacteria). This strain was isolated from soil in
      Woods Hole, MA, as part of the 2014 Microbial Diversity Summer Program at the
      Marine Biological Laboratory in Woods Hole, MA.
AU  - Mariita RM
AU  - Bhatnagar S
AU  - Hanselmann K
AU  - Hossain MJ
AU  - Korlach J
AU  - Boitano M
AU  - Roberts RJ
AU  - Liles MR
AU  - Moss AG
AU  - Leadbetter JR
AU  - Newman DK
AU  - Dawson SC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01504-15.

PMID- 25265418
VI  - 9
DP  - 2014
TI  - Worldwide Occurrence of Integrative Conjugative Element Encoding Multidrug Resistance Determinants in Epidemic Vibrio cholerae O1.
PG  - E108728
AB  - In the last decades, there has been an increase of cholera epidemics caused by
      multidrug resistant strains. Particularly, the integrative and conjugative
      element (ICE) seems to play a major role in the emergence of multidrug resistant
      Vibrio cholerae. This study fully characterized, by whole genome sequencing, new
      ICEs carried by multidrug resistant V. cholerae O1 strains from Nigeria (2010)
      (ICEVchNig1) and Nepal (1994) (ICEVchNep1). The gene content and gene order of
      these two ICEs are the same, and identical to ICEVchInd5, ICEVchBan5 and
      ICEVchHai1 previously identified in multidrug resistant V. cholerae O1. This ICE
      is characterized by dfrA1, sul2, strAB and floR antimicrobial resistance genes,
      and by unique gene content in HS4 and HS5 ICE regions. Screening for ICEs, in
      publicly available V. cholerae genomes, revealed the occurrence and widespread
      distribution of this ICE among V. cholerae O1. Metagenomic analysis found
      segments of this ICE in marine environments far from the direct influence of the
      cholera epidemic. Therefore, this study revealed the epidemiology of a
      spatio-temporal prevalent ICE in V. cholerae O1. Its occurrence and dispersion in
      V. cholerae O1 strains from different continents throughout more than two decades
      can be indicative of its role in the fitness of the current pandemic lineage.
AU  - Marin MA
AU  - Fonseca EL
AU  - Andrade BN
AU  - Cabral AC
AU  - Vicente AC
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2014 9: E108728.

PMID- 23788544
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Methylobacterium mesophilicum Strain SR1.6/6, Isolated from Citrus sinensis.
PG  - e00356-13
AB  - Methylobacterium mesophilicum strain SR1.6/6 is an endophytic bacterium isolated  from a
      surface-sterilized Citrus sinensis branch. Ecological and biotechnological
      aspects of this bacterium, such as the genes involved in its association with the
      host plant and the primary oxidation of methanol, were annotated in the draft
      genome.
AU  - Marinho-Almeida D
AU  - Dini-Andreote F
AU  - Camargo-Neves AA
AU  - Juca-Ramos RT
AU  - Andreote FD
AU  - Carneiro AR
AU  - Oliveira-de-Souza LA
AU  - Caracciolo-Gomes-de-Sa PH
AU  - Ribeiro-Barbosa MS
AU  - Araujo WL
AU  - Silva A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00356-13.

PMID- 
VI  - 0
DP  - 1996
TI  - DNA Methylation.
PG  - 782-791
AB  - DNA methylation in bacteria is most often thought of in its
      role to protect DNA from restriction endonucleases.  In addition to this
      role, however, studies in Escherichia coli have shown that methylated
      bases have other biological functions.  As described below, DNA adenine
      methylation is frequently used to control the rate at which these
      functions exert their effects.  Thus it is primarily used for regulatory
      purposes.
AU  - Marinus MG
PT  - Journal Article
TA  - Methylation of DNA in Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology
JT  - Methylation of DNA in Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology
SO  - Methylation of DNA in Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology 1996 0: 782-791.

PMID- 
VI  - 0
DP  - 1987
TI  - Methylation of DNA.
PG  - 697-702
AB  - None
AU  - Marinus MG
PT  - Journal Article
TA  - Escherichia coli and Salmonella typhimurium: Cellular and molecular biology.
JT  - Escherichia coli and Salmonella typhimurium: Cellular and molecular biology.
SO  - Escherichia coli and Salmonella typhimurium: Cellular and molecular biology. 1987 0: 697-702.

PMID- 
VI  - 0
DP  - 1984
TI  - Methylation of prokaryotic DNA.
PG  - 81-109
AB  - The biological function of methylated bases in DNA of prokaryotes appears to be
      quite different than that of eukaryotes.  In this chapter, most of the
      information presented is derived fom studies with Escherichia coli K-12 simply
      because more is known about DNA methylation in this organism than in any other
      one.  Some data from certain E. coli bacteriophages also will be reviewed, in
      addition to selected aspects about DNA methylation in certain other
      prokaryotes.  Other recent reviews that complement this one are by Razin and
      Friedman (1981) and Hattman (1981).
AU  - Marinus MG
PT  - Journal Article
TA  - DNA Methylation. Biochemistry and Biological Significance.
JT  - DNA Methylation. Biochemistry and Biological Significance.
SO  - DNA Methylation. Biochemistry and Biological Significance. 1984 0: 81-109.

PMID- 10629194
VI  - 182
DP  - 2000
TI  - Recombination is essential for viability of an Escherichia coli dam (DNA adenine methyltransferase) mutant.
PG  - 463-468
AB  - Double mutants of Escherichia coli dam (DNA adenine methyltransferase) strains with ruvA,
      ruvB, or ruvC could not be constructed, whereas dam derivatives with recD, recF, recJ, and
      recR were viable.  The ruv gene products are required for Holliday junction translocation and
      resolution of recombination intermediates.  A dam recG (Holliday junction translocation)
      mutant strain was isolated but at a very much lower frequency than expected.  The inviability
      of a dam lexA (Ind-) host was abrogated by the simultaneous presence of plasmids encoding both
      recA and ruvAB.  This result indicates that of more than 20 SOS genes, only recA and ruvAB
      need to be derepressed to allow for dam mutant survival.  The presence of mutS or mutL
      mutations allowed the construction of dam lexA (Ind-) derivatives.  The requirement for recA,
      recB, recC, ruvA, ruvB, ruvC, and possibly recG gene expression indicates that recombination
      is essential for viability of dam bacteria probably to repair DNA double-strand breaks.  The
      effect of mutS and mutL mutations indicates that DNA mismatch repair is the ultimate source of
      most of these DNA breaks.  The requirement for recombination also suggests an explanation for
      the sensitivity of dam cells to certain DNA-damaging agents.
AU  - Marinus MG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2000 182: 463-468.

PMID- 3327459
VI  - 21
DP  - 1987
TI  - DNA methylation in Escherichia coli.
PG  - 113-131
AB  - None
AU  - Marinus MG
PT  - Journal Article
TA  - Annu. Rev. Genet.
JT  - Annu. Rev. Genet.
SO  - Annu. Rev. Genet. 1987 21: 113-131.

PMID- 3929017
VI  - 200
DP  - 1985
TI  - DNA methylation influences trpR promoter activity in Escherichia coli K-12.
PG  - 185-186
AB  - Methylation of adenine in the GATC-sequence of the -35 region of the trpR
      promoter decreases activity by 2-3 fold.
AU  - Marinus MG
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1985 200: 185-186.

PMID- 4589344
VI  - 127
DP  - 1973
TI  - Location of DNA methylase genes on the Escherichia coli K-12 genetic map.
PG  - 47-55
AB  - The genes responsible for DNA adenine methylation (dam) and DNA cytosine methylation (dcm)
      have been mapped on the E. coli K-12 genetic map. The dam gene is situated at min 65 and the
      gene order cysG-(trpS, dam)-aroB inferred. The dcm gene is located at min 37.5 and the gene
      order is supD-dcm-flaA1. In F' merodiploids, the dam and dcm alleles are recessive.
AU  - Marinus MG
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1973 127: 47-55.

PMID- 791938
VI  - 128
DP  - 1976
TI  - Adenine methylation of Okazaki fragments in Escherichia coli.
PG  - 853-854
AB  - In Escherichia coli polA lig-4 bacteria, the moles percent 6-methyladenine
      content of 10S deoxyribonucleic acid (Okazaki fragments) is 0.96 compared with
      1.4 for bulk desoxyribonucleic acid.
AU  - Marinus MG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1976 128: 853-854.

PMID- 6444406
VI  - 141
DP  - 1980
TI  - Influence of uvrD3, uvrE502, and recL152 mutations on the phenotypes of Escherichia coli K-12 dam mutants.
PG  - 223-226
AB  - The recF143 allele did not alter the phenotypes of dam mutants of Escherichia coli. The uvrD3,
      uvrE502, and recL152 mutations did alter some of the phenotypes of dam bacteria. It was
      concluded that the uvrD, uvrE, and recL gene products are involved in the same
      deoxyribonucleic acid repair pathway as the dam gene product.
AU  - Marinus MG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1980 141: 223-226.

PMID- 6316110
VI  - 192
DP  - 1983
TI  - Insertion mutations in the dam gene of Escherichia coli K-12.
PG  - 288-289
AB  - The dam gene of E. coli can be inactivated by insertion of Tn9 or Mud phage. Strains bearing
      these mutations are viable indicating that the dam gene product is dispensable.
AU  - Marinus MG
AU  - Carraway M
AU  - Frey AZ
AU  - Brown L
AU  - Arraj JA
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1983 192: 288-289.

PMID- 19175412
VI  - 33
DP  - 2009
TI  - Roles of DNA adenine methylation in host-pathogen interactions: mismatch repair, transcriptional regulation, and more.
PG  - 488-503
AB  - The DNA adenine methyltransferase (Dam methylase) of Gammaproteobacteria and the cell
      cycle-regulated methyltransferase (CcrM) methylase of Alphaproteobacteria catalyze an
      identical reaction (methylation of adenosine moieties using S-adenosyl-methionine as a methyl
      donor) at similar DNA targets (GATC and GANTC, respectively). Dam and CcrM are of independent
      evolutionary origin. Each may have evolved from an ancestral restriction-modification system
      that lost its restriction component, leaving an 'orphan' methylase devoted solely to
      epigenetic genome modification. The formation of 6-methyladenine reduces the thermodynamic
      stability of DNA and changes DNA curvature. As a consequence, the methylation state of
      specific adenosine moieties can affect DNA-protein interactions. Well-known examples include
      binding of the replication initiation complex to the methylated oriC, recognition of
      hemimethylated GATCs in newly replicated DNA by the MutHLS mismatch repair complex, and
      discrimination of methylation states in promoters and regulatory DNA motifs by RNA polymerase
      and transcription factors. In recent years, Dam and CcrM have been shown to play roles in
      host-pathogen interactions. These roles are diverse and have only partially been understood.
      Especially intriguing is the evidence that Dam methylation regulates virulence genes in
      Escherichia coli, Salmonella, and Yersinia at the posttranscriptional level.
AU  - Marinus MG
AU  - Casadesus J
PT  - Journal Article
TA  - FEMS Microbiol. Rev.
JT  - FEMS Microbiol. Rev.
SO  - FEMS Microbiol. Rev. 2009 33: 488-503.

PMID- 799245
VI  - 149
DP  - 1976
TI  - Hyper-recombination in dam mutants of Escherichia coli K-12.
PG  - 273-277
AB  - F-prime heterogenotes of dam-3 bacteria segregate F-prime homogenotes at a frequency 30-200
      times higher than the isogenic dam+ strain. A hyperrecombination mutant which shows increased
      recombination between chromosomal duplications was characterized as a dam mutant. The dam-3
      allele causes a reduction in linkage of proximal unselected markers in transconjugants and
      increases the recombination frequency between a pair of closely linked markers. It is
      concluded that dam mutations confer a hyperrecombination phenotype to the cell.
AU  - Marinus MG
AU  - Konrad EB
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1976 149: 273-277.

PMID- 
VI  - 
DP  - 2009
TI  - DNA Methylation.
PG  - 1-51
AB  - DNA methylation in bacteria is most often thought of in its role to protect DNA from
      restriction endonucleases.  In addition to this role, however, studies in Escherichia coli,
      Salmonella enteric serovar Typhimurium (referred to as serovar Typhimurium hereafter), and
      Caulobacter crescentus have shown that methylated bases have other biological functions.  In
      these cases, the methylated bases are not part of a restriction/modification system and the
      enzymes that produce them are often referred to as orphan or solitary DNA methyltransferases.
      The postreplicative DNA methylation produced by this enzyme superimposes on the primary DNA
      sequence secondary information that has significance for DNA transactions such as
      transcription, transposition, initiation of chromosome replication, mRNA utilization, and
      prevention of mutations by DNA repair.  These alterations are brought about in two ways, the
      first being simply a change in the steady-state level of the methyltransferase either up or
      down from normal.  The second mechanism is through the configuration of the nucleotide
      sequence subject to methylation; it can exist as symmetrically methylated, unmethylated, or
      two possible hemi-methylated arrangements.  The details about the changes in DNA transactions
      through alteration of methyltransferase levels or state of methylation sequences form the bulk
      of this review.
AU  - Marinus MG
AU  - Lobner-Olesen A
PT  - Journal Article
TA  - EcoSal-Escherichia coli and Salmonella: Cellular and Molecular Biology
JT  - EcoSal-Escherichia coli and Salmonella: Cellular and Molecular Biology
SO  - EcoSal-Escherichia coli and Salmonella: Cellular and Molecular Biology 2009 : 1-51.

PMID- 4600143
VI  - 85
DP  - 1974
TI  - Biological function for 6-methyladenine residues in the DNA of Escherichia coli K12.
PG  - 309-322
AB  - A strain of Escherichia coli K12 mutant at the dam-3 site contains 0.08 mole % 6-methyl
      adenine as compared to 0.5 mole % in the wild type, and the residual DNA methylation is not
      due to the K12 modification methylase specified by the hsp genes. The dam-3 mutant is more
      sensitive to ultraviolet irradiation and to mitomycin C than the wild type and also shows a
      higher mutability. DNA isolated from the dam-3 mutant contains single stranded breaks that are
      amplified in dam-3 polA12 and dam-3 lig-7 double mutants. A function of dam-specified 6-methyl
      adenine residues in DNA would, therefore, appear to be the protection of DNA from nuclease(s)
      that causes the development of breaks. Combination of dam-3 with polA,recA,recB and recC is
      lethal.
AU  - Marinus MG
AU  - Morris NR
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1974 85: 309-322.

PMID- 167279
VI  - 28
DP  - 1975
TI  - Pleiotropic effects of a DNA adenine methylation mutation (dam-3) in Escherichia coli K12.
PG  - 15-26
AB  - The dam-3 mutation results in a five-fold reduction in the number of 6-methyladenine (6-meA)
      residues in the DNA of E. coli K12 or phage lambda. The DNA of phage fd appears to be devoid
      of 6-meA when propagated on dam-3 bacteria. The phenotypic differences between dam-3 and dam+
      bacteria include: (1) increased free phage in lysogenic dam-3 cultures, (2) increased
      sensitivity to methyl methanesulfonate (MMS), (3) inviability of dam-3 lex-I strains, (4)
      lower molecular weight of DNA in dam-3 bacteria in the absence of DNA ligase and (5) increased
      rate of DNA degradation in dam-3 recA strains.
AU  - Marinus MG
AU  - Morris NR
PT  - Journal Article
TA  - Mutat. Res.
JT  - Mutat. Res.
SO  - Mutat. Res. 1975 28: 15-26.

PMID- 4576399
VI  - 114
DP  - 1973
TI  - Isolation of deoxyribonucleic acid methylase mutants of Escherichia coli K-12.
PG  - 1143-1150
AB  - Fourteen deoxyribonucleic acid (DNA) and 10 ribonucleic acid (RNA) methylation mutants were
      isolated from Escherichia coli K-12 by examining the ability of nucleic acids prepared from
      clones of unselected mutagenized cells to accept methyl groups from wild-type crude extract.
      Eleven of the DNA methylation mutants were deficient in 5-methylcytosine (5-MeC) and were
      designated Dcm. Three DNA methylation mutants were deficient in N6-methyladenine (N6-MeA) and
      were designated Dam. Extracts of the mutants were tested for DNA-cytosine:S-adenosylmethione
      and DNA-adenine:S-adenosylmethionine methyltransferase activities. With one exception, all of
      the mutants had reduced or absent activity. A representative Dcm mutation was located at 36 to
      37 min and a representative Dam mutation was located in the 60- to 66-min region on the
      genetic map. The Dcm mutants had no obvious associated phenotypic abnormality. The Dam mutants
      were defective in their ability to restrict lambda. None of the mutations had the effect of
      being lethal.
AU  - Marinus MG
AU  - Morris NR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1973 114: 1143-1150.

PMID- 6376282
VI  - 28
DP  - 1984
TI  - Correlation of DNA adenine methylase activity with spontaneous mutability in Escherichia coli K-12.
PG  - 123-125
AB  - Using a multicopy plasmid in which the tac promoter has been placed in front of the dam gene
      of Escherichia coli K-12, we show that levels of DNA adenine methylase activity are correlated
      with the spontaneous mutation frequency.
AU  - Marinus MG
AU  - Poteete A
AU  - Arraj JA
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1984 28: 123-125.

PMID- 6257722
VI  - 256
DP  - 1981
TI  - Purification of the gene 0.3 protein of bacteriophage T7, an inhibitor of the DNA restriction system of Escherichia coli.
PG  - 2573-2578
AB  - The gene 0.3 protein of bacteriophage T7 prevents the DNA restriction system of
      Escherichia coli from interfering with T7 infection.  A mutant strain of T7
      that greatly overproduces the 0.3 protein has been constructed and used for
      purification of this protein.  The 0.3 protein was found to be extremely acidic
      and can be separated from virtually all other proteins of the infected cell by
      chromatography on DEAE-cellulose.  Residual contaminating proteins and nucleic
      acids can be removed by gel filtration, but an even simpler final purification
      is possible, because under appropriate conditions the 0.3 protein is soluble in
      high concentrations of ethanol.  Thus, a simple, essentially two-step
      purification can produce about 50 mg of pure 0.3 protein from 30 liters of
      culture.  The purified protein appears to be a dimer of identical subunits.  As
      expected from its known function during infection, the purified 0.3 protein
      inhibits the nuclease and ATPase activities of partially purified EcoB, the DNA
      restriction enzyme of E. coli B, but it does not interfere with several
      different type II restriction endonucleases tested.  The inhibition of EcoB
      appears to require stoichiometric rather than catalytic amounts of 0.3 protein.
AU  - Mark K-K
AU  - Studier FW
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1981 256: 2573-2578.

PMID- 26205873
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Escherichia coli O157:H7 ATCC 35150 and a Nalidixic Acid-Resistant Mutant Derivative.
PG  - e00734-15
AB  - Shiga toxin-producing Escherichia coli strains, occasionally isolated from food,  are of
      public health importance. Here, we report on the 5.30-Mbp draft genome
      sequence of E. coli O157:H7 EDL931 (strain ATCC 35150) and the 5.32-Mbp draft
      genome sequence of a nalidixic acid-resistant mutant derivative used as a
      distinguishable control strain in food-testing laboratories.
AU  - Markell JA
AU  - Koziol AG
AU  - Lambert D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00734-15.

PMID- Not carried by PubMed...
VI  - 64
DP  - 1986
TI  - The response of Type II restriction endonucleases to single base pair mismatches in heteroduplex DNA.
PG  - 13-14
AB  - The Type II restriction endonucleases cleave double-stranded DNA at specific sites within
      short recognition sequences and have proven invaluable in the analysis and manipulation of
      genetic material.  In contrast, the Type I endonucleases, which cleave DNA non-specifically at
      varying distances from their recognition sequences, have played only a minor role in modern
      molecular genetics.  Factors affecting DNA recognition and cleavage have been carefully
      defined.  The resistance of mismatched heteroduplex DNA to digestion was initially reported
      for a Type I enzyme (EcoBI) and this has since been confirmed for a single Type II enzyme
      (EcoRI).  In this paper we extend this finding to four more Type II restriction enzymes,
      BamHI, AccI, KpnI and SmaI, using a novel assay for digestion of heteroduplex DNA.
AU  - Markie D
AU  - Tvrdeich G
AU  - Hill DF
AU  - Poulter R
PT  - Journal Article
TA  - Proc. Univ. Otago Med. Sch.
JT  - Proc. Univ. Otago Med. Sch.
SO  - Proc. Univ. Otago Med. Sch. 1986 64: 13-14.

PMID- 15294304
VI  - 37
DP  - 2004
TI  - A novel strategy for the expression and purification of the DNA methyltransferase, M.AhdI.
PG  - 236-242
AB  - Biochemical and structural studies of the methylase from the type 1 1/2 R-M system AhdI
      require the ability to purify this multisubunit enzyme
      in significant quantities in a soluble and active form. Several
      Escherichia coli expression systems were tested for their ability to
      produce the intact methylase but this could not be achieved in a simple
      co-expression system. Expression experiments were optimised to produce
      high yields of soluble M and S subunits as individual proteins.
      Temperature and conditions of induction proved to be the most useful
      factors and although purification of the S subunit was successful, an
      efficient strategy for the M subunit remained elusive. A novel strategy
      was developed in which individual subunits are expressed separately and
      the bacterial cells mixed before lysis. This method produced a high
      yield of the multi-subunit methylase when purified to homogeneity by
      means of heparin and size-exclusion chromatography. It was found to be
      essential, however, to remove tightly bound DNA by ammonium sulphate
      precipitation in 1 M NaCl. The intact methylase can now be consistently
      produced, avoiding the use of fusion proteins. The purified enzyme is
      stable over long time periods, unlike the individual subunits. This
      method may be of general application where the expression of
      multi-subunit proteins, or indeed their individual components, is
      problematic.
AU  - Marks P
AU  - McGeehan J
AU  - Kneale G
PT  - Journal Article
TA  - Protein Expr. Purif.
JT  - Protein Expr. Purif.
SO  - Protein Expr. Purif. 2004 37: 236-242.

PMID- 12771207
VI  - 31
DP  - 2003
TI  - Purification and characterization of a novel DNA methyltransferase, M.AhdI.
PG  - 2803-2810
AB  - We have cloned the M and S genes of the restriction-modification (R-M) system AhdI and have
      purified the resulting methyltransferase to
      homogeneity. M.AhdI is found to form a 170 kDa tetrameric enzyme having a
      subunit stoichiometry M2S2 (where the M and S subunits are responsible for
      methylation and DNA sequence specificity, respectively). Sedimentation
      equilibrium experiments show that the tetrameric enzyme dissociates to
      form a heterodimer at low concentration, with K(d) approximately 2 microM.
      The intact (tetrameric) enzyme binds specifically to a 30 bp DNA duplex
      containing the AhdI recognition sequence GACN5GTC with high affinity (K(d)
      approximately 50 nM), but at low enzyme concentration the DNA binding
      activity is governed by the dissociation of the tetramer into dimers,
      leading to a sigmoidal DNA binding curve. In contrast, only non-specific
      binding is observed if the duplex lacks the recognition sequence.
      Methylation activity of the purified enzyme was assessed by its ability to
      prevent restriction by the cognate endonuclease. The subunit structure of
      the M.AhdI methyltransferase resembles that of type I MTases, in contrast
      to the R.AhdI endonuclease which is typical of type II systems. AhdI
      appears to be a novel R-M system with properties intermediate between
      simple type II systems and more complex type I systems, and may represent
      an intermediate in the evolution of R-M systems.
AU  - Marks P
AU  - McGeehan J
AU  - Wilson G
AU  - Errington N
AU  - Kneale G
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2003 31: 2803-2810.

PMID- 27056220
VI  - 4
DP  - 2016
TI  - Genome Sequence of a Clinical Staphylococcus aureus Strain from a Prosthetic Joint Infection.
PG  - e00198-16
AB  - Here, we report the genome sequence ofStaphylococcus aureusLYO-S2, an isolate with sequence
      type (ST) 45 that was isolated in 2001 from a prosthetic joint
      infection.
AU  - Marques C
AU  - Franceschi C
AU  - Collin V
AU  - Laurent F
AU  - Chatellier S
AU  - Forestier C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00198-16.

PMID- 28360159
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Corynebacterium pseudotuberculosis Strain PA06 Isolated  from a Subauricular Abscess in an Ovine Host.
PG  - e00083-17
AB  - We report here the draft genome sequence of Corynebacterium pseudotuberculosis PA06, isolated
      from a subauricular abscess in an ovine host. C.
      pseudotuberculosis is a worldwide pathogen of small and large ruminants. The
      genome comprises 2,320,074 bp, with a G+C content of 52.2%, 2,195 coding
      sequences, 48 tRNAs, and three rRNAs.
AU  - Marques JM
AU  - de Moura VA
AU  - Lima AC
AU  - Paixao CT
AU  - Lobato AR
AU  - Alves JT
AU  - Guaraldi AL
AU  - Folador AR
AU  - Ramos RT
AU  - Silva A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00083-17.

PMID- 25883297
VI  - 3
DP  - 2015
TI  - Genome Sequence of Ureaplasma diversum Strain ATCC 49782.
PG  - e00314-15
AB  - Here, we report the complete genome sequence of Ureaplasma diversum strain ATCC 49782. This
      species is of bovine origin, having an association with reproductive
      disorders in cattle, including placentitis, fetal alveolitis, abortion, and birth
      of weak calves. It has a small circular chromosome of 975,425 bp.
AU  - Marques LM
AU  - Guimaraes AM
AU  - Martins HB
AU  - Rezende IS
AU  - Barbosa MS
AU  - Campos GB
AU  - do Nascimento NC
AU  - Dos Santos AP
AU  - Amorim AT
AU  - Santos VM
AU  - Messick JB
AU  - Timenetsky J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00314-15.

PMID- 
VI  - 1002
DP  - 2003
TI  - Potent inhibition of HhaI DNA methylase by the aglycon of 2-(1H)-pyrimidinone riboside (Zebularine) at the G(C)under-barGC recognition domain.
PG  - 154-164
AB  - A short oligodeoxynucleotide (ODN) with 2-(1H)-pyrimidinone at the HhaI DNA methyltransferase
      target site (GCGC) is shown to induce a level of inhibition of methyl transfer and thermal
      stability of the complex with the enzyme identical to that achieved with a similar ODN
      substituted with 5-azacytosine. The drugs responsible for these effects-zebularine and
      5-azacytidine/2'-deoxy-5-azacytidine-are contrasted in terms of chemical stability and
      possible metabolic activation by a brief structure-activit analysis.
AU  - Marquez VE
AU  - Eritja R
AU  - Kelley JA
AU  - Vanbemmel D
AU  - Christman J
PT  - Journal Article
TA  - Therapeutic Oligonucleotides
JT  - Therapeutic Oligonucleotides
SO  - Therapeutic Oligonucleotides 2003 1002: 154-164.

PMID- 14751833
VI  - 1002
DP  - 2003
TI  - Potent inhibition of HhaI DNA methylase by the aglycon of 2-(1H)-pyrimidinone riboside (Zebularine) at the GCGC recognition domain.
PG  - 154-164
AB  - A short oligodeoxynucleotide (ODN) with 2-(1H)-pyrimidinone at the HhaI DNA methyltransferase
      target site (GCGC) is shown to induce a level of
      inhibition of methyl transfer and thermal stability of the complex with
      the enzyme identical to that achieved with a similar ODN substituted with
      5-azacytosine. The drugs responsible for these effects-zebularine and
      5-azacytidine/2'-deoxy-5-azacytidine-are contrasted in terms of chemical
      stability and possible metabolic activation by a brief structure-activity
      analysis.
AU  - Marquez VE
AU  - Eritja R
AU  - Kelley JA
AU  - Vanbemmel D
AU  - Christman JK
PT  - Journal Article
TA  - Ann. NY Acad. Sci.
JT  - Ann. NY Acad. Sci.
SO  - Ann. NY Acad. Sci. 2003 1002: 154-164.

PMID- 
VI  - 9
DP  - 1999
TI  - Oligonucleotides containing 5,6-dihydro-5-azacytosine at CpG sites can produce potent inhibition of DNA cytosine-C5-methyltransferase without covalently binding to the enzyme.
PG  - 415-421
AB  - C5-cytosine methylation of DNA at CpG sites is catalyzed by DNA cytosine-C5-methyltransferase
      in both prokaryotes and eukaryotes.  The mechanism of transfer of the methyl group from the
      cofactor S-adenosyl-L-methionine to the target cytosine occurs in a similar fashion in most
      (if not all) C5-MTases, which share highly conserved sequence motifs in the catalytic and
      AdoMet binding regions.  In mammals, the enzyme is responsible for the maintenance of
      methylation patterns in the genome.  However, aberrant DNA methylation patterns are associated
      with tumorigenesis and are common in cancer.
AU  - Marquez VE
AU  - Goddard A
AU  - Alvarez E
AU  - Ford H Jr
AU  - Christman JK
AU  - Sheikhnejad G
AU  - Brank A
AU  - Marasco CJ
AU  - Suffrin JR
AU  - O'Gara M
AU  - Cheng X
PT  - Journal Article
TA  - Antisense Nucleic Acid Drug Dev.
JT  - Antisense Nucleic Acid Drug Dev.
SO  - Antisense Nucleic Acid Drug Dev. 1999 9: 415-421.

PMID- 11563060
VI  - 20
DP  - 2001
TI  - Inhibition of (cytosine C5)-methyltransferase by oligonucleotides containing flexible (cyclopentane) and conformationally constrained  (bicyclo[3.1.0]hexane) abasic sites.
PG  - 451-459
AB  - Pseudorotationally locked sugar analogues based on bicyclo[3.1.0]-hexane templates were placed
      in DNA duplexes as abasic target sites in the M.HhaI recognition sequence. The binding
      affinity
      of the enzyme increases when the abasic site is constrained to the
      South conformation and decreases when it is constrained to the North
      conformation. A structural understanding of these differences is
      provided.
AU  - Marquez VE
AU  - Wang PY
AU  - Nicklaus MC
AU  - Maier M
AU  - Manoharan M
AU  - Christman JK
AU  - Banavali NK
AU  - Mackerell AD
PT  - Journal Article
TA  - Nucleosides Nucleotides Nucleic Acids
JT  - Nucleosides Nucleotides Nucleic Acids
SO  - Nucleosides Nucleotides Nucleic Acids 2001 20: 451-459.

PMID- 28104655
VI  - 5
DP  - 2017
TI  - First Complete Providencia rettgeri Genome Sequence, the NDM-1-Producing Clinical Strain RB151.
PG  - e01472-16
AB  - Providencia rettgeri is an opportunistic bacterial pathogen of clinical significance due to
      its association with urinary tract infections and multidrug
      resistance. Here, we report the first complete genome sequence of P. rettgeri The
      genome of strain RB151 consists of a 4.8-Mbp chromosome and a 108-kbp
      blaNDM-1-positive plasmid.
AU  - Marquez-Ortiz RA
AU  - Haggerty L
AU  - Sim EM
AU  - Duarte C
AU  - Castro-Cardozo BE
AU  - Beltran M
AU  - Saavedra S
AU  - Vanegas N
AU  - Escobar-Perez J
AU  - Petty NK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01472-16.

PMID- 2703472
VI  - 171
DP  - 1989
TI  - Isolation of a Legionella pneumophila restriction mutant with increased ability to act as a recipient in heterospecific matings.
PG  - 2238-2240
AB  - The ability of Legionella pneumophila to act as a recipient of IncP and IncQ
      plasmids in matings with Escherichia coli varies widely from strain to strain.
      We found that the low efficiency of mating of the Philadelphia-1 strain is due
      to a type II restriction-modification system, and we isolated and characterized
      a Philadelphia-1 mutant that lacks the restriction enzyme activity.
AU  - Marra A
AU  - Shuman HA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1989 171: 2238-2240.

PMID- 7828932
VI  - 152
DP  - 1995
TI  - The transformation frequency of plasmids into Bacillus anthracis is affected by adenine methylation.
PG  - 75-78
AB  - Plasmids pLTV1 and pHV33, capable of replicating in both Gram+ and Gram- bacterial hosts
      (shuttle vectors), when derived from the Escherichia coli strain HB101, were inactive in an
      electro-transformation assay employing the Bacillus anthracis strains delta Ames-1 and delta
      V1B-1 as recipients.  The same plasmids isolated from the DNA methyltransferase
      (MTase)-deficient E. coli strain GM2929 (dam,dcm), were able to transform the B. anthracis
      strains at a frequency of 10/2-10/3 transformants/ug of plasmid DNA.  Efficient transformation
      was also obtained when the plasmids were propagated in strains of B. subtilis 168 (10/2-10/4
      transformants/ug of plasmid DNA).  The B. subtilis strains used are known to harbor
      restriction/modification systems that recognize cytosine as a target for methylation.  In
      contrast, no adenine methylation activities have been reported for these strains.  The data
      presented indicate that DNA containing methylated adenine residues is restricted in the B.
      anthracis strains studied here, resulting in decreased plasmid DNA-mediated transformation
      frequencies.  This inhibition could be alleviated by propagating plasmid species in
      MTase-deficient (dam) strains of E. coli or B. subtilis 168, before their introduction into
      strains of B. anthracis.
AU  - Marrero R
AU  - Welkos SL
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 152: 75-78.

PMID- 24407633
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Synechococcus sp. Strain CB0101, Isolated From the Chesapeake Bay Estuary.
PG  - e01111-13
AB  - Here, we report the draft genome sequence of the estuarine Synechococcus sp. strain CB0101.
      The genomics information of this strain will facilitate the study
      of the poorly understood Synechococcus subcluster 5.2 and how this strain is
      capable of thriving in a dynamic estuarine system, such as the Chesapeake Bay.
AU  - Marsan D
AU  - Wommack KE
AU  - Ravel J
AU  - Chen F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01111-13.

PMID- 26637170
VI  - 10
DP  - 2015
TI  - Genomic Epidemiology of an Endoscope-Associated Outbreak of Klebsiella pneumoniae Carbapenemase (KPC)-Producing K. pneumoniae.
PG  - E0144310
AB  - Increased incidence of infections due to Klebsiella pneumoniae carbapenemase
      (KPC)-producing Klebsiella pneumoniae (KPC-Kp) was noted among patients
      undergoing endoscopic retrograde cholangiopancreatography (ERCP) at a single
      hospital. An epidemiologic investigation identified KPC-Kp and non-KPC-producing,
      extended-spectrum beta-lactamase (ESBL)-producing Kp in cultures from 2
      endoscopes. Genotyping was performed on patient and endoscope isolates to
      characterize the microbial genomics of the outbreak. Genetic similarity of 51 Kp
      isolates from 37 patients and 3 endoscopes was assessed by pulsed-field gel
      electrophoresis (PFGE) and multi-locus sequence typing (MLST). Five patient and 2
      endoscope isolates underwent whole genome sequencing (WGS). Two KPC-encoding
      plasmids were characterized by single molecule, real-time sequencing. Plasmid
      diversity was assessed by endonuclease digestion. Genomic and epidemiologic data
      were used in conjunction to investigate the outbreak source. Two clusters of Kp
      patient isolates were genetically related to endoscope isolates by PFGE. A subset
      of patient isolates were collected post-ERCP, suggesting ERCP endoscopes as a
      possible source. A phylogeny of 7 Kp genomes from patient and endoscope isolates
      supported ERCP as a potential source of transmission. Differences in gene content
      defined 5 ST258 subclades and identified 2 of the subclades as
      outbreak-associated. A novel KPC-encoding plasmid, pKp28 helped define and track
      one endoscope-associated ST258 subclade. WGS demonstrated high genetic
      relatedness of patient and ERCP endoscope isolates suggesting ERCP-associated
      transmission of ST258 KPC-Kp. Gene and plasmid content discriminated the outbreak
      from endemic ST258 populations and assisted with the molecular epidemiologic
      investigation of an extended KPC-Kp outbreak.
AU  - Marsh JW
AU  - Krauland MG
AU  - Nelson JS
AU  - Schlackman JL
AU  - Brooks AM
AU  - Pasculle AW
AU  - Shutt KA
AU  - Doi Y
AU  - Querry AM
AU  - Muto CA
AU  - Harrison LH
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2015 10: E0144310.

PMID- 17266985
VI  - 367
DP  - 2007
TI  - Restriction Endonucleases that Bridge and Excise Two Recognition Sites from DNA.
PG  - 419-431
AB  - Most restriction endonucleases bridge two target sites before cleaving DNA: examples include
      all of the translocating Type I and Type III
      systems, and many Type II nucleases acting at their sites. A subset of
      Type II enzymes, the IIB systems, recognise bipartite sequences, like Type
      I sites, but cut specified phosphodiester bonds near their sites, like
      Type IIS enzymes. However, they make two double-strand breaks, one either
      side of the site, to release the recognition sequence on a short DNA
      fragment; 34 bp long in the case of the archetype, BcgI. It has been
      suggested that BcgI needs to interact with two recognition sites to cleave
      DNA but whether this is a general requirement for Type IIB enzymes had yet
      to be established. Ten Type IIB nucleases were tested against DNA
      substrates with one or two copies of the requisite sequences. With one
      exception, they all bridged two sites before cutting the DNA, usually in
      concerted reactions at both sites. The sites were ideally positioned in
      cis rather than in trans and were bridged through 3-D space, like Type II
      enzymes, rather than along the 1-D contour of the DNA, as seen with Type I
      enzymes. The standard mode of action for the restriction enzymes that
      excise their recognition sites from DNA thus involves concurrent action at
      two DNA sites.
AU  - Marshall JJ
AU  - Gowers DM
AU  - Halford SE
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2007 367: 419-431.

PMID- 21653548
VI  - 39
DP  - 2011
TI  - Concerted action at eight phosphodiester bonds by the BcgI restriction endonuclease.
PG  - 7630-7640
AB  - The BcgI endonuclease exemplifies a subset of restriction enzymes, the Type IIB class, which
      make two double-strand breaks (DSBs) at each copy of
      their recognition sequence, one either side of the site, to excise the
      sequence from the remainder of the DNA. In this study, we show that BcgI
      is essentially inactive when bound to a single site and that to cleave a
      DNA with one copy of its recognition sequence, it has to act in trans,
      bridging two separate DNA molecules. We also show that BcgI makes the two
      DSBs at an individual site in a highly concerted manner. Intermediates cut
      on one side of the site do not accumulate during the course of the
      reaction: instead, the DNA is converted straight to the final products cut
      on both sides. On DNA with two sites, BcgI bridges the sites in cis and
      then generally proceeds to cut both strands on both sides of both sites
      without leaving the DNA. The BcgI restriction enzyme can thus excise two
      DNA segments together, by cleaving eight phosphodiester bonds within a
      single-DNA binding event.
AU  - Marshall JJ
AU  - Smith RM
AU  - Ganguly S
AU  - Halford SE
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2011 39: 7630-7640.

PMID- 20298193
VI  - 38
DP  - 2010
TI  - The Type IIB restriction endonucleases.
PG  - 410-416
AB  - The endonucleases from the Type IIB restriction-modification systems differ from all other
      restriction enzymes. The Type IIB enzymes cleave
      both DNA strands at specified locations distant from their recognition
      sequences, like Type IIS nucleases, but they are unique in that they do
      so on both sides of the site, to liberate the site from the remainder
      of the DNA on a short duplex. The fact that these enzymes cut DNA at
      specific locations mark them as Type II systems, as opposed to the Type
      I enzymes that cut DNA randomly, but in terms of gene organization and
      protein assembly, most Type IIB restriction-modification systems have
      more in common with Type I than with other Type II systems. Our current
      knowledge of the Type IIB systems is reviewed in the present paper.
AU  - Marshall JJT
AU  - Halford SE
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 2010 38: 410-416.

PMID- 26494659
VI  - 3
DP  - 2015
TI  - Genome Sequence of 'Candidatus Thioglobus singularis' Strain PS1, a Mixotroph from the SUP05 Clade of Marine Gammaproteobacteria.
PG  - e01155-15
AB  - Mixotrophic marine bacteria from the SUP05 clade are ubiquitous in the ocean. Here, we
      announce the complete genome sequence of 'Candidatus Thioglobus singularis' strain PS1, the
      first cultured mixotrophic representative from the SUP05 clade.
AU  - Marshall KT
AU  - Morris RM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01155-15.

PMID- 8143739
VI  - 220
DP  - 1994
TI  - The I-CeuI endonuclease: purification and potential role in the evolution of Chlamydomonas group I introns.
PG  - 855-859
AB  - During genetic crosses between the interfertile green algae Chlamydomonas eugametos and
      Chlamydomonas moewusii, the I-CeuI endonuclease encoded by the fifth group I intron (CeLSU.5)
      in the C. eugametos chloroplast large subunit rRNA gene mediates the mobility of this intron
      by introducing a double-strand break near the insertion site of the intron in the
      corresponding C. moewusii intronless allele.  To characterize the biochemical properties of
      this endonuclease, we have purified I-CeuI and determined the optimal reaction conditions for
      cleavage.  I-CeuI activity is maximal at 50oC, pH 10.0, 2.5 mM MgCl2 and in the absence of
      NaCl.  Unlike the well-characterized I-SceI endonuclease, I-CeuI remains stable following
      preincubation in the absence of substrate.  We discuss the role that homing endonucleases may
      have played in the evolution of Chlamydomonas chloroplast group I introns.
AU  - Marshall P
AU  - Davis TB
AU  - Lemieux C
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1994 220: 855-859.

PMID- 1475201
VI  - 20
DP  - 1992
TI  - The I-CeuI endonuclease recognizes a sequence of 19 base pairs and preferentially cleaves the coding strand of the Chlamydomonas moewusii chloroplast large subunit rRNA gene.
PG  - 6401-6407
AB  - The I-CeuI endonuclease is a member of the growing family of homing endonucleases that
      catalyse mobility of group I introns by making a double-strand break at the homing site of
      these introns in cognate intronless alleles during genetics crosses. In a previous study, we
      have shown that a short DNA fragment of 26 bp, encompassing the homing site of the fifth
      intron in the Chlamydomonas eugametos chloroplast large subunit rRNA gene (Ce LSU.5), was
      sufficient for I-CeuI recognition and cleavage. Here, we report the recognition sequence of
      the I-CeuI endonuclease, as determined by random mutagenesis of nucleotide positions adjacent
      to the I-CeuI cleavage site. Single-base substitutions that completely abolish endonuclease
      activity delimit a 15-bp sequence whereas those that reduce the cleavage rate define a 19-bp
      sequence that extends from position -7 to position +12 with respect to the Ce LSU.5 intron
      insertion site. As the other homing endonucleases that have been studied so far, the I-CeuI
      endonuclease recognizes a non-symmetric degenerate sequence. The top strand of the recognition
      sequence is preferred for I-CeuI cleavage and the bottom strand most likely determines the
      rate of double-strand breaks.
AU  - Marshall P
AU  - Lemieux C
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 6401-6407.

PMID- 1916294
VI  - 104
DP  - 1991
TI  - Cleavage pattern of the homing endonuclease encoded by the fifth intron in the chloroplast large subunit rRNA-encoding gene of Chlamydomonas eugametos.
PG  - 241-245
AB  - The fifth group-I intron in the chloroplast large subunit rRNA-encoding gene of Chlamydomonas
      eugametos (CeLSU.5) is mobile during interspecific crosses between C. eugametos and
      Chlamydomonas moewusii. Like the six other mobile introns that have been well characterized so
      far, CeLSU.5 contains a long open reading frame (ceuIR) coding for a site-specific
      endonuclease (I-CeuI) that cleaves the C. moewsuii intronless gene in the vicinity of the
      intron-insertion site. This stimulates gap repair and mediates efficient transfer of the
      intron at its cognate site. By expressing the ceuIR gene in the Escherichia coli vectors
      pKK233-2 and pTRC-99A, we recently demonstrated that the endonuclease is highly toxic to E.
      coli. To eliminate this problem and characterize the cleavage pattern and recognition sequence
      of the I-CeuI endonuclease, we have expressed the ceuIR gene in E. coli under the control of a
      bacteriophage T7 promoter in a tightly regulated M13 system, and developed an in vitro system
      to assay partially purified I-CeuI activity. This allowed us to determine that I-CeuI
      recognizes a sequence of less than 26 bp centered around the insertion site and produces a
      staggered cut 5 bp downstream from this site, yielding 4-nucleotide (CTAA), 3'-OH overhangs.
AU  - Marshall P
AU  - Lemieux C
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1991 104: 241-245.

PMID- 22388749
VI  - 109
DP  - 2012
TI  - Rapid diversification of coevolving marine Synechococcus and a virus.
PG  - 4544-4549
AB  - Marine viruses impose a heavy mortality on their host bacteria, whereas at the
      same time the degree of viral resistance in marine bacteria appears to be high.
      Antagonistic coevolution-the reciprocal evolutionary change of interacting
      species-might reconcile these observations, if it leads to rapid and dynamic
      levels of viral resistance. Here we demonstrate the potential for extensive
      antagonistic coevolution between the ecologically important marine cyanobacterium
      Synechococcus and a lytic virus. In a 6-mo-long replicated chemostat experiment,
      Synechococcus sp. WH7803 and the virus (RIM8) underwent multiple coevolutionary
      cycles, leading to the rapid diversification of both host and virus. Over the
      course of the experiment, we detected between 4 and 13 newly evolved viral
      phenotypes (differing in host range) and between 4 and 11 newly evolved
      Synechococcus phenotypes (differing in viral resistance) in each chemostat.
      Genomic analysis of isolates identified several candidate genes in both the host
      and virus that might influence their interactions. Notably, none of the viral
      candidates were tail fiber genes, thought to be the primary determinants of host
      range in tailed bacteriophages, highlighting the difficulty in generalizing
      results from bacteriophage infecting gamma-Proteobacteria. Finally, we show that
      pairwise virus-host coevolution may have broader community consequences;
      coevolution in the chemostat altered the sensitivity of Synechoccocus to a
      diverse suite of viruses, as well as the virus' ability to infect additional
      Synechococcus strains. Our results indicate that rapid coevolution may contribute
      to the generation and maintenance of Synechococcus and virus diversity and
      thereby influence viral-mediated mortality of these key marine bacteria.
AU  - Marston MF
AU  - Pierciey FJ Jr
AU  - Shepard A
AU  - Gearin G
AU  - Qi J
AU  - Yandava C
AU  - Schuster SC
AU  - Henn MR
AU  - Martiny JB
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2012 109: 4544-4549.

PMID- 24336369
VI  - 1
DP  - 2013
TI  - Genome Sequence of Salmonella bongori Strain N268-08.
PG  - e01018-13
AB  - Volume 1, no. 4, e00580-13, 2013. Page 1: The article title should read as given above. After
      the publication of this article, we were
      made aware of the fact that strain N268-08 was not isolated from a clinical sample.
AU  - Marti R
AU  - Hagens S
AU  - Loessner MJ
AU  - Klumpp J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01018-13.

PMID- 23969046
VI  - 1
DP  - 2013
TI  - Genome Sequence of Salmonella bongori Strain N268-08, a Rare Clinical Isolate.
PG  - e00580-13
AB  - Salmonella bongori is a close relative of the highly virulent members of S. enterica
      subspecies enterica, encompassing more than 2,500 serovars, most of
      which cause human salmonellosis, one of the leading food-borne illnesses. S.
      bongori is only very rarely implicated in infections. We here present the
      sequence of a clinical isolate from Switzerland, S. bongori strain N268-08.
AU  - Marti R
AU  - Hagens S
AU  - Loessner MJ
AU  - Klumpp J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00580-13.

PMID- 28550056
VI  - 83
DP  - 2017
TI  - Biofilm Formation Potential of Heat-Resistant Escherichia coli Dairy Isolates and the Complete Genome of Multidrug-Resistant, Heat-Resistant Strain FAM21845.
PG  - e00628-17
AB  - We tested the biofilm formation potential of 30 heat-resistant and 6 heat-sensitive
      Escherichia coli dairy isolates. Production of curli and
      cellulose, static biofilm formation on polystyrene (PS) and stainless steel
      surfaces, biofilm formation under dynamic conditions (Bioflux), and initial
      adhesion rates (IAR) were evaluated. Biofilm formation varied greatly between
      strains, media, and assays. Our results highlight the importance of the
      experimental setup in determining biofilm formation under conditions of interest,
      as correlation between different assays was often not a given. The
      heat-resistant, multidrug-resistant (MDR) strain FAM21845 showed the strongest
      biofilm formation on PS and the highest IAR and was the only strain that formed
      significant biofilms on stainless steel under conditions relevant to the dairy
      industry, and it was therefore fully sequenced. Its chromosome is 4.9 Mb long,
      and it harbors a total of five plasmids (147.2, 54.2, 5.8, 2.5, and 1.9 kb). The
      strain carries a broad range of genes relevant to antimicrobial resistance and
      biofilm formation, including some on its two large conjugative plasmids, as
      demonstrated in plate mating assays.IMPORTANCE In biofilms, cells are embedded in
      an extracellular matrix that protects them from stresses, such as UV radiation,
      osmotic shock, desiccation, antibiotics, and predation. Biofilm formation is a
      major bacterial persistence factor of great concern in the clinic and the food
      industry. Many tested strains formed strong biofilms, and especially strains such
      as the heat-resistant, MDR strain FAM21845 may pose a serious issue for food
      production. Strong biofilm formation combined with diverse resistances (some
      encoded on conjugative plasmids) may allow for increased persistence,
      coselection, and possible transfer of these resistance factors. Horizontal gene
      transfer may conceivably occur in the food production setting or the
      gastrointestinal tract after consumption.
AU  - Marti R
AU  - Schmid M
AU  - Kulli S
AU  - Schneeberger K
AU  - Naskova J
AU  - Knochel S
AU  - Ahrens CH
AU  - Hummerjohann J
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2017 83: e00628-17.

PMID- 28818913
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Klebsiella pneumoniae 704SK6, an OXA-48- and CTX-M-15-Encoding Wastewater Isolate.
PG  - e00831-17
AB  - The Swiss wastewater isolate Klebsiella pneumoniae 704SK6, encoding OXA-48 and CTX-M-15
      beta-lactamases, was fully sequenced. The assembly resulted in an open
      chromosome of 5,208,104 bp in size (G+C content, 57.6%) and four closed plasmid
      sequences of 209,651, 197,670, 65,998, and 63,605 bp in size.
AU  - Marti R
AU  - Stephan R
AU  - Klumpp J
AU  - Nuesch-Inderbinen M
AU  - Hummerjohann J
AU  - Bagutti C
AU  - Zurfluh K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00831-17.

PMID- 28818912
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Enterobacter cloacae 704SK10, an OXA-48-Encoding Wastewater Isolate.
PG  - e00830-17
AB  - Here we present the complete genome sequence of Enterobacter cloacae 704SK10, a Swiss
      wastewater isolate encoding an OXA-48 carbapenemase. Assembly resulted in
      closed sequences of the 4,876,946-bp chromosome, a 111,184-bp IncF plasmid, and
      an OXA-48-encoding IncL plasmid (63,458 bp) nearly identical to the previously
      described plasmid pOXA-48.
AU  - Marti R
AU  - Stephan R
AU  - Klumpp J
AU  - Nuesch-Inderbinen M
AU  - Hummerjohann J
AU  - Bagutti C
AU  - Zurfluh K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00830-17.

PMID- 11242099
VI  - 27
DP  - 2001
TI  - Chipping away at chromatin.
PG  - 240-241
AB  - When DNA-binding proteins are tethered to dam methylase from Escherichia coli. adenine
      methylation is directed to eukaryotic target
      sites in vivo. Hybridization of methylated DNA to microarrays allows
      binding sites to be displayed genome-wide, providing a versatile
      alternative to chromatin immunoprecipitation.
AU  - Martienssen R
PT  - Journal Article
TA  - Nat. Genet.
JT  - Nat. Genet.
SO  - Nat. Genet. 2001 27: 240-241.

PMID- 11498574
VI  - 293
DP  - 2001
TI  - DNA methylation and epigenetic inheritance in plants and filamentous fungi.
PG  - 1070-1074
AB  - Plants and filamentous fungi share with mammals enzymes responsible for DNA methylation. In
      these organisms, DNA methylation is associated with gene silencing and transposon control.
      However, plants and fungi differ from mammals in the genomic distribution, sequence
      specificity, and heritability of methylation. We consider the role that transposons play in
      establishing methylation patterns and the epigenetic consequences of their perturbation.
AU  - Martienssen RA
AU  - Colot V
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2001 293: 1070-1074.

PMID- 7613094
VI  - 5
DP  - 1995
TI  - DNA methylation in eukaryotes.
PG  - 234-242
AB  - Recent advances have expanded our understanding of the processes underlying the establishment,
      maintenance, and elaboration of DNA methylation patterns in eukaryotes.  The functional
      significance of DNA methylation is sought in a comparison of results on a variety of
      epigenetic phenomena in different eukaryotes.  The recent development of DNA methylation
      mutants in mice, Neurospora, and Arabadopsis will allow traditional genetic dissection to be
      applied to long-standing problems regarding the function and regulation of eukaryotic DNA
      methylation.  Although methylation appears to be important for maintenance of different
      epigenetic states, the mechanism that establishes these states is likely to involve additional
      processes.
AU  - Martienssen RA
AU  - Richards EJ
PT  - Journal Article
TA  - Curr. Opin. Genet. Dev.
JT  - Curr. Opin. Genet. Dev.
SO  - Curr. Opin. Genet. Dev. 1995 5: 234-242.

PMID- 10387089
VI  - 38
DP  - 1999
TI  - Divalent metal dependence of site-specific DNA binding by EcoRV endonuclease.
PG  - 8430-8439
AB  - Measurements of binding equilibria of EcoRV endonuclease to DNA, for a series of base-analogue
      substrates, demonstrate that expression of sequence selectivity is strongly enhanced by the
      presence of Ca2+ ions. Binding constants were determined for short duplex
      oligodeoxynucleotides containing the cognate DNA site, three cleavable noncognate sites, and a
      fully nonspecific site. At pH 7.5 and 100 mM NaCl, the full range of specificity from the
      specific (tightest binding) to nonspecific (weakest binding) sites is 0.9 kcal/mol in the
      absence of metal ions and 5.8 kcal/mol in the presence of Ca2+. Precise determination of
      binding affinities in the presence of the active Mg2+ cofactor was found to be possible for
      substrates retaining up to 1.6% of wild-type activity, as determined by the rate of phosphoryl
      transfer. These measurements show that Ca2+ is a near-perfect analogue for Mg2+ in binding
      reactions of the wild-type enzyme with DNA base-analogue substrates, as it provides identical
      DeltaDeltaG degrees bind values among the cleavable noncognate sites. Equilibrium dissociation
      constants of wild-type and base-analogue sites were also measured for the weakly active EcoRV
      mutant K38A, in the presence of either Mg2+ or Ca2+. In this case, Ca2+ allows expression of a
      greater degree of specificity than does Mg2+. DeltaDeltaG degrees/bind values of K38A toward
      specific versus nonspecific sites are 6.1 kcal/mol with Ca2+ and 3.9 kcal/mol with Mg2+,
      perhaps reflecting metal-specific conformational changes in the ground-state ternary
      complexes. The enhancement of binding specificity provided by divalent metal ions is likely to
      be general to many restriction endonucleases and other metal-dependent nucleic acid-modifying
      enzymes. These results strongly suggest that measurements of DNA binding affinities for EcoRV,
      and likely for many other restriction endonucleases, should be performed in the presence of
      divalent metal ions.
AU  - Martin AM
AU  - Horton NC
AU  - Luseti S
AU  - Reich NO
AU  - Perona JJ
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1999 38: 8430-8439.

PMID- 10074946
VI  - 6
DP  - 1999
TI  - Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease.
PG  - 269-277
AB  - Specific recognition by EcoRV endonuclease of its cognate, sharply bent GATATC site at the
      center TA step occurs solely via hydrophobic interaction with thymine methyl groups.
      Mechanistic kinetic analyses of base analog-substituted DNAs at this position reveal that
      direct readout provides 5 kcal mol(-1) toward specificity, with an additional 6-10 kcal
      mol(-1) arising from indirect readout. Crystal structures of several base analog complexes
      show that the major-groove hydrophobic contacts are crucial to forming required divalent
      metal-binding sites, and that indirect readout operates in part through the sequence-dependent
      free-energy cost of unstacking the center base-pair step of the DNA.
AU  - Martin AM
AU  - Sam MD
AU  - Reich NO
AU  - Perona JJ
PT  - Journal Article
TA  - Nat. Struct. Biol.
JT  - Nat. Struct. Biol.
SO  - Nat. Struct. Biol. 1999 6: 269-277.

PMID- 12504684
VI  - 12
DP  - 2002
TI  - SAM (dependent) I AM: the S-adenosylmethionine-dependent methyltransferase fold.
PG  - 783-793
AB  - The S-adenosylmethionine-dependent methyltransferase enzymes share little sequence identity,
      but incorporate a highly conserved structural
      fold. Surprisingly, residues that bind the common cofactor are poorly
      conserved, although the binding site is localised to the same region of
      the fold. The substrate-binding region of the fold varies enormously.
      Over the past two years, there has been a significant increase in the
      number of structures that are known to incorporate this fold, including
      several uncharacterised proteins and two proteins that lack
      methyltransferase activity.
AU  - Martin JL
AU  - McMillan FM
PT  - Journal Article
TA  - Curr. Opin. Struct. Biol.
JT  - Curr. Opin. Struct. Biol.
SO  - Curr. Opin. Struct. Biol. 2002 12: 783-793.

PMID- 16507099
VI  - 7
DP  - 2006
TI  - REtools: a laboratory program for restriction enzyme work: enzyme selection and reaction condition assistance.
PG  - 98
AB  - ABSTRACT : BACKGROUND : Restriction enzymes are one of the everyday tools used in molecular
      biology. The continuously expanding panel of known
      restriction enzymes (several thousands) renders their optimal use
      virtually impossible without computerized assistance. Several
      manufacturers propose on-line sites that assist scientists in their
      restriction enzyme work, however, none of these sites meet all the actual
      needs of laboratory workers, and they do not take into account the enzymes
      actually present in one's own laboratory. RESULTS : Using FileMaker Pro,
      we developed a stand-alone application which can run on both PCs and
      Macintoshes. We called it REtools, for Restriction Enzyme tools. This
      program, which references all currently known enzymes (>3500), permits the
      creation and update of a personalized list of restriction enzymes actually
      available in one's own laboratory. Upon opening the program, scientists
      will be presented with a user friendly interface that will direct them to
      different menus, each one corresponding to different situations that
      restriction enzyme users commonly encounter. We particularly emphasized
      the ease of use to make REtools a solution that laboratory members would
      actually want to use. CONCLUSION : REtools, a user friendly and easily
      customized program to organize any laboratory enzyme stock, brings a
      software solution that will make restriction enzyme use and reaction
      condition determination straightforward and efficient. The usually
      unexplored potential of isoschizomers also becomes accessible to all,
      since REtools proposes all possible enzymes similar to the one(s) chosen
      by the user. Finally, many of the commonly overlooked subtleties of
      restriction enzyme work, such as methylation requirement, unusual reaction
      conditions, or the number of flanking bases required for cleavage, are
      automatically provided by REtools.
AU  - Martin P
AU  - Boulukos KE
AU  - Pognonec P
PT  - Journal Article
TA  - BMC Bioinformatics
JT  - BMC Bioinformatics
SO  - BMC Bioinformatics 2006 7: 98.

PMID- 23989141
VI  - 69
DP  - 2013
TI  - Structural analysis of DNA-protein complexes regulating the restriction-modification system Esp1396I.
PG  - 962-966
AB  - The controller protein of the type II restriction-modification (RM) system Esp1396I binds to
      three distinct DNA operator sequences upstream
      of the methyltransferase and endonuclease genes in order to regulate
      their expression. Previous biophysical and crystallographic studies
      have shown molecular details of how the controller protein binds to the
      operator sites with very different affinities. Here, two protein-DNA
      co-crystal structures containing portions of unbound DNA from native
      operator sites are reported. The DNA in both complexes shows
      significant distortion in the region between the conserved symmetric
      sequences, similar to that of a DNA duplex when bound by the controller
      protein (C-protein), indicating that the naked DNA has an intrinsic
      tendency to bend when not bound to the C-protein. Moreover, the width
      of the major groove of the DNA adjacent to a bound C-protein dimer is
      observed to be significantly increased, supporting the idea that this
      DNA distortion contributes to the substantial cooperativity found when
      a second C-protein dimer binds to the operator to form the tetrameric
      repression complex.
AU  - Martin RNA
AU  - McGeehan JE
AU  - Ball NJ
AU  - Streeter SD
AU  - Thresh SJ
AU  - Kneale GG
PT  - Journal Article
TA  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
JT  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
SO  - Acta Crystallogr. F Struct. Biol. Cryst. Commun. 2013 69: 962-966.

PMID- 24887147
VI  - 9
DP  - 2014
TI  - Structural and Mutagenic Analysis of the RM Controller Protein C.Esp1396I.
PG  - e98365
AB  - Bacterial restriction-modification (RM) systems are comprised of two complementary enzymatic
      activities that prevent the establishment of foreign DNA in a bacterial cell: DNA methylation
      and DNA restriction. These two activities are tightly regulated to prevent over-methylation or
      auto-restriction. Many Type II RM systems employ a controller (C) protein as a transcriptional
      regulator for the endonuclease gene (and in some cases, the methyltransferase gene also). All
      high-resolution structures of C-protein/DNA-protein complexes solved to date relate to
      C.Esp1396I, from which the interactions of specific amino acid residues with DNA bases and/or
      the phosphate backbone could be observed. Here we present both structural and DNA binding data
      for a series of mutations to the key DNA binding residues of C.Esp1396I. Our results indicate
      that mutations to the backbone binding residues (Y37, S52) had a lesser affect on DNA binding
      affinity than mutations to those residues that bind directly to the bases (T36, R46), and the
      contributions of each side chain to the binding energies are compared. High-resolution X-ray
      crystal structures of the mutant and native proteins showed that the fold of the proteins was
      unaffected by the mutations, but also revealed variation in the flexible loop conformations
      associated with DNA sequence recognition. Since the tyrosine residue Y37 contributes to DNA
      bending in the native complex, we have solved the structure of the Y37F mutant protein/DNA
      complex by X-ray crystallography to allow us to directly compare the structure of the DNA in
      the mutant and native complexes.
AU  - Martin RNA
AU  - McGeehan JE
AU  - Kneale G
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2014 9: e98365.

PMID- 23846278
VI  - 1
DP  - 2013
TI  - Genome Sequence of Lactobacillus gastricus PS3, a Strain Isolated from Human Milk.
PG  - e00489-13
AB  - Lactobacillus gastricus is a mostly unknown lactobacilli species associated with  mucosal
      surfaces. We present the draft annotated genome sequence of L. gastricus
      strain PS3, isolated from a human milk sample, to provide new insights into its
      biology and to characterize those genes related to advantageous technological and
      beneficial properties.
AU  - Martin V
AU  - Cardenas N
AU  - Jimenez E
AU  - Maldonado A
AU  - Rodriguez JM
AU  - Fernandez L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00489-13.

PMID- 22843595
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Streptococcus salivarius PS4, a Strain Isolated from  Human Milk.
PG  - 4466-4467
AB  - Streptococcus salivarius is a commensal species commonly found in the human oropharyngeal
      tract. Some strains of this species have been developed for use as
      oral probiotics, while others have been associated with a variety of
      opportunistic human infections. Here, we report the complete sequence of strain
      PS4, which was isolated from breast milk of a healthy woman.
AU  - Martin V
AU  - Maldonado-Barragan A
AU  - Jimenez E
AU  - Ruas-Madiedo P
AU  - Fernandez L
AU  - Rodriguez JM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4466-4467.

PMID- 17878949
VI  - 2
DP  - 2007
TI  - Metagenomics of the deep mediterranean, a warm bathypelagic habitat.
PG  - e914
AB  - BACKGROUND: Metagenomics is emerging as a powerful method to study the
      function and physiology of the unexplored microbial biosphere, and is
      causing us to re-evaluate basic precepts of microbial ecology and
      evolution. Most marine metagenomic analyses have been nearly exclusively
      devoted to photic waters. METHODOLOGY/PRINCIPAL FINDINGS: We constructed a
      metagenomic fosmid library from 3,000 m-deep Mediterranean plankton, which
      is much warmer (approximately 14 degrees C) than waters of similar depth
      in open oceans (approximately 2 degrees C). We analyzed the library both
      by phylogenetic screening based on 16S rRNA gene amplification from clone
      pools and by sequencing both insert extremities of ca. 5,000 fosmids.
      Genome recruitment strategies showed that the majority of high scoring
      pairs corresponded to genomes from Rhizobiales within the
      Alphaproteobacteria, Cenarchaeum symbiosum, Planctomycetes, Acidobacteria,
      Chloroflexi and Gammaproteobacteria. We have found a community structure
      similar to that found in the aphotic zone of the Pacific. However, the
      similarities were significantly higher to the mesopelagic (500-700 m deep)
      in the Pacific than to the single 4000 m deep sample studied at this
      location. Metabolic genes were mostly related to catabolism, transport and
      degradation of complex organic molecules, in agreement with a prevalent
      heterotrophic lifestyle for deep-sea microbes. However, we observed a high
      percentage of genes encoding dehydrogenases and, among them, cox genes,
      suggesting that aerobic carbon monoxide oxidation may be important in the
      deep ocean as an additional energy source. CONCLUSIONS/SIGNIFICANCE: The
      comparison of metagenomic libraries from the deep Mediterranean and the
      Pacific ALOHA water column showed that bathypelagic Mediterranean
      communities resemble more mesopelagic communities in the Pacific, and
      suggests that, in the absence of light, temperature is a major stratifying
      factor in the oceanic water column, overriding pressure at least over 4000
      m deep. Several chemolithotrophic metabolic pathways could supplement
      organic matter degradation in this most depleted habitat.
AU  - Martin-Cuadrado AB
AU  - Lopez-Garcia P
AU  - Alba JC
AU  - Moreira D
AU  - Monticelli L
AU  - Strittmatter A
AU  - Gottschalk G
AU  - Rodriguez-Valera F
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2007 2: e914.

PMID- 18463691
VI  - 2
DP  - 2008
TI  - Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions.
PG  - 865-886
AB  - Marine planktonic archaea are widespread and abundant in deep oceanic waters but, despite
      their obvious ecological importance, little is known about them. Metagenomic analyses of large
      genome fragments allow access to both gene content and genome structure from single
      individuals of these cultivation-reluctant organisms. We present the comparative analysis of
      22 archaeal genomic clones containing 16S rRNA genes that were selected from four metagenomic
      libraries constructed from meso- and bathypelagic plankton of different oceanic regions (South
      Atlantic, Antarctic Polar Front,
      Adriatic and Ionian Sea; depths from 500 to 3000 m). We sequenced clones of the divergent
      archaeal lineages Group 1A (Crenarchaeota) and Group III (Euryarchaeota) as well as clones
      from the more frequent Group I Crenarchaeota and Group II Euryarchaeota. Whenever possible, we
      analysed
      clones that had identical or nearly identical 16S rRNA genes and that were retrieved from
      distant geographical locations, that is, that defined pan-oceanic operational taxonomic units
      (OTUs). We detected genes involved in nitrogen fixation in Group 1A Crenarchaeota, and genes
      involved in
      carbon fixation pathways and oligopeptide importers in Group I Crenarchaeota, which could
      confirm the idea that these are mixotrophic. A two-component system resembling that found in
      ammoniaoxidizing bacteria was found in Group III Euryarchaeota, while genes for anaerobic
      respiratory
      chains were detected in Group II Euryarchaeota. Whereas gene sequence conservation was high,
      and recombination and gene shuffling extensive within and between OTUs in Group I
      Crenarchaeota, gene sequence conservation was low and global synteny maintained in Group II
      Euryarchaeota. This implies remarkable differences in genome dynamics in Group I Crenarchaeota
      and Group II Euryarchaeota with recombination and mutation being, respectively, the dominant
      genome-shaping forces. These observations, along with variations in GC content, led us to
      hypothesize that the two groups of organisms have fundamentally different lifestyles.
AU  - Martin-Cuadrado AB
AU  - Rodriguez-Valera F
AU  - Moreira D
AU  - Alba JC
AU  - Ivars-Martinez E
AU  - Henn MR
AU  - Talla E
AU  - Lopez-Garcia P
PT  - Journal Article
TA  - ISME J.
JT  - ISME J.
SO  - ISME J. 2008 2: 865-886.

PMID- 24526651
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Sulfonamide Antibiotic-Degrading Microbacterium sp.  Strain C448.
PG  - e01113-13
AB  - We report the draft genome sequence of Microbacterium sp. strain C448, isolated from
      agricultural soil with a decade of exposure to veterinary antibiotics on the
      basis of using sulfamethazine and other antibiotics as the sole sources of
      carbon. The genome sequence revealed that strain C448 harbors several antibiotic
      resistance genes, including sulI.
AU  - Martin-Laurent F
AU  - Marti R
AU  - Waglechner N
AU  - Wright GD
AU  - Topp E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01113-13.

PMID- 24435868
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Hyphomicrobium nitrativorans Strain NL23, a Denitrifying Bacterium Isolated from Biofilm of a Methanol-Fed Denitrification  System Treating Seawater at the Montreal Biodome.
PG  - e01165-13
AB  - Hyphomicrobium nitrativorans strain NL23 has been isolated from the biofilm of a
      denitrification system treating seawater. This strain has the capacity to
      denitrify using methanol as a carbon source. Here, we report the complete genome
      sequence of this strain in an effort to increase understanding of the function of
      this bacterium within the biofilm.
AU  - Martineau C
AU  - Villeneuve C
AU  - Mauffrey F
AU  - Villemur R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01165-13.

PMID- 
VI  - 3
DP  - 2012
TI  - Small molecules DNA methyltransferases inhibitors.
PG  - 263-273
AB  - Methylation catalyzed by the DNA methyltransferases affects the C5 position of cytosine
      residues in DNA. This physiological process is
      active from the embryo conception, throughout all its developmental
      steps, and also later for the maintenance of the adult organism. Excess
      methylated cytosine in tumor suppressor genes is a consistent hallmark
      of human cancers. However, DNA methylation variation is now
      acknowledged to significantly contribute to genetic and common
      diseases. DNA methyltransferases became attractive therapeutic targets
      as DNA demethylation, in vitro, brought cancer cell differentiation and
      apoptosis. Inhibitors are already in use, alone or in combination, to
      treat myeloid malignancies, while clinical assays are ongoing for other
      diseases. DNA methylation and histone modifications are intimately
      correlated with epigenetic heritable modifications of gene expression
      that are independent of changes in the genetic sequence. Common
      initiatives for epigenetic research have built public databases with
      useful resources. The recent discovery of 5-hydroxymethyl cytosine has
      added new questions and challenges for the epigenome community. We
      review here knowledge about DNA methylation to provide researchers with
      the information needed to make more active inhibitors for the benefit
      of patients. Because of space limitations, many important works cannot
      be cited. We refer the reader to reviews containing these references.
AU  - Martinet N
AU  - Michel BY
AU  - Bertrand P
AU  - Benhida R
PT  - Journal Article
TA  - MedChemComm
JT  - MedChemComm
SO  - MedChemComm 2012 3: 263-273.

PMID- 28473392
VI  - 5
DP  - 2017
TI  - Resequencing the Genome of Bifidobacterium breve Strain CECT7263.
PG  - e00299-17
AB  - The probiotic properties of Bifidobacterium breve CECT7263, as well as its safety, have been
      the focus of in several studies since 2008, including the
      sequencing of its genome in 2012. This study aims to complete the available
      genomic data to deepen the knowledge of some phenotypic characteristics of this
      strain.
AU  - Martinez N
AU  - Luque R
AU  - Olivares MM
AU  - Margolles A
AU  - Banuelos O
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00299-17.

PMID- 22461551
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Rahnella sp. Strain Y9602, a Gammaproteobacterium Isolate from Metal- and Radionuclide-Contaminated Soil.
PG  - 2113-2114
AB  - Rahnella sp. strain Y9602 is a gammaproteobacterium isolated from contaminated subsurface
      soils that is capable of promoting uranium phosphate mineralization as
      a result of constitutive phosphatase activity. Here we report the first complete
      genome sequence of an isolate belonging to the genus Rahnella.
AU  - Martinez RJ
AU  - Bruce D
AU  - Detter C
AU  - Goodwin LA
AU  - Han J
AU  - Han CS
AU  - Held B
AU  - Land ML
AU  - Mikhailova N
AU  - Nolan M
AU  - Pennacchio L
AU  - Pitluck S
AU  - Tapia R
AU  - Woyke T
AU  - Sobecky PA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2113-2114.

PMID- 22582378
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Rahnella aquatilis CIP 78.65.
PG  - 3020-3021
AB  - Rahnella aquatilis CIP 78.65 is a gammaproteobacterium isolated from a drinking water source
      in Lille, France. Here we report the complete genome sequence of Rahnella aquatilis CIP 78.65,
      the type strain of R. aquatilis.
AU  - Martinez RJ
AU  - Bruce D
AU  - Detter C
AU  - Goodwin LA
AU  - Han J
AU  - Han CS
AU  - Held B
AU  - Land ML
AU  - Mikhailova N
AU  - Nolan M
AU  - Pennacchio L
AU  - Pitluck S
AU  - Tapia R
AU  - Woyke T
AU  - Sobecky PA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3020-3021.

PMID- 25858845
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Klebsiella pneumoniae Carbapenemase-Producing Acinetobacter baumannii Strain M3AC9-7, Isolated from Puerto Rico.
PG  - e00274-15
AB  - We report the draft genome of a multidrug resistant, Klebsiella pneumoniae carbapenemase
      (KPC)-producing Acinetobacter baumannii strain M3AC9-7 that belongs
      to the novel sequence type, ST250. The draft genome consists of a total length of
      4.09 Mbp and a G+C content of 38.95%.
AU  - Martinez T
AU  - Ropelewski AJ
AU  - Gonzalez-Mendez R
AU  - Vazquez GJ
AU  - Robledo IE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00274-15.

PMID- 27540056
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a Multidrug-Resistant Klebsiella pneumoniae Carbapenemase-Producing Acinetobacter baumannii Sequence Type 2 Isolate from  Puerto Rico.
PG  - e00758-16
AB  - We report here the draft genome sequence of Acinetobacter baumannii strain M3AC14-8, sequence
      type 2 (ST2), carrying a chromosomally carried blaKPC-2 gene.
      The draft genome consists of a total length of 4.11 Mbp and a G+C content of
      39.25%.
AU  - Martinez T
AU  - Ropelewski AJ
AU  - Gonzalez-Mendez R
AU  - Vazquez GJ
AU  - Robledo IE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00758-16.

PMID- 24504004
VI  - 2
DP  - 2014
TI  - Genome Sequence of Streptomyces exfoliatus DSMZ 41693, a Source of Poly(3-Hydroxyalkanoate)-Degrading Enzymes.
PG  - e01272-13
AB  - Here we report the draft genome sequence of Streptomyces exfoliatus DSMZ 41693, which includes
      a gene encoding a poly(3-hydroxyoctanoate) depolymerase, an enzyme
      which can be used for the industrial synthesis of chiral (R)-3-hydroxyalkanoic
      acids. In addition, the genome carries numerous genes involved in the
      biosynthesis of secondary metabolites, including polyketides and terpenes.
AU  - Martinez V
AU  - Hormigo D
AU  - Del Cerro C
AU  - Gomez-de-Santos P
AU  - Garcia-Hidalgo J
AU  - Arroyo M
AU  - Prieto A
AU  - Garcia JL
AU  - de la Mata I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01272-13.

PMID- 10760141
VI  - 35
DP  - 2000
TI  - Homing of a bacterial group II intron with an intron-encoded protein lacking a recognizable endonuclease domain.
PG  - 1405-1412
AB  - RmInt1 is a functional group II intron found in Sinorhizobium meliloti where it interrupts a
      group of IS elements of the IS630-Tc1 family. In contrast to many other group II introns, the
      intron-encoded protein (IEP) of RmInt1 lacks the characteristic conserved part of the Zn
      domain associated with the IEP endonuclease activity. Nevertheless, in this study, we show
      that RmInt1 is capable of inserting into a vector containing the DNA spanning the RmInt1
      target site from the genome of S. meliloti. Efficient homing was also observed in the absence
      of homologous recombination (RecA- strains). In addition, it is shown that RmInt1 is able to
      move to its target in a heterologous host (S. medicae). Homing of RmInt1 occurs very
      efficiently upon DNA target uptake (conjugation/electroporation) by the host cell resulting in
      a proportion of invaded target of 11-30%. Afterwards, the remaining intronless target DNA is
      protected from intron invasion.
AU  - Martinez-Abarca F
AU  - Garcia-Rodriguez FM
AU  - Toro N
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2000 35: 1405-1412.

PMID- 23409262
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of the Alfalfa Symbiont Sinorhizobium/Ensifer meliloti Strain GR4.
PG  - e00174-12
AB  - We present the complete nucleotide sequence of the multipartite genome of
      Sinorhizobium/Ensifer meliloti GR4, a predominant rhizobial strain in an
      agricultural field site. The genome (total size, 7.14 Mb) consists of five
      replicons: one chromosome, two expected symbiotic megaplasmids (pRmeGR4c and
      pRmeGR4d), and two accessory plasmids (pRmeGR4a and pRmeGR4b).
AU  - Martinez-Abarca F
AU  - Martinez-Rodriguez L
AU  - Lopez-Contreras JA
AU  - Jimenez-Zurdo JI
AU  - Toro N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00174-12.

PMID- 27469952
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of an Oceanobacillus sp. Strain Isolated from Soil in a Burial Crypt.
PG  - e00701-16
AB  - We present the draft genome of an Oceanobacillus sp. strain isolated from spores  found in
      soil samples from a burial crypt of the Cathedral of Sant'Antonio Abate
      in Castelsardo, Italy. The data obtained indicated the closest relation of the
      strain with Oceanobacillus caeni.
AU  - Martinez-Ballesteros I
AU  - Arizaga Y
AU  - Bikandi J
AU  - Garaizar J
AU  - Ganau G
AU  - Paglietti B
AU  - Murgia M
AU  - Deligios M
AU  - Rubino S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00701-16.

PMID- 29242216
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of the New Urolithin-Producing Bacterium Gordonibacter urolithinfaciens DSM 27213(T).
PG  - e01120-17
AB  - Gordonibacter urolithinfaciens DSM 27213(T) was isolated from human feces and is  able to
      metabolize ellagic acid (a dietary phenolic compound present in various
      fruits) to urolithins. Here, we report the finished and annotated genome sequence
      of this organism.
AU  - Martinez-Blanch JF
AU  - Ramon D
AU  - Beltran D
AU  - Romo-Vaquero M
AU  - Garcia-Villalba R
AU  - Espin JC
AU  - Tomas-Barberan FA
AU  - Codoner FM
AU  - Selma MV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01120-17.

PMID- 26313942
VI  - 10
DP  - 2015
TI  - Bioinformatics Analysis of the Complete Genome Sequence of the Mango Tree Pathogen Pseudomonas syringae pv. syringae UMAF0158 Reveals Traits Relevant to Virulence and Epiphytic Lifestyle.
PG  - E0136101
AB  - The genome sequence of more than 100 Pseudomonas syringae strains has been
      sequenced to date; however only few of them have been fully assembled, including
      P. syringae pv. syringae B728a. Different strains of pv. syringae cause different
      diseases and have different host specificities; so, UMAF0158 is a P. syringae pv.
      syringae strain related to B728a but instead of being a bean pathogen it causes
      apical necrosis of mango trees, and the two strains belong to different
      phylotypes of pv.syringae and clades of P. syringae. In this study we report the
      complete sequence and annotation of P. syringae pv. syringae UMAF0158 chromosome
      and plasmid pPSS158. A comparative analysis with the available sequenced genomes
      of other 25 P. syringae strains, both closed (the reference genomes DC3000, 1448A
      and B728a) and draft genomes was performed. The 5.8 Mb UMAF0158 chromosome has
      59.3% GC content and comprises 5017 predicted protein-coding genes.
      Bioinformatics analysis revealed the presence of genes potentially implicated in
      the virulence and epiphytic fitness of this strain. We identified several genetic
      features, which are absent in B728a, that may explain the ability of UMAF0158 to
      colonize and infect mango trees: the mangotoxin biosynthetic operon mbo, a gene
      cluster for cellulose production, two different type III and two type VI
      secretion systems, and a particular T3SS effector repertoire. A mutant strain
      defective in the rhizobial-like T3SS Rhc showed no differences compared to
      wild-type during its interaction with host and non-host plants and worms. Here we
      report the first complete sequence of the chromosome of a pv. syringae strain
      pathogenic to a woody plant host. Our data also shed light on the genetic factors
      that possibly determine the pathogenic and epiphytic lifestyle of UMAF0158. This
      work provides the basis for further analysis on specific mechanisms that enable
      this strain to infect woody plants and for the functional analysis of host
      specificity in the P. syringae complex.
AU  - Martinez-Garcia PM
AU  - Rodriguez-Palenzuela P
AU  - Arrebola E
AU  - Carrion VJ
AU  - Gutierrez-Barranquero JA
AU  - Perez-Garcia A
AU  - Ramos C
AU  - Cazorla FM
AU  - Vicente Ad
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2015 10: E0136101.

PMID- 25685259
VI  - 10
DP  - 2015
TI  - Complete genome sequence of Pseudomonas fluorescens strain PICF7, an indigenous root endophyte from olive (Olea europaea L.) and effective biocontrol agent  against Verticillium dahliae.
PG  - 10
AB  - Pseudomonas fluorescens strain PICF7 is a native endophyte of olive roots. Previous studies
      have shown this motile, Gram-negative, non-sporulating bacterium
      is an effective biocontrol agent against the soil-borne fungus Verticillium
      dahliae, the causal agent of one of the most devastating diseases for olive (Olea
      europaea L.) cultivation. Here, we announce and describe the complete genome
      sequence of Pseudomonas fluorescens strain PICF7 consisting of a circular
      chromosome of 6,136,735 bp that encodes 5,567 protein-coding genes and 88
      RNA-only encoding genes. Genome analysis revealed genes predicting factors such
      as secretion systems, siderophores, detoxifying compounds or volatile components.
      Further analysis of the genome sequence of PICF7 will help in gaining insights
      into biocontrol and endophytism.
AU  - Martinez-Garcia PM
AU  - Ruano-Rosa D
AU  - Schiliro E
AU  - Prieto P
AU  - Ramos C
AU  - Rodriguez-Palenzuela P
AU  - Mercado-Blanco J
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 10.

PMID- 27125479
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Burkholderia cenocepacia Strain CEIB S5-2, a Methyl Parathion- and p-Nitrophenol-Degrading Bacterium, Isolated from Agricultural  Soils in Morelos, Mexico.
PG  - e00220-16
AB  - Burkholderia cenocepacia is an opportunistic pathogen that belongs to Burkholderia cepacia
      complex (BCC). Burkholderia cenocepacia strain CEIB S5-2 was
      isolated from agricultural soils in Morelos, Mexico, and previously has shown its
      abilities for bioremediation. In this study, we report the draft genome sequence
      of Burkholderia cenocepacia strain CEIB S5-2.
AU  - Martinez-Ocampo F
AU  - Fernandez LMG
AU  - Lozano-Aguirre BLF
AU  - Popoca-Ursino EC
AU  - Ortiz-Hernandez ML
AU  - Sanchez-Salinas E
AU  - Ramos QF
AU  - Villalobos-Lopez MA
AU  - Dantan-Gonzalez E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00220-16.

PMID- 25744996
VI  - 3
DP  - 2015
TI  - Burkholderia cenocepacia Strain CEIB S5-1, a Rhizosphere-Inhabiting Bacterium with Potential in Bioremediation.
PG  - e00056-15
AB  - Burkholderia cenocepacia is considered an opportunistic pathogen from humans and  may cause
      disease in plants. A bioprospection from a plaguicide-contaminated
      agricultural field in Mexico identified several methyl parathion-degrading
      bacteria. Here, we report the draft genome sequence of B. cenocepacia strain CEIB
      S5-1, which gave us clues into ecological biodiversity.
AU  - Martinez-Ocampo F
AU  - Lozano-Aguirre BLF
AU  - Hernandez-Mendoza A
AU  - Rojas-Espinoza LE
AU  - Popoca-Ursino EC
AU  - Ortiz-Hernandez ML
AU  - Sanchez-Salinas E
AU  - Ramos QF
AU  - Dantan-Gonzalez E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00056-15.

PMID- 27389272
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of 'Candidatus Mycoplasma haemobos,' a Hemotropic Mycoplasma Identified in Cattle in Mexico.
PG  - e00656-16
AB  - We present here the draft genome sequence of the first 'Candidatus Mycoplasma haemobos'
      strain found in cattle in Mexico. This hemotropic mycoplasma causes
      acute and chronic disease in animals. This genome is a starting point for
      studying the role of this mycoplasma in coinfections and synergistic mechanisms
      associated with the disease.
AU  - Martinez-Ocampo F
AU  - Rodriguez-Camarillo SD
AU  - Amaro-Estrada I
AU  - Quiroz-Castaneda RE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00656-16.

PMID- 22365985
VI  - 94
DP  - 2012
TI  - Overexpression of Ipe protein from the coliphage mEp021 induces pleiotropic effects involving hemolysis by HlyE-containing vesicles and cell death.
PG  - 1262-1273
AB  - Lysogenic Escherichia coli K-12 harbouring the prophage mEp021 displays haemolytic activity.
      From a genomic library of mEp021, we identified an open reading frame (ORF 4) that was
      responsible for the haemolytic activity. However, the ORF 4 sequence contains four initiation
      codons in the same frame: ORF 4.1-ORF 4.4, coding for 83-a.a., 82-a.a., 77-a.a. and 72-a.a.
      products, respectively. The expression of the cloned ORF 4.3, or inducer of pleiotropic
      effects (ipe), reproduced the haemolytic phenotype in a native strain carrying the gene hlyE+,
      but not in the mutant hlyE- strain. The overexpression of Ipe induced several pleiotropic
      effects, such as the inhibition of cell growth and the deregulation of cell division, which
      resulted in a mixture of normal and desiccated-like cells: normal-filamentous,
      desiccated-likefilamentous bacilli, minicells etc. Other effects included abnormalities of the
      cell membrane, the production of vesicles containing HlyE, and finally, cell death. These
      events were analysed at the molecular level by microarray assays. The global transcription
      profile of E. coli K-12 strain MC4100, which expressed Ipe after 4 h, revealed differential
      expression of various genes, most of which were related either to cell membrane and murein
      biosynthesis or to cell division. The up-regulation of some of these transcripts was confirmed
      by qRT-PCR. Additional research is needed to determine whether these effects are directly
      related to Ipe activity or are consequences of the cellular responses to putative structural
      damage induced by Ipe.
AU  - Martinez-Penafiel E
AU  - Fernandez-Ramirez F
AU  - Ishida C
AU  - Reyes-Cortes R
AU  - Sepulveda-Robles O
AU  - Guarneros-Pena G
AU  - Bermudez-Cruz RM
AU  - Kameyama L
PT  - Journal Article
TA  - Biochimie
JT  - Biochimie
SO  - Biochimie 2012 94: 1262-1273.

PMID- 29225729
VI  - 12
DP  - 2017
TI  - Draft genome sequence of Bacillus velezensis 2A-2B strain: a rhizospheric inhabitant of Sporobolus airoides (Torr.) Torr., with antifungal activity against  root rot causing phytopathogens.
PG  - 73
AB  - A Bacillus velezensis strain from the rhizosphere of Sporobolus airoides (Torr.)  Torr., a
      grass in central-north Mexico, was isolated during a biocontrol of
      phytopathogens scrutiny study. The 2A-2B strain exhibited at least 60% of growth
      inhibition of virulent isolates of phytopathogens causing root rot. These
      phytopathogens include Phytophthora capsici, Fusarium solani, Fusarium oxysporum
      and Rhizoctonia solani. Furthermore, the 2A-2B strain is an indolacetic acid
      producer, and a plant inducer of PR1, which is an induced systemic resistance
      related gene in chili pepper plantlets. Whole genome sequencing was performed to
      generate a draft genome assembly of 3.953 MB with 46.36% of GC content, and a N50
      of 294,737. The genome contains 3713 protein coding genes and 89 RNA genes.
      Moreover, comparative genome analysis revealed that the 2A-2B strain had the
      greatest identity (98.4%) with Bacillus velezensis.
AU  - Martinez-Raudales I
AU  - De La Cruz-Rodriguez Y
AU  - Alvarado-Gutierrez A
AU  - Vega-Arreguin J
AU  - Fraire-Mayorga A
AU  - Alvarado-Rodriguez M
AU  - Balderas-Hernandez V
AU  - Fraire-Velazquez S
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 73.

PMID- 28963212
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Bacillus velezensis 3A-25B, a Strain with Biocontrol Activity against Fungal and Oomycete Root Plant Phytopathogens, Isolated from  Grassland Soil.
PG  - e01021-17
AB  - Here, we present the draft genome of Bacillus velezensis 3A-25B, which totaled 4.01 Mb with 36
      contigs, 3,948 genes, and a GC content of 46.34%. This strain,
      which demonstrates biocontrol activity against root rot causal phytopathogens in
      horticultural crops and friendly interactions in roots of pepper plantlets, was
      obtained from grassland soil in Zacatecas Province, Mexico.
AU  - Martinez-Raudales I
AU  - De La Cruz-Rodriguez Y
AU  - Vega-Arreguin J
AU  - Alvarado-Gutierrez A
AU  - Fraire-Mayorga A
AU  - Alvarado-Rodriguez M
AU  - Balderas-Hernandez V
AU  - Gomez-Soto JM
AU  - Fraire-Velazquez S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01021-17.

PMID- 26358599
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Klebsiella variicola Plant Isolates.
PG  - e01015-15
AB  - Three endophytic Klebsiella variicola isolates-T29A, 3, and 6A2, obtained from sugar cane
      stem, maize shoots, and banana leaves, respectively-were used for whole-genome sequencing.
      Here, we report the draft genome sequences of circular chromosomes and plasmids. The genomes
      contain plant colonization and cellulases genes. This study will help toward understanding the
      genomic basis of K. variicola interaction with plant hosts.
AU  - Martinez-Romero E
AU  - Silva-Sanchez J
AU  - Barrios H
AU  - Rodriguez-Medina N
AU  - Martinez-Barnetche J
AU  - Tellez-Sosa J
AU  - Gomez-Barreto RE
AU  - Garza-Ramos U
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01015-15.

PMID- 29724839
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Nine New Carnobacterium maltaromaticum Strains Isolated from Diseased Sharks.
PG  - e00354-18
AB  - Here, we report the draft genome sequences of 9 strains of Carnobacterium maltaromaticum
      (SK_LD1 to SK_LD3 and SK_AV1 to SK_AV6), a member of the
      Carnobacteriaceae family (phylum Firmicutes). These strains were isolated from
      the brain and the inner ear of three diseased thresher sharks and two diseased
      salmon sharks. The genome assembly resulted in an average of 3,306,205.9 +/-
      29,143.9 bp and 3,085 +/- 32.67 coding DNA sequences (CDS).
AU  - Martinez-Steele L
AU  - Lowe CG
AU  - Okihiro MS
AU  - Berlemont R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00354-18.

PMID- 26847907
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Four Enterococcus faecium Strains Isolated from Argentine Cheese.
PG  - e01576-15
AB  - We report the draft genome sequences of four Enterococcus faecium strains isolated from
      Argentine regional cheeses. These strains were selected based on
      their technological properties, i.e., their ability to produce aroma compounds
      (diacetyl, acetoin, and 2,3-butanediol) from citrate. The goal of our study is to
      provide further genetic evidence for the rational selection of enterococci
      strains based on their pheno- and genotype in order to be used in cheese
      production.
AU  - Martino GP
AU  - Quintana IM
AU  - Espariz M
AU  - Blancato VS
AU  - Gallina NG
AU  - Esteban L
AU  - Magni C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01576-15.

PMID- 26607892
VI  - 3
DP  - 2015
TI  - Resequencing of the Lactobacillus plantarum Strain WJL Genome.
PG  - e01382-15
AB  - Lactobacillus plantarum strain WJL is a symbiont isolated from the Drosophila melanogaster
      gut. The genome of L. plantarum WJL, first sequenced in 2013, was
      resequenced and rescaffolded in this study. A combination of Sanger and Illumina
      sequencing allowed us to reduce the number of contigs from 102 to 13. This work
      contributes to a better understanding of the genome and function of this
      organism.
AU  - Martino ME
AU  - Bayjanov JR
AU  - Joncour P
AU  - Hughes S
AU  - Gillet B
AU  - Kleerebezem M
AU  - Siezen R
AU  - van Hijum SA
AU  - Leulier F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01382-15.

PMID- 26607887
VI  - 3
DP  - 2015
TI  - Nearly Complete Genome Sequence of Lactobacillus plantarum Strain NIZO2877.
PG  - e01370-15
AB  - Lactobacillus plantarum is a versatile bacterial species that is isolated mostly  from foods.
      Here, we present the first genome sequence of L. plantarum strain
      NIZO2877 isolated from a hot dog in Vietnam. Its two contigs represent a nearly
      complete genome sequence.
AU  - Martino ME
AU  - Bayjanov JR
AU  - Joncour P
AU  - Hughes S
AU  - Gillet B
AU  - Kleerebezem M
AU  - Siezen R
AU  - van Hijum SA
AU  - Leulier F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01370-15.

PMID- 19656368
VI  - 10
DP  - 2009
TI  - Comparative genomic analyses of Streptococcus mutans provide insights into chromosomal shuffling and species-specific content.
PG  - 358
AB  - Background: Streptococcus mutans is the major pathogen of dental caries, and it occasionally
      causes infective endocarditis. While the
      pathogenicity of this species is distinct from other human pathogenic
      streptococci, the species-specific evolution of the genus Streptococcus
      and its genomic diversity are poorly understood.Results: We have
      sequenced the complete genome of S. mutans serotype c strain NN2025,
      and compared it with the genome of UA159. The NN2025 genome is composed
      of 2,013,587 bp, and the two strains show highly conserved core-genome.
      However, comparison of the two S. mutans strains showed a large genomic
      inversion across the replication axis producing an X-shaped symmetrical
      DNA dot plot. This phenomenon was also observed between other
      streptococcal species, indicating that streptococcal genetic
      rearrangements across the replication axis play an important role in
      Streptococcus genetic shuffling. We further confirmed the genomic
      diversity among 95 clinical isolates using long-PCR analysis. Genomic
      diversity in S. mutans appears to occur frequently between insertion
      sequence (IS) elements and transposons, and these diversity regions
      consist of restriction/modification systems, antimicrobial peptide
      synthesis systems, and transporters. S. mutans may preferentially
      reject the phage infection by clustered regularly interspaced short
      palindromic repeats (CRISPRs). In particular, the CRISPR-2 region,
      which is highly divergent between strains, in NN2025 has long repeated
      spacer sequences corresponding to the streptococcal phage
      genome.Conclusion: These observations suggest that S. mutans strains
      evolve through chromosomal shuffling and that phage infection is not
      needed for gene acquisition. In contrast, S. pyogenes tolerates phage
      infection for acquisition of virulence determinants for niche
      adaptation.
AU  - Maruyama F
AU  - Kobata M
AU  - Kurokawa K
AU  - Nishida K
AU  - Sakurai A
AU  - Nakano K
AU  - Nomura R
AU  - Kawabata S
AU  - Ooshima T
AU  - Nakai K
AU  - Hattori M
AU  - Hamada S
AU  - Nakagawa I
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2009 10: 358.

PMID- 24136845
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences of Pseudomonas aeruginosa B3 Strains Isolated from a Cystic Fibrosis Patient Undergoing Antibiotic Chemotherapy.
PG  - e00804-13
AB  - Pseudomonas aeruginosa frequently establishes chronic infections in the airways of patients
      suffering from cystic fibrosis (CF). Here, we report the draft genome
      sequences of four P. aeruginosa B3 strains isolated from a chronically infected
      CF patient undergoing antibiotic chemotherapy.
AU  - Marvig RL
AU  - Jochumsen N
AU  - Johansen HK
AU  - Hoiby N
AU  - Molin S
AU  - Sommer MO
AU  - Jelsbak L
AU  - Folkesson A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00804-13.

PMID- 22887658
VI  - 194
DP  - 2012
TI  - Complete genome sequences of six strains of the genus methylobacterium.
PG  - 4746-4748
AB  - The complete and assembled genome sequences were determined for six strains of the
      alphaproteobacterial genus Methylobacterium, chosen for their key adaptations
      to different plant-associated niches and environmental constraints.
AU  - Marx CJ et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4746-4748.

PMID- 21914887
VI  - 193
DP  - 2011
TI  - Genome Sequence of the Ruminal Bacterium Megasphaera elsdenii.
PG  - 5578-5579
AB  - Megasphaera elsdenii is a Gram-negative ruminal bacterium. It is being investigated as a
      probiotic supplement for ruminants as it may provide
      benefits for energy balance and animal productivity. Furthermore, it is of
      biotechnological interest due to its capability of producing various
      volatile fatty acids. Here we report the complete genome sequence of M.
      elsdenii DSM 20460, the type strain for the species.
AU  - Marx H
AU  - Graf AB
AU  - Tatto NE
AU  - Thallinger GG
AU  - Mattanovich D
AU  - Sauer M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5578-5579.

PMID- 17817807
VI  - 180
DP  - 1973
TI  - Restriction enzymes:  new tools for studying DNA.
PG  - 482-485
AB  - None
AU  - Marx JL
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1973 180: 482-485.

PMID- 7478992
VI  - 23
DP  - 1995
TI  - Dam methylase from Escherichia coli: kinetic studies using modified DNA oligomers: hemimethylated substrates.
PG  - 3648-3655
AB  - We have measured steady-state kinetics of the N6-adenine methyltransferase Dam Mtase using as
      substrates non-selfcomplementary tetradecamer duplexes (d[GCCGGATCTAGACG].d[CGTCTAGATCCGGC])
      containing the hemimethylated GATC target sequence in one or the other strand and
      modifications in the GATC target sequence of the complementary strands.  Modifications
      included substitution of guanine by hypoxanthine (I), thymine by uracil (U) or 5-ethyl-uracil
      (E) and adenine by 2,6-diamino-purine (D).  Thermodynamic parameters were obtained from the
      concentration dependence of the melting temperature (Tm) of the duplexes.  Large differences
      in DNA methylation of duplexes containing single dl for dG substitution of the Dam recognition
      site were observed compared with the canonical substrate, if the substitution involved the
      top strand (on the G.C rich side).  Substitution in either strand by uracil (dU) or
      5-ethyl-uracil (dE) resulted in small perturbation of the methylation patterns.  When
      2,5-diamino-purine (dD) replaced the adenine to be methylated, small, but significant
      methylation was observed.  The kinetic parameters of the methylation reaction were compared
      with the thermodynamic free energies and significant correlation was observed.
AU  - Marzabal S
AU  - DuBois S
AU  - Thielking V
AU  - Cano A
AU  - Eritja R
AU  - Guschlbauer W
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1995 23: 3648-3655.

PMID- 25744993
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Thalassobacter Strains 1CONIMAR09 and 16PALIMAR09, Two  Members of the Roseobacter Lineage Isolated from Coastal Areas of the  Mediterranean Sea around Mallorca Island.
PG  - e00041-15
AB  - We report the draft genome sequence of two new members of the Roseobacter lineage,
      Thalassobacter strains 1CONIMAR09 and 16PALIMAR09, which were isolated
      from the seawater coast of Mallorca Island. Each genome harbored putative genes
      for obtaining energy by chemolithotrophy and making aerobic anoxygenic
      photosynthesis.
AU  - Mas-Llado M
AU  - Pina-Villalonga JM
AU  - Brunet-Galmes I
AU  - Nogales B
AU  - Bosch R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00041-15.

PMID- 24855294
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Two Isolates of the Roseobacter Group, Sulfitobacter sp. Strains 3SOLIMAR09 and 1FIGIMAR09, from Harbors of Mallorca Island  (Mediterranean Sea).
PG  - e00350-14
AB  - We present the draft genome sequences of two isolates of the Roseobacter lineage, 3SOLIMAR09
      and 1FIGIMAR09, which were obtained from harbors of Mallorca Island,
      Spain, and are affiliated with the Sulfitobacter genus. Both isolates harbor the
      complete gene set for protocatechuate catabolism and incomplete pathways for
      several additional monoaromatic compounds.
AU  - Mas-Llado M
AU  - Pina-Villalonga JM
AU  - Brunet-Galmes I
AU  - Nogales B
AU  - Bosch R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00350-14.

PMID- 22207743
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Sphingobium sp. Strain SYK-6, a Degrader of Lignin-Derived Biaryls and Monoaryls.
PG  - 534-535
AB  - Sphingobium sp. strain SYK-6 is able to grow on an extensive variety of lignin-derived biaryls
      and monoaryls, and the catabolic genes for these
      compounds are useful for the production of industrially valuable
      metabolites from lignin. Here we report the complete nucleotide sequence
      of the SYK-6 genome which consists of the 4,199,332-bp-long chromosome and
      the 148,801-bp-long plasmid.
AU  - Masai E
AU  - Kamimura N
AU  - Kasai D
AU  - Oguchi A
AU  - Ankai A
AU  - Fukui S
AU  - Takahashi M
AU  - Yashiro I
AU  - Sasaki H
AU  - Harada T
AU  - Nakamura S
AU  - Katano Y
AU  - Narita-Yamada S
AU  - Nakazawa H
AU  - Hara H
AU  - Katayama Y
AU  - Fukuda M
AU  - Yamazaki S
AU  - Fujita N
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 534-535.

PMID- 29773625
VI  - 6
DP  - 2018
TI  - Complete Genome Sequences of the Potential Zoonotic Pathogens Staphylococcus felis and Staphylococcus kloosii.
PG  - e00404-18
AB  - Coagulase-negative staphylococci (CoNS) are opportunistic pathogens frequently encountered in
      nosocomial infections. Animal-associated CoNS pose a zoonotic risk
      and constitute a potential reservoir for virulence and antimicrobial resistance
      genes. To improve our knowledge of animal-associated CoNS, we sequenced the
      complete genomes of Staphylococcus felis (ATCC 49168) and Staphylococcus kloosii
      (ATCC 43959).
AU  - Mascarenhas DSAC
AU  - Jie R
AU  - Antunes GH
AU  - Alves M
AU  - Pombert JF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00404-18.

PMID- Not carried by PubMed...
VI  - 54
DP  - 1994
TI  - Kinetic and chemical mechanisms of the EcoRI DNA (N6-adenine) methyltransferase.
PG  - 5132B-5133B
AB  - A kinetic analysis of the EcoRI DNA N6-adenine methyltransferase (Mtase) is presented. The
      enzyme catalyzes the S-adenosylmethionine (AdoMet)-dependent methylation of a short, synthetic
      14 base pair DNA substrate and plasmid pBR322 DNA substrate with kcat/Km values of 0.51 x 10/8
      and 4.1 x 10/8 s-1 M-1, respectively. The Mtase is thus one of the most efficient biocatalysts
      known. The steady state kinetic data are consistent with an ordered bi-bi steady-state
      mechanism in which AdoMet binds first, followed by (AdoHcy), is an uncompetitive inhibitor
      with respect to DNA and a competitive inhibitor with respect to AdoMet. Thus, initial DNA
      binding followed by AdoHcy binding leads to formation of a ternary deadend complex
      (Mtase-AdoHcy binding leads to formation of a ternary dead-end complex (Mtase-DNA-AdoHcy). The
      product inhibition patterns and apparent order of substrate binding can be reconciled by a
      mechanism in which the Mtase binds AdoMet and noncanonical DNA randomly but that recognition
      of the canonical site requires AdoMet to be bound. Presteady-state and isotope partition
      analyses starting with the binary Mtase-AdoMet complex confirm its catalytic competence. In
      summary, it was determined that the EcoRI DNA Mtase binds AdoMet and noncanonical DNA randomly
      but recognition of the canonical site requires AdoMet to be bound. It was shown that step(s)
      after methyl transfer limit the overall reaction rate and that methyl transfer at the N6 amino
      moiety of adenine on each strand requires a single binding orientation. Furthermore, it was
      demonstrated that no critical protein residues undergo ionization state changes in the pH
      range 5.5-8.0. However, above pH 8.5 at least four residues in the free enzyme and AdoMet
      bound enzyme and two residues in the central complex (Mtase-DNA-AdoMet) are implicated to be
      critical in binding and/or catalysis; candidate amino acid residues are cysteine (other than
      cysteine 223), lysine, tyrosine, and/or arginine.
AU  - Mashhoon N
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1994 54: 5132B-5133B.

PMID- 15456775
VI  - 279
DP  - 2004
TI  - Functional Characterization of Escherichia coli DNA Adenine Methyltransferase, a Novel Target for Antibiotics.
PG  - 52075-52081
AB  - We have characterized Escherichia coli DNA adenine methyltransferase, a critical regulator of
      bacterial virulence. Steady-state kinetics, product
      inhibition, and isotope exchange studies are consistent with a kinetic
      mechanism in which the cofactor S-adenosylmethionine binds first, followed
      by sequence-specific DNA binding and catalysis. The enzyme has a fast
      methyl transfer step followed by slower product release steps, and we
      directly demonstrate the competence of the enzyme cofactor complex.
      Methylation of adjacent GATC sites is distributive with DNA derived from a
      genetic element that controls the transcription of the adjacent genes.
      This indicates that the first methylation event is followed by enzyme
      release. The affinity of the enzyme for both DNA and S-adenosylmethionine
      was determined. Our studies provide a basis for further structural and
      functional analysis of this important enzyme and for the identification of
      inhibitors for potential therapeutic applications.
AU  - Mashhoon N
AU  - Carroll M
AU  - Pruss C
AU  - Eberhard J
AU  - Ishikawa S
AU  - Estabrook RA
AU  - Reich N
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2004 279: 52075-52081.

PMID- 16760373
VI  - 11
DP  - 2006
TI  - Selective inhibitors of bacterial DNA adenine methyltransferases.
PG  - 497-510
AB  - The authors describe the discovery and characterization of several structural classes of
      small-molecule inhibitors of bacterial DNA
      adenine methyltransferases. These enzymes are essential for bacterial
      virulence (DNA adenine methyltransferase [DAM]) and cell viability
      (cell cycle-regulated methyltransferase [CcrM]). Using a novel
      high-throughput fluorescence-based assay and recombinant DAM and CcrM,
      the authors screened a diverse chemical library. They identified 5
      major structural classes of inhibitors composed of more than 350
      compounds: cyclopentaquinolines, phenyl vinyl furans,
      pyrimidine-diones, thiazolidine-4-ones, and phenyl-pyrroles. DNA
      binding assays were used to identify compounds that interact directly
      with DNA. Potent compounds selective for the bacterial target were
      identified, whereas other compounds showed greater selectivity for the
      mammalian DNA cytosine methyltransferase, Dnmt1. Enzyme inhibition
      analysis identified mechanistically distinct compounds that interfered
      with DNA or cofactor binding. Selected compounds demonstrated
      cell-based efficacy. These small-molecule DNA methyltransferase
      inhibitors provide useful reagents to probe the role of DNA methylation
      and may form the basis of developing novel antibiotics.
AU  - Mashhoon N
AU  - Pruss C
AU  - Carroll M
AU  - Johnson PH
AU  - Reich NO
PT  - Journal Article
TA  - J. Biomol. Screen.
JT  - J. Biomol. Screen.
SO  - J. Biomol. Screen. 2006 11: 497-510.

PMID- 8003477
VI  - 33
DP  - 1994
TI  - Investigation of ionizable residues critical for sequence-specific enzymatic DNA modification: Protein modification and steady-state and pre-steady-state kinetic pH analyses of EcoRI DNA methyltransferase.
PG  - 7113-7119
AB  - Steady- and pre-steady-state pH kinetic analyses are widely used methods to investigate
      important ionizable groups in enzyme-catalyzed reactions. The first such analysis to identify
      ionizable residues critical for sequence-specific modification of DNA is presented. EcoRI DNA
      methyltransferase uses S-adenosyl-L-methionine (AdoMet) to catalyze the N6 methylation of the
      second adenine in the double-stranded DNA sequence GAATTC. The kinetic mechanism was
      previously shown to be steady-state-ordered bi bi in which AdoMet binds first followed by DNA
      addition (Reich, N.O. & Mashhoon, N. (1991) Biochemistry 30, 2933-2939). Steady-state
      parameters are strongly dependent on pH and implicate at least four residues with pKa values
      between 8.2 and 8.9 in the free enzyme and AdoMet-bound enzyme and one residue with an
      apparent pKa of 6.0. The data obtained aer consistent with the enzyme binding the form of
      AdoMet in which the alpha amino group is protonated. Two protein residues with an apparent pKa
      between 8.9 and 9.2 were implicated within the central complex (enzyme-DNA-AdoMet). The
      general insensitivity of all steady-state parameters to pH changes between pH 6.0 and 8.0
      suggests that no critical protein residues undergo ionization-state changes in this range. The
      lack of significant pH-dependent changes in protein fluorescence and DNA thermal stability
      suggests minimal structural changes in either macromolecule. In support of the steady-state
      results single-turnover experiments reveal minimal pH dependence of the methylation rate
      constant between pH 5.53 and 8.6. Thus, no amino acids critical for catalysis undergo
      ionization-state changes in this range. The previously identified site of NEM-mediated
      inactivation of the methyltransferase, cysteine 223 (Everett et al. (1990) J. Biol. Chem. 265,
      17713-17719), has a pKa of 7.9; on the basis of the steady- and pre-steady-state pH
      dependences this cysteine does not directly contribute to catalysis and substrate binding. The
      results are discussed in the context of the requirement for significant enzymatic activation
      of the poorly nucleophilic N6 position.
AU  - Mashhoon N
AU  - Reich NO
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1994 33: 7113-7119.

PMID- 3192615
VI  - 107
DP  - 1988
TI  - A kinetic study of DNA methylation by EcoRI methylase.
PG  - 838a
AB  - The ability of a protein to recognize and subsequently modify a specific
      sequence of bases in DNA is a fundamental biochemical question that is being
      addressed in our laboratory by studying the EcoRI DNA methylase.  EcoRI
      methylase, a 38 kilodalton bacterial protein, requires S-adenosyl methionine
      (AdoMet) to methylate the double stranded DNA sequence GAATTC at the second
      adenine.  Methylation of DNA serves to protect the organism's DNA against
      cleavage by the corresponding endonuclease.  Little is known about the enzyme's
      kinetic mechanism, the order of substrate binding and product release, and the
      rate limiting step in the reaction.  Steady state and pre-steady state analysis
      were used to determine the kinetic mechanism.  Product inhibition with
      S-adenosyl homocysteine is competitive with respect to AdoMet, whereas it is
      non-competititve with respect to DNA.  Data will be presented on the steady
      state kinetic parameters for AdoMet and DNA, the rate limiting step in the
      reaction, and the order of substrate binding and product release.
AU  - Mashhoon N
AU  - Reich NO
PT  - Journal Article
TA  - J. Cell Biol.
JT  - J. Cell Biol.
SO  - J. Cell Biol. 1988 107: 838a.

PMID- 1727392
VI  - 6
DP  - 1992
TI  - An investigation of the chemical mechanism of the EcoRI DNA methyltransferase.
PG  - A333
AB  - The pH dependence of the EcoRI DNA methyltransferase activity was studied under
      steady state and pre-steady state conditions, and with chemical modification
      analysis.  Steady state pH analysis suggests that a residue with a pKa of
      8.5-9.0 is necessary in its protonated form for enzyme activity.  KmDNA
      increases over 250 fold as pH increases from 5.5 to 9.5 and kcat decreases over
      20 fold.  Pre-steady state experiments were performed to measure the
      methylation rate constant under single turnover conditions (>1 s-1 compared to
      the kcat of .124 s-1) and to determine how pH affects this methylation rate
      constant.  Chemical modification of the methylase with N-ethylmaleimide was
      carried out to substantiate the steady state experimental findings.
AU  - Mashhoon N
AU  - Reich NO
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1992 6: A333.

PMID- 2323503
VI  - 4
DP  - 1990
TI  - Analysis of the kinetic and chemical mechanisms of EcoRI methylase.
PG  - A1979
AB  - Our goal is to elucidate the kinetic and chemical mechanisms of the EcoRI DNA
      (adenine-N6)-methyltransferase.  Steady state and pre-steady state kinetic
      experiments suggest an ordered bi bi mechanism in which S-Adenosylmethionine
      (AdoMet) binds first, followed by DNA substrate.  After methyl transfer,
      S-Adenosylhomocysteine (AdoHcy) dissociates followed by methylated DNA.  The
      methyl transfer step is at least nine fold faster than the catalytic turnover
      (kcat).  The kcat and Michaelis constants (Km) for AdoMet with a short 14 base
      pair (14mer) and a long 4363 base pair plasmid DNA substrates are similar (150
      nM).  In contrast, the Km for the plasmid DNA is fifty fold lower than 14mer.
      The specificity constant (kcat/Km) for plasmid DNA is about 50 fold greater
      than for the 14mer, suggesting that EcoRI methylase is a processive enzyme.
      With a kcat/Km ratio of 2.9x10/8 M-1 sec-1 for plasmid DNA, EcoRI methylase is
      among the most efficient enzymes reported.  pH studies implicating specific
      amino acid residues in catalysis and (or) substrate binding will be presented.
AU  - Mashhoon N
AU  - Reich NO
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1990 4: A1979.

PMID- Not carried by PubMed...
VI  - 196
DP  - 1988
TI  - A kinetic study of DNA methylation by EcoRI methylase.
PG  - 96
AB  - The ability of a protein to recognize and subsequently modify a specific
      sequence of bases in DNA is a fundamental biochemical question that is being
      addressed in our laboratory by studying the EcoRI DNA methylase.  EcoRI
      methylase, a 38 kilodalton bacterial protein, requires S-adenosyl methionine
      (AdoMet) to methylate the double stranded DNA sequence GAATTC at the second
      adenine.  Methylation of DNA serves to protect the organism's DNA against
      cleavage by the corresponding endonuclease.  Little is known about the enzyme's
      kinetic mechanism, the order of substrate binding and product release and the
      rate limiting step in the reaction.  Steady state and pre-steady state analysis
      were used to determine the kinetic mechanism.  Product inhibition with
      S-adenosyl homocysteine is competitive with respect to AdoMet, whereas it is
      non-competitive with respect to DNA.  Data will be presented on the steady
      state kinetic parameters for AdoMet and DNA, the rate limiting step in the
      reaction, and the order of substrate binding and product release.
AU  - Mashhoon N
AU  - Reich NO
PT  - Journal Article
TA  - ACS Abstracts
JT  - ACS Abstracts
SO  - ACS Abstracts 1988 196: 96.

PMID- 29650576
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Four Strains of Recently Established Novel Veillonella  Species Isolated from Human Oral Cavities.
PG  - e00259-18
AB  - Veillonella species are known to contribute to the formation of early oral biofilms and tend
      to be prevalent in people with poor oral hygiene status. Here,
      we report the draft genome sequences of 4 oral Veillonella strains that were
      established recently as novel species.
AU  - Mashima I
AU  - Liao YC
AU  - Sabharwal A
AU  - Haase EM
AU  - Nakazawa F
AU  - Scannapieco FA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00259-18.

PMID- 26294617
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Veillonella tobetsuensis ATCC BAA-2400T Isolated from Human Tongue Biofilm.
PG  - e00808-15
AB  - Here, we report the draft genome sequence of Veillonella tobetsuensis ATCC-BAA 2400(T). This
      bacterium has the remarkable ability to form oral biofilms. The
      genome is predicted to encode the necessary enzymes involved in the pathway that
      facilitates the conversion of lactate to propionate.
AU  - Mashima I
AU  - Nakazawa F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00808-15.

PMID- 28034855
VI  - 4
DP  - 2016
TI  - Genome Sequence of Actinomyces naeslundii Strain ATCC 27039, Isolated from an Abdominal Wound Abscess.
PG  - e01443-16
AB  - Here, we present the complete genome sequence of Actinomyces naeslundii strain ATCC 27039,
      isolated from an abdominal wound abscess. This strain is genetically
      transformable and will thus provide valuable information related to its crucial
      role in oral multispecies biofilm development.
AU  - Mashimo C
AU  - Yamane K
AU  - Yamanaka T
AU  - Maruyama H
AU  - Wang PL
AU  - Komasa S
AU  - Okazaki J
AU  - Nambu T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01443-16.

PMID- 19852768
VI  - 47
DP  - 2009
TI  - A dual-activation, adenoviral-based system for the controlled induction of DNa double-strand breaks by the restriction endonuclease SacI.
PG  - 847-854
AB  - Spontaneous damage to DNA is frequent and may lead to cell death, cell senescence, or
      mutations.  DNA double-strand breaks are of special interest because they are highly toxic and
      have been implicated in neurodegeneration, cancer, and aging.  Until now, there has not been a
      reliable system allowing tunable induction of random DSBs without affecting other
      macromolecules or cell functions.  Here, we describe an adenoviral-based,
      doxycycline-mediated, and tamoxifen-dependent system for quantitative introduction of DSBs in
      mammalian cells.  We generated a single adenoviral vector containing a tet-inducible,
      composite SalI restriction endonuclease/estrogen receptor gene, and a constitutively expressed
      reverse transactivator gene.  Transduced mouse embryonic fibroblasts - as well as mouse liver
      cells in vivo - demonstrated a high level of DSBs in response to treatment with doxycycline
      and tamoxifen.  We show that the amount of induced DSBs can be titrated by doxycycline dose
      and duration of treatment.  This system should be useful for studying the processing of
      randomly induced DSBs and their effects on cell fate, without the side effects normally
      associated with radiation or chemical treatment.
AU  - Maslov A
AU  - Metrikin M
AU  - Vijg J
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 2009 47: 847-854.

PMID- 26139726
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Two Pyrazinamide-Resistant Clinical Isolates, Mycobacterium tuberculosis 13-4152 and 13-2459.
PG  - e00758-15
AB  - We report draft genome sequences of two pyrazinamide (PZA)-resistant isolates, Mycobacterium
      tuberculosis 13-4152 and 13-2459. Isolate 13-4152 is PZA resistant,
      though it lacks mutations in known genes of PZA resistance. The comparative
      analysis of these genomes with those stored in GenBank revealed unique mutations,
      which may elucidate new mechanisms of PZA resistance.
AU  - Maslov DA
AU  - Shur KV
AU  - Bekker OB
AU  - Zakharevich NV
AU  - Zaichikova MV
AU  - Klimina KM
AU  - Smirnova TG
AU  - Zhang Y
AU  - Chernousova LN
AU  - Danilenko VN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00758-15.

PMID- 24948763
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of 'Candidatus Cronobacter colletis' NCTC 14934T, a New Species in the Genus Cronobacter.
PG  - e00585-14
AB  - Members of the Cronobacter genus are associated with serious infections in neonates. This is
      the first report of the draft genome sequence for the newly
      proposed species Cronobacter colletis.
AU  - Masood N
AU  - Jackson E
AU  - Moore K
AU  - Farbos A
AU  - Paszkiewicz K
AU  - Dickins B
AU  - McNally A
AU  - Forsythe S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00585-14.

PMID- 24115548
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of a Meningitic Isolate of Cronobacter sakazakii Clonal Complex 4, Strain 8399.
PG  - e00833-13
AB  - The Cronobacter sakazakii clonal lineage defined as clonal complex 4 (CC4), composed of nine
      sequence types, is associated with severe cases of neonatal
      meningitis. To date, only closely related C. sakazakii sequence type 4 (ST4)
      strains have been sequenced. C. sakazakii strain 8399, isolated from a case of
      neonatal meningitis, was sequenced as the first non-ST4 C. sakazakii strain.
AU  - Masood N
AU  - Moore K
AU  - Farbos A
AU  - Hariri S
AU  - Block C
AU  - Paszkiewicz K
AU  - Dickins B
AU  - McNally A
AU  - Forsythe S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00833-13.

PMID- 24072872
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences of Three Newly Identified Species in the Genus Cronobacter, C. helveticus LMG23732T, C. pulveris LMG24059, and C. zurichensis  LMG23730T.
PG  - e00783-13
AB  - Cronobacter helveticus, Cronobacter pulveris, and Cronobacter zurichensis are newly described
      species in the Cronobacter genus, which is associated with
      serious infections of neonates. This is the first report of draft genome
      sequences for these species.
AU  - Masood N
AU  - Moore K
AU  - Farbos A
AU  - Hariri S
AU  - Paszkiewicz K
AU  - Dickins B
AU  - McNally A
AU  - Forsythe S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00783-13.

PMID- 24072871
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Earliest Cronobacter sakazakii Sequence Type 4 Strain, NCIMB 8272.
PG  - e00782-13
AB  - The Cronobacter sakazakii clonal lineage defined as sequence type 4 (ST4) is associated with
      severe cases of neonatal meningitis and persistence in powdered
      infant formula. For genome sequencing of the earliest deposited culture
      collection strain of Cronobacter sakazakii ST4, we used the strain NCIMB 8272,
      originally isolated from milk powder in 1950.
AU  - Masood N
AU  - Moore K
AU  - Farbos A
AU  - Hariri S
AU  - Paszkiewicz K
AU  - Dickins B
AU  - McNally A
AU  - Forsythe S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00782-13.

PMID- Not carried by PubMed...
VI  - 57
DP  - 1996
TI  - What is the origin and role of the large variable region in the M-AluI DNA-(cytosine c5) methyltransferase?
PG  - 1626
AB  - AluI DNA-(cytosine C5)-methyltransferase is part of a restriction-modification system, and
      methylates the 5-carbon of cytosine in the sequence 5'-AGCT-3'.  The amino acid sequences of
      all known 5mC MTases contain ten conserved motifs, and between Motifs VIII and IX have a
      variable region containing one or more Target Recognizing Domains.  TRDs are responsible for
      DNA sequence specificity: monospecific MTases appear to have only one, while multispecific
      MTases have as many as five.  M.AluI has the second largest variable region of all known 5mC
      MTases, and sequence comparisons reveal four candidate TRDs in its variable region.  What is
      the origin and role of this large variable region?  One possibility is that M.AluI evolved
      from a multispecific MTase, or imported its variable region from a multispecific MTase.
      Alternatively, it may have evolved from a monospecific MTase, expanding its variable region by
      partial duplications.  Phylogenetic parsimony analysis and FASTA followed by Spearman's rank
      order correlation coefficient suggested that neither M.AluI nor its variable region is closely
      related to the known multispecific MTases.  The M.AluI pattern, however, is consistent with
      importation of the variable region.  Methylation of AGCT sites accounted for 85-90% of the
      methylating activity, but M.HhaI gave no unexplained methylating activity.  Various insertions
      or deletion mutants failed to identify dispensable portions of the variable region, but a
      sensitive in vivo assay based on McrBC restriction did reveal that the central portion is
      particularly important for activity.  If M.AluI is like the multispecific MTases, which it
      resembles in size, then it might be expected to accommodate a TRD from a multispecific MTase.
      When such a TRD was moved into two locations in the M.AluI variable region, neither construct
      gained a new specificity and both had greatly reduced activity.  Hence, M.AluI behaves in most
      respects like a monospecific MTase, and the remarkable size of its variable region remains to
      be explained.
AU  - Master SS
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1996 57: 1626.

PMID- 9439564
VI  - 257
DP  - 1997
TI  - A genetic and functional analysis of the unusually large variable region in the M.AluI DNA-(cytosine C5)-methyltransferase.
PG  - 14-22
AB  - The M.AluI DNA-(cytosine C5)-methyltransferase (5mC methylase) acts on the sequence
      5'-AGCT-3'.  The amino acid sequences of known 5mC methylases contain ten conserved motifs,
      with a variable region between Motifs VIII and IX that contains one or more
      "target-recognizing domains" responsible for DNA sequence specificity.  Monospecific 5mC
      methylases are believed to have only one TRD, while multi-specific 5mC methylases have as many
      as five.  M.AluI has the second-largest variable region of all known 5mC methylase, and
      sequence analysis reveals five candidate TRDs.  In testing whether M.AluI is in fact
      monospecific it was found that AGCT methylation represents only 80-90% of the methylating
      activity of this enzyme, while control experiments with the enzyme M.HhaI gave no unexplained
      activity.  Because individual TRDs can be deleted from multispecific methylases without
      general loss of activity, a series of insertion and deletion mutants of the M.AluI variable
      region were prepared.  All deletions that removed more than single amino acids from the
      variable region caused significant loss of activity; a sensitive in vivo assay for methylase
      activity based on McrBC restriction suggested that the central portion of the variable region
      is particularly important.  In some cases, multispecific methylases can accommodate a TRD from
      another multispecific methylase, thereby acquiring an additional specificity.  When TRDs were
      removed from a multispecific methylase into two different locations in the variable region of
      M.AluI, all hybrid enzymes had greatly reduced activity and no new specificities.  M.AluI thus
      behaves in most respects as a monospecific methylase despite the remarkable sizeof its
      variable region.
AU  - Master SS
AU  - Blumenthal RM
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1997 257: 14-22.

PMID- 7720955
VI  - 9
DP  - 1995
TI  - Is the M.AluI DNA-(cytosine C5)-methyltransferase monospecific or multispecific?
PG  - A1399
AB  - The AluI DNA-(cytosine C5)-methyltransferase (M.AluI) is part of a type II
      restriction-modification system and methylates cytosine at the 5-carbon position in the
      sequence 5'-AGCT-3'. The predicted amino acid sequences of all known 5-methylcytosine (5mC)
      MTases contain ten conserved motifs, and a variable region which lies between motifs VIII and
      IX. This variable region contains one or more Target Recognition Domains (TRDs) responsible
      for the DNA sequence specificity of the MTase. Monospecific 5mC MTases are believed to have
      only one TRD, while multispecific 5mC methylases have as many as four. M.AluI has the
      second-largest variable region of all known 5mC MTases, and sequence comparisons with the TRDs
      of multispecific MTases reveal four candidate TRDs in the M.AluI variable region. We have
      confirmed that M.AluI is monospecific. Furthermore, we have constructed a series of insertion
      and deletion mutants in order to identify a single contiguous region as the candidate TRD
      responsible for M.AluI 5'-AGCT-3' specificity. In multispecific MTases a TRD is necessary
      and sufficient to confer the cognate specificity, as shown by moving the TRD into another
      multispecific MTase. In monospecific MTases, however, the TRD alone is not sufficient to
      confer the required specificity but requires the presence of at least motif IX from the parent
      MTase. Is M.AluI functionally more closely related to the multispecifics than to other
      monospecifics. We are testing this in collaboration with another laboratory. If M.AluI is like
      the multispecific MTases, than it should accommodate a TRD from a multispecific MTase. When a
      TRD was moved from a multispecific MTase into two different locations in the variable region
      of M.AluI, neither construct gained a new specificity and both had greatly reduced activity.
      To test if the candidate M.AluI TRD is sufficient to confer specificity we are moving it into
      the variable region of a multispecific MTase. From the existing data, it seems as if M.AluI
      behaves in all respects as a monospecific MTase, and the remarkable size of its variable
      region remains to be explained.
AU  - Master SS
AU  - Blumenthal RM
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1995 9: A1399.

PMID- 25477416
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Versatile Alkane-Degrading Bacterium Aquabacterium sp. Strain NJ1.
PG  - e01271-14
AB  - The draft genome sequence of a soil bacterium, Aquabacterium sp. strain NJ1, capable of
      utilizing both liquid and solid alkanes, was deciphered. This is the
      first report of an Aquabacterium genome sequence.
AU  - Masuda H
AU  - Shiwa Y
AU  - Yoshikawa H
AU  - Zylstra GJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01271-14.

PMID- 23929476
VI  - 1
DP  - 2013
TI  - Whole-Genome Sequence of the Purple Photosynthetic Bacterium Rhodovulum sulfidophilum Strain W4.
PG  - e00577-13
AB  - We report the draft genome sequence of the purple photosynthetic bacterium Rhodovulum
      sulfidophilum. The photosynthesis gene cluster comprises two
      segments-a unique feature among photosynthesis gene clusters of purple bacteria.
      The genome information will be useful for further analysis of bacterial
      photosynthesis.
AU  - Masuda S
AU  - Hori K
AU  - Maruyama F
AU  - Ren S
AU  - Sugimoto S
AU  - Yamamoto N
AU  - Mori H
AU  - Yamada T
AU  - Sato S
AU  - Tabata S
AU  - Ohta H
AU  - Kurokawa K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00577-13.

PMID- 18482458
VI  - 8
DP  - 2008
TI  - Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays.
PG  - 76
AB  - BACKGROUND: Syphilis spirochete Treponema pallidum ssp. pallidum remains the enigmatic
      pathogen, since no virulence factors have been identified
      and the pathogenesis of the disease is poorly understood. Increasing rates
      of new syphilis cases per year have been observed recently. RESULTS: The
      genome of the SS14 strain was sequenced to high accuracy by an
      oligonucleotide array strategy requiring hybridization to only three
      arrays (Comparative Genome Sequencing, CGS). Gaps in the resulting
      sequence were filled with targeted dideoxy-terminators (DDT) sequencing
      and the sequence was confirmed by whole genome fingerprinting (WGF). When
      compared to the Nichols strain, 327 single nucleotide substitutions (224
      transitions, 103 transversions), 14 deletions, and 18 insertions were
      found. On the proteome level, the highest frequency of amino acid-altering
      substitution polymorphisms was in novel genes, while the lowest was in
      housekeeping genes, as expected by their evolutionary conservation.
      Evidence was also found for hypervariable regions and multiple regions
      showing intrastrain heterogeneity in the T. pallidum chromosome.
      CONCLUSION: The observed genetic changes do not have influence on the
      ability of Treponema pallidum to cause syphilitic infection, since both
      SS14 and Nichols are virulent in rabbit. However, this is the first
      assessment of the degree of variation between the two syphilis pathogens
      and paves the way for phylogenetic studies of this fascinating organism.
AU  - Matejkova P
AU  - Strouhal M
AU  - Smajs D
AU  - Norris SJ
AU  - Palzkill T
AU  - Petrosino JF
AU  - Sodergren E
AU  - Norton JE
AU  - Singh J
AU  - Richmond TA
AU  - Molla MN
AU  - Albert TJ
AU  - Weinstock GM
PT  - Journal Article
TA  - BMC Microbiol.
JT  - BMC Microbiol.
SO  - BMC Microbiol. 2008 8: 76.

PMID- 29686747
VI  - 13
DP  - 2018
TI  - High-quality draft genome of the methanotroph Methylovulum psychrotolerans Str. HV10-M2 isolated from plant material at a high-altitude environment.
PG  - 10
AB  - Here we present the genome of Methylovulum psychrotolerans strain HV10-M2, a methanotroph
      isolated from Hardangervidda national park (Norway). This strain
      represents the second of the two validly published species genus with a sequenced
      genome. The other is M. miyakonense HT12, which is the type strain of the species
      and the type species of the genus Methylovulum. We present the genome of M.
      psychrotolerants str. HV10-M2 and discuss the differences between M.
      psychrotolerans and M. miyakonense. The genome size of M. psychrotolerans str.
      HV10-M2 is 4,923,400 bp and contains 4415 protein-coding genes, 50 RNA genes and
      an average GC content of 50.88%.
AU  - Mateos-Rivera A
AU  - Islam T
AU  - Marshall IPG
AU  - Schreiber L
AU  - Ovreas L
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2018 13: 10.

PMID- 24030491
VI  - 341
DP  - 2013
TI  - Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts.
PG  - 1514-1517
AB  - The global epidemic of multidrug-resistant Salmonella Typhimurium DT104 provides
      an important example, both in terms of the agent and its resistance, of a widely
      disseminated zoonotic pathogen. Here, with an unprecedented national collection
      of isolates collected contemporaneously from humans and animals and including a
      sample of internationally derived isolates, we have used whole-genome sequencing
      to dissect the phylogenetic associations of the bacterium and its antimicrobial
      resistance genes through the course of an epidemic. Contrary to current tenets
      supporting a single homogeneous epidemic, we demonstrate that the bacterium and
      its resistance genes were largely maintained within animal and human populations
      separately and that there was limited transmission, in either direction. We also
      show considerable variation in the resistance profiles, in contrast to the
      largely stable bacterial core genome, which emphasizes the critical importance of
      integrated genotypic data sets in understanding the ecology of bacterial zoonoses
      and antimicrobial resistance.
AU  - Mather AE et al
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2013 341: 1514-1517.

PMID- 25561339
VI  - 59
DP  - 2015
TI  - Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae at a single institution: insights into endemicity from whole-genome sequencing.
PG  - 1656-1663
AB  - The global emergence of Klebsiella pneumoniae carbapenemase-producing K.
      pneumoniae (KPC-Kp) multilocus sequence type ST258 is widely recognized. Less is
      known about the molecular and epidemiological details of non-ST258 K. pneumoniae
      in the setting of an outbreak mediated by an endemic plasmid. We describe the
      interplay of blaKPC plasmids and K. pneumoniae strains and their relationship to
      the location of acquisition in a U.S. health care institution. Whole-genome
      sequencing (WGS) analysis was applied to KPC-Kp clinical isolates collected from
      a single institution over 5 years following the introduction of blaKPC in August
      2007, as well as two plasmid transformants. KPC-Kp from 37 patients yielded 16
      distinct sequence types (STs). Two novel conjugative blaKPC plasmids (pKPC_UVA01
      and pKPC_UVA02), carried by the hospital index case, accounted for the presence
      of blaKPC in 21/37 (57%) subsequent cases. Thirteen (35%) isolates represented an
      emergent lineage, ST941, which contained pKPC_UVA01 in 5/13 (38%) and pKPC_UVA02
      in 6/13 (46%) cases. Seven (19%) isolates were the epidemic KPC-Kp strain, ST258,
      mostly imported from elsewhere and not carrying pKPC_UVA01 or pKPC_UVA02. Using
      WGS-based analysis of clinical isolates and plasmid transformants, we demonstrate
      the unexpected dispersal of blaKPC to many non-ST258 lineages in a hospital
      through spread of at least two novel blaKPC plasmids. In contrast, ST258 KPC-Kp
      was imported into the institution on numerous occasions, with other blaKPC
      plasmid vectors and without sustained transmission. Instead, a newly recognized
      KPC-Kp strain, ST941, became associated with both novel blaKPC plasmids and
      spread locally, making it a future candidate for clinical persistence and
      dissemination.
AU  - Mathers AJ
AU  - Stoesser N
AU  - Sheppard AE
AU  - Pankhurst L
AU  - Giess A
AU  - Yeh AJ
AU  - Didelot X
AU  - Turner SD
AU  - Sebra R
AU  - Kasarskis A
AU  - Peto T
AU  - Crook D
AU  - Sifri CD
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2015 59: 1656-1663.

PMID- 27594975
VI  - 11
DP  - 2016
TI  - Genomic sequence analysis of a plant-associated Photobacterium halotolerans MELD1: from marine to terrestrial environment?
PG  - 56
AB  - Mercury impacts the function and development of the central nervous system in both humans and
      wildlife by being a potent neurotoxin. Microbial bioremediation
      is an important means of remediation of mercury-contaminated soil. The
      rhizospheric Photobacterium halotolerans strain MELD1 was isolated from mercury
      and dioxin contaminated site from Tainan, Taiwan. It has been shown to reduce
      Hg(2+) to Hg(0). The 4,758,027 bp genome of P. halotolerans MELD1 has a G + C
      content of 50.88 % and contains 4198 protein-coding and 106 RNA genes. Genomic
      analysis revealed the presence of a number of interesting gene cluster that maybe
      involved in heavy metal resistance, rhizosphere competence and colonization of
      the host plant.
AU  - Mathew DC
AU  - Lo SC
AU  - Mathew GM
AU  - Chang KH
AU  - Huang CC
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 56.

PMID- 26044418
VI  - 3
DP  - 2015
TI  - Genome Sequence of Photobacterium halotolerans MELD1, with Mercury Reductase (merA), Isolated from Phragmites australis.
PG  - e00530-15
AB  - Here, we present the whole-genome sequence of Photobacterium halotolerans strain, MELD1,
      isolated from the roots of a terrestrial plant Phragmites australis grown
      in soil heavily contaminated with mercury and dioxin. The genome provides further
      insight into the adaptation of bacteria to the toxic environment from where it
      was isolated.
AU  - Mathew DC
AU  - Mathew GM
AU  - Gicana RG
AU  - Huang CC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00530-15.

PMID- 22628513
VI  - 194
DP  - 2012
TI  - Genome Sequence of Diplorickettsia massiliensis, an Emerging Ixodes ricinus-Associated Human Pathogen.
PG  - 3287
AB  - Diplorickettsia massiliensis is a gammaproteobacterium in the order Legionellales and an agent
      of tick-borne infection. We sequenced the genome from strain 20B,
      isolated from an Ixodes ricinus tick. The genome consists of a 1,727,973-bp
      chromosome but no plasmid and includes 2,269 protein-coding genes and 42 RNA
      genes, including 3 rRNA genes.
AU  - Mathew MJ
AU  - Subramanian G
AU  - Nguyen TT
AU  - Robert C
AU  - Mediannikov O
AU  - Fournier PE
AU  - Raoult D
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3287.

PMID- 27340050
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Two Strains of Paenibacillus glucanolyticus with the Ability To Degrade Lignocellulose.
PG  - e00423-16
AB  - Paenibacillus glucanolyticus 5162, a bacterium isolated from soil, and Paenibacillus
      glucanolyticus SLM1, a bacterium isolated from pulp mill waste, can
      utilize cellulose, hemicellulose and lignin as sole carbon sources for growth.
      These two strains of Paenibacillus glucanolyticus were sequenced using PacBio and
      Illumina MiSeq technologies.
AU  - Mathews SL
AU  - Pawlak J
AU  - Grunden AM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00423-16.

PMID- 22628504
VI  - 194
DP  - 2012
TI  - Genome sequences of two plant growth-promoting fluorescent pseudomonas strains, r62 and r81.
PG  - 3272-3273
AB  - Plant growth-promoting rhizobacterial (PGPR) strains R62 and R81 have previously  been
      isolated and characterized as part of the Indo-Swiss Collaboration in
      Biotechnology. Here we present the draft genome sequences of these two PGPR
      strains, with the aim of unraveling the mechanisms behind their ability to
      promote wheat growth.
AU  - Mathimaran N
AU  - Srivastava R
AU  - Wiemken A
AU  - Sharma AK
AU  - Boller T
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3272-3273.

PMID- 28153885
VI  - 5
DP  - 2017
TI  - First Report on a Cluster of Colistin-Resistant Klebsiella pneumoniae Strains Isolated from a Tertiary Care Center in India: Whole-Genome Shotgun Sequencing.
PG  - e01466-16
AB  - Klebsiella pneumoniae is a nosocomial pathogen with clinical importance due to its increasing
      resistance to carbapenems and colistin. Here, we report the genome
      sequences of eight colistin-resistant K. pneumoniae strains which might help in
      understanding the molecular mechanism of the species. The sequence data indicate
      genomes of ~5.2 to 5.4 Mb, along with several plasmids.
AU  - Mathur P
AU  - Veeraraghavan B
AU  - Devanga RNK
AU  - Inbanathan FY
AU  - Khurana S
AU  - Bhardwaj N
AU  - Kumar S
AU  - Sagar S
AU  - Gupta A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01466-16.

PMID- 8820570
VI  - 4
DP  - 1996
TI  - Genetic barriers among bacteria.
PG  - 69-73
AB  - Barriers to chromosomal gene transfer between bacterial species control their genetic
      isolation.  These barriers, such as different microhabitats, the host ranges of genetic
      exchange vectors and restriction-modification systems, limit gene exchange, but the major
      limitation is genomic sequence divergence.  The mismatch-repair system inhibits interspecies
      recombination, the inducible SOS system stimulates interspecies recombination, while natural
      selection determines the effective recombination frequencies.
AU  - Matic I
AU  - Taddei F
AU  - Radman M
PT  - Journal Article
TA  - Trends Microbiol.
JT  - Trends Microbiol.
SO  - Trends Microbiol. 1996 4: 69-73.

PMID- 27198016
VI  - 4
DP  - 2016
TI  - Genome Sequence of Serratia plymuthica A153, a Model Rhizobacterium for the Investigation of the Synthesis and Regulation of Haterumalides, Zeamine, and  Andrimid.
PG  - e00373-16
AB  - The rhizobacterium Serratia plymuthica A153 is a Gram-negative bacterium belonging to the
      family Enterobacteriaceae Here, we present the genome sequence
      of this strain, which produces multiple bioactive secondary metabolites,
      including the halogenated macrolide oocydin A, the polyamino antibiotic zeamine,
      and the bacterial acetyl-CoA carboxylase inhibitor andrimid.
AU  - Matilla MA
AU  - Drew A
AU  - Udaondo Z
AU  - Krell T
AU  - Salmond GP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00373-16.

PMID- 21183676
VI  - 193
DP  - 2010
TI  - Complete genome of the plant-growth promoting rhizobacterium Pseudomonas putida BIRD-1.
PG  - 1290
AB  - We report the complete sequence of the 5.7-Mbp of Pseudomonas putida BIRD-1, a
      metabolically-versatile plant growth-promoting rhizobacterium that is highly tolerant to
      desiccation, capable of solubilizing inorganic phosphate and iron, and of synthesizing
      phytohormones that stimulate seed germination and plant growth.
AU  - Matilla MA
AU  - Pizarro-Tobias P
AU  - Roca A
AU  - Fernandez M
AU  - Duque E
AU  - Molina L
AU  - Wu X
AU  - van der Lelie D
AU  - Gomez MJ
AU  - Segura A
AU  - Ramos JL
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 193: 1290.

PMID- 28254993
VI  - 5
DP  - 2017
TI  - Genome Sequence of Serratia marcescens MSU97, a Plant-Associated Bacterium That Makes Multiple Antibiotics.
PG  - e01752-16
AB  - Serratia marcescens MSU97 was isolated from the Guayana region of Venezuela due to its ability
      to suppress plant-pathogenic oomycetes. Here, we report the genome
      sequence of MSU97, which produces various antibiotics, including the bacterial
      acetyl-coenzyme A (acetyl-CoA) carboxylase inhibitor andrimid, the chlorinated
      macrolide oocydin A, and the red linear tripyrrole antibiotic prodigiosin.
AU  - Matilla MA
AU  - Udaondo Z
AU  - Krell T
AU  - Salmond GP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01752-16.

PMID- 10640352
VI  - 278
DP  - 2000
TI  - A positive selection vector combining tetracycline resistance that eliminates the need for bacterial plating comprising a modified version of the gene encoding the cytosine-specific DNA-methyltransferase and a modified form of the plasmid pBR322 tetA(C).
PG  - 46-51
AB  - The construction of plasmid pMTet1 that combined positive selection with
      tetracycline-resistance was described. The vector comprised a
      modified version of the gene encoding the cytosine(C-5)-specific
      DNA-methyltransferase (C5-Mtase) MspI and a modified form of the
      plasmid pBR322 tetA(C) gene. This combination of a C5-Mtase gene and
      the tetA(C) derived from plasmid pBR322 permitted the isolation of
      recombinant plasmids in liquid culture which for the first time
      eliminated the need to isolate single, antibiotic-resistant colonies
      and therefore significantly accelerated recombinant plasmid isolation.
      Furthermore, the application of this novel cloning vector, in
      conjunction with chromatographic DNA fractionation, for the
      construction of size-selected recombinant molecules was reported. The
      construction of the plasmid pMTet1 was followed by the DNA
      amplification reaction and nucleic acid chromatography. The plasmid
      pMTet1 facilitated the rapid cloning of DNA molecules generated by
      proof-reading DNA-polymerases and restriction digests using enzymes
      that produced noncohesive termini.
AU  - Matin MM
AU  - Hornby DP
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 2000 278: 46-51.

PMID- 10047908
VI  - 26
DP  - 1998
TI  - Exploring the structural flexibility of 5m-cytosine-DNA methyltransferases.
PG  - S394
AB  - DNA methyltransferases are found in organisms ranging from bacteria to mammals.  They
      recognize specific DNA sequences and transfer a methyl group to adenine or cytosine residues.
      5m-cytosine methyltransferases form the basis of the work considered here, they belong to type
      II restriction-modification systems, which use S-adenosyl-L-methionine as a cofactor to add
      methyl groups to the 5 position of cytosine.  Two families of 5mC Mtases are known;
      mono-specific methyltransferases which recognize and methylate a single DNA sequence, and
      multi-specific Mtases that recognize and modify more than one DNA sequence.
AU  - Matin MM
AU  - Hornby DP
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 1998 26: S394.

PMID- 21229971
VI  - 50
DP  - 2011
TI  - Determinants of Precatalytic Conformational Transitions in the DNA Cytosine Methyltransferase M.HhaI.
PG  - 1465-1473
AB  - The DNA methyltransferase M.HhaI is an excellent model for understanding how recognition of a
      nucleic acid substrate is translated
      into site-specific modification. In this study, we utilize direct,
      real-time monitoring of the catalytic loop position via engineered
      tryptophan fluorescence reporters to dissect the conformational
      transitions that occur in both enzyme and DNA substrate prior to
      methylation of the target cytosine. Using nucleobase analogues in place
      of the target and orphan bases, the kinetics of the base flipping and
      catalytic loop closure rates were determined, revealing that base
      flipping precedes loop closure as the rate-determining step prior to
      methyl transfer. To determine the mechanism by which individual
      specific hydrogen bond contacts at the enzyme DNA interface mediate
      these conformational transitions, nucleobase analogues lacking hydrogen
      bonding groups were incorporated into the recognition sequence to
      disrupt the major groove recognition elements. The consequences of
      binding, loop closure, and catalysis were determined for four contacts,
      revealing large differences in the contribution of individual hydrogen
      bonds to DNA recognition and conformational transitions on the path to
      catalysis. Our results describe how M.HhaI utilizes direct readout
      contacts to accelerate extrication of the target base that offer new
      insights into the evolutionary history of this important class of
      enzymes.
AU  - Matje DM
AU  - Coughlin DF
AU  - Connolly BA
AU  - Dahlquist FW
AU  - Reich NO
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2011 50: 1465-1473.

PMID- 23409782
VI  - 52
DP  - 2013
TI  - Enzyme-Promoted Base Flipping Controls DNA Methylation Fidelity.
PG  - 1677-1685
AB  - A quantitative understanding of how conformational transitions contribute to enzyme catalysis
      and specificity remains a fundamental challenge. A suite of
      biophysical approaches was used to reveal several transient states of the
      enzyme-substrate complexes of the model DNA cytosine methyltransferase M.HhaI.
      Multidimensional, transverse relaxation-optimized nuclear magnetic resonance
      (NMR) experiments show that M.HhaI has the same conformation with noncognate and
      cognate DNA sequences. The high-affinity cognatelike mode requires the formation
      of a subset of protein-DNA interactions that drive the flipping of the target
      base from the helix to the active site. Noncognate substrates lacking these
      interactions undergo slow base flipping, and fluorescence tracking of the
      catalytic loop corroborates the NMR evidence of a loose, nonspecific binding mode
      prior to base flipping and subsequent closure of the catalytic loop. This slow
      flipping transition defines the rate-limiting step for the methylation of
      noncognate sequences. Additionally, we present spectroscopic evidence of an
      intermediate along the base flipping pathway that has been predicted but never
      previously observed. These findings provide important details of how
      conformational rearrangements are used to balance specificity with catalytic
      efficiency.
AU  - Matje DM
AU  - Zhou H
AU  - Smith DA
AU  - Neely RK
AU  - Dryden DT
AU  - Jones AC
AU  - Dahlquist FW
AU  - Reich NO
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2013 52: 1677-1685.

PMID- 4919760
VI  - 104
DP  - 1970
TI  - Host-induced modification/restriction and the utilization of 5-bromouracil by thymineless mutants of Escherichia coli.
PG  - 606-607
AB  - An mk-rk- mutation exerted no measurable effect on 5-bromouracil incorporation
      by a thymineless derivative of Escherichia coli K.
AU  - Matney TS
AU  - MacDougall NLT
AU  - Butler MA
AU  - Suit JC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1970 104: 606-607.

PMID- 28775794
VI  - 12
DP  - 2017
TI  - High-quality genome sequence of the radioresistant bacterium Deinococcus ficus KS 0460.
PG  - 46
AB  - The genetic platforms of Deinococcus species remain the only systems in which massive ionizing
      radiation (IR)-induced genome damage can be investigated in vivo
      at exposures commensurate with cellular survival. We report the whole genome
      sequence of the extremely IR-resistant rod-shaped bacterium Deinococcus ficus KS
      0460 and its phenotypic characterization. Deinococcus ficus KS 0460 has been
      studied since 1987, first under the name Deinobacter grandis, then Deinococcus
      grandis. The D. ficus KS 0460 genome consists of a 4.019 Mbp sequence (69.7% GC
      content and 3894 predicted genes) divided into six genome partitions, five of
      which are confirmed to be circular. Circularity was determined manually by mate
      pair linkage. Approximately 76% of the predicted proteins contained identifiable
      Pfam domains and 72% were assigned to COGs. Of all D. ficus KS 0460 proteins, 79%
      and 70% had homologues in Deinococcus radiodurans ATCC BAA-816 and Deinococcus
      geothermalis DSM 11300, respectively. The most striking differences between D.
      ficus KS 0460 and D. radiodurans BAA-816 identified by the comparison of the KEGG
      pathways were as follows: (i) D. ficus lacks nine enzymes of purine degradation
      present in D. radiodurans, and (ii) D. ficus contains eight enzymes involved in
      nitrogen metabolism, including nitrate and nitrite reductases, that D.
      radiodurans lacks. Moreover, genes previously considered to be important to IR
      resistance are missing in D. ficus KS 0460, namely, for the Mn-transporter nramp,
      and proteins DdrF, DdrJ and DdrK, all of which are also missing in Deinococcus
      deserti. Otherwise, D. ficus KS 0460 exemplifies the Deinococcus lineage.
AU  - Matrosova VY et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 46.

PMID- 
VI  - 63
DP  - 2001
TI  - Genetic transformation of Streptomyces globisporus 1912 strains: restriction barrier and plasmid compatibility.
PG  - 15-21
AB  - Low efficiency of genetic transformation of protoplasts of different strains of Streptomyces
      globisporus 1912 by means of DNA preparations
      of three vectors pIJ487, pGM160 and pWHM4 is explained by the presence of
      a restriction barrier in the recipients. This obstacle can be
      overcome by the use of modified DNA of the same vectors, isolated from
      not numerous transformants. The frequency of transformation by such
      modified vector DNA was increased by two-three orders in comparison
      with initial DNA, isolated from Streptomyces lividans TK24, losing
      restriction-modification system. The vector pCNB4001, containing the
      replicon of endogeneous plasmid pSG1912-1, effectively transformed the
      protoplasts of all S. globisporus 1912 strains. Compatibility of pIJ487
      and pSG1912-1 plasmids and incompatibility of the latter and pWHM4 was
      shown.
AU  - Matselyukh AB
PT  - Journal Article
TA  - Mikrobiol. Zh.
JT  - Mikrobiol. Zh.
SO  - Mikrobiol. Zh. 2001 63: 15-21.

PMID- 20236167
VI  - 12
DP  - 2010
TI  - Selenium controls transcription of paralogous formate dehydrogenase genes in the termite gut acetogen, Treponema primitia.
PG  - 2245-2258
AB  - Summary The termite gut spirochete, Treponema primitia, is a CO(2)-reductive acetogen that is
      phylogenetically distinct from other distantly related and more extensively studied acetogens
      such as Moorella thermoacetica. Research on T. primitia has revealed details about the role of
      spirochetes in CO(2)-reductive acetogenesis, a process important to the mutualism occurring
      between termites and their gut microbial communities. Here, a locus of the T. primitia genome
      containing Wood-Ljungdahl pathway genes for CO(2)-reductive acetogenesis was sequenced. This
      locus contained methyl-branch genes of the pathway (i.e. for the reduction of CO(2) to the
      level of methyl-tetrahydrofolate) including paralogous genes for cysteine and selenocysteine
      (Sec) variants of formate dehydrogenase (FDH) and genes for Sec incorporation. The FDH
      variants affiliated phylogenetically with hydrogenase-linked FDH enzymes, suggesting that T.
      primitia FDH enzymes utilize electrons derived directly from molecular H(2). Sub-nanomolar
      concentrations of selenium decreased transcript levels of the cysteine variant FDH gene.
      Selenium concentration did not markedly influence the level of mRNA upstream of the Sec-codon
      in the Sec variant FDH; however, the level of transcript extending downstream of the Sec-codon
      increased incrementally with increasing selenium concentrations. The features and regulation
      of these FDH genes are an indication that T. primitia may experience dynamic selenium
      availability in its H(2)-rich gut environment.
AU  - Matson EG
AU  - Zhang X
AU  - Leadbetter JR
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2010 12: 2245-2258.

PMID- 27609915
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Helicobacter suis Strain SNTW101, Isolated from a Japanese Patient with Nodular Gastritis.
PG  - e00934-16
AB  - We present here the draft whole-genome shotgun sequence of an uncultivated strain SNTW101 of
      Helicobacter suis, which has been maintained in the stomachs of mice.
      This strain was originally isolated from gastric biopsy specimens of a urea
      breath test-negative Japanese patient suffering from nodular gastritis.
AU  - Matsui H
AU  - Takahashi T
AU  - Murayama SY
AU  - Uchiyama I
AU  - Yamaguchi K
AU  - Shigenobu S
AU  - Suzuki M
AU  - Rimbara E
AU  - Shibayama K
AU  - Overby A
AU  - Nakamura M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00934-16.

PMID- 3032318
VI  - 104
DP  - 1986
TI  - Production of restriction endonucleases from various Salmonella strains of human origin.
PG  - 92-96
AB  - Using a safe procedure for the detection of restriction endonuclease-producing
      strains, 21 restriction-positive strains were found among 120 Salmonella
      strains of human origin.  The designation of the restriction endonucleases and
      their producers was SinI and SinII in Salmonella infantis (11 strains), SblI in
      Salmonella blockley (3 strains), StmI in Salmonella typhimurium, SbaI in
      Salmonella bareilly, SscI in Salmonella schwarzengrund, SthI in Salmonella
      thompson, SanI in Salmonella anatum, SisI in Salmonella Isangi and SbrI in
      Salmonella bredeney.  Activity of all the endonucleases was very high.  No Hsd
      plasmids has been isolated from these restriction endonuclease-producing
      strains in spite of several trials, indicating that the hsd+ gene might be
      carried on chromosomal DNA.
AU  - Matsui M
AU  - Mise K
AU  - Yoshida Y
AU  - Ishidate M
PT  - Journal Article
TA  - Eisei Shikenjo Hokoku
JT  - Eisei Shikenjo Hokoku
SO  - Eisei Shikenjo Hokoku 1986 104: 92-96.

PMID- 20418439
VI  - 76
DP  - 2010
TI  - Species-Specific Type II Restriction-Modification System of Xylella fastidiosa Temecula1.
PG  - 4092-4095
AB  - The transformation efficiency of Xylella fastidiosa can be increased by interfering with
      restriction by the strain-specific type II system
      encoded by the PD1607 and PD1608 genes. Here, we report results for two
      strategies: in vitro methylation using M. SssI and isolation of DNA
      from an Escherichia coli strain expressing the methylase PD1607.
AU  - Matsumoto A
AU  - Igo MM
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2010 76: 4092-4095.

PMID- 16493661
VI  - 63
DP  - 2006
TI  - Crystal structure of intein homing endonuclease II encoded in DNA polymerase gene from hyperthermophilic archaeon Thermococcus kodakaraensis strain KOD1.
PG  - 711-715
AB  - 
AU  - Matsumura H
AU  - Takahashi H
AU  - Inoue T
AU  - Yamamoto T
AU  - Hashimoto H
AU  - Nishioka M
AU  - Fujiwara S
AU  - Takagi M
AU  - Imanaka T
AU  - Kai Y
PT  - Journal Article
TA  - Proteins
JT  - Proteins
SO  - Proteins 2006 63: 711-715.

PMID- 29798920
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Escherichia coli J53, an Azide-Resistant Laboratory Strain Used for Conjugation Experiments.
PG  - e00433-18
AB  - We report here the complete genome sequence of Escherichia coli J53, which is used as a
      recipient in conjugation experiments and is a laboratory strain derived
      from E. coli K-12. This genome sequence will help in the development of a
      comprehensive genetic analysis of conjugative elements.
AU  - Matsumura Y
AU  - Peirano G
AU  - Pitout JDD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00433-18.

PMID- 29930039
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Escherichia coli ME8067, an Azide-Resistant Laboratory Strain Used for Conjugation Experiments.
PG  - e00515-18
AB  - We report here the complete genome sequence of Escherichia coli ME8067, an azide-resistant
      laboratory strain used for conjugation experiments. The ME8067
      genome was closely related to E. coli strain K-12 substrain W3110. This genome
      sequence will support further genetic analysis of conjugative elements.
AU  - Matsumura Y
AU  - Yamamoto M
AU  - Nakano S
AU  - Nagao M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00515-18.

PMID- 26450739
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Streptomyces sp. JHA19, a Strain That Possesses beta-d-Galactofuranosidase Activity.
PG  - e01171-15
AB  - By screening for microbes that exhibit beta-d-galactofuranosidase (Galf-ase) activity, a
      Streptomyces sp. strain, named JHA19, was isolated from a soil sample from Kagawa University,
      Japan, in 2010. Here, we report the results of whole-genome shotgun sequencing and found that
      the strain has four predicted Galf-ase genes.
AU  - Matsunaga E
AU  - Higuchi Y
AU  - Mori K
AU  - Tashiro K
AU  - Kuhara S
AU  - Takegawa K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01171-15.

PMID- 28408688
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Streptomyces sp. JHA26, a Strain That Harbors a PA14 Domain Containing beta-d-Galactofuranosidase.
PG  - e00190-17
AB  - The genome sequence of Streptomyces sp. strain JHA26, the culture supernatant of  which
      exhibited beta-d-galactofuranosidase (Galf-ase) activity, was analyzed to
      search for a Galf-ase-encoding gene. We report here the results of whole-genome
      shotgun sequencing and reveal the identity of a new Galf-ase gene.
AU  - Matsunaga E
AU  - Higuchi Y
AU  - Mori K
AU  - Tashiro K
AU  - Takegawa K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00190-17.

PMID- 16303747
VI  - 12
DP  - 2005
TI  - Complete Genome Sequence of the Facultative Anaerobic Magnetotactic Bacterium Magnetospirillum sp. strain AMB-1.
PG  - 157-166
AB  - Magnetospirillum sp. strain AMB-1 is a Gram-negative alpha-proteobacterium that synthesizes
      nano-sized magnetites, referred to as magnetosomes,
      aligned intracellularly in a chain. The potential of this nano-sized
      material is growing and will be applicable to broad research areas. It has
      been expected that genome analysis would elucidate the mechanism of
      magnetosome formation by magnetic bacteria. Here we describe the genome of
      Magnetospirillum sp. AMB-1 wild type, which consists of a single circular
      chromosome of 4967148 bp. For identification of genes required for
      magnetosome formation, transposon mutagenesis and determination of
      magnetosome membrane proteins were performed. Analysis of a non-magnetic
      transposon mutant library focused on three unknown genes from 2752 unknown
      genes and three genes from 205 signal transduction genes. Partial proteome
      analysis of the magnetosome membrane revealed that the membrane contains
      numerous oxidation/reduction proteins and a signal response regulator that
      may function in magnetotaxis. Thus, oxidation/reduction proteins and
      elaborate multidomain signaling proteins were analyzed. This comprehensive
      genome analysis will enable resolution of the mechanisms of magnetosome
      formation and provide a template to determine how magnetic bacteria
      maintain a species-specific, nano-sized, magnetic single domain and
      paramagnetic morphology.
AU  - Matsunaga T
AU  - Okamura Y
AU  - Fukuda Y
AU  - Wahyudi AT
AU  - Murase Y
AU  - Takeyama H
PT  - Journal Article
TA  - DNA Res.
JT  - DNA Res.
SO  - DNA Res. 2005 12: 157-166.

PMID- 7816625
VI  - 22
DP  - 1994
TI  - The CpG-specific methylase SssI has topoisomerase activity in the presence of Mg2+.
PG  - 5354-5359
AB  - A prokaryotic CpG-specific methylase from Spiroplasma, SssI methylase, is now widely used to
      study the effect of CpG methylation in mammalian cells, and can processively modify cytosines
      in CpG dinucleotides in the absence of Mg2+. In the presence of Mg2+, we found (i) that the
      methylation reaction is distributive rather than processive as a result of the decreased
      affinity of SssI methylase for DNA, and (ii) that a type I-like topoisomerase activity is
      present in SssI methylase preparations. This topoisomerase activity was still present in SssI
      methylase further purified by either SDS-polyacrylamide or isoelectric focusing gel
      electrophoresis. We show that methylase and topoisomerase activities are not functionally
      interdependent, since conditions exist where only one or the other enzymatic activity is
      detectable. The catalytic domains of SssI methylase and prokaryotic topoisomerases show
      similarity at the amino acid level, further supporting the idea that the topoisomerase
      activity is a genuine activity of SssI methylase. Mycoplasmas, including Spiroplasma, have the
      smallest genomes of all living organisms; thus, this condensation of two enzymatic activities
      into the same protein may be a result of genome economy, and may also have functional
      implications for the mechanism of methylation.
AU  - Matsuo K
AU  - Silke J
AU  - Gramatikoff K
AU  - Schaffner W
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1994 22: 5354-5359.

PMID- 15766787
VI  - 244
DP  - 2005
TI  - Restriction and modification of SP10 phage by BsuM of Bacillus subtilis Marburg.
PG  - 335-339
AB  - Bacillus subtilis Marburg has only one intrinsic restriction and modification system BsuM that
      recognizes the CTCGAG (XhoI site)
      sequence. It consists of two operons, BsuMM operon for two cytosine DNA
      methyltransferases, and BsuMR operon for a restriction nuclease and two
      associated proteins of unknown function. In this communication, we
      analyzed the BsuM system by utilizing phage SPIO that possesses more
      than twenty BsuM target sequences on the phage genome. SPIO phages
      grown in the restriction and modification-deficient strain could not
      make plaques on the restriction-proficient BsuMR(+) indicator strain.
      An enforced expression of the wild type BsuMM operon in the BsuMR(+)
      indicator strain, however, allowed more than thousand times more
      plaques. DNA extracted from SPIO phages, thus, propagated became more
      but not completely refractory to XhoI digestion in vitro. Thus, the
      SPIO phage genome DNA is able to be nearly full-methylated but some
      BsuM sites are considered to be unmethylated.
AU  - Matsuoka S
AU  - Asai K
AU  - Sadaie Y
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2005 244: 335-339.

PMID- 2722743
VI  - 171
DP  - 1989
TI  - Streptomyces lipmanii expresses two restriction systems that inhibit plasmid transformation and bacteriophage plaque formation.
PG  - 3128-3132
AB  - Bacteriophage host range studies suggested that several beta-lactam-producing streptomycetes
      express similar restriction-modification systems.  Streptomyces lipmanii LE32 expressed two
      restriction-modification systems, designated SliI and SliII.  A mutant strain, PM87, was
      defective only in SliI restriction but expressed both SliI and SliII modification.
      Streptomyces sp. strain A57986, a natural isolate partially deficient in the expression of
      SliI and SliII restriction, nevertheless modified bacteriophage DNA for both SliI and SliII
      specificities.  Protoplasts of PM87 and A57986 were transformed by several plasmids, and the
      modified plasmids isolated from these strains transformed wild-type S. lipmanii efficiently.
AU  - Matsushima P
AU  - Baltz RH
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1989 171: 3128-3132.

PMID- Not carried by PubMed...
VI  - 89
DP  - 1989
TI  - Restriction and modification in Streptomyces lipmanii.
PG  - 361
AB  - Steptomyces lipmanii and several other beta-lactam antibiotic-producing
      streptomycetes express restriction systems that inhibit plasmid transformation
      and bacteriophage plaque formation.  Bacteriophage host range studies suggested
      that many beta-lactam producers express some common restriction system(s).  We
      isolated a mutant, S. lipmanii PM87, defective in one restriction system (SliI)
      and analyzed restriction and modification of several different bacteriophages
      in PM87 and its parent strain, LE32.  PM87 appears to be proficient in SliI
      modification and expresses a second restriction/modification system, designated
      SliII.  Another beta-lactam producing streptomycete, strain A57986, which was
      naturally less restricting than S. lipmanii, expressed only SliI restriction
      and modification.  PM87 and A57986 were readily transformed by many unmodified
      plasmids; once modified in these hosts the same plasmids were efficiently
      introduced into more restricting strains by transformation.
AU  - Matsushima P
AU  - Baltz RH
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1989 89: 361.

PMID- 3473276
VI  - 206
DP  - 1987
TI  - Highly transformable mutants of Streptomyces fradiae defective in several restriction systems.
PG  - 393-400
AB  - Streptomyces fradiae JS85 is a mutant defective in tylosin production and an
      efficient recipient for conjugal transfer of tylosin genes.  JS85 was
      mutagenized with N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) and derivatives
      defective in restriction were isolated by sequential selection for increased
      transformability by several plasmid DNAs.  From the number of mutation and
      selection cycles required to eliminate most restriction, it was estimated that
      wild type S. fradiae expressed at least five restriction systems.  From the
      patterns of restriction enzyme digestion of chromosomal DNA observed in the
      series of mutants that became progressively less restricting, it was suggested
      that wild type S. fradiae normally expresses modification (and presumably
      restriction) systems similar or analogous to PstI, XhoI, ScaI and EcoRI.  The
      least restricting mutant of S. fradiae was readily transformable by many
      plasmids, including a bifunctional cosmid vector containing a large insert of
      Streptomyces DNA.
AU  - Matsushima P
AU  - Cox KL
AU  - Baltz RH
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1987 206: 393-400.

PMID- 3571169
VI  - 169
DP  - 1987
TI  - Efficient transformation of Amycolatopsis orientalis (Nocardia orientalis) protoplasts by Streptomyces plasmids.
PG  - 2298-2300
AB  - Conditions for efficient transformation of Amycolatopsis orientalis (Nocardia
      orientalis) protoplasts by Streptomyces plasmid cloning vectors were
      identified.  Three streptomycete plasmid origins of replication function in A.
      orientalis, as do the apramycin resistance gene from Escherichia coli, the
      thiostrepton resistance gene from Streptomyces azureus, and the tyrosinase gene
      from Streptomyces antibioticus.  A. orientalis appears to express some
      restriction and modification, because highest transformation frequencies
      (1000000/microgram DNA) were obtained when plasmid pIJ702 was modified in A.
AU  - Matsushima P
AU  - McHenney MA
AU  - Baltz RH
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1987 169: 2298-2300.

PMID- 2542216
VI  - 171
DP  - 1989
TI  - Transduction and transformation of plasmid DNA in Streptomyces fradiae strains that express different levels of restriction.
PG  - 3080-3084
AB  - We constructed nonrestricting strains of Streptomyces fradiae blocked in
      different steps in tylosin biosynthesis.  Plasmid transformation frequencies
      were 10/3 to 10/4-fold higher and bacteriophage plating efficiences were 10/4
      to 10/8-fold higher in the nonrestricting strains than in the restricting
      strains.  The efficiences of transduction of plasmid pRHB101 in S. fradiae
      strains varied by over 1,000-fold, depending on growth conditions, and optimum
      transduction frequencies were obtained when cells were grown to mid-exponential
      phase at 39C.  Under these conditions, restricting and nonrestricting strains
      were transduced at frequencies that differed by only two- to fivefold.
AU  - Matsushima P
AU  - McHenney MA
AU  - Baltz RH
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1989 171: 3080-3084.

PMID- 29545293
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Mn(II)-Oxidizing Pseudomonas resinovorans Strain MO-1.
PG  - e00088-18
AB  - Pseudomonas resinovorans strain MO-1, which possesses a high ability to oxidize Mn(II), has
      been isolated from oligotrophic pond sediment. The draft genome
      sequence consists of 6,252,942 bp and has a G+C content of 63.4%. Strain MO-1 has
      5,694 coding sequences, including 13 putative Mn(II) oxidation genes.
AU  - Matsushita S
AU  - Nakano M
AU  - Aoi Y
AU  - Kindaichi T
AU  - Ozaki N
AU  - Ohashi A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00088-18.

PMID- 21554859
VI  - 409
DP  - 2011
TI  - Increased number of Arginine-based salt bridges contributes to the thermotolerance of thermotolerant acetic acid bacteria, Acetobacter tropicalis SKU1100.
PG  - 120-124
AB  - Thermotolerant acetic acid bacteria (AAB), Acetobacter tropicalis SKU1100,
      can grow above 40 degrees C. To investigate the basis of its
      thermotolerance, we compared the genome of A. tropicalis SKU1100 with that
      of mesophilic AAB strain Acetobacter pasteurianus IFO3283-01. The
      comparative genomic study showed that amino acid substitutions from large
      to small residue and Lys to Arg occur in many orthologous genes.
      Furthermore, comparative modeling study was carried out with the
      orthologous proteins between SKU1100 and IFO3283-01 strains, indicating
      that the number of Arg-based salt bridges increased in protein models.
      Since it has been reported that Arg-based salt bridges are important
      factor for thermo-stability of protein structure, our results strongly
      suggest that the increased number of Arg-based salt bridges may
      contributes to the thermotolerance of A. tropicalis SKU1100 (the
      thermo-stability of proteins in A. tropicalis SKU1100).
AU  - Matsutani M
AU  - Hirakawa H
AU  - Nishikura M
AU  - Soemphol W
AU  - Ali IA
AU  - Yakushi T
AU  - Matsushita K
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 2011 409: 120-124.

PMID- 23580707
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Dihydroxyacetone-Producing Gluconobacter thailandicus Strain NBRC 3255.
PG  - e00118-13
AB  - Here, we report the draft genome sequence of the acetic acid bacterium Glucnobacter
      thailandicus strain NBRC 3255. The draft genome sequence is composed
      of 109 contigs in 3,305,227 bp and contains 3,225 protein-coding genes. Two
      paralogous sets of sldAB operons, which are responsible for dihydroxyacetone
      production from glycerol, were identified.
AU  - Matsutani M
AU  - Kawajiri E
AU  - Yakushi T
AU  - Adachi O
AU  - Matsushita K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00118-13.

PMID- 23723406
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of a Thermophilic Member of the Bacillaceae, Anoxybacillus  flavithermus Strain Kn10, Isolated from the Kan-nawa Hot Spring in Japan.
PG  - e00311-13
AB  - Here, we report the draft genome sequence of the Anoxybacillus flavithermus Kn10  strain (NBRC
      109594), isolated from a water drain of the Kan-nawa Hot Spring in
      Japan. The draft genome sequence is composed of 90 contigs for 2,772,624 bp with
      41.6% G+C content and contains 2,883 protein-coding genes and 80 tRNA genes.
AU  - Matsutani M
AU  - Shirakihara Y
AU  - Imada K
AU  - Yakushi T
AU  - Matsushita K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00311-13.

PMID- 25197448
VI  - 9
DP  - 2014
TI  - Draft genome sequence of Gluconobacter thailandicus NBRC 3257.
PG  - 614-623
AB  - Gluconobacter thailandicus strain NBRC 3257, isolated from downy cherry (Prunus tomentosa), is
      a strict aerobic rod-shaped Gram-negative bacterium. Here, we
      report the features of this organism, together with the draft genome sequence and
      annotation. The draft genome sequence is composed of 107 contigs for 3,446,046 bp
      with 56.17% G+C content and contains 3,360 protein-coding genes and 54 RNA genes.
AU  - Matsutani M
AU  - Suzuki H
AU  - Yakushi T
AU  - Matsushita K
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 614-623.

PMID- 9353259
VI  - 11
DP  - 1997
TI  - A bacterial group II intron encoding reverse transcriptase, maturase, and DNA endonuclease activities: biochemical demonstration of maturase activity and insertion of new genetic information within the intron.
PG  - 2910-2924
AB  - The Lactococcus lactis group II intron Ll.ltrB is similar to mobile yeast mtDNA group II
      introns, which encode reverse transcriptase, RNA maturase, and DNA endonuclease activities for
      site-specific DNA insertion. Here, we show that the Lactococcal intron can be expressed and
      spliced efficiently in Escherichia coli. The intron-encoded protein LtrA has reverse
      transcriptase and RNA maturase activities, with the latter activity shown both in vivo and in
      vitro, a first for any group II intron-encoded protein. As for the yeast mtDNA introns, the
      DNA endonuclease activity of the Lactococcal intron is associated with RNP particles
      containing both the intron-encoded protein and the excised intron RNA. Also, the intron RNA
      cleaves the sense-strand of the recipient DNA by a reverse splicing reaction, whereas the
      intron-encoded protein cleaves the antisense strand. The Lactococcal intron endonuclease can
      be obtained in large quantities by coexpression of the LtrA protein with the intron RNA in E.
      coli or reconstituted in vitro by incubating the expressed LtrA protein with in
      vitro-synthesized intron RNA. Furthermore, the specificity of the endonuclease and reverse
      splicing reactions can be changed predictably by modifying the RNA component. Expression in E.
      coli facilitates the use of group II introns for the targeting of specific foreign sequences
      to a desired site in DNA.
AU  - Matsuura M
AU  - Saldanha R
AU  - Ma H
AU  - Wank H
AU  - Yang J
AU  - Mohr G
AU  - Cavangh S
AU  - Dunny GM
AU  - Belfort M
AU  - Lambowitz AM
PT  - Journal Article
TA  - Genes Dev.
JT  - Genes Dev.
SO  - Genes Dev. 1997 11: 2910-2924.

PMID- 26966200
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Thermodesulfovibrio aggregans TGE-P1T, an Obligately Anaerobic, Thermophilic, Sulfate-Reducing Bacterium in the Phylum Nitrospirae.
PG  - e00089-16
AB  - We report a high-quality draft genome sequence of the type strain (TGE-P1(T)) of
      Thermodesulfovibrio aggregans, an obligately anaerobic, thermophilic,
      sulfate-reducing bacterium in the phylum Nitrospirae. The genome comprises 2.00
      Mb in 16 contigs (3 scaffolds), has a G+C content of 34.5%, and contains 1,998
      predicted protein-encoding genes.
AU  - Matsuura N
AU  - Ohashi A
AU  - Tourlousse DM
AU  - Sekiguchi Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00089-16.

PMID- 26868399
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the Syntrophic Lactate-Degrading Bacterium Tepidanaerobacter syntrophicus JLT.
PG  - e01712-15
AB  - We report here a high-quality draft genome sequence of the type strain (JL) of
      Tepidanaerobacter syntrophicus, an obligately anaerobic and moderately
      thermophilic bacterium, which is able to perform syntrophic lactate degradation
      with hydrogenotrophic methanogens. The genome comprises 2.43 Mb in 9 scaffolds,
      with a G+C content of 38.6%.
AU  - Matsuura N
AU  - Ohashi A
AU  - Tourlousse DM
AU  - Sekiguchi Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01712-15.

PMID- 26383658
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Anaerolinea thermolimosa IMO-1, Bellilinea caldifistulae GOMI-1, Leptolinea tardivitalis YMTK-2, Levilinea saccharolytica KIBI-1, Longilinea arvoryzae KOME-1, Previously Described as Members of the Class Anaerolineae (Chloroflex.
PG  - e00975-15
AB  - Members of the class Anaerolineae in the bacterial phylum Chloroflexi are widespread in a
      range of ecosystems but remain poorly understood. We present here the draft genome sequences
      of the type strains of five Anaerolineae species, Anaerolinea thermolimosa IMO-1, Bellilinea
      caldifistulae GOMI-1, Leptolinea tardivitalis YMTK-2, Levilinea saccharolytica KIBI-1, and
      Longilinea arvoryzae KOME-1.
AU  - Matsuura N
AU  - Tourlousse DM
AU  - Ohashi A
AU  - Hugenholtz P
AU  - Sekiguchi Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00975-15.

PMID- 26450719
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Anaerolineae Strain TC1, a Novel Isolate from a Methanogenic Wastewater Treatment System.
PG  - e01104-15
AB  - We report the draft genome sequence of Anaerolineae bacterium strain TC1, newly isolated from
      a methanogenic wastewater treatment system. The assembly contains 16 contigs in 3 scaffolds
      representing 3,510,630 bp in total with a G+C content of 41.35%. The genome is predicted to
      contain 2,793 protein-coding genes and 56 RNAs.
AU  - Matsuura N
AU  - Tourlousse DM
AU  - Sun L
AU  - Toyonaga M
AU  - Kuroda K
AU  - Ohashi A
AU  - Cruz R
AU  - Yamaguchi T
AU  - Sekiguchi Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01104-15.

PMID- 
VI  - 29
DP  - 2000
TI  - Direct observation of sliding of restriction endonuclease EcoRI on a single DNA molecule.
PG  - 255
AB  - In recent years, a fluorescence microscopy technique has been used to image the dynamics of
      individual DNA and protein molecules.  For the advanced investigation of the molecular
      mechanism in DNA-protein interactions such as sliding of restriction endonucleases on DNA
      molecules, direct observation of a single protein molecule will be significant.  To observe
      dynamics of individual proteins under a fluorescence microscopy on real-time, it requires
      labeling proteins with a fluorescent dye.  In this study, therefore, we developed fluorescent
      labeling system for a restriction endonuclease EcoRI as a model to label DNA binding proteins.
      EcoRI bound on DNA molecules was treated with amine-reactive dye Oregon-Green500.
      Consequently, we found that restriction endonuclease activity of labeled EcoRI was retained,
      even though EcoRI was fluorescently labeled.  Moreover, when DNA-staining dye YOYO-1
      concentration was YOYO-1 : nucleotide pair = 1:100 in molar ratio, EcoRI digested the DNA
      molecules as unstained DNA.  Finally, we observed that fluorescent labeled EcoRI slid on
      stained DNA straightening on 3-APTES-treated cover glass in the absence of Mg2+ using a
      fluorescence microscopy.
AU  - Matsuura S-I
AU  - Hirano K
AU  - Zako T
AU  - Katsura S
AU  - Nagamune T
AU  - Mizuno A
PT  - Journal Article
TA  - Eur. Biophys. J.
JT  - Eur. Biophys. J.
SO  - Eur. Biophys. J. 2000 29: 255.

PMID- 1521769
VI  - 94
DP  - 1992
TI  - Evidence for the existence of a restriction-modification system common to several species of the family Vibronaceae.
PG  - 191-194
AB  - A broad-host-range vibriophage KVP40 originally isolated on Vibrio parahaemolyticus 1010 was
      restricted and modified by strains of at least five Vibrio and one Photobacterium species.
      1010 was a non-restricting host. An anti-restriction mutant KVP40 aar1 was isolated after
      propagating the phage on a restricting host, V. anguillarum VIB36, as well as the parental
      phage grown on VIB36, showed much higher efficiencies of plating on all the restricting hosts
      as compared with the parental phage grown on 1010, indicating that these restricting hosts
      probably share a common restriction-modification system active in vivo on KVP40.
AU  - Matsuzaki S
AU  - Inoue T
AU  - Tanaka S
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1992 94: 191-194.

PMID- 22328756
VI  - 194
DP  - 2012
TI  - Genome Sequence of Pantoea agglomerans Strain IG1.
PG  - 1258-1259
AB  - Pantoea agglomerans is a Gram-negative bacterium that grows symbiotically with various plants.
      Here we report the 4.8-Mb genome sequence of P. agglomerans
      strain IG1. The lipopolysaccharides derived from P. agglomerans IG1 have been
      shown to be effective in the prevention of various diseases, such as bacterial or
      viral infection, lifestyle-related diseases. This genome sequence represents a
      substantial step toward the elucidation of pathways for production of
      lipopolysaccharides.
AU  - Matsuzawa T
AU  - Mori K
AU  - Kadowaki T
AU  - Shimada M
AU  - Tashiro K
AU  - Kuhara S
AU  - Inagawa H
AU  - Soma G
AU  - Takegawa K
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1258-1259.

PMID- 26251495
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Corynebacterium striatum 1961 BR-RJ/09, a Multidrug-Susceptible Strain Isolated from the Urine of a Hospitalized  37-Year-Old Female Patient.
PG  - e00869-15
AB  - Corynebacterium striatum commonly colonizes the normal skin and nasopharyngeal tract of
      humans; however, this potentially pathogenic bacterium has been
      identified as the causative agent of several nosocomial infections. The current
      study describes the draft genome of strain 1961 BR-RJ/09, isolated from the urine
      of a hospitalized patient from Brazil.
AU  - Mattos-Guaraldi AL
AU  - Guimaraes LC
AU  - Santos CS
AU  - Veras AA
AU  - Carneiro AR
AU  - Soares SC
AU  - Ramos JN
AU  - Souza C
AU  - Vieira VV
AU  - Hirata R Jr
AU  - Azevedo V
AU  - Pacheco LG
AU  - Silva A
AU  - Ramos RT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00869-15.

PMID- 29301877
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Enterohemorrhagic and Enteropathogenic Escherichia coli Strains Isolated from Alpacas in Peru.
PG  - e01391-17
AB  - The draft genome sequences of two strains of Escherichia coli, isolated from alpacas in Peru,
      are reported here. ECA1 has been determined to be a strain of
      enterohemorrhagic E. coli and ECB1 a strain of enteropathogenic E. coli These
      pathogens are responsible for hemolytic-uremic syndrome in humans and diarrhea in
      different mammals, respectively.
AU  - Maturrano L
AU  - Aleman M
AU  - Carhuaricra D
AU  - Maximiliano J
AU  - Siuce J
AU  - Luna L
AU  - Rosadio R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01391-17.

PMID- 11266551
VI  - 29
DP  - 2001
TI  - DNA methyltransferases of the cyanobacterium Anabaena PCC 7120.
PG  - 1491-1506
AB  - From the characterization of enzyme activities and the analysis of genomic sequences, the
      complement of DNA methyltransferases (MTases) possessed by the cyanobacterium Anabaena PCC
      7120 has been deduced. Anabaena has nine DNA MTases. Four are associated with Type II
      restriction enzymes (AvaI, AvaII, AvaIII and the newly recognized inactive AvaIV), and five
      are not. Of the latter, four may be classified as solitary MTases, those whose function lies
      outside of a restriction/modification system. The group is defined here based on biochemical
      and genetic characteristics. The four solitary MTases, DmtA/M.AvaVI, DmtB/M.AvaVII,
      DmtC/M.AvaVIII and DmtD/M.AvaIX, methylate at GATC, GGCC, CGATCG and RCCGGY, respectively.
      DmtB methylates cytosines at the N4 position, but its sequence is more similar to N6-adenine
      MTases than to cytosine-specific enzymes, indicating that it may have evolved from the former.
      The solitary MTases, appear to be of ancient origin within cyanobacteria, while the
      restriction MTases appear to have arrived by recent horizontal transfer as did five now
      inactive Type I restriction systems. One Mtase, M.AvaV, cannot reliably be classified as
      either a solitary or restriction MTase. It is structurally unusual and along with a few
      proteins of prokaryotic and eukaryotic origin defines a structural class of MTases distinct
      from all previously described.
AU  - Matveyev AV
AU  - Young KT
AU  - Meng A
AU  - Elhai J
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2001 29: 1491-1506.

PMID- Not included in PubMed...
VI  - 11
DP  - 1985
TI  - Isolation and characterization of a DNA-methylase from Flavobacterium okeanokoites.
PG  - 953-956
AB  - FokI DNA methylase has been isolated from a cell extract of Flavobacterium
      okeanokoites by gel filtration followed by gel chromatography on
      hydroxylapatite.  The purified enzyme methylated the DNA of plasmid pBR322,
      making it resistant to the subsequent action of the site-specific FokI
      endonuclease.  It has been shown that it is the cytosine residues that are
      methylated.  This modification does not protect the DNA from hydrolysis by
      BbvI, BmeI, and EcoRII endonucleases, the recognition sites of which contain
      cytosine, which shows the specific nature of the methylation of DNA by the FokI
      methylase.
AU  - Matvienko NI
AU  - Kramarov VM
AU  - Irismetov AA
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1985 11: 953-956.

PMID- 3036510
VI  - 165
DP  - 1987
TI  - Isolation and some properties of the site-specific endonuclease and methylase Bme216I from Bacillus megaterium 216.
PG  - 565-570
AB  - The site-specific endonuclease Bme216I was isolated as a homogeneous
      preparation by chromatography on phosphocellulose, hydroxyapatite and
      heparin-agarose.  The molecular mass of the enzyme, determined by gel
      filtration and by electrophoresis under denaturing conditions, was found to be
      60 kDa and 30 kDa respectively.  These data indicate that the native enzyme
      consists of two identical subunits.  The enzyme recognized the pentanucleotide
      sequence 5'-G^GACC-3' . 3'-CCTG^G-5' and cleaves the sequence as indicated by
      arrows.  The optimal concentration for endonuclease reaction is 6-7 mM Mg2+.
      The endonuclease relaxes its specificity in the presence of glycerol or
      dimethyl sulfoxide at low Mg2+ concentration (1-3 mM).  Methylase Bme216I,
      which protects DNA against endonuclease Bme216I action by DNA methylation, was
      isolated from the same bacterial strain.
AU  - Matvienko NI
AU  - Kramarov VM
AU  - Pachkunov DM
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1987 165: 565-570.

PMID- Not included in PubMed...
VI  - 177
DP  - 1984
TI  - The recognition sequence of site-specific endonuclease BbvII from Bacillus brevis 80.
PG  - 23-26
AB  - Site-specific endonuclease BbvII from Bacillus brevis 80 recognizes the
      non-symmetrical hexanucleotide and cleaves DNA at distances of 2 and 6
      nucleotides from the recognition site:5'-GAAGACNN^ 3'-CTTCTGNNNNNN^This enzyme
      may be used in molecular cloning for vectors with multiple restriction sites.
AU  - Matvienko NI
AU  - Pachkunov DM
AU  - Kramarov VM
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1984 177: 23-26.

PMID- 1315959
VI  - 20
DP  - 1992
TI  - Bce83I, a restriction endonuclease from Bacillus cereus 83 which recognizes novel nonpalindromic sequence 5'-CTTGAG-3' and is stimulated by S-adenosylmethionine.
PG  - 1803
AB  - Restriction endonuclease Bce83I has been purified by chromatography on blue-sepharose and
      hydroxyapatite. It recognizes 4,6,5,13 and more than 20 sites on pUC18, pBR322, M13mp18,
      lambda and T7 DNA, respectively.
AU  - Matvienko NN
AU  - Kramarov VM
AU  - Ivanov LY
AU  - Matvienko NI
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 1803.

PMID- 8399763
VI  - 58
DP  - 1993
TI  - New site-specific endonuclease and methylase from Bacillus licheniformis 736.
PG  - 1139-1153
AB  - *

      The site-specific endonuclease R.Bli736I and methylase M.Bli736I have been isolated from the

      Bacilus licheniformis strain 736 by blue-agarose, hydroxyapatite-Ultragel and
      heparin-Sepharose

      chromatography. The enzymes are free from interfering impurities. R.Bli736I recognizes the

      sequence:

      

         5'-GGTCTCN^-3'

         3'-CCAGAGNNNNN^-5'

      

      on the DNA and cleaves the DNA as indicated by arrows to form single-stranded 4-nucleotide

      5'-protruding termini. This enzyme is an isoschizomer of Eco31I isolated from E.coli.

      

AU  - Matvienko NN
AU  - Kramarov VM
AU  - Zheleznaya LA
AU  - Matvienko NI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1993 58: 1139-1153.

PMID- 8292647
VI  - 58
DP  - 1993
TI  - Isolation of site-specific endonuclease and methylase from Bacillus cereus 83.
PG  - 1845-1860
AB  - 

       The site-specific endonuclease R.Bce83I and methylase M.Bce83I were isolated from Bacillus

       cereus 83 by three consecutive chromatographies on blue agarose, hydroxyapatite and

       heparin-Sepharose. R.Bce83I recognizes the

       

      

           5'-CTTGAG16N^-3'

           3'-GAACTC14N^-5'

       

      

       sequences on the DNA and cleaves the DNA as indicated by the arrows. The endonuclease is

       stimulated by S-adenosyl-L-methionine and may consequently be referred to as a type IV

       restriction enzyme.

      

AU  - Matvienko NN
AU  - Kramarov VM
AU  - Zheleznaya LA
AU  - Matvienko NI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1993 58: 1845-1860.

PMID- 8385319
VI  - 21
DP  - 1993
TI  - BspLU11I, a novel site specific endonuclease which cleaves 5'-ACATGT-3'.
PG  - 1495
AB  - 
AU  - Matvienko NN
AU  - Zeleznaja LA
AU  - Matvienko NI
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 1495.

PMID- Not included in PubMed...
VI  - 62
DP  - 1997
TI  - Peculiarities of gene expression of the EcoRII modification-restriction system.
PG  - 1314-1318
AB  - The restriction-modification genes of the EcoRII system have been cloned into plasmids under
      control of phage-specific promoters T7 and SP6.  The transcription was induced by cell
      infection with the recombinant M13 phages with the corresponding genes of phage
      RNA-polymerases under control of the Plac-promoter in the presence of IPTG.  The induction
      yields significant amounts of EcoRII DNA-methylase for both phage-specific promoters.  In both
      cases no increase in EcoRII endonuclease expression could be achieved.  We hypothesize that
      the expression of the endonuclease gene is regulated on the translational level.
AU  - Matvienko NN
AU  - Zheleznaya LA
AU  - Chernyshova EE
AU  - Buryanov YI
AU  - Matvienko NI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1997 62: 1314-1318.

PMID- 9275302
VI  - 62
DP  - 1997
TI  - Site-specific DNA-methylase M.BspST5I methylates only one strand of the recognized site.
PG  - 304-306
AB  - We recently isolated a site-specific adenine DNA-methylase, M.BspST5I, which methylates only
      one strand of the recognized site GCA*TC.  The methylated base is indicated by an asterisk.
AU  - Matvienko NN
AU  - Zheleznaya LA
AU  - Zelinskaya NV
AU  - Matvienko NI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1997 62: 304-306.

PMID- 26205869
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Strain ATCC 33958, Reported To Be Elizabethkingia miricola.
PG  - e00828-15
AB  - We report the draft genome of Elizabethkingia strain ATCC 33958, which has been classified as
      Elizabethkingia miricola. Similar to other Elizabethkingia species,
      the ATCC 33958 draft genome contains numerous beta-lactamase genes. ATCC 33958
      also harbors a urease gene cluster which supports classification as E. miricola.
AU  - Matyi SA
AU  - Hoyt PR
AU  - Ayoubi-Canaan P
AU  - Hasan NA
AU  - Gustafson JE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00828-15.

PMID- 23846266
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences of Elizabethkingia meningoseptica.
PG  - e00444-13
AB  - Elizabethkingia meningoseptica is ubiquitous in nature, exhibits a multiple-antibiotic
      resistance phenotype, and causes rare opportunistic
      infections. We now report two draft genome sequences of E. meningoseptica type
      strains that were sequenced independently in two laboratories.
AU  - Matyi SA
AU  - Hoyt PR
AU  - Hosoyama A
AU  - Yamazoe A
AU  - Fujita N
AU  - Gustafson JE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00444-13.

PMID- 25013145
VI  - 2
DP  - 2014
TI  - Draft Genomes of Heterogeneous Vancomycin-Intermediate Staphylococcus aureus Strain MM66 and MM66 Derivatives with Altered Vancomycin Resistance Levels.
PG  - e00688-14
AB  - The draft genomes of heterogeneous vancomycin-intermediate Staphylococcus aureus  (hVISA)
      strain MM66 and MM66 isolates demonstrating altered vancomycin resistance
      levels were produced in an effort to provide information on mutations
      contributing to the vancomycin resistance levels observed in these strains.
AU  - Matyi SA
AU  - Ramaraj T
AU  - Sundararajan A
AU  - Lindquist IE
AU  - Devitt NP
AU  - Schilkey FD
AU  - Lamichhane-Khadka R
AU  - Hoyt PR
AU  - Mudge J
AU  - Gustafson JE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00688-14.

PMID- 29329757
VI  - 90
DP  - 2018
TI  - Challenges of Francisella classification exemplified by an atypical clinical isolate.
PG  - 241-247
AB  - The accumulation of sequenced Francisella strains has made it increasingly apparent that the
      16S rRNA gene alone is not enough to stratify the Francisella
      genus into precise and clinically useful classifications. Continued whole-genome
      sequencing of isolates will provide a larger base of knowledge for targeted
      approaches with broad applicability. Additionally, examination of genomic
      information on a case-by-case basis will help resolve outstanding questions
      regarding strain stratification. We report the complete genome sequence of a
      clinical isolate, designated here as F. novicida-like strain TCH2015, acquired
      from the lymph node of a 6-year-old male. Two features were atypical for F.
      novicida: exhibition of functional oxidase activity and additional gene content,
      including proposed virulence determinants. These differences, which could
      potentially impact virulence and clinical diagnosis, emphasize the need for more
      comprehensive methods to profile Francisella isolates. This study highlights the
      value of whole-genome sequencing, which will lead to a more robust database of
      environmental and clinical genomes and inform strategies to improve detection and
      classification of Francisella strains.
AU  - Matz LM
AU  - Kamdar KY
AU  - Holder ME
AU  - Metcalf GA
AU  - Weissenberger GM
AU  - Meng Q
AU  - Vee V
AU  - Han Y
AU  - Muzny DM
AU  - Gibbs RA
AU  - Johnson CL
AU  - Revell PA
AU  - Petrosino JF
PT  - Journal Article
TA  - Diagn. Microbiol. Infect. Dis.
JT  - Diagn. Microbiol. Infect. Dis.
SO  - Diagn. Microbiol. Infect. Dis. 2018 90: 241-247.

PMID- 22965103
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of the Hydrogenotrophic, Methanogenic Archaeon Methanoculleus bourgensis Strain MS2T, Isolated from a Sewage Sludge Digester.
PG  - 5487-5488
AB  - Methanoculleus bourgensis, of the order Methanomicrobiales, is a dominant methanogenic
      archaeon in many biogas-producing reactor systems fed with renewable
      primary products. It is capable of synthesizing methane via the hydrogenotrophic
      pathway utilizing hydrogen and carbon dioxide or formate as the substrates. Here
      we report the complete and finished genome sequence of M. bourgensis strain
      MS2(T), isolated from a sewage sludge digester.
AU  - Maus I
AU  - Wibberg D
AU  - Stantscheff R
AU  - Eikmeyer FG
AU  - Seffner A
AU  - Boelter J
AU  - Szczepanowski R
AU  - Blom J
AU  - Jaenicke S
AU  - Konig H
AU  - Puhler A
AU  - Schluter A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5487-5488.

PMID- 27340059
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of the Methanogen Methanoculleus bourgensis BA1 Isolated from a Biogas Reactor.
PG  - e00568-16
AB  - Methanoculleus bourgensis BA1, a hydrogenotrophic methanogen, was isolated from a
      laboratory-scale biogas reactor operating under an elevated ammonium
      concentration. Here, the complete genome sequence of M. bourgensis BA1 is
      reported. The availability of the BA1 genome sequence enables detailed
      comparative analyses involving other Methanoculleus spp. representing important
      members of microbial biogas communities.
AU  - Maus I
AU  - Wibberg D
AU  - Winkler A
AU  - Puhler A
AU  - Schnurer A
AU  - Schluter A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00568-16.

PMID- 22301140
VI  - 86
DP  - 2012
TI  - The Genome Sequence of the Emerging Common Midwife Toad Virus Identifies an Evolutionary Intermediate within Ranaviruses.
PG  - 3617-3625
AB  - Worldwide amphibian population declines have been ascribed to global warming,
      increasing pollution levels, and other factors directly related to human
      activities. These factors may additionally be favoring the emergence of novel
      pathogens. In this report, we have determined the complete genome sequence of the
      emerging common midwife toad ranavirus (CMTV), which has caused fatal disease in
      several amphibian species across Europe. Phylogenetic and gene content analyses
      of the first complete genomic sequence from a ranavirus isolated in Europe show
      that CMTV is an amphibian-like ranavirus (ALRV). However, the CMTV genome
      structure is novel and represents an intermediate evolutionary stage between the
      two previously described ALRV groups. We find that CMTV clusters with several
      other ranaviruses isolated from different hosts and locations which might also be
      included in this novel ranavirus group. This work sheds light on the phylogenetic
      relationships within this complex group of emerging, disease-causing viruses.
AU  - Mavian C
AU  - Lopez-Bueno A
AU  - Balseiro A
AU  - Casais R
AU  - Alcami A
AU  - Alejo A
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 2012 86: 3617-3625.

PMID- 22570241
VI  - 86
DP  - 2012
TI  - Complete genome sequence of European sheatfish virus.
PG  - 6365-6366
AB  - Viral diseases are an increasing threat to the thriving aquaculture industry worldwide. An
      emerging group of fish pathogens is formed by several ranaviruses, which have been isolated at
      different locations from freshwater and seawater fish species since 1985.  We report the
      complete genome sequence of European sheatfish ranavirus (ESV), the first ranavirus isolated
      in Europe, which causes high mortality rates in infected sheatfish (Silurus glanis) and in
      other species. Analysis of the genome sequence shows that ESV belongs to the amphibian-like
      ranaviruses and is closely related to the epizootic hematopoietic necrosis virus (EHNV), a
      disease agent geographically confined to the Australian continent and notifiable to the World
      Organization for Animal Health.
AU  - Mavian C
AU  - Lopez-Bueno A
AU  - Fernandez-Somalo MP
AU  - Alcami A
AU  - Alejo A
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 2012 86: 6365-6366.

PMID- 12324371
VI  - 68
DP  - 2002
TI  - Identification of Differences in Genome Content among phlD-Positive Pseudomonas fluorescens Strains by Using PCR-Based Subtractive Hybridization.
PG  - 5170-5176
AB  - Certain 2,4-diacetylphloroglucinol-producing strains of Pseudomonas
      fluorescens colonize roots and suppress soilborne diseases more
      effectively than others from which they are otherwise phenotypically
      almost indistinguishable. We recovered DNA fragments present in the
      superior colonizer P. fluorescens Q8r1-96 but not in the less
      rhizosphere-competent strain Q2-87. Of the open reading frames in 32
      independent Q8r1-96-specific clones, 1 was similar to colicin M from
      Escherichia coli, 3 resembled known regulatory proteins, and 28 had no
      significant match with sequences of known function. Seven clones
      hybridized preferentially to DNA from strains with superior rhizosphere
      competence, and sequences in two others were highly expressed in vitro and
      in the rhizosphere.
AU  - Mavrodi DV
AU  - Mavrodi OV
AU  - McSpadden-Gardener BB
AU  - Landa BB
AU  - Weller DM
AU  - Thomashow LS
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2002 68: 5170-5176.

PMID- 21304644
VI  - 1
DP  - 2009
TI  - Complete genome sequence of Cryptobacterium curtum type strain (12-3).
PG  - 93-100
AB  - Cryptobacterium curtum Nakazawa etal. 1999 is the type species of the genus, and  is of
      phylogenetic interest because of its very distant and isolated position within the family
      Coriobacteriaceae. C. curtum is an asaccharolytic, opportunistic pathogen with a typical
      occurrence in the oral cavity, involved in dental and oral infections like periodontitis,
      inflammations and abscesses. Here we describe the features of this organism, together with the
      complete genome sequence, and annotation. This is the first complete genome sequence of the
      actinobacterial family Coriobacteriaceae, and this 1,617,804 bp long single replicon genome
      with its 1364 protein-coding and 58 RNA genes is part of the Genomic Encyclopedia of Bacteria
      and Archaea project.
AU  - Mavromatis K et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2009 1: 93-100.

PMID- 21304673
VI  - 2
DP  - 2010
TI  - Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IA).
PG  - 9-18
AB  - Alicyclobacillus acidocaldarius (Darland and Brock 1971) is the type species of the larger of
      the two genera in the bacillal family 'Alicyclobacillaceae'. A.
      acidocaldarius is a free-living and non-pathogenic organism, but may also be
      associated with food and fruit spoilage. Due to its acidophilic nature, several
      enzymes from this species have since long been subjected to detailed molecular
      and biochemical studies. Here we describe the features of this organism, together
      with the complete genome sequence and annotation. This is the first completed
      genome sequence of the family 'Alicyclobacillaceae'. The 3,205,686 bp long genome
      (chromosome and three plasmids) with its 3,153 protein-coding and 82 RNA genes is
      part of the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Mavromatis K et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 2: 9-18.

PMID- 22768364
VI  - 6
DP  - 2012
TI  - Permanent draft genome sequence of the gliding predator Saprospira grandis strain Sa g1 (= HR1).
PG  - 210-219
AB  - Saprospira grandis Gross 1911 is a member of the Saprospiraceae, a family in the  class
      'Sphingobacteria' that remains poorly characterized at the genomic level.
      The species is known for preying on other marine bacteria via 'ixotrophy'. S.
      grandis strain Sa g1 was isolated from decaying crab carapace in France and was
      selected for genome sequencing because of its isolated location in the tree of
      life. Only one type strain genome has been published so far from the
      Saprospiraceae, while the sequence of strain Sa g1 represents the second genome
      to be published from a non-type strain of S. grandis. Here we describe the
      features of this organism, together with the complete genome sequence and
      annotation. The 4,495,250 bp long Improved-High-Quality draft of the genome with
      its 3,536 protein-coding and 62 RNA genes is a part of the Genomic Encyclopedia
      of Bacteria and Archaea project.
AU  - Mavromatis K et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 6: 210-219.

PMID- 21304713
VI  - 2
DP  - 2010
TI  - Complete genome sequence of Coraliomargarita akajimensis type strain (04OKA010-24).
PG  - 290-299
AB  - Coraliomargarita akajimensis Yoon et al. 2007 is the type species of the genus
      Coraliomargarita. C. akajimensis is an obligately aerobic, Gram-negative,
      non-spore-forming, non-motile, spherical bacterium that was isolated from
      seawater surrounding the hard coral Galaxea fascicularis. C. akajimensis is of
      special interest because of its phylogenetic position in a genomically
      under-studied area of the bacterial diversity. Here we describe the features of
      this organism, together with the complete genome sequence, and annotation. This
      is the first complete genome sequence of a member of the family Puniceicoccaceae.
      The 3,750,771 bp long genome with its 3,137 protein-coding and 55 RNA genes is a
      part of the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Mavromatis K et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 2: 290-299.

PMID- 21304741
VI  - 3
DP  - 2010
TI  - Complete genome sequence of Vulcanisaeta distributa type strain (IC-017).
PG  - 117-125
AB  - Vulcanisaeta distributa Itoh et al. 2002 belongs to the family Thermoproteaceae in the phylum
      Crenarchaeota. The genus Vulcanisaeta is characterized by a global
      distribution in hot and acidic springs. This is the first genome sequence from a
      member of the genus Vulcanisaeta and seventh genome sequence in the family
      Thermoproteaceae. The 2,374,137 bp long genome with its 2,544 protein-coding and
      49 RNA genes is a part of the Genomic Encyclopedia of Bacteriaand Archaea
      project.
AU  - Mavromatis K et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 3: 117-125.

PMID- 21304743
VI  - 3
DP  - 2010
TI  - Complete genome sequence of Spirochaeta smaragdinae type strain (SEBR 4228).
PG  - 136-144
AB  - Spirochaeta smaragdinae Magot et al. 1998 belongs to the family Spirochaetaceae.  The species
      is Gram-negative, motile, obligately halophilic and strictly
      anaerobic and is of interest because it is able to ferment numerous
      polysaccharides. S. smaragdinae is the only species of the family Spirochaetaceae
      known to reduce thiosulfate or element sulfur to sulfide. This is the first
      complete genome sequence in the family Spirochaetaceae. The 4,653,970 bp long
      genome with its 4,363 protein-coding and 57 RNA genes is a part of the Genomic
      Encyclopedia of Bacteria and Archaea project.
AU  - Mavromatis K et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 3: 136-144.

PMID- 21677851
VI  - 4
DP  - 2011
TI  - Complete genome sequence of Riemerella anatipestifer type strain (ATCC 11845).
PG  - 144-153
AB  - Riemerella anatipestifer (Hendrickson and Hilbert 1932) Segers et al. 1993 is the type species
      of the genus Riemerella, which belongs to the family
      Flavobacteriaceae. The species is of interest because of the position of the
      genus in the phylogenetic tree and because of its role as a pathogen of
      commercially important avian species worldwide. This is the first completed
      genome sequence of a member of the genus Riemerella. The 2,155,121 bp long genome
      with its 2,001 protein-coding and 51 RNA genes consists of one circular
      chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea
      project.
AU  - Mavromatis K et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 4: 144-153.

PMID- 23961311
VI  - 8
DP  - 2013
TI  - Complete genome sequence of the moderate thermophile Anaerobaculum mobile type strain (NGA(T)).
PG  - 47-57
AB  - Anaerobaculum mobile Menes and Muxi 2002 is one of three described species of the genus
      Anaerobaculum, family Synergistaceae, phylum Synergistetes. This anaerobic
      and motile bacterium ferments a range of carbohydrates and mono- and dicarboxylic
      acids with acetate, hydrogen and CO2 as end products. A. mobile NGA(T) is the
      first member of the genus Anaerobaculum and the sixth member of the phylum
      Synergistetes with a completely sequenced genome. Here we describe the features
      of this bacterium, together with the complete genome sequence, and annotation.
      The 2,160,700 bp long single replicon genome with its 2,053 protein-coding and 56
      RNA genes is part of the G enomic E ncyclopedia of Bacteria and Archaea project.
AU  - Mavromatis K et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 47-57.

PMID- 23961309
VI  - 8
DP  - 2013
TI  - Complete genome sequence of the bile-resistant pigment-producing anaerobe Alistipes finegoldii type strain (AHN2437(T)).
PG  - 26-36
AB  - Alistipes finegoldii Rautio et al. 2003 is one of five species of Alistipes with  a validly
      published name: family Rikenellaceae, order Bacteroidetes, class
      Bacteroidia, phylum Bacteroidetes. This rod-shaped and strictly anaerobic
      organism has been isolated mostly from human tissues. Here we describe the
      features of the type strain of this species, together with the complete genome
      sequence, and annotation. A. finegoldii is the first member of the genus
      Alistipes for which the complete genome sequence of its type strain is now
      available. The 3,734,239 bp long single replicon genome with its 3,302
      protein-coding and 68 RNA genes is part of the G enomic E ncyclopedia of Bacteria
      and Archaea project.
AU  - Mavromatis K et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 26-36.

PMID- 16707693
VI  - 188
DP  - 2006
TI  - The genome of the obligately intracellular bacterium Ehrlichia canis reveals themes of complex membrane structure and immune evasion  strategies.
PG  - 4015-4023
AB  - Ehrlichia canis, a small obligately intracellular, tick-transmitted, gram-negative,
      alpha-proteobacterium, is the primary etiologic agent of
      globally distributed canine monocytic ehrlichiosis. Complete genome
      sequencing revealed that the E. canis genome consists of a single circular
      chromosome of 1,315,030 bp predicted to encode 925 proteins, 40 stable RNA
      species, 17 putative pseudogenes, and a substantial proportion of
      noncoding sequence (27%). Interesting genome features include a large set
      of proteins with transmembrane helices and/or signal sequences and a
      unique serine-threonine bias associated with the potential for O
      glycosylation that was prominent in proteins associated with pathogen-host
      interactions. Furthermore, two paralogous protein families associated with
      immune evasion were identified, one of which contains poly(G-C) tracts,
      suggesting that they may play a role in phase variation and facilitation
      of persistent infections. Genes associated with pathogen-host interactions
      were identified, including a small group encoding proteins (n = 12) with
      tandem repeats and another group encoding proteins with eukaryote-like
      ankyrin domains (n = 7).
AU  - Mavromatis K
AU  - Doyle CK
AU  - Lykidis A
AU  - Ivanova N
AU  - Francino MP
AU  - Chain P
AU  - Shin M
AU  - Malfatti S
AU  - Larimer F
AU  - Copeland A
AU  - Detter JC
AU  - Land M
AU  - Richardson PM
AU  - Yu XJ
AU  - Walker DH
AU  - McBride JW
AU  - Kyrpides NC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2006 188: 4015-4023.

PMID- 21304645
VI  - 1
DP  - 2009
TI  - Complete genome sequence of Capnocytophaga ochracea type strain (VPI 2845).
PG  - 101-109
AB  - Capnocytophaga ochracea (Prevot et al. 1956) Leadbetter et al. 1982 is the type species of the
      genus Capnocytophaga. It is of interest because of its location in
      the Flavobacteriaceae, a genomically not yet charted family within the order
      Flavobacteriales. The species grows as fusiform to rod shaped cells which tend to
      form clumps and are able to move by gliding. C. ochracea is known as a
      capnophilic (CO(2)-requiring) organism with the ability to grow under anaerobic
      as well as aerobic conditions (oxygen concentration larger than 15%), here only
      in the presence of 5% CO(2). Strain VPI 2845(T), the type strain of the species,
      is portrayed in this report as a gliding, Gram-negative bacterium, originally
      isolated from a human oral cavity. Here we describe the features of this
      organism, together with the complete genome sequence, and annotation. This is the
      first completed genome sequence from the flavobacterial genus Capnocytophaga, and
      the 2,612,925 bp long single replicon genome with its 2193 protein-coding and 59
      RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Mavrommatis K et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2009 1: 101-109.

PMID- 6285900
VI  - 203
DP  - 1982
TI  - The SalGI restriction endonuclease.  (Enzyme specificity).
PG  - 93-98
AB  - We have analysed the kinetics of DNA cleavage in the reaction between the SalGI
      restriction endonuclease and plasmid pMB9.  This reaction is subject to
      competitive inhibiton by DNA sequences outside the SalGI recognition site; we
      have determined the Km and Vmax. for the reaction of this enzyme at its
      recognition site and the KI for its interaction at other DNA sequences.  We
      conclude that the specificity of DNA cleavage by the enzyme is only partly
      determined by the discrimination it shows for binding at its recognition
      sequence compared with binding to other DNA sequences.
AU  - Maxwell A
AU  - Halford SE
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 1982 203: 93-98.

PMID- 6285898
VI  - 203
DP  - 1982
TI  - The SalGI restriction endonuclease.  (Purification and properties).
PG  - 77-84
AB  - The type II restriction endonuclease SalGI has been purified to near
      homogeneity.  At least 80% of the protein remaining after the final stage of
      the preparation is SalGI restriction endonuclease; no contaminating nucleases
      remain detectable.  The principal form of the protein under both native and
      denaturing conditions is a monomer of Mr about 29000. The optimal conditions
      for both enzyme stability and enzyme activity have been determined.
AU  - Maxwell A
AU  - Halford SE
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 1982 203: 77-84.

PMID- 7215691
VI  - 9
DP  - 1981
TI  - The mechanism of DNA cleavage by restriction endonuclease SalGI.
PG  - 227P
AB  - The SalGI restriction endonuclease cleaves duplex DNA only at its recognition
      site.  Under optimal conditions (pH 8, 10 mM MgCl2), both strands of the DNA
      are cleaved in one concerted reaction:  a covalently closed DNA molecule with
      one SalGI recognition site is converted directly to linear DNA.  But under
      other conditions (viz 1 mM MgCl2), each reaction of this enzyme cleaves either
      one or both strands of the DNA; the covalently closed DNA is now converted into
      either the open-circle or the linear forms, the two being produced
      simultaneously rather than consecutively.  The enzyme will also cleave the DNA
      nicked at the SalGI recognition site but this second reaction is much slower
      than the first.  The SalGI restriction enzyme therefore interacts with DNA by a
      fundamentally different mechanism from some other restriction enzymes such as
      EcoRI.
AU  - Maxwell A
AU  - Halford SE
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 1981 9: 227P.

PMID- 6285899
VI  - 203
DP  - 1982
TI  - The SalGI restriction endonuclease.  Mechanism of DNA cleavage.
PG  - 85-92
AB  - The cleavage of supercoiled DNA of plasmid pMB9 by restriction endonuclease
      SalGI has been studied.  Under the optimal conditions for this reaction, the
      only product is the linear form of the DNA, in which both strands of the duplex
      have been cleaved at the SalGI recognition site.  DNA molecules cleaved in one
      strand at this site were found to be poor substrates for the SalGI enzyme.
      Thus, both strands of the DNA appear to be cleaved in a concerted reaction.
      However, under other conditions, the enzyme cleaves either one or both strands
      of the DNA; the supercoiled substrate is then converted to either open-circle
      or linear forms, the two being produced simultaneously rather than
      consecutively.  We propose a mechanism for the SalGI restriction endonuclease
      which accounts fo the reactions of this enzyme under both optimal and other
      conditions.  These reactions were unaffected by the tertiary structure of the
      DNA.
AU  - Maxwell A
AU  - Halford SE
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 1982 203: 85-92.

PMID- 27834722
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Aggregatibacter actinomycetemcomitans Strain IDH781.
PG  - e01285-16
AB  - We report here the complete genomic sequence and methylome of Aggregatibacter
      actinomycetemcomitans strain IDH781. This rough strain is used extensively as a
      model organism to characterize localized aggressive periodontitis pathogenesis,
      the basic biology and oral cavity colonization of A. actinomycetemcomitans, and
      its interactions with other members of the oral microbiome.
AU  - May AC
AU  - Ehrlich RL
AU  - Balashov S
AU  - Ehrlich GD
AU  - Shanmugam M
AU  - Fine DH
AU  - Ramasubbu N
AU  - Mell JC
AU  - Cugini C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01285-16.

PMID- 29167243
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Aggregatibacter actinomycetemcomitans Strains 310a and  310b.
PG  - e01282-17
AB  - We report the draft genome sequences of Aggregatibacter actinomycetemcomitans strains 310a
      (310-TR) and 310b (310-OS). Strain 310a is a clinical isolate with a
      rough phenotype. Strain 310b is a laboratory-adapted isolate derived from the
      passage of 310a and displays a smooth phenotype.
AU  - May AC
AU  - Ohta H
AU  - Maeda H
AU  - Kokeguchi S
AU  - Cugini C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01282-17.

PMID- 11248100
VI  - 98
DP  - 2001
TI  - Complete genomic sequence of Pasteurella multocida, Pm70.
PG  - 3460-3465
AB  - We present here the complete genome sequence of a common avian clone of Pasteurella multocida,
      Pm70. The genome of Pm70 is a single circular chromosome 2,257,487 base pairs in length and
      contains 2,014 predicted coding regions, 6 ribosomal RNA operons, and 57 tRNAs. Genome-scale
      evolutionary analyses based on pairwise comparisons of 1,197 orthologous sequences between P.
      multocida, Haemophilus influenzae, and Escherichia coli suggest that P. multocida and H.
      influenzae diverged approximately 270 million years ago and the gamma subdivision of the
      proteobacteria radiated about 680 million years ago. Two previously undescribed open reading
      frames, accounting for approximately 1% of the genome, encode large proteins with homology to
      the virulence-associated filamentous hemagglutinin of Bordetella pertussis. Consistent with
      the critical role of iron in the survival of many microbial pathogens, in silico and
      whole-genome microarray analyses identified more than 50 Pm70 genes with a potential role in
      iron acquisition and metabolism. Overall, the complete genomic sequence and preliminary
      functional analyses provide a foundation for future research into the mechanisms of
      pathogenesis and host specificity of this important multispecies pathogen.
AU  - May BJ
AU  - Zhang Q
AU  - Li LL
AU  - Paustian ML
AU  - Whittam TS
AU  - Kapur V
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2001 98: 3460-3465.

PMID- 26472845
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Taylorella equigenitalis Strain ERC_G2224 Isolated from  the Semen of a Lipizzaner Stallion in South Africa.
PG  - e01205-15
AB  - Taylorella equigenitalis is the causative agent of contagious equine metritis (CEM), a
      sexually transmitted infection of horses. We report here the genome sequence of T.
      equigenitalis strain ERC_G2224, isolated in 2015 from a semen sample collected in 1996 from a
      Lipizzaner stallion in South Africa.
AU  - May CE
AU  - Schulman ML
AU  - Howell PG
AU  - Lourens CW
AU  - Gouws J
AU  - Joone C
AU  - Monyai MS
AU  - le Grange M
AU  - Bezuidt OK
AU  - Harper CK
AU  - Guthrie AJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01205-15.

PMID- 26021934
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Mycoplasma synoviae Strain WVU 1853T.
PG  - e00563-15
AB  - A hybrid sequence assembly of the complete Mycoplasma synoviae type strain WVU 1853(T) genome
      was compared to that of strain MS53. The findings support prior
      conclusions about M. synoviae, based on the genome of that otherwise
      uncharacterized field strain, and provide the first evidence of epigenetic
      modifications in M. synoviae.
AU  - May MA
AU  - Kutish GF
AU  - Barbet AF
AU  - Michaels DL
AU  - Brown DR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00563-15.

PMID- 1091619
VI  - 122
DP  - 1975
TI  - Deoxyribonucleic acid-cytosine methylation by host- and plasmid-controlled enzymes.
PG  - 129-138
AB  - Deoxyribonucleic acid (DNA)-cytosine methylation specified by the wild-type Escherichia coli
      K12 mec+ gene and by the N-3 drug resistance (R) factor was studied in vivo and in vitro.
      Phage lambda and fd were propagated in the presence of L-[methyl-3H]methionine in various host
      bacteria. The in vivo labeled DNA was isolated from purified phage and depurinated by formic
      acid-diphenylamine treatment. The resulting pyrimidine oligonucleotide tracts were separated
      according to size and base composition by chromatography on diethylaminoethyl-cellulose in 7 M
      urea at pH 5.5 and 3.5, respectively. The distribution of labeled 5-methylcytosine in DNA
      pyrimidine tracts was identical for phage grown in mec+ and mec- (N-3) cells. For phage lambda
      the major 5-methylcytosine-containing tract was the tripyrimidine, C2T; for both fd.mec- (N-3)
      DNA and fd.mec+ DNA, C2T was the sole 5-methylcytosine-containing tract. When various lambda
      DNAs were methylated to saturation in vitro by crude extracts from mec+ and mec- (N-3) cells,
      the extent of cytosine methylation was the same. This is in contrast to in vivo methylation
      where k.mec- (N-3) DNA contains twice as many 5-methylcytosines per genome as k.mec+ DNA.
      Therefore, we suggest that the K12 met+ cytosine methylase and the N-3 plasmid modification
      methylases are capable of recognizing the same nucleotide sequences, but that the in vivo
      methylation rate is lower in mec+ cells.
AU  - May MS
AU  - Hattman S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1975 122: 129-138.

PMID- 1097428
VI  - 123
DP  - 1975
TI  - Analysis of bacteriophage deoxyribonucleic acid sequences methylated by host- and R-factor-controlled enzymes.
PG  - 768-770
AB  - Phages lambda and fd were propagated in Escherichia coli strains that have
      either host K-12 or the N-3 R-factor deoxyribonucleic acid-cytosine methylase
      activity.  Pyrimidine tracts containing 3H-labeled 5-methylcytosine (MeC) were
      analyzed; in all cases, the major methylated sequence was 5'...C-MeC-T ...3'.
AU  - May MS
AU  - Hattman S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1975 123: 768-770.

PMID- 1727392
VI  - 6
DP  - 1992
TI  - DNA photoaffinity crosslinking to TaqI endonuclease by a phosphorothioate-linked aryl azide.
PG  - A487
AB  - To identify amino acid residues required for the function of TaqI endonuclease
      (cleaves T^CGA), a new type of DNA photoaffinity crosslinking reagent was
      designed.  DNA (16-mer) was chemically synthesized in which a sulphur atom
      replaced a non-bridging phosphate oxygen at the position 5' to the C (scissile
      phosphate).  The two resulting phosphorothioate diasteriomers were separated
      using HPLC (C-18 column) and then alkylated with p-azidophenacyl bromide.  The
      endonuclease bound the modified substrates in a sequence-nonspecific manner and
      was crosslinked in the presence of UV light (366nm) with an efficiency of 25%.
      The TaqI-DNA crosslink was purified from unreacted material by FPLC (MonoQ).
      This species has proven highly resistant to a variety of proteases, and efforts
      are underway to effectively fragment the protein and identify the crosslinked
      residue.  The approach described here should be generally applicable to the
      study of other DNA binding proteins, given the facility of reagent synthesis
      and the flexibility of photoactive crosslinker placement.
AU  - Mayer A
AU  - Barany F
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1992 6: A487.

PMID- Not carried by PubMed...
VI  - 57
DP  - 1996
TI  - Defining the contacts between Taq endonuclease and the DNA phosphate backbone.
PG  - 2359B
AB  - The restriction endonuclease TaqI exhibits extreme specificity for its cognate sequence, TCGA,
      but a direct readout model fails to account for this property.  This study examines the role
      of phosphate contacts in the enzyme-substrate and transition-state complexes.  An S-methyl
      group was introduced into each of the pTpCpGpApNpN internucleotide linkages using a hybrid
      chemical-enzymatic synthesis, in which sulfur substitutions of non-bridging phosphate oxygens
      directed the placement of methyl groups.  The resulting twelve diastereomerically pure
      phosphate-modified substrates were tested for binding and cleavage by TaqI endonuclease.  The
      largest binding effects were produced by pro-Sp methylations at the pTpCpGA phosphates, which
      destablized the enzyme-substrate complex by 1.0-1.6 kcal/mol.  Cleavage of the modified strand
      was inhibited completely by modifications at the TpCpGpA phosphates, and inhibited
      significantly at the TCGApNp phosphates.  Cleavage of both strands was completely inhibited by
      modification of the TCGpA linkage.  Effects on the cleavage of the unmodified strand
      implicated phosphate modifications which caused global perturbations in the structure of the
      transition-state complex.  These results support a model to account for the specificity of
      TaqI, in which sequence-specific phosphate contacts are formed in the transition state, thus
      amplifying the apparent contribution of base contacts to the transition-state complex.  To
      identify amino acid residues which are in contact with the DNA, a sequence-specific
      photoaffinity reagent was designed which exploits the finding that modification of the Rp
      oxygen of the scissile phosphate does not interfere with substrate binding.  Accordingly, the
      scissile phosphate was substituted with an Rp phosphorothioate group to direct the placement
      of the bifunctional reagent, p-azidophenacyl bromide.  TaqI bound the photoaffinity reagent
      specifically and formed a covalent adduct with the enzyme in the presence of UV light.  Upon
      digestion of the covalent complex and isolation of a labeled peptide, the modified amino acid
      was identified as Tyr161.  This residue was changed to phenylalanine by site-directed
      mutagenesis, and the resulting Y161F mutant was characterized.  Removal of the Tyr161 hydroxyl
      group lowered both the kcat and the KM 5-fold, indicating that while this residue may be near
      the scissile phosphate, it is not critically required for catalysis.
AU  - Mayer AN
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1996 57: 2359B.

PMID- 7961873
VI  - 269
DP  - 1994
TI  - Interaction of TaqI endonuclease with the phosphate backbone.
PG  - 29067-29076
AB  - The restriction endonuclease TaqI exhibits extreme specificity for its cognate sequence, TCGA,
      but a direct hydrogen bond readout model fails to account for this property. The present study
      examines the role of phosphate contacts in the enzyme-substrate and transition state
      complexes. An S-methyl group was introduced into each of the pTpCpGpApNpN internucleotide
      linkages using a hybrid chemical-enzymatic synthesis, in which sulfur substitutions of
      nonbridging phosphate oxygens directed the placement of methyl groups. The resulting 12
      diastereomerically pure phosphate-modified substrates were tested for binding and cleavage by
      TaqI. The largest binding effects were induced by pro-Sp methylations at the pTpCpGA
      phosphates, which destabilized the enzyme-substrate complex by 1.0-1.6 kcal/mol. Cleavage of
      the modified strand was inhibited completely by modifications at the TpCpGpA phosphates and
      inhibited significantly at the TCGApNp phosphates. Cleavage of both strands was completely
      inhibited by modification of the TCGpA linkage. Effects on the cleavage of the unmodified
      strand were used to implicate phosphate modifications that caused global perturbations in the
      structure of the transition state complex. These results lend support for a model for the
      specificity of TaqI, in which sequence-specific phosphate contacts are formed in the
      transition state, thus amplifying the apparent contribution of base contacts to transition
      state stabilization.
AU  - Mayer AN
AU  - Barany F
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1994 269: 29067-29076.

PMID- 7883172
VI  - 153
DP  - 1995
TI  - Photoaffinity cross-linking of TaqI restriction endonuclease using an aryl azide linked to the phosphate backbone.
PG  - 1-8
AB  - In an effort to identify amino acid (aa) residues near the active site of TaqI restriction
      endonuclease (ENase), a sequence-specific photoaffinity reagent was designed. This reagent
      exploits the finding that modification of the Rp oxygen of the scissile phosphate does not
      interfere with substrate binding. The TpCGA phosphate was substituted with an Rp
      phosphorothioate group to direct the placement of the heterobifunctional reagent
      p-azidophenacyl bromide. TaqI bound the photoaffinity reagent specifically and formed a
      covalent adduct with the ENase in the presence of UV light. The modified aa was identified as
      Tyr161. This aa was changed to Phe by site-directed mutagenesis, and the resulting Y161F
      mutant was characterized. Removal of the Tyr161 hydroxyl group lowered both the kcat and the
      Km five-fold, indicating that, while this aa may be near the scissile phosphate, it is not
      critically rquired for catalysis.
AU  - Mayer AN
AU  - Barany F
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 153: 1-8.

PMID- 352725
VI  - 90
DP  - 1978
TI  - Optimization of the EcoRI* activity of EcoRI endonuclease.
PG  - 341-344
AB  - None
AU  - Mayer H
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1978 90: 341-344.

PMID- Not included in PubMed...
VI  - 356
DP  - 1975
TI  - Isolierung der Restriktionsendonuclease EcoRI aus einem Antibiotka-Resistenz-freien Stamm von Escherichia coli.
PG  - 253-254
AB  - Der Antibiotikaresistenz-(R-Faktor R1drd16 ist ein durch Deletionsmutation
      entstandenes Derivat des ursprunglichen R1-Faktors, der das Restriktionsenzym
      EcoRI kodiert.  Der R1drd16-Faktor determiniert nur noch Resistenz gegen
      Kanamycin.  Durch weitere Mutation konnte ein Plasmid erhalten werden, das
      keine Antibiotikaresistenz, wohl aber noch die Synthese von EcoRI determiniert.
      Im Grobfermentationsannsatz konnte der E.-coli-Stamm, der diesen mutierten
      R-Faktor tragt, mit einer Ausbeute von 35 g Bakterienfeuchtmasse/Igezuchtet
      werden, ohne dab ein erkennbarer Verlust des Plasmids zu beobachten wr.  Nach
      Zellaufschlub wurden in einem einzigen Fallungsschritt mit
      Cetyltrimetylam-moniumbromid Zellmembran und DNA entfernt.  Bei der
      Chromatographie an  Phosphocellulose und Hydroxyl-apatit verhalt sich das
      Exonuclease-freie Enzym wie EcoRI des ursprunglichen Plasmids.  Auch die
      Spaltungs-produkte von verschiedenen bakteriellen DNAs mit beiden
      Enzympraparationen sind identisch.
AU  - Mayer H
AU  - Goebel W
PT  - Journal Article
TA  - Hoppe Seylers Z. Physiol. Chem.
JT  - Hoppe Seylers Z. Physiol. Chem.
SO  - Hoppe Seylers Z. Physiol. Chem. 1975 356: 253-254.

PMID- 6273788
VI  - 9
DP  - 1981
TI  - ClaI, a new restriction endonuclease from Caryophanon latum L.
PG  - 4833-4845
AB  - From Caryophanon latum L a site specific restriction endonuclease (ClaI) has been purified,
      which recognises the DNA hexanucleotide palindrome 5'-A-T-^C-G-A-T-3'. Staggered cleavage
      generates DNA restriction fragments with 5'-terminal pCG extensions. A ClaI map of
      bacteriophage lambda has been determined, which indicates cleavage inhibition due to adenine
      methylation at overlapping ClaI-GATC recognition sequences. Plasmid pBR322 is cut only once,
      in the tetracycline promoter region, and can, therefore, be used as a vector system for
      cloning fragments derived from ClaI digestions, and in addition for fragments generated by
      TaqI, HpaII, and several other enzymes.
AU  - Mayer H
AU  - Grosschedl R
AU  - Schutte H
AU  - Hobom G
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1981 9: 4833-4845.

PMID- 101530
VI  - 136
DP  - 1978
TI  - Restriction Endonucleases: General Survey Procedure and Survey of Gliding Bacteria.
PG  - 708-713
AB  - Among 120 strains of gliding bacteria which were screened for restriction
      endonucleases, 27 were found positive.  Additionally, three strains carried
      enzymes able to release the supercoiled state of closed circular DNA.  By using
      a new rapid method, restriction endonuclease activity was released by stirring
      about 0.5 g of cells (fresh weight) in a motor-driven glass homogenizer in
      buffer containing Triton X-101, ethylenediaminetetraacetic acid, and
      mercaptoethanol.  A yield from 60 to 80% of the total activity present in the
      cells was obtained with minimal destruction of the cells.  The enzyme activity
      in the crude extract was measured semi-quantitatively be digestion of DNA and
      subsequent separation of the fragments on an agarose slab gel.  The method
      appears to be generally applicable for the extraction of restriction
      endonucleases from gram-negative bacteria on an analytical scale and in a
      modified form for large-scale preparation of restriction enzymes.
AU  - Mayer H
AU  - Reichenbach H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1978 136: 708-713.

PMID- 18708505
VI  - 190
DP  - 2008
TI  - Molecular characterization of a Clostridium difficile bacteriophage and its cloned biologically active endolysin.
PG  - 6734-6740
AB  - Clostridium difficile infection is increasing in both frequency and
      severity, with the emergence of new highly virulent strains highlighting
      the need for more rapid and effective methods of control. Here, we show
      that bacteriophage endolysin can be used to inhibit and kill C. difficile.
      The genome sequence of a novel bacteriophage that is active against C.
      difficile was determined, and the bacteriophage endolysin gene was
      subcloned and expressed in Escherichia coli. The partially purified
      endolysin was active against 30 diverse strains of C. difficile, and
      importantly, this group included strains of the major epidemic ribotype
      027 (B1/NAP1). In contrast, a range of commensal species that inhabit the
      gastrointestinal tract, including several representatives of the
      clostridium-like Firmicutes, were insensitive to the endolysin. This
      endolysin provides a platform for the generation of both therapeutic and
      detection systems to combat the C. difficile problem. To investigate a
      method for the protected delivery and production of the lysin in the
      gastrointestinal tract, we demonstrated the expression of active CD27L
      endolysin in the lactic acid bacterium Lactococcus lactis MG1363.
AU  - Mayer MJ
AU  - Narbad A
AU  - Gasson MJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2008 190: 6734-6740.

PMID- 20581196
VI  - 76
DP  - 2010
TI  - Genomic Sequence and Characterization of the Virulent Bacteriophage {phi}CTP1 from Clostridium tyrobutyricum and Heterologous Expression of Its Endolysin.
PG  - 5415-5422
AB  - The growth of Clostridium tyrobutyricum in developing cheese leads to
      spoilage and cheese blowing. Bacteriophages or their specific lytic
      enzymes may provide a biological control method for eliminating such
      undesirable organisms without affecting other microflora. We isolated the
      virulent bacteriophage phiCTP1 belonging to the Siphoviridae and have
      shown that it is effective in causing lysis of sensitive strains. The
      double-stranded DNA genome of phiCTP1 is 59,199 bp, and sequence analysis
      indicated that it has 86 open reading frames. orf29 was identified as the
      gene coding for the phage endolysin responsible for cell wall degradation
      prior to virion release. We cloned and expressed the ctp1l gene in E. coli
      and demonstrated that the partially purified protein induced lysis of C.
      tyrobutyricum cells and reduced viable counts both in buffer and in milk.
      The endolysin was inactive against a range of clostridial species but did
      show lysis of Clostridium sporogenes, another potential spoilage organism.
      Removal of the C-terminal portion of the endolysin completely abolished
      lytic activity.
AU  - Mayer MJ
AU  - Payne J
AU  - Gasson MJ
AU  - Narbad A
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2010 76: 5415-5422.

PMID- 10676950
VI  - 403
DP  - 2000
TI  - Demethylation of the zygotic paternal genome.
PG  - 501-502
AB  - In mammals, both parental genomes undergo dramatic epigenetic changes after fertilization to
      form the diploid somatic genome.  Here we show that the paternal genome in the mouse is
      significantly and actively demethylated within 6-8 hours of fertilization, before the onset of
      DNA replication, whereas the maternal genome is demethylated after several cleavage divisions.
      This active demethylation of the paternal genome may be associated with epigenetic remodelling
      of sperm chromatin, in order to establish parent-specific developmental programmes during
      early embryogenesis.
AU  - Mayer W
AU  - Niveleau A
AU  - Walter J
AU  - Fundele R
AU  - Haaf T
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2000 403: 501-502.

PMID- 21839719
VI  - 418
DP  - 2011
TI  - Direct and continuous fluorescence-based measurements of Pyrococcus horikoshii DNA N-6 adenine methyltransferase activity.
PG  - 204-212
AB  - N-6 methylation of adenine destabilises duplex DNA and this can increase the proportion of DNA
      that dissociates into single strands. We
      have investigated utilising this property to measure the DNA adenine
      methyltransferase-catalyzed conversion of hemimethylated to fully
      methylated DNA through a simple, direct, fluorescence-based assay. The
      effects of methylation on the kinetics and thermodynamics of
      hybridisation were measured by comparing a fully methylated
      oligonucleotide product and a hemimethylated oligonucleotide substrate
      using a 13-bp duplex labeled on adjacent strands with a fluorophore
      (fluorescein) and quencher (dabcyl). Enzymatic methylation of the
      hemimethylated GATC site resulted in destabilisation of the duplex,
      increasing the proportion of dissociated DNA, and producing an
      observable increase in fluorescence. The assay provides a direct
      measurement of methylation rate in real time and is highly
      reproducible, with a coefficient of variance over 48 independent
      measurements of 3.6%. DNA methylation rates can be measured as low as
      3.55 +/- 1.84 fmol s(-1) in a 96-well plate format, and the assay has
      been used to kinetically characterise the Pyrococcus horikoshii DNA
      adenine methyltransferase.
AU  - Maynard-Smith MD
AU  - McKelvie JC
AU  - Wood RJ
AU  - Harmer JE
AU  - Ranasinghe RT
AU  - Williams CL
AU  - Coomber DM
AU  - Stares AF
AU  - Roach PL
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 2011 418: 204-212.

PMID- Not included in PubMed...
VI  - 79
DP  - 1991
TI  - Nucleolytic activities in Lactococcus lactis subsp. lactis NCDO 497.
PG  - 195-198
AB  - Two nucleolytic activities were detected in Lactococcus lactis subsp. lactis NCDO 497. One of
      them was a specific endonuclease, located in the cytoplasm, with the typical characteristics
      of type II restriction endonucleases. The second activity was a non-specific deoxyribonuclease
      with exocytoplasmic location.
AU  - Mayo B
AU  - Hardisson C
AU  - Brana AF
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1991 79: 195-198.

PMID- 20348264
VI  - 192
DP  - 2010
TI  - Complete genome sequence of the probiotic Lactobacillus casei strain BL23.
PG  - 2647-2648
AB  - The entire genome of Lactobacillus casei BL23, a strain with probiotic properties, has been
      sequenced. The genomes of BL23 and the industrially
      used probiotic strain Shirota YIT 9029 (Yakult) seem to be very similar.
AU  - Maze A et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 2647-2648.

PMID- Not included in PubMed...
VI  - 24
DP  - 1990
TI  - Possible origin and evolution of enzymatic methylation of eukaryotic DNA.  Methylation of cytosine residues in three families of palindromes: RYRY, YYRR, and YYRYRR.
PG  - 16-35
AB  - On the basis of an analysis of the experimental data on the closest neighbors of the
      5-methylcytosine residues in eukaryotic DNA it was established that the regions of methylation
      CG and CNG may be included in three families of palindromes: RYRY, YYRR and YYRYRR.  It was
      shown that the entire variety of methylated sequences detectable in their DNA can arise as a
      result of mutational substitutions 5-MeC -> T, which occur in the deamination of 5-MeC
      residues in prototype portions of each of these families: GCGC, CCGG and CCGCGG.  The question
      of the multiplicity of DNA-methyltransferases in eukaryotes and their evolutionary origin from
      prokaryotic methylases of the second type, which recognize analogous sequences in DNA, is
      discussed.
AU  - Mazin AL
AU  - Vanyushin BF
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1990 24: 16-35.

PMID- 25838479
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Clostridium botulinum Strain 277-00 Type B2.
PG  - e00211-15
AB  - We report the draft genome sequence of Clostridium botulinum strain 277-00, which encodes a
      botulinum neurotoxin B2 associated with a ha gene locus. Strain 277-00
      was isolated from a cheese responsible for an outbreak of botulism in Iran in
      1997. This strain is closed to the bivalent B2/FA strain IBCA10-7060.
AU  - Mazuet C
AU  - Bouchier C
AU  - Popoff MR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00211-15.

PMID- 26221417
VI  - 10
DP  - 2015
TI  - High-quality permanent draft genome sequence of Rhizobium leguminosarum bv. viciae strain GB30; an effective microsymbiont of Pisum sativum growing in Poland.
PG  - 36
AB  - Rhizobium leguminosarum bv. viciae GB30 is an aerobic, motile, Gram-negative,
      non-spore-forming rod that can exist as a soil saprophyte or as a legume
      microsymbiont of Pisum sativum. GB30 was isolated in Poland from a nodule
      recovered from the roots of Pisum sativum growing at Janow. GB30 is also an
      effective microsymbiont of the annual forage legumes vetch and pea. Here we
      describe the features of R. leguminosarum bv. viciae strain GB30, together with
      sequence and annotation. The 7,468,464 bp high-quality permanent draft genome is
      arranged in 78 scaffolds of 78 contigs containing 7,227 protein-coding genes and
      75 RNA-only encoding genes, and is part of the GEBA-RNB project proposal.
AU  - Mazur A
AU  - De Meyer SE
AU  - Tian R
AU  - Wielbo J
AU  - Zebracki K
AU  - Seshadri R
AU  - Reddy T
AU  - Markowitz V
AU  - Ivanova NN
AU  - Pati A
AU  - Woyke T
AU  - Kyrpides NC
AU  - Reeve W
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 36.

PMID- 8784209
VI  - 35
DP  - 1996
TI  - The paradoxical influence of thymine analogues on restriction endonuclease cleavage of oligodeoxynucleotides.
PG  - 11522-11528
AB  - Thymine residues in the DNA of eukaryotes may be replaced occasionally by uracil (U) or
      5-(hydroxymethyl)uracil (H) as consequences of dUMP misincorporation or thymine oxidation,
      respectively.  In this study, we constructed a series of 44-base oligonucleotides containing
      site-specific U or H residues and 5'-fluorescein labels in order to probe the influence of
      such modifications on sequence-specific DNA-protein interactions using several type II
      restriction endonucleases.  We find that substitution within the recognition sites of several
      restriction endonucleases increases initial cleavage velocity by up to an order of magnitude.
      These results contrast dramatically with several previous studies which demonstrated that U
      substitution in short oligonucleotides inhibits or prevents nuclease cleavage.  We propose
      that this apparent paradox results because the rate-limiting step in the cleavage of longer
      oligonucleotides is product release whereas for shorter oligonucelotides substrate binding is
      most probably rate-limiting.  For longer oligonucleotides and DNA, more rapid release of the
      cleaved, substituted oligonucleotides results in more rapid turnover and a faster apparent
      cleavage rate.  The sequence length at which the transition is rate-limiting step occurs
      likely corresponds to the size of th enzyme footprint on its DNA recognition site.  We
      conclude that both U and H do perturb sequence-specific DNA - protein interactions, and the
      magnitude of this effect is site-dependent.
AU  - Mazurek M
AU  - Sowers LC
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1996 35: 11522-11528.

PMID- 2788457
VI  - 28
DP  - 1989
TI  - Effects of functional group changes in the EcoRV recognition site on the cleavage reaction catalyzed by the endonuclease.
PG  - 4616-4622
AB  - Oligodeoxynucleotides have been prepared which contain changes in the
      functional group pattern present in the EcoRV recognition site d(GATATC).
      These modifications involve the deletion of specific functional groups or the
      reversal of the relative positions of functional groups within the canonical
      six base pair recognition site.  The duplex stability of these modified
      oligodeoxynucleotides has been assessed by determining the thermodynamic
      parameters characterizing helix formation.  Steady-state kinetic parameters
      have been used to characterize the interaction of the modified
      oligodeoxynucleotides with the EcoRV endonuclease.  The enzyme is very
      sensitive to the deletion of either of the adenine amino or thymine methyl
      groups, or the reversal of the relative positions of the adenine amino group
      and thymine carboxy group which form an interstrand hydrogen bond in the major
      groove of the B-DNA helix.  Conversely, deletion of the guanine amino group had
      only minimal effects upon the measured kinetic parameters.  Deletion of the
      exocyclic amino group from the inner dA-dT base pair resulted in the fragment
      which interacted with the enzyme on the basis of observed inhibition
      experiments but was not cleaved.  The results suggest that the endonuclease
      interacts with its recognition sequence via contacts in the major groove of the
      B-DNA helix and that both hydrogen bonding to the adenine amino groups and also
      hydrophobic interactions with the thymine methyl groups are involved.
AU  - Mazzarelli J
AU  - Scholtissek S
AU  - McLaughlin LW
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1989 28: 4616-4622.

PMID- 29192087
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of a Clinical Enterococcus faecium Sequence Type 18 Strain  from South Africa.
PG  - e01381-17
AB  - We report the first draft genome sequence of an Enterococcus faecium sequence type 18 (ST18)
      strain isolated from a tuberculosis patient in Africa. The genome
      is comprised of 3,202,539 bp, 501 contigs, 37.70% GC content, 3,202
      protein-encoding genes, and 61 RNA genes. The resistome and virulome of this
      important pathogen are presented herein.
AU  - Mbelle NM
AU  - Maningi NE
AU  - Tshisevhe V
AU  - Modipane L
AU  - Amoako DG
AU  - Osei SJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01381-17.

PMID- 29242225
VI  - 5
DP  - 2017
TI  - First Report of a Whole-Genome Shotgun Sequence of a Clinical Enterococcus faecalis Sequence Type 6 Strain from South Africa.
PG  - e01382-17
AB  - Enterococcus faecalis is a lactic acid-producing Gram-positive bacterium commonly found in the
      intestinal tract of humans and animals; it is implicated in
      multidrug-resistant nosocomial infections. The draft genome of this E. faecalis
      sequence type 6 (ST6) strain consists of 3,215,228 bp, with 37.20% GC content,
      3,048 predicted coding sequences, and 61 RNA genes.
AU  - Mbelle NM
AU  - Maningi NE
AU  - Tshisevhe V
AU  - Modipane L
AU  - Amoako DG
AU  - Osei SJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01382-17.

PMID- 
VI  - 
DP  - 2005
TI  - TILLING for Arabidopsis chromomethylase function.
PG  - 1-66
AB  - In contrast to prokaryotic methyltransferases, comparatively little is known about the
      detailed structure and function of eukaryotic cytosine-5-methyltransferase enzymes.  During
      the course of my thesis work, I identified two DNA methyltransferase homologs that also
      contained a chromodomain (termed "chromomethylases") in Arabidopsis thaliana.  It is thought
      that chromodomains target proteins to interact with specific chromatin determinants; thus
      chromomethylases might be involved in epigenetic silencing by linking chromatin structure to
      DNA methylation.  In addition, the unique structure of the chromomethylases suggest they may
      not play a general role in maintaining CpG DNA methylation patterns, as may be true for the
      Arabidopsis methylase MET1 but, instead, may play a more specialized role in either
      establishing methylation or maintaining methylation on CpNpG or other nonsymmetrical sites.
      The two new genes, CMT2 and CMT3, were studied to determine their biological functions.  The
      goal of my thesis work was to characterize the chromomethylase genes specifically in hopes of
      determining the function of DNA methylation in plants.  Along the way I developed the reverse
      genetics method TILLING (Targeting Induced Local Lesions IN Genomes) and explored genome wide
      methylation targets of CMT3 using methylation profiling.  This work revealed that cmt3 mutants
      appear to have decreased CpNpG methylation while CpG methylation is unaffected.
AU  - McCallum CM
PT  - Journal Article
TA  - Ph.D. Thesis, University of Washington, Seattle, USA
JT  - Ph.D. Thesis, University of Washington, Seattle, USA
SO  - Ph.D. Thesis, University of Washington, Seattle, USA 2005 : 1-66.

PMID- 10748531
VI  - 18
DP  - 2000
TI  - Targeted screening for induced mutations.
PG  - 455-459
AB  - With the accumulation of large-scale sequence data, emphasis in genomics has shifted from
      determining gene structure to testing gene function, and this relies on reverse genetic
      methodology. Here we explore the feasibility of screening for chemically induced mutations in
      target sequences in Arabidopsis thaliana. Our TILLING (Targeting Induced Local Lesions IN
      Genomes) method combines the efficiency of ethyl methanesulfonate (EMS)-induced mutagenesis
      with the ability of denaturing high-performance liquid chromatography (DHPLC) to detect base
      pair changes by heteroduplex analysis. Importantly, this method generates a wide range of
      mutant alleles, is fast and automatable, and is applicable to any organism that can be
      chemically mutagenized.
AU  - McCallum CM
AU  - Comai L
AU  - Greene EA
AU  - Henikoff S
PT  - Journal Article
TA  - Nat. Biotechnol.
JT  - Nat. Biotechnol.
SO  - Nat. Biotechnol. 2000 18: 455-459.

PMID- 23935484
VI  - 9
DP  - 2013
TI  - Genomic analysis of the Kiwifruit pathogen Pseudomonas syringae pv. actinidiae provides insight into the origins of an emergent plant disease.
PG  - E1003503
AB  - The origins of crop diseases are linked to domestication of plants. Most crops
      were domesticated centuries--even millennia--ago, thus limiting opportunity to
      understand the concomitant emergence of disease. Kiwifruit (Actinidia spp.) is an
      exception: domestication began in the 1930s with outbreaks of canker disease
      caused by P. syringae pv. actinidiae (Psa) first recorded in the 1980s. Based on
      SNP analyses of two circularized and 34 draft genomes, we show that Psa is
      comprised of distinct clades exhibiting negligible within-clade diversity,
      consistent with disease arising by independent samplings from a source
      population. Three clades correspond to their geographical source of isolation; a
      fourth, encompassing the Psa-V lineage responsible for the 2008 outbreak, is now
      globally distributed. Psa has an overall clonal population structure, however,
      genomes carry a marked signature of within-pathovar recombination. SNP analysis
      of Psa-V reveals hundreds of polymorphisms; however, most reside within
      PPHGI-1-like conjugative elements whose evolution is unlinked to the core genome.
      Removal of SNPs due to recombination yields an uninformative (star-like)
      phylogeny consistent with diversification of Psa-V from a single clone within the
      last ten years. Growth assays provide evidence of cultivar specificity, with
      rapid systemic movement of Psa-V in Actinidia chinensis. Genomic comparisons show
      a dynamic genome with evidence of positive selection on type III effectors and
      other candidate virulence genes. Each clade has highly varied complements of
      accessory genes encoding effectors and toxins with evidence of gain and loss via
      multiple genetic routes. Genes with orthologs in vascular pathogens were found
      exclusively within Psa-V. Our analyses capture a pathogen in the early stages of
      emergence from a predicted source population associated with wild Actinidia
      species. In addition to candidate genes as targets for resistance breeding
      programs, our findings highlight the importance of the source population as a
      reservoir of new disease.
AU  - McCann HC
AU  - Rikkerink EH
AU  - Bertels F
AU  - Fiers M
AU  - Lu A
AU  - Rees-George J
AU  - Andersen MT
AU  - Gleave AP
AU  - Haubold B
AU  - Wohlers MW
AU  - Guttman DS
AU  - Wang PW
AU  - Straub C
AU  - Vanneste JL
AU  - Rainey PB
AU  - Templeton MD
PT  - Journal Article
TA  - PLoS Pathog.
JT  - PLoS Pathog.
SO  - PLoS Pathog. 2013 9: E1003503.

PMID- 17359257
VI  - 9
DP  - 2007
TI  - Proteorhodopsin photosystem gene clusters exhibit co-evolutionary trends and shared ancestry among diverse marine microbial phyla.
PG  - 846-858
AB  - Since the recent discovery of retinylidene proteins in marine bacteria (proteorhodopsins), the
      estimated abundance and diversity of this gene
      family has expanded rapidly. To explore proteorhodopsin photosystem
      evolutionary and distributional trends, we identified and compared 16
      different proteorhodopsin-containing genome fragments recovered from
      naturally occurring bacterioplankton populations. In addition to finding
      several deep-branching proteorhodopsin sequences, proteorhodopsins were
      found in novel taxonomic contexts, including a betaproteobacterium and a
      planctomycete. Approximately one-third of the proteorhodopsin-containing
      genome fragments analysed, as well as a number of recently reported marine
      bacterial whole genome sequences, contained a linked set of genes required
      for biosynthesis of the rhodopsin chromophore, retinal. Phylogenetic
      analyses of the retinal biosynthetic genes suggested their co-evolution
      and probable coordinated lateral gene transfer into disparate lineages,
      including Euryarchaeota, Planctomycetales, and three different
      proteobacterial lineages. The lateral transfer and retention of genes
      required to assemble a functional proteorhodopsin photosystem appears to
      be a coordinated and relatively frequent evolutionary event. Strong
      selection pressure apparently acts to preserve these light-dependent
      photosystems in diverse marine microbial lineages.
AU  - McCarren J
AU  - DeLong EF
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2007 9: 846-858.

PMID- 22691167
VI  - 12
DP  - 2012
TI  - The distribution of plasmids that carry virulence and resistance genes in Staphylococcus aureus is lineage associated.
PG  - 104
AB  - Background: Staphylococcus aureus is major human and animal pathogen. Plasmids often carry
      resistance genes and virulence genes that can
      disseminate through S. aureus populations by horizontal gene transfer
      (HGT) mechanisms. Sequences of S. aureus plasmids in the public domain
      and data from multi-strain microarrays were analysed to investigate (i)
      the distribution of resistance genes and virulence genes on S. aureus
      plasmids, and (ii) the distribution of plasmids between S. aureus
      lineages.
      Results: A total of 21 plasmid rep gene families, of which 13 were
      novel to this study, were characterised using a previously proposed
      classification system. 243 sequenced plasmids were assigned to 39
      plasmid groups that each possessed a unique combination of rep genes.
      We show some resistance genes (including ermC and cat) and virulence
      genes (including entA, entG, entJ, entP) were associated with specific
      plasmid groups suggesting there are genetic pressures preventing
      recombination of these genes into novel plasmid groups. Whole genome
      microarray analysis revealed that plasmid rep, resistance and virulence
      genes were associated with S. aureus lineages, suggesting
      restriction-modification (RM) barriers to HGT of plasmids between
      strains exist. Conjugation transfer (tra) complex genes were rare.
      Conclusion: This study argues that genetic pressures are
      restraining the spread of resistance and virulence genes amongst S.
      aureus plasmids, and amongst S. aureus populations, delaying the
      emergence of fully virulent and resistant strains.
AU  - McCarthy AJ
AU  - Lindsay JA
PT  - Journal Article
TA  - BMC Microbiol.
JT  - BMC Microbiol.
SO  - BMC Microbiol. 2012 12: 104.

PMID- 16648995
VI  - 44
DP  - 2006
TI  - Digestion of I-PpoI recognition sites in unfavorable sequence contexts achieved by changing the reaction conditions.
PG  - 61-67
AB  - 
AU  - McCarthy CB
AU  - Romanowski V
PT  - Journal Article
TA  - Biochem. Genet.
JT  - Biochem. Genet.
SO  - Biochem. Genet. 2006 44: 61-67.

PMID- 28684579
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of an IMP-7-Producing Pseudomonas aeruginosa Bloodstream Infection Isolate from Australia.
PG  - e00596-17
AB  - IMP-7 is one of the two IMP-type carbapenemases that in Pseudomonas aeruginosa are not limited
      to a geographic area, but it has not been previously reported in
      the Australian setting. We report here the draft genome sequence of an Australian
      P. aeruginosa bloodstream infection isolate that contains IMP-7.
AU  - McCarthy KL
AU  - Jennison A
AU  - Wailan AM
AU  - Paterson DL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00596-17.

PMID- 28818886
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Two Pseudomonas aeruginosa Bloodstream Infection Isolates Associated with Rapid Patient Death.
PG  - e00597-17
AB  - The morbidity and mortality associated with Pseudomonas aeruginosa bloodstream infections are
      significant. New strategies are required to treat such infections.
      We report here the draft genome sequences of two antibiotic-sensitive P.
      aeruginosa bloodstream infection isolates that were associated with rapid death
      in nonneutropenic patients.
AU  - McCarthy KL
AU  - Jennison AV
AU  - Wailan AM
AU  - Paterson DL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00597-17.

PMID- 26021927
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Sulfolobus solfataricus Strain 98/2 and Evolved Derivatives.
PG  - e00549-15
AB  - Sulfolobus solfataricus is a thermoacidophilic crenarcheote with a 3.0-Mb genome. Here, we
      report the genome sequence of S. solfataricus strain 98/2, along with
      several evolved derivatives generated through experimental microbial evolution
      for enhanced thermoacidophily.
AU  - McCarthy S
AU  - Gradnigo J
AU  - Johnson T
AU  - Payne S
AU  - Lipzen A
AU  - Martin J
AU  - Schackwitz W
AU  - Moriyama E
AU  - Blum P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00549-15.

PMID- 19123947
VI  - 10
DP  - 2009
TI  - Genome sequence analysis of Helicobacter pylori strains associated with gastric ulceration and gastric cancer.
PG  - 3
AB  - BACKGROUND: Persistent colonization of the human stomach by Helicobacter
      pylori is associated with asymptomatic gastric inflammation (gastritis)
      and an increased risk of duodenal ulceration, gastric ulceration, and
      non-cardia gastric cancer. In previous studies, the genome sequences of H.
      pylori strains from patients with gastritis or duodenal ulcer disease have
      been analyzed. In this study, we analyzed the genome sequences of an H.
      pylori strain (98-10) isolated from a patient with gastric cancer and an
      H. pylori strain (B128) isolated from a patient with gastric ulcer
      disease. RESULTS: Based on multilocus sequence typing, strain 98-10 was
      most closely related to H. pylori strains of East Asian origin and strain
      B128 was most closely related to strains of European origin. Strain 98-10
      contained multiple features characteristic of East Asian strains,
      including a type s1c vacA allele and a cagA allele encoding an EPIYA-D
      tyrosine phosphorylation motif. A core genome of 1237 genes was present in
      all five strains for which genome sequences were available. Among the 1237
      core genes, a subset of alleles was highly divergent in the East Asian
      strain 98-10, encoding proteins that exhibited <90% amino acid sequence
      identity compared to corresponding proteins in the other four strains.
      Unique strain-specific genes were identified in each of the newly
      sequenced strains, and a set of strain-specific genes was shared among H.
      pylori strains associated with gastric cancer or premalignant gastric
      lesions. CONCLUSION: These data provide insight into the diversity that
      exists among H. pylori strains from diverse clinical and geographic
      origins. Highly divergent alleles and strain-specific genes identified in
      this study may represent useful biomarkers for analyzing geographic
      partitioning of H. pylori and for identifying strains capable of inducing
      malignant or premalignant gastric lesions.
AU  - McClain MS
AU  - Shaffer CL
AU  - Israel DA
AU  - Peek RM Jr
AU  - Cover TL
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2009 10: 3.

PMID- 
VI  - 3
DP  - 1986
TI  - Structural studies on a DNA-EcoRI endonuclease recognition complex.
PG  - 45-68
AB  - The 3 angstrom structure of a co-crystalline recognition complex between EcoRI
      endonuclease and the cognate oligonucleotide TCGCGAATTCGCG was solved by the
      ISIRT method using a platinum isomorphous derivative.  The complex possesses a
      common two-fold symmetry axis which relates both strands of the
      self-complementary oligonucleotide and the two identical subunits of the
      protein dimer.  Each subunit is organized into an alpha/beta domain based on a
      five stranded beta-sheet and an extension, called the arm, which wraps around
      the DNA.  The primary beta-sheet consists of anti-parallel and parallel
      segments which, respectively, contain the sites of DNA strand scission and
      sequence recognition.  (DNA hydrolysis was inhibited via omission of
      magnesium).  The DNA departs significantly from the conformations seen in the
      absence of protein, suggesting that binding of the enzyme is required for their
      stability.  These are termed neo-conformations to distinguish them from those
      which are intrinsically stable in the absence of protein and include the
      torsional type-1 neo-kink which unwinds the DNA by approximately 25 degrees.
      This separates the DNA backbones by approximately 3.5 angstrom without
      unstacking the bases, and is a structural requirement for the recognition
      modules of the protein to gain access to the edges of the bases exposed at the
      bottom of the major groove.  We suspect that there are a finite number of
      structurally feasible neo-conformations which are important for DNA-protein
      interactions in general.
AU  - McClarin JA
AU  - Frederick CA
AU  - Grable J
AU  - Samudzi CT
AU  - Wang B-C
AU  - Greene P
AU  - Boyer HW
AU  - Rosenberg JM
PT  - Journal Article
TA  - Biomolecular Sterodynamics
JT  - Biomolecular Sterodynamics
SO  - Biomolecular Sterodynamics 1986 3: 45-68.

PMID- 3024321
VI  - 234
DP  - 1986
TI  - Structure of the DNA-EcoRI endonuclease recognition complex at 3 angstrom resolution.
PG  - 1526-1541
AB  - The crystal structure of the complex between EcoRI endonuclease and the cognate
      oligonucleotide TCGC-GAATTCGCG provides a detailed example of the structural basis of
      sequence-specific DNA-protein interactions.  The structure was determined, to 3 angstrom
      resolution, by the ISIR (iterative single isomorphous replacement) method with a platinum
      isomorphous derivative.  The complex has twofold symmetry.  Each subunit of the endonuclease
      is organized into an a/b domain consisting of a five-stranded beta sheet, alpha helices, and
      an extension, called the "arm," which wraps around the DNA.  The large beta sheet consists of
      antiparallel and parallel motifs that form the foundations for loops and alpha helices
      responsible for DNA strand scission and sequence-specific recognition, respectively.  The DNA
      cleavage site is located in a cleft that binds the DNA backbone in the vicinity of the
      scissile bond. Sequence specificity is mediated by 12 hydrogen bonds originating from alpha
      helical recognition modules.  Arg200 forms two hydrogen bonds with guanine while Glu144 and
      Arg145 form four hydrogen bonds to adjacent adenine residues. These interactions discriminate
      the EcoRI hexanucleotide GAATTC from all other hexanucleotides because any base substitution
      would require rupture of at least one of these hydrogen bonds.
AU  - McClarin JA
AU  - Frederick CA
AU  - Wang BC
AU  - Greene P
AU  - Boyer HW
AU  - Grable J
AU  - Rosenberg JM
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1986 234: 1526-1541.

PMID- 2828867
VI  - 155
DP  - 1987
TI  - Site-specific cleavage of DNA at 8-, 9-, and 10-bp sequences.
PG  - 22-33
AB  - Site-specific cleavage of DNA at 8-, 9-, and 10-bp sequences had been reported.
      This technique relies on a restriction enzyme, DpnI, which only cuts the sequence
      GATC when both strands are methylated at adenine 3,4;
          5'...GmA T C...3'
          3'...C TmA G...5'
      DpnI does not cut the DNA of most species because they lack this methylated sequence.
AU  - McClelland M
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1987 155: 22-33.

PMID- 6443311
VI  - 21
DP  - 1984
TI  - Selection against dam methylation sites in the genomes of DNA of enterobacteriophages.
PG  - 317-322
AB  - Post replicative methylation of adenine in Escherichia coli DNA to produce G6mATC (where 6mA
      is 6-methyladenine) has been associated with preferential daughter-strand repair and possibly
      regulation of replication. An analysis was undertaken to determine if these, or other, as yet
      unknown roles of GATC, have had an effect on the frequency of GATC in E. coli or bacteriophage
      DNA. It was first ascertained that the most accurate predictions of GATC frequency were based
      on the observed frequencies of GAT and ATC, which would be expected since these predictors
      take into account preferences in codon usage. The predicted frequencies were compared with
      observed GATC frequencies in all available bacterial and phage nucleotide sequences. The
      frequency of GATC was close to the predicted frequency in most genes of E. coli and its RNA
      bacteriophages and in the genes of nonenteric bacteria and their bacteriophages. However, for
      DNA enterobacteriophages the observed frequency of GATC was generally significantly lower than
      predicted when assessed by the chi square test. No elevation in the rate of mutation of 6mA in
      GATC relative to other bases was found when pairs of DNA sequences from closely related phages
      or pairs of homologous genes from enterobacteria were compared, nor was any preferred pathway
      for mutation of 6mA evident in the E. coli DNA bacteriophages. This situation contrasts with
      that of 5-methylcytosine, which is hypermutable, with a preferred pathway to thymine. Thus,
      the low level of GATC in enterobacteriophages is probably due not to 6mA hypermutability, but
      to selection against GATC in order to bypass a GATC mediated host function.
AU  - McClelland M
PT  - Journal Article
TA  - J. Mol. Evol.
JT  - J. Mol. Evol.
SO  - J. Mol. Evol. 1984 21: 317-322.

PMID- 6273810
VI  - 9
DP  - 1981
TI  - The effect of sequence specific DNA methylation on restriction endonuclease cleavage.
PG  - 5859-5866
AB  - Sequence specific DNA methylation sometimes results in the protection of some
      or all of a restriction endonucleases' cleavage sites.  This is usually, but
      not always, the result of methylation of one or both strands of DNA at the site
      characteristic of the corresponding "cognate" modification methylase.  The
      known effects of sequence methylation on restriction endonucleases are
      compiled.
AU  - McClelland M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1981 9: 5859-5866.

PMID- 6278447
VI  - 9
DP  - 1981
TI  - Purification and characterization of two new modification methylases: M.ClaI from Caryophanon latum and M.TaqI from Thermus aquaticus YTI.
PG  - 6795-6804
AB  - A method for detecting Type II modification methylases and determining their methylation site
      by assaying the ability of methylated DNA to be cleaved by heterologous restriction enzymes is
      described and applied to the isolation of the restriction modification methylases from Thermus
      thermophilus HB8, Thermus aquaticus YTI and Caryophanon latum L.  M.TaqI is shown to have a
      methylation specificity identical to M.TthI (TCGmeA). M.ClaI methylates at adenine and
      protects a subset of TthI sites indicating that it methylates the sequence ATCGmeAT.
      Methylation by M.TthI also protects against cleavage by SalI, XhoI and at some HindII, AccI
      and MboI sites.
AU  - McClelland M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1981 9: 6795-6804.

PMID- 6306558
VI  - 11
DP  - 1983
TI  - The effect of site specific methylation on restriction endonuclease cleavage (update).
PG  - r169-r173
AB  - I present here an update of the compilation published in 1981 in this journal
      on the effects of site specific methylation on restriction endonuclease
      cleavage.  The amount of information available has increased by nearly 50%
      since that time.  Table 1 is organized by length of restriction endonuclease
      recognition sequence and then alphabetically by sequence.  Isoschizomers are
      listed alphabetically by name.  Only the effects of methylation at the N6
      position of adenine and C5 of cytosine are considered.  References to the
      purification of restriction enzymes and the determination of their recognition
      sequences can be found in R.J. Roberts review.
AU  - McClelland M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1983 11: r169-r173.

PMID- 6644829
VI  - 19
DP  - 1983
TI  - The frequency and distribution of methylatable DNA sequences in leguminous plant protein coding genes.
PG  - 346-354
AB  - Methylation of higher plant DNA occurs at up to 25% of all cytosines, primarily
      in the sequences CpG and CpNpG, both of which are over 80% methylated in wheat
      and tobacco (Gruenbaum et al. 1981).  CpG and CpNpG frequencies and
      distributions in the known sequences of cloned genes of leguminous plants were
      analyzed.  In this sample CpG occurred at only 49% of the frequency expected if
      the bases were distributed at random.  This lower frequency may be attributed
      to the fixation of mutations generated by a high rate of deamination of
      5-methylcytosine to thymine (Salser 1977).  Consistent with this hypothesis,
      the product of CpG transitions, TpG and CpA, were significantly above their
      expected frequency.  However CpNpG occurred at approximately expected levels
      and there was no significant increase in its transition products CpNpA and
      TpNpG.  Possible explanations for this phenomenon are discussed.  An analysis
      of the distribution of di- and trinucleotides across functionally classified
      regions of genes showed CpG to be asymmetrically distributed.  CpG was on
      average significantly enriched in the 3' flanking regions compared to other
      regions.  This may reflect a methylation-mediated regulatory role for this
      region in some legume genes.
AU  - McClelland M
PT  - Journal Article
TA  - J. Mol. Evol.
JT  - J. Mol. Evol.
SO  - J. Mol. Evol. 1983 19: 346-354.

PMID- 2833730
VI  - 16
DP  - 1988
TI  - Recognition sequences of Type II restriction systems are constrained by the G+C content of host genomes.
PG  - 2283-2294
AB  - I show that the recognition sequences of Type II restriction systems are
      correlated with the G+C content of the host bacterial DNA.  Almost all
      restriction systems with G+C rich tetranucleotide recognition sequences are
      found in species with A+T rich genomes, whereas G+C rich hexanucleotide and
      octanucleotide recognition sequences are found almost exclusively in speciies
      with G+C rich genomes.  Most hexanucleotide recognition sequences found in
      species with A+T rich genomes are A+T rich.  This distribution eliminates a
      substantial proportion of the potential variance in the frequency of
      restriction recognition sequences in the host genomes.  As a consequence,
      almost all restriction recognition sequences, including those eight base pairs
      in length (NotI and SfiI), are predicted to occur with a frequency ranging from
      once every 300 to once every 5,000 base pairs in the host genome.  Since the
      G+C content of bacteriophage DNA and of the host genome are also correlated,
      the data presented is evidence that most TypeII "restriction systems" are
      indeed involved in phage restriction.
AU  - McClelland M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1988 16: 2283-2294.

PMID- 15531882
VI  - 36
DP  - 2004
TI  - Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid.
PG  - 1268-1274
AB  - Salmonella enterica serovars often have a broad host range, and some cause both
      gastrointestinal and systemic disease. But the serovars Paratyphi A
      and Typhi are restricted to humans and cause only systemic disease. It has
      been estimated that Typhi arose in the last few thousand years. The
      sequence and microarray analysis of the Paratyphi A genome indicates that
      it is similar to the Typhi genome but suggests that it has a more recent
      evolutionary origin. Both genomes have independently accumulated many
      pseudogenes among their approximately 4,400 protein coding sequences: 173
      in Paratyphi A and approximately 210 in Typhi. The recent convergence of
      these two similar genomes on a similar phenotype is subtly reflected in
      their genotypes: only 30 genes are degraded in both serovars.
      Nevertheless, these 30 genes include three known to be important in
      gastroenteritis, which does not occur in these serovars, and four for
      Salmonella-translocated effectors, which are normally secreted into host
      cells to subvert host functions. Loss of function also occurs by mutation
      in different genes in the same pathway (e.g., in chemotaxis and in the
      production of fimbriae).
AU  - McClelland M et al
PT  - Journal Article
TA  - Nat. Genet.
JT  - Nat. Genet.
SO  - Nat. Genet. 2004 36: 1268-1274.

PMID- 11677609
VI  - 413
DP  - 2001
TI  - Complete genome sequence of Salmonella enterica serovar typhimurium LT2.
PG  - 852-856
AB  - Salmonella enterica subspecies I, serovar Typhimurium (S. typhimurium), is a leading cause of
      human gastroenteritis, and is used as a mouse model of human typhoid fever. The incidence of
      non-typhoid salmonellosis is increasing worldwide, causing millions of infections and many
      deaths in the human population each year. Here we sequenced the 4,857-kilobase (kb) chromosome
      and 94-kb virulence plasmid of S. typhimurium strain LT2. The distribution of close homologues
      of S. typhimurium LT2 genes in eight related enterobacteria was determined using previously
      completed genomes of three related bacteria, sample sequencing of both S. enterica serovar
      Paratyphi A (S. paratyphi A) and Klebsiella pneumoniae, and hybridization of three unsequenced
      genomes to a microarray of S. typhimurium LT2 genes. Lateral transfer of genes is frequent,
      with 11% of the S. typhimurium LT2 genes missing from S. enterica serovar Typhi (S. typhi),
      and 29% missing from Escherichia coli K12. The 352 gene homologues of S. typhimurium LT2
      confined to subspecies I of S. enterica-containing most mammalian and bird pathogens-are
      useful for studies of epidemiology, host specificity and pathogenesis. Most of these
      homologues were previously unknown, and 50 may be exported to the periplasm or outer membrane,
      rendering them accessible as therapeutic or vaccine targets.
AU  - McClelland M et al
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2001 413: 852-856.

PMID- 1538746
VI  - 355
DP  - 1992
TI  - Biased DNA repair.
PG  - 595-596
AB  - Hennecke et al. report the first in vitro characterization of a DNA mismatch
      endonuclease.  This enzyme, the vsr gene product, initiates very short patch
      repair of E. coli by nicking one strand of the duplex next to the T at a
      mismatched T:G in the sequence CTWG or TWGG.
AU  - McClelland M
AU  - Bhagwat AS
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1992 355: 595-596.

PMID- 2893340
VI  - 16
DP  - 1988
TI  - KGB: a single buffer for all restriction endonucleases.
PG  - 364
AB  - Most recommended restriction buffers contain Na+ and Cl-.  However, in bacteria
      the most abundant intracellular cation and anion are usually potassium and
      glutamate, respectively.  Furthermore, restriction endonucleases cleave DNA in
      potassium glutamate (KGlu) over a much broader concentration range than they do
      in NaCl.  These facts encouraged us to investigate the possibility that we
      could use KGlu in a chloride-free buffer and achieve normal levels of activity
      for all restriction endonucleases.  We have tested fifty-five restriction
      endonucleases for their ability to cleave DNA in a series of KGlu buffers (KGB,
      see Table 1) and compared the level of activity with that found under
      conditions recommended by the vendors (New England Biolabs, Boehringer Mannheim
      Biochem. and International Biotech. Inc.).  Assays were performed as partial
      digests (0.2 units per ug of DNA in 30 ul for 30 min.) and as overnight
      digestions with excess enzyme to ensure that no loss of specificity (start
      activity) occurred.  Most restriction endonucleases, polymerases and ligase
      showed broad KGlu concentration optima and all enzymes functioned in 100 mM
      KGlu (1X KGB).  Reducing agent was not normally required.  Some enzymes worked
      well in concentrations of KGlu over 400 mM (data not presented).  KGB can be
      used to simplify laboratory procedures including double digests, DNA cleavage
      followed by end-labeling, or the digestion of DNA embedded in agarose prior to
      pulsed field gel electrophoresis.  DNA in KGB can be phenol extracted and
      ethanol precipitated using standard protocols.
AU  - McClelland M
AU  - Hanish J
AU  - Nelson M
AU  - Patel Y
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1988 16: 364.

PMID- 2819819
VI  - 15
DP  - 1987
TI  - Restriction endonucleases for pulsed field mapping of bacterial genomes.
PG  - 5985-6005
AB  - Fundamental to many bacterial genome mapping strategies currently under
      development is the need to cleave the genome into a few large DNA fragments
      that can be resolved by pulsed field gel electrophoresis.  Identification of
      endonucleases that infrequently cut a genome is of key importance in this
      process.  We show that the tetranucleotide CTAG is extremely rare in most
      bacterial genomes with G+C contents above 45%.  As a consequence, most of the
      sixteen bacterial genomes we have tested are cleaved less than once every
      100,000 base pairs by one or more endonucleases that have CTAG in their
      recognition sequences:  XbaI (TCTAGA), SpeI (ACTAGT), AvrII (CCTAGG) and NheI
      (GCTAGC).  Similarily, CCG and CGG are the rarest trinucleotides in many
      genomes with G+C content of less than 45%.  Thus, SmaI (CCCGGG), RsrII
      (CGGWCCG), NaeI (GCCGGC) and SacII (CCGCGG) are often suitable endonucleases
      for producing fragments that average over 100,000 base pairs from such genomes.
      Pulsed field gel electrophoresis of the fragments that result from cleavage
      witih endonucleases that cleave only a few times per genome should assist in
      the physical mapping of many prokaryotic genomes.
AU  - McClelland M
AU  - Jones R
AU  - Patel Y
AU  - Nelson M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1987 15: 5985-6005.

PMID- 6322193
VI  - 81
DP  - 1984
TI  - Site-specific cleavage of DNA at 8- and 10-base pair sequences.
PG  - 983-987
AB  - A method is described for cutting DNA at specific sites that are 8 and 10 base
      pairs long.  The DNA is first treated with a specific methylase, either the
      restriction-modification enzyme M. TaqI, which converts the 4-base sequence
      T-C-G-A to T-C-G-mA, or the similar enzyme M. ClaI, which converts the 6-base
      sequence A-T-C-G-A-T to A-T-C-G-mA-T.  The DNA is then cleaved with DpnI, a
      restriction endonuclease that recognizes the sequence G-mA-T-C.  DpnI is unique
      in that it cuts only DNA that is methylated at adenine in both strands of its
      recognition sequence.  In DNAs that are not otherwise methylated at adenine in
      both strands of the sequence G-A-T-C, cleavage by DpnI occurs only at the
      following sequences: 	in the case of M. TaqI methylation, 5' T-C-G-mA- T-C-G-mA
      3'3'mA-G-C- T-mA-G-C- T 5'; in the case of M. ClaI methylation, 5' A- T-C-G-mA-
      T-C-G-mA-T 3'3' T-mA-G-C -T-mA-G-C -T-A 5'.  Specific cutting and cloning at
      these methylase/DpnI-generated sites is shown experimentally.  Further, we
      describe how the above technique can be extended to generate DpnI cleavage
      sites of up to 12 base pairs.  In DNA that contains equal amounts of each base
      distributed at random, 8- and 10-base pair recognition sequences occur, on the
      average, approximately once every 65,000 and 1,000,000 base pairs,
      respectively.  Potential applications, including the development of cloning
      vectors and a rapid method for chromosome walking, are discussed.
AU  - McClelland M
AU  - Kessler LG
AU  - Bittner M
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1984 81: 983-987.

PMID- 1317957
VI  - 20
DP  - 1992
TI  - Effect of site-specific methylation on DNA modification methyltransferases and restriction endonucleases.
PG  - 2145-2157
AB  - We present in Table I an updated list of the sensitivities of over 280 restriction
      endonucleases to the site-specific DNA modifications m4C, m5C, hm5C, and m6A, four
      modifications that are common in DNA prokaryotes, eukaryotes, and their viruses. Table II is a
      list of over 190 characterized DNA methyltransferases. A detailed list of cloned
      restriction-modification genes has been made by Wilson. Table III lists the sensitivities of
      over 20 Type II DNA methyltransferases to m4C, m5C, hm5C, and m6A modification. Most DNA
      methyltransferases are sensitive to non-canonical modifications within their recognition
      sequences, and this sensitivity may differ from that of their restriction endonuclease
      partners. Finally, several restriction endonuclease isoschizomers are known to differ in their
      ability to cleave DNA which has been methylated. Table IV lists over 20 known isoschizomer
      pairs and one isomethylator pair, along with the modified recognition sites at which they
      differ.
AU  - McClelland M
AU  - Nelson M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 2145-2157.

PMID- 2851534
VI  - 5
DP  - 1987
TI  - Enhancement of the apparent cleavage specificities of restriction endonucleases:  applications to megabase mapping of chromosomes.
PG  - 257-282
AB  - Restriction endonucleases generally recognize DNA sequences of four to six base
      pairs.  Therefore, these enzymes cut DNA that contains equal amounts of A,C,G
      and T, distributed at random, into fragments with an average size of 4/4 to 4/6
      base pairs, (256 to 4096 base pairs).  Accordingly, restriction endonuclease
      mapping techniques are appropriate for the analysis of gene-sized DNA
      molecules.  For example, a restriction endonuclease with a six base specificity
      will cut the human genome into approximately 750,000 fragments averaging 4
      kilobase pairs.  However, more specific DNA cutting methods would yield fewer
      and larger fragments, suitable for the analysis of large, complex genomes.
      Techniques have been described for the preparation and separation of DNA
      molecules of one megabase pair or more.  To produce fragments of this size from
      random DNA one must have a recognition sequence which is the log (base 4) of
      1,000,000; approximately ten base pairs.  The genome sizes of various organisms
      and the number of fragments generated by cleavage systems of varying
      specificities are presented in Table 1.  We describe here a number of
      strategies which can be used to increase the apparent specificity of
      restriction endonucleases to produce Average Fragment Sizes (AFS) in the range
      fo 6,000 to 270,000,000 base pairs.  These are:  (1) protection of restriction
      endonuclease recognition sites from cleavage by sequence-specific DNA
      methylation. (2) generation of cleavage sites using sequence-specific DNA
      methylation and a methylation-dependent restriction endonuclease, DpnI.  (3)
      blocking DNA methylases by other methylases.  (4) prediction of rare
      restriction recognition sites for particular genomes based on the non-random
      sequence arrangement of natural DNAs.  We believe that combinations of the
      above-mentioned three methods will provide a framework for the eventual
      molecular dissection of large, complex, DNA molecules.
AU  - McClelland M
AU  - Nelson M
PT  - Journal Article
TA  - Gene Amplif. Anal.
JT  - Gene Amplif. Anal.
SO  - Gene Amplif. Anal. 1987 5: 257-282.

PMID- 2854811
VI  - 74
DP  - 1988
TI  - The effect of site-specific DNA methylation on restriction endonucleases and DNA modification methyltransferases - a review.
PG  - 291-304
AB  - Review of methylation sensitivity.
AU  - McClelland M
AU  - Nelson M
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 291-304.

PMID- 3248722
VI  - 74
DP  - 1988
TI  - The 5'-GGATCC-3' cleavage specificity of BamHI is increased to 5'-CCGGATCCGG-3' by sequential double methylation with M.HpaII and M.BamHI.
PG  - 169-176
AB  - Site-specific DNA methylation is known to block cleavage by a number of
      restriction endonucleases.  We show that methylation at non-canonical DNA
      modification sites can also block methylation by five of 13 DNA
      methyltransferases (MTases) tested.  Furthermore, MTases and endonucleases that
      recognize the same nucleotide sequence can differ in their sensitivity to
      non-canonical methylation.  In particular, BamHI endonuclease can cut
      5'-GGATCm5C efficiently, whereas M.BamHI cannot methylate this modified
      sequence.  Methyltransferase/endonuclease pairs which differ in their
      sensitivity to non-canonical methylation can be exploited to generate rare DNA
      cleavage sites.  For example, we show that M.HpaII, M.BamHI, and BamHI can be
      used sequentially in a three-step procedure to specifically cleave DNA at the
      10-bp sequence 5'-CCGGATCCGG.  Several highly selective DNA cutting strategies
      are made possible by these sequential double methylation-blocking reactions.
AU  - McClelland M
AU  - Nelson M
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 169-176.

PMID- 2987886
VI  - 13
DP  - 1985
TI  - The effect of site specific methylation on restriction endonuclease digestion.
PG  - r201-r207
AB  - None
AU  - McClelland M
AU  - Nelson M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1985 13: r201-r207.

PMID- 2997742
VI  - 13
DP  - 1985
TI  - Purification of MboII methylase (GAAGmA) from Moraxella bovis: site specific cleavage of DNA at nine and ten base pair sequences.
PG  - 7171-7182
AB  - The restriction modification methylase M.MboII has been purified using a sensitive
      oligonucleotide linker assay.  The enzyme methylates the MboII recognition sequence GAAGA at
      adenine to produce GAAGmA.  M.MboII can be used in conjunction with the methylation dependent
      restriction endonuclease DpnI (GmATC) to produce cleavage at the 10 base sequence GAAGATCTTC.
      When M.MboII is used in combination with M.ClaI (ATCGATCGAT), GAAGATCTTC, GAAGATCGAT,
      ATCGATCTTC and ATCGATCGAT, which is equivalent to a nine base recognition site. The use of
      combinations of adenine methylases and DpnI to generate highly selective DNA cleavages at a
      variety of sequences up to fourteen base pairs is discussed.
AU  - McClelland M
AU  - Nelson M
AU  - Cantor CR
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1985 13: 7171-7182.

PMID- 7937074
VI  - 22
DP  - 1994
TI  - Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases.
PG  - 3640-3659
AB  - Restriction endonucleases have site-specific interactions with DNA that can often be inhibited
      by site-specific DNA methylation and other site-specific DNA modifications. However, such
      inhibition cannot generally be predicted. The empirically acquired data on these effects are
      tabulated for over 320 restriction endonucleases. In addition, a table of known site-specific
      DNA modification methyltransferases and their specificities is presented along with EMBL
      database accession numbers for cloned genes.
AU  - McClelland M
AU  - Nelson M
AU  - Raschke E
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1994 22: 3640-3659.

PMID- 15843021
VI  - 348
DP  - 2005
TI  - Continuous assays for DNA translocation using fluorescent triplex dissociation: Application to type I restriction endonucleases.
PG  - 895-915
AB  - Fluorescent assays and accompanying kinetic models are described for the analysis of DNA
      translocation independent of duplex unwinding. A
      triplex binding site (TBS) was introduced into DNA substrates at
      precise loci downstream of recognition sequences for type IA, IB and IC
      restriction endonucleases (EcoKI, EcoAI and EcoR1241, respectively).
      Each endonuclease was incubated (without ATP) with substrates on which
      a hexachlorofluoroscein-labelled triplex-forming oligonucleotide
      (HEX-TFO) was pre-bound. Following addition of ATP, 1-D enzyme motion
      resulted in collision with, and displacement of, the HEX-TFO, producing
      a > twofold increase in fluorescent intensity. Alternatively, a
      decrease in anisotropy following displacement of a rhodamine-labelled
      TFO was monitored. Using rapid mixing in a stopped-flow fluorimeter,
      continuous kinetic profiles were produced in which displacement is
      preceded by a lag-phase, directly proportional to the distance moved.
      For each enzyme, we obtained not only the translocation. rate but also
      information on slow isomerisation step(s) at initiation. Furthermore,
      we demonstrated that enzymes deficient in DNA cleavage but with maximal
      ATPase activity showed initiation and translocation rates identical to
      wild-type, confirming that DNA strand breaks are not a pre-requisite of
      motion.
AU  - McClelland SE
AU  - Dryden DTF
AU  - Szczelkun MD
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2005 348: 895-915.

PMID- 
VI  - 14
DP  - 2004
TI  - The type I and III restriction endonucleases: Structural elements in the molecular motors that process DNA.
PG  - 111-135
AB  - The Type I and III restriction endonucleases are larger, multimeric protein complexes with
      four enzyme activities; DNA methyltransferase, DNA endonuclease, ATPase and DNA translocase.
      It has been demonstrated that ATP-dependent protein motion along DNA is necessary for
      endonuclease activity.  Studies have shown that Type I enzymes remain bound to their
      recognition sites whilst simultaneously translocating adjacent non-specific dsDNA past a
      stationary complex.  This occurs bi-directionally so that two DNA loops are extruded.  An
      equivalent unidirectional mechanism has been suggested for the Type III enzymes.  DNA cleavage
      generally results when the enzymes stall against another restriction enzyme complex.  Both the
      HsdR subunits of the Type I enzymes and the Res subunits of the Type III enzymes carry amino
      acid motifs characteristic of superfamily 2 helicases.  In this review, the structural and
      mechanistic implications of this relationship are discussed and models s!
      uggested for how the ATP-dependent restriction enzymes might couple chemical energy to
      mechanical motion on DNA.
AU  - McClelland SE
AU  - Szczelkun MD
PT  - Journal Article
TA  - Nucleic Acids Mol. Biol.
JT  - Nucleic Acids Mol. Biol.
SO  - Nucleic Acids Mol. Biol. 2004 14: 111-135.

PMID- 28883154
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Marine Bacterium Oceanimonas baumannii ATCC 700832T.
PG  - e01007-17
AB  - The aerobic phenol-degrading Gram-negative rod Oceanimonas baumannii ATCC 700832T was first
      isolated from estuary mud from the River Wear, United Kingdom, in 1983.
      Information on the draft genome sequence for O. baumannii ATCC 700832T is
      included in this announcement. The predicted genome size is 3,809,332 bp, with
      55.88% G+C content.
AU  - McClelland WD
AU  - Trachtenberg AM
AU  - Brennan MA
AU  - MacLea KS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01007-17.

PMID- 30533890
VI  - 7
DP  - 2018
TI  - Complete Genome Sequences of Canadian Epidemic Methicillin-Resistant Staphylococcus aureus Strains CMRSA3 and CMRSA6.
PG  - e00892-18
AB  - Methicillin-resistant Staphylococcus aureus (MRSA) clonal complex 8 (CC8) sequence type 239
      (ST239) represents a predominant hospital-associated MRSA
      sublineage present worldwide. The Canadian epidemic MRSA strains CMRSA3 and
      CMRSA6 are moderately virulent members of this group but are closely related to
      the highly virulent strain TW20. Whole-genome sequencing of CMRSA3 and CMRSA6 was
      conducted to identify genetic determinants associated with their virulence.
AU  - McClure JA
AU  - Shideler SM
AU  - Zhang K
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e00892-18.

PMID- 28572329
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of a Community-Associated Methicillin-Resistant Staphylococcus aureus Hypervirulent Strain, USA300-C2406, Isolated from a Patient  with a Lethal Case of Necrotizing Pneumonia.
PG  - e00461-17
AB  - USA300 is a predominant community-associated methicillin-resistant Staphylococcus aureus
      strain causing significant morbidity and mortality. We present here the
      full annotated genome of a USA300 hypervirulent clinical strain, USA300-C2406,
      isolated from a patient with a lethal case of necrotizing pneumonia, to gain a
      better understanding of USA300 hypervirulence.
AU  - McClure JA
AU  - Zhang K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00461-17.

PMID- 28596402
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of the Methicillin-Resistant Staphylococcus aureus Colonizing Strain M92.
PG  - e00478-17
AB  - M92 is a methicillin-resistant Staphylococcus aureus (MRSA) colonizing strain belonging to
      ST239-MRSA-III. It frequently shows local nasal colonization in our
      hospital staff, but has never been associated with infection. We sequenced the
      complete genome of M92, in order to compare it to highly virulent MRSA strains to
      gain insight into MRSA virulence factors.
AU  - McClure JA
AU  - Zhang K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00478-17.

PMID- 28596400
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of Five Representative Staphylococcus aureus ST398 Strains from Five Major Sequence Heterogeneity Groups of a Diverse Isolate  Collection.
PG  - e00473-17
AB  - Staphylococcus aureus sequence type 398 (ST398) is a rapidly emerging livestock-associated
      strain causing zoonotic disease in humans. The course of
      pathogen evolution remains unclear, prompting whole-genome comparative studies in
      attempts to elucidate this issue. We present the full, annotated genomes of five
      newly isolated representative ST398 strains from five major sequence
      heterogeneity groups of our diverse isolate collection.
AU  - McClure JA
AU  - Zhang K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00473-17.

PMID- 673834
VI  - 5
DP  - 1978
TI  - A restriction enzyme ThaI from the thermophilic mycoplasma Thermoplasma acidophilum.
PG  - 1729-1739
AB  - A type II restriction enzyme (ThaI) has been isolated from the thermophilic
      mycoplasma Thermoplasma acidophilum.  A new method of general application was
      used to determine the DNA sequence cleaved by the enzyme.  ThaI cuts DNA in the
      centre of the sequence CGCG.  Single-stranded DNA is not a substrate.  ThaI
      does not cut T. acidophilum DNA which is presumably modified.  This is the
      first description of a restriction enzyme from a mycoplasma.  Because ThaI is
      easily prepared in large amounts of approximately 105 units per gram of cells,
      it will be a valuable addition to the battery of restriction enzymes used in
      studies of DNA sequences.  It is active at high temperatures and may therefore
      be useful for special purposes requiring more extreme conditions.
AU  - McConnell DJ
AU  - Searcy DG
AU  - Sutcliffe JG
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1978 5: 1729-1739.

PMID- 19276110
VI  - 106
DP  - 2009
TI  - Generation of a nicking enzyme that stimulates site-specific gene conversion from the I-AniI LAGLIDADG homing endonuclease.
PG  - 5099-5104
AB  - Homing endonucleases stimulate gene conversion by generating site-specific DNA double-strand
      breaks that are repaired by homologous recombination.
      These enzymes are potentially valuable tools for targeted gene correction
      and genome engineering. We have engineered a variant of the I-AniI homing
      endonuclease that nicks its cognate target site. This variant contains a
      mutation of a basic residue essential for proton transfer and solvent
      activation in one active site. The cleavage mechanism, DNA-binding
      affinity, and substrate specificity profile of the nickase are similar to
      the wild-type enzyme. I-AniI nickase stimulates targeted gene correction
      in human cells, in cis and in trans, at approximately 1/4 the efficiency
      of the wild-type enzyme. The development of sequence-specific nicking
      enzymes like the I-AniI nickase will facilitate comparative analyses of
      DNA repair and mutagenesis induced by single- or double-strand breaks.
AU  - McConnell SA
AU  - Takeuchi R
AU  - Pellenz S
AU  - Davis L
AU  - Maizels N
AU  - Monnat RJ Jr
AU  - Stoddard BL
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2009 106: 5099-5104.

PMID- 25414513
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Lactococcus lactis Strain AI06, an Endophyte of the Amazonian Acai Palm.
PG  - e01225-14
AB  - We report the genome, in a single chromosome, of Lactococcus lactis strain AI06,  isolated
      from the mesocarp of the acai fruit (Euterpe oleracea) in eastern
      Amazonia, Brazil. This strain is an endophyte of the acai palm and also a
      component of the microbiota of the edible food product.
AU  - McCulloch JA
AU  - de Oliveira VM
AU  - de Almeida PAV
AU  - Perez-Chaparro PJ
AU  - de Almeida LM
AU  - de Vasconcelos JM
AU  - de Oliveira LF
AU  - da Silva DE
AU  - Rogez HL
AU  - Cretenet M
AU  - Mamizuka EM
AU  - Nunes MR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01225-14.

PMID- 26272570
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Staphylococcus aureus FCFHV36, a Methicillin-Resistant Strain Heterogeneously Resistant to Vancomycin.
PG  - e00893-15
AB  - We report here the sequence of the entire chromosome of Staphylococcus aureus strain FCFHV36,
      a methicillin-resistant strain heterogeneously intermediate to
      vancomycin, bearing a type II staphylococcal chromosome cassette mec element
      (SCCmec), belonging to multilocus sequence type (MLST) 105, and isolated from a
      vertebra of a patient with osteomyelitis.
AU  - McCulloch JA
AU  - Silveira AC
AU  - da Costa-Lima-Moraes A
AU  - Perez-Chaparro PJ
AU  - Ferreira SM
AU  - Almeida LM
AU  - d'Azevedo PA
AU  - Mamizuka EM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00893-15.

PMID- 25540352
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Rice Isolate Pseudomonas chlororaphis EA105.
PG  - e01342-14
AB  - Pseudomonas chlororaphis EA105, a strain isolated from rice rhizosphere, has shown
      antagonistic activities against a rice fungal pathogen, and could be
      important in defense against rice blast. We report the draft genome sequence of
      EA105, which is an estimated size of 6.6 Mb.
AU  - McCully LM
AU  - Bitzer AS
AU  - Spence CA
AU  - Bais HP
AU  - Silby MW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01342-14.

PMID- 24459278
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Salmonella enterica Serovar Agona Pulsed-Field Type SAGOXB.0066, Cause of a 2008 Pan-European Outbreak.
PG  - e01219-13
AB  - Salmonella enterica serovar Agona is in the top 10 most common nontyphoidal serovars reported
      in humans in the European Union. Here we report the complete
      genome sequence of an S. enterica serovar Agona isolate, designated 24249, that
      was the cause of a pan-European outbreak in 2008 with 163 confirmed cases
      reported.
AU  - McCusker MP
AU  - Hokamp K
AU  - Buckley JF
AU  - Wall PG
AU  - Martins M
AU  - Fanning S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01219-13.

PMID- Not carried by PubMed...
VI  - 89
DP  - 1989
TI  - A plasmid-encoded restriction-modification system in Mycobacterium avium.
PG  - 167
AB  - We previously described an R-M system in M. avium strain LR25.  This system was
      demonstrated by restriction and host-induced modification of phage JF2.  Curing
      of the plasmids of LR25 produced a strain, LR163, that lacks the R-M system.
      We have now demonstrated the presence of a restriction endonuclease, designated
      MavI, in extracts of LR25 and other M. avium strains.  Cells were grown in
      7H9-Av broth and treated with cycloserine for 16 hr.  Cells were harvested and
      then lysed by sonication.  Debris was removed by centrifugation, and the DNA
      was precipitated with streptomycin sulfate.  The crude lysates were assayed for
      endonuclease activity using various test DNAs.  The digest patterns obtained
      with the extract of LR25 were the same as those produced by XhoI.  Further
      studies showed that MavI cleaves at the same site as XhoI, C^TCGAG.  The enzyme
      was demonstrated in several plasmid-containing strains but was absent from
      LR163.  DNA isolated from the strains having MavI activity ws found to be
      resistant to cleavage by XhoI but sensitive to other endonucleases indicating
      the expected modification.  Modification of some SalI sites was also observed,
      but no corresponding endonuclease activity was detected.
AU  - McDermott PF
AU  - Crawford JT
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1989 89: 167.

PMID- 23814031
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Methicillin-Susceptible Staphylococcus aureus Strain 06BA18369, a Pathogen Associated with Skin and Soft Tissue Infections in Northern  Saskatchewan, Canada.
PG  - e00389-13
AB  - Here, we announce the draft sequence of a representative methicillin-susceptible
      Staphylococcus aureus (MSSA) isolate (06BA18369) whose strain type (spa type
      t311) was commonly isolated from skin and soft tissue coinfections with
      Streptococcus pyogenes. This strain sequence provides insight into a highly
      successful community-associated MSSA strain type.
AU  - McDonald RR
AU  - Golding GR
AU  - Irvine J
AU  - Graham MR
AU  - Tyler S
AU  - Mulvey MR
AU  - Levett PN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00389-13.

PMID- 23814030
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Streptococcus pyogenes Strain 06BA18369, a Human Pathogen Associated with Skin and Soft Tissue Infections in Northern Canada.
PG  - e00387-13
AB  - We report the draft sequence of Streptococcus pyogenes 06BA18369 (emm type 41.2,  sequence
      type 579 [ST579]), isolated from a skin and soft tissue infection (SSTI)
      mixed with Staphylococcus aureus. This genome provides insight into the genetic
      composition of S. pyogenes strains associated with mixed SSTIs.
AU  - McDonald RR
AU  - Golding GR
AU  - Irvine J
AU  - Graham MR
AU  - Tyler S
AU  - Mulvey MR
AU  - Levett PN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00387-13.

PMID- 22628495
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of an Antibiotic-Resistant Propionibacterium acnes Strain,  PRP-38, from the Novel Type IC Cluster.
PG  - 3260-3261
AB  - Propionibacterium acnes, a non-spore-forming, anaerobic Gram-positive bacterium,  is most
      notably recognized for its association with acne vulgaris (I. Kurokawa et
      al., Exp. Dermatol. 18:821-832, 2009). We now present the draft genome sequence
      of an antibiotic-resistant P. acnes strain, PRP-38, isolated from an acne patient
      in the United Kingdom and belonging to the novel type IC cluster.
AU  - McDowell A
AU  - Hunyadkurti J
AU  - Horvath B
AU  - Voros A
AU  - Barnard E
AU  - Patrick S
AU  - Nagy I
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3260-3261.

PMID- 22290972
VI  - 56
DP  - 2012
TI  - Complete Sequence of a Novel 178-Kilobase Plasmid Carrying blaNDM-1 in a Providencia stuartii Strain Isolated in Afghanistan.
PG  - 1673-1679
AB  - In response to global concerns over the spread of the New Delhi metallo-beta-lactamase gene 1,
      bla(NDM-1), a monthly surveillance program was initiated in September 2010. All
      carbapenem-resistant Gram-negative strains forwarded to our facility are screened for this
      gene. To date, 321 carbapenem-resistant isolates, encompassing 11 bacterial species, have been
      tested. In February 2011, two strains of Providencia stuartii, submitted from a military
      hospital in Afghanistan, tested positive for bla(NDM-1). Both strains were identical by
      pulsed-field gel electrophoresis (PFGE). bla(NDM-1) was carried on a large plasmid, pMR0211,
      which was sequenced by emulsion PCR and pyrosequencing. pMR0211 is 178,277 bp in size and
      belongs to incompatibility group A/C. The plasmid consists of a backbone with considerable
      homology to pAR060302 from Escherichia coli, and it retains many of the antibiotic resistance
      genes associated with it. The plasmid also shares common elements with the pNDM-HK plasmid,
      including bla(NDM-1), armA, and sul1. However, gene orientation is reversed, and a 3-kb
      fragment from this region is absent from pMR0211. pMR0211 also contains additional genes,
      including the aminoglycoside-modifying enzyme loci aadA and aac(6'), the quinolone resistance
      gene qnrA, a gene with highest homology to a U32 family peptidase from Shewanella amazonensis,
      and the bla(OXA-10) gene. The finding of this gene in an intrinsically colistin-resistant
      species such as Providencia stuartii is especially worrisome, as it renders the organism
      resistant to nearly every available antibiotic. The presence of multiple insertion sequences
      and transposons flanking the region containing the bla(NDM-1) gene further highlights the
      potential mobility associated with this gene.
AU  - McGann P
AU  - Hang J
AU  - Clifford RJ
AU  - Yang Y
AU  - Kwak YI
AU  - Kuschner RA
AU  - Lesho EP
AU  - Waterman PE
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2012 56: 1673-1679.

PMID- 22210861
VI  - 40
DP  - 2012
TI  - Recognition of dual symmetry by the controller protein C.Esp1396I based on the structure of the transcriptional activation complex.
PG  - 4158-4167
AB  - The controller protein C.Esp1396I regulates the timing of gene expression of the
      restriction-modification (RM) genes of the RM system Esp1396I. The molecular
      recognition of promoter sequences by such transcriptional regulators is poorly
      understood, in part because the DNA sequence motifs do not conform to a
      well-defined symmetry. We report here the crystal structure of the controller
      protein bound to a DNA operator site. The structure reveals how two different
      symmetries within the operator are simultaneously recognized by the homo-dimeric
      protein, underpinned by a conformational change in one of the protein subunits.
      The recognition of two different DNA symmetries through movement of a flexible
      loop in one of the protein subunits may represent a general mechanism for the
      recognition of pseudo-symmetric DNA sequences.
AU  - McGeehan JE
AU  - Ball NJ
AU  - Streeter SD
AU  - Thresh SJ
AU  - Kneale GG
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: 4158-4167.

PMID- 16516922
VI  - 358
DP  - 2006
TI  - Cooperative Binding of the C.AhdI Controller Protein to the C/R Promoter and its Role in Endonuclease Gene Expression.
PG  - 523-531
AB  - The controller (C) proteins of a wide variety of restriction-modification (R-M) systems are
      thought to regulate expression of the endonuclease (R) gene by a genetic switch that ensures
      that methylation precedes endonuclease expression. Previous DNA footprinting experiments with
      C.AhdI have located the binding site upstream of the C and R genes in the AhdI R-M system, and
      the structure of C.AhdI has recently been determined. Here, we provide evidence that the
      binding site can accommodate either one or two dimers of C.AhdI in a concentration-dependent
      manner The dimer binding site is adjacent to the -35 hexamer site required for the interaction
      with RNA polymerase (RNAP); however, co-operative binding of a second dimer blocks this site.
      Optimum DNA binding site sizes for dimer and tetramer formation were determined to be ca 21 bp
      and 34 bp, respectively. The stoichiometry and affinities of relevant DNA-protein complexes
      have been characterised by sedimentation velocity and EMSA using native and mutant promoter
      sequences. Molecular models of the dimer and tetramer complexes have been constructed that are
      consistent with the hydrodynamic data. Our results suggest a mechanism for both positive and
      negative regulation of endonuclease expression, whereby at moderate levels of C.AhdI, the
      protein binds to the promoter as a dimer and stimulates transcription by the interaction with
      RNAP. As the levels of C.AhdI increase further, binding of the second dimer competes with
      RNAP, thus down-regulating transcription of its own gene, and hence that of the endonuclease.
AU  - McGeehan JE
AU  - Papapanagiotou I
AU  - Streeter SD
AU  - Kneale GG
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2006 358: 523-531.

PMID- 14747712
VI  - 60
DP  - 2004
TI  - Crystallization and preliminary X-ray analysis of the controller protein C.Ahdl from Aeromonas hydrophilia.
PG  - 323-325
AB  - Single crystals of purified homodimeric controller protein from Aeromonas hydrophilia (C.AhdI)
      have been grown under several different
      conditions using vapour diffusion. X-ray diffraction data have been
      collected using synchrotron radiation from crystals of both the native
      and a selenomethionine (SeMet) derivative of the protein. The native
      crystal form belongs to space group P2(1) and data were collected to a
      resolution of 2.2 Angstrom. Two crystal forms of the SeMet protein have
      been obtained and were found to belong to space groups P1 and P2(1);
      data have been recorded to 2.0 and 1.7 Angstrom resolution,
      respectively, for the two crystal forms. Three-wavelength MAD data were
      collected to 1.7 Angstrom for the SeMet derivative crystal, which is
      isomorphous with the native P2(1) crystal.
AU  - McGeehan JE
AU  - Streeter S
AU  - Cooper JB
AU  - Mohammed F
AU  - Fox GC
AU  - Kneale GG
PT  - Journal Article
TA  - Acta Crystallogr. D Biol. Crystallogr.
JT  - Acta Crystallogr. D Biol. Crystallogr.
SO  - Acta Crystallogr. D Biol. Crystallogr. 2004 60: 323-325.

PMID- 15713456
VI  - 346
DP  - 2005
TI  - High-resolution crystal structure of the restriction-modification controller protein C.AhdI from Aeromonas hydrophila.
PG  - 689-701
AB  - Restriction/modification (R/M) systems serve to protect the host bacterium from invading
      bacteriophage. The multi-component system includes a methyltransferase, which recognizes and
      methylates a specific DNA sequence, and an endonuclease which recognises the same sequence and
      cleaves within or close to this site. The endonuclease will only cleave DNA that is
      unmethylated at the specific site, thus host DNA is protected while non-host DNA is cleaved.
      However, following DNA replication, expression of the endonuclease must be delayed until the
      host DNA is appropriately methylated. In many R/M systems, this regulation is achieved at the
      transcriptional level via the controller protein, or C-protein.  We have solved the first
      X-ray structure of an R/M controller protein, C.AhdI, to 1.69  resolution using
      selenomethionine MAD. C.AhdI is part of a Type IIH R/M system from the pathogen Aeromonas
      hydrophila. The structure reveals an all-B protein that contains a classical helix-turn-helix
      (HTH) domain and can be assigned to the Xre family of transcriptional regulators. Unlike its
      monomeric structural homologues, an extended helix generates an interface that results in
      dimerisation of the free protein. The dimer is electrostatically polarised and a positively
      charged surface corresponds to the position of the DNA recognition helices of the HTH domain.
      Comparison with the structure of the cI ternary complex suggests that C.AhdI activates
      transcription through direct contact with the 70 subunit of RNA polymerase.
AU  - McGeehan JE
AU  - Streeter S
AU  - Papapanagiotou I
AU  - Fox GC
AU  - Kneale GG
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2005 346: 689-701.

PMID- 18644840
VI  - 36
DP  - 2008
TI  - Structural analysis of the genetic switch that regulates the expression of restriction-modification genes.
PG  - 4778-4787
AB  - Controller (C) proteins regulate the timing of the expression of restriction and modification
      (R-M) genes through a combination of positive and negative feedback circuits. A single dimer
      bound to the operator switches on transcription of the C-gene and the endonuclease gene; at
      higher concentrations, a second dimer bound adjacently switches off these genes. Here we
      report the first structure of a C protein-DNA operator complex, consisting of two C protein
      dimers bound to the native 35 bp operator sequence of the R-M system Esp1396I. The structure
      reveals a role for both direct and indirect DNA sequence recognition. The structure of the DNA
      in the complex is highly distorted, with severe compression of the minor groove resulting in a
      50 degrees bend within each operator site, together with a large expansion of the major groove
      in the centre of the DNA sequence. Cooperative binding between dimers governs the
      concentration-dependent activation-repression switch and arises, in part, from the interaction
      of Glu25 and Arg35 side chains at the dimer-dimer interface. Competition between Arg35 and an
      equivalent residue of the sigma(70) subunit of RNA polymerase for the Glu25 site underpins the
      switch from activation to repression of the endonuclease gene.
AU  - McGeehan JE
AU  - Streeter SD
AU  - Thresh SJ
AU  - Ball N
AU  - Ravelli RB
AU  - Kneale GG
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2008 36: 4778-4787.

PMID- 21440553
VI  - 409
DP  - 2011
TI  - Structural Analysis of a Novel Class of R-M Controller Proteins: C.Csp231I from Citrobacter sp. RFL231.
PG  - 177-188
AB  - Controller proteins play a key role in the temporal regulation of gene expression in bacterial
      restriction-modification (R-M) systems and are
      important mediators of horizontal gene transfer. They form the basis of a
      highly cooperative, concentration-dependent genetic switch involved in
      both activation and repression of R-M genes. Here we present biophysical,
      biochemical, and high-resolution structural analysis of a novel class of
      controller proteins, exemplified by C.Csp231I. In contrast to all
      previously solved C-protein structures, each protein subunit has two extra
      helices at the C-terminus, which play a large part in maintaining the
      dimer interface. The DNA binding site of the protein is also novel, having
      largely AAAA tracts between the palindromic recognition half-sites,
      suggesting tight bending of the DNA. The protein structure shows an
      unusual positively charged surface that could form the basis for wrapping
      the DNA completely around the C-protein dimer.
AU  - McGeehan JE
AU  - Streeter SD
AU  - Thresh SJ
AU  - Taylor JE
AU  - Shevtsov MB
AU  - Kneale GG
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2011 409: 177-188.

PMID- 15784532
VI  - 73
DP  - 2005
TI  - Cloning and sequencing of a genomic island found in the Brazilian purpuric fever clone of Haemophilus influenzae biogroup aegyptius.
PG  - 1927-1938
AB  - A genomic island was identified in the Haemophilus influenzae biogroup
      aegyptius Brazilian purpuric fever (BPF) strain F3031. This island, which
      was also found in other BPF isolates, could not be detected in non-BPF
      biogroup aegyptius strains or in nontypeable or typeable H. influenzae
      strains, with the exception of a region present in the type b Eagan
      strain. This 34,378-bp island is inserted, in reference to H. influenzae
      Rd KW20, within a choline transport gene and contains a mosaic structure
      of Mu-like prophage genes, several hypothetical genes, and genes
      potentially encoding an Erwinia carotovora carotovoricin Er-like
      bacteriocin. The product of the tail fiber ORF in the bacteriocin-like
      region shows a hybrid structure where the C terminus is similar to an H.
      influenzae phage HP1 tail protein implicating this open reading frame in
      altering host specificity for a putative bacteriocin. Significant synteny
      is seen in the entire genomic island with genomic regions from Salmonella
      enterica subsp. enterica serovar Typhi CT18, Photorhabdus luminescens
      subsp. laumondii TT01, Chromobacterium violaceum, and to a lesser extent
      Haemophilus ducreyi 35000HP. In a previous work, we isolated several
      BPF-specific DNA fragments through a genome subtraction procedure, and we
      have found that a majority of these fragments map to this locus. In
      addition, several subtracted fragments generated from an independent
      laboratory by using different but related strains also map to this island.
      These findings underscore the importance of this BPF-specific chromosomal
      region in explaining some of the genomic differences between highly
      invasive BPF strains and non-BPF isolates of biogroup aegyptius.
AU  - McGillivary G
AU  - Tomaras AP
AU  - Rhodes ER
AU  - Actis LA
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2005 73: 1927-1938.

PMID- 18582973
VI  - 75
DP  - 2008
TI  - Isolation and analysis of mRNA from environmental microbial communities.
PG  - 172-176
AB  - The advent of metagenomics has revealed that our planet harbors millions
      of previously undiscovered microbial species. However, functional insights
      into the activities of microbial communities cannot easily be obtained
      using metagenomics. Using transcriptional analyses to study microbial gene
      functions is currently problematic due to difficulties working with
      unstable microbial mRNA as a small fraction of total cellular RNA. Current
      techniques can be expensive and time consuming, and still result in
      significant levels of rRNA contamination. We have adapted techniques to
      rapidly isolate high high-quality RNA from environmental samples and
      developed a simple method for specific isolation of mRNA by size
      separation. This new technique was evaluated by constructing cDNA
      libraries directly from uncultured environmental microbial communities,
      including agricultural soil samples, aquatic flocculants, organic
      composts, mammalian oral and faecal samples, and wastewater sludge. The
      sequencing of a fraction of these cDNA clones revealed a high degree of
      novelty, demonstrating the potential of this approach to capture a large
      number of unique transcripts directly from the environment. To our
      knowledge, this is the first study that uses gel electrophoresis to
      isolate mRNA from microbial communities. We conclude that this method
      could be used to provide insights into the microbial 'metatranscriptome'
      of entire microbial communities. Coupled with high-throughput sequencing
      or the construction of cDNA microarrays, this approach will provide a
      useful tool to study the transcriptional activities of microorganisms,
      including those of entire microbial communities and of non-culturable
      microorganisms.
AU  - McGrath KC
AU  - Thomas-Hall SR
AU  - Cheng CT
AU  - Leo L
AU  - Alexa A
AU  - Schmidt S
AU  - Schenk PM
PT  - Journal Article
TA  - J. Microbiol. Methods
JT  - J. Microbiol. Methods
SO  - J. Microbiol. Methods 2008 75: 172-176.

PMID- 10223975
VI  - 65
DP  - 1999
TI  - Molecular characterization of a phage-encoded resistance system in Lactococcus lactis.
PG  - 1891-1899
AB  - A specific fragment of the genome of Tuc2009, a temperate lactococcal bacteriophage, was shown
      to contain several open reading frames, whose deduced protein products exhibited similarities
      to proteins known to be involved in DNA replication and modification.  In this way, a putative
      single-stranded binding protein, replisome organizer protein, topoisomerase I, and a methylase
      were identified.  When the genetic information coding for the putative replisome organizer
      protein of Tuc2009, Rep2009, was supplied on a high-copy-number plasmid vector, it was shown
      to confer a phage-encoded resistance (Per) phenotype on its lactococcal host UC509.9.  The
      presence of this recombinant plasmid was shown to cause a marked reduction in Tuc2009 DNA
      replication, suggesting that the observed phage resistance was due to titration of a factor,
      or factors, required for Tuc2009 DNA replication.  Further experiments delineated the phage
      resistance-conferring region to a 160-bp fragment rich in direct repeats.  Gel retardation
      experiments, which indicated a protein-DNA interaction between this 160-bp fragment and the
      Rep2009 protein, were performed.  UC509.9 strains harboring plasmids with randomly mutated
      versions of this fragment were shown to display a variable phage resistance phenotype,
      depending on the position of the mutations.
AU  - McGrath S
AU  - Seegers JFML
AU  - Fitzgerald GF
AU  - van Sinderen D
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1999 65: 1891-1899.

PMID- 6993844
VI  - 178
DP  - 1980
TI  - Isolation and characterization of Dam+ revertants and suppressor mutations that modify secondary phenotypes of dam-3 strains of Escherichia coli K-12.
PG  - 309-315
AB  - Bacteria mutant in the dam (DNA adenine methylation) gene and in either recA or recB or recC
      genes are inviable (Virm- phenotype). From crosses between dam-3 bacteria and recA1 or recB21
      recC22 strains, Vrm+ recombinants were recovered. Among these recombinants, Dam+ revertants
      were present which did not show the phenotypes normally associated with dam-3 bacteria. Three
      classes of indirectly suppressed strains (dam 3 genotype) were also recovered which showed
      alterations in the secondary phenotypes normally associated with dam-3 bacteria. These strains
      contained a second unlinked mutation in either mutL or mutS or sin. In addition, mutation in
      either sbcA or sbcB supresses the Vrm-phenotype of dam-3 recB21 recC22 strains.
AU  - McGraw BR
AU  - Marinus MG
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1980 178: 309-315.

PMID- 26203335
VI  - 10
DP  - 2015
TI  - High quality draft genome sequence of Meganema perideroedes str. Gr1(T) and a proposal for its reclassification to the family Meganemaceae fam. nov.
PG  - 23
AB  - Meganema perideroedes Gr1(T) is a filamentous bacterium isolated from an activated sludge
      wastewater treatment plant where it is implicated in poor sludge
      settleability (bulking). M. perideroedes is the sole described species of the
      genus Meganema and of the proposed novel family 'Meganemaceae'. Here we describe
      the features of the type strain Gr1(T) along with its annotated genome sequence.
      The 3,409,949 bp long draft genome consists of 22 scaffolds with 3,033
      protein-coding and 59 RNA genes and is a part of Genomic Encyclopedia of Type
      Strains, Phase I: the one thousand microbial genomes KMG project. Notably, genome
      annotation indicated the potential for facultative methylotrophy. However, the
      ability to utilize methanol as a carbon source could not be empirically
      demonstrated for the type strain or for in situ Meganema spp. strains.
AU  - McIlroy SJ
AU  - Lapidus A
AU  - Thomsen TR
AU  - Han J
AU  - Haynes M
AU  - Lobos E
AU  - Huntemann M
AU  - Pati A
AU  - Ivanova NN
AU  - Markowitz V
AU  - Verbarg S
AU  - Woyke T
AU  - Klenk HP
AU  - Kyrpides N
AU  - Nielsen PH
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 23.

PMID- 17442750
VI  - 104
DP  - 2007
TI  - The genome of Syntrophus aciditrophicus: Life at the thermodynamic limit of microbial growth.
PG  - 7600-7605
AB  - Biochemically, the syntrophic bacteria constitute the missing link in our understanding of
      anaerobic flow of carbon in the biosphere. The completed genome sequence of Syntrophus
      aciditrophicus SB, a model fatty acid- and aromatic acid-degrading syntrophic bacterium,
      provides a glimpse of the composition and architecture of the electron transfer and
      energy-transducing systems needed to exist on marginal energy economies of a syntrophic
      lifestyle. The genome contains 3,179,300 base pairs and 3,169 genes where 1,618 genes were
      assigned putative functions. Metabolic reconstruction of the gene inventory revealed that most
      biosynthetic pathways of a typical Gram-negative microbe were present. A distinctive feature
      of syntrophic metabolism is the need for reverse electron transport; the presence of a unique
      Rnf-type ion-translocating electron transfer complex, menaquinone, and membrane-bound Fe-S
      proteins with associated heterodisulfide reductase domains suggests mechanisms to accomplish
      this task. Previously undescribed approaches to degrade fatty and aromatic acids, including
      multiple AMP-forming CoA ligases and acyl-CoA synthetases seem to be present as ways to form
      and dissipate ion gradients by using a sodium-based energy strategy. Thus, S. aciditrophicus,
      although nutritionally self-sufficient, seems to be a syntrophic specialist with limited
      fermentative and respiratory metabolism. Genomic analysis confirms the S. aciditrophicus
      metabolic and regulatory commitment to a nonconventional mode of life compared with our
      prevailing understanding of microbiology.
AU  - McInerney MJ
AU  - Rohlin L
AU  - Mouttaki H
AU  - Kim U
AU  - Krupp RS
AU  - Rios-Hernandez L
AU  - Sieber J
AU  - Struchtemeyer CG
AU  - Bhattacharyya A
AU  - Campbell JW
AU  - Gunsalus RP
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2007 104: 7600-7605.

PMID- 7705636
VI  - 139
DP  - 1995
TI  - Transduction, restriction and recombination patterns in Escherichia coli.
PG  - 35-43
AB  - Chromosomal DNA from several Escherichia coli reference (ECOR) strains was transducted by
      bacteriophage P1 into E. coli strain K12 W3110 trpA33. Recombination patterns of the
      transductants were determined by restriction fragment length polymorphism over a 40-kb region
      centering on a single marker (trpA+) in the tryptophan operon. These experiments demonstrate
      that transduction between different strains of E. coli can result in recombinational
      replacements that are small in comparison to the entrant molecule (replacements average 8-14
      kb, whereas P1 packages approximately 100 kb) often in a series of discrete segments. The
      transduction patterns generated resemble the natural mosaic sequence patterns of the ECOR
      strains described in previous work. Extensive polymorphisms in the restriction-modification
      systems of the ECOR strains are a possible explanation for the sequence patterns in nature. To
      test this possibility, two transductants were back-transduced into strain K12 W3110 trpA33.
      The resulting patterns were strikingly different from the original transductions. The size of
      the replacements was greater, and no multiple replacements were observed, suggesting a role
      for restriction-modification systems in the transduction patterns and perhaps for the mosaic
      sequence patterns in nature.
AU  - McKane M
AU  - Milkman R
PT  - Journal Article
TA  - Genetics
JT  - Genetics
SO  - Genetics 1995 139: 35-43.

PMID- 16348036
VI  - 55
DP  - 1989
TI  - Localization of separate genetic loci for reduced sensitivity towards small isometric-headed bacteriophage sk1 and prolate-headed bacteriophage c2 on pGBK17 from Lactococcus lactis subsp. lactis KR2.
PG  - 2702-2709
AB  - The mechanism of reduced sensitivity to the small isometric-headed bacteriophage sk1 encoded
      on a 19-kilobase (kb) HpaII fragment subcloned from pKR223 of Lactococcus lactis subsp. lactis
      KR2 was examined. The reduced sensitivity to phage sk1 was due to a modest
      restriction/modification (R/M) system that was not active against prolate-headed phage c2. The
      genetic loci for the R/M system against sk1 and the abortive phage infection (Abi) mechanism
      effective against phage c2 were then localized by restriction mapping, subcloning, and
      deletion analysis. The restriction gene was localized to a region of a 2.7-kb EcoRV fragment
      and included an EcoRI site within that fragment. The modification gene was found to be
      physically separate from the restriction gene and was present on a 1.75-kb BstEII-XbaI
      fragment. The genetic locus for the Abi phenotype against phage c2 was localized to a region
      containing a 1.3-kb EcoRI fragment. Attempts to clone the c2 Abi mechanism independent of the
      sk1 R/M system were unsuccessful, suggesting that expression of the abi genes required
      sequences upstream of the modification gene. Some pGBK17 (vector pGB301 plus a 19-kb HpaII
      insert fragment) transformants exhibited the R/M system against phage sk1 but lost the Abi
      mechanism against phage c2. These transformants contained a 1.2-1.3-kb insertion in the Abi
      region. The data identified genetic loci on a cloned 19-kb HpaII fragment responsible for
      restriction activity and for modification activity against a small isometric-headed phage and
      for Abi activity against prolate-headed phage c2. A putative insertion element was also found
      to inactivate the abi gene(s).
AU  - McKay LL
AU  - Bohanon MJ
AU  - Polzin KM
AU  - Rule PL
AU  - Baldwin KA
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1989 55: 2702-2709.

PMID- 22889062
VI  - 168
DP  - 2013
TI  - Inhibition of Yersinia pestis DNA adenine methyltransferase in vitro by a stibonic acid compound: identification of a potential novel class of antimicrobial agents.
PG  - 172-188
AB  - Background and Purpose Multiple antibiotic resistant strains of plague are emerging, driving a
      need for the development of novel antibiotics
      effective against Yersinia pestis. DNA adenine methylation regulates
      numerous fundamental processes in bacteria and alteration of DNA
      adenine methlytransferase (Dam) expression is attenuating for several
      pathogens, including Y. pestis. The lack of a functionally similar
      enzyme in humans makes Dam a suitable target for development of novel
      therapeutics for plague. Experimental Approach Compounds were evaluated
      for their ability to inhibit Dam activity in a high-throughput
      screening assay. DNA was isolated from Yersinia grown in the presence
      of lead compounds and restricted to determine the effect of inhibitors
      on DNA methylation. Transcriptional analysis was undertaken to
      determine the effect of an active inhibitor on virulence-associated
      phenotypes. Key Results We have identified a series of aryl stibonic
      acids which inhibit Dam in vitro. The most active,
      4-stibonobenzenesulfonic acid, exhibited a competitive mode of
      inhibition with respect to DNA and a Ki of 6.46 nM. One compound was
      found to inhibit DNA methylation in cultured Y. pestis. The effects of
      this inhibition on the physiology of the cell were widespread, and
      included altered expression of known virulence traits, including iron
      acquisition and Type III secretion. Conclusions and Implications We
      have identified a novel class of potent Dam inhibitors. Treatment of
      bacterial cell cultures with these inhibitors resulted in a decrease in
      DNA methylation. Expression of virulence factors was affected,
      suggesting these inhibitors may attenuate bacterial infectivity and
      function as antibiotics.
AU  - McKelvie JC
AU  - Richards MI
AU  - Harmer JE
AU  - Milne TS
AU  - Roach PL
AU  - Oyston PCF
PT  - Journal Article
TA  - Br. J. Pharmacol.
JT  - Br. J. Pharmacol.
SO  - Br. J. Pharmacol. 2013 168: 172-188.

PMID- 6281441
VI  - 154
DP  - 1982
TI  - Cleavage of mammalian repetitive deoxyribonucleic acids by a mammalian site-specific endodeoxyribonuclease.
PG  - 379-384
AB  - We probed the structure of mammalian repetitive DNAs with a site-specific
      mammalian endodeoxyribonuclease, which we recently identified, and which
      apparently represents a common enzyme activity among the mammals (McKenna et
      al., 1981).  With several of the DNAs (e.g. mouse satellite, guinea pig
      beta-satellite, variable repeated spacer DNA from mouse ribosomal genes and
      primate alphoid sequences), the endonuclease activity gave highly specific
      cleavage patterns when the digestion products were analyzed by gel
      electrophoresis.  These patterns were not always identical to those produced by
      microbial restriction enzymes.  However, in other cases (e.g. bovid and caprid
      satellites and guinea pig alpha-satellite) the repetitive DNAs appeared to be
      degraded randomly.  Thus, the mammalian enzyme reveals structural features of
      the repetitive sequences that are not rendered immediately obvious by microbial
      restriction enzyme analysis.  Evidence from mapping data presented here
      suggests that the mammalian site-specific endonucleases are not sequence
      specific but have special affinity for imperfect or hyphenated palindromic
      sequences in repetitive DNAs and in other eukaryrotic DNA sequences.
AU  - McKenna WG
AU  - Brown FL
AU  - Musich PR
AU  - Maio JJ
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1982 154: 379-384.

PMID- 6263915
VI  - 256
DP  - 1981
TI  - Purification and properties of a mammalian endonuclease showing site-specific cleavage of DNA.
PG  - 6435-6443
AB  - An endonuclease activity has been identified from a variety of mammalian
      sources which cleaves native viral DNAs (adenovirus-2, SV40) and mammalian
      repetitive DNA to yield specific, double-stranded DNA segments when the
      cleavage products are analyzed by gel electrophoresis.  The activity has been
      purified 750-fold from bull testes by ammonium sulfate precipitations and ion
      exchange chromatography.  The enzyme has a pH optimum of 7.5 and shows an
      absolute requirement for Mg2+ or Mn2+ and reducing agents in the reaction
      buffer.  It is strongly inhibited by salt and stimulated by glycerol or
      dimethyl sulfoxide.  By glycerol gradient analysis it has a sedimentation
      coefficient of 4.5 S (65,000 daltons if globular) and it may exist as a dimer
      of 6.4 S (130,000 daltons).  The enzyme liberates 3'-OH and 5'-P termini in its
      cleavage of mammalian viral and repetitive DNAs and there is a clear
      nonrandomness in the 5'-terminal nucleotides: purines and 5'-pG in particular
      predominate.  The similarities between the mammalian endonuclease activity and
      the bacterial restriction enzymes may be superficial.  By gel electrophoresis
      the mammalian endonuclease produces its most characteristic series of segments
      with viral DNAs in the molecular weight range of 150,000 to 1,500.000  These
      are true double-stranded intermediate products in the cleavage of high
      molecular weight DNA but they are not end products in the reaction as they
      would be in the case of the bacterial restriction enzymes.  With time, the
      endonuclease degrades viral DNA to shorter and shorter segments without
      releasing acid-soluble nucleotides at any stage in the digestion and the final
      end products are about 120 base pairs long.  The enzyme degrades both double-
      and single-stranded DNA endonucleolytically though it shows site specificity
      (production of discrete segments upon gel electrophoresis) only with the
      double-stranded DNA substrates.
AU  - McKenna WG
AU  - Maio JJ
AU  - Brown FL
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1981 256: 6435-6443.

PMID- 27198022
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Enterococcus faecium ATCC 700221.
PG  - e00386-16
AB  - We report the complete genome sequence of a vancomycin-resistant isolate of Enterococcus
      faecium derived from human feces. The genome comprises one
      chromosome of 2.9 Mb and three plasmids. The strain harbors a plasmid-borne
      vanA-type vancomycin resistance locus and is a member of multilocus sequencing
      type (MLST) cluster ST-17.
AU  - McKenney PT
AU  - Ling L
AU  - Wang G
AU  - Mane S
AU  - Pamer EG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00386-16.

PMID- 24104751
VI  - 31
DP  - 2013
TI  - DREAMing of a patent-free human genome for clinical sequencing.
PG  - 884-887
AB  - Can methylation be the key to challenging the interpretation of existing gene patent claims?
      And can a novel PCR method be used to enable the sequencing of hundreds of genes?  The case
      for the perils of gene patents and the negative impact of a profit motive in scientific
      endeavors has been made.  Often, gene patent discussions will conflate economic and ethical
      concerns while failing to properly define the scope of property or the influence of profit
      motivations.  In an attempt to untangle these two topics, we review the impact of methylation
      on the scope of gene patent property rights and suggest a simple PCR strategy that may
      challenge the interpretation of many patent claims still in force after the US Supreme
      Court's decision in Associaton for Moleuclar Pathology v. Mayriad Genetics.  We also offer an
      alternatie economic perspective on profit motivation and its impact on the ethics of gene
      patents.
AU  - McKernan KJ
AU  - Spangler J
AU  - Helbert Y
AU  - Zhang L
AU  - Tadigotla V
PT  - Journal Article
TA  - Nat. Biotechnol.
JT  - Nat. Biotechnol.
SO  - Nat. Biotechnol. 2013 31: 884-887.

PMID- 2827747
VI  - 26
DP  - 1987
TI  - Effects of functional group changes in the EcoRI recognition site on the cleavage reaction catalyzed by the endonuclease.
PG  - 7238-7245
AB  - Oligodeoxynucleotides have been prepared that contain changes in the functional
      group pattern present in the EcoRI recognition site.  These changes involve
      functional group deletions, functional group reversals, and displaced
      functional groups.  Steady-state kinetic parameters have been used to
      characterize the interaction of these modified recognition sites with the EcoRI
      endonuclease.  Changes in the functional group pattern have varying effects
      upon the cleavage reaction.  Both the exocyclic amino groups of the two adenine
      residues and the methyl groups of the thymine residues appear to interact with
      the endonuclease quite differently.  In both cases efficient catalysis was
      observed when these functional groups were present at the outer dA-dT base
      pair.  Selectivity was decreased by over an order of magnitude largely via
      increases in Km when these functional groups were deleted.  Similar
      modifications at the inner dA-dT base pair did not alter the kinetic parameters
      significantly from those observed with the native sequence.  Addition of an
      amino group to the minor groove at the outer dA-dT base pair resulted in a
      modified recognition site that interacted with the enzyme, on the basis of
      observed competitive inhibition kinetics, but was not cleaved.
AU  - McLaughlin LW
AU  - Benseler F
AU  - Graeser E
AU  - Piel N
AU  - Scholtissek S
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1987 26: 7238-7245.

PMID- 24407632
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Clostridium mangenotii TR, Isolated from the Fecal Material of a Timber Rattlesnake.
PG  - e01107-13
AB  - Here, we report the draft genome sequence of Clostridium mangenotii strain TR, which was
      isolated from the fecal material of a timber rattlesnake. This
      bacterium is nonpathogenic but contains 68 genes involved in virulence, disease,
      and defense.
AU  - McLaughlin RW et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01107-13.

PMID- 26847892
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Actinomyces odontolyticus subsp. actinosynbacter Strain  XH001, the Basibiont of an Oral TM7 Epibiont.
PG  - e01685-15
AB  - Here, we present the draft genome sequence of Actinomyces odontolyticus subsp. actinosynbacter
      strain XH001, isolated from the human oral cavity. Uniquely, it
      was discovered as a host bacterium to the ultrasmall epibiont TM7x, which is the
      first cultivated member of 'Candidatus Saccharibacteria' (formerly candidate
      phylum TM7).
AU  - McLean JS
AU  - Liu Q
AU  - Bor B
AU  - Bedree JK
AU  - Cen L
AU  - Watling M
AU  - To TT
AU  - Bumgarner RE
AU  - He X
AU  - Shi W
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01685-15.

PMID- 26701081
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of 'Candidatus Bacteroides periocalifornicus,' a New Member of the Bacteriodetes Phylum Found within the Oral Microbiome of Periodontitis  Patients.
PG  - e01485-15
AB  - Here we present the draft genome of a distantly related member within the phylum
      Bacteriodetes, 'Candidatus Bacteroides periocalifornicus.' The draft genome
      sequence was assembled with metagenomic data from a patient with periodontitis.
      The closest relative has less than 68% average nucleic identity, supporting a
      novel family within Bacteriodetes.
AU  - McLean JS
AU  - Liu Q
AU  - Thompson J
AU  - Edlund A
AU  - Kelley S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01485-15.

PMID- 23846274
VI  - 1
DP  - 2013
TI  - Genome Sequence of Lactobacillus sakei subsp. sakei LS25, a Commercial Starter Culture Strain for Fermented Sausage.
PG  - e00475-13
AB  - Lactobacillus sakei is a lactic acid bacterium associated primarily with fermented meat and
      fish. Here, we present the draft genome sequence of L. sakei
      subsp. sakei strain LS25, a commercial starter culture strain for fermented
      sausage.
AU  - McLeod A
AU  - Brede DA
AU  - Rud I
AU  - Axelsson L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00475-13.

PMID- 17030794
VI  - 103
DP  - 2006
TI  - The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse.
PG  - 15582-15587
AB  - Rhodococcus sp. RHA1 (RHA1) is a potent polychlorinated biphenyl-degrading soil actinomycete
      that catabolizes a wide range of compounds and
      represents a genus of considerable industrial interest. RHA1 has one of
      the largest bacterial genomes sequenced to date, comprising 9,702,737 bp
      (67% G+C) arranged in a linear chromosome and three linear plasmids. A
      targeted insertion methodology was developed to determine the telomeric
      sequences. RHA1's 9,145 predicted protein-encoding genes are exceptionally
      rich in oxygenases (203) and ligases (192). Many of the oxygenases occur
      in the numerous pathways predicted to degrade aromatic compounds (30) or
      steroids (4). RHA1 also contains 24 nonribosomal peptide synthase genes,
      six of which exceed 25 kbp, and seven polyketide synthase genes, providing
      evidence that rhodococci harbor an extensive secondary metabolism. Among
      sequenced genomes, RHA1 is most similar to those of nocardial and
      mycobacterial strains. The genome contains few recent gene duplications.
      Moreover, three different analyses indicate that RHA1 has acquired fewer
      genes by recent horizontal transfer than most bacteria characterized to
      date and far fewer than Burkholderia xenovorans LB400, whose genome size
      and catabolic versatility rival those of RHA1. RHA1 and LB400 thus appear
      to demonstrate that ecologically similar bacteria can evolve large genomes
      by different means. Overall, RHA1 appears to have evolved to
      simultaneously catabolize a diverse range of plant-derived compounds in an
      O(2)-rich environment. In addition to establishing RHA1 as an important
      model for studying actinomycete physiology, this study provides critical
      insights that facilitate the exploitation of these industrially important
      microorganisms.
AU  - McLeod MP et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2006 103: 15582-15587.

PMID- 19506028
VI  - 37
DP  - 2009
TI  - Extensive DNA mimicry by the ArdA anti-restriction protein and its role in the spread of antibiotic resistance.
PG  - 4887-4897
AB  - The ardA gene, found in many prokaryotes including important pathogenic species, allows
      associated mobile genetic elements to evade the ubiquitous
      Type I DNA restriction systems and thereby assist the spread of resistance
      genes in bacterial populations. As such, ardA contributes to a major
      healthcare problem. We have solved the structure of the ArdA protein from
      the conjugative transposon Tn916 and find that it has a novel extremely
      elongated curved cylindrical structure with defined helical grooves. The
      high density of aspartate and glutamate residues on the surface follow a
      helical pattern and the whole protein mimics a 42-base pair stretch of
      B-form DNA making ArdA by far the largest DNA mimic known. Each monomer of
      this dimeric structure comprises three alpha-beta domains, each with a
      different fold. These domains have the same fold as previously determined
      proteins possessing entirely different functions. This DNA mimicry
      explains how ArdA can bind and inhibit the Type I restriction enzymes and
      we demonstrate that 6 different ardA from pathogenic bacteria can function
      in Escherichia coli hosting a range of different Type I restriction
      systems.
AU  - McMahon SA
AU  - Roberts GA
AU  - Johnson KA
AU  - Cooper LP
AU  - Liu H
AU  - White JH
AU  - Carter LG
AU  - Sanghvi B
AU  - Oke M
AU  - Walkinshaw MD
AU  - Blakely GW
AU  - Naismith JH
AU  - Dryden DT
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: 4887-4897.

PMID- 28082499
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of 15 Staphylococcus aureus Isolates Recovered from Raw Milk and Associated Milk Filters from Victoria, Australia.
PG  - e01463-16
AB  - This study describes draft whole genomes of 15 Staphylococcus aureus isolates from dairy farms
      located in Victoria, Australia. Two novel sequence types (ST3183
      and ST3184) were identified among these isolates.
AU  - McMillan K
AU  - Allnutt TR
AU  - Fox EM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01463-16.

PMID- 22689239
VI  - 194
DP  - 2012
TI  - Genome Sequence of Listeria monocytogenes 07PF0776, a Cardiotropic Serovar 4b Strain.
PG  - 3552
AB  - Listeria monocytogenes is a food-borne bacterial pathogen commonly associated with serious
      invasive infections of the central nervous system or of the
      developing fetus. We present the genome sequence of Listeria monocytogenes
      07PF0776, a serovar 4b isolate from a human myocardial abscess that exhibits
      enhanced invasion of cardiac tissue.
AU  - McMullen PD
AU  - Gillaspy AF
AU  - Gipson J
AU  - Bobo LD
AU  - Skiest DJ
AU  - Freitag NE
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3552.

PMID- 19893622
VI  - 5
DP  - 2009
TI  - Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides.
PG  - E1000714
AB  - Vinyl chloride (VC) is a human carcinogen and widespread priority
      pollutant. Here we report the first, to our knowledge, complete genome
      sequences of microorganisms able to respire VC, Dehalococcoides sp.
      strains VS and BAV1. Notably, the respective VC reductase encoding genes,
      vcrAB and bvcAB, were found embedded in distinct genomic islands (GEIs)
      with different predicted integration sites, suggesting that these genes
      were acquired horizontally and independently by distinct mechanisms. A
      comparative analysis that included two previously sequenced
      Dehalococcoides genomes revealed a contextually conserved core that is
      interrupted by two high plasticity regions (HPRs) near the Ori. These HPRs
      contain the majority of GEIs and strain-specific genes identified in the
      four Dehalococcoides genomes, an elevated number of repeated elements
      including insertion sequences (IS), as well as 91 of 96 rdhAB, genes that
      putatively encode terminal reductases in organohalide respiration. Only
      three core rdhA orthologous groups were identified, and only one of these
      groups is supported by synteny. The low number of core rdhAB, contrasted
      with the high rdhAB numbers per genome (up to 36 in strain VS), as well as
      their colocalization with GEIs and other signatures for horizontal
      transfer, suggests that niche adaptation via organohalide respiration is a
      fundamental ecological strategy in Dehalococccoides. This adaptation has
      been exacted through multiple mechanisms of recombination that are mainly
      confined within HPRs of an otherwise remarkably stable, syntenic,
      streamlined genome among the smallest of any free-living microorganism.
AU  - McMurdie PJ
AU  - Behrens SF
AU  - Muller JA
AU  - Goke J
AU  - Ritalahti KM
AU  - Wagner R
AU  - Goltsman E
AU  - Lapidus A
AU  - Holmes S
AU  - Loffler FE
AU  - Spormann AM
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2009 5: E1000714.

PMID- 24912189
VI  - 111
DP  - 2014
TI  - Control of catalytic efficiency by a coevolving network of catalytic and noncatalytic residues.
PG  - E2376-E2383
AB  - The active sites of enzymes consist of residues necessary for catalysis and structurally
      important noncatalytic residues that together maintain the architecture and function of the
      active site. Examples of evolutionary interactions between catalytic and non-catalytic
      residues have been difficult to define and experimentally validate due to a general
      intolerance of these residues to substitution. Here, using computational methods to predict
      coevolving residues, we identify a network of positions consisting of two catalytic
      metal-binding residues and two adjacent noncatalytic residues in LAGLIDADG homing
      endonucleases (LHEs). Distinct combinations of the four residues in the network map to
      distinct LHE subfamilies, with a striking distribution of the metal-binding Asp (D) and Glu
      (E) residues. Mutation of these four positions in three LHEs-I-LtrI, I-OnuI, and
      I-HjeMI-indicate that the combinations of residues tolerated are specific to each enzyme.
      Kinetic analyses under single-turnover conditions revealed that I-LtrI activity could be
      modulated over an similar to 100-fold range by mutation of residues in the coevolving network.
      I-LtrI catalytic site variants with low activity could be rescued by compensatory mutations at
      adjacent noncatalytic sites that restore an optimal coevolving network and vice versa. Our
      results demonstrate that LHE activity is constrained by an evolutionary barrier of residues
      with strong context-dependent effects. Creation of optimal coevolving active-site networks is
      therefore an important consideration in engineering of LHEs and other enzymes.
AU  - McMurrough TA
AU  - Dickson RJ
AU  - Thibert SMF
AU  - Gloor GB
AU  - Edgell DR
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2014 111: E2376-E2383.

PMID- 12202767
VI  - 30
DP  - 2002
TI  - Characterisation of site-biased DNA methyltransferases: specificity, affinity and subsite relationships.
PG  - 3818-3830
AB  - DNA methylation is now seen as a primary signal in the cell for mediating transcriptional
      repression through chromatin formation. The construction and evaluation of enzymes capable of
      influencing this process in vivo is therefore of significant interest. We have fused the
      C5-cytosine DNA methyltransferases, M.HhaI and M.HpaII, which both methylate 4 bp sequences
      containing a CpG dinucleotide, to a three zinc finger protein recognising a 9 bp DNA sequence.
      DNA methylation analyses demonstrate specific DNA methylation by both enzymes at target sites
      comprising adjacent methyltransferase and zinc finger subsites, targeted M.HpaII being the
      most specific. Binding analysis of the targeted M.HpaII enzyme reveals an 8-fold preference
      for binding to its target site, compared to binding to a zinc finger site alone, and an
      18-fold preference over binding to a methyltransferase site alone, thereby demonstrating
      enhanced binding by the fusion protein, compared to its component proteins. Both DNA binding
      and methylation are specific for the target site up to separations of approximately 40 bp
      between the zinc finger and methyltransferase subsites. Ex vivo plasmid methylation
      experiments are also described that demonstrate targeted methylation. These targeted enzymes,
      however, are shown to be not fully mono-functional, retaining a significant non-targeted
      activity most evident at elevated protein concentrations.
AU  - McNamara AR
AU  - Hurd PJ
AU  - Smith AEF
AU  - Ford KG
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2002 30: 3818-3830.

PMID- 22030749
VI  - 3
DP  - 2011
TI  - The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins.
PG  - 106RA106
AB  - Understanding how the human gut microbiota and host are affected by probiotic bacterial
      strains requires carefully controlled studies in humans and in mouse models of the gut
      ecosystem where potentially confounding variables that are difficult to control in humans can
      be constrained. Therefore, we characterized the fecal microbiomes and metatranscriptomes of
      adult female monozygotic twin pairs through repeated sampling 4 weeks before, 7 weeks during,
      and 4 weeks after consumption of a commercially available fermented milk product (FMP)
      containing a consortium of Bifidobacterium animalis subsp. lactis, two strains of
      Lactobacillus delbrueckii subsp. bulgaricus, Lactococcus lactis subsp. cremoris, and
      Streptococcus thermophilus. In addition, gnotobiotic mice harboring a 15-species model human
      gut microbiota whose genomes contain 58,399 known or predicted protein-coding genes were
      studied before and after gavage with all five sequenced FMP strains. No significant changes in
      bacterial species composition or in the proportional representation of genes encoding known
      enzymes were observed in the feces of humans consuming the FMP. Only minimal changes in
      microbiota configuration were noted in mice after single or repeated gavage with the FMP
      consortium. However, RNA-Seq analysis of fecal samples and follow-up mass spectrometry of
      urinary metabolites disclosed that introducing the FMP strains into mice results in
      significant changes in expression of microbiome-encoded enzymes involved in numerous metabolic
      pathways, most prominently those related to carbohydrate metabolism. B. animalis subsp.
      lactis, the dominant persistent member of the FMP consortium in gnotobiotic mice, up-regulates
      a locus in vivo that is involved in the catabolism of xylooligosaccharides, a class of glycans
      widely distributed in fruits, vegetables, and other foods, underscoring the importance of
      these sugars to this bacterial species. The human fecal metatranscriptome exhibited
      significant changes, confined to the period of FMP consumption, that mirror changes in
      gnotobiotic mice, including those related to plant polysaccharide metabolism. These
      experiments illustrate a translational research pipeline for characterizing the effects of
      FMPs on the human gut microbiome.
AU  - McNulty NP et al
PT  - Journal Article
TA  - Sci. Transl. Med.
JT  - Sci. Transl. Med.
SO  - Sci. Transl. Med. 2011 3: 106RA106.

PMID- 18820018
VI  - 190
DP  - 2008
TI  - Genome Sequence of a Nephritogenic and Highly Transformable M49 Strain of Streptococcus pyogenes.
PG  - 7773-7785
AB  - The 1,815,783-bp genome of a serotype M49 strain of Streptococcus pyogenes
      (group A streptococcus [GAS]), strain NZ131, has been determined. This GAS
      strain (FCT type 3; emm pattern E), originally isolated from a case of
      acute post-streptococcal glomerulonephritis, is unusually competent for
      electrotransformation and has been used extensively as a model organism
      for both basic genetic and pathogenesis investigations. As with the
      previously sequenced S. pyogenes genomes, three unique prophages are a
      major source of genetic diversity. Two clustered regularly interspaced
      short palindromic repeat (CRISPR) regions were present in the genome,
      providing genetic information on previous prophage encounters. A unique
      cluster of genes was found in the pathogenicity island-like emm region
      that included a novel Nudix hydrolase, and, further, this cluster appears
      to be specific for serotype M49 and M82 strains. Nudix hydrolases
      eliminate potentially hazardous materials or prevent the unbalanced
      accumulation of normal metabolites; in bacteria, these enzymes may play a
      role in host cell invasion. Since M49 S. pyogenes strains have been known
      to be associated with skin infections, the Nudix hydrolase and its
      associated genes may have a role in facilitating survival in an
      environment that is more variable and unpredictable than the uniform
      warmth and moisture of the throat. The genome of NZ131 continues to shed
      light upon the evolutionary history of this human pathogen. Apparent
      horizontal transfer of genetic material has led to the existence of highly
      variable virulence-associated regions that are marked by multiple
      rearrangements and genetic diversification while other regions, even those
      associated with virulence, vary little between genomes. The genome regions
      that encode surface gene products that will interact with host targets or
      aid in immune avoidance are the ones that display the most sequence
      diversity. Thus, while natural selection favors stability in much of the
      genome, it favors diversity in these regions.
AU  - McShan WM
AU  - Ferretti JJ
AU  - Karasawa T
AU  - Suvorov AN
AU  - Lin S
AU  - Qin B
AU  - Jia H
AU  - Kenton S
AU  - Najar F
AU  - Wu H
AU  - Scott J
AU  - Roe BA
AU  - Savic DJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2008 190: 7773-7785.

PMID- 25657279
VI  - 3
DP  - 2015
TI  - Draft genome sequences of five new strains of methylophilaceae isolated from lake washington sediment.
PG  - e01511-14
AB  - We sequenced the genomes of five new Methylophilaceae strains isolated from Lake  Washington
      sediment. We used the new sequences to sort these new strains into
      specific Methylophilaceae ecotypes, including one novel ecotype. The new genomes
      expand the known diversity of Methylophilaceae and provide new models for
      studying the ecology of methylotrophy.
AU  - McTaggart TL
AU  - Benuska G
AU  - Shapiro N
AU  - Woyke T
AU  - Chistoserdova L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01511-14.

PMID- 25676775
VI  - 3
DP  - 2015
TI  - Draft Genome of Janthinobacterium sp. RA13 Isolated from Lake Washington Sediment.
PG  - e01588-14
AB  - Sequencing the genome of Janthinobacterium sp. RA13 from Lake Washington sediment is
      announced. From the genome content, a versatile life-style is predicted, but
      not bona fide methylotrophy. With the availability of its genomic sequence,
      Janthinobacterium sp. RA13 presents a prospective model for studying microbial
      communities in lake sediments.
AU  - McTaggart TL
AU  - Shapiro N
AU  - Woyke T
AU  - Chistoserdova L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01588-14.

PMID- 25700420
VI  - 3
DP  - 2015
TI  - Draft genomes of two strains of flavobacterium isolated from lake washington sediment.
PG  - e01597-14
AB  - We report sequencing the genomes of two new Flavobacterium strains isolated from Lake
      Washington sediment. From genomic contents, versatile lifestyles were predicted but not bona
      fide methylotrophy. With the availability of their genomic sequences, the new Flavobacterium
      strains present prospective models for studying microbial communities in lake sediments.
AU  - McTaggart TL
AU  - Shapiro N
AU  - Woyke T
AU  - Chistoserdova L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01597-14.

PMID- 25700412
VI  - 3
DP  - 2015
TI  - Draft Genome of Pseudomonas sp. Strain 11/12A, Isolated from Lake Washington Sediment.
PG  - e01587-14
AB  - We announce here the genome sequencing of Pseudomonas sp. strain 11/12A from Lake Washington
      sediment. From the genome content, a versatile lifestyle is predicted  but not one of bona
      fide methylotrophy. With the availability of its genomic sequence, Pseudomonas sp. 11/12A
      presents a prospective model for studying microbial communities in lake sediments.
AU  - McTaggart TL
AU  - Shapiro N
AU  - Woyke T
AU  - Chistoserdova L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01587-14.

PMID- 23408395
VI  - 6
DP  - 2012
TI  - Complete Genome Sequence of Paenibacillus strain Y4.12MC10, a Novel Paenibacillus lautus strain Isolated from Obsidian Hot Spring in Yellowstone National Park.
PG  - 381-400
AB  - Paenibacillus sp.Y412MC10 was one of a number of organisms isolated from Obsidian Hot Spring,
      Yellowstone National Park, Montana, USA under permit from the
      National Park Service. The isolate was initially classified as a Geobacillus sp.
      Y412MC10 based on its isolation conditions and similarity to other organisms
      isolated from hot springs at Yellowstone National Park. Comparison of 16 S rRNA
      sequences within the Bacillales indicated that Geobacillus sp.Y412MC10 clustered
      with Paenibacillus species, and the organism was most closely related to
      Paenibacillus lautus. Lucigen Corp. prepared genomic DNA and the genome was
      sequenced, assembled, and annotated by the DOE Joint Genome Institute. The genome
      sequence was deposited at the NCBI in October 2009 (NC_013406). The genome of
      Paenibacillus sp. Y412MC10 consists of one circular chromosome of 7,121,665 bp
      with an average G+C content of 51.2%. Comparison to other Paenibacillus species
      shows the organism lacks nitrogen fixation, antibiotic production and social
      interaction genes reported in other paenibacilli. The Y412MC10 genome shows a
      high level of synteny and homology to the draft sequence of Paenibacillus sp.
      HGF5, an organism from the Human Microbiome Project (HMP) Reference Genomes.
      This, combined with genomic CAZyme analysis, suggests an intestinal, rather than
      environmental origin for Y412MC10.
AU  - Mead DA et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 6: 381-400.

PMID- 20624727
VI  - 2
DP  - 2010
TI  - The sequence of a 1.8-mb bacterial linear plasmid reveals a rich evolutionary reservoir of secondary metabolic pathways.
PG  - 212-224
AB  - Plasmids are mobile genetic elements that play a key role in the evolution
      of bacteria by mediating genome plasticity and lateral transfer of useful
      genetic information. Although originally considered to be exclusively
      circular, linear plasmids have also been identified in certain bacterial
      phyla, notably the actinomycetes. In some cases, linear plasmids engage
      with chromosomes in an intricate evolutionary interplay, facilitating the
      emergence of new genome configurations by transfer and recombination or
      plasmid integration. Genome sequencing of Streptomyces clavuligerus ATCC
      27064, a Gram-positive soil bacterium known for its production of a
      diverse array of biotechnologically important secondary metabolites,
      revealed a giant linear plasmid of 1.8 Mb in length. This megaplasmid
      (pSCL4) is one of the largest plasmids ever identified and the largest
      linear plasmid to be sequenced. It contains more than 20% of the putative
      protein-coding genes of the species, but none of these is predicted to be
      essential for primary metabolism. Instead, the plasmid is densely packed
      with an exceptionally large number of gene clusters for the potential
      production of secondary metabolites, including a large number of putative
      antibiotics, such as staurosporine, moenomycin, beta-lactams, and
      enediynes. Interestingly, cross-regulation occurs between chromosomal and
      plasmid-encoded genes. Several factors suggest that the megaplasmid came
      into existence through recombination of a smaller plasmid with the arms of
      the main chromosome. Phylogenetic analysis indicates that heavy traffic of
      genetic information between Streptomyces plasmids and chromosomes may
      facilitate the rapid evolution of secondary metabolite repertoires in
      these bacteria.
AU  - Medema MH
AU  - Trefzer A
AU  - Kovalchuk A
AU  - van den Berg M
AU  - Muller U
AU  - Heijne W
AU  - Wu L
AU  - Alam MT
AU  - Ronning CM
AU  - Nierman WC
AU  - Bovenberg RA
AU  - Breitling R
AU  - Takano E
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2010 2: 212-224.

PMID- 29650568
VI  - 6
DP  - 2018
TI  - Genome Sequence of a Heterotrophic Nitrifier and Aerobic Denitrifier, Paracoccus  denitrificans Strain ISTOD1, Isolated from Wastewater.
PG  - e00210-18
AB  - We report here the draft genome sequence of Paracoccus denitrificans strain ISTOD1 of 4.9 Mb,
      isolated from wastewater. It has been identified as a
      heterotrophic nitrifying and aerobic denitrifying bacterium. Genomic analysis
      revealed genes related to nitrogen and phosphorus removal, showing that the
      strain holds potential for bioremediation and biorefinery uses.
AU  - Medhi K
AU  - Mishra A
AU  - Thakur IS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00210-18.

PMID- 23991259
VI  - 8
DP  - 2013
TI  - Non-contiguous finished genome sequence and description of Bartonella senegalensis sp. nov.
PG  - 279-289
AB  - Bartonella senegalensis sp. nov. strain OS02(T) is the type strain of B. senegalensis sp.
      nov., a new species within the genus Bartonella. This strain,
      whose genome is described here, was isolated in Senegal from the soft tick
      Ornithodoros sonrai, the vector of relapsing fever. B. senegalensis is an
      aerobic, rod-shaped, Gram-negative bacterium. Here we describe the features of
      this organism, together with the complete genome sequence and its annotation. The
      1,966,996 bp-long genome contains 1,710 protein-coding and 46 RNA genes,
      including 6 rRNA genes.
AU  - Mediannikov O
AU  - El Karkouri K
AU  - Diatta G
AU  - Robert C
AU  - Fournier PE
AU  - Raoult D
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 279-289.

PMID- 24501655
VI  - 9
DP  - 2013
TI  - Non-contiguous finished genome sequence and description of Bartonella florenciae  sp. nov.
PG  - 185-196
AB  - Bartonella florenciae sp. nov. strain R4(T) is the type strain of B. florenciae sp. nov., a
      new species within the genus Bartonella. This strain, whose genome is
      described here, was isolated in France from the spleen of the shrew Crocidura
      russula. B. florenciae is an aerobic, rod-shaped, Gram-negative bacterium. Here
      we describe the features of this organism, together with the complete genome
      sequence and its annotation. The 2,010,844 bp-long genome contains 1,909
      protein-coding and 46 RNA genes, including two rRNA operons.
AU  - Mediannikov O
AU  - El Karkouri K
AU  - Robert C
AU  - Fournier PE
AU  - Raoult D
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 9: 185-196.

PMID- 25780502
VI  - 9
DP  - 2014
TI  - High quality draft genome sequence and description of Occidentia massiliensis gen. nov., sp. nov., a new member of the family Rickettsiaceae.
PG  - 9
AB  - The family Rickettsiaceae currently includes two genera: Orientia that contains one species,
      Orientia tsutsugamushi, and Rickettsia that contains 28 species.
      Occidentia massiliensis gen. nov., sp. nov. strain OS118(T) is the type strain of
      O. massiliensis gen. nov., sp. nov., the type species of the new genus Occidentia
      gen. nov. within the family Rickettsiaceae. This strain, whose genome is
      described here, was isolated in France from the soft tick Ornithodoros sonrai
      collected in Senegal. O. massiliensis is an aerobic, rod-shaped, Gram-negative,
      obligate intracellular bacillus that may be cultivated in BME/CTVM2 cells. Here
      we describe the features of O. massiliensis, together with the complete genomic
      sequencing and annotation. The 1,469,252 bp long genome (1 chromosome but no
      plasmid) contains 1,670 protein-coding and 41 RNA genes, including one rRNA
      operon.
AU  - Mediannikov O
AU  - Nguyen TT
AU  - Bell-Sakyi L
AU  - Padmanabhan R
AU  - Fournier PE
AU  - Raoult D
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 9.

PMID- 16169927
VI  - 15
DP  - 2005
TI  - Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125.
PG  - 1325-1335
AB  - A considerable fraction of life develops in the sea at temperatures lower than 15 degrees C.
      Little is known about the adaptive features selected
      under those conditions. We present the analysis of the genome sequence of
      the fast growing Antarctica bacterium Pseudoalteromonas haloplanktis
      TAC125. We find that it copes with the increased solubility of oxygen at
      low temperature by multiplying dioxygen scavenging while deleting whole
      pathways producing reactive oxygen species. Dioxygen-consuming lipid
      desaturases achieve both protection against oxygen and synthesis of lipids
      making the membrane fluid. A remarkable strategy for avoidance of reactive
      oxygen species generation is developed by P. haloplanktis, with
      elimination of the ubiquitous molybdopterin-dependent metabolism. The P.
      haloplanktis proteome reveals a concerted amino acid usage bias specific
      to psychrophiles, consistently appearing apt to accommodate asparagine, a
      residue prone to make proteins age. Adding to its originality, P.
      haloplanktis further differs from its marine counterparts with recruitment
      of a plasmid origin of replication for its second chromosome.
AU  - Medigue C et al
PT  - Journal Article
TA  - Genome Res.
JT  - Genome Res.
SO  - Genome Res. 2005 15: 1325-1335.

PMID- 29567732
VI  - 6
DP  - 2018
TI  - Genome Sequences of 15 Klebsiella sp. Isolates from Sugarcane Fields in Colombia's Cauca Valley.
PG  - e00104-18
AB  - Members of the Klebsiella genus promote plant growth. We report here draft whole-genome
      sequences for 15 Klebsiella sp. isolates from sugarcane fields in
      the Cauca Valley of Colombia. The genomes of these isolates were characterized as
      part of a broader effort to evaluate their utility as endemic plant
      growth-promoting biofertilizers.
AU  - Medina-Cordoba LK
AU  - Chande AT
AU  - Rishishwar L
AU  - Mayer LW
AU  - Marino-Ramirez L
AU  - Valderrama-Aguirre LC
AU  - Valderrama-Aguirre A
AU  - Kostka JE
AU  - Jordan IK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00104-18.

PMID- 21315180
VI  - 16
DP  - 2011
TI  - Advances in the computational development of DNA methyltransferase inhibitors.
PG  - 418-425
AB  - DNA methylation is an epigenetic change that results in the addition of a methyl group at the
      carbon-5 position of cytosine residues. The process is mediated by DNA methyltransferases
      (DNMTs), a family of enzymes for which inhibition is a promising strategy for the treatment of
      cancer and other diseases. Here, we review the current status of the computational studies
      directed to rationalize, at the molecular level, the enzymatic activity of DNMT inhibitors. We
      also review successful virtual screenings to identify inhibitors with novel scaffolds as well
      as the emerging efforts to characterize the dynamic behavior of DNMTs. Thus, computational
      approaches form part of multidisciplinary efforts to further advance epigenetic therapies.
AU  - Medina-Franco JL
AU  - Caulfield T
PT  - Journal Article
TA  - Drug Discovery Today
JT  - Drug Discovery Today
SO  - Drug Discovery Today 2011 16: 418-425.

PMID- 23447100
VI  - 17
DP  - 2013
TI  - Docking of a novel DNA methyltransferase inhibitor identified from high-throughput screening: insights to unveil inhibitors in chemical databases.
PG  - 337-344
AB  - Inhibitors of DNA methyltransferase (DNMT) are attractive compounds not only as potential
      therapeutic agents for the treatment of cancer and
      other diseases, but also as research tools to investigate the role of
      DNMTs in epigenetic events. Recent advances in high-throughput
      screening (HTS) for epigenetic targets and the availability of the
      first crystallographic structure of human DNMT1 encourage the
      integration of research strategies to uncover and optimize the activity
      of DNMT inhibitors. Herein, we present a binding model of a novel
      small-molecule DNMT1 inhibitor obtained by HTS, recently released in a
      public database. The docking model is in agreement with key
      interactions previously identified for established inhibitors using
      extensive computational studies including molecular dynamics and
      structure-based pharmacophore modeling. Based on the chemical structure
      of the novel inhibitor, a sequential computational screening of five
      chemical databases was performed to identify candidate compounds for
      testing. Similarity searching followed by molecular docking of chemical
      databases such as approved drugs, natural products, a DNMT-focused
      library, and a general screening collection, identified at least 108
      molecules with promising DNMT inhibitory activity. The chemical
      structures of all hit compounds are disclosed to encourage the research
      community working on epigenetics to test experimentally the enzymatic
      and demethylating activity in vivo. Five candidate hits are drugs
      approved for other indications and represent potential starting points
      of a drug repurposing strategy.
AU  - Medina-Franco JL
AU  - Yoo J
PT  - Journal Article
TA  - Mol. Diversity
JT  - Mol. Diversity
SO  - Mol. Diversity 2013 17: 337-344.

PMID- 22582377
VI  - 194
DP  - 2012
TI  - Genome Sequence of Pantoea sp. Strain Sc 1, an Opportunistic Cotton Pathogen.
PG  - 3019
AB  - Pantoea is comprised of a broad spectrum of species, including plant pathogens. Here, we
      provide an annotated genome sequence of Pantoea sp. strain Sc 1, which
      was isolated from a diseased cotton boll. This research provides the first genome
      sequence of a bona fide Pantoea sp. insect-vectored cotton pathogen.
AU  - Medrano EG
AU  - Bell AA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3019.

PMID- 26358602
VI  - 3
DP  - 2015
TI  - Genome Sequence of Pantoea ananatis Strain CFH 7-1, Which Is Associated with a Vector-Borne Cotton Fruit Disease.
PG  - e01029-15
AB  - Pantoea ananatis is a bacterium with versatile niches that vary from pathogenic to beneficial.
      We present the genome of strain CFH 7-1, which was recovered from  a diseased greenhouse
      cotton boll previously caged with a field-collected cotton  fleahopper (Pseudatomoscelis
      seriatus). These data will assist in deciphering the infection process.
AU  - Medrano EG
AU  - Bell AA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01029-15.

PMID- 25146146
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of a Klebsiella pneumoniae Strain Isolated from a Known  Cotton Insect Boll Vector.
PG  - e00850-14
AB  - Klebsiella pneumoniae (associated with bacterial pneumonia) was previously isolated from
      Nezara viridula, a significant vector of cotton boll-rot pathogens.
      We provide the first annotated genome sequence of the cotton opportunistic strain
      K. pneumoniae 5-1. This data provides guidance to study the bases of cotton
      pathogenesis by bacteria associated with vectors.
AU  - Medrano EG
AU  - Forray MM
AU  - Bell AA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00850-14.

PMID- 24336368
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Salmonella enterica subsp. enterica Serotype Oranienburg Strain S-76, Isolated from an Aquatic Environment.
PG  - e01017-13
AB  - Salmonella is a widespread microorganism and a common causative agent of food-borne illnesses.
      Salmonella enterica subsp. enterica serotype Oranienburg is
      highly prevalent in surface water from tropical ecosystems and is not commonly
      related to illnesses. Here, we report the first genome sequence of Salmonella
      Oranienburg strain S-76, isolated from an aquatic environment.
AU  - Medrano-Felix A
AU  - Estrada-Acosta M
AU  - Jimenez M
AU  - Gomez-Gil B
AU  - Leon-Felix J
AU  - Amarillas L
AU  - Chaidez C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01017-13.

PMID- 29097461
VI  - 5
DP  - 2017
TI  - Genome Sequences of Acholeplasma laidlawii Strains Differing in Sensitivity to Ciprofloxacin.
PG  - e01189-17
AB  - Acholeplasma laidlawii is a well-suited model for study of the molecular basis of the
      adaptation of mollicutes to environmental conditions. Here we present the
      whole-genome sequences of four strains of A. laidlawii with differential
      sensitivity to ciprofloxacin.
AU  - Medvedeva ES
AU  - Siniagina MN
AU  - Malanin SY
AU  - Boulygina EA
AU  - Malygina TY
AU  - Baranova NB
AU  - Mouzykantov AA
AU  - Davydova MN
AU  - Chernova OA
AU  - Chernov VM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01189-17.

PMID- 8265369
VI  - 21
DP  - 1993
TI  - Restriction endonuclease NciI is not blocked by CpG methylation.
PG  - 5517-5518
AB  - Vertebrate DNA is highly methylated at cytosines in the dinucleotide sequence CpG. Many
      restriction enzymes are unable to cleave DNA if their recognition sequences contain methylated
      CpG, and this property has been used to study the pattern of DNA methylation in higher
      eukaryotes. An enzyme that has recently been used in this way is NciI (recognition sequence
      CCSGG, where S is C or G). It was reported that this enzyme cannot cleave a region of the
      mouse actin promoter when the CpG in its recognition site is methylated on both strands, but
      can cleave when either one or both strands are unmethylated. As a result, NciI has been used
      to monitor the conversion of symmetrically methylated DNA to hemi-methylated DNA in a number
      of systems. Its general use for this purpose depends upon the idea that NciI cannot cleave any
      symmetrically methylated site. We have digested symmetrically methylated and non-methylated
      DNA with NciI, and find that it can cleave both forms to completion, though at markedly
      different rates.
AU  - Meehan RR
AU  - Ulrich E
AU  - Bird AP
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 5517-5518.

PMID- 22923402
VI  - 78
DP  - 2012
TI  - Evidence of in vivo prophage induction during Clostridium difficile infection.
PG  - 7662-7670
AB  - Prophages contribute to the evolution and virulence of most bacterial pathogens,
      but their role in Clostridium difficile is unclear. Here we describe the
      isolation of four Myoviridae phages, MMP01, MMP02, MMP03, and MMP04, that were
      recovered as free viral particles in the filter-sterilized stool supernatants of
      patients suffering from C. difficile infection (CDI). Furthermore, identical
      prophages were found in the chromosomes of C. difficile isolated from the
      corresponding fecal samples. We therefore provide, for the first time, evidence
      of in vivo prophage induction during CDI. We completely sequenced the genomes of
      MMP02 and MMP04, and bioinformatics analyses did not reveal the presence of
      virulence factors but underlined the unique character of MMP04. We also studied
      the mobility of MMP02 and MMP04 prophages in vitro. Both prophages were
      spontaneously induced, with 4 to 5 log PFU/ml detected in the culture
      supernatants of the corresponding lysogens. When lysogens were grown in the
      presence of subinhibitory concentrations of ciprofloxacin, moxifloxacin,
      levofloxacin, or mitomycin C, the phage titers further increased, reaching 8 to 9
      log PFU/ml in the case of MMP04. In summary, our study highlights the extensive
      genetic diversity and mobility of C. difficile prophages. Moreover, antibiotics
      known to represent risk factors for CDI, such as quinolones, can stimulate
      prophage mobility in vitro and probably in vivo as well, which underscores their
      potential impact on phage-mediated horizontal gene transfer events and the
      evolution of C. difficile.
AU  - Meessen-Pinard M
AU  - Sekulovic O
AU  - Fortier LC
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2012 78: 7662-7670.

PMID- 27125486
VI  - 4
DP  - 2016
TI  - High-Quality Draft Genomes from Thermus caliditerrae YIM 77777 and T. tengchongensis YIM 77401, Isolates from Tengchong, China.
PG  - e00312-16
AB  - The draft genomes of Thermus tengchongensis YIM 77401 and T. caliditerrae YIM 77777 are
      2,562,314 and 2,218,114 bp and encode 2,726 and 2,305 predicted genes,
      respectively. Gene content and growth experiments demonstrate broad metabolic
      capacity, including starch hydrolysis, thiosulfate oxidation, arsenite oxidation,
      incomplete denitrification, and polysulfide reduction.
AU  - Mefferd CC et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00312-16.

PMID- 27284152
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Staphylococcus succinus Strain CSM-77, a Moderately Halophilic Bacterium Isolated from a Triassic Salt Mine.
PG  - e00532-16
AB  - Here, we report the draft genome sequence of Staphylococcus succinus strain CSM-77. This
      moderately halophilic bacterium was isolated from the surface of a
      halite sample obtained from a Triassic salt mine.
AU  - Megaw J
AU  - Gilmore BF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00532-16.

PMID- 29371365
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Pantoea ananatis Strain 1.38, a Bacterium Isolated from  the Rhizosphere of Oryza sativa var. Puntal That Shows Biotechnological Potential  as an Inoculant.
PG  - e01547-17
AB  - Pantoea ananatis 1.38 is a strain isolated from the rhizosphere of irrigated rice in southern
      Spain. Its genome was estimated at 4,869,281 bp, with 4,644 coding
      sequences (CDSs). The genome encompasses several CDSs related to plant growth
      promotion, such as that for siderophore metabolism, and virulence genes
      characteristic of pathogenic Pantoea spp. are absent.
AU  - Megias E
AU  - Dos Reis JFB
AU  - Ribeiro RA
AU  - Ollero FJ
AU  - Megias M
AU  - Hungria M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01547-17.

PMID- 26893418
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Pantoea ananatis Strain AMG521, a Rice Plant Growth-Promoting Bacterial Endophyte Isolated from the Guadalquivir Marshes in  Southern Spain.
PG  - e01681-15
AB  - The rice endophyte Pantoea ananatis AMG521 shows several plant growth-promoting properties and
      promotes rice yield increases. Its draft genome was estimated at
      4,891,568 bp with 4,704 coding sequences (CDS). The genome encodes genes for
      N-acylhomoserine lactone (AHL) synthases, AHL hydrolases, hyperadherence (yidQ,
      yidP, and yidR), fusaric acid resistance, and oxidation of lignin, highlighting
      its biotechnological potential.
AU  - Megias E
AU  - Megias M
AU  - Ollero FJ
AU  - Hungria M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01681-15.

PMID- 28751401
VI  - 5
DP  - 2017
TI  - Genome Sequence of Pantoea sp. Strain 1.19, Isolated from Rice Rhizosphere, with  the Capacity To Promote Growth of Legumes and Nonlegumes.
PG  - e00707-17
AB  - Pantoea sp. 1.19, a plant growth-promoting bacterium (PGPB), was isolated from the rhizosphere
      of rice plants in Spain. Its genome, estimated at 3,771,065 bp,
      encodes 3,535 coding sequences (CDSs), carrying genes for synthesis of auxins,
      homoserine lactones, enzymes, siderophores, and quorum sensing. Several CDSs
      emphasize its biotechnological potential as an agriculture inoculant.
AU  - Megias E
AU  - Reis JFB
AU  - Ribeiro RA
AU  - Megias M
AU  - Ollero FJ
AU  - Hungria M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00707-17.

PMID- 28839029
VI  - 5
DP  - 2017
TI  - Genome Sequence of Pantoea ananatis Strain AMG 501, a Plant Growth-Promoting Bacterium Isolated from Rice Leaves Grown in Paddies of Southern Spain.
PG  - e00848-17
AB  - Pantoea ananatis AMG 501 is a plant growth-promoting bacterium isolated from rice leaves. Its
      genome was estimated at 5,102,640 bp with 4,994 coding sequences,
      encompassing genes related to the metabolism of carbohydrates, to the synthesis
      of auxins, siderophores, and homoserine lactones, and to the type I, II, III, IV,
      and VI secretion systems.
AU  - Megias E
AU  - Reis JFB
AU  - Ribeiro RA
AU  - Ollero FJ
AU  - Megias M
AU  - Hungria M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00848-17.

PMID- 26893424
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Two Novel Amoeba-Resistant Intranuclear Bacteria, 'Candidatus Berkiella cookevillensis' and 'Candidatus Berkiella aquae'.
PG  - e01732-15
AB  - 'Candidatus Berkiella cookevillensis' and 'Candidatus Berkiella aquae' are obligate
      intranuclear endosymbionts of freshwater amoebae. Here, we present the
      draft genome sequences of these two bacteria, with total sizes of 2,990,361 bp
      and 3,626,027 bp, respectively.
AU  - Mehari YT
AU  - Arivett BA
AU  - Farone AL
AU  - Gunderson JH
AU  - Farone MB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01732-15.

PMID- 26859667
VI  - 11
DP  - 2016
TI  - Plasmid Characterization and Chromosome Analysis of Two netF+ Clostridium perfringens Isolates Associated with Foal and Canine Necrotizing Enteritis.
PG  - E0148344
AB  - The recent discovery of a novel beta-pore-forming toxin, NetF, which is strongly
      associated with canine and foal necrotizing enteritis should improve our
      understanding of the role of type A Clostridium perfringens associated disease in
      these animals. The current study presents the complete genome sequence of two
      netF-positive strains, JFP55 and JFP838, which were recovered from cases of foal
      necrotizing enteritis and canine hemorrhagic gastroenteritis, respectively.
      Genome sequencing was done using Single Molecule, Real-Time (SMRT)
      technology-PacBio and Illumina Hiseq2000. The JFP55 and JFP838 genomes include a
      single 3.34 Mb and 3.53 Mb chromosome, respectively, and both genomes include
      five circular plasmids. Plasmid annotation revealed that three plasmids were
      shared by the two newly sequenced genomes, including a NetF/NetE toxins-encoding
      tcp-conjugative plasmid, a CPE/CPB2 toxins-encoding tcp-conjugative plasmid and a
      putative bacteriocin-encoding plasmid. The putative beta-pore-forming toxin
      genes, netF, netE and netG, were located in unique pathogenicity loci on
      tcp-conjugative plasmids. The C. perfringens JFP55 chromosome carries 2,825
      protein-coding genes whereas the chromosome of JFP838 contains 3,014
      protein-encoding genes. Comparison of these two chromosomes with three available
      reference C. perfringens chromosome sequences identified 48 (~247 kb) and 81
      (~430 kb) regions unique to JFP55 and JFP838, respectively. Some of these
      divergent genomic regions in both chromosomes are phage- and plasmid-related
      segments. Sixteen of these unique chromosomal regions (~69 kb) were shared
      between the two isolates. Five of these shared regions formed a mosaic of
      plasmid-integrated segments, suggesting that these elements were acquired early
      in a clonal lineage of netF-positive C. perfringens strains. These results
      provide significant insight into the basis of canine and foal necrotizing
      enteritis and are the first to demonstrate that netF resides on a large and
      unique plasmid-encoded locus.
AU  - Mehdizadeh-Gohari I
AU  - Kropinski AM
AU  - Weese SJ
AU  - Parreira VR
AU  - Whitehead AE
AU  - Boerlin P
AU  - Prescott JF
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2016 11: E0148344.

PMID- 26021932
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Uropathogenic Escherichia coli Strain CI5.
PG  - e00558-15
AB  - Escherichia coli represents the primary etiological agent responsible for urinary tract
      infections, one of the most common infections in humans. We report here the
      complete genome sequence of uropathogenic Escherichia coli strain CI5, a clinical
      pyelonephritis isolate used for studying pathogenesis.
AU  - Mehershahi KS
AU  - Abraham SN
AU  - Chen SL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00558-15.

PMID- 28473396
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of the Uropathogenic Escherichia coli Strain NU14.
PG  - e00306-17
AB  - Escherichia coli is the most common bacterium causing urinary tract infections in humans. We
      report here the complete genome sequence of the uropathogenic
      Escherichia coli strain NU14, a clinical pyelonephritis isolate used for studying
      pathogenesis.
AU  - Mehershahi KS
AU  - Chen SL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00306-17.

PMID- 26494662
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Streptococcus agalactiae Serotype III, Multilocus Sequence Type 283 Strain SG-M1.
PG  - e01188-15
AB  - Streptococcus agalactiae (group B Streptococcus) is a common commensal strain in  the human
      gastrointestinal tract that can also cause invasive disease in humans and other animals. We
      report here the complete genome sequence of S. agalactiae SG-M1, a serotype III, multilocus
      sequence type 283 strain, isolated from a Singaporean patient suffering from meningitis.
AU  - Mehershahi KS
AU  - Hsu LY
AU  - Koh TH
AU  - Chen SL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01188-15.

PMID- 17328745
VI  - 268
DP  - 2007
TI  - A Dam methylation mutant of Klebsiella pneumoniae is partially attenuated.
PG  - 187-193
AB  - In Klebsiella pneumoniae, a chromosomal insertion mutation was constructed in the dam gene,
      which encodes DNA adenine methylase (Dam),
      resulting in a mutant unable to methylate specific nucleotides. In some
      bacteria, the Dam methylase has been shown to play an important role in
      virulence gene regulation as well as in methyl-directed mismatch repair
      and the regulation of replication initiation. Disruption of the normal
      Dam function by either eliminating or greatly increasing expression in
      several organisms has been shown to cause attenuation of virulence in
      murine models of infection. In K. pneumoniae, a mutation-eliminating
      Dam function is shown here to result in only partial attenuation
      following intranasal and intraperitoneal infection of Balb/C mice.
AU  - Mehling JS
AU  - Lavender H
AU  - Clegg S
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2007 268: 187-193.

PMID- 24459254
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of the Sugar Cane Endophyte Pseudomonas aurantiaca PB-St2, a Disease-Suppressive Bacterium with Antifungal Activity toward the Plant  Pathogen Colletotrichum falcatum.
PG  - e01108-13
AB  - The endophytic bacterium Pseudomonas aurantiaca PB-St2 exhibits antifungal activity and
      represents a biocontrol agent to suppress red rot disease of sugar
      cane. Here, we report the completely sequenced 6.6-Mb genome of P. aurantiaca
      PB-St2. The sequence contains a repertoire of biosynthetic genes for secondary
      metabolites that putatively contribute to its antagonistic activity and its
      plant-microbe interactions.
AU  - Mehnaz S
AU  - Bauer JS
AU  - Gross H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01108-13.

PMID- Not carried by PubMed...
VI  - 7
DP  - 1993
TI  - Rapid purification of a restriction endonuclease from Escherichia coli RY13.
PG  - 411-414
AB  - A two step method for the purification of the restriction endonuclease EcoRI was developed.
      The first step involved the purification of the enzyme on a Cibacron Blue-F3GA-agarose column,
      followed by a hydroxyapatite column. The enzyme was homogeneous on SDS-PAGE and completely
      free from contaminating nucleases and phosphatases, and can be used for direct DNA hydrolysis.
AU  - Mehra RS
AU  - Malhotra VP
AU  - Rembhotkar GW
PT  - Journal Article
TA  - Biotechnol. Tech.
JT  - Biotechnol. Tech.
SO  - Biotechnol. Tech. 1993 7: 411-414.

PMID- 26966202
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Kocuria rhizophila RF, a Radiation-Resistant Soil Isolate.
PG  - e00095-16
AB  - Kocuria rhizophila RF, a soil isolate from Iran, is a radiation-resistant bacterium. Only a
      limited amount of genomic information for radiation-resistant
      bacteria is currently available. Here, we report the draft genome sequence of
      this bacterium, providing knowledge to aid in the discovery of the genomic basis
      of its resistance to radiation.
AU  - Mehrabadi JF
AU  - Mirzaie A
AU  - Ahangar N
AU  - Rahimi A
AU  - Rokni-Zadeh H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00095-16.

PMID- 22628506
VI  - 194
DP  - 2012
TI  - Genome Sequences of Pseudomonas fragi Strains A22 and B25.
PG  - 3276-3277
AB  - Pseudomonas fragi A22 is a novel isolate that produces bead-like particles (A22B) in its cell
      wall. To explore the genetic basis for the formation of A22B, P.
      fragi A22 and the type strain of the species, P. fragi B25, were subjected to
      genome sequence analysis. Here, we report the draft genome sequences and
      automatic annotation of both strains. These data offer a solid base for related
      studies of P. fragi, including comparative genomics, proteomics, and gene mining.
AU  - Mei Y
AU  - Sun Y
AU  - He J
AU  - Wang Q
AU  - Sun Y
AU  - Shao W
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3276-3277.

PMID- 10092455
VI  - 287
DP  - 1999
TI  - Detection of anticodon nuclease residues involved in tRNALys cleavage specificity.
PG  - 499-510
AB  - The tRNALys-specific anticodon
      nuclease exists in latent form in Escherichia coli strains containing
      the optional prr locus. The latency is a result of a masking
      interaction between the anticodon nuclease core-polypeptide PrrC and
      the Type IC DNA restriction-modification enzyme EcoprrI. Activation of
      the latent enzyme by phage T4-infection elicits cleavage of tRNALys 5'
      to the wobble base, yielding 5'-OH and 2', 3'-cyclic phosphate termini.
      The N-proximal half of PrrC has been implicated with (A/G) TPase and
      EcoprrI interfacing activities. Therefore, residues involved in
      recognition and cleavage of tRNALys were searched for at the C-half.
      Random mutagenesis of the low-G+C portion encoding PrrC residues
      200-313 was performed, followed by selection for loss of anticodon
      nuclease-dependent lethality and production of full-sized PrrC-like
      protein. This process yielded a cluster of missense mutations mapping
      to a region highly conserved between PrrC and two putative Neisseria
      meningitidis MC58 homologues. This cluster included two adjacent
      members that relaxed the inherent enzyme's cleavage specificity. We
      also describe another mode of relaxed specificity, due to mere
      overexpression of PrrC. This mode was shared by wild-type PrrC and the
      other mutant alleles. The additional substrates recognised under the
      promiscuous conditions had, in general, anticodons resembling that of
      tRNALys. Taken together, the data suggest that the anticodon of tRNALys
      harbours anticodon nuclease identity elements and implicates a
      conserved region in PrrC in their recognition.
AU  - Meidler R
AU  - Morad I
AU  - Amitsur M
AU  - Inokuchi H
AU  - Kaufmann G
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1999 287: 499-510.

PMID- 25780495
VI  - 9
DP  - 2014
TI  - Complete genome sequence of DSM 30083(T), the type strain (U5/41(T)) of Escherichia coli, and a proposal for delineating subspecies in microbial  taxonomy.
PG  - 2
AB  - Although Escherichia coli is the most widely studied bacterial model organism and often
      considered to be the model bacterium per se, its type strain was until now
      forgotten from microbial genomics. As a part of the G enomic E ncyclopedia of B
      acteria and A rchaea project, we here describe the features of E. coli DSM
      30083(T) together with its genome sequence and annotation as well as novel
      aspects of its phenotype. The 5,038,133 bp containing genome sequence includes
      4,762 protein-coding genes and 175 RNA genes as well as a single plasmid.
      Affiliation of a set of 250 genome-sequenced E. coli strains, Shigella and
      outgroup strains to the type strain of E. coli was investigated using digital
      DNA:DNA-hybridization (dDDH) similarities and differences in genomic G+C content.
      As in the majority of previous studies, results show Shigella spp. embedded
      within E. coli and in most cases forming a single subgroup of it. Phylogenomic
      trees also recover the proposed E. coli phylotypes as monophyla with minor
      exceptions and place DSM 30083(T) in phylotype B2 with E. coli S88 as its closest
      neighbor. The widely used lab strain K-12 is not only genomically but also
      physiologically strongly different from the type strain. The phylotypes do not
      express a uniform level of character divergence as measured using dDDH, however,
      thus an alternative arrangement is proposed and discussed in the context of
      bacterial subspecies. Analyses of the genome sequences of a large number of E.
      coli strains and of strains from > 100 other bacterial genera indicate a value of
      79-80% dDDH as the most promising threshold for delineating subspecies, which in
      turn suggests the presence of five subspecies within E. coli.
AU  - Meier-Kolthoff JP et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 2.

PMID- 24501643
VI  - 9
DP  - 2013
TI  - Genome sequence of the chemoheterotrophic soil bacterium Saccharomonospora cyanea type strain (NA-134(T)).
PG  - 28-41
AB  - Saccharomonospora cyanea Runmao et al. 1988 is a member of the genus Saccharomonospora in the
      family Pseudonocardiaceae that is moderately well
      characterized at the genome level thus far. Members of the genus
      Saccharomonospora are of interest because they originate from diverse habitats,
      such as soil, leaf litter, manure, compost, surface of peat, moist, over-heated
      grain, and ocean sediment, where they probably play a role in the primary
      degradation of plant material by attacking hemicellulose. Species of the genus
      Saccharomonospora are usually Gram-positive, non-acid fast, and are classified
      among the actinomycetes. S. cyanea is characterized by a dark blue (= cyan blue)
      aerial mycelium. After S. viridis, S. azurea, and S. marina, S. cyanea is only
      the fourth member in the genus for which a completely sequenced (non-contiguous
      finished draft status) type strain genome will be published. Here we describe the
      features of this organism, together with the draft genome sequence, and
      annotation. The 5,408,301 bp long chromosome with its 5,139 protein-coding and 57
      RNA genes was sequenced as part of the DOE funded Community Sequencing Program
      (CSP) 2010 at the Joint Genome Institute (JGI).
AU  - Meier-Kolthoff JP
AU  - Lu M
AU  - Huntemann M
AU  - Lucas S
AU  - Lapidus A
AU  - Copeland A
AU  - Pitluck S
AU  - Goodwin LA
AU  - Han C
AU  - Tapia R
AU  - Potter G
AU  - Land M
AU  - Ivanova N
AU  - Rohde M
AU  - Goker M
AU  - Detter JC
AU  - Woyke T
AU  - Kyrpides NC
AU  - Klenk HP
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 9: 28-41.

PMID- 22675600
VI  - 6
DP  - 2012
TI  - Complete genome sequence of Polynucleobacter necessarius subsp. asymbioticus type strain (QLW-P1DMWA-1(T)).
PG  - 74-83
AB  - Polynucleobacter necessarius subsp. asymbioticus strain QLW-P1DMWA-1(T) is a planktonic
      freshwater bacterium affiliated with the family Burkholderiaceae
      (class Betaproteobacteria). This strain is of interest because it represents a
      subspecies with cosmopolitan and ubiquitous distribution in standing freshwater
      systems. The 16S-23S ITS genotype represented by the sequenced strain comprised
      on average more than 10% of bacterioplankton in its home habitat. While all
      strains of the subspecies P. necessarius asymbioticus are free-living freshwater
      bacteria, strains belonging to the only other subspecies, P. necessarius subsp.
      necessarius are obligate endosymbionts of the ciliate Euplotes aediculatus. The
      two subspecies of P. necessarius are the instances of two closely related
      subspecies that differ in their lifestyle (free-living vs. obligate
      endosymbiont), and they are the only members of the genus Polynucleobacter with
      completely sequenced genomes. Here we describe the features of P. necessarius
      subsp. asymbioticus, together with the complete genome sequence and annotation.
      The 2,159,490 bp long chromosome with a total of 2,088 protein-coding and 48 RNA
      genes is the first completed genome sequence of the genus Polynucleobacter to be
      published and was sequenced as part of the DOE Joint Genome Institute Community
      Sequencing Program 2006.
AU  - Meincke L et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 6: 74-83.

PMID- 26472835
VI  - 3
DP  - 2015
TI  - Genome Sequence of a Urease-Positive Campylobacter lari Strain.
PG  - e01191-15
AB  - Campylobacter lari is frequently isolated from shore birds and can cause illness  in humans.
      Here, we report the draft whole-genome sequence of a urease-positive strain of C. lari that
      was isolated in estuarial water on the coast of Delaware,  USA.
AU  - Meinersmann RJ
AU  - Bono JL
AU  - Lindsey RL
AU  - Genzlinger LL
AU  - Loparev VN
AU  - Oakley BB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01191-15.

PMID- 27834721
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of a Colistin Resistance Gene (mcr-1)-Bearing Isolate of Escherichia coli from the United States.
PG  - e01283-16
AB  - Transmissible colistin resistance conferred by the mcr-1 gene-bearing IncI2 plasmid has been
      recently reported in Escherichia coli in the United States. We
      report here the completed genome sequence of a second E. coli strain isolated
      from swine in the United States that carried the mcr-1 gene on an IncI2-type
      plasmid.
AU  - Meinersmann RJ
AU  - Ladely SR
AU  - Bono JL
AU  - Plumblee JR
AU  - Hall MC
AU  - Genzlinger LL
AU  - Cook KL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01283-16.

PMID- 27587816
VI  - 4
DP  - 2016
TI  - Colistin Resistance mcr-1-Gene-Bearing Escherichia coli Strain from the United States.
PG  - e00898-16
AB  - Transmissible colistin resistance in the form of an mcr-1-gene-bearing plasmid has been
      recently reported in Enterobacteriaceae in several parts of the world.
      We report here the completed genome sequence of an Escherichia coli strain
      isolated from swine in the United States that carried the mcr-1 gene on an
      IncI2-type plasmid.
AU  - Meinersmann RJ
AU  - Ladely SR
AU  - Plumblee JR
AU  - Hall MC
AU  - Simpson SA
AU  - Ballard LL
AU  - Scheffler BE
AU  - Genzlinger LL
AU  - Cook KL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00898-16.

PMID- 11591165
VI  - 40
DP  - 2001
TI  - Dynamic impact of methylation at the m. hhai target site: a solid-state deuterium nmr study.
PG  - 12436-12443
AB  - Base methylation plays an important role in numerous biological functions of DNA, from
      inhibition of cleavage by endonucleases to inhibition of transcription factor binding. Studies
      of nucleic acid structure have shown little differences in unmethylated DNAs and the identical
      sequence containing methylated analogues. We have investigated changes in the local dynamics
      of DNA upon substitution of a methylated cytosine analogue for cytosine using solid-state
      deuterium NMR. In particular, we have observed changes in the local dynamics at the target
      site of the M.HhaI restriction system. These studies observe changes in the amplitudes of the
      local backbone dynamics at the actual target site of the HhaI methyltransferase. This
      conclusion is another indication that the significant result of base methylation is to perturb
      the local dynamics, and therefore the local conformational flexibility, of the DNA helix,
      inhibiting or restricting the protein's ability to manipulate the DNA helix in order to
      perform its chemical alterations.
AU  - Meints GA
AU  - Drobny GP
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2001 40: 12436-12443.

PMID- Not carried by PubMed...
VI  - 3
DP  - 1985
TI  - Chlorella Viruses.
PG  - 180-187
AB  - Although viruses that infect blue-green algae (cyanobacteria) have been
      extensively studied (Sherman and Brown, 1978), little is known about viruses of
      eukaryotic algae (see reviews, Lemke, 1976, Sherman and Brown, 1978, Dodds,
      1979, and Dodds, 1983).  Most viruses or virus-like particles (VLP) in
      eukaryotic algae have been detected by ultrastructural studies, and only a few
      attempts have been made to characterize these particles, primarily because they
      are difficult to obtain in reasonable quantities.  Several factors contribute
      to this lack of material: (i) usually only a few algal cells contained
      particles, (ii) usually the cells only contained particles at one stage of the
      algal life cycle, (iii) usually the cells that had particles did not lyse, and
      (iv) in most cases the particles were not infectious.  These factors, plus the
      fact that some of these particles were present in multicellular filamentous
      algae, have hindered the development of a biological assay for them.  Thus it
      is interesting that we have recently discovered a group of large (negatively
      stained particles are 150 to 190 nm in diameter) polyhedral, dsDNA-containing
      viruses which infect and replicate in certain strains of unicellular,
      eukaryotic, exsymbiont Chlorella-like green algae.  These viruses can be
      produced in large quantities and, most importantly, the viruses can be assayed
      by plaque formation on lawns of the host Chlorella.  These viruses, therefore,
      have the potential to serve as excellent model systems for studying gene
      regulation in a photosynthetic eukaryote in the manner that bacterio phages
      served as model systems for studying gene regulation in bacteria.  This review
      will briefly describe some of the pertinent properties of these viruses,
      focusing primarily on the most studied virus PBCV-1.  A more comprehensive
      review of these viruses is in press (Van Etten et al., 1986).
AU  - Meints RH
AU  - Schuster AM
AU  - Van Etten JL
PT  - Journal Article
TA  - Plant Mol. Biol. Rep.
JT  - Plant Mol. Biol. Rep.
SO  - Plant Mol. Biol. Rep. 1985 3: 180-187.

PMID- 8590483
VI  - 28
DP  - 1995
TI  - Identification of the heterothallic mutation in HO-endonuclease of S. cerevisiae using HO/ho chimeric genes.
PG  - 367-373
AB  - HO-endonuclease initiates a mating-type switch in the yeast S. cerevisiae by making a
      double-strand cleavage in the DNA of the mating-type gene, MAT.  Heterothallic strains of
      yeast have a stable mating type and contain a recessive ho allele.  Here we report the
      sequence of the ho allele; ho has four point mutations all of which encode for substitute
      amino acids.  The fourth mutation is a leucine to histidine substitution within a presumptive
      zinc finger.  Chimeric HO/ho genes were constructed in vivo by converting different parts of
      the sequence of the genomic ho allele to the HO sequence by gene conversion.  HO activity was
      assessed by three bioassays: a mating-type switch, extinction of expression of an a-specific
      reporter gene, and the appearance of Canr Ade- papillae resulting from excision of an
      engineered Ty element containing the HO-endonuclease target site and a SUP4o gene.  We found
      that the replacement of the fourth point mutation in ho to the HO sequence restored HO
      activity to the chimeric endonuclease.
AU  - Meiron H
AU  - Nahon E
AU  - Raveh D
PT  - Journal Article
TA  - Curr. Genet.
JT  - Curr. Genet.
SO  - Curr. Genet. 1995 28: 367-373.

PMID- 1734285
VI  - 355
DP  - 1992
TI  - Type III restriction enzymes need two inversely oriented recognition sites for DNA cleavage.
PG  - 467-469
AB  - Type III restriction/modification enzymes recognize short, nonpalindromic
      sequences that can be methylated on only one strand, with the paradoxical
      consequence that during replication of what is in effect hemimethylated DNA
      totally unmodified sites arise.  Why the unmodified sites are not subject to
      suicidal restriction was not clear.  Here we show that restriction requires two
      unmodified recognition sites that can be separated by different distances but
      which must be in inverse orientation.  All of the unmodified sites in newly
      replicated DNA are of course in the same orientation, which explains why they
      are not restricted.  This result may be of relevance to other manifestations of
      anisotropy in double-stranded DNA, such as genetic imprinting.
AU  - Meisel A
AU  - Bickle TA
AU  - Kruger DH
AU  - Schroeder C
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1992 355: 467-469.

PMID- 1861989
VI  - 19
DP  - 1991
TI  - M.EcoP15I methylates the second adenine in its recognition sequence.
PG  - 3997
AB  - The type III restriction/modification system EcoP15I recognizes the
      non-palindromic sequence 5'-CAGCAG-3'.  The restriction enzyme cleaves the DNA
      25-27 bp to the right of the sequence as written.  The modification methylase
      methylates one of the two adenine residues in the recognition sequence.
      Attempts to determine which of the adenines is methylated by the enzyme were
      foiled by the internal repeated symmetry of the recognition sequence.
AU  - Meisel A
AU  - Kruger DH
AU  - Bickle TA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 3997.

PMID- 7796821
VI  - 14
DP  - 1995
TI  - Type III restriction endonucleases translocate DNA in a reaction driven by recognition site-specific ATP hydrolysis.
PG  - 2958-2966
AB  - Type III restriction/modification systems recognize short non-palindromic sequences, only one
      strand of which can be methylated. Replication of type III-modified DNA produces completely
      unmethylated recognition sites which, according to classical mechanisms of restriction, should
      be signals for restriction. We have shown previously that suicidal restriction by the type III
      enzyme EcoP15I is prevented if all the unmodified sites are in the same orientation:
      restriction by EcoP15I requires a pair of unmethylated, inversely oriented recognition sites.
      We have now addressed the molecular mechanism of site orientation-specific DNA restriction.
      EcoP15I is demonstrated to possess an intrinsic ATPase activity, the potential driving force
      of DNA translocation. The ATPase activity is uniquely recognition site-specific, but
      EcoP15I-modified sites also support the reaction. EcoP15I DNA restriction patterns are shown
      to be predetermined by the enzyme-to-site ratio, in that site-saturating enzyme levels elicit
      cleavage exclusively between the closest pair of head-to-head oriented sites. DNA restriction
      is blocked by Lac repressor bound in the intervening sequence between the two EcoP15I sites.
      These results rule out DNA looping and strongly suggest that cleavage is triggered by the
      close proximity of two convergently tracking EcoP15I-DNA complexes.
AU  - Meisel A
AU  - Mackeldanz P
AU  - Bickle TA
AU  - Kruger DH
AU  - Schroeder C
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1995 14: 2958-2966.

PMID- 
VI  - 
DP  - 2009
TI  - Non-associating heterodimeric DNA methyltransferases as a platform for developing designer methyltransferases.
PG  - 
AB  - The ability to site-specifically methylate a unique DNA sequence within a genome has numerous
      potential uses including 1) a tool for the study of DNA methylation patterns, 2) a tool to
      silence genes of interest, and 3) a potential gene therapy device to correct conditions caused
      by hypomethylation. Current approaches include linking methyltransferases to DNA binding
      domains to localize enzymes next to a target site. This approach has achieved site-biased
      methylation, however the engineered methyltransferases are still active in the absence of
      binding their intended target and methylate non-target sites. We demonstrate an alternative
      strategy in which fragments of a DNA methyltransferase, compromised in their ability to
      methylate DNA, are fused to two zinc fingers designed to bind 9 bp sites flanking a
      methylation site. Using the naturally heterodimeric methyltransferase M.EcoHK31I, we have
      demonstrated that this strategy can yield a methyltransferase capable of a high level of
      methylation at the target site with undetectable levels of methylation at the non-target sites
      in E. coli. The two zinc fingers acted synergistically to target methylation to the desired
      site. However, some nontarget methylation could be detected at higher expression levels of the
      zinc fingermethyltransferase indicating that further improvements will be necessary to attain
      the desired exclusive target specificity.
AU  - Meister GE
PT  - Journal Article
TA  - Ph.D. Thesis, Johns Hopkins University, USA
JT  - Ph.D. Thesis, Johns Hopkins University, USA
SO  - Ph.D. Thesis, Johns Hopkins University, USA 2009 : .

PMID- 
VI  - 236
DP  - 2008
TI  - BIOT 149-Heterodimeric DNA methyltransferases.
PG  - 0
AB  - DNA methylation patterns play an important role in determining gene expression patterns. These
      patterns are of particular interest in embryonic development and in cancer cells, which often
      exhibit abnormal methylation patterns. The ability to control the activity and specificity of
      DNA methyltransferases would have applications in the study of DNA methylation in cells, would
      offer an avenue to control gene expression epigenetically and potentially would allow the
      correction of abnormal methylation patterns for therapeutic purposes. Most known DNA
      methyltransferases are encoded in a single polypeptide chain.  DNA methyltransferases in which
      the activity is encoded by heterodimerizing peptides, offer unique platform for engineering
      DNA methyltransferases with novel properties. The C5-methylcytosine methyltransferases M. AquI
      and M. EcoHK31I each have alpha and beta peptide chains that associate to create a functional
      enzyme. Methylation is not possible without the association of the two fragments.   Truncated
      version of these fragments exhibit decreased association in vitro. We have used an in vivo
      method to determine if the fragment's association is more or less sensitive to these
      truncations in the cellular environment.  Select fragments formed the basis for designed
      methyltransferase libraries that will methylate unique sites.
AU  - Meister GE
AU  - Chandrasegaran S
AU  - Ostermeier M
PT  - Journal Article
TA  - ACS Abstracts
JT  - ACS Abstracts
SO  - ACS Abstracts 2008 236: 0.

PMID- 18835252
VI  - 377
DP  - 2008
TI  - An engineered split M.Hhal-zinc finger fusion lacks the intended methyltransferase specificity.
PG  - 226-230
AB  - The ability to site-specifically methylate DNA in vivo would have wide applicability to the
      study of basic biomedical problems as well as
      enable studies on the potential of site-specific DNA methylation as a
      therapeutic strategy for the treatment of diseases. Natural DNA
      methyltransferases lack the specificity required for these
      applications. Nomura and Barbas [W. Nomura, C.F. Barbas 3rd, In vivo
      site-specific DNA methylation with a designed sequence-enabled DNA
      methylase, J. Am. Chem. Soc. 129 (2007) 8676-8677] have reported that
      an engineered DNA methyltransferase comprised of fragments of M.Hhal
      methyltransferase and zinc finger proteins has very high specificity
      for the chosen target site. Our analysis of this engineered enzyme
      shows that the fusion protein methylates target and non-target sites
      with similar efficiency.
AU  - Meister GE
AU  - Chandrasegaran S
AU  - Ostermeier M
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 2008 377: 226-230.

PMID- 20007601
VI  - 38
DP  - 2010
TI  - Heterodimeric DNA methyltransferases as a platform for creating designer zinc finger methyltransferases for targeted DNA methylation in cells.
PG  - 1749-1759
AB  - The ability to target methylation to specific genomic sites would further the study of DNA
      methylation's biological role and potentially offer a
      tool for silencing gene expression and for treating diseases involving
      abnormal hypomethylation. The end-to-end fusion of DNA methyltransferases
      to zinc fingers has been shown to bias methylation to desired regions.
      However, the strategy is inherently limited because the methyltransferase
      domain remains active regardless of whether the zinc finger domain is
      bound at its cognate site and can methylate non-target sites. We
      demonstrate an alternative strategy in which fragments of a DNA
      methyltransferase, compromised in their ability to methylate DNA, are
      fused to two zinc fingers designed to bind 9 bp sites flanking a
      methylation target site. Using the naturally heterodimeric DNA
      methyltransferase M.EcoHK31I, which methylates the inner cytosine of
      5'-YGGCCR-3', we demonstrate that this strategy can yield a
      methyltransferase capable of significant levels of methylation at the
      target site with undetectable levels of methylation at non-target sites in
      Escherichia coli. However, some non-target methylation could be detected
      at higher expression levels of the zinc finger methyltransferase
      indicating that further improvements will be necessary to attain the
      desired exclusive target specificity.
AU  - Meister GE
AU  - Chandrasegaran S
AU  - Ostermeier M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2010 38: 1749-1759.

PMID- 8223468
VI  - 12
DP  - 1993
TI  - Macroevolution by transposition: drastic modification of DNA recognition by the type I restriction enzyme following Tn5 transposition.
PG  - 4585-4591
AB  - We have characterized a novel mutant of EcoDXXI, a type IC DNA restriction and modification
      (R-M) system, in which the specificity has been altered due to a Tn5 insertion into the middle
      of hsdS, the gene which encodes the polypeptide that confers DNA sequence specificity to both
      the restriction and the modification reactions. Like other type I enzymes, the wild type
      EcoDXXI recognizes a sequence composed of two asymmetrical half sites separated by a spacer
      region: TCA(N7)RTTC. Purification of the EcoDXXI mutant methylase and subsequent in vitro DNA
      methylation assays identified the mutant recognition sequence as an interrupted palindrome,
      TCA(N8)TGA, in which the 5' half site of the wild type site is repeated in inverse
      orientation. The additional base pair in the non-specific spacer of the mutant recognition
      sequence maintains the proper spacing between the two methylatable adenine groups. Sequencing
      of both the wild type and mutant EcoDXXI hsdS genes showed that the Tn5 insertion occurred at
      nucleotide 673 of the 1221 bp gene. This effectively deletes the entire carboxyl-terminal DNA
      binding domain which recognizes the 3' half of the EcoDXXI binding site. The truncated hsdS
      gene still encodes both the amino-terminal DNA binding domain and the conserved repeated
      sequence that defines the length of the recognition site spacer region. We propose that the
      EcoDXXI mutant methylase utilizes two truncated hsdS subunits to recognize its binding site.
      The implications of this finding in terms of subunit interactions and the malleability of the
      type I R-M systems will be discussed.
AU  - Meister J
AU  - MacWilliams M
AU  - Hubner P
AU  - Jutte H
AU  - Skrzypek E
AU  - Piekarowicz A
AU  - Bickle TA
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1993 12: 4585-4591.

PMID- 20675499
VI  - 192
DP  - 2010
TI  - The genome sequence of the cyanobacterium Oscillatoria sp. PCC 6506 reveals several gene clusters responsible for the biosynthesis of toxins  and secondary metabolites.
PG  - 5264-5265
AB  - We report a draft sequence of the genome of Oscillatoria sp. PCC 6506, a cyanobacterium that
      produces anatoxin-a and homoanatoxin-a, two
      neurotoxins, and cylindrospermopsin, a cytotoxin. Beside the clusters of
      genes responsible for the biosynthesis of these toxins, we have found
      other clusters of genes likely involved in the biosynthesis of
      not-yet-identified secondary metabolites.
AU  - Mejean A
AU  - Mazmouz R
AU  - Mann S
AU  - Calteau A
AU  - Medigue C
AU  - Ploux O
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 5264-5265.

PMID- 
VI  - 82
DP  - 2000
TI  - Inactivation of a Spiroplasma citri DNA modification methylase by a virus-like insertion element suggested by DNA sequence.
PG  - 71
AB  - A partial SpV1-like viral DNA sequence in the Spiroplasma citri chromosome, the D3 progenitor,
      was previously implicated as the donor of viral DNA sequences causing recombinational
      instability of insert-containing virus vectors.  Re-examination of the D3 progenitor sequence
      suggested that the virus-like sequence had inserted into a DNA adenine modification methylase
      gene, inactivating it.  Comparison of the D3 progenitor sequence with SpV1-C74 revealed that
      it was more closely related to this virus than to SpV1-R8A2 B and that the point of insertion
      corresponded to an inverted terminal repeat similar to those terminating elements of the IS3
      family of insertion sequences.  The transposases most similar to the SpV1-C74 is probably an
      encapsilated insertion element.
AU  - Melcher U
AU  - Fletcher J
PT  - Journal Article
TA  - J. Plant Pathol.
JT  - J. Plant Pathol.
SO  - J. Plant Pathol. 2000 82: 71.

PMID- 10518300
VI  - 4
DP  - 1999
TI  - Mechanisms of Spiroplasma genome variation associated with SpV1-like viral DNA inferred from sequence comparisons.
PG  - 29-46
AB  - Genomes of Spiroplasma citri strains have rearranged frequently during their evolution, partly
      due to multiple integrated sequences of spiroplasma viruses. To understand better the role of
      viral sequences in genome evolution, we examined available nucleotide sequences of viruslike
      elements in the S. citri chromosome. Comparison of integrated and nonintegrated sequences of
      spiroplasma virus SpV1-C74 DNA suggested that it is an encapsidated form of the circular
      transposition intermediate belonging to an insertion sequence (IS3) family member. One
      SpV1-C74 viral DNA fragment was identified as interrupting the remains of a DNA adenine
      modification methylase gene. A viral DNA insertion of SpV1-R8A2 B DNA had hallmarks of having
      suffered an internal deletion by a site-specific recombination system. Homologous
      recombination likely was responsible for several deletions within viral DNA. A homologous
      recombination event was inferred between part of a viral DNA insertion and a similar
      chromosomal sequence. Dispersed sequences from SpV1-like C4 open reading frames (ORFs) were
      identified as involved in a complex deletion-inversion event. Thus, SpV1-like sequences likely
      have altered spiroplasma genomes by inserting within active genes, destroying their function,
      by providing targets for site-specific recombination, by mediating deletions of sequences
      adjacent to their integration sites, and by providing targets for homologous recombination,
      leading to inversions.
AU  - Melcher U
AU  - Sha Y
AU  - Ye F
AU  - Fletcher J
PT  - Journal Article
TA  - Microb. Comp. Genomics
JT  - Microb. Comp. Genomics
SO  - Microb. Comp. Genomics 1999 4: 29-46.

PMID- 25477405
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Haemophilus influenzae Strain 375 from the Middle Ear of a Pediatric Patient with Otitis Media.
PG  - e01245-14
AB  - Originally isolated from a pediatric patient with otitis media, Haemophilus influenzae strain
      375 (Hi375) has been extensively studied as a model system for
      intracellular invasion of airway epithelial cells and other pathogenesis traits.
      Here, we report its complete genome sequence and methylome.
AU  - Mell JC
AU  - Sinha S
AU  - Balashov S
AU  - Viadas C
AU  - Grassa CJ
AU  - Ehrlich GD
AU  - Nislow C
AU  - Redfield RJ
AU  - Garmendia J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01245-14.

PMID- 28473388
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Nitrobacter vulgaris Strain Ab1, a Nitrite-Oxidizing Bacterium.
PG  - e00290-17
AB  - Here, we present the 3.9-Mb draft genome sequence of Nitrobacter vulgaris strain  Ab1, which
      was isolated from a sewage system in Hamburg, Germany. The analysis of
      its genome sequence will contribute to our knowledge of nitrite-oxidizing
      bacteria and acyl-homoserine lactone quorum sensing in nitrifying bacteria.
AU  - Mellbye BL
AU  - Davis EWII
AU  - Spieck E
AU  - Chang JH
AU  - Bottomley PJ
AU  - Sayavedra-Soto LA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00290-17.

PMID- 28729253
VI  - 5
DP  - 2017
TI  - Genome Sequences of the First WHO Repository of Platelet Transfusion-Relevant Bacterial Reference Strains.
PG  - e00001-17
AB  - To develop novel techniques for improving blood safety, dedicated bacterial strains, which are
      able to persist and to proliferate in blood platelet
      concentrates, are needed. Here, we present draft genome sequences of the four
      bacterial strains approved for the first WHO repository of platelet
      transfusion-relevant bacterial reference strains.
AU  - Mellmann A
AU  - Spindler-Raffel E
AU  - Bletz S
AU  - Prax M
AU  - Bekeredjian-Ding I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00001-17.

PMID- 1650423
VI  - 53
DP  - 1991
TI  - Two site-specific endonucleases of the Cyanobacterium Nostoc linckia.
PG  - 24-28
AB  - Two restrictases Nli387/7I and Nli387/7II have been isolated from
      cyanobacterium Nostoc linckia using chromatography on phosphocellulose, <Mono
      Q> column, and heparin sepharose 4B.  The preparations are described by the
      method of electrophoresis in polyacrylamide gels under denaturating conditions.
      The catalytic properties of the restrictases have been determined:  optimal
      pH 9.0 - 9.5, optimal concentration of Na+ - 5 mM, that of Mg2+ - 6 mM, optimal
      temperature - 37C.  The isolated enzymes are isoschizomers of the restrictases
      AvaI and AvaII.  The point of cutting is determined for enzyme Nli387/7 I.  It
      is shown that restrictase Nli387/7 I is a false isoschizomer of AvaI.
AU  - Melnik AI
AU  - Rebentish BA
AU  - Bolotin AV
AU  - Mendzhul MI
PT  - Journal Article
TA  - Mikrobiol. Zh.
JT  - Mikrobiol. Zh.
SO  - Mikrobiol. Zh. 1991 53: 24-28.

PMID- 27617057
VI  - 11
DP  - 2016
TI  - Complete genome sequence of Desulfurivibrio alkaliphilus strain AHT2(T), a haloalkaliphilic sulfidogen from Egyptian hypersaline alkaline lakes.
PG  - 67
AB  - Desulfurivibrio alkaliphilus strain AHT2(T) is a strictly anaerobic sulfidogenic
      haloalkaliphile isolated from a composite sediment sample of eight hypersaline
      alkaline lakes in the Wadi al Natrun valley in the Egyptian Libyan Desert. D.
      alkaliphilus AHT2(T) is Gram-negative and belongs to the family Desulfobulbaceae
      within the Deltaproteobacteria. Here we report its genome sequence, which
      contains a 3.10 Mbp chromosome. D. alkaliphilus AHT2(T) is adapted to survive
      under highly alkaline and moderately saline conditions and therefore, is relevant
      to the biotechnology industry and life under extreme conditions. For these
      reasons, D. alkaliphilus AHT2(T) was sequenced by the DOE Joint Genome Institute
      as part of the Community Science Program.
AU  - Melton ED
AU  - Sorokin DY
AU  - Overmars L
AU  - Chertkov O
AU  - Clum A
AU  - Pillay M
AU  - Ivanova N
AU  - Shapiro N
AU  - Kyrpides NC
AU  - Woyke T
AU  - Lapidus AL
AU  - Muyzer G
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 67.

PMID- 28943998
VI  - 12
DP  - 2017
TI  - Draft genome sequence of Dethiobacter alkaliphilus strain AHT1T, a gram-positive  sulfidogenic polyextremophile.
PG  - 57
AB  - Dethiobacter alkaliphilus strain AHT1T is an anaerobic, sulfidogenic, moderately
      salt-tolerant alkaliphilic chemolithotroph isolated from hypersaline soda lake
      sediments in northeastern Mongolia. It is a Gram-positive bacterium with low GC
      content, within the phylum Firmicutes. Here we report its draft genome sequence,
      which consists of 34 contigs with a total sequence length of 3.12 Mbp. D.
      alkaliphilus strain AHT1T was sequenced by the Joint Genome Institute (JGI) as
      part of the Community Science Program due to its relevance to bioremediation and
      biotechnological applications.
AU  - Melton ED
AU  - Sorokin DY
AU  - Overmars L
AU  - Lapidus AL
AU  - Pillay M
AU  - Ivanova N
AU  - Del Rio TG
AU  - Kyrpides NC
AU  - Woyke T
AU  - Muyzer G
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 57.

PMID- 24459275
VI  - 2
DP  - 2014
TI  - Genome Sequence of a Helicobacter pylori Strain Isolated from a Mexican Patient with Intestinal Gastric Cancer.
PG  - e01214-13
AB  - Helicobacter pylori strains are the major risk factor for gastric cancer. Strains vary in
      their content of disease-associated genes, so genome-wide analysis of
      cancer-isolated strains will help elucidate their pathogenesis and genetic
      diversity. We present the draft genome sequence of H. pylori isolated from a
      Mexican patient with intestinal gastric cancer.
AU  - Mendez-Tenorio A
AU  - Larios-Serrato V
AU  - Olguin-Ruiz GE
AU  - Sanchez-Vallejo CJ
AU  - Torres-Lopez RC
AU  - Aviles-Jimenez F
AU  - Camorlinga-Ponce M
AU  - Torres J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01214-13.

PMID- 25555740
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Oenococcus oeni Strain X2L (CRL1947), Isolated from Red  Wine of Northwest Argentina.
PG  - e01376-14
AB  - We report the draft genome sequence of Oenococcus oeni strain X2L, a potential starter culture
      of malolactic fermentation, isolated from Malbec wine of
      Argentina. Genes encoding for enzymes involved in the metabolism of malate,
      citrate, and nitrogen compounds, as well as aroma compounds, were found in this
      genome, showing its ability to improve the sensorial characteristics of wines.
AU  - Mendoza LM
AU  - Saavedra L
AU  - Raya RR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01376-14.

PMID- 28878860
VI  - 12
DP  - 2017
TI  - Draft genome sequences of two opportunistic pathogenic strains of Staphylococcus  cohnii isolated from human patients.
PG  - 49
AB  - Herein, we report the draft-genome sequences and annotation of two opportunistic  pathogenic
      strains of Staphylococcus cohnii isolated from humans. One strain
      (SC-57) was isolated from blood from a male patient in May 2006 and the other
      (SC-532) from a catheter from a male patient in June 2006. Similar to other
      genomes of Staphylococcus species, most genes (42%) of both strains are involved
      in metabolism of amino acids and derivatives, carbohydrates and proteins. Eighty
      (4%) genes are involved in virulence, disease, and defense and both species show
      phenotypic low biofilm production and evidence of increased antibiotic resistance
      associated to biofilm production. From both isolates, a new Staphylococcal
      Cassette Chromosome mec was detected: mec class A, ccr type 1. This is the first
      report of whole genome sequences of opportunistic S. cohnii isolated from human
      patients.
AU  - Mendoza-Olazaran S
AU  - Garcia-Mazcorro JF
AU  - Morfin-Otero R
AU  - Villarreal-Trevino L
AU  - Camacho-Ortiz A
AU  - Rodriguez-Noriega E
AU  - Bocanegra-Ibarias P
AU  - Maldonado-Garza HJ
AU  - Dowd SE
AU  - Garza-Gonzalez E
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 49.

PMID- 10643272
VI  - 61
DP  - 1999
TI  - Endonuclease activity in cyanobacteria Anabaena variabilis and Plectonema boryanum involving restriction endonuclease and nuclease.
PG  - 10-14
AB  - Site-specific endodeoxyribonuclease activity was found in crude cell-free extracts of
      cyanobacteria Plectonema boryanum CALU 465 and
      Plectonema edaphycum CALU 262. Cyanobacterium Anabaena variabilis CALU
      458 was shown to possess restriction site-specific endonuclease Ava458I
      which was probably an isoschizomer of CfrI with the recognition site
      PyGGCCPu.
AU  - Mendzhul MI
AU  - Moshinsky ID
AU  - Syrchin SA
PT  - Journal Article
TA  - Mikrobiol. Zh.
JT  - Mikrobiol. Zh.
SO  - Mikrobiol. Zh. 1999 61: 10-14.

PMID- Not carried by PubMed...
VI  - 9
DP  - 1993
TI  - The way of defense of cyanophage LPP-3 DNA against restriction-modification systems in the cells of the cyanobacterium Plectonema boryanum.
PG  - 54-61
AB  - The HPLC method was used to study some peculiarities of the DNA composition of the
      cyanobacterium Plectonema boryanum and cyanophage LPP-3. Analysis of the elution profile of
      the products of DNA acid hydrolysis allow the identification in P. boryanum DNA, in addition
      to the canonical bases, of the presence of 4.5% N-6-methyladenine and 1.2% 5-methyl-cytosine;
      DNA from LPP-3 has 0.8% 5-methycytosine and no N-6-methyladenine. The presence of
      5-methylcytosine was detected only by the application of a modified hydrolysis method using
      HF. Restriction endonuclease isoschizomers, whose hydrolysis of DNA depends on the presence of
      methylated bases in the recognition sites, were used to detect site-specific methylation. The
      comparison of the products of the DNA LPP-3 and P. boryanum fermentative hydrolysis by MspI
      and HpaII; Sau3AI, MboI and DpnI; Apyl and MvaI restrictases enabled the determination that
      DNA from LPP-3 and P. boryanum has a high degree of methylation of the inner cytosine in
      CC(A/T)GG sequences and in P. boryanum the adenine in the GATC site; CCGG sites were not
      methylated in either DNA. It is concluded that dam- and dcm-like modification systems are in
      P. boryanum. The defense of viral DNA against host R-M systems occurs by cytosine methylation
      in the sequence CmC(A/T)GG and counter-selection at BamHI sites.
AU  - Mendzhul MI
AU  - Syrchin SA
AU  - Averkiev AA
AU  - Rebentish BA
PT  - Journal Article
TA  - Biopol. Kletka
JT  - Biopol. Kletka
SO  - Biopol. Kletka 1993 9: 54-61.

PMID- 8220827
VI  - 55
DP  - 1993
TI  - The resistance of the DNA of cyanophage LPP-3 to the action of different restriction endonucleases.
PG  - 47-53
AB  - Data on the study of structural peculiarities of cyanophage LPP-3 DNA are presented in the
      work. The length of cyanophage DNA calculated by means of the enzymatic hydrolysis by
      restrictases is 40+/-3.5 thousand base pairs. Cyanophage LPP-3 DNA was hydrolysed by more than
      50 different restrictases. As a result of screening it was found out that the great number of
      restrictases, which recognized hexanucleotide sequences did not hydrolyse DNA of cyanophage
      LPP-3. A considerable deviation of the number of the observed sites of restriction from their
      theoretically expected number for restrictases, which recognized hexanucleotide sequences did
      not hydrolyse DNA of cyanophage LPP-3. A considerable deviation of the number of the observed
      sites of restriction from their theoretically expected number for restrictases HaeIII and
      Cfr131 was established. Restrictases-isoschizomers with different sensitivity to the
      methylation of the recognition sites -- MspI, HpaII and Sau3A, MboI and DpnI were used to
      check the availability of methylated bases in LPP-3 DNA. Absence of methylated adenine in the
      site GATC and methylated cytosine in the second position of the site CCGG were established.
      The results obtained permit supposing that the expressed counterselection by the sites of
      recognition of many restriction endonucleases takes place in cyanophage LPP-3 DNA. It is
      supposed that apparently, this method of protection of its genome in LPP-3 is one of most
      important but the inconsiderable percentage of site-specific methylation of the virus DNA
      cannot be completely excluded.
AU  - Mendzhul MI
AU  - Syrchin SA
AU  - Rebentish BA
AU  - Averkiev AA
AU  - Busakhina IV
PT  - Journal Article
TA  - Mikrobiol. Zh.
JT  - Mikrobiol. Zh.
SO  - Mikrobiol. Zh. 1993 55: 47-53.

PMID- 26941141
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus CFL1, a Lactic Acid Bacterium Isolated from French Handcrafted Fermented Milk.
PG  - e00052-16
AB  - Lactobacillus delbrueckii subsp. bulgaricus (L. bulgaricus) is a lactic acid bacterium widely
      used for the production of yogurt and cheeses. Here, we report
      the genome sequence of L. bulgaricus CFL1 to improve our knowledge on its
      stress-induced damages following production and end-use processes.
AU  - Meneghel J
AU  - Dugat-Bony E
AU  - Irlinger F
AU  - Loux V
AU  - Vidal M
AU  - Passot S
AU  - Beal C
AU  - Layec S
AU  - Fonseca F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00052-16.

PMID- Not carried by PubMed...
VI  - 14
DP  - 1989
TI  - Cloning and overexpression of EcoRI methylase.
PG  - 37-40
AB  - The author cloned a HindIII fragment of pMB3 plasmid containing part of the coding region for
      EcoRI endonuclease, and the entire sequence for EcoRI methylase downstream of the PL promoter
      of the expression vector pcp 40.  The recombinant was introduced into a lysogenic E. coli
      strain, harboring a lambda phage with a temperature sensitive mutation for the repressor gene
      (c1857). After heat induction, a protein band of apparent molecular mass of 39 Kd, increased
      continuously during 8 hours.  After four hours of thermal induction, the band represented
      nearly 50% of the soluble proteins observed by gel electrophoresis.  At the maximum induction
      time, the methylase activity registered a 15 fold increment over the non-induced state.
AU  - Menendez C
AU  - Bournat JC
AU  - Ramirez JL
PT  - Journal Article
TA  - Interciencia
JT  - Interciencia
SO  - Interciencia 1989 14: 37-40.

PMID- 28751403
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Paenarthrobacter nicotinovorans Hce-1.
PG  - e00727-17
AB  - Paenarthrobacter nicotinovorans Hce-1 is a Gram-positive obligate aerobe actinomycete. We
      report here the complete genome sequence of this organism. The
      genome has a length of 4,174,362 bp and contains 4,568 protein-coding genes, 64
      tRNA operons, and 22 rRNA operons. Its GC content in the gene region is 63.4%.
AU  - Meng J
AU  - Sun X
AU  - Li S
AU  - Liang H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00727-17.

PMID- 26044436
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Rice Endophyte-Associated Isolate Kosakonia oryzae KO348.
PG  - e00594-15
AB  - Kosakonia oryzae KO348 is an endophytic and plant growth-promoting strain isolated from the
      roots of rice in Italy. Here, we report the draft genome
      sequence of Kosakonia oryzae KO348.
AU  - Meng X
AU  - Bertani I
AU  - Abbruscato P
AU  - Piffanelli P
AU  - Licastro D
AU  - Wang C
AU  - Venturi V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00594-15.

PMID- 8832377
VI  - 13
DP  - 1996
TI  - Inhibition of restriction endonuclease activity by DNA binding fluorochromes.
PG  - 945-951
AB  - Activity of type II restriction endonucleases is affected by many common factors including
      buffer composition and sequences flanking the recognition site.  The successful development of
      Optical Mapping relied on optimization of light microscope-based imaging of fluorescently
      labeled DNA molecules during restriction endonuclease digestion.  Little was known about the
      effects of commonly used DNA-fluorochromes on restriction endonuclease activity.  Thus, we
      developed an enzyme activity assay using lambda bacteriophage DNA or adenovirus-2 DNA to
      evaluate the effects of five DNA binding fluorochromes (4'-6-daimidine-2-phenylindole (DAPI),
      ethidium bromide (EtdBr), ethidium bromide homodimer (EthD-1), bis-benzimide (H33258) and
      benzothiazolium-4-quinolinium dimer (TOTO-1)) on the enzymatic activities of eleven type II
      restriction endonucleases (AscI, CspI, DraI, EcoRI, HhaI, HindIII, NotI, RsrII, SfiI, SgrAI
      and SmaI).  We found that the minor groove binding fluorochrome, DAPI, did not measurably
      inhibit activity of this group, with the exception of DraI.  Similarly, another minor groove
      binding fluorochrome H33258 inhibited DraI and NotI (slightly).  The three intercalating
      fluorochromes EtdBr, EthD-1 and TOTO-1, however, variably inhibited the other enzymes.  Since
      beta-mercaptoethanol (BME) is used to discourage photodamage of stained DNA molecules, we also
      assessed its effect on restriction endonuclease activity.  Interestingly, DraI, EcoRI, HhaI,
      HindIII, SfiI and SmaI retained full activities at high concentration of BME (5%), but AscI,
      CspI, NotI, RsrII and SgrAI showed varying sensitivities to the BME.  Isoschizomers CspI and
      RsrII behaved differently to both fluorochromes and BME.  The results presented here should
      provide a basis for further development of new Optical Mapping-based techniques requiring
      fluorescence labeling of other actively imaged enzymatic reactions.
AU  - Meng X
AU  - Cai W
AU  - Schwartz DC
PT  - Journal Article
TA  - J. Biomol. Struct. Dyn.
JT  - J. Biomol. Struct. Dyn.
SO  - J. Biomol. Struct. Dyn. 1996 13: 945-951.

PMID- 
VI  - 63
DP  - 2007
TI  - Purification, crystallization, x-ray diffraction analysis and phasing of an engineered single-chain PvuII restriction endonuclease.
PG  - 836-838
AB  - The restriction endonuclease PvuII from Proteus vulgaris has been converted from its wild-type
      homodimeric form into the enzymatically
      active single-chain variant scPvuII by tandemly joining the two
      subunits through the peptide linker Gly-Ser-Gly-Gly. scPvuII, which is
      suitable for the development of programmed restriction endonucleases
      for highly specific DNA cleavage, was purified and crystallized. The
      crystals diffract to a resolution of 2.35 angstrom and belong to space
      group P4(2), with unit-cell parameters a = b = 101.92, c = 100.28
      angstrom and two molecules per asymmetric unit. Phasing was
      successfully performed by molecular replacement.
AU  - Meramveliotaki C
AU  - Kotsifaki D
AU  - Androulaki M
AU  - Hountas A
AU  - Eliopoulos E
AU  - Kokkinidis M
PT  - Journal Article
TA  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
JT  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
SO  - Acta Crystallogr. F Struct. Biol. Cryst. Commun. 2007 63: 836-838.

PMID- 27684472
VI  - 11
DP  - 2016
TI  - Genomic Analysis Reveals Novel Diversity among the 1976 Philadelphia Legionnaires' Disease Outbreak Isolates and Additional ST36 Strains.
PG  - E0164074
AB  - Legionella pneumophila was first recognized as a cause of severe and potentially
      fatal pneumonia during a large-scale outbreak of Legionnaires' disease (LD) at a
      Pennsylvania veterans' convention in Philadelphia, 1976. The ensuing
      investigation and recovery of four clinical isolates launched the fields of
      Legionella epidemiology and scientific research. Only one of the original
      isolates, "Philadelphia-1", has been widely distributed or extensively studied.
      Here we describe the whole-genome sequencing (WGS), complete assembly, and
      comparative analysis of all Philadelphia LD strains recovered from that
      investigation, along with L. pneumophila isolates sharing the Philadelphia
      sequence type (ST36). Analyses revealed that the 1976 outbreak was due to
      multiple serogroup 1 strains within the same genetic lineage, differentiated by
      an actively mobilized, self-replicating episome that is shared with L.
      pneumophila str. Paris, and two large, horizontally-transferred genomic loci,
      among other polymorphisms. We also found a completely unassociated ST36 strain
      that displayed remarkable genetic similarity to the historical Philadelphia
      isolates. This similar strain implies the presence of a potential clonal
      population, and suggests important implications may exist for considering
      epidemiological context when interpreting phylogenetic relationships among
      outbreak-associated isolates. Additional extensive archival research identified
      the Philadelphia isolate associated with a non-Legionnaire case of "Broad Street
      pneumonia", and provided new historical and genetic insights into the 1976
      epidemic. This retrospective analysis has underscored the utility of
      fully-assembled WGS data for Legionella outbreak investigations, highlighting the
      increased resolution that comes from long-read sequencing and a sequence
      type-matched genomic data set.
AU  - Mercante JW
AU  - Morrison SS
AU  - Desai HP
AU  - Raphael BH
AU  - Winchell JM
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2016 11: E0164074.

PMID- 27563044
VI  - 4
DP  - 2016
TI  - Complete Genome Sequences of the Historical Legionella pneumophila Strains OLDA and Pontiac.
PG  - e00866-16
AB  - Here, we report the complete genome sequences of Legionella pneumophila serogroup 1 strains
      OLDA and Pontiac, which predate the 1976 Philadelphia Legionnaires'
      disease outbreak. Strain OLDA was isolated in 1947 from an apparent sporadic
      case, and strain Pontiac caused an explosive outbreak at a Michigan health
      department in 1968.
AU  - Mercante JW
AU  - Morrison SS
AU  - Raphael BH
AU  - Winchell JM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00866-16.

PMID- 27834711
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Two Marinitoga camini Isolates Producing Bacterioviruses.
PG  - e01261-16
AB  - Here, we present the draft genome sequences of two thermophilic Marinitoga strain members of
      the Thermotogales order, Marinitoga camini DV1155 and Marinitoga
      camini DV1197. These strains were isolated from deep-sea hydrothermal vents of
      the Mid-Atlantic Ridge.
AU  - Mercier C
AU  - Lossouarn J
AU  - Haverkamp T
AU  - Bienvenu N
AU  - Godfroy A
AU  - Cueff-Gauchard V
AU  - Geslin C
AU  - Nesbo C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01261-16.

PMID- 23969057
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of the Arcobacter butzleri Cattle Isolate 7h1h.
PG  - e00655-13
AB  - Arcobacter butzleri strain 7h1h was isolated in the United Kingdom from the feces of a
      clinically healthy dairy cow. The genome of this isolate was sequenced to
      completion. Here, we present the annotation and analysis of the completed 7h1h
      genome, along with a comparison of this genome to the existing A. butzleri
      genomes.
AU  - Merga JY
AU  - Winstanley C
AU  - Williams NJ
AU  - Yee E
AU  - Miller WG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00655-13.

PMID- 23012279
VI  - 194
DP  - 2012
TI  - Genome Sequence of Lactobacillus ingluviei, a Bacterium Associated with Weight Gain in Animals.
PG  - 5697
AB  - We report the draft genome sequence of Lactobacillus ingluviei strain Autruche 4  (CSURP209)
      isolated from an ostrich. L. ingluviei is associated with weight gain
      in mice. This genome sequence may help us understand the obesity-induced
      mechanisms of intestinal bacteria.
AU  - Merhej V
AU  - Armougom F
AU  - Robert C
AU  - Raoult D
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5697.

PMID- 23209252
VI  - 194
DP  - 2012
TI  - Genome Sequence of Bartonella rattaustraliani, a Bacterium Isolated from an Australian Rat.
PG  - 7012
AB  - Bartonella rattaustraliani is a facultative intracellular bacterium isolated from the blood of
      a Rattus sp. in Australia. The present study reports the draft
      genome of B. rattaustraliani strain AUST/NH4 (CSUR B609(T)).
AU  - Merhej V
AU  - Croce O
AU  - Robert C
AU  - Rolain JM
AU  - Raoult D
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 7012.

PMID- 23209253
VI  - 194
DP  - 2012
TI  - Genome Sequence of Bartonella rattimassiliensis, a Bacterium Isolated from European Rattus norvegicus.
PG  - 7013
AB  - Bartonella rattimassiliensis is a facultative intracellular bacterium isolated from the blood
      of Rattus norvegicus in Marseille. The present study reports the
      draft genome of B. rattimassiliensis strain 15908 (CIP 107705(T)).
AU  - Merhej V
AU  - Croce O
AU  - Robert C
AU  - Rolain JM
AU  - Raoult D
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 7013.

PMID- 26388967
VI  - 10
DP  - 2015
TI  - Non-contiguous finished genome sequence and description of Clostridium ihumii sp. nov.
PG  - 63
AB  - Clostridium ihumii strain AP5(T) sp. nov. is a new species within the genus Clostridium. This
      strain, whose genome is described here, was isolated from the stool sample of a 21-year-old
      French Caucasian female with anorexia nervosa. C. ihumii is a Gram-positive, anaerobic
      bacillus. Here we describe the features of this organism, together with the complete genome
      sequence and annotation. The 4,433,668 bp long genome contains 4,076 protein-coding and 85 RNA
      genes, including 9 rRNA genes.
AU  - Merhej V
AU  - Pfleiderer A
AU  - Ramasamy D
AU  - Lagier JC
AU  - Michelle C
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 63.

PMID- 8815499
VI  - 48
DP  - 1996
TI  - Biologia molecular en medicina.  II. Enzimas de restriccion.
PG  - 159-163
AB  - 
AU  - Merino A
AU  - Gamba G
PT  - Journal Article
TA  - Rev. Invest. Clin.
JT  - Rev. Invest. Clin.
SO  - Rev. Invest. Clin. 1996 48: 159-163.

PMID- 25395646
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of the Multiresistant Acinetobacter baumannii Strain AbH12O-A2, Isolated during a Large Outbreak in Spain.
PG  - e01182-14
AB  - We report the complete genome sequence of Acinetobacter baumannii strain AbH12O-A2, isolated
      during a large outbreak in Spain. The genome has 3,875,775 bp
      and 3,526 coding sequences, with 39.4% G+C content. The availability of this
      genome will facilitate the study of the pathogenicity of the Acinetobacter
      species.
AU  - Merino M
AU  - Alvarez-Fraga L
AU  - Gomez MJ
AU  - Aransay AM
AU  - Lavin JL
AU  - Chaves F
AU  - Bou G
AU  - Poza M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01182-14.

PMID- 15653631
VI  - 33
DP  - 2005
TI  - Probing a rate-limiting step by mutational perturbation of AdoMet binding in the HhaI methyltransferase.
PG  - 307-315
AB  - DNA methylation plays important roles via regulation of numerous cellular mechanisms in
      diverse organisms, including humans. The paradigm bacterial methyltransferase (MTase) HhaI
      (M.HhaI) catalyzes the transfer of a methyl group from the cofactor S-adenosyl-L-methionine
      (AdoMet) onto the target cytosine in DNA, yielding 5-methylcytosine and
      S-adenosyl-L-homocysteine (AdoHcy). The turnover rate (kcat) of M.HhaI, and the other two
      cytosine-5 MTases examined, is limited by a step subsequent to methyl transfer; however, no
      such step has so far been identified. To elucidate the role of cofactor interactions during
      catalysis, eight mutants of Trp41, which is located in the cofactor binding pocket, were
      constructed and characterized. The mutants show full proficiency in DNA binding and
      base-flipping, and little variation is observed in the apparent methyl transfer rate kchem as
      determined by rapid-quench experiments using immobilized fluorescent-labeled DNA. However, the
      Trp41 replacements with short side chains substantially perturb cofactor binding (100-fold
      higher KD(AdoMet)and KM(AdoMet))leading to a faster turnover of the enzyme (10-fold higher
      kcat). Our analysis indicates that the rate-limiting breakdown of a long-lived ternary product
      complex is initiated by the dissociation of AdoHcy or the opening of the catalytic loop in the
      enzyme.
AU  - Merkiene E
AU  - Klimasauskas S
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2005 33: 307-315.

PMID- 
VI  - 34
DP  - 2005
TI  - Synergy of substrate binding, base flipping and catalytic loop motions in a DNA methyltransferase.
PG  - 617
AB  - The HhaI methyltransferase transfers a methyl group from cofactor AdoMet onto its target
      cytosine residue in DNA.  Crystal structures revealed that M.HhaI flips its target base out of
      the DNA helix.  This transition is accompanied by a massive motion of a loop in the protein
      which locks the flipped out base in the catalytic site.  We used fluorescence of a unique
      tryptophan residue to specifically monitor cofactor binding.  Equilibrium binding studies
      revealed a highly improved binding of the cofactor AdoMet and the reaction product AdoHcy in
      the presence of specific DNA.  No such effect was observed with non-specific DNA in the case
      of AdoMet, but surprisingly, led to a substantial drop in binding affinity in the case of
      AdoHcy!  To elucidate the role of the catalytic loop in substrate binding we constructed two
      variants of M.HhaI in which large segments of the catalytic loop were entirely removed.
      Although the binary interactions with the substrates and base flipping was almost unaffected
      by the deletions, the synergy of substrate binding in the ternary complexes were completely
      lost.  To 'visualize' the loop motions directly during the reaction cycle we prepared a
      series of double mutants in which a unique tryptophan residue was placed in selected positions
      on the mobile catalytic loop.  Single turnover stopped flow kinetic studies of the mutants
      revealed two conformational transitions of the loop which coincide with the formation of the
      tight ternary complex and the release of products.
AU  - Merkiene E
AU  - Lukinavicius G
AU  - Klimasauskas S
PT  - Journal Article
TA  - Eur. Biophys. J.
JT  - Eur. Biophys. J.
SO  - Eur. Biophys. J. 2005 34: 617.

PMID- Not carried by PubMed...
VI  - 1
DP  - 1997
TI  - Coexistence of single-strand and double-strand DNA cytosine-N4-methyltransferases in the BcnI restriction-modification system.
PG  - 5-8
AB  - Sequence analysis of the BcnI RM system, besides the previously characterized restriction
      endonuclease (bcnIR) and cytosine-N4-methyltransferase (bcnIB), revealed the presence of a
      large open reading frame potentially encoding a second cytosine-N4-methyltransferase (bcnIA).
      The bcnIA gene, when subcloned in E. coli on the pUC19 vector, rendered protection of the
      5'CC(C/G)GG-3' sites against cleavage by the cognate BcnI endonuclease.  The two
      methyltransferases were partially purified, and their activities in vitro were compared using
      various DNA substrates.  Both enzymes act on 5'-CC(C/G)GG-3' sites in double-stranded DNA,
      however, BcnIA can also, at a comparable rate, modify the specific targets in single-stranded
      DNA.  Biological significance of the presence of two distinct methyltransferases in the BcnI
      RM system is discussed.
AU  - Merkiene E
AU  - Vilkaitis G
AU  - Klimasauskas S
PT  - Journal Article
TA  - Biologija
JT  - Biologija
SO  - Biologija 1997 1: 5-8.

PMID- 9628356
VI  - 379
DP  - 1998
TI  - A pair of single-strand and double-strand DNA cytosine-N4 methyltransferases from Bacillus centrosporus.
PG  - 569-571
AB  - Sequence analysis of the BcnI restriction-modification system revealed the presence of an open
      reading frame encoding a second cytosine-N4 methyltransferase, M.BcnIA, in the vicinity of the
      genes specifying the previously characterized cytosine-N4 methyltransferase M.BcnIB and
      restriction endonuclease R.BcnI.  Both methyltransferases were purified from the E. coli cells
      expressing the individual genes, and their enzymatic efficiencies in vitro were compared with
      a variety of DNA substrates.  Both enzymes act on 5'-CC(C/G)GG-3' sites in double-stranded
      DNA, however, M.BcnIA can also, with a comparable efficiency, modify the specific targets in
      single-stranded DNA.  The biological significance of the presence of the tandem
      methyltransferases in the BcnI system is discussed.
AU  - Merkiene E
AU  - Vilkaitis G
AU  - Klimasauskas S
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1998 379: 569-571.

PMID- 10961941
VI  - 28
DP  - 2000
TI  - Kinetics of cofactor binding and catalytic loop movements of HhaI methyltransferase.
PG  - A464
AB  - HhaI methyltransferase (M.HhaI) flips its target cytosine out of the DNA helix and into a
      catalytic site in the enzyme.  This conformational transition of bound DNA is accompanied by a
      large movement of the catalytic loop (over 20 Angstrom) in the enzyme itself.  Our studies
      concentrated on the motions of the catalytic loop and interaction between M.HhaI and its
      cofactor S-adenosyl-L-methionine (AdoMet) which serves as the methyl group donor in the MTase
      reaction.  We found that the intrinsic fluorescence of a unique tryptophan residue (W41) is
      significantly quenched upon binding of cofactor, but is unaffected upon binding of DNA.  A
      series of kinetic association and equilibrium binding studies in the presence of various DNA
      substrates permitted direct determination of kinetic parameters for cofactor binding.  We find
      that non-specific DNA causes a substantial decrease in the affinity of the enzyme toward the
      product AdoHcy but not toward cofactor AdoMet, which suggests a mechanism for cofactor
      reloading during diffusion of MTase over regions of non-specific DNA.  Single-turnover
      experiments revealed a concentration independent transient (2 s^-1) which we tentatively
      attribute to the aforementioned conformational rearrangement of the catalytic loop.  To
      'visualize' the loop motions directly we prepared a series of double mutants in which the
      unique Trp was placed in selected positions on the mobile catalytic loop.  Preliminary
      characterization of the mutant proteins indicates that they are suitable for direct kinetic
      measurement of conformational transitions in the catalytic loop.  Kinetic analysis of these
      transitions using global fitting and simulation is now underway.
AU  - Merkiene E
AU  - Weinhold E
AU  - Klimasauskas S
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 2000 28: A464.

PMID- 8932364
VI  - 24
DP  - 1996
TI  - Statistical evidence for a biochemical pathway of natural, sequence-targeted G/C to C/G transversion mutagenesis in Haemophilus influenzae Rd.
PG  - 4146-4151
AB  - Markov chain analysis of the Haemophilus influenzae Rd genome reveals striking
      under-representation of three palindromic tetranucleotide strings (CCGG, GGCC and CATG),
      accompanied by over-representation of six tetranucleotide strings that are derived from the
      former by exchanging strand location of the two residues making up a G/C nucleotide pair at
      the terminal palindrome position.  Constraints are outlined for a molecular model able to
      explain the phenomenon as the result of sequence-targeted, enzyme-driven G/C to C/G
      transversion mutagenesis.  Possible participation in the process by components of known DNA
      mismatch repair or restriction/modification systems (in particular, cytosine methylation) is
      discussed.  The effect widens the spectrum of enzyme-driven, specific mutagenesis beyond the
      formerly described C/G to T/A transition (VSP repair of Escherichia coli).  Potential
      evolutionary benefits of enzymatic pathways of specific mutagenesis can be envisioned.
AU  - Merkl R
AU  - Fritz HJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1996 24: 4146-4151.

PMID- 1579456
VI  - 20
DP  - 1992
TI  - Statistical evaluation and biological interpretation of non-random abundance in the E. coli K-12 genome of tetra- and pentanucleotide sequences related to VSP DNA mismatch repair.
PG  - 1657-1662
AB  - The abundance of all tetra- and pentanucleotide sequences is calculated for a set of DNA
      sequence data comprising 767,393 nucleotides of the E. coli K-12 genome.  Observed frequencies
      are compared to those expected from a Markov chain prediction algorithm.  Systematic and
      extreme non-random representations are found for special sets of sequences.  These are
      interpreted as arising from incorporation of a 2'-deoxyguanosine residue opposite thymidine
      during replication which, in special sequence contexts, leads to a T/G mismatch that is
      simultaneously substrate for two competing DNA mismatch repair systems: the mutHLS and the VSP
      pathway.  Processing by the former leads to error correction, by the latter to mutation
      fixation.  The significance of the latter process, as demonstrated here, makes it unlikely
      that VSP repair has evolved mainly as a mutation avoidance mechanism.  It is proposed that in
      E. coli K-12, VSP repair, together with DNA cytosine methylation, constitutes a
      mutagenesis/recombination system capable of promoting gene-conversion-like unidirectional
      transfer of short stretches of DNA sequence.
AU  - Merkl R
AU  - Kroeger M
AU  - Rice P
AU  - Fritz H-J
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 1657-1662.

PMID- 3039870
VI  - 163
DP  - 1987
TI  - In vitro sodium bisulfite mutagenesis of restriction endonuclease recognition sites.
PG  - 79-87
AB  - Sodium bisulfite treatment of single-stranded DNA deaminates exposed cytosine
      residues to form uracil, resulting in cytosine-to-thymidine transition
      mutations following DNA replication.  We have used this reaction in vitro to
      destroy the recognition sequences for the restriction endonucleases HindIII and
      XmaI in the aminoglycoside 3'-phosphotransferase I coding region of plasmid
      pUC4K.  This procedure should be applicable to the mutation of any recognition
      sequence of restriction endonucleases which generate cytosine-containing
      single-stranded ends.  The possibility of mutagenesis of restriction sites to
      generate stop codons in coding regions is discussed.
AU  - Merlo DJ
AU  - Thompson DV
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 1987 163: 79-87.

PMID- 8386500
VI  - 59
DP  - 1993
TI  - In vivo methylation in Escherichia coli by the Bacillus subtilis phage Phi3T methyltransferase to protect plasmids from restriction upon transformation of Clostridium acetobutylicum ATCC 824.
PG  - 1077-1081
AB  - The restriction endonuclease Cac824I has been shown to be a major barrier to
      electrotransformation of Clostridium acetobutylicum ATCC 824 (L.D. Mermelstein, N.E. Welker,
      G.N. Bennett, and E.T. Popoutsakis, BioTechnology 10:190-195, 1992). Methylation by the Phi3T
      I methyltransferase encoded by Bacillus subtilis phage Phi3T was shown to protect plasmid DNA
      from restriction by Cac824I. Expression in Escherichia coli of the phi3tI gene (which encodes
      the Phi3TI methyltransferase) from pAN1, which replicates via the p15A origin of replication,
      was sufficient to completely methylate coresident E. coli-C. acetobutylicum shuttle vectors
      with ColE1 origins of replication. Three shuttle vectors (pIMP1, pSYL2, and pSYL7) methylated
      in this manner were used to efficiently electrotransform strain ATCC 824. These vectors could
      not be introduced into strain ATCC 824 when unmethylated because the E. coli portions of the
      plasmids contain a large number of Cac824I sites. This method obviates the need to use B.
      subtilis-C. acetobutylicum shuttle vectors with few Cac824I sites to introduce DNA into C.
      acetobutylicum ATCC 824.
AU  - Mermelstein LD
AU  - Popoutsakis ET
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1993 59: 1077-1081.

PMID- 1368230
VI  - 10
DP  - 1992
TI  - Expression of cloned homologous genes in Clostridium acetobutylicum ATCC 824.
PG  - 190-195
AB  - We have previously cloned the acetone-formation pathway gene, encoding acetoacetate
      deacarboxylase (adc), and butyrate-formation pathway gene, encoding phosphtransbutyrylase
      (ptb), of Clostridium acetobutylicum ATCC 824 in Escherichia coli. Here we report their
      subcloning in Bacillus subtilis and transfer to strain ATCC 824 via electrotransformation,
      where the corresponding enzyme activities were expressed at elevated levels, using pFNK1, a
      new B. subtilis/C. acetobutylicum shuttle vector. Plasmid pFNK1 was used because shuttle
      vectors that function in E. coli were unable to electrotransform ATCC 824 unless they became
      deleted in the E. coli-plasmid regions. The difficulties with shuttle vectors that function in
      E. coli are probably due to the presence of a restriction endonuclease in ATCC 824. This
      endonuclease recognizes the sequence 5'-GCNGC-3', which is prevalent in E. coli plasmids,
      but occurs infrequently in pFNK1 and C. acetobutylicum genes. Cloning of genes in C.
      acetobutylicum is critical for redirecting the cellular metabolism (metabolic engineering) as
      well as for genetic studies of this industrial organism.
AU  - Mermelstein LD
AU  - Welker NE
AU  - Bennett GN
AU  - Papoutsakis ET
PT  - Journal Article
TA  - Biotechnology
JT  - Biotechnology
SO  - Biotechnology 1992 10: 190-195.

PMID- 
VI  - 27
DP  - 1999
TI  - AhdI, a new class of restriction-modification system?
PG  - A126
AB  - Bacterial restriction-modification systems have traditionally been divided into three distinct
      classes, types I, II and III.  Here we report a study of what appears to be a new class of R-M
      systems, exemplified by AhdI.  Analysis of the DNA sequence and gene organization of AhdI has
      revealed that the methyltransferase more closely resembles a type I MTase than a type II.  In
      contrast, the AhdI endonuclease is more characteristic of a type II R-M system.  It is
      possible that the AhdI R-M system is an evolutionary intermediate made up of a type II-like
      endonuclease and a methyltransferase that resembles those found in the multisubunit type I
      systems.  This new class of R-M system has been named type 1-1/2.  The AhdI methyltransferase
      is a multisubunit enzyme containing two subunits, one that shares some degree of sequence
      homology with the type I HsdM subunit and the other with the HsdS subunit found in type I
      MTases.  Whereas the M subunit of AhdI closely resembles a type I HsdM subunit in the sequence
      and size of the protein, the S subunit is only half the size of the type I counterpart.  We
      report here the cloning and characterization of the AhdI methyltransferase.  With experimental
      evidence obtained from gel electrophoresis and analytical gel filtration we have determined
      the stoichiometry of the enzyme and with the use of gel retardation and surface plasmon
      resonance we will address the relationship of the subunit composition to DNA binding by the
      AhdI MTase.
AU  - Mernagh D
AU  - Marks P
AU  - Kneale G
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 1999 27: A126.

PMID- 9628343
VI  - 379
DP  - 1998
TI  - Protein-protein and protein-DNA interactions in the type I restriction endonuclease R.EcoR124I.
PG  - 497-503
AB  - The type I restriction-modification system EcoR124I recognizes and binds to the split DNA
      recognition sequence 5'-GAAN6RTCG-3'.  The methyltransferase, consisting of HsdM and HsdS
      subunits with the composition M2S, can interact with one or more subunits of the HsdR subunit
      to form the endonuclease.  The interaction of the methyltransferase with HsdR has been
      investigated by surface plasmon resonance, showing that there are two non-equivalent binding
      sites for hsdR which differ in binding affinity by at least two orders of magnitude.  DNA
      footprinting experiments using exonuclease III suggest that the addition of HsdR to the
      methyltransferase (at a stoichiometry of either 1:1 or 2:1) increases the stability of the
      resulting DNA-protein complex but does not increase the size of the footprint.  More extensive
      in situ footprinting experiments using copper-phenanthroline on the DNA-protein complexes
      formed by M2S, R1M2S and R2M2S also show no difference in the detailed cleavage pattern, with
      ~18 nucleotides protected on both strands in each complex.  Thus the HsdR subunit(s) of the
      endonuclease stabilize the interaction of the M2S complex with DNA, but do not directly
      contribute to DNA binding.  In addition, the thymidine nucleotide in the tetranucleotide
      recognition sequence GTCG is hyper-reactive to cleavage in each case, suggesting that the DNA
      structure in this region is altered in these complexes.
AU  - Mernagh DR
AU  - Janscak P
AU  - Firman K
AU  - Kneale GG
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1998 379: 497-503.

PMID- 9016653
VI  - 24
DP  - 1996
TI  - High resolution footprinting of a type I methyltransferase reveals a large structural distortion within the DNA recognition site.
PG  - 4853-4858
AB  - The type I DNA methyltransferase M.EcoR124I is a multi-subunit enzyme that binds to the
      sequence GAAN6RTCG, transferring a methyl group from S-adenosylmethionine to a specific
      adenine on each DNA strand.  We have investigated the protein-DNA interactions in the complex
      by DNase I and hydroxyl radical footprinting.  The DNase I footprint is unusually large: the
      protein protects the DNA on both strands for at least two complete turns of the helix,
      indicating that the enzyme completely encloses the DNA in the complex.  The higher resolution
      hydroxyl radical probe shows a smaller, but still extensive, 18 bp footprint encompassing the
      recognition site.  Within this region, however, there is a remarkably hyper-reactive site on
      each strand.  The two sites of enhanced cleavage are co-incident with the two adenines that
      are the target bases for methylation, showing that the DNA is both accessible and highly
      distorted at these sites.  The hydroxyl radical footprint is unaffected by the presence of the
      cofactor S-adenosylmethionine, showing that the distorted DNA structure induced by M.EcoR124I
      is formed during the initial DNA binding reaction and not as a transient intermediate in the
      reaction pathway.
AU  - Mernagh DR
AU  - Kneale GG
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1996 24: 4853-4858.

PMID- 9023108
VI  - 25
DP  - 1997
TI  - DNA binding and subunit interactions in the type I methyltransferase M.EcoR124I.
PG  - 987-991
AB  - The type I DNA methyltransferase M.EcoR124I consists of two methylation subunits (hsdM) and
      one DNA recognition subunit (HsdS).  When expressed independently, HsdS is insoluble, but this
      subunit can be obtained in soluble form as a GST fusion protein.  We show that the HsdS
      subunit, even as a fusion protein, is unable to form a discrete complex with its DNA
      recognition sequence.  When HsdM is added to the HsdS fusion protein, discrete complexes are
      formed but these are unable to methylate DNA.  The two complexes formed correspond to species
      with one or two copies of the HsdM subunit, indicating that blocking the N-terminus of hsdS
      affects one of the HsdM binding sites.  However, removal of the GST moiety from such complexes
      results in tight and specific DNA binding and restores full methylation activity.  The results
      clearly demonstrate the importance of the HsdM subunit for DNA binding, in addition to its
      catalytic role in the methyltransferase reaction.
AU  - Mernagh DR
AU  - Reynolds LA
AU  - Kneale GG
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1997 25: 987-991.

PMID- 9841886
VI  - 336
DP  - 1998
TI  - Interaction of the type I methyltransferase M.EcoR124I with modified DNA substrates: sequence discrimination and base flipping.
PG  - 719-725
AB  - We have analyzed the DNA-protein contacts made between the type I DNA methyltransferase
      M.EcoR124I and its recognition sequence.  The effects of base modifications have been probed
      by measuring the affinity of M.EcoR124I for the modified sequences relative to that for the
      wild-type sequence by using gel-retardation competition assays.  These results, along with
      those from methylation interference footprinting and photo-affinity cross-linking have
      identified the location of potential DNA contacts within the DNA recognition site.
      Substitution of 6-thioguanosine for each of the three specific guanines in the recognition
      sequence leads to a large (10-20-fold) decrease in the strength of DNA binding, indicating the
      importance of hydrogen-bonding interactions in the major groove of DNA.  In contrast,
      replacement of either (or both) of the adenine at the target site for methylation by the
      enzyme, to produce either a base pair mismatch or loss of the base, leads to a marked increase
      in DNA-binding affinity.  The results strongly support the proposal that type I
      methyltransferases employ a base-flipping mechanism to methylate their target base.
AU  - Mernagh DR
AU  - Taylor IA
AU  - Kneale GG
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 1998 336: 719-725.

PMID- 15632435
VI  - 151
DP  - 2005
TI  - A unique nine-gene comY operon in Streptococcus mutans.
PG  - 157-166
AB  - Many Gram-positive and Gram-negative bacteria possess natural competence mechanisms for DNA
      capture and internalization. In Bacillus
      subtilis, natural competence is absolutely dependent upon the presence
      of a seven-gene operon known as the comG operon (comGA-G). In species
      of Streptococcus, this function has been described for a four-gene
      operon (comYA-D in Streptococcus gordonii and cglA-D in Streptococcus
      pneumoniae). In this study, a nine-orf operon (named comYA-I) required
      for natural competence in Streptococcus mutans was identified and
      characterized. Orf analysis of this operon indicates that the first
      four Orfs (ComYA-D) share strong homology with ComYA-D of S. gordonii
      and CgIA-D of S. pneumoniae, the fifth to seventh Orfs (ComYE-G) match
      conserved hypothetical proteins from various species of Streptococcus
      with ComYF possessing a predicted ComGF domain, the eighth Orf (ComYH)
      shows a strong homology to numerous DNA methyltransferases from
      restriction/modification systems, and the ninth Orf (ComYI) is
      homologous to acetate kinase (AckA). RT-PCR analysis of the orf
      junctions confirmed that all nine orfs were present in a single
      transcript, while real-time RT-PCR analysis demonstrated that these
      orfs were expressed at a level very similar to that of the first orf in
      the operon. Mutations were constructed in all nine putative orfs. The
      first seven genes (comYA-G) were found to be essential for natural
      competence, while comYH and comYI had reduced and normal natural
      competence ability, respectively. Analyses of S. mutans comY-luciferase
      reporter fusions indicated that comY expression is growth-phase
      dependent, with maximal expression at an OD600 of about 0(.)2, while
      mutations in ciaH, comC and luxS reduced the level of comY expression.
      In addition, comY operon expression appears to be correlated with
      natural competence ability.
AU  - Merritt J
AU  - Qi FX
AU  - Shi WY
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2005 151: 157-166.

PMID- 25814602
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence and Annotation of Corynebacterium singulare DSM 44357, Isolated from a Human Semen Specimen.
PG  - e00183-15
AB  - Corynebacterium singulare DSM 44357 is a urease-positive microorganism isolated from human
      semen. The complete genome sequence of C. singulare DSM 44357
      comprises 2,830,519 bp with a mean G+C content of 60.12% and 2,581 protein-coding
      genes. The deduced antibiotic resistance pattern of this strain includes
      macrolides, lincosamides, aminoglycosides, chloramphenicol, and tetracyline.
AU  - Merten M
AU  - Brinkrolf K
AU  - Albersmeier A
AU  - Kutter Y
AU  - Ruckert C
AU  - Tauch A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00183-15.

PMID- 9449671
VI  - 125
DP  - 1998
TI  - Sex-specific exons control DNA methyltransferase in mammalian germ cells.
PG  - 889-897
AB  - The spermatozoon and oocyte genomes bear sex-specific methylation patterns that are
      established during gametogenesis and are required for the allele-specific expression of
      imprinted genes in somatic tissues.  The mRNA for Dnmt1, the predominant maintenance and de
      novo DNA (cytosine-5)-methyl transferase in mammals, is present at high levels in postmitotic
      murine germ cells but undergoes alternative splicing of sex-specific 5' exons, which controls
      the production and localization of enzyme during specific stages of gametogenesis.  An
      oocyte-specific 5' exon is associated with the production of very large amounts of active
      Dnmt1 protein, which is truncated at the N terminus and sequestered in the cytoplasm during
      the later stages of oocyte growth, while a spermatocyte-specific 5' exon interferes with
      translation and prevents production of Dnmt1 during the prolonged crossing-over stages of male
      meiosis.  During the course of postnatal oogenesis, Dnmt1 is present at high levels in nuclei
      only in growing dictyate oocytes, a stage during which gynogenetic developmental potential is
      lost and biparental developmental potential is gained.
AU  - Mertineit C
AU  - Yoder JA
AU  - Taketo T
AU  - Laird DW
AU  - Trasler JM
AU  - Bestor TH
PT  - Journal Article
TA  - Development
JT  - Development
SO  - Development 1998 125: 889-897.

PMID- 4343968
VI  - 69
DP  - 1972
TI  - Cleavage of DNA by EcoRI restriction endonuclease generates cohesive ends.
PG  - 3370-3374
AB  - EcoRI restriction endonuclease cleaves duplex DNA at a specific sequence,
      probably 6 nucleotide pairs in length, by making two single-strand staggered
      cleavages, generating 5'-phosphoryl and 3'-hydroxyl termini.  The single-strand
      ends produced at each break have identical and complementary sequences of 4 or
      6 nucleotides in length.  Therefore, the cleavage site possesses a 2-fold
      rotational axis of symmetry perpendicular to the helix axis.  The ends of
      full-length linear SV40 DNA, generated by EcoRI endonuclease cleavage, can be
      joined by Escherichia coli ligase to regenerate duplex, fully infectious,
      covalently-closed circular molecules.  It was further found that all EcoRI
      endonuclease-generated ends are identical and complementary.  Therefore, any
      two DNA molecules with EcoRI sites can be "recombined" at their restriction
      sites by the sequential action of EcoRI endonuclease and DNA ligase to generate
      hybrid DNA molecules.
AU  - Mertz JE
AU  - Davis RW
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1972 69: 3370-3374.

PMID- 
VI  - 2
DP  - 1972
TI  - DNA-restriction enzyme from E. coli K.
PG  - 889-895
AB  - Most strains of E. coli are able to recognize and degrade DNA from foreign E.
      coli strains.  Whether a foreign DNA molecule is degraded depends on certain
      nonheritable properties imparted by the cell from which it is obtained.  These
      properties are called host-controlled modifications.  For example, the result
      of infecting E. coli strain K with phage lambda depends on the host in which
      the phages were last grown.  Phages grown in bacteria possessing the
      modification character mk multiply successfully, but phages from bacteria
      lacking mk do not.  Instead, their DNA is quickly degraded on entering cells of
      strain K.  The ability of strain K to degrade or "restrict" DNA from cells
      lacking mk is itself under genetic control, the responsible character being
      designated rk.  An endonuclease has been shown to be responsible for
      restriction in E. coli K.  It is specifically active against lambda DNA from
      strains lacking mk and is called endonuclease R.K.
AU  - Meselson M
AU  - Yuan R
PT  - Journal Article
TA  - Procedures in Nucleic Acids Research
JT  - Procedures in Nucleic Acids Research
SO  - Procedures in Nucleic Acids Research 1972 2: 889-895.

PMID- 4868368
VI  - 217
DP  - 1968
TI  - DNA restriction enzyme from E. coli.
PG  - 1110-1114
AB  - An endonuclease which degrades foreign DNA has been isolated.  The enzyme
      requires S-adenosylmethionine, ATP and Mg++.
AU  - Meselson M
AU  - Yuan R
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1968 217: 1110-1114.

PMID- 4563439
VI  - 41
DP  - 1972
TI  - Restriction and modification of DNA.
PG  - 447-466
AB  - None
AU  - Meselson M
AU  - Yuan R
AU  - Heywood J
PT  - Journal Article
TA  - Annu. Rev. Biochem.
JT  - Annu. Rev. Biochem.
SO  - Annu. Rev. Biochem. 1972 41: 447-466.

PMID- 23105090
VI  - 194
DP  - 2012
TI  - Genome Sequence of Lactococcus raffinolactis Strain 4877, Isolated from Natural Dairy Starter Culture.
PG  - 6364
AB  - The nonstarter lactic acid bacterium Lactococcus raffinolactis is prevalent in a  wide range
      of environments, such as the dairy environment, but little is known
      about this species. Here, we present the draft genome of Lactococcus
      raffinolactis strain 4877, isolated from a natural mesophilic dairy starter
      culture.
AU  - Meslier V
AU  - Loux V
AU  - Renault P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6364.

PMID- 23144391
VI  - 194
DP  - 2012
TI  - Genome Sequence of Leuconostoc pseudomesenteroides Strain 4882, Isolated from a Dairy Starter Culture.
PG  - 6637
AB  - The nonstarter lactic acid bacterium Leuconostoc pseudomesenteroides is a species widely found
      in the dairy industry and plays a key role in the formation of
      aromatic compounds. Here, we report the first genome sequence of a dairy strain
      of Leuconostoc pseudomesenteroides, which is 2 Mb.
AU  - Meslier V
AU  - Loux V
AU  - Renault P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6637.

PMID- 2842065
VI  - 54
DP  - 1988
TI  - Timing and targeting: the biological functions of Dam methylation in E. coli.
PG  - 735-737
AB  - Postreplicative DNA methylation superimposes on the fixed primary information of the DNA
      sequence secondary information that has significance in the regulation of a variety of
      cellular processes in prokaryotes and eukaryotes.  In many eukaryotes, methylation of cytosine
      residues in defined regions of the genome is involved in a global control of gene activity.
      The methylation pattern may change during development, but once established, it can be stably
      transmitted to daughter cells by the activity of maintenance methyltransferases.  Highly
      methylated regions are often transcriptionally inactive.  In contrast to the situation in
      eukaryotes, the regulatory effects of Dam methylation in Escherichia coli do not arise from
      selective methylation of defined regions of the genome. The Dam DNA methyltransferase
      methylates the N6 position of adenine at all GATC sites.  However, because there is a lag
      between replication and methylation, newly replicated DNA is hemimethylated and therefore
      distinct from the rest of the genome.  The hemimethylated status of new DNA provides a time
      window during which certain cellular processes are activated or suppressed, thus linking these
      processes to the cell cycle.  Moreover, the methylation asymmetry in this window allows
      distinction between parental (methylated) and daughter (unmethylated) DNA strands.  Here we
      discuss the regulatory potential of these two forms of superimposed information.
AU  - Messer W
AU  - Noyer-Weidner M
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1988 54: 735-737.

PMID- 21317328
VI  - 193
DP  - 2011
TI  - Complete Genome Sequences of Two Hemotropic Mycoplasmas, Mycoplasma haemofelis Strain Ohio2 and Mycoplasma suis Strain Illinois.
PG  - 2068-2069
AB  - We report the complete and fully assembled genomes of Mycoplasma haemofelis strain Ohio2 and
      Mycoplasma suis strain Illinois, which are the
      first available genomes of these uncultivatable hemoplasma species. The
      single circular chromosomes of 1,152,484 bp and 742,431 bp for M.
      haemofelis and M. suis, respectively, are typical of mycoplasma species,
      having reduced size and low G+C content (38.8% for M. haemofelis and 31.1%
      for M. suis). Their metabolic pathways are reduced, with evidence of
      adaption to the blood environment.
AU  - Messick JB
AU  - Santos AP
AU  - Guimaraes AM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 2068-2069.

PMID- 27182430
VI  - 11
DP  - 2016
TI  - Complete genome sequence of 'Halanaeroarchaeum sulfurireducens' M27-SA2, a sulfur-reducing and acetate-oxidizing haloarchaeon from the deep-sea hypersaline anoxic lake Medee.
PG  - 35
AB  - Strain M27-SA2 was isolated from the deep-sea salt-saturated anoxic lake Medee, which
      represents one of the most hostile extreme environments on our planet. On
      the basis of physiological studies and phylogenetic positioning this extremely
      halophilic euryarchaeon belongs to a novel genus 'Halanaeroarchaeum' within the
      family Halobacteriaceae. All members of this genus cultivated so far are strict
      anaerobes using acetate as the sole carbon and energy source and elemental sulfur
      as electron acceptor. Here we report the complete genome sequence of the strain
      M27-SA2 which is composed of a 2,129,244-bp chromosome and a 124,256-bp plasmid.
      This is the second complete genome sequence within the genus Halanaeroarchaeum.
      We demonstrate that genome of 'Halanaeroarchaeum sulfurireducens' M27-SA2 harbors
      complete metabolic pathways for acetate and sulfur catabolism and for de novo
      biosynthesis of 19 amino acids. The genomic analysis also reveals that
      'Halanaeroarchaeum sulfurireducens' M27-SA2 harbors two prophage loci and one
      CRISPR locus, highly similar to that of Kulunda Steppe (Altai, Russia) isolate
      'H. sulfurireducens' HSR2(T). The discovery of sulfur-respiring acetate-utilizing
      haloarchaeon in deep-sea hypersaline anoxic lakes has certain significance for
      understanding the biogeochemical functioning of these harsh ecosystems, which are
      incompatible with life for common organisms. Moreover, isolations of
      Halanaeroarchaeum members from geographically distant salt-saturated sites of
      different origin suggest a high degree of evolutionary success in their
      adaptation to this type of extreme biotopes around the world.
AU  - Messina E
AU  - Sorokin DY
AU  - Kublanov IV
AU  - Toshchakov S
AU  - Lopatina A
AU  - Arcadi E
AU  - Smedile F
AU  - La Spada G
AU  - La Cono V
AU  - Yakimov MM
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 35.

PMID- 
VI  - 29
DP  - 1999
TI  - Genetic analysis in the domain Archaea.
PG  - 277-326
AB  - The recognition of the Archaea as a phylogenetic domain at the same hierarchical level as the
      Bacteria or Eukarya is a relatively recent development in the biological sciences.  This
      revision of the classical prokaryotic vs. eukaryotic phylogeny stems largely from the work of
      Carl Woese and his collaborators, and originated in the late 1970's from the study of what
      were then known as methane-producing bacteria.  Utilizing 16S RNA as a molecular marker for
      determining phylogenetic relationships between organisms, Woese and his collaborators showed
      that these organisms were vastly different from the known bacterial species and proposed they
      should be considered as a separate group, designated the Archaebacteria.  Although this
      assertion was hotly contested for many years, its validity has been gradually substantiated by
      a variety of methods and is now widely accepted.  The term Archaebacteria has been replaced by
      Archaea to emphasize the important point that these are not Bacteria.
AU  - Metcalf WW
PT  - Journal Article
TA  - Methods Microbiol.
JT  - Methods Microbiol.
SO  - Methods Microbiol. 1999 29: 277-326.

PMID- 16043709
VI  - 102
DP  - 2005
TI  - The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses.
PG  - 10913-10918
AB  - The completion of the 5,373,180-bp genome sequence of the marine psychrophilic bacterium
      Colwellia psychrerythraea 34H, a model for the study of life in permanently cold environments,
      reveals capabilities important to carbon and nutrient cycling, bioremediation, production of
      secondary metabolites, and cold-adapted enzymes. From a genomic perspective, cold adaptation
      is suggested in several broad categories involving changes to the cell membrane fluidity,
      uptake and synthesis of compounds conferring cryotolerance, and strategies to overcome
      temperature-dependent barriers to carbon uptake. Modeling of three-dimensional protein
      homology from bacteria representing a range of optimal growth temperatures suggests changes to
      proteome composition that may enhance enzyme effectiveness at low temperatures. Comparative
      genome analyses suggest that the psychrophilic lifestyle is most likely conferred not by a
      unique set of genes but by a collection of synergistic changes in overall genome content and
      amino acid composition.
AU  - Methe BA et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2005 102: 10913-10918.

PMID- 14671304
VI  - 302
DP  - 2003
TI  - Genome of Geobacter sulfurreducens: metal reduction in subsurface environments.
PG  - 1967-1969
AB  - The complete genome sequence of Geobacter sulfurreducens, a delta-proteobacterium, reveals
      unsuspected capabilities, including
      evidence of aerobic metabolism, one-carbon and complex carbon metabolism,
      motility, and chemotactic behavior. These characteristics, coupled with
      the possession of many two-component sensors and many c-type cytochromes,
      reveal an ability to create alternative, redundant, electron transport
      networks and offer insights into the process of metal ion reduction in
      subsurface environments. As well as playing roles in the global cycling of
      metals and carbon, this organism clearly has the potential for use in
      bioremediation of radioactive metals and in the generation of electricity.
AU  - Methe BA et al
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2003 302: 1967-1969.

PMID- 
VI  - 0
DP  - 1990
TI  - Group II introns transpose in yeast mitochondria.
PG  - 169-174
AB  - There is a set of genetic phenomena which, first discovered in yeast mitochondrial genetics
      twenty years ago, is still of considerable interest for molecular biologists.  Variously
      described as polarity of transmission and recombination of genetic markers, unidirectional
      gene conversion with coconversion of flanking markers, intron gene conversion, duplicative
      transposition, homing or intron infectivity these phenomena have one feature in common: a
      specific portion of the donor mitochondrial genome, is preferentially transmitted to the
      progeny when compared to other parts of the same genome.  The leading element of this gene
      conversion is an intron and the process is initiated by an intron-encoded-protein which has a
      specific double strand DNA endonuclease activity that cleaves an intronless recipient
      mitochondrial genome at (or in the vicinity of) the site of intron insertion.  For many years
      the phenomenon was restricted to the omega+ intron located in the large rRNA gene but more
      recently it was observed for the ai4 intron of the COX1 gene.  Both omega+ and ai4 belong to
      the group I of intronic RNA structure and code for proteins which share several polypeptide
      motifs in common with RNA maturases.
AU  - Meunier B
AU  - Tian G-L
AU  - Macadre C
AU  - Slonimski PP
AU  - Lazowska J
PT  - Journal Article
TA  - Structure, function and biogenesis of energy transfer systems.
JT  - Structure, function and biogenesis of energy transfer systems.
SO  - Structure, function and biogenesis of energy transfer systems. 1990 0: 169-174.

PMID- 28702355
VI  - 13
DP  - 2017
TI  - Whole Genome sequencing and annotation of halophilic Salinicoccus sp. BAB 3246 isolated from coastal region of Gujarat.
PG  - 30-34
AB  - Salinicoccus sp. BAB 3246 is a halophilic bacterium isolated from a marine water sample
      collected from the coastal region of Gujarat, India, from a surface water stream. Based on
      16sRNA sequencing, the organism was identi and #64257;ed as Salinicoccus sp. BAB3246 (Genebank
      ID:KF889285). The present work was performed to determine the whole genome sequence of the
      organism using Ion Torrent PGM platform followed by assembly using the CLC genomics workbench
      and genome annotation using RAST, BASys and MaGe. The complete genome sequence was 713,204 bp
      identi and #64257;ed by with second largest size for Salinicoccus sp. reported in the NCBI
      genome database. A total of 652 degradative pathways were identi and #64257;ed by KEGG map
      analysis. Comparative genomic analysis revealed Salinicoccus sp.BAB3246 as mosthighly related
      to Salinicoccushalodurans H3B36. Data mining identi and #64257;ed stress response genes and
      operator pathway for degradation of various environmental pollutants. Annotation data and
      analysis indicate potential use in pollution control in industrial in and #64258;uent and
      saline environment.
AU  - Mevada VA
AU  - Patel S
AU  - Pandya JV
AU  - Joshi H
AU  - Patel RK
PT  - Journal Article
TA  - Genomics Data
JT  - Genomics Data
SO  - Genomics Data 2017 13: 30-34.

PMID- 26451236
VI  - 10
DP  - 2015
TI  - Draft genome sequence of Halomonas meridiana R1t3 isolated from the surface microbiota of the Caribbean Elkhorn coral Acropora palmata.
PG  - 75
AB  - Members of the gammaproteobacterial genus Halomonas are common in marine environments.
      Halomonas and other members of the Oceanospirillales have recently
      been identified as prominent members of the surface microbiota of reef-building
      corals. Halomonas meridiana strain R1t3 was isolated from the surface mucus layer
      of the scleractinian coral Acropora palmata in 2005 from the Florida Keys. This
      strain was chosen for genome sequencing to provide insight into the role of
      commensal heterotrophic bacteria in the coral holobiont. The draft genome
      consists of 290 scaffolds, totaling 3.5 Mbp in length and contains 3397
      protein-coding genes.
AU  - Meyer JL
AU  - Dillard BA
AU  - Rodgers JM
AU  - Ritchie KB
AU  - Paul VJ
AU  - Teplitski M
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 75.

PMID- 
VI  - 0
DP  - 1996
TI  - DNA methylation of flower color transgenes in Petunia hybrida.
PG  - 305-317
AB  - Inactivation of transgene constructs that have been introduced into plants is a frequently
      reported phenomenon.  Many such silencing events are associated with DNA methylation, although
      it is still a matter of debate whether de novo methylation is the cause or the consequence of
      gene inactivation.  A correlation between DNA methylation and gene inactivation is not limited
      to transgenes but is also observed for transposable elements and for some, but not all,
      endogenous genes.  Interestingly, changes in methylation patterns that correlate with changes
      in tissue-specific expression have been found in distant upstream regions of some genes,
      indicating that methylation-mediated control of gene expression does not exclusively affect
      promoter regions.
AU  - Meyer P
PT  - Journal Article
TA  - Epigenetic Mechanisms of Gene Regulation
JT  - Epigenetic Mechanisms of Gene Regulation
SO  - Epigenetic Mechanisms of Gene Regulation 1996 0: 305-317.

PMID- 28798176
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Magnetospirillum sp. Strain 15-1, a Denitrifying Toluene Degrader Isolated from a Planted Fixed-Bed Reactor.
PG  - e00764-17
AB  - Here, we report the draft genome sequence of Magnetospirillum sp. 15-1. This strain was
      isolated from a planted fixed-bed reactor based on its ability to
      degrade toluene under anaerobic conditions. The genome assembly consists of 5.4
      Mb in 28 contigs and 5,095 coding sequences containing the genes involved in
      anaerobic toluene degradation.
AU  - Meyer-Cifuentes I
AU  - Fiedler S
AU  - Muller JA
AU  - Kappelmeyer U
AU  - Mausezahl I
AU  - Heipieper HJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00764-17.

PMID- 19878267
VI  - 12
DP  - 2010
TI  - Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME-1 group.
PG  - 422-439
AB  - Microbial consortia mediating the anaerobic oxidation of methane with sulfate are composed of
      methanotrophic Archaea (ANME) and Bacteria related
      to sulfate-reducing Deltaproteobacteria. Cultured representatives are not
      available for any of the three ANME clades. Therefore, a metagenomic
      approach was applied to assess the genetic potential of ANME-1 archaea. In
      total, 3.4 Mbp sequence information was generated based on metagenomic
      fosmid libraries constructed directly from a methanotrophic microbial mat
      in the Black Sea. These sequence data represent, in 30 contigs, about
      82-90% of a composite ANME-1 genome. The dataset supports the hypothesis
      of a reversal of the methanogenesis pathway. Indications for an
      assimilatory, but not for a dissimilatory sulfate reduction pathway in
      ANME-1, were found. Draft genome and expression analyses are consistent
      with acetate and formate as putative electron shuttles. Moreover, the
      dataset points towards downstream electron-accepting redox components
      different from the ones known from methanogenic archaea. Whereas catalytic
      subunits of [NiFe]-hydrogenases are lacking in the dataset, genes for an
      [FeFe]-hydrogenase homologue were identified, not yet described to be
      present in methanogenic archaea. Clustered genes annotated as secreted
      multiheme c-type cytochromes were identified, which have not yet been
      correlated with methanogenesis-related steps. The genes were shown to be
      expressed, suggesting direct electron transfer as an additional possible
      mode to shuttle electrons from ANME-1 to the bacterial sulfate-reducing
      partner.
AU  - Meyerdierks A
AU  - Kube M
AU  - Kostadinov I
AU  - Teeling H
AU  - Glockner FO
AU  - Reinhardt R
AU  - Amann R
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2010 12: 422-439.

PMID- 995649
VI  - 3
DP  - 1976
TI  - Topographical analysis of yeast ribosomal DNA by cleavage with restriction endonucleases.  II. The physical map of EcoRI fragments.
PG  - 2697-2707
AB  - Yeast ribosomal DNA (rDNA) was digested with the restriction endonuclease
      EcoRI.  Eight distinct fragments were obtained with a molecular weight of 4.35
      (1), 1.75 (2), 1.45 (3), 1.07 (4), 0.42 (5), 0.37 (6), 0.26 (7) and 0.22 (8)
      Mdaltons, respectively.  Except for fragment 1 with a molecular wieght of 4.35
      Mdaltons, all fragments are derived from the multiple ribosomal transcription
      units.  The 'spacer' sequences, on the other hand, gave rise to digestion
      products which are very heterogeneous in size.  By analysis of the partial
      digestion products, together with the data obtained by digestion with a
      combination of two restriction enzymes (EcoRI and HindII or HindIII) and
      redigation of the HindII- and HindIII-fragments with EcoRI, the physical map of
      the EcoRI cleavage sites in the ribosomal transcription unit could be
      established.
AU  - Meyerink JH
AU  - Retel J
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1976 3: 2697-2707.

PMID- 1083938
VI  - 2
DP  - 1976
TI  - Topographical analysis of yeast ribosomal DNA by cleavage with restriction endonucleases.
PG  - 393-400
AB  - Yeast ribosomal DNA (rDNA) was digested with the restriction enzymes HindIII,
      HindII and a mixture of HindII and HindIII.  The cleavage products were
      analyzed by electrophoresis on 1.5% agarose gels.  Several distinct bands could
      be observed, which are derived from the redundant ribosomal transcription unit.
      They are superimposed on a rather broad smear of background DNA, representing
      the heterogenous 'spacer' sequences.  From the restriction maps, together with
      data obtained by partial digestion, a physical map for the ribosomal
      transcription unit in yeast could be constructed.
AU  - Meyerink JH
AU  - Retel J
AU  - Planta RJ
AU  - Heidekamp F
PT  - Journal Article
TA  - Mol. Biol. Rep.
JT  - Mol. Biol. Rep.
SO  - Mol. Biol. Rep. 1976 2: 393-400.

PMID- 
VI  - 
DP  - 1987
TI  - Actinophages and restriction endonucleases from Micromonospora species (Actinomycetales).
PG  - 1-117
AB  - In the course of developing a screening procedure for the detection of
      restriction endonucleases in Micromonosporae, an economically important group
      of actinomycetes, previously undiscovered actinophages were isolated from soils
      enriched with Micromonospora species.  The majority of the actinophages
      belonged to Ackermann's type B1 since they had isometric heads, hexagonal in
      shape, and long, noncontractile tails.  The tails were often flexible and
      striated, and some had terminal bulbs.  One actinophage was classified as type
      C1 because of the very short, noncontractile tail and the isometric head.  The
      actinophages all contained double-stranded DNA and had genome sizes ranging
      from approximately 40 to 60 kilobases.  All actinophages were polyvalent except
      for one monovalent isolate specific for M. coerulea (NRRL B16093).  The
      host-ranges of the actinophages were determined on thirty species of
      Micromonospora.  Certain actinophages were also capable of infecting strains of
      Amorphosporangium, Ampullariella and Catellatospora which are actinomycetes of
      the same cell wall chemotype as Micromonosporae (type II).  Whole-cell sugar
      analyses were performed on the Micromonospora species using a newly developed
      thin-layer chromatography (TLC) method.  The TLC method used an
      acetonitrile:water development system, and N-naphthylethylenediamine
      hydrochloride or acid aniline phthalate to visualize hexoses or pentoses,
      respectively.  A comparison of host-range studies and whole-cell sugar analyses
      suggested that xylose may be involved in actinophage receptors for
      Micromonospora species.  The actinophages were used in efficiency of plating
      studies as biological indicators of host-controlled restriction-modification
      activity.  Restriction enzymes were detected and isolated from three strains of
      Micromonospora.  Type II restriction endonucleases werre isolated from
      Micromonospora echinospora ssp. echinospora (ATCC 15837), M. purpurea (ATCC
      15835) and M. zionensis (LL-100-125), and were designated MecI, MpuI and MziI,
      respectively.  Restriction enzymes MecI and MpuI are isoschizomers of XhoI
      (from Xanthomonas holcicola), while MziI is an isoschizomer of PvuII (from
      Proteus vulgaris).  One can speculate that a number of R-M systems remain to be
      identified in Micromonospora species and that the discovery of an enzyme with a
      novel recognition sequence is possible.
AU  - Meyertons JL
PT  - Journal Article
TA  - Ph.D. Thesis, Rutgers University, USA
JT  - Ph.D. Thesis, Rutgers University, USA
SO  - Ph.D. Thesis, Rutgers University, USA 1987 : 1-117.

PMID- Not carried by PubMed...
VI  - 48
DP  - 1988
TI  - Actinophages and restriction endonucleases from Micromonospora species (Actinomycetales).
PG  - 1888
AB  - In the course of developing a screening procedure for the detection of
      restriction endonucleases in micromonosporae, an economically important group
      of actinomycetes, previously undiscovered actinophages were isolated from soils
      enriched with Micromonospora species. The majority of the actinophages belonged
      to Ackermann's type B1 since they had isometric heads, hexagonal in shape, and
      long, noncontractile tails. The tails were often flexible and striated, and
      some had terminal bulbs. One actinophage was classified as type C1 because of
      the very short, noncontractile tail and the isometric head. The actinophages
      all contained double-stranded DNA and had genome sizes ranging from
      approximately 40 to 60 kilobases. All actinophages were polyvalent except for
      one monovalent isolate specific for M. coerulea (NRRL B16092). The host-ranges
      of the actinophages were determined on thirty species of Micromonospora.
      Certain actinophages were also capable of infecting strains of
      Amorphosporangium, Ampullariella and Catellatospora which are Actinomycetes of
      the same cell wall chemotype as Micromonosporae (type II). Whole-cell sugar
      analyses were performed on the Micromonospora species using a newly developed
      thin-layer chromatography (TLC) method. The TLC method used an
      acetonitrile:water development system, and N-naphthylethylenediamine
      hydrochloride or acid aniline phthalate to visualize hexoses or pentoses,
      respectively. A comparison of host-range studies and whole-cell sugar analyses
      suggested that xylose may be involved in actinophage receptors for
      Micromonospora species. The actinophages were used in efficiency of plating
      studies as biological indicators of host-controlled restriction-modification
      activity. Restriction enzymes were detected and isolated from three strains of
      Micromonospora. Type II restriction endonucleases were isolated from
      Micromonospora echinospora ssp. echinospora (ATCC 15837), M. purpurea (ATCC
      15835) and M. zionensis (LL-100-125), and were designed MecI, MpuI and MziI,
      respectively. Restriction enzymes MecI and MpuI are isoschizomers of XhoI (from
      Xanthomonas holcicola), while MziI is an isoschizomer of PvuII (from Proteus
      vulgaris). One can speculate that a number of R-M systems remain to be
      identified in Micromonospora species and that the discovery of an enzyme with a
      novel recognition sequence is possible.
AU  - Meyertons JL
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1988 48: 1888.

PMID- Not included in PubMed...
VI  - 2
DP  - 1987
TI  - Actinophages and restriction enzymes from Micromonospora species (Actinomycetales).
PG  - 293-303
AB  - To develop a screening procedure for the detection of restriction endonucleases
      in Micromonosporae and Catellatosporae based on efficiency of plating, eight
      different actinophages were isolated from soils enriched with Micromonospora
      species and one from Catellatospora-enriched soil.  The lytic actinophages all
      contained double-stranded DNA and the majority appeared, when examined by
      electron microscopy, to belong to Ackermann's type B1 since they had isometric
      heads and noncontractile tails.  One actinophage was classified as type C1
      because of its isometric head and very short noncontractile tail.  The host
      ranges of the actinophages were determined on strains of Micromonospora and
      selected species from other actinomycete genera of cell wall chemotype II.
      Type II restriction enzymes were isolated from M. echinospora ssp. echinospora
      (ATCC 15837), M. purpurea (ATCC 15835) and M. zionensis (LL-100-125) and were
      designated MecI, MpuI, and MziI, respectively.  Restriction enzymes MecI and
      MpuI are isoschizomers of XhoI, while MziI is an isoschizomer of PvuII.
AU  - Meyertons JL
AU  - Tilley BC
AU  - Lechevalier MP
AU  - Lechevalier HA
PT  - Journal Article
TA  - J. Ind. Microbiol.
JT  - J. Ind. Microbiol.
SO  - J. Ind. Microbiol. 1987 2: 293-303.

PMID- 27445380
VI  - 4
DP  - 2016
TI  - Genome Sequence of the Uncommon Streptococcus pyogenes M/emm66 Strain STAB13021,  Isolated from Clonal Clustered Cases in French Brittany.
PG  - e00689-16
AB  - Here, we announce the complete annotated genome sequence of the invasive Streptococcus
      pyogenes strain M/emm66, isolated in 2013 from a subcutaneous
      abscess in new clustered cases in French Brittany.
AU  - Meygret A
AU  - Vincent P
AU  - Moullec S
AU  - Nacazume J
AU  - Adnani Y
AU  - Lavenier D
AU  - Kayal S
AU  - Faili A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00689-16.

PMID- 26380038
VI  - 10
DP  - 2015
TI  - High-quality permanent draft genome sequence of Ensifer meliloti strain 4H41, an  effective salt- and drought-tolerant microsymbiont of Phaseolus vulgaris.
PG  - 34
AB  - Ensifer meliloti 4H41 is an aerobic, motile, Gram-negative, non-spore-forming rod that can
      exist as a soil saprophyte or as a legume microsymbiont of common bean (Phaseolus vulgaris).
      Strain 4H41 was isolated in 2002 from root nodules of P. vulgaris grown in South Tunisia from
      the oasis of Rjim-Maatoug. Strain 4H41 is salt- and drought-tolerant and highly effective at
      fixing nitrogen with P. vulgaris. Here we describe the features of E. meliloti 4H41, together
      with genome sequence information and its annotation. The 6,795,637 bp high-quality permanent
      draft genome is arranged into 47 scaffolds of 47 contigs containing 6,350 protein-coding genes
      and 72 RNA-only encoding genes, and is one of the rhizobial  genomes sequenced as part of the
      DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule
      Bacteria (GEBA-RNB) project proposal.
AU  - Mhamdi R
AU  - Ardley J
AU  - Tian R
AU  - Seshadri R
AU  - Reddy TB
AU  - Pati A
AU  - Woyke T
AU  - Markowitz V
AU  - Ivanova N
AU  - Kyrpides N
AU  - Reeve W
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 34.

PMID- 11536427
VI  - 30
DP  - 2001
TI  - Cloning and sequence analysis of a zebrafish cDNA encoding DNA (cytosine-5)-methyltransferase-1.
PG  - 213-219
AB  - Summary: The zebrafish has become a well-established animal model for the analysis of
      development and of several disease phenotypes. Several of the favorable traits that make it a
      popular model organism would also be beneficial for the study of normal and abnormal
      vertebrate development in which DNA methylation may play a role. We report the determination
      of the full-length cDNA sequence corresponding to the zebrafish DNA (cytosine-5-)
      methyltransferase gene, Dnmt1. It is 4,907 bases long and has an open reading frame predicted
      to encode a 1,499 amino acid protein that is similar in size and sequence to a number of other
      methyltransferases identified in other organisms.
AU  - Mhanni AA
AU  - Yoder JA
AU  - Dubesky C
AU  - McGowan RA
PT  - Journal Article
TA  - Genesis
JT  - Genesis
SO  - Genesis 2001 30: 213-219.

PMID- 7899082
VI  - 23
DP  - 1995
TI  - Functional analysis of Gln-237 mutants of HhaI methyltransferase.
PG  - 620-627
AB  - When the HhaI (cytosine-5) methyltransferase (M.HhaI) binds DNA it causes the target cytosine
      to be flipped 180 degrees out of the helix. The space becomes occupied by two amino acids,
      Ser-87 and Gln-237, which enter the helix from opposite sides and form a hydrogen bond to each
      other. Gln-237 may be involved in specific sequence recognition since it forms three hydrogen
      bonds to the orphan guanosine, which is the partner of the target cytosine. We have prepared
      all 19 mutants of Gln-237 and tested their biochemical properties. We find that mutations of
      this residue greatly affect the stability of the M.HhaI-DNA complex without affecting the
      enzyme's specificity for the target sequence. Surprisingly, all mutants retain detectable
      levels of enzymatic activity.
AU  - Mi S
AU  - Alonso D
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1995 23: 620-627.

PMID- 8506140
VI  - 21
DP  - 1993
TI  - The DNA binding affinity of HhaI methylase is increased by a single amino acid substitution in the catalytic center.
PG  - 2459-2464
AB  - The HhaI methyltransferase recognizes the sequence GCGC and transfers a methyl group to C5 of
      the first cytosine residue. All m5C-methyltransferases contain a highly conserved sequence
      motif called the P-C motif. The cysteine residue of this motif is involved in catalysis by
      forming a covalent bond with the 6-position of cytosine prior to methyl group transfer. For
      the EcoRII methyltransferase, it has been shown that substitution of this catalytic cysteine
      by glycine is cytotoxic to E.coli cells expressing the mutant methyltransferase (Wyszynski et
      al. Nucl. Acids. Res. 20:319,1992). We now show that this observation can be extended to the
      HhaI system and suggest that the cytotoxicity is due to abnormally tight DNA binding by the
      mutant methyltransferase, which probably interferes with replication or transcription.
AU  - Mi S
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 2459-2464.

PMID- 1408795
VI  - 20
DP  - 1992
TI  - How M.MspI and M.HpaII decide which base to methylate.
PG  - 4811-4816
AB  - The HpaII methylase (M.HpaII) recognizes the sequence CCGG and methylates the inner cytosine
      residue. The MspI methylase (MspI) recognizes the same sequence but methylates the outer
      cytosine residue. Both methylases have the usual architecture of 10 well-conserved motifs
      surrounding a variable region, responsible for sequence specific recognition, that is quite
      different in the two methylases. We hav constructed hybrids between these two methylases and
      studied their methylation properties. A hybrid containing the variable region and C-terminal
      sequences from M.MspI methylates the outer cytosine residue. A second hybrid identical to the
      first except that the variable region derives from the M.HpaII methylates the inner cytosine
      residue. Thus the choice of base to be methylated within the recognition sequence is
      determined by the variable region.
AU  - Mi S
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 4811-4816.

PMID- 22203551
VI  - 49
DP  - 2011
TI  - Complete genome of Leptospirillum ferriphilum ML-04 provides insight into its physiology and environmental adaptation.
PG  - 890-901
AB  - Leptospirillum ferriphilum has been identified as the dominant, moderately
      thermophilic, bioleaching microorganism in bioleaching processes. It is an acidic
      and chemolithoautrophic bacterium that gains electrons from ferrous iron
      oxidation for energy production and cell growth. Genetic information about this
      microorganism has been limited until now, which has hindered its further
      exploration. In this study, the complete genome of L. ferripilum ML-04 is
      sequenced and annotated. The bacterium has a single circular chromosome of
      2,406,157 bp containing 2,471 coding sequences (CDS), 2 rRNA operons, 48 tRNA
      genes, a large number of mobile genetic elements and 2 genomic islands. In silico
      analysis shows L. ferriphilum ML-04 fixes carbon through a reductive citric acid
      (rTCA) cycle, and obtains nitrogen through ammonium assimilation. The genes
      related to "cell envelope biogenesis, outer membrane" (6.9%) and "DNA
      replication, recombination and repair" (5.6%) are abundant, and a large number of
      genes related to heavy metal detoxification, oxidative and acidic stress defense,
      and signal transduction pathways were detected. The genomic plasticity, plentiful
      cell envelope components, inorganic element metabolic abilities and stress
      response mechanisms found the base for this organism's survival in the
      bioleaching niche.
AU  - Mi S
AU  - Song J
AU  - Lin J
AU  - Che Y
AU  - Zheng H
AU  - Lin J
PT  - Journal Article
TA  - J. Microbiol.
JT  - J. Microbiol.
SO  - J. Microbiol. 2011 49: 890-901.

PMID- 
VI  - 26
DP  - 2002
TI  - Molecular cloning and sequence analysis of Rana tigrina ranavirus (RTV) DNA methyltransferase gene.
PG  - 157-160
AB  - The complete gene of RTV DNA methyltransferase (MTase) was amplified, cloned and sequenced.
      The ORF consists of 642 bp, which codes for a protein of 214 aa with a predicted molecular
      mass
      of 24.8kD.  Sequence analysis of MTase gene shows much higher identity to the species of genus
      Ranavirus (96%-97%) than to lymphocystis disease virus (56%), the type species of the genus
      Lymphocystivirus, indicating again that RTV was the member of the genus Ranavirus; just as the
      other vertebrate iridoviruses, the MTase gene of RTV contains the first four highly conserved
      motifs of cytosine MTases but the fifth motif, responsible for DNA binding specificity, is
      missing; among the virus of RTV, doctor fish iridovirus and largemouth bass ranavirus, the
      very
      different identity between MTase and MCP gene suggests that the gene used as target to
      estimate the evolution of the iridoviruses should be suitable.
AU  - Miao S
AU  - Li F
AU  - Zhang M
AU  - Wang X
AU  - He J
AU  - Jiang J
PT  - Journal Article
TA  - Shuichan Xuebao
JT  - Shuichan Xuebao
SO  - Shuichan Xuebao 2002 26: 157-160.

PMID- 26089417
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Gluconobacter oxydans NL71, a Strain That Efficiently Biocatalyzes Xylose to Xylonic Acid at a High Concentration.
PG  - e00615-15
AB  - Gluconobacter oxydans NL71, a selected strain in the crude lignocellulosic hydrolysate,
      catalyzed 600 g/liter xylose to 586.3 g/liter xylonic acid at 95.1%
      yield. The biocatalysis of xylose yielded three times higher than the best
      previous output, providing a possibility of the industrial scale utilization of
      lignocellulosic xylose. Due to its promising industrial applications, we
      sequenced the complete genome of strain G. oxydans NL71 to further our
      understanding of its overall metabolism.
AU  - Miao Y
AU  - Zhou X
AU  - Xu Y
AU  - Yu S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00615-15.

PMID- 28642378
VI  - 5
DP  - 2017
TI  - New Genome Sequence of an Echinaceapurpurea Endophyte, Arthrobacter sp. Strain EpSL27, Able To Inhibit Human-Opportunistic Pathogens.
PG  - e00565-17
AB  - We announce here the draft genome sequence of Arthrobacter sp. strain EpSL27, isolated from
      the stem and leaves of the medicinal plant Echinacea purpurea and
      able to inhibit human-pathogenic bacterial strains. The genome sequencing of this
      strain may lead to the identification of genes involved in the production of
      antimicrobial molecules.
AU  - Miceli E
AU  - Presta L
AU  - Maggini V
AU  - Fondi M
AU  - Bosi E
AU  - Chiellini C
AU  - Fagorzi C
AU  - Bogani P
AU  - Di Pilato V
AU  - Rossolini GM
AU  - Mengoni A
AU  - Firenzuoli F
AU  - Perrin E
AU  - Fani R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00565-17.

PMID- 22001176
VI  - 67
DP  - 2012
TI  - ICEPmu1, an integrative conjugative element (ICE) of Pasteurella multocida: structure and transfer.
PG  - 91-100
AB  - BackgroundIntegrative and conjugative elements (ICEs) have not been
      detected in Pasteurella multocida. In this study the multiresistance
      ICEPmu1 from bovine P. multocida was analysed for its core genes and its
      ability to conjugatively transfer into strains of the same and different
      genera.MethodsICEPmu1 was identified during whole genome sequencing.
      Coding sequences were predicted by bioinformatic tools and manually
      curated using the annotation software ERGO. Conjugation into P. multocida,
      Mannheimia haemolytica and Escherichia coli recipients was performed by
      mating assays. The presence of ICEPmu1 and its circular intermediate in
      the recipient strains was confirmed by PCR and sequence analysis.
      Integration sites were sequenced. Susceptibility testing of the
      ICEPmu1-carrying recipients was conducted by broth
      microdilution.ResultsThe 82 214 bp ICEPmu1 harbours 88 genes. The core
      genes of ICEPmu1, which are involved in excision/integration and
      conjugative transfer, resemble those found in a 66 641 bp ICE from
      Histophilus somni. ICEPmu1 integrates into a tRNA(Leu) and is flanked by
      13 bp direct repeats. It is able to conjugatively transfer to P.
      multocida, M. haemolytica and E. coli, where it also uses a tRNA(Leu) for
      integration and produces closely related 13 bp direct repeats. PCR assays
      and susceptibility testing confirmed the presence and the functional
      activity of the ICEPmu1-associated resistance genes in the recipient
      strains.ConclusionsThe observation that the multiresistance ICEPmu1 is
      present in a bovine P. multocida and can easily spread across strain and
      genus boundaries underlines the risk of a rapid dissemination of multiple
      resistance genes, which will distinctly decrease the therapeutic options.
AU  - Michael GB
AU  - Kadlec K
AU  - Sweeney MT
AU  - Brzuszkiewicz E
AU  - Liesegang H
AU  - Daniel R
AU  - Murray RW
AU  - Watts JL
AU  - Schwarz S
PT  - Journal Article
TA  - J. Antimicrob. Chemother.
JT  - J. Antimicrob. Chemother.
SO  - J. Antimicrob. Chemother. 2012 67: 91-100.

PMID- 3731271
VI  - 46
DP  - 1986
TI  - Genetic exchanges between bacteriophage T4 and filamentous fungi?
PG  - 323
AB  - Note the sequence similarity between I-TevI and a protein encoded by a class 1 intron in the
      NADH-dehydrogenase gene of Neurospora crassa.
AU  - Michel F
AU  - Dujon B
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1986 46: 323.

PMID- 27610213
VI  - 11
DP  - 2016
TI  - Draft genome sequence of Enterococcus faecium strain LMG 8148.
PG  - 63
AB  - Enterococcus faecium, traditionally considered a harmless gut commensal, is emerging as an
      important nosocomial pathogen showing increasing rates of
      multidrug resistance. We report the draft genome sequence of E. faecium strain
      LMG 8148, isolated in 1968 from a human in Gothenburg, Sweden. The draft genome
      has a total length of 2,697,490 bp, a GC-content of 38.3 %, and 2,402 predicted
      protein-coding sequences. The isolation of this strain predates the emergence of
      E. faecium as a nosocomial pathogen. Consequently, its genome can be useful in
      comparative genomic studies investigating the evolution of E. faecium as a
      pathogen.
AU  - Michiels JE
AU  - Van den Bergh B
AU  - Fauvart M
AU  - Michiels J
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 63.

PMID- 27594976
VI  - 11
DP  - 2016
TI  - Draft genome sequence of Acinetobacter baumannii strain NCTC 13423, a multidrug-resistant clinical isolate.
PG  - 57
AB  - Acinetobacter baumannii is a pathogen that is becoming increasingly important and causes
      serious hospital-acquired infections. We sequenced the genome of A.
      baumannii NCTC 13423, a multidrug-resistant strain belonging to the international
      clone II group, isolated from a human infection in the United Kingdom in 2003.
      The 3,937,944 bp draft genome has a GC-content of 39.0 % and a total of 3672
      predicted protein-coding sequences. The availability of genome sequences of
      multidrug-resistant A. baumannii isolates will fuel comparative genomic studies
      to help understand the worrying spread of multidrug resistance in this pathogen.
AU  - Michiels JE
AU  - Van den Bergh B
AU  - Fauvart M
AU  - Michiels J
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 57.

PMID- Not carried by PubMed...
VI  - 88
DP  - 1988
TI  - Diamminedichloroplatinum(II) modification of DNA inhibits cutting by restriction endonucleases in a sequence specific manner.
PG  - 164
AB  - cis-Diamminedichloroplatinum(II), cis-DDP, is a potent antitumor agent while
      the trans-isomer is ineffective.  Both have been shown to bind to DNA
      preferentially at guanine.  In this study, [32P]-end-labeled DNA modified with
      cis-DDP or trans-DDP was digested with restriction endonucleases having
      recognition sequences at which DDP is capable of reacting to form bifunctional
      adducts:  BstUI, GG^CG; HinPI, G^CGC; HhaI, GCG^C; and BamHI, G^GATCC.
      Inhibition of cutting by these enzymes was compared to that for ClaI, AT^CGAT,
      as DDP reacts with bases of its recognition site in a monofunctional manner.
      Restriction fragments were subjected to electrophoresis and the amounts of
      radioactivity in each were quantitated by densitometry and liquid scintillation
      spectrophotometry.  Inhibition by trans-DDP was greatest when the base sequence
      GXG was adjacent to, or occluding the cut site.  Thus, two guanines separated
      by a third base appears to be a biologically inhibitory adduct of trans-DDP
      while cis-DDP forms such adducts at lower frequency.  Inhibition by cis-DDP was
      greatest at the BamHI site where it can form crosslinks between adjacent
      guanines.
AU  - Mick JM
AU  - Beck DJ
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1988 88: 164.

PMID- 28495770
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of the Bacterium Bacillus circulans Jordan Strain 32352.
PG  - e00289-17
AB  - Here, we report the complete genome sequence for the Bacillus circulans Jordan strain 32352.
      This species is a soil dwelling bacterium that expresses glycosyl
      hydrolase enzymes degrading pneumococcal capsular polysaccharides.
AU  - Middleton DR
AU  - Lorenz W
AU  - Avci FY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00289-17.

PMID- 
VI  - 
DP  - 1973
TI  - Restriction endonucleases from Haemophilus species: Enzymes for specific fragmentation of DNA.
PG  - 
AB  - Restriction endodeoxyribonucleases cleave DNA at specific recognition sites.  We proposed to
      employ such enzymes as reagents for analysis of DNA.  Screening procedures were begun to
      identify restriction enzymes that would cleave OmegaX174 DNA into unique fragments.
AU  - Middleton JH
PT  - Journal Article
TA  - Ph.D. Thesis
JT  - Ph.D. Thesis
SO  - Ph.D. Thesis 1973 : .

PMID- 4537735
VI  - 10
DP  - 1972
TI  - Specific fragments of PhiX174 deoxyribonucleic acid produced by a restriction enzyme from Haemophilus aegyptius, endonuclease Z.
PG  - 42-50
AB  - A restriction-like enzyme has been purified from Haemophilus aegyptius.  This
      nuclease, endonuclease Z, produces a rapid decrease in the viscosity of native
      calf thymus and H. influenzae deoxyribonucleic acids (DNA), but does not
      degrade homologous DNA.  The specificity of endonuclease Z is different from
      that of the similar endonuclease isolated from H. influenzae (endonuclease R).
      The purified enzyme cleaves the double-stranded replicative form DNA of
      bacteriophage PhiX174 (PhiX174 RF DNA) into at least 11 specific limit
      fragments whose molecular sizes have been estimated by gel electrophoresis.
      The position of these fragments with respect to the genetic map of PhiX174 can
      be determined by using the genetic assay for small fragments of PhiX174 DNA.
AU  - Middleton JH
AU  - Edgell MH
AU  - Hutchison CA III
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1972 10: 42-50.

PMID- 22843596
VI  - 194
DP  - 2012
TI  - Genome Sequence of Pediococcus pentosaceus Strain IE-3.
PG  - 4468
AB  - We report the 1.8-Mb genome sequence of Pediococcus pentosaceus strain IE-3, isolated from a
      dairy effluent sample. The whole-genome sequence of this strain
      will aid in comparative genomics of Pediococcus pentosaceus strains of diverse
      ecological origins and their biotechnological applications.
AU  - Midha S
AU  - Ranjan M
AU  - Sharma V
AU  - Kumari A
AU  - Singh PK
AU  - Korpole S
AU  - Patil PB
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4468.

PMID- 22582385
VI  - 194
DP  - 2012
TI  - Genome Sequence of Xanthomonas citri pv. mangiferaeindicae Strain LMG 941.
PG  - 3031
AB  - We report the 5.1-Mb genome sequence of Xanthomonas citri pv. mangiferaeindicae strain LMG
      941, the causal agent of bacterial black spot in mango. Apart from evolutionary studies, the
      draft genome will be a valuable resource for the epidemiological studies and quarantine of
      this phytopathogen.
AU  - Midha S
AU  - Ranjan M
AU  - Sharma V
AU  - Pinnaka AK
AU  - Patil PB
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3031.

PMID- 26635397
VI  - 44
DP  - 2015
TI  - On the role of steric clashes in methylation control of restriction endonuclease  activity.
PG  - 485-495
AB  - Restriction-modification systems digest non-methylated invading DNA, while protecting host DNA
      against the endonuclease activity by methylation. It is widely believed that the methylated
      DNA would not 'fit' into the binding site of the endonuclease in the productive orientation,
      and thus steric clashes should account for most of the protection. We test this concept
      statistically by grafting methyl groups in silico onto non-methylated DNA in co-crystal
      structures with restriction endonucleases. Clash scores are significantly higher for
      protective than non-protective methylation (P < 0.05% according to the Wilcoxon rank sum
      test). Structural data alone are sufficient to distinguish between protective and
      non-protective DNA methylation with 90% confidence and decision thresholds of 1.1 A and 48 A3
      for the most severe distance-based and cumulative volume-based clash with the protein,
      respectively (0.1 A was deducted from each interatomic distance to allow for coordinate
      errors). The most severe clashes are more pronounced for protective methyl groups attached to
      the nitrogen atoms (N6-methyladenines and N4-methylcytosines) than for C5-methyl groups on
      cytosines. Cumulative clashes are comparable for all three types of protective methylation.
AU  - Mierzejewska K
AU  - Bochtler M
AU  - Czapinska H
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2015 44: 485-495.

PMID- 24966351
VI  - 42
DP  - 2014
TI  - Structural basis of the methylation specificity of R.DpnI.
PG  - 8745-8754
AB  - R.DpnI consists of N-terminal catalytic and C-terminal winged helix domains that  are
      separately specific for the Gm6ATC sequences in Dam-methylated DNA. Here we
      present a crystal structure of R.DpnI with oligoduplexes bound to the catalytic
      and winged helix domains and identify the catalytic domain residues that are
      involved in interactions with the substrate methyl groups. We show that these
      methyl groups in the Gm6ATC target sequence are positioned very close to each
      other. We further show that the presence of the two methyl groups requires a
      deviation from B-DNA conformation to avoid steric conflict. The methylation
      compatible DNA conformation is complementary with binding sites of both R.DpnI
      domains. This indirect readout of methylation adds to the specificity mediated by
      direct favorable interactions with the methyl groups and solvation/desolvation
      effects. We also present hydrogen/deuterium exchange data that support
      'crosstalk' between the two domains in the identification of methylated DNA,
      which should further enhance R.DpnI methylation specificity.
AU  - Mierzejewska K
AU  - Siwek W
AU  - Czapinska H
AU  - Kaus-Drobek M
AU  - Radlinska M
AU  - Skowronek K
AU  - Bujnicki JM
AU  - Dadlez M
AU  - Bochtler M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2014 42: 8745-8754.

PMID- 
VI  - 280
DP  - 2013
TI  - Molecular basis of 6-methyladenine recognition by R.DpnI restriction endonuclease.
PG  - 122-123
AB  - The 6-methyladenine is one of the key epigenetic modifications in prokaryotes.  R.DpnI is the
      best known 6 mA-dependent restriction endonuclease, specific for Dam methylated G6 mATC sites
      and widely used for site-directed mutagenesis.  Our previous studies have shown that R.DpnI
      consists of two domains, an N-terminal catalytic PD-D/E_XK domain and a C-terminal winged
      helix domain and that both independently read out DNA sequence and methylation status.  In our
      first structure of R.DpnI-DNA complex, there is only one substrate oligoduplex per enzyme
      molecule, which is specifically bound to the wH domain and distant from the calalytic domain.
      Hence, the question remained open how the catalytic domain of R.DpnI interacts with its
      target, and how it specifically recognizes the methyl groups which license DNA cleavage.  Such
      a process is difficult to realize with stringency, because attractive van der Waals
      interactions with the small hydrophobic group are relatively weak when compared to repulsive
      ones.  The structures depicting the phenomenon are rare and there is still relatively little
      known about the mechanism of recognition by modification dependent enzymes.  Here, we present
      a high resolution structure of R.DpnI which features both protein domains bound to the target
      DNA.  Recognition of the 6mAs by the catalytic domain is carried out without flipping bases
      out of the helix.  A previously disordered loop wraps around the major groove of the target
      DNA, where both methyl groups are located in close proximity to each other.  The PD-D/E)XK
      domain places the 6mAs in a hydrophobic pocket formed by residues Leu129 and Trp 138.  To the
      best of our knowledge this is the first structure showing how a protein can efficiently detect
      two 6mA modified sites together.
AU  - Mierzejewska K
AU  - Siwek W
AU  - Czapinska H
AU  - Skowronek K
AU  - Bujnicki J
AU  - Bochtler M
PT  - Journal Article
TA  - FEBS J.
JT  - FEBS J.
SO  - FEBS J. 2013 280: 122-123.

PMID- 26847886
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Streptococcus salivarius HSISS4, a Human Commensal Bacterium Highly Prevalent in the Digestive Tract.
PG  - e01637-15
AB  - The human commensal bacterium Streptococcus salivarius plays a major role in the  equilibrium
      of microbial communities of the digestive tract. Here, we report the
      first complete genome sequence of a Streptococcus salivarius strain isolated from
      the small intestine, namely, HSISS4. Its circular chromosome comprises 1,903
      coding sequences and 2,100,988 nucleotides.
AU  - Mignolet J
AU  - Fontaine L
AU  - Kleerebezem M
AU  - Hols P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01637-15.

PMID- 25377696
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Chromobacterium haemolyticum Causing Human Bacteremia Infection in Japan.
PG  - e01047-14
AB  - Chromobacterium haemolyticum is a Gram-negative bacterium displaying remarkable hemolysis
      against human and sheep erythrocytes. In addition, C. haemolyticum
      infects humans, in which the infection mechanism remains unknown. We report here
      the draft genome sequence of C. haemolyticum strain T124, isolated from a young
      patient with sepsis in Japan.
AU  - Miki T
AU  - Okada N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01047-14.

PMID- 23645200
VI  - 79
DP  - 2013
TI  - Comparative Genomics of Bifidobacterium animalis subsp. lactis Reveals a Strict Monophyletic Bifidobacterial Taxon.
PG  - 4304-4315
AB  - Strains of Bifidobacterium animalis subsp. lactis are extensively exploited by
      the food industry as health-promoting bacteria, although the genetic variability
      of members belonging to this taxon has so far not received much scientific
      attention. In this article, we describe the complete genetic makeup of the B.
      animalis subsp. lactis Bl12 genome and discuss the genetic relatedness of this
      strain with other sequenced strains belonging to this taxon. Moreover, a detailed
      comparative genomic analysis of B. animalis subsp. lactis genomes was performed,
      which revealed a closely related and isogenic nature of all currently available
      B. animalis subsp. lactis strains, thus strongly suggesting a closed pan-genome
      structure of this bacterial group.
AU  - Milani C
AU  - Duranti S
AU  - Lugli GA
AU  - Bottacini F
AU  - Strati F
AU  - Arioli S
AU  - Foroni E
AU  - Turroni F
AU  - van Sinderen D
AU  - Ventura M
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2013 79: 4304-4315.

PMID- 25085493
VI  - 80
DP  - 2014
TI  - Genome encyclopaedia of type strains of the genus Bifidobacterium.
PG  - 6290-6302
AB  - Bifidobacteria represent one of the dominant microbial groups that are present in the gut of
      various animals, being particularly prevalent during the suckling stage of life of humans and
      other mammals.  However, the overall genome structure of this group of microorganisms remains
      largely unexplored.  Here, we sequenced the genomes of 42 representative (sub)species across
      the Bifidobacterium genus, and used this information to explore the overall genetic picture of
      this bacterial group.  Furthermore, the here described genomic data were used to reconstruct
      the evolutionary development of the Bifidobacterium genus.  This reconstruction suggests that
      its evolution was substantially influenced by genetic adaptations to obtain access to glycans,
      thereby representing a common and potent evolutionary force in shaping bifidobacterial
      genomes.
AU  - Milani C
AU  - Lugli GA
AU  - Duranti S
AU  - Turroni F
AU  - Bottacini F
AU  - Mangifesta M
AU  - Sanchez B
AU  - Viappiani A
AU  - Mancabelli L
AU  - Taminiau B
AU  - Delcenserie V
AU  - Barrangou R
AU  - Margolles A
AU  - van Sinderen D
AU  - Ventura M
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2014 80: 6290-6302.

PMID- 24164619
VI  - 350
DP  - 2014
TI  - Cytosine DNA methylation influences drug resistance in Escherichia coli through increased sugE expression.
PG  - 100-106
AB  - Escherichia coli K-12 strains contain the orphan cytosine-5 DNA methyltransferase enzyme Dcm
      (DNA cytosine methyltransferase). Two recent reports indicate that Dcm
      has an influence on stationary phase gene expression in E. coli. Herein, we
      demonstrate that dcm knockout cells overexpress the drug resistance transporter
      SugE, which has been linked to ethidium bromide (ETBR) resistance. SugE
      expression also increased in the presence of the DNA methylation inhibitor
      5-azacytidine, suggesting that Dcm-mediated DNA methylation normally represses
      sugE expression. The effect of Dcm on sugE expression is primarily restricted to
      early stationary phase, and RpoS is required for robust sugE expression. Dcm
      knockout cells are more resistant to ETBR than wild-type cells, and
      complementation with a plasmid-borne dcm gene restores ETBR sensitivity. SugE
      knockout cells are more sensitive to ETBR than wild-type cells. These data
      indicate that Dcm influences the sensitivity to an antimicrobial compound through
      changes in gene expression.
AU  - Militello KT
AU  - Mandarano AH
AU  - Varechtchouk O
AU  - Simon RD
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2014 350: 100-106.

PMID- 
VI  - 24
DP  - 2010
TI  - Dcm-mediated cytosine DNA methylation is conserved in Escherichia coli and influences the expression of ribosomal protein genes.
PG  - 78-85
AB  - In Escherichia coli, cytosine DNA methylation is catalyzed by the Dcm (DNA cytosine methylase)
      protein and occurs at the second cytosine in the sequence 5'CCWGG3'. Although the presence
      of cytosine DNA methylation was reported over 35 years ago, the biological role of
      5-methylcytosine in E. coli remains unclear. There is data indicating that Dcm can protect the
      genome against attack by a restriction enzyme that cleaves the same sequence, yet DNA
      methyltransferases in eukaryotes often influence gene expression. In order to gain insight
      into the potential roles of cytosine DNA methylation in E. coli, we: (a) screened 162 strains
      including laboratory strains, pathogens, and recently isolated environmental samples for the
      presence of the full-length dcm gene using the polymerase chain reaction; (b) examined the
      same strains for the presence of 5-methylcytosine at 5'CCWGG3' sites using a restriction
      enzyme isoschizomer digestion assay; and (c) quantified the levels of
      5-methyl-2'-deoxycytidine in selected strains using liquid chromatography tandem mass
      spectrometry. Dcm-mediated cytosine DNA methylation is conserved in all 162 strains examined,
      and the level of 5-methylcytosine ranges from 0.8-1.2% of the cytosines. We also tested the
      hypothesis that Dcm influences gene expression. Gene expression in wild-type and dcm knockout
      cells was compared via qPCR. We focused on ribosomal protein genes, as they have been
      previously demonstrated to contain numerous 5'CCWGG3' sites. We demonstrate that Dcm
      represses expression of ribosomal protein genes during stationary phase, and this may explain
      the ubiquitous presence of this DNA modification pathway. Support for this work was provided
      by the Geneseo Foundation and NIH grant R15AI074035-01.
AU  - Militello KT
AU  - Simon RD
AU  - Qureshi M
AU  - Maines R
AU  - VanHorne ML
AU  - Hennick SM
AU  - Jayakar SK
AU  - Pounder S
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 2010 24: 78-85.

PMID- 22150247
VI  - 328
DP  - 2012
TI  - Conservation of Dcm-mediated cytosine DNA methylation in Escherichia coli.
PG  - 78-85
AB  - In Escherichia coli, cytosine DNA methylation is catalyzed by the DNA cytosine
      methyltransferase (Dcm) protein and occurs at the second
      cytosine in the sequence 5'CCWGG3'. Although the presence of cytosine
      DNA methylation was reported over 35years ago, the biological role of
      5-methylcytosine in E.coli remains unclear. To gain insight into the
      role of cytosine DNA methylation in E.coli, we (1) screened the 72
      strains of the ECOR collection and 90 recently isolated environmental
      samples for the presence of the full-length dcm gene using the
      polymerase chain reaction; (2) examined the same strains for the
      presence of 5-methylcytosine at 5'CCWGG3' sites using a restriction
      enzyme isoschizomer digestion assay; and (3) quantified the levels of
      5-methyl-2'-deoxycytidine in selected strains using liquid
      chromatography tandem mass spectrometry. Dcm-mediated cytosine DNA
      methylation is conserved in all 162 strains examined, and the level of
      5-methylcytosine ranges from 0.86% to 1.30% of the cytosines. We also
      demonstrate that Dcm reduces the expression of ribosomal protein genes
      during stationary phase, and this may explain the highly conserved
      nature of this DNA modification pathway.
AU  - Militello KT
AU  - Simon RD
AU  - Qureshi M
AU  - Maines R
AU  - VanHorne ML
AU  - Hennick SM
AU  - Jayakar SK
AU  - Pounder S
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2012 328: 78-85.

PMID- 9215884
VI  - 146
DP  - 1997
TI  - Recombination and population structure in Escherichia coli.
PG  - 745-750
AB  - A major focus of population genetics, and now of molecular evolution, is the study of gene
      lineages.  Population genetic parameters usually apply to small chromosomal regions rather
      than to the genome as a whole, although genes do not always descend independently of their
      surroundings.  The genome of Escherichia coli strikes me as an unusually favorable theater in
      which to observe the lineages of genes and their relationships with the evolutionary processes
      that operate at the population level.  I should like to trace the developing understanding of
      E. coli's population genetics in  the coexistence of clonality and recombination, the
      recognition of restriction as important to recombination, and the emerging features of its
      genomic structure.
AU  - Milkman R
PT  - Journal Article
TA  - Genetics
JT  - Genetics
SO  - Genetics 1997 146: 745-750.

PMID- 12618387
VI  - 163
DP  - 2003
TI  - Molecular evolution of the Escherichia coli chromosome. VI. Two regions of high effective recombination.
PG  - 475-483
AB  - Two 6- to 8-min regions, centered respectively near 45 min (O-antigen region) and 99 min
      (restriction-modification region) on the Escherichia
      coli chromosome, display unusually high variability among 11 otherwise
      very similar strains. This variation, revealed by restriction fragment
      length polymorphism (RFLP) and nucleotide sequence comparisons, appears to
      be due to a great local increase in the retention frequency of recombinant
      replacements. We infer a two-step mechanism. The first step is the
      acquisition of a small stretch of DNA from a phylogenetically distant
      source. The second is the successful retransmission of the imported DNA,
      together with flanking native DNA, to other strains of E. coli. Each cell
      containing the newly transferred DNA has a very high selective advantage
      until it reaches a high frequency and (in the O-antigen case) is
      recognized by the new host's immune system. A high selective advantage
      increases the probability of retention greatly; the effective
      recombination rate is the product of the basic recombination rate and the
      probability of retention. Nearby nucleotide sequences clockwise from the
      O-antigen (rfb) region are correlated with specific O antigens, confirming
      local hitchhiking. Comparable selection involving imported restriction
      endonuclease genes is proposed for the region near 99 min.
AU  - Milkman R
AU  - Jaeger E
AU  - McBride RD
PT  - Journal Article
TA  - Genetics
JT  - Genetics
SO  - Genetics 2003 163: 475-483.

PMID- 10511538
VI  - 153
DP  - 1999
TI  - Molecular evolution of the escherichia coli chromosome. V. Recombination patterns among strains of diverse origin.
PG  - 539-554
AB  - Incorporation patterns of donor DNA into recipient chromosomes following transduction or
      conjugation have been studied in the progeny of a variety of Escherichia coli crosses in which
      donor and recipient nucleotide sequences differ by 1-3%. Series of contiguous or variously
      spaced PCR fragments have been amplified from each recombinant chromosome and digested with a
      commercial restriction endonuclease previously shown to distinguish the respective parents in
      a given fragment. We conclude that entering donor DNA fragments are frequently abridged (cut
      and shortened) before incorporation, the cutting being due to restriction systems, and the
      shortening presumably due to exonuclease activity. Analysis of several backcrosses confirms,
      and extends to conjugation, the importance of restriction in E. coli recombination in nature.
      The transmission patterns in conjugation are similar to those of transduction, but (as
      expected) on a much larger scale. Asymmetric results of reciprocal crosses imply that mismatch
      frequency is not a major factor. Marked differences among the results of simple crosses
      according to parental strain combinations are consistent with observations that E. coli
      strains in nature vary dramatically in their restriction-modification systems.
AU  - Milkman R
AU  - Raleigh EA
AU  - McKane M
AU  - Cryderman D
AU  - Bilodeau P
AU  - McWeeny K
PT  - Journal Article
TA  - Genetics
JT  - Genetics
SO  - Genetics 1999 153: 539-554.

PMID- 9526646
VI  - 24
DP  - 1998
TI  - Use of the restriction enzyme AvaI and Exo- Bst polymerase in strand displacement amplification.
PG  - 392-396
AB  - Strand displacement amplification is an isothermal in vitro method of amplifying DNA.  This
      technique is based on the ability of a restriction enzyme to nick one strand of a
      hemiphosphorothioated form of its double-stranded recognition site and the ability of a
      polymerase to initiate synthesis at the nick and displace the downstream DNA strand during
      replication.  The method consists of two parts: (i) a target generation process that makes
      copies of the target sequence flanked by nickable restriction sites and (ii) the exponential
      amplification of these modified target sequences by repeated nicking, strand displacement and
      priming of displaced strands, as depicted in Figure 1.  The first SDA system we developed used
      the restriction enzyme HincII and the 3'-5' exonuclease-deficient Klenow fragment of E. coli
      polymerase I.  This system achieves 10^8-fold amplification in 2h at 37-40 C.  More recently,
      we have developed a thermophilic SDA system that operates at 60 C and uses a restriction
      enzyme from Bacillus stearothermophilus and a 3'-5' exonuclease-deficient Klenow fragment of
      a DNA polymerase from B. caldotenax.  This system is faster and more powerful, achieving a
      10^10-fold amplification in 15 min.  It is also more specific, with a significant reduction in
      background amplification.
AU  - Milla MA
AU  - Spears PA
AU  - Pearson RE
AU  - Walker GT
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 1998 24: 392-396.

PMID- 28596399
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequence of Coxiella burnetii Nine Mile RSA439 (Phase II, Clone 4),  a Laboratory Workhorse Strain.
PG  - e00471-17
AB  - Here, we report the whole-genome sequence of Coxiella burnetii Nine Mile RSA439 (phase II,
      clone 4), a laboratory strain used extensively to investigate the
      biology of this intracellular bacterial pathogen. The genome consists of a
      1.97-Mb chromosome and a 37.32-kb plasmid.
AU  - Millar JA
AU  - Beare PA
AU  - Moses AS
AU  - Martens CA
AU  - Heinzen RA
AU  - Raghavan R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00471-17.

PMID- 15263091
VI  - 101
DP  - 2004
TI  - Genetic organization of the psbAD region in phages infecting marine Synechococcus strains.
PG  - 11007-11012
AB  - The discovery of the genes psbA and psbD, encoding the D1 and D2 core components  of the
      photosynthetic reaction center PSII (photosystem II), in the genome of the
      bacteriophage S-PM2 (a cyanomyovirus) that infects marine cyanobacteria begs the
      question as to how these genes were acquired. In an attempt to answer this
      question, it was established that the occurrence of the genes is widespread among
      marine cyanomyovirus isolates and may even extend to podoviruses. The phage psbA
      genes fall into a clade that includes the psbA genes from their potential
      Synechococcus and Prochlorococcus hosts, and thus, this phylogenetic analysis
      provides evidence to support the idea of the acquisition of these genes by
      horizontal gene transfer from their cyanobacterial hosts. However, the phage psbA
      genes form distinct subclades within this lineage, which suggests that their
      acquisition was not very recent. The psbA genes of two phages contain identical
      212-bp insertions that exhibit all of the canonical structural features of a
      group I self-splicing intron. The different patterns of genetic organization of
      the psbAD region are consistent with the idea that the psbA and psbD genes were
      acquired more than once by cyanomyoviruses and that their horizontal transfer
      between phages via a common phage gene pool, as part of mobile genetic modules,
      may be a continuing process. In addition, genes were discovered encoding a
      high-light inducible protein and a putative key enzyme of dark metabolism,
      transaldolase, extending the areas of host-cell metabolism that may be affected
      by phage infection.
AU  - Millard A
AU  - Clokie MR
AU  - Shub DA
AU  - Mann NH
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2004 101: 11007-11012.

PMID- 26564037
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Pandoraea apista LMG 16407 Type Strain.
PG  - e01300-15
AB  - Pandoraea species, in particular Pandoraea apista, are opportunistic, multidrug-resistant
      pathogens in persons with cystic fibrosis (CF). To aid in
      understanding the role of P. apista in CF lung disease, we used Illumina MiSeq
      and nanopore MinION technology to sequence the whole genome of the P. apista LMG
      16407(T).
AU  - Millard AD
AU  - Westblade LF
AU  - LiPuma JJ
AU  - Vavikolanu K
AU  - Read TD
AU  - Pallen MJ
AU  - Burd EM
AU  - Constantinidou CI
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01300-15.

PMID- 8251507
VI  - 32
DP  - 1993
TI  - Cytosine methylation enhances mitomycin C cross-linking.
PG  - 12850-12856
AB  - MitomycinC (M) is a powerful antitumor agent that targets the DNA sequence CpG. Because it is
      likely that this dinucleotide will contain 5-methylcytosine in vivo, we have compared the
      cross-linking efficiency of MC for DNA containing either 5-methylcytosine or normal cytosine
      embedded in random sequence DNA oligomers. We have found that mitomycin C displays a small but
      significant preference for methylated DNA. Recognition of an abnormal methylation pattern in
      the DNA of transformed cells may therefore be one mechanism by which MC exerts its
      chemotherapeutic effects.
AU  - Millard JT
AU  - Beachy TM
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1993 32: 12850-12856.

PMID- 349563
VI  - 75
DP  - 1978
TI  - Phenotypically cryptic EcoRI endonuclease specified by the ColE1 plasmid.
PG  - 1265-1269
AB  - An endonuclease having EcoRI specificity is produced by bacteria containing the
      ColE1 plasmid.  Such bacterial cells fail to express restriction or
      modification functions in vivo, and phage or plasmid DNA obtained from
      ColE1-containing cells has unmodified EcoRI sites that are extracted from
      bacteria that carry ColE1.  No EcoRI DNA methylase activity associated with
      ColE1 has been detected.  The finding of phenotypically cryptic ColE1-dependent
      EcoRI endonuclease activity and the absence of any detectable EcoRI
      modification system in ColE1-containing cells suggest a control mechanism that
      appears to prevent functional expression of the ColE1-determined enzyme in
      vivo.
AU  - Miller CA
AU  - Cohen SN
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1978 75: 1265-1269.

PMID- 26823594
VI  - 4
DP  - 2016
TI  - Genome Sequence of Highly Virulent Pseudomonas aeruginosa Strain VA-134, Isolated from a Burn Patient.
PG  - e01662-15
AB  - Infection with Pseudomonas aeruginosa leads to impairment of healing and many deaths in severe
      burn patients. The phenotypic diversity of P. aeruginosa strains
      makes it difficult to define a therapeutic strategy. Here we report the genome
      sequence of a highly virulent strain of P. aeruginosa, VA-134, isolated from a
      burn patient.
AU  - Miller CL
AU  - Chen T
AU  - Chen P
AU  - Leung KP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01662-15.

PMID- 21398547
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of the Cellulose-Degrading Bacterium Cellulosilyticum lentocellum.
PG  - 2357-2358
AB  - Cellulosilyticum lentocellum DSM 5427 is an anaerobic, endospore-forming member of the
      Firmicutes. We describe the complete genome sequence of this cellulose-degrading bacterium;
      originally isolated from estuarine sediment of a river that received both domestic and paper
      mill waste. Comparative genomics of cellulolytic clostridia will provide insight into factors
      that influence degradation rates.
AU  - Miller DA et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 2357-2358.

PMID- 17603475
VI  - 25
DP  - 2007
TI  - An improved zinc-finger nuclease architecture for highly specific genome editing.
PG  - 778-785
AB  - Genome editing driven by zinc-finger nucleases (ZFNs) yields high gene-modification
      efficiencies (>10%) by introducing a recombinogenic
      double-strand break into the targeted gene. The cleavage event is induced
      using two custom-designed ZFNs that heterodimerize upon binding DNA to
      form a catalytically active nuclease complex. Using the current ZFN
      architecture, however, cleavage-competent homodimers may also form that
      can limit safety or efficacy via off-target cleavage. Here we develop an
      improved ZFN architecture that eliminates this problem. Using
      structure-based design, we engineer two variant ZFNs that efficiently
      cleave DNA only when paired as a heterodimer. These ZFNs modify a native
      endogenous locus as efficiently as the parental architecture, but with a
      >40-fold reduction in homodimer function and much lower levels of
      genome-wide cleavage. This architecture provides a general means for
      improving the specificity of ZFNs as gene modification reagents.
AU  - Miller JC
AU  - Holmes MC
AU  - Wang J
AU  - Guschin DY
AU  - Lee YL
AU  - Rupniewski I
AU  - Beausejour CM
AU  - Waite AJ
AU  - Wang NS
AU  - Kim KA
AU  - Gregory PD
AU  - Pabo CO
AU  - Rebar EJ
PT  - Journal Article
TA  - Nat. Biotechnol.
JT  - Nat. Biotechnol.
SO  - Nat. Biotechnol. 2007 25: 778-785.

PMID- 3277182
VI  - 85
DP  - 1988
TI  - High-voltage electroporation of bacteria:  Genetic transformation of Campylobacter jejuni with plasmid DNA.
PG  - 856-860
AB  - Electroporation permits the uptake of DNA by mammalian cells and plant
      protoplasts because it induces transient permeability of the cell membrane.  We
      investigated the utility of high-voltage electroporation as a method for
      genetic transformation of intact bacterial cells by using the enteric pathogen
      Campylobacter jejuni as a model system.  This report demonstrates that the
      application of high-voltage discharges to bacterial cells permits genetic
      transformation.  Our method involves exposure of a Campylobacter cell
      suspension to a high-voltage exponential decay discharge (5-13 kV/cm) for a
      brief period of time (resistance-capacitance time constant = 2.4-26 msec) in
      the presence of plasmid DNA.  Electrical transformation of C. jejuni results in
      frequencies as high as 1.2 x 10/6 transformants per microgram of DNA.  We have
      investigated the effects of pulse amplitude and duration, cell growth
      conditions, divalent cations, and DNA concentration on the efficiency of
      transformation.  Transformants of C. jejuni obtained by electroporation
      contained structurally intact plasmid molecules.  In addition, evidence is
      presented that indicates that C. jejuni possesses DNA restriction and
      modification systems.  The use of electroporation as a method for transforming
      other bacterial species and guidelines for its implementation are also
      discussed.
AU  - Miller JF
AU  - Dower WJ
AU  - Tompkins LS
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1988 85: 856-860.

PMID- 17165714
VI  - 128
DP  - 2006
TI  - Contrasting Views of the Internal Dynamics of the HhaI Methyltransferase Target DNA Reported by Solution and Solid-State NMR Spectroscopy.
PG  - 15970-15971
AB  - The enzymatic methylation of deoxyribonucleic acid is essential for many biological processes
      and has therefore been studied in considerable detail.  The structure of the ternary complex
      of the HhaI methyltransferase with its DNA target [5'-(dGATAGCGCTATC)-3']2 and the
      methyl-donating cofactor S-adenosyl L-methionine demonstrated that the substrate cytosine is
      extruded from its normally base-paired position.  Through this confirmational change, the
      carbon at the C5 position on the base of the underlined cytosine becomes accessible in the
      enzyme's catalytic pocket.  The interactions observed between the protein and the extruded
      base explain the stabilization of this highly distorted structure but do not provide a
      mechanism or pathway to flip the base outside of the double helix.  What are the energetically
      favorable pathways that allow base extrusion?  Are they sequence dependent?
AU  - Miller PA
AU  - Shajani Z
AU  - Meints GA
AU  - Caplow D
AU  - Goobes G
AU  - Varani G
AU  - Drobny GP
PT  - Journal Article
TA  - J. Am. Chem. Soc.
JT  - J. Am. Chem. Soc.
SO  - J. Am. Chem. Soc. 2006 128: 15970-15971.

PMID- 2987859
VI  - 13
DP  - 1985
TI  - Alpha-putrescinylthymine and the sensitivity of bacteriophage Phi W-14 DNA to restriction endonucleases.
PG  - 2559-2568
AB  - The modified base alpha-putrescinylthymine (putT) in Phi W-14 DNA blocks
      cleavage of the DNA by 17 of 32 Type II restriction endonucleases.  The enzymes
      cleaving the DNA do so to widely varying extents.  The frequencies of cleavage
      of three altered forms of the DNA show that putT blocks recognition sites
      either when it occurs within the site or when it is in a sequence flanking the
      site.  The blocking is dependent on both charge and steric factors.  The charge
      effects can be greater than the steric effects for some of the enzymes tested.
      All the enzymes cleaving Phi W-14 DNA release discrete fragments, showing that
      the distribution of putT is ordered.  The cleavage frequencies for different
      enzymes suggest that the sequence CAputTG occurs frequently in DNA.  Only TaqI
      of the enzymes tested appeared not to be blocked by putT, but it was slowed
      down.  TaqI generated fragments are joinable by T4 DNA ligase.
AU  - Miller PB
AU  - Wakarchuk WW
AU  - Warren RAJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1985 13: 2559-2568.

PMID- 20833805
VI  - 192
DP  - 2010
TI  - Genome Sequence of the Dioxin-Mineralizing Bacterium Sphingomonas wittichii RW1.
PG  - 6101-6102
AB  - Pollutants such as polychlorinated biphenyls and dioxins pose a serious threat to human and
      environmental health. Natural attenuation of these
      compounds by microorganisms provides one promising avenue for their
      removal from contaminated areas. Over the past 2 decades, studies of the
      bacterium Sphingomonas wittichii RW1 have provided a wealth of knowledge
      about how bacteria metabolize chlorinated aromatic hydrocarbons. Here we
      describe the finished genome sequence of S. wittichii RW1 and major
      findings from its annotation.
AU  - Miller TR
AU  - Delcher AL
AU  - Salzberg SL
AU  - Saunders E
AU  - Detter JC
AU  - Halden RU
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 6101-6102.

PMID- 
VI  - 291
DP  - 2001
TI  - Characterization of multiple Campylobacter jejuni type I restriction-modification loci.
PG  - 79
AB  - Type I restriction-modification systems have been found in many bacterial taxa.  Type I
      enzymes are composed of three subunits, encoded by the hsdR, hsdS, and hsdM genes.  All three
      gene products are necessary for restriction, whereas the hsdM and hsdS gene products are
      sufficient for methylation.  To characterize the Campylobacter jejuni type I
      restriction-modification systems, the hsd loci from eight C. jejuni strains were cloned and
      sequence.  The enteric hsd genes and the H. pylori hsd genes are contiguous; however, in C.
      jejuni, intervening ORFs are present between hsdR and hsdS and between hsdS and hsdM.  The
      function of the "RS"  ORF is unknown and the "SM" ORF probably serves no function since it is
      absent in at least two loci.  Based on DNA homology and complementation, the enteric hsd loci
      have been subdivided into five families (IA, IB, IC, ID, and IE).  The hsd loci of C. jejuni
      can also be divided into families: BLAST analysis suggests that the hsd locus of NCTC 81116 is
      homologous to the IB family and the hsd loci of NCTC 11168 and 81-176 are homologous to the ID
      family.  The hsdM gene of C. jejuni RM1221 ("IB") is more homologous to its enteric
      counterparts (E-e-74) than to the hsdM genes of NCTC 11168 (E=e-24) and H. pylori 26695
      (E=e-22).  To determine if additional families exist or if some strains have multiple loci, 39
      C. jejuni strains were amplified with "IB" - and "ID"-specific probes.  Twelve strains could
      not be assigned to either the "IB" or "ID" family, suggesting that at least one additional
      family may exist.  Also, no strain amplified with both the "IB" and "ID" probes; however, the
      presence of one or more strains that contain multiple loci of the same family cannot be
      eliminated.
AU  - Miller WG
PT  - Journal Article
TA  - Int. J. Med. Microbiol.
JT  - Int. J. Med. Microbiol.
SO  - Int. J. Med. Microbiol. 2001 291: 79.

PMID- 29074672
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of the Hippuricase-Positive Campylobacter avium Type Strain LMG 24591.
PG  - e01221-17
AB  - Campylobacter avium is a thermotolerant Campylobacter species that has been isolated from
      poultry. C. avium was also the second hippuricase-positive species
      to be identified within Campylobacter Here, we present the genome sequence of the
      C. avium type strain LMG 24591 (=CCUG 56292T), isolated in 2006 from a broiler
      chicken in Italy.
AU  - Miller WG
AU  - Chapman MH
AU  - Yee E
AU  - Revez J
AU  - Bono JL
AU  - Rossi M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01221-17.

PMID- 27795285
VI  - 4
DP  - 2016
TI  - Complete Genome Sequences of Multidrug-Resistant Campylobacter jejuni Strain 14980A (Turkey Feces) and Campylobacter coli Strain 14983A (Housefly from a  Turkey Farm), Harboring a Novel Gentamicin Resistance Mobile Element.
PG  - e01175-16
AB  - Multidrug resistance (MDR) in foodborne pathogens is a major food safety and public health
      issue. Here we describe whole-genome sequences of two MDR strains
      of Campylobacter jejuni and Campylobacter coli from turkey feces and a housefly
      from a turkey farm. Both strains harbor a novel chromosomal gentamicin resistance
      mobile element.
AU  - Miller WG
AU  - Huynh S
AU  - Parker CT
AU  - Niedermeyer JA
AU  - Kathariou S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01175-16.

PMID- 
VI  - 104
DP  - 2004
TI  - Diversity of Campylobacter type I restriction-modification loci: Induction of hsdS by exogenous DNA.
PG  - 210
AB  - Restriction-modification systems are found in many bacterial taxa and are believed to provide
      a barrier against foreign DNA and bacteriophages.  R-M systems have been classified into three
      types, type I, II, and III.  The type I enzyme is a bifunctional, multi-subunit complex
      containing HsrR, HsdS, and HsdM.  Restriction and modification are represented by the HsdR and
      HsdM proteins, respectively.  HsdS interacts with the target sequence as part of both the
      restriction and modification complexes.  The type I restriction-modification (hsd) genes of 62
      Campylobacter jejuni strains were characterized by DNA sequencing and amplification.  No
      evidence was found that C. jejuni strains contain multiple hsd loci.  Unlike many
      characterized hsd loci from other taxa, intervening open reading frames are present between
      hsdS and the hsdR and hsdM genes.  These ORFs, designated as rlo (R-linked ORF) and mlo
      (M-linked ORF), have no defined function but association of rlo genes with particular hsdS
      alleles may suggest a role in R-M function.  Based on parsimony analysis of amino-acid
      sequences, the C. jejuni hsd loci were assigned to one of three families: 'IAB', 'IC', or
      'IF'.  HsdM proteins within a family are strongly conserved but share little homology with
      HsdM proteins from the other two families.  Also, there is significant diversity within the
      'IAB' hsd family: 8 different 'IAB' hsdS alleles and 7 different 'IAB' rlo alleles have
      been characterized.  Finally, RT-PCR analysis using hsdS-specific primer sets was used to
      assess whether the unique hsdS alleles were expressed.  Expression of only two hsdS alleles
      was detected by RT-PCR from cultures grown on rich media; however, expression of 7 additional
      hsdS alleles was detected after the addition of exogenous DNA to the C. jejuni cells.
AU  - Miller WG
AU  - Keech AM
AU  - Pearson BM
AU  - Wells JM
AU  - Kapitonov VV
AU  - Konkel ME
AU  - Mandrell RE
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 2004 104: 210.

PMID- 15699185
VI  - 151
DP  - 2005
TI  - Diversity within the Campylobacter jejuni type I restriction - modification loci.
PG  - 337-351
AB  - The type I restriction-modification (hsd) systems of 73 Campylobacter jejuni strains were
      characterized according to their DNA and amino acid
      sequences, and/or gene organization. A number of new genes were
      identified which are not present in the sequenced strain NCTC 11168.
      The closely related organism Helicobacter pylori has three type I
      systems; however, no evidence was found that C. jejuni strains contain
      multiple type I systems, although hsd loci are present in at least two
      different chromosomal locations. Also, unlike H. pylori, intervening
      ORFs are present, in some strains, between hsdR and hsdS and between
      hsdS and hsdM. No definitive function can be ascribed to these ORFs,
      designated here as rloA-H ((R) under bar-(l) under bar inked (O) under
      bar RF) and mloA-B ((M) under bar-(l) under bar inked (O) under bar
      RF). Based on parsimony analysis of amino acid sequences to assess
      character relatedness, the C. jejuni type I R-M systems are assigned to
      one of three families: 'IAB', 'IC' or 'IF'. This study confirms that
      HsdM proteins within a family are highly conserved but share little
      homology with HsdM proteins from other families. The 'IC' hsd loci are
      > 99% identical at the nucleoticle level, as are the 'IF' hsd loci.
      Additionally, whereas the nucleoticle sequences of the 'IAB' hsdR and
      hsdM genes show a high degree of similarity, the nucleoticle sequences
      of the 'IAB' hsdS and no genes vary considerably. This diversity
      suggests that recombination between 'IAB' hsd loci would lead not only
      to new hsdS alleles but also to the exchange of no genes; five C.
      jejuni hsd loci are presumably the result of such recombination. The
      importance of these findings with regard to the evolution of C. jejuni
      type I R-M systems is discussed.
AU  - Miller WG
AU  - Pearson BM
AU  - Wells JM
AU  - Parker CT
AU  - Kapitonov VV
AU  - Mandrell RE
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2005 151: 337-351.

PMID- 18713059
VI  - 5
DP  - 2008
TI  - The complete genome sequence and analysis of the human pathogen Campylobacter lari.
PG  - 371-386
AB  - Campylobacter lari is a member of the epsilon subdivision of the Proteobacteria and is part of
      the thermotolerant Campylobacter group, a
      clade that includes the human pathogen C. jejuni. Here we present the
      complete genome sequence of the human clinical isolate, C. lari RM2100.
      The genome of strain RM2100 is approximately 1.53 Mb and includes the 46
      kb megaplasmid pCL2100. Also present within the strain RM2100 genome is a
      36 kb putative prophage, termed CLIE1, which is similar to CJIE4, a
      putative prophage present within the C. jejuni RM1221 genome. Nearly all
      (90%) of the gene content in strain RM2100 is similar to genes present in
      the genomes of other characterized thermotolerant campylobacters. However,
      several genes involved in amino acid biosynthesis and energy metabolism,
      identified previously in other Campylobacter genomes, are absent from the
      C. lari RM2100 genome. Therefore, C. lari RM2100 is predicted to be
      multiply auxotrophic, unable to synthesize eight different amino acids,
      acetyl-coA, and pantothenate. Additionally, strain RM2100 does not contain
      a complete TCA cycle and is missing the CydAB terminal oxidase of the
      respiratory chain. Defects in the amino acid biosynthetic pathways in this
      organism could be potentially compensated by the large number of encoded
      peptidases. Nevertheless, the apparent absence of certain key enzymatic
      functions in strain RM2100 would be expected to have an impact on C. lari
      biology. It is also possible that the reduction in the C. lari metabolic
      machinery is related to its environmental range and host preference.
AU  - Miller WG
AU  - Wang G
AU  - Binnewies TT
AU  - Parker CT
PT  - Journal Article
TA  - Foodborne Pathog. Dis.
JT  - Foodborne Pathog. Dis.
SO  - Foodborne Pathog. Dis. 2008 5: 371-386.

PMID- 26383656
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Campylobacter gracilis ATCC 33236T.
PG  - e01087-15
AB  - The human oral pathogen Campylobacter gracilis has been isolated from periodontal and
      endodontal infections, and also from nonoral head, neck, or lung infections.  This study
      describes the whole-genome sequence of the human periodontal isolate ATCC 33236(T) (=FDC
      1084), which is the first closed genome for C. gracilis.
AU  - Miller WG
AU  - Yee E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01087-15.

PMID- 28546490
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of the Campylobacter helveticus Type Strain ATCC 51209.
PG  - e00398-17
AB  - Campylobacter helveticus has been isolated from domestic dogs and cats. Although  C.
      helveticus is closely related to the emerging human pathogen C. upsaliensis,
      no C. helveticus-associated cases of human illness have been reported. This study
      describes the whole-genome sequence of the C. helveticus type strain ATCC 51209
      (=CCUG 30682T).
AU  - Miller WG
AU  - Yee E
AU  - Bono JL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00398-17.

PMID- 27417840
VI  - 4
DP  - 2016
TI  - Complete Genome Sequences of Campylobacter hyointestinalis subsp. hyointestinalis Strain LMG 9260 and C. hyointestinalis subsp. lawsonii Strain LMG 15993.
PG  - e00665-16
AB  - Campylobacter hyointestinalis is isolated primarily from ruminants and swine, but is also
      occasionally isolated from humans. C. hyointestinalis is currently
      divided into two subspecies, C. hyointestinalis subsp. hyointestinalis and C.
      hyointestinalis subsp. lawsonii This study describes the first closed
      whole-genome sequences of C. hyointestinalis subsp. hyointestinalis isolate LMG
      9260 and C. hyointestinalis subsp. lawsonii isolate LMG 15993.
AU  - Miller WG
AU  - Yee E
AU  - Chapman MH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00665-16.

PMID- 28633450
VI  - 9
DP  - 2017
TI  - Comparative genomics of all three Campylobacter sputorum biovars and a novel cattle-associated C. sputorum clade.
PG  - 1513-1518
AB  - Campylobacter sputorum is a non-thermotolerant campylobacter that is primarily
      isolated from food animals such as cattle and sheep. C. sputorum is also
      infrequently associated with human illness. Based on catalase and urease
      activity, three biovars are currently recognized within C. sputorum: bv. sputorum
      (catalase negative, urease negative), bv. fecalis (catalase positive, urease
      negative), and bv. paraureolyticus (catalase negative, urease positive). A
      multi-locus sequence typing (MLST) method was recently constructed for C.
      sputorum. MLST typing of several cattle-associated C. sputorum isolates suggested
      that they are members of a divergent C. sputorum clade. Although catalase
      positive, and thus technically bv. fecalis, the taxonomic position of these
      strains could not be determined solely by MLST. To further characterize C.
      sputorum, the genomes of four strains, representing all three biovars and the
      divergent clade, were sequenced to completion. Here we present a comparative
      genomic analysis of the four C. sputorum genomes. This analysis indicates that
      the three biovars and the cattle-associated strains are highly-related at the
      genome level with similarities in gene content. Furthermore, the four genomes are
      strongly syntenic with one or two minor inversions. However, substantial
      differences in gene content were observed among the three biovars. Finally,
      although the strain representing the cattle-associated isolates was shown to be
      C. sputorum, it is possible that this strain is a member of a novel C. sputorum
      subspecies; thus, these cattle-associated strains may form a second taxon within
      C. sputorum.
AU  - Miller WG
AU  - Yee E
AU  - Chapman MH
AU  - Bono JL
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2017 9: 1513-1518.

PMID- 25381664
VI  - 6
DP  - 2014
TI  - Comparative genomics of the Campylobacter lari group.
PG  - 3252-3266
AB  - The Campylobacter lari group is a phylogenetic clade within the epsilon
      subdivision of the Proteobacteria and is part of the thermotolerant Campylobacter
      spp., a division within the genus that includes the human pathogen Campylobacter
      jejuni. The C. lari group is currently composed of five species (C. lari,
      Campylobacter insulaenigrae, Campylobacter volucris, Campylobacter
      subantarcticus, and Campylobacter peloridis), as well as a group of strains
      termed the urease-positive thermophilic Campylobacter (UPTC) and other C.
      lari-like strains. Here we present the complete genome sequences of 11 C. lari
      group strains, including the five C. lari group species, four UPTC strains, and a
      lari-like strain isolated in this study. The genome of C. lari subsp. lari strain
      RM2100 was described previously. Analysis of the C. lari group genomes indicates
      that this group is highly related at the genome level. Furthermore, these genomes
      are strongly syntenic with minor rearrangements occurring only in 4 of the 12
      genomes studied. The C. lari group can be bifurcated, based on the flagella and
      flagellar modification genes. Genomic analysis of the UPTC strains indicated that
      these organisms are variable but highly similar, closely related to but distinct
      from C. lari. Additionally, the C. lari group contains multiple genes encoding
      hemagglutination domain proteins, which are either contingency genes or linked to
      conserved contingency genes. Many of the features identified in strain RM2100,
      such as major deficiencies in amino acid biosynthesis and energy metabolism, are
      conserved across all 12 genomes, suggesting that these common features may play a
      role in the association of the C. lari group with coastal environments and
      watersheds.
AU  - Miller WG
AU  - Yee E
AU  - Chapman MH
AU  - Smith TP
AU  - Bono JL
AU  - Huynh S
AU  - Parker CT
AU  - Vandamme P
AU  - Luong K
AU  - Korlach J
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2014 6: 3252-3266.

PMID- 27365359
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Campylobacter iguaniorum Strain RM11343, Isolated from an Alpaca.
PG  - e00646-16
AB  - Campylobacter iguaniorum is a member of the C. fetus group of campylobacters and  is one of
      two Campylobacter taxa isolated from reptiles. This study describes the whole-genome sequence
      of the C. iguaniorum strain RM11343, which was isolated from a California alpaca fecal sample.
AU  - Miller WG
AU  - Yee E
AU  - Huynh S
AU  - Chapman MH
AU  - Parker CT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00646-16.

PMID- 28854596
VI  - 9
DP  - 2017
TI  - Comparative genomic analysis identifies a Campylobacter clade deficient in selenium metabolism.
PG  - 1843-1858
AB  - The nonthermotolerant Campylobacter species C. fetus, C. hyointestinalis, C. iguaniorum, and
      C. lanienae form a distinct phylogenetic clusterwithin the genus.  These species are primarily
      isolated from foraging(swine)or grazing (e.g.,cattle, sheep) animals and cause sporadic and
      infrequent human illness. Previous typing studies identi and #64257;ed three putative novel
      C.lanienae-related taxa, based on either MLST or atpA sequence data. To further characterize
      these putative novel taxa and the C. fetus group as a whole, 76 genomes were sequenced, either
      to completion or to draft level.  The segenomes represent 26 C.lanienae strains and 50 strains
      of the three novel taxa. C. fetus, C. hyointestinalis and C. iguaniorum genomes were
      previously sequenced to completion; therefore, a comparative genomic analysis across the
      entire C. fetus group was conducted (including average nucleotide identity analysis) that
      supports the initial identi and #64257;cation of these three novel Campylobacterspecies.
      Furthermore, C. lanienae and the three putative novel species form a discrete clade within the
      C. fetus group, which we have termed the C. lanienaeclade.  This clade is distinguished from
      other members of the C. fetus group by a reduced genome size and distinct CRISPR/Cas systems.
      Moreover, there are two signature characteristics of the C. lanienae clade. C. lanienae clade
      genomes carry four toten unlinked and similar, but non-identical,  and #64258;agellin genes.
      Additionally, all 76 C. lanienae clade genomes sequenced demonstrate a complete absence of
      genes related to selenium metabolism, including genes encoding the selenocysteine insertion
      machinery, selenoproteins, and the selenocysteinyl tRNA.
AU  - Miller WG
AU  - Yee E
AU  - Lopes BS
AU  - Chapman MH
AU  - Huynh S
AU  - Bono JL
AU  - Parker CT
AU  - Forbes KJ
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2017 9: 1843-1858.

PMID- 26543122
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of the Campylobacter ureolyticus Clinical Isolate RIGS 9880.
PG  - e01291-15
AB  - The emerging pathogen Campylobacter ureolyticus has been isolated from human and  animal
      genital infections, human periodontal disease, domestic and food animals,
      and from cases of human gastroenteritis. We report the whole-genome sequence of
      the human clinical isolate RIGS 9880, which is the first closed genome for C.
      ureolyticus.
AU  - Miller WG
AU  - Yee E
AU  - On SL
AU  - Andersen LP
AU  - Bono JL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01291-15.

PMID- 28619810
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of the Campylobacter cuniculorum Type Strain LMG 24588.
PG  - e00543-17
AB  - Campylobacter cuniculorum is a thermotolerant species isolated from farmed rabbits
      (Oryctolagus cuniculus). Although C. cuniculorum is highly prevalent in
      rabbits farmed for human consumption, the pathogenicity of this organism in
      humans is still unknown. This study describes the whole-genome sequence of the C.
      cuniculorum type strain LMG 24588 (=CCUG 56289T).
AU  - Miller WG
AU  - Yee E
AU  - Revez J
AU  - Bono JL
AU  - Rossi M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00543-17.

PMID- 9324259
VI  - 179
DP  - 1997
TI  - Homing of a group II intron from Lactococcus lactis subsp. lactis ML3.
PG  - 6107-6111
AB  - Ll.ltrB is a functional group II intron located within a gene (ltrB) encoding a conjugative
      relaxase essential for transfer of the lactococcal element pRS01.  In this work, the Ll.ltrB
      intron was shown to be an independent mobile element capable of inserting into an intronless
      allele of the ltrB gene.  Ll.ltrB was not observed to insert into a deletion derivative of the
      ltrB gene in which the intron splice site was removed. In contrast, a second vector containing
      a 271-nucleotide segment of ltrB spanning the Ll.ltrB splice site was shown to be a proficient
      recipient of intron insertion.  Efficient homing was observed in the absence of a functional
      host homologous recombination system.  This work demonstrates that the Ll.ltrB intron is a
      novel site-specific mobile element in lactococci and that group II intron self-transfer is a
      mechanism for intron dissemination among bacteria.
AU  - Mills DA
AU  - Manias DA
AU  - McKay LL
AU  - Dunny GM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1997 179: 6107-6111.

PMID- 8655550
VI  - 178
DP  - 1996
TI  - Splicing of a group II intron involved in the conjugative transfer of pRS01 in Lactococci.
PG  - 3531-3538
AB  - Analysis of a region involved in the conjugative transfer of the lactococcal conjugative
      element pRS01 has revealed a bacterial group II intron.  Splicing of this lactococcal intron
      (designated Ll.ltrB) in vivo resulted in the ligation of two exon messages (ltrBE1 and ltrBE2)
      which encoded a putative conjugative relaxase essential for the transfer of pRS01.  Like many
      group II introns, the Ll.ltrB intron possessed an open reading frame (ltrA) with homology to
      reverse transcriptases.  Remarkably, sequence analysis of ltrA suggested a greater similarity
      to open reading frames encoded by eukaryotic mitochondrial group II introns than to those
      identified to date from other bacteria.  Several insertional mutations within ltrA resulted in
      plasmids exhibiting a conjugative transfer-deficient phenotype.  These results provide the
      first direct evidence for splicing of a prokaryotic group II intron in vivo and suggest that
      conjugative transfer is a mechanism for group II intron dissemination in bacteria.
AU  - Mills DA
AU  - McKay LL
AU  - Dunny GM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1996 178: 3531-3538.

PMID- 
VI  - 103
DP  - 2003
TI  - Insights into the role of cryptic marine plasmids based on sequence analysis.
PG  - N-147
AB  - Knowledge has been gained from the intensive study of a limited group of bacterial plasmids
      particularly those from clinical settings and
      terrestrial environments. The molecular characterization of plasmid
      populations occurring in a wider range of habitats, especially marine,
      is necessary to provide knowledge on plasmid ecology and their
      contributions to the genetic plasticity of microbial communities. DNA
      sequencing and analysis have greatly facilitated the determination of
      putative functions to otherwise 'cryptic' marine plasmids. In
      collaboration with TIGR, we have undertaken whole plasmid sequencing to
      elucidate putative gene functions to gain a better understanding of
      plasmid diversity and ecological roles. A random shotgun method was
      used to obtain DNA sequences from five 'cryptic' marine plasmids
      ranging in size from 9-kb to 80-kb from Vibrio and Shewanella. A
      comparative and systematic analysis of the marine plasmid sequences
      have indicated that p172, a 28.8-kb plasmid from marine Vibrio sp. 172
      encodes partitioning elements, colicin-mediated cell killing,
      restriction modification systems, and natural competence. A co-resident
      replicon in Vibrio sp. 172, p172-A, is a 9.0-kb element that appears to
      be the replicative form of a previously identified Vibrio
      parahaemolyticus phage. A second marine Vibrio strain designated 09022,
      contains a 31.0-kb plasmid, p09022, that remains mostly cryptic,
      however p09022 does encode partitioning elements and a restriction
      modification system related to similar genes on p172. A majority of the
      putative genes from p23023 (52.1-kb) resident in a third Vibrio sp.,
      and p0908 (81.4-kb) isolated from a Shewenella sp., possesses no
      homology to any known ORFs. However, p23023 encodes a putative cell
      adhesion operon, previously reported in non-marine bacterial hosts.
      Sequence analysis demonstrates the capacity to assign putative function
      to cryptic plasmids, but also exemplifies the need for additional
      sequencing and analyzing of marine genes. Such plasmid-encoded
      adhesion, competency and colicin production traits likely provide hosts
      with competitive advantages in marine ecosystems.
AU  - Mills HJ
AU  - Eisen J
AU  - Sobecky PA
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 2003 103: N-147.

PMID- 11951645
VI  - 200
DP  - 2002
TI  - Methods in Molecular Biology. DNA methylation protocols.
PG  - 1-7
AB  - This book provides a set of reproducible protocols for the analysis of DNA methylation and
      methylases. Each technique includes a summary of the basic
      theory, a materials list, step-by-step instructions, and notes for
      avoiding pitfalls. It was written for all researchers investigating
      replication, transcription, growth, differentiation, and carcinogenesis.
      Bibliographical references, illustrations, and an index are included.
AU  - Mills KI
AU  - Ramsahoye BH
PT  - Journal Article
TA  - Methods Mol. Biol.
JT  - Methods Mol. Biol.
SO  - Methods Mol. Biol. 2002 200: 1-7.

PMID- 
VI  - 16
DP  - 2005
TI  - Biochemical mechanisms of intein-mediated protein splicing.
PG  - 233-255
AB  - This chapter discusses the mechanism of the self-catalyzed process by which inteins promote
      both their own excision from a host protein and the direct linkage of the flanking host
      protein segments, the N- and C-exteins, by a peptide bond.  The majority of inteins have a
      nucleophilic amino acid at their N-terminus and asparagine at their C-terminus and are linked
      to a C-extein with an N-terminal nucleophilic amino acid.  These canonical inteins promote
      protein splicing by a four-step mechanism of sequential acyl rearrangements.  Non-canonical
      inteins, which lack either the N-terminal nucleophile or the C-terminal asparagine, promote
      protein splicing by a variant of this mechanism or promote protein cleavage rather than
      splicing.  A remarkable feature of the protein splicing process is that it involves multiple
      steps that are chemically autonomous yet proceed in a highly coordinated manner without side
      reactions unless perturbed by mutation, unnatural exteins, or non-physiological conditions.
      The factors that may serve to integrate protein splicing into a system that ordinarily
      operates efficiently without side reactions are discussed.
AU  - Mills KV
AU  - Paulus H
PT  - Journal Article
TA  - Nucleic Acids Mol. Biol.
JT  - Nucleic Acids Mol. Biol.
SO  - Nucleic Acids Mol. Biol. 2005 16: 233-255.

PMID- 
VI  - 21
DP  - 2011
TI  - A new phage on the 'Mozzarella' block: Bacteriophage 5093 shares a low level of homology with other Streptococcus thermophilus phages.
PG  - 963-969
AB  - Streptococcus thermophilus bacteriophage 5093 is a virulent phage that infects the industrial
      Mozzarella starter CSK939. The genome of phage
      5093 is 37,184 base pairs (bps) containing 50 open reading frames
      (orfs). Genetic analysis revealed that the genome of phage 5093 is
      highly mosaic when compared with other sequenced S. thermophilus
      phages. This is particularly apparent in the late gene cluster with
      regions displaying high homology to prophage sequences of non-dairy
      streptococci and limited homology to either pac or cos-type S.
      thermophilus phages. In addition, a definitive antireceptor gene was
      not observed - suggesting that phage 5093 may have developed a
      different system for host recognition. Interestingly, the phage does
      contain a methylase domain that probably evolved as a phage
      counter-defence mechanism. These findings suggest that phage 5093 may
      represent a third group of S. thermophilus phage and provide the link
      between phages that infect S. thermophilus and its non-dairy ancestors.
AU  - Mills S
AU  - Griffin C
AU  - O'Sullivan O
AU  - Coffey A
AU  - McAuliffe OE
AU  - Meijer WC
AU  - Serrano LM
AU  - Ross RP
PT  - Journal Article
TA  - Int. Dairy Journal
JT  - Int. Dairy Journal
SO  - Int. Dairy Journal 2011 21: 963-969.

PMID- 16472306
VI  - 30
DP  - 2006
TI  - Plasmids of lactococci - genetic accessories or genetic necessities?
PG  - 243-273
AB  - Lactococci are one of the most exploited microorganisms used in the manufacture of food.
      These intensively used cultures are generally characterized by having a rich plasmid
      complement.  It could be argued that it is the plasmid complement of commercially utilized
      cultures that gives them their technical superiority and individuality.  Consequently, it is
      timely to reflect on the desirable characteristics encoded on lactococcal plasmids.  It is
      argued that plasmids play a key role in the evolution of modern starter strains and are a lot
      more than just selfish replicosomes but more essential necessities of intensively used
      commercial starters.  Moreover, the study of plasmid biology provides a genetic blueprint that
      has proved essential for the generation of molecular tools for the genetic improvement of
      Lactococcus lactis.
AU  - Mills S
AU  - McAuliffe OE
AU  - Coffey A
AU  - Fitzgerald GF
AU  - Ross RP
PT  - Journal Article
TA  - FEMS Microbiol. Rev.
JT  - FEMS Microbiol. Rev.
SO  - FEMS Microbiol. Rev. 2006 30: 243-273.

PMID- 11493005
VI  - 311
DP  - 2001
TI  - Analysis of DNA looping interactions by type II restriction enzymes that require two copies of their recognition sites.
PG  - 515-527
AB  - Before cleaving DNA substrates with two recognition sites, the Cfr10I, NgoMIV, NaeI and SfiI
      restriction endonucleases bridge the two sites
      through 3D space, looping out the intervening DNA. To characterise
      their looping interactions, the enzymes were added to plasmids with two
      recognition sites interspersed with two res sites for site-specific
      recombination by Tn21 resolvase, in buffers that contained either EDTA
      or CaCl2 so as to preclude DNA cleavage by the endonuclease; the extent
      to which the res sites were sequestered into separate loops was
      evaluated from the degree of inhibition of resolvase. With Cfr10I, a
      looped complex was detected in the presence but not in the absence of
      Ca2+; it had a lifetime of about 90 seconds. Neither NgoMIV nor NaeI
      gave looped complexes of sufficient stability to be detected by this
      method. In contrast, SfiI with Ca++ produced a looped complex that survived for more than
      seven hours, whereas its looping interaction in
      EDTA lasts for about four minutes. When resolvase was added to a SfiI
      binding reaction in EDTA followed immediately by CaCl2, the looped DNA
      was blocked from recombination while the unlooped DNA underwent
      recombination. By measuring the distribution between looped and
      unlooped DNA at various SfiI concentrations, and by fitting the data to
      a model for DNA binding by a tetrameric protein to two sites in cis, an
      equilibrium constant for the looping interaction was determined. The
      equilibrium constant was essentially independent of the length of DNA
      between the SfiI sites.
AU  - Milsom SE
AU  - Halford SE
AU  - Embleton ML
AU  - Szczelkun MD
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2001 311: 515-527.

PMID- 26988053
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Methylobacterium sp. Strain AMS5, an Isolate from a Soybean Stem.
PG  - e00144-16
AB  - Nonrhizobial Methylobacterium spp. inhabit the phyllosphere of a wide variety of  plants. We
      report here the complete genome sequence of Methylobacterium sp. AMS5,
      which was isolated from a soybean stem. The information is useful for
      understanding the molecular mechanisms of the interaction between nonrhizobial
      Methylobacterium spp. and plants.
AU  - Minami T
AU  - Ohtsubo Y
AU  - Anda M
AU  - Nagata Y
AU  - Tsuda M
AU  - Mitsui H
AU  - Sugawara M
AU  - Minamisawa K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00144-16.

PMID- 19388554
VI  - 56
DP  - 2009
TI  - MICROBE-INDUCED EPIGENETIC ALTERATIONS IN HOST CELLS: THE COMING ERA OF PATHO-EPIGENETICS OF MICROBIAL INFECTIONS A REVIEW.
PG  - 1-19
AB  - It is well documented that the double-stranded DNA (dsDNA) genomes of certain viruses and the
      proviral genomes of retroviruses are regularly
      targeted by epigenetic regulatory mechanisms (DNA methylation, histone
      modifications, binding of regulatory proteins) in infected cells. In
      parallel, proteins encoded by viral genomes may affect the activity of
      a set of cellular promoters by interacting with the very same
      epigenetic regulatory machinery. This may result in epigenetic
      dysregulation and subsequent cellular dysfunctions that may manifest in
      or contribute to the development of pathological changes (e. g.
      initiation and progression of malignant neoplasms; immunodeficiency).
      Bacteria infecting mammals may cause diseases in a similar manner, by
      causing hypermethylation of key cellular promoters at CpG dinucleotides
      (promoter silencing, e. g. by Campylobacter rectus in the placenta or
      by Helicobacter pylori in gastric mucosa). I suggest that in addition
      to viruses and bacteria, other microparasites (protozoa) as well as
      macroparasites (helminths, arthropods, fungi) may induce pathological
      changes by epigenetic reprogramming of host cells they are interacting
      with. Elucidation of the epigenetic consequences of microbe-host
      interactions (the emerging new field of patho-epigenetics) may have
      important therapeutic implications because epigenetic processes can be
      reverted and elimination of microbes inducing patho-epigenetic changes
      may prevent disease development.
AU  - Minarovits J
PT  - Journal Article
TA  - Acta Microbiol. Immunol. Hung.
JT  - Acta Microbiol. Immunol. Hung.
SO  - Acta Microbiol. Immunol. Hung. 2009 56: 1-19.

PMID- 17170133
VI  - 103
DP  - 2006
TI  - Sequence-specific modification of mitochondrial DNA using a chimeric zinc finger methylase.
PG  - 19689-19694
AB  - We used engineered zinc finger peptides (ZFPs) to bind selectively to predetermined sequences
      in human mtDNA. Surprisingly, we found that
      engineered ZFPs cannot be reliably routed to mitochondria by using only
      conventional mitochondrial targeting sequences. We here show that addition
      of a nuclear export signal allows zinc finger chimeric enzymes to be
      imported into human mitochondria. The selective binding of
      mitochondria-specific ZFPs to mtDNA was exemplified by targeting the
      T8993G mutation, which causes two mitochondrial diseases, neurogenic
      muscle weakness, ataxia, and retinitis pigmentosa (NARP) and also
      maternally inherited Leigh's syndrome. To develop a system that allows the
      monitoring of site-specific alteration of mtDNA we combined a ZFP with the
      easily assayed DNA-modifying activity of hDNMT3a methylase. Expression of
      the mutation-specific chimeric methylase resulted in the selective
      methylation of cytosines adjacent to the mutation site. This is a proof of
      principle that it is possible to target and alter mtDNA in a
      sequence-specific manner by using zinc finger technology.
AU  - Minczuk M
AU  - Papworth MA
AU  - Kolasinska P
AU  - Murphy MP
AU  - Klug A
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2006 103: 19689-19694.

PMID- 27795957
VI  - 2016
DP  - 2016
TI  - Resistance of Permafrost and Modern Acinetobacter lwoffii Strains to Heavy Metals and Arsenic Revealed by Genome Analysis.
PG  - 3970831
AB  - We performed whole-genome sequencing of five permafrost strains of Acinetobacter
      lwoffii (frozen for 15-3000 thousand years) and analyzed their resistance genes
      found in plasmids and chromosomes. Four strains contained multiple plasmids
      (8-12), which varied significantly in size (from 4,135 to 287,630 bp) and genetic
      structure; the fifth strain contained only two plasmids. All large plasmids and
      some medium-size and small plasmids contained genes encoding resistance to
      various heavy metals, including mercury, cobalt, zinc, cadmium, copper, chromium,
      and arsenic compounds. Most resistance genes found in the ancient strains of A.
      lwoffii had their closely related counterparts in modern clinical A. lwoffii
      strains that were also located on plasmids. The vast majority of the chromosomal
      resistance determinants did not possess complete sets of the resistance genes or
      contained truncated genes. Comparative analysis of various A. lwoffii and of A.
      baumannii strains discovered a number of differences between them: (i) chromosome
      sizes in A. baumannii exceeded those in A. lwoffii by about 20%; (ii) on the
      contrary, the number of plasmids in A. lwoffii and their total size were much
      higher than those in A. baumannii; (iii) heavy metal resistance genes in the
      environmental A. lwoffii strains surpassed those in A. baumannii strains in the
      number and diversity and were predominantly located on plasmids. Possible reasons
      for these differences are discussed.
AU  - Mindlin S
AU  - Petrenko A
AU  - Kurakov A
AU  - Beletsky A
AU  - Mardanov A
AU  - Petrova M
PT  - Journal Article
TA  - Biomed. Res. Int.
JT  - Biomed. Res. Int.
SO  - Biomed. Res. Int. 2016 2016: 3970831.

PMID- 23405284
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of a Propionibacterium acnes Isolate from a Sarcoidosis  Patient.
PG  - e00016-12
AB  - Propionibacterium acnes is a human skin commensal that resides preferentially within sebaceous
      follicles and is the only microorganism that has been isolated from sarcoid lesions. We report
      the complete genome sequence of P. acnes, which was isolated from a Japanese patient with
      sarcoidosis.
AU  - Minegishi K
AU  - Aikawa C
AU  - Furukawa A
AU  - Watanabe T
AU  - Nakano T
AU  - Ogura Y
AU  - Ohtsubo Y
AU  - Kurokawa K
AU  - Hayashi T
AU  - Maruyama F
AU  - Nakagawa I
AU  - Eishi Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00016-12.

PMID- Not carried by PubMed...
VI  - 51
DP  - 1990
TI  - Comparative analysis of the T2 and T4 DNA [N6-adenine] methyltransferase (dam) genes and characterization of single amino acid substitutions that alter the sequence specificity of their encoded proteins.
PG  - 588B
AB  - Bacteriophage T4 encodes a DNA-[N6-adenine]methyltransferase (Dam) which recognizes primarily
      the sequence GATC in both cytosine- and hydroxymethylcytosine-containing DNA. The
      corresponding enzyme encoded by the related bacteriophage T2 is able to methylate both
      substrates to a greater extent than T4 Dam. The T2 dam gene has been cloned and sequenced, and
      the sequence compared with that of the T4 dam gene. From the coding region, I infer there are
      three amino acid differences, two of which are located in a region of homology (I) that is
      shared by T2 and T4 Dam, Escherichia coli Dam, and the modification enzyme of Streptococcus
      pneumoniae, all of which methylate the sequence 5' GATC 3'. Although the T2 and T4 dam
      promoters are not identical, gene fusion experiments indicate that the T4 promoter produces
      about two-fold more Beta-galactosidase activity than does the T2 promoter. T2 and T4 dam give
      rise to hypermethylating mutants (damh) which exhibit an alteration in sequence specificity;
      that is, they are readily able to methylate non-canonical sites. I have determined that the
      damh mutation in T4 produces a single amino acid change (Pro126 to Ser126) in another region
      of homology (III) shared by the four DNA-adenine methyltransferases. Another mutant, damc, is
      described which methylates GATC in cytosine-containing DNA, but not in
      hydroxymethylcytosine-containing DNA. This mutation alters a single amino acid (Phe127 to
      Val127). The effect of several different amino acids at residue 126 was examined by creating
      an amber codon at that position and comparing the methylation capability of partially purified
      enzymes produced in the presence of various suppressors. No enzyme activity is observed for
      proteins containing phenylalanine, glutamic acid, or histidine at position 126. However,
      insertion of alanine, cysteine, or glycine at residue 126 produces enzymatic activity similar
      to that of Damh. These results suggest that at least two regions of the Dam protein are
      involved in sequence recognition. These regions may be in close proximity to one another in
      the native protein to form a domain that is involved in nucleotide recognition and protein-DNA
      interation.
AU  - Miner Z
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1990 51: 588B.

PMID- 3053648
VI  - 170
DP  - 1988
TI  - Molecular cloning, sequencing, and mapping of the bacteriophage T2 dam gene.
PG  - 5177-5184
AB  - Bacteriophage T2 codes for a DNA-(adenine-N6) methyltransferase (Dam), which is able to
      methylate both cytosine- and hydroxymethylcytosine-containing DNAs to a greater extent than
      the corresponding methyltransferase encoded by bacteriophage T4. We have cloned and sequenced
      the T2 dam gene and compared it with the T4 dam gene. In the Dam coding region, there are 22
      nucleotide differences, 4 of which result in three coding differences (2 are in the same
      codon). Two of the amino acid alterations are located in a region of homology that is shared
      by T2 and T4 Dam, Escherichia coli Dam, and the modification enzyme of Streptococcus
      pneumoniae, all of which methylate the sequence 5'GATC3'. The T2 dam and T4 dam promoters
      are not identical and appear to have slightly different efficiencies; when fused to the E.
      coli lacZ gene, the T4 promoter produces about twofold more beta-galactosidase activity than
      does the T2 promoter. In our first attempt to isolate T2 dam, a truncated gene was cloned on a
      1.67-kilobase XbaI fragment. This construct produces a chimeric protein composed of the first
      163 amino acids of T2 Dam followed by 83 amino acids coded by the pUC18 vector. Surprisingly,
      the chimera has Dam activity, but only on cytosine-containing DNA. Genetic and physical
      analyses place the T2 dam gene at the same respective map location as the T4 dam gene.
      However, relative to T4, T2 contains an insertion of 536 base pairs 5' to the dam gene.
      Southern blot hybridization and computer analysis failed to reveal any homology between this
      insert and either T4 or E. coli DNA.
AU  - Miner Z
AU  - Hattman S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1988 170: 5177-5184.

PMID- 3248730
VI  - 74
DP  - 1988
TI  - Single amino acid changes which alter the sequence specificity of the T4 and T2 (Dam) DNA-adenine methyltransferases.
PG  - 275-276
AB  - Meeting Abstract
AU  - Miner Z
AU  - Schlagman S
AU  - Hattman S
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 275-276.

PMID- 3163924
VI  - 37
DP  - 1988
TI  - Single amino acid changes which alter the sequence specificity of the T4 (dam) DNA-adenine methyltransferase.
PG  - 1811-1812
AB  - Many enteric bacteria contain a DNA adenine methyltransferase (Dam) that methylates the A
      residue in the sequence, GATC. The related T-even phages, T2 and T4 (but not T6), also encode
      Dam methylases; the normal substrate for these enzymes is 5-hydroxymethylcytosine
      (hmC)-containing DNA, since these viruses contain this base in place of C, and the hmC is
      modified further by glucosylation. Nonglucosylating mutants (gt-) have been isolated that are
      different from their gt+ parents in that they are unable to grow on certain strains, such as
      P1 lysogenic hosts. Derivatives of T2 gt- and T4 gt- phage capable of growth on P1 lysogens
      have been isolated; these are designated damh because they exhibit hypermethylation of their
      DNA. Thus, Damh, but not Dam+, methylation protects against P1 restriction of the asymmetric
      sequence, AGACC.
AU  - Miner Z
AU  - Schlagman S
AU  - Hattman S
PT  - Journal Article
TA  - Biochem. Pharmacol.
JT  - Biochem. Pharmacol.
SO  - Biochem. Pharmacol. 1988 37: 1811-1812.

PMID- 2467142
VI  - 13D
DP  - 1989
TI  - The dam DNA-methyltransferases of E. coli and its phages T2 and T4.
PG  - 199
AB  - DNA (adenine-N6) methyltransferases (MTases) recognizing the palindromic tetranucleotide
      sequence, 5'-GATC-3', are encoded by (dam) genes of various bacteriophages (e.g.
      T2,T4,T1,P1) and bacteria (e.g. Escherichia, Salmonella, Neisseria, Streptococcus).  Cloning
      and nucleotide sequence analysis has revealed that these Dam polypeptides contain several
      regions of considerable amino acid sequence homology; and one of these regions (IV) contains a
      sequence motif, (Asp/Asn)-Pro-Pro-(Phe/Tyr), also found in MTases that methylate adenine in
      sequences other than GATC.  The conservation of amino acid sequences among these enzymes
      suggests that they are in domains important for MTase function and specificity; i.e. substrate
      (S-adenosylmethionine, AdoMet) and DNA-nucleotide sequence recognition/interaction.  We have
      been focusing on the Dam MTases of phages T2 and T4, particularly because mutants (dam^h) are
      known that methylate DNA to higher extents than the enzyme from the wild-type (dam+) parent.
      In addition, second site mutants (dam^h dam-x) have been isolated that abolish all DNA
      methylation ability.  The normal substrate for the phage DNA MTases is DNA containing
      5-hydroxymethylcytosine (hmC), because the viruses contain this base in place of C; however,
      C-DNA is still a good substrate for these enzymes.  The two wild-type phage MTases differ in
      that the T2 enzyme adds about twice as many methyl groups per unit DNA than does the T4
      enzyme.  A comparison of the wild-type T2 and T4 Dam+ encoded polypeptides revealed three
      amino acid differences; viz., at positions 20,26,188.  The latter is a conserved changed
      (Asp->Glu) and does not appear to be involved in sequence specificity.  The other two changes
      are located in homology region I, implicating this domain in nucleotide sequence recognition.
      Current efforts to prove this include production of chimeric enzymes and site-directed
      mutagenesis.  We have shown that the dam+ -> dam^h mutation produces a Pro ->Ser change at
      amino acid residue 126.  A Phe -> Val change at residue 127 prevents the MTase from
      methylating hmC-DNA, but not C-DNA.  These two residues are contained in homology region III,
      also implicating this domain in nucleotide sequence recognition.
AU  - Miner Z
AU  - Schlagman S
AU  - Hattman S
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1989 13D: 199.

PMID- 2510127
VI  - 17
DP  - 1989
TI  - Single amino acid changes that alter the DNA sequence specificity of the DNA-[N/6-adenine] methyltransferase (Dam) of bacteriophage T4.
PG  - 8149-8157
AB  - Bacteriophage T4 codes for a DNA-[N/6-adenine] methyltransferase (Dam) which
      recognizes primarily the sequence GATC in both cytosine-and
      hydroxymethylcytosine-containing DNA.  Hypermethylating mutants, dam/h, exhibit
      a relaxation in sequence specificity, that is, they are readily able to
      methylate non-canonical sites.  We have determined that the dam/h mutation
      produces a single amino acid change (Pro/126 to Ser/126) in a region of
      homology (III) shared by three DNA-adenine methyltransferases; viz, T4 Dam,
      Escherichia coli Dam, and the DpnII modification enzyme of Streptococcus
      pneumoniae.  We also describe another mutant, dam/c, which methylates GATC in
      cytosine-containing DNA, but not in hydroxymethylcytosine-containing DNA.  This
      mutation also alters a single amino acid (Phe/127 to Val/127).  These results
      implicate homology region III as a domain involved in DNA sequence recognition.
      The effect of several different amino acids at residue 126 was examined by
      creating a polypeptide chain terminating codon at that position and comparing
      the methylation capability of partially purified enzymes produced in the
      presence of various suppressors.  No enzyme activity is detected when
      phenylalanine, glutamic acid, or histidine is inserted at position 126.
      However, insertion of alanine, cysteine, or glycine at residue 126 produces
      enzymatic activity similar to Dam/h.
AU  - Miner Z
AU  - Schlagman SL
AU  - Hattman S
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 8149-8157.

PMID- 15489423
VI  - 186
DP  - 2004
TI  - The genome sequence of Mycoplasma hyopneumoniae strain 232, the agent of swine mycoplasmosis.
PG  - 7123-7133
AB  - We present the complete genome sequence of Mycoplasma hyopneumoniae, an important member of
      the porcine respiratory disease complex. The genome is
      composed of 892,758 bp and has an average G+C content of 28.6 mol%. There
      are 692 predicted protein coding sequences, the average protein size is
      388 amino acids, and the mean coding density is 91%. Functions have been
      assigned to 304 (44%) of the predicted protein coding sequences, while 261
      (38%) of the proteins are conserved hypothetical proteins and 127 (18%)
      are unique hypothetical proteins. There is a single 16S-23S rRNA operon,
      and there are 30 tRNA coding sequences. The cilium adhesin gene has six
      paralogs in the genome, only one of which contains the cilium binding
      site. The companion gene, P102, also has six paralogs. Gene families
      constitute 26.3% of the total coding sequences, and the largest family is
      the 34-member ABC transporter family. Protein secretion occurs through a
      truncated pathway consisting of SecA, SecY, SecD, PrsA, DnaK, Tig, and
      LepA. Some highly conserved eubacterial proteins, such as GroEL and GroES,
      are notably absent. The DnaK-DnaJ-GrpR complex is intact, providing the
      only control over protein folding. There are several proteases that might
      serve as virulence factors, and there are 53 coding sequences with
      prokaryotic lipoprotein lipid attachment sites. Unlike other mycoplasmas,
      M. hyopneumoniae contains few genes with tandem repeat sequences that
      could be involved in phase switching or antigenic variation. Thus, it is
      not clear how M. hyopneumoniae evades the immune response and establishes
      a chronic infection.
AU  - Minion FC
AU  - Lefkowitz EJ
AU  - Madsen ML
AU  - Cleary BJ
AU  - Swartzell SM
AU  - Mahairas GG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2004 186: 7123-7133.

PMID- 11266550
VI  - 29
DP  - 2001
TI  - Methylation by a mutant T2 DNA [N6-adenine] methyltransferase expands the usage of RecA-assisted endonuclease (RARE) cleavage.
PG  - 1484-1490
AB  - Properties of a mutant bacteriophage T2 DNA [N6-adenine] methyltransferase (T2 Dam MTase) have
      been investigated for its potential utilization in RecA-assisted restriction endonuclease
      (RARE) cleavage. Steady-state kinetic analyses with oligonucleotide duplexes revealed that,
      compared to wild-type T4 Dam, both wild-type T2 Dam and mutant T2 Dam P126S had a 1.5-fold
      higher kcat in methylating canonical GATC sites. Additionally, T2 Dam P126S showed increased
      efficiencies in methylation of non-canonical GAY sites relative to the wild-type enzymes. In
      agreement with these steady-state kinetic data, when bacteriophage  DNA was used as a
      substrate, maximal protection from restriction nuclease cleavage in vitro was achieved on the
      sequences GATC, GATN and GACY, while protection of GACR sequences was less efficient.
      Collectively, our data suggest that T2 Dam P126S can modify 28 recognition sequences. The
      feasibility of using the mutant enzyme in RARE cleavage with BclI and EcoRV endonucleases has
      been shown on phage  DNA and with BclI and DpnII endonucleases on yeast chromosomal DNA
      embedded in agarose.
AU  - Minko I
AU  - Hattman S
AU  - Lloyd RS
AU  - Kossykh V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2001 29: 1484-1490.

PMID- 25237024
VI  - 2
DP  - 2014
TI  - Whole-genome sequences of 24 Brucella strains.
PG  - e00915-14
AB  - Brucella species are intracellular zoonotic pathogens which cause, among other pathologies,
      increased rates of abortion in ruminants. Human infections are
      generally associated with exposure to contaminated and unpasteurized dairy
      products; however Brucellae have been developed as bioweapons. Here we present 17
      complete and 7 scaffolded genome assemblies of Brucella strains.
AU  - Minogue TD et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00915-14.

PMID- 25291776
VI  - 2
DP  - 2014
TI  - Complete Genome Assembly of Escherichia coli ATCC 25922, a Serotype O6 Reference  Strain.
PG  - e00969-14
AB  - We present the complete genome assembly of Escherichia coli ATCC 25922 as submitted to NCBI
      under accession no. CP009072. This strain was originally
      isolated from a clinical sample in Seattle, Washington (1946), and is often used
      in quality control testing. The assembled genome is 5.20 Mb (50.4% G+C content)
      and includes two plasmids.
AU  - Minogue TD
AU  - Daligault HA
AU  - Davenport KW
AU  - Bishop-Lilly KA
AU  - Broomall SM
AU  - Bruce DC
AU  - Chain PS
AU  - Chertkov O
AU  - Coyne SR
AU  - Freitas T
AU  - Frey KG
AU  - Gibbons HS
AU  - Jaissle J
AU  - Redden CL
AU  - Rosenzweig CN
AU  - Xu Y
AU  - Johnson SL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00969-14.

PMID- 25258274
VI  - 2
DP  - 2014
TI  - Complete Genome Assembly of Streptococcus pyogenes ATCC 19615, a Group A beta-Hemolytic Reference Strain.
PG  - e00976-14
AB  - We present the complete genome assembly of Streptococcus pyogenes ATCC 19615 (Rosenbach) as
      submitted to GenBank under accession number CP008926. This group A
      nonmotile beta-hemolytic clinical isolate is used for quality control in a
      variety of commercially available tests. The assembled genome is 1.84 Mb (38.5%
      G+C content) and contains 1,788 coding regions.
AU  - Minogue TD
AU  - Daligault HA
AU  - Davenport KW
AU  - Bishop-Lilly KA
AU  - Broomall SM
AU  - Bruce DC
AU  - Chain PS
AU  - Chertkov O
AU  - Coyne SR
AU  - Freitas T
AU  - Frey KG
AU  - Gibbons HS
AU  - Jaissle J
AU  - Redden CL
AU  - Rosenzweig CN
AU  - Xu Y
AU  - Johnson SL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00976-14.

PMID- 25291772
VI  - 2
DP  - 2014
TI  - Complete Genome Assembly of Reference Strain Ochrobactrum anthropi ATCC 49687.
PG  - e00962-14
AB  - Ochrobactrum anthropi is an occasional cause of nosocomial infections; however, interest in
      the organism lies in its phylogenetic proximity to the genus
      Brucella. Here, we present the 4.9-Mb finished genome of Ochrobactrum anthropi
      ATCC 49687, most commonly used as an exclusionary reference organism.
AU  - Minogue TD
AU  - Daligault HA
AU  - Davenport KW
AU  - Bishop-Lilly KA
AU  - Bruce DC
AU  - Chain PS
AU  - Chertkov O
AU  - Coyne SR
AU  - Freitas T
AU  - Frey KG
AU  - Jaissle J
AU  - Koroleva GI
AU  - Ladner JT
AU  - Palacios GF
AU  - Redden CL
AU  - Xu Y
AU  - Johnson SL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00962-14.

PMID- 25291770
VI  - 2
DP  - 2014
TI  - Draft Genome Assembly of Neisseria lactamica Type Strain A7515.
PG  - e00951-14
AB  - We present the scaffolded genome assembly of Neisseria lactamica type strain A7515 (ATCC
      23970) as submitted to NCBI under accession no. JOVI00000000. This
      type strain of the lactose-fermenting Neisseria species is often used in quality
      control testing and intra-genus phylogenetic analyses. The assembly includes four
      contigs placed into a single scaffold.
AU  - Minogue TD
AU  - Daligault HA
AU  - Davenport KW
AU  - Bishop-Lilly KA
AU  - Bruce DC
AU  - Chain PS
AU  - Chertkov O
AU  - Coyne SR
AU  - Freitas T
AU  - Frey KG
AU  - Jaissle J
AU  - Koroleva GI
AU  - Ladner JT
AU  - Palacios GF
AU  - Redden CL
AU  - Xu Y
AU  - Johnson SL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00951-14.

PMID- 25342683
VI  - 2
DP  - 2014
TI  - Draft Genome Assemblies of Enterobacter aerogenes CDC 6003-71, Enterobacter cloacae CDC 442-68, and Pantoea agglomerans UA 0804-01.
PG  - e01073-14
AB  - The Enterobacteriaceae are environmental and enteric microbes. We sequenced the genomes of two
      Enterobacter reference strains, E. aerogenes CDC 6003-71 and E.
      cloacae CDC 442-68, as well as one near neighbor used as an exclusionary
      reference for diagnostics, Pantoea agglomerans CDC UA0804-01. The genome sizes
      range from 4.72 to 5.55 Mbp and have G+C contents from 54.6 to 55.1%.
AU  - Minogue TD
AU  - Daligault HE
AU  - Davenport KW
AU  - Bishop-Lilly KA
AU  - Bruce DC
AU  - Chain PS
AU  - Coyne SR
AU  - Chertkov O
AU  - Freitas T
AU  - Frey KG
AU  - Jaissle J
AU  - Koroleva GI
AU  - Ladner JT
AU  - Palacios GF
AU  - Redden CL
AU  - Xu Y
AU  - Johnson SL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01073-14.

PMID- 25342681
VI  - 2
DP  - 2014
TI  - Draft Genome Assemblies of Proteus mirabilis ATCC 7002 and Proteus vulgaris ATCC  49132.
PG  - e01064-14
AB  - The pleomorphic swarming bacilli of the genus Proteus are common human gut commensal organisms
      but also the causative agents of recurrent urinary tract
      infections and bacteremia. We sequenced and assembled the 3.99-Mbp genome of
      Proteus mirabilis ATCC 7002 (accession no. JOVJ00000000) and the 3.97-Mbp genome
      of Proteus vulgaris ATCC 49132 (accession no. JPIX00000000), both of which are
      commonly used reference strains.
AU  - Minogue TD
AU  - Daligault HE
AU  - Davenport KW
AU  - Bishop-Lilly KA
AU  - Bruce DC
AU  - Chain PS
AU  - Coyne SR
AU  - Chertkov O
AU  - Freitas T
AU  - Frey KG
AU  - Jaissle J
AU  - Koroleva GI
AU  - Ladner JT
AU  - Palacios GF
AU  - Redden CL
AU  - Xu Y
AU  - Johnson SL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01064-14.

PMID- 25291775
VI  - 2
DP  - 2014
TI  - Complete Genome Assembly of Enterococcus faecalis 29212, a Laboratory Reference Strain.
PG  - e00968-14
AB  - Enterococcus faecalis is a nonmotile Gram-positive coccus, found both as a commensal organism
      in healthy humans and animals and as a causative agent of
      multiple diseases, in particular endocarditis. We sequenced the genome of E.
      faecalis ATCC 29212, a commonly used reference strain in laboratory studies, to
      complete 'finished' annotated assembly (3 Mb).
AU  - Minogue TD
AU  - Daligault HE
AU  - Davenport KW
AU  - Broomall SM
AU  - Bruce DC
AU  - Chain PS
AU  - Coyne SR
AU  - Chertkov O
AU  - Freitas T
AU  - Gibbons HS
AU  - Jaissle J
AU  - Koroleva GI
AU  - Ladner JT
AU  - Palacios GF
AU  - Rosenzweig CN
AU  - Xu Y
AU  - Johnson SL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00968-14.

PMID- 25278526
VI  - 2
DP  - 2014
TI  - Draft Genome Assembly of Pseudomonas aeruginosa Quality Control Reference Strain  Boston 41501.
PG  - e00960-14
AB  - We present the scaffolded genome assembly of Pseudomonas aeruginosa Boston 41501, now publicly
      available in GenBank (JOVK00000000) in 10 contigs placed into a
      single scaffold. The 6.82-Mbp genome contains 66.1% G+C content and 6,295 coding
      sequences, including type 4 pilus and type 3 secretion system production genes.
AU  - Minogue TD
AU  - Daligault HE
AU  - Davenport KW
AU  - Broomall SM
AU  - Bruce DC
AU  - Chain PS
AU  - Coyne SR
AU  - Gibbons HS
AU  - Jaissle J
AU  - Chertkov O
AU  - Freitas T
AU  - Rosenzweig CN
AU  - Xu Y
AU  - Johnson SL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00960-14.

PMID- 22355105
VI  - 109
DP  - 2012
TI  - Hypervariable loci in the human gut virome.
PG  - 3962-3966
AB  - Genetic variation is critical in microbial immune evasion and drug resistance, but variation
      has rarely been studied in complex heterogeneous communities such as the human microbiome. To
      begin to study natural variation, we analyzed DNA viruses present in the lower
      gastrointestinal tract of 12 human volunteers by determining 48 billion bases of viral DNA
      sequence. Viral genomes mostly showed low variation, but 51 loci of approximately 100 bp
      showed extremely high variation, so that up to 96% of the viral genomes encoded unique amino
      acid sequences. Some hotspots of hypervariation were in genes homologous to the bacteriophage
      BPP-1 viral tail-fiber gene, which is known to be hypermutagenized by a unique
      reverse-transcriptase (RT)-based mechanism. Unexpectedly, other hypervariable loci in our data
      were in previously undescribed gene types, including genes encoding predicted Ig-superfamily
      proteins. Most of the hypervariable loci were linked to genes encoding RTs of a single clade,
      which we find is the most abundant clade among gut viruses but only a minor component of
      bacterial RT populations. Hypervariation was targeted to 5'-AAY-3' asparagine codons, which
      allows maximal chemical diversification of the encoded amino acids while avoiding formation of
      stop codons. These findings document widespread targeted hypervariation in the human gut
      virome, identify previously undescribed types of genes targeted for hypervariation, clarify
      association with RT gene clades, and motivate studies of hypervariation in the full human
      microbiome.
AU  - Minot S
AU  - Grunberg S
AU  - Wu G
AU  - Lewis J
AU  - Bushman F
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2012 109: 3962-3966.

PMID- 16701503
VI  - 10
DP  - 2004
TI  - The development of Clostridium difficile genetic systems.
PG  - 75-84
AB  - Clostridum difficile is a major cause of healthcare-associated disease in the western world,
      and is particularly prominent in the elderly. Its
      incidence is rising concomitant with increasing longevity. More
      effective countermeasures are required. However, the pathogenesis of C.
      difficile infection is poorly understood. The lack of effective genetic
      tools is a principal reason for this ignorance. For many years. the
      only tools available for the transfer of genes into C. difficile have
      been conjugative transposons, such as Tn916, delivered via filter
      mating from Bacillus subtilis donors. They insert into a preferred site
      within the genome. Therefore, they may not be employed for classical
      mutagenesis studies, but can be employed to modulate gene function
      through the delivery of antisense RNA. Attempts to develop
      transformation procedures have so far met with little success. However,
      in recent years the situation has been dramatically improved through
      the demonstration of efficient conjugative transfer of both
      replication-proficient and replication-deficient plasmids from
      Escherichia coli donors. This efficient transfer can only be achieved
      in certain strains through negation of the indigenous restriction
      barrier, and is generally most effective when the plasmid employed is
      based on the replicon of the C. difficile plasmid. pCD6.
AU  - Minton N
AU  - Carter G
AU  - Herbert M
AU  - O'Keeffe T
AU  - Purdy D
AU  - Elmore M
AU  - Ostrowski A
AU  - Pennington O
AU  - Davis I
PT  - Journal Article
TA  - Anaerobe
JT  - Anaerobe
SO  - Anaerobe 2004 10: 75-84.

PMID- 27540064
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Brachyspira hyodysenteriae Type Strain B-78 (ATCC 27164).
PG  - e00840-16
AB  - Reported herein is the complete genome sequence of the type strain B-78 (ATCC 27164) of
      Brachyspira hyodysenteriae, the etiological agent of swine dysentery.
      The 3.1-Mb genome consists of a 3.056-Mb chromosome and a 45-kb plasmid, with
      2,617 protein-coding genes, 39 RNA genes, and 40 pseudogenes.
AU  - Mirajkar NS
AU  - Johnson TJ
AU  - Gebhart CJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00840-16.

PMID- 28495781
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Lawsonia intracellularis Strain E40504, Isolated from a  Horse Diagnosed with Equine Proliferative Enteropathy.
PG  - e00330-17
AB  - Reported herein is the draft genome sequence of equine-origin Lawsonia intracellularis strain
      E40504, an obligate intracellular bacterium and the
      etiological agent of equine proliferative enteropathy. The 1.69-Mb draft genome
      sequence includes 1,380 protein-coding genes and 49 RNA genes, and it lacks a
      genomic island reported in swine-origin L. intracellularis strain PHE/MN1-00.
AU  - Mirajkar NS
AU  - Kelley MR
AU  - Gebhart CJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00330-17.

PMID- 25953176
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Arthrobacter chlorophenolicus Strain Mor30.16, Isolated  from the Bean Rhizosphere.
PG  - e00360-15
AB  - Bacteria of the genus Arthrobacter are commonly found in the soil and plant rhizosphere. In
      this study we report the draft genome of Arthrobacter
      chlorophenolicus strain Mor30.16 that was isolated from rhizosphere of beans
      grown in Cuernavaca Morelos, Mexico. This strain promotes growth and ameliorates
      drought stress in bean plants.
AU  - Miranda-Rios JA
AU  - Ramirez-Trujillo JA
AU  - Nova-Franco B
AU  - Lozano-Aguirre BLF
AU  - Iturriaga G
AU  - Suarez-Rodriguez R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00360-15.

PMID- 20660690
VI  - 54
DP  - 2010
TI  - Sequence of pNL194, a 79.3-Kilobase IncN Plasmid Carrying the blaVIM-1 Metallo-{beta}-Lactamase Gene in Klebsiella pneumoniae.
PG  - 4497-4502
AB  - The nucleotide sequence of pNL194, a VIM-1-encoding plasmid, is described.
      pNL194 (79,307-bp) comprised an IncN characteristic segment (38,940-bp)
      and a mosaic structure (40,367-bp) including blaVIM-1, aacA7, aadA1,
      dfrA1, dfrA12, aphA1, strA, strB, and sul1. Tn1000 or Tn5501 insertion
      within fipA probably facilitated recruitment of additional mobile elements
      carrying resistance genes.
AU  - Miriagou V
AU  - Papagiannitsis CC
AU  - Kotsakis SD
AU  - Loli A
AU  - Tzelepi E
AU  - Legakis NJ
AU  - Tzouvelekis LS
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2010 54: 4497-4502.

PMID- 27856594
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the Thermotolerant Cyanobacterium Desertifilum sp. IPPAS B-1220.
PG  - e01304-16
AB  - Here, we report the draft genome of the filamentous cyanobacterium Desertifilum sp. strain
      IPPAS B-1220, isolated from Lake Shar-Nuur, Mongolia. The genome of
      6.1 Mb codes for 5,113 genes. Genome mining revealed 10 clusters for the
      synthesis of bioactive compounds (nonribosomal peptides, polyketides,
      bacteriocins, and lantipeptides) with potential biotechnological or medical
      importance.
AU  - Mironov KS
AU  - Sinetova MA
AU  - Bolatkhan K
AU  - Zayadan BK
AU  - Ustinova VV
AU  - Kupriyanova EV
AU  - Skrypnik AN
AU  - Gogoleva NE
AU  - Gogolev YV
AU  - Los DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01304-16.

PMID- 29437103
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Two Thermotolerant Cyanobacterial Strains Isolated from Hot Springs.
PG  - e01548-17
AB  - We report here two draft cyanobacterial genome sequences, those of Cyanobacterium aponinum
      IPPAS B-1201, isolated from a hot spring in the Turgen Gorge
      (Kazakhstan), and the uncharacterized cyanobacterium IPPAS B-1203, isolated from
      a hot spring in Karlovy Vary (Czech Republic). These two strains were deposited
      at the Collection of Microalgae (IPPAS) of the Timiryazev Institute of Plant
      Physiology.
AU  - Mironov KS
AU  - Sinetova MA
AU  - Kupriyanova EV
AU  - Ustinova VV
AU  - Kozlova AY
AU  - Messineva EM
AU  - Gabrielyan DA
AU  - Bedbenov VS
AU  - Zayadan BK
AU  - Los DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01548-17.

PMID- 6282344
VI  - 47
DP  - 1982
TI  - Purification of specific endonucleases EcoRI and BglII by affinity chromatography.
PG  - 686-694
AB  - Highly active preparations of specific endonucleases EcoRI from E. coli cells and BglII from
      Bacillus globigii cells were obtained by affinity chromatography.  The isolation and
      purification procedures included ultrasonic disintegration of the cells, high-speed
      centrifugation, and chromatography. Dextran blue-Sepharose, folate-Sepharose, and
      phenyl-Sepharose were used as affinity sorbents.  The optimum conditions for sorption and
      elution of the endonucleases without intermediate steps of dialysis and concentration were
      selected.  The consecutive combining of the above-mentioned sorbents with various ligands made
      it possible to achieve highly efficient purification.  The purified enzyme preparations do not
      contain nonspecific nucleases or phosphatases, they are fairly concentrated, and can be used
      for the specific hydrolysis of DNA.
AU  - Miroshnichenko BA
AU  - Naroditskii BS
AU  - Khilko SN
AU  - Platonova N
AU  - Gruber IM
AU  - Tikhonenko TI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1982 47: 686-694.

PMID- 28619793
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Methylocapsa palsarum NE2T, an Obligate Methanotroph from Subarctic Soil.
PG  - e00504-17
AB  - Methylocapsa palsarum NE2T is an aerobic, mildly acidophilic, obligate methanotroph. Similar
      to other Methylocapsa species, it possesses only a
      particulate methane monooxygenase and is capable of atmospheric nitrogen
      fixation. The genome sequence of this typical inhabitant of subarctic wetlands
      and soils also contains genes indicative of aerobic anoxygenic photosynthesis.
AU  - Miroshnikov KK et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00504-17.

PMID- 
VI  - 6
DP  - 2007
TI  - A recombinant lactobacillus strain expressing genes coding for restriction enzymes cleaving the HIV genomes for use as a live  microbicide strategy against heterosexual transmission of HIV.
PG  - 1750-1756
AB  - Using genetically engineered endogenous lactobacillus strains colonizing the vagina mucosa to
      express heterogenous proteins has of
      late joined the novel strategies aimed at developing a microbicides
      against HIV. Using the lactobacillus metabolic genome pathway, we found
      that these bacteria do not naturally produce restriction enzymes, but
      rather, have a number of putative alien genes of the type. In view of
      the antiviral defence role of restriction modification systems (RMS),
      we searched for enzymes that cleave HIV-1, 2 and other SIV genomes
      using theoretical computational methods. With over 200 such enzymes
      identified, we present herein a plasmid vector mediated strategy for
      modifying lactobacillus strains to express RMS islands as an approach
      to developing a live HIV microbicide. This model is transferable to
      other viral infections that find their way into humans through mucosal
      orifices.
AU  - Misaki W
PT  - Journal Article
TA  - Afr. J. Biotechnol.
JT  - Afr. J. Biotechnol.
SO  - Afr. J. Biotechnol. 2007 6: 1750-1756.

PMID- 
VI  - 7
DP  - 2008
TI  - Why bacteria derived R-M nucleic enzymatic peptides are likely efficient therapeutic molecules for use in the design and development of novel HIV inhibitory strategies.
PG  - 1791-1796
AB  - In the past, we have identified, described and isolated over 200 bacteria derived Restriction
      Modification (R-M) nucleic enzymatic peptides as efficient therapeutic molecules for use in
      the development of novel HIV inhibitory strategies. In the issuing months of our publications,
      3 questions have been directed to our work; (1) HIV is an RNA virus, thus restriction peptides
      are impotent as defense peptides. (2) HIV genome is encapsulated in nuclear capsid and viral
      envelope, making access impossible. (3) Human genome contains several palindromes recognizable
      by R-M peptides, making safety delineation critical. This paper serves to provide succinct
      responses to these issues, and highlight critical strategies being employed in ensuring the
      development of safe Microbides and therapeutic vaccines based on this approach.
AU  - Misaki W
PT  - Journal Article
TA  - Afr. J. Biotechnol.
JT  - Afr. J. Biotechnol.
SO  - Afr. J. Biotechnol. 2008 7: 1791-1796.

PMID- 
VI  - 6
DP  - 2007
TI  - Frequency and site mapping of HIV-1/SIVcpz, HIV2/SIVsmm and other SIV gene sequence cleavage by various bacteria restriction enzymes:  Precursors for a novel HIV inhibitory product.
PG  - 1225-1232
AB  - Resistance, toxicity and virologic failure have underlined the need to develop new HIV
      inhibitory products. Base on the natural bacteria
      "restriction modification system" antiviral immune model, we set out to
      analyze the effects of various restriction enzymes on the HIV genome. A
      computer simulated model using Web cutter Version 2.0, and cytogenetic
      analysis. 339 restriction enzymes from Promega database, 10
      HIV-1/SIVcpz genes, 10 HIV-2/SIVsmm genes and 10 other SIV genes. Gene
      sequences were fed into Web cutter 2.0 set to search enzymes with at
      least 6 recognition base pairs ( palindromes). A background in vitro
      cytogenetic control analysis using HIV-1/ SIVcpz GAG, POL and ENV genes
      was done. Of the 339 enzymes used, 238 ( 70.2%) cleaved the HIV-1/
      SIVcpz A1. BY. 97.97BL006  AF193275 genome with 9037 bp compared to 225
      ( 66.4%) and 219 ( 64.6%) for the HIV-2/SIVsmm genome ( 9713 bp) and
      other SIV B. FR. 83. HXB2  LAI  IIIB  BRU  K03455 genome ( 9719 bp),
      respectively. Individual genes had differing but potent susceptibility
      to the enzymes, with a 98.9% Web cutter PPV ( 95% CI, 97.2%99.6%) for
      in vitro cytogenetics. The natural bacteria RMS antiviral immune model
      offers precursors for developing novel HIV and other viral therapeutic
      molecules.
AU  - Misaki W
AU  - Wilson B
AU  - Henry K
PT  - Journal Article
TA  - Afr. J. Biotechnol.
JT  - Afr. J. Biotechnol.
SO  - Afr. J. Biotechnol. 2007 6: 1225-1232.

PMID- 7920544
VI  - 111
DP  - 1993
TI  - Restriction endonucleases: Their characteristics and distribution in pathogenic bacteria.
PG  - 1-12
AB  - Restriction endonucleases have been widely employed in almost all fields of genetic
      engineering including DNA mapping, cloning, sequencing, hybridization, amplification and
      diagnosis. The general characteristics of restriction endonucleases and their reactions are
      reviewed in this paper, together with their distribution in pathogenic bacteria. Many
      restriction endonucleases with novel specificity have been found in these bacteria in our
      laboratory. Some of them are commercially available and have been employed for the molecular
      biologist. Rapid method for detection of restriction endonucleases in pathogenic bacteria is
      also described.
AU  - Mise K
AU  - Miyahara M
PT  - Journal Article
TA  - Eisei Shikenjo Hokoku
JT  - Eisei Shikenjo Hokoku
SO  - Eisei Shikenjo Hokoku 1993 111: 1-12.

PMID- 
VI  - 0
DP  - 1990
TI  - Usefulness in the epidemiology of food poisoning cases of detection of specific restriction endonucleases in some serotypes of Salmonella and Yersinia.
PG  - 127-129
AB  - Restriction endonucleases have been employed as an extremely important tool in
      recombinant DNA technology.  To date, the occurrence of more than 100
      restriction endonucleases with different specificities has been reported.
      Restriction endonucleases have been screened in this laboratory for pathogenic
      bacteria belonging to the Enterobacteriaceae in the hope that: (i) the
      detection of a specific restriction endonuclease is found at a high frequency
      in the species; and (ii) new restriction endonucleases with novel specificities
      might be found in pathogenic bacteria, since screening for restriction
      endonucleases has rarely been carried out.  Here, we report that four
      clinically important food-poisoning bacteria produce specific restriction
      endonucleases at high frequencies.  Some of these are expected to be useful for
      recombinant DNA technology after cloning of their gene into Escherichia coli
      K-12.
AU  - Mise K
AU  - Miyahara M
AU  - Maruyama T
AU  - Kudoh Y
AU  - Ohashi M
PT  - Journal Article
TA  - Microbial Toxins in Foods and Feeds: Cell. Mol. Modes Action
JT  - Microbial Toxins in Foods and Feeds: Cell. Mol. Modes Action
SO  - Microbial Toxins in Foods and Feeds: Cell. Mol. Modes Action 1990 0: 127-129.

PMID- 2989097
VI  - 33
DP  - 1985
TI  - Purification of a new restriction endonuclease, StyI, from Escherichia coli carrying the hsd+ miniplasmid.
PG  - 357-361
AB  - A new restriction endonuclease, StyI, free of contaminating nuclease
      activities, has been isolated from Escherichia coli carrying the hsd+
      miniplasmid of Salmonella typhi origin.  In the presence of 10 mM Mg2+, it
      recognizes and cleaves a hexanucleotide sequence of 5'-C^C(A/T)(A/T)GG.  The
      advantages of the StyI endonuclease include its stability, high yield (more
      than 2 x 103 units/g of wet cells), easy handling of producer cells, and the
      ability to recognize new sequences, CCAAGG and CCTTGG.
AU  - Mise K
AU  - Nakajima K
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1985 33: 357-361.

PMID- 6096226
VI  - 30
DP  - 1984
TI  - Isolation of restriction enzyme EcoVIII, an isoschizomer of HindIII, produced by Escherichia coli E1585-68.
PG  - 79-85
AB  - A restriction endonuclease designated EcoVIII, an isoschizomer of HindIII, was
      isolated from Escherichia coli E1585-68 and purified by dextran-polyethylene
      glycol (DPG) phase partitiion, ammonium sulfate precipitation, phospho- and
      DEAE-cellulose chromatography, and hydroxylapatite chromatography.  The
      purified EcoVIII was stable during the purification procedure and its high
      specific activity required 10 mM Mg2+.  Unlike HindIII, EcoVIII exhibited a
      high specific activity even at low pH (pH 6.3) and showed the highest activity
      at 48C.  Transformation of purified plasmid DNA from E. coli E1585-68 into K-12
      indicated that the EcoVIII gene was carried on a multicopy 4.4-kb miniplasmid.
      EcoVIII seems to be preferable to HindIII for its production and use because of
      easier handling of producer cells and a wider range of activity.
AU  - Mise K
AU  - Nakajima K
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1984 30: 79-85.

PMID- 3000888
VI  - 36
DP  - 1985
TI  - Restriction endonuclease EcoO109 from Escherichia coli H709c with heptanucleotide recognition site 5'-PuG^GNCCPy.
PG  - 363-367
AB  - A new restriction endonuclease, EcoO109, has been isolated from Escherichia
      coli H709c by polyethylenemine (PEI) precipitation, DEAE-cellulose
      chromatography and heparin agarose chromatography.  The yield was high, more
      than 3000 units/g of wet cells.  The EcoO109 endonuclease recognizes and
      cleaves a nucleotide sequence of 5'-PuG^GN C CPy-3' 3'-PyC CN'G^GPu-5'in the
      presence of 10 mM Mg2+.  The enzyme will be useful for structural analysis and
      molecular cloning of DNA because of the stability, high yield and easy handling
      of the producer strain.
AU  - Mise K
AU  - Nakajima K
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1985 36: 363-367.

PMID- 3021586
VI  - 44
DP  - 1986
TI  - Production of restriction endonucleases using multicopy Hsd plasmids occurring naturally in pathogenic Escherichia coli and Shigella boydii.
PG  - 165-169
AB  - A convenient procedure has been devised for detection of restriction
      endonucleases in the Escherichia coli-Shigella group.  With this procedure, two
      restriction endonucleases, designated Sbo13 and EcoT22, were found and later
      were identified as isoschizomers of NruI and AvaIII, respectively.  These
      endonucleases were shown to be produced from small multicopy plasmids.  They
      were isolated from nonpathogenic E. coli into which the plasmids had been
      introduced by transformation, and purified from contaminating nuclease
      activity.  The yield was high, 1000 units/g of wet cells for Sbo13 and 500
      units/g for EcoT22.  Sbo13 and EcoT22 should be preferable to NruI and AvaIII
      because of the high yield and ease in handling the producer cells.
AU  - Mise K
AU  - Nakajima K
AU  - Terakado N
AU  - Ishidate M
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1986 44: 165-169.

PMID- 29437100
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Zhihengliuella sp. Strain ISTPL4, a Psychrotolerant and  Halotolerant Bacterium Isolated from Pangong Lake, India.
PG  - e01533-17
AB  - Zhihengliuella sp. strain ISTPL4, a psychrotolerant bacterium, was isolated from  brackish
      water of the high-altitude Pangong Lake in India. In this study, we
      report its draft genome sequence, which contains 3,529,629 bp with a G+C content
      of 69.84%. The genome is enriched in genes associated with cold adaptation and
      plant growth promotion.
AU  - Mishra A
AU  - Jha G
AU  - Thakur IS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01533-17.

PMID- 24501657
VI  - 9
DP  - 2013
TI  - Non-contiguous finished genome sequence and description of Nosocomiicoccus massiliensis sp. nov.
PG  - 205-219
AB  - Nosocomiicoccus massiliensis strain NP2(T) sp. nov. is the type strain of a new species within
      the genus Nosocomiicoccus. This strain, whose genome is described
      here, was isolated from the fecal flora of an AIDS-infected patient living in
      Marseille, France. N. massiliensis is a Gram-positive aerobic coccus. Here we
      describe the features of this organism, together with the complete genome
      sequence and annotation. The 1,645,244 bp long genome (one chromosome but no
      plasmid) contains 1,738 protein-coding and 45 RNA genes, including 3 rRNA genes.
AU  - Mishra AK
AU  - Edouard S
AU  - Dangui NP
AU  - Lagier JC
AU  - Caputo A
AU  - Blanc-Tailleur C
AU  - Ravaux I
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 9: 205-219.

PMID- 23407265
VI  - 6
DP  - 2012
TI  - Genome sequence and description of Alistipes senegalensis sp. nov.
PG  - 1-16
AB  - Alistipes senegalensis strain JC50(T) is the type strain of A. senegalensis sp. nov., a new
      species within the Alistipes genus. This strain, whose genome is
      described here, was isolated from the fecal flora of an asymptomatic patient. A.
      senegalensis is an anaerobic Gram-negative rod-shaped bacterium. Here we describe
      the features of this organism, together with the complete genome sequence and
      annotation. The 4,017,609 bp long genome (1 chromosome, but no plasmid) contains
      3,113 protein-coding and 50 RNA genes, including 5 rRNA genes.
AU  - Mishra AK
AU  - Gimenez G
AU  - Lagier JC
AU  - Robert C
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 6: 1-16.

PMID- 23991260
VI  - 8
DP  - 2013
TI  - Non contiguous-finished genome sequence and description of Enorma massiliensis gen. nov., sp. nov., a new member of the Family Coriobacteriaceae.
PG  - 290-305
AB  - Enorma massiliensis strain phI(T) is the type strain of E. massiliensis gen. nov., sp. nov.,
      the type species of a new genus within the family
      Coriobacteriaceae, Enorma gen. nov. This strain, whose genome is described here,
      was isolated from the fecal flora of a 26-year-old woman suffering from morbid
      obesity. E. massiliensis strain phI(T) is a Gram-positive, obligately anaerobic
      bacillus. Here we describe the features of this organism, together with the
      complete genome sequence and annotation. The 2,280,571 bp long genome (1
      chromosome but no plasmid) exhibits a G+C content of 62.0% and contains 1,901
      protein-coding and 51 RNA genes, including 3 rRNA genes.
AU  - Mishra AK
AU  - Hugon P
AU  - Lagier JC
AU  - Nguyen TT
AU  - Couderc C
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 290-305.

PMID- 24019985
VI  - 7
DP  - 2013
TI  - Non contiguous-finished genome sequence and description of Peptoniphilus obesi sp. nov.
PG  - 357-369
AB  - Peptoniphilus obesi strain ph1(T) sp. nov., is the type strain of P. obesi sp. nov., a new
      species within the genus Peptoniphilus. This strain, whose genome is
      described here, was isolated from the fecal flora of a 26-year-old woman
      suffering from morbid obesity. P. obesi strain ph1(T) is a Gram-positive,
      obligate anaerobic coccus. Here we describe the features of this organism,
      together with the complete genome sequence and annotation. The 1,774,150 bp long
      genome (1 chromosome but no plasmid) contains 1,689 protein-coding and 29 RNA
      genes, including 5 rRNA genes.
AU  - Mishra AK
AU  - Hugon P
AU  - Lagier JC
AU  - Nguyen TT
AU  - Robert C
AU  - Couderc C
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 7: 357-369.

PMID- 23408485
VI  - 7
DP  - 2012
TI  - Non contiguous-finished genome sequence and description of Peptoniphilus grossensis sp. nov.
PG  - 320-330
AB  - Peptoniphilus grossensis strain ph5(T) sp. nov., is the type strain of Peptoniphilus
      grossensis sp. nov., a new species within the Peptoniphilus genus.
      This strain, whose genome is described here, was isolated from the fecal flora of
      a 26-year-old woman suffering from morbid obesity. P. grossensis strain ph5 is a
      Gram-positive obligate anaerobic coccus. Here we describe the features of this
      organism, together with the complete genome sequence and annotation. The
      2,101,866-bp long genome (1 chromosome but no plasmid) exhibits a G+C content of
      33.9% and contains 2,041 protein-coding and 29 RNA genes, including 3 rRNA genes.
AU  - Mishra AK
AU  - Hugon P
AU  - Robert C
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 7: 320-330.

PMID- 24019986
VI  - 7
DP  - 2013
TI  - Non contiguous-finished genome sequence and description of Peptoniphilus senegalensis sp. nov.
PG  - 370-381
AB  - Peptoniphilus senegalensis strain JC140(T) sp. nov., is the type strain of P. senegalensis sp.
      nov., a new species within the genus Peptoniphilus. This strain,
      whose genome is described here, was isolated from the fecal flora of a healthy
      patient. P. senegalensis strain JC140(T) is an obligate Gram-positive anaerobic
      coccus. Here we describe the features of this organism, together with the
      complete genome sequence and annotation. The 1,840,641 bp long genome (1
      chromosome but no plasmid) exhibits a G+C content of 32.2% and contains 1,744
      protein-coding and 23 RNA genes, including 3 rRNA genes.
AU  - Mishra AK
AU  - Lagier JC
AU  - Nguyen TT
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 7: 370-381.

PMID- 24976895
VI  - 9
DP  - 2013
TI  - Non-contiguous finished genome sequence and description of Holdemania massiliensis sp. nov.
PG  - 395-409
AB  - Holdemania massiliensis strain AP2(T) sp. nov. is the type strain of H. massiliensis sp. nov.,
      a new species within the genus Holdemania. This strain,
      whose genome is described here, was isolated from the fecal flora of a
      21-year-old French Caucasian female suffering from severe restrictive anorexia
      nervosa. H. massiliensis is a Gram-positive, anaerobic bacillus. Here we describe
      the features of this organism, together with the complete genome sequence and
      annotation. The 3,795,625 bp-long genome (one chromosome but no plasmid) contains
      3,461 protein-coding and 49 RNA genes, including 3 rRNA genes.
AU  - Mishra AK
AU  - Lagier JC
AU  - Pfleiderer A
AU  - Nguyen TT
AU  - Caputo A
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 9: 395-409.

PMID- 23459006
VI  - 7
DP  - 2012
TI  - Non-contiguous finished genome sequence and description of Paenibacillus senegalensis sp. nov.
PG  - 70-81
AB  - strain JC66, is the type strain of sp. nov., a new species within the genus . This strain,
      whose genome is described here, was isolated from the fecal flora of
      a healthy patient. strain JC66 is a facultative Gram-negative anaerobic
      rod-shaped bacterium. Here we describe the features of this organism, together
      with the complete genome sequence and annotation. The 5,581,254 bp long genome (1
      chromosome but no plasmid) exhibits a G+C content of 48.2% and contains 5,008
      protein-coding and 51 RNA genes, including 9 rRNA genes.
AU  - Mishra AK
AU  - Lagier JC
AU  - Rivet R
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 7: 70-81.

PMID- 23449949
VI  - 7
DP  - 2012
TI  - Non contiguous-finished genome sequence and description of Peptoniphilus timonensis sp. nov.
PG  - 1-11
AB  - strain JC401 sp. nov. is the type strain of sp. nov., a new species within the genus. This
      strain, whose genome is described here, was isolated from the fecal
      flora of a healthy patient. is an obligate Gram-positive anaerobic coccus. Here
      we describe the features of this organism, together with the complete genome
      sequence and annotation. The 1,758,598 bp long genome (1 chromosome, no plasmid)
      contains 1,922 protein-coding and 22 RNA genes, including 5 rRNA genes.
AU  - Mishra AK
AU  - Lagier JC
AU  - Robert C
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 7: 1-11.

PMID- 23408737
VI  - 6
DP  - 2012
TI  - Non-contiguous finished genome sequence and description of Clostridium senegalense sp. nov.
PG  - 386-395
AB  - Clostridium senegalense strain JC122(T), is the type strain of Clostridium senegalense sp.
      nov., a new species within the genus Clostridium. This strain,
      whose genome is described here, was isolated from the fecal flora of a healthy
      patient. C. senegalense strain JC122(T) is an obligate anaerobic Gram-positive
      rod-shaped bacterium. Here we describe the features of this organism, together
      with the complete genome sequence and annotation. The 3,893,008 bp long genome (1
      chromosome but no plasmid) exhibits a G+C content of 26.8% and contains 3,704
      protein-coding and 57 RNA genes, including 6 rRNA genes.
AU  - Mishra AK
AU  - Lagier JC
AU  - Robert C
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 6: 386-395.

PMID- 23991262
VI  - 8
DP  - 2013
TI  - Genome sequence and description of Timonella senegalensis gen. nov., sp. nov., a  new member of the suborder Micrococcinae.
PG  - 318-335
AB  - Timonella senegalensis strain JC301(T) gen. nov., sp. nov. is the type strain of  T.
      senegalensis gen. nov., sp. nov., a new species within the newly proposed
      genus Timonella. This bacterial strain was isolated from the fecal flora of a
      healthy Senegalese patient. In this report, we detail the features of this
      organism, together with the complete genome sequence and annotation. Timonella
      senegalensis strain JC301(T) exhibits the highest 16S rRNA similarity (95%) with
      Sanguibacter marinus, the closest validly published bacterial species. The genome
      of T. senegalensis strain JC301(T) is 3,010,102-bp long, with one chromosome and
      no plasmid. The genome contains 2,721 protein-coding genes and 72 RNA genes,
      including 5 rRNA genes. The genomic annotation revealed that T. senegalensis
      strain JC301(T) possesses the complete complement of enzymes necessary for the de
      novo biosynthesis of amino acids and vitamins (except for riboflavin and biotin),
      as well as the enzymes involved in the metabolism of various carbon sources,
      chaperone genes, and genes involved in the regulation of polyphosphate and
      glycogen levels.
AU  - Mishra AK
AU  - Lagier JC
AU  - Robert C
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 318-335.

PMID- 24501631
VI  - 8
DP  - 2013
TI  - Non-contiguous finished genome sequence and description of Bacillus massilioanorexius sp. nov.
PG  - 465-479
AB  - Bacillus massilioanorexius strain AP8(T) sp. nov. is the type strain of B. massilioanorexius
      sp. nov., a new species within the genus Bacillus. This strain,
      whose genome is described here, was isolated from the fecal flora of a
      21-year-old Caucasian French female suffering from a severe form of anorexia
      nervosa since the age of 12 years. B. massilioanorexius is a Gram-positive
      aerobic bacillus. Here we describe the features of this organism, together with
      the complete genome sequence and annotation. The 4,616,135 bp long genome (one
      chromosome but no plasmid) contains 4,432 protein-coding and 87 RNA genes,
      including 8 rRNA genes.
AU  - Mishra AK
AU  - Pfleiderer A
AU  - Lagier JC
AU  - Robert C
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 465-479.

PMID- 29122871
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Nonclinical and Clinical Enterobacter cloacae Isolates  Exhibiting Multiple Antibiotic Resistance and Virulence Factors.
PG  - e01218-17
AB  - Enterobacter spp. have been implicated as opportunistic pathogens which over the  years have
      gained resistance toward most of the available therapeutic drugs. We
      sequenced two multidrug-resistant Enterobacter cloacae isolates harboring
      multiple efflux pump genes. These isolates exhibited strain-specific modulation
      of efflux pump protein expression.
AU  - Mishra M
AU  - Patole S
AU  - Mohapatra H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01218-17.

PMID- 
VI  - 
DP  - 2002
TI  - Restriction Endonucleases.
PG  - 62-80
AB  - Luria and Human first described the phenomenon of host-controlled specificity in T-even
      phages.  This was immediately confirmed by Bertani and Weigle in lambda and P2 phages.  In
      these studies it was shown that a particular bacteriophage possessed different efficiencies of
      infection on several closely related strains of bacteria.  However, the progeny of
      bacteriophage which initially plated with a low efficiency was later found to plate
      efficiently after one generation of plating on the same bacterium.  This phenomenon of
      host-controlled specificity was first discovered in T-even phages by Luria and Human  and in
      lambda and P2 phages by Bertani and Weigle.  The epigenetic nature of such host range
      specificity was indicated by the fact that the newly acquired high efficiency of plating on a
      particular bacterial host was lost by the progeny of the same bacteriophage when plated on
      different hosts.  The first host modification unique to T-even phages involved the
      glycosylation of hydroxymethyl cytosine residue.  However, the modification introduced in
      lambda phages was found to be of universal occurrence.  The molecular basis of such host range
      specificity depended on the restriction or modification of certain DNA sequences by
      restriction and modification enzymes (Arber and Dussoix, 1962; Arbor and Linn, 1969).  Foreign
      DNA molecules (lacking appropriate modification) were cleaved by the host restriction
      endonuclease upon entry into the bacterial cell.  During this process some of the phage DNA
      may escape restriction by host endonucleases and instead get modified by methylation of
      adenine or cytosine moieties in DNA and thus acquire the ability to infect the same host
      efficiently in subsequent rounds of infection.  In these series of events, bacterial DNAs
      remain protected because of previous modification of the DNA sequences by methylase.  This
      molecular scenario for the host range specificity by Arber and Dussoix was confirmed by the
      discovery of bacterial restriction-modification enzymes.  The restriction endonucleases widely
      differ in terms of subunit composition, cofactor requirements, and interaction with DNA
      substrate in addition to their specificity for nucleotide sequence as sites of recognition and
      of cleavage or modification.  They are classified under three categories.  These are: type I
      restriction endonuclease, type II restriction endonuclease, and type III restriction
      endonuclease.  Among these three types of restriction endonuclease, type I and type III
      enzymes can be referred to as ATP-dependent restriction endonucleases and the type II enzymes
      can be referred to as ATP-independent restriction endonucleases.  The physiological roles of
      the ATP-dependent restriction endonucleases in biological restriction and modification have
      been genetically identified.  The physiological role of the ATP-independent endonucleases
      remains to be elucidated.  However, the discovery of this group of restriction endonucleases
      has revolutionized molecular biology by facilitating the physical mapping and nucleotide
      sequencing of DNA segments and their amplification by molecular cloning.  The properties of
      the three types of restriction enzymes are compared in Table 4.1.
AU  - Mishra NC
PT  - Journal Article
TA  - Nucleases. Molecular Biology and Applications.
JT  - Nucleases. Molecular Biology and Applications.
SO  - Nucleases. Molecular Biology and Applications. 2002 : 62-80.

PMID- 27365340
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Pseudomonas sp. Strain BMS12, a Plant Growth-Promoting and Protease-Producing Bacterium, Isolated from the Rhizosphere Sediment of Phragmites karka of Chilika Lake, India.
PG  - e00342-16
AB  - We report the 4.51 Mb draft genome of Pseudomonas sp. strain BMS12, a Gram-negative bacterium
      in the class of Gammaproteobacteria, isolated from the rhizospheric sediment of Phragmites
      karka, an invasive weed in Chilika Lake, Odisha, India. The Pseudomonas sp. strain BMS12 is
      capable of producing proteases and is also an efficient plant growth promoter that can be
      useful for various phytoremedial and industrial applications.
AU  - Mishra SR
AU  - Panda AN
AU  - Ray L
AU  - Sahu N
AU  - Mishra G
AU  - Jadhao S
AU  - Suar M
AU  - Adhya TK
AU  - Rastogi G
AU  - Pattnaik AK
AU  - Raina V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00342-16.

PMID- 27365343
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Acinetobacter sp. Strain BMW17, a Cellulolytic and Plant Growth-Promoting Bacterium Isolated from the Rhizospheric Region of Phragmites karka of Chilika Lake, India.
PG  - e00395-16
AB  - We report the 3.16 Mb draft genome of Acinetobacter sp. strain BMW17, a Gram-negative
      bacterium in the class of Gammaproteobacteria, isolated from the rhizospheric region of
      Phragmites karka, an invasive weed in Chilika Lake, Odisha, India. The strain BMW17(T) is
      capable of degrading cellulose and is also  an efficient plant growth promoter that can be
      useful for various phytoremedial and commercial applications.
AU  - Mishra SR
AU  - Ray L
AU  - Panda AN
AU  - Sahu N
AU  - Xess SS
AU  - Jadhao S
AU  - Suar M
AU  - Adhya TK
AU  - Rastogi G
AU  - Pattnaik AK
AU  - Raina V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00395-16.

PMID- 26358596
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence and Methylome of Staphylococcus schleiferi, an Important Cause of Skin and Ear Infections in Veterinary Medicine.
PG  - e01011-15
AB  - Staphylococcus schleiferi, a Gram-positive and coagulase-variable organism, is an
      opportunistic human pathogen and a major cause of skin and soft tissue infections in dogs.
      Here, we report the first S. schleiferi genome sequence and methylome from four canine
      clinical isolates.
AU  - Misic AM
AU  - Cain CL
AU  - Morris DO
AU  - Rankin SC
AU  - Beiting DP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01011-15.

PMID- 8158653
VI  - 238
DP  - 1994
TI  - Salt effects on protein-DNA interactions.  The lambdacI repressor and EcoRI endonuclease.
PG  - 264-280
AB  - In this paper, finite-difference solutions to the nonlinear Poisson-Boltzmann (NLPB) equation
      are used to calculate the salt dependent contribution to the electrostatic DNA binding free
      energy for both the lambdacI repressor and the EcoRI endonuclease. For the protein-DNA systems
      studied, the NLPB method describes nonspecific univalent salt dependent effects on the binding
      free energy which are in excellent agreement with experimental results. In these systems, the
      contribution of the ion atmosphere to the binding free energy substantially destabilizes the
      protein-DNA complexes. The magnitude of this effect involves a macromolecular structure
      dependent redistribution of both cations and anions around the protein and the DNA which is
      dominated by long range electrostatic interactions. We find that the free energy associated
      with global ion redistribution upon binding is more important than changes associated with
      local protein-DNA interactions (ion-pairs) in determining salt effects. The NLPB model reveals
      how long range salt effects can play a significant role on the relative stability of
      protein-DNA complexes with different structures.
AU  - Misra VK
AU  - Hecht JL
AU  - Sharp KA
AU  - Friedman RA
AU  - Honig B
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1994 238: 264-280.

PMID- 26514764
VI  - 3
DP  - 2015
TI  - Draft Whole-Genome Sequence of the Marine Bacterium Idiomarina zobellii KMM 231T.
PG  - e01257-15
AB  - Idiomarina zobellii was isolated from the northwest Pacific Ocean at a depth of 4,000 to 5,000
      m in 1985. The draft whole-genome shotgun sequence of I. zobellii
      KMM 231(T) described in this paper has a predicted length of 2,602,160 bp,
      containing 2,570 total genes, 52 tRNAs, and a G+C content of 47.10%.
AU  - Mithoefer S
AU  - Rheaume BA
AU  - MacLea KS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01257-15.

PMID- 7948908
VI  - 26
DP  - 1994
TI  - The Chlorella virus adenine methyltransferase gene is a strong promoter in plants.
PG  - 85-93
AB  - An upstream region isolated from a eukaryotic algal virus adenine methyltransferase gene was
      tested for promoter function in plants. Fusion of this region to the chloramphenicol
      acetyltransferase reporter gene resulted in significantly higher expression than fusion with
      the cauliflower mosaic virus 35S promoter. Strong levels of expression were also found in
      electroporated monocot plant cells. The promoter activity in transgenic tobacco plants showed
      tissue-specific expression. Leaves had the highest expression followed by stems and flowers.
      The promoter activity was not detected in root tissue. Environmental cues, such as light, and
      the phytohormones auxin and cytokinines had no effect on the promoter's expression. This
      promoter might be utilized to achieve high levels of expression of introduced genes in higher
      plants.
AU  - Mitra A
AU  - Higgins DW
PT  - Journal Article
TA  - Plant Mol. Biol.
JT  - Plant Mol. Biol.
SO  - Plant Mol. Biol. 1994 26: 85-93.

PMID- 8086473
VI  - 1219
DP  - 1994
TI  - Ectopic expression of a viral adenine methyltransferase gene in tobacco.
PG  - 244-249
AB  - Plant genomes contain both methylated adenine and cytosine residues although the roles of
      these methylations are not well understood. A Chlorella virus adenine methyltransferase gene
      under the control of cauliflower mosaic virus 35S promoter in a binary plant transformation
      vector was expressed both in transgenic tobacco plants and transformed tobacco calli. The
      transgenic plants as well as transformed calli produced functional adenine methyltransferase
      enzyme, but the level of expression was higher in tobacco calli. A transgenic tobacco cell
      line that expressed the methyltransferase enzyme and carried an Arabidopsis cab3 gene
      containing a single target site for the adenine methyltransferase enzyme showed that the
      adenine residue was not methylated. HPLC analysis of genomic DNA from transgenic calli also
      showed no detectable levels of methylated adenine residues.
AU  - Mitra A
AU  - Que Q
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1994 1219: 244-249.

PMID- 24158016
VI  - 24
DP  - 2014
TI  - Generation and Analysis of Draft Sequences of 'Stolbur' Phytoplasma from Multiple Displacement Amplification Templates.
PG  - 1-11
AB  - Phytoplasma-associated diseases are reported for more than 1,000 plant species worldwide.
      Only a few genome sequences are available in contrast to the economical importance of these
      bacterial pathogens.  A new strategy was used to retrieve phytoplasma strain-specifric genome
      data.  Multiple displacement amplification was performed on DNA obtained from <3 g of plant
      tissue from tobacco and parsley samples infected with 'stolbur' strains.  Random hexamers
      and Phi29 polymerase were evaluated with and without supplementation by group-assigned
      oligonucleotides providing templates for Illumina's sequencing approach.  Metagenomic drafts
      derived from individual and pooled strain-specific de novo assembles were analyzed.
      Supplementation of the Phi29 reaction with the group-assigned oligonucleotides resulted in an
      about 2-fold enrichment of the percentage of phytoplasma-assigned reads and thereby improved
      assembly results.  The obtained genomic drafts represent the largest datasets available from
      'stolbur' phytoplasmas.  Sequences of the two strains (558 kb, 448 proeins and 516 kb, 346
      proteins, respectively) were annotated allowing the identification of prominent membrane
      proteins and reconstruction of core pathways.  Analysis of a putative truncated sucrose
      phosphorylase provides hints on sugar degradation.  Furthermore, it is shown that drafts
      obtained from repetitive-rich genomes allow only limited analysis on multicopy regions and
      genome completeness.
AU  - Mitrovic J
AU  - Siewert C
AU  - Duduk B
AU  - Hecht J
AU  - Moelling K
AU  - Broecker F
AU  - Beyerlein P
AU  - Buettner C
AU  - Bertaccini A
AU  - Kube M
PT  - Journal Article
TA  - J. Mol. Microbiol. Biotechnol.
JT  - J. Mol. Microbiol. Biotechnol.
SO  - J. Mol. Microbiol. Biotechnol. 2014 24: 1-11.

PMID- 28254979
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Anoxybacillus mongoliensis Strain MB4, a Sulfur-Utilizing Aerobic Thermophile Isolated from a Hot Spring in Tattapani,  Central India.
PG  - e01709-16
AB  - Anoxybacillus mongoliensis strain MB4, an aerobic thermophile, was isolated from  a hot spring
      located in central India. Its first draft genome sequence reported
      in this study comprises 2,807,516 bp and 2,853 protein-coding genes. Detailed
      genomic analysis indicates that it is capable of performing sulfur metabolism.
AU  - Mittal P
AU  - Saxena R
AU  - Sharma VK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01709-16.

PMID- 23814112
VI  - 1
DP  - 2013
TI  - Genome Sequence of the Multiple-beta-Lactam-Antibiotic-Resistant Bacterium Acidovorax sp. Strain MR-S7.
PG  - e00412-13
AB  - Acidovorax sp. strain MR-S7 was isolated from activated sludge in a treatment system for
      wastewater containing beta-lactam antibiotic pollutants. Strain MR-S7
      demonstrates multidrug resistance for various types of beta-lactam antibiotics at
      high levels of MIC. The draft genome sequence clarified that strain MR-S7 harbors
      unique beta-lactamase genes.
AU  - Miura T
AU  - Kusada H
AU  - Kamagata Y
AU  - Hanada S
AU  - Kimura N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00412-13.

PMID- 25125640
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of an Alkane Degrader, Alcanivorax sp. Strain NBRC 101098.
PG  - e00766-14
AB  - Alcanivorax sp. strain NBRC 101098 was isolated from seawater in Japan. Strain NBRC 101098 is
      able to degrade various types of n-alkanes. Here, we report the
      complete genome of strain NBRC 101098.
AU  - Miura T
AU  - Tsuchikane K
AU  - Numata M
AU  - Hashimoto M
AU  - Hosoyama A
AU  - Ohji S
AU  - Yamazoe A
AU  - Fujita N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00766-14.

PMID- 25814615
VI  - 3
DP  - 2015
TI  - Complete Genome Sequences of Sulfurospirillum Strains UCH001 and UCH003 Isolated  from Groundwater in Japan.
PG  - e00236-15
AB  - Sulfurospirillum strains UCH001 and UCH003 were isolated from anaerobic
      cis-1,2-dichloroethene-dechlorinating microbial consortia derived from
      groundwater in Japan. Here, we report the complete genome sequences of strains
      UCH001 and UCH003.
AU  - Miura T
AU  - Uchino Y
AU  - Tsuchikane K
AU  - Ohtsubo Y
AU  - Ohji S
AU  - Hosoyama A
AU  - Ito M
AU  - Takahata Y
AU  - Yamazoe A
AU  - Suzuki K
AU  - Fujita N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00236-15.

PMID- 1791853
VI  - 5
DP  - 1991
TI  - A DNA sequence for the discrimination of Neisseria gonorrhoeae from other Neisseria species.
PG  - 327-335
AB  - A 350 base pair Neisseria gonorrhoeae DNA restriction fragment was cloned after subtractive
      hybridization to Neisseria meningitidis DNA.  This restriction fragment hybridized to 105 out
      of 106 N. gonorrhoeae strains tested.  While three N. meningitidis strains did not hybridize
      to this probe, Neisseria mucosa DNA exhibited cross-hybridization.  This particular clone was
      used to screen a N. gonorrhoeae genomic DNA library.  A positive 2-4 kilobase pair clone was
      shown by DNA sequencing to contain two long open reading frames.  One open reading frame did
      not hybridize to N. mucosa and other Neisseria species, while it retained specificity for the
      original 105 N. gonorrhoeae strains.  This open reading frame also showed significant homology
      to cytosine DNA methyltransferases.
AU  - Miyada CG
AU  - Born TL
PT  - Journal Article
TA  - Mol. Cell. Probes
JT  - Mol. Cell. Probes
SO  - Mol. Cell. Probes 1991 5: 327-335.

PMID- 9675867
VI  - 164
DP  - 1998
TI  - Partial purification and characterization of RalF40I, a class II restriction endonuclease from Ruminococcus albus F-40, which recognizes and cleaves 5'-/GATC-3'.
PG  - 215-218
AB  - Restriction endonuclease RalF40I was purified from cell-free extracts of the rumen
      cellulolytic bacterium Ruminococcus albus F-40 by heparin-Sepharose chromatography.  The
      preparation was active only on DNA substrates that were not Dam-methylated.  RalF40I
      recognizes the 4-bp palindrome, 5'-/GATC-3', and cleaves DNA at the 5' side of G in the
      sequence, producing 5' tetranucleotide protruding ends.  RalF40I is a class II restriction
      endonuclease and an isoschizomer of MboI and DpnII.
AU  - Miyagi T
AU  - Javorsky P
AU  - Pristas P
AU  - Karita S
AU  - Sakka K
AU  - Ohmiya K
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1998 164: 215-218.

PMID- Not carried by PubMed...
VI  - 35
DP  - 1994
TI  - Characterization of restriction endonucleases from Vibrio parahaemolyticus.
PG  - 605-609
AB  - Forty-six restriction endonuclease (ENase)-positive strains were found among 270 strains of
      Vibrio parahaemolyticus tested. Thirty-six ENases were purified and 7 different specificities
      were identified. All are isoschizomers of already-known ENases, i.e., isoschizomers of AvaII,
      AsuI, PmaCI, PstI, Eco31I, EarI, and SapI. It is noteworthy that the majority of V.
      parahaemolyticus ENases recognize non-palindromic or interrupted palindromic sequences.
      Specific ENases with the same specificity were found at a high frequency in some serotypes of
      V. parahaemolyticus.
AU  - Miyahara M
AU  - Fujiwara R
AU  - Mise K
AU  - Shimada T
AU  - Matsushita S
AU  - Kudoh Y
AU  - Ishiwata N
AU  - Tanimura A
PT  - Journal Article
TA  - J. Food. Hyg. Sci. Japan
JT  - J. Food. Hyg. Sci. Japan
SO  - J. Food. Hyg. Sci. Japan 1994 35: 605-609.

PMID- 9057987
VI  - 20
DP  - 1997
TI  - StyD4I restriction-modification system of Salmonella typhi D4: Cloning and sequence analysis.
PG  - 201-203
AB  - A plasmid (5.4 kbp) from Salmonella Typhi D4 has been identified as encoding a restriction and
      modification (R-M) system.  DNA fragments (2537 bp) that carried the genes for the restriction
      endonuclease and methyltransferase encoded on the plasmid were sequenced.  Two divergently
      arranged open reading frames of 957 bp for the restriction endonuclease consisting of 318 aa
      (amino acids) and 1140 bp for the DNA methyltransferase consisting of 379 aa were identified.
      These sequences were similar to the sequences of the SsoII R-M system, including the
      interspace between the two genes.
AU  - Miyahara M
AU  - Ishiwata N
AU  - Yoshida Y
PT  - Journal Article
TA  - Biol. Pharm. Bull.
JT  - Biol. Pharm. Bull.
SO  - Biol. Pharm. Bull. 1997 20: 201-203.

PMID- 8951174
VI  - 19
DP  - 1996
TI  - Isolation and characterization of restriction endonuclease in Plesiomonas shigelloides and Aeromonas species.
PG  - 1506-1507
AB  - Five restriction endonucleases (ENases) and one ENase were found in a screen of 196 strains of
      Plesiomonas shigelloides and 147 strains of Aeromonas species.  Plesiomonas and Aeromonas
      species are classified as Vibrionaceae, identified as food-poisoning bacteria, are closely
      genetically related to each other, and their ENases producing abilities have not been
      reported.  ENases were detected at relatively low frequencies in these species as compared to
      those in other species, such as Salmonella species and Vibrio parahaemolyticus.  All ENases
      were shown to be isoschizomers of already known ENases.  One of the Plesiomonas ENases,
      designated PshBI, recognizing the sequence 5'-AT/TAAT-3' should be useful, since PshBI ENase
      is produced at a high yield of 7000 units/g of wet cells.  The specificities of other ENases
      are also described in this paper.
AU  - Miyahara M
AU  - Kimizuka F
AU  - Kita A
AU  - Matsushita S
AU  - Kudo Y
AU  - Shimada T
AU  - Mise K
PT  - Journal Article
TA  - Biol. Pharm. Bull.
JT  - Biol. Pharm. Bull.
SO  - Biol. Pharm. Bull. 1996 19: 1506-1507.

PMID- 2167629
VI  - 56
DP  - 1990
TI  - Widespread occurrence of specific restriction endonucleases in Salmonella infantis, Salmonella thompson, and Salmonella blockley isolated from humans in Japan.
PG  - 2248-2250
AB  - Specific restriction endonucleases were detected in three serotypes of
      Salmonella spp. isolated from humans in Japan from 1970 to 1987: an
      isoschizomer of AvaII endonuclease at a frequency of 0.91 in Salmonella
      infantis, an isoschizomer of KpnI at a frequency of 0.34 in Salmonella
      thompson, and an isoschziomer of StyI at a frequency of 0.30 in Salmonella
      blockley.  Of interest is that restriction endonuclease-producing S. thompson
      was detected at high frequencies in the 1970s but at low frequencies in the
      1980s.
AU  - Miyahara M
AU  - Kudoh Y
AU  - Mise K
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1990 56: 2248-2250.

PMID- 2833162
VI  - 54
DP  - 1988
TI  - Widespread occurrence of the restriction endonuclease YenI, an isoschizomer of PstI, in Yersinia enterocolitica serotype 08.
PG  - 577-580
AB  - The cold-active restriction endonuclease YenI, an isoschizomer of PstI, was
      found in 12 of 14 Yersinia enterocolitica serotype 08 strains of different
      origins, but not in other serotypes of Y. enterocolitica, Yersinia
      pseudotuberculosis, or Yersinia pestis.  In spite of the limited number of
      strains tested, the result suggests that the detection of YenI endonuclease or
      the gene might result in more rapid determination of the prominently pathogenic
      serotype of Y. enterocolitica.
AU  - Miyahara M
AU  - Maruyama T
AU  - Wake A
AU  - Mise K
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1988 54: 577-580.

PMID- Not included in PubMed...
VI  - 213
DP  - 1988
TI  - Rapid method for detection of restriction endonuclease-producing strains in enteropathogenic bacteria.
PG  - 273-277
AB  - An improved rapid method is described for the detection of restriction
      endonucleases in enteropathogenic bacteria including Salmonella and Escherichia
      coli.  With the improved method, at least six restriction endonucleases with
      different specificity were found in 415 strains tested.  Five of them were
      shown to be isoschizomers of known restriction endonucleases, while one seemed
      to be novel.  Among the isoschizomers, SthI endonuclease (isoschizomer of KpnI)
      in Salmonella thompson appears to be useful; unlike KpnI, SthI generates DNA
      fragments with a 5'-protruding end.
AU  - Miyahara M
AU  - Mise K
PT  - Journal Article
TA  - Anal. Chim. Acta
JT  - Anal. Chim. Acta
SO  - Anal. Chim. Acta 1988 213: 273-277.

PMID- 8335263
VI  - 129
DP  - 1993
TI  - Isolation and characterization of the StyD4I restriction endonuclease a neoschizomer of ScrFI, from Escherichia coli K-12 carrying a small multicopy Hsd Plasmid of Salmonella typhi origin.
PG  - 83-86
AB  - A restriction endonuclease designated StyD4I, a neoschizomer of ScrFI, has been isolated from
      Escherichia coli K-12 carrying a small multicopy host specificity for DNA (Hsd) plasmid of
      Salmonella typhi D4 origin. In the presence of 10 mM Mg2+, StyD4I cleaves the sequence
      5'-/CCNGG-3' and generates a 5-nucleotide cohesive end. StyD4I should be useful for
      recombinant DNA technology, because of the stability and ease in handling the producer cells.
AU  - Miyahara M
AU  - Mise K
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1993 129: 83-86.

PMID- 1563630
VI  - 113
DP  - 1992
TI  - Purification of restriction endonuclease EcoO128I produced by an enteropathogenic Escherichia coli O128Ly3.
PG  - 135-136
AB  - Restriction endonuclease EcoO128I, an isoschizomer of BstEII, was purified from a rough mutant
      of Escherichia coli O128Ly3. EcoO128I should be more convenient for recombinant DNA
      applications than BstEII, because of its improved cleavage activity at 37C.
AU  - Miyahara M
AU  - Mise K
AU  - Kimizuka F
AU  - Matsumoto H
AU  - Terawaki Y
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1992 113: 135-136.

PMID- 2323540
VI  - 66
DP  - 1990
TI  - SshAI restriction endonuclease from Salmonella shikmonah.
PG  - 245-248
AB  - A new type II restriction endonuclease, SshAI, was purified from Salmonella shikmonah TK139 of
      kangaroo origin.  The recognition and cleavage specificity of SshAI was determined to be
      5'-CC/TNAGG-3', identical to that of SauI from Streptomyces aureofaciens and Bsu36I from
      Bacillus subtilis.  Based on closely related and in part overlapping recognition specificities
      of SshAI and other restriction endonucleases, a close evolutionary relationship is proposed
      for all known Salmonella restriction endonucleases.
AU  - Miyahara M
AU  - Nakajima K
AU  - Kawanishi T
AU  - Mise K
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1990 66: 245-248.

PMID- 2139620
VI  - 87
DP  - 1990
TI  - Restriction endonuclease PshAI from Plesiomonas shigelloides with the novel recognition site 5'-GACNN/NNGTC.
PG  - 119-122
AB  - A new restriction endonuclease (ENase), PshAI, has been isolated from
      Plesiomonas shigelloides 319-73, an organism that causes food poisoning in
      humans.  The enzyme was stable and produced a yield of 410 units/g of cells.
      In the presence of 10 mM MgCl2, PshAI recognizes and cleaves the nucleotide
      sequence 5'-GACNN/NNGTC, producing blunt ends.  PshAI will be useful for
      structural analysis and molecular cloning of DNA, because no ENases recognizing
      the sequence GACNNNNGTC have been previously described.
AU  - Miyahara M
AU  - Nakajima K
AU  - Shimada T
AU  - Mise K
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1990 87: 119-122.

PMID- 9401735
VI  - 20
DP  - 1997
TI  - Characterization of two restriction endonucleases, SenPT14bI and SenPT16I, in standard phage-type strains of Salmonella enteritidis.
PG  - 1212-1214
AB  - Two restriction endonucleases were found by screening 38 standard phage strains of Salmonella
      enteritidis.  An isoschizomer of SacII Enase that recognizes the sequence 5'-CCGC/GG-3' was
      identified in S. enteritidis PT14b, and an isoschizomer of XmaIII ENase (5'-C/GGCCG-3') was
      found in S. enteritidis PT16.  It is of special interest that the recognition specifities of
      all known ENases in Salmonella, including those of the S. enteritidis ENases, are very similar
      to each other.
AU  - Miyahara M
AU  - Nakamura A
AU  - Mise K
PT  - Journal Article
TA  - Biol. Pharm. Bull.
JT  - Biol. Pharm. Bull.
SO  - Biol. Pharm. Bull. 1997 20: 1212-1214.

PMID- 1644299
VI  - 117
DP  - 1992
TI  - Isolation and characterization of new restriction endonucleases from Vibrio parahaemolyticus: VpaK32I enzyme with the class-IIS heptanucleotide specificity, GCTCTTCN1/N4.
PG  - 103-106
AB  - Six restriction endonucleases (ENases), classified into four different specificities, were
      found in a screen among 68 reference strains of Vibrio parahaemolyticus of human origin. Five
      of these ENases are isoschizomers of well-know ENases, while the remaining one, designated
      VpaK321, is a novel and highly efficient class-IIS ENase with the heptanucleotide recognition
      site, 5'-GCTCTTC(1/4)-3'.
AU  - Miyahara M
AU  - Shimada T
AU  - Kotani H
AU  - Mise K
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1992 117: 103-106.

PMID- Not carried by PubMed...
VI  - 35
DP  - 1994
TI  - Characterization of restriction endonucleases from Vibrio cholerae non 01.
PG  - 599-604
AB  - Fourteen restriction endonucleases (ENases) were found by screening of 118 O antigen reference
      strains of Vibrio cholerae. Ten of these ENases were partially purified and classified into
      eight specificity categories. All of them were isoschizomers of already-known ENases. It is of
      interest that the isoschizomer of EcoRI ENase designated VchO2I was found in V. cholerae O2,
      since VchO2I, as well as EcoRI, shows high activity at pH 8-9, and most V. cholerae strains
      can grow well in this pH range.
AU  - Miyahara M
AU  - Shimada T
AU  - Mise K
PT  - Journal Article
TA  - J. Food. Hyg. Sci. Japan
JT  - J. Food. Hyg. Sci. Japan
SO  - J. Food. Hyg. Sci. Japan 1994 35: 599-604.

PMID- 9037858
VI  - 114
DP  - 1996
TI  - Purification of EcoO44I restriction endonuclease in Escherichia coli O44 isolated from an affected human.
PG  - 13-15
AB  - A restriction endonuclease (Enase) designated EcoO44I  was purified without non-specific
      nucleases from enteropathogenic Escherichia coli O44 Hiromi strain of affected human origin.
      The yield was 1,100 units/g of wet cells.  The EcoO44I Enase recognized and cleaved the
      specific sequence 5'-GGTCTC-3' (1/5) as was the case with Eco31I or BsaI Enase.  Because of
      the stability and high yield, EcoO44I would be useful for recombinant DNA technology after
      isolation of EcoO44-positive, avirulent mutant strains of E. coli O44 Hiromi.
AU  - Miyahara M
AU  - Shinohara N
AU  - Mise K
PT  - Journal Article
TA  - Eisei Shikenjo Hokoku
JT  - Eisei Shikenjo Hokoku
SO  - Eisei Shikenjo Hokoku 1996 114: 13-15.

PMID- 1598226
VI  - 20
DP  - 1992
TI  - Isolation and identification of restriction endonuclease, SelI from a cyanobacterium, Synechococcus elongatus.
PG  - 2605
AB  - A restriction endonuclease, SelI has been isolated from a thermophilic and unicellular
      cyanobacterium, Synechococcus elongatus. SelI, an isoschizomer of FnuDII, recognizes and
      cleaves at the sequence, 5'-|CGCG-3'.
AU  - Miyake M
AU  - Kotani H
AU  - Asada Y
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 2605.

PMID- 12900422
VI  - 278
DP  - 2003
TI  - Involvement of the VDE homing endonuclease and rapamycin in regulation of the Saccharomyces cerevisiae GSH11 gene encoding the high affinity  glutathione transporter.
PG  - 39632-39636
AB  - The Saccharomyces cerevisiae gene HGT1/GSH11 encodes the high affinity glutathione transporter
      and is repressed by cysteine added to the culture
      medium. It has been found previously that a 5'-upstream cis-element,
      CCGCCACAC, is responsible for regulating GSH11 expression and that several
      proteins bind to this element (Miyake, T., Kanayama, M., Sammoto, H., and
      Ono, B. (2002) Mol. Genet. Genomics 266, 1004-1011). In this report we
      present evidence that the most prominent of these proteins is VDE, known
      previously as the homing endonuclease encoded by VMA1. We show also that
      GSH11 is not expressed in a VDE-deleted strain and that inability to
      express the GSH11 of this strain is overcome by introduction of the coding
      region of VDE or the entire VMA1 gene. It is also found that VDE does not
      cut DNA in the vicinity of the GSH11 cis-element. Rapamycin, an inhibitor
      of the target of rapamycin (TOR) signal-transduction system, is found to
      enhance expression of GSH11 in a VDE-dependent manner under conditions of
      sulfur starvation. These results indicate that GSH11 is regulated by a
      system sensitive to sulfur starvation (presumably via cysteine depletion)
      and a more general system involving the nutritional starvation signal
      mediated by the TOR system. Both systems need to be operational
      (inhibition of TOR and sulfur starvation) for full expression of GSH11.
AU  - Miyake T
AU  - Hiraishi H
AU  - Sammoto H
AU  - Ono B-I
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2003 278: 39632-39636.

PMID- 10492170
VI  - 6
DP  - 1999
TI  - Sequence analysis of Stx2-converting phage VT2-Sa shows a great divergence in early regulation and replication regions.
PG  - 235-240
AB  - In enterohemorrhagic Escherichia coli, Shiga toxin is produced by lysogenic prophages. We have
      isolated the prophage VT2-Sa that is responsible for production of Shiga toxin type 2 protein,
      and determined the complete nucleotide sequence of this phage DNA. The entire DNA sequence
      consisted of 60,942 bp, exhibiting marked similarity to the 933W phage genome. However,
      several differences were observed in the immunity and replication regions, where cI, cII,
      cIII, N, cro, O, and P genes were present: Predicted amino acid sequences of N, cI, cro, O and
      P in the VT2-Sa genome did not show significant similarity to the counterparts of the 933W
      genome; however its cI showed higher similarity to lambda. Furthermore, O and P closely
      resembled those of phage HK022. These observations suggest that the various degrees of
      homology observed in the immunity and replication regions of VT2-Sa could have resulted from
      frequent recombination events among the lambdoid phages, and that these regions play a key
      role as a functional unit for phage propagation in competition with other lambdoid phages.
AU  - Miyamoto H
AU  - Nakai W
AU  - Yajima N
AU  - Fujibayashi A
AU  - Higuchi T
AU  - Sato K
AU  - Matsushiro A
PT  - Journal Article
TA  - DNA Res.
JT  - DNA Res.
SO  - DNA Res. 1999 6: 235-240.

PMID- 12117935
VI  - 70
DP  - 2002
TI  - Organization of the plasmid cpe locus in Clostridium perfringens type A isolates.
PG  - 4261-4272
AB  - Clostridium perfringens type A isolates causing food poisoning have a chromosomal enterotoxin
      gene (cpe), while C. perfringens type A isolates
      responsible for non-food-borne human gastrointestinal diseases carry a
      plasmid cpe gene. In the present study, the plasmid cpe locus of the
      type A non-food-borne-disease isolate F4969 was sequenced to design
      primers and probes for comparative PCR and Southern blot studies of the
      cpe locus in other type A isolates. Those analyses determined that the
      region upstream of the plasmid cpe gene is highly conserved among type
      A isolates carrying a cpe plasmid. The organization of the type A
      plasmid cpe locus was also found to be unique, as it contains IS1469
      sequences located similarly to those in the chromosomal cpe locus but
      lacks the IS1470 sequences found upstream of IS1469 in the chromosomal
      cpe locus. Instead of those upstream IS1470 sequences, a partial open
      reading frame potentially encoding cytosine methylase (dcm) was
      identified upstream of IS1469 in the plasmid cpe locus of all type A
      isolates tested. Similar dcm sequences were also detected in several
      cpe-negative C. perfringens isolates carrying plasmids but not in type
      A isolates carrying a chromosomal cpe gene. Contrary to previous
      reports, sequences homologous to IS1470, rather than IS1151, were found downstream of the
      plasmid cpe gene in most type A isolates
      tested. Those IS1470-like sequences reside in about the same position
      but are oppositely oriented and defective relative to the IS1470
      sequences found downstream of the chromosomal cpe gene. Collectively,
      these and previous results suggest that the cpe plasmid of many type A
      isolates originated from integration of a cpe-containing genetic
      element near the dcm sequences of a C. perfringens plasmid. The
      similarity of the plasmid cpe locus in many type A isolates is
      consistent with horizontal transfer of a common cpe plasmid among C.
      perfringens type A strains.
AU  - Miyamoto K
AU  - Chakrabarti G
AU  - Morino Y
AU  - McClane BA
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2002 70: 4261-4272.

PMID- 16452442
VI  - 188
DP  - 2006
TI  - Complete Sequencing and Diversity Analysis of the Enterotoxin-Encoding Plasmids in Clostridium perfringens Type A Non-Food-Borne Human Gastrointestinal Disease Isolates.
PG  - 1585-1598
AB  - Enterotoxin-producing Clostridium perfringens type A isolates are an
      important cause of food poisoning and non-food-borne human
      gastrointestinal diseases, e.g., sporadic diarrhea (SPOR) and
      antibiotic-associated diarrhea (AAD). The enterotoxin gene (cpe) is
      usually chromosomal in food poisoning isolates but plasmid-borne in
      AAD/SPOR isolates. Previous studies determined that type A SPOR isolate
      F5603 has a plasmid (pCPF5603) carrying cpe, IS1151, and the beta2 toxin
      gene (cpb2), while type A SPOR isolate F4969 has a plasmid (pCPF4969)
      lacking cpb2 and IS1151 but carrying cpe and IS1470-like sequences. By
      completely sequencing these two cpe plasmids, the current study identified
      pCPF5603 as a 75.3-kb plasmid carrying 73 open reading frames (ORFs) and
      pCPF4969 as a 70.5-kb plasmid carrying 62 ORFs. These plasmids share an
      approximately 35-kb conserved region that potentially encodes virulence
      factors and carries ORFs found on the conjugative transposon Tn916. The
      34.5-kb pCPF4969 variable region contains ORFs that putatively encode two
      bacteriocins and a two-component regulator similar to VirR/VirS, while the
      approximately 43.6-kb pCPF5603 variable region contains a functional cpb2
      gene and several metabolic genes. Diversity studies indicated that other
      type A plasmid cpe(+)/IS1151 SPOR/AAD isolates carry a pCPF5603-like
      plasmid, while other type A plasmid cpe(+)/IS1470-like SPOR/AAD isolates
      carry a pCPF4969-like plasmid. Tn916-related ORFs similar to those in
      pCPF4969 (known to transfer conjugatively) were detected in the cpe
      plasmids of other type A SPOR/AAD isolates, as well as in representative
      C. perfringens type B to D isolates carrying other virulence plasmids,
      possibly suggesting that most or all C. perfringens virulence plasmids
      transfer conjugatively.
AU  - Miyamoto K
AU  - Fisher DJ
AU  - Li J
AU  - Sayeed S
AU  - Akimoto S
AU  - McClane BA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2006 188: 1585-1598.

PMID- 21655254
VI  - 6
DP  - 2011
TI  - Identification of Novel Clostridium perfringens Type E Strains That Carry an Iota Toxin Plasmid with a Functional Enterotoxin Gene.
PG  - E20376
AB  - Clostridium perfringens enterotoxin (CPE) is a major virulence factor for
      human gastrointestinal diseases, such as food poisoning and antibiotic
      associated diarrhea. The CPE-encoding gene (cpe) can be chromosomal or
      plasmid-borne. Recent development of conventional PCR cpe-genotyping
      assays makes it possible to identify cpe location (chromosomal or plasmid)
      in type A isolates. Initial studies for developing cpe genotyping assays
      indicated that all cpe-positive strains isolated from sickened patients
      were typable by cpe-genotypes, but surveys of C. perfringens environmental
      strains or strains from feces of healthy people suggested that this assay
      might not be useful for some cpe-carrying type A isolates. In the current
      study, a pulsed-field gel electrophoresis Southern blot assay showed that
      four cpe-genotype untypable isolates carried their cpe gene on a plasmid
      of  approximately 65 kb. Complete sequence analysis of the  approximately
      65 kb variant cpe-carrying plasmid revealed no intact IS elements and a
      disrupted cytosine methyltransferase (dcm) gene. More importantly, this
      plasmid contains a conjugative transfer region, a variant cpe gene and
      variant iota toxin genes. The toxin genes encoded by this plasmid are
      expressed based upon the results of RT-PCR assays. The  approximately 65
      kb plasmid is closely related to the pCPF4969 cpe plasmid of type A
      isolates. MLST analyses indicated these isolates belong to a unique
      cluster of C. perfringens. Overall, these isolates carrying a variant
      functional cpe gene and iota toxin genes represent unique type E strains.
AU  - Miyamoto K
AU  - Yumine N
AU  - Mimura K
AU  - Nagahama M
AU  - Li J
AU  - McClane BA
AU  - Akimoto S
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2011 6: E20376.

PMID- 10780447
VI  - 42
DP  - 1999
TI  - Recognition and cleavage of double-stranded DNA by yeast VMA1-derived endonuclease.
PG  - 197-198
AB  - DNA endonuclease derived from the yeast VMA1-gene product recognizes and cleaves 31 base-pairs
      of double-stranded DNA (dsDNA). Mixtures of the endonuclease (VDE) with a full DNA substrate
      consisting of 34 base-pairs, with nicked substrates each having a nick in either DNA chain,
      and with cleaved substrates each having a cleaved-off chain are prepared. Molecular weights
      (MWs) of eluted peaks from gel filtration columns were estimated from elution profiles in the
      presence of Mg2+ ions. Each mixture exhibited an eluted peak at about 63k MW, larger than the
      MW of VDE unbound to dsDNA. This indicates that VDE and dsDNA substrates form stable
      complexes. The mixture of VDE either with the full substrate or with the nicked substrate
      having a nick in the anti-sense chain eluted an additional 25k-MW peak, which presumably
      corresponds to a cleaved product. The complex of VDE with the full substrate was eluted at
      62k-MW location in the absence of Mg2+ ions and yielded a single crystal. Stable complexes of
      VDE either with the dsDNA substrates or with the cleaved products are obtainable.
AU  - Miyamoto S
AU  - Mizutani R
AU  - Satow Y
AU  - Kawasaki M
AU  - Ohya Y
AU  - Anraku Y
PT  - Journal Article
TA  - Nucleic Acids Symp. Ser.
JT  - Nucleic Acids Symp. Ser.
SO  - Nucleic Acids Symp. Ser. 1999 42: 197-198.

PMID- 30533903
VI  - 7
DP  - 2018
TI  - Complete Genome Sequence of Acidithiobacillus ferridurans JCM 18981.
PG  - e01028-18
AB  - Acidithiobacillus ferridurans is an acidophilic chemolithotrophic bacterium that  can grow in
      the presence of high concentrations of ferrous iron. Here, we present
      the complete 2,921,399-bp genome sequence of the strain A. ferridurans JCM
      18981(T), isolated from uranium mine drainage water.
AU  - Miyauchi T
AU  - Kouzuma A
AU  - Abe T
AU  - Watanabe K
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e01028-18.

PMID- 16963556
VI  - 72
DP  - 2006
TI  - Complete nucleotide sequence of an exogenously isolated plasmid, pLB1, involved in .gamma.-hexachlorocyclohexane degradation.
PG  - 6923-6933
AB  - The alpha-proteobacterial strain Sphingobium japonicum UT26 utilizes a highly chlorinated
      pesticide, gamma-hexachlorocyclohexane (gamma-HCH), as a sole source of carbon and energy, and
      haloalkane dehalogenase LinB catalyzes the second step of gamma-HCH degradation in UT26.
      Functional complementation of a linB mutant of UT26, UT26DB, was performed by the exogenous
      plasmid isolation technique using HCH-contaminated soil, leading to our successful
      identification of a plasmid, pLB1, carrying the linB gene. Complete sequencing analysis of
      pLB1, with a size of 65,998 bp, revealed that it carries (i) 50 totally annotated coding
      sequences, (ii) an IS6100 composite transposon containing two copies of linB, and (iii)
      potential genes for replication, maintenance, and conjugative transfer with low levels of
      similarity to other homologues. A minireplicon assay demonstrated that a 2-kb region
      containing the predicted repA gene and its upstream region of pLB1 functions as an
      autonomously replicating unit in UT26. Furthermore, pLB1 was conjugally transferred from
      UT26DB to other alpha-proteobacterial strains but not to any of the beta- or
      gamma-proteobacterial strains examined to date. These results suggest that this exogenously
      isolated novel plasmid contributes to the dissemination of at least some genes for gamma-HCH
      degradation in the natural environment. To the best of our knowledge, this is the first
      detailed report of a plasmid involved in gamma-HCH degradation.
AU  - Miyazaki R
AU  - Sato Y
AU  - Ito M
AU  - Ohtsubo Y
AU  - Nagata Y
AU  - Tsuda M
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2006 72: 6923-6933.

PMID- 24458096
VI  - 5
DP  - 2014
TI  - A sequence-specific DNA glycosylase mediates restriction-modification in Pyrococcus abyssi.
PG  - 3178
AB  - Restriction-modification systems consist of genes that encode a restriction enzyme and a
      cognate methyltransferase. Thus far, it was believed that restriction enzymes are
      sequence-specific endonucleases that introduce double-strand breaks at specific sites by
      catalysing the cleavages of phosphodiester bonds. Here we report that based on the crystal
      structure and enzymatic activity, one of the restriction enzymes, R.PabI, is not an
      endonuclease but a sequence-specific adenine DNA glycosylase. The structure of the R.PabI-DNA
      complex shows that R.PabI unwinds DNA at a 5'-GTAC-3' site and flips the guanine and adenine
      bases out of the DNA helix to recognize the sequence. R.PabI catalyses the hydrolysis of the
      N-glycosidic bond between the adenine base and the sugar in the DNA and produces two opposing
      apurinic/apyrimidinic (AP) sites. The opposing AP sites are cleaved by heat-promoted beta
      elimination and/or by endogenous AP endonucleases of host cells to introduce a double-strand
      break.
AU  - Miyazono K
AU  - Furuta Y
AU  - Watanabe-Matsui M
AU  - Miyakawa T
AU  - Ito T
AU  - Kobayashi I
AU  - Tanokura M
PT  - Journal Article
TA  - Nat. Commun.
JT  - Nat. Commun.
SO  - Nat. Commun. 2014 5: 3178.

PMID- 17332011
VI  - 35
DP  - 2007
TI  - Novel protein fold discovered in the PabI family of restriction enzymes.
PG  - 1908-1918
AB  - Although structures of many DNA-binding proteins have been solved, they fall into a limited
      number of folds. Here, we describe an approach that
      led to the finding of a novel DNA-binding fold. Based on the behavior of
      Type II restriction-modification gene complexes as mobile elements, our
      earlier work identified a restriction enzyme, R.PabI, and its cognate
      modification enzyme in Pyrococcus abyssi through comparison of closely
      related genomes. While the modification methyltransferase was easily
      recognized, R.PabI was predicted to have a novel 3D structure. We
      expressed cytotoxic R.PabI in a wheat-germ-based cell-free translation
      system and determined its crystal structure. R.PabI turned out to adopt a
      novel protein fold. Homodimeric R.PabI has a curved anti-parallel
      beta-sheet that forms a 'half pipe'. Mutational and in silico DNA-binding
      analyses have assigned it as the double-strand DNA-binding site. Unlike
      most restriction enzymes analyzed, R.PabI is able to cleave DNA in the
      absence of Mg(2+). These results demonstrate the value of genome
      comparison and the wheat-germ-based system in finding a novel DNA-binding
      motif in mobile DNases and, in general, a novel protein fold in
      horizontally transferred genes.
AU  - Miyazono K
AU  - Watanabe M
AU  - Kosinski J
AU  - Ishikawa K
AU  - Kamo M
AU  - Sawasaki T
AU  - Nagata K
AU  - Bujnicki JM
AU  - Endo Y
AU  - Tanokura M
AU  - Kobayashi I
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2007 35: 1908-1918.

PMID- 22123763
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Highly Multidrug-Resistant Pseudomonas aeruginosa NCGM2.S1, a Representative Strain of a Cluster Endemic to  Japan.
PG  - 7010
AB  - We report the completely annotated genome sequence of Pseudomonas aeruginosa NCGM2.S1, a
      representative strain of a cluster endemic to Japan
      with a high level of resistance to carbapenem (MIC >/= 128 mug/ml),
      amikacin (MIC >/= 128 mug/ml), and fluoroquinolone (MIC >/= 128 mug/ml).
AU  - Miyoshi-Akiyama T
AU  - Kuwahara T
AU  - Tada T
AU  - Kitao T
AU  - Kirikae T
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 7010.

PMID- 22535945
VI  - 194
DP  - 2012
TI  - Complete Annotated Genome Sequence of Mycobacterium tuberculosis Erdman.
PG  - 2770
AB  - We report the completely annotated genome sequence of Mycobacterium tuberculosis  Erdman (TMC
      107; ATCC 35801), which is a well-known laboratory strain of M.
      tuberculosis.
AU  - Miyoshi-Akiyama T
AU  - Matsumura K
AU  - Iwai H
AU  - Funatogawa K
AU  - Kirikae T
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2770.

PMID- 22072647
VI  - 193
DP  - 2011
TI  - Genome Sequence of Clinical Isolate Mycobacterium tuberculosis NCGM2209.
PG  - 6792
AB  - We report the annotated genome sequence of a clinical isolate, Mycobacterium tuberculosis
      strain NCGM2209, which belongs to the 'Beijing
      family' and was isolated in Japan.
AU  - Miyoshi-Akiyama T
AU  - Matsumura K
AU  - Kobayashi N
AU  - Maeda S
AU  - Kirikae T
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6792.

PMID- 25458614
VI  - 95
DP  - 2014
TI  - Complete annotated genome sequence of Mycobacterium tuberculosis (Zopf) Lehmann and Neumann (ATCC35812) (Kurono).
PG  - 37-39
AB  - We report the completely annotated genome sequence of Mycobacterium tuberculosis
      (Zopf) Lehmann and Neumann (ATCC35812) (Kurono), which is a used for virulence
      and/or immunization studies. The complete genome sequence of M. tuberculosis
      Kurono was determined with a length of 4,415,078 bp and a G+C content of 65.60%.
      The chromosome was shown to contain a total of 4,340 protein-coding genes, 53
      tRNA genes, one transfer messenger RNA for all amino acids, and 1 rrn operon.
      Lineage analysis based on large sequence polymorphisms indicated that M.
      tuberculosis Kurono belongs to the Euro-American lineage (lineage 4).
      Phylogenetic analysis using whole genome sequences of M. tuberculosis Kurono in
      addition to 22 M. tuberculosis complex strains indicated that H37Rv is the
      closest relative of Kurono based on the results of phylogenetic analysis. These
      findings provide a basis for research using M. tuberculosis Kurono, especially in
      animal models.
AU  - Miyoshi-Akiyama T
AU  - Satou K
AU  - Kato M
AU  - Shiroma A
AU  - Matsumura K
AU  - Tamotsu H
AU  - Iwai H
AU  - Teruya K
AU  - Funatogawa K
AU  - Hirano T
AU  - Kirikae T
PT  - Journal Article
TA  - Tuberculosis
JT  - Tuberculosis
SO  - Tuberculosis 2014 95: 37-39.

PMID- 23012276
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Helicobacter cinaedi Type Strain ATCC BAA-847.
PG  - 5692
AB  - Here we report the completely annotated genome sequence of the Helicobacter cinaedi type
      strain (ATCC BAA-847), which is an emerging pathogen that causes
      cellulitis and bacteremia. The genome sequence will provide new insights into the
      diagnosis, pathogenic mechanisms, and drug resistance of H. cinaedi.
AU  - Miyoshi-Akiyama T
AU  - Takeshita N
AU  - Ohmagari N
AU  - Kirikae T
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5692.

PMID- 22965090
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Streptococcus pyogenes M1 476, Isolated from a Patient with Streptococcal Toxic Shock Syndrome.
PG  - 5466
AB  - Here, we report the completely annotated genome sequence of Streptococcus pyogenes M1 476
      isolated from a patient with streptococcal toxic shock syndrome
      (STSS) during pregnancy. The genome sequence will provide new insights into the
      mechanisms underlying STSS.
AU  - Miyoshi-Akiyama T
AU  - Watanabe S
AU  - Kirikae T
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5466.

PMID- 12095641
VI  - 522
DP  - 2002
TI  - Association of HSP70 with endonucleases allows the expression of otherwise silent mutations.
PG  - 177-182
AB  - A subpopulation of the 70 kDa heat shock protein (HSP70) found within the mitochondria of
      Saccharomyces cerevisiae functions as a stable
      binding partner of the endonuclease SceI. We have previously found that
      the SceI endonuclease monomer recognizes and cleaves a unique, 26 bp
      sequence in vitro. Dimerization with HSP70 changes the specificity of
      SceI, allowing it to cleave at multiple sequences. This study shows
      that SuvI, an ortholog of SceI isolated from a different yeast strain,
      contains two amino acid substitutions, yet it shows the same uni-site
      specificity in its monomeric form. Binding of HSP70 to the SuvI monomer
      confers multi-site specificity that is different from that exhibited by
      the HSP70/SceI heterodimer. Mutation of single residues of SceI to the
      corresponding residue in SuvI provides enzymes with specificities
      intermediate between SceI and SuvI when complexed with HSP70. These
      results suggest that HSP70 interaction with certain endonucleases
      allows the expression of otherwise silent mutations in them, causing a
      change in enzyme cleavage specificity.
AU  - Mizumura H
AU  - Shibata T
AU  - Morishima N
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 2002 522: 177-182.

PMID- 10464305
VI  - 274
DP  - 1999
TI  - Stable association of 70-kDa heat shock protein induces latent multisite specificity of a unisite-specific endonuclease in yeast mitochondria.
PG  - 25682-25690
AB  - The multisite-specific endonuclease Endo.SceI of yeast mitochondria is unique among
      endonucleases because its 50-kDa subunit forms a stable dimer with the mitochondrial 70-kDa
      heat shock protein (mtHSP70), which otherwise fulfills a chaperone function by binding
      transiently to unfolded proteins. Here we show that the mtHSP70 subunit confers broader
      sequence specificity, greater stability, and higher activity on the 50-kDa subunit. The 50-kDa
      subunit alone displayed weaker activity and highly sequence-specific endonuclease activity.
      The 50-kDa protein exists as a heterodimer with mtHSP70 in vivo, allowing Endo.SceI to cleave
      specifically at multiple sites on mitochondrial DNA. Endo.SceI may have evolved from a highly
      specific endonuclease that gained broader sequence specificity after becoming a stable partner
      of mtHSP70.
AU  - Mizumura H
AU  - Shibata T
AU  - Morishima N
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1999 274: 25682-25690.

PMID- 23160125
VI  - 79
DP  - 2013
TI  - Reconstruction of Novel Cyanobacterial Siphovirus Genomes from Mediterranean Metagenomic Fosmids.
PG  - 688-695
AB  - Cellular metagenomes are primarily used for investigating microbial community
      structure and function. However, cloned fosmids from such metagenomes capture
      phage genome fragments that can be used as a source of phage genomes. We show
      that fosmid cloning from cellular metagenomes and sequencing at a high coverage
      is a credible alternative to constructing metaviriomes and allows capturing and
      assembling novel, complete phage genomes. It is likely that phages recovered from
      cellular metagenomes are those replicating within cells during sample collection
      and represent "active" phages, naturally amplifying their genomic DNA and
      increasing chances for cloning. We describe five sets of siphoviral contigs
      (MEDS1, MEDS2, MEDS3, MEDS4 and MEDS5), obtained by sequencing fosmids from the
      cellular metagenome of the deep chlorophyll maximum in the Mediterranean. Three
      of these represent complete siphoviral genomes and two partial ones. These are
      the first set of phage genomes assembled directly from cellular metagenomic
      fosmid libraries. They exhibit low sequence similarities to one another and to
      known siphoviruses, but are remarkably similar in overall genome architecture. We
      present evidence suggesting they infect picocyanobacteria, likely Synechococcus.
      Four of these sets also define a novel branch in the phylogenetic tree of phage
      large subunit terminases. Moreover, some of these siphoviral groups are globally
      distributed and abundant in the oceans, comparable to some known myoviruses and
      podoviruses. This suggests that as more siphoviral genomes become available, we
      will be better able to assess the abundance and influence of this diverse and
      polyphyletic group in the marine habitat.
AU  - Mizuno CM
AU  - Rodriguez-Valera F
AU  - Garcia-Heredia I
AU  - Martin-Cuadrado AB
AU  - Ghai R
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2013 79: 688-695.

PMID- 24348267
VI  - 9
DP  - 2013
TI  - Expanding the marine virosphere using metagenomics.
PG  - e1003987
AB  - Viruses infecting prokaryotic cells (phages) are the most abundant entities of the biosphere
      and contain a largely uncharted
      wealth of genomic diversity. They play a critical role in the biology of their hosts and in
      ecosystem functioning at large. The
      classical approaches studying phages require isolation from a pure culture of the host. Direct
      sequencing approaches have
      been hampered by the small amounts of phage DNA present in most natural habitats and the
      difficulty in applying metaomic
      approaches, such as annotation of small reads and assembly. Serendipitously, it has been
      discovered that cellular
      metagenomes of highly productive ocean waters (the deep chlorophyll maximum) contain
      significant amounts of viral DNA
      derived from cells undergoing the lytic cycle. We have taken advantage of this phenomenon to
      retrieve metagenomic
      fosmids containing viral DNA from a Mediterranean deep chlorophyll maximum sample. This method
      allowed description of
      complete genomes of 208 new marine phages. The diversity of these genomes was remarkable,
      contributing 21 genomic
      groups of tailed bacteriophages of which 10 are completely new. Sequence based methods have
      allowed host assignment
      to many of them. These predicted hosts represent a wide variety of important marine
      prokaryotic microbes like members of
      SAR11 and SAR116 clades, Cyanobacteria and also the newly described low GC Actinobacteria. A
      metavirome constructed
      from the same habitat showed that many of the new phage genomes were abundantly represented.
      Furthermore, other
      available metaviromes also indicated that some of the new phages are globally distributed in
      low to medium latitude ocean
      waters. The availability of many genomes from the same sample allows a direct approach to
      viral population genomics
      confirming the remarkable mosaicism of phage genomes.
AU  - Mizuno CM
AU  - Rodriguez-Valera F
AU  - Kimes NE
AU  - Ghai R
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2013 9: e1003987.

PMID- 1369292
VI  - 54
DP  - 1990
TI  - Purification, properties and determination of recognition sequence and cleavage site of restriction endonuclease from Agrobacterium gelatinovorum IAM 12617, a marine bacterium (AgeI).
PG  - 1797-1802
AB  - A new restriction endonuclease, designated as AgeI, was purified from cell-free
      extracts of a marine bacterium, Agrobacterium gelatinovorum IAM 12617 by
      streptomycin treatment, ammonium sulfate fractionation, combined column
      chromatographies on heparin-Sepharose CL-6B and DEAE-Sepharose CL-6B and FPLC
      on Mono Q (HR 5/5) and Superose 12 (HR 10/30).  The purified enzyme was
      homogenous on SDS-polyacrylamide gel disc electrophoresis and free from other
      phosphatase and exonuclease activities on ligation-recutting test.  The
      relative molecular mass of the enzyme was 24,000 daltons by SDS-polyacrylamide
      gel disc electrophoresis.  The gel filtration using Superose 12 (HR 10/30) gave
      the same calculation (23,000 daltons).  These data indicated that the enzyme is
      a monomer.  The isoelectric point of the enzyme was 6.5.  The purified enzyme
      cleaved lambda and Ad2 DNAs at 10 or more and 5 sites, respectively.  However,
      the purified enzyme did not cleave SV40, PhiX174 RF I, M13mp18 RF I or pBR322
      DNAs.  pBR328 DNA was cleaved at 1 site by the purified enzyme.  The purified
      enzyme worked best at 37C and pH 7.5 in a reaction mixture (50 microliters)
      containing 1.0 micrograms lambda DNA, 10 mM Tris-HCl, 7 mM 2-mercaptoethanol, 7
      mM MgCl2 and 50 mM NaCl.  The purified enzyme did not require monovalent
      cations necessarily for the enzyme reaction.  The enzyme recognized the
      palindromic hexanucleotide DNA sequence 5'-ACCGGT-3' and cut between A and C,
      producing a 5'-cohesive tetranucleotide extension.
AU  - Mizuno H
AU  - Suzuki T
AU  - Akagawa M
AU  - Yamasato K
AU  - Yamada Y
PT  - Journal Article
TA  - Agric. Biol. Chem.
JT  - Agric. Biol. Chem.
SO  - Agric. Biol. Chem. 1990 54: 1797-1802.

PMID- 1369311
VI  - 54
DP  - 1990
TI  - Purification and properties of restriction endonuclease from Deleya marina IAM 14114, a marine bacterium (DmaI).
PG  - 2863-2867
AB  - A restriction endonuclease, designated as DmaI, was purified from cell-free
      extracts of Deleya marina IAM 14114 by streptomycin treatment, ammonium sulfate
      fractionation and two steps of chromatographicy on Heparin-Sepharose CL-6B and
      Mono Q (HR 5/5, FPLC).  The purified enzyme was homogeneous on
      SDS-polyacrylamide gel disk electrophoresis and a ligation-recutting test.  The
      relative molecular mass measurements of the purified enzyme gave 28,000 daltons
      by SDS-polyacrylamide gel disk electrophoresis and 56,000 daltons by gel
      filtration.  These data indicated that the purified enzyme (56,000 daltons) has
      a dimeric structure composed of two 28,000-dalton subunits.  The isoelectric
      point was 5.5.  The purified enzyme worked best at 37C in a reaction mixture
      (50 microliters) containing 1.0 microgram lambda DNA, 10 mM Tris-HCI, 7 mM
      2-mercaptoethanol, 7 mM MgCl2 and 100 mM NaCl (pH 7.5).  The enzyme was stable
      up to 55C and between pH 7.0 and 9.0.  The purified enzyme recognizes the
      palindromic hexanucleotide DNA sequence 5'-CAGCTG-3', cuts between G and C and
      produces a flush end (isoschizomer of PvuII).
AU  - Mizuno H
AU  - Suzuki T
AU  - Yamada Y
AU  - Akagawa M
AU  - Yamasato K
PT  - Journal Article
TA  - Agric. Biol. Chem.
JT  - Agric. Biol. Chem.
SO  - Agric. Biol. Chem. 1990 54: 2863-2867.

PMID- 14646148
VI  - 11
DP  - 2004
TI  - Protein splicing of yeast VMA1-derived endonuclease via thiazolidine intermediates.
PG  - 109-112
AB  - Protein splicing precisely excises out an internal intein segment from a protein precursor,
      and concomitantly ligates the N- and C-terminal extein polypeptides flanking the intein.  A
      recombinant X10SNS bearing N- and C-extein polypeptides has been prepared for the intein
      endonuclease derived from the Saccharomyces cerevisiae VMA1 gene.  X10SNS has replacements of
      C284S, H362N, and C738S, and forms the intein and extein segments in the crystal lattice.  The
      crystal structure of X10SNS revealed a linkage between the N- and C-extein segments, and
      showed that the C284 amino group of the resultant intein segment is in interaction with the
      G283 O atom of the N-extein segment.  A mechanism for the final S-N acyl shift step proposes
      that a tetrahedral intermediate involves a five-membered thiazolidine ring at G283-C738
      junction.  An oxyanion of the thiazolidine intermediate is to be stabilized by the C284 N
      atom.
AU  - Mizutani R
AU  - Anraku Y
AU  - Satow Y
PT  - Journal Article
TA  - J. Synchrotron Radiat.
JT  - J. Synchrotron Radiat.
SO  - J. Synchrotron Radiat. 2004 11: 109-112.

PMID- 11884132
VI  - 316
DP  - 2002
TI  - Protein-splicing reaction via a thiazolidine intermediate: Crystal structure of the VMA1-derived endonuclease bearing the N and C-terminal  propeptides.
PG  - 919-929
AB  - Protein splicing excises an internal intein segment from a protein precursor precisely, and
      concomitantly ligates flanking N and C-extein
      polypeptides at the respective sides of the precursor. Here, a series
      of precursor recombinants bearing 11 N-extein and ten C-extein residues
      is prepared for the intein of the Saccharomyces cerevisiae VMAI-derived
      homing endonuclease referred to as VIDE and as PI-SceI. The recombinant
      with replacements of C284S, H362N, N737S, and C738S is chosen as a
      splice-able precursor model and is then subjected to a 2.1 Angstrom
      resolution crystallographic analysis. The crystal structure shows that
      the introduced extein polypeptides are located in the vicinity of the
      splicing site, and that each of their peptide bonds is in the trans
      conformation. The S284 O-gamma atom located at a distance of 3.1
      Angstrom from the G283 C atom in the N-terminal junction suggests that
      a nucleophilic attack of the C284 S-gamma atom on the G283 C atom forms
      a tetrahedral intermediate containing a five-membered thiazolidine
      ring. The tetrahedral intermediate is supposedly resolved into a
      thioester acyl group upon the cleavage of the linkage between the G283
      C and C284 N atoms, and this thioester acyl formation completes the
      initial steps of N --> S acyl shift at the junction between the
      N-extein and intein. The S738 O-gamma atom in the C-terminal junction
      is placed in close proximity to the S284 O-gamma atom at a distance of
      3.6 Angstrom, and is well suited for another nucleophilic attack on the
      resultant thioester acyl group that is then subjected to the
      transesterification in the next step. The reaction steps proposed for
      the acyl shift are driven entirely by protonation and deprotonation, in
      which proton ingress and egress is balanced within the splicing site.
AU  - Mizutani R
AU  - Nogami S
AU  - Kawasaki M
AU  - Ohya Y
AU  - Anraku Y
AU  - Satow Y
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2002 316: 919-929.

PMID- 28302779
VI  - 5
DP  - 2017
TI  - Genome Sequence of Arcobacter sp. Strain LA11, Isolated from the Abalone Haliotis discus.
PG  - e00032-17
AB  - Arcobacter sp. strain LA11 was isolated from the gut of the abalone Haliotis discus Here, we
      present the annotation and analysis of the draft genome of this
      strain, which is involved in nitrogen metabolism.
AU  - Mizutani Y
AU  - Tanaka R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00032-17.

PMID- 10194386
VI  - 38
DP  - 1999
TI  - A new method for determining the Stereochemistry of DNA cleavage reactions: Application to the SfiI and HpaII restriction endonucleases and to the MuA transposase.
PG  - 4640-4648
AB  - A new method was developed for tracking the stereochemical path of enzymatic cleavage of DNA.
      DNA with a phosphorothioate of known chirality at the scissile bond is cleaved by the enzyme
      in H218O. The cleavage produces a DNA molecule with the 5'-[16O,18O, S]-thiophosphoryl group,
      whose chirality depends on whether the cleavage reaction proceeds by a single-step hydrolysis
      mechanism or by a two-step mechanism involving a protein-DNA covalent intermediate. To
      determine this chirality, the cleaved DNA is joined to an oligonucleotide by DNA ligase. Given
      the strict stereochemistry of the DNA ligase reaction, determined here, the original chirality
      of the phosphorothioate dictates whether the 18O is retained or lost in the ligation product,
      which can be determined by mass spectrometry. This method has advantages over previous methods
      in that it is not restricted to particular DNA sequences, requires substantially less
      material, and avoids purification of the products at intermediate stages in the procedure. The
      method was validated by confirming that DNA cleavage by the EcoRI restriction endonuclease
      causes inversion of configuration at the scissile phosphate. It was then applied to the
      reactions of the SfiI and HpaII endonucleases and the MuA transposase. In all three cases, DNA
      cleavage proceeded with inversion of configuration, indicating direct hydrolysis of the
      phosphodiester bond by water as opposed to a reaction involving a covalent enzyme-DNA
      intermediate.
AU  - Mizuuchi K
AU  - Nobbs TJ
AU  - Halford SE
AU  - Adzuma K
AU  - Qin J
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1999 38: 4640-4648.

PMID- 21129434
VI  - 93
DP  - 2011
TI  - A maturase that specifically stabilizes and activates its cognate group  I intron at high temperatures.
PG  - 533-541
AB  - Folding of large structured RNAs into their functional tertiary structures at high
      temperatures is challenging. Here we show that
      I-Tnal protein, a small LAGLIDADG homing endonuclease encoded by a
      group I intron from a hyperthermophilic bacterium, acts as a maturase
      that is essential for the catalytic activity of this intron at high
      temperatures and physiological cationic conditions. I-Tnal specifically
      binds to and induces tertiary packing of the P4-P6 domain of the
      intron: this RNA protein complex might serve as a thermostable platform
      for active folding of the entire intron. Interestingly, the binding
      affinity of I-Tnal to its cognate intron RNA largely increases with
      temperature; over 30-fold stronger binding at higher temperatures
      relative to 37 degrees C correlates with a switch from an
      entropy-driven (37 degrees C) to an enthalpydriven (55-60 degrees C)
      interaction mode. This binding mode may represent a novel strategy how
      an RNA binding protein can promote the function of its target RNA
      specifically at high temperatures.
AU  - Mo D
AU  - Wu L
AU  - Xu Y
AU  - Ren J
AU  - Wang L
AU  - Huang L
AU  - Wu Q-J
AU  - Bao P
AU  - Xie M-H
AU  - Yin P
AU  - Liu B-F
AU  - Liang Y
AU  - Zhang Y
PT  - Journal Article
TA  - Biochimie
JT  - Biochimie
SO  - Biochimie 2011 93: 533-541.

PMID- 25861391
VI  - 7
DP  - 2015
TI  - Genome sequencing of Clostridium butyricum DKU-01, isolated from infant feces.
PG  - 8
AB  - BACKGROUND: Clostridium butyricum is a butyric acid-producing anaerobic
      bacteriuma, and commonly present as gut microbiota in humans. This species has
      been used as a probiotic for the prevention of diarrhea in humans. In this study,
      we report the draft genome of C. butyricum DKU-01, which was isolated from infant
      feces, to better understand the characteristics of this strain so that it can
      later be used in the development of probiotic products. RESULTS: A total of 79
      contigs generated by hybrid assembly of sequences obtained from Roche 454 and
      Illumina Miseq sequencing systems were investigated. The assembled genome of
      strain DKU-01 consisted of 4,519,722 bp (28.62% G + C content) with a N50 contig
      length of 108,221 bp and 4,037 predicted CDSs. The extracted 16S rRNA gene from
      genome sequences of DKU-01 was similar to Clostridium butyricum with 99.63%
      pairwise similarity. The sequence of strain DKU-01 was compared with previously
      reported genome sequences of C. butyricum. The value of average nucleotide
      identity between strains DKU-01 and C. butyricum 60E3 was 98.74%, making it the
      most similar strain to DKU-01. CONCLUSIONS: We sequenced the DKU-01 strain
      isolated from infant feces, and compared it with the available genomes of C.
      butyricum on a public database. Genes related to Fructooligosaccharide
      utilization were detected in the genome of strain DKU-01 and compared with other
      genera, such as Bifidobacterium and Streptococcus. We found that strain DKU-01
      can metabolize a wide range of carbohydrates in comparative genome result.
      Further analyses of the comparative genome and fermentation study can provide the
      information necessary for the development of strain DKU-01 for probiotics.
AU  - Mo S
AU  - Kim BS
AU  - Yun SJ
AU  - Lee JJ
AU  - Yoon SH
AU  - Oh CH
PT  - Journal Article
TA  - Gut Pathog.
JT  - Gut Pathog.
SO  - Gut Pathog. 2015 7: 8.

PMID- 25744989
VI  - 3
DP  - 2015
TI  - Genome Sequence of Clostridium acetobutylicum GXAS18-1, a Novel Biobutanol Production Strain.
PG  - e00033-15
AB  - Clostridium acetobutylicum is an organism involved in the production of acetone and butanol by
      traditional acetone-butanol-ethanol fermentation (ABE). We report
      the draft genome sequence of C. acetobutylicum strain GXAS18-1, which can produce
      ABE directly from cassava flour.
AU  - Mo X
AU  - Pei J
AU  - Guo Y
AU  - Lin L
AU  - Peng L
AU  - Kou C
AU  - Fan D
AU  - Pang H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00033-15.

PMID- 18448537
VI  - 82
DP  - 2008
TI  - The temperate marine phage PhiHAP-1 of Halomonas aquamarina possesses a linear plasmid-like prophage genome.
PG  - 6618-6630
AB  - A myovirus-like temperate phage, PhiHAP-1, was induced with mitomycin C
      from a Halomonas aquamarina strain isolated from surface waters in the
      Gulf of Mexico. The induced cultures produced significantly more
      virus-like particles (VLPs) (3.73 x 10(10) VLP ml(-1)) than control
      cultures (3.83 x 10(7) VLP ml(-1)) when observed with epifluorescence
      microscopy. The induced phage was sequenced by using linker-amplified
      shotgun libraries and contained a genome 39,245 nucleotides in length with
      a G+C content of 59%. The PhiHAP-1 genome contained 46 putative open
      reading frames (ORFs), with 76% sharing significant similarity (E value of
      <10(-3)) at the protein level with other sequences in GenBank. Putative
      functional gene assignments included small and large terminase subunits,
      capsid and tail genes, an N6-DNA adenine methyltransferase, and
      lysogeny-related genes. Although no integrase was found, the PhiHAP-1
      genome contained ORFs similar to protelomerase and parA genes found in
      linear plasmid-like phages with telomeric ends. Southern probing and PCR
      analysis of host genomic, plasmid, and PhiHAP-1 DNA indicated a lack of
      integration of the prophage with the host chromosome and a difference in
      genome arrangement between the prophage and virion forms. The linear
      plasmid prophage form of PhiHAP-1 begins with the protelomerase gene,
      presumably due to the activity of the protelomerase, while the induced
      phage particle has a circularly permuted genome that begins with the
      terminase genes. The PhiHAP-1 genome shares synteny and gene similarity
      with coliphage N15 and vibriophages VP882 and VHML, suggesting an
      evolutionary heritage from an N15-like linear plasmid prophage ancestor.
AU  - Mobberley JM
AU  - Authement RN
AU  - Segall AM
AU  - Paul JH
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 2008 82: 6618-6630.

PMID- 29439050
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Cyanobacterium sp. Strain HL-69, Isolated from a Benthic Microbial Mat from a Magnesium Sulfate-Dominated Hypersaline Lake.
PG  - e01583-17
AB  - The complete genome sequence of Cyanobacterium sp. strain HL-69 consists of 3,155,247 bp and
      contains 2,897 predicted genes comprising a chromosome and two
      plasmids. The genome is consistent with a halophilic nondiazotrophic phototrophic
      lifestyle, and this organism is able to synthesize most B vitamins and produces
      several secondary metabolites.
AU  - Mobberley JM
AU  - Romine MF
AU  - Cole JK
AU  - Maezato Y
AU  - Lindemann SR
AU  - Nelson WC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01583-17.

PMID- 26384038
VI  - 7
DP  - 2015
TI  - Comprehensive insights in the Mycobacterium avium subsp. paratuberculosis genome using new WGS data of sheep strain JIII-386 from Germany.
PG  - 2585-2601
AB  - Mycobacterium avium (M. a.) subsp. paratuberculosis (MAP) - the etiologic agent of Johne's
      disease - affects cattle, sheep and other ruminants worldwide. To decipher phenotypic
      differences among sheep and cattle strains (belonging to MAP-S [Type-I/III] respectively MAP-C
      [Type-II]) comparative genome analysis needs data from diverse isolates originating from
      different geographic regions of the world. The current study presents the so far best
      assembled genome of a MAP-S-strain: sheep isolate JIII-386 from Germany. One newly sequenced
      cattle isolate (JII-1961, Germany), four published MAP strains of MAP-C and MAP-S from U.S.
      and Australia and M. a. subsp. hominissuis (MAH) strain 104 were used for assembly improvement
      and comparisons. All genomes were annotated by BacProt and results compared with NCBI
      annotation. Corresponding protein-coding sequences (CDSs) were detected, but also CDSs that
      were exclusively determined either by NCBI or BacProt. A new Shine-Dalgarno sequence motif
      (5'AGCTGG3') was extracted. Novel CDSs including PE-PGRS family protein genes and about 80
      non-coding RNAs exhibiting high sequence conservation are presented. Previously found genetic
      differences between MAP-types are partially revised. Four out of ten assumed MAP-S-specific
      large sequence polymorphism regions (LSPSs) are still present in MAP-C strains; new LSPSs were
      identified. Independently of the regional origin of the strains, the number of individual CDSs
      and single nucleotide variants confirm the strong similarity of MAP-C strains and show higher
      diversity among MAP-S strains. This study gives ambiguous results regarding the hypothesis
      that MAP-S is the evolutionary intermediate between MAH and MAP-C, but it clearly shows a
      higher similarity of MAP to MAH than to M. intracellulare.
AU  - Mobius P
AU  - Holzer M
AU  - Felder M
AU  - Nordsiek G
AU  - Groth M
AU  - Kohler H
AU  - Reichwald K
AU  - Platzer M
AU  - Marz M
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2015 7: 2585-2601.

PMID- 28839035
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of JII-1961, a Bovine Mycobacterium avium subsp. paratuberculosis Field Isolate from Germany.
PG  - e00870-17
AB  - Mycobacterium avium subsp. paratuberculosis causes Johne's disease in ruminants and was also
      detected in nonruminant species, including human beings, and in milk
      products. We announce here the 4.829-Mb complete genome sequence of the
      cattle-type strain JII-1961 from Germany, which is very similar to cattle-type
      strains recovered from different continents.
AU  - Mobius P
AU  - Nordsiek G
AU  - Holzer M
AU  - Jarek M
AU  - Marz M
AU  - Kohler H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00870-17.

PMID- 16299387
VI  - 172
DP  - 2006
TI  - Genetic addiction: selfish gene's strategy for symbiosis in the genome.
PG  - 1309-1323
AB  - The evolution and maintenance of the phenomenon of postsegregational host killing or genetic
      addiction are paradoxical. In this phenomenon, a gene complex, once
      established in a genome, programs death of a host cell that has eliminated it.
      The intact form of the gene complex would survive in other members of the host
      population. It is controversial as to why these genetic elements are maintained,
      due to the lethal effects of host killing, or perhaps some other properties are
      beneficial to the host. We analyzed their population dynamics by analytical
      methods and computer simulations. Genetic addiction turned out to be advantageous
      to the gene complex in the presence of a competitor genetic element. The
      advantage is, however, limited in a population without spatial structure, such as
      that in a well-mixed liquid culture. In contrast, in a structured habitat, such
      as the surface of a solid medium, the addiction gene complex can increase in
      frequency, irrespective of its initial density. Our demonstration that genomes
      can evolve through acquisition of addiction genes has implications for the
      general question of how a genome can evolve as a community of potentially selfish
      genes.
AU  - Mochizuki A
AU  - Yahara K
AU  - Kobayashi I
AU  - Iwasa Y
PT  - Journal Article
TA  - Genetics
JT  - Genetics
SO  - Genetics 2006 172: 1309-1323.

PMID- 22535949
VI  - 194
DP  - 2012
TI  - Genomic Comparison between a Virulent Type A1 Strain of Francisella tularensis and Its Attenuated O-Antigen Mutant.
PG  - 2775-2776
AB  - We report the complete genome sequences of TI0902, a highly virulent type A1 strain, and
      TIGB03, a related, attenuated chemical mutant strain. Compared to the
      wild type, the mutant strain had 45 point mutations and a 75.9-kb duplicated
      region that had not been previously observed in Francisella species.
AU  - Modise T
AU  - Ryder C
AU  - Mane SP
AU  - Bandara AB
AU  - Jensen RV
AU  - Inzana TJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2775-2776.

PMID- 6293768
VI  - 13
DP  - 1982
TI  - Studies on sequence recognition by type II restriction and modification enzymes.
PG  - 287-323
AB  - DNA restriction endonucleases and modification methylases are strain-specific
      enzymes responsible for the host-specific barriers to interstrain transfer of
      DNA that have been identified in numerous prokaryotic cell types.  Foreign DNA
      entering a bacterial cell is subject to rapid endonucleolytic hydrolysis if it
      is devoid of the modification characteristic of the particular bacterial
      strain.  The strain specific modification enzyme catalyzes methyl transfer from
      S-adenosyl-L-methionine (AdoMet) to a specific DNA sequence which is
      characteristic of the particular host specificity system.  Thus, cellular DNA
      is rendered resistant to attack by the endogenous restriction enzyme by virtue
      of being methylated at DNA sites that are also recognized by the endonuclease.
AU  - Modrich P
PT  - Journal Article
TA  - CRC Crit. Rev. Biochem.
JT  - CRC Crit. Rev. Biochem.
SO  - CRC Crit. Rev. Biochem. 1982 13: 287-323.

PMID- 232555
VI  - 12
DP  - 1979
TI  - Structures and mechanisms of DNA restriction and modification enzymes.
PG  - 315-369
AB  - Although the phenomenon of host specificity was initially observed in the early
      1950s (Luria & Human, 1952; Bertani & Weigle, 1953), it was nearly a decade
      later that Arber and his colleagues accurately predicted the molecular basis of
      the phenomenon.  Their experiments with bacteriophage lambda demonstrated that
      a given host-specificity system imparts a specific modification of the viral
      DNA, and further, that restriction of DNA lacking the appropriate modificaton
      is a consequence of nucleolytic hydrolysis upon entry into the host cell (Arber
      & Dussoix, 1962; Dussoix & Arber, 1962; Arber, Hattman & Dussoix, 1963).  These
      observations led to their proposal that host specificity is based on a
      two-enzyme system.  They suggested that cells of a given host specificity
      possess a restriction endodeoxyribonuclease that recognizes a unique sequence
      of nucleotide pairs and introduces double strand breaks into unmodified DNA.
      The second component of the system, a modification enzyme, was proposed to
      recognize the same nucleotide sequence and to modify the DNA, yielding a
      species which is no longer subject to hydrolysis by the restriction
      endonuclease.  Moreover, a variety of biological experiments suggested a
      correlation between the phenomenon of modifications and polynucleotide
      methylation (Arber, 1965; Klein & Sauerbier, 1965; Arber & Smith, 1966).  Thus,
      cellular DNA would be resistant to restriction cleavage by virtue of being
      appropriately methylated.  DNA foreign to the cell and lacking the appropriate
      modification would, however, be specifically recognized and hydrolysed by the
      restriction endonuclease.  Such systems then could account for the observed
      barriers to transfer of unmodified DNA elements between prokaryotic cell types.
AU  - Modrich P
PT  - Journal Article
TA  - Q. Rev. Biophys.
JT  - Q. Rev. Biophys.
SO  - Q. Rev. Biophys. 1979 12: 315-369.

PMID- 
VI  - 0
DP  - 1982
TI  - Type-II restriction and modification enzymes.
PG  - 109-154
AB  - I. IntroductionII. Structure of type-II restriction and modification enzymes.III. Methyl
      transfer by type-II modification enzymes.IV. Fidelity of type-II restriction and modification
      enzymes.V. Type-II enzyme-DNA interaction: thermodynamic and Kinetic parameters.VI. Type-II
      enzyme-DNA interaction: DNA determinants important in specific recognition.VII. Concluding
      remarks.
AU  - Modrich P
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleases
JT  - Nucleases
SO  - Nucleases 1982 0: 109-154.

PMID- 332689
VI  - 252
DP  - 1977
TI  - Role of the 2-amino group of deoxyguanosine in sequence recognition by EcoRI restriction and modifcation enzymes.
PG  - 7273-7278
AB  - The dG residues within the EcoRI recognition sequence of ColE1 DNA have been
      selectively replaced with dI.  Methylation of the altered sequence by the EcoRI
      modification enzyme is extremely slow as compared with methyl transfer to the
      natural recognition site.  Since the affinity of the modification enzyme for
      the dI-containing sequence is considerably less than that for the nature
      sequence, we have concluded that the 2-amino group of dG has an important role
      in DNA site recognition by this enzyme.  In contrast, the altered site is
      subject to cleavage by EcoRI endonuclease at rates essentially identical with
      those observed with the natural sequence.  These results strongly suggest that
      the two enzymes utilize different contacts within the EcoRI site and are
      consistent with our conclusion (Rubin, R.A., and Modrich, P. (1977) J. Biol.
      Chem. 252, 7265-7272) that the two proteins interact with their common
      recognition sequence in different ways.
AU  - Modrich P
AU  - Rubin RA
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1977 252: 7273-7278.

PMID- 786985
VI  - 251
DP  - 1976
TI  - EcoRI endonuclease.  Physical and catalytic properties of the homogeneous enzyme.
PG  - 5866-5874
AB  - A procedure for large scale isolation of Escherichia coli RI endonuclease in
      high yield has been developed.  The purified enzyme is homogenous as judged by
      polyacrylamide gel electrophoresis and analytical sedimentation.  The denatured
      and reduced form of the enzyme has a molecular weight of 28,500 -/+ 500.  In
      solution the enzyme exists as a mixture of dimers and tetramers of molecular
      weights 57,000 and 114,000, respectively.  We estimate the dissociation
      constant for tetramer to dimer transition to be less than or approximately
      equal to 1 x 10-7 M.  Steady state kinetic analysis of the endonuclease with
      ColE1 DNA as substrate showed that the enzyme obeys Michaelis-Menten kinetics.
      At 37C the turnover number is four double strand scissions per min, and the Km
      for ColE1 molecules is 8 x 10-9 M.  At 0C the major product of endonuclease
      action contains only one single strand break in the RI site, and such molecules
      can dissociate from the enzyme.  In contrast, at 30C or 37C, two single strand
      breaks are introduced into the RI sequence prior to dissociation of the enzyme.
      A transient enzyme-bound intermediate containing only one break in the RI site
      was observed in studies of a single turnover at 30C.  Kinetic analysis of this
      reaction indicates that the first break is introduced into the RI site with a
      first order rate constant of at elast 40 min-1, while the second cleavage
      occurs with a rate constant of 14 min-1.  Since the turnover number of the
      enzyme at 30C is only 0.72 min-1, these results indicate that the rate-limiting
      step is release of endonuclease from its DNA product.
AU  - Modrich P
AU  - Zabel D
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1976 251: 5866-5874.

PMID- 15464603
VI  - 114
DP  - 2004
TI  - Overexpression and affinity chromatography purification of the Type III restriction endonuclease EcoP15I for use in transcriptome analysis.
PG  - 99-106
AB  - The Type III restriction endonuclease EcoP15I is a multifunctional hetero-oligomeric enzyme
      that recognizes the non-symmetric DNA sequence 5'-CAGCAG. For efficient cleavage, EcoP15I
      needs the interaction with two copies of the recognition sequence that have to be inversely
      oriented in the DNA double strand. The enzyme cuts the upper DNA strand 25-26bp and the lower
      DNA strand 27-28bp, respectively, downstream of the recognition sequence-a distinct feature
      that makes the enzyme particularly valuable for gene expression profiling methods relying on
      the SAGE procedure (Matsumura et al., PNAS 100, 15718, 2003). Because the broader use of this
      transcriptome analysis method requires the availability of larger amounts of restriction
      endonuclease EcoP15I and the enzyme is not commercially available, we have cloned the genes
      coding for the EcoP15I restriction endonuclease into pQE-16 plasmid vector that provides the
      enzyme with a C-terminal 6xHis-tag. After Ni-NTA affinity chromatography and ion exchange
      chromatography on heparin sepharose, we obtained 5mg homogeneous EcoP15I per gram cell pellet
      within 1-2 day(s). Moreover, the C-terminally 6xHis-tagged EcoP15I restriction endonuclease
      shows comparable enzymatic activity as the untagged enzyme.
AU  - Moencke-Buchner E
AU  - Mackeldanz P
AU  - Krueger DH
AU  - Reuter M
PT  - Journal Article
TA  - J. Biotechnol.
JT  - J. Biotechnol.
SO  - J. Biotechnol. 2004 114: 99-106.

PMID- 2834322
VI  - 170
DP  - 1988
TI  - Entry of bacteriophage T7 DNA into the cell and escape from host restriction.
PG  - 2095-2105
AB  - T7 DNA did not become susceptible to degradation by the host restriction
      enzymes EcoB, EcoK, or EcoP1 until 6 to 7 min. after infection (at 30C).
      During this period, T7 gene 0.3 protein is made and inactivates EcoB and EcoK,
      allowing wild-type T7, or even a mutant that has recognition sites flanking
      gene 0.3, to escape restriction by these enzymes.  However, T7 failed to escape
      restriction by EcoP1 even though 0.3 protein was made, evidently because 0.3
      protein is unable to inactivate EcoP1.  How T7 DNA can be accessible to
      transcription but not restriction in the first few minutes of infection is not
      yet understood, but we favor the idea that the entering DNA is initially
      segregated in a special place.  Entry of T7 DNA into the cell is normally
      coupled to transcription.  Tests of degradation of DNAs having their first
      restriction sites different distances from the end of the DNA indicated that
      only the first 1,000 or so base pairs (2.5%) of the molecule enter the cell
      without transcription.  An exception was the only mutant tested that lacks base
      pairs 343 to 393 of T7 DNA; most or all of this DNA entered the cell without
      being transcribed, apparently because it lacks a sequence that normally arrests
      entry.  This block to DNA entry would normally be relieved by the host RNA
      polymerase transcribing from an appropriately situated promoter, but the block
      can also be relieved by T7 RNA polymerase, if supplied by the host cell.  T7
      mutants that lack all three strong early promoters A1, A2, and A3 could grow by
      using a secondary promoter.
AU  - Moffatt BA
AU  - Studier FW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1988 170: 2095-2105.

PMID- 26879123
VI  - 17
DP  - 2016
TI  - Isolation and genome sequencing of four Arctic marine Psychrobacter strains exhibiting multicopper oxidase activity.
PG  - 117
AB  - BACKGROUND: Marine cold-temperature environments are an invaluable source of
      psychrophilic microbial life for new biodiscoveries. An Arctic marine bacterial
      strain collection was established consisting of 1448 individual isolates
      originating from biota, water and sediment samples taken at a various depth in
      the Barents Sea, North of mainland Norway, with an all year round seawater
      temperature of 4 degrees C. The entire collection was subjected to
      high-throughput screening for detection of extracellular laccase activity with
      guaiacol as a substrate. RESULTS: In total, 13 laccase-positive isolates were
      identified, all belonging to the Psychrobacter genus. From the most diverse four
      strains, based on 16S rRNA gene sequence analysis, all originating from the same
      Botryllus sp. colonial ascidian tunicate sample, genomic DNA was isolated and
      genome sequenced using a combined approach of whole genome shotgun and 8 kb
      mate-pair library sequencing on an Illumina MiSeq platform. The genomes were
      assembled and revealed genome sizes between 3.29 and 3.52 Mbp with an average G +
      C content of around 42 %, with one to seven plasmids present in the four strains.
      Bioinformatics based genome mining was performed to describe the metabolic
      potential of these four strains and to identify gene candidates potentially
      responsible for the observed laccase-positive phenotype. Up to two different
      laccase-like multicopper oxidase (LMCO) encoding gene candidates were identified
      in each of the four strains. Heterologous expression of P11F6-LMCO and
      P11G5-LMCO2 in Escherichia coli BL21 (DE3) resulted in recombinant proteins
      exhibiting 2,2'-azino-bis-3-ethylbenzothiazoline-6-sulphonic acid (ABTS) and
      guaiacol oxidizing activity. CONCLUSIONS: Thirteen Psychrobacter species with
      laccase-positive phenotype were isolated from a collection of Arctic marine
      bacteria. Four of the isolates were genome sequenced. The overall genome features
      were similar to other publicly available Psychrobacter genome sequences except
      for P11G5 harboring seven plasmids. However, there were differences at the
      pathway level as genes associated with degradation of phenolic compounds,
      nicotine, phenylalanine, styrene, ethylbenzene, and ethanolamine were detected
      only in the Psychrobacter strains reported in this study while they were absent
      among the other publicly available Psychrobacter genomes. In addition, six gene
      candidates were identified by genome mining and shown to possess T1, T2 and T3
      copper binding sites as the main signature of the three-domain laccases.
      P11F6-LMCO and P11G5-LMCO2 were recombinantly expressed and shown to be active
      when ABTS and guaiacol were used as substrates.
AU  - Moghadam MS
AU  - Albersmeier A
AU  - Winkler A
AU  - Cimmino L
AU  - Rise K
AU  - Hohmann-Marriott MF
AU  - Kalinowski J
AU  - Ruckert C
AU  - Wentzel A
AU  - Lale R
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2016 17: 117.

PMID- 29700155
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of the Obligatory Marine Myxobacterial Strains Enhygromyxa salina SWB005 and SWB007.
PG  - e00324-18
AB  - The two marine myxobacterial strains Enhygromyxa salina SWB005 and SWB007 were isolated from
      coastal soil samples using Escherichia coli as bait for these predatory strains. These strains
      produce unique specialized metabolites. Genomes were assembled into 312 contigs for E. salina
      SWB005 (9.0 Mbp) and 192 contigs for E. salina SWB007 (10.6 Mbp).
AU  - Moghaddam JA
AU  - Poehlein A
AU  - Fisch K
AU  - Alanjary M
AU  - Daniel R
AU  - Konig GM
AU  - Schaberle TF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00324-18.

PMID- 10443440
VI  - 113
DP  - 1999
TI  - Expression of I-SceI in Drosophila to induce DNA double-strand breaks.
PG  - 439-445
AB  - Generation of double-strand breaks in chromosomal DNA induces repair machinery of a cell, and
      is also a necessary step for recombination events.  A system for the directed introduction of
      DSBs into a genome could substantially facilitate progress in understanding DSB repair
      mechanisms and could be used for efficient gene targeting.  The most successful attempts
      toward this goal in Drosophila have utilized the P element transposition system.  However,
      directed introduction of DSBs is still neither highly precise nor efficient, probably in part
      owing to the innate properties of the P element transposase, which although being a
      site-specific DNA binding protein, also has an affinity for nonspecific DNA sequences in
      vitro.  As a result, DSBs generated by P element transposase are distributed randomly in the
      Drosophila genome with the highest frequency close to or at the P element ends.  Site-specific
      endonucleases with sufficiently long recognition sequences potentially could provide a
      solution to this problem.  Among the most specific is the I-SceI endonuclease.  It recognizes
      an 18-bp nonpalindromic sequence and has very low tolerance to nucleotide substitution.
      Theoretically, this recognition site should appear only once in every 6.87 x 10^10 bp, which
      exceeds the size of the Drosophila genome by about 400 times.
AU  - Mogila VA
AU  - Bellaiche Y
AU  - Perrimon N
PT  - Journal Article
TA  - Methods Mol. Biol.
JT  - Methods Mol. Biol.
SO  - Methods Mol. Biol. 1999 113: 439-445.

PMID- 28694917
VI  - 12
DP  - 2017
TI  - Complete genome sequence of Microbulbifer sp. CCB-MM1, a halophile isolated from  Matang Mangrove Forest, Malaysia.
PG  - 36
AB  - Microbulbifer sp. CCB-MM1 is a halophile isolated from estuarine sediment of Matang Mangrove
      Forest, Malaysia. Based on 16S rRNA gene sequence analysis,
      strain CCB-MM1 is a potentially new species of genus Microbulbifer. Here we
      describe its features and present its complete genome sequence with annotation.
      The genome sequence is 3.86 Mb in size with GC content of 58.85%, harbouring 3313
      protein coding genes and 92 RNA genes. A total of 71 genes associated with
      carbohydrate active enzymes were found using dbCAN. Ectoine biosynthetic genes,
      ectABC operon and ask_ect were detected using antiSMASH 3.0. Cell shape
      determination genes, mreBCD operon, rodA and rodZ were annotated, congruent with
      the rod-coccus cell cycle of the strain CCB-MM1. In addition, putative mreBCD
      operon regulatory gene, bolA was detected, which might be associated with the
      regulation of rod-coccus cell cycle observed from the strain.
AU  - Moh TH
AU  - Lau NS
AU  - Furusawa G
AU  - Amirul AA
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 36.

PMID- 25700398
VI  - 3
DP  - 2015
TI  - Analysis of Quorum-Sensing Pantoea stewartii Strain M073A through Whole-Genome Sequencing.
PG  - e00022-15
AB  - Pantoea stewartii strain M073a is a Gram-negative bacterium isolated from a tropical
      waterfall. This strain exhibits quorum-sensing activity. Here, the assembly and annotation of
      its genome are presented.
AU  - Mohamad NI
AU  - Tan WS
AU  - Chang CY
AU  - Keng TK
AU  - Yin WF
AU  - Chan KG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00022-15.

PMID- 25555738
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequence of Quorum-Sensing Vibrio tubiashii Strain T33.
PG  - e01362-14
AB  - Vibrio tubiashii strain T33 was isolated from the coastal waters of Morib, Malaysia, and was
      shown to possess quorum-sensing activity similar to that of its famous relative Vibrio
      fischeri. Here, the assembly and annotation of its genome are presented.
AU  - Mohamad NI
AU  - Yin WF
AU  - Chan KG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01362-14.

PMID- 29051236
VI  - 5
DP  - 2017
TI  - First Complete Genome Sequence of Methicillin-Resistant Staphylococcus aureus Strain SO-1977 Isolated from Khartoum, Sudan.
PG  - e00945-17
AB  - Methicillin-resistant Staphylococcus aureus is increasingly becoming resistant to most
      antibiotics and consequently has become a challenging public health problem
      in Sudan. The present study documented the first complete genome sequence of
      strain SO-1977, isolated from a contaminated wound in Sudan.
AU  - Mohamed SB
AU  - Ali MS
AU  - Alamir FM
AU  - Alyas TB
AU  - Ahmed AE
AU  - Seed AO
AU  - Omer RA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00945-17.

PMID- 26868404
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Cylindrospermopsis sp. Strain CR12 Extracted from the Minimetagenome of a Nonaxenic Unialgal Culture from a Tropical Freshwater Lake.
PG  - e01726-15
AB  - Cylindrospermopsis is known to be one of the major bloom-forming cyanobacterial genera in many
      freshwater environments. We report here the draft genome sequence of a tropical
      Cylindrospermopsis sp. strain, CR12, which is capable of producing the hepatotoxic
      cylindrospermopsin.
AU  - Mohamed-Nor NH
AU  - Tan BF
AU  - Te SH
AU  - Thompson JR
AU  - Gin KY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01726-15.

PMID- 26659679
VI  - 3
DP  - 2015
TI  - Complete Genome Sequences of an Escherichia coli Laboratory Strain and Trimethoprim-Resistant (TMP32XR) Mutant Strains.
PG  - e01434-15
AB  - We report the whole-genome sequences of an Escherichia coli laboratory wild-type  strain and
      trimethoprim-resistant strains (two biological replicates, TMP32XR1
      and TMP32XR2). Compared to the U00096.3 strain, a widely used strain in
      laboratory experiments, the laboratory wild-type strain and the drug-resistant
      strains evolved from this (TMP32XR1 and TMP32XR2) are 13, 24, and 37 bp longer,
      respectively.
AU  - Mohan A
AU  - Bhosle A
AU  - Chandra N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01434-15.

PMID- 25657281
VI  - 3
DP  - 2015
TI  - Complete Genome Sequences of a Mycobacterium smegmatis Laboratory Strain (MC2 155) and Isoniazid-Resistant (4XR1/R2) Mutant Strains.
PG  - e01520-14
AB  - We report the whole genome sequences of a Mycobacterium smegmatis laboratory wild-type strain
      (MC(2) 155) and mutants (4XR1, 4XR2) resistant to isoniazid.
      Compared to Mycobacterium smegmatis MC(2) 155 (NC_008596), a widely used strain
      in laboratory experiments, the MC(2) 155, 4XR1, and 4XR2 strains are 60, 128 and
      93 bp longer, respectively.
AU  - Mohan A
AU  - Padiadpu J
AU  - Baloni P
AU  - Chandra N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01520-14.

PMID- 24016522
VI  - 306
DP  - 2013
TI  - Cell and Molecular Biology of DNA Methyltransferase 1.
PG  - 1-42
AB  - The DNA cytosine methyltransferase 1 (DNMT1) is a ubiquitous nuclear enzyme that catalyzes the
      well-established reaction of placing methyl
      groups on the unmethylated cytosines in methyl-CpG:CpG base pairs in
      the hemimethylated DNA formed by methylated parent and unmethylated
      daughter strands. This activity regenerates fully methylated
      methyl-CpG:methyl-CpG pairs. Despite the straightforward nature of its
      catalytic activity, detailed biochemical, genetic, and developmental
      studies revealed intricate details of the central regulatory role of
      DNMT1 in governing the epigenetic makeup of the nuclear genome. DNMT1
      mediates demethylation and also participates in seemingly wide cellular
      functions unrelated to maintenance DNA methylation. This review brings
      together mechanistic details of maintenance methylation by DNMT1, its
      regulation at transcriptional and posttranscriptional levels, and the
      seemingly unexpected functions of DNMT1 in the context of DNA
      methylation which is central to epigenetic changes that occur during
      development and the process of cell differentiation.
AU  - Mohan KN
AU  - Chaillet JR
PT  - Journal Article
TA  - Int. Rev. Cell Mol. Biol.
JT  - Int. Rev. Cell Mol. Biol.
SO  - Int. Rev. Cell Mol. Biol. 2013 306: 1-42.

PMID- 7698657
VI  - 155
DP  - 1995
TI  - Partial purification and characterisation of Bfi57I and Bfi89I, restriction endonucleases from different strains of Butyrivibrio fibrisolvens.
PG  - 131-132
AB  - Two class-II restriction endonucleases (ENases), Bfi57I and Bfi89I, were partially purified
      from Butyrivibrio fibrisolvens OB157 and OB189, respectively. Bfi57I (isoschizomer Sau3AI) had
      the DNA recognition/cleavage sequence 5'-/GATC-3'; it is not inhibited by Dam methylation,
      but is partially inhibited by M.BamHI methylation. Bfi89I (isoschizomer EaeI) had the
      recognition/cleavage sequence 5'Y/GGCCR-3'; unlike the EaeI isoschizomer it is not fully
      inhibited by M.HaeIII methylation.
AU  - Mohn WW
AU  - Teather RM
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 155: 131-132.

PMID- 10716944
VI  - 14
DP  - 2000
TI  - Rules for DNA target-site recognition by a lactococcal group II intron enable retargeting of the intron to specific DNA sequences.
PG  - 559-573
AB  - Group II intron homing occurs primarily by a mechanism in which the intron RNA reverse splices
      into a DNA target site and is then reverse transcribed by the intron-encoded protein. The DNA
      target site is recognized by an RNP complex containing the intron-encoded protein and the
      excised intron RNA. Here, we analyzed DNA target-site requirements for the Lactococcus lactis
      Ll.LtrB group II intron in vitro and in vivo. Our results suggest a model similar to yeast
      mtDNA introns, in which the intron-encoded protein first recognizes a small number of
      nucleotide residues in double-stranded DNA and causes DNA unwinding, enabling the intron RNA
      to base-pair with the DNA for reverse splicing. Antisense-strand cleavage requires additional
      interactions between the protein and 3' exon. Key nucleotide residues are recognized directly
      by the intron-encoded protein independent of sequence context, and there is a stringent
      requirement for fixed spacing between target site elements recognized by the protein and RNA
      components of the endonuclease. Experiments with DNA substrates containing GC-clamps or
      "bubbles" indicate a requirement for DNA unwinding in the 3' exon but not the distal 5' exon
      region. Finally, by applying the target-site recognition rules, we show that the L1.LtrB
      intron can be modified to insert at new sites in a plasmid-borne thyA gene in Escherichia
      coli. This strategy should be generally applicable to retargeting group II introns and to
      delivering foreign sequences to specific sites in heterologous genomes.
AU  - Mohr G
AU  - Smith D
AU  - Belfort M
AU  - Lambowitz AM
PT  - Journal Article
TA  - Genes Dev.
JT  - Genes Dev.
SO  - Genes Dev. 2000 14: 559-573.

PMID- 27013041
VI  - 4
DP  - 2016
TI  - Fully Closed Genome Sequences of Five Type Strains of the Genus Cronobacter and One Cronobacter sakazakii Strain.
PG  - e00142-16
AB  - Cronobacteris associated with infant infections and the consumption of reconstituted infant
      formula. Here we sequenced and closed six genomes ofC.
      condimenti(T),C. muytjensii(T),C. universalis(T),C. malonaticus(T),C.
      dublinensis(T), andC. sakazakiithat can be used as reference genomes in single
      nucleotide polymorphism (SNP)-based next-generation sequencing (NGS) analysis for
      source tracking investigations.
AU  - Moine D
AU  - Kassam M
AU  - Baert L
AU  - Tang Y
AU  - Barretto C
AU  - Ngom BC
AU  - Klijn A
AU  - Descombes P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00142-16.

PMID- 
VI  - 75
DP  - 1992
TI  - The susceptibility of evolving dairy bacteriophages to restriction enzymes and lactococcal R/M system.
PG  - 114
AB  - One approach to limit phage development during milk fermentation is to use strains insensitive
      to predominant phage species present in cheese plants, particularly prolate (c2) and small
      isometric-headed (P008) species. However this may lead to the emergence of other phage
      species. Recently, we have isolated 7 industrial phages (phi48, phi50,al,bl, cs, d1 from USA
      and UL36 from Canada) able to propagate on Lactococcus lactis LMA12, and except for UL36, also
      on its pTR2030 transconjugants. Electron microscopy and DNA homology studies have placed these
      phages within the P335 species (composed of lytic and temperate types). Molecular analyses
      have shown a relatively high number of restriction sites in their genomes for many
      endonucleases, including ScrFI. The industrial phages, compared to phages sk1, p2, jj50 (P008
      species) and c2, were highly sensitive to 4 plasmid-encoded R/M systems (pTN20, pTRK12,
      pTRK30, pTRK68). The paucity of restriction sites in many phage genomes has been proposed as
      an antirestriction response which has evolved in some lactococcal phages. Since the 7 phages
      studied herein are more sensitive to R/M and their DNA cuts more frequently, this group may
      represent a younger generation of phages that have just recently evolved to lactococci.
AU  - Moineau S
AU  - D'Amelio GE
AU  - Pandian S
AU  - Klaenhammer TR
PT  - Journal Article
TA  - J. Dairy Sci.
JT  - J. Dairy Sci.
SO  - J. Dairy Sci. 1992 75: 114.

PMID- 16348842
VI  - 59
DP  - 1993
TI  - Restriction/modification systems and restriction endonucleases are more effective on lactococcal bacteriophages that have emerged recently in the dairy industry.
PG  - 197-202
AB  - Recently, eight lytic small isometric-headed bacteriophages were isolated from
      cheese-manufacturing plants throughout North America. The eight phages were different, but all
      propagated on one strain, Lactococcus lactis NCK203. On the basis of DNA homology, they were
      classified in the P335 species. Digestion of their genomes in vitro with restriction enzymes
      resulted in an unusually high number of type II endonuclease sites compared with the more
      common lytic phages of the 936 (small isometric-headed) and c2 (prolate-headed) species. In
      vivo, the P335 phages were more sensitive to four distinct lactococcal restriction and
      modification (R/M) systems than phages belonging to the 936 and c2 species. A significant
      correlation was found between the number of restriction sites for endonucleases (purified from
      other bacterial genera) and the relative susceptibility of phages to lactococcal R/M systems.
      Comparisons among these three phage species indicate that the P335 species may have emerged
      most recently in the dairy industry.
AU  - Moineau S
AU  - Pandian S
AU  - Klaenhammer TR
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1993 59: 197-202.

PMID- 16535064
VI  - 61
DP  - 1995
TI  - Expression of a Lactococcus lactis phage resistance mechanism by Streptococcus thermophilus.
PG  - 2461-2466
AB  - The 7.8-kb lactococcal plasmid pSRQ700 encodes the LlaII restriction/modification system which
      recognizes and cleaves the sequence 3'-GATC-5'. When the plasmid pSRQ700 is introduced into
      a phage-sensitive Lactococcus lactis strain, strong phage resistance is conferred by the LlaII
      system. In this report, we show that pSRQ700 cannot replicate in Streptococcus thermophilus.
      However, if cloned into the vector pNZ123, the native LlaII system is expressed and strong
      phage resistance is conferred to various industrial S. thermophilus strains. Resistance
      against phages isolated from yogurt and mozzarella wheys was observed. To our knowledge, this
      is the first report of increased phage resistance in S. thermophilus.
AU  - Moineau S
AU  - Walker SA
AU  - Holler BJ
AU  - Vedamuthu ER
AU  - Vandenbergh PA
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1995 61: 2461-2466.

PMID- 7793939
VI  - 61
DP  - 1995
TI  - Cloning and sequencing of LlaII restriction/modification genes from Lactococcus lactis and relatedness of this system to the Streptococcus pneumoniae DpnII system.
PG  - 2193-2202
AB  - The natural 7.8-kb plasmid pSRQ700 was isolated from Lactococcus lactis subsp. cremoris DCH-4.
      It encodes a restriction/modification system named LlaII. When introduced into a
      phage-sensitive L. lactis strain, pSRQ700 confers strong phage resistance against the three
      most common lactococcal phage species, namely, 936, c2, and P335. The LlaII endonuclease was
      purified and found to cleave the palindromic sequence 5'-GATC-3'. It is an isoschizomer of
      Streptococcus pneumoniae DpnII. The plasmid pSRQ700 was mapped, and the genetic organization
      of LlaII was localized. Cloning and sequencing of the entire LlaII system allowed the
      identification of three open reading frames. The three genes (llaIIA, llaIIB, and llaIIC)
      overlapped and are under one putative promoter. A putative terminator was found at the end of
      llaIIC. The genes llaIIA and llaIIB coded for m6A methyltransferases, and llaIIC coded for an
      endonuclease. The LlaII system shares strong genetic similarities with the DpnII system. The
      deduced amino acid sequence of M.LlaIIA was 75% identical with that of M.DpnII, whereas
      M.LlaIIB was 88% identical with M.DpnA. However, R.LlaII shared only 31% identity with
      R.DpnII.
AU  - Moineau S
AU  - Walker SA
AU  - Vedamuthu ER
AU  - Vandenbergh PA
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1995 61: 2193-2202.

PMID- 2587240
VI  - 17
DP  - 1989
TI  - Isolation and identification of restriction BshKI.
PG  - 8884
AB  - None
AU  - Moissidou A
AU  - Rina M
AU  - Bouriotis V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 8884.

PMID- 2168545
VI  - 18
DP  - 1990
TI  - Restriction endonuclease from thermophilic bacterial species I.  Isolation and characterization of BsiEI.
PG  - 4954
AB  - 
AU  - Mok YK
AU  - Clark DR
AU  - Kam KM
AU  - Shaw PC
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 4954.

PMID- 2251161
VI  - 18
DP  - 1990
TI  - Restriction endonuclease from thermophilic bacterial species II. Isolation and characterization of BsiBl.
PG  - 6740
AB  - None
AU  - Mok YK
AU  - Clark DR
AU  - Kam KM
AU  - Shaw PC
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 6740.

PMID- 2041772
VI  - 19
DP  - 1991
TI  - BsiYI, a novel thermophilic restriction endonuclease that recognizes 5' CCNNNNNNNGG3' and the discovery of a wrongly sequenced site in pACYC177 .
PG  - 2321-2323
AB  - A new type II restriction endonuclease designated BsiYI has been purified from
      a thermophilic soil Bacillus stearothermophilus strain.  This enzyme recognizes
      and cleaves the highly degenerate sequence 5'CCNNNNN^NNGG3'.  During the
      identification of the recognition sequence of BsiYI, we discovered that there
      should be five G nucleotides instead of four at position 1227 - 1230 of the
      plasmid pACYC177.
AU  - Mok YK
AU  - Clark DR
AU  - Kam KM
AU  - Shaw PC
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 2321-2323.

PMID- 29574188
VI  - 660
DP  - 2018
TI  - New bifunctional restriction-modification enzyme AloI isoschizomer (PcoI): Bioinformatics analysis, purification and activity confirmation.
PG  - 8-12
AB  - Type II restriction endonucleases and modification DNA-methyltransferases are key instruments
      of genetic engineering. Recently the number of proteins assigned to
      this group exceeds 8500. Subtype IIC organizes bifunctional
      endonuclease-methyltransferase enzymes and currently consists of 16 described
      members. Here we present phylogenetic tree of 22 new potential bifunctional
      endonucleases. The majority of them are thought to be fusions of a restriction
      nuclease with a DNA-methyltransferase and a target recognition subunit of type I
      restriction-modification systems (R-M-S structure). A RM.AloI isoschizomer from
      Prevotella copri DSM-18205, PcoI, has been cloned, purified and its REase
      activity demonstrated. It cuts DNA in magnesium-dependent manner and demonstrates
      high affinity to DNA, which probably reflects its mechanism of action. This work
      provides additional proves that gene fusion might play an important role in
      evolution of restriction-modification systems and other DNA-modifying proteins.
AU  - Mokrishcheva ML
AU  - Kertesz-Farkas A
AU  - Nikitin DV
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 2018 660: 8-12.

PMID- 
VI  - 
DP  - 2012
TI  - Role of gene fusion in evolution of restriction endonucleases.
PG  - 163-181
AB  - DNA restriction-modification systems (RMS) are prokaryotic tools against invasion of foreign
      DNAs into
      cells (Williams, 2003). They play an important evolutionary role as subcellular barriers
      restricting horizontal
      gene transfer and thereby providing microbial biodiversity. Usually, RMS comprise of a
      restriction
      endonuclease (REase) and modification DNA methyltransferase (MTase) enzyme recognizing
      the same short 4-8 nucleotide sequence. RMS functioning includes methylation of recognition
      DNA sequences
      by MTase. All non-modified sites can be cut by a cognate REase (Williams, 2003). Type II
      REases are indispensable tools in creating recombinant DNA molecules (Skowronek and Bujnicki,
      2007).
      Their widespread practical application has stimulated research to discover and characterize
      more of these
      systems. Currently, more than 10000 different sequences corresponding to REases of type II
      alone are
      listed in REBASE, the database holding all known and many putative RMS (Roberts et al., 2010).
      The high number of known RMS is reflected also in high diversity of their organisation or
      functioning
      and, hypothetically, in multiplicity of their evolutionary pathways. One of these pathways
      could be fusion
      of preexisting ORFs with formation of a gene capable of producing a protein with an array of
      new
      activities and functions. It could be suggested that type IIC RMS carrying both REase and
      MTase in a
      single polypeptide might appear by this mechanism (Roberts et al., 2003). Here we present
      direct evidence
      how a fully functional type IIC REase could appear by fusion of the appropriate genes as a
      result
      of a few point mutations.
AU  - Mokrishcheva ML
AU  - Solonin AS
AU  - Nikitin DV
PT  - Journal Article
TA  - Protein Purification and Analysis
JT  - Protein Purification and Analysis
SO  - Protein Purification and Analysis 2012 : 163-181.

PMID- 21291520
VI  - 11
DP  - 2011
TI  - Fused eco29kIR- and M genes coding for a fully functional hybrid polypeptide as a model of molecular evolution of restriction-modification systems.
PG  - 35
AB  - Background: The discovery of restriction endonucleases and modification DNA
      methyltransferases, key instruments of genetic engineering, opened
      a new era of molecular biology through development of the recombinant
      DNA technology. Today, the number of potential proteins assigned to
      type II restriction enzymes alone is beyond 6000, which probably
      reflects the high diversity of evolutionary pathways. Here we present
      experimental evidence that a new type IIC restriction and modification
      enzymes carrying both activities in a single polypeptide could result
      from fusion of the appropriate genes from preexisting bipartite
      restriction-modification systems.
      Results: Fusion of eco29kIR and M ORFs gave a novel gene encoding
      for a fully functional hybrid polypeptide that carried both restriction
      endonuclease and DNA methyltransferase activities. It has been placed
      into a subclass of type II restriction and modification enzymes - type
      IIC. Its MTase activity, 80% that of the M.Eco29kI enzyme, remained
      almost unchanged, while its REase activity decreased by three times,
      concurrently with changed reaction optima, which presumably can be
      caused by increased steric hindrance in interaction with the substrate.
      In vitro the enzyme preferentially cuts DNA, with only a low level of
      DNA modification detected. In vivo new RMS can provide a 10(2)-fold
      less protection of host cells against phage invasion.
      Conclusions: We propose a molecular mechanism of appearing of type
      IIC restriction-modification and M.SsoII-related enzymes, as well as
      other multifunctional proteins. As shown, gene fusion could play an
      important role in evolution of restriction-modification systems and be
      responsible for the enzyme subclass interconversion. Based on the
      proposed approach, hundreds of new type IIC enzymes can be generated
      using head-to-tail oriented type I, II, and III restriction and
      modification genes. These bifunctional polypeptides can serve a basis
      for enzymes with altered recognition specificities. Lastly, this study
      demonstrates that protein fusion may change biochemical properties of
      the involved enzymes, thus giving a starting point for their further
      evolutionary divergence.
AU  - Mokrishcheva ML
AU  - Solonin AS
AU  - Nikitin DV
PT  - Journal Article
TA  - BMC Evol. Biol.
JT  - BMC Evol. Biol.
SO  - BMC Evol. Biol. 2011 11: 35.

PMID- 11786018
VI  - 315
DP  - 2002
TI  - Structure and activity of a thermostable thymine-DNA glycosylase: Evidence for base twisting to remove mismatched normal DNA bases.
PG  - 373-384
AB  - The repair of T:G mismatches in DNA is key for maintaining bacterial restriction/modification
      systems and gene silencing in higher eukaryotes. T:G mismatch repair can be initiated by a
      specific mismatch glycosylase (MIG) that is homologous to the helix-hairpin-helix (HhH) DNA
      repair enzymes. Here, we present a 2.0 A resolution crystal structure and complementary
      mutagenesis results for this thermophilic HhH MIG enzyme. The results suggest that MIG
      distorts the target thymine nucleotide by twisting the thymine base approximately 90 degrees
      away from its normal anti position within DNA. We propose that functionally significant
      differences exist in DNA repair enzyme extrahelical nucleotide binding and catalysis that are
      characteristic of whether the target base is damaged or is a normal base within a mispair.
      These results explain why pure HhH DNA glycosylases and combined glycosylase/AP lyases cannot
      be interconverted by simply altering their functional group chemistry, and how
      broad-specificity DNA glycosylase enzymes may weaken the glycosylic linkage to allow a variety
      of damaged DNA bases to be excised.
AU  - Mol CD
AU  - Arvai AS
AU  - Begley TJ
AU  - Cunningham RP
AU  - Tainer JA
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2002 315: 373-384.

PMID- 6286422
VI  - 18
DP  - 1982
TI  - The sequence specificity of endonucleases CauI and CauII isolated from Chloroflexus aurantiacus.
PG  - 93-96
AB  - The type II restriction enzymes CauI and CauII, isolated from Chloroflexus
      aurantiacus, recognize and cleave (at the position indicated by an arrow) the
      sequences G^GA/TCC and CC^G/CGG, respectively.  These conclusions are supported
      by the results from restriction site mapping, sequence analysis by partial
      chemical degradation, end-group analysis after lambda exonuclease treatment and
      computer-assisted comparison of DNA sequence data.
AU  - Molemans F
AU  - van Emmelo J
AU  - Fiers W
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1982 18: 93-96.

PMID- 28007851
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Dehalococcoides mccartyi Strain WBC-2, Capable of Anaerobic Reductive Dechlorination of Vinyl Chloride.
PG  - e01375-16
AB  - Dehalococcoides mccartyi strain WBC-2 dechlorinates carcinogen vinyl chloride to  ethene in
      the West Branch Canal Creek (WBC-2) microbial consortium used for bioaugmentation. We
      assembled and closed the complete genome sequence of this prokaryote using metagenomic
      sequencing from an enrichment culture.
AU  - Molenda O
AU  - Tang S
AU  - Edwards EA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01375-16.

PMID- 4911845
VI  - 2
DP  - 1968
TI  - Host-controlled restriction of T-even bacteriophages:  relation of endonuclease I and T-even-induced nucleases to restriction.
PG  - 313-319
AB  - Restriction of nonglucosylated T2 phage (T*2) as a function of bacterial growth
      state was the same for endonuclease I-containing and endonuclease I-deficient
      strains of Escherichia coli B.  Furthermore, E. coli strains with various
      levels of restriction for T2 had comparable endonuclease I activities.  It was
      also found that a T4 mutant temperature-sensitive for gene 46 and 47 functions
      was fully restricted at 42 C.  It therefore appears that neither endonuclease I
      nor the phage-induced nucleases whose activities are blocked by mutations in
      genes 46 and 47 catalyze the initial event in restriction of nonglucosylated
      T-even phages.
AU  - Molholt B
AU  - Fraser D
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1968 2: 313-319.

PMID- 23868128
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of a Pseudomonas putida Clinical Isolate, Strain H8234.
PG  - e00496-13
AB  - We report the complete genome sequence of Pseudomonas putida strain H8234, which  was isolated
      from a hospital patient presenting with bacteremia. This strain has
      a single chromosome (6,870,827 bp) that contains 6,305 open reading frames. The
      strain is not a pathogen but exhibits multidrug resistance associated with 40
      genomic islands.
AU  - Molina L
AU  - Bernal P
AU  - Udaondo Z
AU  - Segura A
AU  - Ramos JL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00496-13.

PMID- 26045557
VI  - 290
DP  - 2015
TI  - Engineering a Nickase on the Homing Endonuclease I-DmoI Scaffold.
PG  - 18534-18544
AB  - Homing endonucleases are useful tools for genome modification because of their capability to
      recognize and cleave specifically large DNA targets. These
      endonucleases generate a DNA double strand break that can be repaired by the DNA
      damage response machinery. The break can be repaired by homologous recombination,
      an error-free mechanism, or by non-homologous end joining, a process susceptible
      to introducing errors in the repaired sequence. The type of DNA cleavage might
      alter the balance between these two alternatives. The use of 'nickases' producing
      a specific single strand break instead of a double strand break could be an
      approach to reduce the toxicity associated with non-homologous end joining by
      promoting the use of homologous recombination to repair the cleavage of a single
      DNA break. Taking advantage of the sequential DNA cleavage mechanism of I-DmoI
      LAGLIDADG homing endonuclease, we have developed a new variant that is able to
      cut preferentially the coding DNA strand, generating a nicked DNA target. Our
      structural and biochemical analysis shows that by decoupling the action of the
      catalytic residues acting on each strand we can inhibit one of them while keeping
      the other functional.
AU  - Molina R
AU  - Marcaida MJ
AU  - Redondo P
AU  - Marenchino M
AU  - Duchateau P
AU  - D'Abramo M
AU  - Montoya G
AU  - Prieto J
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2015 290: 18534-18544.

PMID- 22495931
VI  - 40
DP  - 2012
TI  - Non-specific protein-DNA interactions control I-CreI target binding and cleavage.
PG  - 6936-6945
AB  - Homing endonucleases represent protein scaffolds that provide powerful tools for  genome
      manipulation, as these enzymes possess a very low frequency of DNA
      cleavage in eukaryotic genomes due to their high specificity. The basis of
      protein-DNA recognition must be understood to generate tailored enzymes that
      target the DNA at sites of interest. Protein-DNA interaction engineering of
      homing endonucleases has demonstrated the potential of these approaches to create
      new specific instruments to target genes for inactivation or repair. Protein-DNA
      interface studies have been focused mostly on specific contacts between amino
      acid side chains and bases to redesign the binding interface. However, it has
      been shown that 4 bp in the central DNA sequence of the 22-bp substrate of a
      homing endonuclease (I-CreI), which do not show specific protein-DNA
      interactions, is not devoid of content information. Here, we analyze the
      mechanism of target discrimination in this substrate region by the I-CreI
      protein, determining how it can occur independently of the specific protein-DNA
      interactions. Our data suggest the important role of indirect readout in this
      substrate region, opening the possibility for a fully rational search of new
      target sequences, thus improving the development of redesigned enzymes for
      therapeutic and biotechnological applications.
AU  - Molina R
AU  - Redondo P
AU  - Stella S
AU  - Marenchino M
AU  - D'Abramo M
AU  - Gervasio FL
AU  - Charles EJ
AU  - Valton J
AU  - Grizot S
AU  - Duchateau P
AU  - Prieto J
AU  - Montoya G
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: 6936-6945.

PMID- 25486305
VI  - 22
DP  - 2015
TI  - Visualizing phosphodiester-bond hydrolysis by an endonuclease.
PG  - 65-72
AB  - The enzymatic hydrolysis of DNA phosphodiester bonds has been widely studied, but the chemical
      reaction has not yet been observed. Here we follow the generation of
      a DNA double-strand break (DSB) by the Desulfurococcus mobilis homing
      endonuclease I-DmoI, trapping sequential stages of a two-metal-ion cleavage
      mechanism. We captured intermediates of the different catalytic steps, and this
      allowed us to watch the reaction by 'freezing' multiple states. We observed the
      successive entry of two metals involved in the reaction and the arrival of a
      third cation in a central position of the active site. This third metal ion has a
      crucial role, triggering the consecutive hydrolysis of the targeted
      phosphodiester bonds in the DNA strands and leaving its position once the DSB is
      generated. The multiple structures show the orchestrated conformational changes
      in the protein residues, nucleotides and metals during catalysis.
AU  - Molina R
AU  - Stella S
AU  - Redondo P
AU  - Gomez H
AU  - Marcaida MJ
AU  - Orozco M
AU  - Prieto J
AU  - Montoya G
PT  - Journal Article
TA  - Nat. Struct. Mol. Biol.
JT  - Nat. Struct. Mol. Biol.
SO  - Nat. Struct. Mol. Biol. 2015 22: 65-72.

PMID- 25414508
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Corynebacterium imitans DSM 44264, Isolated from a Five-Month-Old Boy with Suspected Pharyngeal Diphtheria.
PG  - e01210-14
AB  - The complete genome sequence of the type strain Corynebacterium imitans DSM 44264 comprises
      2,565,321 bp with a mean G+C content of 64.26%. The detection of the
      antibiotic resistance genes erm(X), aphA1-IAB, strA-strB, and cmx is fully
      consistent with the previously observed multidrug-resistant pattern of C. imitans
      isolates.
AU  - Mollmann S
AU  - Albersmeier A
AU  - Ruckert C
AU  - Tauch A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01210-14.

PMID- 6253897
VI  - 8
DP  - 1980
TI  - Cleavage of DNA.RNA hybrids by Type II restriction enzymes.
PG  - 2939-2946
AB  - The action of a number of restriction enzymes on DNA.RNA hybrids has been examined using
      hybrids synthesised with RNAs of cucumber mosaic virus as templates. The enzymes EcoRI,
      HindII, SalI, MspI, HhaI, AluI, TaqI and HaeIII cleaved the DNA strand of the hybrids (and
      possibly also the RNA strand) into specific fragments. For four of these enzymes, HhaI, AluI,
      TaqI and HaeIII, comparison of the restriction fragments produced with the known sequences of
      the viral RNAs confirmed that they were recognising and cleaving the DNA strand of the hybrids
      at their correct recognition sequences. It is likely that the ability to utilise DNA.RNA
      hybrids as substrates is a general property of Type II restriction enzymes.
AU  - Molloy PL
AU  - Symons RH
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1980 8: 2939-2946.

PMID- 2833732
VI  - 16
DP  - 1988
TI  - Effect of cytosine methylation on cutting by the restriction enzyme MaeII.
PG  - 2335
AB  - The restriction enzyme MaeII, isolated from Methanococcus aeolicus, recognizes
      and cuts within the sequence ACGT.  The susceptibility of MaeII to inhibition
      by cytosine methylation of interest for studies of gene expression as its
      recognition sequence contains a CG dinucleotide which has the potential to be
      methylated in vertebrate DNA.  In particular its recognition sequence is found
      within the binding sites for at least three mammalian transcription factors -
      the adenovirus major late gene upstream element, CCACGTGA, the cAMP responsive
      element, TGACGTCA, and an adenovirus E2 factor binding site, (T/A)CGTCA.
AU  - Molloy PL
AU  - Watt F
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1988 16: 2335.

PMID- 1810112
VI  - 38
DP  - 1991
TI  - Purification of a new restriction endonuclese from Streptococcus mutans and identification of its recognition sequence.
PG  - 55-60
AB  - SmuEI, a type II restriction endonuclease, has been isolated from Streptococcus mutans
      serotype E, which is an isoschizomer of AvaII recognizes the palindromic pentanucleotide
      sequence 5' GGWCC 3'. Similarly to AvaII, SmuEI cleaves the sequence, G^GWCC generating 5'
      protruding fragment termini.
AU  - Molnar A
AU  - Geck P
AU  - Orosz A
AU  - Kulcsar P
AU  - Nasz I
PT  - Journal Article
TA  - Acta Microbiol. Hung.
JT  - Acta Microbiol. Hung.
SO  - Acta Microbiol. Hung. 1991 38: 55-60.

PMID- 
VI  - 52
DP  - 1998
TI  - Occurrence of restriction and modification systems in ruminal Selenomonades.
PG  - 284
AB  - Bacterial restriction and modification systems consist of a restriction endonuclease plus a
      "cognate" modification methyltransferase having the same specificity. The biological function
      of restriction and modification systems is to protect bacteria from invading phage and plasmid
      DNA. The rumen is one of the most complex and best studied of all microbial ecosystems. In
      addition to protozoa, bacteria and fungi the rumen is known to contain a large and diverse
      population of bacteriophages. These phages probably play a significant role in the population
      dynamics of ruminal bacteria. Thus under ruminal condition possession of restriction and
      modification system can provide bacteria with a selective advantage.
AU  - Molnarova V
AU  - Javorsky P
AU  - Pristas P
PT  - Journal Article
TA  - Chemical Papers-Chemicke Zvesti
JT  - Chemical Papers-Chemicke Zvesti
SO  - Chemical Papers-Chemicke Zvesti 1998 52: 284.

PMID- 16887660
VI  - 5
DP  - 1999
TI  - Prevalence of CTGCAG recognizing restriction and modification systems in ruminal selenomonades.
PG  - 37-41
AB  - Analysis of restriction and modification activities in natural population of Selenomonas
      ruminantium have revealed the prevalence of CTGCAG (PstI isoschizomers) recognizing
      restriction and/or modification systems in these bacteria.  PstI isoschizomeric restriction
      endonucleases were detected in 4 out of 15 strains tested.  In one strain, the PstI
      isoschizomeric restriction system was accompanied by another restriction and modification
      system recognizing the sequence GAATTC (EcoRI isoschizomer).  Four other strains contained
      CTGCAG specific methylases which lacked cognate endonuclease activities.  The presence of
      identical restriction and modification systems in both subspecies of S. ruminantium, as well
      as the occurrence of PstI isoschizomers in various combinations, indicate the possibility of
      horizontal transfer of genes coding for these systems.
AU  - Molnarova V
AU  - Pristas P
AU  - Javorsky P
PT  - Journal Article
TA  - Anaerobe
JT  - Anaerobe
SO  - Anaerobe 1999 5: 37-41.

PMID- 27152321
VI  - 2
DP  - 2016
TI  - Plantazolicin is an ultra-narrow spectrum antibiotic that targets the membrane.
PG  - 207-220
AB  - Plantazolicin (PZN) is a ribosomally synthesized and post-translationally modified natural
      product from Bacillus methylotrophicus FZB42 and Bacillus pumilus. Extensive tailoring to
      twelve of the fourteen amino acid residues in the mature natural product endows PZN with not
      only a rigid, polyheterocyclic structure, but also antibacterial activity. Here we report a
      remarkably discriminatory activity of PZN toward Bacillus anthracis, which rivals a
      previously-described gamma (gamma) phage lysis assay in distinguishing B.
      anthracis from other members of the Bacillus cereus group. We evaluate the underlying cause of
      this selective activity by measuring the RNA expression profile of PZN-treated B. anthracis,
      which revealed significant upregulation of genes within the cell envelope stress response. PZN
      depolarizes the B. anthracis membrane like other cell envelope-acting compounds but uniquely
      localizes to distinct foci within the envelope. Selection and whole-genome sequencing of
      PZN-resistant mutants of B. anthracis implicate a relationship between the action of PZN and
      cardiolipin (CL) within the membrane. Exogenous CL increases the potency of PZN in wild type
      B. anthracis and promotes the incorporation of fluorescently tagged PZN in the cell envelope.
      We propose that PZN localizes to and exacerbates structurally compromised regions of the
      bacterial membrane, which ultimately results in cell lysis.
AU  - Molohon KJ
AU  - Blair PM
AU  - Park S
AU  - Doroghazi JR
AU  - Maxson T
AU  - Hershfield JR
AU  - Flatt KM
AU  - Schroeder NE
AU  - Ha T
AU  - Mitchell DA
PT  - Journal Article
TA  - ACS Infect Dis
JT  - ACS Infect Dis
SO  - ACS Infect Dis 2016 2: 207-220.

PMID- 10737890
VI  - 183
DP  - 2000
TI  - DNA methylation and cancer.
PG  - 145-154
AB  - The methylation of DNA is an epigenetic modification that can play an important role in the
      control of gene expression in mammalian cells. The enzyme involved in this process is DNA
      methyltransferase, which catalyzes the transfer of a methyl group from S-adenosyl-methionine
      to cytosine residues to form 5-methylcytosine, a modified base that is found mostly at CpG
      sites in the genome. The presence of methylated CpG islands in the promoter region of genes
      can suppress their expression. This process may be due to the presence of 5-methylcytosine
      that apparently interferes with the binding of transcription factors or other DNA-binding
      proteins to block transcription. In different types of tumors, aberrant or accidental
      methylation of CpG islands in the promoter region has been observed for many cancer-related
      genes resulting in the silencing of their expression. How this aberrant hypermethylation takes
      place is not known. The genes involved include tumor suppressor genes, genes that suppress
      metastasis and angiogenesis, and genes that repair DNA suggesting that epigenetics plays an
      important role in tumorigenesis. The potent and specific inhibitor of DNA methylation,
      5-aza-2'-deoxycytidine (5-AZA-CdR) has been demonstrated to reactivate the expression most of
      these "malignancy" suppressor genes in human tumor cell lines. These genes may be interesting
      targets for chemotherapy with inhibitors of DNA methylation in patients with cancer and this
      may help clarify the importance of this epigenetic mechanism in tumorigenesis.
AU  - Momparler RL
AU  - Bovenzi V
PT  - Journal Article
TA  - J. Cell. Physiol.
JT  - J. Cell. Physiol.
SO  - J. Cell. Physiol. 2000 183: 145-154.

PMID- 23833139
VI  - 1
DP  - 2013
TI  - Complete Genome Sequences of Helicobacter pylori Rifampin-Resistant Strains.
PG  - e00446-13
AB  - Here we present the complete genome sequences of two Helicobacter pylori rifampin-resistant
      (Rif(r)) strains (Rif1 and Rif2). Rif(r) strains were obtained
      by in vitro selection of H. pylori 26695 on agar plates with 20 microg/ml
      rifampin. The genome data provide insights on the genomic diversity of H. pylori
      under selection by rifampin.
AU  - Momynaliev K
AU  - Chelysheva V
AU  - Selezneva O
AU  - Akopian T
AU  - Alexeev D
AU  - Govorun V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00446-13.

PMID- 16358730
VI  - 39
DP  - 2005
TI  - Nucleotide correspondence between protein-coding sequences of Helicobacter pylori 26695 and J99 strains.
PG  - 945-951
AB  - Comparison of open-reading frames (ORFs) H. pylori 26695 and J99 strains has been revealed
      prevalence of nucleotide replacements as transitions (more than 3%) above transversions (less
      than 1%). Prevalence of nucleotide transitions is caused by high speed of C : G to T : A
      transitions in a coding strand of DNA (3.5-5.3%) and not coding strand (2.9-3.9%). The
      correspondence rate of transversion (A --> C, A --> T, C --> A, C --> G, G --> C, G --> T, T
      --> A and T --> G) did not exceed 0.84%. The highest correspondence frequency between C and T
      was detected in ACGT-ATGT (28.3%) - the site of methylation by active methyltransferase
      M.Hpy99XI in H. pylori 26695 and J99. Thus one can speculate that predominant transition
      taking place in H. pylori is mutation of C into T, which is realized through cytosine
      methylation-deamination mechanism.
AU  - Momynaliev KT
AU  - Rogov SI
AU  - Govorun VM
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2005 39: 945-951.

PMID- 
VI  - 37
DP  - 2003
TI  - Comparative genome analysis of Helicobacter pylori strains.
PG  - 529-536
AB  - DNA macroarrays were used to characterize 17 Helicobacter pylori strains isolated in four
      geographic regions of Russia (Moscow, St.
      Petersburg, Kazan, and Novosibirsk). Of all genes, 1272 (81%) proved to
      occur in all strains and to constitute a functional core of the genome,
      and 293 (18.7%) were strain-specific and greatly varied among the H.
      pylori strains. Most (71%) of the latter had unknown functions; the
      remainder included restriction-modification genes (3-9%), transposition
      genes (2-4%), and genes coding for outer membrane proteins (2-4%). The
      Russian H. pylori strains did not differ in genome organization or in
      the number and distribution of strain-specific genes from strains
      isolated in other countries.
AU  - Momynaliev KT
AU  - Smirnova OV
AU  - Kudryavtseva LV
AU  - Govorun VM
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2003 37: 529-536.

PMID- 15135731
VI  - 3
DP  - 2004
TI  - Functional interactions between the MutL and Vsr proteins of Escherichia coli are dependent on the N-terminus of Vsr.
PG  - 639-647
AB  - The crystal structure of the Escherichia coli Vsr endonuclease bound to a C(T/G)AGG substrate
      revealed that the DNA is held by a pincer composed of
      a trio of aromatic residues which intercalate into the major groove, and
      an N-terminus alpha helix which lies across the minor groove. We have
      constructed an N-terminus truncation (Delta14) which removes most of the
      alpha helix. The mutant is still fairly proficient in mediating very short
      patch repair. However, its endonuclease activity is considerably reduced
      and, in contrast to that of the wild type protein, cannot be stimulated by
      MutL. We had shown previously that excess Vsr in vivo causes mutagenesis,
      probably by inhibiting the participation of MutL in mismatch repair. The
      Delta14 mutant has diminished mutagenicity. In contrast, four
      enzymatically inactive mutants, with intact N-termini, are as mutagenic as
      the wild type protein. On the basis of these results we suggest that MutL
      causes a conformational change in the N-terminus of Vsr which enhances Vsr
      activity, and that this functional interaction between Vsr and MutL
      decreases the ability of MutL to carry out mismatch repair.
AU  - Monastiriakos SK
AU  - Doiron KM
AU  - Siponen MI
AU  - Cupples CG
PT  - Journal Article
TA  - DNA Repair
JT  - DNA Repair
SO  - DNA Repair 2004 3: 639-647.

PMID- 15501656
VI  - 155
DP  - 2004
TI  - Genome-wide comparison reveals great inter- and intraspecies variability in B. pseudomallei and B. mallei pathogens.
PG  - 781-793
AB  - Burkholderia mallei and B. pseudomallei, closely related Gram-negative
      bacteria, are causative agents of serious infectious diseases of humans
      and animals: glanders and melioidosis, respectively. Despite numerous
      studies of these pathogens, the detailed mechanism of their pathogenesis
      is still unknown. The problem is even more complicated due to natural
      variability of B. pseudomallei and B. mallei strains, the understanding of
      which is a prerequisite for rational design of tools for diagnostics,
      prophylaxis and therapy of the diseases. Using a subtractive hybridization
      technique, we compared the genomes of B. pseudomallei C-141 and B. mallei
      C-5 strains. A subtracted library of DNA fragments specific for B.
      pseudomallei C-141 and absent from B. mallei C-5 was obtained and
      analyzed. A variety of differences have been detected and mapped on the
      recently sequenced genome of B. pseudomallei K96243. A comparative
      sequence analysis also revealed considerable genomic differences between
      B. pseudomallei C-141 and B. mallei ATCC 23344 strains sequenced at The
      Institute for Genomic Research (TIGR). We also observed significant
      genomic differences between B. pseudomallei C-141 and B. pseudomallei
      K96243. Some of the differential DNA fragments displayed similarity to
      different mobile elements which have not yet been described for B.
      pseudomallei, whereas the others matched various prophage components,
      components of active transport systems, different enzymes and
      transcription regulators. A substantial proportion of the differential
      clones had no database matches either at the nucleotide or protein level.
      The results provide evidence for great genome-wide variability of B.
      pseudomallei, further confirmed by Southern blot analysis of various B.
      pseudomallei strains. The data obtained can be useful for future
      development of efficient diagnostic tools allowing rapid identification of
      species, strains and isolates of B. mallei and B. pseudomallei.
AU  - Monastyrskaya GS
AU  - Fushan AA
AU  - Abaev IV
AU  - Filyukova OB
AU  - Kostina MB
AU  - Pecherskih E
AU  - Sverdlov ED
PT  - Journal Article
TA  - Res. Microbiol.
JT  - Res. Microbiol.
SO  - Res. Microbiol. 2004 155: 781-793.

PMID- 19250940
VI  - 387
DP  - 2009
TI  - Functional Characterization and Modulation of the DNA Cleavage Efficiency of Type III Restriction Endonuclease EcoP15I in Its Interaction with Two  Sites in the DNA Target.
PG  - 1309-1319
AB  - EcoP15I is a Type III restriction endonuclease requiring the interaction with two inversely
      oriented 5'-CAGCAG recognition sites for efficient DNA
      cleavage. Diverse models have been developed to explain how enzyme
      complexes bound to both sites move toward each other, DNA translocation,
      DNA looping and simple diffusion along the DNA. Conflicting data also
      exist about the impact of cofactor S-adenosyl-l-methionine (AdoMet), the
      AdoMet analogue sinefungin and the bases flanking the DNA recognition
      sequence on EcoP15I enzyme activity. To clarify the functional role of
      these questionable parameters on EcoP15I activity and to optimize the
      enzymatic reaction, we investigated the influence of cofactors, ionic
      conditions, bases flanking the recognition sequence and enzyme
      concentration. We found that AdoMet is not necessary for DNA cleavage.
      Moreover, the presence of AdoMet dramatically impaired DNA cleavage due to
      competing DNA methylation. Sinefungin neither had an appreciable effect on
      DNA cleavage by EcoP15I nor compensated for the second recognition site.
      Moreover, we discovered that adenine stretches on the 5' or 3' side of
      CAGCAG led to preferred cleavage of this site. The length of the adenine
      stretch was pivotal and had to be different on the two sides for most
      efficient cleavage. In the absence of AdoMet and with enzyme in molar
      excess over recognition sites, we observed minor cleavage at two
      communicating DNA sites simultaneously. These results could also be
      exploited in the high-throughput, quantitative transcriptome analysis
      method SuperSAGE to optimize the crucial EcoP15I digestion step.
AU  - Moncke-Buchner E
AU  - Rothenberg M
AU  - Reich S
AU  - Wagenfuhr K
AU  - Matsumura H
AU  - Terauchi R
AU  - Kruger DH
AU  - Reuter M
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2009 387: 1309-1319.

PMID- 28481340
VI  - 49
DP  - 2017
TI  - Widespread adenine N6-methylation of active genes in fungi.
PG  - 964-968
AB  - N6-methyldeoxyadenine (6mA) is a noncanonical DNA base modification present at low levels in
      plant and animal genomes, but its prevalence and association with
      genome function in other eukaryotic lineages remains poorly understood. Here we
      report that abundant 6mA is associated with transcriptionally active genes in
      early-diverging fungal lineages. Using single-molecule long-read sequencing of 16
      diverse fungal genomes, we observed that up to 2.8% of all adenines were
      methylated in early-diverging fungi, far exceeding levels observed in other
      eukaryotes and more derived fungi. 6mA occurred symmetrically at ApT
      dinucleotides and was concentrated in dense methylated adenine clusters
      surrounding the transcriptional start sites of expressed genes; its distribution
      was inversely correlated with that of 5-methylcytosine. Our results show a
      striking contrast in the genomic distributions of 6mA and 5-methylcytosine and
      reinforce a distinct role for 6mA as a gene-expression-associated epigenomic mark
      in eukaryotes.
AU  - Mondo SJ et al
PT  - Journal Article
TA  - Nat. Genet.
JT  - Nat. Genet.
SO  - Nat. Genet. 2017 49: 964-968.

PMID- 26184872
VI  - 43
DP  - 2015
TI  - RNA aptamer inhibitors of a restriction endonuclease.
PG  - 7544-7555
AB  - Restriction endonucleases (REases) recognize and cleave short palindromic DNA sequences,
      protecting bacterial cells against bacteriophage infection by
      attacking foreign DNA. We are interested in the potential of folded RNA to mimic
      DNA, a concept that might be applied to inhibition of DNA-binding proteins. As a
      model system, we sought RNA aptamers against the REases BamHI, PacI and KpnI
      using systematic evolution of ligands by exponential enrichment (SELEX). After 20
      rounds of selection under different stringent conditions, we identified the 10
      most enriched RNA aptamers for each REase. Aptamers were screened for binding and
      specificity, and assayed for REase inhibition. We obtained eight high-affinity
      (Kd approximately 12-30 nM) selective competitive inhibitors (IC50 approximately
      20-150 nM) for KpnI. Predicted RNA secondary structures were confirmed by in-line
      attack assay and a 38-nt derivative of the best anti-KpnI aptamer was sufficient
      for inhibition. These competitive inhibitors presumably act as KpnI binding site
      analogs, but lack the primary consensus KpnI cleavage sequence and are not
      cleaved by KpnI, making their potential mode of DNA mimicry fascinating.
      Anti-REase RNA aptamers could have value in studies of REase mechanism and may
      give clues to a code for designing RNAs that competitively inhibit DNA binding
      proteins including transcription factors.
AU  - Mondragon E
AU  - Maher LJ III
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2015 43: 7544-7555.

PMID- 23969055
VI  - 1
DP  - 2013
TI  - Genome Sequence of the Quorum-Quenching Agrobacterium tumefaciens Strain WRT31.
PG  - e00653-13
AB  - Agrobacterium tumefaciens strain WRT31 is a quorum-sensing signal-degrading bacterium that has
      been isolated from the rhizosphere of tobacco plants. This
      strain belongs to A. tumefaciens genomovar G1, is avirulent on various putative
      host plants, devoid of Ti plasmid, and contains the blcC gene encoding a
      gamma-butyrolactonase.
AU  - Mondy S
AU  - Lalouche O
AU  - Dessaux Y
AU  - Faure D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00653-13.

PMID- 24092790
VI  - 1
DP  - 2013
TI  - Genome Sequence of the Quorum-Sensing-Signal-Producing Nonpathogen Agrobacterium  tumefaciens Strain P4.
PG  - e00798-13
AB  - Agrobacterium tumefaciens P4 is a quorum-sensing-signal-producing bacterium that  has been
      isolated from the tobacco rhizosphere. This strain belongs to
      genomospecies 1 of the A. tumefaciens complex; it is avirulent on various
      putative host plants, devoid of the Ti plasmid, and contains a luxI homolog on
      the At plasmid.
AU  - Mondy S
AU  - Lalouche O
AU  - Dessaux Y
AU  - Faure D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00798-13.

PMID- 18020376
VI  - 46
DP  - 2007
TI  - Probing the two-metal ion mechanism in the restriction endonuclease BamHI.
PG  - 14514-14523
AB  - The choreography of restriction endonuclease catalysis is a long-standing paradigm in
      molecular biology. Bivalent metal ions are
      required almost for all PD..D/ExK type enzymes, but the number of
      cofactors essential for the DNA backbone scission remained ambiguous.
      On the basis of crystal structures and biochemical data for various
      restriction enzymes, three models have been developed that assign
      critical roles for one, two, or three metal ions during the
      phosphodiester hydrolysis. To resolve this apparent controversy, we
      investigated the mechanism of BamHI catalysis using quantum
      mechanical/molecular mechanical simulation techniques and determined
      the activation barriers of three possible pathways that involve a
      Glu-113 or a neighboring water molecule as a general base or an
      external nucleophile that penetrated from bulk solution. The extrinsic
      mechanism was found to be the most favorable with an activation free
      energy of 23.4 kcal/mol, in reasonable agreement with the experimental
      data. On the basis of the effect of the individual metal ions on the
      activation barrier, metal ion A was concluded to be pivotal for the
      reaction, while the enzyme lacking metal ion B still has moderate
      efficiency. Thus, we propose that the catalytic scheme of BamHI does
      not involve a general base for nucleophile generation and requires one
      obligatory metal ion for catalysis that stabilizes the attacking
      nucleophile and coordinates it throughout the nucleophilic attack. Such
      a model may also explain the variation in the number of metal ions in
      the crystal structures and thus could serve as a framework for a
      unified catalytic scheme of type II restriction endonucleases.
AU  - Mones L
AU  - Kulhanek P
AU  - Florian J
AU  - Simon I
AU  - Fuxreiter M
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2007 46: 14514-14523.

PMID- 17214552
VI  - 388
DP  - 2007
TI  - Metal-binding sites at the active site of restriction endonuclease BamHI can conform to a one-ion mechanism.
PG  - 73-78
AB  - The number of metal ions required for phosphoryl transfer in restriction endonucleases is
      still an unresolved question in molecular
      biology. The two Ca2+ and Mn2+ ions observed in the pre- and
      post-reactive complexes of BamHI conform to the classical two-metal ion
      choreography. We probed the Mg2+ cofactor positions at the active site
      of BamHI by molecular dynamics simulations with one and two metal ions
      present and identified several catalytically relevant sites. These can
      mark the pathway of a single ion during catalysis, suggesting its
      critical role, while a regulatory function is proposed for a possible
      second ion.
AU  - Mones L
AU  - Simon I
AU  - Fuxreiter M
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 2007 388: 73-78.

PMID- 16330755
VI  - 102
DP  - 2005
TI  - The genome of Salinibacter ruber: Convergence and gene exchange among hyperhalophilic bacteria and archaea.
PG  - 18147-18152
AB  - Saturated thalassic brines are among the most physically demanding habitats on Earth: few
      microbes survive in them. Salinibacter ruber is among these organisms and has been found
      repeatedly in significant numbers in climax saltern crystallizer communities. The phenotype of
      this bacterium is remarkably similar to that of the hyperhalophilic Archaea (Haloarchaea). The
      genome sequence suggests that this resemblance has arisen through convergence at the
      physiological level (different genes producing similar overall phenotype) and the molecular
      level (independent mutations yielding similar sequences or structures). Several genes and gene
      clusters also derive by lateral transfer from (or may have been laterally transferred to)
      haloarchaea. S. ruber encodes four rhodopsins. One resembles bacterial proteorhodopsins and
      three are of the haloarchaeal type, previously uncharacterized in a bacterial genome. The
      impact of these modular adaptive elements on the cell biology and ecology of S. ruber is
      substantial, affecting salt adaptation, bioenergetics, and photobiology.
AU  - Mongodin EF et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2005 102: 18147-18152.

PMID- 28983003
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of a Strain of Bifidobacterium pseudolongum Isolated from Mouse Feces and Associated with Improved Organ Transplant Outcome.
PG  - e01089-17
AB  - Here, we report the complete genome sequence of Bifidobacterium pseudolongum strain
      UMB-MBP-01, isolated from the feces of C57BL/6J mice. This strain was
      identified in microbiome profiling studies and associated with improved
      transplant outcome in a murine model of cardiac heterotypic transplantation.
AU  - Mongodin EF
AU  - Hittle LL
AU  - Nadendla S
AU  - Brinkman CC
AU  - Xiong Y
AU  - Bromberg JS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01089-17.

PMID- 17194220
VI  - 2
DP  - 2006
TI  - Secrets of Soil Survival Revealed by the Genome Sequence of Arthrobacter aurescens TC1.
PG  - e214
AB  - Arthrobacter sp. strains are among the most frequently isolated, indigenous, aerobic bacterial
      genera found in soils. Member of the genus are metabolically and ecologically diverse and have
      the ability to survive in environmentally harsh conditions for extended periods of time. The
      genome of Arthrobacter aurescens strain TC1, which was originally isolated from soil at an
      atrazine spill site, is composed of a single 4,597,686 basepair (bp) circular chromosome and
      two circular plasmids, pTC1 and pTC2, which are 408,237 bp and 300,725 bp, respectively. Over
      66% of the 4,702 open reading frames (ORFs) present in the TC1 genome could be assigned a
      putative function, and 13.2% (623 genes) appear to be unique to this bacterium, suggesting
      niche specialization. The genome of TC1 is most similar to that of Tropheryma, Leifsonia,
      Streptomyces, and Corynebacterium glutamicum, and analyses suggest that A. aurescens TC1 has
      expanded its metabolic abilities by relying on the duplication of catabolic genes and by
      funneling metabolic intermediates generated by plasmid-borne genes to chromosomally encoded
      pathways. The data presented here suggest that Arthrobacter's environmental prevalence may be
      due to its ability to survive under stressful conditions induced by starvation, ionizing
      radiation, oxygen radicals, and toxic chemicals.
AU  - Mongodin EF
AU  - Shapir N
AU  - Daugherty SC
AU  - DeBoy RT
AU  - Emerson JB
AU  - Shvartsbeyn A
AU  - Radune D
AU  - Vamathevan J
AU  - Riggs F
AU  - Grinberg V
AU  - Khouri HM
AU  - Wackett LP
AU  - Nelson KE
AU  - Sadowsky MJ
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2006 2: e214.

PMID- 25035289
VI  - 466-467
DP  - 2014
TI  - Genome of brown tide virus (AaV), the little giant of the Megaviridae, elucidates NCLDV genome expansion and host-virus coevolution.
PG  - 60-70
AB  - Aureococcus anophagefferens causes economically and ecologically destructive
      "brown tides" in the United States, China and South Africa. Here we report the
      370,920bp genomic sequence of AaV, a virus capable of infecting and lysing A.
      anophagefferens. AaV is a member of the nucleocytoplasmic large DNA virus (NCLDV)
      group, harboring 377 putative coding sequences and 8 tRNAs. Despite being an
      algal virus, AaV shows no phylogenetic affinity to the Phycodnaviridae family, to
      which most algae-infecting viruses belong. Core gene phylogenies, shared gene
      content and genome-wide similarities suggest AaV is the smallest member of the
      emerging clade "Megaviridae". The genomic architecture of AaV demonstrates that
      the ancestral virus had an even smaller genome, which expanded through gene
      duplication and assimilation of genes from diverse sources including the host
      itself - some of which probably modulate important host processes. AaV also
      harbors a number of genes exclusive to phycodnaviruses - reinforcing the
      hypothesis that Phycodna- and Mimiviridae share a common ancestor.
AU  - Moniruzzaman M
AU  - LeCleir GR
AU  - Brown CM
AU  - Gobler CJ
AU  - Bidle KD
AU  - Wilson WH
AU  - Wilhelm SW
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 2014 466-467: 60-70.

PMID- 22919640
VI  - 2
DP  - 2012
TI  - Genetic manipulation of Staphylococci-breaking through the barrier.
PG  - 49
AB  - Most strains of Staphylococcus aureus and Staphylococcus epidermidis possess a strong
      restriction barrier that hinders exchange of DNA. Recently, major advances have been made in
      identifying and characterizing the restriction-modification (RM) systems involved. In
      particular a novel type IV restriction enzyme that recognizes cytosine methylated DNA has been
      shown to be the major barrier to transfer of plasmid DNA from Escherichia coli into S. aureus
      and S. epidermidis. While the conserved type I RM system provides a further barrier. Here we
      review the recent advances in understanding of restriction systems in staphylococci and
      highlight how this has been exploited to improve our ability to manipulate genetically
      previously untransformable strains.
AU  - Monk IR
AU  - Foster TJ
PT  - Journal Article
TA  - Front Cell Infect Microbiol
JT  - Front Cell Infect Microbiol
SO  - Front Cell Infect Microbiol 2012 2: 49.

PMID- 22434850
VI  - 3
DP  - 2012
TI  - Transforming the Untransformable: Application of Direct Transformation To Manipulate Genetically Staphylococcus aureus and Staphylococcus epidermidis.
PG  - e00277
AB  - The strong restriction barrier present in Staphylococcus aureus and Staphylococcus epidermidis
      has limited functional genomic analysis to a
      small subset of strains that are amenable to genetic manipulation.
      Recently, a conserved type IV restriction system termed SauUSI (which
      specifically recognizes cytosine methylated DNA) was identified as the
      major barrier to transformation with foreign DNA. Here we have
      independently corroborated these findings in a widely used laboratory
      strain of S. aureus. Additionally, we have constructed a DNA cytosine
      methyltransferase mutant in the high-efficiency Escherichia coli
      cloning strain DH10B (called DC10B). Plasmids isolated from DC10B can
      be directly transformed into clinical isolates of S. aureus and S.
      epidermidis. We also show that the loss of restriction (both type I and
      IV) in an S. aureus USA300 strain does not have an impact on virulence.
      Circumventing the SauUSI restriction barrier, combined with an improved
      deletion and transformation protocol, has allowed the genetic
      manipulation of previously untransformable strains of these important
      opportunistic pathogens.
      IMPORTANCE Staphylococcal infections place a huge burden on the
      health care sector due both to their severity and also to the economic
      impact of treating the infections because of prolonged hospitalization.
      To improve the understanding of Staphylococcus aureus and
      Staphylococcus epidermidis infections, we have developed a series of
      improved techniques that allow the genetic manipulation of strains that
      were previously refractory to transformation. These developments will
      speed up the process of mutant construction and increase our
      understanding of these species as a whole, rather than just a small
      subset of strains that could previously be manipulated.
AU  - Monk IR
AU  - Shah IM
AU  - Xu M
AU  - Tan MW
AU  - Foster TJ
PT  - Journal Article
TA  - MBio
JT  - MBio
SO  - MBio 2012 3: e00277.

PMID- 26015493
VI  - 6
DP  - 2015
TI  - Complete Bypass of Restriction Systems for Major Staphylococcus aureus Lineages.
PG  - e00308-15
AB  - Staphylococcus aureus is a prominent global nosocomial and community-acquired bacterial
      pathogen. A strong restriction barrier presents a major hurdle for the
      introduction of recombinant DNA into clinical isolates of S. aureus. Here, we
      describe the construction and characterization of the IMXXB series of Escherichia
      coli strains that mimic the type I adenine methylation profiles of S. aureus
      clonal complexes 1, 8, 30, and ST93. The IMXXB strains enable direct,
      high-efficiency transformation and streamlined genetic manipulation of major S.
      aureus lineages. IMPORTANCE: The genetic manipulation of clinical S. aureus
      isolates has been hampered due to the presence of restriction modification
      barriers that detect and subsequently degrade inappropriately methylated DNA.
      Current methods allow the introduction of plasmid DNA into a limited subset of S.
      aureus strains at high efficiency after passage of plasmid DNA through the
      restriction-negative, modification-proficient strain RN4220. Here, we have
      constructed and validated a suite of E. coli strains that mimic the adenine
      methylation profiles of different clonal complexes and show high-efficiency
      plasmid DNA transfer. The ability to bypass RN4220 will reduce the cost and time
      involved for plasmid transfer into S. aureus. The IMXXB series of E. coli strains
      should expedite the process of mutant construction in diverse genetic backgrounds
      and allow the application of new techniques to the genetic manipulation of S.
      aureus.
AU  - Monk IR
AU  - Tree JJ
AU  - Howden BP
AU  - Stinear TP
AU  - Foster TJ
PT  - Journal Article
TA  - MBio
JT  - MBio
SO  - MBio 2015 6: e00308-15.

PMID- 10082660
VI  - 255
DP  - 1999
TI  - Generation of highly site-specific DNA double-strand breaks in human cells by the homing endonucleases I-PpoI and I-CreI.
PG  - 88-93
AB  - We have determined the ability of two well-characterized eukaryotic homing endonucleases,
      I-PpoI from the myxomycete Physarum polycephalum and I-CreI from the green alga Chlamydomonas
      reinhardtii, to generate site-specific DNA double-strand breaks in human cells. These 18-kDa
      proteins cleave highly conserved 15- or 24-bp rDNA homing sites in their respective hosts to
      generate homogeneous 4-base, 3' ends that initiate target intron transposition or "homing."
      We show that both endonucleases can be expressed in human cells and can generate site-specific
      DNA double-strand breaks in 28S rDNA and homing site plasmids. These endonuclease-induced
      breaks can be repaired in vivo, although break repair is mutagenic with the frequent
      generation of short deletions or insertions. I-PpoI and I-CreI should be useful for analyzing
      DNA double-strand break repair in human cells and rDNA.
AU  - Monnat RJ Jr
AU  - Hackmann AFM
AU  - Cantrell MA
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1999 255: 88-93.

PMID- 10512041
VI  - 69
DP  - 1999
TI  - Comparative analysis of the lppA locus in Mycoplasma capricolum subsp. capricolum and Mycoplasma capricolum subsp. capripneumoniae.
PG  - 157-172
AB  - The lppA gene, encoding the lipoprotein named LppA[Mcaca] was characterised in Mycoplasma
      capricolum subsp. capricolum.  It encodes a lipoprotein with an apparent molecular mass of 57
      kDa as determined by SDS-PAGE. Using antibodies directed against recombinant LppA[Mcaca], we
      showed the expression of this lipoprotein in all M. capricolum subsp. capricolum by immunoblot
      analysis. The serum did not cross-react with other members of the Mycoplasma mycoides cluster,
      hence showing that LppA[Mcaca] was antigenically specific to M. capricolum subsp. capricolum.
      The lppA gene was conserved within the subspecies and was used for the development of a
      specific PCR assay for the identification of M. capricolum subsp. capricolum.
      The taxonomically related Mycoplasma capricolum subsp. capripneumoniae (F38) was found to
      contain an lppA-pseudo-gene.  It showed high similarity to functional lppA genes of other
      mycoplasmas in the M. mycoides cluster. However, it contained interrupted open reading frames.
      Moreover, the nucleotide sequence of the lppA pseudo-genes in different strains of M.
      capricolum subsp. capripneumoniae were quite variable. Interestingly, the lppA pseudo-gene had
      a size similar to that of the functional lppA genes of other mycoplasmas of the M. mycoides
      cluster and occupied the same genomic location as the latter ones in the vicinity of the mtlD
      genes. This study showed that all members of the M. mycoides cluster contain each a species-,
      subspecies- respectively type- specific lppA gene analogue which encodes a lipoprotein that
      has structural and functional relationship to the surface lipoprotein LppA [MmymySC],
      previously named P72, of M. mycoides subsp mycoides SC, with the exceptionof M. capricolum
      subsp. capripneumoniae which seems not to express an LppA analogue.
AU  - Monnerat M-P
AU  - Thiaucourt F
AU  - Nicolet J
AU  - Frey J
PT  - Journal Article
TA  - Vet. Microbiol.
JT  - Vet. Microbiol.
SO  - Vet. Microbiol. 1999 69: 157-172.

PMID- 10066658
VI  - 6
DP  - 1999
TI  - Genetic and serological analysis of lipoprotein LppA in Mycoplasma mycoides subsp. mycoides LC and Mycoplasma mycoides subsp. capri.
PG  - 224-230
AB  - The genes encoding the 62-kDa lipoproteins from the Mycoplasma mycoides subsp. mycoides
      large-colony type (LC) strain Y-goat and the M. mycoides subsp. capri strain PG3 were cloned
      and analyzed by sequencing. These two lipoproteins have been named LppA[MmymyLC] and
      LppA[Mmyca], and their corresponding genes have been named lppA[MmymyLC] and lppA[Mmyca],
      respectively. The nucleotide and deduced amino acid sequences of these two lipoproteins showed
      a very high degree of similarity between these two mycoplasmas. Given the sequence data,
      LppA seems to fulfill the same structural functions as the previously described major
      lipoproteins P72 of M. mycoides subsp. mycoides small-colony type and P67 of the Mycoplasma
      species bovine group 7. Based on lppA gene sequences of M. mycoides subsp. mycoides LC and M.
      mycoides subsp. capri type strains, a specific PCR assay was developed so that it amplified
      this gene in all field strains of the two species analyzed in this study but not in the other
      members of the M. mycoides cluster. Analysis of the PCR-amplified lppA genes with frequently
      cutting restriction
      enzymes showed a certain degree of genetic variability which, however, did not cluster the two
      subspecies. This PCR therefore allows a rapid identification of M. mycoides subsp. mycoides LC
      and M. mycoides subsp. capri but does not distinguish between these two closely related
      subspecies. LppA was expressed in Escherichia coli K-12 and used for the production of
      polyclonal mouse antiserum. Antibodies against recombinant LppA[MmymyLC] reacted with a 62 kDa
      protein in all M. mycoides subsp. mycoides LC and M. mycoides subsp. capri type strains and
      field strains tested but not with the other members of the M. mycoides cluster, thus showing
      the antigenic specificity of LppA and further supporting the concept that a close relationship
      exists between these two mycoplasmas.
AU  - Monnerat MP
AU  - Thiaucourt F
AU  - Poveda JB
AU  - Nicolet J
AU  - Frey J
PT  - Journal Article
TA  - Clin. Diagn. Lab. Immunol.
JT  - Clin. Diagn. Lab. Immunol.
SO  - Clin. Diagn. Lab. Immunol. 1999 6: 224-230.

PMID- 22247534
VI  - 194
DP  - 2012
TI  - Genome Sequence of Corynebacterium casei UCMA 3821, Isolated from a Smear-Ripened Cheese.
PG  - 738-739
AB  - Corynebacterium casei is one of the most prevalent species present on the surfaces of
      smear-ripened cheeses, where it contributes to the production
      of the desired organoleptic properties. Here, we report the draft genome
      sequence of Corynebacterium casei UCMA 3821 to provide insights into its
      physiology.
AU  - Monnet C
AU  - Loux V
AU  - Bento P
AU  - Gibrat JF
AU  - Straub C
AU  - Bonnarme P
AU  - Landaud S
AU  - Irlinger F
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 738-739.

PMID- 29954908
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Vibrio harveyi Strain GAN1709, Isolated from Diseased Greater Amberjack (Seriola dumerili) Farmed in Japan.
PG  - e00611-18
AB  - Vibrio harveyi strain GAN1709 was isolated from a diseased greater amberjack farmed in Nomi
      Bay, Japan. Here, we report the draft genome sequence of this
      strain, which comprises 6,265,473 bp, with a G+C content of 44.8%.
AU  - Monno S
AU  - Sugiura H
AU  - Yamashita H
AU  - Kato Y
AU  - Morimitu K
AU  - Imajoh M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00611-18.

PMID- 25059868
VI  - 2
DP  - 2014
TI  - Genome Sequences of Cupriavidus metallidurans Strains NA1, NA4, and NE12, Isolated from Space Equipment.
PG  - e00719-14
AB  - Cupriavidus metallidurans NA1, NA4, and NE12 were isolated from space and
      spacecraft-associated environments. Here, we report their draft genome sequences
      with the aim of gaining insight into their potential to adapt to these
      environments.
AU  - Monsieurs P
AU  - Mijnendonckx K
AU  - Provoost A
AU  - Venkateswaran K
AU  - Ott CM
AU  - Leys N
AU  - Van Houdt R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00719-14.

PMID- 25189592
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Ralstonia pickettii Strains SSH4 and CW2, Isolated from Space Equipment.
PG  - e00887-14
AB  - Ralstonia pickettii SSH4 and CW2 were isolated from space equipment. Here, we report their
      draft genome sequences with the aim of gaining insight into their
      potential to adapt to these environments.
AU  - Monsieurs P
AU  - Mijnendonckx K
AU  - Provoost A
AU  - Venkateswaran K
AU  - Ott CM
AU  - Leys N
AU  - Van Houdt R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00887-14.

PMID- 24336383
VI  - 1
DP  - 2013
TI  - Genome Sequence of Cupriavidus metallidurans Strain H1130, Isolated from an Invasive Human Infection.
PG  - e01051-13
AB  - Cupriavidus metallidurans H1130 was repeatedly isolated from different blood culture sets
      taken from a patient suffering from significant nosocomial
      septicemia. Here, we announce the H1130 genome sequence for use in comparative
      analyses and for exploring the adaptation and pathogenic potential of this
      bacterium.
AU  - Monsieurs P
AU  - Provoost A
AU  - Mijnendonckx K
AU  - Leys N
AU  - Gaudreau C
AU  - Van Houdt R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01051-13.

PMID- 28596406
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Enterobacter cloacae Strains CAPREx E7 and CAPREx E2-2.
PG  - e00488-17
AB  - Enterobacter cloacae strains CAPREx E7 and CAPREx E2-2 were isolated from Ghanaian yams at a
      London market. The draft genome sequences indicate that the
      two strains are similar, with genomes of 5,042,838 and 5,039,930 bp and 56.19%
      and 55.05% G+C content, respectively. Both strains encoded three different
      beta-lactamases, including one of the AmpC family.
AU  - Monson RE
AU  - Honger J
AU  - Rawlinson A
AU  - Salmond GPC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00488-17.

PMID- 28522705
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Colistin-Resistant MCR-1-Producing Escherichia coli ST1850 and ST74 Strains Isolated from Commercial Chicken Meat.
PG  - e00329-17
AB  - We present here the draft genome sequences of two colistin-resistant mcr-1-carrying
      Escherichia coli strains belonging to sequence type 74 (ST74) and
      ST1850, isolated from commercial chicken meat in Brazil. Assembly of this draft
      genome resulted in 5,022,083 and 4,950,681 bp, respectively, revealing the
      presence of the IncX4 plasmid-mediated mcr-1 gene responsible for resistance to
      colistin.
AU  - Monte DF
AU  - Fernandes MR
AU  - Cerdeira L
AU  - de Souza TA
AU  - Mem A
AU  - Franco BDGM
AU  - Landgraf M
AU  - Lincopan N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00329-17.

PMID- 30533911
VI  - 7
DP  - 2018
TI  - Complete Genome Sequence of Rhizobium sp. Strain 11515TR, Isolated from Tomato Rhizosphere in the Philippines.
PG  - e00903-18
AB  - Rhizobium sp. strain 11515TR was isolated from the rhizosphere of tomato in Laguna,
      Philippines. The 7.07-Mb complete genome comprises three replicons, one
      chromosome, and two plasmids, with a G+C content of 59.4% and 6,720
      protein-coding genes. The genome encodes gene clusters supporting rhizosphere
      processes, plant symbiosis, and secondary bioactive metabolites.
AU  - Montecillo AD
AU  - Raymundo AK
AU  - Papa IA
AU  - Aquino GMB
AU  - Rosana ARR
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e00903-18.

PMID- 10666469
VI  - 28
DP  - 2000
TI  - Purification and characterization of the DNA cleavage and recognition site of I-ScaI mitochondrial group I intron encoded endonuclease produced in Escherichia coli.
PG  - 1245-1251
AB  - The second intron in the mitochondrial cytb gene of Saccharomyces capensis, belonging to group
      I, encodes a 280 amino acid protein containing two LAGLIDADG motifs. Genetic and molecular
      studies have previously shown that this protein has a dual function in the wild-type strain.
      It acts as a specific homing endonuclease I-ScaI promoting intron mobility and as a maturase
      promoting intron splicing. Here we describe the synthesis of a universal code equivalent to
      the mitochondrial sequence coding for this protein and the in vitro characterization of I-ScaI
      endonuclease activity, using a truncated mutant form of the protein p28bi2 produced in
      Escherichia coli. We have also determined the cleavage pattern as well as the recognition site
      of p28bi2. It was found that p28bi2 generates a double-strand cleavage downstream from the
      intron insertion site with 4 nt long 3'-overhangs. Mutational analysis of the DNA target site
      shows that p28bi2 recognizes a 16-19 bp sequence from positions -11 to +8 with respect to the
      intron insertion site.
AU  - Monteilhet C
AU  - Dziadkowiec D
AU  - Szczepanek T
AU  - Lazowska J
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2000 28: 1245-1251.

PMID- 2183191
VI  - 18
DP  - 1990
TI  - Purification and characterization of the in vitro activity of I-Sce I, a novel and highly specific endonuclease encoded by a group I intron.
PG  - 1407-1413
AB  - Group I intron encoded proteins represent a novel class of site specific double
      strand endonucleases.  The endonuclease activity of this class of proteins has
      been first demonstrated in vivo for I-Sce I which is encoded  by a
      mitochondrial intron of Saccharomyces cerevisiae.  Assays using crude cell
      extracts have shown that I-Sce I can be used in vitro as a restriction
      endonuclease potentially useful for recombinant DNA technology owing to its
      large recognition sequence (18 nucleotides).  We report here the purification
      and the first detailed analysis of the in vitro activity and properties of
      I-Sce I.
AU  - Monteilhet C
AU  - Perrin A
AU  - Thierry A
AU  - Colleaux L
AU  - Dujon B
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 1407-1413.

PMID- 15305603
VI  - 17
DP  - 2004
TI  - The genome sequence of the gram-positive sugarcane pathogen Leifsonia xyli subsp. xyli.
PG  - 827-836
AB  - The genome sequence of Leifsonia xyli subsp. xyli, which causes ratoon stunting disease and
      affects sugarcane worldwide, was determined. The
      single circular chromosome of Leifsonia xyli subsp. xyli CTCB07 was 2.6 Mb
      in length with a GC content of 68% and 2,044 predicted open reading
      frames. The analysis also revealed 307 predicted pseudogenes, which is
      more than any bacterial plant pathogen sequenced to date. Many of these
      pseudogenes, if functional, would likely be involved in the degradation of
      plant heteropolysaccharides, uptake of free sugars, and synthesis of amino
      acids. Although L. xyli subsp. xyli has only been identified colonizing
      the xylem vessels of sugarcane, the numbers of predicted regulatory genes
      and sugar transporters are similar to those in free-living organisms. Some
      of the predicted pathogenicity genes appear to have been acquired by
      lateral transfer and include genes for cellulase, pectinase, wilt-inducing
      protein, lysozyme, and desaturase. The presence of the latter may
      contribute to stunting, since it is likely involved in the synthesis of
      abscisic acid, a hormone that arrests growth. Our findings are consistent
      with the nutritionally fastidious behavior exhibited by L. xyli subsp.
      xyli and suggest an ongoing adaptation to the restricted ecological niche
      it inhabits.
AU  - Monteiro-Vitorello CB et al
PT  - Journal Article
TA  - Mol. Plant Microbe Interact.
JT  - Mol. Plant Microbe Interact.
SO  - Mol. Plant Microbe Interact. 2004 17: 827-836.

PMID- 24201198
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Leifsonia xyli subsp. cynodontis Strain DSM46306, a Gram-Positive Bacterial Pathogen of Grasses.
PG  - e00915-13
AB  - We announce the complete genome sequence of Leifsonia xyli subsp. cynodontis, a vascular
      pathogen of Bermuda grass. The species also comprises Leifsonia xyli
      subsp. xyli, a sugarcane pathogen. Since these two subspecies have genome
      sequences available, a comparative analysis will contribute to our understanding
      of the differences in their biology and host specificity.
AU  - Monteiro-Vitorello CB
AU  - Zerillo MM
AU  - Van Sluys MA
AU  - Camargo LE
AU  - Kitajima JP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00915-13.

PMID- 6222239
VI  - 189
DP  - 1983
TI  - Restriction and modification in Bacillus subtilis:  expression of the cloned methyltransferase gene from B. subtilis phage SPR in E. coli and B. subtilis.
PG  - 17-20
AB  - Expression of the SPR methyltransferase gene from B. subtilis phage SPR cloned
      into lambda and SPP1 was studied by analyzing the sensitivity of the hybrid
      phage DNAs to restriction by the enzymes HaeIII, MspI, and HpaII.  The
      following results were obtained:  (1) The genes were expressed both in the
      homologous (B. subtilis) and heterologous (E. coli) host. (2) The specificity
      of the expression of the cloned gene was identical to that of the gene in SPR.
      (3) Expression depended on the orientation of the cloned segment within the
      vector DNAs suggesting that vector promoters were involved in transcription.
      The coding strand of the cloned DNA was identified through hybridization with
      SPR mRNA.
AU  - Montenegro MA
AU  - Pawlek B
AU  - Behrens B
AU  - Trautner TA
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1983 189: 17-20.

PMID- 27777646
VI  - 11
DP  - 2016
TI  - A draft genome sequence of Pseudomonas veronii R4: a grapevine (Vitis vinifera L.) root-associated strain with high biocontrol potential.
PG  - 76
AB  - A new plant commensal Pseudomonas veronii isolate (strain R4) was identified from a Xiphinema
      index biocontrol screen. Isolated from grapevine roots from vineyards
      in central Chile, the strain R4 exhibited a slower yet equivalently effective
      nematicide activity as the well-characterized P. protegens CHA0. Whole genome
      sequencing of strain R4 and comparative analysis among the available Pseudomonas
      spp. genomes allowed for the identification of gene clusters that encode putative
      extracellular proteases and lipase synthesis and secretion systems, which are
      proposed to mediate-at least in part-the observed nematicidal activity. In
      addition, R4 strain presented relevant gene clusters related to metal tolerance,
      which is typical in P. veronii. Bioinformatics analyses also showed gene clusters
      associated with plant growth promoting activity, such as indole-3-acetic acid
      synthesis. In addition, the strain R4 genome presented a metabolic gene clusters
      associated with phosphate and ammonia biotransformation from soil, which could
      improve their availability for plants.
AU  - Montes C
AU  - Altimira F
AU  - Canchignia H
AU  - Castro A
AU  - Sanchez E
AU  - Miccono M
AU  - Tapia E
AU  - Sequeida A
AU  - Valdes J
AU  - Tapia P
AU  - Gonzalez C
AU  - Prieto H
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 76.

PMID- 25676753
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Bacillus amyloliquefaciens JJC33M, Isolated from Sugarcane Soils in the Papaloapan Region, Mexico.
PG  - e01519-14
AB  - Bacillus amyloliquefaciens strain JJC33M is a bacterium that produces alpha-amylase (EC
      3.2.1.1) and was isolated from sugarcane soil. Its estimated
      genome size is 3.96 Mb, and it harbors 4,048 coding genes (CDSs).
AU  - Montor-Antonio JJ
AU  - Sachman-Ruiz B
AU  - Lozano L
AU  - Del Moral S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01519-14.

PMID- 23516230
VI  - 1
DP  - 2013
TI  - Genome Sequence of Staphylococcus pseudintermedius Strain E140, an ST71 European-Associated Methicillin-Resistant Isolate.
PG  - e0020712
AB  - We report the first genome sequence of the methicillin-resistant Staphylococcus
      pseudintermedius (MRSP) strain E140, isolated from a canine bite wound infection
      in Denmark. This strain represents the dominant clonal lineage associated with
      canine MRSP infections in Europe.
AU  - Moodley A
AU  - Riley MC
AU  - Kania SA
AU  - Guardabassi L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0020712.

PMID- Not carried by PubMed...
VI  - 17
DP  - 1996
TI  - Synthesis and characterization of dodecanucleotides containing the XhoI recognition sequence with a phosphorothioate group at the cleavage site.
PG  - 1031-1036
AB  - The synthesis and characterization of diastereomeric dodecanucleotides, d[GATCp(s)TCGAGATC],
      containing the recognition sequence of the XhoI restriction endonuclease with a
      phosphorothioate internucleotidic linkage at the cleavage sites are described.  Rp and Sp
      forms of each diastereomerically pure dinucleoside phosphorothioates d[Cp(S)T] were
      presynthesized and used for the addition to the growing oligonucleotide chain as a block.  The
      stereochemistry of dinucleoside phosphorothioate was assigned by 31P NMR spectroscopy, enzyme
      digestion, and reverse-phase HPLC.  XhoI restriction endonuclease cuts only theRp diastereomer
      d[GATCp(s)TCGAGATC].  The rate of hydrolysis is slower than that of the unmodified dodecamer
      d[GATCTCGAGATC].  The phosphorothioate nucleotide is used for determination of the
      stereochemical course of the XhoI catalyzed reaction.
AU  - Moon BJ
AU  - Kim SK
AU  - Kim NH
AU  - Kwon OS
PT  - Journal Article
TA  - Bull. Korean Chem. Soc.
JT  - Bull. Korean Chem. Soc.
SO  - Bull. Korean Chem. Soc. 1996 17: 1031-1036.

PMID- Not carried by PubMed...
VI  - 29
DP  - 1996
TI  - Site-directed mutagenesis studies with restriction endonuclease EcoRV to identify the role of Ile91 in recognition and catalysis.
PG  - 99-104
AB  - Site-directed substitutions were made to change the Ile91 of restriction endonuclease EcoRV to
      either Val, Ala or Gly to identify the role of Ile91 in recognition and catalysis, since
      substitution of Ile91 with Leu afforded dramatic effects on the activity and properties of
      restriction endonuclease EcoRV.  These changes alter the size of the hydrophobic side chain at
      position 91 and thus might have revealed the reason for the altered phenotype of Ile91 Leu.
      However, the properties of Ile91Val and Ile91Ala mutants were much like wild type EcoRV, in
      both activity and metal ion preference.  Ile91Gly had very little activity with either Mg2+ or
      Mn2- as cofactors.  To try to understand the unusual Mn2+ profile of the Ile91Leu mutant, two
      double mutants, Ile91Leu;Asp90Asn and Ile91Leu;Glu45Met were created.  Both double mutants
      were seriously disabled by the second amino acid change. Ile91Leu;Glu45Met had some residual
      activity in the Mn2+ reaction buffer, whereas the Ile91Leu;Asp90Asn displayed no detectable
      activity.
AU  - Moon BJ
AU  - Vipond IB
AU  - Halford SE
PT  - Journal Article
TA  - J. Biochem. Mol. Biol.
JT  - J. Biochem. Mol. Biol.
SO  - J. Biochem. Mol. Biol. 1996 29: 99-104.

PMID- Not carried by PubMed...
VI  - 29
DP  - 1996
TI  - Site-directed mutagenesis of Ile91 of restriction endonuclease EcoRV: Dramatic consequences on the activity and the properties of the enzyme.
PG  - 17-21
AB  - Ile91 of restriction endonuclease EcoRV, which has not been known to take part directly in
      catalytic activity, was substituted with Leu by site-directed mutagenesis.  The Ile91Leu
      mutant shows over 1000-fold less activity than the wild type EcoRV under standard reaction
      condition.  The metal ion dependency of the reaction was altered.  In contrast to the wild
      type EcoRV, the mutant prefers Mn2+ to Mg2+ as the cofactor.  In Mn2+ buffer the mutant is as
      active as the wild type enzyme in Mg2+ buffer.  Like the wild type enzyme, the mutant shows an
      unspecific binding of DNA in gel shift experiments.  In contrast to the wild type enzyme, the
      mutant did not cleave at noncognate sites of DNA under star condition.  Note: this paper was
      published without Dr. S. Halford's knowledge.
AU  - Moon BJ
AU  - Vipond IB
AU  - Halford SE
PT  - Journal Article
TA  - J. Biochem. Mol. Biol.
JT  - J. Biochem. Mol. Biol.
SO  - J. Biochem. Mol. Biol. 1996 29: 17-21.

PMID- 26950323
VI  - 4
DP  - 2016
TI  - Genome Sequence of a Unique t2247-ST692-III Livestock-Associated Methicillin-Resistant Staphylococcus aureus Strain from Chicken Carcass.
PG  - e00026-16
AB  - We report the draft genome sequence of a novel livestock-associated t2247-ST692-III
      methicillin-resistant Staphylococcus aureus strain designated
      K12S0375, which was isolated from a chicken carcass in South Korea. The K12S0375
      strain contains uncommon genes, including antimicrobial resistance genes (tetL
      and tetS) and leukotoxin (lukED), and the genomic distance indicates a single
      lineage in a genome-based phylogenetic tree compared with 459 S. aureus genome
      sequences. This genome sequence will contribute to understanding epidemiological
      and genomic features of the ST692 lineage, including antimicrobial resistance and
      virulence genes.
AU  - Moon DC
AU  - Kim BY
AU  - Tamang MD
AU  - Nam HM
AU  - Jang GC
AU  - Jung SC
AU  - Lee HS
AU  - Park YH
AU  - Lim SK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00026-16.

PMID- 18793728
VI  - 62
DP  - 2008
TI  - Recombinant expression, purification, and characterization of XorKII: A restriction endonuclease from Xanthomonas oryzae pv. oryzae.
PG  - 230-234
AB  - An endonuclease from Xanthomonas oryzae pathovar oryzae (Xoo) KACC10331, XorKII, was
      recombinantlyproduced in Escherichia coli by applying the stationary state induction method,
      which was necessary toprevent the unwanted lysis of E. coli cells. XorKII was purified by
      immobilized metal affinity chromatographyon an FPLC system. The yield was 3.5 mg of XorKII per
      liter of LB medium. The purified recombinantXorKII showed that it recognized and cleaved to
      the same site as PstI. It behaved as a dimer as evidenced
      by the size exclusion chromatography. The specific activity of the purified XorKII was
      determined to be31,300 U/mg. The enzyme activity was monitored by cleaving lambda DNA or YEp24
      plasmid as substrates. The enzyme was the most active at 10 mM Tris-HCl pH 7.0, 10 mM MgCl2, 1
      mM dithiothreitol
      at 37 oC. XorKII was easily inactivated by heating at 65 oC for 5 min, but retained most of
      the original activity after incubation at 37oC for 24 h.
AU  - Moon WJ
AU  - Cho J-Y
AU  - Chae YK
PT  - Journal Article
TA  - Protein Expr. Purif.
JT  - Protein Expr. Purif.
SO  - Protein Expr. Purif. 2008 62: 230-234.

PMID- 24236055
VI  - 8
DP  - 2013
TI  - Pediatric fecal microbiota harbor diverse and novel antibiotic resistance genes.
PG  - E78822
AB  - Emerging antibiotic resistance threatens human health. Gut microbes are an
      epidemiologically important reservoir of resistance genes (resistome), yet prior
      studies indicate that the true diversity of gut-associated resistomes has been
      underestimated. To deeply characterize the pediatric gut-associated resistome, we
      created metagenomic recombinant libraries in an Escherichia coli host using fecal
      DNA from 22 healthy infants and children (most without recent antibiotic
      exposure), and performed functional selections for resistance to 18 antibiotics
      from eight drug classes. Resistance-conferring DNA fragments were sequenced
      (Illumina HiSeq 2000), and reads assembled and annotated with the PARFuMS
      computational pipeline. Resistance to 14 of the 18 antibiotics was found in
      stools of infants and children. Recovered genes included chloramphenicol
      acetyltransferases, drug-resistant dihydrofolate reductases, rRNA
      methyltransferases, transcriptional regulators, multidrug efflux pumps, and every
      major class of beta-lactamase, aminoglycoside-modifying enzyme, and tetracycline
      resistance protein. Many resistance-conferring sequences were mobilizable; some
      had low identity to any known organism, emphasizing cryptic organisms as
      potentially important resistance reservoirs. We functionally confirmed three
      novel resistance genes, including a 16S rRNA methylase conferring aminoglycoside
      resistance, and two tetracycline-resistance proteins nearly identical to a
      bifidobacterial MFS transporter (B. longum s. longum JDM301). We provide the
      first report to our knowledge of resistance to folate-synthesis inhibitors
      conferred by a predicted Nudix hydrolase (part of the folate synthesis pathway).
      This functional metagenomic survey of gut-associated resistomes, the largest of
      its kind to date, demonstrates that fecal resistomes of healthy children are far
      more diverse than previously suspected, that clinically relevant resistance genes
      are present even without recent selective antibiotic pressure in the human host,
      and that cryptic gut microbes are an important resistance reservoir. The observed
      transferability of gut-associated resistance genes to a gram-negative (E. coli)
      host also suggests that the potential for gut-associated resistomes to threaten
      human health by mediating antibiotic resistance in pathogens warrants further
      investigation.
AU  - Moore AM
AU  - Patel S
AU  - Forsberg KJ
AU  - Wang B
AU  - Bentley G
AU  - Razia Y
AU  - Qin X
AU  - Tarr PI
AU  - Dantas G
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2013 8: E78822.

PMID- 6294416
VI  - 98
DP  - 1982
TI  - The average spacing of restriction enzyme recognition sites in DNA.
PG  - 165-169
AB  - The discovery of naturally occurring enzymes which cleave DNA at sites specific to particular
      nucleotide sequences has had a great impact on molecular biology.  The function of these
      enzymes in vivo is to protect bacterial cells from viral invasion by degradation of foreign
      DNA.  Several hundred of these "restriction" enzymes are known and they are a very common tool
      both for analysis and manipulation of DNA.  The overwhelming majority of restriction enzyme
      recognition sites are four to six nucleotides in length and have the remarkable property of
      internal symmetry with respect to nucleotide sequence (i.e. diad symmetry).  A major practical
      offshoot of the characterization of restriction enzymes has been their use in DNA cloning.  In
      addition, comparison of restriction enzyme cleavage patterns has been used analytically to
      assess the similarity of DNA from related organisms-particularly mitochondrial DNA.  As an aid
      in these studies, a number of statistical methods have been devised to analyze data generated
      by comparison of restriction enzyme digestion patterns.  The first of these studies was
      carried out by Upholt and Upholt & Dawid.  This work was revised by Nei & Li and by Gotoh et
      al.  The intent of this note is to add practical detail to these analyses.
AU  - Moore GP
AU  - Moore AR
PT  - Journal Article
TA  - J. Theor. Biol.
JT  - J. Theor. Biol.
SO  - J. Theor. Biol. 1982 98: 165-169.

PMID- 331253
VI  - 4
DP  - 1977
TI  - A restriction endonuclease cleavage map of mouse mitochondrial DNA.
PG  - 1273-1289
AB  - A restriction endonuclease cleavage map is presented for mouse mitochrondrial DNA.  This map
      was constructed by electron microscopic measurements on partial digests containing fixed
      D-loops, and by electrophoretic analysis of partial and complete single enzyme digests, and of
      double digests.  No map differences were detected between mitochrondrial DNA from cultured LA9
      cells and an inbred mouse line for the six endonucleases used.  Three cleavage sites
      recognized by HpaI, five sites recognized by HincII, two sites recognized by PstI and four
      sites recognized by BamI were located with respect to the origin of replication and the EcoRI
      and HinIII sites previously determined by others.  No cleavages were produced by KpnI or SalI.
      The migration of linear DNA with a molecular weight greater than 1 x 10^6 was not a linear
      function of log molecular weight in 1% agarose gels run at 6.6 volts/cm.
AU  - Moore KH
AU  - Johnson PH
AU  - Chandler EW
AU  - Grossman LI
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1977 4: 1273-1289.

PMID- 3031711
VI  - 45
DP  - 1987
TI  - Restriction enzyme cleavage of UV-irradiated DNA:  A comparison of far-UV and mid-UV wavelengths.
PG  - 253-263
AB  - UV-irradiated DNA is less susceptible to restriction by Type II endonucleases
      than unirradiated DNA presumably due to photolesions formed in the recognition
      sites.  Previous reported studies have used 254 nm radiation or 313 nm plus
      acetophenone, both treatments which introduce pyrimidine dimers in preference
      to other photolesions.  To assess the effect of a longer wavelength, at which
      the ratio of pyrimidine dimer formation to the formation of other photolesions
      is reduced, two different DNAs were irradiated with UV of either 254 or 313 nm
      and restricted with suitable restriction endonucleases.  Restriction patterns
      were analysed for novel fragments resulting from UV-induced alteration of
      enzyme recognition sites.  EcoRI restriction of 254 nm irradiated lambda DNA
      produced six novel bands, only three of which were observed following
      restriction of 313 nm irradiated lambda.  These three represented the largest
      fragments resulting from single site blocks.  Novel fragments involving
      adjacent site blocks observed at 254 nm were not found with 313 nm radiation.
      Comparison of 254 nm irradiated pSVgpt to that irradiated at 313 nm, both
      restricted with DraI, revealed a more complex pattern.  Although all sites were
      singly blocked by radiation of both wavelengths, multiple site blocks produced
      by 313 nm radiation did not occur in the order predicted by the 254 nm
      radiation dose response.  These data suggest that certain sites in pSVgpt may
      be more refractory to multiple site blocks than others when irradiated at 313
      nm.
AU  - Moore SP
AU  - McAleer MA
AU  - Moss SH
PT  - Journal Article
TA  - Photochem. Photobiol.
JT  - Photochem. Photobiol.
SO  - Photochem. Photobiol. 1987 45: 253-263.

PMID- 8262917
VI  - 268
DP  - 1993
TI  - Functional expression and properties of tRNALys-specific core anticodon nuclease encoded by Escherichia coli prrC.
PG  - 26842-26849
AB  - Escherichia coli carrying the optional locus prr harbor a latent, tRNALys-specific anticodon
      nuclease, activated by the product of phage T4 stp.  Anticodon nuclease latency is ascribed to
      the masking of prrC, implicated with the enzymatic activity, by flanking, type Ic DNA
      restriction modification genes (prrA, B&D-hsdM, S&R).  Overexpression of plasmid-borne prrC
      elicited anticodon nuclease activity in uninfected E. coli.  In vitro, the prrC-coded core
      activity was indifferent to a synthetic Stp polypeptide, GTP, ATP, and endogenous DNA,
      effectors that synergistically activate the latent enzyme.  Several facts suggested that PrrC
      is highly labile in the absence of the masking proteins.  The core activity decayed with t1/2
      below 1 min at 30oC, and the PrrC portion of a fusion protein was unstable.  Moreover,
      expression of prrC from its own promoter at low plasmid copy number did not allow detection of
      core activity.  Yet, it sufficed for establishment of a latent, T4-inducible enzyme when
      complemented by the masking Hsd proteins, which were provided by another replicon.
      Interaction between the antagonistic components of latent anticodon nuclease was also
      demonstrated immunochemically.  The coupling of anticodon nuclease with a DNA restriction
      modification system may serve to ward off its inadvertent toxicity and maintain it as an
      antiviral contingency.
AU  - Morad I
AU  - Chapman-Shimshoni D
AU  - Amitsur M
AU  - Kaufmann G
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1993 268: 26842-26849.

PMID- 27198028
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Flavihumibacter sp. Strain CACIAM 22H1, a Heterotrophic  Bacterium Associated with Cyanobacteria.
PG  - e00400-16
AB  - Here, we present a draft genome and annotation of Flavihumibacter sp. CACIAM 22H1, isolated
      from Bolonha Lake, Brazil, which will provide further insight into
      the production of substances of biotechnological interest.
AU  - Moraes PH
AU  - Lima AR
AU  - Siqueira AS
AU  - Dall'Agnol LT
AU  - Barauna AR
AU  - Aguiar DC
AU  - Fuzii HT
AU  - Albuquerque KC
AU  - de Lima CP
AU  - Nunes MR
AU  - Vianez-Junior JL
AU  - Goncalves EC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00400-16.

PMID- 22535947
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of a Sucrose-Nonfermenting Epidemic Strain of Vibrio cholerae O1 from Brazil.
PG  - 2772
AB  - We report the genome sequence of Vibrio cholerae strain IEC224, which fails to ferment
      sucrose. It was isolated from a cholera outbreak in the Amazon. The
      defective sucrose phenotype was determined to be due to a frameshift mutation,
      and a molecular marker of the Latin American main epidemic lineage was
      identified.
AU  - Morais LL
AU  - Garza DR
AU  - Loureiro EC
AU  - Nunes KN
AU  - Vellasco RS
AU  - da Silva CP
AU  - Nunes MR
AU  - Thompson CC
AU  - Vicente AC
AU  - Santos EC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2772.

PMID- 23974026
VI  - 195
DP  - 2013
TI  - Role of HynAB and Ech, the only two hydrogenases found in the model sulfate reducer Desulfovibrio gigas.
PG  - 4753
AB  - Sulfate-reducing bacteria are characterized by a high number of hydrogenases, which have been
      proposed to contribute to the overall energy metabolism of the cell, but exactly in what role
      is not clear. Desulfovibrio spp. can produce or consume H2 when growing on organic or
      inorganic substrates in the presence or absence of sulfate. Because of the presence of only
      two hydrogenases encoded in its genome, the periplasmic HynAB and cytoplasmic Ech
      hydrogenases, Desulfovibrio gigas is an excellent model organism for investigation of the
      specific function of each of these enzymes during growth. In this study, we analyzed the
      physiological response to the deletion of the genes that encode the two hydrogenases in D.
      gigas, through the generation of DeltaechBC and DeltahynAB single mutant strains. These
      strains were analyzed for the ability to grow on different substrates, such as lactate,
      pyruvate, and hydrogen, under respiratory and fermentative conditions. Furthermore, the
      expression of both hydrogenase genes in the three strains studied was assessed through
      quantitative reverse transcription-PCR. The results demonstrate that neither hydrogenase is
      essential for growth on lactate-sulfate, indicating that hydrogen cycling is not
      indispensable. In addition, the periplasmic HynAB enzyme has a bifunctional activity and is
      required for growth on H2 or by fermentation of pyruvate. Therefore, this enzyme seems to play
      a dominant role in D. gigas hydrogen metabolism.
AU  - Morais-Silva FO
AU  - Santos CI
AU  - Rodrigues R
AU  - Pereira IA
AU  - Rodrigues-Pousada C
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2013 195: 4753.

PMID- 26966218
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequence of Staphylococcus epidermidis Tu3298.
PG  - e00112-16
AB  - Staphylococcus epidermidis Tu3298 is a frequently used laboratory strain, known for its
      production of epidermin and absence of the icaABCD operon. We report the
      whole-genome sequence of this strain, a 2.5-kb genome containing 2,332 genes.
AU  - Moran JC
AU  - Horsburgh MJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00112-16.

PMID- 8029012
VI  - 22
DP  - 1994
TI  - Splicing defective mutants of the COXI gene of yeast mitochondrial DNA: initial definition of the maturase domain of the group II intron AI2.
PG  - 2057-2064
AB  - Six mutations blocking the function of a seven intron form of the mitochondrial gene encoding
      subunit I of cytochrome c oxidase (COXI) and mapping upstream of exon 3 were isolated and
      characterized.  A cis-dominant mutant of the group IIA intron 1 defines a helical portion of
      the C1 substructure of domain 1 as essential for splicing.  A trans-recessive mutant confirms
      that the intron 1 reading frame encodes a maturase function.  A cis-dominant mutant in exon 2
      was found to have no effect on the splicing of intron 1 or 2.  A trans-recessive mutant,
      located in the group IIA intron 2, demonstrates for the first time that intron 2 encodes a
      maturase.  A genetic dissection of the five missense mutations present in the intron 2 reading
      frame of that strain demonstrates that the maturase defect results from one or both of the
      missense mutations in a newly-recognized conserved sequence called domain X.
AU  - Moran JV
AU  - Mecklenburg KL
AU  - Sass P
AU  - Belcher SM
AU  - Mahnke D
AU  - Lewin A
AU  - Perlman P
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1994 22: 2057-2064.

PMID- 1324475
VI  - 20
DP  - 1992
TI  - Intron 5a of the COXI gene of yeast mitochondrial DNA is a mobile group I intron.
PG  - 4069-4076
AB  - We have found that intron 5a of the COXI gene (aI5a) of yeast mtDNA is a mobile group I intron
      in crosses between strains having or lacking the intron. We have demonstrated the following
      hallmarks of that process: 1) co-conversion of flanking optional intron markers; 2) mutations
      that truncate the intron open reading frame block intron mobility; and 3) the intron open
      reading frame encodes an endonuclease activity that is required for intron movement. The
      endonuclease activity, termed I-SceIV, cleaves the COXI allele lacking aI5a near the site of
      intron insertion, making a four-base staggered cut with 3' OH overhangs. Three cloned DNAs
      derived from different forms of the COXI gene, which differ in primary sequence at up to seven
      nucleotides around the cleavage site, are all good substrates for in vitro I-SceIV cleavage
      activity. Two of the strains from which these substrates derived were tested in crosses and
      are comparably efficient as aI5a recipients. When compared with omega mobility occurring
      simultaneously in one cross, aI5a is less efficient as a mobile element.
AU  - Moran JV
AU  - Wernette CM
AU  - Mecklenburg KL
AU  - Butow RA
AU  - Perlman PS
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 4069-4076.

PMID- 7537853
VI  - 15
DP  - 1995
TI  - Mobile group II introns of yeast mitochrondrial DNA are novel site-specific retroelements.
PG  - 2828-2838
AB  - Group II introns aI1 and aI2 of the yeast mitochondrial COX1 gene are mobile elements that
      encode an intron-specific reverse transcriptase (RT) activity.  We show here that the introns
      of Saccharomyces cerevisiae ID41-6/161 insert site specifically into intronless alleles.  The
      mobility is accompanied by efficient, but highly asymmetric, coconversion of nearby flanking
      exon sequences.  Analysis of mutants shows that the aI2 protein is required for the mobility
      of both aI1 and aI2.  Efficient mobility is dependent on both the RT activity of the
      aI2-encoded protein and a separate function, a putative DNA endonuclease, that is associated
      with the Zn2+ finger-like region of the intron reading frame.  Surprisingly, there appear to
      be two  mobility modes: the major one involves cDNAs reverse transcribed from unspliced
      precursor RNA; the minor one, observed in two mutants lacking detectable RT activity, appears
      to involve DNA level recombination.  A cis-dominant splicing-defective mutant of aI2 continues
      to synthesize cDNAs containing the introns but is completely defective in both mobility modes,
      indicating that the splicing or the structure of the intron is required.  Our results
      demonstrate that the yeast group II intron aI2 is a retroelement that uses novel mobility
      mechanisms.
AU  - Moran JV
AU  - Zimmerly S
AU  - Eskes R
AU  - Kennell JC
AU  - Lambowitz AM
AU  - Butow RA
AU  - Perlman PS
PT  - Journal Article
TA  - Mol. Cell. Biol.
JT  - Mol. Cell. Biol.
SO  - Mol. Cell. Biol. 1995 15: 2828-2838.

PMID- 15602564
VI  - 432
DP  - 2004
TI  - Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment.
PG  - 910-913
AB  - Since the recognition of prokaryotes as essential components of the oceanic food web,
      bacterioplankton have been acknowledged as catalysts of
      most major biogeochemical processes in the sea. Studying heterotrophic
      bacterioplankton has been challenging, however, as most major clades have
      never been cultured or have only been grown to low densities in sea water.
      Here we describe the genome sequence of Silicibacter pomeroyi, a member of
      the marine Roseobacter clade (Fig. 1), the relatives of which comprise
      approximately 10-20% of coastal and oceanic mixed-layer bacterioplankton.
      This first genome sequence from any major heterotrophic clade consists of
      a chromosome (4,109,442 base pairs) and megaplasmid (491,611 base pairs).
      Genome analysis indicates that this organism relies upon a
      lithoheterotrophic strategy that uses inorganic compounds (carbon monoxide
      and sulphide) to supplement heterotrophy. Silicibacter pomeroyi also has
      genes advantageous for associations with plankton and suspended particles,
      including genes for uptake of algal-derived compounds, use of metabolites
      from reducing microzones, rapid growth and cell-density-dependent
      regulation. This bacterium has a physiology distinct from that of marine
      oligotrophs, adding a new strategy to the recognized repertoire for coping
      with a nutrient-poor ocean.
AU  - Moran MA et al
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2004 432: 910-913.

PMID- 16195380
VI  - 102
DP  - 2005
TI  - The players in a mutualistic symbiosis: Insects, bacteria, viruses, and virulence genes.
PG  - 16919-16926
AB  - Aphids maintain mutualistic symbioses involving consortia of coinherited
      organisms. All possess a primary endosymbiont, Buchnera, which compensates
      for dietary deficiencies; many also contain secondary symbionts, such as
      Hamiltonella defensa, which confers defense against natural enemies.
      Genome sequences of uncultivable secondary symbionts have been refractory
      to analysis due to the difficulties of isolating adequate DNA samples. By
      amplifying DNA from hemolymph of infected pea aphids, we obtained a set of
      genomic sequences of H. defensa and an associated bacteriophage. H.
      defensa harbors two type III secretion systems, related to those that
      mediate host cell entry by enteric pathogens. The phage, called APSE-2, is
      a close relative of the previously sequenced APSE-1 but contains intact
      homologs of the gene encoding cytolethal distending toxin (cdtB), which
      interrupts the eukaryotic cell cycle and which is known from a variety of
      mammalian pathogens. The cdtB homolog is highly expressed, and its genomic
      position corresponds to that of a homolog of stx (encoding Shiga-toxin)
      within APSE-1. APSE-2 genomes were consistently abundant in infected pea
      aphids, and related phages were found in all tested isolates of H.
      defensa, from numerous insect species. Based on their ubiquity and
      abundance, these phages appear to be an obligate component of the H.
      defensa life cycle. We propose that, in these mutualistic symbionts,
      phage-borne toxin genes provide defense to the aphid host and are a basis
      for the observed protection against eukaryotic parasites.
AU  - Moran NA
AU  - Degnan PH
AU  - Santos SR
AU  - Dunbar HE
AU  - Ochman H
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2005 102: 16919-16926.

PMID- 29954915
VI  - 6
DP  - 2018
TI  - Genome Sequence of Staphylococcus aureus Ex1, Isolated from a Patient with Spinal Osteomyelitis.
PG  - e00623-18
AB  - Here, we present the genome sequence of Staphylococcus aureus Ex1, isolated in 2015 from a
      patient with spinal osteomyelitis at the Royal Devon and Exeter
      Hospital in the United Kingdom. The availability of the Ex1 genome sequence
      provides a resource for studying the basis for spinal infection and horizontal
      gene transfer in S. aureus.
AU  - Morcrette H
AU  - Morgan MS
AU  - Farbos A
AU  - O'Neill P
AU  - Moore K
AU  - Titball RW
AU  - Studholme DJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00623-18.

PMID- 12496295
VI  - 278
DP  - 2003
TI  - Why do divalent metal ions either promote or inhibit enzymatic reactions? The case of BamHI restriction endonuclease from combined quantum-classical simulations.
PG  - 4381-4384
AB  - Divalent metal ions are essential to many enzymatic reactions involving nucleic acids, but
      their critical and specific role still needs to be uncovered. Restriction endonucleases are a
      prominent group of such metal-requiring enzymes. Large-scale accurate simulations of Mg- and
      Ca-BamHI elucidate the mechanism of the catalytic reaction leading to DNA cleavage and show
      that it involves the concerted action of two metal ions and water molecules. It is also
      established that what is decisive for the dramatically different behavior of magnesium (a
      cocatalyst) and calcium (an inhibitor) are kinetic factors and not the properties of the
      pre-reactive states of the enzymes. A new perspective is opened for the understanding of the
      functional role of metal ions in biological processes.
AU  - Mordasini T
AU  - Curioni A
AU  - Andreoni W
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2003 278: 4381-4384.

PMID- 20861243
VI  - 84
DP  - 2010
TI  - Marine prasinovirus genomes show low evolutionary divergence and acquisition of protein metabolism genes by horizontal gene transfer.
PG  - 12555-12563
AB  - Although marine picophytoplankton are at the base of the global food
      chain, accounting for half of the planetary primary production, they are
      outnumbered 10 to 1 and are largely controlled by hugely diverse
      populations of viruses. Eukaryotic microalgae form a ubiquitous and
      particularly dynamic fraction of such plankton, with environmental clone
      libraries from coastal regions sometimes being dominated by one or more of
      the three genera Bathycoccus, Micromonas, and Ostreococcus (class
      Prasinophyceae). The complete sequences of two double-stranded (dsDNA)
      Bathycoccus, one dsDNA Micromonas, and one new dsDNA Ostreococcus virus
      genomes are described. Genome comparison of these giant viruses revealed a
      high degree of conservation, both for orthologous genes and for synteny,
      except for one 36-kb inversion in the Ostreococcus lucimarinus virus and
      two very large predicted proteins in Bathycoccus prasinos viruses. These
      viruses encode a gene repertoire of certain amino acid biosynthesis
      pathways never previously observed in viruses that are likely to have been
      acquired from lateral gene transfer from their host or from bacteria.
      Pairwise comparisons of whole genomes using all coding sequences with
      homologous counterparts, either between viruses or between their
      corresponding hosts, revealed that the evolutionary divergences between
      viruses are lower than those between their hosts, suggesting either
      multiple recent host transfers or lower viral evolution rates.
AU  - Moreau H
AU  - Piganeau G
AU  - Desdevises Y
AU  - Cooke R
AU  - Derelle E
AU  - Grimsley N
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 2010 84: 12555-12563.

PMID- 26358589
VI  - 3
DP  - 2015
TI  - Genome Sequences of Two Strains of Salmonella enterica Serovar Enteritidis Isolated from Shell Eggs.
PG  - e00954-15
AB  - This report presents the complete genome sequences of two Salmonella enterica serovar
      Enteritidis strains bearing the pulsed-field gel electrophoresis profile  JEGX01.0004, which
      were isolated from the internal contents of eggs.
AU  - Moreau MR
AU  - Wijetunge DS
AU  - Kurundu HEM
AU  - Jayarao BM
AU  - Kariyawasam S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00954-15.

PMID- 27738024
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Three Endophyte Strains of Pseudomonas fluorescens Isolated from Miscanthus giganteus.
PG  - e00965-16
AB  - We report here the draft genome sequence of three Pseudomonas fluorescens strains (L111, L228,
      and L321) isolated from Miscanthus giganteus The draft genome
      analyses uncovered a group of genes involved in the biosynthesis of secondary
      metabolites and for plant growth promotion.
AU  - Moreira AS
AU  - Germaine KJ
AU  - Lloyd A
AU  - Lally RD
AU  - Galbally PT
AU  - Ryan D
AU  - Dowling DN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00965-16.

PMID- 7669297
VI  - 19
DP  - 1995
TI  - Minimum duplex requirements for restriction enzyme cleavage near the termini of linear DNA fragments.
PG  - 56-59
AB  - Restriction endonucleases differ in their ability to cleave close to the ends of linear DNA
      fragments, each requiring a characteristic minimum number of base pairs adjacent to their
      recognition sites for efficient cleavage. Quantitative cleavage close to either end of a
      linear DNA fragment is crucial when carrying out digests at adjacent restriction sites within
      cloning vector polylinkers or when trimming the ends of polymerase chain reaction (PCR)
      products prior to cloning. In the former case, incomplete digestion by the second restriction
      enzyme (following linearization by the first) would be undetectable by gel electrophoresis,
      yet could result in an unacceptably high background level of transformants following ligation
      of the insert. In the latter case, recovery of a cloned PCR product is dependent upon
      generation of the desired overhangs at either end of the amplified product prior to cloning.
      Incorporation of restriction sites within PCR primers for future cloning steps has become an
      important factor in primer design: If not enough bases are added upstream from each site, then
      the corresponding enzyme will not cut the PCR product.
AU  - Moreira RF
AU  - Noren CJ
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 1995 19: 56-59.

PMID- 28209836
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of a Vibrio harveyi Strain Associated with Vibriosis in Pacific White Shrimp (Litopenaeus vannamei).
PG  - e01662-16
AB  - Vibrio harveyi is a Gram-negative bacterium associated with vibriosis in penaeid  shrimp.
      Here, we report the draft genome sequence of a V. harveyi strain isolated
      from Pacific white shrimp (Litopenaeus vannamei) during a vibriosis outbreak. The
      availability of this genome will aid future studies of vibriosis in shrimp
      aquaculture.
AU  - Moreno E
AU  - Parks M
AU  - Pinnell LJ
AU  - Tallman JJ
AU  - Turner JW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01662-16.

PMID- 25767244
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Bordetella avium Nh1210, an Outbreak Strain of Lockjaw Syndrome.
PG  - e00120-15
AB  - Bordetella avium is a highly contagious bacterium that infects the upper respiratory tract of
      birds. B. avium Nh1210 is an outbreak strain of lockjaw
      syndrome in juvenile cockatiel chicks (Nymphicus hollandicus). Here, we report
      the draft genome sequence of strain Nh1210.
AU  - Moreno LZ
AU  - Knobl T
AU  - Grespan AA
AU  - Felizardo MR
AU  - Gomes CR
AU  - Ferreira TS
AU  - Xavier-de-Oliveira MG
AU  - Myriantheus L
AU  - Moreno AM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00120-15.

PMID- 26472831
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Brazilian Leptospira noguchii Serogroup Panama Strain U73, Isolated from Cattle.
PG  - e01179-15
AB  - Leptospira noguchii is a current zoonotic pathogen in Brazil. Here, we report the draft genome
      sequence of the Brazilian L. noguchii serogroup Panama strain U73, isolated from asymptomatic
      cattle urine.
AU  - Moreno LZ
AU  - Loureiro AP
AU  - Miraglia F
AU  - Matajira CE
AU  - Kremer FS
AU  - Eslabao MR
AU  - Dellagostin OA
AU  - Lilenbaum W
AU  - Moreno AM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01179-15.

PMID- 29880594
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Brazilian Leptospira interrogans Serovar Pomona Strain GR5, Isolated from Apparently Healthy Gilt.
PG  - e00491-18
AB  - Leptospira interrogans serovar Pomona is one of the most important serovars associated with
      worldwide porcine leptospirosis, and its infection is
      characterized by high antibody titers and the establishment of a renal carrier
      state. Here, we present the draft genome sequence of Leptospira interrogans
      serovar Pomona strain GR5 isolated from apparently healthy gilt in Brazil.
AU  - Moreno LZ
AU  - Miraglia F
AU  - de Oliveira CH
AU  - Vasconcellos SA
AU  - Heinemann MB
AU  - Moreno AM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00491-18.

PMID- 28596401
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Pseudomonas chlororaphis ATCC 9446, a Nonpathogenic Bacterium with Bioremediation and Industrial Potential.
PG  - e00474-17
AB  - Pseudomonas chlororaphis strain ATCC 9446 is a biocontrol-related organism. We report here its
      draft genome sequence assembled into 35 contigs consisting of
      6,783,030 bp. Genome annotation predicted a total of 6,200 genes, 6,128 coding
      sequences, 81 pseudogenes, 58 tRNAs, 4 noncoding RNAs (ncRNAs), and 41
      frameshifted genes.
AU  - Moreno-Avitia F
AU  - Lozano L
AU  - Utrilla J
AU  - Bolivar F
AU  - Escalante A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00474-17.

PMID- 24422886
VI  - 15
DP  - 2014
TI  - Genomic comparison of sporeforming bacilli isolated from milk.
PG  - 26
AB  - BACKGROUND: Sporeformers in the order Bacillales are important contributors to spoilage of
      pasteurized milk. While only a few Bacillus and Viridibacillus strains can grow in milk at 6
      degrees C, the majority of Paenibacillus isolated from pasteurized fluid milk can grow under
      these conditions. To gain a better understanding of genomic features of these important
      spoilage organisms and to identify candidate genomic features that may facilitate cold growth
      in milk, we performed a comparative genomic analysis of selected dairy associated sporeformers
      representing isolates that can and cannot grow in milk at 6 degrees C. RESULTS: The genomes
      for seven Paenibacillus spp., two Bacillus spp., and one Viridibacillus sp. isolates were
      sequenced. Across the genomes sequenced, we identified numerous genes encoding antimicrobial
      resistance mechanisms, bacteriocins, and pathways for synthesis of non-ribosomal peptide
      antibiotics. Phylogenetic analysis placed genomes representing Bacillus, Paenibacillus and
      Viridibacillus into three distinct well supported clades and further classified the
      Paenibacillus strains characterized here into three distinct clades, including (i) clade I,
      which contains one strain able to grow at 6 degrees C in skim milk broth and one strain not
      able to grow under these conditions, (ii) clade II, which contains three strains able to grow
      at 6 degrees C in skim milk broth, and (iii) clade III, which contains two strains unable to
      grow under these conditions. While all Paenibacillus genomes were found to include multiple
      copies of genes encoding beta-galactosidases, clade II strains showed significantly higher
      numbers of genes encoding these enzymes as compared to clade III strains. Genome comparison of
      strains able to grow at 6 degrees C and strains unable to grow at this temperature identified
      numerous genes encoding features that might facilitate the growth of Paenibacillus in milk at
      6 degrees C, including peptidases with cold-adapted features (flexibility and disorder regions
      in the protein structure) and cold-adaptation related proteins (DEAD-box helicases, chaperone
      DnaJ). CONCLUSIONS: Through a comparative genomics approach we identified a number of genomic
      features that may relate to the ability of selected Paenibacillus strains to cause spoilage of
      refrigerated fluid milk. With additional experimental evidence, these data will facilitate
      identification of targets to detect and control Gram positive spore formers in fluid milk.
AU  - Moreno-Switt AI
AU  - Andrus AD
AU  - Ranieri ML
AU  - Orsi RH
AU  - Ivy R
AU  - den Bakker HC
AU  - Martin NH
AU  - Wiedmann M
AU  - Boor KJ
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2014 15: 26.

PMID- 23865498
VI  - 14
DP  - 2013
TI  - Genomic characterization provides new insight into Salmonella phage diversity.
PG  - 481
AB  - Background Salmonella is a widely distributed foodborne pathogen that causes tens of millions
      of salmonellosis cases globally every year. While the genomic diversity of Salmonella is
      increasingly well studied, our knowledge of Salmonella phage genomic diversity is still rather
      limited, despite the contributions of both lysogenic and lytic phages to Salmonella virulence,
      diversity and ecology (e.g., through horizontal gene transfer and Salmonella lysis). To gain a
      better understanding of phage diversity in a specific ecological niche, we sequenced 22
      Salmonella phages isolated from a number of dairy farms from New York State (United States)
      and analyzed them using a comparative genomics approach. Results Classification of the 22
      phages according to the presence/absence of orthologous genes allowed for classification into
      8 well supported clusters. In addition to two phage clusters that represent novel virulent
      Salmonella phages, we also identified four phage clusters that each contained previously
      characterized phages from multiple continents. Our analyses also identified two clusters of
      phages that carry putative virulence (e.g., adhesins) and antimicrobial resistance (tellurite
      and bicyclomycin) genes as well as virulent and temperate transducing phages. Insights into
      phage evolution from our analyses include (i) identification of DNA metabolism genes that may
      facilitate nucleotide synthesis in phages with a G+C % distinct from Salmonella, and (ii)
      evidence of Salmonella phage tailspike and fiber diversity due to both single nucleotide
      polymorphisms and major re-arrangements, which may affect the host specificity of Salmonella
      phages. Conclusions Genomics-based characterization of 22 Salmonella phages isolated from
      dairy farms allowed for identification of a number of novel Salmonella phages. While the
      comparative genomics analyses of these phages provide a number of new insights in the
      evolution and diversity of Salmonella phages, they only represent a first glimpse into the
      diversity of Salmonella phages that is likely to be discovered when phages from different
      environments are characterized.
AU  - Moreno-Switt AI
AU  - Orsi RH
AU  - den Bakker HC
AU  - Vongkamjan K
AU  - Altier C
AU  - Wiedmann M
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2013 14: 481.

PMID- 25502684
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Erwinia oleae, a Bacterium Associated with Olive Knots Caused by Pseudomonas savastanoi pv. savastanoi.
PG  - e01308-14
AB  - Erwinia oleae is a nonpathogenic bacterial species isolated from olive knots caused by
      Pseudomonas savastanoi pv. savastanoi. Since the presence of E. oleae
      in the knots increases disease severity, interspecies interactions with the
      pathogen are hypothesized. Here, we report the first draft genome sequence of the
      E. oleae type strain.
AU  - Moretti C
AU  - Cortese C
AU  - Passos-da-Silva D
AU  - Venturi V
AU  - Firrao G
AU  - Buonaurio R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01308-14.

PMID- 25278521
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Pseudomonas savastanoi pv. savastanoi Strain DAPP-PG 722, Isolated in Italy from an Olive Plant Affected by Knot Disease.
PG  - e00864-14
AB  - Olive knot disease, caused by the bacterium Pseudomonas savastanoi pv. savastanoi, seriously
      affects olive trees in the Mediterranean basin. Here, we
      report the draft genome sequence of P. savastanoi pv. savastanoi DAPP-PG 722, a
      strain isolated in Italy from an olive plant affected by knot disease.
AU  - Moretti C
AU  - Cortese C
AU  - Passos-da-Silva D
AU  - Venturi V
AU  - Ramos C
AU  - Firrao G
AU  - Buonaurio R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00864-14.

PMID- 25103763
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of a Hypersensitive Reaction-Inducing Pantoea agglomerans Strain Isolated from Olive Knots Caused by Pseudomonas savastanoi pv. savastanoi.
PG  - e00774-14
AB  - Pantoea agglomerans strains inducing a hypersensitive reaction in tobacco leaves  are
      frequently isolated inside olive knots caused by Pseudomonas savastanoi pv.
      savastanoi. Here, we report the draft genome sequence of the Italian P.
      agglomerans strain, which is able to increase olive knot disease severity when
      coinoculated with P. savastanoi pv. savastanoi.
AU  - Moretti C
AU  - Cortese C
AU  - Passos-da-Silva D
AU  - Venturi V
AU  - Torelli E
AU  - Firrao G
AU  - Buonaurio R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00774-14.

PMID- 29867913
VI  - 9
DP  - 2018
TI  - Beyond the Limits: tRNA Array Units in Mycobacterium Genomes.
PG  - 1042
AB  - tRNA array unit, a genomic region presenting an intriguing high tRNA gene number
      and density, was supposed to occur only in few bacteria phyla, particularly
      Firmicutes. Here, we identified and characterized an abundance and diversity of
      tRNA array units in Mycobacterium associated genomes. These genomes comprised
      chromosome, bacteriophages and plasmids from mycobacteria. Firstly, we had
      identified 32 tRNA genes organized in an array unit within a mycobacteria plasmid
      genome and therefore, we hypothesized the presence of such structures in
      Mycobacterium genus. However, at the time, bioinformatics tools only predict tRNA
      genes, not characterizing their arrangement as arrays. In order to test our
      hypothesis, we developed and applied an in-house Perl script that identified tRNA
      genes organization as an array unit. This survey included a total of 7,670
      complete and drafts genomes of Mycobacterium genus, 4312 mycobacteriophage
      genomes and 40 mycobacteria plasmids. We showed that tRNA array units are
      abundant in genomes associated to the Mycobacterium genus, mainly in
      Mycobacterium abscessus complex species, being spread in chromosome, prophage,
      and plasmid genomes. Moreover, other non-coding RNA species (tmRNA and structured
      RNA) were also identified in these regions. Our results revealed that tRNA array
      units are not restrict, as previously assumed, to few bacteria phyla and genomes
      being present in one of the most diverse bacteria genus. We also provide a
      bioinformatics tool that allows further exploration of this issue in huge genomic
      databases. The presence of tRNA array units in plasmids and bacteriophages,
      associated with horizontal gene transfer, and in a bacteria genus that explores
      diverse niches, are indicatives that tRNA array units have impact in the bacteria
      biology.
AU  - Morgado SM
AU  - Vicente AC
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2018 9: 1042.

PMID- 9758783
VI  - 64
DP  - 1998
TI  - Characterization of an extremely thermostable restriction enzyme, PspGI, from a Pyrococcus strain and cloning of the PspGI restriction-modification system in Escherichia coli.
PG  - 3669-3673
AB  - An extremely thermostable restriction endonuclease, PspGI, was purified from Pyrococcus sp.
      strain GI-H.  PspGI is an isoschizomer of EcoRII and cleaves DNA before the first C in the
      sequence 5' ^CCWGG 3' (W is A or T).  PspGI digestion can be carried out at 65 to 85 C.  To
      express PspGI at high levels, the PspGI restriction-modification genes (pspGIR and pspGIM)
      were cloned in Escherichia coli.  M.PspGI contains the conserved sequence motifs of
      alpha-aminomethyltransferases; therefore, it must be an N4-cytosine methylase.  M.PspGI shows
      53% similarity to (44% identity with) its isoschizomer, M.MvaI from Micrococcus variabilis.
      In a segment of 87 amino acid residues, PspGI shows significant sequence similarity to EcoRII
      and to regions of SsoII and StyD4I which have a closely related recognition sequence (5'
      ^CCNGG 3').  PspGI was expressed in E. coli via a T7 expression system.  Recombinant PspGI
      was purified to near homogeneity and had a half-life of 2 h at 95 C.  PspGI remained active
      following 30 cycles of thermocycling; thus, it can be used in DNA-based diagnostic
      applications.
AU  - Morgan R
AU  - Xiao J-P
AU  - Xu S-Y
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1998 64: 3669-3673.

PMID- 
VI  - 
DP  - 2009
TI  - Rational engineering of DNA binding and cleavage specificity in a family of Type II restriction endonucleases.
PG  - 1-190
AB  - Type II restriction endonucleases serve as important tools for molecular biology. Although
      enzymes recognizing 274 unique sequences are known, it would be desirable to be able to create
      'designer endonucleases' to cut at sequences of choice rather than rely on the limited
      number of natural isolates. However, these endonucleases have proved remarkably resistant to
      all attempts to engineer changes in their recognition specificity. The Type II endonucleases
      typically exhibit little sequence similarity. This study has identified a new family of
      unusual Type II endonucleases through genome mining that do share a great deal of sequence
      conservation. Twenty individual members of this family were biochemically characterized and
      all recognize unique DNA sequences. These enzymes also employ a unique mode of modification,
      in that they modify only one DNA strand for host protection against the action of the
      endonuclease. This family of single-strand-modifying enzymes serves as the archetype for a new
      restriction endonuclease subclass, the Type IIL group. Because these enzymes encode
      endonuclease, methyltransferase and specificity functions in the same polypeptide, alterations
      to the recognition domain result in a coordinated change in specificity for both host
      protection and endonuclease activity. To alter recognition specificity, multiple sequence
      alignments of the recognition sequences and protein sequences were created and interrogated to
      identify correlations between position-specific amino acid residues and position-specific DNA
      base recognition. Correlations were identified between pairs of amino acid positions and the
      DNA bases recognized at three separate recognition positions. Enzymes having new recognition
      specificity were then created by altering the amino acid residues at the correlating positions
      to residues correlated with recognition of a desired new DNA base. Using this approach three
      positions in the recognition sequences have been altered singly and in combination to create a
      dozen novel Type II endonucleases having predictable new recognition sequences. From this work
      it is now possible to rationally engineer hundreds of new Type II restriction endonucleases
      specificities. These results move us closer to the goal of creating 'designer restriction
      endonucleases' that recognize and cleave at any desired DNA sequence.
AU  - Morgan RD
PT  - Journal Article
TA  - Ph.D. Thesis, Boston University
JT  - Ph.D. Thesis, Boston University
SO  - Ph.D. Thesis, Boston University 2009 : 1-190.

PMID- 2835752
VI  - 16
DP  - 1988
TI  - MseI, a unique restriction endonuclease from Micrococcus species which recognizes 5'T^TAA 3'.
PG  - 3104
AB  - A new typeII restriction endonuclease, MseI, has been isolated from Micrococcus
      species (NEB446).  MseI recognizes the palindromic sequence 5'TTAA3' and
      cleaves between the two T residues to produce a 2 base 5' extension: T/TAA.
AU  - Morgan RD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1988 16: 3104.

PMID- 27231364
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence and Methylome Analysis of Bacillus globigii ATCC 49760.
PG  - e00427-16
AB  - Bacillus subtilis (Ehrenburg) Cohn ATCC 49760, deposited as Bacillus globigii, is the source
      strain for the restriction enzymes BglI and BglII. Its complete
      sequence and full methylome were determined using single-molecule real-time
      (SMRT) sequencing.
AU  - Morgan RD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00427-16.

PMID- 18931376
VI  - 36
DP  - 2008
TI  - MmeI: a minimal Type II restriction-modification system that only modifies one DNA strand for host protection.
PG  - 6558-6570
AB  - MmeI is an unusual Type II restriction enzyme that is useful for generating long sequence
      tags. We have cloned the MmeI
      restriction-modification (R-M) system and found it to consist of a single
      protein having both endonuclease and DNA methyltransferase activities. The
      protein comprises an amino-terminal endonuclease domain, a central DNA
      methyltransferase domain and C-terminal DNA recognition domain. The
      endonuclease cuts the two DNA strands at one site simultaneously, with
      enzyme bound at two sites interacting to accomplish scission. Cleavage
      occurs more rapidly than methyl transfer on unmodified DNA. MmeI modifies
      only the adenine in the top strand, 5'-TCCRAC-3'. MmeI endonuclease
      activity is blocked by this top strand adenine methylation and is
      unaffected by methylation of the adenine in the complementary strand,
      5'-GTYGGA-3'. There is no additional DNA modification associated with the
      MmeI R-M system, as is required for previously characterized Type IIG R-M
      systems. The MmeI R-M system thus uses modification on only one of the two
      DNA strands for host protection. The MmeI architecture represents a
      minimal approach to assembling a restriction-modification system wherein a
      single DNA recognition domain targets both the endonuclease and DNA
      methyltransferase activities.
AU  - Morgan RD
AU  - Bhatia TK
AU  - Lovasco L
AU  - Davis TB
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2008 36: 6558-6570.

PMID- 11154070
VI  - 381
DP  - 2000
TI  - Characterization of the specific DNA nicking activity of restriction endonuclease N.BstNBI.
PG  - 1123-1125
AB  - N.BstNBI is a unique restriction endonuclease isolated from Bacillus stearothermophilus, We
      have characterized the recognition sequence and
      the cleavage site of N.BstNBI. Mapping of cleavage sites of N.BstNBI
      showed that it recognizes an asymmetric sequence, 5' GAGTC 3', and
      cleaves only on the top strand 4 base pairs away from its recognition
      sequence. To verify the nicking activity of N.BstNBI, we have
      constructed two plasmids containing a single recognition sequence
      (pNB1) or no recognition site (pNB0). When pNB1 and pNB0 were incubated
      with the enzyme, N.BstNBI nicked only the plasmid pNB1, suggesting that
      N.BstNBI is a specific nicking endonuclease.
AU  - Morgan RD
AU  - Calvet C
AU  - Demeter M
AU  - Agra R
AU  - Kong HM
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 2000 381: 1123-1125.

PMID- 8996109
VI  - 183
DP  - 1996
TI  - Molecular cloning and expression of NlaIII restriction-modification system in E. coli.
PG  - 215-218
AB  - The NlaIII restriction enzyme isolated from Neisseria lactamica recognizes the sequence
      5'-CATG-3', cleaving after the G to generate a four base 3' overhang.  The NlaIII methylase
      and a portion of the NlaIII endonuclease gene were cloned into E. coli by the methylase
      selection method, and the remaining portion of the NlaIII endonuclease gene was cloned by
      inverse PCR.  The nucleotide sequence of the endonuclease gene and the methylase gene were
      determined.  The NlaIII endonuclease gene is 693 bp, encoding a protein with a predicted
      molecular weight of 26,487.  The NlaIII methylase gene was identical with that previously
      reported [Labbe, D., Joltke, H.J. and Lau, P.C. (1990)  Cloning and characterization of two
      tandemly arranged DNA methyltransferase genes of Neisseria lactamica: an adenine-specific
      M.NlaIII and a cytosine-type methylase.  Mol. Gen. genet. 224, 101-110].  The endonuclease and
      methylase genes overlap by four bases and are transcribed in the same orientation.  The
      endonuclease gene was cloned into an improved T7 vector, and a high level of NlaIII
      endonuclease expression was achieved in E. coli.
AU  - Morgan RD
AU  - Camp RR
AU  - Wilson GG
AU  - Xu S-Y
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1996 183: 215-218.

PMID- 2821501
VI  - 15
DP  - 1987
TI  - A unique type II restriction endonuclease from Acinetobacter lwoffi N.
PG  - 7201
AB  - A new type II restriction endonuclease, AlwN I, has been isolated from
      Acinetobacter lwoffi N (NEB 419).  AlwN I recognizes the interrupted
      palindromic sequence 5' CAGNNNCTG 3' and cleaves between the 3' N and C to
      produce a 3 base 3' extension.
AU  - Morgan RD
AU  - Dalton M
AU  - Stote R
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1987 15: 7201.

PMID- 19578066
VI  - 37
DP  - 2009
TI  - The MmeI family: type II restriction-modification enzymes that employ single-strand modification for host protection.
PG  - 5208-5221
AB  - The type II restriction endonucleases form one of the largest families of
      biochemically-characterized proteins. These endonucleases typically share
      little sequence similarity, except among isoschizomers that recognize the
      same sequence. MmeI is an unusual type II restriction endonuclease that
      combines endonuclease and methyltransferase activities in a single
      polypeptide. MmeI cuts DNA 20 bases from its recognition sequence and
      modifies just one DNA strand for host protection. Using MmeI as query we
      have identified numerous putative genes highly similar to MmeI in database
      sequences. We have cloned and characterized 20 of these MmeI homologs.
      Each cuts DNA at the same distance as MmeI and each modifies a conserved
      adenine on only one DNA strand for host protection. However each enzyme
      recognizes a unique DNA sequence, suggesting these enzymes are undergoing
      rapid evolution of DNA specificity. The MmeI family thus provides a rich
      source of novel endonucleases while affording an opportunity to observe
      the evolution of DNA specificity. Because the MmeI family enzymes employ
      modification of only one DNA strand for host protection, unlike previously
      described type II systems, we propose that such single-strand modification
      systems be classified as a new subgroup, the type IIL enzymes, for Lone
      strand DNA modification.
AU  - Morgan RD
AU  - Dwinell EA
AU  - Bhatia TK
AU  - Lang EM
AU  - Luyten YA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: 5208-5221.

PMID- 19567736
VI  - 37
DP  - 2009
TI  - Rational engineering of type II restriction endonuclease DNA binding and cleavage specificity.
PG  - 5222-5233
AB  - The type II restriction endonucleases are indispensible tools for molecular biology. Although
      enzymes recognizing nearly 300 unique
      sequences are known, the ability to engineer enzymes to recognize any
      sequence of choice would be valuable. However, previous attempts to
      engineer new recognition specificity have met limited success. Here we
      report the rational engineering of multiple new type II specificities. We
      recently identified a family of MmeI-like type II endonucleases that have
      highly similar protein sequences but different recognition specificity. We
      identified the amino-acid positions within these enzymes that determine
      position specific DNA base recognition at three positions within their
      recognition sequences through correlations between their aligned
      amino-acid residues and aligned recognition sequences. We then altered the
      amino acids at the identified positions to those correlated with
      recognition of a desired new base to create enzymes that recognize and cut
      at predictable new DNA sequences. The enzymes so altered have similar
      levels of endonuclease activity compared to the wild-type enzymes. Using
      simple and predictable mutagenesis in this family it is now possible to
      create hundreds of unique new type II restriction endonuclease
      specificities. The findings suggest a simple mechanism for the evolution
      of new DNA specificity in Nature.
AU  - Morgan RD
AU  - Luyten YA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: 5222-5233.

PMID- 27580720
VI  - 44
DP  - 2016
TI  - Novel m4C modification in type I restriction-modification systems.
PG  - 9413-9425
AB  - We identify a new subgroup of Type I Restriction-Modification enzymes that modify cytosine in
      one DNA strand and adenine in the opposite strand for host
      protection. Recognition specificity has been determined for ten systems using
      SMRT sequencing and each recognizes a novel DNA sequence motif. Previously
      characterized Type I systems use two identical copies of a single
      methyltransferase (MTase) subunit, with one bound at each half site of the
      specificity (S) subunit to form the MTase. The new m4C-producing Type I systems
      we describe have two separate yet highly similar MTase subunits that form a
      heterodimeric M1M2S MTase. The MTase subunits from these systems group into two
      families, one of which has NPPF in the highly conserved catalytic motif IV and
      modifies adenine to m6A, and one having an NPPY catalytic motif IV and modifying
      cytosine to m4C. The high degree of similarity among their cytosine-recognizing
      components (MTase and S) suggest they have recently evolved, most likely from the
      far more common m6A Type I systems. Type I enzymes that modify cytosine
      exclusively were formed by replacing the adenine target recognition domain (TRD)
      with a cytosine-recognizing TRD. These are the first examples of m4C modification
      in Type I RM systems.
AU  - Morgan RD
AU  - Luyten YA
AU  - Johnson SA
AU  - Clough EM
AU  - Clark TA
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2016 44: 9413-9425.

PMID- 3054512
VI  - 8
DP  - 1988
TI  - Inducible expression and cytogenic effects of the EcoRI restriction endonuclease in chinese hamster ovary cells.
PG  - 4204-4211
AB  - The cytogenic endpoints of sister chromatid exchange (SCE) and chromosome
      aberrations are widely used as indicators of DNA damage induced by mutagenic
      carcinogens.  Chromosome aberrations appear to result directly from DNA
      double-strand breaks, but the lesion(s) giving rise to SCE formation remains
      unknown.  Most compounds that induce SCEs induce a spectrum of lesions in DNA.
      To investigate the role of double-strand breakage in SCE formation, we
      constructed a plasmid that gives rise to one specific lesion, a staggered-end
      ("cohesive") DNA double-strand break.  This plasmid, designated pMENs, contains
      a selectable marker, neo, which is a bacterial gene for neomycin resistance,
      and the coding sequence for the bacterial restriction endonuclease EcoRI
      attached to the mouse metallothionein gene promoter.  EcoRI recognizes G^AATTC
      sequences in DNA and makes DNA double-strand breaks with four nucleotides
      overhanging as staggered ends.  Cells transfected with pMENS were resistant to
      the antibiotic G418 and contained an integrated copy of the EcoRI gene,
      detectable by DNA filter hybridization.  The addition of the heavy metal CdSO4
      resulted in the intracellular production of EcoRI, as measured by an anti-EcoRI
      antibody.  Cytogenetic analysis after the addition of CdSO4 indicated a
      dramatic increase in the frequency of chromosome aberrations but very little
      effect on SCE frequency.  Although there was some intercellular heterogeneity,
      these results confirm that DNA double-strand breaks do result in chromosome
      aberrations but that these breaks are not sufficient to give rise to SCE
      formation.
AU  - Morgan WF
AU  - Fero ML
AU  - Land MC
AU  - Winegar RA
PT  - Journal Article
TA  - Mol. Cell. Biol.
JT  - Mol. Cell. Biol.
SO  - Mol. Cell. Biol. 1988 8: 4204-4211.

PMID- 29025949
VI  - 5
DP  - 2017
TI  - Genome Sequence of Saccharomyces cerevisiae Strain Kagoshima No. 2, Used for Brewing the Japanese Distilled Spirit Shochu.
PG  - e01126-17
AB  - 
AU  - Mori K
AU  - Kadooka C
AU  - Masuda C
AU  - Muto A
AU  - Okutsu K
AU  - Yoshizaki Y
AU  - Takamine K
AU  - Futagami T
AU  - Tamaki H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01126-17.

PMID- 24676729
VI  - 64
DP  - 2014
TI  - Thermotoga profunda sp. nov. and Thermotoga caldifontis sp. nov., anaerobic thermophilic bacteria isolated from terrestrial hot springs.
PG  - 2128-2136
AB  - Two thermophilic, strictly anaerobic, Gram-negative bacteria, designated strains
      AZM34c06(T) and AZM44c09(T), were isolated from terrestrial hot springs in Japan.
      The optimum growth conditions for strain AZM34c06(T) were 60 degrees C, pH 7.4 and 0 %
      additional NaCl, and those for strain AZM44c09(T) were 70 degrees C, pH
      7.4 and 0 % additional NaCl. Complete genome sequencing was performed for both strains,
      revealing genome sizes of 2.19 Mbp (AZM34c06(T)) and 2.01 Mbp (AZM44c09(T)). Phylogenetic
      analyses based on 16S rRNA gene sequences and the concatenated predicted amino acid sequences
      of 33 ribosomal proteins showed that both strains belonged to the genus Thermotoga. The
      closest relatives of strains
      AZM34c06(T) and AZM44c09(T) were the type strains of Thermotoga lettingae (96.0 % similarity
      based on the 16S rRNA gene and 84.1 % similarity based on ribosomal
      proteins) and Thermotoga hypogea (98.6 and 92.7 % similarity), respectively.
      Using blast, the average nucleotide identity was 70.4-70.5 % when comparing strain AZM34c06(T)
      and T. lettingae TMO(T) and 76.6 % when comparing strain
      AZM44c09(T) and T. hypogea NBRC 106472(T). Both values are far below the 95 % threshold value
      for species delineation. In view of these data, we propose the inclusion of the two isolates
      in the genus Thermotoga within two novel species, Thermotoga profunda sp. nov. (type strain
      AZM34c06(T) = NBRC 106115(T) = DSM
      23275(T)) and Thermotoga caldifontis sp. nov. (type strain AZM44c09(T) = NBRC
      106116(T) = DSM 23272(T)).
AU  - Mori K
AU  - Yamazoe A
AU  - Hosoyama A
AU  - Ohji S
AU  - Fujita N
AU  - Ishibashi J
AU  - Kimura H
AU  - Suzuki K
PT  - Journal Article
TA  - Int. J. Syst. Evol. Microbiol.
JT  - Int. J. Syst. Evol. Microbiol.
SO  - Int. J. Syst. Evol. Microbiol. 2014 64: 2128-2136.

PMID- 25146138
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Falsirhodobacter sp. Strain alg1, an Alginate-Degrading  Bacterium Isolated from Fermented Brown Algae.
PG  - e00826-14
AB  - Falsirhodobacter sp. alg1 is an alginate-degrading bacterium, the second species  from the
      nonphototrophic bacterial genus Falsirhodobacter. We report the first
      draft genome of a bacterium from this genus and point out possible important
      features related to alginate assimilation and its evolutionary aspects.
AU  - Mori T
AU  - Takahashi M
AU  - Tanaka R
AU  - Shibata T
AU  - Kuroda K
AU  - Ueda M
AU  - Takeyama H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00826-14.

PMID- 25999559
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Aeromonas caviae 8LM, Isolated from Stool Culture of a Child with Diarrhea.
PG  - e00524-15
AB  - Aeromonas spp. are Gram-negative rods ubiquitous in aquatic environments; however, some
      species are able to cause a variety of infections in humans. Here,
      we report the draft genome sequence of Aeromonas caviae 8LM isolated from stool
      culture from a child with diarrhea in southern Brazil.
AU  - Moriel B
AU  - Cruz LM
AU  - Dallagassa CB
AU  - Faoro H
AU  - de Souza EM
AU  - Pedrosa FO
AU  - Rego FG
AU  - Picheth G
AU  - Fadel-Picheth CM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00524-15.

PMID- 20439758
VI  - 107
DP  - 2010
TI  - Identification of protective and broadly conserved vaccine antigens from the genome of Extraintestinal Pathogenic Escherichia coli (ExPEC).
PG  - 9072-9077
AB  - Extraintestinal pathogenic Escherichia coli (ExPEC) are a common cause of disease in both
      mammals and birds. A vaccine to prevent such infections would be desirable given the
      increasing antibiotic resistance of these bacteria. We have determined the genome
      sequence of ExPEC IHE3034 (ST95) isolated from a case of neonatal
      meningitis and compared this to available genome sequences of
      other ExPEC strains and a few nonpathogenic E. coli. We found
      19 genomic islands present in the genome of IHE3034, which are
      absent in the nonpathogenic E. coli isolates. By using subtractive
      reverse vaccinology we identified 230 antigens present in ExPEC
      but absent (or present with low similarity) in nonpathogenic
      strains. Nine antigens were protective in a mouse challenge model.
      Some of them were also present in other pathogenic non-ExPEC
      strains, suggesting that a broadly protective E. coli vaccine may
      be possible. The gene encoding the most protective antigen was
      detected in most of the E. coli isolates, highly conserved in
      sequence and found to be exported by a type II secretion system
      which seems to be nonfunctional in nonpathogenic strains.
AU  - Moriel DG et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2010 107: 9072-9077.

PMID- 10946233
VI  - 460
DP  - 2000
TI  - Three-dimensional structural views of damaged-DNA recognition: T4 endonuclease V, E. coli Vsr protein, and human nucleotide excision repair factor XPA.
PG  - 257-275
AB  - Genetic information is frequently disturbed by introduction of modified or mismatch bases into
      duplex DNA, and hence all organisms contain DNA repair systems to restore normal genetic
      information by removing such damaged bases or nucleotides and replacing them by correct ones.
      The understanding of this repair mechanism is a central subject in cell biology. This review
      focuses on the three-dimensional structural views of damaged DNA recognition by three
      proteins. The first protein is T4 endonuclease V (T4 endo V), which catalyzes the first
      reaction step of the excision repair pathway to remove pyrimidine-dimers (PD) produced within
      duplex DNA by UV irradiation. The crystal structure of this enzyme complexed with DNA
      containing a thymidine-dimer provided the first direct view of DNA lesion recognition by a
      repair enzyme, indicating that the DNA kink coupled with base flipping-out is important for
      damaged DNA recognition. The second is very short patch repair (Vsr) endonuclease, which
      recognizes a TG mismatch within the five base pair consensus sequence. The crystal structure
      of this enzyme in complex with duplex DNA containing a TG mismatch revealed a novel mismatch
      base pair recognition scheme, where three aromatic residues intercalate from the major groove
      into the DNA to strikingly deform the base pair stacking but the base flipping-out does not
      occur. The third is human nucleotide excision repair (NER) factor XPA, which is a major
      component of a large protein complex. This protein has been shown to bind preferentially to
      UV- or chemical carcinogen-damaged DNA. The solution structure of the XPA central domain,
      essential for the interaction of damaged DNA, was determined by NMR. This domain was found to
      be divided mainly into a (Cys)4-type zinc-finger motif subdomain for replication protein A
      (RPA) recognition and the carboxyl terminal subdomain responsible for DNA binding.
AU  - Morikawa K
AU  - Shirakawa M
PT  - Journal Article
TA  - Mutat. Res.
JT  - Mutat. Res.
SO  - Mutat. Res. 2000 460: 257-275.

PMID- 8391397
VI  - 23
DP  - 1993
TI  - A sequence-specific endonuclease, Endo.SceI, can efficiently induce gene conversion in yeast mitochondria lacking a major exonuclease.
PG  - 537-541
AB  - Endo.SceI most likely initiates homologous recombination of the yeast mitochondrial genome
      through sequence-specific double-strand scission of DNA.  According to the double-strand
      break-repair model for the mechanism of homologous recombination, DNA ends created by
      sequence-specific endonucleases have to be processed by exonucleases.  The major mitochondrial
      exonuclease (encoded by NUC1) has been shown to greatly affect the length of conversion tracts
      at the 21S rRNA locus when site-specific gene conversion is induced by omega endonuclease.  In
      order to examine the role of the NUC1 nuclease in the Endo.SceI-induced recombination,
      recombination frequencies were measured after crossing of parental strains either in the
      presence or absence of NUC1 nuclease activity.  The frequency of gene conversion in the oli2
      locus induced by Endo.SceI was not reduced by disruption of the NUC1 gene.  This result
      strongly implicates the presence of multiple exonucleases for the processing of the DNA ends
      created by sequence-specific endonucleases.
AU  - Morishima N
AU  - Nakagawa K-I
AU  - Shibata T
PT  - Journal Article
TA  - Curr. Genet.
JT  - Curr. Genet.
SO  - Curr. Genet. 1993 23: 537-541.

PMID- 2203771
VI  - 265
DP  - 1990
TI  - A subunit of yeast site-specific endonuclease SceI is a mitochondrial version of the 70-kDa heat shock protein.
PG  - 15189-15197
AB  - Endo.SceI of Saccharomyces cerevisiae is a heterodimeric site-specific
      endonuclease, which is distinguishable from prokaryotic restriction
      endonucleases in the mode of recognition of its cleavage site.  We have used
      monoclonal antibodies specific to the larger subunit (75 kDa) of Endo.SceI to
      isolate the gene for the subunit (ENS1) from S. cerevisiae.  Unexpectedly ENS1
      was found to encode a 70-kDa heat shock protein-related polypeptide and to be
      identical to recently cloned SSC1.  Subcellular fractionation experiments on
      yeast cells revealed that the primary target site of the larger subunit is
      mitochondria, where almost all the Endo.SceI activity is localized.  Molecular
      genetic analysis of ENS1 demonstrated its indispensability for growth and the
      requirement of a high level of its expression at the sporulation and
      germination stages.  The data suggest that ENS1 plays an important role,
      especially at these differentiation stages.
AU  - Morishima N
AU  - Nakagawa K-I
AU  - Yamamoto E
AU  - Shibata T
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1990 265: 15189-15197.

PMID- 1294675
VI  - 64
DP  - 1992
TI  - SceI: an endonuclease with multiple cutting sites induces homologous genetic recombination.
PG  - 1420-1431
AB  - A review.
AU  - Morishima N
AU  - Shibata T
PT  - Journal Article
TA  - Seikagaku
JT  - Seikagaku
SO  - Seikagaku 1992 64: 1420-1431.

PMID- 1947180
VI  - 36
DP  - 1991
TI  - Sequence-specific endonucleases involved in genetic recombination.
PG  - 1716-1720
AB  - 
AU  - Morishima N
AU  - Shibata T
PT  - Journal Article
TA  - Tanpakushitsu Kakusan Koso
JT  - Tanpakushitsu Kakusan Koso
SO  - Tanpakushitsu Kakusan Koso 1991 36: 1716-1720.

PMID- 18487258
VI  - 15
DP  - 2008
TI  - Comparative Genome Analysis of Lactobacillus reuteri and Lactobacillus fermentum Reveal a Genomic Island for Reuterin and Cobalamin Production.
PG  - 151-161
AB  - Lactobacillus reuteri is a heterofermentative lactic acid bacterium that naturally inhabits
      the gut of humans and other animals. The probiotic
      effects of L. reuteri have been proposed to be largely associated with the
      production of the broad-spectrum antimicrobial compound reuterin during
      anaerobic metabolism of glycerol. We determined the complete genome
      sequences of the reuterin-producing L. reuteri JCM 1112(T) and its closely
      related species Lactobacillus fermentum IFO 3956. Both are in the same
      phylogenetic group within the genus Lactobacillus. Comparative genome
      analysis revealed that L. reuteri JCM 1112(T) has a unique cluster of 58
      genes for the biosynthesis of reuterin and cobalamin (vitamin B(12)). The
      58-gene cluster has a lower GC content and is apparently inserted into the
      conserved region, suggesting that the cluster represents a genomic island
      acquired from an anomalous source. Two-dimensional nuclear magnetic
      resonance (2D-NMR) with (13)C(3)-glycerol demonstrated that L. reuteri JCM
      1112(T) could convert glycerol to reuterin in vivo, substantiating the
      potential of L. reuteri JCM 1112(T) to produce reuterin in the intestine.
      Given that glycerol is shown to be naturally present in feces, the
      acquired ability to produce reuterin and cobalamin is an adaptive
      evolutionary response that likely contributes to the probiotic properties
      of L. reuteri.
AU  - Morita H
AU  - Toh H
AU  - Fukuda S
AU  - Horikawa H
AU  - Oshima K
AU  - Suzuki T
AU  - Murakami M
AU  - Hisamatsu S
AU  - Kato Y
AU  - Takizawa T
AU  - Fukuoka H
AU  - Yoshimura T
AU  - Itoh K
AU  - O'Sullivan DJ
AU  - McKay LL
AU  - Ohno H
AU  - Kikuchi J
AU  - Masaoka T
AU  - Hattori M
PT  - Journal Article
TA  - DNA Res.
JT  - DNA Res.
SO  - DNA Res. 2008 15: 151-161.

PMID- 25883283
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Bifidobacterium kashiwanohense JCM 15439T, Isolated from Feces from a Healthy Japanese Infant.
PG  - e00255-15
AB  - We isolated Bifidobacterium kashiwanohense JCM 15439 from the feces of a healthy  Japanese
      infant and proposed it as the type strain of a novel species within the
      genus Bifidobacterium. Here, we report the complete genome sequence of this
      organism.
AU  - Morita H
AU  - Toh H
AU  - Nakano A
AU  - Oshima K
AU  - Takagi M
AU  - Suda W
AU  - Tanabe S
AU  - Hattori M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00255-15.

PMID- 19820099
VI  - 191
DP  - 2009
TI  - Complete genome sequence of probiotic Lactobacillus rhamnosus ATCC 53103.
PG  - 7630-7631
AB  - Lactobacillus rhamnosus is a facultatively heterofermentative lactic acid bacterium and is
      frequently isolated from human gastrointestinal mucosa of healthy individuals. L. rhamnosus
      ATCC 53103 isolated from a healthy human intestinal flora is one of the most widely used and
      well-documented probiotics. Here we report the finished and annotated genome sequence of this
      organism.
AU  - Morita H
AU  - Toh H
AU  - Oshima K
AU  - Murakami M
AU  - Taylor TD
AU  - Igimi S
AU  - Hattori M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2009 191: 7630-7631.

PMID- 27034488
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Leuconostoc mesenteroides 213M0, Isolated from Traditional Fermented Mare Milk Airag in Bulgan Aimag, Mongolia.
PG  - e00178-16
AB  - Leuconostoc mesenteroides213M0 was isolated from traditional fermented mare milk  airag in
      Bulgan Aimag, Mongolia. This strain produces a listericidal
      bacteriocin-like inhibitory substance. Here, we report the draft genome sequence
      of this organism.
AU  - Morita H
AU  - Toh H
AU  - Oshima K
AU  - Nakano A
AU  - Hano C
AU  - Yoshida S
AU  - Bolormaa T
AU  - Burenjargal S
AU  - Nguyen CT
AU  - Tashiro K
AU  - Arakawa K
AU  - Miyamoto T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00178-16.

PMID- 27013047
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Leuconostoc mesenteroides 406 Isolated from the Traditional Fermented Mare Milk Airag in Tuv Aimag, Mongolia.
PG  - e00166-16
AB  - Leuconostoc mesenteroides406 was isolated from the traditional fermented mare milk airag in
      Tuv Aimag, Mongolia. This strain produces an antilisterial
      bacteriocin. Here, we report the draft genome sequence of this organism.
AU  - Morita H
AU  - Toh H
AU  - Oshima K
AU  - Nakano A
AU  - Hano C
AU  - Yoshida S
AU  - Nguyen TT
AU  - Wulijideligen TK
AU  - Arakawa K
AU  - Miyamoto T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00166-16.

PMID- 21829716
VI  - 6
DP  - 2011
TI  - Complete Genome Sequence and Comparative Analysis of the Fish Pathogen Lactococcus garvieae.
PG  - E23184
AB  - Lactococcus garvieae causes fatal haemorrhagic septicaemia in fish such as
      yellowtail. The comparative analysis of genomes of a virulent strain Lg2
      and a non-virulent strain ATCC 49156 of L. garvieae revealed that the two
      strains shared a high degree of sequence identity, but Lg2 had a 16.5-kb
      capsule gene cluster that is absent in ATCC 49156. The capsule gene
      cluster was composed of 15 genes, of which eight genes are highly
      conserved with those in exopolysaccharide biosynthesis gene cluster often
      found in Lactococcus lactis strains. Sequence analysis of the capsule gene
      cluster in the less virulent strain L. garvieae Lg2-S, Lg2-derived strain,
      showed that two conserved genes were disrupted by a single base pair
      deletion, respectively. These results strongly suggest that the capsule is
      crucial for virulence of Lg2. The capsule gene cluster of Lg2 may be a
      genomic island from several features such as the presence of insertion
      sequences flanked on both ends, different GC content from the chromosomal
      average, integration into the locus syntenic to other lactococcal genome
      sequences, and distribution in human gut microbiomes. The analysis also
      predicted other potential virulence factors such as haemolysin. The
      present study provides new insights into understanding of the virulence
      mechanisms of L. garvieae in fish.
AU  - Morita H
AU  - Toh H
AU  - Oshima K
AU  - Yoshizaki M
AU  - Kawanishi M
AU  - Nakaya K
AU  - Suzuki T
AU  - Miyauchi E
AU  - Ishii Y
AU  - Tanabe S
AU  - Murakami M
AU  - Hattori M
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2011 6: E23184.

PMID- 18618709
VI  - 73
DP  - 2008
TI  - Crystal structure of a putative DNA methylase TTHA0409 from Thermus thermophilus HB8.
PG  - 259-264
AB  - To protect the cell from exogenous DNA, most species have DNA modification methylase.  It is
      also reported that DNA methylation is essentially involved in bacterial virulence.  Many
      restriction-modification systems have been researched, and several three-dimensional
      structures of R-M enzymes have been determined.  DNA modification methylases catalyze the
      transfer of a methyl group to DNA from S-adenosyl-L-methionine, which is consequently
      converted to S-adenosyl-L-homocysteine.  These enzymes are categorized into the following two
      classes based on the position of the transferred methyl group on the DNA bases: endocyclic
      MTases and exocyclic amino MTases.  Endocyclic MTases methylate the C5 position of a cytosine
      base, whereas exocyclic amino MTases methylate the N6 position of an adenine base or N4
      position of a cytosine base.  Furtermore, the exocyclic amino MTases are subdivided into six
      classes, namely, alpha, beta, gamma, delta and epsilon, based on their amino acid sequences.
AU  - Morita R
AU  - Ishikawa H
AU  - Nakagawa N
AU  - Kuramitsu S
AU  - Masui R
PT  - Journal Article
TA  - Proteins
JT  - Proteins
SO  - Proteins 2008 73: 259-264.

PMID- 29930046
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Lactobacillus plantarum Strain LQ80, Selected for Preparation of Fermented Liquid Feed for Pigs.
PG  - e00530-18
AB  - Lactobacillus plantarum LQ80 is a strain isolated from liquid feed for pigs. We determined the
      complete genome sequence of this strain using the PacBio RS II
      platform. LQ80 contained a single circular chromosome of 3,230,192 bp, with
      44.66% G+C content and seven plasmids.
AU  - Moriya N et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00530-18.

PMID- 1641344
VI  - 20
DP  - 1992
TI  - Isolation and characterization of a restriction enzyme BspO4I from an alkalophilic bacterium.
PG  - 3781
AB  - A type II restriction enzyme, BspO4I, has been isolated from Bacillus sp 0-4 (ATCC 21536), an
      alkalophilic bacterium. The enzyme was an isoschizomer of PvuII, recognizing the six base
      palindromic sequence of 5'CAGCTG3' and cleaves between G and C residues to produce
      blunt-ended cleavage products. Bsp04I was partially purified from a cell-free extract using
      column chromatography on DEAE-cellulose, heparin-cellulofine and phosphocellulose. Optimal
      conditions for the enzyme activity were pH 8.5, 20 mM MgCl2, 250 mM monovalent cation (NaCl or
      KCl), 10 mM 2-mercaptoethanol at 40oC. The cleavage site of BspO4I was determined by primer
      extension experiments and indicated that BspO4I recognizes and cleaves the following sequence:
      5'CAG^CTG3'
      3'GTC^GAC5'.
AU  - Moriya S
AU  - Yanagawa S
AU  - Aoki N
AU  - Iwabuchi M
AU  - Inoue T
AU  - Ando T
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 3781.

PMID- 27313289
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Methylobacterium populi P-1M, Isolated from Pink-Pigmented Household Biofilm.
PG  - e00458-16
AB  - Methylobacterium populi P-1M is isolated from the pink-pigmented household biofilm. Here, we
      present the complete genome sequence of P-1M, consisting of one
      chromosome of 5,705,640 bp and five plasmids of 64,864 bp, 59,879 bp, 42,569 bp,
      41,417 bp, and 29,506 bp.
AU  - Morohoshi T
AU  - Ikeda T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00458-16.

PMID- 25323715
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of N-Acylhomoserine Lactone-Producing Pseudomonas sp. Strain StFLB209, Isolated from Potato Phyllosphere.
PG  - e01037-14
AB  - Pseudomonas sp. strain StFLB209 is isolated from the potato leaf and produces N-acylhomoserine
      lactone quorum-sensing signal compounds. Here, we present the
      6,332,373-bp complete genome sequence of StFLB209, with a G+C content of 60.7%,
      which carries 5,598 protein-coding genes, 6 rRNA operons, and 69 tRNA genes.
AU  - Morohoshi T
AU  - Kato T
AU  - Someya N
AU  - Ikeda T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01037-14.

PMID- 25291777
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Chryseobacterium sp. Strain StRB126, an N-Acylhomoserine Lactone-Degrading Bacterium Isolated from Potato Root.
PG  - e00952-14
AB  - Chryseobacterium sp. strain StRB126 was isolated from a potato root and showed
      N-acylhomoserine lactone-degrading activity. Here, we present the complete
      5,503,743-bp genome sequence of StRB126, which has a G+C content of 35.6% and
      carries 4,828 protein-coding genes, six rRNA operons, and 80 tRNA genes.
AU  - Morohoshi T
AU  - Wang WZ
AU  - Someya N
AU  - Ikeda T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00952-14.

PMID- 21357489
VI  - 193
DP  - 2011
TI  - Genome Sequence of Microbacterium testaceum StLB037, an N-Acylhomoserine Lactone-Degrading Bacterium Isolated from Potato Leaves.
PG  - 2072-2073
AB  - Microbacterium testaceum is an endophytic Gram-positive bacterium that resides within plant
      hosts. M. testaceum StLB037 was isolated from potato
      leaves and shows N-acylhomoserine lactone-degrading activity. Here, we
      present the 3.98-Mb complete genome sequence of StLB037, with an average
      GC content of 70.28%.
AU  - Morohoshi T
AU  - Wang WZ
AU  - Someya N
AU  - Ikeda T
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 2072-2073.

PMID- 26687717
VI  - 44
DP  - 2015
TI  - Temporal dynamics of methyltransferase and restriction endonuclease accumulation  in individual cells after introducing a restriction-modification system.
PG  - 790-800
AB  - Type II restriction-modification (R-M) systems encode a restriction endonuclease  that cleaves
      DNA at specific sites, and a methyltransferase that modifies same
      sites protecting them from restriction endonuclease cleavage. Type II R-M systems
      benefit bacteria by protecting them from bacteriophages. Many type II R-M systems
      are plasmid-based and thus capable of horizontal transfer. Upon the entry of such
      plasmids into a naive host with unmodified genomic recognition sites,
      methyltransferase should be synthesized first and given sufficient time to
      methylate recognition sites in the bacterial genome before the toxic restriction
      endonuclease activity appears. Here, we directly demonstrate a delay in
      restriction endonuclease synthesis after transformation of Escherichia coli cells
      with a plasmid carrying the Esp1396I type II R-M system, using single-cell
      microscopy. We further demonstrate that before the appearance of the Esp1396I
      restriction endonuclease the intracellular concentration of Esp1396I
      methyltransferase undergoes a sharp peak, which should allow rapid methylation of
      host genome recognition sites. A mathematical model that satisfactorily describes
      the observed dynamics of both Esp1396I enzymes is presented. The results reported
      here were obtained using a functional Esp1396I type II R-M system encoding both
      enzymes fused to fluorescent proteins. Similar approaches should be applicable to
      the studies of other R-M systems at single-cell level.
AU  - Morozova N
AU  - Sabantsev A
AU  - Bogdanova E
AU  - Fedorova Y
AU  - Maikova A
AU  - Vedyaykin A
AU  - Rodic A
AU  - Djordjevic M
AU  - Khodorkovskii M
AU  - Severinov K
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2015 44: 790-800.

PMID- 818976
VI  - 108
DP  - 1976
TI  - Restriction in Myxococcus virescens.
PG  - 227-230
AB  - 1.  The plating efficiency of bacteriophage MX-1 on Myococcus xanthus strains A
      and B and M. virescens V2 were compared.  Comparison of strains V2 and A
      suggest that V2 is restrictive and A is not (restriction coefficient was
      approximately 8).  A derivative of M. virescens V2 (strain V2-9) was obtained
      by repeated exposure of strain V2 to ultraviolet radiation.  Strain V2-9 was
      also unrestrictive.  Strain B is apparently unrestrictive too but analysis of
      phenotypic changes in phage derived from hosts V2, B and A suggested that some
      of the host-cell processes differ from orthodox restriction and modification.
      2.  Cell-free extracts from M. virescens V2 were fractionated by ion-exchange
      chromatography and two restriction endonucleases, R. MviV2I and R. MviV2II were
      identified.  Nuclease I was found to hydrolyse coliphage lambda DNA at
      apparently one site only and MX-1 DNA at approximately 10 sites; nuclease II
      was found to hydrolyse MX-1 DNA at a very large number of sites and its
      restriction sequence was of comparable frequency with that of R.EcoRII.
      "Modified MX-1 DNA", obtained from phage whose last host was M. virescens V2
      was hydroxlysed by nuclease II but not by nuclease I.  The significance of
      these findings for restriction in myxococci is discussed.
AU  - Morris DW
AU  - Parish JH
PT  - Journal Article
TA  - Arch. Microbiol.
JT  - Arch. Microbiol.
SO  - Arch. Microbiol. 1976 108: 227-230.

PMID- 18178732
VI  - 190
DP  - 2008
TI  - Genomic characterization of mycobacteriophage giles: evidence for phage acquisition of host DNA by illegitimate recombination.
PG  - 2172-2182
AB  - A characteristic feature of bacteriophage genomes is that they are
      architecturally mosaic, with each individual genome representing a unique
      assemblage of individual exchangeable modules. Plausible mechanisms for
      generating mosaicism include homologous recombination at shared boundary
      sequences of module junctions, illegitimate recombination in a
      non-sequence-directed process, and site-specific recombination. Analysis
      of the novel mycobacteriophage Giles genome not only extends our current
      perspective on bacteriophage genetic diversity, with more than 60% of the
      genes unrelated to other mycobacteriophages, but offers novel insights
      into how mosaic genomes are created. In one example, the
      integration/excision cassette is atypically situated within the structural
      gene operon and could have moved there either by illegitimate
      recombination or more plausibly via integrase-mediated site-specific
      recombination. In a second example, a DNA segment has been recently
      acquired from the host bacterial chromosome by illegitimate recombination,
      providing further evidence that phage genomic mosaicism is generated by
      nontargeted recombination processes.
AU  - Morris P
AU  - Marinelli LJ
AU  - Jacobs-Sera D
AU  - Hendrix RW
AU  - Hatfull GF
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2008 190: 2172-2182.

PMID- 27231373
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Pseudomonas fluorescens LBUM636, a Strain with Biocontrol Capabilities against Late Blight of Potato.
PG  - e00446-16
AB  - Herein provided is the full-genome sequence of Pseudomonas fluorescens LBUM636. This strain is
      a plant growth-promoting rhizobacterium (PGPR) which produces
      phenazine-1-carboxylic acid, an antibiotic involved in the biocontrol of numerous
      plant pathogens, including late blight of potato caused by the plant pathogen
      Phytophthora infestans.
AU  - Morrison CK
AU  - Novinscak A
AU  - Gadkar VJ
AU  - Joly DL
AU  - Filion M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00446-16.

PMID- 24620832
VI  - 11
DP  - 2014
TI  - Complete genome analysis of a frog virus 3 (FV3) isolate and sequence comparison with isolates of differing levels of virulence.
PG  - 46
AB  - BACKGROUND: Frog virus 3 (FV3) is the type species of the genus Ranavirus, and in
      the past few decades, FV3 infections have resulted in considerable morbidity and
      mortality in a range of wild and cultivated amphibian species in the Americas,
      Europe, and Asia. The reasons for the pathogenicity of FV3 are not well
      understood. FINDINGS: We investigated three FV3 isolates designated SSME, wt-FV3,
      and aza-Cr, and reported that our wt-FV3 and aza-Cr strains showed similar levels
      of virulence, while SSME was the least virulent in an in vivo study with
      Lithiobates pipiens tadpoles. Using 454 GS-FLX sequencing technology, we
      sequenced SSME and compared it to the published wt-FV3 genome. SSME had multiple
      amino acid deletions in ORFs 49/50L, 65L, 66L, and 87L, which may explain its
      reduced virulence. We also investigated repeat regions and found that repeat copy
      number differed between isolates, with only one group of 3 isolates and 1 pair of
      isolates being identical at all 3 locations. CONCLUSIONS: In this study we have
      shown that genetic variability is present between closely related FV3 isolates,
      both in terms of deletions/insertions, and even more so at select repeat
      locations. These genomic areas with deletions/insertions may represent regions
      that affect virulence, and therefore require investigation. Furthermore, we have
      identified repeat regions that may prove useful in future phylogeographical
      tracking and identification of ranaviral strains across different environmental
      regions.
AU  - Morrison EA
AU  - Garner S
AU  - Echaubard P
AU  - Lesbarreres D
AU  - Kyle CJ
AU  - Brunetti CR
PT  - Journal Article
TA  - Virol. J.
JT  - Virol. J.
SO  - Virol. J. 2014 11: 46.

PMID- 
VI  - 104
DP  - 2004
TI  - Homing endonuclease I-CreI mutants with substitutions at residues 30, 32 and 38 include altered specificity derivatives.
PG  - 313
AB  - The homing endonuclease I-CreI recognizes and cleaves a specific 22 base pair DNA sequence.
      The amino acid contacts responsible for DNA recognition have been identified; three such
      residues that cooperate to interact with a particular target site base pair are N30, S32, and
      Q38.  In order to study how these residues function in DNA recognition and cleavage, as well
      as the interactions bertween the residues themselves, we employed site-directed mutagenesis to
      alter the amino acids at these positions.  Resulting I-CreI derivatives were then assayed in
      vivo in an Escherichia coli based system for cleavage activity against appropriate DNA
      targets.  A number of active I-CreI derivatives altered at these positions have been isolated
      and characterized both in vivo and in vitro.  Our results demonstrate that it is possible to
      isolate derivatives of I-CreI altered at residues 30, 32 and 38 that exhibit novel DNA
      recognition properties.
AU  - Morrison HA
AU  - Seligman LM
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 2004 104: 313.

PMID- 
VI  - 
DP  - 1991
TI  - Deoxyribonucleic acid restriction/modification systems and gene transfer strategies in Ruminococcus albus 8 and Ruminococcus flavofaciens FD-1.
PG  - 1-134
AB  - One goal critical to the use of recombinant DNA technologies with rumen bacteria is the
      establishment of a stable DNA transfer system. Research to date has shown that Ruminococcus
      can be classified as a genus resistant to transformation, and that electroporation may offer
      the only means to introduce foreign DNA. This thesis aims to elucidate and solve limitations
      to the utilization of electroporation with Ruminococcus albus 8 and Ruminococcus flavefaciens
      FD-1. The limited degradation of DNA by restriction enzymes and confirmation of plasmid uptake
      were given priority, although the consequences of incompatible plasmid replicons and failure
      in the expression of selectable markers cannot be overlooked. Fluorescent labelled dextrans
      were used in place of plasmid DNA and indicated that electroporation resulted in the uptake of
      macromolecules. Type-II endonuclease activities were present in most strains of Ruminococcus
      tested. However, the cell-free extract of R. flavefaciens FD-1 did not provide a simple DNA
      protection strategy, so the restriction/modification systems of R. albus 8 and R. flavefaciens
      FD-1 were studied in more detail. Plasmids derived from a dam proficient Escherichia coli
      background are protected against the Type-IIS restriction enzyme of R. albus 8. Adenine
      methylation by M.TaqI and a methylase from Chlorella will inhibit DNA cleavage by RflFI and
      RFlFII, respectively. The initial electroporation experiments utilizing methylated DNA were
      unsuccessful in yielding phenotypic transformants of R. albus 8. Plasmid DNA isolated directly
      from Ruminococcus would be a valuable tool in addressing some of the problems still affecting
      gene transfer. The plasmid pBAW301, present in R. flavefaciens strain R13c2, was isolated and
      is sufficiently small to facilitate construction of potential shuttle vectors as well as broad
      host range, chimeric plasmids. Knowledge of DNA modification in Ruminococcus has been
      obtained. Other species possessing stable plasmids and gene/s encoding antibiotic resistance
      have also been identified. Greater emphasis can now be placed on the electroporation technique
      itself, as well as a wider range of selective markers. Ruminococcus ssp. required further
      investigation if model genetic systems are to be developed and some of the proposed goals of
      molecular biology research for this genus are to be fully realized.
AU  - Morrison M
PT  - Journal Article
TA  - Ph.D. Thesis, University of Illinois, USA
JT  - Ph.D. Thesis, University of Illinois, USA
SO  - Ph.D. Thesis, University of Illinois, USA 1991 : 1-134.

PMID- 7958770
VI  - 122
DP  - 1994
TI  - The restriction endonuclease RflFII, isolated from Ruminococcus flavefaciens FD-1, recognizes the sequence 5'-AGTACT-3', and is inhibited by site-specific adenine methylation.
PG  - 181-185
AB  - Molecular studies of the rumen bacterium Ruminococcus flavefaciens are constrained by the lack
      of stable gene transfer system. We report here on the characterization of RflFII, a
      restriction endonuclease isolated from R. flavefaciens FD-1. The enzyme is an isoschizomer of
      ScaI, and cleavage of the DNA is blunt-ended, between the internal TA dinucleotide sequence of
      5'-AGTACT-3'. Chromosomal DNA preparations were used to demonstrate that adenine methylation
      of DNA within the sequence 5'-GTAC-3' inhibits both RflFII and the restriction endonucleases
      RsaI and ScaI. Chromosomal DNA from R. flavefaciens FD-1 is also host modified to protect
      against cleavage by ScaI.
AU  - Morrison M
AU  - Mackie RI
AU  - White BA
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1994 122: 181-185.

PMID- 1539994
VI  - 58
DP  - 1992
TI  - Partial characterization of a DNA restriction endonuclease from Ruminococcus flavefaciens FD-1 and its inhibition by site-specific adenine methylation.
PG  - 66-69
AB  - The principal DNA restriction-modification system of the cellulolytic ruminal
      bacterium Ruminococcus flavefaciens FD-1 is described.  The restriction
      endonuclease RflFI could be separated from cell extracts by phosphocellulose
      and heparin-sepharose chromatography.  Restriction enzyme digests utilizing
      RflFI alone or in combination with SalI, a restriction enzyme isolated from
      Streptomyces albus G, showed that the DNA sequence recognized by RflFI either
      overlapped or was the same as that recognized by SalI.  DNA sequence analysis
      confirmed that RflFI was identical in activity to SalI, with the recognition
      sequence being 5'-GTCGAC-3' and cleavage occurring between G and T.  Adenine
      methylation within this sequence can be catalyzed in vitro by TaqI methylase,
      and this inhibited the cleavage of plasmid DNA molecules by RflFI and SalI.
      Chromosomal DNA from R. flavefaciens FD-1 is also methylated within this DNA
      sequence because neither restriction endonuclease could degrade this DNA
      substrate.  These findings provide a means to protect plasmid molecules from
      degradation prior to gene transfer experiments with R. flavefaciens FD-1.
AU  - Morrison M
AU  - Mackie RI
AU  - White BA
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1992 58: 66-69.

PMID- 1547946
VI  - 111
DP  - 1992
TI  - Partial purification and characterization of Ral8I, a class-IIS restriction endonuclease from Ruminococcus albus 8 which recognizes 5'-GGATC .
PG  - 105-108
AB  - Heparin-agarose chromatography was used to isolate a restriction endonuclease (ENase) from the
      cellulolytic Gram + anaerobe, Ruminococcus albus 8. The enzyme, Ral8I, was eluted from the
      column using 230-310 mM Na+. However, the preparation was active only with DNA substrates that
      were not Dam-methylated. Moreover the restriction fragment pattern generated from simian virus
      40 (SV40) DNA was not consistent with the expected number of Dam-methylation sites. Alignment
      of the Dam-methylation sites in SV40 DNA indicated that Ral8I may actually recognize the
      asymmetric sequence, GGATC. This was confirmed by nucleotide (nt) sequence analysis and,
      further, Ral8I was found to cause cleavage of the DNA approx. 5 nt downstream from the
      recognition sequence. Ral8I can therefore be classified as a type-IIS restriction endonuclease
      and is an isoschizomer of AlwI, BinI and BthII.
AU  - Morrison M
AU  - Mackie RI
AU  - White BA
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1992 111: 105-108.

PMID- Not carried by PubMed...
VI  - 0
DP  - 1992
TI  - Restriction-modification systems in Ruminococcus and development of a gene transfer system.
PG  - 301-303
AB  - 
AU  - Morrison M
AU  - Mackie RI
AU  - White BA
PT  - Journal Article
TA  - Aust. Microbiol.
JT  - Aust. Microbiol.
SO  - Aust. Microbiol. 1992 0: 301-303.

PMID- 27445383
VI  - 4
DP  - 2016
TI  - Complete Genome Sequences of Three Outbreak-Associated Legionella pneumophila Isolates.
PG  - e00696-16
AB  - We report here the complete genome sequences of three Legionella pneumophila isolates that are
      associated with a Legionnaires' disease outbreak in New York in
      2012. Two clinical isolates (D7630 and D7632) and one environmental isolate
      (D7631) were recovered from this outbreak. A single isolate-specific virulence
      gene was found in D7632. These isolates were included in a large study evaluating
      the genomic resolution of various bioinformatics approaches for L. pneumophila
      serogroup 1 isolates.
AU  - Morrison SS
AU  - Desai HP
AU  - Mercante JW
AU  - Lapierre P
AU  - Raphael BH
AU  - Musser K
AU  - Winchell JM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00696-16.

PMID- 25573935
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Legionella pneumophila D-5864, a Serogroup 6 Strain.
PG  - e01379-14
AB  - Legionella pneumophila is the leading etiology of legionellosis infections in North America
      and Europe. Here we report the draft genome sequence of L.
      pneumophila D-5864, a serogroup 6 strain, which was isolated from a bronchial
      alveolar lavage specimen of a male patient from Arizona in 2009. Genes within the
      lipopolysaccharide (LPS)-biosynthesis region could potentially be determinants of
      serogroup specificity.
AU  - Morrison SS
AU  - Kozak-Muiznieks NA
AU  - Sammons S
AU  - Rowe LA
AU  - Frace M
AU  - Winchell JM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01379-14.

PMID- 4343967
VI  - 69
DP  - 1972
TI  - Cleavage of Simian Virus 40 DNA at a unique site by a bacterial restriction enzyme.
PG  - 3365-3369
AB  - The RI restriction endonuclease of Escherichia coli converts covalently-closed
      circular Simian Virus 40 (SV40) DNA to unit-length linear duplex molecules.
      Cleavage occurs at a unique site, since denaturation and renaturation of these
      linear molecules yield linear but no circular molecules.  The distance from the
      cleavage site to the SV40 DNA sequence contained in the adenovirus-SV40 hybrid,
      Ad2+ND1, is 0.11 of the length of SV40 DNA.  T4 gene 32 protein binds to SV40
      DNA in a region 0.45 of the length of SV40 DNA from the RI cleavage site.  E.
      coli B restriction endonuclease can cleave SV40 DNA at several sites.
AU  - Morrow JF
AU  - Berg P
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1972 69: 3365-3369.

PMID- 15956212
VI  - 102
DP  - 2005
TI  - Recruitment of DNA methyltransferase I to DNA repair sites.
PG  - 8905-8909
AB  - In mammalian cells, the replication of genetic and epigenetic information is directly coupled;
      however, little is known about the maintenance of epigenetic information in DNA repair. Using
      a laser microirradiation system to introduce DNA lesions at defined subnuclear sites, we
      tested whether the major DNA methyltransferase (Dnmt1) or one of the two de novo
      methyltransferases (Dnmt3a, Dnmt3b) are recruited to sites of DNA repair in vivo. Time lapse
      microscopy of microirradiated mammalian cells expressing GFP-tagged Dnmt1, Dnmt3a, or Dnmt3b1
      together with red fluorescent protein-tagged proliferating cell nuclear antigen (PCNA)
      revealed that Dnmt1 and PCNA accumulate at DNA damage sites as early as 1 min after
      irradiation in S and non-S phase cells, whereas recruitment of Dnmt3a and Dnmt3b was not
      observed. Deletion analysis showed that Dnmt1 recruitment was mediated by the PCNA-binding
      domain. These data point to a direct role of Dnmt1 in the restoration of epigenetic
      information during DNA repair.
AU  - Mortusewicz O
AU  - Schermelleh L
AU  - Walter J
AU  - Cardoso MC
AU  - Leonhardt H
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2005 102: 8905-8909.

PMID- Not carried by PubMed...
VI  - 91
DP  - 1991
TI  - Characteristics of a restriction endonuclease from the Cyanobacterium Nostoc PCC 7121 and protection of DNA with Eco 47 II methylase.
PG  - 155
AB  - In order to investigate the structure and function of the cytochrome b6-f
      complex, we are trying to develop procedures for gene transfer into and gene
      replacement in Nostoc PCC 7121, a heterotrophic cyanobacterium from which the
      cytochrome b6-f genes have been cloned and sequenced.  Restriction
      endonucleases in Nostoc are being investigated as possible barriers to
      transformation.  A restriction endonuclease which we designated Nsp7121I has
      been isolated and partially purified.  The DNA recognition sequence (GGNCC) for
      this endonuclease was established by comparison of Nsp7171I restriction digests
      of plasmid and bacteriophage DNAs with computer generated restriction fragment
      profiles.  Plasmid encoded Eco47II methylase protected DNA against restriction
      by the Nostoc endonuclease.  Unmodified plasmids previously used in
      transformation attempts were cleaved at multiple sites.  Thus one barrier to
      transformation has been identified and a modification methylase is available
      for its circumvention.  Work is in progress to test transformation of Nostoc
      PCC 7121 with Eco47II protected DNA.
AU  - Moser D
AU  - Kallas T
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1991 91: 155.

PMID- 8215799
VI  - 160
DP  - 1993
TI  - Characterization of a restriction barrier and electrotransformation of the cyanobacterium Nostoc PCC-7121.
PG  - 229-237
AB  - We have investigated host restriction as a barrier to transformation and developed a method
      for gene transfer into the previously untransformable, heterotrophic cyanobacterium Nostoc PCC
      7121. A restriction endonuclease, designed Nsp7121I, has been partialy purified by
      phosphocellulose chromatography of Nostoc cell extracts. Comparisons of Nsp7121I digests of
      bacteriophage lambda and plasmid DNAs with computer-generated restriction fragment profiles
      showed that Nsp7121I is an isoschizomer of restriction endonucleases, such as AsuI, Nsp75241V,
      Sau96I, and Eco4711, that recognize the sequence GGNCC. Cleavage by Nsp71211 within this
      sequence was confirmed by sequence analysis of DNA fragments cleaved at a unique Nsp7121I
      site. These date further suggested that cleavage occurs after the first G (5'-G/GNCC-3') in
      this site to generate a three base 5' overhang. Nsp7121I degraded all plasmids used in
      previous transformation attempts but modification of these DNA molecules by Eco47II methylase
      effectively prevented digestion by Nsp7121I. Plasmids premethylated by passage through
      Escherichia coli carrying a plasmid-encoded Eco47II methylase have now been used in an
      electroporation procedure to transform Nostoc PCC 7121 to neomycin resistance at frequencies
      as high as one transformant per 1000 viable cells. Transformation and stable replication
      within Nostoc of one of the transforming plasmids (pRL25), was confirmed by recovery of pRL25,
      in its original form, from transformants. Conjugal transfer of pRL25 from E. coli into Nostoc
      was also possible but at much lower efficiency than by electroporation. These findings
      establish the basis for genetic analysis of Nostoc PCC 7121, from which genes for
      photosynthetic electron transport have been cloned.
AU  - Moser DP
AU  - Zarka D
AU  - Kallas T
PT  - Journal Article
TA  - Arch. Microbiol.
JT  - Arch. Microbiol.
SO  - Arch. Microbiol. 1993 160: 229-237.

PMID- 231678
VI  - 135
DP  - 1979
TI  - Specific Recombination in Vitro Promoted by the Restriction Endonuclease HgaI.
PG  - 517-524
AB  - We describe the use of the restriction endonuclease HgaI from Haemophilus
      gallinarum for the efficient construction in vitro of recombinant molecules.
      Using bacteriophage f1 DNA, we show that only HgaI fragments that were
      orginally adjacent on the genome are ligated, that upon ligation infectious
      molecules are reassembled with high efficiency, and that recombinant genomes
      can thus be easily constructed.  The method relies upon the unique properties
      of HgaI and is applicable to any viral or plasmid DNA that contains several
      HgaI recognition sites.
AU  - Moses P
AU  - Horiuchi K
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1979 135: 517-524.

PMID- 22461555
VI  - 194
DP  - 2012
TI  - Genome Sequence of 'Candidatus Nitrosopumilus salaria' BD31, an Ammonia-Oxidizing Archaeon from the San Francisco Bay Estuary.
PG  - 2121-2122
AB  - Ammonia-oxidizing archaea (AOA) play important roles in nitrogen and carbon cycling in marine
      and terrestrial ecosystems. Here, we present the draft genome
      sequence for the ammonia-oxidizing archaeon 'Candidatus Nitrosopumilus salaria'
      BD31, which was enriched in culture from sediments of the San Francisco Bay
      estuary. The genome sequences revealed many similarities to the genome of
      Nitrosopumilus maritimus.
AU  - Mosier AC
AU  - Allen EE
AU  - Kim M
AU  - Ferriera S
AU  - Francis CA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2121-2122.

PMID- 22461554
VI  - 194
DP  - 2012
TI  - Genome Sequence of 'Candidatus Nitrosoarchaeum limnia' BG20, a Low-Salinity Ammonia-Oxidizing Archaeon from the San Francisco Bay Estuary.
PG  - 2119-2120
AB  - Here, we present the draft genome sequence of 'Candidatus Nitrosoarchaeum limnia' BG20, an
      ammonia-oxidizing archaeon enriched in culture from low-salinity
      sediments of the San Francisco Bay estuary. The genome sequence revealed many
      similarities to the previously sequenced genome of 'Ca. Nitrosoarchaeum limnia'
      SFB1 (enriched from a nearby site in San Francisco Bay) and is representative of
      a clade of ammonia-oxidizing archaea (AOA) found in low-salinity habitats
      worldwide.
AU  - Mosier AC
AU  - Allen EE
AU  - Kim M
AU  - Ferriera S
AU  - Francis CA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2119-2120.

PMID- 
VI  - 101
DP  - 2001
TI  - Characterization of a restriction endonuclease isolated from Bacillus subtilis F2.
PG  - 457
AB  - Usefulness of restriction system with their high substrate specificities for ds-DNA, and the
      processing of the free or packaged
      DNA during uptake into Bacillus subtilis cells made us study about the
      restriction enzyme activity of one of our laboratory isolate, Bacillus
      subtilis F2 which have been used for the propagation of the newly
      isolated PAK phage. During the life cycle of PAK phage in Bacillus
      subtilis F2 host, it has been noticed that DNA of phage get fragmented
      in vivo, therefore, it becomes important to explore the endonuclease
      activity in this strain. A cell bound enzyme was isolated from Bacillus
      subtilis F2, and was characterized in crude extract of bacterial cell
      pellet. The enzyme showed to have endonuclease activity on
      bacteriophage lambda DNA and other DNA as well. Interestingly, lambda
      DNA seems to have very few cut sites. Another important characteristic
      of this enzyme is to have optimum pH shifted toward alkaline range,
      which is 8.5 among of 182 known restriction enzymes. The optimum
      temperature found to be 40 C. It seems to work at high salt
      concentration. Lysates extracted at pH 6 and 6.5 have shown
      endonuclease activity with a new profile of lambda DNA fragmentation of
      lysate extracted at pH 7.5. Hence BsuF2 is a type II restriction enzyme
      it seems to have high potential to be used as a genetic tool in
      molecular biology.
AU  - Motamedchaboki K
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 2001 101: 457.

PMID- 26184941
VI  - 3
DP  - 2015
TI  - Draft Whole-Genome Sequence and Annotation of Xenorhabdus griffiniae Strain BMMCB Associated with the South African Entomopathogenic Nematode Steinernema khoisanae  Strain BMMCB.
PG  - e00785-15
AB  - Xenorhabdus griffiniae strain BMMCB (LDNM00000000) belongs to the family Enterobacteriaceae
      and was isolated from the South African entomopathogenic
      nematode Steinernema khoisanae strain BMMCB (GenBank accession no. KT027382).
      Here, we report the draft whole-genome sequence of X. griffinae strain BMMCB with
      a genome size of 4,183,779 bp and 44.7% G+C content. The NCBI Prokaryotic
      Automatic Annotation Pipeline (PGAAP) revealed 3,970 genes.
AU  - Mothupi B
AU  - Featherston J
AU  - Gray V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00785-15.

PMID- 21720041
VI  - 59
DP  - 2011
TI  - Inhibition of Restriction Enzymes EcoRI, BamHI and HindIII by Phenethylphenylphthalimides Derived from Thalidomide.
PG  - 880-884
AB  - We discovered inhibitors of the restriction enzymes EcoRI, BamHI and HindIII by screening our
      library of compounds with a
      phenethylphenylphthalimide skeleton, based on alpha-glucosidase
      inhibitors and liver X receptor antagonists derived from thalidomide.
      Structural development afforded the potent restriction enzyme
      inhibitors 25 and 26.
AU  - Motoshima K
AU  - Ishikawa M
AU  - Hashimoto Y
AU  - Sugita K
PT  - Journal Article
TA  - Chem. Pharm. Bull. (Tokyo)
JT  - Chem. Pharm. Bull. (Tokyo)
SO  - Chem. Pharm. Bull. (Tokyo) 2011 59: 880-884.

PMID- 30249635
VI  - 115
DP  - 2018
TI  - Glyphosate perturbs the gut microbiota of honey bees.
PG  - 10305-10310
AB  - Glyphosate, the primary herbicide used globally for weed control, targets the
      5-enolpyruvylshikimate-3-phosphate synthase (EPSPS)
      enzyme in the shikimate pathway found in plants and some
      microorganisms. Thus, glyphosate may affect bacterial symbionts
      of animals living near agricultural sites, including pollinators such
      as bees. The honey bee gut microbiota is dominated by eight
      bacterial species that promote weight gain and reduce pathogen
      susceptibility. The gene encoding EPSPS is present in almost all
      sequenced genomes of bee gut bacteria, indicating that they are
      potentially susceptible to glyphosate. We demonstrated that the
      relative and absolute abundances of dominant gut microbiota
      species are decreased in bees exposed to glyphosate at concentrations
      documented in the environment. Glyphosate exposure of
      young workers increased mortality of bees subsequently exposed
      to the opportunistic pathogen Serratia marcescens. Members of
      the bee gut microbiota varied in susceptibility to glyphosate,
      largely corresponding to whether they possessed an EPSPS of class
      I (sensitive to glyphosate) or class II (insensitive to glyphosate).
      This basis for differences in sensitivity was confirmed using
      in vitro experiments in which the EPSPS gene from bee gut bacteria
      was cloned into Escherichia coli. All strains of the core bee gut
      species, Snodgrassella alvi, encode a sensitive class I EPSPS, and
      reduction in S. alvi levels was a consistent experimental result.
      However, some S. alvi strains appear to possess an alternative
      mechanism of glyphosate resistance. Thus, exposure of bees to
      glyphosate can perturb their beneficial gut microbiota, potentially
      affecting bee health and their effectiveness as pollinators.
AU  - Motta EVS
AU  - Kwong WK
AU  - Moran NA
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2018 115: 10305-10310.

PMID- 28495767
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of 12 Isolates of Listeria monocytogenes Belonging to Serotypes 1/2a, 1/2b, and 4b Obtained from Food Products and Food-Processing  Environments in Canada.
PG  - e00258-17
AB  - Listeria monocytogenes is the etiological agent for an often fatal foodborne illness known as
      listeriosis. Here, we present the complete genome sequences of
      12 L. monocytogenes isolates representing the three most common serotypes of this
      pathogen (1/2a, 1/2b, and 4b), collected in Canada from different food products
      and environmental sources.
AU  - Mottawea W
AU  - Chen S
AU  - Saleh-Lakha S
AU  - Belanger S
AU  - Ogunremi D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00258-17.

PMID- 25642218
VI  - 5
DP  - 2014
TI  - A comparative analysis of methylome profiles of Campylobacter jejuni sheep abortion isolate and gastroenteric strains using PacBio data.
PG  - 782
AB  - Campylobacter jejuni is a leading cause of human gastrointestinal disease and small ruminant
      abortions in the United States. The recent emergence of a highly
      virulent, tetracycline-resistant C. jejuni subsp. jejuni sheep abortion clone
      (clone SA) in the United States, and that strain's association with human
      disease, has resulted in a heightened awareness of the zoonotic potential of this
      organism. Pacific Biosciences' Single Molecule, Real-Time sequencing technology
      was used to explore the variation in the genome-wide methylation patterns of the
      abortifacient clone SA (IA3902) and phenotypically distinct
      gastrointestinal-specific C. jejuni strains (NCTC 11168 and 81-176). Several
      notable differences were discovered that distinguished the methylome of IA3902
      from that of 11168 and 81-176: identification of motifs novel to IA3902,
      genome-specific hypo- and hypermethylated regions, strain level variability in
      genes methylated, and differences in the types of methylation motifs present in
      each strain. These observations suggest a possible role of methylation in the
      contrasting disease presentations of these three C. jejuni strains. In addition,
      the methylation profiles between IA3902 and a luxS mutant were explored to
      determine if variations in methylation patterns could be identified that might
      explain the role of LuxS-dependent methyl recycling in IA3902 abortifacient
      potential.
AU  - Mou KT
AU  - Muppirala UK
AU  - Severin AJ
AU  - Clark TA
AU  - Boitano M
AU  - Plummer PJ
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2014 5: 782.

PMID- 25197461
VI  - 9
DP  - 2014
TI  - Complete Genome sequence of Burkholderia phymatum STM815(T), a broad host range and efficient nitrogen-fixing symbiont of Mimosa species.
PG  - 763-774
AB  - Burkholderia phymatum is a soil bacterium able to develop a nitrogen-fixing symbiosis with
      species of the legume genus Mimosa, and is frequently found
      associated specifically with Mimosa pudica. The type strain of the species, STM
      815(T), was isolated from a root nodule in French Guiana in 2000. The strain is
      an aerobic, motile, non-spore forming, Gram-negative rod, and is a highly
      competitive strain for nodulation compared to other Mimosa symbionts, as it also
      nodulates a broad range of other legume genera and species. The 8,676,562 bp
      genome is composed of two chromosomes (3,479,187 and 2,697,374 bp), a megaplasmid
      (1,904,893 bp) and a plasmid hosting the symbiotic functions (595,108 bp).
AU  - Moulin L et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 763-774.

PMID- 23405314
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Rhizobium mesoamericanum STM3625, a Nitrogen-Fixing Symbiont of Mimosa pudica Isolated in French Guiana (South America).
PG  - e00066-12
AB  - Rhizobium mesoamericanum STM3625 is a Mimosa pudica symbiont isolated in French Guiana. This
      strain serves as a model bacterium for comparison of adaptation to mutualism (symbiotic
      traits, bacterial genetic programs for plant infection) between alpha and beta rhizobial
      symbionts of Mimosa pudica.
AU  - Moulin L
AU  - Mornico D
AU  - Melkonian R
AU  - Klonowska A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00066-12.

PMID- 18424798
VI  - 36
DP  - 2008
TI  - Crystal structures of I-SceI complexed to nicked DNA substrates: snapshots of intermediates along the DNA cleavage reaction pathway.
PG  - 3287-3296
AB  - I-SceI is a homing endonuclease that specifically cleaves an 18-bp double-stranded DNA. I-SceI
      exhibits a strong preference for cleaving the bottom strand DNA. The published structure of
      I-SceI bound to an uncleaved DNA substrate provided a mechanism for bottom strand cleavage but
      not for top strand cleavage. To more fully elucidate the I-SceI catalytic mechanism, we
      determined the X-ray structures of I-SceI in complex with DNA substrates that are nicked in
      either the top or bottom strands. The structures resemble intermediates along the DNA cleavage
      reaction. In a structure containing a nick in the top strand, the spatial arrangement of metal
      ions is similar to that observed in the structure that contains uncleaved DNA, suggesting that
      cleavage of the bottom strand occurs by a common mechanism regardless of whether this strand
      is cleaved first or second. In the structure containing a nick in the bottom strand, a new
      metal binding site is present in the active site that cleaves the top strand. This new metal
      and a candidate nucleophilic water molecule are correctly positioned to cleave the top strand
      following bottom strand cleavage, providing a plausible mechanism for top strand cleavage.
AU  - Moure CM
AU  - Gimble FS
AU  - Quiocho FA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2008 36: 3287-3296.

PMID- 14636596
VI  - 334
DP  - 2003
TI  - The crystal structure of the gene targeting homing endonuclease I-SceI reveals the origins of its target site specificity.
PG  - 685-695
AB  - The I-SceI homing endonuclease enhances gene targeting by introducing double-strand breaks at
      specific chromosomal loci, thereby increasing the
      recombination frequency. Here, we report the crystal structure of the
      enzyme complexed to its DNA substrate and Ca(2+) determined at 2.25A
      resolution. The structure shows the prototypical beta-saddle of LAGLIDADG
      homing endonucleases that is contributed by two pseudo-symmetric domains.
      The high specificity of I-SceI is explained by the large number of
      protein-DNA contacts, many that are made by a long beta-hairpin loop that
      reaches into the major groove of the DNA. The DNA minor groove is
      compressed at the catalytic center, bringing the two scissile
      phosphodiester bonds into close proximity. The protein-Ca(2+)-DNA
      structure shows the protein bound to its DNA substrate in a pre-reactive
      state that is defined by the presence of two asymmetric active sites, one
      of which appears poised to first cleave the DNA bottom strand.
AU  - Moure CM
AU  - Gimble FS
AU  - Quiocho FA
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2003 334: 685-695.

PMID- 12219083
VI  - 9
DP  - 2002
TI  - Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition sequence.
PG  - 764-770
AB  - The first X-ray structures of an intein-DNA complex, that of the two-domain homing
      endonuclease PI-SceI bound to its 36-base pair DNA substrate, have been determined in the
      presence and absence of Ca(2+). The DNA shows an asymmetric bending pattern, with a major 50
      degrees bend in the endonuclease domain and a minor 22 degrees bend in the splicing domain
      region. Distortions of the DNA bound to the endonuclease domain cause the insertion of the two
      cleavage sites in the catalytic center. DNA binding induces changes in the protein
      conformation. The two overlapping non-identical active sites in the endonucleolytic center
      contain two Ca(+2) ions that coordinate to the catalytic Asp residues. Structure analysis
      indicates that the top strand may be cleaved first.
AU  - Moure CM
AU  - Gimble FS
AU  - Quiocho FA
PT  - Journal Article
TA  - Nat. Struct. Biol.
JT  - Nat. Struct. Biol.
SO  - Nat. Struct. Biol. 2002 9: 764-770.

PMID- 
VI  - 16
DP  - 2005
TI  - The structure and function of intein-associated homing endonucleases.
PG  - 257-271
AB  - Homing endonucleases are a large group of proteins that are characterized by their ability to
      recognize long (14-40 base pairs, bp) asymmetric or pseudo-palindromic double-stranded DNA
      sequences as cleavage sites.  By cleaving DNA, they assist in the homing process of their
      encoding genes into other genes.  Homing endonucleases include both intron-encoded and intein-
      (for intervening protein) associated members that self-splice at the mRNA and protein level,
      respectively.  Those inteins that contain associated endonuclease domains are especially
      interesting due to their bifunctionality and their exceptionally long DNA recognition
      abilities.  With two exceptions, all of the approximately 160 inteins that have been
      characterized to date are associated with the LAGLIDADG homing endonuclease subfamily, which
      also includes numerous intron-encoded endonucleases.  This chapter is devoted mainly to the
      structural studies of intein-associated LAGLIDADG homing endonucleases that have revealed the
      domain organization and architecture of this type of protein, providing insights into the
      combination of protein splicing and site-specific DNA recognition and cleavage across a single
      peptide chain.  The knowledge gained in these structure-function studies has been successfully
      exploited in biotechnology to devise systems for protein purification and to study
      protein-protein interactions using the splicing capability of inteins, and in gene targeting
      studies, which use their rare-cutting endonuclease properties.  These applications are
      discussed in other chapters in this volume.
AU  - Moure CM
AU  - Quiocho FA
PT  - Journal Article
TA  - Nucleic Acids Mol. Biol.
JT  - Nucleic Acids Mol. Biol.
SO  - Nucleic Acids Mol. Biol. 2005 16: 257-271.

PMID- 7922307
VI  - 4
DP  - 1994
TI  - Adaptive evolution of highly mutable loci in pathogenic bacteria.
PG  - 24-33
AB  - Bacteria have specific loci that are highly mutable.  We argue that the coexistence within
      bacterial genomes of such 'contingency' genes with high mutation rates, and 'housekeeping'
      genes with low mutation rates, is the result of adaptive evolution, and facilitates the
      efficient exploration of phenotypic solutions to unpredictable aspects of the host environment
      while minimizing deleterious effects on fitness.
AU  - Moxon ER
AU  - Rainey PB
AU  - Nowak MA
AU  - Lenski RE
PT  - Journal Article
TA  - Curr. Biol.
JT  - Curr. Biol.
SO  - Curr. Biol. 1994 4: 24-33.

PMID- 25146142
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Nominated Type Strain of 'Ferrovum myxofaciens,' an  Acidophilic, Iron-Oxidizing Betaproteobacterium.
PG  - e00834-14
AB  - 'Ferrovum myxofaciens' is an iron-oxidizing betaproteobacterium with widespread distribution
      in acidic low-temperature environments, such as acid mine drainage
      streams. Here, we describe the genomic features of this novel acidophile and
      investigate the relevant metabolic pathways that enable its survival in these
      environments.
AU  - Moya-Beltran A
AU  - Cardenas JP
AU  - Covarrubias PC
AU  - Issotta F
AU  - Ossandon FJ
AU  - Grail BM
AU  - Holmes DS
AU  - Quatrini R
AU  - Johnson DB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00834-14.

PMID- 10415493
VI  - 870
DP  - 1999
TI  - Detecting alien genes in bacterial genomes.
PG  - 314-329
AB  - We present new methods for calculating codon bias of a group of genes or an individual gene
      relative to a standard gene class.  This method is suitable for identifying alien (e.g.,
      horizonatally transferred) and highly expressed genes.  In yeast and several bacterial
      genomes, highly expressed genes typically include ribosomal protein genes, elongation factors,
      chaperonins (heat shock proteins), and a subset of genes involved in glycolysis generally
      essential in exponential growth.  Highly expressed genes of the Synechocystis genome feature
      several photosystem II genes, and highly expressed genes in several methanogens (Methanococcus
      jannaschii, M. thermoautotrophicum) are essential for methanogenesis.  Alien genes mostly
      consist of ORFs of unknown function, transposases, prophage genes, and
      restriction/modification enzymes.  Notably, nuclear ribosomal proteins of yeast are highly
      expressed, whereas mitochondrial ribosomal protein genes appear to be alien genes.  Alien
      genes often occur in clusters, suggesting in these cases that transfer events entail several
      genes.
AU  - Mrazek J
AU  - Karlin S
PT  - Journal Article
TA  - Ann. NY Acad. Sci.
JT  - Ann. NY Acad. Sci.
SO  - Ann. NY Acad. Sci. 1999 870: 314-329.

PMID- 16701584
VI  - 11
DP  - 2005
TI  - Occurrence of restriction-modification systems in ruminal butyrate-producing bacteria.
PG  - 280-284
AB  - Thirty-five strains of ruminal bacteria belonging to the former Butyrivibrio fibrisolvens
      species were screened for the presence of
      site-specific restriction endonuclease and modification
      methyltransferase activities. Seven strains possessed endonuclease
      activities detectable in crude cell extracts. The recognition sequences
      and optimal reaction conditions for seven of them were determined. Five
      enzymes were found to be isoschizomers of type II endonucleases (EcoRV,
      Nsil, Asel (2x) and Saul), one was type IIS (FokI) and two remained
      unknown. The optimal reaction buffer was found to be a low ionic
      strength buffer and all enzymes possessed sufficient activity at 39
      degrees C. The presence of DNA modification among all strains was also
      determined. Most of the methylation activities correlated with
      restriction activities, yet some strains possessed unaccompanied
      modification methyltransferases.
AU  - Mrazek J
AU  - Piknova M
AU  - Pristas P
AU  - Kopecny J
PT  - Journal Article
TA  - Anaerobe
JT  - Anaerobe
SO  - Anaerobe 2005 11: 280-284.

PMID- 18334533
VI  - 36
DP  - 2008
TI  - Real-time kinetics of restriction-modification gene expression after entry into a new host cell.
PG  - 2581-2593
AB  - Most type II restriction-modification (R-M) systems produce separate restriction endonuclease
      (REase) and methyltransferase (MTase) proteins.
      After R-M system genes enter a new cell, protective MTase must appear
      before REase to avoid host chromosome cleavage. The basis for this
      apparent temporal regulation is not well understood. PvuII and some other
      R-M systems appear to achieve this delay by cotranscribing the REase gene
      with the gene for an autogenous transcription activator/repressor (the 'C'
      protein C.PvuII). To test this model, bacteriophage M13 was used to
      introduce the PvuII genes into a bacterial population in a relatively
      synchronous manner. REase mRNA and activity appeared approximately 10 min
      after those of the MTase, but never rose if there was an inactivating
      pvuIIC mutation. Infection with recombinant M13pvuII phage had little
      effect on cell growth, relative to infection with parental M13. However,
      infection of cells pre-expressing C.PvuII led to cessation of growth. This
      study presents the first direct demonstration of delayed REase expression,
      relative to MTase, when type II R-M genes enter a new host cell.
      Surprisingly, though the C and REase genes are cotranscribed, the pvuIIC
      portion of the mRNA was more abundant than the pvuIIR portion after stable
      establishment of the R-M system.
AU  - Mruk I
AU  - Blumenthal RM
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2008 36: 2581-2593.

PMID- 19126580
VI  - 37
DP  - 2009
TI  - Tuning the relative affinities for activating and repressing operators of a temporally regulated restriction-modification system.
PG  - 983-998
AB  - Most type II restriction-modification (R-M) systems produce separate endonuclease (REase) and
      methyltransferase (MTase) proteins. After R-M
      genes enter a new cell, MTase activity must appear before REase or the
      host chromosome will be cleaved. Temporal control of these genes thus has
      life-or-death consequences. PvuII and some other R-M systems delay
      endonuclease expression by cotranscribing the REase gene with the upstream
      gene for an autogenous activator/repressor (C protein). C.PvuII was
      previously shown to have low levels early, but positive feedback later
      boosts transcription of the C and REase genes. The MTase is expressed
      without delay, and protects the host DNA. C.PvuII binds to two sites
      upstream of its gene: O(L), associated with activation, and O(R),
      associated with repression. Even when symmetry elements of each operator
      are made identical, C.PvuII binds preferentially to O(L). In this study,
      the intra-operator spacers are shown to modulate relative C.PvuII
      affinity. In light of a recently reported C.Esp1396I-DNA co-crystal
      structure, in vitro and in vivo effects of altering O(L) and O(R) spacers
      were determined. The results suggest that the GACTnnnAGTC consensus is the
      primary determinant of C.PvuII binding affinity, with intra-operator
      spacers playing a fine-tuning role that affects mobility of this R-M
      system.
AU  - Mruk I
AU  - Blumenthal RM
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: 983-998.

PMID- 14600245
VI  - 149
DP  - 2003
TI  - Characterization of the LlaCl methyltransferase from Lactococcus lactis subsp cremoris W15 provides new insights into the biology of type II  restriction-modification systems.
PG  - 3331-3341
AB  - The gene encoding the LlaCI methyltransferase (M.LlaCI) from Lactococcus lactis subsp.
      cremoris W15 was overexpressed in Escherichia coli. The
      enzyme was purified to apparent homogeneity using three consecutive steps
      of chromatography on phosphocellulose, blue-agarose and Superose 12HR,
      yielding a protein of M(r) 31 300+/-1000 under denaturing conditions. The
      exact position of the start codon AUG was determined by protein
      microsequencing. This enzyme recognizes the specific palindromic sequence
      5'-AAGCTT-3'. Purified M.LlaCI was characterized. Unlike many other
      methyltransferases, M.LlaCI exists in solution predominantly as a dimer.
      It modifies the first adenine residue at the 5' end of the specific
      sequence to N(6)-methyladenine and thus is functionally identical to the
      corresponding methyltransferases of the HindIII (Haemophilus influenzae
      Rd) and EcoVIII (Escherichia coli E1585-68) restriction-modification
      systems. This is reflected in the identity of M.LlaCI with M.HindIII and
      M.EcoVIII noted at the amino acid sequence level (50 % and 62 %,
      respectively) and in the presence of nine sequence motifs conserved among
      N(6)-adenine beta-class methyltransferases. However, polyclonal antibodies
      raised against M.EcoVIII cross-reacted with M.LlaCI but not with
      M.HindIII. Restriction endonucleases require Mg(2+) for phosphodiester
      bond cleavage. Mg(2+) was shown to be a strong inhibitor of the M.LlaCI
      enzyme and its isospecific homologues. This observation suggests that
      sensitivity of the M.LlaCI to Mg(2+) may strengthen the restriction
      activity of the cognate endonuclease in the bacterial cell. Other
      biological implications of this finding are also discussed.
AU  - Mruk I
AU  - Cichowicz M
AU  - Kaczorowski T
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2003 149: 3331-3341.

PMID- 17468281
VI  - 73
DP  - 2007
TI  - A rapid and efficient method for cloning genes of type II restriction-modification systems by use of a killer plasmid.
PG  - 4286-4293
AB  - We present a method for cloning restriction-modification (R-M) systems that is based on the
      use of a lethal plasmid (pKILLER). The plasmid
      carries a functional gene for a restriction endonuclease having the
      same DNA specificity as the R-M system of interest. The first step is
      the standard preparation of a representative, plasmid-borne genomic
      library. Then this library is transformed with the killer plasmid. The
      only surviving bacteria are those which carry the gene specifying a
      protective DNA methyltransferase. Conceptually, this in vivo selection
      approach resembles earlier methods in which a plasmid library was
      selected in vitro by digestion with a suitable restriction
      endonuclease, but it is much more efficient than those methods. The new
      method was successfully used to clone two R-M systems, BstZ1II from
      Bacillus stearothermophilus 14P and Csp231I from Citrobacter sp. strain
      RFL231, both isospecific to the prototype HindIII R-M system.
AU  - Mruk I
AU  - Kaczorowski T
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2007 73: 4286-4293.

PMID- 12732532
VI  - 69
DP  - 2003
TI  - Genetic organization and molecular analysis of the EcoVIII restriction-modification system of Escherichia coli E1585-68 and its comparison with isospecific homologs.
PG  - 2638-2650
AB  - The EcoVIII restriction-modification (R-M) system is carried by the Escherichia coli E1585-68
      natural plasmid pEC156 (4,312 bp). The two genes
      were cloned and characterized. The G+C content of the EcoVIII R-M system
      is 36.1%, which is significantly lower than the average G+C content of
      either plasmid pEC156 (43.6%) or E. coli genomic DNA (50.8%). The
      difference suggests that there is a possibility that the EcoVIII R-M
      system was recently acquired by the genome. The 921-bp EcoVIII
      endonuclease (R. EcoVIII) gene (ecoVIIIR) encodes a 307-amino-acid protein
      with an M(r) of 35,554. The convergently oriented EcoVIII
      methyltransferase (M. EcoVIII) gene (ecoVIIIM) consists of 912 bp that
      code for a 304-amino-acid protein with an M(r) of 33,930. The exact
      positions of the start codon AUG were determined by protein
      microsequencing. Both enzymes recognize the specific palindromic sequence
      5'-AAGCTT-3'. Preparations of EcoVIII R-M enzymes purified to homogeneity
      were characterized. R. EcoVIII acts as a dimer and cleaves a specific
      sequence between two adenine residues, leaving 4-nucleotide 5' protruding
      ends. M. EcoVIII functions as a monomer and modifies the first adenine
      residue at the 5' end of the specific sequence to N(6)-methyladenine.
      These enzymes are thus functionally identical to the corresponding enzymes
      of the HindIII (Haemophilus influenzae Rd) and LlaCI (Lactococcus lactis
      subsp. cremoris W15) R-M systems. This finding is reflected by the levels
      of homology of M. EcoVIII with M. HindIII and M. LlaCI at the amino acid
      sequence level (50 and 62%, respectively) and by the presence of nine
      sequence motifs conserved among m(6) N-adenine beta-class
      methyltransferases. The deduced amino acid sequence of R. EcoVIII shows
      weak homology with its two isoschizomers, R. HindIII (26%) and R. LlaCI
      (17%). A catalytic sequence motif characteristic of restriction
      endonucleases was found in the primary structure of R. EcoVIII
      (D(108)X(12)DXK(123)), as well as in the primary structures of R. LlaCI
      and R. HindIII. Polyclonal antibodies raised against R. EcoVIII did not
      react with R. HindIII, while anti-M. EcoVIII antibodies cross-reacted with
      M. LlaCI but not with M. HindIII. R. EcoVIII requires Mg(II) ions for
      phosphodiester bond cleavage. We found that the same ions are strong
      inhibitors of the M. EcoVIII enzyme. The biological implications of this
      finding are discussed.
AU  - Mruk I
AU  - Kaczorowski T
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2003 69: 2638-2650.

PMID- 23945938
VI  - 42
DP  - 2013
TI  - To be or not to be: regulation of restriction-modification systems and other toxin-antitoxin systems.
PG  - 70-86
AB  - One of the simplest classes of genes involved in programmed death is that containing the
      toxin-antitoxin (TA) systems of prokaryotes. These systems are composed of an intracellular
      toxin and an antitoxin that neutralizes its effect. These systems, now classified into five
      types, were initially discovered because some of them allow the stable maintenance of mobile
      genetic elements in a microbial population through postsegregational killing or the death of
      cells that have lost these systems. Here, we demonstrate parallels between some TA systems and
      restriction-modification systems (RM systems). RM systems are composed of a restriction enzyme
      (toxin) and a modification enzyme (antitoxin) and limit the genetic flux between lineages with
      different epigenetic identities, as defined by sequence-specific DNA methylation. The
      similarities between these systems include their postsegregational killing and their effects
      on global gene expression. Both require the finely regulated expression of a toxin and
      antitoxin. The antitoxin (modification enzyme) or linked protein may act as a transcriptional
      regulator. A regulatory antisense RNA recently identified in an RM system can be compared with
      those RNAs in TA systems. This review is intended to generalize the concept of TA systems in
      studies of stress responses, programmed death, genetic conflict and epigenetics.
AU  - Mruk I
AU  - Kobayashi I
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2013 42: 70-86.

PMID- 21459843
VI  - 39
DP  - 2011
TI  - Antisense RNA associated with biological regulation of a restriction-modification system.
PG  - 5622-5632
AB  - Restriction-modification systems consist of a modification enzyme that methylates a specific
      DNA sequence and a restriction endonuclease that cleaves DNA lacking this epigenetic
      signature. Their gene expression should be finely regulated because their potential to attack
      the host bacterial genome needs to be controlled. In the EcoRI system, where the restriction
      gene is located upstream of the modification gene in the same orientation, we previously
      identified intragenic reverse promoters affecting gene expression. In the present work, we
      identified a small (88 nt) antisense RNA (Rna0) transcribed from a reverse promoter (P(REV0))
      at the 3' end of the restriction gene. Its antisense transcription, as measured by
      transcriptional gene fusion, appeared to be terminated by the P(M1,M2) promoter. P(M1,M2)
      promoter-initiated transcription, in turn, appeared to be inhibited by P(REV0). Mutational
      inactivation of P(REV0) increased expression of the restriction gene. The biological
      significance of this antisense transcription is 2-fold. First, a mutation in P(REV0) increased
      restriction of incoming DNA. Second, the presence of the antisense RNA gene (ecoRIA) in trans
      alleviated cell killing after loss of the EcoRI plasmid (post-segregational killing). Taken
      together, these results strongly suggested the involvement of an antisense RNA in the
      biological regulation of this restriction-modification system.
AU  - Mruk I
AU  - Liu Y
AU  - Ge L
AU  - Kobayashi I
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2011 39: 5622-5632.

PMID- 17933763
VI  - 35
DP  - 2007
TI  - Regulatory circuit based on autogenous activation-repression: roles of C-boxes and spacer sequences in control of the PvuII  restriction-modification system.
PG  - 6935-6952
AB  - Type II restriction-modification (R-M) systems comprise a restriction endonuclease (REase) and
      a protective methyltransferase (MTase). After R-M
      genes enter a new cell, MTase must appear before REase or the chromosome
      will be cleaved. PvuII and some other R-M systems achieve this delay by
      cotranscribing the REase gene with the gene for an autogenous
      transcription activator (the controlling or 'C' protein C.PvuII). This
      study reveals, through in vivo titration, that C.PvuII is not only an
      activator but also a repressor for its own gene. In other systems, this
      type of circuit can result in oscillatory behavior. Despite the use of
      identical, symmetrical C protein-binding sequences (C-boxes) in the left
      and right operators, C.PvuII showed higher in vitro affinity for O(L) than
      for O(R), implicating the spacer sequences in this difference. Mutational
      analysis associated the repression with O(R), which overlaps the promoter
      -35 hexamer but is otherwise dispensable for activation. A nonrepressing
      mutant exhibited poor establishment in new cells. Comparing
      promoter-operator regions from PvuII and 29 R-M systems controlled by C
      proteins revealed that the most-highly conserved sequence is the
      tetranucleotide spacer separating O(L) from O(R). Any changes in that
      spacer reduced the stability of C.PvuII-operator complexes and abolished
      activation.
AU  - Mruk I
AU  - Rajesh P
AU  - Blumenthal RM
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2007 35: 6935-6952.

PMID- 11591138
VI  - 46
DP  - 2001
TI  - Characterization of pEC156, a ColE1-Type Plasmid from Escherichia coli E1585-68 That Carries Genes of the EcoVIII Restriction-Modification System.
PG  - 128-139
AB  - The complete 4312-bp sequence of the pEC156 plasmid from Escherichia coli E1585-68, which
      carries genes encoding the EcoVIII restriction-modification (R-M) system, an isoschizomer of
      HindIII from Haemophilus influenzae, has been determined. Two clustered and convergently
      oriented open reading frames, large enough to encode genes of the EcoVIII R-M system, were
      found. The transcriptional start points were mapped by the primer extension method. The
      relative molecular masses of the EcoVIII endonuclease and EcoVIII methyltransferase deduced
      from the nucleotide sequence are 35,554 and 33,910, respectively. Nucleotide sequence analysis
      of pEC156 suggests that this plasmid is a ColE1-type replicon. It consists of an origin of
      replication and two untranslated genes encoding RNA I and RNA II, both involved in the
      regulation of plasmid DNA replication. The replication region also contains the gene encoding
      a 64-aa Rom-like protein. Inactivation of the putative rom gene by insertion of a
      kanamycin-resistance cassette resulted in 4.5-fold increase in pEC156-derived plasmid copy
      number in E. coli cells. All of these elements (RNA I, RNA II, and rom) reveal a high level of
      similarity to ColE1 homologs. The replication of all ColE1-type plasmids is dependent on the
      activity of E. coli DNA polymerase I. It was shown that a pEC156 derivative (pIB8) carrying an
      antibiotic resistance gene indeed failed to replicate in an E. coli polA12(ts) mutant at 43
      degrees C, and its copy number was reduced in the E. coli pcnB80 mutant. These results prove
      that pEC156 is a ColE1-type replicon. Copyright 2001 Academic Press.
AU  - Mruk I
AU  - Sektas M
AU  - Kaczorowski T
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 2001 46: 128-139.

PMID- 26769940
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Algoriphagus sp. Strain NH1, a Multidrug-Resistant Bacterium Isolated from Coastal Sediments of the Northern Yellow Sea in China.
PG  - e01555-15
AB  - Algoriphagus sp. NH1 is a multidrug-resistant bacterium isolated from coastal sediments of the
      northern Yellow Sea in China. Here, we report the draft genome
      sequence of NH1, with a size of 6,131,579 bp, average G+C content of 42.68%, and
      5,746 predicted protein-coding sequences.
AU  - Mu D
AU  - Zhao J
AU  - Wang Z
AU  - Chen G
AU  - Du Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01555-15.

PMID- 28619811
VI  - 5
DP  - 2017
TI  - Full-Genome Sequence of Listeria monocytogenes Strain H34, Isolated from a Newborn with Sepsis in Uruguay.
PG  - e00544-17
AB  - The foodborne pathogen Listeria monocytogenes causes severe disease mainly in the vulnerable
      populations of the young, old, pregnant, and immunocompromised. Here,
      we present the genome sequence of L. monocytogenes H34, a serotype 1/2b, lineage
      I, sequence type 489 (ST489) strain, isolated from a neonatal sepsis case in
      Uruguay.
AU  - Muchaamba F
AU  - Guldimann C
AU  - Tasara T
AU  - Mota MI
AU  - Braga V
AU  - Varela G
AU  - Algorta G
AU  - Klumpp J
AU  - Jermini M
AU  - Stephan R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00544-17.

PMID- 1652638
VI  - 31
DP  - 1991
TI  - High transformable mutants of Streptomyces aureofaciens containing restriction-modification systems.
PG  - 141-147
AB  - Streptomyces aureofaciens 13 is a mutant defective in chlortetracycline
      production. It was chosen as a potentially useful host for gene cloning in
      investigations of the organization of the biosynthetic genes for the
      tetracycline antibiotic pathway.  From the Streptomyces aureofaciens 13 strain,
      three suitable clones were used for our work.  The conditions for optimal
      formation and efficient transformation of protoplasts with plasmid DNAs have
      been determined.  Transformation frequencies of about 10/4 to 10/5 per
      microgram of plasmid DNA were obtained when plasmids were isolated from
      Streptomyces strains.  From the patterns of restriction enzyme digestion of
      plasmid DNA isolated from Streptomyces aureofaciens transformants, it was
      observed that the clones express modification systems which render plasmid DNAs
      resistant to cleavage by HindIII and EcoRI.  Additionally, one of the clones
      produces the restriction endonuclease Sau13I (isoschizomer of SauI).  The
      presence of the restriction-modification system of Sau13I does not reduce the
      efficiency of plasmid transformation.  Note: Sau13I is already used for an
      isoschizomer of AsuI from Staphylococcus aureus.
AU  - Muchova J
AU  - Lacova B
AU  - Godany A
AU  - Sevcikova B
PT  - Journal Article
TA  - J. Basic Microbiol.
JT  - J. Basic Microbiol.
SO  - J. Basic Microbiol. 1991 31: 141-147.

PMID- 26769924
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Helicobacter pylori Strain 29CaP Isolated from a Mexican Patient with Gastric Cancer.
PG  - e01512-15
AB  - Helicobacter pylori infection is a risk factor for the development of gastric cancer and other
      gastroduodenal diseases. We report here the complete genome
      sequence of H. pylori strain 29CaP, isolated from a Mexican patient with gastric
      cancer. The genomic data analysis revealed a cag-negative H. pylori strain that
      contains a prophage sequence.
AU  - Mucito-Varela E
AU  - Castillo-Rojas G
AU  - Cevallos MA
AU  - Lozano L
AU  - Merino E
AU  - Lopez-Leal G
AU  - Lopez-Vidal Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01512-15.

PMID- 26744372
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Helicobacter pylori Strain 7C Isolated from a Mexican Patient with Chronic Gastritis.
PG  - e01503-15
AB  - Helicobacter pylori-induced gastritis is a risk factor for developing gastric pathologies.
      Here, we report the complete genome sequence of a
      multidrug-resistant H. pylori strain isolated from a chronic gastritis patient in
      Mexico City, Mexico. Nonvirulent VacA and cag-pathogenicity island (PAI)
      genotypes were found, but the presence of a potential mobilizable plasmid
      carrying an IS605 element is of outstanding interest.
AU  - Mucito-Varela E
AU  - Castillo-Rojas G
AU  - Cevallos MA
AU  - Lozano L
AU  - Merino E
AU  - Lopez-Leal G
AU  - Lopez-Vidal Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01503-15.

PMID- 12356742
VI  - 21
DP  - 2002
TI  - EcoRII: a restriction enzyme evolving recombination functions?
PG  - 5262-5268
AB  - The restriction endonuclease EcoRII requires the cooperative interaction with two copies of
      the sequence 5'CCWGG for DNA cleavage. We found by limited proteolysis that EcoRII has a
      two-domain structure that enables this particular mode of protein-DNA interaction. The
      C-terminal domain is a new restriction endonuclease, EcoRII-C. In contrast to the wild-type
      enzyme, EcoRII-C cleaves DNA specifically at single 5'CCWGG sites. Moreover, substrates
      containing two or more cooperative 5'CCWGG sites are cleaved much more efficiently by
      EcoRII-C than by EcoRII. The N-terminal domain binds DNA specifically and attenuates the
      activity of EcoRII by making the enzyme dependent on a second 5'CCWGG site. Therefore, we
      suggest that a precursor EcoRII endonuclease acquired an additional DNA-binding domain to
      enable the interaction with two 5'CCWGG sites. The current EcoRII molecule could be an
      evolutionary intermediate between a site-specific endonuclease and a protein that functions
      specifically with two DNA sites such as recombinases and transposases. The combination of
      these functions may enable EcoRII to accomplish its own propagation similarly to transposons.
AU  - Mucke M
AU  - Grelle G
AU  - Behlke J
AU  - Kraft R
AU  - Kruger DH
AU  - Reuter M
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 2002 21: 5262-5268.

PMID- 14576294
VI  - 31
DP  - 2003
TI  - Diversity of Type II restriction endonucleases that require two DNA recognition sites.
PG  - 6079-6084
AB  - Orthodox Type IIP restriction endonucleases, which are commonly used in molecular biological
      work, recognize a single palindromic DNA recognition
      sequence and cleave within or near this sequence. Several new studies have
      reported on structural and biochemical peculiarities of restriction
      endonucleases that differ from the orthodox in that they require two
      copies of a particular DNA recognition sequence to cleave the DNA. These
      two sites requiring restriction endonucleases belong to different subtypes
      of Type II restriction endonucleases, namely Types IIE, IIF and IIS. We
      compare enzymes of these three types with regard to their DNA recognition
      and cleavage properties. The simultaneous recognition of two identical DNA
      sites by these restriction endonucleases ensures that single unmethylated
      recognition sites do not lead to chromosomal DNA cleavage, and might
      reflect evolutionary connections to other DNA processing proteins that
      specifically function with two sites.
AU  - Mucke M
AU  - Kruger DH
AU  - Reuter M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2003 31: 6079-6084.

PMID- 10903314
VI  - 275
DP  - 2000
TI  - Imaging DNA loops induced by restriction endonuclease EcoRII. A single amino acid substitution uncouples target recognition from cooperative DNA interaction and cleavage.
PG  - 30631-30637
AB  - EcoRII is a type IIE restriction endonuclease characterized by a highly cooperative reaction
      mechanism that depends on simultaneous binding of the dimeric enzyme molecule to two copies of
      its DNA recognition site. Transmission electron microscopy provided direct evidence that
      EcoRII mediates loop formation of linear DNA containing two EcoRII recognition sites. Specific
      DNA binding of EcoRII revealed a symmetrical DNase I footprint occupying 16-18 bases. Single
      amino acid replacement of Val(258) by Asn yielded a mutant enzyme that was unaffected in
      substrate affinity and DNase I footprinting properties, but exhibited a profound decrease in
      cooperative DNA binding and cleavage activity. Because the electrophoretic mobility of the
      mutant enzyme-DNA complexes was significantly higher than that of the wild-type, we
      investigated if mutant V258N binds as a monomer to the substrate DNA. Analysis of the
      molecular mass of mutant V258N showed a high percentage of protein monomers in solution. The
      dissociation constant of mutant V258N confirmed a 350-fold decrease of the enzyme dimerization
      capability. We conclude that Val(258) is located in a region of EcoRII involved in
      homodimerization. This is the first report of a specific amino acid replacement in a
      restriction endonuclease leading to the loss of dimerization and DNA cleavage while retaining
      specific DNA binding.
AU  - Mucke M
AU  - Lurz R
AU  - Mackeldanz P
AU  - Behlke J
AU  - Kruger DH
AU  - Reuter M
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2000 275: 30631-30637.

PMID- 11832480
VI  - 277
DP  - 2002
TI  - Asymmetric photocross-linking pattern of restriction endonuclease EcoRII to the DNA recognition sequence.
PG  - 14288-14293
AB  - The EcoRII homodimer engages two of its recognition sequences (5'-CCWGG) simultaneously and
      is therefore a type IIE restriction endonuclease. To identify the amino acids of EcoRII that
      interact specifically with the recognition sequence, we photocross-linked EcoRII with
      oligonucleotide substrates that contained only one recognition sequence for EcoRII. In this
      recognition sequence, we substituted either 5-iododeoxycytidine for each C or
      5-iododeoxyuridine for A, G, or T. These iodopyrimidine bases were excited using a UV laser to
      result in covalent cross-linking products. The yield of EcoRII photocross-linked to the 5'-C
      of the 5'-CCAGG strand of the recognition sequence was 45%. However, we could not
      photocross-link EcoRII to the 5'-C of the 5'-CCTGG strand. Thus, the contact of EcoRII to
      the bases of the recognition sequence appears to be asymmetric, unlike that expected for most
      type II restriction endonucleases. Tryptic digestion of free and of cross-linked EcoRII,
      followed by high performance liquid chromatography (HPLC) separation of the individual
      peptides and Edman degradation, identified amino acids 25-49 of EcoRII as the cross-linking
      peptide. Mutational analysis of the electron-rich amino acids His(36) and Tyr(41) of this
      peptide indicates that Tyr(41) is the amino acid involved in the cross-link and that it
      therefore contributes to specific DNA recognition by EcoRII.
AU  - Mucke M
AU  - Pingoud V
AU  - Grelle G
AU  - Kraft R
AU  - Kruger DH
AU  - Reuter M
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2002 277: 14288-14293.

PMID- 11575924
VI  - 312
DP  - 2001
TI  - DNA cleavage by type II restriction-modification enzyme EcoP15I is independent of spacer distance between two head to head oriented recognition sites.
PG  - 687-698
AB  - The type III restriction-modification enzyme EcoP15I requires the interaction of two
      unmethylated, inversely oriented recognition sites 5'-CAGCAG in head to head configuration to
      allow an efficient DNA cleavage. It has been hypothesized that two convergent
      DNA-translocating enzyme-substrate complexes interact to form the active cleavage complex and
      that translocation is driven by ATP hydrolysis. Using a half-automated, fluorescence-based
      detection method, we investigated how the distance between two inversely oriented recognition
      sites affects DNA cleavage efficiency. We determined that EcoP15I cleaves DNA efficiently even
      for two adjacent head to head or tail to tail oriented target sites. Hence, DNA translocation
      appears not to be required for initiating DNA cleavage in these cases. Furthermore, we report
      here that EcoP15I is able to cleave single-site substrates. When we analyzed the interaction
      of EcoP15I with DNA substrates containing adjacent target sites in the presence of
      non-hydrolyzable ATP analogues, we found that cleavage depended on the hydrolysis of ATP.
      Moreover, we show that cleavage occurs at only one of the two possible cleavage positions of
      an interacting pair of target sequences. When EcoP15I bound to a DNA substrate containing one
      recognition site in the absence of ATP, we observed a 36 nucleotide DNaseI-footprint that is
      asymmetric on both strands. All of our footprinting experiments showed that the enzyme did not
      cover the region around the cleavage site. Analyzing a DNA fragment with two head to head
      oriented recognition sites, EcoP15I protected 27-33 nucleotides around the recognition
      sequence, including an additional region of 26 bp between both cleavage sites. For all DNA
      substrates examined, the presence of ATP caused altered footprinting patterns. We assume that
      the altered patterns are most likely due to a conformational change of the enzyme. Overall,
      our data further refine the tracking-collision model for type III restriction enzymes.
AU  - Mucke M
AU  - Reich S
AU  - Moncke-Buchner E
AU  - Reuter M
AU  - Kruger DH
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2001 312: 687-698.

PMID- 6288656
VI  - 152
DP  - 1982
TI  - Transformation of restriction endonuclease phenotype in Streptococcus pneumoniae.
PG  - 183-190
AB  - The genetic basis of the unique restriction endonuclease DpnI, that cleaves
      only at a methylated sequence, 5'-GmeATC-3', and of the complementary
      endonuclease DpnII, which cleaves at the same sequence when it is not
      methylated, was investigated.  Different strains of Streptococcus pneumoniae
      isolated from patients contained either DpnI (two isolates) or DpnII (six
      isolates).  The latter strains also contained DNA methylated at the 5'-GATC-3'
      sequence.  A restrictable bacteriophage, HB-3, was used to characterize the
      various strains and to select for transformants.  One laboratory strain
      contained neither DpnI nor DpnII.  It was probably derived from a
      DpnI-containing strain, and its DNA was not methylated at 5'-GATC-3'.  Cells of
      this strain were transformed to the DpnI restriction phenotype by DNA from a
      DpnI-containing strain and to the DpnII restriction phenotype by DNA from
      DpnII-containing strain.  Neither cross-transformation, that is, transformation
      to one phenotype by DNA from a strain of the other phenotype, nor spontaneous
      conversion was observed.  Extracts of transformants to the new restriction
      phenotype were shown to contain the corresponding endonuclease.
AU  - Muckerman CC
AU  - Springhorn SS
AU  - Greenberg B
AU  - Lacks SA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1982 152: 183-190.

PMID- 
VI  - 0
DP  - 1993
TI  - Homing endonucleases.
PG  - 111-143
AB  - *

      I. Introduction

      II. Historic review

      III. General characteristics of homing endonucleases

              A. Endonuclease-mediated homing

              B. Endonuclease ORF location

              C. Endonuclease expression

              D. Sequence motifs

                      1. The LAGLI-DADG motif

                      2. The GIY-YIG motif

                      3. The zinc finger motif

                      4. Unclassified

              E. Target recognition and cleavage specificity

                      1. General properties

                      2. Genetic studies

                      3. Physical studies

      IV. Evolutionary considerations

              A. Evidence for mobility of endonuclease genes

              B. Invasion and its aftermath

              C. Endonuclease properties that potentiate invasiveness

              D. Down-regulation of endonuclease expression

              E. Cross-species transfer

      

AU  - Mueller JE
AU  - Bryk M
AU  - Loizos N
AU  - Belfort M
PT  - Journal Article
TA  - Nucleases
JT  - Nucleases
SO  - Nucleases 1993 0: 111-143.

PMID- 8595885
VI  - 10
DP  - 1996
TI  - Intron mobility in phage T4 occurs in the context of recombination-dependent DNA replication by way of multiple pathways.
PG  - 351-364
AB  - Numerous group I introns in both prokaryotes and euykaryotes behave as mobile genetic
      elements.  The functional requirements for intron mobility were determined in the T4 phage
      system using an in vivo assay to measure intron homing with wild-type and mutant derivatives.
      Thus, it was demonstrated that intron mobility occurs in the context of phage
      recombination-dependent replication, a pathway that uses overlapping subsets of replication
      and recombination functions.  The functional requirements for intron homing and the nature of
      recombinant products are only partially consistent with the accepted double-strand-break
      repair model for intron inheritance, and implicate additional homing pathways.  Whereas
      ambiguities in resolvase requirements and underrepresentation of crossover recombination
      products are difficult to rationalize strictly by DSBR, these properties are most readily
      consistent with a synthesis-dependent strand annealing pathway.  The pathways share common
      features in the strand invasion steps, but differ in subsequent repair synthesis and
      resolution steps, influencing the genetic consequences of the intron transfer event.
AU  - Mueller JE
AU  - Clyman J
AU  - Huang Y-J
AU  - Parker MM
AU  - Belfort M
PT  - Journal Article
TA  - Genes Dev.
JT  - Genes Dev.
SO  - Genes Dev. 1996 10: 351-364.

PMID- 8804310
VI  - 10
DP  - 1996
TI  - Exon coconversion biases accompanying intron homing: battle of the nucleases.
PG  - 2158-2166
AB  - Intron homing in phage T4 occurs in the context of recombination-dependent replication, by
      virtue of intron-encoded endonucleolytic activity.  After the td intron endonuclease I-TevI
      cleaves the intronless recipient 23 and 25 nucleotides upstream of the intron insertion site,
      exonucleolytic degradation is required for recombination to proceed.  This resection process
      results in coconversion of exon sequences flanking the intron.  In a genetic system designed
      to study coconversion of flanking markers, we demonstrate that although there is a
      bidirectional polarity gradient, coconversion can be highly asymmetric.  Furthermore, we show
      that the coconversion of flanking markers favors exon I sequences, upstream of the I-TevI
      cleavage site.  These data are consistent with the asymmetric features of the homing pathways
      that have been invoked for intron mobility in phage T4.  Moreover, these results are in accord
      with the finding that once the td homing-site substrate is cleaved, I-TevI remains bound to
      the downstream cleavage product, protecting against exonucleolytic degradation, and thereby
      limiting the extent of coconversion into exon II.  The results suggest that recombination
      events are influenced by a competition between the homing endonuclease and exonucleases for
      sequences downstream of the I-TevI cleavage site, thereby implying a role for the homing
      endonuclease in the repair process.
AU  - Mueller JE
AU  - Smith D
AU  - Belfort M
PT  - Journal Article
TA  - Genes Dev.
JT  - Genes Dev.
SO  - Genes Dev. 1996 10: 2158-2166.

PMID- 8521829
VI  - 14
DP  - 1995
TI  - Intron-encoded endonuclease I-TevI binds as a monomer to effect sequential cleavage via conformational changes in the td homing site.
PG  - 5724-5735
AB  - I-TevI, the intron-encoded endonuclease from the thymidylate synthase (td) gene of
      bacteriophage T4, binds its DNA substrate across the minor groove in a sequence-tolerant
      fashion.  We demonstrate here that the 28 kDa I-TevI binds the extensive 37 bp td homing site
      as a monomer and significantly distorts its substrate.  In situ cleavage assays and phasing
      analyses indicate that upon nicking the bottom strand of the td homing site, I-TevI induces a
      directed bend of 38o towards the major groove near the cleavage site.  Formation of the bent
      I-TevI-DNA complex is proposed to promote top-strand cleavage of the homing site.
      Furthermore, reductions in the degree of distortion and in the efficiency of binding
      base-substitution variants of the td homing site indicate that sequences flanking the cleavage
      site contribute to the I-TevI-induced conformational change.  These results, combined with
      genetic, physical and computer-modeling studies, form the basis of a model, wherein I-TevI
      acts as a hinged monomer to induce a distortion that widens the minor groove, facilitating
      access to the top-strand cleavage site.  The model is compatible with both unmodified DNA and
      glucosylated hydroxymethylcytosine-containing DNA, as exists in the T-even phages.
AU  - Mueller JE
AU  - Smith D
AU  - Bryk M
AU  - Belfort M
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1995 14: 5724-5735.

PMID- 27516524
VI  - 4
DP  - 2016
TI  - Genome Sequence of Corynebacterium pseudotuberculosis Strain PA02 Isolated from an Ovine Host in the Amazon.
PG  - e00838-16
AB  - In this work, we report the complete genome sequence of Corynebacterium pseudotuberculosis
      strain PA02 isolated from an ovine host. The genome contains
      2,328,435 bp, a 52.2% G+C content, 2,035 coding sequences, 12 rRNA operons, 45
      tRNAs, and 14 predicted pseudogenes.
AU  - Muge GR
AU  - Veras AA
AU  - de Sa PH
AU  - Cavalcante AL
AU  - Alves JT
AU  - Morais E
AU  - Silva AG
AU  - Guimaraes LC
AU  - Azevedo V
AU  - Folador AR
AU  - Silva A
AU  - Ramos RT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00838-16.

PMID- 22328744
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of the Thermophilic Bacterium Geobacillus thermoleovorans CCB_US3_UF5.
PG  - 1239
AB  - Geobacillus thermoleovorans CCB_US3_UF5 is a thermophilic bacterium isolated from a hot spring
      in Malaysia. Here, we report the complete genome of G.
      thermoleovorans CCB_US3_UF5, which shows high similarity to the genome of
      Geobacillus kaustophilus HTA 426 in terms of synteny and orthologous genes.
AU  - Muhd SMK
AU  - Abdul RAY
AU  - Saito JA
AU  - Hou S
AU  - Alam M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1239.

PMID- 9405154
VI  - 274
DP  - 1997
TI  - Temperature-sensitive mutants of the EcoRI endonuclease.
PG  - 722-737
AB  - The EcoRI endonuclease is an important recombinant DNA tool and a paradigm of
      sequence-specific DNA-protein interactions.  We have isolated temperature sensitive EcoRI
      endonuclease mutants (R56Q, G78D, P90S, V97I, R105K, M157I, C218Y, A235E, M255I, T261I and
      L263F) and characterized activity in vivo and in vitro.  Although the majority were TS for
      function in vivo, all of the mutant enzymes were stably expressed and largely soluble at both
      30oC and 42oC in vivo and none of the mutants was found to be TS in vitro.  These findings
      suggest that these mutations may affect folding of the enzyme at elevated temperature in vivo.
      Both non-conservative and conservative substitutions occurred but were not correlated with
      severity of the mutation.  Of the 12 residues identified, 11 are conserved between EcoRI and
      the isoschizomer RsrI (which shares 50% identity), a further indication that these residues
      are critical for EcoRI structure and function.  Inspection of the 2.8 A resolution X-ray
      crystal structure of the wild-type EcoRI endonuclease-DNA complex revealed that: (1) the TS
      mutations cluster in one half of the globular enzyme; (2) several of the substituted residues
      interact with each other; (3) most mutations would be predicted to disrupt local structures;
      (4) two mutations may affect the dimer interface (G78D and A235E); (5) one mutation (P90S)
      occurred in a residue that is part of, or immediately adjacent to, the EcoRI active site and
      which is conserved in the distantly related EcoRV endonuclease.  Finally, one class of mutants
      restricted phage in vivo and was active in vitro, whereas a second class did not restrict and
      was inactive in vitro.  The two classes of mutants may differ in kinetic properties or
      cleavage mechanism.  In summary, these mutations provide insights into EcoRI structure and
      function, and complement previous genetic, biochemical, and structural analyses.
AU  - Muir RS
AU  - Flores H
AU  - Zinder ND
AU  - Model P
AU  - Soberon X
AU  - Heitman J
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1997 274: 722-737.

PMID- 27174281
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Hydrocarbon-Degrading Staphylococcus saprophyticus Strain CNV2, Isolated from Crude Oil-Contaminated Soil from the Noonmati Oil  Refinery, Guwahati, Assam, India.
PG  - e00370-16
AB  - Here, we report the 2.6 Mb draft genome sequence of hydrocarbon-degrading Staphylococcus
      saprophyticus strain CNV2, isolated from oil-contaminated soil in
      Guwahati, India. CNV2 contains 2,545 coding sequences and has a G+C content of
      33.2%. This is the first report of the genome sequence of an S. saprophyticus
      adapted to an oil-contaminated environment.
AU  - Mukherjee A
AU  - Chettri B
AU  - Langpoklakpam JS
AU  - Singh AK
AU  - Chattopadhyay D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00370-16.

PMID- 27174279
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Hydrocarbon-Degrading Enterobacter cloacae Strain S1:CND1, Isolated from Crude Oil-Contaminated Soil from the Noonmati Oil  Refinery, Guwahati, Assam, India.
PG  - e00367-16
AB  - We report here the 4.57-Mb draft genome sequence of hydrocarbon-degrading Enterobacter cloacae
      strain S1:CND1 isolated from oil-contaminated soil in
      Guwahati, India. S1:CND1 contains 4,205 coding sequences and has a G+C content of
      57.45%. This is the first report of the genome sequence of an E. cloacae adapted
      to an oil-contaminated environment.
AU  - Mukherjee A
AU  - Chettri B
AU  - Langpoklakpam JS
AU  - Singh AK
AU  - Chattopadhyay D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00367-16.

PMID- 26203325
VI  - 10
DP  - 2015
TI  - High quality draft genome sequence and analysis of Pontibacter roseus type strain SRC-1(T) (DSM 17521(T)) isolated from muddy waters of a drainage system in Chandigarh, India.
PG  - 8
AB  - Pontibacter roseus is a member of genus Pontibacter family Cytophagaceae, class Cytophagia.
      While the type species of the genus Pontibacter actiniarum was
      isolated in 2005 from a marine environment, subsequent species of the same genus
      have been found in different types of habitats ranging from seawater, sediment,
      desert soil, rhizosphere, contaminated sites, solar saltern and muddy water. Here
      we describe the features of Pontibacter roseus strain SRC-1(T) along with its
      complete genome sequence and annotation from a culture of DSM 17521(T). The
      4,581,480 bp long draft genome consists of 12 scaffolds with 4,003 protein-coding
      and 50 RNA genes and is a part of Genomic Encyclopedia of Type Strains: KMG-I
      project.
AU  - Mukherjee S et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 8.

PMID- 28604660
VI  - 35
DP  - 2017
TI  - 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life.
PG  - 676-683
AB  - We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of
      Bacteria and Archaea (GEBA) initiative, selected to maximize
      sequence coverage of phylogenetic space. These genomes double the number of
      existing type strains and expand their overall phylogenetic diversity by 25%.
      Comparative analyses with previously available finished and draft genomes reveal
      a 10.5% increase in novel protein families as a function of phylogenetic
      diversity. The GEBA genomes recruit 25 million previously unassigned metagenomic
      proteins from 4,650 samples, improving their phylogenetic and functional
      interpretation. We identify numerous biosynthetic clusters and experimentally
      validate a divergent phenazine cluster with potential new chemical structure and
      antimicrobial activity. This Resource is the largest single release of reference
      genomes to date. Bacterial and archaeal isolate sequence space is still far from
      saturated, and future endeavors in this direction will continue to be a valuable
      resource for scientific discovery.
AU  - Mukherjee S et al
PT  - Journal Article
TA  - Nat. Biotechnol.
JT  - Nat. Biotechnol.
SO  - Nat. Biotechnol. 2017 35: 676-683.

PMID- 27365353
VI  - 4
DP  - 2016
TI  - Genome Sequence of the Red Pigment-Forming Meiothermus taiwanensis Strain RP Isolated from Paniphala Hot Spring, India.
PG  - e00629-16
AB  - Here we report the draft genome sequence of Meiothermus taiwanensis strain RP (MCC 2966),
      isolated from the Paniphala hot spring of India, which contains genes encoding for enzymes of
      the methyl erythritol 4-phosphate (MEP) pathway of isoprenoid biosynthesis and carotenoid
      backbone synthesis.
AU  - Mukherjee T
AU  - Bose S
AU  - Sen U
AU  - Roy C
AU  - Rameez MJ
AU  - Ghosh W
AU  - Mukhopadhyay SK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00629-16.

PMID- 24051321
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Sphingobium sp. Strain HDIPO4, an Avid Degrader of Hexachlorocyclohexane.
PG  - e00749-13
AB  - Sphingobium sp. strain HDIPO4 was isolated from a hexachlorocyclohexane (HCH) dumpsite and
      degraded HCH isomers rapidly. The draft genome sequence of HDIPO4
      (~4.7 Mbp) contains 143 contigs and 4,646 coding sequences with a G+C content of
      65%.
AU  - Mukherjee U
AU  - Kumar R
AU  - Mahato NK
AU  - Khurana JP
AU  - Lal R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00749-13.

PMID- 25081263
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Amycolatopsis mediterranei DSM 40773, a Tangible Antibiotic Producer.
PG  - e00752-14
AB  - Amycolatopsis mediterranei DSM 40773 has been of special interest as successors of this strain
      are in use for the commercial production of rifamycin B. Here we
      present the draft genome sequence (~10 Mb) of this strain, which contains 108
      contigs, 9,198 genes, and has a G+C content of 71.3%.
AU  - Mukherjee U
AU  - Saxena A
AU  - Kumari R
AU  - Singh P
AU  - Lal R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00752-14.

PMID- 10809703
VI  - 182
DP  - 2000
TI  - Distinctiveness of genotypes of Helicobacter pylori in Calcutta India.
PG  - 3219-3227
AB  - The genotypes of 78 strains of Helicobacter pylori from Calcutta, India (55 from ulcer
      patients and 23 from more-benign infections), were studied, with a focus on putative virulence
      genes and neutral DNA markers that were likely to be phylogenetically informative. PCR tests
      indicated that 80 to 90% of Calcutta strains carried the cag pathogenicity island (PAI) and
      potentially toxigenic vacAs1 alleles of the vacuolating cytotoxin gene (vacA), independent of
      disease status. This was higher than in the West (where cag PAI(+) vacAs1 genotypes are
      disease associated) but lower than in east Asia. The iceA2 gene was weakly disease associated
      in Calcutta, whereas in the West the alternative but unrelated iceA1 gene at the same locus is
      weakly disease associated. DNA sequence motifs of vacAm1 (middle region) alleles formed a
      cluster that was distinct from those of east Asia and the West, whereas the cagA sequences of
      Calcutta and Western strains were closely related. An internal deletion found in 20% of
      Calcutta iceA1 genes was not seen in any of approximately 200 strains studied from other
      geographic regions and thus seemed to be unique to this H. pylori population. Two mobile DNAs
      that were rare in east Asian strains were also common in Calcutta. About 90% of Calcutta
      strains were metronidazole resistant. These findings support the idea that H. pylori gene
      pools differ regionally and emphasize the potential importance of studies of Indian and other
      non-Western H. pylori populations in developing a global understanding of this gastric
      pathogen and associated disease.
AU  - Mukhopadhyay AK
AU  - Kersulyte D
AU  - Jeong JY
AU  - Datta S
AU  - Ito Y
AU  - Chowdhury A
AU  - Chowdhury S
AU  - Santra A
AU  - Bhattacharya SK
AU  - Azuma T
AU  - Nair GB
AU  - Berg DE
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2000 182: 3219-3227.

PMID- 26294629
VI  - 3
DP  - 2015
TI  - Genome Sequence of a Burkholderia pseudomallei Clinical Isolate from a Patient with Community-Acquired Pneumonia and Septicemia.
PG  - e00915-15
AB  - Here, we report the draft genome sequence of Burkholderia pseudomallei CM_Manipal, the
      causative agent of melioidosis isolated from a diabetic patient
      in Manipal, southern India. The draft genome consists of 107 contigs and is
      7,209,157 bp long. A total of 5,600 coding sequences (CDSs), 60 tRNAs, 12 rRNAs,
      and one noncoding RNA (ncRNA) were predicted from this assembly.
AU  - Mukhopadhyay C
AU  - Vandana KE
AU  - Chaitanya TA
AU  - Shaw T
AU  - Bhat HV
AU  - Chakrabarty S
AU  - Paul B
AU  - Mallya S
AU  - Murali TS
AU  - Satyamoorthy K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00915-15.

PMID- 9862213
VI  - 11
DP  - 1998
TI  - Protein engineering of BamHI restriction endonuclease: replacement of Cys54 by Ala enhances catalytic activity.
PG  - 931-935
AB  - Chemical modification studies of BamHI endonuclease indicated the importance of the cysteine
      residue in catalysis.  Of the three cysteine residues at position 34, 54 and 64 in the BamHI
      endonuclease Cys54 and Cys64 are at the DNA-protein interface.  The co-crystal structure of
      the BamHI-DNA complex, however, does not indicate any role of cysteines either in binding or
      catalysis.  In the context of strong biochemical evidence, Cys54 in BamHI was changed to Ala54
      to investigate its role in catalysis.  The mutation was carried out by PCR overlap extension,
      the mutant gene was cloned and characterized by sequencing.  The mutant BamHI was expressed
      and purified to homogeneity and the kinetic parameters (KM and kcat) of the wild type and the
      C54A mutant were determined.  The mutation results in up to ~40% enhancement of kcat and some
      increase in KM.  These in vitro results were also supported by in vivo SOS induction assays:
      the C54A mutant gene under the T7 promoter caused complete lysis in JH139 in absence of T7 RNA
      polymerase whereas the wild-type gene gave deep blue colonies under the same conditions.  The
      results suggest no direct role in Cys54 in catalysis, but it can influence the catalytic
      activity through Val57 backbone contact seen in the co-crystal structure.
AU  - Mukhopadhyay P
AU  - Roy KB
PT  - Journal Article
TA  - Protein Eng.
JT  - Protein Eng.
SO  - Protein Eng. 1998 11: 931-935.

PMID- 28473398
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Dolosigranulum pigrum from a Patient with Interstitial Lung Disease Using Single-Molecule Real-Time Sequencing Technology.
PG  - e00317-17
AB  - The whole genome sequence of Dolosigranulum pigrum isolated from the blood of a patient with
      interstitial lung disease was sequenced with the Pacific Biosciences
      RS II platform. The genome size is 2.1 Mb with 2,127 annotated coding sequences;
      it contained two clustered regularly interspaced short palindromic repeats
      (CRISPR)/CRISPR-associated proteins (Cas) systems.
AU  - Mukhopadhyay R
AU  - Joaquin J
AU  - Hogue R
AU  - Fitzgerald S
AU  - Jospin G
AU  - Mars K
AU  - Eisen JA
AU  - Chaturvedi V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00317-17.

PMID- 28450518
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of a Paenalcaligenes hominis Strain Isolated from a Paraplegic Patient with Neurogenic Bladder Using Single-Molecule Real-Time  Sequencing Technology.
PG  - e00252-17
AB  - The genome of Paenalcaligenes hominis, isolated from a paraplegic patient with neurogenic
      bladder, was sequenced with the Pacific Biosciences RSII platform. The
      genome size is 2.68 Mb and includes 3,096 annotated coding sequences, including
      genes associated with quinone cofactors, which play crucial roles in the
      virulence of Gram-negative bacteria.
AU  - Mukhopadhyay R
AU  - Joaquin J
AU  - Hogue R
AU  - Kilaru A
AU  - Jospin G
AU  - Mars K
AU  - Eisen JA
AU  - Chaturvedi V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00252-17.

PMID- 20870763
VI  - 192
DP  - 2010
TI  - High-redundancy draft sequencing of 15 clinical and environmental burkholderia strains.
PG  - 6313-6314
AB  - The Gram-negative Burkholderia genus includes several species of intracellular bacterial
      pathogens that pose substantial risk to humans. In
      this study, we have generated draft genome sequences of 15 strains of B.
      oklahomensis, B. pseudomallei, B. thailandensis, and B. ubonensis to an
      average sequence read coverage of 25- to 40-fold.
AU  - Mukhopadhyay S
AU  - Thomason MK
AU  - Lentz S
AU  - Nolan N
AU  - Willner K
AU  - Gee JE
AU  - Glass MB
AU  - Inglis TJ
AU  - Merritt A
AU  - Levy A
AU  - Sozhamannan S
AU  - Mateczun A
AU  - Read TD
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 6313-6314.

PMID- 29724830
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Bacillus pumilus SCAL1, an Endophytic Heat-Tolerant Plant Growth-Promoting Bacterium.
PG  - e00306-18
AB  - Bacillus pumilus strain SCAL1 is an endophytic, thermophilic plant that was isolated from the
      leaf of a plant, Solanum lycopersicum L., in Sindh, Pakistan.
      B. pumilus strain SCAL1 has usually exhibited high resistance to environmental
      stresses, with a growth temperature ranging from 30 to 60 degrees C. An
      approximately 3.75-Mb draft genome was assembled into 68 contigs.
AU  - Mukhtar T
AU  - Afridi MS
AU  - McArthur R
AU  - Van Hamme JD
AU  - Rineau F
AU  - Mahmood T
AU  - Amna S
AU  - Zahid M
AU  - Salam A
AU  - Khan MN
AU  - Ali F
AU  - Mehmood S
AU  - Bangash N
AU  - Chaudhary HJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00306-18.

PMID- Not included in PubMed...
VI  - 65
DP  - 1993
TI  - Restriction and modification systems: unrestricted frontiers.
PG  - 509-511
AB  - Report on Saxton's River Meeting, July 1993
AU  - Mukund MA
PT  - Journal Article
TA  - Curr. Sci.
JT  - Curr. Sci.
SO  - Curr. Sci. 1993 65: 509-511.

PMID- 4343959
VI  - 69
DP  - 1972
TI  - Specificity of the break produced by restricting endonuclease R in Simian virus 40 DNA, as revealed by partial denaturation mapping.
PG  - 3215-3219
AB  - Superhelical circular (form 1) SV40 DNA was converted to linear molecules by
      the action of a partially purified restriction enzyme of resistance transfer
      factor-R of Escherichia coli.  The resulting linear DNA molecules are full
      length, as judged by their sedimentation through alkaline sucrose gradient and
      by direct observation in an electron microscope.  Nicked circular (form II) DNA
      was found as an intermediate in the conversion of form I DNA to linear DNA.
      Analysis of partial denaturation maps obtained by alkaline denaturation of the
      unit-length linear molecules showed that the break in SV40 DNA occurred at a
      specific site on the DNA.
AU  - Mulder C
AU  - Delius H
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1972 69: 3215-3219.

PMID- 26044437
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Triclosan-Degrading Bacterium Sphingomonas sp. Strain YL-JM2C, Isolated from a Wastewater Treatment Plant in China.
PG  - e00603-15
AB  - Sphingomonas sp. strain YL-JM2C was isolated from a wastewater treatment plant in Xiamen,
      China, by enrichment on triclosan. The bacterium is of special interest
      because of its ability to degrade triclosan. Here, we present a draft genome
      sequence of the microorganism and its functional annotation. To our best
      knowledge, this is the first report of a draft genome sequence of a
      triclosan-degrading bacterium.
AU  - Mulla SI
AU  - Hu A
AU  - Xu H
AU  - Yu CP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00603-15.

PMID- 25977432
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Staphylococcus carnosus subsp. utilis LTH 7013, Isolated from South Tyrolean Ham.
PG  - e00456-15
AB  - Staphylococcus carnosus is used as a starter culture in meat fermentation, where  it
      contributes to color formation and produces aromatic compounds. Here, we
      report the first draft genome sequence of an S. carnosus subsp. utilis strain,
      LTH 7013, isolated from South Tyrolean ham, with potential application as a
      starter culture.
AU  - Muller A
AU  - Huptas C
AU  - Wenning M
AU  - Schmidt H
AU  - Weiss A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00456-15.

PMID- 27688338
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Staphylococcus carnosus LTH 3730.
PG  - e01038-16
AB  - Specific strains of the apathogenic coagulase-negative species Staphylococcus carnosus are
      frequently used as meat starter cultures, as they contribute to
      color formation and the production of aroma compounds. Here, we report the
      complete genome sequence of S. carnosus LTH 3730, a strain isolated from a
      fermented fish product.
AU  - Muller A
AU  - Klumpp J
AU  - Schmidt H
AU  - Weiss A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01038-16.

PMID- 17432936
VI  - 3
DP  - 2007
TI  - A tale of two oxidation states: bacterial colonization of arsenic-rich environments.
PG  - e53
AB  - Microbial biotransformations have a major impact on contamination by toxic elements, which
      threatens public health in developing and industrial
      countries. Finding a means of preserving natural environments-including
      ground and surface waters-from arsenic constitutes a major challenge
      facing modern society. Although this metalloid is ubiquitous on Earth,
      thus far no bacterium thriving in arsenic-contaminated environments has
      been fully characterized. In-depth exploration of the genome of the
      beta-proteobacterium Herminiimonas arsenicoxydans with regard to
      physiology, genetics, and proteomics, revealed that it possesses
      heretofore unsuspected mechanisms for coping with arsenic. Aside from
      multiple biochemical processes such as arsenic oxidation, reduction, and
      efflux, H. arsenicoxydans also exhibits positive chemotaxis and motility
      towards arsenic and metalloid scavenging by exopolysaccharides. These
      observations demonstrate the existence of a novel strategy to efficiently
      colonize arsenic-rich environments, which extends beyond oxidoreduction
      reactions. Such a microbial mechanism of detoxification, which is possibly
      exploitable for bioremediation applications of contaminated sites, may
      have played a crucial role in the occupation of ancient ecological niches
      on earth.
AU  - Muller D et al
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2007 3: e53.

PMID- 23144412
VI  - 194
DP  - 2012
TI  - Genome Sequence of 'Candidatus Microthrix parvicella' Bio17-1, a Long-Chain-Fatty-Acid-Accumulating Filamentous Actinobacterium from a Biological    Wastewater Treatment Plant.
PG  - 6670-6671
AB  - 'Candidatus Microthrix' bacteria are deeply branching filamentous actinobacteria  which
      occur at the water-air interface of biological wastewater treatment plants,
      where they are often responsible for foaming and bulking. Here, we report the
      first draft genome sequence of a strain from this genus: 'Candidatus Microthrix
      parvicella' strain Bio17-1.
AU  - Muller EE
AU  - Pinel N
AU  - Gillece JD
AU  - Schupp JM
AU  - Price LB
AU  - Engelthaler DM
AU  - Levantesi C
AU  - Tandoi V
AU  - Luong K
AU  - Baliga NS
AU  - Korlach J
AU  - Keim PS
AU  - Wilmes P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6670-6671.

PMID- 29075368
VI  - 12
DP  - 2017
TI  - First draft genome sequence of a strain belonging to the Zoogloea genus and its gene expression in situ.
PG  - 64
AB  - The Gram-negative beta-proteobacterium Zoogloea sp. LCSB751 (LMG 29444) was newly isolated
      from foaming activated sludge of a municipal wastewater treatment plant.
      Here, we describe its draft genome sequence and annotation together with a
      general physiological and genomic analysis, as the first sequenced representative
      of the Zoogloea genus. Moreover, Zoogloea sp. gene expression in its environment
      is described using metatranscriptomic data obtained from the same treatment
      plant. The presented genomic and transcriptomic information demonstrate a
      pronounced capacity of this genus to synthesize poly-beta-hydroxyalkanoate within
      wastewater.
AU  - Muller EEL
AU  - Narayanasamy S
AU  - Zeimes M
AU  - Laczny CC
AU  - Lebrun LA
AU  - Herold M
AU  - Hicks ND
AU  - Gillece JD
AU  - Schupp JM
AU  - Keim P
AU  - Wilmes P
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 64.

PMID- 23929484
VI  - 1
DP  - 2013
TI  - Genome Sequence of Serratia plymuthica Strain S13, an Endophyte with Germination- and Plant-Growth-Promoting Activity from the Flower of Styrian Oil Pumpkin.
PG  - e00594-13
AB  - The bacterium Serratia plymuthica strain S13 was demonstrated to colonize various
      plant-associated microhabitats and to suppress damping-off diseases. The
      completed genome sequence has a size of 5.5 Mb, containing 4,957 putative
      protein-encoding regions, and will be used to identify genetic determinants
      enabling the bacterium to escort a plant's entire life cycle.
AU  - Muller H
AU  - Furnkranz M
AU  - Grube M
AU  - Berg G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00594-13.

PMID- 23516179
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of the Sugar Beet Endophyte Pseudomonas poae RE*1-1-14,  a Disease-Suppressive Bacterium.
PG  - e0002013
AB  - The endophytic bacterium Pseudomonas poae RE*1-1-14 shows broad antagonistic activity and is
      applied to seeds as a biocontrol agent to suppress late root rot
      in the sugar beet. The completely sequenced 5.5-Mb genome reveals genes that
      putatively contribute to this antagonistic activity and the intimate
      plant-microbe interaction.
AU  - Muller H
AU  - Zachow C
AU  - Alavi M
AU  - Tilcher R
AU  - Krempl PM
AU  - Thallinger GG
AU  - Berg G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0002013.

PMID- 21097611
VI  - 193
DP  - 2010
TI  - The Complete Genome Sequences of three Erwinia amylovora Phages Isolated in North America and a Bacteriophage Induced from an Erwinia tasmaniensis  Strain.
PG  - 795-796
AB  - Fire blight, a plant disease of economical importance caused by Erwinia amylovora, may be
      controlled by application of bacteriophages. Here we
      provide the complete genome sequences and the annotation of three E.
      amylovora-specific phages isolated in North America and genomic
      information about a bacteriophage induced by mitomycin C-treatment of an
      E. tasmaniensis strain, antagonistic for E. amylovora. The American phages
      resemble two already described viral genomes, whereas the E. tasmaniensis
      phage displays a singular genomic sequence in BLAST searches.
AU  - Muller I
AU  - Kube M
AU  - Reinhardt R
AU  - Jelkmann W
AU  - Geider K
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 193: 795-796.

PMID- 23661486
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Myxococcus xanthus Wild-Type Strain DZ2, a Model Organism for Predation and Development.
PG  - e00217-13
AB  - Myxococcus xanthus is a member of the Myxococcales order within the Deltaproteobacteria
      subdivision. The myxobacteria reside in soil, have relatively
      large genomes, and display complex life cycles. Here, we report the whole-genome
      shotgun sequence of strain DZ2, which includes unique genes not found previously
      in strain DK1622.
AU  - Muller S
AU  - Willett JW
AU  - Bahr SM
AU  - Darnell CL
AU  - Hummels KR
AU  - Dong CK
AU  - Vlamakis HC
AU  - Kirby JR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00217-13.

PMID- 23788552
VI  - 1
DP  - 2013
TI  - Draft Genome of a Type 4 Pilus Defective Myxococcus xanthus Strain, DZF1.
PG  - e00392-13
AB  - Myxococcus xanthus is a member of the Myxococcales order within the deltaproteobacterial
      subdivision. Here, we report the whole-genome shotgun
      sequence of the type IV pilus (T4P) defective strain DZF1, which includes many
      genes found in strain DZ2 but absent from strain DK1622.
AU  - Muller S
AU  - Willett JW
AU  - Bahr SM
AU  - Scott JC
AU  - Wilson JM
AU  - Darnell CL
AU  - Vlamakis HC
AU  - Kirby JR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00392-13.

PMID- 18662788
VI  - 62
DP  - 2008
TI  - Cloning, purification and initial characterization of E. coli McrA, a putative 5-methylcytosine-specific nuclease.
PG  - 98-103
AB  - Expression strains of Escherichia coli BL21(DE3) overproducing the E. coli m(5)C McrA
      restriction protein were produced by cloning the mcrA coding
      sequence behind a T7 promoter. The recombinant mcrA minus BL21(DE3) host
      produces active McrA as evidenced by its acquired ability to selectively
      restrict the growth of T7 phage containing DNA methylated in vitro by
      HpaII methylase. The mcrA coding region contains several non-optimal E.
      coli triplets. Addition of the pACYC-RIL tRNA encoding plasmid to the
      BL21(DE3) host increased the yield of recombinant McrA (rMcrA) upon
      induction about 5- to 10-fold. McrA protein expressed at 37 degrees C is
      insoluble but a significant fraction is recovered as soluble protein after
      autoinduction at 20 degrees C. rMcrA protein, which is predicted to
      contain a Cys(4)-Zn(2+) finger and a catalytically important histidine
      triad in its putative nuclease domain, binds to several metal chelate
      resins without addition of a poly-histidine affinity tag. This feature was
      used to develop an efficient protocol for the rapid purification of nearly
      homogeneous rMcrA. The native protein is a dimer with a high alpha-helical
      content as measured by circular dichroism analysis. Under all conditions
      tested purified rMcrA does not have measurable nuclease activity on HpaII
      methylated (Cm(5)CGG) DNA, although the purified protein does specifically
      bind HpaII methylated DNA. These results have implications for
      understanding the in vivo activity of McrA in "restricting"
      m(5)C-containing DNA and suggest that rMcrA may have utility as a reagent
      for affinity purification of DNA fragments containing m(5)C residues.
AU  - Mulligan EA
AU  - Dunn JJ
PT  - Journal Article
TA  - Protein Expr. Purif.
JT  - Protein Expr. Purif.
SO  - Protein Expr. Purif. 2008 62: 98-103.

PMID- 20015968
VI  - 38
DP  - 2010
TI  - Differential binding of Escherichia coli McrA protein to DNA sequences that contain the dinucleotide m5CpG.
PG  - 1997-2005
AB  - The Escherichia coli McrA protein, a putative C(5)-methylcytosine/C(5)-hydroxyl
      methylcytosine-specific nuclease, binds
      DNA with symmetrically methylated HpaII sequences (Cm5CGG), but its
      precise recognition sequence remains undefined. To determine McrA's
      binding specificity, we cloned and expressed recombinant McrA with a
      C-terminal StrepII tag (rMcrA-S) to facilitate protein purification and
      affinity capture of human DNA fragments with m5C residues. Sequence
      analysis of a subset of these fragments and electrophoretic mobility shift
      assays with model methylated and unmethylated oligonucleotides suggest
      that N(Y > R) m5CGR is the canonical binding site for rMcrA-S. In addition
      to binding HpaII-methylated double-stranded DNA, rMcrA-S binds DNA
      containing a single, hemimethylated HpaII site; however, it does not bind
      if A, C, T or U is placed across from the m5C residue, but does if I is
      opposite the m5C. These results provide the first systematic analysis of
      McrA's in vitro binding specificity.
AU  - Mulligan EA
AU  - Hatchwell E
AU  - McCorkle SR
AU  - Dunn JJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2010 38: 1997-2005.

PMID- 20656798
VI  - 16
DP  - 2010
TI  - A group II intron encodes a functional LAGLIDADG homing endonuclease and self-splices under moderate temperature and ionic conditions.
PG  - 1818-1831
AB  - A group II intron encoding a protein belonging to the LAGLIDADG family of homing endonucleases
      was identified in the mitochondrial rns gene of
      the filamentous fungus Leptographium truncatum, and the catalytic
      activities of both the intron and its encoded protein were
      characterized. A model of the RNA secondary structure indicates that
      the intron is a member of the IIB1 subclass and the open reading frame
      is inserted in ribozyme domain III. In vitro assays carried out with
      two versions of the intron, one in which the open reading frame was
      removed and the other in which it was present, demonstrate that both
      versions of the intron readily self-splice at 37 degrees C and at a
      concentration of MgCl2 as low as 6 mM. The open reading frame encodes a
      functional LAGLIDADG homing endonuclease that cleaves 2 (top strand)
      and 6 (bottom strand) nucleotides (nt) upstream of the intron insertion
      site, generating 4 nt 3' OH overhangs. In vitro splicing assays carried
      out in the absence and presence of the intron-encoded protein indicate
      that the protein does not enhance intron splicing, and RNA-binding
      assays show that the protein does not appear to bind to the intron RNA
      precursor transcript. These findings raise intriguing questions
      concerning the functional and evolutionary relationships of the two
      components of this unique composite element.
AU  - Mullineux ST
AU  - Costa M
AU  - Bassi GS
AU  - Michel F
AU  - Hausner G
PT  - Journal Article
TA  - RNA
JT  - RNA
SO  - RNA 2010 16: 1818-1831.

PMID- 3266858
VI  - 74
DP  - 1988
TI  - Investigation of sequence homology in a group of type-II restriction/modification isoschizomers.
PG  - 245-251
AB  - We have dissected the cloned PstI M and R genes to make DNA hybridization
      probes spanning most of the sequence.  These subclones, and also the intact
      sequence, were used to search for nucleic acid homology by Southern blot in the
      DNA from twelve organisms which produce PstI isoschizomers.  One of these
      probes, a 206-bp fragment from the N-terminal domain of the endonuclease,
      showed significant hybridisation in four strains (Escherichia coli strains
      RFL48, RFL49 and RFL83, and Streptomyces albus P).  No significant
      hybridisation was detected with other parts  of the PstI proteins and the known
      sequences of other type-II systems that recognise different sites.  We
      postulate a possible recognition domain within the M.PstI methyltransferase
      based on similarity to the M.PaeR7 and M.TaqI methyltransferases.
AU  - Mullings R
AU  - Bennett SP
AU  - Brown NL
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 245-251.

PMID- Not included in PubMed...
VI  - 37
DP  - 1986
TI  - Type II restriction endonucleases from Bacillus sphaericus.
PG  - 237-240
AB  - We report the isolation and characterisation of 3 Type II restriction
      endonucleases from Bacillus sphaericus.  These are BspAI (an isoschizomer of
      Sau3AI) in strain JL4B; BspBI and BspBII (isoschizomers of PstI and AsuI) in
      strain JL14.  These are the first reports of these activities in B. sphaericus
      and the first citation of an AsuI isoschizomer in a member of the genus
      Bacillus.  We briefly discuss the possible uses in vitro and significance in
      vivo of these enzymes.
AU  - Mullings R
AU  - Evans LR
AU  - Brown NL
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1986 37: 237-240.

PMID- 22180811
VI  - 5
DP  - 2011
TI  - Genome sequence of Haemophilus parasuis strain 29755.
PG  - 61-68
AB  - Haemophilus parasuis is a member of the family Pasteurellaceae and is the etiologic agent of
      Glasser's disease in pigs, a systemic syndrome associated with
      only a subset of isolates. The genetic basis for virulence and systemic spread of
      particular H. parasuis isolates is currently unknown. Strain 29755 is an invasive
      isolate that has long been used in the study of Glasser's disease. Accordingly,
      the genome sequence of strain 29755 is of considerable importance to
      investigators endeavoring to understand the molecular pathogenesis of H.
      parasuis. Here we describe the features of the 2,224,137 bp draft genome sequence
      of strain 29755 generated from 454-FLX pyrosequencing. These data comprise the
      first publicly available genome sequence for this bacterium.
AU  - Mullins MA
AU  - Register KB
AU  - Bayles DO
AU  - Dyer DW
AU  - Kuehn JS
AU  - Phillips GJ
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 5: 61-68.

PMID- 14636159
VI  - 378
DP  - 2003
TI  - Comparative analysis of DNA methylation patterns in transgenic Drosophila overexpressing mouse DNA methyltransferases.
PG  - 763-768
AB  - DNA methyltransferases (Dnmts) mediate the epigenetic modification of eukaryotic genomes.
      Mammalian DNA methylation patterns are established and
      maintained by co-operative interactions among the Dnmt proteins Dnmt1,
      Dnmt3a and Dnmt3b. Owing to their simultaneous presence in mammalian
      cells, the activities of individual Dnmt have not yet been determined.
      This includes a fourth putative Dnmt, namely Dnmt2, which has failed to
      reveal any activity in previous assays. We have now established transgenic
      Drosophila strains that allow for individual overexpression of all known
      mouse Dnmts. Quantitative analysis of genomic cytosine methylation levels
      demonstrated a robust Dnmt activity for the de novo methyltransferases
      Dnmt3a and Dnmt3b. In addition, we also detected a weak but significant
      activity for Dnmt2. Subsequent methylation tract analysis by genomic
      bisulphite sequencing revealed that Dnmt3 enzymes preferentially
      methylated CpG dinucleotides in a processive manner, whereas Dnmt2
      methylated isolated cytosine residues in a non-CpG dinucleotide context.
      Our results allow a direct comparison of the activities of mammalian Dnmts
      and suggest a significant functional specialization of these enzymes.
AU  - Mund C
AU  - Musch T
AU  - Strodicke M
AU  - Assmann B
AU  - Li E
AU  - Lyko F
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 2003 378: 763-768.

PMID- 23275511
VI  - 79
DP  - 2013
TI  - Rapid and Sensitive Method To Identify Mycobacterium avium subsp paratuberculosis in Cow's Milk by DNA Methylase Genotyping.
PG  - 1612-1618
AB  - Paratuberculosis is an infectious, chronic, and incurable disease that affects ruminants,
      caused by Mycobacterium avium subsp. paratuberculosis. This bacterium is shed primarily
      through feces of infected cows but can be also excreted in colostrum and milk and might
      survive pasteurization. Since an association of genomic sequences of M. avium subsp.
      paratuberculosis in patients with Crohn's disease has been described; it is of interest to
      rapidly detect M. avium subsp. paratuberculosis in milk for human consumption. IS900 insertion
      is used as a target for PCR amplification to identify the presence of M. avium subsp.
      paratuberculosis in biological samples. Two target sequences were selected: IS1 (155 bp) and
      IS2 (94 bp). These fragments have a 100% identity among all M. avium subsp. paratuberculosis
      strains sequenced. M. avium subsp. paratuberculosis was specifically concentrated from milk
      samples by immunomagnetic separation prior to performing PCR. The amplicons were characterized
      using DNA methylase Genotyping, i.e., the amplicons were methylated with 6-methyl-adenine and
      digested with restriction enzymes to confirm their identity. The methylated amplicons from 100
      CFU of M. avium subsp. paratuberculosis can be visualized in a Western blot format using an
      anti-6-methyl-adenine monoclonal antibody. The use of DNA methyltransferase genotyping coupled
      to a scintillation proximity assay allows for the detection of up to 10 CFU of M. avium subsp.
      paratuberculosis per ml of milk. This test is rapid and sensitive and allows for automation
      and thus multiple samples can be tested at the same time.
AU  - Mundo SL
AU  - Gilardoni LR
AU  - Hoffman FJ
AU  - Lopez OJ
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2013 79: 1612-1618.

PMID- 10948096
VI  - 68
DP  - 2000
TI  - Characterization of a shiga toxin 2e-converting bacteriophage from an Escherichia coli strain of human origin.
PG  - 4850-4855
AB  - An infectious Shiga toxin (Stx) 2e-converting bacteriophage (phiP27) was
      isolated from Stx2e-producing Escherichia coli ONT:H(-) isolate 2771/97
      originating from a patient with diarrhea. The phage could be transduced to
      E. coli laboratory strain DH5alpha, and we could show that lysogens were
      able to produce biologically active toxin in a recA-dependent manner. By
      DNA sequence analysis of a 6,388-bp HindIII restriction fragment of
      phiP27, we demonstrated that the stx(2e) gene was located directly
      downstream of ileZ and argO tRNA genes. Although no analogue of an
      antiterminator Q encoding gene was present on this fragment, a lysis
      cassette comprising two holin genes which are related to the holin genes
      of Pseudomonas aeruginosa phage phiCTX and a gene homologous to the
      endolysin gene gp19 of phage PS3 were detected. The results of our study
      demonstrated for the first time that Stx2e can be encoded in the genome of
      an infectious bacteriophage.
AU  - Muniesa M
AU  - Recktenwald J
AU  - Bielaszewska M
AU  - Karch H
AU  - Schmidt H
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2000 68: 4850-4855.

PMID- 21886856
VI  - 4
DP  - 2011
TI  - Complete genome sequence of Rhodospirillum rubrum type strain (S1).
PG  - 293-302
AB  - Rhodospirillum rubrum (Esmarch 1887) Molisch 1907 is the type species of the genus
      Rhodospirillum, which is the type genus of the family Rhodospirillaceae in
      the class Alphaproteobacteria. The species is of special interest because it is
      an anoxygenic phototroph that produces extracellular elemental sulfur (instead of
      oxygen) while harvesting light. It contains one of the most simple photosynthetic
      systems currently known, lacking light harvesting complex 2. Strain S1(T) can
      grow on carbon monoxide as sole energy source. With currently over 1,750 PubMed
      entries, R. rubrum is one of the most intensively studied microbial species, in
      particular for physiological and genetic studies. Next to R. centenum strain SW,
      the genome sequence of strain S1(T) is only the second genome of a member of the
      genus Rhodospirillum to be published, but the first type strain genome from the
      genus. The 4,352,825 bp long chromosome and 53,732 bp plasmid with a total of
      3,850 protein-coding and 83 RNA genes were sequenced as part of the DOE Joint
      Genome Institute Program DOEM 2002.
AU  - Munk AC et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 4: 293-302.

PMID- 21886861
VI  - 4
DP  - 2011
TI  - Complete genome sequence of Tsukamurella paurometabola type strain (no. 33).
PG  - 342-351
AB  - Tsukamurella paurometabola corrig. (Steinhaus 1941) Collins et al. 1988 is the type species of
      the genus Tsukamurella, which is the type genus to the family
      Tsukamurellaceae. The species is not only of interest because of its isolated
      phylogenetic location, but also because it is a human opportunistic pathogen with
      some strains of the species reported to cause lung infection, lethal meningitis,
      and necrotizing tenosynovitis. This is the first completed genome sequence of a
      member of the genus Tsukamurella and the first genome sequence of a member of the
      family Tsukamurellaceae. The 4,479,724 bp long genome contains a 99,806 bp long
      plasmid and a total of 4,335 protein-coding and 56 RNA genes, and is a part of
      the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Munk AC et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 4: 342-351.

PMID- 21304662
VI  - 1
DP  - 2009
TI  - Complete genome sequence of Stackebrandtia nassauensis type strain (LLR-40K-21).
PG  - 234-241
AB  - Stackebrandtia nassauensis Labeda and Kroppenstedt (2005) is the type species of  the genus
      Stackebrandtia, and a member of the actinobacterial family
      Glycomycetaceae. Stackebrandtia currently contains two species, which are
      differentiated from Glycomyces spp. by cellular fatty acid and menaquinone
      composition. Strain LLR-40K-21(T) is Gram-positive, aerobic, and nonmotile, with
      a branched substrate mycelium and on some media an aerial mycelium. The strain
      was originally isolated from a soil sample collected from a road side in Nassau,
      Bahamas. Here we describe the features of this organism, together with the
      complete genome sequence and annotation. This is the first complete genome
      sequence of the actinobacterial suborder Glycomycineae. The 6,841,557 bp long
      single replicon genome with its 6487 protein-coding and 53 RNA genes is part of
      the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Munk C et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2009 1: 234-241.

PMID- 28705973
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of Three Xanthomonas citri Strains from Texas.
PG  - e00609-17
AB  - The complete genome sequences of three Xanthomonas citri strains isolated from lime trees in
      Texas were found to belong to the Aw group. All carried nearly
      identical large plasmids with similarity to those of a citrus canker strain from
      India and to xanthomonads from Africa and Colombia. All three strains harbored
      unusual pthA homologs.
AU  - Munoz BA
AU  - Santillana G
AU  - Mavrodieva V
AU  - Liu Z
AU  - Nakhla M
AU  - Gabriel DW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00609-17.

PMID- 20846960
VI  - 39
DP  - 2011
TI  - Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus.
PG  - 729-743
AB  - Homing endonucleases recognize long target DNA sequences generating an accurate double-strand
      break that promotes gene targeting through
      homologous recombination. We have modified the homodimeric I-CreI
      endonuclease through protein engineering to target a specific DNA sequence
      within the human RAG1 gene. Mutations in RAG1 produce severe combined
      immunodeficiency (SCID), a monogenic disease leading to defective immune
      response in the individuals, leaving them vulnerable to infectious
      diseases. The structures of two engineered heterodimeric variants and one
      single-chain variant of I-CreI, in complex with a 24-bp oligonucleotide of
      the human RAG1 gene sequence, show how the DNA binding is achieved through
      interactions in the major groove. In addition, the introduction of the
      G19S mutation in the neighborhood of the catalytic site lowers the
      reaction energy barrier for DNA cleavage without compromising DNA
      recognition. Gene-targeting experiments in human cell lines show that the
      designed single-chain molecule preserves its in vivo activity with higher
      specificity, further enhanced by the G19S mutation. This is the first time
      that an engineered meganuclease variant targets the human RAG1 locus by
      stimulating homologous recombination in human cell lines up to 265 bp away
      from the cleavage site. Our analysis illustrates the key features for a la
      carte procedure in protein-DNA recognition design, opening new
      possibilities for SCID patients whose illness can be treated ex vivo.
AU  - Munoz IG et al
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2011 39: 729-743.

PMID- 29348357
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Bacillus subtilis 2C-9B, a Strain with Biocontrol Potential against Chili Pepper Root Pathogens and Tolerance to Pb and Zn.
PG  - e01502-17
AB  - Bacillus subtilis 2C-9B, obtained from the rhizosphere of wild grass, exhibits inhibition
      against root rot causal pathogens in Capsicum annuum, Pb and Zn
      tolerance, and plant growth promotion in medium supplemented with Pb. The genome
      of B. subtilis 2C-9B was sequenced and the draft genome assembled, with a length
      of 4,215,855 bp and 4,723 coding genes.
AU  - Munoz-Moreno CY
AU  - De La Cruz-Rodriguez Y
AU  - Vega-Arreguin J
AU  - Alvarado-Rodriguez M
AU  - Gomez-Soto JM
AU  - Alvarado-Gutierrez A
AU  - Fraire-Velazquez S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01502-17.

PMID- 15102813
VI  - 72
DP  - 2004
TI  - Partial analysis of the genomes of two nontypeable Haemophilus influenzae otitis media isolates.
PG  - 3002-3010
AB  - In 1995, The Institute for Genomic Research completed the genomic sequence of a rough
      derivative of Haemophilus influenzae serotype d,
      strain KW20. This sequence, though extremely useful in understanding
      the basic biology of H. influenzae, has yet to provide significant
      insight into our understanding of disease caused by nontypeable H.
      influenzae (NTHI), because serotype d strains are not generally
      pathogens. In contrast, NTHI strains are frequently mucosal pathogens
      and are the primary pathogens of chronic otitis media as well as a
      significant cause of acute otitis media in children. Thus, it is of
      great importance to further understand their biology. We used a
      DNA-based microarray approach to identify genes present in a clinical
      isolate of NTHI that were absent from strain Rd. We also sequenced the
      genome of a second NTHI isolate from a child with chronic otitis media
      to threefold coverage and then used an array of bioinformatics tools to
      identify genes present in this NTHI strain but absent from strain Rd.
      These methods were complementary in approach and results. We
      identified, in both strains, homologues of H. influenzae lav, an
      autotransported protein of unknown function; tna4, which encodes
      tryptophanase; as well as a homologue of Pasteurella multocida tsaA,
      which encodes an alkyl peroxidase that may play a role in protection
      against reactive oxygen species. We also identified a number of
      putative restriction-modification systems, bacteriophage genes and
      transposon-related genes. These data provide new insight that
      complements and extends our ongoing analysis of NTHI virulence
      determinants.
AU  - Munson RS
AU  - Harrison A
AU  - Gillaspy A
AU  - Ray WC
AU  - Carson M
AU  - Armbruster D
AU  - Gipson J
AU  - Gipson M
AU  - Johnson L
AU  - Lewis L
AU  - Dyer DW
AU  - Bakaletz LO
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2004 72: 3002-3010.

PMID- 27174266
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Algoriphagus sp. Strain M8-2, Isolated from a Brackish Lake.
PG  - e00347-16
AB  - Algoriphagus sp. strain M8-2 was isolated from a brackish lake, Lake Sanaru, in Hamamatsu,
      Japan, as a filterable bacterium through a 0.22-microm-pore-size
      membrane filter. We report here the complete nucleotide sequence of the M8-2
      genome (a 3,882,610-bp chromosome).
AU  - Muraguchi Y
AU  - Kushimoto K
AU  - Ohtsubo Y
AU  - Suzuki T
AU  - Dohra H
AU  - Kimbara K
AU  - Shintani M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00347-16.

PMID- 16256694
VI  - 29
DP  - 2001
TI  - Photo-cross-linked oligonucleotide duplex as a decoy-DNA for inhibition of restriction endonuclease activity.
PG  - 223-233
AB  - As a novel type of regulator molecule for DNA-recognizing proteins, a photo-cross-linked
      oligonucleotide duplex was designed and synthesized,
      The molecule regulated the activity of a restriction endonuclease by
      being recognized as a substrate. This type of regulating molecule is
      regarded as a decoy-DNA. 4,5',8-[4-Aminoethylaminomethyl]-trioxaten
      (aeAMT) was conjugated with art oligodeoxyribonucleotide (ODN) at the 5'-end and the aeAMT
      was cross-linked with the thymine residue of the
      complementary oligonucleotide upon UVA irradiation. The terminally
      cross-linked oligonucleotides, singly clipped (SC) decoy-DNA, acquired
      thermal stability, An oligonucleoside phosphorothioate (OPT) was also
      introduced as one or both components, yielding three types of
      decoy-DNAs, SC-ODN-ODN (SC.DD), SC-OPT-ODN (SC.SD). and SC-OPT-OPT
      (SC.SS). The SC decoy-DNAs inhibited the function of the restriction
      endonuclease, AatII, in a sequence-specific and concentration-dependent
      manner with an appreciable IC50 value (1.3 microM for SC.DD, 0.016 microM for
      SC.SD. 0.002 microM for SC.SS). The SC decoy-DNAs were found to be
      effective for regulating the DNA recognizing proteins.
AU  - Murakami A
AU  - Yamamoto Y
AU  - Namba M
AU  - Iwase R
AU  - Yamaoka T
PT  - Journal Article
TA  - Bioorg. Chem.
JT  - Bioorg. Chem.
SO  - Bioorg. Chem. 2001 29: 223-233.

PMID- 1368602
VI  - 54
DP  - 1990
TI  - The restriction endonuclease GinI of Gluconobacter cerinus IFO 3260, an isoschizomer of BamHI, has a monomeric structure.
PG  - 2747-2749
AB  - Type II restriction endonucleases, which are indispensable for gene
      manipulation and gene analysis, are widely found in the Procaryotae such as
      bacteria and cyanobacteria.  During the course of our studies, we reported a
      new restriction endonuclease ApaLI from cells of Acetobacter pasteurianus IFO
      13753.  We have found that the restriction endonuclease GceinI, an isoschizomer
      of BamHI, has a monomeric structure different from the BamHI endonuclease.
      This paper is concerned with the purification and properties of the restriction
      endonuclease GceinI of Gluconobacter cerinus.  Note this enzyme is incorrectly
      called GceinI in this paper.  It should be GinI.
AU  - Murakami M
AU  - Mizuno H
AU  - Yamada Y
PT  - Journal Article
TA  - Agric. Biol. Chem.
JT  - Agric. Biol. Chem.
SO  - Agric. Biol. Chem. 1990 54: 2747-2749.

PMID- 1368524
VI  - 54
DP  - 1990
TI  - A new restriction endonuclease from Bacteroides distasonis (BdiI).
PG  - 275-277
AB  - Authors have changed the name to BdiSI to avoid confusion.
AU  - Murakami M
AU  - Ozawa O
AU  - Kanematsu T
AU  - Yamada Y
PT  - Journal Article
TA  - Agric. Biol. Chem.
JT  - Agric. Biol. Chem.
SO  - Agric. Biol. Chem. 1990 54: 275-277.

PMID- 2062662
VI  - 19
DP  - 1991
TI  - Characterization of restriction endonuclease CbiI, an isoschizomer of AsuII, from Clostridium bifermentans strain B-4.
PG  - 3458
AB  - We have found that an extremely large amount of a restriction endonuclease, designated CbiI,
      is produced within the cells of Clostridium bifermentans strain B-4.  CbiI was purified from
      cell extracts by combined high performance liquid chromatographies on DEAE-Toyopearlpak 650M.
      TSKgel DEAE-5PW, TSKgel HA-1000 and TSKgel G3000SW.  The purified enzyme (0.4 mg protein from
      1.7 g cell extract) was homogeneous on polyacrylamide gel disc electrophoresis (PAGDE).  The
      relative molecular mass of the enzyme was calculated as 49,000 daltons by gel filtration and
      by SDS-PAGE.  These data indicated that CbiI has a monomeric structure.
AU  - Murakami M
AU  - Ozawa O
AU  - Kanematsu T
AU  - Yamada Y
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 3458.

PMID- 1368669
VI  - 55
DP  - 1991
TI  - Characterization of restriction endonuclease BdiSI, an isoschizomer of SfeI, from Bacteroides distasonis strain S-7.
PG  - 261-263
AB  - This paper describes the purification and properties of the restriction
      endonuclease BdiSI, an isoschizomer of SfeI (CTRYAG).
AU  - Murakami M
AU  - Ozawa O
AU  - Kanematsu T
AU  - Yamada Y
PT  - Journal Article
TA  - Agric. Biol. Chem.
JT  - Agric. Biol. Chem.
SO  - Agric. Biol. Chem. 1991 55: 261-263.

PMID- 1369291
VI  - 54
DP  - 1990
TI  - Purification, properties and recognition sequence and cleavage site determinations of restriction endonuclease from Acetobacter pasteurianus IFO 13753 (ApaLI).
PG  - 1791-1796
AB  - A new restriction endonuclease, designated as ApaLI, was purified from
      cell-free extracts of Acetobacter pasteurianus IFO 13753 by streptomycin
      treatment, ammonium sulfate fractionation, combined column chromatographies on
      heparin-Sepharose CL-6B and DEAE-Sepharose CL-6B and Fast Protein Liquid
      Chromatography on Mono Q HR 5/5.  The purified enzyme was homogenous on
      polyacrylamide gel disc electrophoresis.  The molecular weight of the purified
      enzyme was calculated as 26,000 daltons by gel filtration using Sephadex G-200,
      and the isoelectric point of the purified enzyme was 4.8 by ampholine
      sucrose-density gradient isoelectric focusing.  The purified enzyme cleaves
      lambda, Ad2, SV40, M13mp18 RF I, PhiX174 RF I and pBR322 DNAs at 4, 7, 0, 0, 1
      and 3 sites, respectively.  The purified enzyme worked best at 37C and pH 8.0
      in a reaction mixture (50 microliters) containing 1.0 micrograms lambda DNA, 10
      mM Tris-HCI, 7 mM 2-mercaptoethanol, 7 mM MgCl2 and 25 mM NaCl.  However, the
      purified enzyme did not require NaCl necessarily for the enzyme reaction.  The
      purified enzyme recognized the palindromic hexanucleotide DNA sequence,
      5'-GTGCAC-3' and cut between G and T, producing a 5'-cohesive tetranucleotide
      extension.
AU  - Murakami M
AU  - Yamada Y
PT  - Journal Article
TA  - Agric. Biol. Chem.
JT  - Agric. Biol. Chem.
SO  - Agric. Biol. Chem. 1990 54: 1791-1796.

PMID- 2825125
VI  - 15
DP  - 1987
TI  - Cleavage by the restriction endonuclease Asp718, an isoschizomer of KpnI, is sensitive to Escherichia coli Dcm methylation.
PG  - 9085
AB  - While attempting to use Asp718, a KpnI isoschizomer, to subclone KpnI fragments from pAn602, a
      plasmid known to have two KpnI sites, I found that one of these sites was cut very poorly by
      this enzyme. DNA sequence analysis showed that the poorly cut site overlapped the sequence
      CCAGG, an Escherichia coli Dcm methylation site. When this plasmid DNA was propagated in E.
      coli GM31 (dcm-6), a host which does not methylate this site, and digested with either Asp718
      or KpnI both sites were cut to completion.
AU  - Mural RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1987 15: 9085.

PMID- 24652982
VI  - 2
DP  - 2014
TI  - Genome Sequences of Four Clinical Staphylococcus aureus Strains with Diverse Drug Resistance Profiles Isolated from Diabetic Foot Ulcers.
PG  - e00204-14
AB  - Staphylococcus aureus is a major pathogen associated with diabetic foot ulcer infections. To
      gain insight into their pathogenicity and virulence potential, we
      report draft genome sequences of four strains of Staphylococcus aureus, isolated
      from diabetic foot ulcers, showing profiles with various degrees of resistance to
      common antibiotics.
AU  - Murali TS
AU  - Paul B
AU  - Parikh H
AU  - Singh RP
AU  - Kavitha S
AU  - Bhat MK
AU  - Satyamoorthy K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00204-14.

PMID- 12029035
VI  - 184
DP  - 2002
TI  - Complete nucleotide sequence of plasmid Rts1: implications for evolution of large plasmid genomes.
PG  - 3194-3202
AB  - Rts1, a large conjugative plasmid originally isolated from Proteus vulgaris, is a prototype
      for the IncT plasmids and exhibits pleiotropic thermosensitive phenotypes. Here we report the
      complete nucleotide sequence of Rts1. The genome is 217,182 bp in length and contains 300
      potential open reading frames                        (ORFs). Among these, the products of 141
      ORFs, including 9 previously identified genes, displayed significant sequence similarity to
      known proteins. The set of genes responsible for the conjugation function of Rts1 has been
      identified. A broad array of genes related to diverse processes of DNA metabolism were also
      identified. Of particular interest was the presence of tus-like genes that could be involved
      in replication termination. Inspection of the overall genome organization revealed that the
      Rts1 genome is composed of four large modules, providing an example of modular evolution of
      plasmid genomes.
AU  - Murata T
AU  - Ohnishi M
AU  - Ara T
AU  - Kaneko J
AU  - Han CG
AU  - Li YF
AU  - Takashima K
AU  - Nojima H
AU  - Nakayama K
AU  - Kaji A
AU  - Kamio Y
AU  - Miki T
AU  - Mori H
AU  - Ohtsubo E
AU  - Terawaki Y
AU  - Hayashi T
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2002 184: 3194-3202.

PMID- 23516221
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Bacillus thuringiensis subsp. thuringiensis Strain IS5056, an Isolate Highly Toxic to Trichoplusia ni.
PG  - e0010813
AB  - The genome sequence of the entomopathogen Bacillus thuringiensis subsp. thuringiensis strain
      IS5056 was determined. The chromosome is composed of
      5,491,935 bp. In addition, IS5056 harbors 14 plasmids ranging from 6,880 to
      328,151 bp, four of which contain nine insecticidal protein genes, cry1Aa3,
      cry1Ab21, cry1Ba1, cry1Ia14, cry2Aa9, cry2Ab1, vip1, vip2, and vip3Aa10.
AU  - Murawska E
AU  - Fiedoruk K
AU  - Bideshi DK
AU  - Swiecicka I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0010813.

PMID- 2001684
VI  - 10
DP  - 1991
TI  - Cleavage of a four-way DNA function by a restriction enzyme spanning the point of strand exchange.
PG  - 713-718
AB  - The four-way DNA junction is believed to fold in the presence of metal ions
      into an X-shaped structure, in which there is pairwise coaxial stacking of
      helical arms.  A restriction enzyme MboII has been used to probe this
      structure.  A junction was constructed containing a recognition site for MboII
      in one helical arm, positioned such that stacking of arms would result in
      cleavage in a neighbouring arm.  Strong cleavage was observed, at the sites
      expected on the basis of coaxial stacking.  An additional cleavage was seen
      corresponding to the formation of an alternative stacking isomer, suggesting
      that the two isomeric forms are in dynamic equilibrium in solution.
AU  - Murchie AIH
AU  - Portugal J
AU  - Lilley DMJ
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1991 10: 713-718.

PMID- 1840140
VI  - 77
DP  - 1991
TI  - Sequence-specific endonucleases from the cyanobacterium Nostoc sp. ATCC 29132.
PG  - 1-4
AB  - The nitrogen-fixing cyanobacterium Nostoc sp. ATCC 29132 was shown to contain
      two sequence-specific endonucleases.  Nsp(29132) I was an isoschizomer of
      AsuII, and Nsp(29132) II was an isoschizomer of BamHI.  Nsp(29132) II was shown
      to generate ends that could be ligated to those generated by BamHI.
AU  - Muro-Pastor AM
AU  - Herrero A
AU  - Flores E
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1991 77: 1-4.

PMID- 25269955
VI  - 15
DP  - 2014
TI  - Methyltransferases acquired by lactococcal 936-type phage provide protection against restriction endonuclease activity.
PG  - 831
AB  - Background: So-called 936-type phages are among the most frequently isolated phages in dairy
      facilities utilising Lactococcus lactis starter cultures. Despite extensive efforts to control
      phage proliferation and decades of research, these phages continue to negatively impact cheese
      production in terms of the final product quality and consequently, monetary return.Results:
      Whole genome sequencing and in silico analysis of three 936-type phage genomes identified
      several putative (orphan) methyltransferase (MTase)-encoding genes located within the
      packaging and replication regions of the genome. Utilising SMRT sequencing, methylome analysis
      was performed on all three phages, allowing the identification of adenine modifications
      consistent with N-6 methyladenine sequence methylation, which in some cases could be
      attributed to these phage-encoded MTases. Heterologous gene expression revealed that M.
      Phi145I/M. Phi93I and M. Phi93DAM, encoded by genes located within the packaging module,
      provide protection against the restriction enzymes HphI and DpnII, respectively, representing
      the first functional MTases identified in members of 936-type phages.Conclusions: SMRT
      sequencing technology enabled the identification of the target motifs of MTases encoded by the
      genomes of three lytic 936-type phages and these MTases represent the first functional MTases
      identified in this species of phage. The presence of these MTase-encoding genes on 936-type
      phage genomes is assumed to represent an adaptive response to circumvent host encoded
      restriction-modification systems thereby increasing the fitness of the phages in a dynamic
      dairy environment.
AU  - Murphy J
AU  - Klumpp J
AU  - Mahony J
AU  - O'Connell-Motherway M
AU  - Nauta A
AU  - van Sinderen D
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2014 15: 831.

PMID- 24123737
VI  - 79
DP  - 2013
TI  - Bacteriophage Orphan DNA Methyltransferases: Insights from Their Bacterial Origin, Function, and Occurrence.
PG  - 7547
AB  - Type II DNA methyltransferases (MTases) are enzymes found ubiquitously in the prokaryotic
      world, where they play important roles in several cellular processes, such as host protection
      and epigenetic regulation. Three classes of type II MTases have been identified thus far in
      bacteria which function in transferring a methyl group from S-adenosyl-L-methionine (SAM) to a
      target nucleotide base, forming N-6-methyladenine (class I), N-4-methylcytosine (class II), or
      C-5-methylcytosine (class III). Often, these MTases are associated with a cognate restriction
      endonuclease (REase) to form a restriction-modification (R-M) system protecting bacterial
      cells from invasion by foreign DNA. When MTases exist alone, which are then termed orphan
      MTases, they are believed to be mainly involved in regulatory activities in the bacterial
      cell. Genomes of various lytic and lysogenic phages have been shown to encode multi-and
      mono-specific orphan MTases that have the ability to confer protection from restriction
      endonuclea ses of their bacterial host(s). The ability of a phage to overcome R-M and other
      phage-targeting resistance systems can be detrimental to particular biotechnological processes
      such as dairy fermentations. Conversely, as phages may also be beneficial in certain areas
      such as phage therapy, phages with additional resistance to host defenses may prolong the
      effectiveness of the therapy. This minireview will focus on bacteriophage-encoded MTases,
      their prevalence and diversity, as well as their potential origi n and function.
AU  - Murphy J
AU  - Mahony J
AU  - Ainsworth S
AU  - Nauta A
AU  - van Sinderen D
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2013 79: 7547.

PMID- 17981979
VI  - 190
DP  - 2008
TI  - Dam methyltransferase is required for stable lysogeny of the Shiga toxin (Stx2)-encoding bacteriophage 933W of enterohemorrhagic Escherichia coli O157 : H7.
PG  - 438-441
AB  - Shiga toxin 2 (Stx2), one of the principal virulence factors of enterohemorrhagic Escherichia
      coli, is encoded by 933W, a lambda-like
      prophage. 933W prophage induction contributes to Stx2 production, and
      here, we provide evidence that Dam methyltransferase is essential for
      maintenance of 933W lysogeny. Our findings are consistent with the idea
      that the 933W prophage has a relatively low threshold for induction,
      which may promote Stx2 production during infection.
AU  - Murphy KC
AU  - Ritchie JM
AU  - Waldor MK
AU  - Lobner-Olesen A
AU  - Marinus MG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2008 190: 438-441.

PMID- 11872734
VI  - 184
DP  - 2002
TI  - Lack of regulation of the modification-dependent restriction enzyme McrBC in Escherichia coli.
PG  - 1794-1795
AB  - Restriction alleviation (RA) by the type I restriction enzyme EcoKI is caused by treatments
      that damage DNA. RA is due to proteolysis of the EcoKI HsdR subunit by the ClpXP ATP-dependent
      protease. Here we show that the modification-dependent enzyme McrBC is not subject to RA,
      although it is moderately sensitive to ClpAP.
AU  - Murphy M
AU  - Schmid NS
AU  - Bickle TA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2002 184: 1794-1795.

PMID- 17993521
VI  - 190
DP  - 2008
TI  - Three pathogenicity islands of Vibrio cholerae can excise from the chromosome and form circular intermediates.
PG  - 636-647
AB  - Vbrio pathogenicity island-2 (VPI-2) is a 57-kb region integrated at a transfer RNA
      (tRNA)-serine locus that encompasses VC1758 to VC1809 on
      the V. cholerae N16961 genome and is present in pandemic isolates.
      VPI-2 encodes a P4-like integrase, a restriction modification system, a
      Mu phage-like region, and a sialic acid metabolism region, as well as
      neuraminidase (VC1784), which is a glycosylhydrolase known to release
      sialic acid from sialoglycoconjugates to unmask GM1 gangliosides, the
      receptor for cholera toxin. We examined the tRNA-serine locus among the
      sequenced V. cholerae genomes and identified five variant VPI-2
      regions, four of which retained the sialometabolism region. Three
      variant VPI-2 regions contained a type three secretion system. By using
      an inverse nested PCR approach, we found that the VPI-2 region can form
      an extrachromosomal circular intermediate (CI) molecule after precise
      excision from its tRNA-serine attachment site. We constructed a
      knockout mutant of VC1758 (int) with V. cholerae strain N16961 and
      found that no excision PCR product was produced, indicating that a
      functional cognate, VPI-2 integrase, is required for excision. The
      Vibrio seventh pandemic island-I (VSP-I) and VSP-II regions are present
      in V. cholerae 01 El Tor and 0139 serogroup isolates. Novel regions are
      present at the VSP-I insertion site in strain MZO-3 and at the VSP-II
      insertion site in strain 623-39. VSP-II is a 27-kb region that
      integrates at a tRNA-methionine locus, is flanked by direct repeats,
      and encodes a P4-like integrase. We show that VSP-II can excise and
      form a CI and that the cognate VSP-II integrase is required for
      excision. Interestingly, VSP-I is not inserted at a tRNA locus and does
      encode a XerDC-like recombinase, but similar to VPI-2 and VSP-II, VSP-I
      does excise from the genome to form a CI. These results show that all
      three pathogenicity islands can excise from the chromosome, which is
      likely a first step in their horizontal transfer.
AU  - Murphy RA
AU  - Boyd EF
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2008 190: 636-647.

PMID- 23034806
VI  - 40
DP  - 2012
TI  - The methylomes of six bacteria.
PG  - 11450-11462
AB  - Six bacterial genomes, Geobacter metallireducens GS-15, Chromohalobacter salexigens, Vibrio
      breoganii 1C-10, Bacillus cereus ATCC 10987, Campylobacter jejuni subsp. jejuni 81-176 and C.
      jejuni NCTC 11168, all of which had previously been sequenced using other platforms were
      re-sequenced using single-molecule, real-time (SMRT) sequencing specifically to analyze their
      methylomes. In every case a number of new N6-methyladenine (m6A) and N4-methylcytosine (m4C)
      methylation patterns were discovered and the DNA methyltransferases (MTases) responsible for
      those methylation patterns were assigned. In 15 cases, it was possible to match MTase genes
      with MTase recognition sequences without further sub-cloning. Two Type I restriction systems
      required sub-cloning to differentiate their recognition sequences, while four MTase genes that
      were not expressed in the native organism were sub-cloned to test for viability and
      recognition sequences. Two of these proved active. No attempt was made to detect 5-
      methylcytosine (m5C) recognition motifs from the SMRT sequencing data because this
      modification produces weaker signals using current methods.  However, all predicted m6A and
      m4C MTases were detected unambiguously. This study shows that the addition of SMRT sequencing
      to traditional sequencing approaches gives a wealth of useful functional information about a
      genome showing not only which MTase genes are active but also revealing their recognition
      sequences.
AU  - Murray IA
AU  - Clark TA
AU  - Morgan RD
AU  - Boitano M
AU  - Anton BP
AU  - Luong K
AU  - Fomenkov A
AU  - Turner SW
AU  - Korlach J
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: 11450-11462.

PMID- 29228259
VI  - 46
DP  - 2018
TI  - The non-specific adenine DNA methyltransferase M.EcoGII.
PG  - 840-848
AB  - We describe the cloning, expression and characterization of the first truly non-specific
      adenine DNA methyltransferase, M.EcoGII. It is encoded in the genome
      of the pathogenic strain Escherichia coli O104:H4 C227-11, where it appears to
      reside on a cryptic prophage, but is not expressed. However, when the gene
      encoding M.EcoGII is expressed in vivo - using a high copy pRRS plasmid vector
      and a methylation-deficient E. coli host-extensive in vivo adenine methylation
      activity is revealed. M.EcoGII methylates adenine residues in any DNA sequence
      context and this activity extends to dA and rA bases in either strand of a
      DNA:RNA-hybrid oligonucleotide duplex and to rA bases in RNAs prepared by in
      vitro transcription. Using oligonucleotide and bacteriophage M13mp18 virion DNA
      substrates, we find that M.EcoGII also methylates single-stranded DNA in vitro
      and that this activity is only slightly less robust than that observed using
      equivalent double-stranded DNAs. In vitro assays, using purified recombinant
      M.EcoGII enzyme, demonstrate that up to 99% of dA bases in duplex DNA substrates
      can be methylated thereby rendering them insensitive to cleavage by multiple
      restriction endonucleases. These properties suggest that the enzyme could also be
      used for high resolution mapping of protein binding sites in DNA and RNA
      substrates.
AU  - Murray IA
AU  - Morgan RD
AU  - Luyten Y
AU  - Fomenkov A
AU  - Correa IR Jr
AU  - Dai N
AU  - Allaw MB
AU  - Zhang X
AU  - Cheng X
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2018 46: 840-848.

PMID- 20702422
VI  - 38
DP  - 2010
TI  - Sequence-specific cleavage of RNA by Type II restriction enzymes.
PG  - 8257-8268
AB  - The ability of 223 Type II restriction endonucleases to hydrolyze RNA-DNA heteroduplex
      oligonucleotide substrates was assessed. Despite the
      significant topological and sequence asymmetry introduced when one strand
      of a DNA duplex is substituted by RNA we find that six restriction enzymes
      (AvaII, AvrII, BanI, HaeIII, HinfI and TaqI), exclusively of the Type IIP
      class that recognize palindromic or interrupted-palindromic DNA sequences,
      catalyze robust and specific cleavage of both RNA and DNA strands of such
      a substrate. Time-course analyses indicate that some endonucleases
      hydrolyze phosphodiester bonds in both strands simultaneously whereas
      others appear to catalyze sequential reactions in which either the DNA or
      RNA product accumulates more rapidly. Such strand-specific variation in
      cleavage susceptibility is both significant (up to orders of magnitude
      difference) and somewhat sequence dependent, notably in relation to the
      presence or absence of uracil residues in the RNA strand. Hybridization to
      DNA oligonucleotides that contain endonuclease recognition sites can be
      used to achieve targeted hydrolysis of extended RNA substrates produced by
      in vitro transcription. The ability to 'restrict' an RNA-DNA hybrid,
      albeit with a limited number of restriction endonucleases, provides a
      method whereby individual RNA molecules can be targeted for site-specific
      cleavage in vitro.
AU  - Murray IA
AU  - Stickel SK
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2010 38: 8257-8268.

PMID- 11780
VI  - 159
DP  - 1976
TI  - Isolation and characterization of two sequence-specific endonucleases from Anabaena variabilis.
PG  - 317-322
AB  - Two endonucleases, AvaI and AvaII, were isolated from Anabaena variabilis on
      the basis of their ability to make a limited number of breaks at specific
      points in bacteriophage lambda DNA.  Neither enzyme has cofactor requirements
      beyond Mg2+.  Endonuclease AvaI makes eight breaks in the phage lambda
      chromosome at which the 5'-terminal sequence is pPy-C-G-N.  AvaII endonuclease
      cuts phage lambda DNA more extensively, yielding fragments with the 5'-terminal
      sequence G-T-C-N or G-A-C-N.  Neither enzyme generates cohesive ends.
AU  - Murray K
AU  - Hughes SG
AU  - Brown JS
AU  - Bruce SA
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 1976 159: 317-322.

PMID- 
VI  - 10
DP  - 1975
TI  - Restriction enzymes and the cloning of eukaryotic DNA.
PG  - 193-207
AB  - If bacteriophage lambda that has been grown on Escherichia coli strain C is transferred to E.
      coli strain K, its efficiency of growth is impaired by several orders of magnitude, but those
      phage that survive on strain K subsequently grow normally upon it.  If the surviving phage are
      then transferred back to strain C they grow with normal efficiency, but if after this growth
      on strain C they are again transferred to strain K, the reduced efficiency of growth is once
      more observed.  This is an example of the general phenomenon of host-controlled restriction.
      Experiments with 32P-labelled phage showed that the impairment of phage growth was correlated
      with the ability of the restricting host strain to degrade the phage DNA to acid-soluble
      products, a property that the original host strain lacked and which was attributed to a
      host-specific endonuclease.  It is clearly necessary for the bacterial cell to protect its own
      DNA from the action of this enzyme and this it does by methylation of certain bases (adenine
      to 6-methylamino purine or, less commonly, cytosine to 5-methyl cytosine) as was demonstrated
      by the analysis of DNA from phage f1 that had been propagated on restricting and
      non-restricting strains of E. coli.  This process of host-controlled modification explains why
      those phage that survive restriction subsequently grow normally upon the restricting strain:
      their DNA is methylated by the host modification methylase and therefore survives attack by
      the restriction endonuclease.
AU  - Murray K
AU  - Murray NE
AU  - Brammar WJ
PT  - Journal Article
TA  - FEBS J.
JT  - FEBS J.
SO  - FEBS J. 1975 10: 193-207.

PMID- 4367574
VI  - 14
DP  - 1974
TI  - The primary structure of DNA.
PG  - 117-185
AB  - Brown and Todd, in 1952, summarized the evidence then available and proposed
      the now generally accepted structure for deoxyribonucleic acid, in which the
      deoxynucleoside units are linked by 3',5'-phosphodiester bonds.
AU  - Murray K
AU  - Old RW
PT  - Journal Article
TA  - Prog. Nucleic Acid Res. Mol. Biol.
JT  - Prog. Nucleic Acid Res. Mol. Biol.
SO  - Prog. Nucleic Acid Res. Mol. Biol. 1974 14: 117-185.

PMID- 11782494
VI  - 148
DP  - 2002
TI  - Immigration control of DNA in bacteria: self versus non-self.
PG  - 3-20
AB  - Bacteria commonly endow their DNA with an identity mark.  When DNA is transferred from one
      bacterium to another strain of the same species, DNA that lacks the identification mark of the
      recipient strain is recognized as 'foreign' rather than 'self'.  Foreign DNA is commonly
      degraded.  The first evidence for this discriminatory process was the demonstration of a
      barrier, albeit incomplete, to the productive infection of Escherichia coli strain K-12 by
      bacteriophage lambda previously propagated in either E. coli strain C or E. coli strain B.
      Much later it was proven that the growth of phages in E. coli K-12 can be 'restricted' by an
      endonuclease, a restriction enzyme (EcoKI), which attacks foreign DNA.  Occasionally phages
      escape restriction and they, like the resident bacterial chromosome, acquire a protective
      identification mark from a strain-specific modification enzyme that methylates defined bases
      within a specific target sequence.  This sequence-specific modification identifies the
      immediate provenance of bacterial, or phage, DNA.
AU  - Murray NE
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2002 148: 3-20.

PMID- 10839821
VI  - 64
DP  - 2000
TI  - Type I restriction systems: sophisticated molecular machines.
PG  - 412-434
AB  - Restriction enzymes are well known as reagents widely used by molecular biologists for genetic
      manipulation and analysis, but these reagents represent only one class (type II) of a wider
      range of enzymes that recognize specific nucleotide sequences in DNA molecules and detect the
      provenance of the DNA on the basis of specific modifications to their target sequence. Type I
      restriction and modification (R-M) systems are complex; a single multifunctional enzyme can
      respond to the modification state of its target sequence with the alternative activities of
      modification or restriction. In the absence of DNA modification, a type I R-M enzyme behaves
      like a molecular motor, translocating vast stretches of DNA towards itself before eventually
      breaking the DNA molecule. These sophisticated enzymes are the focus of this review, which
      will emphasize those aspects that give insights into more general problems of molecular and
      microbial biology. Current molecular experiments explore target recognition, intramolecular
      communication, and enzyme activities, including DNA translocation. Type I R-M systems are
      notable for their ability to evolve new specificities, even in laboratory cultures. This
      observation raises the important question of how bacteria protect their chromosomes from
      destruction by newly acquired restriction specifities. Recent experiments demonstrate
      proteolytic mechanisms by which cells avoid DNA breakage by a type I R-M system whenever their
      chromosomal DNA acquires unmodified target sequences. Finally, the review will reflect the
      present impact of genomic sequences on a field that has previously derived information almost
      exclusively from the analysis of bacteria commonly studied in the laboratory.
AU  - Murray NE
PT  - Journal Article
TA  - Microbiol. Mol. Biol. Rev.
JT  - Microbiol. Mol. Biol. Rev.
SO  - Microbiol. Mol. Biol. Rev. 2000 64: 412-434.

PMID- 16545077
VI  - 34
DP  - 2006
TI  - The impact of phage lambda: from restriction to recombineering.
PG  - 203-207
AB  - Experiments using phage lambda provided early insights into important molecular mechanisms,
      including genetic recombination and the control of
      gene expression. Before recombinant DNA technology, the use of lambda,
      most particularly lambda transducing phages, illustrated the importance of
      cloning bacterial genes, already providing some insight into how to use
      cloned genes to advantage. Subsequently, lambda made significant
      contributions to recombinant DNA technology, including the early
      generation of genomic and cDNA libraries. More recently, lambda genes
      associated with recombination have enabled techniques referred to as
      'recombineering' to be developed. These techniques permit the refined
      manipulation, including mutation, of foreign genes in Escherichia coli and
      their subsequent return to the donor organism.
AU  - Murray NE
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 2006 34: 203-207.

PMID- 8095080
VI  - 17C
DP  - 1993
TI  - Type I restriction enzymes of enteric bacteria.
PG  - 152
AB  - The multifunctional type I restriction and modification (R/M) enzymes are encoded by three
      genes (hsdR, hsdM and hsdS). These enzymes recognize asymmetric, bipartite target sequences
      and their alternative responses of either restriction or modification are determined by the
      methylation state of the target sequence. Three discrete families of type I R/M systems have
      been described (A,B and C), and we now present evidence for a fourth. This new system and the
      enzymes of families IA and IB are all encoded by allelic genes. Members of a family are highly
      conserved, but differ in their specificity (A) subunits; each of two recognition domains of
      the S subunit confers specificity for one of the two components of the target sequence.
      Members of different families are dissimilar in all of their three subunits. Even when encoded
      by allelic genes, amino acid identity may be only about 20%. The diversity of type I R/M
      systems will be reviewed in relation to their natural distribution and their evolutionary
      relationships. Horizontal transfer of hsd genes between species and frequency-dependent
      selection for alternative specificities are invoked to explain the high levels of variability.
      Comparative analyses of polypeptides identify conserved sequences within the M polypeptides
      common to methyltransferases (mtases) in general and adenine mtases in particular, and within
      the R polypeptides features in common with ATP-dependent helicases. We have made mutations in
      some of these conserved regions and have isolated other mutants on the basis of a change in
      response to the methylation state of the target sequence. The latter mutations mimic the
      effect of a phage encoded polypeptide (Ral) that can enhance modification and ameliorate
      restriction. The mtase component of EcoK, the type I R/M system found in E.coli K-12, has been
      purified and characterized, particularly in terms of binding to target sequences and to the
      cofactor S-adenosylmethionine. The properties of the wild-type mtase and some mutant
      derivatives will be reported.
AU  - Murray NE
AU  - Barcus VA
AU  - Campbell AJB
AU  - Dryden DTF
AU  - Kelleher JE
AU  - Powell LM
AU  - Willcock D
AU  - Sharp PM
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1993 17C: 152.

PMID- 4767461
VI  - 81
DP  - 1973
TI  - Restriction of bacteriophage lambda by Escherichia coli K.
PG  - 395-407
AB  - Derivatives of phage lambda, for which the numbers and positions of the
      recognition sites for endonuclease R, EcoK are known, were used as substrates
      for the Escherichia coli K restriction system in vivo and in vitro.  A single
      unmodified recognition site was sufficient for a DNA molecule to be bound and
      broken by the K restriction enzyme.  Although discrete fragments of DNA were
      not produced, the breaks were made preferentially in the proximity of the
      recognition site.  Breakage of a DNA molecule with only one recognition site
      required a 10 to 40-fold higher concentration of restriction enzyme than
      breakage of a DNA molecule with two or more recognition sites, but these
      substrates were all equally effective in a binding assay for the enzyme.  The
      polynucleotide kinase reaction provided no evidence for new 5'-terminal
      sequences generated by restriction in vitro; the 5' termini were either
      refractory to the polynucleotide kinase reaction or had no sequence
      specificity.
AU  - Murray NE
AU  - Batten PL
AU  - Murray K
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1973 81: 395-407.

PMID- 4579451
VI  - 77
DP  - 1973
TI  - The trpE gene of Escherichia coli K contains a recognition sequence for the K-restriction system.
PG  - 615-624
AB  - A recognition sequence for the K-restriction system has been localized within
      the trpE gene of Escherichia coli.  Mutations conferring resistance to
      restriction do not always inactivate the E gene.  By selecting for phage
      mutants which have simultaneously lost two restriction-recognition sites, one
      in trpE and the other near gene N of phage lambda, we have isolated deletions
      which localize a site of action of the N protein betwen cIII and N itself.
AU  - Murray NE
AU  - Brammar WJ
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1973 77: 615-624.

PMID- 8412658
VI  - 9
DP  - 1993
TI  - Conservation of motifs within the unusually variable polypeptide sequences of type I restriction and modification enzymes.
PG  - 133-143
AB  - Type I restriction enzymes comprise three subunits encoded by genes designated hsdR, hsdM, and
      hsdS; S confers sequence specificity. Three families of enzymes are known and within families,
      but not between, hsdM and hsdR are conserved. Consequently, interfamily comparisons of M and R
      sequences focus on regions of putative functional significance, , while both inter- and
      intrafamily comparisons address the origin, nature and role of diversity of type I restriction
      systems. We have determined the sequence of the hsdR gene for EcoAI, thus making available
      sequences of all three hsd genes of one representative from each family. The predicted R
      polypeptide sequences share conserved regions with one superfamily of putative helicases,
      so-called DEAD box proteins; these conserved sequences may be associated with the
      ATP-dependent translocation of DNA that precedes restriction. We also present hsdM and hsdR
      sequences for EcoEI, a member of the same family as EcoAI. The sequences of the M and R genes
      of EcoAI and EcoEI are at least as divergent as typical genes from Escherichia coli and
      Salmonella, perhaps as the result of selection favouring diversity of restriction
      specificities combined with lateral transfer among different species.
AU  - Murray NE
AU  - Daniel AS
AU  - Cowan GM
AU  - Sharp PM
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1993 9: 133-143.

PMID- 4568839
VI  - 120
DP  - 1973
TI  - DNA targets for the Escherichia coli K restriction system analysed genetically in recombinants between phages Phi80 and lambda.
PG  - 261-281
AB  - Genetic analyses demonstrate the segregation of three targets for the K
      restriction system in h80-lambda hybrid phages.  Mutations in each of these
      three targets have been isolated and shown to confer resistance in cis but not
      in trans.  Two of the three targets (sk-1 and sk-2) have been located on the
      lambda genome:  sk-1 is right of gene R and sk-2 is between genes cIII and N.
      The third target is in the phi80 genome right of, but close to, att.  Phage
      lambda lacking both sk-1 and sk-2 retains at least 3 targets for the K
      restriction system.
AU  - Murray NE
AU  - de Ritis PM
AU  - Foster LA
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1973 120: 261-281.

PMID- 6329689
VI  - 1
DP  - 1982
TI  - Structural homologies among type I restriction-modification systems.
PG  - 535-539
AB  - Structural homologies among different restriction systems of Escherichia coli
      and several Salmonella species have been investigated by immunological methods
      using antibodies prepared against two subunits of the E. coli K12 restriction
      enzyme, and by DNA hybridization experiments using different fragments of the
      E. coli K12 hsd genes as probes.  The results with both techniques show a
      strong homology between the E. coli K12 and B restriction-modification systems,
      weaker but nevertheless marked homology between E. coli K12 and the Salmonella
      systems SB, SP, and SQ and, surprisingly, no homology between the E. coli K12
      and A systems.
AU  - Murray NE
AU  - Gough JA
AU  - Suri B
AU  - Bickle TA
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1982 1: 535-539.

PMID- 4608939
VI  - 251
DP  - 1974
TI  - Manipulation of restriction targets in phage lambda to form receptor chromosomes for DNA fragments.
PG  - 476-481
AB  - Fragments of DNA from derivatives of phage lambda having either one or two
      targets for R.EcoRI have been joined in new combinations to give biologically
      active phage genomes.  These include two classes of deletion mutants; in one,
      only the DNA between targets is deleted, but in the second the deletions are
      more extensive.  Other fragments of DNA have been inserted into these phage
      chromosomes.
AU  - Murray NE
AU  - Murray K
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1974 251: 476-481.

PMID- 17593976
VI  - 2
DP  - 2007
TI  - A Full-Genomic Sequence-Verified Protein-Coding Gene Collection for Francisella tularensis.
PG  - E577
AB  - The rapid development of new technologies for the high throughput (HT)
      study of proteins has increased the demand for comprehensive plasmid clone
      resources that support protein expression. These clones must be
      full-length, sequence-verified and in a flexible format. The generation of
      these resources requires automated pipelines supported by software
      management systems. Although the availability of clone resources is
      growing, current collections are either not complete or not fully
      sequence-verified. We report an automated pipeline, supported by several
      software applications that enabled the construction of the first
      comprehensive sequence-verified plasmid clone resource for more than 96%
      of protein coding sequences of the genome of F. tularensis, a highly
      virulent human pathogen and the causative agent of tularemia. This clone
      resource was applied to a HT protein purification pipeline successfully
      producing recombinant proteins for 72% of the genes. These methods and
      resources represent significant technological steps towards exploiting the
      genomic information of F. tularensis in discovery applications.
AU  - Murthy T
AU  - Rolfs A
AU  - Hu Y
AU  - Shi Z
AU  - Raphael J
AU  - Moreira D
AU  - Kelley F
AU  - McCarron S
AU  - Jepson D
AU  - Taycher E
AU  - Zuo D
AU  - Mohr SE
AU  - Fernandez M
AU  - Brizuela L
AU  - Labaer J
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2007 2: E577.

PMID- 24604649
VI  - 2
DP  - 2014
TI  - Comparative Genomic Analysis of Multidrug-Resistant Pseudomonas aeruginosa Clinical Isolates VRFPA06 and VRFPA08 with VRFPA07.
PG  - e00140-14
AB  - Pseudomonas aeruginosa isolates harboring acquired drug-resistant genes lead to increased
      mortality. Here, we have sequenced and annotated the genomes of two
      multidrug-resistant (MDR) P. aeruginosa isolates and a susceptible P. aeruginosa
      clinical isolate evidencing divergent antibiotic susceptibilities. Genomic
      analysis showed insight on the different genomic strategies adapted by P.
      aeruginosa to combat antimicrobial effects.
AU  - Murugan N
AU  - Malathi J
AU  - Umashankar V
AU  - Madhavan HN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00140-14.

PMID- 24019992
VI  - 7
DP  - 2013
TI  - Thermus oshimai JL-2 and T. thermophilus JL-18 genome analysis illuminates pathways for carbon, nitrogen, and sulfur cycling.
PG  - 449-468
AB  - The complete genomes of Thermus oshimai JL-2 and T. thermophilus JL-18 each consist of a
      circular chromosome, 2.07 Mb and 1.9 Mb, respectively, and two
      plasmids ranging from 0.27 Mb to 57.2 kb. Comparison of the T. thermophilus JL-18
      chromosome with those from other strains of T. thermophilus revealed a high
      degree of synteny, whereas the megaplasmids from the same strains were highly
      plastic. The T. oshimai JL-2 chromosome and megaplasmids shared little or no
      synteny with other sequenced Thermus strains. Phylogenomic analyses using a
      concatenated set of conserved proteins confirmed the phylogenetic and taxonomic
      assignments based on 16S rRNA phylogenetics. Both chromosomes encode a complete
      glycolysis, tricarboxylic acid (TCA) cycle, and pentose phosphate pathway plus
      glucosidases, glycosidases, proteases, and peptidases, highlighting highly
      versatile heterotrophic capabilities. Megaplasmids of both strains contained a
      gene cluster encoding enzymes predicted to catalyze the sequential reduction of
      nitrate to nitrous oxide; however, the nitrous oxide reductase required for the
      terminal step in denitrification was absent, consistent with their incomplete
      denitrification phenotypes. A sox gene cluster was identified in both
      chromosomes, suggesting a mode of chemolithotrophy. In addition, nrf and psr gene
      clusters in T. oshmai JL-2 suggest respiratory nitrite ammonification and
      polysulfide reduction as possible modes of anaerobic respiration.
AU  - Murugapiran SK et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 7: 449-468.

PMID- 23405355
VI  - 1
DP  - 2013
TI  - Whole Genome Sequencing of Thermus oshimai JL-2 and Thermus thermophilus JL-18, Incomplete Denitrifiers from the United States Great Basin.
PG  - e00106-12
AB  - The strains Thermus oshimai JL-2 and Thermus thermophilus JL-18 each have a circular
      chromosome, 2.07 Mb and 1.9 Mb in size, respectively, and each has two plasmids ranging from
      0.27 Mb to 57.2 kb. The megaplasmid of each strain contains a gene cluster for the reduction
      of nitrate to nitrous oxide, consistent with their incomplete denitrification phenotypes.
AU  - Murugapiran SK et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00106-12.

PMID- 2355911
VI  - 10
DP  - 1990
TI  - Characterization of I-Ppo, an intron-encoded endonuclease that mediates homing of a group I intron in the ribosomal DNA of Physarum polycephalum.
PG  - 3386-3396
AB  - A novel and only recently recognized class of enzymes is composed of the site-specific
      endonucleases encoded by some group I introns. We have characterized several aspects of I-Ppo,
      the endonuclease that mediates the mobility of intron 3 in the ribosomal DNA of Physarum
      polycephalum. This intron is unique among mobile group I introns in that it is located in
      nuclear DNA. We found that I-Ppo is encoded by an open reading frame in the 5' half of intron
      3, upstream of the sequences required for self-splicing of group I introns. Either of two AUG
      initiation codons could start this reading frame, one near the beginning of the intron and the
      other in the upstream exon, leading to predicted polypeptides of 138 and 160 amino acid
      residues. The longer polypeptide was the major form translated in vitro in a reticulocyte
      extract. From nuclease assays of proteins synthesized in vitro with partially deleted DNAs, we
      conclude that both polypeptides possess endonuclease activity. We also have expressed I-Ppo in
      Escherichia coli, using a bacteriophage T7 RNA polymerase expression system. The longer
      polypeptide also was the predominant form made in this system. It showed enzymatic activity in
      bacteria in vivo, as demonstrated by the cleavage of a plasmid carrying the target site. Like
      several other intron-encoded endonucleases, I-Ppo makes a four-base staggered cut in its
      ribosomal DNA target sequence, very near the site where intron 3 becomes integrated in crosses
      of intron 3-containing and intron 3-lacking Physarum strains.
AU  - Muscarella DE
AU  - Ellison EL
AU  - Ruoff BM
AU  - Vogt VM
PT  - Journal Article
TA  - Mol. Cell. Biol.
JT  - Mol. Cell. Biol.
SO  - Mol. Cell. Biol. 1990 10: 3386-3396.

PMID- 2536594
VI  - 56
DP  - 1989
TI  - A mobile group I intron in the nuclear DNA of Physarum polycephalum.
PG  - 443-454
AB  - We have shown that a strain-specific group I intron (intron 3) in the nuclear extrachromosomal
      rDNA of Physarum polycephalum is a mobile element. Shortly after mating of amoebae from
      intron-lacking and intron-containing strains, intron 3 transposes in a site-specific manner
      into all available recipient molecules. The transposition appears to occur by gene conversion,
      as evidenced by the co-conversion of adjacent sequences and by double strand breakage observed
      in some of the recipient rDNA molecules. We infer that the double strand break is induced by
      an endonuclease encoded by intron 3, since in vitro transcription and translation of the
      cloned intron leads to the synthesis of an enzymatically active, site-specific nuclease. This
      is the first demonstration of the transposition of a nuclear intron in an experimental
      setting, and provides a rare example of a protein encoded by an RNA polymerase I transcript.
AU  - Muscarella DE
AU  - Vogt VM
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1989 56: 443-454.

PMID- 26392840
VI  - 10
DP  - 2015
TI  - Draft genome sequence of 'Treponema phagedenis' strain V1, isolated from bovine digital dermatitis.
PG  - 67
AB  - 'Treponema phagedenis' is considered to be a key agent in the pathogenesis of bovine digital
      dermatitis, an infectious foot condition of economic and animal welfare importance. We hereby
      report the draft sequence of 'T. phagedenis' strain V1. The draft genome assembly consists
      of 51 scaffolds comprising 3,129,551 bp and a GC-content of 39.9 %. Putative pathogenicity
      related factors have been identified in the genome that can be used in future studies to gain
      insight into  the pathogenic mechanisms of 'T. phagedenis'.
AU  - Mushtaq M
AU  - Manzoor S
AU  - Pringle M
AU  - Rosander A
AU  - Bongcam-Rudloff E
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 67.

PMID- 8346041
VI  - 21
DP  - 1993
TI  - BseRI a novel restriction endonuclease from a Bacillus species which recognizes the sequence 5'...GAGGAG...3'.
PG  - 3585
AB  - BseRI, a unique Type IIS restriction endonuclease, has been isolated from Bacillus species R
      (CAMB 2669). BseRI recognizes a six base pair non-palindromic sequence 5'-GAGGAG-3' and
      cleaves double stranded DNA ten nucleotides beyond this sequence on the top strand and eight
      nucleotides beyond the sequence on the complementary strand to produce a two nucleotide 3'
      extension.
AU  - Mushtaq R
AU  - Naeem S
AU  - Sohail A
AU  - Riazuddin S
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 3585.

PMID- 3654762
VI  - 105
DP  - 1987
TI  - Effects of cytosine methylation on the activity of restriction enzymes.
PG  - 155a
AB  - Restriction cleavage of DNA is a major tool in the characterization eukaryotic
      genes.  Cleavage by a restriction enzyme requires only that the DNA contain the
      recognition site for the enzyme and that it not be modified so as to prohibit
      the hydrolytic reaction.  In mammals, the DNA is modified in some of the
      5'-CG-3' doublets by C5 methylation of cytosine (5mC).  The 5mC inhibits the
      cleavage activity of some nucleases, but does not affect others.  However, the
      effect of 5mC on most restriction enzyme activities has not been thoroughly
      documented.  The studies presented address this need.  Single stranded pTZ19U
      and pTZ19R plasmid DNAs were hybridized with the universal and reverse M13
      sequencing primers, respectively.  These primed templates were extended by DNA
      polI with dATP, dGTP, dTTP and either dCTP or d5mCTP, generating double strand
      substrates in which one strand was completely methylated at all cytosine
      positions.  These substrates were treated with 12 restriction enzymes, each
      with a single cleavage site in the polyclonal region of these vectors.  AccI,
      Asp718, SacI, SalI and SmaI were inactive on the hemimethylated substrates.
      HindIII, KpnI, PstI and XbaI were active but exhibited modified specificities.
      BamHI, EcoRI and HincII activitiies were not affected by 5mC.  These results
      indicate that cytosine methylation can affect restriction cleavage either by
      inhibition or by alteration of the selected cleavage site.  In addition, the
      data confirm that isoschizomers are affected differently by methylation of the
      same site.
AU  - Musich PR
PT  - Journal Article
TA  - J. Cell Biol.
JT  - J. Cell Biol.
SO  - J. Cell Biol. 1987 105: 155a.

PMID- 26607889
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Eight Nontypeable Haemophilus influenzae Strains Previously Characterized Using an Electrophoretic Typing Scheme.
PG  - e01374-15
AB  - Nontypeable Haemophilus influenzae is an important cause of human disease. Strains were
      selected for genome sequencing to represent the breadth of
      nontypeable strains within the species, as previously defined by the
      electrophoretic mobility of 16 metabolic enzymes.
AU  - Mussa HJ
AU  - VanWagoner TM
AU  - Morton DJ
AU  - Seale TW
AU  - Whitby PW
AU  - Stull TL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01374-15.

PMID- 30124845
VI  - 73
DP  - 2018
TI  - Phylogenomics of colistin-susceptible and resistant XDR Acinetobacter baumannii.
PG  - 2952-2959
AB  - Background: Acinetobacter baumannii is a healthcare-associated pathogen with high rates of
      carbapenem resistance. Colistin is now routinely used for treatment of
      infections by this pathogen. However, colistin use has been associated with
      development of resistance to this agent. Objectives: To elucidate the
      phylogenomics of colistin-susceptible and -resistant A. baumannii strain pairs
      from a cohort of hospitalized patients at a tertiary medical centre in the USA.
      Methods: WGS data from 21 pairs of colistin-susceptible and -resistant, XDR
      clinical strains were obtained and compared using phylogeny of aligned genome
      sequences, assessment of pairwise SNP differences and gene content. Results:
      Fourteen patients had colistin-resistant strains that were highly genetically
      related to their own original susceptible strain with a median pairwise SNP
      distance of 5.5 (range 1-40 SNPs), while seven other strain pairs were divergent
      with >/=84 SNP differences. In addition, several strains from different patients
      formed distinct clusters on the phylogeny in keeping with closely linked
      transmission chains. The majority of colistin-resistant strains contained
      non-synonymous mutations within the pmrAB locus suggesting a central role for
      pmrAB mutations in colistin resistance. Excellent genotype-phenotype correlation
      was also observed for carbapenems, aminoglycosides and tetracyclines.
      Conclusions: The findings suggest that colistin resistance in the clinical
      setting arises through both in vivo evolution from colistin-susceptible strains
      and reinfection by unrelated colistin-resistant strains, the latter of which may
      involve patient-to-patient transmission.
AU  - Mustapha MM
AU  - Li B
AU  - Pacey MP
AU  - Mettus RT
AU  - McElheny CL
AU  - Marshall CW
AU  - Ernst RK
AU  - Cooper VS
AU  - Doi Y
PT  - Journal Article
TA  - J. Antimicrob. Chemother.
JT  - J. Antimicrob. Chemother.
SO  - J. Antimicrob. Chemother. 2018 73: 2952-2959.

PMID- 27688339
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Four Hospital-Associated Pseudomonas putida Isolates.
PG  - e01039-16
AB  - We present here the draft genome sequences of four Pseudomonas putida isolates belonging to a
      single clone suspected for nosocomial transmission between
      patients and a bronchoscope in a tertiary hospital. The four genome sequences
      belong to a single lineage but contain differences in their mobile genetic
      elements.
AU  - Mustapha MM
AU  - Marsh JW
AU  - Ezeonwuka CD
AU  - Pasculle AW
AU  - Pacey MP
AU  - Querry AM
AU  - Muto CA
AU  - Harrison LH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01039-16.

PMID- 29472331
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Escherichia coli 81009, a Representative of the Sequence Type 131 C1-M27 Clade with a Multidrug-Resistant Phenotype.
PG  - e00056-18
AB  - The sequence type 131 (ST131)-H30 clone is responsible for a significant proportion of
      multidrug-resistant extraintestinal Escherichia coli infections.
      Recently, the C1-M27 clade of ST131-H30, associated with blaCTX-M-27, has
      emerged. The complete genome sequence of E. coli isolate 81009 belonging to this
      clone, previously used during the development of ST131-specific monoclonal
      antibodies, is reported here.
AU  - Mutti M
AU  - Sonnevend A
AU  - Pal T
AU  - Junttila S
AU  - Ekker H
AU  - Galik B
AU  - Gyenesei A
AU  - Nagy G
AU  - Nagy E
AU  - Szijarto V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00056-18.

PMID- 29449394
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Lactobacillus paracasei DUP 13076, Which Exhibits Potent Antipathogenic Effects against Salmonella enterica Serovars Enteritidis,  Typhimurium, and Heidelberg.
PG  - e00065-18
AB  - Lactobacillus paracasei DUP 13076 demonstrates antagonistic effects against the foodborne
      pathogens Salmonella enterica serovars Enteritidis, Typhimurium, and
      Heidelberg in coculture and in vitro experiments. Here, we report the draft
      genome sequence of Lactobacillus paracasei DUP 13076, which has a circular
      chromosome of 3,048,314 bp and a G+C content of 46.3%.
AU  - Muyyarikkandy MS
AU  - Alqahtani FH
AU  - Mandoiu I
AU  - Amalaradjou MA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00065-18.

PMID- 29449386
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Lactobacillus rhamnosus NRRL B-442, a Potential Probiotic Strain.
PG  - e00046-18
AB  - Lactic acid bacteria are known to exhibit probiotic properties through various mechanisms,
      including competitive exclusion, pathogen inhibition, production of
      antimicrobial substances, and maintenance of eubiosis. Here, we present the draft
      genome sequence of a novel probiotic strain, Lactobacillus rhamnosus strain NRRL
      B-442, which exhibits potent antivirulence activity against Salmonella enterica.
AU  - Muyyarikkandy MS
AU  - Alqahtani FH
AU  - Mandoiu I
AU  - Amalaradjou MA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00046-18.

PMID- 21475584
VI  - 4
DP  - 2011
TI  - Complete genome sequence of 'Thioalkalivibrio sulfidophilus' HL-EbGr7.
PG  - 23-35
AB  - 'Thioalkalivibrio sulfidophilus' HL-EbGr7 is an obligately chemolithoautotrophic,
      haloalkaliphilic sulfur-oxidizing bacterium (SOB) belonging to the
      Gammaproteobacteria. The strain was found to predominate a full-scale bioreactor,
      removing sulfide from biogas. Here we report the complete genome sequence of
      strain HL-EbGr7 and its annotation. The genome was sequenced within the Joint
      Genome Institute Community Sequencing Program, because of its relevance to the
      sustainable removal of sulfide from bio- and industrial waste gases.
AU  - Muyzer G
AU  - Sorokin DY
AU  - Mavromatis K
AU  - Lapidus A
AU  - Clum A
AU  - Ivanova N
AU  - Pati A
AU  - d'Haeseleer P
AU  - Woyke T
AU  - Kyrpides NC
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 4: 23-35.

PMID- 22675584
VI  - 5
DP  - 2011
TI  - Complete genome sequence of Thioalkalivibrio sp. K90mix.
PG  - 341-355
AB  - Thioalkalivibrio sp. K90mix is an obligately chemolithoautotrophic, natronophilic
      sulfur-oxidizing bacterium (SOxB) belonging to the family Ectothiorhodospiraceae within the
      Gammaproteobacteria. The strain was isolated from a mixture of sediment samples obtained from
      different soda lakes located in the Kulunda Steppe (Altai, Russia) based on its extreme
      potassium carbonate tolerance as an enrichment method. Here we report the complete ge-nome
      sequence of strain K90mix and its annotation. The genome was sequenced within the Joint Genome
      Institute Community Sequencing Program, because of its relevance to the sus-tainable removal
      of sulfide from wastewater and gas streams.
AU  - Muyzer G
AU  - Sorokin DY
AU  - Mavromatis K
AU  - Lapidus A
AU  - Foster B
AU  - Sun H
AU  - Ivanova N
AU  - Pati A
AU  - D'haeseleer P
AU  - Woyke T
AU  - Kyripides NC
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 5: 341-355.

PMID- 16825665
VI  - 16
DP  - 2006
TI  - Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringens.
PG  - 1031-1040
AB  - Clostridium perfringens is a Gram-positive, anaerobic spore-forming bacterium commonly found
      in soil, sediments, and the human
      gastrointestinal tract. C. perfringens is responsible for a wide spectrum
      of disease, including food poisoning, gas gangrene (clostridial
      myonecrosis), enteritis necroticans, and non-foodborne gastrointestinal
      infections. The complete genome sequences of Clostridium perfringens
      strain ATCC 13124, a gas gangrene isolate and the species type strain, and
      the enterotoxin-producing food poisoning strain SM101, were determined and
      compared with the published C. perfringens strain 13 genome. Comparison of
      the three genomes revealed considerable genomic diversity with >300 unique
      "genomic islands" identified, with the majority of these islands unusually
      clustered on one replichore. PCR-based analysis indicated that the large
      genomic islands are widely variable across a large collection of C.
      perfringens strains. These islands encode genes that correlate to
      differences in virulence and phenotypic characteristics of these strains.
      Significant differences between the strains include numerous novel mobile
      elements and genes encoding metabolic capabilities, strain-specific
      extracellular polysaccharide capsule, sporulation factors, toxins, and
      other secreted enzymes, providing substantial insight into this medically
      important bacterial pathogen.
AU  - Myers GS et al
PT  - Journal Article
TA  - Genome Res.
JT  - Genome Res.
SO  - Genome Res. 2006 16: 1031-1040.

PMID- 27811102
VI  - 4
DP  - 2016
TI  - Genome Sequence of Prosthecochloris sp. Strain CIB 2401 of the Phylum Chlorobi.
PG  - e01222-16
AB  - To date, only 13 genomes of green sulfur bacteria (family Chlorobiaceae) have been sequenced.
      The sequenced strains do not cover the full phylogenetic
      diversity of the family. We determined the complete genome sequence of
      Prosthecochloris sp. strain CIB 2401, thereby increasing the genome information
      for the poorly represented marine Chlorobiaceae.
AU  - Nabhan S
AU  - Bunk B
AU  - Sproer C
AU  - Liu Z
AU  - Bryant DA
AU  - Overmann J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01222-16.

PMID- 28336595
VI  - 5
DP  - 2017
TI  - Genome Sequence of Creatinine-Fermenting Tissierella creatinophila Strain KRE 4T  (DSM 6911).
PG  - e00051-17
AB  - Tissierella creatinophila strain KRE 4T (DSM 6911) is a strictly anaerobic,
      creatinine-fermenting, and creatine-fermenting organism, which has been isolated
      from sewage sludge. The draft genome consists of one circular chromosome (2.5 Mb)
      and harbors 2,533 predicted protein-encoding genes.
AU  - Nacke H
AU  - Daniel R
AU  - Poehlein A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00051-17.

PMID- 
VI  - 0
DP  - 2006
TI  - BstKTI, a new dam-sensitive neoschizomer of restriction endonuclease MboI, which is able to cleave 5 hemimethylated substrate.
PG  - 5-10
AB  - The strain Bacillus stearothermophilus KT, a producer of a new restriction endonuclease
      BstKTI, which is the neoschizomer of restrictase MboI that recognizes the sequence
      5'-GATC-3', has been found. The preparation of the enzyme was obtained, and its properties
      were studied including substrate specificity and cleavage position in DNA. It was shown that
      DNA hydrolysis occurred in position 5'-GAT^C-3'. Unlike the other isoschizomers of the
      restriction endonuclease MboI, BstKTI is sensitive to dam-methylation, but it is able to
      cleave the adenine-hemimethylated substrate. Moreover, BstKTI is capable of cleaving the
      sequence 5'-GATC-3' that contains the modified cytosine in position C5.
AU  - Nadeev AN
AU  - Chernukhin VA
AU  - Sevastyanova OO
AU  - Tomilova YE
AU  - Shinkarenko NM
AU  - Evdokimov AA
AU  - Degtyarev SK
PT  - Journal Article
TA  - Biotekhnologiya
JT  - Biotekhnologiya
SO  - Biotekhnologiya 2006 0: 5-10.

PMID- 11948154
VI  - 184
DP  - 2002
TI  - Mobility of a restriction-modification system revealed by its genetic context in three hosts.
PG  - 2411-2419
AB  - The flow of genes among prokaryotes plays a fundamental role in shaping bacterial evolution,
      and restriction-modification systems can modulate this flow. However, relatively little is
      known about the distribution and movement of restriction-modification systems themselves. We
      have isolated and characterized the genes for restriction-modification systems from two
      species of Salmonella, S. enterica serovar Paratyphi A and S. enterica serovar Bareilly. Both
      systems are closely related to the PvuII restriction-modification system and share its target
      specificity. In the case of S. enterica serovar Paratyphi A, the restriction endonuclease is
      inactive, apparently due to a mutation in the subunit interface region. Unlike the
      chromosomally located Salmonella systems, the PvuII system is plasmid borne. We have completed
      the sequence characterization of the PvuII plasmid pPvu1, originally from Proteus vulgaris,
      making this the first completely sequenced plasmid from the genus Proteus. Despite the
      pronounced similarity of the three restriction-modification systems, the flanking sequences in
      Proteus and Salmonella are completely different. The SptAI and SbaI genes lie between an
      equivalent pair of bacteriophage P4-related open reading frames, one of which is a putative
      integrase gene, while the PvuII genes are adjacent to a mob operon and a XerCD recombination
      (cer) site.
AU  - Naderer M
AU  - Brust JR
AU  - Knowle D
AU  - Blumenthal RM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2002 184: 2411-2419.

PMID- 22291460
VI  - 6
DP  - 2012
TI  - Staphylococcus aureus eye infections in two Indian hospitals: emergence of ST772 as a major clone.
PG  - 165-173
AB  - PURPOSE: The purpose of this study was to perform molecular characterization of Staphylococcus
      aureus isolates causing a variety of eye infections from two major eye care hospitals in
      India. METHODS: Twenty-four isolates from Aravind Eye Hospital, Madurai, India, and nine
      isolates from LV Prasad Eye Institute, Bhubaneswar, India, representing severe to nonsevere
      eye infections like microbial keratitis to lacrimal sac abscess, were characterized.
      Staphylococcal cassette chromosome mec typing, multilocus sequence typing, accessory gene
      regulator typing, staphylococcal protein A typing, and pulsed field gel electrophoresis were
      used, along with determination of the presence of Panton-Valentine leucocidin toxin and
      endotoxin gene cluster among each sequence type. RESULTS: The majority of eye infections, both
      severe and nonsevere, were caused by sequence type (ST)772, positive for the Panton-Valentine
      leucocidin gene, and carrying methicillin-resistant staphylococcal cassette chromosome mec
      type V cassette (22/33, 67%). Some of the other sequence types that caused severe eye
      infections were ST1 (9%), 5 (3%), 72 (6%), 88 (3%), 121 (3%), and 672 (3%).
      This is the first report of the presence of ST1 and 88 in India. CONCLUSION:
      Although the number of isolates included in this study was small, most of the eye infections
      were caused by community-associated S. aureus where patients had no history of hospitalization
      or treatment in the past year. In the case of six severe infections, patients were admitted
      for surgeries and there is probability of hospital infection. In addition, only
      methicillin-resistant S. aureus isolates carrying staphylococcal cassette chromosome mec type
      V were detected. Epidemic methicillin-resistant Staphylococcus aureus 15 (ST22) is a major ST
      found in health care as well as community settings in non-eye infections in India, but only
      one methicillin-sensitive S. aureus isolate belonging to ST22 was detected.
      Predominantly ST772, along with a few other STs, caused the 33 eye infections studied.
AU  - Nadig S
AU  - Velusamy N
AU  - Lalitha P
AU  - Kar S
AU  - Sharma S
AU  - Arakere G
PT  - Journal Article
TA  - Clinical Ophthalmology
JT  - Clinical Ophthalmology
SO  - Clinical Ophthalmology 2012 6: 165-173.

PMID- 27540048
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Aeromonas dhakensis Strain F2S2-1, Isolated from the Skin Surface of an Indian Oil Sardine (Sardinella longiceps).
PG  - e00494-16
AB  - Draft genome sequencing of Aeromonas dhakensis strain F2S2-1, isolated from the skin surface
      of an Indian oil sardine (Sardinella longiceps), has been carried
      out. The draft genome was roughly 4.7 Mb in size with 61.7% G+C content.
      Annotation of the genome yielded 4,337 genes coding for proteins, tRNAs, and
      rRNAs. Annotation also revealed the presence of 52 genes linked to resistance to
      antibiotics/toxic compounds. Pathway analysis revealed the presence of novobiocin
      biosynthetic genes and genes for biosynthesis of a siderophore group on
      nonsynthetic peptides.
AU  - Nadiga M
AU  - Vaidyanathan VV
AU  - Thayumanavan T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00494-16.

PMID- 12588991
VI  - 23
DP  - 2003
TI  - Karyopherin-mediated nuclear import of the homing endonuclease VMA1-derived endonuclease is required for self-propagation of the  coding region.
PG  - 1726-1736
AB  - VMA1-derived endonuclease (VDE), a site-specific endonuclease in Saccharomyces cerevisiae,
      enters the nucleus to generate a double-strand
      break in the VDE-negative allelic locus, mediating the self-propagating
      gene conversion called homing. Although VDE is excluded from the nucleus
      in mitotic cells, it relocalizes at premeiosis, becoming localized in both
      the nucleus and the cytoplasm in meiosis. The nuclear localization of VDE
      is induced by inactivation of TOR kinases, which constitute central
      regulators of cell differentiation in S. cerevisiae, and by nutrient
      depletion. A functional genomic approach revealed that at least two
      karyopherins, Srp1p and Kap142p, are required for the nuclear localization
      pattern. Genetic and physical interactions between Srp1p and VDE imply
      direct involvement of karyopherin-mediated nuclear transport in this
      process. Inactivation of TOR signaling or acquisition of an extra nuclear
      localization signal in the VDE coding region leads to artificial nuclear
      localization of VDE and thereby induces homing even during mitosis. These
      results serve as evidence that VDE utilizes the host systems of nutrient
      signal transduction and nucleocytoplasmic transport to ensure the
      propagation of its coding region.
AU  - Nagai Y
AU  - Nogami S
AU  - Kumagai-Sano F
AU  - Ohya Y
PT  - Journal Article
TA  - Mol. Cell. Biol.
JT  - Mol. Cell. Biol.
SO  - Mol. Cell. Biol. 2003 23: 1726-1736.

PMID- 28912335
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Klebsiella pneumoniae OK8, a Multidrug-Resistant Mouse and Human Pathogen.
PG  - e01018-17
AB  - We report here the draft genome sequence of Klebsiella pneumoniae OK8, a multidrug-resistant
      strain which was isolated in 1976 from a human and is known
      to be a mouse pathogen.
AU  - Nagamalleswari E
AU  - Nagaraja V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01018-17.

PMID- 28854737
VI  - 45
DP  - 2017
TI  - Restriction endonuclease triggered bacterial apoptosis as a mechanism for long time survival.
PG  - 8423-8434
AB  - Programmed cell death (PCD) under certain conditions is one of the features of bacterial
      altruism. Given the bacterial diversity and varied life style,
      different PCD mechanisms must be operational that remain largely unexplored. We
      describe restriction endonuclease (REase) mediated cell death by an apoptotic
      pathway, beneficial for isogenic bacterial communities. Cell death is pronounced
      in stationary phase and when the enzyme exhibits promiscuous DNA cleavage
      activity. We have elucidated the molecular mechanism of REase mediated cell
      killing and demonstrate that released nutrients from dying cells support the
      growth of the remaining cells in the population. These findings illustrate a new
      intracellular moonlighting role for REases which are otherwise established host
      defence arsenals. REase induced PCD appears to be a cellular design to replenish
      nutrients for cells undergoing starvation stress and the phenomenon could be wide
      spread in bacteria, given the abundance of restriction-modification (R-M) systems
      in the microbial population.
AU  - Nagamalleswari E
AU  - Rao S
AU  - Vasu K
AU  - Nagaraja V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2017 45: 8423-8434.

PMID- 23072305
VI  - 51
DP  - 2012
TI  - Ca(2+) binding to the ExDxD motif regulates the DNA cleavage specificity of a promiscuous endonuclease.
PG  - 8939-8949
AB  - Most of the restriction endonucleases (REases) are dependent on Mg(2+) for DNA cleavage, and
      in general, Ca(2+) inhibits their activity. R.KpnI, an HNH active
      site containing betabetaalpha-Me finger nuclease, is an exception. In presence of
      Ca(2+), the enzyme exhibits high-fidelity DNA cleavage and complete suppression
      of Mg(2+)-induced promiscuous activity. To elucidate the mechanism of unusual
      Ca(2+)-mediated activity, we generated alanine variants in the putative Ca(2+)
      binding motif, E(132)xD(134)xD(136), of the enzyme. Mutants showed decreased
      levels of DNA cleavage in the presence of Ca(2+). We demonstrate that ExDxD
      residues are involved in Ca(2+) coordination; however, the invariant His of the
      catalytic HNH motif acts as a general base for nucleophile activation, and the
      other two active site residues, D148 and Q175, also participate in
      Ca(2+)-mediated cleavage. Insertion of a 10-amino acid linker to disrupt the
      spatial organization of the ExDxD and HNH motifs impairs Ca(2+) binding and
      affects DNA cleavage by the enzyme. Although ExDxD mutant enzymes retained
      efficient cleavage at the canonical sites in the presence of Mg(2+), the
      promiscuous activity was greatly reduced, indicating that the carboxyl residues
      of the acidic triad play an important role in sequence recognition by the enzyme.
      Thus, the distinct Ca(2+) binding motif that confers site specific cleavage upon
      Ca(2+) binding is also critical for the promiscuous activity of the Mg(2+)-bound
      enzyme, revealing its role in metal ion-mediated modulation of DNA cleavage.
AU  - Nagamalleswari E
AU  - Vasu K
AU  - Nagaraja V
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2012 51: 8939-8949.

PMID- 9629533
VI  - 13
DP  - 1998
TI  - 1513-DMIa and 1513-DMIb, DNA methyltransferase inhibitors produced by Streptomyces sp. strain no. 1513.
PG  - 135-146
AB  - Two new methyltransferase inhibitors were isolated from the culture filtrate of Streptomyces
      sp. strain No. 1513 and named 1513-DMIa and 1513-DMIb.  1513-DMIa and 1513-DMIb were
      distinguished in certain properties from DMI-1, DMI-2, DMI-3 and DMI-4 previously reported.
      The molecular weight of 1513-DMIa and 1513-DMIb were estimated to be 576 and 8400 from the
      results of FAB-MS and gel filtration, respectively.  The inhibitory activities of 1513-DMIa
      and 1513-DMIb were shown to be pH- and temperature-dependent and both inhibited M.EcoRI in an
      uncompetitive manner with respect to DNA or S-adenosylmethionine (SAM).
AU  - Nagao K
AU  - Suzuki K
AU  - Hamada S
AU  - Yahara S
AU  - Yamamura R
AU  - Uyeda M
PT  - Journal Article
TA  - J. Enzym. Inhib.
JT  - J. Enzym. Inhib.
SO  - J. Enzym. Inhib. 1998 13: 135-146.

PMID- 8835936
VI  - 10
DP  - 1996
TI  - DMI-2 and DMI-3, DNA methyltransferase inhibitors produced by Streptomyces sp. strain no. 560.
PG  - 115-124
AB  - Streptomyces sp. strain no. 560 produces several types of DNA methyltransferase inhibitors in
      the culture filtrate.  Two of them, DMI-2 and DMI-3, were distinguished from the previously
      reported DMI-1 by their inhibitory spectrum and inhibition characteristics against DNA
      methyltransferase.  The molecular weights of DMI-2 and DMI-3 were 854 and 435, respectively.
      The structure of DMI-2 was determined to be
      4R,6aR,10S,10aS-8-acetyl-6a.10a-d:hydroxy-2-methoxy-12-methyl-10-[4-[3-hydroxy-3,5-dimethy
      tetrahydropyran-1-yloxy)-5-methylcyclohexan-1-yloxyl-1,4,6,7,9-pentaoxo-1,4,6,6a,7,8,9,10,10a
      The chemical structure of DMI-2 was established as a tautomer of duiomycin which is an
      antitumor antibiotic produced by Streptomyces sp. 1725.  DMI-2 and DMI-3 showed strong
      inhibition against N6-methyladenine-DNA methyltransferase (M.EcoRI).  DMI-2 inhibited M.EcoRI
      in a competitive manner with respect to plasmid pUC19 used as DNA substrate and in an
      uncompetitive manner with respect to S-adenosylmethionine (SAM) used as methyl donor.  DMI-3
      inhibited M.EcoRI in a competitive manner with respect to plasmid pUC19 and SAM.  The
      inhibitory activities of both inhibitors depended upon the pH and temperature in the assay
      media.
AU  - Nagao K
AU  - Suzuki K
AU  - Tokunaga J
AU  - Miyazaki H
AU  - Katayama N
AU  - Mitsuyama R
AU  - Uyeda M
PT  - Journal Article
TA  - J. Enzym. Inhib.
JT  - J. Enzym. Inhib.
SO  - J. Enzym. Inhib. 1996 10: 115-124.

PMID- 25931606
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Rhodovulum sulfidophilum DSM 2351, an Extracellular Nucleic Acid-Producing Bacterium.
PG  - e00388-15
AB  - Rhodovulum sulfidophilum DSM 2351 is the nonsulfur photosynthetic bacterium that  efficiently
      releases nucleic acids into the extracellular milieu, which leads to
      flocculation. In this study, we determined the complete genome sequence of R.
      sulfidophilum DSM 2351, which will provide new insights into the mechanism of its
      unique nucleic acid release.
AU  - Nagao N
AU  - Hirose Y
AU  - Misawa N
AU  - Ohtsubo Y
AU  - Umekage S
AU  - Kikuchi Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00388-15.

PMID- 2991768
VI  - 316
DP  - 1985
TI  - A hybrid recognition sequence in a recombinant restriction enzyme and the evolution of DNA sequence specificity.
PG  - 371-372
AB  - Early attempts to generate new restriction specificities by recombination
      between allelic restriction-modification systems have been unsuccessful.
      Bullas et al. succeeded in isolating a new specificity, SQ, in Salmonella that
      they interpreted as being the result of a recombination event betwen the
      parental strains, Salmonella typhimurium and S. potsdam, which encode the SB
      and SP restriction systems, respectively.  This interpretation has recently
      been confirmed by DNA heteroduplex studies with the SB, SP and SQ structural
      genes.  We have determined the DNA sequences recognized by the SB and SP
      enzymes and found that, like all type I restriction sequences, they are split
      into two specific domains by a spacer of nonspecific sequence that, for both SB
      and SP, is 6 base pairs (bp) long.  We have now determined the sequence
      recognized by the recombinant SQ enzyme and find that it is a hybrid between
      the SB and SP sequences, containing one specific domain from each parental
      strain.  This result implies that each of the two specific domains is
      recognized by a physically distinct part of the enzyme.
AU  - Nagaraja V
AU  - Shepherd JCW
AU  - Bickle TA
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1985 316: 371-372.

PMID- 2989535
VI  - 182
DP  - 1985
TI  - Two Type I restriction enzymes from Salmonella species.  Purification and DNA recognition sequences.
PG  - 579-587
AB  - We have purified the type I restriction enzymes SB and SP from Salmonella typhimurium and S.
      potsdam, respectively, and determined the DNA sequences that they recognize.  These sequences
      resemble those previously determined for the type I enzymes, EcoB, EcoK and EcoA, in that the
      specific part of the sequence is divided into two domains by a spacer of non-specific sequence
      that has a fixed length for each enzyme.  Two main differences from the previously determined
      sequences are seen.  Both of the new sequences are degenerate and one of them, SB, has one
      trinucleotide and one pentanucleotide-specific domain rather than the trinucleotide and
      tetranucleotide domains seen for all of the other enzymes.  The only conserved features of the
      recognition sequences are the adenosyl residues that are methylated in the modification
      reaction.  For all of the enzymes these are situated ten or 11 base-pairs apart, one on each
      strand of the DNA.  This suggests that the enzymes bind to DNA along one face of the double
      helix making protein-DNA interaction in two successive major grooves with most of the
      non-specific spacer sequence in the intervening minor groove.
AU  - Nagaraja V
AU  - Shepherd JCW
AU  - Pripfl T
AU  - Bickle TA
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1985 182: 579-587.

PMID- 2987794
VI  - 13
DP  - 1985
TI  - The nucleotide sequence recognized by the Escherichia coli D type I restriction and modification enzyme.
PG  - 389-399
AB  - A type I restriction endonuclease from a new isolate of Escherichia coli (E.
      coli E166) has been purified and characterized.  The enzyme, EcoD, has a
      recognition sequence similar in overall structure to the previously determined
      type I enzyme sequences, an exception being that it is degenerate.  The
      sequence is 5'-T-T-A-N-N-N-N-N-N-N-N-G-T-C-Y-3'
      3'-A-A-T-N-N-N-N-N-N-N-N-C-A-G-R-5'where Y is a pyrimidine, R is a purine and N
      can be any nucleotide.  The enzyme methylates adenosyl residues in both strands
      of the DNA that are separated by ten base pairs, suggesting that the enzyme
      interacts with DNA along one face of the helix making contacts in two
      successive major grooves.
AU  - Nagaraja V
AU  - Stieger M
AU  - Nager C
AU  - Hadi SM
AU  - Bickle TA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1985 13: 389-399.

PMID- 
VI  - 0
DP  - 1985
TI  - New variations of an old theme:  Type I restriction enzymes and their recognition sequences.
PG  - 62-78
AB  - None
AU  - Nagaraja V
AU  - Suri B
AU  - Shepherd JCW
AU  - Bickle TA
PT  - Journal Article
TA  - Gene Manipulation and Expression
JT  - Gene Manipulation and Expression
SO  - Gene Manipulation and Expression 1985 0: 62-78.

PMID- 20544019
VI  - 5
DP  - 2010
TI  - De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads.
PG  - E10922
AB  - State-of-the-art DNA sequencing technologies are transforming the life
      sciences due to their ability to generate nucleotide sequence information
      with a speed and quantity that is unapproachable with traditional Sanger
      sequencing. Genome sequencing is a principal application of this
      technology, where the ultimate goal is the full and complete sequence of
      the organism of interest. Due to the nature of the raw data produced by
      these technologies, a full genomic sequence attained without the aid of
      Sanger sequencing has yet to be demonstrated.We have successfully
      developed a four-phase strategy for using only next-generation sequencing
      technologies (Illumina and 454) to assemble a complete microbial genome de
      novo. We applied this approach to completely assemble the 3.7 Mb genome of
      a rare Geobacter variant (KN400) that is capable of unprecedented current
      production at an electrode. Two key components of our strategy enabled us
      to achieve this result. First, we integrated the two data types early in
      the process to maximally leverage their complementary characteristics. And
      second, we used the output of different short read assembly programs in
      such a way so as to leverage the complementary nature of their different
      underlying algorithms or of their different implementations of the same
      underlying algorithm.The significance of our result is that it
      demonstrates a general approach for maximizing the efficiency and success
      of genome assembly projects as new sequencing technologies and new
      assembly algorithms are introduced. The general approach is a meta
      strategy, wherein sequencing data are integrated as early as possible and
      in particular ways and wherein multiple assembly algorithms are
      judiciously applied such that the deficiencies in one are complemented by
      another.
AU  - Nagarajan H
AU  - Butler JE
AU  - Klimes A
AU  - Qiu Y
AU  - Zengler K
AU  - Ward J
AU  - Young ND
AU  - Methe BA
AU  - Palsson BO
AU  - Lovley DR
AU  - Barrett CL
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2010 5: E10922.

PMID- 28336596
VI  - 5
DP  - 2017
TI  - Whole-Genome Shotgun Sequence of Escherichia coli Strain MN067 from India, a Commensal Bacterium with Potent Pathogenic Ability.
PG  - e00054-17
AB  - Escherichia coli is one of the most frequently prevalent pathogens, causing infections in
      health care settings throughout the world. Here, we report the
      whole-genome sequence of MN067, a commensal bacterium with a pathogenic
      potential.
AU  - Nagarjuna D
AU  - Gaind R
AU  - Dhanda RS
AU  - Yadav M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00054-17.

PMID- 22689232
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Phototrophic Betaproteobacterium Rubrivivax gelatinosus IL144.
PG  - 3541-3542
AB  - Rubrivivax gelatinosus is a facultative photoheterotrophic betaproteobacterium living in
      freshwater ponds, sewage ditches, activated sludge, and food processing
      wastewater. There have not been many studies on photosynthetic
      betaproteobacteria. Here we announce the complete genome sequence of the
      best-studied phototrophic betaproteobacterium, R. gelatinosus IL-144 (NBRC
      100245).
AU  - Nagashima S
AU  - Kamimura A
AU  - Shimizu T
AU  - Nakamura-Isaki S
AU  - Aono E
AU  - Sakamoto K
AU  - Ichikawa N
AU  - Nakazawa H
AU  - Sekine M
AU  - Yamazaki S
AU  - Fujita N
AU  - Shimada K
AU  - Hanada S
AU  - Nagashima KV
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3541-3542.

PMID- 20817768
VI  - 192
DP  - 2010
TI  - Complete Genome Sequence of the Representative {gamma}-Hexachlorocyclohexane-Degrading Bacterium Sphingobium japonicum  UT26.
PG  - 5852-5853
AB  - Sphingobium japonicum strain UT26 utilizes gamma-hexachlorocyclohexane (gamma-HCH), a man-made
      chlorinated pesticide that causes serious
      environmental problems due to its toxicity and long persistence, as a sole
      source of carbon and energy. Here, we report the complete genome sequence
      of UT26, which consists of two chromosomes and three plasmids. The 15 lin
      genes involved in gamma-HCH degradation are dispersed on the two
      chromosomes and one of the three plasmids.
AU  - Nagata Y
AU  - Ohtsubo Y
AU  - Endo R
AU  - Ichikawa N
AU  - Ankai A
AU  - Oguchi A
AU  - Fukui S
AU  - Fujita N
AU  - Tsuda M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 5852-5853.

PMID- 21310712
VI  - 39
DP  - 2011
TI  - Regulation of gene expression in restriction-modification system Eco29kI.
PG  - 4653-4663
AB  - The Eco29kI restriction-modification (R-M) system consists of two partially overlapping genes,
      eco29kIR, encoding a restriction endonuclease
      and eco29kIM, encoding methyltransferase. The two genes are thought to
      form an operon with the eco29kIR gene preceding the eco29kIM gene. Such an
      organization is expected to complicate establishment of plasmids
      containing this R-M system in naive hosts, since common logic dictates
      that methyltransferase should be synthesized first to protect the DNA from
      cleavage by the endonuclease. Here, we characterize the Eco29kI gene
      transcription. We show that a separate promoter located within the
      eco29kIR gene is sufficient to synthesize enough methyltransferase to
      completely modify host DNA. We further show that transcription from two
      intragenic antisense promoters strongly decreases the levels of eco29kIR
      gene transcripts. The antisense transcripts act by preventing translation
      initiation from the bicistronic eco29kIR-eco29kIM mRNA and causing its
      degradation. Both eco29kIM and antisense promoters are necessary for
      Eco29kI genes establishment and/or stable maintenance, indicating that
      they jointly contribute to coordinated expression of Eco29kI genes.
AU  - Nagornykh M
AU  - Zakharova M
AU  - Protsenko A
AU  - Bogdanova E
AU  - Solonin AS
AU  - Severinov K
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2011 39: 4653-4663.

PMID- 18672793
VI  - 44
DP  - 2008
TI  - Regulation of gene expression in a type II restriction-modification system.
PG  - 606-615
AB  - Type II restriction-modification systems are comprised of a restriction endonuclease and
      methyltransferase. The enzymes are coded by individual genes and recognize the same DNA
      sequence. Endonuclease makes a double-stranded break in the recognition site, and
      methyltransferase covalently modifies DNA bases within the recognition site, thereby
      preventing cleavage by the endonuclease. The concerted action of these enzymes plays the role
      of a primitive immune system and protects the bacterial host cell from invasion by foreign
      (for example, viral) DNA. However, uncontrolled expression of restriction-modification system
      genes can result in the death of a bacterial host cell because of endonuclease cleavage of the
      host DNA. In the present review, data on the regulation of expression of the type II
      restriction-modification enzymes genes are discussed.
AU  - Nagornykh MO
AU  - Bogdanova ES
AU  - Protsenko AS
AU  - Solonin AS
AU  - Zakharova MV
AU  - Severinov KV
PT  - Journal Article
TA  - Genetika
JT  - Genetika
SO  - Genetika 2008 44: 606-615.

PMID- 29255570
VI  - 12
DP  - 2017
TI  - The complete genome sequence of Ensifer meliloti strain CCMM B554 (FSM-MA), a highly effective nitrogen-fixing microsymbiont of Medicago truncatula Gaertn.
PG  - 75
AB  - Strain CCMM B554, also known as FSM-MA, is a soil dwelling and nodule forming, nitrogen-fixing
      bacterium isolated from the nodules of the legume Medicago
      arborea L. in the Maamora Forest, Morocco. The strain forms effective nitrogen
      fixing nodules on species of the Medicago, Melilotus and Trigonella genera and is
      exceptional because it is a highly effective symbiotic partner of the two most
      widely used accessions, A17 and R108, of the model legume Medicago truncatula
      Gaertn. Based on 16S rRNA gene sequence, multilocus sequence and average
      nucleotide identity analyses, FSM-MA is identified as a new Ensifer meliloti
      strain. The genome is 6,70 Mbp and is comprised of the chromosome (3,64 Mbp)
      harboring 3574 predicted genes and two megaplasmids, pSymA (1,42 Mbp) and pSymB
      (1,64 Mbp) with respectively 1481 and 1595 predicted genes. The average GC
      content of the genome is 61.93%. The FSM-MA genome structure is highly similar
      and co-linear to other E. meliloti strains in the chromosome and the pSymB
      megaplasmid while, in contrast, it shows high variability in the pSymA plasmid.
      The large number of strain-specific sequences in pSymA as well as strain-specific
      genes on pSymB involved in the biosynthesis of the lipopolysaccharide and
      capsular polysaccharide surface polysaccharides may encode novel symbiotic
      functions explaining the high symbiotic performance of FSM-MA.
AU  - Nagymihaly M
AU  - Vasarhelyi BM
AU  - Barriere Q
AU  - Chong TM
AU  - Balint B
AU  - Bihari P
AU  - Hong KW
AU  - Horvath B
AU  - Ibijbijen J
AU  - Amar M
AU  - Farkas A
AU  - Kondorosi E
AU  - Chan KG
AU  - Gruber V
AU  - Ratet P
AU  - Mergaert P
AU  - Kereszt A
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 75.

PMID- 29097471
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Two Lactobacillus casei Strains Isolated from Cheddar Cheese and a Fermented Milk Drink.
PG  - e01235-17
AB  - MiSeq Illumina shotgun sequencing technology was used to sequence two Lactobacillus casei
      strains, designated strains GCRL 163 and MJA 12. The
      estimated genome sizes for GCRL 163 and MJA 12 were 2.9 Mb and 3.1 Mb, with
      46.35% and 46.31% GC contents, respectively.
AU  - Nahar A
AU  - Baker AL
AU  - Bowman JP
AU  - Britz ML
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01235-17.

PMID- 28883137
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Three Sub-Antarctic Rhodococcus spp., Including Two Novel Psychrophilic Genomospecies.
PG  - e00898-17
AB  - The draft genome sequences of three sub-Antarctic Rhodococcus sp. strains-1159, 1163, and
      1168-are reported here. The estimated genome sizes were 7.09 Mb with a
      62.3% GC content for strain 1159, 4.45 Mb with a 62.3% GC content for strain
      1163, and 5.06 Mb with a 62.10% GC content for strain 1168.
AU  - Nahar A
AU  - Baker AL
AU  - Charleston MA
AU  - Bowman JP
AU  - Britz ML
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00898-17.

PMID- 29025939
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Two Novel Sub-Antarctic Williamsia Species.
PG  - e01047-17
AB  - Illumina MiSeq shotgun sequencing technology was used to sequence the genomes of  two novel
      sub-Antarctic Williamsia species, designated strains 1135 and 1138. The
      estimated genome sizes for strains 1135 and 1138 are 5.99 Mb and 6.08 Mb,
      respectively. This genome sequence information will aid in understanding the
      lipid metabolic pathways of cold-tolerant Williamsia species.
AU  - Nahar A
AU  - Baker AL
AU  - Charleston MA
AU  - Bowman JP
AU  - Britz ML
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01047-17.

PMID- 28385836
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Subantarctic Rhodococcus sp. Strain 1139.
PG  - e00090-17
AB  - The draft genome sequence of subantarctic Rhodococcus sp. strain 1139 is reported here. The
      genome size is 7.04 Mb with high G+C content (62.3%) and it contains a
      large number of genes involved in lipid synthesis. This lipid synthesis system is
      characteristic of oleaginous Actinobacteria, which are of interest for biofuel
      production.
AU  - Nahar A
AU  - Baker AL
AU  - Charleston MA
AU  - Britz ML
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00090-17.

PMID- 29220374
VI  - 12
DP  - 2017
TI  - A blaOXA-181-harbouring multi-resistant ST147 Klebsiella pneumoniae isolate from Pakistan that represent an intermediate stage towards pan-drug resistance.
PG  - e0189438
AB  - Carbapenem resistant Klebsiella pneumoniae (CR-KP) infections are an
      ever-increasing global issue, especially in the Indian subcontinent. Here we
      report genetic insight into a blaOXA-181 harbouring Klebsiella pneumoniae,
      belonging to the pandemic lineage ST147, that represents an intermediate stage
      towards pan-drug resistance. The CR-KP isolate DA48896 was isolated from a
      patient from Pakistan and was susceptible only to tigecycline and colistin. It
      harboured blaOXA-181 and was assigned to sequence type ST147. Analysis from whole
      genome sequencing revealed a very high sequence similarity to the previously
      sequenced pan-resistant K. pneumoniae isolate MS6671 from the United Arab
      Emirates. The two isolates are very closely related with only 46 chromosomal
      nucleotide differences, 14 indels and differences in plasmid content. Both carry
      a substantial number of plasmid-borne and chromosomally encoded resistance
      determinants. Interestingly, the two differences in susceptibility between the
      isolates could be attributed to DA48896 lacking an insertion of blaOXA-181 into
      the mgrB gene that results in colistin resistance in MS6671 and SNPs affecting
      AcrAB efflux pump expression likely to result in tigecycline resistance. These
      differences between the otherwise very similar isolates indicate that strong
      selection has occurred for resistance towards these last-resort drugs and
      illustrates the trajectory of resistance evolution of OXA-181-producing versions
      of the ST147 international risk clone.
AU  - Nahid F
AU  - Zahra R
AU  - Sandegren L
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2017 12: e0189438.

PMID- 9469831
VI  - 26
DP  - 1998
TI  - Targeting a truncated Ho-endonuclease of yeast to novel DNA sites with foreign zinc fingers.
PG  - 1233-1239
AB  - Ho-endonuclease of the yeast, Saccharomyces cerevisiae, initiates a mating type switch by
      making a site-specific double strand break in the mating type gene, MAT.  Ho is a dodecamer
      endonuclease and shares six of the seven intein motifs with PI-SceI endonuclease, an intein
      encoded by the VMAI gene.  We show that a 113 residue truncated Ho-endonuclease starting at
      intein motif C initiates a mating type switch in yeast.  Ho is the only dodecamer endonuclease
      with zinc finers.  To see whether they have a role in determining site specificity we
      exchanged them for zinc fingers of the yeast transcription factor, Swi5.  A chimeric
      endonuclease comprising the dodecamer motifs of Ho (C-E) and the zinc finger domain of Swi5
      cleaves a Swi5 substrate plasmid in vivo.  A similar chimera with the zinc fingers of Sp1
      cleaves a GC box rich substrate plasmid.  These experiments delineate a catalytic fragment of
      Ho-endonuclease that can be fused to various DNA binding moieties in the design of chimeric
      endonucleases with new site specificities.
AU  - Nahon E
AU  - Raveh D
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1998 26: 1233-1239.

PMID- 26251496
VI  - 3
DP  - 2015
TI  - Draft Whole-Genome Sequence and Annotation of the Entomopathogenic Bacterium Xenorhabdus khoisanae Strain MCB.
PG  - e00872-15
AB  - We report here the draft genome sequence of Xenorhabdus khoisanae strain MCB, a Gram-negative
      bacterium and symbiont of a Steinernema entomopathogenic nematode.
      The genome assembly consists of 266 contigs covering 4.68 Mb. Genome annotation
      revealed 3,869 protein-coding sequences, with a G+C content of 43.5%.
AU  - Naidoo S
AU  - Featherston J
AU  - Gray VM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00872-15.

PMID- 26514768
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence and Assembly of Photorhabdus heterorhabditis Strain VMG, a  Bacterial Symbiont Associated with the Entomopathogenic Nematode Heterorhabditis   zealandica.
PG  - e01279-15
AB  - Here, we report the draft genome sequence of Photorhabdus heterorhabditis strain  VMG, a
      symbiont of the entomopathogenic nematode Heterorhabditis zealandica in
      South Africa. The draft genome sequence is 4,878,919 bp long and contains 4,023
      protein-coding genes. The genome assembly contains 262 contigs with a G+C content
      of 42.22%.
AU  - Naidoo S
AU  - Mothupi B
AU  - Featherston J
AU  - Mpangase PT
AU  - Gray VM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01279-15.

PMID- 21378186
VI  - 193
DP  - 2011
TI  - Whole genome sequencing of Staphylococcus aureus strain RN4220, a key laboratory strain used in virulence research, identifies mutations that  affect not only virulence factors but also the fitness of the strain.
PG  - 2332-2335
AB  - S. aureus RN4220, a cloning intermediate, is sometimes used in virulence, resistance and
      metabolic studies. Using whole genome sequencing, we showed that RN4220 differs from NCTC8325
      and contains a number of genetic polymorphisms that affect both virulence and general fitness,
      thus implying caution in using this strain for these studies.
AU  - Nair D
AU  - Memmi G
AU  - Hernandez D
AU  - Bard J
AU  - Beaume M
AU  - Gill S
AU  - Francois P
AU  - Cheung AL
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 2332-2335.

PMID- 18524787
VI  - 15
DP  - 2008
TI  - Genome sequence determination of Porphyromonas gingivalis strain ATCC 33277 and genomic comparison with strain W83 revealed extensive genome rearrangements in P. gingivalis.
PG  - 215-225
AB  - The gram-negative anaerobic bacterium Porphyromonas gingivalis is a major causative agent of
      chronic periodontitis. Porphyromonas gingivalis strains
      have been classified into virulent and less-virulent strains by mouse
      subcutaneous soft tissue abscess model analysis. Here, we present the
      whole genome sequence of P. gingivalis ATCC 33277, which is classified as
      a less-virulent strain. We identified 2090 protein-coding sequences
      (CDSs), 4 RNA operons, and 53 tRNA genes in the ATCC 33277 genome. By
      genomic comparison with the virulent strain W83, we identified 461 ATCC
      33277-specific and 415 W83-specific CDSs. Extensive genomic rearrangements
      were observed between the two strains: 175 regions in which genomic
      rearrangements have occurred were identified. Thirty-five of those genomic
      rearrangements were inversion or translocation and 140 were simple
      insertion, deletion, or replacement. Both strains contained large numbers
      of mobile elements, such as insertion sequences, miniature inverted-repeat
      transposable elements (MITEs), and conjugative transposons, which are
      frequently associated with genomic rearrangements. These findings indicate
      that the mobile genetic elements have been deeply involved in the
      extensive genome rearrangement of P. gingivalis and the occurrence of many
      of the strain-specific CDSs. We also describe here a very unique feature
      of MITE400, which we renamed MITEPgRS (MITE of P. gingivalis with
      Repeating Sequences).
AU  - Naito M
AU  - Hirakawa H
AU  - Yamashita A
AU  - Ohara N
AU  - Shoji M
AU  - Yukitake H
AU  - Nakayama K
AU  - Toh H
AU  - Yoshimura F
AU  - Kuhara S
AU  - Hattori M
AU  - Hayashi T
AU  - Nakayama K
PT  - Journal Article
TA  - DNA Res.
JT  - DNA Res.
SO  - DNA Res. 2008 15: 215-225.

PMID- 26645327
VI  - 0
DP  - 2015
TI  - The complete genome sequencing of Prevotella intermedia strain OMA14 and a subsequent fine-scale, intra-species genomic comparison reveal an unusual amplification of conjugative and mobile transposons and a novel Prevotella-lineage-specific repeat.
PG  - dsv032
AB  - Prevotella intermedia is a pathogenic bacterium involved in periodontal diseases. Here, we
      present the complete genome sequence of a clinical strain, OMA14, of
      this bacterium along with the results of comparative genome analysis with strain
      17 of the same species whose genome has also been sequenced, but not fully
      analysed yet. The genomes of both strains consist of two circular chromosomes:
      the larger chromosomes are similar in size and exhibit a high overall linearity
      of gene organizations, whereas the smaller chromosomes show a significant size
      variation and have undergone remarkable genome rearrangements. Unique features of
      the Pre. intermedia genomes are the presence of a remarkable number of essential
      genes on the second chromosomes and the abundance of conjugative and mobilizable
      transposons (CTns and MTns). The CTns/MTns are particularly abundant in the
      second chromosomes, involved in its extensive genome rearrangement, and have
      introduced a number of strain-specific genes into each strain. We also found a
      novel 188-bp repeat sequence that has been highly amplified in Pre. intermedia
      and are specifically distributed among the Pre. intermedia-related species. These
      findings expand our understanding of the genetic features of Pre. intermedia and
      the roles of CTns and MTns in the evolution of bacteria.
AU  - Naito M
AU  - Ogura Y
AU  - Itoh T
AU  - Shoji M
AU  - Okamoto M
AU  - Hayashi T
AU  - Nakayama K
PT  - Journal Article
TA  - DNA Res.
JT  - DNA Res.
SO  - DNA Res. 2015 0: dsv032.

PMID- Not carried by PubMed...
VI  - 13
DP  - 1995
TI  - Cell death programmed by selfish genes -- or, why are there restriction enzymes?
PG  - 1444-1447
AB  - 
AU  - Naito T
AU  - Kobayashi I
PT  - Journal Article
TA  - Jikken Igaku
JT  - Jikken Igaku
SO  - Jikken Igaku 1995 13: 1444-1447.

PMID- 7846533
VI  - 267
DP  - 1995
TI  - Selfish behavior of restriction-modification systems.
PG  - 897-899
AB  - Plasmids carrying gene pairs encoding type II DNA restriction endonucleases and their cognate
      modification enzymes were shown to have increased stability in Escherichia coli. The
      descendants of cells that had lost these genes appeared unable to modify a sufficient number
      of recognition sites in their chromosomes to protect them from lethal attack by the remaining
      restriction enzyme molecules. The capacity of these genes to act as a selfish symbiont is
      likely to have contributed to the evolution of restriction-modification gene pairs.
AU  - Naito T
AU  - Kusano K
AU  - Kobayashi I
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1995 267: 897-899.

PMID- 9628334
VI  - 379
DP  - 1998
TI  - Selfish restriction modification genes: Resistance of a resident R/M plasmid to displacement by an incompatible plasmid mediated by host killing.
PG  - 429-436
AB  - Previous work from this laboratory demonstrated that plasmids carrying a type II
      restriction-modification gene complex are not easily lost from their bacterial host because
      plasmid-free segregant cells are killed through chromosome cleavage.  Here, we have followed
      the course of events that takes place when an Escherichia coli recBC sbcA strain carrying a
      plasmid coding for the PaeR7I restriction-modification gene complex is transformed by a
      plasmid with an identical origin of replication.  The number of transformants that appeared
      was far fewer than with the restriction-minus (r-) control.  Most of the transformants were
      very small.  After prolonged incubation, the number and the size of the colonies increased,
      but this increase never attained the level of the r- control.  Most of the transformed
      colonies retained the drug-resistance of the resident, r+m+ plasmid.  These results indicate
      that post-segregational host killing occurs when a plasmid bearing an R/M gene complex is
      displaced by an incompatible plasmid.  Such cell killing eliminates the competitor plasmid
      along with the host and, thus, would allow persistence of the R/M plasmid in the neighboring,
      clonal host cells in nature.  This phenomenon is reminiscent of mammalian apoptosis and other
      forms of altruistic cell death strategy against infection.  This type of resistance to
      displacement was also studied in a wild type Escherichia coli strain that was normal for
      homologous recombination.  A number of differences between the recBC sbcA strain and the rec+
      strain were observed and these will be discussed.
AU  - Naito Y
AU  - Naito T
AU  - Kobayashi I
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1998 379: 429-436.

PMID- 28839022
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Streptomyces sp. TN58, a Producer of Acyl Alpha-l-Rhamnopyranosides.
PG  - e00828-17
AB  - Streptomyces sp. TN58, isolated from a Tunisian soil sample, produces several natural
      products, including acyl alpha-l-rhamnopyranosides. It possesses a 7.6-Mb
      linear chromosome. This is, to our knowledge, the first genome sequence of a
      microorganism known to produce acyl alpha-l-rhamnopyranosides, and it will be
      helpful to study the biosynthesis of these specialized metabolites.
AU  - Najah S
AU  - Chong TM
AU  - Gerbaud C
AU  - Chan KG
AU  - Mellouli L
AU  - Pernodet JL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00828-17.

PMID- 29348341
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Escherichia coli Strain SN137, a Bacterium with Extracellular Proteolytic Activity on Immunoglobulins and Persistence in Human  Tissue Blood.
PG  - e01455-17
AB  - The draft genome sequence of Escherichia coli strain SN137 is reported here. The  genome
      comprises 172 contigs, corresponding to 4.9 Mb with 50% G+C content, and
      contains several genes related to pathogenicity that explain its survival in
      human hematic tissue.
AU  - Najera-Hernandez S
AU  - Sanchez-Alonso MP
AU  - Anastacio-Marcelino E
AU  - Negrete-Abascal E
AU  - Vazquez-Cruz C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01455-17.

PMID- 21576332
VI  - 79
DP  - 2011
TI  - Complete genome sequence of the marine fish pathogen Vibrio anguillarum harboring the pJM1 virulence plasmid and genomic comparison with other virulent strans of V. anguillarum and V. ordalii.
PG  - 2889-2900
AB  - We dissected the complete genome sequence of the O1 serotype strain Vibrio anguillarum
      775(pJM1) and determined the draft genomic sequences of plasmidless strains of serotype O1
      (strain 96F) and O2B (strain RV22) and V. ordalii. All strains harbor two chromosomes, but 775
      also harbors the virulence plasmid pJM1, which carries the anguibactin-producing and cognate
      transport genes, one of the main virulence factors of V. anguillarum. Genomic analysis
      identified eight genomic islands in chromosome 1 of V. anguillarum 775(pJM1) and two in
      chromosome 2. Some of them carried potential virulence genes for the biosynthesis of O
      antigens, hemolysins, and exonucleases as well as others for sugar transport and metabolism.
      The majority of genes for essential cell functions and pathogenicity are located on chromosome
      1. In contrast, chromosome 2 contains a larger fraction (59%) of hypothetical genes than does
      chromosome 1 (42%). Chromosome 2 also harbors a superintegron, as well as host "addiction"
      genes that are typically found on plasmids. Unique distinctive properties include homologues
      of type III secretion system genes in 96F, homologues of V. cholerae zot and ace toxin genes
      in RV22, and the biofilm formation syp genes in V. ordalii. Mobile genetic elements, some of
      them possibly originated in the pJM1 plasmid, were very abundant in 775, resulting in the
      silencing of specific genes, with only few insertions in the 96F and RV22 chromosomes.
AU  - Naka H
AU  - Dias GM
AU  - Thompson CC
AU  - Dubay C
AU  - Thompson FL
AU  - Crossa JH
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2011 79: 2889-2900.

PMID- 2828049
VI  - 171
DP  - 1988
TI  - Subunit structure of a yeast site-specific endodeoxyribonuclease, endoSceI.  A study using monoclonal antibodies.
PG  - 23
AB  - EndoSceI is a eucaryotic site-specific endoDNase of 120 kDa that causes
      double-stranded scission at well-defined sites, but is distinguishable from
      procaryotic restriction endonucleases by its mode of sequence recognition and
      lack of related specific DNA modification.  In purified preparations of
      endoSceI, only two polypeptide species of 75 kDa (75-kDa peptide) and 50 kDa
      (50-kDa peptide) are detected in apparently equal amounts.  We prepared mouse
      monoclonal IgGs that bound specifically to the 75-kDa peptide (but not the
      50-kDa peptide) without inhibiting the endoSceI activity.  Immunoprecipitation
      experiments with these IgGs revealed that the 75-kDa peptide and the 50-kDa
      peptide are physically associated with each other and with the endonucleolytic
      activity.  Full endoSceI activity was recovered by mixing the purified 75-kDa
      peptide and the partially purified 50-kDa peptide, each of which exhibited
      little or no endonuclease activity alone.  These observations indicate that
      endoSceI consists of two non-identical subunits of 75 kDa and 50 kDa, and that
      both subunits are required for full enzyme activity.
AU  - Nakagawa K-I
AU  - Hashikawa J-I
AU  - Makino O
AU  - Ando T
AU  - Shibata T
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1988 171: 23.

PMID- 1628629
VI  - 11
DP  - 1992
TI  - An endonuclease with multiple cutting sites, Endo.SceI, initiates genetic recombination at its cutting site in yeast mitochondria.
PG  - 2707-2715
AB  - Endo.SceI is a mitochondrial sequence-specific endonuclease which has multiple cutting sites.
      In order to examine the possible role of Endo.SceI in homologus recombination, we analyzed the
      mode of recombination upon mating using antibiotic resistance markers on the mitochondrial
      genome. The segregation of a marker located very close to one of the Endo.SceI cutting sites
      showed a disparity (polarized segregation, i.e. gene conversion). This gene conversion
      depended on the presence of the functional Endo.SceI gene. In vivo cutting of mitochondrial
      DNA upon mating was detected at the cutting site in the antibiotic marker region, which also
      depended on the Endo.SceI activity. These results suggest that mitochrondrial recombination is
      induced by cleavage of mitochondrial DNA by this sequence-specific endonuclease. This is the
      first demonstration that a sequence-specific endonuclease with multiple cutting sites induces
      genetic recombination.
AU  - Nakagawa K-I
AU  - Morishima N
AU  - Shibata T
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1992 11: 2707-2715.

PMID- 1988456
VI  - 266
DP  - 1991
TI  - A maturase-like subunit of the sequence-specific endonuclease Endo.SceI from yeast mitochondria.
PG  - 1977-1984
AB  - Some yeast strains possess a sequence-specific endonuclease, Endo.SceI, which is a
      heterodimeric enzyme localized in mitochondria.  The larger subunit (75 kDa) of Endo.SceI,
      encoded by a nuclear gene (ENS1), is transported from the cytosol into the mitochondria.  In
      this study, we determined the partial amino acid sequence of the smaller subunit (50 kDa) of
      Endo.SceI.  The determined sequence matched well the partial sequence deduced from a
      mitochondrial open reading frame (RF3).  The RF3 locus is known to exhibit polymorphism since
      this reading frame in some yeast strains is supposed to encode a maturase-like protein,
      whereas in other strains, the frame is interrupted by GC clusters, which thus break the frame.
      Southern blot analysis of various yeast strains showed that the continuity of RF3 is
      correlated with the presence of Endo.SceI activity.  These data indicate that the continuous
      RF3 sequence is a functional gene (ENS2) coding for the smaller subunit of Endo.SceI.  The
      results of cytoduction, by which the continuous RF3 sequence was transferred into a yeast
      strain lacking mitochondrial DNA, confirmed this conclusion.  This study suggests the
      involvement of Endo.SceI in genetic recombination of mitochondrial DNA.
AU  - Nakagawa K-I
AU  - Morishima N
AU  - Shibata T
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1991 266: 1977-1984.

PMID- 23924784
VI  - 8
DP  - 2014
TI  - Allying with armored snails: the complete genome of gammaproteobacterial endosymbiont.
PG  - 40-51
AB  - Deep-sea vents harbor dense populations of various animals that have their specific symbiotic
      bacteria. Scaly-foot gastropods, which are snails with mineralized scales covering the sides
      of its foot, have a gammaproteobacterial endosymbiont in their enlarged esophageal glands and
      diverse epibionts on the surface of their scales.  In this study, we report the complete
      genome sequencing of gammaproteobacterial endosymbiont.  The endosymbiont genome displays
      features consistent with ongoing genome reduction such as large proportions of pseudogenes and
      insertion elements.  The genome encodes functions commonly found in deep-sea vent
      chemoautotrophs such as sulfur oxidation and carbon fixation.  Stable carbon isotope
      (13C)-labeling experiments confirmed the endosymbiont chemoautotrophy.  The genome also
      includes an intact hydrogenase gene cluster that potentially has been horizontally transferred
      from phylogenetically distant bacteria.  Notable findings include the presence and
      transcription of genes for flagellar assembly, through which proteins are potentially exported
      from bacterium to the host.  Symbionts of snail individuals exhibited extreme genetic
      homogeneity, showing only two synonymous changes in 19 different genes (13810 positions in
      total) determined for 32 individual gastropods collected from a single colony at one time.
      The extremely low genetic individuality in endosymbionts probably reflects that the stringent
      symbiont selection by host prevents the random genetic drift in the small population of
      horizontally transmitted symbiont.  This study is the first complete genome analysis of
      gastropod endosymbiont and offers an opportunity to study genome evolution in a recently
      evolved endosymbiont.
AU  - Nakagawa S
AU  - Shimamura S
AU  - Takaki Y
AU  - Suzuki Y
AU  - Murakami S
AU  - Watanabe T
AU  - Fujiyoshi S
AU  - Mino S
AU  - Sawabe T
AU  - Maeda T
AU  - Makita H
AU  - Nemoto S
AU  - Nishimura S
AU  - Watanabe H
AU  - Watsuji T
AU  - Takai K
PT  - Journal Article
TA  - ISME J.
JT  - ISME J.
SO  - ISME J. 2014 8: 40-51.

PMID- 17615243
VI  - 104
DP  - 2007
TI  - Deep-sea vent epsilon-proteobacterial genomes provide insights into emergence of pathogens.
PG  - 12146-12150
AB  - Deep-sea vents are the light-independent, highly productive ecosystems driven primarily by
      chemolithoautotrophic microorganisms, in particular by
      epsilon-Proteobacteria phylogenetically related to important pathogens. We
      analyzed genomes of two deep-sea vent epsilon-Proteobacteria strains,
      Sulfurovum sp. NBC37-1 and Nitratiruptor sp. SB155-2, which provide
      insights not only into their unusual niche on the seafloor, but also into
      the origins of virulence in their pathogenic relatives, Helicobacter and
      Campylobacter species. The deep-sea vent epsilon-proteobacterial genomes
      encode for multiple systems for respiration, sensing and responding to
      environment, and detoxifying heavy metals, reflecting their adaptation to
      the deep-sea vent environment. Although they are nonpathogenic, both
      deep-sea vent epsilon-Proteobacteria share many virulence genes with
      pathogenic epsilon-Proteobacteria, including genes for virulence factor
      MviN, hemolysin, invasion antigen CiaB, and the N-linked glycosylation
      gene cluster. In addition, some virulence determinants (such as the
      H(2)-uptake hydrogenase) and genomic plasticity of the pathogenic
      descendants appear to have roots in deep-sea vent epsilon-Proteobacteria.
      These provide ecological advantages for hydrothermal vent
      epsilon-Proteobacteria who thrive in their deep-sea habitat and are
      essential for both the efficient colonization and persistent infections of
      their pathogenic relatives. Our comparative genomic analysis suggests that
      there are previously unrecognized evolutionary links between important
      human/animal pathogens and their nonpathogenic, symbiotic,
      chemolithoautotrophic deep-sea relatives.
AU  - Nakagawa S
AU  - Takaki Y
AU  - Shimamura S
AU  - Reysenbach AL
AU  - Takai K
AU  - Horikoshi K
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2007 104: 12146-12150.

PMID- Not carried by PubMed...
VI  - 40
DP  - 1996
TI  - Types and uses of restriction enzymes.
PG  - 826-835
AB  - A review (in japanese).
AU  - Nakagawahara K
AU  - Mori M
AU  - Mioka C
PT  - Journal Article
TA  - Rinsho Kensa
JT  - Rinsho Kensa
SO  - Rinsho Kensa 1996 40: 826-835.

PMID- 11805295
VI  - 99
DP  - 2002
TI  - HemK, a class of protein methyl transferase with similarity to DNA methyl transferases, methylates polypeptide chain release factors, and hemK knockout induces defects in translational termination.
PG  - 1473-1478
AB  - HemK, a universally conserved protein of unknown function, has high amino acid similarity with
      DNA-(adenine-N6) methyl transferases (MTases). A certain mutation in hemK gene rescues the
      photosensitive phenotype of a ferrochelatase-deficient (hemH) mutant in Escherichia coli. A
      hemK knockout strain of E. coli not only suffered severe growth defects, but also showed a
      global shift in gene expression to anaerobic respiration, as determined by microarray
      analysis, and this shift may lead to the abrogation of photosensitivity by reducing the
      oxidative stress. Suppressor mutations that abrogated the growth defects of the hemK knockout
      strain were isolated and shown to be caused by a threonine to alanine change at codon 246 of
      polypeptide chain release factor (RF) 2, indicating that hemK plays a role in translational
      termination. Consistent with such a role, the hemK knockout strain showed an enhanced rate of
      read-through of nonsense codons and induction of transfer-mRNA-mediated tagging of proteins
      within the cell. By analysis of the methylation of RF1 and RF2 in vivo and in vitro, we showed
      that HemK methylates RF1 and RF2 in vitro within the tryptic fragment containing the conserved
      GGQ motif, and that hemK is required for the methylation within the same fragment of, at
      least, RF1 in vivo. This is an example of a protein MTase containing the DNA MTase motif and
      also a protein-(glutamine-N5) MTase.
AU  - Nakahigashi K
AU  - Kubo N
AU  - Narita S
AU  - Shimaoka T
AU  - Goto S
AU  - Oshima T
AU  - Mori H
AU  - Maeda M
AU  - Wada C
AU  - Inokuchi H
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2002 99: 1473-1478.

PMID- 27999625
VI  - 11
DP  - 2016
TI  - Genome sequence and overview of Oligoflexus tunisiensis Shr3T in the eighth class Oligoflexia of the phylum Proteobacteria.
PG  - 90
AB  - Oligoflexus tunisiensis Shr3T is the first strain described in the newest (eighth) class
      Oligoflexia of the phylum Proteobacteria. This strain was isolated
      from the 0.2-mum filtrate of a suspension of sand gravels collected in the Sahara
      Desert in the Republic of Tunisia. The genome of O. tunisiensis Shr3T is
      7,569,109 bp long and consists of one scaffold with a 54.3% G + C content. A
      total of 6,463 genes were predicted, comprising 6,406 protein-coding and 57 RNA
      genes. Genome sequence analysis suggested that strain Shr3T had multiple terminal
      oxidases for aerobic respiration and various transporters, including the
      resistance-nodulation-cell division-type efflux pumps. Additionally, gene
      sequences related to the incomplete denitrification pathway lacking the final
      step to reduce nitrous oxide (N2O) to nitrogen gas (N2) were found in the O.
      tunisiensis Shr3T genome. The results presented herein provide insight into the
      metabolic versatility and N2O-producing activity of Oligoflexus species.
AU  - Nakai R
AU  - Fujisawa T
AU  - Nakamura Y
AU  - Baba T
AU  - Nishijima M
AU  - Karray F
AU  - Sayadi S
AU  - Isoda H
AU  - Naganuma T
AU  - Niki H
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 90.

PMID- 27365350
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Aurantimicrobium minutum Type Strain KNCT, a Planktonic Ultramicrobacterium Isolated from River Water.
PG  - e00616-16
AB  - Aurantimicrobium minutum type strain KNC(T) is a planktonic ultramicrobacterium isolated from
      river water in western Japan. Strain KNC(T) has an extremely small, streamlined genome of
      1,622,386 bp comprising 1,575 protein-coding sequences. The genome annotation suggests that
      strain KNC(T) has an actinorhodopsin-based photometabolism.
AU  - Nakai R
AU  - Fujisawa T
AU  - Nakamura Y
AU  - Nishide H
AU  - Uchiyama I
AU  - Baba T
AU  - Toyoda A
AU  - Fujiyama A
AU  - Naganuma T
AU  - Niki H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00616-16.

PMID- 
VI  - 63
DP  - 2013
TI  - Molecular identification and characterization of type III restriction-modification (R-M) gene cluster in Campylobacter lari.
PG  - 1629-1637
AB  - Although the human clinical strain of Campylobacter lari (RM2100) has been shown not to carry
      any type III restriction-modification (R-M) systems, an R-M genes cluster was identified
      downstream of the full-length cytolethal distending toxin gene operon in the urease-positive
      thermophilic Campylobacter (UPTC) CF89-12 strain. Two possible open reading frames (ORFs) for
      restriction endonuclease and methyltransferase were predicted to encode peptides of 947 and
      613 amino acid residues with calculated mo ecular weights of 111 and 70.8 kDa, respectively.
      Two putative promoters consisting of the consensus sequences and two probable ribosome binding
      sites for the two ORFs were also identified. Reverse transcription PCR identified
      co-transcription of the R-M genes in the cells. The existence of an S-adenosyl
      methionine-binding motif in the N-terminal conserved region of the possible ORF for the M
      gene, and seven conserved helicase motifs in the R gene were also identified. PCR and Southern
      blot hybridization a nalyses for type III R-M enzyme genes with some of the C. lari isolates
      including UPTC gave positive signals. UPTC isolates were shown to carry type III R-M enzyme
      genes, with a relatively high frequency.
AU  - Nakajima T
AU  - Matsubara K
AU  - Ueno H
AU  - Kagawa S
AU  - Moore JE
AU  - Millar BC
AU  - Matsuda M
PT  - Journal Article
TA  - Ann. Microbiol. (Paris)
JT  - Ann. Microbiol. (Paris)
SO  - Ann. Microbiol. (Paris) 2013 63: 1629-1637.

PMID- 28360156
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Tersicoccus phoenicis DSM 30849T, Isolated from a Cleanroom for Spacecraft Assembly, and Tersicoccus sp. Strain Bi-70, Isolated  from a Freshwater Lake.
PG  - e00079-17
AB  - Here, we report the draft genome sequences of Tersicoccus phoenicis DSM 30849T, isolated from
      a spacecraft assembly cleanroom at the National Aeronautics and
      Space Administration (NASA), and Tersicoccus sp. strain Bi-70, isolated from Lake
      Biwa, the largest lake in Japan. These genome sequences facilitate our
      understanding of the adaptation of these closely related strains to different
      habitats.
AU  - Nakajima Y
AU  - Yoshizawa S
AU  - Nakamura K
AU  - Ogura Y
AU  - Hayashi T
AU  - Kogure K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00079-17.

PMID- 28935744
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Rubricoccus marinus SG-29T, a Marine Bacterium within the Family Rhodothermaceae, Which Contains Two Different Rhodopsin Genes.
PG  - e00990-17
AB  - Here, we report the draft genome sequence of Rubricoccus marinus SG-29T, a bacterium isolated
      from the western North Pacific Ocean. R. marinus SG-29T
      possesses two different types of rhodopsin genes and belongs to the family
      Rhodothermaceae, with which halophilic, thermophilic, and marine bacteria are
      associated.
AU  - Nakajima Y
AU  - Yoshizawa S
AU  - Park S
AU  - Kumagai Y
AU  - Wong SK
AU  - Ogura Y
AU  - Hayashi T
AU  - Kogure K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00990-17.

PMID- 3027659
VI  - 14
DP  - 1986
TI  - Inhibition of restriction endonuclease NciI cleavage by phosphorothioate groups and its application to oligonucleotide-directed mutagenesis.
PG  - 9679-9698
AB  - M13 RF IV DNA where phosphorothioate groups are incorporated at restriction
      endonuclease NciI recognition sites in the (-)strand is efficiently nicked by
      the action of this enzyme.  Incubation of such nicked DNA with exonuclease III
      produces gapped DNA.  The gap can be filled by reaction with deoxynucleoside
      triphosphates and DNA polymerase I.  When this sequence of reactions is
      performed with DNA containing a mismatch oligonucleotide primer in the
      (-)-strand mutational frequencies of 70 - 90% can be obtained upon
      transformation.  The general nature of this methodology has been further shown
      to be applicable to other restriction enzymes such as HindII, PstI and FspI.
      The mutational frequency obtained using these enzymes is between 40 - 80%
      mainly because of less efficient nicking and gapping.  Studies on inhibition of
      NciI cleavage show that in addition to a phosphorothioate group at the position
      of cleavage an additional group in the 5'-neighbouring position is necessary
      for complete inhibition.
AU  - Nakamaye KL
AU  - Eckstein F
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1986 14: 9679-9698.

PMID- 11473387
VI  - 38
DP  - 2001
TI  - Characteristics of mutations generated through digestion with restriction enzyme and ligation in plasmid DNA.
PG  - 46-54
AB  - Recently, the use of restriction enzymes has been extended to studies in which rare events
      such as mutation and mistakes in DNA repair are
      examined. In these studies, the specificity of restriction enzymes
      becomes critical. To clarify the nature of the rare unexpected events
      occurring in the process of cutting of DNA with restriction enzymes
      then ligating it, we studied the molecular characteristics of
      unexpected plasmid DNAs that were retrieved as mutants of the plasmid
      after transfection to E. coli. The plasmid used was pUR288, containing
      lacZ as a marker of mutation. It was digested with restriction enzymes
      under the conditions recommended by the supplier of the enzymes and
      under the presence of DMSO, which is known to induce star activity of
      the enzymes. Comparisons of mutant frequencies and of nucleotide
      sequences of the mutants found in the different conditions indicated
      that nonspecific endonucleolytic activity similar to that found under
      star activity was present under the recommended conditions and,
      further, was responsible for the creation of deletion-type mutations.
      The frequency of these events ranged from 10^-5 to 10^-3, depending
      on the kind of restriction enzymes analyzed. Although the levels of the
      nonspecificity were not high, they should be considered in assays such
      as mutation and mistakes in DNA repair, where rare events are examined.
AU  - Nakamura S
AU  - Ikehata H
AU  - Ono T
PT  - Journal Article
TA  - Environ. Mol. Mutagen.
JT  - Environ. Mol. Mutagen.
SO  - Environ. Mol. Mutagen. 2001 38: 46-54.

PMID- 
VI  - 17
DP  - 1999
TI  - Atomic force microscope observation of plasmid deoxyribose nucleic acid with restriction enzyme.
PG  - 288-293
AB  - We have observed plasmid deoxyribose nucleic acid, in real space images, before and after
      treating with restriction enzyme (PvuII or HincII) using an atomic force microscope.  The
      enzyme is recognized on DNA even in the absence of Mg2+ ions.  In the presence of Mg2+, on the
      other hand, direct evidence was obtained that the enzyme could bind to circular plasmid DNA
      without cutting and cleaved it at the site corresponding to the specificity.  Lengths of the
      DNA fragments observed by AFM were consistent with the values estimated by agarose gel
      electrophoresis.  In addition, as substrates for the AFM observation, rutile TiO2(110) single
      crystal surface was found to be effective in expanding and fixing the DNA molecules as
      straight chains along the stepped surface.
AU  - Nakamura T
AU  - Maeda Y
AU  - Oka T
AU  - Tabata H
AU  - Futai M
AU  - Kawai T
PT  - Journal Article
TA  - J. Vac. Sci. Technol. B
JT  - J. Vac. Sci. Technol. B
SO  - J. Vac. Sci. Technol. B 1999 17: 288-293.

PMID- 14621292
VI  - 10
DP  - 2003
TI  - Complete genome structure of Gloeobacter violaceus PCC 7421, a cyanobacterium that lacks thylakoids.
PG  - 137-145
AB  - The nucleotide sequence of the entire genome of a cyanobacterium Gloeobacter violaceus PCC
      7421 was determined. The genome of G. violaceus
      was a single circular chromosome 4,659,019 bp long with an average GC
      content of 62%. No plasmid was detected. The chromosome comprises 4430
      potential protein-encoding genes, one set of rRNA genes, 45 tRNA genes
      representing 44 tRNA species and genes for tmRNA, B subunit of RNase P,
      SRP RNA and 6Sa RNA. Forty-one percent of the potential protein-encoding
      genes showed sequence similarity to genes of known function, 37% to
      hypothetical genes, and the remaining 22% had no apparent similarity to
      reported genes. Comparison of the assigned gene components with those of
      other cyanobacteria has unveiled distinctive features of the G. violaceus
      genome. Genes for PsaI, PsaJ, PsaK, and PsaX for Photosystem I and PsbY,
      PsbZ and Psb27 for Photosystem II were missing, and those for PsaF, PsbO,
      PsbU, and PsbV were poorly conserved. cpcG for a rod core linker peptide
      for phycobilisomes and nblA related to the degradation of phycobilisomes
      were also missing. Potential signal peptides of the presumptive products
      of petJ and petE for soluble electron transfer catalysts were less
      conserved than the remaining portions. These observations may be related
      to the fact that photosynthesis in G. violaceus takes place not in
      thylakoid membranes but in the cytoplasmic membrane. A large number of
      genes for sigma factors and transcription factors in the LuxR, LysR, PadR,
      TetR, and MarR families could be identified, while those for major
      elements for circadian clock, kaiABC were not found. These differences may
      reflect the phylogenetic distance between G. violaceus and other
      cyanobacteria.
AU  - Nakamura Y et al
PT  - Journal Article
TA  - DNA Res.
JT  - DNA Res.
SO  - DNA Res. 2003 10: 137-145.

PMID- 12240836
VI  - 9
DP  - 2002
TI  - Complete genome structure of the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 (supplement).
PG  - 135-148
AB  - none
AU  - Nakamura Y et al
PT  - Journal Article
TA  - DNA Res.
JT  - DNA Res.
SO  - DNA Res. 2002 9: 135-148.

PMID- 12240834
VI  - 9
DP  - 2002
TI  - Complete genome structure of the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1.
PG  - 123-130
AB  - The entire genome of a thermophilic unicellular cyanobacterium, Thermosynechococcus elongatus
      BP-1, was sequenced. The genome consisted of a circular chromosome 2,593,857 bp long, and no
      plasmid was detected. A total of 2475 potential protein-encoding genes, one set of rRNA genes,
      42 tRNA genes representing 42 tRNA species and 4 genes for small structural RNAs were assigned
      to the chromosome by similarity search and computer prediction. The translated products of 56%
      of the potential protein-encoding genes showed sequence similarity to experimentally
      identified and predicted proteins of known function, and the products of 34% of these genes
      showed sequence similarity to the translated products of hypothetical genes. The remaining 10%
      lacked significant similarity to genes for predicted proteins in the public DNA databases.
      Sixty-three percent of the T. elongatus genes showed significant sequence similarity to those
      of both Synechocystis sp. PCC 6803 and Anabaena sp. PCC 7120, while 22% of the genes were
      unique to this species, indicating a high degree of divergence of the gene information among
      cyanobacterial strains. The lack of genes for typical fatty acid desaturases and the presence
      of more genes for heat-shock proteins in comparison with other mesophilic cyanobacteria may be
      genomic features of thermophilic strains. A remarkable feature of the genome is the presence
      of 28 copies of group II introns, 8 of which contained a presumptive gene for maturase/reverse
      transcriptase. A trace of genome rearrangement mediated by the group II introns was also
      observed.
AU  - Nakamura Y et al
PT  - Journal Article
TA  - DNA Res.
JT  - DNA Res.
SO  - DNA Res. 2002 9: 123-130.

PMID- 25395639
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Marine Flavobacterium Nonlabens Strains NR17, NR24, NR27, NR32, NR33, and Ara13.
PG  - e01165-14
AB  - Here, we present the draft genome sequences of six carotenoid producers affiliated with
      Nonlabens spp. isolated from marine environments in both the
      northern and southern parts of Japan. The genomic information will help to
      elucidate the function and evolution of carotenoid synthetic gene clusters not
      only in the genus Nonlabens but also in the family Flavobacteriaceae.
AU  - Nakanishi M
AU  - Meirelles P
AU  - Suzuki R
AU  - Takatani N
AU  - Mino S
AU  - Suda W
AU  - Oshima K
AU  - Hattori M
AU  - Ohkuma M
AU  - Hosokawa M
AU  - Miyashita K
AU  - Thompson FL
AU  - Niwa A
AU  - Sawabe T
AU  - Sawabe T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01165-14.

PMID- 21294449
VI  - 67
DP  - 2010
TI  - Molecular and comparative analyses of the full-length cytolethal distending toxin (cdt) gene operon and its adjacent genetic loci from urease-positive thermophilic  Campylobacter (UPTC) organisms.
PG  - 208-215
AB  - Molecular and comparative analyses of the full-length cytolethal distending toxin (cdt) gene
      operon and its adjacent genetic loci (2.7-9.4 kilo base pairs in
      length) are carried out with 12 urease-positive thermophilic Campylobacter (UPTC)
      isolates using several polymerase chain reaction (PCR) primer pairs. Three
      putative open reading frames (ORFs) for cdtA, cdtB and cdtC, two putative
      promoters and a hypothetically intrinsic rho-independent transcription terminator
      were identified in all the operons of the 12 UPTC isolates examined. Although the
      number of amino acid residues slightly varied for the putative cdtA and cdtC
      ORFs, those for the cdtB were similar among all the UPTC isolates, as well as the
      six urease-negative (UN) C. lari examined previously. Regarding the cdt genes in
      UPTC CF89-12, each ORF commenced with an ATG start codon and terminated with a
      TAG stop codon for cdtA and cdtB and a TAA for cdtC. Start and stop codons of the
      three ORFs for the other 11 UPTC isolates were identical to those from the UPTC
      CF89-12 isolate except for the TTG start codon for cdtC in the two isolates
      (NCTC12892 and 12893) and the TGA stop codon for cdtA in five isolates (A1, A2,
      A3, 89049 and 92251). Two putative promoter structures, consisting of sequences
      at the -35-like (TTAATA) and -10-like (TATTAA) regions, as well as the start
      codon (ATG), were identified for the transcriptional promoter, immediately
      upstream of the cdtA gene in all the 12 isolates, Although the genetic
      heterogeneity of the cdtB gene locus occurred in all 28 C. lari isolates (n = 16
      UN C. lari; n = 12 UPTC) examined, all nine amino acid-specific DNase residues
      were completely conserved in all their cdtB genes. Variable gene insertions with
      heterogeneous order and combinations occurred between cdtC and lpxB genes in the
      all UPTC organisms examined.
AU  - Nakanishi S
AU  - Tazumi A
AU  - Moore JE
AU  - Millar BC
AU  - Matsuda M
PT  - Journal Article
TA  - Br. J. Biomed. Sci.
JT  - Br. J. Biomed. Sci.
SO  - Br. J. Biomed. Sci. 2010 67: 208-215.

PMID- 27587811
VI  - 4
DP  - 2016
TI  - First Complete Genome Sequence of the Skin-Improving Lactobacillus curvatus Strain FBA2, Isolated from Fermented Vegetables, Determined by PacBio  Single-Molecule Real-Time Technology.
PG  - e00884-16
AB  - The first complete genome sequence of Lactobacillus curvatus was determined by PacBio RS II.
      The single circular chromosome (1,848,756 bp, G+C content of 42.1%)
      of L. curvatus FBA2, isolated from fermented vegetables, contained low G+C
      regions (26.9% minimum) and 43 sets of >1,000-bp identical sequence pairs. No
      plasmids were detected.
AU  - Nakano K et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00884-16.

PMID- 29472335
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Lactococcus lactis subsp. lactis G50 with Immunostimulating Activity, Isolated from Napier Grass.
PG  - e00069-18
AB  - Lactococcus lactis subsp. lactis G50 is a strain with immunostimulating activity, isolated
      from Napier grass (Pennisetum purpureum). We determined the complete
      genome sequence of this strain using the PacBio RS II platform. The single
      circular chromosome consists of 2,346,663 bp, with 35.03% G+C content and no
      plasmids.
AU  - Nakano K
AU  - Minami M
AU  - Shinzato M
AU  - Shimoji M
AU  - Ashimine N
AU  - Shiroma A
AU  - Ohki S
AU  - Nakanishi T
AU  - Tamotsu H
AU  - Teruya K
AU  - Satou K
AU  - Moriya N
AU  - Kimoto-Nira H
AU  - Kobayashi M
AU  - Hagi T
AU  - Nomura M
AU  - Suzuki C
AU  - Hirano T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00069-18.

PMID- 26294631
VI  - 3
DP  - 2015
TI  - First Complete Genome Sequence of Pseudomonas aeruginosa (Schroeter 1872) Migula  1900 (DSM 50071T), Determined Using PacBio Single-Molecule Real-Time Technology.
PG  - e00932-15
AB  - The first complete genome sequence of the type strain Pseudomonas aeruginosa (Schroeter 1872)
      Migula 1900 (DSM 50071(T)) was determined in a single contig by
      PacBio RS II. The genome (6,317,050 bp, G+C content of 66.52%) contained 10 sets
      of >1,000-bp identical sequence pairs and 183 tandem repeats.
AU  - Nakano K
AU  - Terabayashi Y
AU  - Shiroma A
AU  - Shimoji M
AU  - Tamotsu H
AU  - Ashimine N
AU  - Ohki S
AU  - Shinzato M
AU  - Teruya K
AU  - Satou K
AU  - Hirano T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00932-15.

PMID- 26227598
VI  - 3
DP  - 2015
TI  - First Complete Genome Sequence of Clostridium sporogenes DSM 795T, a Nontoxigenic Surrogate for Clostridium botulinum, Determined Using PacBio Single-Molecule  Real-Time Technology.
PG  - e00832-15
AB  - The first complete genome sequence of Clostridium sporogenes DSM 795(T), a nontoxigenic
      surrogate for Clostridium botulinum, was determined in a single
      contig using the PacBio single-molecule real-time technology. The genome
      (4,142,990 bp; G+C content, 27.98%) included 86 sets of >1,000-bp identical
      sequence pairs and 380 tandem repeats.
AU  - Nakano K
AU  - Terabayashi Y
AU  - Shiroma A
AU  - Shimoji M
AU  - Tamotsu H
AU  - Ashimine N
AU  - Ohki S
AU  - Shinzato M
AU  - Teruya K
AU  - Satou K
AU  - Hirano T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00832-15.

PMID- 10845458
VI  - 41
DP  - 2000
TI  - A tobacco NtMET1 cDNA encoding a DNA methyltransferase: Molecular characterization and abnormal phenotypes of transgenic tobacco plants.
PG  - 448-457
AB  - A cDNA encoding a DNA methyltransferase, with a predicted polypeptide of 1556 amino acid
      residues containing all motifs conserved in this
      enzyme family, was isolated from tobacco plants, and the corresponding
      gene was designated as NtMET1, RNA blot analysis indicated NtMET1
      transcripts to accumulate in dividing tissues of tobacco plants, and
      they could be detected during the S phase in synchronized dividing BY2
      cells. In situ hybridization revealed the transcripts to be localized
      exclusively in actively proliferating tissues around axillary apical
      meristem. In order to ascertain physiological roles, transgenic tobacco
      plants that had the antisense construct were made and examined for
      phenotypes. Methylation levels of genomic DNA from transgenic plants
      significantly decreased in comparison with wild-type levels, and
      distinct phenotypic changes including small leaves, short internodes
      and abnormal flower morphology were noted. Microscopic observation
      revealed that leaf structure differed between transgenic and wild-type
      plants. These results suggest that NtMET1 functions during DNA
      replication, and that DNA methylation plays an important role in plant
      morphogenesis.
AU  - Nakano Y
AU  - Steward N
AU  - Sekine M
AU  - Kusano T
AU  - Sano H
PT  - Journal Article
TA  - Plant Cell Physiol.
JT  - Plant Cell Physiol.
SO  - Plant Cell Physiol. 2000 41: 448-457.

PMID- 
VI  - 12
DP  - 2001
TI  - Relation between restriction modification genes and genome rearrangements suggested from genome sequence comparison within genus  Neisseria.
PG  - 398-399
AB  - Restriction-modification gene complexes, such as EcoRI, encode two enzymatic functions,
      restriction and modification.  A restriction enzyme will recognize a specific sequence in DNA
      and cut the DNA unless it is methylated by a cognate modification enzyme.  RM systems will
      defend bacterial cells by attacking incoming foreign DNA.  It is widely held that bacteria
      have evolved RM systems and maintain them in order to protect their genome from invasion by
      foreign DNA such as bacteriophages and plasmids.
AU  - Nakao K
AU  - Chinen A
AU  - Nobusato A
AU  - Fujitani Y
AU  - Uchiyama I
AU  - Kobayashi I
PT  - Journal Article
TA  - Genome Inf. Ser.
JT  - Genome Inf. Ser.
SO  - Genome Inf. Ser. 2001 12: 398-399.

PMID- 27313287
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Three Strains of Ehrlichia ruminantium, a Tick-Borne Pathogen of Ruminants, Isolated from Zimbabwe, The Gambia, and Ghana.
PG  - e00453-16
AB  - The rickettsial bacterium Ehrlichia ruminantium is the causative pathogen of heartwater in
      ruminants. Here, we report the draft genome sequences of three
      strains of E. ruminantium, namely, the Crystal Springs strain from Zimbabwe, the
      Kerr Seringe strain from The Gambia, and the Sankat 430 strain from Ghana.
AU  - Nakao R
AU  - Jongejan F
AU  - Sugimoto C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00453-16.

PMID- 29599160
VI  - 6
DP  - 2018
TI  - Whole-Genome Sequence of Acetobacter orientalis Strain FAN1, Isolated from Caucasian Yogurt.
PG  - e00201-18
AB  - In traditional Caucasian yogurt, Acetobacter orientalis bacteria play important roles in the
      fermentation of milk in concert with Lactococcus bacteria. In this
      study, an A. orientalis strain, FAN1, was newly isolated from commercially
      available Caucasian yogurt, and its whole-genome sequence was determined,
      identifying two circular DNAs.
AU  - Nakashima N
AU  - Tamura T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00201-18.

PMID- 24501649
VI  - 9
DP  - 2013
TI  - Complete genome sequence of Arthrobacter sp. strain FB24.
PG  - 106-116
AB  - Arthrobacter sp. strain FB24 is a species in the genus Arthrobacter Conn and Dimmick 1947, in
      the family Micrococcaceae and class Actinobacteria. A number of
      Arthrobacter genome sequences have been completed because of their important role
      in soil, especially bioremediation. This isolate is of special interest because
      it is tolerant to multiple metals and it is extremely resistant to elevated
      concentrations of chromate. The genome consists of a 4,698,945 bp circular
      chromosome and three plasmids (96,488, 115,507, and 159,536 bp, a total of
      5,070,478 bp), coding 4,536 proteins of which 1,257 are without known function.
      This genome was sequenced as part of the DOE Joint Genome Institute Program.
AU  - Nakatsu CH
AU  - Barabote R
AU  - Thompson S
AU  - Bruce D
AU  - Detter C
AU  - Brettin T
AU  - Han C
AU  - Beasley F
AU  - Chen W
AU  - Konopka A
AU  - Xie G
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 9: 106-116.

PMID- 12782309
VI  - 544
DP  - 2003
TI  - An archaeal homing endonuclease I-PogI cleaves at the insertion site of the neighboring intron, which has no nested open reading frame.
PG  - 165-170
AB  - Homing endonucleases (HEs) of the LAGLIDADG family cleave intron/inteinless cognate DNA at, or
      near, the insertion site (IS) of
      their own intron/intein. Here, we describe a notable exception to this
      rule. Two introns, Pog.S1205 (length 32 bp) and Pog.S1213 (664 bp), whose
      ISs are 8 bp apart, exist within the 16S rRNA gene of the archaeon
      Pyrobaculum oguniense. Pog.S1213 harbors a nested open reading frame (ORF)
      encoding a 22 kDa monomeric protein, I-PogI, which contains two LAGLIDADG
      motifs and has optimal DNA cleavage activity at 90 degrees C.
      Intriguingly, I-PogI cleaves the Pog.S1205-less substrate DNA in the
      presence or absence of Pog.S1213. The cleavage site (CS) of I-PogI does
      not coincide with the IS of Pog.S1213 but with that of Pog.S1205. Thus,
      I-PogI activity both promotes the homing of its own intron, Pog.S1213, and
      guarantees co-conversion of the ORF-less intron Pog.S1205.
AU  - Nakayama H
AU  - Morinaga Y
AU  - Nomura N
AU  - Nunoura T
AU  - Sako Y
AU  - Uchida A
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 2003 544: 165-170.

PMID- 17069851
VI  - 365
DP  - 2007
TI  - Structure of a hyperthermophilic archaeal homing endonuclease, I-Tsp061I: Contribution of cross-domain polar networks to thermostability.
PG  - 362-378
AB  - A novel LAGLIDADG-type homing endonuclease (HEase), I-TspO61I, from the hyperthermophilic
      archaeon Thermoproteus sp. IC-061 16 S rRNA gene
      (rDNA) intron was characterized with respect to its structure,
      catalytic properties and thermostability. It was found that I-Tsp061I
      is a HEase isoschizomer of the previously described I-PogI and exhibits
      the highest thermostability among the known LAGLIDADG-type HEases.
      Determination of the crystal structure of I-Tsp061I at 2.1 A resolution
      using the multiple isomorphous replacement and anomalous scattering
      method revealed that the overall fold is similar to that of other known
      LAGLIDADG-type HEases, despite little sequence similarity between
      I-TspO61I and those HEases. However, I-Tsp061I contains important
      cross-domain polar networks, unlike its mesophilic counterparts.
      Notably, the polar network Tyr6-Asp104-His180-107O-HOH12-104O-Asn177
      exists across the two packed a-helices containing both the LAGLIDADG
      catalytic motif and the GxxxG hydrophobic helix bundle motif. Another
      important structural feature is the salt-bridge network
      Asp29-Arg31-GIu182 across N and C-terminal domain interface, which
      appears to contribute to the stability of the domain/domain packing. On
      the basis of these structural analyses and extensive mutational
      studies, we conclude that such cross-domain polar networks play key
      roles in stabilizing the catalytic center and domain packing, and
      underlie the hyperthermostability of T-Tsp061I.
AU  - Nakayama H
AU  - Shimamura T
AU  - Imagawa T
AU  - Shirai N
AU  - Itoh T
AU  - Sako Y
AU  - Miyano M
AU  - Sakuraba H
AU  - Ohshima T
AU  - Nomura N
AU  - Tsuge H
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2007 365: 362-378.

PMID- 17668112
VI  - 6
DP  - 2007
TI  - Monitoring of three distinct structures of restriction enzyme complexes using characteristic fluorescence from site-selectively incorporated solvatochromic probe.
PG  - 836-841
AB  - The local change in the three different structures of restriction enzyme BamHI, which include
      DNA-free dimer and non-specific and
      specific complexes with DNA, were detected by the fluorescence from a
      site-selectively introduced solvatochromic fluorophore
      N-beta-L-alanyl-5-(N,N-dimethylamino)naphthalene-1-sulfonamide
      (DanAla). According to the crystal structure, alpha-helices of the
      non-specific complex containing Ile82, Glu86 and Trp206 residues are
      converted into random coil by the formation of specific complex with a
      substrate. To understand the microenvironmental change caused by the
      structural transition around these positions, the DanAla probe was
      site-specifically introduced into the positions, and steady-state and
      time-resolved fluorescence was observed. The steady-state fluorescence
      gave us information that the rigidity of the polypeptide chains would
      be enhanced by the formation of the specific complex. The time-resolved
      fluorescence supported that the change in a water molecule-accessible
      space was induced by DNA-binding. We revealed that the change in
      rigidity and solvation around the specific positions was detected by
      the characteristic fluorescence using the combination of steady-state
      and time-resolved fluorescence techniques.
AU  - Nakayama K
AU  - Endo M
AU  - Fujitsuka M
AU  - Majima T
PT  - Journal Article
TA  - Photochem. Photobiolog.
JT  - Photochem. Photobiolog.
SO  - Photochem. Photobiolog. 2007 6: 836-841.

PMID- 
VI  - 229
DP  - 2005
TI  - Photochemical regulation of the activity of a restriction enzyme BamHI using an azobenzene moiety incorporated into the dimer interface.
PG  - U399-U400
AB  - We describe the control of enzymatic activity by photochemical regulation of protein-protein
      interaction.  Restriction enzyme BamHI has a typical dimer interface with salt-bridge network
      and need the dimer formation to show the activity.  Using this enzyme, we designed the
      photochemically controllable BamHI, which has a photofunctional molecule in the dimer
      interface for inactivation, and initiates the activity with photoirradiation (366 nm).
      Photoisomerizable trans-phenylazophenylalanine (trans-azoAla) was site-selectively introduced
      at 132 position in the dimer interface.  The photofunctional BamHI showed no activity, and the
      following photoisomerization induced the activity.  These results suggest that, the bulky
      trans-azoAla may induce the misalignment of the two BamHI monomers as an inactive dimer form,
      while the compact cis-azoAla may allow the specific hydrogen bondings in the dimer interface
      as similar to the wild-type BamHI.  By employing the phosoisomerization of azoAla residue, we
      have successfully constructed photofunctional BamHI which is activated by photoirradiation.
AU  - Nakayama K
AU  - Endo M
AU  - Majima T
PT  - Journal Article
TA  - ACS Abstracts
JT  - ACS Abstracts
SO  - ACS Abstracts 2005 229: U399-U400.

PMID- 16287231
VI  - 16
DP  - 2005
TI  - A hydrophilic azobenzene-bearing amino acid for photochemical control of a restriction enzyme BamHI.
PG  - 1360-1366
AB  - A novel hydrophilic and negatively charged azobenzene-bearing amino acid,
      4'-carboxyphenylazophenylalanine (azoAla 1), has been designed
      and synthesized for investigation of the photochemical regulation of
      the enzyme activity. The properties of photoisomerization and thermal
      stability of the cis-isomer were similar to those of a commonly used
      phenylazophenylalanine (azoAla 2). For photochemical control of the
      enzyme, these two azobenzene-bearing amino acids were incorporated into
      the specific position at the dimer interface of a restriction enzyme
      BamHI. These trans-azobenzene derivatives in the BamHI suppressed the
      enzymatic activity, and the following photoirradiation at 366 nm
      induced the recovery of its activity. Although the activities of both
      azoAla-BamHI mutants were same level after a long time irradiation, the
      recovery of the activity of azoAla 1-BamHI was faster than that of
      azoAla 2-BamHI with a short time irradiation. This result suggests that
      the negatively charged carboxylate group introduced into an azobenzene
      moiety affects the behavior of azoAla in the protein scaffold during
      the trans-cis photoisomerization.
AU  - Nakayama K
AU  - Endo M
AU  - Majima T
PT  - Journal Article
TA  - Bioconjugate Chem.
JT  - Bioconjugate Chem.
SO  - Bioconjugate Chem. 2005 16: 1360-1366.

PMID- 18508905
VI  - 15
DP  - 2008
TI  - The Whole-genome Sequencing of the Obligate Intracellular Bacterium Orientia tsutsugamushi Revealed Massive Gene Amplification During  Reductive Genome Evolution.
PG  - 185-199
AB  - Scrub typhus ('Tsutsugamushi' disease in Japanese) is a mite-borne infectious disease. The
      causative agent is Orientia tsutsugamushi, an
      obligate intracellular bacterium belonging to the family Rickettsiaceae of
      the subdivision alpha-Proteobacteria. In this study, we determined the
      complete genome sequence of O. tsutsugamushi strain Ikeda, which comprises
      a single chromosome of 2 008 987 bp and contains 1967 protein coding
      sequences (CDSs). The chromosome is much larger than those of other
      members of Rickettsiaceae, and 46.7% of the sequence was occupied by
      repetitive sequences derived from an integrative and conjugative element,
      10 types of transposable elements, and seven types of short repeats of
      unknown origins. The massive amplification and degradation of these
      elements have generated a huge number of repeated genes (1196 CDSs,
      categorized into 85 families), many of which are pseudogenes (766 CDSs),
      and also induced intensive genome shuffling. By comparing the gene content
      with those of other family members of Rickettsiacea, we identified the
      core gene set of the family Rickettsiaceae and found that, while much more
      extensive gene loss has taken place among the housekeeping genes of
      Orientia than those of Rickettsia, O. tsutsugamushi has acquired a large
      number of foreign genes. The O. tsutsugamushi genome sequence is thus a
      prominent example of the high plasticity of bacterial genomes, and
      provides the genetic basis for a better understanding of the biology of O.
      tsutsugamushi and the pathogenesis of 'Tsutsugamushi' disease.
AU  - Nakayama K
AU  - Yamashita A
AU  - Kurokawa K
AU  - Morimoto T
AU  - Ogawa M
AU  - Fukuhara M
AU  - Urakami H
AU  - Ohnishi M
AU  - Uchiyama I
AU  - Ogura Y
AU  - Ooka T
AU  - Oshima K
AU  - Tamura A
AU  - Hattori M
AU  - Hayashi T
PT  - Journal Article
TA  - DNA Res.
JT  - DNA Res.
SO  - DNA Res. 2008 15: 185-199.

PMID- 29026213
VI  - 7
DP  - 2017
TI  - Genomic divergence within non-photosynthetic cyanobacterial endosymbionts in rhopalodiacean diatoms.
PG  - 13075
AB  - Organelle acquisitions via endosymbioses with prokaryotes were milestones in the
      evolution of eukaryotes. Still, quite a few uncertainties have remained for the
      evolution in the early stage of organellogenesis. In this respect, rhopalodiacean
      diatoms and their obligate cyanobacterial endosymbionts, called spheroid bodies,
      are emerging as new models for the study of organellogenesis. The genome for the
      spheroid body of Epithemia turgida, a rhopalodiacean diatom, has unveiled its
      unique metabolic nature lacking the photosynthetic ability. Nevertheless, the
      genome sequence of a spheroid body from a single lineage may not be sufficient to
      depict the evolution of these cyanobacterium-derived intracellular structures as
      a whole. Here, we report on the complete genome for the spheroid body of
      Rhopalodia gibberula, a lineage distinct from E. turgida, of which genome has
      been fully determined. Overall, features in genome structure and metabolic
      capacity, including a lack of photosynthetic ability, were highly conserved
      between the two spheroid bodies. However, our comparative genomic analyses
      revealed that the genome of the R. gibberula spheroid body exhibits a lower
      non-synonymous substitution rate and a slower progression of pseudogenisation
      than those of E. turgida, suggesting that a certain degree of diversity exists
      amongst the genomes of obligate endosymbionts in unicellular eukaryotes.
AU  - Nakayama T
AU  - Inagaki Y
PT  - Journal Article
TA  - Sci. Rep.
JT  - Sci. Rep.
SO  - Sci. Rep. 2017 7: 13075.

PMID- 25049384
VI  - 111
DP  - 2014
TI  - Complete genome of a nonphotosynthetic cyanobacterium in a diatom reveals recent adaptations to an intracellular lifestyle.
PG  - 11407-11412
AB  - The evolution of mitochondria and plastids from bacterial endosymbionts were key
      events in the origin and diversification of eukaryotic cells. Although the
      ancient nature of these organelles makes it difficult to understand the earliest
      events that led to their establishment, the study of eukaryotic cells with
      recently evolved obligate endosymbiotic bacteria has the potential to provide
      important insight into the transformation of endosymbionts into organelles.
      Diatoms belonging to the family Rhopalodiaceae and their endosymbionts of
      cyanobacterial origin (i.e., "spheroid bodies") are emerging as a useful model
      system in this regard. The spheroid bodies, which appear to enable rhopalodiacean
      diatoms to use gaseous nitrogen, became established after the divergence of
      extant diatom families. Here we report what is, to our knowledge, the first
      complete genome sequence of a spheroid body, that of the rhopalodiacean diatom
      Epithemia turgida. The E. turgida spheroid body (EtSB) genome was found to
      possess a gene set for nitrogen fixation, as anticipated, but is reduced in size
      and gene repertoire compared with the genomes of their closest known free-living
      relatives. The presence of numerous pseudogenes in the EtSB genome suggests that
      genome reduction is ongoing. Most strikingly, our genomic data convincingly show
      that the EtSB has lost photosynthetic ability and is metabolically dependent on
      its host cell, unprecedented characteristics among cyanobacteria, and
      cyanobacterial symbionts. The diatom-spheroid body endosymbiosis is thus a unique
      system for investigating the processes underlying the integration of a bacterial
      endosymbiont into eukaryotic cells.
AU  - Nakayama T
AU  - Kamikawa R
AU  - Tanifuji G
AU  - Kashiyama Y
AU  - Ohkouchi N
AU  - Archibald JM
AU  - Inagaki Y
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2014 111: 11407-11412.

PMID- 9600985
VI  - 95
DP  - 1998
TI  - Restriction-modification gene complexes as selfish gene entities: roles of a regulatory system in their establishment, maintenance, and apoptotic mutual exclusion.
PG  - 6442-6447
AB  - We have reported some type II restriction-modification gene complexes on plasmids resist
      displacement by an incompatible plasmid through postsegregational host killing.  Such selfish
      behavior may have contributed to the spread and maintenance of RM systems.  Here we analyze
      the role of regulatory genes, often found linked to RM gene complexes, in their interaction
      with the host and the other RM gene complexes.  We identified the C gene of EcoRV as a
      positive regulator of restriction.  A C mutation eliminated postsegregational killing by
      EcoRV.  The C system has been proposed to allow establishment of RM systems in new hosts by
      delaying the appearance of restriction activity.  Consistent with this proposal, bacteria
      pre-expressing ecoRVC were transformed at a reduced efficiency by plasmids carrying the EcoRV
      RM gene complex.  Cells carrying the BamHI RM gene complex were transformed at a reduced
      efficiency by a plasmid carrying a PvuII RM gene complex, which shares the same C specificity.
      The reduction most likely was caused by chromosome cleavage at unmodified PvuII sites by
      prematurely expressed PvuII restriction enzyme.  Therefore, association of the C genes of the
      same specificity with RM gene complexes of different sequence specificities can confer on a
      resident RM gene complex the capacity to abort establishment of a second, incoming RM gene
      complex.  This phenomenon, termed "apoptotic mutual exclusion," is reminiscent of suicidal
      defense against virus infection programmed by other selfish elements.  PvuIIC and bamHIC genes
      define one incompatibility group of exclusion whereas ecoRVC gene defines another.
AU  - Nakayama Y
AU  - Kobayashi I
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1998 95: 6442-6447.

PMID- 7883187
VI  - 153
DP  - 1995
TI  - Cloning and sequencing of a previously unidentified gene that is involved in the biosynthesis of heme in Escherichia coli.
PG  - 67-70
AB  - We have isolated a number of porphyrin (Por)-synthesis mutants as light-resistant revertants
      of a light-sensitive strain delta visA (hemH) of Escherichia coli that accumulates protoPor IX
      in the cell.  Among such mutants, we found a double mutant (H103) with mutations in hemA and
      in a new gene downstream of hemA. This new gene, designated hemK, was located at 27 min on the
      linkage map of the E. coli chromosome. By nucleotide (nt) sequencing, it was demonstrated that
      hemK forms part of the hemA-prfA-hemK operon and encodes 225 amino acids that show no
      significant homology to any protein in the standard databases. The mutant strain H103 formed
      small colonies and showed no catalase activity even in the presence of 5-aminolevulinic acid
      (ALA), indicating its inability to catalyze a step in the biosynthesis of heme from ALA. An
      extract of H103 cells has readily detectable ALA dehydratase and porphobilinogen deaminase
      activities. H103 cells carrying a plasmid that included only hemA as an insert accumulated
      protoPor and coproPor, but showed no sensitivity to light, a result that suggests that it may
      be deficient in protoporphyrinogen oxidase activity.
AU  - Nakayashiki T
AU  - Nishimura K
AU  - Inokuchi H
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 153: 67-70.

PMID- 18997032
VI  - 75
DP  - 2009
TI  - Functional Analysis of MmeI from Methanol Utilizer Methylophilus methylotrophus, a Subtype IIC Restriction-Modification Enzyme Related to Type I Enzymes.
PG  - 212-223
AB  - MmeI from Methylophilus methylotrophus belongs to the type II restriction-modification
      enzymes. It recognizes an asymmetric DNA
      sequence, 5'-TCCRAC-3' (R indicates G or A), and cuts both strands at
      fixed positions downstream of the specific site. This particular
      feature has been exploited in transcript profiling of complex genomes
      (using serial analysis of gene expression technology). We have shown
      previously that the endonucleolytic activity of MmeI is strongly
      dependent on the presence of S-adenosyl-L-methionine (J. Nakonieczna,
      J. W. Zmijewski, B. Banecki, and A. J. Podhajska, Mol. Biotechnol. 37:
      127-135, 2007), which puts MmeI in subtype IIG. The same cofactor is
      used by MmeI as a methyl group donor for modification of an adenine in
      the upper strand of the recognition site to N-6-methyladenine. Both
      enzymatic activities reside in a single polypeptide (919 amino acids
      [aa]), which puts MmeI also in subtype IIC of the
      restriction-modification systems. Based on a molecular model, generated
      with the use of bioinformatic tools and validated by site-directed
      mutagenesis, we were able to localize three functional domains in the
      structure of the MmeI enzyme: (i) the N-terminal portion containing the
      endonucleolytic domain with the catalytic Mg2+-binding motif
      D-70-X-9-EXK82, characteristic for the PD-(D/E)XK superfamily of
      nucleases; (ii) a central portion (aa 310 to 610) containing nine
      sequence motifs conserved among N-6-adenine gamma-class DNA
      methyltransferases; (iii) the C-terminal portion (aa 610 to 919)
      containing a putative target recognition domain. Interestingly, all
      three domains showed highest similarity to the corresponding elements
      of type I enzymes rather than to classical type II enzymes. We have
      found that MmeI variants deficient in restriction activity (D70A, E80A,
      and K82A) can bind and methylate specific nucleotide sequence. This
      suggests that domains of MmeI responsible for DNA restriction and
      modification can act independently. Moreover, we have shown that a
      single amino acid residue substitution within the putative target
      recognition domain (S807A) resulted in a MmeI variant with a higher
      endonucleolytic activity than the wild-type enzyme.
AU  - Nakonieczna J
AU  - Kaczorowski T
AU  - Obarska-Kosinska A
AU  - Bujnicki JM
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2009 75: 212-223.

PMID- 17914173
VI  - 37
DP  - 2007
TI  - Binding of MmeI restriction-modification enzyme to its specific recognition sequence is stimulated by S-adenosyl-L-methionine.
PG  - 127-135
AB  - Restriction endonucleases serve as a very good model for studying specific protein-DNA
      interaction. MmeI is a very interesting
      restriction endonuclease, but although it is useful in Serial Analysis
      of Gene Expression, still very little is known about the mechanism of
      its interaction with DNA. MmeI is a unique enzyme as besides cleaving
      DNA it also methylates specific sequence. For endonucleolytic activity
      MmeI requires Mg(II) and S-adenosyl-L-methionine (AdoMet). AdoMet is a
      methyl donor in the methylation reaction, but its requirement for DNA
      cleavage remains unclear. In the present article we investigated MmeI
      interaction with DNA with the use of numerous methods. Our
      electrophoretic mobility shift assay revealed formation of two types of
      specific protein-DNA complexes. We speculate that faster migrating
      complex consists of one protein molecule and one DNA fragment whereas,
      slower migrating complex, which appears in the presence of AdoMet, may
      be a dimer or multimer form of MmeI interacting with specific DNA.
      Additionally, using spectrophotometric measurements we showed that in
      the presence of AdoMet, MmeI protein undergoes conformational changes.
      We think that such change in the enzyme structure, upon addition of
      AdoMet, may enhance its specific binding to DNA. In the absence of
      AdoMet MmeI binds DNA to the much lower extent.
AU  - Nakonieczna J
AU  - Zmijewski JW
AU  - Banecki B
AU  - Podhajska AJ
PT  - Journal Article
TA  - Mol. Biotechnol.
JT  - Mol. Biotechnol.
SO  - Mol. Biotechnol. 2007 37: 127-135.

PMID- 27834698
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Leptospira alstonii Serovar Room22 Strain GWTS #1.
PG  - e01230-16
AB  - We report here the complete genome sequence of Leptospira alstonii serovar Room22 strain GWTS
      #1. This is the first isolate of L. alstonii to be cultured from a
      mammal and in western Europe, and it represents a new serovar of pathogenic
      leptospires.
AU  - Nally JE
AU  - Bayles DO
AU  - Hurley D
AU  - Fanning S
AU  - McMahon BJ
AU  - Arent Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01230-16.

PMID- 21075921
VI  - 193
DP  - 2010
TI  - Genome Sequence of Leuconostoc fallax KCTC 3537.
PG  - 588-589
AB  - Leuconostoc fallax is known to be present during the manufacturing process of kimchi, the
      best-known traditional Korean dish. Here, we present the
      draft genome sequence of the type strain Leuconostoc fallax KCTC 3537
      (1,638,971 bp, with a G+C content of 37.5%), which consists of 30 large
      contigs (>100 bp in size).
AU  - Nam SH
AU  - Choi SH
AU  - Kang A
AU  - Kim DW
AU  - Kim DS
AU  - Kim RN
AU  - Kim A
AU  - Park HS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 193: 588-589.

PMID- 21148735
VI  - 193
DP  - 2011
TI  - Genome Sequence of Lactobacillus coryniformis subsp. coryniformis KCTC 3167.
PG  - 1014-1015
AB  - Lactobacillus coryniformis subsp. coryniformis is known to be present during the manufacturing
      process of kimchi, the best-known traditional Korean dish. Here, we present the draft genome
      sequence of Lactobacillus coryniformis subsp. coryniformis type strain KCTC 3167 (2,964,752
      bp, with a G+C content of 42.8%), which consists of 55 scaffolds.
AU  - Nam SH
AU  - Choi SH
AU  - Kang A
AU  - Kim DW
AU  - Kim DS
AU  - Kim RN
AU  - Kim A
AU  - Park HS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 1014-1015.

PMID- 21257766
VI  - 193
DP  - 2011
TI  - Genome Sequence of Lactobacillus farciminis KCTC 3681.
PG  - 1790-1791
AB  - Lactobacillus farciminis is one of the most prevalent lactic acid bacteria present during the
      manufacturing process of kimchi, the best-known traditional Korean dish. Here, we present the
      draft genome sequence of the type strain Lactobacillus farciminis KCTC 3681 (2,498,309 bp,
      with a G+C content of 36.4%), which consists of 5 scaffolds.
AU  - Nam SH
AU  - Choi SH
AU  - Kang A
AU  - Kim DW
AU  - Kim RN
AU  - Kim A
AU  - Kim DS
AU  - Park HS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 1790-1791.

PMID- 21183665
VI  - 193
DP  - 2010
TI  - Genome Sequence of Lactobacillus animalis KCTC 3501.
PG  - 1280-1281
AB  - Lactobacillus animalis is one of the most prevalent lactic acid bacteria present during the
      manufacturing process of kimchi, the best-known traditional Korean dish. Here, we present the
      draft genome sequence of the type strain Lactobacillus animalis KCTC 3501 (1,882,795 bp, with
      a G+C content of 41.1%), which consists of 7 scaffolds.
AU  - Nam SH
AU  - Choi SH
AU  - Kang A
AU  - Kim DW
AU  - Kim RN
AU  - Kim A
AU  - Kim DS
AU  - Park HS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 193: 1280-1281.

PMID- 20952569
VI  - 192
DP  - 2010
TI  - Genome Sequence of Leuconostoc argentinum KCTC 3773.
PG  - 6490-6491
AB  - Leuconostoc argentinum is one of the most prevalent lactic acid bacteria present during the
      manufacturing process of kimchi, the best-known
      traditional Korean dish. Here, we present the draft genome sequence of
      type strain KCTC 3773 of Leuconostoc argentinum (1,720,683 bp, with a G+C
      content of 42.9%), which consists of 98 large contigs (>100 bp in size).
AU  - Nam SH
AU  - Choi SH
AU  - Kang A
AU  - Kim DW
AU  - Kim RN
AU  - Kim A
AU  - Park HS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 6490-6491.

PMID- 21914862
VI  - 193
DP  - 2011
TI  - Genome Sequence of Lactobacillus suebicus KCTC 3549.
PG  - 5532-5533
AB  - Lactobacillus suebicus is important in the generation of particular flavors and in other
      ripening processes associated with apple mash. Here,
      we present the draft genome sequence of the type strain Lactobacillus
      suebicus KCTC 3549 (2,656,936 bp, with a G+C content of 39.0%), which
      consists of 143 large contigs (>100 bp).
AU  - Nam SH
AU  - Choi SH
AU  - Kang A
AU  - Kim DW
AU  - Kim RN
AU  - Kim DS
AU  - Kim A
AU  - Park HS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5532-5533.

PMID- 22461550
VI  - 194
DP  - 2012
TI  - Genome Sequence of Lactobacillus fructivorans KCTC 3543.
PG  - 2111-2112
AB  - Lactobacillus fructivorans is important in the generation of particular flavors and in other
      ripening processes associated with fermented food. Here, we present
      the draft genome sequence of the type strain Lactobacillus fructivorans KCTC 3543
      (1,373,326 bp, with a G+C content of 38.9%), which consists of 5 scaffolds. The
      genome sequence was obtained by using a whole-genome shotgun strategy with Roche
      454 GS (FLX Titanium) pyrosequencing, and all of the reads were assembled using
      Newbler Assembler 2.3.
AU  - Nam SH
AU  - Choi SH
AU  - Kang A
AU  - Lee KS
AU  - Kim DW
AU  - Kim RN
AU  - Kim DS
AU  - Park HS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2111-2112.

PMID- 21994929
VI  - 193
DP  - 2011
TI  - Genome Sequence of Leuconostoc carnosum KCTC 3525.
PG  - 6100-6101
AB  - We announce the draft genome sequence of the type strain Leuconostoc carnosum KCTC 3525
      (3,234,408 bp with a G+C content of 40.9%), one of the
      most prevalent lactic acid bacteria present during the manufacturing
      process of vacuum-packaged meats, which consists of 2,407 large contigs
      (>500 bp in size). The genome sequence was obtained by a whole-genome
      shotgun strategy using Roche 454 GS (FLX Titanium) pyrosequencing, and all
      of the reads were assembled using Newbler Assembler 2.3.
AU  - Nam SH
AU  - Kim A
AU  - Choi SH
AU  - Kang A
AU  - Kim DW
AU  - Kim RN
AU  - Kim DS
AU  - Park HS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6100-6101.

PMID- 23045483
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Staphylococcus vitulinus F1028, a Strain Isolated from a Block of Fermented Soybean.
PG  - 5961-5962
AB  - Staphylococcus vitulinus is a coagulase-negative staphylococcus in the family
      Staphylococcaceae. This report describes the draft genome sequence of S.
      vitulinus F1028, which was isolated from a traditional Korean soybean food
      (meju). This 2.56-Mbp genome sequence is the first S. vitulinus genome of a
      strain isolated from a fermented soybean product.
AU  - Nam YD
AU  - Chung WH
AU  - Seo MJ
AU  - Lim SI
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5961-5962.

PMID- 23045498
VI  - 194
DP  - 2012
TI  - Genome Sequence of Staphylococcus lentus F1142, a Strain Isolated from Korean Soybean Paste.
PG  - 5987
AB  - This report describes the draft genome sequence of Staphylococcus lentus F1142, which was
      isolated from a Korean fermented soybean paste (doenjang). The draft
      genome sequence contained 2.79 Mbp with a G+C content of 31.8%; this is the first
      S. lentus genome to be reported.
AU  - Nam YD
AU  - Chung WH
AU  - Seo MJ
AU  - Lim SI
AU  - Yi SH
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5987.

PMID- 22740667
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Gillisia sp. Strain CBA3202, a Novel Member of the Genus Gillisia, Which Belongs to the Family Flavobacteriaceae.
PG  - 3739
AB  - Gillisia sp. strain CBA3202, which belongs to the family Flavobacteriaceae, was isolated from
      sand of the seashore on Jeju Island, Republic of Korea. The draft
      genome of Gillisia sp. CBA3202 contains 2,981,404 bp with a G+C content of 34.9%.
      This is the second genome sequence of the Gillisia strains.
AU  - Nam YD
AU  - Lee HW
AU  - Lee M
AU  - Yim KJ
AU  - Kim KN
AU  - Roh SW
AU  - Kim D
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3739.

PMID- 23045499
VI  - 194
DP  - 2012
TI  - Genome Sequence of Lysinibacillus boronitolerans F1182, Isolated from a Traditional Korean Fermented Soybean Product.
PG  - 5988
AB  - Lysinibacillus is a Gram-positive, rod-shaped, and round-spore-forming bacterial  genus of the
      family Bacillaceae. We analyzed the genome sequence of
      Lysinibacillus boronitolerans F1182, isolated from a traditional Korean fermented
      soybean product. The genome sequence contained 4.46 Mbp with a G+C content of
      37.5%. This is the first report of an L. boronitolerans genome.
AU  - Nam YD
AU  - Seo MJ
AU  - Lim SI
AU  - Lee SY
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5988.

PMID- 23045503
VI  - 194
DP  - 2012
TI  - Genome Sequence of Kocuria atrinae C3-8, Isolated from Jeotgal, a Traditional Korean Fermented Seafood.
PG  - 5996
AB  - Kocuria is a Gram-positive coccus, catalase-positive, coagulase-negative, strictly aerobic
      bacterial genus in the family Micrococcaceae. Kocuria atrinae
      C3-8 was isolated from a traditional Korean fermented seafood. This study
      describes the first genome sequence of K. atrinae strain C3-8, which has a
      3.19-Mbp genome and a G+C content of 63.8%.
AU  - Nam YD
AU  - Seo MJ
AU  - Lim SI
AU  - Park SL
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5996.

PMID- 26430041
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Rothia mucilaginosa Strain NUM-Rm6536, Isolated from  a Human Oral Cavity.
PG  - e01122-15
AB  - Here, we present the complete genome sequence of Rothia mucilaginosa NUM-Rm6536,  a strain
      isolated from the tongue plaque of a healthy human adult. This strain is amenable to genetic
      manipulation by transformation and so provides a useful foundation for more detailed
      investigation of this species.
AU  - Nambu T
AU  - Tsuzukibashi O
AU  - Uchibori S
AU  - Mashimo C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01122-15.

PMID- 28034856
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Rothia aeria Type Strain JCM 11412, Isolated from Air in the Russian Space Laboratory Mir.
PG  - e01444-16
AB  - Here, we present the complete genome sequence of Rothia aeria type strain JCM 11412, isolated
      from air in the Russian space laboratory Mir. Recently, there has
      been an increasing number of reports on infections caused by R. aeria The genomic
      information will enable researchers to identify the pathogenicity of this
      organism.
AU  - Nambu T
AU  - Tsuzukibashi O
AU  - Uchibori S
AU  - Yamane K
AU  - Yamanaka T
AU  - Maruyama H
AU  - Wang PL
AU  - Mugita N
AU  - Morioka H
AU  - Takahashi K
AU  - Komasa Y
AU  - Mashimo C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01444-16.

PMID- 26294638
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Prevotella intermedia Strain 17-2.
PG  - e00951-15
AB  - Prevotella intermedia, a Gram-negative black-pigmented anaerobic rod, is frequently isolated
      from not only periodontal pockets but also purulent
      infections. We report here the complete genome sequence of P. intermedia strain
      17-2, which is a non-exopolysaccharide-producing variant obtained from
      exopolysaccharide (EPS)-producing P. intermedia strain 17 stock culture.
AU  - Nambu T
AU  - Yamane K
AU  - Maruyama H
AU  - Mashimo C
AU  - Yamanaka T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00951-15.

PMID- 9620804
VI  - 393
DP  - 1998
TI  - Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex.
PG  - 386-389
AB  - Cytosine residues in the sequence 5'CpG (cytosine-guanine) are often postsynthetically
      methylated in animal genomes.  CpG methylation is involved in long-term silencing of certain
      genes during mammalian development and in repression of viral genomes.  The methyl-CpG-binding
      proteins MeCP1 and MeCP2 interact specifically with methylated DNA and mediate transcriptional
      repression.  Here we study the mechanism of repression by MeCP2, an abundant nuclear protein
      that is essential for mouse embryogenesis.  MeCP2 binds tightly to chromosomes in a
      methylation-dependent manner.  It contains a transcriptional-repression domain that can
      function at a distance in vitro and in vivo.  We show that a region of MeCP2 that localizes
      with the TRD associates with a corepressor complex containing the transcriptional repressor
      mSin3A and histone deacetylases.  Transcriptional repression in vivo is relieved by the
      deacetylase inhibitor trichostatin A, indicating the deacetylation of histones (and/or of
      other proteins) is an essential component of this repression mechanism.  The data suggest that
      two global mechanisms of gene regulation, DNA methylation and histone deacetylation, can be
      linked by MeCP2.
AU  - Nan X
AU  - Ng H-H
AU  - Johnson CA
AU  - Laherty CD
AU  - Turner BM
AU  - Eisenman RN
AU  - Bird A
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1998 393: 386-389.

PMID- 27198020
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a Novel Acidophilic Iron-Oxidizing Firmicutes Species, 'Acidibacillus ferrooxidans' (SLC66T).
PG  - e00383-16
AB  - Here, we present the draft genome sequence of the type strain of 'Acidibacillus
      ferrooxidans,' a mesophilic, heterotrophic, and acidophilic bacterium that was
      isolated from mine spoilage subjected to accelerated weathering in humidity cell
      tests carried out by the former U.S. Bureau of Mines in Salt Lake City, UT.
AU  - Nancucheo I
AU  - Oliveira R
AU  - Dall'Agnol H
AU  - Johnson DB
AU  - Grail B
AU  - Holanda R
AU  - Nunes GL
AU  - Cuadros-Orellana S
AU  - Oliveira G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00383-16.

PMID- 25197432
VI  - 9
DP  - 2014
TI  - Complete genome sequence of Mesorhizobium ciceri bv. biserrulae type strain (WSM1271(T)).
PG  - 462-472
AB  - Mesorhizobium ciceri bv. biserrulae strain WSM1271(T) was isolated from root nodules of the
      pasture legume Biserrula pelecinus growing in the Mediterranean
      basin. Previous studies have shown this aerobic, motile, Gram negative,
      non-spore-forming rod preferably nodulates B. pelecinus - a legume with many
      beneficial agronomic attributes for sustainable agriculture in Australia. We
      describe the genome of Mesorhizobium ciceri bv. biserrulae strain WSM1271(T)
      consisting of a 6,264,489 bp chromosome and a 425,539 bp plasmid that together
      encode 6,470 protein-coding genes and 61 RNA-only encoding genes.
AU  - Nandasena K et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 462-472.

PMID- 25236617
VI  - 25
DP  - 2015
TI  - Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles.
PG  - 129-141
AB  - Burkholderia pseudomallei (Bp) is the causative agent of the infectious disease melioidosis.
      To investigate population diversity, recombination, and horizontal
      gene transfer in closely related Bp isolates, we performed whole-genome
      sequencing (WGS) on 106 clinical, animal, and environmental strains from a
      restricted Asian locale. Whole-genome phylogenies resolved multiple genomic
      clades of Bp, largely congruent with multilocus sequence typing (MLST). We
      discovered widespread recombination in the Bp core genome, involving hundreds of
      regions associated with multiple haplotypes. Highly recombinant regions exhibited
      functional enrichments that may contribute to virulence. We observed
      clade-specific patterns of recombination and accessory gene exchange, and provide
      evidence that this is likely due to ongoing recombination between clade members.
      Reciprocally, interclade exchanges were rarely observed, suggesting mechanisms
      restricting gene flow between clades. Interrogation of accessory elements
      revealed that each clade harbored a distinct complement of
      restriction-modification (RM) systems, predicted to cause clade-specific patterns
      of DNA methylation. Using methylome sequencing, we confirmed that representative
      strains from separate clades indeed exhibit distinct methylation profiles.
      Finally, using an E. coli system, we demonstrate that Bp RM systems can inhibit
      uptake of non-self DNA. Our data suggest that RM systems borne on mobile
      elements, besides preventing foreign DNA invasion, may also contribute to
      limiting exchanges of genetic material between individuals of the same species.
      Genomic clades may thus represent functional units of genetic isolation in Bp,
      modulating intraspecies genetic diversity.
AU  - Nandi T et al
PT  - Journal Article
TA  - Genome Res.
JT  - Genome Res.
SO  - Genome Res. 2015 25: 129-141.

PMID- 29371363
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Bacillus velezensis CN026 Exhibiting Antagonistic Activity against Gram-Negative Foodborne Pathogens.
PG  - e01543-17
AB  - We report here the complete genome sequence of Bacillus velezensis strain CN026,  a member of
      the B. subtilis group, which is known for its many industrial
      applications. The genome contains 3,995,812 bp and displays six gene clusters
      potentially involved in strain CN026's activity against Gram-negative foodborne
      pathogens.
AU  - Nannan C
AU  - Gillis A
AU  - Caulier S
AU  - Mahillon J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01543-17.

PMID- 29798921
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Streptomyces lunaelactis MM109(T), Isolated from Cave Moonmilk Deposits.
PG  - e00435-18
AB  - Streptomyces lunaelactis MM109(T) is a ferroverdin A (anticholesterol) producer isolated from
      cave moonmilk deposits. The complete genome sequence of MM109(T)
      was obtained by combining Oxford Nanopore MinION and Illumina HiSeq and MiSeq
      technologies, revealing an 8.4-Mb linear chromosome and two plasmids, pSLUN1
      (127,264 bp, linear) and pSLUN2 (46,827 bp, circular).
AU  - Naome A
AU  - Maciejewska M
AU  - Calusinska M
AU  - Martinet L
AU  - Anderssen S
AU  - Adam D
AU  - Tenconi E
AU  - Deflandre B
AU  - Coppieters W
AU  - Karim L
AU  - Hanikenne M
AU  - Baurain D
AU  - Delfosse P
AU  - van Wezel GP
AU  - Rigali S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00435-18.

PMID- 21283796
VI  - 6
DP  - 2011
TI  - In vivo characterization of the homing endonuclease within the polB gene in the halophilic archaeon Haloferax volcanii.
PG  - e15833
AB  - Inteins are parasitic genetic elements, analogous to introns that excise themselves at the
      protein level by self-splicing, allowing the formation
      of functional non-disrupted proteins. Many inteins contain a homing
      endonuclease (HEN) gene, and rely on its activity for horizontal
      propagation. In the halophilic archaeon, Haloferax volcanii, the gene
      encoding DNA polymerase B (polB) contains an intein with an annotated but
      uncharacterized HEN. Here we examine the activity of the polB HEN in vivo,
      within its natural archaeal host. We show that this HEN is highly active,
      and able to insert the intein into both a chromosomal target and an
      extra-chromosomal plasmid target, by gene conversion. We also demonstrate
      that the frequency of its incorporation depends on the length of the
      flanking homologous sequences around the target site, reflecting its
      dependence on the homologous recombination machinery. Although several
      evolutionary models predict that the presence of an intein involves a
      change in the fitness of the host organism, our results show that a strain
      deleted for the intein sequence shows no significant changes in growth
      rate compared to the wild type.
AU  - Naor A
AU  - Lazary R
AU  - Barzel A
AU  - Papke RT
AU  - Gophna U
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2011 6: e15833.

PMID- 24982068
VI  - 58
DP  - 2014
TI  - Colistin heteroresistance in Enterobacter cloacae is associated with cross-resistance to the host antimicrobial lysozyme.
PG  - 5594-5597
AB  - Here, we describe the first identification of colistin-heteroresistant
      Enterobacter cloacae in the United States. Treatment of this isolate with
      colistin increased the frequency of the resistant subpopulation and induced
      cross-resistance to the host antimicrobial lysozyme. This is the first
      description of heteroresistance conferring cross-resistance to a host
      antimicrobial and suggests that clinical treatment with colistin may
      inadvertently select for bacteria that are resistant to components of the host
      innate immune system.
AU  - Napier BA
AU  - Band V
AU  - Burd EM
AU  - Weiss DS
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2014 58: 5594-5597.

PMID- 27516520
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Comamonas thiooxydans Strain S23T (DSM 17888T), a Thiosulfate-Oxidizing Bacterium Isolated from a Sulfur Spring in India.
PG  - e00834-16
AB  - The genus Comamonas contains species isolated from various environments, such as  termite
      guts, wetlands, activated sludge, soil, humans, and fresh water. Here, we
      report the draft genome sequence of Comamonas thiooxydans strain S23(T) capable
      of oxidizing thiosulfate under mixotrophic growth conditions. Based upon draft
      genome sequencing, the genome is 5.3 Mb and encodes 4,767 proteins. The Comamonas
      thiooxydans whole-genome sequence will help understand the metabolic diversity in
      sulfur oxidation pathways.
AU  - Narayan KD
AU  - Badhai J
AU  - Whitman WB
AU  - Das SK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00834-16.

PMID- 23788533
VI  - 1
DP  - 2013
TI  - Whole-Genome Sequences of Four Clinical Isolates of Mycobacterium tuberculosis from Tamil Nadu, South India.
PG  - e00186-13
AB  - We report the annotated genome sequences of four clinical isolates of Mycobacterium
      tuberculosis from Tamil Nadu, India.
AU  - Narayanan S
AU  - Deshpande U
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00186-13.

PMID- Not included in PubMed...
VI  - 40
DP  - 1981
TI  - A new type II restriction enzyme from Haemophilus influenzae.
PG  - 1848
AB  - We have previously reported a new Type II restriction activity (Hin GUII) from
      Haemophilus influenzae (Fed. Proc. 27: 1415, 1978).  These cells also possess
      an isoschizomer of HhaI.  These two enzyme activities can be separated by
      chromatography of the cell extract on phosphocellulose and single-stranded DNA
      agarose.  Two possible recognition sequences were predicted for Hin GUII by the
      computer program RESITE (Tolstoshev, C. and Blakesley, R., manuscript in prep.)
      from the lengths of the eight fragments generated by digestion of PhiX174 RF
      DNA.  By comparison of digestion products of SV40 (11 fragments) and pBR322 (12
      fragments) DNAs, the sequence GGATG/CATCC was predicted.  This was confirmed by
      mapping each on the Hin GUII sites PhiX174 RF DNA and direct DNA sequencing of
      3 cleavage sites on PhiX174 RF and one site on pBR322 DNAs.  Hin GUII is a
      member of a unique group of Type II restriction enzymes which bind to a
      specific sequence and cleave at another site.  The Hin GUII cleavage site is
      situated 9-11 bases 3' to the recognition sequence GGATG/CATCC.
AU  - Nardone G
AU  - Blakesley R
PT  - Journal Article
TA  - Fed. Proc.
JT  - Fed. Proc.
SO  - Fed. Proc. 1981 40: 1848.

PMID- 3505900
VI  - 5
DP  - 1987
TI  - The enzymes of the BamHI restriction-modification system.
PG  - 147-184
AB  - The remarkable sequence specificity of Type II restriction endonucleases and
      their cognate methyl transferases has recently placed them under the scrutiny
      of nucleic acid enzymology.  From a biochemical perspective, their
      comparatively uncomplicated reaction requirements, intermediate size and
      concise, well-defined recognition sites has made them attractive models for the
      investigation of specific protein-nucleic acid interactions.  The solution of
      the same DNA sequence recognition problem by the enzymes of a
      restriction-modification system has led to interesting questions concerning
      structure-function relationships between these genetically distinct proteins.
      Further study of restriction-modification enzymes should promote a better
      understanding of the patterns and principles of protein-nucleic acid
      interactions.  The type II restriction-modification enzymes of Bacillus
      amyloliquefaciens H recognizes the duplex, symmetrical sequence 5'-GGATCC-3'.
      In the presence of Mg+2 the endonuclease catalyzes double stranded cleavage
      between the guanines, generating 5'-phophoryl and 3'-hydroxyl staggered
      termini.  The methylase catalyzes methyl group transfer from
      S-adenosyl-L-methionine to the C5 position of the internal cytosines.
      Methylation prevents cleavage by the endonuclease and is the presumed host
      controlled mechanism for the protection of endogenous DNA.  The specificity of
      the methyl acceptor must be as stringent as the position of strand scission
      since methylation of the external cytosines or the 6-amino groups of the
      adenines does not prevent cleavage.  We have been involved with the
      purification and characterization of these enzymes.  Emphasis has been placed
      on their catalytic properties and mechanisms of sequence discrimination.
AU  - Nardone G
AU  - Chirikjian JG
PT  - Journal Article
TA  - Gene Amplif. Anal.
JT  - Gene Amplif. Anal.
SO  - Gene Amplif. Anal. 1987 5: 147-184.

PMID- 2323503
VI  - 4
DP  - 1990
TI  - Changes in the kinetics of the BamHI restriction/modification enzymes with systematic alterations of the bases flanking the recognition site.
PG  - A1794
AB  - Several type II restriction enzymes exhibit different reaction kinetics with
      identical recognition sites in a given DNA molecule.  Kinetic preferences have
      been ascribed to different sequences flanking each recognition site.  Using
      site-specific mutagenesis, we have made 30 M13mp8 linear DNA substrates having
      mutations within the first 3 nucleotides on both flanks of the single BamHI
      site.  The advantages of these substrates are the constant position of the
      BamHI site relative to the DNA termini, the elimination of changes in secondary
      structure induced by supercoiling and the retention of all the flanking
      sequences except for the specified base changes.  Initial reaction velocities
      were determined in the presence of saturating DNA.  The greater difference in
      cleavage rates was 5 fold.  No correlation was found between flanking G/C
      content and reaction kinetics.  The endonuclease was sensitive to the position
      of base substitution.  C and T in flanking positions 1 and 2 produced the
      greatest reduction in velocites.  A in the second position of either flank
      produced the greatest increase in velocity.  Double or triple substitutions of
      A or T did not generate additive kinetic effects.  The methylase prefers
      substrates containing A in flanking positions 1 and 2 but is inhibited by this
      base in position 3.  T substitutions reduced methylation rates.
AU  - Nardone G
AU  - Connaughton JF
AU  - Kaloss W
AU  - Chirikjian JG
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1990 4: A1794.

PMID- 3017963
VI  - 261
DP  - 1986
TI  - Differences in the Kinetic Properties of BamHI Endonuclease and Methylase with Linear DNA Substrates.
PG  - 12128-12133
AB  - BamHI endonuclease and methylase were found to exhibit a kinetic preference for linear pBR322
      DNA substrates containing the recognition site in a central location.  The Km values for
      substrates having the recognition site in a terminal location were approximately 3-fold
      greater than those with a centrally located site.  This phenomenon may be partially due to
      facilitated transfer of the enzymes to the recognition site over nonspecific flanking
      sequences.  The exploitation of facilitated transfer by these enzymes has been inferred from
      studies demonstrating kinetic preferences for longer DNA substrates.  The reaction rates of
      the endonuclease were 9-fold greater with full-length pBR322 DNA than with a 74-base pair
      derivative.  The methylase exhibits a kinetic preference for longer substrates but only under
      conditions of comparatively higher DNA concentrations.  In addition, the methylase has the
      property of increasing long chain preference with increasing salt concentrations up to 120 mM.
      Increasing salt concentrations decreased the endonuclease's preference for longer substrates.
      Nonspecific inhibition studies revealed qualitative and quantitative differences between the
      two enzymes under catalytic conditions. These studies suggest that BamHI endonuclease and
      methylase interact with nonspecific DNA in different ways.
AU  - Nardone G
AU  - George J
AU  - Chirikjian JG
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1986 261: 12128-12133.

PMID- 6469968
VI  - 259
DP  - 1984
TI  - Sequence-specific BamHI methylase.
PG  - 10357-10362
AB  - BamHI methylase has been purified to apparent homogeneity.  The isolated form
      of the enzyme is a single polypeptide with a molecular weight of 56,000 as
      determined by sodium dodecyl sulfate-polyacrylamide electrophoresis.  Unlike
      BamHI endonuclease, which is isolated as a dimer and higher aggregates, the
      methylase has no apparent higher form.  The methylase requires
      S-adenosyl-L-methionine as the methyl-group donor and is inhibited by Mg2+.
      The enzyme is also inhibited by 2,3-butanedione and reagents specific for
      sulfhydryl groups, such as N-ethylmaleimide, which suggests a role for arginine
      and cysteine residues, respectively.  DNA efficiently protects the enzyme
      against the butanedione modification while S-adeno-sylmethionine has no effect.
      In contrast, S-adenosyl-methionine protects against cysteine modification
      while DNA produces only small amounts of protection.  Studies on the mechanism
      of methylation indicate that both strands of the recognition sequence are
      modified in a single binding event.  The sequence specificity of the methylase
      is relaxed upon the addition of glycerol in the reaction mixture.  In the
      presence of 30% glycerol the enzyme methylates sequences that are also
      recognized by BamHI endonuclease when acting under conditions of relaxed
      specificity.
AU  - Nardone G
AU  - George J
AU  - Chirikjian JG
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1984 259: 10357-10362.

PMID- 3956763
VI  - 45
DP  - 1986
TI  - Kinetics of BamHI endonuclease cleavage of form I SV40 DNA.
PG  - 1504
AB  - BamHI endonuclease recognizes the symmetrical, duplex sequence 5'-GGATCC-3' and cleaves
      between the guanines on both strands.  The kinetic mechanism of the enzyme was investigated
      with form [3H]-SV40 DNA which contains a single BamHI site.  The time course data was analyzed
      by numerical integration of the rate equation and a coordinated non-linear least squares
      analysis in terms of the rate constants.  The kinetic model used was that postulated for the
      EcoRI endonuclease.  	k1	k2	k3	k4E + 1 - EI 5 EII 5 EIII5 E + III	k1k-567 k5E + II	To simplify
      the analysis it was assumed that k1 and k-1 were large with respect to k2 and that k4 were not
      distinguished.  In reactions containing 12 nM DNA 2 nM endonuclease an excellent fit to the
      model was obtained with k2 = 0.192 min-1 +/- 0.0019, k3 (k4) = 1.190 +/- 0.042 and k5/k-5 =
      1.07 +- 0.067.  Unlike EcoRI endonuclease, the cleavage of the first strand is slower with
      this substrate. This analysis is useful in substantiating the model as well as providing
      self-consistent values for the rate constants.  These studies wre being extended to other DNA
      substrates (supported by USPS Grant GM 27701).
AU  - Nardone G
AU  - Wastney M
AU  - Hensley P
AU  - Chirikjian JG
PT  - Journal Article
TA  - Fed. Proc.
JT  - Fed. Proc.
SO  - Fed. Proc. 1986 45: 1504.

PMID- 2203775
VI  - 265
DP  - 1990
TI  - DNA structural polymorphism modulates the kinetics of superhelical DNA cleavage by BamHI restriction endonucleases.
PG  - 15308-15315
AB  - A compartmental model developed by Hensley (Hensley, P., Nardone, G.,
      Chirikjian, J.G., and Wastney, M.E., (1990) J. Biol. Chem. 265, 15300-15307)
      for analysis of the time courses of the cleavage of superhelical DNA substrates
      by the restriction endonuclease, BamHI, has been used to quantify the effects
      of changes in temperature, ionic strength, superhelical density, and the DNA
      substrate on the binding and strand cleavage processes.  Studies reported here
      indicate that changes in topology may be introduced into the DNA substrate
      solely as a result of the plasmid preparation process and in the absence of
      covalent bond cleavage and ligation.  These changes in topology have
      qualitatively different effects on the kinetics than those promoted by changes
      in the superhelical density.  The former are removed by briefly warming the DNA
      prior to assay, suggesting that they are only kinetically stable, while the
      latter changes are not affected by heating.  Increasing the [NaCl] from 0.0 M
      to 0.1 M increases the overall rate of plasmid cleavage by increasing both the
      rates of cleavage and enzyme DNA association.  To describe the decrease in the
      overall cleavage rate observed in 0.15 M NaCl, an ionic strength-dependent
      rate-determining structural transition in the DNA substrate was incorporated
      into the model.  The largest changes in the rate of the cleavage process
      resulted from changes in the DNA substrate.  For the SV40 substrate compared to
      pBR322, the rate constants describing the two association processes and the
      first bond cleavage event were increased 6- to 7-fold.  The rate of the second
      bond cleavage process was not affected.  These changes may be due to
      differences in the flanking sequences.
AU  - Nardone G
AU  - Wastney ME
AU  - Hensley P
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1990 265: 15308-15315.

PMID- 26823600
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Bacillus amyloliquefaciens Strain RHNK22, Isolated from  Rhizosphere with Biosurfactant (Surfactin, Iturin, and Fengycin) and Antifungal  Activity.
PG  - e01682-15
AB  - Bacillus amyloliquefaciens strain RHNK22 isolated from groundnut rhizosphere showed direct and
      indirect plant growth-promoting traits along with biosurfactant activity and reduction in
      surface tension of water. Biosurfactants were identified as lipopeptides (surfactin, iturin,
      and fengycin) by molecular and biochemical analysis in our studies.
AU  - Narendra-Kumar P
AU  - Swapna TH
AU  - Sathi RK
AU  - Archana K
AU  - Nageshwar L
AU  - Nalini S
AU  - Khan MY
AU  - Hameeda B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01682-15.

PMID- 28883135
VI  - 5
DP  - 2017
TI  - Insights into the Draft Genome Sequence of a Haitian Variant Vibrio cholerae Strain Isolated from a Clinical Setting in Kerala, South India.
PG  - e00843-17
AB  - We report here the draft genome sequence of a Haitian variant Vibrio cholerae strain, W4-13,
      isolated from Kerala, South India, possessing cholera toxin gene
      in chromosomes I and II. The sequence will be useful to achieve a profound
      understanding on its evolution, with emphasis on its pathogenesis and antibiotic
      resistance.
AU  - Narendrakumar L
AU  - Suryaletha K
AU  - Reghunathan D
AU  - Prasannakumar M
AU  - Thomas S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00843-17.

PMID- 27034500
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Methanoculleus horonobensis Strain JCM 15517, Methanoculleus thermophilus Strain DSM 2373, and Methanofollis ethanolicus Strain  JCM 15103, Hydrogenotrophic Methanogens Belonging to the Family  Methanomicrobiaceae.
PG  - e00199-16
AB  - The familyMethanomicrobiaceaecomprises hydrogen- and formate-utilizing methanogens. Genome
      sequencing of nine species ofMethanomicrobiaceaehas been
      conducted so far. Here, we report three additional draft genome sequences
      ofMethanomicrobiaceae, those ofMethanoculleus horonobensisJCM 15517
      (=T10(T)),Methanoculleus thermophilusDSM 2373 (=CR-1(T)), andMethanofollis
      ethanolicusJCM 15103 (=HASU(T)).
AU  - Narihiro T
AU  - Kusada H
AU  - Yoneda Y
AU  - Tamaki H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00199-16.

PMID- 26941138
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Syntrophomonas wolfei subsp. methylbutyratica Strain 4J5T (JCM 14075), a Mesophilic Butyrate- and 2-Methylbutyrate-Degrading Syntroph.
PG  - e00047-16
AB  - Syntrophomonas wolfei subsp. methylbutyratica strain 4J5(T) (=JCM 14075(T)) is a  mesophilic
      bacterium capable of degrading butyrate and 2-methylbutyrate through
      syntrophic cooperation with a partner methanogen. The draft genome sequence is
      3.2 Mb, with a G+C content of 45.5%.
AU  - Narihiro T
AU  - Nobu MK
AU  - Tamaki H
AU  - Kamagata Y
AU  - Liu WT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00047-16.

PMID- 6264706
VI  - 2
DP  - 1981
TI  - Current methods for the isolation of specific endonucleases.
PG  - 26-28
AB  - Various schemes and methods used to isolate specific endonucleases from bacteria are
      discussed.  The advantages of employing affinity chromatography to purify restrictases are
      shown with special reference to the isolation of a set of enzymes from B. globigii.  In
      particular, the utilization, in the first stage of purification, of Sepharose 4 B with the
      group-specific ligand Cibacron blue "sewed on" to it, made it possible to eliminate nucleic
      acids and the bulk of protein and to obtain, already after this stage, an enzyme suitable for
      physical mapping.  Additional purification of the enzyme activity maintaining fractions made
      it possible to achieve mutual separation of the enzymes BglI and BglII and BglI and BglIII and
      at the same time to ride of admixtures of nonspecific activities (the purification was done on
      heparin Sepharose).  It is concluded that using affinity chromatography enzymes suitable for
      genetic engineering work can be obtained rapidly and with a high recovery rate.
AU  - Naroditsky BS
AU  - Khilko SN
AU  - Loparev VN
PT  - Journal Article
TA  - Vestn. Akad. Med. Nauk SSSR
JT  - Vestn. Akad. Med. Nauk SSSR
SO  - Vestn. Akad. Med. Nauk SSSR 1981 2: 26-28.

PMID- 28450514
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of MPKL 26, the Type Strain of the Novel Species Sinomonas  mesophila.
PG  - e00247-17
AB  - Sinomonas mesophila MPKL 26T can produce silver nanoparticles. Here, we present the 4.0-Mb
      genome of this type strain, which contains 47 scaffolds with an N50 scaffold length of 261,266
      bp. The availability of the genome sequence will provide a better understanding of strain MPKL
      26T and the genus Sinomonas.
AU  - Narsing-Rao MP
AU  - Jiao JY
AU  - Liu L
AU  - Fang BZ
AU  - Zhang XT
AU  - Chen W
AU  - Zhao J
AU  - Xiao M
AU  - Li WJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00247-17.

PMID- Not carried by PubMed...
VI  - 87
DP  - 1987
TI  - Isolation of a DNA methyltransferase gene, M.CviBIII, from Chlorella virus NC-1A.
PG  - 314
AB  - As an initial step in the study of DNA restriction-modification systems of
      viruses which infect a eucaryotic green alga, Chlorella, we have isolated the
      gene for one methyltransferase, M.CviBIII, from virus NC-1A in Escherichia coli
      plasmid pUC8.  M.CviBIII methylates A in TCGA sequences.  DNA from E. coli
      strains harboring the recombinant plasmid, pNC-1A.14, is resistant to digestion
      by SalI (GTCGAC) and TaqI (TCGA) as well as methylation by the bacterial
      methylase, M.TaqI.  M.CviBIII activity in crude extracts from these E. coli
      strains methylates SalI sites in lambda DNA in an in vitro protection assay.
      Transposon Tn5 mutagenesis localized the M.CviBIII gene to a 1.5 kbp region on
      pNC-1A.14.  Nucleic acid hybridization studies have produced several findings:
      (i) Five of the 29 other Chlorella viruses described in the literature contain
      a gene homologous to M.CviBIII. (ii) Spontaneous mutants of NC-1A, the DNA from
      which is sensitive to TaqI and SalI, have the M.CviBIII gene deleted.  (iii)
      Transcription of the M.CviBIII gene is under temporal control; a 1.4 kb mRNA
      species can be detected with pNC-1A.14 probes only during the early stages of
      NC-1A infection of Chlorella cells.
AU  - Narva KE
AU  - Skrdla MP
AU  - Wendell DL
AU  - Van Etten JL
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1987 87: 314.

PMID- 3248728
VI  - 74
DP  - 1988
TI  - The amino acid sequence of the eukaryotic DNA [N6-adenine]methyltransferase, M.CviBIII, has regions of similarity with the prokaryotic isoschizomer M.TaqI and other DNA [N6-adenine] methyltransferases.
PG  - 253-259
AB  - the sequences of the genes encoding M.CviBIII (from virus NC-1A which infects a
      eukaryotic alga) [Narva et al., Nucleic Acids Res. 15 (1987) 9807-9823] and
      M.TaqI (from the bacterium Thermus aquaticus) [Slatko et al., Nucleic Acids
      Res. 15 (1987) 9781-9796] have been determined recently.  Both enzymes
      methylate adenine in the sequence TCGA.  We have compared the predicted amino
      acid sequences of these two methyltransferases (MTases), with each other and
      with ten other N6A-MTases and find regions of similarity.  M.CviBIII and M.TaqI
      were most closely related followed by M.PaeR7, whose recognition sequence
      (CTCGAG) contains the M.TaqI/M.CviBIII recognition sequence TCGA, and M.PstI,
      whose recognition sequence is CTGCAG.  All of the N6-MTases contain the
      sequence Asp/Asn-Pro-Pro-Tyr (B-P-P-Y) referred to by Hattman et al. [J.
      Bacteriol. 164 (1985) 932-937] as region IV.  The predicted secondary structure
      of this region forms a finger-like structure (Beta finger) containing a
      Beta-pleated sheet (...XXXB), two Beta-turns (P-P) followed by another
      Beta-pleated sheet [Y/FXXX...].
AU  - Narva KE
AU  - Van Etten JL
AU  - Slatko BE
AU  - Benner JS
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 253-259.

PMID- 3320956
VI  - 15
DP  - 1987
TI  - Molecular cloning and characterization of the gene encoding the DNA methyltransferase, M.CviBIII, from Chlorella virus NC-1A.
PG  - 9807-9823
AB  - The gene encoding the DNA methyltransferase, M.CviBIII, from Chlorella virus NC-1A was cloned
      and expressed in E. coli plasmid pUC8. Plasmid (pNC-1A.14.8) encoded M.CviBIII methylates
      adenine in TCGA sequences both in vivo in E. coli and in vitro. Transposon Tn5 mutagenesis
      localized the M.CviBIII functional domain to a 1.5 kbp region of pNC-1A.14.8 and also
      indicated that a virus promoter directs transcription of the gene in E. coli. The 2.1 kbp
      insert containing the M.CviBIII gene was sequenced and a single open reading frame of 1131 bp
      was identified within the domain determined by Tn5 mutagenesis. When the M.CviBIII gene was
      fused in-frame with the 19 amino-terminal codons of lacZ a 45 kD polypeptide was identified in
      maxicells as predicted by the DNA sequence. The M.CviBIII gene was not essential for virus
      replication since a virus M.CviBIII deletion mutant also replicated in Chlorella.
AU  - Narva KE
AU  - Wendell DL
AU  - Skrdla MP
AU  - Van Etten JL
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1987 15: 9807-9823.

PMID- 15028702
VI  - 186
DP  - 2004
TI  - Comparative Genomics of Two Leptospira interrogans Serovars Reveals Novel Insights into Physiology and Pathogenesis.
PG  - 2164-2172
AB  - Leptospira species colonize a significant proportion of rodent populations
      worldwide and produce life-threatening infections in accidental hosts,
      including humans. Complete genome sequencing of Leptospira interrogans
      serovar Copenhageni and comparative analysis with the available Leptospira
      interrogans serovar Lai genome reveal that despite overall genetic
      similarity there are significant structural differences, including a large
      chromosomal inversion and extensive variation in the number and
      distribution of insertion sequence elements. Genome sequence analysis
      elucidates many of the novel aspects of leptospiral physiology relating to
      energy metabolism, oxygen tolerance, two-component signal transduction
      systems, and mechanisms of pathogenesis. A broad array of transcriptional
      regulation proteins and two new families of afimbrial adhesins which
      contribute to host tissue colonization in the early steps of infection
      were identified. Differences in genes involved in the biosynthesis of
      lipopolysaccharide O side chains between the Copenhageni and Lai serovars
      were identified, offering an important starting point for the elucidation
      of the organism's complex polysaccharide surface antigens. Differences in
      adhesins and in lipopolysaccharide might be associated with the adaptation
      of serovars Copenhageni and Lai to different animal hosts. Hundreds of
      genes encoding surface-exposed lipoproteins and transmembrane outer
      membrane proteins were identified as candidates for development of
      vaccines for the prevention of leptospirosis.
AU  - Nascimento AL et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2004 186: 2164-2172.

PMID- 29700154
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Bacillus sp. Strain M21, Isolated from the Arid Area of  Matmata, Tunisia.
PG  - e00323-18
AB  - Bacillus sp. strain M21 was isolated from an environmental sample. In antibacterial
      screenings, the strain inhibited growth of Gram-positive and
      Gram-negative test strains. The genome was assembled into 69 contigs with a total
      size of 5.178 Mb. The strain contains at least nine biosynthetic gene clusters
      for the production of specialized metabolites.
AU  - Nasfi Z
AU  - Poehlein A
AU  - Harms H
AU  - Goralski E
AU  - Fisch KM
AU  - Daniel R
AU  - Konig GM
AU  - Schaberle TF
AU  - Bachoual R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00323-18.

PMID- 21108814
VI  - 11
DP  - 2010
TI  - Genome sequence of adherent-invasive Escherichia coli and comparative genomic analysis with other E. coli pathotypes.
PG  - 667
AB  - ABSTRACT: BACKGROUND: Adherent and invasive Escherichia coli (AIEC) are
      commonly found in ileal lesions of Crohn's Disease (CD) patients, where
      they adhere to intestinal epithelial cells and invade into and survive in
      epithelial cells and macrophages, thereby gaining access to a typically
      restricted host niche. Colonization leads to strong inflammatory responses
      in the gut suggesting that AIEC could play a role in CD immunopathology.
      Despite extensive investigation, the genetic determinants accounting for
      the AIEC phenotype remain poorly defined. To address this, we present the
      complete genome sequence of an AIEC, revealing the genetic blueprint for
      this disease-associated E. coli pathotype. Results - We sequenced the
      complete genome of E. coli NRG857c (O83:H1), a clinical isolate of AIEC
      from the ileum of a Crohn's Disease patient. Our sequence data confirmed a
      phylogenetic linkage between AIEC and extraintestinal pathogenic E. coli
      causing urinary tract infections and neonatal meningitis. The comparison
      of the NRG857c AIEC genome with other pathogenic and commensal E. coli
      allowed for the identification of unique genetic features of the AIEC
      pathotype, including 41 genomic islands, and unique genes that are found
      only in strains exhibiting the adherent and invasive phenotype.
      CONCLUSIONS: Up to now, the virulence-like features associated with AIEC
      are detectable only phenotypically. AIEC genome sequence data will
      facilitate the identification of genetic determinants implicated in
      invasion and intracellular growth, as well as enable functional genomic
      studies of AIEC gene expression during health and disease.
AU  - Nash JH
AU  - Villegas A
AU  - Kropinski AM
AU  - Aguilar-Valenzuela R
AU  - Konczy P
AU  - Mascarenhas M
AU  - Ziebell K
AU  - Torres AG
AU  - Karmali MA
AU  - Coombes BK
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2010 11: 667.

PMID- 25999571
VI  - 3
DP  - 2015
TI  - Draft Whole-Genome Sequence of Morganella morganii Serotype O:1ab.
PG  - e00453-15
AB  - Morganella morganii is a facultative pathogen of humans, causing urinary tract and
      postsurgical infections. Here, we report a high-quality draft assembly of the
      O:1ab serotype.
AU  - Nash JH
AU  - Young NM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00453-15.

PMID- 2987036
VI  - 185
DP  - 1985
TI  - Relaxation of PvuII recognition sequence.
PG  - 101-104
AB  - The substrate specificity of PvuII endonuclease is relaxed in the presence of
      dimethyl sulfoxide.  The new recognition sequences cleaved in pBR322 DNA have
      been found to be CCGCTG, CATCTG, CAGATG, CAGGTG and CAGCGG.
AU  - Nasri M
AU  - Sayadi S
AU  - Thomas D
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1985 185: 101-104.

PMID- 2823216
VI  - 15
DP  - 1987
TI  - Alteration of the specificity of PvuII restriction endonuclease.
PG  - 7677-7687
AB  - The restriction endonuclease PvuII which cleaves the sequence CAG^CTG, at the
      position indicated by the arrow, was found to decrease its substrate
      specificity in the presence of organic solvents.  Thirty-three sites, that we
      have named PvuII* sites, were identified on the nucleotide sequence of pBR322
      DNA.  The new recognition sequences cleaved in pBR322 DNA, at the positions
      indicated by the arrows, were shown to be AAGCTG, GAGCTG, CNGCTG, CANCTG,
      CAGNTG, CAGCNG, CAGCTC and CAGCTT.  (TAGCTG and the complementary sequence
      CAGCTA are not present in pBR322 DNA).  From these recognition sequences, we
      deduced that PvuII* activity recognizes and cleaves degenerate sequences which
      differ from the standard PvuII sequence CAGCTG at only one of the recognition
      site.  Any substitution can occur at any one of the six positions in the
      hexanucleotide sequence.  The optimum incubation medium for PvuII* activity was
      found to be:  10-50 mM Tris-HCl, pH 8.5, 12-15 mM MgCl2, 50 mM NaCl, 10%
      ethanol + 10% dimethylsulfoxide (DMSO).
AU  - Nasri M
AU  - Thomas D
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1987 15: 7677-7687.

PMID- 2852477
VI  - 542
DP  - 1988
TI  - Increase of the potentialities of restriction endonucleases by specificity relaxation in the presence of organic solvents.
PG  - 255-265
AB  - None
AU  - Nasri M
AU  - Thomas D
PT  - Journal Article
TA  - Ann. NY Acad. Sci.
JT  - Ann. NY Acad. Sci.
SO  - Ann. NY Acad. Sci. 1988 542: 255-265.

PMID- 3003698
VI  - 14
DP  - 1986
TI  - Relaxation of recognition sequence of specific endonuclease HindIII.
PG  - 811-821
AB  - Under the standard reaction conditions, the restriction endonuclease HindIII
      cleaves double-stranded DNA, within the recognition sequence -A^AGCTT- at the
      position indicated by the arrow.  In the presence of Dimethyl sulfoxide the
      substrate specificity of this enzyme is reduced and cleavages occur at
      additional sites.  We have determined the secondary sites in pBR322 DNA
      recognized by HindIII endonuclease under relaxed conditions and found that it
      cleaves the hexanucleotides:  G^AGCTT, A^GGCTT, A^TGCTT, A^ATCTT, A^AGCAT,
      A^AGCGT, A^AGCTC,  at the positions indicated by the arrows, producing
      fragments with cohesive ends.
AU  - Nasri M
AU  - Thomas D
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1986 14: 811-821.

PMID- 3022712
VI  - 45
DP  - 1986
TI  - The reactions of SacI, PvuII and EcoRI endonucleases.
PG  - 997-1005
AB  - A new approach to the mechanism study of DNA restriction is suggested.  It is
      based on enzymatic hydrolysis of DNA in the presence of organic solvent.  We
      found that in the presence of DMSO (10% v/v), the superhelical cleavage of
      pBR322 DNA by restriction endonucleases SacI and EcoRI proceeds with extensive
      accumulation of an intermediate, the single-nicked circular DNA, while with
      PvuII endonuclease the superhelical form is converted directly to the linear
      form.
AU  - Nasri M
AU  - Thomas D
PT  - Journal Article
TA  - Biomed. Biochim. Acta
JT  - Biomed. Biochim. Acta
SO  - Biomed. Biochim. Acta 1986 45: 997-1005.

PMID- 2840851
VI  - 15
DP  - 1987
TI  - Immobilization of the restriction endonucleases PvuII and HindIII.
PG  - 119-130
AB  - The effects of several chemical reagents on the activity of the restriction
      endonucleases PvuII and HindIII were investigated.  Carbodiimide, which reacts
      preferentially with carboxyl groups, was found to inactivate these enzymes.
      This specific effect could be prevented by Mg2+ cation.  pBR322 DNA, which
      contains PvuII and PvuII sites and HindIII and HindIII sites, did not protect
      the enzymes from the carbodiimide.  On the other hand, glutaraldehyde, which
      reacts primarily with lysine residues, inactivates PvuII and HindIII enzymes.
      This specific effect could not be prevented by pBR322 DNA.  Preincubation with
      high concentrations of N-ethylmaleimide, which reacts with sulfhydryl groups,
      caused slight inhibition of PvuII activity, but had no effect on the activity
      of HindIII enzyme.  The effects of glutaraldehyde , carbodiimide, and
      N-ethylmaleimide on other restriction endonucleases were also investigated.
      Restriction endonucleases PvuII and HindIII were immobilized by covalent
      coupling to various insoluble carriers.  Both immobilized enzymes retained
      partial enzyme activities, when immobilized through phenolic groups and were
      stable for at least two months.
AU  - Nasri M
AU  - Thomas D
PT  - Journal Article
TA  - Appl. Biochem. Biotechnol.
JT  - Appl. Biochem. Biotechnol.
SO  - Appl. Biochem. Biotechnol. 1987 15: 119-130.

PMID- 25883273
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Bacillus amyloliquefaciens AP183 with Antibacterial Activity against Methicillin-Resistant Staphylococcus aureus.
PG  - e00162-15
AB  - Bacillus amyloliquefaciens AP183 expresses secondary metabolites that inhibit the growth of
      methicillin-resistant Staphylococcus aureus (MRSA). Here, we present a
      ~3.99-Mbp draft genome sequence of AP183 with the aims of providing insights into
      the genomic basis of its antibacterial mechanisms and exploring its potential use
      in preventing MRSA skin colonization.
AU  - Nasrin S
AU  - Hossain MJ
AU  - Liles MR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00162-15.

PMID- 29674542
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Six Multidrug-Resistant Clinical Strains of Acinetobacter baumannii, Isolated at Two Major Hospitals in Kuwait.
PG  - e00264-18
AB  - Acinetobacter baumannii is an important opportunistic pathogen in global health care settings.
      Its dissemination and multidrug resistance pose an issue with
      treatment and outbreak control. Here, we present draft genome assemblies of six
      multidrug-resistant clinical strains of A. baumannii isolated from patients
      admitted to one of two major hospitals in Kuwait.
AU  - Nasser K
AU  - Mustafa AS
AU  - Khan MW
AU  - Purohit P
AU  - Al-Obaid I
AU  - Dhar R
AU  - Al-Fouzan W
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00264-18.

PMID- 9325303
VI  - 272
DP  - 1997
TI  - Catalytic and DNA binding properties of PvuII restriction endonuclease mutants.
PG  - 25761-25767
AB  - The role of particular residues of the PvuII endonuclease in DNA binding and cleavage was
      studied by mutational analysis using a number of in vivo and in vitro approaches.  While
      confirming the importance of residues predicted to be involved directly in function by the
      crystal structure, the analysis led to several striking results. Aspartate 34, which contacts
      the central base pair of the PvuII site (5'-CAGCTG-3') through the minor groove, plays a
      critical role in binding specificity.  A D34G mutant binds with high affinity to any of the
      sequences in the set CANNTG, although its low level of cleavage activity acts only on the
      wild-type site.  In addition, a His to Ala mutation at the residue that contacts the central
      G, and is predicted to be blocked by PvuII methylation, still requires the PvuII methylase to
      be maintained in vivo, arguing against this hypothesis as the only mechanism for methylation
      protection.  Finally, four of the five mutations that reduce cleavage activity while still
      exhibiting binding in the gel shift assay are at residues that form DNA- or subunit-subunit
      contacts rather than in the catalytic center.  This provides further evidence for a strong
      linkage between specific binding and catalysis.
AU  - Nastri HG
AU  - Evans PD
AU  - Walker IH
AU  - Riggs PD
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1997 272: 25761-25767.

PMID- 6275797
VI  - 212
DP  - 1981
TI  - Effect of sulfhydryl group inhibitors on restriction endonuclease activities.
PG  - 611-617
AB  - The activity of restriction endonuclease BamHI was abolished by
      p-mercuribenzoate and 5,5'-dithiobis(2-nitrobenzoic acid).  The activity of
      restriction endonuclease PvuI was abolished by p-mercuribenzoate.  The activity
      of none of the eight other restriction endonucleases tested could be abolished
      by the sulfydryl group inhibitors.  Despite the general practice of inclusion
      of sulfhydryl reducing agents in reaction mixtures containing restriction
      endonucleases it appears that most of these enzymes function without the active
      participation of a -SH moiety.
AU  - Nath K
PT  - Journal Article
TA  - Arch. Biochem. Biophys.
JT  - Arch. Biochem. Biophys.
SO  - Arch. Biochem. Biophys. 1981 212: 611-617.

PMID- 6101045
VI  - 1
DP  - 1981
TI  - Cleavage properties of site-specific restriction endonucleases.
PG  - 113-130
AB  - *

        I. Introduction

       II. Site preference by restriction endonucleases

      III. Perturbations in restriction-endonuclease cleavage properties

       IV. Application of manipulated restriction endonuclease cleavage

        V. Summary

      

AU  - Nath K
AU  - Azzolina BA
PT  - Journal Article
TA  - Gene Amplif. Anal.
JT  - Gene Amplif. Anal.
SO  - Gene Amplif. Anal. 1981 1: 113-130.

PMID- 1099456
VI  - 257
DP  - 1975
TI  - Generation of discrete yeast DNA fragments by endonuclease RI.
PG  - 155-157
AB  - Fine structure genetic analysis has shown that the ilv1 gene of yeast,
      Saccharomyces cerevisiae, is multifunctional.  The ilv1 gene product, threonine
      deaminase, shows catalytic activity, as well as participating in multivalent
      repression of other enzymes involved in isoleucine-valine biosynthetic
      pathways.  A better understanding of the regulatory role of the ilv1 gene
      product and other proteins, such as isoleucyl-tRNA synthetase, which in
      addition to the ilv1 gene product seems to regulate ilv2 and ilv3 gene
      expression, could be obtained if a pure preparation of the various ilv genes
      were isolated in large quantities.  One way of isolating the genes would be to
      use restriction enzymes to cleave yeast DNA which contains normal ilv genes and
      join the fragments to a bacterial plasmid.  Because of the similarity of the
      isoleucine-valine pathways in yeast and Escherichia coli, the fused DNA could
      then be transformed into a strain of E. coli with a deletion in the particular
      ilv gene.  Restriction enzyme-cleaved DNA from various sources has been
      amplified by growth in E. coli.  We have found that restriction enzyme EcoRI
      treatment of yeast DNA results in not only a reduction in the size of total DNA
      but also the generation of several distinct species of homogeneous size DNAs
      some of which are derived from ribosomal genes and others from mitochondrial
      genes.
AU  - Nath K
AU  - Bollon AP
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1975 257: 155-157.

PMID- 11829499
VI  - 316
DP  - 2002
TI  - Bending and flexibility of methylated and unmethylated EcoRI DNA.
PG  - 7-17
AB  - We used cyclization kinetics experiments and Monte Carlo simulations to determine a structural
      model for a DNA decamer containing the EcoRI restriction site. Our findings agree well with
      recent crystal and NMR structures of the EcoRI dodecamer, where an overall bend of seven
      degrees is distributed symmetrically over the molecule. Monte Carlo simulations indicate that
      the sequence has a higher flexibility, assumed to be isotropic, compared to that of a
      "generic" DNA sequence. This model was used as a starting point for the investigation of the
      effect of cytosine methylation on DNA bending and flexibility. While methylation did not
      affect bend magnitude or direction, it resulted in a reduction in bending flexibility and
      under-winding of the methylated nucleotides. We demonstrate that our approach can augment the
      understanding of DNA structure and dynamics by adding information about the global structure
      and flexibility of the sequence. We also show that cyclization kinetics can be used to study
      the properties of modified nucleotides.
AU  - Nathan D
AU  - Crothers DM
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2002 316: 7-17.

PMID- 3248731
VI  - 74
DP  - 1988
TI  - Characterization of clones of the BamHI methyltransferase gene.
PG  - 35-36
AB  - Meeting Abstract
AU  - Nathan PD
AU  - Brooks JE
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 35-36.

PMID- 2467142
VI  - 13D
DP  - 1989
TI  - Characterization of clones of the BamHI methyltransferase gene.
PG  - 212
AB  - The BamHI type II restriction-modification system from Bacillus
      amyloliquefaciensH, recognizes the sequence 5'-GGATCC.  We are characterizing
      different subclones of the BamHI methyltransferase (MTase) gene.  One clone
      carries a 2.2-kb HindIII fragment (pBamM2.2) that contains the MTase gene and
      the N-terminal end of the endonuclease gene.  A second clone carries a 1.8-kb
      XmnI-HindIII fragment (pBamM1.8) that contains the MTase gene and a portion of
      the ORF located in the intergenic region.  These two clones differ in their
      compatibility with McrB (modified cytosine restriction).  Only the plasmid
      pBamM1.8 is restricted by McrB+ hosts.  Two approaches are being used to
      investigate the different McrB compatibilites.  First, we have found that cells
      containing pBamM1.8 produce significantly greater amounts of BamHI MTase than
      cells containing pBamM2.2.  Second, we have found that a disruption of plasmid
      pBamM2.2 in the intergenic ORF results in the loss of McrB compatibility.
      Together, these results suggest that the higher level of MTase from pBamM1.8 is
      responsible for the McrB restriction, and that the region located between the
      two genes affects the level of MTase produced.
AU  - Nathan PD
AU  - Brooks JE
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1989 13D: 212.

PMID- Not carried by PubMed...
VI  - 89
DP  - 1989
TI  - Regulation of the BamHI restriction-modification system.
PG  - 180
AB  - The BamHI restriction-modification (RM) system recognizes the sequence
      5'-GGATCC.  The endonuclease cleaves to leave a 5' GATC extension.  The
      methyltransferase (MTase) modifies the internal cytosine residue to give
      GGATmCC.  We have investigated clones of the BamHI MTase gene, pBamM1.8 and
      pBamM2.2, that differ in their restriction by the McrB (modified cytosine
      restriction) system of Escherichia coli, only pBamM1.8 is restricted by McrB+
      cells.  We have found that cells containing pBamM1.8 produce more MTase than
      cells containing pBamM2.2.  We suggest that the higher expression of MTase by
      cells containing pBamM1.8 is responsible for the McrB restriction.  By using
      linkers to disrupt the plasmid pBamM2.2, we have identified and subcloned a
      genetic region involved in the McrB effect.  This region contains a small open
      reading frame (ORF) that lies between the BamHI RM genes.  Recently we have
      investigated the effect of the ORF region on the endonuclease gene.  Cells that
      contain a plasmid with the BamHI RM system disrupted in the ORF region produce
      a lower level of endonuclease.  Moreover, endonuclease levels are restored when
      the cells are cotransformed with the ORF containing plasmid.  These results
      syggest that the region located between the two genes is important in
      controlling the expression of both BamHI MTase and endonuclease.
AU  - Nathan PD
AU  - Brooks JE
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1989 89: 180.

PMID- 4365016
VI  - 33
DP  - 1974
TI  - Use of restriction endonucleases in analyzing the genome of simian virus 40.
PG  - 1135-1138
AB  - Bacterial restriction endonucleases have been used to cleave SV40 DNA at
      specific sites.  The resulting fragments have been ordered in the molecule,
      resulting in a physical cleavage map of the SV40 chromosome.  With this map as
      a reference, sites of initiation and termination of DNA replication have been
      located, as have regions of the genome expressed early and late in productively
      infected cells.  The 5' - 3' orientation of each strand of SV40 DNA has also
      been determined; from this information and prior identification of the early
      and late template strands, the direction of early and late transcription could
      be deduced.
AU  - Nathans D
AU  - Adler SP
AU  - Brockman WW
AU  - Danna KJ
AU  - Lee TNH
AU  - Sack GH Jr
PT  - Journal Article
TA  - Fed. Proc.
JT  - Fed. Proc.
SO  - Fed. Proc. 1974 33: 1135-1138.

PMID- 166604
VI  - 44
DP  - 1975
TI  - Restriction endonucleases in the analysis and restructuring of DNA molecules.
PG  - 273-293
AB  - Restriction enzymes are endodeoxyribonucleases that recognize specific
      nucleotide sequences in double stranded DNA and cleave both strands of the
      duplex.  In the cell of origin each restriction enzyme is part of a
      restriction-modification (R-M) system, consisting of the restriction
      endonuclease and a matched modification enzyme which recognizes and modifies
      (generally by methylation) the same nucleotide sequence in DNA recognized by
      the restriction enzyme.  Modification thus protects cellular DNA from
      restriction; however, foreign (unmodified) DNA is cleaved by the restriction
      endonuclease and further degraded by other enzymes.  Such R-M systems, first
      detected by phage restriction and modification, are widespread in bacteria and
      are thought to play a role in eliminating foreign DNA that gains entrance to
      the cell via viruses or as naked DNA.  The biochemistry and genetics of R-M
      systems have recently been reviewed.  The usefulness of restriction
      endonucleases in the analysis and restructuring of DNA, which is the topic of
      this review, rests on the fact that some of the restriction enzymes cleave DNA
      at specific nucleotide sequences.  These cleavage site-specific endonucleases
      are thus analogous to specific proteolytic enzymes and are proving as useful in
      the study of DNA structure and function as trypsin and chymotrypsin have been
      in protein analysis.  After the first characterization of a restriction
      endonuclease from Escherichia coli strain K in 1968, there was a curious lag in
      the application of restriction enzymes as analytical tools.  In a sense this
      delay was fortunate, since the enzymes isolated initially are in the class now
      known to be nonspecific in their cleavage sites.  However, after the discovery
      of cleavage site-specific endonucleases, there was immediate applicaton of
      these enzymes to the analysis of viral genomes.  In the past three years there
      has been an almost explosive rate of discovery of new site-specific restriction
      enzymes and rapid application to physical mapping of chromosomes, nucleotide
      sequence analysis of DNA, isolation of genes, and restructuring of DNA
      molecules.  Our purpose is to review these recent developments.
AU  - Nathans D
AU  - Smith HO
PT  - Journal Article
TA  - Annu. Rev. Biochem.
JT  - Annu. Rev. Biochem.
SO  - Annu. Rev. Biochem. 1975 44: 273-293.

PMID- 21935417
VI  - 6
DP  - 2011
TI  - Pseudomonas aeruginosa AES-1 exhibits increased virulence gene expression during chronic infection of cystic fibrosis lung.
PG  - E24526
AB  - Pseudomonas aeruginosa, the leading cause of morbidity and mortality in people
      with cystic fibrosis (CF), adapts for survival in the CF lung through both
      mutation and gene expression changes. Frequent clonal strains such as the
      Australian Epidemic Strain-1 (AES-1), have increased ability to establish
      infection in the CF lung and to superimpose and replace infrequent clonal
      strains. Little is known about the factors underpinning these properties.
      Analysis has been hampered by lack of expression array templates containing
      CF-strain specific genes. We sequenced the genome of an acute infection AES-1
      isolate from a CF infant (AES-1R) and constructed a non-redundant micro-array
      (PANarray) comprising AES-1R and seven other sequenced P. aeruginosa genomes. The
      unclosed AES-1R genome comprised 6.254Mbp and contained 6957 putative genes,
      including 338 not found in the other seven genomes. The PANarray contained 12,543
      gene probe spots; comprising 12,147 P. aeruginosa gene probes, 326
      quality-control probes and 70 probes for non-P. aeruginosa genes, including phage
      and plant genes. We grew AES-1R and its isogenic pair AES-1M, taken from the same
      patient 10.5 years later and not eradicated in the intervening period, in our
      validated artificial sputum medium (ASMDM) and used the PANarray to compare gene
      expression of both in duplicate. 675 genes were differentially expressed between
      the isogenic pairs, including upregulation of alginate, biofilm, persistence
      genes and virulence-related genes such as dihydroorotase, uridylate kinase and
      cardiolipin synthase, in AES-1M. Non-PAO1 genes upregulated in AES-1M included
      pathogenesis-related (PAGI-5) genes present in strains PACS2 and PA7, and
      numerous phage genes. Elucidation of these genes' roles could lead to targeted
      treatment strategies for chronically infected CF patients.
AU  - Naughton S
AU  - Parker D
AU  - Seemann T
AU  - Thomas T
AU  - Turnbull L
AU  - Rose B
AU  - Bye P
AU  - Cordwell S
AU  - Whitchurch C
AU  - Manos J
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2011 6: E24526.

PMID- 18085543
VI  - 9
DP  - 2008
TI  - Genetic selection of cyclic peptide dam methyltransferase inhibitors.
PG  - 194-197
AB  - Enzymatic methylation of specific DNA bases is fundamental to the survival and propagation of
      a variety of organisms, including humans.  DNA methyltransferases control and regulate a
      variety of cellular processes, and due to the central role these processes play in the
      organism's lifecycle, bacterial methyltransferases are attractive targets for the development
      of new antibiotics.  The Escherichia coli dam methyltransferase protein is an N-6 adenine
      methyltransferase that methylates the GATC palindrome by transfer of a methyl group from
      S-adenosyl-L-methionine.  EcoDam functions in a number of diverse and important cellular
      processes, the most well studied being postreplicative DNA mismatch repair and control of DNA
      replication.  In uropathogenic E. coli, EcoDam activity is required for conversion to and
      maintenance of the virulent phenotype.
AU  - Naumann TA
AU  - Tavassoli A
AU  - Benkovic SJ
PT  - Journal Article
TA  - Chembiochem
JT  - Chembiochem
SO  - Chembiochem 2008 9: 194-197.

PMID- 21212233
VI  - 187
DP  - 2011
TI  - Genetic Evidence That DNA Methyltransferase DRM2 Has a Direct Catalytic Role in RNA-Directed DNA Methylation in Arabidopsis thaliana.
PG  - 977-979
AB  - RNA-directed DNA methylation (RdDM) is a small RNA-mediated epigenetic modification in plants.
      We report here the identification of DOMAINS
      REARRANGED METHYLTRANSFERASE 2 (DRM2) in a forward screen for mutants
      defective in RdDM in Arabidopsis thaliana. The finding of a mutation in
      the presumptive active site argues in favor of direct catalytic
      activity for DRM2.
AU  - Naumann U
AU  - Daxinger L
AU  - Kanno T
AU  - Eun C
AU  - Long QA
AU  - Lorkovic ZJ
AU  - Matzke M
AU  - Matzke AJM
PT  - Journal Article
TA  - Genetics
JT  - Genetics
SO  - Genetics 2011 187: 977-979.

PMID- 25169862
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Fish Pathogen Yersinia ruckeri Strain 37551, Serotype O1b, Isolated from Diseased, Vaccinated Atlantic Salmon (Salmo salar) in  Chile.
PG  - e00858-14
AB  - We sequenced the genome of a motile O1b Yersinia ruckeri field isolate from Chile, which is
      causing enteric redmouth disease (ERM) in vaccinated Atlantic
      salmon (Salmo salar). The draft genome has 3,775,486 bp, a G+C content of 47.1%,
      and is predicted to contain 3,406 coding sequences.
AU  - Navas E
AU  - Bohle H
AU  - Henriquez P
AU  - Grothusen H
AU  - Bustamante F
AU  - Bustos P
AU  - Mancilla M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00858-14.

PMID- 25593256
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Thermus sp. Isolate 2.9, Obtained from a Hot Water Spring Located in Salta, Argentina.
PG  - e01414-14
AB  - Thermus sp. isolate 2.9 was obtained from a hot water spring in Salta, Argentina. Here, we
      report the draft genome sequence (2,485,434 bp) of this isolate, which
      consists of 11 scaffolds of >10 kbp and 2,719 protein-coding sequences.
AU  - Navas LE
AU  - Berretta MF
AU  - Ortiz EM
AU  - Benintende GB
AU  - Amadio AF
AU  - Zandomeni RO
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01414-14.

PMID- 28360155
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Bacillus thuringiensis INTA Fr7-4.
PG  - e00076-17
AB  - We report here the complete annotated 6,035,547-bp draft genome sequence of Bacillus
      thuringiensis INTA Fr7-4. This strain contains three cry8 and two vip1
      and vip2 insecticidal toxin genes.
AU  - Navas LE
AU  - Berretta MF
AU  - Ortiz EM
AU  - Sauka DH
AU  - Benintende GB
AU  - Zandomeni RO
AU  - Amadio AF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00076-17.

PMID- 23704179
VI  - 1
DP  - 2013
TI  - Genome Sequence of Lactobacillus plantarum Strain UCMA 3037.
PG  - e00251-13
AB  - Nucleic acid of the strain Lactobacillus plantarum UCMA 3037, isolated from raw milk camembert
      cheese in our laboratory, was sequenced. We present its draft
      genome sequence with the aim of studying its functional properties and
      relationship to the cheese ecosystem.
AU  - Naz S
AU  - Tareb R
AU  - Bernardeau M
AU  - Vaisse M
AU  - Lucchetti-Miganeh C
AU  - Rechenmann M
AU  - Vernoux JP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00251-13.

PMID- 2445354
VI  - 13
DP  - 1987
TI  - Cleavage of synthetic RNA-DNA hybrids with restriction endonucleases BamHI and Sau3AI.
PG  - 928-933
AB  - Synthetic oligodeoxyribonucleotides, containing one or two ribonucleotides in
      the recognition sequence, and RNA-DNA hybrids were tested for their activity in
      cleavage with BamHI and Sau3AI endonucleases.  The replacement of dG with G in
      the first position of BamHI-site (GGATCC) of one of the chains does not affect
      the rate of the BamHI hydrolysis.  The similar heteroduplex, containing G
      residue in the second position, displays a decreased rate of the BamHI
      hydrolysis of the modified strand and to a lesser extent, of the unmodified
      complementary strand.  Oligodeoxyribonucleotides in complex with
      oligoribonucleotides can be cleaved with the excess of BamHI and Sau3AI
      oligoribonucleotides remaining intact.
AU  - Nazarenko IA
AU  - Gorbunov YA
AU  - Malysgin EG
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1987 13: 928-933.

PMID- 28626548
VI  - 8
DP  - 2017
TI  - Nonomuraea sp. ATCC 55076 harbors the largest actinomycete chromosome to date and the kistamicin biosynthetic gene cluster.
PG  - 780-788
AB  - Glycopeptide antibiotics (GPAs) have served as potent clinical drugs and as an inspiration to
      chemists in various disciplines. Among known GPAs, complestatin, chloropeptin, and kistamicin
      are unique in that they contain an unusual indole-phenol crosslink. The mechanism of formation
      of this linkage is unknown, and to date, the biosynthetic gene cluster of only one GPA with an
      indole-phenol crosslink, that of complestatin, has been identified. Here, we report the genome
      sequence of the kistamicin producer Nonomuraea sp. ATCC 55076. We find that this strain
      harbours the largest actinobacterial chromosome to date, consisting of a single linear
      chromosome of 13.1 Mbp. AntiSMASH analysis shows that 32 biosynthetic gene clusters and 10% of
      the genome are devoted to production of secondary metabolites, which include
      1,6-dihydroxyphenazine and nomuricin, a new anthraquinone-type pentacyclic compound that we
      report herein. The kistamicin gene cluster (kis) was identified bioinformatically. A unique
      feature of kis is that it contains two cytochrome P450 enzymes, which likely catalyze three
      crosslinking reactions. These findings set the stage for examining the biosynthesis of
      kistamicin and its unusual indole-phenol crosslink in the future.
AU  - Nazari B
AU  - Forneris CC
AU  - Gibson MI
AU  - Moon K
AU  - Schramma KR
AU  - Setedsayamdost MR
PT  - Journal Article
TA  - MedChemComm
JT  - MedChemComm
SO  - MedChemComm 2017 8: 780-788.

PMID- 22843604
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of the Soil Bacterium Burkholderia terrae Strain BS001, Which Interacts with Fungal Surface Structures.
PG  - 4480-4481
AB  - Burkholderia terrae BS001 is a soil bacterium which was originally isolated from  the
      mycosphere of the ectomycorrhizal fungus Laccaria proxima. It exhibits a
      range of fungus-interacting traits which reveal its propensity to actively
      interact at fungal interfaces. Here, we present the approximately 11.5-Mb (G+C
      content, 61.52%) draft genome sequence of B. terrae BS001 with the aim of
      providing insight into the genomic basis of its ecological success in
      fungus-affected soil settings.
AU  - Nazir R
AU  - Hansen MA
AU  - Sorensen S
AU  - van Elsas JD
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4480-4481.

PMID- 25125646
VI  - 2
DP  - 2014
TI  - Whole-genome sequences of three symbiotic endozoicomonas strains.
PG  - e00802-14
AB  - Members of the genus Endozoicomonas associate with a wide range of marine organisms. Here, we
      report on the whole-genome sequencing, assembly, and
      annotation of three Endozoicomonas type strains. These data will assist in
      exploring interactions between Endozoicomonas organisms and their hosts, and it
      will aid in the assembly of genomes from uncultivated Endozoicomonas spp.
AU  - Neave MJ
AU  - Michell CT
AU  - Apprill A
AU  - Voolstra CR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00802-14.

PMID- 19223329
VI  - 37
DP  - 2009
TI  - Atomic force microscopy of the EcoKI Type I DNA restriction enzyme bound to DNA shows enzyme dimerization and DNA looping.
PG  - 2053-2063
AB  - Atomic force microscopy (AFM) allows the study of single protein-DNA interactions such as
      those observed with the Type I
      Restriction-Modification systems. The mechanisms employed by these systems
      are complicated and understanding them has proved problematic. It has been
      known for years that these enzymes translocate DNA during the restriction
      reaction, but more recent AFM work suggested that the archetypal EcoKI
      protein went through an additional dimerization stage before the onset of
      translocation. The results presented here extend earlier findings
      confirming the dimerization. Dimerization is particularly common if the
      DNA molecule contains two EcoKI recognition sites. DNA loops with dimers
      at their apex form if the DNA is sufficiently long, and also form in the
      presence of ATPgammaS, a non-hydrolysable analogue of the ATP required for
      translocation, indicating that the looping is on the reaction pathway of
      the enzyme. Visualization of specific DNA loops in the protein-DNA
      constructs was achieved by improved sample preparation and analysis
      techniques. The reported dimerization and looping mechanism is unlikely to
      be exclusive to EcoKI, and offers greater insight into the detailed
      functioning of this and other higher order assemblies of proteins
      operating by bringing distant sites on DNA into close proximity via DNA
      looping.
AU  - Neaves KJ
AU  - Cooper LP
AU  - White JH
AU  - Carnally SM
AU  - Dryden DT
AU  - Edwardson JM
AU  - Henderson RM
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: 2053-2063.

PMID- 7607506
VI  - 157
DP  - 1995
TI  - Analysis of overlapping cDNA clones specific for a putative second DNA methyltransferase-encoding gene in Arabidopsis thaliana.
PG  - 269-272
AB  - We have isolated and sequenced overlapping cDNA clones specific for a putative second DNA
      methyltransferase (MTase)-encoding gene (MTase11) from Arabidopsis thaliana (At) recently
      described as a genomic DNA fragment.  The gene seems to be present as a single copy in the At
      genome and is transcribed into a 2.2-kb messenger detectable only in young seedlings.  Using
      sequence comparison we found structural differences between the cDNA clones and the previously
      reported genomic fragment.  The amino-acid sequence deduced from the 1.8-kb cDNA sequence
      shows the occurrence of the conserved motif number VI characteristic for m5C-MTases.  Northern
      and Southern analysis detects no cross-hybridization with the originally described
      MTase-encoding At gene (MTase1).
AU  - Nebendahl A
AU  - Baumlein H
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 269-272.

PMID- Not included in PubMed...
VI  - 31
DP  - 1995
TI  - Plasmid profiles and stability of industrial strains of lactococci.
PG  - 1210-1217
AB  - Industrial lactococci strains, usually cultivated on agar with hydrolized milk, are
      characterized by an increased instability with respect to their ability to utilize lactose on
      an enriched M21 medium.  Plasmid profiles of 14 industrial strains of Lactococcus lactis subs.
      lactis and of a large number of segregants phenotypically differing in sugar-fermenting
      ability and phage sensitivity were examined.  Four out of 14 strains segregated Lac-Gal-
      clones, i.e., simultaneously lost the ability to utilize lactose and galactose.  All
      phage-sensitive segregants retained systems of DNA restriction and modification.  Segregants
      sensitive to the phage lethal effect were found.  These segregants possibly retained the
      defense mechanism against phages manifested as an abortive infection.  In the majority of lac-
      segregants, large plasmids of 40 to 55 kb were lost, although changes in plasmid profiles of
      many Lac- segregants were not detected.
AU  - Nechaeva AA
AU  - Kalinina NA
AU  - Sukhodolets VV
PT  - Journal Article
TA  - Genetika
JT  - Genetika
SO  - Genetika 1995 31: 1210-1217.

PMID- 2657723
VI  - 86
DP  - 1989
TI  - Determinants of EcoRI endonuclease sequence discrimination.
PG  - 3579-3583
AB  - The arginine at position 200 of EcoRI endonuclease is thought to make two
      hydrogen bonds to the guanine of the sequence GAATTC and thus be an important
      determinant of sequence discrimination.  Arg-200 was replaced by each of the
      other 29 naturally occurring amino acids, and the mutant endonucleases were
      assessed for activities in vivo and in vitro.  The mutant endonuclease with
      lysine at position 200 exhibits the most in vivo activity of all the position
      200 mutants, although the in vitro activity is less than 1/100th of wild-type
      activity.  Five other mutants show more drastically reduced levels of in vivo
      activity (Cys, Pro, Val, Ser, and Trp).  The Cys, Val, and Ser mutant enzymes
      appear to have in vivo activity which is specific for the wild-type canonical
      site despite the loss of hydrogen bonding potential at position 200.  The Pro
      and Trp mutants retain in vivo activity which is independent of the presence of
      the EcoRI methylase.  In crude cell lysates, only the Cys mutant shows a very
      low level of in vitro activity.  None of the mutant enzymes show a preference
      for alternative sites in assays in vitro.  The implications of these results
      are discussed.
AU  - Needels MC
AU  - Fried SR
AU  - Love R
AU  - Rosenberg JM
AU  - Boyer HW
AU  - Greene PJ
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1989 86: 3579-3583.

PMID- 3470568
VI  - 11C
DP  - 1987
TI  - Cassette mutagenesis of EcoRI endonuclease.
PG  - 209
AB  - From inspection of the x-ray crystal structure of the DNA-EcoRI endonuclease
      recognition complex, regions of the protein which are responsible for binding
      specificity and catalysis were inferred.  Based on this structural information,
      we have subjected the EcoRI endonuclease gene to site directed mutagenesis.  In
      the first round of mutagenesis we used mismatched oligonucleotides to introduce
      a small number of conservative substitutions into the putative recognition
      regions.  In order to extend this analysis, we have now engineered several
      unique restriction sites into the EcoRI endonuclease gene bracketing
      potentially important regions.  For example, we have introduced sites which
      bracket the N-terminal residues of each of the recognition helices.  Also, the
      introduction of flanking BstEII and SpeI sites around residue 130 has allowed
      us to test a model for the mechanism of phosphodiester hydrolysis.  Based on
      the crystal structure of the protein-DNA complex, it is possible that Lys 130
      participates in general acid catalysis of this reaction.  Employing cassette
      mutagenesis, we have generated mutants of the EcoRI endonuclease gene which
      encode a variety of different amino acids at position 130.  The mutant gene
      products are being characterized and the effect on catalysis of different
      substitutions at position 130 is being assessed.
AU  - Needels MC
AU  - Reich NO
AU  - Boyer HW
AU  - Greene P
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1987 11C: 209.

PMID- 29437113
VI  - 6
DP  - 2018
TI  - Genome Sequence of Hydrogenovibrio sp. Strain SC-1, a Chemolithoautotrophic Sulfur and Iron Oxidizer.
PG  - e01581-17
AB  - Hydrogenovibrio sp. strain SC-1 was isolated from pyrrhotite incubated in situ in the marine
      surface sediment of Catalina Island, CA. Strain SC-1 has demonstrated
      autotrophic growth through the oxidation of thiosulfate and iron. Here, we
      present the 2.45-Mb genome sequence of SC-1, which contains 2,262 protein-coding
      genes.
AU  - Neely C
AU  - Bou KC
AU  - Cervantes A
AU  - Diaz R
AU  - Escobar A
AU  - Ho K
AU  - Hoefler S
AU  - Smith HH
AU  - Abuyen K
AU  - Savalia P
AU  - Nealson KH
AU  - Emerson D
AU  - Tully B
AU  - Barco RA
AU  - Amend J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01581-17.

PMID- 16340006
VI  - 33
DP  - 2005
TI  - Time-resolved fluorescence of 2-aminopurine as a probe of base flipping in M.HhaI-DNA complexes.
PG  - 6953-6960
AB  - DNA base flipping is an important mechanism in molecular enzymology, but its study is limited
      by the lack of an accessible and reliable diagnostic technique. A series of crystalline
      complexes of a DNA methyltransferase, M.HhaI, and its cognate DNA, in which a fluorescent
      nucleobase analogue, 2-aminopurine (AP), occupies defined positions with respect the target
      flipped base, have been prepared and their structures determined at higher than 2 A
      resolution. From time-resolved fluorescence measurements of these single crystals, we have
      established that the fluorescence decay function of AP shows a pronounced, characteristic
      response to base flipping: the loss of the very short (approximately 100 ps) decay component
      and the large increase in the amplitude of the long (approximately 10 ns) component. When AP
      is positioned at sites other than the target site, this response is not seen. Most
      significantly, we have shown that the same clear response is apparent when M.HhaI complexes
      with DNA in solution, giving an unambiguous signal of base flipping. Analysis of the AP
      fluorescence decay function reveals conformational heterogeneity in the DNA-enzyme complexes
      that cannot be discerned from the present X-ray structures.
AU  - Neely RK
AU  - Daujotyte D
AU  - Grazulis S
AU  - Magennis SW
AU  - Dryden DTF
AU  - Klimasauskas S
AU  - Jones AC
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2005 33: 6953-6960.

PMID- 18479503
VI  - 9
DP  - 2008
TI  - The BsaHI Restriction-Modification System: Cloning, Sequencing and Analysis of Conserved Motifs.
PG  - 48
AB  - ABSTRACT: BACKGROUND: Restriction and modification enzymes typically recognise short DNA
      sequences of between two and eight bases in length.
      Understanding the mechanism of this recognition represents a significant
      challenge that we begin to address for the BsaHI restriction-modification
      system, which recognises the six base sequence GRCGYC. RESULTS: The DNA
      sequences of the genes for the BsaHI methyltransferase, bsaHIM, and
      restriction endonuclease, bsaHIR, have been determined (GenBank accession
      #EU386360), cloned and expressed in E.coli. Both the restriction
      endonuclease and methyltransferase enzymes share significant homology with
      a group of 6 other enzymes comprising the RM systems HgiDI and HgiGI and
      the putative HindVP, NlaCORFDP, NpuORFC228P and SplZORFNP RM systems. A
      sequence alignment of these homologues shows that their amino acid
      sequences are largely conserved and highlights several motifs of interest.
      One such conserved motif was identified at the C-terminal end of the
      bsaHIR gene as a potential DNA-recognising region of the enzyme. A
      mutational analysis of these amino acids is consistent with this
      assignment. Sequence alignment of the methyltransferase gene reveals a
      motif that may be used as a diagnostic tool to define the recognition
      sequences of the cytosine C5 methyltransferases. CONCLUSIONS: We have
      identified a region of the R.BsaHI enzyme that is likely involved in DNA
      recognition. Analysis of the amino acid sequence of the BsaHI
      methyltransferase enzyme led us to propose two new motifs that can be used
      in the diagnosis of the recognition sequence of the cytosine
      C5-methyltransferases.
AU  - Neely RK
AU  - Roberts RJ
PT  - Journal Article
TA  - BMC Mol. Biol.
JT  - BMC Mol. Biol.
SO  - BMC Mol. Biol. 2008 9: 48.

PMID- 19740769
VI  - 37
DP  - 2009
TI  - Time-resolved fluorescence studies of nucleotide flipping by restriction enzymes.
PG  - 6859-6870
AB  - Restriction enzymes Ecl18kI, PspGI and EcoRII-C, specific for interrupted 5-bp target
      sequences, flip the central base pair of these sequences into
      their protein pockets to facilitate sequence recognition and adjust the
      DNA cleavage pattern. We have used time-resolved fluorescence spectroscopy
      of 2-aminopurine-labelled DNA in complex with each of these enzymes in
      solution to explore the nucleotide flipping mechanism and to obtain a
      detailed picture of the molecular environment of the extrahelical bases.
      We also report the first study of the 7-bp cutter, PfoI, whose recognition
      sequence (T/CCNGGA) overlaps with that of the Ecl18kI-type enzymes, and
      for which the crystal structure is unknown. The time-resolved fluorescence
      experiments reveal that PfoI also uses base flipping as part of its DNA
      recognition mechanism and that the extrahelical bases are captured by PfoI
      in binding pockets whose structures are quite different to those of the
      structurally characterized enzymes Ecl18kI, PspGI and EcoRII-C. The
      fluorescence decay parameters of all the enzyme-DNA complexes are
      interpreted to provide insight into the mechanisms used by these four
      restriction enzymes to flip and recognize bases and the relationship
      between nucleotide flipping and DNA cleavage.
AU  - Neely RK
AU  - Tamulaitis G
AU  - Chen K
AU  - Kubala M
AU  - Siksnys V
AU  - Jones AC
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: 6859-6870.

PMID- 2646288
VI  - 171
DP  - 1989
TI  - Construction and shuttling of novel bifunctional vectors for Streptomyces spp. and Escherichia coli.
PG  - 1569-1573
AB  - Shuttle vectors for gene transfer between Streptomyces spp. and Escherichia
      coli have been constructed by fusion of an artificial multicopy E. coli
      replicon and DNA fragments of pIJ702.  Stable transfer to Streptomyces lividans
      was obtained.  Marked differences in transformation efficiency were observed
      when plasmid DNA isolated from E. coli GM119 was used instead of that from
      strain HB101.
AU  - Neesen K
AU  - Volckaert G
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1989 171: 1569-1573.

PMID- 8129950
VI  - 5
DP  - 1993
TI  - Protein splicing: selfish genes invade cellular proteins.
PG  - 971-976
AB  - Protein splicing is a series of enzymatic events involving intramolecular
      protein breakage, rejoining and intron homing, in which introns are able to promote the
      recombinative transposition of their own coding sequences.  Eukaryotic and prokaryotic
      spliced proteins have conserved similar gene structure, but little amino acid identity.  The
      genes coding for these spliced proteins contain internal in-frame introns that encode
      polypeptides that apparently self-excise from the resulting host protein sequences.
      Excision of the 'protein intron' is coupled with joining of the two flanking protein regions
      encoded by exons of the host gene.  Some introns of this type encode DNA endonucleases,
      related to Group I RNA intron gene products, that stimulate gene conversion and self-
      transmission.
AU  - Neff NF
PT  - Journal Article
TA  - Curr. Opin. Cell Biol.
JT  - Curr. Opin. Cell Biol.
SO  - Curr. Opin. Cell Biol. 1993 5: 971-976.

PMID- 25103767
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Hexachlorohexane (HCH)-Degrading Sphingobium lucknowense Strain F2T, Isolated from an HCH Dumpsite.
PG  - e00788-14
AB  - Sphingobium lucknowense F2(T), isolated from the hexachlorocylcohexane (HCH) dumpsite located
      in Ummari village, Lucknow, India, rapidly degrades HCH isomers.
      Here we report the draft genome of strain F2 (4.4 Mbp), consisting of 4,910
      protein coding genes with an average G+C content of 64.3%.
AU  - Negi V
AU  - Lata P
AU  - Sangwan N
AU  - Kumar-Gupta S
AU  - Das S
AU  - Rao DL
AU  - Lal R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00788-14.

PMID- 29326222
VI  - 6
DP  - 2018
TI  - Genome Sequence of Actinobacillus seminis Strain ATCC 15768, a Reference Strain of Ovine Pathogens That Causes Infections in Reproductive Organs.
PG  - e01453-17
AB  - The draft genome sequence of Actinobacillus seminis strain ATCC 15768 is reported here. The
      genome comprises 22 contigs corresponding to 2.36 Mb with 40.7% G+C
      content and contains several genes related to virulence, including a putative RTX
      protein.
AU  - Negrete-Abascal E
AU  - Montes-Garcia F
AU  - Vaca-Pacheco S
AU  - Leyto-Gil AM
AU  - Fragoso-Garcia E
AU  - Carvente-Garcia R
AU  - Perez-Agueros S
AU  - Castelan-Sanchez HG
AU  - Garcia-Molina A
AU  - Villamar TE
AU  - Sanchez-Alonso P
AU  - Vazquez-Cruz C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01453-17.

PMID- 26966210
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Three Flavobacterium psychrophilum Strains Isolated from Coldwater Disease Outbreaks at Three Production Hatcheries.
PG  - e00035-16
AB  - We report here the genome sequences of three Flavobacterium psychrophilum strains causing a
      bacterial coldwater disease (BCWD) outbreak, isolated from infected
      rainbow trout from hatcheries in Montana and South Dakota. The availability of
      these virulent outbreak-causing strain genome sequences will help further
      understand the pathogenesis of BCWD.
AU  - Neiger R
AU  - Thomas M
AU  - Das S
AU  - Barnes M
AU  - Fletcher B
AU  - Snekvik K
AU  - Thompson J
AU  - Scaria J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00035-16.

PMID- 3271523
VI  - 6
DP  - 1988
TI  - Site-specific chemical modification of B-Z junctions in supercoiled DNA as detected by nuclease S1 digestion, inhibition of restriction cleavage and nucleotide sequencing.
PG  - 261-273
AB  - Structural distortions on the boundary between right-handed and left-
      handed segments in the superhelical plasmid pPK2 (a derivative of pUC19 containing (dC-
      dG)n segments cloned into polylinker) were studied by means of chemical probes.  Strong
      osmium tetroxide, pyridine (Os,py) modification of DNA at native superhelical density (sigma)
      was found in four thymines surrounding the (dC-dG)13 segment.  These results correlated  with
      restriction cleavage inhibition (due to modification): BamHI cleavage was strongly  inhibited,
      unlike the neighboring XbaI and SalI (weak or no inhibition).  In the (dC-dG)8  segment
      considerably weaker modification of the B-Z junctions was observed,
      accompanied by weak inhibition of BamHI cleavage, while the neighboring SmaI and KpnI
      were not affected.  Os,py modification of DNA at native sigma was not detected by nuclease S1
      cleavage at and (dC-dG)n segment.  However, this enzyme recognized and cleaved at the  B-Z
      junction, osmium modified at more negative sigma.  The results obtained with the glyoxal  and
      diethyl pyrocarbonate modification support the idea of very narrow B-Z junctions at  native
      sigma.
AU  - Nejedly K
AU  - Matyasek R
AU  - Palecek E
PT  - Journal Article
TA  - J. Biomol. Struct. Dyn.
JT  - J. Biomol. Struct. Dyn.
SO  - J. Biomol. Struct. Dyn. 1988 6: 261-273.

PMID- 17069852
VI  - 365
DP  - 2007
TI  - Plasmid-encoded Antirestriction Protein ArdA Can Discriminate between Type I Methyltransferase and Complete Restriction-Modification System.
PG  - 284-297
AB  - Many promiscuous plasmids encode the antirestriction proteins ArdA (alleviation of restriction
      of DNA) that specifically affect the
      restriction activity of heterooligomeric type I restriction-modification
      (R-M) systems in Escherichia coli cells. In addition, a lot of the
      putative ardA genes encoded by plasmids and bacterial chromosomes are
      found as a result of sequencing of complete genomic sequences, suggesting
      that ArdA proteins and type I R-M systems that seem to be widespread among
      bacteria may be involved in the regulation of gene transfer among
      bacterial genomes. Here, the mechanism of antirestriction action of ArdA
      encoded by IncI plasmid ColIb-P9 has been investigated in comparison with
      that of well-studied T7 phage-encoded antirestriction protein Ocr using
      the mutational analysis, retardation assay and His-tag affinity
      chromatography. Like Ocr, ArdA protein was shown to be able to efficiently
      interact with EcoKI R-M complex and affect its in vivo and in vitro
      restriction activity by preventing its interaction with specific DNA.
      However, unlike Ocr, ArdA protein has a low binding affinity to EcoKI
      Mtase and the additional C-terminal tail region (VF-motif) is needed for
      ArdA to efficiently interact with the type I R-M enzymes. It seems likely
      that this ArdA feature is a basis for its ability to discriminate between
      activities of EcoKI Mtase (modification) and complete R-M system
      (restriction) which may interact with unmodified DNA in the cells
      independently. These findings suggest that ArdA may provide a very
      effective and delicate control for the restriction and modification
      activities of type I systems and its ability to discriminate against DNA
      restriction in favour of the specific modification of DNA may give some
      advantage for efficient transmission of the ardA-encoding promiscuous
      plasmids among different bacterial populations.
AU  - Nekrasov SV
AU  - Agafonova OV
AU  - Belogurova NG
AU  - Delver EP
AU  - Belogurov AA
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2007 365: 284-297.

PMID- 29066327
VI  - 154
DP  - 2018
TI  - Genome and Methylome Variation in Helicobacter pylori With a cag Pathogenicity Island During Early Stages of Human Infection.
PG  - 612-623.e7
AB  - BACKGROUND and AIMS: Helicobacter pylori is remarkable for its genetic variation; yet, little
      is known about its genetic changes during early stages of human
      infection, as the bacteria adapt to their new environment. We analyzed genome and
      methylome variations in a fully virulent strain of H pylori during experimental
      infection. METHODS: We performed a randomized Phase I/II, observer-blind,
      placebo-controlled study of 12 healthy, H pylori-negative adults in Germany from
      October 2008 through March 2010. The volunteers were given a prophylactic vaccine
      candidate (n = 7) or placebo (n = 5) and then challenged with H pylori strain
      BCM-300. Biopsy samples were collected and H pylori were isolated. Genomes of the
      challenge strain and 12 reisolates, obtained 12 weeks after (or in 1 case, 62
      weeks after) infection were sequenced by single-molecule, real-time technology,
      which, in parallel, permitted determination of genome-wide methylation patterns
      for all strains. Functional effects of genetic changes observed in H pylori
      strains during human infection were assessed by measuring release of interleukin
      8 from AGS cells (to detect cag pathogenicity island function), neutral red
      uptake (to detect vacuolating cytotoxin activity), and adhesion assays. RESULTS:
      The observed mutation rate was in agreement with rates previously determined from
      patients with chronic H pylori infections, without evidence of a mutation burst.
      A loss of cag pathogenicity island function was observed in 3 reisolates. In
      addition, 3 reisolates from the vaccine group acquired mutations in the
      vacuolating cytotoxin gene vacA, resulting in loss of vacuolization activity. We
      observed interstrain variation in methylomes due to phase variation in genes
      encoding methyltransferases. CONCLUSIONS: We analyzed adaptation of a fully
      virulent strain of H pylori to 12 different volunteers to obtain a robust
      estimate of the frequency of genetic and epigenetic changes in the absence of
      interstrain recombination. Our findings indicate that the large amount of genetic
      variation in H pylori poses a challenge to vaccine development.
      ClinicalTrials.gov no: NCT00736476.
AU  - Nell S
AU  - Estibariz I
AU  - Krebes J
AU  - Bunk B
AU  - Graham DY
AU  - Overmann J
AU  - Song Y
AU  - Sproer C
AU  - Yang I
AU  - Wex T
AU  - Korlach J
AU  - Malfertheiner P
AU  - Suerbaum S
PT  - Journal Article
TA  - Gastroenterology
JT  - Gastroenterology
SO  - Gastroenterology 2018 154: 612-623.e7.

PMID- 9279140
VI  - 11
DP  - 1997
TI  - Characterization of a non-type II restriction/modification system on plasmid PJW565 from Lactococcus lactis subsp. cremoris W56.
PG  - A1035
AB  - Lactococcus lactis subsp. cremoris W56 contains several plasmid encoded
      restriction-modification systems.  The 12.826 kb plasmid pJW565 exhibits a non-type II
      activity, designated LlaBII, and displays resistance against small-isometric-headed phages p2
      and SK1.  The entire plasmid has been sequenced.  Sequence analysis revealed that the R/M
      system was encoded by at least two genes, carrying code for the 231 amino acid protein
      designated llabiiM, and the 1376 amino acid protein designated llabiiR.  Both genes were
      preceded by putative promoter and RBS sequences.  The two genes were separated by 1
      nucleotide, indicating polycistronic transcription.  The predicted proteins (M.LlaBII and
      R.LlaBII) showed homology to several adenine-specific methyltransferases and an E. coli type I
      restriction enzyme, respectively.  Apart from the putative genes involved in the R/M system
      activity and the genes involved in replication, pJW565 contained several open reading frames
      with no known function or homology to existing sequencing data in the EMBL or Genbank
      databases.  In vitro studies of LlaBII activity revealed that the cofactor ATP was essential,
      and the methyl-group donor Adomet stimulated LlaBII endonuclease activity.
AU  - Nellemann LJ
AU  - Aamand JL
AU  - Madsen A
AU  - Josephsen J
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1997 11: A1035.

PMID- 24675861
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence for the Fusarium Head Blight Antagonist Bacillus amyloliquefaciens Strain TrigoCor 1448.
PG  - e00219-14
AB  - We present the complete genome sequence for Bacillus amyloliquefaciens TrigoCor 1448 (ATCC
      202152), a bacterial biological control agent for Fusarium head blight
      in wheat. We compare it to its closest relative, B. amyloliquefaciens strain
      AS43.3.
AU  - Nelson BA
AU  - Ramaiya P
AU  - Lopez-de-Leon A
AU  - Kumar R
AU  - Crinklaw A
AU  - Jolkovsky E
AU  - Crane JM
AU  - Bergstrom GC
AU  - Rey MW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00219-14.

PMID- 8807872
VI  - 3
DP  - 1996
TI  - Base eversion and shuffling by DNA methyltransferases.
PG  - 419-423
AB  - The structures of two DNA cytosine methyltransferases reveal two novel methods of gaining
      access to the substrate cytosine residue, both of which involve eversion of the cytosine in a
      process that may require DNA bending.  In one instance there is also widespread base shuffling
      and distortion of the DNA.
AU  - Nelson HCM
AU  - Bestor TH
PT  - Journal Article
TA  - Chem. Biol.
JT  - Chem. Biol.
SO  - Chem. Biol. 1996 3: 419-423.

PMID- 2159636
VI  - 18
DP  - 1990
TI  - FseI, a new type II restriction endonuclease that recognizes the octanucleotide sequence 5' GGCCGGCC 3' .
PG  - 2061-2064
AB  - A Type II restriction endonuclease, designated FseI, has been partially purified from a
      Frankia species (NRRL 18528). This enzyme cleaves Adenovirus 2 DNA at three sites, but does
      not cleave the DNAs from bacteriophages lambda, T7 and PhiX174, the animal virus SV40, pUC18
      and pBR322. FseI recognizes the octanucleotide sequence 5' GGCCGG^CC 3' and cleaves as
      indicated by the arrow. The frequency of occurrence of FseI sites within sequenced regions of
      the human genome is similar to that for NotI sites.
AU  - Nelson JM
AU  - Miceli SM
AU  - Lechevalier MP
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 2061-2064.

PMID- 12949112
VI  - 185
DP  - 2003
TI  - Complete genome sequence of the oral pathogenic bacterium Porphyromonas gingivalis strain W83.
PG  - 5591-5601
AB  - The complete 2,343,479-bp genome sequence of the gram-negative, pathogenic oral bacterium
      Porphyromonas gingivalis strain W83, a major contributor to
      periodontal disease, was determined. Whole-genome comparative analysis
      with other available complete genome sequences confirms the close
      relationship between the Cytophaga-Flavobacteria-Bacteroides (CFB) phylum
      and the green-sulfur bacteria. Within the CFB phyla, the genomes most
      similar to that of P. gingivalis are those of Bacteroides thetaiotaomicron
      and B. fragilis. Outside of the CFB phyla the most similar genome to P.
      gingivalis is that of Chlorobium tepidum, supporting the previous
      phylogenetic studies that indicated that the Chlorobia and CFB phyla are
      related, albeit distantly. Genome analysis of strain W83 reveals a range
      of pathways and virulence determinants that relate to the novel biology of
      this oral pathogen. Among these determinants are at least six putative
      hemagglutinin-like genes and 36 previously unidentified peptidases. Genome
      analysis also reveals that P. gingivalis can metabolize a range of amino
      acids and generate a number of metabolic end products that are toxic to
      the human host or human gingival tissue and contribute to the development
      of periodontal disease.
AU  - Nelson KE et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2003 185: 5591-5601.

PMID- 15115801
VI  - 32
DP  - 2004
TI  - Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome   components of this species.
PG  - 2386-2395
AB  - The genomes of three strains of Listeria monocytogenes that have been associated with
      food-borne illness in the USA were subjected to whole
      genome comparative analysis. A total of 51, 97 and 69 strain-specific
      genes were identified in L.monocytogenes strains F2365 (serotype 4b,
      cheese isolate), F6854 (serotype 1/2a, frankfurter isolate) and H7858
      (serotype 4b, meat isolate), respectively. Eighty-three genes were
      restricted to serotype 1/2a and 51 to serotype 4b strains. These strain-
      and serotype-specific genes probably contribute to observed differences in
      pathogenicity, and the ability of the organisms to survive and grow in
      their respective environmental niches. The serotype 1/2a-specific genes
      include an operon that encodes the rhamnose biosynthetic pathway that is
      associated with teichoic acid biosynthesis, as well as operons for five
      glycosyl transferases and an adenine-specific DNA methyltransferase. A
      total of 8603 and 105 050 high quality single nucleotide polymorphisms
      (SNPs) were found on the draft genome sequences of strain H7858 and strain
      F6854, respectively, when compared with strain F2365. Whole genome
      comparative analyses revealed that the L.monocytogenes genomes are
      essentially syntenic, with the majority of genomic differences consisting
      of phage insertions, transposable elements and SNPs.
AU  - Nelson KE et al
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2004 32: 2386-2395.

PMID- 10360571
VI  - 399
DP  - 1999
TI  - Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima.
PG  - 323-329
AB  - The 1,860,725-base pair genome of Thermotoga maritima MSB8 contains 1,877 predicted coding
      regions, 1,014 (54%) of which have functional assignments and 863 (46%) of which are of
      unknown function. Genome analysis reveals numerous pathways involved in degradation of sugars
      and plant polysaccharides, and 108 genes that have orthologues only in the genomes of other
      thermophilic Eubacteria and Archaea.  Of the Eubacteria sequenced to date, T. maritima has the
      highest percentage (24%) of genes that are most similar to archaeal genes.  Eighty-one
      archaeal-like genes are clustered in 15 regions of the T. maritima genome that range in size
      from 4 to 20 kilobases.  Conservation of gene order between T. maritima and Archaea in many of
      the clustered regions suggests that lateral gene transfer may have occurred between
      thermophilic Eubacteria and Archaea.
AU  - Nelson KE et al
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1999 399: 323-329.

PMID- 9628333
VI  - 379
DP  - 1998
TI  - Chlorella viruses encode multiple DNA methyltransferases.
PG  - 423-428
AB  - The >320 kb dsDNA genomes of 16 viruses which infect Chlorella strain NC64A and 5 viruses
      infecting Chlorella strain Pbi were tested for their sensitivity/resistance to more than 80
      DNA restriction endonucleases.  From the known methylation sensitivities of these enzymes to
      site-specific 5-methylcytosine and N6-methyladenine DNA modifications, we deduce that the 16
      NC64A viruses encode at least 13 different sequence-specific DNA methyltransferases and the 5
      Pbi viruses encode at least 7 sequence-specific DNA methyltransferases.  Each DNA
      methyltransferase has a 2 to 4 base pair DNA recognition sequence.  Some individual viruses
      encode as many as ten different DNA methyltransferases, making these chlorella virus genomes
      among the most concentrated sources of DNA methyltransferase genes known.
AU  - Nelson M
AU  - Burbank DE
AU  - Van Etten JL
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1998 379: 423-428.

PMID- 6087274
VI  - 12
DP  - 1984
TI  - Alteration of apparent restriction endonuclease recognition specificities by DNA methylases.
PG  - 5165-5173
AB  - An in vitro method of altering the apparent cleavage specificities of
      restriction endonucleases was developed using DNA modification methylases.
      This method was used to reduce the number of cleavage sites for 34 restriction
      endonucleases.  In particular, single-site cleavages were achieved for NheI in
      Adeno-2 DNA and for AccI and HincII in pBR322 DNA by specifically methylating
      all but one recognition sequence.
AU  - Nelson M
AU  - Christ C
AU  - Schildkraut I
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1984 12: 5165-5173.

PMID- 3033612
VI  - 15
DP  - 1987
TI  - The effect of site-specific methylation on restriction-modification enzymes.
PG  - r219-r230
AB  - Previous tabulations of restriction endonuclease sensitivities to site-specific
      DNA methylation have shown that these endonucleases cannot cut particular DNA
      recognition sequences which have been methylated at 4mC, 5mC or 6mA.  Since our
      previous tabulation in this journal the major new additions are extensive data
      on 4mC.  We have altered our notation to incorporate the 4mC data and added a
      number of footnotes.  Fine structural details of cleavage reactions, rate
      differences on hemi- and bi-methylated substrates, and experimental
      discrepancies are noted where such data is available.
AU  - Nelson M
AU  - McClelland M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1987 15: r219-r230.

PMID- 2828871
VI  - 155
DP  - 1987
TI  - Purification and assay of Type II DNA methylases.
PG  - 32-41
AB  - Site-specific DNA methylases (S-adenosylmethionine:  DNA methyltransferases)
      have a variety of uses in DNA analytical procedures.  Methylases may be used as
      probes for DNA conformation, in recombinant DNA cloning strategies, or in
      combination with restriction endonucleases to generate rare or novel DNA
      cleavage specificities.  DNA methylases have been purified from a number of
      different sources.
AU  - Nelson M
AU  - McClelland M
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1987 155: 32-41.

PMID- 2541418
VI  - 17
DP  - 1989
TI  - Effect of site-specific methylation on DNA modification methyltransferases and restriction endonucleases.
PG  - r389-r415
AB  - Review of the effects of methylation.
AU  - Nelson M
AU  - McClelland M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: r389-r415.

PMID- 1645875
VI  - 19
DP  - 1991
TI  - Site-specific methylation: effect on DNA modification methyltransferases and restriction endonucleases.
PG  - 2045-2071
AB  - We present in Table I an updated list of the sensitivities of over 240
      restriction endonucleases to the site-specific DNA modifications m4C, m5C,
      hm5C, and m6A, four modifications that are common in DNA prokaryotes,
      eukaryotes, and their viruses (Mc2, Mc5, Mc8, Mc11, Ne3, Ne4).  Table II is a
      list of over 130 characterized DNA methyltransferases.  A detailed list of
      cloned restriction-modification genes has been made Wilson (Wi4).  Table III
      lists the sensitivities of over 20 Type II DNA methyltransferases to m4C, m5C,
      hm5C, and m6A modification.  Most DNA methyltransferases are sensitive to
      non-canonical modifications within their recognition sequences (Bu5, Mc10, Ne3,
      Po4), and this sensitivity may differ from that of their restriction
      endonuclease partners.  Finally, several restriction endonuclease isoschizomers
      are known to differ in their ability to cleave DNA which has been methylated.
      Table IV lists over 20 known isoschizomer pairs and one isomethylator pair,
      along with the modified recognition sites at which they differ.
AU  - Nelson M
AU  - McClelland M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 2045-2071.

PMID- Not carried by PubMed...
VI  - 18
DP  - 1989
TI  - Chromosome mapping at the megabase level: Guidelines for choosing restriction endonucleases for pulsed field gel mapping.
PG  - 1-3
AB  - A review.
AU  - Nelson M
AU  - McClelland M
PT  - Journal Article
TA  - Promega Notes
JT  - Promega Notes
SO  - Promega Notes 1989 18: 1-3.

PMID- 1336094
VI  - 216
DP  - 1992
TI  - Use of DNA methyltransferase/endonuclease enzyme combinations for megabase mapping of chromosomes.
PG  - 279-303
AB  - Based on a knowledge of the methylation sensitivities of restriction-modification enzymes, and
      the specificities of bacterial DNA methyltransferases, it is possible to mix and match
      site-specific DNA methylation and restriction endonuclease cleavage reactions to produce rare
      or novel DNA cleavages (Dobritsa and Dobritsa, 1980); Nelson et al., 1984; McClelland et al.,
      1985) Detailed procedures for the purification, assay and use of methylase/endonuclease
      combinations in sequential two-step reactions were described in a previous volume of this
      series (McClelland, 1987, Nelson and McClelland, 1987; Nelson and Shildkraut, 1987).
      Three-step procedures have also been described, based upon methylase/endonuclease combinations
      and sequence-specific masking by bacterial repressor proteins (Koob and Szybalski, 1980,
      polypyrimidine triplexes (Maher et al, 1989; Hanvey et al 1989), or other DNA
      methyltransferases (McClelland and Nelson, 1987; McClelland and Nelson, 1988a; Posfai and
      Szybalski, 1988). This article describes four selected DNA methylase/ endonuclease
      combinations which may be used for megabase mapping of chromosome fragments in the size range
      from 100 kb-2000 kb, paying special attention to features of these reactions which have
      sometimes proven problematic.
AU  - Nelson M
AU  - McClelland M
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1992 216: 279-303.

PMID- 8392715
VI  - 21
DP  - 1993
TI  - Effect of site-specific methylation on restriction endonucleases and DNA modification methyltransferases.
PG  - 3139-3154
AB  - We present in Table I an updated list of the sensitivities of 298 restriction endonucleases
      and 20 DNA methyltransferases to site-specific modification at 4-methylcytosine (m4C),
      5-methylcytosine (m5C), 5-hydroxymethylcytosine (hm5C), and 6-methyladenine (m6A), four
      modifications that are common in the DNA of prokaryotes, eukaryotes, and their viruses. In
      addition, new information is included on restriction endonuclease cleavage at sites modified
      with 5-hydroxymethyluracil (hm5U). Knowledge of the sensitivity of restriction endonucleases
      to site-specific modification can be used to study cellular DNA methylation. Several
      restriction-modification enzymes share the same recognition sequence specificity, but have
      different sensitivities to site-specific methylation. Table II lists 32 known isoschizomer
      pairs and one isomethylator pair, along with the modified recognition sites at which they
      differ.
AU  - Nelson M
AU  - Raschke E
AU  - McClelland M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 3139-3154.

PMID- 2828873
VI  - 155
DP  - 1987
TI  - The use of DNA methylases to alter the apparent recognition specificities of restriction endonucleases.
PG  - 41-48
AB  - DNA methylases can be used to alter the apparent recognition specificity of
      restriction endonucleases.  These altered specificities are unique and increase
      the list of cleavage sequences which can be utilized by molecular biologists.
AU  - Nelson M
AU  - Schildkraut I
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1987 155: 41-48.

PMID- 
VI  - 0
DP  - 1993
TI  - DNA methyltransferases and DNA-site-specific endonucleases encoded by chlorella viruses.
PG  - 186-211
AB  - Large polyhedral (diameter of 150 to 190 nm) dsDNA-containing (>30 kbp) viruses which infect
      certain unicellular, eukaryotic, chlorella-like green algae are common in fresh water
      collected throught the world (Van Etten et al, 1985; Schuster et al. 1986; Zhang et al., 1988;
      Reisser et al., 1988; Yamada et al., 1991). The hosts for these lytic chlorella viruses are
      exsymbiotic Chlorella strains NC64A and Pbi, originally isolated from the protozoan Paramecium
      bursaria. Chlorella viruses, which can be produced in large quantities, are the first viruses
      infecting a photosynthetic eukaryotic organism which can be plaque assayed (Van Etten et al.,
      1983) and have been given family status with the name Phycodnaviridae (Francki et al., 1991).
      A comprehensive review on the chlorella viruses has recently been published (Van Etten et al.,
      1991).
AU  - Nelson M
AU  - Zhang Y
AU  - Van Etten JL
PT  - Journal Article
TA  - DNA Methylation: Molecular Biology and Biological Significance
JT  - DNA Methylation: Molecular Biology and Biological Significance
SO  - DNA Methylation: Molecular Biology and Biological Significance 1993 0: 186-211.

PMID- 25657285
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of the Novel Leech Symbiont Mucinivorans hirudinis M3T.
PG  - e01530-14
AB  - Mucinivorans hirudinis M3(T) was isolated from the digestive tract of the medicinal leech,
      Hirudo verbana, and is the type species of a new genus within
      the Rikenellaceae. Here, we report the complete annotated genome sequence of this
      bacterium.
AU  - Nelson MC
AU  - Bomar L
AU  - Graf J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01530-14.

PMID- 25635018
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Yersinia ruckeri Strain CSF007-82, Etiologic Agent of Red Mouth Disease in Salmonid Fish.
PG  - e01491-14
AB  - We present the complete, closed, and finished chromosomal and extrachromosomal genome
      sequences of Yersinia ruckeri strain CSF007-82, the etiologic agent of
      enteric red mouth disease in salmonid fish. The chromosome is 3,799,036 bp with a
      G+C content of 47.5% and encodes 3,530 predicted coding sequences (CDS), 7
      ribosomal operons, and 80 tRNAs.
AU  - Nelson MC
AU  - LaPatra SE
AU  - Welch TJ
AU  - Graf J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01491-14.

PMID- 27492003
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Lactococcus garvieae Strain PAQ102015-99, an Outbreak Strain Isolated from a Commercial Trout Farm in the Northwestern United States.
PG  - e00781-16
AB  - We announce the draft genome assembly of Lactococcus garvieae strain PAQ102015-99, a recently
      isolated strain from an outbreak of lactococcosis at a
      commercial trout farm in the northwestern United States. The draft genome
      comprises 14 contigs totaling 2,068,357 bp with an N50 of 496,618 bp and average
      G+C content of 38%.
AU  - Nelson MC
AU  - Varney JS
AU  - Welch TJ
AU  - Graf J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00781-16.

PMID- 8441677
VI  - 21
DP  - 1993
TI  - Restriction endonuclease cleavage of 5-methyl-deoxycytosine hemimethylated DNA at high enzyme-to-substrate ratios.
PG  - 681-686
AB  - We have investigated the ability of a large number of restriction enzymes to digest
      non-canonically hemimethylated DNA at high enzyme-to-substrate ratios. A single-stranded
      unmethylated phagemid was used as a template to complete synthesis of the second strand using
      5-methyl-dCTP to substitute for all the deoxycytosine residues. A fragment of this
      double-stranded hemimethylated DNA which contains the multiple cloning site region was used as
      a substrate. For all the enzymes tested, at least some degree of protection from digestion is
      observed. Sites completely protected from digestion by their cognate enzymes are SalI, BstXI,
      SacI, SacII, SmaI, SstI, XhoI, PstI, HinfI, BamHI and AccI. Sites partially protected from
      digestion by their cognate enzymes are XbaI, HindIII, KpnI, SpeI, ClaI, EcoRI and PvuII.
      Knowledge of the sensitivity of commonly used restriction enzymes to hemimethylated substrates
      is useful for several applications, which will be discussed.
AU  - Nelson PS
AU  - Papas TS
AU  - Schweinfest CW
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 681-686.

PMID- 27540060
VI  - 4
DP  - 2016
TI  - Genome Sequence of a Multidrug-Resistant Strain of Bacillus pumilus, CB01, Isolated from the Feces of an American Crow, Corvus brachyrhynchos.
PG  - e00807-16
AB  - Avian species have the potential to serve as important reservoirs for the spread  of
      pathogenic microorganisms. Here, we report the genome sequence of a
      drug-resistant strain of Bacillus pumilus, CB01, isolated from the feces of an
      American crow, Corvus brachyrhynchos.
AU  - Nelson RL
AU  - Castro MA
AU  - Katti M
AU  - Eisen JA
AU  - Van Laar TA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00807-16.

PMID- 26159520
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of a Highly Virulent Rabbit Staphylococcus aureus Strain.
PG  - e00461-15
AB  - We report the draft genome sequence of Staphylococcus aureus Sp17, a typical highly virulent
      (HV) rabbit strain. As current medicine apparently fails to
      effectively reduce disease and economical losses caused by this organism, it is
      essential to gain better insight on its genomic arrangement.
AU  - Nemet Z
AU  - Albert E
AU  - Nagy T
AU  - Olasz F
AU  - Barta E
AU  - Kiss J
AU  - Dan A
AU  - Banyai K
AU  - Hermans K
AU  - Biksi I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00461-15.

PMID- 23405328
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences of Four Nosocomial Methicillin-Resistant Staphylococcus aureus (MRSA) Strains (PPUKM-261-2009, PPUKM-332-2009, PPUKM-377-2009, and  PPUKM-775-2009) Representative of Dominant MRSA Pulsotypes Circulating in a  Malaysian University T.
PG  - e00103-12
AB  - Here, we report the draft genome sequences of four nosocomial methicillin-resistant
      Staphylococcus aureus strains (PPUKM-261-2009, PPUKM-332-2009, PPUKM-377-2009, and
      PPUKM-775-2009) isolated from a university teaching hospital in Malaysia. Three of the strains
      belong to sequence type 239 (ST239), which has been associated with sustained hospital
      epidemics worldwide.
AU  - Neoh HM
AU  - Mohamed-Hussein ZA
AU  - Tan XE
AU  - Abd-Rahman BRRM
AU  - Hussin S
AU  - Mohamad ZN
AU  - Jamal R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00103-12.

PMID- 2620059
VI  - 28
DP  - 1989
TI  - Solution structure of the EcoRI DNA sequence: Refinement of NMR-derived distance geometry structures by NOESY spectrum back-calculations.
PG  - 10008-10021
AB  - The solution structure of the self-complementary DNA duplex [d(CGCGAATTCGCG)]2,
      which contains the EcoRI restriction site sequence GAATTC at the center, has
      been studied by two-dimensional nuclear magnetic resonance spectroscopy.
      Time-dependent nuclear Overhauser effect spectra were used to obtain the
      initial cross-relaxation rates between 155 pairs of protons.  These initial
      cross-relaxation rates were converted into interproton distances and entered
      into a distance (bounds) matrix.  A distance geometry algorithm (DSPACE) was
      used to create embedded starting structures and to refine these structures
      until they showed good agreement with the distance matrix; symmetry constraints
      were included in the refinement procedure, making the two strands in the
      refined distanced geometry structures virtually identical and significantly
      improving the agreement with the distance matrix.  The NOESY spectrum for one
      of these distance geometry was then calculated from the explicit coordinates by
      numerically integrating all the z-magnetization transfer pathways among
      neighboring protons within a specified radius. Distances in this distance
      geometry structure that did not agree with the experimental NOESY time course
      were then adjusted accordingly.  This process was iterated until a good
      agreement between calculated and experimental NOESY spectra was reached.  The
      final structure, which generates good agreement with the experimental NOESY
      spectrum, display kinks at the C3-G4 base step and at the A6-T7 base step that
      appear to be similar to those reported for the EcoRI restriction site DNA bound
      to its endonuclease.  The solution structure is not the same as the crystal
      structure of this DNA duplex.
AU  - Nerdal W
AU  - Hare DR
AU  - Reid BR
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1989 28: 10008-10021.

PMID- 25477415
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of C:P1.5-1,10-8:F3-6:ST-11 Meningococcal Clinical Isolate  Associated with a Cluster on a Cruise Ship.
PG  - e01263-14
AB  - Meningococcal serogroup C strains, in particular those belonging to the ST-11 clonal complex,
      are known to cause invasive diseases worldwide. We report the
      genome sequence of a Neisseria meningitidis strain linked to a cluster of cases
      of invasive meningococcal disease on a cruise ship that was described in 2012.
AU  - Neri A
AU  - Fazio C
AU  - Ciammaruconi A
AU  - Anselmo A
AU  - Fortunato A
AU  - Palozzi A
AU  - Vacca P
AU  - Fillo S
AU  - Lista F
AU  - Stefanelli P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01263-14.

PMID- 24074865
VI  - 155
DP  - 2013
TI  - Dnmt3L Antagonizes DNA Methylation at Bivalent Promoters and Favors DNA Methylation at Gene Bodies in ESCs.
PG  - 121-134
AB  - The de novo DNA methyltransferase 3-like (Dnmt3L) is a catalytically inactive DNA
      methyltransferase that cooperates with Dnmt3a and Dnmt3b to methylate DNA. Dnmt3L
      is highly expressed in mouse embryonic stem cells (ESCs), but its function in
      these cells is unknown. Through genome-wide analysis of Dnmt3L knockdown in ESCs,
      we found that Dnmt3L is a positive regulator of methylation at the gene bodies of
      housekeeping genes and, more surprisingly, is also a negative regulator of
      methylation at promoters of bivalent genes. Dnmt3L is required for the
      differentiation of ESCs into primordial germ cells (PGCs) through the activation
      of the homeotic gene Rhox5. We demonstrate that Dnmt3L interacts with the
      Polycomb PRC2 complex in competition with the DNA methyltransferases Dnmt3a and
      Dnmt3b to maintain low methylation levels at the H3K27me3 regions. Thus, in ESCs,
      Dnmt3L counteracts the activity of de novo DNA methylases to maintain
      hypomethylation at promoters of bivalent developmental genes.
AU  - Neri F
AU  - Krepelova A
AU  - Incarnato D
AU  - Maldotti M
AU  - Parlato C
AU  - Galvagni F
AU  - Matarese F
AU  - Stunnenberg HG
AU  - Oliviero S
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 2013 155: 121-134.

PMID- 16309397
VI  - 7
DP  - 2005
TI  - Lateral gene transfer and phylogenetic assignment of environmental fosmid clones.
PG  - 2011-2026
AB  - Metagenomic data, especially sequence data from large insert clones, are
      most useful when reasonable inferences about phylogenetic origins of
      inserts can be made. Often, clones that bear phylotypic markers (usually
      ribosomal RNA genes) are sought, but sometimes phylogenetic assignments
      have been based on the preponderance of blast hits obtained with predicted
      protein coding sequences (CDSs). Here we use a cloning method which
      greatly enriches for ribosomal RNA-bearing fosmid clones to ask two
      questions: (i) how reliably can we judge the phylogenetic origin of a
      clone (that is, its RNA phylotype) from the sequences of its CDSs? and
      (ii) how much lateral gene transfer (LGT) do we see, as assessed by CDSs
      of different phylogenetic origins on the same fosmid? We sequenced 12 rRNA
      containing fosmid clones, obtained from libraries constructed using DNA
      isolated from Baltimore harbour sediments. Three of the clones are from
      bacterial candidate divisions for which no cultured representatives are
      available, and thus represent the first protein coding sequences from
      these major bacterial lineages. The amount of LGT was assessed by making
      phylogenetic trees of all the CDSs in the fosmid clones and comparing the
      phylogenetic position of the CDS to the rRNA phylotype. We find that the
      majority of CDSs in each fosmid, 57-96%, agree with their respective rRNA
      genes. However, we also find that a significant fraction of the CDSs in
      each fosmid, 7-44%, has been acquired by LGT. In several cases, we can
      infer co-transfer of functionally related genes, and generate hypotheses
      about mechanism and ecological significance of transfer.
AU  - Nesbo CL
AU  - Boucher Y
AU  - Dlutek M
AU  - Doolittle WF
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2005 7: 2011-2026.

PMID- 25814596
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Beneficial Rhizobacterium Pseudomonas fluorescens DSM 8569, a Natural Isolate of Oilseed Rape (Brassica napus).
PG  - e00137-15
AB  - Pseudomonas fluorescens DSM 8569 represents a natural isolate of the rhizosphere  of oilseed
      rape (Brassica napus) in Germany and possesses antagonistic potential
      toward the fungal pathogen Verticillium. We report here the draft genome sequence
      of strain DSM 8569, which comprises 5,914 protein-coding sequences.
AU  - Nesemann K
AU  - Braus-Stromeyer SA
AU  - Thuermer A
AU  - Daniel R
AU  - Braus GH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00137-15.

PMID- 25814594
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Phenazine-Producing Pseudomonas fluorescens Strain 2-79.
PG  - e00130-15
AB  - Pseudomonas fluorescens strain 2-79, a natural isolate of the rhizosphere of wheat (Triticum
      aestivum L.), possesses antagonistic potential toward several
      fungal pathogens. We report the draft genome sequence of strain 2-79, which
      comprises 5,674 protein-coding sequences.
AU  - Nesemann K
AU  - Braus-Stromeyer SA
AU  - Thuermer A
AU  - Daniel R
AU  - Mavrodi DV
AU  - Thomashow LS
AU  - Weller DM
AU  - Braus GH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00130-15.

PMID- 29167255
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of Two Plant-Associated Pseudomonas putida Isolates with Increased Heavy-Metal Tolerance.
PG  - e01330-17
AB  - We report here the complete genome sequences of two Pseudomonas putida isolates recovered from
      surface-sterilized roots of Sida hermaphrodita The two isolates
      were characterized by an increased tolerance to zinc, cadmium, and lead.
      Furthermore, the strains showed typical plant growth-promoting properties, such
      as the production of indole acetic acid, cellulolytic enzymes, and siderophores.
AU  - Nesme J
AU  - Cania B
AU  - Zadel U
AU  - Scholer A
AU  - Plaza GA
AU  - Schloter M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01330-17.

PMID- 369620
VI  - 44
DP  - 1979
TI  - Isolation and properties of DNA-cytosine-methylase I from Escherichia coli MRE 600.
PG  - 130-140
AB  - DNA-cytosine-methylase I was isolated and purified to homogeneity.  The yield
      made up to about 30% of total activity.  The enzyme molecular weight as
      determined by centrifugation in a sucrose gradient, by gel filtration and by
      electrophoresis in polyacrylamide gel in the presence of sodium dodecyl sulfate
      was found to be 45000.  The Michaelis constant was 1,8.10-6 M for SAM and
      2.10-4 M for DNA.  DNA-cytosine-methylase I modifies phage lambda DNA in 60
      sites.  This modification does not protect DNA from the effects of restriction
      endonucleases HpaII and BsuRI.  The enzyme methylates DNA in the nucleotide
      sequence: 5'...Pu-MC-C-G-G-Py...3'.
AU  - Nesterenko VF
AU  - Buryanov YI
AU  - Baev AA
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1979 44: 130-140.

PMID- 6245841
VI  - 250
DP  - 1980
TI  - Determination of DNA-cytosine methylase I (M. Eco MRE600I) in plasmid CoLA.
PG  - 1265-1267
AB  - None
AU  - Nesterenko VF
AU  - Buryanov YI
AU  - Baev AA
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1980 250: 1265-1267.

PMID- 20569209
VI  - 48
DP  - 2010
TI  - Enzymatic approaches and bisulfite sequencing cannot distinguish between 5-methylcytosine and 5-hydroxymethylcytosine in DNA.
PG  - 317-319
AB  - DNA cytosine methylation (5mC) is highly abundant in mammalian cells and is associated with
      transcriptional repression. Recently, hydroxymethylcytosine
      (hmC) has been detected at high levels in certain human cell types; however,
      its roles are unknown. Due to the structural similarity between 5mC and hmC,
      it is unclear whether 5mC analyses can discriminate between these nucleotides.
      Here we show that 5mC and hmC are experimentally indistinguishable using
      established 5mC mapping methods, thereby implying that existing 5mC data
      sets will require careful re-evaluation in the context of the possible presence of
      hmC. Potential differential enrichment of 5mC and hmC DNA sequences
      may be facilitated using a 5mC monoclonal antibody.
AU  - Nestor C
AU  - Ruzov A
AU  - Meehan RR
AU  - Dunican DS
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 2010 48: 317-319.

PMID- Not included in PubMed...
VI  - 7
DP  - 1981
TI  - An effective method for isolation of restriction endonucleases.
PG  - 790-791
AB  - A modification of the published method for isolating the restriction
      endonucleases is proposed.  The modification involves the use of Triton X-100
      containing buffers at all steps of the isolation procedure which results in a
      2-12-fold increase in the yield of enzymes depending on the strain of bacteria.
AU  - Netesov SV
AU  - Grachev SA
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1981 7: 790-791.

PMID- 11862704
VI  - 36
DP  - 2002
TI  - Comparative study of the M.BstF5I-1 and M.BstF5I-3 DNA methyltransferases from the Bacillus stearothermophilus F5 restriction-modification system.
PG  - 136-143
AB  - The BstF5I restriction-modification system from Bacillus stearothermophilus F5, unlike all
      known restriction-modification
      systems, contains three genes encoding DNA methyltransferases. In
      addition to revealing two DNA methylases responsible for modification
      of adenine in different DNA strands, it has been first shown that one
      bacterial cell has two DNA methylases, M.BstF5I-1 and M.BstF5I-3, with
      similar substrate specificity. The boundaries of the gene for DNA
      methyltransferase M.BstF5I-1 have been verified. The bstF5IM-1 gene was
      cloned in pJW and expressed in Escherichia coli. Homogeneous samples of
      M.BstF5I-1 and M.BstF5I-3 were obtained by chromatography with
      different sorbents. The main kinetic parameters have been determined
      for M.BstF5I-1 and M.BstF5I-3, both modifying adenine in the
      recognition site 5'-GGATG-3'.
AU  - Netesova NA
AU  - Golikova LN
AU  - Ovetchkina LG
AU  - Evdokimov AA
AU  - Malygin EG
AU  - Gololobova NS
AU  - Gonchar DA
AU  - Degtyarev SK
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2002 36: 136-143.

PMID- 24501629
VI  - 8
DP  - 2013
TI  - Non-contiguous finished genome sequence of plant-growth promoting Serratia proteamaculans S4.
PG  - 441-449
AB  - Serratia proteamaculans S4 (previously Serratia sp. S4), isolated from the rhizosphere of wild
      Equisetum sp., has the ability to stimulate plant growth and
      to suppress the growth of several soil-borne fungal pathogens of economically
      important crops. Here we present the non-contiguous, finished genome sequence of
      S. proteamaculans S4, which consists of a 5,324,944 bp circular chromosome and a
      129,797 bp circular plasmid. The chromosome contains 5,008 predicted genes while
      the plasmid comprises 134 predicted genes. In total, 4,993 genes are assigned as
      protein-coding genes. The genome consists of 22 rRNA genes, 82 tRNA genes and 58
      pseudogenes. This genome is a part of the project 'Genomics of four rapeseed
      plant growth-promoting bacteria with antagonistic effect on plant pathogens'
      awarded through the 2010 DOE-JGI's Community Sequencing Program.
AU  - Neupane S et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 441-449.

PMID- 23450001
VI  - 7
DP  - 2012
TI  - Complete genome sequence of the plant-associated Serratia plymuthica strain AS13.
PG  - 22-30
AB  - AS13 is a plant-associated , isolated from rapeseed roots. It is of special interest because
      of its ability to inhibit fungal pathogens of rapeseed and to
      promote plant growth. The complete genome of AS13 consists of a 5,442,549 bp
      circular chromosome. The chromosome contains 4,951 protein-coding genes, 87 tRNA
      genes and 7 rRNA operons. This genome was sequenced as part of the project
      entitled 'Genomics of four rapeseed plant growth promoting bacteria with
      antagonistic effect on plant pathogens' within the 2010 DOE-JGI Community
      Sequencing Program (CSP2010).
AU  - Neupane S et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 7: 22-30.

PMID- 22768360
VI  - 6
DP  - 2012
TI  - Complete genome sequence of Serratia plymuthica strain AS12.
PG  - 165-173
AB  - A plant-associated member of the family Enterobacteriaceae, Serratia plymuthica strain AS12
      was isolated from rapeseed roots. It is of scientific interest
      because it promotes plant growth and inhibits plant pathogens. The genome of S.
      plymuthica AS12 comprises a 5,443,009 bp long circular chromosome, which consists
      of 4,952 protein-coding genes, 87 tRNA genes and 7 rRNA operons. This genome was
      sequenced within the 2010 DOE-JGI Community Sequencing Program (CSP2010) as part
      of the project entitled 'Genomics of four rapeseed plant growth promoting
      bacteria with antagonistic effect on plant pathogens'.
AU  - Neupane S et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 6: 165-173.

PMID- 22675598
VI  - 6
DP  - 2012
TI  - Complete genome sequence of the rapeseed plant-growth promoting Serratia plymuthica strain AS9.
PG  - 54-62
AB  - Serratia plymuthica are plant-associated, plant beneficial species belonging to the family
      Enterobacteriaceae. The members of the genus Serratia are ubiquitous
      in nature and their life style varies from endophytic to free-living. S.
      plymuthica AS9 is of special interest for its ability to inhibit fungal pathogens
      of rapeseed and to promote plant growth. The genome of S. plymuthica AS9
      comprises a 5,442,880 bp long circular chromosome that consists of 4,952
      protein-coding genes, 87 tRNA genes and 7 rRNA operons. This genome is part of
      the project entitled 'Genomics of four rapeseed plant growth promoting bacteria
      with antagonistic effect on plant pathogens' awarded through the 2010 DOE-JGI
      Community Sequencing Program (CSP2010).
AU  - Neupane S et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 6: 54-62.

PMID- 27257206
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Arthrobacter enclensis NCIM 5488T for Secondary Metabolism.
PG  - e00497-16
AB  - Here, we report the draft genome sequence of Arthrobacter enclensis NCIM 5488(T), an
      actinobacterium isolated from a marine sediment sample from Chorao Island,
      Goa, India. This draft genome sequence consists of 4,226,231 bp with a G+C
      content of 67.08%, 3,888 protein-coding genes, 50 tRNAs, and 10 rRNAs. Analysis
      of the genome using bioinformatics tools such as antiSMASH and NaPDoS showed the
      presence of many unique natural product biosynthetic gene clusters.
AU  - Neurgaonkar PS
AU  - Dharne MS
AU  - Dastager SG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00497-16.

PMID- 12060740
VI  - 99
DP  - 2002
TI  - A theoretical examination of the factors controlling the catalytic efficiency of the DNA-(adenine-N6)-methyltransferase from Thermus aquaticus.
PG  - 7922-7927
AB  - Ab initio and density functional calculations have been carried out to more fully understand
      the factors controlling the catalytic activity of the Thermus aquaticus DNA methyltransferase
      (M.TaqI) in the N-methylation at the N6 of an adenine nucleobase. The noncatalyzed reaction
      was modeled as a methyl transfer from trimethylsulfonium to the N6 of adenine. Activation
      barriers of 32.0 kcal/mol and 24.0 kcal/mol were predicted for the noncatalyzed reaction in
      the gas phase by MP2/6-31+G(d,p)//HF/6-31+G(d,p) and B3LYP/6-31+G(d,p) calculations,
      respectively. Calculations performed to evaluate the effect of substrate positioning in the
      active site of MTaqI on the reaction determine the barrier to be 23.4 kcal/mol and 17.3
      kcal/mol for the MP2/6-31+G(d,p)//HF/6-31+G(d,p) and B3LYP/6-31+G(d,p) gas phase calculations,
      respectively. The effect of hydrogen bonding between the N6 of adenine and the terminal oxygen
      of Asn-105 on the activation barrier was also studied. A formamide molecule was modeled into
      the system to mimic the function of active site residue Asn-105. The activation barrier for
      this reaction was found to be 21.8 kcal/mol and 15.8 kcal/mol as determined from the
      MP2/6-31+G(d,p)//HF/6-31+G(d,p) and B3LYP/6-31+G(d,p) calculations, respectively. This result
      predicts a contribution of less than 2 kcal/mol to the lowering of the activation barrier from
      amide hydrogen bonding between formamide and N6 of adenine. Comparison of the reaction
      coordinates suggest that it is not the hydrogen bonding of the Asn-105 that lends to the
      catalytic prowess of the enzyme since the organization of the substrates in the active site of
      the enzyme has a far greater effect on reducing the activation barrier. The results also
      suggest a stepwise mechanism for the removal of the hydrogen from the N6 of adenine as opposed
      to a concerted reaction in which a proton is abstracted simultaneously with the transfer of
      the methyl group. The hydrogen on the N6 of the intermediate methyl adenine product is far
      more acidic than in the reactant complex and may be subsequently abstracted by basic groups in
      the active site that are too weak to abstract the proton before the full sp3 hybridization of
      the attacking nitrogen.
AU  - Newby AER
AU  - Lau EY
AU  - Bruice TC
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2002 99: 7922-7927.

PMID- 6257701
VI  - 256
DP  - 1981
TI  - DNA Sequences of Structural Genes for EcoRI DNA Restriction and Modified Enzymes.
PG  - 2131-2139
AB  - We have determined the sequence of a 2210-base pair DNA segment containing genes required for
      expression of EcoRI DNA restriction and modification phenotypes.  Polypeptide sequences
      encoded within the two longest open reading frames in this region are in agreement with NH2-
      and C00H-terminal sequences of the two EcoRI enzymes (Rubin, R.A., Modrich, P., and Vanaman,
      T.C. (1981) J. Biol. Chem. 256, 2140-2142), indicating that these are structural genes for the
      two proteins.  The DNA sequence encoding EcoRI endonuclease specifies a 277-residue
      polypeoptide (Mr = 31,063) while the methylase gene encodes a 326-residue protein (Mr =
      38,048).  Genes for the two proteins are nonoverlapping, being separated by a 29-nucleotide
      intercistronic region. Analysis of each polypeptide and its gene sequence for internal regions
      of homology led to identification of a striking 4-fold repeat of Leu-Ile-Lys within the
      methylase and a tandem repeat within the endonuclease, both of which are unlikely on the basis
      of chance.  Comparison of DNA and polypeptide sequences also demonstrated a limited, but
      statistically significant, region of homology between EcoRI endonuclease and methylase primary
      structures. However, the general lack of homology between the two polypeptides suggests
      different evolutionary origins for the two proteins.  The two enzymes also differ markedly at
      higher levels of structure as judged by circular dichroism and prediction of secondary
      structure by the probabilistic method of Chou and Fasman (Chou, P.Y., and Fasman, G.D. (1978)
      Adv. Enzymol. 47, 45-148).  Thus, despite their ability to interact with the same DNA
      sequence, the EcoRI enzymes have quite distinct structural properties.
AU  - Newman AK
AU  - Rubin RA
AU  - Kim SH
AU  - Modrich P
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1981 256: 2131-2139.

PMID- 9736624
VI  - 17
DP  - 1998
TI  - Crystal structure of restriction endonuclease BglI bound to its interrupted DNA recognition sequence.
PG  - 5466-5476
AB  - The crystal structure of the type II restriction endonuclease BglI bound to DNA containing its
      specific recognition sequence has been determined at 2.2 A resolution.  This is the first
      structure of a restriction endonuclease that recognizes and cleaves an interrupted DNA
      sequence, producing 3' overhanging ends.  BglI is a homodimer that binds its specific DNA
      sequence with the minor groove facing the protein.  Parts of the enzyme reach into both the
      major and minor grooves to contact the edges of the bases within the recognition half-sites.
      The arrangement of active site residues is strikingly similar to other restriction
      endonucleases, but the coordination of two calcium ions at the active site gives new insight
      into the catalytic mechanism.  Surprisingly, the core of a BglI subunit displays a striking
      similarity to subunits of EcoRV and PvuII, but the dimer structure is dramatically different.
      The BglI DNA complex demonstrates, for the first time, that a conserved subunit fold can
      dimerize in more than one way, resulting in different DNA cleavage patterns.
AU  - Newman M
AU  - Lunnen K
AU  - Wilson G
AU  - Greci J
AU  - Schildkraut I
AU  - Phillips SEV
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1998 17: 5466-5476.

PMID- 8081758
VI  - 2
DP  - 1994
TI  - Structure of restriction endonuclease BamHI phased at 1.95 A resolution by MAD analysis.
PG  - 439-452
AB  - Type II restriction endonucleases recognize DNA sequences that vary between four to eight base
      pairs, and require only Mg2+ as a cofactor to catalyze the hydrolysis of DNA. Their protein
      sequences display a surprising lack of similarity, and no recurring structural motif analogous
      to the helix-turn-helix or the zinc finger of transcription factors, has yet been discovered.
      We have determined the crystal structure of restriction endonuclease BamHI at 1.95 A
      resolution. The structure was solved by combining phase information derived from
      multi-wavelength X-ray data by algebraic and maximum likelihood methods. The BamHI subunit
      consists of a central beta-sheet with alpha-helices on both sides. The dimer configuration
      reveals a large cleft which could accommodate B-form DNA. Mutants of the enzyme that are
      deficient in cleavage are located at or near the putative DNA-binding cleft. BamHI and
      endonuclease EcoRI share a common core motif (CCM) consisting of five beta-strands and two
      helices. It remains to be determined if other restriction enzymes also contain the CCM. The
      structure of BamHI provides the first clear evidence that there may be substantial structural
      homology amongst restriction enzymes, even though it is undetectable at the sequence level.
AU  - Newman M
AU  - Strzelecka T
AU  - Dorner LF
AU  - Schildkraut I
AU  - Aggarwal AK
PT  - Journal Article
TA  - Structure
JT  - Structure
SO  - Structure 1994 2: 439-452.

PMID- 7624794
VI  - 269
DP  - 1995
TI  - Structure of BamHI endonuclease bound to DNA: partial folding and unfolding on DNA binding.
PG  - 656-663
AB  - The crystal structure of restriction endonuclease BamHI complexed to DNA has been determined
      at 2.2 angstrom resolution.  The DNA binds in the cleft and retains a B-DNA type of
      conformation.  The enzyme, however, undergoes a series of conformational changes, including
      rotation of subunits and folding of disordered regions.  The most striking conformational
      change is the unraveling of carboxyl-terminal alpha helices to form partially disordered
      "arms".  The arm from one subunit fits into the minor groove while the arm from the symmetry
      related subunit follows the DNA sugar-phosphate backbone.  Recognition of DNA base pairs
      occurs primarily in the major groove, with a few interactions occurring in the minor groove.
      Tightly bound water molecules play an equally important role as side chain and main chain
      atoms in the recognition of base pairs.  The complex also provides new insights into the
      mechanism by which the enzyme catalyzes the hydrolysis of DNA phosphodiester groups.
AU  - Newman M
AU  - Strzelecka T
AU  - Dorner LF
AU  - Schildkraut I
AU  - Aggarwal AK
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1995 269: 656-663.

PMID- 8145855
VI  - 368
DP  - 1994
TI  - Structure of restriction endonuclease BamHI and its relationship to EcoRI.
PG  - 660-664
AB  - Type II restriction endonucleases are characterized by the remarkable specificity with which
      they cleave specific DNA sequences. Surprisingly, their protein sequences are in most cases
      unrelated, and no recurring structural motif has yet been identified. We have determined the
      structure of restriction endonuclease BamHI at 1.95 angstrom resolution. BamHI shows striking
      resemblance to the structure of endonuclease EcoRI, despite the lack of sequence similarity
      between them. We also observe some curious differences between the two structures, and propose
      an evolutionary scheme that may explain them. The active site of BamHI is structurally similar
      to the active sites of EcoRI and EcoRV, but the mechanism by which BamHI activates a water
      molecule for nucleophilic attack may be different.
AU  - Newman M
AU  - Strzelecka T
AU  - Dorner LF
AU  - Schildkraut I
AU  - Aggarwal AK
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1994 368: 660-664.

PMID- Not carried by PubMed...
VI  - 51
DP  - 1991
TI  - Investigation of the sequence-specific DNA/protein interactions of the EcoRV restriction enzyme.
PG  - 3366B
AB  - The EcoRV restriction enzyme from Escherichia coli recognises the sequence GATATC on double
      stranded DNA and cuts between the central residues with very high specificity.  The self
      complementary dodecadeoxynucleotide dGACGATATCGTC which contains the EcoRV recognition site
      (underlined) is also a substrate for the endonuclease.  The thesis describes the synthesis of
      fourteen dodecamers of the above parent sequence in which the functional groups of the central
      ATAT residues accessible to the protein via the DNA major and minor grooves have been
      systematically and sequentially deleted.  Conservative contact deletions were achieved by the
      substitution of the two deoxyadenosine residues in turn with the base analogues purine
      deoxyriboside (dP), 7-deazadeoxyadenosine (d7CA) and 3-deazadeoxyadenosine (d3CA).  Similarly
      the two thymidine residues were substituted with deoxyuridine (dU), 5-methyl-2-pyrimidinone
      deoxyriboside (d4HT), 4-thiothymidine (d4ST) and 2-thiothymidine (d2ST).  To obtain the
      complete set of analogues, efficient synthetic routes for the formation of derivatives of
      d4HT, d4ST and d2ST suitable for oligodeoxynucleotide synthesis using the cyanoethyl
      phosphoramidite approach are described (also see Connolly
AU  - Newman PC
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1991 51: 3366B.

PMID- 2271627
VI  - 29
DP  - 1990
TI  - Incorporation of a complete set of deoxyadenosine and thymidine analogues suitable for the study of protein nucleic acid interactions into oligodeoxynucleotides.  Application to the EcoRV restriction endonuclease and modification methylase.
PG  - 9891-9901
AB  - A complete set of dA and T analogues designed for the study of protein DNA
      interactions has been prepared.  These modified bases have been designed by
      considering the groups on the dA and T bases that are accessible to proteins
      when these bases are incorporated into double-helical B-DNA [Seeman, N.C.,
      Rosenberg, J.M. and Rich, A. (1976) Proc. Natl. Acad. Sci. USA 73, 804-808].
      Each of the positions on the two bases, having the potential to interact with
      proteins, have been subject to nondisruptive, conservative change.  Typically a
      particular group (e.g., the 6-amino group of dA or the 5-methyl of T) has been
      replaced with a hydrogen atom.  Occasionally keto groups (the 2- and 4-keto
      oxygen atoms of T) have been replaced with sulfur.  The base set has been
      incorporated into the self-complementary dodecamer d(GACGATATCGTC) at the
      central d(ATAT) sequence.  Melting temperature determination shows that the
      modified bases do not destabilize the double helix.  Additionally, circular
      dichroism spectroscoy shows that almost all the altered bases have very little
      effect on overall oligodeoxynucleotide conformation and that most of the
      modified oligomers have a B-DNA type structure.  d(GATATC) is the recognition
      sequence for the EcoRV restriction modification system.  Initial rate
      measurements (at a single oligodeoxynucleotide concentration of 20 microM) have
      been carried out with both the EcoRV restriction endonuclease and modification
      methylase.  This has enabled a preliminary identification of the groups of the
      dA and T bases within the d(GATATC) sequence that make important contacts to
      both proteins.
AU  - Newman PC
AU  - Nwosu VU
AU  - Williams DM
AU  - Cosstick R
AU  - Seela F
AU  - Connolly BA
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1990 29: 9891-9901.

PMID- 2271628
VI  - 29
DP  - 1990
TI  - Interaction of the EcoRV restriction endonuclease with the deoxyadenosine and thymidine bases in its recognition hexamer d(GATATC).
PG  - 9902-9910
AB  - A set of dA and T analogues suitable for the study of protein DNA interactions
      have been incorporated into the central d(ATAT) sequence within
      d(GACGATATCGTC).  The individual analogues have one potential protein contact
      (either a hydrogen-bonding group or a CH3 group capable of a van der Waals
      interaction) deleted.  In general, the modified bases do not perturb the
      overall structure of the dodecamer, enabling results obtained to be simply
      interpreted in terms of loss of protein DNA contacts.  We have used the
      modified oligodeoxynucleotide set to study the recognition of DNA by the EcoRV
      restriction endonuclease [recognition sequence d(GATATC)].  The kcat and Km
      values for the set have been determined, and a comparison with results seen
      with the parent oligodeoxynucleotide (containing no modified bases) has been
      carried out.  Three classes of results are seen.  First, some analogues lead to
      no change in kinetic parameters, meaning no enzyme contact at the altered site.
      Second (this is seen for most of the modified oligodeoxynucleotides), a drop
      in the kcat/Km ratio relative to the parent is observed.  This comes mainly
      from a decrease in kcat, implying that the endonuclease uses the interaction
      under study to lower the transition-state barrier rather than to bind the
      substrate.  Analyses of these results show that the drop in kcat/Km is what
      would be expected for the simple loss of a hydrogen bond or a CH3 contact
      between the enzyme and the oligodeoxynucleotide.  This implies a contact of
      these types at these sites.  Third, some analogue-containing
      oligodeoxynucleotides are not substrates; i.e., the kcat/Km drop is much
      greater than would be expected for loss of a single hydrogen bond or CH3
      contact.  These results are interpreted in terms of a cooperative mechanism
      whereby the loss of one interaction causes a rearrangement at the enzyme active
      site leading to a consequent loss of further protein substrate contacts.
      However, in these cases gross structural changes in the oligodeoxynucleotide
      conformation cannot be excluded.  It is found that the endonuclease makes very
      many interactions to the d(ATAT) sequence within its d(GATATC) recognition
      site, and these occur in both the major and minor grooves.  The results
      obtained have been used to explain how the enzyme achieves the high degree of
      cleavage specificity for d(GATATC) as compared to all other sequences.
AU  - Newman PC
AU  - Williams DM
AU  - Cosstick R
AU  - Seela F
AU  - Connolly BA
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1990 29: 9902-9910.

PMID- 19638978
VI  - 101
DP  - 2009
TI  - MicroRNA-143 targets DNA methyltransferases 3A in colorectal cancer.
PG  - 699-706
AB  - BACKGROUND: MicroRNAs (miRNAs) are 19-25-nucleotides regulatory non-protein-coding RNA
      molecules that regulate the expressions of a
      wide variety of genes, including some involved in cancer development.
      In this study, we investigated the possible role of miR-143 in
      colorectal cancer (CRC).METHODS: Expression levels of human mature
      miRNAs were examined using real-time PCR-based expression arrays on
      paired colorectal carcinomas and adjacent non-cancerous colonic
      tissues. The downregulation of miR-143 was further evaluated in colon
      cancer cell lines and in paired CRC and adjacent non-cancerous colonic
      tissues by qRT-PCR. Potential targets of miR-143 were defined. The
      functional effect of miR-143 and its targets was investigated in human
      colon cancer cell lines to confirm miRNA-target association.RESULTS:
      Both real-time PCR-based expression arrays and qRT-PCR showed that
      miR-143 was frequently downregulated in 87.5% (35 of 40) of colorectal
      carcinoma tissues compared with their adjacent non-cancerous colonic
      tissues. Using in silico predictions, DNA methyltranferase 3A (DNMT3A)
      was defined as a potential target of miR-143. Restoration of the
      miR-143 expression in colon cell lines decreased tumour cell growth and
      soft-agar colony formation, and downregulated the DNMT3A expression in
      both mRNA and protein levels. DNMT3A was shown to be a direct target of
      miR-143 by luciferase reporter assay. Furthermore, the miR-143
      expression was observed to be inversely correlated with DNMT3A mRNA and
      protein expression in CRC tissues.CONCLUSION: Our findings suggest that
      miR-143 regulates DNMT3A in CRC. These findings elucidated a
      tumour-suppressive role of miR-143 in the epigenetic aberration of CRC,
      providing a potential development of miRNA-based targeted approaches
      for CRC therapy. British Journal of Cancer (2009) 101, 699-706. doi:
      10.1038/sj.bjc.6605195 www.bjcancer.com Published online 28 July 2009
AU  - Ng EKO
AU  - Tsang WP
AU  - Ng SSM
AU  - Jin HC
AU  - Yu J
AU  - Li JJ
AU  - Roecken C
AU  - Ebert MPA
AU  - Kwok TT
AU  - Sung JJY
PT  - Journal Article
TA  - Br. J. Cancer
JT  - Br. J. Cancer
SO  - Br. J. Cancer 2009 101: 699-706.

PMID- 30351265
VI  - 67
DP  - 2018
TI  - A mutation in anti-sigma factor MAB_3542c may be responsible for tigecycline resistance in Mycobacterium abscessus.
PG  - 1676-1681
AB  - In this study, we characterized 7C, a spontaneous mutant selected from tigecycline-susceptible
      Mycobacterium abscessus
      ATCC 19977. Whole-genome sequencing (WGS) was used to identify possible resistance
      determinants in this mutant.
      Compared to the wild-type, 7C demonstrated resistance to tigecycline as well as
      cross-resistance to imipenem, and had a
      slightly retarded growth rate. WGS and subsequent biological verifications showed that these
      phenotypes were caused by a
      point mutation in MAB_3542c, which encodes an RshA-like protein. In Mycobacterium
      tuberculosis, RshA is an anti-sigma
      factor that negatively regulates the heat/oxidative stress response mechanisms. The MAB_3542c
      mutation may represent a
      novel determinant of tigecycline resistance. We hypothesize that this mutation may dysregulate
      the stress-response
      pathways which have been shown to be linked to antibiotic resistance in previous studies.
AU  - Ng HF
AU  - Tan JL
AU  - Zin T
AU  - Yap SF
AU  - Ngeow YF
PT  - Journal Article
TA  - J. Med. Microbiol.
JT  - J. Med. Microbiol.
SO  - J. Med. Microbiol. 2018 67: 1676-1681.

PMID- 23405310
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the First Isolate of Extensively Drug-Resistant (XDR) Mycobacterium tuberculosis in Malaysia.
PG  - e00056-12
AB  - The emergence of the global threat of extensively drug-resistant (XDR) Mycobacterium
      tuberculosis reveals weaknesses in tuberculosis management and diagnostic services. We report
      the draft genome sequence of the first extensively drug-resistant Mycobacterium tuberculosis
      strain isolated in Malaysia. The sequence was also compared against a reference strain to
      elucidate the polymorphism that is related to their extensive resistance.
AU  - Ng KP
AU  - Yew SM
AU  - Chan CL
AU  - Chong J
AU  - Tang SN
AU  - Soo-Hoo TS
AU  - Na SL
AU  - Hassan H
AU  - Ngeow YF
AU  - Hoh CC
AU  - Lee KW
AU  - Yee WY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00056-12.

PMID- 11016950
VI  - 97
DP  - 2000
TI  - Genome sequence of Halobacterium species NRC-1.
PG  - 12176-12181
AB  - We report the complete sequence of an extreme halophile, Halobacterium sp. NRC-1, harboring a
      dynamic 2,571,010-bp genome containing 91 insertion sequences
      representing 12 families and organized into a large chromosome and 2 related
      minichromosomes. The Halobacterium NRC-1 genome codes for 2,630 predicted
      proteins, 36% of which are unrelated to any previously reported. Analysis of the
      genome sequence shows the presence of pathways for uptake and utilization of
      amino acids, active sodium-proton antiporter and potassium uptake systems,
      sophisticated photosensory and signal transduction pathways, and DNA replication,
      transcription, and translation systems resembling more complex eukaryotic
      organisms. Whole proteome comparisons show the definite archaeal nature of this
      halophile with additional similarities to the Gram-positive Bacillus subtilis and
      other bacteria. The ease of culturing Halobacterium and the availability of
      methods for its genetic manipulation in the laboratory, including construction of
      gene knockouts and replacements, indicate this halophile can serve as an
      excellent model system among the archaea.
AU  - Ng WV et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2000 97: 12176-12181.

PMID- 9847077
VI  - 8
DP  - 1998
TI  - Snapshot of a large dynamic replicon in a halophilic archaeon: Megaplasmid or minichromosome?
PG  - 1131-1141
AB  - Extremely halophilic archaea, which flourish in hypersaline environments, are known to contain
      a variety of large dynamic replicons. Previously, the analysis of one such replicon, pNRC100,
      in Halobacterium sp. strain NRC-1, showed that it undergoes high-frequency insertion sequence
      element-mediated insertions and deletions, as well as inversions via recombination between
      39-kb-long inverted repeats. Now, the complete sequencing of pNRC100, a 191,346-bp circle, has
      shown the presence of 27 IS elements representing eight families.  A total of 176 ORFs or
      likely genes of 850-bp average size were found, 39 of which were repeated within the large
      IRs. More than one-half of the ORFs are likely to represent novel genes that have no known
      homologs in the databases. Among ORFs with previously characterized homologs, three different
      copies of putative plasmid replication and four copies of partitioning genes were found,
      suggesting that pNRC100 evolved from IS element-mediated fusions of several smaller plasmids.
      Consistent with this idea, putative genes typically found on plasmids, including those
      encoding a restriction-modification system and arsenic resistance, as well as buoyant
      gas-filled vesicles and a two-component regulatory system, were found on pNRC100.  However,
      additional putative genes not expected on an extrachromosomal element, such as those encoding
      an electron transport chain cytochrome d oxidase, DNA nucleotide synthesis enzymes thioredoxin
      and thioredoxin reductase, and eukaryotic-like TATA-binding protein transcription factors and
      a chromosomal replication initiator protein were also found.  A multi-step IS element-mediated
      process is proposed to account for the acquisition of these chromosomal genes.  The finding of
      essential genes on pNRC100 and its property of resistance to curing suggest that this replicon
      may be evolving into a new chromosome.
AU  - Ng WV
AU  - Ciufo SA
AU  - Smith TM
AU  - Bumgarner RE
AU  - Baskin D
AU  - Faust J
AU  - Hall B
AU  - Loretz C
AU  - Seto J
AU  - Slagel J
AU  - Hood L
AU  - DasSarma S
PT  - Journal Article
TA  - Genome Res.
JT  - Genome Res.
SO  - Genome Res. 1998 8: 1131-1141.

PMID- 23990576
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Mycobacterium massiliense Strain M159, Showing Phenotypic Resistance to beta-Lactam and Tetracycline Antibiotics.
PG  - e00669-13
AB  - Mycobacterium massiliense is a nontuberculous mycobacterium associated with human infections.
      We report here the draft genome sequence of M. massiliense strain
      M159, isolated from the bronchial aspirate of a patient who had a pulmonary
      infection. This strain showed genotypic and in vitro resistance to a number of
      tetracyclines and beta-lactam antibiotics.
AU  - Ngeow YF
AU  - Leong ML
AU  - Wong YL
AU  - Wong GJ
AU  - Tan JL
AU  - Wee WY
AU  - Ong CS
AU  - Pang YK
AU  - Choo SW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00669-13.

PMID- 23045507
VI  - 194
DP  - 2012
TI  - Genomic Analysis of Mycobacterium abscessus Strain M139, Which Has an Ambiguous Subspecies Taxonomic Position.
PG  - 6002-6003
AB  - Mycobacterium abscessus is a ubiquitous, rapidly growing species of nontuberculous
      mycobacteria that colonizes organic surfaces and is frequently
      associated with opportunistic infections in humans. We report here the draft
      genome sequence of Mycobacterium abscessus strain M139, which shows genomic
      features reported to be characteristic of both Mycobacterium abscessus subsp.
      abscessus and Mycobacterium abscessus subsp. massiliense.
AU  - Ngeow YF
AU  - Wee WY
AU  - Wong YL
AU  - Tan JL
AU  - Ongi CS
AU  - Ng KP
AU  - Choo SW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6002-6003.

PMID- 22887681
VI  - 194
DP  - 2012
TI  - Genomic Analysis of Mycobacterium massiliense Strain M115, an Isolate from Human  Sputum.
PG  - 4786
AB  - We report the draft genome sequence of a clinical isolate, strain M115, identified as
      Mycobacterium massiliense, a member of the newly created taxon of
      Mycobacterium abscessus subspecies bolletii comb. nov.
AU  - Ngeow YF
AU  - Wong YL
AU  - Lokanathan N
AU  - Wong GJ
AU  - Ong CS
AU  - Ng KP
AU  - Choo SW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4786.

PMID- 22815444
VI  - 194
DP  - 2012
TI  - Genome Sequence of Mycobacterium massiliense M18, Isolated from a Lymph Node Biopsy Specimen.
PG  - 4125
AB  - Mycobacterium massiliense is a rapidly growing mycobacterial species. The pathogenicity of
      this subspecies is not well known. We report here the annotated
      genome sequence of M. massiliense strain M18, which was isolated from a lymph
      node biopsy specimen from a Malaysian patient suspected of having tuberculous
      cervical lymphadenitis.
AU  - Ngeow YF
AU  - Wong YL
AU  - Tan JL
AU  - Arumugam R
AU  - Wong GJ
AU  - Ong CS
AU  - Ng KP
AU  - Choo SW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4125.

PMID- 23144407
VI  - 194
DP  - 2012
TI  - Genome Sequence of Mycobacterium abscessus Strain M152.
PG  - 6662
AB  - Mycobacterium abscessus is an environmental bacterium with increasing clinical relevance.
      Here, we report the annotated whole-genome sequence of M. abscessus
      strain M152.
AU  - Ngeow YF
AU  - Wong YL
AU  - Tan JL
AU  - Ong CS
AU  - Ng KP
AU  - Choo SW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6662.

PMID- 27056238
VI  - 4
DP  - 2016
TI  - Permanent Draft Genome Sequence for Frankia sp. Strain CeD, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina equistifolia Grown in  Senegal.
PG  - e00265-16
AB  - Frankiastrain CeD is a member ofFrankialineage Ib that is able to reinfect plants of
      theCasuarinafamilies. Here, we report a 5.0-Mbp draft genome sequence with a
      G+C content of 70.1% and 3,847 candidate protein-encoding genes.
AU  - Ngom M
AU  - Oshone R
AU  - Hurst SG IV
AU  - Abebe-Akele F
AU  - Simpson S
AU  - Morris K
AU  - Sy MO
AU  - Champion A
AU  - Thomas WK
AU  - Tisa LS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00265-16.

PMID- 29930069
VI  - 6
DP  - 2018
TI  - High-Quality Draft Single-Cell Genome Sequence of the NS5 Marine Group from the Coastal Red Sea.
PG  - e00565-18
AB  - The uncultured NS5 marine group represents one of the most ubiquitous flavobacterial
      bacterioplankton associated with marine blooms in the pelagic
      ocean. Here, we present a single-cell genome sampled from coastal waters in the
      Red Sea that represents the first high-quality draft genome sequence within the
      NS5 lineage.
AU  - Ngugi DK
AU  - Stingl U
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00565-18.

PMID- 29748404
VI  - 6
DP  - 2018
TI  - High-Quality Draft Single-Cell Genome Sequence Belonging to the Archaeal Candidate Division SA1, Isolated from Nereus Deep in the Red Sea.
PG  - e00383-18
AB  - Candidate division SA1 encompasses a phylogenetically coherent archaeal group ubiquitous in
      deep hypersaline anoxic brines around the globe. Recently, the
      genome sequences of two cultivated representatives from hypersaline soda lake
      sediments were published. Here, we present a single-cell genome sequence from
      Nereus Deep in the Red Sea that represents a putatively novel family within SA1.
AU  - Ngugi DK
AU  - Stingl U
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00383-18.

PMID- 26337889
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Klebsiella pneumoniae Carbapenemase-Producing K. pneumoniae Siphophage Sushi.
PG  - e00994-15
AB  - Klebsiella pneumoniae is a Gram-negative bacterium in the family Enterobacteriaceae. It is
      associated with numerous nosocomial infections, including respiratory and urinary tract
      infections in humans. The following reports the complete genome sequence of K. pneumoniae
      carbapenemase-producing K. pneumoniae T1-like siphophage Sushi and describes its major
      features.
AU  - Nguyen DT
AU  - Lessor LE
AU  - Cahill JL
AU  - Rasche ES
AU  - Kuty EGF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00994-15.

PMID- 12630312
VI  - 47
DP  - 2002
TI  - Identification of the EcoKI and EcoR124I type I restriction-modification enzyme subunits by non-equilibrium pH gradient two-dimensional gel electrophoresis.
PG  - 641-648
AB  - Effectively optimized and reproducible procedure for monitoring the composition of type I
      restriction-modification endonucleases EcoKI and
      EcoR124I by non-equilibrium pH gradient two-dimensional (2-D) gel
      electrophoresis is described. Three subunits of the enzyme complex,
      which widely differ from one another in their isoelectric points and
      molar mass, were identified in crude cell extracts of E. coli. For the
      first time all three subunits of both EcoKI and EcoR124I were detected
      as distinct spots on a single 2-D gel. A sensitive immunoblotting
      procedure was suggested suitable for routine use in determining the
      identity of individual subunits. Potential application of this method
      for detailed studies of regulation of the function and stoichiometry of
      the enzyme complexes is discussed.
AU  - Nguyen LD
AU  - Cajthamlova K
AU  - Nguyen HT
AU  - Weiser J
AU  - Holubova I
AU  - Weiserova M
PT  - Journal Article
TA  - Folia Microbiol. (Praha)
JT  - Folia Microbiol. (Praha)
SO  - Folia Microbiol. (Praha) 2002 47: 641-648.

PMID- 27257192
VI  - 4
DP  - 2016
TI  - Complete and Closed Genome Sequences of 10 Salmonella enterica subsp. enterica Serovar Anatum Isolates from Human and Bovine Sources.
PG  - e00447-16
AB  - Salmonella enterica is an important pathogen transmitted by numerous vectors. Genomic
      comparisons of Salmonella strains from disparate hosts have the potential
      to further our understanding of mechanisms underlying host specificities and
      virulence. Here, we present the closed genome and plasmid sequences of 10
      Salmonella enterica subsp. enterica serovar Anatum isolates from bovine and human
      sources.
AU  - Nguyen SV
AU  - Harhay DM
AU  - Bono JL
AU  - Smith TP
AU  - Fields PI
AU  - Dinsmore BA
AU  - Santovenia M
AU  - Kelley CM
AU  - Wang R
AU  - Bosilevac JM
AU  - Harhay GP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00447-16.

PMID- 27811097
VI  - 4
DP  - 2016
TI  - Complete, Closed Genome Sequences of 10 Salmonella enterica subsp. enterica Serovar Typhimurium Strains Isolated from Human and Bovine Sources.
PG  - e01212-16
AB  - Salmonella enterica is a leading cause of enterocolitis for humans and animals. S. enterica
      subsp. enterica serovar Typhimurium infects a broad range of hosts.
      To facilitate genomic comparisons among isolates from different sources, we
      present the complete genome sequences of 10 S Typhimurium strains, 5 each
      isolated from human and bovine sources.
AU  - Nguyen SV
AU  - Harhay DM
AU  - Bono JL
AU  - Smith TP
AU  - Fields PI
AU  - Dinsmore BA
AU  - Santovenia M
AU  - Kelley CM
AU  - Wang R
AU  - Bosilevac JM
AU  - Harhay GP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01212-16.

PMID- 26159535
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Carbofuran-Mineralizing Novosphingobium sp. Strain KN65.2.
PG  - e00764-15
AB  - Complete mineralization of the N-methylcarbamate insecticide carbofuran, including
      mineralization of the aromatic moiety, appears to be confined to
      sphingomonad isolates. Here, we report the first draft genome sequence of such a
      sphingomonad strain, i.e., Novosphingobium sp. KN65.2, isolated from
      carbofuran-exposed agricultural soil in Vietnam.
AU  - Nguyen TP
AU  - De Mot R
AU  - Springael D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00764-15.

PMID- 21531805
VI  - 193
DP  - 2011
TI  - Complete genome sequence and immunoproteomic analyses of the fish bacterial pathogen Streptococcus parauberis.
PG  - 3356-3366
AB  - Although Streptococcus parauberis is known as a bacterial pathogen associated with bovine
      udder mastitis, it has recently become one of the
      major causative agents of olive flounder (Paralichthys olivaceus)
      streptococcosis in northeast Asia, causing massive mortality resulting in
      severe economic losses. S. parauberis contains two serotypes, and it is
      likely that capsular polysaccharide antigens serve to differentiate the
      serotypes. In the present study, the complete genome sequence of S.
      parauberis (serotype I) was determined using the GS-FLX system to
      investigate its phylogeny, virulence factors, and antigenic proteins. S.
      parauberis possesses a single chromosome of 2,143,887 bp containing 1,868
      predicted coding sequences (CDSs) with an average GC content of 35.6%.
      Whole-genome dot plot analysis and phylogenetic analysis of a 60 kDa
      chaperonin-encoding gene and the GAPDH-encoding gene showed that the
      strain was evolutionarily closely related to S. uberis. S. parauberis
      antigenic proteins were analyzed using an immunoproteomic technique.
      Twenty-one antigenic protein spots were identified in S. parauberis, by
      reaction with an antiserum obtained from S. parauberis-challenged olive
      flounder. This work provides the foundation needed to understand more
      clearly the relationship between pathogen and host, and develops new
      approaches toward prophylactic and therapeutic strategies to deal with
      streptococcosis in fish. The work also provides a better understanding of
      the physiology and evolution of a significant representative of the
      Streptococcaceae.
AU  - Nho SW
AU  - Hikima JI
AU  - Cha IS
AU  - Park SB
AU  - Jang HB
AU  - Del Castillo CS
AU  - Kondo H
AU  - Hirono I
AU  - Aoki T
AU  - Jung TS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3356-3366.

PMID- 25197456
VI  - 9
DP  - 2014
TI  - Complete genome sequence of a plant associated bacterium Bacillus amyloliquefaciens subsp. plantarum UCMB5033.
PG  - 718-725
AB  - Bacillus amyloliquefaciens subsp. plantarum UCMB5033 is of special interest for its ability to
      promote host plant growth through production of stimulating
      compounds and suppression of soil borne pathogens by synthesizing antibacterial
      and antifungal metabolites or priming plant defense as induced systemic
      resistance. The genome of B. amyloliquefaciens UCMB5033 comprises a 4,071,167 bp
      long circular chromosome that consists of 3,912 protein-coding genes, 86 tRNA
      genes and 10 rRNA operons.
AU  - Niazi A
AU  - Manzoor S
AU  - Bejai S
AU  - Meijer J
AU  - Bongcam-Rudloff E
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 718-725.

PMID- 28663301
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Streptococcus pyogenes Strain M3KCL.
PG  - e00610-17
AB  - We present here the draft genome sequence of Streptococcus pyogenes strain M3KCL. The assembly
      contains 1,864,059 bp in 60 contigs. This strain is an M3 strain
      close to MGAS315 but produces SpeB. It was isolated from the blood of a human
      patient with an invasive infection in 2009.
AU  - Nicholls C
AU  - Kump A
AU  - Ford S
AU  - Gonser R
AU  - Cho KH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00610-17.

PMID- 29773626
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences for a Diverse Set of Isolates from 10 Neisseria Species.
PG  - e00409-18
AB  - Neisseria is a diverse genus that includes commensal and pathogenic species that  pose a
      public health threat. While the pathogenic species have been studied
      extensively, many of the commensals have limited genomic information available.
      Here, we present draft genome sequences for a diverse set of 37 isolates from 10
      Neisseria species.
AU  - Nichols M
AU  - Topaz N
AU  - Wang X
AU  - Wang X
AU  - Boxrud D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00409-18.

PMID- 26659691
VI  - 3
DP  - 2015
TI  - Complete Genome Sequences for Two Strains of a Novel Fastidious, Partially Acid-Fast, Gram-Positive Corynebacterineae Bacterium, Derived from Human Clinical  Samples.
PG  - e01462-15
AB  - Here we report the complete genome sequences of two strains of the novel fastidious, partially
      acid-fast, Gram-positive bacillus 'Lawsonella
      clevelandensis' (proposed). Their clinical relevance and unusual growth
      characteristics make them intriguing candidates for whole-genome sequencing.
AU  - Nicholson AC
AU  - Bell M
AU  - Humrighouse BW
AU  - McQuiston JR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01462-15.

PMID- 26966213
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Strains Representing Each of the Elizabethkingia Genomospecies Previously Determined by DNA-DNA Hybridization.
PG  - e00045-16
AB  - Draft genome sequences of Elizabethkingia meningoseptica and representatives of each of its
      four historically described genomospecies were sequenced here.
      Preliminary analysis suggests that Elizabethkingia miricola belongs to
      genomospecies 2, and both Elizabethkingia anophelis and Elizabethkingia
      endophytica are most similar to genomospecies 1.
AU  - Nicholson AC
AU  - Humrighouse BW
AU  - Graziano JC
AU  - Emery B
AU  - McQuiston JR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00045-16.

PMID- 27313304
VI  - 4
DP  - 2016
TI  - Complete Genome Sequences of Four Strains from the 2015-2016 Elizabethkingia anophelis Outbreak.
PG  - e00563-16
AB  - The complete circularized genome sequences of selected specimens from the largest known
      Elizabethkingia anophelis outbreak to date are described here. Genomic
      rearrangements observed among the outbreak strains are discussed.
AU  - Nicholson AC
AU  - Whitney AM
AU  - Emery BD
AU  - Bell ME
AU  - Gartin JT
AU  - Humrighouse BW
AU  - Loparev VN
AU  - Batra D
AU  - Sheth M
AU  - Rowe LA
AU  - Juieng P
AU  - Knipe K
AU  - Gulvik C
AU  - McQuiston JR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00563-16.

PMID- 26337876
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Strain H5989 of a Novel Devosia Species.
PG  - e00934-15
AB  - The CDC Special Bacteriology Reference Laboratory (SBRL) collection of human clinical
      pathogens contains several strains from the genus Devosia, usually found environmentally. We
      provide here the complete genome of strain H5989, which was isolated from a human
      cerebrospinal fluid (CSF) specimen and represents a putative novel species in the genus
      Devosia.
AU  - Nicholson AC
AU  - Whitney AM
AU  - Humrighouse B
AU  - Emery B
AU  - Loparev V
AU  - McQuiston JR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00934-15.

PMID- 27811114
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of the Neonatal Meningitis-Causing Escherichia coli Strain NMEC O18.
PG  - e01239-16
AB  - Neonatal meningitis Escherichia coli (NMEC) is a common agent of neonatal bacterial
      meningitis, causing high neonatal mortality and neurologic sequelae in
      its victims. Here, we present the complete genome sequence of NMEC O18 (also
      known as NMEC 58), a highly virulent (O18ac:K1, ST416) strain.
AU  - Nicholson BA
AU  - Wannemuehler YM
AU  - Logue CM
AU  - Li G
AU  - Nolan LK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01239-16.

PMID- 27811098
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of the Avian-Pathogenic Escherichia coli Strain APEC O18.
PG  - e01213-16
AB  - Avian-pathogenic Escherichia coli (APEC) is the causative agent of colibacillosis, a disease
      that affects all facets of poultry production
      worldwide, resulting in multimillion dollar losses annually. Here, we report the
      genome sequence of an APEC O18 sequence type 95 (ST95) strain associated with
      disease in a chicken.
AU  - Nicholson BA
AU  - Wannemuehler YM
AU  - Logue CM
AU  - Li G
AU  - Nolan LK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01213-16.

PMID- 25013141
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Bordetella bronchiseptica Swine Isolate KM22.
PG  - e00670-14
AB  - Bordetella bronchiseptica swine isolate KM22 has been used in experimental infections of swine
      as a model of clinical B. bronchiseptica infections within
      swine herds and to study host-to-host transmission. Here we report the draft
      genome sequence of KM22.
AU  - Nicholson TL
AU  - Shore SM
AU  - Bayles DO
AU  - Register KB
AU  - Kingsley RA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00670-14.

PMID- 27617056
VI  - 11
DP  - 2016
TI  - An improved high-quality draft genome sequence of Carnobacterium inhibens subsp.  inhibens strain K1(T).
PG  - 65
AB  - Despite their ubiquity and their involvement in food spoilage, the genus Carnobacterium
      remains rather sparsely characterized at the genome level.
      Carnobacterium inhibens K1(T) is a member of the Carnobacteriaceae family within
      the class Bacilli. This strain is a Gram-positive, rod-shaped bacterium isolated
      from the intestine of an Atlantic salmon. The present study determined the genome
      sequence and annotation of Carnobacterium inhibens K1(T). The genome comprised
      2,748,608 bp with a G + C content of 34.85 %, which included 2621 protein-coding
      genes and 116 RNA genes. The strain contained five contigs corresponding to
      presumptive plasmids of sizes: 19,036; 24,250; 26,581; 65,272; and 65,904 bp.
AU  - Nicholson WL
AU  - Davis CL
AU  - Shapiro N
AU  - Huntemann M
AU  - Clum A
AU  - Reddy TB
AU  - Pillay M
AU  - Markowitz V
AU  - Varghese N
AU  - Pati A
AU  - Ivanova N
AU  - Kyrpides N
AU  - Woyke T
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 65.

PMID- 23950115
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Serratia liquefaciens Strain ATCC 27592.
PG  - e00548-13
AB  - We report the complete genome sequence of Serratia liquefaciens strain ATCC 27592, which was
      previously identified as capable of growth under low-pressure
      conditions. To the best of our knowledge, this is the first announcement of the
      complete genome sequence of an S. liquefaciens strain.
AU  - Nicholson WL
AU  - Leonard MT
AU  - Fajardo-Cavazos P
AU  - Panayotova N
AU  - Farmerie WG
AU  - Triplett EW
AU  - Schuerger AC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00548-13.

PMID- 1354453
VI  - 12
DP  - 1992
TI  - Converting restriction sites by filling in 5' extensions.
PG  - 512-514
AB  - None
AU  - Nickoloff JA
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 1992 12: 512-514.

PMID- 3020559
VI  - 83
DP  - 1986
TI  - A 23-base-pair DNA sequence from the MAT locus stimulates intergenic recombination in yeast.
PG  - 7831-7835
AB  - HO nuclease is a site-specific double-strand endonuclease present in haploid Saccharomyces
      cerevisiae undergoing mating type interconversion. HO nuclease initiates mating type
      interconversion by making a double-strand break within the MAT locus. To define the
      recognition site for the enzyme in vitro, we have constructed a number of point mutations and
      deletions within or adjacent to the HO recognition site. Digestion of these substrates with HO
      in vitro reveals that the minimal recognition site is 18 base pairs long, although several
      shorter substrates and substrates containing point mutations are cleaved at low levels in
      vitro. A 24-base-pair HO recognition site stimulates homologous recombination when present in
      a region unrelated to MAT. Recombinants arise from both gene conversion and crossover events.
      The identification of the HO recognition site provides a way of introducing a defined
      initiation site for recombination.
AU  - Nickoloff JA
AU  - Chen EY
AU  - Heffron F
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1986 83: 7831-7835.

PMID- 16822325
VI  - 7
DP  - 2006
TI  - Complete genome sequence of Shigella flexneri 5b and comparison with Shigella flexneri 2a.
PG  - 173
AB  - ABSTRACT: BACKGROUND: Shigella bacteria cause dysentery, which remains a significant threat to
      public health. Shigella flexneri is the most common
      species in both developing and developed countries. Five Shigella genomes
      have been sequenced, revealing dynamic and diverse features. To
      investigate the intra-species diversity of S. flexneri genomes further, we
      have sequenced the complete genome of S. flexneri 5b strain 8401
      (abbreviated Sf8401) and compared it with S. flexneri 2a (Sf301). RESULTS:
      The Sf8401 chromosome is 4.5-Mb in size, a little smaller than that of
      Sf301, mainly because the former lacks the SHI-1 pathogenicity island
      (PAI). Compared with Sf301, there are 6 inversions and one translocation
      in Sf8401, which are probably mediated by insertion sequences (IS). There
      are clear differences in the known PAIs between these two genomes. The
      bacteriophage SfV segment remaining in SHI-O of Sf8401 is clearly larger
      than the remnants of bacteriophage SfII in Sf301. SHI-1 is absent from
      Sf8401 but a specific related protein is found next to the pheV locus.
      SHI-2 is involved in one intra-replichore inversion near the origin of
      replication, which may change the expression of iut/iuc genes. Moreover,
      genes related to the glycine-betaine biosynthesis pathway are present only
      in Sf8401 among the known Shigella genomes. CONCLUSIONS: Our data show
      that the two S. flexneri genomes are very similar, which suggests a high
      level of structural and functional conservation between the two serotypes.
      The differences reflect different selection pressures during evolution.
      The ancestor of S. flexneri probably acquired SHI-1 and SHI-2 before SHI-O
      was integrated and the serotypes diverged. SHI-1 was subsequently deleted
      from the S. flexneri 5b genome by recombination, but stabilized in the S.
      flexneri 2a genome. These events may have contributed to the differences
      in pathogenicity and epidemicity between the two serotypes of S. flexneri.
AU  - Nie H
AU  - Yang F
AU  - Zhang X
AU  - Yang J
AU  - Chen L
AU  - Wang J
AU  - Xiong Z
AU  - Peng J
AU  - Sun L
AU  - Dong J
AU  - Xue Y
AU  - Xu X
AU  - Chen S
AU  - Yao Z
AU  - Shen Y
AU  - Jin Q
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2006 7: 173.

PMID- 19329537
VI  - 15
DP  - 2009
TI  - A conformational switch in the DiGIR1 ribozyme involved in release and folding of the downstream I-DirI mRNA.
PG  - 958-967
AB  - DiGIR1 is a group I-like cleavage ribozyme found as a structural domain within a nuclear
      twin-ribozyme group I intron. DiGIR1 catalyzes
      cleavage by branching at an Internal Processing Site (IPS) leading to
      formation of a lariat cap at the 5'-end of the 3'-cleavage product. The
      3'-cleavage product is subsequently processed into an mRNA encoding a
      homing endonuclease. By analysis of combinations of 5'- and
      3'-deletions, we identify a hairpin in the 5'-UTR of the mRNA (HEG P1)
      that is formed by conformational switching following cleavage. The
      formation of HEG P1 inhibits the reversal of the branching reaction,
      thus giving it directionality. Furthermore, the release of the mRNA is
      a consequence of branching rather than hydrolytic cleavage. A model is
      put forward that explains the release of the I-DirI mRNA with a lariat
      cap and a structured 5'-UTR as a direct consequence of the DiGIR1
      branching reaction. The role of HEG P1 in GIR1 branching is reminiscent
      of that of hairpin P-1 in splicing of the Tetrahymena rRNA group I
      intron and illustrates a general principle in RNA-directed RNA
      processing.
AU  - Nielsen H
AU  - Einvik C
AU  - Lentz TE
AU  - Hedegaard MM
AU  - Johansen SD
PT  - Journal Article
TA  - RNA
JT  - RNA
SO  - RNA 2009 15: 958-967.

PMID- 16141078
VI  - 309
DP  - 2005
TI  - An mRNA is capped by a 2', 5' lariat catalyzed by a group I-like ribozyme.
PG  - 1584-1587
AB  - Twin-ribozyme introns are formed by two ribozymes belonging to the group I family and occur in
      some ribosomal RNA transcripts. The group I-like
      ribozyme, GIR1, liberates the 5' end of a homing endonuclease messenger
      RNA in the slime mold Didymium iridis. We demonstrate that this cleavage
      occurs by a transesterification reaction with the joining of the first and
      the third nucleotide of the messenger by a 2',5'-phosphodiester linkage.
      Thus, a group I-like ribozyme catalyzes an RNA branching reaction similar
      to the first step of splicing in group II introns and spliceosomal
      introns. The resulting short lariat, by forming a protective 5' cap, might
      have been useful in a primitive RNA world.
AU  - Nielsen H
AU  - Westhof E
AU  - Johansen S
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2005 309: 1584-1587.

PMID- 25685261
VI  - 9
DP  - 2014
TI  - Draft genome sequence of Bacillus azotoformans MEV2011, a (Co-) denitrifying strain unable to grow with oxygen.
PG  - 23
AB  - Bacillus azotoformans MEV2011, isolated from soil, is a microaerotolerant obligate
      denitrifier, which can also produce N2 by co-denitrification. Oxygen is
      consumed but not growth-supportive. The draft genome has a size of 4.7 Mb and
      contains key genes for both denitrification and dissimilatory nitrate reduction
      to ammonium.
AU  - Nielsen M
AU  - Schreiber L
AU  - Finster K
AU  - Schramm A
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 23.

PMID- 26413196
VI  - 10
DP  - 2015
TI  - Draft genome sequence of Bacillus azotoformans MEV2011, a (Co-) denitrifying strain unable to grow with oxygen.
PG  - 4
AB  - Bacillus azotoformans MEV2011, isolated from soil, is a microaerotolerant obligate
      denitrifier, which can also produce N2 by co-denitrification. Oxygen is
      consumed but not growth-supportive. The draft genome has a size of 4.7 Mb and
      contains key genes for both denitrification and dissimilatory nitrate reduction
      to ammonium.
AU  - Nielsen M
AU  - Schreiber L
AU  - Finster K
AU  - Schramm A
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 4.

PMID- 1962210
VI  - 254
DP  - 1991
TI  - Sequence-selective recognition of DNA by strand displacement with a Thymine-substituted polyamide.
PG  - 1497-1500
AB  - A polyamide nucleic acid (PNA) was designed by detaching the deoxyribose
      phosphate backbone of DNA in a computer model and replacing it with an achiral
      polyamide backbone.  On the basis of this model, oligomers consisting of
      thymine-linked aminoethylglycyl units were prepared.  These oligomers recognize
      their complementary target in double-stranded DNA by strand displacement.  The
      displacement is made possible by the extraordinarily high stability of the
      PNA-DNA hybrids.  The results show that the backbone of DNA can be replaced by
      a polyamide, with the resulting oligomer retaining base-specificity
      hybridization.
AU  - Nielsen PE
AU  - Egholm M
AU  - Berg RH
AU  - Buchardt O
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1991 254: 1497-1500.

PMID- 8382793
VI  - 21
DP  - 1993
TI  - Sequence specific inhibition of DNA restriction enzyme cleavage by PNA.
PG  - 197-200
AB  - Plasmids containing double-stranded 10-mer PNA (peptide nucleic acid chimera) targets
      proximally flanked by two restriction enzyme sites were challenged with the complementary PNA
      or PNAs having one or two mismatches, and the effect on the restriction enzyme cleavage of the
      flanking sites was assayed. The following PNAs were used: T10-LysNH2, T5CT4-LysNH2 and
      T2CT2CT4-LysNH2 and the corresponding targets cloned into pUC19 were flanked by BamHI, SalI or
      PstI sites, respectively. In all cases it was found that complete inhibition of restriction
      enzyme cleavage was obtained with the complementary PNA, a significantly reduced effect was
      seen with a PNA having one mismatch, and no effect was seen with a PNA having two mismatches.
      These results show that PNA can be used as sequence specific blockers of DNA recognizing
      proteins.
AU  - Nielsen PE
AU  - Egholm M
AU  - Berg RH
AU  - Buchardt O
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 197-200.

PMID- 25676756
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of MCPA-Degrading Sphingomonas sp. Strain ERG5, Isolated from a Groundwater Aquifer in Denmark.
PG  - e01529-14
AB  - Sphingomonas sp. strain ERG5 was isolated from a bacterial community, originating from a
      groundwater aquifer polluted with low pesticide concentrations. This
      bacterium degrades 2-methyl-4-chlorophenoxyacetic acid (MCPA) in a wide spectrum
      of concentrations and has been shown to function in bioaugmented sand filters.
      Genes associated with MCPA degradation are situated on a putative conjugative
      plasmid.
AU  - Nielsen TK
AU  - Kot W
AU  - Sorensen SR
AU  - Hansen LH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01529-14.

PMID- 26021936
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Isoproturon-Mineralizing Sphingomonas sp. SRS2, Isolated from an Agricultural Field in the United Kingdom.
PG  - e00569-15
AB  - Sphingomonas sp. SRS2 was the first described pure strain that is capable of mineralizing the
      phenylurea herbicide isoproturon and some of its related
      compounds. This strain has been studied thoroughly and shows potential for
      bioremediation purposes. We present the draft genome sequence of this bacterium,
      which will aid future studies.
AU  - Nielsen TK
AU  - Sorensen SR
AU  - Hansen LH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00569-15.

PMID- 29276572
VI  - 12
DP  - 2017
TI  - Genome sequence of the model plant pathogen Pectobacterium carotovorum SCC1.
PG  - 87
AB  - Bacteria of the genus Pectobacterium are economically important plant pathogens that cause
      soft rot disease on a wide variety of plant species. Here, we report
      the genome sequence of Pectobacterium carotovorum strain SCC1, a Finnish soft rot
      model strain isolated from a diseased potato tuber in the early 1980's. The
      genome of strain SCC1 consists of one circular chromosome of 4,974,798 bp and one
      circular plasmid of 5524 bp. In total 4451 genes were predicted, of which 4349
      are protein coding and 102 are RNA genes.
AU  - Niemi O
AU  - Laine P
AU  - Koskinen P
AU  - Pasanen M
AU  - Pennanen V
AU  - Harjunpaa H
AU  - Nykyri J
AU  - Holm L
AU  - Paulin L
AU  - Auvinen P
AU  - Palva ET
AU  - Pirhonen M
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 87.

PMID- 15377793
VI  - 101
DP  - 2004
TI  - Structural flexibility in the Burkholderia mallei genome.
PG  - 14246-14251
AB  - The complete genome sequence of Burkholderia mallei ATCC 23344 provides
      insight into this highly infectious bacterium's pathogenicity and
      evolutionary history. B. mallei, the etiologic agent of glanders, has come
      under renewed scientific investigation as a result of recent concerns
      about its past and potential future use as a biological weapon. Genome
      analysis identified a number of putative virulence factors whose function
      was supported by comparative genome hybridization and expression profiling
      of the bacterium in hamster liver in vivo. The genome contains numerous
      insertion sequence elements that have mediated extensive deletions and
      rearrangements of the genome relative to Burkholderia pseudomallei. The
      genome also contains a vast number (>12,000) of simple sequence repeats.
      Variation in simple sequence repeats in key genes can provide a mechanism
      for generating antigenic variation that may account for the mammalian
      host's inability to mount a durable adaptive immune response to a B.
      mallei infection.
AU  - Nierman WC et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2004 101: 14246-14251.

PMID- 11259647
VI  - 98
DP  - 2001
TI  - Complete genome sequence of Caulobacter crescentus.
PG  - 4136-4141
AB  - The complete genome sequence of Caulobacter crescentus was determined to be 4,016,942 base
      pairs in a single circular chromosome encoding 3,767 genes. This organism, which grows in a
      dilute aquatic environment, coordinates the cell division cycle and multiple cell
      differentiation events. With the annotated genome sequence, a full description of the genetic
      network that controls bacterial differentiation, cell growth, and cell cycle progression is
      within reach. Two-component signal transduction proteins are known to play a significant role
      in cell cycle progression. Genome analysis revealed that the C. crescentus genome encodes a
      significantly higher number of these signaling proteins (105) than any bacterial genome
      sequenced thus far. Another regulatory mechanism involved in cell cycle progression is DNA
      methylation. The occurrence of the recognition sequence for an essential DNA methylating
      enzyme that is required for cell cycle regulation is severely limited and shows a bias to
      intergenic regions. The genome contains multiple clusters of genes encoding proteins essential
      for survival in a nutrient poor habitat. Included are those involved in chemotaxis, outer
      membrane channel function, degradation of aromatic ring compounds, and the breakdown of
      plant-derived carbon sources, in addition to many extracytoplasmic function sigma factors,
      providing the organism with the ability to respond to a wide range of environmental
      fluctuations. C. crescentus is, to our knowledge, the first free-living alpha-class
      proteobacterium to be sequenced and will serve as a foundation for exploring the biology of
      this group of bacteria, which includes the obligate endosymbiont and human pathogen Rickettsia
      prowazekii, the plant pathogen Agrobacterium tumefaciens, and the bovine and human pathogen
      Brucella abortus.
AU  - Nierman WC et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2001 98: 4136-4141.

PMID- 23990581
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Sphingobium chinhatense Strain IP26T, Isolated from a Hexachlorocyclohexane Dumpsite.
PG  - e00680-13
AB  - Sphingobium chinhatense strain IP26(T) is a conducive hexachlorocyclohexane (HCH) degrader
      isolated from a heavily contaminated (450 mg HCH/g soil) HCH dumpsite.
      IP26(T) degrades alpha-, beta-, gamma-, and delta-HCH, which are highly
      persistent in the environment. Here we report the draft genome sequence (~5.8
      Mbp) of this strain.
AU  - Niharika N
AU  - Sangwan N
AU  - Ahmad S
AU  - Singh P
AU  - Khurana JP
AU  - Lal R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00680-13.

PMID- 1561078
VI  - 20
DP  - 1992
TI  - Oligodeoxynucleotides containing 4-thiothymidine and 6-thiodeoxyguanosine as affinity labels for the Eco RV restriction endonuclease and modification methylase.
PG  - 1209-1214
AB  - 4-Thiothymidine and 6-thiodeoxyguanosine were incorporated into synthetic
      dodecamers containing the recognition site d(GATATC) of the enzymes EcoRV
      endonuclease and EcoRV methyltransferase.  Upon irradiation with long
      wavelength UV light (340- 360 nm), these oligodeoxynucleotides were
      photochemically crosslinked to both enzymes.  The yields were up to 35% with
      the methyltransferase, but lower (up to 6%) with the endonuclease.
      Oligodeoxynucleotides containing 4-thiothymidine generally gave higher yields
      of crosslinking than those containing 6-thiodeoxyguanosine.  Although both
      specific (i.e. those containing the d(GATATC) sequence) and non-specific
      (lacking this sequence) photoreactive oligodeoxynucleotides gave rise to
      crosslinked products, the use of a non-reactive, competitive substrate
      oligodeoxynucleotide suppressed the crosslinking, indicating that the reaction
      takes place at the enzymes' active sites.  Oligodeoxynucleotides containing
      4-thiocyanatothymidine or 6-thiocyanatodeoxyguanosine were also prepared by
      treatment of the title oligomers with CNBr and KCN.  The dodecamers containing
      4-thiocyanatothymidine were found to covalently modify both enzymes under
      study, with levels of crosslinking reaching up to 42% with the endonuclease and
      up to 12% with the methyltransferase.  No crosslinking was observed with
      oligodeoxynucleotides containing 6-thiocyanatodeoxyguanosine.
AU  - Nikiforov TT
AU  - Connolly BA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 1209-1214.

PMID- 12821318
VI  - 30
DP  - 2003
TI  - Construction of an overproducing strain, purification, and biochemical characterization of the 6His-Eco29kI restriction endonuclease.
PG  - 26-31
AB  - We constructed a strain of Escherichia coli overproducing 6His-tagged Eco29kI by placing the
      coding sequence under control of a strong
      bacteriophage T5 promoter. The yield of 6His-Eco29kI restriction
      endonuclease expression could be increased to about 20% of the total
      cellular protein, but inclusion bodies formed consisting of insoluble
      6His-Eco29kI protein. We developed a fast and effective protocol for
      purification of the homogeneous enzyme from both soluble and insoluble
      fractions and established their identity by catalytic activity assay. The
      isolated enzymes were tested for recognition specificity and optimal
      reaction conditions as a function of NaCl and KCl concentrations,
      temperature, and pH compared with the native Eco29kI restriction
      endonuclease. The 6His-tagged enzyme retained the specificity of the
      native protein but had an altered optimum of its catalytic reaction.
AU  - Nikitin D
AU  - Mokrishcheva M
AU  - Denjmukhametov M
AU  - Pertzev A
AU  - Zakharova M
AU  - Solonin A
PT  - Journal Article
TA  - Protein Expr. Purif.
JT  - Protein Expr. Purif.
SO  - Protein Expr. Purif. 2003 30: 26-31.

PMID- 17604705
VI  - 1774
DP  - 2007
TI  - 6His-Eco29kI methyltransferase methylation site and kinetic mechanism characterization.
PG  - 1014-1019
AB  - A new type 11 6His-Eco29kI DNA methyltransferase was tested for methylation site (CC(Me)GCGG)
      and catalytic reaction optimal
      conditions. With high substrate concentrations, an inhibitory effect of
      DNA, but not AdoMet, on its activity was observed. Isotope partitioning
      and substrate preincubation assays showed that the enzyme-AdoMet
      complex is catalytically active. Considering effect of different
      concentrations of DNA and AdoMet on initial velocity, ping-pong
      mechanisms were ruled out. According to data obtained, the enzyme
      appears to work by preferred ordered bi-bi mechanism with AdoMet as
      leading substrate.
AU  - Nikitin D
AU  - Mokrishcheva M
AU  - Solonin A
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 2007 1774: 1014-1019.

PMID- 
VI  - 0
DP  - 2012
TI  - Bifunctional prokaryotic DNA-methyltransferases.
PG  - 71-87
AB  - Restriction-modification systems are prokaryotic tools against invasion of foreign DNAs into
      cells.  They reduce horizontal gene transfer, thus stimulating microbial biodiversity.
      Usually, they consist of a restriction endonuclease and a modification DNA methyltransferase
      enzyme recognizing the same short 4-8 nucleotide sequence.  MTase is responsible for methyl
      group transfer to adenine or cytosine nucleotides within the target sequence, thus preventing
      its hydrolysis by cognate REase.  Up to now, more than 20 000 different RMS have been
      collected in the REBASE, the database holding all known, and many putative RMS.  Many of these
      RMS have head-to-tail gene orientation, thus providing, by our hypothesis, the possibility of
      gene fusion through point mutations or genome rearrangements such as deletions, insertions,
      inversions or translocation.  These events could be responsible for the origin of bifunctional
      restriction enzymes of type IIC such as AloI, BcgI, BseMII, BseRI, BsgI, BspLU11III, CjeI,
      Eco57I, HaeIV, MmeI, PpiI, TstI and TspWGI; bifunctional MTases such as FokI and LlaI, and
      regulatory SsoII-related MTases.
AU  - Nikitin DV
AU  - Kertesz-Farkas A
AU  - Solonin AS
AU  - Mokrishcheva ML
PT  - Journal Article
TA  - Methylation - from DNA, RNa and histones to diseases and treatment
JT  - Methylation - from DNA, RNa and histones to diseases and treatment
SO  - Methylation - from DNA, RNa and histones to diseases and treatment 2012 0: 71-87.

PMID- 
VI  - 77
DP  - 2012
TI  - Binding of DNA methyltransferase M.Ecl18 to operator-promoter region decreases its methylating activity.
PG  - 392-397
AB  - The type II bifunctional DNA methyltransferase (MTase) Ecl18 that is able to control
      transcription of its own gene was studied kinetically. Based on initial velocity dependences
      from S-adenosyl-L-methionine (AdoMet) and target DNA and substrate preincubation assays, it is
      proposed that the enzyme apparently works by a rapid equilibrium ordered bi-bi mechanism with
      DNA binding first. By measuring the enzyme activity depending on DNA and AdoMet at different
      fixed concentrations of the operator sequence oligonucleotide, it was found that its binding
      has noncompetitive inhibitory effect on Ecl18 MTase activity.
AU  - Nikitin DV
AU  - Mokrishcheva ML
AU  - Solonin AS
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 2012 77: 392-397.

PMID- 22803949
VI  - 77
DP  - 2012
TI  - Binding of DNA methyltransferase M.Ecl18 to operator-promoter region decreases its methylating activity.
PG  - 307-311
AB  - The type II bifunctional DNA methyltransferase (MTase) Ecl18 that is able to control
      transcription of its own gene was studied kinetically.
      Based on initial velocity dependences from S-adenosyl-L-methionine
      (AdoMet) and target DNA and substrate preincubation assays, it is
      proposed that the enzyme apparently works by a rapid equilibrium
      ordered bi-bi mechanism with DNA binding first. By measuring the enzyme
      activity depending on DNA and AdoMet at different fixed concentrations
      of the operator sequence oligonucleotide, it was found that its binding
      has noncompetitive inhibitory effect on Ecl18 MTase activity.
AU  - Nikitin DV
AU  - Mokrishcheva ML
AU  - Solonin AS
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2012 77: 307-311.

PMID- 25953165
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of an Enterotoxigenic Bacteroides fragilis Clinical Isolate.
PG  - e00450-15
AB  - Here we present the complete genome sequence of Bacteroides fragilis isolate BOB25. It is an
      enterotoxigenic isolate that was obtained from a stool sample of
      a patient with dysbiosis.
AU  - Nikitina AS
AU  - Kharlampieva DD
AU  - Babenko VV
AU  - Shirokov DA
AU  - Vakhitova MT
AU  - Manolov AI
AU  - Shkoporov AN
AU  - Taraskina AE
AU  - Manuvera VA
AU  - Lazarev VN
AU  - Kostryukova ES
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00450-15.

PMID- 25237028
VI  - 2
DP  - 2014
TI  - Genome Sequence of Pectobacterium atrosepticum Strain 21A.
PG  - e00935-14
AB  - We report the annotated genome sequence of the enterobacterial plant pathogen Pectobacterium
      atrosepticum strain 21A, isolated in Belarus from potato stem with
      blackleg symptoms.
AU  - Nikolaichik Y
AU  - Gorshkov V
AU  - Gogolev Y
AU  - Valentovich L
AU  - Evtushenkov A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00935-14.

PMID- 15888729
VI  - 33
DP  - 2005
TI  - Common patterns in type II restriction enzyme binding sites.
PG  - 2726-2733
AB  - Restriction enzymes are among the best studied examples of DNA binding proteins. In order to
      find general patterns in DNA recognition sites, which may reflect important properties of
      protein-DNA interaction, we analyse the binding sites of all known type II restriction
      endonucleases. We find a significantly enhanced GC content and discuss three explanations for
      this phenomenon. Moreover, we study patterns of nucleotide order in recognition sites. Our
      analysis reveals a striking accumulation of adjacent purines (R) or pyrimidines (Y). We
      discuss three possible reasons: RR/YY dinucleotides are characterized by (i) stronger H-bond
      donor and acceptor clusters, (ii) specific geometrical properties and (iii) a low stacking
      energy. These features make RR/YY steps particularly accessible for specific protein-DNA
      interactions. Finally, we show that the recognition sites of type II restriction enzymes are
      underrepresented in host genomes and in phage genomes.
AU  - Nikolajewa S
AU  - Byer A
AU  - Friedel M
AU  - Hollunder J
AU  - Wilhelm T
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2005 33: 2726-2733.

PMID- 6395868
VI  - 9
DP  - 1984
TI  - Sequence Specificity of Isolated DNA-Cytosine Methylases from Shigella Sonnei 47 Cells.
PG  - 771-781
AB  - Five individual DNA-cytosine methylases differing in pI (isoelectric point) values are present
      in Shigella sonnei 47 cells.  The sequence specificity of each of those was determined 'in
      vitro' by a highly efficient combined approach that included pyrimidine tract (isostic)
      analysis, identification of the immediate neighborhood of the methylated base within the
      recognition sequence and the calculation method.  The enzyme with pI 5.3 (Msso 5,3) is the
      counterpart of the RSso 47II in the Sso 47II restriction-modification system and methylates
      the internal cytosine residue of the 'palindromic' 5'-C-C-N-G-G-3' sequence.  The enzymes
      with pI 6.2 (Msso 6,2) and 7.4 (MSso 7,4) exhibit identical specificity upon methylation of
      the 'palindromic' 5'-Py-C-N-G-Pu-3' sequence, but differ in the pI values of the proteins.
      The enzyme with pI 4.2 (MSso 4,2) recognizes the unique tetranucleotide 5'-C-C-C-C-3'
      sequence and methylates the second cytosine residue at the 5'-end of the sequence.  The
      enzyme with pI 8.4 (MSso 8,4) methylates the centrol cytosine residue within the degenerative
      trinucleotide 5'-(Pu)-C-C-3' sequence. MSso5,3', MSso6,2', and MSso7,4 are presumed to
      belong to the 'family' of sequence-specific (EcoRII-like) enzymes. These DNA-cytosine
      methylases are likely to be evolutionarily related to EcoRII and to have undergone a
      sufficient genetic drift so as to recognize similar (but more degenerative) nucleotide
      sequences.
AU  - Nikolskaya I
AU  - Lopatina N
AU  - Suchkov S
AU  - Kartashova I
AU  - Debov S
PT  - Journal Article
TA  - Biochem. Int.
JT  - Biochem. Int.
SO  - Biochem. Int. 1984 9: 771-781.

PMID- 369609
VI  - 561
DP  - 1979
TI  - Specificity and functions of guanine methylase of Shigella sonnei DDVI phage.
PG  - 232-239
AB  - DNA methylase methylating adenine with formation of 6-methylamino-purine has
      been identified in Shigella sonnei 1188 cells which are the natural host of
      DDVI phage.  At the same time, in DNA of DDVI phage replicating both in Sh.
      sonnei 1188 cells and Escherichia coli B cells 7-methylguanine was found as the
      only minor base in amounts of 0.25 and 0.27 mol per 100 mos of nucleotides,
      respectively.  The extract of the infected cells was found to contain both
      kinds of DNA methylases; virus-specific guanine methylase and cellular adenine
      methylase.  The place of 6-methylaminopurine in DNA of this phage is explained
      by reversible inhibition of the cell enzyme in the infected cells.  The amount
      of methyl groups transferred by DDVI-specific methylase on DNA does not depend
      on the specifics of the infected cells and is similar in the case of unmodified
      SD phage DNA and DNA of T2 phase methylated by E. coli B enzyme.  Guanine
      methylase has been shown to be a DDVI-induced modification enzyme and to
      protect against restriction of B-type. It methylates double-stranded DNAs only
      and is inhibited by S-adenosylhomocysteine.
AU  - Nikolskaya I
AU  - Tediashvili M
AU  - Lopatina N
AU  - Chanishvili TG
AU  - Debov S
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1979 561: 232-239.

PMID- 322735
VI  - 42
DP  - 1977
TI  - Fractionation and purification of DNA methylases and specific endonucleases from cells of Escherichia coli SK.
PG  - 598-608
AB  - Fractionation and purification of DNA methylases and specific endonucleases from cells of
      Escherichia coli SK responsible for DNA specificity to host prokaryotic cells were studied.
      The most efficient purification was achieved by precipitation of proteins by 60% saturated
      ammonium sulfate with subsequent chromatography on CM-cellulose and concentration of fractions
      by dialysis against glycerol.  Under these conditions the methylase activity produced 4
      discrete fractions.  Due to purification the specific activity of methylases increased
      11-20-fold in various fractions.  Methylase from the first (A) and fourth (BII) peaks
      catalyzed the methylation of cytosine to produce 5-methylcytosine; methylase from the third
      peak (BI) methylated adenine to produce 6-methylaminopurine.  The chemical specificity of the
      second peak (B) methylase could not be established due to very high lability of the enzyme in
      this fraction.  Specific endonuclease was found in the gradient zones eluted by 0.1-0.2M and
      0.65-0.75M NaCl.   It is assumed that those enzymes providing for DNA hydrolysis up to the
      formation of high-molecular discrete fragments, are restriction endonucleases of the SK
      system.  The results obtained strongly suggest the existence of several types of methylases
      and restricting endonucleases in E. coli SK cells.
AU  - Nikolskaya II
AU  - Aleksandrova SS
AU  - Lopatina NG
AU  - Debov SS
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1977 42: 598-608.

PMID- 353533
VI  - 20
DP  - 1978
TI  - Fractionation and specificity of DNA methylases from the Escherichia coli SK cells.
PG  - 17-24
AB  - Specificity of DNA methylation enzymes from the E. coli SK cells and conditions for their
      separation have been investigated.  Column chromatography on carboxymethylcellulose permits
      fractionation of methylase activity into six discrete peaks whose specificity to the
      methylated base has been determined in vitro with H3-SAM as precursor.  All methylases
      specific for adenine produced 6'-methylaminopurine, all methylases specific for cytosine
      yielded 5'-methylcytosine.  The first enzymatic activity peak containing cytosine methylase
      free of traces of adenine-methylating activity (E1), and the second peak containing both the
      enzymes (E2) were not adsorbed on the ion exchanger and went off the column with the effluent
      (column buffer).  Adenine specific methylase E2 is retarded to a small extent during the
      passage through the column.  The second adenine methylase (W) was characterized by weak bonds
      with the ion exchanger and was removed when washing the column with column buffer.  The
      elution with NaCl gradient produced successively three enzymatic activity peaks: adenine
      methylase (GI), cytosine methylase (GII), and one more adenine methylase (GIII) removed from
      the column by 0.16M, 0.24M and 0.43M NaCl respectively.  Using a new modification of the
      complementary methylation test, the specificity with regard to recognition site was examined
      for all enzymes, except for W and GIII, which were extremely unstable.  The adenine methylases
      E2 and GI and the cytosine methylases E1 and GII were shown to recognize different sites and
      to be different enzymes.  In view of the drastic differences in their chromatographic behavior
      and physical stability, the adenine methylases W and GIII are probably also different enzymes.
AU  - Nikolskaya II
AU  - Aleksandrova SS
AU  - Lopatina NG
AU  - Debov SS
PT  - Journal Article
TA  - Mol. Cell. Biochem.
JT  - Mol. Cell. Biochem.
SO  - Mol. Cell. Biochem. 1978 20: 17-24.

PMID- 2823497
VI  - 0
DP  - 1987
TI  - Molecular and medical aspects of DNA modification.
PG  - 23-29
AB  - The role of methylation in the cell's life cycle is considered with special
      reference to regulation of transcription in pro- and eukaryotes.  In
      eukaryotes, an inverse correlation exists between levels of gene expression and
      methylation, as is illustrated by experiments with eukaryotic viruses.  In the
      case of bacteriophages, the expression of viral genes may be regulated through
      methylation both negatively and positively.  The modifying role of methylation
      enzymes in prokaryotes, based on the identity or overlap of recognition sites
      in methylases and restriction endonucleses, is analyzed at length.
AU  - Nikolskaya II
AU  - Debov SS
PT  - Journal Article
TA  - Vestn. Akad. Med. Nauk SSSR
JT  - Vestn. Akad. Med. Nauk SSSR
SO  - Vestn. Akad. Med. Nauk SSSR 1987 0: 23-29.

PMID- Not included in PubMed...
VI  - 0
DP  - 1983
TI  - Enzymes of the new system of the host specificity Sso47II.
PG  - 5-10
AB  - The DNA host specificity systems SsoI and SsoII are present in Sh. sonnei 47 cells.  The
      R.SsoII and M.SsoII were isolated from these cells and purified by means of affinity,
      ion-exchange, hydrophobic chromatography and isoelectric focusing.  The fine structure of
      R.SsoII and M.SsoII recognition sites was the following: ^CC*NGG.  The pI of M.SsoII was found
      to be 5.3 as determined by isoelectric focusing.  M.SsoII transfers methyl groups to the inner
      cytosine in the recognition sequence CC*NGG.  R.SsoII and M.SsoII are isoshiso- and
      isomethymeric of EcoRII type correspondingly with the SsoII recognition sequence being more
      degenerative.
AU  - Nikolskaya II
AU  - Karpetz LZ
AU  - Kartashova M
AU  - Lopatina NG
AU  - Skripkin EA
AU  - Suchkov SV
AU  - Uporova TM
AU  - Gruber IM
AU  - Debov SS
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1983 0: 5-10.

PMID- 386287
VI  - 7
DP  - 1979
TI  - Determination of the recognition sites of cytosine DNA-methylases from Escherichia coli SK.
PG  - 517-528
AB  - Two different cytosine DNA-methylases, NI and GII, are present in Escherichia
      coli SK.  The GII methylase recognizes the five-member symmetric sequence:
      5'...NpCpCpApGpGpN...3'.  This sequence is identical with the recognition site
      of the hsp II type determined by RII plasmid but, in contrast to RII methylase,
      the GII enzyme methylates cytosine located on the 5' side of the site.  By
      analogy with the isoshizomery of the restricting endonucleases, RII and GII DNA
      methylaeses may be called isomethymers which recognize the same site but
      methylate different bases.  Since the phage of the SK and hsp II phenotypes is
      effectively restricted in respective cells it may be assumed that the
      isomethymeric modification does not provide any protection against the
      corresponding restrictases.  NI methylase recognizes the five-member symmetric
      site which represents an inverted sequence of the GII site:
      5'...NpGpGpApCpCpN...3'.  In this case cytosine at the 3'-end of the
      recognition site is methylated.
AU  - Nikolskaya II
AU  - Lopatina NG
AU  - Anikeicheva NV
AU  - Debov SS
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1979 7: 517-528.

PMID- 794697
VI  - 13
DP  - 1976
TI  - The host specificity system in Escherichia coli SK.
PG  - 79-87
AB  - E. coli SK has its own enzyme system providing DNA host specificity which differs from the
      known types of specificity in E. coli K12 and E. coli B.  Modification and restriction are
      observed when the PBVI or PBV3 phages are transferred from E. coli SK to E. coli B or K12 (and
      back).  A methylase has been isolated from E. coli SK cells and partly purified.  This
      methylase catalyzes in vitro transfer of the labeled methyl groups from S-adenosylmethionine
      to DNA of both phage and tissue origin which gives rise to 5'-methylcytosine and
      6'-methylaminopurine.  The methylase preparations isolated from the cells at stationary phase
      have proved to be 1.5-1.7 times as active as the enzyme from cells at the logarithmic growth
      stage.  The extract of E. coli SK cells infected with the phage SD cannot methylate DNA in
      vitro.  This fact is due to de novo synthesis of the enzyme which degrades SAM to
      5'-methylthioadenosine and homoserine.  This enzyme is not found in cells infected with the
      SD phage in the presence of chloroamphenicol.  The activity of the enzyme which degrades SAM
      is highest between the 4th and the 5th minutes of infection.  Thus it may be assumed that this
      enzyme, most probably, is an early virus specific protein and prevents in vivo methylation of
      the phage DNA.
AU  - Nikolskaya II
AU  - Lopatina NG
AU  - Chaplygina NM
AU  - Debov SS
PT  - Journal Article
TA  - Mol. Cell. Biochem.
JT  - Mol. Cell. Biochem.
SO  - Mol. Cell. Biochem. 1976 13: 79-87.

PMID- 7012581
VI  - 35
DP  - 1981
TI  - On heterogeneity of DNA methylases from Escherichia coli SK cells.
PG  - 3-10
AB  - The presence in E. coli SK cells of five different DNA-methylases differing in specificity to
      the methylated sequence is documented has been proven.  Two enzymes methylate cytosine with
      the formation of 5'-methylcytosine and three enzymes methylate adenine with formation of
      6'-methylaminopurine.  A method for simultaneous isolation of the five individual enzymes
      including gel filtration on Biogel A-0.5 M is proposed.  The direct evidence has been
      presented showing that the additional methylation test in our method modification actually can
      discriminate between enzymes differing in sensitive sites.
AU  - Nikolskaya II
AU  - Lopatina NG
AU  - Debov SS
PT  - Journal Article
TA  - Mol. Cell. Biochem.
JT  - Mol. Cell. Biochem.
SO  - Mol. Cell. Biochem. 1981 35: 3-10.

PMID- 329898
VI  - 42
DP  - 1977
TI  - Some peculiarities of phage DDVI-specific methylases.
PG  - 828-832
AB  - Two types of methylases are found in the cellular extract of Escherichia coli B, infected with
      phage DDVI.  One of them is a cellular enzyme, which methylates adenine to form
      6-methylaminopurine and is repressed in the infected cell in vivo.  The second type, which is
      not found in the non-infected cell, is specific for phage DDVI and induces the formation of
      7-methylguanine.  Both enzymes recognize various sites, which accounts for variation in the
      ratio 6-MAP/7-MG in heterologous DNAs between 2.07 in phage Sd DNA and 0.40 in phage DDII DNA.
      During in vitro incubation with homologous methylases phage DDVI DNA and especially phage T2
      DNA are subjected to further methylation, which is probably indicative of their
      undermethylation in vivo.  The DDVI-specific enzyme, similar to B-specific type, methylates
      DNA with a normal set of nitrogenous bases (phages Sd and DDII0, as well as DNAs containing
      5-oxymethylcytosine and glucose (phages T2 and DDVI).  Both methylases under study use only
      native double-helical DNA as substrate and are strongly inhibited by S-adenosylhomocysteine.
      Phage DDVI methylase is characterized by low stability.
AU  - Nikolskaya II
AU  - Lopatina NG
AU  - Dedov SS
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1977 42: 828-832.

PMID- 3068540
VI  - 10
DP  - 1988
TI  - Modifying methylase SsoI from Shigella sonnei 47 cells.
PG  - 26-30
AB  - A simple and fast method for isolation and purification of SsoI methylase from
      the bacterial strain Shigella sonnei 47 has been proposed.  The enzyme is a
      modifying component of the host cell specificity system and protects the
      acceptor DNA from hydrolysis by restriction endonuclease SsoI and EcoRI.  The
      method is based on hydrophobic chromatography of ammonium sulphate fraction on
      phenylsepharose.  The enzyme preparation obtained is devoid of specific and
      nonspecific endonucleases and is stable at storage in 30% glycerol during a
      year.  The conditions of manifestation of "star" activity by the enzyme were
      studied.
AU  - Nikolskaya II
AU  - Lopatina NG
AU  - Lopareva EN
AU  - Posypanova AM
AU  - Debov SS
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1988 10: 26-30.

PMID- 351945
VI  - 24
DP  - 1978
TI  - On the effect of S-nucleosyl homocysteines on activity of several DNA methylases.
PG  - 252-255
AB  - The effect was studied of S-adenosyl, -uridyl, -cytidyl and -inosyl homocysteines on the
      activity of bacterial adenine and cytosine methylases from E. coli CK as well as on guanine
      methylase specific for DDVI phage.  S-adenosyl homocysteine was shown to be a strong inhibitor
      of methylation; 10 microM of the substance inhibited all the enzymes studied by 98-99%.  Use
      of total enzymatic preparations did not show any difference in the affinity of S-uridyl,
      -cytidyl and -inosyl homocysteines to various DNA methylases studied.  All these preparations
      inhibited DNA methylases by 55-65%.  Increase in the concentration of inhibitor up to 20
      microM did not elevate the inhibitory effect.  Action of S-nucleosyl homocysteines did not
      depend on the type of acceptor DNA.
AU  - Nikolskaya II
AU  - Lopatina NG
AU  - Rekunova VN
AU  - Yurkevich AM
AU  - Debov SS
PT  - Journal Article
TA  - Vopr. Med. Khim.
JT  - Vopr. Med. Khim.
SO  - Vopr. Med. Khim. 1978 24: 252-255.

PMID- 3893435
VI  - 10
DP  - 1985
TI  - Sequence specificity of isolated DNA-adenine methylases from Mycobacterium smegmatis (butyricum) and Shigella sonnei 47 cells.
PG  - 405-413
AB  - A set of four individual DNA-adenine methylases differing in pI (isoelectric point) values
      (MMbu4.2', MMbu6.4', MMbu7.3' and MMbu8.7), and a sole methylating enzyme with the same
      base specificity (MSso9.5) are present in M. smegmatis (butyricum) and S. sonnei 47 cells,
      respectively.  The sequence specificity of each of those was studied in vitro by a combined
      approach that comprised isostich (purine tract) analysis and identification of the immediate
      neighbourhood of the methylated base within the sequence methylated.  The MSso9.5 recognition
      site has been established as the hexanucleotide 'palindromic' 5'-G-A*-A-T-T-C-3' sequence
      which is structurally similar to the analogous M.EcoRI recognition site.  However, in contrast
      to M.EcoRI, MSso 9.5 methylates the 5'-end adenine residue in the sequence and thus it
      appears to be an isometimer of M.EcoRI.  By means of the same approach, the partial nucleotide
      sequences methylated by each of the four individual M. butyricum enzymes were determined.
      MMbu7.3 and MMbu8.7 exhibit the identical sequence specificity upon methylation of the
      degenerative trinucleotide 5'-Py-A*-Py-3' sequence and thus these enzymes are assumed to
      represent the different molecular forms of the methylase.  MMbu4.2 methylates the
      5'-G-G-A*-3' sequence and thus it is of a great value as the tool for negating effects of
      the R.BamHI and R.AvaII-type restriction.  MMbu6.4 is of a particular interest on account of
      its unique DNA methylation pattern which is distinguished in the pronounced clustering of
      purine bases in the 5'-Pu-Pu-Pu-Pu-Pu-3' sequence methylated.
AU  - Nikolskaya II
AU  - Lopatina NG
AU  - Sharkova EV
AU  - Suchkov SV
AU  - Somodi P
AU  - Foldes I
AU  - Debov SS
PT  - Journal Article
TA  - Biochem. Int.
JT  - Biochem. Int.
SO  - Biochem. Int. 1985 10: 405-413.

PMID- 6385983
VI  - 7
DP  - 1983
TI  - Isoelectric focusing of bacterial DNA methylases.
PG  - 605-615
AB  - The multiplicity of bacterial DNA methylases has been shown for new microorganisms,
      Mycobacteria and Shigella, by a double-step procedure including column chromatography followed
      by isoelectric focusing of the total methylase fraction.  The profiles of the DNA methylating
      activity of Sh.sonnei 47 and M. butyricum strains were studied.  Sh. Sonnei 47 cells were
      found to contain five different proteins responsible for DNA methylation and having pI 4.2,
      5.3, 6.2, 8.4 and 9.2.  Four M. butyricum methylases were represented by proteins with pI 4.2,
      6.0, 8.0 and 9.0.
AU  - Nikolskaya II
AU  - Sharkova EV
AU  - Suchkov SV
AU  - Karpets LZ
AU  - Debov SS
AU  - Somodi P
AU  - Foldes I
PT  - Journal Article
TA  - Biochem. Int.
JT  - Biochem. Int.
SO  - Biochem. Int. 1983 7: 605-615.

PMID- 3331085
VI  - 15
DP  - 1987
TI  - Factors of activation and stabilization of DNA-methylases from Shigella Sonnei 47 and Mycobacterium smegmatis butyricum cells.
PG  - 127-138
AB  - A comparative study of factors of activation and stabilization of individual
      DNA-methylases from two bacterial strains - Shigella sonnei 47 and
      Mycobacterium smegmatis butyricum - isolated by isoelectrofocusing in a pH
      gradient has been carried out.  Storage of enzymes at +4C (pH 7.5) is
      accompanied by periodic changes in the methylating activity.  No such changes
      are observed when the enzymes are stored at pI of the protein.  In this case
      the methylases with alkaline or close to neutral values of pI remain stable
      over a period of at least two weeks, whereas acidic proteins are irreversibly
      inactivated by the end of a two-week period.  A stabilizing effect of BSA on
      DNA-methylases of Sso47 and Mbu strains has been demonstrated.  A direct
      correlation between the stabilizing effect of BSA and the degree of enzyme
      purity has been established.  Ca2+ appear to be a universal activator of
      methylases of the above strains; these cations produce a potent, although a
      short-term effect and can be used in the production of enzyme preparations with
      a high specific activity in DNA recombinant technology.  Protease inhibitors do
      not exert any appreciable effect on the methylase activity upon storage.
      Storage at -20C and at neutral pH leads to complete inactivation of all
      DNA-methylases within 24 hours.  In this case glycerol is fairly ineffective as
      a stabiliziing agent.
AU  - Nikolskaya II
AU  - Sharkova EV
AU  - Suchkov SV
AU  - Lopatina NG
AU  - Habar K
AU  - Somodi P
AU  - Foldes I
AU  - Debov SS
PT  - Journal Article
TA  - Biochem. Int.
JT  - Biochem. Int.
SO  - Biochem. Int. 1987 15: 127-138.

PMID- 373252
VI  - 6
DP  - 1978
TI  - System of host specificity and the DNA methylases of Shigellae and their phages.
PG  - 724-731
AB  - In Shigella sonnei cells there is a host DNA specificity system responsible for modification
      and restriction of DDII phage.  DNA methylase from Shigella stutzeri cells is specific for
      adenine and catalyses the appearance of 6'-methylaminopurine in the acceptory DNA.
      Methylases from Shigella sonnei cells are specific for adenine and cytosine and provide for
      the presence of 6'-methylaminopurine and 5'-methylcytosine in DNA.  The modifying activity
      of these cells may be equally likely associated with both the enzymes.  A simplified version
      of the additional methylation test has been developed for the study of enzyme specificity.
      The results of additional and cross methylation suggest that several adenine methylases are
      present in the cells of these Shigella, one of these enzymes being shared by Shigella stutzeri
      and Shigella sonnei.  The DNA's isolated from Shigella sonnei and Shigella stutzeri cells are
      undermethylated and in vitro undergo additional methylation upon incubation with the
      appropriate enzyme.
AU  - Nikolskaya II
AU  - Tediashvili MG
AU  - Vasileva MB
AU  - Chanishvili TG
AU  - Debov SS
PT  - Journal Article
TA  - Vopr. Virusol.
JT  - Vopr. Virusol.
SO  - Vopr. Virusol. 1978 6: 724-731.

PMID- 359056
VI  - 43
DP  - 1978
TI  - Investigation of methylation character and DNA methylases specificity in Shigella.
PG  - 1228-1232
AB  - The nature and content of minor bases in DNA of 3 Shigella strains are investigated.  DNA's
      from Shigella stutzeri 2, S. sonnei 1188 and S. sonnei 311 are found to contain 0.43, 0.56 and
      0.45 mol. % of N6-methyladenine respectively.  5-methylcytosine (0.16%) is discovered in S.
      sonnei 311.  Substrate specificity of adenine methylase from S. sonnei 1188 with respect to
      phage DNA's of different host modification is investigated.  Recognition sites for guanine
      methylase of DDVI phage and for adenine methylase of S. sonnei 1188 turned out to be
      different.  DNA of DDII phage grown in S. stutzeri 2 cells does not accept methyl groups under
      the treatment with S. sonnei 1188 extracts, but it is methylated by Escherichia coli extract.
      Adenine methylases of S. sonnei 1188 and S. stutzeri 2 are suggested to be either the same
      enzyme, or enzymes, which recognition sites are partially overlapped.
AU  - Nikolskaya II
AU  - Tediashvili MI
AU  - Chanishvili TG
AU  - Debov SS
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1978 43: 1228-1232.

PMID- 7245875
VI  - 2
DP  - 1981
TI  - Specificity and properties of DNA methylases in Shigella.
PG  - 16-21
AB  - The specificity of and several properties of whole DNA methylase preparations from two
      Shigella strains, S. sonnei 47843 and S. flexneri, were studied.  Both kinds of preparation
      contained adenine and cytosine methylases which led to the presence of 6-methylaminopurine and
      5-methylcytosine in the bacterial DNAs.  The concentrations of these in the S. sonnei DNA were
      0.47 and 0.43 mole per 100 moles of nucleotides, respectively; the corresponding figures for
      the S. flexneri DNAs were 0.42 and 0.38.  In vitro study of substrate specificity showed both
      DNAs to be undermethylated in vivo and to be sensitive substrates for their "own" enzyme.  The
      best acceptors for methyl groups were the thymus and phage Cd DNAs.  The denatured DNA
      specimens did not undergo methylation.  The methylase activities of both strains were
      inhibited by 95-97% by S-adenosylhomocysteine present in an amount of 10 micromoles.
AU  - Nikolskaya II
AU  - Uporova TM
AU  - Tereshina EV
AU  - Gruber IM
AU  - Zhdanova LG
AU  - Debov SS
PT  - Journal Article
TA  - Vestn. Akad. Med. Nauk SSSR
JT  - Vestn. Akad. Med. Nauk SSSR
SO  - Vestn. Akad. Med. Nauk SSSR 1981 2: 16-21.

PMID- 764884
VI  - 40
DP  - 1975
TI  - Identification of DNA methylases in cells of Escherichia coli CK.
PG  - 1081-1086
AB  - It was established that E. coli CK cells contain a methylase which catalyzes
      the incorporation of CH3 groups into tissue and phage DNAs in vitro in the
      presence of the methyl group donor S-adenosyl-L-methionine.  During isolation
      and purification the enzyme was found in the fraction of 30-60% saturation by
      ammonium sulfate and its specific activity increased 1.9-fold.  The methylase
      was active in both phosphate and tris-HCl buffers at pH 6.5-7.5 and did not
      require Mg ions, EDTA, or dithiothreitol.  The enzyme recognized specific
      nucleotide sequences in all the DNAs investigated and had broader substrate
      specificity than the analogous enzyme from E. coli B.  The methylase of E. coli
      CK was most active with thymus DNA.  The methylase from rat liver nuclei was
      inactive in relation to the DNA of bacteriophages.
AU  - Nikolskaya II
AU  - Vanyushin BF
AU  - Mardashev SR
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1975 40: 1081-1086.

PMID- 6290273
VI  - 145
DP  - 1982
TI  - Structure at restriction endonuclease MboI cleavage sites protected by actinomycin D or distamycin A.
PG  - 360-364
AB  - Restriction endonuclease MboI cleavage of DNA was inhibited by actinomycin D
      and distamycin A.  The two inhibitors protected different subsets of the 8
      cleavage sites in polyoma DNA.  The cleavage reactions were analyzed both in
      the presence of minimal inhibitory concentrations of the compounds and at
      higher concentrations, allowing cleavage at only 1 site/DNA molecule.  The
      experiments showed that cleavage sites most efficiently protected by
      actinomycin D had putative inhibitor binding sites as a distance of 1-2 base
      pairs from the MboI recognition sequence.  Distamycin A, in contrast,
      apparently has to bind immediately adjacent to the MboI recognition sequence to
      protect from cleavage.
AU  - Nilsson M-G
AU  - Skarped C
AU  - Magnusson G
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1982 145: 360-364.

PMID- 30521042
VI  - 
DP  - 2018
TI  - Hexameric assembly of the AAA+ protein McrB is necessary for GTPase activity.
PG  - 
AB  - McrBC is one of the three modification-dependent restriction enzymes encoded by the
      Escherichia coli K12 chromosome. Amongst restriction enzymes, McrBC and its
      close homologues are unique in employing the AAA+ domain for GTP
      hydrolysis-dependent activation of DNA cleavage. The GTPase activity of McrB is
      stimulated by the endonuclease subunit McrC. It had been reported previously that
      McrB and McrC subunits oligomerise together into a high molecular weight species.
      Here we conclusively demonstrate using size exclusion chromatography coupled
      multi-angle light scattering (SEC-MALS) and images obtained by electron
      cryomicroscopy that McrB exists as a hexamer in solution. Furthermore, based on
      SEC-MALS and SAXS analyses of McrBC and the structure of McrB, we propose that
      McrBC is a complex of two McrB hexamers bridged by two subunits of McrC, and that
      the complete assembly of this complex is integral to its enzymatic activity. We
      show that the nucleotide-dependent oligomerisation of McrB precedes GTP
      hydrolysis. Mutational studies show that, unlike other AAA+ proteins, the
      catalytic Walker B aspartate is required for oligomerisation.
AU  - Nirwan N
AU  - Singh P
AU  - Mishra GG
AU  - Johnson CM
AU  - Szczelkun MD
AU  - Inoue K
AU  - Vinothkumar KR
AU  - Saikrishnan K
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2018 : .

PMID- 24233588
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Loktanella cinnabarina LL-001T, Isolated from Deep-Sea Floor Sediment.
PG  - e00927-13
AB  - This report describes the draft genome sequence of Loktanella cinnabarina LL-001(T), which was
      the first isolated strain from deep-sea floor sediment of
      the genus Loktanella. The draft genome sequence contains 3,896,245 bp, with a G+C
      content of 66.7%.
AU  - Nishi S
AU  - Tsubouchi T
AU  - Takaki Y
AU  - Koyanagi R
AU  - Satoh N
AU  - Maruyama T
AU  - Hatada Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00927-13.

PMID- 24285661
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Mycobacterium bovis 04-303, a Highly Virulent Strain from Argentina.
PG  - e00931-13
AB  - Mycobacterium bovis strain 04-303 was isolated from a wild boar living in a free-ranging field
      in Argentina. This work reports the draft genome sequence of
      this highly virulent strain and the genomic comparison of its major
      virulence-related genes with those of M. bovis strain AF2122/97 and Mycobacterium
      tuberculosis strain H37Rv.
AU  - Nishibe C
AU  - Canevari CAB
AU  - Dalla CR
AU  - Pinto BJ
AU  - Varuzza L
AU  - Cataldi AA
AU  - Bernardelli A
AU  - Bigi F
AU  - Blanco FC
AU  - Zumarraga MJ
AU  - Almeida NF
AU  - Araujo FR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00931-13.

PMID- 22772895
VI  - 15
DP  - 2013
TI  - Genome DNA Sequence Variation, Evolution, and Function in Bacteria and Archaea.
PG  - 19-24
AB  - Comparative genomics has revealed that variations in bacterial and archaeal genome DNA
      sequences cannot be explained by only neutral mutations. Virus resistance and plasmid
      distribution systems have resulted in changes in bacterial and archaeal genome sequences
      during evolution. The restriction-modification system, a virus resistance system, leads to
      avoidance of palindromic DNA sequences in genomes. Clustered, regularly interspaced, short
      palindromic repeats (CRISPRs) found in genomes represent yet another virus resistance system.
      Comparative genomics has shown that bacteria and archaea have failed to gain any DNA with GC
      content higher than the GC content of their chromosomes. Thus, horizontally transferred DNA
      regions have lower GC content than the host chromosomal DNA does. Some nucleoid-associated
      proteins bind DNA regions with low GC content and inhibit the expression of genes contained in
      those regions. This form of gene repression is another type of virus resistance system. On the
      other hand, bacteria and archaea have used plasmids to gain additional genes. Virus resistance
      systems influence plasmid distribution. Interestingly, the restriction-modification system and
      nucleoid-associated protein genes have been distributed via plasmids. Thus, GC content and
      genomic signatures do not reflect bacterial and archaeal evolutionary relationships.
AU  - Nishida H
PT  - Journal Article
TA  - Curr. Issues Mol. Biol.
JT  - Curr. Issues Mol. Biol.
SO  - Curr. Issues Mol. Biol. 2013 15: 19-24.

PMID- 2994012
VI  - 13
DP  - 1985
TI  - Type II restriction endonucleases cleave single-stranded DNAs in general.
PG  - 5747-5759
AB  - Restriction endonucleases (13 out of 18 species used for the test) were
      certified to cleave single-stranded(ss)DNA.  Such enzymes as AvaII, HaeII,
      DdeI, AluI, Sau3AI, AccII, TthHB81 and HapII were newly reported to cleave
      ssDNA.  A model to account for the cleavage of ssDNA by restriction enzyes was
      proposed with supportive data.  The essential part of the model was that
      restriction enzymes preferentially cleave transiently formed secondary
      structures (called canonical structures) in ssDNA composed of two recognition
      sequences with two fold rotational symmetry.  This means that a restriction
      enzyme can cleave ssDNAs in general so far as the DNAs have the sequences of
      restriction sites for the enzyme, and that the rate of cleavage depends on the
      stabilities of canonical structures.
AU  - Nishigaki K
AU  - Kaneko Y
AU  - Wakuda H
AU  - Husimi Y
AU  - Tanaka T
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1985 13: 5747-5759.

PMID- 30533927
VI  - 7
DP  - 2018
TI  - Draft Genome Sequences of Lawsonia intracellularis Swine Strains Causing Proliferative Enteropathy in Japan.
PG  - e01021-18
AB  - The draft genome sequences of three strains of Lawsonia intracellularis, an obligate
      intracellular animal pathogen responsible for causing proliferative
      enteropathy, obtained from swine in different prefectures in Japan revealed the
      absence of a genomic island previously reported to be linked to host adaptation
      and to high genomic diversity, despite geographical proximity.
AU  - Nishikawa S
AU  - Ogawa Y
AU  - Eguchi M
AU  - Rambukkana A
AU  - Shimoji Y
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e01021-18.

PMID- 27389264
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Nonagglutinating Lactococcus garvieae Strain 122061 Isolated from Yellowtail in Japan.
PG  - e00592-16
AB  - Nonagglutinating Lactococcus garvieae has been isolated from diseased farmed yellowtail in
      Japan since 2012. In this study, the complete genome and plasmid
      sequence of nonagglutinating L. garvieae strain 122061 was determined, to our
      knowledge, for the first time.
AU  - Nishiki I
AU  - Oinaka D
AU  - Iwasaki Y
AU  - Yasuike M
AU  - Nakamura Y
AU  - Yoshida T
AU  - Fujiwara A
AU  - Nagai S
AU  - Katoh M
AU  - Kobayashi T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00592-16.

PMID- 6099355
VI  - 96
DP  - 1984
TI  - A possible correlation between DNA conformation and the mode of action of restriction enzymes.
PG  - 1807-1811
AB  - The cutting modes of restriction endonucleases which recognize
      tetradeoxyribonucleotide sequences are classified into two groups.  d(GGCC) and
      d(CGCG), for example, are cut to produce blunt ends, while d(CCGG) and d(GCGC)
      are cut to produce two-base-long cohesive ends.  A conformational analysis by
      the Calladine-Dickerson method indicates that d(GGCC) and d(CGCG) should have a
      roll angle of successive base-pairs open towards the major groove at the
      central (second) base-pair step.  On the other hand, d(CCGG) and d(GCGC) have
      such open roll angles at the first and third base-pair steps.  It is suggested
      that, in general, the cutting mode of a tetramer-specific enzyme depends
      primarily upon the substrate conformation, rather than upon the enzyme.
      Similar correlations between the mode of action and substrate conformation are
      also suggested for hexamer-specific enzymes.
AU  - Nishimura Y
AU  - Tsuboi M
PT  - Journal Article
TA  - J. Biochem. (Tokyo)
JT  - J. Biochem. (Tokyo)
SO  - J. Biochem. (Tokyo) 1984 96: 1807-1811.

PMID- 12840036
VI  - 13
DP  - 2003
TI  - Comparative complete genome sequence analysis of the amino acid replacements responsible for the thermostability of Corynebacterium efficiens.
PG  - 1572-1579
AB  - Corynebacterium efficiens is the closest relative of Corynebacterium glutamicum,  a species
      widely used for the industrial production of amino acids. C. efficiens
      but not C. glutamicum can grow above 40 degrees C. We sequenced the complete C.
      efficiens genome to investigate the basis of its thermostability by comparing its
      genome with that of C. glutamicum. The difference in GC content between the
      species was reflected in codon usage and nucleotide substitutions. Our
      comparative genomic study clearly showed that there was tremendous bias in amino
      acid substitutions in all orthologous ORFs. Analysis of the direction of the
      amino acid substitutions suggested that three substitutions are important for the
      stability of the C. efficiens proteins: from lysine to arginine, serine to
      alanine, and serine to threonine. Our results strongly suggest that the
      accumulation of these three types of amino acid substitutions correlates with the
      acquisition of thermostability and is responsible for the greater GC content of
      C. efficiens.
AU  - Nishio Y
AU  - Nakamura Y
AU  - Kawarabayasi Y
AU  - Usuda Y
AU  - Kimura E
AU  - Sugimoto S
AU  - Matsui K
AU  - Yamagishi A
AU  - Kikuchi H
AU  - Ikeo K
AU  - Gojobori T
PT  - Journal Article
TA  - Genome Res.
JT  - Genome Res.
SO  - Genome Res. 2003 13: 1572-1579.

PMID- 9742242
VI  - 26
DP  - 1998
TI  - Characterization of two intein homing endonucleases encoded in the DNA polymerase gene of Pyrococcus kodakaraensis strain KOD1.
PG  - 4409-4412
AB  - Two intein endonucleases, denoted PI-PkoI and PI-PkoII, in the DNA polymerase gene of the
      hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1 were expressed in Escherichia coli
      and the recombinant endonucleases were characterized.  Both endonucleases were thermostable
      and cleaved their inteinless DNA sequences leaving four base 3'-hydroxyl overhangs.  PI-PkoII
      and the activity of PI-PkoII was enhanced at higher potassium ion concentrations (1M).
      Recognition sequences were also determined using synthetic oligonucleotides inserted into
      plasmid pUC19.  It was shown that DNA sequences of 19 and 16 bp are needed for cleavage by
      PI-PkoI and PI-PkoII, respectively.  PI-PkoII could cleave the downstream junction region
      between intein-encoding and mature DNA polymerase regions and cleavage by PI-PkoII could be
      detected even when chromosomal DNA of P. kodakaraensis KOD1 was used as substrate.  Therefore,
      it is suggested that these endonucleases are switching endonucleases whose function lies in
      the rearrangement of chromosomal DNA.
AU  - Nishioka M
AU  - Fujiwara S
AU  - Takagi M
AU  - Imanaka T
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1998 26: 4409-4412.

PMID- 
VI  - 43
DP  - 2002
TI  - Correlation between maternal inheritance of chloroplast genes and a chloroplast-resident DNA methyltransferase in the green alga, Chlamydomonas reinhardtii.
PG  - s32
AB  - Chloroplast DNA of Chlamydomonas reinhardtii is maternally inherited.  Methylation mapping and
      indirect immunofluorescence analyses revealed that chloroplast DNA of mating type plus (mt+)
      gametes is heavily methylated while that of mating type minus (mt-) gametes is not.  To
      clarify the relationship between methylation and maternal inheritance of chloroplast DNA, we
      isolated a cDNA encoding a DNA methyltransferase.  The deduced protein, CrMET1 was transferred
      to chloroplasts, shown by GFP analyses.  Upon gametogenesis, CrMET1 transcripts clearly
      increased in mt+ but not in mt- cells.  These experiments suggest that the CrMET1 protein is
      located in chloroplasts and that it specifically methylates chloroplast DNA in mt+ gametes.
      This conclusion was further strengthened by the observation that, during gametogenesis, CrMET1
      is expressed in a mt- mutant, mat-1, whose chloroplast DNA is heavily methylated in gametes
      and paternally inherited.  The results provide evidence that cytosine methylation plays a
      critical role in maternal inheritance of chloroplast genes.
AU  - Nishiyama R
AU  - Ito M
AU  - Yamaguchi Y
AU  - Koizumi N
AU  - Sano H
PT  - Journal Article
TA  - Plant Cell Physiol.
JT  - Plant Cell Physiol.
SO  - Plant Cell Physiol. 2002 43: s32.

PMID- 11983892
VI  - 99
DP  - 2002
TI  - A chloroplast-resident DNA methyltransferase is responsible for hypermethylation of chloroplast genes in Chlamydomonas maternal gametes.
PG  - 5925-5930
AB  - Chloroplast DNA of the green alga Chlamydomonas reinhardtii is maternally inherited.
      Methylation mapping directly revealed that,
      before mating, chloroplast DNA of maternal (mating type plus; mt(+))
      gametes is heavily methylated whereas that of paternal (mating type
      minus; mt(-)) gametes is not. Indirect immunofluorescence analyses with
      anti-5-methylcytosine mAbs visually showed methylation to occur
      exclusively in chloroplast DNA of mt+ gametes, and not in mt- gametes
      or nuclear DNA of either mt. To clarify the relationship between
      methylation and maternal inheritance of chloroplast DNA, we have
      isolated and characterized a cDNA encoding a DNA methyltransferase. The
      deduced protein, CrMET1, consists of 1,344 aa and contains a conserved
      catalytic domain at the C terminal and a nonconserved N-terminal
      region. The predicted N-terminal region has an arginine-rich domain,
      suggesting CrMET1 is transferred to chloroplasts. This finding could be
      directly shown by green fluorescent protein epifluorescence microscopy
      analyses. CrMET1 transcripts were found to be absent in both mt(+) and
      mt(-) vegetative cells. Upon gametogenesis, however, transcript levels
      clearly increased in mt(+) but not mt(-) cells. These experiments
      suggest that the CrMET1 protein is located in chloroplasts and that it
      specifically methylates cytosine residues of chloroplast DNA in mt+
      gametes. This conclusion was further strengthened by the observation
      that, during gametogenesis, CrMET1 is expressed in a mt(-) mutant,
      mat-1, whose chloroplast DNA is heavily methylated in gametes and
      paternally inherited. The results provide evidence that cytosine
      methylation plays a critical role in maternal inheritance of
      chloroplast genes in C. reinhardtii.
AU  - Nishiyama R
AU  - Ito M
AU  - Yamaguchi Y
AU  - Koizumi N
AU  - Sano H
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2002 99: 5925-5930.

PMID- 15514055
VI  - 168
DP  - 2004
TI  - Role of a nonselective de novo DNA methyltransferase in maternal inheritance of chloroplast genes in the green alga, Chlamydomonas  reinhardtii.
PG  - 809-816
AB  - In the green alga, Chlamydomonas, chloroplast DNA is maternally transmitted to the offspring.
      We previously hypothesized that the
      underlying molecular mechanism involves specific methylation of
      maternal gamete DNA before mating, protecting against degradation. To
      obtain direct evidence for this, we focused on a DNA methyltransferase,
      DMT1, which was previously shown to be localized in chloroplasts. The
      full-length DMT1 protein with a molecular mass of 150 kD was expressed
      in insect cells, and its catalytic activity was determined. In vitro
      assays using synthetic DNA indicated methylation of all cytosine
      residues, with no clear selectivity in terms of the neighboring
      nucleotides. Subsequently, transgenic paternal cells constitutively
      expressing DMTI were constructed and direct methylation mapping assays
      of their DNA showed a clear nonselective methylation of chloroplast
      DNA. When transgenic paternal cells were crossed with wild-type
      maternal cells, the frequency of biparental and paternal offspring of
      chloroplasts increased up to 23% while between wild-type strains it was
      similar to3%. The results indicate that DMT1 is a novel type of DNA
      methyltransferase with a nonselective cytosine methylation activity,
      and that chloroplast DNA methylation by DMT1 is one of factors
      influencing maternal inheritance of chloroplast genes.
AU  - Nishiyama R
AU  - Wada Y
AU  - Mibu M
AU  - Yamaguchi Y
AU  - Shimogawara K
AU  - Sano H
PT  - Journal Article
TA  - Genetics
JT  - Genetics
SO  - Genetics 2004 168: 809-816.

PMID- 17429158
VI  - 53
DP  - 2007
TI  - Cloning and characterization of a new hetero-gene cluster of nonribosomal peptide synthetase and polyketide synthase from the cyanobacterium Microcystis aeruginosa K-139.
PG  - 17-27
AB  - Two nonribosomal peptide synthetase genes responsible for the biosynthesis
      of microcystin and micropeptin in Microcystis aeruginosa K-139 have been
      identified. A new nonribosomal peptide synthetase gene, psm3, was
      identified in M. aeruginosa K-139. The gene is a cluster extending 30 kb
      and comprising 13 bidirectionally transcribed open reading frames arranged
      in two putative operons. psm3 encodes four adenylation proteins, one
      polyketide synthase, and several unique proteins, especially Psm3L
      consisting of halogenase, acyl-CoA binding protein-like protein, and acyl
      carrier protein. Alignment of the binding pocket of the adenylation domain
      and an ATP-PPi exchange analysis using a recombinant protein with the
      adenylation domain of Psm3B showed that Psm3G and Psm3B activate aspartic
      acid and tyrosine, respectively. Although disruption of psm3 did not
      reveal the product produced by Psm3, we identified microviridin B and
      aeruginosin K139 in the cells of M. aeruginosa K-139. The above-mentioned
      results indicated that M. aeruginosa possesses at least five nonribosomal
      peptide synthetase gene clusters.
AU  - Nishizawa A
AU  - Arshad AB
AU  - Nishizawa T
AU  - Asayama M
AU  - Fujii K
AU  - Nakano T
AU  - Harada K
AU  - Shirai M
PT  - Journal Article
TA  - J. Gen. Appl. Microbiol.
JT  - J. Gen. Appl. Microbiol.
SO  - J. Gen. Appl. Microbiol. 2007 53: 17-27.

PMID- 20834156
VI  - 74
DP  - 2010
TI  - Isolation and Molecular Characterization of a Multicellular Cyanobacterium, Limnothrix/Pseudanabaena sp Strain ABRG5-3.
PG  - 1827-1835
AB  - A cyanobacterium, semi-filamentous multicellular strain ABRG5-3, was isolated and its unique
      nature was characterized. This axenic strain
      formal colonies and was motile on an agarose plate. The 16S rRNA gene
      of ABRG5-3 exhibited similarities to those of the Limnothrix and
      Pseudanabaena strains, which are known as filamentous and
      nonheterocystous cyanobacteria. Peaks in absorbance for the
      accumulation of chlorophyll a, phycocyanin, and phycoerythrin were
      observed in the cell extract. Natural separation of the pigments
      occurred in the supernatant of the autolysed cells. The cell lysis was
      promoted by osmotic shocks and lysozyme treatments. Chlorophyll a and
      total DNA were abundantly recovered from the cells. Analysis of the
      restriction-modification system for genomic DNA revealed novel
      diversity. Moreover, we made a successful attempt to create
      antibiotic-resistant strains by conjugation with a foreign plasmid,
      which indicates that strain ABRG5-3 is transformable.
AU  - Nishizawa T
AU  - Hanami T
AU  - Hirano E
AU  - Miura T
AU  - Watanabe Y
AU  - Takanezawa A
AU  - Komatsuzaki M
AU  - Ohta H
AU  - Shirai M
AU  - Asayama M
PT  - Journal Article
TA  - Biosci. Biotechnol. Biochem.
JT  - Biosci. Biotechnol. Biochem.
SO  - Biosci. Biotechnol. Biochem. 2010 74: 1827-1835.

PMID- 27563047
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Streptomyces parvulus 2297, Integrating Site-Specifically with Actinophage R4.
PG  - e00875-16
AB  - Streptomyces parvulus 2297, which is a host for site-specific recombination according to
      actinophage R4, is derived from the type strain ATCC 12434. Species
      of S. parvulus are known as producers of polypeptide antibiotic actinomycins and
      have been considered for industrial applications. We herein report for the first
      time the complete genome sequence of S. parvulus 2297.
AU  - Nishizawa T
AU  - Miura T
AU  - Harada C
AU  - Guo Y
AU  - Narisawa K
AU  - Ohta H
AU  - Takahashi H
AU  - Shirai M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00875-16.

PMID- 22328754
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of the Denitrifying and N2O-Reducing Bacterium Azoarcus  sp. Strain KH32C.
PG  - 1255
AB  - We report the finished and annotated genome sequence of a denitrifying and N(2)O-reducing
      betaproteobacterium, Azoarcus sp. strain KH32C. The genome is
      composed of one chromosome and one megaplasmid and contains genes for
      plant-microbe interactions and the gene clusters for aromatic-compound
      degradations.
AU  - Nishizawa T
AU  - Tago K
AU  - Oshima K
AU  - Hattori M
AU  - Ishii S
AU  - Otsuka S
AU  - Senoo K
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1255.

PMID- 28883152
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of Seven Strains Composing a Model Bacterial Community  of Maize Roots.
PG  - e00997-17
AB  - Previously, we assembled a model bacterial community of maize roots. Here, we report the
      complete genome sequences of the seven strains composing the
      community.
AU  - Niu B
AU  - Kolter R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00997-17.

PMID- 21952539
VI  - 193
DP  - 2011
TI  - The Genome of the Plant Growth-Promoting Rhizobacterium Paenibacillus polymyxa M-1 Contains Nine Sites Dedicated to Nonribosomal Synthesis of  Lipopeptides and Polyketides.
PG  - 5862-5863
AB  - The genome of Paenibacillus polymyxa M-1 consisted of a 5.8-Mb chromosome and a 360-kb
      plasmid. Nine sites were dedicated to nonribosomal synthesis
      of lipopeptides and polyketides. Eight of them were located at the
      chromosome, while one gene cluster predicted to encode an unknown
      secondary metabolite was present on the plasmid.
AU  - Niu B
AU  - Rueckert C
AU  - Blom J
AU  - Wang Q
AU  - Borriss R
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5862-5863.

PMID- 18644379
VI  - 382
DP  - 2008
TI  - Engineering Variants of the I-SceI Homing Endonuclease with Strand-specific and Site-specific DNA-nicking Activity.
PG  - 188-202
AB  - The number of strand-specific nicking endonucleases that are currently available for
      laboratory procedures and applications in vivo is limited,
      and none is sufficiently specific to nick single target sites within
      complex genomes. The extreme target specificity of homing endonucleases
      makes them attractive candidates for engineering high-specificity nicking
      endonucleases. I-SceI is a monomeric homing enzyme that recognizes an 18
      bp asymmetric target sequence, and cleaves both DNA strands to leave
      3'-overhangs of 4 bp. In single turnover experiments using plasmid
      substrates, I-SceI generates transient open circle intermediates during
      the conversion of supercoiled to linear DNA, indicating that the enzyme
      cleaves the two DNA strands sequentially. A novel hairpin substrate was
      used to demonstrate that although wild-type I-SceI cleaves either the top
      or bottom DNA strand first to generate two nicked DNA intermediates, the
      enzyme has a preference for cleaving the bottom strand. The kinetics data
      are consistent with a parallel sequential reaction mechanism. Substitution
      of two pseudo-symmetric residues, Lys122 and Lys223, markedly reduces top
      and bottom-strand cleavage, respectively, to generate enzymes with
      significant strand- and sequence-specific nicking activity. The two active
      sites are partially interdependent, since alterations to one site affect
      the second. The kinetics analysis is consistent with X-ray crystal
      structures of I-SceI/DNA complexes that reveal a role for the lysines in
      establishing important solvent networks that include nucleophilic water
      molecules thought to attack the scissile phosphodiester bonds.
AU  - Niu Y
AU  - Tenney K
AU  - Li H
AU  - Gimble FS
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2008 382: 188-202.

PMID- 17369272
VI  - 35
DP  - 2007
TI  - Topology of Type II REases revisited; structural classes and the common conserved core.
PG  - 2227-2237
AB  - Type II restriction endonucleases (REases) are deoxyribonucleases that cleave DNA sequences
      with remarkable specificity. Type II REases are highly divergent in sequence as well as in
      topology, i.e. the connectivity of secondary structure elements. A widely held assumption is
      that a structural core of five beta-strands flanked by two alpha-helices is common to these
      enzymes. We introduce a systematic procedure to enumerate secondary structure elements in an
      unambiguous and reproducible way, and use it to analyze the currently available X-ray
      structures of Type II REases. Based on this analysis, we propose an alternative definition of
      the core, which we term the alphabetaalpha-core. The alphabetaalpha-core includes the most
      frequently observed secondary structure elements and is not a sandwich, as it consists of a
      five-strand beta-sheet and two alpha-helices on the same face of the beta-sheet. We use the
      alphabetaalpha-core connectivity as a basis for grouping the Type II REases into distinct
      structural classes. In these new structural classes, the connectivity correlates with the
      angles between the secondary structure elements and with the cleavage patterns of the REases.
      We show that there exists a substructure of the alphabetaalpha-core, namely a common conserved
      core, ccc, defined here as one alpha-helix and four beta-strands common to all Type II REase
      of known structure.
AU  - Niv MY
AU  - Ripoll DR
AU  - Vila JA
AU  - Liwo A
AU  - Vanamee ES
AU  - Aggarwal AK
AU  - Weinstein H
AU  - Scheraga HA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2007 35: 2227-2237.

PMID- 17972284
VI  - 71
DP  - 2008
TI  - Identification of GATC- and CCGG-recognizing Type II REases and their putative specificity-determining positions using Scan2S--a novel motif scan algorithm with  optional secondary structure constraints.
PG  - 631-640
AB  - Restriction endonucleases (REases) are DNA-cleaving enzymes that have become indispensable
      tools in molecular biology. Type II REases are highly divergent in
      sequence despite their common structural core, function and, in some cases,
      common specificities towards DNA sequences. This makes it difficult to identify
      and classify them functionally based on sequence, and has hampered the efforts of
      specificity-engineering. Here, we define novel REase sequence motifs, which
      extend beyond the PD-(D/E)XK hallmark, and incorporate secondary structure
      information. The automated search using these motifs is carried out with a newly
      developed fast regular expression matching algorithm that accommodates long
      patterns with optional secondary structure constraints. Using this new tool,
      named Scan2S, motifs derived from REases with specificity towards GATC- and
      CGGG-containing DNA sequences successfully identify REases of the same
      specificity. Notably, some of these sequences are not identified by standard
      sequence detection tools. The new motifs highlight potential
      specificity-determining positions that do not fully overlap for the GATC- and the
      CCGG-recognizing REases and are candidates for specificity re-engineering.
AU  - Niv MY
AU  - Skrabanek L
AU  - Roberts RJ
AU  - Scheraga HA
AU  - Weinstein H
PT  - Journal Article
TA  - Proteins
JT  - Proteins
SO  - Proteins 2008 71: 631-640.

PMID- 27738038
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of 11399, a Transformable Citrus-Pathogenic Strain of Xylella fastidiosa.
PG  - e01124-16
AB  - The draft genome of Xylella fastidiosa subsp. pauca strain 11399, a transformable
      citrus-pathogenic strain, is reported here. The 11399 genome size is 2,690,704 bp
      and has a G+C content of 52.7%. The draft genome of 11399 reveals the absence of
      four type I restriction-modification system genes.
AU  - Niza B
AU  - Merfa MV
AU  - Alencar VC
AU  - Menegidio FB
AU  - Nunes LR
AU  - Machado MA
AU  - Takita MA
AU  - de Souza AA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01124-16.

PMID- 
VI  - 
DP  - 2002
TI  - Cloning and studying of the cleavage flexibility of some type IIs  restriction endonucleases.
PG  - 1-226
AB  - More than 3000 bacterial samples were screened for restriction
      enzymes.  Three new specificities were found and a few isoschizomers with
      interesting properties.  Two of these isoschizomers: BceAI, an isoschizomer
      of BcefI (ACGGC) and BspCNI, an isoschizomer of BseMII (CTCAG), belonging
      to the subgroup of Type IIs restriction enzymes were cloned as well as the
      prototype of BceAI, BcefI.  These two cloned isoschizomers and one other,
      BpuCI, a neoschizomer of Ecil (GGCGGA), were studied for their cleavage
      flexibility alongside that of their prototypes.  These studies were carried
      out on different DNA substrates.  The conformation as well as the bending
      mode of these DNA substrates were predicted using computer programs.  The
      flexibility of the 3 pairs of enzymes studied was as follows:  For BceAI
      and BcefI, their preferred site was 12/14 and their alternative site was
      11/13.  For BspCNI and BseMII, for some sequences their preferred site was
      10/8, for other sequences the preferred site was 9/7 and some sequences
      were cleaved at both positions with the same rate.  For BpuCI and Ecil, the
      preferred site for BpuCI was 12/10 and its alternative site was 13/11.  The
      preferred site for EciI was 11/9 and its alternative site was 12/10.  These
      cleavage positions and rates were determined to be sequence-dependent as
      well as influenced by the conformation of the protein (enzyme).  Based on
      the prediction of the conformation and bending mode of the different
      substrates together with the results of the cleavage positions and rates,
      allowed the following conclusions.  For sequences presenting an anisotropic
      bending mode, the cleavage position tended to be further away from the
      recognition sequence.  For sequences presenting an isotropic bending mode,
      the cleavage tended to occur closer to the recognition sequence.
AU  - Nkenfou C
PT  - Journal Article
TA  - Ph.D. Thesis, University of Yaounde I, Cameroon
JT  - Ph.D. Thesis, University of Yaounde I, Cameroon
SO  - Ph.D. Thesis, University of Yaounde I, Cameroon 2002 : 1-226.

PMID- 25523769
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Solvent-Tolerant Clostridium beijerinckii Strain SA-1.
PG  - e01310-14
AB  - We report the complete genome sequence of Clostridium beijerinckii SA-1, derived  by directed
      evolution from C. beijerinckii NCIMB 8052, selecting for enhanced
      solvent tolerance. This sequence allows for accurate placement of SA-1 as C.
      beijerinckii, permits functional analyses of mutant phenotypes, and suggests
      methods for distinguishing SA-1 from its parent.
AU  - Noar J
AU  - Makwana ST
AU  - Bruno-Barcena JM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01310-14.

PMID- 23792740
VI  - 1
DP  - 2013
TI  - Complete Genome Sequences of Azotobacter vinelandii Wild-Type Strain CA and Tungsten-Tolerant Mutant Strain CA6.
PG  - e00313-13
AB  - We report the complete genome sequences of Azotobacter vinelandii mutant strain CA6 and its
      parent wild-type strain, CA. When fixing nitrogen, strain CA6
      displays slow growth and impaired molybdate uptake, tolerance to tungstates, and
      production of hydrogen gas, compared to results for strain CA. Comparing these
      genome sequences may provide a genetic basis for these mutant phenotypes.
AU  - Noar JD
AU  - Bruno-Barcena JM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00313-13.

PMID- Not carried by PubMed...
VI  - 8
DP  - 1997
TI  - SfiI: An unconventional restriction enzyme.
PG  - 10-11
AB  - Abrief review of SfiI
AU  - Nobbs TF
AU  - Wentzell LM
AU  - Szczelkum MD
AU  - Halford SE
PT  - Journal Article
TA  - The NEB Transcript
JT  - The NEB Transcript
SO  - The NEB Transcript 1997 8: 10-11.

PMID- 7563060
VI  - 252
DP  - 1995
TI  - DNA cleavage at two recognition sites by the SfiI restriction endonuclease: Salt dependence of Cis and Trans interactions between distant DNA sites.
PG  - 399-411
AB  - At low ionic strength, the SfiI restriction enzyme cleaved at similar rates both supercoiled
      and linear DNA with two SfiI sites and linear DNA with one SfiI site.  For the substrates with
      two sites, the majority of the DNA was converted directly to products cut at both sites; the
      enzyme appears to bind to two sites before catalyzing its reactions, looping out the
      intervening DNA.  At high ionic strength, linear DNA with one SfiI site was not cut at all,
      linear DNA with two sites was cleaved slowly while supercoiled DNA with two sites was cleaved
      rapidly, though only half of the DNA with two sites was cut at both sites; the DNA that had
      been cut at one site was not cleaved again at the remaining site.  The singly cut product must
      therefore have been generated by a reaction incorporating both sites.  All DNA cleavage
      reactions by SfiI thus involve the tetrameric enzyme bound to two copies of its recognition
      sequence, but weakened DNA-protein interactions at high ionic strength can cause this complex
      to dissociate before cleaving both sites.  Intramolecular interactions between distant DNA
      sites are generally thought to be enhanced by supercoiling and to be more stable than
      intermolecular interactions.  The preference of SfiI at high ionic strength for substrates
      with two sites over substrates with one site and, in the former case, for supercoiled over
      linear DNA, validates this view.  At low ionic strength, the similar rates with the different
      substrates may be due to rate-limiting product dissociation.
AU  - Nobbs TJ
AU  - Halford SE
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1995 252: 399-411.

PMID- 9698558
VI  - 281
DP  - 1998
TI  - DNA excision by the SfiI restriction endonuclease.
PG  - 419-432
AB  - A mechanism for the precise excision of DNA between two target sites was elucidated by
      analyzing the individual steps during the reactions of the SfiI endonuclease on a plasmid with
      two SfiI sites.  Previous studies had indicated that SfiI is a tetrameric protein that binds
      to two copies of its recognition site before cleaving both sites in both strands.  In this
      study, the concerted cleavage of four phosphodiester bonds was shown to arise from four
      consecutive reactions that had similar values for their intrinsic rate constants.  Each
      reaction is presumably mediated by one of the four active sites in the tetramer and all four
      were generally completed within the life-time of the complex between the protein and two
      recognition sites, though products cleaved in one or two phosphodiester bonds were also
      detected following premature dissociation of the enzyme-substrate complex at elevated
      temperatures.  At the physiological temperature for this enzyme, all four bonds were cleaved
      within one minute but the subsequent dissociation of the enzyme-product complex, liberating
      the excised segment of DNA, took about one hour.  The tetrameric structure of SfiI was
      confirmed by equilibrium centrifugation.
AU  - Nobbs TJ
AU  - Szczelkun MD
AU  - Wentzell LM
AU  - Halford SE
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1998 281: 419-432.

PMID- 9628364
VI  - 379
DP  - 1998
TI  - Phosphorothioate substrates for the SfiI restriction endonuclease.
PG  - 599-604
AB  - Oligodeoxynucleotides carrying the recognition sequence for the SfiI endonuclease were
      synthesized with phosphorothioates at the cleavage site.  The Rp and Sp diasteroisomers of the
      oligonucleotides were separated by HPLC using a mobile phase containing L-cysteine.  The
      duplex with Rp phosphorothioates was cleaved very slowly in the presence of Mg2+, though
      virtually complete cleavage was obtained with Mn2+.  No significant cleavage of the duplex
      with Sp phosphorothioates occurred with either Mg2+ or Mn2+.  When added to a plasmid with one
      SfiI site, the duplexes with either Rp or Sp phosphorothioates inhibited the rate at which
      SfiI cleaved the plasmid: a control duplex with oxyester linkages enhanced the rate of plasmid
      cleavage.  In contrast to type IIe nucleases such as EcoRII and NaeI, which can be activated
      by non-hydrolysable analogues of their substrates, SfiI reactions require four susceptible
      phosphodiester bonds.
AU  - Nobbs TJ
AU  - Williams SA
AU  - Connolly BA
AU  - Halford SE
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1998 379: 599-604.

PMID- 2165592
VI  - 18
DP  - 1990
TI  - An improved method for partial restriction digestion of ultraviolet irradiated DNA.
PG  - 4288
AB  - None
AU  - Nobile C
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 4288.

PMID- 24503990
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Syntrophorhabdus aromaticivorans Strain UI, a Mesophilic Aromatic Compound-Degrading Syntroph.
PG  - e01064-13
AB  - Syntrophorhabdus aromaticivorans strain UI is a mesophilic bacterium capable of degrading
      aromatic substrates in syntrophic cooperation with a partner
      methanogen. The draft genome sequence is 3.7 Mb, with a G+C content of 52.0%.
AU  - Nobu MK
AU  - Narihiro T
AU  - Tamaki H
AU  - Qiu YL
AU  - Sekiguchi Y
AU  - Woyke T
AU  - Goodwin L
AU  - Davenport KW
AU  - Kamagata Y
AU  - Liu WT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01064-13.

PMID- 11163966
VI  - 259
DP  - 2000
TI  - Diversity of restriction-modification gene homologues in Helicobacter pylori.
PG  - 89-98
AB  - The complete genome sequences of two Helicobacter pylori strains have recently become
      available. We have searched them for homologues of restriction-modification genes. One strain
      (26695) carried 52 such homologues, and the other (J99) carried 53. Their sequence alignments
      were arranged in the form of a phylogenetic tree and compared with the tree based on rRNA. The
      trees showed that the homologues are scattered among diverse groups of bacteria. They also
      revealed high polymorphism within the species - there are 42 pairs with high homology, 10
      specific to 26695, and 11 specific to J99. Many of the restriction-modification homologues
      were characterized by a GC content lower than that of the average gene in the genome. Some of
      the restriction-modification homologues showed a different codon use bias from the average
      genes. These observations are interpreted in terms of horizontal transfer of the
      restriction-modification genes.
AU  - Nobusato A
AU  - Uchiyama I
AU  - Kobayashi I
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 2000 259: 89-98.

PMID- 11163967
VI  - 259
DP  - 2000
TI  - Insertion with long target duplication: a mechanism for gene mobility suggested from comparison of two related bacterial genomes.
PG  - 99-108
AB  - The complete genome sequences of two closely related organisms - two Helicobacter pylori
      strains - have recently become available. Comparison of these genomes at single base pair
      level has suggested the presence of a mechanism for bacterial gene mobility - insertion with
      long target duplications. This mechanism is formally similar to classical transposon
      insertion, but the duplication is much longer, often in the range of 100bp.  Restriction
      and/or modification enzyme genes are often within or adjacent to the insertion. A similar
      process may have mediated insertion of the cag+ pathogenicity island in H. pylori. A similar
      structure was identified in comparisons between Neisseria meningitidis and Neisseria
      gonorrhoeae genomes. We hypothesize that this mechanism, as well as two other types of
      polymorphism linked with restriction-modification genes (insertion accompanied by target
      deletion and a tripartite structure composed of  substitution/inversion/deletion), have
      resulted from attack by restriction enzymes on the chromosome.
AU  - Nobusato A
AU  - Uchiyama I
AU  - Ohashi S
AU  - Kobayashi I
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 2000 259: 99-108.

PMID- 29607926
VI  - 41
DP  - 2018
TI  - Characterization of the SN35N Strain-Specific Exopolysaccharide Encoded in the Whole Circular Genome of a Plant-Derived Lactobacillus plantarum.
PG  - 536-545
AB  - Lactobacillus plantarum SN35N, which has been previously isolated from pear,
      secretes exopolysaccharide (EPS). The aim of the present study is to characterize
      the EPS chemically and to find the EPS-biosynthesizing gene cluster. The present
      study demonstrates that the strain produces an acidic EPS carrying phosphate
      residue, which is composed of glucose, galactose, and mannose at a molecular
      ratio of 15.0 : 5.7 : 1.0. We also show that acidic EPS strongly inhibits the
      catalytic activity of hyaluronidase (EC 3.2.1.35), promoting an inflammatory
      reaction. In the present study, we also determined the complete genome sequence
      of the SN35N strain, demonstrating that the genome is a circular DNA with 3267626
      bp, and the number of predicted coding genes is 3146, with a GC content of
      44.51%. In addition, the strain harbors four plasmids, designated pSN35N-1, -2,
      -3, and -4. Although four EPS-biosynthesizing genes, designated lpe1, lpe2, lpe3,
      and lpe4, are present in the SN35N chromosomal DNA, another EPS gene cluster,
      lpe5, is located in the pSN35N-3 plasmid, composed of 35425 bp. EPS low-producing
      mutants, which were obtained by treating SN35N cells with novobiocin, lost the
      lpe5 gene cluster in the plasmid-curing experiment, suggesting that the gene
      cluster for the biosynthesis of acidic EPS is present in the plasmid. The present
      study shows the chemical characterization of the acidic EPS and its inhibitory
      effect to the hyaluronidase.
AU  - Noda M
AU  - Shiraga M
AU  - Kumagai T
AU  - Danshiitsoodol N
AU  - Sugiyama M
PT  - Journal Article
TA  - Biol. Pharm. Bull.
JT  - Biol. Pharm. Bull.
SO  - Biol. Pharm. Bull. 2018 41: 536-545.

PMID- 29726956
VI  - 164
DP  - 2018
TI  - A novel structure of exopolysaccharide produced by a plant-derived lactic acid bacterium Lactobacillus paracasei IJH-SONE68.
PG  - 87-92
AB  - A lactic acid bacterium Lactobacillus paracasei IJH-SONE68, which was isolated
      from a fig leaf by our group, was found to produce both acidic and neutral
      exopolysaccharides (EPSs). The nuclear magnetic resonance analysis demonstrates
      that the former EPS is composed primarily of mannose, and the latter one consists
      of the alpha-1, 6-linked glycan chains made of N-acetylglucosamine (GlcNAc). The
      presence of alpha-1, 6-linked GlcNAc polysaccharide is first reported in
      prokaryotes. Furthermore, to reveal the EPS-biosynthetic gene organization in the
      IJH-SONE68 strain, in the present study, we determined the whole-genome sequence.
AU  - Noda M
AU  - Sugimoto S
AU  - Hayashi I
AU  - Danshiitsoodol N
AU  - Fukamachi M
AU  - Sugiyama M
PT  - Journal Article
TA  - J. Biochem. (Tokyo)
JT  - J. Biochem. (Tokyo)
SO  - J. Biochem. (Tokyo) 2018 164: 87-92.

PMID- 29903810
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Lactococcus sp. Strain NtB2 (JCM 32569), Isolated from the Gut of the Higher Termite Nasutitermes takasagoensis.
PG  - e00445-18
AB  - Lactic acid bacteria are widely distributed in the termite gut. Here, we report the draft
      genome sequence of Lactococcus sp. strain NtB2, which was isolated from
      the gut of a wood-feeding higher termite.
AU  - Noda S
AU  - Aihara C
AU  - Yuki M
AU  - Ohkuma M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00445-18.

PMID- 14634013
VI  - 279
DP  - 2004
TI  - DNA recognition by the homing endonuclease PI-SceI involves a divalent metal ion cofactor-induced conformational change.
PG  - 6794-6804
AB  - PI-SceI, a homing endonuclease of the IAGLIDADG family, consists of two domains involved in
      DNA cleavage and protein splicing, respectively.
      Both domains cooperate in binding the recognition sequence. Comparison
      of the structures of PI-SceI in the absence and presence of substrate
      reveals major conformational changes in both the protein and DNA.
      Notably, in the protein-splicing domain the loop comprising residues
      53-70 and adopts a "closed" conformation, thus enabling it to interact
      with the DNA. We have studied the dynamics of DNA binding and
      subsequent loop movement by fluorescence techniques. Six amino acids in
      loop53-70 were individually replaced by cysteine and modified by
      fluorescein. The interaction of the modified PI-SceI variants with the
      substrate, unlabeled or labeled with tetramethylrhodamine, was analyzed
      in equilibrium and stopped-flow experiments. A kinetic scheme was
      established describing the interaction between PI-SceI and DNA. It is
      noteworthy that the apparent hinge-flap motion of loop53-70 is only
      observed in the presence of a divalent metal ion cofactor. Substitution
      of the major Mg2+-binding ligands in PI-SceI, Asp-218 and Asp-326, by
      Asn or "nicking" PI-SceI with trypsin at Arg-277, which interferes with
      formation of an active enzyme-substrate complex, both prevent the
      conformational change of loop53-70. Deletion of the loop inactivates
      the enzyme. We conclude that loop53-70 is an important structural
      element that couples DNA recognition by the splicing domain with DNA
      cleavage by the catalytic domain and as such "communicates" with the
      Mg2+ binding sites at the catalytic centers.
AU  - Noel AJ
AU  - Wende W
AU  - Pingoud A
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2004 279: 6794-6804.

PMID- 26893425
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of 'Candidatus Methanomethylophilus' sp. 1R26, Enriched from Bovine Rumen, a Methanogenic Archaeon Belonging to the  Methanomassiliicoccales Order.
PG  - e01734-15
AB  - Here, we present the draft genome of 'Candidatus Methanomethylophilus' sp. 1R26,  a member
      of the newly described Methanomassiliicoccales order of Euryarcheaota.
      The enrichment culture was established from bovine rumen contents and produced
      methane from trimethylamine and methanol. The draft genome contains genes for
      methanogenesis from methylated compounds.
AU  - Noel SJ
AU  - Hojberg O
AU  - Urich T
AU  - Poulsen M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01734-15.

PMID- 12112231
VI  - 19
DP  - 2002
TI  - Homing at an extragenic locus mediated by VDE (PI-Scel) in  Saccharomyces cerevisiae.
PG  - 773-782
AB  - PI-SceI (VDE), a homing endonuclease with protein splicing activity,  is a genomic parasite in
      the VMA1 gene of Saccharomyces cerevisiae. In a
      heterozygous diploid of the VDE-less VMA1 allele and a VDE-containing VMA1
      allele, VDE specifically cleaves its recognition sequence (VRS) in the
      VDE-less VMA1 allele at meiosis, followed by 'homing', i.e. a conversion
      to a VDE-containing allele. We found that upon VDE expression, homing of a
      marker gene at an extragenic locus occurs only when a 45 bp element
      containing the VRS is inserted at its allelic site, while mutants of VDE
      with no endonuclease activity lack authentic extragenic homing activity.
      Thus, both the VRS and VDE are required for homing. Insertion of the VRS
      in a homozygous diploid significantly lowered the spore germination
      ability, indicating that a template for gene repair at its allelic locus
      is essential for efficient homing and survival of yeast cells. Copyright
      (C) 2002 John Wiley Sons, Ltd.
AU  - Nogami S
AU  - Fukuda T
AU  - Nagai Y
AU  - Yabe S
AU  - Sugiura M
AU  - Mizutani R
AU  - Satow Y
AU  - Anraku Y
AU  - Ohya Y
PT  - Journal Article
TA  - Yeast
JT  - Yeast
SO  - Yeast 2002 19: 773-782.

PMID- 25540341
VI  - 2
DP  - 2014
TI  - Whole-Genome Sequence of Borrelia garinii Strain 935T Isolated from Ixodes persulcatus in South Korea.
PG  - e01298-14
AB  - We report here the genome sequence of Borrelia garinii strain 935T isolated from  Ixodes
      persulcatus in South Korea. The 1,176,739 bp (G+C content, 27.73%) genome
      consists of 1,194 coding regions, 4 rRNA genes, and 33 aminoacyl-tRNA synthetase
      genes. This is the first whole-genome report of a Korean Borrelia species
      isolate.
AU  - Noh Y
AU  - Kim SY
AU  - Lee YS
AU  - Kim DW
AU  - Kwon T
AU  - Hwang KJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01298-14.

PMID- 21304669
VI  - 1
DP  - 2009
TI  - Complete genome sequence of Rhodothermus marinus type strain (R-10).
PG  - 283-290
AB  - Rhodothermus marinus Alfredsson et al. 1995 is the type species of the genus and  is of
      phylogenetic interest because the Rhodothermaceae represent the deepest
      lineage in the phylum Bacteroidetes. R. marinus R-10(T) is a Gram-negative,
      non-motile, non-spore-forming bacterium isolated from marine hot springs off the
      coast of Iceland. Strain R-10(T) is strictly aerobic and requires slightly
      halophilic conditions for growth. Here we describe the features of this organism,
      together with the complete genome sequence, and annotation. This is the first
      complete genome sequence of the genus Rhodothermus, and only the second sequence
      from members of the family Rhodothermaceae. The 3,386,737 bp genome (including a
      125 kb plasmid) with its 2914 protein-coding and 48 RNA genes is part of the
      Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Nolan M et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2009 1: 283-290.

PMID- 21304675
VI  - 2
DP  - 2010
TI  - Complete genome sequence of Streptosporangium roseum type strain (NI 9100).
PG  - 29-37
AB  - Streptosporangium roseum Crauch 1955 is the type strain of the species which is the type
      species of the genus Streptosporangium. The 'pinkish coiled
      Streptomyces-like organism with a spore case' was isolated from vegetable garden
      soil in 1955. Here we describe the features of this organism, together with the
      complete genome sequence and annotation. This is the first completed genome
      sequence of a member of the family Streptosporangiaceae, and the second largest
      microbial genome sequence ever deciphered. The 10,369,518 bp long genome with its
      9421 protein-coding and 80 RNA genes is a part of the Genomic Encyclopedia of
      Bacteria and Archaea project.
AU  - Nolan M et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 2: 29-37.

PMID- 21304670
VI  - 1
DP  - 2009
TI  - Complete genome sequence of Streptobacillus moniliformis type strain (9901).
PG  - 300-307
AB  - Streptobacillus moniliformis Levaditi et al. 1925 is the type and sole species of the genus
      Streptobacillus, and is of phylogenetic interest because of its
      isolated location in the sparsely populated and neither taxonomically nor
      genomically much accessed family 'Leptotrichiaceae' within the phylum
      Fusobacteria. The 'Leptotrichiaceae' have not been well characterized,
      genomically or taxonomically. S. moniliformis,is a Gram-negative, non-motile,
      pleomorphic bacterium and is the etiologic agent of rat bite fever and Haverhill
      fever. Strain 9901(T), the type strain of the species, was isolated from a
      patient with rat bite fever. Here we describe the features of this organism,
      together with the complete genome sequence and annotation. This is only the
      second completed genome sequence of the order Fusobacteriales and no more than
      the third sequence from the phylum Fusobacteria. The 1,662,578 bp long chromosome
      and the 10,702 bp plasmid with a total of 1511 protein-coding and 55 RNA genes
      are part of the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Nolan M et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2009 1: 300-307.

PMID- 21304747
VI  - 3
DP  - 2010
TI  - Complete genome sequence of Ferrimonas balearica type strain (PAT).
PG  - 174-182
AB  - Ferrimonas balearica Rossello-Mora et al. 1996 is the type species of the genus Ferrimonas,
      which belongs to the family Ferrimonadaceae within the
      Gammaproteobacteria. The species is a Gram-negative, motile, facultatively
      anaerobic, non spore-forming bacterium, which is of special interest because it
      is a chemoorganotroph and has a strictly respiratory metabolism with oxygen,
      nitrate, Fe(III)-oxyhydroxide, Fe(III)-citrate, MnO(2), selenate, selenite and
      thiosulfate as electron acceptors. This is the first completed genome sequence of
      a member of the genus Ferrimonas and also the first sequence from a member of the
      family Ferrimonadaceae. The 4,279,159 bp long genome with its 3,803
      protein-coding and 144 RNA genes is a part of the Genomic Encyclopedia of
      Bacteria and Archaea project.
AU  - Nolan M et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 3: 174-182.

PMID- 28495758
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Enterohemorrhagic Escherichia coli O103:H2 Strains Isolated from Feces of Feedlot Cattle.
PG  - e00094-17
AB  - The enterohemorrhagic pathotype represents a minor proportion of the Escherichia  coli O103
      strains shed in the feces of cattle. We report here the genome
      sequences of 43 strains of enterohemorrhagic E. coli (EHEC) O103:H2 isolated from
      feedlot cattle feces. The genomic analysis will provide information on the
      genetic diversity and virulence potential of bovine EHEC O103.
AU  - Noll LW
AU  - Worley JN
AU  - Yang X
AU  - Shridhar PB
AU  - Bai J
AU  - Meng J
AU  - Caragea D
AU  - Nagaraja TG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00094-17.

PMID- 28546486
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Enteropathogenic Escherichia coli O103 Strains Isolated from Feces of Feedlot Cattle.
PG  - e00387-17
AB  - Enteropathogenic Escherichia coli (EPEC) pathotype represents a minor proportion  of E. coli
      O103 strains shed in the feces of feedlot cattle. The draft genome
      sequences of 13 strains of EPEC O103 are reported here. The availability of the
      genome sequences will help in the assessment of genetic diversity and virulence
      potential of bovine EPEC O103.
AU  - Noll LW
AU  - Worley JN
AU  - Yang X
AU  - Shridhar PB
AU  - Bai J
AU  - Meng J
AU  - Caragea D
AU  - Nagaraja TG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00387-17.

PMID- 11466286
VI  - 183
DP  - 2001
TI  - Genome sequencing and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum.
PG  - 4823-4838
AB  - The genome sequence of the solvent-producing bacterium Clostridium acetobutylicum ATCC 824 has
      been determined by the shotgun approach.  The genome consists of a 3.94-Mb chromosome and a
      192-kb megaplasmid that contains the majority of genes responsible for solvent production.
      Comparison of C. acetobutylicum to Bacillus subtilis reveals significant local conservation of
      gene order, which has not been seen in comparisons of other genomes with similar, or, in some
      cases closer, phylogenetic proximity.  This conservation allows the prediction of many
      previously undetected operons in both bacteria.  However, the C. acetobutylicum genome also
      contains a significant number of predicted operons that are shared with distantly related
      bacteria and archaea but not with B. subtilis.  Phylogenetic analysis is compatible with the
      dissemination of such operons by horizontal transfer.  The enzymes of the solventogenesis
      pathway and of the cellulosome of C. acetobutylicum comprise a new set of metabolic capacities
      not previously represented in the collection of complete genomes.  These enzymes show a
      complex pattern of evolutionary affinities, emphasizing the role of lateral gene exchange in
      the evolution of the unique metabolic profile of the bacterium.  Many of the sporulation genes
      identified in B. subtilis are missing in C. acetobutylicum, which suggests major differences
      in the sporulation process.  Thus, comparative analysis reveals both significant conservation
      of the genome organization and pronounced differences in many systems that reflect unique
      adaptive strategies of the two gram-positive bacteria.
AU  - Nolling J et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2001 183: 4823-4838.

PMID- 1512204
VI  - 174
DP  - 1992
TI  - Characterization of the archaeal, plasmid-encoded type II restriction-modification system MthTI from Methanobacterium thermoformicicum THF: Homology to the bacterial NgoPII system from Neisseria gonorrhoeae.
PG  - 5719-5726
AB  - A restriction-modification system, designated MthTI, was localized on plasmid pFV1 from the
      thermophilic archaeon Methanobacterium thermoformicicum THF. The MthTI system is a new member
      of the family of GGCC-recognizing restriction-modification systems. Functional expression of
      the archaeal MthTI genes was obtained in Escherichia coli. The mthTIR and mthTIM genes are 843
      and 990 bp in size and code for proteins of 281 (32,102 Da) and 330 (37,360 Da) amino acids,
      respectively. The deduced amino acids sequences of M.MthTI showed high similarity with that of
      the isospecific methyltransferases M.NgoPII and M.HaeIII. In addition, extensive sequence
      similarity on the amino acid level was observed for the endonucleases R.MthTI and R.NgoPII.
      Moreover, the endonuclease and methyltransferase genes of the thermophilic MthTI system and
      those of Neisseria gonorrhoeae NgoPII system show identical organizations and high (54.5%)
      nucleotide identity. This finding suggests horizontal transfer of restriction-modification
      systems between members of the domains Bacteria and Archaea.
AU  - Nolling J
AU  - de Vos WM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1992 174: 5719-5726.

PMID- 1408820
VI  - 20
DP  - 1992
TI  - Identification of the CTAG-recognizing restriction-modification systems MthZI and MthFI from Methanobacterium thermoformicicum and characterization of the plasmid-encoded mthZIM gene.
PG  - 5047-5052
AB  - Two CTAG-recognizing restriction and modification (R/M) systems, designated MthZI and MthFI,
      were identified in the thermophilic archaeon Methanobacterium thermoformicicum strains Z-245
      and FTF, respectively. Further analysis revealed that the methyltransferase (MTase) genes are
      plasmid-located in both strains. The plasmid pFZ1-encoded mthZIM gene of strain Z-245 was
      further characterized by subcloning and expression studies in Escherichia coli followed by
      nucleotide sequence analysis. The mthZIM gene is 1065 bp in size and may code for a protein of
      355 amino acids (Mr 42,476 Da). The deduced amino acid sequence of the M.MthZI enzyme shares
      substantial similarity with four distinct regions from several m4C and m6A-MTases, and
      contains the TSPPY motif that is so far only found in m4C-MTases. Partially overlapping with
      the mthZIM gene and in reverse orientation, an additional ORF was identified with a size of
      606 bp potentially coding for a protein of 202 amino acids (mr 23.710 Da). This ORF is
      suggested to encode the corresponding endonuclease R.MthZI.
AU  - Nolling J
AU  - de Vos WM
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 5047-5052.

PMID- Not included in PubMed...
VI  - 139
DP  - 1993
TI  - PhiF1 and PhiF3, two novel virulent, archaeal phages infecting different thermophilic strains of the genus Methanobacterium.
PG  - 2511-2516
AB  - Two virulent archaeal phages, PhiF1 and PhiF3, were isolated that were capable of infecting
      different thermophilic members of the genus Methanobacterium. Both phages exhibited a similar
      morphology consisting of a polyhedral head and tail, but differed considerably in their host
      specificities and the size and topology of their genomes. Phage PhiF1 contained a linear,
      double-stranded DNA genome of 85+/-5 kb in size and showed a broad host range including M.
      thermoformicicum strains Z-245, FTF FF1, FF3 and CSM3, and M. thermoautotrophicum strain H. In
      contrast, PhiF3 phage particles contained a circular or terminally redundant linear genome,
      comprising approximately 36+/-2 kb double-stranded DNA, and could only be propagated on M.
      thermoformicicum strain FF3. Hybridization experiments did not reveal similarity between the
      genomes of PhiF1 and PhiF3 nor between both phages and genomic DNA from different thermophilic
      members of the genus Methanobacterium or DNA from phage M1 of M. thermoautotrophicum Marburg.
      A physical map of both phage genomes was constructed. The DNA of phage phiF1 was found to
      contain multiple GGCC sites which form the target for the restriction-modification (R/M)
      system MthTI of M. thermoformicicum THF. In contrast, the DNA of PhiF1 contained only a single
      CTAG site recognized by the R/M systems MthZI and MthFI of M. thermoformicicum Z-245 and FTF,
      respectively. The distribution of these sites correlates well with the capacity of PhiF1 to
      infect M. thermoformicicum strains Z-245 and FTF but not strain THF.
AU  - Nolling J
AU  - Groffen A
AU  - De Vos WM
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1993 139: 2511-2516.

PMID- 1336177
VI  - 20
DP  - 1992
TI  - Modular organization of related Archaeal plasmids encoding different restriction-modification systems in Methanobacterium thermoformicicum.
PG  - 6501-6507
AB  - Nucleotide sequence comparison of the related 13513-bp plasmid pFV1 and the 11014-bp plasmid
      pFZ1 from the thermophilic Archaeon Methanobacterium thermoformicicum THF and Z-245,
      respectively, revealed a homologous, approximately 8.2 kb backbone structure that is
      interrupted by plasmid-specific elements. Various highly conserved palindromic structures and
      an ORF that could code for an NTP-binding protein were identified within the backbone
      structure and may be involved in plasmid maintenance and replication. Each plasmid contains at
      comparable locations a module which specifies components of different restriction-modificaton
      (R/M) systems. The R/M module of pFV1 contained, in addition to the genes of the
      GGCC-recognizing R/M system MthTI, an ORF which may be involved in repair of G-T mismatches
      generated by deamination of m5C at high temperatures.
AU  - Nolling J
AU  - Van Eeden JM
AU  - Eggen RIL
AU  - de Vos WM
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 6501-6507.

PMID- 16049020
VI  - 33
DP  - 2005
TI  - I-Apel: A novel intron-encoded LAGLIDADG homing endonuclease from the archaeon, Aeropyrum pernix K1.
PG  - 5017
AB  - Over 50 introns have been reported in archaeal rRNA genes (rDNAs), a subset of which nests
      putative homing endonuclease (HEase) genes. Here, we report the identification and
      characterization of a novel archaeal LAGLIDADG-type HEase, I-ApeI, encoded by the ApeK1.S908
      intron within the 16S rDNA of Aeropyrum pernix K1. I-ApeI consists of 222 amino acids and
      harbors two LAGLIDADG-like sequences. It recognizes the 20 bp non-palindromic sequence
      5'-GCAAGGCTGAAAC TTAAAGG and cleaves target DNA to produce protruding tetranucleotide 3'
      ends. Either Mn2+ or Co2+ can be substituted for Mg2+ as a cofactor in the cleavage reaction.
      Of the 20 bases within the minimal recognition site, 7 are essential for cleavage and are
      located at positions proximal to the cleavage sites.
AU  - Nomura N
AU  - Morinaga Y
AU  - Shirai N
AU  - Sako Y
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2005 33: 5017.

PMID- 18984620
VI  - 36
DP  - 2008
TI  - Recognition of a common rDNA target site in archaea and eukarya by analogous LAGLIDADG and His-Cys box homing endonucleases.
PG  - 6988-6998
AB  - The presence of a homing endonuclease gene (HEG) within a microbial intron or intein empowers
      the entire element with the ability to invade
      genomic targets. The persistence of a homing endonuclease lineage
      depends in part on conservation of its DNA target site. One such rDNA
      sequence has been invaded both in archaea and in eukarya, by LAGLIDADG
      and His-Cys box homing endonucleases, respectively. The bases encoded
      by this target include a universally conserved ribosomal structure,
      termed helix 69 (H69) in the large ribosomal subunit. This region forms
      the 'B2a' intersubunit bridge to the small ribosomal subunit, contacts
      bound tRNA in the A-and P-sites, and acts as a trigger for ribosome
      disassembly through its interactions with ribosome recycling factor. We
      have determined the DNA-bound structure and specificity profile of an
      archaeal LAGLIDADG homing endonuclease (I-Vdi141I) that recognizes this
      target site, and compared its specificity with the analogous eukaryal
      His-Cys box endonuclease I-PpoI. These homodimeric endonuclease
      scaffolds have arrived at similar specificity profiles across their
      common biological target and analogous solutions to the problem of
      accommodating conserved asymmetries within the DNA sequence, but with
      differences at individual base pairs that are fine-tuned to the
      sequence conservation of archaeal versus eukaryal ribosomes.
AU  - Nomura N
AU  - Nomura Y
AU  - Sussman D
AU  - Klein D
AU  - Stoddard BL
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2008 36: 6988-6998.

PMID- 17583340
VI  - 129
DP  - 2007
TI  - In Vivo Site-Specific DNA Methylation with a Designed Sequence-Enabled DNA Methylase.
PG  - 8676-8677
AB  - As an alternative to the continual expression of transcriptional repressors to turn off genes
      after they have served their purpose, nature has developed epigenetic strategies that result
      in the covalent modification of DNA itself to induce heritable gene silencing.  Mounting
      evidence supports the notion that once a genomic region has been targeted for silencing by
      acquisition of one or more covalent epigenetic marks, mark can be propagated and may influence
      acquisition of others.  If epigenetic modifications can be made specifically by the addition
      of targeted exogenous agents, new approaches to transcriptional therapy should result.
AU  - Nomura W
AU  - Barbas CF III
PT  - Journal Article
TA  - J. Am. Chem. Soc.
JT  - J. Am. Chem. Soc.
SO  - J. Am. Chem. Soc. 2007 129: 8676-8677.

PMID- 20560430
VI  - 82
DP  - 2010
TI  - Development of site-specific DNA methylase for epigenetic regulation of gene expression.
PG  - 393-397
AB  - 
AU  - Nomura W
AU  - Masuda A
AU  - Tamamura H
PT  - Journal Article
TA  - Seikagaku
JT  - Seikagaku
SO  - Seikagaku 2010 82: 393-397.

PMID- 
VI  - 45
DP  - 2009
TI  - Site-selective cytosine methylation by a split DNA methylase.
PG  - 491-492
AB  - Cytosine methylation plays pivotal roles in gene expression.  Methylation pattern in genome is
      heritable, then the effect of methylation is largely influenced across generation.  Truly
      specific methylation has been a challenging problem because fusion methylases with zinc finger
      domain still methylate the native sites as background.  To avoid this, split methylase domains
      were constructed.  These domains were designed to assemble only on the zinc finger target site
      with high specificity.  The split methylase showed it works as specific methylase to the
      target sites.
AU  - Nomura W
AU  - Tamamura H
AU  - Barbas CF III
PT  - Journal Article
TA  - Pept. Sci.
JT  - Pept. Sci.
SO  - Pept. Sci. 2009 45: 491-492.

PMID- 7607520
VI  - 157
DP  - 1995
TI  - A novel Streptomyces restriction endonuclease, Sse1825I, cleaving at 5'-GG/GWCCC-3'.
PG  - 323-324
AB  - We isolated and characterized from a Streptomyces species a new class-II restriction
      endonuclease, which recognizes the palindromic heptanucleotide sequence: 5'-GG/GWCCC
      3'-CCCWG/GG (where W=A or T) and cleaves double-stranded DNA after the second G in this
      sequence.  This Sse1825I enzyme cleaves phage lambda DNA at one site, adenovirus type 2 DNA at
      eight sites, but does not cleave pBR322, SV40, ColE1, pUC18 and pUC19, and replicative forms
      of M13mp18 and M13mp19, and PhiX174 DNAs.
AU  - Nomura Y
AU  - Ishino Y
AU  - Kimizuka F
AU  - Kato I
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 323-324.

PMID- 1369313
VI  - 54
DP  - 1990
TI  - Purification and properties of a new restriction endonuclease, MxaI, from Myxococcus xanthus F18E.
PG  - 3011-3012
AB  - Gliding bacteria have an unusual cell cycle, which consists of vegetative
      growth, the formation of a swarm, and the development of fruiting bodies and
      microcysts.  Only one restriction endonuclease of these bacteria has been
      reported.  Here, we screened 103 strains of Myxococcus species isolated from
      soil and detected endonuclease activity in nine strains.  One strain,
      Myxococcus xanthus F18E, produced a restriction endonuclease, MxaI, that is a
      new isoschizomer of SacI.  We identified the recognition and cleavage sites of
      MxaI and compared the properties of this enzyme with those of SacI.
AU  - Nomura Y
AU  - Kotani H
AU  - Kita K
AU  - Sadaoka A
AU  - Hiraoka N
AU  - Nakamura T
AU  - Abe N
AU  - Izaki K
PT  - Journal Article
TA  - Agric. Biol. Chem.
JT  - Agric. Biol. Chem.
SO  - Agric. Biol. Chem. 1990 54: 3011-3012.

PMID- 16513756
VI  - 188
DP  - 2006
TI  - Complete genome sequence of the dehalorespiring bacterium Desulfitobacterium hafniense Y51 and comparison with Dehalococcoides ethenogenes 195 - bacterium genomic comparison and genome sequencing for use in bioremediation.
PG  - 2262-2274
AB  - AUTHOR ABSTRACT - Desulfitobacterium strains have the ability to dechlorinate halogenated
      compounds under anaerobic conditions by
      dehalorespiration. The complete genome of the tetrachloroethene
      (PCE)-dechlorinating strain Desulfitobacterium hafniense Y51 is a
      5,727,534-bp circular chromosome harboring 5,060 predicted protein
      coding sequences. This genome contains only two reductive dehalogenase
      genes, a lower number than reported in most other dehalorespiring
      strains. More than 50 members of the dimethyl sulfoxide reductase
      superfamily and 30 paralogs of the flavoprotein subunit of the fumarate
      reductase are encoded as well. A remarkable feature of the genome is
      the large number of O-demethylase paralogs, which allow utilization of
      lignin-derived phenyl methyl ethers as electron donors. The large
      genome reveals a more versatile microorganism that can utilize a larger
      set of specialized electron donors and acceptors than previously
      thought. This is in sharp contrast to the PCE-dechlorinating strain
      Dehalococcoides ethenogenes 195, which has a relatively small genome
      with a narrow metabolic repertoire. A genomic comparison of these two
      very different strains allowed us to narrow down the potential
      candidates implicated in the dechlorination process. Our results
      provide further impetus to the use of desulfitobacteria as tools for
      bioremediation.
AU  - Nonaka H
AU  - Keresztes G
AU  - Shinoda Y
AU  - Ikenaga Y
AU  - Abe M
AU  - Naito K
AU  - Inatomi KFK
AU  - Inui M
AU  - Yukawa H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2006 188: 2262-2274.

PMID- 
VI  - 84
DP  - 2003
TI  - Direct observation of the searching mechanism of restriction enzymes using multiple optical traps.
PG  - 304a
AB  - Restriction enzymes recognize specific sequences in dsDNA.  Once they find their target
      sequence, they cut the DNA at that site.  This cutting is evolved in bacteria to protect
      itself against foreign DNA.  The searching mechanism for finding the target sequence is
      important, because the number of non-specific sites is usually larger than the number of
      specific sites.  Therefore, it's unlikely that the initial encounter of the enzyme with the
      DNA will be at the target sequence.  To visualize the possible sliding, hopping and jumping of
      a restriction enzyme during the searching process, the translocation of EcoRI enzymes is
      analyzed using a three-bead-assay created with multiple optical traps.  In this assay
      biotinylated EcoRI enzymes are bound to streptavidin-coated beads.  Such coated beads are
      offered to a DNA molecule held between two beads kept in optical tweezers.  Movement of a
      coated bead is tracked with video microscopy and the forces exerted by the enzyme on the DNA
      are measured using the traps.  Here we report our first results on the movement by EcoRI
      during the searching process for the target sequence.  Such direct observation of restriction
      enzymes during the searching for and recognition of the target sequence provides us with new
      insights into the dynamics of these enzyme-DNA interactions.
AU  - Noom MC
AU  - van den Broek B
AU  - Wuite GJL
PT  - Journal Article
TA  - Biophys. J.
JT  - Biophys. J.
SO  - Biophys. J. 2003 84: 304a.

PMID- 24811681
VI  - 545
DP  - 2014
TI  - A comparative genomic analysis of the alkalitolerant soil bacterium Bacillus lehensis G1.
PG  - 253-261
AB  - Bacillus lehensis G1 is a Gram-positive, moderately alkalitolerant bacterium
      isolated from soil samples. B. lehensis produces cyclodextrin glucanotransferase
      (CGTase), an enzyme that has enabled the extensive use of cyclodextrin in
      foodstuffs, chemicals, and pharmaceuticals. The genome sequence of B. lehensis G1
      consists of a single circular 3.99Mb chromosome containing 4017 protein-coding
      sequences (CDSs), of which 2818 (70.15%) have assigned biological roles, 936
      (23.30%) have conserved domains with unknown functions, and 263 (6.55%) have no
      match with any protein database. Bacillus clausii KSM-K16 was established as the
      closest relative to B. lehensis G1 based on gene content similarity and 16S rRNA
      phylogenetic analysis. A total of 2820 proteins from B. lehensis G1 were found to
      have orthologues in B. clausii, including sodium-proton antiporters, transport
      proteins, and proteins involved in ATP synthesis. A comparative analysis of these
      proteins and those in B. clausii and other alkaliphilic Bacillus species was
      carried out to investigate their contributions towards the alkalitolerance of the
      microorganism. The similarities and differences in alkalitolerance-related genes
      among alkalitolerant/alkaliphilic Bacillus species highlight the complex
      mechanism of pH homeostasis. The B. lehensis G1 genome was also mined for
      proteins and enzymes with potential viability for industrial and commercial
      purposes.
AU  - Noor YM
AU  - Samsulrizal NH
AU  - Jema'on NA
AU  - Low KO
AU  - Ramli AN
AU  - Alias NI
AU  - Damis SI
AU  - Fuzi SF
AU  - Isa MN
AU  - Murad AM
AU  - Raih MF
AU  - Bakar FD
AU  - Najimudin N
AU  - Mahadi NM
AU  - Illias RM
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 2014 545: 253-261.

PMID- 29773632
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Oyster Isolate Vibrio vulnificus Env1.
PG  - e00421-18
AB  - Vibrio vulnificus, a ubiquitous inhabitant of coastal marine environments, has been isolated
      from a variety of sources. It is an opportunistic pathogen of both
      marine animals and humans. Here, the genome sequence of V. vulnificus Env1, an
      environmental isolate resistant to predation by the ciliate Tetrahymena
      pyriformis, is reported.
AU  - Noorian P
AU  - Sun S
AU  - McDougald D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00421-18.

PMID- 18032435
VI  - 36
DP  - 2008
TI  - Unconventional GIY-YIG homing endonuclease encoded in group I introns in closely related strains of the Bacillus cereus group.
PG  - 300-310
AB  - Several group I introns have been previously found in strains of the Bacillus cereus group at
      three different insertion sites in the nrdE gene
      of the essential nrdIEF operon coding for ribonucleotide reductase. Here,
      we identify an uncharacterized group IA intron in the nrdF gene in 12
      strains of the B. cereus group and show that the pre-mRNA is efficiently
      spliced. The Bacillus thuringiensis ssp. pakistani nrdF intron encodes a
      homing endonuclease, denoted I-BthII, with an unconventional GIY-(X)8-YIG
      motif that cleaves an intronless nrdF gene 7 nt upstream of the intron
      insertion site, producing 2-nt 3' extensions. We also found four
      additional occurrences of two of the previously reported group I introns
      in the nrdE gene of 25 sequenced B. thuringiensis and one B. cereus
      strains, and one non-annotated group I intron at a fourth nrdE insertion
      site in the B. thuringiensis ssp. Al Hakam sequenced genome. Two strains
      contain introns in both the nrdE and the nrdF genes. Phylogenetic studies
      of the nrdIEF operon from 39 strains of the B. cereus group suggest
      several events of horizontal gene transfer for two of the introns found in
      this operon.
AU  - Nord D
AU  - Sjoberg BM
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2008 36: 300-310.

PMID- 17496101
VI  - 189
DP  - 2007
TI  - A Functional Homing Endonuclease in the Bacillus anthracis nrdE Group I Intron.
PG  - 5293-5301
AB  - The essential Bacillus anthracis nrdE gene carries a self-splicing group I intron with a
      putative homing endonuclease belonging to the GIY-YIG
      family. Here, we show that the nrdE pre-mRNA is spliced and that the
      homing endonuclease cleaves an intronless nrdE gene 5 nucleotides (nt)
      upstream of the intron insertion site, producing 2-nt 3' extensions. We
      also show that the sequence required for efficient cleavage spans at least
      4 bp upstream and 31 bp downstream of the cleaved coding strand. The
      position of the recognition sequence in relation to the cleavage position
      is as expected for a GIY-YIG homing endonuclease. Interestingly, nrdE
      genes from several other Bacillaceae were also susceptible to cleavage,
      with those of Bacillus cereus, Staphylococcus epidermidis (nrdE1), B.
      anthracis, and Bacillus thuringiensis serovar konkukian being better
      substrates than those of Bacillus subtilis, Bacillus lichenformis, and S.
      epidermidis (nrdE2). On the other hand, nrdE genes from Lactococcus
      lactis, Escherichia coli, Salmonella enterica serovar Typhimurium, and
      Corynebacterium ammoniagenes were not cleaved. Intervening sequences
      (IVSs) residing in protein-coding genes are often found in enzymes
      involved in DNA metabolism, and the ribonucleotide reductase nrdE gene is
      a frequent target for self-splicing IVSs. A comparison of nrdE genes from
      seven gram-positive low-G+C bacteria, two bacteriophages, and Nocardia
      farcinica showed five different insertion sites for self-splicing IVSs
      within the coding region of the nrdE gene.
AU  - Nord D
AU  - Torrents E
AU  - Sjoberg BM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2007 189: 5293-5301.

PMID- 2605243
VI  - 28
DP  - 1989
TI  - Structure and dynamics of a fluorescent DNA oligomer containing the EcoRI recognition sequence: fluorescence, molecular dynamics, and NMR studies.
PG  - 9095-9103
AB  - The self-complementary DNA decamer duplex d(CTGAATTCAG)2 and its modified counterpart
      d(CTGA[2AP]TTCAG)2, where the innermost adenine (6-aminopurine) has been replaced with the
      fluorescent analogue 2-aminopurine (2AP), have been studied by fluorescence and NMR
      spectroscopy and simulated by molecular dynamics.  Both decamers are recognized and cleaved by
      the EcoRI restriction endonuclease.  2D NMR results show that both decamers have a standard
      B-type conformation below 20oC, though a disturbance exists to the 5' side of the 2AP site
      which may originate from increased local mobility.  The fluorescence and fluorescence
      anisotropy decays of both decamers, as well as the one containing 2AP in only one chain, were
      studied as a function of temperature.  The data show that the 2AP base exists in a
      temperature-dependent distribution of states and shows rapid motions, suggesting
      interconversion among these states on a time scale of about 10^-10s.  The integrated
      fluorescence of the decamer with 2AP in both chains shows a large increase around the helix
      melting temperature whereas the decamer with one 2AP shows only a mild increase, showing that
      the mixed helix has a different structural transition as sensed by the 2AP base.  The data
      suggest a model of conformational states which have distinct fluorescence decay times.  The
      various states may differ in the degree of base stacking.  Fluctuations in the degree of
      stacking of the A or 2AP base are supported by molecular dynamics simulations, which
      additionally show that the 2AP-T or A-T base pair hydrogen bonds remain intact during these
      large motions.
AU  - Nordlund TM
AU  - Andersson S
AU  - Nilsson L
AU  - Rigler R
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1989 28: 9095-9103.

PMID- 6257650
VI  - 145
DP  - 1981
TI  - Deoxyribonucleic acid modifications and restriction endonuclease production in Neisseria gonorrhoeae.
PG  - 788-795
AB  - Modification of gonococcal deoxyribonucleic acid (DNA) was investigated, and the relationship
      with endonuclease production was explored.  Both chromosomal and plasmid DNA from different
      gonococcal strains, irrespective of their plasmid content, was poorly cleaved by the
      restriction endonucleases HaeII, HaeIII, SacII, and BamHI.  The fragment pattern of the Tn3
      segment present on the 7.2-kilobase gonococcal resistance plasmid, when compared to its known
      DNA sequence, allowed us to conclude that the HaeIII and BamHI resistance was due to
      modification of these sites.  A comparison of the fragment pattern of the resistance plasmid,
      when isolated from Escherichia coli or Neisseria gonorrhoeae, revealed that the resistance of
      HaeII must also be due to modification of its recognition sequence.  Isoschizomers of HaeII
      and HaeIII can be found in isolates of N. gonorrhoeae (NgoI and NgoII, respectively).  A new
      restriction endonuclease in gonococci, NgoIII, with a specificity similar to SacII, is
      reported here.  High-pressure liquid chromatography of gonococcal DNA showed the presence of
      5-methylcytosine.  It is suggested that the methylation of cytosine residues in the HaeII
      (NgoI), HaeIII (NgoII), and SacII (NgoIII) recognition sites is the basis for the resistance
      of gonococcal DNA to cleavage by these enzymes.  This methylation may be part of a
      host-restriction modification system.  In two out of five gonococcal strains the sequence
      -GATC- was modified.  One strain unable to modify this sequence was a spontaneous mutant of a
      strain carrying such a modifying function. [ The enzyme called NgoI in this abstract has been
      renamed NgoHI, Jan/1998. ] [ The enzyme called NgoII in this abstract has been renamed NgoHII,
      Jan/1998. ] [ The enzyme called NgoIII in this abstract has been renamed NgoKIII, Jan/1998. ]
AU  - Norlander L
AU  - Davies JK
AU  - Hagblom P
AU  - Normark S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1981 145: 788-795.

PMID- 26950319
VI  - 4
DP  - 2016
TI  - Genome Sequence of Pseudomonas aeruginosa Strain DK1-NH57388A, a Stable Mucoid Cystic Fibrosis Isolate.
PG  - e00008-16
AB  - Pseudomonas aeruginosa is an important opportunistic pathogen associated with chronic
      pulmonary infections and mortality in cystic fibrosis (CF) patients.
      Here, we present the complete genome sequence of stable mucoid P. aeruginosa
      strain DK1-NH57388A, a CF isolate which has previously been used to establish
      chronic lung infections in an animal model.
AU  - Norman A
AU  - Ciofu O
AU  - Amador CI
AU  - Hoiby N
AU  - Jelsbak L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00008-16.

PMID- 22887672
VI  - 194
DP  - 2012
TI  - Genome Sequence of Radiation-Resistant Modestobacter marinus Strain BC501, a Representative Actinobacterium That Thrives on Calcareous Stone Surfaces.
PG  - 4773-4774
AB  - Here we report the full genome sequence of Modestobacter marinus strain BC501, an
      actinobacterial isolate that thrives on stone surfaces. The generated chromosome
      is circular, with a length of 5.57 Mb and a G+C content of 74.13%, containing
      5,445 protein-coding genes, 48 tRNAs, and 3 ribosomal operons.
AU  - Normand P
AU  - Gury J
AU  - Pujic P
AU  - Chouaia B
AU  - Crotti E
AU  - Brusetti L
AU  - Daffonchio D
AU  - Vacherie B
AU  - Barbe V
AU  - Medigue C
AU  - Calteau A
AU  - Ghodhbane-Gtari F
AU  - Essoussi I
AU  - Nouioui I
AU  - Abbassi-Ghozzi I
AU  - Gtari M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4773-4774.

PMID- Not carried by PubMed...
VI  - 94
DP  - 1994
TI  - Identification of a DNA methylase gene homologue in Borrelia burgdorferi.
PG  - 125
AB  - DNA methylation may play an important role in DNA mismatch repair, DNA replication and

      recombination, and gene expression. DNA methylases are enzymes that transfer methyl groups

      from donor S-adenosylmethionine to the adenine or cytosine residues within a recognizable DNA

      sequence, thereby preventing digestion at the site and protecting host DNA. The dcm gene

      product of Escherichia coli methylates the C5 position (m5C) of the internal cytosine in the

      sequence CC(A/T)GG. Cytosine (dcm) methylation is prevalent in Borrelia burgdorferi. In this

      study, we examine the B. burgdorferi, 297 genome for the presence of the dcm gene homologue.

      

      An oligonucleotide (21 nucleotides) was synthesized to target a consensus sequence for the

      prokaryotic cytosine methyltransferases. The oligonucleotide was labeled at the 3' end by the

      addition of digoxigenin-11-ddUTP using terminal transferase. The labeled oligonucleotide was

      used to probe genome B. burgdorferi, 297 DNA. The probe hybridized strongly to chromosomal DNA

      in addition to the ospA/ospB plasmid and a 28.4-kb plasmid. These results suggest that a dcm

      homologue is present in B. burgdorferi.

      

AU  - Norton Hughes CA
AU  - Johnson RC
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1994 94: 125.

PMID- 967694
VI  - 3
DP  - 1976
TI  - Protection of particular cleavage sites of restriction endonucleases by distamycin A and actinomycin D.
PG  - 2293-2301
AB  - It is shown here that distamycin A and actinomycin D can protect the
      recognition sites of endo R.EcoRI, EcoRII, HindII, HindIII, HpaI and HpaII from
      the attack of these restriction endonucleases.  At proper distamycin
      concentrations only two endo R.EcoRI sites of phage lambda DNA are available
      for the restriction enzyme - sRI1 and sRI4.  This phenomenon results in the
      appearance of large DNA fragments comprising several consecutive fragments of
      endo R.EcoRI complete cleavage.  The distamycin fragments isolated from the
      agarose gels can be subsequently cleaved by endo R.EcoRI with the yield of the
      fragments of complete digestion.  We have compared the effect of distamycin A
      and actinomycin D on a number of restriction endonucleases having different
      nucleotide sequences in the recogniton sites and established that antibiotic
      action depends on the nucleotide sequences of the recognition sites and their
      closest environment.
AU  - Nosikov VV
AU  - Braga EA
AU  - Karlishev AV
AU  - Zhuze AL
AU  - Polyanovsky OL
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1976 3: 2293-2301.

PMID- 909774
VI  - 4
DP  - 1977
TI  - Protection of particular endonuclease R.HindIII cleavage sites by distamycin A, propyl-distamycin and netropsin.
PG  - 2263-2273
AB  - It is shown that three related antibiotics, distamycin A, propyl-distamycin and netropsin, can
      protect certain endo R.HindIII cleavage sites from attack by endonuclease, giving rise, after
      endo R.HindIII digestion, to larger DNA fragments.  Bacteriophage lambda DNA has six
      recognition sites for HindIII enzyme.  Three of these sites: shindIII 2, 3 and 6 can be
      protected from nuclease action by all the antibiotics used.  Propyl-distamycin protects partly
      shindIII 5, too.  Netropsin protects partly sites shindIII5 and 4, while distamycin A protects
      all the sites but shindIII 1 so the HindII digestion produces only two large fragments of
      lambda DNA.
AU  - Nosikov VV
AU  - Sain B
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1977 4: 2263-2273.

PMID- 4538974
VI  - 112
DP  - 1972
TI  - Molecular events accompanying the fixation of genetic information in Haemophilus heterospecific transformation.
PG  - 751-760
AB  - Heterospecific transformation between Haemophilus influenzae and H.
      parainfluenzae was investigated by isopycnic analysis of deoxyribonucleic acid
      (DNA) extracts of 3H-labeled transforming cells that had been exposed to
      32P-labeled, heavy transforming DNA.  The density distribution of genetic
      markers from the resident DNA and from the donor DNA was determined by
      transformation assay of fractions from CsCl gradients, both species being used
      as recipients.  About 50% of the 32P atoms in H. parainfluenzae donor DNA taken
      up by H. influenzae cells were transferred to resident DNA, and only a small
      amount of the label was lost under conditions of little cell growth.  There was
      less transfer in the reciprocal cross, and almost half of the donor label was
      lost.  In both crosses,the transferred donor material transformed for the donor
      marker considerably more efficiently when assayed on the donor species than on
      the recipient species, indicating that at least some of the associated 32P
      atoms are contained in relatively long stretches of donor DNA.  When the
      transformed cultures were incubated under growth conditions, the donor marker
      associated with recipient DNA transformed the donor species with progressively
      decreasing efficiency.  The data indicate that the low heterospecific
      transformation between H. influenzae and H. parainfluenzae  may be due partly
      to events occurring before association of donor and resident DNA but results
      mostly from events that occur after the association of the two DNA
      preparations.
AU  - Notani NK
AU  - Setlow JK
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1972 112: 751-760.

PMID- 28924022
VI  - 67
DP  - 2017
TI  - Pan-genomic analyses identify key Helicobacter pylori pathogenic loci modified by carcinogenic host microenvironments.
PG  - 1793-1804
AB  - OBJECTIVE: Helicobacter pylori is the strongest risk factor for gastric cancer;
      however, the majority of infected individuals do not develop disease.
      Pathological outcomes are mediated by complex interactions among bacterial, host
      and environmental constituents, and two dietary factors linked with gastric
      cancer risk are iron deficiency and high salt. We hypothesised that prolonged
      adaptation of H. pylori to in vivo carcinogenic microenvironments results in
      genetic modification important for disease. DESIGN: Whole genome sequencing of
      genetically related H. pylori strains that differ in virulence and targeted H.
      pylori sequencing following prolonged exposure of bacteria to in vitro
      carcinogenic conditions were performed. RESULTS: A total of 180 unique single
      nucleotide polymorphisms (SNPs) were identified among the collective genomes when
      compared with a reference H. pylori genome. Importantly, common SNPs were
      identified in isolates harvested from iron-depleted and high salt carcinogenic
      microenvironments, including an SNP within fur (FurR88H). To investigate the
      direct role of low iron and/or high salt, H. pylori was continuously cultured in
      vitro under low iron or high salt conditions to assess fur genetic variation.
      Exposure to low iron or high salt selected for the FurR88H variant after only 5
      days. To extend these results, fur was sequenced in 339 clinical H. pylori
      strains. Among the isolates examined, 17% (40/232) of strains isolated from
      patients with premalignant lesions harboured the FurR88H variant, compared with
      only 6% (6/107) of strains from patients with non-atrophic gastritis alone
      (p=0.0034). CONCLUSION: These results indicate that specific genetic variation
      arises within H. pylori strains during in vivo adaptation to conditions conducive
      for gastric carcinogenesis.
AU  - Noto JM
AU  - Chopra A
AU  - Loh JT
AU  - Romero-Gallo J
AU  - Piazuelo MB
AU  - Watson M
AU  - Leary S
AU  - Beckett AC
AU  - Wilson KT
AU  - Cover TL
AU  - Mallal S
AU  - Israel DA
AU  - Peek RM
PT  - Journal Article
TA  - Gut
JT  - Gut
SO  - Gut 2017 67: 1793-1804.

PMID- 18083809
VI  - 190
DP  - 2008
TI  - Gene acquisition at the insertion site for SCCmec, the genomic island conferring methicillin resistance in Staphylococcus aureus.
PG  - 1276-1283
AB  - Staphylococcus aureus becomes resistant to methicillin by acquiring a
      genomic island, known as staphylococcal chromosome cassette mec (SCCmec),
      which contains the methicillin resistance determinant, mecA. SCCmec is
      site-specifically integrated into the staphylococcal chromosome at a locus
      known as the SCCmec attachment site (attB). In an effort to gain a better
      understanding of the potential that methicillin-sensitive S. aureus (MSSA)
      isolates have for acquiring SCCmec, the nucleotide sequences of attB and
      surrounding DNA regions were examined in a diverse collection of 42 MSSA
      isolates. The chromosomal region surrounding attB varied among the
      isolates studied and appears to be a common insertion point for acquired
      foreign DNA. Insertions of up to 15.1 kb were found containing open
      reading frames with homology to enterotoxin genes,
      restriction-modification systems, transposases, and several sequences that
      have not been previously described in staphylococci. Two groups,
      containing eight and four isolates, had sequences found in known SCCmec
      elements, suggesting SCCmec elements may have evolved through repeated DNA
      insertions at this locus. In addition, the attB sequences of the majority
      of MSSA isolates in this collection differ from the attB sequences of
      strains for which integrase-mediated SCCmec insertion or excision has been
      demonstrated, suggesting that some S. aureus isolates may lack the ability
      to site-specifically integrate SCCmec into their chromosomes.
AU  - Noto MJ
AU  - Kreiswirth BN
AU  - Monk AB
AU  - Archer GL
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2008 190: 1276-1283.

PMID- 8096319
VI  - 7
DP  - 1993
TI  - Regulation of pyelonephritis-associated pili phase-variation in Excherichia coli: binding of the PapI and the Lrp regulatory proteins is controlled by DNA methylation.
PG  - 545-553
AB  - Expression of pyelonephritis-associated pili (Pap) in Escherichia coli is under a
      phase-variation control mechanism in which individual cells alternate between pili+ (ON) and
      pili- (OFF) states through a process involving DNA methylation by deoxyadenosine methylase
      (Dam). Methylation of two GATC sites (GATC1028 and GATC1130) within the pap regulatory region
      is differentially inhibited in phase ON and phase OFF cells. The GATC1028 site of phase ON
      cells is non-methylated and the GATC1130 site is fully methylated. Conversely, in phase OFF
      cells the GATC1028 site is fully methylated whereas the GATC1130 site is non-methylated. Two
      transcriptional activators, PapI and Lrp (leucine-responsive regulatory protein), are required
      for this specific methylation inhibition. DNA footprint analysis using non-methylated pap DNAs
      indicates that Lrp binds to a region surrounding the GATC1130 site, whereas PapI does not
      appear to bind to pap regulatory DNA. However, addition of Lrp and PapI together results in an
      additional DNaseI footprint around the GATC1028 site. Moreover, Dam methylation inhibits
      binding of Lrp/PapI near the GATC1028 site and alters binding of Lrp at the GATC1130 site. Our
      results support a model in which Dam and Lrp/PapI compete for binding near the GATC1028 site,
      regulating the methylation state of this GATC site and consequently, the pap transcription
      state.
AU  - Nou X
AU  - Skinner B
AU  - Braaten B
AU  - Blyn L
AU  - Hirsch D
AU  - Low D
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1993 7: 545-553.

PMID- 23846272
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Frankia sp. Strain BMG5.12, a Nitrogen-Fixing Actinobacterium Isolated from Tunisian Soils.
PG  - e00468-13
AB  - Members of the actinomycete genus Frankia form a nitrogen-fixing symbiosis with 8 different
      families of actinorhizal plants. We report a draft genome sequence for
      Frankia sp. strain BMG5.12, a nitrogen-fixing actinobacterium isolated from
      Tunisian soils with the ability to infect Elaeagnus angustifolia and Myrica gale.
AU  - Nouioui I et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00468-13.

PMID- 28074122
VI  - 12
DP  - 2017
TI  - High quality draft genome of Nakamurella lactea type strain, a rock actinobacterium, and emended description of Nakamurella lactea.
PG  - 4
AB  - Nakamurella lactea DLS-10T, isolated from rock in Korea, is one of the four type  strains of
      the genus Nakamurella. In this study, we describe the high quality
      draft genome of N. lactea DLS-10T and its annotation. A summary of phenotypic
      data collected from previously published studies was also included. The genome of
      strain DLS-10T presents a size of 5.82 Mpb, 5100 protein coding genes, and a C +
      G content of 68.9%. Based on the genome analysis, emended description of N.
      lactea in terms of G + C content was also proposed.
AU  - Nouioui I
AU  - Goker M
AU  - Carro L
AU  - Montero-Calasanz MD
AU  - Rohde M
AU  - Woyke T
AU  - Kyrpides NC
AU  - Klenk HP
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 4.

PMID- 27231368
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Frankia Strain G2, a Nitrogen-Fixing Actinobacterium Isolated from Casuarina equisetifolia and Able To Nodulate Actinorhizal Plants of  the Order Rhamnales.
PG  - e00437-16
AB  - Frankia sp. strain G2 was originally isolated from Casuarina equisetifolia and is
      characterized by its ability to nodulate actinorhizal plants of the Rhamnales
      order, but not its original host. It represents one of the largest Frankia
      genomes so far sequenced (9.5 Mbp).
AU  - Nouioui I
AU  - Gtari M
AU  - Goker M
AU  - Ghodhbane-Gtari F
AU  - Tisa LS
AU  - Fernandez MP
AU  - Normand P
AU  - Huntemann M
AU  - Clum A
AU  - Pillay M
AU  - Varghese N
AU  - Reddy TB
AU  - Ivanova N
AU  - Woyke T
AU  - Kyrpides NC
AU  - Klenk HP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00437-16.

PMID- 27660670
VI  - 11
DP  - 2016
TI  - Genome sequence of Candidatus Arsenophonus lipopteni, the exclusive symbiont of a blood sucking fly Lipoptena cervi (Diptera: Hippoboscidae).
PG  - 72
AB  - Candidatus Arsenophonus lipopteni (Enterobacteriaceae, Gammaproteobacteria) is an obligate
      intracellular symbiont of the blood feeding deer ked, Lipoptena cervi
      (Diptera: Hippoboscidae). The bacteria reside in specialized cells derived from
      host gut epithelia (bacteriocytes) forming a compact symbiotic organ
      (bacteriome). Compared to the closely related complex symbiotic system in the
      sheep ked, involving four bacterial species, Lipoptena cervi appears to maintain
      its symbiosis exclusively with Ca. Arsenophonus lipopteni. The genome of 836,724
      bp and 24.8 % GC content codes for 667 predicted functional genes and bears the
      common characteristics of sequence economization coupled with obligate
      host-dependent lifestyle, e.g. reduced number of RNA genes along with the rRNA
      operon split, and strongly reduced metabolic capacity. Particularly, biosynthetic
      capacity for B vitamins possibly supplementing the host diet is highly
      compromised in Ca. Arsenophonus lipopteni. The gene sets are complete only for
      riboflavin (B2), pyridoxine (B6) and biotin (B7) implying the content of some B
      vitamins, e.g. thiamin, in the deer blood might be sufficient for the insect
      metabolic needs. The phylogenetic position within the spectrum of known
      Arsenophonus genomes and fundamental genomic features of Ca. Arsenophonus
      lipopteni indicate the obligate character of this symbiosis and its independent
      origin within Hippoboscidae.
AU  - Novakova E
AU  - Hypsa V
AU  - Nguyen P
AU  - Husnik F
AU  - Darby AC
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 72.

PMID- 29439044
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Rhodococcus sp. Strain M8, Which Can Degrade a Broad Range of Nitriles.
PG  - e01526-17
AB  - Rhodococcus sp. strain M8 is a nitrile-degrading bacterium isolated from
      acrylonitrile-contaminated sites. This strain produces the enzymes for sequential
      nitrile degradation, cobalt-type nitrile hydratase, and amidase in large amounts.
      Its draft genome sequence, announced here, has an estimated size of 6.3 Mbp.
AU  - Novikov AD
AU  - Lavrov KV
AU  - Kasianov AS
AU  - Gerasimova TV
AU  - Yanenko AS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01526-17.

PMID- 26823582
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Pseudomonas brassicacearum LBUM300, a Disease-Suppressive Bacterium with Antagonistic Activity toward Fungal, Oomycete,  and Bacterial Plant Pathogens.
PG  - e01623-15
AB  - Pseudomonas brassicacearum LBUM300, a plant rhizosphere-inhabiting bacterium, produces
      2,4-diacetylphloroglucinol and hydrogen cyanide and has shown
      antagonistic activity against the plant pathogens Verticillium dahliae,
      Phytophthora cactorum, and Clavibacter michiganensis subsp. michiganensis. Here,
      we report the complete genome sequence of P. brassicacearum LBUM300.
AU  - Novinscak A
AU  - Gadkar VJ
AU  - Joly DL
AU  - Filion M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01623-15.

PMID- 8181713
VI  - 117
DP  - 1994
TI  - Characterization of restriction endonuclease AjoI from Acinetobacter johnsonii.
PG  - 97-102
AB  - A new type II restriction endonuclease, named AjoI, was detected in Acinetobacter johnsonii.
      The enzyme AjoI, an isoschizomer of PstI, recognized the hexanucleotide sequence
      [5'-CTGCA/G-3'], with a cleavage site generating fragments of DNA with protruding cohesive
      3' termini.
AU  - Nowak A
AU  - Kur J
AU  - Gospodarek E
AU  - Bielawski K
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1994 117: 97-102.

PMID- 20386741
VI  - 6
DP  - 2010
TI  - De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis.
PG  - E1000891
AB  - Filamentous fungi are of great importance in ecology, agriculture, medicine, and
      biotechnology. Thus, it is not surprising that genomes for more than 100
      filamentous fungi have been sequenced, most of them by Sanger sequencing. While
      next-generation sequencing techniques have revolutionized genome resequencing,
      e.g. for strain comparisons, genetic mapping, or transcriptome and ChIP analyses,
      de novo assembly of eukaryotic genomes still presents significant hurdles,
      because of their large size and stretches of repetitive sequences. Filamentous
      fungi contain few repetitive regions in their 30-90 Mb genomes and thus are
      suitable candidates to test de novo genome assembly from short sequence reads.
      Here, we present a high-quality draft sequence of the Sordaria macrospora genome
      that was obtained by a combination of Illumina/Solexa and Roche/454 sequencing.
      Paired-end Solexa sequencing of genomic DNA to 85-fold coverage and an additional
      10-fold coverage by single-end 454 sequencing resulted in approximately 4 Gb of
      DNA sequence. Reads were assembled to a 40 Mb draft version (N50 of 117 kb) with
      the Velvet assembler. Comparative analysis with Neurospora genomes increased the
      N50 to 498 kb. The S. macrospora genome contains even fewer repeat regions than
      its closest sequenced relative, Neurospora crassa. Comparison with genomes of
      other fungi showed that S. macrospora, a model organism for morphogenesis and
      meiosis, harbors duplications of several genes involved in
      self/nonself-recognition. Furthermore, S. macrospora contains more polyketide
      biosynthesis genes than N. crassa. Phylogenetic analyses suggest that some of
      these genes may have been acquired by horizontal gene transfer from a distantly
      related ascomycete group. Our study shows that, for typical filamentous fungi, de
      novo assembly of genomes from short sequence reads alone is feasible, that a
      mixture of Solexa and 454 sequencing substantially improves the assembly, and
      that the resulting data can be used for comparative studies to address basic
      questions of fungal biology.
AU  - Nowrousian M
AU  - Stajich JE
AU  - Chu M
AU  - Engh I
AU  - Espagne E
AU  - Halliday K
AU  - Kamerewerd J
AU  - Kempken F
AU  - Knab B
AU  - Kuo HC
AU  - Osiewacz HD
AU  - Poggeler S
AU  - Read ND
AU  - Seiler S
AU  - Smith KM
AU  - Zickler D
AU  - Kuck U
AU  - Freitag M
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2010 6: E1000891.

PMID- 24370935
VI  - 84
DP  - 2014
TI  - A single CMT methyltransferase homolog is involved in CHG DNA methylation and development of Physcomitrella patens.
PG  - 719-735
AB  - C-5 DNA methylation is an essential mechanism controlling gene expression and developmental
      programs in a variety of organisms. Though the role of DNA methylation has been intensively
      studied in mammals and Arabidopsis, little is known about the evolution of this mechanism. The
      chromomethylase (CMT) methyltransferase family is unique to plants and was found to be
      involved in DNA methylation in Arabidopsis, maize and tobacco. The moss Physcomitrella patens,
      a model for early terrestrial plants, harbors a single homolog of the CMT protein family
      designated as PpCMT. Our phylogenetic analysis suggested that the CMT family is unique to
      embryophytes and its earliest known member PpCMT belongs to the CMT3 subfamily. Thus, P.
      patens may serve as a model to study the ancient functions of the CMT3 family. We have
      generated a Delta Ppcmt deletion mutant which demonstrated that PpCMT is essential for P.
      patens protonema and gametophore development and is involved in CHG methylation as
      demonstrated at four distinct genomic loci. PpCMT protein accumulation pattern correlated with
      proliferating cells and was sub-localized to the nucleus as predicted from its function. Taken
      together, our results suggested that CHG DNA methylation mediated by CMT has been employed
      early in land plant evolution to control developmental programs during both the vegetative and
      reproductive haploid phases along the plant life cycle.
AU  - Noy-Malka C
AU  - Yaari R
AU  - Itzhaki R
AU  - Mosquna A
AU  - Gershovitz NA
AU  - Katz A
AU  - Ohad N
PT  - Journal Article
TA  - Plant Mol. Biol.
JT  - Plant Mol. Biol.
SO  - Plant Mol. Biol. 2014 84: 719-735.

PMID- 2854806
VI  - 74
DP  - 1988
TI  - A novel mcrB-based Escherichia coli K-12 vector system and its use in analyzing the genetic determinants for the McrB nuclease.
PG  - 177-178
AB  - Meeting Abstract
AU  - Noyer-Weidner M
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 177-178.

PMID- 3550384
VI  - 205
DP  - 1986
TI  - Cytosine-specific DNA modification interferes with plasmid establishement in Escherichia coli K12:  Involvement of rgl B.
PG  - 469-475
AB  - Several chimeric pBR322/328 derivatives containing genes for cytosine-specific
      DNA methyltransferases (Mtases) can be transformed into the Escherichia coli
      K12/E. coli B hybrid strains HB101 and RR1 but not into other commonly used E.
      coli K12 strains.  In vitro methylation of cytosine residues in pBR328 and
      other unrelated plasmids also reduces their potential to transform such
      methylation sensitive strains, albeit to a lesser degree than observed with
      plasmids containing Mtase genes.  The extent of reduced transformability
      depends on the target specificity of the enzyme used for in vitro modification.
      The role of a host function in the discrimination against methylated plasmids
      was verified by the isolation of K12 mutants which tolerate cytosine methylated
      DNA.  The mutations map in the vicinity of the serB locus.  This and other data
      indicate that the host rg/B function is involved in the discrimination against
      modified DNA.
AU  - Noyer-Weidner M
AU  - Diaz R
AU  - Reiners L
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1986 205: 469-475.

PMID- 3928442
VI  - 35
DP  - 1985
TI  - DNA methyltransferase genes of Bacillus subtilis phages: structural relatedness and gene expression.
PG  - 143-150
AB  - The DNA methyltransferase (Mtase) genes of temperate Bacillus subtilis phages
      Phi3T, Rho11 and SPbeta were cloned and expressed in Escherichia coli.  Each
      gene specifies a 47-kDal protein, which modifies BsuR (GGCC) and Fnu4HI (GCNGC)
      target sequences.  Transcription is controlled by phage promoters located on
      the cloned fragments.  The direction of transcription and the approximate
      position of the Mtase genes were determined.  DNA/DNA hybridization experiments
      revealed close structural relatedness of the Phi3T, Rho11 and SPbeta genes.  A
      significant degree of homology was also found among these genes and the Mtase
      gene of related phage SPR, which codes for an enzyme with different
      modification specificity.  These results suggest a common ancestor of the
      different phage Mtase genes.  Phage Z, the only BsuR-sensitive member of this
      phage group, lacks a modification gene, but contains regions homologous to
      sequences flanking the SPR, Phi3T, Rho11 and SPbeta Mtase genes.
AU  - Noyer-Weidner M
AU  - Jentsch S
AU  - Kupsch J
AU  - Bergbauer M
AU  - Trautner TA
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1985 35: 143-150.

PMID- 6302313
VI  - 46
DP  - 1983
TI  - Restriction and modification in Bacillus subtilis: DNA methylation potential of the related bacteriophages Z, SPR, SPbeta, Phi3T, and Rho11.
PG  - 446-453
AB  - The DNA methylation capacity and some other properties of the related temperate
      Bacillus subtilis phages Z, SPR, SPbeta, Phi3T, and Rho11 are compared.  With
      phage mutants affected in their methylation potential, we show that phage-coded
      methyltransferase genes are interchangeable among the phages studied.  DNA/DNA
      hybridization experiments indicate that phage methyltransferase genes are
      structurally related, whereas no such relationship is observed to a bacterial
      gene, specifying a methyltransferase with the same specificity.
AU  - Noyer-Weidner M
AU  - Jentsch S
AU  - Pawlek B
AU  - Gunthert U
AU  - Trautner TA
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1983 46: 446-453.

PMID- 6264152
VI  - 38
DP  - 1981
TI  - Restriction and modification in Bacillus subtilis: gene coding for a BsuR-specific modification methyltransferase in the temperate bacteriophage Phi3T.
PG  - 1077-1080
AB  - The resistance of Phi3T DNA to degradation by the restriction enzyme BsuR or
      its isoschizomer HaeIII is due to obligatory modification of such DNA.
      Biochemical and genetical experiments indicate that Phi3T codes for a
      methyltransferase, which methylates Phi3T DNA itself or heterologous DNA at
      target sites 5'-GG*CC.
AU  - Noyer-Weidner M
AU  - Pawlek B
AU  - Jentsch S
AU  - Gunthert U
AU  - Trautner TA
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1981 38: 1077-1080.

PMID- 3049249
VI  - 66
DP  - 1988
TI  - Highly efficient positive selection of recombinant plasmids using a novel rglB-based Escherichia coli K-12 vector system.
PG  - 269-278
AB  - We have developed pBR328-derived vectors which allow highly efficient positive
      selection of recombinant plasmids.  The system is based on the rglB-coded
      restriction activity of Escherichia coli K-12 directed against 5-methylcytosine
      (5mC)-containing DNA.  The vectors code for cytosine-specific,
      temperature-sensitive DNA methyltransferases (ts-Mtases), whose specificity
      elicits RglB restriction.  5mC-free vector DNA - a prerequisite to allow
      establishment of such plasmids in cells expressing the RglB nuclease activity -
      can be prepared from cultures grown at 42C.  At 30C the vector plasmids are
      vulnerable to RglB restriction due to the expression of suicidal Mtase
      activity.  Cloning a DNA fragment into the ts-Mtase-coding gene disrupts the
      lethal methylation and thus permits selection of such recombinant plasmids at
      30C.  The standard vector used, pBN73, contains unique recognition sites for
      nine restriction enzymes within the ts-Mtase-coding gene, which can be used
      independently or in combination for the construction of recombinant plasmids
      selectable by the rglB-coded activity.  Plasmid pBN74, which carries the
      determinants for both the ts-Mtase and the RglB nuclease, contains seven unique
      sites within the ts-Mtase-coding gene.  While selection of recombinant plasmids
      derived from pBN73 obligatorily requires the employment of rglB+ strains,
      selection of pBN74 derivatives can be performed independent of the E. coli host
      genotype.  It remains to be elucidated whether positive selection of
      pBN74-derived recombinant plasmids can also be achieved in hosts other than E.
      coli.  Plasmids pBN73, pBN74 and the recombinants are structurally stable.
      Generally applicable procedures, as developed during the establishment of this
      vector system, are described; they allow the isolation of ts-Mtases and
      facilitate the cloning of genes coding for nucleases directed against
      5mC-containing DNA.
AU  - Noyer-Weidner M
AU  - Reiners-Schramm L
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 66: 269-278.

PMID- 
VI  - 0
DP  - 1993
TI  - Methylation of DNA in prokaryotes.
PG  - 39-108
AB  - A much wider variety of biological functions of postreplicative DNA methylation is observed in
      prokaryotes than in eukaryotes. In eukaryotes DNA methylation is primarily a means of the
      control of gene expression. Many chapters of this book are devoted to various aspects of this
      function. In prokaryotes, DNA methylation affects such diverse phenomena as determination of
      accessiblity of DNA to digestion by endonucleases, control of initiation of DNA replication,
      and the definition of origins of packaging in the maturation of phage DNA, which will be dealt
      with in this article. We shall also be concerned with enzymes which facilitate methylation,
      the DNA methyltransferases. In the eukaryotes, as far as we know at this time, the various DNA
      methyltransferases encountered represent a rather homogenous group, whereas in prokaryotes, we
      find a very diverse set of DNA methyltransferases. Beyond their biological significance, DNA
      methyltransferases represent a remarkable class of enzyme in their own right. Not only are
      they paradigms for sequence specific DNA binding proteins, but they also show specificity in
      their catalytic interaction with defined DNA sequences. Furthermore, their universal
      distribution, the multitude of enzymes with different or identical specificities observed
      among prokaryotes and the obligatory coexistence of isospecific restriction and methylating
      enzymes in restriction/modification systems make DNA methyltransferases choice candidates for
      evolutionary studies.
AU  - Noyer-Weidner M
AU  - Trautner TA
PT  - Journal Article
TA  - DNA Methylation: Molecular Biology and Biological Significance
JT  - DNA Methylation: Molecular Biology and Biological Significance
SO  - DNA Methylation: Molecular Biology and Biological Significance 1993 0: 39-108.

PMID- 7937131
VI  - 22
DP  - 1994
TI  - M.Phi3TII: a new monospecific DNA (cytosine-C5) methyltransferase with pronounced amino acid sequence similarity to a family of adenine-N6-DNA-methyltransferases.
PG  - 4066-4072
AB  - The temperate B.subtilis phages Phi3T and Rho11s code, in addition to the multispecific DNA
      (cytosine-C5) methyltransferases (C5-MTases) M.Phi3TI and M.Rho11sI, which were previously
      characterized, for the identical monospecific C5-MTases M.Phi3TII and M.Rho11s.II. These
      enzymes modify the C of TCGA sites, a novel target specificity among C5-MTases. The primary
      sequence of M.Phi3TII (326 amino acids) shows all conserved motifs typical of the building
      plan of C5-MTases. The degree of relatedness between M.Phi3TII and all other mono- or
      multispecific C5-MTases ranges from 30-40% amino acid identity. Particularly M.Phi3TII does
      not show pronounced similarity to M.Phi3TI indicating that both MTase genes were not generated
      from one another but were acquired independently by the phage. The amino terminal part of the
      M.Phi3TII (preceding the variable region 'V'), which predominantly constitutes the catalytic
      domain of the enzyme, exhibits pronounced sequence similarity to the amino termini of a family
      of A-N6-MTases, which -- like M. TaqI -- recognize the general sequence TNNA. This suggests
      that recently described similarities in the general three dimensional organization of C5- and
      A-N6-MTases imply divergent evolution of these enzymes originating from a common molecular
      ancestor.
AU  - Noyer-Weidner M
AU  - Walter J
AU  - Terschuren P-A
AU  - Chai S
AU  - Trautner TA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1994 22: 4066-4072.

PMID- 7816649
VI  - 22
DP  - 1994
TI  - M.Phi3TII: a new monospecific DNA (cytosine-C5) methyltransferase with pronounced amino acid sequence similarity to a family of adenine-N6-DNA-methyltransferases.
PG  - 5517-5523
AB  - The temperate B.subtilis phages Phi3T and Rho11S code, in addition to the multispecific DNA
      (cytosine-C5) methyltransferases (C5-MTases) M.Phi3TI and M.Rho11SI, which were previously
      characterized, for the identical monospecific C5-MTases M.Phi3TII and M.Rho11SII. These
      enzymes modify the C of TCGA sites, a novel target specificity among C5-MTases. The primary
      sequence of M.Phi3TII (326 amino acids) shows all conserved motifs typical of the building
      plan of C5-MTases. The degree of relatedness between M.Phi3TII and all other mono- or
      multispecific C5-MTases ranges from 30-40% amino acid identity. Particularly M.Phi3TII does
      not show pronounced similarity to M.Phi3TI indicating that both Mtase genes were not generated
      from one another but were acquired independently by the phage. The amino terminal part of the
      M.Phi3TII (preceding the variable region 'V'), which predominantly constitutes the catalytic
      domain of the enzyme, exhibits pronounced sequence similarity to the amino termini of a family
      of A-N6-MTases, which -- like M. TaqI -- recognize the general sequence TNNA. This suggests
      that recently described similarities in the general three dimensional organization of C5- and
      A-N6-MTases imply divergent evolution of these enzymes originating from a common molecular
      ancestor.
AU  - Noyer-Weidner M
AU  - Walter J
AU  - Terschuren P-A
AU  - Chai S
AU  - Trautner TA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1994 22: 5517-5523.

PMID- 26380640
VI  - 10
DP  - 2015
TI  - High-quality permanent draft genome sequence of the extremely osmotolerant diphenol degrading bacterium Halotalea alkalilenta AW-7(T), and emended description of the genus Halotalea.
PG  - 52
AB  - Members of the genus Halotalea (family Halomonadaceae) are of high significance since they can
      tolerate the greatest glucose and maltose concentrations ever reported for known bacteria and
      are involved in the degradation of industrial effluents. Here, the characteristics and the
      permanent-draft genome sequence and  annotation of Halotalea alkalilenta AW-7(T) are
      described. The microorganism was  sequenced as a part of the Genomic Encyclopedia of Type
      Strains, Phase I: the one thousand microbial genomes (KMG) project at the DOE Joint Genome
      Institute, and it is the only strain within the genus Halotalea having its genome sequenced.
      The genome is 4,467,826 bp long and consists of 40 scaffolds with 64.62 % average GC  content.
      A total of 4,104 genes were predicted, comprising of 4,028 protein-coding and 76 RNA genes.
      Most protein-coding genes (87.79 %) were assigned to a putative function. Halotalea
      alkalilenta AW-7(T) encodes the catechol and protocatechuate degradation to beta-ketoadipate
      via the beta-ketoadipate and protocatechuate ortho-cleavage degradation pathway, and it
      possesses the genetic ability to detoxify fluoroacetate, cyanate and acrylonitrile. An emended
      description of the genus Halotalea Ntougias et al. 2007 is also provided in order to describe
      the delayed fermentation ability of the type strain.
AU  - Ntougias S
AU  - Lapidus A
AU  - Copeland A
AU  - Reddy TB
AU  - Pati A
AU  - Ivanova NN
AU  - Markowitz VM
AU  - Klenk HP
AU  - Woyke T
AU  - Fasseas C
AU  - Kyrpides NC
AU  - Zervakis GI
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 52.

PMID- 25197463
VI  - 9
DP  - 2014
TI  - High quality draft genome sequence of Olivibacter sitiensis type strain (AW-6(T)), a diphenol degrader with genes involved in the catechol pathway.
PG  - 783-793
AB  - Olivibacter sitiensis Ntougias et al. 2007 is a member of the family Sphingobacteriaceae,
      phylum Bacteroidetes. Members of the genus Olivibacter are
      phylogenetically diverse and of significant interest. They occur in diverse
      habitats, such as rhizosphere and contaminated soils, viscous wastes, composts,
      biofilter clean-up facilities on contaminated sites and cave environments, and
      they are involved in the degradation of complex and toxic compounds. Here we
      describe the features of O. sitiensis AW-6(T), together with the permanent-draft
      genome sequence and annotation. The organism was sequenced under the Genomic
      Encyclopedia for Bacteria and Archaea (GEBA) project at the DOE Joint Genome
      Institute and is the first genome sequence of a species within the genus
      Olivibacter. The genome is 5,053,571 bp long and is comprised of 110 scaffolds
      with an average GC content of 44.61%. Of the 4,565 genes predicted, 4,501 were
      protein-coding genes and 64 were RNA genes. Most protein-coding genes (68.52%)
      were assigned to a putative function. The identification of 2-keto-4-pentenoate
      hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase-coding genes indicates
      involvement of this organism in the catechol catabolic pathway. In addition,
      genes encoding for beta-1,4-xylanases and beta-1,4-xylosidases reveal the
      xylanolytic action of O. sitiensis.
AU  - Ntougias S
AU  - Lapidus A
AU  - Han J
AU  - Mavromatis K
AU  - Pati A
AU  - Chen A
AU  - Klenk HP
AU  - Woyke T
AU  - Fasseas C
AU  - Kyrpides NC
AU  - Zervakis GI
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 783-793.

PMID- 25657274
VI  - 3
DP  - 2015
TI  - Genome Sequencing of 10 Helicobacter pylori Pediatric Strains from Patients with  Nonulcer Dyspepsia and Peptic Ulcer Disease.
PG  - e01488-14
AB  - We present draft genome sequences of 10 Helicobacter pylori clinical strains isolated from
      children. This will be important for future studies of comparative
      genomics in order to better understand the virulence determinants underlying
      peptic ulcer disease.
AU  - Nunes A
AU  - Rocha R
AU  - Vale FF
AU  - Vieira L
AU  - Sampaio DA
AU  - Dias R
AU  - Gomes JP
AU  - Oleastro M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01488-14.

PMID- 21169198
VI  - 39
DP  - 2011
TI  - Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group.
PG  - 3204-3223
AB  - The domain Archaea has historically been divided into two phyla, the Crenarchaeota and
      Euryarchaeota. Although regarded as members of the
      Crenarchaeota based on small subunit rRNA phylogeny, environmental
      genomics and efforts for cultivation have recently revealed two novel
      phyla/divisions in the Archaea; the 'Thaumarchaeota' and 'Korarchaeota'.
      Here, we show the genome sequence of Candidatus 'Caldiarchaeum
      subterraneum' that represents an uncultivated crenarchaeotic group. A
      composite genome was reconstructed from a metagenomic library previously
      prepared from a microbial mat at a geothermal water stream of a
      sub-surface gold mine. The genome was found to be clearly distinct from
      those of the known phyla/divisions, Crenarchaeota (hyperthermophiles),
      Euryarchaeota, Thaumarchaeota and Korarchaeota. The unique traits suggest
      that this crenarchaeotic group can be considered as a novel archaeal
      phylum/division. Moreover, C. subterraneum harbors an ubiquitin-like
      protein modifier system consisting of Ub, E1, E2 and small Zn RING finger
      family protein with structural motifs specific to eukaryotic system
      proteins, a system clearly distinct from the prokaryote-type system
      recently identified in Haloferax and Mycobacterium. The presence of such a
      eukaryote-type system is unprecedented in prokaryotes, and indicates that
      a prototype of the eukaryotic protein modifier system is present in the
      Archaea.
AU  - Nunoura T
AU  - Takaki Y
AU  - Kakuta J
AU  - Nishi S
AU  - Sugahara J
AU  - Kazama H
AU  - Chee GJ
AU  - Hattori M
AU  - Kanai A
AU  - Atomi H
AU  - Takai K
AU  - Takami H
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2011 39: 3204-3223.

PMID- 24604648
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Stenotrophomonas maltophilia Strain 5BA-I-2, a Soil Isolate and a Member of a Phylogenetically Basal Lineage.
PG  - e00134-14
AB  - Stenotrophomonas maltophilia is an omnipresent environmental bacterium emerging as an
      opportunistic human pathogen and exhibiting multidrug resistance. Here, we
      report the draft genome sequence of S. maltophilia strain 5BA-I-2, a soil isolate
      and a member of a phylogenetically basal lineage.
AU  - Nunvar J
AU  - Elhottova D
AU  - Chronakova A
AU  - Schneider B
AU  - Licha I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00134-14.

PMID- 4044519
VI  - 164
DP  - 1985
TI  - Procaryotic and Eucaryotic Traits of DNA Methylation in Spiroplasmas (Mycoplasmas).
PG  - 19-24
AB  - Differences in the type of base methylated (cytosine or adenine) and in the
      extent of methylation were detected by high-pressure liquid chromatography in
      the DNAs of five spiroplasmas.  Nearest neighbor analysis and digestion by
      restriction enzyme isoschizomers also revealed differences in methylation
      sequence specificity.  Whereas in Spiroplasma floricola and Spiroplasma sp.
      strain PPS-1 5-methylcytosine was found on the 5' side of each of the four
      major bases, the cytosine in Spiroplasma apis DNA was methylated only when its
      3' neighboring base was adenine or thymine.  In Spiroplasma sp. strain MQ-1
      over 95% of the methylated cytosine was in C-G sequences.  Essentially all of
      the C-G sequences in the MQ-1 DNA were methylated.  Partially purified extracts
      of S. apis and Spiroplasma sp. strain MQ-1 were used to study substrate and
      sequence specificity of the methylase activity.  Methylation by the MQ-1 enzyme
      was exclusively at C-G sequences, resembling in this respect eucaryotic DNA
      methylases.  However, the MQ-1 emthylase differed from eucaryotic methylases by
      showing high activity on nonmethylated DNA duplexes, low activity with
      hemimethylated DNA duplexes, and no activity on single-stranded DNA.
AU  - Nur I
AU  - Szyf M
AU  - Razin A
AU  - Glaser G
AU  - Rottem S
AU  - Razin S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1985 164: 19-24.

PMID- 29748411
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Staphylococcus aureus Strain HD1410, Isolated from a Persistent Nasal Carrier.
PG  - e00411-18
AB  - We report here the draft genome sequence of a Staphylococcus aureus strain isolated from the
      nares of an 18-year-old female healthy persistent-carrier
      individual, and it was used to investigate S. aureus-specific immune responses in
      colonized and noncolonized individuals.
AU  - Nurjadi D
AU  - Boutin S
AU  - Dalpke A
AU  - Heeg K
AU  - Zanger P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00411-18.

PMID- Not included in PubMed...
VI  - 15
DP  - 1993
TI  - Design of compact multiple cloning sites.
PG  - 209-213
AB  - Cloning procedures in molecular biology are usually enhanced by the availability of desired
      restriction sites in vectors engineering for cloning or expression purposes. In the absence of
      such sites, cloning required blunt ends or the addition of linkers, which requires more
      manipulation, both being less efficient. During the past decade, many vectors have been
      developed that have a multiple cloning site (MCS) containing many restriction sites found only
      once within each vector. An ideal MCS would be one that has many unique restriction sites that
      would satisfy general cloning needs. The upper limit to the number of restriction sites that
      can be placed in an MCS is usually determined by the absence of identical recognition
      specificities in the rest of the vector and the functional length available for the MCS. Here
      we present a simple method to design compact MCSs which are 50% shorter than presently
      available MCSs as a result of the presence of restriction sites that overlap each other.
AU  - Nurminsky DI
AU  - Hartl DL
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 1993 15: 209-213.

PMID- Not carried by PubMed...
VI  - 71
DP  - 1971
TI  - The role of methylation in host-induced modification of Salmonella bacteriophage P3.
PG  - 196
AB  - The temperate Salmonella potsdam bacteriophage P3 lyses E. coli K with high
      efficiency.  It is modified in this passage and subsequently restricted by S.
      potsdam.  Studies with P-32 tagged phage showed that the E. coli passed P3
      phage were adsorbing to S. potsdam, however, and infecting their DNA.  When a
      methionine requiring mutant of S. potsdam was deprived of methionine and
      infected with restricted P3 phage, the restriction was reduced to less than
      half of its former value.  Experiments employing adenine-2-H3 revealed that the
      unrestricted phage DNA from S. potsdam has about 1.2% as many MAP groups as
      adenine whereas the restricted phage DNA from E. coli has about 0.6%.
AU  - Nutter RL
AU  - Bullas LR
AU  - Siapco BJ
AU  - Pearson C
PT  - Journal Article
TA  - Bacteriol. Proc.
JT  - Bacteriol. Proc.
SO  - Bacteriol. Proc. 1971 71: 196.

PMID- 4561208
VI  - 10
DP  - 1972
TI  - Change in methylation of Salmonella bacteriophage P3 deoxyribonucleic acid with host-controlled modification by Escherichia coli.
PG  - 560-562
AB  - Modification of bacteriophage P3 by passage through Escherichia coli K was
      correlated with a 54% decrease in the content of 6-methylaminopurine in the
      phage deoxyribonucleic acid.
AU  - Nutter RL
AU  - Bullas LR
AU  - Siapco BS
AU  - Pearson CA
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1972 10: 560-562.

PMID- 28572306
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Listeria monocytogenes, Isolated from Fresh Leaf Vegetables in Owerri City, Nigeria.
PG  - e00354-17
AB  - Here, we report the draft genome sequences of three Listeria monocytogenes isolates from fresh
      leaves collected in Nigeria, belonging to sequence types ST5
      and ST155 (sublineages SL5 and SL155, respectively).
AU  - Nwaiwu O
AU  - Moura A
AU  - Thouvenot P
AU  - Rees C
AU  - Leclercq A
AU  - Lecuit M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00354-17.

PMID- 2828884
VI  - 209
DP  - 1987
TI  - Cloning of two type II methylase genes that recognise asymmetric nucleotide sequences:  FokI and HgaI.
PG  - 570-574
AB  - The modification genes of Flavobacterium okeanokoites and Haemophilus
      gallinarum have been cloned into the vector of pBR322 and expressed in
      Escherichia coli cells.  FokI methylase gene is contained on a 3.80 kb piece of
      F. okeanokoites DNA.  Plasmid constructs carrying this fragment of DNA are
      resistant to digestion by FokI restriction endonuclease but are sensitive to
      cleavage by HindIII, EcoRI and PstI.  Unmodified lambda DNA molecules, exposed
      in vitro to cell extracts prepared from cells harbouring this plasmid, became
      resistant to digestion by FokI.  The smallest HgaI methylase clone carries the
      pBR322 plasmid containing a 3.50 kb piece of H. gallinarum DNA.  This plasmid
      is resistant to digestion by HgaI.  Neither the FokI nor the HgaI restriction
      endonuclease was detected in either clone.  This is the first report of cloning
      modification genes whose protein products recognise asymmetric nucleotide
      sequences.
AU  - Nwankwo D
AU  - Wilson G
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1987 209: 570-574.

PMID- 7607514
VI  - 157
DP  - 1995
TI  - Cloning of a pair of genes encoding isoschizomeric restriction endonucleases from Bacillus species: the BspEI and BspMII restriction and modification systems.
PG  - 31-35
AB  - The respective genes (R-M) encoding restriction and modification systems from two Bacillus
      species which recognize the same nucleotide sequence, 5'TCCGGA, have been cloned and
      expressed in Escherichia coli.  The BspEI R-M genes were cloned on a 3.6-kb HindIII fragment,
      whereas the BspMII R-M genes were cloned on three contiguous HindIII fragments totalling 9.8
      kb.  Upon thermal induction, E. coli carrying the bspEIR clones under the control of the phage
      lambda PL promoter, express high levels of R.BspEI (106 units/g wet cell paste).  The
      bspMIIR  gene, on the other hand, is only poorly expressed (about 4 x 10/3 units/g wet cell
      paste) following induction.  Although the enzymes of both R-M systems recognize the same
      sequence and  the restriction endonucleases (ENases) cleave DNA at the same position, the
      modification specified by the methyltransferases (MTases) differ.  The internal cytosine is
      the site for M.BspMII modification (TCmeCGGA), whereas the external cytosine is modified by
      M.BspEI.
AU  - Nwankwo DO
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 31-35.

PMID- 8964488
VI  - 173
DP  - 1996
TI  - The XmnI restriction-modification system: cloning, expression, sequence organization and similarity between the R and M genes.
PG  - 121-127
AB  - The xmn1RM genes from Xanthomonas manihotis 7AS1 have been cloned and expressed in Escherichia
      coli.  The nucleotide (nt) sequences of both genes were determined.  The XmnI
      methyltransferase (Mtase)-encoding gene is 1861 bp in length and codes for 620 amino acids
      (aa) (68,660 Da).  The restriction endonuclease (Enase)-encoding gene is 969 bp long and
      therefore codes for a 319-aa protein (35,275 Da).  The two genes are aligned tail to tail and
      they overlap at their respective stop codons.  About 4 x 10^4 units/g wet cell paste of R.XmnI
      was obtained following IPTG induction in a suitable E. coli host.  The xmnIR gene is expressed
      from the T7 promoter.  M.XmnI probably modifies the first A in the sequence, GAA(N)4TTC.  The
      xmnIR and M genes contain regions of conserved similarity and probably evolved from a common
      ancestor.  M.XmnI is losely related to M.EcoRI.  The XmnI R-M system and the type-I R-M
      systems probably derived from a common ancestor.
AU  - Nwankwo DO
AU  - Lynch JJ
AU  - Moran LS
AU  - Fomenkov A
AU  - Slatko BE
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1996 173: 121-127.

PMID- 9034320
VI  - 185
DP  - 1997
TI  - Cloning and expression of AatII restriction-modification system.
PG  - 105-109
AB  - The genes encoding the AatII restriction endonuclease and methylase from Acetobacter aceti
      have been cloned and expressed in Escherichia coli.  The nucleotide sequences of aatIIM and
      aatIIR genes were determined.  The aatIIM and aatIIR genes are 996 bp and 1038 bp,
      respectively, encoding the 331-aa methylase with a predicted molecular mass of 36.9 kDa, and
      the 345-aa AatII restriction endonuclease with a predicted molecular mass of 38.9 kDa.  The
      two genes overlap by 4 base pairs and are transcribed in the same orientation.  The aatIIRM
      genes are located next to a putative gene for plasmid mobilization.  A stable overproducing
      strain was constructed, in which the aatIIM gene was expressed from a pSC101-derived plasmid.
      The aatIIR gene was inserted into a modified T7 expression vector that carries transcription
      terminators upstream from the T7 promoter.  The recombinant AatII restriction endonuclease was
      purified to near homogeneity by chromatography through DEAE Sepharose, Heparin Sepharose, and
      phosphocellulose columns.
AU  - Nwankwo DO
AU  - Maunus RE
AU  - Xu S-Y
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1997 185: 105-109.

PMID- 7959067
VI  - 150
DP  - 1994
TI  - Cloning, analysis and expression of the HindIII R-M-encoding genes.
PG  - 75-80
AB  - The genes encoding the HindIII restriction endonuclease (R.HindIII ENase) and
      methyltransferase (M.HindIII MTase) from Haemophilus influenzae Rd were cloned and expressed
      in Escherichia coli and their nucleotide (nt) sequences were determined. The genes are
      transcribed in the same orientation, with the ENase-encoding gene (hindIIIR) preceding the
      MTase-encoding gene (hindIIIM). The two genes overlap by several nt. The ENase is predicted to
      be 300 amino acids (aa) in length (34950 Da); the MTase is predicted to be 309 aa (35550 Da).
      The HindIII ENase and MTase activities increased approx. 20-fold when the genes were brought
      under the control of an inducible lambda pL promoter. Highly purified HindIII ENase and MTase
      proteins were prepared and their N-terminal aa sequences determined. In H. influenzae Rd, the
      HindIII R-M genes are located between the holC and valS genes; they are not closely linked to
      the HindII R-M genes.
AU  - Nwankwo DO
AU  - Moran LS
AU  - Slatko BE
AU  - Waite-Rees PA
AU  - Dorner LF
AU  - Benner JS
AU  - Wilson GG
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1994 150: 75-80.

PMID- 2456254
VI  - 64
DP  - 1988
TI  - Cloning and expression of the MspI restriction and modification genes.
PG  - 1-8
AB  - The genes for the MspI restriction (R) and modification enzymes (recognition
      sequence CCGG) have been cloned into Escherichia coli using the vector pBR322.
      Clones carrying both genes have been isolated from libraries prepared with
      EcoRI, HindIII and BamHI.  The smallest fragment that encodes both activities
      is a 3.6-kb HindIII fragment.  Plasmids purified from the clones are fully
      resistant to digestion by MspI, indicating that the modification gene is
      functional in E. coli.  The clones remain sensitive to phage infection,
      however, indicating that the endonuclease is dysfunctional.  When the R gene is
      brought under the control of the inducible leftward promoter from phage lambda,
      the level of endonuclease increases and the level of methylase decreases,
      suggesting that the genes are transcribed in opposite directions.
AU  - Nwankwo DO
AU  - Wilson GG
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 64: 1-8.

PMID- 1590763
VI  - 283
DP  - 1992
TI  - Overexpression of the wild-type gene coding for Escherichia coli DNA adenine methylase (dam).
PG  - 745-750
AB  - The gene coding for Escherichia coli dam methylase was isolated from a dam+ K12 strain by the
      PCR method. The gene was subcloned into an overexpression vector under the control of the
      strong lambdaPL promoter. The resultant construct produced the dam methylase at about 20% of
      total cellular protein. Purification of the protein was achieved with two chromatography
      columns and yielded 6 mg of pure methylase per gram cell paste. The methylase readily
      methylates the synthetic dodecamer GACTGATCAGTC containing its recognition sequence. It also
      methylates a synthetic dodecamer containing the EcoRV recognition sequence GATATC. However,
      methyl transfer is to the second adenine in the EcoRV sequence.
AU  - Nwosu VU
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 1992 283: 745-750.

PMID- 2836798
VI  - 16
DP  - 1988
TI  - The cloning, purification and characterization of the EcoRV modification methylase.
PG  - 3705-3720
AB  - The gene for the EcoRV methylase has been cloned into a plasmid under control
      of the strong lambda PL promoter and overexpressed in E. coli.  This plasmid,
      pVIC1, gives reliable overexpression of the methylase at levels of about 20% of
      total protein.  Maximum yields of soluble protein are achieved after about 6
      hours of induction.  If the cells are harvested later than this much of the
      enzyme is found in the pellet fraction following centrifugation.  A two column
      purification scheme using phosphocellulose and Blue-Sepharose chromatography
      has been developed.  This yielded pure methylase in amounts of 5mg per gram E.
      coli cell paste.  The enzyme is monomeric and methylates the first
      deoxyadenosine residue in its recognition sequence GATATC.
AU  - Nwosu VU
AU  - Connolly BA
AU  - Halford SE
AU  - Garnett J
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1988 16: 3705-3720.

PMID- 
VI  - 0
DP  - 2001
TI  - Enhanced DNA cleavage by mercury(II) porphyrin at a low concentration of HaeIII restriction enzyme.
PG  - 932-933
AB  - Mercury(II) porphyrin enhanced DNA cleavage in the presence of 0.2 units per microL of HaeIII
      at which concentration the restriction enzyme
      could not cleave DNA in the absence of the porphyrin. This was ascribed
      to the synergistic effect of the bound Hg2+ ions to DNA and the
      intercalated free base porphyrin, released from the mercury(II)
      porphyrin complex upon binding to DNA, which was confirmed by
      UV-visible and CD spectroscopic measurements.
AU  - Nyarko E
AU  - Tabata M
AU  - Watanabe K
PT  - Journal Article
TA  - Chem. Lett.
JT  - Chem. Lett.
SO  - Chem. Lett. 2001 0: 932-933.

PMID- 28522717
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Undomesticated Bacillus subtilis Strain NCIB 3610.
PG  - e00364-17
AB  - Bacillus subtilis is a Gram-positive bacterium that serves as an important experimental
      system. B. subtilis NCIB 3610 is an undomesticated strain that
      exhibits phenotypes lost from the more common domesticated laboratory strains.
      Here, we announce the complete genome sequence of DK1042, a genetically competent
      derivative of NCIB 3610.
AU  - Nye TM
AU  - Schroeder JW
AU  - Kearns DB
AU  - Simmons LA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00364-17.

PMID- 7607475
VI  - 157
DP  - 1995
TI  - Restriction-modification systems in Lactococcus lactis.
PG  - 13-18
AB  - Several restriction-modification (R-M) systems have been identified in Lactococcus lactis.
      Most of the systems have been plasmid encoded and function as phage-resistance mechanisms. At
      least five different type-II R-M systems, LlaAI, LlaBI, LlaCI, LlaDI and LlaEI, were
      identified in isolates from a mixed Cheddar starter culture. LlaAI and LlaBI recognized the
      DNA sequences 5'-/GATC-3' and 5'-C/TRYAG-3', respectively. The genes coding for the LlaAI
      and LlaBI R-M systems have been cloned and sequenced. The LlaAI R-M system had two genes
      coding for methyltransferases (MTases) and one gene coding for a restriction endonuclease
      (ENase). The MTases showed high homology to the MTases from DpnII. The LlaBI R-M system had
      one gene coding for a MTase and one gene coding for an ENase.
AU  - Nyengaard N
AU  - Vogensen FK
AU  - Josephsen J
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 13-18.

PMID- 8294035
VI  - 136
DP  - 1993
TI  - LlaAI and LlaBI, two type-II restriction endonucleases from Lactococcus lactis subsp. cremoris W9 and W56 recognizing, respectively, 5'-/GATC-3' and 5'-C/TRYAG-3'.
PG  - 371-372
AB  - Two type-II restriction endonucleases have been purified from Lactococus lactis subsp.
      cremoris W9 and W56, the strains isolated from a mixed Cheddar starter. Their characterization
      showed that LlaAI was an isoschizomer of MboI from Moraxella bovis with the cleaving sequence
      5'-/GATC-3' being sensitive to methylation of the adenine residue; LlaBI was an isoschizomer
      to SfcI from Streptococcus faecium with the cleaving sequence 5'C/TRYAG-3'. Both LlaAI and
      LlaBI restriction-modification (R-M) systems are encoded by the plasmids, respectively, pFW094
      and pJW563, protecting the harboring strain against phage attack.
AU  - Nyengaard N
AU  - Vogensen FK
AU  - Josephsen J
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1993 136: 371-372.

PMID- 8795244
VI  - 62
DP  - 1996
TI  - Cloning and analysis of the restriction-modification system LlaBI, a bacteriophage resistance system from Lactococcus lactis subsp. cremoris W56.
PG  - 3494-3498
AB  - The genes coding for the type II restriction-modification (R/M) system LlaBI, which recognized
      the sequence 5'-C/TRYAG-3', have been cloned from a plasmid in Lactococcus lactis subsp.
      cremoris W56 and sequenced.  The DNA sequence predicts an endonuclease of 299 amino acids (33
      kDa) and a methylase of 580 amino acids (65 kDa).  A 4.0-kb HindIII fragment in pSA3 was able
      to restrict bacteriophages, showing that the cloned R/M system can function as a phage defense
      mechanism in L. lactis.
AU  - Nyengaard NR
AU  - Falkenberg-Klok J
AU  - Josephsen J
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1996 62: 3494-3498.

PMID- 24069019
VI  - 4
DP  - 2013
TI  - Coupled high-throughput functional screening and next generation sequencing for identification of plant polymer decomposing enzymes in metagenomic libraries.
PG  - 282
AB  - Recent advances in sequencing technologies generate new predictions and
      hypotheses about the functional roles of environmental microorganisms. Yet, until
      we can test these predictions at a scale that matches our ability to generate
      them, most of them will remain as hypotheses. Function-based mining of
      metagenomic libraries can provide direct linkages between genes, metabolic traits
      and microbial taxa and thus bridge this gap between sequence data generation and
      functional predictions. Here we developed high-throughput screening assays for
      function-based characterization of activities involved in plant polymer
      decomposition from environmental metagenomic libraries. The multiplexed assays
      use fluorogenic and chromogenic substrates, combine automated liquid handling and
      use a genetically modified expression host to enable simultaneous screening of
      12,160 clones for 14 activities in a total of 170,240 reactions. Using this
      platform we identified 374 (0.26%) cellulose, hemicellulose, chitin, starch,
      phosphate and protein hydrolyzing clones from fosmid libraries prepared from
      decomposing leaf litter. Sequencing on the Illumina MiSeq platform, followed by
      assembly and gene prediction of a subset of 95 fosmid clones, identified a broad
      range of bacterial phyla, including Actinobacteria, Bacteroidetes, multiple
      Proteobacteria sub-phyla in addition to some Fungi. Carbohydrate-active enzyme
      genes from 20 different glycoside hydrolase (GH) families were detected. Using
      tetranucleotide frequency (TNF) binning of fosmid sequences, multiple enzyme
      activities from distinct fosmids were linked, demonstrating how
      biochemically-confirmed functional traits in environmental metagenomes may be
      attributed to groups of specific organisms. Overall, our results demonstrate how
      functional screening of metagenomic libraries can be used to connect microbial
      functionality to community composition and, as a result, complement large-scale
      metagenomic sequencing efforts.
AU  - Nyyssonen M
AU  - Tran HM
AU  - Karaoz U
AU  - Weihe C
AU  - Hadi MZ
AU  - Martiny JB
AU  - Martiny AC
AU  - Brodie EL
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2013 4: 282.

PMID- 29301893
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of a Red-Pigmented Janthinobacterium sp. Native to the Hudson Valley Watershed.
PG  - e01429-17
AB  - Water samples from the Hudson Valley watershed indicate that the area is host to  many
      violacein-producing bacterial isolates. Here, we report the draft
      whole-genome sequence of Janthinobacterium sp. strain BJB412, an isolate lacking
      violacein production yet containing genes responsible for prodigiosin, biofilm
      production, and quorum sensing, like its purple-pigmented counterparts.
AU  - O'Brien K
AU  - Perron GG
AU  - Jude BA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01429-17.

PMID- 26489930
VI  - 16
DP  - 2015
TI  - Pangenome analysis of Bifidobacterium longum and site-directed mutagenesis through by-pass of restriction-modification systems.
PG  - 832
AB  - BACKGROUND: Bifidobacterial genome analysis has provided insights as to how these
      gut commensals adapt to and persist in the human GIT, while also revealing
      genetic diversity among members of a given bifidobacterial (sub)species.
      Bifidobacteria are notoriously recalcitrant to genetic modification, which
      prevents exploration of their genomic functions, including those that convey
      (human) health benefits. METHODS: PacBio SMRT sequencing was used to determine
      the whole genome seqeunces of two B. longum subsp. longum strains. The B. longum
      pan-genome was computed using PGAP v1.2 and the core B. longum phylogenetic tree
      was constructed using a maximum-likelihood based approach in PhyML v3.0.
      M.blmNCII was cloned in E. coli and an internal fragment if arfBarfB was cloned
      into pORI19 for insertion mutagenesis. RESULTS: In this study we present the
      complete genome sequences of two Bifidobacterium longum subsp. longum strains.
      Comparative analysis with thirty one publicly available B. longum genomes allowed
      the definition of the B. longum core and dispensable genomes. This analysis also
      highlighted differences in particular metabolic abilities between members of the
      B. longum subspecies infantis, longum and suis. Furthermore, phylogenetic
      analysis of the B. longum core genome indicated the existence of a novel
      subspecies. Methylome data, coupled to the analysis of restriction-modification
      systems, allowed us to substantially increase the genetic accessibility of B.
      longum subsp. longum NCIMB 8809 to a level that was shown to permit site-directed
      mutagenesis. CONCLUSIONS: Comparative genomic analysis of thirty three B. longum
      representatives revealed a closed pan-genome for this bifidobacterial species.
      Phylogenetic analysis of the B. longum core genome also provides evidence for a
      novel fifth B. longum subspecies. Finally, we improved genetic accessibility for
      the strain B. longum subsp. longum NCIMB 8809, which allowed the generation of a
      mutant of this strain.
AU  - O'Callaghan A
AU  - Bottacini F
AU  - O'Connell-Motherway M
AU  - van Sinderen D
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2015 16: 832.

PMID- 28495762
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of 25 Listeria monocytogenes Isolates Associated with Human Clinical Listeriosis in Ireland.
PG  - e00184-17
AB  - Listeria monocytogenes is a Gram-positive opportunistic pathogen that is the causative agent
      of listeriosis. Here, we report the draft genome sequences of 25
      L. monocytogenes strains isolated from patients with clinical listeriosis in the
      Republic of Ireland between 2013 and 2015.
AU  - O'Callaghan A
AU  - Hilliard A
AU  - Morgan CA
AU  - Culligan EP
AU  - Leong D
AU  - DeLappe N
AU  - Hill C
AU  - Jordan K
AU  - Cormican M
AU  - Gahan CGM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00184-17.

PMID- 21690406
VI  - 108
DP  - 2011
TI  - Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved host-colonization factor.
PG  - 11217-11222
AB  - Development of the human gut microbiota commences at birth, with bifidobacteria being among
      the first colonizers of the sterile newborn gastrointestinal tract. To date, the genetic basis
      of Bifidobacterium colonization and persistence remains poorly understood. Transcriptome
      analysis of the Bifidobacterium breve UCC2003 2.42-Mb genome in a murine colonization model
      revealed differential expression of a type IVb tight adherence (Tad) pilus-encoding gene
      cluster designated "tad(2003)." Mutational analysis demonstrated that the tad(2003) gene
      cluster is essential for efficient in vivo murine gut colonization, and immunogold
      transmission electron microscopy confirmed the presence of Tad pili at the poles of B. breve
      UCC2003 cells. Conservation of the Tad pilus-encoding locus among other B. breve strains and
      among sequenced Bifidobacterium genomes supports the notion of a ubiquitous pili-mediated host
      colonization and persistence mechanism for bifidobacteria.
AU  - O'Connell-Motherway M et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2011 108: 11217-11222.

PMID- 21261927
VI  - 2
DP  - 2009
TI  - Overcoming the restriction barrier to plasmid transformation and targeted mutagenesis in Bifidobacterium breve UCC2003.
PG  - 321-332
AB  - In silico analysis of the Bifidobacterium breve UCC2003 genome predicted two distinct loci,
      which encode three different restriction/modification systems, each comprising a modification
      methylase and a restriction endonuclease.  Based on sequence homology and observed protection
      against restriction we conclude that the first restriction endonuclease, designated BbrI, is
      an isoschizomer of BbeI, the second, BbrII, is a neoschizomer of SalI, while the third,
      BbrIII, is an isoschizomer of PstI.  Expression of each of the B. breve UCC2003
      methylase-encoding genes in B. breve JCM 7017 established that BbrII and BbrIII are active and
      restrict incoming DNA.  By exploiting knowledge on restriction/modification in B. breve
      UCC2003 we successfully increased the transformation efficiency to a level that allows the
      reliable generation of mutants by homologous recombination using a non-replicative plasmid.
AU  - O'Connell-Motherway M
AU  - O'Driscoll J
AU  - Fitzgerald GF
AU  - van Sinderen D
PT  - Journal Article
TA  - Micro. Biotech.
JT  - Micro. Biotech.
SO  - Micro. Biotech. 2009 2: 321-332.

PMID- 24743599
VI  - 9
DP  - 2014
TI  - Identification of Restriction-Modification Systems of Bifidobacterium animalis subsp. lactis CNCM I-2494 by SMRT Sequencing and Associated Methylome Analysis.
PG  - e94875
AB  - Bifidobacterium animalis subsp. lactis CNCM I-2494 is a component of a commercialized
      fermented dairy product for which beneficial effects on health has
      been studied by clinical and preclinical trials. To date little is known about
      the molecular mechanisms that could explain the beneficial effects that
      bifidobacteria impart to the host. Restriction-modification (R-M) systems have
      been identified as key obstacles in the genetic accessibility of bifidobacteria,
      and circumventing these is a prerequisite to attaining a fundamental
      understanding of bifidobacterial attributes, including the genes that are
      responsible for health-promoting properties of this clinically and industrially
      important group of bacteria. The complete genome sequence of B. animalis subsp.
      lactis CNCM I-2494 is predicted to harbour the genetic determinants for two type
      II R-M systems, designated BanLI and BanLII. In order to investigate the
      functionality and specificity of these two putative R-M systems in B. animalis
      subsp. lactis CNCM I-2494, we employed PacBio SMRT sequencing with associated
      methylome analysis. In addition, the contribution of the identified R-M systems
      to the genetic accessibility of this strain was assessed.
AU  - O'Connell-Motherway M
AU  - Watson D
AU  - Bottacini F
AU  - Clark TA
AU  - Roberts RJ
AU  - Korlach J
AU  - Garault P
AU  - Chervaux C
AU  - van-Hylckama-Vlieg JE
AU  - Smokvina T
AU  - van-Sinderen D
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2014 9: e94875.

PMID- 26450742
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Rheinheimera sp. KL1, Isolated from a Freshwater Lake in Southern Saskatchewan, Canada.
PG  - e01177-15
AB  - Rheinheimera sp. KL1 was isolated from an algal bloom in Katepwa Lake, Saskatchewan, Canada.
      The isolate shares genetic and physiological similarities with Rheinheimera tangshanensis. The
      genome is estimated to be 4,295,060 bp in length with a GC content of 46.37%. Sequence
      analysis suggests the strain carries a previously uncharacterized prophage.
AU  - O'Connor BR
AU  - Perry BJ
AU  - Yost CK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01177-15.

PMID- 6299889
VI  - 20
DP  - 1982
TI  - Expression of the EcoRI restriction-modification system and the construction of positive-selection cloning vectors.
PG  - 219-229
AB  - The genes encoding the EcoRI restriction-modification (R/M) system have been
      separately cloned onto compatible plasmids.  We have shown that the EcoRI
      restriction gene is expressed in the total absence of methylase enzyme and
      confirmed that a temperature-sensitive mutant is defective in EcoRI
      modification activity at higher temperatures.  Insertion of transcriptional
      terminators into the restriction gene had no detectable effect on EcoRI
      modification activity.  This strongly suggests that a separate promoter exists
      for the methylase gene.  Analysis of the published sequence shows that the
      methylase gene promoter may overlap with the COOH-terminal region of the
      endonuclease structural gene.  The temperature-sensitive EcoRI system has been
      exploited in the construction of two plasmid cloning vectors, pLV57 and pLV59,
      which can be used to select positively for transformants bearing recombinant
      plasmids; cloning of a DNA fragment into pLV57 or pLV59 at the unique HindIII,
      BglII, or PstI sites inactivates the EcoRI restriction gene and permits the
      hybrid plasmid to survive at 37C.  The temperature-sensitive modification
      activity of these vectors should also facilitate the introduction of EcoRI
      linkers into DNA cloned in this way.
AU  - O'Connor CD
AU  - Humphreys GO
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1982 20: 219-229.

PMID- 6091034
VI  - 12
DP  - 1984
TI  - RsrII - a novel restriction endonuclease with a heptanucleotide recognition site.
PG  - 6701-6708
AB  - A sequence-specific endonuclease present in extracts of Rhodopseudomonas
      sphaeroides 630 has been purified and characterized.  The enzyme, RsrII,
      recognises and cleaves the palindromic heptanucleotide sequence:  5' -
      CG^G(A/T)CCG - 3' By virtue of its unusual specificity, RsrII cuts most DNA
      molecules very infrequently which should facilitate the physical mapping of
      large genomes.
AU  - O'Connor CD
AU  - Metcalf E
AU  - Wrighton CJ
AU  - Harris TJR
AU  - Saunders JR
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1984 12: 6701-6708.

PMID- 2443481
VI  - 169
DP  - 1987
TI  - Highly repressible expression system for cloning genes that specify potentially toxic proteins.
PG  - 4457-4462
AB  - A highly repressible expression vector system that allows the cloning of potentially
      deleterious genes has been constructed.  Undesired expression of a cloned gene was prevented
      (I) at the level of initiation of transcription, by the presence of the strong but highly
      repressible leftward promoter of bacteriophage lambda, lambda PL, and (ii) at the level of
      transcript elongation or translation, through synthesis of antisense RNA complementary to the
      mRNA of the cloned gene.  The system was tested by measuring the inhibition of expression of
      traT, the gene for the TraT major outer membrane lipoprotein.  Direct detection and functional
      assays indicated that an essentially complete inhibition of traT expression was obtained.  As
      a further test of the system, the gene encoding the EcoRI restriction endonuclease was cloned
      in the absence of the gene of the corresponding protective EcoRI modification methylase.
      Transformants harboring this construct were only viable when both repression controls were
      operational.
AU  - O'Connor CD
AU  - Timmis KN
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1987 169: 4457-4462.

PMID- 2828860
VI  - 155
DP  - 1987
TI  - RsrII:  a restriction endonuclease with a heptanucleotide recognition sequence.
PG  - 11-15
AB  - The purple nonsulfur photosynthetic bacterium Rhodopseudomonas sphaeroides 630
      produces two restriction endonucleases, RsrI and RsrII, that can be isolated
      free of contaminating endonucleases and exonucleases.  Although RsrI is an
      isoschizomer of the well-characterized Escherichia coli restriction enzyme
      EcoRI, RsrII is the only enzyme described to date that recognizes and cleaves a
      palindromic heptanucleotide sequence.  We describe here an improved procedure
      for the purification of RsrII and discuss some uses of the enzymes.
AU  - O'Connor CD
AU  - Walker JNB
AU  - Saunders JR
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1987 155: 11-15.

PMID- 21873199
VI  - 108
DP  - 2011
TI  - Minimization of the Legionella pneumophila genome reveals chromosomal regions involved in host range expansion.
PG  - 14733-14740
AB  - Legionella pneumophila is a bacterial pathogen of amoebae and humans.
      Intracellular growth requires a type IVB secretion system that
      translocates at least 200 different proteins into host cells. To
      distinguish between proteins necessary for growth in culture and those
      specifically required for intracellular replication, a screen was
      performed to identify genes necessary for optimal growth in nutrient-rich
      medium. Mapping of these genes revealed that the L. pneumophila chromosome
      has a modular architecture consisting of several large genomic islands
      that are dispensable for growth in bacteriological culture. Strains
      lacking six of these regions, and thus 18.5% of the genome, were viable
      but required secondary point mutations for optimal growth. The
      simultaneous deletion of five of these genomic loci had no adverse effect
      on growth of the bacterium in nutrient-rich media. Remarkably, this
      minimal genome strain, which lacked 31% of the known substrates of the
      type IVB system, caused only marginal defects in intracellular growth
      within mouse macrophages. In contrast, deletion of single regions reduced
      growth within amoebae. The importance of individual islands, however,
      differed among amoebal species. The host-specific requirements of these
      genomic islands support a model in which the acquisition of foreign DNA
      has broadened the L. pneumophila host range.
AU  - O'Connor TJ
AU  - Adepoju Y
AU  - Boyd D
AU  - Isberg RR
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2011 108: 14733-14740.

PMID- 23469340
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Enterococcus faecalis PC1.1, a Candidate Probiotic Strain Isolated from Human Feces.
PG  - e00160-12
AB  - is commonly isolated from the gastrointestinal tract of healthy infants and adults, where it
      contributes to host health and well-being. We describe here the
      draft genome sequence of PC1.1, a candidate probiotic strain isolated from human
      feces.
AU  - O'Cuiv P
AU  - Klaassens ES
AU  - Smith WJ
AU  - Mondot S
AU  - Durkin AS
AU  - Harkins DM
AU  - Foster L
AU  - McCorrison J
AU  - Torralba M
AU  - Nelson KE
AU  - Morrison M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00160-12.

PMID- 24503986
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Enterococcus faecium PC4.1, a Clade B Strain Isolated from Human Feces.
PG  - e00022-14
AB  - Enterococcus faecium is commonly isolated from the human gastrointestinal tract;  however,
      important intraspecies variations exist with relevance for host health
      and well-being. Here, we describe the draft genome sequence of E. faecium PC4.1,
      a clade B strain isolated from human feces.
AU  - O'Cuiv P
AU  - Klaassens ES
AU  - Smith WJ
AU  - Mondot S
AU  - Durkin AS
AU  - Harkins DM
AU  - Foster L
AU  - McCorrison J
AU  - Torralba M
AU  - Nelson KE
AU  - Morrison M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00022-14.

PMID- 25953187
VI  - 3
DP  - 2015
TI  - Genome Sequence of Halomonas sp. Strain KO116, an Ionic Liquid-Tolerant Marine Bacterium Isolated from a Lignin-Enriched Seawater Microcosm.
PG  - e00402-15
AB  - Halomonas sp. strain KO116 was isolated from Nile Delta Mediterranean Sea surface water
      enriched with insoluble organosolv lignin. It was further screened for
      growth on alkali lignin minimal salts medium agar. The strain tolerates the ionic
      liquid 1-ethyl-3-methylimidazolium acetate. Its complete genome sequence is
      presented in this report.
AU  - O'Dell KB
AU  - Woo HL
AU  - Utturkar S
AU  - Klingeman D
AU  - Brown SD
AU  - Hazen TC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00402-15.

PMID- 24435863
VI  - 2
DP  - 2014
TI  - The Genome of the Predominant Equine Lactobacillus Species, Lactobacillus equi, Is Reflective of Its Lifestyle Adaptations to an Herbivorous Host.
PG  - e01155-13
AB  - We report the draft genome sequence of Lactobacillus equi strain DPC6820, isolated from equine
      feces. L. equi is a predominant Lactobacillus species in the
      horse hindgut microbiota. An examination of the genome identified genes and
      enzymes highlighting L. equi adaptations to the herbivorous gastrointestinal
      tract of the horse, including fructan hydrolases. This genome sequence may help
      us further understand the microbial ecology of the equine hindgut and the
      influence lactobacilli have on it.
AU  - O'Donnell MM
AU  - Harris HM
AU  - O'Toole PW
AU  - Ross RP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01155-13.

PMID- 16135222
VI  - 57
DP  - 2005
TI  - A dichotomous epigenetic mechanism governs expression of the LlaJI restriction/modification system.
PG  - 1532-1544
AB  - The LlaJI restriction/modification (R/M) system is comprised of two 5mC MTase-encoding genes,
      llaJIM1 and llaJIM2, and two genes required for
      restriction activity, llaJIR1 and llaJIR2. Here, we report the
      molecular mechanism by which this R/M system is transcriptionally
      regulated. The recognition sequence for the LlaJI MTases was deduced to
      be 5'GACGC'3 for M1.LlaJI and 5'GCGTC'3 for M2.LlaJI, thus together
      constituting an asymmetric complementary recognition site. Two
      recognition sequences for both LlaJI MTases are present within the
      LlaJI promoter region, indicative of an epigenetic role. Following in
      vivo analysis of expression of the LlaJI promoter, we established that
      both LlaJI MTases were required for complete transcriptional
      repression. A mutational analysis and DNA binding studies of this
      promoter revealed that the methylation of two specific cytosines by
      M2.LlaJI within this region was required to trigger the specific and
      high affinity binding of M1.LlaJI, which serves to regulate expression
      of the LlaJI operon. This regulatory system therefore represents the
      amalgamation of an epigenetic stimulation coupled to the formation of a
      MTase/repressor:promoter complex.
AU  - O'Driscoll J
AU  - Fitzgerald GF
AU  - van Sinderen D
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2005 57: 1532-1544.

PMID- 15345443
VI  - 70
DP  - 2004
TI  - Lactococcal plasmid pNP40 encodes a novel, temperature-sensitive restriction-modification system.
PG  - 5546-5556
AB  - A novel restriction-modification system, designated LlaJI, was identified on pNP40, a
      naturally occurring 65-kb plasmid from Lactococcus lactis. The system comprises four adjacent
      similarly oriented genes that are predicted to encode two m(5)C methylases and two restriction
      endonucleases. The LlaJI system, when cloned into a low-copy-number vector, was shown to
      confer resistance against representatives of the three most common lactococcal phage species.
      This phage resistance phenotype was found to be strongly temperature dependent, being most
      effective at 19 degrees C. A functional analysis confirmed that the predicted
      methylase-encoding genes, llaJIM1 and llaJIM2, were both required to mediate complete
      methylation, while the assumed restriction enzymes, specified by llaJIR1 and llaJIR2, were
      both necessary for the complete restriction phenotype. A Northern blot analysis revealed that
      the four LlaJI genes are part of a 6-kb operon and that the relative abundance of the
      LlaJI-specific mRNA in the cells does not appear to contribute to the observed
      temperature-sensitive profile. This was substantiated by use of a LlaJI promoter-lacZ fusion,
      which further revealed that the LlaJI operon appears to be subject to transcriptional
      regulation by an as yet unidentified element(s) encoded by pNP40.
AU  - O'Driscoll J
AU  - Glynn F
AU  - Cahalane O
AU  - O'Connell-Motherway M
AU  - Fitzgerald GF
AU  - van Sinderen D
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2004 70: 5546-5556.

PMID- 16952955
VI  - 188
DP  - 2006
TI  - Sequence Analysis of the Lactococcal Plasmid pNP40: a Mobile Replicon for Coping with Environmental Hazards.
PG  - 6629-6639
AB  - The conjugative lactococcal plasmid pNP40, identified in Lactococcus lactis subsp.
      diacetylactis DRC3, possesses a potent complement of bacteriophage resistance systems, which
      has stimulated its application as a fitness-improving, food-grade genetic element for
      industrial starter cultures. The complete sequence of this plasmid allowed the mapping of
      previously known functions including replication, conjugation, bacteriocin resistance, heavy
      metal tolerance, and bacteriophage resistance. In addition, functions for cold shock
      adaptation and DNA damage repair were identified, further confirming pNP40's contribution to
      environmental stress protection. A plasmid cointegration event appears to have been part of
      the evolution of pNP40, resulting in a "stockpiling" of bacteriophage resistance systems.
AU  - O'Driscoll J
AU  - Glynn F
AU  - Fitzgerald GF
AU  - van Sinderen D
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2006 188: 6629-6639.

PMID- 16646963
VI  - 6
DP  - 2006
TI  - A genetic dissection of the LlaJI restriction cassette reveals insights on a novel bacteriophage resistance system.
PG  - 40
AB  - ABSTRACT: BACKGROUND: Restriction/modification systems provide the dual function of protecting
      host DNA against restriction by methylation of appropriate bases within their recognition
      sequences, and restriction of foreign invading un-methylated DNA, such as promiscuous plasmids
      or infecting bacteriphage. The plasmid-encoded LlaJI restriction/modification system from
      Lactococcus lactis recognizes an asymmetric, complementary DNA sequence, consisting of
      5-GACGC-3 in one strand and 5-GCGTC-3 in the other and provides a prodigious barrier to
      bacteriophage infection. LlaJI is comprised of four similarly oriented genes, encoding two
      5mC-MTases (M1.LlaJI and M2.LlaJI) and two subunits responsible for restriction activity
      (R1.LlaJI and R2.LlaJI). Here we employ a detailed genetic analysis of the LlaJI restriction
      determinants in an attempt to characterize mechanistic features of this unusual
      hetero-oligomeric endonuclease. RESULTS: Detailed bioinformatic analysis confirmed the
      presence of a conserved GTP binding and hydrolysis domain within the C-terminal half of the
      R1.LlaJI amino acid sequence whilst the N-terminal half appeared to be entirely unique. This
      domain architecture was homologous with that of the B subunit of the GTP-dependent,
      methyl-specific McrBC endonuclease from E.coli K-12. R1.LlaJI did not appear to contain a
      catalytic centre, whereas this conserved motif; PD...D/EXK, was clearly identified within the
      amino acid sequence for R2.LlaJI. Both R1.LlaJI and R2.LlaJI were found to be absolutely
      required for detectable LlaJI activity in vivo. The LlaJI restriction subunits were purified
      and examined in vitro, which allowed the assignment of R1.LlaJI as the sole specificity
      determining subunit, whilst R2.LlaJI is believed to mediate DNA cleavage. CONCLUSIONS: The
      hetero-subunit structure of LlaJI, wherein one subunit mediates DNA binding whilst the other
      subunit is predicted to catalyze strand hydrolysis distinguishes LlaJI from previously
      characterized restriction-modification systems. Furthermore, this distinction is accentuated
      by the fact that whilst LlaJI behaves as a conventional Type IIA system in vivo, in that it
      restricts un-methylated DNA, it resembles the Type IV McrBC endonuclease, an enzyme specific
      for methylated DNA. A number of similar restriction determinants were identified in the
      database and it is likely LlaJI together with these homologous systems, comprise a new subtype
      of the Type II class incorporating features of Type II and Type IV systems.
AU  - O'Driscoll J
AU  - Heiter DF
AU  - Wilson GG
AU  - Fitzgerald GF
AU  - Roberts R
AU  - van Sinderen D
PT  - Journal Article
TA  - BMC Microbiol.
JT  - BMC Microbiol.
SO  - BMC Microbiol. 2006 6: 40.

PMID- 9288926
VI  - 247
DP  - 1997
TI  - Expression, purification, mass spectrometry, crystallization and multiwavelength anomalous diffraction of selenomethionyl PvuII DNA methyltransferase (cytosine-N4-specific).
PG  - 1009-1018
AB  - The type II DNA-methyltransferase (cytosine N4-specific) M.PvuII was overexpressed in
      Escherichia coli, starting from the internal translation initiator at Met14.  Selenomethionine
      was efficiently incorporated into this short form of M.PvuII by a strain prototrophic for
      methionine.  Both native and selenomethionyl M.PvuII were purified to apparent homogeneity by
      a two-column chromatography procedure.  The yield of purified protein was approximately 1.8
      mg/g bacterial paste.  Mass spectrometry analysis of selenomethionyl M.PvuII revealed three
      major forms that probably differ in the degree of selenomethionine incorporation and the
      extent of selenomethionine oxidation.  Amino acid sequencing and mass spectrometry analysis of
      selenomethionine-containing peptides suggests that Met30, Met51, and Met261 were only
      partially replaced by selenomethionine.  Furthermore, amino acid 261 may be preferentially
      oxidized in both native and selenomethionyl form.  Selenomethionyl and native M.PvuII were
      crystallized separately as binary complexes of the methyl donor S-adenosyl-L-methionine in the
      monoclinic space group P21.  Two complexes were present per asymmetric unit.  Six out of nine
      selenium positions (per molecule), including the three that were found to be partially
      substituted, were identified crystallographically.
AU  - O'Gara M
AU  - Adams GM
AU  - Gong W
AU  - Kobayashi R
AU  - Blumenthal RM
AU  - Cheng X
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1997 247: 1009-1018.

PMID- 9783745
VI  - 5
DP  - 1998
TI  - Structures of HhaI methyltransferase complexed with substrates containing mismatches at the target base.
PG  - 872-877
AB  - Three structures have been determined for complexes between HhaI methyltransferase (M.HhaI)
      and oligonucleotides containing a G:A, G:U or G:AP (AP = abasic or apurinic/apyrimidinic)
      mismatch at the target base pair. The mismatched adenine, uracil and abasic site are all
      flipped out of the DNA helix and located in the enzyme's active-site pocket, adopting the
      same conformation as in the flipped-out normal substrate. These results, particularly the
      flipped-out abasic deoxyribose sugar, provide insight into the mechanism of base flipping. If
      the process involves the protein pushing the base out of the helix, then the push must take
      place not on the base, but rather on the sugar-phosphate backbone. Thus rotation of the DNA
      backbone is probably the key to base flipping.
AU  - O'Gara M
AU  - Horton JR
AU  - Roberts RJ
AU  - Cheng X
PT  - Journal Article
TA  - Nat. Struct. Biol.
JT  - Nat. Struct. Biol.
SO  - Nat. Struct. Biol. 1998 5: 872-877.

PMID- 8800212
VI  - 261
DP  - 1996
TI  - Enzymatic C5-cytosine methylation of DNA: Mechanistic implications of new crystal structures for HhaI methyltransferase-DNA-AdoHcy complexes.
PG  - 634-645
AB  - The refined crystal structures of HhaI methyltransferase complexed with cognate unmethylated
      or methylated DNA together with S-adenosyl-L-homocysteine, along with the previously-solved
      binary and covalent ternary structures, offer a detailed picture of the active site at
      individual stages throughout the reaction cycle.  This picture supports and extends a proposed
      mechanism for C5-cytosine methylation that may be general for the whole family of C5-cytosine
      methyltransferases.  The structures of the two new complexes have been refined to
      crystallographic R-factors of 0.189 and 0.178, respectively, at 2.7 A resolution.  We observe
      that both unmethylated 2'-deoxycytidine and 5-methyl-2'-deoxycytidine flip out of the DNA
      helix and fit into the active site of the enzyme.  The catalytic sulfur atom of Cys81
      interacts strongly with C6.  The C5 methyl group of the flipped 5-methyl-2'-deoxycytidine is
      bent ~50o out of the plane of the cytosine ring and towards the sulfur atom of
      S-adenosyl-L-homocysteine.  This unusual position is probably due to partial sp3 character at
      C5 and C6 and to steric effects of the conserved amino acid residues Pro80 and Cys81.  Two
      water molecules are held near the hydrophobic edge (C5 and C6) of the flipped cytosine by two
      conserved amino acid residues (Gln82 and Asn304) and the phosphoryl oxygen atom of the
      phosphate group 3' to the flipped nucleotide, and one of them may serve as the general base
      for eliminating the proton from C5.  Protonation of the cytosine N3 during the methylation
      reaction may involve Glu119, which itself might be protonated via a water-mediated interaction
      between the terminal carboxyl group of Glu119 and the amino group of the methionine moiety of
      S-adenosyl-L-methionine.  The cofactor thus plays two key roles in the reaction.
AU  - O'Gara M
AU  - Klimasauskas S
AU  - Roberts RJ
AU  - Cheng X
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1996 261: 634-645.

PMID- 7607477
VI  - 157
DP  - 1995
TI  - Structure-based sequence alignment of three AdoMet-dependent DNA methyltransferases.
PG  - 135-138
AB  - M.HhaI, M.TaqI and COMT are DNA methyltransferases (MTases) which catalyze the transfer of a
      methyl group from the cofactor AdoMet to C5 of cytosine, to N6 of adenine and to a hydroxyl
      group of catechol, respectively.  The larger catalytic domains of the bilobal proteins, M.HhaI
      and M.TaqI, and the entire single domain of COMT have an alpha/beta structure containing a
      mixed central beta-sheet.  These domains have very similar folding.  By allowing appropriate
      'insertions' or 'deletions' in the bakbones of the three structures, it was possible to
      find more conserved motifs in M.TaqI and COMT.  The similarity in protein folding and the
      equivalence of amino-acid sequences revealed by the structural alignment indicate that many
      AdoMet-dependent MTases may share a common catalytic domain structure.
AU  - O'Gara M
AU  - McCloy K
AU  - Malone T
AU  - Cheng X
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 135-138.

PMID- 8918941
VI  - 263
DP  - 1996
TI  - A structural basis for the preferential binding of hemimethylated DNA by HhaI DNA methyltransferase.
PG  - 597-606
AB  - The crystal structure of HhaI methyltransferase complexed with non-palindromic duplex DNA,
      containing a hemimethylated recognition sequence, and with the cofactor analog
      S-adenosyl-L-homocysteine (AdoHcy), has been determined.  The structure provides an
      explanation for the stronger affinities of DNA methyltransferases for hemimethylated DNA than
      for unmethylated or fully methylated DNA in the presence of AdoHcy.  The unmethylated target
      2'-deoxycytidine flips out of the DNA helix and the CH group at position 5 makes van der
      Waals' contacts with the sulfur atom of AdoHcy.  Selectivity/preference for hemimethylated
      over fully methylated DNA may thus reflect interactions among the chemical substituent (H or
      CH3) at the C5 position of the flipped cytosine, protein and the bound AdoHcy.  The
      5-methyl-2'-deoxycytidine on the complementary strand remains in the DNA helix, with the
      methyl group almost perpendicular to the carboxylate group of Glu239, which is part of the
      sequence recognition loop.  Thus, selectivity/preference for hemimethylated over unmethylated
      DNA appears to result largely from van der Waals' contacts between the planar Glu239
      carboxylate and the methyl group of the 5-methyl-2'-deoxycytidine.  Furthermore, the positive
      electrostatic potential originating from the bound AdoHcy extends to the DNA phosphate groups
      flanking the flipped cytosine.  The increased binding to DNA by long-range electrostatic
      interactions should also occur with the methyl donor S-adenosyl-L-methionine.
AU  - O'Gara M
AU  - Roberts RJ
AU  - Cheng X
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1996 263: 597-606.

PMID- 10080885
VI  - 287
DP  - 1999
TI  - Structure of a binary complex of HhaI methyltransferase with S-adenosyl-L-methionine formed in the presence of a short non-specific DNA oligonucleotide.
PG  - 201-209
AB  - We have determined a structure for a complex formed between HhaI methyltransferase and
      S-adenosyl-L-methionine in the presence of a non-specific short oligonucleotide.  M.HhaI binds
      to the non-specific short oligonucleotides in solution.  Although no DNA is incorporated in
      the crystal, AdoMet binds in a primed orientation, identical with that observed in the ternary
      complex of the enzyme, cognate DNA, and AdoMet or S-adenosyl-L-homocysteine.  This orientation
      differs from the previously observed unprimed orientation in the M.HhaI-AdoMet binary complex,
      where the S+-CH3 unit of AdoMet is protected by a favorable cation-pi interaction with Trp41.
      The structure suggests that the presence of DNA can guide AdoMet into the primed orientation.
      These results shed new light on the proposed ordered mechanism of binding and explains the
      stable association between Ado-Met and M.HhaI.
AU  - O'Gara M
AU  - Zhang X
AU  - Roberts RJ
AU  - Cheng X
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1999 287: 201-209.

PMID- 28360181
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Three Cellulolytic Bacillus licheniformis Strains Isolated from Imperial Geyser, Amphitheater Springs, and Whiterock Springs inside  Yellowstone National Park.
PG  - e00065-17
AB  - Novel cellulolytic microorganisms are becoming more important for rapidly growing biofuel
      industries. This paper reports the draft genome sequences of Bacillus licheniformis strains
      YNP2-TSU, YNP3-TSU, and YNP5-TSU. These cellulolytic isolates were collected from several
      hydrothermal features inside Yellowstone National Park.
AU  - O'Hair JA
AU  - Li H
AU  - Thapa S
AU  - Scholz M
AU  - Zhou S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00065-17.

PMID- 28254968
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Bacillus licheniformis Strain YNP1-TSU Isolated from Whiterock Springs in Yellowstone National Park.
PG  - e01496-16
AB  - Novel cellulolytic microorganisms can potentially influence second-generation biofuel
      production. This paper reports the draft genome sequence of Bacillus
      licheniformis strain YNP1-TSU, isolated from hydrothermal-vegetative microbiomes
      inside Yellowstone National Park. The assembled sequence contigs predicted 4,230
      coding genes, 66 tRNAs, and 10 rRNAs through automated annotation.
AU  - O'Hair JA
AU  - Li H
AU  - Thapa S
AU  - Scholz MB
AU  - Zhou S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01496-16.

PMID- 29650585
VI  - 6
DP  - 2018
TI  - Draft Genomic Sequences of Chromobacterium sp. nov. Strains MWU13-2610 and MWU14-2602, Isolated from Wild Cranberry Bogs in Massachusetts.
PG  - e00332-18
AB  - Chromobacterium sp. nov. strains MWU13-2610 and MWU14-2602 were isolated from cranberry bogs
      in the Cape Cod National Seashore. These nonpigmented bacteria
      represent two new presumptive species of the rapidly growing genus
      Chromobacterium Gene homologs are present for multiple antibiotic resistance,
      virulence functions, and prophages.
AU  - O'Hara-Hanley K
AU  - Harrison A
AU  - Soby SD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00332-18.

PMID- 25695747
VI  - 10
DP  - 2015
TI  - Analysis of the Campylobacter jejuni genome by SMRT DNA sequencing identifies restriction-modification motifs.
PG  - e0118533
AB  - Campylobacter jejuni is a leading bacterial cause of human gastroenteritis. The goal of this
      study was to analyze the C. jejuni F38011 strain, recovered from an
      individual with severe enteritis, at a genomic and proteomic level to gain
      insight into microbial processes. The C. jejuni F38011 genome is comprised of
      1,691,939 bp, with a mol.% (G+C) content of 30.5%. PacBio sequencing coupled with
      REBASE analysis was used to predict C. jejuni F38011 genomic sites and enzymes
      that may be involved in DNA restriction-modification. A total of five putative
      methylation motifs were identified as well as the C. jejuni enzymes that could be
      responsible for the modifications. Peptides corresponding to the deduced amino
      acid sequence of the C. jejuni enzymes were identified using proteomics. This
      work sets the stage for studies to dissect the precise functions of the C. jejuni
      putative restriction-modification enzymes. Taken together, the data generated in
      this study contributes to our knowledge of the genomic content, methylation
      profile, and encoding capacity of C. jejuni.
AU  - O'Loughlin JL
AU  - Eucker TP
AU  - Chavez JD
AU  - Samuelson DR
AU  - Neal-McKinney J
AU  - Gourley CR
AU  - Bruce JE
AU  - Konkel ME
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2015 10: e0118533.

PMID- 11092936
VI  - 56
DP  - 2000
TI  - Crystallization and preliminary X-ray diffraction analysis of MspI restriction endonuclease in complex with its cognate DNA.
PG  - 1652-1655
AB  - The MspI restriction endonuclease is a type II restriction enzyme. Unlike all other
      restriction enzymes with known structures, MspI recognizes the palindromic tetranucleotide
      sequence 5'-C/CGG and cleaves it as indicated by the '/' to produce DNA products with 5'
      two-base overhangs. Owing to the nature of its cleavage pattern, it is likely that MspI would
      represent a new structural class of restriction endonucleases.  Crystals of the dimeric MspI
      restriction enzyme bound to a duplex DNA molecule containing the specific recognition sequence
      have been obtained by vapor-diffusion techniques in the presence of polyethylene glycol as
      precipitant. The crystals belong to the monoclinic space group P2(1), with unit-cell
      parameters a = 50.2, b = 131.6, c = 59.3 Angstroms, beta = 109.7 degrees. The crystals contain
      one dimeric complex in the asymmetric unit.  A complete native data set has been collected to
      a resolution of 2.05 Angstroms by cryo-crystallographic methods, with an R(merge) of 4.0%.
AU  - O'Loughlin TJ
AU  - Xu Q
AU  - Kucera RB
AU  - Dorner LF
AU  - Sweeney S
AU  - Schildkraut I
AU  - Guo H-C
PT  - Journal Article
TA  - Acta Crystallogr. D Biol. Crystallogr.
JT  - Acta Crystallogr. D Biol. Crystallogr.
SO  - Acta Crystallogr. D Biol. Crystallogr. 2000 56: 1652-1655.

PMID- 9405658
VI  - 94
DP  - 1997
TI  - The restriction-modification genes of Escherichia coli K-12 may not be selfish: They do not resist loss and are readily replaced by alleles conferring different specificities.
PG  - 14596-14601
AB  - Type II restriction and modification genes have been described as selfish because they have
      been shown to impose selection for the maintenance of the plasmid that encodes them. In our
      experiments, the type I R-M system EcoKI does not behave in the same way.  The genes
      specifying EcoKI are, however, normally residents of the chromosome and therefore our analyses
      were extended to monitor the deletion of chromosomal genes rather than loss of plasmid vector.
      If EcoKI were to behave in the same way as the plasmid-encoded type II R-M systems, the loss
      of the relevant chromosomal genes by mutation of recombination should lead to cell death
      because the cell would become deficient in modification enzyme and the bacterial chromosome
      would be vulnerable to the restriction endonuclease.  Our data contradict this prediction;
      they reveal that functional type I R-M genes in the chromosome are readily replaced by mutant
      alleles and by alleles encoding a type I R-M system of different specificity.  The acquisition
      of allelic genes conferring a new sequence specificity, but not the loss of the resident
      genes, is dependent on the product of an unlinked gene, one predicted to be relevant to
      control of expression of the genes that encode EcoKI.  Our evidence suggests that not all R-M
      systems are evolving as "selfish" units; rather, the diversity and distribution of the family
      of type I enzymes we have investigated require an alternative selective pressure.
AU  - O'Neill M
AU  - Chen A
AU  - Murray NE
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1997 94: 14596-14601.

PMID- 9843515
VI  - 17
DP  - 1998
TI  - Localization of a protein-DNA interface by random mutagenesis.
PG  - 7118-7127
AB  - The type I restriction and modification enzymes do not possess obvious DNA-binding motifs
      within their target recognition domains of 150-180 amino acids.  To identify residues involved
      in DNA recognition, changes were made in the amino-TRD of EcoKI by random mutagenesis.  Most
      of the 101 substitutions affecting 79 residues had no effect on the phenotype.  Changes at
      only seven positions caused the loss of restriction and modification activities.  The seven
      residues identified by mutation are not randomly distributed throughout the primary sequence
      of the TRD: five are within the interval between residues 80 and 110.  Sequence analyses have
      led to the suggestion that the TRDs of type I restriction enzymes include a tertiary structure
      similar to the TRD of the HhaI methyltransferase, and to a model for a DNA-protein interface
      in EcoKI.  In this model, the residues within the interval identified by the five mutations
      are close to the protein-DNA interface.  Three additional residues close to the DNA in the
      model were changed; each substitution impaired both activities.  Proteins from twelve mutants
      were purified: six from mutants with partial or wild-type activity and six from mutants
      lacking activity.  There is a strong correlation between phenotype and DNA-binding affinity,
      as determined by fluorescence anisotropy.
AU  - O'Neill M
AU  - Dryden DTF
AU  - Murray NE
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1998 17: 7118-7127.

PMID- 11273713
VI  - 307
DP  - 2001
TI  - Target recognition by EcoKI: the recognition domain is robust and restriction-deficiency commonly results from the proteolytic control of enzyme activity.
PG  - 951-963
AB  - We report a genetic and biochemical analysis of a target recognition domain (TRD) of EcoKI, a
      type I restriction and modification enzyme. The TRDs of type I R-M systems are within the
      specificity subunit (HsdS) and HsdS confers sequence specificity to a complex endowed with
      both restriction and modification activities. Random mutagenesis has revealed that most
      substitutions within the amino TRD of EcoKI, a region comprising 157 amino acid residues, have
      no detectable effect on the phenotype of the bacterium, even when the substitutions are non-
      conservative. The structure of the TRD appears to be robust. All but one of the six
      substitutions that confer a restriction-deficient, modification-deficient (r(-)m(-)) phenotype
      were found to be in the interval between residues 80 and 110, a region predicted by sequence
      comparisons to form part of the protein-DNA interface. Additional site-directed mutations
      affecting this interval commonly impair both restriction and modification. However, we show
      that an r(-) phenotype cannot be taken as evidence that the EcoKI complex lacks endonuclease
      activity; in response to even a slightly impaired modification efficiency, the endonuclease
      activity of EcoKI is destroyed by a process dependent upon the ClpXP protease. Enzymes from
      mutants with an r(-)m(-) phenotype commonly retain some sequence-specific activity; methylase
      activity can be detected on hemimethylated DNA substrates and residual endonuclease activity
      is implied whenever the viability of the r(-)m(-) bacterium is dependent on ClpXP. Conversely,
      the viability of ClpX(-) r(-)m(-) bacteria can be used as evidence for little, or no,
      endonuclease activity. Of 14 mutants with an r(-)m(-) phenotype, only six are viable in the
      absence of ClpXP. The significance of four of the six residues (G91, G105, F107 and G141) is
      enhanced by the finding that even conservative substitutions for these residues impair
      modification, thereby conferring an r(-)m(-) phenotype.
AU  - O'Neill M
AU  - Powell LM
AU  - Murray NE
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2001 307: 951-963.

PMID- 9797334
VI  - 64
DP  - 1998
TI  - Design of a phage-insensitive lactococcal dairy starter via sequential transfer of naturally occurring conjugative plasmids.
PG  - 4618-4622
AB  - The plasmid-free Lactococcus lactis subsp. cremoris MG1614 is highly phage sensitive and lacks
      lactose fermenting ability (Lac) and primary casein degrading ability (Prt). Food grade gene
      transfer systems were used to sequentially superimpose different phage defense systems on this
      background, resulting in a gradual increase in resistance to bacteriophage in the derivatives.
      pLP712, encoding Lac and Prt, was then transferred to one of these hosts, into which plasmids
      encoding adsorption inhibition, restriction modification, and abortive infection had already
      been introduced. This resulted in a phage-resistant strain which was successfully used as a
      single-strain starter for cheddar cheese manufacture under industrial conditions.
AU  - O'Sullivan D
AU  - Coffey A
AU  - Fitzgerald GF
AU  - Hill C
AU  - Ross RP
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1998 64: 4618-4622.

PMID- 11157264
VI  - 67
DP  - 2001
TI  - Naturally occurring lactococcal plasmid pAH90 links bacteriophage resistance and mobility functions to a food-grade selectable markerpotential use to impart phage resistance to dairy fermentation starter culture.
PG  - 929-937
AB  - Phage resistance plasmid pAH90 (26,490 bp) of Lactococcus lactis subsp. lactis biovar.
      diacetylactis DPC721 is a natural cointegrate plasmid
      formed by homologous recombination between the type I
      restriction-modification specificity determinants (hsdS) of plasmid
      pAH33 (6,159 bp) and plasmid pAH82 (20,331 bp), giving rise to a
      phage-sensitive mutant following phage challenge. The recombinant event
      is favored by phage infection. The nucleotide sequence of pAH90 was
      determined, identifying 24 open reading frames responsible for
      restriction-modification, phage adsorption inhibition, plasmid
      replication, cadmium resistance, cobalt transport and conjugative
      mobilization phenotypes. The cadmium resistance property, encoded by
      the cadA gene, facilitated the selection of pAH90 in other
      phage-sensitive lactococci after electroporation. The fortuitous
      association of multiple phage resistance systems, which acted at
      different stages in the phage lytic cycle, with a food-grade selectable
      marker on a mobilizable plasmid makes pAH90 an ideal candidate for use
      in food-grade starter culture improvement in industrial dairy
      fermentations.
AU  - O'Sullivan D
AU  - Ross RP
AU  - Twomey DP
AU  - Fitzgerald GF
AU  - Hill C
AU  - Coffey A
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2001 67: 929-937.

PMID- 10844674
VI  - 36
DP  - 2000
TI  - Novel type I restriction specificities through domain shuffling of HsdS subunits in lactococcus lactis.
PG  - 866-875
AB  - This study identifies a natural system in Lactococcus lactis, in which a restriction
      modification specificity subunit resident on a 6159 bp plasmid (pAH33) alters the specificity
      of a functional R/M mechanism encoded by a 20.3 kb plasmid, pAH82. The new specificity was
      identified after phenotypic and molecular analysis of a 26.5 kb co-integrate plasmid (pAH90),
      which was detected after bacteriophage challenge of the parent strain. Analysis of the regions
      involved in the co-integration revealed that two novel hybrid hsdS genes had been formed
      during the co-integration event. The HsdS chimeras had interchanged the C- and N-terminal
      variable domains of the parent subunits, generating two new restriction specificities.
      Comparison of the parent hsdS genes with other type I specificity determinants revealed that
      the region of the hsdS genes responsible for the co-integration event is highly conserved
      among lactococcal type I hsdS determinants. Thus, as hsdS determinants are widespread in the
      genus Lactococcus, new restriction specificities may evolve rapidly after homologous
      recombination between these genes. This study demonstrates that, similar to previous
      observations in Gram-negative bacteria, a Gram-positive bacterium can acquire novel
      restriction specificities naturally through domain shuffling of resident HsdS subunits.
AU  - O'Sullivan D
AU  - Twomey DP
AU  - Coffey A
AU  - Hill C
AU  - Fitzgerald GF
AU  - Ross RP
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2000 36: 866-875.

PMID- 8586237
VI  - 85
DP  - 1995
TI  - C.LlaI is a bifunctional regulatory protein of the LlaI restriction modification operon from Lactococcus lactis.
PG  - 591-595
AB  - Strains of Lactococcus lactis are used commercially as starter bacteria in dairy
      fermentations.  Bacteriophage attack of these bacteria represents a major problem in the
      industry.  Plasmid-borne phage resistance traits have been found naturally in some strains and
      the mobilization of these plasmids into desired industrial starter strains has provided a
      dynamic new source of cultures in the industry.  One of these plasmids, pTR2030, has been
      studied extensively in this laboratory and shown to encode two phage-resistance determinants;
      the AbiA abortive infection mechanism and the LlaI restriction modification system.  The LlaI
      methylase is a bifunctional type IIS methylase with 39% identity to M.FokI and is encoded by
      1.9 kb on pTR2030, ~5 kb upstream from the abiA gene.  The LlaI restriction component is
      encoded by three genes, llaI.1, llaI.2, llaI.3, positioned downstream from llaIM. A
      GTP-binding site on the deduced protein from llaI.2 suggests that LlaI restriction is probably
      energy-dependent.  Data bank searches did not reveal any significant homologies with these
      deduced proteins, except for the GTP-binding motif on LlaI.2 with a corresponding motif on the
      Escherichia coli McrB protein, which is part of a GTP-dependent, multi-subunit restriction
      enzyme.  From the molecular studies on the LlaI R/M system, it is suggested that the LlaI
      restriction enzyme is a novel type with properties reminiscent of both type IIS and type I
      enzymes.
AU  - O'Sullivan DJ
AU  - Klaenhammer TR
PT  - Journal Article
TA  - Dev. Biol. Stand.
JT  - Dev. Biol. Stand.
SO  - Dev. Biol. Stand. 1995 85: 591-595.

PMID- 9535090
VI  - 27
DP  - 1998
TI  - Control of expression of LlaI restriction in Lactococcus lactis.
PG  - 1009-1020
AB  - The plasmid encoded LlaI R/M sytem from Lactococcus lactis ssp. lactis consists of a bidomain
      methylase, with close evolutionary ties to type IIS methylases, and a tri-subunit restriction
      complex.  Both the methylase and restriction subunits are encoded on a polycistronic 6.9 kb
      operon.  In this study, the 5' end of the llaI 6.9 kb transcript was determined by primer
      extension analysis to be 254 bp upstream from the first R/M gene on the operon, llaIM.
      Deletion of this promoter region abolished LlaI restriction in L. lactis.  Analysis of the
      intervening sequence revealed a 72-amino-acid open reading frame, designated llaIC, with a
      conserved ribosome binding site and helix-turn-helix domain.  Overexpression of llaIC in
      Escherichia coli with a T7 expression vector produced the predicted protein of 8.2 kDa.
      Mutation and in trans complementation analysis indicated that C.LlaI positively enhanced LlaI
      restriction activity in vivo.  Northern analysis and transcriptional fusions of the llaI
      promoter to a lacZ reporter gene indicated that C.LlaI did not enhance transcription of the
      llaI operon.  Databank searches with the deduced protein sequence for llaIC revealed
      significant homologies to the E. coli Rop regulatory and mRNA stabilizer protein.
      Investigation of the effect of C.LlaI on enhancement of LlaI restriction in L. lactis revealed
      that growth at elevated temperatures (40oC) completely abolished any enhancement of
      restriction activity.  These data provide molecular evidence for a mechanism on how the
      expression of a restriction system in a prokaryote can be drastically reduced during elevated
      growth temperatures, by a small regulatory protein.
AU  - O'Sullivan DJ
AU  - Klaenhammer TR
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1998 27: 1009-1020.

PMID- 7528201
VI  - 177
DP  - 1995
TI  - In vivo restriction by LlaI is encoded by three genes, arranged in an operon with llaIM, on the conjugative Lactococcus plasmid pTR2030.
PG  - 134-143
AB  - The LlaI restriction and modification (R/M) system is encoded on pTR2030, a 46.2-kb
      conjugative plasmid from Lactococcus lactis. The llaI methylase gene, sequenced previously,
      encodes a functional type IIS methylase and is located approximately 5 kb upstream from the
      abiA gene, encoding abortive phage resistance. In this study, the sequence of the region
      between llaIM and abiA was determined and revealed four consecutive open reading frames
      (ORFs). Northern (RNA) analysis showed that the four ORFs were part of a 7-kb operon with llaM
      and the downstream abiA gene on a separate transcriptional unit. The deduced protein sequence
      of ORF2 revealed a P-loop consensus motif for ATP/GTP-binding sites and a three-part consensus
      motif for GTP-binding proteins. Data bank searches with the deduced protein sequences for all
      four ORFs revealed no homology except for ORF2 with McrB, in three regions that coincided with
      the GTP-binding motifs in both proteins. To phenotypically analyze the llaI operon, a 9.0-kb
      fragment was cloned into a high-copy-number lactococcal shuttle vector, pTRKH2. The resulting
      construct, pTRK370, exhibited a significantly higher level of in vivo restriction and
      modification in L. lactis NCK203 than the low-copy-number parental plasmid, pTR2030. A
      combination of deletion constructions and frameshift mutations indicated that the first three
      ORFs were involved in LlaI restriction, and they were therefore designated llaI.1, llaI.2, and
      llaI.3. Mutating llaI.1 completely abolished restriction, while disrupting llaI.2 or llaI.3
      allowed an inefficient restriction of phage DNA to occur, manifested primarily by a variable
      plaque phenotype. ORF4 had no discernible effect on in vivo restriction. A frameshift mutation
      in llaIM proved lethal to L. lactis NCK203, implying that the restriction component was active
      without the modification subunit. These results suggested that the LlaI R/M system is unlike
      any other R/M system studied to date and has diverged from the type IIS class of restriction
      enzymes by acquiring some characteristics reminiscent of type I enzymes.
AU  - O'Sullivan DJ
AU  - Zagula K
AU  - Klaenhammer TR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1995 177: 134-143.

PMID- 19265535
VI  - 9
DP  - 2009
TI  - Comparative genomics of lactic acid bacteria reveals a niche-specific gene set.
PG  - 50
AB  - Background: The recently sequenced genome of Lactobacillus helveticus DPC4571 [1] revealed a
      dairy organism with significant homology (75% of
      genes are homologous) to a probiotic bacteria Lb. acidophilus NCFM [2].
      This led us to hypothesise that a group of genes could be determined
      which could define an organism's niche.
      Results: Taking 11 fully sequenced lactic acid bacteria (LAB) as
      our target, (3 dairy LAB, 5 gut LAB and 3 multi-niche LAB), we
      demonstrated that the presence or absence of certain genes involved in
      sugar metabolism, the proteolytic system, and restriction modification
      enzymes were pivotal in suggesting the niche of a strain. We identified
      9 niche specific genes, of which 6 are dairy specific and 3 are gut
      specific. The dairy specific genes identified in Lactobacillus
      helveticus DPC4571 were lhv 1161 and lhv 1171, encoding components of
      the proteolytic system, lhv 1031 lhv 1152, lhv 1978 and lhv 0028
      encoding restriction endonuclease genes, while bile salt hydrolase
      genes lba 0892 and lba 1078, and the sugar metabolism gene lba 1689
      from Lb. acidophilus NCFM were identified as gut specific genes.
      Conclusion: Comparative analysis revealed that if an organism had
      homologs to the dairy specific geneset, it probably came from a dairy
      environment, whilst if it had homologs to gut specific genes, it was
      highly likely to be of intestinal origin.
      We propose that this "barcode" of 9 genes will be a useful initial
      guide to researchers in the LAB field to indicate an organism's ability
      to occupy a specific niche.
AU  - O'Sullivan O
AU  - O'Callaghan J
AU  - Sangrador-Vegas A
AU  - McAuliffe O
AU  - Slattery L
AU  - Kaleta P
AU  - Callanan M
AU  - Fitzgerald GF
AU  - Ross RP
AU  - Beresford T
PT  - Journal Article
TA  - BMC Microbiol.
JT  - BMC Microbiol.
SO  - BMC Microbiol. 2009 9: 50.

PMID- 10206690
VI  - 145
DP  - 1999
TI  - Structural and functional analysis of pCI65st, a 6.5 kb plasmid from Streptococcus thermophilus NDI-6.
PG  - 127-134
AB  - The 6.5 kb cryptic plasmid pCI65st from Streptococcus thermophilus NDI-6, a strain isolated
      from the Indian fermented milk dahi, was subcloned and sequenced. Five putative ORFs were
      identified. ORF1 could encode a 315 aa polypeptide almost identical to the RepA protein of
      previously sequenced S. thermophilus plasmids, indicating that pCI65st is one of the pC194
      group of small gram-positive rolling-circle plasmids. ORFs 2 and 4 were virtually identical
      and could specify proteins of approximately 150 aa with significant similarity to the small
      heat-shock proteins described from a variety of gram-positive bacteria. ORF3 could encode a
      415 aa protein similar to enolase, an enzyme involved in glycolysis and gluconeogenesis. ORF5
      could encode a 412 aa protein which had high similarity to the HsdS (specificity) proteins of
      type I restriction-modification systems. Variants of strain NDI-6 which lacked pCI65st were
      readily isolated after subculture of the parent strain at 32 degrees C. The plasmid-bearing
      parent culture was significantly more resistant to a temperature shift from 42 degrees C to 62
      degrees C than its plasmid-free variant and expressed proteins which corresponded with the
      predicted translation products from ORF2 and ORF4. In addition, plasmid-free mutants were
      lysed in broth by bacteriophages to which the parent culture was resistant.
AU  - O'Sullivan T
AU  - van Sinderen D
AU  - Fitzgerald G
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 1999 145: 127-134.

PMID- 24812213
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the First Isolate of Extensively Drug-Resistant Mycobacterium tuberculosis in New Zealand.
PG  - e00319-14
AB  - Extensively drug-resistant (XDR) tuberculosis has now been described in >90 countries
      worldwide. The first case of XDR tuberculosis (XDR-TB) in New Zealand
      was recorded in 2010. We report the draft whole-genome sequence of the New
      Zealand isolate, NZXDR1, and describe a number of single-nucleotide polymorphisms
      that relate to drug resistance.
AU  - O'Toole RF
AU  - Johari BM
AU  - Mac AM
AU  - Rogers TR
AU  - Bower JE
AU  - Basu I
AU  - Freeman JT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00319-14.

PMID- 21622758
VI  - 193
DP  - 2011
TI  - Draft genome sequence of Bacteroides vulgatus PC510, a strain isolated from human feces.
PG  - 4025-4026
AB  - Although Bacteroides vulgatus is one of the most prevalent microorganisms in the human
      gastrointestinal tract little is known about the genetic
      potential of this species. Here we describe the annotated draft genome
      sequence of B. vulgatus PC510 isolated from human faeces.
AU  - O-Cuiv P
AU  - Klaassens ES
AU  - Durkin AS
AU  - Harkins DM
AU  - Foster L
AU  - McCorrison J
AU  - Torralba M
AU  - Nelson KE
AU  - Morrison M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4025-4026.

PMID- 10665836
VI  - 84
DP  - 1999
TI  - DNA methylation analysis: a review of current methodologies.
PG  - 389-400
AB  - The relationship between levels of DNA methylation and gene activity has been known for some
      time. Many of the early procedures developed gave only
      somewhat limited information about methylation patterns, for example, the total level of
      5-methyl cytosine in the genome or the frequency of methylation of cytosines within
      certain restriction sites. However, in the last few years, there has been an explosion of
      interest in DNA methylation, and with it, many new and powerful techniques have
      been developed to facilitate its study. In this paper, the key techniques currently available
      are reviewed and the advantages, disadvantages, and potential artifacts of each are
      discussed.
AU  - Oakeley EJ
PT  - Journal Article
TA  - Pharmacol. Ther.
JT  - Pharmacol. Ther.
SO  - Pharmacol. Ther. 1999 84: 389-400.

PMID- 10524317
VI  - 27
DP  - 1999
TI  - Quantification of 5-methylcytosine in DNA by the chloroacetaldehyde reaction.
PG  - 744-746
AB  - The study of changes in genome-wide levels of DNA methylation has become a key focus for
      understanding the epigenetic regulation of gene expression. Many procedures exist to study DNA
      methylation, falling into two categories: gene-specific and genome-wide. Genome-wide
      methylation analysis is best performed by DNA hydrolysis followed by HPLC; however, it
      requires access to an HPLC machine, which is not always available. Alternative procedures,
      such as the radioactive labeling of CpG sites using SssI DNA methyltransferase, have been
      developed to address this problem, but it can only monitor CpG methylation changes, and CpNpG
      methylation is not detected. Here, we present a method for the analysis of DNA methylation in
      any sequence context by fluorescent labeling. We present control analyses using synthetic
      oligonucleotides of known methylation levels and a comparison of genomic DNA from two
      transgenic tobacco lines known to differ in their methylation levels. The results indicate
      that hygromycin-induced hypermethylation acts equally on all classes of methylatable cytosine,
      perhaps indicating a common mechanism.
AU  - Oakeley EJ
AU  - Schmitt F
AU  - Jost JP
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 1999 27: 744-746.

PMID- 24407854
VI  - 6
DP  - 2014
TI  - Genome Degeneration and Adaptation in a Nascent Stage of Symbiosis.
PG  - 76-93
AB  - Symbiotic associations between animals and microbes are ubiquitous in nature, with an
      estimated15%of all insect species harboring
      intracellular bacterial symbionts. Most bacterial symbionts sharemany genomic features
      including small genomes, nucleotide composition
      bias, high coding density, and a paucity ofmobileDNA, consistent with long-term host
      association. In this study,wefocus on
      the early stages of genome degeneration in a recently derived insect-bacterial mutualistic
      intracellular association. We present the
      completegenomesequenceandannotationof Sitophilusoryzae primary endosymbiont (SOPE).We
      alsopresent the finishedgenome
      sequence and annotation of strainHS, a close free-living relative of SOPEand other insect
      symbionts of the Sodalis-allied clade,whose
      gene inventory is expected to closely resemble the putative ancestor of this group.
      Structural, functional, and evolutionary analyses
      indicate that SOPE has undergone extensive adaptation toward an insect-associated lifestyle in
      a very short timeperiod. The genome
      of SOPE is large in sizewhen compared withmany ancient bacterial symbionts; however, almost
      half of the protein-coding genes in
      SOPE are pseudogenes. There is also evidence for relaxed selection on the remaining intact
      protein-coding genes. Comparative
      analyses of the whole-genome sequence of strain HS and SOPE highlight numerous genomic
      rearrangements, duplications, and
      deletions facilitated by a recent expansion of insertions sequence elements, some of which
      appear to have catalyzed adaptive
      changes. Functional metabolic predictions suggest that SOPE has lost the ability to synthesize
      several essential amino acids and
      vitamins. Analyses of the bacterial cell envelope and genes encoding secretion systems suggest
      that these structures and elements
      have become simplified in the transition to a mutualistic association.
AU  - Oakeson KF
AU  - Gil R
AU  - Clayton AL
AU  - Dunn DM
AU  - von Niederhausern AC
AU  - Hamil C
AU  - Aoyagi A
AU  - Duval B
AU  - Baca A
AU  - Silva FJ
AU  - Vallier A
AU  - Jackson DG
AU  - Latorre A
AU  - Weiss RB
AU  - Heddi A
AU  - Moya A
AU  - Dale C
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2014 6: 76-93.

PMID- 27198026
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of an Oxalate-Degrading Strain of Clostridium sporogenes from the Gastrointestinal Tract of the White-Throated Woodrat (Neotoma albigula).
PG  - e00392-16
AB  - The gastrointestinal tract of the white-throated woodrat Neotoma albigula harbors a diverse
      microbial population that functions in the degradation of ingested
      plant secondary compounds. Here, we present the draft genome sequence and
      annotation of Clostridium sporogenes strain 8-O, a novel oxalate-degrading
      bacterium isolated from the feces of N. albigula.
AU  - Oakeson KF
AU  - Miller A
AU  - Dale C
AU  - Dearing D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00392-16.

PMID- 12452967
VI  - 93
DP  - 2002
TI  - The complete nucleotide sequence of the Vibrio harveyi bacteriophage VHML.
PG  - 1089-1098
AB  - Aims: To determine the complete nucleotide sequence of the bacteriophage VHML and establish a
      hypothesis for the virulence conversion caused by
      VHML infection of Vibrio harveyi. Methods and Results: The complete
      nucleotide sequence of VHML was determined (43 193 bp) and used to
      identify putative genes. The translated products of these genes were
      compared with reported sequences to assign hypothetical functions. All
      anticipated structural genes and putative genes for lysogeny were
      identified. In addition, we found a complete N6-adenine methyltransferase
      (Dam) gene that appeared to have an essential site for ADP-ribosylating
      toxins at the C-terminal of the translated product. Conclusions: Virulence
      conversion of V. harveyi by VHML may be associated with Dam
      transcriptional regulation. The Dam gene may also encode for a toxin
      component similar to ADP-ribosylating toxins. Significance and Impact of
      Study: This manuscript lays the foundation for understanding the virulence
      of toxin-producing V. harveyi. Further research into aspects discussed
      here will lead to a greater comprehension regarding the invertebrate
      disease vibriosis and its control in the farming of these animals.
AU  - Oakey HJ
AU  - Cullen BR
AU  - Owens L
PT  - Journal Article
TA  - J. Appl. Microbiol.
JT  - J. Appl. Microbiol.
SO  - J. Appl. Microbiol. 2002 93: 1089-1098.

PMID- 12387882
VI  - 530
DP  - 2002
TI  - Folding transition of large DNA completely inhibits the action of a restriction endonuclease as revealed by single-chain observation.
PG  - 143-146
AB  - The biochemical characteristics of lambda DNA chains in folded/unfolded states upon cleavage
      by the restriction enzyme ApaLI were investigated in the presence of spermine. These
      characteristics of DNA chains depending on their higher-order structure were studied at the
      single-molecule level using fluorescence microscopy. With a low concentration of spermine,
      lambda DNA takes a random coiled conformation and allows digestion by the enzyme, while under
      a high concentration of spermine, lambda DNA takes a compact folded structure and inhibits
      such attack. Together with comparative experiments on short oligomeric DNA, our results
      suggest that the transition in the higher-order structure causes on/off-type switching of
      sensitivity to the enzyme.
AU  - Oana H
AU  - Tsumoto K
AU  - Yoshikawa Y
AU  - Yoshikawa K
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 2002 530: 143-146.

PMID- 16614449
VI  - 34
DP  - 2006
TI  - Structural model for the multisubunit Type IC restriction-modification DNA methyltransferase M.EcoR124I in complex with DNA.
PG  - 1992-2005
AB  - Recent publication of crystal structures for the putative DNA-binding subunits (HsdS) of the
      functionally uncharacterized Type I
      restriction-modification (R-M) enzymes MjaXIP and MgeORF438 have provided
      a convenient structural template for analysis of the more extensively
      characterized members of this interesting family of multisubunit molecular
      motors. Here, we present a structural model of the Type IC M.EcoR124I DNA
      methyltransferase (MTase), comprising the HsdS subunit, two HsdM subunits,
      the cofactor AdoMet and the substrate DNA molecule. The structure was
      obtained by docking models of individual subunits generated by
      fold-recognition and comparative modelling, followed by optimization of
      inter-subunit contacts by energy minimization. The model of M.EcoR124I has
      allowed identification of a number of functionally important residues that
      appear to be involved in DNA-binding. In addition, we have mapped onto the
      model the location of several new mutations of the hsdS gene of M.EcoR124I
      that were produced by misincorporation mutagenesis within the central
      conserved region of hsdS, we have mapped all previously identified
      DNA-binding mutants of TRD2 and produced a detailed analysis of the
      location of surface-modifiable lysines. The model structure, together with
      location of the mutant residues, provides a better background on which to
      study protein-protein and protein-DNA interactions in Type I R-M systems.
AU  - Obarska A
AU  - Blundell A
AU  - Feder M
AU  - Vejsadova S
AU  - Sisakova E
AU  - Weiserova M
AU  - Bujnicki JM
AU  - Firman K
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2006 34: 1992-2005.

PMID- 18164032
VI  - 376
DP  - 2008
TI  - HsdR Subunit of the Type I Restriction-Modification Enzyme EcoR124I: Biophysical Characterisation and Structural Modelling.
PG  - 438-452
AB  - Type I restriction-modification (RM) systems are large, multifunctional enzymes composed of
      three different subunits. HsdS and HsdM form a complex
      in which HsdS recognizes the target DNA sequence, and HsdM carries out
      methylation of adenosine residues. The HsdR subunit, when associated with
      the HsdS-HsdM complex, translocates DNA in an ATP-dependent process and
      cleaves unmethylated DNA at a distance of several thousand base-pairs from
      the recognition site. The molecular mechanism by which these enzymes
      translocate the DNA is not fully understood, in part because of the
      absence of crystal structures. To date, crystal structures have been
      determined for the individual HsdS and HsdM subunits and models have been
      built for the HsdM-HsdS complex with the DNA. However, no structure is
      available for the HsdR subunit. In this work, the gene coding for the HsdR
      subunit of EcoR124I was re-sequenced, which showed that there was an error
      in the published sequence. This changed the position of the stop codon and
      altered the last 17 amino acid residues of the protein sequence. An
      improved purification procedure was developed to enable HsdR to be
      purified efficiently for biophysical and structural analysis. Analytical
      ultracentrifugation shows that HsdR is monomeric in solution, and the
      frictional ratio of 1.21 indicates that the subunit is globular and fairly
      compact. Small angle neutron-scattering of the HsdR subunit indicates a
      radius of gyration of 3.4 nm and a maximum dimension of 10 nm. We
      constructed a model of the HsdR using protein fold-recognition and
      homology modelling to model individual domains, and small-angle neutron
      scattering data as restraints to combine them into a single molecule. The
      model reveals an ellipsoidal shape of the enzymatic core comprising the
      N-terminal and central domains, and suggests conformational heterogeneity
      of the C-terminal region implicated in binding of HsdR to the HsdS-HsdM
      complex.
AU  - Obarska-Kosinska A
AU  - Taylor JE
AU  - Callow P
AU  - Orlowski J
AU  - Bujnicki JM
AU  - Kneale GG
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2008 376: 438-452.

PMID- 24675865
VI  - 2
DP  - 2014
TI  - Genome Sequence of a Hyperthermophilic Archaeon, Thermococcus nautili 30-1, That  Produces Viral Vesicles.
PG  - e00243-14
AB  - Thermococcus nautili 30-1 (formerly Thermococcus nautilus), an anaerobic hyperthermophilic
      marine archaeon, was isolated in 1999 from a deep-sea
      hydrothermal vent during the Amistad campaign. Here, we present the complete
      sequence of T. nautili, which is able to produce membrane vesicles containing
      plasmid DNA. This property makes T. nautili a model organism to study horizontal
      gene transfer.
AU  - Oberto J
AU  - Gaudin M
AU  - Cossu M
AU  - Gorlas A
AU  - Slesarev A
AU  - Marguet E
AU  - Forterre P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00243-14.

PMID- 12705678
VI  - 9
DP  - 2003
TI  - VO1, a temperate bacteriophage of the type 19A multiresistant epidemic 8249 strain of Streptococcus pneumoniae: Analysis of variability of  lytic and putative C5 methyltransferase genes.
PG  - 7-15
AB  - A temperate bacteriophage (VO1) has been isolated from the Streptococcus pneumoniae type 19F
      multiresistant epidemic 8249 strain (South African
      strain). Structural analysis of the specific integration site, protein
      composition, restriction patterns, and molecular dissection of the lytic
      system of this phage revealed high sequence similarity with MM1, a
      temperate phage from the Spain23F-1 strain of pneumococcus, another
      multiresistant epidemic clone. The different pneumococcal strains
      sequenced so far exhibit an identical and single attB located in the same
      site of the genome. Remarkably, the LytA amidase coded by VO1 showed clear
      differences with that of the host bacterium in contrast with the situation
      previously documented for bacterial- and phage-coded amidases of
      pneumococcus. In addition, a new gene (orfmet) putatively coding for a C5
      methyltransferase has been identified. A noticeable variability affecting
      the presence (or absence) of this supernumerary gene(s) in the same region
      of the genomes of three otherwise highly similar phages (i.e., VO1, MM1,
      and HB-3) suggests frequent recombinational events leading to introduce
      variability in this genome region. The peculiarities of genes like lytA
      and orfmet in VO1 provide interesting insights on mechanisms of horizontal
      transfer and lysogenic state co-evolution.
AU  - Obregon V
AU  - Garcia P
AU  - Lopez R
AU  - Garcia JL
PT  - Journal Article
TA  - Microb. Drug Resist.
JT  - Microb. Drug Resist.
SO  - Microb. Drug Resist. 2003 9: 7-15.

PMID- 25593247
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Quorum-Sensing and Biofilm-Producing Pseudomonas aeruginosa Strain Pae221, Belonging to the Epidemic High-Risk Clone Sequence Type  274.
PG  - e01343-14
AB  - Pseudomonas aeruginosa Pae221 is a clinical isolate from blood culture. Pae221 was found to be
      a strong quorum-sensing and biofilm-producing strain and also
      demonstrates a notable production of phenazines. This strain belongs to sequence
      type 274 (ST274), an epidemic high-risk clone. Here, we report the draft genome
      sequence of P. aeruginosa Pae221.
AU  - Ocampo-Sosa AA
AU  - Fernandez-Martinez M
AU  - Cabot G
AU  - Pena C
AU  - Tubau F
AU  - Oliver A
AU  - Martinez-Martinez L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01343-14.

PMID- 
VI  - 39
DP  - 2005
TI  - Genome sequence of Xanthomonas oryzae pv. oryzae suggests contribution of large numbers of effector genes and insertion sequences to its race diversity.
PG  - 275-287
AB  - The plant-pathogenic prokaryote Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight,
      one of the most important diseases of rice.  The bacterium is a model organism for the
      analysis of plant-pathogen interaction, because more than 30 races differing in virulence and
      25 resistance genes in rice have been reported to date.  We present here the complete genome
      sequence of Xoo strain MAFF 311018.  The size of the genome was 4,940,217 bp, in a single
      circular chromosome.  The genome structure of Xoo MAFF 311018 was characterized by large
      numbers of effector (avr) genes of the avrBs3/pth family and insertion sequences (Iss).  RFLP
      analysis of diverse strains using ISxo1 as a probe suggests that the prevalence of mobile
      elements in this species, which can bring about genome inversions and rearrangement, may have
      played a major role in generating the high degree of genetic diversity and race
      differentiation characteristic of this pathogen.  The Xoo MAFF 311018 sequence was also highly
      similar to those of X. axonopodis pv. citri and X. campestris pv. campestris with the
      exception of the large number of effectors and IS elements, and numerous inversions and
      rearrangements.
AU  - Ochiai H
AU  - Inoue Y
AU  - Takeya M
AU  - Sasaki A
AU  - Kaku H
PT  - Journal Article
TA  - Japan Agricultural Research Quarterly
JT  - Japan Agricultural Research Quarterly
SO  - Japan Agricultural Research Quarterly 2005 39: 275-287.

PMID- Not carried by PubMed...
VI  - 23
DP  - 1989
TI  - Restriction endonucleases from Phormidium lapideum, a strain of filamentous and thermophilic Cyanobacteria.
PG  - 184-191
AB  - A couple of restriction endonucleases, PlaI and PlaII, have been purified from
      a filamentous and thermophilic cyanobacterium, Phormidium lapideum.  PlaI
      proved to be an isoschizomer of HaeIII and cleaved the site GG^CC and was a
      monomeric protein that had a molecular weight of about 40 kilodaltons.  PlaII
      was an isoschizomer of Nsp(7524)V and recognized the site TTCGAA and was
      estimated as a heterotetrameric protein (alpha2,beta2).  PlaII has an apparent
      molecular mass of 176 kilodaltons and that of the alpha subunit was 63
      kilodaltons, beta subunit 31 kilodaltons.  Characteristics of PlaI and PlaII
      were investigated in comparison with that of the respective isoschizomers,
      HaeIII and Nsp(7524)V.
AU  - Ochiai H
AU  - Shibata H
AU  - Sawa Y
AU  - Ashida N
PT  - Journal Article
TA  - Bull. Fac. Agr. Shimane Univ.
JT  - Bull. Fac. Agr. Shimane Univ.
SO  - Bull. Fac. Agr. Shimane Univ. 1989 23: 184-191.

PMID- 4957400
VI  - 5
DP  - 1966
TI  - Purification and properties of deoxyribonucleic acid methylase from Bacillus subtilis.
PG  - 761-773
AB  - DNA methylase was purified about 100-fold from Bacillus subtilis strain 6633.
      The novel features of this enzyme are as follows: (1) During growth of
      bacteria, enzyme activity was detected principally in the early exponential
      phase.  (2) The enzyme catalyzes the methylation of both native and
      heat-denatured DNA.  (3) The product of the enzymatic methylation of DNA was
      5-methylcytosine (5MC) only.  (4) The extent of the methylation of both native
      and heat-denatured bacterial DNA is approximately proportional to its GC
      (guanine plus cytosine) content.  The higher the per cent GC in DNA, the
      greater the extent of methylation that takes place, even if the ratio of 5MC to
      total cytosine residues in DNA is considered.  The possibility of the selective
      methylation of one strand of DNA was also examined by using B. subtilis
      bacteriophage 2C DNA, whose strands, after denaturation, can be fractionated
      because of a bias in base composition.  The H and L strands of phage 2C DNA
      were separated by MAK column chromatography or by centrifugation in alkaline
      CsCl density gradients, and it was found that both strands were equally
      methylated in vivo and in vitro.
AU  - Oda K
AU  - Marmur J
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1966 5: 761-773.

PMID- 
VI  - 64
DP  - 2001
TI  - DNA methyltransferase 1 is essential for establishment of trophoblast stem cells in culture.
PG  - 175-176
AB  - DNA methylation patterns in mammals are stage- and tissue-specific.  This suggests that
      methylation patterns contribute to proper cell differentiation and/or to the maintenance of
      cellular characteristics.  Several different DNA methyltransferases exist that both establish
      and maintain proper methylation patterns.  Dnmt1 is largely a maintenance methyltransferase
      that ensures an established methylation pattern is inherited by daughter cells.  Disruption of
      Dnmt1 causes growth delay at gastrulation and homozygous mutants are embryonic lethal.  To
      evaluate the role of Dnmt1 in placental development, we attempted to establish trophoblast
      stem cells from homozygous Dnmt1 hypomorphic mutant embryos.  TS cells exclusively contribute
      to the trophoblast lineage in vivo in chimeras.  At the blastocyst stage, TS cells appear in
      the polar trophectoderm, which is adjacent to the inner cell mass.  TS cells can be maintained
      in culture with media supplemented with FGF-4, and differentiate into several subtypes of
      trophoblast cells.  To establish homozygous mutant TS cells, we used blastocysts from
      heterozygous matings.  The 39 blastocysts from 6 female mice were incubated in FGF4-contained
      medium with feeder cells.  Of 39 blastocysts, 28 generated stem cell colonies; 3 were
      homozygous, 10 were wild type, 13 were heterozygous clones, and 2 could not be genotyped, but
      were probably also homozygous.  All clones were passed two more times and most (70-80%) of
      wild type and heterozygous clones survived.  However, no homozygous clone survived beyond the
      second passage.  Some autonomous differentiation was observed in the homozygous TS cells.  Our
      results indicate that Dnmt1-hypomorphic TS cells cannot be established in cell culture, as
      normal and heterozygous TS cells can.  This is in contrast to Dnmt1-hypomorphic embryonic stem
      cells, which can be maintained in culture.  These data suggest that the trophoblast lineage is
      more dependent on Dnmt1 than the embryo proper.
AU  - Oda M
AU  - Tanaka S
AU  - Shiota K
PT  - Journal Article
TA  - Biol. Reprod.
JT  - Biol. Reprod.
SO  - Biol. Reprod. 2001 64: 175-176.

PMID- 11313473
VI  - 21
DP  - 2001
TI  - Mobile self-splicing Group I introns from the psbA gene of Chlamydomonas reinhardtii: highly efficient homing of an exogenous intron containing its own promoter.
PG  - 3472-3481
AB  - Introns 2 and 4 of the psbA gene of Chlamydomonas reinhardtii chloroplasts (Cr.psbA2 and
      Cr.psbA4, respectively) contain large free-standing open reading frames (ORFs). We used
      transformation of an intronless-psbA strain (IL) to test whether these introns undergo homing.
      Each intron, plus short exon sequences, was cloned into a chloroplast expression vector in
      both orientations and then cotransformed into IL along with a spectinomycin resistance marker
      (16S rrn). For Cr.psbA2, the sense construct gave nearly 100% cointegration of the intron
      whereas the antisense construct gave 0%, consistent with homing. For Cr.psbA4, however, both
      orientations produced highly efficient cointegration of the intron. Efficient cointegration of
      Cr.psbA4 also occurred when the intron was introduced as a restriction fragment lacking any
      known promoter. Deletion of most of the ORF, however, abolished cointegration of the intron,
      consistent with homing. The Cr.psbA4 constructs also contained a
      3-(3,4-dichlorophenyl)-1,1-dimethylurea resistance marker in exon 5, which was always present
      when the intron integrated, thus demonstrating exon coconversion. Remarkably, primary
      selection for this marker gave >100-fold more transformants (>10,000/?g of DNA) than did the
      spectinomycin resistance marker. A trans homing assay was developed for Cr.psbA4; the
      ORF-minus intron integrated when the ORF was cotransformed on a separate plasmid. This assay
      was used to identify an intronic region between bp -88 and -194 (relative to the ORF) that
      stimulated homing and contained a possible bacterial (-10, -35)-type promoter. Primer
      extension analysis detected a transcript that could originate from this promoter. Thus, this
      mobile, self-splicing intron also contains its own promoter for ORF expression. The
      implications of these results for horizontal intron transfer and organelle transformation are
      discussed.
AU  - Odom OW
AU  - Holloway SP
AU  - Deshpande NN
AU  - Lee J
AU  - Herrin DL
PT  - Journal Article
TA  - Mol. Cell. Biol.
JT  - Mol. Cell. Biol.
SO  - Mol. Cell. Biol. 2001 21: 3472-3481.

PMID- 21398558
VI  - 193
DP  - 2011
TI  - The complete genome sequence of the hemotrophic Mycoplasma suis_KI3806.
PG  - 2369-2370
AB  - Mycoplasma suis, a member of the hemotrophic mycoplasma (HM) group, parasitize erythrocytes of
      pigs. Increasing evidences suggest that M. suis is also a zoonotic agent. Highly pathogenic
      strains of M. suis (e.g. M. suis_KI3806) have been demonstrated to invade erythrocytes. This
      complete sequenced and manually annotated genome of M. suis_KI3806 is the first available from
      this species and from all HM. The DNA was isolated from blood-samples of experimentally
      infected pigs due to the lack of an in vitro cultivation system. The small circular chromosome
      of 709270 bp with an unexpected-high number of hypothetical proteins and limited transport and
      metabolic capacities could reflect the unique life-style of HM on the surface of erythrocytes.
AU  - Oehlerking J
AU  - Kube M
AU  - Felder KM
AU  - Matter D
AU  - Wittenbrink MM
AU  - Schwarzenbach S
AU  - Kramer MM
AU  - Hoelzle K
AU  - Hoelzle LE
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 2369-2370.

PMID- 2142667
VI  - 89
DP  - 1990
TI  - Probing the function of individual amino acid residues in the DNA binding site of the EcoRI restriction endonuclease by analysing the toxicity of genetically engineered mutants.
PG  - 19-27
AB  - We have developed an assay that allows analysis of the activity of EcoRI
      restriction endonuclease (ENase) and its mutants in vivo.  This assay is based
      on the fact that wild type (wt) EcoRI ENase is toxic for Escherichia coli cells
      not expressing the EcoRI methyltransferase (MTase).  The viability factor
      defined by the ratio of the viable counts of E. coli cultures having or not
      having expressed the ecoRIR gene for a defined time is 10-6 for wt EcoRI ENase
      and close to one for a totally inactive EcoRI ENase mutant.  While the EcoRI
      MTase (M.EcoRI) provides substantial protection against the toxic effects of
      the wt EcoRI ENase and several of the mutants, some mutants become more toxic
      in the presence of M.EcoRI.  Twenty-four different DNA-binding-site mutants of
      EcoRI ENase were characterized in their activity in vivo with this assay.  The
      results obtained allow us to conclude that the structural integrity of the
      region at and around aa 200 seems to be very critical for the enzymatic
      function of EcoRI ENase: nonconservative replacements there lead to viability
      factors of 1-10/2.  While our results indicate that the region around aa 144
      and 145 is also involved in the EcoRI ENase-catalyzed reaction, it is also
      evident that the effects of mutation there are not as large:  viability factors
      of approx. 10-3 are obtained even for drastic replacements.  These results are
      discussed in the light of the x-ray structure analysis of an EcoRI ENase-DNA
      recognition complex.
AU  - Oelgeschlager T
AU  - Geiger R
AU  - Ruter T
AU  - Alves J
AU  - Fliess A
AU  - Pingoud A
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1990 89: 19-27.

PMID- 29085076
VI  - 3
DP  - 2018
TI  - DISARM is a widespread bacterial defence system with broad anti-phage activities.
PG  - 90-98
AB  - The evolutionary pressure imposed by phage predation on bacteria and archaea has  resulted in
      the development of effective anti-phage defence mechanisms, including
      restriction-modification and CRISPR-Cas systems. Here, we report on a new defence
      system, DISARM (defence island system associated with restriction-modification),
      which is widespread in bacteria and archaea. DISARM is composed of five genes,
      including a DNA methylase and four other genes annotated as a helicase domain, a
      phospholipase D (PLD) domain, a DUF1998 domain and a gene of unknown function.
      Engineering the Bacillus paralicheniformis 9945a DISARM system into Bacillus
      subtilis has rendered the engineered bacteria protected against phages from all
      three major families of tailed double-stranded DNA phages. Using a series of gene
      deletions, we show that four of the five genes are essential for DISARM-mediated
      defence, with the fifth (PLD) being redundant for defence against some of the
      phages. We further show that DISARM restricts incoming phage DNA and that the B.
      paralicheniformis DISARM methylase modifies host CCWGG motifs as a marker of self
      DNA akin to restriction-modification systems. Our results suggest that DISARM is
      a new type of multi-gene restriction-modification module, expanding the arsenal
      of defence systems known to be at the disposal of prokaryotes against their
      viruses.
AU  - Ofir G
AU  - Melamed S
AU  - Sberro H
AU  - Mukamel Z
AU  - Silverman S
AU  - Yaakov G
AU  - Doron S
AU  - Sorek R
PT  - Journal Article
TA  - Nature Microbiology
JT  - Nature Microbiology
SO  - Nature Microbiology 2018 3: 90-98.

PMID- 25838474
VI  - 3
DP  - 2015
TI  - High-Quality Draft Genome Sequence of Actinobacterium Kibdelosporangium sp. MJ126-NF4, Producer of Type II Polyketide Azicemicins, Using Illumina and PacBio   Technologies.
PG  - e00114-15
AB  - Here, we report the high-quality draft genome sequence of actinobacterium Kibdelosporangium
      sp. MJ126-NF4, producer of the type II polyketide azicemicins,
      obtained using Illumina and PacBio sequencing technologies. The 11.75-Mbp genome
      contains >11,000 genes and 22 polyketide and nonribosomal peptide natural product
      gene clusters.
AU  - Ogasawara Y
AU  - Torrez-Martinez N
AU  - Aragon AD
AU  - Yackley BJ
AU  - Weber JA
AU  - Sundararajan A
AU  - Ramaraj T
AU  - Edwards JS
AU  - Melancon CEIII
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00114-15.

PMID- 11557893
VI  - 293
DP  - 2001
TI  - Mechanisms of evolution in Rickettsia conorii and R. prowazekii.
PG  - 2093-2098
AB  - Rickettsia conorii is an obligate intracellular bacterium that causes Mediterranean spotted
      fever in humans. We determined the 1,268,755-nucleotide complete genome sequence of R.
      conorii, containing 1374 open reading frames. This genome exhibits 804 of the 834 genes of the
      previously determined R. prowazekii genome plus 552 supplementary open reading frames and a
      10-fold increase in the number of repetitive elements. Despite these differences, the two
      genomes exhibit a nearly perfect colinearity that allowed the clear identification of
      different stages of gene alterations with gene remnants and 37 genes split in 105 fragments,
      of which 59 are transcribed. A 38-kilobase sequence inversion was dated shortly after the
      divergence of the genus.
AU  - Ogata H
AU  - Audic S
AU  - Renesto-Audiffren P
AU  - Fournier P-E
AU  - Barbe V
AU  - Samson D
AU  - Roux V
AU  - Cossart P
AU  - Weissenbach J
AU  - Claverie J-M
AU  - Raoult D
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2001 293: 2093-2098.

PMID- 16703114
VI  - 2
DP  - 2006
TI  - Genome sequence of Rickettsia bellii illuminates the role of amoebae in gene exchanges between intracellular pathogens.
PG  - e76
AB  - The recently sequenced Rickettsia felis genome revealed an unexpected plasmid carrying several
      genes usually associated with DNA transfer,
      suggesting that ancestral rickettsiae might have been endowed with a
      conjugation apparatus. Here we present the genome sequence of Rickettsia
      bellii, the earliest diverging species of known rickettsiae. The 1,552,076
      base pair-long chromosome does not exhibit the colinearity observed
      between other rickettsia genomes, and encodes a complete set of putative
      conjugal DNA transfer genes most similar to homologues found in
      Protochlamydia amoebophila UWE25, an obligate symbiont of amoebae. The
      genome exhibits many other genes highly similar to homologues in
      intracellular bacteria of amoebae. We sought and observed sex pili-like
      cell surface appendages for R. bellii. We also found that R. bellii very
      efficiently multiplies in the nucleus of eukaryotic cells and survives in
      the phagocytic amoeba, Acanthamoeba polyphaga. These results suggest that
      amoeba-like ancestral protozoa could have served as a genetic "melting
      pot" where the ancestors of rickettsiae and other bacteria promiscuously
      exchanged genes, eventually leading to their adaptation to the
      intracellular lifestyle within eukaryotic cells.
AU  - Ogata H
AU  - La Scola B
AU  - Audic S
AU  - Renesto P
AU  - Blanc G
AU  - Robert C
AU  - Fournier PE
AU  - Claverie JM
AU  - Raoult D
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2006 2: e76.

PMID- 15984913
VI  - 3
DP  - 2005
TI  - The genome sequence of Rickettsia felis identifies the first putative conjugative plasmid in an obligate intracellular parasite.
PG  - e248
AB  - We sequenced the genome of Rickettsia felis, a flea-associated obligate intracellular
      alpha-proteobacterium causing spotted fever in humans.
      Besides a circular chromosome of 1,485,148 bp, R. felis exhibits the first
      putative conjugative plasmid identified among obligate intracellular
      bacteria. This plasmid is found in a short (39,263 bp) and a long (62,829
      bp) form. R. felis contrasts with previously sequenced Rickettsia in terms
      of many other features, including a number of transposases, several
      chromosomal toxin-antitoxin genes, many more spoT genes, and a very large
      number of ankyrin- and tetratricopeptide-motif-containing genes.
      Host-invasion-related genes for patatin and RickA were found. Several
      phenotypes predicted from genome analysis were experimentally tested:
      conjugative pili and mating were observed, as well as beta-lactamase
      activity, actin-polymerization-driven mobility, and hemolytic properties.
      Our study demonstrates that complete genome sequencing is the fastest
      approach to reveal phenotypic characters of recently cultured obligate
      intracellular bacteria.
AU  - Ogata H
AU  - Renesto P
AU  - Audic S
AU  - Robert C
AU  - Blanc G
AU  - Fournier PE
AU  - Parinello H
AU  - Claverie JM
AU  - Raoult D
PT  - Journal Article
TA  - PLoS Biology
JT  - PLoS Biology
SO  - PLoS Biology 2005 3: e248.

PMID- 9000384
VI  - 31
DP  - 1997
TI  - Group-I introns in the cytochrome c oxidase genes of Dictyostelium discoideum: two related ORFs in one loop of a group-I intron, a cox1/2 hybrid gene and an unusually large cox3 gene.
PG  - 80-88
AB  - The DNA sequences of cytochrome oxidase (subunits 1, 2 and 3) genes of the cellular slime mold
      Dictyostelium discoideum mitochondria were determined.  The genes for subunits 1 and 2 have a
      single continuous ORF (COX1/2) which contains four group-I introns.  The insertion sites of
      the two group-I introns (DdOX1/2.2 and DdOX1/2.3) coincide with those of fungal and algal
      group-I introns, as well as a liverwort group-I intron, in the cytochrome oxidase subunit 1.
      Interestingly, intron DdOX1/2.2 has two free-standing ORFs in a loop (L8) which have similar
      amino-acid sequences and are homologous to ai4 DNA endonuclease (I-Sce II) and bi4 RNA
      maturase found in group-I introns of Saccharomyces cerevisiae mitochondrial DNA.  Two group-I
      introns (DdOX1/2.3 and DdOX1/2.4) also have a free-standing ORF in loop 1 and loop 2,
      respectively.  These results show that these group-I introns and the intronic ORFs have
      evolved from the same ancestral origin, but that these ORFs have been propagated
      independently.
AU  - Ogawa S
AU  - Matsuo K
AU  - Angata K
AU  - Yanagisawa K
AU  - Tanaka Y
PT  - Journal Article
TA  - Curr. Genet.
JT  - Curr. Genet.
SO  - Curr. Genet. 1997 31: 80-88.

PMID- 9210597
VI  - 191
DP  - 1997
TI  - A site-specific DNA endonuclease specified by one of two ORFs encoded by a group I intron in Dictyostelium discoideum mitochondrial DNA.
PG  - 115-121
AB  - The second intron (DdOX1/2.2) of Dictyostelium discoideum cytochrome oxidase subunit 1/2 fused
      gene has two free-standing ORF genes (Dd ai2a and Dd ai2b) in a loop, which have similar amino
      acid sequences and are homologous to aI4 DNA endonuclease (I-SceII) of Saccharomyces
      cerevisiae.  To elucidate the functions of these ORFs, we cloned the ORFs into an expression
      vector and introduced the composite vectors into E. coli.  The expression of Dd ai2a in E.
      coli caused growth inhibition and degradation of the E. coli genomic DNA.  To determine
      whether Dd ai2a protein is a homing type DNA endonuclease, the ability to cleave the homing
      site of its intron in vivo was examined.  Dd ai2a cleaved only one strand of intronless DNA
      sequence at the site which coincides with the I-SceII cleavage recognition site.  We suppose
      that Dd ai2a functions actually as a homing type DNA endonuclease in D. discoideum
      mitochondria by virtue of other factors.  To obtain further information about the relationship
      between the existence of introns and the mating system, we carried out in vitro self-splicing
      assay and polymerase chain reaction analysis using 13 strains of the cellular slime mold.
AU  - Ogawa S
AU  - Naito K
AU  - Angata K
AU  - Morio T
AU  - Urushihara H
AU  - Tanaka Y
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1997 191: 115-121.

PMID- 21478354
VI  - 193
DP  - 2011
TI  - The Genome of Erysipelothrix rhusiopathiae, the Causative Agent of Swine Erysipelas, Reveals New Insights into the Evolution of Firmicutes and the Organism's Intracellular Adaptations.
PG  - 2959-2971
AB  - Erysipelothrix rhusiopathiae is a Gram-positive bacterium that represents
      a new class, Erysipelotrichia, in the phylum Firmicutes. The organism is a
      facultative intracellular pathogen that causes swine erysipelas, as well
      as a variety of diseases in many animals. Here, we report the first
      complete genome sequence analysis of a member of the class
      Erysipelotrichia. The E. rhusiopathiae genome (1,787,941 bp) is one of the
      smallest genomes in the phylum Firmicutes. Phylogenetic analyses based on
      the 16S rRNA gene and 31 universal protein families suggest that E.
      rhusiopathiae is phylogenetically close to Mollicutes, which comprises
      Mycoplasma species. Genome analyses show that the overall features of the
      E. rhusiopathiae genome are similar to those of other Gram-positive
      bacteria; it possesses a complete set of peptidoglycan biosynthesis genes,
      two-component regulatory systems, and various cell wall-associated
      virulence factors, including a capsule and adhesins. However, it lacks
      many orthologous genes for the biosynthesis of wall teichoic acids (WTA)
      and lipoteichoic acids (LTA) and the dltABCD operon, which is responsible
      for d-alanine incorporation into WTA and LTA, suggesting that the organism
      has an atypical cell wall. In addition, like Mollicutes, its genome shows
      a complete loss of fatty acid biosynthesis pathways and lacks the genes
      for the biosynthesis of many amino acids, cofactors, and vitamins,
      indicating reductive genome evolution. The genome encodes nine antioxidant
      factors and nine phospholipases, which facilitate intracellular survival
      in phagocytes. Thus, the E. rhusiopathiae genome represents evolutionary
      traits of both Firmicutes and Mollicutes and provides new insights into
      its evolutionary adaptations for intracellular survival.
AU  - Ogawa Y
AU  - Ooka T
AU  - Shi F
AU  - Ogura Y
AU  - Nakayama K
AU  - Hayashi T
AU  - Shimoji Y
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 2959-2971.

PMID- 22123768
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of the Hyperthermophilic Archaeon Thermococcus sp. Strain AM4, Capable of Organotrophic Growth and Growth at the Expense  of Hydrogenogenic or Sulfidogenic Oxidation of Carbon Monoxide.
PG  - 7019-7020
AB  - Analysis of the complete genome of Thermococcus sp. strain AM4, which was the first
      lithotrophic Thermococcales isolate described and the first
      archaeal isolate to exhibit a capacity for hydrogenogenic carboxydotrophy,
      reveals a proximity with Thermococcus gammatolerans, corresponding to
      close but distinct species that differ significantly in their lithotrophic
      capacities.
AU  - Oger P
AU  - Sokolova TG
AU  - Kozhevnikova DA
AU  - Chernyh NA
AU  - Bartlett DH
AU  - Bonch-Osmolovskaya EA
AU  - Lebedinsky AV
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 7019-7020.

PMID- 26769929
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of the Hyperthermophilic and Piezophilic Archaeon Thermococcus barophilus Ch5, Capable of Growth at the Expense of Hydrogenogenesis  from Carbon Monoxide and Formate.
PG  - e01534-15
AB  - We report here the complete sequence and fully manually curated annotation of the genome of
      strain Ch5, a new member of the piezophilic hyperthermophilic species
      Thermococcus barophilus.
AU  - Oger P
AU  - Sokolova TG
AU  - Kozhevnikova DA
AU  - Taranov EA
AU  - Vannier P
AU  - Lee HS
AU  - Kwon KK
AU  - Kang SG
AU  - Lee JH
AU  - Bonch-Osmolovskaya EA
AU  - Lebedinsky AV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01534-15.

PMID- 29472326
VI  - 6
DP  - 2018
TI  - Complete Genome Sequences of 11 Type Species from the Thermococcus Genus of Hyperthermophilic and Piezophilic Archaea.
PG  - e00037-18
AB  - We report here the genome sequences of the type strains of the species Thermococcus barossii,
      T. celer, T. chitonophagus, T. gorgonarius, T. pacificus,
      T. peptonophilus, T. profundus, T. radiotolerans, T. siculi, and T. thioreducens,
      as well as the prototype of a possible type strain of a novel Thermococcus
      species, strain P6.
AU  - Oger PM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00037-18.

PMID- 28209839
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of the Hyperthermophilic Piezophilic Archaeon Pyrococcus kukulkanii NCB100 Isolated from the Rebecca's Roost Hydrothermal Vent in the  Guaymas Basin.
PG  - e01667-16
AB  - Members of the order Thermococcales are common inhabitants of high-temperature hydrothermal
      vent systems (black smokers) that are represented in clone libraries
      mostly by isolates from the Thermococcus genus. We report the complete sequence
      of a novel species from the Pyrococcus genus, P. kukulkanii strain NCB100, which
      has been isolated from a flange fragment of the Rebecca's Roost hydrothermal vent
      system in the Guaymas Basin.
AU  - Oger PM
AU  - Callac N
AU  - Oger-Desfeux C
AU  - Hughes S
AU  - Gillet B
AU  - Jebbar M
AU  - Godfroy A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01667-16.

PMID- 21421756
VI  - 193
DP  - 2011
TI  - Draft Genome Sequence of Caloramator australicus strain RC3T a thermoanaerobe from the Great Artesian Basin of Australia.
PG  - 2664-2665
AB  - Caloramator australicus strain RC3(T) (JCM 15081(T) = KCTC 5601(T)) is the type strain of a
      newly identified thermophilic species, which was isolated from red-coloured microbial mats
      that thrive at 66  degrees C in the runoff channel of a Great Artesian Basin bore (New Lorne
      bore, registered number 17263) in outback Queensland, Australia. The ability of C. australicus
      strain to use metals as terminal electron acceptors has led to concerns that it could colonise
      and enhance corrosion of the metal casing of Great Artesian Basin bore-well pipes, and this
      could subsequently lead to bore failure and loss of water availability for the community which
      is so reliant on it. The genome of C. australicus strain has been sequenced, and annotation of
      the  approximately  2.65 Mb sequence indicates that the attributes are consistent with
      physiological and phenotypic traits.
AU  - Ogg CD
AU  - Patel BK
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 2664-2665.

PMID- 22123756
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of NBRC 3288, a Unique Cellulose-Nonproducing Strain of Gluconacetobacter xylinus Isolated from Vinegar.
PG  - 6997-6998
AB  - Gluconacetobacter xylinus is involved in the industrial production of cellulose. We have
      determined the genome sequence of G. xylinus NBRC 3288,
      a cellulose-nonproducing strain. Comparative analysis of genomes of G.
      xylinus NBRC 3288 with those of the cellulose-producing strains clarified
      the genes important for cellulose production in Gluconacetobacter.
AU  - Ogino H
AU  - Azuma Y
AU  - Hosoyama A
AU  - Nakazawa H
AU  - Matsutani M
AU  - Hasegawa A
AU  - Otsuyama K
AU  - Matsushita K
AU  - Fujita N
AU  - Shirai M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6997-6998.

PMID- 28183752
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Two Strains of Salmonella enterica Serovar Typhimurium  Displaying Different Virulence in an Experimental Chicken Model.
PG  - e01526-16
AB  - Salmonella enterica serovar Typhimurium strains 22495 and 22792, obtained from wild birds,
      were found to display different virulence attributes in an
      experimental chicken model. Closed genome sequences were assembled after
      sequencing with the Roche 454 and Illumina MiSeq platforms. An additional plasmid
      was present in the more virulent strain 22495.
AU  - Ogunremi D
AU  - Blais B
AU  - Huang H
AU  - Wang L
AU  - Elmufti M
AU  - Allain R
AU  - Hazelwood J
AU  - Grenier C
AU  - Amoako K
AU  - Savic M
AU  - Fattahi GN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01526-16.

PMID- 25156331
VI  - 15
DP  - 2014
TI  - High resolution assembly and characterization of genomes of Canadian isolates of Salmonella Enteritidis.
PG  - 713
AB  - BACKGROUND: There is a need to characterize genomes of the foodborne pathogen,
      Salmonella enterica serovar Enteritidis (SE) and identify genetic information
      that could be ultimately deployed for differentiating strains of the organism, a
      need that is yet to be addressed mainly because of the high degree of clonality
      of the organism. In an effort to achieve the first characterization of the
      genomes of SE of Canadian origin, we carried out massively parallel sequencing of
      the nucleotide sequence of 11 SE isolates obtained from poultry production
      environments (n = 9), a clam and a chicken, assembled finished genomes and
      investigated diversity of the SE genome. RESULTS: The median genome size was
      4,678,683 bp. A total of 4,833 chromosomal genes defined the pan genome of our
      field SE isolates consisting of 4,600 genes present in all the genomes, i.e.,
      core genome, and 233 genes absent in at least one genome (accessory genome).
      Genome diversity was demonstrable by the presence of 1,360 loci showing single
      nucleotide polymorphism (SNP) in the core genome which was used to portray the
      genetic distances by means of a phylogenetic tree for the SE isolates. The
      accessory genome consisted mostly of previously identified SE prophage sequences
      as well as two, apparently full- sized, novel prophages namely a 28 kb sequence
      provisionally designated as SE-OLF-10058 (3) prophage and a 43 kb sequence
      provisionally designated as SE-OLF-10012 prophage. CONCLUSIONS: The number of
      SNPs identified in the relatively large core genome of SE is a reflection of
      substantial diversity that could be exploited for strain differentiation as shown
      by the development of an informative phylogenetic tree. Prophage sequences can
      also be exploited for SE strain differentiation and lineage tracking. This work
      has laid the ground work for further studies to develop a readily adoptable
      laboratory test for the subtyping of SE.
AU  - Ogunremi D
AU  - Devenish J
AU  - Amoako K
AU  - Kelly H
AU  - Dupras AA
AU  - Belanger S
AU  - Wang LR
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2014 15: 713.

PMID- 27257199
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Lactobacillus plantarum BFE 5092 Isolated from Maasai Fermented Milk.
PG  - e00481-16
AB  - The draft genome of Lactobacillus plantarum BFE 5092 isolated from the Maasai traditional
      fermented milk product kule naoto was sequenced, and sequence
      analysis showed the assembled genome size to be 3,285,094 bp, containing a
      predicted total of 3,111 protein-encoding genes, 17 rRNAs, and 70 tRNAs.
AU  - Oguntoyinbo FA
AU  - Cho GS
AU  - Brinks E
AU  - Fiedler G
AU  - Kabisch J
AU  - Koberg S
AU  - Bockelmann W
AU  - Neve H
AU  - Kang YG
AU  - Yun D
AU  - Kim AR
AU  - Narbad A
AU  - Franz CM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00481-16.

PMID- 24926054
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Two Genetic Variant Strains of Edwardsiella piscicida,  JF1305 and RSB1309, Isolated from Olive Flounder (Paralichythys olivaceus) and  Red Sea Bream (Pagrus major) Cultured in Japan, Respectively.
PG  - e00546-14
AB  - Edwardsiella piscicida is a new species discovered within the group of organisms
      traditionally classified as Edwardsiella tarda. We present draft genome sequences
      of two variant strains of E. piscicida, JF1305 and RSB1309. Differences in
      protein-coding sequence between these isolates are associated with virulence,
      disease, and defense, suggesting differences in pathogenicity.
AU  - Oguro K
AU  - Tamura K
AU  - Yamane J
AU  - Shimizu M
AU  - Yamamoto T
AU  - Ikawa T
AU  - Ohnishi K
AU  - Oshima S
AU  - Imajoh M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00546-14.

PMID- 24855302
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Streptococcus parauberis Strain SK-417, Isolated from Diseased Sebastes ventricosus in Kagoshima, Japan.
PG  - e00453-14
AB  - Streptococcus parauberis strain SK-417 was isolated from the brain of a diseased  Sebastes
      ventricosus, collected from an aquaculture farm in April 2013 in
      Kagoshima Prefecture, Japan. The draft genome sequence, obtained with a 454 GS
      Junior sequencing system, consists of 33 large contigs of >500 bp, totaling
      1,958,836 bp, and has a G+C content of 35.4%.
AU  - Oguro K
AU  - Yamane J
AU  - Yamamoto T
AU  - Ohnishi K
AU  - Oshima S
AU  - Imajoh M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00453-14.

PMID- 21914876
VI  - 193
DP  - 2011
TI  - Whole-Genome Sequence of the Xylanase-Producing Mesoflavibacter zeaxanthinifaciens Strain S86.
PG  - 5557
AB  - We isolated Mesoflavibacter zeaxanthinifaciens S86 as xylanase-producing bacteria from
      seawater sampled in Micronesia. Analysis of the M.
      zeaxanthinifaciens genome revealed that it contains a single circular
      chromosome of 3,704,661 bp with 3,249 putative open reading frames.
AU  - Oh C
AU  - Heo SJ
AU  - De Zoysa M
AU  - Affan A
AU  - Jung WK
AU  - Park HS
AU  - Lee Y
AU  - Lee J
AU  - Yoon KT
AU  - Kang DH
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5557.

PMID- 21994933
VI  - 193
DP  - 2011
TI  - Complete genome sequence of strain s85, a novel member of the family flavobacteriaceae.
PG  - 6107
AB  - An agar-degrading marine bacterium identified as a novel member of the family
      Flavobacteriaceae (strain S85) was isolated from seawater in
      Micronesia. The sequenced strain S85 genome is composed of 3,384,629 bp in
      a circular chromosome, which includes 2,883 complete open reading frames.
AU  - Oh C
AU  - Kwon YK
AU  - Heo SJ
AU  - De Zoysa M
AU  - Affan A
AU  - Lee Y
AU  - Lee J
AU  - Choi YU
AU  - Park HS
AU  - Jung KH
AU  - Lee HY
AU  - Kang DH
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6107.

PMID- 21914866
VI  - 193
DP  - 2011
TI  - Complete genome sequence of the agarase-producing marine bacterium strain s89, representing a novel species of the genus alteromonas.
PG  - 5538
AB  - We report here the annotated genome sequence of the marine bacterium Alteromonas sp. S89 and
      the identification of six genes coding for
      agar-degrading enzymes. The sequenced Alteromonas sp. S89 genome is
      composed of a 3,864,871-bp circular chromosome that includes 3,236
      complete open reading frames.
AU  - Oh C
AU  - Zoysa MD
AU  - Kwon YK
AU  - Heo SJ
AU  - Affan A
AU  - Jung WK
AU  - Park HS
AU  - Lee J
AU  - Son SK
AU  - Yoon KT
AU  - Kang DH
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5538.

PMID- 19168610
VI  - 191
DP  - 2009
TI  - The Complete Genome Sequence of Erythrobacter litoralis HTCC2594.
PG  - 2419-2420
AB  - Erythrobacter litoralis has been known as a bacteriochlorophyll a-containing aerobic
      anoxygenic phototrophic bacterium. Here we announce
      the complete genome sequence of E. litoralis HTCC2594 that is devoid of
      phototrophic potential. E. litoralis HTCC2594, isolated by
      dilution-to-extinction culturing from seawater, could not carry out
      aerobic anoxygenic phototrophy and lacked genes for bacteriochlorophyll a
      biosynthesis and photosynthetic reaction center proteins.
AU  - Oh HM
AU  - Giovannoni SJ
AU  - Ferriera S
AU  - Johnson J
AU  - Cho JC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2009 191: 2419-2420.

PMID- 19767438
VI  - 191
DP  - 2009
TI  - Complete Genome Sequence of Robiginitalea biformata HTCC2501.
PG  - 7144-7145
AB  - Robiginitalea biformata HTCC2501, isolated by dilution-to-extinction culturing from the
      Sargasso Sea, has been known as an aerobic chemoheterotroph with carotenoid pigments and
      dimorphic growth phases. Here we announce the complete genome sequence of R. biformata
      HTCC2501 that contained genes for carotenoid biosynthesis and several macromolecule-degrading
      enzymes.
AU  - Oh HM
AU  - Giovannoni SJ
AU  - Lee K
AU  - Ferriera S
AU  - Johnson J
AU  - Cho JC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2009 191: 7144-7145.

PMID- 20601481
VI  - 192
DP  - 2010
TI  - Genome Sequence of an Oligotrophic Marine Gammaproteobacterium HTCC2143 Isolated from Oregon Coast.
PG  - 4530-4531
AB  - Strain HTCC2143 was isolated from Oregon Coast surface waters using dilution-to-extinction
      culturing. Here we present the genome of strain
      HTCC2143 from BD1-7 clade of the oligotrophic marine Gammaproteobacteria
      group (OMG). The genome of HTCC2143 encodes genes for carotenoid
      biosynthesis, proteorhodopsin, and genes that have potential
      biotechnological significance: epoxide hydrolases, Baeyer-Villiger
      monooxygenases, and polyketide synthases.
AU  - Oh HM
AU  - Kang I
AU  - Ferriera S
AU  - Giovannoni SJ
AU  - Cho JC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 4530-4531.

PMID- 21515764
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Strain IMCC9063 Belonging to SAR11 subgroup 3, Isolated from the Arctic Ocean.
PG  - 3379-3380
AB  - Strain IMCC9063 is a novel isolate of the SAR11 clade and is distantly related to other
      cultured representatives in this clade. The strain was
      isolated off the coast of Svalbard, Norway by applying high-throughput
      culturing methods based on dilution-to-extinction. Here we present the
      finished genome sequence of strain IMCC9063.
AU  - Oh HM
AU  - Kang I
AU  - Lee K
AU  - Jang Y
AU  - Lim SI
AU  - Cho JC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3379-3380.

PMID- 21037002
VI  - 193
DP  - 2010
TI  - Complete Genome Sequence of Parvularcula bermudensis HTCC2503T, the type species of the order 'Parvularculales' in the Alphaproteobacteria.
PG  - 305-306
AB  - The order 'Parvularculales' represents the seventh order in the class Alphaproteobacteria.
      Parvularcula bermudensis, the type species of the order, was isolated from the Sargasso Sea
      using dilution-to-extinction culturing. We present here the complete genome sequence of
      Parvularcula bermudensis HTCC2503(T) that contains genes for carotenoid biosynthesis,
      dimethylsulfoniopropionate demethylase, and transduction-like gene transfer agents.
AU  - Oh HM
AU  - Kang I
AU  - Vergin KL
AU  - Kang D
AU  - Rhee KH
AU  - Giovannoni SJ
AU  - Cho JC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 193: 305-306.

PMID- 21036991
VI  - 193
DP  - 2010
TI  - Genome Sequence of Oceanicaulis sp. HTCC2633, Isolated from the Western Sargasso Sea.
PG  - 317-318
AB  - The genus Oceanicaulis represents dimorphic rods that were originally isolated from a marine
      dinoflagellate. Here we announce the genome sequence of Oceanicaulis sp. strain HTCC2633,
      isolated by dilution-to-extinction culturing from the Sargasso Sea. The genome information of
      strain HTCC2633 indicates a chemoorganotrophic way of life of this strain.
AU  - Oh HM
AU  - Kang I
AU  - Vergin KL
AU  - Lee K
AU  - Giovannoni SJ
AU  - Cho JC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 193: 317-318.

PMID- 21037013
VI  - 193
DP  - 2010
TI  - Complete Genome Sequence of strain HTCC2170, a Novel Member of the Genus Maribacter in the Family Flavobacteriaceae.
PG  - 303-304
AB  - Strain HTCC2170 was isolated from surface waters off the Oregon coast using
      dilution-to-extinction culturing. Here we present the finished genome sequence of a marine
      bacterium, Maribacter sp. HTCC2170. Maribacter sp. HTCC2170 is predicted to be a facultatively
      aerobic chemoorganotroph that is capable of macromolecule degradation and anaerobic
      respiration based on genomic sequence analysis.
AU  - Oh HM
AU  - Kang I
AU  - Yang SJ
AU  - Jang Y
AU  - Vergin KL
AU  - Giovannoni SJ
AU  - Cho JC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 193: 303-304.

PMID- 20382761
VI  - 192
DP  - 2010
TI  - Complete genome sequence of 'Candidatus Puniceispirillum marinum' IMCC1322, a representative of the SAR116 clade in the Alphaproteobacteria.
PG  - 3240-3241
AB  - The complete genome sequence of 'Candidatus Puniceispirillum marinum' IMCC1322, the first
      cultured representative of the SAR116 clade in the
      Alphaproteobacteria, is reported here. The genome contains genes for
      proteorhodopsin, aerobic-type carbon monoxide dehydrogenase,
      dimethylsulfoniopropionate demethylase, and C(1) compound metabolism. The
      genome information proposes the SAR116 group to be metabolic generalists
      in ocean nutrient cycling.
AU  - Oh HM
AU  - Kwon KK
AU  - Kang I
AU  - Kang SG
AU  - Lee JH
AU  - Kim SJ
AU  - Cho JC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 3240-3241.

PMID- 21572000
VI  - 193
DP  - 2011
TI  - Genome Sequence of Strain IMCC9480, a Xanthorhodopsin-bearing Betaproteobacterium Isolated from the Arctic Ocean.
PG  - 3421
AB  - Strain IMCC9480 is a novel member of the family Oxalobacteraceae of the Betaproteobacteria,
      isolated from the Arctic Ocean by
      dilution-to-extinction culturing. Here we present the draft genome
      sequence of strain IMCC9480. The genome is predicted to contain genes for
      xanthorhodopsin, retinoid biosynthesis, carbon monoxide dehydrogenase, and
      C1 metabolism.
AU  - Oh HM
AU  - Lee K
AU  - Jang Y
AU  - Kang I
AU  - Kim HJ
AU  - Kang TW
AU  - Kim SY
AU  - Cho JC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3421.

PMID- 16788065
VI  - 103
DP  - 2006
TI  - The complete genome sequence of a chronic atrophic gastritis Helicobacter pylori strain: Evolution during disease progression.
PG  - 9999-10004
AB  - Helicobacter pylori produces acute superficial gastritis in nearly all of its human hosts.
      However, a subset of individuals develops chronic atrophic gastritis (ChAG), a condition
      characterized in part by diminished numbers of acid-producing parietal cells and increased
      risk for development of gastric adenocarcinoma. Previously, we used a gnotobiotic transgenic
      mouse model with an engineered ablation of parietal cells to show that loss of parietal cells
      provides an opportunity for a H. pylori isolate from a patient with ChAG (HPAG1) to bind to,
      enter, and persist within gastric stem cells. This finding raises the question of how ChAG
      influences H. pylori genome evolution, physiology, and tumorigenesis. Here we describe the
      1,596,366-bp HPAG1 genome. Custom HPAG1 Affymetrix GeneChips, representing 99.6% of its
      predicted ORFs, were used for whole-genome genotyping of additional H. pylori ChAG isolates
      obtained from Swedish patients enrolled in a case-control study of gastric cancer, as well as
      ChAG- and cancer-associated isolates from an individual who progressed from ChAG to gastric
      adenocarcinoma. The results reveal a shared gene signature among ChAG strains, as well as
      genes that may have been lost or gained during progression to adenocarcinoma. Whole-genome
      transcriptional profiling of HPAG1's response to acid during in vitro growth indicates that
      genes encoding components of metal uptake and utilization pathways, outer membrane proteins,
      and virulence factors are among those associated with H. pylori's adaptation to ChAG.
AU  - Oh JD
AU  - Kling-Backhed H
AU  - Giannakis M
AU  - Xu J
AU  - Fulton RS
AU  - Fulton LA
AU  - Cordum HS
AU  - Wang C
AU  - Elliott G
AU  - Edwards J
AU  - Mardis ER
AU  - Engstrand LG
AU  - Gordon JI
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2006 103: 9999-10004.

PMID- 25377713
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of a Novel SAR11 Clade Species Abundant in a Tibetan Lake.
PG  - e01137-14
AB  - SAR11 clade bacteria are abundant and play a key role in the nutrient cycles of marine and,
      presumably, inland aquatic environments. We report here the draft
      genome sequence of a novel species in the SAR11 cluster, reconstructed from a
      metagenomic data set obtained from a Tibetan lake.
AU  - Oh S
AU  - Zhang R
AU  - Wu QL
AU  - Liu WT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01137-14.

PMID- 28705979
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Bacillus altitudinis YNP4-TSU, Isolated from Yellowstone National Park.
PG  - e00631-17
AB  - Undisturbed hot springs inside Yellowstone National Park remain a dynamic biome for novel
      cellulolytic thermophiles. We report here the draft genome sequence of
      one of these isolates, Bacillus altitudinis YNP4-TSU.
AU  - OHair JA
AU  - Li H
AU  - Thapa S
AU  - Scholz M
AU  - Zhou S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00631-17.

PMID- 24526630
VI  - 2
DP  - 2014
TI  - The Complete Genome Sequence of Pseudomonas putida NBRC 14164T Confirms High Intraspecies Variation.
PG  - e00029-14
AB  - Pseudomonas putida has attracted much interest for its environmental, industrial,
      biotechnological, and clinical importance. Here, we report the complete genome
      sequence of the type strain P. putida NBRC 14164. This genome sequence will
      assist to further elucidate the molecular mechanisms of the characteristic traits
      among strains belonging to the species P. putida.
AU  - Ohji S
AU  - Yamazoe A
AU  - Hosoyama A
AU  - Tsuchikane K
AU  - Ezaki T
AU  - Fujita N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00029-14.

PMID- 24459258
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Alkaliphilic and Xylanolytic Paenibacillus sp. Strain JCM 10914, Isolated from the Gut of a Soil-Feeding Termite.
PG  - e01144-13
AB  - Panibacillus sp. strain JCM 10914 is a xylanolytic alkaliphile isolated from the  gut of a
      soil-feeding termite. Its draft genome sequence revealed various genes
      for hydrolytic enzymes and will facilitate studies on adaptation to the highly
      alkaline gut environment and its role in digesting soil organic matter in the
      gut.
AU  - Ohkuma M
AU  - Yuki M
AU  - Oshima K
AU  - Suda W
AU  - Oshida Y
AU  - Kitamura K
AU  - Iida T
AU  - Hattori M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01144-13.

PMID- 24604644
VI  - 2
DP  - 2014
TI  - Genome Sequence of a Bacillus anthracis Outbreak Strain from Zambia, 2011.
PG  - e00116-14
AB  - In August 2011, an anthrax outbreak occurred among Hippopotamus amphibius hippopotamuses and
      humans in Zambia. Here, we report the draft genome sequence of
      the Bacillus anthracis outbreak strain CZC5, isolated from tissues of H.
      amphibius hippopotamuses that had died in the outbreak area.
AU  - Ohnishi N
AU  - Maruyama F
AU  - Ogawa H
AU  - Kachi H
AU  - Yamada S
AU  - Fujikura D
AU  - Nakagawa I
AU  - Hang'ombe MB
AU  - Thomas Y
AU  - Mweene AS
AU  - Higashi H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00116-14.

PMID- 18375553
VI  - 190
DP  - 2008
TI  - Genome sequence of the streptomycin-producing microorganism Streptomyces griseus IFO 13350.
PG  - 4050-4060
AB  - We determined the complete genome sequence of Streptomyces griseus IFO 13350, a soil bacterium
      producing an antituberculosis agent, streptomycin, which is the first aminoglycoside
      antibiotic, discovered more than 60 years ago. The linear chromosome consists of 8,545,929
      base pairs (bp), with an average G+C content of 72.2%, predicting 7,138 open reading frames,
      six rRNA operons (16S-23S-5S), and 66 tRNA genes. It contains extremely long terminal inverted
      repeats (TIRs) of 132,910 bp each. The telomere's nucleotide sequence and secondary
      structure, consisting of several palindromes with a loop sequence of 5'-GGA-3', are
      different from those of typical telomeres conserved among other Streptomyces species. In
      accordance with the difference, the chromosome has pseudogenes for a conserved terminal
      protein (Tpg) and a telomere-associated protein (Tap), and a novel pair of Tpg and Tap
      proteins is instead encoded by the TIRs. Comparisons with the genomes of two related species,
      Streptomyces coelicolor A3(2) and Streptomyces avermitilis, clarified not only the
      characteristics of the S. griseus genome but also the existence of 24 Streptomyces-specific
      proteins. The S. griseus genome contains 34 gene clusters or genes for the biosynthesis of
      known or unknown secondary metabolites. Transcriptome analysis using a DNA microarray showed
      that at least four of these clusters, in addition to the streptomycin biosynthesis gene
      cluster, were activated directly or indirectly by AdpA, which is a central transcriptional
      activator for secondary metabolism and morphogenesis in the A-factor (a gamma-butyrolactone
      signaling molecule) regulatory cascade in S. griseus.
AU  - Ohnishi Y
AU  - Ishikawa J
AU  - Hara H
AU  - Suzuki H
AU  - Ikenoya M
AU  - Ikeda H
AU  - Yamashita A
AU  - Hattori M
AU  - Horinouchi S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2008 190: 4050-4060.

PMID- 18192396
VI  - 190
DP  - 2008
TI  - Maintenance forced by a restriction-modification system can be modulated by a region in its modification enzyme not essential for methyltransferase activity.
PG  - 2039-2049
AB  - Several type II restriction-modification gene complexes can force their maintenance on their
      host bacteria by killing cells that have lost them
      in a process called postsegregational killing or genetic addiction. It
      is likely to proceed by dilution of the modification enzyme molecule
      during rounds of cell division following the gene loss, which exposes
      unmethylated recognition sites on the newly replicated chromosomes to
      lethal attack by the remaining restriction enzyme molecules. This
      process is in apparent contrast to the process of the classical types
      of postsegregational killing systems, in which built-in metabolic
      instability of the antitoxin allows release of the toxin for lethal
      action after the gene loss. In the present study, we characterize a
      mutant form of the EcoRII gene complex that shows stronger capacity in
      such maintenance. This phenotype is conferred by an L80P amino acid
      substitution (T239C nucleotide substitution) mutation in the
      modification enzyme. This mutant enzyme showed decreased DNA
      methyltransferase activity at a higher temperature in vivo and in vitro
      than the nonmutated enzyme, although a deletion mutant lacking the
      N-terminal 83 amino acids did not lose activity at either of the
      temperatures tested. Under a condition of inhibited protein synthesis,
      the activity of the L80P mutant was completely lost at a high
      temperature. In parallel, the L80P mutant protein disappeared more
      rapidly than the wild-type protein. These results demonstrate that the
      capability of a restriction-modification system in forcing maintenance
      on its host can be modulated by a region of its antitoxin, the
      modification enzyme, as in the classical postsegregational killing
      systems.
AU  - Ohno S
AU  - Handa N
AU  - Watanabe-Matsui M
AU  - Takahashi N
AU  - Kobayashi I
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2008 190: 2039-2049.

PMID- 8667030
VI  - 67
DP  - 1996
TI  - Molecular cloning and characterization of annexin V-binding proteins with highly hydrophilic peptide structure.
PG  - 89-97
AB  - We previously reported that annexin V promoted the survival of cultured rat neocortical
      neurons.  In an effort to elucidate the mechanism underlying this neurotrophic activity of
      annexin V, we have attempted to identify the target or binding proteins of annexin V in
      neuronal cells.  Herein, we screened an embryonic day 17 rat brain cDNA library by western
      blot using glutathione S-transferase-annexin V fusion protein as a probe and then isolated
      four clones showing binding to annexin V in a ca2+ - and phospholipid-dependent manner.
      Although these cDNAs encoded different polypeptides, all four polypeptides shared the unique
      feature of containing highly hydrophilic stretches with high Lys, Glu, and Ser contents.
      Deduced amino acid sequences of two clones showed high homology with human X-linked Helicase2
      (XH2) and DNA (cytosine-5) methyltransferase (DMTase) sequences, whereas the other two were
      not related to any known peptide sequence.  These results suggest that XH2 and DMTase are
      candidates for annexin V-binding proteins and thus may mediate the biological activity of
      annexin V.
AU  - Ohsawa K
AU  - Imai Y
AU  - Ito D
AU  - Kohsaka S
PT  - Journal Article
TA  - J. Neurochem.
JT  - J. Neurochem.
SO  - J. Neurochem. 1996 67: 89-97.

PMID- 11751814
VI  - 184
DP  - 2002
TI  - Molecular organization of intrinsic restriction and modification genes BsuM of Bacillus subtilis Marburg.
PG  - 381-389
AB  - Transcriptional analysis and disruption of five open reading frames (ORFs), ydiO, ydiP, ydiR,
      ydiS, and ydjA, in the prophage 3 region of the chromosome of Bacillus subtilis Marburg
      revealed that they are component genes of the intrinsic BsuM restriction and modification
      system of this organism. The classical mutant strain RM125, which lacks the restriction and
      modification system of B. subtilis Marburg, lacks the prophage 3 region carrying these five
      ORFs. These ORFs constitute two operons, the ydiO-ydiP operon and the ydiR-ydiS-ydjA operon,
      both of which are expressed during the logarithmic phase of growth. The predicted gene
      products YdiO and YdiP are the orthologues of cytosine DNA methyltransferases. The predicted
      YdiS product is an orthologue of restriction nucleases, while the predicted YdiR and YdjA
      products have no apparent paralogues and orthologues whose functions are known. Disruption of
      the ydiR-ydiS-ydjA operon resulted in enhanced transformation by plasmid DNA carrying multiple
      BsuM target sequences. Disruption of ydiO or ydiP function requires disruption of at least one
      of the following genes on the chromosome: ydiR, ydiS, and ydjA. The degrees of methylation of
      the BsuM target sequences on chromosomal DNAs were estimated indirectly by determining the
      susceptibility to digestion with XhoI (an isoschizomer of BsuM) of DNAs extracted from the
      disruptant strains. Six XhoI (BsuM) sites were examined. XhoI digested at the XhoI sites in
      the DNAs from disruptants with disruptions in both operons, while XhoI did not digest at the
      XhoI sites in the DNAs from the wild-type strain or from the disruptants with disruptions in
      the ydiR-ydiS-ydjA operon. Therefore, the ydiO-ydiP operon and the ydiR-ydiS-ydjA operon are
      considered operons that are responsible for BsuM modification and BsuM restriction,
      respectively.
AU  - Ohshima H
AU  - Matsuoka S
AU  - Asai K
AU  - Sadaie Y
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2002 184: 381-389.

PMID- 8095080
VI  - 17C
DP  - 1993
TI  - A novel meiosis-induced site-specific endonuclease activity in yeast mitochondria.
PG  - 174
AB  - Sequence-specific endonucleases in eukaryotic cells have been shown to play a crucial role in
      the initiation of genetic recombination. We have found a sequence-specific DNA endonuclease
      activity that cuts DNAs of phage Phi105c and phage Phix174 in a cell-free extracts of a
      synchronously-sporulating strain (SK1) of S. cerevisiae. The preparation from SK1 cells in
      early meiotic phase had 40-fold higher activity than that in exponential growing phase.
      Subcellular fractionation revealed that this activity is condensed in the crude mitochondrial
      fraction. In addition, the activity to cut Phi105c DNA was not detected in the extract from
      p-mutant (large deletion mutations that block all mitochondrial protein synthesis) of the SK1
      strain. Furthermore, the ability to produce the endonuclease was able to be transferred into a
      po strain by mitochondrial transfer through cytoduction. Comparison of nucleotide sequences
      around the cutting sites in Phi 105c and Phix174 DNA suggests that the endonuclease recognizes
      a -20 base pair sequence and generates ends with 4 base-5' overhang. The sequences around the
      cutting sites are different from those by an other yeast mitochondrial endonucleases. As well
      as other yeast mitochondrial sequence-specific endonucleases, the endonuclease in SK1 strain
      is speculated to initiate gene conversion in the mitochondrial genome.
AU  - Ohta K
AU  - Keszenman-Pereyra D
AU  - Nicolas A
AU  - Shibata T
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1993 17C: 174.

PMID- 8602156
VI  - 250
DP  - 1996
TI  - Endo.SK1: an inducible site-specific endonuclease from yeast mitochondria.
PG  - 395-404
AB  - Site-specific endonucleases have been found in various eukaryotic organelles such
      as mitochondria, chloroplasts and nuclei.  These endonucleases initiate site-specific or
      homologous
      gene conversion in mitochondrial and nuclear DNA.  Here, we report a new site-specific
      endonuclease activity, Endo.SK1, identified in mitochondria of strain SK1, a homothallic
      diploid
      strain of Saccharomyces cerevisiae.  Nucleotide sequences around the Endo.SK1-cleavage sites
      are
      different from those of known yeast site-specific endonucleases.  The Endo.SK1 activity is, at
      least partly, specified by a gene in the Sk1-derived mitochondria.  A novel feature of the
      Endo.SK1 activity is its inducibility: the endonuclease activity was induced by ca. 40-fold by
      transfer of cells from a glucose medium into an acetate medium, and was then repressed.  This
      transient induction was independent of the ploidy level of the cells, and coincided with
      induction of
      fumarase, a mitochondrial enzyme involved in the TCA cycle.  Co-induction and co-repression of
      the mitochondrial site-specific endonuclease activity and a respiration-related enzyme
      indicate that
      the endonuclease activity is regulated in response to physiological conditions, and suggest a
      possible role for the endonuclease in mitochondrial DNA metabolism.
AU  - Ohta K
AU  - Nicolas A
AU  - Keszenman-Pereyra D
AU  - Shibata T
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1996 250: 395-404.

PMID- 25593249
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Novosphingobium sp. Strain MBES04, Isolated from Sunken  Wood from Suruga Bay, Japan.
PG  - e01373-14
AB  - This report describes the draft genome sequence of Novosphingobium sp. strain MBES04, isolated
      from sunken wood from Suruga Bay, Japan, which is capable of
      degrading a wide range of lignin-related aromatic monomers. The draft genome
      sequence contains 5,361,448 bp, with a G+C content of 65.4%.
AU  - Ohta Y
AU  - Nishi S
AU  - Kobayashi K
AU  - Tsubouchi T
AU  - Iida K
AU  - Tanizaki A
AU  - Kurosawa K
AU  - Adachi A
AU  - Nishihara M
AU  - Sato R
AU  - Hasegawa R
AU  - Hatada Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01373-14.

PMID- 29700143
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Sphingobium sp. Strain YG1, a Lignin Model Dimer-Metabolizing Bacterium Isolated from Sediment in Kagoshima Bay, Japan.
PG  - e00267-18
AB  - Sphingobium sp. strain YG1 is a lignin model dimer-metabolizing bacterium newly isolated from
      sediment in Kagoshima, Japan, at a depth of 102 m. Here, we report
      the complete genome nucleotide sequence of strain YG1.
AU  - Ohta Y
AU  - Shimane Y
AU  - Nishi S
AU  - Ichikawa J
AU  - Kurosawa K
AU  - Tsubouchi T
AU  - Ishii S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00267-18.

PMID- 18776676
VI  - 72
DP  - 2008
TI  - Restriction on conjugational transfer of pLS20 in Bacillus subtilis 168.
PG  - 2472-2475
AB  - Conjugational transfer of pLS20 in Bacillus subtilis Marburg 168 is restricted by the BsuM
      restriction modification system. Restriction
      efficiency was measured using pLS20 derivatives possessing various
      numbers of XhoI sites, which are known to be recognized by BsuM. An
      increase in XhoI sites clearly reduced the conjugational efficiency of
      pLS20 as compared with that of pUB110 plasmid lacking XhoI.
AU  - Ohtani N
AU  - Sato M
AU  - Tomita M
AU  - Itaya M
PT  - Journal Article
TA  - Biosci. Biotechnol. Biochem.
JT  - Biosci. Biotechnol. Biochem.
SO  - Biosci. Biotechnol. Biochem. 2008 72: 2472-2475.

PMID- 22212656
VI  - 16
DP  - 2012
TI  - The third plasmid pVV8 from Thermus thermophilus HB8: isolation, characterization, and sequence determination.
PG  - 237-244
AB  - The extremely thermophilic bacterium Thermus thermophilus is a model organism for structural
      biology and systems biology, and the so-called "Structural and Functional Whole-Cell Project
      for T. thermophilus HB8" is in progress. The released genomic sequence of the strain HB8 is
      composed of chromosome, pTT27 megaplasmid, and pTT8 plasmid. In this paper, however, a third
      plasmid was demonstrated and its sequence was determined. Although this plasmid pVV8 had been
      reported before, limited information and an unfortunate dropout in the substrain, whose
      genomic sequence was determined, would have prevented the plasmid from coming to public
      attention. The intrinsic circular plasmid, which was estimated to be six to ten copies in a
      cell, is 81151 bp and its G + C content is 68%. Among the identified 91 ORFs, a single gene
      has been experimentally analyzed before and is known as xylose isomerase. The phnCDEGHIJKLMX
      operon related to phosphonate metabolism, alkaline phosphatase, putative transcriptional
      regulators, several sets of toxin-antitoxin system, and transposase-like ORFs are also encoded
      on the pVV8 plasmid. Although association with cell aggregation was the one phenotypic
      characteristic of the plasmid that had been reported, it was never confirmed. Comparison of T.
      thermophilus HB8 strains suggests that the pVV8 is nonessential for growth.
AU  - Ohtani N
AU  - Tomita M
AU  - Itaya M
PT  - Journal Article
TA  - Extremophiles
JT  - Extremophiles
SO  - Extremophiles 2012 16: 237-244.

PMID- 24179121
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Ralstonia pickettii DTP0602, a 2,4,6-Trichlorophenol  Degrader.
PG  - e00903-13
AB  - Ralstonia pickettii strain DTP0602 utilizes 2,4,6-trichlorophenol as its sole carbon and
      energy source. Here, we report the complete genome sequence of strain
      DTP0602, which comprises three chromosomes and no plasmids. We also found that
      the two had gene clusters responsible for the degradation of
      2,4,6-trichlorophenol are located on the 2.9-Mb chromosome 2.
AU  - Ohtsubo Y
AU  - Fujita N
AU  - Nagata Y
AU  - Tsuda M
AU  - Iwasaki T
AU  - Hatta T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00903-13.

PMID- 24482516
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Pseudomonas sp. Strain TKP, Isolated from a gamma-Hexachlorocyclohexane-Degrading Mixed Culture.
PG  - e01241-13
AB  - Pseudomonas sp. strain TKP does not degrade gamma-hexachlorocyclohexane (gamma-HCH), but it
      persistently coexists with the gamma-HCH-degrading
      Sphingobium sp. strain TKS in a mixed culture enriched by gamma-HCH. Here, we
      report the complete genome sequence of strain TKP, which consists of one circular
      chromosome with a size of 7 Mb.
AU  - Ohtsubo Y
AU  - Kishida K
AU  - Sato T
AU  - Tabata M
AU  - Kawasumi T
AU  - Ogura Y
AU  - Hayashi T
AU  - Tsuda M
AU  - Nagata Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01241-13.

PMID- 23209225
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Acidovorax sp. Strain KKS102, a Polychlorinated-Biphenyl Degrader.
PG  - 6970-6971
AB  - We report the complete genome sequence of Acidovorax sp. strain KKS102, a
      polychlorinated-biphenyl-degrading strain isolated from a soil sample in Tokyo.
      The genome contains a single circular 5,196,935-bp chromosome and no plasmids.
AU  - Ohtsubo Y
AU  - Maruyama F
AU  - Mitsui H
AU  - Nagata Y
AU  - Tsuda M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6970-6971.

PMID- 26543118
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of a Phenanthrene Degrader, Burkholderia sp. HB-1 (NBRC  110738).
PG  - e01283-15
AB  - The phenanthrene-degrading Burkholderia sp. HB-1 was isolated from a phenanthrene-enrichment
      culture seeded with a pristine farm soil sample. We
      report the complete genome sequence of HB-1, which has been deposited to the
      stock culture (NBRC 110738) at Biological Resource Center, National Institute of
      Technology and Evaluation (NITE), Tokyo, Japan. The genome of strain HB-1
      comprises two circular chromosomes of 4.1 Mb and 3.1 Mb. The finishing was
      facilitated by the computational tools GenoFinisher, AceFileViewer, and
      ShortReadManager.
AU  - Ohtsubo Y
AU  - Moriya A
AU  - Kato H
AU  - Ogawa N
AU  - Nagata Y
AU  - Tsuda M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01283-15.

PMID- 26472829
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Polyvinyl Alcohol-Degrading Strain Sphingopyxis sp. 113P3 (NBRC 111507).
PG  - e01169-15
AB  - Strain 113P3 was isolated from activated sludge and identified as a polyvinyl alcohol
      (PVA)-degrading Pseudomonas species; it was later reidentified as Sphingopyxis species. Only
      three genes are directly relevant to the metabolism of PVA and comprise the pva operon, which
      was deposited as accession no. AB190228. Here, we report the complete genome sequence of
      strain 113P3, which has been conserved as a stock culture (NBRC 111507) at the Biological
      Resource Center, National Institute of Technology and Evaluation (NITE) (Tokyo, Japan). The
      genome of strain 113P3 is composed of a 4.4-Mb circular chromosome and a 243-kb plasmid. The
      whole finishing was conducted in silico except for four PCRs. The sequence corresponding to
      AB190288 exists on the chromosome.
AU  - Ohtsubo Y
AU  - Nagata Y
AU  - Numata M
AU  - Tsuchikane K
AU  - Hosoyama A
AU  - Yamazoe A
AU  - Tsuda M
AU  - Fujita N
AU  - Kawai F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01169-15.

PMID- 26659674
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Sphingopyxis macrogoltabida Type Strain NBRC 15033, Originally Isolated as a Polyethylene Glycol Degrader.
PG  - e01401-15
AB  - Sphingopyxis macrogoltabida strain 203, the type strain of the species, grew on polyethylene
      glycol (PEG) and has been deposited to the stock culture at the
      Biological Resource Center, National Institute of Technology and Evaluation
      (NITE), under the number NBRC 15033. Here, we report the complete genome sequence
      of strain NBRC 15033. Unfortunately, genes for PEG degradation were missing.
AU  - Ohtsubo Y
AU  - Nagata Y
AU  - Numata M
AU  - Tsuchikane K
AU  - Hosoyama A
AU  - Yamazoe A
AU  - Tsuda M
AU  - Fujita N
AU  - Kawai F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01401-15.

PMID- 26659673
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of a Polypropylene Glycol-Degrading Strain, Microbacterium sp. No. 7.
PG  - e01400-15
AB  - Microbacterium (formerly Corynebacterium) sp. No. 7 was isolated from activated sludge as a
      polypropylene glycol (PPG)-assimilating bacterial strain. Its
      oxidative PPG degradation has been proposed on the basis of PPG dehydrogenase
      activity and the metabolic products. Here, we report the complete genome sequence
      of Microbacterium sp. No. 7. The genome of the strain No. 7 is composed of a
      4,599,046-bp circular chromosome and two linear plasmids. The whole finishing was
      conducted in silico with aids of the computational tools GenoFinisher and
      AceFileViewer. Strain No. 7 is available from the Biological Resource Center,
      National Institute of Technology and Evaluation (NITE) (Tokyo, Japan).
AU  - Ohtsubo Y
AU  - Nagata Y
AU  - Numata M
AU  - Tsuchikane K
AU  - Hosoyama A
AU  - Yamazoe A
AU  - Tsuda M
AU  - Fujita N
AU  - Kawai F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01400-15.

PMID- 26634754
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Polypropylene Glycol- and Polyethylene Glycol-Degrading Sphingopyxis macrogoltabida Strain EY-1.
PG  - e01399-15
AB  - Strain EY-1 was isolated from a microbial consortium growing on a random polymer  of ethylene
      oxide and propylene oxide. Strain EY-1 grew on polyethylene glycol
      and polypropylene glycol and identified as Sphingopyxis macrogoltabida. Here, we
      report the complete genome sequence of Sphingopyxis macrogoltabida EY-1. The
      genome of strain EY-1 is comprised of a 4.76-Mb circular chromosome, and five
      plasmids. The whole finishing was conducted in silico, with aids of computational
      tools GenoFinisher and AceFileViewer. Strain EY-1 is available from Biological
      Resource Center, National Institute of Technology and Evaluation (Tokyo, Japan)
      (NITE).
AU  - Ohtsubo Y
AU  - Nagata Y
AU  - Numata M
AU  - Tsuchikane K
AU  - Hosoyama A
AU  - Yamazoe A
AU  - Tsuda M
AU  - Fujita N
AU  - Kawai F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01399-15.

PMID- 27284143
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Sphingopyxis terrae Strain 203-1 (NBRC 111660), a Polyethylene Glycol Degrader.
PG  - e00530-16
AB  - The complete genome sequence of Sphingopyxis terrae strain 203-1, which is capable of growing
      on polyethylene glycol, was determined. The genome consisted
      of a chromosome with a size of 3.98 Mb and a plasmid with a size of 4,328 bp. The
      strain was deposited to the National Institute of Technology and Evaluation
      (Tokyo, Japan) under the number NBRC 111660.
AU  - Ohtsubo Y
AU  - Nonoyama S
AU  - Nagata Y
AU  - Numata M
AU  - Tsuchikane K
AU  - Hosoyama A
AU  - Yamazoe A
AU  - Tsuda M
AU  - Fujita N
AU  - Kawai F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00530-16.

PMID- 27284142
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Sphingopyxis macrogoltabida Strain 203N (NBRC 111659), a Polyethylene Glycol Degrader.
PG  - e00529-16
AB  - We determined the complete genome sequence of Sphingopyxis macrogoltabida strain  203N, a
      polyethylene glycol degrader. Because the PacBio assembly (285x coverage)
      seemed to be full of nucleotide-level mismatches, the Newbler assembly of MiSeq
      mate-pair and paired-end data was used for finishing and the PacBio assembly was
      used as a reference. The PacBio assembly carried 414 nucleotide mismatches over
      5,953,153 bases of the 203N genome.
AU  - Ohtsubo Y
AU  - Nonoyama S
AU  - Nagata Y
AU  - Numata M
AU  - Tsuchikane K
AU  - Hosoyama A
AU  - Yamazoe A
AU  - Tsuda M
AU  - Fujita N
AU  - Kawai F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00529-16.

PMID- 24459257
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Pseudomonas aeruginosa MTB-1, Isolated from a Microbial Community Enriched by the Technical Formulation of  Hexachlorocyclohexane.
PG  - e01130-13
AB  - Pseudomonas aeruginosa MTB-1 does not degrade gamma-hexachlorocyclohexane (gamma-HCH), but
      this bacterium persistently coexists with a gamma-HCH-degrading
      strain, Sphingomonas sp. MM-1, in a microbial community enriched by the technical
      formulation of HCH. Here we report the complete MTB-1 genome sequence, with a
      6.6-Mb circular chromosome.
AU  - Ohtsubo Y
AU  - Sato T
AU  - Kishida K
AU  - Tabata M
AU  - Ogura Y
AU  - Hayashi T
AU  - Tsuda M
AU  - Nagata Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01130-13.

PMID- 6321178
VI  - 139
DP  - 1984
TI  - Recognition by restriction endonuclease EcoRI of deoxyoctanucleotides containing modified sugar moieties.
PG  - 447-450
AB  - The deoxyribooctanucleotide d(G-G-A-A-T-T-C-C), containing the recognition sequence for EcoRI,
      d(G-A-A-T-T-C), and analogs containing modified sugar moieties were tested for their activity
      in cleavage with EcoRI.  These analogs, with replacement in the third position from the 5'
      end, were synthesized using 9-b-D-arabinosyladenine (aA), 2'-deoxy-2'-fluoroadenosine (Afl)
      and adenosine (rA).  Duplex formation by the three analogs was confirmed by measurements of
      ultraviolet/temperature profiles.  It was found that EcoRI cleaved these duplexes less
      efficiently than d(G-G-A-A-T-T-C-C).  The adenosine-containing analog d(G-G)-rA-d(A-T-T-C-C)
      was cleaved much more slowly than d(G-G)-aA-d(A-T-T-C-C) and d(G-G-Afl-A-T-T-C-C).  The
      corresponding ribooctamer G-G-A-A-U-U-C-C showed a higher melting temperature than the
      deoxyoctamers but its duplex was not cleaved by this enzyme.  An analog with
      2'-deoxy-2'-fluoroguanosine at the second position was cleaved by the endonuclease faster
      than the natural deoxyoctamer.
AU  - Ohtsuka E
AU  - Ishino Y
AU  - Ibaraki K
AU  - Ikehara M
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1984 139: 447-450.

PMID- 6284393
VI  - 30
DP  - 1982
TI  - Studies on deoxynucleic acids and related compounds.  IV. Syntheses of an octanucleotide containing a recognition site for restriction enzyme EcoRI and of an arabinosyladenine analog.
PG  - 874-880
AB  - An octanucleotide containing a recognition site for EcoRI and its
      arabinosyladenine (araA) analog, dGGAATTCC and dGGaraAATTCC, were synthesized
      by the phosphotriester approach with phosphoro-p-anisidate as the protecting
      group for 3'-phosphodiesters.  araA was converted to
      5'-dimethoxytrityl-N,2'-O-O-benzoyl 3'-p-chlorophenyl phosphate and condensed
      with N-benzoyldeoxyadenosine 3'-p-chlorophenyl phosphoro-p-anisidate to yield
      the protected araAdAp.  Other deoxynucleotide blocks (dAAp, dGGp) were prepared
      similarly and condensed with a 5'-deblocked dTTCC block having the 3'-O-benzoyl
      group after removal of the p-anisidate group with isoamyl nitrite.
AU  - Ohtsuka E
AU  - Morisawa H
AU  - Ikehara M
PT  - Journal Article
TA  - Chem. Pharm. Bull. (Tokyo)
JT  - Chem. Pharm. Bull. (Tokyo)
SO  - Chem. Pharm. Bull. (Tokyo) 1982 30: 874-880.

PMID- 25323726
VI  - 2
DP  - 2014
TI  - Whole-Genome Sequence of Mycobacterium kyorinense.
PG  - e01062-14
AB  - We report here the first draft genome sequence of Mycobacterium kyorinense, which was
      described in 2009 and exhibits significant pathogenicity to humans.
AU  - Ohtsuka K
AU  - Ohnishi H
AU  - Nozaki E
AU  - Pais RJ
AU  - Tortoli E
AU  - Yonetani S
AU  - Matsushima S
AU  - Tateishi Y
AU  - Matsumoto S
AU  - Watanabe T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01062-14.

PMID- 27856588
VI  - 4
DP  - 2016
TI  - Genome Sequence of an Acinetobacter baumannii Strain Carrying Three Acquired Carbapenemase Genes.
PG  - e01290-16
AB  - The emergence of multiple-carbapenemase-producing Acinetobacter strains has been  a serious
      concern during the past decade. Here, we report the draft genome
      sequence of an Acinetobacter baumannii strain isolated from a Japanese patient
      with three acquired carbapenemase genes: blaNDM-1, blaTMB-1, and blaOXA-58.
AU  - Oinuma KI
AU  - Suzuki M
AU  - Sato K
AU  - Nakaie K
AU  - Niki M
AU  - Takizawa E
AU  - Niki M
AU  - Shibayama K
AU  - Yamada K
AU  - Kakeya H
AU  - Kaneko Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01290-16.

PMID- Not included in PubMed...
VI  - 69
DP  - 1990
TI  - Inhibition of restriction endonucleases by commercial polysaccharides.
PG  - 360-361
AB  - Commercial polysaccharide preparations were investigated for their restriction
      enzyme-inhibitory activities.  Dextran sulfate (S content 18.5%) and laminaran
      from Eisenia arborea (0.88%) had marked inhibitory activity and haparin (13.1%)
      and iota-, kappa-, and lambda-carrageenans (3.0, 3.8, and 4.3%) showed moderate
      inhibition.  The effects of sulfation level and the structure of the
      carbohydrate moiety on the inhibitory activity were discussed.
AU  - Oishi K
AU  - Aoi S
AU  - Ehara Y
AU  - Otsuka Y
AU  - Shimamura K
AU  - Higuchi Y
AU  - Nomoto M
PT  - Journal Article
TA  - J. Ferment. Bioeng.
JT  - J. Ferment. Bioeng.
SO  - J. Ferment. Bioeng. 1990 69: 360-361.

PMID- 20435723
VI  - 192
DP  - 2010
TI  - Genome Sequence of Lactobacillus crispatus ST1.
PG  - 3547-3548
AB  - Lactobacillus crispatus is a common member of the beneficial microbiota present in the
      vertebrate gastrointestinal and human genitourinary tracts.
      Here, we report the genome sequence of L. crispatus ST1, a chicken isolate
      displaying strong adherence to vaginal epithelial cells.
AU  - Ojala T
AU  - Kuparinen V
AU  - Koskinen JP
AU  - Alatalo E
AU  - Holm L
AU  - Auvinen P
AU  - Edelman S
AU  - Westerlund-Wikstrom B
AU  - Korhonen TK
AU  - Paulin L
AU  - Kankainen M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 3547-3548.

PMID- 15735669
VI  - 24
DP  - 2005
TI  - De novo DNA methyltransferases Dnmt3a and Dnmt3b primarily mediate the cytotoxic effect of 5-aza-2'-deoxycytidine.
PG  - 3091-3099
AB  - The deoxycytidine analog 5-aza-2'-deoxycitidine (5-aza-dC) is a potent chemotherapeutic agent
      effective against selective types of cancer. The molecular mechanism by which 5-aza-dC induces
      cancer cell death, however, is not fully understood. It has been accepted that the mechanism
      of toxicity is due to the covalent binding between the DNA methyltransferase (Dnmt) and
      5-aza-dC-substituted DNA. In order to define which member of the Dnmt family plays a dominant
      role in the cytotoxicity, we examined the effect of 5-aza-dC on cell growth and apoptosis in
      various Dnmt null mutant embryonic stem (ES) cells. Of interest, Dnmt3a-Dnmt3b double null ES
      cells were highly resistant to 5-aza-dC when compared to wild type, Dnmt3a null, Dnmt3b null,
      or Dnmt1 null ES cells. The cellular sensitivity to 5-aza-dC correlated well with the
      expression status of Dnmt3 in both undifferentiated and differentiated ES cells. When
      exogenous Dnmt3a or Dnmt3b was expressed in double null ES cells, the sensitivity to 5-aza-dC
      was partially restored. These results suggest that the cytotoxic effect of 5-aza-dC may be
      mediated primarily through Dnmt3a and Dnmt3b de novo DNA methyltransferases. Further, the
      ability to form Dnmt-DNA adducts was similar in Dnmt1 and Dnmt3, and the expression level of
      Dnmt3 was not higher than that of Dnmt1 in ES cells. Therefore, Dnmt3-DNA adducts may be more
      effective for inducing apoptosis than Dnmt1-DNA adducts. These results imply a therapeutic
      potential of 5-aza-dC to cancers expressing Dnmt3.
AU  - Oka M
AU  - Meacham AM
AU  - Hamazaki T
AU  - Rodic N
AU  - Chang L-J
AU  - Terada N
PT  - Journal Article
TA  - Oncogene
JT  - Oncogene
SO  - Oncogene 2005 24: 3091-3099.

PMID- 24887199
VI  - 9
DP  - 2014
TI  - Comparative Genomic Characterization of a Thailand-Myanmar Isolate, MS6, of Vibrio cholerae O1 El Tor, Which Is Phylogenetically Related to a 'US Gulf Coast' Clone.
PG  - E98120
AB  - BACKGROUND: The cholera outbreaks in Thailand during 2007-2010 were exclusively
      caused by the Vibrio cholerae O1 El Tor variant carrying the cholera toxin gene
      of the classical biotype. We previously isolated a V. cholerae O1 El Tor strain
      from a patient with diarrhea and designated it MS6. Multilocus sequence-typing
      analysis revealed that MS6 is most closely related to the U. S. Gulf Coast clone
      with the exception of two novel housekeeping genes. METHODOLOGY/PRINCIPAL
      FINDINGS: The nucleotide sequence of the genome of MS6 was determined and
      compared with those of 26 V. cholerae strains isolated from clinical and
      environmental sources worldwide. We show here that the MS6 isolate is distantly
      related to the ongoing seventh pandemic V. cholerae O1 El Tor strains. These
      strains differ with respect to polymorphisms in housekeeping genes, seventh
      pandemic group-specific markers, CTX phages, two genes encoding predicted
      transmembrane proteins, the presence of metY (MS6_A0927) or hchA/luxR in a highly
      conserved region of the V. cholerae O1 serogroup, and a superintegron (SI). We
      found that V. cholerae species carry either hchA/luxR or metY and that the V.
      cholerae O1 clade commonly possesses hchA/luxR, except for MS6 and U. S. Gulf
      Coast strains. These findings illuminate the evolutionary relationships among V.
      cholerae O1 strains. Moreover, the MS6 SI carries a quinolone-resistance gene
      cassette, which was closely related with those present in plasmid-borne integrons
      of other gram-negative bacteria. CONCLUSIONS/SIGNIFICANCE: Phylogenetic analysis
      reveals that MS6 is most closely related to a U. S. Gulf Coast clone, indicating
      their divergence before that of the El Tor biotype strains from a common V.
      cholerae O1 ancestor. We propose that MS6 serves as an environmental aquatic
      reservoir of V. cholerae O1.
AU  - Okada K
AU  - Na-Ubol M
AU  - Natakuathung W
AU  - Roobthaisong A
AU  - Maruyama F
AU  - Nakagawa I
AU  - Chantaroj S
AU  - Hamada S
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2014 9: E98120.

PMID- 26079534
VI  - 21
DP  - 2015
TI  - Characterization of 3 Megabase-Sized Circular Replicons from Vibrio cholerae.
PG  - 1262-1263
AB  - To the Editor: Prokaryotes typically have a single circular chromosome.  However, some
      bacteria have >1 chromosome.  Vibrio bacteria, for example, have 2 circular chromosomes: 1
      (Ch1) and 2 (Ch2).  Most recognizable genes responsible for essential cell functions and
      pathogenicity are located on Ch1.  Ch2 is also thought to encode some genes essential for
      normal cell function and those associated with virulence.  Both chromosomes are controlled
      coordinately in their replicon and segregation.  Evidence suggests that Ch2 was originally a
      mega-plasmid captured by an ancestral Vibrio species.  We report the characterization of
      recent isolates of V. cholera 01 from Thailand that carry a novel gigantic replicon (Rep.3) in
      addition to Ch1 and Ch2.
AU  - Okada K
AU  - Natakuathung W
AU  - Na-Ubol M
AU  - Roobthaisong A
AU  - Wongboot W
AU  - Maruyama F
AU  - Nakagawa I
AU  - Chantaroj S
AU  - Hamada S
PT  - Journal Article
TA  - Emerg. Infect. Dis.
JT  - Emerg. Infect. Dis.
SO  - Emerg. Infect. Dis. 2015 21: 1262-1263.

PMID- 24831150
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Bordetella bronchiseptica S798, an Isolate from a Pig with Atrophic Rhinitis.
PG  - e00436-14
AB  - Bordetella bronchiseptica colonizes the respiratory tracts of a wide variety of mammals and
      causes a range of diseases, from lethal pneumonia to asymptomatic
      chronic infection. We report the complete genome sequence of Bordetella
      bronchiseptica strain S798, isolated from a pig with atrophic rhinitis in Japan.
AU  - Okada K
AU  - Ogura Y
AU  - Hayashi T
AU  - Abe A
AU  - Kuwae A
AU  - Horiguchi Y
AU  - Abe H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00436-14.

PMID- 4899947
VI  - 18
DP  - 1969
TI  - Host-controlled restriction and modification of Salmonella typhimurium.
PG  - 81-97
AB  - Since the discovery of sexuality in bacteria, hybridization between Escherichia
      coli and Salmonella strains has been intensively studied by a number of
      workers.  Despite initial uniformal negative results, hybrids did occur at much
      lower frequencies than those between E. coli strains.  In the mating of
      Salmonella, Hfr strains of E. coli have been employed as donors.  The hybrids
      were viable and more fertile as recipients than the parent Salmonella strains,
      in the sense of the frequency of hybrid formation per donor cell.  It was not
      known, however, whether this barrier in gene exchange between these species
      might be poor mating capacity or poor integration capacity or both.  In the
      present paper, I shall show that fertile mutants, which were selected for
      abnormally increased recipient ability in the transmission of an R factor 222
      from E. coli (R+), are simultaneously accompanied by acquisition of the
      increased recipient ability for E. coli chromosome and some alteration of
      host-controlled restriction and modification as to R factors and phage P22.
AU  - Okada M
PT  - Journal Article
TA  - Keio J. Med.
JT  - Keio J. Med.
SO  - Keio J. Med. 1969 18: 81-97.

PMID- 25356467
VI  - 122
DP  - 2014
TI  - Emergence of type I restriction modification system-negative emm1 type Streptococcus pyogenes clinical isolates in Japan.
PG  - 914-921
AB  - Streptococcus pyogenes emm1 type is the dominant cause of streptococcal toxic shock syndrome
      (STSS) in Japan and many other developed countries. Recently, the number of STSS patients in
      Japan was reported to be increasing. Hence, we analyzed the S. pyogenes clinical isolates
      detected in Japan after 2005. We found that the regions encoding the Spy1908-1910
      two-component regulatory system and the adjacent type I restriction modification system were
      deleted in some emm1 type isolates. The isolates with the deletion were detected only in the
      emm1 strains that were isolated between 2010 and 2013, but not before 2010. Twenty-six of 46
      (56.5%) emm1 type isolates were isolated in 2010-2013, and among these isolates, five of seven
      (71.4%) emm1 type STSS isolates were shown to have that deletion. PFGE and PCR analysis for
      the presence of several pyrogenic exotoxin-related genes suggested that the emm1 isolates with
      and without the deletion shared the same genetic background. The emm1 isolates with the
      deletion could incorporate exogenous plasmids by experimental electroporation transformation
      far more efficiently. These results suggested that the novel emm1 isolates have occupied a
      fairly large part of total emm1 isolates.
AU  - Okada R
AU  - Matsumoto M
AU  - Zhang Y
AU  - Isaka M
AU  - Tatsuno I
AU  - Hasegawa T
PT  - Journal Article
TA  - APMIS
JT  - APMIS
SO  - APMIS 2014 122: 914-921.

PMID- 26564047
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of a Benzo[a]pyrene-Degrading Bacterium, Olleya sp. Strain  ITB9.
PG  - e01328-15
AB  - Olleya sp. ITB9 is a benzo[a]pyrene-degrading bacterium, isolated from surface water near a
      waste treatment plant at Tokyo Bay, Japan. Here, we present the
      draft genome sequence of this strain, which consists of 58 contigs corresponding
      to 3.4 Mb and a G+C content of 31.2%.
AU  - Okai M
AU  - Watanabe A
AU  - Ishida M
AU  - Urano N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01328-15.

PMID- 24948769
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of a Legionella pneumophila Serogroup 4 Strain Causing Legionellosis.
PG  - e00602-14
AB  - Here, we report the draft genome sequence of the Legionella pneumophila Nagoya-1  strain,
      serogroup 4, which was isolated from a clinical sample from a patient
      with legionellosis. Several virulence-associated genes, including those encoding
      the type IV (Dot/Icm) secretion system and effector proteins, were highly
      conserved.
AU  - Okamoto A
AU  - Lee H
AU  - Yabutani M
AU  - Yamada K
AU  - Ohta M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00602-14.

PMID- 12197712
VI  - 124
DP  - 2002
TI  - Site-specific discrimination of cytosine and 5-methylcytosine in duplex DNA by peptide nucleic acids.
PG  - 10262-10263
AB  - For site-specific discrimination of cytosine (C) and 5-methylcytosine ((m)C) in duplex DNA, we
      developed a new method using peptide nucleic acids (PNAs). The combination of a PNA-assisted
      DNA displacement complex and a fluorescein-labeled probe oligomer allowed the detection of
      (m)C at the defined sites in target DNA using a restriction enzyme. After treatment of the
      complex with a restriction enzyme, strong fluorescence emission was observed for the complex
      containing C at the target site, whereas the fluorescence intensity for the complex containing
      (m)C was extremely weak.
AU  - Okamoto A
AU  - Tanabe K
AU  - Saito I
PT  - Journal Article
TA  - J. Am. Chem. Soc.
JT  - J. Am. Chem. Soc.
SO  - J. Am. Chem. Soc. 2002 124: 10262-10263.

PMID- 27881541
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequences of Two Manganese(II)-Oxidizing Bacteria, Bosea sp. Strain  BIWAKO-01 and Alphaproteobacterium Strain U9-1i.
PG  - e01309-16
AB  - This report describes the whole-genome sequences of two Mn(II)-oxidizing bacteria, filamentous
      Mn oxide microparticle-forming Bosea sp. strain BIWAKO-01
      and alphaproteobacterium strain U9-1i.
AU  - Okano K
AU  - Furuta S
AU  - Ichise S
AU  - Miyata N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01309-16.

PMID- 25792056
VI  - 3
DP  - 2015
TI  - Genome Sequence of Microcystis aeruginosa Strain NIES-44.
PG  - e00135-15
AB  - Microcystis aeruginosa is a typical algal bloom-forming cyanobacterium. This report describes
      the whole-genome sequence of a non-microcystin-producing strain
      of Microcystis aeruginosa, NIES-44, which was isolated from a Japanese lake.
AU  - Okano K
AU  - Miyata N
AU  - Ozaki Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00135-15.

PMID- 26227601
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequence of the Microcystin-Degrading Bacterium Sphingopyxis sp. Strain C-1.
PG  - e00838-15
AB  - This report describes the whole-genome sequence of an alkalitolerant microcystin-degrading
      bacterium, Sphingopyxis sp. strain C-1, isolated from a
      lake in China.
AU  - Okano K
AU  - Shimizu K
AU  - Maseda H
AU  - Kawauchi Y
AU  - Utsumi M
AU  - Itayama T
AU  - Zhang Z
AU  - Sugiura N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00838-15.

PMID- 
VI  - 18
DP  - 2000
TI  - DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation in mouse early development.
PG  - 468-471
AB  - 
AU  - Okano M
PT  - Journal Article
TA  - Jikken Igaku
JT  - Jikken Igaku
SO  - Jikken Igaku 2000 18: 468-471.

PMID- 
VI  - 20
DP  - 2001
TI  - DNA methylation and DNA methyltransferases in mammals.
PG  - 381-386
AB  - 
AU  - Okano M
PT  - Journal Article
TA  - Saibo Kogaku
JT  - Saibo Kogaku
SO  - Saibo Kogaku 2001 20: 381-386.

PMID- 10555141
VI  - 99
DP  - 1999
TI  - DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development.
PG  - 247-257
AB  - The establishment of DNA methylation patterns requires de novo methylation that occurs
      predominantly during early development and gametogenesis in mice.  Here we demonstrate that
      two recently identified DNA methyltransferases, Dnmt3a and Dnmt3b, are essential for de novo
      methylation and for mouse development.  Inactivation of both genes by gene targeting blocks de
      novo methylation in ES cells and early embryos, but it has no effect on maintenance of
      imprinted methylation patterns.  Dnmt3a and Dnmt3b also exhibit nonoverlapping functions in
      development, with Dnmt3b specifically required for methylation of centromeric minor satellite
      repeats.  Mutations of human DNMT3B are found in ICF syndrome, a developmental defect
      characterized by hypomethylation of pericentromeric repeats.  Our results indicate that both
      Dnmt3a and Dnmt3b function as de novo methyltransferases that play important roles in normal
      development and disease.
AU  - Okano M
AU  - Bell DW
AU  - Haber DA
AU  - Li E
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1999 99: 247-257.

PMID- 12163712
VI  - 132
DP  - 2002
TI  - Genetic analyses of DNA methyltransferase genes in mouse model system.
PG  - 2462S-2465S
AB  - DNA methylation regulates important biological processes and is involved in tumorigenesis and
      several human diseases, such as Rett and immunodeficiency, centromeric instability and facial
      anomalies (ICF). The major objective of our research is to investigate the roles of DNA
      methylation in mammals through genetic analysis of DNA methyltransferase genes in mouse and
      human. Previously, we found that Dnmt1 knockout embryonic stem (ES) cells are capable of
      methylating retroviral DNA de novo. In search of enzymes responsible for de novo methylation,
      we have cloned a novel family of mammalian DNA methyltransferase genes, Dnmt3a and Dnmt3b.
      Although extensive sequence similarity was found between Dnmt3a and Dnmt3b, little homology
      was observed between Dnmt1 and Dnmt3a/3b in the catalytic domain as well as in the N-terminal
      domain. Additionally, biochemical analysis revealed that, unlike Dnmt1, neither Dnmt3a nor
      Dnmt3b had a strong preference to hemimethylated DNA substrates. Genetic analysis demonstrated
      that Dnmt3a and Dnmt3b were required for de novo methylation activities in ES cells and during
      early embryogenesis and were essential for early development. Interestingly, phenotype
      analyses of single homozygous mice for either Dnmt3a or Dnmt3b suggested that the functions of
      Dnmt3a and Dnmt3b also were required at the late developmental stage and even at the adult
      stage.
AU  - Okano M
AU  - Li E
PT  - Journal Article
TA  - J. Nutr.
JT  - J. Nutr.
SO  - J. Nutr. 2002 132: 2462S-2465S.

PMID- 10575238
VI  - 86
DP  - 1999
TI  - Assignment of cytosine-5 DNA methyltransferases Dnmt3a and Dnmt3b to mouse chromosome bands 12A2-A3 and 2H1 by in situ hybridization.
PG  - 333-334
AB  - Methylation of cytosine at the C-5 position is a major form of DNA modification in vertebrates
      and plays important roles in regulation of gene expression and development.  Previously, only
      one mammalian cytosine-5 methyltransferase (now termed Dnmt1) was known and shown to be
      required for maintaining global DNA methylation levels.  Recently, we cloned a family of novel
      cytosine-5 methyltransferase genes, termed Dnmt3a and Dnmt3b, which do not share sequence
      similarities to any known eukaryotic cytosine-5 methyltransferase genes.  Expression pattern
      and biological analysis suggest that Dnmt3a and Dnmt3b are probably responsible for de novo
      methylation, a key process by which DNA methylation patterns are established during
      development.  In this study we have mapped chromosome locations of Dnmt3a and Dnmt3b to
      12A2-A3 and 2H1, respectively, by FISH.
AU  - Okano M
AU  - Takebayashi S
AU  - Okumura K
AU  - Li E
PT  - Journal Article
TA  - Cytogenet. Cell Genet.
JT  - Cytogenet. Cell Genet.
SO  - Cytogenet. Cell Genet. 1999 86: 333-334.

PMID- 9592134
VI  - 26
DP  - 1998
TI  - Dnmt2 is not required for de novo and maintenance methylation of viral DNA in embryonic stem cells.
PG  - 2536-2540
AB  - We have shown previously that de novo methylation activities persist in mouse embryonic stem
      cells homozygous for a null mutation of Dnmt1 that encodes the major DNA cytosine
      methyltransferase.  In this study, we have cloned a putative mammalian DNA methyltransferase
      gene, termed Dnmt2, that is homologous to pmt1 of fission yeast.  Different from pmt1 in which
      the catalytic Pro-Pro-Cys motif is 'mutated' to Pro-Ser-Cys, Dnmt2 contains all the
      conserved methyltransferase motifs, thus likely encoding a functional cytosine
      methyltransferase.  However, baculovirus-expressed Dnmt2 protein failed to methylate DNA in
      vitro.  To investigate whether Dnmt2 functions as a DNA methyltransferase in vivo, we
      inactivated the Dnmt2 gene by targeted deletion of the putative catalytic PPC motif in ES
      cells.  We showed that endogenous virus was fully methylated in Dnmt2-deficient mutant ES
      cells.  Furthermore, newly integrated retrovirus DNA was methylated de novo in infected mutant
      ES cells as efficiently as in wild-type cells.  These results indicate that Dnmt2 is not
      essential for global de novo or maintenance methylation of DNA in ES cells.
AU  - Okano M
AU  - Xie S
AU  - Li E
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1998 26: 2536-2540.

PMID- 9662389
VI  - 19
DP  - 1998
TI  - Cloning and characterization of a family of novel mammalian DNA (cytosine-5) methyltransferases.
PG  - 219-220
AB  - De novo methylation of genomic DNA is a developmentally regulated process that is believed to
      play a pivotal role in regulation of genomic imprinting and X-chromosome inactivation in
      mammals.  Aberrant de novo methylation of growth regulatory genes has been associated with
      tumorigenesis in humans.  We have shown previously that de novo methylation persists in
      embryonic stem cells lacking Dnmt1, which encodes the constitutive DNA methyltransferase Dnmt1
      (or MT1), indicating the existence of independently encoded de novo methyltransferases.
AU  - Okano M
AU  - Xie S
AU  - Li E
PT  - Journal Article
TA  - Nat. Genet.
JT  - Nat. Genet.
SO  - Nat. Genet. 1998 19: 219-220.

PMID- 12068627
VI  - 36
DP  - 2002
TI  - Comparison of the homologous SfeI and LlaBI restriction-modification  systems.
PG  - 432-437
AB  - A fragment containing the SfeI restriction-modification system (RMS)  operon was cloned from a
      Streptococcus faecalis SE72 plasmid. Nucleotide sequence analysis revealed its high (99.2%)
      homology to the operon for Lactococcus lactis subsp. cremoris W56 LlaBI RMS recognizing the
      same site, 5'-CTRYAG-3'. A substantial difference was that SfeI RMS operon had an additional
      198-bp fragment and a larger gene for the putative control protein. No homology was observed
      between operon-flanking sequences of the two closely related species, suggesting horizontal
      transfer of the operon.
AU  - Okhapkina SS
AU  - Netesova NA
AU  - Golikova LN
AU  - Seregina EV
AU  - Sosnovtsev SV
AU  - Abdurashitov MA
AU  - Degtyarev SK
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2002 36: 432-437.

PMID- 25237016
VI  - 2
DP  - 2014
TI  - Genome Sequence of Bacillus anthracis STI, a Sterne-Like Georgian/Soviet Vaccine  Strain.
PG  - e00853-14
AB  - The Bacillus anthracis strain STI is a Soviet vaccine strain that lacks the pXO2  plasmid.
      Previous data indicate that this isolate forms a new branch within the
      B. anthracis sub-group originally identified as A. Br.008/009.
AU  - Okinaka RT
AU  - Challacombe J
AU  - Drees K
AU  - Birdsell DN
AU  - Janke N
AU  - Naumann A
AU  - Seymour M
AU  - Hornstra H
AU  - Schupp J
AU  - Sahl J
AU  - Foster JT
AU  - Pearson T
AU  - Turnbull P
AU  - Keim P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00853-14.

PMID- 28473382
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Seven 4-Formylaminooxyvinylglycine Producers Belonging  to the Pseudomonas fluorescens Species Complex.
PG  - e00277-17
AB  - Vinylglycines are nonproteinogenic amino acids that inhibit amino acid metabolism and ethylene
      production. Here, we report the draft genome sequences of seven
      isolates of Pseudomonas that produce 4-formylaminooxyvinylglycine, a compound
      known to inhibit the germination of grasses and the growth of specific
      plant-pathogenic bacteria.
AU  - Okrent RA
AU  - Manning VA
AU  - Trippe KM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00277-17.

PMID- 28126940
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Bacillus sp. FMQ74, a Dairy-Contaminating Isolate from Raw Milk.
PG  - e01512-16
AB  - Representatives of the genus Bacillus are common milk contaminants that cause spoilage and
      flavor alterations of dairy products. Bacillus sp. FMQ74 was
      isolated from raw milk on a Danish dairy farm. To elucidate the genomic basis of
      this strain's survival in the dairy industry, a high-quality draft genome was
      produced.
AU  - Okshevsky M
AU  - Regina VR
AU  - Marshall IP
AU  - Schreiber L
AU  - Meyer RL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01512-16.

PMID- 10217496
VI  - 145
DP  - 1999
TI  - Genome organization is not conserved between Bacillus cereus and Bacillus subtilis.
PG  - 621-631
AB  - The opportunistic pathogen Bacillus cereus is the genetically stable member of a group of
      closely related bacteria including the insect pathogen Bacillus thuringiensis and the
      mammalian pathogen Bacillus anthracis. Physical maps of B. cereus and B. thuringiensis strains
      show considerable variations in discrete parts of the chromosome, suggesting that certain
      genome regions are more prone to rearrangements. B. cereus belongs to the same subgroup of
      Bacillus species as Bacillus subtilis, by both phenotypic and rRNA sequence classification.
      The analysis of 80 kb of genome sequence sampled from different regions of the B. cereus ATCC
      10987 chromosome is reported.  Analysis of the sequence and comparison of the localization of
      the putative genes with that of B. subtilis orthologues show the following: (1) gene
      organization is not conserved between B. cereus and B. subtilis; (2) several putative genes
      are more closely related to genes from other bacteria and archaea than to B. subtilis, or may
      be absent in B. subtilis 168; (3) B. cereus contains a 155 bp repetitive sequence that is not
      present in B. subtilis. By hybridization, this repeat is present in all B. cereus and B.
      thuringiensis strains so far investigated.
AU  - Okstad OA
AU  - Hegna I
AU  - Lindback T
AU  - Rishovd A-L
AU  - Kolsto A-B
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 1999 145: 621-631.

PMID- 8233834
VI  - 21
DP  - 1993
TI  - Isolation and characterization of the modification methylase M.SauLPI from Streptomyces aureofaciens B-96.
PG  - 4843
AB  - In our previous work we reported the presence of a GCC/GGC recognizing restriction system in
      tetracycline producing strains of Streptomyces aureofaciens. In this paper we describe the
      characterization of the cognate modification DNA methyltransferase M.SauLPI from
      S.aureofaciens strain B-96.
AU  - Oktavcovca B
AU  - Godany A
AU  - Pristas P
AU  - Stevcikova B
AU  - Farkasovska J
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 4843.

PMID- 22452844
VI  - 27
DP  - 2012
TI  - Complete Genome Sequence of Bradyrhizobium sp. S23321: Insights into Symbiosis Evolution in Soil Oligotrophs.
PG  - 306-315
AB  - Bradyrhizobium sp. S23321 is an oligotrophic bacterium isolated from paddy field soil.
      Although S23321 is
      phylogenetically close to Bradyrhizobium japonicum USDA110, a legume symbiont, it is unable to
      induce root nodules
      in siratro, a legume often used for testing Nod factor-dependent nodulation. The genome of
      S23321 is a single circular
      chromosome, 7,231,841 bp in length, with an average GC content of 64.3%. The genome contains
      6,898 potential
      protein-encoding genes, one set of rRNA genes, and 45 tRNA genes. Comparison of the genome
      structure between
      S23321 and USDA110 showed strong colinearity; however, the symbiosis islands present in
      USDA110 were absent
      in S23321, whose genome lacked a chaperonin gene cluster (groELS3) for symbiosis regulation
      found in USDA110.
      A comparison of sequences around the tRNA-Val gene strongly suggested that S23321 contains an
      ancestral-type
      genome that precedes the acquisition of a symbiosis island by horizontal gene transfer.
      Although S23321 contains a
      nif (nitrogen fixation) gene cluster, the organization, homology, and phylogeny of the genes
      in this cluster were more
      similar to those of photosynthetic bradyrhizobia ORS278 and BTAi1 than to those on the
      symbiosis island of USDA110.
      In addition, we found genes encoding a complete photosynthetic system, many ABC transporters
      for amino acids and
      oligopeptides, two types (polar and lateral) of flagella, multiple respiratory chains, and a
      system for lignin monomer
      catabolism in the S23321 genome. These features suggest that S23321 is able to adapt to a wide
      range of environments,
      probably including low-nutrient conditions, with multiple survival strategies in soil and
      rhizosphere.
AU  - Okubo T et al
PT  - Journal Article
TA  - Microbes Environ.
JT  - Microbes Environ.
SO  - Microbes Environ. 2012 27: 306-315.

PMID- 23396330
VI  - 79
DP  - 2013
TI  - Soil oligotrophic bacterium Agromonas oligotrophica (Bradyrhizobium oligotrophicum) is a nitrogen-fixing symbiont of Aeschynomene indica as suggested by genome analysis.
PG  - 2542-2551
AB  - Agromonas oligotrophica (Bradyrhizobium oligotrophicum) S58T is a nitrogen-fixing oligotrophic
      bacterium isolated from paddy field soil that is able to grow in extra-low nutrient
      environments.  Here, the complete genome sequence of S58 was determined.  The S58 genome was
      found to comprise a circular chromosome of 8,264,165 bp with an average GC content of 65.1%
      lacking nodABC genes and typical symbiosis island.  The genome showed a high level of
      similarity to the genomes of Bradyrhizobium sp. ORS278 and Bradyrizobium sp. BTAil including
      nitrogen fixation and photosynthesis gene clusters, which nodulate an aquatic legume plant,
      Aeschynomene indica, in a Nod factor-independent manner.  Although non-symbiotic
      (brady)rhizobia are significant components of rhizobial populations in soil, we found that
      most genes important for nodule development (ndv) and symbiotic nitrogen fixation (nif and
      fix) with A. indica were well conserved between the ORS278 and S58 genomes.  Therefore, we
      performed inoculation experiments with five A. oligotrophica strians (S58, S42, S55, S72, and
      S80).  Surpirsingly, all five strains of A. oligotrophica formed effective nitrogen-fixing
      nodules on the roots and/or stems of A. indica with differentiated bacteroids.  Non-symbiotic
      (brady)rhizobia are known to be significant components of rhizobial populations without
      symbiosis isoland or symbiotic plasmids in soil, but the present results indicate that
      soil-dwelling A. oligotrophica generally possesses the ability to establish symbiosis with A.
      indica is a common trait of nodABC- and symbiosis island-lacking strains within the members of
      photosynthetic Bradyrhizobium clade including A. oligotrophica.
AU  - Okubo T
AU  - Fukushima S
AU  - Itakura M
AU  - Oshima K
AU  - Longtonglang A
AU  - Teaumroong N
AU  - Mitsui H
AU  - Hattori M
AU  - Hattori R
AU  - Hattori T
AU  - Minamisawa K
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2013 79: 2542-2551.

PMID- 12734795
VI  - 20
DP  - 2003
TI  - Occurrence, horizontal transfer and degeneration of VDE intein family in Saccharomycete yeasts.
PG  - 563-573
AB  - VDE is a homing endonuclease gene originally discovered as an intervening element in VMA1s of
      Saccharomyces cerevisiae. There have been two
      independent subfamilies of VDE, one from S. cerevisiae strain X2180-1A and
      the other from Saccharomyces sp. DH1-1A in the host VMA1 gene, and they
      share the identity of 96.3%. In order to search the occurrence,
      intra/interspecies transfer and molecular degeneration of VDE, complete
      sequences of VMA1 in 10 strains of S. cerevisiae, eight species of
      saccharomycete yeasts, Candida glabrata and Kluyveromyces lactis were
      determined. We found that six of 10 S. cerevisiae strains contain VDEs
      99.7-100% identical to that of the strain X2180-1A, one has no VDE,
      whereas the other three harbour VDEs 100% identical to that of the strain
      DH1-1A. S. carlsbergensis has two VMA1s, one being 99.8% identical to that
      of the strain X2180-1A with VDE 100% identical to that of the strain
      DH1-1A and the other containing the same VMA1 in S. pastorianus with no
      VDE. This and other evidence indicates that intra/interspecies
      transmissions of VDEs have occurred among saccharomycete yeasts.
      Phylogenetic analyses of VMA1 and VDE suggest that the S. cerevisiae VDEs
      had branched earlier than other VDEs from an ancestral VDE and had invaded
      into the host loci as relatively late events. The two VDEs seemed to
      degenerate in individual host loci, retaining their splicing capacity
      intact. The degeneration of the endonuclease domains was distinct and, if
      compared, its apparent rate was much faster than that of the
      protein-splicing domains.
AU  - Okuda Y
AU  - Sasaki D
AU  - Nogami S
AU  - Kaneko Y
AU  - Ohya Y
AU  - Anraku Y
PT  - Journal Article
TA  - Yeast
JT  - Yeast
SO  - Yeast 2003 20: 563-573.

PMID- 21622755
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Melissococcus plutonius ATCC 35311.
PG  - 4029-4030
AB  - We report the first completely annotated genome sequence of Melissococcus plutonius ATCC
      35311. M. plutonius is a one genus one species bacterium,
      and the etiological agent of European foulbrood of the honey bee. The
      genome sequence will provide new insights into the molecular mechanisms
      underlying its pathogenicity.
AU  - Okumura K
AU  - Arai R
AU  - Okura M
AU  - Kirikae T
AU  - Takamatsu D
AU  - Osaki M
AU  - Miyoshi-Akiyama T
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4029-4030.

PMID- 23416996
VI  - 79
DP  - 2013
TI  - Genetic Analysis of Capsular Polysaccharide Synthesis Gene Clusters from All Serotypes of Streptococcus suis: Potential Mechanisms for the Generation of Capsular Variation.
PG  - 2796-2806
AB  - Streptococcus suis strains are classified into 35 serotypes on the basis of the
      antigenicity of their capsular polysaccharides (CPs). CP synthesis genes are
      known to be clustered on the chromosome (cps gene cluster). The entire cps gene
      clusters of S. suis have so far been sequenced in 15 serotypes and found to be
      located between orfZ and aroA. In this study, to provide comprehensive
      information about S. suis CPs, we sequenced the entire cps gene clusters of the
      remaining serotypes and analyzed the complete set of S. suis cps gene clusters.
      Among the 35 cps gene clusters, 22 were located between orfZ and aroA, whereas
      the other 13 were flanked by other gene(s) on the chromosomes, and the
      chromosomal locus was classified into five patterns. By clustering analysis, the
      predicted products of cps genes found in the 35 serotypes were assigned into 291
      homology groups, and all serotypes possessed a serotype-specific gene, except for
      serotypes 1, 2, 1/2 and 14. Because of the presence of genes encoding flippase
      (wzx) and polymerase (wzy), CPs of all serotypes were thought to be synthesized
      by the Wzx/Wzy pathway. Our data also implied the possibility of the transfer of
      the entire or partial cps gene clusters among S. suis strains, as well as the
      influence of spontaneous mutations in a single or a few genes on the antigenicity
      of some serotypes. Accumulation of these gene transfers and small-scale mutations
      may have generated the antigenic diversity of S. suis CPs.
AU  - Okura M
AU  - Takamatsu D
AU  - Maruyama F
AU  - Nozawa T
AU  - Nakagawa I
AU  - Osaki M
AU  - Sekizaki T
AU  - Gottschalk M
AU  - Kumagai Y
AU  - Hamada S
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2013 79: 2796-2806.

PMID- 26089418
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Bacillus anthracis Strains Stored for Several Decades in Japan.
PG  - e00633-15
AB  - We report the draft genome sequences of Bacillus anthracis strains Shikan-NIID, 52-40-NIAH,
      and 44-NIAH stored in Japan and belonging to the A3 cluster.
AU  - Okutani A
AU  - Osaki M
AU  - Takamatsu D
AU  - Kaku Y
AU  - Inoue S
AU  - Morikawa S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00633-15.

PMID- 25977425
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Alicycliphilus sp. B1, an N-Acylhomoserine Lactone-Producing Bacterium, Isolated from Activated Sludge.
PG  - e00424-15
AB  - We report here the draft genome sequence of Alicycliphilus sp. B1, isolated from  activated
      sludge in a wastewater treatment plant of an electronic component
      factory as an N-acylhomoserine lactone-producing strain. The draft genome is
      7,465,959 bp in length, with 59 large contigs. About 7,391 protein-coding genes,
      82 tRNAs, and 13 rRNAs are predicted from this assembly.
AU  - Okutsu N
AU  - Morohoshi T
AU  - Ikeda T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00424-15.

PMID- 24994793
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Marine Actinomycete Streptomyces sp. Strain NTK 937, Producer of the Benzoxazole Antibiotic Caboxamycin.
PG  - e00534-14
AB  - Streptomyces sp. strain NTK 937 is the producer of the benzoxazole antibiotic caboxamycin,
      which has been shown to exert inhibitory activity against
      Gram-positive bacteria, cytotoxic activity against several human tumor cell
      lines, and inhibition of the enzyme phosphodiesterase. In this genome
      announcement, we present a draft genome sequence of Streptomyces sp. NTK 937 in
      which we identified at least 35 putative secondary metabolite biosynthetic gene
      clusters.
AU  - Olano C
AU  - Cano-Prieto C
AU  - Losada AA
AU  - Bull AT
AU  - Goodfellow M
AU  - Fiedler HP
AU  - Mendez C
AU  - Salas JA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00534-14.

PMID- 25676749
VI  - 3
DP  - 2015
TI  - Genome Sequences of Three Salmonella enterica subsp. enterica Serovar Infantis Strains from Healthy Broiler Chicks in Hungary and in the United Kingdom.
PG  - e01468-14
AB  - The genome sequences of three strains of Salmonella enterica subsp. enterica serovar Infantis
      isolated from broiler chickens in 1994 and 2004 in Hungary and
      in the 1980s in the United Kingdom are reported here. A sequence comparison
      should improve our understanding of the evolution of the genome and spread of S.
      Infantis in poultry.
AU  - Olasz F
AU  - Nagy T
AU  - Szabo M
AU  - Kiss J
AU  - Szmolka A
AU  - Barta E
AU  - van Tonder A
AU  - Thomson N
AU  - Barrow P
AU  - Nagy B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01468-14.

PMID- 1095757
VI  - 92
DP  - 1975
TI  - Recognition Sequence of Restriction Endonuclease III from Hemophilus influenzae.
PG  - 331-339
AB  - An endonuclease, R.HindIII, prepared from Hemophilus influenzae strain Rd,
      degrades foreign DNA, but not homologous DNA.  Phage T7 DNA is also resistant
      to the enzyme.  Fragments of phage lambda DNA produced by treatment with
      R.HindIII have been labelled at their 5' termini and analysis of the
      radioactive nucleotides in pancreatic DNAase digests of these fragments
      revealed a single 5' terminal sequence.  From this and other data we conclude
      that the enzyme recognizes and cleaves DNA at the following nucleotide
      sequence, 3' -N-T-T-C-G-A-A-N- 5' 5' -N-A-A-G-C-T-T-N- 3' giving termini
      bearing short cohesive ends.
AU  - Old R
AU  - Murray K
AU  - Roizes G
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1975 92: 331-339.

PMID- 16790780
VI  - 74
DP  - 2006
TI  - Identification of Markers for Helicobacter pylori Strains Isolated from Children with Peptic Ulcer Disease by Suppressive Subtractive Hybridization.
PG  - 4064-4074
AB  - Peptic ulcer disease (PUD) occurs after a long-term Helicobacter pylori
      infection. However, the disease can develop earlier, and rare cases have
      been observed in children, suggesting that these H. pylori strains may be
      more virulent. We used suppressive subtractive hybridization for
      comparative genomics between H. pylori strains isolated from a 5-year-old
      child with duodenal ulcer and from a sex- and age-matched child with
      gastritis only. The prevalence of the 30 tester-specific subtracted
      sequences was determined on a collection of H. pylori strains from
      children (15 ulcers and 30 gastritis) and from adults (46 ulcers and 44
      gastritis). Two of these sequences, jhp0562 (80.0% versus 33.3%, P =
      0.008) and jhp0870 (80.0% versus 36.7%, P = 0.015), were highly associated
      with PUD in children and a third sequence, jhp0828, was less associated
      (40.0% versus 10.0%, P = 0.048). Among adult strains, none of the 30
      sequences was associated with PUD. However, both jhp0562 and jhp0870 were
      less prevalent in adenocarcinoma strains than in PUD strains from children
      and adults, the difference being statistically significant for jhp0870. In
      conclusion, two H. pylori genes were identified as being strongly
      associated with PUD in children, and their putative roles as an outer
      membrane protein for jhp0870 and in lipopolysaccharide biosynthesis for
      jhp0562, suggest that they may be novel virulence factors of H. pylori.
AU  - Oleastro M
AU  - Monteiro L
AU  - Lehours P
AU  - Megraud F
AU  - Menard A
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2006 74: 4064-4074.

PMID- 
VI  - 59
DP  - 1999
TI  - Cloning and characterization of the 5-methylcytosine methyltransferase gene in maize plants and tissue cultures.
PG  - 4638
AB  - The genomic sequence of maize containing the methyltransferase gene called Zmet1 was
      successfully cloned and sequenced.  Seven clones were identified from a genomic library by
      using a highly conserved region from an Arabidopsis EST homologous to the Met1
      methyltransferase gene as a probe.  The assembled genomic sequence of four overlapping clones
      covers both the 5' and 3' flanking regions of the maize methyltransferase gene totaling
      7,955 nucleotides.  Sequence alignments with the Arabidopsis Met1 cDNA revealed that the open
      reading frame of Zmet1 encodes a putative protein of 1,525 amino acids, which is interrupted
      in the genomic sequence by ten introns.  Northern analysis confirmed this result by the
      identification of a single 4.6 kb RNA transcript.  The structure of the Zmet1 methylase is
      similar to the other eukaryotic maintenance methylases; a large N-terminal domain of 1,054
      amino  acids linked to a smaller C-terminal domain of 471 amino acids by a lysine-rich
      sequence.  Zmet1 is highly expressed in actively dividing cells, namely in seedling tissue and
      rapidly dividing callus tissue.  Restriction analysis suggests that there are at least two
      Zmet1 loci in the maize genome, one of which maps to the short arm of chromosome 7 in bin 2.
      The percent of 5-methylcytosine in maize DNA was shown to be dependent on the type of tissue
      and the stage in development.  Although the amount of repetitive DNA remained stable in the
      overall G/C to A/T ratio, methylation levels were found to significantly decrease from
      15-day-old embryos to one-week-old seedlings.  Remethylation occurs between the first and
      second week of seedling growth.  These changes indicate that there are both de novo
      methylation and demethylation activities in early development.  The methylation pattern at
      four low-copy sequences remained unchanged throughout plant and callus development except for
      a possible hypermethylation event in the third month of cell culture.  However, there was
      significant demethylation in the repetitive sequences, rDNA and COS 12, throughout an eight
      month period in tissue culture.  The identification of stages or tissues which are undergoing
      demethylation and de novo methylation may be important in identifying undiscovered methylase
      and demethylase enzymes, developmentally regulated genes, as well as interacting proteins that
      may regulate methylase functions.
AU  - Olhoft PM
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1999 59: 4638.

PMID- 10858352
VI  - 44
DP  - 2000
TI  - Genetic organization of the downstream region of the mecA element in methicillin-resistant Staphylococcus aureus isolates carrying different polymorphisms of this region.
PG  - 1906-1910
AB  - We describe here the genetic organization of the mec element downstream of
      the mecA gene in 34 different methicillin-resistant Staphylococcus aureus
      (MRSA) clinical isolates carrying 13 of the most frequent polymorphisms of
      mecA and representing the major epidemic clones of MRSA. All polymorphisms
      carried three common genetic elements: the hypervariable region, a copy of
      IS431, and a unique 2-kb sequence (downstream constant segment, or dcs)
      for which no homologous sequences are found in data banks. Polymorphisms
      of the downstream region were shown to be caused by the presence of
      linearized plasmids flanked by insertion sequences (pUB110, pT181, and
      pI258) and the autonomous insertion sequence IS256.
AU  - Oliveira DC
AU  - Wu SW
AU  - de Lencastre H
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2000 44: 1906-1910.

PMID- 25278529
VI  - 2
DP  - 2014
TI  - Genome Sequence of Lactococcus lactis subsp. lactis NCDO 2118, a GABA-Producing Strain.
PG  - e00980-14
AB  - Lactococcus lactis subsp. lactis NCDO 2118 is a nondairy lactic acid bacterium, a xylose
      fermenter, and a gamma-aminobutyric acid (GABA) producer isolated from
      frozen peas. Here, we report the complete genome sequence of L. lactis NCDO 2118,
      a strain with probiotic potential activity.
AU  - Oliveira LC et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00980-14.

PMID- 27979934
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Type Strain Campylobacter fetus subsp. fetus ATCC 27374.
PG  - e01344-16
AB  - Campylobacter fetus subsp. fetus is a zoonotic bacterium important for animal and public
      health. The complete sequencing and annotation of the genome of the type
      strain C. fetus subsp. fetus ATCC 27374 are reported here.
AU  - Oliveira LM
AU  - Resende DM
AU  - Dorneles EM
AU  - Horacio EC
AU  - Alves FL
AU  - Goncalves LO
AU  - Tavares GS
AU  - Stynen AP
AU  - Lage AP
AU  - Ruiz JC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01344-16.

PMID- 25240511
VI  - 10
DP  - 2014
TI  - First report of Corynebacterium pseudotuberculosis from caseous lymphadenitis lesions in Black Alentejano pig (Sus scrofa domesticus).
PG  - 218
AB  - BACKGROUND: Corynebacterium pseudotuberculosis is the etiologic agent of caseous
      lymphadenitis, a common disease in small ruminant populations throughout the
      world and responsible for a significant economic impact for producers. CASE
      PRESENTATION: To our knowledge, this is the first characterization of C.
      pseudotuberculosis from caseous lymphadenitis lesions in Black Alentejano pig
      (Sus scrofa domesticus). In this study, phenotypic and genotypic identification
      methods allocated the swine isolates in C. pseudotuberculosis biovar ovis. The
      vast majority of the isolates were able to produce phospholipase D and were
      susceptible to most of the antimicrobial compounds tested. Macrorestriction
      patterns obtained by Pulsed Field Gel Electrophoresis (PFGE) grouped the C.
      pseudotuberculosis in two clusters with a high similarity index, which reveals
      their clonal relatedness. Furthermore, swine isolates were compared with C.
      pseudotuberculosis from caprines and PFGE patterns also showed high similarity,
      suggesting the prevalence of dominant clones and a potential cross-dissemination
      between these two animal hosts. CONCLUSIONS: This work represents the first
      report of Corynebacterium pseudotuberculosis from caseous lymphadenitis lesions
      in Black Alentejano pig and alerts for the importance of the establishment of
      suitable control and sanitary management practices to control the infection and
      avoid further dissemination of this important pathogen to other animal hosts.
AU  - Oliveira M
AU  - Barroco C
AU  - Mottola C
AU  - Santos R
AU  - Lemsaddek A
AU  - Tavares L
AU  - Semedo-Lemsaddek T
PT  - Journal Article
TA  - BMC Vet. Res.
JT  - BMC Vet. Res.
SO  - BMC Vet. Res. 2014 10: 218.

PMID- 25120263
VI  - 42
DP  - 2014
TI  - The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts.
PG  - 10618-10631
AB  - The roles of restriction-modification (R-M) systems in providing immunity against horizontal
      gene transfer (HGT) and in stabilizing mobile genetic elements (MGEs)
      have been much debated. However, few studies have precisely addressed the
      distribution of these systems in light of HGT, its mechanisms and its vectors. We
      analyzed the distribution of R-M systems in 2261 prokaryote genomes and found
      their frequency to be strongly dependent on the presence of MGEs, CRISPR-Cas
      systems, integrons and natural transformation. Yet R-M systems are rare in
      plasmids, in prophages and nearly absent from other phages. Their abundance
      depends on genome size for small genomes where it relates with HGT but saturates
      at two occurrences per genome. Chromosomal R-M systems might evolve under cycles
      of purifying and relaxed selection, where sequence conservation depends on the
      biochemical activity and complexity of the system and total gene loss is
      frequent. Surprisingly, analysis of 43 pan-genomes suggests that solitary R-M
      genes rarely arise from the degradation of R-M systems. Solitary genes are
      transferred by large MGEs, whereas complete systems are more frequently
      transferred autonomously or in small MGEs. Our results suggest means of testing
      the roles for R-M systems and their associations with MGEs.
AU  - Oliveira PH
AU  - Touchon M
AU  - Rocha EP
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2014 42: 10618-10631.

PMID- 27140615
VI  - 113
DP  - 2016
TI  - Regulation of genetic flux between bacteria by restriction-modification systems.
PG  - 5658-5663
AB  - Restriction-modification (R-M) systems are often regarded as bacteria's innate immune
      systems, protecting cells from infection by mobile genetic elements
      (MGEs). Their diversification has been recently associated with the emergence of
      particularly virulent lineages. However, we have previously found more R-M
      systems in genomes carrying more MGEs. Furthermore, it has been suggested that
      R-M systems might favor genetic transfer by producing recombinogenic
      double-stranded DNA ends. To test whether R-M systems favor or disfavor genetic
      exchanges, we analyzed their frequency with respect to the inferred events of
      homologous recombination and horizontal gene transfer within 79 bacterial
      species. Genetic exchanges were more frequent in bacteria with larger genomes and
      in those encoding more R-M systems. We created a recognition target motif
      predictor for Type II R-M systems that identifies genomes encoding systems with
      similar restriction sites. We found more genetic exchanges between these genomes,
      independently of their evolutionary distance. Our results reconcile previous
      studies by showing that R-M systems are more abundant in promiscuous species,
      wherein they establish preferential paths of genetic exchange within and between
      lineages with cognate R-M systems. Because the repertoire and/or specificity of
      R-M systems in bacterial lineages vary quickly, the preferential fluxes of
      genetic transfer within species are expected to constantly change, producing
      time-dependent networks of gene transfer.
AU  - Oliveira PH
AU  - Touchon M
AU  - Rocha EP
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2016 113: 5658-5663.

PMID- 17369815
VI  - 25
DP  - 2007
TI  - Complete genome sequence of the erythromycinproducing bacterium Saccharopolyspora erythraea NRRL23338.
PG  - 447-453
AB  - Saccharopolyspora erythraea is used for the industrial-scale production of the antibiotic
      erythromycin A, derivatives of which play a vital role in medicine. The sequenced chromosome
      of this soil bacterium comprises 8,212,805 base pairs, predicted to encode 7,264 genes. It is
      circular, like those of the pathogenic actinomycetes Mycobacterium tuberculosis and
      Corynebacterium diphtheriae, but unlike the linear chromosomes of the model actinomycete
      Streptomyces coelicolor A3(2) and the closely related Streptomyces avermitilis. The S.
      erythraea genome contains at least 25 gene clusters for production of known or predicted
      secondary metabolites, at least 72 genes predicted to confer resistance to a range of common
      antibiotic classes and many sets of duplicated genes to support its saprophytic lifestyle. The
      availability of the genome sequence of S. erythraea will improve insight into its biology and
      facilitate rational development of strains to generate high-titer producers of clinically
      important antibiotics.
AU  - Oliynyk M
AU  - Samborskyy M
AU  - Lester JB
AU  - Mironenko T
AU  - Scott N
AU  - Dickens S
AU  - Haydock SF
AU  - Leadlay PF
PT  - Journal Article
TA  - Nat. Biotechnol.
JT  - Nat. Biotechnol.
SO  - Nat. Biotechnol. 2007 25: 447-453.

PMID- 1848100
VI  - 30
DP  - 1991
TI  - Ability of DNA and spermidine to affect the activity of restriction endonucleases from several bacterial species.
PG  - 2543-2549
AB  - Previous work has described the novel ability to modulate in vitro the activity
      of restriction endonuclease NaeI from Nocardia aerocoligenes by using cleavable
      DNA and spermidine [Conrad & Topal (1989) Proc. Natl. Acad. Sci. 86,
      9707-9711].  In this paper we report the results of a study of 49 type II
      restriction enzymes from a variety of bacterial species.  On the basis of the
      rates of cleavage observed, we found that in addition to expected cleavable
      sites a number of enzymes had slow and resistant cognate recognition sites.
      Resistant sites were identified for BspMI, NaeI, and NarI; slow sites were
      identified for HpaII, NaeI, and SacII.  Cleavage of these sites was found to be
      signficantly enhanced by the addition of cleavable DNA or spermidine.  We
      demonstrate that for BspMI, as for NaeI, activator DNAs increased Vmax without
      altering Km, whereas for HpaII, NarI, and SacII activator DNAs decreased Km
      without changing Vmax.  Comparison among the Kms for NaeI cleavage of several
      different substrates demonstrated that distant DNA sequences can affect DNA
      recognition by the activated enzyme.  Our observations extend DNA activation of
      the Nocardia NaeI endonuclease to restriction endonucleases from Nocardia
      argentinensis (NarI), Bacillus species M (BspMI), Haemophilus parainfluenza
      (HpaII), and Streptomyces achromogenes (SacII).  In addition, activation has
      now been found to affect slow as well as resistant recognition sites.
AU  - Oller AR
AU  - Vanden Broek W
AU  - Conrad M
AU  - Topal MD
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1991 30: 2543-2549.

PMID- 25301653
VI  - 2
DP  - 2014
TI  - Draft Genome of Chilean Honeybee (Apis mellifera) Gut Strain Lactobacillus kunkeei MP2.
PG  - e01013-14
AB  - Here, we report the first draft genome sequence of Lactobacillus kunkeei strain MP2, isolated
      from a Chilean honeybee gut. The sequenced genome has a total size
      of 1.58 Mb distributed into 44 contigs and 1,356 protein-coding sequences.
AU  - Olmos A
AU  - Henriquez-Piskulich P
AU  - Sanchez C
AU  - Rojas-Herrera M
AU  - Moreno-Pino M
AU  - Gomez M
AU  - Rodriguez DaSR
AU  - Maracaja-Coutinho V
AU  - Aldea P
AU  - Trombert AN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01013-14.

PMID- 25883295
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Marine Isolates of Thalassomonas viridans and Thalassomonas actiniarum.
PG  - e00297-15
AB  - Thalassomonas viridans and Thalassomonas actiniarum are aerobic Gram-negative bacilli which
      belong to a genus that has not received much attention, even
      though, as demonstrated here by the sequencing of their genomes, they are quite
      different from their closest relatives in current databases. Their genomes are
      relatively large at 7.7 and 7.4 Mb, respectively. This brief report describes the
      first draft genomes for any Thalassomonas species.
AU  - Olonade I
AU  - van Zyl LJ
AU  - Trindade M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00297-15.

PMID- 2271600
VI  - 29
DP  - 1990
TI  - Investigation of the inhibitory role of phosphorothioate internucleotidic linkages on the catalytic activity of the restriction endonuclease EcoRV.
PG  - 9546-9551
AB  - The inhibitory effect of phosphorothioate residues, located within one strand
      of double-stranded DNA, on the hydrolytic activity of the restriction
      endonuclease EcoRV was investigated.  Specific incorporation of a
      phosphorothioate group at the site of cleavage yielded the sequence
      5'-GATsATC-3'.  This modified sequence was cleaved at a relative rate of 0.1
      compared to the unmodified substrate.  Substrates 5'-GATsAsTC-3' and
      5'-GsATsATC-3', both containing one additional phosphorothioate substitution,
      were linearized at a rate of 0.04 relative to unmodified DNA.  However, under
      the same conditions, fully dAMPS-substituted DNA was found to be virtually
      resistant to the hydrolytic activity of EcoRV.  Further experiments showed that
      double-stranded DNA fragments generated by PCR containing phosphorothioate
      groups within both strands are potent inhibitors of EcoRV catalysis.  The
      inhibition was independent of whether the inhibitor fragment contained an EcoRV
      recognition site.  We concluded that substitution of the phosphate group at the
      site of cleavage by a phosphorothioate residue decreases the rate of
      EcoRV-catalyzed hydrolysis most significantly.  Substitution of other phosphate
      groups within the recognition sequence plays a limited role in enzyme
      inhibition.  The presence of multiple dNMPS residues at regions of the DNA
      removed from the EcoRV recognition site may decrease the amount of enzyme
      available for catalysis by nonspecific binding to EcoRV.
AU  - Olsen DB
AU  - Kotzorek G
AU  - Eckstein F
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1990 29: 9546-9551.

PMID- 2387858
VI  - 265
DP  - 1990
TI  - Inhibition of the restriction endonuclease BanII using modified DNA substrates.
PG  - 14389-14394
AB  - The restriction endonuclease BanII catalyzes the cleavage of double-stranded
      DNA and recognizes the degenerate sequence 5'-GPuGCPyC-3'.  The polylinker of
      M13mp18 contains one such sequence, 5'-GAGCTC-3'.  The three other possible
      sites recognized by the enzyme were prepared by site-directed mutagenesis.  The
      substitution of phosphate groups by phosphorothioate residues at some positions
      within the various recognition sites had relatively little effect on the rate
      of cleavage of the DNA.  However, when the DNA contained a phosphorothioate
      group at the site of cleavage the rate of linearization of the DNA was
      decreased by a factor of 9.  Interestingly, DNA which contained an additional
      phosphorothioate internucleotidic linkage immediately 3'-outside the
      recognition site could not be linearized by the enzyme.  The results indicate
      that an important contact between enzyme and substrate is perturbed by the
      presence of the sulfur atom at this position.
AU  - Olsen DB
AU  - Kotzorek G
AU  - Sayers JR
AU  - Eckstein F
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1990 265: 14389-14394.

PMID- Not carried by PubMed...
VI  - 10
DP  - 1991
TI  - Interaction of restriction endonucleases with phosphorothioate-containing DNA.
PG  - 665-667
AB  - The requirements for inhibition of cleavage of phosporothioate-containing DNA
      by the restriction enzymes BanII and EcoRV with respect to number and position
      of these groups was determined.
AU  - Olsen DB
AU  - Sayers JR
AU  - Kotzorek G
AU  - Eckstein F
PT  - Journal Article
TA  - Nucleosides and Nucleotides
JT  - Nucleosides and Nucleotides
SO  - Nucleosides and Nucleotides 1991 10: 665-667.

PMID- 25953185
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Three Escherichia coli Strains with Different In Vivo Pathogenicities in an Avian (Ascending) Infection Model of the Oviduct.
PG  - e00399-15
AB  - Here, we present three draft genome sequences of Escherichia coli strains that experimentally
      were proven to possess low (strain D2-2), intermediate
      (Chronic_salp), or high virulence (Cp6salp3) in an avian (ascending) infection
      model of the oviduct.
AU  - Olsen RH
AU  - Thofner IC
AU  - Pors SE
AU  - Christensen H
AU  - Bisgaard M
AU  - Christensen JP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00399-15.

PMID- 28729898
VI  - 12
DP  - 2017
TI  - Draft genome sequences of strains Salinicola socius SMB35T, Salinicola sp. MH3R3-1 and Chromohalobacter sp. SMB17 from the Verkhnekamsk potash mining region  of Russia.
PG  - 39
AB  - Halomonads are moderately halophilic bacteria that are studied as models of prokaryotic
      osmoadaptation and sources of enzymes and chemicals for
      biotechnological applications. Despite the progress in understanding the
      diversity of these organisms, our ability to explain ecological, metabolic, and
      biochemical traits of halomonads at the genomic sequence level remains limited.
      This study addresses this gap by presenting draft genomes of Salinicola socius
      SMB35T, Salinicola sp. MH3R3-1 and Chromohalobacter sp. SMB17, which were
      isolated from potash mine tailings in the Verkhnekamsk salt deposit area of
      Russia. The analysis of these genomes confirmed the importance of ectoines and
      quaternary amines to the capacity of halomonads to tolerate osmotic stress and
      adapt to hypersaline environments. The study also revealed that Chromohalobacter
      and Salinicola share 75-90% of the predicted proteome, but also harbor a set of
      genus-specific genes, which in Salinicola amounted to approximately 0.5 Mbp.
      These genus-specific genome segments may contribute to the phenotypic diversity
      of the Halomonadaceae and the ability of these organisms to adapt to changing
      environmental conditions and colonize new ecological niches.
AU  - Olsson BE
AU  - Korsakova ES
AU  - Anan'ina LN
AU  - Pyankova AA
AU  - Mavrodi OV
AU  - Plotnikova EG
AU  - Mavrodi DV
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 39.

PMID- 3019239
VI  - 13
DP  - 1986
TI  - Effect of glutaraldehyde on the activity of some DNA restriction endonucleases.
PG  - 29-35
AB  - The effect of the bifunctional crosslinking reagent glutaraldehyde on the
      activity of the restriction enzymes BamHI, HindIII, EcoRI, and Tth111I was
      investigated.  The four enzymes exhibited differential sensitivity to
      inactivation.  Tth111I was the most sensitive, with activity losses occurring
      at levels of 0.0025% and above.  HindIII was the most stable of the four and
      remained fully active at concentrations as high as 0.075%.  Addition of BSA to
      incubation mixtures generally had a stabilizing effect.  Implications of these
      results for the design of glutaraldehyde-based methods for the immobilization
      of restriction endonucleases are discussed.
AU  - Olszewski J
AU  - Wasserman BP
PT  - Journal Article
TA  - Appl. Biochem. Biotechnol.
JT  - Appl. Biochem. Biotechnol.
SO  - Appl. Biochem. Biotechnol. 1986 13: 29-35.

PMID- 29192074
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Leuconostoc citreum CW28 Isolated from Pozol, a Pre-Hispanic Fermented Corn Beverage.
PG  - e01283-17
AB  - Leuconostoc citreum CW28 was isolated from pozol, a Mayan fermented corn beverage. This strain
      produces a cell-associated inulosucrase, the first
      described in bacteria. Its draft genome sequence, announced here, has an
      estimated size of 1.98 Mb and harbors 1,915 coding genes, 12 rRNAs, 68 tRNAs, 17
      putative pseudogenes, and 1 putative phage.
AU  - Olvera C
AU  - Santamaria RI
AU  - Bustos P
AU  - Vallejo C
AU  - Montor JJ
AU  - Wacher C
AU  - Lopez MA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01283-17.

PMID- 26543120
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences for Five Strains of Trabulsiella odontotermitis, Isolated  from Heterotermes sp. Termite Gut.
PG  - e01289-15
AB  - Trabulsiella odontotermitis represents a novel species in the genus Trabulsiella  with no
      complete genome reported yet. Here, we describe the draft genome
      sequences of five isolates from termites present in the north of Mexico, which
      have an interesting pool of genes related to cellulose degradation with
      biotechnological application.
AU  - Olvera-Garcia M
AU  - Fontes-Perez H
AU  - Chavez-Martinez A
AU  - Ruiz BO
AU  - Rodriguez-Almeida FA
AU  - Sanchez-Flores A
AU  - Corral-Luna A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01289-15.

PMID- 28774988
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Mycobacterium peregrinum Isolated from an HIV-Positive Patient in South Africa.
PG  - e00759-17
AB  - Here, we report a draft genome sequence of Mycobacterium peregrinum obtained from a sputum
      sample of a South African HIV-infected patient with suspected pulmonary
      tuberculosis. The genome described here comprises 6,931,852 bp, revealing 66.2%
      G+C content, 6,808 coding sequences, and 81 RNA genes.
AU  - Omar SV
AU  - Allam M
AU  - Joseph L
AU  - Mtshali S
AU  - Ismail NA
AU  - Ismail A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00759-17.

PMID- 25301661
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Two Antimicrobial-Producing Burkholderia sp. Strains, MSh1 and MSh2, Isolated from Malaysian Tropical Peat Swamp Forest Soil.
PG  - e01032-14
AB  - We report the draft genome sequences of two antimicrobial-producing isolates, Burkholderia sp.
      strains MSh1 and MSh2, which were isolated from tropical peat
      swamp forest soil. Putative genes related to different antimicrobial production
      have been annotated in both genome sequences.
AU  - Ong KS
AU  - Aw YK
AU  - Gan HM
AU  - Yule CM
AU  - Lee SM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01032-14.

PMID- 22461552
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Typhi P-stx-12.
PG  - 2115-2116
AB  - We report here the complete genome sequence of Salmonella enterica subsp. enterica serovar
      Typhi P-stx-12, a clinical isolate obtained from a typhoid
      carrier in India.
AU  - Ong SY
AU  - Pratap CB
AU  - Wan X
AU  - Hou S
AU  - Abdul RAY
AU  - Saito JA
AU  - Nath G
AU  - Alam M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2115-2116.

PMID- 24019994
VI  - 7
DP  - 2013
TI  - The Genomic Blueprint of Salmonella enterica subspecies enterica serovar Typhi P-stx-12.
PG  - 483-496
AB  - Salmonella enterica subspecies enterica serovar Typhi is a rod-shaped, Gram-negative,
      facultatively anaerobic bacterium. It belongs to the family
      Enterobacteriaceae in the class Gammaproteobacteria, and has the capability of
      residing in the human gallbladder by forming a biofilm and hence causing the
      person to become a typhoid carrier. Here we present the complete genome of
      Salmonella enterica subspecies enterica serotype Typhi strain P-stx-12, which was
      isolated from a chronic carrier in Varanasi, India. The complete genome comprises
      a 4,768,352 bp chromosome with a total of 98 RNA genes, 4,691 protein-coding
      genes and a 181,431 bp plasmid. Genome analysis revealed that the organism is
      closely related to Salmonella enterica serovar Typhi strain Ty2 and Salmonella
      enterica serovar Typhi strain CT18, although their genome structure is slightly
      different.
AU  - Ong SY
AU  - Pratap CB
AU  - Wan X
AU  - Hou S
AU  - Rahman AY
AU  - Saito JA
AU  - Nath G
AU  - Alam M
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 7: 483-496.

PMID- 26744374
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a Virulent Pectobacterium carotovorum subsp. brasiliense Isolate Causing Soft Rot of Cucumber.
PG  - e01530-15
AB  - Pectobacterium carotovorum subsp. brasiliense causes soft rot and blackleg diseases on
      potatoes, ornamentals, and other crops of economic importance. Here,
      we report a draft genome sequence of a highly virulent P. carotovorum subsp.
      brasiliense strain, PcbHPI01, isolated from a cucumber in South Africa.
AU  - Onkendi EM
AU  - Ramesh AM
AU  - Kwenda S
AU  - Naidoo S
AU  - Moleleki L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01530-15.

PMID- 8364503
VI  - 16
DP  - 1993
TI  - Nucleosides and nucleotides. CXIX. Inhibition of DNA-cytosine methylase HhaI by a self-complementary oligonucleotide containing 5-fluorocytosine.
PG  - 529-533
AB  - A self-complementary decadeoxyribonucleotide, 5'd(GAAGFGCTTC)3', containing 5-fluorocytosine
      (F) in substitution for cytosine at the methylation site of DNA-cytosine methylase HhaI
      (mHhaI) has been synthesized M.HhaI was inhibited by the pre-incubation of the enzyme with
      d(GAAGFGCTTC).
AU  - Ono A
AU  - Matsuo Y
AU  - Matsuda A
AU  - Ueda T
PT  - Journal Article
TA  - Biol. Pharm. Bull.
JT  - Biol. Pharm. Bull.
SO  - Biol. Pharm. Bull. 1993 16: 529-533.

PMID- 6320131
VI  - 12
DP  - 1983
TI  - Oligodeoxynucleotides containing 7-deazaadenine: synthesis and recognition by restriction.
PG  - 67-70
AB  - Deoxydecanucleotides containing a recognition sequence of BglII and Sau3AI, and their
      7-deazaadenine analogs were synthesized by the phosphotriester method.  The decanucleotides
      containing 7-deazaadenine in place of adenine were partially or strongly resistant to the
      hydrolysis by these restriction endonucleases.
AU  - Ono A
AU  - Ohtani Y
AU  - Sato M
AU  - Ueda T
PT  - Journal Article
TA  - Nucleic Acids Symp. Ser.
JT  - Nucleic Acids Symp. Ser.
SO  - Nucleic Acids Symp. Ser. 1983 12: 67-70.

PMID- 6096813
VI  - 12
DP  - 1984
TI  - Synthesis of deoxyoligonucleotides containing 7-deazaadenine: recognition and cleavage by restriction endonuclease BglII and Sau3AI.
PG  - 8939-8949
AB  - Deoxydecanucleotides having a recognition sequence of BglII and Sau3AI, and
      their 7-deazaadenine analogs were synthesized.  The decanucleotides containing
      7-deazaadenine in place of adenine were partially resistant to the hydrolysis
      by Sau3AI and strongly resistant to that by BglII.  A new hypothesis on the
      mode of recognition and cleavage of specific nucleotide sequences by BglII,
      recognizing one strand and cleaving the other strand, is presented.
AU  - Ono A
AU  - Sato M
AU  - Ohtani Y
AU  - Ueda T
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1984 12: 8939-8949.

PMID- 3029671
VI  - 15
DP  - 1987
TI  - Synthesis of decadeoxyribonucleotides containing N6-methyladenine, N4-methylcytosine, and 5-methylcytosine: recognition and cleavage by restriction endonucleases (nucleosides and nucleotides part 74).
PG  - 219-232
AB  - The naturally-occurring modified bases, N6-methyladenine, N4-methylcytosine,
      and 5-methylcytosine were chemically introduced in place of the adenine or
      cytosine in the decadeoxyribonucleotides containing recognition sequences of
      BglII, Sau3AI, MboI and MflI.  The modified oligomers bind to the enzymes but
      the rates of cleavage by the enzymes are variable.
AU  - Ono A
AU  - Ueda T
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1987 15: 219-232.

PMID- 3031618
VI  - 15
DP  - 1987
TI  - Minor-groove-modified oligonucleotides: synthesis of decadeoxynucleotides containing hypoxanthine, N2-methylguanine and 3-deazaadenine, and their interactions with restriction endonucleases BglII, Sau3AI, and MboI.
PG  - 3059-3072
AB  - Decadeoxynucleotides containing hypoxanthine, N2-methylguanine, 3-deazaadenine in the
      recognition sequences of restriction endonucleases BglII, Sau3AI, and MboI were synthesized.
      These decanucleotides modified in the base moieties facing into the minor groove were strongly
      resistant to hydrolysis by BglII and partially resistant to that of Sau3AI and MboI.  The
      decadeoxynucleotide containing 3-deazaadenine in place of adenine was bound to BglII strongly,
      whereas the nucleotides containing hypoxanthine and N2-methylguanine were bound less tightly.
AU  - Ono A
AU  - Ueda T
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1987 15: 3059-3072.

PMID- 22582379
VI  - 194
DP  - 2012
TI  - Genome Sequence of Shigella flexneri Serotype 5a Strain M90T Sm.
PG  - 3022
AB  - Bacteria of the genus Shigella are a major cause of death worldwide (L. von Seidlein et al.,
      PLoS Med. 3:e353, 2006). We sequenced the genome of Shigella flexneri strain M90T Sm (serotype
      5a) and compared it to the published genome sequence of S. flexneri strain 8401 (serotype 5b).
AU  - Onodera NT
AU  - Ryu J
AU  - Durbic T
AU  - Nislow C
AU  - Archibald JM
AU  - Rohde JR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3022.

PMID- 25342671
VI  - 2
DP  - 2014
TI  - First Genome Sequence of Potential Mycotoxin-Degrading Bacterium Devosia nanyangense DDB001.
PG  - e00922-14
AB  - Devosia sp. nov. DDB001, isolated from mycotoxin-contaminated soil, is a potential
      mycotoxin-degrading alphaproteobacterium. To our knowledge, this is the
      first draft genome announcement of a Devosia species.
AU  - Onyango M
AU  - Wang Y
AU  - Nickel O
AU  - Zhao C
AU  - Zhang X
AU  - Hartke A
AU  - Hemberger J
AU  - Cemic F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00922-14.

PMID- 17687327
VI  - 448
DP  - 2007
TI  - DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA.
PG  - 714-717
AB  - Mammals use DNA methylation for the heritable silencing of retrotransposons and imprinted
      genes and for the inactivation of the X
      chromosome in females. The establishment of patterns of DNA methylation
      during gametogenesis depends in part on DNMT3L, an enzymatically inactive
      regulatory factor that is related in sequence to the DNA
      methyltransferases DNMT3A and DNMT3B. The main proteins that interact in
      vivo with the product of an epitope-tagged allele of the endogenous Dnmt3L
      gene were identified by mass spectrometry as DNMT3A2, DNMT3B and the four
      core histones. Peptide interaction assays showed that DNMT3L specifically
      interacts with the extreme amino terminus of histone H3; this interaction
      was strongly inhibited by methylation at lysine 4 of histone H3 but was
      insensitive to modifications at other positions. Crystallographic studies
      of human DNMT3L showed that the protein has a carboxy-terminal
      methyltransferase-like domain and an N-terminal cysteine-rich domain.
      Cocrystallization of DNMT3L with the tail of histone H3 revealed that the
      tail bound to the cysteine-rich domain of DNMT3L, and substitution of key
      residues in the binding site eliminated the H3 tail-DNMT3L interaction.
      These data indicate that DNMT3L recognizes histone H3 tails that are
      unmethylated at lysine 4 and induces de novo DNA methylation by
      recruitment or activation of DNMT3A2.
AU  - Ooi SK
AU  - Qiu C
AU  - Bernstein E
AU  - Li K
AU  - Jia D
AU  - Yang Z
AU  - Erdjument-Bromage H
AU  - Tempst P
AU  - Lin SP
AU  - Allis CD
AU  - Cheng X
AU  - Bestor TH
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2007 448: 714-717.

PMID- 26537224
VI  - 7
DP  - 2015
TI  - Defining the genome features of Escherichia albertii, an emerging enteropathogen closely related to Escherichia coli.
PG  - 3170-3179
AB  - Escherichia albertii is a recently recognized close relative of E. coli. This
      emerging enteropathogen possesses a type III secretion system (T3SS) encoded by
      the locus of enterocyte effacement (LEE), similar to enteropathogenic and
      enterohemorrhagic E. coli (EPEC and EHEC). Shiga toxin-producing strains have
      also been identified. The genomic features of E. albertii, particularly
      differences from other Escherichia species, have not yet been well clarified.
      Here, we sequenced the genome of 29 E. albertii strains (3 complete and 26 draft
      sequences) isolated from multiple sources and performed intra-species and
      intra-genus genomic comparisons. The sizes of the E. albertii genomes range from
      4.5 Mb to 5.1 Mb, smaller than those of E. coli strains. Intra-species genomic
      comparisons identified five phylogroups of E. albertii. Intra-genus genomic
      comparison revealed that the possible core genome of E. albertii comprises 3,250
      genes, whereas that of the genus Escherichia comprises 1,345 genes. Our analysis
      further revealed several unique or notable genetic features of E. albertii,
      including those responsible for known biochemical features and virulence factors
      and a possibly active second T3SS known as ETT2 (E. coli T3SS 2) that is
      inactivated in E. coli. Although this organism has been observed to be non-motile
      in vitro, genes for flagellar biosynthesis are fully conserved;
      chemotaxis-related genes have been selectively deleted. Based on these results,
      we have developed a nested PCR system to directly detect E. albertii. Our data
      define the genomic features of E. albertii and provide a valuable basis for
      future studies of this important emerging enteropathogen.
AU  - Ooka T
AU  - Ogura Y
AU  - Katsura K
AU  - Seto K
AU  - Kobayashi H
AU  - Kawano K
AU  - Tokuoka E
AU  - Furukawa M
AU  - Harada S
AU  - Yoshino S
AU  - Seto J
AU  - Ikeda T
AU  - Yamaguchi K
AU  - Murase K
AU  - Gotoh Y
AU  - Imuta N
AU  - Nishi J
AU  - Gomes TA
AU  - Beutin L
AU  - Hayashi T
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2015 7: 3170-3179.

PMID- 21742888
VI  - 193
DP  - 2011
TI  - Genome sequences of Alicycliphilus denitrificans strains BC and K601T.
PG  - 5028-5029
AB  - Alicycliphilus denitrificans strain BC and A. denitrificans strain K601(T) degrade cyclic
      hydrocarbons. These strains have been isolated from a
      mixture of wastewater treatment plant material and benzene polluted soil
      and from a wastewater treatment plant, respectively, suggesting their role
      in bioremediation of soil and water. Although the strains are
      phylogenetically closely related, there are some clear physiological
      differences. The hydrocarbon cyclohexanol, for example, can be degraded by
      strain K601(T), but not by strain BC. Furthermore, both strains can use
      nitrate and oxygen as an electron acceptor, but only strain BC can use
      chlorate as electron acceptor. To better understand nitrate and chlorate
      reduction mechanisms coupled to the oxidation of cyclic compounds, the
      genomes of A. denitrificans strain BC and K601(T) were sequenced. Here, we
      report the complete genome sequences of A. denitrificans strain BC and
      K601(T).
AU  - Oosterkamp MJ et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5028-5029.

PMID- 27932652
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of the Nonylphenol-Degrading Bacterium Sphingobium cloacae JCM 10874T.
PG  - e01358-16
AB  - Sphingobium cloacae JCM 10874T can degrade phenolic endocrine-disrupting chemicals,
      nonylphenol, and octylphenol. Here, we report the complete genome
      sequence of the JCM 10874T strain.
AU  - Ootsuka M
AU  - Nishizawa T
AU  - Ohta H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01358-16.

PMID- 26139713
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of a Multidrug-Resistant Acinetobacter baumannii Strain from Chile.
PG  - e00687-15
AB  - Acinetobacter baumannii strain Ab5 was isolated in the year 2007 in Chile, being  one of the
      first multidrug-resistant (MDR) cases reported in the country. Here,
      we present the very first draft genome sequence of an MDR Chilean strain, which
      shows the presence of diverse resistance and acquired virulence genes.
AU  - Opazo A
AU  - Lopes BS
AU  - Garcia P
AU  - Dominguez YM
AU  - Lima C
AU  - Bello-Toledo H
AU  - Gonzalez-Rocha G
AU  - Amyes SG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00687-15.

PMID- 27563049
VI  - 4
DP  - 2016
TI  - Genome Sequence of a Lactococcus lactis Strain Isolated from Salmonid Intestinal  Microbiota.
PG  - e00881-16
AB  - Lactococcus lactis is a common inhabitant of the intestinal microbiota of salmonids,
      especially those in aquaculture systems. Here, we present a genome
      sequence of a Lactococcus lactis strain isolated from the intestinal contents of
      rainbow trout reared in Chile.
AU  - Opazo R
AU  - Gajardo F
AU  - Ruiz M
AU  - Romero J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00881-16.

PMID- 29700144
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Methylomonas denitrificans Strain FJG1, an Obligate Aerobic Methanotroph That Can Couple Methane Oxidation with Denitrification.
PG  - e00276-18
AB  - Methylomonas denitrificans strain FJG1 is a member of the gammaproteobacterial methanotrophs.
      The sequenced genome of FJG1 reveals the presence of genes that
      encode methane, methanol, formaldehyde, and formate oxidation. It also contains
      genes that encode enzymes for nitrate reduction to nitrous oxide, consistent with
      the ability of FJG1 to couple denitrification with methane oxidation.
AU  - Orata FD
AU  - Kits KD
AU  - Stein LY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00276-18.

PMID- 27417846
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Four Bacterial Strains Isolated from a Polymicrobial Culture of Naked (N-Type) Emiliania huxleyi CCMP1516.
PG  - e00674-16
AB  - Strains of Sulfitobacter spp., Erythrobacter sp., and Marinobacter sp. were isolated from a
      polymicrobial culture of the naked (N-type) haptophyte Emiliania
      huxleyi strain CCMP1516. The genomes encode genes for the production of
      phytohormones, vitamins, and the consumption of their hosts' metabolic
      by-products, suggesting symbiotic interactions within this polymicrobial culture.
AU  - Orata FD
AU  - Rosana AR
AU  - Xu Y
AU  - Simkus DN
AU  - Bramucci AR
AU  - Boucher Y
AU  - Case RJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00674-16.

PMID- 25137193
VI  - 86
DP  - 2014
TI  - Sequence Specific Detection of Restriction Enzymes at DNA-Modified Carbon Nanotube Field Effect Transistors.
PG  - 8628-8633
AB  - Protein-DNA interactions play a central role in many cellular processes, and their
      misregulation has been implicated in a number of human diseases. Thus, there is a pressing
      need for the development of analytical strategies for interrogating the binding of proteins to
      DNA. Herein, we report the electrical monitoring of a prototypical DNA-binding protein, the
      PvuII restriction enzyme, at microfluidic-encapsulated, DNA-modified carbon nanotube field
      effect transistors. Our integrated platform enables the sensitive, sequence specific detection
      of PvuII at concentrations as low as 0.5 pM in a volume of 0.025 mu L (corresponding to
      similar to 7500 proteins). These figures of merit compare favorably to state of the art values
      reported for alternative fluorescent and electrical assays. The overall detection strategy
      represents a step toward the massively parallel electrical monitoring, identification, and
      quantification of protein DNA interactions at arrayed nanoscale devices.
AU  - Ordinario DD
AU  - Burke AM
AU  - Long P
AU  - Jocson J-M
AU  - Wang H
AU  - Dickson MN
AU  - Gorodetsky AA
PT  - Journal Article
TA  - Anal. Chem.
JT  - Anal. Chem.
SO  - Anal. Chem. 2014 86: 8628-8633.

PMID- 23792747
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Propionibacterium avidum Strain 44067, Isolated from  a Human Skin Abscess.
PG  - e00337-13
AB  - Propionibacterium avidum is an anaerobic Gram-positive bacterium that forms part  of the
      normal human cutaneous microbiota, colonizing moist areas such as the
      vestibule of the nose, axilla, and perineum. Here we present the complete genome
      sequence of P. avidum strain 44067, which was isolated from a carbuncle of the
      trunk.
AU  - Ordogh L
AU  - Hunyadkurti J
AU  - Voros A
AU  - Horvath B
AU  - Szucs A
AU  - Urban E
AU  - Kereszt A
AU  - Kondorosi E
AU  - Nagy I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00337-13.

PMID- 23887911
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Polyextremophilic Exiguobacterium sp. Strain S17, Isolated from Hyperarsenic Lakes in the Argentinian Puna.
PG  - e00480-13
AB  - Exiguobacterium sp. strain S17 is a moderately halotolerant, arsenic-resistant bacterium that
      was isolated from Laguna Socompa stromatolites in the Argentinian
      Puna. The draft genome sequence suggests potent enzyme candidates that are
      essential for survival under multiple environmental extreme conditions, such as
      high levels of UV radiation, elevated salinity, and the presence of critical
      arsenic concentrations.
AU  - Ordonez OF
AU  - Lanzarotti E
AU  - Kurth D
AU  - Gorriti MF
AU  - Revale S
AU  - Cortez N
AU  - Vazquez MP
AU  - Farias ME
AU  - Turjanski AG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00480-13.

PMID- 21981907
VI  - 12
DP  - 2011
TI  - Genomic and proteomic analyses of Mycobacterium bovis BCG Mexico 1931 reveal a diverse immunogenic repertoire against tuberculosis infection.
PG  - 493
AB  - BACKGROUND: Studies of Mycobacterium bovis BCG strains used in different
      countries and vaccination programs show clear variations in the genomes
      and immune protective properties of BCG strains. The aim of this study was
      to characterise the genomic and immune proteomic profile of the BCG 1931
      strain used in Mexico. RESULTS: BCG Mexico 1931 has a circular chromosome
      of 4,350,386 bp with a G+C content and numbers of genes and pseudogenes
      similar to those of BCG Tokyo and BCG Pasteur. BCG Mexico 1931 lacks
      Region of Difference 1 (RD1), RD2 and N-RD18 and one copy of IS6110,
      indicating that BCG Mexico 1931 belongs to DU2 group IV within the BCG
      vaccine genealogy. In addition, this strain contains three new RDs, which
      are 53 (RDMex01), 655 (RDMex02) and 2,847 bp (REDMex03) long, and 55
      single-nucleotide polymorphisms representing non-synonymous mutations
      compared to BCG Pasteur and BCG Tokyo. In a comparative proteomic
      analysis, the BCG Mexico 1931, Danish, Phipps and Tokyo strains showed
      812, 794, 791 and 701 protein spots, respectively. The same analysis
      showed that BCG Mexico 1931 shares 62% of its protein spots with the BCG
      Danish strain, 61% with the BCG Phipps strain and only 48% with the BCG
      Tokyo strain. Thirty-nine reactive spots were detected in BCG Mexico 1931
      using sera from subjects with active tuberculosis infections and positive
      tuberculin skin tests. CONCLUSIONS: BCG Mexico 1931 has a smaller genome
      than the BCG Pasteur and BCG Tokyo strains. Two specific deletions in BCG
      Mexico 1931 are described (RDMex02 and RDMex03). The loss of RDMex02
      (fadD23) is associated with enhanced macrophage binding and RDMex03
      contains genes that may be involved in regulatory pathways. We also
      describe new antigenic proteins for the first time.
AU  - Orduna P
AU  - Cevallos MA
AU  - de Leon SP
AU  - Arvizu A
AU  - Hernandez-Gonzalez IL
AU  - Mendoza-Hernandez G
AU  - Lopez-Vidal Y
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2011 12: 493.

PMID- 16235556
VI  - 39
DP  - 2005
TI  - MethylIMapper: a method for high-throughput, multilocus bisulfite sequence analysis and reporting.
PG  - 464-468
AB  - Understanding the phenotypic contribution of epigenetic components is making DNA methylation
      pattern analysis more important in higher eukaryotic genomes as well as human disease.
      Bisulfite sequencing protocols report DNA methylation occupancy information as a positive
      assay output that allows methylation patterns to be elucidated from particular developmental
      or disease states.  Reported here is a new method for bisulfite sequencing project management,
      data analysis, and site-specific methylation test development that is designed for integration
      in high-throughput genomic and bioinformatics analyses.
AU  - Ordway JM
AU  - Bedell JA
AU  - Citek RW
AU  - Nunberg AN
AU  - Jeddeloh JA
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 2005 39: 464-468.

PMID- 6279378
VI  - 263
DP  - 1982
TI  - A new site-specific endonuclease from Streptomyces -- SgrII.
PG  - 217-220
AB  - At the present time 21 restriction enzymes have been isolated from various
      species of Streptomyces.  According to the genetic data of T.A. Voeikova, the
      same restriction-modification systems tested with the acid of actinophage Pg81,
      have been detected in the strains S. griseus, Kr. 20 and Rcg 2, a recombinant
      obtained in a cross of S. coelicolor A3/2 and S. griseus Kr. 15.  In this work
      we describe the isolation and characterization of a new type of restriction
      enzyme, called SgrII.  These enzymes have been subsequently renamed Sgr20I and
      Scg2I.
AU  - Orekhov AV
AU  - Rebentish BA
AU  - Debabov VG
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1982 263: 217-220.

PMID- 2547697
VI  - 25
DP  - 1989
TI  - Restriction of shuttle Escherichia coli - Streptomyces plasmids in Streptomyces Lividans 66.
PG  - 614-625
AB  - The shuttle Escherichia coli - Streptomyces plasmids were used to transform S. lividans 66.
      Plasmid DNAs isolated from this strain transform it 10-1000-fold more efficiently than DNAs
      from E. coli. A rare transformant cured of the most restricted plasmid is a more efficient
      recipient of plasmid DNA from E. coli and has the property of R+/-M+ mutant. Restriction in S.
      lividans 66 correlates with the appearance in DNA from E. coli of the sites susceptible to
      Scg2I restriction endonuclease. The latter was isolated earlier from recombinant strain Rcg2,
      a hybrid between S. griseus Kr. 15 and S. coelicolor A3(2). Scg2I possesses the recognition
      sequence CC(T/A)GG, like EcoRII, MvaI and Eco dcm methylase. The DNA resistant to Scg2I
      cleavage retained this ability after in vitro modification by EcoRII methylase. So, the
      resistance of DNA to Scg2I cleavage is not connected with methylation at 4th and 5th position
      of second cytosine in the recognition sequence. Neither restriction of plasmid DNA in S.
      lividans 66 is dependent on dcm modification in E. coli, though its dependence on dam
      modification is not excluded. It is assumed that the restriction in S. lividans 66 is
      specified by endonuclease analogous to Scg2I.
AU  - Orekhov AV
AU  - Strokina IV
AU  - Foors AR
PT  - Journal Article
TA  - Genetika
JT  - Genetika
SO  - Genetika 1989 25: 614-625.

PMID- 28818894
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Chilean Antarctic Pseudomonas sp. Strain K2I15.
PG  - e00771-17
AB  - We announce the draft genome sequence of Pseudomonas sp. strain K2I15, isolated from the
      rhizosphere of Deschampsia antarctica Desv. The genome sequence had
      6,645,031 bp with a G+C content of 60.4%. This genome provides insights into the
      niche adaptation, prophage carriage, and evolution of this specific Antarctic
      bacteria.
AU  - Orellana P
AU  - Pavon A
AU  - Cespedes S
AU  - Salazar L
AU  - Gutierrez A
AU  - Castillo D
AU  - Corsini G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00771-17.

PMID- 17242028
VI  - 23
DP  - 2007
TI  - I-Ssp6803I: the first homing endonuclease from the PD-(D/E)XK superfamily exhibits an unusual mode of DNA recognition.
PG  - 527-530
AB  - Motivation: Restriction endonucleases (REases) and homing endonucleases (HEases) are
      biotechnologically important enzymes. Nearly all
      structurally characterized REases belong to the PD-(D/E) XK superfamily
      of nucleases, while most HEases belong to an unrelated LAGLIDADG
      superfamily. These two protein folds are typically associated with very
      different modes of protein-DNA recognition, consistent with the
      different mechanisms of action required to achieve high specificity.
      REases recognize short DNA sequences using multiple contacts per base
      pair, while HEases recognize very long sites using a few contacts per
      base pair, thereby allowing for partial degeneracy of the target
      sequence. Thus far, neither REases with the LAGLIDADG fold, nor HEases
      with the PD-(D/E) XK fold, have been found.Results: Using protein fold
      recognition, we have identified the first member of the PD-(D/E) XK
      superfamily among homing endonucleases, a cyanobacterial enzyme
      I-Ssp6803I. We present a model of the I-Ssp6803I-DNA complex based on
      the structure of Type II restriction endonuclease R. BglI and predict
      the active site and residues involved in specific DNA sequence
      recognition by I-Ssp6803I. Our finding reveals a new unexpected
      evolutionary link between HEases and REases and suggests how PD-(D/E)
      XK nucleases may develop a 'HEase-like' way of interacting with the
      extended DNA sequence. This in turn may be exploited to study the
      evolution of DNA sequence specificity and to engineer nucleases with
      new substrate specificities.Contact: iamb@genesilico.pl.
AU  - Orlowski J
AU  - Boniecki M
AU  - Bujnicki JM
PT  - Journal Article
TA  - Bioinformatics
JT  - Bioinformatics
SO  - Bioinformatics 2007 23: 527-530.

PMID- 18456708
VI  - 36
DP  - 2008
TI  - Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses.
PG  - 3552-3569
AB  - For a very long time, Type II restriction enzymes (REases) have been a paradigm of ORFans:
      proteins with no detectable similarity to each other and to any other protein in the database,
      despite common cellular and biochemical function. Crystallographic analyses published until
      January 2008 provided high-resolution structures for only 28 of 1637 Type II REase sequences
      available in the Restriction Enzyme database (REBASE). Among these structures, all but two
      possess catalytic domains with the common PD-(D/E)XK nuclease fold. Two structures are
      unrelated to the others: R.BfiI exhibits the phospholipase D (PLD) fold, while R.PabI has a
      new fold termed 'half-pipe'. Thus far, bioinformatic studies supported by site-directed
      mutagenesis have extended the number of tentatively assigned REase folds to five (now
      including also GIY-YIG and HNH folds identified earlier in homing endonucleases) and provided
      structural predictions for dozens of REase sequences without experimentally solved structures.
      Here, we present a comprehensive study of all Type II REase sequences available in REBASE
      together with their homologs detectable in the nonredundant and environmental samples
      databases at the NCBI. We present the summary and critical evaluation of structural
      assignments and predictions reported earlier, new classification of all REase sequences into
      families, domain architecture analysis and new predictions of three-dimensional folds. Among
      289 experimentally characterized (not putative) Type II REases, whose apparently full-length
      sequences are available in REBASE, we assign 199 (69%) to contain the PD-(D/E)XK domain. The
      HNH domain is the second most common, with 24 (8%) members. When putative REases are taken
      into account, the fraction of PD-(D/E)XK and HNH folds changes to 48% and 30%, respectively.
      Fifty-six characterized (and 521 predicted) REases remain unassigned to any of the five REase
      folds identified so far, and may exhibit new architectures. These enzymes are proposed as the
      most interesting targets for structure determination by high-resolution experimental methods.
      Our analysis provides the first comprehensive map of sequence-structure relationships among
      Type II REases and will help to focus the efforts of structural and functional genomics of
      this large and biotechnologically important class of enzymes.
AU  - Orlowski J
AU  - Bujnicki JM
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2008 36: 3552-3569.

PMID- 18951880
VI  - 377
DP  - 2008
TI  - Mutational analysis and a structural model of methyl-directed restriction enzyme Mrr.
PG  - 862-866
AB  - The Mrr protein of Escherichia coli K12 is a cryptic Type IV restriction endonuclease whose
      activity appears to be triggered by high
      pressure stress. In this report We used high pressure to isolate and
      analyze several Mrr mutants, and generated a new structural model of
      the Mrr protein. The activity of a number of spontaneous and
      Strategically Constructed Mrr mutants is discussed in the light of this
      model, providing a first insight into the Structure-function
      relationships of the Mrr enzyme.
AU  - Orlowski J
AU  - Mebrhatu MT
AU  - Michiels CW
AU  - Bujnicki JM
AU  - Aertsen A
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 2008 377: 862-866.

PMID- 23270491
VI  - 13
DP  - 2012
TI  - Genomic basis of broad host range and environmental adaptability of Rhizobium tropici CIAT 899 and Rhizobium sp. PRF 81 which are used in inoculants for common bean (Phaseolus vulgaris L.).
PG  - 735
AB  - ABSTRACT: BACKGROUND: Rhizobium tropici CIAT 899 and Rhizobium sp. PRF 81 are
      alpha-Proteobacteria that establish nitrogen-fixing symbioses with a range of
      legume hosts. These strains are broadly used in commercial inoculants for
      application to common bean (Phaseolus vulgaris) in South America and Africa. Both
      strains display intrinsic resistance to several abiotic stressful conditions such
      as low soil pH and high temperatures, which are common in tropical environments,
      and to several antimicrobials, including pesticides. The genetic determinants of
      these interesting characteristics remain largely unknown. RESULTS: Genome
      sequencing revealed that CIAT 899 and PRF 81 share a highly-conserved symbiotic
      plasmid (pSym) that is present also in Rhizobium leucaenae CFN 299, a rhizobium
      displaying a similar host range. This pSym seems to have arisen by a
      co-integration event between two replicons. Remarkably, three distinct nodA genes
      were found in the pSym, a characteristic that may contribute to the broad host
      range of these rhizobia. Genes for biosynthesis and modulation of plant-hormone
      levels were also identified in the pSym. Analysis of genes involved in stress
      response showed that CIAT 899 and PRF 81 are well equipped to cope with low pH,
      high temperatures and also with oxidative and osmotic stresses. Interestingly,
      the genomes of CIAT 899 and PRF 81 had large numbers of genes encoding
      drug-efflux systems, which may explain their high resistance to antimicrobials.
      Genome analysis also revealed a wide array of traits that may allow these strains
      to be successful rhizosphere colonizers, including surface polysaccharides,
      uptake transporters and catabolic enzymes for nutrients, diverse iron-acquisition
      systems, cell wall-degrading enzymes, type I and IV pili, and novel T1SS and T5SS
      secreted adhesins. CONCLUSIONS: Availability of the complete genome sequences of
      CIAT 899 and PRF 81 may be exploited in further efforts to understand the
      interaction of tropical rhizobia with common bean and other legume hosts.
AU  - Ormeno-Orrillo E et al
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2012 13: 735.

PMID- 29798911
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Rhizobium sophoriradicis H4, a Nitrogen-Fixing Bacterium Associated with the Leguminous Plant Phaseolus vulgaris on the Coast of Peru.
PG  - e00241-18
AB  - The genome sequence of Rhizobium sophoriradicis H4, a nitrogen-fixing bacterium isolated from
      the common bean (Phaseolus vulgaris) in Peru, is reported here. The
      genome assembly revealed a 6.44-Mbp genome which was distributed into 95 contigs,
      with N50 and L50 values of 293 kbp and 9, respectively. The genome contained
      6,312 coding sequence (CDS) genes and 52 RNA genes (49 tRNAs and 3 rRNAs).
AU  - Ormeno-Orrillo E
AU  - Aguilar-Cuba Y
AU  - Zuniga-Davila D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00241-18.

PMID- 23209196
VI  - 194
DP  - 2012
TI  - Genome Sequences of Burkholderia sp. Strains CCGE1002 and H160, Isolated from Legume Nodules in Mexico and Brazil.
PG  - 6927
AB  - The genome sequences of Burkholderia sp. strains CCGE1002 from Mexico and H160 from Brazil,
      isolated from legume nodules, are reported. Their gene contents in
      relation to plant-microbe interactions and xenobiotic degradation are discussed.
AU  - Ormeno-Orrillo E
AU  - Rogel MA
AU  - Chueire LM
AU  - Tiedje JM
AU  - Martinez-Romero E
AU  - Hungria M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6927.

PMID- 29519840
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of the Symbiotic Strain Bradyrhizobium icense LMTR 13(T), Isolated from Lima Bean (Phaseolus lunatus) in Peru.
PG  - e00146-18
AB  - The complete genome sequence of Bradyrhizobium icense LMTR 13(T), a root nodule bacterium
      isolated from the legume Phaseolus lunatus, is reported here. The
      genome consists of a circular 8,322,773-bp chromosome which codes for a large and
      novel symbiotic island as well as genes putatively involved in soil and root
      colonization.
AU  - Ormeno-Orrillo E
AU  - Rogel MA
AU  - Zuniga-Davila D
AU  - Martinez-Romero E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00146-18.

PMID- 28007857
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the Commensal Escherichia coli Strain F-18.
PG  - e01416-16
AB  - Here, we report the draft genome sequence of Escherichia coli strain F-18, originally isolated
      from the feces of a healthy individual in 1977. The draft genome is 5,246,829 bp, with a G+C
      content of 50.50%, and it encodes 4,933 predicted coding sequences (CDSs), 10 rRNAs, and 84
      tRNAs.
AU  - Ormsby MJ
AU  - Johnson SA
AU  - Wall DM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01416-16.

PMID- 19348764
VI  - 96
DP  - 2009
TI  - Intrinsic Dynamics of Restriction Endonuclease EcoO109I Studied by Molecular Dynamics Simulations and X-Ray Scattering Data Analysis.
PG  - 2808-2822
AB  - EcoO109I is a type II restriction endonuclease that functions as a dimer in solution. Upon DNA
      binding to the enzyme, the two subunits
      rotate counterclockwise relative to each other, as the two catalytic
      domains undergo structural changes to capture the cognate DNA. Using a
      150-ns molecular dynamics simulation, we investigated the intrinsic
      dynamics of the DNA-free enzyme in solution to elucidate the
      relationship between enzyme dynamics and structural changes. The
      simulation revealed that the enzyme is considerably flexible, and thus
      exhibits large fluctuations in the radius of gyration. The small-angle
      x-ray scattering profile calculated from the simulation, including
      scattering from explicit hydration water, was in agreement with the
      experimentally observed profile. Principal component analysis revealed
      that the major dynamics were represented by the open-close and
      counterclockwise motions: the former is required for the enzyme to
      access DNA, whereas the latter corresponds to structural changes upon
      DNA binding. Furthermore, the intrinsic dynamics in the catalytic
      domains were consistent with motions capturing the cognate DNA. These
      results indicate that the structure of EcoO109I is intrinsically
      flexible in the direction of its functional movement, to facilitate
      effective structural changes for sequence-specific DNA recognition and
      processing.
AU  - Oroguchi T
AU  - Hashimoto H
AU  - Shimizu T
AU  - Sato M
AU  - Ikeguchi M
PT  - Journal Article
TA  - Biophys. J.
JT  - Biophys. J.
SO  - Biophys. J. 2009 96: 2808-2822.

PMID- 28818898
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Two Unclassified Chitinophagaceae Bacteria, IBVUCB1 and IBVUCB2, Isolated from Environmental Samples.
PG  - e00787-17
AB  - We report here the draft genome sequences of two Chitinophagaceae bacteria, IBVUCB1 and
      IBVUCB2, assembled from metagenomes of surface samples from
      freshwater lakes. The genomes are >99% complete and may represent new genera
      within the Chitinophagaceae family, indicating a larger diversity than currently
      identified.
AU  - Orr RJS
AU  - Rombauts S
AU  - Van de Peer Y
AU  - Shalchian-Tabrizi K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00787-17.

PMID- 28839038
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Two Unclassified Bacteria, Sphingomonas sp. Strains IBVSS1 and IBVSS2, Isolated from Environmental Samples.
PG  - e00894-17
AB  - We report here the draft genome sequences of Sphingomonas sp. IBVSS1 and IBVSS2,  two bacteria
      assembled from the metagenomes of surface samples from freshwater
      lakes. The genomes are >99% complete and may represent new species within the
      Sphingomonas genus, indicating a larger diversity than currently identified.
AU  - Orr RJS
AU  - Rombauts S
AU  - Van de Peer Y
AU  - Shalchian-Tabrizi K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00894-17.

PMID- 28839037
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Two Unclassified Bacteria, Hydrogenophaga sp. Strains IBVHS1 and IBVHS2, Isolated from Environmental Samples.
PG  - e00884-17
AB  - We report here the draft genome sequences of Hydrogenophaga sp. strains IBVHS1 and IBVHS2, two
      bacteria assembled from the metagenomes of surface samples from
      freshwater lakes. The genomes are >95% complete and may represent new species
      within the Hydrogenophaga genus, indicating a larger diversity than currently
      identified.
AU  - Orr RJS
AU  - Rombauts S
AU  - Van de Peer Y
AU  - Shalchian-Tabrizi K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00884-17.

PMID- 25377698
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Bacillus coagulans GBI-30, 6086, a Widely Used Spore-Forming Probiotic Strain.
PG  - e01080-14
AB  - Bacillus coagulans GBI-30, 6086 is a safe strain, already available on the market, and
      characterized by certified beneficial effects. The draft genome
      sequence presented here constitutes the first pillar toward the identification of
      the molecular mechanisms responsible for its positive features and safety.
AU  - Orru L
AU  - Salvetti E
AU  - Cattivelli L
AU  - Lamontanara A
AU  - Michelotti V
AU  - Capozzi V
AU  - Spano G
AU  - Keller D
AU  - Cash H
AU  - Martina A
AU  - Torriani S
AU  - Felis GE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01080-14.

PMID- 29903806
VI  - 6
DP  - 2018
TI  - Whole-Genome Sequences of Two Listeria monocytogenes Serovar 1/2a Strains Responsible for a Severe Listeriosis Outbreak in Central Italy.
PG  - e00236-18
AB  - We report the whole-genome sequences of two Listeria monocytogenes strains responsible for a
      severe invasive listeriosis outbreak in central Italy that
      occurred in 2015 and 2016. These two strains differ by a single band in their
      pulsed-field gel electrophoresis (PFGE) profiles.
AU  - Orsini M
AU  - Cornacchia A
AU  - Patavino C
AU  - Torresi M
AU  - Centorame P
AU  - Acciari VA
AU  - Ruolo A
AU  - Marcacci M
AU  - Ancora M
AU  - Di Domenico M
AU  - Mangone I
AU  - Blasi G
AU  - Duranti A
AU  - Camma C
AU  - Pomilio F
AU  - Migliorati G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00236-18.

PMID- 25814605
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequencing of Mycoplasma mycoides subsp. mycoides Italian Strain 57/13, the Causative Agent of Contagious Bovine Pleuropneumonia.
PG  - e00197-15
AB  - Mycoplasma mycoides subsp. mycoides is generally considered one of most pathogenic Mycoplasma
      species, and it is the etiological agent of contagious
      bovine pleuropneumonia (CBPP). Here, we present the annotated genome sequence of
      M. mycoides subsp. mycoides Italian strain 57/13, isolated in 1992 during CBPP
      outbreaks in Italy.
AU  - Orsini M
AU  - Krasteva I
AU  - Marcacci M
AU  - Ancora M
AU  - Ciammaruconi A
AU  - Gentile B
AU  - Lista F
AU  - Pini A
AU  - Scacchia M
AU  - Sacchini F
AU  - Camma C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00197-15.

PMID- 26294627
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of 19 Salmonella enterica Serovar Typhimurium [4,5:i:-] Strains Resistant to Nalidixic Acid from a Long-Term Outbreak in Italy.
PG  - e00911-15
AB  - Here, we present the draft genome sequences of 19 Salmonella enterica serovar Typhimurium
      monophasic variant [4,5:i:-] strains involved in a long-term
      salmonellosis outbreak that occurred in central Italy in 2013 to 2014.
AU  - Orsini M
AU  - Mangone I
AU  - DiPasquale A
AU  - Perticara S
AU  - Sacchini L
AU  - Cito F
AU  - Iannetti S
AU  - Marcacci M
AU  - Ancora M
AU  - Calistri P
AU  - Di Giannatale E
AU  - Camma C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00911-15.

PMID- 29954895
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of the Antimicrobial-Producing Strain Paenibacillus elgii AC13.
PG  - e00573-18
AB  - A Paenibacillus elgii strain isolated from soil samples from Cerrado, Brazil, showed
      antimicrobial activity. Its genome sequence was acquired (GS20 FLX
      Titanium 454 platform) and comprises 108 contigs (N50, 198,427 bp) and 6,810
      predicted sequences. Here, we shed some light on the antimicrobial genes of the
      strain, including a nonribosomal peptide synthetase (NRPS) module identified as
      part of a pelgipeptin gene cluster.
AU  - Ortega DB
AU  - Costa RA
AU  - Pires AS
AU  - Araujo TF
AU  - Araujo JF
AU  - Kurokawa AS
AU  - Magalhaes BS
AU  - Reis AMM
AU  - Franco OL
AU  - Kruger RH
AU  - Pappas GJ Jr
AU  - Barreto CC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00573-18.

PMID- 21515771
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of a beneficial plant root-associated bacterium Pseudomonas brassicacearum.
PG  - 3146
AB  - To shed light on the genetic equipment of the beneficial plant-associated bacterium
      Pseudomonas brassicacearum, we sequenced the whole genome of the
      strain NFM421. Its genome consists of one chromosome equipped with a
      repertoire of plant growth beneficial factors. In addition a complete T3SS
      and two complete T6SS were identified. We report here the first genome
      sequence of this species.
AU  - Ortet P
AU  - Barakat M
AU  - Lalaouna D
AU  - Fochesato S
AU  - Barbe V
AU  - Vacherie B
AU  - Santaella C
AU  - Heulin T
AU  - Achouak W
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3146.

PMID- 28385837
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Microbacterium oleivorans Strain A9, a Bacterium Isolated from Chernobyl Radionuclide-Contaminated Soil.
PG  - e00092-17
AB  - Here, we present the draft genome sequence of Microbacterium oleivorans strain A9, a
      uranium-tolerant actinobacterium which has been isolated from
      radionuclide-contaminated soil from the Chernobyl exclusion zone. It is composed
      of 22 contigs totaling 2,954,335 bp and contains 2,813 coding DNA sequences, one
      cluster of rRNA genes, and 45 tRNA genes.
AU  - Ortet P
AU  - Gallois N
AU  - Piette L
AU  - Long J
AU  - Berthomieu C
AU  - Armengaud J
AU  - Barakat M
AU  - Chapon V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00092-17.

PMID- 26184933
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Geobacillus sp. Isolate T6, a Thermophilic Bacterium Collected from a Thermal Spring in Argentina.
PG  - e00743-15
AB  - Geobacillus sp. isolate T6 was collected from a thermal spring in Salta, Argentina. The draft
      genome sequence (3,767,773 bp) of this isolate is
      represented by one major scaffold of 3,46 Mbp, a second one of 207 kbp, and 20
      scaffolds of <13 kbp. The assembled sequences revealed 3,919 protein-coding
      genes.
AU  - Ortiz EM
AU  - Berretta MF
AU  - Navas LE
AU  - Benintende GB
AU  - Amadio AF
AU  - Zandomeni RO
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00743-15.

PMID- 23209200
VI  - 194
DP  - 2012
TI  - Genome Sequence and Comparative Genomics Analysis of a Vibrio cholerae O1 Strain  Isolated from a Cholera Patient in Malaysia.
PG  - 6933
AB  - The genome sequence analysis of a clinical Vibrio cholerae VC35 strain from an outbreak case
      in Malaysia indicates multiple genes involved in host adaptation
      and a novel Na(+)-driven multidrug efflux pump-coding gene in the genome of
      Vibrio cholerae with the highest similarity to VMA_001754 of Vibrio mimicus
      VMA223.
AU  - Osama A
AU  - Gan HM
AU  - Teh CS
AU  - Yap KP
AU  - Thong KL
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6933.

PMID- 28572318
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of Two Geographically Distinct Legionella micdadei Clinical Isolates.
PG  - e00436-17
AB  - Legionella is a highly diverse genus of intracellular bacterial pathogens that cause
      Legionnaire's disease (LD), an often severe form of pneumonia. Two L.
      micdadei sp. clinical isolates, obtained from patients hospitalized with LD from
      geographically distinct areas, were sequenced using PacBio SMRT cell technology,
      identifying incomplete phage regions, which may impact virulence.
AU  - Osborne AJ
AU  - Jose BR
AU  - Perry J
AU  - Smeele Z
AU  - Aitken J
AU  - Gardner PP
AU  - Slow S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00436-17.

PMID- 29192086
VI  - 5
DP  - 2017
TI  - High-Quality Draft Genome Sequence of Curtobacterium sp. Strain Ferrero.
PG  - e01378-17
AB  - Here, we present the high-quality draft genome sequence of Curtobacterium sp. strain Ferrero,
      an actinobacterium belonging to a novel species isolated as an
      environmental contaminant in a bacterial cell culture. The assembled genome of
      3,694,888 bp in 49 contigs has a G+C content of 71.6% and contains 3,516
      predicted genes.
AU  - Osdaghi E
AU  - Forero SN
AU  - Bolot S
AU  - Fischer-Le SM
AU  - Jacques MA
AU  - Portier P
AU  - Carrere S
AU  - Koebnik R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01378-17.

PMID- 28636609
VI  - 12
DP  - 2017
TI  - Genomic and phenotypic characterisation of fluoroquinolone resistance mechanisms in Enterobacteriaceae in Durban, South Africa.
PG  - E0178888
AB  - Resistance to fluoroquinolones (FQ) is being increasingly reported and found to
      be mediated by efflux pumps, plasmid-mediated quinolone resistance genes (PMQR)
      and mutations in gyrA, gyrB, parC and parE. However, studies reporting on FQ
      resistance mechanisms (FQRM), particularly in Africa, are focused mostly on
      Salmonella. This study used a whole-genome-based approach to describe FQRM in
      forty-eight clinical Enterobacteriaceae isolates comprising of Klebsiella
      pneumoniae (n = 21), Serratia marcescens (n = 12), Enterobacter spp. (n = 10),
      Citrobacter freundii (n = 3), Escherichia coli (n = 1), and Klebsiella
      michiganensis (n = 1) with reduced susceptibility to FQ in Enterobacteriaceae.
      All the isolates exhibited exceptionally high-level resistance (MIC of 4-512mg/L)
      to all three FQs, which could not be reversed by carbonyl cyanide m-chlorophenyl
      hydrazine (CCCP), verapamil (VRP) or reserpine (RSP). PMQR genes such as oqxAB (n
      = 43), aac(6')-Ib-cr (n = 28), and qnr(S1, B1, B2, B9, B49, B66) (n = 23) were
      identified without transposons or integrons in their immediate environments.
      Multiple and diverse mutations were found in gyrA (including S83I/Y and
      T/I83I/T), gyrB, parC and parE, which were clonally specific. There were vertical
      and horizontal transmission of high-level FQ resistance in Enterobacteriaceae in
      hospitals in Durban, South Africa, which are mediated by efflux, PMQR genes, and
      gyrA, gyrB, parC and parE mutations.
AU  - Osei-Sekyere J
AU  - Amoako DG
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2017 12: E0178888.

PMID- 28798190
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Thiohalobacter thiocyanaticus Strain FOKN1, a Neutrophilic Halophile Capable of Thiocyanate Degradation.
PG  - e00799-17
AB  - A draft genome sequence of a neutrophilic halophile capable of thiocyanate degradation,
      Thiohalobacter thiocyanaticus FOKN1, was determined using a PacBio
      RSII sequencer. A 3.23-Mb circular genome sequence was assembled, in which 3,026
      gene-coding sequences, 45 tRNAs, and 1 rrn operon were annotated.
AU  - Oshiki M
AU  - Fukushima T
AU  - Kawano S
AU  - Nakagawa J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00799-17.

PMID- 25883286
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of an Anaerobic Ammonium-Oxidizing Bacterium, 'Candidatus Brocadia sinica'.
PG  - e00267-15
AB  - A draft genome sequence of an anaerobic ammonium-oxidizing (anammox) bacterium, 'Candidatus
      Brocadia sinica,' was determined by pyrosequencing and by screening a
      fosmid library. A 4.07-Mb genome sequence comprising 3 contigs was assembled, in
      which 3,912 gene-coding regions, 47 tRNAs, and a single rrn operon were
      annotated.
AU  - Oshiki M
AU  - Shinyako-Hata K
AU  - Satoh H
AU  - Okabe S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00267-15.

PMID- 
VI  - 75
DP  - 2000
TI  - Restriction and modification system genes of Bacillus subtilis.
PG  - 380
AB  - We found a set of genes for DNA restriction and modification in the third prophage region of
      the Bacillus subtilis chromosome, where only five orfs are found in the 12kb region.  Two orfs
      code for proteins similar to DNA methylation enzymes and constitute an operon.  The other
      three orfs make another operon and the middle orf codes for a protein similar to DNA
      restriction enzyme.  They must be RM system genes which recognize XhoI site and are deleted in
      a classical RM strain of Bacillus subtilis.  XhoI sites on the DNA extracted only from RM
      knockout strain could be digested with XhoI, indicating they are involved in restriction and
      modification of Bacillus subtilis chromosome.
AU  - Oshima H
AU  - Asai K
AU  - Sadaie Y
PT  - Journal Article
TA  - Genes Genet. Syst.
JT  - Genes Genet. Syst.
SO  - Genes Genet. Syst. 2000 75: 380.

PMID- 26159526
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Streptomyces incarnatus NRRL8089, which Produces the Nucleoside Antibiotic Sinefungin.
PG  - e00715-15
AB  - A draft genome sequence of Streptomyces incarnatus NRRL8089, which produces the nucleoside
      antibiotic sinefungin, is described here. The genome contains
      8,897,465 bp in 76 contigs and 8,266 predicted genes. Interestingly, the genome
      encodes an open reading frame for selenocysteine-containing formate
      dehydrogenase-O and the selenoprotein biosynthetic gene cluster selABCD.
AU  - Oshima K
AU  - Hattori M
AU  - Shimizu H
AU  - Fukuda K
AU  - Nemoto M
AU  - Inagaki K
AU  - Tamura T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00715-15.

PMID- 25977411
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Scardovia inopinata JCM 12537T, Isolated from Human Dental Caries.
PG  - e00481-15
AB  - Scardovia inopinata JCM 12537(T) was isolated from human dental caries. Here, we  report the
      complete genome sequence of this organism. This paper is the first
      report to demonstrate the fully sequenced and completely annotated genome of an
      S. inopinata strain.
AU  - Oshima K
AU  - Hayashi J
AU  - Toh H
AU  - Nakano A
AU  - Omori E
AU  - Hattori Y
AU  - Morita H
AU  - Honda K
AU  - Hattori M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00481-15.

PMID- 25977413
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Parascardovia denticolens JCM 12538T, Isolated from Human Dental Caries.
PG  - e00485-15
AB  - Parascardovia denticolens JCM 12538(T) was isolated from human dental caries. Here, we report
      the complete genome sequence of this organism. This paper is the
      first report demonstrating the completely sequenced and assembled genome of P.
      denticolens.
AU  - Oshima K
AU  - Hayashi J
AU  - Toh H
AU  - Nakano A
AU  - Shindo C
AU  - Komiya K
AU  - Morita H
AU  - Honda K
AU  - Hattori M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00485-15.

PMID- 25858849
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Gardnerella vaginalis Strain JCM 11026T, Isolated from Vaginal Tracts of Women.
PG  - e00286-15
AB  - Gardnerella vaginalis strain JCM 11026(T) was isolated from vaginal tracts of women. Here, we
      report the complete genome sequence of this organism.
AU  - Oshima K
AU  - Hisamatsu S
AU  - Toh H
AU  - Nakano A
AU  - Kiuchi M
AU  - Kuroyanagi H
AU  - Morita H
AU  - Hattori M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00286-15.

PMID- 8905239
VI  - 3
DP  - 1996
TI  - A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map (supplement).
PG  - 211-223
AB  - none
AU  - Oshima T et al
PT  - Journal Article
TA  - DNA Res.
JT  - DNA Res.
SO  - DNA Res. 1996 3: 211-223.

PMID- 8905232
VI  - 3
DP  - 1996
TI  - A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min Region on the linkage map.
PG  - 137-155
AB  - The 718,122 base pair sequence of the Escherichia coli K-12 genome corresponding to the region
      from 12.7 to 28.0 minutes on the genetic map is described.  This region contains at least 681
      potential open reading frames, of which 277 (41%) have been previously identified, 147 (22%)
      are homologous to other known genes, 139 (20%) are identical or similar to the hypothetical
      genes registered in databases, and the remaining 118 (17%) do not show a significant
      similarity to any other gene.  In this region, we assigned a cluster of cit genes encoding
      multienzyme citrate lyase, two clusters of fimbrial genes and a set of lysogenic phage genes
      encoding integrase, excisionase and repressor in the e14 genetic element.  In addition, a new
      valine tRNA gene, designated valZ, and a family of long directly repeated sequences, LDR-A, -B
      and -C, were found.
AU  - Oshima T et al
PT  - Journal Article
TA  - DNA Res.
JT  - DNA Res.
SO  - DNA Res. 1996 3: 137-155.

PMID- 12139615
VI  - 45
DP  - 2002
TI  - Genome-wide analysis of deoxyadenosine methyltransferase-mediated control of gene expression in Escherichia coli.
PG  - 673-695
AB  - Deoxyadenosine methyltransferase (Dam) methylates the deoxyadenine residues in 5'-GATC-3'
      sequences and is important in many cellular processes in Escherichia coli. We performed a
      computational analysis of the entire E. coli genome and confirmed that GATC sequences are
      distributed unevenly in regulatory regions, which suggests that Dam might regulate gene
      transcription. To test this, a high-density DNA microarray of 4097 E. coli genes was
      constructed and used to assess the gene expression profiles of the wild type and the
      dam-16::kam mutant strain grown under four different conditions. We also used two-dimensional
      electrophoretic analysis of the proteome to assess the protein profiles. The expression of a
      large number of genes was affected by the dam deficiency. Genes involved in aerobic
      respiration, stress and SOS responses, amino acid metabolism and nucleotide metabolism were
      expressed at higher levels in the mutant cells, especially in aerobic conditions. In contrast,
      transcription of genes participating in anaerobic respiration, flagella biosynthesis,
      chemotaxis and motility was decreased in the dam mutant strain under both aerobic and low
      aerobic conditions. Thus, Dam-controlled genes are involved in adjusting the metabolic and
      respiratory pathways and bacterial motility to suit particular environmental conditions. The
      promoters of most of these Dam-controlled genes were also found to contain GATC sequences that
      overlap with recognition sites for two global regulators, fumarate nitrate reduction (Fnr) and
      catabolite activator protein (CRP). We propose that Dam-mediated methylation plays an
      important role in the global regulation of genes, particularly those with Fnr and CRP binding
      sites.
AU  - Oshima T
AU  - Wada C
AU  - Kawagoe Y
AU  - Ara T
AU  - Maeda M
AU  - Masuda Y
AU  - Hiraga S
AU  - Mori H
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2002 45: 673-695.

PMID- 29545306
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Methylovulum psychrotolerans Sph1(T), an Obligate Methanotroph from Low-Temperature Environments.
PG  - e01488-17
AB  - Methylovulum psychrotolerans Sph1(T) is an aerobic, obligate methanotroph, which  was isolated
      from cold methane seeps in West Siberia. This bacterium possesses
      only a particulate methane monooxygenase and is widely distributed in
      low-temperature environments. Strain Sph1(T) has the genomic potential for
      biosynthesis of hopanoids required for the maintenance of intracytoplasmic
      membranes.
AU  - Oshkin IY
AU  - Miroshnikov KK
AU  - Belova SE
AU  - Korzhenkov AA
AU  - Toshchakov SV
AU  - Dedysh SN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01488-17.

PMID- 26769948
VI  - 4
DP  - 2016
TI  - Permanent Draft Genome Sequences for Two Variants of Frankia sp. Strain CpI1, the First Frankia Strain Isolated from Root Nodules of Comptonia peregrina.
PG  - e01588-15
AB  - Frankia stains CpI1-S and CpI1-P are members of Frankia lineage Ia that are able  to reinfect
      plants of the Betulaceae and Myricaceae families. Here, we report two
      7.6-Mbp draft genome sequences with 6,396 and 6,373 candidate protein-coding
      genes for CpI1-S and CpI1-P, respectively.
AU  - Oshone R
AU  - Hurst SG IV
AU  - Abebe-Akele F
AU  - Simpson S
AU  - Morris K
AU  - Thomas WK
AU  - Tisa LS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01588-15.

PMID- 27198023
VI  - 4
DP  - 2016
TI  - Permanent Draft Genome Sequence of Frankia sp. Strain Allo2, a Salt-Tolerant Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Allocasuarina.
PG  - e00388-16
AB  - Frankia sp. strain Allo2 is a member of Frankia lineage Ib, which is able to reinfect plants
      of the Casuarinaceae family, and exhibits a high level of salt
      tolerance compared to other isolates. Here, we report the 5.3-Mbp draft genome
      sequence of Frankia sp. strain Allo2 with a G+C content of 70.0% and 4,224
      candidate protein-encoding genes.
AU  - Oshone R
AU  - Ngom M
AU  - Abebe-Akele F
AU  - Simpson S
AU  - Morris K
AU  - Sy MO
AU  - Champion A
AU  - Thomas WK
AU  - Tisa LS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00388-16.

PMID- 29954903
VI  - 6
DP  - 2018
TI  - Complete Draft Genome Sequence of an Extended-Spectrum beta-Lactamase-Producing Citrobacter freundii Strain Recovered from the Intestine of a House Sparrow (Passer domesticus) in Germany, 2017.
PG  - e00599-18
AB  - Here, we announce the genome of an extended-spectrum beta-lactamase-producing Citrobacter
      freundii strain isolated from the cecum of a house sparrow that was
      found dead in Berlin-Lichtenberg, Germany, in 2017. This isolate exhibits
      increased MICs for several antimicrobials and a comprehensive set of acquired
      resistance determinants potentially involved in horizontal gene transfer.
AU  - Osieka V
AU  - Grobbel M
AU  - Schmoger S
AU  - Szentiks CA
AU  - Irrgang A
AU  - Kasbohrer A
AU  - Tenhagen BA
AU  - Hammerl JA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00599-18.

PMID- 12954781
VI  - 31
DP  - 2003
TI  - Crystal structure of MboIIA methyltransferase.
PG  - 5440-5448
AB  - DNA methyltransferases (MTases) are sequence-specific enzymes which transfer a methyl group
      from S-adenosyl-L-methionine (AdoMet) to the amino
      group of either cytosine or adenine within a recognized DNA sequence.
      Methylation of a base in a specific DNA sequence protects DNA from
      nucleolytic cleavage by restriction enzymes recognizing the same DNA
      sequence. We have determined at 1.74 A resolution the crystal structure of
      a beta-class DNA MTase MboIIA (M.MboIIA) from the bacterium Moraxella
      bovis, the smallest DNA MTase determined to date. M.MboIIA methylates the
      3' adenine of the pentanucleotide sequence 5'-GAAGA-3'. The protein
      crystallizes with two molecules in the asymmetric unit which we propose to
      resemble the dimer when M.MboIIA is not bound to DNA. The overall
      structure of the enzyme closely resembles that of M.RsrI. However, the
      cofactor-binding pocket in M.MboIIA forms a closed structure which is in
      contrast to the open-form structures of other known MTases.
AU  - Osipiuk J
AU  - Walsh MA
AU  - Joachimiak A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2003 31: 5440-5448.

PMID- 1320190
VI  - 233
DP  - 1992
TI  - The integrated state of the rolling-circle plasmid pTB913 in the composite Bacillus plasmid pTB19.
PG  - 462-468
AB  - pTB19, a 27 kb plasmid originating from a thermophilic Bacillus species,
      contains integrated copies of two rolling-circle type plasmids on a 10.6
      kb DNA fragment. In the present study we analysed the part of pTB19 that
      contains the rolling-circle plasmid pTB913 and the region in between the
      two rolling-circle plasmids. We show that, in the integrated state, pTB913
      was flanked by a 55 bp direct repeat that duplicated part of the
      replication initiation gene repB. Since repB was interrupted, the
      integrated pTB913 could not initiate rolling-circle replication.
      Autonomously replicating pTB913 was produced from pTB19, probably through
      recombination between the 55 bp direct repeats; this was a rare event.
      Since the second integrated rolling-circle type plasmid also contained a
      non-functional replication initiation gene, replication of pTB19 must be
      controlled by the RepA determinant. Theta-type replication, controlled by
      RepA is likely to account for the high stability of pTB19. In between the
      two integrated rolling-circle plasmids was present an open reading frame
      (447 codons) which could encode a protein of unknown function.
AU  - Oskam L
AU  - Hillenga DJ
AU  - Venema G
AU  - Bron S
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1992 233: 462-468.

PMID- 28975015
VI  - 12
DP  - 2017
TI  - High-quality draft genome sequence of Ensifer meliloti Mlalz-1, a microsymbiont of Medicago laciniata (L.) miller collected in Lanzarote, Canary Islands, Spain.
PG  - 58
AB  - 10.1601/nm.1335 Mlalz-1 (INSDC = ATZD00000000) is an aerobic, motile, Gram-negative,
      non-spore-forming rod that was isolated from an effective
      nitrogen-fixing nodule of Medicago laciniata (L.) Miller from a soil sample
      collected near the town of Guatiza on the island of Lanzarote, the Canary
      Islands, Spain. This strain nodulates and forms an effective symbiosis with the
      highly specific host M. laciniata. This rhizobial genome was sequenced as part of
      the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and
      Archaea-Root Nodule Bacteria (GEBA-RNB) sequencing project. Here the features of
      10.1601/nm.1335 Mlalz-1 are described, together with high-quality permanent draft
      genome sequence information and annotation. The 6,664,116 bp high-quality draft
      genome is arranged in 99 scaffolds of 100 contigs, containing 6314 protein-coding
      genes and 74 RNA-only encoding genes. Strain Mlalz-1 is closely related to
      10.1601/nm.1335 10.1601/strainfinder?urlappend=%3Fid%3DIAM+12611 T,
      10.1601/nm.1334 A 321T and 10.1601/nm.17831
      10.1601/strainfinder?urlappend=%3Fid%3DORS+1407 T, based on 16S rRNA gene
      sequences. gANI values of >/=98.1% support the classification of strain Mlalz-1
      as 10.1601/nm.1335. Nodulation of M. laciniata requires a specific nodC allele,
      and the nodC gene of strain Mlalz-1 shares >/=98% sequence identity with nodC of
      M. laciniata-nodulating 10.1601/nm.1328 strains, but </=93% with nodC of
      10.1601/nm.1328 strains that nodulate other Medicago species. Strain Mlalz-1 is
      unique among sequenced 10.1601/nm.1335 strains in possessing genes encoding
      components of a T2SS and in having two versions of the adaptive acid tolerance
      response lpiA-acvB operon. In 10.1601/nm.1334 strain
      10.1601/strainfinder?urlappend=%3Fid%3DWSM+419, lpiA is essential for enhancing
      survival in lethal acid conditions. The second copy of the lpiA-acvB operon of
      strain Mlalz-1 has highest sequence identity (> 96%) with that of 10.1601/nm.1334
      strains, which suggests genetic recombination between strain Mlalz-1 and
      10.1601/nm.1334 and the horizontal gene transfer of lpiA-acvB.
AU  - Osman WAM
AU  - van Berkum P
AU  - Leon-Barrios M
AU  - Velazquez E
AU  - Elia P
AU  - Tian R
AU  - Ardley J
AU  - Gollagher M
AU  - Seshadri R
AU  - Reddy TBK
AU  - Ivanova N
AU  - Woyke T
AU  - Pati A
AU  - Markowitz V
AU  - Baeshen MN
AU  - Baeshen NN
AU  - Kyrpides N
AU  - Reeve W
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 58.

PMID- 25342676
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Iron-Oxidizing, Acidophilic, and Halotolerant 'Thiobacillus prosperus' Type Strain DSM 5130.
PG  - e01042-14
AB  - 'Thiobacillus prosperus' is a halotolerant mesophilic acidophile that gains energy through
      iron and sulfur oxidation. Its physiology is poorly understood.
      Here, we describe the principal genomic features of the type strain of T.
      prosperus, DSM 5130. This is the first public genome sequence of an acidophilic
      halotolerant bacterium.
AU  - Ossandon FJ
AU  - Cardenas JP
AU  - Corbett M
AU  - Quatrini R
AU  - Holmes DS
AU  - Watkin E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01042-14.

PMID- 10383952
VI  - 181
DP  - 1999
TI  - Characterization of a dam mutant of Serratia marcescens and nucleotide sequence of the dam region.
PG  - 3880-3885
AB  - The DNA of Serratia marcescens has N6-adenine methylation in GATC sequences. Among
      2-aminopurine-sensitive mutants isolated from S. marcescens Sr41, one was identified which
      lacked GATC methylation. The mutant showed up to 30-fold increased spontaneous mutability and
      enhanced mutability after treatment with 2-aminopurine, ethyl methanesulfonate, or UV light.
      The gene (dam) coding for the adenine methyltransferase (Dam enzyme) of S. marcescens was
      identified on a gene bank plasmid which alleviated the 2-aminopurine sensitivity and the
      higher mutability of a dam-13::Tn9 mutant of Escherichia coli. Nucleotide sequencing revealed
      that the deduced amino acid sequence of Dam (270 amino acids; molecular mass, 31.3 kDa) has
      72% identity to the Dam enzyme of E. coli. The dam gene is located between flanking genes
      which are similar to those found to the sides of the E. coli dam gene. The results of
      complementation studies indicated that like Dam of E. coli and unlike Dam of Vibrio cholerae,
      the Dam enzyme of S. marcescens plays an important role in mutation avoidance by allowing the
      mismatch repair enzymes to discriminate between the parental and newly synthesized strands
      during correction of replication errors.
AU  - Ostendorf T
AU  - Cherepanov P
AU  - deVries J
AU  - Wachernagel W
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1999 181: 3880-3885.

PMID- 6298065
VI  - 20
DP  - 1982
TI  - Ethidium-bromide-inhibited restriction endonucleases cleave one strand of circular DNA.
PG  - 121-125
AB  - We analyzed the effect of ethidium bromide (EtBr) on the cleavage of closed
      circular pBR322 DNA molecules by six restriction enzymes which make staggered
      or flush cuts (EcoRI, HindIII, BglI, PstI, HincII, PvuII).  EtBr concentrations
      and reaction temperatures were determined at which DNA molecules with
      single-strand breaks were the major reaction product of digestion by all the
      enzymes.  However, the amounts of intermediates which could be isolated
      differed for various enzymes.  The results extend previous studies, showing
      that sequential cleavage of the DNA strands probably is a general property of
      restriction endonucleases.
AU  - Osterlund M
AU  - Luthman H
AU  - Nilsson SV
AU  - Magnusson G
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1982 20: 121-125.

PMID- 3167042
VI  - 27
DP  - 1988
TI  - 5-Fluorocytosine in DNA is a mechanism-based inhibitor of HhaI methylase.
PG  - 5204-5210
AB  - 5-Fluorodeoxycytidine (FdCyd) was incorporated into a synthetic DNA polymer
      containing the GCGC recognition sequence of HhaI methylase to give a polymer
      with about 80% FdCyd.  In the absence of AdoMet, poly(FdC-dG) bound
      competitively with respect to poly(dG-dC) (Ki=3nM).  In the presence of AdoMet,
      the analogue caused a time-dependent, first-order (k=0.05 min-1) inactivation
      of the enzyme.  There is an ordered mechanism of binding in which enzyme first
      binds to poly(FdC-dG), then binds to AdoMet, and subsequently forms stable,
      inactive complexes.  The complexes did not dissociate over the course of 3 days
      and were stable to heat (95C) in the prsence of 1% SDS.  Gel filtration of a
      complex formed with HhaI methylase, poly(FdC-dG), and [methyl-3H]AdoMet gave a
      peak of radioactivity eluting near the void volume.  Digestion of the DNA in
      the complex resulted in a reduction of the molecular weight to the size of the
      methylase, and the radioactivity in this peak was shown to be associated with
      protein.  These data indicate that the complexes contain covalently bound HhaI
      methylase, poly(FdC-dG), and methyl groups and that 5-fluorodeoxycytidine is a
      mechanism-based inactivator of the methylase.  By analogy with other
      pyrimidine-modifying enzymes and recent studies on the mechanism of HhaI
      methylase (Wu & Santi, 1987), these results suggest that an enzyme nucleophile
      attacks FdCyd residues at C-6, activating the 5-position for one-carbon
      transfer.  Subsequent transfer of the methyl group of AdoMet to the activated
      FdCyd forms a stable complex in which the enzyme is covalently bound to the
      6-position of FdCyd in the polymer and a methyl group is attached to C-5.  The
      effect of 5-fluorodeoxycytidine on the inhibition of DNA-cytosine
      methyltransferases is thus due to irreversible, covalent inactivation.
AU  - Osterman DG
AU  - DePillis GD
AU  - Wu JC
AU  - Matsuda A
AU  - Santi DV
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1988 27: 5204-5210.

PMID- 24948393
VI  - 15
DP  - 2014
TI  - Genome sequencing of two Neorhizobium galegae strains reveals a noeT gene responsible for the unusual acetylation of the nodulation factors.
PG  - 500
AB  - BACKGROUND: The species Neorhizobium galegae comprises two symbiovars that induce
      nodules on Galega plants. Strains of both symbiovars, orientalis and officinalis,
      induce nodules on the same plant species, but fix nitrogen only in their own host
      species. The mechanism behind this strict host specificity is not yet known. In
      this study, genome sequences of representatives of the two symbiovars were
      produced, providing new material for studying properties of N. galegae, with a
      special interest in genomic differences that may play a role in host specificity.
      RESULTS: The genome sequences confirmed that the two representative strains are
      much alike at a whole-genome level. Analysis of orthologous genes showed that N.
      galegae has a higher number of orthologs shared with Rhizobium than with
      Agrobacterium. The symbiosis plasmid of strain HAMBI 1141 was shown to transfer
      by conjugation under optimal conditions. In addition, both sequenced strains have
      an acetyltransferase gene which was shown to modify the Nod factor on the residue
      adjacent to the non-reducing-terminal residue. The working hypothesis that this
      gene is of major importance in directing host specificity of N. galegae could
      not, however, be confirmed. CONCLUSIONS: Strains of N. galegae have many genes
      differentiating them from strains of Agrobacterium, Rhizobium and Sinorhizobium.
      However, the mechanism behind their ecological difference is not evident.
      Although the final determinant for the strict host specificity of N. galegae
      remains to be identified, the gene responsible for the species-specific
      acetylation of the Nod factors was identified in this study. We propose the name
      noeT for this gene to reflect its role in symbiosis.
AU  - Osterman J
AU  - Marsh J
AU  - Laine P
AU  - Zeng Z
AU  - Alatalo E
AU  - Sullivan JT
AU  - Young JP
AU  - Thomas-Oates J
AU  - Paulin L
AU  - Lindstrom K
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2014 15: 500.

PMID- 6313628
VI  - 156
DP  - 1983
TI  - Molecular cloning with bifunctional plasmid vectors in Bacillus subtilis:  Isolation of a spontaneous mutant of Bacillus subtilis with enhanced transformability for Escherichia coli-propagated chimeric plasmid DNA.
PG  - 934-936
AB  - Hybrid plasmid DNA cloned in Escherichia coli undergoes deletions when returned
      to competent Bacillus subtilis, even in defined restriction and modification
      mutants of strain 168.  We have isolated a mutant of B. subtilis MI112 which is
      stably transformed at high frequency by chimeric plasmid DNA propagated in E.
      coli.
AU  - Ostroff GR
AU  - Pene JJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1983 156: 934-936.

PMID- 6319968
VI  - 193
DP  - 1984
TI  - Molecular cloning with bifunctional plasmid vectors in Bacillus subtilis.  II.  Transfer of sequences propagated in Escherichia coli to B. subtilis.
PG  - 306-311
AB  - Recombinant plasmid DNA cloned in E. coli via the bifunctional vector pDH5060
      suffered deletions when returned to B. subtilis.  However, DNA preparations of
      identical chimeras containing homologous or heterologous sequences stably
      transformed B. subtilis at high efficiency when isolated from B. subtilis.  The
      vector pDH5060, however, was not affected and could be stably shuttled between
      E. coli and B. subtilis at high frequency.  These problems affected the
      transfer of clone pools and individual chimeras, irrespective of the
      restriction or recombination phenotype of B. subtilis recipients.  Deleted
      chimeras lost at least one end of cloned inserts, and in most cases, flanking
      plasmid sequences.  Single plasmid forms (intact or deleted) were isolated from
      several hundred individual Cmr-transformants.  This suggests that events
      leading to deletion of chimeric plasmid DNA occur during transformation by
      restriction of unmodified insert sequences propagated in the intermediate host,
      E. coli.  This conclusion is discussed with regard to the mechanism of plasmid
      transformation in B. subtilis.
AU  - Ostroff GR
AU  - Pene JJ
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1984 193: 306-311.

PMID- 26430024
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Bacillus licheniformis S127, Isolated from a Sheep Udder Clinical Infection.
PG  - e00971-15
AB  - Bacillus licheniformis is a Gram-positive biofilm- and endospore-forming bacterium, which
      contaminates dairy products and can be pathogenic to humans. The draft genome sequencing for
      B. licheniformis strain S127 is reported here, providing genetic data relevant to the ability
      of this strain to sustain its survival in the dairy industry.
AU  - Ostrov I
AU  - Sela N
AU  - Freed M
AU  - Khateb N
AU  - Kott-Gutkowski M
AU  - Inbar D
AU  - Shemesh M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00971-15.

PMID- 1937043
VI  - 106
DP  - 1991
TI  - Combinatorial mutagenesis of three major groove-contacting residues of EcoRI: single and double amino acid replacements retaining methyltransferase-sensitive activities.
PG  - 7-12
AB  - A library of mutant ecoRIR genes encoding EcoRI restriction endonuclease was
      generated using trinucleotide blocks and a combination of recombinant DNA
      procedures, including primer extension and the polymerase chain reaction.
      Codons corresponding to three amino acids (E144, R145 and R200), previously
      implicated in the specific, recognition of the DNA substrate, were
      combinatorially mutated so as to generate a library that potentially contains
      all 8000 possible single, double and triple aa replacements, in a balanced
      distribution.  Inspection of the phenotypes of Escherichia coli colonies
      bearing the mutant genes showed that several of them retained activities that
      were deleterious to the cells but were still protected by the EcoRI
      methyltransferase.  These included new enzyme variants, including
      non-conservative single (Thr or Val for Glu144) and double (Val for Glu144 and
      Thr for Arg145) replacements.
AU  - Osuna J
AU  - Flores H
AU  - Soberon X
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1991 106: 7-12.

PMID- 9127487
VI  - 25
DP  - 1997
TI  - Purification of (His)6EcoRV [recombinant restriction endonuclease EcoRV fused to a (His)6 affinity domain] by metal-chelate affinity chromatography.
PG  - 109-115
AB  - The chromatographic purification of (His)6EcoRV, a fusion protein consisting of a
      hexahistidine affinity domain and restriction endonuclease EcoRV produced from recombinant
      Escherichia coli, led to high product concentrations (>-1 mg/ml) in the preparative mode.
      Increasing the amount of applied crude cell homogenate caused competition with host-specific
      proteins, leading to a decrease of recovery and purity of the fusion protein.  Reduction of
      host-specific proteins was achieved by pre-adsorption on to a DEAE anion-exchange sorbent.
      This, in combination with 0.5-1 M NaCl in the adsorption buffer, assured a purity >95% and a
      total protein recovery of ~34% in the preparative mode.  Contamination of the product with
      about 2 mol of Ni(II)/mol of (His)6EcoRV was found due to metal-ion transfer to the N-terminal
      high affinity binding site at (His)6.  Tris(carboxymethyl)ethylenediamine (TED)-Sepharose was
      employed as an Ni(II) adsorber.  One passage of Ni(II)-contaminated protein solutions through
      the TED-Sepharose column resulted in a decrease in the Ni(II) content in the (His)6EcoRV
      fractions below the detection limit (~0.02 mg/l) of the atomic-adsorption spectrophotometer.
AU  - Oswald T
AU  - Hornbostel G
AU  - Rinas U
AU  - Anspach FB
PT  - Journal Article
TA  - Biotechnol. Appl. Biochem.
JT  - Biotechnol. Appl. Biochem.
SO  - Biotechnol. Appl. Biochem. 1997 25: 109-115.

PMID- 8660518
VI  - 236
DP  - 1996
TI  - Chloramphenicol resistance interferes with purification of histidine-tagged fusion proteins from recombinant Escherichia coli.
PG  - 357-358
AB  - The production of oligohistidine-tagged fusion proteins has become a widespread technique in
      order to facilitate recombinant protein purification by using immobilized metal ion affinity
      chromatography (IMAC).  In many cases a one-step purification procedure is sufficient to
      obtain the protein of interest as 95% pure.  However, several host-specific proteins have been
      identified which show a high affinity to the IMAC materials and are copurified with the
      oligohistidine-tagged fusion protien.  Here we describe impaired purification of (His)6-tagged
      fusion proteins by IMAC from chloramphenicol-resistant Escherichia coli cells.
AU  - Oswald T
AU  - Rinas U
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 1996 236: 357-358.

PMID- 7765822
VI  - 42
DP  - 1994
TI  - Comparison of N-terminal affinity fusion domains: effect on expression level and product heterogeneity of recombinant restriction endonuclease EcoRV.
PG  - 73-77
AB  - The influence of different N-terminal affinity fusion domains on the product heterogeneity of
      recombinant proteins expressed in Escherichia coli was investigated. N-Terminal extended forms
      of the restriction endonuclease EcoRV with either glutathione-S-transferase [GST], histidine
      hexapeptide [(His)6], or a combination of GST and (His)6 [GST-(His)6] were compared to native
      EcoRV with respect to expression level, susceptibility to inclusion body formation and protein
      fragmentation. Fingerprinting of product heterogeneity was done by using two-dimensional (2-D)
      non-equilibrium pH-gradient electrophoresis with subsequent immunoblotting. Fusion proteins
      containing GST were poorly expressed compared to native EcoRV. In addition, GST fusion
      proteins were highly susceptible to in vivo aggregation and fragmentation and displayed more
      heterogeneity on 2-D immunoblots. However, the sole presence of oligohistidine at the
      N-terminus of EcoRV proved to be advantageous. Fragmentation of (His)6-EcoRV was not observed
      and 2-D immunoblots did not show heterogeneous forms of the recombinant protein. In addition,
      fusion of the histidine-hexapeptide to the N-terminus of native EcoRV increased the expression
      level of the recombinant protein twofold compared to native EcoRV. Inclusion body formation of
      the (His)6-EcoRV fusion protein was intensive when cells were grown at 37oC but not at 30oC.
      The advantage of oligohistidine fusion to EcoRV was finally demonstrated by purifying soluble
      (His)6-EcoRV in a single-step procedure from crude cell lysates using immobilized metal
      chelate affinity chromatography.
AU  - Oswald T
AU  - Wende W
AU  - Pingoud A
AU  - Rinas U
PT  - Journal Article
TA  - Appl. Microbiol. Biotechnol.
JT  - Appl. Microbiol. Biotechnol.
SO  - Appl. Microbiol. Biotechnol. 1994 42: 73-77.

PMID- 19834512
VI  - 10
DP  - 2009
TI  - Structural basis for recognition of H3K4 methylation status by the DNA methyltransferase 3A ATRX-DNMT3-DNMT3L domain.
PG  - 1235-1241
AB  - DNMT3 proteins are de novo DNA methyltransferases that are responsible for the establishment
      of DNA methylation patterns in mammalian genomes. Here,
      we have determined the crystal structures of the ATRX-DNMT3-DNMT3L (ADD)
      domain of DNMT3A in an unliganded form and in a complex with the
      amino-terminal tail of histone H3. Combined with the results of
      biochemical analysis, the complex structure indicates that DNMT3A
      recognizes the unmethylated state of lysine 4 in histone H3. This finding
      indicates that the recruitment of DNMT3A onto chromatin, and thereby de
      novo DNA methylation, is mediated by recognition of the histone
      modification state by its ADD domain. Furthermore, our biochemical and
      nuclear magnetic resonance data show mutually exclusive binding of the ADD
      domain of DNMT3A and the chromodomain of heterochromatin protein 1alpha to
      the H3 tail. These results indicate that de novo DNA methylation by DNMT3A
      requires the alteration of chromatin structure.
AU  - Otani J
AU  - Nankumo T
AU  - Arita K
AU  - Inamoto S
AU  - Ariyoshi M
AU  - Shirakawa M
PT  - Journal Article
TA  - EMBO Rep.
JT  - EMBO Rep.
SO  - EMBO Rep. 2009 10: 1235-1241.

PMID- 26679583
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Pedobacter sp. Strain Hv1, an Isolate from Medicinal Leech Mucosal Castings.
PG  - e01469-15
AB  - The Pedobacter sp. Hv1 strain was isolated from the medicinal leech, Hirudo verbana, mucosal
      castings. These mucosal sheds have been demonstrated to play a
      role in horizontal symbiont transmission. Here, we report the draft 4.9 Mbp
      genome sequence of Pedobacter sp. strain Hv1.
AU  - Ott BM
AU  - Beka L
AU  - Graf J
AU  - Rio RV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01469-15.

PMID- Not included in PubMed...
VI  - 24
DP  - 1985
TI  - 31P NMR spectral analysis of the dodecamer d(CGCGAATTCGCG).
PG  - 2530-2535
AB  - The resonances in the 31P NMR spectrum of the dodecamer d(CGCGAATTCGCG) have
      been assigned by use of regiospecific labeling with oxygen-17.  At 19C the
      resonsances of 9 of the 11 dinucleoside phosphates are resolved.  Most
      noticeably, different chemical shifts are observed for the phosphates of d(GpC)
      at positions 2 and 10 as well as for d(CpG) at positions 1,3,9, and 11,
      indicating that the position in an oligonucleotide influences the chemical
      shift.  For the central d(GAATTC) portion of this dodecamer, a close
      relationship between the chemical shift of the phosphate groups and their
      position in the sequence of the oligonucleotide exists, in that the more
      central the phosphate residue is the more the signal appears at higher field.
      This finding parallels that found for the octamer d(GGAATTCC) [Connolly, B.A. &
      Eckstein, F. (1984) Biochemistry 23,5523-5527].  The signals of the phosphate
      residues at positions 3 and 9, however, are found at lower field strength than
      expected from their position in the sequence, indicating a break in
      conformation at these two locations.  A discontinuity of structure is also
      observed at these positions in the X-ray structure of this dodecamer
      [Dickerson, R.F., & Drew, H.R. (1981) J. Mol. Biol. 149, 761-786] as shown by
      the anomalous twist angles between the third and fourth as well as the ninth
      and tenth base pairs.  The dependence of the chemical shift on temperature
      indicates different mobilities for each of the 11 phosphate groups.  There
      seems to be no fraying at the ends but conformational changes particularly at
      the central A-T base pairs at the center of the molecule, consistent with the
      data obtained by H NMR spectroscopy [Patel, D.J., Kozlowski, S.A., Marky, L.A.,
      Broka, C., Rice, J.A., Itakura, K., & Breslauer, K.J. (1982) Biochemistry 21,
      428-436].
AU  - Ott J
AU  - Eckstein F
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1985 24: 2530-2535.

PMID- 19357771
VI  - 4
DP  - 2009
TI  - dndDB: a database focused on phosphorothioation of the DNA backbone.
PG  - e5132
AB  - BACKGROUND: The Dnd DNA degradation phenotype was first observed during electrophoresis of
      genomic DNA from Streptomyces lividans more than 20
      years ago. It was subsequently shown to be governed by the five-gene dnd
      cluster. Similar gene clusters have now been found to be widespread among
      many other distantly related bacteria. Recently the dnd cluster was shown
      to mediate the incorporation of sulphur into the DNA backbone via a
      sequence-selective, stereo-specific phosphorothioate modification in
      Escherichia coli B7A. Intriguingly, to date all identified dnd clusters
      lie within mobile genetic elements, the vast majority in laterally
      transferred genomic islands. METHODOLOGY: We organized available data from
      experimental and bioinformatics analyses about the DNA phosphorothioation
      phenomenon and associated documentation as a dndDB database. It contains
      the following detailed information: (i) Dnd phenotype; (ii) dnd gene
      clusters; (iii) genomic islands harbouring dnd genes; (iv) Dnd proteins
      and conserved domains. As of 25 December 2008, dndDB contained data
      corresponding to 24 bacterial species exhibiting the Dnd phenotype
      reported in the scientific literature. In addition, via in silico
      analysis, dndDB identified 26 syntenic dnd clusters from 25 species of
      Eubacteria and Archaea, 25 dnd-bearing genomic islands and one dnd plasmid
      containing 114 dnd genes. A further 397 other genes coding for proteins
      with varying levels of similarity to Dnd proteins were also included in
      dndDB. A broad range of similarity search, sequence alignment and
      phylogenetic tools are readily accessible to allow for to individualized
      directions of research focused on dnd genes. CONCLUSION: dndDB can
      facilitate efficient investigation of a wide range of aspects relating to
      dnd DNA modification and other island-encoded functions in host organisms.
      dndDB version 1.0 is freely available at http://mml.sjtu.edu.cn/dndDB/.
AU  - Ou HY
AU  - He X
AU  - Shao Y
AU  - Tai C
AU  - Rajakumar K
AU  - Deng Z
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2009 4: e5132.

PMID- 8127646
VI  - 22
DP  - 1994
TI  - The restriction enzyme BanI is inhibited by dcm-methylation of the GGCGCm5C site.
PG  - 108
AB  - We constructed a synthetic tRNAlys,3 gene that was cloned into pUC9. A BanI site was
      introduced at the 3' end to allow run-off transcription by T7 RNA polymerase. Surprisingly,
      we were unable to digest this BanI site, while three BanI sites in the pUC9 plasmid were
      efficiently cleaved (Figure 1, lane 7). Similar results were obtained upon prolonged
      incubation at either 37 degrees C or 50 degrees C which is the optimal temperature for BanI
      (results not shown). Since BanI recognizes different sequences (G/GPyPuCC), this could be due
      to site-preference. However, the BanI site in the tRNA gene was identical to one of the pUC9
      sites (GGCGCC). Inspection of the downstream sequences indicated the presence of an
      overlapping dcm-methylation site (GGCGCCAGG). Because the plasmid was grown in a dcm+ host
      (DH5), this will result in C5-methylation of the final C of the BanI site (GGCGCm5C). Next, we
      grew pUC-tRNAlys3 in a dcm-host (GM48), which resulted in complete digestion of the plasmid
      (lane 3). These results indicate that the BanI enzyme is not active on GGCGCm5C sites.
AU  - Oude Essink BB
AU  - Berkhout B
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1994 22: 108.

PMID- 29495512
VI  - 9
DP  - 2018
TI  - Characterizing the DNA Methyltransferases of Haloferax volcanii via Bioinformatics, Gene Deletion, and SMRT Sequencing.
PG  - E129
AB  - DNA methyltransferases (MTases), which catalyze the methylation of adenine and cytosine bases
      in DNA, can occur in bacteria and archaea alongside cognate
      restriction endonucleases (REases) in restriction-modification (RM) systems or
      independently as orphan MTases. Although DNA methylation and MTases have been
      well-characterized in bacteria, research into archaeal MTases has been limited. A
      previous study examined the genomic DNA methylation patterns (methylome) of the
      halophilic archaeon Haloferax volcanii, a model archaeal system which can be
      easily manipulated in laboratory settings, via single-molecule real-time (SMRT)
      sequencing and deletion of a putative MTase gene (HVO_A0006). In this follow-up
      study, we deleted other putative MTase genes in H. volcanii and sequenced the
      methylomes of the resulting deletion mutants via SMRT sequencing to characterize
      the genes responsible for DNA methylation. The results indicate that deletion of
      putative RM genes HVO_0794, HVO_A0006, and HVO_A0237 in a single strain abolished
      methylation of the sole cytosine motif in the genome (C(m4)TAG). Amino acid
      alignments demonstrated that HVO_0794 shares homology with characterized cytosine
      CTAG MTases in other organisms, indicating that this MTase is responsible for
      C(m4)TAG methylation in H. volcanii. The CTAG motif has high density at only one
      of the origins of replication, and there is no relative increase in CTAG motif
      frequency in the genome of H. volcanii, indicating that CTAG methylation might
      not have effectively taken over the role of regulating DNA replication and
      mismatch repair in the organism as previously predicted. Deletion of the putative
      Type I RM operon rmeRMS (HVO_2269-2271) resulted in abolished methylation of the
      adenine motif in the genome (GCA(m6)BN(6)VTGC). Alignments of the MTase
      (HVO_2270) and site specificity subunit (HVO_2271) demonstrate homology with
      other characterized Type I MTases and site specificity subunits, indicating that
      the rmeRMS operon is responsible for adenine methylation in H. volcanii. Together
      with HVO_0794, these genes appear to be responsible for all detected methylation
      in H. volcanii, even though other putative MTases (HVO_C0040, HVO_A0079) share
      homology with characterized MTases in other organisms. We also report the
      construction of a multi-RM deletion mutant (DeltaRM), with multiple RM genes
      deleted and with no methylation detected via SMRT sequencing, which we anticipate
      will be useful for future studies on DNA methylation in H. volcanii.
AU  - Ouellette M
AU  - Gogarten JP
AU  - Lajoie J
AU  - Makkay AM
AU  - Papke RT
PT  - Journal Article
TA  - Genes (Basel)
JT  - Genes (Basel)
SO  - Genes (Basel) 2018 9: E129.

PMID- 25904898
VI  - 6
DP  - 2015
TI  - Genome-wide DNA methylation analysis of Haloferax volcanii H26 and identification of DNA methyltransferase related PD-(D/E)XK nuclease family protein HVO_A0006.
PG  - 251
AB  - Restriction-modification (RM) systems have evolved to protect the cell from invading DNAs and
      are composed of two enzymes: a DNA methyltransferase and a
      restriction endonuclease. Although RM systems are present in both archaeal and
      bacterial genomes, DNA methylation in archaea has not been well defined. In order
      to characterize the function of RM systems in archaeal species, we have made use
      of the model haloarchaeon Haloferax volcanii. A genomic DNA methylation analysis
      of H. volcanii strain H26 was performed using PacBio single molecule real-time
      (SMRT) sequencing. This analysis was also performed on a strain of H. volcanii in
      which an annotated DNA methyltransferase gene HVO_A0006 was deleted from the
      genome. Sequence analysis of H26 revealed two motifs which are modified in the
      genome: C(m4)TAG and GCA(m6)BN6VTGC. Analysis of the DeltaHVO_A0006 strain
      indicated that it exhibited reduced adenine methylation compared to the parental
      strain and altered the detected adenine motif. However, protein domain
      architecture analysis and amino acid alignments revealed that HVO_A0006 is
      homologous only to the N-terminal endonuclease region of Type IIG RM proteins and
      contains a PD-(D/E)XK nuclease motif, suggesting that HVO_A0006 is a PD-(D/E)XK
      nuclease family protein. Further bioinformatic analysis of the HVO_A0006 gene
      demonstrated that the gene is rare among the Halobacteria. It is surrounded by
      two transposition genes suggesting that HVO_A0006 is a fragment of a Type IIG RM
      gene, which has likely been acquired through gene transfer, and affects
      restriction-modification activity by interacting with another RM system
      component(s). Here, we present the first genome-wide characterization of DNA
      methylation in an archaeal species and examine the function of a DNA
      methyltransferase related gene HVO_A0006.
AU  - Ouellette M
AU  - Jackson L
AU  - Chimileski S
AU  - Papke RT
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2015 6: 251.

PMID- 28057747
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Akkermansia glycaniphila Strain PytT, a Mucin-Degrading Specialist of the Reticulated Python Gut.
PG  - e01098-16
AB  - Akkermansia glycaniphila is a novel Akkermansia species that was isolated from the intestine
      of the reticulated python and shares the capacity to degrade mucin
      with the human strain Akkermansia muciniphila MucT Here, we report the complete
      genome sequence of strain PytT of 3,074,121 bp. The genomic analysis reveals
      genes for mucin degradation and aerobic respiration.
AU  - Ouwerkerk JP
AU  - Koehorst JJ
AU  - Schaap PJ
AU  - Ritari J
AU  - Paulin L
AU  - Belzer C
AU  - de Vos WM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01098-16.

PMID- 11195593
VI  - 26
DP  - 2000
TI  - The oligomerization of phage T4 DNA-(adenine-N-6)-methyltransferase and its effect on the catalytic characteristics of the enzyme.
PG  - 940-943
AB  - The structural and catalytic properties of the phage T4 DNA-(adenine-N-6)-methyltransferase
      (EC 2.1;1.72) were studied at
      different enzyme-substrate concentration ratios by chemical
      cross-linking of the protein subunits and by measuring the presteady
      state kinetics of the reactions. Various structural states of the
      methyltransferase were correlated with its catalytic activity, and it
      was shown that the oligomeric forms of the enzyme are catalytically
      active but are characterized by the reaction parameters different from
      those of the monomer.
AU  - Ovechkina LG
AU  - Zinoviev VV
AU  - Gorbunov YA
AU  - Malygin EG
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 2000 26: 940-943.

PMID- 29437102
VI  - 6
DP  - 2018
TI  - Complete Nucleotide Sequence of an Escherichia coli Sequence Type 410 Strain Carrying blaNDM-5 on an IncF Multidrug Resistance Plasmid and blaOXA-181 on an  IncX3 Plasmid.
PG  - e01542-17
AB  - Using Nanopore sequencing, we describe here the circular genome of an Escherichia coli
      sequence type 410 (ST410) strain with five closed plasmids. A large 111-kb
      incompatibility group F (IncF) plasmid harbored blaNDM-5 and 16 other resistance
      genes. A 51-kb IncX3 plasmid carried QnrS1 and blaOXA-181E. coli isolates with
      both blaNDM-5 and blaOXA-181 carbapenemases are rare.
AU  - Overballe-Petersen S
AU  - Roer L
AU  - Ng K
AU  - Hansen F
AU  - Justesen US
AU  - Andersen LP
AU  - Stegger M
AU  - Hammerum AM
AU  - Hasman H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01542-17.

PMID- 24356826
VI  - 1
DP  - 2013
TI  - Draft genome sequences for oil-degrading bacterial strains from beach sands impacted by the deepwater horizon oil spill.
PG  - e01015-13
AB  - We report the draft genome sequences of 10 proteobacterial strains isolated from  beach sands
      contaminated with crude oil discharged from the Deepwater Horizon
      spill, which were cultivated under aerobic and anaerobic conditions with crude
      oil as the sole carbon source. All strains contain multiple putative genes
      belonging to hydrocarbon degradation pathways.
AU  - Overholt WA
AU  - Green SJ
AU  - Marks KP
AU  - Venkatraman R
AU  - Prakash O
AU  - Kostka JE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01015-13.

PMID- 
VI  - 22
DP  - 1998
TI  - The construction of a mammalian transfection vector for expression of cytosine-5 specific DNA methyltransferase gene M.MspI in cultured cells.
PG  - 161-170
AB  - The expression vectors are designed for expression and purification of normal or recombinant
      genes of interest.  There is a wide variety of stable and transferable selectable mammalian
      expression vectors.  The vector pCDM8 and its derivatives, pcDNAI/Ampicillin are widely used
      for cloning and analyzing of genes in higher eukaryotic cells.  The vectors pRC/CMV, pcDNA3
      and pRC/RSV are designed for high-level expression of recombinant genes in mammalian cells.
      In the present study, we have been able to transfect and express the monospecific bacterial
      (Moraxella sp.) cytosine-5 DNA methyltransferase M.MspI gene in cultured cells within a newly
      constructed mammalian transfection vector.  We have constructed a very efficient, stable or
      transferable eukaryotic expression vector analogous to the well-known expression system in COS
      cells.  A bacterial cytosine-5 MTase gene with a vertebrate nuclear targeting signal SV40 VP1
      and marker enzyme glutathione-S-transferase genes were transferred into the eukaryotic shuttle
      vector pcDNA3 using a PCR based method.  This novel plasmid which contains a strong
      cytomegalovirus and T7 promoters and the SV40 origin of replication for autonomous replication
      in mammalian cells was called pOZT4.  Human kidney epithelial 293 and CHO cells were
      transfected with pOZT4 which was encoding the fusion gene and it was established that the
      genomic DNA of both cells were methylated at the CCCG sites by the active enzyme.
AU  - Ozdemir O
PT  - Journal Article
TA  - Turkish J. Biol.
JT  - Turkish J. Biol.
SO  - Turkish J. Biol. 1998 22: 161-170.

PMID- 
VI  - 22
DP  - 1998
TI  - In vivo DNA methylation of Escherichia coli DH5a and top10F' strains by bacterial cytosine-5 methyltransferase M.MspI.
PG  - 143-151
AB  - At the chromatin level, methylated CpG dinucleotides are R.MspI resistant compared with
      nonmethylated counterparts.  The DNA of two E. coli strains was analyzed following
      transformation with bacterial cytosine-5-methyltransferase gene M.MspI in the mammalian
      transfection vector pcDNA3.  Expression of the M.MspI was tested by R.MspI digestion.  The
      results suggest that the DNA of both strains was fully methylated at the CCGG sequences, by
      the active enzyme under the control of T7 and cytomegalovirus promoters.  Methylated DNA
      cannot be digested and it exhibits higher fragment sizes in 1% agarose gel in contrast to the
      untransformed cell DNAs in vivo.
AU  - Ozdemir O
AU  - Hornby D
PT  - Journal Article
TA  - Turkish J. Biol.
JT  - Turkish J. Biol.
SO  - Turkish J. Biol. 1998 22: 143-151.

PMID- 23045505
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of the Pseudomonas aeruginosa Bloodstream Isolate PABL056.
PG  - 5999
AB  - Pseudomonas aeruginosa is an important cause of disease in hospitalized and immunocompromised
      patients. The genome of P. aeruginosa is among the largest of
      bacteria pathogenic to humans. We present the draft genome sequence of P.
      aeruginosa strain PABL056, a human bloodstream isolate with the largest genome
      yet reported in P. aeruginosa.
AU  - Ozer EA
AU  - Allen JP
AU  - Hauser AR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5999.

PMID- 25212612
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Acinetobacter baumannii Strain ABBL099, a Multidrug-Resistant Clinical Outbreak Isolate with a Novel Multilocus Sequence  Type.
PG  - e00738-14
AB  - Acinetobacter baumannii is associated with hospital-acquired infections and can cause
      persistent outbreaks. Here we report the draft genome sequence of ABBL099,
      a multidrug-resistant clinical isolate of A. baumannii belonging to a novel
      sequence type and representative of clonal isolates cultured from patients at one
      institution over a 4-year time period.
AU  - Ozer EA
AU  - Fitzpatrick MA
AU  - Hauser AR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00738-14.

PMID- 28935729
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Clostridioides difficile Epidemic Strain DH/NAP11/106/ST-42, Isolated from Stool from a Pediatric Patient with Diarrhea.
PG  - e00923-17
AB  - We report here the complete genome sequence of Clostridioides difficile strain
      DH/NAP11/106/ST-42, which is now the most common strain causing C. difficile
      infection among U.S. adults. This strain was isolated from the stool from a
      hospitalized pediatric patient with frequent relapses of C. difficile infection.
AU  - Ozer EA
AU  - Hauser AR
AU  - Gerding DN
AU  - Espinosa RO
AU  - Hecht DW
AU  - Kociolek LK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00923-17.

PMID- 27231362
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a Multidrug-Resistant Klebsiella quasipneumoniae subsp.  similipneumoniae Isolate from a Clinical Source.
PG  - e00422-16
AB  - We report here the draft genome sequence of a multidrug-resistant clinical isolate of
      Klebsiella quasipneumoniae subsp. similipneumoniae, KP_Z4175. This
      strain, isolated as part of a hospital infection-control screening program, is
      resistant to multiple beta-lactam antibiotics, aminoglycosides, and
      trimethoprim-sulfamethoxazole.
AU  - Ozer EA
AU  - Morris AR
AU  - Krapp F
AU  - Henry CS
AU  - Tyo KE
AU  - Lathem WW
AU  - Hauser AR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00422-16.

PMID- 16900141
VI  - 24
DP  - 2006
TI  - Specificity by design - The specificity of a homing endonuclease has been altered using computational modeling of the protein-DNA interface.
PG  - 954-955
AB  - Endonucleases that cleave DNA with high specificity have been exploited in biotechnology for
      gene cloning and for nuclease-induced recombination.  As methods are developed that can
      retarget such proteins to recognize any endogenous DNA site of interest, they should become
      powerful tools that facilitate new approaches in gene therapy and genome editing.  In this
      context, a recent Nature paper by David Baker and colleagues marks an important milestone.
      The work builds on Barry Stoddard's long-standing interest in the study of homing
      endonucleases and on recent studies from the Baker laboratory in which a computational model
      of the protein-DNA interface was tested and optimized.  Using this model, Baker and colleagues
      have now designed a variant of the I-MsoI homing endonuclease that binds and cleaves DNA at a
      new site.  Their experiment had a relatively modest goal -- only one base pair was changed in
      each recognition half-site -- but it nonetheless represents a critical conceptual and
      methodological advance for the field.
AU  - Pabo CO
PT  - Journal Article
TA  - Nat. Biotechnol.
JT  - Nat. Biotechnol.
SO  - Nat. Biotechnol. 2006 24: 954-955.

PMID- 26586891
VI  - 3
DP  - 2015
TI  - Draft Genome of Thermanaerothrix daxensis GNS-1, a Thermophilic Facultative Anaerobe from the Chloroflexi Class Anaerolineae.
PG  - e01354-15
AB  - We present the draft genome of Thermanaerothrix daxensis GNS-1, a thermophilic member of the
      Chloroflexi phylum. This organism was initially characterized as a
      nonmotile, strictly anaerobic fermenter; however, genome analysis demonstrates
      that it encodes genes for a flagellum and multiple pathways for aerobic and
      anaerobic respiration.
AU  - Pace LA
AU  - Hemp J
AU  - Ward LM
AU  - Fischer WW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01354-15.

PMID- 23788540
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Rhodococcus rhodnii Strain LMG5362, a Symbiont of Rhodnius prolixus (Hemiptera, Reduviidae, Triatominae), the Principle Vector of  Trypanosoma cruzi.
PG  - e00329-13
AB  - We report the 4,385,577-bp high-quality draft assembly of the bacterial symbiont  Rhodococcus
      rhodnii strain LMG5362, isolated from the gut of Rhodnius prolixus
      (Hemiptera, Reduviidae, Triatominae), the principle vector of the protozoan
      Trypanosoma cruzi, the etiological agent of Chagas disease. This sequence might
      provide useful information for subsequent studies of the symbiotic relationship
      between Rd. prolixus and Rc. rhodnii, while also providing a starting point for
      the development of biotechnological applications for the control of Rd. prolixus.
AU  - Pachebat JA
AU  - van Keulen G
AU  - Whitten MM
AU  - Girdwood S
AU  - Del Sol R
AU  - Dyson PJ
AU  - Facey PD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00329-13.

PMID- 22514549
VI  - 3
DP  - 2012
TI  - A Role for Sigma Factor sigma(E) in Corynebacterium pseudotuberculosis Resistance to Nitric Oxide/Peroxide Stress.
PG  - 126
AB  - Pathogenic intracellular bacteria can respond to antimicrobial mechanisms of the
      host cell through transient activation of stress-responsive genes by alternative
      sigma (sigma) factors of the RNA polymerase. We evaluated the contribution of the
      extracytoplasmic function sigma factor sigma(E) for Corynebacterium
      pseudotuberculosis resistance to stress conditions resembling those found
      intracellularly during infection. A sigE-null mutant strain (DeltasigE) of this
      bacterium was more susceptible in vitro to acidic pH, cell surface stressors, and
      biologically relevant concentrations of nitric oxide (NO). The same mutant strain
      was unable to persist in C57BL/6 mice but remained infective in mice lacking
      inducible nitric oxide synthase (iNOS), confirming the significance of sigma(E)
      for resistance to nitric oxide/peroxide stress in vivo. High-throughput proteomic
      analysis identified NO-responsive extracellular proteins of C. pseudotuberculosis
      and demonstrated the participation of sigma(E) in composition of this bacterium's
      exoproteome.
AU  - Pacheco LG
AU  - Castro TL
AU  - Carvalho RD
AU  - Moraes PM
AU  - Dorella FA
AU  - Carvalho NB
AU  - Slade SE
AU  - Scrivens JH
AU  - Feelisch M
AU  - Meyer R
AU  - Miyoshi A
AU  - Oliveira SC
AU  - Dowson CG
AU  - Azevedo V
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2012 3: 126.

PMID- 29299109
VI  - 12
DP  - 2017
TI  - The draft genome of Brucella abortus strain Ba col-B012, isolated from a dairy farm in Narino, Colombia, bring new insights into the epidemiology of biovar 4  strains.
PG  - 89
AB  - 
AU  - Pacheco-Montealegre M
AU  - Patino RE
AU  - Torres L
AU  - Jimenez S
AU  - Rodriguez JL
AU  - Caro-Quintero A
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 89.

PMID- 6091684
VI  - 9
DP  - 1983
TI  - Site-specific endonuclease BmeI from Bacillus Megaterium 216.
PG  - 127-129
AB  - A site-specific endonuclease BmeI has been isolated from Bacillus megaterium
      216 by gel filtration on ultragel AcA-44 with a subsequent chromatography on
      heparin-sepharose 6B.  On the double-stranded DNA the endonuclease recognizes
      the pentanucleotide sequence 5' - GG (A) CC - 3' 3' - CC (T) GG - 5' and
      hydrolyzes it in the points shown by arrows.  At gel filtration the
      endonuclease is eluted in the volume corresponding to a molecular mass of
      60,000.
AU  - Pachkunov DM
AU  - Kramarov BM
AU  - Dobritsa AP
AU  - Matvienko NI
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1983 9: 127-129.

PMID- 19900415
VI  - 391
DP  - 2010
TI  - Biomolecular response of oxanine in DNA strands to T4 polynucleotide kinase, T4 DNA ligase, and restriction enzymes.
PG  - 118-122
AB  - Oxanine (Oxa) generated from guanine (Gua) by NO- or HNO2-induced nitrosative oxidation, has
      been thought to cause mutagenic problems in
      cellular systems. In this study, the response of Oxa to different
      enzymatic functions was explored to understand how similarly it can
      participate in biomolecular reactions compared to the natural base,
      Gua. The phosphorylation efficiency of the T4 polynucleotide kinase was
      highest when Oxa was located on the 5'-end of single stranded DNAs
      compared to when other nucleobases were in this position. The order of
      phosphorylation efficiency was as follows, Oxa > Gua > adenine (Ade)
      similar to thymine (Thy) > cylosine (Cyt) Base-pairing of Oxa and Cyt
      (Oxa Cyt) between the ligation fragment and template was found to
      influence the ligation performance of the T4 DNA ligase to a lesser
      degree compared to Gua:Cyt. In addition, EcoRl and BglII showed higher
      cleavage activities on DNA substrates containing Oxa:Cyt than those
      containing Gua:Cyt, while BamHl, HindIII and EcoRV showed lower
      cleavage activity; however, this decrease in activity was relatively
      small.
AU  - Pack SP
AU  - Doi A
AU  - Choi YS
AU  - Kodaki T
AU  - Makino K
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 2010 391: 118-122.

PMID- 11239007
VI  - 29
DP  - 2001
TI  - OliI, a unique restriction endonuclease that recognizes the discontinuous sequence 5'-CACNN/NNGTG-3'.
PG  - e30
AB  - A new type II restriction endonuclease designated OliI has been partially purified from the
      halophilic bacterium Oceanospirillum linum 4-5D. OliI recognizes the interrupted
      hexanucleotide palindrome 5'-CACNNNNGTG-3' and cleaves it in the center generating
      blunt-ended DNA fragments.
AU  - Padegimiene E
AU  - Maneliene Z
AU  - Petrusyte M
AU  - Janulaitis A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2001 29: e30.

PMID- 2832390
VI  - 170
DP  - 1988
TI  - Restriction analysis and quantitative estimation of methylated bases of filamentous and unicellular cyanobacterial DNAs.
PG  - 1934-1939
AB  - The DNAs of strains of three cyanobacterial genera (Anabaena, Plectonema, and Synechococcus)
      were found to be partially or fully resistant to many restriction endonucleases. This could be
      due to the absence of specific sequences or to modifications, rendering given sequences
      resistant to cleavage. The latter explanation is substantiated by the content of
      N6-methyladenine and 5-methylcytosine in these genomes, which is high in comparison with that
      in other bacterial genomes. dcm- and dam-like methylases are present in the three strains
      (based on the restriction patterns obtained with the appropriate isoschizomeric enzymes).
      Their contribution to the overall content of methyladenine and methylcytosine in the genomes
      was calculated. Partial methylation of GATC sequences was observed in Anabaena DNA. In
      addition, the GATC methylation patterns might not have been random in the three cyanobacterial
      DNA preparations, as revealed by the appearance of discrete fragments (possibly of plasmid
      origin) withstanding cleavage by DpnI (which requires the presence of methyladenine in the
      GATC sequence).
AU  - Padhy RN
AU  - Hottat FG
AU  - Coene MM
AU  - Hoet PP
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1988 170: 1934-1939.

PMID- 26494682
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Aeromonas caviae Strain 429865 INP, Isolated from a Mexican Patient.
PG  - e01240-15
AB  - Aeromonas caviae is an emerging human pathogen. Here, we report the draft genome  sequence of
      Aeromonas caviae strain 429865 INP which shows the presence of various putative
      virulence-related genes.
AU  - Padilla JC
AU  - Bustos P
AU  - Castro-Escarpulli G
AU  - Sanchez-Varela A
AU  - Palma-Martinez I
AU  - Arzate-Barbosa P
AU  - Garcia-Perez CA
AU  - Lopez-Lopez MJ
AU  - Gonzalez V
AU  - Guo X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01240-15.

PMID- 25197488
VI  - 9
DP  - 2014
TI  - Genome sequence and description of Corynebacterium ihumii sp. nov.
PG  - 1128-1143
AB  - Corynebacterium ihumii strain GD7(T) sp. nov. is proposed as the type strain of a new species,
      which belongs to the family Corynebacteriaceae of the class
      Actinobacteria. This strain was isolated from the fecal flora of a 62 year-old
      male patient, as a part of the culturomics study. Corynebacterium ihumii is a
      Gram positive, facultativly anaerobic, nonsporulating bacillus. Here, we describe
      the features of this organism, together with the high quality draft genome
      sequence, annotation and the comparison with other member of the genus
      Corynebacteria. C. ihumii genome is 2,232,265 bp long (one chromosome but no
      plasmid) containing 2,125 protein-coding and 53 RNA genes, including 4 rRNA
      genes. The whole-genome shotgun sequence of Corynebacterium ihumii strain GD7(T)
      sp. nov has been deposited in EMBL under accession number GCA_000403725.
AU  - Padmanabhan R
AU  - Dubourg G
AU  - Lagier JC
AU  - Couderc C
AU  - Michelle C
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 1128-1143.

PMID- 25197489
VI  - 9
DP  - 2014
TI  - Non-contiguous finished genome sequence and description of Collinsella massiliensis sp. nov.
PG  - 1144-1158
AB  - Collinsella massiliensis strain GD3(T) is the type strain of Collinsella massiliensis sp.
      nov., a new species within the genus Collinsella. This strain,
      whose genome is described here, was isolated from the fecal flora of a
      53-year-old French Caucasoid woman who had been admitted to intensive care unit
      for Guillain-Barre syndrome. Collinsella massiliensis is a Gram-positive,
      obligate anaerobic, non motile and non sporulating bacillus. Here, we describe
      the features of this organism, together with the complete genome sequence and
      annotation. The genome is 2,319,586 bp long (1 chromosome, no plasmid), exhibits
      a G+C content of 65.8% and contains 2,003 protein-coding and 54 RNA genes,
      including 1 rRNA operon.
AU  - Padmanabhan R
AU  - Dubourg G
AU  - Nguyen TT
AU  - Couderc C
AU  - Rossi-Tamisier M
AU  - Caputo A
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 1144-1158.

PMID- 24501636
VI  - 8
DP  - 2013
TI  - Non-contiguous finished genome sequence and description of Megasphaera massiliensis sp. nov.
PG  - 525-538
AB  - Megasphaera massiliensis strain NP3(T) sp. nov. is the type strain of Megasphaera massiliensis
      sp. nov., a new species within the genus Megasphaera. This strain,
      whose genome is described here, was isolated from the fecal flora of an
      HIV-infected patient. M. massiliensis is a Gram-negative, obligate anaerobic
      coccobacillus. Here we describe the features of this organism, together with the
      complete genome sequence and annotation. The 2,661,757 bp long genome (1
      chromosome but no plasmid) contains 2,577 protein-coding and 61 RNA genes,
      including 5 rRNA genes.
AU  - Padmanabhan R
AU  - Lagier JC
AU  - Dangui NP
AU  - Michelle C
AU  - Couderc C
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 525-538.

PMID- 25301642
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Necropsobacter rosorum Strain P709T.
PG  - e00913-14
AB  - Necropsobacter is a recently described genus that contains a single species, N. rosorum, and
      belongs to the family Pasteurellaceae. Here, we present the draft
      genome of N. rosorum strain P709(T), which is the first genome sequence from this
      species.
AU  - Padmanabhan R
AU  - Robert C
AU  - Fenollar F
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00913-14.

PMID- 21475592
VI  - 4
DP  - 2011
TI  - Complete genome sequence of Desulfobulbus propionicus type strain (1pr3).
PG  - 100-110
AB  - Desulfobulbus propionicus Widdel 1981 is the type species of the genus Desulfobulbus, which
      belongs to the family Desulfobulbaceae. The species is of
      interest because of its great implication in the sulfur cycle in aquatic
      sediments, its large substrate spectrum and a broad versatility in using various
      fermentation pathways. The species was the first example of a pure culture known
      to disproportionate elemental sulfur to sulfate and sulfide. This is the first
      completed genome sequence of a member of the genus Desulfobulbus and the third
      published genome sequence from a member of the family Desulfobulbaceae. The
      3,851,869 bp long genome with its 3,351 protein-coding and 57 RNA genes is a part
      of the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Pagani I et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 4: 100-110.

PMID- 21677852
VI  - 4
DP  - 2011
TI  - Complete genome sequence of Marivirga tractuosa type strain (H-43).
PG  - 154-162
AB  - Marivirga tractuosa (Lewin 1969) Nedashkovskaya et al. 2010 is the type species of the genus
      Marivirga, which belongs to the family Flammeovirgaceae. Members of
      this genus are of interest because of their gliding motility. The species is of
      interest because representative strains show resistance to several antibiotics,
      including gentamicin, kanamycin, neomycin, polymixin and streptomycin. This is
      the first complete genome sequence of a member of the family Flammeovirgaceae.
      Here we describe the features of this organism, together with the complete genome
      sequence and annotation. The 4,511,574 bp long chromosome and the 4,916 bp
      plasmid with their 3,808 protein-coding and 49 RNA genes are a part of the
      Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Pagani I et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 4: 154-162.

PMID- 10938631
VI  - 62
DP  - 2000
TI  - Individual- and population-based diversity in restriction-modification systems.
PG  - 759-774
AB  - Restriction-modification (RM) systems are cognate gene complexes that code for an endonuclease
      and a methylase. They are often thought to have developed in bacteria as protection against
      invading genetic material, e.g., phage DNA. The high diversity of RM systems, as observed in
      nature, is often ascribed to the coevolution of RM systems (which 'invent' novel types) and
      phages. However, the extent to which phages are insensitive to RM systems casts doubts on the
      effectiveness of RM systems as protection against infection and thereby on the reason for the
      diversity of RM systems. We present an eco-evolutionary model in order to study the evolution
      of the diversity of RM systems. The model predicts that in general diversity of RM systems is
      high. More importantly, the diversity of the RM systems is expressed either at the individual
      level or at the population level. In the first case all individuals carry RM systems of all
      sequence specificities, whereas in the second case they carry only one RM system or no RM
      systems at all. Nevertheless, in the second case the same number of sequence specificities are
      present in the population.
AU  - Pagie L
AU  - Hogeweg P
PT  - Journal Article
TA  - Bull. Math. Biol.
JT  - Bull. Math. Biol.
SO  - Bull. Math. Biol. 2000 62: 759-774.

PMID- 23045493
VI  - 194
DP  - 2012
TI  - Genome Sequence of Legionella tunisiensis Strain LegMT, a New Legionella Species  Isolated from Hypersaline Lake Water.
PG  - 5978
AB  - Legionella tunisiensis is a gammaproteobacterium from the class Legionellaceae, growing in
      amoebae. We sequenced the genome from strain LegM(T). It is composed
      of 3,508,121 bp and contains 4,747 protein-coding genes and 38 RNA genes,
      including 3 rRNA genes.
AU  - Pagnier I
AU  - Boughalmi M
AU  - Croce O
AU  - Robert C
AU  - Raoult D
AU  - La Scola B
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5978.

PMID- 24501638
VI  - 8
DP  - 2013
TI  - Non-contiguous finished genome sequence and description of Anaerococcus pacaensis sp. nov., a new species of anaerobic bacterium.
PG  - 548-560
AB  - Anaerococcus pacaensis strain 9403502(T), is the type strain of Anaerococcus pacaensis sp.
      nov., a new species within a new genus Anaerococcus. This strain,
      whose genome is described here, was isolated from a blood sample. A. pacaensis
      strain 9403502(T) is an obligate anaerobic Gram-positive coccus. Here we describe
      the features of this organism, together with the complete genome sequence and
      annotation. The 2.36 Mbp long genome exhibits a G+C content of 35.05% and
      contains 2,186 protein-coding and 72 RNA genes, including 3 rRNA genes.
AU  - Pagnier I
AU  - Croce O
AU  - Robert C
AU  - Raoult D
AU  - La Scola B
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 548-560.

PMID- 24503989
VI  - 2
DP  - 2014
TI  - Genome Sequence of Legionella anisa, Isolated from a Respiratory Sample, Using an Amoebal Coculture Procedure.
PG  - e00031-14
AB  - Legionella anisa is a gammaproteobacterium from the class Legionellaceae, which is responsible
      for nosocomial pneumonia. We sequenced the genome from the L.
      anisa strain Linanisette, which was recovered from a clinical sample using an
      amoebal coculture procedure but not with standard culture methods.
AU  - Pagnier I
AU  - Croce O
AU  - Robert C
AU  - Raoult D
AU  - La Scola B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00031-14.

PMID- 25197492
VI  - 9
DP  - 2014
TI  - Non-contiguous finished genome sequence and description of Anaerococcus provenciensis sp. nov.
PG  - 1198-1210
AB  - Anaerococcus provenciensis strain 9402080(T) sp. nov. is the type strain of A. provenciensis
      sp. nov., a new species within the genus Anaerococcus. This strain
      was isolated from a cervical abscess sample. A. provenciensis is a Gram-positive
      anaerobic cocci. Here, we describe the features of this organism, together with
      the complete genome sequence and annotation. The 2.26 Mbp long genome contains
      2099 protein-coding and 57 RNA genes including 8 rRNA genes and exhibits a G+C
      content of 33.48%.
AU  - Pagnier I
AU  - Croce O
AU  - Robert C
AU  - Raoult D
AU  - La Scola B
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 1198-1210.

PMID- 25197455
VI  - 9
DP  - 2014
TI  - Non-contiguous finished genome sequence and description of Fenollaria massiliensis gen. nov., sp. nov., a new genus of anaerobic bacterium.
PG  - 704-717
AB  - Fenollaria massiliensis strain 9401234(T), is the type strain of Fenollaria massiliensis gen.
      nov., sp. nov., a new species within a new genus Fenollaria.
      This strain, whose genome is described here, was isolated from an osteoarticular
      sample. F. massiliensis strain 9401234(T) is an obligate anaerobic Gram-negative
      bacillus. Here we describe the features of this organism, together with the
      complete genome sequence and annotation. The 1.71 Mbp long genome exhibits a G+C
      content of 34.46% and contains 1,667 protein-coding and 30 RNA genes, including 3
      rRNA genes.
AU  - Pagnier I
AU  - Croce O
AU  - Robert C
AU  - Raoult D
AU  - La Scola B
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 704-717.

PMID- 23012280
VI  - 194
DP  - 2012
TI  - Genome Sequence of Reyranella massiliensis, a Bacterium Associated with Amoebae.
PG  - 5698
AB  - Reyranella massiliensis is an Alphaproteobacterium member of the class Rhodospirillaceae,
      growing in amoebae. We sequenced the genome of type strain
      521(T). It is composed of a 5,792,218-bp chromosome and encodes 5,675
      protein-coding genes and 53 RNA genes, including 3 rRNA genes.
AU  - Pagnier I
AU  - Croce O
AU  - Robert C
AU  - Raoult D
AU  - La Scola B
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5698.

PMID- 23209256
VI  - 194
DP  - 2012
TI  - Genome Sequence of Afipia birgiae, a Rare Bacterium Associated with Amoebae.
PG  - 7018
AB  - Afipia birgiae is an alphaproteobacterium from the family Bradyrhizobiaceae, growing in
      amoebae, and a potential human pathogen. We sequenced the genome of
      type strain 34632(T). It is composed of 5,325,467 bp and contains 5,160
      protein-coding genes and 53 RNA genes, including 3 rRNA genes.
AU  - Pagnier I
AU  - Croce O
AU  - Robert C
AU  - Raoult D
AU  - La Scola B
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 7018.

PMID- 25323728
VI  - 2
DP  - 2014
TI  - Genome Sequence of Legionella massiliensis, Isolated from a Cooling Tower Water Sample.
PG  - e01068-14
AB  - We present the draft genome sequence of Legionella massiliensis strain LegA(T), recovered from
      a cooling tower water sample, using an amoebal coculture
      procedure. The strain described here is composed of 4,387,007 bp, with a G+C
      content of 41.19%, and its genome has 3,767 protein-coding genes and 60 predicted
      RNA genes.
AU  - Pagnier I
AU  - Croce O
AU  - Robert C
AU  - Raoult D
AU  - La Scola B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01068-14.

PMID- 6099579
VI  - 8
DP  - 1984
TI  - Purification of EcoRI endonuclease on heparin sepharose-4B column chromatography.
PG  - 41-45
AB  - Restriction endonucleases play a very important role in genetic engineering and
      DNA mapping.  Among hundreds of restriction endonucleases, the EcoRI enzyme is
      the most useful and widely investigated enzyme.  After sonication and
      ultracentrifugation, crude extracts of E. coli RY 13 were purified by employing
      the polyethyleneimine precipitate, ammonium sulfate precipitate and heparin
      Sepharose-4B affinity column chromatography.  The EcoRI enzyme were purified at
      about 42 fold and the specific activity was about 100,000 U/mg of protein.  The
      whole purification procedure was finished within two days.  The recovery was
      about 42%.  The enzyme was sufficiently concentrated for direct specific DNA
      hydrolysis.
AU  - Pai S-H
AU  - Chuang J-Z
AU  - Kou M-C
AU  - Hsu T-T
PT  - Journal Article
TA  - Proc. Natl. Sci. Counc. Repub. China B
JT  - Proc. Natl. Sci. Counc. Repub. China B
SO  - Proc. Natl. Sci. Counc. Repub. China B 1984 8: 41-45.

PMID- 13941102
VI  - 19
DP  - 1963
TI  - Cooperative infection by host-modified lambda phage.
PG  - 565-572
AB  - Host-modified lambda which arises by phage growth in Escherichia coli strain C
      plates with an efficiency of 10-3 to 10-4 on E. coli strain K when infection is
      performed at a low multiplicity.  The occasional infection which results arises
      from the presence in K populations of rare cells in which lambda.C is capable
      of multiplying.  When several lambda.C phage particles infect a single K cell,
      a form of cooperative infection, analogous to multiplicity reactivation,
      occurs, such that at high multiplicities more than 10% of the infected cells
      yield progeny.  The latent period and burst size are normal when lambda.C
      infects strain K either singly or multiply.  In both cases all the progeny that
      are formed in a single cycle of growth are of the unrestricted or lambda.K
      type.  The occurrence of cooperative infection is explained by assuming that
      the restriction present in host modification is applied independently to
      genetic structures smaller than the entire phage chromosome.  Each susceptible
      site has a small chance of escaping restriction, and undamaged sites in
      separate phage chromosomes can complement each other to produce an infection.
      The quantitative dependence of the number of successful infections upon the
      multiplicity of infection suggests that approximately 10 independent phage
      sites are involved, each with approximately a 15% change of surviving.
AU  - Paigen K
AU  - Weinfeld H
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1963 19: 565-572.

PMID- 27795252
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Enterococcus faecalis Strain F165 Isolated from a Urinary Tract Infection.
PG  - e01084-16
AB  - We report here a draft genome sequence of Enterococcus faecalis strain F165 isolated from a
      urine specimen in South Brazil. The genome size was 3,049,734 bp,
      with a G+C content of 37.38%, and genes related to antimicrobial resistance and
      adherence were found in the strain. These findings are consistent with
      pathogenesis of E. faecalis species.
AU  - Paim TG
AU  - Pieta L
AU  - Prichula J
AU  - Sambrano GE
AU  - Soares R
AU  - Bello AD
AU  - Frazzon J
AU  - d'Azevedo PA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01084-16.

PMID- 27795253
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Brazilian Escherichia coli Uropathogenic Strain E2.
PG  - e01085-16
AB  - Escherichia coli is a common pathogen recovered from cystitis infections. In this report, we
      announce the draft genome sequence of strain E2 isolated from the
      urine specimen from a female patient in South Brazil. The genome assembly has
      5,081,209 bp, a G+C content of 50.57%, and virulence factors associated with both
      enteroaggregative and uropathogenic E. coli strains.
AU  - Paim TG
AU  - Pieta L
AU  - Prichula J
AU  - Sambrano GE
AU  - Soares R
AU  - Caierao J
AU  - Frazzon J
AU  - d'Azevedo PA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01085-16.

PMID- 26798099
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Two Salmonella enterica Serotype Infantis Strains Isolated from a Captive Western Lowland Gorilla (Gorilla gorilla gorilla) and a  Cohabitant Black and White Tegu (Tupinambis merianae) in Brazil.
PG  - e01590-15
AB  - The draft genome sequences of two Salmonella enterica serotype Infantis isolates  are reported
      here. One of the strains was isolated from a western lowland gorilla
      (Gorilla gorilla gorilla) with colitis. The second strain was isolated from a
      reptile that inhabited the same premises. Whole-genome sequencing demonstrated
      that these isolates were not clonal.
AU  - Paixao TA
AU  - Coura FM
AU  - Malta MC
AU  - Tinoco HP
AU  - Pessanha AT
AU  - Pereira FL
AU  - Leal CA
AU  - Heinemann MB
AU  - Figueiredo HC
AU  - Santos RL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01590-15.

PMID- 12079351
VI  - 319
DP  - 2002
TI  - Complete nucleotide sequence and likely recombinatorial origin of bacteriophage T3.
PG  - 1115-1132
AB  - We report the complete genome sequence (38,208 bp) of bacteriophage T3 and
      provide a bioinformatic comparative analysis with other completely
      sequenced members of the T7 group of phages. This comparison suggests that
      T3 has evolved from a recombinant between a T7-like coliphage and a
      yersiniophage. To assess this, recombination between T7 and the Yersinia
      enterocolitica serotype O:3 phage phiYeO3-12 was accomplished in vivo;
      coliphage progeny from this cross were selected that had many biological
      properties of T3. This represents the first experimentally observed
      recombination between lytic phages whose normal hosts are different
      bacterial genera.
AU  - Pajunen MI
AU  - Elizondo MR
AU  - Skurnik M
AU  - Kieleczawa J
AU  - Molineux IJ
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2002 319: 1115-1132.

PMID- 
VI  - 98
DP  - 2009
TI  - Study on recognization and cleavage characteristics of restriction enzyme Bci528I.
PG  - 50-51
AB  - We find that restriction enzyme Bci528I isolated Bacillus circulans 528 recognizes
      pallindromic hexanucleotide sequence.
AU  - Pak CM
AU  - Kim UY
AU  - Ra SR
PT  - Journal Article
TA  - Choson Minjujuui Inmin Konghwaguk Kwahagwon Tongbo
JT  - Choson Minjujuui Inmin Konghwaguk Kwahagwon Tongbo
SO  - Choson Minjujuui Inmin Konghwaguk Kwahagwon Tongbo 2009 98: 50-51.

PMID- 26324280
VI  - 59
DP  - 2015
TI  - Whole-Genome Sequencing Identifies Emergence of a Quinolone Resistance Mutation in a Case of Stenotrophomonas maltophilia Bacteremia.
PG  - 7117-7120
AB  - Whole-genome sequences for Stenotrophomonas maltophilia serial isolates from a bacteremic
      patient before and after development of levofloxacin resistance were
      assembled de novo and differed by one single-nucleotide variant in smeT, a
      repressor for multidrug efflux operon smeDEF. Along with sequenced isolates from
      five contemporaneous cases, they displayed considerable diversity compared
      against all published complete genomes. Whole-genome sequencing and complete
      assembly can conclusively identify resistance mechanisms emerging in S.
      maltophilia strains during clinical therapy.
AU  - Pak TR
AU  - Altman DR
AU  - Attie O
AU  - Sebra R
AU  - Hamula CL
AU  - Lewis M
AU  - Deikus G
AU  - Newman LC
AU  - Fang G
AU  - Hand J
AU  - Patel G
AU  - Wallach F
AU  - Schadt EE
AU  - Huprikar S
AU  - van Bakel H
AU  - Kasarskis A
AU  - Bashir A
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2015 59: 7117-7120.

PMID- 23833129
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Salinibacillus aidingensis Strain MSP4, an Obligate Halophilic Bacterium Isolated from a Salt Crystallizer of the Rann of Kutch,  India.
PG  - e00253-13
AB  - We report the 7.42-Mbp draft whole genome sequence of Salinibacillus aidingensis  strain MSP4,
      an obligate halophilic bacterium, isolated from a salt crystallizer
      of the Rann of Kutch in India. Analysis of the genome of this organism will lead
      to a better understanding of the genes and metabolic pathways involved in
      imparting osmotolerance.
AU  - Pal KK
AU  - Dey R
AU  - Sherathia D
AU  - Dalsania T
AU  - Savsani K
AU  - Patel I
AU  - Thomas M
AU  - Ghorai S
AU  - Vanpariya S
AU  - Rupapara R
AU  - Acharya N
AU  - Rawal P
AU  - Joshi P
AU  - Sukhadiya B
AU  - Mandaliya M
AU  - Saxena AK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00253-13.

PMID- 24371204
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of an Obligate and Moderately Halophilic Bacterium, Thalassobacillus devorans Strain MSP14, the First Draft Genome of the Genus  Thalassobacillus.
PG  - e01103-13
AB  - We report the 3.93-Mbp first draft genome sequence of a species of the genus Thalassobacillus,
      Thalassobacillus devorans strain MSP14, a moderate but obligate
      halophile, isolated from a salt crystallizer of the Little Rann of Kutch, India.
      Exploring the genome of this organism will facilitate understanding the
      mechanism(s) of its obligate halophilism.
AU  - Pal KK
AU  - Dey R
AU  - Sherathia D
AU  - Sukhadiya B
AU  - Dalsania T
AU  - Patel I
AU  - Savsani K
AU  - Thomas M
AU  - Vanpariya S
AU  - Mandaliya M
AU  - Rupapara R
AU  - Rawal P
AU  - Ghorai S
AU  - Bhayani S
AU  - Shah A
AU  - Saxena AK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01103-13.

PMID- 24407642
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of a Moderately Halophilic Bacillus megaterium Strain, MSP20.1, Isolated from a Saltern of the Little Rann of Kutch, India.
PG  - e01134-13
AB  - The 4.37-Mbp draft genome of a moderately halophilic Bacillus megaterium strain,  MSP20.1,
      isolated from a saltern of the Little Rann of Kutch, India, is reported
      here. To understand the mechanism(s) of moderate halophilism and to isolate the
      gene(s) involved in osmotolerance and adaptation, the genome of MSP20.1 was
      sequenced.
AU  - Pal KK
AU  - Dey R
AU  - Sherathia D
AU  - Vanpariya S
AU  - Patel I
AU  - Dalsania T
AU  - Savsani K
AU  - Sukhadiya B
AU  - Mandaliya M
AU  - Thomas M
AU  - Ghorai S
AU  - Rupapara R
AU  - Rawal P
AU  - Shah A
AU  - Bhayani S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01134-13.

PMID- 24136852
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Extremely Halophilic Bacillus sp. Strain SB49, Isolated from a Salt Crystallizer Pond of the Little Rann of Kutch, India.
PG  - e00869-13
AB  - Here we report the draft whole-genome sequence (3.72 Mbp) of Bacillus sp. strain  SB49, an
      extremely halophilic bacterium isolated from a salt crystallizer pond of
      the Little Rann of Kutch in India. Unraveling the genome of this organism will
      facilitate understanding and isolation of the genes involved in imparting extreme
      osmotolerance.
AU  - Pal KK
AU  - Dey R
AU  - Thomas M
AU  - Sherathia D
AU  - Dalsania T
AU  - Patel I
AU  - Savsani K
AU  - Ghorai S
AU  - Vanpariya S
AU  - Sukhadiya B
AU  - Mandaliya M
AU  - Rupapara R
AU  - Rawal P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00869-13.

PMID- 24115544
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Bacillus sp. Strain SB47, an Obligate Extreme Halophile  Isolated from a Salt Pan of the Little Rann of Kutch, India.
PG  - e00816-13
AB  - Here, we report the 4.46-Mbp draft genome sequence of Bacillus sp. strain SB47, an extreme
      halophile isolated from a salt pan of the Little Rann of Kutch, India.
      Exploring the genome of this organism will facilitate the understanding and
      isolation of the gene(s) involved in its extreme osmotolerance.
AU  - Pal KK
AU  - Dey R
AU  - Thomas M
AU  - Sherathia D
AU  - Dalsania T
AU  - Patel I
AU  - Savsani K
AU  - Ghorai S
AU  - Vanpariya S
AU  - Sukhadiya B
AU  - Mandaliya M
AU  - Rupapara R
AU  - Rawal P
AU  - Saxena AK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00816-13.

PMID- 25908145
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Paenibacillus sp. Strain IHBB 10380 Using PacBio Single-Molecule Real-Time Sequencing Technology.
PG  - e00356-15
AB  - The complete genome sequence of 5.77 Mb is reported for Paenibacillus sp. strain  IHBB 10380,
      isolated from the cold desert area of the northwestern Himalayas and
      exhibiting amylase and cellulase activities. The gene-coding clusters predicted
      the presence of genes for hydrolytic enzymes in the genome.
AU  - Pal M
AU  - Swarnkar MK
AU  - Thakur R
AU  - Kiran S
AU  - Chhibber S
AU  - Singh AK
AU  - Gulati A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00356-15.

PMID- 26564043
VI  - 3
DP  - 2015
TI  - Genome Sequence of Hydrocarbon-Degrading Cronobacter sp. Strain DJ34 Isolated from Crude Oil-Containing Sludge from the Duliajan Oil Fields, Assam, India.
PG  - e01321-15
AB  - We report here the 4,856,096-bp draft genome sequence of hydrocarbon-degrading Cronobacter sp.
      strain DJ34 isolated from crude oil-containing sludge from the
      Duliajan oil fields, India. DJ34 contains genes that mediate hydrocarbon
      degradation, metal resistance, and biosurfactant production. This is the first
      report of the genome sequence of Cronobacter sp. inhabiting an oil-contaminated
      environment.
AU  - Pal S
AU  - Das Banerjee T
AU  - Roy A
AU  - Sar P
AU  - Kazy SK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01321-15.

PMID- 28729282
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Actinomycessucciniciruminis Strain Am4T, Isolated from Cow Rumen Fluid.
PG  - e01587-16
AB  - Actinomyces succiniciruminis strain Am4T, isolated from cow rumen fluid, can metabolize a
      range of substrates including complex carbohydrates to organic
      acids. Here, we report a 3.33-Mbp draft genome of Actinomyces succiniciruminis.
AU  - Palakawong NaAS
AU  - Hornung B
AU  - Ravikumar VA
AU  - Plugge W
AU  - Plugge CM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01587-16.

PMID- 28209819
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Actinomyces glycerinitolerans Strain G10T, Isolated from Sheep Rumen Fluid.
PG  - e01589-16
AB  - Actinomyces glycerinitolerans strain G10T, which was isolated from sheep rumen fluid, can
      metabolize a range of substrates, including complex carbohydrates to
      organic acids (OAs). Here, we report a 3.69-Mbp draft genome of Actinomyces
      glycerinitolerans.
AU  - Palakawong NaAS
AU  - Strepis N
AU  - Pristas P
AU  - Plugge CM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01589-16.

PMID- 28360157
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Streptococcus caviae Strain Cavy grass 6T, Isolated from Domesticated Guinea Pig Fecal Samples.
PG  - e00080-17
AB  - Streptococcus caviae strain Cavy grass 6T, isolated from fecal samples of pet guinea pigs, can
      metabolize a range of plant mono- and disaccharides, as well as polymeric carbohydrates. Here,
      we report the draft genome sequence of this strain, which comprises 2.11 Mb.
AU  - Palakawong-Na-Ayudthaya S
AU  - Marshall IPG
AU  - Schreiber L
AU  - Plugge CM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00080-17.

PMID- 24501645
VI  - 9
DP  - 2013
TI  - Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701(T)) and emended description of the  genus Thermanaerovibrio.
PG  - 57-70
AB  - Thermanaerovibrio velox Zavarzina et al. 2000 is a member of the Synergistaceae,  a family in
      the phylum Synergistetes that is already well-characterized at the
      genome level. Members of this phylum were described as Gram-negative staining
      anaerobic bacteria with a rod/vibrioid cell shape and possessing an atypical
      outer cell envelope. They inhabit a large variety of anaerobic environments
      including soil, oil wells, wastewater treatment plants and animal
      gastrointestinal tracts. They are also found to be linked to sites of human
      diseases such as cysts, abscesses, and areas of periodontal disease. The
      moderately thermophilic and organotrophic T. velox shares most of its morphologic
      and physiologic features with the closely related species, T. acidaminovorans. In
      addition to Su883(T), the type strain of T. acidaminovorans, stain Z-9701(T) is
      the second type strain in the genus Thermanaerovibrio to have its genome sequence
      published. Here we describe the features of this organism, together with the
      non-contiguous genome sequence and annotation. The 1,880,838 bp long chromosome
      (non-contiguous finished sequence) with its 1,751 protein-coding and 59 RNA genes
      is a part of the G enomic E ncyclopedia of Bacteria and Archaea project.
AU  - Palaniappan K et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 9: 57-70.

PMID- 29674544
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Marinobacter flavimaris LMG 23834(T), Which Is Potentially Useful in Bioremediation.
PG  - e00273-18
AB  - The complete genome sequence of the halophilic strain Marinobacter flavimaris LMG 23834(T) is
      presented here. The genomic information of this type strain will be
      useful for taxonomic purposes and for its potential use in bioremediation
      studies.
AU  - Palau M
AU  - Boujida N
AU  - Manresa A
AU  - Minana-Galbis D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00273-18.

PMID- 2822529
VI  - 6
DP  - 1987
TI  - Inhibition of restriction endonuclease cleavage due to site-specific chemical modification of the B-Z junction in supercoiled DNA.
PG  - 327-341
AB  - Structural distortions on the boundary between right-handed B and left-handed Z
      DNA segments in plasmid pRW751 (a derivative of pBR322 containing (dC-dG)13 and
      (dC-dG)16 segments) were studied by means of chemical probes.  Samples of
      supercoiled DNA were treated with the respective chemical probe, linearized
      with EcoRI and inhibition of BamHI (whose recognition sequence GGATCC lies on
      the boundary between the (dC-dG)n segments and the pBR322 nucleotide sequence)
      cleavage was tested.  Treatment with osmium tetroxide in the presence of
      pyridine or 2,2'-bipyridine, respectively, resulted in a strong inhibition of
      the BamHI cleavage at both restriction sites, provided the (dC-dG)n segments
      were in the left-handed form.  In the presence of 2,2'-bipyridine submillimolar
      concentrations of OsO4 (at 26C) were sufficient to induce the inhibition of
      BamHI.  Chloroacetaldehyde was used as a probe reacting selectively with atoms
      involved in the Watson-Crick hydrogen bonding.  Similarly as in the case of
      osmium tetroxide treatment of pRW751 with this agent resulted in the inhibition
      of BamHI cleavage.  It was concluded that the B-Z junction regions in pRW751
      contain few solitary bases with disturbed hydrogen bonding or non-Watson-Crick
      base pairs.
AU  - Palecek E
AU  - Boublikova P
AU  - Galazka G
AU  - Klysik J
PT  - Journal Article
TA  - Gen. Physiol. Biophys.
JT  - Gen. Physiol. Biophys.
SO  - Gen. Physiol. Biophys. 1987 6: 327-341.

PMID- 12917641
VI  - 424
DP  - 2003
TI  - The genome of a motile marine Synechococcus.
PG  - 1037
AB  - Marine unicellular cyanobacteria are responsible for an estimated 20-40% of chlorophyll
      biomass and carbon fixation in the oceans. Here we have
      sequenced and analysed the 2.4-megabase genome of Synechococcus sp. strain
      WH8102, revealing some of the ways that these organisms have adapted to
      their largely oligotrophic environment. WH8102 uses organic nitrogen and
      phosphorus sources and more sodium-dependent transporters than a model
      freshwater cyanobacterium. Furthermore, it seems to have adopted
      strategies for conserving limited iron stores by using nickel and cobalt
      in some enzymes, has reduced its regulatory machinery (consistent with the
      fact that the open ocean constitutes a far more constant and buffered
      environment than fresh water), and has evolved a unique type of swimming
      motility. The genome of WH8102 seems to have been greatly influenced by
      horizontal gene transfer, partially through phages. The genetic material
      contributed by horizontal gene transfer includes genes involved in the
      modification of the cell surface and in swimming motility. On the basis of
      its genome, WH8102 is more of a generalist than two related marine
      cyanobacteria.
AU  - Palenik B
AU  - Brahamsha B
AU  - Larimer FW
AU  - Land M
AU  - Hauser L
AU  - Chain P
AU  - Lamerdin J
AU  - Regala W
AU  - Allen EE
AU  - McCarren J
AU  - Paulsen I
AU  - Dufresne A
AU  - Partensky F
AU  - Webb EA
AU  - Waterbury J
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2003 424: 1037.

PMID- 16938853
VI  - 103
DP  - 2006
TI  - Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment.
PG  - 13555-13559
AB  - Coastal aquatic environments are typically more highly productive and dynamic than open ocean
      ones. Despite these differences, cyanobacteria
      from the genus Synechococcus are important primary producers in both types
      of ecosystems. We have found that the genome of a coastal cyanobacterium,
      Synechococcus sp. strain CC9311, has significant differences from an open
      ocean strain, Synechococcus sp. strain WH8102, and these are consistent
      with the differences between their respective environments. CC9311 has a
      greater capacity to sense and respond to changes in its (coastal)
      environment. It has a much larger capacity to transport, store, use, or
      export metals, especially iron and copper. In contrast, phosphate
      acquisition seems less important, consistent with the higher concentration
      of phosphate in coastal environments. CC9311 is predicted to have
      differences in its outer membrane lipopolysaccharide, and this may be
      characteristic of the speciation of some cyanobacterial groups. In
      addition, the types of potentially horizontally transferred genes are
      markedly different between the coastal and open ocean genomes and suggest
      a more prominent role for phages in horizontal gene transfer in
      oligotrophic environments.
AU  - Palenik B
AU  - Ren Q
AU  - Dupont CL
AU  - Myers GS
AU  - Heidelberg JF
AU  - Badger JH
AU  - Madupu R
AU  - Nelson WC
AU  - Brinkac LM
AU  - Dodson RJ
AU  - Durkin AS
AU  - Daugherty SC
AU  - Sullivan SA
AU  - Khouri H
AU  - Mohamoud Y
AU  - Halpin R
AU  - Paulsen IT
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2006 103: 13555-13559.

PMID- 29225728
VI  - 12
DP  - 2017
TI  - The complete genome sequence of the rumen bacterium Butyrivibrio hungatei MB2003.
PG  - 72
AB  - Butyrivibrio hungatei MB2003 was isolated from the plant-adherent fraction of rumen contents
      from a pasture-grazed New Zealand dairy cow, and was selected for
      genome sequencing in order to examine its ability to degrade plant
      polysaccharides. The genome of MB2003 is 3.39 Mb and consists of four replicons;
      a chromosome, a secondary chromosome or chromid, a megaplasmid and a small
      plasmid. The genome has an average G + C content of 39.7%, and encodes 2983
      putative protein-coding genes. MB2003 is able to use a variety of monosaccharide
      substrates for growth, with acetate, butyrate and formate as the principal
      fermentation end-products, and the genes encoding these metabolic pathways have
      been identified. MB2003 is predicted to encode an extensive repertoire of CAZymes
      with 78 GHs, 7 CEs, 1 PL and 78 GTs. MB2003 is unable to grow on xylan or pectin,
      and its role in the rumen appears to be as a utilizer of monosaccharides,
      disaccharides and oligosaccharides made available by the degradative activities
      of other bacterial species.
AU  - Palevich N
AU  - Kelly WJ
AU  - Leahy SC
AU  - Altermann E
AU  - Rakonjac J
AU  - Attwood GT
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 72.

PMID- 29748406
VI  - 6
DP  - 2018
TI  - Draft Genome Sequencing of an Acinetobacter ursingii Isolate from Healthy Human Skin, Carrying Multidrug Resistance Genes.
PG  - e00394-18
AB  - In this paper, we report the data from whole-genome shotgun sequencing of an Acinetobacter
      ursingii isolate from healthy human skin of the forearm. The
      bacterial genome includes 3,473 genes and carries beta-lactamase resistance genes
      as well as resistance genes for several heavy metals.
AU  - Palkova L
AU  - Minarik G
AU  - Soltys K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00394-18.

PMID- 27469965
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Photorhabdus luminescens Strain DSPV002N Isolated from Santa Fe, Argentina.
PG  - e00744-16
AB  - Here, we report the draft genome sequence of Photorhabdus luminescens strain DSPV002N, which
      consists of 177 contig sequences accounting for 5,518,143 bp,
      with a G+C content of 42.3% and 4,701 predicted protein-coding genes (CDSs). From
      these, 27 CDSs exhibited significant similarity with insecticidal toxin proteins
      from Photorhabdus luminescens subsp. laumondii TT01.
AU  - Palma L
AU  - Del Valle EE
AU  - Frizzo L
AU  - Berry C
AU  - Caballero P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00744-16.

PMID- 24625875
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Bacillus thuringiensis Serovar Tolworthi Strain Na205-3, an Isolate Toxic for Helicoverpa armigera.
PG  - e00187-14
AB  - We report here the complete annotated 6,510,053-bp draft genome sequence of Bacillus
      thuringiensis serovar tolworthi strain Na205-3, which is toxic for
      Helicoverpa armigera. This strain potentially contains nine insecticidal toxin
      genes homologous to cry1Aa12, cry1Ab1, cry1Ab8, cry1Ba1, cry1Af1, cry1Ia10,
      vip1Bb1, vip2Ba2, and vip3Aa6.
AU  - Palma L
AU  - Munoz D
AU  - Murillo J
AU  - Caballero P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00187-14.

PMID- 8200522
VI  - 143
DP  - 1994
TI  - The dam and dcm strains of Escherichia coli--a review.
PG  - 1-12
AB  - The construction of a variety of strains deficient in the methylation of adenine and cytosine
      residues in DNA by the methyltransferases (MTases) Dam and Dcm has allowed the study of the
      role of these enzymes in the biology of Escherichia coli. Dam methylation has been shown to
      play a role in coordinating DNA replication initiation. DNA mismatch repair and the regulation
      of expression of some genes. The regulation of expression of dam has been found to be complex
      and influenced by five promoters. A role for Dcm methylation in the cell remains elusive and
      dcm- cells have no obvious phenotype, dam- and dcm- strains have a range of uses in molecular
      biology and bacterial genetics, including preparation of DNA for restriction by some
      restriction endonucleases, for transformation into other bacterial species, nucleotide
      sequencing and site-directed mutagenesis. A variety of assays are available for rapid
      detection of both the Dam and Dcm phenotypes. A number of restriction systems in E. coli have
      been described which recognise foreign DNA methylation, but ignore Dam and Dcm methylation.
      Here, we describe the most commonly used mutant alleles of dam and dcm and the characteristics
      of a variety of the strains that carry these genes. A description of several plasmids that
      carry dam gene constructs is also included.
AU  - Palmer BR
AU  - Marinus MG
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1994 143: 1-12.

PMID- 20207762
VI  - 192
DP  - 2010
TI  - High-quality draft genome sequences of 28 Enterococcus sp. isolates.
PG  - 2469-2470
AB  - The enterococci are low-GC Gram-positive bacteria that have emerged as leading causes of
      hospital-acquired infection. They are also commensals of
      the gastrointestinal tract of healthy humans and most other animals with
      gastrointestinal flora and are important for food fermentations. Here we
      report the availability of draft genome sequences for 28 enterococcal
      strains of diverse origin, including the species Enterococcus faecalis, E.
      faecium, E. casseliflavus, and E. gallinarum.
AU  - Palmer KL
AU  - Carniol K
AU  - Manson JM
AU  - Heiman D
AU  - Shea T
AU  - Young S
AU  - Zeng Q
AU  - Gevers D
AU  - Feldgarden M
AU  - Birren B
AU  - Gilmore MS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 2469-2470.

PMID- 26937267
VI  - 11
DP  - 2016
TI  - Draft genome sequences of Pantoea agglomerans and Pantoea vagans isolates associated with termites.
PG  - 23
AB  - The genus Pantoea incorporates many economically and clinically important species. The
      plant-associated species, Pantoea agglomerans and Pantoea vagans,
      are closely related and are often isolated from similar environments. Plasmids
      conferring certain metabolic capabilities are also shared amongst these two
      species. The genomes of two isolates obtained from fungus-growing termites in
      South Africa were sequenced, assembled and annotated. A high number of
      orthologous genes are conserved within and between these species. The difference
      in genome size between P. agglomerans MP2 (4,733,829 bp) and P. vagans MP7
      (4,598,703 bp) can largely be attributed to the differences in plasmid content.
      The genome sequences of these isolates may shed light on the common traits that
      enable P. agglomerans and P. vagans to co-occur in plant- and insect-associated
      niches.
AU  - Palmer M
AU  - de Maayer P
AU  - Poulsen M
AU  - Steenkamp ET
AU  - van Zyl E
AU  - Coutinho TA
AU  - Venter SN
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 23.

PMID- 23300246
VI  - 4
DP  - 2013
TI  - Broad Conditions Favor the Evolution of Phase-Variable Loci.
PG  - e00430-12
AB  - Simple sequence repeat (SSR) tracts produce stochastic on-off switching, or phase variation,
      in the expression of a panoply of
      surface molecules in many bacterial commensals and pathogens. A change
      to the number of repeats in a tract may alter the phase of the
      translational reading frame, which toggles the on-off state of the
      switch. Here, we construct an in silico SSR locus with mutational
      dynamics calibrated to those of the Haemophilus influenzae mod locus.
      We simulate its evolution in a regimen of two alternating environments,
      simultaneously varying the selection coefficient, s, and the epoch
      length, T. Some recent work in a simpler (two-locus) model suggested
      that stochastic switching in a regimen of two alternating environments
      may be evolutionarily favored only if the selection coefficients in the
      two environments are nearly equal ('symmetric') or selection is very
      strong. This finding was puzzling, as it greatly restricted the
      conditions under which stochastic switching might evolve. Instead, we
      find agreement with other recent theoretical work, observing selective
      utility for stochastic switching if the product sT is large enough for
      the favored state to nearly fix in both environments. Symmetry is
      required neither in s nor in sT. Because we simulate finite populations
      and use a detailed model of the SSR locus, we are also able to examine
      the impact of population size and of several SSR locus parameters. Our
      results indicate that conditions favoring evolution and maintenance of
      SSR loci in bacteria are quite broad.
      IMPORTANCE Bacteria experience frequent changes of environment
      during the infection cycle. One means to rapidly adapt is stochastic
      switching: a bacterial lineage will stochastically produce a variety of
      genotypes, so that some descendants will survive if the environment
      changes. Stochastic switching mediated by simple sequence repeat (SSR)
      loci is widespread among bacterial commensals and pathogens and
      influences critical interactions with host surfaces or immune
      effectors, thereby affecting host persistence, transmission, and
      virulence. Here, we use the most detailed in silico model of an SSR
      locus to date, with its phase variation calibrated to match the mod
      locus of Haemophilus influenzae. The type III restriction-modification
      system encoded by mod participates in the regulation of multiple other
      genes; thus, SSR-mediated phase variation of mod has far-reaching
      cis-regulatory effects. This coupling of phase-variable switching to
      complex phenotypic effects has been described as the 'phasevarion' and
      is central to understanding the infection cycle of bacterial commensals
      and pathogens.
AU  - Palmer ME
AU  - Lipsitch M
AU  - Moxon ER
AU  - Bayliss CD
PT  - Journal Article
TA  - MBio
JT  - MBio
SO  - MBio 2013 4: e00430-12.

PMID- 25593259
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Probiotic Strain Lactobacillus acidophilus ATCC 4356.
PG  - e01421-14
AB  - We present the 1,956,699-bp draft genome sequence of Lactobacillus acidophilus strain ATCC
      4356. Comparative genomic analysis revealed 99.96% similarity with L.
      acidophilus NCFM NC_006814.3 and 99.97% with La-14 NC_021181.2 genomes.
AU  - Palomino MM
AU  - Allievi MC
AU  - Fina MJ
AU  - Waehner PM
AU  - Prado AM
AU  - Sanchez RC
AU  - Ruzal SM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01421-14.

PMID- 29449405
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Lactobacillus helveticus ATCC 12046.
PG  - e01595-17
AB  - Lactobacillus helveticus is a lactic acid bacterium used traditionally in the dairy industry,
      especially in the manufacture of cheeses. We present here the
      2,141,841-bp draft genome sequence of L. helveticus strain ATCC 12046, a
      potential starter strain for improving cheese production.
AU  - Palomino MM
AU  - Burguener GF
AU  - Campos J
AU  - Allievi M
AU  - Fina-Martin J
AU  - Prado AM
AU  - Fernandez DoPDA
AU  - Ruzal SM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01595-17.

PMID- 27013050
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequence of Bacillus sp. SDLI1, Isolated from the Social Bee Scaptotrigona depilis.
PG  - e00174-16
AB  - We announce the complete genome sequence ofBacillussp. strain SDLI1, isolated from larval gut
      of the stingless beeScaptotrigona depilis The 4.13-Mb circular
      chromosome harbors biosynthetic gene clusters for the production of antimicrobial
      compounds.
AU  - Paludo CR
AU  - Ruzzini AC
AU  - Silva-Junior EA
AU  - Pishchany G
AU  - Currie CR
AU  - Nascimento FS
AU  - Kolter RG
AU  - Clardy J
AU  - Pupo MT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00174-16.

PMID- 26918090
VI  - 11
DP  - 2016
TI  - Draft genome sequence of Sphingomonas paucimobilis strain LCT-SP1 isolated from the Shenzhou X spacecraft of China.
PG  - 18
AB  - Sphingomonas paucimobilis strain LCT-SP1 is a glucose-nonfermenting Gram-negative,
      chemoheterotrophic, strictly aerobic bacterium. The major feature
      of strain LCT-SP1, isolated from the Chinese spacecraft Shenzhou X, together with
      the genome draft and annotation are described in this paper. The total size of
      strain LCT-SP1 is 4,302,226 bp with 3,864 protein-coding and 50 RNA genes. The
      information gained from its sequence is potentially relevant to the elucidation
      of microbially mediated corrosion of various materials.
AU  - Pan L
AU  - Zhou H
AU  - Li J
AU  - Huang B
AU  - Guo J
AU  - Zhang XL
AU  - Gao LC
AU  - Xu C
AU  - Liu CT
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 18.

PMID- 28619791
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Aeromonas hydrophila Strain BSK-10 (Serotype O97), Isolated from Carassius carassius with Motile Aeromonad Septicemia in China.
PG  - e00497-17
AB  - We report here a draft genome sequence of Aeromonas hydrophila strain BSK-10, belonging to
      serotype O97, isolated from crucian carp (Carassius carassius) with
      motile aeromonad septicemia in Zhejiang, China. The assembly resulted in 34
      scaffolds totaling approximately 4.97 Mb, with an average G+C content of 60.97%
      and 4,594 predicted coding genes.
AU  - Pan X
AU  - Lin L
AU  - Xu Y
AU  - Yuan X
AU  - Yao J
AU  - Yin W
AU  - Hao G
AU  - Shen J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00497-17.

PMID- Not carried by PubMed...
VI  - 36
DP  - 1991
TI  - A new Type II restriction endonuclease, BsaOI, from Bacillus stearothermophilus.
PG  - 1231-1232
AB  - A new Type II restriction endonuclease, BsaOI, has been isolated from the thermophile Bacillus
      stearothermophilus O-122. This enzyme cleaves pBR322 DNA at 7 sites, pUC19 DNA at 5 sites and
      PhiX174 DNA at one site.
AU  - Pan XS
AU  - Chen ZF
PT  - Journal Article
TA  - Chinese Sci. Bull.
JT  - Chinese Sci. Bull.
SO  - Chinese Sci. Bull. 1991 36: 1231-1232.

PMID- 26629309
VI  - 10
DP  - 2015
TI  - Complete genome sequence and characterization of the haloacid-degrading Burkholderia caribensis MBA4.
PG  - 114
AB  - Burkholderia caribensis MBA4 was isolated from soil for its capability to grow on haloacids.
      This bacterium has a genome size of 9,482,704 bp. Here we report the
      genome sequences and annotation, together with characteristics of the genome. The
      complete genome sequence consists of three replicons, comprising 9056
      protein-coding genes and 80 RNA genes. Genes responsible for dehalogenation and
      uptake of haloacids were arranged as an operon. While dehalogenation of
      haloacetate would produce glycolate, three glycolate operons were identified. Two
      of these operons contain an upstream glcC regulator gene. It is likely that the
      expression of one of these operons is responsive to haloacetate. Genes
      responsible for the metabolism of dehalogenation product of halopropionate were
      also identified.
AU  - Pan Y
AU  - Kong KF
AU  - Tsang JS
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 114.

PMID- 26823586
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of the Exopolysaccharide-Producing Burkholderia caribensis Type Strain MWAP64.
PG  - e01636-15
AB  - We report the complete genome sequence of Burkholderia caribensis MWAP64 (LMG 18531), which
      was isolated from soil for its proficiency in producing large
      amounts of exopolysaccharide that help form microaggregates in a vertisol. There
      are four replicons with a total size of 9,032,119 bp.
AU  - Pan Y
AU  - Kong KF
AU  - Tsang JS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01636-15.

PMID- 27491986
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Pseudoalteromonas tetraodonis Strain MQS005, a Bacterium with Potential Quorum-Sensing Regulation.
PG  - e00724-16
AB  - We present here the draft genome sequence of Pseudoalteromonas tetraodonis strain MQS005, a
      bacterium possessing potential quorum-sensing regulatory activity. This
      strain was isolated from water from the South China Sea, People's Republic of
      China. The assembly consists of 4,252,538 bp and contains 144 contigs, with a G+C
      content of 41.85%.
AU  - Pan Y
AU  - Wang Y
AU  - Yan X
AU  - Mazumder A
AU  - Liang Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00724-16.

PMID- 21478353
VI  - 193
DP  - 2011
TI  - Whole-genome sequences of four Mycobacterium bovis BCG vaccine strains.
PG  - 3152-3153
AB  - Bacille Calmette-Guerin (BCG) is the only vaccine available against tuberculosis (TB).
      Currently there are a number of BCG strains that are in
      use, which exhibit biochemical and genetic differences. We report the
      genome sequences of four BCG strains representing different lineages,
      which will help to design more effective TB vaccines.
AU  - Pan Y
AU  - Yang X
AU  - Duan J
AU  - Lu N
AU  - Leung AS
AU  - Tran V
AU  - Hu Y
AU  - Wu N
AU  - Liu D
AU  - Wang Z
AU  - Yu X
AU  - Chen C
AU  - Zhang Y
AU  - Wan K
AU  - Liu J
AU  - Zhu B
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3152-3153.

PMID- 21478350
VI  - 193
DP  - 2011
TI  - The genome sequence of spinosyns-producing bacterium Saccharopolyspora spinosa NRRL 18395.
PG  - 3150-3151
AB  - Saccharopolyspora spinosa is a Gram-positive bacterium that produces spinosad, a well-known
      biodegradable insecticide used for agricultural
      pests control and has an excellent environmental and mammalian
      toxicological profile. Here, we present the first draft genome sequence of
      the type strain Saccharopolyspora spinosa NRRL 18395, which consists of 22
      scaffolds.
AU  - Pan Y
AU  - Yang X
AU  - Li J
AU  - Zhang R
AU  - Hu Y
AU  - Zhou Y
AU  - Wang J
AU  - Zhu B
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3150-3151.

PMID- 25451047
VI  - 59
DP  - 2015
TI  - Identification of capsular types in carbapenem-resistant Klebsiella pneumoniae strains by wzc sequencing and implications in capsule depolymerase treatment.
PG  - 1038-1047
AB  - Klebsiella pneumoniae is an important human pathogen associated with a variety of
      diseases and the prevalence of multiple drug resistant K. pneumoniae (MDRKP) was
      rapidly increasing. Here we determined the capsular types of 85
      carbapenem-resistant K. pneumoniae (CRKP) by wzc sequencing and investigated the
      presence of carbapenemases and integrons among CRKP. Ten strains (12%) of the
      CRKP was positive for carbapenemase (IMP: 6/85, KPC: 3/85, and VIM: 1/85).
      Capsular type K64 accounted for 32 (38%) of CRKP, followed by K62 (13%), K24
      (8%), KN2 (7%) and K28 (6%). Sequence types (STs) were determined by multilocus
      sequence typing (MLST) and the results indicated that ST11 which accounted for
      47% (40/85) of these CRKP was the major ST. We further isolated a K64 specific
      capsule depolymerase (K64dep) which can enhance serum and neutrophil killing in
      vitro and increase survival rate in K64 K. pneumoniae inoculated mice. The
      toxicity study demonstrated that mice treated with K64dep showed normal
      biochemical parameters and no significant histopathological changes of liver,
      kidney and spleen, indicating enzyme treatment did not cause toxicity in mice.
      Therefore, the findings of capsular type clustering among CRKP and an effective
      treatment of capsule depolymerase for MDRKP infections are important for
      capsule-based vaccine development and therapy.
AU  - Pan YJ
AU  - Lin TL
AU  - Lin YT
AU  - Su PA
AU  - Chen CT
AU  - Hsieh PF
AU  - Hsu CR
AU  - Chen CC
AU  - Hsieh YC
AU  - Wang JT
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2015 59: 1038-1047.

PMID- 6098533
VI  - 31
DP  - 1984
TI  - Practical consequences of restriction site symmetry.
PG  - 291-294
AB  - Because of the palindromic character of most 6-bp restriction sites, filling-in
      and ligation of the protruding ends create symmetric sequences which include
      new 6-bp restriction sites.  The old site is, in most cases, lost.  After
      cleavage at the new palindromic site and removal of the protruding ends, a new
      center of symmetry is created which is often part of yet another 6-bp
      restriction site.  A compilation of potential and available sites as presented
      should prove useful in genetic engineering.
AU  - Panayotatos N
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1984 31: 291-294.

PMID- 28428296
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of Mycobacterium kansasii Strains Isolated from Rhesus  Macaques.
PG  - e00187-17
AB  - Mycobacterium kansasii is a nontuberculous mycobacterium. It causes opportunistic infections
      with pulmonary and extrapulmonary manifestations. We report here the
      complete genome sequences of two M. kansasii strains isolated from rhesus
      macaques. We performed genome comparisons with human and environmental isolates
      of M. kansasii to assess the genomic diversity of this species.
AU  - Panda A
AU  - Nagaraj S
AU  - Zhao X
AU  - Tettelin H
AU  - DeTolla LJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00187-17.

PMID- 27365341
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Halobacillus sp. Strain KGW1, a Moderately Halophilic and Alkaline Protease-Producing Bacterium Isolated from the Rhizospheric Region of Phragmites karka from Chilika Lake, Odisha, India.
PG  - e00361-16
AB  - Halobacillus sp. strain KGW1 is a moderately halophilic, rod shaped, Gram-positive, yellow
      pigmented, alkaline protease-producing bacterium isolated from a water sample from Chilika
      Lake, Odisha, India. Sequencing of bacterial DNA assembled a 3.68-Mb draft genome. The genome
      annotation analysis showed various gene clusters for tolerance to stress, such as elevated pH,
      salt concentration, and toxic metals.
AU  - Panda AN
AU  - Mishra SR
AU  - Ray L
AU  - Sahu N
AU  - Acharya A
AU  - Jadhao S
AU  - Suar M
AU  - Adhya TK
AU  - Rastogi G
AU  - Pattnaik AK
AU  - Raina V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00361-16.

PMID- 26251497
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Three Pectobacterium Strains Causing Blackleg of Potato: P. carotovorum subsp. brasiliensis ICMP 19477, P. atrosepticum ICMP 1526,  and P. carotovorum subsp. carotovorum UGC32.
PG  - e00874-15
AB  - Blackleg is a disease caused by several species of Pectobacterium that results in losses to
      potato crops worldwide. Here, we report the draft genomes of three
      taxonomically and geographically distinct blackleg-causing strains of
      Pectobacterium: P. carotovorum subsp. brasiliensis ICMP 19477, P. atrosepticum
      ICMP 1526, and P. carotovorum subsp. carotovorum UGC32. Comparison of these
      genomes will support the identification of common traits associated with their
      capacity to cause blackleg.
AU  - Panda P
AU  - Fiers MW
AU  - Lu A
AU  - Armstrong KF
AU  - Pitman AR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00874-15.

PMID- 26251498
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence for ICMP 5702, the Type Strain of Pectobacterium carotovorum subsp. carotovorum That Causes Soft Rot Disease on Potato.
PG  - e00875-15
AB  - Pectobacterium species are economically important bacteria that cause soft rotting of potato
      tubers in the field and in storage. Here, we report the draft
      genome sequence of the type strain for P. carotovorum subsp. carotovorum, ICMP
      5702 (ATCC 15713). The genome sequence of ICMP 5702 will provide an important
      reference for future phylogenomic and taxonomic studies of the phytopathogenic
      Enterobacteriaceae.
AU  - Panda P
AU  - Lu A
AU  - Armstrong KF
AU  - Pitman AR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00875-15.

PMID- 26988040
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequences of Staphylococcus haemolyticus Isolated from Infected Eyes and Healthy Conjunctiva in Bhubaneswar, India.
PG  - e00099-16
AB  - Staphylococcus haemolyticus, an opportunistic pathogen, is known to exhibit multidrug
      resistance and produce biofilm. We sequenced the genome of four
      multidrug resistant, biofilm forming isolates from infected eyes and asymptomatic
      healthy conjunctiva.
AU  - Panda S
AU  - Singh DV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00099-16.

PMID- 28770026
VI  - 12
DP  - 2017
TI  - Neisseria lactamica Y92-1009 complete genome sequence.
PG  - 41
AB  - We present the high quality, complete genome assembly of Neisseria lactamica Y92-1009 used to
      manufacture an outer membrane vesicle (OMV)-based vaccine, and a
      member of the Neisseria genus. The strain is available on request from the Public
      Health England Meningococcal Reference Unit. This Gram negative, dipplococcoid
      bacterium is an organism of worldwide clinical interest because human
      nasopharyngeal carriage is related inversely to the incidence of meningococcal
      disease, caused by Neisseria meningitidis. The organism sequenced was isolated
      during a school carriage survey in Northern Ireland in 1992 and has been the
      subject of a variety of laboratory and clinical studies. Four SMRT cells on a
      RSII machine by Pacific Biosystems were used to produce a complete, closed genome
      assembly. Sequence data were obtained for a total of 30,180,391 bases from 2621
      reads and assembled using the HGAP algorithm. The assembly was corrected using
      short reads obtained from an Illumina HiSeq 2000instrument. This resulted in a
      2,146,723 bp assembly with approximately 460 fold mean coverage depth and a GC
      ratio of 52.3%.
AU  - Pandey AK
AU  - Cleary DW
AU  - Laver JR
AU  - Maiden MCJ
AU  - Didelot X
AU  - Gorringe A
AU  - Read RC
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 41.

PMID- 29702132
VI  - 278
DP  - 2018
TI  - Complete genome sequence of Bacillus velezensis QST713: A biocontrol agent that protects Agaricus bisporus crops against the green mould disease.
PG  - 10-19
AB  - Bacillus subtilis QST713 is extensively used as a biological control agent in agricultural
      fields including in the button mushroom culture, Agaricus bisporus.
      This last use exploits its inhibitory activity against microbial pathogens such
      as Trichoderma aggressivum f. europaeum, the main button mushroom green mould
      competitor. Here, we report the complete genome sequence of this bacterium with a
      genome size of 4 233 757bp, 4263 predicted genes and an average GC content of
      45.9%. Based on phylogenomic analyses, strain QST713 is finally designated as
      Bacillus velezensis. Genomic analyses revealed two clusters encoding potential
      new antimicrobials with NRPS and TransATPKS synthetase. B. velezensis QST713
      genome also harbours several genes previously described as being involved in
      surface colonization and biofilm formation. This strain shows a strong ability to
      form in vitro spatially organized biofilm and to antagonize T. aggressivum. The
      availability of this genome sequence could bring new elements to understand the
      interactions with micro or/and macroorganisms in crops.
AU  - Pandin C
AU  - Le Coq D
AU  - Deschamps J
AU  - Vedie R
AU  - Rousseau T
AU  - Aymerich S
AU  - Briandet R
PT  - Journal Article
TA  - J. Biotechnol.
JT  - J. Biotechnol.
SO  - J. Biotechnol. 2018 278: 10-19.

PMID- 23788547
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Antarctic Psychrophilic Bacterium Pseudomonas syringae Strain Lz4W.
PG  - e00377-13
AB  - The psychrophilic bacterium Pseudomonas syringae strain Lz4W was isolated from soil samples
      from Antarctica to decipher the mechanisms of low-temperature
      adaptation. We report here the 4.982-Mb draft genome sequence of P. syringae
      Lz4W. This sequence will provide insights into the genomic basis of the
      psychrophilicity of this bacterium.
AU  - Pandiyan A
AU  - Ray MK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00377-13.

PMID- 29773613
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Two Chemosynthetic Arcobacter Strains Isolated from Hydraulically Fractured Wells in Marcellus and Utica Shales.
PG  - e00159-18
AB  - Genome sequences were obtained for two isolates of the genus Arcobacter from saline fluids
      produced from hydraulically fractured shale gas wells in the
      Marcellus and Utica formations. These genomes provide insight into microbial
      sulfur cycles occurring in a high-salt deep terrestrial shale environment.
AU  - Panescu J
AU  - Daly RA
AU  - Wrighton KC
AU  - Mouser PJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00159-18.

PMID- 26402569
VI  - 21
DP  - 2015
TI  - Methicillin-Susceptible, Vancomycin-Resistant Staphylococcus aureus, Brazil.
PG  - 1844-1848
AB  - We report characterization of a methicillin-susceptible,
      vancomycin-resistant bloodstream isolate of Staphylococcus aureus recovered from a patient in
      Brazil. Emergence of vancomycin resistance in methicillin-susceptible S. aureus would indicate
      that this resistance trait might be poised to disseminate more rapidly among S. aureus and
      represents a major public health threat.
AU  - Panesso D et al
PT  - Journal Article
TA  - Emerg. Infect. Dis.
JT  - Emerg. Infect. Dis.
SO  - Emerg. Infect. Dis. 2015 21: 1844-1848.

PMID- 23357425
VI  - 432
DP  - 2013
TI  - Functional characterization of a rice de novo DNA methyltransferase, OsDRM2, expressed in Escherichia coli and yeast.
PG  - 157-162
AB  - DNA methylation of cytosine nucleotides is an important epigenetic modification that occurs in
      most eukaryotic organisms and is established and maintained by various DNA methyltransferases
      together with their co-factors. There are two major categories of DNA methyltransferases: de
      novo and maintenance. Here, we report the isolation and functional characterization of a de
      novo methyltransferase, named OsDRM2, from rice (Oryza sativa L.). The full-length coding
      region of OsDRM2 was cloned and transformed into Escherichia coil and Saccharomyces
      cerevisiae. Both of these organisms expressed the OsDRM2 protein, which exhibited stochastic
      de novo methylation activity in vitro at CG, CHG, and CHH di- and tri-nucleotide patterns. Two
      lines of evidence demonstrated the de novo activity of OsDRM2: (1) a 5'-CCGG-3' containing
      DNA fragment that had been pre-treated with OsDRM2 protein expressed in E. coli was protected
      from digestion by the CG-methylation-sensitive isoschizomer HpaII; (2) methylation-sensitive
      amplified polymorphism (MSAP) analysis of S. cerevisiae genomic DNA from transformants that
      had been introduced with OsDRM2 revealed CG and CHG methylation levels of 3.92-9.12%, and
      2.88-6.93%, respectively, whereas the mock control S. cerevisiae DNA did not exhibit cytosine
      methylation. These results were further supported by bisulfite sequencing of the 18S rRNA and
      EAF5 genes of the transformed S. cerevisiae, which exhibited different DNA methylation
      patterns, which were observed in the genomic DNA. Our findings establish that OsDRM2 is an
      active de novo DNA methyltransferase gene with conserved activity in both prokaryotic and
      eukaryotic non-host species. (C) 2013 Elsevier Inc. All rights reserved.
AU  - Pang J
AU  - Dong M
AU  - Li N
AU  - Zhao Y
AU  - Liu B
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 2013 432: 157-162.

PMID- 26014286
VI  - 5
DP  - 2015
TI  - Novel insights into the pathogenicity of epidemic Aeromonas hydrophila ST251 clones from comparative genomics.
PG  - 9833
AB  - Outbreaks in fish of motile Aeromonad septicemia (MAS) caused by Aeromonas
      hydrophila have caused a great concern worldwide. Here, for the first time, we
      provide two complete genomes of epidemic A. hydrophila strains isolated in China.
      To gain an insight into the pathogenicity of epidemic A. hydrophila, we performed
      comparative genomic analyses of five epidemic strains belonging to sequence type
      (ST) 251, together with the environmental strain ATCC 7966(T). We found that the
      known virulence factors, including a type III secretion system, a type VI
      secretion system and lateral flagella, are not required for the high virulence of
      the ST251 clonal group. Additionally, our work identifies three utilization
      pathways for myo-inositol, sialic acid and L-fucose providing clues regarding the
      factors that underlie the epidemic and virulent nature of ST251 A. hydrophila.
      Based on the geographical distribution and biological resources of the ST251
      clonal group, we conclude that ST251 is a high-risk clonal group of A. hydrophila
      which may be responsible for the MAS outbreaks in China and the southeastern
      United States.
AU  - Pang M
AU  - Jiang J
AU  - Xie X
AU  - Wu Y
AU  - Dong Y
AU  - Kwok AH
AU  - Zhang W
AU  - Yao H
AU  - Lu C
AU  - Leung FC
AU  - Liu Y
PT  - Journal Article
TA  - Sci. Rep.
JT  - Sci. Rep.
SO  - Sci. Rep. 2015 5: 9833.

PMID- 24009121
VI  - 1
DP  - 2013
TI  - Whole-Genome Sequence of Mycobacterium abscessus Clinical Strain V06705.
PG  - e00690-13
AB  - Infection caused by Mycobacterium abscessus strains is a growing cause of concern in both
      community-acquired and health care-associated diseases, as these
      organisms naturally display multiple drug resistances. We report an annotated
      draft genome sequence of M. abscessus strain V06705 obtained from a patient in
      France.
AU  - Pang S
AU  - Renvoise A
AU  - Perret C
AU  - Guinier M
AU  - Chelghoum N
AU  - Brossier F
AU  - Capton E
AU  - Jarlier V
AU  - Sougakoff W
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00690-13.

PMID- 10779951
VI  - 34
DP  - 2000
TI  - Statistical analysis of complete bacterial genomes: Avoidance of palindromes and restriction-modification systems.
PG  - 246-252
AB  - Absence of 4, 5, and 6-letter palindromes is observed in genome sequences of a broad spectrum
      of bacteria. Recognition sites of
      restrictases of a particular species (or of a species closely related
      to it) comprise a significant portion of such palindromes. A
      significant role is played by the horizontal transfer of genes that
      encode the restriction-modification systems (R-M systems). In organisms
      that are practically isolated from the effects of such systems (for
      example, in Mycoplasma), such phenomenon is not observed. Common trends
      to preference and "avoidance" of nucleotides were studied in
      representatives of 33 bacterial families on the basis available
      bacterial genomes. The results of the study present additional data on
      intra- and interrelationships in established taxonomic groups.
AU  - Panina EM
AU  - Mironov AA
AU  - Gelfand MS
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2000 34: 246-252.

PMID- 22923796
VI  - 86
DP  - 2012
TI  - Complete genome sequence of Caulobacter crescentus bacteriophage phiCbK.
PG  - 10234-10235
AB  - phiCbK is a B3 morphotype bacteriophage of the Siphoviridae family that infects Caulobacter
      crescentus, the preeminent model system for bacterial cell cycle studies. The last 4 decades
      of research with phiCbK as a genetic and cytological tool to study the biology of the host
      warrant an investigation of the phage genome composition. Herein, we report the complete
      genome sequence of phiCbK and highlight unusual features that emerged from its annotation. The
      complete genome analysis of the phiCbK phage provides new insight into its characteristics and
      potential interactions with its Caulobacter crescentus host, setting the stage for future
      functional studies with phiCbK.
AU  - Panis G
AU  - Lambert C
AU  - Viollier PH
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 2012 86: 10234-10235.

PMID- 11406597
VI  - 20
DP  - 2001
TI  - The McrBC restriction endonuclease assembles into a ring structure in the presence of G nucleotides.
PG  - 3210-3217
AB  - McrBC from Escherichia coli K-12 is a restriction enzyme that belongs to the family of AAA(+)
      proteins and cuts DNA containing modified cytosines. Two proteins are expressed from the mcrB
      gene: a full-length version, McrB(L), and a short version, McrB(S). McrB(L) binds specifically
      to the methylated recognition site and is, therefore, the DNA-binding moiety of the McrBC
      endonuclease. McrB(S) is devoid of DNA-binding activity. We observed that the quaternary
      structure of the endonuclease depends on binding of the cofactors. In gel filtration
      experiments, McrB(L) and McrB(S) form high molecular weight oligomers in the presence of
      Mg(2+) and GTP, GDP or GTP-gamma-S. Oligomerization did not require the presence of DNA and
      was independent of GTP hydrolysis. Electron micrographs of negatively stained McrB(L) and
      McrB(S) revealed ring-shaped particles with a central channel. Mass analysis by scanning
      transmission electron microscopy indicates that McrB(L) and McrB(S) form single heptameric
      rings as well as tetradecamers. In the presence of McrC, a subunit that is essential for DNA
      cleavage, the tetradecameric species was the major form of the endonuclease.
AU  - Panne D
AU  - Muller SA
AU  - Wirtz S
AU  - Engel A
AU  - Bickle TA
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 2001 20: 3210-3217.

PMID- 9736625
VI  - 17
DP  - 1998
TI  - McrBS, a modulator peptide for McrBC activity.
PG  - 5477-5483
AB  - McrBC is a methylation-dependent endonuclease from Escherichia coli K-12.  The enzyme
      recognizes DNA with modified cytosine preceded by a purine.  McrBC restricts DNA that contains
      at least two methylated recognition sites separated by 40-80 bp.  Two gene products, McrBL and
      McrBS, are produced from the mcrB gene and one, McrC, from the mcrC gene.  DNA cleavage in
      vitro requires McrBL, McrC, GTP and Mg2+.  We found that DNA cleavage was optimal at a ratio
      of 3-5 McrBL per molecule of McrC, suggesting that formation of a multisubunit complex with
      several molecules of McrBL is required for cleavage.  To understand the role of McrBS, we have
      purified the protein and analyzed its role in vitro.  At the optimal ratio of 3-5 McrBL per
      molecule of McrC, McrBS acted as an inhibitor of DNA cleavage.  Inhibition was due to
      sequestration of McrC and required the presence of GTP, suggesting that the interaction is GTP
      dependent.  If McrC was in excess, a condition resulting in suboptimal DNA cleavage, addition
      of McrBS enhanced DNA cleavage, presumably due to sequestration of excess McrC.  We suggest
      that the role of McrBS is to modulate McrBC activity by binding to McrC.
AU  - Panne D
AU  - Raleigh EA
AU  - Bickle TA
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1998 17: 5477-5483.

PMID- 10388557
VI  - 290
DP  - 1999
TI  - The McrBC endonuclease translocates DNA in a reaction dependent on GTP hydrolysis.
PG  - 49-60
AB  - McrBC specifically recognizes and cleaves methylated DNA in a reaction dependent on GTP
      hydrolysis. DNA cleavage requires at least two recognition sites that are optimally separated
      by 40-80 bp, but can be spaced as far as 3 kb apart. The nature of the communication between
      two recognition sites was analyzed on DNA substrates containing one or two recognition sites.
      DNA cleavage of circular DNA required only one methylated recognition site, whereas the
      linearized form of this substrate was not cleaved. However, the linearized substrate was
      cleaved if a Lac repressor was bound adjacent to the recognition site. These results suggest a
      model in which communication between two remote sites is accomplished by DNA translocation
      rather than looping. A mutant protein with defective GTPase activity cleaved substrates with
      closely spaced recognition sites, but not substrates where the sites were further apart. This
      indicates that McrBC translocates DNA in a reaction dependent on GTP hydrolysis. We suggest
      that DNA cleavage occurs by the encounter of two DNA-translocating McrBC complexes, or can be
      triggered by non-specific physical obstacles like the Lac repressor bound on the enzyme's
      path along DNA. Our results indicate that McrBC belongs to the general class of DNA "motor
      proteins", which use the free energy associated with nucleoside 5'-triphosphate hydrolysis to
      translocate along DNA.
AU  - Panne D
AU  - Raleigh EA
AU  - Bickle TA
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1999 290: 49-60.

PMID- 27274783
VI  - 11
DP  - 2016
TI  - Comparing polysaccharide decomposition between the type strains Gramella echinicola KMM 6050(T) (DSM 19838(T)) and Gramella portivictoriae  UST040801-001(T) (DSM 23547(T)), and emended description of Gramella echinicola  Nedashkovskaya et al. 2005 emend.
PG  - 37
AB  - Strains of the genus Gramella (family Flavobacteriacae, phylum Bacteroidetes) were isolated
      from marine habitats such as tidal flat sediments, coastal surface
      seawater and sea urchins. Flavobacteriaceae have been shown to be involved in the
      decomposition of plant and algal polysaccharides. However, the potential to
      decompose polysaccharides may differ tremendously even between species of the
      same genus. Gramella echinicola KMM 6050(T) (DSM 19838(T)) and Gramella
      portivictoriae UST040801-001(T) (DSM 23547(T)) have genomes of similar lengths,
      similar numbers of protein coding genes and RNA genes. Both genomes encode for a
      greater number of peptidases compared to 'G. forsetii'. In contrast to the genome
      of 'G. forsetii', both genomes comprised a smaller set of CAZymes. Seven
      polysaccharide utilization loci were identified in the genomes of DSM 19838(T)
      and DSM 23547(T). Both Gramella strains hydrolyzed starch, galactomannan,
      arabinoxylan and hydroxyethyl-cellulose, but not pectin, chitosan and cellulose
      (Avicel). Galactan and xylan were hydrolyzed by strain DSM 19838(T), whereas
      strain DSM 23547(T) hydrolyzed pachyman and carboxy-methyl cellulose.
      Conclusively, both Gramella type strains exhibit characteristic physiological,
      morphological and genomic differences that might be linked to their habitat.
      Furthermore, the identified enzymes mediating polysaccharide decomposition, are
      of biotechnological interest.
AU  - Panschin I et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 37.

PMID- 28572324
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Vancomycin-Resistant Clinical Isolate Staphylococcus aureus VRS3b.
PG  - e00452-17
AB  - We report here the draft genome sequence of the vancomycin-resistant strain Staphylococcus
      aureus VRS3b. The 2.8-Mb genome, assembled into 46 contigs,
      harbored 2,915 putative coding sequences. The G+C content of the genome was
      32.7%.
AU  - Panthee S
AU  - Paudel A
AU  - Hamamoto H
AU  - Sekimizu K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00452-17.

PMID- 28450502
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Salmonella enterica subsp. enterica Serovar Typhimurium Strains Isolated from Chicken and Swine Carcasses in Two Distinct Geographical  Regions from Rio de Janeiro State, Brazil.
PG  - e00197-17
AB  - Salmonella enterica subsp. enterica serovar Typhimurium is a surveyed worldwide serotype with
      well-characterized genomes for several different strains. In
      Brazil, very few studies have submitted whole-genome sequences to GenBank. This
      genome may be useful to analyze the genetic mechanisms comparable to those of
      other related studies conducted in Brazil and globally.
AU  - Panzenhagen PHN
AU  - Cabral CC
AU  - Suffys PN
AU  - Aquino MHC
AU  - Franco RM
AU  - Pereira VLA
AU  - Rodrigues DP
AU  - Conte-Junior CA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00197-17.

PMID- 29437087
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of 11 Salmonella enterica Serovar Typhimurium Strains Isolated from Human Systemic and Nonsystemic Sites in Brazil.
PG  - e01223-17
AB  - Salmonella enterica serovar Typhimurium strains isolated from systemic sites outside
      sub-Saharan Africa have been rarely sequenced. Here, we report the draft
      genome sequences of S Typhimurium sequence type 19 (ST19) (n = 9), ST1649 (n =
      1), and ST313 (n = 1) strains isolated from human systemic (e.g., blood) and
      nonsystemic (e.g., stool and wounds) sites in Brazil.
AU  - Panzenhagen PHN
AU  - Paul NC
AU  - Conte JCA
AU  - Costa RG
AU  - Rodrigues DP
AU  - Shah DH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01223-17.

PMID- 29167264
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of Two Strains of the Meat Spoilage Bacterium Brochothrix thermosphacta Isolated from Ground Chicken.
PG  - e01357-17
AB  - Brochothrix thermosphacta is an important meat spoilage bacterium. Here we report the genome
      sequences of two strains of B. thermosphacta isolated from ground
      chicken. The genome sequences were determined using long-read PacBio
      single-molecule real-time (SMRT) technology and are the first complete genome
      sequences reported for B. thermosphacta.
AU  - Paoli GC
AU  - Wijey C
AU  - Nguyen LH
AU  - Chen CY
AU  - Yan X
AU  - Irwin PL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01357-17.

PMID- 11487702
VI  - 13
DP  - 2001
TI  - Maize chromomethylase Zea methyltransferase2 is required for CpNpG methyl ation.
PG  - 1919-1928
AB  - A cytosine DNA methyltransferase containing a chromodomain, Zea methyltransferase2 (Zmet2),
      was cloned from maize. The sequence of ZMET2 is similar to that of the Arabidopsis
      chromomethylases CMT1 and CMT3, with C-terminal motifs characteristic of eukaryotic and
      prokaryotic DNA methyltransferases. We used a reverse genetics approach to determine the
      function of the Zmet2 gene. Plants homozygous for a Mutator transposable element insertion
      into motif IX had a 13% reduction in methylated cytosines. DNA gel blot analysis of these
      plants with methylation-sensitive restriction enzymes and bisulfite sequencing of a 180-bp
      knob sequence showed reduced methylation only at CpNpG sites. No reductions in methylation
      were observed at CpG or asymmetric sites in heterozygous or homozygous mutant plants. Our
      research shows that chromomethylase Zmet2 is required for in vivo methylation of CpNpG
      sequences.
AU  - Papa CM
AU  - Springer NM
AU  - Muszynski MG
AU  - Meeley R
AU  - Kaeppler SM
PT  - Journal Article
TA  - Plant Cell
JT  - Plant Cell
SO  - Plant Cell 2001 13: 1919-1928.

PMID- 
VI  - 
DP  - 2008
TI  - The effect of active site mutations on the homodimeric behavior of the PvuII restriction endonuclease.
PG  - 1-233
AB  - The PvuII restriction endonuclease, a homodimer of two 18 kDa subunits, belongs to the type II
      family of restriction enzymes. As a part of the Proteus vulgaris RM system, it specifically
      cleaves the 5'-CAG|CTG-3' sequence in the presence of Mg2+ ions. Located in the active site
      of PvuII, Tyrosine 94 has previously been shown to be involved in the metal ion binding by the
      enzyme. The profile of the Ca2+ dependence of the DNA binding to the Y94F variant is shown to
      be clearly biphasic. The application of a sequential binding model yielded two weak binding
      constants in the upper phase with a coupling energy (delta G degrees coop) at -0.3, while two
      tight binding constants are shown for the lower phase with -1.4 kcal/mole interaction energy.
      The similar metal binding pattern between the Y94F and the WT PvuII for Mg2+, Ca2+, Tb3+ and
      Eu3+ in the absence of DNA is also shown. The application of 1H-15N HSQC spectroscopy in the
      presence of Ca2+ and DNA and the chemical denaturation of the Y94F variant confirm the
      conformational impact of Tyr94. It is concluded that the removal of the aromatic iii hydroxyl
      group of Tyr94 slightly repositions the metal ions in the active site of PvuII affecting the
      intra and/or inter-subunit interactions among the metal binding sites. The single chain (SC)
      PvuII bearing a covalent linker between the two subunits is utilized in the exploration of the
      modes of cooperativity among the metal binding sites. The heterodimeric WT|E68A-SC PvuII was
      prepared and studied in parallel to the WTSC homodimer. Global analysis of DNA binding
      isotherms at different Ca2+ concentrations for the WT|E68A-SC variant returned an
      intra-subunit delta G degrees coop at +1.6 and +1.0 kcal/mole in the absence and presence of
      DNA, respectively. Combined with similar analysis for the WT-SC variant, the corresponding
      values for the inter-subunit delta G degrees coop are shown at -2.8 and -1.1 kcal/mole for the
      occupation of two sites simultaneously. The sequential binding of metal ions in the absence
      and presence of DNA is overall unfavorable with significant negative interaction being
      observed between the metal sites. It is shown that the effect of Ca2+ ions on DNA binding is
      greater than the effect of the DNA on the affinity for metal ions. The cleavage of plasmid DNA
      under single turnover conditions reveals a similar dependence of the nicking and linearization
      rates on the concentration of Mg2+ ions for the WT-SC and the WT|E68A-SC PvuII. The series of
      events leading to the linear product (DNA association, nicking, release of the intermediate,
      re-association and linearization) in the presence of metal ions in one PvuII subunit is not
      significantly slower than the synchronized double strand cleavage in the presence of metal
      ions in both PvuII subunits.
AU  - Papadakos GA
PT  - Journal Article
TA  - Ph.D. Thesis, University of Missouri
JT  - Ph.D. Thesis, University of Missouri
SO  - Ph.D. Thesis, University of Missouri 2008 : 1-233.

PMID- 22408241
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of the Dairy Isolate Streptococcus macedonicus ACA-DC 198.
PG  - 1838-1839
AB  - The species Streptococcus macedonicus is associated with the food environment, especially with
      fermented dairy products. Here we present the complete 2.1-Mb
      genome sequence of strain ACA-DC 198, which was isolated from naturally fermented
      Greek kasseri cheese.
AU  - Papadimitriou K
AU  - Ferreira S
AU  - Papandreou NC
AU  - Mavrogonatou E
AU  - Supply P
AU  - Pot B
AU  - Tsakalidou E
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1838-1839.

PMID- 27660795
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequence of the Cheese Isolate Streptococcus macedonicus 679.
PG  - e01025-16
AB  - It is well recognized that Streptococcus macedonicus can populate artisanal fermented foods,
      especially those of dairy origin. However, the safety of S.
      macedonicus remains to be established. Here, we present the whole-genome sequence
      of strain 679, which was isolated from a French uncooked semihard cheese made
      with cow milk.
AU  - Papadimitriou K
AU  - Mavrogonatou E
AU  - Bolotin A
AU  - Tsakalidou E
AU  - Renault P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01025-16.

PMID- 23629721
VI  - 57
DP  - 2013
TI  - Characterization of pKP1433, a Novel KPC-2-Encoding Plasmid from Klebsiella pneumoniae ST340.
PG  - 3427-3429
AB  - The nucleotide sequence of pKP1433 (55417 bp), a blaKPC-2-carrying plasmid from
      Klebsiella pneumoniae sequence type 340 was determined. pKP1433 displayed
      extensive sequence and structural similarities with the IncN plasmids possessing
      the KPC-2-encoding Tn4401b isoform. However, replication, partitioning, and
      stability of pKP1433 were determined by sequences related to diverse non-IncN
      plasmids.
AU  - Papagiannitsis CC
AU  - Miriagou V
AU  - Giakkoupi P
AU  - Tzouvelekis LS
AU  - Vatopoulos AC
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2013 57: 3427-3429.

PMID- 20956594
VI  - 55
DP  - 2011
TI  - Sequence of pR3521, an IncB Plasmid from Escherichia coli Encoding ACC-4, SCO-1, and TEM-1 {beta}-Lactamases.
PG  - 376-381
AB  - The sequence of pR3521, a self-transmissible plasmid from Escherichia
      coli, was determined. pR3521 (110,416 bp) comprised a contiguous IncB
      sequence (84,034 bp) sharing extensive similarities with IncI replicons
      and an acquired region (26,382 bp) carrying sequences of diverse origin,
      containing bla(ACC-4), bla(SCO-1), bla(TEM-1b) (two copies), strA, strB,
      sul2, and aacC2.
AU  - Papagiannitsis CC
AU  - Tzouvelekis LS
AU  - Kotsakis SD
AU  - Tzelepi E
AU  - Miriagou V
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2011 55: 376-381.

PMID- 17426137
VI  - 35
DP  - 2007
TI  - DNA structural deformations in the interaction of the controller protein C.AhdI with its operator sequence.
PG  - 2643-2650
AB  - Controller proteins such as C.AhdI regulate the expression of bacterial
      restriction-modification genes, and ensure that methylation of the host DNA precedes
      restriction by delaying transcription of the endonuclease. The operator DNA sequence to which
      C.AhdI binds consists of two adjacent binding sites, O(L) and O(R). Binding of C.AhdI to O(L)
      and to O(L) + O(R) has been investigated by circular permutation DNA-bending assays and by
      circular dichroism (CD) spectroscopy. CD indicates considerable distortion to the DNA when
      bound by C.AhdI. Binding to one or two sites to form dimeric and tetrameric complexes
      increases the CD signal at 278 nm by 40 and 80% respectively, showing identical local
      distortion at both sites. In contrast, DNA-bending assays gave similar bend angles for both
      dimeric and tetrameric complexes (47 and 38 degrees , respectively). The relative orientation
      of C.AhdI dimers in the tetrameric complex and the structural role of the conserved Py-A-T
      sequences found at the centre of C-protein-binding sites are discussed.
AU  - Papapanagiotou I
AU  - Streeter SD
AU  - Cary PD
AU  - Kneale GG
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2007 35: 2643-2650.

PMID- 23814106
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Moderately Halophilic Bacterium Marinobacter lipolyticus Strain SM19.
PG  - e00379-13
AB  - Marinobacter lipolyticus strain SM19, isolated from saline soil in Spain, is a moderately
      halophilic bacterium belonging to the class Gammaproteobacteria. Here,
      we report the draft genome sequence of this strain, which consists of a 4.0-Mb
      chromosome and which is able to produce the halophilic enzyme lipase LipBL.
AU  - Papke RT
AU  - de la Haba RR
AU  - Infante-Dominguez C
AU  - Perez D
AU  - Sanchez-Porro C
AU  - Lapierre P
AU  - Ventosa A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00379-13.

PMID- 21725006
VI  - 193
DP  - 2011
TI  - Genome sequence of the ethanol-producing Zymomonas mobilis subsp. mobilis lectotype strain ATCC 10988.
PG  - 5051-5052
AB  - Zymomonas mobilis ATCC 10988 is the type strain of the Z. mobilis subsp. mobilis taxon,
      members of which are some of the most rigorous
      ethanol-producing bacteria. Isolated from Agave cactus fermentations in
      Mexico, ATCC 10988 is of the first Z. mobilis strains to be described and
      studied. Its robustness in sucrose-substrate fermentations, physiological
      characteristics, large number of plasmids and overall genomic plasticity
      render this strain important to the study of the species. Here we report
      the finishing and annotation of the ATCC 10988 chromosomal and plasmid
      genome.
AU  - Pappas KM
AU  - Kouvelis VN
AU  - Saunders E
AU  - Brettin TS
AU  - Bruce D
AU  - Detter C
AU  - Balakireva M
AU  - Han C
AU  - Savvakis G
AU  - Kyrpides NC
AU  - Typas MA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5051-5052.

PMID- 17305528
VI  - 7
DP  - 2007
TI  - Meganucleases and DNA double-strand break-induced recombination: Perspectives for gene therapy.
PG  - 49-66
AB  - Meganucleases are sequence-specific endonucleases recognizing large (> 12 bp) sequence sites
      and several laboratories have used these proteins
      to induce highly efficient gene targeting in mammalian cells. The
      recent development of artificial endonucleases with tailored
      specificities has opened the door for a wide range of new applications,
      including therapeutic ones: redesigned endonucleases cleaving chosen
      sequences could be used to in gene therapy to correct mutated genes or
      introduce transgenes in chosen loci. Such "targeted" approaches
      markedly differ from current gene therapy strategies based on the
      random insertion of a complementing virus-borne transgene. As a
      consequence, they should bypass the odds of random insertion.
      Artificial fusion proteins including Zinc-Finger binding domains have
      provided important proofs of concept, however the toxicity of these
      proteins is still an issue. Today custom-designed homing endonucleases,
      the natural meganucleases, could represent an efficient alternative.
      After a brief description of the origin of the technology, current
      systems based on redesigned endonucleases will be presented, with a
      special emphasis on the recent advances in homing endonuclease
      engineering. Finally, we will discuss the main issues that will need to
      be addressed in order to bring this promising technology to the
      patient.
AU  - Paques F
AU  - Duchateau P
PT  - Journal Article
TA  - Curr. Gene Ther.
JT  - Curr. Gene Ther.
SO  - Curr. Gene Ther. 2007 7: 49-66.

PMID- 7991539
VI  - 91
DP  - 1994
TI  - Interspecific transfer of mitochondrial genes in fungi and creation of a homologous hybrid gene.
PG  - 11807-11810
AB  - In eukaryotes, horizontal gene transfer is a rare event.  Here we show that the mitochondrial
      genome of a lower fungus, Allomyces macrogynus, has an extra DNA segment not present in a
      close relative, Allomyces arbusculus.  This insert consists of the C terminus of a foreign
      gene encoding a subunit of the ATP synthetase complex (atp6) plus an open reading frame
      encoding an endonuclease.  The inserted atp6 portion is fused in phase to the resident gene,
      resulting in expression of a hybrid atp6 gene and the displacement of the original C-terminal
      atp6 region.  We present evidence that this insertion may have been acquired by interspecific
      transfer and we discuss the possible role of the endonuclease in this process.
AU  - Paquin B
AU  - Laforest M-J
AU  - Lang BF
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1994 91: 11807-11810.

PMID- 8636971
VI  - 255
DP  - 1996
TI  - The mitochondrial DNA of Allomyces macrogynus: the complete genomic sequence from an ancestral fungus.
PG  - 688-701
AB  - We have determined the complete nucleotide sequence of the circular mitochondrial DNA (mtDNA)
      of the chytridiomycete fungus, Allomyces macrogynus (57,473 bp; A + T content 60.5%).  The
      identified genes that are typical for most fungal mitochondria include those for the large
      (rnl) and small subunit (rns) ribosomal RNAs, a complete set of 25 tRNAs, three ATPase
      subunits (atp6, atp8 and atp9), apocytochrome b (cob), three subunits of the cytochrome
      oxidase complex (cox1, cox2 and cox3), and seven subunits of the NADH dehydrogenase complex
      (nad1, nad2, nad3, nad4, nad4L, nad5 and nad6).  A total of 28 introns of both groups are
      found, some of which contain open reading frames (ORFs) coding for potential endonucleases
      (group I) or reverse-transcriptases (group II).  All  mitochondrial genes are transcribed from
      the same DNA strand, as is the case in many other eufungi.  Particular features of the A.
      macrogynus mtDNA include: (1) the first documented case of a fungal mitochondrial ribosomal
      protein gene (rps3) that is clearly identified by similarity with bacterial homologues; (2)
      four unique ORFs; (3) the presence of an insert in the atp6 gene that may have been acquired
      by interspecific transfer; (4) more than 67 short, highly structured and conserved DNA
      elements inserted in intergenic spacers, introns, and variable regions of the rnl and rns
      genes: these elements are unusually G + C rich; (5) rRNA structures that resemble more closely
      those of eubacteria than their counterparts in other fungal mitochondria.  The high degree of
      conservation of the A. macrogynus mitochondrial rRNA secondary structures, the existence of a
      mitochondrial rps3 gene (common to protist but unique in fungal mtDNAs), and phylogenetic
      relationships inferred from highly conserved protein genes, demonstrate consistently the
      ancestral character of this fungal mitochondrial genome.
AU  - Paquin B
AU  - Lang BF
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1996 255: 688-701.

PMID- 8536320
VI  - 28
DP  - 1995
TI  - Intron-encoded open reaading frame of the GIY-YIG subclass in a plastid gene.
PG  - 97-99
AB  - Group-I introns, containing open reading frames that code for homing endonucleases, are widely
      distributed amongst eukaryotic organellar genomes.  However, endonucleases of the GIY-YIG
      subclass have a restricted distribution in mitochondria and bacteriophages, and have never
      been observed in plastids.  We have found the GIY-YIG motif in an intronic ORF within the
      previously published psbA gene sequence from Chlamydomonas reinhardtii chloroplasts.  Based on
      phylogenetic analysis and an evaluation of amino-acid substitutions, this ORF is not closely
      related to any of the other GIY-YIG ORFs.  These results suggest that GIY-YIG ORFs have a
      longer evolutionary history than previously assumed.
AU  - Paquin B
AU  - O'Kelly CJ
AU  - Lang BF
PT  - Journal Article
TA  - Curr. Genet.
JT  - Curr. Genet.
SO  - Curr. Genet. 1995 28: 97-99.

PMID- 29674531
VI  - 6
DP  - 2018
TI  - Complete Genome Sequencing of 10 Brucella abortus Biovar 3 Strains Isolated from  Water Buffalo.
PG  - e00180-18
AB  - Brucellosis is a zoonotic disease that affects both humans and animals. Its distribution is
      global, concentrated in the Mediterranean area, India, Central
      Asia, and Latin America. Here, we present a complete genome assembly of 10
      Brucella abortus strains isolated from water buffaloes farmed in the Campania
      region of Italy.
AU  - Paradiso R
AU  - Orsini M
AU  - Criscuolo D
AU  - Borrelli R
AU  - Valvini O
AU  - Camma C
AU  - Chiusano ML
AU  - Galiero G
AU  - Borriello G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00180-18.

PMID- 29599153
VI  - 6
DP  - 2018
TI  - Complete Genome Sequencing of Eight Brucella abortus Biovar 1 Strains Isolated from Water Buffalo.
PG  - e00179-18
AB  - Brucellosis is a zoonotic disease caused by bacteria of the genus Brucella The disease is
      endemic in many areas, causing chronic infections responsible for
      reproductive disorders in infected animals. Here, we present eight complete
      genome assemblies of eight Brucella abortus strains isolated from water buffaloes
      farmed in the Campania region.
AU  - Paradiso R
AU  - Orsini M
AU  - Riccardi MG
AU  - Cecere B
AU  - Cerrone A
AU  - Camma C
AU  - Chiusano ML
AU  - Galiero G
AU  - Borriello G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00179-18.

PMID- 28899344
VI  - 18
DP  - 2017
TI  - Bacteriophages are the major drivers of Shigella flexneri serotype 1c genome plasticity: a complete genome analysis.
PG  - 722
AB  - BACKGROUND: Shigella flexneri is the primary cause of bacillary dysentery in the
      developing countries. S. flexneri serotype 1c is a novel serotype, which is found
      to be endemic in many developing countries, but little is known about its genomic
      architecture and virulence signatures. We have sequenced for the first time, the
      complete genome of S. flexneri serotype 1c strain Y394, to provide insights into
      its diversity and evolution. RESULTS: We generated a high-quality reference
      genome of S. flexneri serotype 1c using the hybrid methods of long-read
      single-molecule real-time (SMRT) sequencing technology and short-read MiSeq
      (Illumina) sequencing technology. The Y394 chromosome is 4.58 Mb in size and
      shares the basic genomic features with other S. flexneri complete genomes.
      However, it possesses unique and highly modified O-antigen structure comprising
      of three distinct O-antigen modifying gene clusters that potentially came from
      three different bacteriophages. It also possesses a large number of hypothetical
      unique genes compared to other S. flexneri genomes. CONCLUSIONS: Despite a high
      level of structural and functional similarities of Y394 genome with other S.
      flexneri genomes, there are marked differences in the pathogenic islands. The
      diversity in the pathogenic islands suggests that these bacterial pathogens are
      well adapted to respond to the selection pressures during their evolution, which
      might contribute to the differences in their virulence potential.
AU  - Parajuli P
AU  - Adamski M
AU  - Verma NK
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2017 18: 722.

PMID- 29025955
VI  - 5
DP  - 2017
TI  - Genome Sequence of Pseudomonas putida Strain ASAD, an Acetylsalicylic Acid-Degrading Bacterium.
PG  - e01169-17
AB  - Pseudomonas putida strain ASAD was isolated from compost because of its ability to utilize
      aspirin (acetylsalicylic acid) as a carbon and energy source. We
      report the draft genome sequence of strain ASAD, with an estimated length of 6.9
      Mb. Study of this isolate will provide insight into the aspirin biodegradation
      pathway.
AU  - Parales RE
AU  - Navara R
AU  - Gettys R
AU  - Huang JJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01169-17.

PMID- 21591120
VI  - 35
DP  - 2007
TI  - Demonstration of REBASE-assisted restriction mapping to determine the recognition site of unknown restriction endonucleases.
PG  - 337-341
AB  - An important step in the characterization of a new restriction enzyme involves determination
      of its recognition site. Comparison of its DNA
      substrate digestion fragment patterns with those obtained using enzymes
      of known specificity indicates whether the enzyme recognizes a novel
      sequence or is an isoschizomer of already existing prototype. REBASE
      (Restriction Enzyme dataBASE: hftp://www.neb.com/rebase)-assisted
      restriction mapping is described in this paper for a rare cutter [TspMI
      (REBASE No. 7191)] and a frequent cutter [Bfll (REBASE No. 4910)] as a
      practical exercise for undergraduate students to understand how to
      determine recognition sequence of a REase.
AU  - Parashar V
AU  - Capalash N
AU  - Sharma P
PT  - Journal Article
TA  - Biochem. Mol. Biol. Educ.
JT  - Biochem. Mol. Biol. Educ.
SO  - Biochem. Mol. Biol. Educ. 2007 35: 337-341.

PMID- 16847605
VI  - 72
DP  - 2006
TI  - TspMI, a thermostable isoschizomer of XmaI (5' C/CCGGG 3'): characterization and single molecule imaging with DNA - involving vector-mediated gene transfer and expression in host cell with restriction endonuclease activity.
PG  - 917-923
AB  - AUTHOR ABSTRACT - TspMI, a thermostable isoschizomer of XmaI from a Thermus sp., has been
      characterized. The enzyme was purified to homogeneity using Cibacron-Blue 3GA agarose, Heparin
      agarose, SP sephadex C50, and Mono-Q fast protein liquid chromatography and was found to be a
      homodimer of 40 kDa. Restriction mapping and run-off sequencing of TspMI-cleaved DNA ends
      depicted that it cleaved at 5'C/CCGGG3' to generate a four-base, 5'-CCGG overhang. The
      enzyme was sensitive to methylation of second and third cytosines in its recognition sequence.
      TspMI worked optimally at 60 degrees C with 6 mM Mg2+, no Na+/K+, and showed no star activity
      in the presence of 25% glycerol. The enzyme could efficiently digest the DNA labeled with a
      higher concentration of YOYO-I (one dye molecule to one nucleotide), making it a useful
      candidate for real-time imaging experiments. Single molecule interaction between TspMI and
      lambda DNA was studied using total internal reflection fluorescence microscopy. The enzyme
      survived 30 polymerase chain reaction (PCR) cycles in the presence of 10% glycerol and 0.5 M
      trehalose without any activity loss and, hence, is suitable for incorporation in
      restriction-endonuclease-mediated selective-PCR for various applications.
AU  - Parashar V
AU  - Capalash N
AU  - Xu SY
AU  - Sako Y
AU  - Sharma P
PT  - Journal Article
TA  - Appl. Microbiol. Biotechnol.
JT  - Appl. Microbiol. Biotechnol.
SO  - Appl. Microbiol. Biotechnol. 2006 72: 917-923.

PMID- 20959287
VI  - 39
DP  - 2011
TI  - MethylViewer: computational analysis and editing for bisulfite sequencing and methyltransferase accessibility protocol for individual  templates (MAPit) projects.
PG  - e5
AB  - Bisulfite sequencing is a widely-used technique for examining cytosine DNA methylation at
      nucleotide resolution along single DNA strands.
      Probing with cytosine DNA methyltransferases followed by bisulfite
      sequencing (MAPit) is an effective technique for mapping protein-DNA
      interactions. Here, MAPit methylation footprinting with M.CviPI, a GC
      methyltransferase we previously cloned and characterized, was used to
      probe hMLH1 chromatin in HCT116 and RKO colorectal cancer cells.
      Because M. CviPI-probed samples contain both CG and GC methylation, we
      developed a versatile, visually-intuitive program, called MethylViewer,
      for evaluating the bisulfite sequencing results. Uniquely, MethylViewer
      can simultaneously query cytosine methylation status in
      bisulfite-converted sequences at as many as four different user-defined
      motifs, e.g. CG, GC, etc., including motifs with degenerate bases. Data
      can also be exported for statistical analysis and as
      publication-quality images. Analysis of hMLH1 MAPit data with
      MethylViewer showed that endogenous CG methylation and accessible GC
      sites were both mapped on single molecules at high resolution.
      Disruption of positioned nucleosomes on single molecules of the PHO5
      promoter was detected in budding yeast using M.CviPII, increasing the
      number of enzymes available for probing protein-DNA interactions.
      MethylViewer provides an integrated solution for primer design and
      rapid, accurate and detailed analysis of bisulfite sequencing or MAPit
      datasets from virtually any biological or biochemical system.
AU  - Pardo CE
AU  - Carr IM
AU  - Hoffman CJ
AU  - Darst RP
AU  - Markham AF
AU  - Bonthron DT
AU  - Kladde MP
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2011 39: e5.

PMID- Not included in PubMed...
VI  - 132
DP  - 1995
TI  - Site-specific restriction endonucleases in Bacillus licheniformis.
PG  - 285-289
AB  - We systematically studied site-specific restriction endonucleases in Bacillus licheniformis
      strains and detected endonuclease activity in 25 of 217 strains tested.  Three different
      activities were obtained.  One of these activities detected in 21 strains was the most
      representative within the species and produced a banding pattern, after digestion of lambda
      DNA, identical to that seen with ClaI.  Two other strains isolated from soil samples from
      China and USA were found to produce a DNA-cleaving enzyme with the same recognition sequence
      as BsaI.  One producer strain, isolated from a Peruvian soil sample, possessed a mixture of
      two isoschizomers, ClaI and BsaI.  Finally, one strain produced an endonuclease activity, not
      previously described in B. licheniformis, that showed the same recognition sites as Bsu36I.
AU  - Parini C
AU  - Fortina MG
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1995 132: 285-289.

PMID- 30338024
VI  - 13
DP  - 2018
TI  - First genome sequencing and comparative analyses of Corynebacterium pseudotuberculosis strains from Mexico.
PG  - 21
AB  - Corynebacterium pseudotuberculosis is a pathogenic bacterium which has been rapidly spreading
      all over the world, causing economic losses in the agricultural
      sector and sporadically infecting humans. Six C. pseudotuberculosis strains were
      isolated from goats, sheep, and horses with distinct abscess locations. For the
      first time, Mexican genomes of this bacterium were sequenced and studied in
      silico. All strains were sequenced using Ion Personal Genome Machine sequencer,
      assembled using Newbler and SPAdes software. The automatic genome annotation was
      done using the software RAST and in-house scripts for transference, followed by
      manual curation using Artemis software and BLAST against NCBI and UniProt
      databases. The six genomes are publicly available in NCBI database. The analysis
      of nucleotide sequence similarity and the generated phylogenetic tree led to the
      observation that the Mexican strains are more similar between strains from the
      same host, but the genetic structure is probably more influenced by
      transportation of animals between farms than host preference. Also, a putative
      drug target was predicted and in silico analysis of 46 strains showed two gene
      clusters capable of differentiating the biovars equi and ovis: Restriction
      Modification system and CRISPR-Cas cluster.
AU  - Parise D
AU  - Parise MTD
AU  - Viana MVC
AU  - Munoz-Bucio AV
AU  - Cortes-Perez YA
AU  - Arellano-Reynoso B
AU  - Diaz-Aparicio E
AU  - Dorella FA
AU  - Pereira FL
AU  - Carvalho AF
AU  - Figueiredo HCP
AU  - Ghosh P
AU  - Barh D
AU  - Gomide ACP
AU  - Azevedo VAC
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2018 13: 21.

PMID- 23083487
VI  - 13
DP  - 2012
TI  - The genome sequence of Propionibacterium acidipropionici provides insights into its biotechnological and industrial potential.
PG  - 562
AB  - ABSTRACT: BACKGROUND: Synthetic biology allows the development of new biochemical
      pathways for the production of chemicals from renewable sources. One major
      challenge is the identification of suitable microorganisms to hold these pathways
      with sufficient robustness and high yield. In this work we analyzed the genome of
      the propionic acid producer Actinobacteria Propionibacterium acidipropionici
      (ATCC 4875). RESULTS: The assembled P. acidipropionici genome has 3,656,170 base
      pairs (bp) with 68.8% G + C content and a low-copy plasmid of 6,868 bp. We
      identified 3,336 protein coding genes, approximately 1000 more than P.
      freudenreichii and P. acnes, with an increase in the number of genes putatively
      involved in maintenance of genome integrity, as well as the presence of an
      invertase and genes putatively involved in carbon catabolite repression. In
      addition, we made an experimental confirmation of the ability of P.
      acidipropionici to fix CO2, but no phosphoenolpyruvate carboxylase coding gene
      was found in the genome. Instead, we identified the pyruvate carboxylase gene and
      confirmed the presence of the corresponding enzyme in proteome analysis as a
      potential candidate for this activity. Similarly, the phosphate acetyltransferase
      and acetate kinase genes, which are considered responsible for acetate formation,
      were not present in the genome. In P. acidipropionici, a similar function seems
      to be performed by an ADP forming acetate-CoA ligase gene and its corresponding
      enzyme was confirmed in the proteome analysis. CONCLUSIONS: Our data shows that
      P. acidipropionici has several of the desired features that are required to
      become a platform for the production of chemical commodities: multiple pathways
      for efficient feedstock utilization, ability to fix CO2, robustness, and
      efficient production of propionic acid, a potential precursor for valuable
      3-carbon compounds.
AU  - Parizzi LP
AU  - Grassi MC
AU  - Llerena LA
AU  - Carazzolle MF
AU  - Queiroz VL
AU  - Lunardi I
AU  - Zeidler AF
AU  - Teixeira PJ
AU  - Mieczkowski P
AU  - Rincones J
AU  - Pereira GA
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2012 13: 562.

PMID- 28935749
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Actinobacillus pleuropneumoniae Strain KL 16 (Serotype 1).
PG  - e01025-17
AB  - Actinobacillus pleuropneumoniae is a bacterial pathogen causing highly contagious porcine
      pleuropneumonia. Due to limited information on this species, it is
      difficult to study the biology of A. pleuropneumoniae at the genome level. Here,
      we report the fully annotated genome sequence of A. pleuropneumoniae strain KL
      16.
AU  - Park BS
AU  - Han J
AU  - Shin DJ
AU  - Jeong YJ
AU  - Lee N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01025-17.

PMID- 19574415
VI  - 58
DP  - 2009
TI  - Two variants of staphylococcal cassette chromosome mec type IVA in community-associated meticillin-resistant Staphylococcus aureus strains in South Korea.
PG  - 1314-1321
AB  - Meticillin-resistant Staphylococcus aureus (MRSA) strains harbouring staphylococcal cassette
      chromosome mec (SCCmec) type IVA are known to be more prevalent in South Korea than in other
      countries. Variations in the SCCmec IVA structure have been identified, including in sequence
      type (ST)
      1 and ST72 strains. This study compared and investigated the genetic characteristics of two
      subtypes common in South Korea. Type IVA SCCmec of
      ST1 strains was characterized by type IV features with the linearized pUB110 at the junkyard
      (J) 3 region. However, that of ST72 strains carried a variant class B mec complex, ccrA2, with
      an identity of approximately 96 % and the linearized pUB110 at the J3 region. In SCCmec of
      ST72 strains, the organization of the class B variant and the J3 region may be more similar to
      that of type IA than to other types, but the ccr type and other J regions seemed to be derived
      from type IV. These genetic characteristics showed that type IVA appears to result from the
      dynamic genetic exchange and recombination of SCC DNA.
AU  - Park C
AU  - Shin HH
AU  - Kwon EY
AU  - Choi SM
AU  - Kim SH
AU  - Park SH
AU  - Choi JH
AU  - Yoo JH
AU  - Lee DG
AU  - Shin WS
PT  - Journal Article
TA  - J. Med. Microbiol.
JT  - J. Med. Microbiol.
SO  - J. Med. Microbiol. 2009 58: 1314-1321.

PMID- 21151881
VI  - 8
DP  - 2010
TI  - Domain swapping in allosteric modulation of DNA specificity.
PG  - e1000554
AB  - SgrAI is a type IIF restriction endonuclease that cuts an unusually long recognition sequence
      and exhibits allosteric self-modulation of cleavage
      activity and sequence specificity. Previous studies have shown that DNA
      bound dimers of SgrAI oligomerize into an activated form with higher DNA
      cleavage rates, although previously determined crystal structures of SgrAI
      bound to DNA show only the DNA bound dimer. A new crystal structure of the
      type II restriction endonuclease SgrAI bound to DNA and Ca(2+) is now
      presented, which shows the close association of two DNA bound SgrAI
      dimers. This tetrameric form is unlike those of the homologous enzymes
      Cfr10I and NgoMIV and is formed by the swapping of the amino-terminal 24
      amino acid residues. Two mutations predicted to destabilize the swapped
      form of SgrAI, P27W and P27G, have been made and shown to eliminate both
      the oligomerization of the DNA bound SgrAI dimers as well as the
      allosteric stimulation of DNA cleavage by SgrAI. A mechanism involving
      domain swapping is proposed to explain the unusual allosteric properties
      of SgrAI via association of the domain swapped tetramer of SgrAI bound to
      DNA into higher order oligomers.
AU  - Park CK
AU  - Joshi HK
AU  - Agrawal A
AU  - Ghare MI
AU  - Little EJ
AU  - Dunten PW
AU  - Bitinaite J
AU  - Horton NC
PT  - Journal Article
TA  - PLoS Biology
JT  - PLoS Biology
SO  - PLoS Biology 2010 8: e1000554.

PMID- 21075933
VI  - 193
DP  - 2010
TI  - Complete Genome Sequence of Japanese Erwinia Strain Ejp617, a Bacterial Shoot Blight Pathogen of Pear.
PG  - 586-587
AB  - The Japanese Erwinia strain Ejp617 is a plant pathogen that causes bacterial shoot blight of
      pear (BSBP) in Japan. Here, we report the
      complete genome sequence of strain Ejp617 isolated from Nashi pears in
      Japan to provide for further valuable insight among related Erwinia
      species.
AU  - Park DH
AU  - Thapa SP
AU  - Choi BS
AU  - Kim WS
AU  - Hur JH
AU  - Cho JM
AU  - Lim JS
AU  - Choi IY
AU  - Lim CK
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 193: 586-587.

PMID- 23144398
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of the Novel Enteric Bacterium Galloisinimonas intestini B14T KCTC 32180, Isolated from the Gut of a Galloisiana Species (Notoptera:  Grylloblattidae) Fossil Insect.
PG  - 6648
AB  - We report the 3.74-Mb genome sequence of Galloisinimonas intestini B14(T), isolated from the
      gut of one of the world's rarest insect species, Galloisiana
      sp., collected at a Mosan cave, Moonkyung, Gyungsangbook-do, South Korea. Strain
      B14(T) is a novel genus candidate of the family Enterobacteriaceae.
AU  - Park DS
AU  - Bae KS
AU  - Kim H
AU  - Shin KS
AU  - Choi SH
AU  - Kim DS
AU  - Kim BW
AU  - Oh HW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6648.

PMID- 25428979
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Chryseobacterium sp. Strain P1-3, a Keratinolytic Bacterium Isolated from Poultry Waste.
PG  - e01237-14
AB  - Chryseobacterium sp. strain P1-3, harboring keratin degrading activity, has recently been
      isolated from poultry waste. Here, we report the 4.6-Mbp draft
      genome sequence of the keratinolytic bacterium with a G+C content of 37.0% and
      4,087 protein-coding genes.
AU  - Park GS
AU  - Hong SJ
AU  - Lee CH
AU  - Khan AR
AU  - Ullah I
AU  - Jung BK
AU  - Choi J
AU  - Kwak Y
AU  - Back CG
AU  - Jung HY
AU  - Shin JH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01237-14.

PMID- 24029767
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Entomopathogenic Bacterium Photorhabdus temperata Strain M1021, Isolated from Nematodes.
PG  - e00747-13
AB  - Photorhabdus temperata strain M1021 is an entomopathogenic bacterium belonging to the family
      Enterobacteriaceae and is symbiotically associated with nematodes. The
      draft genome sequence of P. temperata strain M1021 consists of 5,598,253 bp with
      a G+C content of 43.7%, and it has 6,120 protein-coding genes.
AU  - Park GS
AU  - Khan AR
AU  - Hong SJ
AU  - Jang EK
AU  - Ullah I
AU  - Jung BK
AU  - Choi J
AU  - Yoo NK
AU  - Park KJ
AU  - Shin JH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00747-13.

PMID- 27491992
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Two Ureolytic Bacteria Isolated from Concrete Block Waste.
PG  - e00762-16
AB  - We sequenced genomes of two ureolytic bacteria, Bacillus sp. JH7 and Sporosarcina sp. HYO08,
      which were isolated from concrete waste and have a potential for
      biocementation applications.
AU  - Park H
AU  - Park B
AU  - Kim HJ
AU  - Park W
AU  - Choi IG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00762-16.

PMID- 23409270
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of a Humic Substance-Degrading Paenibacillus sp. Isolated from the Subarctic Grasslands at Low Temperature.
PG  - e00170-12
AB  - The Paenibacillus sp. strain PAMC 26794 was isolated from the tundra grasslands in Alaska for
      its high ability to degrade humic acids. We sequenced the PAMC
      26794 genome to discover the degradative genes for natural humic substances and
      we propose the degradation pathway(s) of an abundant bacterial group (genus
      Paenibacillus) that inhabits cold environments.
AU  - Park HJ
AU  - Kim D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00170-12.

PMID- 22815453
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Arctic Marine Bacterium Pseudoalteromonas issachenkonii  PAMC 22718.
PG  - 4140
AB  - The psychrotolerant Pseudoalteromonas issachenkonii PAMC 22718 was isolated for its higher
      chitinase and protease activities from cold seawater in the Kara Sea,
      Arctic. Here, we present the draft genome sequence of PAMC 22718 to provide
      further information for the ecological function of the genus Pseudoalteromonas in
      a cold marine environment.
AU  - Park HJ
AU  - Shin SC
AU  - Kim D
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4140.

PMID- 23405349
VI  - 1
DP  - 2013
TI  - Draft genome sequence of a subarctic humic substance-degrading pseudomonad.
PG  - e00070-12
AB  - The Pseudomonas sp. PAMC 26793 was isolated because of its high ability to degrade humic acids
      from a subarctic grassland in Alaska. We sequenced the PAMC 26793 genome to discover the genes
      for degradation of natural humic substances and to provide further information for the
      degradation process of soil bacteria in a low-temperature environment.
AU  - Park HJ
AU  - Shin SC
AU  - Kim D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00070-12.

PMID- 28280026
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Clinical Isolates of Serotype 6E Streptococcus pneumoniae from Five Asian Countries.
PG  - e01728-16
AB  - Although serotype 6E Streptococcus pneumoniae consistently expresses capsules of  either
      vaccine-serotype 6A or 6B, certain genetic variants of serotype 6E may
      evade vaccine induced immunity. Thus, draft genome sequences from five clinical
      isolates of serotype 6E from each of five different Asian countries have been
      generated to provide insight into the genomic diversity in serotype 6E strains.
AU  - Park IH
AU  - Baek JY
AU  - Song JH
AU  - Ko KS
AU  - Kim KH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01728-16.

PMID- 23051057
VI  - 13
DP  - 2012
TI  - Comparative genomics of the classical Bordetella subspecies: the evolution and exchange of virulence-associated diversity amongst closely related pathogens.
PG  - 545
AB  - ABSTRACT: BACKGROUND: The classical Bordetella subspecies are phylogenetically
      closely related, yet differ in some of the most interesting and important
      characteristics of pathogens, such as host range, virulence and persistence. The
      compelling picture from previous comparisons of the three sequenced genomes was
      of genome degradation, with substantial loss of genome content (up to 24%)
      associated with adaptation to humans. RESULTS: For a more comprehensive picture
      of lineage evolution, we employed comparative genomic and phylogenomic analyses
      using seven additional diverse, newly sequenced Bordetella isolates. Genome-wide
      single nucleotide polymorphism (SNP) analysis supports a reevaluation of the
      phylogenetic relationships between the classical Bordetella subspecies, and
      suggests a closer link between ovine and human B. parapertussis lineages than has
      been previously proposed. Comparative analyses of genome content revealed that
      only 50% of the pan-genome is conserved in all strains, reflecting substantial
      diversity of genome content in these closely related pathogens that may relate to
      their different host ranges, virulence and persistence characteristics.
      Strikingly, these analyses suggest possible horizontal gene transfer (HGT) events
      in multiple loci encoding virulence factors, including O-antigen and pertussis
      toxin (Ptx). Segments of the pertussis toxin locus (ptx) and its secretion system
      locus (ptl) appear to have been acquired by the classical Bordetella subspecies
      and are divergent in different lineages, suggesting functional divergence in the
      classical Bordetellae. CONCLUSIONS: Together, these observations, especially in
      key virulence factors, reveal that multiple mechanisms, such as point mutations,
      gain or loss of genes, as well as HGTs, contribute to the substantial phenotypic
      diversity of these versatile subspecies in various hosts.
AU  - Park J
AU  - Zhang Y
AU  - Buboltz AM
AU  - Zhang X
AU  - Schuster SC
AU  - Ahuja U
AU  - Liu M
AU  - Miller JF
AU  - Sebaihia M
AU  - Bentley SD
AU  - Parkhill J
AU  - Harvill ET
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2012 13: 545.

PMID- 21317338
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Vibrio vulnificus MO6-24/O.
PG  - 2062-2063
AB  - Vibrio vulnificus is the causative agent of life-threatening septicemia and severe wound
      infections. Here, we announce the complete annotated
      genome sequence of V. vulnificus MO6-24/O, isolated from a patient with
      septicemia. When it is compared with previously known V. vulnificus
      genomes, the genome of this bacterium shows a unique genetic makeup,
      including phagelike elements, carbohydrate metabolism-related genes, and
      the superintegron.
AU  - Park JH
AU  - Cho YJ
AU  - Chun J
AU  - Seok YJ
AU  - Lee JK
AU  - Kim KS
AU  - Lee KH
AU  - Park SJ
AU  - Choi SH
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 2062-2063.

PMID- 22072649
VI  - 193
DP  - 2011
TI  - Draft Genome Sequence of the Biocontrol Bacterium Pseudomonas putida B001, an Oligotrophic Bacterium That Induces Systemic Resistance to Plant  Diseases.
PG  - 6795-6796
AB  - Pseudomonas putida B001 is a rhizobacterium that was isolated on the basis of its abilities to
      grow under low-nutrient conditions and induce systemic
      resistance against bacterial, fungal, and viral diseases of plants. Here
      we report the draft genome sequence and automatic annotation of strain
      B001. Comparison of this sequence to the sequenced genome of P. putida
      KT2440 points to a subset of gene functions that may be related to the
      defense-inducing functions of B001.
AU  - Park JY
AU  - Han SH
AU  - Lee JH
AU  - Han YS
AU  - Lee YS
AU  - Rong X
AU  - McSpadden GBB
AU  - Park HS
AU  - Kim YC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6795-6796.

PMID- 22038960
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Multidrug-Resistant Acinetobacter baumannii Strain 1656-2, Which Forms Sturdy Biofilm.
PG  - 6393-6394
AB  - Acinetobacter baumannii is a Gram-negative bacterium causing nosocomial infections worldwide.
      To gain quick insight into the molecular basis of
      biofilm formation in A. baumannii, we determined the complete genome
      sequence of A. baumannii strain 1656-2, which forms sturdy biofilm and is
      resistant to multiple drugs.
AU  - Park JY
AU  - Kim S
AU  - Kim SM
AU  - Cha SH
AU  - Lim SK
AU  - Kim J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6393-6394.

PMID- 24092782
VI  - 1
DP  - 2013
TI  - Genome Sequence of Streptococcus parauberis Strain KCTC11980, Isolated from Diseased Paralichthys olivaceus.
PG  - e00780-13
AB  - Streptococcus parauberis is a coccoid, nonmotile, alpha-hemolytic, Gram-positive  bacterium of
      the Streptococcaceae family. Streptococcus parauberis strain
      KCTC11980 was isolated from the kidney of a diseased olive flounder collected
      from an aquaculture farm on Jeju Island in 2010. The 2.12-Mb genome sequence
      consists of 44 large contigs in 16 scaffolds and contains 2,214 predicted
      protein-coding genes, with a G+C content of 35.4%.
AU  - Park MA
AU  - Kwon MG
AU  - Hwang JY
AU  - Jung SH
AU  - Kim DW
AU  - Park JY
AU  - Kim JS
AU  - Na YJ
AU  - Kim MY
AU  - Kim DS
AU  - Chae SH
AU  - Seo JS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00780-13.

PMID- 27858139
VI  - 101
DP  - 2017
TI  - Lactobacillus plantarum HAC01 regulates gut microbiota and adipose tissue accumulation in a diet-induced obesity murine model.
PG  - 1605-1614
AB  - The functional features of Lactobacillus plantarum HAC01 (HAC01), isolated from
      fermented Korean kimchi, were studied with regard to the fat mass,
      immunometabolic biomarkers and dysbiosis in a diet-induced obesity (DIO) murine
      model. L. rhamnosus GG (LGG) served as reference strain and a PBS-treated group
      as control. The administration of L. plantarum HAC01 resulted in reduction of the
      mesenteric adipose depot, the conjunctive tissue closely associated with the
      gastrointestinal tract, where lipid oxidative gene expression was upregulated
      compared to the control group. Metagenome analysis of intestinal microbiota
      showed that both strains HAC01 and LGG influenced specific bacterial families
      such as the Lachnospiraceae and Ruminococcaceae rather than the phyla Firmicutes
      and Bacteroidetes as a whole. The relative abundance of the Lachnospiraceae
      (phylum Firmicutes) was significantly higher in both LAB-treated groups than in
      the control. Comparing the impact of the two Lactobacillus strains on microbial
      composition in the gut also suggests strain-specific effects. The study
      emphasises the need for deeper studies into functional specificity of a probiotic
      organism at the strain level. Alleviation of obesity-associated dysbiosis by
      modulation of the gut microbiota appears to be associated with "indicator"
      bacterial taxa such as the family Lachnospiraceae. This may provide further
      insight into mechanisms basic to the mode of probiotic action against obesity and
      associated dysbiosis.
AU  - Park S
AU  - Ji Y
AU  - Jung HY
AU  - Park H
AU  - Kang J
AU  - Choi SH
AU  - Shin H
AU  - Hyun CK
AU  - Kim KT
AU  - Holzapfel WH
PT  - Journal Article
TA  - Appl. Microbiol. Biotechnol.
JT  - Appl. Microbiol. Biotechnol.
SO  - Appl. Microbiol. Biotechnol. 2017 101: 1605-1614.

PMID- 23090406
VI  - 68
DP  - 2012
TI  - Structural characterization of a modification subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016.
PG  - 1570-1577
AB  - In multifunctional type I restriction enzymes, active methyl-transferases (MTases) are
      constituted of methylation (HsdM) and
      specificity (HsdS) subunits. In this study, the crystal structure of a
      putative HsdM subunit from Vibrio vulnificus YJ016 (vvHsdM) was
      elucidated at a resolution of 1.80 angstrom. A cofactor-binding site
      for S-adenosyl-L-methionine (SAM, a methyl-group donor) is formed
      within the C-terminal domain of an alpha/beta-fold, in which a number
      of residues are conserved, including the GxGG and (N/D) PP(F/Y) motifs,
      which are likely to interact with several functional moieties of the
      SAM methyl-group donor. Comparison with the N6 DNA MTase of Thermus
      aquaticus and other HsdM structures suggests that two aromatic rings
      (Phe199 and Phe312) in the motifs that are conserved among the HsdMs
      may sandwich both sides of the adenine ring of the recognition sequence
      so that a conserved Asn residue (Asn309) can interact with the N6 atom
      of the target adenine base (a methyl-group acceptor) and locate the
      target adenine base close to the transferred SAM methyl group.
AU  - Park S-Y
AU  - Lee H-J
AU  - Song J-M
AU  - Sun J
AU  - Hwang H-J
AU  - Nishi K
AU  - Kim J-S
PT  - Journal Article
TA  - Acta Crystallogr. D Biol. Crystallogr.
JT  - Acta Crystallogr. D Biol. Crystallogr.
SO  - Acta Crystallogr. D Biol. Crystallogr. 2012 68: 1570-1577.

PMID- 25091334
VI  - 5
DP  - 2014
TI  - Metabolic engineering of Corynebacterium glutamicum for L-arginine production.
PG  - 4618
AB  - L-Arginine is an important amino acid for diverse industrial and health product
      applications. Here we report the development of metabolically engineered
      Corynebacterium glutamicum ATCC 21831 for the production of L-arginine. Random
      mutagenesis is first performed to increase the tolerance of C. glutamicum to
      L-arginine analogues, followed by systems metabolic engineering for further
      strain improvement, involving removal of regulatory repressors of arginine
      operon, optimization of NADPH level, disruption of L-glutamate exporter to
      increase L-arginine precursor and flux optimization of rate-limiting L-arginine
      biosynthetic reactions. Fed-batch fermentation of the final strain in 5 l and
      large-scale 1,500 l bioreactors allows production of 92.5 and 81.2 g l(-1) of
      L-arginine with the yields of 0.40 and 0.35 g L-arginine per gram carbon source
      (glucose plus sucrose), respectively. The systems metabolic engineering strategy
      described here will be useful for engineering Corynebacteria strains for the
      industrial production of L-arginine and related products.
AU  - Park SH
AU  - Kim HU
AU  - Kim TY
AU  - Park JS
AU  - Kim SS
AU  - Lee SY
PT  - Journal Article
TA  - Nat. Commun.
JT  - Nat. Commun.
SO  - Nat. Commun. 2014 5: 4618.

PMID- 22815446
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of the Sulfur-Oxidizing Bacterium 'Candidatus Sulfurovum sediminum' AR, Which Belongs to the Epsilonproteobacteria.
PG  - 4128-4129
AB  - Sulfur-oxidizing bacteria are common microorganisms in a variety of sulfide-rich
      environments. They play important roles in the global sulfur cycle on earth.
      Here, we present a high-quality draft genome sequence of a sulfur-oxidizing
      bacterium, 'Candidatus Sulfurovum sediminum' strain AR, which belongs to the
      class Epsilonproteobacteria and dominated an enrichment culture from a marine
      sediment collected off Svalbard, within the Arctic Circle. Its genome contains
      genes for sulfur oxidation and carbon fixation. The size of the draft genome is
      2.12 Mb, and the G+C content is 39.4%.
AU  - Park SJ
AU  - Ghai R
AU  - Martin-Cuadrado AB
AU  - Rodriguez-Valera F
AU  - Jung MY
AU  - Kim JG
AU  - Rhee SK
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4128-4129.

PMID- 23209211
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of an Ammonia-Oxidizing Archaeon, 'Candidatus Nitrosopumilus sediminis' AR2, from Svalbard in the Arctic Circle.
PG  - 6948-6949
AB  - Ammonia-oxidizing archaea (AOA) typically predominate over ammonia-oxidizing bacteria in
      marine sediments. We herein present the draft genome sequence of an
      ammonia-oxidizing archaeon, 'Candidatus Nitrosopumilus sediminis' AR2, which was
      enriched in culture from a marine sediment obtained off Svalbard, within the
      Arctic Circle. The typical genes involved in archaeal ammonia oxidation and
      carbon fixation necessary for chemolithoautotrophic growth were observed.
      Interestingly, the AR2 genome sequence was revealed to possess, uniquely among
      cultivated AOA from marine environments, a capability for urea utilization.
AU  - Park SJ
AU  - Kim JG
AU  - Jung MY
AU  - Kim SJ
AU  - Cha IT
AU  - Ghai R
AU  - Martin-Cuadrado AB
AU  - Rodriguez-Valera F
AU  - Rhee SK
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6948-6949.

PMID- 23209206
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of an Ammonia-Oxidizing Archaeon, 'Candidatus Nitrosopumilus koreensis' AR1, from Marine Sediment.
PG  - 6940-6941
AB  - Ammonia-oxidizing archaea (AOA) are ubiquitous in various marine environments and play
      important roles in the global nitrogen and carbon cycles. We here present a
      high-quality draft genome sequence of an ammonia-oxidizing archaeon, 'Candidatus
      Nitrosopumilus koreensis' AR1, which was found to dominate an ammonia-oxidizing
      enrichment culture in marine sediment off Svalbard, the Arctic Circle. Despite a
      significant number of nonoverlapping genes (ca. 30%), similarities of this strain
      to 'Candidatus Nitrosopumilus maritimus' were revealed by core genes for archaeal
      ammonia oxidation and carbon fixation, G+C content, and extensive synteny
      conservation.
AU  - Park SJ
AU  - Kim JG
AU  - Jung MY
AU  - Kim SJ
AU  - Cha IT
AU  - Kwon K
AU  - Lee JH
AU  - Rhee SK
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6940-6941.

PMID- 22038973
VI  - 193
DP  - 2011
TI  - Genome Sequence of Brachybacterium squillarum M-6-3T, Isolated from Salt-Fermented Seafood.
PG  - 6416-6417
AB  - Brachybacterium squillarum M-6-3(T) was isolated from salt-fermented seafood in Korea and
      belongs to the Dermabacteraceae, a rather isolated
      family within the actinobacterial suborder Micrococcineae. Here, we
      present the draft genome sequence of the type strain Brachybacterium
      squillarum M-6-3(T) (3,191,479 bp), a Gram-positive bacterium with high
      (72.8%) G+C content.
AU  - Park SK
AU  - Roh SW
AU  - Whon TW
AU  - Bae JW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6416-6417.

PMID- 24336380
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Fusobacterium nucleatum subsp. animalis ChDC F324, Isolated from a Human Subgingival Plaque in the Republic of Korea.
PG  - e01042-13
AB  - Five subspecies of Fusobacterium nucleatum have been classified: animalis, nucleatum,
      polymorphum, vincentii, and fusiforme. F. nucleatum subsp. animalis
      ChDC F324 (KCOM 1325) was isolated from a human subgingival plaque in the
      Republic of Korea. Here, we report the draft genome sequence of the strain.
AU  - Park SN
AU  - Cho E
AU  - Kim HS
AU  - Kim DS
AU  - Jung J
AU  - Baek JH
AU  - Kyong LY
AU  - Jo E
AU  - Chang YH
AU  - Hwan SJ
AU  - Choi SH
AU  - Kang J
AU  - Choi Y
AU  - Kong SW
AU  - Han SE
AU  - Park HS
AU  - Kim H
AU  - Kook JK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01042-13.

PMID- 24336379
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Fusobacterium nucleatum subsp. nucleatum ChDC F316, Isolated from a Human Peri-implantitis Lesion in the Republic of Korea.
PG  - e01041-13
AB  - Fusobacterium nucleatum is a Gram-negative anaerobe and is one of the causative agents of
      periodontal diseases, including peri-implantitis. Fusobacterium
      nucleatum subsp. nucleatum ChDC F316 (KCOM 1322) was isolated from a human
      peri-implantitis lesion. Here, we report the draft genome sequence of this
      strain.
AU  - Park SN
AU  - Cho E
AU  - Kim HS
AU  - Kim DS
AU  - Jung J
AU  - Baek JH
AU  - Kyong LY
AU  - Jo E
AU  - Chang YH
AU  - Hwan SJ
AU  - Choi SH
AU  - Kang J
AU  - Choi Y
AU  - Park HS
AU  - Kim H
AU  - Kook JK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01041-13.

PMID- 24336378
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Fusobacterium nucleatum subsp. vincentii ChDC F8, Isolated from a Human Subgingival Plaque in the Republic of Korea.
PG  - e01040-13
AB  - Fusobacterium nucleatum is a Gram-negative, nonmotile, obligately anaerobic rod bacterium
      which might play an important role in the initiation and progression of
      periodontal diseases. F. nucleatum subsp. vincentii ChDC F8 (KCOM 1231) was
      isolated from a human gingivitis lesion. Here, we report the draft genome
      sequence of the strain.
AU  - Park SN
AU  - Cho E
AU  - Kim HS
AU  - Kim DS
AU  - Jung J
AU  - Baek JH
AU  - Kyong LY
AU  - Jo E
AU  - Chang YH
AU  - Hwan SJ
AU  - Kim J
AU  - Choi SH
AU  - Kang J
AU  - Choi Y
AU  - Park HS
AU  - Kim H
AU  - Kook JK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01040-13.

PMID- 24459284
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Fusobacterium nucleatum ChDC F145, ChDC F174, ChDC F206, and ChDC F300, Isolated from Human Subgingival Plaques in the Republic of  Korea.
PG  - e01233-13
AB  - Recently, five strains were isolated from human subgingival plaques and were proposed as a
      novel subspecies of Fusobacterium nucleatum. Here, we report the
      draft genome sequences of the strains, except one for which the draft sequence
      was already introduced.
AU  - Park SN
AU  - Cho E
AU  - Lim YK
AU  - Kim HS
AU  - Kim DS
AU  - Jung J
AU  - Baek JH
AU  - Jo E
AU  - Chang YH
AU  - Shin JH
AU  - Choi SH
AU  - Kang J
AU  - Choi Y
AU  - Park HS
AU  - Kim H
AU  - Kook JK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01233-13.

PMID- 23105064
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Fusobacterium nucleatum ChDC F128, Isolated from a Periodontitis Lesion.
PG  - 6322-6323
AB  - Fusobacterium nucleatum is classified into five subspecies. F. nucleatum ChDC F128 was
      isolated from a periodontitis lesion and proposed as a new subspecies
      based on the comparison of the nucleotide sequences of the RNA polymerase beta
      subunit and zinc protease genes. Here, we report the draft genome sequence of the
      strain.
AU  - Park SN
AU  - Kong SW
AU  - Kim HS
AU  - Park MS
AU  - Lee JW
AU  - Cho E
AU  - Lim YK
AU  - Choi MH
AU  - Chang YH
AU  - Shin JH
AU  - Park HS
AU  - Choi SH
AU  - Kook JK
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6322-6323.

PMID- 22965077
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Fusobacterium nucleatum subsp. fusiforme ATCC 51190T.
PG  - 5445-5446
AB  - Fusobacterium nucleatum, one of the major causative bacteria of periodontitis, is classified
      into five subspecies (nucleatum, polymorphum, vincentii, animalis, and
      fusiforme) on the basis of the several phenotypic characteristics and DNA
      homology. This is the first report of the draft genome sequence of F. nucleatum
      subsp. fusiforme ATCC 51190(T).
AU  - Park SN
AU  - Kong SW
AU  - Park MS
AU  - Lee JW
AU  - Cho E
AU  - Lim YK
AU  - Choi MH
AU  - Kim HS
AU  - Chang YH
AU  - Shin JH
AU  - Park HS
AU  - Choi SH
AU  - Kook JK
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5445-5446.

PMID- 23105077
VI  - 194
DP  - 2012
TI  - Genome Sequence of Pectobacterium carotovorum subsp. carotovorum Strain PCC21, a  Pathogen Causing Soft Rot in Chinese Cabbage.
PG  - 6345-6346
AB  - Pectobacterium carotovorum is a plant-pathogenic enterobacterium responsible for  soft rot in
      various commercially important plants. Here we report the complete
      genome sequence and automatic annotation of strain PCC21.
AU  - Park TH
AU  - Choi BS
AU  - Choi AY
AU  - Choi IY
AU  - Heu S
AU  - Park BS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6345-6346.

PMID- 17180708
VI  - 34
DP  - 2007
TI  - Molecular cloning and characterization of the DNA adenine methyltransferase gene in Feldmannia sp virus.
PG  - 177-183
AB  - The genome of Feldmannia sp. virus (FsV), a marine brown alga virus, contains a putative DNA
      adenine methyltransferase (dam) gene of 1,245
      bp that encodes a polypeptide of 45.8 kDa. A BLAST search with the FsV
      dam gene showed high amino acid identity to two putative
      methyltransferase genes, ORF B29 of Feldmannia irregularis virus
      (FirrV, 54%) and ORF129 of Ectocarpus siliculosus virus (EsV, 36%); and
      a PSI BLAST search revealed similarity to the N-6-adenine
      methyltransferases (MTases) of other species. Most conserved motifs of
      beta-class MTases were observed in the FsV dam gene. However, neither
      of the highly conserved sequences in motifs I (FxGxG) or IV
      [(S/N/D)PP(Y/F/W)] perfectly matched those in the FsV dam gene. The
      highly conserved DPPY consensus sequence in motif IV was NTPW in the
      FsV dam gene, perfectly matching the sequences in ORF B29 of FirrV and
      ORF129 of EsV. Therefore, the dam genes in brown algae viruses may
      belong to a yet undiscovered group. The FsV Dam protein expressed from
      the cloned FsV dam gene methylated E. coli chromosomal DNA. This is the
      first report showing that a virus infecting marine filamentous brown
      algae encodes a functional Dam protein.
AU  - Park Y
AU  - Kim G-D
AU  - Choi T-J
PT  - Journal Article
TA  - Virus Genes
JT  - Virus Genes
SO  - Virus Genes 2007 34: 177-183.

PMID- 25359915
VI  - 2
DP  - 2014
TI  - Whole-Genome Sequence of Mycobacterium tuberculosis Korean Strain KIT87190.
PG  - e01103-14
AB  - Mycobacterium tuberculosis is a contagious agent that causes tuberculosis. A specific type
      (called the K cluster) of M. tuberculosis with 10 copies of IS6110
      in restriction fragment length polymorphism (RFLP) has been found in about 4% of
      M. tuberculosis isolates in Korea. Here, we report the complete genome sequence
      of M. tuberculosis Korean strain KIT87190 belonging to the K cluster.
AU  - Park YK
AU  - Kang H
AU  - Yoo H
AU  - Lee SH
AU  - Roh H
AU  - Kim HJ
AU  - Ryoo S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01103-14.

PMID- 27088668
VI  - 66
DP  - 2016
TI  - Dermabacter jinjuensis sp. nov., a novel species of the genus Dermabacter isolated from a clinical specimen.
PG  - 2573-2577
AB  - A Gram-stain-positive, catalase-positive, facultatively anaerobic, non-motile,
      coryneform bacterium, designated strain 32(T), was isolated from a closed pus
      sample from a patient having finger necrosis in Korea. Strain 32(T) was
      considered as representing a novel species according to its initial
      identification by matrix-assisted laser desorption/ionization-time-of-flight MS.
      Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 32(T)
      belonged to the genus Dermabacter and was closely related to Dermabacter hominis
      DSM 7083(T) (=ATCC 49369(T)) (98.34 % similarity). Optimal growth was observed at
      30-40 degrees C and pH 7. Growth occurred in the presence of 0-6 % (w/v) NaCl.
      Menaquinones MK-8, MK-7 and MK-9 were the major respiratory quinones. The major
      polar lipids were phosphatidylethanolamine, phosphatidylcholine, glycolipid and
      two unknown lipids. The major cellular fatty acids were anteiso-C17 : 0,
      anteiso-C15 : 0, iso-C16 : 0 and iso-C15 : 0. The DNA G+C content of strain 32(T)
      was 62.58 mol%, and the mean level of DNA-DNA relatedness between strain 32(T)
      and D. hominis ATCC 49369(T) was 49+/-1.6 %. Based on the phenotypic and
      genotypic characteristics, strain 32(T) is confirmed to represent a novel species
      of the genus Dermabacter, for which the name Dermabacter jinjuensis sp. nov. is
      proposed. The type strain is 32(T) (=NCCP 16133(T)=DSM 101003(T)).
AU  - Park YK
AU  - Lee KM
AU  - Lee WK
AU  - Cho MJ
AU  - Lee HS
AU  - Cho YG
AU  - Lee YC
AU  - Lee WK
AU  - Seong WK
AU  - Hwang KJ
PT  - Journal Article
TA  - Int. J. Syst. Evol. Microbiol.
JT  - Int. J. Syst. Evol. Microbiol.
SO  - Int. J. Syst. Evol. Microbiol. 2016 66: 2573-2577.

PMID- 2854098
VI  - 73
DP  - 1988
TI  - A simple and rapid method to obtain substitution mutations in Escherichia coli:  isolation of a dam deletion/insertion mutation.
PG  - 531-535
AB  - We describe the isolation of a strain of Escherichia coli bearing a deletion/insertion (i.e.,
      a substitution mutation) in the dam gene (dam-16). The mutagenesis protocol used should be
      applicable to any cloned non-essential gene of E. coli. The substitution mutation confers
      resistance to kanamycin and can easily be transferred to other strains by standard genetic
      techniques. The amount of Dam methyltransferase (MTase) in dam-16 strains as determined either
      in vitro or in vivo is below the level of detection. We conclude that the Dam MTase is not
      required for viability of E. coli.
AU  - Parker B
AU  - Marinus MG
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 73: 531-535.

PMID- 24233585
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Thompson  Strain RM6836.
PG  - e00900-13
AB  - Salmonella enterica subsp. enterica serovar Thompson strain RM6836 was isolated from lettuce
      in 2002. We report here the complete sequence and annotation of the
      genome of S. Thompson RM6836. This is the first reported complete genome sequence
      for S. Thompson and it will enhance our understanding of this serovar and provide
      another point for comparative studies between Salmonella enterica strains.
AU  - Parker CT
AU  - Gorski L
AU  - Huynh S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00900-13.

PMID- 26586897
VI  - 3
DP  - 2015
TI  - Complete Genome Sequences of Two Outbreak Strains of Salmonella enterica subsp. enterica Serovar Thompson Associated with Cilantro.
PG  - e01365-15
AB  - Salmonella enterica subsp. enterica serovar Thompson strains RM1984 (CADPH-99A2334) and RM1986
      (CADPH-99A2345) are associated with a 1999 outbreak in
      contaminated cilantro. We report here the complete genome sequences and
      annotation of these two S. Thompson strains. These genomes are distinct and
      provide additional data for our understanding of S. enterica.
AU  - Parker CT
AU  - Huynh S
AU  - Gorski L
AU  - Cooper KK
AU  - Miller WG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01365-15.

PMID- 28232429
VI  - 5
DP  - 2017
TI  - Genomic Sequence of Campylobacter jejuni subsp. jejuni HS:19 Penner Serotype Reference Strain RM3420.
PG  - e01701-16
AB  - Campylobacter jejuni subsp. jejuni infections are a leading cause of foodborne gastroenteritis
      and the most prevalent antecedent to Guillain-Barre syndrome
      (GBS). Penner serotype HS:19 is among several capsular types shown to be markers
      for GBS. This study describes the genome of C. jejuni subsp. jejuni HS:19 Penner
      reference strain RM3420.
AU  - Parker CT
AU  - Huynh S
AU  - Heikema AP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01701-16.

PMID- 27795263
VI  - 4
DP  - 2016
TI  - Complete Genomic Sequence of Campylobacter jejuni subsp. jejuni HS:19 Strain RM1285 Isolated from Packaged Chicken.
PG  - e01100-16
AB  - Poultry products serve as the main source of Campylobacter jejuni subsp. jejuni infections in
      humans. C. jejuni subsp. jejuni infections are a leading cause of
      foodborne gastroenteritis and are a prevalent antecedent to Guillain-Barre
      syndrome. This study describes the genome of C. jejuni subsp. jejuni HS:19 strain
      RM1285, isolated from packaged chicken in California.
AU  - Parker CT
AU  - Huynh S
AU  - Heikema AP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01100-16.

PMID- 26543130
VI  - 3
DP  - 2015
TI  - Complete Genome Sequences of Campylobacter jejuni Strains RM3196 (233.94) and RM3197 (308.95) Isolated from Patients with Guillain-Barre Syndrome.
PG  - e01312-15
AB  - Infections with Campylobacter jejuni subsp. jejuni are a leading cause of foodborne
      gastroenteritis and the most prevalent infection preceding
      Guillain-Barre syndrome (GBS). This study describes the genomes of C. jejuni
      subsp. jejuni HS:41 strains RM3196 (233.94) and RM3197 (308.95) that were
      isolated from patients with GBS in Cape Town, South Africa.
AU  - Parker CT
AU  - Huynh S
AU  - Heikema AP
AU  - Cooper KK
AU  - Miller WG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01312-15.

PMID- 24723721
VI  - 2
DP  - 2014
TI  - Genome Sequence of Bacterial Interference Strain Staphylococcus aureus 502A.
PG  - e00284-14
AB  - Staphylococcus aureus 502A was a strain used in bacterial interference programs
      during the 1960s and early 1970s. Infants were deliberately colonized with 502A
      with the goal of preventing colonization with more invasive strains. We present
      the completed genome sequence of this organism.
AU  - Parker D
AU  - Narechania A
AU  - Sebra R
AU  - Deikus G
AU  - Larussa S
AU  - Ryan C
AU  - Smith H
AU  - Prince A
AU  - Mathema B
AU  - Ratner AJ
AU  - Kreiswirth B
AU  - Planet PJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00284-14.

PMID- 10581262
VI  - 153
DP  - 1999
TI  - Intron homing with limited exon homology. Illegitimate double-strand-break repair in intron acquisition by phage t4.
PG  - 1513-1523
AB  - The td intron of bacteriophage T4 encodes a DNA endonuclease that initiates intron homing to
      cognate intronless alleles by a double-strand-break (DSB) repair process. A genetic assay was
      developed to analyze the relationship between exon homology and homing efficiency. Because
      models predict exonucleolytic processing of the cleaved recipient leading to homologous strand
      invasion of the donor allele, the assay was performed in wild-type and exonuclease-deficient
      (rnh or dexA) phage. Efficient homing was supported by exon lengths of 50 bp or greater,
      whereas more limited exon lengths led to a precipitous decline in homing levels. However,
      extensive homology in one exon still supported elevated homing levels when the other exon was
      completely absent. Analysis of these "one-sided" events revealed recombination junctions at
      ectopic sites of microhomology and implicated nucleolytic degradation in illegitimate DSB
      repair in T4. Interestingly, homing efficiency with extremely limiting exon homology was
      greatly elevated in phage deficient in the 3'-5' exonuclease, DexA, suggesting that the
      length of 3' tails is a major determinant of the efficiency of DSB repair. Together, these
      results suggest that illegitimate DSB repair may provide a means by which introns can invade
      ectopic sites.
AU  - Parker MM
AU  - Belisle M
AU  - Belfort M
PT  - Journal Article
TA  - Genetics
JT  - Genetics
SO  - Genetics 1999 153: 1513-1523.

PMID- 10688204
VI  - 403
DP  - 2000
TI  - The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences.
PG  - 665-668
AB  - Campylobacter jejuni, from the delta-epsilon group of proteobacteria, is a microaerophilic,
      Gram-negative, flagellate, spiral bacterium-properties it shares with the related gastric
      pathogen Helicobacter pylori.  It is the leading cause of bacterial food-borne diarrhoeal
      disease throughout the world.  In addition, infection with C. jejuni is the most frequent
      antecedent to a form of neuromuscular paralysis known as Guillain-Barre syndrome.  Here we
      report the genome sequence of C. jejuni NCTC11168.  C. jejuni has a circular chromosome of
      1,641,481 base pairs (30.6% G+C) which is predicted to encode 1,654 proteins and 54 stable RNA
      species.  The genome is unusual in that there are virtually no insertion sequences or
      phage-associated sequences and very few repeat sequences.  One of the most striking findings
      in the genome was the presence of hypervariable sequences.  These short homopolymeric runs of
      nucleotides were commonly found in genes encoding the biosynthesis or modification of surface
      structures, or in closely linked genes of unknown function.  The apparently high rate of
      variation of these homopolymeric tracts may be important in the survival strategy of C.
      jejuni.
AU  - Parkhill J et al
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2000 403: 665-668.

PMID- 11586360
VI  - 413
DP  - 2001
TI  - Genome sequence of Yersinia pestis, the causative agent of plague.
PG  - 523-527
AB  - The Gram-negative bacterium Yersinia pestis is the causative agent of the systemic invasive
      infectious disease classically referred to as plague, and has been responsible for three human
      pandemics: the Justinian plague (sixth to eighth centuries), the Black Death (fourteenth to
      nineteenth centuries) and modern plague (nineteenth century to the present day). The recent
      identification of strains resistant to multiple drugs and the potential use of Y. pestis as an
      agent of biological warfare mean that plague still poses a threat to human health. Here we
      report the complete genome sequence of Y. pestis strain CO92, consisting of a 4.65-megabase
      (Mb) chromosome and three plasmids of 96.2 kilobases (kb), 70.3 kb and 9.6 kb. The genome is
      unusually rich in insertion sequences and displays anomalies in GC base-composition bias,
      indicating frequent intragenomic recombination. Many genes seem to have been acquired from
      other bacteria and viruses (including adhesins, secretion systems and insecticidal toxins).
      The genome contains around 150 pseudogenes, many of which are remnants of a redundant
      enteropathogenic lifestyle. The evidence of ongoing genome fluidity, expansion and decay
      suggests Y. pestis is a pathogen that has undergone large-scale genetic flux and provides a
      unique insight into the ways in which new and highly virulent pathogens evolve.
AU  - Parkhill J et al
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2001 413: 523-527.

PMID- 10761919
VI  - 404
DP  - 2000
TI  - Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491.
PG  - 502-506
AB  - Neisseria meningitidis causes bacterial meningitis and is therefore responsible for
      considerable morbidity and mortality in both the developed and the developing world.
      Meningococci are opportunistic pathogens that colonize the nasopharynges and oropharynges of
      asymptomatic carriers. For reasons that are still mostly unknown, they occasionally gain
      access to the blood, and subsequently to the cerebrospinal fluid, to cause septicaemia and
      meningitis. N. meningitidis strains are divided into a number of serogroups on the basis of
      the immunochemistry of their capsular polysaccharides; serogroup A strains are responsible for
      major epidemics and pandemics of meningococcal disease, and therefore most of the morbidity
      and mortality associated with this disease. Here we have determined the complete genome
      sequence of a serogroup A strain of Neisseria meningitidis, Z2491. The sequence is 2,184,406
      base pairs in length, with an overall G+C content of 51.8%, and contains 2,121 predicted
      coding sequences. The most notable feature of the genome is the presence of many hundreds of
      repetitive elements, ranging from short repeats, positioned either singly or in large multiple
      arrays, to insertion sequences and gene duplications of one kilobase or more. Many of these
      repeats appear to be involved in genome fluidity and antigenic variation in this important
      human pathogen.
AU  - Parkhill J et al
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2000 404: 502-506.

PMID- 11677608
VI  - 413
DP  - 2001
TI  - Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18.
PG  - 848-852
AB  - Salmonella enterica serovar Typhi (S. typhi) is the aetiological agent of typhoid fever, a
      serious invasive bacterial disease of humans with an annual global burden of approximately 16
      million cases, leading to 600,000 fatalities. Many S. enterica serovars actively invade the
      mucosal surface of the intestine but are normally contained in healthy individuals by the
      local immune defence mechanisms. However, S. typhi has evolved the ability to spread to the
      deeper tissues of humans, including liver, spleen and bone marrow. Here we have sequenced the
      4,809,037-base pair (bp) genome of a S. typhi (CT18) that is resistant to multiple drugs,
      revealing the presence of hundreds of insertions and deletions compared with the Escherichia
      coli genome, ranging in size from single genes to large islands. Notably, the genome sequence
      identifies over two hundred pseudogenes, several corresponding to genes that are known to
      contribute to virulence in Salmonella typhimurium. This genetic degradation may contribute to
      the human-restricted host range for S. typhi. CT18 harbours a 218,150-bp
      multiple-drug-resistance incH1 plasmid (pHCM1), and a 106,516-bp cryptic plasmid (pHCM2),
      which shows recent common ancestry with a virulence plasmid of Yersinia pestis.
AU  - Parkhill J et al
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2001 413: 848-852.

PMID- 27151790
VI  - 4
DP  - 2016
TI  - Draft Genome of Shewanella frigidimarina Ag06-30, a Marine Bacterium Isolated from Potter Peninsula, King George Island, Antarctica.
PG  - e00289-16
AB  - We present the draft genome of Shewanella frigidimarina Ag06-30, a marine bacterium from King
      George Island, Antarctica, which encodes the carbapenemase
      SFP-1. The assembly contains 4,799,218 bp (G+C content 41.24%). This strain
      harbors several mobile genetic elements that provide insight into lateral gene
      transfer and bacterial plasticity and evolution.
AU  - Parmeciano DiNG
AU  - Vazquez SC
AU  - MacCormack WP
AU  - Iriarte A
AU  - Quiroga C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00289-16.

PMID- 1312486
VI  - 300
DP  - 1992
TI  - Detection of elsamicin-DNA binding specificity by restriction enzyme cleavage.
PG  - 25-29
AB  - The sequence specificity of elsamicin A, an anti-tumour antibotic, binding to
      DNA was elucidated considering the inhibition of the rate of digestion of
      linearised pBR322 DNA by AatII, ClaI, EcoRI, HindIII and NruI restriction
      enzymes.  Elsamicin A inhibits the rate of digestion by NruI (recognition
      sequence TCG/CGA) to a greater extent than it does for the other enzymes, thus
      evidencing the sequence-selective binding of elsamicin to CGC regions in DNA.
      Our results also show the important role of the neighbouring sequences in the
      elsamicin A-DNA interactions and their effects on the cleavage by restriction
      enzymes.
AU  - Parraga A
AU  - Portugal J
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1992 300: 25-29.

PMID- 23189158
VI  - 7
DP  - 2012
TI  - Sequence of Two Plasmids from Clostridium perfringens Chicken Necrotic Enteritis Isolates and Comparison with C. perfringens Conjugative Plasmids.
PG  - E49753
AB  - Twenty-six isolates of Clostridium perfringens of different MLST types from
      chickens with necrotic enteritis (NE) (15 netB-positive) or from healthy chickens
      (6 netB-positive, 5 netB-negative) were found to contain 1-4 large plasmids, with
      most netB-positive isolates containing 3 large and variably sized plasmids which
      were more numerous and larger than plasmids in netB-negative isolates. NetB and
      cpb2 were found on different plasmids consistent with previous studies. The
      pathogenicity locus NELoc1, which includes netB, was largely conserved in these
      plasmids whereas NeLoc3, present in the cpb2 containing plasmids, was less well
      conserved. A netB-positive and a cpb2-positive plasmid were likely to be
      conjugative, and the plasmids were completely sequenced. Both plasmids possessed
      the intact tcp conjugative region characteristic of C. perfringens conjugative
      plasmids. Comparative genomic analysis of nine CpCPs, including the two plasmids
      described here, showed extensive gene rearrangements including pathogenicity
      locus and accessory gene insertions around rather than within the backbone
      region. The pattern that emerges from this analysis is that the major
      toxin-containing regions of the variety of virulence-associated CpCPs are
      organized as complex pathogenicity loci. How these different but related CpCPs
      can co-exist in the same host has been an unanswered question. Analysis of the
      replication-partition region of these plasmids suggests that this region controls
      plasmid incompatibility, and that CpCPs can be grouped into at least four
      incompatibility groups.
AU  - Parreira VR
AU  - Costa M
AU  - Eikmeyer F
AU  - Blom J
AU  - Prescott JF
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2012 7: E49753.

PMID- 17222143
VI  - 9
DP  - 2007
TI  - Analysis of environmental transcriptomes by DNA microarrays.
PG  - 453-464
AB  - In this work we investigated the correlations between global gene expression patterns and
      environmental parameters in natural ecosystems. We
      studied the preferential gene expression of the iron oxidizer bacterium
      Leptospirillum ferrooxidans to adapt its physiology to changes in the
      physicochemical parameters in its natural medium. Transcriptome analysis
      by DNA microarrays can proportionate an instant picture about the
      preferential gene expression between two different environmental samples.
      However, this type of analysis is very difficult and complex in natural
      ecosystems, mainly because of the broad biodiversity and multiple
      environmental parameters that may affect gene expression. The necessity of
      high-quality RNA preparations as well as complicated data analysis are
      also technological limitations. The low prokaryotic diversity of the
      extremely acidic and iron-rich waters of the Tinto River (Spain)
      ecosystem, where L. ferrooxidans is abundant, allows the opportunity to
      achieve global gene expression studies and to associate gene function with
      environmental parameters. We applied a total RNA amplification protocol
      validated previously for the amplification of the environmental
      transcriptome (meta-transcriptome). The meta-transcriptome of two sites
      from the Tinto River mainly differing in the salt and oxygen contents were
      amplified and analysed by a L. ferrooxidans DNA microarray. The results
      showed a clear preferential induction of genes involved in certain
      physicochemical parameters like: high salinity (ectAB, otsAB), low oxygen
      concentration (cydAB), iron uptake (fecA-exbBD-tonB), oxidative stress
      (carotenoid synthesis, oxyR, recG), potassium (kdpBAC) or phosphate
      concentrations (pstSCAB), etc. We conclude that specific gene expression
      patterns can be useful indicators for the physiological conditions in a
      defined ecosystem. Also, the upregulation of certain genes and operons
      reveals information about the environmental conditions (nutrient
      limitations, stresses, etc.).
AU  - Parro V
AU  - Moreno-Paz M
AU  - Gonzalez-Toril E
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2007 9: 453-464.

PMID- 12927537
VI  - 331
DP  - 2003
TI  - DNA Recognition by the EcoRV Restriction Endonuclease Probed using Base Analogues.
PG  - 1005-1016
AB  - The EcoRV restriction endonuclease recognises palindromic GATATC sequences and cuts between
      the central T and dA bases in a reaction that has an
      absolute requirement for a divalent metal ion, physiologically Mg(2+). Use
      has been made of base analogues, which delete hydrogen bonds between the
      protein and DNA (or hydrophobic interactions in the case of the 5-CH(3)
      group of thymine), to evaluate the roles of the outer two base-pairs
      (GATATC) in DNA recognition. Selectivity arises at both the binding steps
      leading to the formation of the enzyme-DNA-metal ion ternary complex
      (assayed by measuring the dissociation constant in the presence of the
      non-reactive metal Ca(2+)) and the catalytic step (evaluated using
      single-turnover hydrolysis in the presence of Mg(2+)), with each
      protein-DNA contact contributing to recognition. With the A:T base-pair,
      binding was reduced by the amount expected for the simple loss of a single
      contact; much more severe effects were observed with the G:C base-pair,
      suggesting additional conformational perturbation. Most of the modified
      bases lowered the rate of hydrolysis; furthermore, the presence of an
      analogue in one strand of the duplex diminished cutting at the second,
      unmodified strand, indicative of communication between DNA binding and the
      active site. The essential metal ion Mg(2+) plays a key role in mediating
      interactions between the DNA binding site and active centre and in many
      instances rescue of hydrolysis was seen with Mn(2+). It is suggested that
      contacts between the GATATC site are required for tight binding and for
      the correct assembly of metal ions and bound water at the catalytic site,
      functions important in providing acid/base catalysis and transition state
      stabilisation.
AU  - Parry D
AU  - Moon SA
AU  - Liu HH
AU  - Heslop P
AU  - Connolly BA
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2003 331: 1005-1016.

PMID- 22461556
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Oceanimonas sp. GK1, a Halotolerant Bacterium from Gavkhouni Wetland in Iran.
PG  - 2123-2124
AB  - Oceanimonas sp. GK1 (IBRC-M 10197) is a marine halotolerant gammaproteobacterium  which was
      characterized as producing large amounts of poly-beta-hydroxybutyrate.
      Here we present the whole-genome sequence of Oceanimonas sp. GK1, which consists
      of a single circular chromosome of 3,514,537 bp and two plasmids 8,462 and 4,245
      bp in length.
AU  - Parsa YL
AU  - Azarbaijani R
AU  - Sarikhan S
AU  - Mousavi H
AU  - Ramezani M
AU  - Amoozegar MA
AU  - Shahzadeh FA
AU  - Salekdeh GH
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2123-2124.

PMID- 12730200
VI  - 278
DP  - 2003
TI  - Gene cluster of Arthrobacter ilicis Ru61a involved in the degradation of quinaldine to anthranilate: characterization and functional expression of the quinaldine 4-oxidase qoxLMS genes.
PG  - 27483-27494
AB  - A genetic analysis of the anthranilate pathway of quinaldine degradation was
      performed. A 23-kb region of DNA from Arthrobacter ilicis Ru61a was cloned into
      the cosmid pVK100. Although Escherichia coli clones containing the recombinant
      cosmid did not transform quinaldine, cosmids harboring the 23-kb region, or a
      10.8-kb stretch of this region, conferred to Pseudomonas putida KT2440 the
      ability to cometabolically convert quinaldine to anthranilate. The 10.8-kb
      fragment thus contains the genes coding for quinaldine 4-oxidase (Qox),
      1H-4-oxoquinaldine 3-monooxygenase, 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase,
      and N-acetylanthranilate amidase. The qoxLMS genes coding for the molybdopterin
      cytosine dinucleotide-(MCD-), FeSI-, FeSII-, and FAD-containing Qox were inserted
      into the expression vector pJB653, generating pKP1. Qox is the first
      MCD-containing enzyme to be synthesized in a catalytically fully competent form
      by a heterologous host, P. putida KT2440 pKP1; the catalytic properties and the
      UV-visible and EPR spectra of Qox purified from P. putida KT2440 pKP1 were
      essentially like those of wild-type Qox. This provides a starting point for the
      construction of protein variants of Qox by site-directed mutagenesis. Downstream
      of the qoxLMS genes, a putative gene whose deduced amino acid sequence showed 37%
      similarity to the cofactor-inserting chaperone XdhC was located. Additional open
      reading frames identified on the 23-kb segment may encode further enzymes (a
      glutamyl tRNA synthetase, an esterase, two short-chain dehydrogenases/reductases,
      an ATPase belonging to the AAA family, a 2-hydroxyhepta-2,4-diene-1,7-dioate
      isomerase/5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase-like protein, and an
      enzyme of the mandelate racemase group) and hypothetical proteins involved in
      transcriptional regulation, and metabolite transport.
AU  - Parschat K
AU  - Hauer B
AU  - Kappl R
AU  - Kraft R
AU  - Huttermann J
AU  - Fetzner S
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2003 278: 27483-27494.

PMID- 17337569
VI  - 189
DP  - 2007
TI  - Complete Nucleotide Sequence of the 113-Kilobase Linear Catabolic Plasmid pAL1 of Arthrobacter nitroguajacolicus Ru61a and Transcriptional Analysis of Genes Involved in Quinaldine Degradation.
PG  - 3855-3867
AB  - The nucleotide sequence of the linear catabolic plasmid pAL1 from the 2-methylquinoline
      (quinaldine)-degrading strain Arthrobacter nitroguajacolicus Ru61a comprises 112,992 bp. A
      total of 103 open reading frames (ORFs) were identified on pAL1, 49 of which had no
      annotatable function. The ORFs were assigned to the following functional groups: (i)
      catabolism of quinaldine and anthranilate, (ii) conjugation, and (iii) plasmid maintenance and
      DNA replication and repair. The genes for conversion of quinaldine to anthranilate are
      organized in two operons that include ORFs presumed to code for proteins involved in assembly
      of the quinaldine-4-oxidase holoenzyme, namely, a MobA-like putative molybdopterin cytosine
      dinucleotide synthase and an XdhC-like protein that could be required for insertion of the
      molybdenum cofactor. Genes possibly coding for enzymes involved in anthranilate degradation
      via 2-aminobenzoyl coenzyme A form another operon. These operons were expressed when cells
      were grown on quinaldine or on aromatic compounds downstream in the catabolic pathway.
      Single-stranded 3' overhangs of putative replication intermediates of pAL1 were predicted to
      form elaborate secondary structures due to palindromic and superpalindromic terminal
      sequences; however, the two telomeres appear to form different structures. Sequence analysis
      of ORFs 101 to 103 suggested that pAL1 codes for one or two putative terminal proteins,
      presumed to be covalently bound to the 5' termini, and a multidomain telomere-associated
      protein (Tap) comprising 1,707 amino acids. Even if the putative proteins encoded by ORFs 101
      to 103 share motifs with the Tap and terminal proteins involved in telomere patching of
      Streptomyces linear replicons, their overall sequences and domain structures differ
      significantly.
AU  - Parschat K
AU  - Overhage J
AU  - Strittmatter AW
AU  - Henne A
AU  - Gottschalk G
AU  - Fetzner S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2007 189: 3855-3867.

PMID- 28175269
VI  - 9
DP  - 2017
TI  - Genome-Guided Insights Reveal Organophosphate-Degrading Brevundimonas diminuta as Sphingopyxis wildii and Define Its Versatile Metabolic Capabilities and Environmental Adaptations.
PG  - 77-81
AB  - The complete genome sequence of Brevundimonas diminuta represented a chromosome (
      approximately 4.15 Mb) and two plasmids (pCMS1 and pCMS2) with sizes of 65,908
      and 30,654 bp, respectively. The sequence of the genome showed no significant
      similarity with the known bacterial genome sequences, instead showed weak
      similarity with the members of different genera of family, Sphingomonadaceae.
      Contradicting existing taxonomic position, the core genome-guided phylogenetic
      tree placed B. diminuta in the genus Sphingopyxis and showed sufficient
      genome-to-genome distance warranting a new species name. Reflecting the strains
      ability to grow in harsh environments, the genome-contained genetic repertoire
      required for mineralization of several recalcitrant man-made aromatic compounds.
AU  - Parthasarathy S
AU  - Azam S
AU  - Lakshman-Sagar A
AU  - Narasimha-Rao V
AU  - Gudla R
AU  - Parapatla H
AU  - Yakkala H
AU  - Ghanta-Vemuri S
AU  - Siddavattam D
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2017 9: 77-81.

PMID- 22926566
VI  - 56
DP  - 2012
TI  - pEl1573 carrying blaIMP-4 from Sydney, Australia, is closely related to other IncL/M plasmids.
PG  - 6029-6032
AB  - Complete sequencing of pEl1573, a representative IncL/M plasmid carrying blaIMP-4 from Sydney,
      Australia, revealed a ~60 kb backbone almost identical to those of IncL/M plasmids
      pCTX-M3,from Poland, and pCTX-M360, from China, and less closely related to pNDM-HK, pOXA-48a
      and pEL60, suggesting different lineages. The ~28 kb Tn2-derived multiresistance region in
      pEl1573 is inserted in the same location as those in pCTX-M3 and pNDM-HK and shares some of
      the same components, but has undergone rearrangements.
AU  - Partridge SR
AU  - Ginn AN
AU  - Paulsen IT
AU  - Iredell JR
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2012 56: 6029-6032.

PMID- 21859935
VI  - 55
DP  - 2011
TI  - Recombination in IS26 and Tn2 in the Evolution of Multiresistance Regions Carrying blaCTX-M-15 on Conjugative IncF Plasmids from Escherichia coli.
PG  - 4971-4978
AB  - CTX-M-15 now appears to be the dominant extended-spectrum beta-lactamase
      worldwide, and a number of different factors may contribute to this
      success. These include associations between bla(CTX-M-15) and particular
      plasmids (IncF) and/or strains, such as Escherichia coli ST131, as well as
      the genetic contexts in which this gene is found. We previously identified
      bla(CTX-M-15) as the dominant ESBL gene in the western Sydney area,
      Australia, and found that it was carried mainly on IncF or IncI1 plasmids.
      Here, we have mapped the multiresistance regions of the 11 conjugative
      plasmids with one or more IncF replicons obtained from that survey and
      conducted a limited comparison of plasmid backbones. Two plasmids with
      only an IncFII replicon appear to be very similar to the published
      plasmids pC15-1a and pEK516. The remaining nine plasmids, with multiple
      IncF replicons, have multiresistance regions related to those of pC15-1a
      and pEK516, but eight contain additional modules previously found in
      resistance plasmids from different geographic locations that carry a
      variety of different resistance genes. Differences between the
      multiresistance regions are largely due to IS26-mediated deletions,
      insertions, and/or rearrangements, which can explain the observed variable
      associations between bla(CTX-M-15) and certain other resistance genes. We
      found no evidence of independent movement of bla(CTX-M-15) or of a large
      multiresistance region between different plasmid backbones. Instead,
      homologous recombination between common components, such as IS26 and Tn2,
      appeared to be more important in creating new multiresistance regions, and
      this may be coupled with recombination in plasmid backbones to reassort
      multiple IncF replicons as well as components of multiresistance regions.
AU  - Partridge SR
AU  - Zong Z
AU  - Iredell JR
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2011 55: 4971-4978.

PMID- 28774966
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Citrobacter freundii Myophage Mijalis.
PG  - e00228-17
AB  - Citrobacter freundii is responsible for various opportunistic nosocomial infections. Phage
      therapies against C. freundii may prove useful in human
      medicine for treatment of infections caused by the ubiquitous bacteria. Here, we
      announce the complete genome sequence of the C. freundii Felix O1-like myophage
      Mijalis and present its features.
AU  - Parvataneni S
AU  - Mijalis EM
AU  - Kuty EGF
AU  - Rasche ES
AU  - Liu M
AU  - Gill JJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00228-17.

PMID- 7591067
VI  - 63
DP  - 1995
TI  - Host restriction phenotypes of Salmonella typhi and Salmonella gallinarum.
PG  - 4329-4335
AB  - Salmonella typhi and Salmonella gallinarum phenotypes correlated with mouse host restriction
      have been identified by using in vitro and in vivo systems. S. typhi is capable of entering
      the murine intestinal epithelium via M cells, as is Salmonella typhimurium, which causes
      systemic infection in the mouse.  But, unlike S. typhimurium, S. typhi does not destroy the
      epithelium and is cleared from the Peyer's patches soon after M-cell entry, S. gallinarum
      appears to be incapable of entering the murine Peyer's patch epithelium.  Our in vitro
      evidence suggests that S. gallinarum is taken up in murine phagocytic cells by a mechanism
      different from that of S. typhimurium.  S. typhimurium is taken up at a higher frequency and
      is maintained at higher viable counts throughout a 24-h time course in a murine
      macrophage-like cell line than are S. gallinarum and S. typhi.
AU  - Pascopella L
AU  - Raupach B
AU  - Ghori N
AU  - Monack D
AU  - Falkow S
AU  - Small PLC
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 1995 63: 4329-4335.

PMID- 26337875
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Pseudomonas putida JLR11, a Facultative Anaerobic 2,4,6-Trinitrotoluene Biotransforming Bacterium.
PG  - e00904-15
AB  - We report the draft genome sequence of Pseudomonas putida JLR11, a facultative anaerobic
      bacterium that has been studied in detail for its capacity to use the explosive
      2,4,6-trinitrotoluene (TNT) as a nitrogen source. The sequence confirms the mechanisms used by
      this versatile strain to reduce and assimilate nitrogen from TNT.
AU  - Pascual J
AU  - Udaondo Z
AU  - Molina L
AU  - Segura A
AU  - Esteve-Nunez A
AU  - Caballero A
AU  - Duque E
AU  - Ramos JL
AU  - van Dillewijn P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00904-15.

PMID- 2990125
VI  - 4
DP  - 1985
TI  - Search for DNA host specificity system in Salmonella typhi.
PG  - 3-6
AB  - Seventeen pure lines of S. typhi bacteriophages have been obtained from mother races O and Vi;
      of these, three were used to study 152 S. typhi strains with a view to detecting their DNA
      host specificity systems.  10 S. typhi strains having the DNA host specificity system have
      been detected by the rough determination of the lytic spectrum and the cross titration of
      phage Vi IX.
AU  - Pashenkov AL
AU  - Nikolskaya II
AU  - Nigmatullin TG
AU  - Debov SS
PT  - Journal Article
TA  - Zh. Mikrobiol. Epidemiol. Immunobiol.
JT  - Zh. Mikrobiol. Epidemiol. Immunobiol.
SO  - Zh. Mikrobiol. Epidemiol. Immunobiol. 1985 4: 3-6.

PMID- 29519833
VI  - 6
DP  - 2018
TI  - Genome Sequence of Enterococcus faecium Strain ICIS 96 Demonstrating Intermicrobial Antagonism Associated with Bacteriocin Production.
PG  - e00126-18
AB  - We report here the complete genome sequence of Enterococcus faecium strain ICIS 96, which was
      isolated from the feces of a horse. Bacteriological
      characterization of strain ICIS 96 revealed the absence of pathogenicity factors,
      while its spectrum of antagonistic activity was found to be broad, having
      activities associated with both Gram-positive and Gram-negative bacteria.
      Analysis of the E. faecium ICIS 96 genome revealed five genes associated with
      antimicrobial activity (enterocin [ent] A, ent B, lactobin A/cerein 7b, and ent
      L50 A/B). No genes that correlate with human pathogenicity were identified.
AU  - Pashkova TM
AU  - Vasilchenko AS
AU  - Khlopko YA
AU  - Kochkina EE
AU  - Kartashova OL
AU  - Sycheva MV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00126-18.

PMID- 25428963
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Leuconostoc citreum Strain NRRL B-742.
PG  - e01179-14
AB  - Leuconostoc citreum belongs to the group of lactic acid bacteria and plays an important role
      in fermented foods of plant origin. Here, we report the complete
      genome of the Leuconostoc citreum strain NRRL B-742, isolated in 1954 for its
      capacity to produce dextran.
AU  - Passerini D
AU  - Vuillemin M
AU  - Laguerre S
AU  - Amari M
AU  - Loux V
AU  - Gabriel V
AU  - Robert H
AU  - Morel S
AU  - Monsan P
AU  - Gabriel B
AU  - Fontagne-Faucher C
AU  - Remaud-Simeon M
AU  - Moulis C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01179-14.

PMID- 23661482
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Erwinia toletana, a Bacterium Associated with Olive Knots Caused by Pseudomonas savastanoi pv. Savastanoi.
PG  - e00205-13
AB  - Erwinia toletana was first reported in 2004 as a bacterial species isolated from  olive knots
      caused by the plant bacterium Pseudomonas savastanoi pv. savastanoi.
      Recent studies have shown that the presence of this bacterium in the olive knot
      environment increases the virulence of the disease, indicating possible
      interspecies interactions with P. savastanoi pv. savastanoi. Here, we report the first draft
      genome sequence of an E. toletana strain.
AU  - Passos-da-Silva D
AU  - Devescovi G
AU  - Paszkiewicz K
AU  - Moretti C
AU  - Buonaurio R
AU  - Studholme DJ
AU  - Venturi V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00205-13.

PMID- 23190728
VI  - 7
DP  - 2013
TI  - By their genes ye shall know them: genomic signatures of predatory bacteria.
PG  - 756-769
AB  - Predatory bacteria are taxonomically disparate, exhibit diverse predatory
      strategies and are widely distributed in varied environments. To date, their
      predatory phenotypes cannot be discerned in genome sequence data thereby limiting
      our understanding of bacterial predation, and of its impact in nature. Here, we
      define the 'predatome,' that is, sets of protein families that reflect the
      phenotypes of predatory bacteria. The proteomes of all sequenced 11 predatory
      bacteria, including two de novo sequenced genomes, and 19 non-predatory bacteria
      from across the phylogenetic and ecological landscapes were compared. Protein
      families discriminating between the two groups were identified and quantified,
      demonstrating that differences in the proteomes of predatory and non-predatory
      bacteria are large and significant. This analysis allows predictions to be made,
      as we show by confirming from genome data an over-looked bacterial predator. The
      predatome exhibits deficiencies in riboflavin and amino acids biosynthesis,
      suggesting that predators obtain them from their prey. In contrast, these genomes
      are highly enriched in adhesins, proteases and particular metabolic proteins,
      used for binding to, processing and consuming prey, respectively. Strikingly,
      predators and non-predators differ in isoprenoid biosynthesis: predators use the
      mevalonate pathway, whereas non-predators, like almost all bacteria, use the DOXP
      pathway. By defining predatory signatures in bacterial genomes, the predatory
      potential they encode can be uncovered, filling an essential gap for measuring
      bacterial predation in nature. Moreover, we suggest that full-genome proteomic
      comparisons are applicable to other ecological interactions between microbes, and
      provide a convenient and rational tool for the functional classification of
      bacteria.
AU  - Pasternak Z
AU  - Pietrokovski S
AU  - Rotem O
AU  - Gophna U
AU  - Lurie-Weinberger MN
AU  - Jurkevitch E
PT  - Journal Article
TA  - ISME J.
JT  - ISME J.
SO  - ISME J. 2013 7: 756-769.

PMID- 24786951
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Fervidicella metallireducens Strain AeBT, an Iron-Reducing Thermoanaerobe from the Great Artesian Basin.
PG  - e00345-14
AB  - The genome sequence of Fervidicella metallireducens strain AeB(T), a curved, heterotrophic,
      thermoanaerobic, and iron-reducing bacterium isolated from a gray
      microbial mat colonizing the free-flowing waters of a Great Artesian Basin (GAB)
      bore well located in outback Queensland, Australia, is reported here. The
      analysis of the 2.9-Mb sequence indicates that the attributes of the genome are
      consistent with its physiological and phenotypic traits.
AU  - Patel BK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00345-14.

PMID- 25676761
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Anoxybacillus Strain BCO1, Isolated from a Thermophilic  Microbial Mat Colonizing the Outflow of a Bore Well of the Great Artesian Basin  of Australia.
PG  - e01547-14
AB  - Anoxybacillus strain BCO1, isolated from a thermophilic (50 degrees C) microbial  mat
      colonizing an outflow of a Great Artesian bore well of Australia, possessed a
      genome of ~2.8 Mb, with a G+C content of 41.7 mol%, and encoded 3,205 genes.
AU  - Patel BK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01547-14.

PMID- 26847908
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Caloramator mitchellensis, a Thermoanaerobe Isolated from the Waters of the Great Artesian Basin.
PG  - e01578-15
AB  - The genome sequence of Caloramator mitchellensis strain VF08, a rod-shaped, heterotrophic,
      strictly anaerobic bacterium isolated from the free-flowing waters
      of a Great Artesian Basin (GAB) bore well located in Mitchell, an outback
      Queensland town in Australia, is reported here. The analysis of the 2.42-Mb
      genome sequence indicates that the attributes of the genome are consistent with
      its physiological and phenotypic traits.
AU  - Patel BK
AU  - Te'o VS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01578-15.

PMID- 8107862
VI  - 367
DP  - 1994
TI  - A molecular handshake.
PG  - 688-690
AB  - Review of the M.HhaI/DNA crystal structure paper.
AU  - Patel DJ
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1994 367: 688-690.

PMID- 22535942
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Pseudomonas fuscovaginae, a Broad-Host-Range Pathogen of Plants.
PG  - 2765-2766
AB  - Pseudomonas fuscovaginae was first reported as a pathogen of rice causing sheath  rot in
      plants grown at high altitudes. P. fuscovaginae is now considered a
      broad-host-range plant pathogen causing disease in several economically important
      plants. We report what is, to our knowledge, the first draft genome sequence of a
      P. fuscovaginae strain.
AU  - Patel HK
AU  - Passos-da-Silva D
AU  - Devescovi G
AU  - Maraite H
AU  - Paszkiewicz K
AU  - Studholme DJ
AU  - Venturi V
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2765-2766.

PMID- 
VI  - 0
DP  - 1993
TI  - The domain structure of the DNA specificity subunit of type I restriction endonucleases. I. Cloning, mutagenesis and over-production of the EcoR124 DNA methyltransferase.
PG  - 179-187
AB  - Type I restriction endonucleases consist of three subunits encoded by the genes hsdR, hsdM and
      hsdS.  The hsdS gene product is responsible for DNA specificity and together with the hsdM
      gene product is sufficient for modification (methylation) of the DNA recognition sequence;
      hsdR is required for endonuclease activity.  The endonuclease requires ATP, SAM and Mg2+ as
      cofactors while the DNA methyltransferase requires only SAM and Mg2+.  Evidence has been
      presented to support the hypothesis that the HsdS protein has two domains responsible for DNA
      recognition, separated by a spacer region.  The EcoR124 R-M system is of particular interest
      in that an alternative DNA specificity (EcoR124/3) has been identified which differs from the
      EcoR124 DNA specificity by the presence of an extra non-specific nucleotide:  EcoR124 -
      GAANNNNNNRTCG (or GAAN6RTCG), EcoR124/3 - GAANNNNNNNRTCG (or GAAN7RTCG).  EcoR124 and its
      variant form EcoR124/3 have been cloned producing the recombinant plasmids pCP1005 and pUNG31
      respectively, their transcripts mapped, the genes sequenced and low levels of the endonuclease
      have been purified.  These data show that they are members of a new sub-class of type I R-M
      systems: type IC.  The only difference between EcoR124 and EcoR124/3 lies within their hsdS
      genes.  The EcoR124/3 hsdS gene has an extra copy of a 12-bp repeat within the predicted
      spacer region (repeated twice in EcoR124 and three times in EcoR124/3).
AU  - Patel J
AU  - Firman K
PT  - Journal Article
TA  - Proc. Eur. Meet. Genet. Transform.
JT  - Proc. Eur. Meet. Genet. Transform.
SO  - Proc. Eur. Meet. Genet. Transform. 1993 0: 179-187.

PMID- 1551595
VI  - 112
DP  - 1992
TI  - High-level expression of the cloned genes encoding the subunits of and intact DNA methyltransferase, M.EcoR124.
PG  - 21-27
AB  - We have cloned the genes coding for the two subunits (HsdM and HsdS) of the
      type-I DNA methyltransferase (MTase), M.EcoR124, into the specially constructed
      expression vector, pJ119.  These subunit have been synthesized together as an
      intact MTase.  WE have also cloned the individual subunit-encoding genes under
      the control of the T7 gene 10 promoter or the lacUV5 promoter.  High levels of
      expression have been obtained in all cases.  While HsdM was found to be
      soluble, HsdS was insoluble.  However, in the presence of the co-produced HsdM
      subunit, HsdS was found in the soluble fraction as part of an active MTase.  We
      have partially purified the cloned multi-subunit enzyme and shown that it is
      capable of DNA methylation both in vivo and in vitro.
AU  - Patel J
AU  - Taylor I
AU  - Dutta CF
AU  - Kneale G
AU  - Firman K
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1992 112: 21-27.

PMID- Not carried by PubMed...
VI  - 10
DP  - 1991
TI  - Interaction of a minor groove binder with a fluorescent DNA oligomer containing the EcoRI recognition sequence.
PG  - 547-548
AB  - The minor groove binding drug netropsin quenches the 2-aminopurine (2AP)
      fluorescence in the duplex d(CTGA(2AP)TTCAG)2.  Drug binding constants, K
      approx.10/5 M-1 were established between 5-25C.  A preliminary evaluation of
      the thermodynamic data indicated a predominantly entropy driven interaction.
AU  - Patel N
AU  - Graslund A
AU  - Berglund H
AU  - Nilsson L
AU  - Rigler R
AU  - McLaughlin LW
PT  - Journal Article
TA  - Nucleosides and Nucleotides
JT  - Nucleosides and Nucleotides
SO  - Nucleosides and Nucleotides 1991 10: 547-548.

PMID- 24503980
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Petroleum Hydrocarbon-Degrading Pseudomonas aeruginosa Strain PK6, Isolated from the Saurashtra Region of Gujarat, India.
PG  - e00002-14
AB  - Pseudomonas aeruginosa strain PK6, a potential petroleum hydrocarbon-degrading soil bacterium,
      was isolated from a site contaminated by a petroleum hydrocarbon
      spill from an automobile service station in Junagadh, Gujarat, India. Here, we
      provide the 6.04-Mb draft genome sequence of strain PK6, which has genes encoding
      enzymes for potential and related metabolic pathways of the strain.
AU  - Patel PA
AU  - Kothari VV
AU  - Kothari CR
AU  - Faldu PR
AU  - Domadia KK
AU  - Rawal CM
AU  - Bhimani HD
AU  - Parmar NR
AU  - Nathani NM
AU  - Koringa PG
AU  - Joshi CG
AU  - Kothari RK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00002-14.

PMID- 11352575
VI  - 308
DP  - 2001
TI  - Prokaryotic DNA polymerase I: evolution, structure, and "base flipping" mechanism for nucleotide selection.
PG  - 823-837
AB  - Accurate transmission of DNA material from one generation to the next is crucial for prolonged
      cell survival. Following the discovery of DNA polymerse I in Escherichia coli, the DNA
      polymerase I class of enzymes has served as the prototype for studies on structural and
      biochemical mechanisms of DNA replication. Recently, a series of genomic, mutagenesis and
      structural investigations have provided key insights into how Pol I class of enzymes function
      and evolve. X-ray crystal structures of at least three Pol I class of enzymes have been solved
      in the presence of DNA and dNTP, thus allowing a detailed description of a productive
      replication complex. Rapid-quench stop-flow studies have helped define individual steps during
      nucleotide incorporation and conformational changes that are rate limiting during catalysis.
      Studies in our laboratory have generated large libraries of active mutant enzymes (8000)
      containing a variety of substitutions within the active site, some of which exhibit altered
      biochemical properties. Extensive genomic information of Pol I has recently become available,
      as over 50 polA genes from different prokaryotic species have been sequenced. In light of
      these advancements, we review here the structure-function relationships of Pol I, and we
      highlight those interactions that are responsible for the high fidelity of DNA synthesis. We
      present a mechanism for "flipping" of the complementary template base to enhance interactions
      with the incoming nucleotide substrate during DNA synthesis.
AU  - Patel PH
AU  - Suzuki M
AU  - Adman E
AU  - Shinkai A
AU  - Loeb LA
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2001 308: 823-837.

PMID- 29748405
VI  - 6
DP  - 2018
TI  - High-Quality Whole-Genome Sequences for 77 Shiga Toxin-Producing Escherichia coli Strains Generated with PacBio Sequencing.
PG  - e00391-18
AB  - Shiga toxin-producing Escherichia coli (STEC) is an enteric foodborne pathogen that can cause
      mild to severe illness. Here, we report the availability of
      high-quality whole-genome sequences for 77 STEC strains generated using the
      PacBio sequencing platform.
AU  - Patel PN
AU  - Lindsey RL
AU  - Garcia-Toledo L
AU  - Rowe LA
AU  - Batra D
AU  - Whitley SW
AU  - Drapeau D
AU  - Stoneburg D
AU  - Martin H
AU  - Juieng P
AU  - Loparev VN
AU  - Strockbine N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00391-18.

PMID- 25398322
VI  - 70
DP  - 2015
TI  - Genome sequence and phenotypic characterization of Caulobacter segnis.
PG  - 355-363
AB  - Caulobacter segnis is a unique species of Caulobacter that was initially deemed
      Mycoplana segnis because it was isolated from soil and appeared to share a number
      of features with other Mycoplana. After a 16S rDNA analysis showed that it was
      closely related to Caulobacter crescentus, it was reclassified C. segnis. Because
      the C. segnis genome sequence available in GenBank contained 126 pseudogenes, we
      compared the original sequencing data to the GenBank sequence and determined that
      many of the pseudogenes were due to sequence errors in the GenBank sequence.
      Consequently, we used multiple approaches to correct and reannotate the C. segnis
      genome sequence. In total, we deleted 247 bp, added 14 bp, and changed 8 bp
      resulting in 233 fewer bases in our corrected sequence. The corrected sequence
      contains only 15 pseudogenes compared to 126 in the original annotation.
      Furthermore, we found that unlike Mycoplana, C. segnis divides by fission,
      producing swarmer cells that have a single, polar flagellum.
AU  - Patel S
AU  - Fletcher B
AU  - Scott DC
AU  - Ely B
PT  - Journal Article
TA  - Curr. Microbiol.
JT  - Curr. Microbiol.
SO  - Curr. Microbiol. 2015 70: 355-363.

PMID- 2786192
VI  - 17
DP  - 1989
TI  - Methylation at overlapping dam (Gm6ATC) sites does not block cleavage by the NruI (TCGCGA) isoschizomer restriction endonucleases AmaI, SalDI and Sbo13I.
PG  - 3613
AB  - AmaI, NruI, SalDI and Sbo13I endonucleases were tested for sensitivity to TCGCGm6A at an
      overlapping dam site in Ad2 DNA (pos 7723). NruI cleavage was blocked by m6A modification, but
      the other endonucleases were not.
AU  - Patel Y
AU  - Nelson M
AU  - McClelland M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 3613.

PMID- 2158082
VI  - 18
DP  - 1990
TI  - Cleavage at the twelve-base-pair sequence 5'-TCTAGATCTAGA-3' using M.XbaI (TCTAGm6A) methylation and DpnI (Gm6A/TC) cleavage .
PG  - 1603-1607
AB  - The DNA methylase M.XbaI was isolated from an E. coli recombinant clone.  We
      deduce that the enzyme methylates at the sequence 5'-TCTAGm6A-3'.  In
      combination with the methylation-dependent restriction endonuclease, DpnI
      (5'-Gm6A/TC-3'), DNA cleavage occurs at the sequence 5'-TCTAGA/TCTAGA-3'.  This
      twelve-base-pair site should occur once every 16,000,000 base pairs in a random
      sequence of DNA.  The exceptional rarity of the M.XbaI/DpnI sequence makes it
      an ideal candidate for transpositional integration of a unique cleavage site
      into bacterial genomes.  Retrotransposition into mammalian genomes is also an
      attractive possibility.
AU  - Patel Y
AU  - Van Cott E
AU  - Wilson GG
AU  - McClelland M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 1603-1607.

PMID- 29519834
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence and Annotation of the Phytopathogenic Ralstonia pickettii (Previously Burkholderia glumae) Strain ICMP-8657.
PG  - e00128-18
AB  - Strain ICMP-8657 was formerly taxonomically classified as Burkholderia glumae and reported to
      be the producer of an antibacterial pyrazole derivative. Here, we
      report the draft genome sequence of ICMP-8657, which failed to demonstrate the
      biosynthetic capacity to produce the stated antibacterial compound, leading to
      its taxonomic reclassification as Ralstonia pickettii ICMP-8657.
AU  - Paterson J
AU  - Gross H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00128-18.

PMID- 23409266
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Rhodococcus opacus Strain M213 Shows a Diverse Catabolic Potential.
PG  - e00144-12
AB  - Soil-borne Gram-positive bacteria from the genus Rhodococcus metabolize a range of aromatic
      hydrocarbons and also produce a variety of value-added products, such
      as triacylglycerols and steroids. We report the draft genome sequence of
      Rhodococcus opacus strain M213 (9,193,504 bp with a G+C content of 66.99%),
      providing a comprehensive understanding of the repertoire of metabolic genes of
      this strain.
AU  - Pathak A
AU  - Green SJ
AU  - Ogram A
AU  - Chauhan A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00144-12.

PMID- 29930041
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Pseudomonas sp. Strain B1, Isolated from a Contaminated  Sediment.
PG  - e00518-18
AB  - The draft genome sequence of Pseudomonas sp. strain B1, isolated from a contaminated soil, is
      reported. The genome comprises 6,706,934 bases, 6,059
      coding sequences, and 70 RNAs and has a G+C content of 60.3%. A suite of
      biodegradative genes, many located on genomic islands, were identified from
      strain B1, further enhancing our understanding of the versatile pseudomonads.
AU  - Pathak A
AU  - Jaswal R
AU  - Stothard P
AU  - Brooks S
AU  - Chauhan A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00518-18.

PMID- 29930048
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Serratia sp. Strain S1B, Isolated from Mercury-Contaminated Soil.
PG  - e00534-18
AB  - We report here the draft genome sequence of Serratia sp. strain S1B, comprising 7,710,841
      bases, 7,075 coding sequences, a G+C content of 45.9%, and 138 RNAs.
      Notably, a repertoire of biodegradative genes, several occurring on genomic
      islands, was also identified, which enhances our understanding of the
      environmental relevance of Serratia spp.
AU  - Pathak A
AU  - Jaswal R
AU  - Xu X
AU  - Chauhan A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00534-18.

PMID- 29167258
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of an Indian Marine Cyanobacterial Strain with Fast Growth  and High Polyglucan Content.
PG  - e01334-17
AB  - Marine cyanobacteria play an important role in global carbon cycling and are a potential
      source of polyglucans for biotechnological purposes. This report
      provides the draft sequence of an Indian marine cyanobacterium, Synechococcus
      elongatus BDU 130192, which shows fast growth and high polyglucan content. The
      genome sequence will help in understanding the unique properties of this
      organism.
AU  - Pathania R
AU  - Ahmad A
AU  - Srivastava S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01334-17.

PMID- 22180809
VI  - 5
DP  - 2011
TI  - Non-contiguous finished genome sequence of the opportunistic oral pathogen Prevotella multisaccharivorax type strain (PPPA20).
PG  - 41-49
AB  - Prevotella multisaccharivorax Sakamoto et al. 2005 is a species of the large genus Prevotella,
      which belongs to the family Prevotellaceae. The species is of
      medical interest because its members are able to cause diseases in the human oral
      cavity such as periodontitis, root caries and others. Although 77 Prevotella
      genomes have already been sequenced or are targeted for sequencing, this is only
      the second completed genome sequence of a type strain of a species within the
      genus Prevotella to be published. The 3,388,644 bp long genome is assembled in
      three non-contiguous contigs, harbors 2,876 protein-coding and 75 RNA genes and
      is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Pati A et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 5: 41-49.

PMID- 21304650
VI  - 1
DP  - 2009
TI  - Complete genome sequence of Saccharomonospora viridis type strain (P101).
PG  - 141-149
AB  - Saccharomonospora viridis (Schuurmans et al. 1956) Nonomurea and Ohara 1971 is the type
      species of the genus Saccharomonospora which belongs to the family
      Pseudonocardiaceae. S. viridis is of interest because it is a Gram-negative
      organism classified among the usually Gram-positive actinomycetes. Members of the
      species are frequently found in hot compost and hay, and its spores can cause
      farmer's lung disease, bagassosis, and humidifier fever. Strains of the species
      S. viridis have been found to metabolize the xenobiotic pentachlorophenol (PCP).
      The strain described in this study has been isolated from peat-bog in Ireland.
      Here we describe the features of this organism, together with the complete genome
      sequence, and annotation. This is the first complete genome sequence of the
      family Pseudonocardiaceae, and the 4,308,349 bp long single replicon genome with
      its 3906 protein-coding and 64 RNA genes is part of the Genomic Encyclopedia of
      Bacteria and Archaea project.
AU  - Pati A et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2009 1: 141-149.

PMID- 21304677
VI  - 2
DP  - 2010
TI  - Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022).
PG  - 49-56
AB  - Sphaerobacter thermophilus Demharter et al. 1989 is the sole and type species of  the genus
      Sphaerobacter, which is the type genus of the family
      Sphaerobacteraceae, the order Sphaerobacterales and the subclass
      Sphaerobacteridae. Phylogenetically, it belongs to the genomically little studied
      class of the Thermomicrobia in the bacterial phylum Chloroflexi. Here, the genome
      of strain S 6022(T) is described which is an obligate aerobe that was originally
      isolated from an aerated laboratory-scale fermentor that was pulse fed with
      municipal sewage sludge. We describe the features of this organism, together with
      the complete genome and annotation. This is the first complete genome sequence of
      the thermomicrobial subclass Sphaerobacteridae, and the second sequence from the
      chloroflexal class Thermomicrobia. The 3,993,764 bp genome with its 3,525
      protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria
      and Archaea project.
AU  - Pati A et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 2: 49-56.

PMID- 21304710
VI  - 2
DP  - 2010
TI  - Complete genome sequence of Brachyspira murdochii type strain (56-150).
PG  - 260-269
AB  - Brachyspira murdochii Stanton et al. 1992 is a non-pathogenic, host-associated spirochete of
      the family Brachyspiraceae. Initially isolated from the intestinal
      content of a healthy swine, the 'group B spirochaetes' were first described as
      Serpulina murdochii. Members of the family Brachyspiraceae are of great
      phylogenetic interest because of the extremely isolated location of this family
      within the phylum 'Spirochaetes'. Here we describe the features of this organism,
      together with the complete genome sequence and annotation. This is the first
      completed genome sequence of a type strain of a member of the family
      Brachyspiraceae and only the second genome sequence from a member of the genus
      Brachyspira. The 3,241,804 bp long genome with its 2,893 protein-coding and 40
      RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Pati A et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 2: 260-269.

PMID- 21304714
VI  - 2
DP  - 2010
TI  - Complete genome sequence of Arcobacter nitrofigilis type strain (CI).
PG  - 300-308
AB  - Arcobacter nitrofigilis (McClung et al. 1983) Vandamme et al. 1991 is the type species of the
      genus Arcobacter in the family Campylobacteraceae within the
      Epsilonproteobacteria. The species was first described in 1983 as Campylobacter
      nitrofigilis [1] after its detection as a free-living, nitrogen-fixing
      Campylobacter species associated with Spartina alterniflora Loisel roots [2]. It
      is of phylogenetic interest because of its lifestyle as a symbiotic organism in a
      marine environment in contrast to many other Arcobacter species which are
      associated with warm-blooded animals and tend to be pathogenic. Here we describe
      the features of this organism, together with the complete genome sequence, and
      annotation. This is the first complete genome sequence of a type stain of the
      genus Arcobacter. The 3,192,235 bp genome with its 3,154 protein-coding and 70
      RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Pati A et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 2: 300-308.

PMID- 21475586
VI  - 4
DP  - 2011
TI  - Complete genome sequence of Bacteroides helcogenes type strain (P 36-108).
PG  - 45-53
AB  - Bacteroides helcogenes Benno et al. 1983 is of interest because of its isolated phylogenetic
      location and, although it has been found in pig feces and is known
      to be pathogenic for pigs, occurrence of this bacterium is rare and it does not
      cause significant damage in intensive animal husbandry. The genome of B.
      helcogenes P 36-108(T) is already the fifth completed and published type strain
      genome from the genus Bacteroides in the family Bacteroidaceae. The 3,998,906 bp
      long genome with its 3,353 protein-coding and 83 RNA genes consists of one
      circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and
      Archaea project.
AU  - Pati A et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 4: 45-53.

PMID- 21677858
VI  - 4
DP  - 2011
TI  - Complete genome sequence of Oceanithermus profundus type strain (506).
PG  - 210-220
AB  - Oceanithermus profundus Miroshnichenko et al. 2003 is the type species of the genus
      Oceanithermus, which belongs to the family Thermaceae. The genus currently
      comprises two species whose members are thermophilic and are able to reduce
      sulfur compounds and nitrite. The organism is adapted to the salinity of sea
      water, is able to utilize a broad range of carbohydrates, some proteinaceous
      substrates, organic acids and alcohols. This is the first completed genome
      sequence of a member of the genus Oceanithermus and the fourth sequence from the
      family Thermaceae. The 2,439,291 bp long genome with its 2,391 protein-coding and
      54 RNA genes consists of one chromosome and a 135,351 bp long plasmid, and is a
      part of the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Pati A et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 4: 210-220.

PMID- 21677859
VI  - 4
DP  - 2011
TI  - Complete genome sequence of Cellulophaga lytica type strain (LIM-21).
PG  - 221-232
AB  - Cellulophaga lytica (Lewin 1969) Johansen et al. 1999 is the type species of the  genus
      Cellulophaga, which belongs to the family Flavobacteriaceae within the
      phylum 'Bacteroidetes' and was isolated from marine beach mud in Limon, Costa
      Rica. The species is of biotechnological interest because its members produce a
      wide range of extracellular enzymes capable of degrading proteins and
      polysaccharides. After the genome sequence of Cellulophaga algicola this is the
      second completed genome sequence of a member of the genus Cellulophaga. The
      3,765,936 bp long genome with its 3,303 protein-coding and 55 RNA genes consists
      of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria
      and Archaea project.
AU  - Pati A et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 4: 221-232.

PMID- 28250895
VI  - 12
DP  - 2017
TI  - High-quality-draft genome sequence of the fermenting bacterium Anaerobium acetethylicum type strain GluBS11T (DSM 29698).
PG  - 24
AB  - Anaerobium acetethylicum strain GluBS11T belongs to the family Lachnospiraceae within the
      order Clostridiales. It is a Gram-positive, non-motile and strictly
      anaerobic bacterium isolated from biogas slurry that was originally enriched with
      gluconate as carbon source (Patil, et al., Int J Syst Evol Microbiol
      65:3289-3296, 2015). Here we describe the draft genome sequence of strain
      GluBS11T and provide a detailed insight into its physiological and metabolic
      features. The draft genome sequence generated 4,609,043 bp, distributed among 105
      scaffolds assembled using the SPAdes genome assembler method. It comprises in
      total 4,132 genes, of which 4,008 were predicted to be protein coding genes, 124
      RNA genes and 867 pseudogenes. The G + C content was 43.51 mol %. The annotated
      genome of strain GluBS11T contains putative genes coding for the pentose
      phosphate pathway, the Embden-Meyerhoff-Parnas pathway, the Entner-Doudoroff
      pathway and the tricarboxylic acid cycle. The genome revealed the presence of
      most of the necessary genes required for the fermentation of glucose and
      gluconate to acetate, ethanol, and hydrogen gas. However, a candidate gene for
      production of formate was not identified.
AU  - Patil Y
AU  - Muller N
AU  - Schink B
AU  - Whitman WB
AU  - Huntemann M
AU  - Clum A
AU  - Pillay M
AU  - Palaniappan K
AU  - Varghese N
AU  - Mikhailova N
AU  - Stamatis D
AU  - Reddy TB
AU  - Daum C
AU  - Shapiro N
AU  - Ivanova N
AU  - Kyrpides N
AU  - Woyke T
AU  - Junghare M
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 24.

PMID- 29122870
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Clinical and Nonclinical Isolates of Klebsiella spp. Exhibiting Nonheritable Tolerance toward Antimicrobial Compounds.
PG  - e01217-17
AB  - A clinical isolate and a nonclinical isolate of Klebsiella pneumoniae were found  to exhibit
      nonheritable tolerance in response to antimicrobial compounds. The
      draft genome sequences of both isolates are presented here.
AU  - Patole S
AU  - Mishra M
AU  - Mohapatra H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01217-17.

PMID- 20829291
VI  - 156
DP  - 2010
TI  - Twenty-eight divergent polysaccharide loci specifying within- and amongst-strain capsule diversity in three strains of Bacteroides fragilis.
PG  - 3255-3269
AB  - Comparison of the complete genome sequence of Bacteroides fragilis 638R, originally isolated
      in the USA, was made with two previously
      sequenced strains isolated in the UK (NCTC 9343) and Japan (YCH46). The
      presence of 10 loci containing genes associated with polysaccharide
      (PS) biosynthesis, each including a putative Wzx flippase and Wzy
      polymerase, was confirmed in all three strains, despite a lack of
      cross-reactivity between NCTC 9343 and 638R surface PS-specific
      antibodies by immunolabelling and microscopy. Genomic comparisons
      revealed an exceptional level of PS biosynthesis locus diversity. Of
      the 10 divergent PS-associated loci apparent in each strain, none is
      similar between NCTC 9343 and 638R. YCH46 shares one locus with NCTC
      9343, confirmed by mAb labelling, and a second different locus with
      638R, making a total of 28 divergent PS biosynthesis loci amongst the
      three strains. The lack of expression of the phase-variable large
      capsule (LC) in strain 638R, observed in NCTC 9343, is likely to be due
      to a point mutation that generates a stop codon within a putative
      initiating glycosyltransferase, necessary for the expression of the LC
      in NCTC 9343. Other major sequence differences were observed to arise
      from different numbers and variety of inserted extra-chromosomal
      elements, in particular prophages. Extensive horizontal gene transfer
      has occurred within these strains, despite the presence of a
      significant number of divergent DNA restriction and modification
      systems that act to prevent acquisition of foreign DNA. The level of
      amongst-strain diversity in PS biosynthesis loci is unprecedented.
AU  - Patrick S
AU  - Blakely GW
AU  - Houston S
AU  - Moore J
AU  - Abratt VR
AU  - Bertalan M
AU  - Cerdeno-Tarraga AM
AU  - Quail MA
AU  - Corton N
AU  - Corton C
AU  - Bignell A
AU  - Barron A
AU  - Clark L
AU  - Bentley SD
AU  - Parkhill J
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2010 156: 3255-3269.

PMID- 25523765
VI  - 2
DP  - 2014
TI  - Draft Whole-Genome Sequences of 10 Serogroup O6 Enterotoxigenic Escherichia coli  Strains.
PG  - e01274-14
AB  - Entertotoxigenic Escherichia coli (ETEC) is a major cause of global diarrhea, resulting in
      approximately 200 million occurrences and 300,000 to 400,000 deaths
      annually, primarily in children under the age of five. Here, we announce the
      release of the draft genomes of 10 ETEC isolates belonging to serogroup O6.
AU  - Pattabiraman V
AU  - Bopp CA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01274-14.

PMID- 26044422
VI  - 3
DP  - 2015
TI  - Draft Whole-Genome Sequences of Nine Enterotoxigenic Escherichia coli Serogroup O6 Strains.
PG  - e00564-15
AB  - Enterotoxigenic Escherichia coli (ETEC) is an important cause of diarrhea in children under
      the age of 5 years and in adults living in developing countries, as well as in travelers to
      these countries. In this announcement, we release the draft whole-genome sequences of 10 ETEC
      serogroup O6 strains.
AU  - Pattabiraman V
AU  - Bopp CA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00564-15.

PMID- 27660794
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a Diazotrophic, Plant Growth-Promoting Rhizobacterium of the Pseudomonas syringae Complex.
PG  - e01023-16
AB  - We report here the draft genome sequence of Pseudomonas syringae GR12-2, a nitrogen-fixing,
      plant growth-promoting bacterium, isolated from the rhizosphere
      of an Arctic grass. The 6.6-Mbp genome contains 5,676 protein-coding genes,
      including a nitrogen-fixation island similar to that in P. stutzeri.
AU  - Patten CL
AU  - Jeong H
AU  - Blakney AJ
AU  - Wallace N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01023-16.

PMID- 4019414
VI  - 163
DP  - 1985
TI  - Evidence for two restriction-modification systems in Halobacterium cutirubrum.
PG  - 783-784
AB  - Data from plating experiments indicated that Halobacterium cutirubrum NRC34001
      has at least two separate restriction-modifiction systems.  A spontaneous or
      induced loss of one or both systems resulted in four restriction-modification
      phenotypes.  There was a positive correlation between changes in gas
      vacuolation phenotypes and either restriction-modifiction system.
AU  - Patterson NH
AU  - Pauling C
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1985 163: 783-784.

PMID- 20729368
VI  - 192
DP  - 2010
TI  - Genome sequence of the solvent-producing bacterium Clostridium carboxidivorans strain P7T.
PG  - 5554-5555
AB  - Clostridium carboxidivorans strain P7(T) is a strictly anaerobic acetogenic bacterium that
      produces acetate, ethanol, butanol, and
      butyrate. The C. carboxidivorans genome contains all the genes for the
      carbonyl branch of the Wood-Ljungdahl pathway for CO(2) fixation, and it
      encodes enzymes for conversion of acetyl coenzyme A into butanol and
      butyrate.
AU  - Paul D
AU  - Austin FW
AU  - Arick T
AU  - Bridges SM
AU  - Burgess SC
AU  - Dandass YS
AU  - Lawrence ML
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 5554-5555.

PMID- 18539730
VI  - 190
DP  - 2008
TI  - Genome sequence of the chemolithoautotrophic bacterium Oligotropha carboxidovorans OM5T.
PG  - 5531-5532
AB  - Oligotropha carboxidovorans OM5(T) (DSM 1227, ATCC 49405) is a
      chemolithoautotrophic bacterium with the capability to utilize carbon
      monoxide, carbon dioxide, and hydrogen. It is also capable of
      heterotrophic growth under appropriate environmental conditions. Here we
      report the annotated genome sequence of the circular chromosome of this
      organism.
AU  - Paul D
AU  - Bridges S
AU  - Burgess SC
AU  - Dandass Y
AU  - Lawrence ML
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2008 190: 5531-5532.

PMID- 24503993
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Filamentous Cyanobacterium Leptolyngbya sp. Strain Heron Island J, Exhibiting Chromatic Acclimation.
PG  - e01166-13
AB  - Leptolyngbya sp. strain Heron Island is a cyanobacterium exhibiting chromatic acclimation.
      However, this strain has strong interactions with other bacteria,
      making it impossible to obtain axenic cultures for sequencing. A protocol
      involving an analysis of tetranucleotide frequencies, G+C content, and BLAST
      searches has been described for separating the cyanobacterial scaffolds from
      those of its cooccurring bacteria.
AU  - Paul R
AU  - Jinkerson RE
AU  - Buss K
AU  - Steel J
AU  - Mohr R
AU  - Hess WR
AU  - Chen M
AU  - Fromme P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01166-13.

PMID- 12271122
VI  - 99
DP  - 2002
TI  - The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts.
PG  - 13148-13153
AB  - The 3.31-Mb genome sequence of the intracellular pathogen and potential bioterrorism agent,
      Brucella suis, was determined. Comparison of B. suis with Brucella melitensis has defined a
      finite set of differences that could be responsible for the differences in virulence and host
      preference between these organisms, and indicates that phage have played a significant role in
      their divergence. Analysis of the B. suis genome reveals transport and metabolic capabilities
      akin to soil/plant-associated bacteria. Extensive gene synteny between B. suis chromosome 1
      and the genome of the plant symbiont Mesorhizobium loti emphasizes the similarity between this
      animal pathogen and plant pathogens and symbionts. A limited repertoire of genes homologous to
      known bacterial virulence factors were identified.
AU  - Paulsen I et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2002 99: 13148-13153.

PMID- 12663927
VI  - 299
DP  - 2003
TI  - Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis.
PG  - 2071-2074
AB  - The complete genome sequence of Enterococcus faecalis V583, a vancomycin-resistant clinical
      isolate, revealed that more than a quarter
      of the genome consists of probable mobile or foreign DNA. One of the
      predicted mobile elements is a previously unknown vanB
      vancomycin-resistance conjugative transposon. Three plasmids were
      identified, including two pheromone-sensing conjugative plasmids, one
      encoding a previously undescribed pheromone inhibitor. The apparent
      propensity for the incorporation of mobile elements probably contributed
      to the rapid acquisition and dissemination of drug resistance in the
      enterococci.
AU  - Paulsen IT et al
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2003 299: 2071-2074.

PMID- 15980861
VI  - 23
DP  - 2005
TI  - Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5.
PG  - 873-878
AB  - Pseudomonas fluorescens Pf-5 is a plant commensal bacterium that inhabits the rhizosphere and
      produces secondary metabolites that suppress soilborne
      plant pathogens. The complete sequence of the 7.1-Mb Pf-5 genome was
      determined. We analyzed repeat sequences to identify genomic islands that,
      together with other approaches, suggested P. fluorescens Pf-5's recent
      lateral acquisitions include six secondary metabolite gene clusters, seven
      phage regions and a mobile genomic island. We identified various features
      that contribute to its commensal lifestyle on plants, including broad
      catabolic and transport capabilities for utilizing plant-derived
      compounds, the apparent ability to use a diversity of iron siderophores,
      detoxification systems to protect from oxidative stress, and the lack of a
      type III secretion system and toxins found in related pathogens. In
      addition to six known secondary metabolites produced by P. fluorescens
      Pf-5, three novel secondary metabolite biosynthesis gene clusters were
      also identified that may contribute to the biocontrol properties of P.
      fluorescens Pf-5.
AU  - Paulsen IT et al
PT  - Journal Article
TA  - Nat. Biotechnol.
JT  - Nat. Biotechnol.
SO  - Nat. Biotechnol. 2005 23: 873-878.

PMID- 24029754
VI  - 1
DP  - 2013
TI  - Genome Sequence of the Melanin-Producing Extremophile Aeromonas salmonicida subsp. pectinolytica Strain 34melT.
PG  - e00675-13
AB  - The genome of Aeromonas salmonicida subsp. pectinolytica strain 34mel(T), isolated from a
      heavily polluted river, contains several genomic islands and
      putative virulence genes. The identification of genes involved in resistance to
      different kinds of stress sheds light on the mechanisms used by this strain to
      thrive in an extreme environment.
AU  - Pavan ME
AU  - Pavan EE
AU  - Lopez NI
AU  - Levin L
AU  - Pettinari MJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00675-13.

PMID- 3163393
VI  - 12D
DP  - 1988
TI  - A DNA binding protein acts as a transcriptional roadblock.
PG  - 145
AB  - What results when an elongating RNA polymerase encounters DNA-bound protein is
      of general interest.  To ask if a protein bound tightly to a specific sequence
      blocks further elongation by E. coli RNA polymerase, transcription on templates
      associated with a mutant of the EcoRI endonuclease has been studied in vitro.
      This protein (E111G) binds to the wild type recognition sequence with high
      affinity yet carries out no appreciable cleavage.  When a DNA template
      containing one EcoRI site is transcribed in the presence of E111G and
      rifampicin, two RNA products are seen:  a full-length runoff transcript and a
      truncated RNA species whose 3' endpoint is immediately upstream of the EcoRI
      recognition sequence.  Under conditions of complete binding by E111G, the
      shorter transcript is the major RNA species appearing.  Blockage appears
      long-lived and not dependent on the DNA sequence context upstream of the EcoRI
      site.  During steady state transcription an additional RNA 3' endpoint, due to
      a second RNA polymerase stalled behind the first, is seen.  From analysis of
      the RNA 3' ends, the position of the 3' terminal ribonucleotide with respect to
      the leading edge of the RNA polymerase ternary complex has been located.
AU  - Pavco PA
AU  - Steege DA
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1988 12D: 145.

PMID- 17689048
VI  - 90
DP  - 2007
TI  - Plant cytosine-5 DNA methyltransferases: Structure, function, and molecular evolution.
PG  - 530-541
AB  - A detailed analysis of the structure and function, along with evolutionary aspects, of the
      main plant cytosine-5 DNA
      methyltransferases (C5-MTases) is presented. The evolutionary
      relationships between the already known and four candidate plant
      C5-MTases identified in this work were investigated using the distance,
      maximum-parsimony, and maximum-likelihood approaches. The topologies of
      the trees were overall congruent: four monophyletic groups
      corresponding to the four plant C5-MTase families were clearly
      distinguished. In addition, sequence analyses of the plant C5-MTase
      target recognition domain sequences were performed and phylogenetic
      trees were reconstructed showing that there is good conservation among
      but not within the plant C5-MTase families. Furthermore, a conserved
      dipeptide that plays an important role in flipping the target base into
      the catalytic site of the C5-MTases was identified in all plant
      C5-MTases under study.
AU  - Pavlopoulou A
AU  - Kossida S
PT  - Journal Article
TA  - Genomics
JT  - Genomics
SO  - Genomics 2007 90: 530-541.

PMID- 19135144
VI  - 93
DP  - 2009
TI  - Phylogenetic analysis of the eukaryotic RNA (cytosine-5)-methyltransferases.
PG  - 350-357
AB  - RNA (cytosine-5)-methyltransferases (RCMTs) have been characterized both in prokaryotic and
      eukaryotic organisms. The RCMT family, however, remains largely uncharacterized, as opposed to
      the family of DNA (cytosine-5)-methyltransferases which has been studied in depth. In the
      present study, an in silico identification of the putative 5-methylcytosine RNA-generating
      enzymes in the eukaryotic genomes was performed. A comprehensive phylogenetic analysis of the
      putative eukaryotic RCMT-related proteins has been performed in order to redefine subfamilies
      within the RCMT family. Five distinct eukaryotic subfamilies were identified, including the
      three already known (NOP2, NCL1 and YNL022c), one novel subfamily (RCMT9) and a fifth one
      which hitherto was considered to exist exclusively in prokaryotes (Fmu). The potential
      evolutionary relationships among the different eukaryotic RCMT subfamilies were also
      investigated.  Furthermore, the results of this study add further support to a previous
      hypothesis that RCMTs represent evolutionary intermediates of RNA
      (uridine-5)-methyltransferases and DNA (cytosine-5)-methyltransferases.
AU  - Pavlopoulou A
AU  - Kossida S
PT  - Journal Article
TA  - Genomics
JT  - Genomics
SO  - Genomics 2009 93: 350-357.

PMID- 26294625
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Antarctic Pseudomonas sp. Strain KG01 with Full Potential for Biotechnological Applications.
PG  - e00906-15
AB  - We report here the draft genome sequence of a free-living psychrotolerant, Pseudomonas sp.
      strain KG01, isolated from an Antarctic soil sample and
      displaying interesting antimicrobial and surfactant activities. The sequence is
      6.3 Mb long and includes 5,648 predicted-coding sequences.
AU  - Pavlov MS
AU  - Lira F
AU  - Martinez JL
AU  - Olivares J
AU  - Marshall SH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00906-15.

PMID- 15073287
VI  - 150
DP  - 2004
TI  - Evolution of genomic islands by deletion and tandem accretion by site-specific recombination: ICESt1-related elements from Streptococcus thermophilus.
PG  - 759-774
AB  - The 34 734-bp integrative and potentially conjugative element (putative ICE)
      ICESt1 has been previously found to be site-specifically integrated in the 3' end
      of the fda locus of Streptococcus thermophilus CNRZ368. Four types of genomic
      islands related to ICESt1 are integrated in the same position in seven other
      strains of S. thermophilus. One of these elements, ICESt3, harbours conjugation
      and recombination modules closely related to those of ICESt1 and excises by
      site-specific recombination. Two other types of elements, CIME19258 and CIME302,
      are flanked by site-specific attachment sites closely related to attL and attR of
      ICESt1 and ICESt3, whereas Delta CIME308 only possesses a putative attR site;
      none of these three elements carry complete conjugation and recombination
      modules. ICESt1 contains a functional internal recombination site, attL', that is
      almost identical to attL of CIME19258. The recombination between attL' and attR
      of ICESt1 leads to the excision of the expected circular molecule (putative ICE);
      a cis-mobilizable element (CIME) flanked by an attL site and an attB' site
      remains integrated into the 3' end of fda. Furthermore, sequences that could be
      truncated att sites were found within ICESt1, ICESt3 and CIME302. All together,
      these data suggest that these genomic islands evolved by deletion and tandem
      accretion of ICEs and CIMEs resulting from site-specific recombination. A model
      for this evolution is proposed and its application to other genomic islands is
      discussed.
AU  - Pavlovic G
AU  - Burrus V
AU  - Gintz B
AU  - Decaris B
AU  - Guedon G
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2004 150: 759-774.

PMID- 
VI  - 84
DP  - 2004
TI  - Characterization and evolution of a family of integrative and potentially conjugative or mobilizable elements from Streptococcus  thermophilus.
PG  - 7-14
AB  - The integrative and conjugative elements (ICEs) excise by site-specific recombination.
      self-transfer the resulting circular form by conjugation
      and integrate into the genome of the recipient bacterium. The 34.7-kb
      element from Streptococcus thermophilus CNRZ368, ICEStl, excises and
      integrates by site-specific recombination. This element also possesses
      a conjugation module distantly related to that of the conjugative
      transposon Tn9l6 from Enterococcus faecalis. Therefore, ICEStl is
      probably an ICE. Four types of elements related to ICEStl are
      integrated into the same location as ICEStl in seven other strains of
      S. thermophilus. One of these elements, ICESt3, is probably an ICE
      whereas the three others (CIMEs) would have arisen from ICEs by
      deletion of the conjugation and recombination modules. These elements
      also encode functions that are not involved in element maintenance or
      transfer, Such as restriction-modification systems. Each of these
      elements has a chimerical Structure resulting from the acquisition of
      modules from different origins. Sequence analyses indicate that these
      elements are involved in horizontal transfers with various species of
      dairy or pathogenic lactic acid bacteria. DeltaCIME308 has exchanged
      restriction-modification and cadmium resistance modules with plasmids.
      CIME19258 has acquired a cadmium resistance module by the integration
      of an ICE related to Tn9l6 within the CIME. The site-specific
      recombination between an internal anL-related site and attR of ICEStl
      leads to the excision of a circular molecule which could be another
      ICE, ICEt2, suggesting that ICEStl has arisen by accretion of a CIME
      and ICEt2. CIME302, ICESt2 and ICESt3 would also have arisen by
      site-specific accretion of CIMEs and ICEs and/or mobilization of CIMEs
      by ICEs. An ICE would integrate by site-specific recombination in the
      attR site of a CIME; then the CIME-ICE would excise by site-specific
      recombination and transfer by conjugation.
AU  - Pavlovic G
AU  - Burrus V
AU  - Toulmay A
AU  - Choulet F
AU  - Decaris B
AU  - Guedon G
PT  - Journal Article
TA  - Lait
JT  - Lait
SO  - Lait 2004 84: 7-14.

PMID- 28818897
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Bacillus sp. Strain K2I17, Isolated from the Rhizosphere of Deschampsia antarctica Desv.
PG  - e00786-17
AB  - We present here the draft genome sequence of Bacillus sp. strain K2I17, which was isolated
      from the rhizosphere of Deschampsia antarctica Desv. The genomic
      sequence contained 6,113,341 bp. This genome provides insights into the possible
      new biomedical and biotechnical applications of this specific Antarctic
      bacterium.
AU  - Pavon A
AU  - Orellana P
AU  - Salazar L
AU  - Cespedes S
AU  - Muino L
AU  - Gutierrez A
AU  - Castillo D
AU  - Corsini G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00786-17.

PMID- 23144385
VI  - 194
DP  - 2012
TI  - Genome Sequence of Janibacter hoylei MTCC8307, Isolated from the Stratospheric Air.
PG  - 6629-6630
AB  - Janibacter hoylei MTCC8307 was isolated from stratospheric air at an altitude of  41.4 km over
      Hyderabad, India. Here, we present the draft genome of Janibacter
      hoylei MTCC8307, which contains 3,139,099 bp with a G+C content of 72.8 mol%,
      2,972 protein-coding genes, and 57 structural RNAs.
AU  - Pawar SP
AU  - Dhotre DP
AU  - Shetty SA
AU  - Chowdhury SP
AU  - Chaudhari BL
AU  - Shouche YS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6629-6630.

PMID- 26044439
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Burkholderia sp. MR1, a Methylarsenate-Reducing Bacterial Isolate from Florida Golf Course Soil.
PG  - e00608-15
AB  - To elucidate the environmental organoarsenical biocycle, we isolated a soil organism,
      Burkholderia sp. MR1, which reduces relatively nontoxic pentavalent
      methylarsenate to the more toxic trivalent methylarsenite, with the goal of
      identifying the gene for the reductase. Here, we report the draft genome sequence
      of Burkholderia sp. MR1.
AU  - Pawitwar SS
AU  - Utturkar SM
AU  - Brown SD
AU  - Yoshinaga M
AU  - Rosen BP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00608-15.

PMID- 15684412
VI  - 33
DP  - 2005
TI  - Inference of relationships in the 'twilight zone' of homology using a combination of bioinformatics and site-directed mutagenesis: a case study   of restriction endonucleases Bsp6I and PvuII.
PG  - 661-671
AB  - Thus far, identification of functionally important residues in Type II restriction
      endonucleases (REases) has been difficult using conventional
      methods. Even though known REase structures share a fold and marginally
      recognizable active site, the overall sequence similarities are
      statistically insignificant, unless compared among proteins that recognize
      identical or very similar sequences. Bsp6I is a Type II REase, which
      recognizes the palindromic DNA sequence 5'GCNGC and cleaves between the
      cytosine and the unspecified nucleotide in both strands, generating a
      double-strand break with 5'-protruding single nucleotides. There are no
      solved structures of REases that recognize similar DNA targets or generate
      cleavage products with similar characteristics. In straightforward
      comparisons, the Bsp6I sequence shows no significant similarity to REases
      with known structures. However, using a fold-recognition approach, we have
      identified a remote relationship between Bsp6I and the structure of PvuII.
      Starting from the sequence-structure alignment between Bsp6I and PvuII, we
      constructed a homology model of Bsp6I and used it to predict functionally
      significant regions in Bsp6I. The homology model was supported by
      site-directed mutagenesis of residues predicted to be important for
      dimerization, DNA binding and catalysis. Completing the picture of
      sequence-structure-function relationships in protein superfamilies becomes
      an essential task in the age of structural genomics and our study may
      serve as a paradigm for future analyses of superfamilies comprising
      strongly diverged members with little or no sequence similarity.
AU  - Pawlak SD
AU  - Radlinska M
AU  - Chmiel AA
AU  - Bujnicki JM
AU  - Skowronek KJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2005 33: 661-671.

PMID- 
VI  - 272
DP  - 2005
TI  - Fold-recognition, homology modeling and mutagenesis of restriction enzyme Bsp6I.
PG  - 95
AB  - Identification of functionally important residues in type II restriction enzymes (REases) has
      been difficult using conventional methods. Even though known REase structures share a common
      fold and marginally recognizable active site, the overall sequence similarities are
      statistically insignificant, unless compared among proteins that recognize identical or very
      similar sequences. Bsp6I is a Type II REase, which recognizes the palindromic DNA sequence
      5'GCNGC and cleaves between the cytosine and the unspecified nucleotide in both strands,
      generating a double strand break with 5'-protruding single nucleotides. There are no solved
      structures of REases that recognize similar DNA targets or generate cleavage products with
      similar characteristics. The Bsp6I sequence shows no significant similarity to REases with
      known structures. However, using a protein fold-recognition approach, we have identified a
      remote relationship between Bsp6I and the structure of PvuII, which allowed us to construct a
      homology model of Bsp6I and use it to predict functionally important regions and residues in
      Bsp6I. The model of the Bsp6I structure was built using the "Frankenstein's monster" method
      and tested by the characterization of the effects of single amino acid substitutions of
      residues predicted to be directly involved in involved in cleavage, DNA-binding and
      dimerization. The endonuclease activity of an extensive panel of mutants was tested in vivo
      using the bacteriophage lambda-plating assay. All mutations in residues predicted as
      catalytic, involved in DNA binding dimerization decreased the restriction level to less than
      1% of the wild type (wt) activity. A subset of mutants exhibiting different levels of
      reduction of the in vivo activity was recloned into an expression vector, overexpressed,
      purified and tested in an in vitro cleavage assay. The results agreed with the in vivo
      analyses, thus corroborating the model-based predictions. Our study represents an example of
      how the computational protein fold-recognition followed by model-based identification and
      experimental validation of functionally important residues can be used to reduce the "white
      spaces" on the structural map of a protein superfamily by providing links between known
      structures and the sequences of their remote homologs. Confident identification of a protein
      fold, which is very difficult in the case of restriction enzymes, is important for the
      selection of targets for high-resolution studies. Completing the picture of
      sequence-structure-function relationships in protein superfamilies becomes an essential task
      in the age of structural genomics and our study may serve as a paradigm for future analyses.
AU  - Pawlak SD
AU  - Skowronek K
AU  - Radlinska M
AU  - Bujnicki JM
PT  - Journal Article
TA  - FEBS J.
JT  - FEBS J.
SO  - FEBS J. 2005 272: 95.

PMID- 28408665
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of 13 Colombian Helicobacter pylori Strains Isolated from  Pacific Coast and Andean Residents.
PG  - e00113-17
AB  - We present here the draft genomes of 13 Helicobacter pylori strains isolated from Colombian
      residents on the Pacific coast (n = 6) and in the Andes mountains (n =
      7), locations that differ in gastric cancer risk. These 13 strains were obtained
      from individuals with diagnosed gastric lesions.
AU  - Pazos A
AU  - Kodaman N
AU  - Piazuelo MB
AU  - Romero-Gallo J
AU  - Sobota RS
AU  - Israel DA
AU  - Bravo LE
AU  - Morgan DR
AU  - Wilson KT
AU  - Correa P
AU  - Peek RM Jr
AU  - Williams SM
AU  - Schneider BG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00113-17.

PMID- 14529619
VI  - 333
DP  - 2003
TI  - S-Adenosyl Methionine Prevents Promiscuous DNA Cleavage by the EcoP1I type III Restriction Enzyme.
PG  - 321-335
AB  - DNA cleavage by the type III restriction endonuclease EcoP1I was analysed on circular and
      catenane DNA in a variety of buffers with different salts.
      In the presence of the cofactor S-adenosyl methionine (AdoMet), and
      irrespective of buffer, only substrates with two EcoP1I sites in inverted
      repeat were susceptible to cleavage. Maximal activity was achieved at a
      Res2Mod2 to site ratio of approximately 1:1 yet resulted in cleavage at
      only one of the two sites. In contrast, the outcome of reactions in the
      absence of AdoMet was dependent upon the identity of the monovalent buffer
      components, in particular the identity of the cation. With Na+, cleavage
      was observed only on substrates with two sites in inverted repeat at
      elevated enzyme to site ratios (>15:1). However, with K+ every substrate
      tested was susceptible to cleavage above an enzyme to site ratio of
      approximately 3:1, including a DNA molecule with two directly repeated
      sites and even a DNA molecule with a single site. Above an enzyme to site
      ratio of 2:1, substrates with two sites in inverted repeat were cleaved at
      both cognate sites. The rates of cleavage suggested two separate events: a
      fast primary reaction for the first cleavage of a pair of inverted sites;
      and an order-of-magnitude slower secondary reaction for the second
      cleavage of the pair or for the first cleavage of all other site
      combinations. EcoP1I enzymes mutated in either the ATPase or nuclease
      motifs did not produce the secondary cleavage reactions. Thus, AdoMet
      appears to play a dual role in type III endonuclease reactions: Firstly,
      as an allosteric activator, promoting DNA association; and secondly, as a
      "specificity factor", ensuring that cleavage occurs only when two
      endonucleases bind two recognition sites in a designated orientation.
      However, given the right conditions, AdoMet is not strictly required for
      DNA cleavage by a type III enzyme.
AU  - Peakman LJ
AU  - Antognozzi M
AU  - Bickle TA
AU  - Janscak P
AU  - Szczelkun MD
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2003 333: 321-335.

PMID- 15302916
VI  - 32
DP  - 2004
TI  - DNA communications by Type III restriction endonucleases - confirmation of 1D translocation over 3D looping.
PG  - 4166-4174
AB  - DNA cleavage by Type III restriction enzymes is governed strictly by the relative arrangement
      of recognition sites on a DNA substrate.  Xendonuclease activity is usually only triggered by
      sequences in head-to-head orientation. Tens to thousands of base pairs can separate these
      sites. Long distance communication over such distances could occur by either one-dimensional
      (1D) DNA translocation or 3D DNA looping. To distinguish between these alternatives, we
      analysed the activity of EcoPI and EcoP15I on DNA catenanes in which the recognition sites
      were either on the same or separate rings. While substrates with a pair of sites located on
      the same ring were cleaved efficiently, catenanes with sites on separate rings were not
      cleaved. These results exclude a simple 3D DNA-looping activity. To characterize the
      interactions further, EcoPI was incubated with plasmids carrying two recognition sites
      interspersed with two 21res sites for site-specific recombination by Tn21 resolvase;
      inhibition of recombination would indicate the formation of stable DNA loops. No inhibition
      was observed, even under conditions where EcoPI translocation could also occur.
AU  - Peakman LJ
AU  - Szczelkun MD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2004 32: 4166-4174.

PMID- 19401438
VI  - 37
DP  - 2009
TI  - S-Adenosyl homocysteine and DNA ends stimulate promiscuous nuclease activities in the Type III restriction endonuclease EcoPI.
PG  - 3934-3945
AB  - In the absence of the methyl donor S-adenosyl methionine and under certain permissive reaction
      conditions, EcoPI shows non-specific endonuclease
      activity. We show here that the cofactor analogue S-adenosyl homocysteine
      promotes this promiscuous DNA cleavage. Additionally, an extensive
      exonuclease-like processing of the DNA is also observed that can even
      result in digestion of non-specific DNA in trans. We suggest a model for
      how DNA communication events initiating from non-specific sites, and in
      particular free DNA ends, could produce the observed cleavage patterns.
AU  - Peakman LJ
AU  - Szczelkun MD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: 3934-3945.

PMID- 21742875
VI  - 193
DP  - 2011
TI  - Genome sequence of the newly isolated chemolithoautotrophic Bradyrhizobiaceae strain SG-6C.
PG  - 5057
AB  - Strain SG-6C (DSM 23264, CCM 7827) is a chemolithoautotrophic bacterium, of the family
      Bradyrhizobiaceae. It can also grow heterotrophically under
      appropriate environmental conditions. Here we report the annotated genome
      sequence of this strain in a single 4.3-Mb circular scaffold.
AU  - Pearce SL
AU  - Pandey R
AU  - Dorrian SJ
AU  - Russell RJ
AU  - Oakeshott JG
AU  - Pandey G
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5057.

PMID- 23833131
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Ralstonia sp. Strain GA3-3, Isolated from Australian Suburban Soil.
PG  - e00414-13
AB  - Ralstonia sp. strain GA3-3 is a hexachlorocyclohexane (HCH)-degrading bacterial strain
      isolated from suburban soil in Canberra, Australia. The genome of strain
      GA3-3 was sequenced to investigate its ability to degrade alpha-HCH. Here, we
      report the annotated genome sequence of this strain.
AU  - Pearce SL
AU  - Pushiri H
AU  - Oakeshott JG
AU  - Russell RJ
AU  - Pandey G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00414-13.

PMID- 17873037
VI  - 189
DP  - 2007
TI  - The Complete Genome Sequence of Campylobacter jejuni Strain 81116 (NCTC11828).
PG  - 8402-8403
AB  - Campylobacter jejuni is a major human enteric pathogen that displays genetic variability via
      genomic reorganization and phase variation. This
      variability can adversely affect the outcomes and reproducibility of
      experiments. C. jejuni strain 81116 (NCTC11828) has been suggested to be a
      genetically stable strain (G. Manning, B. Duim, T. Wassenaar, J. A.
      Wagenaar, A. Ridley, and D. G. Newell, Appl. Environ. Microbiol.
      67:1185-1189, 2001), is amenable to genetic manipulation, and is infective
      for chickens. Here we report the finished annotated genome sequence of C.
      jejuni strain 81116.
AU  - Pearson BM
AU  - Gaskin DJ
AU  - Segers RP
AU  - Wells JM
AU  - Nuijten PJ
AU  - Mvan VAH
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2007 189: 8402-8403.

PMID- 24336384
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of the Campylobacter coli Clinical Isolate 15-537360.
PG  - e01056-13
AB  - Campylobacter coli strain 15-537360 was originally isolated in 2001 from a 42-year-old patient
      with gastroenteritis. Here, we report its complete genome
      sequence, which comprises a 1.7-Mbp chromosome and a 29-kbp conjugative cryptic
      plasmid. This is the first complete genome sequence of a clinical isolate of C.
      coli.
AU  - Pearson BM
AU  - Rokney A
AU  - Crossman LC
AU  - Miller WG
AU  - Wain J
AU  - van Vliet AH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01056-13.

PMID- 21994932
VI  - 193
DP  - 2011
TI  - The Draft Genome of Planococcus donghaensis MPA1U2 Reveals Nonsporulation Pathways Controlled by a Conserved Spo0A Regulon.
PG  - 6106
AB  - The Planococcaceae are extreme survivors, having been cultured from environments such as deep
      sea sediments, marine solar salterns, glaciers,
      permafrost, Antarctic deserts, and sea ice brine. The family contains both
      sporulating and nonsporulating genera. Here we present the unclosed, draft
      genome sequence of Planococcus donghaensis strain MPA1U2, a nonsporulating
      psychrotrophic bacterium isolated from surface coastal water of the
      Pacific Ocean.
AU  - Pearson MD
AU  - Noller HF
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6106.

PMID- 18375554
VI  - 190
DP  - 2008
TI  - Complete genome sequence of uropathogenic Proteus mirabilis, a master of both adherence and motility.
PG  - 4027-4037
AB  - The gram-negative enteric bacterium Proteus mirabilis is a frequent cause of urinary tract
      infections in individuals with long-term indwelling
      catheters or with complicated urinary tracts (e.g., due to spinal cord
      injury or anatomic abnormality). P. mirabilis bacteriuria may lead to
      acute pyelonephritis, fever, and bacteremia. Most notoriously, this
      pathogen uses urease to catalyze the formation of kidney and bladder
      stones or to encrust or obstruct indwelling urinary catheters. Here we
      report the complete genome sequence of P. mirabilis HI4320, a
      representative strain cultured in our laboratory from the urine of a
      nursing home patient with a long-term (> or =30 days) indwelling urinary
      catheter. The genome is 4.063 Mb long and has a G+C content of 38.88%.
      There is a single plasmid consisting of 36,289 nucleotides. Annotation of
      the genome identified 3,685 coding sequences and seven rRNA loci. Analysis
      of the sequence confirmed the presence of previously identified virulence
      determinants, as well as a contiguous 54-kb flagellar regulon and 17 types
      of fimbriae. Genes encoding a potential type III secretion system were
      identified on a low-G+C-content genomic island containing 24 intact genes
      that appear to encode all components necessary to assemble a type III
      secretion system needle complex. In addition, the P. mirabilis HI4320
      genome possesses four tandem copies of the zapE metalloprotease gene,
      genes encoding six putative autotransporters, an extension of the atf
      fimbrial operon to six genes, including an mrpJ homolog, and genes
      encoding at least five iron uptake mechanisms, two potential type IV
      secretion systems, and 16 two-component regulators.
AU  - Pearson MM et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2008 190: 4027-4037.

PMID- 519761
VI  - 18
DP  - 1979
TI  - Patchwork structure of a bovine satellite DNA.
PG  - 883-893
AB  - According to a previous restriction nuclease analysis, bovine 1.706 satellite
      DNA (density 1.706 g/cm3 in CsCl) is organized in an unusual structure of
      superimposed long- and short-range repeats (Streeck and Zachau, 1978).  We have
      now determined the nucleotide sequence of this satellite DNA in both cloned
      fragments and fragments from the total satellite DNA.  Each long-range repeat
      unit (about 2350 bp) is divided into four segments.  Each segment consists of
      different variants of a basic 23 bp sequence which is itself composed of a
      dodecanucleotide and a related undecanucleotide.  A total of 2400 nucleotides
      have been sequenced.  Detailed analysis of the sequence divergence reveals that
      both the overall extent of divergence and the frequency of base changes at
      individual positions of the 23 bp repeats are characteristically different in
      the various segments.  Preferentially methylated sites and a high incidence of
      symmetry elements are found.  In two of the four segments, 22 of 23 bp of the
      prototype sequence are included in six overlapping elements of dyad symmetry
      and in a palindrome.  A scheme for the evolution of the satellite DNA from a
      basic dodecanucleotide is proposed which is based on the different degrees of
      divergence for the various repeats superimposed in this satellite DNA.
AU  - Pech M
AU  - Streeck RE
AU  - Zachau HG
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1979 18: 883-893.

PMID- 29439041
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of the Novel Cellulolytic, Anaerobic, Thermophilic Bacterium Herbivorax saccincola Type Strain GGR1, Isolated from a Lab Scale  Biogas Reactor as Established by Illumina and Nanopore MinION Sequencing.
PG  - e01493-17
AB  - The cellulolytic bacterium Herbivorax saccincola strain GGR1, which represents the type strain
      of this species, was isolated from the in vivo enriched
      cellulose-binding community of a lab scale thermophilic biogas reactor. Here, we
      report the complete genome sequence of H. saccincola GGR1(T), the first isolated
      member of the genus Herbivorax.
AU  - Pechtl A
AU  - Ruckert C
AU  - Maus I
AU  - Koeck DE
AU  - Trushina N
AU  - Kornberger P
AU  - Schwarz WH
AU  - Schluter A
AU  - Liebl W
AU  - Zverlov VV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01493-17.

PMID- 24874683
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of the Subsurface, Mesophilic Sulfate-Reducing Bacterium Desulfovibrio aespoeensis Aspo-2.
PG  - e00509-14
AB  - Desulfovibrio aespoeensis Aspo-2, DSM 10631(T), is a mesophilic, hydrogenotrophic
      sulfate-reducing bacterium sampled from a 600-m-deep subsurface aquifer in hard
      rock under the island of Aspo in southeastern Sweden. We report the genome
      sequence of this bacterium, which is a 3,629,109-bp chromosome; plasmids were not
      found.
AU  - Pedersen K
AU  - Bengtsson A
AU  - Edlund J
AU  - Rabe L
AU  - Hazen T
AU  - Chakraborty R
AU  - Goodwin L
AU  - Shapiro N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00509-14.

PMID- 24903867
VI  - 2
DP  - 2014
TI  - Genome Sequence of Leuconostoc mesenteroides subsp. cremoris Strain T26, Isolated from Mesophilic Undefined Cheese Starter.
PG  - e00485-14
AB  - Leuconostoc is the main group of heterofermentative bacteria found in mesophilic  dairy
      starters. They grow in close symbiosis with the Lactococcus population and
      are able to degrade citrate. Here we present a draft genome sequence of
      Leuconostoc mesenteroides subsp. cremoris strain T26.
AU  - Pedersen TB
AU  - Kot WP
AU  - Hansen LH
AU  - Sorensen SJ
AU  - Broadbent JR
AU  - Vogensen FK
AU  - Ardo Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00485-14.

PMID- 24903866
VI  - 2
DP  - 2014
TI  - Genome Sequences of Two Leuconostoc pseudomesenteroides Strains Isolated from Danish Dairy Starter Cultures.
PG  - e00484-14
AB  - The lactic acid bacterium Leuconostoc pseudomesenteroides can be found in mesophilic cheese
      starters, where it produces aromatic compounds from, e.g.,
      citrate. Here, we present the draft genome sequences of two L.
      pseudomesenteroides strains isolated from traditional Danish cheese starters.
AU  - Pedersen TB
AU  - Kot WP
AU  - Hansen LH
AU  - Sorensen SJ
AU  - Broadbent JR
AU  - Vogensen FK
AU  - Ardo Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00484-14.

PMID- 12705866
VI  - 113
DP  - 2003
TI  - 
PG  - 171-182
AB  - Bacteriophages are the most abundant organisms in the biosphere and play major roles in the
      ecological balance of microbial life. The genomic
      sequences of ten newly isolated mycobacteriophages suggest that the
      bacteriophage population as a whole is amazingly diverse and may represent
      the largest unexplored reservoir of sequence information in the biosphere.
      Genomic comparison of these mycobacteriophages contributes to our
      understanding of the mechanisms of viral evolution and provides compelling
      evidence for the role of illegitimate recombination in horizontal genetic
      exchange. The promiscuity of these recombination events results in the
      inclusion of many unexpected genes including those implicated in
      mycobacterial latency, the cellular and immune responses to mycobacterial
      infections, and autoimmune diseases such as human lupus. While the role of
      phages as vehicles of toxin genes is well established, these observations
      suggest a much broader involvement of phages in bacterial virulence and
      the host response to bacterial infections.
AU  - Pedulla ML et al
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 2003 113: 171-182.

PMID- Not included in PubMed...
VI  - 39
DP  - 1996
TI  - Expression of ICEA, a novel ulcer-associated H. pylori gene, is induced by contact with gastric epithelial cells and is associated with enhanced mucosal IL-8.
PG  - A71
AB  - cagA+tox+ H. pylori strains are linked with peptic ulceration but most persons infected with
      such isolates remain disease-free; thus, other unidentified virulence genes may be important
      in pathogenesis.  For H. pylori, adherence to gastric epithelium may provide a stimulus for
      induction of virulence gene expression.  iceA is a novel H. pylori gene that is selectively
      up-regulated following contact with gastric epithelial cells.  The aims of this study were to
      characterize iceA allellic diversity, correlate iceA genotypes with H. pylori virulence
      determinants, peptic ulcer disease and in vivo IL-8 production, and examine expression of iceA
      alleles following contact with gastric epithelial cells.
AU  - Peek RM Jr
AU  - Thompson SA
AU  - Atherton JC
AU  - Blaser MJ
AU  - Miller GG
PT  - Journal Article
TA  - Gut
JT  - Gut
SO  - Gut 1996 39: A71.

PMID- 25858826
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Supercritical CO2-Tolerant Bacteria Bacillus subterraneus MITOT1 and Bacillus cereus MIT0214.
PG  - e00140-15
AB  - We report draft genome sequences of Bacillus subterraneus MITOT1 and Bacillus cereus MIT0214
      isolated through enrichment of samples from geologic sequestration
      sites in pressurized bioreactors containing a supercritical (sc) CO2 headspace.
      Their genome sequences expand the phylogenetic range of sequenced bacilli and
      allow characterization of molecular mechanisms of scCO2 tolerance.
AU  - Peet KC
AU  - Thompson JR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00140-15.

PMID- 25767231
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Two Strains of Serratia spp. from the Midgut of the Malaria Mosquito Anopheles gambiae.
PG  - e00090-15
AB  - Here, we report the annotated draft genome sequences of two strains of Serratia spp., Ag1 and
      Ag2, isolated from the midgut of two different strains of Anopheles
      gambiae. The genomes of these two strains are almost identical.
AU  - Pei D
AU  - Hill-Clemons C
AU  - Carissimo G
AU  - Yu W
AU  - Vernick KD
AU  - Xu J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00090-15.

PMID- 29167265
VI  - 5
DP  - 2017
TI  - Complete Circularized Genome Sequences of Four Strains of Elizabethkingia anophelis, Including Two Novel Strains Isolated from Wild-Caught Anopheles  sinensis.
PG  - e01359-17
AB  - We provide complete circularized genome sequences of two mosquito-derived Elizabethkingia
      anophelis strains with draft sequences currently in the public
      domain (R26 and Ag1), and two novel E. anophelis strains derived from a different
      mosquito species, Anopheles sinensis (AR4-6 and AR6-8). The genetic similarity of
      all four mosquito-derived strains is remarkable.
AU  - Pei D
AU  - Nicholson AC
AU  - Jiang J
AU  - Chen H
AU  - Whitney AM
AU  - Villarma A
AU  - Bell M
AU  - Humrighouse B
AU  - Rowe LA
AU  - Sheth M
AU  - Batra D
AU  - Juieng P
AU  - Loparev VN
AU  - McQuiston JR
AU  - Lan Y
AU  - Ma Y
AU  - Xu J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01359-17.

PMID- 2784394
VI  - 245
DP  - 1989
TI  - Oligonucleotide duplexes containing CC(A/T)GG stimulate cleavage of refractory DNA by restriction endonuclease EcoRII.
PG  - 141-144
AB  - Some DNA species are resistant towards the restriction endonuclease EcoRII
      despite the presence of unmodified recognition sites.  We show that 14
      base-pair oligonucleotide duplexes containing the EcoRII recognition site
      5'-CC(A/T)GG are cleaved by this enzyme and are able to stimulate EcoRII
      cleavage of such resistant DNA molecules (e.g. DNA of bacterial virus T3).  A
      direct correlation between the concentration of oligonucleotide duplex
      molecules and the degree of EcoRII digestion of the primarily resistant DNA is
      observed.  This indicates a stoichiometric rather than a catalytic mode of
      enzyme activation.  An excess of DNA devoid of EcoRII sites (non-site DNA, e.g.
      MvaI-digested T7 DNA) does not interfere with the activity of EcoRII.
AU  - Pein C-D
AU  - Reuter M
AU  - Cech D
AU  - Kruger DH
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1989 245: 141-144.

PMID- 1923799
VI  - 19
DP  - 1991
TI  - Activation of restriction endonuclease EcoRII does not depend on the cleavage of stimulator DNA.
PG  - 5139-5142
AB  - The restriction endonuclease EcoRII is unable to cleave DNA molecules when
      recognition sites are very far apart.  The enzyme, however can be activated in
      the presence of DNA molecules with a high frequency of EcoRII sites or by
      oligonucleotides containing recognition sites:  Addition of the activator
      molecules stimulates cleavage of the refractory substrate.  We now show that
      endonucleolysis of the stimulator molecules is not a necessary prerequisite of
      enzyme activation.  A total EcoRII digest of pBR322 DNA or oligonucleotide
      duplexes with simulated EcoRII ends (containing the 5' phosphate group), as
      well as oligonucleotide duplexes containing modified bases within the EcoRII
      site, making them resistant to cleavage, are all capable of enzyme activation.
      For activation EcoRII requires interaction with at least two recognition sites.
      The two sites may be on the same DNA molecule, on different oligonucleotide
      duplexes, or on one DNA molecule and one oligonucleotide duplex.  The
      efficiency of functional intramolecular cooperation decreases with increasing
      distance between the sites.  Intermolecular site interaction is inversely
      related to the size of the stimulator oligonucleotide duplex.  The data are in
      agreement with a model whereby EcoRII simultaneously interacts with two
      recognition sites in the active complex, but cleavage of the site serving as an
      allosteric activator is not necessary.
AU  - Pein C-D
AU  - Reuter M
AU  - Meisel A
AU  - Cech D
AU  - Kruger DH
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 5139-5142.

PMID- 2827129
VI  - SS18
DP  - 1987
TI  - Interaction of the MvaI restriction enzyme with synthetic DNA fragments.
PG  - 225-228
AB  - The cleavage of synthetic DNA duplexes by the restriction endonuclease MvaI has
      been studied.  The main result of the cleavage experiments is that MvaI cleaves
      unmodified duplexes in two single strand scissions in separate events and that
      the two strands are cleaved at significantly different rates.  One strand nicks
      within the recognition site do not affect the cleavage.  Furthermore, neither a
      pyrophosphate internucleotide bond modification in one strand nor the absence
      of one phosphate group at the central dA-residue of the recognition site
      inhibits the cleavage of the second strand.
AU  - Pein CD
AU  - Cech D
AU  - Gromova ES
AU  - Orezkaya TS
AU  - Shabarova ZA
AU  - Kubareva EA
PT  - Journal Article
TA  - Nucleic Acids Symp. Ser.
JT  - Nucleic Acids Symp. Ser.
SO  - Nucleic Acids Symp. Ser. 1987 SS18: 225-228.

PMID- 9628360
VI  - 379
DP  - 1998
TI  - Establishment of a hybrid SalI-HgiDII type II restriction-modification system.
PG  - 583-584
AB  - In the SalI system, endonuclease activity can be only achieved in the presence of a functional
      modification gene.  Thus, the DNA methyltransferase is involved in the control of restriction.
      By fusion of the restriction gene of the SalI system to the modification gene of the
      isospecific HgiDII system a hybrid type II restriction-modification system was created.
      Although in the hybrid situation the level of endonuclease activity was significantly lower
      than in the natural system, the HgiDII modification enzyme clearly supports SalI restriction.
      The mechanism by which the two isospecific methyltransferases control restriction is currently
      under study.
AU  - Pelaez AI
AU  - Ribas-Aparicio RM
AU  - Gomez A
AU  - Rodicio MR
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1998 379: 583-584.

PMID- 
VI  - 20
DP  - 2003
TI  - Target site cleavage by the homing endonuclease I-SpomI from fission yeast mitochondria.
PG  - S47
AB  - Proteins encoded by mobile group I introns promote invasion into target DNAs.  The LAGLIDADG
      homing endonuclease I-SpomI from the intron cox1Ilb of S. pombe mitochondria recognizes a
      target DNA-sequence of 20bp.  As other representatives of this enzyme class I-SpomI generates
      a 4nt 3' overhang.  Because of the length of the recognition sequence it can be employed for
      the induction of specific double strand brakes in vitro and in vivo.  Since the recognition
      site is almost palindromic, we changed it in such a way to give rise to a complete palindrome.
      Since one of those variants was cut as well as the wild-type sequence, we assume that the
      enzyme forms dimers and only one of the two LAGLIDADG-motifs is involved in the recognition of
      the DNA-substrate.  An antibody against I-SpomI allows the determination of the active form in
      mitochondrial extracts of the fission yeast.  Furthermore we introduced mutations into both
      LADLIDADG-motifs: in motif P1 the aspartic residues were changed into alanine, in P2 the two
      glutamic residues.  Inactivation of one of those motifs employed in the cutting mechanism was
      supposed to result in a DNA single strand break actively of the mutant protein.  The
      experiments were done in parallel with I-SceI from S. cerevisiae to have a direct comparison
      between the different enzymes.  Enzymes with nicking activity can serve to study as well the
      repair mechanisms of SSB and to give insights into the cutting mechanism of LAGLIDADG homing
      endonucleases.
AU  - Pellenz S
AU  - Dujon B
AU  - Schafer B
PT  - Journal Article
TA  - Yeast
JT  - Yeast
SO  - Yeast 2003 20: S47.

PMID- 12187383
VI  - 55
DP  - 2002
TI  - Characterization of the I-SpomI endonuclease from fission yeast: Insights into the evolution of a group I intron-encoded homing  endonuclease.
PG  - 302-313
AB  - The first group I intron in the cox1 gene (cox1I1b) of the mitochondrial genome of the fission
      yeast Schizosaccharomyces pombe is
      a mobile DNA element. The mobility is dependent on an endonuclease
      protein that is encoded by an intronic open reading frame (ORF). The
      intron-encoded endonuclease is a typical member of the LAGLIDADG
      protein family of endonucleases with two consensus motifs. In addition
      to this, analysis of several intron mutants revealed that this protein
      is required for intron splicing. However, this protein is one of the
      few group I intron-encoded proteins that functions in RNA splicing
      simultaneously with its DNA endonuclease activity. We report here on
      the biochemical characterization of the endonuclease activity of this
      protein artificially expressed in Escherichia coli. Although the
      intronic ORF is expressed as a fusion protein with the upstream exon in
      vivo, the experiments showed that a truncated translation product
      consisting of the C-terminal 304 codons of the cox1I1b ORF restricted
      to loop 8 of the intron RNA secondary structure is sufficient for the
      specific endonuclease activity in vitro. Based on the results, we
      speculate on the evolution of site-specific homing endonucleases
      encoded by group I introns in eukaryotes.
AU  - Pellenz S
AU  - Harington A
AU  - Dujon B
AU  - Wolf K
AU  - Schaefer B
PT  - Journal Article
TA  - J. Mol. Evol.
JT  - J. Mol. Evol.
SO  - J. Mol. Evol. 2002 55: 302-313.

PMID- 18245282
VI  - 190
DP  - 2008
TI  - "Candidatus Cloacamonas acidaminovorans": genome sequence reconstruction provides a first glimpse of a new bacterial division.
PG  - 2572-2579
AB  - Many microorganisms live in anaerobic environments. Most of these microorganisms have not yet
      been cultivated. Here, we present, from a
      metagenomic analysis of an anaerobic digester of a municipal wastewater
      treatment plant, a reconstruction of the complete genome of a bacterium
      belonging to the WWE1 candidate division. In silico proteome analysis
      indicated that this bacterium might derive most of its carbon and energy
      from the fermentation of amino acids, and hence, it was provisionally
      classified as "Candidatus Cloacamonas acidaminovorans." "Candidatus
      Cloacamonas acidaminovorans" is probably a syntrophic bacterium that is
      present in many anaerobic digesters. This report highlights how
      environmental sequence data might provide genomic and functional
      information about a new bacterial clade whose members are involved in
      anaerobic digestion.
AU  - Pelletier E
AU  - Kreimeyer A
AU  - Bocs S
AU  - Rouy Z
AU  - Gyapay G
AU  - Chouari R
AU  - Riviere D
AU  - Ganesan A
AU  - Daegelen P
AU  - Sghir A
AU  - Cohen GN
AU  - Medigue C
AU  - Weissenbach J
AU  - Le Paslier D
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2008 190: 2572-2579.

PMID- 12923091
VI  - 185
DP  - 2003
TI  - The SopEPhi Phage Integrates into the ssrA Gene of Salmonella enterica Serovar Typhimurium A36 and Is Closely Related to the Fels-2 Prophage.
PG  - 5182-5191
AB  - Salmonella spp. are enteropathogenic gram-negative bacteria that use a large array of
      virulence factors to colonize the host, manipulate host
      cells, and resist the host's defense mechanisms. Even closely related
      Salmonella strains have different repertoires of virulence factors.
      Bacteriophages contribute substantially to this diversity. There is
      increasing evidence that the reassortment of virulence factor repertoires
      by converting phages like the GIFSY phages and SopEPhi may represent an
      important mechanism in the adaptation of Salmonella spp. to specific hosts
      and to the emergence of new epidemic strains. Here, we have analyzed in
      more detail SopEPhi, a P2-like phage from Salmonella enterica serovar
      Typhimurium DT204 that encodes the virulence factor SopE. We have cloned
      and characterized the attachment site (att) of SopEPhi and found that its
      47-bp core sequence overlaps the 3' terminus of the ssrA gene of serovar
      Typhimurium. Furthermore, we have demonstrated integration of SopEPhi into
      the cloned attB site of serovar Typhimurium A36. Sequence analysis of the
      plasmid-borne prophage revealed that SopEPhi is closely related to (60 to
      100% identity over 80% of the genome) but clearly distinct from the Fels-2
      prophage of serovar Typhimurium LT2 and from P2-like phages in the serovar
      Typhi CT18 genome. Our results demonstrate that there is considerable
      variation among the P2-like phages present in closely related Salmonella
      spp.
AU  - Pelludat C
AU  - Mirold S
AU  - Hardt WD
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2003 185: 5182-5191.

PMID- 17020552
VI  - 264
DP  - 2006
TI  - A novel ICE in the genome of Shewanella putrefaciens W3-18-1: comparison with the SXT/R391 ICE-like elements.
PG  - 80-88
AB  - A novel R391-like ICE (integrating conjugative element) has been detected in the  4.2 MB
      genome of Shewanella putrefaciens W3-18-1 located on three different
      contigs. Assembly of the ICE encoding contigs based on similarity with R391
      revealed a mosaic element of plasmid, phage and transposon-like sequences typical
      of SXT/R391 ICE-like elements. The element, which is 110 057 bp in length, was
      highly similar to R391 sequences, with most related ORFs showing >96% amino acid
      sequence identity. The element, designated ICESpuPO1, contained a number of
      inserts determining resistance to copper and other heavy metals and a
      broad-spectrum RND efflux pump similar to antibiotic efflux systems. The element
      was integrated into the Shewanella prfC gene in a manner similar to related
      ICE-like elements. The chromosomal element junctions contained a 17-bp
      SXT/R391-like attL and attR site and an unannotated ORF between attL and the ICE
      integrase encoding a putative recombinational directional factor necessary for
      excision, with 100% amino acid identity to the R391 ORF4 product.
AU  - Pembroke JT
AU  - Piterina AV
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2006 264: 80-88.

PMID- 22328767
VI  - 194
DP  - 2012
TI  - Draft Genome of Pseudomonas stutzeri Strain ZoBell (CCUG 16156), a Marine Isolate and Model Organism for Denitrification Studies.
PG  - 1277-1278
AB  - Pseudomonas stutzeri strain ZoBell, formerly a strain of Pseudomonas perfectomarina (CCUG
      16156 = ATCC 14405), is a model organism for
      denitrification. It was isolated by ZoBell in 1944 from a marine sample, and here
      we report the first genome draft of a strain assigned to genomovar 2 of the
      species P. stutzeri.
AU  - Pena A
AU  - Busquets A
AU  - Gomila M
AU  - Bosch R
AU  - Nogales B
AU  - Garcia-Valdes E
AU  - Lalucat J
AU  - Bennasar A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1277-1278.

PMID- 23516224
VI  - 1
DP  - 2013
TI  - Draft Genome of Pseudomonas stutzeri Strain NF13, a Nitrogen Fixer Isolated from  the Galapagos Rift Hydrothermal Vent.
PG  - e0011313
AB  - Pseudomonas stutzeri strain NF13 was isolated from a water sample taken at a hydrothermal vent
      in the Galapagos rift. It was selected for its ability to
      metabolize sulfur compounds and to grow diazotrophically. Here, we report the
      first draft genome of a member of genomovar 19 of the species.
AU  - Pena A
AU  - Busquets A
AU  - Gomila M
AU  - Mayol J
AU  - Bosch R
AU  - Nogales B
AU  - Garcia-Valdes E
AU  - Bennasar A
AU  - Lalucat J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0011313.

PMID- 27594974
VI  - 11
DP  - 2016
TI  - High quality draft genome sequences of Pseudomonas fulva DSM 17717(T), Pseudomonas parafulva DSM 17004(T) and Pseudomonas cremoricolorata DSM 17059(T)  type strains.
PG  - 55
AB  - Pseudomonas has the highest number of species out of any genus of Gram-negative bacteria and
      is phylogenetically divided into several groups. The Pseudomonas
      putida phylogenetic branch includes at least 13 species of environmental and
      industrial interest, plant-associated bacteria, insect pathogens, and even some
      members that have been found in clinical specimens. In the context of the Genomic
      Encyclopedia of Bacteria and Archaea project, we present the permanent,
      high-quality draft genomes of the type strains of 3 taxonomically and
      ecologically closely related species in the Pseudomonas putida phylogenetic
      branch: Pseudomonas fulva DSM 17717(T), Pseudomonas parafulva DSM 17004(T) and
      Pseudomonas cremoricolorata DSM 17059(T). All three genomes are comparable in
      size (4.6-4.9 Mb), with 4,119-4,459 protein-coding genes. Average nucleotide
      identity based on BLAST comparisons and digital genome-to-genome distance
      calculations are in good agreement with experimental DNA-DNA hybridization
      results. The genome sequences presented here will be very helpful in elucidating
      the taxonomy, phylogeny and evolution of the Pseudomonas putida species complex.
AU  - Pena A
AU  - Busquets A
AU  - Gomila M
AU  - Mulet M
AU  - Gomila RM
AU  - Reddy TB
AU  - Huntemann M
AU  - Pati A
AU  - Ivanova N
AU  - Markowitz V
AU  - Garcia-Valdes E
AU  - Goker M
AU  - Woyke T
AU  - Klenk HP
AU  - Kyrpides N
AU  - Lalucat J
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 55.

PMID- 28428293
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Bacillus cereus LA2007, a Human-Pathogenic Isolate Harboring Anthrax-Like Plasmids.
PG  - e00181-17
AB  - We present the genome sequence of Bacillus cereus LA2007, a strain isolated in 2007 from a
      fatal pneumonia case in Louisiana. Sequence-based genome analysis
      revealed that LA2007 carries a plasmid highly similar to Bacillus anthracis pXO1,
      including the genes responsible for the production and regulation of anthrax
      toxin.
AU  - Pena-Gonzalez A
AU  - Marston CK
AU  - Rodriguez-R LM
AU  - Kolton CB
AU  - Garcia-Diaz J
AU  - Theppote A
AU  - Frace M
AU  - Konstantinidis KT
AU  - Hoffmaster AR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00181-17.

PMID- 24501644
VI  - 9
DP  - 2013
TI  - Genome sequence and description of the heavy metal tolerant bacterium Lysinibacillus sphaericus strain OT4b.31.
PG  - 42-56
AB  - Lysinibacillus sphaericus strain OT4b.31 is a native Colombian strain having no larvicidal
      activity against Culex quinquefasciatus and is widely applied in the
      bioremediation of heavy-metal polluted environments. Strain OT4b.31 was placed
      between DNA homology groups III and IV. By gap-filling and alignment steps, we
      propose a 4,096,672 bp chromosomal scaffold. The whole genome (consisting of
      4,856,302 bp long, 94 contigs and 4,846 predicted protein-coding sequences)
      revealed differences in comparison to the L. sphaericus C3-41 genome, such as
      syntenial relationships, prophages and putative mosquitocidal toxins.
      Sphaericolysin B354, the coleopteran toxin Sip1A and heavy metal resistance
      clusters from nik, ars, czc, cop, chr, czr and cad operons were identified.
      Lysinibacillus sphaericus OT4b.31 has applications not only in bioremediation
      efforts, but also in the biological control of agricultural pests.
AU  - Pena-Montenegro TD
AU  - Dussan J
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 9: 42-56.

PMID- 25685257
VI  - 10
DP  - 2015
TI  - Genome sequence and description of the mosquitocidal and heavy metal tolerant strain Lysinibacillus sphaericus CBAM5.
PG  - 2
AB  - Lysinibacillus sphaericus CBAM5, was isolated from subsurface soil of oil well explorations in
      the Easter Planes of Colombia. This strain has potential in
      bioremediation of heavy-metal polluted environments and biological control of
      Culex quinquefasciatus. According to the phylogenetic analysis of 16S rRNA gene
      sequences, the strain CBAM5 was assigned to the Lysinibacillus sphaericus
      taxonomic group 1 that comprises mosquito pathogenic strains. After a combination
      assembly-integration, alignment and gap-filling steps, we propose a 4,610,292 bp
      chromosomal scaffold. The whole genome (consisting of 5,146,656 bp long, 60
      contigs and 5,209 predicted-coding sequences) revealed strong functional and
      syntenial similarities to the L. sphaericus C3-41 genome. Mosquitocidal (Mtx),
      binary (Bin) toxins, cereolysin O, and heavy metal resistance clusters from nik,
      ars, czc, mnt, ter, cop, cad, and znu operons were identified.
AU  - Pena-Montenegro TD
AU  - Lozano L
AU  - Dussan J
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 2.

PMID- 18031983
VI  - 91
DP  - 2008
TI  - Characterization of ST-4821 complex, a unique Neisseria meningitidis clone.
PG  - 78-87
AB  - Ten outbreaks of a new serogroup C meningococcal disease emerged during
      2003-2005 in China. The multilocus sequence typing results indicated that
      unique sequence type 4821 clone meningococci were responsible for these
      outbreaks. Herein, we determined the entire genomic DNA sequence of
      serogroup C isolate 053442, which belongs to ST-4821. Comparison of 053442
      gene contents with other meningococcal genomes shows that they have
      similar characteristics, including thousands of repetitive elements and
      simple sequence repeats, numerous phase-variable genes, and similar
      virulence-related factors. However, many strain-specific regions were
      found in each genome. We also present the results of a genomic comparison
      of 28 ST-4821 complex isolates that were isolated from different
      serogroups using comparative genomic hybridization analysis. Genome
      comparison between the newly emerged hyperinvasive isolates belonging to
      different serogroups will further our understanding of their respective
      pathogenetic mechanisms.
AU  - Peng J
AU  - Yang L
AU  - Yang F
AU  - Yang J
AU  - Yan Y
AU  - Nie H
AU  - Zhang X
AU  - Xiong Z
AU  - Jiang Y
AU  - Cheng F
AU  - Xu X
AU  - Chen S
AU  - Sun L
AU  - Li W
AU  - Shen Y
AU  - Shao Z
AU  - Liang X
AU  - Xu J
AU  - Jin Q
PT  - Journal Article
TA  - Genomics
JT  - Genomics
SO  - Genomics 2008 91: 78-87.

PMID- 25999580
VI  - 3
DP  - 2015
TI  - Genome Sequence of Bacillus coagulans P38, an Efficient Polymer-Grade l-Lactate Producer from Cellulosic Substrates.
PG  - e00495-15
AB  - Bacillus coagulans P38 is an efficient polymer-grade l-lactic acid producer from  a cellulosic
      carbon source. Here, the draft 3.37-Mb genome sequence of this
      potential strain may provide useful information to further improve the strain
      performance for higher titers and, importantly, to understand the mechanism of
      its high tolerance for 2-furfural.
AU  - Peng L
AU  - Song L
AU  - Sun L
AU  - Cai Y
AU  - Wang L
AU  - Yu B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00495-15.

PMID- 28450503
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Potassium Feldspar-Solubilizing Bacterium Ensifer adhaerens L18.
PG  - e00199-17
AB  - Ensifer adhaerens L18, isolated from potassium feldspar mining area soil, was found to be
      capable of solubilizing K from an insoluble K-bearing mineral source.
      Here, we report the draft genome sequence and annotation of the
      feldspar-solubilizing bacterium Ensifer adhaerens L18. These data provide the
      basis to investigate the relative impact of bacteria in feldspar solubilizing and
      the molecular mechanism of the potassium feldspar's dissolution.
AU  - Peng Q
AU  - Yi L
AU  - Peng Q
AU  - Peng Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00199-17.

PMID- 29301896
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of the Vanadium-Leaching Bacterium Pseudomonas chlororaphis Strain L19.
PG  - e00966-17
AB  - Pseudomonas chlororaphis strain L19, isolated from stone coal soil, has the ability to perform
      bioleaching to release vanadium ions from mineral ore. Here,
      we report the draft genome sequence and annotation of the vanadium-leaching
      bacterium Pseudomonas chlororaphis L19. These data provide information for
      understanding the genomic properties and mineral bioleaching mechanisms of strain
      L19.
AU  - Peng Q
AU  - Yi L
AU  - Zhou L
AU  - Peng Q
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00966-17.

PMID- 26044430
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Thermoanaerobacter sp. Strain YS13, a Novel Thermophilic Bacterium.
PG  - e00584-15
AB  - Here, we report the draft genome sequence of Thermoanerobacter sp. YS13, isolated from a
      geothermal hot spring in Yellowstone National Park, which consists of
      2,713,030 bp with a mean G+C content of 34.05%. A total of 2,779 genes, including
      2,707 protein-coding genes, 12 rRNAs, and 59 tRNAs were identified.
AU  - Peng T
AU  - Pan S
AU  - Christopher L
AU  - Sparling R
AU  - Levin DB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00584-15.

PMID- 16885309
VI  - 72
DP  - 2006
TI  - Discovery of a marine bacterium producing 4-hydroxybenzoate and its alkyl esters, parabens.
PG  - 5556-5561
AB  - Chemically synthesized 4-hydroxybenzoate (4HBA) is widely used in the chemical
      and electrical industries as a material for producing polymers such as those of
      the liquid crystal type. Its alkyl esters, called parabens, have been the most
      widely used preservatives by the food and cosmetic industries. We report here for
      the first time a microorganism, a marine bacterium, which biosynthesizes these
      petrochemical products. The marine bacterial strain, A4B-17, which was found to
      belong to the genus Microbulbifer on the basis of its rRNA and gyrB sequences,
      was isolated from an ascidian in the coastal waters of Palau. Strain A4B-17 was,
      surprisingly, found to produce 10 mg/liter of 4HBA, together with its butyl (24
      mg/liter), heptyl (0.4 mg/liter), and nonyl (6 mg/liter) esters. We therefore
      characterized 23 other marine bacteria belonging to the genus Microbulbifer,
      which our institute had previously isolated from various marine environments, and
      found that these bacteria also produced 4HBA, although with low production levels
      (less than one-fifth of that produced by A4B-17). We also show that the alkyl
      esters of 4HBA produced by strain A4B-17 were effective in preventing the growth
      of yeasts, molds, and gram-positive bacteria.
AU  - Peng X
AU  - Adachi K
AU  - Chen C
AU  - Kasai H
AU  - Kanoh K
AU  - Shizuri Y
AU  - Misawa N
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2006 72: 5556-5561.

PMID- 26827796
VI  - 581
DP  - 2016
TI  - Genomic characterization of Pasteurella multocida HB01, a serotype A bovine isolate from China.
PG  - 85-93
AB  - Pasteurellamultocida infects various domestic and feral animals, generally causing clinical
      disease. To investigate P. multocida disease in cattle, we sequenced the complete genome of P.
      multocida HB01 (GenBank accession CP006976), a serotype A organism isolated from a cow in
      China. The genome is composed of a single circular chromosome of 2,416,068 base pairs
      containing 2212 protein-coding sequences, 6 ribosomal rRNA operons,
      and 56 tRNA genes. The present study confirms that P. multocida HB01 possesses a more complete
      metabolic pathway with an intact trichloroacetic acid cycle for anabolism compared with A.
      pleuropneumoniae and Haemophilus parasuis. This is the first time that this metabolic
      mechanism of P. multocida has been described. We also identified a full spectrum of genes
      related to known virulence factors of P. multocida. The differences
      in virulence factors between strains of different serotypes and origins were also compared.
      This comprehensive comparative genome analysis will help in further studies of the metabolic
      pathways, genetic basis of serotype, and virulence of P. multocida.
AU  - Peng Z
AU  - Liang W
AU  - Liu W
AU  - Wu B
AU  - Tang B
AU  - Tan C
AU  - Zhou R
AU  - Chen H
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 2016 581: 85-93.

PMID- 27340071
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Enterococcus hirae R17, a Daptomycin-Resistant Bacterium Isolated from Retail Pork in China.
PG  - e00605-16
AB  - Daptomycin-resistant Enterococcus hirae R17 was isolated from retail pork sold at a free-trade
      market in Beijing, China. The complete genome sequence of R17
      contains a circular 2,886,481-bp chromosome and a circular 73,574-bp plasmid.
      Genes involved in cell envelope homeostasis of this bacterium were identified by
      whole-genome analysis.
AU  - Peng Z
AU  - Wang W
AU  - Hu Y
AU  - Li F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00605-16.

PMID- 7791212
VI  - 249
DP  - 1995
TI  - Phage T4-coded Stp: double-edged effector of coupled DNA and tRNA-restriction systems.
PG  - 857-868
AB  - The optional Escherichia coli prr locus encodes two physically associated restriction systems:
      the type IC DNA restriction-modification enzyme EcoprrI and the tRNALys-specific anticodon
      nuclease, specified by the PrrC polypeptide. Anticodon nuclease is kept latent as a result of
      this interaction. The activation of anticodon nuclease, upon infection by phage T4, may cause
      depletion of tRNALys and, consequently, abolition of T4 protein synthesis. However, this
      effect is counteracted by the repair of tRNALys in consecutive reactions catalysed by the
      phage enzymes polynucleotide kinase and RNA ligase. Stp, a short polypeptide encoded by phage
      T4, has been implicated with activation of the anticodon nuclease. Here we confirm this notion
      and also demonstrate a second function of Stp: inhibition of EcoprrI restriction. Both effects
      depend, in general, on the same residues within the N-proximal 18 residue region of Stp. We
      propose that Stp alters the conformation of EcoprrI and, consequently, of PrrC, allowing
      activation of the latent anticodon nuclease. Presumably, Stp evolved to offset a DNA
      restriction system of the host cell but was turned, eventually, against the phage as an
      activator of the appended tRNA restriction enzyme.
AU  - Penner M
AU  - Morad I
AU  - Snyder L
AU  - Kaufmann G
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1995 249: 857-868.

PMID- 25792058
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Corynebacterium minutissimum, an Opportunistic Pathogen and the Causative Agent of Erythrasma.
PG  - e00139-15
AB  - Corynebacterium minutissimum was first isolated in 1961 from infection sites of patients
      presenting with erythrasma, a common cutaneous infection characterized
      by a rash. Since its discovery, C. minutissimum has been identified as an
      opportunistic pathogen in immunosuppressed cancer and HIV patients. Here, we
      report the whole-genome sequence of C. minutissimum.
AU  - Penton PK
AU  - Tyagi E
AU  - Humrighouse BW
AU  - McQuiston JR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00139-15.

PMID- 8441645
VI  - 21
DP  - 1993
TI  - I-SceIII: A novel group I intron-encoded endonuclease from the yeast mitochondria.
PG  - 358
AB  - Re-engineered gene with "good" codons and expressed in E. coli. Cleavage site determined.
AU  - Perea J
AU  - Desdouets C
AU  - Schapira M
AU  - Jacq C
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 358.

PMID- 25838495
VI  - 3
DP  - 2015
TI  - Whole-Genome Shotgun Sequence of the Keratinolytic Bacterium Lysobacter sp. A03,  Isolated from the Antarctic Environment.
PG  - e00246-15
AB  - Lysobacter sp. strain A03 is a protease-producing bacterium isolated from decomposing-penguin
      feathers collected in the Antarctic environment. This strain
      has the ability to degrade keratin at low temperatures. The A03 genome sequence
      provides the possibility of finding new genes with biotechnological potential to
      better understand its cold-adaptation mechanism and survival in cold
      environments.
AU  - Pereira JQ
AU  - Ambrosini A
AU  - Sant'Anna FH
AU  - Tadra-Sfeir M
AU  - Faoro H
AU  - Pedrosa FO
AU  - Souza EM
AU  - Brandelli A
AU  - Passaglia LM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00246-15.

PMID- 25745011
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Six Actinobacillus pleuropneumoniae Serotype 8 Brazilian Clinical Isolates: Insight into New Applications.
PG  - e01585-14
AB  - Actinobacillus pleuropneumoniae is the causative agent of swine pleuropneumonia,  a highly
      contagious disease associated with pigs of all ages that results in
      severe economic losses to the industry. Here, we report for the first time six
      genome sequences of A. pleuropneumoniae clinical isolates of serotype 8, found
      worldwide.
AU  - Pereira MF
AU  - Rossi CC
AU  - de Carvalho FM
AU  - de Almeida LG
AU  - Souza RC
AU  - de Vasconcelos AT
AU  - Bazzolli DM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01585-14.

PMID- 26430043
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Xanthomonas arboricola pv. juglandis 417, a Copper-Resistant Strain Isolated from Juglans regia L.
PG  - e01126-15
AB  - Here, we report the complete genome sequence of Xanthomonas arboricola pv. juglandis 417, a
      copper-resistant strain isolated from a blighted walnut fruit (Juglans regia L. cv. Chandler).
      The genome consists of a single chromosome (5,218 kb).
AU  - Pereira UP
AU  - Gouran H
AU  - Nascimento R
AU  - Adaskaveg JE
AU  - Goulart LR
AU  - Dandekar AM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01126-15.

PMID- 6099022
VI  - 12
DP  - 1984
TI  - Use of different media for growing the producers of restricting enzyme XbaI.
PG  - 48-50
AB  - The possibility of using culture media prepared from local ingredients and
      intended for growing the producers of restricting enzyme XbaI has been
      demonstrated.  The yield of restricting enzyme XbaI per g of crude biomass,
      obtained with the use of peptone-yeast medium prepared from ingredients
      supplied by Difco Laboratories (USA), has proved to be 4 times greater than
      that obtained with the use of peptone-yeast medium prepared from local
      ingredients.  At the same time the use of casein-saline medium ensures the
      yield of the enzyme, similar to that obtained with the use of peptone-yeast
      medium prepared from ingredients supplied by Difco Laboratories, but with a
      greater content of nonspecific nucleases.
AU  - Perelman EV
AU  - Shtanchaeva SM
AU  - Bulk VF
AU  - Tarasov AP
AU  - Bakh NL
AU  - Semina IS
PT  - Journal Article
TA  - Zh. Mikrobiol. Epidemiol. Immunobiol.
JT  - Zh. Mikrobiol. Epidemiol. Immunobiol.
SO  - Zh. Mikrobiol. Epidemiol. Immunobiol. 1984 12: 48-50.

PMID- 14606940
VI  - 68
DP  - 2003
TI  - Cloning and sequencing of the gene of site-specific nickase N.BspD6I.
PG  - 1203-1207
AB  - A fragment of chromosomal DNA from Bacillus species D6 containing the gene of nickase N.BspD6I
      and the regions adjacent to its 5;- and 3;-ends was cloned and sequenced. The nucleotide
      sequence of the nickase gene, except of one neutral change, is homologous to the nicking
      endonuclease N.BstNBI gene sequenced by Higgens et al. (2001). After integration of a PCR-copy
      of the nickase gene into an expression vector pET28b under the control of the phage T7
      promoter, specific nicking activity was detected in the lysates of transformed E. coli cells.
AU  - Perevyazova TA
AU  - Rogulin EA
AU  - Zheleznaya LA
AU  - Matvienko NI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 2003 68: 1203-1207.

PMID- 26316636
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Paenibacillus larvae MEX14, Isolated from Honey Bee Larvae from the Xochimilco Quarter in Mexico City.
PG  - e00968-15
AB  - Paenibacillus larvae strain MEX14 is a facultative anaerobic endospore-forming bacterium that
      infects Apis mellifera larvae. Strain MEX14 was isolated from domestic bee larvae collected in
      a backyard in Mexico City. The estimated genome  size was determined to be 4.18 Mb, and it
      harbors 4,806 protein coding genes (CDSs).
AU  - Perez-de-la-Rosa D
AU  - Perez-de-la-Rosa JJ
AU  - Cossio-Bayugar R
AU  - Miranda-Miranda E
AU  - Lozano L
AU  - Bravo-Diaz MA
AU  - Rocha-Martinez MK
AU  - Sachman-Ruiz B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00968-15.

PMID- 27103715
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of an Atypical Strain of Streptococcus pneumoniae Serotype  19A Isolated from Cerebrospinal Fluid.
PG  - e00277-16
AB  - We present here the draft genome sequence of ITALIC! Streptococcus pneumoniaestrain
      MTY32702340SN814 isolated in Monterrey, Mexico, from a girl with
      bacterial meningitis. The strain belongs to the atypical and multidrug-resistant
      serogroup 19A. This is the first report in the literature of sequence type 3936
      (ST3936) in ITALIC! S. pneumoniaeserotype 19A.
AU  - Perez-Maya AA
AU  - Hinojosa-Robles RM
AU  - Barcenas-Walls JR
AU  - Rojas-Martinez A
AU  - Barrera-Saldana HA
AU  - Ortiz-Lopez R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00277-16.

PMID- 27034499
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Streptococcus pneumoniae Serotype 19A, a Blood Clinical Isolate from Northeast Mexico.
PG  - e00195-16
AB  - We report here the draft genome sequence of aStreptococcus pneumoniaestrain isolated in
      Monterrey, Mexico, MTY1662SN214, from a man with purpura fulminans.
      The strain belongs to the invasive and multidrug-resistant serogroup 19A,
      sequence type 320 (ST320). The draft genome sequence consists of 60 large
      contigs, a total of 2,069,474 bp, and has a G+C content of 39.7%.
AU  - Perez-Maya AA
AU  - Hinojosa-Robles RM
AU  - Barcenas-Walls JR
AU  - Vignau-Cantu A
AU  - Barrera-Saldana HA
AU  - Ortiz-Lopez R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00195-16.

PMID- 28883144
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of a blaOXA-58-Producing Acinetobacter baumannii Strain  Isolated from a Mexican Hospital.
PG  - e00949-17
AB  - In this study, we present the complete genome sequence of a blaOXA-58-producing Acinetobacter
      baumannii strain, sampled from a Mexican hospital and not related
      to the international clones.
AU  - Perez-Oseguera A
AU  - Castro-Jaimes S
AU  - Salgado-Camargo AD
AU  - Silva-Sanchez J
AU  - Garza-Gonzalez E
AU  - Castillo-Ramirez S
AU  - Cevallos MA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00949-17.

PMID- 27979937
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Pediococcus parvulus 2.6, a Probiotic beta-Glucan Producer Strain.
PG  - e01381-16
AB  - We report here the draft genome sequence of the probiotic Pediococcus parvulus 2.6, a lactic
      acid bacterial strain isolated from ropy cider. The bacterium
      produces a prebiotic and immunomodulatory exopolysaccharide, and this is the
      first strain of the P. parvulus species whose genome has been characterized.
AU  - Perez-Ramos A
AU  - Mohedano ML
AU  - Puertas A
AU  - Lamontanara A
AU  - Orru L
AU  - Spano G
AU  - Capozzi V
AU  - Duenas MT
AU  - Lopez P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01381-16.

PMID- 12142409
VI  - 184
DP  - 2002
TI  - Short-sequence tandem and nontandem DNA repeats and endogenous hydrogen peroxide production contribute to genetic instability of Streptococcus   pneumoniae.
PG  - 4392-4399
AB  - Loss-of-function mutations in the following seven pneumococcal genes were detected and
      analyzed: pspA, spxB, xba, licD2, lytA, nanA, and atpC.
      Factors associated with these mutations included (i) frameshifts caused by
      reversible gain and loss of single bases within homopolymeric repeats as
      short as 6 bases, (ii) deletions caused by recombinational events between
      nontandem direct repeats as short as 8 bases, and (iii) substitutions of
      guanine residues caused at an increased frequency by the high levels of
      hydrogen peroxide (>2 mM) typically generated by this species under
      aerobic growth conditions. The latter accounted for a frequency as high as
      2.8 x 10(-6) for spontaneous mutation to resistance to optochin and was
      10- to 200-fold lower in the absence of detectable levels of H2O2. Some of
      these mutations appear to have been selected for in vivo during
      pneumococcal infection, perhaps as a consequence of immune pressure or
      oxidative stress.
AU  - Pericone CD
AU  - Bae D
AU  - Shchepetov M
AU  - McCool T
AU  - Weiser JN
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2002 184: 4392-4399.

PMID- 24158560
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of the Escherichia coli PMV-1 Strain, a Model Extraintestinal Pathogenic E. coli Strain Used for Host-Pathogen Interaction  Studies.
PG  - e00913-13
AB  - Escherichia coli is a highly versatile species, causing diverse intestinal and extraintestinal
      infections. Here, we present the complete genome sequence of
      PMV-1, an O18:K1 extraintestinal pathogenic E. coli (ExPEC) strain that is used
      as a model for peritonitis in mice and was useful for deciphering the innate
      immune response triggered by ExPEC infections.
AU  - Peris-Bondia F
AU  - Muraille E
AU  - Van Melderen L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00913-13.

PMID- 
VI  - 16
DP  - 2005
TI  - Inteins - A historical perspective.
PG  - 193-210
AB  - Protein splicing elements, termed inteins, were first identified in 1990.  Since then,
      post-translational protein splicing has been demonstrated and the self-catalytic mechanism
      deciphered.  The robust nature of these single turnover enzymes is evidenced by the expanding
      list of naturally occurring variations in the protein splicing mechanism.  Protein splicing
      must be efficient and neutral, and must not cause detrimental effects to the spliced extein;
      otherwise, selective pressure would lead to intein loss.  Inteins are probably ancient
      elements, but their original function can only be speculated upon, because invasion by homing
      endonucleases mobilized them into new locations and converted them into selfish DNA.  To date,
      there is no evidence of regulation of protein splicing in native systems.  The sporadic
      distribution of inteins may relate more to the types of genes found in mobile elements capable
      of spreading inteins, than to the function of those genes.  Inteins tend to be found in
      conserved host protein motifs, which may be due to conservation of homing endonuclease
      recognition sites, difficulty in removing inteins from essential regions or the ease of
      accepting an insertion sequence in a conserved substrate or cofactor binding site designed to
      interact with the environment.  The ability to cleave peptide bonds, to ligate protein
      fragments and to generate carboxy-terminal alpha-thioesters have made inteins the fastest
      growing tool for protein engineering and biotechnology.
AU  - Perler FB
PT  - Journal Article
TA  - Nucleic Acids Mol. Biol.
JT  - Nucleic Acids Mol. Biol.
SO  - Nucleic Acids Mol. Biol. 2005 16: 193-210.

PMID- 11398469
VI  - 334
DP  - 2001
TI  - Hyperthermophilic inteins.
PG  - 270-280
AB  - Inteins are intervening sequences that are posttranslationally excised from protein
      precursors.  They are the protein equivalent of introns, which are intervening sequences that
      splice from precursor RNAs.  The sequences flanking both sides of the intein are called
      exteins.  During protein splicing, the intein is excised from a precursor protein and the
      flanking exteins are joined by a peptide bond.  This ligation of exteins differentiates
      protein splicing from other forms of proteolytic processing.  The self-catalytic protein
      splicing reaction is mediated by the intein plus the first carboxy-extein amino acid, which
      are capable of splicing in heterologous exteins.  However, each intein has its own "substrate"
      specificity that dictates allowable proximal extein residues.  As of December 31, 1999, there
      were 100 putative inteins listed in the Intein Registry, representing all three domains of
      life (see InBase2 at http://www.neb.com/neb/intins.html); 74% of these inteins are found in
      thermophilic organisms, mainly Archaea.  Thermophilic inteins were among the first inteins
      discovered and played a key role in establishing protein splicing as a fundamental method of
      protein biosynthesis.  The proof that inteins were spliced from precursor proteins rather than
      from precursor RNAs and the mechanism of protein splicing were initially demonstrated using
      archaeal inteins.  Since their discovery in 1990, inteins have been harnessed to perform
      numerous protein engineering processes.
AU  - Perler FB
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 2001 334: 270-280.

PMID- 9847224
VI  - 27
DP  - 1999
TI  - InBase, the New England Biolabs Intein Database.
PG  - 346-347
AB  - Inteins are intervening sequences that splice as proteins, not RNA.  InBase, the New England
      Biolabs Intein Database (http://www.neb.com/neb.inteins.html), is a comprehensive on-line
      database that includes the Intein Registry, along with detailed information about each intein
      and its host protein, tabulated comparisons and a comprehensive bibliography including papers
      in press.
AU  - Perler FB
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1999 27: 346-347.

PMID- 1608969
VI  - 89
DP  - 1992
TI  - Intervening sequences in an Archaea DNA polymerase gene.
PG  - 5577-5581
AB  - The DNA polymerase gene from the Archaea Thermococcus litoralis has been cloned and expressed
      in Escherichia coli. It is split by two intervening sequences (IVSs) that form one continuous
      open reading frame with three polymerase exons. To our knowledge, neither IVS is similar to
      previously described introns. However, the deduced amino acid sequences of both IVSs are
      similar to open reading frames present in mobile group I introns. The second IVS (IVS2)
      encodes an endonuclease, I-TliI, that cleaves at the exon 2-exon 3 junction after IVS2 has
      been deleted. IVS2 self-splices in E. coli to yield active polymerase, but processing is
      abolished if the IVS2 reading frame is disrupted. Silent changes in the DNA sequence at the
      exon 2-IVS2 junction that maintain the original protein sequence do not inhibit splicing.
      These data suggest that protein rather than mRNA splicing may be responsible for production of
      the mature polymerase.
AU  - Perler FB
AU  - Comb DG
AU  - Jack WE
AU  - Moran LS
AU  - Qiang B
AU  - Kucera RB
AU  - Benner J
AU  - Slatko BE
AU  - Nwankwo DO
AU  - Hempstead SK
AU  - Carlow CKS
AU  - Jannasch H
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1992 89: 5577-5581.

PMID- 8165123
VI  - 22
DP  - 1994
TI  - Protein splicing elements: inteins and exteins--a definition of terms and recommended nomenclature.
PG  - 1125-1127
AB  - Several archaeal, eubacterial and eucaryotic genes have been identified with in-frame
      insertions that are excised at the protein level, not at the RNA level. This process is termed
      protein splicing. Initially, a single precursor polypeptide is synthesized. The intervening
      protein sequences is then excised from within the precursor, and the flanking protein
      sequences are joined. Thus, protein splicing results in the production of two proteins from a
      single primary translation product, the internal protein and the protein formed by the joining
      of the external sequences. The removal of the internal segment, concomitant with the formation
      of a normal peptide bond joining the external polypeptide sequences, distinguishes protein
      splicing from simple autoproteolysis. The rapid production of the mature products suggests
      that protein splicing is very efficient. The protein precursor rarely accumulates, even when
      the native gene is expressed in heterologous systems, both in vivo and in vitro. Evidence to
      date suggests that protein splicing is autocatalytic.
AU  - Perler FB
AU  - Davis EO
AU  - Dean GE
AU  - Gimble FS
AU  - Jack WE
AU  - Neff N
AU  - Noren CJ
AU  - Thorner J
AU  - Belfort M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1994 22: 1125-1127.

PMID- 
VI  - 105
DP  - 2005
TI  - Phylogenetic evidence for horizontal gene transfer of type I restriction and modification (hsd) genes among highly homogenous Salmonella strains.
PG  - 284
AB  - Previous studies from our laboratory have documented the prevalence of horizontal gene
      transfer (HGT) among strains of Salmonella enterica subspecies I. In comparing subspecies, a
      recombination gradient was noted wherein the incidence of HGT is inversely correlated with the
      genetic diversity separating individual strains. These findings suggested that there are
      barriers, either genetic or ecological, that restrict exchange between disparate serovars of
      Salmonella. The compatibility of restriction-modification (R-M) systems among strains has been
      proposed as one explanation to account for the contrasting recombination rates. To explore
      this possibility, 40 closely-related strains of the highly homogenous Typhimurium complex were
      compared by cladistic analysis of the hsd genes, R, M, and S, which compose the type I R-M
      system in Salmonella enterica subspecies I. The resultant trees revealed a prominent role for
      HGT in the evolution of the hsd operon. Several Salmonella strains were found to be
      evolutionarily discordant when hsd gene trees were compared to known markers of S. enterica
      chromosome evolution (e.g., mdh). Additionally, several distinct clusters of mdh and mutS
      alleles were coalesced into single hsd clades for the three type I R-M loci. Analyses of
      congruence among hsd genes showed nearly unanimous discordance, the only exception being the
      hsdM/S2 comparison (p = 1.0). This finding would suggest that the type I R-M operon is
      anevolutionary mosaic, subject to numerous HGT events. This conclusion is further supported by
      the identification of unique cassettes of sequence at two sites in hsdS. The hsdS2 segment
      comprised two distinct sequences while the hsdS3 segment contained one of three unique
      alleles. One of the hsdS3 alleles showed high homology to an E. coli hsd insert, suggesting a
      recent cross-species transfer of this sequence. These data demonstrate that HGT has been a
      common occurrence in hsd gene evolution and indicate an overall genetic compatibility among
      closely-related salmonellae. This may explain in part why Salmonella known to share homologous
      genomes and common niches are permitted to exchange DNA more freely.
AU  - Perlloni A
AU  - Brown EW
AU  - LeClerc JE
AU  - Cebula TA
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 2005 105: 284.

PMID- 30533889
VI  - 7
DP  - 2018
TI  - Complete Genome Sequence of Stenotrophomonas maltophilia AB550, an Environmental  Solar Radiation- and Multidrug-Resistant Strain Isolated in Western Australia.
PG  - e00914-18
AB  - We report here the complete genome sequence of Stenotrophomonas maltophilia AB550, a
      multidrug- and solar radiation-resistant strain isolated from the
      effluents of an urban wastewater treatment plant in Western Australia. The genome
      consists of a single 4.9-Mb chromosome.
AU  - Permala RR
AU  - Glady-Croue J
AU  - Watkin ELJ
AU  - Ramsay JP
AU  - Croue JP
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e00914-18.

PMID- 11206551
VI  - 409
DP  - 2001
TI  - Genome sequence of enterohaemorrhagic Escherichia coli O157:H7.
PG  - 529-533
AB  - The bacterium Escherichia coli O157:H7 is a worldwide threat to public health and has been
      implicated in many outbreaks of haemorrhagic colitis, some of which included fatalities caused
      by haemolytic uraemic syndrome.  Close to 75,000 cases of O157:H7 infection are now estimated
      to occur annually in the United States.  The severity of disease, the lack of effective
      treatment and the potential for large-scale outbreaks from contaminated food supplies have
      propelled intensive research on the pathogenesis and detection of E. coli O157:H7.  Here we
      have sequenced the genome of E. coli O157:H7 to identify candidate genes responsible for
      pathogenesis, to develop better methods of strain detection and to advance our understanding
      of the evolution of E. coli, through comparison with the genome of the non-pathogenic
      laboratory strain E. coli K-12.  We find that lateral gene transfer is far more extensive than
      previously anticipated.  In fact, 1,387 new genes encoded in strain-specific clusters of
      diverse sizes were found in O157:H7.  These include candidate virulence factors, alternative
      metabolic capacities, several prophages and other new functions - all of which could be
      targets for surveillance.
AU  - Perna NT et al
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2001 409: 529-533.

PMID- 21993298
VI  - 40
DP  - 2012
TI  - Illuminating the reaction pathway of the FokI restriction endonuclease by fluorescence resonance energy transfer.
PG  - 1203-1213
AB  - The FokI restriction endonuclease is a monomeric protein that recognizes an asymmetric
      sequence and cleaves both DNA strands at fixed loci downstream of the
      site. Its single active site is positioned initially near the recognition
      sequence, distant from its downstream target 13 nucleotides away. Moreover, to
      cut both strands, it has to recruit a second monomer to give an assembly with two
      active sites. Here, the individual steps in the FokI reaction pathway were
      examined by fluorescence resonance energy transfer (FRET). To monitor DNA binding
      and domain motion, a fluorescence donor was attached to the DNA, either
      downstream or upstream of the recognition site, and an acceptor placed on the
      catalytic domain of the protein. A FokI variant incapable of dimerization was
      also employed, to disentangle the signal due to domain motion from that due to
      protein association. Dimerization was monitored separately by using two samples
      of FokI labelled with donor and acceptor, respectively. The stopped-flow studies
      revealed a complete reaction pathway for FokI, both the sequence of events and
      the kinetics of each individual step.
AU  - Pernstich C
AU  - Halford SE
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: 1203-1213.

PMID- 116010
VI  - 31
DP  - 1979
TI  - Restriction cleavage map of SP01 DNA: general location of early, middle, and late genes.
PG  - 156-171
AB  - A detailed restriction endonuclease map for the genome of Bacillus subtilis phage SP01 is
      presented. Sites of cleavage for the restriction
      enzymes BglII, EcoRI, HaeIII, and SalI were determined. This physical map
      showed that SP01 DNA was 140 kilobases in length and contained a repeated
      sequence of 12.4 kilobases at its termini. Combined with previously
      published information, we were also able to identify the general locations
      of genes expressed at early, middle, or late times in the phage lytic
      cycle. In particular, early genes were largely clustered in the terminal
      repeats, whereas a major cluster of late genes was located in the
      left-central portion of the genome.
AU  - Pero J
AU  - Hannett NM
AU  - Talkington C
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1979 31: 156-171.

PMID- 
VI  - 223
DP  - 2002
TI  - Structural pathways of phosphoryl transfer in type II restriction endonucleases.
PG  - C-38-C-39
AB  - Crystal structures of EcoRV endonuclease bound to DNA and divalent metal
      ions have elucidated important aspects of the structural pathway of DNA
      bending, the stereochemical mechanism of catalysis, and the coupling of
      sequence selectivity to phosphoryl transfer. Three distinct divalent metal
      ion binding sites have been located in the vicinity of the scissile DNA
      phosphates, while a fourth site specific to manganese is found at the
      interface of the enzyme with the DNA flanks. Mutational analysis of
      active-site residues places important constraints on the reaction mechanism,
      and suggests that moderate-range electrostatic effects play an important
      role in facilitating rate enhancement. Measurements of the pH and
      metal-dependence of the chemical step, by rapid-quench kinetics, lend
      support to a detailed model of the reaction pathway derived from the crystal
      structures. Comparisons of the EcoRV mechanism with those of other
      restriction endonucleases offer further insight into the origins of
      catalytic power.
AU  - Perona JJ
PT  - Journal Article
TA  - ACS Abstracts
JT  - ACS Abstracts
SO  - ACS Abstracts 2002 223: C-38-C-39.

PMID- 12431439
VI  - 28
DP  - 2002
TI  - Type II restriction endonucleases.
PG  - 353-364
AB  - Type II restriction endonucleases have emerged as important paradigms for the study of
      protein-nucleic acid interactions. This is due to their ability to catalyse phosphodiester
      bond cleavage with very large rate enhancements while also maintaining exquisite sequence
      selectivities. The principles and methods developed to analyze site-specific binding and
      catalysis for restriction endonucleases can be applied to other enzymes which also operate on
      nucleic acids. This paper reviews biochemical and structural approaches to characterization of
      these enzymes, with particular attention to the multiple crucial roles of divalent metal ions,
      the possibilities for use of alternative substrates in binding and catalytic experiments, the
      strategies for exploring the detailed chemistry of phosphoryl transfer, and the use of X-ray
      crystallography to provide descriptions of conformational pathways at specific, nonspecific,
      and noncognate DNA sites.
AU  - Perona JJ
PT  - Journal Article
TA  - Methods
JT  - Methods
SO  - Methods 2002 28: 353-364.

PMID- 
VI  - 35
DP  - 2000
TI  - Catalytic mechanism of EcoRV endonuclease derived from crystal structures and transient kinetics.
PG  - 9-17
AB  - High-resolution cocrystal structures of wild-type and mutant forms of EcoRV endonuclease bound
      to duplex DNA and divalent metal ions allow construction of a detailed model for the
      pre-transition state configuration.  Three distinct metal-ion binding sites have been revealed
      in different structural analyses.  In particular, a new site (site I) was recently found in a
      ternary complex of the T93A mutant bound to cognate DNA and Ca2+ ions.  The same site is
      occupied by Ca2+, Mg2+ or Mn2+ in three high-resolution structures of EcoRV bound to duplex
      DNA containing 3'S-phosphorothiolate linkages (3'-PS) at the scissile phosphates.  Each of
      these four structures traps a pre-transition state conformation in which the DNA is not
      cleaved.  The new site I metal is ligated through an inner-sphere water molecule to the
      phosphate group located 3' to the scissile phosphate.  A second inner-sphere water on this
      metal is positioned approximately in-line for attack on the scissile phosphate.  These
      structures corroborate the observation that the pro-SP phosphoryl oxygen on the adjacent
      3'-phosphate cannot be modified without severe loss of catalytic efficiency.  Together with
      previous cocrystal structures, these data allow construction of a detailed model for the
      pre-transition state configuration in EcoRV.  This model features three divalent metal ions
      per active site, and invokes assistance in the bond-making step by a conserved lysine, which
      stabilizes the attacking hydroxide ion nucleophile.  The model is supported by pre-steady
      state and single-turnover kinetic data, in which the metal and pH-dependencies of the
      phosphoryl transfer step are directly evaluated.  The structural equivalence of key groups,
      conserved in the active sites of many type II restriction endonucleases, suggests that
      ligation of a catalytic divalent metal ion to the adjacent 3'-phosphate may occur in many
      type II restriction enzymes.
AU  - Perona JJ
AU  - Horton NC
AU  - Sam MD
PT  - Journal Article
TA  - Transactions ACA
JT  - Transactions ACA
SO  - Transactions ACA 2000 35: 9-17.

PMID- 9367757
VI  - 273
DP  - 1997
TI  - Conformational transitions and structural deformability of EcoRV endonuclease revealed by crystallographic analysis.
PG  - 207-225
AB  - The structures of wild-type and mutant forms of the unliganded EcoRV endonuclease dimer have
      been determined at 2.4 angstroms resolution in a new crystal lattice.  Comparison of these
      structures with that of the free enzyme determined with different packing constraints shows
      that the conformations of the domain interfaces are not conserved between crystal forms.  The
      unliganded enzyme and the enzyme-DNA complex delineate two distinct quaternary states
      separated by a 25 degree intersubunit rotation, but considerable conformational heterogeneity,
      of the order of 10^6 domain rotations, exists within each of these states.  Comparison of the
      free enzyme structure between the two crystal forms further reveals that the C-terminal 28
      amino acid residues are disordered and undergo an extensive local folding transition upon DNA
      binding.  Introduction of the mutation T93A at the DNA-binding cleft causes large-scale
      effects on the protein conformation.  Structural changes in the mutated unliganded enzyme
      propagate some 20 to 25 angstroms to the dimerization interface and lead to a rearrangement of
      monomer subunits.  Comparative analysis of these structures, a new structure of the enzyme
      cocrystallized with DNA and calcium ions, and previously determined cocrystal structures
      suggests important roles for a number of amino acid residues in facilitating the intersubunit
      motions and local folding transitions.  In particular, the T93A structure reveals a pathway
      through the protein, by which DNA-binding may cause the domain movements required for proper
      alignment of catalytic groups.  The key active-site residue Glu45 is located on a flexible
      helix inside the pathway, and this provides a direct means by which essential catalytic
      functions are coupled to the protein conformational change.  It appears that indirect
      perturbation of the Glu45 conformation via an altered quaternary structure may be a
      contributing factor to the decreased catalytic efficiency of T93A, and this mechanism may also
      explain the diminished activities of other active site variants of EcoRV.
AU  - Perona JJ
AU  - Martin AM
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1997 273: 207-225.

PMID- 10666705
VI  - 17
DP  - 2000
TI  - A diverse population of introns in the nuclear ribosomal genes of ericoid mycorrhizal fungi includes elements with sequence similarity to endonuclease-coding genes.
PG  - 44-59
AB  - Ericoid mycorrhizal fungi form symbioses with the roots of members of the Ericales. Although
      only two genera have been identified in culture,
      the taxonomic diversity of ericoid symbionts is certainly wider.
      Genetic variation among 40 ericoid fungal isolates was investigated in
      this study. PCR amplification of the nuclear small-subunit ribosomal
      DNA (SSU rDNA) and of the internal transcribed spacer (ITS), followed
      by sequencing, led to the discovery of DNA insertions of various sizes
      in the SSU rDNA of most isolates. They reached sizes of almost 1,800 bp
      and occurred in up to five different insertion sites. Their positions
      and sizes were generally correlated with morphological and ITS-RFLP
      grouping of the isolates, although some insertions were found to be
      optional among isolates of the same species, and insertions were not
      always present in all SSU rDNA repeats within an isolate. Most
      insertions were identified as typical group I introns, possessing the
      conserved motifs characteristic of this group. However, other
      insertions lack these motifs and form a distinct group that includes
      other fungal ribosomal introns. Alignments with almost 70 additional
      sequences from fungal nuclear SSU rDNA introns indicate that introns
      inserted at the same site along the rDNA gene are generally homologous,
      but they also suggest the possibility of some horizontal transfers. Two
      of the ericoid fungal introns showed strong homology with a conserved
      motif found in endonuclease genes from nuclear rDNA introns.
AU  - Perotto S
AU  - Nepote-Fus P
AU  - Saletta L
AU  - Bandi C
AU  - Young JPW
PT  - Journal Article
TA  - Mol. Biol. Evol.
JT  - Mol. Biol. Evol.
SO  - Mol. Biol. Evol. 2000 17: 44-59.

PMID- 23979735
VI  - 57
DP  - 2013
TI  - Novel Pseudo-Staphylococcal Cassette Chromosome mec Element ({Psi}SCCmec57395) in Methicillin-Resistant Staphylococcus pseudintermedius CC45.
PG  - 5509-5515
AB  - Genetic characterization of methicillin-resistant Staphylococcus pseudintermedius
      (MRSP) from Thailand and Israel revealed the presence of a predominant atypical
      clonal lineage which was not typeable by SmaI-PFGE and SCCmec typing. All the
      atypical isolates (n = 34) belonged to CC45 (30 ST45 and 2 ST179 isolates, 1 ST57
      isolate, and 1 ST85 isolate). The isolates originated from healthy and diseased
      dogs and cats, as well as from the environment of one clinic. Cfr9I-pulsed-field
      gel electrophoresis (Cfr9I-PFGE) and dru typing permitted the further distinction
      of CC45 isolates from the two different countries. Microarray analysis identified
      genes that confer resistance to beta-lactams (mecA; blaZ), aminoglycosides
      [aac(6')-Ie-aph(2')-Ia; aph(3')-III; ant(6)-Ia], macrolides and lincosamides
      [erm(B)], tetracyclines [tet(M)], trimethoprim [dfr(G)], streptothricin (sat4),
      and chloramphenicol (catpC221). Fluoroquinolone resistance was attributed to
      specific amino acid substitutions, i.e., Ser84Leu in GyrA and Ser80Ile and
      Asp84Asn in GrlA. A novel pseudo-staphylococcal cassette chromosome
      (PsiSCCmec57395) element was identified in MRSP strain 57395 (sequence type ST45)
      by whole-genome sequencing. The 12,282-bp PsiSCCmec57395 element contained a
      class C1 mec gene complex but no ccr genes. In addition to the methicillin
      resistance gene mecA, PsiSCCmec57395 also carried determinants of resistance to
      heavy metals, such as arsenic, cadmium, and copper. Bsu36I restriction analysis
      of the PsiSCCmec57395 element amplified by long-range PCR revealed the presence
      of PsiSCCmec57395 in the 33 additional isolates of MRSP CC45. The PsiSCCmec57395
      element represents a new class of SCCmec and has been identified in MRSP of CC45,
      which is a predominant clonal lineage in Israel and Thailand.
AU  - Perreten V
AU  - Chanchaithong P
AU  - Prapasarakul N
AU  - Rossano A
AU  - Blum SE
AU  - Elad D
AU  - Schwendener S
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2013 57: 5509-5515.

PMID- 8335007
VI  - 12
DP  - 1993
TI  - Asymmetrical recognition and activity of the I-SceI endonuclease on its site and on intron-exon junctions.
PG  - 2939-2947
AB  - Group I intron-encoded endonucleases represent a new class of double strand cutting
      endonucleases whose function is to initiate the homing of introns by generating double strand
      breaks in site-specific sequences. We have studied the mechanism of interaction of the I-SceI
      endonuclease with different DNA substrates derived from its natural site in the intron-less
      gene or from intron-exon junctions in the gene with an intron. We show that the enzyme
      recognizes it asymmetrical site with high affinity binding to the sequence corresponding to
      the downstream exon followed by binding to the upstream exon and catalysis of phosphodiester
      bond hydrolysis. Asymmetrical nicking activity is observed as an intermediate of the cleavage
      reaction. In the intron-containing gene, the enzyme recognizes the downstream intron-exon
      junction without any cleavage activity. This binding raises the possibility of a specific
      function of homing endonucleases in either gene expression or intron homing steps subsequent
      to DNA cleavage.
AU  - Perrin A
AU  - Buckle M
AU  - Dujon B
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1993 12: 2939-2947.

PMID- 23133404
VI  - 8
DP  - 2012
TI  - A Bacteriophage-Encoded J-Domain Protein Interacts with the DnaK/Hsp70 Chaperone and Stabilizes the Heat-Shock Factor sigma(32) of Escherichia coli.
PG  - E1003037
AB  - The universally conserved J-domain proteins (JDPs) are obligate cochaperone
      partners of the Hsp70 (DnaK) chaperone. They stimulate Hsp70's ATPase activity,
      facilitate substrate delivery, and confer specific cellular localization to
      Hsp70. In this work, we have identified and characterized the first functional
      JDP protein encoded by a bacteriophage. Specifically, we show that the ORFan gene
      057w of the T4-related enterobacteriophage RB43 encodes a bona fide JDP protein,
      named Rki, which specifically interacts with the Escherichia coli host
      multifunctional DnaK chaperone. However, in sharp contrast with the three known
      host JDP cochaperones of DnaK encoded by E. coli, Rki does not act as a generic
      cochaperone in vivo or in vitro. Expression of Rki alone is highly toxic for
      wild-type E. coli, but toxicity is abolished in the absence of endogenous DnaK or
      when the conserved J-domain of Rki is mutated. Further in vivo analyses revealed
      that Rki is expressed early after infection by RB43 and that deletion of the rki
      gene significantly impairs RB43 proliferation. Furthermore, we show that
      mutations in the host dnaK gene efficiently suppress the growth phenotype of the
      RB43 rki deletion mutant, thus indicating that Rki specifically interferes with
      DnaK cellular function. Finally, we show that the interaction of Rki with the
      host DnaK chaperone rapidly results in the stabilization of the heat-shock factor
      sigma(32), which is normally targeted for degradation by DnaK. The mechanism by
      which the Rki-dependent stabilization of sigma(32) facilitates RB43 bacteriophage
      proliferation is discussed.
AU  - Perrody E
AU  - Cirinesi AM
AU  - Desplats C
AU  - Keppel F
AU  - Schwager F
AU  - Tranier S
AU  - Georgopoulos C
AU  - Genevaux P
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2012 8: E1003037.

PMID- 29097468
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Delftia acidovorans RAY209, a Plant Growth-Promoting  Rhizobacterium for Canola and Soybean.
PG  - e01224-17
AB  - Herein, we report the genome sequence of Delftia acidovorans strain RAY209, a plant
      growth-promoting rhizobacterium that is used in commercial inoculants for
      canola and soybean. The genome of RAY209 has a consensus of 6,528,879 bp and an
      estimated 5,721 coding sequences.
AU  - Perry BJ
AU  - Bergsveinson J
AU  - Tambalo DD
AU  - Yost CK
AU  - Khan NH
AU  - Whiting M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01224-17.

PMID- 26203323
VI  - 10
DP  - 2015
TI  - Genome sequence of the soil bacterium Corynebacterium callunae type strain DSM 20147(T).
PG  - 5
AB  - Corynebacterium callunae DSM 20147(T) is a member of the genus Corynebacterium which contains
      Gram-positive and non-spore forming bacteria with a high G + C
      content. C. callunae was isolated during a screening for l-glutamic acid
      producing bacteria and belongs to the aerobic and non-haemolytic corynebacteria.
      As this is a type strain in a subgroup of industrial relevant bacteria for many
      of which there are also complete genome sequence available, knowledge of the
      complete genome sequence might enable genome comparisons to identify production
      relevant genetic loci. This project, describing the 2.84 Mbp long chromosome and
      the two plasmids, pCC1 (4.11 kbp) and pCC2 (85.02 kbp), with their 2,647
      protein-coding and 82 RNA genes, will aid the Genomic Encyclopedia of Bacteria
      and Archaea project.
AU  - Persicke M
AU  - Albersmeier A
AU  - Bednarz H
AU  - Niehaus K
AU  - Kalinowski J
AU  - Ruckert C
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 5.

PMID- 29724838
VI  - 6
DP  - 2018
TI  - Genome Sequence of Lysinibacillus sphaericus, a Lignin-Degrading Bacterium Isolated from Municipal Solid Waste Soil.
PG  - e00353-18
AB  - We report here the draft genome sequence of Lysinibacillus sphaericus strain A1,  a potential
      lignin-degrading bacterium isolated from municipal solid waste (MSW)
      soil and capable of enhancing gas release from lignocellulose-containing soil.
AU  - Persinoti GF
AU  - Paixao DAA
AU  - Bugg TDH
AU  - Squina FM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00353-18.

PMID- 22123767
VI  - 193
DP  - 2011
TI  - Genome Sequence of 'Candidatus Frankia datiscae' Dg1, the Uncultured Microsymbiont from Nitrogen-Fixing Root Nodules of the Dicot Datisca  glomerata.
PG  - 7017-7018
AB  - Members of the noncultured clade of Frankia enter into root nodule symbioses with actinorhizal
      species from the orders Cucurbitales and
      Rosales. We report the genome sequence of a member of this clade
      originally from Pakistan but obtained from root nodules of the American
      plant Datisca glomerata without isolation in culture.
AU  - Persson T et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 7017-7018.

PMID- 19129491
VI  - 106
DP  - 2009
TI  - Identification of Rhodococcus fascians cytokinins and their modus operandi to reshape the plant.
PG  - 929-934
AB  - Decades ago, the importance of cytokinins (CKs) during Rhodococcus
      fascians pathology had been acknowledged, and an isopentenyltransferase
      gene had been characterized in the fas operon of the linear virulence
      plasmid, but hitherto, no specific CK(s) could be associated with
      virulence. We show that the CK receptors AHK3 and AHK4 of Arabidopsis
      thaliana are essential for symptom development, and that the CK perception
      machinery is induced upon infection, underlining its central role in the
      symptomatology. Three classical CKs [isopentenyladenine, trans-zeatin, and
      cis-zeatin (cZ)] and their 2-methylthio (2MeS)-derivatives were identified
      by CK profiling of both the pathogenic R. fascians strain D188 and its
      nonpathogenic derivative D188-5. However, the much higher CK levels in
      strain D188 suggest that the linear plasmid is responsible for the
      virulence-associated production. All R. fascians CKs were recognized by
      AHK3 and AHK4, and, although they individually provoked typical CK
      responses in several bioassays, the mixture of bacterial CKs exhibited
      clear synergistic effects. The cis- and 2MeS-derivatives were poor
      substrates of the apoplastic CK oxidase/dehydrogenase enzymes and the
      latter were not cytotoxic at high concentrations. Consequently, the
      accumulating 2MeScZ (and cZ) in infected Arabidopsis tissue contribute to
      the continuous stimulation of tissue proliferation. Based on these
      results, we postulate that the R. fascians pathology is based on the local
      and persistent secretion of an array of CKs.
AU  - Pertry I
AU  - Vaclavikova K
AU  - Depuydt S
AU  - Galuszka P
AU  - Spichal L
AU  - Temmerman W
AU  - Stes E
AU  - Schmulling T
AU  - Kakimoto T
AU  - Van Montagu MC
AU  - Strnad M
AU  - Holsters M
AU  - Tarkowski P
AU  - Vereecke D
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2009 106: 929-934.

PMID- 10752077
VI  - 36
DP  - 2000
TI  - Restriction endonucleases from various bacterial strains displaying an ice-nucleating activity.
PG  - 13-16
AB  - Six strains containing Type II site-specific endonucleases were selected from a collection of
      45
      ice-nucleating bacterial strains isolated from the
      rhizosphere of plants growing in various geographical regions.
      Endonucleases Pfl21I, Psp8I, and Psp23I were isolated and purified
      from two Pseudomonas sp. strains and a Pseudomonas fluorescens strain.
      Restriction endonucleases Pfl21I and Psp23I were shown to recognize and
      cleave the DNA nucleotide sequence 5'-CTGCA^G-3'.
      Endonuclease Psp8I recognized and cleaved the DNA nucleotide sequence
      5'-G^GATCC-3'. These endonucleases were found to be true
      isoschizomers of PstI and BamHI, respectively.
AU  - Pertsev AV
AU  - Denmukhametov MM
AU  - Anoshkin AG
AU  - Ariskina EV
AU  - Berezin IA
AU  - Solonin AS
AU  - Kuzmin NP
PT  - Journal Article
TA  - Prikl. Biokhim. Mikrobiol.
JT  - Prikl. Biokhim. Mikrobiol.
SO  - Prikl. Biokhim. Mikrobiol. 2000 36: 13-16.

PMID- Not included in PubMed...
VI  - 62
DP  - 1997
TI  - Isolation of a strain overproducing endonuclease Eco29kI: Purification and characterization of the homogeneous enzyme.
PG  - 858-867
AB  - The physical map of the plasmid pSACII1 carrying the genes of the restriction-modification
      system Eco29kI (isoschizomer of SacII) was determined.  The cloning of the Eco29kI
      endonuclease methylase genes into the plasmid vector pUC129 produced recombinant strain
      Escherichia coli K802 [pECO29A15] with Eco29kI synthesis level about 100 times higher than in
      the parent strain.  The restriction endonuclease was purified from Escherichia coli K802
      [pECO29A15] cells to near homogeneity using column chromatography sequentially on
      phosphocellulose, hydroxyapatite, and heparin-Sepharose and rechromatography on
      phosphocellulose.  Biochemical characterization of the homogeneous R.Eco29kI is given.  The
      enzyme has molecular mass 24.5 kD and is present in the solution as a monomer.
AU  - Pertzev AV
AU  - Kravetz AN
AU  - Mayorov SG
AU  - Zakharova MV
AU  - Solonin AS
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1997 62: 858-867.

PMID- 1579502
VI  - 20
DP  - 1992
TI  - Eco29kI, a novel plasmid encoded restriction endonuclease from Escherichia coli.
PG  - 1991
AB  - Eco29kI is a type II restriction endonuclease from clinical strain Escherichia coli 29
      isolated in Kiev. The genes for the Eco29kI restriction modification system were located on
      one of its plasmids, namely pSACII1 about 4.0 kb in size as was determined by plasmid
      transformation of E. coli K802 (Figure 1) according to (1) except that the phage Phi 80 vir
      was used for selection of clones.
AU  - Pertzev AV
AU  - Ruban NM
AU  - Zakharova MV
AU  - Beletzkaja IV
AU  - Petrov SI
AU  - Kravetz AN
AU  - Solonin AS
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 1991.

PMID- 26450740
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Xanthomonas translucens pv. graminis Pathotype Strain CFBP 2053.
PG  - e01174-15
AB  - Strains of Xanthomonas translucens pv. graminis cause bacterial wilt on several forage
      grasses. A draft genome sequence of pathotype strain CFBP 2053 was generated to facilitate the
      discovery of new pathogenicity factors and to develop diagnostic tools for the species X.
      translucens.
AU  - Pesce C
AU  - Bolot S
AU  - Berthelot E
AU  - Bragard C
AU  - Cunnac S
AU  - Fischer-Le SM
AU  - Portier P
AU  - Arlat M
AU  - Gagnevin L
AU  - Jacques MA
AU  - Noel LD
AU  - Carrere S
AU  - Koebnik R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01174-15.

PMID- 25676771
VI  - 3
DP  - 2015
TI  - High-Quality Draft Genome Sequence of the Xanthomonas translucens pv. cerealis Pathotype Strain CFBP 2541.
PG  - e01574-14
AB  - Xanthomonas translucens pv. cerealis is the causal agent of bacterial leaf streak on true
      grasses. The genome of the pathotype strain CFBP 2541 was sequenced in
      order to decipher mechanisms that provoke disease and to elucidate the role of
      transcription activator-like (TAL) type III effectors in pathogenicity.
AU  - Pesce C
AU  - Bolot S
AU  - Cunnac S
AU  - Portier P
AU  - Fischer-Le SM
AU  - Jacques MA
AU  - Gagnevin L
AU  - Arlat M
AU  - Noel LD
AU  - Carrere S
AU  - Bragard C
AU  - Koebnik R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01574-14.

PMID- 23105050
VI  - 194
DP  - 2012
TI  - Complete Genome Sequences of Desulfosporosinus orientis DSM765T, Desulfosporosinus youngiae DSM17734T, Desulfosporosinus meridiei DSM13257T, and  Desulfosporosinus acidiphilus DSM22704T.
PG  - 6300-6301
AB  - Desulfosporosinus species are sulfate-reducing bacteria belonging to the Firmicutes. Their
      genomes will give insights into the genetic repertoire and
      evolution of sulfate reducers typically thriving in terrestrial environments and
      able to degrade toluene (Desulfosporosinus youngiae), to reduce Fe(III)
      (Desulfosporosinus meridiei, Desulfosporosinus orientis), and to grow under
      acidic conditions (Desulfosporosinus acidiphilus).
AU  - Pester M et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6300-6301.

PMID- 9573156
VI  - 180
DP  - 1998
TI  - Isolation and characterization of three Streptococcus pneumoniae transformation-specific loci by use of a lacZ reporter insertion vector.
PG  - 2701-2710
AB  - Although more than a dozen new proteins are produced when Streptococcus pneumoniae cells
      become competent for genetic transformation, only a few of the corresponding genes have been
      identified to date.  To find genes responsible for the production of competence-specific
      proteins, a random lacZ transcriptional fusion library was constructed in S. pneumoniae by
      using the insertional lacZ reporter vector pEVP3.  Screening the library for clones with
      competence-specific B-galactosidase production yielded three insertion mutants with induced
      beta-Gal levels of about 4, 10, and 40 Miller units.  In all three clones, activation of the
      lacZ reporter correlated with competence and depended on competence-stimulating peptide.
      Chromosomal loci adjacent to the integrated vector were subcloned from the insertion mutants,
      and their nucleotide sequences were determined.  Genes at two of the loci exhibited strong
      similarity to parts of Bacillus subtilis com operons.  One locus contained open reading frames
      homologous to the comEA and comEC genes in B. subtilis but lacked a comEB homolog.  A second
      locus contained four ORFs with homology to the B. subtilis comG gene ORFs 1 to 4, but comG
      gene ORFs 5 to 7 were replaced in S. pneumoniae with an ORF encoding a protein homologous to
      transport ATP-binding proteins.  Genes at all three loci were confirmed to be required for
      transformation by mutagenesis using pEVP3 for insertion duplications or an erm cassette for
      gene disruptions.
AU  - Pestova EV
AU  - Morrison DA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1998 180: 2701-2710.

PMID- 8655518
VI  - 178
DP  - 1996
TI  - Genes associated with the meningococcal capsule complex are also found in Neisseria gonorrhoeae.
PG  - 3342-3345
AB  - A homolog of the meningococcal cps locus region E has been identified in Neisseria gonorrhoeae
      immediately upstream of the gonococcal region D locus.  Region E has no detectable function in
      capsule biosynthesis in Neisseria meningitidis or in lipopolysaccharide biosynthesis in either
      organism.  The open reading frame is homologous to proteins of unknown function in Escherichia
      coli and Haemophilus influenzae.  Further analysis of the N. meningitidis cps cluster has
      identified a second copy of region D encoding three additional open reading frames, including
      homologs of DNA methyltransferases.  The organization of the region D and E genes in N.
      gonorrhoeae and N. meningitidis in relation to the cps genes provides some insight into the
      evolutionary origin of encapsulation in N. meningitidis.
AU  - Petering H
AU  - Hammerschmidt S
AU  - Frosch M
AU  - van Putten JPM
AU  - Ison CA
AU  - Robertson BD
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1996 178: 3342-3345.

PMID- 
VI  - 
DP  - 2003
TI  - Changing the sequence specificity of the restriction endonuclease EcoRI.
PG  - 1-167
AB  - EcoRI is one of the best studied restriction endonucleases of type II.  It recognizes the
      palindromic DNA sequence GAATTC with high specificity and cleaves it between G and A in the
      presence of Mg2+ ions.  This specific recognition is due to a highly complex and redundant
      network of hydrogen bonds, ionic and hydrophobic contacts.  In order to change the sequence
      specificity of the enzyme concerning the GC base pair at the end of the recognition sequence
      three amino acid residues (Met137, Arg200 and Arg203) were mutated.  Met137 was replaced by
      Asn, Cys, Gln, Leu and Lys, Arg200 by Lys and Tyr and Arg203 by Lys.  Already the single
      mutation M137Q results in an obvious change of specificity, because of its preference for
      5-methyl cytosine instead of cytosine during cleavage experiments with both
      oligodeoxynucleotide and plasmid substrates depending on the sequence context within the DNA.
      All other mutants at amino acid Met137 revealed a strong reduction of cleavage activity.  Thus
      only the single mutant M137Q was used as a starting point for further mutations within one
      protein.  The four mutations M137Q, R200K, R200Y and R203K were combined with each other to
      form any variation possible in order to generate multiple mutants.  Except for M137Q/R203K all
      mutants showed heavy loss of cleavage activity.  The mutant M137Q/R203K revealed an increased
      ability to cleave star sites.  In this case the stringent coupling of specific DNA recognition
      and catalysis is relaxed and the cleavage of DNA also takes place even if there are more
      interrupted DNA contacts than those to the GC base pair.  By combining the double mutation
      M137Q/R203K with R200Y an enzyme was created, that despite very low activity was able to
      cleave all four palindromic hexamer variations with a central AATT sequence at star
      conditions, whereas the sequence CAATTG was obviously preferred.  Thus an alteration of
      sequence specificity was obtained for the triple mutant M137Q/R200Y/R203K.
AU  - Peters I
PT  - Journal Article
TA  - Ph.D. Thesis, Germany
JT  - Ph.D. Thesis, Germany
SO  - Ph.D. Thesis, Germany 2003 : 1-167.

PMID- 
VI  - 
DP  - 2007
TI  - New applications of (S)-adenosyl-L-methionine analogues with protein methyltransferases and click chemistry for sequence specific protein labelling.
PG  - 1-126
AB  - 
AU  - Peters W
PT  - Journal Article
TA  - Ph.D. Thesis, Germany
JT  - Ph.D. Thesis, Germany
SO  - Ph.D. Thesis, Germany 2007 : 1-126.

PMID- 26543110
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Two Propionibacterium acnes Strains Isolated from Progressive Macular Hypomelanosis Lesions of Human Skin.
PG  - e01250-15
AB  - Propionibacterium acnes is a Gram-positive bacterium that is prevalent on human skin. It has
      been associated with skin disorders such as acne vulgaris and
      progressive macular hypomelanosis (PMH). Here, we report draft genome sequences
      of two type III P. acnes strains, PMH5 and PMH7, isolated from PMH skin lesions.
AU  - Petersen R
AU  - Lomholt HB
AU  - Scholz CF
AU  - Bruggemann H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01250-15.

PMID- 8226701
VI  - 175
DP  - 1993
TI  - Analysis of the genetic requirements for viability of Escherichia coli K-12 DNA adenine methylase (dam) mutants.
PG  - 7505-7508
AB  - RecBCD protein, necessary for Escherichia coli dam mutant viability, is directly required for
      DNA repair. Recombination genes recF+, recN+, recO+, and recQ+ are not essential for dam
      mutant viability; they are required for recBC sbcBC dam mutant survival, mutH, mutL, or mutS
      mutations do not suppress subinduction of SOS genes in dam mutants.
AU  - Peterson KR
AU  - Mount DW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1993 175: 7505-7508.

PMID- 3932821
VI  - 201
DP  - 1985
TI  - Viability of Escherichia coli K-12 DNA adenine methylase (dam) mutants requires increased expression of specific genes in the SOS regulon.
PG  - 14-19
AB  - We have examined the level of expression of the SOS regulon in cells lacking DNA adenine
      methylase activity (dam-). Mud (Ap,lac) fusions to several SOS operons (recA, lexA, uvrA,
      uvrB,uvrD, sulA, dinD and dinF) were found to express higher levels of beta-galactosidase in
      dam- strains than in isogenic dam+ strains. The attempted construction of dam- strains that
      were also mutant in one of several SOS genes indicated that the viability of
      methylase-deficient strains correlates with the inactivation of the SOS repressor (LexA
      protein). Consistent with this, the wild-type functions of two LexA-repressed genes (recA and
      ruv) appear to be required for dam- strain viability.
AU  - Peterson KR
AU  - Wertman KF
AU  - Mount DW
AU  - Marinus MG
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1985 201: 14-19.

PMID- 3956763
VI  - 45
DP  - 1986
TI  - Prediction of restriction endonuclease site distribution based on dinucleotide frequency.
PG  - 1850
AB  - Most analyses of the frequency of restriction endonuclease recognition sites
      have assumed a random distribution of nucleotides.  Nearest neighbor analysis
      and the sequence of nucleic acids indicate that the distribution of nucleotides
      is nonrandom at least at the dinucleotide level.  Recent analyses have made use
      of the nonrandom dinucleotide distribution observed in sequenced nucleic acids
      to predict the frequency of restriction endonuclease sites.  The frequency of
      sites in DNAs which have not been extensively sequenced can also be predicted
      using the dinucleotide frequencies measured by nearest neighbor analysis.
      Taking into account the dinucleotide bias, the site frequencies for a large
      number of restriction endonucleases have been calculated for the DNAs from
      several organisms.  Some restriction endonucleases which have the same base
      composition in their recognition sites [e.g. EcoRV (GATATC) and HindIII
      (AAGCTT)] have widely different site frequencies in the DNA from some
      organisms.  The observed distribution of DNA fragments generated by selected
      restriction endonucleases correlates with the predicted frequency of the
      recognition site.  This type of analysis should be useful in the selection of
      suitable restriction endonucleases for mapping genomic DNAs, for generating DNA
      fragments for subcloning, and for screening for restriction fragment length
      polymorphisms.
AU  - Peterson RC
PT  - Journal Article
TA  - Fed. Proc.
JT  - Fed. Proc.
SO  - Fed. Proc. 1986 45: 1850.

PMID- 2908508
VI  - 6
DP  - 1988
TI  - Prediction of the frequencies of restriction endonuclease recognition sequences using di- and mononucleotide frequencies.
PG  - 34-39
AB  - The calculation of probabilities of nucleotide sequences from the freqeuencies
      of dinucleotides is described.  The dinucleotide and mononucleotide frequencies
      used can be obtained from nearest neighbor analysis or from databank sequences.
      If dinucleotide and mononucleotide frequencies from nearest neighbor analysis
      are used, probabilities for oligonucleotides can be calculated for genomes in
      which there is little or no sequence data.  Within a given genome, a broad
      range of probabilities for hexanucleotide palindromes with the same base
      composition is predicted and shown.
AU  - Peterson RC
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 1988 6: 34-39.

PMID- 16321401
VI  - 355
DP  - 2005
TI  - GATC flanking sequences regulate Dam activity: evidence for how Dam specificity may influence pap expression.
PG  - 459-472
AB  - Escherichia coli DNA adenine methyltransferase (Dam) plays essential roles in DNA replication,
      mismatch repair and gene regulation. The differential methylation by Dam of the two GATC
      sequences in the pap promoter regulates the expression of pili genes necessary for
      uropathogenic E.coli cellular adhesion. Dam processively methylates GATC sites in various DNA
      substrates, yet the two pap GATC sites are not processively methylated. We previously proposed
      that the flanking sequences surrounding the two pap GATC sites contribute to the enzyme's
      distributive methylation. We show here that replacement of the poorly methylated pap GATC
      sites with sites predicted to be processively methylated indeed results in an increase in Dam
      processivity. The increased processivity is due to a change in the methyltransfer kinetics and
      not the binding efficiency of Dam. A competition experiment in which the flanking sequences of
      only one pap GATC site were altered demonstrates that the GATC flanking sequences directly
      regulate the enzyme's catalytic efficiency. The GATC flanking sequences in Dam-regulated
      promoters in E.coli and other bacteria are similar to those in the pap promoter. Gene
      regulation from some of these promoters involves mechanisms and proteins that are quite
      different from those in the pap operon. Further, GATC sequences previously identified to
      remain unmethylated within the E.coli genome, but whose function remains largely unassigned,
      are flanked by sequences predicted to be poorly methylated. We conclude that the GATC flanking
      sequences may be critical for expression of pap and other Dam-regulated genes by affecting the
      activity of Dam at such sites and, thus, its processivity. A model is proposed, illustrating
      how the sequences flanking the GATC sites in Dam-regulated promoters may contribute to this
      epigenetic mechanism of gene expression, and how flanking sequences contribute to the diverse
      biological roles of Dam.
AU  - Peterson SN
AU  - Reich NO
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2005 355: 459-472.

PMID- 18706913
VI  - 383
DP  - 2008
TI  - Competitive Lrp and Dam assembly at the pap regulatory region: implications for mechanisms of epigenetic regulation.
PG  - 92-105
AB  - Escherichia coli DNA adenine methyltransferase (Dam) and Leucine-responsive regulatory protein
      (Lrp) are key regulators of the pap operon, which codes for
      the pilus proteins necessary for uropathogenic E. coli cellular adhesion. The pap
      operon is regulated by a phase variation mechanism in which the methylation
      states of two GATC sites in the pap regulatory region and the binding position of
      Lrp determine whether the pilus genes are expressed. The post-replicative
      reassembly of Dam, Lrp, and the local regulator PapI onto a hemimethylated pap
      intermediate is a critical step of the phase variation switching mechanism and is
      not well understood. We show that Lrp, in the presence and in the absence of PapI
      and nonspecific DNA, specifically protects pap regulatory GATC sites from Dam
      methylation when allowed to compete with Dam for assembly on unmethylated and
      hemimethylated pap DNA. The methylation protection is dependent upon the
      concentration of Lrp and does not occur with non-regulatory GATC sites. Our data
      suggest that only at low Lrp concentrations will Dam compete effectively for
      binding and methylation of the proximal GATC site, leading to a phase switch
      resulting in the expression of pili.
AU  - Peterson SN
AU  - Reich NO
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2008 383: 92-105.

PMID- 22887652
VI  - 194
DP  - 2012
TI  - Complete Genome Sequences of Corynebacterium pseudotuberculosis Strains 3/99-5 and 42/02-A, Isolated from Sheep in Scotland and Australia, Respectively.
PG  - 4736-4737
AB  - Here, we report the whole-genome sequences of two ovine-pathogenic Corynebacterium
      pseudotuberculosis isolates: strain 3/99-5, which represents the
      first C. pseudotuberculosis genome originating from the United Kingdom, and
      42/02-A, the second from Australia. These genome sequences will contribute to the
      objective of determining the global pan-genome of this bacterium.
AU  - Pethick FE et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4736-4737.

PMID- 23516198
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Oxytetracycline-Producing Bacterium Streptomyces rimosus ATCC 10970.
PG  - e0006313
AB  - We report the draft genome of Streptomyces rimosus (ATCC 10970), a soil isolate that produces
      oxytetracycline, a commercially important and clinically useful
      antibiotic.
AU  - Pethick FE
AU  - Macfadyen AC
AU  - Tang Z
AU  - Sangal V
AU  - Liu TT
AU  - Chu J
AU  - Kosec G
AU  - Petkovic H
AU  - Guo M
AU  - Kirby R
AU  - Hoskisson PA
AU  - Herron PR
AU  - Hunter IS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0006313.

PMID- 2159641
VI  - 18
DP  - 1990
TI  - Some restriction endonucleases tolerate single mismatches of the pyrimidine-purine type.
PG  - 2159-2162
AB  - DNAs from phage mutants M13mp18 and M13mp18/MP-1 were used to construct two
      closed circular heteroduplexes.  One of them carried the sequence 5'-CCTGGG-3'
      3'-GGGCCC-5' with a T-G mismatch at the position 6248.  The other carried the
      sequence  5'-CCCGGG-3' 3'-GGACCC-5' with a C-A mismatch at the same position.
      Heteroduplexes were exposed to 7 restriction endonucleases having recognition
      sites within the sequence  5'-CCCGGG-3'  3'-GGGCCC-5' and to 1 restriction
      endonuclease having a recognition site within the sequence  5'-CCTGGG-3'
      3'-GGACCC-5'.  All tested enzymes cleaved at least one mismatch-containing
      sequence although with reduced efficiency.  SmaI and XmaI tolerated both
      mismatch-containing sequences.  AvaI, HpaII, MspI, NciI and NspIII were able to
      tolerate only the T-G containing sequence while BstNI was able to tolerate only
      the C-A containing sequence.  It is inferred that the tolerance displayed by
      SmaI and XmaI depends on the presence of either the original purines or the
      original pyrimidines in mismatches of both the T-G and C-A type and that all
      other tested enzymes require the presence of the original purines in mismatches
      of both types.
AU  - Petranovic M
AU  - Petranovic D
AU  - Dohet C
AU  - Brooks P
AU  - Radman M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 2159-2162.

PMID- 1661374
VI  - 25
DP  - 1991
TI  - A spectrophotometric method for studying the cleavage of DNA duplexes by restriction endonucleases.
PG  - 1424-1426
AB  - A spectrophotometric method for continuously monitoring the cleavage of DNA duplexes by type
      II restriction endonucleases was proposed.  The time course of cleavage of a 14-membered DNA
      duplex by MvaI endonuclease was obtained.  The spectrophotometric method is characterized by
      rapidity and high precision in determining the kinetic parameters of the reaction.  It can be
      recommended for testing preparations for the presence of restriction endonucleases, rapid
      determination of the activity of any restriction endonucleases, highly precise quantitative
      analysis of the restriction enzyme catalysed reactions.
AU  - Petrauskene O
AU  - Kubareva EA
AU  - Gromova ES
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1991 25: 1424-1426.

PMID- 9541001
VI  - 425
DP  - 1998
TI  - EcoRII endonuclease has two identical DNA-binding sites and cleaves one of two co-ordinated recognition sites in one catalytic event.
PG  - 29-34
AB  - EcoRII is a typical restriction enzyme that cleaves DNA using a two-site mechanism.  EcoRII
      endonuclease is unable to cleave DNA which contains a small number of EcoRII recognition sites
      but the enzyme activity can be stimulated in the presence of DNA with a high frequency of
      EcoRII sites.  To investigate the mechanism of activation, the kinetics of stimulated EcoRII
      cleavage has been studied.  A 14 bp substrate activated the cleavage of the 71 bp substrate,
      containing one EcoRII recognition site (trans-activation) by a competitive mechanism: the
      activator increased substrate binding but not catalysis.  The activation increased if the
      substrate concentration decreased and if the activator had a lower affinity for the enzyme
      than the substrate.  The introduction of the second recognition site into the 71 bp duplex
      also enabled cleavage of this substrate (cis-activation).  Pyrophosphate bonds were
      incorporated into one of two recognition sites to switch off the cleavage of the
      phosphodiester bonds.  Analysis of cleavage products of these modified substrates showed that
      EcoRII cuts one of two coordinated recognition sites in one catalytic event.
AU  - Petrauskene OV
AU  - Babkina OV
AU  - Tashlitsky VN
AU  - Kazankov GM
AU  - Gromova ES
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1998 425: 29-34.

PMID- 7607486
VI  - 157
DP  - 1995
TI  - DNA duplexes containing methylated bases or non-nucleotide inserts in the recognition site are cleaved by restriction endonuclease R.EcoRII in presence of canonical substrate.
PG  - 173-176
AB  - DNA duplexes containing the natural methylated bases N6-methyladenine (m6Ade),
      N4-methylcytosine (m4Cyt) or C5-methylcytosine (m5Cyt) in one strand of the recognition
      sequence are resistant to EcoRII restriction endonuclease (R.EcoRII).  Hydrolysis of these
      modified duplexes was observed in the presence of the canonical substrate.  Incorporation of
      m4Cyt or m5Cyt into both strands of the recognition sequence precludes such activation by a
      canonical substrate.  R.EcoRII also fails to cleave substrate analogs in which one of the
      nucleosides in the recognition site is replaced by the 1,2-dideoxyribose (D) or by
      1,3-propanediol (Prd) (modeling DNA with an abasic site).  The hydrolysis of DNA duplexes with
      non-nucleotide inserts is also activated in the presence of canonical substrate.  Thus, the
      two-substrate mechanism of EcoRII-DNA interaction allows hydrolysis of apurinic/apyrimidinic
      and hemimethylated DNA.
AU  - Petrauskene OV
AU  - Gromova ES
AU  - Romanova EA
AU  - Volkov EM
AU  - Oretskaya TS
AU  - Shabarova ZA
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 173-176.

PMID- 8117292
VI  - 198
DP  - 1994
TI  - Two subunits of EcoRII restriction endonuclease interact with two DNA recognition sites.
PG  - 885-890
AB  - The cleavage of a 14 base pair DNA duplex containing one EcoRII recognition site by EcoRII
      restriction endonuclease (R.EcoRII) was studied in single turnover experiments with varying
      enzyme concentrations in the micromolar range. The reaction rate increased with enzyme
      concentration until a ratio of one dimeric R.EcoRII enzyme to two double stranded
      olionucleotide molecules. Excess of R.EcoRII lead to inhibition of cleavage. Maximum cleavage
      was also found with pBR322 DNA containing six EcoRII recognition sites at a ratio of one
      dimeric enzyme to two EcoRII recognition sites of the plasmid DNA. At higher ratios inhibition
      was observed. These observations indicate that the active enzyme complex is formed when two
      subunits of the enzyme interact with two R. EcoRII recognition sites.
AU  - Petrauskene OV
AU  - Karpova EA
AU  - Gromova ES
AU  - Guschlbauer W
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1994 198: 885-890.

PMID- 8747543
VI  - 37
DP  - 1995
TI  - Use of UV spectroscopy for the study of nucleic acid cleavage by E.coli RNase H and restriction endonucleases.
PG  - 1127-1135
AB  - A one-step spectrophotometric method for monitoring of nucleic acid cleavage by ribonuclease H
      from E.coli and type II restriction endonucleases has been proposed.  It is based on recording
      the increase in the UV absorbance at 260 nm during the course of enzymatic reaction.  Duplexes
      stable under the reaction conditions were chosen as substrates for the enzymes being studied.
      In order to obtain duplex dissociation following their cleavage by the enzyme appropriate
      temperature conditions were selected.  The spectrophotometric method may be applied for rapid
      testing of the nuclease activity in protein preparations as well as for precise quantitative
      analysis of nucleic acid degradation by enzymes.  This method may be successfully employed in
      kinetic studies of nucleic acid - protein interactions.
AU  - Petrauskene OV
AU  - Krynetskaya NF
AU  - Tashlitsky VN
AU  - Belkov VM
AU  - Kubareva EA
AU  - Gromova ES
AU  - Guschlbauer W
AU  - Shabarova ZA
PT  - Journal Article
TA  - Biochem. Mol. Biol. Int.
JT  - Biochem. Mol. Biol. Int.
SO  - Biochem. Mol. Biol. Int. 1995 37: 1127-1135.

PMID- 8316237
VI  - 27
DP  - 1993
TI  - Synthetic DNA duplexes as a tool in studying the mechanism of EcoRII activation.
PG  - 507-518
AB  - The efficiency of EcoRII cleavage of synthetic DNA duplexes with one EcoRII recognition site
      decreases with increasing substrate length. This enzyme virtually fails to cleave DNA duplexes
      longer than 215 bp. However, EcoRII cleaves long DNA duplexes with one recognition site in the
      presence of 11-14 bp substrates. The extent of hydrolysis activation depends on the length and
      concentration of the added substrate. A model system is suggested for studying the molecular
      and kinetic mechanism of EcoRII activation. This system includes a 30-bp substrate with one
      EcoRII recognition site, and DNA duplexes as activating substrates that contain modified
      heterocyclic bases and internucleotide phosphate groups. DNA duplexes with a modified EcoRII
      recognition site may activate hydrolysis of the 30-bp substrate and of phage T3 DNA. Their
      catalytic effect on the cleavage of extended duplexes depends on the type of modification and
      its localization in the recognition site. Cooperative interaction of EcoRII with two
      recognition sites in DNA has been shown to be essential for the functioning of the enzyme.
AU  - Petrauskene OV
AU  - Kubareva EA
AU  - Gromova ES
AU  - Pein C-D
AU  - Cech D
AU  - Shabarova ZA
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1993 27: 507-518.

PMID- 1396668
VI  - 208
DP  - 1992
TI  - Mechanism of the interaction of EcoRII restriction endonuclease with two recognition sites - probing of modified DNA duplexes as activators of the enzyme.
PG  - 617-622
AB  - The efficiency of cleavage of DNA duplexes with single EcoRII recognition sites by the EcoRII
      restriction endonuclease decreases with increasing substrate length. DNA duplexes of more than
      215 bp are not effectively cleaved by this enzyme. Acceleration of the hydrolysis of long
      single-site substrates by EcoRII is observed in the presence of 11-14 bp substrates. The
      stimulation of hydrolysis depends on the length and concentration of the second substrate. To
      study the mechanism of EcoRII endonuclease stimulation, DNA duplexes with base analogs and
      modified internucleotide phosphate groups in the EcoRII site have been investigated as
      activators. These modified duplexes are cleaved by EcoRII enzyme with different efficiences or
      are not cleaved at all. It has been discovered that the resistance of some of them can be
      overcome by incubation with a susceptible canonical substrate. The acceleration of cleavage of
      long single-site substrates depends on the type of modification of the activator. The modified
      DNA duplexes can activate EcoRII catalyzed hydrolysis if they can be cleaved by EcoRII
      themselves or in the presence of the second canonical substrate. It has been demonstrated that
      EcoRII endonuclease interacts in a cooperative way with two recognition sites in DNA. The
      cleavage of one of the recognition sites depends on the cleavage of the other. We suggest that
      the activator is not an allosteric effector but acts as a second substrate.
AU  - Petrauskene OV
AU  - Kubareva EA
AU  - Gromova ES
AU  - Shabarova ZA
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1992 208: 617-622.

PMID- 7610047
VI  - 23
DP  - 1995
TI  - The interaction of DNA duplexes containing 2-aminopurine with restriction endonucleases EcoRII and SsoII.
PG  - 2192-2197
AB  - Oligonucleotides containing 2-aminopurine (2-AP) in place of G or A in the recognition site of
      EcoRII (CCT/AGG) or SsoII (CCNGG) restriction endonucleases have been synthesized in order to
      investigate the specific interaction of DNA with these enzymes. Physicochemical properties (CD
      spectra and melting behaviour) have shown that DNA duplexes containing 2-aminopurine exist
      largely in a stable B-like form. 2-Aminopurine base paired with cytidine, however, essentially
      influences the helix structure. The presence of a 2-AP.C mismatch strongly reduces the
      stability of the duplexes in comparison with the natural double strand, indicated by a
      biphasic melting behaviour. SsoII restriction endonuclease recognizes and cleaves the modified
      substrate with a 2-AP.T mismatch in the centre of the recognition site, but it does not cleave
      the duplexes containing 2-aminopurine in place of inner and outer G, or both. EcoRII
      restriction endonuclease does not cleave duplexes containing 2-aminopurine at all. The
      two-substrate mechanism of EcoRII-DNA interaction, however, allows hydrolysis of the duplex
      containing 2-aminopurine in place of adenine in the presence of the canonical substrate.
AU  - Petrauskene OV
AU  - Schmidt S
AU  - Karyagina AS
AU  - Nikolskaya II
AU  - Gromova ES
AU  - Cech D
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1995 23: 2192-2197.

PMID- 9035738
VI  - 61
DP  - 1996
TI  - Kinetic modeling of allosteric interaction of EcoRII restriction endonuclease with two DNA sites.
PG  - 1257-1269
AB  - The effect of correlations between kinetic parameters of two inducible substrates on
      allosteric activation of EcoRII endonuclease hydrolysis of one substrate was studied.  The
      pairs of DNA duplexes were constructed that were the substrates of EcoRII restriction
      endonuclease or their analogs and had different kinetic constants of interaction with the
      enzyme; the effects of their concentrations on mutual hydrolysis induction were studied.  A
      kinetic mechanism is suggested considering the allosteric effects of two DNA recognition sites
      on a dimeric molecule of EcoRII.  Mathematic modelling was used to analyze the kinetic
      mechanism and evaluate optimal characteristics of the inductor.  Thus, activation increases
      when substrate concentration decreases, enzyme binding of two inductor or substrate molecules
      decreases, binding of one substrate molecule increases versus binding of one inductor
      molecule, and kcat of the enzyme-substrate complex including one substrate and one inductor
      increases.
AU  - Petrauskene OV
AU  - Tashlitsky VN
AU  - Brevnov MG
AU  - Bakman Y
AU  - Gromova ES
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1996 61: 1257-1269.

PMID- 10798530
VI  - 17
DP  - 2000
TI  - DNA duplexes containing altered sugar residues as probes of EcoRII and MvaI endonuclease interactions with sugar-phosphate backbone.
PG  - 857-870
AB  - Oligonucleotides containing 1-(beta-D-2'-deoxy-threo-pentofuranosyl)cytosine (dCx) and/or
      1-(beta-D-2'-deoxy-threo-pentofuranosyl)thymine (dTx) in place of dC and dT residues in the
      EcoRII and MvaI recognition site CC(A/T)GG were synthesized in order to investigate specific
      recognition of the DNA sugar-phosphate backbone by EcoRII and MvaI restriction endonucleases.
      In 2'-deoxyxylosyl moieties of dCx and dTx, 3'-hydroxyl groups were inverted, which perturbs
      the related individual phosphates. Introduction of a single 2'-deoxyxylosyl moiety into a dC
      x dG pair resulted in a minor destabilization of double-stranded DNA structure. In the case of
      a dA x dT pair the effect of a 2'-deoxyxylose incorporation was much more pronounced.
      Multiple dCx modifications and their combination with dTx did not enhance the destabilization
      effect. Hydrolysis of dCx-containing DNA duplexes by EcoRII endonuclease was blocked and
      binding affinity was strongly dependent on the location of an altered sugar. A DNA duplex
      containing a dTx residue was cleaved by the enzyme, but kcat/K(M) was slightly reduced. In
      contrast, MvaI endonuclease efficiently cleaved both types of sugar-altered substrate analogs.
      However it did not cleave conformationally perturbed scissile bonds, when the corresponding
      unmodified bonds were perfectly hydrolyzed in the same DNA duplexes. Based on these data the
      possible contributions of individual phosphates in the recognition site to substrate
      recognition and catalysis by EcoRII were proposed. We observed strikingly non-equivalent
      inputs for different phosphates with respect to their effect on EcoRII-DNA complex formation.
AU  - Petrauskene OV
AU  - Yakovleva JN
AU  - Alekseev YI
AU  - Subach FV
AU  - Babkina OV
AU  - Gromova ES
PT  - Journal Article
TA  - J. Biomol. Struct. Dyn.
JT  - J. Biomol. Struct. Dyn.
SO  - J. Biomol. Struct. Dyn. 2000 17: 857-870.

PMID- Not included in PubMed...
VI  - 12
DP  - 1986
TI  - Synthesis of oligodeoxynucleotides containing N4-methylcytosine.
PG  - 1597-1603
AB  - With deoxyuridine as starting material, N4-methyldeoxycytidine and its fully protected
      mononucleotide, suitable for oligonucleotide synthesis, have been prepared.  By means of the
      phosphotriester approach, the fully protected mononucleotide was used for the synthesis of
      seven dodecadeoxynucleotides containing either m4C or m5C in various positions of the CCCGGG
      sequence, the recognition site of some restriction endonucleases.
AU  - Petrauskiene LJ
AU  - Klimasauskas SJ
AU  - Butkus VV
AU  - Janulaitis A
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1986 12: 1597-1603.

PMID- 25377702
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Two Clostridium botulinum Group II (Nonproteolytic) Type B Strains (DB-2 and KAPB-3).
PG  - e01111-14
AB  - Clostridium botulinum is important for food safety and studies of neurotoxins associated with
      human botulism. We present the draft genome sequences of two
      strains belonging to group II type B: one collected from Pacific Ocean sediments
      (DB-2) and another obtained during a botulism outbreak (KAPB-3).
AU  - Petronella N
AU  - Kenwell R
AU  - Pagotto F
AU  - Pightling AW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01111-14.

PMID- 8832107
VI  - 42
DP  - 1996
TI  - Sequence-specific DNA modification in Acetobacter xylinum.
PG  - 759-767
AB  - Two cryptic plasmids have been discovered in Acetobacter xylinum B42 and in its derivative
      PEA-1, a cellulose defective mutant.  These two plasmids were designated pAX1 and pAX2 (50 and
      105 in size, respectively).  A restriction map was constructed for pAX1.  Attempts to cure
      these plasmids were unsuccessful.  Enzyme restriction analysis showed that these plasmids
      contain protected EcoRI and ApoI sites.  Using Southern blot and hybridization techniques, the
      protection was extended to chromosomal DNA.  Enzyme restriction analysis of several plasmids,
      from different origins and containing different incompatibility groups, isolated from strain
      PEA-1 also showed EcoRI and ApoI protection.  The presence of modifications on specific
      sequences was not found in A. xylinum 8747.  These results strongly suggest the presence of a
      modification system in A. xylinum B42 that recognizes the tetranucleotide 5'-AATT.
AU  - Petroni EA
AU  - Bocca SN
AU  - Ielpi L
PT  - Journal Article
TA  - Cell. Mol. Biol. (Noisy-le-grand)
JT  - Cell. Mol. Biol. (Noisy-le-grand)
SO  - Cell. Mol. Biol. (Noisy-le-grand) 1996 42: 759-767.

PMID- 2362828
VI  - 18
DP  - 1990
TI  - Altered specificity of restriction endonucleases HinfI.
PG  - 3666
AB  - None
AU  - Petronzio T
AU  - Schildkraut I
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 3666.

PMID- 16980500
VI  - 188
DP  - 2006
TI  - Chromosome Rearrangement and Diversification of Francisella tularensis Revealed by the Type B (OSU18) Genome Sequence.
PG  - 6977-6985
AB  - The gamma-proteobacterium Francisella tularensis is one of the most
      infectious human pathogens, and the highly virulent organism F. tularensis
      subsp. tularensis (type A) and less virulent organism F. tularensis subsp.
      holarctica (type B) are most commonly associated with significant disease
      in humans and animals. Here we report the complete genome sequence and
      annotation for a low-passage type B strain (OSU18) isolated from a dead
      beaver found near Red Rock, Okla., in 1978. A comparison of the F.
      tularensis subsp. holarctica sequence with that of F. tularensis subsp.
      tularensis strain Schu4 (P. Larsson et al., Nat. Genet. 37:153-159, 2005)
      highlighted genetic differences that may underlie different pathogenicity
      phenotypes and the evolutionary relationship between type A and type B
      strains. Despite extensive DNA sequence identity, the most significant
      difference between type A and type B isolates is the striking amount of
      genomic rearrangement that exists between the strains. All but two
      rearrangements can be attributed to homologous recombination occurring
      between two prominent insertion elements, ISFtu1 and ISFtu2. Numerous
      pseudogenes have been found in the genomes and are likely contributors to
      the difference in virulence between the strains. In contrast, no
      rearrangements have been observed between the OSU18 genome and the genome
      of the type B live vaccine strain (LVS), and only 448 polymorphisms have
      been found within non-transposase-coding sequences whose homologs are
      intact in OSU18. Nonconservative differences between the two strains
      likely include the LVS attenuating mutation(s).
AU  - Petrosino JF
AU  - Xiang Q
AU  - Karpathy SE
AU  - Jiang H
AU  - Yerrapragada S
AU  - Liu Y
AU  - Gioia J
AU  - Hemphill L
AU  - Gonzalez A
AU  - Raghavan TM
AU  - Uzman A
AU  - Fox GE
AU  - Highlander S
AU  - Reichard M
AU  - Morton RJ
AU  - Clinkenbeard KD
AU  - Weinstock GM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2006 188: 6977-6985.

PMID- 23029591
VI  - 6
DP  - 2012
TI  - Whole Genome Sequence of Treponema pallidum ssp. pallidum, Strain Mexico A, Suggests Recombination between Yaws and Syphilis Strains.
PG  - E1832
AB  - BACKGROUND: Treponema pallidum ssp. pallidum (TPA), the causative agent of
      syphilis, and Treponema pallidum ssp. pertenue (TPE), the causative agent of
      yaws, are closely related spirochetes causing diseases with distinct clinical
      manifestations. The TPA Mexico A strain was isolated in 1953 from male, with
      primary syphilis, living in Mexico. Attempts to cultivate TPA Mexico A strain
      under in vitro conditions have revealed lower growth potential compared to other
      tested TPA strains. METHODOLOGY/PRINCIPAL FINDINGS: The complete genome sequence
      of the TPA Mexico A strain was determined using the Illumina sequencing
      technique. The genome sequence assembly was verified using the whole genome
      fingerprinting technique and the final sequence was annotated. The genome size of
      the Mexico A strain was determined to be 1,140,038 bp with 1,035 predicted ORFs.
      The Mexico A genome sequence was compared to the whole genome sequences of three
      TPA (Nichols, SS14 and Chicago) and three TPE (CDC-2, Samoa D and Gauthier)
      strains. No large rearrangements in the Mexico A genome were found and the
      identified nucleotide changes occurred most frequently in genes encoding putative
      virulence factors. Nevertheless, the genome of the Mexico A strain, revealed two
      genes (TPAMA_0326 (tp92) and TPAMA_0488 (mcp2-1)) which combine TPA- and TPE-
      specific nucleotide sequences. Both genes were found to be under positive
      selection within TPA strains and also between TPA and TPE strains.
      CONCLUSIONS/SIGNIFICANCE: The observed mosaic character of the TPAMA_0326 and
      TPAMA_0488 loci is likely a result of inter-strain recombination between TPA and
      TPE strains during simultaneous infection of a single host suggesting horizontal
      gene transfer between treponemal subspecies.
AU  - Petrosova H
AU  - Zobanikova M
AU  - Cejkova D
AU  - Mikalova L
AU  - Pospisilova P
AU  - Strouhal M
AU  - Chen L
AU  - Qin X
AU  - Muzny DM
AU  - Weinstock GM
AU  - Smajs D
PT  - Journal Article
TA  - PLoS Neglected Trop. Dis.
JT  - PLoS Neglected Trop. Dis.
SO  - PLoS Neglected Trop. Dis. 2012 6: E1832.

PMID- 20582239
VI  - 1
DP  - 2009
TI  - Bioinformatic identification of novel methyltransferases.
PG  - 163-175
AB  - Methylation of DNA, protein and even RNA species are integral processes in epigenesis. Enzymes
      that catalyze these reactions using the donor S-adenosylmethionine fall into several
      structurally distinct classes. The members in each class share sequence similarity that can be
      used to identify additional methyltransferases. Here, we characterize these classes and in
      silico approaches to infer protein function. Computational methods, such as hidden Markov
      model profiling and the Multiple Motif Scanning program, can be used to analyze known
      methyltransferases and relay information into the prediction of new ones. In some cases, the
      substrate of methylation can be inferred from hidden Markov model sequence similarity
      networks. Functional identification of these candidate species is much more difficult; we
      discuss one biochemical approach.
AU  - Petrossian T
AU  - Clarke S
PT  - Journal Article
TA  - Epigenomics
JT  - Epigenomics
SO  - Epigenomics 2009 1: 163-175.

PMID- 19128472
VI  - 10
DP  - 2009
TI  - Computational methods to identify novel methyltransferases.
PG  - 7
AB  - 1.2% of the yeast genes are estimated to encode enzymes that catalyze the transfer of a methyl
      group from S-adenosylmethionine to protein, nucleic acid, lipid, and small molecule
      substrates.  These enzymes function in biosynthesis, regulating metabolic pathways and
      controlling gene expressiopn, including writing the histone code.  BLAST and MEM/MAST analysis
      using the amino acid sequence of motifs have previously generated a list of putative Class I
      methyltransferases.  Recently we have used a combination of a new search algorithm and
      structural information to refine this analysis.  This study utilizes these updated methods of
      identifying motifs and scanning the proteome to predict new members of the different families
      of methyltransferases in different organisms.  These new members may function in novel
      pathways or new modes of regulation.
AU  - Petrossian TC
AU  - Clarke SG
PT  - Journal Article
TA  - BMC Bioinformatics
JT  - BMC Bioinformatics
SO  - BMC Bioinformatics 2009 10: 7.

PMID- 27056234
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Streptococcus mitis Strain SVGS_061 Isolated from a Neutropenic Patient with Viridans Group Streptococcal Shock Syndrome.
PG  - e00259-16
AB  - Streptococcus mitisfrequently causes invasive infections in neutropenic cancer patients, with
      a subset of patients developing viridans group streptococcal (VGS)
      shock syndrome. We report here the first complete genome sequence ofS.
      mitisstrain SVGS_061, which caused VGS shock syndrome, to help elucidate the
      pathogenesis of severe VGS infection.
AU  - Petrosyan V
AU  - Holder M
AU  - Ajami NJ
AU  - Petrosino JF
AU  - Sahasrabhojane P
AU  - Thompson EJ
AU  - Kalia A
AU  - Shelburne SA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00259-16.

PMID- 9480433
VI  - 31
DP  - 1997
TI  - Interaction of T4 phage DNA-[N6-adenine]-methyltransferase with substrates containing defective recognition sites.
PG  - 973-977
AB  - The effect of the structure of the recognition site GATC in a substrate duplex on its complex
      form ation with DNA-[N6-adenine]-methyltransferase of T4 phage was studied.  The gel
      retardation method was employed to reveal the complexes.  As compared with the native
      duplexes, the majority of defective duplexes had the same or even better affinity to T4 MTase;
      however, no correlation was found between the complex stability and effectiveness of the
      duplexes as substrates for methylation.  Apparently, formation of a stale enzyme-DNA complex
      does not require continuity of the two strands of the duplex and perfect base pairing in the
      recognition site.  A half of the constituents of the recognition site suffices for stable
      complexes with T4 MTase to form.  Deoxyguanosine residues in both strands of the modified GATC
      are shown to be indispensable for complex formation.
AU  - Petrov NA
AU  - Gorbunov YA
AU  - Malygin EG
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1997 31: 973-977.

PMID- 9480432
VI  - 31
DP  - 1997
TI  - Substrate complexes of DNA-[N6-adenine]-methyltransferases of T-even phages registered by the gel retardation method.
PG  - 966-972
AB  - DNA-[N6-adenine]-methyltransferases of T4 and T2 phages (T4 and T2 Mtases) recognize, in
      double-stranded DNA, the palindrome GATC and catalyze the transfer of the methyl group from
      S-adenosyl-L-methionine (SAM) to position N6 of the adenine residue.  The gel retardation
      method was used to study the relative effectiveness of complex formation of T4 and T2 MTases
      with oligonucleotide substrates of varying length containing GATC in the middle of the duplex.
      It is shown that T4 MTase forms stable complexes with 20-mer duplexes bearing a nonmodified or
      hemimethylated GATC site.  The binding of the duplex to T4 MTase is enhanced in the presence
      of SAM.  Parameters of the interaction of SAM with MTase not bound and bound with the 20-mer
      duplex are determined.  T2 MTase, which has a higher catalytic activity than the T4 enzyme,
      forms less stable complexes with oligonucleotides.  Thus, there is no direct relation between
      the stability of the enzyme-substrate complexes and the catalytic activity.
AU  - Petrov NA
AU  - Gorbunov YA
AU  - Naumochkin AN
AU  - Malygin EG
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1997 31: 966-972.

PMID- 21029436
VI  - 7
DP  - 2010
TI  - Genomes of the T4-related bacteriophages as windows on microbial genome evolution.
PG  - 292
AB  - ABSTRACT: The T4-related bacteriophages are a group of bacterial viruses
      that share morphological similarities and genetic homologies with the
      well-studied Escherichia coli phage T4, but that diverge from T4 and each
      other by a number of genetically determined characteristics including the
      bacterial hosts they infect, the sizes of their linear double-stranded
      (ds) DNA genomes and the predicted compositions of their proteomes. The
      genomes of about 40 of these phages have been sequenced and annotated over
      the last several years and are compared here in the context of the factors
      that have determined their diversity and the diversity of other microbial
      genomes in evolution. The genomes of the T4 relatives analyzed so far
      range in size between ~160,000 and ~250,000 base pairs (bp) and are
      mosaics of one another, consisting of clusters of homology between them
      that are interspersed with segments that vary considerably in genetic
      composition between the different phage lineages. Based on the known
      biological and biochemical properties of phage T4 and the proteins encoded
      by the T4 genome, the T4 relatives reviewed here are predicted to share a
      genetic core, or "Core Genome" that determines the structural design of
      their dsDNA chromosomes, their distinctive morphology and the process of
      their assembly into infectious agents (phage morphogenesis). The Core
      Genome appears to be the most ancient genetic component of this phage
      group and constitutes a mere 12-15% of the total protein encoding
      potential of the typical T4-related phage genome. The high degree of
      genetic heterogeneity that exists outside of this shared core suggests
      that horizontal DNA transfer involving many genetic sources has played a
      major role in diversification of the T4-related phages and their spread to
      a wide spectrum of bacterial species domains in evolution. We discuss some
      of the factors and pathways that might have shaped the evolution of these
      phages and point out several parallels between their diversity and the
      diversity generally observed within all groups of interrelated dsDNA
      microbial genomes in nature.
AU  - Petrov VM
AU  - Ratnayaka S
AU  - Nolan JM
AU  - Miller ES
AU  - Karam JD
PT  - Journal Article
TA  - Virol. J.
JT  - Virol. J.
SO  - Virol. J. 2010 7: 292.

PMID- 21926218
VI  - 77
DP  - 2011
TI  - Prevention of Gordonia and Nocardia Stabilized Foam Formation by Using Bacteriophage GTE7.
PG  - 7864-7867
AB  - Most activated sludge treatment plants suffer from the presence of foams
      on the surfaces of their aeration reactors. These are often stabilized by
      hydrophobic mycolic acid-synthesizing actinobacterial species. A
      polyvalent Siphoviridae phage, GTE7, which lysed several Gordonia and
      Nocardia species, is described here. Its genome has a modular structure
      similar to that described for Rhodococcus phage ReqiDocB7. In
      laboratory-scale experiments, we showed that GTE7 prevents stabilization
      of foams by these Gordonia and Nocardia species.
AU  - Petrovski S
AU  - Seviour RJ
AU  - Tillett D
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2011 77: 7864-7867.

PMID- 6304654
VI  - 11
DP  - 1983
TI  - Sequence-specific responses of restriction endonucleases to bromodeoxyuridine substitution in mammalian DNA.
PG  - 2495-2510
AB  - Substitution of BrdU for dT in mammalian DNA alters the rates of DNA cleavage
      by restriction endonucleases in a manner that can be related to the specificity
      of cleavage.  A formula is proposed that describes inhibitory and stimulatory
      contributions arising from the substitution of a Br atom for the CH3 group on
      T.  The larger Br atom is postulated to sterically hinder the nuclease from
      binding to adjacent groups in the DNA cleavage site, while allowing a tighter
      binding to itself.  The inhibition caused by steric hindrance is predicted to
      vary inversely with distance from the point of cleavage, whereas the
      stimulation caused by tighter binding is predicted to be independent of
      distance.  The resultant formula gives a good fit to the data obtained for
      thirteen different restriction nucleases of known specificity.  The parameters
      in the formula appear to be simple functions of ionic strength.  This formula
      can be used to predict the effect of BrdU substitution on any endonuclease
      whose specificity of cleavage is known.
AU  - Petruska J
AU  - Horn D
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1983 11: 2495-2510.

PMID- 2854813
VI  - 74
DP  - 1988
TI  - Restriction endonucleases of a new type.
PG  - 89-91
AB  - Meeting Abstract
AU  - Petrusyte M
AU  - Bitinaite J
AU  - Menkevicius S
AU  - Klimasauskas S
AU  - Butkus V
AU  - Janulaitis A
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 89-91.

PMID- 8506146
VI  - 21
DP  - 1993
TI  - Bsp1407I, a restriction endonuclease from Bacillus stearothermophilus, which recognizes novel palindromic sequence 5'-T^GTACA-3'.
PG  - 2514
AB  - A new type II restriction endonuclease, Bsp1407I, has been isolated from Bacillus
      stearothermophilus RFL1407. Bsp1407I recognizes the palindromic hexanucleotide 5'- TGTACA-3'
      generating 5'-protruding tetranucleotide. Bsp1407I cuts lambda DNA at five sites, SV40 at two
      sites and does not cleave phiX174 and pBR322 DNA. We found that the computer calculated number
      of fragments that would be generated at the sequences 5'-TGTACA, correlated with the observed
      cleavage frequency of the above mentioned substrates. Double digestion with Bsp1407I and
      Bsp1201 (ApaI), Pfl23II(SplI), Eco81I(SauI) and XhoI were used to map the Bsp1407I sites on
      lambda DNA. The mapped positions matched those predicted by cleavage at the sequence
      5'-TGTACA. The cleavage site of Bsp1407I was determined using a synthetic oligonucleotide
      duplex which contains the Bsp1407I recognition sequence:
      5'-GAGTGTACACTC-3'
      3'-CTCACATGTGAG-5'.
AU  - Petrusyte M
AU  - Rudokas K
AU  - Maneliene Z
AU  - Kiuduliene E
AU  - Butkus V
AU  - Janulaitis A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 2514.

PMID- 2824154
VI  - 295
DP  - 1987
TI  - New types of restriction endonucleases.
PG  - 1250-1253
AB  - The restriction enzymes GsuI and Eco57I are described.  The cleavage sites were
      characterized as CTGGAG (16/14) for GsuI and CTGAAG (16/14) for Eco57I.  Both
      enzymes are activated by SAM.  Complete fragmentation was not possible!
      Endonuclease and methylase activities could not be separated for Eco57I.  For
      GsuI no methylase activity was detected.
AU  - Petrusyte MP
AU  - Bitinaite JB
AU  - Kersulyte DR
AU  - Menkevicius SJ
AU  - Butkus VV
AU  - Janulaitis A
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1987 295: 1250-1253.

PMID- 6277627
VI  - 121
DP  - 1982
TI  - Isolation and some properties of the restriction endonuclease BcnI from Bacillus centrosporus.
PG  - 377-381
AB  - A specific type-II restriction endonuclease BcnI from Bacillus centrosporus has
      been purified to electrophoretic homogeneity in three chromatographic steps.
      Around 15 micrograms of such a preparation can be isolated from 1g of the cell
      paste.  The yield of the enzyme is higher than that of any type-II restriction
      endonuclease so far reported.The molecular weight of the enzyme determined by
      gel filtration and polyacrylamide gel electrophoresis in the presence of sodium
      dodecyl sulphate equals 27500 and 28000 respectively.  The activity of the
      restriction endonuclease is maximal at pH 9.2 and 40-45C.  The optimal
      magnesium concentration was estimated to be 7.5mM.  The activity of BcnI may
      also be observed in the presence of Co2+, Mn2+, Ni2+ and Zn2+ but it is
      markedly less than in the presence of Mg2+.
AU  - Petrusyte MP
AU  - Janulaitis A
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1982 121: 377-381.

PMID- Not included in PubMed...
VI  - 7
DP  - 1981
TI  - Specific methylase from Bacillus centrosporus.
PG  - 1885-1887
AB  - A new site-specific methylase, BcnI, has been isolated from the Bacillus centrosporus strain.
      The enzyme recognizes the sequence 5'CmC (C/G)GG in double-stranded DNA and methylating the
      underlined cytosine residue.
AU  - Petrusyte MP
AU  - Janulaitis A
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1981 7: 1885-1887.

PMID- 26251502
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Enteroinvasive Escherichia coli O96:H19 Associated with a Severe Foodborne Outbreak.
PG  - e00883-15
AB  - We present here the complete genome sequence of a strain of enteroinvasive Escherichia coli
      O96:H19 from a severe foodborne outbreak in a canteen in Italy
      in 2014. The complete genome may provide important information about the acquired
      pathogenicity of this strain and the transition between commensal and pathogenic
      E. coli.
AU  - Pettengill EA
AU  - Hoffmann M
AU  - Binet R
AU  - Roberts RJ
AU  - Payne J
AU  - Allard M
AU  - Michelacci V
AU  - Minelli F
AU  - Morabito S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00883-15.

PMID- 24407634
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Saccharopolyspora rectivirgula.
PG  - e01117-13
AB  - We have sequenced the genome of Saccharopolyspora rectivirgula, the causative agent of
      farmer's lung disease. The draft genome consists of 182 contigs totaling
      3,977,051 bp, with a GC content of 68.9%.
AU  - Pettersson BM
AU  - Behra PR
AU  - Manduva S
AU  - Das S
AU  - Dasgupta S
AU  - Bhattacharya A
AU  - Kirsebom LA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01117-13.

PMID- 19897651
VI  - 192
DP  - 2010
TI  - The Citrobacter rodentium genome sequence reveals convergent evolution with human pathogenic Escherichia coli.
PG  - 525-538
AB  - Citrobacter rodentium (formally Citrobacter freundii biotype 4280) is a
      highly infectious pathogen that causes colitis and transmissible colonic
      hyperplasia in mice. In common with enteropathogenic and enterohemorrhagic
      Escherichia coli (EPEC and EHEC, respectively), C. rodentium exploits a
      type III secretion system (T3SS) to induce attaching and effacing (A/E)
      lesions that are essential for virulence. Here, we report the fully
      annotated genome sequence of the 5.3-Mb chromosome and four plasmids
      harbored by C. rodentium strain ICC168. The genome sequence revealed key
      information about the phylogeny of C. rodentium and identified 1,585 C.
      rodentium-specific (without orthologues in EPEC or EHEC) coding sequences,
      10 prophage-like regions, and 17 genomic islands, including the locus for
      enterocyte effacement (LEE) region, which encodes a T3SS and effector
      proteins. Among the 29 T3SS effectors found in C. rodentium are all 22 of
      the core effectors of EPEC strain E2348/69. In addition, we identified a
      novel C. rodentium effector, named EspS. C. rodentium harbors two type VI
      secretion systems (T6SS) (CTS1 and CTS2), while EHEC contains only one
      T6SS (EHS). Our analysis suggests that C. rodentium and EPEC/EHEC have
      converged on a common host infection strategy through access to a common
      pool of mobile DNA and that C. rodentium has lost gene functions
      associated with a previous pathogenic niche.
AU  - Petty NK
AU  - Bulgin R
AU  - Crepin VF
AU  - Cerdeno-Tarraga AM
AU  - Schroeder GN
AU  - Quail MA
AU  - Lennard N
AU  - Corton C
AU  - Barron A
AU  - Clark L
AU  - Toribio AL
AU  - Parkhill J
AU  - Dougan G
AU  - Frankel G
AU  - Thomson NR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 525-538.

PMID- 26251503
VI  - 3
DP  - 2015
TI  - Genome Sequence of the Acidophilic Sulfate-Reducing Peptococcaceae Strain CEB3.
PG  - e00886-15
AB  - We report the draft genome of the Peptococcaceae strain CEB3 that originated from an acidic
      (pH 2.5) stream draining an abandoned copper mine. Strain CEB3 is one
      of the very few reported acidophilic sulfate-reducing isolates. The 5.04-Mb draft
      genome harbors 5,069 predicted protein-encoding and 66 RNA genes.
AU  - Petzsch P
AU  - Poehlein A
AU  - Johnson DB
AU  - Daniel R
AU  - Schlomann M
AU  - Muhling M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00886-15.

PMID- 26251501
VI  - 3
DP  - 2015
TI  - Genome Sequence of the Moderately Acidophilic Sulfate-Reducing Firmicute Desulfosporosinus acididurans (Strain M1T).
PG  - e00881-15
AB  - Microbial dissimilatory sulfate reduction is commonplace in many anaerobic environments,
      though few acidophilic bacteria are known to mediate this process.
      We report the 4.64-Mb draft genome of the type strain of the moderate acidophile
      Desulfosporosinus acididurans, which was isolated from acidic sediment in a river
      draining the Soufriere volcano, Montserrat.
AU  - Petzsch P
AU  - Poehlein A
AU  - Johnson DB
AU  - Daniel R
AU  - Schlomann M
AU  - Muhling M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00881-15.

PMID- 28232435
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Mycobacterium chimaera Type Strain Fl-0169.
PG  - e01620-16
AB  - We report here the draft genome sequence of the type strain Mycobacterium chimaera Fl-0169, a
      member of the Mycobacterium avium complex (MAC). M. chimaera
      Fl-0169T was isolated from a patient in Italy and is highly similar to strains of
      M. chimaera isolated in Ireland, although Fl-0169T possesses unique virulence
      genes.
AU  - Pfaller S
AU  - Tokarev V
AU  - Kessler C
AU  - McLimans C
AU  - Gomez-Alvarez V
AU  - Wright J
AU  - King D
AU  - Lamendella R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01620-16.

PMID- 27516507
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of the Cyanobacterium Anabaena sp. 33047.
PG  - e00809-16
AB  - This study presents the complete nucleotide sequence of Anabaena sp. ATCC 33047 (Anabaena CA),
      a filamentous, nitrogen-fixing marine cyanobacterium, which under
      salt stress conditions accumulates sucrose internally. The elucidation of the
      genome will contribute to the understanding of cyanobacterial diversity.
AU  - Pfeffer S
AU  - Brown RM Jr
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00809-16.

PMID- 27516506
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of a Gluconacetobacter hansenii ATCC 23769 Isolate, AY201, Producer of Bacterial Cellulose and Important Model Organism for the Study  of Cellulose Biosynthesis.
PG  - e00808-16
AB  - The cellulose producer and model organism used for the study of cellulose biosynthesis,
      Gluconacetobacter hansenii AY201, is a variant of G. hansenii ATCC
      23769. We report here the complete nucleotide sequence of G. hansenii AY201,
      information which may be utilized to further the research into understanding the
      genes necessary for cellulose biosynthesis.
AU  - Pfeffer S
AU  - Mehta K
AU  - Brown RM Jr
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00808-16.

PMID- 27516505
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Gluconacetobacter hansenii Strain NQ5 (ATCC 53582), an Efficient Producer of Bacterial Cellulose.
PG  - e00785-16
AB  - This study reports the release of the complete nucleotide sequence of Gluconacetobacter
      hansenii strain NQ5 (ATCC 53582). This strain was isolated by
      R. Malcolm Brown, Jr. in a sugar mill in North Queensland, Australia, and is an
      efficient producer of bacterial cellulose. The elucidation of the genome will
      contribute to the study of the molecular mechanisms necessary for cellulose
      biosynthesis.
AU  - Pfeffer S
AU  - Mehta K
AU  - Brown RM Jr
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00785-16.

PMID- 28408681
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Komagataeibacter hansenii Strain SC-3B.
PG  - e00169-17
AB  - This study reports the release of the complete nucleotide sequence of Komagataeibacter
      hansenii SC-3B, a new efficient producer of cellulose.
      Elucidation of the genome may provide more information to aid in understanding
      the genes necessary for cellulose biosynthesis.
AU  - Pfeffer S
AU  - Santos R
AU  - Ebels M
AU  - Bordbar D
AU  - Brown RM Jr
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00169-17.

PMID- 28408680
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Komagataeibacter hansenii LMG 23726T.
PG  - e00168-17
AB  - This study reports the release of the complete nucleotide sequence of Komagataeibacter
      hansenii LMG 23726T This organism is a cellulose producer, and
      its genome may provide more information to aid in the understanding of the genes
      necessary for cellulose biosynthesis.
AU  - Pfeffer S
AU  - Santos R
AU  - Ebels M
AU  - Bordbar D
AU  - Brown RM Jr
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00168-17.

PMID- 28408679
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Komagataeibacter hansenii Strain HUM-1.
PG  - e00167-17
AB  - This study reports the release of the complete nucleotide sequence of Komagataeibacter
      hansenii HUM-1, a new efficient producer of cellulose.
      Elucidation of the genome may provide more information to aid in understanding
      the genes necessary for cellulose biosynthesis.
AU  - Pfeffer S
AU  - Santos R
AU  - Ebels M
AU  - Bordbar D
AU  - Brown RM Jr
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00167-17.

PMID- 27540066
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of a Novel Strain of Cyanobacterium, Anabaena sp. 4-3.
PG  - e00842-16
AB  - We report the complete nucleotide sequence of Anabaena sp. 4-3, an efficient producer of
      sucrose. It was isolated from salt flats near the University of Texas
      Marine Science Institute in Port Aransas, Texas. The genome may provide insight
      into the utilization of cyanobacteria as a source for biofuels.
AU  - Pfeffer S
AU  - Sowa S
AU  - Brown RM Jr
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00842-16.

PMID- 2463790
VI  - 268
DP  - 1989
TI  - Polypeptide composition and an immunological analysis of DNA methyltransferases from different species.
PG  - 388-392
AB  - The cross-reactivity of the monoclonal anti-human placental DNA
      methyltransferase antibody M2B10 with DNA methyltransferases isolated from
      other species was investigated.  This antibody immunoprecipitates DNA
      methyltransferases from mammalian cells, i.e., human placenta, mouse P815
      cells, and rat liver cells.  No cross-reactivity is observed with DNA
      methyltransferases from wheat germ and with bacterial DNA methyltransferases
      HpaII and EcoRI.  The mammalian enzymes are characterized by polypeptides of
      molecular mass 150-190 kDa.  Polypeptides smaller than 190 kDa are presumably
      generated by proteolysis of the native 190-kDa DNA methyltransferase.  Trypsin
      digestion of the 190-kDa polypeptide isolated from mouse cells results in
      progressive appearance of DNA methyltransferase polypeptides of 150-190, 110,
      100, and 52-60 kDa.
AU  - Pfeifer GP
AU  - Kohlmaier L
AU  - Tomassetti A
AU  - Schleicher R
AU  - Follmann H
AU  - Pfohl-Leszkowicz A
AU  - Dirheimer G
AU  - Drahovsky D
PT  - Journal Article
TA  - Arch. Biochem. Biophys.
JT  - Arch. Biochem. Biophys.
SO  - Arch. Biochem. Biophys. 1989 268: 388-392.

PMID- 18313895
VI  - 91
DP  - 2008
TI  - Evolution in the laboratory: The genome of Halobacterium salinarum strain R1 compared to that of strain NRC-1.
PG  - 335-346
AB  - We report the sequence of the Halobacterium salinarum strain R1 chromosome and its four
      megaplasmids. Our set of protein-coding genes is supported by
      extensive proteomic and sequence homology data. The structures of the
      plasmids, which show three large-scale duplications (adding up to 100 kb),
      were unequivocally confirmed by cosmid analysis. The chromosome of strain
      R1 is completely colinear and virtually identical to that of strain NRC-1.
      Correlation of the plasmid sequences revealed 210 kb of sequence that
      occurs only in strain R1. The remaining 350 kb shows virtual sequence
      identity in the two strains. Nevertheless, the number and overall
      structure of the plasmids are largely incompatible. Also, 20% of the
      protein sequences differ despite the near identity at the DNA sequence
      level. Finally, we report genome-wide mobility data for insertion
      sequences from which we conclude that strains R1 and NRC-1 originate from
      the same natural isolate. This exemplifies evolution in the laboratory.
AU  - Pfeiffer F
AU  - Schuster SC
AU  - Broicher A
AU  - Falb M
AU  - Palm P
AU  - Rodewald K
AU  - Ruepp A
AU  - Soppa J
AU  - Tittor J
AU  - Oesterhelt D
PT  - Journal Article
TA  - Genomics
JT  - Genomics
SO  - Genomics 2008 91: 335-346.

PMID- 25197494
VI  - 9
DP  - 2014
TI  - Non-contiguous finished genome sequence and description of Alistipes ihumii sp. nov.
PG  - 1221-1235
AB  - Alistipes ihumii strain AP11(T) sp. nov. is the type strain of A. ihumii sp. nov., a new
      species within the genus Alistipes. This strain, whose genome is
      described here, was isolated from the fecal flora of a 21-year-old French
      Caucasian female, suffering from a severe restrictive form of anorexia nervosa
      since the age of 12 years. A. ihumii is a Gram-negative anaerobic bacillus. Here
      we describe the features of this organism, together with the complete genome
      sequence and annotation. The 2,753,264 bp long genome (one chromosome but no
      plasmid) contains 2,254 protein-coding and 47 RNA genes, including 3 rRNA genes.
AU  - Pfleiderer A
AU  - Mishra AK
AU  - Lagier JC
AU  - Robert C
AU  - Caputo A
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 1221-1235.

PMID- 22237545
VI  - 6
DP  - 2012
TI  - Dinitrogen fixation in a unicellular chlorophyll d-containing cyanobacterium.
PG  - 1367-1377
AB  - Marine cyanobacteria of the genus Acaryochloris are the only known organisms that
      use chlorophyll d as a photosynthetic pigment. However, based on chemical
      sediment analyses, chlorophyll d has been recognized to be widespread in oceanic
      and lacustrine environments. Therefore it is highly relevant to understand the
      genetic basis for different physiologies and possible niche adaptation in this
      genus. Here we show that unlike all other known isolates of Acaryochloris, the
      strain HICR111A, isolated from waters around Heron Island, Great Barrier Reef,
      possesses a unique genomic region containing all the genes for the structural and
      enzymatically active proteins of nitrogen fixation and cofactor biosynthesis.
      Their phylogenetic analysis suggests a close relation to nitrogen fixation genes
      from certain other marine cyanobacteria. We show that nitrogen fixation in
      Acaryochloris sp. HICR111A is regulated in a light-dark-dependent fashion. We
      conclude that nitrogen fixation, one of the most complex physiological traits
      known in bacteria, might be transferred among oceanic microbes by horizontal gene
      transfer more often than anticipated so far. Our data show that the two powerful
      processes of oxygenic photosynthesis and nitrogen fixation co-occur in one and
      the same cell also in this branch of marine microbes and characterize
      Acaryochloris as a physiologically versatile inhabitant of an ecological niche,
      which is primarily driven by the absorption of far-red light.
AU  - Pfreundt U
AU  - Stal LJ
AU  - Voss B
AU  - Hess WR
PT  - Journal Article
TA  - ISME J.
JT  - ISME J.
SO  - ISME J. 2012 6: 1367-1377.

PMID- 23469351
VI  - 1
DP  - 2013
TI  - Genome Sequence of Naphthalene-Degrading Soil Bacterium Pseudomonas putida CSV86.
PG  - e00234-12
AB  - CSV86, a soil isolate, preferentially utilizes naphthalene over glucose as a source of carbon
      and energy. We present the draft genome sequence, which is 6.4
      Mb in size; analysis suggests the chromosomal localization of genes coding for
      naphthalene utilization. The operons coding for glucose and other aromatic
      compounds might also be annotated in another study.
AU  - Phale PS
AU  - Paliwal V
AU  - Raju SC
AU  - Modak A
AU  - Purohit HJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00234-12.

PMID- 19412177
VI  - 41
DP  - 2009
TI  - Retrotransposon silencing and telomere integrity in somatic cells of Drosophila depends on the cytosine-5 methyltransferase DNMT2.
PG  - 696-702
AB  - Here we show that the cytosine-5 methyltransferase DNMT2 controls retrotransposon silencing in
      Drosophila somatic cells. In Drosophila,
      significant DNMT2-dependent DNA methylation occurs during early
      embryogenesis. Suppression of white gene silencing by Mt2 (Dnmt2) null
      mutations in variegated P[w(+)] element insertions identified functional
      targets of DNMT2. The enzyme controls DNA methylation at retrotransposons
      in early embryos and initiates histone H4K20 trimethylation catalyzed by
      the SUV4-20 methyltransferase. In somatic cells, loss of DNMT2 eliminates
      H4K20 trimethylation at retrotransposons and impairs maintenance of
      retrotransposon silencing. In Dnmt2 and Suv4-20 null genotypes,
      retrotransposons are strongly overexpressed in somatic but not germline
      cells, where retrotransposon silencing depends on an RNAi mechanism. DNMT2
      also controls integrity of chromosome 2R and 3R telomeres. In Dnmt2 null
      strains, we found stable loss of the subtelomeric clusters of defective
      Invader4 elements. Together, these results demonstrate a previously
      unappreciated role of DNA methylation in retrotransposon silencing and
      telomere integrity in Drosophila.
AU  - Phalke S
AU  - Nickel O
AU  - Walluscheck D
AU  - Hortig F
AU  - Onorati MC
AU  - Reuter G
PT  - Journal Article
TA  - Nat. Genet.
JT  - Nat. Genet.
SO  - Nat. Genet. 2009 41: 696-702.

PMID- 17660435
VI  - 153
DP  - 2007
TI  - Comparative genomic analysis of mycobacteriophage Tweety: evolutionary insights and construction of compatible site-specific integration vectors for mycobacteria.
PG  - 2711-2723
AB  - Mycobacteriophage Tweety is a newly isolated phage of Mycobacterium
      smegmatis. It has a viral morphology with an isometric head and a long
      flexible tail, and forms turbid plaques from which stable lysogens can
      be
      isolated. The Tweety genome is 58 692 bp in length, contains 109
      protein-coding genes, and shows significant but interrupted nucleotide
      sequence similarity with the previously described mycobacteriophages
      Llij,
      PMC and Che8. However, overall the genome possesses mosaic architecture,
      with gene products being related to other mycobacteriophages such as
      Che9d, Omega and Corndog. A gene encoding an integrase of the
      tyrosine-recombinase family is located close to the centre of the
      genome,
      and a putative attP site has been identified within a short intergenic
      region immediately upstream of int. This Tweety attP-int cassette was
      used
      to construct a new set of integration-proficient plasmid vectors that
      efficiently transform both fast- and slow-growing mycobacteria through
      plasmid integration at a chromosomal locus containing a tRNA(Lys) gene.
      These vectors are maintained well in the absence of selection and are
      completely compatible with integration vectors derived from
      mycobacteriophage L5, enabling the simple construction of complex
      recombinants with genes integrated simultaneously at different
      chromosomal
      positions.
AU  - Pham TT
AU  - Jacobs-Sera D
AU  - Pedulla ML
AU  - Hendrix RW
AU  - Hatfull GF
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2007 153: 2711-2723.

PMID- 29317751
VI  - 8
DP  - 2018
TI  - Methylation in Mycobacterium tuberculosis is lineage specific with associated mutations present globally.
PG  - 160
AB  - DNA methylation is an epigenetic modification of the genome involved in regulating crucial
      cellular processes, including transcription and chromosome
      stability. Advances in PacBio sequencing technologies can be used to robustly
      reveal methylation sites. The methylome of the Mycobacterium tuberculosis complex
      is poorly understood but may be involved in virulence, hypoxic survival and the
      emergence of drug resistance. In the most extensive study to date, we
      characterise the methylome across the 4 major lineages of M. tuberculosis and 2
      lineages of M. africanum, the leading causes of tuberculosis disease in humans.
      We reveal lineage-specific methylated motifs and strain-specific mutations that
      are abundant globally and likely to explain loss of function in the respective
      methyltransferases. Our work provides a set of sixteen new complete reference
      genomes for the Mycobacterium tuberculosis complex, including complete lineage 5
      genomes. Insights into lineage-specific methylomes will further elucidate
      underlying biological mechanisms and other important phenotypes of the
      epi-genome.
AU  - Phelan J
AU  - de Sessions PF
AU  - Tientcheu L
AU  - Perdigao J
AU  - Machado D
AU  - Hasan R
AU  - Hasan Z
AU  - Bergval IL
AU  - Anthony R
AU  - McNerney R
AU  - Antonio M
AU  - Portugal I
AU  - Viveiros M
AU  - Campino S
AU  - Hibberd ML
AU  - Clark TG
PT  - Journal Article
TA  - Sci. Rep.
JT  - Sci. Rep.
SO  - Sci. Rep. 2018 8: 160.

PMID- 26205866
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Mycobacterium lentiflavum CSUR P1491.
PG  - e00817-15
AB  - We announce the draft genome sequence of Mycobacterium lentiflavum strain CSUR P1491, a
      nontuberculous mycobacterium responsible for opportunistic potentially
      life-threatening infections in immunocompromised patients. The genome described
      here comprises a 6,818,507-bp chromosome exhibiting a 65.75% G+C content, 6,354
      protein-coding genes, and 75 RNA genes.
AU  - Phelippeau M
AU  - Croce O
AU  - Robert C
AU  - Raoult D
AU  - Drancourt M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00817-15.

PMID- 26205865
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Mycobacterium europaeum Strain CSUR P1344.
PG  - e00816-15
AB  - We report the draft genome sequence of Mycobacterium europaeum strain CSUR P1344, a slowly
      growing mycobacterium of the Mycobacterium simiae complex and
      opportunistic respiratory tract colonizer and pathogen. This genome of 6,152,523
      bp exhibits a 68.18% G+C content, encoding 5,814 predicted proteins and 74 RNAs.
AU  - Phelippeau M
AU  - Croce O
AU  - Robert C
AU  - Raoult D
AU  - Drancourt M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00816-15.

PMID- 25013147
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Mycobacterium neoaurum Strain DSM 44074T.
PG  - e00699-14
AB  - We report the draft genome sequence of Mycobacterium neoaurum strain DSM 44074(T), a
      nontuberculosis species responsible for opportunistic infections in
      immunocompromised patients. The strain described here is composed of 5,536,033
      bp, with a G+C content of 66.24%, and carries 5,274 protein-coding genes and 72
      RNA genes.
AU  - Phelippeau M
AU  - Robert C
AU  - Croce O
AU  - Raoult D
AU  - Drancourt M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00699-14.

PMID- 23869018
VI  - 341
DP  - 2013
TI  - Pandoraviruses: amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes.
PG  - 281-286
AB  - Ten years ago, the discovery of Mimivirus, a virus infecting Acanthamoeba,
      initiated a reappraisal of the upper limits of the viral world, both in terms of
      particle size (>0.7 micrometers) and genome complexity (>1000 genes), dimensions
      typical of parasitic bacteria. The diversity of these giant viruses (the
      Megaviridae) was assessed by sampling a variety of aquatic environments and their
      associated sediments worldwide. We report the isolation of two giant viruses, one
      off the coast of central Chile, the other from a freshwater pond near Melbourne
      (Australia), without morphological or genomic resemblance to any previously
      defined virus families. Their micrometer-sized ovoid particles contain DNA
      genomes of at least 2.5 and 1.9 megabases, respectively. These viruses are the
      first members of the proposed "Pandoravirus" genus, a term reflecting their lack
      of similarity with previously described microorganisms and the surprises expected
      from their future study.
AU  - Philippe N
AU  - Legendre M
AU  - Doutre G
AU  - Coute Y
AU  - Poirot O
AU  - Lescot M
AU  - Arslan D
AU  - Seltzer V
AU  - Bertaux L
AU  - Bruley C
AU  - Garin J
AU  - Claverie JM
AU  - Abergel C
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2013 341: 281-286.

PMID- 26398358
VI  - 10
DP  - 2015
TI  - In Vivo Evolution of Bacterial Resistance in Two Cases of Enterobacter aerogenes Infections during Treatment with Imipenem.
PG  - E0138828
AB  - Infections caused by multidrug resistant (MDR) bacteria are a major concern
      worldwide. Changes in membrane permeability, including decreased influx and/or
      increased efflux of antibiotics, are known as key contributors of bacterial MDR.
      Therefore, it is of critical importance to understand molecular mechanisms that
      link membrane permeability to MDR in order to design new antimicrobial
      strategies. In this work, we describe genotype-phenotype correlations in
      Enterobacter aerogenes, a clinically problematic and antibiotic resistant
      bacterium. To do this, series of clinical isolates have been periodically
      collected from two patients during chemotherapy with imipenem. The isolates
      exhibited different levels of resistance towards multiple classes of antibiotics,
      consistently with the presence or the absence of porins and efflux pumps.
      Transport assays were used to characterize membrane permeability defects.
      Simultaneous genome-wide analysis allowed the identification of putative
      mutations responsible for MDR. The genome of the imipenem-susceptible isolate G7
      was sequenced to closure and used as a reference for comparative genomics. This
      approach uncovered several loci that were specifically mutated in MDR isolates
      and whose products are known to control membrane permeability. These were omp35
      and omp36, encoding the two major porins; rob, encoding a global AraC-type
      transcriptional activator; cpxA, phoQ and pmrB, encoding sensor kinases of the
      CpxRA, PhoPQ and PmrAB two-component regulatory systems, respectively. This
      report provides a comprehensive analysis of membrane alterations relative to
      mutational steps in the evolution of MDR of a recognized nosocomial pathogen.
AU  - Philippe N
AU  - Maigre L
AU  - Santini S
AU  - Pinet E
AU  - Claverie JM
AU  - Davin-Regli AV
AU  - Pages JM
AU  - Masi M
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2015 10: E0138828.

PMID- 25593245
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Four Closely Linked Vibrio vulnificus Isolates from the Biotype 1 Environmental Genotype.
PG  - e01317-14
AB  - Biotype 1 of Vibrio vulnificus, which causes severe invasive intestinal and wound infections,
      is split into two genotypes with all previously sequenced clinical
      isolates from the C genotypes. We report here the whole-genome sequencing of two
      clinical isolates and two closely linked oyster isolates from the E genotype for
      comparative studies.
AU  - Phillips KE
AU  - Schipma MJ
AU  - Satchell KJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01317-14.

PMID- 24652973
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Israeli Outbreak-Associated Vibrio vulnificus Biotype 3  Clinical Isolate BAA87.
PG  - e00032-14
AB  - Vibrio vulnificus is a seafood-associated pathogen that causes severe wound and intestinal
      infections. Biotype 3 of V. vulnificus emerged in 1996 as the cause of
      an Israeli outbreak associated with the handling of infected tilapia. Here, we
      describe the whole-genome sequence of the ATCC biotype 3 clinical isolate BAA87
      (CDC9530-96).
AU  - Phillips KE
AU  - Schipma MJ
AU  - Satchell KJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00032-14.

PMID- 
VI  - 
DP  - 2005
TI  - Cloning and characterization of a methyl-dependent restriction endonuclease and a cell cycle regulating DNA methyltransferase from Zymomonas mobilis subspecies mobilis CP4.
PG  - 1-220
AB  - A Zymomonas mobilis CP4 genomic library was screened using the E. coli indicator strains
      AP1-200-9 and ER1992 to isolate clones of enzymes that cause DNA damage.  Sequence analysis of
      positive clones identified two open reaading frames encoding DNA modification enzymes: (a) a
      924 base pair open reading frame with sequence similarity to mrr, a methyl-dependant
      restriction endonuclease, which was designated ZmCP4mrr, and (2) a 1149 bp open reading frame
      with amino acid sequence similarity to ccrM, a cell cycle regulating DNA methyltransferase,
      which was designated ZmCP4ccM.  Sequence analysis indicates that ZmCP4mrr is a solitary
      methyl-dependent restriction endonuclease without a cognate DNA methyltransferase.
      Transformation of Eschichia coli K12 strains with various DNA methyltransferase backgrounds
      demonstrated that a plasmid borne ZmCP4mrr gene readily transforms E. coli strains that
      experess dcm, hsdM, and EcoKccrM DNA methyltransferases, indicating that ZmCP4Mrr does not
      recognize and restrict sites methylated by these DNA methyltransferases.  E. coli strains that
      express the dam DNA methyltransferase could only be transformed if expression of plasmid borne
      ZmCP4mrr was repressed.  Subsequent induction of ZmCP4mrr expression in these cells resulted
      in inhibition of growth and cell death, indicating that ZmCP4Mrr specifically restricts Dam
      N6-adenine methylated DNA (5'-GmATC-3').  Plasmid DNA originating from dam deficient E. coli
      strains did not improve transformation efficiency, indicating that Z. mobilis CP4 has a
      restriction system in addition to ZmCP4Mrr contributing to low frequency of gene transfer from
      foreign DNA.  Sequence analysis indicates that AmCP4ccrM is a solitary DNA methyltransferase
      with two possible in-frame translation initiation sites.  A ribosomal binding site containing
      a sequence, 5'-AGGA-3', conserved in Z. mobilis promoters of highly expressed genes is
      located adjacent to the first possible translation initiation site and not the second,
      suggesting that ZmCP4ccrM is being expressed from the first translational initiation site. The
      specificity for ZmCP4CcrM methylation was directly determined to be the N6-adenine of its
      recognition site 5'-GANTC-3'.  Z. mobilis CP4 cells overexpressing ZmCP4ccrM exhibited a
      subpopulation of filamentous cells, ranging from 10-90 uM in length, with multiple
      chromosomes.  Overexpression of ZmCP4ccrM caused disruption of normal cell division and
      chromosomal segregation, suggesting that ZmCP4CcrM is involved in cell cycle regulation.
AU  - Phillips PL
PT  - Journal Article
TA  - Ph.D. Thesis, Univ. of Florida, Gainesville
JT  - Ph.D. Thesis, Univ. of Florida, Gainesville
SO  - Ph.D. Thesis, Univ. of Florida, Gainesville 2005 : 1-220.

PMID- 7656019
VI  - 1
DP  - 1994
TI  - Induced flip.
PG  - 76-77
AB  - Hhal methyltransferase, caught in the act of methylating a cytosine on a DNA substrate,
      reveals how the enzyme overcomes the problem of chemically modifying bases in the relatively
      inaccessible environment of the DNA duplex.
AU  - Phillips SEV
PT  - Journal Article
TA  - Nat. Struct. Biol.
JT  - Nat. Struct. Biol.
SO  - Nat. Struct. Biol. 1994 1: 76-77.

PMID- 28982992
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Methylobacterium radiotolerans Strain MAMP 4754, a Bacterial Endophyte Isolated from Combretum erythrophyllum in South Africa.
PG  - e00976-17
AB  - We announce here the draft genome sequence of Methylobacterium radiotolerans strain MAMP 4754,
      isolated from the roots of the medicinal plant Combretum
      erythrophyllumM. radiotolerans has a genome size of 7,389,282 bp with 7,166 genes
      and a G+C content of 70.5%.
AU  - Photolo MM
AU  - Mavumengwana V
AU  - Serepa-Dlamini MH
AU  - Tlou MG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00976-17.

PMID- 22408239
VI  - 194
DP  - 2012
TI  - Draft Genome of Halomonas Species Strain GFAJ-1 (ATCC BAA-2256).
PG  - 1835-1836
AB  - Halomonas strain GFAJ-1 was reported in Science magazine to be a remarkable microbe for which
      there was 'arsenate in macromolecules that normally contain phosphate, most notably nucleic
      acids.' The draft genome of the bacterium was determined (NCBI accession numbers AHBC01000001
      through AHBC01000103). It appears to be a typical gamma proteobacterium.
AU  - Phung LT
AU  - Silver S
AU  - Trimble WL
AU  - Gilbert JA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1835-1836.

PMID- 22933773
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Alcaligenes faecalis subsp. faecalis NCIB 8687 (CCUG 2071).
PG  - 5153
AB  - Alcaligenes faecalis subsp. faecalis NCIB 8687, the betaproteobacterium from which arsenite
      oxidase had its structure solved and the first 'arsenate gene
      island' identified, provided a draft genome of 3.9 Mb in 186 contigs (with the
      largest 15 comprising 90% of the total) for this opportunistic pathogen species.
AU  - Phung LT
AU  - Trimble WL
AU  - Meyer F
AU  - Gilbert JA
AU  - Silver S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5153.

PMID- 18270594
VI  - 3
DP  - 2008
TI  - Genome sequence of the saprophyte Leptospira biflexa provides insights into the evolution of Leptospira and the pathogenesis of leptospirosis.
PG  - e1607
AB  - Leptospira biflexa is a free-living saprophytic spirochete present in aquatic environments. We
      determined the genome sequence of L. biflexa,
      making it the first saprophytic Leptospira to be sequenced. The L. biflexa
      genome has 3,590 protein-coding genes distributed across three circular
      replicons: the major 3,604 chromosome, a smaller 278-kb replicon that also
      carries essential genes, and a third 74-kb replicon. Comparative sequence
      analysis provides evidence that L. biflexa is an excellent model for the
      study of Leptospira evolution; we conclude that 2052 genes (61%) represent
      a progenitor genome that existed before divergence of pathogenic and
      saprophytic Leptospira species. Comparisons of the L. biflexa genome with
      two pathogenic Leptospira species reveal several major findings. Nearly
      one-third of the L. biflexa genes are absent in pathogenic Leptospira. We
      suggest that once incorporated into the L. biflexa genome, laterally
      transferred DNA undergoes minimal rearrangement due to physical
      restrictions imposed by high gene density and limited presence of
      transposable elements. In contrast, the genomes of pathogenic Leptospira
      species undergo frequent rearrangements, often involving recombination
      between insertion sequences. Identification of genes common to the two
      pathogenic species, L. borgpetersenii and L. interrogans, but absent in L.
      biflexa, is consistent with a role for these genes in pathogenesis.
      Differences in environmental sensing capacities of L. biflexa, L.
      borgpetersenii, and L. interrogans suggest a model which postulates that
      loss of signal transduction functions in L. borgpetersenii has impaired
      its survival outside a mammalian host, whereas L. interrogans has retained
      environmental sensory functions that facilitate disease transmission
      through water.
AU  - Picardeau M et al
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2008 3: e1607.

PMID- 16125907
VI  - 157
DP  - 2006
TI  - Strain variability in the DNA immigration control region (ICR) of Xylella fastidiosa.
PG  - 254-262
AB  - The genome of the bacterium Xylella fastidiosa contains four ORFs (XF2721, XF2725, XF2739 and
      XF0295) related to the restriction
      modification type I system, ordinarily named R-M. This system belongs
      to the DNA immigration control region (ICR). Each CIRF is related to
      different operon structures, which are homologues among themselves and
      with subunit Hsd R from the endonuclease coding genes. In addition,
      these ORFs are highly homologous to genes in Pseudomonas aeruginosa,
      Methylococcus capsulatus str. Bath, Legionella pneumophila,
      Helicobacter pylori, Xanthomonas oryzae pv. Oryzae and Silicibacter
      pomeroyi, as well as to genes from X. fastidiosa strains that infect
      grapevine, almond and oleander plants. This study was carried out on
      R-M ORFs from forty-three X. fastidiosa strains isolated from citrus,
      coffee, grapevine, periwinkle, almond and plum trees, in order to
      assess the genetic diversity of these loci through PCR-RFLP. PCR-RFLP
      analysis of the four ORFs related to the R-M system from these strains
      enabled the detection of haplotypes for these loci. When the haplotypes
      were defined, wide genetic diversity and a large range of similar
      strains originating from different hosts were observed. This analysis
      also provided information indicating differences in population genetic
      structures, which led to detection of different levels of gene transfer
      among the groups of strains.
AU  - Picchi SC
AU  - Vilas-Boas LA
AU  - Ceresini PC
AU  - de Macedo-Lemos EG
AU  - Lemos MV
PT  - Journal Article
TA  - Res. Microbiol.
JT  - Res. Microbiol.
SO  - Res. Microbiol. 2006 157: 254-262.

PMID- 27563050
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Cellulolytic and Xylanolytic Cellulomonas sp. Strain B6  Isolated from Subtropical Forest Soil.
PG  - e00891-16
AB  - Cellulomonas sp. strain B6 was isolated from a subtropical forest soil sample and presented
      (hemi)cellulose-degrading activity. We report here its draft genome
      sequence, with an estimated genome size of 4 Mb, a G+C content of 75.1%, and
      3,443 predicted protein-coding sequences, 92 of which are glycosyl hydrolases
      involved in polysaccharide degradation.
AU  - Piccinni F
AU  - Murua Y
AU  - Ghio S
AU  - Talia P
AU  - Rivarola M
AU  - Campos E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00891-16.

PMID- 6449403
VI  - 11
DP  - 1980
TI  - An easy method for the selection of restriction- and modification-deficient mutants of Escherichia coli K-12.
PG  - 173-175
AB  - An easy and rapid method for selecting restriction- and modification-
      defective mutants of
      Escherichia coli K-12 is described. This method employs selection of tetracycline-resistant
      lysogens after
      infection with lambda::Tn10 phage and results in a high yield of spontaneous rk-mk- and
      rk-mk- mutants.
AU  - Piechaczyk M
AU  - Jeanteur P
AU  - Louarn J-M
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1980 11: 173-175.

PMID- 1741304
VI  - 20
DP  - 1992
TI  - PamI and PamII restriction endonucleases from Phormidium ambiguum.
PG  - 619
AB  - PamI and PamII are type II restriction endonucleases from the Cyanobacterial
      strain Phormidium ambiguum GOM (CCALA Hindak 1965/117).  PamI and PamII are
      isoschizomers of MstI and AcyI respectively.  The enzymes were purified using
      two chromatographic steps: 1) phosphocellulose, 2) DEAE-sephadex G-25.  The
      enzymes were free of contaminating nuclease activity.  All digestions were
      performed at 37C in a buffer containing 50 mM NaCl, 10 mM Tris-HCl (pH 7.5), 10
      mM MgCl2.
AU  - Piechula S
AU  - Kim SC
AU  - Podhajska AJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 619.

PMID- 1480496
VI  - 20
DP  - 1992
TI  - Isolation and identification of the restriction endonuclease PtaI from Phormidium tadzschicicum, an isoschizomer of BspMII.
PG  - 6738
AB  - PtaI is a type II restriction endonuclease from the cyanobacterial strain Phormidium
      tadzschicicum. PtaI recognizes the sequence TCCGGA and cleaves between T and C. It is an
      isoschizomer of BspMII.
AU  - Piechula S
AU  - Kur J
AU  - Bielawski K
AU  - Podhajska AJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 6738.

PMID- 7607516
VI  - 157
DP  - 1995
TI  - Purification and characterization of two restriction endonucleases isolated from Phormidium inundatum.
PG  - 315-316
AB  - We have isolated two restriction endonucleases, PinBI and PinBII, from the cyanobacterial
      strain Phormidium inundatum, and identified them as isoschizomers of AvaIII and BspMII,
      respectively.
AU  - Piechula S
AU  - Kur J
AU  - Woszczyk J
AU  - Podhajska AJ
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 315-316.

PMID- 8734423
VI  - 5
DP  - 1996
TI  - Isolation and characterization of the restriction endonuclease PpeI from Phormidium persicinum.
PG  - 97-99
AB  - PpeI is a type II restriction endonuclease isolated from cyanobacterial strain
      Phormidium persicinum.  The endonuclease PpeI, an isoschizomer of ApaI, recognizes the
      hexanucleotide sequence (5'-GGGCC/C-3') and cleaves, after the second C, producing
      four nucleotide 3'-cohesive ends.
AU  - Piechula S
AU  - Piosik J
AU  - Bielawski K
AU  - Podhajska AJ
PT  - Journal Article
TA  - Mol. Biotechnol.
JT  - Mol. Biotechnol.
SO  - Mol. Biotechnol. 1996 5: 97-99.

PMID- 1904151
VI  - 19
DP  - 1991
TI  - Isolation and identification of two new Synechococcus-derived restriction endonucleases, SleI and SspAI isoschizomers of EcoRII.
PG  - 2782
AB  - Two new type-II restriction endonucleases, SleI and SspAI, have been isolated
      from Synechococcus leopoliensis.  Strain 1402-1 was obtained from the Institut
      Pasteur Culture Collection of Cyanobacterial Strains.  Synechococcus sp. AN6301
      was obtained from Pflanzenphysiologisches Institut, Universitat Gottingen,
      Nikolausberg, FRG.  Both strains were grown aerobically at 30C in BG medium
      under fluorescent light.  The cells were harvested and stored in liquid
      nitrogen.  Frozen cells were disrupted by sonication.  Purification of the
      enzymes was carried out by the following steps: (I) DEAE-cellulose
      chromatography (II) DNA-cellulose chromatography, (III) QAE-Sephadex
      chromatography.  The digestion pattern of pBR322 DNA with BstNI was identical
      to the patterns obtained with SleI and SspAI, indicating that SleI and SspAI
      are isoschizomers of BstNI, and therefore, of its isoschizomer EcoRII.  It was
      found that SleI and SspAI enzymes generate 5 nucleotide (nt) cohesive ends, as
      assessed by digestion of lambda DNA and fill-in reaction with T7 DNA
      polymerase, [alpha-35S]dATP and the other dNTPs.  EcoRII and BstNI recognize
      the same sequence, but cut between different nt generating 5-nt and 1-nt
      cohesive ends, respectively.  Generally following the approach described by
      Brown et al., we have directly determined the sequence of the cleavage site of
      SleI and SspAI in M13mp18 double stranded DNA.  The first restriction site
      recognized by EcoRII is located 167 nt from the first nt of the 17-mer
      sequencing primer, and thus can easily be sequenced.  We found that the SleI
      and SspAI cut sites (represented by arrows) are shifted by two nt (Fig. 2)
      within the recognition site with respect to the BstNI cuts (represented by
      dots), and thus are identical to the EcoRII cuts.
AU  - Piechula S
AU  - Skowron PM
AU  - Piatyszek M
AU  - Podhajska AJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 2782.

PMID- 11430404
VI  - 198
DP  - 2001
TI  - Mesophilic cyanobacteria producing thermophilic restriction endonucleases.
PG  - 135-140
AB  - When searching for the site-specific endonucleases in several strains of Phormidium we made
      the following observations. Among the 16 strains
      that originated from 15 species of Phormidium. 12 produced one or more
      restriction enzymes, of which two produced the highly thermophilic
      restriction endonucleases PtaI and PpaAII with their optimum activity
      at 65-80 C, which is far above the lethal temperature for the
      host microorganism (40 C). These two temperature-resistant
      enzymes are isoschizomers of known BspMII and TaqI endonucleases,
      respectively. The presence of the thermophilic TaqI isoschizomer does
      not seem to play any role in the mesophilic host microorganism, which
      does not even contain an active cognate methyltransferase. Among the
      remaining 10 strains, six produced isoschizomers of endonucleases which
      we first described in cyanobacteria, namely: PfuAII (NdeI), PinBII and
      PtaI(BspMII). PlaAII (RsaI), PpaAII PpeI (ApaI). Two enzymes, PauAII
      (AhaIII) and PfaAII (NdeI), belong to a group of a very rarely
      occurring isoschizomers. Out of 21 cyanobacterial endonucleases
      investigated by us, Four were active in a wide range of temperatures
      (from 15 to 60 C) which also extended the optimal growth
      temperature of the hosts. We assume that our observation on the
      presence of temperature-resistant restriction enzymes in mesophilic
      hosts supports the idea of horizontal gene transfer. Restriction
      modification systems may be an excellent tool for investigation of that
      phenomenon.
AU  - Piechula S
AU  - Waleron K
AU  - Swiatek W
AU  - Biedrzycka I
AU  - Podhajska AJ
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2001 198: 135-140.

PMID- 6286981
VI  - 157
DP  - 1982
TI  - HineI is an isoschizomer of HinfIII restriction endonuclease.
PG  - 373-381
AB  - HineI is a restriction enzyme isolated from Haemophilus influenzae strain Re.
      Like other type III restriction endonucleases it requires ATP for cleavage and
      S-adenosyl-methionine for methylation of DNA.  This enzyme recognises the same
      sequence as HinfIII (Piekarowicz et al., 1981) and cleaves and methylates DNA
      in a manner similar to all type III restriction enzymes.
AU  - Piekarowicz A
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1982 157: 373-381.

PMID- 4545336
VI  - 6
DP  - 1974
TI  - The influence of methionine deprivation on restriction properties of Haemophilus influenzae Rd and Ra strains.
PG  - 71-74
AB  - The influence of methionine starvation on the restriction properties of H.
      influenzae Rd and Ra has been examined.  It was shown that the methionine
      deprivation of Rd and Ra cells does not change their capacity to restrict HPlcl
      phage.  These results suggest that S-adenosylmethionine may not be required for
      the action of H. influenzae Rd and Ra restriction endonucleases.
AU  - Piekarowicz A
PT  - Journal Article
TA  - Acta Microbiol. Pol. A
JT  - Acta Microbiol. Pol. A
SO  - Acta Microbiol. Pol. A 1974 6: 71-74.

PMID- 6099947
VI  - 31
DP  - 1984
TI  - Preferential cleavage by restriction endonuclease HinfIII.
PG  - 453-464
AB  - The efficiency of endonucleolytic scission by restriction endonuclease HinfIII
      varies markedly for different recognition sites.  The relative frequencies of
      cleavage at these sites have been determined on the basis of analysis of
      specific unit length linear molecules formed.  The efficiency of restriction
      reaction depends also on the number of recognition sites in the DNA substrate.
      Cleavage by HinfIII in the absence or presence of S-adenosylmethionine is
      observed only when at least three recognition sites are present.  HinfIII also
      shows preferential methylation of certain sites observable even for a substrate
      with one recognition site.  The nucleotide sequences at sites cleaved or
      methylated at high frequency have been compared.
AU  - Piekarowicz A
PT  - Journal Article
TA  - Acta Biochim. Pol.
JT  - Acta Biochim. Pol.
SO  - Acta Biochim. Pol. 1984 31: 453-464.

PMID- 7526612
VI  - 43
DP  - 1994
TI  - Identification of a new restriction endonuclease R.NciII, from Neisseria cinerea.
PG  - 103-105
AB  - Site-specific restriction endonuclease R.NciII has been purified from Neisseria cinerea strain
      32615. The enzyme recognizes the sequence 5'GATC3' and its activity is inhibited by the
      presence of methylated adenine residue within the recognition sequence.
AU  - Piekarowicz A
PT  - Journal Article
TA  - Acta Microbiol. Pol.
JT  - Acta Microbiol. Pol.
SO  - Acta Microbiol. Pol. 1994 43: 103-105.

PMID- 7740976
VI  - 43
DP  - 1994
TI  - DNA methyltransferases of Neisseria gonorrhoeae.
PG  - 269-277
AB  - The DNA of both prokaryotic and eukaryotic organisms can undergo postreplicative modification.
      The most widely known type of modification is the addition of the methyl groups to either
      cytosine or adenine residues.  This process is carried out by the enzymes called DNA
      methyltransferases or MTases.  Methylation by all types of MTases requires
      S-adenosylmethionine (SAM).  The function of SAM is in most of the cases limited to serving as
      a methyl group donor.  In the case of Escherichia coli Dam MTase, however, it also affects
      binding of the enzyme to the target site.
AU  - Piekarowicz A
PT  - Journal Article
TA  - Acta Microbiol. Pol.
JT  - Acta Microbiol. Pol.
SO  - Acta Microbiol. Pol. 1994 43: 269-277.

PMID- 1081329
VI  - 8
DP  - 1975
TI  - Host specificity of DNA in Haemophilus influenzae:  The physiological and genetical bases of instability of restriction and modification of DNA in strain RD.
PG  - 119-130
AB  - Further investigations of the instability of restriction and modification
      properties of H. influenzae Rd strain were carried out.  It has been shown that
      the instable properties of hsd HindI system are maintained even after transfer
      of this system to another H. influenzae strain.  The expression of hsd HindI
      system is very sensitive to various physiological changes which do not
      influence the other hsd systems present in the same Rd strain.  The instability
      of hsd HindI system is postulated to be connected with some regulator gene(s).
AU  - Piekarowicz A
AU  - Baj J
PT  - Journal Article
TA  - Acta Microbiol. Pol. A
JT  - Acta Microbiol. Pol. A
SO  - Acta Microbiol. Pol. A 1975 8: 119-130.

PMID- 6267295
VI  - 146
DP  - 1981
TI  - The DNA sequence recognised by the HinfIII restriction endonuclease.
PG  - 167-172
AB  - HinfIII is a type III restriction enzyme (Kaue & Piekarowicz, 1978) isolated
      from Haemophilus influenzae Rf.  Like other type III restriction endonucleases,
      the enzyme also catalyses the modification of susceptible DNA.  It requires ATP
      for DNA cleavage and S-adenosyl methionine for DNA methylation.  We have
      determined the DNA sequence recognised by HinfIII to be: 5'-C-G-A-A-T-3'
      3'-G-C-T-T-A-5' In restriction, the enzyme cleaves the DNA about 25 base-pairs
      to the right of this sequence.  In the modification reaction only one of the
      strands is methylated, that containing the 5'-C-G-A-A-T-3' sequence.
AU  - Piekarowicz A
AU  - Bickle TA
AU  - Shepherd JCW
AU  - Ineichen K
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1981 146: 167-172.

PMID- 6265646
VI  - 144
DP  - 1980
TI  - Cleavage and methylation of DNA by the restriction endonuclease HinfIII isolated from Haemophilus influenzae Rf.
PG  - 415-429
AB  - HinfIII is a restriction enzyme isolated from Haemophilus influenzae strain Rf. It requires
      ATP for cleavage and S-adenosyl-methionine for methylation of DNA. This enzyme can be present
      in two forms: one with AdoMet bound to it, and a second form free of this cofactor.  In the
      presence of AdoMet and ATP the enzyme cleaves ColE1 DNA molecules once, to produce unit-length
      linear molecules.  The HinfIII endonuclease cleaves at unique sites, though not every site on
      every molecule is cut.  The five HinfIII cleavage sites were mapped relative to the EcoRI
      restriction endonuclease cleavage site.  If AdoMet is omitted from the enzyme reaction
      mixture, the second form of HinfIII enzyme cleaves ColE1 DNA into several fragments.  An
      average of 6.2 +/- 1 methyl groups are transferred to ColE1 DNA from AdoMet.  The methyl
      groups were mapped relative to the HaeIII restriction endonuclease fragments.  The position of
      methylation sites correlates well with the cleavage sites. The restriction activity of the
      HinfIII enzyme shows some dependence upon the structure of the substrate DNA.  The linear
      molecule of ColE1 DNA is a poorer substrate than the supercoiled molecules.  Lambda DNA
      fragments with molecular weights smaller than approximately 2,000,000 are not cleaved by
      HinfIII enzyme, but since they can be methylated the enzyme is able to recognize the specific
      sequences on these fragments.
AU  - Piekarowicz A
AU  - Brzezinski R
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1980 144: 415-429.

PMID- 65103
VI  - 25
DP  - 1976
TI  - Host specificity of DNA in Haemophilus influenzae: DNA restriction enzyme from H. Influenzae Rf232.
PG  - 307-312
AB  - A restriction endonuclease has been partially purified from Haemophilus
      influenzae Rf232 containing the genetically determined system of restriction
      and modification of DNA.  The enzyme requires ATP for the degradation of
      transfecting phage DNA.
AU  - Piekarowicz A
AU  - Brzezinski R
AU  - Kauc L
PT  - Journal Article
TA  - Acta Microbiol. Pol.
JT  - Acta Microbiol. Pol.
SO  - Acta Microbiol. Pol. 1976 25: 307-312.

PMID- 1080342
VI  - 7
DP  - 1975
TI  - Host Specificity of DNA in Haemophilus influenzae:  The in vivo Action of the Restriction Endonucleases on Phage and Bacterial DNA.
PG  - 51-65
AB  - In Haemophilus influenzae strains only the type 1 of the restriction
      endonucleases have an in vivo effect on phage and bacterial transforming DNA.
      The type 2 of restriction endonucleases which act very efficiently in vitro are
      completely inactive in vivo.  The reasons for this inactivity is unknown.
AU  - Piekarowicz A
AU  - Brzezinski R
AU  - Kauc L
PT  - Journal Article
TA  - Acta Microbiol. Pol. A
JT  - Acta Microbiol. Pol. A
SO  - Acta Microbiol. Pol. A 1975 7: 51-65.

PMID- 10581668
VI  - 48
DP  - 1999
TI  - Cloning of the Dam methyltransferase gene from Haemophilus influenzae bacteriophage HP1.
PG  - 123-129
AB  - The putative product of orf13 from the genome of Haemophilus influenzae HP1 bacteriophage
      shows homology only to bacteriophage T1 Dam methyltransferase, and a weak similarity to the
      conserved amino acids sequence motifs characteristic of m6A-methyltransferases.  Especially
      interesting is the lack of characteristic motif I responsible for binding of
      S-adenosylmethionine.  Despite this fact, a DNA sequence of HP1 bacteriophage of Haemophilus
      influenzae encoding methyltransferase activity was cloned and expressed in Escherichia coli
      using pMPMT4omega expression vector.  The cloned methyltransferase recognizes the sequence
      5'-GATC-3' and methylates an adenine residue.  The enzyme methylates both double- and
      single-stranded DNA substrates.
AU  - Piekarowicz A
AU  - Bujnicki J
PT  - Journal Article
TA  - Acta Microbiol. Pol.
JT  - Acta Microbiol. Pol.
SO  - Acta Microbiol. Pol. 1999 48: 123-129.

PMID- 4537971
VI  - 116
DP  - 1972
TI  - Host specificity of DNA in Haemophilus influenzae:  the two restriction and modification systems in strain Ra.
PG  - 11-25
AB  - Rough R strains of Haemophilus influenzae derived from the smooth (S) serotypes
      Sa, Sb, Sd, Se and Sf each carry DNA restriction and modification systems.  The
      DNA host specificity determined by Re and Rf may be the same but is different
      from that for Ra, Rb and Rd all of which can be distinguished from one another.
      Strain Ra carries two genetically distinct host specificity systems Al and A2
      each of which is able to restrict Haemophilus phage HP1, and each of which
      confers a specific modification on phage grown in strain Ra.  Among
      restriction-deficient mutants isolated from strain Ra, seven of the eight
      possible phenotypes for these two systems were obtained after either one or two
      mutational steps.
AU  - Piekarowicz A
AU  - Glover SW
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1972 116: 11-25.

PMID- 3002797
VI  - 154
DP  - 1986
TI  - The DNA sequence recognized by the EcoDXXI restriction endonuclease.
PG  - 295-298
AB  - EcoDXXI is a type-I restriction enzyme coded for by the plasmid pDXX1.  Like
      other type-I restriction endonucleases, the enzyme catalyses the modification
      of susceptible DNA.  We have determined the DNA sequence recognised by EcoDXXI
      to be:5'-TCANNNNNNNATTC-3' 3'-AGTNNNNNNNTAAG-5'where N can be any nucleotide.
      This sequence has an overall structure very similar to previously determined
      type-I sequences.
AU  - Piekarowicz A
AU  - Goguen JD
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1986 154: 295-298.

PMID- 2996888
VI  - 152
DP  - 1985
TI  - The EcoDXXI restriction and modification system of Escherichia coli ET7.  Purification, subunit structure and properties of the restriction endonuclease.
PG  - 387-393
AB  - The Escherichia coli plasmid pDXX1 codes for a new restriction-modification system. The
      specific restriction endonuclease coded by this system has been purified by a procedure that
      includes phosphocellulose and heparin-agarose chromatography. Sedimentation on glycerol
      gradients showed one peak of activity with a value of about 12S. The highly purified enzyme
      require ATP and Mg2+ for activity as well as S-adenosylmethionine, although some
      S-adenosylmethionine molecules are probably bound to the enzyme. The enzyme does not cleave
      lambda DNA at well-defined sites and has a strong non-modified DNA-dependent ATPase activity.
      The enzyme has also methylase activity acting against non-modified DNA. te is repeated in
      inverse orientation. The additional base pair in the non-specific spacer of the mutant
      recognition sequence maintains the proper spacing between the two methylatable adenine groups.
      Sequencing of both the wild type and mutant EcoDXXI hsdS genes showed that the Tn5 insertion
      occurred at nucleotide 673 of the 1221 bp gene. This effectively deletes the entire
      carboxyl-terminal DNA binding domain which recognizes the 3' half of the EcoDXXI binding
      site. The truncated hsdS gene still encodes both the amino-terminal DNA binding domain and the
      conserved repeated sequence that defines the length of the recognition site spacer region. We
      propose that the EcoDXXI mutant methylase utilizes two truncated hsdS subunits to recognize
      its binding site. The implications of this finding in terms of subunit interactions and the
      malleability of the type I R-M systems will be discussed.
AU  - Piekarowicz A
AU  - Goguen JD
AU  - Skrzypek E
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1985 152: 387-393.

PMID- 10547285
VI  - 293
DP  - 1999
TI  - The HaeIV restriction modification system of Haemophilus aegyptius is encoded by a single polypeptide.
PG  - 1055-1065
AB  - The HaeIV restriction endonuclease (ENase) belongs to a distinct class of ENases,
      characterized by its ability to cleave double-stranded DNA on both sides of its recognition
      sequence, excising a short DNA fragment that includes the recognition sequence. The gene
      encoding the HaeIV ENase was cloned from Haemophilus aegyptius into pUC19 using a previously
      described system that does not need the knowledge that a particular ENase is produced by a
      bacterial strain. DNA sequence analysis of the insert contained on this plasmid identified a
      single open reading frame (ORF), with the predicted protein having an apparent molecular mass
      of approximately 110 kDa. The protein encoded by this ORF was purified to homogeneity from
      Escherichia coli strain ER1944 carrying the haeIVRM gene on a recombinant plasmid under the
      control of the inducible ara promoter. The protein possessed both ENase and methyltransferase
      (MTase) activities. Amino acid sequence analysis was able to identify several conserved motifs
      found in DNA MTases, located in the middle of the protein. The enzyme recognizes the
      interrupted palindromic sequence 5' GAPyNNNNNPuTC 3', cleaving double-stranded DNA on both
      strands upstream and downstream of the recognition sequence, releasing an approximately 33 bp
      fragment. The ENase possessed an absolute requirement only for Mg(+2). ATP had no influence on
      ENase or MTase activities. The ENase made the first strand cleavage randomly on either side of
      the recognition sequence, but the second cleavage occurred more slowly. The MTase activity
      modified symmetrically located adenine residues on both strands within the recognition
      sequence yielding N6-methyl adenine. Furthermore, the MTase was active as a dimer.
AU  - Piekarowicz A
AU  - Golaszewska M
AU  - Sunday AO
AU  - Siwinska M
AU  - Stein DC
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1999 293: 1055-1065.

PMID- 4545801
VI  - 81
DP  - 1974
TI  - Host specificity of DNA in Haemophilus influenzae: Similarity between host-specificity types of Haemophilus influenzae Re and Rf.
PG  - 405-411
AB  - Strain Re of Haemophilus influenzae carries two genetically distinct
      host-specificity systems EI and E2 each of which is able to restrict
      Haemophilus phage HPIcI and each of which confers a specific modification upon
      phage grown in strain Re.  These two systems are apparently identical to the
      host-specificity systems of H. influenzae Rf F1 and F2.
AU  - Piekarowicz A
AU  - Kalinowska J
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1974 81: 405-411.

PMID- 4545904
VI  - 81
DP  - 1974
TI  - Host specificity of DNA in Haemophilus influenzae: The restriction and modification systems in strains Rb and Rf.
PG  - 391-403
AB  - Haemophilus influenzae Rf possesses two distinct host specificity systems FI
      and F2 each of which is able to restrict and modify Haemophilus phage HPICI,
      while strain Rb posseses only one system, B.  Among restriction-deficient
      mutants isolated from strain Rf, the r-m+ as well as r-m- phenotypes for these
      two systems were obtained after either one or two mutational steps.  The FI
      system was introduced into H. influenzae Rd by genetic transformation to show
      that the DI and FI systems are not allelic.
AU  - Piekarowicz A
AU  - Kauc L
AU  - Glover SW
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1974 81: 391-403.

PMID- 11555298
VI  - 41
DP  - 2001
TI  - Analysis of type I restriction modification systems in the Neisseriaceae: Genetic organization and properties of the gene products.
PG  - 1199-1210
AB  - The hsd locus (host specificity of DNA) was identified in the Neisseria gonorrhoeae genome.
      The DNA fragment encoding this locus produced an active restriction and modification (R/M)
      system when cloned into Escherichia coli. This R/M system was designated NgoAV. The cloned
      genomic fragment (7800 bp) has the potential to encode seven open reading frames (ORFs).
      Several of these ORFs had significant homology with other proteins found in the databases:
      ORF1, the hsdM, a methylase subunit (HsdM); ORF2, a homologue of dinD; ORF3, a homologue of
      hsdS; ORF4, a homologue of hsdS; and ORF5, an endonuclease subunit hsdR. The endonuclease and
      methylase subunits possessed strongest protein sequence homology to the EcoR124II R/M system,
      indicating that NgoAV belongs to the type IC R/M family. Deletion analysis showed that only
      ORF3 imparted the sequence specificity of the RM.NgoAV system, which recognizes an interrupted
      palindrome sequence (GCAN8TGC). The genetic structure of ORF3 (208 amino acids) is almost
      identical to the structure of the 5' truncated hsdS genes of EcoDXXI or EcoR124II R/M systems
      obtained by in vitro manipulation. Genomic sequence analysis allowed us to identify hsd loci
      with a very high homology to RM.NgoAV in two strains of Neisseria meningitidis. However,
      significant differences in the organization and structure of the hsdS genes in both these
      systems suggests that, if functional, they would possess recognition sites that differ from
      the gonococcus and from themselves.
AU  - Piekarowicz A
AU  - Klyz A
AU  - Kwiatek A
AU  - Stein DC
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2001 41: 1199-1210.

PMID- 10333562
VI  - 47
DP  - 1998
TI  - Sensitivity of the restriction endonucleases HaeIII, BsrI, EaeI and CfrI to cytosine N4-methylation.
PG  - 405-407
AB  - HaeIII, BsrI and NgoII are isochizomers that recognize the sequence GGCC while EaeI and CfrI
      recognize the overlapping sequence YGGCCR. It has previously been shown that all these enzymes
      are inhibited by cytosine C5-methylation within the recognition sequence. The methylation
      sensitivities of these enzymes to cytosine N4-methylation have not been previously reported.
      In this paper we present data demonstrating that all these enzymes, except NgoII, are
      inhibited by cytosine N4-methylation of the second 5' cytosine residue within the recognition
      sequence.
AU  - Piekarowicz A
AU  - Radlinska M
PT  - Journal Article
TA  - Acta Microbiol. Pol.
JT  - Acta Microbiol. Pol.
SO  - Acta Microbiol. Pol. 1998 47: 405-407.

PMID- Not included in PubMed...
VI  - 44
DP  - 1996
TI  - DNA methyltransferases of Neisseria gonorrhoeae.
PG  - 205-210
AB  - An individual strain of Neisseria gonorrhoeae may produce up to 16 different DNA
      methyltransferases.  We have used a novel cloning system that is able to detect MTase clones
      in the absence of direct selection to identify different MTase clones.  The characterization
      of six of these clones showed that MTase genes are linked to restriction endonuclease systems
      but none of these six R-M systems are genetically linked on the chromosome.  The initial
      characterization of four other clones indicates that none of the encoded MTase genes are
      linked to the restriction endonuclease systems.  On the other hand, several of these MTases
      show genetical linkage on the chromosome.  Four of these MTase clones have been characterized
      by DNA sequence analysis, and the open reading frames encoding each of these MTases have been
      identified.  These MTases belong either to the 5mC or N4mC group of MTases.  Some of the 5mC
      MTases show the presence of typical MTase conserved motifs.  However, some other cloned 5mC
      MTase show the lack of these motifs.
AU  - Piekarowicz A
AU  - Radlinska M
AU  - Wiernicka-Gnas M
PT  - Journal Article
TA  - Bull. Acad. Pol. Sci. [Biol]
JT  - Bull. Acad. Pol. Sci. [Biol]
SO  - Bull. Acad. Pol. Sci. [Biol] 1996 44: 205-210.

PMID- 8934670
VI  - 44
DP  - 1995
TI  - Identification of a new restriction endonuclease R.BcrAI from Bacillus cremoris.
PG  - 315-316
AB  - Site specific restriction endonuclease R.BcrAI has been purified from Bacillus cremoris.  The
      enzyme recognizes the sequence 5' CTCTTC 3'.
AU  - Piekarowicz A
AU  - Skowronek K
PT  - Journal Article
TA  - Acta Microbiol. Pol.
JT  - Acta Microbiol. Pol.
SO  - Acta Microbiol. Pol. 1995 44: 315-316.

PMID- 6158837
VI  - 29
DP  - 1980
TI  - Specific restriction endonucleases from Haemophilus influenzae JC9.
PG  - 151-156
AB  - Two types of restriction endonucleases have been isolated from Haemophilus
      influenzae.  The presence of type III restriction enzymes is in vivo correlated
      with the activity against Haemophilus phages HP1, S2 and N3 (Piekarowicz,
      Brzezinski and Kauc, 1975, Kauc and Piekarowicz, 1978).
AU  - Piekarowicz A
AU  - Stasiak A
AU  - Stanczak J
PT  - Journal Article
TA  - Acta Microbiol. Pol.
JT  - Acta Microbiol. Pol.
SO  - Acta Microbiol. Pol. 1980 29: 151-156.

PMID- 7607465
VI  - 157
DP  - 1995
TI  - Purification and characterization of a new DNA methyltransferase from Neisseria gonorrhoeae.
PG  - 101-102
AB  - A new DNA methyltransferase, M.NgoBVII, was isolated from Neisseria gonorrhoeae strain WR302.
      M.NgoVII recognizes the sequence 5'-GCNGC-3'.
      [ The enzyme called NgoBVII in this abstract has been renamed NgoBXII, Jan/1998. ]
AU  - Piekarowicz A
AU  - Stein DC
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 101-102.

PMID- 7530896
VI  - 43
DP  - 1994
TI  - Improvement of the strain for the rapid identification of genes encoding restriction and modification enzymes.
PG  - 229-231
AB  - The E. coli AP1-200-9 strain used for rapid identification of genes encoding restriction and
      modification enzymes carries a temperature sensitive lacZ gene fused to the damage-inducible
      dinD locus. A derivative of this strain was constructed that has a wild-type form of this
      locus which allows for a more efficient identification of recombinant plasmids encoding
      restriction and modification enzymes.
AU  - Piekarowicz A
AU  - Weglenska A
PT  - Journal Article
TA  - Acta Microbiol. Pol.
JT  - Acta Microbiol. Pol.
SO  - Acta Microbiol. Pol. 1994 43: 229-231.

PMID- 3141904
VI  - 16
DP  - 1988
TI  - Identification of a new restriction endonuclease, R.NgoBI, from Neisseria gonorrhoeae.
PG  - 9868
AB  - As a species, Neisseria gonorrhoeae produces five restriction endonucleases, and several other
      DNA methyltransferases.  We have purified a methyltransferase that recognizes the sequence 5'
      TCACC 3' and report here the purification from N. gonorrhoeae WR302 of a restriction
      endonuclease, R.NgoBI, that also recognizes this sequence.  Purification scheme:  The
      purification scheme employed was as previously described (2) except the (NH4)2SO4 precipitate
      was dissolved in buffer A (20 mM KPO4, 1 mM EDTA, 10% glycerol, 10 mM 2-mercaptoethanol, pH
      7.5) before being purified by chromatography through a 2x20 cm phosphocellulose column.  The
      enzyme activity eluted at 0.15 M NaCl. Active fractions were further purified through an Accel
      QMA column and active fractions eluted at 0.1 M NaCl.  The recognition sequence for R.NgoBI
      was determined by digesting lambda DNA with it and comparing the banding pattern obtained with
      computer generated patterns obtained with all known enzymes.  The data indicated that this
      enzyme cleaved lambda DNA at the same sequence as HphI.  Figure 1 is a comparison of the
      fragments obtained after digesting pUC8 with NgoBI and HphI.  The restriction enzyme was most
      active in a buffer containing 25 mM Tris-HCl, 25 mM KCl, 10 mM MgCl2, 2 mM 2-mercaptoethanol,
      pH 7.8.
      [ The enzyme called NgoBI in this abstract has been renamed NgoBVIII, Jan/1998. ]
AU  - Piekarowicz A
AU  - Yuan R
AU  - Stein DC
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1988 16: 9868.

PMID- 3135534
VI  - 16
DP  - 1988
TI  - Purification and characterization of DNA methyltransferases from Neisseria gonorrhoeae.
PG  - 5957-5972
AB  - Three DNA methyltransferases, M.NgoAI, and M.NgoBI and M.NgoBII, free of any nuclease
      activities were isolated from Neisseria gonorrhoeae strains WR220 and MUG116 respectively.
      M.NgoAI recognizes the sequence 5' GGCC 3' and methylates the first 5' cytosine on both
      strands.  M.NgoBI and M.NgoBII recognize 5' TCACC 3' and 5' GTANNNNNCTC 3' respectively.
      M.NgoBII 5' GTANNNNNmCTC 3'.
      [ The enzyme called NgoAI in this abstract has been renamed NgoGII, Jan/1998. ]
      [ The enzyme called NgoBI in this abstract has been renamed NgoBVIII, Jan/1998. ]
      [ The enzyme called NgoBII in this abstract has been renamed NgoBIX, Jan/1998. ]
AU  - Piekarowicz A
AU  - Yuan R
AU  - Stein DC
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1988 16: 5957-5972.

PMID- 2854809
VI  - 74
DP  - 1988
TI  - Construction of a temperature-sensitive mutation for the direct identification of plasmids encoding DNA methyltransferases.
PG  - 233-235
AB  - Meeting Abstract
AU  - Piekarowicz A
AU  - Yuan R
AU  - Stein DC
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 233-235.

PMID- 3150364
VI  - 74
DP  - 1988
TI  - Neisseria gonorrhoeae M.NgoAI DNA methyltransferase:  physical and catalytic properties of the homogeneous enzyme.
PG  - 93-97
AB  - A DNA methyltransferase, M.NgoAI, was purified to homogeneity from Neisseria
      gonorrhoeae strain WR220 by successive column chromatography.  Its Mr is 25000,
      as determined by both gel filtration and denaturing polyacrylamide gel
      electrophoresis.  Maximal enzymatic activity was obtained in 50 mM Tris.HCl (pH
      7.4), 10 mM EDTA, with incubation at 37C.  An apparent Km value for
      S-adenosylmethionine and 5'-GGCC sites was determined to be 1.25 microM and
      89.6 nM, respectively.
AU  - Piekarowicz A
AU  - Yuan R
AU  - Stein DC
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 93-97.

PMID- 2513556
VI  - 17
DP  - 1989
TI  - Cleavage of DNA by HaeII is inhibited by the presence of 5-methylcytosine at the second cytosine within the recognition sequence.
PG  - 10132
AB  - None
AU  - Piekarowicz A
AU  - Yuan R
AU  - Stein DC
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 10132.

PMID- 1851562
VI  - 19
DP  - 1991
TI  - A new method for the rapid identification of genes encoding restriction and modification enzymes.
PG  - 1831-1835
AB  - We have constructed derivatives of Escherichia coli that can be used for the
      rapid identification of recombinant plasmids encoding DNA restriction enzymes
      and methyltransferases.  The induction of the DNA-damage inducible SOS response
      by the Mcr and Mrr systems, in the presence of methylated DNA, is used to
      select plasmids encoding DNA methyltransferases.  The strains of E. coli that
      we have constructed are temperature-sensitive for the Mcr and Mrr systems and
      have been further modified to include a lacZ gene fused to the damage-inducible
      dinD locus of E. coli.  The detection of recombinant plasmids encoding DNA
      methyltransferases and restriction enzymes is a simple, one step procedure that
      is based on the induction at the restrictive temperature of the lacZ gene.
      Transformants encoding DNA methyltransferase genes are detected on LB agar
      plates supplemented with X-gal as blue colonies.  Using this method, we have
      cloned a variety of DNA methyltransferase genes from diverse species such as
      Neisseria, Haemophilus, Treponema, Pseudomonas, Xanthomonas and
      Saccharopolyspora.
AU  - Piekarowicz A
AU  - Yuan R
AU  - Stein DC
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 1831-1835.

PMID- 1987114
VI  - 173
DP  - 1991
TI  - Isolation of temperature-sensitive McrA and McrB mutations and complementation analysis of the McrBC region of Escherichia coli K-12.
PG  - 150-155
AB  - We isolated temperature-sensitive mcrA and mcrBC mutants of Escherichia coli.
      At 42C, they were unable to restrict the T-even bacteriophages T6gt and Tegt or
      plasmids encoding cloned DNA methylase genes whose specificities confer
      sensitivity to the McrA and McrBC nucleases.  Complementation analysis of the
      McrBC region (mcrB251) with the complete cloned McrBC system or a derivative
      with mcrB alone indicated that the mutation shows an absolute defect for the
      restriction of DNA containing hydroxymethylcytosine and a thermosensitive
      defect for the restriction of DNA containing methylcytosine.  The properties of
      the McrA temperature-sensitive mutants suggest that some of these mutations can
      also influence the restriction of DNA containing hydroxymethylcytosine or
      methylcytosine residues.
AU  - Piekarowicz A
AU  - Yuan R
AU  - Stein DC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1991 173: 150-155.

PMID- 9299347
VI  - 272
DP  - 1997
TI  - Characterization of the interaction between the restriction endonuclease McrBC from E. coli and its cofactor GTP.
PG  - 190-199
AB  - McrBC, a GTP-dependent restriction enzyme from E. coli K-12, cleaves DNA containing methylated
      cytosine residues 40 to 80 residues apart and 3'-adjacent to a purine residue
      (pumCN40-80PumC).  The presence of the three consensus sequences characteristic for guanine
      nucleotide binding proteins in one of the two subunits of McrBC suggests that this subunit is
      responsible for GTP binding and hydrolysis.  We show here that (i) McrB binds GTP with an
      affinity of 106 M^-1 and that GTP binding stabilizes McrB against thermal denaturation.  (ii)
      McrB binds GDP about 50-fold and ATP at least three orders of magnitude more weakly than GTP.
      (iii) McrB hydrolyzes GTP in the presence of Mg2+ with a steady-state rate of approximately
      0.5 min^-1.  (iv) McrC stimulates GTP hydrolysis 30-fold, but substrate DNA has no detectable
      effect on the GTPase activity of McrB, neither by itself nor in the presence of McrC.  (v)
      Substitution of N339 and N376 with alanine allowed us to identify NTAD (339 to 342) rather
      than NKKA (376 to 379) as the equivalent of the third consensus sequence motif characteristic
      for guanine nucleotide binding proteins, NKXD.
AU  - Pieper U
AU  - Brinkmann T
AU  - Kruger T
AU  - Noyer-Weidner M
AU  - Pingoud A
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1997 272: 190-199.

PMID- 11955074
VI  - 41
DP  - 2002
TI  - The GTP-dependent restriction enzyme McrBC from Escherichia coli forms high-molecular mass complexes with DNA and produces a cleavage pattern with a characteristic 10-base pair repeat.
PG  - 5245-5254
AB  - The GTP-dependent restriction enzyme McrBC consists of two polypeptides: one (McrB) that is
      responsible for GTP binding and hydrolysis as well as DNA binding and another (McrC) that is
      responsible for DNA cleavage. It recognizes two methylated or hemimethylated RC sites (R(m)C)
      at a distance of approximately 30 to more than 2000 base pairs and cleaves the DNA close to
      one of the two R(m)C sites. This process is strictly coupled to GTP hydrolysis and involves
      the formation of high-molecular mass complexes. We show here using footprinting techniques,
      surface plasmon resonance, and scanning force microscopy experiments that in the absence of
      McrC, McrB binds to a single R(m)C site. If a second R(m)C site is present on the DNA, it is
      occupied independently by McrB. Whereas the DNA-binding domain of McrB forms 1:1 complexes
      with each R(m)C site and shows a clear footprint on both R(m)C sites, full-length McrB forms
      complexes with a stoichiometry of at least 4:1 at each R(m)C site, resulting in a slightly
      more extended footprint. In the presence of McrC, McrB forms high-molecular mass complexes of
      unknown stoichiometry, which are considerably larger than the complexes formed with McrB
      alone. In these complexes and when GTP is present, the DNA is cleaved next to one of the R(m)C
      sites at distances differing by one to five helical turns, suggesting that in the McrBC-DNA
      complex only a few topologically well-defined phosphodiester bonds of the DNA are accessible
      for the nucleolytic center of McrC.
AU  - Pieper U
AU  - Groll DH
AU  - Wunsch S
AU  - Gast FU
AU  - Speck C
AU  - Mucke N
AU  - Pingoud A
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2002 41: 5245-5254.

PMID- 11955073
VI  - 41
DP  - 2002
TI  - A mutational analysis of the PD...D/EXK motif suggests that McrC harbors the catalytic center for DNA cleavage by the GTP-dependent restriction enzyme McrBC from Escherichia coli.
PG  - 5236-5244
AB  - McrBC is a unique restriction enzyme which binds specifically to the bipartite recognition
      sequence RmCNa~30-2000RmC and in the
      presence of GTP translocates the DNA and cleaves both strands at
      multiple positions within the two RmC "half-sites". It is known that
      McrBC is composed of two subunits: McrB which binds and hydrolyzes GTP
      and specifically interacts with DNA and McrC whose function is not
      clear but which has been suspected to harbor the catalytic center for
      DNA cleavage. A multiple-sequence alignment of the amino acid sequence
      of Escherichia coli McrC and of six presumably homologous open reading
      frames from various bacterial species shows that a sequence motif found
      in many restriction enzymes, but also in other nucleases, the
      PD....D/EXK motif, is conserved among these sequences. A mutational
      analysis, in which the carboxylates (aspartic acid in McrC) of this
      motif were substituted with alanine or asparagine and lysine was
      substituted with alanine or arginine, strongly suggests that Asp244,
      Asp257, and Lys259 represent the catalytic center of E. coli McrC.
      Whereas the variants D244A (or -N), D257A (or -N), and K259A are
      inactive in DNA cleavage (K259R has residual DNA cleavage activity),
      they interact with McrB like wild-type McrC, as can be deduced from the
      finding that they stimulate the McrB-catalyzed GTP hydrolysis to the
      same extent as wild-type McrC. Thus, whereas McrC variants defective in
      DNA cleavage can stimulate the GTPase activity of McrB, the DNase
      activity of McrC is not supported by McrB variants defective in GTP
      hydrolysis.
AU  - Pieper U
AU  - Pingoud A
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2002 41: 5236-5244.

PMID- 10497020
VI  - 292
DP  - 1999
TI  - The GTP-binding domain of McrB: More than just a variation on common theme?
PG  - 547-556
AB  - The methylation-dependent restriction endonuclease McrBC from Escherichia coli K12 cleaves DNA
      containing two R(m)C dinucleotides separated by about 40 to 2000 base-pairs. McrBC is unique
      in that cleavage is totally dependent on GTP hydrolysis. McrB is the GTP binding and
      hydrolyzing subunit, whereas MrC stimulates its GTP hydrolysis. The C-terminal part of McrB
      contains the sequences characteristic for GTP-binding proteins, consisting of the GxxxxGK(S/T)
      motif (position 201-208), followed by the DxxG motif (position 300-303). The third motif
      (NKxD) is present only in a non-canonical form (NTAD 333-336). Here we report a mutational
      analysis of the putative GTP-binding domain of McrB. Amino acid substitutions were initially
      performed in the three proposed GTP-binding motifs. Whereas substitutions in motif 1 (P203V)
      and 2 (D300N) show the expected, albeit modest effects, mutation in the motif 3 is at variance
      with the expectations. Unlike the corresponding EF-Tu and ras -p21 variants, the D336N
      mutation in McrB does not change the nucleotide specificity from GTP to XTP, but results in a
      lack of GTPase stimulation by McrC. The finding that McrB is not a typical G protein motivated
      us to perform a search for similar sequences in DNA databases. Eight microbial sequences were
      found, mainly from unfinished sequencing projects, with highly conserved sequence blocks
      within a presumptive GTP-binding domain. From the five sequences showing the highest homology,
      17 invariant charged or polar residues outside the classical three GTP-binding motifs were
      identified and subsequently exchanged to alanine. Several mutations specifically affect GTP
      affinity and/or GTPase activity. Our data allow us to conclude that McrB is not a typical
      member of the superfamily of GTP-binding proteins, but defines a new subfamily within the
      superfamily of GTP-binding proteins, together with similar prokaryotic proteins of as yet
      unidentified function.
AU  - Pieper U
AU  - Schweitzer T
AU  - Groll DH
AU  - Gast F-U
AU  - Pingoud A
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1999 292: 547-556.

PMID- 10595586
VI  - 380
DP  - 1999
TI  - Defining the location and function of domains of McrB by deletion mutagenesis.
PG  - 1225-1230
AB  - The GTP-dependent restriction endonuclease McrBC of E. coli K12, which recognizes
      cytosine-methylated DNA, consists of two protein subunits, McrB and McrC. We have investigated
      the structural assignment and interdependence of the McrB subunit functions, namely (i)
      specific DNA recognition and (ii) GTP binding and hydrolysis. Extending earlier work, we have
      produced McrB variants comprising N- and C-terminal fragments. The variants McrB1-162 and
      McrB1-170 are still capable of specific DNA binding. McrB169-465 shows GTP binding and
      hydrolysis characteristics indistinguishable from full-length McrB as well as wild-type like
      interaction with McrC. Thus, DNA and GTP binding are spatially separated on the McrB molecule,
      and the respective domains function quite independently.
AU  - Pieper U
AU  - Schweitzer T
AU  - Groll DH
AU  - Pingoud A
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1999 380: 1225-1230.

PMID- 27348220
VI  - 11
DP  - 2016
TI  - Genomic Diversity of Enterotoxigenic Strains of Bacteroides fragilis.
PG  - e0158171
AB  - Enterotoxigenic (ETBF) strains of Bacteroides fragilis are the subset of strains  that secrete
      a toxin called fragilysin (Bft). Although ETBF strains are known to
      cause diarrheal disease and have recently been associated with colorectal cancer,
      they have not been well characterized. By sequencing the complete genome of four
      ETBF strains, we found that these strains exhibit considerable variation at the
      genomic level. Only a small number of genes that are located primarily in the Bft
      pathogenicity island (BFT PAI) and the flanking CTn86 conjugative transposon are
      conserved in all four strains and a fifth strain whose genome was previously
      sequenced. Interestingly, phylogenetic analysis strongly suggests that the BFT
      PAI was acquired by non-toxigenic (NTBF) strains multiple times during the course
      of evolution. At the phenotypic level, we found that the ETBF strains were less
      fit than the NTBF strain NCTC 9343 and were susceptible to a growth-inhibitory
      protein that it produces. The ETBF strains also showed a greater tendency to form
      biofilms, which may promote tumor formation, than NTBF strains. Although the
      genomic diversity of ETBF strains raises the possibility that they vary in their
      pathogenicity, our experimental results also suggest that they share common
      properties that are conferred by different combinations of non-universal genetic
      elements.
AU  - Pierce JV
AU  - Bernstein HD
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2016 11: e0158171.

PMID- 25792064
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Xanthomonas sacchari Strain LMG 476.
PG  - e00146-15
AB  - We report the high-quality draft genome sequence of Xanthomonas sacchari strain LMG 476,
      isolated from sugarcane. The genome comparison of this strain with a
      previously sequenced X. sacchari strain isolated from a distinct environmental
      source should provide further insights into the adaptation of this species to
      different habitats and its evolution.
AU  - Pieretti I
AU  - Bolot S
AU  - Carrere S
AU  - Barbe V
AU  - Cociancich S
AU  - Rott P
AU  - Royer M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00146-15.

PMID- 20017926
VI  - 10
DP  - 2009
TI  - The complete genome sequence of Xanthomonas albilineans provides new insights into the reductive genome evolution of the xylem-limited Xanthomonadaceae.
PG  - 616
AB  - BACKGROUND: The Xanthomonadaceae family contains two xylem-limited plant
      pathogenic bacterial species, Xanthomonas albilineans and Xylella
      fastidiosa. X. fastidiosa was the first completely sequenced plant
      pathogen. It is insect-vectored, has a reduced genome and does not possess
      hrp genes which encode a Type III secretion system found in most plant
      pathogenic bacteria. X. fastidiosa was excluded from the Xanthomonas group
      based on phylogenetic analyses with rRNA sequences. RESULTS: The complete
      genome of X. albilineans was sequenced and annotated. X. albilineans,
      which is not known to be insect-vectored, also has a reduced genome and
      does not possess hrp genes. Phylogenetic analysis using X. albilineans
      genomic sequences showed that X. fastidiosa belongs to the Xanthomonas
      group. Order of divergence of the Xanthomonadaceae revealed that X.
      albilineans and X. fastidiosa experienced a convergent reductive genome
      evolution during their descent from the progenitor of the Xanthomonas
      genus. Reductive genome evolutions of the two xylem-limited
      Xanthomonadaceae were compared in light of their genome characteristics
      and those of obligate animal symbionts and pathogens. CONCLUSION: The two
      xylem-limited Xanthomonadaceae, during their descent from a common
      ancestral parent, experienced a convergent reductive genome evolution.
      Adaptation to the nutrient-poor xylem elements and to the cloistered
      environmental niche of xylem vessels probably favoured this convergent
      evolution. However, genome characteristics of X. albilineans differ from
      those of X. fastidiosa and obligate animal symbionts and pathogens,
      indicating that a distinctive process was responsible for the reductive
      genome evolution in this pathogen. The possible role in genome reduction
      of the unique toxin albicidin, produced by X. albilineans, is discussed.
AU  - Pieretti I
AU  - Royer M
AU  - Barbe V
AU  - Carrere S
AU  - Koebnik R
AU  - Cociancich S
AU  - Couloux A
AU  - Darrasse A
AU  - Gouzy J
AU  - Jacques MA
AU  - Lauber E
AU  - Manceau C
AU  - Mangenot S
AU  - Poussier S
AU  - Segurens B
AU  - Szurek B
AU  - Verdier V
AU  - Arlat M
AU  - Rott P
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2009 10: 616.

PMID- 21378179
VI  - 193
DP  - 2011
TI  - Genome Sequence of Neisseria meningitidis serogroup B strain H44/76.
PG  - 2371-2372
AB  - Neisseria meningitidis is an obligate human pathogen. While it is a frequent commensal of the
      upper respiratory tract, in some individuals the bacterium spreads to the bloodstream causing
      meningitis and/or sepsis, serious conditions with high morbidity and mortality. Here we report
      the availability of the genome sequence of the widely used serogroup B laboratory strain
      H44/76.
AU  - Piet JR
AU  - Huis IVRA
AU  - van Schaik BD
AU  - van Kampen AH
AU  - Baas F
AU  - van de Beek D
AU  - Pannekoek Y
AU  - van der Ende A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 2371-2372.

PMID- 26679596
VI  - 3
DP  - 2015
TI  - Complete Genome Sequences of Two Listeria monocytogenes Serovars, 1/2a and 4b, Isolated from Dairy Products in Brazil.
PG  - e01494-15
AB  - Listeria monocytogenes is the foodborne pathogen responsible for a bacterial infection called
      listeriosis. Here, we present the whole-genome sequences of two
      L. monocytogenes serovars, 1/2a and 4b, which are considered the most prevalent
      in food processing plants and listeriosis outbreaks, respectively.
AU  - Pieta L
AU  - Campos FS
AU  - Mariot RF
AU  - Prichula J
AU  - de Moura TM
AU  - Frazzon AP
AU  - Frazzon J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01494-15.

PMID- 23733949
VI  - 110
DP  - 2013
TI  - Structure of the archaeal head-tailed virus HSTV-1 completes the HK97 fold story.
PG  - 10604-10609
AB  - It has been proposed that viruses can be divided into a small number of
      structure-based viral lineages. One of these lineages is exemplified by bacterial
      virus Hong Kong 97 (HK97), which represents the head-tailed dsDNA bacteriophages.
      Seemingly similar viruses also infect archaea. Here we demonstrate using genomic
      analysis, electron cryomicroscopy, and image reconstruction that the major coat
      protein fold of newly isolated archaeal Haloarcula sinaiiensis tailed virus 1 has
      the canonical coat protein fold of HK97. Although it has been anticipated
      previously, this is physical evidence that bacterial and archaeal head-tailed
      viruses share a common architectural principle. The HK97-like fold has previously
      been recognized also in herpesviruses, and this study expands the HK97-like
      lineage to viruses from all three domains of life. This is only the second
      established lineage to include archaeal, bacterial, and eukaryotic viruses. Thus,
      our findings support the hypothesis that the last common universal ancestor of
      cellular organisms was infected by a number of different viruses.
AU  - Pietila MK
AU  - Laurinmaki P
AU  - Russell DA
AU  - Ko CC
AU  - Jacobs-Sera D
AU  - Hendrix RW
AU  - Bamford DH
AU  - Butcher SJ
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2013 110: 10604-10609.

PMID- 9514260
VI  - 7
DP  - 1998
TI  - Modular organization of inteins and C-terminal autocatalytic domains.
PG  - 64-71
AB  - Analysis of the conserved sequence features of inteins (protein "introns") reveals that they
      are composed of three distinct modular domains.  The N-terminal and C-terminal domains are
      predicted to perform different parts of the autocatalytic protein splicing reaction.  An
      optional endonuclease domain is shown to correspond to different types of homing endonucleases
      in different inteins.  The N domain contains motifs predicted to catalyze the first steps of
      protein splicing, leading to the cleavage of the intein N terminus from its protein host.
      Intein N domain motifs are also found in C-terminal autocatalytic domains present in hedgehog
      and other protein families.  Specific residues in the N domain of intein and CADs are proposed
      to form a charge relay system involved in cleaving their N-termini.  The intein C domain is
      apparently unique to inteins and contains motifs that catalyze the final protein splicing
      steps: ligation of the intein flanks and cleavage of its C terminus to release the free intein
      and spliced host protein.  All intein EN domains known thus far have dodecapeptide (DOD,
      LAGLI-DADG) type homing endonuclease motifs.  This work identifies an EN domain with an HNH
      homing-endonuclease motif and two new small inteins with no EN domains.  One of these small
      inteins might be inactive or a "pseudo intein".  The results suggest a modular architecture
      for inteins, clarify their origin and relationship to other protein families, and extend
      recent experimental findings on the functional roles of intein N, C and EN motifs.
AU  - Pietrokovski S
PT  - Journal Article
TA  - Protein Sci.
JT  - Protein Sci.
SO  - Protein Sci. 1998 7: 64-71.

PMID- 11485819
VI  - 17
DP  - 2001
TI  - Intein spread and extinction in evolution.
PG  - 465-472
AB  - Inteins are selfish DNA elements found within coding regions. They are translated with their
      host protein, but then catalyze their own
      excision and the formation of a peptide bond between their flanking
      protein regions. Understanding what drives and selects inteins is
      relevant for assessing whether they have unidentified biological
      functions and whether they can invade and become established in new
      genes and organisms. Inteins are suggested to have been present and
      more common in the progenitors of eukaryotes and prokaryotes. In these
      cells, inteins had some beneficial function or had evolved from an
      unknown beneficial protein. Since then, this putative benefit has been
      lost and inteins are gradually becoming extinct. The proteins in which
      inteins are currently found are proposed to be proteins vital for the
      survival of the organism, where intein removal is most difficult.
AU  - Pietrokovski S
PT  - Journal Article
TA  - Trends Genet.
JT  - Trends Genet.
SO  - Trends Genet. 2001 17: 465-472.

PMID- 7756989
VI  - 3
DP  - 1994
TI  - Conserved sequence features of inteins (protein introns) and their use in identifying new inteins and related proteins.
PG  - 2340-2350
AB  - Inteins (protein introns) are internal portions of protein sequences that are
      posttranslationally excised while the flanking regions are spliced together, making an
      additional protein product.  Inteins have been found in a number of homologous genes in
      yeast, mycobacteria, and extreme thermophile archaebacteria.  The inteins are probably
      multifunctional, autocatalyzing their own splicing, and some were also shown to be DNA
      endonucleases.  The splice junction regions and two regions similar to homing
      endonucleases were thought to be the only common sequence features of inteins.  This
      work analyzed all published intein sequences with recently developed methods for detecting
      weak, conserved sequence features.  The methods complemented each other in the
      identification and assessment of several patterns characterizing the intein sequences.  New
      intein conserved features are discovered and the known ones are quantitatively described
      and localized.  The general sequence description of all the known inteins is derived from
      the motifs and their relative positions.  The intein sequence description is used to search
      the
      sequence databases for intein-like proteins.  A sequence region in a mycobacterial open
      reading frame possessing all of the intein motifs and absent from sequences homologous to
      both of its flanking sequences is identified as an intein.  A newly discovered putative intein
      in red algae chloroplasts is found not to contain the endonuclease motifs present in all other
      inteins.  The yeast HO endonuclease is found to have an overall intein-like structure and a
      few viral polyprotein cleavage sites are found to be significantly similar to the inteins
      amino-end splice junction motif.  The intein features described may serve for detection of
      intein sequences.
AU  - Pietrokovski S
PT  - Journal Article
TA  - Protein Sci.
JT  - Protein Sci.
SO  - Protein Sci. 1994 3: 2340-2350.

PMID- 8783935
VI  - 12
DP  - 1996
TI  - A new intein in cyanobacteria and its significance for the spread of inteins.
PG  - 287-288
AB  - Inteins are protein 'introns' encoded inside the polypeptide sequence of
      other proteins.  The inteins splice out post-translationally by a proteolytic cleavage and
      ligation process.  Inteins appear to autocatalyze their own excision and some are site-
      specific endonucleases.  Inteins are mobile genetic elements and at least one can home, that
      is, insert a copy of its DNA into its integration site in an intein-less allele.  Fifteen
      inteins
      have been found in various organisms, including mycobacteria, thermophilic
      archaebacteria, yeast and chloroplast of red alga.  Inteins are not very similar to one
      another, but homologous sites in archaebacterial DNA polymerases and in mycobacterial
      gyrase-A proteins contain homologous inteins.  However, the mycobacterial RecA proteins
      and DNA polymerases also contain different inteins in different integration sites.
AU  - Pietrokovski S
PT  - Journal Article
TA  - Trends Genet.
JT  - Trends Genet.
SO  - Trends Genet. 1996 12: 287-288.

PMID- 25059873
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Listeria monocytogenes Strain LI0521 (syn. HPB7171), Isolated in 1983 during an Outbreak in Massachusetts Caused by Contaminated  Cheese.
PG  - e00729-14
AB  - Listeria monocytogenes, a pathogenic food-borne bacterium, is the causative agent of both
      sporadic and outbreak cases of human listeriosis. Here, we present the
      genome sequence of L. monocytogenes reference strain LI0521, isolated during an
      outbreak involving contaminated cheese, which has been used as the model during
      several proteomic studies.
AU  - Pightling AW
AU  - Lin M
AU  - Pagotto F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00729-14.

PMID- 26067972
VI  - 3
DP  - 2015
TI  - Genome Sequence of Listeria monocytogenes Strain HPB5415, Collected during a 2008 Listeriosis Outbreak in Canada.
PG  - e00637-15
AB  - Listeria monocytogenes strain HPB5415-isolated from deli meat-was found in 2008 to have the
      same pulsed-field gel electrophoresis patterns as a clinical strain
      (08-5923). However, whether nucleotide differences (single nucleotide
      polymorphisms [SNPs]) exist between their genomes was not determined. We
      sequenced the L. monocytogenes strain HPB5415 genome and identified 52 SNPs
      relative to strain 08-5923.
AU  - Pightling AW
AU  - Pagotto F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00637-15.

PMID- 25103765
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Cronobacter sakazakii Clonal Complex 45 Strain HPB5174,  Isolated from a Powdered Infant Formula Facility in Ireland.
PG  - e00778-14
AB  - Cronobacter sakazakii is a food-borne pathogenic bacterium that may cause severe  illness in
      neonates and the elderly. We present the genome sequence of a rare
      strain (ST40, CC45), commonly found in multiple food processing facilities and in
      powdered infant formula and only indicted in a single clinical case.
AU  - Pightling AW
AU  - Pagotto F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00778-14.

PMID- 27634991
VI  - 4
DP  - 2016
TI  - Genome Sequence of the Listeria monocytogenes Food Isolate HPB913, Collected in Canada in 1993.
PG  - e00911-16
AB  - Listeria monocytogenes is a pathogenic bacterium of importance to public health and food
      safety agencies. We present the genome sequence of the serotype 1/2a L.
      monocytogenes food isolate HPB913, which was collected in Canada in 1993 as part
      of an investigation into a sporadic case of foodborne illness.
AU  - Pightling AW
AU  - Rand H
AU  - Strain E
AU  - Pagotto F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00911-16.

PMID- 27491990
VI  - 4
DP  - 2016
TI  - Genome Sequence of Listeria monocytogenes Strain HPB2088 (Serotype 1/2a), an Environmental Isolate Collected in Canada in 1994.
PG  - e00760-16
AB  - Listeria monocytogenes is a foodborne pathogen that causes severe illness. Thus,  ongoing
      efforts at real-time whole-genome sequencing are of utmost importance.
      However, it is also important that retrospective analyses that place these data
      into context be performed. Here, we present the genome sequence of strain
      HPB2088, which was collected in 1994.
AU  - Pightling AW
AU  - Rand H
AU  - Strain E
AU  - Pagotto F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00760-16.

PMID- 
VI  - 2000
DP  - 2000
TI  - Efficient synthesis of S-adenosyl-L-homocysteine natural product analogues and their use to elucidate the structural determinant for cofactor binding of the DNA methyltransferase M.HhaI.
PG  - 549-555
AB  - 5'-Acetylthio-5'-deoxy-2',3'-O-isopropylideneadenosine was directly prepared from
      commercially available 2',3'-O-isopropylideneadenosine and thioacetic acid under Mitsunobu
      conditions in almost quantitative yield.  In situ cleavage of the acetylthio function of
      5'-Acetylthio-5'-deoxy-2',3'-O-isopropylideneadenosine followed by coupling with different
      alkyl bromides proceeded with high yields.  Deprotection of the obtained 5'-thionucleosides
      yielded the S-adenosyl-L-homocysteine analogues decarboxylated AdHcy, deaminated AdoHcy and
      5'-[3-(cyano)propylthio]-5'-deoxyadenosine in good overall yields.  Direct deprotection of
      the thionucleoside 5'-Acetylthio-5'-deoxy-2',3'-O-isopropylideneadenosine delivered
      5'-thio-5'-deoxyadenosine in excellent yield.  In addition, binding constants of these
      AdoHcy analogues and the DNA methyltransferase M.HhaI were determined in a fluorescence assay.
AU  - Pignot M
AU  - Pljevaljcic G
AU  - Weinhold E
PT  - Journal Article
TA  - Eur. J. Org. Chem.
JT  - Eur. J. Org. Chem.
SO  - Eur. J. Org. Chem. 2000 2000: 549-555.

PMID- 
VI  - 37
DP  - 1998
TI  - Coupling of a nucleoside with DNA by a methyltransferase.
PG  - 2888-2891
AB  - S-Adenosyl-L-methionine-dependent methyltransferases catalyze the transfer of the activated
      methyl group from the cofactor S-adenosyl-L-methionine to sulfur, nitrogen, oxygen, and carbon
      acceptors (Scheme 1) of small molecules, phospholipids, proteins, RNA and DNA with high
      specificity.  The transfer of larger chemical entities in a Mtase-catalyzed reaction has not
      been reported and thus represents an interesting challenge for bioorganic chemists.  In
      principal, covalent linking of the activated methyl group with the gamma-C atom of 1 would
      yield a three-membered thiiranium compound, which could lead to a coupling of the whole
      cofactor to the target substrate.  Since thiiranium compounds are known to be unstable in
      nucleophilic solvents, we concentrated on the more stable aziridine analogues, which can be
      activated as alkylating reagents upon protonation of their ring nitrogen atom.
      N-adenosylaziridine was synthesized by nucleophilic substitution of the tosylate group of
      5'-deoxy-5'-tosyladenosine (tosyl=Ts=toluene-4-sulfonyl) with aziridine (Scheme 2).
AU  - Pignot M
AU  - Siethoff C
AU  - Linscheid M
AU  - Weinhold E
PT  - Journal Article
TA  - Angew. Chem. Int. Ed. Engl.
JT  - Angew. Chem. Int. Ed. Engl.
SO  - Angew. Chem. Int. Ed. Engl. 1998 37: 2888-2891.

PMID- 
VI  - 53
DP  - 2008
TI  - On the distinction of the mechanisms of DNA cleavage by restriction enzymes - The I-, II-, and III-type molecular motors.
PG  - 858-867
AB  - A comparative physical description is given for the functioning of various restriction enzymes
      and for their processes of DNA cleavage.
      The previously proposed model system of kinetic equations is applied to
      the I- and III-type enzymes, which use ATP molecules as an energy
      source, while the II-type enzymes work thanks to catalytic reactions
      with participation of an electric field. All the enzymes achieved
      bending and twisting DNA, providing for either the linear motion of the
      II-type enzyme along the DNA chain or the DNA translocation by the
      I-and III-type enzymes due to moving chiral kinks. A comparative
      estimation of the considered linear and angular velocities is
      performed. The role of stalling forces for enzyme-DNA complexes, which
      induce the observed cutting of the DNA either inside the enzyme (II) or
      in some "weak" places outside enzymes I and III, which results in the
      supercoiling of the DNA, is shown. The role of ionic screening for the
      described processes is discussed.
AU  - Pikin SA
PT  - Journal Article
TA  - Crystallogr. Rep.
JT  - Crystallogr. Rep.
SO  - Crystallogr. Rep. 2008 53: 858-867.

PMID- 
VI  - 508
DP  - 2009
TI  - On the DNA cleavage by restriction enzymes - molecular motors with polarization properties.
PG  - 403-413
AB  - In the paper, on the general physical basis, the attempt was done to explain the operation of
      restriction enzymes of different types.  The physical model lies in the DNA deformation in the
      protein zone which is caused by catalytic processes taking place here.  It is shown that some
      phenomena are similar to liquid-crystalline effects.  The DNA molecule either forms locally a
      chiral kink moving together with a protein (the II type enzymes) or realizes the translocation
      through protein (the I and III type enzymes).  The velocity of linear motion of the enzymes
      was estimated on the basis of proper kinetic equations which include the action of a
      longitudinal stalling force, the role of this force in DNA cleavage being different for
      different enzymes.  The supercoiling of DNA during tis translocation is discussed.
AU  - Pikin SA
PT  - Journal Article
TA  - Mol. Cryst. Liq. Cryst.
JT  - Mol. Cryst. Liq. Cryst.
SO  - Mol. Cryst. Liq. Cryst. 2009 508: 403-413.

PMID- 
VI  - 54
DP  - 2009
TI  - Physical aspects of the structure and function of helicases as rotary molecular motors.
PG  - 929-936
AB  - Helicases were shown to have common physical properties with rotary molecular motors, such as
      F (0) F (1)-ATP synthase and type I
      restriction-modification (RM) enzymes. The necessary conditions for
      action of molecular motors are chirality, the presence of the C (2) (or
      lower) symmetry axis within rather large atomic groups, and
      polarization properties. The estimates were made for the material
      parameters of helicases, which translocate DNA due to moving chiral
      kinks without DNA cleavage and are characterized by higher viscosity,
      low mobility, and smaller chiral kinetic coefficients than type II RM
      enzymes. This paper discusses the efficiency of helicases with opposite
      polarities that drive DNA translocation in opposite directions.
AU  - Pikin SA
PT  - Journal Article
TA  - Crystallogr. Rep.
JT  - Crystallogr. Rep.
SO  - Crystallogr. Rep. 2009 54: 929-936.

PMID- 15212796
VI  - 236
DP  - 2004
TI  - Different restriction and modification phenotypes in ruminal lactate-utilizing bacteria.
PG  - 91-95
AB  - Analysis of restriction and modification activities in lactate-utilizing bacteria belonging to
      the Megasphaera elsdenii and Mitsuokella multiacida species revealed the presence of
      GATC-specific, MboI isospecific, restriction-modification (R-M) systems in all strains tested.
      While restriction endonucleases isolated from M. elsdenii strains were found to be sensitive
      to Dam methylation, enzymes from M. multiacida cleaved DNA irrespective of Dam methylation.
      The comparison of type 11 R-M systems specificities in three closely related lactate-utilizing
      ruminal bacterial species indicated complete lack of restriction and/or modification enzymes
      previously characterized from Selenomonas ruminantium in tested M. elsdenii and M. multiacida
      strains. R-M systems are believed to represent the main defense tool against phage infection.
      Based on the results of our experiments it could be assumed that M. elsdenii and M. multiacida
      use the different strategy for bacteriophage protection compared to S. ruminantium.
AU  - Piknova M
AU  - Filova M
AU  - Javorsky P
AU  - Pristas P
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2004 236: 91-95.

PMID- 16328890
VI  - 32
DP  - 2005
TI  - A Unique Pair of GATC Specific DNA Methyltransferases in Mitsuokella multiacida.
PG  - 281-284
AB  - Two GATC specific methylases together with Sau3AI isoschizomeric restriction endonuclease were
      partially characterized in Mitsuokella
      multiacida 46/5. This is the first report on the presence of solitary Dam
      methyltransferase alongside GATC specific restriction-modification system
      resulting in the unusual two-fold methylation of the GATC motifs.
AU  - Piknova M
AU  - Filova M
AU  - Javorsky P
AU  - Pristas P
PT  - Journal Article
TA  - Mol. Biol. Rep.
JT  - Mol. Biol. Rep.
SO  - Mol. Biol. Rep. 2005 32: 281-284.

PMID- 16102910
VI  - 251
DP  - 2005
TI  - Multiple restriction-modification systems are present in rumen treponemes.
PG  - 99
AB  - Type II restriction endonucleases were purified by heparin-sepharose followed by ion
      chromatography from Treponema strains. The results
      indicate that in addition to frequently cutting GATC-specific
      restriction enzymes, the tested strains also possess rarely cutting
      endonucleases. The purified restriction endonucleases represent four
      different sequence specificities, comprising isoschizomers of Drdl,
      AflII, Tth111II and NdeI. The data presented show that three rumen
      Treponema strains possess altogether seven type II
      restriction-modification systems. Thus, individual Treponema strains
      may be considered an interesting source of multiple type II restriction
      enzymes.
AU  - Piknova M
AU  - Javorsky P
AU  - Pristas P
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2005 251: 99.

PMID- 
VI  - 69
DP  - 2004
TI  - Some evolutionary aspects of biology of the type II restriction-modification systems.
PG  - 15-28
AB  - Restriction-modification (R-M) systems occur exclusively among prokaryotic organisms, mainly
      bacteria, and they represent the main protection mechanism against bacteriophage infections.
      R-M systems comprise two enzymatic activities: a restriction endonuclease activity that
      specifically cleaves DNA; and a corresponding methyltransferase activity that specifically
      methylates the DNA, thereby protecting the genome of the host bacterium from cleavage by a
      partner's restriction enzyme.  There are three main groups of R-M systems called Types I, II
      and III and recently a new Type IV has been added to accommodate a class of methyl-dependent
      restriction enzymes.  R-M systems are widely distributed among bacteria and more than 3500
      restriction enzymes and 600 methyltransferases have been identified to date.  The most
      abundant are type II R-M systems, which form a very large family of enzymes of similar
      function.  Considering the dissimilarities in amino acid sequences and, paradoxically,
      structural resemblances of restriction enzymes, it is very hard to decide whether restriction
      endonucleases are the outcome of divergent evolution from a very distant ancestor or whether
      they evolved independently.  While generally accepted that R-M systems act as barrier against
      genetic exchanges, there is increasing evidence for their behavior as mobile genetic elements.
AU  - Piknova M
AU  - Pristas P
AU  - Javorsky P
PT  - Journal Article
TA  - Biol. Listy
JT  - Biol. Listy
SO  - Biol. Listy 2004 69: 15-28.

PMID- 15227796
VI  - 49
DP  - 2004
TI  - GATC-specific restriction-modification systems in ruminal bacteria.
PG  - 191-193
AB  - The GATC-specific restriction and modification activities were analyzed in 11 major bacterial
      representatives of ruminal microflora.
      Modification phenotype was observed in 13 out of 40 ruminal strains.
      MboI isoschizomeric restriction endonucleases were detected in 10
      bacterial strains tested; three strains lacked any detectable
      corresponding endonuclease activity. The only examined strain of
      Mitsuokella multiacida was found to possess a different type of
      endonuclease activity. This is the first report on restriction activity
      in ruminal treponemes M. multiacida and Megasphaera elsdenii.
AU  - Piknova M
AU  - Pristas P
AU  - Javorsky P
PT  - Journal Article
TA  - Folia Microbiol. (Praha)
JT  - Folia Microbiol. (Praha)
SO  - Folia Microbiol. (Praha) 2004 49: 191-193.

PMID- 15214731
VI  - 38
DP  - 2004
TI  - GATC-specific restriction and modification systems in treponemes.
PG  - 311-314
AB  - Aims: To investigate the presence of GATC-specific modification and restriction activities in
      rumen isolates of Treponema sp.
      Methods: The presence of N-6-methyladenine within GATC (Dam)
      sequences was analysed using isoschizomeric restriction endonucleases
      having different sensitivities to the methylation of the target
      sequence. A fast screening method was used for testing of site-specific
      endonuclease activities directly in crude cell extracts. Three out of
      six rumen isolates of Treponema sp. showed restriction activities.
      Restriction endonucleases were further purified by Heparin-Sepharose
      chromatography. Using PCR and specific primers, no sequence homologous
      to the T. pallidum dam gene was found.
      Conclusions: Three rumen treponemal strains were documented to
      possess MboI isoschizomeric restriction- modification systems.
      Significance: This is the first report on restriction activity in
      rumen treponemes.
AU  - Piknova M
AU  - Pristas P
AU  - Javorsky P
AU  - Kasperowic A
AU  - Michalowski T
PT  - Journal Article
TA  - Lett. Appl. Microbiol.
JT  - Lett. Appl. Microbiol.
SO  - Lett. Appl. Microbiol. 2004 38: 311-314.

PMID- 27389258
VI  - 4
DP  - 2016
TI  - Complete Genome Sequences of 11 Haemophilus ducreyi Isolates from Children with Cutaneous Lesions in Vanuatu and Ghana.
PG  - e00459-16
AB  - Haemophilus ducreyi causes chancroid and has recently been shown to be a significant cause of
      cutaneous lesions in tropical or subtropical regions where
      yaws is endemic. Here, we report the draft genome assemblies for 11 cutaneous
      strains of Haemophilus ducreyi, isolated from children in Vanuatu and Ghana.
AU  - Pillay A
AU  - Katz SS
AU  - Abrams AJ
AU  - Ballard RC
AU  - Simpson SV
AU  - Taleo F
AU  - Lahra MM
AU  - Batra D
AU  - Rowe L
AU  - Trees DL
AU  - Asiedu K
AU  - Chen CY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00459-16.

PMID- 8636983
VI  - 257
DP  - 1996
TI  - Activation of a yeast pseudo DNA methyltransferase by deletion of a single amino acid.
PG  - 804-813
AB  - The biological methylation of cytosine bases in DNA is central to such diverse phenomena as
      restriction and modification in bacteria, repeat induced point-mutation (RIPing) in fungi and
      for programming gene expression patterns in vertebrates.  Structural studies on HhaI DNA
      methyltransferase, together with the sequence comparisons of around 40 cytosine-specific DNA
      methyltransferases, have recently provided a molecular framework for understanding the
      mechanism of action of the related group of enzymes that catalyse this base modification.
      There are, however, a number of organisms, including Saccharomyces cerevisiae,
      Schizosaccharomyces pombe and Drosophila melanogaster, which have no detectable DNA
      methylation.  Here we report that the product of the pmt1 gene recently identified in S.
      pombe, which contains most of the primary structure elements of a typical cytosine-specific
      DNA methyltransferase, is catalytically inert owing to the insertion of a Ser residue between
      the Pro-Cys motif found at the active site of all such DNA methyltransferases.  Following
      deletion of this Ser residue, catalytic activity is restored and, using a range of DNA binding
      experiments, it is shown that the enzyme recognises and methylates the sequence CC(A/T)GG, the
      same sequence that is modified by the product of the Escherichia coli dcm gene.  The pmt gene
      of S. pombe therefore encodes a pseudo DNA methyltransferase, which we have called psiM.SpoI.
AU  - Pinarbasi E
AU  - Elliott J
AU  - Hornby DP
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1996 257: 804-813.

PMID- 9628362
VI  - 379
DP  - 1998
TI  - Substitution of the conserved phenylalanine in the S-adenosyl-L-methionine binding site of M.MspI with tyrosine modifies the kinetic properties of the enzyme.
PG  - 591-594
AB  - Cytosine (C-5)-specific DNA methyltransferases share a set of ten conserved motifs distributed
      evenly throughout the entire polypeptide chain.  The first conserved motif contains a Phe,
      which is intimately associated with cofactor recognition.  In the pseudo-DNA methyltransferase
      M.SpoI, encoded by the pmt1 gene in Schizosaccharomyces pombe, a Tyr replaces this Phe
      residue.  We describe the properties of a mutant form of M.MspI, a typical cytosine
      (C-5)-specific DNA methyltransferase, in which Tyr replaces the conserved Phe.  This mutant
      shows differences in ternary complex formation and in the pattern of covalent complex
      formation with an inhibitory, fluorinated DNA duplex which may be due to anomalous hydrogen
      bonding between the mutant Tyr hydroxyl group and the catalytic loop of the enzyme or through
      interference with cofactor binding.
AU  - Pinarbasi E
AU  - Kan MS
AU  - Duran C
AU  - Ford GC
AU  - Hornby DP
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1998 379: 591-594.

PMID- Not carried by PubMed...
VI  - 20
DP  - 1996
TI  - Subcloning and expression of a cDNA encoding a Schizosaccharomyces pombe putative C-5 DNA methyltransferase.
PG  - 325-331
AB  - The pmt1+ gene, which shows a striking similarity to bacterial C-5 DNA methyltransferases, has
      recently been isolated from Schizosaccharomyces pombe.  In this study, we have subcloned pmt1+
      cDNA into the bacterial expression vector pET14b, which contains a sequence coding six
      histidine residues upstream of the coding site so that the recombinant protein possesses a
      histidine tag (Hig-Tag) at its N-terminus.  The constructed vector, which we have called
      pETSPO1, encoding the pmt1+ cDNA, was then introduced into E. coli BL21 (DE3)pLysS cells and
      the expressed recombinant protein was purified to homogeneity by nickel-chelate-affinity
      chromatography.  Approximately 5 mg of His-Tag-pmt1+ fusion protein was purified from one
      liter of induced culture.
AU  - Pinarbasi E
AU  - Pinarbasi H
AU  - Hornby DP
PT  - Journal Article
TA  - Turkish J. Biol.
JT  - Turkish J. Biol.
SO  - Turkish J. Biol. 1996 20: 325-331.

PMID- 12297020
VI  - 35
DP  - 2002
TI  - Recombinant alpha and beta subunits of M.AquI constitute an active DNA methyltransferase.
PG  - 348-351
AB  - AquI DNA methyltransferase, M.AquI, catalyses the transfer of a methyl group from
      S-adenosyl-L-methionine to the C5 position of the outermost
      deoxycytidine base in the DNA sequence 5'CYCGRG3'. M.AquI is encoded by
      two overlapping ORFs (termed a and P) instead of the single ORF that is
      customary for Class II methyltransferase genes. The structural
      organization of the M.AquI protein sequence is quite similar to that of
      other bacteria] C5-DNA methyltransferases. Ten conserved motifs are
      also present in the correct order, but only on two polypeptides. We
      separately subcloned the genes that encode the alpha and beta subunits
      of M.AquI into expression vectors. The overexpressed His-fusion alpha
      and beta subunits of the enzyme were purified to homogeneity in a
      single step by Nickel-chelate affinity chromatography. The purified
      recombinant proteins were assayed for biological activity by an in
      vitro DNA tritium transfer assay. The alpha and beta subunits of M.AquI
      alone have no DNA methyltransferase activity, but when both subunits
      are included in the assay, an active enzyme that catalyses the transfer
      of the methyl group from S-adenosyl-L-methionine to DNA is
      reconstituted. We also showed that the beta subunit alone contains all
      of the information that is required to generate recognition of specific
      DNA duplexes in the absence of the alpha subunit.
AU  - Pinarbasi H
AU  - Pinarbasi E
AU  - Hornby D
PT  - Journal Article
TA  - J. Biochem. Mol. Biol.
JT  - J. Biochem. Mol. Biol.
SO  - J. Biochem. Mol. Biol. 2002 35: 348-351.

PMID- 
VI  - 25
DP  - 2001
TI  - Substitution of the conserved cysteine with glycine (Cys82Gly) of Agmenellum quadruplicatum methylase AquI (M.AquI) is not cytotoxic to  E. coli.
PG  - 177-184
AB  - Cytosine 5 DNA methyltransferases share ten conserved motifs. Motif IV contains an absolutely
      conserved proline-cysteine dipeptide. The
      cysteine residue of this motif is involved in catalysis by forming a
      covalent bond with the 6-position of cytosine prior to methyl group
      transfer. AquI DNA methyltransferase recognising the sequence CCCGGG is
      a heterodimer unlike other C5 DNA methyltransferases. We changed the
      conserved cysteine (Cys82) of M.AquI to serine and glycine. The
      presence of mutations was confirmed by automated DNA sequencing.
      Mutants were tested by in vivo plasmid protection assay and also by
      transformation into mcrA+BC+ strain of E. coli. Replacement of the
      conserved cysteine with serine led to an apparent loss of the
      methyltransferring ability of the enzyme. Interestingly, it was found
      that substitution of cysteine with glycine is not cytotoxic to E. coli
      in the case of M.AquI.
AU  - Pinarbasi H
AU  - Pinarbasi E
AU  - Hornby DP
PT  - Journal Article
TA  - Turkish J. Biol.
JT  - Turkish J. Biol.
SO  - Turkish J. Biol. 2001 25: 177-184.

PMID- 12562799
VI  - 185
DP  - 2003
TI  - The small subunit of M.AquI is responsible for sequence-specific DNA recognition and binding in the absence of the catalytic domain.
PG  - 1284-1288
AB  - AquI DNA methyltransferase (M. AquI) catalyzes the transfer of a methyl group from
      S-adenosyl-L-methionine to the C5 position of the outermost
      deoxycytidine base in the DNA sequence 5'-CCCGGG-3'. M. AquI is a
      heterodimer in which the polypeptide chain is separated at the junction
      between the two equivalent structural domains in the related enzyme M.
      HhaI. Recently, we reported the subcloning, overexpression, and
      purification of the subunits (alpha and beta) of M. AquI separately. Here
      we describe the DNA binding properties of M. AquI. The results presented
      here indicate that the beta subunit alone contains all of the information
      for sequence-specific DNA recognition and binding. The first step in the
      sequence-specific recognition of DNA by M. AquI involves the formation of
      binary complex with the target recognition domain in conjunction with
      conserved sequence motifs IX and X, found in all known C5 DNA
      methyltransferases, contained in the beta subunit. The alpha subunit
      enhances the binding of the beta subunit to DNA specifically and
      nonspecifically. It is likely that the addition of the alpha subunit to
      the beta subunit stabilizes the conformation of the beta subunit and
      thereby enhances its affinity for DNA indirectly. Addition of
      S-adenosyl-L-methionine and its analogues S-adenosyl-L-homocysteine and
      sinefungin enhances binding, but only in the presence of the alpha
      subunit. These compounds did not have any effect on DNA binding by the
      beta subunit alone. Using a 30-mer oligodeoxynucleotide substrate
      containing 5-fluorodeoxycytidine (5-FdC), it was found that the beta
      subunit alone did not form a covalent complex with its specific sequence
      in the absence or presence of S-adenosyl-L-methionine. However, the
      addition of the alpha subunit to the beta subunit led to the formation of
      a covalent complex with specific DNA sequence containing 5-FdC.
AU  - Pinarbasi H
AU  - Pinarbasi E
AU  - Hornby DP
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2003 185: 1284-1288.

PMID- 
VI  - 60
DP  - 2000
TI  - Multitiered regulation of 5-cytosine DNA methyltransferase expression.
PG  - 5938
AB  - The methylation of DNA at the 5 position of the cytosine moiety within CpG dinucleotides
      sequences forms a complex pattern which delimits non-expressed genes.  For many years,
      especially through studies of the correlation between methylation and gene silencing,
      researchers have tried to decipher this genomic subtext.  Probably, a better way to achieve an
      understanding of DNA methylation is by first elucidating what regulates the apparatus
      responsible for its establishment.  The DNA MeTase is the enzyme responsible for the catalysis
      of the DNA methylation reaction.  It was therefore the objective of this thesis to define some
      of the factors that regulate the expression of this enzyme.  Preceding work had described a
      promoter for the gene encoding the DNA MeTase.  Recent data has prompted some to put in doubt
      the validity of this promoter.  In the first part of this thesis I present a report which
      describes a selection between two possible promoters for the DNA MeTase gene effected by
      methylation in P19 cells.  This data not only revalidates the previous description of the
      promoter, but adds a new level of possible control.  In the second part, I elucidated the
      elements within the minimal region of the aforementioned promoter which are necessary for
      activity.  The results illustrate that most of the sequence plays a role in the promoter
      function, and pRb is found to be able to modulate the activity in a novel cooperation between
      AP1 and Sp1 which is absolutely necessary for the promoter to fulfil its purpose.  The third
      part of the thesis is based on an effort to investigate the generality of oncogenic control of
      DNA MeTase expression.  The promoter was previously demonstrated to be responsive to the
      Ras/AP1 pathway leading to oncogenesis.  Therefore, another oncogene, the SV40 large T
      antigen, known to act through a separate pathway from Ras and AP1, was transfected into BALB/c
      3T3 cells in order to see how the expression of the DNA MeTase would be affected during this
      transformation.  It was found that T antigen, through its actions on pRb, can induce DNA
      MeTase expression by stabilizing its mRNA.  These studies establish that the DNA MeTase is a
      nodal point of control by oncogenes and tumor suppressors which may need this enzyme in order
      to execute their effects on the cell.
AU  - Pinard M
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 2000 60: 5938.

PMID- 9033675
VI  - 7
DP  - 1996
TI  - Regulation of cytosine DNA methyltransferase expression by tumor suppressors.
PG  - 174a
AB  - In mammalian genomes, 60-80% of CpG dinucleotide sequences are methylated on the cytosine 5'
      position.  These methylated sequences are distributed in a tissue specific pattern which is
      correlated with gene silencing.  Recent data suggest a critical role for DNA MeTase in
      oncogenesis.  The DNA methyltransferase gene expression has previously been shown to respond
      to the oncogenic Ras pathway via AP-1 sites found in its promoter.  The effective silencing of
      certain tumor suppressors by DNA methylation has also been demonstrated.  We hypothesize that
      DNA MeTase acts as a pivotal point in the cross-talk between oncogenes and tumor suppressors.
      In order to elucidate the effect of tumor suppressors on DNA MeTase expression, the SV40 T
      antigen was stably transfected into BalbC3T3 cells to inhibit pRb activity.  We demonstrate
      that expression of T antigen includes expression of DNA MeTase RNA as determined by RNAase
      protection, of DNA MeTase protein as shown by Western blot analysis and of DNA MeTase activity
      as assessed by an enzymatic activity assay.  DNA MeTase induction is at least partly
      transcriptional as shown by nuclear Run-off assays.  By Southern blot assays we have observed
      differences in the levels of methylation in several CpG island genes although not all to the
      same extent.  Therefore, we clearly show that T antigen affects the regulation of DNA MeTase
      and, in consequence, affects the methylation of specific genes.  These results may be the
      first to show a feedback regulation of DNA MeTase by tumor suppressors which may mean that the
      DNA MeTase is a center point in growth regulation by both oncogenes and tumor suppressors.
AU  - Pinard M
AU  - Szyf M
PT  - Journal Article
TA  - Mol. Biol. Cell
JT  - Mol. Biol. Cell
SO  - Mol. Biol. Cell 1996 7: 174a.

PMID- 2982605
VI  - 147
DP  - 1985
TI  - Spermidine increases the accuracy of type II restriction endonucleases.  Suppression of cleavage at degenerate, non-symmetrical sites.
PG  - 105-109
AB  - The non-specific cleavage of DNA by type II restriction endonucleases (BamHI,
      BsuRI, EcoRI, EcoRV, HindIII, PstI and SalI) can be effectively suppressed by
      spermidine in millimolar concentrations, regardless of whether the non-specific
      cleavage is induced by high concentrations of enzyme under optimal buffer
      conditions or by high pH, low ionic strength, organic solvents and Mn2+ ions.
      The increased specificity of restriction endonucleases in the presence of
      spermidine is due to an enhancement of the cleavage rate at the canonical site
      and a slowing down of the cleavage rate at related sites.  It is argued that
      spermidine is essential for the high accuracy of restriction endonucleases in
      vivo.
AU  - Pingoud A
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1985 147: 105-109.

PMID- 3675865
VI  - 368
DP  - 1987
TI  - Site-directed mutagenesis of the EcoRI restriction endonuclease.
PG  - 1093
AB  - EcoRI is the only restriction endonuclease for which detailed structural
      information is available.  Based on this information we have begun to study the
      involvement of individual amino acid residues in the recognition process and in
      catalysis by site directed mutagenesis.  In an effort to identify the essential
      Glu and His residues of EcoRI we have replaced Glu 96, Glu 111, Glu 144 by Gln
      and His 14, His 31 and His 114 by Asn.  All these single point mutations
      drastically lower the catalytic effectivity of EcoRI, mainly by affecting the
      kcat-value.  The Glu 96 mutant, furthermore, shows reduced specificity towards
      its DNA substrate.  At present these results can only in part be explained by
      the 3D structure of the EcoRI recognition complex as deduced from the x-ray
      analysis of an EcoRI oligodeoxynucleotide complex crystallized in the absence
      of Mg2+.
AU  - Pingoud A
AU  - Alves J
AU  - Fliess A
AU  - Geiger R
AU  - Rueter T
AU  - Wolfes H
PT  - Journal Article
TA  - Biol. Chem. Hoppe Seyler
JT  - Biol. Chem. Hoppe Seyler
SO  - Biol. Chem. Hoppe Seyler 1987 368: 1093.

PMID- 19082972
VI  - 16
DP  - 1993
TI  - Restriction Enzymes.
PG  - 107-200
AB  - A review focussing on the practical aspects of the use of these enzymes.
AU  - Pingoud A
AU  - Alves J
AU  - Geiger R
PT  - Journal Article
TA  - Methods Mol. Biol.
JT  - Methods Mol. Biol.
SO  - Methods Mol. Biol. 1993 16: 107-200.

PMID- 15770420
VI  - 62
DP  - 2005
TI  - Type II restriction endonucleases: structure and mechanism.
PG  - 685-707
AB  - Type II restriction endonucleases are components of restriction modification systems that
      protect bacteria and archaea against invading
      foreign DNA. Most are homodimeric or tetrameric enzymes that cleave DNA
      at defined sites of 4 - 8 bp in length and require Mg2+ ions for
      catalysis. They differ in the details of the recognition process and
      the mode of cleavage, indicators that these enzymes are more diverse
      than originally thought. Still, most of them have a similar structural
      core and seem to share a common mechanism of DNA cleavage, suggesting
      that they evolved from a common ancestor. Only a few restriction
      endonucleases discovered thus far do not belong to the PD...D/ExK
      family of enzymes, but rather have active sites typical of other
      endonuclease families. The present review deals with new developments
      in the field of Type II restriction endonucleases. One of the more
      interesting aspects is the increasing awareness of the diversity of
      Type II restriction enzymes. Nevertheless, structural studies
      summarized herein deal with the more common subtypes. A major emphasis
      of this review will be on target site location and the mechanism of
      catalysis, two problems currently being addressed in the literature.
AU  - Pingoud A
AU  - Fuxreiter M
AU  - Pingoud V
AU  - Wende W
PT  - Journal Article
TA  - Cell. Mol. Life Sci.
JT  - Cell. Mol. Life Sci.
SO  - Cell. Mol. Life Sci. 2005 62: 685-707.

PMID- 2610941
VI  - 370
DP  - 1989
TI  - Functional sites of the EcoRI restriction endonuclease probed by site directed mutagenesis.
PG  - 943-944
AB  - The EcoRI restriction endonuclease recognizes with high specificity the double
      stranded DNA sequence G^AATTC/CTTAA^G and in the presence of Mg2+ cleaves the
      DNA as indicated.  A 3 Angstrom X-ray structure analysis of an EcoRI-DNA
      complex, crystallized in the absence of Mg2+, indicates that the amino acid
      residues in positions 144 and 145 as well as 200 are involved in DNA binding.
      Site directed mutagenesis experiments have shown that their involvement in the
      recognition process, however, is more intricate than proposed by the authors of
      the X-ray structure analysis.  To define more precisely the role of these and
      adjacent amino acids we have produced single and double mutants of EcoRI with
      amino acid replacements in position 144, 145, 147 as well as 199, 200, 203 and
      analyzed their activity in vivo and in vitro after purification to homogeneity.
      The results of the in vivo assay allows us to conclude that the structural
      integrity of the region at and around position 200 is very critical for the
      enzymatic function of EcoRI:  nonconservative mutations lead to a dramatic
      decrease in activity.  In contrast, the region around position 144 and 145
      seems to be of minor importance for the enzymatic activity:  non-conservative
      mutations in this region have similar moderate effects as conservative
      mutations.  The analysis of the purified EcoRI mutants confirms these results.
      In addition, they demonstrate that some mutants which have a very low activity
      are still specific for the EcoRI site (Arg200->Gly), while others show a
      relaxed specificity (Arg200->Glu or Gln and Asn199->Asp).  The Asn199->Asp
      mutant, furthermore, attacks preferentially the central phosphodiester bond in
      its degenerate hexanucleotide recognition sequence.  Taken together our results
      suggest that not only Glu144, Arg145 and Arg200 are involved in specificity
      determining interactions but other amino acids as well.  The recognition
      process, furthermore, does not only depend on hydrogen bonds but also on the
      overall complementarity of charge dipoles, and presumably is highly redundant.
      We have begun to locate the catalytic center and the Mg2+ binding site of
      EcoRI.  Two candidate regions were analyzed:
      1.  92GGIVEVKD - DYGEWR
      2. 126LLVGKRGDQDLMAAG
      which show a homology to a consensus sequence proposed to be involved in Mg2+
      binding in a variety of polymerases.  Preliminary results demonstrate that the
      second region is more critical than the first one for the catalytic action of
      EcoRI.
AU  - Pingoud A
AU  - Geiger R
AU  - Alves J
AU  - Oelgeschlager T
AU  - Ruter T
PT  - Journal Article
TA  - Biol. Chem. Hoppe Seyler
JT  - Biol. Chem. Hoppe Seyler
SO  - Biol. Chem. Hoppe Seyler 1989 370: 943-944.

PMID- 11557805
VI  - 29
DP  - 2001
TI  - Structure and function of type II restriction endonucleases.
PG  - 3705-3727
AB  - More than 3000 type II restriction endonucleases have been discovered. They recognize short,
      usually palindromic, sequences of 4-8 bp and, in the presence of Mg(2+), cleave the DNA within
      or in close proximity to the recognition sequence. The orthodox type II enzymes are homodimers
      which recognize palindromic sites. Depending on particular features subtypes are classified.
      All structures of restriction enzymes show a common structural core comprising four
      beta-strands and one alpha-helix. Furthermore, two families of enzymes can be distinguished
      which are structurally very similar (EcoRI-like enzymes and EcoRV-like enzymes). Like other
      DNA binding proteins, restriction enzymes are capable of non-specific DNA binding, which is
      the prerequisite for efficient target site location by facilitated diffusion. Non-specific
      binding usually does not involve interactions with the bases but only with the DNA backbone.
      In contrast, specific binding is characterized by an intimate interplay between direct
      (interaction with the bases) and indirect (interaction with the backbone) readout. Typically
      approximately 15-20 hydrogen bonds are formed between a dimeric restriction enzyme and the
      bases of the recognition sequence, in addition to numerous van der Waals contacts to the bases
      and hydrogen bonds to the backbone, which may also be water mediated. The recognition process
      triggers large conformational changes of the enzyme and the DNA, which lead to the activation
      of the catalytic centers. In many restriction enzymes the catalytic centers, one in each
      subunit, are represented by the PD...D/EXK motif, in which the two carboxylates are
      responsible for Mg(2+) binding, the essential cofactor for the great majority of enzymes. The
      precise mechanism of cleavage has not yet been established for any enzyme, the main
      uncertainty concerns the number of Mg(2+) ions directly involved in cleavage. Cleavage in the
      two strands usually occurs in a concerted fashion and leads to inversion of configuration at
      the phosphorus. The products of the reaction are DNA fragments with a 3'-OH and a
      5'-phosphate.
AU  - Pingoud A
AU  - Jeltsch A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2001 29: 3705-3727.

PMID- 9210460
VI  - 246
DP  - 1997
TI  - Recognition and cleavage of DNA by type-II restriction endonucleases.
PG  - 1-22
AB  - Restriction endonucleases are enzymes which recognize short DNA sequences and cleave the DNA
      in both strands.  Depending on the enzymological properties different types are distinguished.
      Type II restriction endonucleases are homodimers which recognize short palindromic sequences
      4-8 bp in length and, in the presence of Mg2+, cleave the DNA within or next to the
      recognition site.  They are capable of non-specific binding to DNA and make use of linear
      diffusion to locate their target site.  Binding and recognition of the specific site involves
      contacts to the bases of the recognition sequence and the phosphodiester backbone over
      approximately 10-12 bp.  In general, recognition is highly redundant which explains the
      extreme specificity of these enzymes.  Specific binding is accompanied by conformational
      changes over both the protein and the DNA.  This mutual induced fit leads to the activation of
      the catalytic centers.  The precise mechanism of cleavage has not yet been established for any
      restriction endonuclease.  Currently two models are discussed: the substrate-assisted
      catalysis mechanism and the two-metal-ion mechanism.  Structural similarities identified
      between EcoRI, EcoRV, BamHI, PvuII and Cfr10I suggest that many type II restriction
      endonucleases are not only functionally but also evolutionarily related.  A review.
AU  - Pingoud A
AU  - Jeltsch A
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1997 246: 1-22.

PMID- Not included in PubMed...
VI  - 376
DP  - 1995
TI  - Mechanism of DNA recognition and cleavage by restriction enzymes.
PG  - S138
AB  - The crystal structure analyses of specific DNA complexes of EcoRI, EcoRV and PvuII have
      greatly aided in our understanding of how these enzymes recognize and cleave their DNA
      substrate.  Many questions, however, remain, in particular, how is the target site located,
      what is the relative contribution of direct and indirect readout for the recognition process,
      how do the two subunits of the homodimeric restriction enzymes cooperate in recognition as
      well as cleavage, and, what is the precise mechanism of phosphodiester bond hydrolysis.  Using
      EcoRV as a model restriction enzyme we have tried to answer some of these questions.  It is
      apparent from our studies that EcoRV makes use of facilitated diffusion along the DNA to
      locate its target site and that Mg ions are required for specific binding which leads to a
      pronounced DNA bending.  During recognition, contacts are formed to the bases and the
      backbone: base contacts are in general more important than phosphate contacts, the latter,
      however, are needed for binding, linear diffusion and to make sites with different flanking
      sequences equally accessible for EcoRV,  Mutants of EcoRV have been constructed that exhibit
      preferences for sites containing a modified base or backbone as well as for certain flanking
      sequences.  We have shown that the two identical subnits of EcoRV communicate with each other
      in DNA recognition, not, however, in catalysis per se.  Accordingly, artifical heterodimers
      could be produced that exhibit a pronounced nicking activity.  While the catalytic amino acid
      residues and the stereochemical course for the reaction have been identfied for EcoRV, it is
      still not clear how the attacking hydroxide ion is generated and how many metal ions are
      involved in the catalytic mechanism.  Based on the current experimental evidence, we believe
      that a water molecule is activated by the phosphate residue 3' to the scissile phosphodiester
      bond, that only one Mg ion is needed to polarize the P-O bond, to stabilize the transition
      state and to supply a water molecule for protonation of the leaving group.  It is becoming
      increasingly clear that restriction enzymes, which in general do not share significant
      sequence homology, have structural and mechanistic features in common.  Indeed, using a
      genotypic and phenotypic analysis it has been possible to demonstrate a common evolutionary
      history for these enzymes.
AU  - Pingoud A
AU  - Jeltsch A
AU  - Lanio T
AU  - Schulze C
AU  - Selent U
AU  - Stahl F
AU  - Wende W
AU  - Wenz C
PT  - Journal Article
TA  - Biol. Chem. Hoppe Seyler
JT  - Biol. Chem. Hoppe Seyler
SO  - Biol. Chem. Hoppe Seyler 1995 376: S138.

PMID- 
VI  - 2
DP  - 2001
TI  - Enzymes that keep DNA under control.
PG  - 271-276
AB  - Life demands not only the faithful and controlled replication of DNA but, in addition, many
      other enzymatic processes involving DNA, including topoisomerase action, recombination,
      repair, restriction and modification.  These topics and their interrelationships were
      discussed at the IUBMB symposium in Bangalore (India) on DNA enzymes: structures and
      mechanisms (December 1-3, 2000), which was organized by V. Nagaraja and D.N. Rao (Bangalore,
      India) and brought together about 200 scientists from all over the world.  Whereas most
      presentations focused on detailed biochemical and genetic mechanisms, several reminded us that
      enzymes and DNA are components of complex living organisms that live, die and evolve.
AU  - Pingoud A
AU  - Jeltsch A
AU  - Maxwell A
AU  - Sherratt D
PT  - Journal Article
TA  - EMBO Rep.
JT  - EMBO Rep.
SO  - EMBO Rep. 2001 2: 271-276.

PMID- 
VI  - 9
DP  - 2003
TI  - Homing endonucleases - multifaceted tools for genome engineering.
PG  - 592-595
AB  - 
AU  - Pingoud A
AU  - Pingoud V
AU  - Wende W
PT  - Journal Article
TA  - BIOspektrum
JT  - BIOspektrum
SO  - BIOspektrum 2003 9: 592-595.

PMID- 17621297
VI  - 25
DP  - 2007
TI  - Precision genome surgery.
PG  - 743-744
AB  - Zinc finger nucleases hold great potential for gene therapy as they allow one to cleave DNA at
      a chosen target sequence.  Unfortunately, however, they also cleave prolifically at off-target
      sites, resulting in unacceptable toxicity.  Two papers in this issue, by Miller et al. and
      Szczepek et al., show that off-target cleavage can be greatly reduced by rationally
      redesigning the ZFN dimer interface to inhibit homodimerization.  The goal of gene therapy is
      to repair genetic defects without othewise modifying the genome.  One of the most promising
      strategies for gene correction is homologous recombination.  In this approach, the correct DNA
      sequence is saupplied in trans and is integrated into the genome by an endogenous mechanism of
      site-specific recombination.  Ideally, the deficient gene is replaced with a functional copy
      in its natural context while leaving the rest of the genome untouched.  Homologous
      recombination can also be used for gene inactivation, insertion or deletion.
AU  - Pingoud A
AU  - Silva GH
PT  - Journal Article
TA  - Nat. Biotechnol.
JT  - Nat. Biotechnol.
SO  - Nat. Biotechnol. 2007 25: 743-744.

PMID- 1892579
VI  - 8
DP  - 1991
TI  - Identification of functional sites in the EcoRV restriction endonuclease by site-directed mutagenesis.
PG  - A165
AB  - Guided by the X-ray structure analysis of a crystalline EcoRV d(GGGATATCCC)
      complex (Winkler, unpublished) we have replaced various amino acid residues in
      EcoRV by site-directed mutagenesis in order to identify those amino acids which
      participate in the binding and cleavage of DNA.  Mutant enzymes were isolated
      and characterized physico-chemically and biochemically.  Our results show that
      three regions are of importance for DNA binding: region I around Ser183,
      Asn185, Thr186 and Asn188, region II around Gln69 and Asn70 and region III
      comprising the C-terminus.  The conservative substitution of these amino acids
      leads to mutant enzymes of no or considerably reduced activity but unaltered
      specificity, indicating that the process of recognition is tightly coupled to
      catalysis and highly redundant.  Region I contains a sequence motif
      (-SerGlyXXXAsnIIeXSer-) which is also found in other restriction enzymes
      recognizing the sequence G--/--C or G-/-C, the dashes representing A or T.
      Region III is homologous to a sequence found in SmaI.  Presumably the catalytic
      center is formed by Asp74 and Asp90, which may serve to bind Mg2+ and activate
      water for a nucleophilic attack, and Lys92 which may hold the scissile
      phosphodiester bond in place.  The mutation of Asp74 to Gln leads to a nearly
      inactive enzyme.  Other mutations are currently being characterized.  It is
      noteworthy that in EcoRI a similar sequence motif (-ProAsp...Glu(Asp)XLys-) is
      found in the vicinity of the scissile phosphodiester bond.
AU  - Pingoud A
AU  - Thielking V
AU  - Selent U
AU  - Kohler E
AU  - Liedtke M
AU  - Wolfes H
AU  - Pieper U
AU  - Geiger R
AU  - Winkler FK
PT  - Journal Article
TA  - J. Biomol. Struct. Dyn.
JT  - J. Biomol. Struct. Dyn.
SO  - J. Biomol. Struct. Dyn. 1991 8: A165.

PMID- 6098296
VI  - 23
DP  - 1984
TI  - Effect of polyamines and basic proteins on cleavage DNA by restriction endonucleases.
PG  - 5697-5703
AB  - We have investigated the effect of the polyamines spermine, spermidine, and
      putrescine and the prokaryotic histone-like proteins NS1 and NS2 on the
      restriction endonuclease EcoRI catalyzed cleavage of plasmid and bacteriophage
      DNAs.  At low concentrations of spermine and spermidine, the rate of DNA
      cleavage by EcoRI is increased, while high concentrations of spermine as well
      as of spermidine are inhibitory.  These phenomena are also observed with other
      restriction endonucleases.  They are, therefore, probably due to the
      interaction of the polyamines with the DNA.  Putrescine does not have such an
      effect within the concentration range investigated.  Remarkably, low
      concentrations of spermine and spermidine very efficiently suppress EcoRI
      activity.  An inhibition of the EcoRI-catalyzed cleavage of DNA is also
      observed with NS1 and NS2, an effect that can be mimicked with other basic
      proteins that interact with DNA.  The results are discussed in terms of the
      mechanism of restriction in vivo.
AU  - Pingoud A
AU  - Urbanke C
AU  - Alves J
AU  - Ehbrecht H-J
AU  - Zabeau M
AU  - Gualerzi C
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1984 23: 5697-5703.

PMID- 17437711
VI  - 15
DP  - 2007
TI  - A sliding restriction enzyme pauses.
PG  - 391-393
AB  - In this issue of Structure, Aggarwal and colleagues (Townson et al., 2007) present the crystal
      structure of the restriction endonuclease BstYI in
      complex with a near-cognate substrate. This structure most likely reflects
      the conformation BstYI adopts as it scans DNA and pauses upon encountering
      a site similar to its recognition sequence.
AU  - Pingoud A
AU  - Wende W
PT  - Journal Article
TA  - Structure
JT  - Structure
SO  - Structure 2007 15: 391-393.

PMID- 21560218
VI  - 12
DP  - 2011
TI  - Generation of Novel Nucleases with Extended Specificity by Rational and Combinatorial Strategies.
PG  - 1495-1500
AB  - After the discovery of DNA as the molecule carrying the hereditary information of all living
      organisms, DNA processing enzymes, in particular restriction endonucleases, led to the
      development of recombinant DNA technology. Today, in the postgenomic era, a steadily growing
      number of entire genome sequences is available.  The emerging genome-engineering technology
      requires more sophisticated nucleases with very high specificity, that ideally target a unique
      sequence in a complex genome.  The design and control of these rare-cutting endonucleases by
      using rational and evolutionary strategies is the focus of this Minireview.
AU  - Pingoud A
AU  - Wende W
PT  - Journal Article
TA  - Chembiochem
JT  - Chembiochem
SO  - Chembiochem 2011 12: 1495-1500.

PMID- 24878924
VI  - 42
DP  - 2014
TI  - Type II restriction endonucleases-a historical perspective and more.
PG  - 7489-7527
AB  - This article continues the series of Surveys and Summaries on restriction endonucleases
      (REases) begun this year in Nucleic Acids Research. Here we discuss 'Type II' REases, the
      kind used for DNA analysis and cloning. We focus on their biochemistry: what they are, what
      they do, and how they do it. Type II REases are produced by prokaryotes to combat
      bacteriophages. With extreme accuracy, each recognizes a particular sequence in
      double-stranded DNA and cleaves at a fixed position within or nearby. The discoveries of these
      enzymes in the 1970s, and of the uses to which they could be put, have since impacted every
      corner of the life sciences. They became the enabling tools of molecular biology, genetics and
      biotechnology, and made analysis at the most fundamental levels routine. Hundreds of different
      REases have been discovered and are available commercially. Their genes have been cloned,
      sequenced and overexpressed. Most have been characterized to some extent, but few have been
      studied in depth. Here, we describe the original discoveries in this field, and the properties
      of the first Type II REases investigated. We discuss the mechanisms of sequence recognition
      and catalysis, and the varied oligomeric modes in which Type II REases act. We describe the
      surprising heterogeneity revealed by comparisons of their sequences and structures.
AU  - Pingoud A
AU  - Wilson GG
AU  - Wende W
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2014 42: 7489-7527.

PMID- 12798682
VI  - 329
DP  - 2003
TI  - PspGI, a type II restriction endonuclease from the extreme thermophile Pyrococcus sp.: structural and functional studies to investigate an evolutionary relationship with several mesophilic restriction enzymes.
PG  - 913-929
AB  - We present here the first detailed biochemical analysis of an archaeal restriction enzyme.
      PspGI shows sequence similarity to SsoII, EcoRII,
      NgoMIV and Cfr10I, which recognize related DNA sequences. We demonstrate
      here that PspGI, like SsoII and unlike EcoRII or NgoMIV and Cfr10I,
      interacts with and cleaves DNA as a homodimer and is not stimulated by
      simultaneous binding to two recognition sites. PspGI and SsoII differ in
      their basic biochemical properties, viz. stability against chemical
      denaturation and proteolytic digestion, DNA binding and the pH, MgCl(2)
      and salt-dependence of their DNA cleavage activity. In contrast, the
      results of mutational analyses and cross-link experiments show that PspGI
      and SsoII have a very similar DNA binding site and catalytic center as
      NgoMIV and Cfr10I (whose crystal structures are known), and presumably
      also as EcoRII, in spite of the fact that these enzymes, which all
      recognize variants of the sequence -/CC-GG- (/ denotes the site of
      cleavage), are representatives of different subgroups of type II
      restriction endonucleases. A sequence comparison of all known restriction
      endonuclease sequences, furthermore, suggests that several enzymes
      recognizing other DNA sequences also share amino acid sequence
      similarities with PspGI, SsoII and EcoRII in the region of the presumptive
      active site. These results are discussed in an evolutionary context.
AU  - Pingoud V
AU  - Conzelmann C
AU  - Kinzebach S
AU  - Sudina A
AU  - Metelev V
AU  - Kubareva E
AU  - Bujnicki JM
AU  - Lurz R
AU  - Luder G
AU  - Xu SY
AU  - Pingoud A
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2003 329: 913-929.

PMID- 16880975
VI  - 1
DP  - 2005
TI  - Identification of base-specific contacts in protein-DNA complexes by photocrosslinking and mass spectrometry: A case study using the  restriction endonuclease SsoII.
PG  - 135-141
AB  - Specific protein-nucleic acid interactions are of paramount importance for the propagation,
      maintenance and expression of genetic information.  Restriction endonucleases serve as model
      systems to study the mechanisms of DNA recognition by proteins.  SsoII is a Type II
      restriction endonuclease that recognizes the double stranded sequence / CCNGG and cleaves it
      in the presence of Mg2+-ions, as indicated.  SsoII shows sequence similarity over a stretch of
      ~70 amino acid residues with several other restriction endonucleases that recognize a similar
      sequence as SsoII (Cfr10I, EcoRII, NgoMIV, PspGI).  In the NgoMIV this stretch is involved in
      DNA recognition and cleavage, as shown by the crystal structure analysis of an enzyme-product
      complex.  To find out whether the presumptive DNA recognition region in SsoII is indeed in
      contact with DNA we have photocrosslinked SsoII with an oligodeoxyribonucleotide in which the
      first guanine of the recognition sequence was replaced by 5-iodouracil.  Following digestion
      by trypsin, the peptide-oligodeoxyribonucleotide conjugate was purified by Fe3+-IMAC and then
      incubated with hydrogen fluoride, which hydrolyzes the oligodeoxyribonucleotide to yield the
      peptide-deoxyuridine conjugate.  The site of photocrosslinking was identified by MALDI-TOF-MS
      and MALDI-TOF-MS/MS to be Trp189, adjacent to Arg188, which aligns with Arg194 in NgoMIV,
      involved in recognition of the second guanine in the NgoMIV recognition sequence G/CCGGC.
      This result confirms previously published conclusions drawn on the basis of a mutational
      analysis of SsoII.  The methodology that was employed here can be used in principle to
      identify the DNA binding site of any protein.
AU  - Pingoud V
AU  - Geyer H
AU  - Geyer R
AU  - Kubareva E
AU  - Bujnicki JM
AU  - Pingoud A
PT  - Journal Article
TA  - Mol. BioSyst.
JT  - Mol. BioSyst.
SO  - Mol. BioSyst. 2005 1: 135-141.

PMID- 9609720
VI  - 37
DP  - 1998
TI  - Structural and functional analysis of the homing endonuclease PI-SceI by limited proteolytic cleavage and molecular cloning of partial digestion products.
PG  - 8233-8243
AB  - PI-SceI is a member of an unusual class of rare cutting homing endonucleases produced by an
      autocatalytic protein splicing from a precursor.  To analyze the structural and functional
      domain organization of the endonuclease PI-SceI and to examine whether the DNA binding
      activity can be structurally separated from the catalytic activity, we performed limited
      proteolytic digestion experiments with various proteases.  Two protease-resistant fragments
      spanning the N- and C-terminal halves of the nuclease were identified using different
      proteases which cleave the protein in the same region. Each fragment contains one of the two
      conserved LAGLIDADG motifs.  The products of the limited proteolytic digests were shown to
      remain associated and to exhibit specific DNA binding but to be inactive in DNA cleavage.
      Different from what is observed with native PI-SceI, only one complex is formed as shown in an
      electrophoretic mobility shift assay.  Expression clones for the N- and C-terminal protein
      fragments obtained by tryptic digestion were constructed, and the proteins PI-SceI-N and
      PI-SceI-C were purified.  Only PI-SceI-N exhibits DNA binding activity.  Bending experiments
      with PI-SceI-N, a mixture of PI-SceI-N and PI-SceI-C, as well as the products of the limited
      tryptic digest show that a DNA substrate with the full length recognition sequence is bent by
      45 degrees.  This degree of bending is also observed with a DNA containing only the right side
      of the recognition sequence, corresponding to one of the DNA cleavage products of PI-SceI.
      Our results demonstrate that the N-terminal half of PI-SceI which lacks one of the two
      LAGLDADG motifs is able to bind to DNA specifically and to induce one of the distortions
      observed to occur in the process of DNA binding by PI-SceI.  These results are discussed in
      light of the recently solve crystal structure of PI-SceI and used to refine a model for the
      mechanism of DNA binding and cleavage by PI-SceI.
AU  - Pingoud V
AU  - Grindl W
AU  - Wende W
AU  - Thole H
AU  - Pingoud A
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1998 37: 8233-8243.

PMID- 11827971
VI  - 277
DP  - 2002
TI  - Evolutionary relationship between different subgroups of restriction endonucleases.
PG  - 14306-14314
AB  - The type II restriction endonuclease SsoII shows sequence similarity with 10 other restriction
      endonucleases, among them the type IIE
      restriction endonuclease EcoRII, which requires binding to an effector
      site for efficient DNA cleavage, and the type IIF restriction
      endonuclease NgoMIV, which is active as a homotetramer and cleaves DNA
      with two recognition sites in a concerted reaction. We show here that
      SsoII is an orthodox type II enzyme, which is active as a homodimer and
      does not require activation by binding to an effector site.
      Nevertheless, it shares with EcoRII and NgoMIV a very similar
      DNA-binding site and catalytic center as shown here by a mutational
      analysis, indicative of an evolutionary relationship between these
      three enzymes. We suggest that a similar relationship exists between
      other orthodox type II, type IIE, and type IIF restriction
      endonucleases. This may explain why similarities may be more pronounced
      between members of different subtypes of restriction enzymes than among
      the members of a given subtype.
AU  - Pingoud V
AU  - Kubareva E
AU  - Stengel G
AU  - Friedhoff P
AU  - Bujnicki JM
AU  - Urbanke C
AU  - Sudina A
AU  - Pingoud A
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2002 277: 14306-14314.

PMID- 15563460
VI  - 280
DP  - 2005
TI  - Specificity changes in the evolution of Type II restriction endonucleases - A biochemical and bioinformatic analysis of restriction  enzymes that recognize unrelated sequences.
PG  - 4289-4298
AB  - How restriction enzymes with their different specificities and mode of cleavage evolved has
      been a long standing question in evolutionary
      biology. We have recently shown that several Type II restriction
      endonucleases, namely SsoII (down arrow CCNGG), PspGI (^CCWGG), Eco-RII (^CCWGG), NgoMIV
      (G^CCGGC), and Cfr10I (R^CCGGY), which recognize similar DNA sequences (as indicated, where ^
      denotes cleavage position), share limited
      sequence similarity over an interrupted stretch of approximately 70 amino
      acid residues with MboI, a Type II restriction endonuclease from
      Moraxella bovis (Pingoud, V., Conzelmann, C., Kinzebach, S., Sudina,
      A., Metelev, V., Kubareva, E., Bujnicki, J.M., Lurz, R., Luder, G., Xu,
      S. Y., and Pingoud, A. (2003) J. Mol. Biol 329, 913-929). Nevertheless,
      MboI has a dissimilar DNA specificity (^GATC) compared with
      these enzymes. In this study, we characterize MboI in detail to
      determine whether it utilizes a mechanism of DNA recognition similar to
      SsoII, PspGI, EcoRII, NgoMIV, and Cfr10I. Mutational analyses and
      photocross-linking experiments demonstrate that MboI exploits the
      stretch of approximately 70 amino acids for DNA recognition and cleavage.
      It is therefore likely that MboI shares a common evolutionary origin
      with SsoII, PspGI, EcoRII, NgoMIV, and Cfr10I. This is the first
      example of a relatively close evolutionary link between Type
      II restriction enzymes of widely different specificities.
AU  - Pingoud V
AU  - Sudina A
AU  - Geyer H
AU  - Bujnicki JM
AU  - Lurz R
AU  - Luder G
AU  - Morgan R
AU  - Kubareva E
AU  - Pingoud A
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2005 280: 4289-4298.

PMID- 10187809
VI  - 274
DP  - 1999
TI  - Photocross-linking of the homing endonuclease PI-SceI to its recognition sequence.
PG  - 10235-10243
AB  - PI-SceI is an intein-encoded protein that belongs to the LAGLIDADG family of homing
      endonucleases.  According to the crystal structure and mutational studies, this endonuclease
      consists of two domains, one responsible for protein splicing, the other for DNA cleavage, and
      both presumably for DNA binding.  To define the DNA binding site of PI-SceI,
      photocross-linking was used to identify amino acid residues in contact with DNA.  Sixty-three
      double-stranded oligodeoxynucleotides comprising the minimal recognition sequence and
      containing single 5-iodopyrimidine substitutions in almost all positions of the recognition
      sequence were synthesized and irradiated in the presence of PI-SceI with a helium/cadmium
      laser (325 nm).  The best cross-linking yield (approximately 30%) was obtained with an
      oligodeoxynucleotide with a 5-iododeoxyuridine at position +9 in the bottom strand.  The
      subsequent analysis showed that cross-linking had occurred with amino acid His-333, 6 amino
      acids after the second LAGLIDADG motif.  With the H333A variant of PI-SceI or in the presence
      of excess unmodified oligodeoxynucleotide, no cross-linking was observed, indicating the
      specificity of the cross-linking reaction.  Chemical modification of His residues in PI-SceI
      by diethylpyrocarbonate leads to a substantial reduction in the binding and cleavage activity
      of PI-SceI.  This inactivation can be suppressed by substrate binding.  This result further
      supports the finding that at least one His residue is in close contact to the DNA.  Based on
      these and published results, conclusions are drawn regarding the DNA binding site of PI-SceI.
AU  - Pingoud V
AU  - Thole H
AU  - Christ F
AU  - Grindl W
AU  - Wende W
AU  - Pingoud A
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1999 274: 10235-10243.

PMID- 19682999
VI  - 393
DP  - 2009
TI  - On the Divalent Metal Ion Dependence of DNA Cleavage by Restriction Endonucleases of the EcoRI Family.
PG  - 140-160
AB  - Restriction endonucleases of the PD...D/EXK family need Mg(2+) for DNA cleavage. Whereas
      Mg(2+) (or Mn(2+)) promotes catalysis, Ca(2+) (without
      Mg(2+)) only supports DNA binding. The role of Mg(2+) in DNA cleavage by
      restriction endonucleases has elicited many hypotheses, differing mainly
      in the number of Mg(2+) involved in catalysis. To address this problem, we
      measured the Mg(2+) and Mn(2+) concentration dependence of DNA cleavage by
      BamHI, BglII, Cfr10I, EcoRI, EcoRII (catalytic domain), MboI, NgoMIV,
      PspGI, and SsoII, which were reported in co-crystal structure analyses to
      bind one (BglII and EcoRI) or two (BamHI and NgoMIV) Me(2+) per active
      site. DNA cleavage experiments were carried out at various Mg(2+) and
      Mn(2+) concentrations at constant ionic strength. All enzymes show a
      qualitatively similar Mg(2+) and Mn(2+) concentration dependence. In
      general, the Mg(2+) concentration optimum (between approximately 1 and 10
      mM) is higher than the Mn(2+) concentration optimum (between approximately
      0.1 and 1 mM). At still higher Mg(2+) or Mn(2+) concentrations, the
      activities of all enzymes tested are reduced but can be reactivated by
      Ca(2+). Based on these results, we propose that one Mg(2+) or Mn(2+) is
      critical for restriction enzyme activation, and binding of a second Me(2+)
      plays a role in modulating the activity. Steady-state kinetics carried out
      with EcoRI and BamHI suggest that binding of a second Mg(2+) or Mn(2+)
      mainly leads to an increase in K(m), such that the inhibitory effect of
      excess Mg(2+) or Mn(2+) can be overcome by increasing the substrate
      concentration. Our conclusions are supported by molecular dynamics
      simulations and are consistent with the structural observations of both
      one and two Me(2+) binding to these enzymes.
AU  - Pingoud V
AU  - Wende W
AU  - Friedhoff P
AU  - Reuter M
AU  - Alves J
AU  - Jeltsch A
AU  - Mones L
AU  - Fuxreiter M
AU  - Pingoud A
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2009 393: 140-160.

PMID- 26769942
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Two Novel Acidimicrobiaceae Members from an Acid Mine Drainage Biofilm Metagenome.
PG  - e01563-15
AB  - Bacteria belonging to the family Acidimicrobiaceae are frequently encountered in  heavy
      metal-contaminated acidic environments. However, their phylogenetic and
      metabolic diversity is poorly resolved. We present draft genome sequences of two
      novel and phylogenetically distinct Acidimicrobiaceae members assembled from an
      acid mine drainage biofilm metagenome.
AU  - Pinto AJ
AU  - Sharp JO
AU  - Yoder MJ
AU  - Almstrand R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01563-15.

PMID- 30410642
VI  - 13
DP  - 2018
TI  - Draft genome sequence of Bacillus amyloliquefaciens subsp. plantarum strain Fito_F321, an endophyte microorganism from Vitis vinifera with biocontrol potential.
PG  - 30
AB  - Bacillus amyloliquefaciens subsp. plantarum strain Fito_F321 is a naturally occurring strain
      in vineyard, with the ability to colonise grapevine and which
      unveils a naturally antagonistic potential against phytopathogens of grapevine,
      including those responsible for the Botryosphaeria dieback, a GTD disease. Herein
      we report the draft genome sequence of B. amyloliquefaciens subsp. plantarum
      Fito_F321, isolated from the leaf of Vitis vinifera cv. Merlot at Bairrada
      appellation (Cantanhede, Portugal). The genome size is 3,856,229 bp, with a GC
      content of 46.54% that contains 3697 protein-coding genes, 86 tRNA coding genes
      and 5 rRNA genes. The draft genome of strain Fito_F321 allowed to predict a set
      of bioactive compounds as bacillaene, difficidin, macrolactin, surfactin and
      fengycin that due to their antimicrobial activity are hypothesized to be of
      utmost importance for biocontrol of grapevine diseases.
AU  - Pinto C
AU  - Sousa S
AU  - Froufe H
AU  - Egas C
AU  - Clement C
AU  - Fontaine F
AU  - Gomes AC
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2018 13: 30.

PMID- 29167244
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Planktic Cyanobacterium Tychonema bourrellyi, Isolated from Alpine Lentic Freshwater.
PG  - e01294-17
AB  - We describe here the draft genome sequence of the cyanobacterium Tychonema bourrellyi,
      assembled from a metagenome of a nonaxenic culture. The strain
      (FEM_GT703) was isolated from a freshwater sample taken from Lake Garda, Italy.
      The draft genome sequence represents the first assembled T. bourrellyi strain.
AU  - Pinto F
AU  - Tett A
AU  - Armanini F
AU  - Asnicar F
AU  - Boscaini A
AU  - Pasolli E
AU  - Zolfo M
AU  - Donati C
AU  - Salmaso N
AU  - Segata N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01294-17.

PMID- 29437085
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Novel Pseudomonas, Flavobacterium, and Sediminibacterium Species Strains from a Freshwater Ecosystem.
PG  - e00009-18
AB  - Freshwater ecosystems represent 0.01% of the water on Earth, but they support 6%  of global
      biodiversity that is still mostly uncharacterized. Here, we describe
      the genome sequences of three strains belonging to novel species in the
      Pseudomonas, Flavobacterium, and Sediminibacterium genera recovered from a water
      sample of Lake Garda, Italy.
AU  - Pinto F
AU  - Tett A
AU  - Armanini F
AU  - Asnicar F
AU  - Boscaini A
AU  - Pasolli E
AU  - Zolfo M
AU  - Donati C
AU  - Salmaso N
AU  - Segata N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00009-18.

PMID- 24204251
VI  - 9
DP  - 2013
TI  - Transcriptional Regulation of Culex pipiens Mosquitoes by Wolbachia Influences Cytoplasmic Incompatibility.
PG  - E1003647
AB  - Cytoplasmic incompatibility (CI) induced by the endosymbiont Wolbachia pipientis
      causes complex patterns of crossing sterility between populations of the Culex
      pipiens group of mosquitoes. The molecular basis of the phenotype is yet to be
      defined. In order to investigate what host changes may underlie CI at the
      molecular level, we examined the transcription of a homolog of the Drosophila
      melanogaster gene grauzone that encodes a zinc finger protein and acts as a
      regulator of female meiosis, in which mutations can cause sterility. Upregulation
      was observed in Wolbachia-infected C. pipiens group individuals relative to
      Wolbachia-cured lines and the level of upregulation differed between lines that
      were reproductively incompatible. Knockdown analysis of this gene using RNAi
      showed an effect on hatch rates in a Wolbachia infected Culex molestus line.
      Furthermore, in later stages of development an effect on developmental
      progression in CI embryos occurs in bidirectionally incompatible crosses. The
      genome of a wPip Wolbachia strain variant from Culex molestus was sequenced and
      compared with the genome of a wPip variant with which it was incompatible. Three
      genes in inserted or deleted regions were newly identified in the C. molestus
      wPip genome, one of which is a transcriptional regulator labelled wtrM. When this
      gene was transfected into adult Culex mosquitoes, upregulation of the grauzone
      homolog was observed. These data suggest that Wolbachia-mediated regulation of
      host gene expression is a component of the mechanism of cytoplasmic
      incompatibility.
AU  - Pinto SB
AU  - Stainton K
AU  - Harris S
AU  - Kambris Z
AU  - Sutton ER
AU  - Bonsall MB
AU  - Parkhill J
AU  - Sinkins SP
PT  - Journal Article
TA  - PLoS Pathog.
JT  - PLoS Pathog.
SO  - PLoS Pathog. 2013 9: E1003647.

PMID- 3663209
VI  - 147
DP  - 1987
TI  - Adenine methylation in zein genes.
PG  - 1082-1087
AB  - This paper reports the novel finding of adenine methylation in higher plants. Comparison of
      restriction patterns of genomic maize DNA digested with enzymes MboI and Sau3AI enabled us to
      detect the existence of adenine methylation in zein genes. Adenine methylation within or
      around zein genes turned out to be similar in endosperm (where zeins are actively synthesized)
      and in seedling tissue (where zein genes are not expressed). Furthermore, adenine methylation
      patterns were found to be similar both in wild-type and opaque-2 mutant plants. These lines of
      evidence suggest that adenine methylation is unrelated to the regulation of gene expression.
AU  - Pintor-Toro JA
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1987 147: 1082-1087.

PMID- 23814109
VI  - 1
DP  - 2013
TI  - Genome Sequence of Plesiomonas shigelloides Strain 302-73 (Serotype O1).
PG  - e00404-13
AB  - Plesiomonas shigelloides, the only species of the genus, is an emergent pathogenic bacterium
      associated with human diarrheal and extraintestinal disease.
      We present the whole-genome sequence analysis of the representative strain for
      the O1 serotype (strain 302-73), providing a tool for studying bacterial
      outbreaks, virulence factors, and accurate diagnostic methods.
AU  - Pique N
AU  - Aquilini E
AU  - Alioto T
AU  - Minana-Galbis D
AU  - Tomas JM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00404-13.

PMID- 26404589
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Pseudomonas aeruginosa Phage vB_PaeM_CEB_DP1.
PG  - e00918-15
AB  - vB_PaeM_CEB_DP1 is a Pseudomonas aeruginosa bacteriophage (phage) belonging to the
      Pbunalikevirus genus of the Myoviridae family of phages. It was isolated from hospital sewage.
      vB_PaeM_CEB_DP1 is a double-stranded DNA (dsDNA) phage, with a genome of 66,158 bp, containing
      89 predicted open reading frames.
AU  - Pires DP
AU  - Sillankorva S
AU  - Kropinski AM
AU  - Lu TK
AU  - Azeredo J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00918-15.

PMID- 25860355
VI  - 10
DP  - 2015
TI  - Genome-Wide Methylation Patterns in Salmonella enterica Subsp. enterica Serovars.
PG  - e0123639
AB  - The methylation of DNA bases plays an important role in numerous biological processes
      including development, gene expression, and DNA replication. Salmonella
      is an important foodborne pathogen, and methylation in Salmonella is implicated
      in virulence. Using single molecule real-time (SMRT) DNA-sequencing, we sequenced
      and assembled the complete genomes of eleven Salmonella enterica isolates from
      nine different serovars, and analysed the whole-genome methylation patterns of
      each genome. We describe 16 distinct N6-methyladenine (m6A) methylated motifs,
      one N4-methylcytosine (m4C) motif, and one combined m6A-m4C motif. Eight of these
      motifs are novel, i.e., they have not been previously described. We also
      identified the methyltransferases (MTases) associated with 13 of the motifs. Some
      motifs are conserved across all Salmonella serovars tested, while others were
      found only in a subset of serovars. Eight of the nine serovars contained a unique
      methylated motif that was not found in any other serovar (most of these motifs
      were part of Type I restriction modification systems), indicating the high
      diversity of methylation patterns present in Salmonella.
AU  - Pirone-Davies C
AU  - Hoffmann M
AU  - Roberts RJ
AU  - Muruvanda T
AU  - Timme RE
AU  - Strain E
AU  - Luo Y
AU  - Payne J
AU  - Luong K
AU  - Song Y
AU  - Tsai YC
AU  - Boitano M
AU  - Clark TA
AU  - Korlach J
AU  - Evans PS
AU  - Allard MW
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2015 10: e0123639.

PMID- 967673
VI  - 3
DP  - 1976
TI  - Two restriction endonucleases from Bacillus globigii.
PG  - 1747-1760
AB  - The sites of action of the restriction enzyme BglII on lambda DNA are mapped. This enzyme
      recognises the sequence 5'...AGATCT...3' and makes staggered cuts producing sticky ends. In
      lambda DNA, the second A in this sequence is methylated about 50% of the time by a bacterial
      methylase absent in E. coli dam-. In contrast to BglII, BglI makes many cuts in lambda DNA and
      produces 5' terminals which are not substrates for polynucleotide kinase.
AU  - Pirrotta V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1976 3: 1747-1760.

PMID- 6246381
VI  - 65
DP  - 1980
TI  - General purification schemes for restriction endonucleases.
PG  - 89-95
AB  - The range of organisms used for the production of restriction enzymes and the
      various properties of these enzymes is such that it is difficult to devise a
      purification scheme of general application.  the combination of
      polyethyleneimine precipitation and chromatography on heparin-agarose discussed
      in this article has a sufficiently wide applicability and a number of
      advantages to recommend it as the backbone of a general purification scheme or
      as a first approach in the isolation of new restriction endonuclease
      activities.  In individual cases, however, additions or modifications of this
      procedure are necessary to optimize the results.  In this article we will first
      present the basic procedure and then discuss alternatives or modifications
      suitable to certain particular cases.
AU  - Pirrotta V
AU  - Bickle TA
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1980 65: 89-95.

PMID- 21304740
VI  - 3
DP  - 2010
TI  - Complete genome sequence of Thermosediminibacter oceani type strain (JW/IW-1228P).
PG  - 108-116
AB  - Thermosediminibacter oceani (Lee et al. 2006) is the type species of the genus
      Thermosediminibacter in the family Thermoanaerobacteraceae. The anaerobic,
      barophilic, chemoorganotrophic thermophile is characterized by straight to curved
      Gram-negative rods. The strain described in this study was isolated from a core
      sample of deep sea sediments of the Peruvian high productivity upwelling system.
      This is the first completed genome sequence of a member of the genus
      Thermosediminibacter and the seventh genome sequence in the family
      Thermoanaerobacteraceae. The 2,280,035 bp long genome with its 2,285
      protein-coding and 63 RNA genes is a part of the Genomic Encyclopedia of Bacteria
      and Archaea project.
AU  - Pitluck S et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 3: 108-116.

PMID- 21304733
VI  - 3
DP  - 2010
TI  - Non-contiguous finished genome sequence of Aminomonas paucivorans type strain (GLU-3).
PG  - 285-293
AB  - Aminomonas paucivorans Baena et al. 1999 is the type species of the genus Aminomonas, which
      belongs to the family Synergistaceae. The species is of
      interest because it is an asaccharolytic chemoorganotrophic bacterium which
      ferments quite a number of amino acids. This is the first finished genome
      sequence (with one gap in a rDNA region) of a member of the genus Aminomonas and
      the third sequence from the family Synergistaceae. The 2,630,120 bp long genome
      with its 2,433 protein-coding and 61 RNA genes is a part of the
      GenomicEncyclopedia ofBacteria andArchaea project.
AU  - Pitluck S et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 3: 285-293.

PMID- 21475587
VI  - 4
DP  - 2011
TI  - Complete genome sequence of Calditerrivibrio nitroreducens type strain (Yu37-1).
PG  - 54-62
AB  - Calditerrivibrio nitroreducens Iino et al. 2008 is the type species of the genus
      Calditerrivibrio. The species is of interest because of its important role in the
      nitrate cycle as nitrate reducer and for its isolated phylogenetic position in
      the Tree of Life. Here we describe the features of this organism, together with
      the complete genome sequence and annotation. This is the third complete genome
      sequence of a member of the family Deferribacteraceae. The 2,216,552 bp long
      genome with its 2,128 protein-coding and 50 RNA genes is a part of the Genomic
      Encyclopedia of Bacteria and Archaea project.
AU  - Pitluck S et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 4: 54-62.

PMID- 9279140
VI  - 11
DP  - 1997
TI  - Effects of increasing DCM expression on Vsr repair of site specific and related sequences.
PG  - A1369
AB  - DCM, the only cytosine methylase in Escherichia coli, methylates the second cytosine of this
      specific site: CCAGG.  However, overexpression of dcm leads to methylation of other related
      sequences as well.  5-methylcytosine spontaneously deaminates to thymine.  Vsr repairs T/G
      mismatches, and restores the cytosine both at CTAGG sites and at related sequences.  Our
      experiments aim to demonstrate what sequences are methylated by Dcm and which ones are
      repaired by Vsr, and show if there is overlap between the two.  We have regulated the
      expression of Dcm by placing dcm under the PBAD promoter and by varying the concentration of
      arabinose from 0% to 0.2%.  The results showed variation over 3 orders of magnitude in Dcm
      expression.  Further work will be done to analyze Vsr repair.
AU  - Pitsikas P
AU  - Cupples C
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1997 11: A1369.

PMID- Not carried by PubMed...
VI  - 99
DP  - 1999
TI  - Fate of Dcm cytosine methylase after treatment of Escherichia coli with 5-Azacytidine.
PG  - 334
AB  - 5-azacytidine is a chemotherapeutic agent used in the treatment of leukemia.  When
      incorporated into DNA as 5-azacytosine, it causes C-to-G transversion mutations.  In addition,
      when it replaces cytosine in methylase recognition sites, transfer of the methyl group cannot
      take place, and the enzyme remains covalently bound to the DNA.  The resulting inactivation of
      the methyltransferase leads to DNA demethylation.  We are interested in determining how the
      DNA-methylase complexes are removed, how the DNA is repaired, and what becomes of the enzyme.
      As a first step, we have made an antibody to Dcm, the sole cytosine methylase in Escherichia
      coli, and used it to quantify the levels of free protein present in the cells after treatment
      with 5-azacytidine.  We find that levels of analog which are sufficient to cause an increase
      in C-to-G mutations result in a large reduction in the amount of Dcm.  The levels of an
      enzymatically inactive mutant are unaffected.  Transcription of the dcm gene is apparently not
      autoregulated.  We are currently combining western analysis with Southern analysis to
      determine the fate of the DNA/protein complexes.
AU  - Pitsikas P
AU  - Cupples CG
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1999 99: 334.

PMID- 29431605
VI  - 0
DP  - 2018
TI  - Multifactorial chromosomal variants regulate polymyxin resistance in extensively drug-resistant Klebsiella pneumoniae.
PG  - 0
AB  - Extensively drug-resistant Klebsiella pneumoniae (XDR-KP) infections cause high
      mortality and are disseminating globally. Identifying the genetic basis
      underpinning resistance allows for rapid diagnosis and treatment. XDR isolates
      sourced from Greece and Brazil, including 19 polymyxin-resistant and five
      polymyxin-susceptible strains, were subjected to whole genome sequencing.
      Seventeen of the 19 polymyxin-resistant isolates harboured variations upstream or
      within mgrB. The most common mutation identified was an insertion at nucleotide
      position 75 in mgrB via an ISKpn26-like element in the ST258 lineage and ISKpn13
      in one ST11 isolate. Three strains acquired an IS1 element upstream of mgrB and
      another strain had an ISKpn25 insertion at 133 bp. Other isolates had truncations
      (C28STOP, Q30STOP) or a missense mutation (D29E) affecting mgrB. Complementation
      assays revealed all mgrB perturbations contributed to resistance. Missense
      mutations in phoQ (T281M, G385C) were also found to facilitate resistance.
      Several variants in phoPQ co-segregating with the ISKpn26-like insertion were
      identified as potential partial suppressor mutations. Three ST258 samples were
      found to contain subpopulations with different resistance-conferring mutations,
      including the ISKpn26-like insertion colonizing with a novel mutation in pmrB
      (P158R), both confirmed via complementation assays. These findings highlight the
      broad spectrum of chromosomal modifications which can facilitate and regulate
      resistance against polymyxins in K. pneumoniae.
AU  - Pitt ME
AU  - Elliott AG
AU  - Cao MD
AU  - Ganesamoorthy D
AU  - Karaiskos I
AU  - Giamarellou H
AU  - Abboud CS
AU  - Blaskovich MA
AU  - Cooper MA
AU  - Coin LJ
PT  - Journal Article
TA  - Microbial Genomics
JT  - Microbial Genomics
SO  - Microbial Genomics 2018 0: 0.

PMID- 5334975
VI  - 87
DP  - 1964
TI  - Effect of phage-controlled restriction on genetic links in bacterial crosses.
PG  - 1256-1257
AB  - Arber and Dussoix (J. Mol. Biol. 5:18, 1962) demonstrated that
      lambda-bacteriophage, when grown on Escherichia coli K-12, plates with an
      efficiency of 1 on E. coli K-12 but with an efficiency of only 2 X 10-5 on E.
      coli K-12 (P1) which is lysogenic for bacteriophage Pl.  They showed that the
      low efficiency of plating is a result of the breakdown of the
      lambda-deoxyribonucleic acid (DNA) injected into the Pl lysogenic host. The
      present paper reports some studies of recombination between a P1 sensitive Hfr,
      AB2229, and a P1 lysogenic recipient, AB2147, in which two effects of
      restriction on the recovery of recombinants were observed.
AU  - Pittard J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1964 87: 1256-1257.

PMID- 22328764
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of the Beer Spoilage Organism Pediococcus claussenii ATCC BAA-344T.
PG  - 1271-1272
AB  - Pediococcus claussenii is a common brewery contaminant. We have sequenced the chromosome and
      plasmids of the type strain P. claussenii ATCC BAA-344. A ropy
      variant was chosen for sequencing to obtain genetic information related to growth
      in beer, as well as exopolysaccharide and possibly biofilm formation by this
      organism.
AU  - Pittet V
AU  - Abegunde T
AU  - Marfleet T
AU  - Haakensen M
AU  - Morrow K
AU  - Jayaprakash T
AU  - Schroeder K
AU  - Trost B
AU  - Byrns S
AU  - Bergsveinson J
AU  - Kusalik A
AU  - Ziola B
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1271-1272.

PMID- 22247527
VI  - 194
DP  - 2012
TI  - Genome Sequence of Lactobacillus rhamnosus ATCC 8530.
PG  - 726
AB  - Lactobacillus rhamnosus is found in the human gastrointestinal tract and is important for
      probiotics. We became interested in L. rhamnosus isolate
      ATCC 8530 in relation to beer spoilage and hops resistance. We report here
      the genome sequence of this isolate, along with a brief comparison to
      other available L. rhamnosus genome sequences.
AU  - Pittet V
AU  - Ewen E
AU  - Bushell BR
AU  - Ziola B
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 726.

PMID- 28509398
VI  - 105
DP  - 2017
TI  - The multicomponent antirestriction system of phage P1 is linked to capsid morphogenesis.
PG  - 399-412
AB  - Bacterial Type I restriction-modification (R-M) systems present a major barrier to foreign DNA
      entering the bacterial cell. The temperate phage P1 packages
      several proteins into the virion that protect the phage DNA from host
      restriction. Isogenic P1 deletion mutants were used to reconstitute the
      previously described restriction phenotypes associated with darA and darB. While
      P1DeltadarA and P1DeltadarB produced the expected phenotypes, deletions of
      adjacent genes hdf and ddrA also produced darA-like phenotypes and deletion of
      ulx produced a darB-like phenotype, implicating several new proteins of
      previously unknown function in the P1 dar antirestriction system. Interestingly,
      disruption of ddrB decreased P1's sensitivity to EcoB and EcoK restriction.
      Proteomic analysis of purified virions suggests that packaging of antirestriction
      components into P1 virions follows a distinct pathway that begins with the
      incorporation of DarA and Hdf and concludes with DarB and Ulx. Electron
      microscopy analysis showed that hdf and darA mutants also produce abnormally high
      proportions of virions with aberrant small heads, which suggests Hdf and DarA
      play a role in capsid morphogenesis. The P1 antirestriction system is more
      complex than previously realized and is comprised of multiple proteins including
      DdrA, DdrB, Hdf, and Ulx in addition to DarA and DarB.
AU  - Piya D
AU  - Vara L
AU  - Russell WK
AU  - Young R
AU  - Gill JJ
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2017 105: 399-412.

PMID- 26048971
VI  - 212
DP  - 2015
TI  - Parallel Epidemics of Community-Associated Methicillin-Resistant Staphylococcus aureus USA300 Infection in North and South America.
PG  - 1874-1882
AB  - BACKGROUND: The community-associated methicillin-resistant Staphylococcus aureus
      (CA-MRSA) epidemic in the United States is attributed to the spread of the USA300
      clone. An epidemic of CA-MRSA closely related to USA300 has occurred in northern
      South America (USA300 Latin-American variant, USA300-LV). Using phylogenomic
      analysis, we aimed to understand the relationships between these 2 epidemics.
      METHODS: We sequenced the genomes of 51 MRSA clinical isolates collected between
      1999 and 2012 from the United States, Colombia, Venezuela, and Ecuador.
      Phylogenetic analysis was used to infer the relationships and times since the
      divergence of the major clades. RESULTS: Phylogenetic analyses revealed 2
      dominant clades that segregated by geographical region, had a putative common
      ancestor in 1975, and originated in 1989, in North America, and in 1985, in South
      America. Emergence of these parallel epidemics coincides with the independent
      acquisition of the arginine catabolic mobile element (ACME) in North American
      isolates and a novel copper and mercury resistance (COMER) mobile element in
      South American isolates. CONCLUSIONS: Our results reveal the existence of 2
      parallel USA300 epidemics that shared a recent common ancestor. The simultaneous
      rapid dissemination of these 2 epidemic clades suggests the presence of shared,
      potentially convergent adaptations that enhance fitness and ability to spread.
AU  - Planet PJ et al
PT  - Journal Article
TA  - J. Infect. Dis.
JT  - J. Infect. Dis.
SO  - J. Infect. Dis. 2015 212: 1874-1882.

PMID- 23405291
VI  - 1
DP  - 2013
TI  - Genome Sequence of the Human Abscess Isolate Streptococcus intermedius BA1.
PG  - e00117-12
AB  - Streptococcus intermedius is a human pathogen with a propensity for abscess formation. We
      report a high-quality draft genome sequence of S. intermedius strain BA1, an isolate from a
      human epidural abscess. This sequence provides insight into the biology of S. intermedius and
      will aid investigations of pathogenicity.
AU  - Planet PJ
AU  - Rampersaud R
AU  - Hymes SR
AU  - Whittier S
AU  - Della-Latta PA
AU  - Narechania A
AU  - Daugherty SC
AU  - Santana-Cruz I
AU  - Desalle R
AU  - Ravel J
AU  - Ratner AJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00117-12.

PMID- 23580708
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences of Five Yersinia pseudotuberculosis ST19 Isolates and One  Isolate Variant.
PG  - e00122-13
AB  - We report the first draft genome sequences of five Yersinia pseudotuberculosis isolates of
      sequence type (ST) 19 and of a variant from one of the five isolates.
      The total length of assemblies ranged from 4,226,485 bp to 4,274,148 bp,
      including between 3,808 and 3,843 predicted coding sequences.
AU  - Platonov ME
AU  - Blouin Y
AU  - Evseeva VV
AU  - Afanas'ev MV
AU  - Pourcel C
AU  - Balakhonov SV
AU  - Vergnaud G
AU  - Anisimov AP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00122-13.

PMID- 26804559
VI  - 26
DP  - 2016
TI  - Bacterial Autoimmunity Due to a Restriction-Modification System.
PG  - 404-409
AB  - Restriction-modification (RM) systems represent a minimal and ubiquitous biological system of
      self/non-self discrimination in prokaryotes [1], which
      protects hosts from exogenous DNA [2]. The mechanism is based on the balance
      between methyltransferase (M) and cognate restriction endonuclease (R). M tags
      endogenous DNA as self by methylating short specific DNA sequences called
      restriction sites, whereas R recognizes unmethylated restriction sites as
      non-self and introduces a double-stranded DNA break [3]. Restriction sites are
      significantly underrepresented in prokaryotic genomes [4-7], suggesting that the
      discrimination mechanism is imperfect and occasionally leads to autoimmunity due
      to self-DNA cleavage (self-restriction) [8]. Furthermore, RM systems can promote
      DNA recombination [9] and contribute to genetic variation in microbial
      populations, thus facilitating adaptive evolution [10]. However, cleavage of
      self-DNA by RM systems as elements shaping prokaryotic genomes has not been
      directly detected, and its cause, frequency, and outcome are unknown. We quantify
      self-restriction caused by two RM systems of Escherichia coli and find that, in
      agreement with levels of restriction site avoidance, EcoRI, but not EcoRV,
      cleaves self-DNA at a measurable rate. Self-restriction is a stochastic process,
      which temporarily induces the SOS response, and is followed by DNA repair,
      maintaining cell viability. We find that RM systems with higher restriction
      efficiency against bacteriophage infections exhibit a higher rate of
      self-restriction, and that this rate can be further increased by stochastic
      imbalance between R and M. Our results identify molecular noise in RM systems as
      a factor shaping prokaryotic genomes.
AU  - Pleska M
AU  - Qian L
AU  - Okura R
AU  - Bergmiller T
AU  - Wakamoto Y
AU  - Kussell E
AU  - Guet CC
PT  - Journal Article
TA  - Curr. Biol.
JT  - Curr. Biol.
SO  - Curr. Biol. 2016 26: 404-409.

PMID- 1551570
VI  - 130
DP  - 1992
TI  - Site-specific recombination determined by I-SceI, a mitochondrial group I intron-encoded endonuclease expressed in the yeast nucleus.
PG  - 451-460
AB  - The Saccharomyces cerevisiae mitochondrial endonuclease I-SceI creates a double-strand break
      as the initiating step in the gene conversional transfer of the omega+ intron to omega- DNA.
      We have expressed a glactose-inducible synthetic I-SceI gene in the nucleus of yeast that also
      carries the I-SceI recognition site on a plasmid substrate.  We find that the
      galactose-induced I-SceI protein can be active in the nucleus and efficiently catalyze
      recombination.  With a target plasmid containing direct repeats of the Escherichia coli lacZ
      gene, one copy of which is interrupted by a 24-bp cutting site, galactose induction produces
      both deletions and gene conversions.  Both the kinetics and the proportion of deletions and
      gene conversions are very similar to analogous events initiated by a galactose-inducible HO
      endonuclease gene.  We also find that, in a rad52 mutant strain, the repair of double-strand
      breaks initiated by I-SceI and by HO are similarly affected: the formation of deletions is
      reduced, but not eliminated.  Altogether, these results suggest either that the two
      endonucleases act in the same way after double-strand break formation or that the two
      endonucleases are not involved in subsequent steps.
AU  - Plessis A
AU  - Perrin A
AU  - Haber JE
AU  - Dujon B
PT  - Journal Article
TA  - Genetics
JT  - Genetics
SO  - Genetics 1992 130: 451-460.

PMID- 12643710
VI  - 125
DP  - 2003
TI  - Design of a new fluorescent cofactor for DNA methyltransferases and sequence-specific labeling of DNA.
PG  - 3486-3492
AB  - Sequence-specific labeling of DNA is of immense interest for analytical and functional studies
      of DNA. We present a novel approach for
      sequence-specific labeling of DNA using a newly designed fluorescent
      cofactor for the DNA methyltransferase from Thermus aquaticus (M.TaqI).
      Naturally, M.TaqI catalyzes the nucleophilic attack of the exocyclic amino
      group of adenine within the double-stranded 5'-TCGA-3' DNA sequence onto
      the methyl group of the cofactor S-adenosyl-L-methionine (AdoMet) leading
      to methyl group transfer. The design of a new fluorescent cofactor for
      covalent labeling of DNA was based on three criteria: (1) Replacement of
      the methionine side chain of the natural cofactor AdoMet by an aziridinyl
      residue leads to M.TaqI-catalyzed nucleophilic ring opening and coupling
      of the whole nucleoside to DNA. (2) The adenosyl moiety is the molecular
      anchor for cofactor binding. (3) Attachment of a fluorophore via a
      flexible linker to the 8-position of the adenosyl moiety does not block
      cofactor binding. According to these criteria the new fluorescent cofactor
      8-amino[1'-(N'-dansyl)-4'-aminobutyl]-5'-(1-aziridinyl)-5'-deoxyadenosi
      ne (3) was synthesized. 3 binds about 4-fold better than the natural
      cofactor AdoMet to M.TaqI and is coupled with a short duplex
      oligodeoxynucleotide by M.TaqI. The identity of the expected modified
      nucleoside was verified by electrospray ionization mass spectrometry after
      enzymatic fragmentation of the product duplex. In addition, the new
      cofactor 3 was used to sequence-specifically label plasmid DNA in a
      M.TaqI-catalyzed reaction.
AU  - Pljevaljcic G
AU  - Pignot M
AU  - Weinhold E
PT  - Journal Article
TA  - J. Am. Chem. Soc.
JT  - J. Am. Chem. Soc.
SO  - J. Am. Chem. Soc. 2003 125: 3486-3492.

PMID- 15197308
VI  - 283
DP  - 2004
TI  - Sequence-specific DNA labeling using methyltransferases.
PG  - 145-161
AB  - Sequence-specific labeling of native deoxyribonucleic acid (DNA) still represents a
      more-or-less unsolved problem. Difficulties mainly arise from
      the necessity to combine two different functions: sequence-specific
      recognition of DNA and covalent bond formation between the label and DNA.
      DNA methyltransferases (MTases) naturally possess these two functions and
      transfer a methyl group from the cofactor S-adenosyl-L-methionine (AdoMet)
      to adenine or cytosine residues within specific DNA sequences, typically
      ranging from two to eight base pairs. Unfortunately, the methyl group
      itself is a very limited reporter group and it would be desirable to
      transfer larger chemical entities with DNA MTases. Replacement of the
      methionine side chain of the natural cofactor AdoMet by an aziridinyl
      residue leads to the synthetic cofactor N-adenosylaziridine, which is
      quantitatively, base- and sequence-specifically coupled with DNA in a DNA
      MTase-catalyzed reaction. By attaching interesting reporter groups to a
      suitable position of N-adenosylaziridine a large variety of new synthetic
      cofactors are obtained for sequence-specific labeling of DNA. This method
      is illustrated by coupling primary amino groups and biotin to short duplex
      oligodeoxynucleotides or plasmid DNA using the DNA MTase M.TaqI.
AU  - Pljevaljcic G
AU  - Schmidt F
AU  - Peschlow A
AU  - Weinhold E
PT  - Journal Article
TA  - Methods Mol. Biol.
JT  - Methods Mol. Biol.
SO  - Methods Mol. Biol. 2004 283: 145-161.

PMID- 17654629
VI  - 8
DP  - 2007
TI  - Quantitative labeling of long plasmid DNA with nanometer precision.
PG  - 1516-1519
AB  - 
AU  - Pljevaljcic G
AU  - Schmidt F
AU  - Scheidig AJ
AU  - Lurz R
AU  - Weinhold E
PT  - Journal Article
TA  - Chembiochem
JT  - Chembiochem
SO  - Chembiochem 2007 8: 1516-1519.

PMID- 14997517
VI  - 5
DP  - 2004
TI  - Sequence-specific methyltransferase-induced labeling of DNA (SMILing DNA).
PG  - 265-269
AB  - A new concept for sequence-specific labeling of DNA by using chemically modified cofactors for
      DNA methyltransferases is presented. Replacement
      of the amino acid side chain of the natural cofactor
      S-adenosyl-L-methionine with an aziridine group leads to a cofactor
      suitable for DNA methyltransferase-catalyzed sequence-specific coupling
      with DNA. Sequence-specifically fluorescently labeled plasmid DNA was
      obtained by using the DNA methyltransferase from Thermus aquaticus
      (M.TaqI) as catalyst and attaching a fluorophore to the aziridine
      cofactor. First results suggest that all classes of DNA
      methyltransferases with different recognition sequences can be used. In
      addition, this novel method for DNA labeling should be applicable to a
      wide variety of reporter groups.
AU  - Pljevaljcic G
AU  - Schmidt F
AU  - Weinhold E
PT  - Journal Article
TA  - Chembiochem
JT  - Chembiochem
SO  - Chembiochem 2004 5: 265-269.

PMID- 23450070
VI  - 7
DP  - 2012
TI  - Complete genome sequence of Syntrophobacter fumaroxidans strain (MPOB(T)).
PG  - 91-106
AB  - strain MPOB is the best-studied species of the genus . The species is of interest because of
      its anaerobic syntrophic lifestyle, its involvement in the conversion
      of propionate to acetate, H and CO during the overall degradation of organic
      matter, and its release of products that serve as substrates for other
      microorganisms. The strain is able to ferment fumarate in pure culture to CO and
      succinate, and is also able to grow as a sulfate reducer with propionate as an
      electron donor. This is the first complete genome sequence of a member of the
      genus and a member genus in the family . Here we describe the features of this
      organism, together with the complete genome sequence and annotation. The
      4,990,251 bp long genome with its 4,098 protein-coding and 81 RNA genes is a part
      of the Microbial Genome Program (MGP) and the Genomes to Life (GTL) Program
      project.
AU  - Plugge CM
AU  - Henstra AM
AU  - Worm P
AU  - Swarts DC
AU  - Paulitsch-Fuchs AH
AU  - Scholten JC
AU  - Lykidis A
AU  - Lapidus AL
AU  - Goltsman E
AU  - Kim E
AU  - McDonald E
AU  - Rohlin L
AU  - Crable BR
AU  - Gunsalus RP
AU  - Stams AJ
AU  - McInerney MJ
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 7: 91-106.

PMID- 3118961
VI  - 69
DP  - 1987
TI  - The role of dam methylation in controlling gene expression.
PG  - 439-443
AB  - The E. coli gene dam encodes an adenine-specific methylase which converts all adenine residues
      in the sequence GATC into 6-methyl adenine. dam type methylases seem to be ubiquitous in
      Enterobacteriaceae and Haemophilus, since DNA from these strains cross hybridizes with the
      cloned dam gene and they contain DNA resistant to MboI cleavage, which only cleaves
      non-methylated DNA. However, dam methylation is absent from most species of eubacteria not
      phylogenetically related to E. coli and presumably evolved late in prokaryotic evolution. At
      least, one reason why people have become more aware of dam (and dcm) methylation in the last
      decade is because certain restriction enzymes are sensitive to DNA methylation and hence
      overlapping dam and restriction sites are not cleaved. A third phenotype for the dam mutations
      has been described in the literature: that of controlling the level of expression of a
      miscellaneous selection of genes with GATC sequences in their promoter regions. It is this
      third phenotype which is the subject of this paper, but initially it is worth summarizing the
      evidence for the dam methylation affecting other phenotypes of the E. coli bacteria.
AU  - Plumbridge J
PT  - Journal Article
TA  - Biochimie
JT  - Biochimie
SO  - Biochimie 1987 69: 439-443.

PMID- 25999570
VI  - 3
DP  - 2015
TI  - Genome Sequence of Lactococcus lactis subsp. cremoris Mast36, a Strain Isolated from Bovine Mastitis.
PG  - e00449-15
AB  - The genome sequence of Lactococcus lactis subsp. cremoris Mast36, isolated from bovine
      mastitis, is reported here. This strain was shown to be able to grow in
      milk and still possess genes of vegetable origin. The genome also contains a
      cluster of genes associated with pathogenicity.
AU  - Plumed-Ferrer C
AU  - Gazzola S
AU  - Fontana C
AU  - Bassi D
AU  - Cocconcelli PS
AU  - von Wright A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00449-15.

PMID- 10074068
VI  - 181
DP  - 1999
TI  - Sequence of Shiga toxin 2 phage 933W from Escherichia coli O157:H7: Shiga toxin as a phage late-gene product.
PG  - 1767-1778
AB  - Lysogenic bacteriophages are major vehicles for the transfer of genetic
      information between bacteria, including pathogenicity and/or virulence
      determinants. In the enteric pathogen Escherichia coli O157:H7, which
      causes hemorrhagic colitis and hemolytic-uremic syndrome, Shiga toxins 1
      and 2 (Stx1 and Stx2) are phage encoded. The sequence and analysis of the
      Stx2 phage 933W is presented here. We find evidence that the toxin genes
      are part of a late-phage transcript, suggesting that toxin production may
      be coupled with, if not dependent upon, phage release during lytic growth.
      Another phage gene, stk, encodes a product resembling eukaryotic
      serine/threonine protein kinases. Based on its position in the sequence,
      Stk may be produced by the prophage in the lysogenic state, and, like the
      YpkA protein of Yersinia species, it may interfere with the signal
      transduction pathway of the mammalian host. Three novel tRNA genes present
      in the phage genome may serve to increase the availability of rare tRNA
      species associated with efficient expression of pathogenicity
      determinants: both the Shiga toxin and serine/threonine kinase genes
      contain rare isoleucine and arginine codons. 933W also has homology to
      lom, encoding a member of a family of outer membrane proteins associated
      with virulence by conferring the ability to survive in macrophages, and
      bor, implicated in serum resistance.
AU  - Plunkett G III
AU  - Rose DJ
AU  - Durfee TJ
AU  - Blattner FR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1999 181: 1767-1778.

PMID- Not carried by PubMed...
VI  - 93
DP  - 1993
TI  - Detection of restriction endonuclease activity in Streptococcus thermophilus ST132.
PG  - 330
AB  - Genetic development of Streptococcus thermophilus (ST), an important industrial bacterium in
      dairy fermentations, requires the understanding of enzymes that influence the survival and
      replication of transforming DNAs. We have detected a new restriction endonuclease (R-ENase),
      designated as Sth132I, in sonically disrupted cell extracts of strain ST132. Ion exchange
      chromatography (DEAE-cellulose) of crude extracts with a continuous salt gradient resolved
      Sth132I (50-100mM Kcl) and nonspecific exonucleases which coprecipitated by ammonium sulfate
      fractionation. Sth132I had several recognition sites on PhiX174 (5.38 kbp), a single site each
      on pVA736 (7.6 kbp) and pERB (2.2 kbp) but failed to digest pBR322 (4.36 kbp) and lambda DNA.
      Single, double and triple digestions performed on the model pER8 (a native plasmid of ST108)
      allowed tentative positioning of the Sth132I recognition sie at coordinate 0.22 kbp but the
      enzyme was not identifiable as one of the known single-restriction R-NEses. Sth132I required
      Mg++ and retained activity up to 55oC.
AU  - Poch MT
AU  - Somkuti GA
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1993 93: 330.

PMID- 7612245
VI  - 43
DP  - 1995
TI  - Isolation of SagI, a new HaeIII isoschizomer from Streptococcus agalactiae.
PG  - 282-284
AB  - A new HaeIII isoschizomer from Streptococcus agalactiae was isolated by a single-step
      purification method. The highly active restriction endonuclease, SagI, was free of nonspecific
      nuclease activity and was suitable for use in molecular biology procedures. The rapid
      isolation procedure may be applicable for the recovery of other restriction endonucleases from
      bacteria.
AU  - Poch MT
AU  - Somkuti GA
PT  - Journal Article
TA  - Appl. Microbiol. Biotechnol.
JT  - Appl. Microbiol. Biotechnol.
SO  - Appl. Microbiol. Biotechnol. 1995 43: 282-284.

PMID- Not carried by PubMed...
VI  - 94
DP  - 1994
TI  - Rapid isolation of restriction endonucleases from Streptococci.
PG  - 385
AB  - Streptococcus thermophilus can be genetically-engineered to favorably alter characteristics of
      fermented dairy products.  However, endogeneous restriction-modification systems in these
      bacteria can influence the survival and replication of transforming DNAs. A rapid, microscale
      Heparin Sepharose CL-6B affinity gel procedure was developed for detection of restriction
      endonucleases (RE-Nases) in S. thermophilus and other Streptococcus species.
      RE-Nase-containing extracts free of DNA, RNA and nonspecific nuclease activity were produced
      for forty or more strains daily. RE-Nase activity was detected in 10 of 44 strains of
      Streptococci assayed.        	SagI, a new isoschizomer of HaeIII was purified using this
      single-step method from S. agalactiae. This highly active isoschizomer (12,000 U/g of dry
      cells) was free of nonspecific nuclease activity and was suitable for use in molecular biology
      procedures. The isolation procedures was applicable for the rapid isolation of RE-Nases from
      other lactic acid bacteria.
AU  - Poch MT
AU  - Somkuti GA
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1994 94: 385.

PMID- Not carried by PubMed...
VI  - 7
DP  - 1993
TI  - Rapid screening of lactic acid bacteria for restriction endonuclease activity.
PG  - 781-784
AB  - A rapid microscale heparin Sepharose CL-6B affinity gel procedure was developed for detecting
      restriction endonuclease (RE-Nase) activity in a variety of lactic acid bacteria.
      Re-Nase-containing extracts free of DNA, RNA and nonspecific nuclease activity can be produced
      for forty or more strains daily and only 10-12 ml of each log phase culture as required for
      screening. RE-Nase activity was tested in several streptococci and lactobacilli. With
      appropriate modifications, this procedure should allow rapid detection of RE-Nase activity in
      other bacterial species.
AU  - Poch MT
AU  - Somkuti GA
PT  - Journal Article
TA  - Biotechnol. Tech.
JT  - Biotechnol. Tech.
SO  - Biotechnol. Tech. 1993 7: 781-784.

PMID- 9305765
VI  - 195
DP  - 1997
TI  - Sth132I, a novel class-IIS restriction endonuclease of Streptococcus thermophilus ST132.
PG  - 201-206
AB  - The Sth132I restriction endonuclease (R.Sth132I) was detected in Streptococcus thermophilus
      ST132 and purified to near homogeneity by heparin Sepharose CL-6B affinity chromatography.
      Fragments from Sth132I digestion of plasmid DNA were subcloned into pUC19 in Escherichia coli
      DH5a and sequenced.  Sequence analysis of inserts and their ligation junction sites revealed
      that Sth132I is a novel class-IIS restriction endonuclease, which recognizes the
      non-palindromic sequence 5'-CCCG(N)4-3' 3'-GGGC(N)8-5'.
AU  - Poch MT
AU  - Somkuti GA
AU  - Solaiman DKY
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1997 195: 201-206.

PMID- 27516519
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Tepidiphilus thermophilus Strain JHK30T (JCM 19170T) Isolated from a Terrestrial Hot Spring in India.
PG  - e00832-16
AB  - Tepidiphilus thermophilus strain JHK30(T) was isolated from a hot spring at Surajkund,
      Jharkhand, India. It is a Gram-negative rod, nonsporulating, aerobic,
      and motile. The estimated genome is 2.3 Mb, with 2,186 protein-coding sequences.
AU  - Poddar A
AU  - Lepcha RT
AU  - Whitman WB
AU  - Das SK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00832-16.

PMID- 23130356
VI  - 59
DP  - 2012
TI  - A rapid and simple method for detection of type II restriction endonucleases in cells of bacteria with high activity of nonspecific nucleases.
PG  - 669-672
AB  - In this work we describe a novel, rapid and simple microscale procedure for identification of
      restriction endonuclease activity in bacteria
      lysates, which contain high levels of non-specific DNA nucleases.
AU  - Podgorska B
AU  - Kujawska G
AU  - Skurzewski M
AU  - Batsko O
AU  - Kaczorowski T
PT  - Journal Article
TA  - Acta Biochim. Pol.
JT  - Acta Biochim. Pol.
SO  - Acta Biochim. Pol. 2012 59: 669-672.

PMID- 1479906
VI  - 216
DP  - 1992
TI  - Conferring new specificities on restriction enzymes: cleavage at any predetermined site by combining adapter oligodeoxynucleotide and Class-IIS enzyme.
PG  - 303-309
AB  - 
AU  - Podhajska AJ
AU  - Kim SC
AU  - Szybalski W
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1992 216: 303-309.

PMID- 3007287
VI  - 40
DP  - 1985
TI  - Conversion of the FokI endonuclease to a universal restriction enzyme:  cleavage of phage M13mp7 DNA at predetermined sites.
PG  - 175-182
AB  - Endonuclease FokI belongs to class IIS of restriction enzymes, for which the
      DNA cut points lie outside the enzyme-recognition sites.  This permitted
      conferring new cleavage specificities by combining FokI with tailored
      oligodeoxynucleotide adapters.  Such adapters carry a single-stranded (ss)
      target-recognition domain, complementary to the selected ss target DNA, and a
      double-stranded (ds) enzyme-recognition site.  Neither enzyme nor adapter alone
      has endonucleolytic activity toward phage M13mp7 ss DNA, whereas the
      enzyme-adapter complex cleaves this ss target DNA at the particular sites fore
      ordained by the sequence of the ss domain of the adapter.  Two kinds of
      adapters (32 and 34 nucleotides long), with opposing orientations of the
      asymmetric FokI recognition site, were constructed and shown to direct specific
      cleavage under a variety of conditions.  In addition to FokI, other class IIS
      enzymes, HphI, MboII and BbvI, which alone do not cleave ss DNA, are suitable
      for construction of tailored enzyme-adapter complexes with predictable cleavage
      specificities.  This report provides a preliminary experimental confirmation
      for the proposal of Szybalski [Gene 40 (1985) 169-173] for the design of
      adapter-enzyme complexes with novel and predictable specificities.
      Theoretically, using this approach any sequence could be precisely cleaved at a
      predetermined point.
AU  - Podhajska AJ
AU  - Szybalski W
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1985 40: 175-182.

PMID- 25081264
VI  - 2
DP  - 2014
TI  - First Insights into the Genome of the Amino Acid-Metabolizing Bacterium Clostridium litorale DSM 5388.
PG  - e00754-14
AB  - Clostridium litorale is a Gram-positive, rod-shaped, and spore-forming bacterium, which is
      able to use amino acids such as glycine, sarcosine, proline, and betaine
      as single carbon and energy sources via Stickland reactions. The genome consists
      of a circular chromosome (3.41 Mb) and a circular plasmid (27 kb).
AU  - Poehlein A
AU  - Alghaithi HS
AU  - Chandran L
AU  - Chibani CM
AU  - Davydova E
AU  - Dhamotharan K
AU  - Ge W
AU  - Gutierrez-Gutierrez DA
AU  - Jagirdar A
AU  - Khonsari B
AU  - Nair KP
AU  - Daniel R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00754-14.

PMID- 28522720
VI  - 5
DP  - 2017
TI  - First Insight into the Genome Sequence of Clostridium thermobutyricum DSM 4928, a Butyrate-Producing Moderate Thermophile.
PG  - e00367-17
AB  - The moderately thermophilic and Gram-positive bacterium Clostridium thermobutyricum is
      strictly anaerobic and forms subterminally located endospores.
      It was isolated from horse manure compost. C. thermobutyricum produces butyrate
      as the main fermentation product. The draft genome consists of one circular
      chromosome (3.425 Mb) and contains 3,201 predicted protein-coding genes.
AU  - Poehlein A
AU  - Anbalagan A
AU  - Nagel A
AU  - Daniel R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00367-17.

PMID- 24926057
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Amino Acid-Utilizing Eubacterium acidaminophilum al-2 (DSM 3953).
PG  - e00573-14
AB  - Eubacterium acidaminophilum is a strictly anaerobic, Gram-positive, rod-shaped
      bacterium which belongs to cluster XI of the Clostridia. It ferments amino acids
      by a Stickland reaction. The genome harbors a chromosome (2.25 Mb) and a
      megaplasmid (0.8 Mb). It contains several gene clusters coding for
      selenocysteine-containing, glycine-derived, and amino acid-degrading reductases.
AU  - Poehlein A
AU  - Andreesen JR
AU  - Daniel R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00573-14.

PMID- 25931608
VI  - 3
DP  - 2015
TI  - First Insights into the Genome of the N-Methylhydantoin-Degrading Clostridium sp. Strain FS41 (DSM 6877).
PG  - e00394-15
AB  - Clostridium sp. strain FS41 (DSM 6877) is a strictly anaerobic and Gram-positive
      spindle-shaped rod. This spore-forming bacterium is able to degrade
      N-methylhydantoin, with N-carbamoylsarcosine and sarcosine as intermediates. The
      genome consists of one replicon (6.28 Mb) and harbors 5,735 predicted
      protein-coding genes.
AU  - Poehlein A
AU  - Bandera A
AU  - Horne D
AU  - Maier J
AU  - Pawlowicz D
AU  - Siebert V
AU  - Daniel R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00394-15.

PMID- 26450731
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of the Type Strain of the Acetogenic Bacterium Moorella  thermoacetica DSM 521T.
PG  - e01159-15
AB  - Here we report the closed genome sequence of the type strain Moorella thermoacetica DSM
      521(T), an acetogenic bacterium, which is able to grow autotrophically on H2 + CO2 and/or CO,
      using the Wood-Ljungdahl pathway. The genome consists of a circular chromosome (2.53 Mb).
AU  - Poehlein A
AU  - Bengelsdorf FR
AU  - Esser C
AU  - Schiel-Bengelsdorf B
AU  - Daniel R
AU  - Durre P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01159-15.

PMID- 28007862
VI  - 4
DP  - 2016
TI  - Genome Sequence of the Acetogenic Bacterium Acetobacterium wieringae DSM 1911T.
PG  - e01430-16
AB  - Here, we report the draft genome sequence of Acetobacterium wieringae DSM 1911T,  an
      anaerobic, autotrophic, acetogenic, d,l-lactate-utilizing bacterium. The genome consists of a
      chromosome (3.88 Mb) and 3,620 predicted protein-encoding genes.
AU  - Poehlein A
AU  - Bengelsdorf FR
AU  - Schiel-Bengelsdorf B
AU  - Daniel R
AU  - Durre P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01430-16.

PMID- 26404607
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Purine-Degrading Gottschalkia purinilyticum (Formerly Clostridium purinilyticum) WA1 (DSM 1384).
PG  - e01088-15
AB  - Here, we report the draft genome sequence of Gottschalkia purinilyticum (formerly Clostridium
      purinilyticum) WA1, an anaerobic bacterium specialized on degradation of purines (including
      adenine) and glycine, which uses the selenoprotein glycine  reductase for substrate
      degradation. The genome consists of a single chromosome (3.40 Mb).
AU  - Poehlein A
AU  - Bengelsdorf FR
AU  - Schiel-Bengelsdorf B
AU  - Daniel R
AU  - Durre P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01088-15.

PMID- 26184942
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Rnf- and Cytochrome-Containing Autotrophic Acetogen Clostridium aceticum DSM 1496.
PG  - e00786-15
AB  - Here, we report the closed genome sequence of Clostridium aceticum, an Rnf- and
      cytochrome-containing autotrophic acetogen that is able to convert CO2 and H2 to
      acetate using the Wood-Ljungdahl pathway. The genome consists of a circular
      chromosome (4.2 Mbp) and a small circular plasmid (5.7 kbp).
AU  - Poehlein A
AU  - Bengelsdorf FR
AU  - Schiel-Bengelsdorf B
AU  - Gottschalk G
AU  - Daniel R
AU  - Durre P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00786-15.

PMID- 28522721
VI  - 5
DP  - 2017
TI  - First Insights into the Genome Sequence of the Alkaliphilic Thermotolerant Bacterium Clostridium thermoalcaliphilum JW/YL23-2T.
PG  - e00368-17
AB  - Clostridium thermoalcaliphilum is an obligate anaerobic and rod-shaped bacterium  isolated
      from sewage sludge. It is an alkaliphilic thermotolerant organism and
      utilizes sucrose, glucose, fructose, maltose, cellobiose, amino acids, and
      Casamino Acids as substrates. The draft genome comprises 2.031 Mbp and 2,027
      predicted protein-coding genes.
AU  - Poehlein A
AU  - Berg A
AU  - Welsing G
AU  - Daniel R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00368-17.

PMID- 29724835
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of the Hydrogenogenic Carboxydotroph Moorella stamsii DSM 26271.
PG  - e00345-18
AB  - The spore-forming, thermophilic, and obligate anaerobic bacterium Moorella stamsii was
      isolated from digester sludge. Apart from its ability to use carbon
      monoxide for growth, M. stamsii harbors several enzymes for the use of different
      sugars. The draft genome has a size of 3,329 Mb and contains 3,306 predicted
      protein-encoding genes.
AU  - Poehlein A
AU  - Boer T
AU  - Steensen K
AU  - Daniel R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00345-18.

PMID- 29650586
VI  - 6
DP  - 2018
TI  - First Insight into the Genome Sequence of Clostridium vincentii DSM 10228, Isolated from Sediment of the McMurdo Ice Shelf, Antarctica.
PG  - e00334-18
AB  - Clostridium vincentii is an obligate anaerobic, saccharophilic, psychrophilic, Gram-positive,
      motile, and rod-shaped bacterium. It was isolated from a pond
      sediment of the McMurdo Ice Shelf, Antarctica. C. vincentii produces acetate and
      formate as main fermentation products. The draft genome consists of one
      chromosome (3.506 Mb) with 3,379 predicted protein-encoding genes.
AU  - Poehlein A
AU  - Bolz S
AU  - Fischer B
AU  - Daniel R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00334-18.

PMID- 29724845
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of the Butanoic Acid-Producing Bacterium Clostridium luticellarii DSM 29923, Used for Strong Aromatic Chinese Liquor Production.
PG  - e00377-18
AB  - The strictly anaerobic, Gram-positive bacterium Clostridium luticellarii, which has straight
      or slightly curved rod-shaped cells, polar endospores, and
      peritrichous flagella, is used for the production of strong aromatic Chinese
      liquors. C. luticellarii is able to produce butanoic acid. The draft genome
      sequence consists of 3.757 Mbp, including 3,632 predicted protein-encoding genes.
AU  - Poehlein A
AU  - Bremekamp R
AU  - Lutz VT
AU  - Schulz LM
AU  - Daniel R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00377-18.

PMID- 23704177
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Desulfotignum phosphitoxidans DSM 13687 Strain FiPS-3.
PG  - e00227-13
AB  - We report the 5.008-Mbp assembled draft genome sequence of Desulfotignum phosphitoxidans
      strain FiPS-3 (DSM 13687), which gains metabolic energy from the
      oxidation of phosphite to phosphate. Its genome provides insights into the
      composition and architecture of the phosphite-utilizing and energy-transducing
      systems required to live with phosphite as electron donor.
AU  - Poehlein A
AU  - Daniel R
AU  - Simeonova DD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00227-13.

PMID- 26566425
VI  - 10
DP  - 2015
TI  - Genome sequence of Pedobacter glucosidilyticus DD6b, isolated from zooplankton Daphnia magna.
PG  - 100
AB  - The phosphite assimilating bacterium, P. glucosidilyticus DD6b, was isolated from the gut of
      the zooplankton Daphnia magna. Its 3,872,381 bp high-quality draft
      genome is arranged into 93 contigs containing 3311 predicted protein-coding and
      41 RNA-encoding genes. This genome report presents the specific properties and
      common features of P. glucosidilyticus DD6b genome in comparison with the genomes
      of P. glucosidilyticus type strain DSM 23,534, and another five Pedobacter type
      strains with publicly available completely sequenced genomes. Here, we present
      the first journal report on P. glucosidilyticus genome sequence and provide
      information on a new specific physiological determinant of P. glucosidilyticus
      species.
AU  - Poehlein A
AU  - Daniel R
AU  - Simeonova DD
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 100.

PMID- 28798180
VI  - 5
DP  - 2017
TI  - First Insights into the Genome Sequence of Pseudomonas oleovorans DSM 1045.<jour_book>Genome Announc.
PG  - e00774-17
AB  - The Gram-negative proteobacterium Pseudomonas oleovorans DSM 1045 is considered a promising
      source for enzymes of biotechnological interest, e.g., hydrolases and
      transaminases. Here, we present a draft sequence of its 4.86-Mb genome, enabling
      the identification of novel biocatalysts.
AU  - Poehlein A
AU  - Daniel R
AU  - Thurmer A
AU  - Bollinger A
AU  - Thies S
AU  - Katzke N
AU  - Jaeger KE
PT  - Journal Article
TA  - 
JT  - 
SO  -  2017 5: e00774-17.

PMID- 24356841
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Methanotrophic Gammaproteobacterium Methyloglobulus  morosus DSM 22980 Strain KoM1.
PG  - e01078-13
AB  - Here, we report the draft genome sequence of the methanotrophic gammaproteobacterium
      Methyloglobulus morosus DSM 22980 strain KoM1, which is
      proposed to be the type species for the novel genus Methyloglobulus. The genome
      (4.143 Mb) consists of a single circular chromosome and harbors genes for
      2-aminoethylphosphonate (ciliatine) biosynthesis.
AU  - Poehlein A
AU  - Deutzmann JS
AU  - Daniel R
AU  - Simeonova DD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01078-13.

PMID- 26865909
VI  - 11
DP  - 2016
TI  - Genome sequence of Shinella sp. strain DD12, isolated from homogenized guts of starved Daphnia magna.
PG  - 14
AB  - Shinella sp. strain DD12, a novel phosphite assimilating bacterium, has been isolated from
      homogenized guts of 4 days starved zooplankton Daphnia magna. Here
      we report the draft genome of this bacterium, which comprises 7,677,812 bp and
      7505 predicted protein-coding genes.
AU  - Poehlein A
AU  - Freese H
AU  - Daniel R
AU  - Simeonova DD
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 14.

PMID- 25212623
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Serratia sp. Strain DD3, Isolated from the Guts of Daphnia magna.
PG  - e00903-14
AB  - We report the draft genome sequence of Serratia sp. strain DD3, a gammaproteobacterium from
      the family Enterobacteriaceae. It was isolated from
      homogenized guts of Daphnia magna. The genome size is 5,274 Mb.
AU  - Poehlein A
AU  - Freese HM
AU  - Daniel R
AU  - Simeonova DD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00903-14.

PMID- 27174286
VI  - 4
DP  - 2016
TI  - First Insights into the Genome of the Moderately Thermophilic Bacterium Clostridium tepidiprofundi SG 508T.
PG  - e00379-16
AB  - The moderately thermophilic bacterium Clostridium tepidiprofundi is Gram-positive and belongs
      to clostridial cluster I. It was isolated from a hydrothermal vent
      chimney. Substrates utilized by C. tepidiprofundi include casein, peptone,
      tryptone, yeast extract, beef extract, starch, maltose, and glucose. The genome
      consists of one replicon (3.06 Mb).
AU  - Poehlein A
AU  - Friedrich I
AU  - Kruger L
AU  - Daniel R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00379-16.

PMID- 28522716
VI  - 5
DP  - 2017
TI  - First Insights into the Genome Sequence of the Cellulolytic Bacterium Clostridium hungatei DSM 14427.
PG  - e00363-17
AB  - Clostridium hungatei is an obligate anaerobic and spore-forming bacterium, which  was isolated
      from soil. It ferments carbohydrates, such as cellulose or
      d-glucose. C. hungatei is able to fix nitrogen. The draft genome consists of 1
      chromosome (4.902 Mb) with 4,246 predicted protein-coding genes.
AU  - Poehlein A
AU  - Funkner K
AU  - Schuler MA
AU  - Daniel R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00363-17.

PMID- 28082491
VI  - 5
DP  - 2017
TI  - Genome Sequence of Uric Acid-Fermenting Eubacterium angustum DSM 1989T (MK-1).
PG  - e01439-16
AB  - Eubacterium angustum DSM 1989T (MK-1) is a strictly anaerobic and uric acid-, xanthine-, and
      guanine-fermenting organism isolated from sewage sludge. The draft
      genome consists of one circular chromosome (2.4 Mb) and harbors 2,397 predicted
      protein-encoding genes.
AU  - Poehlein A
AU  - Galperin MY
AU  - Andreesen JR
AU  - Daniel R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01439-16.

PMID- 28619808
VI  - 5
DP  - 2017
TI  - First Insights into the Genome Sequence of Clostridium oryzae DSM 28571, Isolated from the Soil of a Japanese Rice Field.
PG  - e00539-17
AB  - Clostridium oryzae was originally isolated from the soil of a Japanese rice field. C. oryzae
      represents a novel species within the genus Clostridium and is
      associated with anaerobic rice straw degradation. Here, we present the draft
      genome sequence of C. oryzae DSM 28571 (5.076 Mbp), containing 4,590 predicted
      protein-coding genes.
AU  - Poehlein A
AU  - Gippert AL
AU  - Bierenbroodspot MJ
AU  - Daniel R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00539-17.

PMID- 24029766
VI  - 1
DP  - 2013
TI  - First Insights into the Genome of the Gram-Negative, Endospore-Forming Organism Sporomusa ovata Strain H1 DSM 2662.
PG  - e00734-13
AB  - The genome of Sporomusa ovata strain H1 DSM 2662, an anaerobic, Gram-negative
      endospore-forming bacterium, was sequenced. S. ovata uses N-methyl compounds,
      primary alcohols, fatty acids, and H2 and CO2 as energy and carbon sources to
      produce acetate. The genome harbors one chromosome, which encodes proteins
      typical for sporulation.
AU  - Poehlein A
AU  - Gottschalk G
AU  - Daniel R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00734-13.

PMID- 25700415
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of the Nitrogen-Fixing and Solvent-Producing Clostridium pasteurianum DSM 525.
PG  - e01591-14
AB  - Here, we report on the closed genome sequence of Clostridium pasteurianum DSM 525, which is an
      anaerobic, Gram-positive and endospore-forming organism. C. pasteurianum can fix N2 and
      produce solvents such as butanol and 1,3-propanediol  from carbohydrates. The genome consists
      of a single 4,350,673-bp replicon.
AU  - Poehlein A
AU  - Grosse-Honebrink A
AU  - Zhang Y
AU  - Minton NP
AU  - Daniel R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01591-14.

PMID- 24285650
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of the Solvent Producer Clostridium saccharobutylicum NCP262 (DSM 13864).
PG  - e00997-13
AB  - Clostridium saccharobutylicum was employed for the production of acetone and butanol in South
      Africa until the 1970s. The genome comprises a single replicon
      (5,107,814 bp) harboring all the genes necessary for solvent production and the
      degradation of various organic compounds, such as fructose, cellobiose, sucrose,
      and mannose.
AU  - Poehlein A
AU  - Hartwich K
AU  - Krabben P
AU  - Ehrenreich A
AU  - Liebl W
AU  - Durre P
AU  - Gottschalk G
AU  - Daniel R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00997-13.

PMID- 29700158
VI  - 6
DP  - 2018
TI  - First Insights into the Genome Sequence of Clostridium thermopalmarium DSM 5974,  a Butyrate-Producing Bacterium Isolated from Palm Wine.
PG  - e00338-18
AB  - Clostridium thermopalmarium is a moderate thermophilic, rod-shaped, and endospore-forming
      bacterium, which was isolated from palm wine in Senegal.
      Butyrate is produced from a broad variety of sugar substrates. Here, we present
      the draft genome sequence of C. thermopalmarium DSM 5974 (2.822 Mb) containing
      2,665 predicted protein-encoding genes.
AU  - Poehlein A
AU  - Hettwer E
AU  - Mohnike L
AU  - Daniel R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00338-18.

PMID- 29622618
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of the Methanococcus maripaludis Type Strain JJ (DSM 2067), a Model for Selenoprotein Synthesis in Archaea.
PG  - e00237-18
AB  - Methanococcus maripaludis type strain JJ (DSM 2067) is an important organism because it serves
      as a model for primary energy metabolism and hydrogenotrophic
      methanogenesis and is amenable to genetic manipulation. The complete genome (1.7
      Mb) harbors 1,815 predicted protein-encoding genes, including 9 encoding
      selenoproteins.
AU  - Poehlein A
AU  - Heym D
AU  - Quitzke V
AU  - Fersch J
AU  - Daniel R
AU  - Rother M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00237-18.

PMID- 28572314
VI  - 5
DP  - 2017
TI  - First Insights into the Genome of the Cr(VI)-Reducing Bacterium Clostridium chromiireducens DSM 23318.
PG  - e00420-17
AB  - Clostridium chromiireducens is an obligate, anaerobic, Gram-positive, rod-shaped, and
      spore-forming bacterium that is able to reduce Cr(VI). The draft genome
      consists of one chromosome (5,448 Mb) and contains 4,773 predicted
      protein-encoding genes.
AU  - Poehlein A
AU  - Hoche N
AU  - Mehr A
AU  - Daniel R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00420-17.

PMID- 29371353
VI  - 6
DP  - 2018
TI  - First Insights into the Draft Genome Sequence of the Endophyte Paenibacillus amylolyticus Strain GM1FR, Isolated from Festuca rubra L.
PG  - e01516-17
AB  - Paenibacillus amylolyticus strain GM1FR is an endophyte isolated from aerial plant tissues of
      Festuca rubra L. Here, we report the draft genome sequence (7.3
      Mb) of GM1FR containing 6,241 protein-coding genes, some of which are potentially
      involved in plant growth promotion and biocontrol.
AU  - Poehlein A
AU  - Hollensteiner J
AU  - Granzow S
AU  - Wemheuer B
AU  - Vidal S
AU  - Wemheuer F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01516-17.

PMID- 29700162
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of the Thermophilic Acetogen Moorella humiferrea DSM 23265.
PG  - e00357-18
AB  - Moorella humiferrea is an endospore-forming, anaerobic, and thermophilic bacterium which was
      isolated from a terrestrial hydrothermal spring. M.
      humiferrea is able to use humic acid or 10-anthraquinone-2,6-disulfonate as an
      electron-shuttling compound for growth and Fe(III) reduction. The genome has a
      size of 2.629 Mb and contains 2,668 predicted protein-coding genes.
AU  - Poehlein A
AU  - Keyl A
AU  - Milsch JC
AU  - Daniel R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00357-18.

PMID- 25323722
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of the Solvent Producer Clostridium saccharoperbutylacetonicum Strain DSM 14923.
PG  - e01056-14
AB  - Clostridium saccharoperbutylacetonicum strain DSM 14923 is known as a butanol-producing
      bacterium. Various organic compounds such as glucose, fructose,
      sucrose, mannose, and cellobiose are fermented. The genome consists of one
      chromosome and one circular megaplasmid. C. saccharoperbutylacetonicum was used
      in industrial fermentation processes to produce the solvents acetone, butanol,
      and ethanol.
AU  - Poehlein A
AU  - Krabben P
AU  - Durre P
AU  - Daniel R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01056-14.

PMID- 21742890
VI  - 193
DP  - 2011
TI  - Complete genome sequence of the type strain Cupriavidus necator N-1.
PG  - 5017
AB  - Here we announce the complete genome sequence of the copper-resistant bacterium Cupriavidus
      necator N-1, the type strain of the genus
      Cupriavidus. The genome consists of two chromosomes and two circular
      plasmids. Based on genome comparison the chromosomes of C. necator N-1
      share a high degree of similarity with the two chromosomal replicons of
      the bioplastic-producing hydrogen bacterium Ralstonia eutropha H16. The
      two strains differ in their plasmids and the presence of hydrogenase
      genes, which are absent in strain N-1.
AU  - Poehlein A
AU  - Kusian B
AU  - Friedrich B
AU  - Daniel R
AU  - Bowien B
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5017.

PMID- 26272578
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Purine-Degrading Clostridium cylindrosporum HC-1 (DSM 605).
PG  - e00917-15
AB  - Here, we report the draft genome sequence of Clostridium cylindrosporum HC-1, a purine- and
      glycine-fermenting anaerobe, which uses selenoprotein glycine
      reductase for substrate degradation. The genome consists of a single chromosome
      (2.72 Mb) and a circular plasmid (14.4 kb).
AU  - Poehlein A
AU  - Montoya SJD
AU  - Bengelsdorf FR
AU  - Schiel-Bengelsdorf B
AU  - Daniel R
AU  - Durre P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00917-15.

PMID- 27198019
VI  - 4
DP  - 2016
TI  - First Insights into the Genome Sequence of the Halophilic Archaeon Halalkalicoccus paucihalophilus (DSM 24557).
PG  - e00382-16
AB  - Halalkalicoccus paucihalophilus is an extremely halophilic, Gram-negative, and nonmotile
      coccus-like archaeon, which was originally isolated from the Lop Nur
      region in the northwest of China. The genome consists of a single replicon (3.98
      Mbp). H. paucihalophilus is able to utilize mannose, which is unique for members
      of this genus.
AU  - Poehlein A
AU  - Mucek K
AU  - Enders M
AU  - Pankok F
AU  - Daniel R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00382-16.

PMID- 28336608
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Klebsiella pneumoniae subsp. pneumoniae ATCC 9621.
PG  - e01718-16
AB  - We present here the 5.561-Mbp assembled draft genome sequence of Klebsiella pneumoniae subsp.
      pneumoniae ATCC 9621, a phosphite- and
      organophosphonate-assimilating Gammaproteobacterium. The genome harbors 5,179
      predicted protein-coding genes.
AU  - Poehlein A
AU  - Najdenski H
AU  - Simeonova DD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01718-16.

PMID- 28082509
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Flavobacterium succinicans Strain DD5b.
PG  - e01492-16
AB  - We present the first 3.315-Mbp assembled draft genome sequence of Flavobacterium  succinicans
      strain DD5b. This bacterium is a phosphite-assimilating
      representative of the genus Flavobacterium isolated from guts of the zooplankton
      Daphnia magna.
AU  - Poehlein A
AU  - Najdenski H
AU  - Simeonova DD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01492-16.

PMID- 29724844
VI  - 6
DP  - 2018
TI  - First Insight into the Genome Sequence of Clostridium liquoris DSM 100320, a Butyrate- and Ethanol-Producing Bacterium.
PG  - e00376-18
AB  - Clostridium liquoris is a strictly anaerobic, Gram-positive, nonmotile, spore-forming,
      rod-shaped bacterium. The major fermentation products from glucose
      are ethanol and butyrate. C. liquoris was isolated from a 20-year-old liquor
      fermentation pit. The draft genome sequence consists of a chromosome (2.892 Mb)
      harboring 2,788 predicted protein-encoding genes.
AU  - Poehlein A
AU  - Neubauer H
AU  - Niemeyer P
AU  - Daniel R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00376-18.

PMID- 26221421
VI  - 10
DP  - 2015
TI  - Genome sequence of Clostridium sporogenes DSM 795(T), an amino acid-degrading, nontoxic surrogate of neurotoxin-producing Clostridium botulinum.
PG  - 40
AB  - Clostridium sporogenes DSM 795 is the type strain of the species Clostridium sporogenes, first
      described by Metchnikoff in 1908. It is a Gram-positive,
      rod-shaped, anaerobic bacterium isolated from human faeces and belongs to the
      proteolytic branch of clostridia. C. sporogenes attracts special interest because
      of its potential use in a bacterial therapy for certain cancer types. Genome
      sequencing and annotation revealed several gene clusters coding for proteins
      involved in anaerobic degradation of amino acids, such as glycine and betaine via
      Stickland reaction. Genome comparison showed that C. sporogenes is closely
      related to C. botulinum. The genome of C. sporogenes DSM 795 consists of a
      circular chromosome of 4.1 Mb with an overall GC content of 27.81 mol% harboring
      3,744 protein-coding genes, and 80 RNAs.
AU  - Poehlein A
AU  - Riegel K
AU  - Konig SM
AU  - Leimbach A
AU  - Daniel R
AU  - Durre P
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 40.

PMID- 27198021
VI  - 4
DP  - 2016
TI  - First Insights into the Draft Genome of Clostridium colicanis DSM 13634, Isolated from Canine Feces.
PG  - e00385-16
AB  - Clostridium colicanis DSM 13634 is a strictly anaerobic, rod-shaped, and spore-forming
      bacterium. It produces acids from common sugars such as glucose and
      fructose. The draft genome consists of one chromosome (2.6 Mbp) and contains
      2,159 predicted protein-encoding genes.
AU  - Poehlein A
AU  - Schilling T
AU  - Bhaskar SNU
AU  - Daniel R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00385-16.

PMID- 27081148
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of the Amino Acid-Fermenting Clostridium propionicum X2  (DSM 1682).
PG  - e00294-16
AB  - Clostridium propionicumis a strict anaerobic, Gram positive, rod-shaped bacterium that belongs
      to the clostridial cluster XIVb. The genome consists of one replicon
      (3.1 Mb) and harbors 2,936 predicted protein-encoding genes. The genome encodes
      all enzymes required for fermentation of the amino acids alpha-alanine,
      beta-alanine, serine, threonine, and methionine.
AU  - Poehlein A
AU  - Schlien K
AU  - Chowdhury NP
AU  - Gottschalk G
AU  - Buckel W
AU  - Daniel R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00294-16.

PMID- 27340077
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Methanobrevibacter curvatus DSM11111, Methanobrevibacter cuticularis DSM11139, Methanobrevibacter filiformis DSM11501,   and Methanobrevibacter oralis DSM7256.
PG  - e00617-16
AB  - Here, the draft genome sequences of four different Methanobrevibacter species are presented.
      Three of the Methanobrevibacter species (M. curvatus, M. cuticularis,
      and M. filiformis) have been isolated from the termite hindgut, while M. oralis
      was isolated from human subgingival plaque.
AU  - Poehlein A
AU  - Seedorf H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00617-16.

PMID- 28860249
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Sphingomonas mucosissima DSM 17494 and Sphingomonas dokdonensis DSM 21029.
PG  - e00889-17
AB  - Sphingomonas mucosissima and Sphingomonas dokdonensis are Gram-negative chemoheterotrophic
      strictly aerobic rods or cocci. The genomes (3.453 Mb and
      3.587 Mb, respectively) contain 3,279 and 3,329 predicted protein-encoding genes,
      respectively. The genome of S. dokdonensis harbors a 90-kb plasmid.
AU  - Poehlein A
AU  - Wubbeler JH
AU  - Daniel R
AU  - Steinbuchel A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00889-17.

PMID- 23516204
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Clostridium stercorarium subsp. stercorarium Strain DSM 8532, a Thermophilic Degrader of Plant Cell Wall Fibers.
PG  - e0007313
AB  - Clostridium stercorarium strain DSM 8532 is a thermophilic bacterium capable of efficiently
      degrading polysaccharides in plant biomass and converting the
      resulting sugars to ethanol and acetate. The complete genome sequence of 2.96 Mbp
      reveals a multitude of genes for hydrolytic enzymes and enables further study of
      the organism and its enzymes, and their exploitation for biotechnological
      processes.
AU  - Poehlein A
AU  - Zverlov VV
AU  - Daniel R
AU  - Schwarz WH
AU  - Liebl W
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0007313.

PMID- 1408773
VI  - 20
DP  - 1992
TI  - BpuAI, a novel BbsI and BbvII isoschizomer from Bacillus pumilus recognizing 5'-GAAGAC-3'.
PG  - 4664
AB  - We have isolated BpuAI, a novel class-IIs restriction endonuclease from Bacillus pumilus
      recognizing the sequence 5'-GAAGAC-3', cutting at N2-3' and N6-5'. High amounts of
      activity can be purified due to a fast protocol and the presence of high amounts of specific
      activity in the crude extract.
AU  - Pogge von Strandmann R
AU  - Stadtler R
AU  - Walter T
AU  - Frey B
AU  - Kaluza K
AU  - Hengstenberg W
AU  - Schmitz G
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 4664.

PMID- 3259576
VI  - 263
DP  - 1988
TI  - On the mechanism of DNA-adenine methylase.
PG  - 7461-7464
AB  - Experiments were performed to determine whether EcoRI methylase catalyzes the
      transfer of the methyl group of S-adenosylmethionine (a) directly to the N6 of
      adenine in DNA or (b) initially to N1 to give N1-methyladenine followed by
      isomerization of the N1-methylamino and 6-NH2 to give N6-methyladenine (Dimroth
      rearrangement).  A facile synthesis of highly enriched [6-15N]deoxyadenosine
      and a dodecamer substrate of EcoRI methylase with [6-15N]adenine in the
      methylation site are reported.  In the product of EcoRI enzymatic methylation,
      all of the isotope remains at the N6 position of the N6-methyladenine product.
      It is concluded that, contrary to existing chemical precedent, the methylation
      occurs by direct transfer from S-adenosylmethionine to the N6 of adenine in
      DNA.
AU  - Pogolotti AL
AU  - Ono A
AU  - Subramaniam R
AU  - Santi DV
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1988 263: 7461-7464.

PMID- 6279395
VI  - 123
DP  - 1982
TI  - Temperature dependence of the activity of DNA-modifying enzymes: endonucleases and DNA ligase.
PG  - 141-152
AB  - The activities of 17 endonucleases: the restriction endonucleases AvaI, BamHI,
      EcoRI, HindIII, PstI and SalI, which cleave pBR322 DNA once: AluI, AvaII, CfoI,
      HaeIII, HhaI, HinfI, HpaII and TaqI, which cut pBR322 DNA several times, and
      three "unspecific" nucleases (S1 nuclease, staphylococcal nuclease and DNase I
      from bovine pancreas) were determined between 0C and 65C.  The reaction was
      followed by the disappearance of covalently closed circular pBR322 DNA, using
      the alkaline ethidium fluorescence assay of Morgan et al. [Nucl. Acids Res.
      (1979) 7, 547-594]; the activity of T4 DNA ligase was similarly measured by the
      conversion of nicked circular DNA to closed circular DNA.  For each enzyme,
      small aliquots of the same solution were incubated at different temperatures
      simultaneously in a temperature gradient device, resulting in a high relative
      precision.  The experimental results are summarized by the simplest possible
      theoretical description, using linear or exponential kinetics and apparent
      activation energies Ea for the enzymatic reaction, Ei for the enzyme
      inactivation and Ti for the inactivation temperature.  To a good approximation
      these three parameters suffice for describing the temperature dependence of the
      activity of most of the enzymes.
AU  - Pohl FM
AU  - Thomae R
AU  - Karst A
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1982 123: 141-152.

PMID- 28619809
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Pseudoruegeria sp. SK021, a Representative of the Marine Roseobacter Group, Isolated from North Sea Sediment.
PG  - e00541-17
AB  - Pseudoruegeria sp. SK021 is a member of the Roseobacter group, isolated under aerobic
      conditions from North Sea sediment. The draft genome comprises 3.95 Mb
      and contains 3,747 protein-coding sequences. Although the strain is nonmotile
      under laboratory conditions, the entire set of genes for the formation of a
      flagellar apparatus was found.
AU  - Pohlner M
AU  - Marshall I
AU  - Schreiber L
AU  - Cypionka H
AU  - Engelen B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00541-17.

PMID- 29903812
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Nine Strains of Brochothrix thermosphacta, Carnobacterium divergens, Lactobacillus algidus, Lactobacillus fuchuensis,  Lactococcus piscium, Leuconostoc gelidum subsp. gasicomitatum, Pseudomonas  lundensis, and Weissella viridesc.
PG  - e00479-18
AB  - In this study, we present the draft genome sequences of nine strains from various
      psychrotrophic species identified in meat products and being recognized as
      important emerging food spoilers. Many of these species have only one or few
      strains being sequenced, and this work will contribute to the improvement of the
      overall genomic knowledge about them.
AU  - Poirier S
AU  - Coeuret G
AU  - Champomier-Verges MC
AU  - Chaillou S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00479-18.

PMID- 10828056
VI  - 275
DP  - 2000
TI  - Structural Insights into the Protein Splicing Mechanism of PI-SceI.
PG  - 16408-16413
AB  - PI-SceI is a member of a class of proteins (inteins) that excise themselves from a precursor
      protein and in the process ligate the flanking protein sequences (exteins). We report here the
      2.1-A resolution crystal structure of a PI-SceI miniprecursor (VMA29) containing 10 N-terminal
      extein residues and 4 C-terminal extein residues. Mutations at the N- and C-terminal splicing
      junctions, blocking in vivo protein splicing, allowed the miniprecursor to be purified and
      crystallized. The structure reveals both the N- and C-terminal scissile peptide bonds to be in
      distorted trans conformations (tau approximately 100 degrees ). Modeling of the wild-type
      PI-SceI based on the VMA29 structure indicates a large conformational change (movement of >9
      A) must occur to allow transesterification to be completed. A zinc atom was discovered at the
      C-terminal splicing junction. Residues Cys(455), His(453), and Glu(80) along with a water
      molecule (Wat(53)) chelate the zinc atom. The crystal structure of VMA29 has captured the
      intein in its pre-spliced state.
AU  - Poland BW
AU  - Xu MQ
AU  - Quiocho FA
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2000 275: 16408-16413.

PMID- 29371348
VI  - 6
DP  - 2018
TI  - Genome Sequence of Verrucomicrobium sp. Strain GAS474, a Novel Bacterium Isolated from Soil.
PG  - e01451-17
AB  - Verrucomicrobium sp. strain GAS474 was isolated from the mineral soil of a temperate deciduous
      forest in central Massachusetts. Here, we present the
      complete genome sequence of this phylogenetically novel organism, which consists
      of a total of 3,763,444 bp on a single scaffold, with a 65.8% GC content and
      3,273 predicted open reading frames.
AU  - Pold G
AU  - Conlon EM
AU  - Huntemann M
AU  - Pillay M
AU  - Mikhailova N
AU  - Stamatis D
AU  - Reddy TBK
AU  - Daum C
AU  - Shapiro N
AU  - Kyrpides N
AU  - Woyke T
AU  - DeAngelis KM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01451-17.

PMID- 29437089
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Three Strains of a Novel Rhizobiales Species Isolated from Forest Soil.
PG  - e01452-17
AB  - Three strains of a novel Rhizobiales species were isolated from temperate deciduous forest
      soil in central Massachusetts. Their genomes consist of 9.09 to
      10.29 Mb over 3 to 4 scaffolds each and indicate that diverse nitrogenous
      compounds are used by these organisms.
AU  - Pold G
AU  - Huntemann M
AU  - Pillay M
AU  - Mikhailova N
AU  - Stamatis D
AU  - Reddy TBK
AU  - Daum C
AU  - Shapiro N
AU  - Kyrpides N
AU  - Woyke T
AU  - DeAngelis KM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01452-17.

PMID- 25999577
VI  - 3
DP  - 2015
TI  - Genome Sequence of Anoxybacillus thermarum AF/04T, Isolated from the Euganean Hot Springs in Abano Terme, Italy.
PG  - e00490-15
AB  - Anoxybacillus thermarum AF/04(T) was isolated from the Euganean hot springs in Abano Terme,
      Italy. The present work reports a high-quality draft genome sequence
      of strain AF/04(T). This work also provides useful insights into glycoside
      hydrolases, glycoside transferases, and sugar transporters that may be involved
      in cellular carbohydrate metabolism.
AU  - Poli A
AU  - Nicolaus B
AU  - Chan KG
AU  - Kahar UM
AU  - Chan CS
AU  - Goh KM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00490-15.

PMID- 
VI  - 10
DP  - 2000
TI  - Site-specific endonucleases of Streptomycetes.
PG  - 13-15
AB  - Production of restriction enzymes is widespread among soil streptomycetes. More than 15% of
      fresh soil isolates showed this ability. Of eight strains showing enzyme activity, seven
      formed isoschizomers of AsuII. Enzymes with such specificity were not previously found amongst
      streptomycetes.  Enzymes of restriction-modification (RM} systems are present in large amounts
      in streptomycetes and some strains are strong producers of endonucleases (e.g., SacI, SacII,
      SalGI). Streptomycetes also produce isoschizomers of EcoRI, PstI and others. Studies on these
      enzymes are valuable for understanding regulation and functioning of RM systems, actual
      production of the enzymes themselves and for pharmaceutical and other biotechnological
      applications (Rodicio & Chater, 1988}. The aim of the present study was to investigate the
      amount of restrictases among fresh soil isolates.
AU  - Polishchuk LV
AU  - Lukyanchuk VV
AU  - Matselyuch BP
PT  - Journal Article
TA  - Actinomycetes
JT  - Actinomycetes
SO  - Actinomycetes 2000 10: 13-15.

PMID- 242001
VI  - 72
DP  - 1975
TI  - Specificity of substrate recognition by the EcoRI restriction endonuclease.
PG  - 3310-3314
AB  - The substrate specificity of the EcoRI restriction endonuclease can be varied
      in vitro by changing the pH and the ionic environment of the reaction.
      Phosphodiester bond cleavage occurs at a DNA hexanucleotide sequence
      d(N-G-A-A-T-T-C-N) d(N-C-T-T-A-A-G-N)	when the ionic strength is high, 100mM
      Tris-HCl, 50 mM NaCl, 5 mM MgCl2, and the pH is approximately 7.3.  Lowering
      the ionic strength to 25 mM Tris-HCl, 2 mM MgCl2, and adjusting the pH to 8.5
      reduces the recognition specificity of the EcoRI endonuclease to the
      tetranucleotide sequence, d(N-A-A-T-T-N) d(N-T-T-A-A-N)	The enzymatic activity
      responsible for this substrate recognition is referred to as EcoRI*.  Cleavage
      of pVH51 plasmid DNA under EcoRI* conditions results in a number of partial
      digest fragments, some of which disappear slowly over a prolonged digestion
      period.  This suggests that different recognition sites are cleaved at
      different rates.  Comparison of DNA fragment patterns of modified and
      unmodified pVH51 DNA indicates that the canonical EcoRI sequence is the most
      rapidly cleaved site under EcoRI* conditions.  DNA modified in vivo by the
      EcoRI methylase is not cleaved by the EcoRI endonuclease under standard
      conditions, but is cleaved under EcoRI* conditions at sites other than the
      standard EcoRI substrate.
AU  - Polisky B
AU  - Greene P
AU  - Garfin DE
AU  - McCarthy BJ
AU  - Goodman HM
AU  - Boyer HW
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1975 72: 3310-3314.

PMID- 2788270
VI  - 17
DP  - 1989
TI  - MscI, a type II restriction endonuclease from Micrococcus species which recognizes 5' TGGCCA 3' .
PG  - 5858
AB  - None
AU  - Polisson C
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 5858.

PMID- 3264065
VI  - 16
DP  - 1988
TI  - AseI, a restriction endonuclease from Aquaspirillum serpens which recognizes 5'ATTAAT3'.
PG  - 10365
AB  - AseI and AseII, type II restriction endonucleases, have been isolated from
      Aquaspirillum serpens (NEB#448).  AseI, an isoschizomer of VspI, recognizes the
      six base palindromic sequence 5'ATTAAT3', and cleaves 3' of the 5' T, to
      generate a two base 5' overhang, 5' AT^TAAT3'.  AseII is an isoschizomer of
      NciI (data not shown).
AU  - Polisson C
AU  - Morgan RD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1988 16: 10365.

PMID- 2838810
VI  - 16
DP  - 1988
TI  - BsrI, a unique restriction endonuclease from Bacillus stearothermophilus which recognizes 5'ACTGG3'.
PG  - 5205
AB  - A new type II restriction endonuclease, BsrI, has been isolated from Bacillus
      stearothermophilus (NEB#447).  BsrI recognizes the five base non-palindromic
      sequence 5' ACTGG 3'.  It cleaves one nucleotide outside of the recognition
      sequence on one strand, and within the recognition sequence on the opposite
      strand, to generate a two base 3' overhang.
AU  - Polisson C
AU  - Morgan RD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1988 16: 5205.

PMID- 2170952
VI  - 18
DP  - 1990
TI  - AciI, a unique restriction endonuclease from Arthrobacter citreus which recognizes 5' CCGC3'.
PG  - 5911
AB  - None
AU  - Polisson C
AU  - Morgan RD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 5911.

PMID- 2542897
VI  - 17
DP  - 1989
TI  - DrdI, a unique restriction endonuclease from Deinococcus radiodurans which recognizes 5'GACN6GTC3'.
PG  - 3316
AB  - None
AU  - Polisson C
AU  - Morgan RD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 3316.

PMID- 3263622
VI  - 16
DP  - 1988
TI  - EarI, a restriction endonuclease from Enterobacter aerogenes which recognizes 5'CTCTTC3'.
PG  - 9872
AB  - EarI, a TypeII restriction endonuclease, has been isolated from Enterobacter aerogenes
      (NEB#450).  EarI, an isoschizomer of Ksp632I, recognizes the six base non-palindromic sequence
      5'CTCTTC3', and cleaves one nucleotide 3' of the 3' cytosine on one strand, and four
      nucleotides 5' of the 5' guanine on the opposite strand, to generate a three base 5'
      overhang.  The single cleavage site of EarI on SV40 DNA was mapped to approximately position
      4450 by analysis against BglI, EcoRI and TaqI cleaved SV40 DNA (figure 1, lanes B-E).  The
      sequence 5'CTCTTC3' occurs at position 4437.  The number and sizes of the fragments
      generated by digestion with EarI on eight DNA molecules (119 sites) match the computer
      predicted number and sizes of the fragments that would be generated by cleavage at the
      sequence 5'CTCTTC3'.  EarI has the following number of recognition sites on these commonly
      used DNAs:  pUC19, 3; pBR322, 2; phiX174, 2; M13mp18, 2; SV40, 1; Adeno2, 29; T7, 46; and
      Lambda, 34 (fig. 1, lanes F-l).  From these data we conclude that EarI recognizes the sequence
      5'CTCTTC3'.  The crude extract contained approximately 8,000 units EarI per gram of cells.
      The cleavage site of EarI was determined by cleavage of a primed synthesis reaction.  Using
      M13mp18 DNA as template with an appropriate primer, the four standard dideoxy DNA sequencing
      reactions were performed and a fifth reaction containing no dideoxy terminations was extended
      through the EarI site.  The fifth reaction was terminated by heat treatment.  EarI was added
      to the fifth reaction.  The cleaved product resulted in a single band (fig. II, lane -) which
      comigrates with the first 3'nucleotide outside of the recognition sequence.  The addition of
      Klenow subsequent to EarI digestion resulted in a single band, three nucleotides longer,
      comigrating with the fourth 3' nucleotide outside of the recognition sequence (fig. II, lane
      +).  These results indicate that EarI cleaves one nucleotide 3' of the recognition sequence
      on the 5'CTCTTC3' strand, and four nucleotides 5' of the 5' G on the opposite strand
      sequence 5'GAAGAG3', generating a three base 5' overhang.
      5'CTCTTCN3'
      3'GAGAAGNNNN5'.
AU  - Polisson C
AU  - Morgan RD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1988 16: 9872.

PMID- 1614876
VI  - 20
DP  - 1992
TI  - ApoI, a unique restriction endonuclease from Arthrobacter protophormiae which recognizes 5' RAATTY-3'.
PG  - 2888
AB  - ApoI, a novel type II restriction endonuclease, has been isolated from Arthrobacter
      protophormiae (NEB#723). ApoI recognizes the six base palindromic sequence 5' R|AATTY 3',
      and cleaves after the first base pair, as indicated by the arrow, to create a four base 5'
      extension.
AU  - Polisson C
AU  - Robinson D
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 2888.

PMID- 22570478
VI  - 287
DP  - 2012
TI  - Proximal Recognition Sites Facilitate Intrasite Hopping by DNA Adenine Methyltransferase MECHANISTIC EXPLORATION OF EPIGENETIC GENE REGULATION.
PG  - 22873-22881
AB  - The methylation of adenine in palindromic 5'-GATC-3' sites by Escherichia coli Dam supports
      diverse roles, including the essential
      regulation of virulence genes in several human pathogens. As a result
      of a unique hopping mechanism, Dam methylates both strands of the same
      site prior to fully dissociating from the DNA, a process referred to as
      intrasite processivity. The application of a DpnI restriction
      endonuclease-based assay allowed the direct interrogation of this
      mechanism with a variety of DNA substrates. Intrasite processivity is
      disrupted when the DNA flanking a single GATC site is longer than 400
      bp on either side. Interestingly, the introduction of a second GATC
      site within this flanking DNA reinstates intrasite methylation of both
      sites. Our results show that intrasite methylation occurs only when
      GATC sites are clustered, as is found in gene segments both known and
      postulated to undergo in vivo epigenetic regulation by Dam methylation.
      We propose a model for intrasite methylation in which Dam bound to
      flanking DNA is an obligate intermediate. Our results provide insights
      into how intrasite processivity, which appears to be context-dependent,
      may contribute to the diverse biological roles that are carried out by
      Dam.
AU  - Pollak AJ
AU  - Reich NO
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2012 287: 22873-22881.

PMID- 27313308
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Kosmotoga sp. Strain DU53 and Kosmotoga arenicorallina  S304.
PG  - e00570-16
AB  - Here, we announce the draft genome sequences of two thermophilic Thermotogae bacteria:
      Kosmotoga sp. strain DU53, isolated from a continental oil reservoir,
      and Kosmotoga arenicorallina, isolated from hydrothermal sediments. The sequences
      will provide further insight into evolution of the Kosmotogales.
AU  - Pollo SM
AU  - Charchuk R
AU  - Nesbo CL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00570-16.

PMID- 19376855
VI  - 191
DP  - 2009
TI  - The Escherichia coli Mismatch Repair Protein MutL Recruits the Vsr and MutH Endonucleases in Response to DNA Damage.
PG  - 4041-4043
AB  - The activities of the Vsr and MutH endonucleases of Escherichia coli are stimulated by MutL.
      The interaction of MutL with each enzyme is enhanced
      in vivo by 2-aminopurine treatment and by inactivation of the mutY gene.
      We hypothesize that MutL recruits the endonucleases to sites of DNA
      damage.
AU  - Polosina YY
AU  - Mui J
AU  - Pitsikas P
AU  - Cupples CG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2009 191: 4041-4043.

PMID- 27284131
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Aeribacillus pallidus Strain 8m3, a Thermophilic Hydrocarbon-Oxidizing Bacterium Isolated from the Dagang Oil Field (China).
PG  - e00500-16
AB  - The draft genome sequence of Aeribacillus pallidus strain 8m3, a thermophilic aerobic
      oil-oxidizing bacterium isolated from production water from the Dagang
      high-temperature oil field, China, is presented here. The genome is annotated to
      provide insights into the genomic and phenotypic diversity of the genus
      Aeribacillus.
AU  - Poltaraus AB
AU  - Sokolova DS
AU  - Grouzdev DS
AU  - Ivanov TM
AU  - Malakho SG
AU  - Korshunova AV
AU  - Rozanov AS
AU  - Tourova TP
AU  - Nazina TN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00500-16.

PMID- 27491973
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Geobacillus subterraneus Strain K, a Hydrocarbon-Oxidizing Thermophilic Bacterium Isolated from a Petroleum Reservoir   in Kazakhstan.
PG  - e00782-16
AB  - The draft genome sequence of Geobacillus subterraneus strain K, a thermophilic aerobic
      oil-oxidizing bacterium isolated from production water of the Uzen
      high-temperature oil field in Kazakhstan, is presented here. The genome is
      annotated for elucidation of the genomic and phenotypic diversity of thermophilic
      alkane-oxidizing bacteria.
AU  - Poltaraus AB
AU  - Sokolova DS
AU  - Grouzdev DS
AU  - Ivanov TM
AU  - Malakho SG
AU  - Korshunova AV
AU  - Tourova TP
AU  - Nazina TN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00782-16.

PMID- 26227604
VI  - 3
DP  - 2015
TI  - Isolation, Identification, Whole-Genome Sequencing, and Annotation of Four Bacillus Species, B. anthracis RIT375, B. circulans RIT379, B. altitudinis  RIT380, and B. megaterium RIT381, from Internal Stem Tissue of the Insulin Plant   Costus igneus.
PG  - e00847-15
AB  - Here, we report the isolation, identification, whole-genome sequencing, and annotation of four
      Bacillus species from internal stem tissue of the insulin
      plant Costus igneus, grown in Puerto Rico. The plant is of medicinal importance,
      as extracts from its leaves have been shown to lower blood sugar levels of
      hyperglycemic rats.
AU  - Polter SJ
AU  - Caraballo AA
AU  - Lee YP
AU  - Eng WW
AU  - Gan HM
AU  - Wheatley MS
AU  - Savka MA
AU  - Thomas BN
AU  - Hudson AO
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00847-15.

PMID- 17438034
VI  - 75
DP  - 2007
TI  - Genome sequence of a clinical isolate of Campylobacter jejuni from Thailand.
PG  - 3425-3433
AB  - Campylobacter jejuni CG8486, which belongs to the HS4 complex, was isolated from a patient
      with inflammatory diarrhea in Thailand.  This strain caused a diarrheal disease in ferrets
      comparable to that caused by C. jejuni strain 81-176, but it was much less invasive for
      epithelial cells in vitro than 81-176.  Complete genome sequencing of CG8486 revealed a
      1.65-Mb genome that was very similar to the other two published genomes of clinical isolates
      of C. jejuni, the genomes of 81-176 and NCTC 11168, with a limited number of CG8486-specific
      genes mapping outside the hypervariable carbohydrate biosynthesis loci.  These data suggest
      that the genes required for induction of inflammatory diarrhea are among the genes shared by
      CG8486 and 81-176 but that either major changes in the carbohydrate loci and/or more subtle
      changes in other genes may modulate virulence.
AU  - Poly F
AU  - Read T
AU  - Tribble DR
AU  - Baqar S
AU  - Lorenzo M
AU  - Guerry P
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2007 75: 3425-3433.

PMID- 18809665
VI  - 76
DP  - 2008
TI  - Characterization of two Campylobacter jejuni strains for use in volunteer experimental-infection studies.
PG  - 5655-5667
AB  - The development of vaccines against Campylobacter jejuni would be facilitated by
      the ability to perform phase II challenge studies. However, molecular mimicry of
      the lipooligosaccharide (LOS) of most C. jejuni strains with human gangliosides
      presents safety concerns about the development of Guillain-Barre syndrome.
      Clinical isolates of C. jejuni that appeared to lack genes for the synthesis of
      ganglioside mimics were identified by DNA probe analyses. Two clinical isolates
      from Southeast Asia (strains BH-01-0142 and CG8421) were determined to express
      the LOS type containing N-acetyl quinovosamine. No ganglioside structures were
      observed to be present in the LOSs of these strains, and pyrosequence analyses of
      the genomes of both strains confirmed the absence of genes involved in
      ganglioside mimicry. The capsule polysaccharide (CPS) of BH-01-0142 was
      determined to be composed of galactose (Gal), 6-deoxy-ido-heptose, and, in
      smaller amounts, D-glycero-D-ido-heptose, and the CPS of CG8421 was observed to
      contain Gal, 6-deoxy-altro-heptose, N-acetyl-glucosamine, and minor amounts of
      6-deoxy-3-O-Me-altro-heptose. Both CPSs were shown to carry
      O-methyl-phosphoramidate. The two genomes contained strain-specific zones, some
      of which could be traced to a plasmid origin, and both contained a large
      chromosomal insertion related to the CJEI3 element of C. jejuni RM1221. The
      genomes of both strains shared a high degree of similarity to each other and,
      with the exception of the capsule locus of CG8421, to the type strain of the HS3
      serotype, TGH9011.
AU  - Poly F
AU  - Read TD
AU  - Chen YH
AU  - Monteiro MA
AU  - Serichantalergs O
AU  - Pootong P
AU  - Bodhidatta L
AU  - Mason CJ
AU  - Rockabrand D
AU  - Baqar S
AU  - Porter CK
AU  - Tribble D
AU  - Darsley M
AU  - Guerry P
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2008 76: 5655-5667.

PMID- 15872262
VI  - 43
DP  - 2005
TI  - Genomic diversity in Campylobacter jejuni: Identification of C-jejuni 81-176-specific genes.
PG  - 2330-2338
AB  - Since the publication of the complete genomic sequence of Campylobacter jejuni NCTC 11168 in
      February 2000, evidence has been compiling that
      suggests C. jejuni strains exhibit high genomic diversity. In order to
      investigate this diversity, the unique genomic DNA sequences from a
      nonsequenced Campylobacter strain, C. jejuni 81-176, were identified by
      comparison with C. jejuni NCTC 11168 by using a shotgun DNA microarray
      approach. Up to 63 kb of new chromosomal DNA sequences unique to this
      pathogen were obtained. Eighty-six open reading frames were identified
      by the presence of uninterrupted coding regions encoding a minimum of
      40 amino acids. In addition, this study shows that the whole-plasmid
      shotgun microarray approach is effective and provides a comprehensive
      coverage of DNA regions that differ between two closely related
      genomes. The two plasmids harbored by this Campylobacter strain, pTet
      and pVir, were also sequenced, with coverages of 2.5- and 2.9-fold,
      respectively, representing 72 and 92% of their complete nucleotide
      sequences. The unique chromosomal genes encode proteins involved in
      capsule and lipooligosaccharide biosynthesis, restriction and
      modification systems, and respiratory metabolism. Several of these
      unique genes are likely associated with C. jejuni 81-176 fitness and
      virulence. Interestingly, the comparison of C. jejuni 81-176 unique
      genes with those of C. jejuni ATCC 43431 revealed a single gene which
      encodes a probable TraG-like protein. The product of this gene might be
      associated with the mechanism of C. jejuni invasion into epithelial
      cells. In conclusion, this study extends the repertoire of C. jejuni
      genes and thus will permit the construction of a composite and more
      comprehensive microarray of C. jejuni.
AU  - Poly F
AU  - Threadgill D
AU  - Stintzi A
PT  - Journal Article
TA  - J. Clin. Microbiol.
JT  - J. Clin. Microbiol.
SO  - J. Clin. Microbiol. 2005 43: 2330-2338.

PMID- 15231810
VI  - 186
DP  - 2004
TI  - Identification of Campylobacter jejuni ATCC 43431-specific genes by whole microbial genome comparisons.
PG  - 4781-4795
AB  - This study describes a novel approach to identify unique genomic DNA sequences from the
      unsequenced strain C. jejuni ATCC 43431 by comparison with the sequenced strain C. jejuni NCTC
      11168. A shotgun DNA microarray was constructed by arraying 9,600 individual DNA fragments
      from a C. jejuni ATCC 43431 genomic library onto a glass slide. DNA fragments unique to C.
      jejuni ATCC 43431 were identified by competitive hybridization to the array with genomic DNA
      of C. jejuni NCTC 11168. The plasmids containing unique DNA fragments were sequenced, allowing
      the identification of up to 130 complete and incomplete genes. Potential biological roles were
      assigned to 66% of the unique open reading frames. The mean G+C content of these unique genes
      (26%) differs significantly from the G+C content of the entire C. jejuni genome (30.6%). This
      suggests that they may have been acquired through horizontal gene transfer from an organism
      with a G+C content lower than that of C. jejuni. Because the two C. jejuni strains differ by
      Penner serotype, a large proportion of the unique ATCC 43431 genes encode proteins involved in
      lipooligosaccharide and capsular biosynthesis, as expected. Several unique open reading frames
      encode enzymes which may contribute to genetic variability, i.e., restriction-modification
      systems and integrases. Interestingly, many of the unique C. jejuni ATCC 43431 genes show
      identity with a possible pathogenicity island from Helicobacter hepaticus and components of a
      potential type IV secretion system. In conclusion, this study provides a valuable resource to
      further investigate Campylobacter diversity and pathogenesis.
AU  - Poly F
AU  - Threadgill D
AU  - Stintzi A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2004 186: 4781-4795.

PMID- 2545058
VI  - 3
DP  - 1989
TI  - Development of a culture medium for bacteria of the genus Haemophilus, producing restriction endonucleases.
PG  - 3-8
AB  - A culture medium for the cultivation of hemophilic bacteria, containing acidic
      casein hydrolysate, aminopeptide and fodder yeast extract, has been proposed.
      The growth-stimulating properties of this medium have been studied on 5 strains
      producing restrictases differing in their specificity.  In growing these
      producer strains in a model AHKYM-2 fermenter with the supply of carbohydrate
      substrates (glucose, sucrose, glycerin) the yield of biomass, considered to be
      high for hemophilic bacteria (10-14 g wet weight from 1 liter of the medium),
      has been achieved.  As shown on H. influenzae Rc B-2297 used as an example, an
      increase in the yield of microbial biomass leads to a decrease in restrictase
      specific activity.
AU  - Polyachenko VM
AU  - Melnikova VA
AU  - Gruber IM
AU  - Smirnova GA
AU  - Raskin BM
PT  - Journal Article
TA  - Zh. Mikrobiol. Epidemiol. Immunobiol.
JT  - Zh. Mikrobiol. Epidemiol. Immunobiol.
SO  - Zh. Mikrobiol. Epidemiol. Immunobiol. 1989 3: 3-8.

PMID- 160751
VI  - 17
DP  - 1979
TI  - Regulation of restriction endonuclease activity with antibiotics.
PG  - 307-321
AB  - Restriction-modification systems were made known in the early 1960's.  Active investigation,
      however, has begun in the last years.  These systems serve to protect the bacterial cell from
      invasion by foreign DNA.  Simultaneously, restriction enzymes are widely used as a tool for
      specific DNA cleavage and obtaining of recombinant DNA molecules in vitro.
AU  - Polyanovsky OL
AU  - Nosikov VV
AU  - Zhuze AL
AU  - Braga EA
AU  - Karlyshev AV
PT  - Journal Article
TA  - Adv. Enzyme Regul.
JT  - Adv. Enzyme Regul.
SO  - Adv. Enzyme Regul. 1979 17: 307-321.

PMID- 15689527
VI  - 22
DP  - 2005
TI  - Evolutionary diversification of DNA methyltransferases in eukaryotic Genomes.
PG  - 1119-1128
AB  - In eukaryotes, C5-cytosine methylation is a common mechanism associated with a variety of
      functions such as gene regulation or control of
      genomic stability. Different subfamilies of eukaryotic
      methyltransferases (MTases) have been identified, mainly in metazoa,
      plants, and fungi. In this paper, we used hidden Markov models to
      detect MTases in completed or almost completed eukaryotic genomes,
      including different species of Protozoa. A phylogenetic analysis of
      MTases enabled us to define six subfamilies of MTases, including two
      new subfamilies. The dnmt1 subfamily that includes all the known MTases
      with a maintenance activity seems to be absent in the Protozoa. The
      dnmt2 subfamily seems to be the most widespread, being present even in
      the nonmethylated Dictyostelium discoideum. We also found two dnmt2
      members in the bacterial genus Geobacter, suggesting that horizontal
      transfers of MTases occurred between eukaryotes and prokaryotes. Even
      if the direction of transfer cannot be determined, this relationship
      might be useful for understanding the function of this enigmatic
      subfamily of MTases. Globally, our analysis reveals a great diversity
      of MTases in eukaryotes, suggesting the existence of different
      methylation systems. Our results also suggest acquisitions and losses
      of different MTases in every eukaryotic lineage studied and that some
      eukaryotes appear to be devoid of methylation.
AU  - Ponger L
AU  - Li WH
PT  - Journal Article
TA  - Mol. Biol. Evol.
JT  - Mol. Biol. Evol.
SO  - Mol. Biol. Evol. 2005 22: 1119-1128.

PMID- 28878861
VI  - 12
DP  - 2017
TI  - Genome sequence of the sulfur-oxidizing Bathymodiolus thermophilus gill endosymbiont.
PG  - 50
AB  - Bathymodiolus thermophilus, a mytilid mussel inhabiting the deep-sea hydrothermal vents of the
      East Pacific Rise, lives in symbiosis with chemosynthetic
      Gammaproteobacteria within its gills. The intracellular symbiont population
      synthesizes nutrients for the bivalve host using the reduced sulfur compounds
      emanating from the vents as energy source. As the symbiont is uncultured,
      comprehensive and detailed insights into its metabolism and its interactions with
      the host can only be obtained from culture-independent approaches such as
      genomics and proteomics. In this study, we report the first draft genome sequence
      of the sulfur-oxidizing symbiont of B. thermophilus, here tentatively named
      Candidatus Thioglobus thermophilus. The draft genome (3.1 Mb) harbors 3045
      protein-coding genes. It revealed pathways for the use of sulfide and thiosulfate
      as energy sources and encodes the Calvin-Benson-Bassham cycle for CO2 fixation.
      Enzymes required for the synthesis of the tricarboxylic acid cycle intermediates
      oxaloacetate and succinate were absent, suggesting that these intermediates may
      be substituted by metabolites from external sources. We also detected a
      repertoire of genes associated with cell surface adhesion, bacteriotoxicity and
      phage immunity, which may perform symbiosis-specific roles in the B. thermophilus
      symbiosis.
AU  - Ponnudurai R
AU  - Sayavedra L
AU  - Kleiner M
AU  - Heiden SE
AU  - Thurmer A
AU  - Felbeck H
AU  - Schluter R
AU  - Sievert SM
AU  - Daniel R
AU  - Schweder T
AU  - Markert S
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 50.

PMID- 21298013
VI  - 6
DP  - 2011
TI  - Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution.
PG  - E16329
AB  - Mycobacteriophages are viruses that infect mycobacterial hosts such as
      Mycobacterium smegmatis and Mycobacterium tuberculosis. All
      mycobacteriophages characterized to date are dsDNA tailed phages, and have
      either siphoviral or myoviral morphotypes. However, their genetic
      diversity is considerable, and although sixty-two genomes have been
      sequenced and comparatively analyzed, these likely represent only a small
      portion of the diversity of the mycobacteriophage population at large.
      Here we report the isolation, sequencing and comparative genomic analysis
      of 18 new mycobacteriophages isolated from geographically distinct
      locations within the United States. Although no clear correlation between
      location and genome type can be discerned, these genomes expand our
      knowledge of mycobacteriophage diversity and enhance our understanding of
      the roles of mobile elements in viral evolution. Expansion of the number
      of mycobacteriophages grouped within Cluster A provides insights into the
      basis of immune specificity in these temperate phages, and we also
      describe a novel example of apparent immunity theft. The isolation and
      genomic analysis of bacteriophages by freshman college students provides
      an example of an authentic research experience for novice scientists.
AU  - Pope WH et al
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2011 6: E16329.

PMID- 27340062
VI  - 4
DP  - 2016
TI  - Genome Sequences of Gordonia terrae Phages Benczkowski14 and Katyusha.
PG  - e00578-16
AB  - Bacteriophages Katyusha and Benczkowski14 are newly isolated phages that infect Gordonia
      terrae 3612. Both have siphoviral morphologies with isometric heads and
      long tails (500 nm). The genomes are 75,380 bp long and closely related, and the
      tape measure genes (9 kbp) are among the largest to be identified.
AU  - Pope WH et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00578-16.

PMID- 27284148
VI  - 4
DP  - 2016
TI  - Draft Genome Assembly of the Bloom-Forming Cyanobacterium Nodularia spumigena Strain CENA596 in Shrimp Production Ponds.
PG  - e00466-16
AB  - We report here the draft genome assembly of the brackish cyanobacterium Nodularia spumigena
      strain CENA596 isolated from a shrimp production pond in Rio Grande do
      Sul, Brazil. The draft genome consists of 291 contigs with a total size of
      5,189,679 bp. Secondary metabolite annotations resulted in several predicted gene
      clusters, including those responsible for encoding the hepatotoxin nodularin.
AU  - Popin RV
AU  - Rigonato J
AU  - Abreu VA
AU  - Andreote AP
AU  - Silveira SB
AU  - Odebrecht C
AU  - Fiore MF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00466-16.

PMID- 2830710
VI  - 24
DP  - 1987
TI  - The location of genes coding the specific modification and restriction system in the recombinant E. coli strain tF.
PG  - 9-12
AB  - The recombinant Escherichia coli tF strain has been shown to have its own specific
      modification and restriction system.  In order to establish the location of genes, coding this
      system a plasmid has been isolated from the investigated strain, which substantiates the
      resistance to streptomycin.  The plasmid DNA has been transformed into a recipient strain, E.
      coli O, which has no modification and restriction system of its own.  The newly obtained E.
      coli O (ptF) transformants also have proved negative with regard to their testing for the
      presence of a specific modification and restriction system.  The conclusion follows that the
      genes, coding the modification and restriction system of the E. coli tF strain are not located
      in the plasmid isolated from it.
AU  - Popovski B
PT  - Journal Article
TA  - Vet. Med. Nauki
JT  - Vet. Med. Nauki
SO  - Vet. Med. Nauki 1987 24: 9-12.

PMID- 3024387
VI  - 23
DP  - 1986
TI  - Structure and mechanisms of action of restrictional endonucleases.
PG  - 13-17
AB  - The structure and the mode of restrictional endonucleases are dealt with in
      detail.  Described are some more important representatives of the three types
      of endonucleases.  Stated are their role and place in present-day molecular
      biology.
AU  - Popovski B
PT  - Journal Article
TA  - Vet. Med. Nauki
JT  - Vet. Med. Nauki
SO  - Vet. Med. Nauki 1986 23: 13-17.

PMID- 2823452
VI  - 24
DP  - 1987
TI  - Phenotypic characteristics of a new modificational and restriction system in Escherichia coli.
PG  - 19-24
AB  - It has been demonstrated phenotypically that there exists a new
      modification-and-restrictional system as synthesized by the recombinant
      Escherichia coli tF strain.  A series of passages of the T3 and T7 phages and
      their mutants in E. coli tF has made it possible to ascertain a specific
      modification of the phage DNA, which was shown to be induced by the host
      strain.  The high level of adsorption of these phages on the cell surface of E.
      coli tF has ruled out the possibility of the existance of a nonclassical
      modification and restriction of DNA.  In view of the further characterizing of
      this modificational-and-restrictional system of E. coli tF it has been
      comparatively studied with the already known modification-and-restrictional
      systems isolated from various Escherichia coli strains.  Results have shown
      that no identity exists between the tested systems and the one in E. coli tF.
      It is stated that the new modificational-and-restrictional system of E. coli tF
      belongs to none of the three known types of restrictional endonucleases.
AU  - Popovski B
PT  - Journal Article
TA  - Vet. Med. Nauki
JT  - Vet. Med. Nauki
SO  - Vet. Med. Nauki 1987 24: 19-24.

PMID- 27540078
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the Sulfate-Reducing Bacterium Desulfotomaculum copahuensis Strain CINDEFI1 Isolated from the Geothermal Copahue System, Neuquen, Argentina.
PG  - e00870-16
AB  - Desulfotomaculum copahuensis strain CINDEFI1 is a novel spore-forming sulfate-reducing
      bacterium isolated from the Copahue volcano area, Argentina. Here, we present its draft genome
      in which we found genes related with the anaerobic respiration of sulfur compounds similar to
      those present in the Copahue environment.
AU  - Poratti GW
AU  - Yaakop AS
AU  - Chan CS
AU  - Urbieta MS
AU  - Chan KG
AU  - Ee R
AU  - Tan-Guan-Sheng A
AU  - Goh KM
AU  - Donati ER
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00870-16.

PMID- 25792062
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Lactobacillus kunkeei AR114 Isolated from Honey Bee Gut.
PG  - e00144-15
AB  - Lactobacillus kunkeei is a common inhabitant in honey bee gut, being present in several parts
      of the world. Here, we describe the draft genome of L. kunkeei
      AR114, an isolate from late foraging season in Norway.
AU  - Porcellato D
AU  - Frantzen C
AU  - Rangberg A
AU  - Umu OC
AU  - Gabrielsen C
AU  - Nes IF
AU  - Amdam GV
AU  - Diep DB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00144-15.

PMID- 25035319
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Enterococcus hirae Strain INF E1 Isolated from Cultured  Milk.
PG  - e00498-14
AB  - Here, we present the draft genome of Enterococcus hirae INF E1, found as a contaminant in
      cultured milk and studied for its ability to metabolize milk fat
      globule membrane glycoconjugates.
AU  - Porcellato D
AU  - Ostlie HM
AU  - Skeie SB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00498-14.

PMID- 24812215
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Geobacillus sp. Strain FW23, Isolated from a Formation Water Sample.
PG  - e00352-14
AB  - The thermophilic Geobacillus sp. strain FW23 was isolated from the Mehsana oil wells in
      Gujrat, India, during a screening for oil-degrading bacteria. Here, we
      report the draft genome sequence of Geobacillus sp. FW23, which may help reveal
      the genomic differences between this strain and the earlier reported species of
      the genus Geobacillus.
AU  - Pore SD
AU  - Arora P
AU  - Dhakephalkar PK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00352-14.

PMID- 29146852
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Agrobacterium tumefaciens Biovar 1 Strain 186, Isolated  from Walnut.
PG  - e01232-17
AB  - Agrobacterium tumefaciens biovar 1 strain 186 was isolated from a walnut tree expressing crown
      gall symptoms. The draft genome sequence of this strain harbored
      genes for crown gall formation and will be useful for understanding its virulence
      on Paradox, the predominant hybrid rootstock used for the cultivation of English
      walnut in California.
AU  - Poret-Peterson AT
AU  - Bhatnagar S
AU  - McClean AE
AU  - Kluepfel DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01232-17.

PMID- 23950122
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of emm Type 14 Streptococcus pyogenes Strain HSC5.
PG  - e00612-13
AB  - Streptococcus pyogenes causes a greater diversity of human disease than any other bacterial
      pathogen. Here, we present the complete genome sequence of the emm type
      14 S. pyogenes strain HSC5. This strain is a robust producer of the cysteine
      protease SpeB and is capable of producing infection in several different animal
      models.
AU  - Port GC
AU  - Paluscio E
AU  - Caparon MG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00612-13.

PMID- 26139722
VI  - 3
DP  - 2015
TI  - Complete Genome Sequences of emm6 Streptococcus pyogenes JRS4 and Parental Strain D471.
PG  - e00725-15
AB  - We report the complete genome assemblies of the group A Streptococcus pyogenes serotype emm6
      strain D471 and its streptomycin-resistant derivative JRS4. Both of
      these well-studied laboratory strains have been extensively characterized over
      the past three decades and have been instrumental in the discovery of multiple
      aspects of streptococcal pathogenesis.
AU  - Port GC
AU  - Paluscio E
AU  - Caparon MG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00725-15.

PMID- 21622735
VI  - 193
DP  - 2011
TI  - Genome Sequence of Rhodobacter sphaeroides strain WS8N.
PG  - 4027-4028
AB  - R. sphaeroides is a metabolically diverse photosynthetic alpha-proteobacterium found
      ubiquitously in soil and in fresh water
      habitats. Here we present the annotated genome sequence of Rhodobacter
      sphaeroides WS8N.
AU  - Porter SL
AU  - Wilkinson DA
AU  - Byles ED
AU  - Wadhams GH
AU  - Taylor S
AU  - Saunders NJ
AU  - Armitage JP
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4027-4028.

PMID- 10500219
VI  - 96
DP  - 1999
TI  - DNA adenine methylase mutants of Salmonella typhimurium show defects in protein secretion, cell invasion, and M cell cytotoxicity.
PG  - 11578-11583
AB  - Mutants of Salmonella typhimurium lacking DNA adenine methylase are attenuated for virulence
      in BALB/c mice.  LD(50) values of a DNA adenine methylation (Dam)(-) mutant are at least
      10(3)- to 10(4)-fold higher than those of the parental strain when administrated by oral or
      intraperitoneal routes. Dam(-) mutants are unable to proliferate in target organs but persist
      in low numbers in these locations. Efficient protection to challenge with the virulent
      parental strain is observed in mice infected with a Dam(-) mutant. Use of the ileal loop assay
      shows that Dam(-) mutants are less cytotoxic to M cells and fail to invade enterocytes. In the
      tissue culture model, lack of DNA adenine methylation causes reduced ability to invade
      nonphagocytic cells. In contrast, no effect is observed either in intracellular proliferation
      within nonphagocytic cells or in survival within macrophages. The invasion defect of Dam(-)
      mutants is correlated with a distinct pattern of secreted proteins, which is observed in both
      PhoP(+) and PhoP(-) backgrounds. Altogether, our observations suggest a multifactorial role of
      Dam methylation in Salmonella virulence.
AU  - Portillo FGD
AU  - Pucciarelli MG
AU  - Casadesus J
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1999 96: 11578-11583.

PMID- 29593690
VI  - 9
DP  - 2018
TI  - A Validation Approach of an End-to-End Whole Genome Sequencing Workflow for Source Tracking of Listeria monocytogenes and Salmonella enterica.
PG  - 446
AB  - Whole genome sequencing (WGS), using high throughput sequencing technology,
      reveals the complete sequence of the bacterial genome in a few days. WGS is
      increasingly being used for source tracking, pathogen surveillance and outbreak
      investigation due to its high discriminatory power. In the food industry, WGS
      used for source tracking is beneficial to support contamination investigations.
      Despite its increased use, no standards or guidelines are available today for the
      use of WGS in outbreak and/or trace-back investigations. Here we present a
      validation of our complete (end-to-end) WGS workflow for Listeria monocytogenes
      and Salmonella enterica including: subculture of isolates, DNA extraction,
      sequencing and bioinformatics analysis. This end-to-end WGS workflow was
      evaluated according to the following performance criteria: stability,
      repeatability, reproducibility, discriminatory power, and epidemiological
      concordance. The current study showed that few single nucleotide polymorphism
      (SNPs) were observed for L. monocytogenes and S. enterica when comparing genome
      sequences from five independent colonies from the first subculture and five
      independent colonies after the tenth subculture. Consequently, the stability of
      the WGS workflow for L. monocytogenes and S. enterica was demonstrated despite
      the few genomic variations that can occur during subculturing steps.
      Repeatability and reproducibility were also demonstrated. The WGS workflow was
      shown to have a high discriminatory power and has the ability to show genetic
      relatedness. Additionally, the WGS workflow was able to reproduce published
      outbreak investigation results, illustrating its capability of showing
      epidemiological concordance. The current study proposes a validation approach
      comprising all steps of a WGS workflow and demonstrates that the workflow can be
      applied to L. monocytogenes or S. enterica.
AU  - Portmann AC
AU  - Fournier C
AU  - Gimonet J
AU  - Ngom-Bru C
AU  - Barretto C
AU  - Baert L
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2018 9: 446.

PMID- 11841209
VI  - 41
DP  - 2002
TI  - Insertion of a reversible redox switch into a rare-cutting DNA endonuclease.
PG  - 2184-2190
AB  - Target sites for homing endonucleases occur infrequently in complex genomes. As a consequence,
      these enzymes can be used in mammalian systems to introduce double-strand breaks at
      recognition sites inserted within defined loci to study DNA repair by homologous and
      nonhomologous recombination. Using homing endonucleases for gene targeting in vivo would be
      more feasible if temporal or spatial regulation of their enzymatic activity were possible.
      Here, we show that the DNA cleavage activity of the yeast PI-SceI homing endonuclease can be
      turned on and off using a redox switch. Two cysteine pairs (Cys-64/Cys-344 and Cys-67/Cys-365)
      were separately inserted into flexible DNA binding loop(s) to create disulfide bonds that lock
      the endonuclease into a nonproductive conformation. The cleavage activities of the reduced
      Cys-64/Cys-344 and Cys-67/Cys-365 variants are similar or slightly lower than that of the
      control protein, but the activities of the proteins in the oxidized state are decreased more
      than 30-fold. Modulating the activity of the proteins is easily accomplished by adding or
      removing the reducing agent. We show that defects in DNA binding account for the decreased DNA
      cleavage activities of the proteins containing disulfide bonds. Interestingly, the
      Cys-67/Cys-365 variant toggles between two different DNA binding conformations under reducing
      and oxidizing conditions, which may permit the identification of structural differences
      between the two states. These studies demonstrate that homing endonuclease activity can be
      controlled using a molecular switch.
AU  - Posey KL
AU  - Gimble FS
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2002 41: 2184-2190.

PMID- 15280510
VI  - 32
DP  - 2004
TI  - Evolution of divergent DNA recognition specificities in VDE homing endonucleases from two yeast species.
PG  - 3947-3956
AB  - Homing endonuclease genes (HEGs) are mobile DNA elements that are thought to confer no benefit
      to their host. They encode site-specific DNA endonucleases that perpetuate the element within
      a species population by homing and disseminate it between species by horizontal transfer.
      Several yeast species contain the VMA1 HEG that encodes the intein-associated VMA1-derived
      endonuclease (VDE). The evolutionary state of VDEs from 12 species was assessed by assaying
      their endonuclease activities. Only two enzymes are active, PI-ZbaI from Zygosaccharomyces
      bailii and PI-ScaI from Saccharomyces cariocanus. PI-ZbaI cleaves the Z.bailii recognition
      sequence significantly faster than the Saccharomyces cerevisiae site, which differs at six
      nucleotide positions. A mutational analysis indicates that PI-ZbaI cleaves the S.cerevisiae
      substrate poorly due to the absence of a contact that is analogous to one made in PI-SceI
      between Gln-55 and nucleotides +9/+10. PI-ZbaI cleaves the Z.bailii substrate primarily due to
      a single base-pair substitution (A/T+5  T/A+5). Structural modeling of the PI-ZbaI/DNA complex
      suggests that Arg-331, which is absent in PI-SceI, contacts T/A+5, and the reduced activity
      observed in a PI-ZbaI R331A mutant provides evidence for this interaction. These data
      illustrate that homing endonucleases evolve altered specificity as they adapt to recognize
      alternative target sites.
AU  - Posey KL
AU  - Koufopanou V
AU  - Burt A
AU  - Gimble FS
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2004 32: 3947-3956.

PMID- 6096817
VI  - 12
DP  - 1984
TI  - Structure of the gene coding for the sequence-specific DNA-methyltransferase of the B. subtilis phage SPR.
PG  - 9039-9049
AB  - The nucleotide sequence of the gene coding for the 5'GGCC and 5'CCGG specific
      DNA methyltransferase of the Bacillus subtilis phage SPR was determined by the
      Maxam-Gilbert procedure.  Transcriptional and translational signals of the
      sequence were assigned with the help of S1 mapping and translation in E. coli
      minicells.  The gene codes for a 49 kd polypeptide.  The amino acid sequence of
      the SPR methylase shows regions of homology with the sequence of the
      5'-GGCC-specific BspRI modification methylase.
AU  - Posfai G
AU  - Baldauf F
AU  - Erdei S
AU  - Posfai J
AU  - Venetianer P
AU  - Kiss A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1984 12: 9039-9049.

PMID- 1923753
VI  - 19
DP  - 1991
TI  - Complementation by detached parts of GGCC-specific DNA methyltransferases.
PG  - 4843-4847
AB  - Individually inactive N- and C-terminal fragments of the m5C-methyltransferase
      M.BspRI can complement each other resulting in specific, in vivo methylation of
      the DNA.  This was shown by cloning the coding regions for N- and C-terminal
      parts of the enzyme in compatible plasmids and co-transforming them into E.
      coli cells.  The enzyme could be detached at several different sites, producing
      either non-overlapping or partially overlapping fragments capable of
      complementation.  Reconstitution of the active methyltransferase from inactive
      fragments was demonstrated in vitro, as well.  Another GGCC-specific
      methyltransferase, M.BsuRI, showed a similar complementation phenomenon.
      Moreover, interspecies complmentation was observed between appropriate
      fragments of the two closely related enzymes M.BspRI and M.BsuRI.  Fragments of
      structurally and functionally more different methyltransferases were unable to
      complement each other.
AU  - Posfai G
AU  - Kim SC
AU  - Szilak L
AU  - Kovacs A
AU  - Venetianer P
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 4843-4847.

PMID- 6313947
VI  - 170
DP  - 1983
TI  - Structure of the Bacillus sphaericus R modification methylase gene.
PG  - 597-610
AB  - A 2500 base-pair segment of Bacillus sphaericus R DNA cloned in Escherichia
      coli has previously been shown to carry the functional BspRI modification
      methylase gene.  The approximate location of the gene on this DNA segment and
      its direction of transcription were established by subcloning experiments.  The
      nucleotide sequence of the relevant region was determined by the Maxam-Gilbert
      procedure.  An open reading frame that can code for a 424 amino acid protein
      was found.  The calculated molecular weight (48,264) of this protein is in fair
      agreement with previous estimates (50,000 to 52,000).  The synthesis of this
      protein was demonstrated in E. coli minicells.  The initiation point of
      transcription by E. coli RNA polymerase was localized by in vitro transcription
      experiments.  The open reading frame starts 29 base-pairs downstream from the
      transcription initiation site and it is preceded by a sequence showing
      extensive Shine-Dalgarno complementarity.  Subcloning experiments and
      translation in minicells suggest that after removal of this translational
      initiation site, a secondary start site 29 amino acids downstream can also
      start translation in E. coli and this shorter protein retains the methylase
      activity.  The overall base composition of the gene and the codon usage
      indicate a strong preference for A.T base-pairs.
AU  - Posfai G
AU  - Kiss A
AU  - Erdei S
AU  - Posfai J
AU  - Venetianer P
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1983 170: 597-610.

PMID- 3556326
VI  - 50
DP  - 1986
TI  - Overproduction of the Bacillus sphaericus R modification methylase in Escherichia coli and its purification to homogeneity.
PG  - 63-67
AB  - A DNA fragment containing the information coding for the GGCC-specific Bacillus
      sphaericus R modification methylase, BspR, was inserted into plasmid vector
      pKK223-3 under the control of the strong and inducible tac promoter, and
      transformed into Escherichia coli HB101.  Upon induction this strain
      accumulated the methylase enzyme (while cell growth was inhibited) up to
      several percent of total cellular protein.  Homogeneous methylase could be
      prepared in three purification steps.
AU  - Posfai G
AU  - Kiss A
AU  - Venetianer P
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1986 50: 63-67.

PMID- 2840643
VI  - 16
DP  - 1988
TI  - Increasing the FokI cleavage specificity from 5 to 7 base pairs by two-step methylation.
PG  - 6245
AB  - Non-cognate methylation of specific nucleotides of the recognition sequence
      could inhibit the methylase but not the endonuclease of the same
      restriction-modification system.  This permits an increase in the cleavage
      specificity of the restriction enzyme by two-step methylation of the DNA, as
      shown here for the three-component M.MspI-M.FokI-FokI combination, changing
      FokI specificity from 5 to 7 bp.  The cleavage specificity of FokI is
      5'-GGATG(N)9/13.  M.FokI methylates only one strand of the recognition site
      resulting in GGmATG sequence.  MspI and FokI sites can overlap in the 7-bp
      sequence CCGGATG or in the 8-bp sequence CCGGGATG.  Methylation of such sites
      by M.MspI (methylation specificity:  mCCGG) produces non-cognate methylation of
      the overlapping FokI sites, resulting in  (a)G GATG    CmCTAC or (b)GGATG
      mCCTAC sequences, respectively.  We show here that in case (a), M.FokI is
      inhibited and FokI is unaffected (Fig. 2, lanes 3 and 2, respectively), while
      in case (b), M.FokI is unaffected and FokI is partially inhibited (Fig. 2,
      lanes 6 and 5, respectively, where M.HpaII was used to produce the (b) type
      non-cognate methylation of FokI sites on the same 7-bp sequences).  As a
      result, when the DNA is premethylated by M.MspI, M.FokI cannot methylate those
      7-bp CCGGATG sequences (which thus remain susceptible to FokI), whereas all
      other FokI sites would be methylated and thus protected from FokI cleavage.
      However, cleavage by FokI at the CCGGATG sites may not be complete (max 90%),
      because M.FokI has some residual affinity to the sites premethylated by M.MspI,
      especially when excess M.FokI is used (data not shown).  Nevertheless, in many
      cases this does not affect the applicability of the system.
AU  - Posfai G
AU  - Szybalski W
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1988 16: 6245.

PMID- 3265686
VI  - 69
DP  - 1988
TI  - A simple method for locating methylated bases in DNA, as applied to detect asymmetric methylation by M.FokIA.
PG  - 147-151
AB  - Class-IIS restriction enzymes, which cut the DNA outside their recognition sequence, could be
      used for locating the bases methylated by a DNA-modification methylase.  This is possible
      because methylation of the class-IIS cut sites does not interfere with the cleavage.  The
      method consists of (i) selection of a nucleotide sequence with appropriate overlap between the
      methylase recognition site and the class-IIS enzyme cut site, (ii) methylation using
      S-adenosylmethionine as [3H]methyl donor, (iii) cleavage of the methylated sequence with the
      class-IIS enzyme, (iv) separation of the cleavage products and identification of the
      3H-labelled fragment.  Using this simple and straightforward method, we have shown that
      M.FokIA is an adenine methylase and methylates asymmetrically one strand of the FokI
      recognition site, resulting in the
      5'-GGmATG(N)9
      CC TAC(N)13
      sequence.  In addition, it was observed that another class-IIS restriction enzyme, SfaNI, is
      completely inhibited by methylation of its recognition site,  5'-GCA TC/CGTmAG, by M.FokIA.
AU  - Posfai G
AU  - Szybalski W
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 69: 147-151.

PMID- 3074006
VI  - 74
DP  - 1988
TI  - A simple method for locating methylated bases in DNA using class-IIS restriction enzymes.
PG  - 179-181
AB  - Meeting Abstract
AU  - Posfai G
AU  - Szybalski W
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 179-181.

PMID- 2717398
VI  - 17
DP  - 1989
TI  - Predictive motifs derived from cytosine methyltransferases.
PG  - 2421-2435
AB  - Thirteen bacterial DNA methyltransferases that catalyze the formation of
      5-methylcytosine within specific DNA sequences possess related structures.
      Similar building blocks (motifs), containing invariant positions, can be found
      in the same order in all thirteen sequences.  Five of these blocks are highly
      conserved while a further five contain weaker similarities.  One block, which
      has the most invariant residues, contains the proline-cysteine dipeptide of the
      proposed catalytic site.  A region in the second half of each sequence is
      unusually variable both in length and sequence composition.  Those
      methyltransferases that exhibit significant homology in this region share
      common specificity in DNA recognition.  The five highly conserved motifs can be
      used to discriminate the known 5-methylcytosine forming methyltransferases from
      all other methyltransferases of known sequence, and from all other identified
      proteins in the PIR, GenBank and EMBL databases.  These five motifs occur in a
      mammalian methyltransferase responsible for the formation of 5-methylcytosine
      within CG dinucleotides.  By searching the unidentified open reading frames
      present in the GenBank and EMBL databases, two potential 5-methylcytosine
      forming methyltransferases have been found.
AU  - Posfai J
AU  - Bhagwat AS
AU  - Posfai G
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 2421-2435.

PMID- 3248729
VI  - 74
DP  - 1988
TI  - Sequence motifs specific for cytosine methyltransferases.
PG  - 261-265
AB  - Using a new alignment method, the sequences of 13 m5C methyltransferases
      (MTases) have been examined.  Five extremely well-conserved blocks of sequence
      have been detected and have been used as fixed points for the alignment of the
      13 sequences.  Following this initial alignment, five further blocks of
      similarity have been identified to give a total of ten recognizable blocks of
      sequence homology that are all arranged in a common order.  The structures of
      these MTases consist of a variable-length N-terminal arm followed by eight
      well-conserved blocks each separated by small variable-length regions.  A large
      variable-length segment of 90 to 270 amino acids (aa) then follows.  After this
      are two blocks, and a variable-length C-terminal segment completes the
      sequence.  Within the final alignment, 20 aa in the protein sequences, and 86
      nucleotides in the nucleotide sequences are invariant.  The strongest
      conservation is found in proximity to a suspected functional site that contains
      the dipeptide proline-cysteine.  Consensus patterns can be defined for the five
      best conserved blocks and, when used as search motifs, are able to clearly
      distinguish between the m5C MTases and all other identified proteins in the PIR
      database.  This suggests they may be of use in identifying putative MTases
      among protein sequences of unknown function.
AU  - Posfai J
AU  - Bhagwat AS
AU  - Roberts RJ
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 261-265.

PMID- 2467142
VI  - 13D
DP  - 1989
TI  - Predictive motifs of cytosine methylases.
PG  - 213
AB  - Fourteen bacterial DNA methyltransferases that catalyze the formation of
      5-methylcytosine within specific DNA sequences possess related structures.
      Similar building blocks (motifs), containing invariant positions, can be found
      in the same order in all fourteen sequences.  Five of these blocks are highly
      conserved while a further five contain weaker similarities.  One block which
      has the most invariant residues, contains the proline-cysteine dipeptide of the
      proposed catalytic site.  A region in the second half of each sequence is
      unusually variable both in length and sequence composition.  Those
      methyltransferases that exhibit significant homology in this region share
      common specificity in DNA recognition.  The five highly conserved motifs can be
      used to discriminate the known 5-methylcytosine forming methyltransferases from
      all other methyltransferases of known sequence and from all other identified
      proteins in the PIR, GenBank and EMBL databases.  These five motifs occur in
      the eukaryotic mammalian methyltransferase.  By searching the unidentified open
      reading frames present in the GenBank and EMBL databases two potential cytosine
      methyltransferases have been found that were not recognized previously.
AU  - Posfai J
AU  - Roberts RJ
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1989 13D: 213.

PMID- 21396108
VI  - 12
DP  - 2011
TI  - Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper.
PG  - 146
AB  - BACKGROUND: Bacterial spot of tomato and pepper is caused by four Xanthomonas
      species and is a major plant disease in warm humid climates. The four species are
      distinct from each other based on physiological and molecular characteristics.
      The genome sequence of strain 85-10, a member of one of the species, Xanthomonas
      euvesicatoria (Xcv) has been previously reported. To determine the relationship
      of the four species at the genome level and to investigate the molecular basis of
      their virulence and differing host ranges, draft genomic sequences of members of
      the other three species were determined and compared to strain 85-10. RESULTS: We
      sequenced the genomes of X. vesicatoria (Xv) strain 1111 (ATCC 35937), X.
      perforans (Xp) strain 91-118 and X. gardneri (Xg) strain 101 (ATCC 19865). The
      genomes were compared with each other and with the previously sequenced Xcv
      strain 85-10. In addition, the molecular features were predicted that may be
      required for pathogenicity including the type III secretion apparatus, type III
      effectors, other secretion systems, quorum sensing systems, adhesins,
      extracellular polysaccharide, and lipopolysaccharide determinants. Several novel
      type III effectors from Xg strain 101 and Xv strain 1111 genomes were
      computationally identified and their translocation was validated using a reporter
      gene assay. A homolog to Ax21, the elicitor of XA21-mediated resistance in rice,
      and a functional Ax21 sulfation system were identified in Xcv. Genes encoding
      proteins with functions mediated by type II and type IV secretion systems have
      also been compared, including enzymes involved in cell wall deconstruction, as
      contributors to pathogenicity. CONCLUSIONS: Comparative genomic analyses revealed
      considerable diversity among bacterial spot pathogens, providing new insights
      into differences and similarities that may explain the diverse nature of these
      strains. Genes specific to pepper pathogens, such as the O-antigen of the
      lipopolysaccharide cluster, and genes unique to individual strains, such as novel
      type III effectors and bacteriocin genes, have been identified providing new
      clues for our understanding of pathogen virulence, aggressiveness, and host
      preference. These analyses will aid in efforts towards breeding for broad and
      durable resistance in economically important tomato and pepper cultivars.
AU  - Potnis N
AU  - Krasileva K
AU  - Chow V
AU  - Almeida NF
AU  - Patil PB
AU  - Ryan RP
AU  - Sharlach M
AU  - Behlau F
AU  - Dow JM
AU  - Momol M
AU  - White FF
AU  - Preston JF
AU  - Vinatzer BA
AU  - Koebnik R
AU  - Setubal JC
AU  - Norman DJ
AU  - Staskawicz BJ
AU  - Jones JB
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2011 12: 146.

PMID- 29954905
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Bacillus altitudinis Lc5, a Biocontrol and Plant Growth-Promoting Endophyte Strain Isolated from Indigenous Black Rice of Manipur.
PG  - e00601-18
AB  - We report here the 3.6-Mb draft genome of Bacillus altitudinis Lc5, a potential plant growth
      promoter and an active antagonistic endophyte of black rice. This
      genome study will provide better insights into the strain's mechanisms for plant
      growth promotion and biocontrol, thus facilitating its application in organic
      agriculture.
AU  - Potshangbam M
AU  - Sahoo D
AU  - Verma P
AU  - Verma S
AU  - Kalita MC
AU  - Indira DS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00601-18.

PMID- 6286593
VI  - 151
DP  - 1982
TI  - Exonuclease activity from Pseudomonas aeruginosa which is missing in phenotypically restrictionless mutants.
PG  - 1204-1209
AB  - A phenotypically restrictionless strain of Pseudomonas aeruginosa was found to
      lack a deoxyribonuclease specific for linear duplex DNA.  The purified enzyme
      had an optimum pH of 8.5, required MgCl2 (10 mM) for maximum activity, and did
      not require ATP.  Neither the degradation of heat-denatured DNA nor the
      degradation of bacteriophage F116 DNA was detected.  The genome of
      bacteriophage F116 was shown to possess single-stranded terminal regions, which
      account for the resistance to degradation and for the ability of the phage to
      transfect restriction-proficient strains.
AU  - Potter AA
AU  - Loutit JS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1982 151: 1204-1209.

PMID- 6094546
VI  - 259
DP  - 1984
TI  - Cleavage of phosphorothioate-substituted DNA by restriction endonucleases.
PG  - 14243-14248
AB  - M13 RF DNA was synthesized in vitro in the presence of various single
      deoxynucleoside 5'-O-(1-thiotriphosphate) phosphorothioate analogues, and the
      three other appropriate deoxynucleoside triphosphates using a M13
      (+)-single-stranded template, Escherichia coli DNA polymerase I and T4 DNA
      ligase.  The resulting DNAs contained various restriction endonuclease
      recognition sequences which had been modified at their cleavage points in the
      (-)-strand by phosphorothioate substitution.  The behavior of the restriction
      enzymes AvaI, BamHI, EcoRI, HindIII, and SalI towards these substituted DNAs
      was investigated.  EcoRI, BamHI, and HindIII were found to cleave appropriate
      phosphorothioate-substituted DNA at a reduced rate compared to normal M13 RF
      DNA, and by a two-step process in which all of the DNA is converted to an
      isolable intermediate nicked molecule containing a specific discontinuity at
      the respective recognition site presumably in the (+)-strand.  By contrast,
      SalI cleaved substituted DNA effectively without the intermediacy of a nicked
      form.  AvaI, however, is only capable of cleaving the unsubstituted (+)-strand
      in appropriately modified DNA.
AU  - Potter BVL
AU  - Eckstein F
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1984 259: 14243-14248.

PMID- 28729267
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the blaOXA-436- and blaNDM-1-Harboring Shewanella putrefaciens SA70 Isolate.
PG  - e00644-17
AB  - We sequenced a carbapenem-resistant Shewanella putrefaciens isolate cultured from the sink
      handle of a Pakistan hospital room. Assembly annotation indicates that
      the isolate has a chromosomal blaOXA-436 carbapenemase and a plasmid-borne
      blaNDM-1 gene. To our knowledge, this is the first report of a Shewanella species
      harboring blaNDM.
AU  - Potter RF
AU  - D'Souza AW
AU  - Wallace MA
AU  - Shupe A
AU  - Patel S
AU  - Gul D
AU  - Kwon JH
AU  - Andleeb S
AU  - Burnham CA
AU  - Dantas G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00644-17.

PMID- 401500
VI  - 129
DP  - 1977
TI  - Two-dimensional restriction analysis of the Bacillus subtilis genome: gene purification and ribosomal ribonucleic acid gene organization.
PG  - 492-500
AB  - With two-dimensional restriction enzyme analysis we have been able to cleave
      the Bacillus subtilis genome and resolve the resulting deoxyribonucleic acid
      (DNA) segments into discrete bands on agarose gels.  A general procedure for
      gene purification has been developed by coupling multidimensional restriction
      analysis with a biological assay for gene detection.  The organization of
      ribosomal ribonucleic acid (rRNA) genes was studied by hybridizing 16S and 23S
      rRNA probes to the two-dimensional DNA banding patterns.
AU  - Potter SS
AU  - Bott KF
AU  - Newbold JE
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1977 129: 492-500.

PMID- 17660407
VI  - 153
DP  - 2007
TI  - A putative DNA adenine methyltransferase is involved in Yersinia pseudo tuberculosis pathogenicity.
PG  - 2426-2434
AB  - Some adenine methyltransferases have been shown not only to protect specific DNA restriction
      sites from cleavage by a restriction
      endonuclease, but also to play a role in various bacterial processes
      and sometimes in bacterial virulence. This study focused on a type I
      restriction-modification system (designated yrml) of Y.
      pseudotuberculosis. This system is composed of three adjacent genes
      which could potentially encode an N-6-adenine DNA methylase (YamA), an
      enzyme involved in site-specific recognition (YrsA) and a restriction
      endonuclease (YreA). Screening of 85 isolates of Y. pestis and Y.
      pseudotuberculosis indicated that the yrml system has been lost by Y.
      pestis and that yamA (but not yrsA or yreA) is present in all Y
      pseudotuberculosis strains tested, suggesting that it may be important
      at some stages of the epidemiological cycle of this species. To further
      investigate the role of yamA in Y pseudo tuberculosis survival,
      multiplication or virulence, a Delta yamA mutant of Y
      pseudotuberculosis IP32953 was constructed by allelic exchange with a
      kanamycin cassette. The fact that Delta yamA mutants were obtained
      indicated that this gene is not essential for Y pseudotuberculosis
      viability. The IP32953 Delta yamA mutant strain grew as well as the
      wild-type in a rich medium at both 28 degrees C and 37 degrees C. It
      also grew normally in a chemically defined medium at 28 degrees C, but
      exhibited a growth defect at 37 degrees C. In contrast to the Dam
      adenine methyltransferase, a mutation in yamA did not impair the
      functions of DNA repair or resistance to detergents. However, the Delta
      yamA mutant exhibited a virulence defect in a mouse model of
      intragastric infection. The in silico analysis indicated that the
      chromosomal region carrying the Y pseudotuberculosis yrml locus has
      been replaced in Y. pestis by a horizontally acquired region which
      potentially encodes another methyltransferase. YamA might thus be
      dispensable for Y. pestis growth and virulence because this species has
      acquired another gene fulfilling the same functions.
AU  - Pouillot F
AU  - Fayolle C
AU  - Carniel E
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2007 153: 2426-2434.

PMID- 29242227
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of the Kiwifruit Pathogen Pseudomonas syringae pv. actinidiae Biovar 5, Originating from Japan.
PG  - e01409-17
AB  - We present the first complete genome sequence of a copper-resistant biovar 5 strain of a
      bacterial pathogen of kiwifruit, Pseudomonas syringae pv. actinidiae.
      Comparison with the genome sequence of a copper-sensitive biovar 5 isolate
      indicates that copper resistance is encoded on a plasmid.
AU  - Poulter R
AU  - Taiaroa G
AU  - Sumpter N
AU  - Stockwell P
AU  - Butler M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01409-17.

PMID- 17046294
VI  - 44
DP  - 2007
TI  - The nuclear-encoded inteins of fungi.
PG  - 153-179
AB  - An intein is a protein sequence embedded within a precursor protein that is excised during
      protein maturation. Inteins were first found
      encoded in the VMA gene of Saccharomyces cerevisiae. Subsequently, they
      have been found in diverse organisms (eukaryotes, archaea, eubacteria
      and viruses). The VMA intein has been found in various saccharomycete
      yeasts but not in other fungi. Different inteins have now been found
      widely in the fungi (ascomycetes, basidiomycetes, zygomycetes and
      chytrids) and in diverse proteins. A protein distantly related to
      inteins, but closely related to metazoan hedgehog proteins, has been
      described from Glomeromycota. Many of the newly described inteins
      contain homing endonucleases and some of these are apparently active.
      The enlarged fungal intein data set permits insight into the evolution
      of inteins, including the role of horizontal transfer in their
      persistence. The diverse fungal inteins provide a resource for
      biotechnology using their protein splicing or homing endonuclease
      capabilities.
AU  - Poulter RTM
AU  - Goodwin TJD
AU  - Butler MI
PT  - Journal Article
TA  - Fungal Genet. Biol.
JT  - Fungal Genet. Biol.
SO  - Fungal Genet. Biol. 2007 44: 153-179.

PMID- 2834268
VI  - 24
DP  - 1988
TI  - Cloning of the restriction-modification genes of Bacillus centrosporus in Escherichia coli.
PG  - 210-215
AB  - Using the pBR327 vector we have produced a genomic library of Bacillus
      centrosporus.  The total plasmid DNA of the library was cleaved by the
      restriction endonuclease BcnI and then transformed in Escherichia coli RR1.
      Among the transformants obtained we identified two clones possessing
      restriction and DNA modification profiles of BcnI and containing 13.3 kb and
      9.05 kb plasmids, respectively.  Restriction mapping of both plasmids showed
      that they contained two sites for HindIII, one site for Eco31I, and one site
      for Eco47III located at equal distances.  Deletion mapping of the recombinant
      plasmids confirmed that this was the region of the location of the BcnI
      restriction-modification genes.  On the basis of the results obtained we
      discuss the special features of cloning of the restriction-modification genes.
AU  - Povilionis PI
AU  - Lubys AA
AU  - Janulaitis A
PT  - Journal Article
TA  - Genetika
JT  - Genetika
SO  - Genetika 1988 24: 210-215.

PMID- 2547699
VI  - 25
DP  - 1989
TI  - Investigation of methyl-cytosine specific restriction in Escherichia coli K-12.
PG  - 753-755
AB  - Experiments on transformation of Escherichia coli K-12 cells by plasmids
      carrying RM systems with different recognition sites containing
      5-methylcytosine have shown that the gene mcrB dtermines the function of
      restriction.  The data obtained made it possible to believe that E. coli
      possesses no restriction system recognizing specifically cytosine methylated in
      position 4.
AU  - Povilionis PI
AU  - Lubys AA
AU  - Vaisvila RI
AU  - Kulakauskas ST
AU  - Janulaitis A
PT  - Journal Article
TA  - Genetika
JT  - Genetika
SO  - Genetika 1989 25: 753-755.

PMID- 16347091
VI  - 51
DP  - 1986
TI  - Resistance to in vitro restriction of DNA from lactic streptococcal bacteriophage c6A.
PG  - 1358-1360
AB  - DNA isolated from streptococcal bacteriophage c6A was cut only infrequently by
      many restriction endonucleases.  Fragments of c6A DNA cloned in Escherichia
      coli plasmids were similarly resistant to cleavage.  We conclude that the low
      frequency of cleavage is due to an unusually low number of restriction enzyme
      recognition sequences in c6A DNA.
AU  - Powell IB
AU  - Davidson BE
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1986 51: 1358-1360.

PMID- 9799635
VI  - 283
DP  - 1998
TI  - The DNA binding characteristics of the trimeric EcoKI methyltransferase and its partially assembled dimeric form determined by fluorescence polarization and DNA footprint.
PG  - 947-961
AB  - The type I DNA restriction and modification systems of enteric bacteria display several
      enzymatic activities due to their oligomeric structure.  Partially assembled forms of the
      EcoKI enzyme from E. coli K12 can display specific DNA binding properties and modification
      methyltransferase activity.  The heterodimer of one specificity (S) subunit and one
      modification (M) subunit can only bind DNA whereas  the addition of a second modification
      subunit to form M2S1 also confers methyltransferase activity.  We have examined the DNA
      binding specificity of M1S1 and M2S1 using the change in fluorescence anisotropy which occurs
      on binding of a DNA probe labelled with a hexachlorofluorescein fluorophore.  The dimer has
      much weaker affinity for the EcoKI target sequence than the trimer and slightly less ability
      to discriminate against other DNA sequences.  Binding of both proteins is strongly dependent
      on salt concentration.  The fluorescence results compare favorably with those obtained with
      the gel retardation method.  DNA footprinting using exonucleaseIII and DNaseI, and methylation
      interference show no asymmetry, with both DNA strands being protected by the dimer and the
      trimer.  This indicates that the dimer is a mixture of the two possible forms, M1S1 and S1M1.
      The dimer has a footprint on the DNA substrate of the same length as the trimer implying that
      the modification subunits are located on either side of the DNA helical axis rather than lying
      along the helical axis.
AU  - Powell LM
AU  - Connolly BA
AU  - Dryden DTF
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1998 283: 947-961.

PMID- 9799636
VI  - 283
DP  - 1998
TI  - Sequence-specific DNA binding by EcoKI, a type IA DNA restriction enzyme.
PG  - 963-976
AB  - The type I DNA restriction and modification enzymes of prokaryotes are multimeric enzymes that
      cleave unmethylated, foreign DNA in a complex process involving recognition of the methylation
      status of a DNA target sequence, extensive translocation of DNA in both directions towards the
      enzyme bound at the target sequence, ATP hydrolysis, which is believed to drive the
      translocation possibly via a helicase mechanism, and eventual endonucleolytic cleavage of the
      DNA.  We have examined the DNA binding affinity and exonuclease III footprint of the EcoKI
      type IA restriction enzyme on oligonucleotide duplexes that either contain or lack the target
      sequence.  The influence of the cofactors, S-adenosyl methionine and ATP, on binding to DNA of
      different methylation states has been assessed.  EcoKI in the absence of ATP, with or without
      S-adenosyl methionine, binds tightly even to DNA lacking the target site and the exonuclease
      footprint is large, approximately 45 base-pairs.  The protection is weaker on DNA lacking the
      target site.  Partially assembled EcoKI lacking one or both of the subunits essential for DNA
      cleavage, is unable to bind tightly to DNA lacking the target site but can bind tightly to the
      recognition site.  The addition of ATP to EcoKI, in the presence of AdoMet, allows tight
      binding only to the target site and the footprint shrinks to 30 base pairs, almost identical
      to that of the modification enzyme which makes up the core of EcoKI.  The same effect occurs
      when S-adenosyl homocysteine or sinefungin are substituted for S-adenosyl methionine, and ADP
      or ATPgammaS are substituted for ATP.  It is proposed that the DNA binding surface of EcoKI
      comprises three regions: a "core" region which recognizes the target sequence and which is
      present on the modification enzyme, and a region on each DNA cleavage subunit.  The cleavage
      subunits make tight contacts to any DNA molecule in the absence of cofactors, but this contact
      is weakened in the presence of cofactors to allow the protein conformational changes required
      for DNA translocation when a target site is recognized by the core modification enzyme.  This
      weakening of the interaction between the DNA cleavage subunits and the DNA could allow more
      access of exonuclease III to DNA and account for the shorter footprint.
AU  - Powell LM
AU  - Dryden DTF
AU  - Murray NE
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1998 283: 963-976.

PMID- 8230207
VI  - 234
DP  - 1993
TI  - DNA recognition by the EcoK methyltransferase. The influence of DNA methylation and the cofactor S-adenosyl-L-methionine.
PG  - 60-71
AB  - The methyltransferase of the EcoK type I restriction/modification system is trimeric, M2S1,
      where the S subunit determines the sequence specificity of the enzyme. The methyltransferase
      has a strong preference for hemimethylated substrate DNA and therefore, we have investigated
      the effect of the methylation state of DNA on binding by the enzyme, together with the effects
      on binding of the cofactor S-adenosyl-L-methionine. Our results indicate that the
      methyltransferase has two non-interacting S-adenosyl-L-methionine binding sites, each with a
      dissociation constant of 3.60 (+-0.42)uM determined by equilibrium dialysis, or 2.21 (+-0.29)
      uM determined by the displacement of a fluorescent probe. Ultraviolet light-induced
      crosslinking showed that S-adenosyl-L-methionine binds strongly only to the modification (M)
      subunits. Changes in the sedimentation velocity of the methyltransferases imply a protein
      conformational change due to S-adenosyl-L-methionine binding. Gel retardation results show
      that the binding of S-adenosyl-L-methionine to the methyltransferase enhances binding to both
      specific and non-specific DNAs, but the enhancement is greater for the specific DNA.
      Differences in binding affinities contribute to the recognition of the specific nucleotide
      sequence AAC(N)6GTGC by the methyltransferase in preference to a non-specific sequence. In
      contrast, although the complexes of unmodified and hemimethylated DNAs with the
      methyltransferase have different mobilities in non-denaturing gels, there appears to be no
      contribution of binding affinity to the distinction between these two substrates. Therefore,
      the preference for the hemimethylated substrate must be due to a difference in catalysis.
AU  - Powell LM
AU  - Dryden DTF
AU  - Willcock DF
AU  - Pain RH
AU  - Murray NE
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1993 234: 60-71.

PMID- 12568936
VI  - 103
DP  - 2003
TI  - Assembly of EcoKI DNA methyltransferase requires the C-terminal region of the HsdM modification subunit.
PG  - 129-137
AB  - The methyltransferase component of type I DNA restriction and modification systems comprises
      three subunits, one DNA sequence specificity subunit and
      two DNA modification subunits. Limited proteolysis of the EcoKI
      methyltransferase shows that a 55-kDa N-terminal fragment of the 59-kDa
      modification subunit is resistant to degradation. We have purified this
      fragment and determined by mass spectrometry that proteolysis removes 43
      or 44 amino acids from the C-terminus. The fragment fails to interact with
      the other subunits even though it still possesses secondary and tertiary
      structure and the ability to bind the S-adenosylmethionine cofactor. We
      conclude that the C-terminal region of the modification subunit of EcoKI
      is essential for the assembly of the EcoKI methyltransferase.
AU  - Powell LM
AU  - Lejeune E
AU  - Hussain FS
AU  - Cronshaw AD
AU  - Kelly SM
AU  - Price NC
AU  - Dryden DT
PT  - Journal Article
TA  - Biophys. Chem.
JT  - Biophys. Chem.
SO  - Biophys. Chem. 2003 103: 129-137.

PMID- 7731811
VI  - 23
DP  - 1995
TI  - S-adenosyl methionine alters the DNA contacts of the EcoKI methyltransferase.
PG  - 967-974
AB  - The EcoKI methyltransferase methylates two adenines on opposite strands of its bipartite DNA
      recognition sequence AAC(N6)GTGC. The enzyme has a strong preference for hemimethylated DNA
      substrates, but the methylation state of the DNA does not influence its binding affinity.
      Methylation interference was used to compare the contacts made by the EcoKI methyltransferase
      with unmodified, hemimethylated or fully modified DNAs. Contacts were seen at or near the N7
      position of guanine, in the major groove, for all of the guanines in the EcoKI recognition
      sequence, and at two guanines on the edge of the intervening spacer sequence. The presence of
      the cofactor and methyl donor S-adenosyl methionine had a striking effect on the interference
      pattern for unmodified DNA which could not be mimicked by the presence of the cofactor
      analogue S-adenosyl homocysteine. In contrast, S-adenosyl methionine had no effect on the
      interference patterns for either kind of hemimethylated DNA, or for fully modified DNA.
      Differences between the interference patterns for the unmodified DNA provide evidence that
      methylation of the target sequence influences the conformation of the protein-DNA interface,
      and illustrate the importance of S-adenosyl methionine in the distinction between unmodified
      and methylated DNA by the methyltransferase.
AU  - Powell LM
AU  - Murray NE
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1995 23: 967-974.

PMID- 24385572
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Alga-Aggregating Bacterium Bacillus sp. Strain RP1137.
PG  - e00973-13
AB  - Bacillus sp. strain RP1137 is a bacterium that is able to rapidly and efficiently aggregate
      biofuel-producing microalgae. By 16S rRNA gene sequencing, it was found
      to be related to the industrially important Bacillus megaterium. Here, we report
      the draft genome sequence of Bacillus sp. strain RP1137.
AU  - Powell RJ
AU  - Bachvaroff TR
AU  - Hill RT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00973-13.

PMID- 23516209
VI  - 1
DP  - 2013
TI  - Genome Sequence of Cronobacter sakazakii SP291, a Persistent Thermotolerant Isolate Derived from a Factory Producing Powdered Infant Formula.
PG  - e0008213
AB  - Cronobacter is an opportunistic pathogen associated with meningitis in neonates.  Based on
      long-term surveillance of a powdered infant formula production facility,
      a persistent and thermotolerant isolate, denoted Cronobacter sakazakii SP291, was
      detected. Here we report the complete genome along with the sequences of three
      plasmids identified in this organism.
AU  - Power KA
AU  - Yan Q
AU  - Fox EM
AU  - Cooney S
AU  - Fanning S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0008213.

PMID- 24356836
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Lactobacillus crispatus EM-LC1, an Isolate with Antimicrobial Activity Cultured from an Elderly Subject.
PG  - e01070-13
AB  - Here we report the 1.86-Mb draft genome sequence of Lactobacillus crispatus EM-LC1, a fecal
      isolate with antimicrobial activity. This genome sequence is
      expected to provide insights into the antimicrobial activity of L. crispatus and
      improve our knowledge of its potential probiotic traits.
AU  - Power SE
AU  - Harris HM
AU  - Bottacini F
AU  - Ross RP
AU  - O'Toole PW
AU  - Fitzgerald GF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01070-13.

PMID- 24090403
VI  - 14
DP  - 2013
TI  - Efficient and accurate whole genome assembly and methylome profiling of E. coli.
PG  - 675
AB  - BACKGROUND: With the price of next generation sequencing steadily decreasing, bacterial genome
      assembly is now accessible to a wide range of researchers. It is
      therefore necessary to understand the best methods for generating a genome
      assembly, specifically, which combination of sequencing and bioinformatics
      strategies result in the most accurate assemblies. Here, we sequence three E.
      coli strains on the Illumina MiSeq, Life Technologies Ion Torrent PGM, and
      Pacific Biosciences RS. We then perform genome assemblies on all three datasets
      alone or in combination to determine the best methods for the assembly of
      bacterial genomes. RESULTS: Three E. coli strains - BL21(DE3), Bal225, and
      DH5alpha - were sequenced to a depth of 100x on the MiSeq and Ion Torrent
      machines and to at least 125x on the PacBio RS. Four assembly methods were
      examined and compared. The previously published BL21(DE3) genome
      [GenBank:AM946981.2], allowed us to evaluate the accuracy of each of the
      BL21(DE3) assemblies. BL21(DE3) PacBio-only assemblies resulted in a 90%
      reduction in contigs versus short read only assemblies, while N50 numbers
      increased by over 7-fold. Strikingly, the number of SNPs in PacBio-only
      assemblies were less than half that seen with short read assemblies (~20 SNPs vs.
      ~50 SNPs) and indels also saw dramatic reductions (~2 indel >5 bp in PacBio-only
      assemblies vs. ~12 for short-read only assemblies). Assemblies that used a
      mixture of PacBio and short read data generally fell in between these two
      extremes. Use of PacBio sequencing reads also allowed us to call covalent base
      modifications for the three strains. Each of the strains used here had a known
      covalent base modification genotype, which was confirmed by PacBio sequencing.
      CONCLUSION: Using data generated solely from the Pacific Biosciences RS, we were
      able to generate the most complete and accurate de novo assemblies of E. coli
      strains. We found that the addition of other sequencing technology data offered
      no improvements over use of PacBio data alone. In addition, the sequencing data
      from the PacBio RS allowed for sensitive and specific calling of covalent base
      modifications.
AU  - Powers JG
AU  - Weigman VJ
AU  - Shu J
AU  - Pufky JM
AU  - Cox D
AU  - Hurban P
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2013 14: 675.

PMID- 21131493
VI  - 193
DP  - 2010
TI  - Genome Sequence of an Erwinia amylovora Strain with Restricted Pathogenicity to Rubus Plants.
PG  - 785-786
AB  - Here we present the genome of a strain of Erwinia amylovora, the fire blight pathogen, with
      restricted pathogenicity to Rubus spp. Comparative
      genomics of ATCC BAA-2158 with E. amylovora strains from non-Rubus hosts
      identified significant genetic differences but supports the inclusion of
      this strain within the species E. amylovora.
AU  - Powney R
AU  - Smits TH
AU  - Sawbridge T
AU  - Frey B
AU  - Blom J
AU  - Frey JE
AU  - Plummer KM
AU  - Beer SV
AU  - Luck J
AU  - Duffy B
AU  - Rodoni B
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 193: 785-786.

PMID- Not carried by PubMed...
VI  - 9
DP  - 1994
TI  - Sequence-specific DNA affinity chromatography: Application of a group specific adsorbent for the isolation of restriction endonucleases.
PG  - 543-546
AB  - Several rapid and effective methods have been described to obtain restriction endonucleases
      suitable for commercial exploitation. However lengthy and laborious protocols have been
      necessary to obtain homogeneous enzymes. The use of sequence-specific DNA affinity
      chromatography to purify restriction endonucleases EcoRI and SphI to near homogeneity in a two
      step procedure has been recently reported. However, the high cost of these adsorbents is a
      limiting factor for their wider application. The application of a sequence-specific DNA
      affinity ligand containing recognition sequences for 34 restriction endonucleases as
      group-specific ligand for the isolation of restriction endonucleases is now reported. Crude
      samples of six restriction endonucleases namely BshFI, BamHI, SmaI, SacII, PvuII and SalI were
      shown to bind to this adsorbent and could be eluted at different Kcl concentrations with
      purification factors obtained varying from 8 to greater than 300 fold and recoveries from
      75-94%. Furthermore, restriction endonuclease BshFI, an isoschizomer of HaeIII from the
      microorganism Bacillus sphaericus was purified to near homogeneity employing a two step
      procedure which involves DNA cellulose chromatography and oligonucleotide ligand affinity
      chromatography.
AU  - Pozidis C
AU  - Vlatakis G
AU  - Bouriotis V
PT  - Journal Article
TA  - Prog. Biotechnol.
JT  - Prog. Biotechnol.
SO  - Prog. Biotechnol. 1994 9: 543-546.

PMID- 8383139
VI  - 630
DP  - 1993
TI  - Sequence-specific DNA affinity chromatography: application of a group-specific adsorbent for the isolation of restriction endonucleases.
PG  - 151-157
AB  - The use of sequence-specific DNA affinity adsorbents for the isolation of restriction
      endonuclease EcoRI and SphI to near homogeneity has been reported. However, the high cost of
      these adsorbents is a limiting factor for their wider application. This paper reports the
      application of sequence-specific DNA affinity ligands containing recognition sequences for 34
      restriction endonucleases as group specific ligands in the isolation of restriction
      endonuclease. Crude samples of six restriction endonucleases, namely BshFI, BamHI, SmaI,
      SacII, PvuII and SalI, were shown to bind to these adsorbents and could be eluted at different
      KCl concentrations. High purification factors and recoveries were obtained. Restriction
      endonuclease BshFI, an isoschizomer of HaeIII, from the microorganism Bacillus sphaericus was
      purified to near homogeneity employing a two-step procedure which involves DNA-cellulose
      chromatography and oligonucleotide-ligand affinity chromatography. The enzyme exists as a
      monomer with an apparent relative molecular mass of 34000 as determined by both sodium dodecyl
      sulphate-polyacrylamide gel electrophoresis and size exclusion chromatography.
AU  - Pozidis C
AU  - Vlatakis G
AU  - Bouriotis V
PT  - Journal Article
TA  - J. Chromatogr.
JT  - J. Chromatogr.
SO  - J. Chromatogr. 1993 630: 151-157.

PMID- 22740659
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Staphylococcus aureus 118 (ST772), a Major Disease Clone from India.
PG  - 3727-3728
AB  - We report the draft genome sequence of an ST772 Staphylococcus aureus disease isolate carrying
      staphylococcal cassette chromosome mec (SCCmec) type V from a
      pyomyositis patient. Our de novo short read assembly is approximately 2.8 Mb and
      encodes a unique Panton-Valentine leukocidin (PVL) phage with structural genes
      similar to those of varphi7247PVL and novel lysogenic genes at the N termini.
AU  - Prabhakara S
AU  - Khedkar S
AU  - Loganathan RM
AU  - Chandana S
AU  - Gowda M
AU  - Arakere G
AU  - Seshasayee AS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3727-3728.

PMID- 27081143
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of an Environmental trh+ Vibrio parahaemolyticus K23 Strain Isolated from Kerala, India.
PG  - e00282-16
AB  - Vibrio parahaemolyticusis the leading cause of seafood-related gastroenteritis. Here, we
      report the draft genome sequence of atrh(+)strain,V.
      parahaemolyticusK23, isolated from seafood. The sequence will be useful for
      comparative analysis between environmental and clinical isolates ofV.
      parahaemolyticus.
AU  - Prabhakaran DM
AU  - Chowdhury G
AU  - Pazhani GP
AU  - Ramamurthy T
AU  - Thomas S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00282-16.

PMID- 25744986
VI  - 3
DP  - 2015
TI  - Genome Sequences of the Lignin-Degrading Pseudomonas sp. Strain YS-1p and Rhizobium sp. Strain YS-1r Isolated from Decaying Wood.
PG  - e00019-15
AB  - Pseudomonas sp. strain YS-1p and Rhizobium sp. strain YS-1r were isolated from a
      lignin-degrading enrichment culture. The isolates degraded lignin-derived
      monomers, dimers, alkali lignin, and, to a smaller extent (3% to 5%), lignin in
      switch grass and alfalfa. Genome analysis revealed the presence of a variety of
      lignin-degrading genes.
AU  - Prabhakaran M
AU  - Couger MB
AU  - Jackson CA
AU  - Weirick T
AU  - Fathepure BZ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00019-15.

PMID- 25540348
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Elizabethkingia meningoseptica, Isolated from a Postoperative Endophthalmitis Patient.
PG  - e01335-14
AB  - We present the draft genome assembly of an Elizabethkingia meningoseptica strain  isolated
      from a 67-year-old postoperative endophthalmitis patient who suffered
      loss of vision in the right eye. The draft genome assembly has 167 contigs with a
      total size of 4,019,665 bp encoding multiple drug-resistant genes.
AU  - Pradeep BE
AU  - Mahalingam N
AU  - Manivannan B
AU  - Padmanabhan K
AU  - Nilawe P
AU  - Gurung G
AU  - Chhabra A
AU  - Nagaraja V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01335-14.

PMID- 23383081
VI  - 8
DP  - 2013
TI  - The First Genomic and Proteomic Characterization of a Deep-Sea Sulfate Reducer: Insights into the Piezophilic Lifestyle of Desulfovibrio piezophilus.
PG  - E55130
AB  - Desulfovibrio piezophilus strain C1TLV30(T) is a piezophilic anaerobe that was
      isolated from wood falls in the Mediterranean deep-sea. D. piezophilus represents
      a unique model for studying the adaptation of sulfate-reducing bacteria to
      hydrostatic pressure. Here, we report the 3.6 Mbp genome sequence of this
      piezophilic bacterium. An analysis of the genome revealed the presence of seven
      genomic islands as well as gene clusters that are most likely linked to life at a
      high hydrostatic pressure. Comparative genomics and differential proteomics
      identified the transport of solutes and amino acids as well as amino acid
      metabolism as major cellular processes for the adaptation of this bacterium to
      hydrostatic pressure. In addition, the proteome profiles showed that the
      abundance of key enzymes that are involved in sulfate reduction was dependent on
      hydrostatic pressure. A comparative analysis of orthologs from the
      non-piezophilic marine bacterium D. salexigens and D. piezophilus identified
      aspartic acid, glutamic acid, lysine, asparagine, serine and tyrosine as the
      amino acids preferentially replaced by arginine, histidine, alanine and threonine
      in the piezophilic strain. This work reveals the adaptation strategies developed
      by a sulfate reducer to a deep-sea lifestyle.
AU  - Pradel N
AU  - Ji B
AU  - Gimenez G
AU  - Talla E
AU  - Lenoble P
AU  - Garel M
AU  - Tamburini C
AU  - Fourquet P
AU  - Lebrun R
AU  - Bertin P
AU  - Denis Y
AU  - Pophillat M
AU  - Barbe V
AU  - Ollivier B
AU  - Dolla A
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2013 8: E55130.

PMID- 7821556
VI  - 22
DP  - 1994
TI  - DNA methylation in plants: involvement of two different methyltransferases.
PG  - 297S
AB  - The DNA of higher eukaryotes is methylated at carbon 5 of some cytosine residues. In
      vertebrates, 3 to 8% of cytosine residues are methylated, whereas in plants as many as 30% of
      the total cytosines are methylated. The higher content of methylated cytosine in the DNA of
      some plants could be partly attributed to their large genome with many repetitive sequences.
      However, in the vertebrate genome 5-methylcytosine (5mC) is largely confined to CG
      dinucleotides, whereas in higher plants both CG dinucleotides and CNG trinucleotides are
      methylated. In non-vascular plants, methylation appears to occur only at CNG trinucleotides.
      Methylation of DNA in plants, as in vertebrates, is implicated in the regulation of gene
      expression; an effect that may be direct, through DNA:transcription factor interaction, or
      indirect via an alteration in chromatin structure.
AU  - Pradhan S
AU  - Adams RLP
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 1994 22: 297S.

PMID- 7757118
VI  - 7
DP  - 1995
TI  - Distinct CG and CNG DNA methyltransferases in Pisum sativum.
PG  - 471-481
AB  - DNA methyltransferase activity, present in low salt extracts of nuclei from young pea shoot
      apices, has been fractionated into two different species by assaying with model substrates.
      The CG methyltransferase (an unstable enzyme believed to be of 140 kDa) methylates cytosine
      only in oligonucleotides with CG and CI dinucleotide targets while an enzyme of 110 kDa (the
      CNG methyltransferase) methylates the cytosines in 5'-CAG-3' and 5'-CTG-3' target
      sequences, especially when hemimethylated, but not in 5'-CCG-3' nor in 5'-CGG-3' target
      sequences present in oligonucleotides.
AU  - Pradhan S
AU  - Adams RLP
PT  - Journal Article
TA  - Plant J.
JT  - Plant J.
SO  - Plant J. 1995 7: 471-481.

PMID- 10551868
VI  - 274
DP  - 1999
TI  - Recombinant human DNA (cytosine-5) methyltransferase.
PG  - 33002-33010
AB  - A method is described to express and purify human DNA (cytosine-5) methyltransferase (human
      DNMT1) using a protein splicing (intein) fusion partner in a baculovirus expression vector.
      The system produces ~1 mg of intact recombinant enzyme >95% pure per 1.5 x 10^9 insect cells.
      The protein lacks any affinity tag and is identical to the native enzyme except for the two
      C-terminal amino acids, proline and glycine, that were substituted for lysine and aspartic
      acid for optimal cleavage from the intein affinity tag. Human DNMT1 was used for steady-state
      kinetic analysis with poly(dI-dC).poly(dI-dC) and unmethylated and hemimethylated 36- and
      75-mer oligonucleotides. The turnover number (k(cat)) was 131-237 h(-1) on
      poly(dI-dC).poly(dI-dC), 1.2-2.3 h(-1) on unmethylated DNA, and 8.3-49 h(-1) on hemimethylated
      DNA. The Michaelis constants for DNA (K(m)(CG)) and S-adenosyl-L-methionine (AdoMet)
      (K(m)(AdoMet)) ranged from 0.33-1.32 and 2.6-7.2 muM, respectively, whereas the ratio of
      k(cat)/K(m)(CG) ranged from 3.9 to 44 (237-336 for poly(dI-dC).poly(dI-dC)) x 10(6) M(-1)
      h(-1). The preference of the enzyme for hemimethylated, over unmethylated, DNA was 7-21-fold.
      The values of k(cat) on hemimethylated DNAs showed a 2-3-fold difference, depending upon which
      strand was pre-methylated. Furthermore, human DNMT1 formed covalent complexes with substrates
      containing 5-fluoro-CNG, indicating that substrate specificity extended beyond the canonical
      CG dinucleotide. These results show that, in addition to maintenance methylation, human DNMT1
      may also carry out de novo and non-CG methyltransferase activities in vivo.
AU  - Pradhan S
AU  - Bacolla A
AU  - Wells RD
AU  - Roberts RJ
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1999 274: 33002-33010.

PMID- 9469828
VI  - 26
DP  - 1998
TI  - Isolation, characterization and baculovirus-mediated expression of cDNA encoding cytosine DNA methyltransferase from Pisum sativum.
PG  - 1214-1222
AB  - A series of overlapping clones complementy to the Arabidopsis cytosine-5 DNA methyltransferase
      has been isolated from pea cDNA libraries.  The assembled nucleic acid sequence contains an
      open reading frame of 4761 bp encoding a protein of 1554 amino acids.  Like other eukaryotic
      C-5 MTases, the inferred protein has a presumed regulatory N-terminal region linked to a
      catalytic C-terminal domain, which has eight of the ten conserved motifs found in prokaryotic
      C-5 MTases.  The pea C-5 MTase has 65% identity at the nucleotide level and 61% identity at
      the protein level, with the Arabidopsis C-5 MTase.  The catalytic domain of the pea enzyme
      shares 78% identity with Arabidopsis and ~52% identity with murine and human C-5 MTases,
      including the relative position of the proline-cysteine dipeptides of the catalytic center.
      Using the conserved region of the cDNA as a probe, we have identified a transcript of 5 kb.
      Southern blot analysis of pea genomic DNA with the above probe indicates the presence of a
      single gene.  Using poly(A)+ RNA from different developmental stages and different tissues, we
      have observed that expression is confined mostly to the rapidly dividing tissues of the plant.
      Expression of this assembled cDNA in a baculovirus system gives a protein of ~174 kDa.  The
      expressed protein can be cross-linked, in an AdoMet-dependent manner, to duplex
      oligonucleotide substrates containing FdC in place of target cytosines in either CG or CAG/CTG
      sequences.
AU  - Pradhan S
AU  - Cummings M
AU  - Roberts RJ
AU  - Adams RLP
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1998 26: 1214-1222.

PMID- 12731873
VI  - 42
DP  - 2003
TI  - Allosteric activator domain of maintenance human DNA (cytosine-5) methyltransferase and its role in methylation spreading.
PG  - 5321-5332
AB  - The human maintenance DNA (cytosine-5) methyltransferase (hDNMT1) consists of a large
      N-terminal regulatory domain fused to a catalytic C-terminal
      domain by randomly repeated Gly-Lys dipeptides. Several N-terminal
      deletion mutants of hDNMT1 were made, purified, and tested for substrate
      specificity. Deletion mutants lacking 121, 501, 540, or 580 amino acids
      from the N-terminus still functioned as DNA methyltransferases, methylated
      CG sequences, and preferred hemimethylated to unmethylated DNA, as did the
      full-length hDNMT1. Methylated DNA stimulated methylation spreading on
      unmethylated CpG sequences for the full-length and the 121 amino acid
      deletion hDNMT1 equally well but not for the mutants lacking 501, 540, or
      580 amino acids, indicating the presence of an allosteric activation
      determinant between amino acids 121 and 501. Peptides from the N- and
      C-termini bound methylated DNA independently. Point mutation analysis
      within the allosteric region revealed that amino acids 284-287 (KKHR) were
      involved in methylated DNA-mediated allosteric activation. Allosteric
      activation was reduced in the double point mutant enzymes D25 (K284A and
      K285A) and D12 (H286A and R287A). Retinoblastoma gene product (Rb), a
      negative regulator of DNA methylation, bound to the allosteric site of
      hDNMT1 and inhibited methylation, suggesting Rb may regulate methylation
      spreading.
AU  - Pradhan S
AU  - Esteve PO
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2003 42: 5321-5332.

PMID- 14585271
VI  - 109
DP  - 2003
TI  - Mammalian DNA (cytosine-5) methyltransferases and their expression.
PG  - 6-16
AB  - Two classes of functional DNA (cytosine-5) methyltransferases have been discovered in mammals
      to date. One class methylates the unmodified DNA and
      is designated as the de novo enzyme, whereas the other maintains the
      methylation status of the daughter strand during DNA replication and thus
      is referred to as a maintenance DNA methyltransferase. Each enzyme
      catalyzes methyl group transfer from S-adenosyl-L-methionine to cytosine
      bases in DNA. During methylation the enzyme flips its target base out of
      the DNA duplex into a typically concave catalytic pocket. This flipped
      cytosine base is then a substrate for the enzyme-catalyzed reaction. The
      newly formed 5-methylcytosine confers epigenetic information on the
      parental genome without altering nucleotide sequences. This epigenetic
      information is inherited during DNA replication and cell division. In
      mammals, DNA methylation participates in gene expression, protection of
      the genome against selfish DNA, parental imprinting, mammalian X
      chromosome inactivation, developmental regulation, T cell development, and
      various diseases.
AU  - Pradhan S
AU  - Esteve PO
PT  - Journal Article
TA  - Clin. Immunol.
JT  - Clin. Immunol.
SO  - Clin. Immunol. 2003 109: 6-16.

PMID- 7607510
VI  - 157
DP  - 1995
TI  - CG and CNG methyltransferases in plants.
PG  - 289-291
AB  - We have purified two distinct DNA methyltransferases from pea shoot tips and analyzed their
      sequence specificity using synthetic oligodeoxyribonucleotide substrates and chemical
      sequencing methods.  One methylates only CG target sequences, whereas the other methylates
      only CAG or CTG target sequences.  We have found no evidence for methylation of the 5'
      cytosine in CCG target sequences either in vivo or in vitro.  Using amino-acid sequence data,
      PCR-amplified fragments from conserved sequences and heterologous probes, we have isolated
      several cDNA clones that react with mRNA molecules of different sizes.
AU  - Pradhan S
AU  - Houlston C
AU  - Cummings M
AU  - Adams RLP
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 289-291.

PMID- 11847125
VI  - 21
DP  - 2002
TI  - The retinoblastoma gene product interacts with maintenance human DNA (cytosine-5) methyltransferase and modulates its activity.
PG  - 779-788
AB  - The mammalian DNA (cytosine-5) methyltransferase (Dnmt1) is involved in the maintenance of
      methylation patterns in the genome during DNA replication and development.  The retinoblastoma
      gene product, Rb, is a cell cycle regulator protein that represses transcription by recruiting
      histone deacetylase (HDAC1).  In vivo, histone deacetylase associates with Dnmt1.  Here we
      show that Rb itself associates with human Dnmt1 (hDnmt1) independently of its own
      phosphorylation status.  Methyltransferase activity was co-purified with Rb.  The regulatory
      domain of hDnmt1 binds strongly to the B and C pockets of Rb (amino acids 701-872) and
      inhibits methyltransferase activity by disruption of the hDnmt1-DNA binary complex.  Weak
      interaction of Rb pockets A and B with Dnmt1 was also observed.  Overexpression of Rb leads to
      hypomethylation of the cellular DNA, suggesting that Rb may modulate Dnmt1 activity during DNA
      replication in the cell cycle.
AU  - Pradhan S
AU  - Kim GD
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 2002 21: 779-788.

PMID- 10790376
VI  - 19
DP  - 2000
TI  - Hybrid mouse-prokaryotic DNA (cytosine-5) methyltransferases retain the specificity of the parental C-terminal domain.
PG  - 2103-2114
AB  - The mouse (cytosine-5) DNA methyltransferase (Dnmt1) consists of a regulatory N-terminal and a
      catalytic C-terminal domain, which are fused by a stretch of Gly-Lys dipeptide repeats. The
      C-terminal region contains all of the conserved motifs found in other cytosine-5 DNA
      methyltransferases including the relative position of the catalytic Pro-Cys dipeptide. In
      prokaryotes, the methyltransferases are simpler and lack the regulatory N-terminal domain. We
      constructed three hybrid methyltransferases, containing the intact N-terminus of the murine
      Dnmt1 and most of the coding sequences from M.HhaI (GCGC), M.HpaII (CCGG) or M.SssI (CG).
      These hybrids are biologically active when expressed in a baculovirus system and show the
      specificity of the parental C-terminal domain. Expression of these recombinant constructs
      leads to de novo methylation of both host and viral genomes in a sequence-specific manner.
      Steady-state kinetic analyses were performed on the murine Dnmt1-HhaI hybrid using
      poly(dG-dC).poly (dG-dC), unmethylated and hemimethylated oligonucleotides as substrates. The
      enzyme has a slow catalytic turnover number of 4.38 h(-1) for poly(dG-dC). poly(dG-dC), and
      exhibits 3-fold higher catalytic efficiency for hemimethylated substrates.
AU  - Pradhan S
AU  - Roberts RJ
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 2000 19: 2103-2114.

PMID- 9358180
VI  - 25
DP  - 1997
TI  - Baculovirus-mediated expression and characterization of the full-length murine DNA methyltransferase.
PG  - 4666-4673
AB  - The original cDNA sequence reported for the murine DNA methyltransferase was not full length.
      Recently, additional cDNA sequences have been reported that lie upstream of the original and
      contain an extended open reading frame with three additional ATGs in frame with the coding
      region.  Genomic DNA upstream of this ATG contains two more ATGs in frame and no obvious
      splice site.  We have constructed, and expressed in baculovirus, MTase clones that begin at
      each of these four ATGs and examined their properties.  Constructs beginning with any of the
      first three ATGs as their initiator methionines give a predominant DNA MTase band of ~185 kDa
      on SDS-PAGE corresponding to translational initiation at the third ATG.  The fourth ATG
      construct gives a much smaller protein band of 173 kDa.  The 185 kDa protein was purified by
      HPLC, characterized by mass spectrometry and has a measured molecular mass of 184+/- 0.5 kDa.
      All of these MTases were functional in vitro and steady state kinetic analysis showed that the
      recombinant proteins exhibit similar kinetic properties irrespective of their length.  The
      homogeneous recombinant enzyme from the fourth ATG construct shows a 2.5-fold preference for a
      hemi-methylated DNA substrate as compared to an unmethylated substrate, whereas the 185 kDa
      protein is equally active on both substrates.  The kinetic properties of the recombinant
      enzyme are similar to those reported for the native MTase derived from murine erythroleukemia
      cells.  The new clones are capable of yielding large quantities of intact MTases for further
      structural and functional studies.
AU  - Pradhan S
AU  - Talbot D
AU  - Sha M
AU  - Benner J
AU  - Hornstra L
AU  - Li E
AU  - Jaenisch R
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1997 25: 4666-4673.

PMID- 27795257
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Extremely Drug-Resistant Pseudomonas aeruginosa (ST357)  Strain CMC_VB_PA_B22862 Isolated from a Community-Acquired Bloodstream Infection.
PG  - e01092-16
AB  - Extremely drug-resistant Pseudomonas aeruginosa strains causing severe infections have become
      a serious concern across the world. Here, we report draft genome
      sequence of P. aeruginosa with an extremely drug-resistant profile isolated from
      a patient with community-acquired bloodstream infection in India.
AU  - Pragasam AK
AU  - Yesurajan F
AU  - Doss CGP
AU  - George B
AU  - Devanga RNK
AU  - Walia K
AU  - Veeraraghavan B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01092-16.

PMID- 22328760
VI  - 194
DP  - 2012
TI  - Whole-Genome Shotgun Sequencing of Lactobacillus rhamnosus MTCC 5462, a Strain with Probiotic Potential.
PG  - 1264-1265
AB  - Lactobacillus rhamnosus MTCC 5462 was isolated from infant gastrointestinal flora. The strain
      exhibited an ability to reduce cholesterol and stimulate
      immunity. The strain has exhibited positive results in alleviating
      gastrointestinal discomfort and good potential as a probiotic. We sequenced the
      whole genome of the strain and compared it to the published genome sequence of
      Lactobacillus rhamnosus GG (ATCC 53103).
AU  - Prajapati JB
AU  - Khedkar CD
AU  - Chitra J
AU  - Suja S
AU  - Mishra V
AU  - Sreeja V
AU  - Patel RK
AU  - Ahir VB
AU  - Bhatt VD
AU  - Sajnani MR
AU  - Jakhesara SJ
AU  - Koringa PG
AU  - Joshi CG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1264-1265.

PMID- 21705605
VI  - 193
DP  - 2011
TI  - Whole-Genome Shotgun Sequencing of an Indian-Origin Lactobacillus helveticus Strain, MTCC 5463, with Probiotic Potential.
PG  - 4282-4283
AB  - Lactobacillus helveticus MTCC 5463 was isolated from a vaginal swab from a healthy adult
      female. The strain exhibited potential probiotic properties,
      with their beneficial role in the gastrointestinal tract and their ability
      to reduce cholesterol and stimulate immunity. We sequenced the whole
      genome and compared it with the published genome sequence of Lactobacillus
      helveticus DPC4571.
AU  - Prajapati JB
AU  - Khedkar CD
AU  - Chitra J
AU  - Suja S
AU  - Mishra V
AU  - Sreeja V
AU  - Patel RK
AU  - Ahir VB
AU  - Bhatt VD
AU  - Sajnani MR
AU  - Jakhesara SJ
AU  - Koringa PG
AU  - Joshi CG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4282-4283.

PMID- Not carried by PubMed...
VI  - 91
DP  - 1991
TI  - Study of the expression of hsd genes of E. coli K-12 after conjugal transfer.
PG  - 165
AB  - The enzyme for DNA restriction and modification in E. coli K-12 is encoded by
      three contiguous genes: hsdRK (restriction), hsdMK (modification) and hsdSK
      (specificity).  Two promoters are known pres upstream of hsdRK, and pmod
      upstream of hsdMK and hsdSK.  F plasmids carrying the wild-type hsd genes can
      be transferred to a non-K modified recipient (e.g., E. coli) without killing
      the recipient strain.  Thus there must be control at either the
      transcriptional, translational or post-translational level which allows the
      modification of the recipient's chromosome, thereby preventing its restriction.
      F plasmids carrying various hsd-lacZ operon fusions were constructed and
      subsequent F transfer experiments showed simultaneous expression of both pres
      and pmod promoters, and thus no control at the transcriptional level was
      indicated.  Further we have isolated a mutant of E. coli C which is killed
      (efficiency of transfer <10/4) upon conjugal transfer of the wild type hsd
      genes, suggesting a genetic basis for this control phenomenon.  A plasmid
      expressing the R subunit was then introduced into this mutant as well as into
      wild type E. coli C.  Subsequent conjugal transfer of an F plasmid carrying the
      hsdRK hsdM+K hsdS+K genes into this mutant resulted in complementation between
      the incoming M and S subunits with the pre-existing R subunit, as evidenced by
      the killing of the mutant recipient.  However, in the case of the wild type
      recipient strain harboring the plasmid expressing the R subunit, modification
      of the recipient DNA occurred, resulting in successful conjugation.  This
      suggests that there is control of the incoming hsd gene expression in the
      recipient at the post-translational level.
AU  - Prakash A
AU  - Chung S
AU  - Ryu J-I
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1991 91: 165.

PMID- 1827085
VI  - 99
DP  - 1991
TI  - Genomic hsd-Mu(lac) operon fusion mutants of Escherichia coli K-12.
PG  - 9-14
AB  - Genomic (chromosomal) hsd-Mu(lac) operon fusions have been constructed in two
      strains of Escherichia coli K-12 for the three hsd genes, hsdRK, hsdMK and
      hsdSK, using MudX and lambda placMu53.  Expression of hsdK mutants ranged from
      16 to 74 units (u) (with a mean of 52 u) for fusions to promoter Pres and
      ranged from 26-75 u (also with a mean of 52 u) for fusions to promoter Pmod.
      The expression of the two hsdK promoters was measured in different stages of
      growth.  The Pres fusion mutant showed a lag in Beta-galactosidase (BetaGal)
      production, as compared to the Pmod fusion mutant.  One rK-mK mutant (JR205)
      showed more than ten times the BetaGal activity of other insertion mutants.
      The activity of this mutant decreased by 20-fold upon the transfer of F101-102,
      which includes the wild-type hsd region.  Positive gene-dosage effect was
      observed using F' plasmids containing the hsd-lacZ region.
AU  - Prakash A
AU  - Valinluck B
AU  - Ryu J-I
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1991 99: 9-14.

PMID- 28086066
VI  - 67
DP  - 2017
TI  - Description of Auricoccucs indicus gen. nov., sp. nov., isolated from skin of human ear.
PG  - 1212-1218
AB  - In present study, a Gram-stain-positive, non-motile, non-spore-forming, small
      spherical bacterium, strain S31T was isolated from skin surface (external ear
      lobe) of a healthy human subject and characterized using polyphasic approach of
      bacterial taxonomy. Based on 1507 bp 16S rRNA gene sequence comparison, strain
      S31T showed highest (92.8%, AY119686) sequence similarity with Macrococcus
      brunensis CCUG 47200T followed by Macrococcus caseolyticus DSM 20597T (92.7%
      AP009484) and formed a separate clade with 65% bootstrap support. The DNA G+C
      content was found to be 34 mol%. Anteiso C15:0, Anteiso C17:0 and iso C16:0 are
      the predominant fatty acids in fatty acid methyl ester (FAME) profile of strain
      S31T. It contained A3alpha type peptidoglycan with L-Lys- Gly3-L-Ala peptide.
      Comparative study of morphological and physiological traits indicated that strain
      S31T phenetically diverged from its closest relatives. Based on morphological,
      chemotaxonomic and genotypic data, strain S31T showed sufficient delineations
      from its closest relatives of family Staphylococcaceae and is proposed as a new
      genus Auricoccus with Auricoccus indicus as type species of the genus. Strain
      S31T (CCUG 69858T = KCTC 33611T = MCC 3027T) is the type strain of the species.
AU  - Prakash O
AU  - Muduli S
AU  - Kumar R
AU  - Kumari C
AU  - Nimonkar Y
AU  - Shouche YS
AU  - Sharma R
PT  - Journal Article
TA  - Int. J. Syst. Evol. Microbiol.
JT  - Int. J. Syst. Evol. Microbiol.
SO  - Int. J. Syst. Evol. Microbiol. 2017 67: 1212-1218.

PMID- 21925114
VI  - 10
DP  - 2011
TI  - Complete Genome Sequences of Rat and Mouse Segmented Filamentous Bacteria, a Potent Inducer of Th17 Cell Differentiation.
PG  - 273-284
AB  - Segmented filamentous bacteria (SFB) are noncultivable
      commensals inhabiting the gut of various vertebrate
      species and have been shown to induce Th17
      cells in mice. We present the complete genome
      sequences of both rat and mouse SFB isolated from
      SFB-monocolonized hosts. The rat and mouse SFB
      genomes each harbor a single circular chromosome
      of 1.52 and 1.59 Mb encoding 1346 and 1420
      protein-coding genes, respectively. The overall nucleotide
      identity between the two genomes is 86%, and
      the substitution rate was estimated to be similar to
      that of the free-living E. coli. SFB genomes encode
      typical genes for anaerobic fermentation and spore
      and flagella formation, but lack most of the amino
      acid biosynthesis enzymes, reminiscent ofpathogenic
      Clostridia, exhibiting large dependency on the host.
      However, SFB lack most of the clostridial virulencerelated
      genes. Comparative analysis with clostridial
      genomes suggested possible mechanisms for host
      responses and specific adaptations in the intestine.
AU  - Prakash T
AU  - Oshima K
AU  - Morita H
AU  - Fukuda S
AU  - Imaoka A
AU  - Kumar N
AU  - Sharma VK
AU  - Kim S-W
AU  - Takahashi M
AU  - Saitou N
AU  - Taylor TD
AU  - Ohno H
AU  - Umesaki Y
AU  - Hattori M
PT  - Journal Article
TA  - Cell Host Microbe
JT  - Cell Host Microbe
SO  - Cell Host Microbe 2011 10: 273-284.

PMID- 8264523
VI  - 241
DP  - 1993
TI  - The expression and regulation of hsdK genes after conjugative transfer.
PG  - 491-496
AB  - The type I restriction and modification genes of Escherichia coli can be transferred to other
      non-modified strains by conjugation without killing the recipient, implying that the
      restriction function must be regulated. In this study, two isogenic F plasmids (r+k and r-K)
      served as donors in quantitative conjugation experiments with various restriction-deficient
      strains of E. coli and Salmonella typhimurium. Conjugation studies with hsd:lacZ operon
      fusions in F' plasmids indicate that both the hsdK promoters, Pres and Pmod, express
      simultaneously following conjugative transfer. Thus these genes do not appear to be regulated
      at the transcriptional level. A spontaneous mutant of E. coli C was discovered that is
      presumably killed upon conjugative transfer of the hsdK genes (defined as a Crc- phenotype).
      The gene that is defective in the mutant was tentatively designated hsdC (control). Hfr gene
      replacement studies led to the localization of the putative hsdC gene between 6 and 16 min on
      the E. coli genetic map.
AU  - Prakash-Cheng A
AU  - Chung SS
AU  - Ryu J-I
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1993 241: 491-496.

PMID- 8393010
VI  - 175
DP  - 1993
TI  - Delayed expression of in vivo restriction activity following conjugal transfer of Escherichia coli hsdk (restriction-modification) genes.
PG  - 4905-4906
AB  - Following conjugal transfer of the hsdk genes (hsdRK, hsdMk, and hsdSk) of Escherichia coli
      K-12, restriction activity was first detected only after approximately 15 generations, whereas
      modification activity was observed immediately. This sequential expression explains the
      establishment of hsdk genes in a nonmodified host and suggests regulation of restriction
      activity after conjugal transfer.
AU  - Prakash-Cheng A
AU  - Ryu J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1993 175: 4905-4906.

PMID- 28321010
VI  - 32
DP  - 2017
TI  - Discovery and Complete Genome Sequence of a Bacteriophage from an Obligate Intracellular Symbiont of a Cellulolytic Protist in the Termite Gut.
PG  - 112-117
AB  - Termites depend nutritionally on their gut microbes, and protistan, bacterial, and archaeal
      gut communities have been extensively studied.  However, limited information is available on
      viruses in the termite gut.  We herein report the complete genome sequence (99,517 bp) of a
      phage obtained during a genome analysis of "Candidatus Azobacteroides pseudotrichonymphae"
      phylotype ProJPt-1, which is an obligate intracellular symbiont of the cellulolytic protest
      Pseudotrichonympha sp. in the gut of the termite Prorhinotermes japonicas.  The genome of the
      phage, designated ProJPt-Bp1, was circular or circularly permuted, and was not integrated into
      the two circular chromosomes or five circular plasmids composing the host ProJPt-1 genome.
      The phage was putatively affiliated with the order Caudovirales based on sequence similarities
      with several phage-related genes; however, most of the 52 protein-coding sequences had no
      significant homology to sequences in the databases.  The phage genome contained a tRNA-Gln
      (CAG) gene, which showed the highest sequence similarity to the tRNA-Gln (CAG) gene, the phage
      tRNA gene may compensate for differences in codon usage bias between the phage and host
      genomes.  The phage genome also contained a non-coding region with high nucleotide sequence
      similarity to a region in one of the host plasmids.  No other phage-related sequences were
      found in the host ProJPt-1 genome.  To the best of our knowledge, this is the first report of
      a phage from an obligate, mutualistic endosymbiont permanently associated with eukaryotic
      cells.
AU  - Pramono AK
AU  - Kuwahara H
AU  - Itoh T
AU  - Toyoda A
AU  - Yamada A
AU  - Hongoh Y
PT  - Journal Article
TA  - Microbes Environ.
JT  - Microbes Environ.
SO  - Microbes Environ. 2017 32: 112-117.

PMID- Not carried by PubMed...
VI  - 3
DP  - 1987
TI  - Thermostability of nucleic acid and restriction endonuclease template synthesis enzymes from extremely thermophilic archebacteria.
PG  - 440-446
AB  - A study has been made of the thermostability of DNA-dependent RNA polymerases, DNA-dependent
      DNA polymerases, and restriction endonucleases from extremely thermophilic archebacteria. The
      optimum temperature for enzyme catalytic activity (T opt) lay in the optimum temperature
      region for growth of the organisms involved: at 85C for RNA polymerases from Thermoproteus
      tenax and Desulfurococcus mucosus, at 55-65C and 70-75C for three DNA polymerases and
      restrictase SuaI from Sulfolobus acidocaldarius, respectively, and at 55-60C for DNA
      polymerase and restrictase ThaI from Thermoplasma acidophilum. All the enzymes investigated
      were highly stable at temperatures up to T opt.
AU  - Prangishvili DA
AU  - Chinchaladze DZ
AU  - Chelidze MG
PT  - Journal Article
TA  - Biotekhnologiya
JT  - Biotekhnologiya
SO  - Biotekhnologiya 1987 3: 440-446.

PMID- 2822145
VI  - 52
DP  - 1987
TI  - Isolation and properties of a restriction endonuclease SuaI from the thermoacidophilic archaebacterium Sulfolobus acidocaldarius.
PG  - 1043-1050
AB  - A new restriction endonuclease SuaI was isolated from the thermoacidophilic
      archaebacterium Sulfolobus acidocaldarius.  The enzyme is an isoschizomer of
      BspRI; it recognizes the tetranucleotide GGCC and cleaves DNA in the center of
      this sequence.  SuaI requires Mg2+, the optimal concentration being 6 mM.  KCl
      at concentrations above 25 mM significantly inhibits the enzyme activity.  The
      pH optimum lies within the range of 6-7 at 70C, the temperature optimum is at
      70-75C.  the enzyme is highly stable at temperatures up to 80C.  DNA of S.
      acidocaldarius is not cleaved by the enzyme.
AU  - Prangishvili DA
AU  - Vashakidze RP
AU  - Chelidze MG
AU  - Chinchaladze DZ
AU  - Tsalkalamanidze NV
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1987 52: 1043-1050.

PMID- 2996942
VI  - 192
DP  - 1985
TI  - A restriction endonuclease SuaI from the thermoacidophilic archaebacterium Sulfolobus acidocaldarius.
PG  - 57-60
AB  - A type II restriction endonuclase (SuaI) has been isolated from the
      thermoacidophilic archaebacterium Sulfolobus acidocaldarius.  The enzyme is an
      isoschizomer of BspRI.  It does not cut S. acidocaldarius DNA, as the
      recognition sequence GGCC in this DNA contains modified nucleotide(s).  The
      enzyme is most active at 60-70C and is highly thermostable.
AU  - Prangishvili DA
AU  - Vashakidze RP
AU  - Chelidze MG
AU  - Gabriadze IY
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1985 192: 57-60.

PMID- 16084831
VI  - 335
DP  - 2005
TI  - Deinococcus radiodurans strain R1 contains N6-methyladenine in its genome.
PG  - 412-416
AB  - Methylation of DNA is known to be involved in DNA repair mechanisms in bacteria. Deinococcus
      radiodurans strain R1 on exposure to high
      radiation undergoes significant DNA damage, which is repaired without
      mutations. However, the presence of modified nucleotides has not been
      reported in its genome. We report here the detection of
      N6-methyladenine in the genome of D. radiodurans strain R1 using
      immunochemical techniques. This N6-methyladenine is not a part of GATC
      restriction-modification system. D. radiodurans cell extract also
      exhibited a DNA adenine methyltransferase activity which was reduced in
      the early post-irradiation recovery phase.
AU  - Prasad BJ
AU  - Sabnis K
AU  - Deobagkar DD
AU  - Deobagkar DN
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 2005 335: 412-416.

PMID- 29146855
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Entomopathogenic Brevibacillus laterosporus Strain Lak 1210, an Alkaliphilic Chitin Degrader.
PG  - e01251-17
AB  - We announce here the draft genome sequence of Brevibacillus laterosporus strain Lak 1210,
      isolated from mangrove soil. This alkaliphilic strain is an efficient
      chitin degrader and has the ability to control insects and inhibit
      phytopathogenic fungi. The assembly consists of 5,082,926 bp, with 4,321
      protein-coding sequences and a GC content of 41.15%.
AU  - Prasanna L
AU  - Moharana TR
AU  - Sheikh N
AU  - Arravapalli VR
AU  - Kumaraswamy T
AU  - Eijsink VGH
AU  - Nalam MR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01251-17.

PMID- 
VI  - 
DP  - 2009
TI  - Modulation of restriction enzyme PvuII activity by metal ion cofactors.
PG  - 
AB  - Many nucleases require cofactors (usually Mg2+) for activity. Metal ions like Ca2+, Mn2+,
      Tb3+, Eu3+ etc., can bind at the active site and have varying effects on the enzymatic
      activity. In a crystal structure with DNA, two Ca2+ ions were bound to the active site of each
      PvuII monomer, and the metals share the ligands. Ca2+ ions promote DNA binding and not
      cleavage in many nucleases. We explored the role of Mg2+ and Ca2+ binding at the metal binding
      sites of PvuII to elucidate the role of each metal site. Ca2+ binding at the catalytic metal
      site would inhibit the cleavage activity,
      whereas its binding at the regulatory site can have varied effects. In EcoRV enzyme, it was
      seen that Ca2+ at the regulatory site increases the activity of the enzyme. We monitored the
      cleavage kinetics of PvuII in presence of mixed metals. The cleavage kinetics data for Ca2+
      and Mg2+ set were modeled using parameters from previous studies on PvuII. Our global analysis
      on single turnover cleavage kinetics datasets show best fit to a model in which mixed metal
      species are formed and active. The cleavage rate constants for the mixed metal species ranged
      from 0.01-0.08 sec-1, which is similar to the rate when only one metal is bound. From earlier
      work in our lab, Tb3+ was shown to have a tight (2 iM) binding site and a weak binding site in
      PvuII. The difference in affinity allows one site to be filled with Tb3+ and the other with
      another metal. Indirect Tb3+ luminescence spectroscopy of the Tb3+ bound to enzyme in presence
      of other metals indicates that Ca2+ and Mn2+ displace Tb3+ from the enzyme. This was observed
      by the decrease in the luminescence intensity of E-Tb3+ complex with the addition of Ca2+/Mn2+
      ions. Under similar conditions, the addition of Mg2+ ions to the E-Tb3+ complex results in an
      increase in the signal observed. This indicates the formation of the mixed species
      E-Tb3+-Mg2+. No enzymatic activity was detected for the enzyme with the addition of Mg2+ to
      the E-Tb3+ complex, whereas with the addition of Mn2+ ions there was detectable activity.
      The observed activity with Mn2+ ion was due to the displacement of Tb3+ ions from the active
      site, forming the active EMn2+Mn2+ species. Although the E-Mg2+-Tb3+ species is catalytically
      inactive, it does bind the DNA as confirmed by fluorescence anisotropy using nonhydrolyzable
      phosphoramidate DNA.
AU  - Prasannan CB
PT  - Journal Article
TA  - Ph.D. Thesis, University of Missouri
JT  - Ph.D. Thesis, University of Missouri
SO  - Ph.D. Thesis, University of Missouri 2009 : .

PMID- 29748397
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Staphylococcus haemolyticus Type Strain SGAir0252.
PG  - e00229-18
AB  - Staphylococcus haemolyticus is a coagulase-negative staphylococcal species that is part of the
      skin microbiome and an opportunistic human pathogen. The strain
      SGAir0252 was isolated from tropical air samples collected in Singapore, and its
      complete genome comprises one chromosome of 2.63 Mb and one plasmid of 41.6 kb.
AU  - Premkrishnan BNV et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00229-18.

PMID- Not included in PubMed...
VI  - 33
DP  - 1986
TI  - DNA methylase activities in a Neisseria gonorrhoeae extract.
PG  - 37-41
AB  - Resistance of Neisseria gonorrhoeae DNA to cleavage by various restriction endonucleases
      suggests the existence of modification enzymes which protect the corresponding recognition
      sequences. We indeed found methylase activities in N. gonorrhoeae extracts. These activities
      lead to the methylation of adenine and cytosine residues in bacteriophage lambda DNA and DNA
      from an Escherichia coli Dam- strain. They also result in partial protection of lambda DNA to
      cleavage by the restriction endonucleases HaeII, HaeIII, BamHI and SacII.
AU  - Prere MF
AU  - Fayet O
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1986 33: 37-41.

PMID- 2996414
VI  - 136A
DP  - 1985
TI  - Susceptibility of Neisseria Gonorrhoeae DNA to Cleavage by Restriction Endonuclease KpnI.
PG  - 329-338
AB  - We compared the susceptibility of Escherichia coli and Neisseria gonorrhoeae
      DNA to cleavage by KpnI and found that KpnI has a lower affinity for gonococcal
      DNA.  Site-specific methylation is suggested as the cause of this altered
      affinity.
AU  - Prere MF
AU  - Fayet O
PT  - Journal Article
TA  - Ann. Inst. Pasteur Microbiol.
JT  - Ann. Inst. Pasteur Microbiol.
SO  - Ann. Inst. Pasteur Microbiol. 1985 136A: 329-338.

PMID- 2996413
VI  - 136A
DP  - 1985
TI  - DNA modification in Neisseria gonorrhoeae: Resistance of DNA of 19 strains to cleavage by restriction enzymes.
PG  - 323-328
AB  - Site-specific modification is frequently encountered in the DNA of bacteria.  It is generally
      due to the methylation of either a cytosine or an adenine in short sequences 4- to
      6-base-pairs long.  One way to reveal the presence of site-specific methylation in a DNA
      sample is to demonstrate its resistance to cleavage by a restriction endonuclease.  In
      Neisseria gonorrhoeae, studies performed in a limited number of strains revealed that their
      DNA is resistant to digestion by several restriction enzymes.  Those included HaeII, HaeIII,
      SacII, BamHI, NarI and KpnI.  In order to determine whether this pattern of resistance is a
      general property, or if there is variation from strain to strain, we have analyzed the DNA of
      a collection of 19 gonococcal strains for resistance to various restriction endonucleases.  We
      have also investigated the plasmid content of these strains to determine whether this
      correlates with a given resistance pattern.
AU  - Prere MF
AU  - Fayet O
PT  - Journal Article
TA  - Ann. Inst. Pasteur Microbiol.
JT  - Ann. Inst. Pasteur Microbiol.
SO  - Ann. Inst. Pasteur Microbiol. 1985 136A: 323-328.

PMID- 27151804
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Pseudomonas sp. EpS/L25, Isolated from the Medicinal Plant Echinacea purpurea and Able To Synthesize Antimicrobial Compounds.
PG  - e00346-16
AB  - We announce here the draft genome sequence of Pseudomonas sp. strain EpS/L25, isolated from
      the stem/leaves of the medicinal plant Echinacea purpurea This
      genome will allow for comparative genomics in order to identify genes associated
      with the production of bioactive compounds and antibiotic resistance.
AU  - Presta L
AU  - Bosi E
AU  - Fondi M
AU  - Maida I
AU  - Perrin E
AU  - Miceli E
AU  - Maggini V
AU  - Bogani P
AU  - Firenzuoli F
AU  - Di Pilato V
AU  - Rossolini GM
AU  - Mengoni A
AU  - Fani R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00346-16.

PMID- 27469957
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of the Antimicrobial Producers Pseudomonas sp. TAA207 and  Pseudomonas sp. TAD18 Isolated from Antarctic Sediments.
PG  - e00728-16
AB  - We report here the draft genome sequence of the Pseudomonas sp. TAA207 and Pseudomonas sp.
      TAD18 strains, isolated from Antarctic sediments during a summer
      campaign near coastal areas of Terra Nova Bay (Antarctica). Genome sequence
      knowledge allowed the identification of genes associated with the production of
      bioactive compounds and antibiotic resistance. Furthermore, it will be
      instrumental for comparative genomics and the fulfillment of both basic and
      application-oriented investigations.
AU  - Presta L
AU  - Inzucchi I
AU  - Bosi E
AU  - Fondi M
AU  - Perrin E
AU  - Maida I
AU  - Miceli E
AU  - Tutino ML
AU  - Lo GA
AU  - de Pascale D
AU  - Fani R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00728-16.

PMID- 27198032
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Flavobacterium sp. Strain TAB 87, Able To Inhibit the Growth of Cystic Fibrosis Bacterial Pathogens Belonging to the Burkholderia  cepacia Complex.
PG  - e00410-16
AB  - We report here the draft genome sequence of the Flavobacterium sp. TAB 87 strain, isolated
      from Antarctic seawater during a summer campaign near the French
      Antarctic station Dumont d'Urville (60 degrees 40'S, 40 degrees 01'E). It will
      allow for comparative genomics and the fulfillment of both fundamental and
      application-oriented investigations. It allowed the recognition of genes
      associated with the production of bioactive compounds and antibiotic resistance.
AU  - Presta L
AU  - Inzucchi I
AU  - Bosi E
AU  - Fondi M
AU  - Perrin E
AU  - Miceli E
AU  - Tutino ML
AU  - Lo GA
AU  - de Pascale D
AU  - Fani R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00410-16.

PMID- 2856420
VI  - 3
DP  - 1986
TI  - A possible role for DNA restriction in bacterial evolution.
PG  - 296-299
AB  - The phenomena of restriction and modification (R-M) were first described more
      than 30 years ago and it is now more than 20 years since Arber & Dussoix
      proposed, rightly, that R-M was due to the action of endonucleases and
      methylases acting at the same DNA sequences.  Briefly, the endonuclease (or
      restriction enzyme) recognizes a specific DNA sequence as a signal to cleave
      the DNA unless the sequence has previously been methylated by a modification
      methylase of the same sequence specificity.  The DNA of a cell carrying a R-M
      system will normally be modified and is therefore not a substrate for the
      restriction enzyme.  The only natural substrate for a restriction enzyme is
      invasive foreign DNA containing unmethylated recognition sequences.
      Restriction is independent of the mode of introduction of the DNA into the
      cell, and phage infection, plasmid conjugation or transformation all lead to
      restriction.
AU  - Price C
AU  - Bickle TA
PT  - Journal Article
TA  - Microbiol. Sci.
JT  - Microbiol. Sci.
SO  - Microbiol. Sci. 1986 3: 296-299.

PMID- 3265670
VI  - 16
DP  - 1988
TI  - Evolution of DNA sequence specificity in type I restriction enzymes.
PG  - 942-943
AB  - None
AU  - Price C
AU  - Bickle TA
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 1988 16: 942-943.

PMID- 8095080
VI  - 17C
DP  - 1993
TI  - Evolution of DNA sequence specificity in type 1C restriction and modification systems.
PG  - 151
AB  - The type I restriction-modification (R-M) systems of the Enterobacteriaceae form three
      genetically complementing families, one of which is the type 1C family. All type I R-M systems
      recognize DNA sequences that are asymmetric and split into two by a spacer that can have any
      sequence but which, for a given R-M system, has fixed length. The specific DNA-binding
      components of both restriction and modification enzymes are the products of the hsdS genes,
      which form complexes with the hsdM and hsdR gene products. Within a family of type I systems
      the hsdS genes have a characteristic structure with two variable regions, each coding a
      protein domain (called Target Recognition Domains, TRD) that recognizes one half of the
      recognition sequence, and two (three in one case) conserved regions that are thought to code
      regions of the protein that are important for protein-protein interactions. The type IA and IC
      R-M systems are so far the only DNA binding protein that have been show to alter their binding
      specificity by natural means. Type IA enzymes can reassort their TRDs by recombination within
      a conserved region of the hsdS gene, leading to the production of enzymes that have new,
      hybrid recognition sequences. Type IC systems (and, presumable, type IB systems, although it
      has not yet been demonstrated) can also change their specificity in this way. In addition type
      IC systems can change the length of the central conserved region of the hsdS gene by unequal
      crossing over at a 12 bp long repeated sequence. This leads to enzymes that recognize the same
      specific sequence but with different lengths of non-specific spacer. We have discovered yet a
      third way in which type IC enzymes can change their specificity. We have recovered a mutant
      that has a transposon inserted in the middle of the hsdS gene and which nevertheless produces
      an active R-M system with altered sequence specificity. The structure of the mutant enzymes
      and the sequence that it recognizes with be presented. The sequence is the only known type I
      recognition sequence that is palindromic. Finally, we will present data on a type IC R-M
      system of as yet unknown DNA specificity that appears to be on a transposable element. This
      system is particulary interesting because it is closely integrated, both genetically and
      physically, with an RNA restriction system that is specific for cells infected by T even
      phages.
AU  - Price C
AU  - Gubler M
AU  - Braguglia D
AU  - Meister J
AU  - Tyndall C
AU  - Piekarowicz A
AU  - Bickle TA
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1993 17C: 151.

PMID- 2784505
VI  - 205
DP  - 1989
TI  - Basis for changes in DNA recognition by the EcoR124 and EcoR124/3 Type I DNA restriction and modification enzymes.
PG  - 115-125
AB  - EcoR124I and EcoR124/3I are type I DNA restriction and modification systems.
      The EcoR124/3I system arose from the EcoR124I system some 15 years ago and at
      the electron microscopic DNA heteroduplex level the genes for both systems are
      still apparently identical.  We have shown that the DNA sequences recognized by
      the two systems are GAA(N6)RTCG for EcoR124I and GAA(N7)RTCG for EcoR124/3I.
      The sequences thus differ only in the length of the non-specific spacer.  This
      difference nevertheless places the two specific domains of the EcoR124/3I
      recognition sequence 0.34 nm further apart and rotates them 36C with respect to
      those of EcoR124I, which implies major structural differences in the proteins
      recognizing these sequences.  We have now determined the nucleotide sequences
      of the hsdS and hsdM genes of both systems and of the hsdR gene of EcoR124/3I.
      The hsdS gene products provide DNA sequence specificity in both restriction and
      modification, the hsdM gene products are necessary for modification and all
      three hsd gene products are required for restriction.  The only difference that
      we have detected between the two systems is that a 12 base-pair sequence
      towards the middle of the hsdS gene is repeated twice in the EcoR124I gene and
      three times in the EcoR124/3I gene.  We have deleted one of the repeats in the
      EcoR124/3I gene and shown that this changes the specificity to that of
      EcoR124I.  Thus, the extra four amino acids in the middle of the EcoR124/3I
      hsdS gene product, which in an alpha-helical configuration would extend 0.6 nm,
      are sufficient to explain the differences in sequence recognition.  We suggest
      that this kind of specificity change should not be rare in Nature.
AU  - Price C
AU  - Lingner J
AU  - Bickle TA
AU  - Firman K
AU  - Glover SW
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1989 205: 115-125.

PMID- 3040396
VI  - 167
DP  - 1987
TI  - EcoR124 and EcoR124/3:  the first members of a new family of type I restriction and modification systems.
PG  - 111-115
AB  - We have purified the EcoR124 and EcoR124/3 restriction enzymes and shown that
      they are type I enzymes by several criteria:  subunit composition, DNA and
      S-adenosylmethionine-dependent ATPase activity, and site-specific DNA methylase
      activity.  By immunochemical criteria these enzymes are related to each other
      but are unrelated to the two previously investigated families of type I
      restriction enzymes.  They form therefore a new family which we call type IC.
      The arrangement of the structural genes coding for these enzymes and their
      transcriptional organisation have been determined.  These are different from
      the common arrangement found for the other two families of type I enzymes.
AU  - Price C
AU  - Pripfl T
AU  - Bickle TA
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1987 167: 111-115.

PMID- 3038525
VI  - 6
DP  - 1987
TI  - DNA recognition by a new family of type I restriction enzymes:  a unique relationship between two different DNA specificities.
PG  - 1493-1497
AB  - The DNA sequences recognized by the allelic type I restriction enzymes EcoR124
      and EcoR124/3 were determined.  EcoR124 recognizes 5'-GAA(N6)RTCG-3' and
      EcoR124/3 recognizes 5'-GAA(N7)RTCG-3'.  These are typical of sequences
      recognized by type I recognition enzymes in that they consist of two specific
      domains separated by a non-specific spacer sequence.  For these two enzymes,
      the specific sequences are identical but the length of the non-specific spacer
      is different.  The specific domains of EcoR124/3 are thus 3.4 angstroms further
      apart than those of EcoR124 and rotated with respect to each other through a
      further 36 degrees.
AU  - Price C
AU  - Shepherd JCW
AU  - Bickle TA
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1987 6: 1493-1497.

PMID- 28385830
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequences of Burkholderia pseudomallei Isolates Exhibiting Decreased Meropenem Susceptibility.
PG  - e00053-17
AB  - We report here paired isogenic Burkholderia pseudomallei genomes obtained from three patients
      receiving intravenous meropenem for melioidosis treatment, with
      post-meropenem isolates developing decreased susceptibility. Two genomes were
      finished, and four were drafted to improved high-quality standard. These genomes
      will be used to identify meropenem resistance mechanisms in B. pseudomallei.
AU  - Price EP
AU  - Smith ML
AU  - Paxinos EE
AU  - Tallon LJ
AU  - Sadzewicz L
AU  - Sengamalay N
AU  - Baird RW
AU  - Currie BJ
AU  - Sarovich DS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00053-17.

PMID- 29769716
VI  - 557
DP  - 2018
TI  - Mutant phenotypes for thousands of bacterial genes of unknown function.
PG  - 503-509
AB  - One-third of all protein-coding genes from bacterial genomes cannot be annotated  with a
      function. Here, to investigate the functions of these genes, we present
      genome-wide mutant fitness data from 32 diverse bacteria across dozens of growth
      conditions. We identified mutant phenotypes for 11,779 protein-coding genes that
      had not been annotated with a specific function. Many genes could be associated
      with a specific condition because the gene affected fitness only in that
      condition, or with another gene in the same bacterium because they had similar
      mutant phenotypes. Of the poorly annotated genes, 2,316 had associations that
      have high confidence because they are conserved in other bacteria. By combining
      these conserved associations with comparative genomics, we identified putative
      DNA repair proteins; in addition, we propose specific functions for poorly
      annotated enzymes and transporters and for uncharacterized protein families. Our
      study demonstrates the scalability of microbial genetics and its utility for
      improving gene annotations.
AU  - Price MN et al
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2018 557: 503-509.

PMID- 27777649
VI  - 11
DP  - 2016
TI  - Genome sequences and annotation of two urinary isolates of E. coli.
PG  - 79
AB  - The genus Escherichia includes pathogens and commensals. Bladder infections (cystitis) result
      most often from colonization of the bladder by uropathogenic E.
      coli strains. In contrast, a poorly defined condition called asymptomatic
      bacteriuria results from colonization of the bladder with E. coli strains without
      symptoms. As part of an on-going attempt to identify and characterize the newly
      discovered female urinary microbiota, we report the genome sequences and
      annotation of two urinary isolates of E. coli: one (E78) was isolated from a
      female patient who self-reported cystitis; the other (E75) was isolated from a
      female patient who reported that she did not have symptoms of cystitis. Whereas
      strain E75 is most closely related to an avian extraintestinal pathogen, strain
      E78 is a member of a clade that includes extraintestinal strains often found in
      the human bladder. Both genomes are uncommonly rich in prophages.
AU  - Price TK
AU  - Mehrtash A
AU  - Kalesinskas L
AU  - Malki K
AU  - Hilt EE
AU  - Putonti C
AU  - Wolfe AJ
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 79.

PMID- 27908986
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a Urinary Isolate of Lactobacillus crispatus.
PG  - e01278-16
AB  - While Lactobacillus crispatus contributes to the stability of normal vaginal microbiota, its
      role in urinary health remains unclear. As part of an on-going
      attempt to characterize the female urinary microbiota, we report the genome
      sequence of an L. crispatus strain isolated from a woman displaying no lower
      urinary tract symptoms.
AU  - Price TK
AU  - Shaheen M
AU  - Kalesinskas L
AU  - Malki K
AU  - Hilt EE
AU  - Putonti C
AU  - Wolfe AJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01278-16.

PMID- 27303749
VI  - 1
DP  - 2016
TI  - CRISPR-Cas and Restriction-Modification Act Additively against Conjugative Antibiotic Resistance Plasmid Transfer in Enterococcus faecalis.
PG  - e00064-16
AB  - Enterococcus faecalis is an opportunistic pathogen and a leading cause of nosocomial
      infections. Conjugative pheromone-responsive plasmids are
      narrow-host-range mobile genetic elements (MGEs) that are rapid disseminators of
      antibiotic resistance in the faecalis species. Clustered regularly interspaced
      short palindromic repeat (CRISPR)-Cas and restriction-modification confer
      acquired and innate immunity, respectively, against MGE acquisition in bacteria.
      Most multidrug-resistant E. faecalis isolates lack CRISPR-Cas and possess an
      orphan locus lacking cas genes, CRISPR2, that is of unknown function. Little is
      known about restriction-modification defense in E. faecalis. Here, we explore the
      hypothesis that multidrug-resistant E. faecalis strains are immunocompromised. We
      assessed MGE acquisition by E. faecalis T11, a strain closely related to the
      multidrug-resistant hospital isolate V583 but which lacks the ~620 kb of
      horizontally acquired genome content that characterizes V583. T11 possesses the
      E. faecalis CRISPR3-cas locus and a predicted restriction-modification system,
      neither of which occurs in V583. We demonstrate that CRISPR-Cas and
      restriction-modification together confer a 4-log reduction in acquisition of the
      pheromone-responsive plasmid pAM714 in biofilm matings. Additionally, we show
      that the orphan CRISPR2 locus is functional for genome defense against another
      pheromone-responsive plasmid, pCF10, only in the presence of cas9 derived from
      the E. faecalis CRISPR1-cas locus, which most multidrug-resistant E. faecalis
      isolates lack. Overall, our work demonstrated that the loss of only two loci led
      to a dramatic reduction in genome defense against a clinically relevant MGE,
      highlighting the critical importance of the E. faecalis accessory genome in
      modulating horizontal gene transfer. Our results rationalize the development of
      antimicrobial strategies that capitalize upon the immunocompromised status of
      multidrug-resistant E. faecalis. IMPORTANCE Enterococcus faecalis is a bacterium
      that normally inhabits the gastrointestinal tracts of humans and other animals.
      Although these bacteria are members of our native gut flora, they can cause
      life-threatening infections in hospitalized patients. Antibiotic resistance genes
      appear to be readily shared among high-risk E. faecalis strains, and multidrug
      resistance in these bacteria limits treatment options for infections. Here, we
      find that CRISPR-Cas and restriction-modification systems, which function as
      adaptive and innate immune systems in bacteria, significantly impact the spread
      of antibiotic resistance genes in E. faecalis populations. The loss of these
      systems in high-risk E. faecalis suggests that they are immunocompromised, a
      tradeoff that allows them to readily acquire new genes and adapt to new
      antibiotics.
AU  - Price VJ
AU  - Huo W
AU  - Sharifi A
AU  - Palmer KL
PT  - Journal Article
TA  - 
JT  - 
SO  -  2016 1: e00064-16.

PMID- Not carried by PubMed...
VI  - 1
DP  - 1991
TI  - Determination of substrate specificity of restriction endonuclease Tru9I.
PG  - 57-59
AB  - Tru9I, type II restriction endonuclease, has been isolated from Thermus ruber
      9.  The recognition sequence and cleavage point of restriction endonuclease
      Tru9I have been determined as 5'T^TAA.  Tru9I is an isoschizomer of MseI.
AU  - Prichodko EA
AU  - Rechnukova NI
AU  - Degtyarev SK
PT  - Journal Article
TA  - Sib. Biol. J.
JT  - Sib. Biol. J.
SO  - Sib. Biol. J. 1991 1: 57-59.

PMID- Not carried by PubMed...
VI  - 1
DP  - 1990
TI  - General method for determining the sites of DNA cleavage by restriction endonucleases.
PG  - 12-16
AB  - A method for determining substrate specificity of large block cleaving restrictases is
      suggested. Plasmid vectors pUBS18 and pUBS19, that permit labelling at one end of a Bse21I
      site for rapid DNA sequencing were constructed. Restriction endonuclease BimI recognizing the
      sequence TT^CGAA was isolated from the bacterial strain Brevibacterium immotum.
AU  - Prichodko GG
AU  - Degtyarev SK
AU  - Rechkunova NI
AU  - Sosnovsev SV
AU  - Tchigikov VE
PT  - Journal Article
TA  - Biotekhnologiya
JT  - Biotekhnologiya
SO  - Biotekhnologiya 1990 1: 12-16.

PMID- Not carried by PubMed...
VI  - 4
DP  - 1988
TI  - A modified method for determining the sites of DNA cleavage by restriction endonucleases.
PG  - 618-620
AB  - The modification merely involves labelling the 3' end of restriction fragments
      using Klenow so as to avoid problems of the extra phosphate group which arise
      when kinase-labelled fragments are compared with chemically degraded fragments.
AU  - Prichodko GG
AU  - Petrov NA
AU  - Chizhikov VE
AU  - Degtyarev SK
PT  - Journal Article
TA  - Biotekhnologiya
JT  - Biotekhnologiya
SO  - Biotekhnologiya 1988 4: 618-620.

PMID- Not carried by PubMed...
VI  - 14
DP  - 1988
TI  - Establishing the substrate specificity of restriction endonuclease Bsu15I.
PG  - 108-109
AB  - The recognition sequence and cleavage point of restriction endonuclease Bsu15I has been
      determined as 5'AT^CGAT.
AU  - Prichodko GG
AU  - Petrov NA
AU  - Repin VE
AU  - Degtyarev SK
PT  - Journal Article
TA  - Izv. Sib. Otd. Akad. Nauk SSSR
JT  - Izv. Sib. Otd. Akad. Nauk SSSR
SO  - Izv. Sib. Otd. Akad. Nauk SSSR 1988 14: 108-109.

PMID- Not carried by PubMed...
VI  - 1
DP  - 1991
TI  - Determination of substrate specificity of restriction endonuclease Acc65I.
PG  - 59-60
AB  - The recognition sequence and cleavage point of restriction endonuclease Acc65I
      have been determined as 5'G^GTACC.
AU  - Prichodko GG
AU  - Rechnukova NI
AU  - Repin VE
AU  - Degtyarev SK
PT  - Journal Article
TA  - Sib. Biol. J.
JT  - Sib. Biol. J.
SO  - Sib. Biol. J. 1991 1: 59-60.

PMID- 26769928
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Enterococcus faecalis Strain P8-1 Isolated from Wild  Magellanic Penguin (Spheniscus magellanicus) Feces on the South Coast of Brazil.
PG  - e01531-15
AB  - Enterococcus faecalis strains have a ubiquitous nature that allows them to survive in
      different niches. Studies involving enterococci isolated from marine
      animals are scarce. Therefore, in this study, we report the complete genome
      sequence of E. faecalis strain P8-1 isolated from feces of a Magellanic penguin
      on the south coast of Brazil.
AU  - Prichula J
AU  - Campos FS
AU  - Pereira RI
AU  - Cardoso LA
AU  - Wachholz GR
AU  - Pieta L
AU  - Mariot RF
AU  - de Moura TM
AU  - Tavares M
AU  - d'Azevedo PA
AU  - Frazzon J
AU  - Frazzon AP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01531-15.

PMID- 
VI  - 1
DP  - 2002
TI  - Identification of horizontally acquired genetic elements in Helicobacter pylori and other prokaryotes using oligonucleotide difference analysis.
PG  - 2-15
AB  - The Helicobacter pylori genome contains genetic elements believed to have been horizontally
      acquired. We compared a Markov chain method dependent on genomic oligonucleotide frequencies
      with
      methods based upon G + C content to identify potential horizontally acquired gene clusters.
      Compared with G +
      C content analysis, oligonucleotide difference analysis (ODA) identified a unique set of
      genes, with a few genes
      shared by the two methods. However, each method identified a large number of cag island and
      plasticity zone
      genes, with 12-18% identified by both. ODA also was applicable to other prokaryotes,
      identifying as foreign
      prophages in Bacillus subtilis, insertion elements in Campylobacter jejuni, genes with
      repetitive elements in
      Mycobacterium tuberculosis, and the integron island in Vibrio cholerae. GATC, the cognate
      sequence for the
      hpyIII restriction-modification system in H. pylori, is substantially underrepresented in the
      plasticity zone,
      suggesting a role for that R-M system in limiting horizontal transfer events. That GATC is not
      substantially
      underrepresented in the cag island suggests that the two islands likely have different
      origins. The information
      provided by ODA is complementary to G + C content for identifying horizontal acquisitions in
      prokaryotes.
AU  - Pride DT
AU  - Blaser MJ
PT  - Journal Article
TA  - Genome Lett.
JT  - Genome Lett.
SO  - Genome Lett. 2002 1: 2-15.

PMID- 24903879
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of a Moderately Virulent Aeromonas hydrophila Strain, pc104A, Isolated from Soil of a Catfish Pond in West Alabama.
PG  - e00554-14
AB  - Aeromonas hydrophila pc104A is a moderately virulent strain isolated from the soil of a
      catfish pond in west Alabama in 2010. Its full genome is 5,023,829 bp.
      The availability of this genome will allow comparative genomics to identify the
      virulence genes that are important for pathogenesis or immunogens for the purpose
      of vaccine development.
AU  - Pridgeon JW
AU  - Zhang D
AU  - Zhang L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00554-14.

PMID- 24903878
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of a Virulent Strain, Streptococcus iniae ISET0901, Isolated from Diseased Tilapia.
PG  - e00553-14
AB  - Streptococcus iniae ISET0901 is a virulent strain isolated in 2007 from diseased  tilapia. Its
      full genome is 2,070,856 bp. The availability of this genome will
      allow comparative genomics to identify virulence genes important for the
      pathogenesis of streptococcosis caused by S. iniae, as well as possible
      immunogens for vaccine development.
AU  - Pridgeon JW
AU  - Zhang D
AU  - Zhang L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00553-14.

PMID- 24874684
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of the Attenuated Novobiocin-Resistant Streptococcus iniae Vaccine Strain ISNO.
PG  - e00510-14
AB  - Streptococcus iniae ISNO is an attenuated novobiocin-resistant vaccine strain. Its full genome
      is 2,070,182 bp in length. The availability of this genome will
      allow comparative genomics to identify potential virulence genes important for
      pathogenesis of S. iniae and potential mechanisms associated with novobiocin
      resistance in this strain.
AU  - Pridgeon JW
AU  - Zhang D
AU  - Zhang L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00510-14.

PMID- 24855300
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of the Highly Virulent Aeromonas hydrophila AL09-71 Isolated from Diseased Channel Catfish in West Alabama.
PG  - e00450-14
AB  - Aeromonas hydrophila AL09-71 was isolated from diseased channel catfish in west Alabama during
      a 2009 disease outbreak. The full genome of A. hydrophila AL09-71
      is 5,023,861 bp. The availability of this genome will allow comparative genomics
      to identify genes involved in pathogenesis or immunogens for the purpose of
      vaccine development.
AU  - Pridgeon JW
AU  - Zhang D
AU  - Zhang L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00450-14.

PMID- 14983040
VI  - 101
DP  - 2004
TI  - The genome sequence of the probiotic intestinal bacterium Lactobacillus johnsonii NCC 533.
PG  - 2512-2517
AB  - Lactobacillus johnsonii NCC 533 is a member of the acidophilus group of intestinal
      lactobacilli that has been extensively studied for their "probiotic" activities that include,
      pathogen inhibition, epithelial cell attachment, and immunomodulation. To gain insight into
      its physiology and identify genes potentially involved in interactions with the host, we
      sequenced and analyzed the 1.99-Mb genome of L. johnsonii NCC 533. Strikingly, the organism
      completely lacked genes encoding biosynthetic pathways for amino acids, purine nucleotides,
      and most cofactors. In apparent compensation, a remarkable number of uncommon and often
      duplicated amino acid permeases, peptidases, and phosphotransferase-type transporters were
      discovered, suggesting a strong dependency of NCC 533 on the host or other intestinal microbes
      to provide simple monomeric nutrients. Genome analysis also predicted an abundance (>12) of
      large and unusual cell-surface proteins, including fimbrial subunits, which may be involved in
      adhesion to glycoproteins or other components of mucin, a characteristic expected to affect
      persistence in the gastrointestinal tract (GIT). Three bile salt hydrolases and two bile acid
      transporters, proteins apparently critical for GIT survival, were also detected. In silico
      genome comparisons with the >95% complete genome sequence of the closely related Lactobacillus
      gasseri revealed extensive synteny punctuated by clear-cut insertions or deletions of single
      genes or operons. Many of these regions of difference appear to encode metabolic or structural
      components that could affect the organisms competitiveness or interactions with the GIT
      ecosystem.
AU  - Pridmore RD
AU  - Berger B
AU  - Desiere F
AU  - Vilanova D
AU  - Barretto C
AU  - Pittet A-C
AU  - Zwahlen M-C
AU  - Rouvet M
AU  - Altermann E
AU  - Barrangou R
AU  - Mollet B
AU  - Mercenier A
AU  - Klaenhammer T
AU  - Arigoni F
AU  - Schell MA
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2004 101: 2512-2517.

PMID- 17999959
VI  - 283
DP  - 2008
TI  - Generation and analysis of mesophilic variants of the thermostable archaeal I-DmoI homing endonuclease.
PG  - 4364-4374
AB  - The hyperthermophilic archaeon Desulfurococcus mobilis I-DmoI protein belongs to the family of
      proteins known as homing endonucleases (HEs).
      HEs are highly specific DNA-cleaving enzymes that recognize long
      stretches of DNA and are powerful tools for genome engineering. Because
      of its monomeric nature, I-DmoI is an ideal scaffold for generating
      mutant enzymes with novel DNA specificities, similarly reported for
      homodimeric HEs, but providing single chain endonucleases instead of
      dimers. However, this would require the use of a mesophilic variant
      cleaving its substrate at temperatures of 37 C and below. We have
      generated mesophilic mutants of I-DmoI, using a single round of
      directed evolution that relies on a functional assay in yeast. The
      effect of mutations identified in the novel proteins has been
      investigated. These mutations are located distant to the DNA-binding
      site and cause changes in the size and polarity of buried residues,
      suggesting that they act by destabilizing the protein. Two of the novel
      proteins have been produced and analyzed in vitro. Their overall
      structures are similar to that of the parent protein, but they are
      destabilized against thermal and chemical denaturation. The
      temperature-dependent activity profiles for the mutants shifted toward
      lower temperatures with respect to the wild-type activity profile.
      However, the most destabilized mutant was not the most active at low
      temperatures, suggesting that other effects, like local structural
      distortions and/or changes in the protein dynamics, also influence
      their activity. These mesophilic I-DmoI mutants form the basis for
      generating new variants with tailored DNA specificities.
AU  - Prieto J
AU  - Epinat JC
AU  - Redondo P
AU  - Ramos E
AU  - Padro D
AU  - Cedrone F
AU  - Montoya G
AU  - Paques F
AU  - Blanco FJ
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2008 283: 4364-4374.

PMID- 22283548
VI  - 47
DP  - 2012
TI  - Molecular scissors for in situ cellular repair.
PG  - 207-221
AB  - The engineering of protein-DNA interactions in different protein scaffolds may provide
      'toolkits' to modify the genome. Homing
      endonucleases are powerful tools for genome manipulation through
      homologous recombination, as these enzymes possess a very low frequency
      of DNA cleavage in eukaryotic genomes due to their high specificity.
      Therefore, the combination of a precise 'cutter' with the presence of a
      natural or modified homologous DNA donor provides a potentially useful
      means to modify the genome. However, the basis of protein-DNA
      recognition must be understood to generate tailored enzymes that target
      the DNA at sites of interest. The engineering of homing endonucleases
      and alternative scaffolds, such as zinc fingers or transcription
      activator-like effector domains, has demonstrated the potential of
      these approaches to create new specific instruments to target genes for
      inactivation or repair. Customized homing endonucleases targeting
      selected human genes can excise or correct regions of genes implicated
      in monogenic diseases, thereby representing important tools for
      intervention in eukaryotic genomes.
AU  - Prieto J
AU  - Molina R
AU  - Montoya G
PT  - Journal Article
TA  - Crit. Rev. Biochem. Mol. Biol.
JT  - Crit. Rev. Biochem. Mol. Biol.
SO  - Crit. Rev. Biochem. Mol. Biol. 2012 47: 207-221.

PMID- 27303901
VI  - 72
DP  - 2016
TI  - Structure of the I-SceI nuclease complexed with its dsDNA target and three catalytic metal ions.
PG  - 473-479
AB  - Homing endonucleases are highly specific DNA-cleaving enzymes that recognize and  cleave long
      stretches of DNA. The engineering of these enzymes provides
      instruments for genome modification in a wide range of fields, including gene
      targeting. The homing endonuclease I-SceI from the yeast Saccharomyces cerevisiae
      has been purified after overexpression in Escherichia coli and its crystal
      structure has been determined in complex with its target DNA. In order to
      evaluate the number of ions that are involved in the cleavage process, thus
      determining the catalytic mechanism, crystallization experiments were performed
      in the presence of Mn(2+), yielding crystals that were suitable for X-ray
      diffraction analysis. The crystals belonged to the orthorhombic space group
      P212121, with unit-cell parameters a = 80.11, b = 80.57, c = 130.87 A, alpha =
      beta = gamma = 90 degrees . The self-rotation function and the Matthews
      coefficient suggested the presence of two protein-DNA complexes in the asymmetric
      unit. The crystals diffracted to a resolution limit of 2.9 A using synchrotron
      radiation. From the anomalous data, it was determined that three cations are
      involved in catalysis and it was confirmed that I-SceI follows a two-metal-ion
      DNA-strand cleavage mechanism.
AU  - Prieto J
AU  - Redondo P
AU  - Merino N
AU  - Villate M
AU  - Montoya G
AU  - Blanco FJ
AU  - Molina R
PT  - Journal Article
TA  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
JT  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
SO  - Acta Crystallogr. F Struct. Biol. Cryst. Commun. 2016 72: 473-479.

PMID- 17452357
VI  - 35
DP  - 2007
TI  - The C-terminal loop of the homing endonuclease I-CreI is essential for site recognition, DNA binding and cleavage1.
PG  - 3262-3271
AB  - Meganucleases are sequence-specific endonucleases with large cleavage sites that can be used
      to induce efficient homologous gene targeting in
      cultured cells and plants. These enzymes open novel perspectives for
      genome engineering in a wide range of fields, including gene therapy. A
      new crystal structure of the I-CreI dimer without DNA has allowed the
      comparison with the DNA-bound protein. The C-terminal loop displays a
      different conformation, which suggests its implication in DNA binding. A
      site-directed mutagenesis study in this region demonstrates that whereas
      the C-terminal helix is negligible for DNA binding, the final C-terminal
      loop is essential in DNA binding and cleavage. We have identified two
      regions that comprise the Ser138-Lys139 and Lys142-Thr143 pairs whose
      double mutation affect DNA binding in vitro and abolish cleavage in vivo.
      However, the mutation of only one residue in these sites allows DNA
      binding in vitro and cleavage in vivo. These findings demonstrate that the
      C-terminal loop of I-CreI endonuclease plays a fundamental role in its
      catalytic mechanism and suggest this novel site as a region to take into
      account for engineering new endonucleases with tailored specificity.
AU  - Prieto J
AU  - Redondo P
AU  - Padro D
AU  - Arnould S
AU  - Epinat JC
AU  - Paques F
AU  - Blanco FJ
AU  - Montoya G
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2007 35: 3262-3271.

PMID- 9750328
VI  - 27
DP  - 1998
TI  - Two restriction endonucleases in Selenomonas ruminantium subsp. lactilytica.
PG  - 83-85
AB  - Crude protein extract from a recently isolated ruminal bacterium identified as Selenomonas
      ruminantium subsp. lactilytica specifically cleaved DNA.  This ability was due to the presence
      of two site-specific restriction endonucleases.  SrlI, a NaeI isoschizomer, recognizes the
      5'-GCCGGC-3' sequence.  SrlII, an NsiI isoschizomer, recognizes 5'-ATGCAT-3'.
AU  - Pristas P
AU  - Fliegerova K
AU  - Javorsky P
PT  - Journal Article
TA  - Lett. Appl. Microbiol.
JT  - Lett. Appl. Microbiol.
SO  - Lett. Appl. Microbiol. 1998 27: 83-85.

PMID- 1508727
VI  - 20
DP  - 1992
TI  - Characterization of restriction endonuclease activities in tetracycline producing strains of Streptomyces aureofaciens.
PG  - 4364
AB  - We have tested several strains of streptomyces aureofaciens from different sources for
      restriction endonuclease. In all tested tetracycline producing strains (B-96, NMU, 16, R8/26)
      restriction endonuclease was isolated and characterized (SauLPI, SauNI, SauSI, SauHPI
      respectively). Previously described restriction endonuclease from strain S.aureofaciens R8/26I
      (1) was renamed for SauHPI in this report. Endonucleases were purified from cell extracts by
      phosphocellulose and heparin-sepharose chromatography according to (2) with minor
      modifications. The restriction endonucleases were free of contaminating nucleases activity.
      All isolated restriction endonucleases produced the same cleavage pattern on tested DNA
      substrates. Computer-derived mapping data predict the sequence 5'-GCCGCC-3'. The comparison
      of cleavage patterns of pBR322 by S.aureofaciens restrictases to NaeI confirmed the
      recognition sequence (Figure 1).
AU  - Pristas P
AU  - Godany A
AU  - Sevcikova B
AU  - Oktavcova B
AU  - Farkasovska J
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 4364.

PMID- 
VI  - 37
DP  - 1997
TI  - Restriction-modification systems in ruminal bacteria: occurrence and some evolutionary implications.
PG  - 74-75
AB  - Type II restriction modification systems involve a DNA methyltransferase and an endonuclease
      of the same recognition sequence specificity.  It is generally accepted that these systems act
      primarily to protect bacteria from foreign DNA, particularly from infection by bacteriophages.
      The study of the biology of restriction-modification systems has revealed some general
      features and it has been shown that the composition of the bacterial chromosome and the
      restriction-modification systems present within cells are evolutionarily linked.  Restriction
      endonucleases have been found in bacteria from all taxonomic and ecological groups.  Ruminal
      bacteria have been shown to be a promising source of these enzymes.  Up to now ten restriction
      endonucleases have been isolated from bacteria of this ecological group.  Our studies on
      variability of endonucleolytic activity in S. ruminantium have demonstrated a high frequency
      and diversity of restriction endonucleases in this species, and at least ten different
      specificities have been characterized.  In addition the observed frequency of restriction
      endonucleases, which were present in more than one-third of strains tested, is higher than
      observed in bacteria from other ecological groups.  A high frequency of restriction
      endonucleases in S. ruminantium can also be inferred from the analysis of DNA.  Using the
      method of Karlin et al., it was shown that average counts of perfect 4- and 6- base pairs
      palindromes observed within S. ruminantium DNA are lower than in other bacteria, and even
      lower than those observed among phage DNAs.  The observed low frequency of short palindromes
      is therefore in good agreement with the high frequency of restriction endonucleases observed
      in this genus.  Similarly other ruminal bacteria show lower counts of palindromes than would
      be predicted from a random distribution.  We suppose that the consistently low frequencies of
      4-bp and 6-bp palindromes observed within the DNA of ruminal bacteria is probably a result of
      the variety and multiplicity of restriction systems found in bacteria from this ecological
      group.  Possibly, there is a correlation between bacterial population density and the
      frequency of restriction endonucleases.  Bacterial counts in the rumen are higher than in any
      other environment.  Together with the high bacterial counts, there are also unusually high
      concentrations of bacteriophages.  If the protection of cells from bacteriophage infection is
      a primary role of restriction-modification systems, these systems should be more frequent in
      the rumen than in environments with lower populations of bacteriophages.  In such a strongly
      competitive ecosystem as the rumen of herbivorous animals the possession of restriction
      activity can provide a selective advantage for survival of both the individual bacterial clone
      and the species as a whole.
AU  - Pristas P
AU  - Javorsky P
PT  - Journal Article
TA  - Reprod. Nutr. Dev.
JT  - Reprod. Nutr. Dev.
SO  - Reprod. Nutr. Dev. 1997 37: 74-75.

PMID- 
VI  - 57
DP  - 2002
TI  - Diversity of restriction and modification phenotypes in local population of rumen bacterium Selenomonas ruminantium.
PG  - 777-782
AB  - Type II restriction endonuclease activities detected in various strains of Selenomonas
      ruminantium species, coming from genetically homogenous
      local population, were characterised. The recognition sequence of
      Srl55DI was determined to be 5'-G/AATTC-3', identical to that of EcoRI.
      Srl5DI restriction endonuclease recognises 5'-CTGCA/G-3' sequence and
      is true isoschizomer of PstI. The Srl56DI restriction endonuclease was
      found to recognise and cleave 5-C/TRYAG-3' sequence and is true
      isoschizomer of SfcI. All other restriction activities characterised
      were duplicates of restriction endonucleases, which have previously
      been detected in bacteria of S. ruminantium species. In total, 9
      different restriction endonucleases were found in the tested bacteria.
      Much higher variability of modification phenotypes was observed, when
      totally 13 types of modification profiles were found in the studied S.
      ruminantium strains. Chromosomal DNA isolated from S. ruminantium
      strains was found to be refractive to cleavage by various restriction
      enzymes, implying the presence of methylase activities additional to
      those required for protection against the cellular endonucleases. While
      extremely diverse in restriction and modification phenotypes the tested
      strains showed very low genetic diversity, when all but one strain
      produced identical profiles in ARDREA analysis. Based on close
      similarity of the tested strains the lateral gene transfer is proposed
      as a source of the observed diversity of restriction and modification
      phenotypes in S. ruminantium.
AU  - Pristas P
AU  - Molnarova V
AU  - Javorsky P
PT  - Journal Article
TA  - Biologia (Bratisl)
JT  - Biologia (Bratisl)
SO  - Biologia (Bratisl) 2002 57: 777-782.

PMID- 11501482
VI  - 46
DP  - 2001
TI  - Restriction and modification systems of ruminal bacteria.
PG  - 71-72
AB  - A high frequency of type II restriction endonuclease activities was detected in Selenomonas
      ruminantium but not in other rumen bacteria tested. Eight different restriction endonucleases
      were characterized in 17 strains coming from genetically homogeneous local populations.
      Chromosomal DNA isolated from S. ruminantium strains was found to be refractory to cleavage by
      various restriction enzymes, implying the presence of methylase activities additional to those
      required for protection against the cellular endonucleases. The presence of Dam methylation
      was detected in S. ruminantium strains as well as in several other species belonging to the
      Sporomusa sub-branch of low G + C Gram-positive bacteria (Megasphaera elsdenii, Mitsuokella
      multiacidus).
AU  - Pristas P
AU  - Molnarova V
AU  - Javorsky P
PT  - Journal Article
TA  - Folia Microbiol. (Praha)
JT  - Folia Microbiol. (Praha)
SO  - Folia Microbiol. (Praha) 2001 46: 71-72.

PMID- 9791949
VI  - 38
DP  - 1998
TI  - Detection of N6-methyladenine in GATC sequences of Selenomonas ruminantium.
PG  - 283-287
AB  - The presence of N6-methyladenine in GATC sequences in DNA of Selenomonas ruminantium was
      investigated using sensitive methylation discriminating isoschizomeric restriction enzyme
      analysis.  Methylated adenine was detected in 8 out of 18 tested strains belonging to the
      subsp. lactilytica of S. ruminantium.  No corresponding restriction activity was detected in
      three tested strains.  No GATC methylation was detected in 3 analyzed S. ruminantium subsp.
      ruminantium strains.
AU  - Pristas P
AU  - Molnarova V
AU  - Javorsky P
PT  - Journal Article
TA  - J. Basic Microbiol.
JT  - J. Basic Microbiol.
SO  - J. Basic Microbiol. 1998 38: 283-287.

PMID- 15980893
VI  - 51
DP  - 2005
TI  - Underrepresentation of short palindromes in Selenomonas ruminantium DNA: evidence for horizontal gene transfer of restriction and  modification systems?
PG  - 315-318
AB  - Molecular analysis of isolates of the rumen bacterium Selenomonas ruminantium revealed a high
      variety and frequency of site-specific
      (restriction) endonucleases. While all known S. ruminantium restriction
      and modification systems recognize hexanucleotide sequences only,
      consistently low counts of both 6-bp and 4-bp palindromes were found in
      DNA sequences of S. ruminantium. Statistical analysis indicated that
      there is some correlation between the degree of underrepresentation of
      tetranucleotide words and the number of known restriction endonucleases
      for a given sequence. Control analysis showed the same correlation in
      lambda DNA but not in human adenovirus DNA. Based on the data
      presented, it could be proposed that there is a much higher historical
      occurrence of restriction and modification systems in S. ruminantium
      and (or) frequent horizontal gene transfer of restriction and
      modification gene complexes.
AU  - Pristas P
AU  - Piknova M
PT  - Journal Article
TA  - Can. J. Microbiol.
JT  - Can. J. Microbiol.
SO  - Can. J. Microbiol. 2005 51: 315-318.

PMID- 8042908
VI  - 161
DP  - 1994
TI  - Restriction endonucleases from Selenomonas ruminantium which recognize and cleave 5'-AT/TAAT-3'.
PG  - 439-441
AB  - Two natural isolates from fallow-deer rumen identified as Selenomonas ruminantium were found
      to produce a restriction endonuclease which we called Sru4DI. This enzyme was isolated from
      cell extracts by phosphocellulose chromatography. Analysis of the Sru4DI recognition site
      showed that Sru4DI recognizes the hexanucleotide sequence 5'-AT/TAAT-3' generating 5'
      dinucleotide protruding ends upon cleavage and thus is a true isoschizomer of VspI, a
      restriction enzyme isolated from Vibrio sp.
AU  - Pristas P
AU  - Vanat I
AU  - Godany A
AU  - Javorsky P
PT  - Journal Article
TA  - Arch. Microbiol.
JT  - Arch. Microbiol.
SO  - Arch. Microbiol. 1994 161: 439-441.

PMID- 7789798
VI  - 158
DP  - 1995
TI  - Isolation and characterization of a new restriction endonuclease, Sru30DI, from Selenomonas ruminantium.
PG  - 139-140
AB  - The restriction endonuclease (ENase) Sru30DI, an isoschizomer of StuI, which recognizes the
      sequence 5'-AGG/CCT-3', was purified from a natural isolate of Selenomonas ruminantium. The
      ENase was isolated from cell extracts using single-step purification by phosphocellulose
      column chromatography. Activity of Sru30DI is inhibited by overlapping Dcm methylation. The
      ENase is extremely stable at 37oC and is active over a wide range of pH, temperature and salt
      concentrations.
AU  - Pristas P
AU  - Vanat I
AU  - Javorsky P
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 158: 139-140.

PMID- 18454331
VI  - 42
DP  - 1997
TI  - Variability of endonucleolytic activity indicates high genetic diversity within the natural population of Selenomonas ruminantium.
PG  - 121-124
AB  - The population of bacteria of Selenomonas ruminantium species in the rumen of fallow-deer was
      analyzed using endonucleolytic activity assay and plasmid profiles, indicating the presence of
      the different specificity nucleases, have been observed.  Site-specific endonucleases were
      detected in 17 out of 45 strains tested.  In other strains a various level of non-specific
      activity was detected.  Plasmid DNAs ranging in size from 0.9 to more than 25 kbp were
      detected in 60% of strains analyzed.  No or little correlation was observed between the
      endonuclease activity and the plasmid content.  The presence of different specificity
      endonucleases, as well as differences of plasmid profiles of isolates possessing identical
      specific activity indicate that the population of S. ruminantium in the rumen of an individual
      animal consists of at least 10 different clones.
AU  - Pristas P
AU  - Vanat I
AU  - Javorsky P
PT  - Journal Article
TA  - Folia Microbiol. (Praha)
JT  - Folia Microbiol. (Praha)
SO  - Folia Microbiol. (Praha) 1997 42: 121-124.

PMID- 23887905
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences of Four Dickeya dianthicola and Four Dickeya solani Strains.
PG  - e00087-12
AB  - Dickeya dianthicola and 'Dickeya solani' are currently the dominant bacterial pathogens of
      potatoes in Europe. Here, we present the draft genome sequences of
      four strains of each pathogen.
AU  - Pritchard L
AU  - Humphris S
AU  - Baeyen S
AU  - Maes M
AU  - Van Vaerenbergh J
AU  - Elphinstone J
AU  - Saddler G
AU  - Toth I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00087-12.

PMID- 24265502
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences of 17 Isolates of the Plant Pathogenic Bacterium Dickeya.
PG  - e00978-13
AB  - Dickeya (formerly Erwinia chrysanthemi) species cause diseases on a wide range of crops and
      ornamental plants worldwide. Here we present the draft sequences of 17
      Dickeya isolates spanning four Dickeya species, including five isolates that are
      currently unassigned to a species.
AU  - Pritchard L
AU  - Humphris S
AU  - Saddler GS
AU  - Elphinstone JG
AU  - Pirhonen M
AU  - Toth IK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00978-13.

PMID- 24510257
VI  - 1123
DP  - 2014
TI  - Bioinformatic Identification of Homing Endonucleases and Their Target Sites.
PG  - 27-35
AB  - Homing endonuclease genes (HEGs) are a large, phylogenetically diverse superfamily of enzymes
      with high specificity for especially long target sites. The public genomic sequence databases
      contain thousands of HEGs. This is a large and diverse arsenal of potential genome editing
      tools. To make use of this natural resource, one needs to identify candidate HEGs. Due to
      their special relationship with a host gene, it is also possible to predict their cognate
      target sequences. Here I describe the HomeBase algorithm that was developed to this end. A
      detailed description of the computational pipeline is provided with emphasis on technical and
      methodological caveats of the approach.
AU  - Privman E
PT  - Journal Article
TA  - Methods Mol. Biol.
JT  - Methods Mol. Biol.
SO  - Methods Mol. Biol. 2014 1123: 27-35.

PMID- 27422870
VI  - 44
DP  - 2016
TI  - Structural insight into DNA-assembled oligochromophores: crystallographic analysis of pyrene- and phenanthrene-modified DNA in complex with BpuJI  endonuclease.
PG  - 7079-7089
AB  - The use of the DNA duplex as a supramolecular scaffold is an established approach for the
      assembly of chromophore aggregates. In the absence of detailed structural
      insight, the characterization of thus assembled oligochromophores is, today,
      largely based on solution-phase spectroscopy. Here, we describe the crystal
      structures of three DNA-organized chromophore aggregates. DNA hybrids containing
      non-nucleosidic pyrene and phenanthrene building blocks were co-crystallized with
      the recently described binding domain of the restriction enzyme BpuJI. Crystal
      structures of these complexes were determined at 2.7, 1.9 and 1.6 A resolutions.
      The structures reveal aromatic stacking interactions between pyrene and/or
      phenanthrene units within the framework of the B-DNA duplex. In hybrids
      containing a single modification in each DNA strand near the end of the duplex,
      the two polyaromatic hydrocarbons are engaged in a face-to-face stacking
      orientation. Due to crystal packing and steric effects, the terminal GC base pair
      is disrupted in all three crystal structures, which results in a non-perfect
      stacking arrangement of the aromatic chromophores in two of the structures. In a
      hybrid containing a total of three pyrenes, crystal lattice induced end-to-end
      stacking of individual DNA duplexes leads to the formation of an extended
      aromatic pi-stack containing four co-axially arranged pyrenes. The aromatic
      planes of the stacked pyrenes are oriented in a parallel way. The study
      demonstrates the value of co-crystallization of chemically modified DNA with the
      recombinant binding domain of the restriction enzyme BpuJI for obtaining detailed
      structural insight into DNA-assembled oligochromophores.
AU  - Probst M
AU  - Aeschimann W
AU  - Chau TT
AU  - Langenegger SM
AU  - Stocker A
AU  - Haner R
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2016 44: 7079-7089.

PMID- 27635013
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Legionella jamestowniensis Isolated from a Patient with  Chronic Respiratory Disease.
PG  - e01007-16
AB  - Legionella jamestowniensis can be found in the environment in various water samples, in wet
      soil, and in compost facilities, but evidence of its human
      pathogenicity has not yet been demonstrated. Here, we report the first draft
      genome sequence of an L. jamestowniensis isolate, derived from a patient
      suffering from a chronic respiratory disease.
AU  - Prochazka B
AU  - Indra A
AU  - Hasenberger P
AU  - Blaschitz M
AU  - Wagner L
AU  - Wewalka G
AU  - Sorschag S
AU  - Schmid D
AU  - Ruppitsch W
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01007-16.

PMID- 22740681
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Serratia sp. Strain M24T3, Isolated from Pinewood Disease Nematode Bursaphelenchus xylophilus.
PG  - 3764
AB  - Here we report the draft genome sequence of Serratia sp. strain M24T3, which is associated
      with pinewood nematode Bursaphelenchus xylophilus, the causative agent
      of pine wilt disease. Serratia sp. strain M24T3 has been identified as a
      bionematocide for B. xylophilus in vitro, and multiple genes potentially involved
      in virulence and nematotoxity were identified.
AU  - Proenca DN
AU  - Espirito SC
AU  - Grass G
AU  - Morais PV
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3764.

PMID- 22887683
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Pseudomonas sp. Strain M47T1, Carried by Bursaphelenchus xylophilus Isolated from Pinus pinaster.
PG  - 4789-4790
AB  - The draft genome sequence of Pseudomonas sp. strain M47T1, carried by the Bursaphelenchus
      xylophilus pinewood nematode, the causative agent of pine wilt
      disease, is presented. In Pseudomonas sp. strain M47T1, genes that make this a
      plant growth-promoting bacterium, as well as genes potentially involved in
      nematotoxicity, were identified.
AU  - Proenca DN
AU  - Espirito SC
AU  - Grass G
AU  - Morais PV
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4789-4790.

PMID- 28904742
VI  - 12
DP  - 2017
TI  - Draft genome sequence of the cellulolytic endophyte Chitinophaga costaii A37T2T.
PG  - 53
AB  - Here we report the draft genome sequence of Chitinophaga costai A37T2T (=CIP 110584T, =LMG
      27458T), which was isolated from the endophytic community of Pinus
      pinaster tree. The total genome size of C. costaii A37T2T is 5.07 Mbp, containing
      4204 coding sequences. Strain A37T2T encoded multiple genes likely involved in
      cellulolytic, chitinolytic and lipolytic activities. This genome showed 1145
      unique genes assigned into 109 Cluster of Orthologous Groups in comparison with
      the complete genome of C. pinensis DSM 2588T. The genomic information suggests
      the potential of the strain A37T2T to interact with the plant metabolism. As
      there are only a few bacterial genomes related to Pine Wilt Disease, this work
      provides a contribution to the field.
AU  - Proenca DN
AU  - Whitman WB
AU  - Shapiro N
AU  - Woyke T
AU  - Kyrpides NC
AU  - Morais PV
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 53.

PMID- 6374428
VI  - 4
DP  - 1984
TI  - 5-methylcytosine is not detectable in Saccharomyces cerevisiae.
PG  - 985-988
AB  - We examined the DNA of Saccharomyces cerevisiae by both HpaII-MspI restriction enzyme
      digestion and high-performance liquid chromatography analysis for the possible presence of
      5-methylcytosine.  Both of these methods failed to detect cytosine methylation within this
      yeast DNA; i.e. there is <1 5-methylcytosine per 3,100 to 6,000 cytosine residues.
AU  - Proffitt JH
AU  - Davie JR
AU  - Swinton D
AU  - Hattman S
PT  - Journal Article
TA  - Mol. Cell. Biol.
JT  - Mol. Cell. Biol.
SO  - Mol. Cell. Biol. 1984 4: 985-988.

PMID- 12853608
VI  - 31
DP  - 2003
TI  - Pseudocomplementary PNAs as selective modifiers of protein activity on duplex DNA: the case of type IIs restriction enzymes.
PG  - 3929-3935
AB  - This study evaluates the potential of pseudocomplementary peptide nucleic acids (pcPNAs) for
      sequence-specific modification of enzyme activity
      towards double-stranded DNA (dsDNA). To this end, we analyze the ability
      of pcPNA-dsDNA complexes to site-selectively interfere with the action of
      four type IIs restriction enzymes. We have found that pcPNA-dsDNA
      complexes exhibit a different degree of DNA protection against
      cleaving/nicking activity of various isoschizomeric endonucleases under
      investigation (PleI, MlyI and N.BstNBI) depending on their type and mutual
      arrangement of PNA-binding and enzyme recognition/cleavage sites. We have
      also found that the pcPNA targeting to closely located PleI or BbsI
      recognition sites on dsDNA generates in some cases the nicking activity of
      these DNA cutters. At the same time, MlyI endonuclease, a PleI
      isoschizomer, does not exhibit any DNA nicking/cleavage activity, being
      completely blocked by the nearby pcPNA binding. Our results have general
      implications for effective pcPNA interference with the performance of
      DNA-processing proteins, thus being important for prospective applications
      of pcPNAs.
AU  - Protozanova E
AU  - Demidov VV
AU  - Nielsen PE
AU  - Frank-Kamenetskii MD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2003 31: 3929-3935.

PMID- 12231505
VI  - 3
DP  - 2002
TI  - Tailoring the activity of restriction endonuclease PleI by PNA-induced DNA looping.
PG  - 956-961
AB  - DNA looping is one of the key factors allowing proteins bound to different DNA sites to signal
      one another via direct contacts. We demonstrate that DNA looping can be generated in an
      arbitrary chosen site by sequence-directed targeting of double-stranded DNA with
      pseudocomplementary peptide-nucleic acids (pcPNAs). We designed pcPNAs to mask the DNA from
      cleavage by type IIs restriction enzyme PleI while not preventing the enzyme from binding to
      its primary DNA recognition site. Direct interaction between two protein molecules (one bound
      to the original recognition site and the other to a sequence-degenerated site) results in a
      totally new activity of PleI: it produces a nick near the degenerate site. The PNA-induced
      nicking efficiency varies with the distance between the two protein-binding sites in a phase
      with the DNA helical periodicity. Our findings imply a general approach for the fine-tuning of
      proteins bound to DNA sites well separated along the DNA chain.
AU  - Protozanova E
AU  - Demidov VV
AU  - Soldatenkov V
AU  - Chasovskikh S
AU  - Frank-Kamenetskii MD
PT  - Journal Article
TA  - EMBO Rep.
JT  - EMBO Rep.
SO  - EMBO Rep. 2002 3: 956-961.

PMID- 19592424
VI  - 37
DP  - 2009
TI  - Transcription regulation of restriction-modification system Ecl18kI.
PG  - 5322-5330
AB  - Restriction-modification (R-M) system Ecl18kI is representative of R-M systems whose
      coordinated transcription is achieved through a separate
      DNA-binding domain of the methyltransferase. M.Ecl18kI recognizes an
      operator sequence located in the noncoding region that separates the
      divergently transcribed R and M genes. Here we show that, contrary to
      previous predictions, the two ecl18kI promoters are not divergent, but
      actually face one another. The binding of M.Ecl18kI to its operator
      prevents RNA polymerase (RNAP) binding to the M promoter by steric
      exclusion, but has no direct effect on RNAP interaction with the R
      promoter. The start point for R transcription is located outside of the
      intergenic region, opposite the initiation codon of the M gene. Regulated
      transcription of the potentially toxic ecl18kI R gene is accomplished (i)
      at the stage of promoter complex formation, through direct competition
      from complexes formed at the M promoter, and (ii) at the stage of promoter
      clearance, since R promoter-bound RNAP escapes the promoter more slowly
      than RNAP bound to the M promoter.
AU  - Protsenko A
AU  - Zakharova M
AU  - Nagornykh M
AU  - Solonin A
AU  - Severinov K
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: 5322-5330.

PMID- 30533920
VI  - 7
DP  - 2018
TI  - Complete Genome Sequence of the Industrial Fast-Acidifying Strain Streptococcus thermophilus N4L.
PG  - e01029-18
AB  - Streptococcus thermophilus is one of the most used dairy starters for the production of yogurt
      and cheese. We report here the complete genome sequence of
      the industrial strain S. thermophilus N4L, which is used in dairy technology for
      its fast-acidifying phenotype.
AU  - Proust L
AU  - Loux V
AU  - Martin V
AU  - Magnabosco C
AU  - Pedersen M
AU  - Monnet V
AU  - Juillard V
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e01029-18.

PMID- 12374837
VI  - 184
DP  - 2002
TI  - The dilemma of phage taxonomy illustrated by comparative genomics of sfi21-like siphoviridae in lactic acid bacteria.
PG  - 6026-6036
AB  - The complete genome sequences of two dairy phages, Streptococcus thermophilus phage 7201 and
      Lactobacillus casei phage A2, are reported. Comparative genomics reveals that both phages are
      members of the recently proposed Sfi21-like genus of Siphoviridae, a widely distributed phage
      type in low-GC-content gram-positive bacteria. Graded relatedness, the hallmark of evolving
      biological systems, was observed when different Sfi21-like phages were compared. Across the
      structural module, the graded relatedness was represented by a high level of DNA sequence
      similarity or protein sequence similarity, or a shared gene map in the absence of sequence
      relatedness. This varying range of relatedness was found within Sfi21-like phages from a
      single species as demonstrated by the different prophages harbored by Lactococcus lactis
      strain IL1403. A systematic dot plot analysis with 11 complete L. lactis phage genome
      sequences revealed a clear separation of all temperate phages from two classes of virulent
      phages. The temperate lactococcal phages share DNA sequence homology in a patchwise fashion
      over the nonstructural gene cluster. With respect to structural genes, four DNA homology
      groups could be defined within temperate L. lactis phages. Closely related structural modules
      for all four DNA homology groups were detected in phages from Streptococcus or Listeria,
      suggesting that they represent distinct evolutionary lineages that have not uniquely evolved
      in L. lactis. It seems reasonable to base phage taxonomy on data from comparative genomics.
      However, the peculiar modular nature of phage evolution creates ambiguities in the definition
      of phage taxa by comparative genomics. For example, depending on the module on which the
      classification is based, temperate lactococcal phages can be classified as a single phage
      species, as four distinct phage species, or as two if not three different phage genera. We
      propose to base phage taxonomy on comparative genomics of a single structural gene module
      (head or tail genes). This partially phylogeny-based taxonomical system still mirrors some
      aspects of the current International Committee on Taxonomy in Virology classification system.
      In this system the currently sequenced lactococcal phages would be grouped into five genera:
      c2-, sk1, Sfi11-, r1t-, and Sfi21-like phages.
AU  - Proux C
AU  - Van Sinderen D
AU  - Suarez J
AU  - Garcia P
AU  - Ladero V
AU  - Fitzgerald GF
AU  - Desiere F
AU  - Brussow H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2002 184: 6026-6036.

PMID- 6777630
VI  - 180
DP  - 1980
TI  - Transformation and transduction of Bacillus subtilis strains with the BsuR restriction-modification system by means of modified and unmodified DNA of pUB110 plasmid.
PG  - 135-138
AB  - During transformation of B. subtilis cells with the BsuR restriction-modification system by
      means of pUB110 plasmid, restriction and modification of the plasmid DNA occurs.  The effect
      of restriction on the transformation frequency is relatively weak, bringing about a 20-fold
      decrease only.  When using cells of a modifying recipient, the frequency of AR9 phage-mediated
      transduction of unmodified plasmid DNA is also relatively little decreased.  The frequency of
      transduction by chromosomal markers, under the same conditions, falls much lower.
AU  - Prozorov AA
AU  - Belova TS
AU  - Surikov NN
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1980 180: 135-138.

PMID- 24732980
VI  - 9
DP  - 2014
TI  - Vibrio vulnificus Phage PV94 Is Closely Related to Temperate Phages of V. cholerae and Other Vibrio Species.
PG  - E94707
AB  - BACKGROUND: Vibrio vulnificus is an important pathogen which can cause serious
      infections in humans. Yet, there is limited knowledge on its virulence factors
      and the question whether temperate phages might be involved in pathogenicity, as
      is the case with V. cholerae. Thus far, only two phages (SSP002 and VvAW1)
      infecting V. vulnificus have been genetically characterized. These phages were
      isolated from the environment and are not related to Vibrio cholerae phages. The
      lack of information on temperate V. vulnificus phages prompted us to isolate
      those phages from lysogenic strains and to compare them with phages of other
      Vibrio species. RESULTS: In this study the temperate phage PV94 was isolated from
      a V. vulnificus biotype 1 strain by mitomycin C induction. PV94 is a myovirus
      whose genome is a linear double-stranded DNA of 33,828 bp with 5'-protruding
      ends. Sequence analysis of PV94 revealed a modular organization of the genome.
      The left half of the genome comprising the immunity region and genes for the
      integrase, terminase and replication proteins shows similarites to V. cholerae
      kappa phages whereas the right half containing genes for structural proteins is
      closely related to a prophage residing in V. furnissii NCTC 11218. CONCLUSION: We
      present the first genomic sequence of a temperate phage isolated from a human V.
      vulnificus isolate. The sequence analysis of the PV94 genome demonstrates the
      wide distribution of closely related prophages in various Vibrio species.
      Moreover, the mosaicism of the PV94 genome indicates a high degree of horizontal
      genetic exchange within the genus Vibrio, by which V. vulnificus might acquire
      virulence-associated genes from other species.
AU  - Pryshliak M
AU  - Hammerl JA
AU  - Reetz J
AU  - Strauch E
AU  - Hertwig S
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2014 9: E94707.

PMID- 14338791
VI  - 11
DP  - 1965
TI  - Replication and host modification of DNA transferred during bacterial mating.
PG  - 829-838
AB  - An experiment is presented which shows that during the course of bacterial
      mating between Escherichia coli F-prime (lambda) male and an E. coli (lambda)
      female, the transferred lambda prophages all replicate.  This strongly suggests
      that all the transferred F-prime factors carrying the lambda prophage replicate
      during the mating.  A separate experiment, employing host-induced modification,
      shows that at least 20% of the strands injected into the female are synthesized
      in the male just prior to injection.  It is argued that all the injected DNA
      replicates in the male just prior to injection, and that most of the newly made
      strands are not endowed with the host-induced modification properties normally
      associated with DNA synthesized in the male.
AU  - Ptashne M
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1965 11: 829-838.

PMID- 7596142
VI  - S21
DP  - 1995
TI  - Regulated expression of restriction endonuclease activity in mammalian cells.
PG  - 327
AB  - DNA double-strand breaks (dsbs) are the primary lethal lesion in cells exposed to ionizing
      radiation (IR).  Detecting cellular responses specific to the dsbs formed by IR is hampered by
      a broad spectrum of damage.  Transfer of restriction enzymes (REs) into mammalian cells
      affords access to dsbs in the absence of other lesions; however, this approach is not
      quantitatively radiomimetic due to the variable introduction of REs into cells in quantities
      ranging from none to much greater than average.  While this effect might be eliminated by
      regulated, homogeneous RE gene expression in mammalian cells, such a strategy has been limited
      by leaky transcriptional control.  Braselman et al. reported stringent regulation by estrogen
      of a chimeric transcription factor::estrogen receptor (ER) fusion protein activity in
      mammalian cells in an effort to create a radiomimetic dsb model system tightly controlled by
      estrogen.  PCR was used to modify a RE gene (PvuII) to allow efficient translation in
      eucaryotic cells; expression of the modified gene in E. coli verified function by phage
      restriction.  This gene was installed in a mammalian expression system expected to afford
      estrogen-dependent regulation; the resulting construct has been transferred into rodent cells.
      Recovery of robust G418-resistant stable transfectants at similar frequencies of RE
      gene-containing and control constructs (in the absence of estrogen) indicates that any basal
      PvuII expression in the former case occurs at a level tolerated by the cells.  Preliminary
      results suggest cytotoxicity associated with estrogenic steroid exposure in the former, but
      not the latter, cells.  The dependence of killing on estrogen exposure duration is currently
      under investigation, as is the ability of putative RE-induced dsb to function as sublethal
      damage with respect to subsequent IR exposure.  Direct measurement of dsb yields will be
      performed using pulse field gels.  The PvuII gene has been engineered for regulated mammalian
      cell expression.  This system apparently affords tight control of intracellular RE activity by
      estrogen, providing a means to study quantitative DNA dsb effects in the absence of other
      changes generated in X-irradiated cells.  Current results will be presented.
AU  - Pu AT
AU  - Radany EH
PT  - Journal Article
TA  - J. Cell. Biochem.
JT  - J. Cell. Biochem.
SO  - J. Cell. Biochem. 1995 S21: 327.

PMID- 11932461
VI  - 148
DP  - 2002
TI  - Envelope instability in DNA adenine methylase mutants of Salmonella  enterica.
PG  - 1171-1182
AB  - Mutants of Salmonella enterica serovar Typhimurium lacking DNA
      adenine (Dam) methylase show reduced secretion of invasion effectors
      encoded in the Salmonella-pathogenicity island 1 (SPI-1). Concomitant with
      this alteration, a high number and quantity of extracellular proteins are
      detected in cultures of Dam(-) mutants. This study shows by subcellular
      fractionation analysis that the presence of numerous extracellular proteins
      in cultures of Dam(-) mutants is linked to an exacerbated release of
      membrane particulate material. The membrane 'leaky' phenotype and the
      impaired functionality of type III secretion systems were, however,
      unrelated since exacerbated release of proteins to the medium was evident
      in Dam(-) strains carrying mutations in either SPI-1 (invA, invJ) or
      flagellar (flhD) genes. This result supports the view that Dam methylation
      controls a plethora of cellular processes. Electron microscopy analysis
      demonstrated that the accumulation of membrane particulate material occurs
      preferentially as vesicles in stationary cultures of Dam(-) strains. In
      addition, a reduction in the relative amount of peptidoglycan-associated
      lipoprotein (PAL), TolB, OmpA and murein lipoprotein (Lpp) bound to
      peptidoglycan was observed in actively growing Dam(-) mutants. The
      existence of an envelope defect was further confirmed by the increased
      sensitivity to deoxycholate exhibited by Dam(-) mutants, mostly during
      exponential growth. Unexpectedly, lack of Dam methylation neither increased
      envelope instability nor impaired the association of PAL-Tol-Lpp proteins
      to the peptidoglycan in Escherichia coli. Accordingly, E. coli Dam(-)
      mutants did not show sensitivity to deoxycholate. Altogether, these results
      indicate that, besides its role in modulating the secretion of effectors by
      the SPI-1-encoded type III apparatus, Dam methylation controls cell
      envelope integrity in S. enterica.
AU  - Pucciarelli MG
AU  - Prieto AI
AU  - Casadesus J
AU  - Portillo FGD
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2002 148: 1171-1182.

PMID- 11962209
VI  - 38
DP  - 2002
TI  - Entomapathogenic bacteria Bacillus thuringiensis as producers of restriction endonucleases.
PG  - 140-144
AB  - A total of 115 collection strains of Bacillus thuringiensis, belonging to various subspecies,
      have been studied for the presence of DNA restriction-modification systems.  Restriction
      endonucleases of 13 strains have been isolated and characterized.  No considerable
      correlations between the taxonomic positions of the bacteria and the specificities of the
      endonucleases isolated have been detected.  It is concluded that the enzymes with identical
      specificities are present in both the crystalliferous and acrystalliferous strains of the same
      subspecies.
AU  - Puchkova LI
AU  - Kalmykova GV
AU  - Burtseva LI
AU  - Repin VE
PT  - Journal Article
TA  - Prikl. Biokhim. Mikrobiol.
JT  - Prikl. Biokhim. Mikrobiol.
SO  - Prikl. Biokhim. Mikrobiol. 2002 38: 140-144.

PMID- Not carried by PubMed...
VI  - 1
DP  - 1990
TI  - Streptomyces fradiae is the producer of the restriction endonuclease Sfr274I.
PG  - 32-34
AB  - Experiments were carried out to assay for restrictase producers in
      microorganisms from the Streptomyces genus.  Streptomyces fradiae Ac 149 was
      found to be a producer of the restriction endonuclease Sfr274I - an
      isoschizomer of the restrictase XhoI (recognition site CTCGAG).
AU  - Puchkova LI
AU  - Krivopalova GN
AU  - Andreeva IS
AU  - Selina AV
AU  - Serov GD
AU  - Rechkunova NI
AU  - Degtyarev SK
PT  - Journal Article
TA  - Izv. Sib. Otd. Akad. Nauk SSSR
JT  - Izv. Sib. Otd. Akad. Nauk SSSR
SO  - Izv. Sib. Otd. Akad. Nauk SSSR 1990 1: 32-34.

PMID- 11852561
VI  - 38
DP  - 2002
TI  - Testing and isolation of high-purity restriction endonucleases.
PG  - 20-24
AB  - A new method of testing restriction nucleases is proposed.  This method is based on
      high-temperature treatment of crude cell extracts.  Disrupted cells were heated at 50-60 C,
      centrifuged, and assayed for restrictases.  This method provides the opportunity for screening
      new enzymes in microbial strains enriched with nonspecific restrictases.  High-temperature
      treatment of cell extracts of certain producers reduces the number of steps of the procedure
      used for isolating high-purity restrictases; the resulting preparations are capable of
      maintaining high enzymatic activity during long-term storage.  It was shown that
      high-temperature treatment can be applied not only to thermophilic but also to mesophilic
      strains of microorganisms of different taxa.
AU  - Puchkova LI
AU  - Ushakova TA
AU  - Mikhailova VK
AU  - Serov GD
AU  - Krivopalova GN
AU  - Repin VE
PT  - Journal Article
TA  - Prikl. Biokhim. Mikrobiol.
JT  - Prikl. Biokhim. Mikrobiol.
SO  - Prikl. Biokhim. Mikrobiol. 2002 38: 20-24.

PMID- 8255757
VI  - 21
DP  - 1993
TI  - Homologous recombination in plant cells in enhanced by in vivo induction of double strand breaks into DNA by a site-specific endonuclease.
PG  - 5034-5040
AB  - Induction of double strand breaks (DSBs) is coupled to meiotic and mitotic recombination in
      yeast. We show that also in a higher eukaryote induction of DSBs is directly correlated with a
      strong enhancement of recombination frequencies. We cotransfected Nicotiana plumbaginifolia
      protopasts with a plasmid carrying a synthetic I-SceI gene, coding for a highly sequence
      specific endonuclease, together with recombination substrates carrying an I-SceI-site adjacent
      to their homologous sequences. We measured efficiencies of extrachromosomal recombination,
      using a well established transient B-glucuronidase (GUS) assay. GUS enzyme activities were
      strongly increased when a plasmid carrying the I-SceI gene in sense but not in antisense
      orientation with respect to the promoter was included in the transfections. The in vivo
      induced DSBs were detected in the recombination substrates by Southern blotting, demonstrating
      that the yeast enzyme is functional in plant cells. At high ratios of transfected I-SceI-genes
      to I-SceI-sites the majority of the I-SceI-sites in the recombination substrates are cleaved,
      indicating that the induction of the DSBs is the rate limiting step in the described
      recombination reaction. These results imply that in vivo induction of transient breaks at
      specific sites in the plant genome could allow foreign DNA to be targeted to these sites via
      homologous recombination.
AU  - Puchta H
AU  - Dujon B
AU  - Hohn B
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 5034-5040.

PMID- 29700137
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of the Extremely Desiccation-Tolerant Cyanobacterium Gloeocapsopsis sp. Strain AAB1.
PG  - e00216-18
AB  - Gloeocapsopsis sp. strain AAB1 is an extremely desiccation-tolerant cyanobacterium isolated
      from translucent quartz stones from the Atacama Desert
      (Chile). Here, we report its draft genome sequence, which consists of 137 contigs
      with an approximately 5.4-Mb genome size. The annotation revealed 5,641 coding
      DNA sequences, 38 tRNA genes, and 5 rRNA genes.
AU  - Puente-Sanchez F
AU  - Gonzalez-Silva C
AU  - Parro V
AU  - Tamames J
AU  - Azua-Bustos A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00216-18.

PMID- 27688325
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the Deep-Subsurface Actinobacterium Tessaracoccus lapidicaptus IPBSL-7T.
PG  - e01078-16
AB  - The type strain of Tessaracoccus lapidicaptus was isolated from the deep subsurface of the
      Iberian Pyrite Belt (southwest Spain). Here, we report its
      draft genome, consisting of 27 contigs with a ~3.1-Mb genome size. The annotation
      revealed 2,905 coding DNA sequences, 45 tRNA genes, and three rRNA genes.
AU  - Puente-Sanchez F
AU  - Pieper DH
AU  - Arce-Rodriguez A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01078-16.

PMID- 27284133
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Lactobacillus collinoides CUPV237, an Exopolysaccharide  and Riboflavin Producer Isolated from Cider.
PG  - e00506-16
AB  - Lactobacillus collinoides CUPV237 is a strain isolated from a Basque cider. Lactobacillus
      collinoides is one of the most frequent species found in cider from
      Spain, France, or England. A notable feature of the L. collinoides CUPV237 strain
      is its ability to produce exopolysaccharides.
AU  - Puertas AI
AU  - Capozzi V
AU  - Llamas MG
AU  - Lopez P
AU  - Lamontanara A
AU  - Orru L
AU  - Russo P
AU  - Spano G
AU  - Duenas MT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00506-16.

PMID- 9931007
VI  - 38
DP  - 1999
TI  - Functional roles of the conserved aromatic amino acid residues at position 108 (Motif IV) and position 196 (Motif VIII) in base flipping and catalysis by the N6-adenine DNA methyltransferase from Thermus aquaticus.
PG  - 1426-1434
AB  - The DNA methyltransferase from Thermus aquaticus catalyzes the transfer of the activated
      methyl group of S-adenosyl-L-methionine to the N6 position of adenine within the
      double-stranded DNA sequence 5'-TCGA-3'.  To achieve catalysis M.TaqI flips the target
      adenine out of the DNA helix.  On the basis of the three-dimensional structure of M.TaqI in
      complex with the cofactor and its structural homology to the C5-cytosine DNA Mtase from
      Haemophilus haemolyticus, Tyr108 and Phe196 were suggested to interact with the extrahelical
      adenine.  The functional roles of these two aromatic amino acid residues in M.TaqI were
      investigated by mutational analysis.  The obtained mutant Mtases were analyzed in an improved
      kinetic assay, and their ability to flip the target base was studied in a fluorescence-based
      assay using a duplex oligodeoxynucleotide containing the fluorescent base analogue
      2-aminopurine at the target position.  While the mutant Mtases containing the aromatic amino
      acid Trp at position 108 or 196 (Y108W and F196W) showed almost wild-type catalytic activity,
      the mutant Mtases with the nonaromatic amino acid Ala (Y108A and F196A) had a strongly reduced
      catalytic constant.  Y108A was still able to flip the target base, whereas F196A was strongly
      impaired in base flipping.  These results indicate that Phe196 is important for stabilizing
      the extrahelical target adenine and suggest that Tyr108 is involved in placing the
      extrahelical target base in an optimal position for methyl group transfer.  Since both
      aromatic amino acids belong to the conserved motifs IV and XIII found in N6-adenine and
      N4-cytosine DNA Mtases as well as in N6-adenine RNA Mtases, a similar function of aromatic
      amino acid residues within these motifs is expected for the different Mtases.
AU  - Pues H
AU  - Bleimling N
AU  - Holz B
AU  - Wolcke J
AU  - Weinhold E
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1999 38: 1426-1434.

PMID- 503858
VI  - 7
DP  - 1979
TI  - A thermostable, sequence-specific restriction endonuclease from Bacillus stearothermophilus: BstPI.
PG  - 1429-1444
AB  - A restriction endonuclease, BstPI, was purified from a strain of B.
      stearothermophilus, and its cleavage specificity was determined.  The enzyme
      cleaves at palindromic sites of the general structure: 5' -G^-G-T-N-A-C-C- 3'
      3' -C-C-A-N-T-G^-G- 5' where N-N' can be any base pair.  It produces
      phosphorylated 5'-termini which are single stranded over a length of 5
      nucleotides.  Ends generated by cleavage with BstPI can be rejoined by DNA
      ligase.
AU  - Pugatsch T
AU  - Weber H
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1979 7: 1429-1444.

PMID- 29348339
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Strains TRE 1, TRE D, TRE H, and TRI 7, Isolated from Tamarins and Belonging to Four Putative Novel Bifidobacterium Species.
PG  - e01449-17
AB  - Bifidobacterium sp. strains TRE 1, TRE D, TRE H, and TRI 7 were isolated from two tamarins
      housed in Parco Natura Viva, Garda Zoological Park S.r.l. (Bussolengo,
      Verona, Italy). These strains belong to four putative novel species of the genus
      Bifidobacterium The genome sizes were 2.7 Mb for TRE 1, 2.7 Mb for TRE D, 2.4 Mb
      for TRE H, and 2.7 Mb for TRI 7. The average GC contents were 63.18% for TRE 1,
      58.27% for TRE D, 57.11% for TRE H, and 63.79% for TRI 7.
AU  - Puglisi E
AU  - Mattarelli P
AU  - Modesto M
AU  - Bonetti A
AU  - Spiezio C
AU  - Sandri C
AU  - Morelli L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01449-17.

PMID- 18927608
VI  - 3
DP  - 2008
TI  - Re-assembly of the genome of Francisella tularensis subsp. holarctica OSU18.
PG  - E3427
AB  - Francisella tularensis is a highly infectious human intracellular pathogen
      that is the causative agent of tularemia. It occurs in several major
      subtypes, including the live vaccine strain holarctica (type B). F.
      tularensis is classified as category A biodefense agent in part because a
      relatively small number of organisms can cause severe illness. Three
      complete genomes of subspecies holarctica have been sequenced and
      deposited in public archives, of which OSU18 was the first and the only
      strain for which a scientific publication has appeared. We re-assembled
      the OSU18 strain using both de novo and comparative assembly techniques,
      and found that the published sequence has two large inversion
      mis-assemblies. We generated a corrected assembly of the entire genome
      along with detailed information on the placement of individual reads
      within the assembly. This assembly will provide a more accurate basis for
      future comparative studies of this pathogen.
AU  - Puiu D
AU  - Salzberg SL
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2008 3: E3427.

PMID- 26607894
VI  - 3
DP  - 2015
TI  - Genome Sequence of the Atypical Symbiotic Frankia R43 Strain, a Nitrogen-Fixing and Hydrogen-Producing Actinobacterium.
PG  - e01387-15
AB  - Frankia strain R43 is a nitrogen-fixing and hydrogen-producing symbiotic actinobacterium that
      was isolated from nodules of Casuarina cunninghamiana but
      infects only Elaeagnaceae. This communication reports the genome of the strain
      R43 and provides insights into the microbe genomics and physiological potentials.
AU  - Pujic P
AU  - Bolotin A
AU  - Fournier P
AU  - Sorokin A
AU  - Lapidus A
AU  - Richau KH
AU  - Briolay J
AU  - Mebarki F
AU  - Normand P
AU  - Sellstedt A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01387-15.

PMID- 21304663
VI  - 1
DP  - 2009
TI  - Complete genome sequence of Slackia heliotrinireducens type strain (RHS 1).
PG  - 234-241
AB  - Slackia heliotrinireducens (Lanigan 1983) Wade et al. 1999 is of phylogenetic interest because
      of its location in a genomically yet uncharted section of the
      family Coriobacteriaceae, within the deep branching Actinobacteria. Strain RHS
      1(T) was originally isolated from the ruminal flora of a sheep. It is a
      proteolytic anaerobic coccus, able to reductively cleave pyrrolizidine alkaloids.
      Here we describe the features of this organism, together with the complete genome
      sequence, and annotation. This is the first complete genome sequence of the genus
      Slackia, and the 3,165,038 bp long single replicon genome with its 2798
      protein-coding and 60 RNA genes is part of the Genomic Encyclopedia of Bacteria
      and Archaea project.
AU  - Pukall R et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2009 1: 234-241.

PMID- 21304666
VI  - 1
DP  - 2009
TI  - Complete genome sequence of Jonesia denitrificans type strain (Prevot 55134).
PG  - 262-269
AB  - Jonesia denitrificans (Prevot 1961) Rocourt et al. 1987 is the type species of the genus
      Jonesia, and is of phylogenetic interest because of its isolated
      location in the actinobacterial suborder Micrococcineae. J. denitrificans is
      characterized by a typical coryneform morphology and is able to form irregular
      nonsporulating rods showing branched and club-like forms. Coccoid cells occur in
      older cultures. J. denitrificans is classified as a pathogenic organism for
      animals (vertebrates). The type strain whose genome is described here was
      originally isolated from cooked ox blood. Here we describe the features of this
      organism, together with the complete genome sequence and annotation. This is the
      first completed genome sequence of a member of the genus for which a complete
      genome sequence is described. The 2,749,646 bp long genome with its 2558
      protein-coding and 71 RNA genes is part of the Genomic Encyclopedia of Bacteria
      and Archaea project.
AU  - Pukall R et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2009 1: 262-269.

PMID- 21304701
VI  - 2
DP  - 2010
TI  - Complete genome sequence of Kribbella flavida type strain (IFO 14399).
PG  - 186-193
AB  - The genus Kribbella consists of 15 species, with Kribbella flavida (Park et al. 1999) as the
      type species. The name Kribbella was formed from the acronym of the
      Korea Research Institute of Bioscience and Biotechnology, KRIBB. Strains of the
      various Kribbella species were originally isolated from soil, potato, alum slate
      mine, patinas of catacombs or from horse racecourses. Here we describe the
      features of K. flavida together with the complete genome sequence and annotation.
      In addition to the 5.3 Mbp genome of Nocardioides sp. JS614, this is only the
      second completed genome sequence of the family Nocardioidaceae. The 7,579,488 bp
      long genome with its 7,086 protein-coding and 60 RNA genes and is part of the
      Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Pukall R et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 2: 186-193.

PMID- 21304704
VI  - 2
DP  - 2010
TI  - Complete genome sequence of Conexibacter woesei type strain (ID131577).
PG  - 212-219
AB  - The genus Conexibacter (Monciardini et al. 2003) represents the type genus of the family
      Conexibacteraceae (Stackebrandt 2005, emend. Zhi et al. 2009) with
      Conexibacter woesei as the type species of the genus. C. woesei is a
      representative of a deep evolutionary line of descent within the class
      Actinobacteria. Strain ID131577(T) was originally isolated from temperate forest
      soil in Gerenzano (Italy). Cells are small, short rods that are motile by
      peritrichous flagella. They may form aggregates after a longer period of growth
      and, then as a typical characteristic, an undulate structure is formed by
      self-aggregation of flagella with entangled bacterial cells. Here we describe the
      features of the organism, together with the complete sequence and annotation. The
      6,359,369 bp long genome of C. woesei contains 5,950 protein-coding and 48 RNA
      genes and is part of the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Pukall R et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 2: 212-219.

PMID- 21677853
VI  - 4
DP  - 2011
TI  - Complete genome sequence of Deinococcus maricopensis type strain (LB-34).
PG  - 163-172
AB  - Deinococcus maricopensis (Rainey and da Costa 2005) is a member of the genus Deinococcus,
      which is comprised of 44 validly named species and is located within
      the deeply branching bacterial phylum Deinococcus-Thermus. Strain LB-34(T) was
      isolated from a soil sample from the Sonoran Desert in Arizona. Various species
      of the genus Deinococcus are characterized by extreme radiation resistance, with
      D. maricopensis being resistant in excess of 10 kGy. Even though the genomes of
      three Deinococcus species, D. radiodurans, D. geothermalis and D. deserti, have
      already been published, no special physiological characteristic is currently
      known that is unique to this group. It is therefore of special interest to
      analyze the genomes of additional species of the genus Deinococcus to better
      understand how these species adapted to gamma- or UV ionizing-radiation. The
      3,498,530 bp long genome of D. maricopensis with its 3,301 protein-coding and 66
      RNA genes consists of one circular chromosome and is a part of the Genomic
      Encyclopedia of Bacteria and Archaea project.
AU  - Pukall R et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 4: 163-172.

PMID- 6225697
VI  - 104
DP  - 1983
TI  - Effects of high levels of DNA adenine methylation on methyl-directed mismatch repair in Escherichia coli.
PG  - 571-582
AB  - Two methods were used in an attempt to increase the efficiency and strand
      selectivity of methyl-directed mismatch repair of bacteriophage lambda
      heteroduplexes in E. coli.  Previous studies of such repair used lambda DNA
      that was only partially methylated as the source of methylated chains.  Also,
      transfection was carried out in methylating strains.  Either of these factors
      might have been responsible for the incompleteness of the strand selectivity
      observed previously.  In the first approach to increasing strand selectivity,
      heteroduplexes were transfected into a host deficient in methylation, but no
      changes in repair frequencies were observed.  In the second approach,
      heteroduplexes were prepared using DNA that had been highly methylated in vitro
      with purified DNA adenine methylase as the source of methylated chains.  In
      heteroduplexes having a repairable cI/+ mismatch, strand selectivity was indeed
      enhanced.  In heteroduplexes with one chain highly methylated and the
      complementary chain unmethylated, the frequency of repair on the unmethylated
      chain increased to nearly 100%.  Heteroduplexes with both chains highly
      methylated were not repaired at a detectable frequency.  Thus, chains highly
      methylated by DNA adenine methylase were refractory to mismatch repair by this
      system, regardless of the methylation of the complementary chain.  These
      results support the hypothesis that methyl-directed mismatch repair acts to
      correct errors of replication, thus lowering the mutation rate.
AU  - Pukkila PJ
AU  - Peterson J
AU  - Herman G
AU  - Modrich P
AU  - Meselson M
PT  - Journal Article
TA  - Genetics
JT  - Genetics
SO  - Genetics 1983 104: 571-582.

PMID- 21463507
VI  - 12
DP  - 2011
TI  - Genome-wide analysis of the role of GlnR in Streptomyces venezuelae provides new insights into global nitrogen regulation in actinomycetes.
PG  - 175
AB  - ABSTRACT: BACKGROUND: GlnR is an atypical response regulator found in
      actinomycetes that modulates the transcription of genes in response to
      changes in nitrogen availability. We applied a global in vivo approach to
      identify the GlnR regulon of Streptomyces venezuelae, which, unlike many
      actinomycetes, grows in a diffuse manner that is suitable for
      physiological studies. Conditions were defined that facilitated analysis
      of GlnR-dependent induction of gene expression in response to rapid
      nitrogen starvation. Microarray analysis identified global transcriptional
      differences between glnR+ and glnR mutant strains under varying nitrogen
      conditions. To differentiate between direct and indirect regulatory
      effects of GlnR, chromatin immuno-precipitation (ChIP) using antibodies
      specific to a FLAG-tagged GlnR protein, coupled with microarray analysis
      (ChIP-chip), was used to identify GlnR binding sites throughout the S.
      venezuelae genome. RESULTS: GlnR bound to its target sites in both
      transcriptionally active and apparently inactive forms. Thirty-six GlnR
      binding sites were identified by ChIP-chip analysis allowing derivation of
      a consensus GlnR-binding site for S. venezuelae. GlnR-binding regions were
      associated with genes involved in primary nitrogen metabolism, secondary
      metabolism, the synthesis of catabolic enzymes and a number of
      transport-related functions. CONCLUSIONS: The GlnR regulon of S.
      venezuelae is extensive and impacts on many facets of the organism's
      biology. GlnR can apparently bind to its target sites in both
      transcriptionally active and inactive forms.
AU  - Pullan ST
AU  - Chandra G
AU  - Bibb MJ
AU  - Merrick M
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2011 12: 175.

PMID- 
VI  - 7
DP  - 2018
TI  - Closed genome sequence using hybrid Nanopore/Illumina assembly of a Bacillus anthracis isolate from an animal-skin-drum-associated anthrax case in the UK.
PG  - e00802-18
AB  - Hybrid de novo assembly of Illumina/Nanopore reads produced a complete genome sequence of the
      chromosome and two virulence plasmids of a
      Bacillus anthracis isolate from a fatal anthrax case in the United Kingdom linked to imported
      animal skins/drums; this provides a high-quality representative sequence for this lineage.
AU  - Pullan ST
AU  - Miles RW
AU  - Lewandowski K
AU  - Vipond R
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e00802-18.

PMID- 14651626
VI  - 51
DP  - 2004
TI  - The Pasteurella multocida toxin is encoded within a lysogenic bacteriophage.
PG  - 255-269
AB  - Toxigenic strains of Pasteurella multocida produce a 146 kDa toxin (PMT)
      that acts as a potent mitogen. Sequence analysis of the structural gene
      for PMT, toxA, previously suggested it was horizontally acquired, because
      it had a low G + C content relative to the P. multocida genome. To address
      this, the sequence of DNA flanking toxA was determined. The sequence
      analysis showed the presence of homologues to bacteriophage tail protein
      genes and a bacteriophage antirepressor, suggesting that the toxin gene
      resides within a prophage. In addition to phage genes, the toxA flanking
      DNA contained a homologue of a restriction/modification system that was
      shown to be functional. The presence of a bacteriophage was demonstrated
      in spent medium from toxigenic P. multocida isolates. Its production was
      increased by mitomycin C addition, a treatment that is known to induce the
      lytic cycle of many temperate bacteriophages. The genomes of
      bacteriophages from three different toxigenic P. multocida strains had
      similar but not identical restriction profiles, and were approximately
      45-50 kb in length. The prophages from two of these had integrated at the
      same site in the chromosome, in a tRNA gene. Southern blot analysis
      confirmed that these bacteriophages contained the toxA gene.
AU  - Pullinger GD
AU  - Bevir T
AU  - Lax AJ
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2004 51: 255-269.

PMID- 18794283
VI  - 76
DP  - 2008
TI  - Identification of Salmonella enterica serovar Dublin-specific sequences by subtractive hybridization and analysis of their role in intestinal colonization and systemic translocation in cattle.
PG  - 5310-5321
AB  - Salmonella enterica serovar Dublin is a host-restricted serovar associated
      with typhoidal disease in cattle. In contrast, the fowl-associated serovar
      S. enterica serovar Gallinarum is avirulent in calves, yet it invades
      ileal mucosa and induces enteritis at levels comparable to those induced
      by S. enterica serovar Dublin. Suppression subtractive hybridization was
      employed to identify S. enterica serovar Dublin strain SD3246 genes absent
      from S. enterica serovar Gallinarum strain SG9. Forty-one S. enterica
      serovar Dublin fragments were cloned and sequenced. Among these, 24
      mobile-element-associated genes were identified, and 12 clones exhibited
      similarity with sequences of known or predicted function in other
      serovars. Three S. enterica serovar Dublin-specific regions were
      homologous to regions from the genome of Enterobacter sp. strain 638.
      Sequencing of fragments adjacent to these three sequences revealed the
      presence of a 21-kb genomic island, designated S. enterica serovar Dublin
      island 1 (SDI-1). PCR analysis and Southern blotting showed that SDI-1 is
      highly conserved within S. enterica serovar Dublin isolates but rarely
      found in other serovars. To probe the role of genes identified by
      subtractive hybridization in vivo, 24 signature-tagged S. enterica serovar
      Dublin SD3246 mutants lacking loci not present in Salmonella serovar
      Gallinarum SG9 were created and screened by oral challenge of cattle.
      Though attenuation of tagged SG9 and SD3246 Salmonella pathogenicity
      island-1 (SPI-1) and SPI-2 mutant strains was detected, no obvious defects
      of these 24 mutants were detected. Subsequently, a DeltaSDI-1 mutant was
      found to exhibit weak but significant attenuation compared with the parent
      strain in coinfection of calves. SDI-1 mutation did not impair invasion,
      intramacrophage survival, or virulence in mice, implying that SDI-1 does
      not influence fitness per se and may act in a host-specific manner.
AU  - Pullinger GD
AU  - Dziva F
AU  - Charleston B
AU  - Wallis TS
AU  - Stevens MP
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2008 76: 5310-5321.

PMID- 24762937
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Lysobacter capsici AZ78, a Bacterium Antagonistic to Plant-Pathogenic Oomycetes.
PG  - e00325-14
AB  - Lysobacter capsici AZ78, isolated from tobacco rhizosphere, effectively controls  Phytophthora
      infestans and Plasmopara viticola on tomato and grapevine plants, respectively. We report the
      first draft genome sequence of the L. capsici species.
AU  - Puopolo G
AU  - Sonego P
AU  - Engelen K
AU  - Pertot I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00325-14.

PMID- Not carried by PubMed...
VI  - 13
DP  - 1996
TI  - Validation of radioactive methods in the quality control of DNA restriction enzymes.
PG  - 197-200
AB  - In this paper two radioactive substrates obtained from lambda DNA digested with the
      restriction enzyme HpaII were evaluated for the detection of 5' to 3', 3' to 5' single and
      double stranded-DNA dependent exonuclease and phosphatase activities found in DNA restriction
      and modifying enzyme preparations.  A cloning simulation assay was performed using the same
      conditions established for the radioactive assay taking into account enzyme units and pmols of
      DNA ends used as substrate.  As a result, it was found that for degradation of the radioactive
      DNA substrate per enzyme unit below 0.5%, the false positives in the cloning simulation assay
      became less than 5%.  Finally, the use of the radiolabeled [gamma 32P] ATP lambda HpaII DNA
      substrate to detect 5' to 3' single stranded-DNA dependent exonuclease and phosphatase
      contaminating activities is described at certain critical steps of the purification process of
      the restriction enzyme KpnI.
AU  - Pupo E
AU  - Perez E
AU  - Trujillo LE
AU  - Miranda F
AU  - Gonzalez E
AU  - Brito J
PT  - Journal Article
TA  - Biotecnol. Apl.
JT  - Biotecnol. Apl.
SO  - Biotecnol. Apl. 1996 13: 197-200.

PMID- 25608871
VI  - 16
DP  - 2015
TI  - A pipeline for completing bacterial genomes using in silico and wet lab approaches.
PG  - S7
AB  - Despite the large volume of genome sequencing data produced by next-generation sequencing
      technologies and the highly sophisticated software dedicated to handling these types of data,
      gaps are commonly found in draft genome assemblies. The existence of gaps compromises our
      ability to take full advantage of the genome data. This study aims to identify a practical
      approach for biologists to complete their own genome assemblies using commonly available tools
      and resources. A pipeline was developed to assemble complete genomes primarily from the next
      generation sequencing
      (NGS) data. The input of the pipeline is paired-end Illumina sequence reads, and the output is
      a high quality complete genome sequence. The pipeline alternates the employment of
      computational and biological methods in
      seven steps. It combines the strengths of de novo assembly, reference-based assembly,
      customized programming, public databases utilization, and wet lab experimentation. The
      application of the pipeline is demonstrated by the
      completion of a bacterial genome, Thermotoga sp. strain RQ7, a hydrogen-producing strain. The
      developed pipeline provides an example of effective integration of computational and
      biological principles. It highlights the complementary roles that in silico and wet lab
      methodologies play in bioinformatical studies. The constituting principles and methods are
      applicable to similar studies on both prokaryotic and eukaryotic genomes.
AU  - Puranik R
AU  - Quan G
AU  - Werner J
AU  - Zhou R
AU  - Xu Z
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2015 16: S7.

PMID- 24371207
VI  - 1
DP  - 2013
TI  - Genome Sequence of the Pigment-Producing Bacterium Pseudogulbenkiania ferrooxidans, Isolated from Loktak Lake.
PG  - e01115-13
AB  - The whole genome of a pigment-producing isolate from a lake in northern India,
      Pseudogulbenkiania ferrooxidans strain EGD-HP2, has been sequenced to study the
      spectrum of biosynthesis of secondary metabolites. The genome annotation data
      revealed an operon for violacein, which showed homology with the reported operon
      of a Chromobacterium sp., and also a quinone cofactor.
AU  - Puranik S
AU  - Talkal R
AU  - Qureshi A
AU  - Khardenavis A
AU  - Kapley A
AU  - Purohit HJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01115-13.

PMID- 12406220
VI  - 46
DP  - 2002
TI  - Conjugative transfer of clostridial shuttle vectors from Escherichia coli to Clostridium difficile through circumvention of the restriction  barrier.
PG  - 439-452
AB  - Progress towards understanding the molecular basis of virulence in Clostridium difficile has
      been hindered by the lack of effective gene transfer systems. We have now, for the first time,
      developed procedures that may be used to introduce autonomously replicating vectors into this
      organism through their conjugative, oriT-based mobilization from Escherichia coli donors.
      Successful transfer was achieved through the use of a plasmid replicon isolated from an
      indigenous C. difficile plasmid, pCD6, and through the characterization and subsequent
      circumvention of host restriction/modification (RM) systems. The characterized replicon is the
      first C. difficile plasmid replicon to be sequenced and encodes a large replication protein
      (RepA) and a repetitive region composed of a 35 bp iteron sequence repeated seven times.
      Strain CD6 has two RM systems, CdiCD6I/M.CdiCD6I and CdiCD6II/M.CdiCD6II, with equivalent
      specificities to Sau96I/M. Sau96I (5'-GGNmCC-3') and Mbol/M. Mbol (5'-GmATC-3')
      respectively. A second strain (CD3) possesses a type IIs restriction enzyme, CdiI, which
      cleaves the sequence 5'-CATCG-3' between the fourth and fifth nucleotide to give a
      blunt-ended fragment. This is the first time that an enzyme with this specificity has been
      reported. The sequential addition of this site to vectors showed that each site caused between
      a five- and 16-fold reduction in transfer efficiency. The transfer efficiencies achieved with
      both strains equated to between 1.0x10^-6 and 5.5x10^-5 transconjugants per donor.
AU  - Purdy D
AU  - O'Keeffe TA
AU  - Elmore M
AU  - Herbert M
AU  - McLeod A
AU  - Bokori-Brown M
AU  - Ostrowski A
AU  - Minton NP
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2002 46: 439-452.

PMID- 20227382
VI  - 498
DP  - 2010
TI  - Identification of a second DNA binding site in human DNA methyltransferase 3A by substrate inhibition and domain deletion.
PG  - 13-22
AB  - The human DNA methyltransferase 3A (DNMT3A) is essential for establishing DNA methylation
      patterns. Knowing the key factors involved
      in the regulation of mammalian DNA methylation is critical to
      furthering understanding of embryonic development and designing
      therapeutic approaches targeting epigenetic mechanisms. We observe
      substrate inhibition for the full length DNMT3A but not for its
      isolated catalytic domain, demonstrating that DNMT3A has a second
      binding site for DNA. Deletion of recognized domains of DNMT3A reveals
      that the conserved PWWP domain is necessary for substrate inhibition
      and forms at least part of the allosteric DNA binding site. The PWWP
      domain is demonstrated here to bind DNA in a cooperative manner with mu
      M affinity. No clear sequence preference was observed, similar to
      previous observations with the isolated PWWP domain of Dnmt3b but with
      one order of magnitude weaker affinity. Potential roles for a low
      affinity, low specificity second DNA binding site are discussed.
AU  - Purdy MM
AU  - Holz-Schietinger C
AU  - Reich NO
PT  - Journal Article
TA  - Arch. Biochem. Biophys.
JT  - Arch. Biochem. Biophys.
SO  - Arch. Biochem. Biophys. 2010 498: 13-22.

PMID- 
VI  - 232
DP  - 2006
TI  - Modulation of mammalian DNA methyltransferase activity by RNA.
PG  - 244
AB  - Recent studies indicate potential interactions between mammalian DNA methyltransferase enzymes
      and RNA.  Transcriptional silencing by short or antisense RNA's directed to promoter regions
      has been proposed to involve an RNA directed DNA methylation component, though this remains
      controversial.  Binding of duplex RNA to the DNMT3 isoforms has been demonstrated, along with
      inhibition of DNMT1 by single stranded DNA.  The present work shows that an ss RNA is a more
      potent DNMT1 inhibitor than the corresponding ssDNA.  ssRNA, being more abundant than ssDNA,
      may represent an endogenous DNMT1 inhibitor.  Preliminary results indicate that an RNA/DNA
      hybrid duplex, suggested in some mechanisms for RNA directed DNA methylation, is a poor DNMT1
      substrate.  Studies on interactions of the DNMT3 isoforms with ssRNA and RNA/DNA duplexes are
      underway.
AU  - Purdy MM
AU  - Reich NO
PT  - Journal Article
TA  - ACS Abstracts
JT  - ACS Abstracts
SO  - ACS Abstracts 2006 232: 244.

PMID- 
VI  - 20
DP  - 2006
TI  - DNA binding by HhaI DNA methyltransferase domain interface mutants.
PG  - A901
AB  - The bacterial HhaI DNA methyltransferase (M.HhaI) is a structurally and mechanistically
      characterized member of the cytosine C-5 DNA
      methyltransferase family. A Statistical Coupling Analysis, which uses
      genetic covariation to estimate energetic coupling between protein
      residues, was performed on this enzyme family. This analysis identified
      a network of co-evolving residues centered on two regions - the
      catalytic loop and domain interface, both of which were previously
      implicated by crystallography in large scale conformational changes
      upon DNA binding. Mutation of several domain interface residues in
      M.HhaI resulted in 6 - 100 fold decreases in DNA affinity, despite their 7 - 20 angstrom
      distances from the DNA. The effects of these
      mutations suggest a role of this network in positioning or moving the
      two domains and the importance of proper domain positioning in DNA
      binding. The crystal structure of the I308A mutant was solved to 2.2
      angstrom resolution. It is unclear if this mutation alters the
      structure enough to explain the 35 fold loss in DNA affinity,
      suggesting that this mutation may perturb the domain - domain motions
      necessary for DNA binding.
AU  - Purdy MM
AU  - Reich NO
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 2006 20: A901.

PMID- 
VI  - 230
DP  - 2005
TI  - DNA binding and hemimethylation preference of HhaI DNA methyltransferase domain interface mutants.
PG  - U626
AB  - Recent studies indicate potential interactions between mammalian DNA methyltransferase (DNMT)
      enzymes and RNA. Transcriptional silencing by short or antisense RNA's directed to promoter
      regions has been proposed to involve an RNA directed DNA methylation component, though this
      remains controversial. Binding of duplex RNA to the DNMT3 isoforms has been demonstrated,
      along with inhibition of DNMT1 by single stranded (ss) DNA. The present work shows that an ss
      RNA is a more potent DNMT1 inhibitor than the corresponding ss DNA. ss RNA, being more
      abundant than ss DNA, may represent an endogenous DNMT1 inhibitor. Preliminary results
      indicate that an RNA/DNA hybrid duplex, suggested in some mechanisms for RNA directed DNA
      methylation, is a poor DNMT1 substrate. Studies on interactions of the DNMT3 isoforms with ss
      RNA and RNA/DNA duplexes are underway.
AU  - Purdy MM
AU  - Reich NO
PT  - Journal Article
TA  - ACS Abstracts
JT  - ACS Abstracts
SO  - ACS Abstracts 2005 230: U626.

PMID- 1322528
VI  - 20
DP  - 1992
TI  - A new affinity reagent for the site-specific, covalent attachment of DNA to active-site nucleophiles: application to the EcoRI and RsrI restriction and modification enzymes.
PG  - 3713-3719
AB  - A modified oligodeoxyribonucleotide duplex containing an unnatural internucleotide
      trisubstituted 3' to 5' pyrophosphate bond in one strand
      [5'(oligo1)3'-P(OCH3)P-5'(oligo2)3'] reacts with nucleophiles in aqueous media by acting
      as a phosphorylating affinity reagent. When interacted with a protein, a portion of the
      oligonucleotide [-P-5'(oligo2)3'] becomes attached to an amino acid nucleophilic group
      through a phosphate of the O-methyl-modified pyrophosphate linkage. We demonstate the affinity
      labeling of nucleophilic groups at the active sites of the EcoRI and RsrI restriction and
      modification enzymes with an oligodeoxyribonucleotide duplex containg a modified scissile bond
      in the EcoRI recognitin site. With the EcoRI and RsrI endonuclease in molar excess
      approximately 1% of the oligonucleotide becomes attached to the protein and with the companion
      methyltransferases the yield approaches 40% for the EcoRI enzyme and 30% for the RsrI
      methyltransferase. Crosslinking proceeds only upon formation of a sequence-specific enzyme-DNA
      complex and generates a covalent bond between the 3'-phosphate of the modified pyrophosphate
      in the substrate and a nucleophilic group at the active site of the enzymes. The reaction
      results in the elimination of an oligodeoxyribonucleotide remnant that contains the
      3'-O-methylphosphate [5'(oligo1)3'-P(OCH3)] derived from the modified phosphate of the
      pyrophosphate linkage. Hydrolysis properties of the covalent protein-DNA adducts indicate that
      phosphoamide (P-N) bonds are formed with the EcoRI endonuclease and methyltransferase.
AU  - Purmal AA
AU  - Shabarova ZA
AU  - Gumport RI
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 3713-3719.

PMID- 6088201
VI  - 276
DP  - 1984
TI  - Interaction of EcoRII restriction and modification enzymes with DNA duplexes containing pyrophosphate bonds.
PG  - 992-995
AB  - 
AU  - Purmal AA
AU  - Vinogradova MN
AU  - Elov AA
AU  - Gromova ES
AU  - Drutsa VL
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1984 276: 992-995.

PMID- 26893420
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Paenibacillus etheri sp. nov. SH7T, a Methyl Tert-Butyl  Ether Degrader.
PG  - e01696-15
AB  - We report here the draft genome sequence of Paenibacillus etheri sp. nov. SH7(T)  (= CECT
      8558(T) = DSM 29760(T)), isolated from a hydrocarbon-contaminated soil
      pilot plant in Granada, Spain. The bacterium was isolated and sequenced due to
      its methyl tert-butyl ether (MTBE)-degrading properties.
AU  - Purswani J
AU  - Guisado IM
AU  - Gonzalez-Lopez J
AU  - Pozo C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01696-15.

PMID- 6310500
VI  - 11
DP  - 1983
TI  - Isolation and characterisation of DraI, a type II restriction endonuclease recognising a sequence containing only A:T basepairs, and inhibition of its activity by uv irradiation of substrate DNA.
PG  - 5467-5474
AB  - A type II restriction endonuclease, DraI, isolated from Deinococcus radiophilus
      ATCC 27603 recognises the palindromic hexanucleotide sequence5'-T-T-T^A-A-A-3'
      3'-A-A-A^T-T-T-5'and cleaves it, as indicated by the arrows, to produce
      blunt-ended fragments.  The yield of enzyme is 100 to 1000 times that of the
      only other known type II restriction endonuclease that recognises a sequence
      composed solely of A:T basepairs, the isoschizomer AhaIII.  Ultraviolet
      irradiation of the DNA substrate at relatively low doses inhibits the activity
      of DraI by "protecting" the recognition sequence and this may be exploited to
      give control of partial digestion of DNA by DraI.
AU  - Purvis IJ
AU  - Moseley BEB
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1983 11: 5467-5474.

PMID- 23833132
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Pandoraea sp. Strain SD6-2, Isolated from Lindane-Contaminated Australian Soil.
PG  - e00415-13
AB  - Pandoraea sp. strain SD6-2 is a delta-hexachlorocyclohexane-degrading bacterial strain
      isolated from lindane-contaminated soil in Queensland, Australia. The
      genome of SD6-2 was sequenced to investigate its ability to degrade
      delta-hexachlorocyclohexane. Here we report the annotated genome sequence of this
      strain.
AU  - Pushiri H
AU  - Pearce SL
AU  - Oakeshott JG
AU  - Russell RJ
AU  - Pandey G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00415-13.

PMID- 28684577
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Micrococcus luteus (Schroeter) Cohn (ATCC 12698).
PG  - e00576-17
AB  - The actinobacterium Micrococcus luteus can be found in a wide variety of habitats. Here, we
      report the 2,411,958-bp draft genome sequence of the type
      strain M. leuteus (Schroeter) Cohn (ATCC 12698). Characteristic of this taxa, the
      genome sequence has a high G+C content, 73.14%.
AU  - Putonti C
AU  - Cudone E
AU  - Kalesinskas L
AU  - Engelbrecht KC
AU  - Koenig DW
AU  - Wolfe AJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00576-17.

PMID- 28684576
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Enterococcus faecalis ATCC BAA-2128.
PG  - e00575-17
AB  - While a part of the native gut microflora, the Gram-positive bacterium Enterococcus faecalis
      can lead to serious infections elsewhere in the body. The
      draft genome of E. faecalis strain ATCC BAA-2128, isolated from piglet feces, was
      examined. This draft genome consists of 42 contigs, 12 of which exhibit homology
      to annotated plasmids.
AU  - Putonti C
AU  - Kalesinskas L
AU  - Cudone E
AU  - Engelbrecht KC
AU  - Koenig DW
AU  - Wolfe AJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00575-17.

PMID- 28684583
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Two ATCC Staphylococcus aureus subsp. aureus Strains.
PG  - e00618-17
AB  - Draft genome sequences for Staphylococcus aureus subsp. aureus Rosenbach ATCC 14458 and ATCC
      27217 strains were investigated. The genome sizes were 2,880,761
      bp and 2,759,100 bp, respectively. Strain ATCC 14458 was assembled into 39
      contigs, including 3 plasmids, and strain ATCC 27217 was assembled into 25
      contigs, including 2 plasmids.
AU  - Putonti C
AU  - Kalesinskas L
AU  - Cudone E
AU  - Engelbrecht KC
AU  - Koenig DW
AU  - Wolfe AJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00618-17.

PMID- 28684584
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Staphylococcus epidermidis (Winslow and Winslow) Evans (ATCC 14990).
PG  - e00619-17
AB  - Here, we report the draft genome sequence for the type strain Staphylococcus epidermidis
      (Winslow and Winslow) Evans (ATCC 14990). The assembly consisted of
      2,457,519 bp with an observed G+C content of 32.04%. Thirty-seven contigs were
      produced, including two putative plasmids, with a 296.8x coverage and an N50 of
      180,848 bp.
AU  - Putonti C
AU  - Kalesinskas L
AU  - Cudone E
AU  - Engelbrecht KC
AU  - Koenig DW
AU  - Wolfe AJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00619-17.

PMID- 29439036
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of an Active Heterotrophic Nitrifier-Denitrifier, Cupriavidus pauculus UM1.
PG  - e00028-18
AB  - Here, we present the draft genome sequence of Cupriavidus pauculus UM1, a metal-resistant
      heterotrophic nitrifier-denitrifier capable of synthesizing
      nitrite from pyruvic oxime. The size of the genome is 7,402,815 bp with a GC
      content of 64.8%. This draft assembly consists of 38 scaffolds.
AU  - Putonti C
AU  - Polley N
AU  - Castignetti D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00028-18.

PMID- 8367284
VI  - 21
DP  - 1993
TI  - A quantitative assay to measure the relative DNA-binding affinity of pyrrolo[2,1-c][1,4]benzodiazepine (PBD) antitumor antibiotics based on the inhibition of restriction endonuclease BamHI.
PG  - 3671-3675
AB  - An assay has been developed (restriction endonuclease digestion assay - RED100) based on
      inhibition of the restriction endonuclease BamHI that is capable of quantitive evaluation of
      the relative DNA-binding affinity of pyrrolo[2,1-c][1,4]benzodiazepine (PBD) antitumor
      antibiotics. This method provides comparable results to those obtained from thermal
      denaturation and ethidium bromide displacement assays but is much more sensitive,
      discriminating between molecules of similar structure such as DC-81, iso-DC-81 and
      neothramycin. The results reveal a trend between relative DNA-binding affinity and in vitro
      cytotoxicity for the PBDs in two tumour cell lines studied.
AU  - Puvvada MS
AU  - Hartley JA
AU  - Jenkins TC
AU  - Thurston DE
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 3671-3675.

PMID- 29449392
VI  - 6
DP  - 2018
TI  - Closed Genome Sequence of Phytopathogen Biocontrol Agent Bacillus velezensis Strain AGVL-005, Isolated from Soybean.
PG  - e00057-18
AB  - We report here the closed and near-complete genome sequence and annotation of Bacillus
      velezensis strain AGVL-005, a bacterium isolated from soybean seeds in
      Brazil and used for phytopathogen biocontrol.
AU  - Pylro VS
AU  - Dias ACF
AU  - Andreote FD
AU  - Morais DK
AU  - Varani AM
AU  - Andreote CCF
AU  - Bernardo ERA
AU  - Zucchi T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00057-18.

PMID- 25431621
VI  - 7
DP  - 2014
TI  - Expansion of the genetic toolkit for metabolic engineering of Clostridium pasteurianum: chromosomal gene disruption of the endogenous CpaAI restriction  enzyme.
PG  - 163
AB  - BACKGROUND: Clostridium pasteurianum is one of the most promising biofuel producers within the
      genus Clostridium owing to its unique metabolic ability to
      ferment glycerol into butanol. Although an efficient means is available for
      introducing foreign DNA to C. pasteurianum, major genetic tools, such as gene
      knockout, knockdown, or genome editing, are lacking, preventing metabolic
      engineering of C. pasteurianum. RESULTS: Here we present a methodology for
      performing chromosomal gene disruption in C. pasteurianum using the programmable
      lactococcus Ll.ltrB group II intron. Gene disruption was initially found to be
      impeded by inefficient electrotransformation of Escherichia coli-C. pasteurianum
      shuttle vectors, presumably due to host restriction. By assessing the ability of
      various vector deletion derivatives to electrotransform C. pasteurianum and
      probing the microorganism's methylome using next-generation sequence data, we
      identified a new C. pasteurianum Type I restriction-methylation system, CpaAII,
      with a predicted recognition sequence of 5'-AAGNNNNNCTCC-3' (N = A, C, G, or T).
      Following rescue of high-level electrotransformation via mutation of the sole
      CpaAII site within the shuttle vectors, we retargeted the intron to the cpaAIR
      gene encoding the CpaAI Type II restriction endonuclease (recognition site of
      5'-CGCG-3'). Intron insertion was potentially hindered by low retrohoming
      efficiency, yet this limitation could be overcome by a procedure for enrichment
      of the intron insertion. The resulting DeltacpaAIR mutant strain was efficiently
      electrotransformed with M.FnuDII-unmethylated plasmid DNA. CONCLUSIONS: The
      markerless and plasmidless DeltacpaAIR mutant strain of C. pasteurianum developed
      in this study can serve as a general host strain for future genetic and metabolic
      manipulation. Further, the associated gene disruption protocol should not only
      serve as a guide for chromosomal gene inactivation studies involving mobile group
      II introns, but also prove invaluable for applying metabolic engineering
      strategies to C. pasteurianum.
AU  - Pyne ME
AU  - Moo-Young M
AU  - Chung DA
AU  - Chou CP
PT  - Journal Article
TA  - Biotechnol. Biofuels.
JT  - Biotechnol. Biofuels.
SO  - Biotechnol. Biofuels. 2014 7: 163.

PMID- 23570573
VI  - 6
DP  - 2013
TI  - Development of an electrotransformation protocol for genetic manipulation of Clostridium pasteurianum.
PG  - 50
AB  - Background: Reducing the production cost of, and increasing revenues from, industrial biofuels
      will greatly facilitate their proliferation
      and co-integration with fossil fuels. The cost of feedstock is the
      largest cost in most fermentation bioprocesses and therefore represents
      an important target for cost reduction. Meanwhile, the biorefinery
      concept advocates revenue growth through complete utilization of
      by-products generated during biofuel production. Taken together, the
      production of biofuels from low-cost crude glycerol, available in
      oversupply as a by-product of bioethanol production, in the form of
      thin stillage, and biodiesel production, embodies a remarkable
      opportunity to advance affordable biofuel development. However, few
      bacterial species possess the natural capacity to convert glycerol as a
      sole source of carbon and energy into value-added bioproducts. Of
      particular interest is the anaerobe Clostridium pasteurianum, the only
      microorganism known to convert glycerol alone directly into butanol,
      which currently holds immense promise as a high-energy biofuel and bulk
      chemical. Unfortunately, genetic and metabolic engineering of C.
      pasteurianum has been fundamentally impeded due to lack of an efficient
      method for deoxyribonucleic acid (DNA) transfer.
      Results: This work reports the development of an
      electrotransformation protocol permitting high-level DNA transfer to C.
      pasteurianum ATCC 6013 together with accompanying selection markers and
      vector components. The CpaAI restriction-modification system was found
      to be a major barrier to DNA delivery into C. pasteurianum which we
      overcame by in vivo methylation of the recognition site (5'-CGCG-3')
      using the M. FnuDII methyltransferase. With proper selection of the
      replication origin and antibiotic-resistance marker, we initially
      electroporated methylated DNA into C. pasteurianum at a low efficiency
      of 2.4 x 10(1) transformants mu g(-1) DNA by utilizing conditions
      common to other clostridial electroporations. Systematic investigation
      of various parameters involved in the cell growth, washing and pulse
      delivery, and outgrowth phases of the electrotransformation procedure
      significantly elevated the electrotransformation efficiency, up to 7.5
      x 10(4) transformants mu g(-1) DNA, an increase of approximately three
      order of magnitude. Key factors affecting the electrotransformation
      efficiency include cell-wall-weakening using glycine, ethanol-mediated
      membrane solubilization, field strength of the electric pulse, and
      sucrose osmoprotection.
      Conclusions: C. pasteurianum ATCC 6013 can be electrotransformed at
      a high efficiency using appropriately methylated plasmid DNA. The
      electrotransformation method and tools reported here should promote
      extensive genetic manipulation and metabolic engineering of this
      biotechnologically important bacterium.
AU  - Pyne ME
AU  - Moo-Young M
AU  - Chung DA
AU  - Chou CP
PT  - Journal Article
TA  - Biotechnol. Biofuels.
JT  - Biotechnol. Biofuels.
SO  - Biotechnol. Biofuels. 2013 6: 50.

PMID- 25103768
VI  - 2
DP  - 2014
TI  - Improved Draft Genome Sequence of Clostridium pasteurianum Strain ATCC 6013 (DSM  525) Using a Hybrid Next-Generation Sequencing Approach.
PG  - e00790-14
AB  - We present an improved draft genome sequence for Clostridium pasteurianum strain  ATCC 6013
      (DSM 525), the type strain of the species and an important
      solventogenic bacterium with industrial potential. Availability of a
      near-complete genome sequence will enable strain engineering of this promising
      bacterium.
AU  - Pyne ME
AU  - Utturkar S
AU  - Brown SD
AU  - Moo-Young M
AU  - Chung DA
AU  - Chou CP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00790-14.

PMID- 3032219
VI  - 65
DP  - 1987
TI  - Restriction of single-stranded M13 DNA using synthetic oligonucleotides:  the structural requirement of restriction enzymes.
PG  - 50-55
AB  - A targeted ss (single stranded) DNA cleavage technique is reported which
      involves the use of synthetic oligomers complementary to the ss M12 DNA
      polylinker.  BamHI, SmaI, and KpnI restriction enzymes were tested with a
      partial duplex DNA formed from ss M13 DNA and a nested series of fragments
      derived from a synthetic 21-mer which were complementary to the polylinker
      region.  These enzymes require up to two flanking nucleotides in addition to
      the hexameric recognition site for efficient cleavage.  This technique could be
      useful for effecting unique cleavages of DNA with enzymes which generally give
      a large number of fragments and for strategies of ss DNA manipulation.
AU  - Qi GR
AU  - Wong P
AU  - Cedergren R
PT  - Journal Article
TA  - Biochem. Cell Biol.
JT  - Biochem. Cell Biol.
SO  - Biochem. Cell Biol. 1987 65: 50-55.

PMID- 22693604
VI  - 7
DP  - 2012
TI  - Comparative Geno-Plasticity Analysis of Mycoplasma bovis HB0801 (Chinese Isolate).
PG  - E38239
AB  - Mycoplasma bovis pneumonia in cattle has been epidemic in China since 2008. To
      investigate M. bovis pathogenesis, we completed genome sequencing of strain
      HB0801 isolated from a lesioned bovine lung from Hubei, China. The genomic
      plasticity was determined by comparing HB0801 with M. bovis strain ATCC(R)
      25523/PG45 from cow mastitis milk, Chinese strain Hubei-1 from lesioned lung
      tissue, and 16 other Mycoplasmas species. Compared to PG45, the genome size of
      HB0801 was reduced by 11.7 kb. Furthermore, a large chromosome inversion (580 kb)
      was confirmed in all Chinese isolates including HB0801, HB1007, a strain from cow
      mastitis milk, and Hubei-1. In addition, the variable surface lipoproteins (vsp)
      gene cluster existed in HB0801, but contained less than half of the genes, and
      had poor identity to that in PG45, but they had conserved structures. Further
      inter-strain comparisons revealed other mechanisms of gene acquisition and loss
      in HB0801 that primarily involved insertion sequence (IS) elements, integrative
      conjugative element, restriction and modification systems, and some lipoproteins
      and transmembrane proteins. Subsequently, PG45 and HB0801 virulence in cattle was
      compared. Results indicated that both strains were pathogenic to cattle. The
      scores of gross pathological assessment for the control group, and the PG45- and
      HB0801-infected groups were 3, 13 and 9, respectively. Meanwhile the scores of
      lung lesion for these three groups were 36, 70, and 69, respectively. In
      addition, immunohistochemistry detection demonstrated that both strains were
      similarly distributed in lungs and lymph nodes. Although PG45 showed slightly
      higher virulence in calves than HB0801, there was no statistical difference
      between the strains (P>0.05). Compared to Hubei-1, a total of 122 SNP loci were
      disclosed in HB0801. In conclusion, although genomic plasticity was thought to be
      an evolutionary advantage, it did not apparently affect virulence of M. bovis
      strains in cattle.
AU  - Qi J
AU  - Guo A
AU  - Cui P
AU  - Chen Y
AU  - Mustafa R
AU  - Ba X
AU  - Hu C
AU  - Bai Z
AU  - Chen X
AU  - Shi L
AU  - Chen H
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2012 7: E38239.

PMID- 15901698
VI  - 187
DP  - 2005
TI  - Novel molecular features of the fibrolytic intestinal bacterium Fibrobacter intestinalis not shared with Fibrobacter succinogenes as  determined by suppressive subtractive hybridization.
PG  - 3739-3751
AB  - Suppressive subtractive hybridization was conducted to identify unique genes coding for plant
      cell wall hydrolytic enzymes and other properties
      of the gastrointestinal bacterium Fibrobacter intestinalis DR7 not shared
      by Fibrobacter succinogenes S85. Subtractive clones from F. intestinalis
      were sequenced and assembled to form 712 nonredundant contigs with an
      average length of 525 bp. Of these, 55 sequences were unique to F.
      intestinalis. The remaining contigs contained 764 genes with BLASTX
      similarities to other proteins; of these, 80% had the highest similarities
      to proteins in F. succinogenes, including 30 that coded for carbohydrate
      active enzymes. The expression of 17 of these genes was verified by
      Northern dot blot analysis. Of genes not exhibiting BLASTX similarity to
      F. succinogenes, 30 encoded putative transposases, 6 encoded restriction
      modification genes, and 45% had highest similarities to proteins in other
      species of gastrointestinal bacteria, a finding suggestive of either
      horizontal gene transfer to F. intestinalis or gene loss from F.
      succinogenes. Analysis of contigs containing segments of two or more
      adjacent genes revealed that only 35% exhibited BLASTX similarity and were
      in the same orientation as those of F. succinogenes, indicating extensive
      chromosomal rearrangement. The expression of eight transposases, and three
      restriction-modification genes was confirmed by Northern dot blot
      analysis. These data clearly document the maintenance of carbohydrate
      active enzymes in F. intestinalis necessitated by the preponderance of
      polysaccharide substrates available in the ruminal environment. It also
      documents substantive changes in the genome from that of F. succinogenes,
      which may be related to the introduction of the array of transposase and
      restriction-modification genes.
AU  - Qi M
AU  - Nelson KE
AU  - Daugherty SC
AU  - Nelson WC
AU  - Hance IR
AU  - Morrison M
AU  - Forsberg CW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2005 187: 3739-3751.

PMID- 21304594
VI  - 6
DP  - 2011
TI  - Genome Sequence Analyses of Pseudomonas savastanoi pv. glycinea and Subtractive Hybridization-Based Comparative Genomics with Nine Pseudomonads.
PG  - E16451
AB  - Bacterial blight, caused by Pseudomonas savastanoi pv. glycinea (Psg), is a
      common disease of soybean. In an effort to compare a current field isolate with
      one isolated in the early 1960s, the genomes of two Psg strains, race 4 and B076,
      were sequenced using 454 pyrosequencing. The genomes of both Psg strains share
      more than 4,900 highly conserved genes, indicating very low genetic diversity
      between Psg genomes. Though conserved, genome rearrangements and recombination
      events occur commonly within the two Psg genomes. When compared to each other,
      437 and 163 specific genes were identified in B076 and race 4, respectively. Most
      specific genes are plasmid-borne, indicating that acquisition and maintenance of
      plasmids may represent a major mechanism to change the genetic composition of the
      genome and even acquire new virulence factors. Type three secretion gene clusters
      of Psg strains are near identical with that of P. savastanoi pv. phaseolicola
      (Pph) strain 1448A and they shared 20 common effector genes. Furthermore, the
      coronatine biosynthetic cluster is present on a large plasmid in strain B076, but
      not in race 4. In silico subtractive hybridization-based comparative genomic
      analyses with nine sequenced phytopathogenic pseudomonads identified dozens of
      specific islands (SIs), and revealed that the genomes of Psg strains are more
      similar to those belonging to the same genomospecies such as Pph 1448A than to
      other phytopathogenic pseudomonads. The number of highly conserved genes (core
      genome) among them decreased dramatically when more genomes were included in the
      subtraction, suggesting the diversification of pseudomonads, and further
      indicating the genome heterogeneity among pseudomonads. However, the number of
      specific genes did not change significantly, suggesting these genes are indeed
      specific in Psg genomes. These results reinforce the idea of a species complex of
      P. syringae and support the reclassification of P. syringae into different
      species.
AU  - Qi M
AU  - Wang D
AU  - Bradley CA
AU  - Zhao Y
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2011 6: E16451.

PMID- 29301882
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Streptomyces sp. Strain JV178, a Producer of Clifednamide-Type Polycyclic Tetramate Macrolactams.
PG  - e01401-17
AB  - Here, we report the draft genome sequence of Streptomyces sp. JV178, a strain originating from
      Connecticut (USA) garden soil. This strain produces the
      polycyclic tetramate macrolactam compounds clifednamides A and B. The draft
      genome contains 10.65 Mb, 9,045 predicted protein coding sequences, and several
      natural product biosynthetic loci.
AU  - Qi Y
AU  - D'Alessandro JM
AU  - Blodgett JAV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01401-17.

PMID- 22587291
VI  - 108
DP  - 2012
TI  - Evolutionary Dynamics of Restriction Site Avoidance.
PG  - 158105
AB  - Molecular noise in bacterial restriction-modification systems can cause rare events of host
      DNA cleavage at restriction sites. Such
      noise-induced selective pressure may result in evolved sequences
      exhibiting restriction site avoidance. We identify a two-state regime
      of evolutionary dynamics, in which populations either develop avoidance
      or go extinct. Using perturbation theory, we show that equilibrium
      sequence statistics exhibit power-law scaling in the ratio of
      restriction strength to mutation rate. Noise levels comparable to
      mutation rates can be sufficient to evolve detectable avoidance.
AU  - Qian L
AU  - Kussell E
PT  - Journal Article
TA  - Phys. Rev. Lett.
JT  - Phys. Rev. Lett.
SO  - Phys. Rev. Lett. 2012 108: 158105.

PMID- 27932643
VI  - 4
DP  - 2016
TI  - Genome Sequence of Burkholderia plantarii ZJ171, a Tropolone-Producing Bacterial  Pathogen Responsible for Rice Seedling Blight.
PG  - e01318-16
AB  - Burkholderia plantarii is the causal agent of rice seedling blight. Here, we report the draft
      genome sequence of B. plantarii, which contains 8,020,831 bp,
      with a G+C content of 68.66% and a predicted 7,688 coding sequences. The
      annotated genome sequence will provide further insight into its pathogenicity.
AU  - Qian Y
AU  - Matsumoto H
AU  - Li W
AU  - Zhu G
AU  - Hashidoko Y
AU  - Hu Y
AU  - Wang M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01318-16.

PMID- 24950734
VI  - 33
DP  - 2014
TI  - Genome-wide identification and expression profiling of DNA methyltransferase gene family in maize.
PG  - 1661-1672
AB  - In this study, we identified eight DNA MTase genes in maize and the diversity of expression
      patterns of them was presented by EST mining, microarray and semi-quantitative expression
      profile analyses.DNA methylation plays a pivotal role in promoting genomic stability through
      diverse biological processes including regulation of gene expression during development and
      chromatin organization. Although this important biological process is mainly regulated by
      several conserved Cytosine-5 DNA methyltransferases encoded by a smaller multigene family in
      plants, investigation of the plant C5-MTase-encoding gene family will serve to elucidate the
      epigenetic mechanism diversity in plants. Recently, genome-wide identification and
      evolutionary analyses of the C5-MTase-encoding gene family have been characterized in multiple
      plant species including Arabidopsis, rice, carrot and wheat. However, little is known
      regarding the C5-MTase-encoding genes in the entire maize genome. Here, genome-wide
      identification and expression profile analyses of maize C5-MTase-encoding genes (ZmMETs) were
      performed from the latest version of the maize (B73) genome. Phylogenetic analysis indicated
      that the orthologs from the three species (maize, Arabidopsis and rice) were categorized into
      four classes. Chromosomal location of these genes revealed that they are unevenly distributed
      on 6 of all 10 chromosomes with three chromosomal/segmental duplication events, suggesting
      that gene duplication played a key role in expansion of the maize C5-MTase-encoding gene
      family. Furthermore, EST expression data mining, microarray data and semi-quantitative
      expression profile analyses detected in the leaves by two different abiotic stress treatments
      have demonstrated that these genes had temporal and spatial expression pattern and exhibited
      different expression levels in stress treatments, suggesting that functional diversification
      of ZmMET genes family. Overall, our study will serve to present signification insights to
      explore the plant C5-MTase!
      -encodin
      g gene expression and function and also be beneficial for future experimental research to
      further unravel the mechanisms of epigenetic regulation in plants.
AU  - Qian Y
AU  - Xi Y
AU  - Cheng B
AU  - Zhu S
PT  - Journal Article
TA  - Plant Cell
JT  - Plant Cell
SO  - Plant Cell 2014 33: 1661-1672.

PMID- 2111266
VI  - 88
DP  - 1990
TI  - The apparent specificity of NotI (5'-GCGGCCGC-3') is enhanced by M.FnuDII or M.BepI methyltransferases (5'-mCGCG-3'): cutting bacterial chromosomes into a few large pieces .
PG  - 101-105
AB  - The restriction endonuclease (ENase) NotI is blocked by methylation within its
      recognition sequence at 5'GCGGCmCGC-3'.  This sensitivity to methylation can be
      used to enhance the specificity of NotI in vivo and in vitro.  Modification by
      M.FnuDII or M.BepI methyltransferases (MTase)(5'-mCGCG-3') will block NotI
      (5'-GCGGCCGC-3') cleavage at overlapping MTase/ENase sites 5'-CGCGGCCGC-3'
      (equivalent to 5'-GCGGCCGCG-3'), and increase the apparent cleavage specificity
      of NotI about twofold.  This cross-protection procedure reduces the number of
      NotI fragments in the genomes of Escherichia coli and Bacillus subtilis, as
      resolved by pulsed field electrophoresis.  Application of this method to large
      DNAs in vitro requires the preparation of highly purified DNA MTases.
AU  - Qiang B-Q
AU  - McClelland M
AU  - Poddar S
AU  - Spokauskas A
AU  - Nelson M
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1990 88: 101-105.

PMID- 6330673
VI  - 12
DP  - 1984
TI  - A type II restriction endonuclease with an eight nucleotide specificity from Streptomyces fimbriatus.
PG  - 4507-4515
AB  - A new site-specific endonuclease, SfiI, has been isolated from Streptomyces
      fimbriatus.  This is the first report of a type II restriction endonuclease
      whose recognition specificity requires eight nucleotides.  SfiI cleaves the
      sequence, GGCCNNNN^NGGCC, symmetrically to produce a three base, 3' extension.
AU  - Qiang B-Q
AU  - Schildkraut I
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1984 12: 4507-4515.

PMID- 3008082
VI  - 14
DP  - 1986
TI  - Two unique restriction endonucleases from Neisseria lactamica.
PG  - 1991-1999
AB  - Two new site-specific endonucleases, NlaIII and NlaIV, have been isolated from
      Neisseria lactamica.  NlaIII recognizes the sequence, CATG, and cleaves 3' of
      the sequence to produce a four base 3' extension.  NlaIV recognizes the
      sequence, GGNNCC, and cleaves between the two N's to produce blunt ended
      fragments.
AU  - Qiang B-Q
AU  - Schildkraut I
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1986 14: 1991-1999.

PMID- 2828862
VI  - 155
DP  - 1987
TI  - NotI and SfiI:  restriction endonucleases with octanucleotide recognition sequences.
PG  - 15-21
AB  - While there are over 500 reported Type II restriction endonucleases, only two,
      NotI and SfiI, require an octanucleotide recognition sequence.  These two
      endonucleases cleave DNA less frequently than conventional tetranucleotide-,
      pentanucleotide-, and hexanucleotide-recognizing restriction endonucleases.  On
      average, NotI and SfiI will cleave DNA only once every 64,000 nucleotides.
      With the advent of physical methods that can separate very large DNA molecules,
      NotI and SfiI have become useful analytical reagents for molecular biologists.
      NotI is isolated from the bacterium Nocardia otitidis-caviarum ATCC 14630, and
      recognizes the DNA sequence     5'...GC^GGCCGC...3'     3'...CGCCGG^CG...5'
      cleaving the phosphodiester bonds in both strands as indicated.  SfiI is
      isolated from the bacterium Streptomyces fimbriatus ATCC 25051 and recognizes
      the DNA sequence     5'...GGCCNNNN^NGGCC...3'     3'...CCGGN^NNNNCCGG...5'
      cleaving the phosphodiester bonds in both strands as indicated.
AU  - Qiang B-Q
AU  - Schildkraut I
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1987 155: 15-21.

PMID- 23105086
VI  - 194
DP  - 2012
TI  - Whole-Genome Sequence of Nocardiopsis alba Strain ATCC BAA-2165, Associated with  Honeybees.
PG  - 6358-6359
AB  - The actinomycete Nocardiopsis alba was reportedly associated with honeybees in separate
      occurrences. We report the complete genome of Nocardiopsis alba ATCC
      BAA-2165 isolated from honeybee guts. It will provide insights into the
      metabolism and genetic regulatory networks of this genus of bacteria that enable
      them to live in a range of environments.
AU  - Qiao J
AU  - Chen L
AU  - Li Y
AU  - Wang J
AU  - Zhang W
AU  - Chen S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6358-6359.

PMID- 24526631
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Root-Colonizing Bacterium Bacillus sp. Strain PTS-394.
PG  - e00038-14
AB  - Here, we report the high-quality draft genome sequence of Bacillus sp. strain PTS-394,
      isolated from the rhizosphere of tomatoes grown on Putuo Mountain
      (Xiamen, Fujian province, China), which exhibited excellent colonization ability
      on plant roots. The 4.0-Mb genome uncovered the mechanism for its potential root
      colonization ability and may provide novel insights into plant-bacterium
      interactions.
AU  - Qiao J
AU  - Liu Y
AU  - Liang X
AU  - Hu Y
AU  - Du Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00038-14.

PMID- 22843597
VI  - 194
DP  - 2012
TI  - Genome Sequence of Staphylococcus capitis QN1, Which Causes Infective Endocarditis.
PG  - 4469-4470
AB  - Staphylococcus capitis is a subtype of coagulase-negative staphylococci (CoNS) which could
      emerge as a significant pathogen causing infective endocarditis,
      prosthetic valve endocarditis, and late-onset sepsis. We isolated S. capitis
      strain QN1 from the skin swab sample of a female. Here we prepared a genome
      sequence for this strain consisting of 30 contigs totaling 2,430,101 bases and a
      GC content of 32.76%.
AU  - Qin N
AU  - Ding W
AU  - Yao J
AU  - Su K
AU  - Wu L
AU  - Li L
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4469-4470.

PMID- 22815455
VI  - 194
DP  - 2012
TI  - Genome Sequence of Aerococcus viridans LL1.
PG  - 4143
AB  - Aerococcus viridans is a catalase-negative Gram-positive bacterium and has been described as
      an airborne organism widely distributed in the hospital environment
      or in clinical specimens. We isolated A. viridans strain LL1 from indoor dust
      samples collected by a patient. Here, we prepared a genome sequence for this
      strain consisting of 31 contigs totaling 1,994,039 bases and a GC content of
      39.42%.
AU  - Qin N
AU  - Zheng B
AU  - Yang F
AU  - Chen Y
AU  - Guo J
AU  - Hu X
AU  - Li L
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4143.

PMID- 20703316
VI  - 5
DP  - 2011
TI  - Comparative genomics reveals a deep-sea sediment-adapted life style of Pseudoalteromonas sp. SM9913.
PG  - 274-284
AB  - Deep-sea sediment is one of the most important microbial-driven ecosystems, yet it is not well
      characterized. Genome sequence analyses of deep-sea sedimentary bacteria would shed light on
      the understanding of this ecosystem. In this study, the complete genome of deep-sea
      sedimentary bacterium Pseudoalteromonas sp. SM9913 (SM9913) is described and compared with
      that of the closely related Antarctic surface sea-water ecotype Pseudoalteromonas haloplanktis
      TAC125 (TAC125). SM9913 has fewer dioxygenase genes than TAC125, indicating a possible
      sensitivity to reactive oxygen species. Accordingly, experimental results showed that SM9913
      was less tolerant of H(2)O(2) than TAC125. SM9913 has gene clusters related to both polar and
      lateral flagella biosynthesis. Lateral flagella, which are usually present in deep-sea
      bacteria and absent in the related surface bacteria, are important for the survival of SM9913
      in deep-sea environments. With these two flagellar systems, SM9913 can swim in sea water and
      swarm on the sediment particle surface, favoring the acquisition of nutrients from particulate
      organic matter and reflecting the particle-associated alternative lifestyle of SM9913 in the
      deep sea. A total of 12 genomic islands were identified in the genome of SM9913 that may
      confer specific features unique to SM9913 and absent from TAC125, such as drug and heavy metal
      resistance. Many signal transduction genes and a glycogen production operon were also present
      in the SM9913 genome, which may help SM9913 respond to food pulses and store carbon and energy
      in a deep-sea environment.
AU  - Qin QL
AU  - Li Y
AU  - Zhang YJ
AU  - Zhou ZM
AU  - Zhang WX
AU  - Chen XL
AU  - Zhang XY
AU  - Zhou BC
AU  - Wang L
AU  - Zhang YZ
PT  - Journal Article
TA  - ISME J.
JT  - ISME J.
SO  - ISME J. 2011 5: 274-284.

PMID- 22628500
VI  - 194
DP  - 2012
TI  - Genome Sequence of Proteorhodopsin-Containing Sea Ice Bacterium Glaciecola punicea ACAM 611T.
PG  - 3267
AB  - Here, we report the draft genome sequence of Antarctic sea ice bacterium Glaciecola punicea
      ACAM 611(T), the type species of the genus Glaciecola. A
      blue-light-absorbing proteorhodopsin gene is present in the 3.08-Mb genome. This
      genome sequence can facilitate the study of the physiological metabolisms and
      ecological roles of sea ice bacteria.
AU  - Qin QL
AU  - Xie BB
AU  - Shu YL
AU  - Rong JC
AU  - Zhao DL
AU  - Zhang XY
AU  - Chen XL
AU  - Zhou BC
AU  - Zhang YZ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3267.

PMID- 20398413
VI  - 11
DP  - 2010
TI  - The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea environment and ecological role in sedimentary organic nitrogen degradation.
PG  - 247
AB  - BACKGROUND: Zunongwangia profunda SM-A87, which was isolated from deep-sea
      sediment, is an aerobic, gram-negative bacterium that represents a new
      genus of Flavobacteriaceae. This is the first sequenced genome of a
      deep-sea bacterium from the phylum Bacteroidetes. RESULTS: The Z. profunda
      SM-A87 genome has a single 5 128 187-bp circular chromosome with no
      extrachromosomal elements and harbors 4 653 predicted protein-coding
      genes. SM-A87 produces a large amount of capsular polysaccharides and
      possesses two polysaccharide biosynthesis gene clusters. It has a total of
      130 peptidases, 61 of which have signal peptides. In addition to
      extracellular peptidases, SM-A87 also has various extracellular enzymes
      for carbohydrate, lipid and DNA degradation. These extracellular enzymes
      suggest that the bacterium is able to hydrolyze organic materials in the
      sediment, especially carbohydrates and proteinaceous organic nitrogen.
      There are two clustered regularly interspaced short palindromic repeats in
      the genome, but their spacers do not match any sequences in the public
      sequence databases. SM-A87 is a moderate halophile. Our protein
      isoelectric point analysis indicates that extracellular proteins have
      lower predicted isoelectric points than intracellular proteins. SM-A87
      accumulates organic osmolytes in the cell, so its extracelluar proteins
      are more halophilic than its intracellular proteins. CONCLUSION: Here, we
      present the first complete genome of a deep-sea sedimentary bacterium from
      the phylum Bacteroidetes. The genome analysis shows that SM-A87 has some
      common features of deep-sea bacteria, as well as an important capacity to
      hydrolyze sedimentary organic nitrogen.
AU  - Qin QL
AU  - Zhang XY
AU  - Wang XM
AU  - Liu GM
AU  - Chen XL
AU  - Xie BB
AU  - Dang HY
AU  - Zhou BC
AU  - Yu J
AU  - Zhang YZ
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2010 11: 247.

PMID- 22374958
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Marine Streptomyces sp. Strain W007, Which Produces Angucyclinone Antibiotics with a Benz[a]anthracene Skeleton.
PG  - 1628-1629
AB  - A series of angucyclinone antibiotics have been isolated from marine Streptomyces sp. strain
      W007 and identified. Here, a draft genome sequence of Streptomyces sp.
      W007 is presented. The genome contains an intact biosynthetic gene cluster for
      angucyclinone antibiotics, which provides insight into the combinatorial
      biosynthesis of angucyclinone antibiotics produced by marine streptomycetes.
AU  - Qin S
AU  - Zhang H
AU  - Li F
AU  - Zhu B
AU  - Zheng H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1628-1629.

PMID- 22328752
VI  - 194
DP  - 2012
TI  - Draft Genome Sequences of Two Legionella dumoffii Strains, TEX-KL and NY-23.
PG  - 1251-1252
AB  - Legionella (Fluoribacter) dumoffii is one of the agents causing Legionnaires' disease. Here,
      we used Illumina second-generation sequencing technology to
      decipher for the first time the whole-genome sequences of two strains of this
      species, TEX-KL and NY-23. The assembly results for both strains consist of one
      chromosome and two plasmids.
AU  - Qin T
AU  - Cui Y
AU  - Cen Z
AU  - Liang T
AU  - Ren H
AU  - Yang X
AU  - Zhao X
AU  - Liu Z
AU  - Xu L
AU  - Li D
AU  - Song Y
AU  - Yang R
AU  - Shao Z
AU  - Song Y
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1251-1252.

PMID- 
VI  - 230
DP  - 2005
TI  - Efficient manipulation of nanoparticle-bound DNA by restriction endonuclease.
PG  - U1077
AB  - 
AU  - Qin W
AU  - Yung LYL
PT  - Journal Article
TA  - ACS Abstracts
JT  - ACS Abstracts
SO  - ACS Abstracts 2005 230: U1077.

PMID- 21268065
VI  - 112
DP  - 2011
TI  - Usp7 and Uhrf1 Control Ubiquitination and Stability of the Maintenance DNA Methyltransferase Dnmt1.
PG  - 439-444
AB  - In mammals Dnmt1 is the DNA methyltransferase chiefly responsible for maintaining genomic
      methylation patterns through DNA replication
      cycles, but how its maintenance activity is controlled is still not
      well understood. Interestingly, Uhrf1, a crucial cofactor for
      maintenance of DNA methylation by Dnmt1, is endowed with E3 ubiquitin
      ligase activity. Here, we show that both Dnmt1 and Uhrf1 coprecipitate
      with ubiquitin specific peptidase 7 (Usp7), a de-ubiquitinating enzyme.
      Overexpression of Uhrf1 and Usp7 resulted in opposite changes in the
      ubiquitination status and stability of Dnmt1. Our findings suggest
      that, by balancing Dnmt1 ubiquitination, Usp7 and Uhrf1 fine tune Dnmt1
      stability.
AU  - Qin WH
AU  - Leonhardt H
AU  - Spada F
PT  - Journal Article
TA  - J. Cell. Biochem.
JT  - J. Cell. Biochem.
SO  - J. Cell. Biochem. 2011 112: 439-444.

PMID- 17096530
VI  - 7
DP  - 2006
TI  - Efficient manipulation of nanoparticle-bound DNA via restriction endonuclease.
PG  - 3047-3051
AB  - As a programmable biopolymer, DNA has shown great potential in the fabrication and
      construction of nanometer-scale assemblies and devices.
      In this report, we described a strategy for efficient manipulation of
      gold nanoparticle-bound DNA using restriction endonuclease. The
      digestion efficiency of this restriction enzyme was studied by varying
      the surface coverage of stabilizer, the size of nanoparticles, as well
      as the distance between the nanoparticle surface and the enzyme-cutting
      site of particle-bound DNA. We found that the surface coverage of
      stabilizer is crucial for achieving high digestion efficiency. In
      addition, this stabilizer surface coverage can be tailored by varying
      the ion strength of the system. Based on the results of polyacrylamide
      gel electrophoresis and fluorescent study, a high digestion efficiency
      of 90+% for particle-bound DNA was achieved for the first time. This
      restriction enzyme manipulation can be considered as an additional
      level of control of the particle-bound DNA and is expected to be
      applied to manipulate more complicated nanostructures assembled by DNA.
AU  - Qin WJ
AU  - Yung LYL
PT  - Journal Article
TA  - Biomacromolecules
JT  - Biomacromolecules
SO  - Biomacromolecules 2006 7: 3047-3051.

PMID- 17069642
VI  - 15
DP  - 2006
TI  - Genome sequences of the honey bee pathogens Paenibacillus larvae and Ascosphaera apis.
PG  - 715-718
AB  - Genome sequences offer a broad view of host-pathogen interactions at the systems
      biology level. With the completion of the sequence of the honey bee, interest in
      the relevant pathogens is heightened. Here we report the genome sequences of two
      of the major pathogens of honey bees, the bacterium Paenibacillus larvae
      (causative agent for American foulbrood disease) and the fungus Ascosphaera apis.
      (causative agent for chalkbrood disease). Ongoing efforts to characterize the
      genomes of these species can be used to understand and mitigate the effects of
      two important pathogens, and will provide a contrast with pathogenic, benign and
      freeliving relatives.
AU  - Qin X
AU  - Evans JD
AU  - Aronstein KA
AU  - Murray KD
AU  - Weinstock GM
PT  - Journal Article
TA  - Insect Mol. Biol.
JT  - Insect Mol. Biol.
SO  - Insect Mol. Biol. 2006 15: 715-718.

PMID- 25540347
VI  - 2
DP  - 2014
TI  - Genome Sequences of Three Highly Copper-Resistant Salmonella enterica subsp. I Serovar Typhimurium Strains Isolated from Pigs in Denmark.
PG  - e01334-14
AB  - Salmonella typhimurium is the causative agent of typhoid fever, which causes nearly 21.7
      million illnesses and 217,000 deaths around the world each year.
      Here, we describe the draft genome sequences of the Salmonella typhimurium
      strains S7, S15, and S23, isolated from copper-fed pigs in Denmark and containing
      additional putative determinants conferring resistances to copper and other
      metals and metalloids.
AU  - Qin Y
AU  - Hasman H
AU  - Aarestrup FM
AU  - Alwathnani HA
AU  - Rensing C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01334-14.

PMID- 27833718
VI  - 11
DP  - 2016
TI  - Two draft genome sequences of Pseudomonas jessenii strains isolated from a copper contaminated site in Denmark.
PG  - 86
AB  - Pseudomonas jessenii C2 and Pseudomonas jessenii H16 were isolated from low-Cu and high-Cu
      industrially contaminated soil, respectively. P. jessenii H16
      displayed significant resistance to copper when compared to P. jessenii C2. Here
      we describe genome sequences and interesting features of these two strains. The
      genome of P. jessenii C2 comprised 6,420,113 bp, with 5814 protein-coding genes
      and 67 RNA genes. P. jessenii H16 comprised 6,807,788 bp, with 5995
      protein-coding genes and 70 RNA genes. Of special interest was a specific
      adaptation to this harsh copper-contaminated environment as P. jessenii H16
      contained a novel putative copper resistance genomic island (GI) of around 50,000
      bp.
AU  - Qin Y
AU  - Wang D
AU  - Brandt KK
AU  - Rensing C
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 86.

PMID- 8329215
VI  - 20
DP  - 1993
TI  - Overcoming restriction of Streptomyces hygroscopicus 10-22 by the modification of S. fradiae -- An attempt to develop a transformation system for S. hygroscopicus 10-22.
PG  - 180-184
AB  - No transformant was obtained when pIJ702 (tsr, mel+) from S. lividans TK24 was used to
      transform S. hygroscopicus 10-22. pIJ702 isolated from S. fradiae ATCC 10745, however, was
      transformed into 10-22 at a frequency of 10/3-10/4 tranformants/ug DNA. Among the transformant
      colonies, only 1/1000 of them were black in colour (mel+) while a great majority of them
      remained white (mel-). The plasmid pIJ702 band was only visualized on agarose gels from the
      black colonies but not from the white colonies. However, when pIJ702 isolated from both black
      and white transformants were used to transform S. lividans TK24, the mel gene was expressed
      normally in the recipients. The preparation was also successful in transforming S.
      hygroscopicus 10-22, and again gave rise to 1/1000 of black colonies only. When the 10-22
      (pIJ702) black colonies were plated on non-selective medium, among the majority of black
      colonies grown, there were a few white colonies, which proved to be host mutants of 10-22.
      These mutants were transformable by pIJ702 and homogeneous black colonies were obtained.
AU  - Qin Z
AU  - Deng Z
AU  - Zhou Q
AU  - Chen H
PT  - Journal Article
TA  - I Chuan Hsueh Pao
JT  - I Chuan Hsueh Pao
SO  - I Chuan Hsueh Pao 1993 20: 180-184.

PMID- 8144475
VI  - 176
DP  - 1994
TI  - Development of a gene cloning system for Streptomyces hygroscopicus subsp. yingchengensis, a producer of three useful antifungal compounds, by elimination of three barriers to DNA transfer.
PG  - 2090-2095
AB  - Streptomyces hygroscopicus 10-22 could not be transformed with any of the commonly used
      Streptomyces plasmid vectors and was resistant to plaque formation by the Streptomyces phages
      C31 and R4. Repeated selection resulted in the isolation of derivatives of S. hygroscopicus
      10-22 that could be transformed with pIJ101- and pJV1-derived cloning vectors and of
      restriction-deficient derivatives that could accept DNA propagated in Streptomyces lividans
      66. These new strains, which include three that still produce the original antibiotics, can be
      used as hosts for gene cloning. Insertion of nonreplicating vectors by homologous
      recombination and transposition of Tn4560 were demonstrated in S. hygroscopicus 10-22.
AU  - Qin Z
AU  - Peng K
AU  - Zhou X
AU  - Lliang R
AU  - Zhou Q
AU  - Chen H
AU  - Hopwood DA
AU  - Kieser T
AU  - Deng Z
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1994 176: 2090-2095.

PMID- 11836534
VI  - 9
DP  - 2002
TI  - The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds.
PG  - 217-224
AB  - The PWWP domain is a weakly conserved sequence motif found in >60 eukaryotic proteins,
      including the mammalian DNA methyltransferases Dnmt3a and Dnmt3b. These proteins often contain
      other chromatin-association domains. A 135-residue PWWP domain from mouse Dnmt3b (amino acids
      223--357) has been structurally characterized at 1.8 A resolution. The N-terminal half of this
      domain resembles a barrel-like five-stranded structure, whereas the C-terminal half contains a
      five-helix bundle. The two halves are packed against each other to form a single structural
      module that exhibits a prominent positive electrostatic potential. The PWWP domain alone binds
      DNA in vitro, probably through its basic surface. We also show that recombinant Dnmt3b2
      protein (a splice variant of Dnmt3b) and two N-terminal deletion mutants (Delta218 and
      Delta369) have approximately equal methyl transfer activity on unmethylated and hemimethylated
      CpG-containing oligonucleotides. The Delta218 protein, which includes the PWWP domain, binds
      DNA more strongly than Delta369, which lacks the PWWP domain.
AU  - Qiu C
AU  - Sawada K
AU  - Zhang X
AU  - Cheng X
PT  - Journal Article
TA  - Nat. Struct. Biol.
JT  - Nat. Struct. Biol.
SO  - Nat. Struct. Biol. 2002 9: 217-224.

PMID- 18599839
VI  - 154
DP  - 2008
TI  - ClpXP proteases positively regulate alginate overexpression and mucoid conversion in Pseudomonas aeruginosa.
PG  - 2119-2130
AB  - Overproduction of the exopolysaccharide alginate and conversion to a mucoid
      phenotype in Pseudomonas aeruginosa are markers for the onset of chronic lung
      infection in cystic fibrosis (CF). Alginate production is regulated by the
      extracytoplasmic function (ECF) sigma factor AlgU/T and the cognate anti-sigma
      factor MucA. Many clinical mucoid isolates carry loss-of-function mutations in
      mucA. These mutations, including the most common mucA22 allele, cause C-terminal
      truncations in MucA, indicating that an inability to regulate AlgU activity by
      MucA is associated with conversion to the mucoid phenotype. Here we report that a
      mutation in a stable mucoid strain derived from the parental strain PAO1,
      designated PAO581, that does not contain the mucA22 allele, was due to a
      single-base deletion in mucA (DeltaT180), generating another type of C-terminal
      truncation. A global mariner transposon screen in PAO581 for non-mucoid isolates
      led to the identification of three regulators of alginate production, clpP
      (PA1801), clpX (PA1802), and a clpP paralogue (PA3326, designated clpP2). The
      PAO581 null mutants of clpP, clpX and clpP2 showed decreased AlgU transcriptional
      activity and an accumulation of haemagglutinin (HA)-tagged N-terminal MucA
      protein with an apparent molecular mass of 15 kDa. The clpP and clpX mutants of a
      CF mucoid isolate revert to the non-mucoid phenotype. The ClpXP and ClpP2
      proteins appear to be part of a proteolytic network that degrades the cytoplasmic
      portion of truncated MucA proteins to release the sequestered AlgU, which drives
      alginate biosynthesis.
AU  - Qiu D
AU  - Eisinger VM
AU  - Head NE
AU  - Pier GB
AU  - Yu HD
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2008 154: 2119-2130.

PMID- 23811511
VI  - 79
DP  - 2013
TI  - Combined Genomics and Experimental Analyses of Respiratory Characteristics of Shewanella putrefaciens W3-18-1.
PG  - 5250-5257
AB  - It has previously been shown that the Shewanella putrefaciens W3-18-1 strain produces
      remarkably high current in microbial fuel cells (MFCs)
      and can form magnetite at 0 degrees C. To explore the underlying
      mechanisms, we developed a genetic manipulation method by deleting the
      restriction-modification system genes of the SGI1 (Salmonella genome
      island 1)-like prophage and analyzed the key genes involved in
      bacterial respiration. W3-18-1 has less respiratory flexibility than
      the well-characterized S. oneidensis MR-1 strain, as it possesses fewer
      cytochrome c genes and lacks the ability to oxidize sulfite or reduce
      dimethyl sulfoxide (DMSO) and timethylamine oxide (TMAO). W3-18-1 lacks
      the hydrogen-producing Fe-only hydrogenase, and the hydrogen-oxidizing
      Ni-Fe hydrogenase genes were split into two separate clusters. Two
      periplasmic nitrate reductases (NapDAGHB and NapDABC) were functionally
      redundant in anaerobic growth of W3-18-1 with nitrate as the electron
      acceptor, though napDABC was not regulated by Crp. Moreover, nitrate
      respiration started earlier in W3-18-1 than in MR-1 (with NapDAGHB
      only) under microoxic conditions. These results indicate that
      Shewanella putrefaciens W3-18-1 is well adapted to habitats with higher
      oxygen levels. Taken together, the results of this study provide
      valuable insights into bacterial genome evolution.
AU  - Qiu D
AU  - Wei H
AU  - Tu Q
AU  - Yang Y
AU  - Xie M
AU  - Chen J
AU  - Pinkerton MH
AU  - Liang Y
AU  - He Z
AU  - Zhou J
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2013 79: 5250-5257.

PMID- Not carried by PubMed...
VI  - 20
DP  - 1989
TI  - Database management system for recognition sequences and sequences assembly of restriction endonuclease and methylase.
PG  - 185-187
AB  - None
AU  - Qiu J
AU  - Ren J
PT  - Journal Article
TA  - Zhongguo Yaoke Daxue Xuebao
JT  - Zhongguo Yaoke Daxue Xuebao
SO  - Zhongguo Yaoke Daxue Xuebao 1989 20: 185-187.

PMID- 26012582
VI  - 65
DP  - 2015
TI  - Diaphorobacter polyhydroxybutyrativorans sp. nov., a novel poly(3-hydroxybutyrate-co-3-hydroxyvalerate)-degrading bacterium isolated from biofilms.
PG  - 2913-2918
AB  - A novel Gram-stain-negative, facultatively aerobic and rod-shaped strain,
      designated SL-205(T), was isolated from the biofilms of a denitrifying reactor
      using poly(3-hydoxybutyrate-co-3-hydroxyvalerate) as the sole carbon source in
      Beijing, PR China. A polyphasic taxonomic characterization was performed on the
      novel isolate. Phylogenetic analyses based on the 16S rRNA gene sequence revealed
      that strain SL-205(T) is a member of the genus Diaphorobacter. High levels of 16S
      rRNA gene sequence similarity were found between strain SL-205(T) and
      Diaphorobacter nitroreducens NA10B(T) (99.4%) and Diaphorobacter oryzae RF3(T)
      (98.5%), respectively. However, the DNA-DNA relatedness values between strain
      SL-205(T) and D. nitroreducens NA10B(T) and D. oryzae RF3(T) were 57 +/- 1% and
      45 +/- 1.5%, respectively. The G+C content of the genomic DNA of strain SL-205(T)
      was 66.8 mol%. The major fatty acids consisted of summed feature 3 (including C16
      : 1omega7c and/or iso-C15 : 0 2-OH), C16 : 0 and C18 : 1omega7c. Ubiquinone Q-8
      was the only respiratory quinone; the polar lipid profile comprised
      phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and one
      uncharacterized phospholipid. We conclude that strain SL-205(T) represents a
      novel species of the genus Diaphorobacter for which the name Diaphorobacter
      polyhydroxybutyrativorans is proposed; the type strain is SL-205(T) ( = ACCC
      19739(T) = DSM 29460(T)).
AU  - Qiu T
AU  - Zuo Z
AU  - Gao J
AU  - Gao M
AU  - Han M
AU  - Sun L
AU  - Zhang L
AU  - Wang X
PT  - Journal Article
TA  - Int. J. Syst. Evol. Microbiol.
JT  - Int. J. Syst. Evol. Microbiol.
SO  - Int. J. Syst. Evol. Microbiol. 2015 65: 2913-2918.

PMID- 19376907
VI  - 75
DP  - 2009
TI  - Identification and Characterization of a Novel Gene Involved in the trans-Specific Nematicidal Activity of Photorhabdus luminescens LN2.
PG  - 4221-4223
AB  - Photorhabdus luminescens subsp. akhurstii LN2 from Heterorhabditis indica
      LN2 showed nematicidal activity against axenic Heterorhabditis
      bacteriophora H06 infective juveniles (IJs). Transposon mutagenesis
      identified an LN2 mutant that supports the growth of H06 nematodes. Tn5
      disrupted the namA gene, encoding a novel 364-residue protein and
      involving the nematicidal activity. The green fluorescent protein-labeled
      namA mutant was unable to colonize the intestines of H06 IJs.
AU  - Qiu X
AU  - Han R
AU  - Yan X
AU  - Liu M
AU  - Cao L
AU  - Yoshiga T
AU  - Kondo E
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2009 75: 4221-4223.

PMID- 25502667
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence and Annotation of the Entomopathogenic Bacterium Photorhabdus luminescens LN2, Which Shows Nematicidal Activity against  Heterorhabditis bacteriophora H06 Nematodes.
PG  - e01268-14
AB  - We present here the 5.6-Mb genome sequence of Photorhabdus luminescens strain LN2, a
      Gram-negative bacterium that is a symbiont of Heterorhabditis indica LN2
      and shows nematicidal activity against Heterorhabditis bacteriophora H06
      nematodes.
AU  - Qiu X
AU  - Zhan ZB
AU  - Yan X
AU  - Han R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01268-14.

PMID- 28751395
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Terrimicrobium sacchariphilum NM-5T, a Facultative Anaerobic Soil Bacterium of the Class Spartobacteria.
PG  - e00666-17
AB  - We report here a high-quality draft genome sequence of Terrimicrobium sacchariphilum strain
      NM-5T, a facultative anaerobic, mesophilic, fermentative
      bacterium belonging to the class Spartobacteria of the phylum Verrucomicrobia The
      genome comprises 4,751,807 bp in three contigs and has a G+C content of 60.19%.
      Annotation predicted 4,175 protein-coding sequences and 54 RNAs.
AU  - Qiu YL
AU  - Tourlousse DM
AU  - Matsuura N
AU  - Ohashi A
AU  - Sekiguchi Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00666-17.

PMID- 28729272
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Paludibacter jiangxiensis NM7T, a Propionate-Producing Fermentative Bacterium.
PG  - e00667-17
AB  - We report here a high-quality draft genome sequence of Paludibacter jiangxiensis  strain NM7T,
      a mesophilic, anaerobic, propionate-producing fermentative bacterium
      within the family Porphyromonadaceae of the phylum Bacteroidetes The genome
      comprises 3,664,884 bp in four contigs, has a G+C content of 42.92%, and contains
      2,949 protein-coding sequences and 62 RNAs.
AU  - Qiu YL
AU  - Tourlousse DM
AU  - Matsuura N
AU  - Ohashi A
AU  - Sekiguchi Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00667-17.

PMID- 27136327
VI  - 23
DP  - 2016
TI  - Structure of a group II intron in complex with its reverse transcriptase.
PG  - 549-557
AB  - Bacterial group II introns are large catalytic RNAs related to nuclear spliceosomal introns
      and eukaryotic retrotransposons. They self-splice, yielding
      mature RNA, and integrate into DNA as retroelements. A fully active group II
      intron forms a ribonucleoprotein complex comprising the intron ribozyme and an
      intron-encoded protein that performs multiple activities including reverse
      transcription, in which intron RNA is copied into the DNA target. Here we report
      cryo-EM structures of an endogenously spliced Lactococcus lactis group IIA intron
      in its ribonucleoprotein complex form at 3.8-A resolution and in its
      protein-depleted form at 4.5-A resolution, revealing functional coordination of
      the intron RNA with the protein. Remarkably, the protein structure reveals a
      close relationship between the reverse transcriptase catalytic domain and
      telomerase, whereas the active splicing center resembles the spliceosomal Prp8
      protein. These extraordinary similarities hint at intricate ancestral
      relationships and provide new insights into splicing and retromobility.
AU  - Qu G
AU  - Kaushal PS
AU  - Wang J
AU  - Shigematsu H
AU  - Piazza CL
AU  - Agrawal RK
AU  - Belfort M
AU  - Wang HW
PT  - Journal Article
TA  - Nat. Struct. Mol. Biol.
JT  - Nat. Struct. Mol. Biol.
SO  - Nat. Struct. Mol. Biol. 2016 23: 549-557.

PMID- 26139718
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Rhodococcus sp. Strain IcdP1 Shows Diverse Catabolic  Potential.
PG  - e00711-15
AB  - The complete genome sequence of Rhodococcus sp. strain IcdP1 is presented here. This organism
      was shown to degrade a broad range of high-molecular-weight
      polycyclic aromatic hydrocarbons and organochlorine pesticides. The sequence data
      can be used to predict genes for xenobiotic biodegradation and metabolism.
AU  - Qu J
AU  - Miao LL
AU  - Liu Y
AU  - Liu ZP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00711-15.

PMID- 26067966
VI  - 3
DP  - 2015
TI  - Genome Sequence of an Indigoid-Producing Strain, Pseudomonas sp. PI1.
PG  - e00622-15
AB  - Pseudomonas sp. strain PI1 can cometabolize indole in the presence of phenol to produce
      various indigoids. Here, we present a 7.2-Mb draft genome sequence of
      strain PI1, which may provide insight into the study of phenol-indole
      cometabolism and its application in aromatic bioremediation and wastewater
      treatment processes.
AU  - Qu Y
AU  - Liu Z
AU  - Shen W
AU  - Li S
AU  - Tang H
AU  - Xu P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00622-15.

PMID- 23405319
VI  - 1
DP  - 2013
TI  - Genome Sequence of Sphingomonas xenophaga QYY, an Anthraquinone-Degrading Strain.
PG  - e00031-12
AB  - Sphingomonas xenophaga QYY is an efficient anthraquinone-degrading strain. Here,  we present a
      4.2-Mb assembly of the first genome sequence of S. xenophaga. We have annotated 36 coding
      sequences (CDSs) encoding aromatic catabolism and 216 CDSs responsible for toxic resistance
      and stress response, which may provide insights into the degradation of complex aromatics.
AU  - Qu Y
AU  - Zhang X
AU  - Yu H
AU  - Tang H
AU  - Shen E
AU  - Zhou H
AU  - Ma Q
AU  - Cao X
AU  - Zhou J
AU  - Xu P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00031-12.

PMID- 
VI  - 41
DP  - 2000
TI  - Dual flipping and novel motifs of DNA methyltransferase.
PG  - 79
AB  - Structural superimposition of three resolved structures of DNA cytosine methyltransferase
      (DCMTase) M.HhaI revealed the dual flipping feature of the enzyme and the cofactor
      S-adenosyl-L-methionine (SAM) or its demethylated form, S-adenosyl-L-homocysteine (SAH).  In
      the absence of DNA, enzyme-bound SAM is solvent exposed.  In the presence of DNA, SAM flips
      from the surface of the enzyme into the catalytic site and complements the flipped out
      cytosine methylation target in DNA.  Analysis of amino acid residues interacting with the
      cofactor identified 16 contact amino acid residues for unflipped SAM and 24 residues for
      flipped SAM/SAH in M.HhaI.  These contact residues are also conserved in higher eukaryotic
      DCMTases.  Human Dnmt1 and M.HhaI bound to SAH and DNA and M.HhaI bound to flipped SAM reveals
      that SAH and flipped SAM are coordinated in the same binding pocket.  Analysis of the
      cofactor-interacting residues in M.HhaI, human Dnmt1 and other known DCMTases enabled us to
      define two novel flipped SAM/SAH binding sequence motifs expressed in the same order in all
      DCMTases, providing a specific tool for analysis of related proteins.  High sequence homology
      of the cofactor interacting residues implies their conserved function and further underlines
      the structural and functional similarity between bacterial M.HhaI and human Dnmt1 DCMTases.
      Our findings also support the alternative binding mechanism in which SAM binding precedes DNA
      binding in M.HhaI.
AU  - Quada JC
AU  - Izbicka E
AU  - Rashidi HH
PT  - Journal Article
TA  - Proc. Amer. Assoc. Cancer Res.
JT  - Proc. Amer. Assoc. Cancer Res.
SO  - Proc. Amer. Assoc. Cancer Res. 2000 41: 79.

PMID- 26067973
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Bacterium Pseudomonas putida CBB5, Which Can Utilize Caffeine as a Sole Carbon and Nitrogen Source.
PG  - e00640-15
AB  - Pseudomonas putida CBB5 was isolated from soil by enriching for growth on caffeine
      (1,3,7-trimethylxanthine). The draft genome of this strain is 6.9 Mb,
      with 5,941 predicted coding sequences. It includes the previously studied Alx
      gene cluster encoding alkylxanthine N-demethylase enzymes and other genes that
      enable the degradation of purine alkaloids.
AU  - Quandt EM
AU  - Summers RM
AU  - Subramanian MV
AU  - Barrick JE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00640-15.

PMID- 29270251
VI  - 12
DP  - 2017
TI  - Draft genome sequence of Acidithiobacillus thiooxidans CLST isolated from the acidic hypersaline Gorbea salt flat in northern Chile.
PG  - 84
AB  - 10.1601/nm.2199 CLST is an extremely acidophilic gamma-proteobacteria that was isolated from
      the Gorbea salt flat, an acidic hypersaline environment in northern
      Chile. This kind of environment is considered a terrestrial analog of ancient
      Martian terrains and a source of new material for biotechnological applications.
      10.1601/nm.2199 plays a key role in industrial bioleaching; it has the capacity
      of generating and maintaining acidic conditions by producing sulfuric acid and it
      can also remove sulfur layers from the surface of minerals, which are detrimental
      for their dissolution. CLST is a strain of 10.1601/nm.2199 able to tolerate
      moderate chloride concentrations (up to 15 g L(-1) Cl(-)), a feature that is
      quite unusual in extreme acidophilic microorganisms. Basic microbiological
      features and genomic properties of this biotechnologically relevant strain are
      described in this work. The 3,974,949 bp draft genome is arranged into 40
      scaffolds of 389 contigs containing 3866 protein-coding genes and 75 RNAs
      encoding genes. This is the first draft genome of a halotolerant 10.1601/nm.2199
      strain. The release of the genome sequence of this strain improves representation
      of these extreme acidophilic Gram negative bacteria in public databases and
      strengthens the framework for further investigation of the physiological
      diversity and ecological function of 10.1601/nm.2199 populations.
AU  - Quatrini R
AU  - Escudero LV
AU  - Moya-Beltran A
AU  - Galleguillos PA
AU  - Issotta F
AU  - Acosta M
AU  - Cardenas JP
AU  - Nunez H
AU  - Salinas K
AU  - Holmes DS
AU  - Demergasso C
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 84.

PMID- 9197539
VI  - 190
DP  - 1997
TI  - Chlorella virus SC-1A encodes at least five functional and one nonfunctional DNA methyltransferases.
PG  - 237-244
AB  - Chlorella virus SC-1A encodes at least six DNA methyltransferases: four N6-methyldeoxyadenine
      (m6A) Mtases, M.CviSI (TGCmA), M.CviSII (CmATG), M.CviSIII (TCGmA) and M.CviSIV (GmATC), one
      5-methyldeoxycytosine (m5C) Mtase, M.CviSV (~RCmCG), and one nonfunctional m5C MTase,
      M.CviSVI, which is homologous to the MTase M.CviJI [RGmC(T/C/G)] produced by another chlorella
      virus IL-3A.  Genes encoding three of the SC-1A m6A MTases (M.CviSI, M.CviSII, and M.CviSIII)
      and the nonfunctional m5C MTase were cloned and sequenced.  Neither M.CviSI nor M.CviSIII
      genes hybridized to genes for their respective isomethylomers, M.CviRI and M.CviBIII, from
      other chlorella viruses.  However, the M.CviSII gene hybridized strongly to its M.CviAII
      isomethylomer gene from virus PBCV-1.  Like the prototype chlorella virus PBCV-1, the SC-1A
      genome contains inverted terminal repeats, one of which is adjacent to the nonfunctional m5C
      MTase.  The three cloned m6A MTase genes are distributed throughout the approx. 345 kb SC-1A
      genome.
AU  - Que Q
AU  - Zhang Y
AU  - Nelson M
AU  - Ropp S
AU  - Burbank DE
AU  - Van Etten JL
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1997 190: 237-244.

PMID- 30533899
VI  - 7
DP  - 2018
TI  - Draft Genome Sequences of Isolates from Sediments of the River Elbe That Are Highly Tolerant to Diclofenac.
PG  - e00849-18
AB  - Here, we report the genome sequences of one Achromobacter and four Pseudomonas strains
      isolated from sediments of the River Elbe which are highly tolerant
      toward the xenobiotic target compound diclofenac, a nonsteroidal
      anti-inflammatory drug (NSAID) and emerging contaminant.
AU  - Quesada JM
AU  - Aguilar I
AU  - de la Torre J
AU  - Wittich RM
AU  - van Dillewijn P
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e00849-18.

PMID- 24812216
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Elizabethkingia meningoseptica Isolated from a Traumatic Wound.
PG  - e00355-14
AB  - We report the draft genome assembly of Elizabethkingia meningoseptica strain 502. The sample
      was isolated from the wound of a repatriated military serviceperson
      who suffered major trauma from an improvised explosive device (IED), resulting in
      wounds with extensive environmental contamination. E. meningoseptica was isolated
      from wounds in both legs. The draft genome assembly has 21 contigs with a total
      size of 3,960,744 bases. The genome contains genes encoding 26 putative
      beta-lactamases.
AU  - Quick J
AU  - Constantinidou C
AU  - Pallen MJ
AU  - Oppenheim B
AU  - Loman NJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00355-14.

PMID- 29097465
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Escherichia coli O113:H21 Strains Recovered from a Major Produce Production Region in California.
PG  - e01203-17
AB  - Shiga toxin-producing Escherichia coli is a foodborne and waterborne pathogen and is
      responsible for outbreaks of human gastroenteritis. This report documents the
      draft genome sequences of seven O113:H21 strains recovered from livestock,
      wildlife, and soil samples recovered from a major agricultural region for leafy
      greens in California, USA.
AU  - Quinones B
AU  - Yambao JC
AU  - Lee BG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01203-17.

PMID- 7220347
VI  - 9
DP  - 1981
TI  - In vitro methylation of DNA with HpaII methylase.
PG  - 633-646
AB  - The enzyme HpaII methylase extracted and partially purified from Haemophilus
      parainfluenza catalyzes the methylation of the tetranucleotide sequence CCGG at
      the internal cytosine.  The enzyme will methylate this sequence if both DNA
      strands are unmethylated or if only one strand is unmethylated.  Conditions
      have been developed for producing fully methylated DNA from various sources.
      In vitro methylation of this site protects the DNA against digestion by the
      restriction enzyme HpaII as well as the enzyme SmaI which recognizes the
      hexanucleotide sequence CCCGGG.  These properties make this enzyme a valuable
      tool for analyzing methylation in eukaryotic DNA where the sequence CCGG is
      highly methylated.  The activity of this methylase on such DNA indicates the
      degree of undermethylation of the CCGG sequence.  Several examples show that
      this technique can be used to detect small changes in the methylation state of
      eukaryotic DNA.
AU  - Quint A
AU  - Cedar H
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1981 9: 633-646.

PMID- 2644046
VI  - 56
DP  - 1989
TI  - Intron mobility in the T-even phages:  high frequency inheritance of group I introns promoted by intron open reading frames.
PG  - 455-465
AB  - Intron mobility in the T-even phages has been demonstrated. Efficient nonreciprocal conversion
      of intron minus (In-) alleles to intron plus (In+) occurred for the td and sunY genes, but not
      for nrdB. Conversion to In+ was absolutely dependent on expression of the respective intron
      open reading frame (ORF). Introns were inserted at their cognate sites in an intronless phage
      genome via an RNA-independent, DNA-based, duplicative recombination event that was stimulated
      by exon homology. The fd intron ORF product directs the endonucleolytic cleavage of DNA,
      targeting the site of intron integration. A 21 nucleotide deletion of the integration site
      abolished high frequency intron inheritance. These experiments provide a novel example of gene
      conversion in prokaryotes, while suggesting a molecular rationale for the inconsistent
      distribution of introns within highly conserved exon contexts of the T-even phage genomes.
AU  - Quirk SM
AU  - Bell-Pedersen D
AU  - Belfort M
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1989 56: 455-465.

PMID- 30533934
VI  - 7
DP  - 2018
TI  - Draft Genome Sequence of Mycoplasma wenyonii, a Second Hemotropic Mycoplasma Species Identified in Mexican Bovine Cattle.
PG  - e00875-18
AB  - The hemotropic mycoplasma (hemoplasma) Mycoplasma wenyonii is an animal pathogen  that affects
      bovine cattle health. Here, we present the draft genome sequence of
      the hemoplasma M. wenyonii strain INIFAP02 found in cattle from Mexico.
AU  - Quiroz-Castaneda RE
AU  - Martinez-Ocampo F
AU  - Dantan-Gonzalez E
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e00875-18.

PMID- 24407637
VI  - 2
DP  - 2014
TI  - Genome Sequence of Lactobacillus plantarum EGD-AQ4, Isolated from Fermented Product of Northeast India.
PG  - e01122-13
AB  - We present a draft genome sequence of Lactobacillus plantarum strain EGD-AQ4, isolated from
      nonalcoholic fermented bamboo shoot products of Northeast India.
      The size of the draft genome sequence is the largest among all the reported
      genome sequences of Lactobacillus plantarum, thus enabling the exploration of new
      gene clusters involved in various functional and probiotic attributes.
AU  - Qureshi A
AU  - Itankar Y
AU  - Ojha R
AU  - Mandal M
AU  - Khardenavis A
AU  - Kapley A
AU  - Purohit HJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01122-13.

PMID- 
VI  - 0
DP  - 2000
TI  - Isolation-purification of a new restriction endonuclease, CglI and its optimum reaction condition.
PG  - 36-38
AB  - A new restriction endonuclease CglI is isolated and purified from Corynebacterium glutamicum
      165 by a ultrasonication, Biogel filtered phosphocellulose and DEAE-cellulose column
      chromatography.  We establish some reasonable reaction condition for the purified restriction
      endonuclease, CglI.
AU  - Ra SR
AU  - Ri DC
PT  - Journal Article
TA  - Choson Minjujuui Inmin Konghwaguk Kwahagwon Tongbo
JT  - Choson Minjujuui Inmin Konghwaguk Kwahagwon Tongbo
SO  - Choson Minjujuui Inmin Konghwaguk Kwahagwon Tongbo 2000 0: 36-38.

PMID- 11327769
VI  - 308
DP  - 2001
TI  - Conformational flexibility in T4 endonuclease VII revealed by crystallography: implications for substrate binding and cleavage.
PG  - 311-323
AB  - The structure of the N62D mutant of the junction-resolving endonuclease VII (EndoVII) from
      phage T4 has been refined at 1.3 A, and a second wild-type crystal form solved and refined at
      2.8 A resolution. Comparison of the mutant with the wild-type protein structure in two
      different crystal environments reveals considerable conformational flexibility at the dimer
      level affecting the substrate-binding cleft, the dimerization interface and the orientation of
      the C-terminal domains. The opening of the DNA-binding cleft, the orientation of the
      C-terminal domains relative to the central dimerization domain as well as the relative
      positioning of helices in the dimerization interface appear to be sensitive to the crystal
      packing environment. The highly unexpected rearrangement within the extended hydrophobic
      interface does change the contact surface area but keeps the number of hydrophobic contacts
      about the same and will therefore not require significant energy input. The conformational
      flexibility most likely is of functional significance for the broad substrate specificity of
      EndoVII. Binding of sulphate ions in the mutant structure and their positions relative to the
      active-site metal ions and residues known to be essential for catalysis allows us to propose a
      possible catalytic mechanism. A comparison with the active-site geometries of other
      magnesium-dependent nucleases, among them the homing endonuclease I-PpoI and Serratia
      endonuclease, shows common features, suggesting related catalytic mechanisms. Copyright 2001
      Academic Press.
AU  - Raaijmakers H
AU  - Toro I
AU  - Birkenbihl R
AU  - Kemper B
AU  - Suck D
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2001 308: 311-323.

PMID- 2957724
VI  - 27
DP  - 1987
TI  - Restriction alleviation of phage lambda in Escherichia coli K-12 cells after gamma-irradiation.
PG  - 563-564
AB  - In gamma-irradiated cells of Escherichia coli K-12 restriction alleviation of an unmodified
      phage lambda is only observed in AB1157 strain.  No restriction alleviation by gamma-rays is
      registered in AB1157 mutants (recA and ssb-1).
AU  - Rabinkova EV
AU  - Torosyan MV
AU  - Fradkin GE
PT  - Journal Article
TA  - Radiobiologiia
JT  - Radiobiologiia
SO  - Radiobiologiia 1987 27: 563-564.

PMID- 14766539
VI  - 70
DP  - 2004
TI  - Diversity of phage types among archived cultures of the demerec collection of Salmonella enterica serovar Typhimurium strains.
PG  - 664-669
AB  - The existence of several thousand Salmonella enterica serovar Typhimurium LT2 and LT7 cultures
      originally collected by M. Demerec and
      sealed in agar stab vials for 33 to 46 years is a resource for
      evolutionary and mutational studies. Cultures from 74 of these vials,
      descendants of cells sealed and stored in nutrient agar stabs several
      decades ago, were phage typed by the Callow and Felix, Lilleengen, and
      Anderson systems. Among 53 LT2 archived strains, 16 had the same phage
      type as the nonarchival sequenced LT2 strain. The other 37 archived
      cultures differed in phage typing pattern from the sequenced strain.
      These 37 strains were divided into 10 different phage types. Among the
      19 LT7 strains, only one was similar to the parent by phage typing,
      while 18 were different. These 18 strains fell into eight different
      phage types. The typing systems were developed to track epidemics from
      source to consumer, as well as geographic spread. The value of phage
      typing is dependent upon the stability of the phage type of any given
      strain throughout the course of the investigation. Thus, the variation
      over time observed in these archived cultures is particularly
      surprising. Possible mechanisms for such striking diversity may include
      loss of prophages, prophage mosaics as a result of recombination
      events, changes in phage receptor sites on the bacterial cell surface,
      or mutations in restriction-modification systems.
AU  - Rabsch W
AU  - Helm RA
AU  - Eisenstark A
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2004 70: 664-669.

PMID- 15551059
VI  - 183
DP  - 2005
TI  - The genome sequence of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1.
PG  - 27-36
AB  - Recent research on microbial degradation of aromatic and other refractory compounds in anoxic
      waters and soils has revealed that nitrate-reducing
      bacteria belonging to the Betaproteobacteria contribute substantially to
      this process. Here we present the first complete genome of a metabolically
      versatile representative, strain EbN1, which metabolizes various aromatic
      compounds, including hydrocarbons. A circular chromosome (4.3 Mb) and two
      plasmids (0.21 and 0.22 Mb) encode 4603 predicted proteins. Ten anaerobic
      and four aerobic aromatic degradation pathways were recognized, with the
      encoding genes mostly forming clusters. The presence of paralogous gene
      clusters (e.g., for anaerobic phenylacetate oxidation), high sequence
      similarities to orthologs from other strains (e.g., for anaerobic phenol
      metabolism) and frequent mobile genetic elements (e.g., more than 200
      genes for transposases) suggest high genome plasticity and extensive
      lateral gene transfer during metabolic evolution of strain EbN1. Metabolic
      versatility is also reflected by the presence of multiple respiratory
      complexes. A large number of regulators, including more than 30
      two-component and several FNR-type regulators, indicate a finely tuned
      regulatory network able to respond to the fluctuating availability of
      organic substrates and electron acceptors in the environment. The absence
      of genes required for nitrogen fixation and specific interaction with
      plants separates strain EbN1 ecophysiologically from the closely related
      nitrogen-fixing plant symbionts of the Azoarcus cluster. Supplementary
      material on sequence and annotation are provided at the Web page
      http://www.micro-genomes.mpg.de/ebn1/.
AU  - Rabus R
AU  - Kube M
AU  - Heider J
AU  - Beck A
AU  - Heitmann K
AU  - Widdel F
AU  - Reinhardt R
PT  - Journal Article
TA  - Arch. Microbiol.
JT  - Arch. Microbiol.
SO  - Arch. Microbiol. 2005 183: 27-36.

PMID- 15305914
VI  - 6
DP  - 2004
TI  - The genome of Desulfotalea psychrophila, a sulfate-reducing bacterium from permanently cold Arctic sediments.
PG  - 887-902
AB  - Summary Desulfotalea psychrophila is a marine sulfate-reducing delta-proteobacterium that is
      able to grow at in situ temperatures below 0
      degrees C. As abundant members of the microbial community in permanently
      cold marine sediments, D. psychrophila-like bacteria contribute to the
      global cycles of carbon and sulfur. Here, we describe the genome sequence
      of D. psychrophila strain LSv54, which consists of a 3 523 383 bp circular
      chromosome with 3118 predicted genes and two plasmids of 121 586 bp and 14
      663 bp. Analysis of the genome gave insight into the metabolic properties
      of the organism, e.g. the presence of TRAP-T systems as a major route for
      the uptake of C(4)-dicarboxylates, the unexpected presence of genes from
      the TCA cycle, a TAT secretion system, the lack of a beta-oxidation
      complex and typical Desulfovibrio cytochromes, such as c(553), c(3) and
      ncc. D. psychrophila encodes more than 30 two-component regulatory
      systems, including a new Ntr subcluster of hybrid kinases, nine putative
      cold shock proteins and nine potentially cold shock-inducible proteins. A
      comparison of D. psychrophila's genome features with those of the only
      other published genome from a sulfate reducer, the hyperthermophilic
      archaeon Archaeoglobus fulgidus, revealed many striking differences, but
      only a few shared features.
AU  - Rabus R
AU  - Ruepp A
AU  - Frickey T
AU  - Rattei T
AU  - Fartmann B
AU  - Stark M
AU  - Bauer M
AU  - Zibat A
AU  - Lombardot T
AU  - Becker I
AU  - Amann J
AU  - Gellner K
AU  - Teeling H
AU  - Leuschner WD
AU  - Glockner FO
AU  - Lupas AN
AU  - Amann R
AU  - Klenk HP
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2004 6: 887-902.

PMID- 23908277
VI  - 1
DP  - 2013
TI  - First Insights into the Completely Annotated Genome Sequence of Bacillus licheniformis Strain 9945A.
PG  - e00525-13
AB  - Strains of the species Bacillus licheniformis are widely used in biotechnology for the
      production of enzymes and antibiotics (M. Schallmey, A. Singh, and O. P.
      Ward, Can. J. Microbiol. 50:1-17, 2004). However, research and application of B.
      licheniformis strains are adversely affected by poor genetic accessibility. Thus,
      for a closer inspection of natural competence in B. licheniformis, the genome of
      strain 9945A, of which derivatives are known to be naturally competent (C. B.
      Thorne and H. B. Stull, J. Bacteriol. 91:1012-1020, 1966), was completely
      sequenced and manually annotated.
AU  - Rachinger M
AU  - Volland S
AU  - Meinhardt F
AU  - Daniel R
AU  - Liesegang H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00525-13.

PMID- 24462975
VI  - 99
DP  - 2014
TI  - Improving the efficiency of plasmid transformation in Shewanella oneidensis MR-1 by removing ClaI restriction site.
PG  - 35-37
AB  - Here we demonstrate that elimination of ClaI restriction site from the sequence of a plasmid
      DNA increases the efficiency of transformation of Shewanella oneidensis MR-1 significantly. To
      achieve reliable transformation of S. oneidensis MR-1 plasmids either lacking ClaI site or
      isolated from primary transformants of S. oneidensis should be used. (C) 2014 Published by
      Elsevier B.V.
AU  - Rachkevych N
AU  - Sybirna K
AU  - Boyko S
AU  - Boretsky Y
AU  - Sibirny A
PT  - Journal Article
TA  - J. Microbiol. Methods
JT  - J. Microbiol. Methods
SO  - J. Microbiol. Methods 2014 99: 35-37.

PMID- 29599154
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Two Novel Salmonella enterica subsp. enterica Strains Isolated from Low-Moisture Foods with Applications in Food Safety Research.
PG  - e00183-18
AB  - The genomes of two strains of Salmonella enterica subsp. enterica serovar Cubana  and serovar
      Muenchen, isolated from dry hazelnuts and chia seeds, respectively,
      were sequenced using the Illumina MiSeq platform, assembled de novo using the
      overlap-layout-consensus method, and aligned to their respective most identical
      sequence genome scaffolds using MUMMER and BLAST searches.
AU  - Radford DR
AU  - Leon-Velarde CG
AU  - Chen S
AU  - Hamidi OAM
AU  - Balamurugan S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00183-18.

PMID- 11720311
VI  - 50
DP  - 2001
TI  - Cloning of enterohemorrhagic Escherichia coli Phage VT-2 Dam methyltransferase.
PG  - 161-167
AB  - Enterobacterial GATC-specific DNA adenine methyltransferase plays an essential role in
      regulation of DNA replication, methyl-directed mismatch repair, transposition and gene
      expression.  In Salmonella typhimurium it has been shown to directly control virulence.  In
      this paper we report cloning and expression of the dam gene from the Shiga toxin-producing
      VT2-Sa prophage of enterohemorrhagic Escherichia coli O157.  Comparisons of the predicted
      amino acid sequence indicates that Dam methyltransferases of E. coli phages VT2-Sa, 933W, T1
      and Haemophilus influenzae phage HP1 make up a separate subgroup of adenine-N6
      methyltransferases.  These proteins are similar to the gamma subfamily of
      amino-methyltransferases in respect to the linear order of sequence motifs and the presence of
      the hallmark "NPPY" tetrapeptide.  However, they apparently lack an autonomous
      target-recognizing domain at the C-terminus of the catalytic domain and therefore we propose
      to dub them as a "mini-gamma" subfamily.
AU  - Radlinska M
AU  - Bujnicki JM
PT  - Journal Article
TA  - Acta Microbiol. Pol.
JT  - Acta Microbiol. Pol.
SO  - Acta Microbiol. Pol. 2001 50: 161-167.

PMID- 11720315
VI  - 50
DP  - 2001
TI  - Site-directed mutagenesis defines the catalytic aspartate in the active site of the atypical DNA: m4C methyltransferase M.NgoMXV.
PG  - 97-105
AB  - M.NgoMXV is one of the few atypical DNA:m4C methyltransferases that does not possess a serine
      residue in its predicted active site.  We previously reported a homology model of M.NgoMXV and
      argued that the aspartate side chain at a corresponding position, similarly to some
      DNA:m6A-specific enzymes, is essential for the methyltransferase activity (Radlinska et al.
      1999).  Here we reported the corrected amino acid sequence of M.NgoMXV and the analysis of
      substitution of D68 with alanine or serine, which both render the enzyme totally inactive.
AU  - Radlinska M
AU  - Bujnicki JM
PT  - Journal Article
TA  - Acta Microbiol. Pol.
JT  - Acta Microbiol. Pol.
SO  - Acta Microbiol. Pol. 2001 50: 97-105.

PMID- 10651285
VI  - 37
DP  - 1999
TI  - Structural characterization of two tandemly arranged DNA methyltransferase genes from Neisseria gonorrhoeae MS11: N4-cytosine specific M.NgoMXV and nonfunctional 5-cytosine-type M.NgoMorf2P.
PG  - 717-728
AB  - Two adjacent genes encoding DNA methyltransferases (MTases) of Neisseria gonorrhoeae MS11, an
      active N4-cytosine specific M. NgoMXV and an inactive 5-cytosine type M.NgoMorf2P, were cloned
      into Escherichia coli and sequenced. We analyzed the deduced amino acid sequence of both gene
      products and localized conserved regions characteristic for DNA MTases. Structure prediction,
      threading-derived alignments, and comparison with the common fold for DNA MTases allowed for
      construction of super-secondary and tertiary models for M.NgoMorf2P and M.NgoMXV,
      respectively. These models helped in identification of amino acids and structural elements
      essential for function of both enzymes. The implications of this putative structural model on
      the catalytic mechanism of M.NgoMXV and its possible relation to the common ancestor of modern
      DNA amino-MTases are also discussed.
AU  - Radlinska M
AU  - Bujnicki JM
AU  - Piekarowicz A
PT  - Journal Article
TA  - Proteins
JT  - Proteins
SO  - Proteins 1999 37: 717-728.

PMID- 15558546
VI  - 58
DP  - 2005
TI  - Identification of amino acids important for target recognition by the DNA:m(5)C methyltransferase M.NgoPII by alanine-scanning mutagenesis  of residues at the protein-DNA interface.
PG  - 263-270
AB  - DNA:m(5)C MTases comprise a catalytic domain with conserved residues of the active site and a
      strongly diverged TRD with variable residues
      involved in DNA recognition and binding. To date, crystal structures of
      2 DNA:m(5)C MTases complexed with the substrate DNA have been obtained;
      however, for none of these enzymes has the importance of the whole set
      of DNA-binding residues been comprehensively studied. We built a
      comparative model of M.NgoPII, a close homologue and isomethylomer of
      M.HaeIII, and systematically analyzed the effect of alanine
      substitutions for the complete set of amino acid residues from its TRD
      predicted to be important for DNA binding and target recognition. Our
      data demonstrate that only 1 Arg residue is indispensable for the MTase
      activity in vivo and in vitro, and that mutations of only a few other
      residues cause significant reduction of the activity in vitro, with
      little effect on the activity in vivo. The identification of
      dispensable protein-DNA contacts in the wild-type MTase will serve as a
      platform for exhaustive combinatorial mutagenesis aimed at the design
      of new contacts, and thus construction of enzyme variants that retain
      the activity but exhibit potentially new substrate preferences.
AU  - Radlinska M
AU  - Kondrzycka-Dada A
AU  - Piekarowicz A
AU  - Bujnicki JM
PT  - Journal Article
TA  - Proteins
JT  - Proteins
SO  - Proteins 2005 58: 263-270.

PMID- 9865616
VI  - 379
DP  - 1998
TI  - Cloning and characterization of the gene encoding a new DNA methyltransferase from Neisseria gonorrhoeae.
PG  - 1391-1395
AB  - A HindIII fragment of N. gonorrhoeae MS11 DNA coding for DNA methyltransferase activity was
      cloned and expressed in E. coli AP1-200-9 cells.  The sequence of 4681 bp was determined, and
      its analysis revealed two open reading frames sharing some similarity with known DNA MTases.
      ORF1 encodes an active N4mC MTase (M.NgoMV).  The enzyme modifies only one strand of double
      stranded DNA and preferentially recognizes the sequence GCCHR although it is able to methylate
      other sites.  The exact recognition sequence cannot be precisely defined due to a relaxed
      specificity.  The second ORF shows high homology to 5mC Mtases, but we were unable to
      demonstrate DNA methylating activity of its product either in vivo or in vitro.
AU  - Radlinska M
AU  - Piekarowicz A
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1998 379: 1391-1395.

PMID- 16450842
VI  - 54
DP  - 2005
TI  - Cloning and preliminary characterization of a GATC-specific beta(2)-class DNA:m(6)A methyltransferase encoded by transposon Tn1549  from Enterococcus spp.
PG  - 249-252
AB  - A recent study revealed a subfamily of N6-adenine (m(6)A) methyltransferases that comprises a
      few functionally studied eukaryotic
      members acting on mRNA and prokaryotic members acting on DNA as well as
      numerous uncharacterized open reading frames. Here, we report cloning
      and functional characterization of a prokaryotic member of this family
      encoded by transposon Tn1549 from Enterococcus spp.
AU  - Radlinska M
AU  - Piekarowicz A
AU  - Galimand M
AU  - Bujnicki JM
PT  - Journal Article
TA  - Pol. J. Microbiol.
JT  - Pol. J. Microbiol.
SO  - Pol. J. Microbiol. 2005 54: 249-252.

PMID- 10333555
VI  - 47
DP  - 1998
TI  - Novel procedure for the detection of 5-methylcytosine.
PG  - 327-334
AB  - Bisulfite converts non-methylated cytosine in DNA to uracil leaving 5-methylcytosine
      unaltered.  In this communication, we present a new approach omitting the conventional PCR
      amplification step.  Bisulfite-converted methylated DNA is directly sequenced.  The
      effectiveness of the new protocol is demonstrated by using it for the detection of
      5-methylation of cytosine residues introduced by three different DNA methyltransferases
      (M.HaeIII, M.HpaII and M.HhaI).  A simple experimental system useful to determine the sequence
      specificity of DNA methyltransferases is also presented.
AU  - Radlinska M
AU  - Skowronek K
PT  - Journal Article
TA  - Acta Microbiol. Pol.
JT  - Acta Microbiol. Pol.
SO  - Acta Microbiol. Pol. 1998 47: 327-334.

PMID- 1829421
VI  - 121-125
DP  - 1991
TI  - Ultraviolet light induction of lambda from dcm host strains alleviates EcoRII restriction of phage.
PG  - 121-126
AB  - A new form of restriction alleviation is demonstrated for phage induced by ultraviolet light
      from dcm strains of Escherichia coli K-12. EcoRII restriction of the induced phage is
      alleviated, which is the first report of Type II restriction alleviation. Unlike previously
      reported restriction alleviation, the increase in phage-plating efficiency is not dependent
      upon irradiation of the plating host for its induction.
AU  - Radnedge L
AU  - Pinney RJ
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1991 121-125: 121-126.

PMID- 25201645
VI  - 15
DP  - 2014
TI  - Unusual genome complexity in Lactobacillus salivarius JCM1046.
PG  - 771
AB  - BACKGROUND: Lactobacillus salivarius strains are increasingly being exploited for
      their probiotic properties in humans and animals. Dissemination of antibiotic
      resistance genes among species with food or probiotic-association is undesirable
      and is often mediated by plasmids or integrative and conjugative elements. L.
      salivarius strains typically have multireplicon genomes including circular
      megaplasmids that encode strain-specific traits for intestinal survival and
      probiotic activity. Linear plasmids are less common in lactobacilli and show a
      very limited distribution in L. salivarius. Here we present experimental evidence
      that supports an unusually complex multireplicon genome structure in the porcine
      isolate L. salivarius JCM1046. RESULTS: JCM1046 harbours a 1.83 Mb chromosome,
      and four plasmids which constitute 20% of the genome. In addition to the known
      219 kb repA-type megaplasmid pMP1046A, we identified and experimentally validated
      the topology of three additional replicons, the circular pMP1046B (129 kb), a
      linear plasmid pLMP1046 (101 kb) and pCTN1046 (33 kb) harbouring a conjugative
      transposon. pMP1046B harbours both plasmid-associated replication genes and
      paralogues of chromosomally encoded housekeeping and information-processing
      related genes, thus qualifying it as a putative chromid. pLMP1046 shares limited
      sequence homology or gene synteny with other L. salivarius plasmids, and its
      putative replication-associated protein is homologous to the RepA/E proteins
      found in the large circular megaplasmids of L. salivarius. Plasmid pCTN1046
      harbours a single copy of an integrated conjugative transposon (Tn6224) which
      appears to be functionally intact and includes the tetracycline resistance gene
      tetM. CONCLUSION: Experimental validation of sequence assemblies and plasmid
      topology resolved the complex genome architecture of L. salivarius JCM1046. A
      high-coverage draft genome sequence would not have elucidated the genome
      complexity in this strain. Given the expanding use of L. salivarius as a
      probiotic, it is important to determine the genotypic and phenotypic organization
      of L. salivarius strains. The identification of Tn6224-like elements in this
      species has implications for strain selection for probiotic applications.
AU  - Raftis EJ
AU  - Forde BM
AU  - Claesson MJ
AU  - O'Toole PW
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2014 15: 771.

PMID- 22201792
VI  - 17
DP  - 2012
TI  - Mechanistic insights into type III restriction enzymes.
PG  - 1094-1107
AB  - Type III restriction-modification (R-M) enzymes need to interact with two separate
      unmethylated DNA sequences in indirectly repeated, head-to-head orientations for efficient
      cleavage to occur at a defined location next to only one of the two sites. However, cleavage
      of sites that are not in head-to-head orientation have been observed to occur under certain
      reaction conditions in vitro. ATP hydrolysis is required for the long-distance communication
      between the sites prior to cleavage. Type III R-M enzymes comprise two subunits, Res and Mod
      that form a homodimeric Mod(2) and a heterotetrameric Res(2)Mod(2) complex. The Mod subunit in
      M-2 or R2M2 complex recognizes and methylates DNA while the Res subunit in R2M2 complex is
      responsible for ATP hydrolysis, DNA translocation and cleavage. A vast majority of biochemical
      studies on Type III R-M enzymes have been undertaken using two closely related enzymes, EcoP1I
      and EcoP15I. Divergent opinions about how the long-distance interaction between the
      recognition sites exist and at least three mechanistic models based on 1D- diffusion and/or
      3D-DNA looping have been proposed.
AU  - Raghavendra NK
AU  - Bheemanaik S
AU  - Rao DN
PT  - Journal Article
TA  - Front. Biosci.
JT  - Front. Biosci.
SO  - Front. Biosci. 2012 17: 1094-1107.

PMID- 16026759
VI  - 334
DP  - 2005
TI  - Exogenous AdoMet and its analogue sinefungin differentially influence DNA cleavage by R.EcoP15I-Usefulness in SAGE.
PG  - 803-811
AB  - While it has been demonstrated that AdoMet is required for DNA cleavage by Type III
      restriction enzymes, here we show that in the presence of
      exogenous AdoMet, the head-to-head oriented recognition sites are cleaved
      only on a supercoiled DNA. On a linear DNA, exogenous AdoMet strongly
      drives methylation while inhibiting cleavage reaction. Strikingly, the AdoMet
      analogue sinefungin results in cleavage at all recognition sites
      irrespective of the topology of DNA. The cleavage reaction in the presence
      of sinefungin is ATP dependent. The site of cleavage is comparable with
      that in the presence of AdoMet. The use of EcoP15I restriction in presence
      of sinefungin as an improved tool for serial analysis of gene expression
      is discussed.
AU  - Raghavendra NK
AU  - Rao DN
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 2005 334: 803-811.

PMID- 12655005
VI  - 31
DP  - 2003
TI  - Functional cooperation between exonucleases and endonucleases - basis for the evolution of restriction enzymes.
PG  - 1888-1896
AB  - Many types of restriction enzymes cleave DNA away from their recognition site. Using the type
      III restriction enzyme, EcoP15I, which cleaves DNA
      25-27 bp away from its recognition site, we provide evidence to show that
      an intact recognition site on the cleaved DNA sequesters the restriction
      enzyme and decreases the effective concentration of the enzyme. EcoP15I
      restriction enzyme is shown here to perform only a single round of DNA
      cleavage. Significantly, we show that an exonuclease activity is essential
      for EcoP15I restriction enzyme to perform multiple rounds of DNA cleavage.
      This observation may hold true for all restriction enzymes cleaving DNA
      sufficiently far away from their recognition site. Our results highlight
      the importance of functional cooperation in the modulation of enzyme
      activity. Based on results presented here and other data on
      well-characterised restriction enzymes, a functional evolutionary
      hierarchy of restriction enzymes is discussed.
AU  - Raghavendra NK
AU  - Rao DN
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2003 31: 1888-1896.

PMID- 15501920
VI  - 32
DP  - 2004
TI  - Unidirectional translocation from recognition site and a necessary interaction with DNA end for cleavage by Type III restriction enzyme.
PG  - 5703-5711
AB  - Type III restriction enzymes have been demonstrated to require two unmethylated asymmetric
      recognition sites oriented head-to-head to elicit
      double-strand break 25-27 bp downstream of one of the two sites. The
      proposed DNA cleavage mechanism involves ATP-dependent DNA translocation.
      The sequence context of the recognition site was suggested to influence
      the site of DNA cleavage by the enzyme. In this investigation, we
      demonstrate that the cleavage site of the R.EcoP15I restriction enzyme
      does not depend on the sequence context of the recognition site.
      Strikingly, this study demonstrates that the enzyme can cleave linear DNA
      having either recognition sites in the same orientation or a single
      recognition site. Cleavage occurs predominantly at a site proximal to the
      DNA end in the case of multiple site substrates. Such cleavage can be
      abolished by the binding of Lac repressor downstream (3' side) but not
      upstream (5' side) of the recognition site. Binding of HU protein has also
      been observed to interfere with R.EcoP15I cleavage activity. In accordance
      with a mechanism requiring two enzyme molecules cooperating to elicit
      double-strand break on DNA, our results convincingly demonstrate that the
      enzyme translocates on DNA in a 5' to 3' direction from its recognition
      site and indicate a switch in the direction of enzyme motion at the DNA
      ends. This study demonstrates a new facet in the mode of action of these
      restriction enzymes.
AU  - Raghavendra NK
AU  - Rao DN
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2004 32: 5703-5711.

PMID- 27231353
VI  - 4
DP  - 2016
TI  - Genome Sequence of Psychrobacter cibarius Strain W1.
PG  - e00078-16
AB  - Here, we report the draft genome sequence of Psychrobacter cibarius strain W1, which was
      isolated at a slaughterhouse in Denmark. The 3.63-Mb genome sequence
      was assembled into 241 contigs.
AU  - Raghupathi PK
AU  - Herschend J
AU  - Roder HL
AU  - Sorensen SJ
AU  - Burmolle M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00078-16.

PMID- 27034481
VI  - 4
DP  - 2016
TI  - Draft Genome Assembly of Two Pseudoclavibacter helvolus Strains, G8 and W3, Isolated from Slaughterhouse Environments.
PG  - e00077-16
AB  - We report the draft genome sequences of twoPseudoclavibacter helvolusstrains. Strain G8 was
      isolated from a meat chopper and strain W3 isolated from the wall
      of a small slaughterhouse in Denmark. The two annotated genomes are 3.91 Mb and
      4.00 Mb in size, respectively.
AU  - Raghupathi PK
AU  - Herschend J
AU  - Roder HL
AU  - Sorensen SJ
AU  - Burmolle M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00077-16.

PMID- 27034480
VI  - 4
DP  - 2016
TI  - Genome Sequence of Kocuria varians G6 Isolated from a Slaughterhouse in Denmark.
PG  - e00076-16
AB  - We report here the first draft genome sequence ofKocuria variansG6, which was isolated from a
      meat chopper at a small slaughterhouse in Denmark. The 2.90-Mb
      genome sequence consists of 95 contigs and contains 2,518 predicted
      protein-coding genes.
AU  - Raghupathi PK
AU  - Herschend J
AU  - Roder HL
AU  - Sorensen SJ
AU  - Burmolle M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00076-16.

PMID- 26798084
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Lysinibacillus sphaericus B1-CDA, a Bacterium That Accumulates Arsenic.
PG  - e00999-15
AB  - Here, we report the genomic sequence and genetic composition of an arsenic-resistant
      bacterium, Lysinibacillus sphaericus B1-CDA. Assembly of the
      sequencing reads revealed that the genome size is ~4.5 Mb, encompassing ~80% of
      the chromosomal DNA.
AU  - Rahman A
AU  - Nahar N
AU  - Jass J
AU  - Olsson B
AU  - Mandal A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00999-15.

PMID- 27257201
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Enterobacter cloacae B2-DHA, a Chromium-Resistant Bacterium.
PG  - e00483-16
AB  - Previously, we reported a chromium-resistant bacterium, Enterobacter cloacae B2-DHA, isolated
      from the landfills of tannery industries in Bangladesh. Here, we
      investigated its genetic composition using massively parallel sequencing and
      comparative analysis with other known Enterobacter genomes. Assembly of the
      sequencing reads revealed a genome of ~4.21 Mb in size.
AU  - Rahman A
AU  - Nahar N
AU  - Olsson B
AU  - Mandal A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00483-16.

PMID- 26679576
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Streptococcus anginosus J4211, a Clinical Isolate.
PG  - e01440-15
AB  - Streptococcus anginosus is an opportunistic human pathogen that causes abscesses  of the
      brain, liver, and other organs. Here, we announce the complete genome
      sequence of a clinically isolated strain of S. anginosus J4211. The genome
      sequence contains two prophages and multiple mobile genetic elements.
AU  - Rahman M
AU  - Nguyen SV
AU  - McCullor KA
AU  - King CJ
AU  - Jorgensen JH
AU  - McShan WM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01440-15.

PMID- 28705984
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Eggerthia catenaformis Strain MAR1 Isolated from Saliva  of Healthy Humans.
PG  - e00638-17
AB  - Here, we report the draft genome sequence of Eggerthia catenaformis MAR1 isolated during a
      screen for d-cycloserine-resistant bacteria from the saliva of healthy
      humans. Analysis of the genome reveals that the strain has the potential to be a
      human pathogen and carries genes related to virulence and antibiotic resistance.
AU  - Rahman MA
AU  - Mullany P
AU  - Roberts AP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00638-17.

PMID- 
VI  - 
DP  - 2006
TI  - Roles of DNA and histone methyltransferases during zebrafish development.
PG  - 1-160
AB  - The research work presented in this dissertation describes the roles of the major DNA
      methyltransferases and histone methyltransferases in zebrafish development.  DNA and histone
      methylation are two key processes that regulate transcription of genes in mammals.  Both of
      these processes are essential for proper development of an organism and their misregulation
      leads to multiple diseases including cancer.  A better understanding of these two processes
      will help us understand how an organism develops and will also help in designing more
      effective drugs against cancer.  Chapter 1 is an introduction on DNA and histone methylation
      and the enzymes which catalyze these processes.  This chapter summarizes the literature on the
      normal various organisms including zebrafish, how abnormalities in this process lead to
      cancer, the protein structure and function of the known DNA methyltransferases and findings
      about relationship between histone methylation and DNA methylation.  Chapter 2 describes the
      function of DNA methyltransferase-1 during zebrafish development.  The focus of the studies
      described in this chapter is on the function of this enzyme during later differentiation
      during tissue-specific development.  Also, the epistatic relationship between Dnmt1 and
      Suv39h1, the major H3K9 methyltransferase, is described in this chapter.  Chapter 3 shows our
      findings about role of Dnmt3, a member of other sub-class of DNA methyltransferase family,
      during zebrafish development.  Here I have shown novel roles of this enzyme during development
      of vertebrate brain.  In Chapter 4, I have described our novel findings regarding the role of
      Dnmt2, a mysterious DNA/RNA methyltransferase, during zebrafish development.  Here, I have
      also described the importance of its function in the cytoplasm.  Chapter 5 is an attempt to
      compare the phenotypes obtained by knocking-down protein levels of different DNA
      methyltransferases.  This chapter is the crux of our studies which shows striking similarities
      and differences of in vivo functions of different classes of DNA methyltransferases.  In
      Chapter 6, the main conclusions of my work are summarized.  I have also discussed the
      implications of our findings and the future approaches to unravel the mysteries of
      developmental functions of DNA methyltransferases.
AU  - Rai K
PT  - Journal Article
TA  - Ph.D. Thesis, Univ. of Utah
JT  - Ph.D. Thesis, Univ. of Utah
SO  - Ph.D. Thesis, Univ. of Utah 2006 : 1-160.

PMID- 28408686
VI  - 5
DP  - 2017
TI  - Permanent Draft Genome Sequence of the French Bean Symbiont Rhizobium sp. Strain  RSm-3 Isolated from the Eastern Himalayan Region of India.
PG  - e00175-17
AB  - The genus Rhizobium contains many species able to form nitrogen-fixing nodules on plants of
      the legume family. Here, we report the 6.9-Mbp draft genome sequence of
      Rhizobium sp. strain RSm-3, with a G+C content of 61.4% and 6,511 candidate
      protein-coding genes.
AU  - Rai R
AU  - Swanson E
AU  - Sarkar I
AU  - Lama D
AU  - Abebe-Aleke F
AU  - Simpson S
AU  - Morris K
AU  - Thomas WK
AU  - Kar P
AU  - Gtari M
AU  - Sen A
AU  - Tisa LS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00175-17.

PMID- 25301660
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of FT9, a Novel Bacillus cereus Strain Isolated from a Brazilian Thermal Spring.
PG  - e01027-14
AB  - A Bacillus cereus strain, FT9, isolated from a hot spring in the midwest region of Brazil, had
      its entire genome sequenced.
AU  - Raiol T
AU  - De-Souza MT
AU  - Oliveira JV
AU  - Silva HS
AU  - Orem JC
AU  - Cavalcante DA
AU  - Almeida NF
AU  - Telles GP
AU  - Setubal JC
AU  - Brigido MM
AU  - Torres FA
AU  - Stadler PS
AU  - Walter ME
AU  - Moraes LM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01027-14.

PMID- 22965084
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Mycobacterium massiliense.
PG  - 5455
AB  - Mycobacterium massiliense is a rapidly growing bacterium associated with opportunistic
      infections. The genome of a representative isolate (strain GO 06)
      recovered from wound samples from patients who underwent arthroscopic or
      laparoscopic surgery was sequenced. To the best of our knowledge, this is the
      first announcement of the complete genome sequence of an M. massiliense strain.
AU  - Raiol T
AU  - Ribeiro GM
AU  - Maranhao AQ
AU  - Bocca AL
AU  - Silva-Pereira I
AU  - Junqueira-Kipnis AP
AU  - Brigido MM
AU  - Kipnis A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5455.

PMID- 7785768
VI  - 226
DP  - 1995
TI  - A bisulfite method of 5-methylcytosine mapping that minimizes template degradation.
PG  - 161-166
AB  - The bisulfite method is a highly sensitive approach to 5-methylcytosine mapping that utilizes
      the capability of the polymerase chain reaction to exponentially amplify DNA. We have observed
      that the bisulfite reaction results in a significant level of template degradation due to DNA
      depurination.  Furthermore, our data suggest that the DNA fragmentation which occurs limits
      the sensitivity of the method.  We describe a simple solution to limit degradation of the DNA
      template.
AU  - Raizis AM
AU  - Schmitt F
AU  - Jost J-P
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 1995 226: 161-166.

PMID- Not carried by PubMed...
VI  - 70
DP  - 1991
TI  - Heat shock-induced relaxation of restriction enzyme specificity in Escherichia coli.
PG  - 91-101
AB  - Methylated and hydroxymethylated cytosine containing DNA was restricted by
      proteins encoded by the mcrBC (rglB) loci of E. coli.  In vivo, RglB proteins
      recognize and cleave hmCT2 and hmCT4 DNAs at 30C and 42C but hmCT6 DNA was
      unaffected at both temperatures.  However, cells carrying the rglB genes cloned
      on pBR322 (pDSS17) did not restrict hmCT6 at 30C, but hmCT6 DNA was cleaved
      efficiently at 42C.  Heat shock treatment for five minutes was enough to induce
      this promiscuity in recognition specificity.  We call this activity RglB star.
      A single copy of rglB located on the chromosome or cloned on a low copy vector
      pMU575 failed to show RglB star activity.  De novo protein synthesis was not
      required for the manifestation of RglB star activity.
AU  - Raja MC
AU  - Dharmalingam K
PT  - Journal Article
TA  - J. Genetics
JT  - J. Genetics
SO  - J. Genetics 1991 70: 91-101.

PMID- 24201206
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Enterococcus raffinosus Strain CFTRI 2200, Isolated from Infant Fecal Material.
PG  - e00932-13
AB  - The complete genome sequence of Enterococcus raffinosus strain CFTRI 2200, isolated from the
      fecal material of a 7-month-old infant, is reported. The
      complete genome consists of 4.237 Mbp with a G+C content of 39.47% and 4,242
      protein-coding genes, 54 tRNAs, and 46 rRNAs.
AU  - Rajagopal K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00932-13.

PMID- 21197443
VI  - 2010
DP  - 2010
TI  - Characterization of pPCP1 Plasmids in Yersinia pestis Strains Isolated from the Former Soviet Union.
PG  - 760-819
AB  - Complete sequences of 9.5-kb pPCP1 plasmids in three Yersinia pestis strains from the former
      Soviet Union (FSU) were determined and compared with those of pPCP1 plasmids in three
      well-characterized, non-FSU Y.
      pestis strains (KIM, CO92, and 91001). Two of the FSU plasmids were from strains C2614 and
      C2944, isolated from plague foci in Russia, and one plasmid was from strain C790 from
      Kyrgyzstan. Sequence analyses identified four sequence types among the six plasmids. The pPCP1
      plasmids in the FSU strains were most genetically related to the pPCP1 plasmid in the KIM
      strain and least related to the pPCP1 plasmid in Y. pestis 91001. The FSU strains generally
      had larger pPCP1 plasmid copy numbers compared to strain CO92. Expression of the plasmid's
      pla gene was significantly (P </= .05) higher in strain C2944 than in strain CO92. Given
      pla's role in Y. pestis virulence, this difference may have important implications for the
      strain's virulence.
AU  - Rajanna C
AU  - Revazishvili T
AU  - Rashid MH
AU  - Chubinidze S
AU  - Bakanidze L
AU  - Tsanava S
AU  - Imnadze P
AU  - Bishop-Lilly KA
AU  - Sozhamannan S
AU  - Gibbons HS
AU  - Morris JG
AU  - Sulakvelidze A
PT  - Journal Article
TA  - Int. J. Microbiol.
JT  - Int. J. Microbiol.
SO  - Int. J. Microbiol. 2010 2010: 760-819.

PMID- 25657280
VI  - 3
DP  - 2015
TI  - Draft Genome of Escherichia coli O146 Isolate from Maulana Azad Medical College,  New Delhi, India.
PG  - e01515-14
AB  - Here, we report the draft genome sequence of enteropathogenic Escherichia coli (EPEC) O146
      strain isolated from a 1-year-old child with acute diarrhea in Delhi
      who recovered completely. The multidrug transporter (mdtABCD) gene, responsible
      for drug resistance, is present. The strain also contains the astA gene, an
      additional virulence determinant.
AU  - Rajeshwari K
AU  - Uppal B
AU  - Singh R
AU  - Malakar AK
AU  - Chikara SK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01515-14.

PMID- 28153891
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Klebsiella pneumoniae AWD5.
PG  - e01531-16
AB  - Here, we report the draft genome sequence of Klebsiella pneumoniae strain AWD5, isolated from
      an automobile workshop in India. The de novo assembly resulted in a
      4,807,409 bp genome containing 25 rRNA genes, 81 tRNAs, and 4,636 coding
      sequences (CDS). It carries important genes for polyaromatic hydrocarbon
      degradation and benzoate degradation.
AU  - Rajkumari J
AU  - Singha LP
AU  - Pandey P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01531-16.

PMID- 25908134
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Streptococcus iniae YSFST01-82, Isolated from Olive Flounder in Jeju, South Korea.
PG  - e00319-15
AB  - Streptococcus iniae is associated with morbidity in commercial fish species, especially in
      olive flounders (Paralichthys olivaceus), and was recently
      identified as an emerging human pathogen. Here, we report the complete 2.09-Mb
      genome sequence of S. iniae strain YSFST01-82, isolated from an olive flounder
      with streptococcosis disease in Jeju, South Korea.
AU  - Rajoo S
AU  - Jeon W
AU  - Park K
AU  - Yoo S
AU  - Yoon I
AU  - Lee H
AU  - Ahn J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00319-15.

PMID- 
VI  - 121
DP  - 1999
TI  - Protein-modulated DNA electron transfer.
PG  - 5615-5616
AB  - Long-range oxidative damage to the 5'-guanine of 5'-GG-3' sequences in DNA readily occurs
      as a result of electron migration through the pi-stack on long-range electron transfer, since
      upon binding, the protein induces and stabilizes a pi-gap using a novel DNA base-flipping
      mechanism.  Long-range oxidation of 5'-GG-3' sites was first shown with a rhodium
      intercalator.  The rhodium photochemistry bound to DNA yields base photooxidation upon
      irradiation at low energy (365nm), whereas irradiation at high energy (313 nm) leads to direct
      strand scission, marking the sites of intercalation.  Other DNA-bound photooxidants also
      promote DNA damage at long range.
AU  - Rajski SR
AU  - Kumar S
AU  - Roberts RJ
AU  - Barton JK
PT  - Journal Article
TA  - J. Am. Chem. Soc.
JT  - J. Am. Chem. Soc.
SO  - J. Am. Chem. Soc. 1999 121: 5615-5616.

PMID- 8095080
VI  - 17C
DP  - 1993
TI  - McrBC, a novel multisubunit GTP-dependent restriction endonuclease.
PG  - 152
AB  - The McrBC system is one of four restriction systems used by E. coli K-12 to monitor the origin
      of invading DNA and determine its fate. Like McrA and Mrr, the McrBC system is specific for
      modified DNA. The system is encoded by two genes of low GC composition flanked by two similar
      dyad symmetries, suggesting that the system may have been imported from elsewhere. Both genes
      are required for restriction in vivo of a variety of modified targets, including those with
      5-methylcytosine, 5-hydroxymethylcytosine and N4-methylcytosine. A few modified targets are
      sensitive to restriction mediated by mcrB in the absence of mcrC. Three proteins are expressed
      from the two genes. Only two of the three are required for in vitro activity. The in vitro
      cleavage activity reflects the in vivo properties of the system in its requirement for a
      modified substrate and in the spectrum of site-specific modifications that are sensitive to
      cleavage. GTP is required for cleavage. Non-hydrolysable analogues of GTP inhibit the
      reaction, as does ATP. Our current model is that cleavage requires the sequence
      RmC(N40-80)RmC, with multiple cleavage positions on both strands distributed within the spacer
      region. The roles played by the two proteins are under investigation genetically. Twelve mcrB
      mutants with dominant phenotypes have been isolated. These fall into three phenotypic classes.
      All are defective in McrC-dependent restriction; they differ in their ability in vivo to
      inhibit restriction by wild type genes in trans and in their ability to carry out
      McrC-independent restriction. Sequence analysis reveals that each class corresponds to a
      particular portion of the protein, one of which is the GTP-binding site motif identified in
      the polypeptide sequence of McrB.
AU  - Raleigh E
AU  - Dila D
AU  - Sutherland E
AU  - Kelleher J
AU  - Moran L
AU  - Slatko B
AU  - Briggs P
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1993 17C: 152.

PMID- 1316984
VI  - 6
DP  - 1992
TI  - Organization and function of the mcrBC genes of Escherichia coli K-12.
PG  - 1079-1086
AB  - Many natural DNA sequences are restricted in Escherichia coli K-12, not only by the classic
      Type I restriction system EcoK, but also by one of three modification-specific restriction
      systems found in K-12. The McrBC system is the best studied of these. We infer from the base
      composition of the mcrBC genes that they were imported from an evolutionarily distant source.
      The genes are located in a hypervariable cluster of restriction genes that may play a
      significant role in generation of species identity in enteric bacteria. Restriction activity
      requires the products of two genes for activity both in vivo and in vitro. The mcrB gene
      elaborates two protein products, only one of which is required for activity in vitro, but both
      of which contain a conserved amino acid sequence motif identified as a possible GTP-binding
      site. The mcrC gene product contains a leucine heptad repeat that could play a role in
      protein-protein interactions. McrBC activity in vivo and in vitro depends on the presence of
      modified cytosine in a specific sequence context; three different modifications are
      recognized. The in vitro activity of this novel multi-subunit restriction enzyme displays an
      absolute requirement for GTP as a cofactor.
AU  - Raleigh EA
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1992 6: 1079-1086.

PMID- 2821354
VI  - 152
DP  - 1987
TI  - Restriction and modification in vivo by Escherichia coli K12.
PG  - 130-141
AB  - This chapter focuses on how restriction of newly introduced DNA by Escherichia coli can
      interfere with cloning and subcloning work, and in particular on how the pattern of
      methylation of the DNA influences this. A principal aim is to acquaint the reader with three
      E. coli restriction systems that attack DNA only when it is appropriately methylated. The
      second part of this chapter describes biological restriction and modification in general
      terms. The third part discusses the particular restriction systems found in E. coli K12, first
      briefly the familiar K and P1 restriction systems, and then in detail the methyl-specific
      McrA, McrB and Mrr systems. Some common strains are discussed with special reference to their
      restriction phenotypes. The fourth part briefly reviews the E. coli methylation functions, Dam
      and Dcm, as they affect sensitivity to digestion of DNA in vitro.
AU  - Raleigh EA
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1987 152: 130-141.

PMID- 2013582
VI  - 173
DP  - 1991
TI  - Nomenclature relating to restriction of modified DNA in Escherichia coli.
PG  - 2707-2709
AB  - At least three restriction systems that attack DNA containing naturally
      modified bases have been found in common Escherichia coli K-12 strains.  These
      systems are McrA, McrBC, and Mrr.  A brief summary of the genetic and phenotype
      properties so far observed in laboratory strains is set forth, together with a
      proposed nomenclature for describing these properties.
AU  - Raleigh EA
AU  - Benner J
AU  - Bloom F
AU  - Braymer HD
AU  - DeCruz E
AU  - Dharmalingam K
AU  - Heitman J
AU  - Noyer-Weidner M
AU  - Piekarowicz A
AU  - Kretz PL
AU  - Short JM
AU  - Woodcock D
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1991 173: 2707-2709.

PMID- 
VI  - 
DP  - 1998
TI  - Restriction modification systems: where they are and what they do.
PG  - 78-92
AB  - The review concentrates on restriction-modification in the context of bacterial genome
      evolution and how the systems affect bacterial populations.  RM systems regulate the entry of
      foreign DNA into cells.  A model of how the systems work is shown in Figure 8-1.  Foreign DNA
      is restricted by a restriction endonuclease that recognizes a specific sequence and cleaves
      the DNA unless the sequence is protected. Typically, a modification methyltransferase confers
      protection, by methylating a particular base within the sequence recognized by the restriction
      enzyme, thereby rendering it resistant to cleavage.  Alternatively, however, some restriction
      enzymes recognize a sequence only when it is methylated.  In this case, methylation of a
      suitable base confers sensitivity to restriction and protection arises from failure to
      methylate the relevant sequence.  Both sorts of restriction can act to limit the transfer of
      DNA into cells.  One key feature of RM is that the systems can be effective only if they are
      variable and fluid within a bacterial population.  Modifications made to foreign DNA escaping
      restriction are epigenetic, i.e., not heritable.
AU  - Raleigh EA
AU  - Brooks JE
PT  - Journal Article
TA  - Bacterial Genomes
JT  - Bacterial Genomes
SO  - Bacterial Genomes 1998 : 78-92.

PMID- 2831502
VI  - 15
DP  - 1988
TI  - McrA and McrB restriction phenotypes of some E. coli strains and implications for gene cloning.
PG  - 1563-1575
AB  - The McrA and McrB (modified cytosine restriction) systems of E. coli interfere
      with incoming DNA containing methylcytosine.  DNA from many organisms,
      including all mammalian and plant DNA, is expected to be sensitive, and this
      could interfere with cloning experiments.  The McrA and B phenotypes of a few
      strains have been reported previously.  The Mcr phenotypes of 94 strains,
      primarily derived from E. coli K12, are tabulated here.  We briefly review some
      evidence suggesting that McrB restriction of mouse-modified DNA does occur in
      vivo and does in fact interfere with cloning of specific mouse sequences.
AU  - Raleigh EA
AU  - Murray NE
AU  - Revel H
AU  - Blumenthal RM
AU  - Westaway D
AU  - Reith AD
AU  - Rigby PWJ
AU  - Elhai J
AU  - Hanahan D
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1988 15: 1563-1575.

PMID- 1569746
VI  - 16B
DP  - 1992
TI  - Molecular analysis of McrBC, a GTP-dependent restriction endonuclease from E. coli K-12.
PG  - 21
AB  - The McrBC system is one of three modification-dependent restriction systems used by E. coli
      K-12 to monitor the origin of invading DNA and determine its fate. The system is encoded by
      two genes of low GC composition flanked by two similar dyad symmetries, suggesting that the
      system may have been imported from elsewhere. Both genes are required for restriction in vivo
      of a variety of modified targets, including those with 5-methylcytosine,
      5-hydroxymethylcytosine and N4-methylcytosine. Three proteins are expressed from the two
      genes, two of which are required for in vitro activity. For each of these proteins (McrBL and
      McrC), constructs that forced translation initiation at either of two potential start codons
      yielded enzymatically active product. One of each was purified to >90% purity. The in vitro
      cleavage activity reflected the in vivo properties of the system in its requirement for a
      modified substrate and in the spectrum of site-specific modifications that were sensitive to
      cleavage. GTP was required for cleavage. Non-hydrolysable analogues of GTP inhibited the
      reaction, as did ATP. We are unaware of any other nuclease with an absolute requirement for a
      guanosine nucleotide. The nature of the cleavage site was examined further by mapping sites on
      natural substrates, delimiting the cleavage site by primer extension, and cleaving synthetic
      oligonucleotide model substrates. Different sites are cleaved with differing efficiencies. Our
      current model is that cleavage requires the sequence RmC(N40-70)RmC, with multiple cleavage
      positions on both strands distributed within the spacer region.
AU  - Raleigh EA
AU  - Sutherland E
AU  - Dila D
AU  - Briggs P
AU  - Kelleher J
AU  - Coe L
AU  - Slatko B
AU  - Moran L
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1992 16B: 21.

PMID- 2548920
VI  - 122
DP  - 1989
TI  - Genetic and physical mapping of the mcrA (rglA) and mcrB (rglB) loci of Escherichia coli K-12.
PG  - 279-296
AB  - We have genetically analyzed, cloned and physically mapped the modified
      cytosine-specific restriction determinants mcrA (rglA) and mcrB (rglB) of
      Escherichia coli K-12.  The independently discovered Rgl and Mcr restriction
      systems are shown to be identical by three criteria:  1) mutants with the RglA-
      or RglB- phenotypes display the corresponding McrA- or McrB- phenotypes, and
      vice versa; 2) the gene(s) for RglA and McrA reside together at one locus,
      while gene(s) for RglB and McrB are coincident at a different locus; and 3)
      RglA+ and RglB+ recombinant clones complement for the corresponding
      Mcr-deficient lesions.  The mcrA (rglA) gene(s) is on the excisable element
      e14, just clockwise of purB at 25 min.  The mcrB (rglB) gene(s), at 99 min, is
      in a cluster of restriction functions that includes hsd and mrr, determinants
      of host-specific restriction (EcoK) and methyladenine-specific restriction
      respectively.  Gene order is mcrB-hsdS-hsdM-hsdR-mrr-serB.  Possible models for
      the acquisition of these restriction determinants by enteric bacteria are
      discussed.
AU  - Raleigh EA
AU  - Trimarchi R
AU  - Revel H
PT  - Journal Article
TA  - Genetics
JT  - Genetics
SO  - Genetics 1989 122: 279-296.

PMID- 3024165
VI  - 83
DP  - 1986
TI  - Escherichia coli K-12 restricts DNA containing 5-methylcytosine.
PG  - 9070-9074
AB  - We have observed that plasmids containing certain cloned modification methylase genes of type
      II restriction-modification systems cannot be transformed into many laboratory strains of
      Escherichia coli K-12.  The investigation of this phenomenon, reported here, has revealed (i)
      DNA containing 5-methylcytosine is biologically restricted by these strains, while DNA
      containing 6-methyladenine is not; (ii) restriction is due to two genetically distinct systems
      that differ in their sequence specificities, which we have named mcrA and mcrB (for modified
      cytosine restriction).  Since 5-methylcytosine containing DNA is widespread in nature, the Mcr
      systems probably have a broad biological role. Mcr restriction may seriously interfere with
      molecular cloning of 5-methylcytosine-containing foreign DNAs.  The Mcr phenotypes of some
      commonly used strains of E. coli K-12 are reported.
AU  - Raleigh EA
AU  - Wilson G
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1986 83: 9070-9074.

PMID- 8509345
VI  - 175
DP  - 1993
TI  - Leptospira genomes are modified at 5'-GTAC.
PG  - 3913-3915
AB  - Genomic DNAs of 14 strains from seven species of the spirochete Leptospira were resistant to
      cleavage by the restriction endonuclease RsaI (5'-GTAC). A modified base comigrating with m4C
      was detected by chromatography. Genomic DNAs from other spirochetes, Borrelia group VS461, and
      Serpulina strains were not resistant to RsaI digestion. Modification at 5'-GTAm4C may occur
      in most or all strains of all species of Leptospira but not in all genera of spirochetes.
      Genus-wide DNA modification has rarely been observed in bacteria.
AU  - Ralph D
AU  - Que Q
AU  - Van Etten JL
AU  - McClelland M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1993 175: 3913-3915.

PMID- 14192537
VI  - 36
DP  - 1964
TI  - A new property of phage group II Staphylococcus aureus strains:  Host restriction of phage K14.
PG  - 1-16
AB  - Various strains of Staphylococcus aureus which type exclusively with phages of
      lytic group II were found to modify phage K14 so that its ability to form
      plaques on host K1N was lessened.  The restricted phage formed plaques with
      high efficiency on all strains of lytic group II.  In general, it plated at
      lower titres on strains of lytic groups I, II, IV, and on some strains of
      miscellaneous typing characteristics; however, there were some variations among
      separate cultures of the same strains.  For example, the restricted phage
      plated at high titre on strains 52A/79a, 73, and 44A, but formed significantly
      fewer numbers of plaques on strain 52A, 79b and on a second culture of 44A.
      Strain K1N was found to dissociate into apt (K1H1) and non-apt (K1N2) forms.
      The probability of plaque development by restricted phage on strain K1N was
      dependent upon the nutritional state of the cocci and also upon the proportion
      of apt and non-apt cells.  The restriction of phage K14 was eliminated during
      its propagation on all strains other than lytic group II.  The unrestricted
      progeny particles tended to assay at equal titre on all the indicator strains.
      In all cases the genotype of the phage - susceptibility to
      host-control-remained unchanged.  The observations add to existing data which
      indicate that strains of phage group II form a genetically distinct group.  The
      suggestion is made that this phenomenon might help in taxonomic classifiction
      of strains of S. aureus.
AU  - Ralston DJ
AU  - Baer BS
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1964 36: 1-16.

PMID- 14949003
VI  - 80
DP  - 1952
TI  - Phage multiplication on two hosts, isolation and activity of variants of Staphylococcus phage P1.
PG  - 217-220
AB  - Analysis of phage activity by titration on two hosts has revealed the presence
      of variants hitherto undetected in stock phage P1.  One isolate, Phage 14,
      exhibits great changes in titration ratio on passage through the two hosts K1
      and WF 145.  Produced on K1 cells, the ratio of free phage assayed on two hosts
      is 1.3, whereas made on 145 cells,the free phage titrates in a ratio 145/K1 of
      ca 40.  This occurs regardless of the host employed in previous passage and is
      reproduced in the very first burst from infected cells.  Attempts to isolate
      different strains from this phage by usual plaque isolation technics were not
      successful.  The high ratio obtained with free phage made on 145 cells could
      not be explained on the basis of differences in adsorption onto or latent
      periods in the two hosts.  The difference was traced to the production of a
      large number of particles from host 145 which adsorbed on K1 but formed no
      plaques.  No evidence was found for an inhibitor of K1 activity associated with
      phage 14 production on 145 cells.  Heat inactivation destroyed phage activity
      for K1 cells much more rapidly than for 145 cells.  There was no interaction of
      heat killed and active phage on exposure to 59C. Evidence has been accumulated
      which indicates that the phage P14 is altered on passage through host 145.  The
      fact that phage particles surviving a heat treatment which destroyed all
      activity for K1 cells produce on strain 145 a mixture of two phages (one active
      on K1 and on - or both - active on strain 145) points to an unusual host effect
      on virus reproduction.
AU  - Ralston DJ
AU  - Kruger AP
PT  - Journal Article
TA  - Proc. Soc. Exp. Biol. Med.
JT  - Proc. Soc. Exp. Biol. Med.
SO  - Proc. Soc. Exp. Biol. Med. 1952 80: 217-220.

PMID- 29599150
VI  - 6
DP  - 2018
TI  - Genome Sequence of Coxiella-Like Endosymbiont Strain CLE-RmD, a Bacterial Agent in the Cattle Tick (Rhipicephalus microplus) Deutsch Strain.
PG  - e00003-18
AB  - We report a partial genome sequence for the Coxiella-like endosymbiont strain CLE-RmD,
      assembled from metagenomics data obtained from the southern cattle tick
      (Rhipicephalus microplus) Deutsch strain.
AU  - Ramaiah A
AU  - Dasch GA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00003-18.

PMID- 7705589
VI  - 108
DP  - 1995
TI  - Restriction enzyme systems of Helicobacter pylori.
PG  - A200
AB  - To date, the analysis of H. pylori using methods such as RFLP's, PCR and pulsed field gel
      electrophoresis, has revealed considerable genetic diversity from strain to strain.  Due to
      this diversity, there are as yet no methods for classifying this organism.  Also there are
      considerable differences in the transformability of different clinical isolates, some being
      easily transformable while others are not.  It has therefore been postulated that the organism
      may have restriction-modification systems which differ among isolates.  Restriction enzymes
      are produced by bacteria that cleave DNA at specific recognition sequences; these bacteria
      therefore have a modification system to methylate their own DNA at the recognition sites to
      protect it from cleavage.  No restriction enzymes have been described in H. pylori so far.
      Since restriction-modification systems are highly conserved in a given strain of a pathogenic
      organism, this can be a reliable method for classifying clinical isolates.  We cultured eleven
      H. pylori isolates on Campylobacter agar Skirrow (Difco) plates supplemented with 10%
      defibrinated sheep blood (Remel) in microaerobic chambers.  Cells were resuspended in a
      suitable buffer and sonicated.  Protein extracts were prepared by precipitation with 60%
      ammonium sulfate and subsequent dialysis, and these were used for restriction digests.
      Preliminary digests were done using a standard DNA template, the plasmid pBR322, which has a
      known restriction map and DNA sequence.  The patterns of these digests suggested the existence
      of restriction enzymes.  The site specificity of the restriction enzymes was elucidated using
      pBR322 that was linearized and labelled at one end with 32P.  Partial digests of the 32P
      labelled DNA with Hp extracts were fractionated by electrophoresis on polyacrylamide and
      agarose gels alongside appropriate radiolabelled markers.  By determining the sizes of the
      fragments of DNA generated we were able to determine the restriction sites on pBR322.  The
      various clinical isolates studied by us so far all have distinct restriction patterns.  Two
      have so far been identified.  The enzyme present in Hp 32 has a specificity corresponding to
      Sau96I while that in Hp 64 corresponds to DdeI.  Work is currently under way in our laboratory
      to identify the restriction enzymes in other clinical isolates.  We anticipate that this will
      yield a pattern that will form the bais for a classification system for H. pylori strains.
AU  - Ramakrishna J
AU  - Mathee K
AU  - Plaut AG
AU  - Wright A
PT  - Journal Article
TA  - Gastroenterology
JT  - Gastroenterology
SO  - Gastroenterology 1995 108: A200.

PMID- Not included in PubMed...
VI  - 17
DP  - 1992
TI  - Molecular cloning and sequencing of mcrA locus and identification of McrA protein in Escherichia coli.
PG  - 217-232
AB  - The Mcr systems (previously known as Rgl systems) of Escherichia coli recognize and cleave
      specific sequences carrying methylated or hydroxymethylated cytosines.  We have cloned the
      mcrA gene and determined its nucleotide sequence.  An 831 base pair sequence encodes the McrA
      protein.  Analysis of the sequence data reveals that there are additional ORFs internal to the
      above.  A phage T7 expression system was used to determine the protein products encoded by the
      cloned mcrA gene.  The results clearly show that a 31 kDa polypeptide is responsible for McrA
      activity.  This is in agreement with the molecular weight deduced from sequence data.  McrA
      protein was found to be localized in the outer membrane of Escherichia coli.  To our knowledge
      this is the first restriction enzyme localized in the outer membrane of Escherichia coli.
AU  - Ramalingam R
AU  - Prasad R
AU  - Shivapriya R
AU  - Dharmalingam K
PT  - Journal Article
TA  - J. Biosci.
JT  - J. Biosci.
SO  - J. Biosci. 1992 17: 217-232.

PMID- 21094162
VI  - 405
DP  - 2011
TI  - Creating Designed Zinc-Finger Nucleases with Minimal Cytotoxicity.
PG  - 630-641
AB  - Zinc-finger nucleases (ZFNs) have emerged as powerful tools for delivering a targeted genomic
      double-strand break (DSB) to either stimulate local
      homologous recombination with investigator-provided donor DNA or induce
      gene mutations at the site of cleavage in the absence of a donor by
      nonhomologous end joining both in plant cells and in mammalian cells,
      including human cells. ZFNs are formed by fusing zinc-finger proteins to
      the nonspecific cleavage domain of the FokI restriction enzyme.
      ZFN-mediated gene targeting yields high gene modification efficiencies
      (>10%) in a variety of cells and cell types by delivering a recombinogenic
      DSB to the targeted chromosomal locus, using two designed ZFNs. The
      mechanism of DSB by ZFNs requires (1) two ZFN monomers to bind to their
      adjacent cognate sites on DNA and (2) the FokI nuclease domains to
      dimerize to form the active catalytic center for the induction of the DSB.
      In the case of ZFNs fused to wild-type FokI cleavage domains, homodimers
      may also form; this could limit the efficacy and safety of ZFNs by
      inducing off-target cleavage. In this article, we report further
      refinements to obligate heterodimer variants of the FokI cleavage domain
      for the creation of custom ZFNs with minimal cellular toxicity. The
      efficacy and efficiency of the reengineered obligate heterodimer variants
      of the FokI cleavage domain were tested using the green fluorescent
      protein gene targeting reporter system. The three-finger and four-finger
      zinc-finger protein fusions to the REL_DKK pair among the newly generated
      FokI nuclease domain variants appear to eliminate or greatly reduce the
      toxicity of designer ZFNs to human cells.
AU  - Ramalingam S
AU  - Kandavelou K
AU  - Rajenderan R
AU  - Chandrasegaran S
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2011 405: 630-641.

PMID- 26184952
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of a Novel Nicotine-Degrading Bacterium, Pseudomonas plecoglossicida TND35.
PG  - e01162-14
AB  - Pseudomonas plecoglossicida TND35 is a potent nicotine-degrading bacterium. The draft genome
      sequence of strain TND35 contains 6,209,227 bp, 5,511 coding genes,
      and a G+C content of 62.3%. It encompasses genes related to catabolism of
      nicotine, N-heterocyclic aromatic compounds, heavy metal degradation, and butanol
      biosynthesis.
AU  - Raman G
AU  - Sakthivel N
AU  - Park S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01162-14.

PMID- 19181848
VI  - 106
DP  - 2009
TI  - Type III restriction enzymes communicate in 1D without looping between their target sites.
PG  - 1748-1753
AB  - To cleave DNA, Type III restriction enzymes must communicate the relative orientation of two
      asymmetric recognition sites over hundreds of base
      pairs. The basis of this long-distance communication, for which ATP
      hydrolysis by their helicase domains is required, is poorly understood.
      Several conflicting DNA-looping mechanisms have been proposed, driven
      either by active DNA translocation or passive 3D diffusion. Using
      single-molecule DNA stretching in combination with bulk-solution assays,
      we provide evidence that looping is both highly unlikely and unnecessary,
      and that communication is strictly confined to a 1D route. Integrating our
      results with previous data, a simple communication scheme is concluded
      based on 1D diffusion along DNA.
AU  - Ramanathan SP
AU  - van Aelst K
AU  - Sears A
AU  - Peakman LJ
AU  - Diffin FM
AU  - Szczelkun MD
AU  - Seidel R
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2009 106: 1748-1753.

PMID- 8384465
VI  - 14
DP  - 1993
TI  - Ambient temperature-stable molecular biology reagents.
PG  - 470-474
AB  - We have processed biological materials to generate several reagents that are ambient
      temperature stable and ready to use. Stabilized biomolecules in a glassy matrix of
      carbohydrate polymers offer water-soluble reagents for complex molecular biology applications.
      This approach is particulary useful for reagent systems composed of enzymes, nucleotides and
      other components dispensed in single-use aliquots. Reconstitution of the glassy matrix
      delivers buffered enzymes and/or nucleotides for restriction, modification, sequencing and/or
      amplification of nucleic acids. These ambient-temperature-stable reagents allow a high level
      of reproducibility as they minimize the potential for pipetting errors. They also provide
      advantages in shipping, storage and subsequent handling. Added convenience includes
      elimination of setup time, cross contamination and refrigeration. Applications of
      ambient-temperature-stable biological reagents for routine molecular biology methods are
      presented.
AU  - Ramanujam R
AU  - Heaster J
AU  - Huang C
AU  - Jolly J
AU  - Koelbl J
AU  - Lively C
AU  - Ogutu E
AU  - Ting E
AU  - Treml S
AU  - Aldous B
AU  - Hatley R
AU  - Mathias S
AU  - Franks F
AU  - Burdick B
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 1993 14: 470-474.

PMID- 25301662
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Vancomycin-Susceptible Staphylococcus aureus Related to Heterogeneous Vancomycin-Intermediate S. aureus.
PG  - e01033-14
AB  - We report the draft genome sequences of three vancomycin-susceptible methicillin-resistant
      Staphylococcus aureus strains. S. aureus strain MV8 is a
      sequence type 8 (ST-8) staphylococcal cassette chromosome mec element type IV
      (SCCmec IV) derivative, while the other two strains (S. aureus MM25 and MM61) are
      ST-5 SCCmec II strains. MM61 is also closely related to the heterogeneous
      vancomycin-intermediate S. aureus strain MM66.
AU  - Ramaraj T
AU  - Matyi SA
AU  - Sundararajan A
AU  - Lindquist IE
AU  - Devitt NP
AU  - Schilkey FD
AU  - Lamichhane-Khadka R
AU  - Hoyt PR
AU  - Mudge J
AU  - Gustafson JE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01033-14.

PMID- 24699955
VI  - 2
DP  - 2014
TI  - Improved Hybrid Genome Assemblies of Two Strains of Bacteroides xylanisolvens, SD_CC_1b and SD_CC_2a, Obtained Using Illumina and 454 Sequencing Technologies.
PG  - e00237-14
AB  - Bacteroides xlyanisolvens strains (SD_CC_1b, SD_CC_2a) isolated from human feces  were grown
      on crystalline cellulose. Cellulolytic properties are not common in Bacteroides species. Here,
      we report improved genome sequences of both of the B. xlyanisolvens strains.
AU  - Ramaraj T
AU  - Sundararajan A
AU  - Schilkey FD
AU  - Delvecchio VG
AU  - Donlon M
AU  - Ziemer C
AU  - Mudge J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00237-14.

PMID- 25197477
VI  - 9
DP  - 2014
TI  - Non contiguous-finished genome sequence and description of Enorma timonensis sp.  nov.
PG  - 970-986
AB  - Enorma timonensis strain GD5(T) sp. nov., is the type strain of E. timonensis sp. nov., a new
      member of the genus Enorma within the family Coriobacteriaceae. This
      strain, whose genome is described here, was isolated from the fecal flora of a
      53-year-old woman hospitalized for 3 months in an intensive care unit. E.
      timonensis is an obligate anaerobic rod. Here we describe the features of this
      organism, together with the complete genome sequence and annotation. The
      2,365,123 bp long genome (1 chromosome but no plasmid) contains 2,060
      protein-coding and 52 RNA genes, including 4 rRNA genes.
AU  - Ramasamy D
AU  - Dubourg G
AU  - Robert C
AU  - Caputo A
AU  - Papazian L
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 970-986.

PMID- 23408663
VI  - 7
DP  - 2012
TI  - Genome sequence and description of Aeromicrobium massiliense sp. nov.
PG  - 246-257
AB  - Aeromicrobium massiliense strain JC14(T)sp. nov. is the type strain of Aeromicrobium
      massiliense sp. nov., a new species within the genus Aeromicrobium.
      This strain, whose genome is described here, was isolated from the fecal
      microbiota of an asymptomatic patient. Aeromicrobium massiliense is an aerobic
      rod-shaped gram-positive bacterium. Here we describe the features of this
      organism, together with the complete genome sequence and annotation. The
      3,322,119 bp long genome contains 3,296 protein-coding and 51 RNA genes.
AU  - Ramasamy D
AU  - Kokcha S
AU  - Lagier JC
AU  - Nguyen TT
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 7: 246-257.

PMID- 23991258
VI  - 8
DP  - 2013
TI  - Non contiguous-finished genome sequence and description of Bacillus massiliosenegalensis sp. nov.
PG  - 264-278
AB  - Bacillus massiliosenegalensis strain JC6(T) sp. nov. is the type strain of Bacillus
      massiliosenegalensis sp. nov., a new species within the genus Bacillus.
      This strain was isolated from the fecal flora of a healthy Senegalese patient. B.
      massiliosenegalensis is an aerobic Gram-positive rod-shaped bacterium. Here we
      describe the features of this organism, together with the complete genome
      sequence and annotation. The 4,981,278-bp long genome comprises a 4,957,301-bp
      chromosome and a 23,977-bp plasmid. The chromosome contains 4,925 protein-coding
      and 72 RNA genes, including 4 rRNA genes. The plasmid contains 29 protein-coding
      genes.
AU  - Ramasamy D
AU  - Lagier JC
AU  - Gorlas A
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 264-278.

PMID- 23991263
VI  - 8
DP  - 2013
TI  - Non contiguous-finished genome sequence and description of Dielma fastidiosa gen. nov., sp. nov., a new member of the Family Erysipelotrichaceae.
PG  - 336-351
AB  - Dielma fastidiosa strain JC13(T) gen. nov., sp. nov. is the type strain of D. fastidiosa gen.
      nov., sp. nov., the type species of a new genus within the family
      Erysipelotrichaceae. This strain, whose draft genome is described here, was
      isolated from the fecal flora of a healthy 16-year-old male Senegalese volunteer.
      D. fastidiosa is a Gram-negative anaerobic rod. Here we describe the features of
      this organism, together with the complete genome sequence and annotation. The
      3,574,031 bp long genome comprises a 3,556,241-bp chromosome and a 17,790-bp
      plasmid. The chromosome contains 3,441 protein-coding and 50 RNA genes, including
      3 rRNA genes, whereas the plasmid contains 17 protein-coding genes.
AU  - Ramasamy D
AU  - Lagier JC
AU  - Nguyen TT
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 336-351.

PMID- 25197491
VI  - 9
DP  - 2014
TI  - Genome sequence and description of Bacteroides timonensis sp. nov.
PG  - 1181-1197
AB  - Bacteroides timonensis strain AP1(T) (= CSUR P194 = DSM 26083) is the type strain of B.
      timonensis sp. nov. This strain, whose genome is described here, was
      isolated from the fecal flora of a 21-year-old French Caucasoid female who
      suffered from severe anorexia nervosa. Bacteroides timonensis is a Gram-negative,
      obligate anaerobic bacillus. Here we describe the features of this organism,
      together with the complete genome sequence and annotation. The 7,130,768 bp long
      genome (1 chromosome, no plasmid) exhibits a G+C content of 43.3% and contains
      5,786 protein-coding and 59 RNA genes, including 2 rRNA genes.
AU  - Ramasamy D
AU  - Lagier JC
AU  - Rossi-Tamisier M
AU  - Pfleiderer A
AU  - Michelle C
AU  - Couderc C
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 1181-1197.

PMID- 25212629
VI  - 2
DP  - 2014
TI  - Whole-Genome Sequencing of Streptomycin-Resistant Mycobacterium tuberculosis Isolate VRFCWCF MRTB 180 Reveals Novel and Potential Mutations for Resistance.
PG  - e00919-14
AB  - We announce the draft genome sequence of a streptomycin monoresistant Mycobacterium
      tuberculosis strain (VRFCWCF MRTB 180) isolated from sputum of a
      clinically suspected tuberculosis patient.
AU  - Ramasubban G
AU  - Lakshmipathy D
AU  - Vetrivel U
AU  - Kulandai LT
AU  - Madhavan HN
AU  - Sridhar R
AU  - Meenakshi N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00919-14.

PMID- 
VI  - 0
DP  - 2018
TI  - Insights on a founder effect: the case of Xylella fastidiosa in the Salento area of Apulia, Italy.
PG  - 0
AB  - Summary. Xylella fastidiosa causing disease on different plant species has been reported in
      several European countries, since 2013. Based on multilocus sequence typing (MLST) results,
      there is evidence of repeated introductions of the pathogen in Spain and France. In contrast,
      in the Salento area of Apulia (Puglia) in Southern Italy, the existence of a unique Apulian
      MLST genotype of X. fastidiosa, causing the olive quick decline syndrome (OQDS; also referred
      to as CoDiRO or ST53) was proven, and this was tentatively ascribed to X. fastidiosa subsp.
      pauca. In order to acquire information on intra population diversity European Food Safety
      Authority (EFSA) has strongly called for the characterization of X. fastidiosa isolates from
      Apulia to produce the necessary data to better understand strain diversity and evolution. In
      this work, for the first time the existence of sub-variants within a set of  14 ST53 isolates
      of X. fastidiosa collected from different locations was searched using DNA typing methods
      targeting the whole pathogen genome. Invariably, VNTR, RAPD and rep-PCR (ERIC and BOX motifs)
      analyses indicated that all tested isolates possessed the same genomic fingerprint, supporting
      the existence of predominant epidemiological strain in Apulia. To further explore the degree
      of clonality within this population, two isolates from two different Salento areas (Taviano
      and Ugento) were completely sequenced using PacBio SMRT technology. The whole genome map and
      sequence comparisons revealed that both isolates are nearly identical, showing less than
      0.001% nucleotide diversity. However, the complete and circularized Salento-1 and Salento-2
      genome sequences were different, in genome and plasmid size, from the reference strain 9a5c of
      X. fastidiosa subsp. pauca (from citrus), and showed a PCR-proved large genome inversion of
      about 1.7 Mb. Genome-wide indices ANIm and dDDH indicated that the three isolates of X.
      fastidiosa from Salento (Apulia, Italy), namely Salento-1, Salento-2, and De Donno, whose
      complete genome sequence has been recently released, share a very recent common ancestor. This
      highlights the importance of continuous and extensive monitoring of molecular variation of
      this invasive pathogen to understand evolution of adaptive traits, and the necessity for
      adoption of all possible measures to reduce the risk of new introductions that may augment
      pathogen diversity.
AU  - Ramazzotti M
AU  - Cimaglia F
AU  - Gallo A
AU  - Ranaldi F
AU  - Surico G
AU  - Mita G
AU  - Bleve G
AU  - Marchi G
PT  - Journal Article
TA  - Phytopathol. Mediterr.
JT  - Phytopathol. Mediterr.
SO  - Phytopathol. Mediterr. 2018 0: 0.

PMID- 6246338
VI  - 65
DP  - 1980
TI  - Purification and properties of the SstI endonuclease.
PG  - 170-173
AB  - The SstI endonuclease is a restriction enzyme purified from a Streptomyces species which has
      been named Streptomyces stanford and is available from the American Type Culture Collection as
      ATCC No. 29415.  A crude lysate of these cells appears to cleave phage lambda DNA into two
      large fragments and phage lambda plac5 DNA into three large fragments.  SstI endonuclease is
      the major endonuclease which can be found in the lysate.  The enzyme produces cohesive ends
      and seems to cut most DNAs tested at rare sites.
AU  - Rambach A
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1980 65: 170-173.

PMID- 10339549
VI  - 96
DP  - 1999
TI  - DNA methylation is a reversible biological signal.
PG  - 6107-6112
AB  - The pattern of DNA methylation plays an important role in regulating different genome
      functions.  To test the hypothesis that DNA methylation is a reversible biochemical process,
      we purified a DNA demethylase from human cells that catalyzes the cleavage of a methyl residue
      from 5-methyl cytosine and its release as methanol.  We show that similar to DNA
      methyltransferase, DNA demethylase shows CpG dinucleotide specificity, can demethylate mdCpdG
      sites in different sequence contexts, and demethylates both fully methylated and
      hemimethylated DNA.  Thus, contrary to the commonly accepted model, DNA methylation is a
      reversible signal, similar to other physiological biochemical modifications.
AU  - Ramchandani S
AU  - Bhattacharya SK
AU  - Cervoni N
AU  - Szyf M
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1999 96: 6107-6112.

PMID- 9628348
VI  - 379
DP  - 1998
TI  - Genomic structure of the human DNA methyltransferase gene.
PG  - 535-540
AB  - We determined the genomic  structure of the gene encoding human DNA methyltransferase.  Six
      overlapping human genomic DNA clones which include all of the known cDNA sequence were
      isolated.  Analysis of these clones demonstrates that the human DNA MTase gene consists of at
      least 40 exons and 39 introns spanning a distance of 60 kilobases.  Elucidation of the
      chromosomal organization of the human DNA MTase gene provides the template for future
      structure-function analysis of the properties of mammalian DNA MTase.
AU  - Ramchandani S
AU  - Bigey P
AU  - Szyf M
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1998 379: 535-540.

PMID- 9012845
VI  - 94
DP  - 1997
TI  - Inhibition of tumorigenesis by a cytosine-DNA, methyltransferase, antisense oligodeoxynucleotide.
PG  - 684-689
AB  - This paper tests the hypothesis that cytosine DNA methyltransferase (DNA MeTase) is a
      candidate target for anticancer therapy.  Several observations have suggested recently that
      hyperactivation of DNA MeTase plays a critical role in initiation and progression of cancer
      and that its up-regulation is a component of the Ras oncogenic signaling pathway.  We show
      that a phosphorothioate-modified, antisense oligodeoxynucleotide directed against the DNA
      MeTase mRNA reduces the level of DNA MeTase mRNA, inhibits DNA MeTase activity, and inhibits
      anchorage independent growth of Y1 adrenocortical carcinoma cells ex vivo in a dose-dependent
      manner.  Injection of DNA MeTase antisense oligodeoxynucleotides i.p. inhibits the growth of
      Y1 tumors in syngeneic LAF1 mice, reduces the level of DNA MeTase, and induces demethylation
      of the adrenocortical-specific gene C21 and its expression in tumors in vivo.  These results
      support the hypothesis that an increase in DNA MeTase activity is critical for tumorigenesis
      and is reversible by pharmacological inhibition of DNA MeTase.
AU  - Ramchandani S
AU  - MacLeod AR
AU  - Pinard M
AU  - von Hofe E
AU  - Szyf M
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1997 94: 684-689.

PMID- 9033675
VI  - 7
DP  - 1996
TI  - A novel RNA element mediates the cell cycle dependent posttranscriptional regulation of DNA methyltransferase.
PG  - 302a
AB  - DNA methyltransferase is the enzyme responsible for methylation of DNA at CpG dinucleotide
      sequences.  Patterns of methylation have been shown to be an important control over gene
      regulation.  Recent evidence has linked the disregulation of the DNA MeTase to oncogenesis.
      The only mechanism of regulation of DNA MeTase gene expression thoroughly studied has been
      transcriptional.  However, in untransformed cells the regulation of DNA MeTase has been
      described to be posttranscriptional and dependent on the cell cycle.  The stability of DNA
      MeTase mRNA is dependent on protein synthesis as the stability of the message is enhanced at
      G0 upon the addition of cycloheximide.  Differential mRNA stabilities can be conferred by the
      make-up of a transcript's 3' untranslated region (3'UTR).  Homology comparison between the
      3' UTR's of the human, mouse, and chicken DNA MeTases have revealed two stretches of greater
      than 90% homology between all three mRNAs and the AU content of these stretches is greater
      than 85%.  To test the hypothesis that this sequence element regulates DNA MeTase mRNA it has
      been inserted 3' to the rabbit-beta-globin gene and transfected into BALB/c 3T3 fibroblast
      cells.  The chimeric globin-MeTase 3'UTR stability profile and its regulation with the cell
      cycle recapitulates that of the endogenous DNA MeTase mRNA.  Our data suggests that a sequence
      element in the DNA MeTase 3' UTR is a novel cell-cycle dependent regulator of mRNA stability.
AU  - Ramchandani S
AU  - Szyf M
PT  - Journal Article
TA  - Mol. Biol. Cell
JT  - Mol. Biol. Cell
SO  - Mol. Biol. Cell 1996 7: 302a.

PMID- Not included in PubMed...
VI  - 55
DP  - 1994
TI  - Cloning of the human DNA methyltransferase gene.
PG  - A137
AB  - During the process of carcinogenesis it has been observed that DNA methylation is deregulated.
      Increasing levels of DNA methyltransferase (DNA MeTase) mRNA has been shown to parallel the
      progression of cells through neoplasia to tumour cells. At least two levels of regulation of
      the mouse DNA MeTase have been shown; at the transcriptional level, via its promoter, and at
      the post transcriptional level in a cell cycle dependent fashion. Previously in our lab, the
      mouse 5' region was identified and was shown to be regulated by known oncogenic pathways. The
      sequence of the complete DNA MeTase gene has not yet been reported. Identifying the promoter
      of the human gene along with its complete genomic sequence is essential for a thorough study
      of the mechanisms involved in the multi-tiered regulation of DNA MeTase and to understand
      it's deregulation in cancer. Using a probe generated by PCR of the human DNA MeTase cDNA
      (position +156 to +507), a human genomic library was screened and a clone of approximately 22
      kilobases (kb) was isolated. It was found that this clone contains the complete coding
      sequence of the DNA MeTase enzyme. Sequence analysis along with restriction enzyme digests
      have allowed us to construct a partial map of the physical structure of the human DNA MeTase
      gene. This partial structure has already revealed some interesting aspects related to the
      genetic evolution of the human DNA MeTase. First, the proposed catalytic domain of the human
      DNA MeTase is extremely homologous to all other cytosine DNA MeTases, even to those that are
      found in bacteria, and this catalytic domain is conserved within one complete exon in the
      human gene. This is very different from the structure of the 5' region of the gene, which is
      fragmented into numerous little introns and exons. Within one of the small introns that have
      been identified, a trinucleotide repeat of ATG occurs (9 times in a row), and this repeat is
      upstream of the proposed start site of translation. Trinucleotide repeat expansion has been
      shown to be a genetic hot spot of mutation, but even more interesting is the nature of the
      repeat, ATG, which is the translation start codon and this repeat appears to be in frame with
      the "normal" coding sequence. The implications being that possible alternative
      methyltransferases may be translated under certain conditions such as cancer.
AU  - Ramchandani SK
AU  - Rouleau J
AU  - Szyf M
PT  - Journal Article
TA  - Am. J. Hum. Genet.
JT  - Am. J. Hum. Genet.
SO  - Am. J. Hum. Genet. 1994 55: A137.

PMID- 24874667
VI  - 2
DP  - 2014
TI  - Genome Sequencing of Ralstonia solanacearum Biovar 3, Phylotype I, Strains Rs-09-161 and Rs-10-244, Isolated from Eggplant and Chili in India.
PG  - e00323-14
AB  - Ralstonia solanacearum Indian strains Rs-09-161 and Rs-10-244 were isolated from  the coastal
      region of Goa and from the Andaman Islands. We report the draft
      genome sequences of these representative isolates infecting solanaceous
      vegetables in India.
AU  - Ramesh R
AU  - Gaitonde S
AU  - Achari G
AU  - Asolkar T
AU  - Singh NP
AU  - Carrere S
AU  - Genin S
AU  - Peeters N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00323-14.

PMID- 28183757
VI  - 5
DP  - 2017
TI  - Genome Sequence of the Filamentous Actinomycete Kitasatospora viridifaciens.
PG  - e01560-16
AB  - The vast majority of antibiotics are produced by filamentous soil bacteria called
      actinomycetes. We report here the genome sequence of the tetracycline producer
      'Streptomyces viridifaciens' DSM 40239. Given that this species has the hallmark
      signatures characteristic of the Kitasatospora genus, we previously proposed to
      rename this organism Kitasatospora viridifaciens.
AU  - Ramijan K
AU  - van Wezel GP
AU  - Claessen D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01560-16.

PMID- 21282446
VI  - 55
DP  - 2011
TI  - Genomic Analysis of Acinetobacter baumannii A118 by Comparison of Optical Maps: Identification of Structures Related to its Susceptibility Phenotype.
PG  - 1520-1526
AB  - Acinetobacter baumannii A118, a naturally competent clinical isolate, is unusually susceptible
      to several antibiotics. Comparison of the optical map of strain A118 with in silico-generated
      restriction maps of sequenced genomes and sequence analyses showed that the AbaR region,
      commonly found inserted within the comM gene in other isolates, is missing in strain A118,
      which could in part explain the susceptible phenotype exhibited by this isolate. These
      comparative studies also showed differences in regions where genes coding for functions that
      may be involved in drug resistance or susceptibility are located. Further sequencing
      demonstrated that cat and blaADC, named blaADC-55, are present but that a tet(A) gene usually
      found in other strains is not. In addition, carO and pbp2, which may play a role in
      susceptibility to carbapenems, are present in strain A118. These findings support the idea
      that A. baumannii strains possess multiple mechanisms that contribute to antibiotic
      resistance, and the presence of some of them is not sufficient for a resistant phenotype. The
      results shown here indicate that optical mapping is a useful tool for preliminary comparative
      genomic analysis.
AU  - Ramirez MS
AU  - Adams MD
AU  - Bonomo RA
AU  - Centron D
AU  - Tolmasky ME
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2011 55: 1520-1526.

PMID- 24948759
VI  - 2
DP  - 2014
TI  - Genome Sequences of Two Carbapenemase-Resistant Klebsiella pneumoniae ST258 Isolates.
PG  - e00558-14
AB  - Klebsiella pneumoniae, an ESKAPE group (Enterococcus faecium, Staphylococcus aureus,
      Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa,
      and Enterobacter species) pathogen, has acquired multiple antibiotic resistance
      genes and is becoming a serious public health threat. Here, we report the genome
      sequences of two representative strains of K. pneumoniae from the emerging K.
      pneumoniae carbapenemase (KPC) outbreak in northeast Ohio belonging to sequence
      type 258 (ST258) (isolates Kb140 and Kb677, which were isolated from blood and
      urine, respectively). Both isolates harbor a blaKPC gene, and strain Kb140
      carries blaKPC-2, while Kb677 carries blaKPC-3.
AU  - Ramirez MS
AU  - Xie G
AU  - Johnson S
AU  - Davenport K
AU  - van Duin D
AU  - Perez F
AU  - Bonomo RA
AU  - Chain P
AU  - Tolmasky ME
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00558-14.

PMID- 21421005
VI  - 66
DP  - 2011
TI  - Nucleotide sequence of Pseudomonas aeruginosa conjugative plasmid pUM505 containing virulence and heavy-metal resistance genes.
PG  - 7-18
AB  - We determined the complete nucleotide sequence of conjugative plasmid
      pUM505 isolated from a clinical strain of Pseudomonas aeruginosa. The
      plasmid had a length of 123,322bp and contained 138 complete coding
      regions, including 46% open reading frames encoding hypothetical proteins.
      pUM505 can be considered a hybrid plasmid because it presents two
      well-defined regions. The first region corresponded to a larger DNA
      segment with homology to a pathogenicity island from virulent Pseudomonas
      strains; this island in pUM505 was comprised of genes probably involved in
      virulence and genes encoding proteins implicated in replication,
      maintenance and plasmid transfer. Sequence analysis identified pil genes
      encoding a type IV secretion system, establishing pUM505 as a member of
      the family of IncI1 plasmids. Plasmid pUM505 also contained virB4/virD4
      homologues, which are linked to virulence in other plasmids. The second
      region, smaller in length, contains inorganic mercury and chromate
      resistance gene clusters both flanked by putative mobile elements.
      Although no genes for antibiotic resistance were identified, when pUM505
      was transferred to a recipient strain of P. aeruginosa it conferred
      resistance to the fluoroquinolone ciprofloxacin. pUM505 also conferred
      resistance to the superoxide radical generator paraquat. pUM505 could
      provide Pseudomonas strains with a wide variety of adaptive traits such as
      virulence, heavy-metal and antibiotic resistance and oxidative stress
      tolerance which can be selective factors for the distribution and
      prevalence of this plasmid in diverse environments, including hospitals
      and heavy metal contaminated soils.
AU  - Ramirez-Diaz MI
AU  - Diaz-Magana A
AU  - Meza-Carmen V
AU  - Johnstone L
AU  - Cervantes C
AU  - Rensing C
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 2011 66: 7-18.

PMID- 28302784
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Francisella noatunensis subsp. orientalis STIR-GUS-F2f7, a Highly Virulent Strain Recovered from Diseased Red Nile Tilapia Farmed in  Europe.
PG  - e01555-16
AB  - A highly virulent strain of Francisella noatunensis subsp. orientalis, STIR-GUS-F2f7, was
      isolated from moribund red Nile tilapia (Oreochromis
      niloticus) farmed in Europe. In this communication, the complete genome
      sequencing of this bacterium is reported.
AU  - Ramirez-Paredes JG
AU  - Larsson P
AU  - Wehner S
AU  - Bekaert M
AU  - Ohrman C
AU  - Metselaar M
AU  - Thompson KD
AU  - Richards RH
AU  - Penman DJ
AU  - Adams A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01555-16.

PMID- 23144380
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Corynebacterium pseudotuberculosis Cp316 Strain, Isolated  from the Abscess of a Californian Horse.
PG  - 6620-6621
AB  - The bacterium Corynebacterium pseudotuberculosis is of major veterinary importance because it
      affects livestock, particularly sheep, goats, and horses,
      in several countries, including Australia, Brazil, the United States, and Canada,
      resulting in significant economic losses. In the present study, we describe the
      complete genome of the Corynebacterium pseudotuberculosis Cp316 strain, biovar
      equi, isolated from the abscess of a North American horse.
AU  - Ramos RT et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6620-6621.

PMID- 29622610
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of the 1,4-Dioxane-Degrading Bacterium Pseudonocardia dioxanivorans BERK-1.
PG  - e00207-18
AB  - Pseudonocardia dioxanivorans strain BERK-1 grows aerobically with 1,4-dioxane as  its sole
      substrate. Reported here is its draft genome sequence, with a size of
      7.1 Mbp. Key genes are highlighted in this article. BERK-1 exhibits a reduced
      level of cell aggregation and adherence to surfaces compared to those of P.
      dioxanivorans CB1190, giving it an apparent advantage for movement through soil.
AU  - Ramos-Garcia AA
AU  - Shankar V
AU  - Saski CA
AU  - Hsiang T
AU  - Freedman DL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00207-18.

PMID- 25858824
VI  - 3
DP  - 2015
TI  - Rethinking the Niche of Upper-Atmosphere Bacteria: Draft Genome Sequences of Bacillus aryabhattai C765 and Bacillus aerophilus C772, Isolated from Rice  Fields.
PG  - e00094-15
AB  - Here, we report two genome sequences of endospore-forming bacteria isolated from  the rice
      fields of Comporta, Portugal, identified as Bacillus aryabhattai C765
      and Bacillus aerophilus C772. Both species were previously identified in air
      samples from the upper atmosphere, but our findings suggest their presence in a
      wider range of environmental niches.
AU  - Ramos-Silva P
AU  - Brito PH
AU  - Serrano M
AU  - Henriques AO
AU  - Pereira-Leal JB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00094-15.

PMID- 10805783
VI  - 97
DP  - 2000
TI  - Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a.
PG  - 5237-5242
AB  - Current evidence indicates that methylation of cytosine in mammalian DNA is restricted to both
      strands of the symmetrical sequence CpG, although there have been sporadic reports that
      sequences other than CpG may also be methylated. We have used a dual-labeling nearest neighbor
      technique and bisulphite genomic sequencing methods to investigate the nearest neighbors of
      5-methylcytosine residues in mammalian DNA. We find that embryonic stem cells, but not somatic
      tissues, have significant cytosine-5 methylation at CpA and, to a lesser extent, at CpT. As
      the expression of the de novo methyltransferase Dnmt3a correlates well with the presence of
      non-CpG methylation, we asked whether Dnmt3a might be responsible for this modification.
      Analysis of genomic methylation in transgenic Drosophila expressing Dnmt3a reveals that Dnmt3a
      is predominantly a CpG methylase but also is able to induce methylation at CpA and at CpT.
AU  - Ramsahoye BH
AU  - Biniszkiewicz D
AU  - Lyko F
AU  - Clark V
AU  - Bird AP
AU  - Jaenisch R
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2000 97: 5237-5242.

PMID- 9241230
VI  - 25
DP  - 1997
TI  - Restriction endonuclease isoschizomers ItaI, BsoFI and Fsp4HI are characterized by differences in their sensitivities to CpG methylation.
PG  - 3196-3198
AB  - BsoFI, ItaI and Fsp4HI are isoschizomers of Fnu4HI (5'-GC/NGC-3').  Both Fnu4HI and BsoFI
      have previously been shown to be inhibited by cytosine-specific methylation within the
      recognition sequence.  Fnu4HI is inhibited if either the internal cytosine at position 2 or
      the external cytosine at position 5 of the restriction sequence is methylated, but the precise
      nature of the methylation sensitivity of BsoFI is unclear from the literature.  The
      methylation sensitivities of ItaI and Fsp4HI have not previously been reported.  By
      methylating the plasmid pUC18 with M.SssI (a DNA cytosine-5'-methyltransferase with a
      specificity for CpG), we have determined that ItaI is sensitive only to methylation of
      internal CpG sites within the restriction sequence.  The methylation sensitivity of Fsp4HI is
      identical to that of Fnu4HI, being inhibited by methylation of either internal CpG sites or
      overlapping CpG sites.  BsoFI, like the other isoschizomers tested, is sensitive to a
      combination of internal and overlapping CpG methylation.  BsoFI is also sensitive to
      overlapping CpG methylation (in the absence of internal CpG methylation) if CpG overlap with
      both sides of the recognition sequence.  Sites containing one overlapping CpG (in the absence
      of internal CpG) are cut when methylated but show marked individual variation in their rates
      of cleavage.  Considerable variation in the rate of cleavage by BsoFI is also observed at
      sites containing only internal methylated CpG.  Some sites are cut slowly, whilst others fail
      to cut even after prolonged incubation with excess of enzyme.
AU  - Ramsahoye BH
AU  - Burnett AK
AU  - Taylor C
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1997 25: 3196-3198.

PMID- 25767232
VI  - 3
DP  - 2015
TI  - High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from  Uranium(VI)-Contaminated Groundwater.
PG  - e00092-15
AB  - Desulfovibrio carbinoliphilus subsp. oakridgensis FW-101-2B is an anaerobic, organic
      acid/alcohol-oxidizing, sulfate-reducing delta-proteobacterium. FW-101-2B
      was isolated from contaminated groundwater at The Field Research Center at Oak
      Ridge National Lab after in situ stimulation for heavy metal-reducing conditions.
      The genome will help elucidate the metabolic potential of sulfate-reducing
      bacteria during uranium reduction.
AU  - Ramsay BD et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00092-15.

PMID- 8619995
VI  - 35
DP  - 1996
TI  - Kinetics of the interaction between DNA and the type IC restriction enzyme EcoR124II.
PG  - 3746-3753
AB  - Optical waveguide mode spectroscopy was used to determine the binding constants characterizing
      the interaction of EcoR124II, a type IC restriction modification enzyme from Salmonella
      typhimurium, with DNA.  The DNA is immobilized on the surface of an optical waveguide, and the
      enzyme is introduced in bulk solution flowing over the DNA under controlled hydrodynamic
      conditions.  The binding kinetics of the protein to the DNA can be directly observed and the
      number of bound protein molecules per base pair determined to a high accuracy.  Dissociation
      of the protein was measured by switching flowing protein to protein-free buffer.  Binding to
      two different kinds of DNA, with and without the specific sequence recognized by EcoR124II,
      was investigated.  Protein binding and dissociation (M-RnonspecificM-S binding), quantified by
      association and dissociation rate coefficients ka and kd, were the same for both types, but
      the DNA carrying the recognition site showed an additional process, M-RirreversibleM-S
      association (i.e. dissociation was not observed on the time scale of the experiments) of the
      protein, quantified by a rate coefficient ks.  Some inferences regarding the mechanism of base
      pair searching are made from the measured ka, kd and ks values.
AU  - Ramsden JJ
AU  - Dreier J
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1996 35: 3746-3753.

PMID- 28218897
VI  - 14
DP  - 2017
TI  - Mapping DNA methylation with high-throughput nanopore sequencing.
PG  - 411-413
AB  - DNA chemical modifications regulate genomic function. We present a framework for  mapping
      cytosine and adenosine methylation with the Oxford Nanopore Technologies
      MinION using this nanopore sequencer's ionic current signal. We map three
      cytosine variants and two adenine variants. The results show that our model is
      sensitive enough to detect changes in genomic DNA methylation levels as a
      function of growth phase in Escherichia coli.
AU  - Rand AC
AU  - Jain M
AU  - Eizenga JM
AU  - Musselman-Brown A
AU  - Olsen HE
AU  - Akeson M
AU  - Paten B
PT  - Journal Article
TA  - Nat. Methods
JT  - Nat. Methods
SO  - Nat. Methods 2017 14: 411-413.

PMID- 22965136
VI  - 41
DP  - 2013
TI  - Sensitive and selective amplification of methylated DNA sequences using helper-dependent chain reaction in combination with a methylation-dependent restriction enzymes.
PG  - e15
AB  - We have developed a novel technique for specific amplification of rare methylated DNA
      fragments in a high background of unmethylated sequences
      that avoids the need of bisulphite conversion. The
      methylation-dependent restriction enzyme GlaI is used to selectively
      cut methylated DNA. Then targeted fragments are tagged using specially
      designed 'helper' oligonucleotides that are also used to maintain
      selection in subsequent amplification cycles in a process called
      'helper-dependent chain reaction'. The process uses disabled primers
      called 'drivers' that can only prime on each cycle if the helpers
      recognize specific sequences within the target amplicon. In this way,
      selection for the sequence of interest is maintained throughout the
      amplification, preventing amplification of unwanted sequences. Here we
      show how the method can be applied to methylated Septin 9, a promising
      biomarker for early diagnosis of colorectal cancer. The GlaI digestion
      and subsequent amplification can all be done in a single tube. A
      detection sensitivity of 0.1% methylated DNA in a background of
      unmethylated DNA was achieved, which was similar to the
      well-established Heavy Methyl method that requires bisulphite-treated
      DNA.
AU  - Rand KN
AU  - Young GP
AU  - Ho T
AU  - Molloy PL
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2013 41: e15.

PMID- 26966214
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Mesorhizobium sp. UFLA 01-765, a Multitolerant, Efficient Symbiont and Plant Growth-Promoting Strain Isolated from Zn-Mining Soil  Using Leucaena leucocephala as a Trap Plant.
PG  - e00050-16
AB  - We report the 7.4-Mb draft genome sequence of Mesorhizobium sp. strain UFLA 01-765, a
      Gram-negative bacterium of the Phyllobacteriaceae isolated from
      Zn-mining soil in Minas Gerais, Brazil. This strain promotes plant growth,
      efficiently fixes N2 in symbiosis with Leucaena leucocephala on multicontaminated
      soil, and has potential for application in bioremediation of marginal lands.
AU  - Rangel WM
AU  - Thijs S
AU  - Moreira FM
AU  - Weyens N
AU  - Vangronsveld J
AU  - Van Hamme JD
AU  - Bottos EM
AU  - Rineau F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00050-16.

PMID- 29348338
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of a Novel Bacterium, Pseudomonas sp. Strain MR 02, Capable of Pyomelanin Production, Isolated from the Mahananda River at Siliguri, West  Bengal, India.
PG  - e01443-17
AB  - The draft genome sequence of a novel strain, Pseudomonas sp. MR 02, a pyomelanin-producing
      bacterium isolated from the Mahananda River at Siliguri,
      West Bengal, India, is reported here. This strain has a genome size of 5.94 Mb,
      with an overall G+C content of 62.6%. The draft genome reports 5,799 genes (mean
      gene length, 923 bp), among which 5,503 are protein-coding genes, including the
      genes required for the catabolism of tyrosine or phenylalanine for the
      characteristic production of homogentisic acid (HGA). Excess HGA, on excretion,
      auto-oxidizes and polymerizes to form pyomelanin.
AU  - Ranjan VK
AU  - Saha T
AU  - Mukherjee S
AU  - Chakraborty R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01443-17.

PMID- 27660778
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Clostridium sp. Strain W14A Isolated from a Cellulose-Degrading Biofilm in a Landfill Leachate Microcosm.
PG  - e00985-16
AB  - Here, we report the draft genome of Clostridium sp. strain W14A, isolated from the anaerobic,
      cellulolytic biofilm of a cotton string sample incubated in a
      landfill leachate microcosm. The draft genome comprises 131 contigs, 3,823,510
      bp, 51.5% G+C content, and 4,119 predicted coding domain sequences.
AU  - Ransom-Jones E
AU  - McDonald JE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00985-16.

PMID- 29700150
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of the Putative Marine Pathogen Aquimarina sp. Strain I32.4.
PG  - e00313-18
AB  - Aquimarina sp. strain I32.4 (formerly Aquimarina sp. 'homaria') is a putative pathogen
      involved in epizootic shell disease in the American lobster (Homarus
      americanus). We report here the draft genome sequence for Aquimarina sp. strain
      I32.4 and describe virulence factors that may provide insight into its mechanism
      of pathogenicity.
AU  - Ranson HJ
AU  - LaPorte J
AU  - Spinard E
AU  - Chistoserdov AY
AU  - Gomez-Chiarri M
AU  - Nelson DR
AU  - Rowley DC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00313-18.

PMID- 29724832
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Loktanella maritima Strain YPC211, a Commensal Bacterium of the American Lobster (Homarus americanus).
PG  - e00314-18
AB  - Loktanella maritima strain YPC211 was isolated from the American lobster (Homarus americanus).
      We report here the draft genome sequence for L. maritima YPC211 and
      identify genes of potential importance to its role within the microbial
      community.
AU  - Ranson HJ
AU  - LaPorte J
AU  - Spinard E
AU  - Gomez-Chiarri M
AU  - Nelson DR
AU  - Rowley DC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00314-18.

PMID- 9580708
VI  - 26
DP  - 1998
TI  - Direct visualization of site-specific and strand-specific DNA methylation patterns in automated DNA sequencing data.
PG  - 2505-2507
AB  - We report here a simple method of directly visualizing in automated DNA sequencing
      chromatograms DNA methylations of different types including cytosine
      methylations in Hpa II and dcm sites as well as adenine methylations in dam
      sites. This is made possible by the observation that the extent of incorporation
      of fluorescently labeled dideoxynucleotides is influenced by the methylated bases
      in template DNA. This simple approach involves routine automated DNA sequencing
      without any prior treatment of DNA specific for detecting DNA methylation.
AU  - Rao BS
AU  - Buckler-White A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1998 26: 2505-2507.

PMID- 26936325
VI  - 18
DP  - 2016
TI  - Active and Adaptive Legionella CRISPR-Cas reveals a recurrent challenge to the pathogen.
PG  - 1319-1338
AB  - CRISPR-Cas systems are widely recognized as critical genome defense systems that protect
      microbes from external threats such as bacteriophage infection. Several isolates of the
      intracellular pathogen Legionella pneumophila possess multiple CRISPR-Cas systems (Type I-C,
      Type I-F, and Type II-B), yet the targets of these systems remain unknown. With the recent
      observation that at least one of these systems (II-B) plays a non-canonical role in supporting
      intracellular replication, the possibility remained that these systems are vestigial genome
      defense systems co-opted for other purposes. Our data indicate this is not the case. Using an
      established plasmid transformation assay, we demonstrate Type I-C, I-F, and II-B CRISPR-Cas
      provide protection against spacer targets. We observe efficient laboratory acquisition of new
      spacers under " priming" conditions, in which initially incomplete target elimination leads to
      the generation of new spacers and ultimate loss of the invasive DNA. Critically, we identify
      the first known target of L. pneumophila CRISPR-Cas: a 30 kilobase episome of unknown function
      whose interbacterial transfer is guarded against by CRISPR-Cas. We provide evidence that the
      element can subvert CRISPR-Cas by mutating its targeted sequences - but that primed spacer
      acquisition may limit this mechanism of escape. Rather than generally impinging on bacterial
      fitness, this element drives a host-specialization event - with improved fitness in
      Acanthamoeba but a reduced ability to replicate in other hosts and conditions. These
      observations add to a growing body of evidence that host-range restriction can serve as an
      existential threat to L. pneumophila in the wild.
AU  - Rao C
AU  - Guyard C
AU  - Pelaz C
AU  - Wasserscheid J
AU  - Bondy-Denomy J
AU  - Dewar K
AU  - Ensminger AW
PT  - Journal Article
TA  - Cell. Microbiol.
JT  - Cell. Microbiol.
SO  - Cell. Microbiol. 2016 18: 1319-1338.

PMID- 23863841
VI  - 42
DP  - 2014
TI  - Type III restriction-modification enzymes: a historical perspective.
PG  - 45-55
AB  - Restriction endonucleases interact with DNA at specific sites leading to cleavage of DNA.
      Bacterial DNA is protected from restriction endonuclease cleavage by modifying the DNA using a
      DNA methyltransferase. Based on their molecular structure, sequence recognition, cleavage
      position and cofactor requirements, restriction-modification (R-M) systems are classified into
      four groups. Type III R-M enzymes need to interact with two separate unmethylated DNA
      sequences in inversely repeated head-to-head orientations for efficient cleavage to occur at a
      defined location (25-27 bp downstream of one of the recognition sites). Like the Type I R-M
      enzymes, Type III R-M enzymes possess a sequence-specific ATPase activity for DNA cleavage.
      ATP hydrolysis is required for the long-distance communication between the sites before
      cleavage. Different models, based on 1D diffusion and/or 3D-DNA looping, exist to explain how
      the long-distance interaction between the two recognition sites takes place. Type III R-M
      systems are found in most sequenced bacteria. Genome sequencing of many pathogenic bacteria
      also shows the presence of a number of phase-variable Type III R-M systems, which play a role
      in virulence. A growing number of these enzymes are being subjected to biochemical and genetic
      studies, which, when combined with ongoing structural analyses, promise to provide details for
      mechanisms of DNA recognition and catalysis.
AU  - Rao DN
AU  - Dryden DT
AU  - Bheemanaik S
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2014 42: 45-55.

PMID- 2708308
VI  - 171
DP  - 1989
TI  - Characterization of mutations of the bacteriophage P1 mod gene encoding the recognition subunit of the EcoPI restriction and modification system.
PG  - 2347-2352
AB  - This study characterized several mutations of the bacteriophage P1 mod gene.
      This gene codes for the subunit of the EcoPI restriction enzyme that is
      responsible for DNA sequence recognition and for modification methylation.  We
      cloned the mutant mod genes into expression vectors and purified the mutant
      proteins to near homogeneity.  Two of the mutant mod genes studied were the c2
      clear-plaque mutants described by Scott (Virology 41:66-71, 1970).  These
      mutant proteins can recognize EcoPI sites in DNA and direct restriction but are
      unable to modify DNA.  Methylation assays as well as S-adenosylmethionine (SAM)
      binding studies showed that the c2 mutants are methylation deficient because
      they do not bind SAM, and we conclude that the mutations destroy the
      SAM-binding site.  Both of the c2 mutations lie within a region of the EcoPI
      mod gene that is not conserved when compared with the mod gene of the related
      EcoPI5 system.  EcoPI5 and EcoPI recognize different DNA sequences, and we
      believe that this region of the protein may code for the DNA-binding site of
      the enzyme.  The other mutants characterized were made by site-directed
      mutagenesis at codon 240.  Evidence is presented that one of them, Ser-240
      ->Pro, simultaneously lost the capacity to bind SAM and may also have changed
      its DNA sequence specificity.
AU  - Rao DN
AU  - Eberle H
AU  - Bickle TA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1989 171: 2347-2352.

PMID- 2585503
VI  - 209
DP  - 1989
TI  - Cloning, over-expression and the catalytic properties of the EcoP15 modification methylase from Escherichia coli.
PG  - 599-606
AB  - The EcoP15 modification methylase gene from the p15B plasmid of Escherichia
      coli 15T- has been cloned and expressed at high levels in a plasmid vector
      system.  We have purified the enzyme to near homogeneity in large amounts and
      have studied some of its enzymatic properties.  Initial rates of methyl
      transfer are first order in methylase concentration and, with a pUC19 DNA as
      substrate, the reaction proceeds by a random mechanism in which either DNA or
      S-adenosylmethionine can bind to the free enzyme.  After methyltransfer to DNA,
      the methylated DNA and S-adenosylhomocysteine appear to dissociate in random
      order.  As expected in such a mechanism, S-adenosylhomocysteine is a
      non-competitive inhibitor with respect to both S-adenosylmethionine and DNA.
      DNA-dependent substrate inhibition by S-adenosylmethionine at concentrations
      not much above its KM suggests that release of methylated DNA may be the
      rate-limiting step.  This suggestion is strengthened by the fact that a mutant
      of the closely related EcoP1 does not show such substrate inhibition.
AU  - Rao DN
AU  - Page MGP
AU  - Bickle TA
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1989 209: 599-606.

PMID- 10697406
VI  - 64
DP  - 2000
TI  - ATP-dependent restriction enzymes.
PG  - 1-63
AB  - The phenomenon of restriction and modification (R-M) was first observed in the course of
      studies on bacteriophages in the early 1950s. It was only in the 1960s that work of Arber and
      colleagues provided a molecular explanation for the host specificity. DNA restriction and
      modification enzymes are responsible for the host-specific barriers to interstrain and
      interspecies transfer of genetic information that have been observed in a variety of bacterial
      cell types. R-M systems comprise an endonuclease and a methyltransferase activity. They serve
      to protect bacterial cells against bacteriophage infection, because incoming foreign DNA is
      specifically cleaved by the restriction enzyme if it contains the recognition sequence of the
      endonuclease. The DNA is protected from cleavage by a specific methylation within the
      recognition sequence, which is introduced by the methyltransferase. Classic R-M systems are
      now divided into three types on the basis of enzyme complexity, cofactor requirements, and
      position of DNA cleavage, although new systems are being discovered that do not fit readily
      into this classification. This review concentrates on multisubunit, multifunctional
      ATP-dependent restriction enzymes. A growing number of these enzymes are being subjected to
      biochemical and genetic studies that, when combined with ongoing structural analyses, promise
      to provide detailed models for mechanisms of DNA recognition and catalysis. It is now clear
      that DNA cleavage by these enzymes involves highly unusual modes of interaction between the
      enzymes and their substrates. These unique features of mechanism pose exciting questions and
      in addition have led to the suggestion that these enzymes may have biological functions beyond
      that of restriction and modification. The purpose of this review is to describe the exciting
      developments in our understanding of how the ATP-dependent restriction enzymes recognize
      specific DNA sequences and cleave or modify DNA.
AU  - Rao DN
AU  - Saha S
AU  - Krishnamurthy V
PT  - Journal Article
TA  - Prog. Nucleic Acid Res. Mol. Biol.
JT  - Prog. Nucleic Acid Res. Mol. Biol.
SO  - Prog. Nucleic Acid Res. Mol. Biol. 2000 64: 1-63.

PMID- Not included in PubMed...
VI  - 18
DP  - 1996
TI  - Development of Chainia as a host for xlanase gene cloning: evidence for occurrence of a restriction-modification system.
PG  - 327-332
AB  - Conditions for genetic transformation of the xylanase-negative (X-) strain of
      Chainia with pIJ 702 were optimized.  The growth of Chainia at 30oC for 36-40h and addition of
      gelatin (1%) to the medium resulted in the maximum yield of protoplasts and regeneration
      efficiency.  Poor transformation efficiency of Chainia (X-) protoplasts by native pIJ 702
      versus
      improved efficiency (16 transformants/ug of plasmid DNA) by prior heating of protoplasts at
      42oC
      for 10 min suggests the occurrence of a restriction system in Chainia.  Increased
      transformation
      efficiency by passage of the plasmid through Chainia together with the altered methylation
      status of
      the transformant plasmid presents evidence for the existence of an operative modification
      system in
      Chainia.  Development of thiostrepton resistance and formation of melamin pigment in Chainia
      (X-
      ) by transformation with pIJ 702 reveal that genes from Streptomyces can be functionally
      expressed by Chainia (X-).
AU  - Rao M
AU  - Suvarna K
AU  - Srinivasan MC
AU  - Vasanti D
PT  - Journal Article
TA  - Biotechnol. Lett.
JT  - Biotechnol. Lett.
SO  - Biotechnol. Lett. 1996 18: 327-332.

PMID- 22689243
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of 'Candidatus Hamiltonella defensa,' an Endosymbiont of the Whitefly Bemisia tabaci.
PG  - 3558
AB  - 'Candidatus Hamiltonella defensa' is a facultative endosymbiont of the whitefly Bemisia
      tabaci. Herein, we report the first draft genome sequence of 'Candidatus
      Hamiltonella defensa' from the invasive Mediterranean cryptic species of the B.
      tabaci complex. The 1.84-Mbp genome sequence comprises 404 contigs and contains
      1,806 predicted protein-coding genes.
AU  - Rao Q
AU  - Wang S
AU  - Su YL
AU  - Bing XL
AU  - Liu SS
AU  - Wang XW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3558.

PMID- 22887655
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Rickettsia sp. Strain MEAM1, Isolated from the Whitefly  Bemisia tabaci.
PG  - 4741-4742
AB  - We report the draft genome sequence of the Rickettsia sp. strain MEAM1, which is  a
      facultative symbiont from an invasive species of the whitefly Bemisia tabaci.
      The total length of the assembled genome is approximately 1.24 Mb, with 335
      scaffolds and 1,247 coding sequences predicted within the genome.
AU  - Rao Q
AU  - Wang S
AU  - Zhu DT
AU  - Wang XW
AU  - Liu SS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4741-4742.

PMID- 24874680
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Field Isolate Brucella melitensis Strain Bm IND1 from India.
PG  - e00497-14
AB  - Brucella spp. are facultative intracellular bacterial pathogens causing the zoonotic disease
      brucellosis. Here, we report the draft genome sequence of the
      Brucella melitensis strain from India designated Bm IND1, isolated from stomach
      contents of an aborted goat fetus.
AU  - Rao SB
AU  - Gupta VK
AU  - Kumar M
AU  - Hegde NR
AU  - Splitter GA
AU  - Reddanna P
AU  - Radhakrishnan GK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00497-14.

PMID- 24889424
VI  - 17
DP  - 2015
TI  - A genomic island integrated into recA of Vibrio cholerae contains a divergent recA and provides multi-pathway protection from DNA damage.
PG  - 1090-1102
AB  - Lateral gene transfer (LGT) has been crucial in the evolution of the cholera
      pathogen, Vibrio cholerae. The two major virulence factors are present on two
      different mobile genetic elements, a bacteriophage containing the cholera toxin
      genes and a genomic island (GI) containing the intestinal adhesin genes.
      Non-toxigenic V. cholerae in the aquatic environment are a major source of novel
      DNA that allows the pathogen to morph via LGT. In this study, we report a novel
      GI from a non-toxigenic V. cholerae strain containing multiple genes involved in
      DNA repair including the recombination repair gene recA that is 23% divergent
      from the indigenous recA and genes involved in the translesion synthesis pathway.
      This is the first report of a GI containing the critical gene recA and the first
      report of a GI that targets insertion into a specific site within recA. We show
      that possession of the island in Escherichia coli is protective against DNA
      damage induced by UV-irradiation and DNA targeting antibiotics. This study
      highlights the importance of genetic elements such as GIs in the evolution of V.
      cholerae and emphasizes the importance of environmental strains as a source of
      novel DNA that can influence the pathogenicity of toxigenic strains.
AU  - Rapa RA
AU  - Islam A
AU  - Monahan LG
AU  - Mutreja A
AU  - Thomson N
AU  - Charles IG
AU  - Stokes HW
AU  - Labbate M
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2015 17: 1090-1102.

PMID- 28153889
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of Legionella pneumophila subsp. fraseri Strains Detroit-1 and Dallas 1E.
PG  - e01525-16
AB  - We report here the complete genome sequences of two of the earliest known strains of
      Legionella pneumophila subsp. fraseri Detroit-1 is serogroup 1 and was
      isolated from a lung biopsy specimen in 1977. Dallas 1E is serogroup 5 and was
      isolated in 1978 from a cooling tower.
AU  - Raphael BH
AU  - Kozak-Muiznieks NA
AU  - Morrison SS
AU  - Mercante JW
AU  - Winchell JM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01525-16.

PMID- 23469350
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Type Strain Clostridium pasteurianum DSM 525 (ATCC 6013), a Promising Producer of Chemicals and Fuels.
PG  - e00232-12
AB  - Clostridium pasteurianum, an anaerobic bacterium able to utilize atmospheric free nitrogen for
      biosynthesis, has recently been proven to be a promising producer of chemicals and fuels, such
      as 1,3-propanediol and n-butanol. Here, we report the high-quality draft genome sequence of
      DSM 525, a type strain of C. pasteurianum.
AU  - Rappert S
AU  - Song L
AU  - Sabra W
AU  - Wang W
AU  - Zeng AP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00232-12.

PMID- 8217304
VI  - 10
DP  - 1993
TI  - Comprehensive restriction enzyme lists to update to any DNA sequence computer program.
PG  - 49-60
AB  - Restriction enzyme lists are presented for the practical working geneticist to update any DNA
      computer program. These lists combine formerly scattered information and contain all presently
      known restriction enzymes with a unique recognition sequence, a cut site, or methylation
      (in)sensitivity. The lists are in the shortest possible form to also be functional with small
      DNA computer programs, and will produce clear restriction maps without any redundancy or loss
      of information. The lists discern between commercial and noncommercial enzymes, and prototype
      enzymes and different isoschizomers are cross-referenced. Differences in general methylation
      sensitivities and (in)sensitivities against Dam and Dcm methylases of Escherichia coli are
      indicated. Commercial methylases and intron-encoded endonucleases are included. An address
      list is presented to contact commercial suppliers. The lists are constantly updated and
      available in electronic form as pure US ASCI filed, and in formats for the DNA computer
      programs DNA-Strider for Apple Macintosh, and DNAsis for IBM personal computers or compatibles
      via e-mail from the internet address: NETSERV@EMBLHEIDELBERG.DE by sending only the message
      HELP RELIBRARY.
AU  - Raschke E
PT  - Journal Article
TA  - Genet. Anal. Tech. Appl.
JT  - Genet. Anal. Tech. Appl.
SO  - Genet. Anal. Tech. Appl. 1993 10: 49-60.

PMID- 26950326
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Three Novel Clostridium Isolates from Northern Iraq.
PG  - e00033-16
AB  - Three Clostridium sp. strains were isolated from soil and sediment collected from the
      Kurdistan region of Iraq. All three isolates were found to harbor putative
      prophages, with a CRISPR-Cas system found in strains C105KSO13 and C105KSO14.
AU  - Rashid SR
AU  - Clokie MR
AU  - Millard AD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00033-16.

PMID- 28883146
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Gluten-Hydrolyzing Bacterium Bacillus subtilis GS 188, Isolated from Wheat Sourdough.
PG  - e00952-17
AB  - The draft genome sequence of Bacillus subtilis GS 188, a novel spore-forming probiotic
      bacterium with gluten-hydrolyzing potential, was isolated from wheat
      sourdough and provides deep insights into the beneficial features of this strain
      for its use in the preparation of gluten-reduced wheat foods for humans with
      celiac disease.
AU  - Rashmi BS
AU  - Gayathri D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00952-17.

PMID- 21793740
VI  - 365
DP  - 2011
TI  - Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany.
PG  - 709-717
AB  - BACKGROUND: A large outbreak of diarrhea and the hemolytic-uremic syndrome
      caused by an unusual serotype of Shiga-toxin-producing Escherichia coli
      (O104:H4) began in Germany in May 2011. As of July 22, a large number of
      cases of diarrhea caused by Shiga-toxin-producing E. coli have been
      reported--3167 without the hemolytic-uremic syndrome (16 deaths) and 908
      with the hemolytic-uremic syndrome (34 deaths)--indicating that this
      strain is notably more virulent than most of the Shiga-toxin-producing E.
      coli strains. Preliminary genetic characterization of the outbreak strain
      suggested that, unlike most of these strains, it should be classified
      within the enteroaggregative pathotype of E. coli. METHODS: We used
      third-generation, single-molecule, real-time DNA sequencing to determine
      the complete genome sequence of the German outbreak strain, as well as the
      genome sequences of seven diarrhea-associated enteroaggregative E. coli
      serotype O104:H4 strains from Africa and four enteroaggregative E. coli
      reference strains belonging to other serotypes. Genomewide comparisons
      were performed with the use of these enteroaggregative E. coli genomes, as
      well as those of 40 previously sequenced E. coli isolates. RESULTS: The
      enteroaggregative E. coli O104:H4 strains are closely related and form a
      distinct clade among E. coli and enteroaggregative E. coli strains.
      However, the genome of the German outbreak strain can be distinguished
      from those of other O104:H4 strains because it contains a prophage
      encoding Shiga toxin 2 and a distinct set of additional virulence and
      antibiotic-resistance factors. CONCLUSIONS: Our findings suggest that
      horizontal genetic exchange allowed for the emergence of the highly
      virulent Shiga-toxin-producing enteroaggregative E. coli O104:H4 strain
      that caused the German outbreak. More broadly, these findings highlight
      the way in which the plasticity of bacterial genomes facilitates the
      emergence of new pathogens.
AU  - Rasko DA et al
PT  - Journal Article
TA  - N. Engl. J. Med.
JT  - N. Engl. J. Med.
SO  - N. Engl. J. Med. 2011 365: 709-717.

PMID- 14960714
VI  - 32
DP  - 2004
TI  - The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1.
PG  - 977-988
AB  - We sequenced the complete genome of Bacillus cereus ATCC 10987, a non-lethal dairy isolate in
      the same genetic subgroup as Bacillus anthracis. Comparison of the chromosomes demonstrated
      that B.cereus ATCC 10987 was more similar to B.anthracis Ames than B.cereus ATCC 14579, while
      containing a number of unique metabolic capabilities such as urease and xylose utilization and
      lacking the ability to utilize nitrate and nitrite. Additionally, genetic mechanisms for
      variation of capsule carbohydrate and flagella surface structures were identified. Bacillus
      cereus ATCC 10987 contains a single large plasmid (pBc10987, of  208 kb, that is similar in
      gene content and organization to B.anthracis pXO1 but is lacking the pathogenicity-associated
      island containing the anthrax lethal and edema toxin complex genes. The chromosomal similarity
      of B.cereus ATCC 10987 to B.anthracis Ames, as well as the fact that it contains a large
      pXO1-like plasmid, may make it a possible model for studying B.anthracis plasmid biology and
      regulatory cross-talk.
AU  - Rasko DA
AU  - Ravel J
AU  - Okstad OA
AU  - Helgason E
AU  - Cer RZ
AU  - Jiang L
AU  - Shores KA
AU  - Fouts DE
AU  - Tourasse NJ
AU  - Angiuoli SV
AU  - Kolonay J
AU  - Nelson WC
AU  - Kolsto A-B
AU  - Fraser CM
AU  - Read TD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2004 32: 977-988.

PMID- 20587501
VI  - 38
DP  - 2010
TI  - BspRI restriction endonuclease: cloning, expression in Escherichia coli and sequential cleavage mechanism.
PG  - 7155-7166
AB  - The GGCC-specific restriction endonuclease BspRI is one of the few Type IIP restriction
      endonucleases, which were suggested to be a monomer. Amino
      acid sequence information obtained by Edman sequencing and mass
      spectrometry analysis was used to clone the gene encoding BspRI. The
      bspRIR gene is located adjacently to the gene of the cognate modification
      methyltransferase and encodes a 304 aa protein. Expression of the bspRIR
      gene in Escherichia coli was dependent on the replacement of the native
      TTG initiation codon with an ATG codon, explaining previous failures in
      cloning the gene using functional selection. A plasmid containing a single
      BspRI recognition site was used to analyze kinetically nicking and
      second-strand cleavage under steady-state conditions. Cleavage of the
      supercoiled plasmid went through a relaxed intermediate indicating
      sequential hydrolysis of the two strands. Results of the kinetic analysis
      of the first- and second-strand cleavage are consistent with cutting the
      double-stranded substrate site in two independent binding events. A
      database search identified eight putative restriction-modification systems
      in which the predicted endonucleases as well as the methyltransferases
      share high sequence similarity with the corresponding protein of the BspRI
      system. BspRI and the related putative restriction endonucleases belong to
      the PD-(D/E)XK nuclease superfamily.
AU  - Rasko T
AU  - Der A
AU  - Klement E
AU  - Slaska-Kiss K
AU  - Posfai E
AU  - Medzihradszky KF
AU  - Marshak DR
AU  - Roberts RJ
AU  - Kiss A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2010 38: 7155-7166.

PMID- 10931923
VI  - 28
DP  - 2000
TI  - DNA bending induced by DNA (cytosine-5) methyltransferases.
PG  - 3083-3091
AB  - DNA bending induced by six DNA (cytosine-5) methyltransferases was studied using circular
      permutation gel mobility shift assay. The following bend angles were obtained: M.BspRI
      (GG(m5)CC), 46-50 degrees; M.HaeIII (GG(m5)CC), 40-43 degrees; M.SinI (GGW(m5)CC), 34-37
      degrees; M.Sau96I (GGN(m5)CC), 52-57 degrees; M.HpaII (C(m5)CGG), 30 degrees; and M.HhaI
      (G(m5)CGC), 13 degrees. M.HaeIII was also tested with fragments carrying a methylated binding
      site, and it was found to induce a 32 degrees bend. A phase-sensitive gel mobility shift
      assay, using a set of DNA fragments with a sequence-directed bend and a single
      methyltransferase binding site, indicated that M.HaeIII and M.BspRI bend DNA toward the
      minor groove. The DNA curvature induced by M.HaeIII contrasts with the lack of DNA bend
      observed for a covalent M.HaeIII-DNA complex in an earlier X-ray study. Our results and data
      from other laboratories show a correlation between the bending properties and the recognition
      specificities of (cytosine-5) methyltransferases: enzymes recognizing a cytosine 3' to the
      target cytosine tend to induce greater bends than enzymes with guanine in this position. We
      suggest that the observed differences indicate different mechanisms employed by (cytosine-5)
      methyltransferases to stabilize the helix after the target base has flipped out.
AU  - Rasko T
AU  - Finta C
AU  - Kiss A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2000 28: 3083-3091.

PMID- 26893427
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Type Strain Streptococcus gordonii ATCC 10558.
PG  - e01745-15
AB  - Streptococcus gordonii ATCC 10558(T) was isolated from a patient with infective endocarditis
      in 1946 and announced as a type strain in 1989. Here, we report the
      2,154,510-bp draft genome sequence of S. gordonii ATCC 10558(T). This sequence
      will contribute to knowledge about the pathogenesis of infective endocarditis.
AU  - Rasmussen LH
AU  - Dargis R
AU  - Christensen JJ
AU  - Skovgaard O
AU  - Nielsen XC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01745-15.

PMID- 7607492
VI  - 157
DP  - 1995
TI  - Growth-rate-dependent transcription initiation from the dam P2 promoter.
PG  - 213-215
AB  - Transcription of the dam gene in Escherichia coli is dependent on growth rate.  Using
      single-copy promoter::lacZYA fusions we found that of the five promoter regions which affect
      dam expression, only the P2 promoter shows growth-rate dependence.  The determinants for
      growth-rate control must lie in the region -52 to +27 relative to the transcription start
      point.
AU  - Rasmussen LJ
AU  - Lobner-Olesen A
AU  - Marinus MG
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 213-215.

PMID- 8487553
VI  - 17E
DP  - 1993
TI  - Regulation of expression of the dam methyltransferase gene (dam) from Escherichi coli.
PG  - 303
AB  - The level of Dam protein (DNA adenine methyltransferase) in E. coli is critical for the
      efficient action of Dam-directed mismatch repair and synchronous initiation of chromosome
      replication from oriC. A drastic increase or decrease from the normal level of 130 molecules
      per cell causes hypermutability and asynchronous initiation. The Dam methyltransferase is
      encoded by the dam gene located at 74 min on the genetic map. The dam gene is part of a
      transcriptional unit which includes five promoters and at least four genes: aroK (shikimic
      acids kinase I), aroB (3-dehydroquinate synthase), urf74.3 (an unidentified open reading
      frame) and dam (Dam methyltransferase). As a first step to elucidate the mechanism of
      regulation we have found that the expression of the dam gene is growth rate regulated and
      coordinated with cell growth. In order to determine the region responsible for this regulation
      we have separated and characterized the promoters individually.
AU  - Rasmussen LJ
AU  - Marinus MG
AU  - Lcbner-Olesen A
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1993 17E: 303.

PMID- 7934887
VI  - 12
DP  - 1994
TI  - Novel growth rate control of dam gene expression in Escherichia coli.
PG  - 631-638
AB  - Transcription of the dam gene in Escherichia coli is growth rate regulated by a mechanism
      distinct from that used for ribosomal RNA gene promoters.
      Single-copy operon fusions to lacZ indicated that the major promoter, P2,
      is responsible for most or all of the growth rate dependence. Promoter P2
      is a typical sigma 70 promoter with 18 bp spacing between the -10 and -35
      hexamers. Primer extension analysis was used to show that there was no
      inhibition of transcription from promoter P2 in cells induced for the
      stringent response. Beta-galactosidase specific activity from a
      single-copy dam::lacZ fusion was unaffected by either excess rrnB RNA or
      the level of Fis protein. Thus growth rate control of dam gene expression
      differs from that of the rRNA and tRNA genes by its lack of response to
      stringent control, ribosomal feedback and enhanced transcription by Fis
      protein. We devised a procedure for selection of mutant cells in which dam
      gene expression was unregulated. One such mutant (cde-4), obtained by
      miniTn10 insertion, showed the same level of beta-galactosidase activity
      at all growth rates tested. In contrast, growth rate-dependent expression
      of the rrnB gene was unaffected by cde-4 confirming the different modes of
      regulation. The cde-4::miniTn10 insertion is located close to kilobase 670
      on the physical map in or near the lipB gene.
AU  - Rasmussen LJ
AU  - Marinus MG
AU  - Lobner-Olesen A
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1994 12: 631-638.

PMID- 
VI  - 1
DP  - 1998
TI  - Dam-directed DNA mismatch repair.
PG  - 205-228
AB  - Base mismatches in duplex DNA are repaired by a variety of systems in Escherichia coli,
      including: Very Short Patch repair; MutY-dependent repair; and DNA adenine
      methyltransferase-directed DNA mismatch repair.  The first two systems have a restricted
      substrate specificity (T.G and A.G mismatches, respectively), whereas the third system can
      repair 11 out of the 12 possible base mispairs with only the C.C mismatch being refractory.
      There is no known repair pathway for C.C mismatches in duplex DNA.  The DDMR pathway also acts
      on insertions/deletions ("loops") of up to 4 bases.  In this chapter are reviewed the VSP
      repair and DDMR systems with emphasis on the latter.  The MutY-pathway is discussed in Chapter
      6.
AU  - Rasmussen LJ
AU  - Samson L
AU  - Marinus MG
PT  - Journal Article
TA  - DNA Damage and Repair
JT  - DNA Damage and Repair
SO  - DNA Damage and Repair 1998 1: 205-228.

PMID- 11234385
VI  - 35
DP  - 2001
TI  - Alleviation of type I restriction in Escherichia coli K12 in the presence of the arsR gene from pKW301 of Acidiphilium multivorum AIU 301.
PG  - 79-82
AB  - A study was made of the antirestriction activity of Acidiphilium multivorum AIU 301 ArsR, a
      repressor of the ars operon which confers resistance to arsenite and arsenate and is on
      pKW301. In Escherichia coli, arsR cloned under the control of Plac in a multi-copy vector
      alleviated restriction of nonmodified lambda DNA by a factor of 120, six times more
      efficiently than its analogs of conjugal plasmids R64 (incI1) and R773 (incFI). Amino acid
      sequence analysis showed that the three ArsR proteins have a homologous region of 38 residues,
      including the antirestriction motif, in their N domains, whereas the motif is in the C domain
      in the Ard proteins. The other regions are nonhomologous, and pKW301 ArsR is 33 residues
      shorter than R64 and R773 ArsRs. The total charge is -4 in pKW301 ArsR and +2 in R64 and R733
      ArsRs. A total negative charge was assumed to contribute to the antirestriction activity.
AU  - Rastorguev SM
AU  - Zavilgelskii GB
AU  - Suzuki K
AU  - Sakka K
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2001 35: 79-82.

PMID- 12669426
VI  - 39
DP  - 2003
TI  - Role of "antirestriction" motif in functional activity of antirestriction protein ArdA pKM101 (IncN).
PG  - 286-292
AB  - A number of mutant forms of the antirestriction protein ArdA encoded by the ardA gene located
      in a transmissive IncN plasmid pKM101 have been
      constructed. Proteins belonging to the Ard family are specific inhibitors
      of type I restriction--modification enzymes. Single mutational
      substitutions of negatively charged amino acid residues located in the
      "antirestriction motif" with hydrophobic alanine, E134A, E137A, D144A, or
      a double substitution E134A, E137A do not affect the antirestriction
      activity (Ard) of ArdA but almost completely abolish the antimodification
      activity (Amd). Mutational substitutions F107D and A110D in the assumed
      interface ArdA, which determines contact between monomers in the active
      dimer (Ard)2, cause an approximately 100-fold decrease in the
      antirestriction protein activity. It is hypothesized that the ArdA protein
      forms two complexes with the type I restriction--modification enzyme
      (R2M2S): (1) with a specific region in the S subunit involved in contact
      with the sK site in DNA; and (2) with a nonspecific region in the R
      subunit involved in DNA translocation and degradation by restriction
      endonucleases. The association of ArdA with the specific region inhibits
      restriction endonuclease and methyltransferase activities simultaneously,
      whereas the association of ArdA with a nonspecific region inhibits only
      restriction endonuclease activity of the R2M2S enzyme.
AU  - Rastorguev SM
AU  - Zavilgelsky GB
PT  - Journal Article
TA  - Genetika
JT  - Genetika
SO  - Genetika 2003 39: 286-292.

PMID- 9598970
VI  - 426
DP  - 1998
TI  - IncI1 plasmid R64 encodes the ArsR protein that alleviates type I restriction.
PG  - 21-23
AB  - The host-controlled EcoK restriction of unmodified phage lambda was five-fold alleviated in
      the wild-type Escherichia coli strain K12 carrying the R64 plasmid of the incompatibility
      group I1. The relevant gene was mapped between the origin of vegetative replication (rep,
      oriV) and the tet(r) gene about 60 kbp downstream from the origin of transfer, oriT. We cloned
      this gene inside the 613 bp long EcoRI-PstI fragment and sequenced it. Only one 351 bp long
      open reading frame (ORF) starting at 124 bp from the beginning of the insert was found in the
      sequence. Computer search in the current databases revealed that the putative protein is
      identical to the ArsR protein specified by the IncFI plasmid R773. ArsR is a repressor of the
      arsenical resistance (ars) operon, arsRDABC. There are no arsABC genes in the R64 plasmid
      since plasmid R64- (or pSR8)-mediated resistance of E. coli K12 cells to the arsenicals
      arsenate and arsenite was not detected. The gene arsR and the antirestriction genes ard (ardA
      and ardB) are non-homologous. However, comparison of the deduced amino acid sequence of ArsR
      with the ArdA and ArdB sequences revealed only one small region of similarity, a 9 amino acid
      motif found in different antirestriction proteins that is hypothesized to be an interaction
      site for antirestriction proteins with restriction endonucleases.
AU  - Rastorguev SM
AU  - Zavilgelsky GB
AU  - Tchurikov NA
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1998 426: 21-23.

PMID- 17195251
VI  - 8
DP  - 2007
TI  - Reversible inactivation of the CG specific Sssl DNA (cytosine-C5)-methyltransferase with a photocleavable protecting group.
PG  - 202-207
AB  - Caging of proteins by conjugation with a photocleavable group is a powerful approach for
      reversibly blocking enzymatic activity. Here we
      describe the covalent modification of the bacterial Sssl DNA
      methyltransferase (M.Sssl) with the cysteine-specific reagent
      4,5-dimethoxy-2-nitrobenzyibromide (DMNBB). M.Sssl contains two
      cysteine residues; replacement of the active-site Cys141 with Ser
      resulted in an approximately 700-fold loss of enzymatic activity; this
      indicates an important role for this residue in catalysis. However,
      replacement of Cys368 with Ala did not affect methyltransferase
      activity. Treatment of the Cys368Ala mutant enzyme with DMNBB led to an
      almost complete loss of activity. Irradiation of the inactivated enzyme
      with near-ultraviolet light (320400 nm) restored 60% of the catalytic
      activity. This indicates that caging by DMNBB can be used for the
      reversible inactivation of M.Sssl.
AU  - Rathert P
AU  - Rasko T
AU  - Roth M
AU  - Slaska-Kiss K
AU  - Pingoud A
AU  - Kiss A
AU  - Jeltsch A
PT  - Journal Article
TA  - Chembiochem
JT  - Chembiochem
SO  - Chembiochem 2007 8: 202-207.

PMID- 8370544
VI  - 131
DP  - 1993
TI  - A new restriction endonuclease, TspEI, from the genus Thermus that generates cohesive termini compatible with those of EcoRI.
PG  - 83-86
AB  - The detection, isolation and properties of the restriction endonuclease TspEI are described.
      The canonical recognition sequence (AATT) is the same as the 4-bp core of the 6-bp sequence
      (GAATTC) of EcoRI. Hydrolysis occurs 5' to the palindromic tetramer so that TspEI produces
      the same cohesive termini as EcoRI. TspEI therefore has an obvious application in producing
      partial digests of DNA for ligation to EcoRI-digested cloning vectors.
AU  - Raven NDH
AU  - Kelly CD
AU  - Carter ND
AU  - Eastlake P
AU  - Brown C
AU  - Williams RAD
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1993 131: 83-86.

PMID- 8415002
VI  - 21
DP  - 1993
TI  - Tsp45I, a new thermostable site-specific endonuclease that cleaves the recognition sequence 5'-GTSAC-3'.
PG  - 4397
AB  - A site-specific nuclease from Thermus strain 45 was purified by ammonium sulphate
      fractionation and then by chromatography on Phospho-Ultrogel, DEAE-Fractogel 650 M, and
      Sephadex G200 columns. The Mr by gel filtration was 80 kD, and a single band on SDS-PAGE was
      estimated as 38 kD. On the basis of the fragment pattern of digests of pBR322 and phiX174 RF
      DNA< and by reference to reported fragment sizes for these substrates, it was concluded that
      the recognition site was GTSAC. This was confirmed by the identity of Tsp45I patterns with
      those predicted by computer simulations of substrate hydrolysis at this site (kindly provided
      by R.Roberts), and by the agreement between observed and expected fragment sized for digests
      of lambda DNA, M13mp18RF DNA, pHC624 and pUC18. The optimum activity was observed at 65oC in
      10 mM Tris chloride buffer, pH7.3 at 25oC containing no NaCl, l mM MgCl2, 2 mM dithiothreitol
      and 100 mg/l albumin. The enzyme has a low requirement for inorganic ions, indeed activity was
      detected even when magnesium ions were omitted from the assay buffer. The cleavage points were
      determined by the primed synthesis method from the M13 -40 sequencing primer on a recognition
      site provided by two complementary synthetic oligonucleotides 5'CCGTCGACGTGACGGATCCCC and 5'
      GGGGATCCGTCACGTCGACGG that were annealed together and digested with SalI and BamHI. The
      central fragment that contained the recognition site was ligated into M13mp8 digested with the
      same enzymes and DNA was extracted and purified. The hydrolysis sites of Tsp45I (Figure 1) lie
      outside the recognition site, 5' to the G residues in each strand: 5'^GTGAC-3', 3'-CACTG^5'.
AU  - Raven NDH
AU  - Williams RAD
AU  - Smith KE
AU  - Kelly CD
AU  - Carter ND
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 4397.

PMID- 353810
VI  - 75
DP  - 1978
TI  - Nucleotide sequence of the recognition site for the restriction-modification enzyme of Escherichia coli B.
PG  - 2266-2270
AB  - The nucleotide sequence of the recognition site for the restriction-modifiction
      enzyme of Escherichia coli B (SB site) has been determined.  The recognition
      site is a 15-nucleotide sequence consisting of the trimer 5'TGA3', followed by
      an 8-nucleotide domain of variable sequence, which in turn is followed by the
      tetramer 5'TGCT3'.  The sequence has no 2-fold rotational symmetry.  Single
      base changes in the constant nucleotide domains result in the loss of
      sensitivity to both restriction and modification.  Our data are also consistent
      with modification occurring by methylation of two adenine residues per SB site:
      one on the adenine of the trimer 5'TGA3' and the other on the complementary
      strand on the adenine complementary to the first thymine of the tetramer
      5'TGCT3'.  All nine independently isolated spontaneous mutants at the SB1 site
      of bacteriophage f1 are caused by a C-to-T transversion.  Mutations at the SB2
      site are caused by various single base changes.
AU  - Ravetch JV
AU  - Horiuchi K
AU  - Zinder ND
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1978 75: 2266-2270.

PMID- 2989655
VI  - 198
DP  - 1985
TI  - Transposon mutagenesis and genetic mapping of the rglA and rglB loci of Escherichia coli.
PG  - 390-392
AB  - The rglA and rglB genes code for two different proteins which cleave the
      hydroxymethylated cytosine residues of T-even phages.  We isolated Tn10 and Tn5
      insertion mutants of the above genes and of the genes in and around the rglA
      and rglB loci.  These insertions were used to cocnstruct a detailed genetic
      map.  Our results show that the rglA gene maps at 25.24 min and the rglB gene
      at 98.39 min on the standard Escherichia coli K12 genetic map.
AU  - Ravi RS
AU  - Sozhamannan S
AU  - Dharmalingam K
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1985 198: 390-392.

PMID- 19114480
VI  - 191
DP  - 2009
TI  - Complete genome sequence of the anaerobic, protein-degrading hyperthermophilic crenarchaeon Desulfurococcus kamchatkensis.
PG  - 2371-2379
AB  - Desulfurococcus kamchatkensis is an anaerobic organotrophic hyperthermophilic crenarchaeon
      isolated from a terrestrial hot spring. Its
      genome consists of a single circular chromosome of 1365223 bp with no
      extrachromosomal elements. A total of 1474 protein-coding genes were
      annotated of which 205 are exclusive for D. kamchatkensis. The search for
      a replication origin site revealed a single region coinciding with a
      global extreme of the nucleotide composition disparity curve and
      containing a set of crenarchaeal-type origin recognition boxes. Unlike in
      most archaea, two genes encoding homologs of eukaryotic initiator proteins
      Orc1/Cdc6 are located distantly from this site. A number of mobile
      elements are present in the genome, including seven transposons
      representing IS607 and IS200/IS605 families, and multiple copies of
      miniature inverted repeat transposable elements. Two large clusters of
      regularly interspaced repeats are present; none of the spacer sequences
      matches with known archaeal extrachromosomal elements except that one
      spacer matches the sequence of a resident gene of D. kamchatkensis. Many
      of the predicted metabolic enzymes are associated with the fermentation of
      peptides and sugars, including more than thirty peptidases with diverse
      specificities, a number of polysaccharide degradation enzymes, and many
      transporters. Consistently, the genome encodes both enzymes of the
      modified Embden-Meyerhof pathway of glucose oxidation and a set of enzymes
      needed for gluconeogenesis. The genome structure and content reflect the
      organism's nutritionally diverse, competitive natural environment
      periodically invaded by viruses and other mobile elements.
AU  - Ravin NV
AU  - Mardanov AV
AU  - Beletsky AV
AU  - Kublanov IV
AU  - Kolganova TV
AU  - Lebedinsky AV
AU  - Chernyh NA
AU  - Bonch-Osmolovskaya EA
AU  - Skryabin KG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2009 191: 2371-2379.

PMID- 11948159
VI  - 184
DP  - 2002
TI  - A conserved C-terminal region in Gp71 of the small isometric-head phage LL-H and ORF474 of the prolate-head phage JCL1032 is implicated in  specificity of adsorption of phage to its host, Lactobacillus  delbrueckii.
PG  - 2455-2459
AB  - Thirty-five phage-resistant mutants of Lactobacillus delbrueckii subsp. lactis ATCC 15808 were
      selected. Thirty-three of these mutants were
      assigned to the Bes group, while the remaining two were grouped under
      the Ads designation. Bes group mutants adsorbed phage LL-H but did not
      allow efficient phage development. Preliminary evidence suggests that
      these strains exhibit a mutation that changes the DNA specificity of a
      restriction-modification system. The Ads group mutants did not adsorb
      the small isometric-head phage LL-H. The results suggest that there are
      at least three different types of phage receptors in L. delbrueckii:
      two that are specific for small isometric-head phages and one that is
      specific for prolate-head phage JCL1032. Five LL-H host-range mutants
      which could overcome the adsorption block (a-type mutants) were
      selected and investigated by sequencing the genes g71 and g17, which
      encode minor and major tail proteins, respectively. Each of the a-type
      mutants carried a nucleotide change at the 3' end of gene g71. No
      mutations were observed in gene g17. Comparison of the gene product of
      g71 of phage LL-H with its homolog in JCL1032 (ORF474) showed that
      these proteins had very similar C-terminal regions. No similarities
      were found at the N-terminal part of the proteins. We conclude that the
      C-terminal portion of the protein encoded by g71 of phage LL-H and its
      homolog in phage JCL1032 determines the adsorption specificities of
      these phages on L. delbrueckii.
AU  - Ravin V
AU  - Raisanen L
AU  - Alatossava T
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2002 184: 2455-2459.

PMID- 10860722
VI  - 299
DP  - 2000
TI  - Genomic sequence and analysis of the atypical temperate bacteriophage N15.
PG  - 53-73
AB  - N15 is a temperate bacteriophage that forms stable lysogens in Escherichia coli. While its
      virion is morphologically very similar to
      phage lambda and its close relatives, it is unusual in that the
      prophage form replicates autonomously as a linear DNA molecule with
      closed hairpin telomeres. Here, we describe the genomic architecture of
      N15, and its global pattern of gene expression, which reveal that N15
      contains several plasmid-derived genes that are expressed in N15
      lysogens. The tel site, at which processing occurs to form the prophage
      ends is close to the center of the genome in a similar location to that
      occupied by the attachment site, attP, in lambda and its relatives and
      defines the boundary between the left and right arms. The left arm
      contains a long cluster of structural genes that are closely related to
      those of the lambda-like phages, but also includes homologs of umuD',
      which encodes a DNA polymerase accessory protein, and the plasmid
      partition genes, sopA and sopB. The right arm likewise contains a
      mixture of apparently phage- and plasmid-derived genes including genes
      encoding plasmid replication functions, a phage repressor, a
      transcription antitermination system, as well as phage host cell lysis
      genes and two putative DNA methylases. The unique structure of the N15
      genome suggests that the large global population of bacteriophages may
      exhibit a much greater diversity of genomic architectures than was
      previously recognized.
AU  - Ravin V
AU  - Ravin N
AU  - Casjens S
AU  - Ford ME
AU  - Hatfull GF
AU  - Herdrix RW
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2000 299: 53-73.

PMID- 25940918
VI  - 4
DP  - 2015
TI  - Comparative genomics of Pseudomonas syringae pv. syringae strains B301D and HS191 and insights into intrapathovar traits associated with plant pathogenesis.
PG  - 553-573
AB  - Pseudomonas syringae pv. syringae is a common plant-associated bacterium that
      causes diseases of both monocot and dicot plants worldwide. To help delineate
      traits critical to adaptation and survival in the plant environment, we generated
      complete genome sequences of P. syringae pv. syringae strains B301D and HS191,
      which represent dicot and monocot strains with distinct host specificities.
      Intrapathovar comparisons of the B301D (6.09 Mb) and HS191 (5.95 Mb plus a 52 kb
      pCG131 plasmid) genomes to the previously sequenced B728a genome demonstrated
      that the shared genes encompass about 83% of each genome, and include genes for
      siderophore biosynthesis, osmotolerance, and extracellular polysaccharide
      production. Between 7% and 12% of the genes are unique among the genomes, and
      most of the unique gene regions carry transposons, phage elements, or IS elements
      associated with horizontal gene transfer. Differences are observed in the type
      III effector composition for the three strains that likely influences host range.
      The HS191 genome had the largest number at 25 of effector genes, and seven
      effector genes are specific to this monocot strain. Toxin production is another
      major trait associated with virulence of P. syringae pv. syringae, and HS191 is
      distinguished by genes for production of syringopeptin SP25 and mangotoxin.
AU  - Ravindran A
AU  - Jalan N
AU  - Yuan JS
AU  - Wang N
AU  - Gross DC
PT  - Journal Article
TA  - Microbiologyopen
JT  - Microbiologyopen
SO  - Microbiologyopen 2015 4: 553-573.

PMID- 22887673
VI  - 194
DP  - 2012
TI  - Whole-Genome Shotgun Sequencing of the Extremophile Alkalibacillus haloalkaliphilus C-5, of Indian Origin.
PG  - 4775
AB  - Alkalibacillus haloalkaliphilus C-5 is a haloalkaliphilic bacterium that was isolated from a
      soil sample from the salty Sambhar Lake, Rajasthan, India. The
      organism is capable of alkaline protease production under conditions of pH 10 and
      10% (wt/vol) salt. We sequenced and have reported the whole genome of
      Alkalibacillus haloalkaliphilus C-5, of Indian origin, for the first time.
AU  - Rawal CM
AU  - Raval VH
AU  - Bhimani HD
AU  - Bhensdadia DV
AU  - Kothari CR
AU  - Patel AB
AU  - Bhatt VD
AU  - Parmar NR
AU  - Sajnani MR
AU  - Koringa PG
AU  - Joshi CG
AU  - Kothari RK
AU  - Singh SP
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4775.

PMID- 23450133
VI  - 7
DP  - 2012
TI  - Complete genome sequence of Terriglobus saanensis type strain SP1PR4(T), an Acidobacteria from tundra soil.
PG  - 59-69
AB  - SP1PR4 is a novel species of the genus . is of ecological interest because it is  a
      representative of the phylum , which are dominant members of bacterial soil
      microbiota in Arctic ecosystems. is a cold-adapted acidophile and a versatile
      heterotroph utilizing a suite of simple sugars and complex polysaccharides. The
      genome contained an abundance of genes assigned to metabolism and transport of
      carbohydrates including gene modules encoding for carbohydrate-active enzyme
      (CAZyme) family involved in breakdown, utilization and biosynthesis of diverse
      structural and storage polysaccharides. SP1PR4 represents the first member of
      genus with a completed genome sequence, consisting of a single replicon of
      5,095,226 base pairs (bp), 54 RNA genes and 4,279 protein-coding genes. We infer
      that the physiology and metabolic potential of is adapted to allow for resilience
      to the nutrient-deficient conditions and fluctuating temperatures of Arctic
      tundra soils.
AU  - Rawat SR
AU  - Mannisto MK
AU  - Starovoytov V
AU  - Goodwin L
AU  - Nolan M
AU  - Hauser L
AU  - Land M
AU  - Davenport KW
AU  - Woyke T
AU  - Haggblom MM
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 7: 59-69.

PMID- 25197431
VI  - 9
DP  - 2014
TI  - Complete genome sequence of Granulicella tundricola type strain MP5ACTX9(T), an Acidobacteria from tundra soil.
PG  - 449-461
AB  - Granulicella tundricola strain MP5ACTX9(T) is a novel species of the genus Granulicella in
      subdivision 1 Acidobacteria. G. tundricola is a predominant
      member of soil bacterial communities, active at low temperatures and nutrient
      limiting conditions in Arctic alpine tundra. The organism is a cold-adapted
      acidophile and a versatile heterotroph that hydrolyzes a suite of sugars and
      complex polysaccharides. Genome analysis revealed metabolic versatility with
      genes involved in metabolism and transport of carbohydrates, including gene
      modules encoding for the carbohydrate-active enzyme (CAZy) families for the
      breakdown, utilization and biosynthesis of diverse structural and storage
      polysaccharides such as plant based carbon polymers. The genome of G. tundricola
      strain MP5ACTX9(T) consists of 4,309,151 bp of a circular chromosome and five
      mega plasmids with a total genome content of 5,503,984 bp. The genome comprises
      4,705 protein-coding genes and 52 RNA genes.
AU  - Rawat SR
AU  - Mannisto MK
AU  - Starovoytov V
AU  - Goodwin L
AU  - Nolan M
AU  - Hauser L
AU  - Land M
AU  - Davenport KW
AU  - Woyke T
AU  - Haggblom MM
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 449-461.

PMID- 24501646
VI  - 9
DP  - 2013
TI  - Complete genome sequence of Granulicella mallensis type strain MP5ACTX8(T), an acidobacterium from tundra soil.
PG  - 71-82
AB  - Granulicella mallensis MP5ACTX8(T) is a novel species of the genus Granulicella in subdivision
      1of Acidobacteria. G. mallensis is of ecological interest being a
      member of the dominant soil bacterial community active at low temperatures and
      nutrient limiting conditions in Arctic alpine tundra. G. mallensis is a
      cold-adapted acidophile and a versatile heterotroph that hydrolyzes a suite of
      sugars and complex polysaccharides. Genome analysis revealed metabolic
      versatility with genes involved in metabolism and transport of carbohydrates.
      These include gene modules encoding the carbohydrate-active enzyme (CAZyme)
      family involved in breakdown, utilization and biosynthesis of diverse structural
      and storage polysaccharides including plant based carbon polymers. The genome of
      Granulicella mallensis MP5ACTX8(T) consists of a single replicon of 6,237,577
      base pairs (bp) with 4,907 protein-coding genes and 53 RNA genes.
AU  - Rawat SR
AU  - Mannisto MK
AU  - Starovoytov V
AU  - Goodwin L
AU  - Nolan M
AU  - Hauser LJ
AU  - Land M
AU  - Davenport KW
AU  - Woyke T
AU  - Haggblom MM
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 9: 71-82.

PMID- 25977418
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Cupriavidus basilensis 4G11, Isolated from the Oak Ridge Field Research Center Site.
PG  - e00322-15
AB  - Cupriavidus basilensis 4G11 was isolated from groundwater at the Oak Ridge Field  Research
      Center (FRC) site. Here, we report the complete genome sequence and
      annotation of Cupriavidus basilensis 4G11. The genome contains 8,421,483 bp,
      7,661 predicted protein-coding genes, and a total GC content of 64.4%.
AU  - Ray J
AU  - Waters RJ
AU  - Skerker JM
AU  - Kuehl JV
AU  - Price MN
AU  - Huang J
AU  - Chakraborty R
AU  - Arkin AP
AU  - Deutschbauer A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00322-15.

PMID- 24029759
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Ammonia-Producing Aeromonas sp. MDS8 Strain MCC2167 from Sludge of a Dairy Effluent Treatment Plant.
PG  - e00710-13
AB  - The draft genome sequence of an amylase-, protease-, lipase-, oxidase-, and catalase-producing
      Gram-negative bacillus (Aeromonas sp. MDS8 strain MCC2167)
      with the ability to produce ammonia during 16 h of growth at 37 degrees C,
      isolated from dairy sludge, with a size of 4,841,753 bp and a G+C content of
      63.1%, is reported here.
AU  - Raychaudhuri S
AU  - Saha A
AU  - Ghoshal T
AU  - Thakur AR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00710-13.

PMID- 26966196
VI  - 4
DP  - 2016
TI  - Genome Sequence of Elizabethkingia anophelis Strain EaAs1, Isolated from the Asian Malaria Mosquito Anopheles stephensi.
PG  - e00084-16
AB  - We sequenced the genome of a strain of the Gram-negative bacterial species Elizabethkingia
      anophelis, which is an important component of the Anopheles mosquito microbiome. This genome
      sequence will add to the list of resources used to examine host-microbe interactions in
      mosquitoes.
AU  - Raygoza-Garay JA
AU  - Hughes GL
AU  - Koundal V
AU  - Rasgon JL
AU  - Mwangi MM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00084-16.

PMID- 30533907
VI  - 7
DP  - 2018
TI  - Draft Genome Sequence and Brief History of Rhodovulum sp. Strain BSW8.
PG  - e00983-18
AB  - Rhodovulum is a marine Gram-negative purple photosynthetic bacterial genus that is a member of
      the Alphaproteobacteria. Strain BSW8 is a variant that does not
      appear to make a polysaccharide slime capsule, and its genome sequence further
      contributes to the diversity of sequenced genomes belonging to this genus.
AU  - Rayyan AA
AU  - Meyer TE
AU  - Kyndt JA
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e00983-18.

PMID- 
VI  - 0
DP  - 1978
TI  - Methylated bases in the single-stranded DNA phages.
PG  - 165-175
AB  - The widespread occurrence of methylated bases in the DNA of living organisms and the
      species-specific pattern of DNA methylation (Hall 1971) strongly suggest that these methyl
      groups play an important biological role.  At the present time, however, few biological
      processes can be correlated with methylated bases in DNA.  Most of the methylated bases in the
      bacterial chromosome are not related to the modificatiton activity in these cells, since
      bacteria that are devoid of a restriction-modification (R-M) system still methylate their own
      DNA.  The function of these methyl groups, as well as of those found in eukaryotic cell DNA,
      is obscure.  The single-stranded DNA bacteriophages, which possess a few methyl groups per
      genome, are ideal tools for studying the role of DNA methylation.  Thus, the filamentous
      bacteriophages f1, fd, and M13 have been investigated with respect to the function of the
      methylated bases in the R-M phenomena (Arber 1968).  The isometric phage PhiX174, which is not
      subject to R-M and is propagated in Escherichia coli C, a strain devoid of any known R-M
      system, was chosen to study the role of methylated bases not related to R-M.  A single methyl
      group has been found in the PhiX genome and it has been suggested that this group is essential
      in the final stages of phage maturation.
AU  - Razin A
PT  - Journal Article
TA  - The Single-Stranded DNA Phages
JT  - The Single-Stranded DNA Phages
SO  - The Single-Stranded DNA Phages 1978 0: 165-175.

PMID- 
VI  - 11
DP  - 1989
TI  - DNA methylases.
PG  - 1-11
AB  - A review.
AU  - Razin A
PT  - Journal Article
TA  - Genet. Eng. (N Y)
JT  - Genet. Eng. (N Y)
SO  - Genet. Eng. (N Y) 1989 11: 1-11.

PMID- 6261297
VI  - 25
DP  - 1981
TI  - DNA methylation and its possible biological roles.
PG  - 33-52
AB  - Bases modified by methylation have been known to occur at a low frequency in DNA for more than
      three decades.  This modification of DNA is carried out by specific methyltransferases (DNA
      methylases) that transfer the chemically active methyl group from S-adenosylmethionine
      (AdoMet) to either carbon 5 of cytosine residues or the exocyclic amino group attached to
      carbon 6 of adenine residues of the DNA chain.
      I. Introduction.
      II.  Methylases and their specificity.
      A. Substrate specificity.
      B. Sequence specificity.
      III. Distribution of methylated bases along the chromosome.
      A. Distribution with respect to DNA sequences.
      B. Distribution with respect to chromosomal proteins.
      C. Distribution with respect to chromosome ultrastructure.
      D. Methylated and unmethylated domains.
      IV. The mode of methylation in vivo.
      A. Semiconservative methylation.
      B. DeNovo methylation.
      C. "Origins" of methylation.
      V. Possible functions of methylated bases in DNA.
      A. Cell differentiation and gene activity.
      B. Restriction and modification.
      C. Interplay between DNA replication and methylation.
      D. Mutation, recombination, and repair.
      VI. Conclusions and prospects. References.
AU  - Razin A
AU  - Friedman J
PT  - Journal Article
TA  - Prog. Nucleic Acid Res. Mol. Biol.
JT  - Prog. Nucleic Acid Res. Mol. Biol.
SO  - Prog. Nucleic Acid Res. Mol. Biol. 1981 25: 33-52.

PMID- 127165
VI  - 2
DP  - 1975
TI  - Studies on the biological role of DNA methylation:  inhibition of methylation and maturation of the bacteriophage PhiX174 by nicotinamide.
PG  - 1967-1974
AB  - Nicotinamide was found to be a potent inhibitor of DNA methylation in vivo without
      interferring with protein or DNA synthesis.  The inhibition of DNA methylation in a
      phage-infected cell resulted in a parallel decrease in the production of viable virus
      particles.  In vitro experiments revealed that nicotinamide inhibits DNA methylase activity in
      a competitive fashion with respect to S-adenosylmethionine and non-competitively with respect
      to DNA. These results were interpreted to mean that DNA methylation is an essential step in
      the process of maturation of the bacteriophage PhiChi174.
AU  - Razin A
AU  - Goren D
AU  - Friedman J
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1975 2: 1967-1974.

PMID- 7433124
VI  - 8
DP  - 1980
TI  - Methylated bases in mycoplasmal DNA.
PG  - 1383-1390
AB  - The DNAs of four Mycoplasma and one Acholeplasma species were found to contain methylated
      bases.  All of the five species contained 6-methyladenine (m6Ade), the methylated base
      characteristic of prokaryotic DNA.  The extent of methylation of adenine residues in the
      mycoplasmal DNA ranged from 0.2% in Mycoplasma capricolum to about 2% in Mycoplasma arginini
      and Mycoplasma hyorhinis with intermediate methylation values for Mycoplasma orale and
      Acholeplasma laidlawii DNAs.  About 5.8% of the cytosine residues in M. hyorhinis DNA were
      methylated also.  Analysis of cell culture DNA for the presence of m6Ade as a means for
      detection of contamination by mycoplasmas, and the phylogenetic implications of the finding of
      methylated bases in mycoplasmal DNAs are discussed.
AU  - Razin A
AU  - Razin S
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1980 8: 1383-1390.

PMID- 6254144
VI  - 210
DP  - 1980
TI  - DNA methylation and gene function.
PG  - 604-610
AB  - In most higher organisms, DNA is modified after synthesis by the enzymatic conversion of many
      cytosine residues to 5-methylcytosine.  For several years, control of gene activity by DNA
      methylation has been recognized as a logically attractive possibility, but experimental
      support has proved elusive.  However, there is now reason to believe, from recent studies,
      that DNA methylation is a key element in the hierarchy of control mechanisms that govern
      vertebrate gene function and differentiation.
AU  - Razin A
AU  - Riggs D
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1980 210: 604-610.

PMID- 842826
VI  - 77
DP  - 1977
TI  - Analysis of 5-methylcytosine in DNA.
PG  - 370-377
AB  - A method for analyzing 5-methylcytosine in DNA by gas chromatography is described.  The method
      is based on degradation of the DNA to its free bases by treatment with trifluoroacetic acid
      and gas chromatography of the trimethylsilyl derivatives of the free bases.  Chromatography of
      microgram amounts of derivatized material is conducted at isothermal conditions using a 3%
      SE-30 or 2% OV-225 column.  The peak areas corresponding to cytosine and 5-methylcytosine are
      used to calculate the 5-methylcytosine/cytosine molar ratio in DNA.  The lower limit for
      detection of 5-methylcytosine in DNA by this method is a 5-methylcytosine/cytosine molar ratio
      of 0.001.
AU  - Razin A
AU  - Sedat J
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 1977 77: 370-377.

PMID- 6253948
VI  - 8
DP  - 1980
TI  - Studies on the biological role of DNA methylation; IV.  Mode of methylation of DNA in E. coli cells.
PG  - 1783-1792
AB  - Two pairs of restriction enzyme isoschizomers were used to study in vivo
      methylation of E. coli and extrachromosomal DNA.  By use of the restriction
      enzymes MboI (which cleaves only the unmethylated GATC sequence) and its
      isoschizomer Sau3A (indifferent to a methylated adenine at this sequence), we
      found that all the GATC sites in E. coli and in extrachromosomal DNAs are
      symmetrically methylated on both strands.  The calculated number of GATC sites
      in E. coli DNA can account for all its m6Ade residues.  Foreign DNA, like mouse
      mtDNA, which is not methylated at GATC sites became fully methylated at these
      sequences when introduced by transfection into E. coli cells.  This experiment
      provides the first evidence for the operation of a de novo methylation
      mechanism for E. coli methylases not involved in restriction modification.
      When the two restriction enzyme isoschizomers, EcoRII and ApyI, were used to
      analyze the methylation pattern of CCA/TGG sequences in E. coli C and PhiX174
      DNA, it was found that all these sites are methylated.  The number of CCA/TGG
      sites in E. coli C DNA does not account for all m5Cyt residues.
AU  - Razin A
AU  - Urieli S
AU  - Pollack Y
AU  - Gruenbaum Y
AU  - Glaser G
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1980 8: 1783-1792.

PMID- 10684935
VI  - 28
DP  - 2000
TI  - Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39.
PG  - 1397-1406
AB  - The genome sequences of Chlamydia trachomatis mouse pneumonitis (MoPn) strain Nigg (1 069 412
      nt) and Chlamydia pneumoniae strain AR39 (1 229 853 nt) were determined using a random shotgun
      strategy. The MoPn genome exhibited a general conservation of gene order and content with the
      previously sequenced C. trachomatis serovar D. Differences between C. trachomatis strains were
      focused on an ~50 kb 'plasticity zone' near the termination origins. In this region MoPn
      contained three copies of a novel gene encoding a >3000 amino acid toxin homologous to a
      predicted toxin from Escherichia coli 0157:H7 but had apparently lost the tryptophan
      biosyntheis genes found in serovar D in this region. The C. pneumoniae AR39 chromosome was
      >99.9% identical to the previously sequenced C. pneumoniae CWL029 genome, however, comparative
      analysis identified an invertible DNA segment upstream of the uridine kinase gene which was in
      different orientations in the two genomes. AR39 also contained a novel 4524 nt circular
      single-stranded (ss)DNA bacteriophage, the first time a virus has been reported infecting C.
      pneumoniae. Although the chlamydial genomes were highly conserved, there were intriguing
      differences in key nucleotide salvage pathways: C. pneumoniae has a uridine kinase gene for
      dUTP production, MoPn has a uracil phosphororibosyl transferase, while C. trachomatis serovar
      D contains neither gene. Chromosomal comparison revealed that there had been multiple large
      inversion events since the species divergence of C. trachomatis and C. pneumoniae, apparently
      oriented around the axis of the origin of replication and the termination region. The striking
      synteny of the Chlamydia genomes and prevalence of tandemly duplicated genes are evidence of
      minimal chromosome rearrangement and foreign gene uptake, presumably owing to the ecological
      isolation of the obligate intracellular parasites. In the absence of genetic analysis,
      comparative genomics will continue to provide insight into the virulence mechanisms of these
      important human pathogens.
AU  - Read TD et al
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2000 28: 1397-1406.

PMID- 12682364
VI  - 31
DP  - 2003
TI  - Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the   Chlamydiaceae.
PG  - 2134-2147
AB  - The genome of Chlamydophila caviae (formerly Chlamydia psittaci, GPIC isolate) (1 173 390 nt
      with a plasmid of 7966 nt) was determined,
      representing the fourth species with a complete genome sequence from the
      Chlamydiaceae family of obligate intracellular bacterial pathogens. Of
      1009 annotated genes, 798 were conserved in all three other completed
      Chlamydiaceae genomes. The C.caviae genome contains 68 genes that lack
      orthologs in any other completed chlamydial genomes, including tryptophan
      and thiamine biosynthesis determinants and a ribose-phosphate
      pyrophosphokinase, the product of the prsA gene. Notable amongst these was
      a novel member of the virulence-associated invasin/intimin family (IIF) of
      Gram-negative bacteria. Intriguingly, two authentic frameshift mutations
      in the ORF indicate that this gene is not functional. Many of the unique
      genes are found in the replication termination region (RTR or plasticity
      zone), an area of frequent symmetrical inversion events around the
      replication terminus shown to be a hotspot for genome variation in
      previous genome sequencing studies. In C.caviae, the RTR includes several
      loci of particular interest including a large toxin gene and evidence of
      ancestral insertion(s) of a bacteriophage. This toxin gene, not present in
      Chlamydia pneumoniae, is a member of the YopT effector family of type
      III-secreted cysteine proteases. One gene cluster (guaBA-add) in the RTR
      is much more similar to orthologs in Chlamydia muridarum than those in the
      phylogenetically closest species C.pneumoniae, suggesting the possibility
      of horizontal transfer of genes between the rodent-associated Chlamydiae.
      With most genes observed in the other chlamydial genomes represented,
      C.caviae provides a good model for the Chlamydiaceae and a point of
      comparison against the human atherosclerosis-associated C.pneumoniae. This
      crucial addition to the set of completed Chlamydiaceae genome sequences is
      enabling dissection of the roles played by niche-specific genes in these
      important bacterial pathogens.
AU  - Read TD et al
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2003 31: 2134-2147.

PMID- 12721629
VI  - 423
DP  - 2003
TI  - The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria.
PG  - 81-86
AB  - Bacillus anthracis is an endospore-forming bacterium that causes inhalational anthrax. Key
      virulence genes are found on plasmids
      (extra-chromosomal, circular, double-stranded DNA molecules) pXO1 (ref. 2)
      and pXO2 (ref. 3). To identify additional genes that might contribute to
      virulence, we analysed the complete sequence of the chromosome of B.
      anthracis Ames (about 5.23 megabases). We found several chromosomally
      encoded proteins that may contribute to pathogenicity--including
      haemolysins, phospholipases and iron acquisition functions--and identified
      numerous surface proteins that might be important targets for vaccines and
      drugs. Almost all these putative chromosomal virulence and surface
      proteins have homologues in Bacillus cereus, highlighting the similarity
      of B. anthracis to near-neighbours that are not associated with anthrax.
      By performing a comparative genome hybridization of 19 B. cereus and
      Bacillus thuringiensis strains against a B. anthracis DNA microarray, we
      confirmed the general similarity of chromosomal genes among this group of
      close relatives. However, we found that the gene sequences of pXO1 and
      pXO2 were more variable between strains, suggesting plasmid mobility in
      the group. The complete sequence of B. anthracis is a step towards a
      better understanding of anthrax pathogenesis.
AU  - Read TD et al
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2003 423: 81-86.

PMID- 12004073
VI  - 296
DP  - 2002
TI  - Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis.
PG  - 2028-2033
AB  - Comparison of the whole-genome sequence of Bacillus anthracis isolated from a victim of a
      recent bioterrorist anthrax attack with a reference
      reveals 60 new markers that include single nucleotide polymorphisms
      (SNPs), inserted or deleted sequences, and tandem repeats. Genome
      comparison detected four high-quality SNPs between the two sequenced B.
      anthracis chromosomes and seven differences among different preparations
      of the reference genome. These markers have been tested on a collection of
      anthrax isolates and were found to divide these samples into distinct
      families. These results demonstrate that genome-based analysis of
      microbial pathogens will provide a powerful new tool for investigation of
      infectious disease outbreaks.
AU  - Read TD
AU  - Salzberg SL
AU  - Pop M
AU  - Shumway M
AU  - Umayam L
AU  - Jiang L
AU  - Holtzapple E
AU  - Busch JD
AU  - Smith KL
AU  - Schupp JM
AU  - Solomon D
AU  - Keim P
AU  - Fraser CM
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2002 296: 2028-2033.

PMID- 1508042
VI  - 6
DP  - 1992
TI  - Evasion of type I and type II DNA restriction systems by IncI1 plasmid Collb-P9 during transfer by bacterial conjugation.
PG  - 1933-1941
AB  - Transmission of unmodified plasmid CoIIb-P9 by bacterial conjugation is markedly resistant to
      restriction compared with transfer by transformation. One process allowing evasion of type I
      and II restriction systems involves conjugative transfer of multiple copies of the plasmid. A
      more specialized evasion mechanism requires the Ard (alleviation of restriction of DNA) system
      encoded by CoIIb. The ard gene is transferred early in conjugation and specifically alleviates
      DNA restriction by all known families of type I enzyme, including EcoK.  CoIIb has no effect
      on EcoK modification but this activity is impaired by multicopy recombinant plasmids
      supporting overexpression of ard. Genetic evidence shows that Ard protects CoIIb from EcoK
      restriction following conjugative transfer and that this protection requires expression of the
      gene on the immigrant plasmid. It is proposed that carriage of ard facilitates transfer of
      CoIIb between its natural enterobacterial hosts and that the route of DNA entry is important
      to the restriction-evasion mechanism.
AU  - Read TD
AU  - Thomas AT
AU  - Wilkins BM
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1992 6: 1933-1941.

PMID- 8554531
VI  - 312
DP  - 1995
TI  - DNA binding and methyl transfer catalysed by mouse DNA methyltransferase.
PG  - 855-861
AB  - By using a purified fraction of mouse DNA methyltransferase we have shown, by gel-retardation
      analysis, that the enzyme forms a low-affinity complex preferentially with hemimethylated DNA;
      the complexes formed with unmethylated or with fully methylated DNA are of even lower
      affinity, and only very weak interaction occurs with DNA lacking CG dinucleotides.
      Interaction is inhibited by N-ethylmaleimide.  Methyl transfer from S-adenosyl-methionine is
      associated with the release of the fully methylated product from the complex.  Complexes
      formed with the intact enzyme are extremely large, but limited trypsin treatment allows a
      major complex to enter the gel.  DNA binding is not inhibited by this limited proteolysis of
      the native enzyme.
AU  - Reale A
AU  - Lindsay H
AU  - Saluz HP
AU  - Pradhan S
AU  - Adams RLP
AU  - Jost J-P
AU  - Strom R
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 1995 312: 855-861.

PMID- 6298063
VI  - 20
DP  - 1982
TI  - Nostoc PCC7524, a cyanobacterium which contains five sequence-specific deoxyribonucleases.
PG  - 103-110
AB  - Five nucleotide sequence-specific deoxyribonucleases present in cell-free
      extracts of the filamentous cyanobacterium Nostoc PCC7524 have been purified
      and characterized.  One of these enzymes, designated Nsp(7524)I cleaves at a
      new kind of nucleotide sequence, i.e. 5'-PuCATG^Py-3'.  The other four
      restriction enzymes in this organism, designated Nsp(7524)II, Nsp(7524)III,
      Nsp(7524)IV and Nsp(7524)V, are isoschizomers of enzymes which have been
      previously described.  The cleavage site of Nsp(7524)II which is an
      isoschizomer of SduI was determined.
AU  - Reaston J
AU  - Duyvesteyn MGC
AU  - de Waard A
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1982 20: 103-110.

PMID- Not carried by PubMed...
VI  - 3
DP  - 1994
TI  - A new site-specific endodeoxyribonuclease FmuI from the strain Flavobacterium multivorum.
PG  - 15-16
AB  - A new site-specific endodeoxyribonuclease (restrictase) has been isolated from the strain
      Flavobacterium multivorum and some of its characteristics were examined. It was named FmuI and
      shown to determine the following nucleotide sequence: 5'-GGNC/C-3'. The new restrictase
      turned out to be a false isoschizomer (or an alternative prototype) of the enzyme AsuI.
AU  - Rebentish BA
AU  - Bolotin AP
AU  - Grachova IM
AU  - Ren LS
AU  - Uyan JM
PT  - Journal Article
TA  - Biotekhnologiya
JT  - Biotekhnologiya
SO  - Biotekhnologiya 1994 3: 15-16.

PMID- 25657273
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Mycobacterium setense Type Strain DSM-45070 and the Nonpathogenic Strain Manresensis, Isolated from the Bank of the Cardener River in  Manresa, Catalonia, Spain.
PG  - e01485-14
AB  - We present here the draft genome sequences of two Mycobacterium setense strains.  One of them
      corresponds to the M. setense type strain DSM-45070, originally
      isolated from a patient with a posttraumatic chronic skin abscess. The other one
      corresponds to the nonpathogenic M. setense strain Manresensis, isolated from the
      Cardener River crossing Manresa, Catalonia, Spain. A comparative genomic analysis
      shows a smaller genome size and fewer genes in M. setense strain Manresensis
      relative to those of the type strain, and it shows the genome segments unique to
      each strain.
AU  - Rech G
AU  - Vilaplana C
AU  - Velasco J
AU  - Pluvinet R
AU  - Santin S
AU  - Prat C
AU  - Julian E
AU  - Alcaide F
AU  - Comas I
AU  - Sumoy L
AU  - Cardona PJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01485-14.

PMID- Not carried by PubMed...
VI  - 5
DP  - 1989
TI  - Stability of the secondary structure of the oligonucleotide substrates.  The effect of Ecodam DNA-methylase.
PG  - 43-49
AB  - Oligonucleotide complexes containing various defects in the Ecodam methylase recognition site
      have been investigated for their stability. A partial duplex structure for the single-stranded
      20-base long oligonucleotide containing a self-complementary hexanucleotide sequence is
      observed only below 5C. Other complexes melt within the narrow temperature range of 22-31C in
      30 mM of potassium-phosphate buffer, pH 7.8. The presence of the Ecodam methylase results in
      an increase of the melting point of the complex at least by 5C.
AU  - Rechkunova NI
AU  - Lokhov SG
AU  - Gorbunov YA
AU  - Zinovev VV
AU  - Buryanov YI
AU  - Malygin EG
PT  - Journal Article
TA  - Biopol. Kletka
JT  - Biopol. Kletka
SO  - Biopol. Kletka 1989 5: 43-49.

PMID- 2836720
VI  - 22
DP  - 1988
TI  - Effects of oligonucleotide structure on the kinetic values of the interaction with BamHI endonuclease.
PG  - 217-223
AB  - Kinetic values of the BamHI endonuclease interaction with synthetic oligonucleotides,
      containing some defects, have been determined.  These defects were: the absence of the one
      internucleotide phosphate in the GGATCC sequence; substitution of a phosphate linkage by a
      methylphosphonate one; 5'-protruding end of the double-stranded oligonucleotide substrate.
      Some modifications resulted in the increase of the initial rates of cleavage due to higher
      Vmax values for these substrates.  Several structural defects in the oligonucleotide
      substrates have been shown to intensify the formation of productive complexes with the enzyme,
      which can be explained by the significant role of the polynucleotide chain kinds in the
      recognition process.  Studies on oligonucleotides with different defects made it possible to
      reveal the phosphate groups essential for the interaction with BamHI endonuclease.
AU  - Rechkunova NI
AU  - Ovetchkina LG
AU  - Jashina LN
AU  - Vtorushina IA
AU  - Gorbunov JA
AU  - Zinoviev VV
AU  - Malygin EG
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1988 22: 217-223.

PMID- Not carried by PubMed...
VI  - 3
DP  - 1987
TI  - Dimerization of Ecodam-methylase induced by the oligonucleotide substrate.
PG  - 152-154
AB  - The Ecodam-methylase has been investigated for its interaction with the 20-base
      oligonucleotide duplex containing the enzyme recognition site. An increase of the enzyme
      molecular weight was detected by the gel-filtration and sucrose density gradient
      centrifugation methods. The maximal value of the complex molecular weight was observed when
      concentrations of the enzyme and the substrate were equal. The results obtained prove the
      formation of the dimeric enzyme form in the presence of the substrate.
AU  - Rechkunova NI
AU  - Zinovev VV
AU  - Malygin EG
AU  - Gorbunov YA
AU  - Popov SG
AU  - Nesterenko VF
AU  - Buryanov YI
PT  - Journal Article
TA  - Biopol. Kletka
JT  - Biopol. Kletka
SO  - Biopol. Kletka 1987 3: 152-154.

PMID- 3026483
VI  - 908
DP  - 1987
TI  - The cleavage of single-stranded DNA by the isoschizomeric restriction endonuclease HhaI and CfoI.
PG  - 90-96
AB  - The cleavage of single-stranded (ss) M13mp8(+) DNA by the isoschizomeric restriction
      endonucleases HhaI and CfoI has been investigated.  The two enzymes differ considerably in
      their ability to cleave ssDNA.  HhaI cleaves ssDNA about two orders of magnitude faster than
      does CfoI, although both enzymes show the same activity when assayed on double-stranded DNA.
      From the cleavage of oligonucleotides and of M13mp8(+) DNA fragments it is concluded that
      cleavage of ssDNA occurs via transiently formed double-stranded hairpin structures.  A rough
      correlation exists between the stability of the secondary structures and the cleavage
      efficiency.
AU  - Reckmann B
AU  - Krauss G
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1987 908: 90-96.

PMID- 11895953
VI  - 70
DP  - 2002
TI  - The nucleotide sequence of Shiga toxin (Stx) 2e-encoding phage phiP27 is not related to other Stx phage genomes, but the modular genetic structure is Conserved.
PG  - 1896-1908
AB  - In this study we determined the complete nucleotide sequence of Shiga
      toxin 2e-encoding bacteriophage phi P27, isolated from the Shiga
      toxin-producing Escherichia coli patient isolate 2771/97. phi P27 is
      integrated as a prophage in the chromosomal yecE gene. This integration
      generates identity segments of attL and attR sites with lengths of 11
      nucleotides. The integrated prophage genome has a size of 42,575 bp. We
      identified 58 open reading frames (ORFs), each with a length of >150
      nucleotides. The deduced proteins of 44 ORFs showed significant homologies
      to other proteins present in sequence databases, whereas 14 putative
      proteins did not. For 29 proteins, we could deduce a putative function.
      Most of these are related to the basic phage propagation cycle. The phi
      P27 genome represents a mosaic composed of genetic elements which are
      obviously derived from related and unrelated phages. We identified five
      short linker sequences of 22 to 151 bp in the phi P27 sequence which have
      also been detected in a couple of other lambdoid phages. These linkers are
      located between functional modules in the phage genome and are thought to
      play a role in genetic recombination. Although the overall DNA sequence of
      phi P27 is not highly related to other known phages, the data obtained
      demonstrate a typical lambdoid genome structure.
AU  - Recktenwald J
AU  - Schmidt H
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2002 70: 1896-1908.

PMID- 
VI  - 1
DP  - 1996
TI  - DNA restriction and modification systems.
PG  - 773-781
AB  - The phenomenon of restriction and modification was first observed in the course of studies on
      bacterial viruses in the early 1950s.  Several authors reported that certain strains of
      bacteria inhibited ("restricted") the growth of bacterial viruses previously propagated on a
      different strain.  The molecular explanation for this effect was discovered in the early
      1960s: the restriction of viral growth was due to endonucleolytic cleavage of the viral DNA by
      site-specific endonucleases.  Some of these restriction endonucleases were found to possess
      very useful properties, and their subsequent exploitation in the 1970s was the key to the
      development of genetic engineering technology.
AU  - Redaschi N
AU  - Bickle TA
PT  - Journal Article
TA  - Escherichia coli and Salmonella: Cellular and Molecular Biology
JT  - Escherichia coli and Salmonella: Cellular and Molecular Biology
SO  - Escherichia coli and Salmonella: Cellular and Molecular Biology 1996 1: 773-781.

PMID- 8636982
VI  - 257
DP  - 1996
TI  - Posttranscriptional regulation of EcoP1I and EcoP15I restriction activity.
PG  - 790-803
AB  - Efficient establishment of a DNA restriction-modification (R-M) system in a non-modified cell
      requires a tight control of the potentially lethal activity of the restriction enzyme.  The
      type III R-M systems EcoP1I and EcoP15I can be transferred to non-modified Escherichia coli
      cells by transfection, conjugation or transformation and become established without
      difficulty.  Modification activity is expressed immediately after the R-M genes enter the
      cell, whereas the expression of restriction activity is delayed until complete protection of
      the cellular DNA is achievedby methylation.  We have shown by Western blot analysis that the
      expression of the modification polypeptide subunit positively regulates the amount of
      restriction subunit present in the cell.  The finding that ribosomal alterations affected the
      expression of restriction activity pointed to additional control at the translational level.
      The analysis of EcoP1I expression in E. coli strains mutated in either of the ribosomal
      proteins S12 (rpsL) or S4 (rpsD) suggests that the level of in vivo restriction activity can
      be modulated both by a decrease in the efficiency of translation and by varying ribosomal
      accuracy conditions.  In addition, we have preliminary evidence from in vivo gene fusion
      studies that the res gene may code for more than one gene product.
AU  - Redaschi N
AU  - Bickle TA
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1996 257: 790-803.

PMID- 24201199
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Psychrobacter aquaticus Strain CMS 56T, Isolated from a  Cyanobacterial Mat Sample Collected from Water Bodies in the McMurdo Dry Valley  Region of Antarctica.
PG  - e00918-13
AB  - We report the 3.2-Mb draft genome sequence of Psychrobacter aquaticus strain CMS  56(T),
      isolated from a cyanobacterial mat sample collected from a water body in
      the McMurdo Dry Valley region of Antarctica.
AU  - Reddy GS
AU  - Ara S
AU  - Singh A
AU  - Kumar PA
AU  - Shivaji S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00918-13.

PMID- 25414505
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Cryobacterium roopkundensis Strain RuGl7, Isolated from  a Soil Sample in the Vicinity of Roopkund Lake, Himalayas, India.
PG  - e01206-14
AB  - We report the 4.36-Mb genome of Cryobacterium roopkundensis strain RuGl7, isolated from a soil
      sample collected in the periphery of Roopkund Lake, Himalayas, India. The draft genome
      consists of 4,356,863 bp, 4,048 protein-coding sequences, and 50 RNAs, with 65.3% G+C DNA
      content.
AU  - Reddy GS
AU  - Sreenivas A
AU  - Shivaji S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01206-14.

PMID- 10788323
VI  - 298
DP  - 2000
TI  - Binding of EcoP15I DNA methyltransferase to DNA reveals a large structural distortion within the recognition sequence.
PG  - 597-610
AB  - EcoP15I DNA methyltransferase, a member of the type III restriction-modification system, binds
      to the sequence 5'-CAGCAG-3' transferring a methyl group from S-adenosyl-l-methionine to the
      second adenine base. We have investigated protein-DNA interactions in the methylase-DNA
      complex by three methods. Determination of equilibrium dissociation constants indicated that
      the enzyme had higher affinity for DNA containing mismatches at the target base within the
      recognition sequence. Potassium permanganate footprinting studies revealed that there was a
      hyper-reactive permanganate cleavage site coincident with adenine that is the target base for
      methylation. More importantly, to detect DNA conformational alterations within the enzyme-DNA
      complexes, we have used a fluorescence-based assay. When EcoP15I DNA methyltransferase bound
      to DNA containing 2-aminopurine substitutions within the cognate sequence, an eight to tenfold
      fluorescent enhancement resulting from enzymatic flipping of the target adenine base was
      observed. Furthermore, fluorescence spectroscopy analysis showed that the changes attributable
      to structural distortion were specific for only the bases within the recognition sequence.
      More importantly, we observed that both the adenine bases in the recognition site appear to be
      structurally distorted to the same extent. While the target adenine base is probably flipped
      out of the DNA duplex, our results also suggest that fluorescent enhancements could be derived
      from protein-DNA interactions other than base flipping. Taken together, our results support
      the proposed base flipping mechanism for adenine methyltransferases.
AU  - Reddy YV
AU  - Rao DN
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2000 298: 597-610.

PMID- 9726999
VI  - 273
DP  - 1998
TI  - Probing the role of cysteine residues in the EcoP15I DNA methyltransferase.
PG  - 23866-23876
AB  - Chemical modification using thiol-directed agents and site-directed mutagenesis has been used
      to investigate the role of cysteine residues of EcoP15I DNA methyltransferase.  Irreversible
      inhibition of enzymatic activity was provoked by chemical modification of the enzyme by
      N-ethylmaleimide and iodoacetamide.  5,5'-Dithiobis(2-nitrobenzoic acid) titration of the
      enzyme under nondenaturing and denaturing conditions confirmed the presence of six cysteine
      residues without any disulfides in the protein.  Aware that relatively bulky reagents
      inactivate the methyltransferase by directly occluding the substrate-binding site or by
      locking the methyltransferase in an inactive conformation, we used site-directed mutagenesis
      to sequentially replace each of the six cysteines in the protein at positions 30, 213, 344,
      434, 553, and 577.  All the resultant mutation methylases except for the C344S and C344A
      enzymes retained significant activity as assessed by in vivo and in vitro assays.  The effects
      of the substitutions on the function of EcoP15I DNA methyltransferase were investigated by
      substrate binding assays, activity measurements, and steady-state kinetic analysis of
      catalysis.  Our results clearly indicate that the cysteines at positions other than 344 are
      not essential for activity.  In contrast, the C344A enzyme showed a marked loss of enzymatic
      activity.  More importantly, whereas the inactive C344A mutant enzyme bound
      S-adenosyl-L-methionine, it failed to bind to DNA.  Furthermore, in double and triple mutants
      where two or three cysteine residues were replaced by serine, all such mutants in which the
      cysteine at position 344 was changed, were inactive.  Taken together, these results
      convincingly demonstrate that the Cys-344 is necessary for enzyme activity and indicate an
      essential role for it in DNA binding.
AU  - Reddy YVR
AU  - Rao DN
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1998 273: 23866-23876.

PMID- 9573173
VI  - 180
DP  - 1998
TI  - Cloning and physical mapping of the EcoRI fragments of the giant linear plasmid SCP1.
PG  - 2796-2799
AB  - A cosmid library was constructed for the 350-kb giant linear plasmid SCP1
      and aligned on a successive linear map. Only a 0.8-kb gap has remained
      uncloned in the terminal inverted repeats close to both ends. Partial
      digestion of the aligned cosmids with EcoRI and hybridization with the
      flanking fragments of the vector enabled physical mapping of all of the
      EcoRI fragments. On this map, the methylenomycin biosynthetic gene
      cluster, the insertion sequence IS466, and the sapCDE genes coding for
      spore-associated proteins were localized.
AU  - Redenbach M
AU  - Ikeda K
AU  - Yamasaki M
AU  - Kinashi H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1998 180: 2796-2799.

PMID- 8843436
VI  - 21
DP  - 1996
TI  - A set of ordered cosmids and a detailed genetic and physical map for the 8 Mb Streptomyces coelicolor A3(2) chromosome.
PG  - 77-96
AB  - A Supercos-1 library carrying chromosomal DNA of a plasmid-free derivative of Streptomyces
      coelicolor A3(2) was organized into an ordered encyclopaedia of overlapping clones by
      hybridization. The minimum set of overlapping clones representing the entire chromosome (with
      three short gaps) consists of 319 cosmids. The average insert size is 37.5 kb and the set of
      clones therefore divides the chromosome into 637 alternating unique and overlapping segments
      which have an average length of approx. 12.5 kb. More than 170 genes, gene clusters and other
      genetic markers were mapped to their specific segment by hybridization to the encyclopaedia.
      Genes could be cloned by direct transformation and complementation of S. coelicolor mutants
      with cosmids isolated from Escherichia coli, selecting for insertion into the chromosome by
      homologous recombination. As in other streptomycetes, the ends of the chromosome have long
      terminal inverted repeats.
AU  - Redenbach M
AU  - Kieser HM
AU  - Denapaite D
AU  - Eichner A
AU  - Cullum J
AU  - Kinashi H
AU  - Hopwood DA
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1996 21: 77-96.

PMID- 24637769
VI  - 70
DP  - 2014
TI  - Crystallization and preliminary X-ray diffraction analysis of the homing endonuclease I-CvuI from Chlorella vulgaris in complex with its target DNA.
PG  - 256-259
AB  - Homing endonucleases are highly specific DNA-cleaving enzymes that recognize long stretches of
      DNA. The engineering of these enzymes provides novel instruments for genome modification in a
      wide range of fields, including gene targeting, by inducing specific double-strand breaks.
      I-CvuI is a homing endonuclease from the green alga Chlorella vulgaris. This enzyme was
      purified after overexpression in Escherichia coli. Crystallization experiments of I-CvuI in
      complex with its DNA target in the presence of Mg2+ yielded crystals suitable for X-ray
      diffraction analysis. The crystals belonged to the orthorhombic space group P2(1)2(1)2(1),
      with unit-cell parameters a = 62.83, b = 83.56, c = 94.40 angstrom. The self-rotation function
      and the Matthews coefficient suggested the presence of one protein-DNA complex per asymmetric
      unit. The crystals diffracted to a resolution limit of 1.9 angstrom using synchrotron
      radiation.
AU  - Redondo P
AU  - Merino N
AU  - Villate M
AU  - Blanco FJ
AU  - Montoya G
AU  - Molina R
PT  - Journal Article
TA  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
JT  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
SO  - Acta Crystallogr. F Struct. Biol. Cryst. Commun. 2014 70: 256-259.

PMID- 18987743
VI  - 456
DP  - 2008
TI  - Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases.
PG  - 107-111
AB  - Xeroderma pigmentosum is a monogenic disease characterized by hypersensitivity to ultraviolet
      light. The cells of xeroderma pigmentosum
      patients are defective in nucleotide excision repair, limiting their
      capacity to eliminate ultraviolet-induced DNA damage, and resulting in a
      strong predisposition to develop skin cancers. The use of rare cutting DNA
      endonucleases-such as homing endonucleases, also known as
      meganucleases-constitutes one possible strategy for repairing DNA lesions.
      Homing endonucleases have emerged as highly specific molecular scalpels
      that recognize and cleave DNA sites, promoting efficient homologous gene
      targeting through double-strand-break-induced homologous recombination.
      Here we describe two engineered heterodimeric derivatives of the homing
      endonuclease I-CreI, produced by a semi-rational approach. These two
      molecules-Amel3-Amel4 and Ini3-Ini4-cleave DNA from the human XPC gene
      (xeroderma pigmentosum group C), in vitro and in vivo. Crystal structures
      of the I-CreI variants complexed with intact and cleaved XPC target DNA
      suggest that the mechanism of DNA recognition and cleavage by the
      engineered homing endonucleases is similar to that of the wild-type
      I-CreI. Furthermore, these derivatives induced high levels of specific
      gene targeting in mammalian cells while displaying no obvious
      genotoxicity. Thus, homing endonucleases can be designed to recognize and
      cleave the DNA sequences of specific genes, opening up new possibilities
      for genome engineering and gene therapy in xeroderma pigmentosum patients
      whose illness can be treated ex vivo.
AU  - Redondo P
AU  - Prieto J
AU  - Munoz IG
AU  - Alibes A
AU  - Stricher F
AU  - Serrano L
AU  - Cabaniols JP
AU  - Daboussi F
AU  - Arnould S
AU  - Perez C
AU  - Duchateau P
AU  - Paques F
AU  - Blanco FJ
AU  - Montoya G
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2008 456: 107-111.

PMID- 18084082
VI  - 63
DP  - 2007
TI  - Crystallization and preliminary x-ray diffraction analysis on the homing endonuclease I-Dmo-I in complex with its target DNA.
PG  - 1017-1020
AB  - Homing endonucleases are highly specific DNA-cleaving enzymes that recognize long stretches of
      base pairs. The availability of these
      enzymes has opened novel perspectives for genome engineering in a wide
      range of fields, including gene therapy, by taking advantage of the
      homologous gene-targeting enhancement induced by a double-strand break.
      I-Dmo-I is a well characterized homing endonuclease from the archaeon
      Desulfurococcus mobilis. The enzyme was cloned and overexpressed in
      Escherichia coli. Crystallization experiments of I-Dmo-I in complex
      with its DNA target in the presence of Ca2+ and Mg2+ yielded crystals
      that were suitable for X-ray diffraction analysis. The crystals
      belonged to the monoclinic space group P2(1), with unit-cell parameters
      a = 106.75, b = 70.18, c = 106.85 angstrom, alpha = gamma = 90, beta =
      119.93 degrees. The self-rotation function and the Matthews coefficient
      suggested the presence of three protein-DNA complexes per asymmetric
      unit. The crystals diffracted to a resolution limit of 2.6 angstrom
      using synchrotron radiation at the Swiss Light Source (SLS) and the
      European Synchrotron Radiation Facility (ESRF).
AU  - Redondo P
AU  - Prieto J
AU  - Ramos E
AU  - Blanco FJ
AU  - Montoya G
PT  - Journal Article
TA  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
JT  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
SO  - Acta Crystallogr. F Struct. Biol. Cryst. Commun. 2007 63: 1017-1020.

PMID- 22328765
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Biocontrol Strain Pseudomonas fluorescens F113.
PG  - 1273-1274
AB  - Pseudomonas fluorescens F113 is a plant growth-promoting rhizobacterium (PGPR) that has
      biocontrol activity against fungal plant pathogens and is a model for
      rhizosphere colonization. Here, we present its complete genome sequence, which
      shows that besides a core genome very similar to those of other strains sequenced
      within this species, F113 possesses a wide array of genes encoding specialized
      functions for thriving in the rhizosphere and interacting with eukaryotic
      organisms.
AU  - Redondo-Nieto M et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1273-1274.

PMID- 24812220
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Erwinia mallotivora BT-MARDI, Causative Agent of Papaya  Dieback Disease.
PG  - e00375-14
AB  - Erwinia mallotivora was isolated from papaya trees infected with dieback disease, which were
      planted at the Malaysian Agricultural Research and Development Institute (MARDI), Malaysia.
      Here, we report a draft genome sequence of E. mallotivora BT-MARDI, which offers an important
      source of information for understanding pathogen and host interaction during papaya dieback
      development.
AU  - Redzuan RA
AU  - Bakar NA
AU  - Rozano L
AU  - Badrun R
AU  - Amin NM
AU  - Raih MFM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00375-14.

PMID- 8185912
VI  - 16
DP  - 1994
TI  - An improved method for detection of 5-methylcytosine by PCR-based genomic sequencing.
PG  - 416-417
AB  - 
AU  - Reeben M
AU  - Prydz H
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 1994 16: 416-417.

PMID- 3074015
VI  - 74
DP  - 1988
TI  - Cloning, purification and characterization of the HincII and HindII methyltransferases from Haemophilus influenzae.
PG  - 37
AB  - Meeting Abstract
AU  - Rees PA
AU  - Nwankwo DO
AU  - Wilson GG
AU  - Benner JS
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 37.

PMID- 6247618
VI  - 178
DP  - 1980
TI  - Unusual behaviour of SPO1 DNA with respect to restriction and modification enzymes recognizing the sequence 5'-G-G-C-C.
PG  - 229-231
AB  - SPO1 DNA contains only 5 cleavage sites for restriction enzymes which recognize
      and cleave the sequence 5'-G-G-C-C (HaeIII or BsuR).  Fragments of SPO1 DNA
      cloned in E. coli to substitute 5'-hydroxymethyluracil (HMU) by thymine (T)
      remain resistant to HaeIII indicating that this unexpectedly small number of
      cleavages by HaeIII is not correlated with the presence of HMU in the normal
      phage DNA.  It was previously shown that SPO1 is neither subject to B. subtilis
      R restriction (Trautner et al., 1974) nor modification in vivo (Gunthert et
      al., 1975).  We now show that SPO1 DNA can however be restricted and modified
      in vitro.
AU  - Reeve JN
AU  - Amann E
AU  - Tailor R
AU  - Gunthert U
AU  - Scholz K
AU  - Trautner TA
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1980 178: 229-231.

PMID- 24976896
VI  - 9
DP  - 2013
TI  - Complete genome sequence of Mesorhizobium australicum type strain (WSM2073(T)).
PG  - 410-419
AB  - Mesorhizobium australicum strain WSM2073(T) was isolated from root nodules on the pasture
      legume Biserrula pelecinus growing in Australia in 2000. This aerobic,
      motile, gram negative, non-spore-forming rod is poorly effective in N2 fixation
      on B. pelecinus and has gained the ability to nodulate B. pelecinus following in
      situ lateral transfer of a symbiosis island from the original inoculant strain
      for this legume, Mesorhizobium ciceri bv. biserrulae WSM1271. We describe that
      the genome size of M. australicum strain WSM2073(T) is 6,200,534 bp encoding
      6,013 protein-coding genes and 67 RNA-only encoding genes. This genome does not
      contain any plasmids but has a 455.7 kb genomic island from Mesorhizobium ciceri
      bv. biserrulae WSM1271 that has been integrated into a phenylalanine-tRNA gene.
AU  - Reeve W et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 9: 410-419.

PMID- 24976894
VI  - 9
DP  - 2013
TI  - Genome sequence of the Lebeckia ambigua-nodulating 'Burkholderia sprentiae' strain WSM5005(T.).
PG  - 385-394
AB  - 'Burkholderia sprentiae' strain WSM5005(T) is an aerobic, motile, Gram-negative,
      non-spore-forming rod that was isolated in Australia from an effective N2-fixing
      root nodule of Lebeckia ambigua collected in Klawer, Western Cape of South
      Africa, in October 2007. Here we describe the features of 'Burkholderia
      sprentiae' strain WSM5005(T), together with the genome sequence and its
      annotation. The 7,761,063 bp high-quality-draft genome is arranged in 8 scaffolds
      of 236 contigs, contains 7,147 protein-coding genes and 76 RNA-only encoding
      genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint
      Genome Institute 2010 Community Sequencing Program.
AU  - Reeve W et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 9: 385-394.

PMID- 24976886
VI  - 9
DP  - 2013
TI  - Complete genome sequence of Mesorhizobium opportunistum type strain WSM2075(T.).
PG  - 294-303
AB  - Mesorhizobium opportunistum strain WSM2075(T) was isolated in Western Australia in 2000 from
      root nodules of the pasture legume Biserrula pelecinus that had been
      inoculated with M. ciceri bv. biserrulae WSM1271. WSM2075(T) is an aerobic,
      motile, Gram negative, non-spore-forming rod that has gained the ability to
      nodulate B. pelecinus but is completely ineffective in N2 fixation with this
      host. This report reveals that the genome of M. opportunistum strain WSM2075(T)
      contains a chromosome of size 6,884,444 bp, encoding 6,685 protein-coding genes
      and 62 RNA-only encoding genes. The genome contains no plasmids, but does harbor
      a 455.7 kb genomic island from Mesorhizobium ciceri bv. biserrulae WSM1271 that
      has been integrated into a phenylalanine-tRNA gene.
AU  - Reeve W et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 9: 294-303.

PMID- 24976885
VI  - 9
DP  - 2013
TI  - Genome sequence of the Trifolium rueppellianum -nodulating Rhizobium leguminosarum bv. trifolii strain WSM2012.
PG  - 283-293
AB  - Rhizobium leguminosarum bv. trifolii WSM2012 (syn. MAR1468) is an aerobic, motile,
      Gram-negative, non-spore-forming rod that was isolated from an
      ineffective root nodule recovered from the roots of the annual clover Trifolium
      rueppellianum Fresen growing in Ethiopia. WSM2012 has a narrow, specialized host
      range for N2-fixation. Here we describe the features of R. leguminosarum bv.
      trifolii strain WSM2012, together with genome sequence information and
      annotation. The 7,180,565 bp high-quality-draft genome is arranged into 6
      scaffolds of 68 contigs, contains 7,080 protein-coding genes and 86 RNA-only
      encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE
      Joint Genome Institute 2010 Community Sequencing Program.
AU  - Reeve W et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 9: 283-293.

PMID- 24976884
VI  - 9
DP  - 2013
TI  - Genome sequence of the lupin-nodulating Bradyrhizobium sp. strain WSM1417.
PG  - 273-282
AB  - Bradyrhizobium sp. strain WSM1417 is an aerobic, motile, Gram-negative, non-spore-forming rod
      that was isolated from an effective nitrogen (N2) fixing
      root nodule of Lupinus sp. collected in Papudo, Chile, in 1995. However, this
      microsymbiont is a poorly effective N2 fixer with the legume host Lupinus
      angustifolius L.; a lupin species of considerable economic importance in both
      Chile and Australia. The symbiosis formed with L. angustifolius produces less
      than half of the dry matter achieved by the symbioses with commercial inoculant
      strains such as Bradyrhizobium sp. strain WSM471. Therefore, WSM1417 is an
      important candidate strain with which to investigate the genetics of effective N2
      fixation in the lupin-bradyrhizobia symbioses. Here we describe the features of
      Bradyrhizobium sp. strain WSM1417, together with genome sequence information and
      annotation. The 8,048,963 bp high-quality-draft genome is arranged in a single
      scaffold of 2 contigs, contains 7,695 protein-coding genes and 77 RNA-only
      encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE
      Joint Genome Institute 2010 Community Sequencing Program.
AU  - Reeve W et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 9: 273-282.

PMID- 24976883
VI  - 9
DP  - 2013
TI  - Genome sequence of the South American clover-nodulating Rhizobium leguminosarum bv. trifolii strain WSM597.
PG  - 264-272
AB  - Rhizobium leguminosarum bv. trifolii strain WSM597 is an aerobic, motile, Gram-negative,
      non-spore-forming rod isolated from a root nodule of the annual
      clover Trifolium pallidum L. growing at Glencoe Research Station near Tacuarembo,
      Uruguay. This strain is generally ineffective for nitrogen (N2) fixation with
      clovers of Mediterranean, North American and African origin, but is effective on
      the South American perennial clover T. polymorphum Poir. Here we describe the
      features of R. leguminosarum bv. trifolii strain WSM597, together with genome
      sequence information and annotation. The 7,634,384 bp high-quality-draft genome
      is arranged in 2 scaffolds of 53 contigs, contains 7,394 protein-coding genes and
      87 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part
      of the DOE Joint Genome Institute 2010 Community Sequencing Program.
AU  - Reeve W et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 9: 264-272.

PMID- 24976882
VI  - 9
DP  - 2013
TI  - Genome sequence of the Ornithopus/Lupinus-nodulating Bradyrhizobium sp. strain WSM471.
PG  - 254-263
AB  - Bradyrhizobium sp. strain WSM471 is an aerobic, motile, Gram-negative, non-spore-forming rod
      that was isolated from an effective nitrogen- (N2) fixing
      root nodule formed on the annual legume Ornithopus pinnatus (Miller) Druce
      growing at Oyster Harbour, Albany district, Western Australia in 1982. This
      strain is in commercial production as an inoculant for Lupinus and Ornithopus.
      Here we describe the features of Bradyrhizobium sp. strain WSM471, together with
      genome sequence information and annotation. The 7,784,016 bp high-quality-draft
      genome is arranged in 1 scaffold of 2 contigs, contains 7,372 protein-coding
      genes and 58 RNA-only encoding genes, and is one of 20 rhizobial genomes
      sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing
      Program.
AU  - Reeve W et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 9: 254-263.

PMID- 24976881
VI  - 9
DP  - 2013
TI  - Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain TA1.
PG  - 243-253
AB  - Rhizobium leguminosarum bv. trifolii strain TA1 is an aerobic, motile, Gram-negative,
      non-spore-forming rod that is an effective nitrogen fixing
      microsymbiont on the perennial clovers originating from Europe and the
      Mediterranean basin. TA1 however is ineffective with many annual and perennial
      clovers originating from Africa and America. Here we describe the features of R.
      leguminosarum bv. trifolii strain TA1, together with genome sequence information
      and annotation. The 8,618,824 bp high-quality-draft genome is arranged in a 6
      scaffold of 32 contigs, contains 8,493 protein-coding genes and 83 RNA-only
      encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE
      Joint Genome Institute 2010 Community Sequencing Program.
AU  - Reeve W et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 9: 243-253.

PMID- 21304679
VI  - 2
DP  - 2010
TI  - Complete genome sequence of Rhizobium leguminosarum bv trifolii strain WSM2304, an effective microsymbiont of the South American clover Trifolium polymorphum.
PG  - 66-76
AB  - Rhizobium leguminosarum bv trifolii is the effective nitrogen fixing microsymbiont of a
      diverse range of annual and perennial Trifolium (clover)
      species. Strain WSM2304 is an aerobic, motile, non-spore forming, Gram-negative
      rod, isolated from Trifolium polymorphum in Uruguay in 1998. This microsymbiont
      predominated in the perennial grasslands of Glencoe Research Station, in Uruguay,
      to competitively nodulate its host, and fix atmospheric nitrogen. Here we
      describe the basic features of WSM2304, together with the complete genome
      sequence, and annotation. This is the first completed genome sequence for a
      nitrogen fixing microsymbiont of a clover species from the American center of
      origin. We reveal that its genome size is 6,872,702 bp encoding 6,643
      protein-coding genes and 62 RNA only encoding genes. This multipartite genome was
      found to contain 5 distinct replicons; a chromosome of size 4,537,948 bp and four
      circular plasmids of size 1,266,105 bp, 501,946 bp, 308,747 bp and 257,956 bp.
AU  - Reeve W et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 2: 66-76.

PMID- 21304680
VI  - 2
DP  - 2010
TI  - Complete genome sequence of the Medicago microsymbiont Ensifer (Sinorhizobium) medicae strain WSM419.
PG  - 77-86
AB  - Ensifer (Sinorhizobium) medicae is an effective nitrogen fixing microsymbiont of  a diverse
      range of annual Medicago (medic) species. Strain WSM419 is an aerobic,
      motile, non-spore forming, Gram-negative rod isolated from a M. murex root nodule
      collected in Sardinia, Italy in 1981. WSM419 was manufactured commercially in
      Australia as an inoculant for annual medics during 1985 to 1993 due to its
      nitrogen fixation, saprophytic competence and acid tolerance properties. Here we
      describe the basic features of this organism, together with the complete genome
      sequence, and annotation. This is the first report of a complete genome sequence
      for a microsymbiont of the group of annual medic species adapted to acid soils.
      We reveal that its genome size is 6,817,576 bp encoding 6,518 protein-coding
      genes and 81 RNA only encoding genes. The genome contains a chromosome of size
      3,781,904 bp and 3 plasmids of size 1,570,951 bp, 1,245,408 bp and 219,313 bp.
      The smallest plasmid is a feature unique to this medic microsymbiont.
AU  - Reeve W et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 2: 77-86.

PMID- 25197439
VI  - 9
DP  - 2014
TI  - Genome sequence of the Listia angolensis microsymbiont Microvirga lotononidis strain WSM3557(T.).
PG  - 540-550
AB  - Microvirga lotononidis is a recently described species of root-nodule bacteria that is an
      effective nitrogen- (N2) fixing microsymbiont of the symbiotically
      specific African legume Listia angolensis (Welw. ex Bak.) B.-E. van Wyk & Boatwr.
      M. lotononidis possesses several properties that are unusual in root-nodule
      bacteria, including pigmentation and the ability to grow at temperatures of up to
      45 degrees C. Strain WSM3557(T) is an aerobic, motile, Gram-negative,
      non-spore-forming rod isolated from a L. angolensis root nodule collected in
      Chipata, Zambia in 1963. This is the first report of a complete genome sequence
      for the genus Microvirga. Here we describe the features of Microvirga lotononidis
      strain WSM3557(T), together with genome sequence information and annotation. The
      7,082,538 high-quality-draft genome is arranged in 18 scaffolds of 104 contigs,
      contains 6,956 protein-coding genes and 84 RNA-only encoding genes, and is one of
      20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010
      Community Sequencing Program.
AU  - Reeve W et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 540-550.

PMID- 21304718
VI  - 2
DP  - 2010
TI  - Complete genome sequence of Rhizobium leguminosarum bv. trifolii strain WSM1325,  an effective microsymbiont of annual Mediterranean clovers.
PG  - 347-356
AB  - Rhizobium leguminosarum bv trifolii is a soil-inhabiting bacterium that has the capacity to be
      an effective nitrogen fixing microsymbiont of a diverse range of
      annual Trifolium (clover) species. Strain WSM1325 is an aerobic, motile,
      non-spore forming, Gram-negative rod isolated from root nodules collected in 1993
      from the Greek Island of Serifos. WSM1325 is produced commercially in Australia
      as an inoculant for a broad range of annual clovers of Mediterranean origin due
      to its superior attributes of saprophytic competence, nitrogen fixation and
      acid-tolerance. Here we describe the basic features of this organism, together
      with the complete genome sequence, and annotation. This is the first completed
      genome sequence for a microsymbiont of annual clovers. We reveal that its genome
      size is 7,418,122 bp encoding 7,232 protein-coding genes and 61 RNA-only encoding
      genes. This multipartite genome contains 6 distinct replicons; a chromosome of
      size 4,767,043 bp and 5 plasmids of size 828,924 bp, 660,973 bp, 516,088 bp,
      350,312 bp and 294,782 bp.
AU  - Reeve W et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 2: 347-356.

PMID- 25197447
VI  - 9
DP  - 2014
TI  - Genome sequence of the Medicago-nodulating Ensifer meliloti commercial inoculant  strain RRI128.
PG  - 602-613
AB  - Ensifer meliloti strain RRI128 is an aerobic, motile, Gram-negative, non-spore-forming rod.
      RRI128 was isolated from a nodule recovered from the roots
      of barrel medic (Medicago truncatula) grown in the greenhouse and inoculated with
      soil collected from Victoria, Australia. The strain is used in commercial
      inoculants in Australia. RRI128 nodulates and forms an effective symbiosis with a
      diverse range of lucerne cultivars (Medicago sativa) and several species of
      annual medic (M. truncatula, Medicago littoralis and Medicago tornata), but forms
      an ineffective symbiosis with Medicago polymorpha. Here we describe the features
      of E. meliloti strain RRI128, together with genome sequence information and
      annotation. The 6,900,273 bp draft genome is arranged into 156 scaffolds of 157
      contigs, contains 6,683 protein-coding genes and 87 RNA-only encoding genes, and
      is one of 100 rhizobial genomes sequenced as part of the DOE Joint Genome
      Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria
      (GEBA-RNB) project.
AU  - Reeve W
AU  - Ballard R
AU  - Drew E
AU  - Tian R
AU  - Brau L
AU  - Goodwin L
AU  - Huntemann M
AU  - Han J
AU  - Tatiparthi R
AU  - Chen A
AU  - Mavrommatis K
AU  - Markowitz V
AU  - Palaniappan K
AU  - Ivanova N
AU  - Pati A
AU  - Woyke T
AU  - Kyrpides N
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 602-613.

PMID- 25197437
VI  - 9
DP  - 2014
TI  - Genome sequence of Ensifer medicae strain WSM1115; an acid-tolerant Medicago-nodulating microsymbiont from Samothraki, Greece.
PG  - 514-526
AB  - Ensifer medicae strain WSM1115 forms effective nitrogen fixing symbioses with a range of
      annual Medicago species and is used in commercial inoculants in
      Australia. WSM1115 is an aerobic, motile, Gram-negative, non-spore-forming rod.
      It was isolated from a nodule recovered from the root of burr medic (Medicago
      polymorpha) collected on the Greek Island of Samothraki. WSM1115 has a broad host
      range for nodulation and N2 fixation capacity within the genus Medicago, although
      this does not extend to all medic species. WSM1115 is considered saprophytically
      competent in moderately acid soils (pH(CaCl2) 5.0), but it has failed to persist
      at field sites where soil salinity exceeded 10 ECe (dS/m). Here we describe the
      features of E. medicae strain WSM1115, together with genome sequence information
      and its annotation. The 6,861,065 bp high-quality-draft genome is arranged into 7
      scaffolds of 28 contigs, contains 6,789 protein-coding genes and 83 RNA-only
      encoding genes, and is one of 100 rhizobial genomes sequenced as part of the DOE
      Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root
      Nodule Bacteria (GEBA-RNB) project.
AU  - Reeve W
AU  - Ballard R
AU  - Howieson J
AU  - Drew E
AU  - Tian R
AU  - Brau L
AU  - Munk C
AU  - Davenport K
AU  - Chain P
AU  - Goodwin L
AU  - Pagani I
AU  - Huntemann M
AU  - Mavrommatis K
AU  - Pati A
AU  - Markowitz V
AU  - Ivanova N
AU  - Woyke T
AU  - Kyrpides N
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 514-526.

PMID- 24976880
VI  - 9
DP  - 2013
TI  - Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain SRDI943.
PG  - 232-242
AB  - Rhizobium leguminosarum bv. trifolii SRDI943 (strain syn. V2-2) is an aerobic, motile,
      Gram-negative, non-spore-forming rod that was isolated from a root nodule
      of Trifolium michelianum Savi cv. Paradana that had been grown in soil collected
      from a mixed pasture in Victoria, Australia. This isolate was found to have a
      broad clover host range but was sub-optimal for nitrogen fixation with T.
      subterraneum (fixing 20-54% of reference inoculant strain WSM1325) and was found
      to be totally ineffective with the clover species T. polymorphum and T. pratense.
      Here we describe the features of R. leguminosarum bv. trifolii strain SRDI943,
      together with genome sequence information and annotation. The 7,412,387 bp
      high-quality-draft genome is arranged into 5 scaffolds of 5 contigs, contains
      7,317 protein-coding genes and 89 RNA-only encoding genes, and is one of 100
      rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010
      Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB)
      project.
AU  - Reeve W
AU  - Drew E
AU  - Ballard R
AU  - Melino V
AU  - Tian R
AU  - De Meyer S
AU  - Brau L
AU  - Ninawi M
AU  - Daligault H
AU  - Davenport K
AU  - Erkkila T
AU  - Goodwin L
AU  - Gu W
AU  - Munk C
AU  - Teshima H
AU  - Xu Y
AU  - Chain P
AU  - Kyrpides N
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 9: 232-242.

PMID- 24976879
VI  - 9
DP  - 2013
TI  - Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain SRDI565.
PG  - 220-231
AB  - Rhizobium leguminosarum bv. trifolii SRDI565 (syn. N8-J) is an aerobic, motile, Gram-negative,
      non-spore-forming rod. SRDI565 was isolated from a nodule
      recovered from the roots of the annual clover Trifolium subterraneum subsp.
      subterraneum grown in the greenhouse and inoculated with soil collected from New
      South Wales, Australia. SRDI565 has a broad host range for nodulation within the
      clover genus, however N2-fixation is sub-optimal with some Trifolium species and
      ineffective with others. Here we describe the features of R. leguminosarum bv.
      trifolii strain SRDI565, together with genome sequence information and
      annotation. The 6,905,599 bp high-quality-draft genome is arranged into 7
      scaffolds of 7 contigs, contains 6,750 protein-coding genes and 86 RNA-only
      encoding genes, and is one of 100 rhizobial genomes sequenced as part of the DOE
      Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root
      Nodule Bacteria (GEBA-RNB) project.
AU  - Reeve W
AU  - Drew E
AU  - Ballard R
AU  - Melino V
AU  - Tian R
AU  - De Meyer S
AU  - Brau L
AU  - Ninawi M
AU  - Teshima H
AU  - Goodwin L
AU  - Chain P
AU  - Liolios K
AU  - Pati A
AU  - Mavromatis K
AU  - Ivanova N
AU  - Markowitz V
AU  - Woyke T
AU  - Kyrpides N
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 9: 220-231.

PMID- 25197490
VI  - 9
DP  - 2014
TI  - Genome sequence of Microvirga lupini strain LUT6(T), a novel Lupinus alphaproteobacterial microsymbiont from Texas.
PG  - 1159-1167
AB  - Microvirga lupini LUT6(T) is an aerobic, non-motile, Gram-negative, non-spore-forming rod that
      can exist as a soil saprophyte or as a legume
      microsymbiont of Lupinus texensis. LUT6(T) was isolated in 2006 from a nodule
      recovered from the roots of the annual L. texensis growing in Travis Co., Texas.
      LUT6(T) forms a highly specific nitrogen-fixing symbiosis with endemic L.
      texensis and no other Lupinus species can form an effective nitrogen-fixing
      symbiosis with this isolate. Here we describe the features of M. lupini LUT6(T),
      together with genome sequence information and its annotation. The 9,633,614 bp
      improved high quality draft genome is arranged into 160 scaffolds of 1,366
      contigs containing 10,864 protein-coding genes and 87 RNA-only encoding genes,
      and is one of 20 rhizobial genomes sequenced as part of a DOE Joint Genome
      Institute 2010 Community Sequencing Project.
AU  - Reeve W
AU  - Parker M
AU  - Tian R
AU  - Goodwin L
AU  - Teshima H
AU  - Tapia R
AU  - Han C
AU  - Han J
AU  - Liolios K
AU  - Huntemann M
AU  - Pati A
AU  - Woyke T
AU  - Mavromatis K
AU  - Markowitz V
AU  - Ivanova N
AU  - Kyrpides N
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 1159-1167.

PMID- 25780496
VI  - 9
DP  - 2014
TI  - Genome sequence of the Lotus corniculatus microsymbiont Mesorhizobium loti strain R88B.
PG  - 3
AB  - Mesorhizobium loti strain R88B was isolated in 1993 in the Rocklands range in Otago, New
      Zealand from a Lotus corniculatus root nodule. R88B is an aerobic,
      Gram-negative, non-spore-forming rod. This report reveals the genome of M. loti
      strain R88B contains a single scaffold of size 7,195,110 bp which encodes 6,950
      protein-coding genes and 66 RNA-only encoding genes. This genome does not harbor
      any plasmids but contains the integrative and conjugative element ICEMlSym(R7A),
      also known as the R7A symbiosis island, acquired by horizontal gene transfer in
      the field environment from M. loti strain R7A. It also contains a mobilizable
      genetic element ICEMladh(R88B), that encodes a likely adhesin gene which has
      integrated downstream of ICEMlSym(R7A), and three acquired loci that together
      allow the utilization of the siderophore ferrichrome. This rhizobial genome is
      one of 100 sequenced as part of the DOE Joint Genome Institute 2010 Genomic
      Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.
AU  - Reeve W
AU  - Sullivan J
AU  - Ronson C
AU  - Tian R
AU  - Brau L
AU  - Davenport K
AU  - Goodwin L
AU  - Chain P
AU  - Woyke T
AU  - Lobos E
AU  - Huntemann M
AU  - Pati A
AU  - Mavromatis K
AU  - Markowitz V
AU  - Ivanova N
AU  - Kyrpides N
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 3.

PMID- 26380641
VI  - 10
DP  - 2015
TI  - High-Quality draft genome sequence of the Lotus spp. microsymbiont Mesorhizobium  loti strain CJ3Sym.
PG  - 54
AB  - Mesorhizobium loti strain CJ3Sym was isolated in 1998 following transfer of the integrative
      and conjugative element ICEMlSym(R7A), also known as the R7A symbiosis island, in a laboratory
      mating from the donor M. loti strain R7A to a nonsymbiotic recipient Mesorhizobium strain CJ3.
      Strain CJ3 was originally isolated from a field site in the Rocklands range in New Zealand in
      1994. CJ3Sym  is an aerobic, Gram-negative, non-spore-forming rod. This report reveals the
      genome of M. loti strain CJ3Sym currently comprises 70 scaffolds totaling 7,563,725 bp. The
      high-quality draft genome is arranged in 70 scaffolds of 71 contigs, contains 7,331
      protein-coding genes and 70 RNA-only encoding genes, and  is part of the GEBA-RNB project
      proposal.
AU  - Reeve W
AU  - Sullivan J
AU  - Ronson C
AU  - Tian R
AU  - Munk C
AU  - Han C
AU  - Reddy TB
AU  - Seshadri R
AU  - Woyke T
AU  - Pati A
AU  - Markowitz V
AU  - Ivanova N
AU  - Kyrpides N
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 54.

PMID- 25197433
VI  - 9
DP  - 2014
TI  - Genome sequence of Ensifer arboris strain LMG 14919(T); a microsymbiont of the legume Prosopis chilensis growing in Kosti, Sudan.
PG  - 473-483
AB  - Ensifer arboris LMG 14919(T) is an aerobic, motile, Gram-negative, non-spore-forming rod that
      can exist as a soil saprophyte or as a legume
      microsymbiont of several species of legume trees. LMG 14919(T) was isolated in
      1987 from a nodule recovered from the roots of the tree Prosopis chilensis
      growing in Kosti, Sudan. LMG 14919(T) is highly effective at fixing nitrogen with
      P. chilensis (Chilean mesquite) and Acacia senegal (gum Arabic tree or gum
      acacia). LMG 14919(T) does not nodulate the tree Leucena leucocephala, nor the
      herbaceous species Macroptilium atropurpureum, Trifolium pratense, Medicago
      sativa, Lotus corniculatus and Galega orientalis. Here we describe the features
      of E. arboris LMG 14919(T), together with genome sequence information and its
      annotation. The 6,850,303 bp high-quality-draft genome is arranged into 7
      scaffolds of 12 contigs containing 6,461 protein-coding genes and 84 RNA-only
      encoding genes, and is one of 100 rhizobial genomes sequenced as part of the DOE
      Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root
      Nodule Bacteria (GEBA-RNB) project.
AU  - Reeve W
AU  - Tian R
AU  - Brau L
AU  - Goodwin L
AU  - Munk C
AU  - Detter C
AU  - Tapia R
AU  - Han C
AU  - Liolios K
AU  - Huntemann M
AU  - Pati A
AU  - Woyke T
AU  - Mavrommatis K
AU  - Markowitz V
AU  - Ivanova N
AU  - Kyrpides N
AU  - Willems A
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 473-483.

PMID- 28270909
VI  - 12
DP  - 2017
TI  - High-quality permanent draft genome sequence of the Bradyrhizobium elkanii type strain USDA 76T, isolated from Glycine max (L.) Merr.
PG  - 26
AB  - Bradyrhizobium elkanii USDA 76T (INSCD = ARAG00000000), the type strain for Bradyrhizobium
      elkanii, is an aerobic, motile, Gram-negative, non-spore-forming
      rod that was isolated from an effective nitrogen-fixing root nodule of Glycine
      max (L. Merr) grown in the USA. Because of its significance as a microsymbiont of
      this economically important legume, B. elkanii USDA 76T was selected as part of
      the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and
      Archaea-Root Nodule Bacteria sequencing project. Here the symbiotic abilities of
      B. elkanii USDA 76T are described, together with its genome sequence information
      and annotation. The 9,484,767 bp high-quality draft genome is arranged in 2
      scaffolds of 25 contigs, containing 9060 protein-coding genes and 91 RNA-only
      encoding genes. The B. elkanii USDA 76T genome contains a low GC content region
      with symbiotic nod and fix genes, indicating the presence of a symbiotic island
      integration. A comparison of five B. elkanii genomes that formed a clique
      revealed that 356 of the 9060 protein coding genes of USDA 76T were unique,
      including 22 genes of an intact resident prophage. A conserved set of 7556 genes
      were also identified for this species, including genes encoding a general
      secretion pathway as well as type II, III, IV and VI secretion system proteins.
      The type III secretion system has previously been characterized as a host
      determinant for Rj and/or rj soybean cultivars. Here we show that the USDA 76T
      genome contains genes encoding all the type III secretion system components,
      including a translocon complex protein NopX required for the introduction of
      effector proteins into host cells. While many bradyrhizobial strains are unable
      to nodulate the soybean cultivar Clark (rj1), USDA 76T was able to elicit nodules
      on Clark (rj1), although in reduced numbers, when plants were grown in Leonard
      jars containing sand or vermiculite. In these conditions, we postulate that the
      presence of NopX allows USDA 76T to introduce various effector molecules into
      this host to enable nodulation.
AU  - Reeve W
AU  - van Berkum P
AU  - Ardley J
AU  - Tian R
AU  - Gollagher M
AU  - Marinova D
AU  - Elia P
AU  - Reddy TB
AU  - Pillay M
AU  - Varghese N
AU  - Seshadri R
AU  - Ivanova N
AU  - Woyke T
AU  - Baeshen MN
AU  - Baeshen NA
AU  - Kyrpides N
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 26.

PMID- 22046404
VI  - 6
DP  - 2011
TI  - Rates of Mutation and Host Transmission for an Escherichia coli Clone over 3 Years.
PG  - E26907
AB  - Although over 50 complete Escherichia coli/Shigella genome sequences are
      available, it is only for closely related strains, for example the O55:H7
      and O157:H7 clones of E. coli, that we can assign differences to
      individual evolutionary events along specific lineages. Here we sequence
      the genomes of 14 isolates of a uropathogenic E. coli clone that persisted
      for 3 years within a household, including a dog, causing a urinary tract
      infection (UTI) in the dog after 2 years. The 20 mutations observed fit a
      single tree that allows us to estimate the mutation rate to be about 1.1
      per genome per year, with minimal evidence for adaptive change, including
      in relation to the UTI episode. The host data also imply at least 6 host
      transfer events over the 3 years, with 2 lineages present over much of
      that period. To our knowledge, these are the first direct measurements for
      a clone in a well-defined host community that includes rates of mutation
      and host transmission. There is a concentration of non-synonymous
      mutations associated with 2 transfers to the dog, suggesting some
      selection pressure from the change of host. However, there are no changes
      to which we can attribute the UTI event in the dog, which suggests that
      this occurrence after 2 years of the clone being in the household may have
      been due to chance, or some unknown change in the host or environment. The
      ability of a UTI strain to persist for 2 years and also to transfer
      readily within a household has implications for epidemiology, diagnosis,
      and clinical intervention.
AU  - Reeves PR
AU  - Liu B
AU  - Zhou Z
AU  - Li D
AU  - Guo D
AU  - Ren Y
AU  - Clabots C
AU  - Lan R
AU  - Johnson JR
AU  - Wang L
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2011 6: E26907.

PMID- 26941148
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Alcaligenes faecalis Strain IITR89, an Indole-Oxidizing  Bacterium.
PG  - e00067-16
AB  - We report the draft genome sequence of Alcaligenes faecalis strain IITR89, a bacterium able to
      form indigo by utilizing indole as the sole carbon source. The
      Alcaligenes species is increasingly reported for biodegradation of diverse
      toxicants and thus complete sequencing may provide insight into biodegradation
      capabilities and other phenotypes.
AU  - Regar RK
AU  - Gaur VK
AU  - Mishra G
AU  - Jadhao S
AU  - Kamthan M
AU  - Manickam N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00067-16.

PMID- 26941147
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Acinetobacter baumannii IITR88, a Bacterium Degrading Indoles and Other Aromatic Compounds.
PG  - e00065-16
AB  - Here, we report the 4.16-Mb draft genome sequence of an indole-degrading bacterium,
      Acinetobacter baumannii IITR88, isolated from the Bhagirathi river in
      India. A total of 4,069 coding regions (CDSs), 3 rRNAs, and 52 tRNAs were
      predicted. Genes for the degradation of indoles, phenylacetaldehyde,
      anthranilate, and several other aromatic compounds were present.
AU  - Regar RK
AU  - Gaur VK
AU  - Mishra G
AU  - Jadhao S
AU  - Kamthan M
AU  - Manickam N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00065-16.

PMID- 28630206
VI  - 61
DP  - 2017
TI  - Rapid and Consistent Evolution of Colistin Resistance in Extensively Drug-Resistant Pseudomonas aeruginosa during Morbidostat Culture.
PG  - e00043-17
AB  - Colistin is a last resort antibiotic commonly used against multidrug-resistant strains of
      Pseudomonas aeruginosa To investigate the potential for in-situ evolution of resistance
      against colistin and to map the molecular targets of colistin resistance, we exposed two P.
      aeruginosa isolates to colistin using a continuous culture device known as morbidostat. As a
      result, colistin resistance reproducibly increased 10-fold within ten days, and 100-fold
      within 20 days, along with highly stereotypic, yet strain specific mutation patterns. The
      majority of mutations hit the pmrAB two component signaling system and genes involved in
      lipopolysaccharide (LPS) synthesis, including lpxC, pmrE, and migA We tracked the frequencies
      of all arising mutations by whole genome deep sequencing every 3-4 days to provide a detailed
      picture of the dynamics of resistance evolution, including competition and displacement among
      multiple resistant sub-populations. In seven out of 18 cultures, we observed mutations in mutS
      along with a mutator phenotype that seemed to facilitate resistance evolution.
AU  - Regenbogen B
AU  - Willmann M
AU  - Steglich M
AU  - Bunk B
AU  - Nubel U
AU  - Peter S
AU  - Neher RA
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2017 61: e00043-17.

PMID- 25792043
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Six Bordetella hinzii Isolates Acquired from Avian and  Mammalian Hosts.
PG  - e00081-15
AB  - Bordetella hinzii is a Gram-negative bacterium known to infect poultry, humans, rabbits, and
      rodents. It is an opportunistic pathogen in immunocompromised
      humans, and some strains cause mild to moderate respiratory disease in turkeys.
      Little is known as to the degree of genetic diversity within the species or the
      genetic basis for virulence. Here, we report the genome sequences of six isolates
      of B. hinzii acquired from humans, rabbits, or turkeys. These data provide a
      framework for refining the population structure of the genus, establishing
      relationships among genetically distinct isolates, and developing an
      understanding of the possible virulence mechanisms of the bacterium.
AU  - Register KB
AU  - Ivanov YV
AU  - Harvill ET
AU  - Brinkac L
AU  - Kim M
AU  - Losada L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00081-15.

PMID- 25908122
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of 53 Genetically Distinct Isolates of Bordetella bronchiseptica Representing 11 Terrestrial and Aquatic Hosts.
PG  - e00152-15
AB  - Bordetella bronchiseptica infects a variety of mammalian and avian hosts. Here, we report the
      genome sequences of 53 genetically distinct isolates acquired from
      a broad range of terrestrial and aquatic animals. These data will greatly
      facilitate ongoing efforts to better understand the evolution, host adaptation,
      and virulence mechanisms of B. bronchiseptica.
AU  - Register KB
AU  - Ivanov YV
AU  - Jacobs N
AU  - Meyer JA
AU  - Goodfield LL
AU  - Muse SJ
AU  - Smallridge WE
AU  - Brinkac L
AU  - Kim M
AU  - Sanka R
AU  - Harvill ET
AU  - Losada L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00152-15.

PMID- 25700413
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of an Extensively Drug-Resistant Mycobacterium tuberculosis Manu-Ancestor Spoligo-International Type 523 Isolate from Thailand.
PG  - e01589-14
AB  - We present the draft genome sequence of DS-16780, with a rare spoligo-international type (SIT)
      523 (777777777777771) genotype, which reveals an extensively drug-resistant Mycobacterium
      tuberculosis (XDR-TB) phenotype. The isolate is a representative of clonal XDR-TB from the
      western part of Thailand.
AU  - Regmi SM
AU  - Chaiprasert A
AU  - Coker OO
AU  - Disratthakit A
AU  - Prammananan T
AU  - Suriyaphol P
AU  - Yik-Ying T
AU  - Twee HO
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01589-14.

PMID- 21193609
VI  - 193
DP  - 2010
TI  - Defining the plasmid-encoded restriction-modification systems of the Lyme disease spirochete Borrelia burgdorferi.
PG  - 1161-1171
AB  - The restriction-modification (R-M) systems of many bacteria present a barrier to the stable
      introduction of foreign DNA. The Lyme disease spirochete Borrelia burgdorferi has two
      plasmid-encoded putative R-M genes, bbe02 and bbq67, whose presence limits transformation by
      shuttle vector DNA from E. coli. We show that both the bbe02 and bbq67 loci in recipient B.
      burgdorferi limit transformation with shuttle vector DNA from E. coli, irrespective of its
      dam, dcm, or hsd methylation status. However, plasmid DNA purified from B. burgdorferi
      transformed naive B. burgdorferi much more efficiently than plasmid DNA from E. coli,
      particularly when the bbe02 and bbq67 genotypes of the B. burgdorferi DNA source matched that
      of the recipient. We detected adenine methylation of plasmid DNA prepared from B. burgdorferi
      that carried bbe02 and bbq67. These results indicate that the bbe02 and bbq67 loci of B.
      burgdorferi encode distinct R-M enzymes that methylate endogenous DNA and cleave foreign DNA
      lacking the same sequence-specific modification. Our findings have basic implications for
      horizontal gene transfer among B. burgdorferi strains with distinct plasmid contents. Further
      characterization and identification of the nucleotide sequences recognized by BBE02 and BBQ67
      will facilitate efficient genetic manipulation of this pathogenic spirochete.
AU  - Rego ROM
AU  - Bestor A
AU  - Rosa PA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 193: 1161-1171.

PMID- 28473385
VI  - 5
DP  - 2017
TI  - Draft Whole-Genome Sequences of Multidrug-Resistant Escherichia coli O157:H7 Strains Isolated from Feedlot Cattle Treated with Growth-Promoting Agents.
PG  - e00284-17
AB  - Enterohemorrhagic Escherichia coli serotype O157:H7 is a major cause of foodborne outbreaks
      and hemolytic-uremic syndrome. Here, we report the draft genome
      sequences of three antibiotic-resistant E. coli O157:H7 strains isolated from
      feedlot cattle. These draft genome sequences will aid in the development of
      sequence-based tools for the detection of virulence and antimicrobial resistance
      genotypes.
AU  - Rehman MA
AU  - Carrillo C
AU  - Malouin F
AU  - Diarra MS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00284-17.

PMID- 26404595
VI  - 3
DP  - 2015
TI  - Complete Genome and Plasmid Sequences of Three Canadian Strains of Salmonella enterica subsp. enterica Serovar Enteritidis Belonging to Phage Types 8, 13, and  13a.
PG  - e01017-15
AB  - Salmonella enterica subsp. enterica serovar Enteritidis is a prominent cause of human
      salmonellosis frequently linked to poultry products. In Canada, S. Enteritidis phage types 8,
      13, and 13a predominate among both clinical and poultry isolates. Here, we report the complete
      genome and plasmid sequences of poultry isolates of these three phage types.
AU  - Rehman MA
AU  - Labbe G
AU  - Ziebell K
AU  - Johnson RP
AU  - Nash JH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01017-15.

PMID- 24762938
VI  - 2
DP  - 2014
TI  - Complete Genome Sequences of 16 Canadian Strains of Salmonella enterica subsp. enterica Serovar Enteritidis.
PG  - e00330-14
AB  - Salmonella enterica subsp. enterica serovar Enteritidis is an important zoonotic food-borne
      pathogen causing serious human illnesses frequently linked to poultry products. Here, we
      report fully assembled genome sequences of 16 S. Enteritidis strains with common pulsed-field
      gel electrophoresis (PFGE) and phage types (8, 13, 13a, and 14b) that predominate in North
      America.
AU  - Rehman MA
AU  - Ziebell K
AU  - Nash JH
AU  - Kropinski AM
AU  - Ross A
AU  - Al-Lami M
AU  - Boerlin P
AU  - Chui L
AU  - Devenish J
AU  - Bekal S
AU  - Graham M
AU  - Amoako KK
AU  - Johnson RP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00330-14.

PMID- 24786953
VI  - 2
DP  - 2014
TI  - High-Quality Draft Whole-Genome Sequences of 162 Salmonella enterica subsp. enterica Serovar Enteritidis Strains Isolated from Diverse Sources in Canada.
PG  - e00348-14
AB  - We report the high-quality draft genome sequences of 162 strains of Salmonella enterica subsp.
      enterica serovar Enteritidis representing diverse phage types and
      pulsed-field gel electrophoresis (PFGE) profiles. The analysis of these genomes
      will enable the identification of markers that are useful for differentiating
      strains of this highly clonal serovar and will provide insights into the
      evolution, virulence, and epidemiology of the strains.
AU  - Rehman MA
AU  - Ziebell K
AU  - Nash JH
AU  - Kropinski AM
AU  - Zong Z
AU  - Nafziger E
AU  - Boerlin P
AU  - Chui L
AU  - Devenish J
AU  - Bekal S
AU  - Graham M
AU  - Johnson RP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00348-14.

PMID- 24051312
VI  - 1
DP  - 2013
TI  - Multiple Genome Sequences of Helicobacter pylori Strains of Diverse Disease and Antibiotic Resistance Backgrounds from Malaysia.
PG  - e00687-13
AB  - Helicobacter pylori causes human gastroduodenal diseases, including chronic gastritis and
      peptic ulcer disease. It is also a major microbial risk factor for
      the development of gastric adenocarcinoma and mucosa-associated lymphoid tissue
      (MALT) lymphoma. Twenty-one strains with different ethnicity, disease, and
      antimicrobial susceptibility backgrounds were sequenced by use of Illumina HiSeq
      and PacBio RS platforms.
AU  - Rehvathy V
AU  - Tan MH
AU  - Gunaletchumy SP
AU  - Teh X
AU  - Wang S
AU  - Baybayan P
AU  - Singh S
AU  - Ashby M
AU  - Kaakoush NO
AU  - Mitchell HM
AU  - Croft LJ
AU  - Goh KL
AU  - Loke MF
AU  - Vadivelu J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00687-13.

PMID- Not carried by PubMed...
VI  - 194
DP  - 1987
TI  - High resolution mapping of the DNA-protein interface in the EcoRI DNA methylase system.
PG  - 63
AB  - This monomeric, S-Adenosyl-Methionine (SAM) dependent enzyme recognizes the
      palindromic double stranded DNA sequence 5' GAATTC 3' and methylates the
      exocyclic amino of the second adenine.  As part of our effort to understand the
      origins of sequence specific DNA binding we are characterizing the interactions
      between the methylase and its DNA substrate.  The experimental methods include
      the use of small, well defined oligonucleotides in conjunction with DNase I and
      hydroxy radical (PNAS (1986) 83 5469) mapping.  Results with altered flanking
      DNA sequences, hemimethylated recognition sequences, and modulation of binding
      via SAM (and SAM analogs) will be presented.
AU  - Reich NO
AU  - Danzitz MJ
PT  - Journal Article
TA  - ACS Abstracts
JT  - ACS Abstracts
SO  - ACS Abstracts 1987 194: 63.

PMID- 1536835
VI  - 31
DP  - 1992
TI  - EcoRI DNA methyltransferase-DNA interactions.
PG  - 1937-1945
AB  - We present a novel strategy with synthetic hemimethylated DNA substrates
      containing uracil for thymine and inosine for guanosine replacements and EcoRI
      DNA methyltransferase to characterize the importance of major groove
      hydrophobic groups to the sequence-specific modification of DNA.  The bacterial
      MTase uses S-adenosyl-L-methionine to methylate the double-stranded DNA site
      5'GAATTC3' at the N6 position of the central adenosine of each strand.  Uracil
      substitution in either strand at the outer thymine (5'GAATUC3') causes 2.2- and
      1.7-fold improvements in specificity (kcat/KmDNA).  The fact that the
      specificity constant for the substrate containing uracil in both strands is
      identifical to the value expected for noninteracting substitutions suggests
      that no significant methyltransferase-DNA interactions are altered beyond the
      site of etiher substitution.  Similar analysis of the internal thymine
      (5'GAAUTC3') also shows these methyl groups to make a negative contribution to
      specificity, although the observed non-additivity with the doubly modified
      substrate clearly shows methyltransferase-DNA interactions beyond the site of
      substitution to be affected in this case.  To further probe the effect of
      analogue incorporation on methyltransferase-DNA interactions beyond the site of
      substitution, the relatively silent and additive uracil changes (5'GAATUC3')
      were combined with inosine for guanosine substitutions (e.g., 5'IAATTC3') known
      to have significant negative effects on specificity.  In contrast to the
      additivity observed with the outer thymines, these studies show significant
      changes in methyltransferase-DNA interactions caused by the removal of the
      thymine methyls.  Our results implicate a complex and flexible
      methyltransferase-DNA interface in which subtle structural changes in the
      substrate are transmitted over the entire canonical site.  Thermal stability
      analyses and determination of Delta H and Delta S for the double- to
      single-stranded transition for single and doubly substituted substrates show no
      additivity.  This suggests that structural changes in the DNA alone may occur
      beyond the site of substitution.  Interestingly, substrates with widely varying
      enthalpy and entropy terms show similar specificity with the Mtase, suggesting
      the Mtase is insensitive to the underlying conformational differences.
AU  - Reich NO
AU  - Danzitz MJ
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1992 31: 1937-1945.

PMID- 1754395
VI  - 19
DP  - 1991
TI  - Non-additivity of sequence-specific enzyme-DNA interactions in the EcoRI DNA methyltransferase.
PG  - 6587-6594
AB  - We describe a novel strategy to characterize protein-DNA interactions involving
      monomeric enzymes such as DNA methyltransferases (Mtases).  This strategy is
      applied to our investigation of the EcoRI DNA Mtase, which binds its double
      stranded recognition site 5'-G-AATTC-3' and methylates the central adenosine of
      each strand using S-adenosyl-L-methionine as the methyl donor.  We show that
      prior methylation of adenosine in either strand does not perturb catalysis.  In
      contrast, substrates substituted with deoxyinosine at either guanosine position
      (T-BM15 and T15-BM) show the minor groove residing N2 amino group of both
      guanosines contribute to DNA recognition since specificity constants for the
      modified substrates are reduced 13 and 39 fold.  Similar analysis of a
      substrate containing deoxyinosine at both positions (T15-BM15) clearly shows
      that some communication occurs between the sites.  To determine the extent to
      which structural changes in the DNA alone contribute to this lack of
      additivity, we performed DNA melting analysis of the singly and doubly
      substituted substrates, and also found nonadditivity.  Although our functional
      and structural analyses suggest that deoxyinosine incorporation causes long
      range conformational effects, the similarity of Km(AdoMet) for all substrates
      suggests that no large-scale structural changes occur in the Mtase-DNA-AdoMet
      complex.  Our results support the following conclusions: 1) The non-additivity
      shown in this system contrasts with the widespread demonstration of additivity
      involving repressors (Lehming et al., 1990; Takeda et al., 1989; Ebright et
      al., 1987), suggesting that sequence discrimination by enzymes may involve more
      complex mechanisms.  Further, this non-additivity precludes quantitative
      assignment of individual interactions and we suggest that future analyses of
      this and related enzyme systems with base analogs include detailed information
      about the long range structural consequences of individual substitutions.  2)
      Although T15-BM and T-BM15 are shown to be radically different by thermodynamic
      analysis, the similar specificity constants with the Mtase suggest that the
      underlying structural differences (e.g., altered helical parameters of the DNA)
      are not critical for sequence-recognition.  3) The significance of minor groove
      Mtase-DNA interactions to specificity is confirmed.
AU  - Reich NO
AU  - Danzitz MJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 6587-6594.

PMID- 2323503
VI  - 4
DP  - 1990
TI  - Mechanisms of substrate discrimination in the EcoRI DNA methylase.
PG  - A1793
AB  - We have investigated how this prokaryotic Type II DNA methylase selectively
      modifies the second adenine in the double stranded canonical site, 5' GAATTC
      3'.  Non-selfcomplementary 14 basepair DNA substrates have been submitted to
      detailed functional analysis by comparisons of true steady-state kinetic
      parameters.  Modifications within the recognition hexanucleotide include  i)
      methylation of one strand, ii) removal of single sites of (potential)
      methylase-DNA interaction (e.g. minor groove H-bond donor, major groove
      thymidine-methyl) iii) substitution of basepairs within the recognition site.
      Prior methylation of one strand does not effect kinetic parameters (Kcat, Km or
      Kcat/Km).  A significant contribution toward specificity (kcat/Km)DNA derives
      from minor groove interactions; this is largely a result of increases in KmDNA.
      In contrast, discrimination against substrates related by single basepair
      changes occur through decreases in kcat of up to one million fold.  No effects
      on KmAdoMet were detected for any DNA substrate.  The structural integrity of
      the modified DNA substrates was determined with melting temperature and second
      site analyses.
AU  - Reich NO
AU  - Danzitz MJ
AU  - Osti F
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1990 4: A1793.

PMID- Not carried by PubMed...
VI  - 194
DP  - 1987
TI  - Functional analysis of cysteines in the EcoRI DNA methylase.
PG  - 64
AB  - This monomeric, S-adenosyl-methionine (SAM) dependent enzyme recognizes the
      palindromic double stranded DNA sequence 5' GAATTC 3' and methylates the
      exocyclic amino of the second adenine.  As part of our effort to understand the
      origins of sequence specific DNA binding we are characterizing the functional
      significance of the enzyme's seven cysteines (326 total amino acids).  Cysteine
      labeling experiments with N-Ethyl-Maleimide (NEM) lead to inactivation of
      enzyme activity.  Substrate and cofactor (SAM) protection are being used to
      implicate specific cysteines.  Proteolytic digestion of 3H NEM labeled enzyme
      followed by amino acid sequencing affords the assignment of specific
      cysteine(s).
AU  - Reich NO
AU  - DiMichele L
PT  - Journal Article
TA  - ACS Abstracts
JT  - ACS Abstracts
SO  - ACS Abstracts 1987 194: 64.

PMID- 2341412
VI  - 265
DP  - 1990
TI  - Identification of peptides involved in S-Adenosylmethionine binding in the EcoRI DNA methylase.
PG  - 8929-8934
AB  - The Mr 38,050 monomeric EcoRI DNA methylase is part of a bacterial
      restriction-modification system.  The methylase transfers the methyl group from
      S-adenosylmethionine (AdoMet) to the second adenine in the double-stranded DNA
      sequence 5'-GAATTC-3'.  We have used the radiolabeled photoaffinity analog
      8-azido-S-adenosylmethionine (8-N3-AdoMet) to identify peptides at the AdoMet
      binding site in the binary methylase-cofactor analog complex.  The dissociation
      constants in the absence of DNA for the analog and AdoMet are 12.9 and 4.8
      microM, respectively.  The apparent kcat and Km values, obtained with the
      double-stranded DNA substrate 5'-CGCGAATTCGCG-3', are 5.0 s-1 and 0.710 microM
      (8-N3-AdoMet) and 4.3 s-1 and 0.335 microM (AdoMet).  Photolabeling by
      8-N3-AdoMet occurs upon irradiation with ultraviolet light and is inhibited by
      AdoMet.  Digestion of the adducted methylase with subtilisin generated several
      radiolabeled peptides.  Peptide sequencing from independent photolabeling
      experiments revealed two radiolabeled peptides containing amino acids 206-212
      and 213-221.  Instability of the adducted peptides precluded assignment of
      modified amino acids.
AU  - Reich NO
AU  - Everett EA
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1990 265: 8929-8934.

PMID- 2007130
VI  - 30
DP  - 1991
TI  - Structural and functional analysis of EcoRI DNA methyltransferase by proteolysis.
PG  - 2940-2946
AB  - Native EcoRI DNA methyltransferase (Mtase, Mr 38050) is proteolyzed by trypsin
      to generate an intermediate 36-kDa fragment (p36) followed by the formation of
      two polypeptides of Mr23000 and 13000 (p23 and p13, respectively).  Protein
      sequence analysis of the tryptic fragments indicates that p36 results from
      removal of the first 14 or 16 amino acids, p23 spans residues 15-216, and p13
      spans residues 217-325.  The relative resistance to further degradation of p23
      and p13 suggests stable domain structures.  This is further supported by the
      generation of similar fragments with SV8 endoprotease which has entirely
      different peptide specificities.  Our results suggest that Mtase is a
      two-domain protein connected by a highly flexible interdomain hinge.  The
      putative hinge region encompasses previously identified peptides implicated in
      AdoMet binding [Reich, N.O. & Everett, E. (1990) J. Biol. Chem. 265, 8929-8934]
      and catalysis [Everett et al. (1990) J. Biol. Chem. 265, 17713-17719].
      Protection studies with DNA, S-adenosylmethionine (AdoMet),
      S-adenosylhomocysteine (AdoHcy), and sinefungin (AdoMet analogue) show that the
      Mtase undergoes significant conformational changes upon ligand binding.
      Trypsinolysis of the AdoMet-bound form of the Mtase generates different
      fragments, and the AdoMet-bound form is over 800 times more stable than unbound
      Mtase.  The sequence-specific ternary complex (Mtase-DNA-sinefungin) is 2000
      times more resistant to degradation by trypsin; cleavage eventually generates
      26- and 12-kDa fragments which span residues 104-325 and 1-103, respectively
      (p26 and p12).  The first 14 or 16 amino acids of the Mtase are not essential
      since p36 retains activity.  Activity analysis of the p26 and p12 mixture also
      indicates retention of activity.  Therefore, either p26 is catalytically active
      or the two fragments remain associated to create a functional enzyme.  The
      former rationale is supported by the fact that for EcoRI Mtase, all peptide
      regions implicated in DNA binding, AdoMet binding, and catalysis residue in the
      p26 fragment.
AU  - Reich NO
AU  - Maegley KA
AU  - Shoemaker DD
AU  - Everett E
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1991 30: 2940-2946.

PMID- 8486619
VI  - 268
DP  - 1993
TI  - Presteady state kinetics of an S-adenosylmethionine-dependent enzyme.
PG  - 9191-9193
AB  - We present the first presteady state kinetic analysis of an S-adenosylmethionine-dependent
      enzyme. The target enzyme is the bacterial EcoRI DNA methyltransferase, which transfers the
      methyl group to the second adenine in the DNA sequence GAATTC. The rate constant for
      conversion of the central complex (enzyme-DNA-S-adenosylmethionine) to products
      (enzyme-methylated DNA-S-adenosylhomocysteine) (41 +/- 7 s-1) is over 300-fold faster than
      kcat, consistent with our demonstration that steps after methyltransfer are rate-limiting
      (Reich, N.O., and Mashhoon, N. (1991) Biochemistry 30, 2933-2939). Methyltransfer at the N6
      amino moiety of adenine on each strand requires a single binding orientation.
AU  - Reich NO
AU  - Mashhoon N
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1993 268: 9191-9193.

PMID- 2341414
VI  - 265
DP  - 1990
TI  - Inhibition of EcoRI DNA methylase with cofactor analogs.
PG  - 8966-8970
AB  - Four analogs of the natural cofactor S-adenosylmethionine (AdoMet) were tested
      for their ability to bind and inhibit the prokaryotic enzyme, EcoRI adenine DNA
      methylase.  The EcoRI methylase transfers the methyl group from AdoMet to the
      second adenine in the double-stranded DNA sequence 5' GAATTC 3'.  Dissociation
      constants (KD) of the binary methylase-analog complexes obtained in the absence
      of DNA with S-adenosylhomocysteine (AdoHcy), sinefungin, N-methyl-AdoMet, and
      N-ethylAdoMet are 225, 43, >1000, and >2000 microM, respectively.  In the
      presence of a DNA substrate, all four analogs show simple competitive
      inhibition with respect to AdoMet.  The product of the enzymic reaction,
      AdoHcy, is a poor inhibitor of the enzyme (KI(AdoHcy)=9 microM; KM(AdoMet)=0.60
      microM).  Two synthetic analogs, N-methyl-AdoMet and N-ethyl-AdoMet, were also
      shown to be poor inhibitors with KI values of 50 and >1000 microM,
      respectively.  In contrast, the naturally occurring analog sinefungin was shown
      to be a highly potent inhibitor (KI=10 microM).  Gel retardation assays confirm
      that the methylase-DNA-sinefungin complex is sequence-specific.  The ternary
      complex is the first sequence-specific complex detected for any DNA methylase.
      Potential applications to structural studies of methylase-DNA interations are
      discussed.
AU  - Reich NO
AU  - Mashhoon N
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1990 265: 8966-8970.

PMID- 2007129
VI  - 30
DP  - 1991
TI  - Kinetic mechanism of the EcoRI DNA methyltransferase.
PG  - 2933-2939
AB  - We present kinetic analysis of the EcoRI DNA N6-adenosine methyltransferase
      (Mtase).  The enzyme catalyzes the S-adenosylmethionine (AdoMet)-dependent
      methylation of a short, synthetic 14 base pair DNA substrate and plasmid pBR322
      DNA substrate with kcat/Km values of 0.51 x 10/8 and 4.1 x 10/8 S-1-M-1,
      respectively.  The Mtase is thus one of the most efficient biocatalysts known.
      Our data are consistent with an ordered bi-bi steady-state mechanism in which
      AdoMet binds first, followed by DNA addition.  One of the reaction products,
      S-adenosylhomocysteine (AdoHcy), is an uncompetitive inhibitor with respect to
      DNA and a competititive inhibitor with respect to AdoMet.  Thus, initial DNA
      binding followed by AdoHcy binding leads to formation of a ternary dead-end
      complex (Mtase-DNA-AdoHcy).  We suggest that the product inhibition patterns
      and apparent order of substrate binding can be reconciled by a mechanism in
      which the Mtase binds AdoMet and noncanonical DNA randomly but that recognition
      of the canonical site requires AdoMet to be bound.  Pre-steady-state and
      isotope partitition analyses starting with the binary Mtase-AdoMet complex
      confirm its catalytic competence.  Moreover, the methyl transfer step is at
      least 10 times faster than catalytic turnover.
AU  - Reich NO
AU  - Mashhoon N
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1991 30: 2933-2939.

PMID- 2467142
VI  - 13D
DP  - 1989
TI  - Structure-function analysis of enzyme-DNA interactions in the EcoRI DNA methylase.
PG  - 213
AB  - Our goal is to understand the molecular basis of DNA sequence recognition and
      the modulation of this process by the cofactor S-adenosylmethionine, [AdoMet]
      in this prokaryotic system.  The kinetic mechanism and the rate determining
      step[s] have been elucidated: AdoMet binds first, followed by the double
      stranded DNA substrate [5'GAATTC3'].  Rapid transfer of the methyl group to the
      DNA in the ternary methylase-AdoMet-DNA complex is followed by rate limiting
      step[s].  One portion of the methylase involved in AdoMet binding has been
      identified:  it is a flexible peptide connecting two stable domains.  This
      flexible hinge region and the domains were characterized using photo affinity
      analogs, in vitro proteolysis, and peptide sequencing.  Hydroxy radical
      footprinting and synthetic oligonucleotides have been used to characterize the
      methylase-DNA topology.  Moreover, DNA substrates with modified bases [uracil,
      inosine, deaza-adenine, etc.] have been submitted to comparative specificity
      analysis [kcat/KM].  Data from both analyses will be presented; the
      contribution to overall specificity deriving from individual methylase-DNA
      interactions has been elucidated.
AU  - Reich NO
AU  - Mashhoon N
AU  - Everett E
AU  - Danzitz M
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1989 13D: 213.

PMID- 1639813
VI  - 267
DP  - 1992
TI  - In vitro specificity of EcoRI DNA methyltransferase.
PG  - 15802-15807
AB  - The sequence selectivity of enzyme-DNA interactions was analyzed by comparing discrimination
      between synthetic oligonucleotides containing the canonical site GAATTC and altered DNA
      sequences with the EcoRI DNA methyltransferase. The specificities (kcat/Km DNA) are decreased
      from 5- to 23,000-fold relative to the unmodified site. For several substrates the decrease in
      kcat makes a disproportionate contribution to the specificity difference, suggesting that
      discrimination is mediated by the placement of critical catalytic residues rather than binding
      interaction. This is supported by our observation that specificity changes are generally not
      followed by changes in the stability of the methyltransferase-DNA complexes. Also, base pair
      substitution near the site of methylation results in greater decreases in complex stability,
      suggesting that recognition and catalytic mechanisms overlap.
AU  - Reich NO
AU  - Olsen C
AU  - Osti F
AU  - Murphy J
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1992 267: 15802-15807.

PMID- Not carried by PubMed...
VI  - 203
DP  - 1992
TI  - In vitro and in vivo specificity analysis of the EcoRI DNA methyltransferase.
PG  - 113-BIOL
AB  - The EcoRI DNA methyltransferase modifies the second adenine in the site GAATTC using the
      cofactor S-adenosylmethionine. We determined the in vitro sequence-selectivity with a family
      of related hemimethylated 14mers (X=methyladenosine):
      5' GGCGGAATTCGCGG 3'
      3' CCGCCTTXAGCGCC 5'
      Comparisons of true kcat, KmDNA, KmAdoMet and Kcat/KmDNA show specificity decreases from 5
      (GAATCC) to 23,000 (GGATTC) fold (top strand shown). For several substrates the decrease in
      kcat makes a disproportionate contribution toward specificity, suggesting that discrimination
      is mediated by the placement of critical catalytic residues. Further evidence for this
      conclusion is provided by our observation that the stability of the methyltransferase-DNA
      complexes (determined by gel shift analysis) do not generally follow specificity changes. In
      contrast, no methylation of noncanonical sites was detectable in vivo. We used three assays to
      show that TAATTC, CAATTC, GTATTC, GGATTC and GAGTTC are not methylated in vivo under
      conditions where the canonical site is protected. A possible reconciliation of these results
      with our in vitro data is that noncanonical methylation does occur in vivo but is actively
      repaired. The possible involvement of the recently identified mrr (methylated adenine
      recognition and repair) locus in this capacity is being investigated.
AU  - Reich NO
AU  - Olsen C
AU  - Osti F
AU  - Murphy J
AU  - Smith D
AU  - Crowder S
PT  - Journal Article
TA  - ACS Abstracts
JT  - ACS Abstracts
SO  - ACS Abstracts 1992 203: 113-BIOL.

PMID- 1727392
VI  - 6
DP  - 1992
TI  - In vitro and in vivo specificity analysis of the EcoRI DNA methyltransferase.
PG  - A217
AB  - The EcoRI DNA methyltransferase modifies the second adenine in the site GAATTC
      using the cofactor S-adenosylmethionine.  We determined the in vitro
      sequence-selectivity with a family of related hemimethylated 14mers
      X=methyladenosine):
      5' GGCCGGAATTCGCGG 3'
      3' CCGGCCTTXAGCGCC 5'
      Comparisons of true kcat, KDNA, KmAdomet and kcat/KmDNA show specificity
      decreases from 5(GAATCC) to 23,000 (GGATTC) fold (top strand shown).  For
      several substrates the decrease in kcat makes a disproportionate contribution
      toward specificity, suggesting that discrimination is mediated by the placement
      of critical catalytic residues.  Further evidence for this conclusion is
      provided by our observation that the stability of the methyltransferase-DNA
      complexes (determined by gel shift analysis) do not generally follow
      specificity changes.  In constrast, no methylation of noncanonical sites was
      detectable in vivo.  We used three assays to show that TAATTC, CAATTC, GTATTC,
      GGATTC and GAGTTC are not methylated in vivo under conditions where the
      canonical site is protected.  A possible reconciliation of these results with
      our in vitro data is that noncanonical methylation does occur in vivo but is
      actively repaired.  The possible involvement of the recently identified mrr
      (methylated adenine recognition and repair) locus in this capacity is being
      investigated.
AU  - Reich NO
AU  - Olsen C
AU  - Osti F
AU  - Murphy J
AU  - Smith D
AU  - Crowder S
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1992 6: A217.

PMID- Not included in PubMed...
VI  - 31
DP  - 1992
TI  - In vitro and in vivo specificity analysis of the EcoRI DNA methyltransferase.
PG  - 2208
AB  - The EcoRI DNA methyltransferase modifies the second adenine in the site GAATTC
      using the cofactor S-adenosylmethionine.  We determined the in vitro sequence
      selectivity with a family of related hemimethylated 14mers (X =
      methyladenosine):
      5'GGCGGAATTCGCGG3'
      3'CCGCCTTXAGCGCC5'
      Comparisons of true kcat, KmDNA, KmAdoMet, and kcat/Km DNA show specificity
      decreases from 5-(GAATCC) to 23000-(GGATTC) fold (top strand shown).  For
      several substrates the decrease in kcat makes a disproportionate contribution
      toward specificity, suggesting that discrimination is mediated by the placement
      of critical catalytic residues.  Further evidence for this conclusion is
      provided by our observation that the stability of the methyltransferase-DNA
      complexes (determined by gel shift analysis) do not generally follow
      specificity changes.  In contrast, no methylation of noncanonical sites was
      detectable in vivo.  We used three assays to show that TAATTC, CAATTC, GTATTC,
      GGATTC, and GAGTTC are not methylated in vivo under conditions where the
      canonical site is protected.  A possible reconciliation of these results with
      our in vitro data is that noncanonical methylation does occur in vivo but is
      actively repaired.  The possible involvement of the recently identified mrr
      (methylated adenine recognition and repair locus in this capacity is being
      investigated.
AU  - Reich NO
AU  - Olsen C
AU  - Osti F
AU  - Murphy J
AU  - Smith D
AU  - Crowder S
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1992 31: 2208.

PMID- Not included in PubMed...
VI  - 61
DP  - 1992
TI  - In vitro and in vivo specificity analysis of the EcoRI DNA methyltransferase.
PG  - A217
AB  - The EcoRI DNA methyltransferase modifies the second adenine in the site GAATTC
      using the cofactor S-adenosylmethionine.  We determined the in vitro
      sequence-selectivity with a family of related hemimethylated 14mers
      (X-methyladenosine): top 5GGCGGAATTCGCGG3/5CCGCGAXTTCCGCC3' bottom.
      Comparisons of the true kcat, KDNA, KmAdoMet and kcat/KmDNA show specificity
      decreases from 5(GAATCC) to 23,000 (GGATTC) fold (top strand shown).  For
      several substrates the decrease in kcat makes a disproportionate contribution
      toward specificity, suggesting that discrimination is mediated by the placement
      of critical catalytic residues.  Further evidence for this conclusion is
      provided by our observation that the stability of the methyltransferase-DNA
      complexes (determined by gel shift analysis) do not generally follow
      specificity changes.  In contrast, no methylation of noncanonical sites was
      detectable in vivo.  We used three assays to show that TAATTC, CAATTC, GTATTC,
      GGATTC and GAGTTC are not methylated in vivo under conditions where the
      canonical site is protected.  A possible reconciliation of these results with
      our in vitro data is that noncanonical methylation does occur in vivo but is
      actively repaired.  The possible involvement of the recently identified mrr
      (methylated adenine recognition and repair) locus in this capacity is being
      investigated.
AU  - Reich NO
AU  - Olsen C
AU  - Osti F
AU  - Murphy J
AU  - Smith D
AU  - Crowder S
PT  - Journal Article
TA  - Biophys. J.
JT  - Biophys. J.
SO  - Biophys. J. 1992 61: A217.

PMID- 
VI  - 41
DP  - 2000
TI  - The enzymology of epigenetics: Mechanism and inhibition of mammalian DNA cytosine methyltransferase.
PG  - 346-347
AB  - The major DNA cytosine methyltransferase in mammals, Dnmt1, is potently inhibited by a novel
      allosteric inhibitor.  The inhibitor decreases DNA methylation in mammalian cells.  Other
      compounds that decrease cellular DNA methylation levels have been shown to reverse
      tumorigenesis in animals.  Thus, our inhibitor is being tested in tumor cell lines as a new
      anticancer therapeutic.  The expression of newly integrated viral DNA is often stopped by DNA
      methylation.  "DNA methylation spreading" results from the "activation" of the enzyme by
      proximal 5-methylcytosine groups adjacent to the target CpG that undergoes methylation.  This
      occurs primarily in single-stranded DNA, the 5-methylcytosine can be anywhere from 3 to 27
      nucleotides removed from the CpG, and the effect is due to an increased affinity of the enzyme
      for its substrate.  Our results have implications for the potential methylation-dependent
      silencing of genes during gene therapy.  Dnmt1 prefers hemimethylated substrates; this occurs
      during the initial attack at the C6 position of the target cytosine, rather than the
      subsequent methyl transfer step.  Dnmt1 catalyzes the exchange of the C5 hydrogen of cytosine,
      but only in the presence of the natural cofactor AdoMet, or certain cofactor analogs.  Similar
      results were reported for the related deamination reaction catalyzed by bacterial enzymes,
      suggesting that exchange and demamination occur through similar reaction intermediates.  Our
      results suggest that Dnmt1 may not be mutagenic under the conditions previously demonstrated
      for the bacterial enzyme.
AU  - Reich NO
AU  - Svedruzic Z
AU  - Flynn J
AU  - Aubol B
PT  - Journal Article
TA  - Proc. Amer. Assoc. Cancer Res.
JT  - Proc. Amer. Assoc. Cancer Res.
SO  - Proc. Amer. Assoc. Cancer Res. 2000 41: 346-347.

PMID- 
VI  - 
DP  - 2003
TI  - Reaction mechanism of type III restriction endonuclease EcoP151 and possible application in molecular diagnostics.
PG  - 1-100
AB  - EcoP15I is a multifunctional, hetero-oligomeric Type III restriction enzyme.  Type III
      restriction enzymes are of general interest in medicine and functional genome analysis because
      they cut DNA 25 bp downstream of their recognition site.  EcoP15I recognises the DNA sequence
      5'-CAGCAG and needs two inverse oriented recognition sites for effective DNA cleavage.
      According to the present translocation collision model DNA cleavage was proposed to result
      from ATP dependent DNA translocation, which is expected to induce DNA loop formation, and
      collision of two enzyme-DNA complexes.  Experiments show that EcoP15 moves rather in a
      three-dimensional than in a 'sliding' process in search for its recognition site.
      Huntington's disease is a progressive neurodegenerative disorder with autosomal-dominant
      inheritance.  The disease is caused by a CAG trinucleotide repeat expansion located in the
      first exon of the HD gene.  To diagnose the illness the exact determination of the number of
      CAG repeats is necessary.  This study shows that the number of CAG repeats in the HD gene can
      be determined by restriction of the DNA with the endonuclease EcoP15I and subsequent
      high-resolution analysis of the restriciton fragment pattern using the ALPexpress DNA Analysis
      System.  Here, for the first time DNA translocation by the Type III restriction enzyme EcoP15I
      is demonstrated.  The postulated EcoP15-DNA loops are visualised using scanning force
      microscopy.  This confirms the translocation-collision model for DNA cleavage by EcoP15.
      Similarities and differences between the DNA cleavage processes of the Type III restriciton
      enzyme EcoP15I and other restriction enzymes are discussed.
AU  - Reich S
PT  - Journal Article
TA  - Ph.D. Thesis, Germany
JT  - Ph.D. Thesis, Germany
SO  - Ph.D. Thesis, Germany 2003 : 1-100.

PMID- 15276827
VI  - 341
DP  - 2004
TI  - Scanning force microscopy of DNA translocation by the type III restriction enzyme EcoP15I.
PG  - 337-343
AB  - Type III restriction enzymes are multifunctional heterooligomeric enzymes that cleave DNA at a
      fixed position downstream of a non-symmetric recognition site. For effective DNA cleavage
      these restriction enzymes need the presence of two unmethylated, inversely oriented
      recognition sites in the DNA molecule. DNA cleavage was proposed to result from ATP-dependent
      DNA translocation, which is expected to induce DNA loop formation, and collision of two
      enzyme-DNA complexes. We used scanning force microscopy to visualise the protein interaction
      with linear DNA molecules containing two EcoP15I recognition sites in inverse orientation. In
      the presence of the cofactors ATP and Mg2+, EcoP15I molecules were shown to bind specifically
      to the recognition sites and to form DNA loop structures. One of the origins of the
      protein-clipped DNA loops was shown to be located at an EcoP15I recognition site, the other
      origin had an unspecific position in between the two EcoP15I recognition sites. The data
      demonstrate for the first time DNA translocation by the Type III restriction enzyme EcoP15I
      using scanning force microscopy. Moreover, our study revealed differences in the
      DNA-translocation processes mediated by Type I and Type III restriction enzymes.
AU  - Reich S
AU  - Gossl D
AU  - Reuter M
AU  - Rabe JP
AU  - Kruger DH
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2004 341: 337-343.

PMID- 
VI  - 28
DP  - 2000
TI  - DNA cleavage by the restriction endonuclease EcoP15I.
PG  - A331
AB  - The type III restriction endonuclease EcoP15I recognizes the asymmetric DNA sequence
      5'-CAGCAG and cleaves it 25-27 bp downstream.  Two unmethylated, inversely oriented
      recognition sites in head-to-head configuration (5'-CAGCAG...NNN...CTGCTG) are preferred
      substrates in DNA cleavage.  An intrinsic ATPase activity is the potential driving force of
      DNA translocation bringing two EcoP15I-DNA complexes together.  In this work we investigated
      EcoP15I cleavage efficiency in dependence on distance of two inversely oriented recognition
      sites.  We showed that EcoP15I proceeds to cleave DNA efficiently even in the case of two
      adjacent head-to-head oriented recognition sites, but cleavage rate rapidly diminished with
      increasing distance of two tail-to-tail oriented recognition sites.  EcoP15I cleavage was
      abolished in the presence of non-hydrolysable ATP analogs instead of ATP, even on substrates
      with recognition sites in close vicinity.  This confirmed a role of ATP hydrolysis for the
      phosphodiester bond cleavage.  Furthermore, DNaseI footprint experiments were performed to get
      insight into the spatial requirements of the enzyme on substrate DNA with one recognition site
      and revealed a 36 base-footprint rather symmetrical in both strands.  It became evident that
      the enzyme did not cover the region around the cleavage site.  Presence of ATP caused a change
      in the footprint pattern.  Analyzing a DNA fragment with two head-to-head oriented recognition
      sites, an additional region between the two cooperative cleavage sites was protected against
      DNaseI digestion.  Our experimental data allow a refinement of the tracking-collision model
      discussed for type III enzymes and give suggestions on the spatial organization of the
      collision complex.
AU  - Reich S
AU  - Mucke M
AU  - Moncke-Buchner E
AU  - Reuter M
AU  - Kruger DH
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 2000 28: A331.

PMID- 28183769
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Edwardsiella hoshinae ATCC 35051.
PG  - e01605-16
AB  - Edwardsiella hoshinae is a Gram-negative facultative anaerobe that has primarily  been
      isolated from avians and reptiles. We report here the complete and annotated
      genome sequence of an isolate from a monitor lizard (Varanus sp.), which contains
      a chromosome of 3,811,650 bp and no plasmids.
AU  - Reichley SR
AU  - Waldbieser GC
AU  - Lawrence ML
AU  - Griffin MJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01605-16.

PMID- 26337892
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of an Edwardsiella piscicida-Like Species, Recovered from Tilapia in the United States.
PG  - e01004-15
AB  - An Edwardsiella piscicida-like species is a Gram-negative facultative anaerobe that causes
      disease in some fish species. In this report, we present the complete and annotated genome of
      isolate LADL05-105, recovered from cultured tilapia reared in Louisiana, which contains a
      chromosome of 4,142,037 bp and no plasmids.
AU  - Reichley SR
AU  - Waldbieser GC
AU  - Lawrence ML
AU  - Griffin MJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01004-15.

PMID- 28619788
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Edwardsiella ictaluri Isolate RUSVM-1 Recovered from  Nile Tilapia (Oreochromis niloticus) in the Western Hemisphere.
PG  - e00390-17
AB  - Edwardsiella ictaluri is a Gram-negative bacillus that has recently been implicated in disease
      outbreaks in tilapia and zebrafish. We report here the
      complete and annotated genome sequence of an isolate from a Nile tilapia
      (Oreochromis niloticus), which contains a chromosome of 3,630,639 bp and two
      plasmids.
AU  - Reichley SR
AU  - Waldbieser GC
AU  - Soto E
AU  - Lawrence ML
AU  - Griffin MJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00390-17.

PMID- 26112788
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Edwardsiella tarda Isolate FL95-01, Recovered from Channel Catfish.
PG  - e00682-15
AB  - Edwardsiella tarda is a Gram-negative facultative anaerobe that has been isolated from fish,
      reptiles, amphibians, and mammals, including humans. This is a report
      of the complete and annotated genome of isolate FL95-01, recovered from channel
      catfish (Ictalurus punctatus).
AU  - Reichley SR
AU  - Waldbieser GC
AU  - Tekedar HC
AU  - Lawrence ML
AU  - Griffin MJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00682-15.

PMID- 27881536
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Edwardsiella piscicida Isolate S11-285 Recovered from Channel Catfish (Ictalurus punctatus) in Mississippi, USA.
PG  - e01259-16
AB  - Edwardsiella piscicida is a recently described Gram-negative facultative anaerobe and an
      important pathogen to many wild and cultured fish species worldwide. Here,
      we report the complete and annotated genome of E. piscicida isolate S11-285
      recovered from channel catfish (Ictalurus punctatus), consisting of a chromosome
      of 3,923,603 bp and 1 plasmid.
AU  - Reichley SR
AU  - Waldbieser GC
AU  - Tekedar HC
AU  - Lawrence ML
AU  - Griffin MJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01259-16.

PMID- 26205870
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of an Edwardsiella piscicida-Like Species Isolated from  Diseased Grouper in Israel.
PG  - e00829-15
AB  - The Edwardsiella piscicida-like sp. is a Gram-negative facultative anaerobe that  causes
      disease in some fish species. We report here the complete genome sequence
      of a virulent isolate from a diseased white grouper (Epinephelus aeneus) raised
      on the Red Sea in Israel, which contains a chromosome of 3,934,167 bp and no
      plasmids.
AU  - Reichley SR
AU  - Waldbieser GC
AU  - Ucko M
AU  - Colorni A
AU  - Dubytska L
AU  - Thune RL
AU  - Lawrence ML
AU  - Griffin MJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00829-15.

PMID- 11327870
VI  - 40
DP  - 2001
TI  - Binding and recognition of GATATC target sequences by the EcoRV restriction endonuclease: A study using fluorescent oligonucleotides and fluorescence polarization.
PG  - 2484-2494
AB  - Oligonucleotides labeled with hexachlorofluorescein (hex) have enabled the interaction of the
      restriction endonuclease EcoRV with DNA to be
      evaluated using fluorescence anisotropy. The sensitivity of hex allowed
      measurements at oligonucleotide concentrations as low as 1 nM, enabling
      KD values in the low nanomolar range to be measured. Both direct
      titration, i.e., addition of increasing amounts of the endonuclease to
      hex-labeled oligonucleotides, and displacement titration, i.e.,
      addition of unlabeled oligonucleotide to preformed
      hex-oligonucleotide/EcoRV endonuclease complexes, have been used for KD
      determination. Displacement titration is the method of choice;
      artifacts due to any direct interaction of the enzyme with the dye are
      eliminated, and higher fluorescent-labeled oligonucleotide
      concentrations may be used, improving signal-to-noise ratio. Using this
      approach (with three different oligonucleotides) we found that the
      EcoRV restriction endonuclease showed a preference of between 1.5 and
      6.5 for its GATATC target sequence at pH 7.5 and 100 mM NaCl, when the
      divalent cation Ca2+ is absent. As expected, both the presence of Ca2+
      and a decrease in pH value stimulated the binding of specific sequences
      but had much less effect on nonspecific ones.
AU  - Reid SL
AU  - Parry D
AU  - Liu H-H
AU  - Connolly BA
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2001 40: 2484-2494.

PMID- 7953517
VI  - 4
DP  - 1994
TI  - Imprinting with and without methylation.
PG  - 145-147
AB  - Methyltransferase-deficient mice reveal that DNA methylation is required for the somatic-cell
      maintenance of parental imprinting, which alters the expression of a gene according to the
      parent from which it was inherited.
AU  - Reik W
AU  - Allen ND
PT  - Journal Article
TA  - Curr. Biol.
JT  - Curr. Biol.
SO  - Curr. Biol. 1994 4: 145-147.

PMID- 10581015
VI  - 23
DP  - 1999
TI  - Dissecting de novo methylation.
PG  - 380-382
AB  - The methylation of DNA is fundamental to mammalian development.  This is vividly illustrated
      by the fact that mouse embryos deficient in Dnmt1, a DNA methyltransferase that methylates
      cytosine groups, die as a result of genome-wide demethylation.  Dnmt1 seems to be the main
      enzyme responsible for maintaining methylation after each round of DNA replication.  But
      studies of Dnmt1-deficient embryonic stem cells have revealed that other enzymes must exist to
      methylate the genome de novo after the wave of global demethylation that occurs during early
      embryonic development.  Okano et al. recently reported that murine Dnmt3a and Dnmt3b are the
      long-sought mammalian de novo methyltransferases.  Their findings, as well as those of Xu et
      al. and Hansen et al., also show that mutations of DNMT3B cause a disorder associated with
      immunodeficiency, centromere instability and facial anomalies (ICF syndrome).  This disorder
      is the only known human condition with constitutive abnormalities in DNA methylation.
AU  - Reik W
AU  - Kelsey G
AU  - Walter J
PT  - Journal Article
TA  - Nat. Genet.
JT  - Nat. Genet.
SO  - Nat. Genet. 1999 23: 380-382.

PMID- 9610405
VI  - 8
DP  - 1998
TI  - Imprinting mechanisms in mammals.
PG  - 154-164
AB  - Imprinting is a genetic mechanism that determines expression or repression of genes according
      to their parental origin.  Some imprinted genes occur in clusters in the genome.  Recent work
      using transgenic mice shows that multiple cis-acting sequences are needed for correct
      imprinting.  Mutation analysis in a normal chromosomal context reveals the importance of
      imprinting centers for regional establishment or maintenance of imprinting in a cluster.
      Elements that contribute to the function of imprinting centers and regional propagation of the
      imprints are CpG-rich differentially methylated regions (that during development retain
      germline imposed methylation or demethylation), direct repeat clusters, and unusual RNA's
      (antisense, non-translated etc.).  The interaction of these cis elements with transacting
      factors such as methylase and chromatin factors establishes a hierarchical control system with
      local and regional effects.
AU  - Reik W
AU  - Walter J
PT  - Journal Article
TA  - Current Opinion in Genetics
JT  - Current Opinion in Genetics
SO  - Current Opinion in Genetics 1998 8: 154-164.

PMID- 21546587
VI  - 157
DP  - 2011
TI  - Application of suppressive subtractive hybridization to the identification of genetic differences between two Lactococcus garvieae strains showing distinct differences in virulence for rainbow trout and mouse.
PG  - 2106-2119
AB  - Lactococcus garvieae is the causative microbial agent of lactococcosis, an important and
      damaging fish disease in aquaculture. This bacterium has also been isolated from vegetables,
      milk, cheese, meat and sausages, from cow and buffalo as a mastitis agent, and even from
      humans, as an opportunistic infectious agent. In this work pathogenicity experiments were
      performed in rainbow trout and mouse models with strains isolated from human (L. garvieae HF)
      and rainbow trout (L. garvieae UNIUDO74; henceforth referred to as 074). The mean LD(50) value
      in rainbow trout obtained for strain 074 was 2.1x10(2)+/-84 per fish. High doses of the
      bacteria caused specific signs of disease as well as histological alterations in mice. In
      contrast, strain HF did not prove to be pathogenic either for rainbow trout or for mice. Based
      on these virulence differences, two suppressive subtractive hybridizations were carried out to
      identify unique genetic sequences present in L. garvieae HF (SSHI) and L. garvieae 074
      (SSHII). Differential dot-blot screening of the subtracted libraries allowed the
      identification of 26 and 13 putative ORFs specific for L. garvieae HF and L. garvieae 074,
      respectively. Additionally, a PCR-based screening of 12 of the 26 HF-specific putative ORFs
      and the 13 074-specific ones was conducted to identify their presence/absence in 25 L.
      garvieae strains isolated from different origins and geographical areas. This study
      demonstrates the existence of genetic heterogeneity within L. garvieae isolates and provides a
      more complete picture of the genetic background of this bacterium.
AU  - Reimundo P
AU  - Rivas AJ
AU  - Osorio CR
AU  - Mendez J
AU  - Perez-Pascual D
AU  - Navais R
AU  - Gomez E
AU  - Sotelo M
AU  - Lemos ML
AU  - Guijarro JA
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2011 157: 2106-2119.

PMID- 9580672
VI  - 26
DP  - 1998
TI  - Identifying 5-methylcytosine and related modifications in DNA genomes.
PG  - 2255-2264
AB  - Intense interest in the biological roles of DNA methylation, particularly in eukaryotes, has
      produced at least eight different methods for identifying 5-methylcytosine and related
      modifications in DNA genomes.  However, the utility of each method depends not only on its
      simplicity but on its specificity, resolution, sensitivity and potential artifacts.  Since
      these parameters affect the interpretation of data, they should be considered in any
      application.  Therefore, we have outlined the principles and applications of each method,
      quantitatively evaluated their specificity, resolution and sensitivity, identified potential
      artifacts and suggested solutions, and discussed a paradox in the distribution of m5C in
      mammalian genomes that illustrates how methodological limitations can affect interpretation of
      data.  Hopefully, the information and analysis provided here will guide new investigators
      entering this exciting field.
AU  - Rein T
AU  - DePamphilis ML
AU  - Zorbas H
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1998 26: 2255-2264.

PMID- 2020550
VI  - 19
DP  - 1991
TI  - BfaI, a new MaeI isoschizomer from Bacteroides fragilis, recognizes the sequence 5' C^TAG 3'.
PG  - 1152
AB  - A new type II restriction endonuclease, BfaI, has been isolated from
      Bacteroides fragilis (NEB #668).  BfaI recognizes the four base sequence 5'
      CTAG 3' and cleaves between the C and the T residues to produce a 2 base 5'
      extension; C/TAG.
AU  - Reinecke SN
AU  - Morgan RD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 1152.

PMID- 29348358
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Kyrpidia sp. Strain EA-1, a Thermophilic Knallgas Bacterium, Isolated from the Azores.
PG  - e01505-17
AB  - Kyrpidia sp. strain EA-1 is a thermophilic hydrogen-oxidizing bacterium isolated  from
      hydrothermal systems at Sao Miguel Island, Portugal. Here, we present the
      complete genome sequence of the strain assembled to a single circular chromosome.
      The genome spans 3,352,175 bp, with a GC content of 58.7%.
AU  - Reiner JE
AU  - Lapp CJ
AU  - Bunk B
AU  - Sproer C
AU  - Overmann J
AU  - Gescher J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01505-17.

PMID- 17307879
VI  - 104
DP  - 2007
TI  - Use of plasmon coupling to reveal the dynamics of DNA bending and cleavage by single EcoRV restriction enzymes.
PG  - 2667-2672
AB  - Pairs of Au nanoparticles have recently been proposed as "plasmon rulers" based on the
      dependence of their light scattering on the interparticle distance. Preliminary work has
      suggested that plasmon rulers can be used to measure and monitor dynamic distance changes over
      the 1- to 100-nm length scale in biology. Here, we substantiate that plasmon rulers can be
      used to measure dynamical biophysical processes by applying the ruler to a system that has
      been investigated extensively by using ensemble kinetic measurements: the cleavage of DNA by
      the restriction enzyme EcoRV. Temporal resolutions of up to 240 Hz were obtained, and the
      end-to-end extension of up to 1,000 individual dsDNA enzyme substrates could be simultaneously
      monitored for hours. The kinetic parameters extracted from our single-molecule cleavage
      trajectories agree well with values obtained in bulk through other methods and confirm well
      known features of the cleavage process, such as DNA bending before cleavage. Previously
      unreported dynamical information is revealed as well, for instance, the degree of softening of
      the DNA just before cleavage. The unlimited lifetime, high temporal resolution, and high
      signal/noise ratio make the plasmon ruler a unique tool for studying macromolecular assemblies
      and conformational changes at the single-molecule level.
AU  - Reinhard BM
AU  - Sheikholeslami S
AU  - Mastroianni A
AU  - Alivisatos AP
AU  - Liphardt J
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2007 104: 2667-2672.

PMID- 29748399
VI  - 6
DP  - 2018
TI  - Complete Genome Sequences of 10 Yersinia pseudotuberculosis Isolates Recovered from Wild Boars in Germany.
PG  - e00266-18
AB  - We report here the draft genome sequences of 10 Yersinia pseudotuberculosis isolates recovered
      from tonsils of wild boars hunted between 2015 and 2016 in
      Germany. Whole-genome sequencing and bioinformatic analyses were performed to
      assess the diversity of Y. pseudotuberculosis, which may result in human
      infections caused by the consumption of game meat.
AU  - Reinhardt M
AU  - Hammerl JA
AU  - Hertwig S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00266-18.

PMID- Not carried by PubMed...
VI  - 56
DP  - 1996
TI  - The crystal structure of HaeIII methylase covalently complexed to DNA: An extrahelical cytosine and rearranged base pairing.
PG  - 3746B
AB  - Many organisms expand the information content of their genome through enzymatic methylation of
      cytosine residues.  The structure of M.HaeIII, a bacterial DNA (cytosine-5) methyltransferase
      (DCMtase), bound covalently to DNA, is presented here.  The structure has been solved by X-ray
      diffraction using the multiple isomorphous replacement method.  It has been refined to 2.8 A
      with a crystallographic Rfree-value of 32.6% (R-value of 22.6%) and root mean square
      deviations from ideal values of 0.012 Angstroms and 2.3 degrees for bond lengths and angles,
      respectively.  In the M.HaeIII-DNA complex, the substrate cytosine is extruded from the DNA
      helix and inserted into the active site of the enzyme, as was observed for another DCMtase,
      M.HhaI.  The DNA is bound in a cleft between the two domains of the protein and is distorted
      from the characteristic B-form conformation at its recognition sequence.  A comparison of
      structures shows that the M.HaeIII complex differs from that of M.HhaI in that the remaining
      bases in the M.HaeIII recognition sequence undergo an extensive rearrangement in their
      pairing.  In this process, the bases are unstacked, and a gap 8 Angstroms long opens in the
      DNA.
AU  - Reinisch KM
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1996 56: 3746B.

PMID- 8176750
VI  - 238
DP  - 1994
TI  - Crystallization and preliminary crystallographic anlaysis of a DNA (cytosine-5)-methyltransferase from Haemophilus aegyptius bound covalently to DNA.
PG  - 626-629
AB  - A DNA (cytosine)-5-methyltransferase from Haemophilus aegyptius (M.HaeIII), which catalyzes
      methyl transfer from S-adenosyl-L-methionine to DNA, has been crystallized as a covalent
      complex with a suicide oliogonucleotide substrate. Crystals of the co-complex were grown by
      vapor diffusion with hanging droplets, using polyethylene glycol 3500 as the precipitant. The
      crystals belong to the orthorhombic space group P212121; the unit cell parameters are a=57.6A,
      b=108.0A, c=155.8A with two protein-DNA complexes in the asymmetric unit. Complete sets of
      native and derivative data have been collected to 2.7A using a laboratory source.
AU  - Reinisch KM
AU  - Chen L
AU  - Verdine GL
AU  - Lipscomb WN
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1994 238: 626-629.

PMID- 7606780
VI  - 82
DP  - 1995
TI  - The crystal structure of HaeIII methyltransferase covalently complexed to DNA: an extrahelical cytosine and rearranged base pairing.
PG  - 143-153
AB  - Many organisms expand the information content of their genome through enzymatic methylation of
      cytosine residues.  Here we report the 2.8 A crystal structure of a bacterial DNA
      (cytosine-5)-methyltransferase (DCMtase), M. HaeIII, bound covalently to DNA.  In this
      complex, the substrate cytosine is extruded from the DNA helix and inserted into the active
      site of the enzyme, as has been observed for another DCMtase, M.HhaI.  The DNA is bound in a
      cleft between the two domains of the protein and is distorted from the characteristic B-form
      conformation at its recognition sequence.  A comparison of structures shows a variation in the
      mode of DNA recognition: M.HaeIII differs from M.HhaI in that the remaining bases in its
      recognition sequence undergo an extensive rearrangement in their pairing.  In this process,
      the bases are unstacked, and a gap 8 A long opens in the DNA.
AU  - Reinisch KM
AU  - Chen L
AU  - Verdine GL
AU  - Lipscomb WN
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1995 82: 143-153.

PMID- 28774990
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Achromobacter denitrificans PR1.
PG  - e00762-17
AB  - Achromobacter denitrificans strain PR1 was isolated from an enrichment culture able to use
      sulfamethoxazole as an energy source. Here, we describe the complete
      genome of this strain sequenced by Illumina MiSeq and Oxford Nanopore MinION.
AU  - Reis AC
AU  - Kroll K
AU  - Gomila M
AU  - Kolvenbach BA
AU  - Corvini PFX
AU  - Nunes OC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00762-17.

PMID- 10464180
VI  - 181
DP  - 1999
TI  - Bacterial DNA Methylation: a Cell Cycle Regulator?
PG  - 5135-5139
AB  - A MiniReview of the role of CcrM (M.CcrMI) and Dam (M.EcoDam) methylases in regulating various
      cellular processes such as DNA replication, cell-cycle and others.
AU  - Reisenauer A
AU  - Kahng LS
AU  - McCollum S
AU  - Shapiro L
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1999 181: 5135-5139.

PMID- 12234936
VI  - 21
DP  - 2002
TI  - DNA methylation affects the cell cycle transcription of the CtrA global regulator in Caulobacter.
PG  - 4969-4977
AB  - The Caulobacter chromosome changes progressively from the fully methylated to the
      hemimethylated state during DNA replication. These changes in DNA methylation could signal
      differential binding of regulatory proteins to activate or repress transcription. The gene
      encoding CtrA, a key cell cycle regulatory protein, is transcribed from two promoters. The P1
      promoter fires early in S phase and contains a GAnTC sequence that is recognized by the CcrM
      DNA methyltransferase. Using analysis of CcrM mutant strains, transcriptional reporters
      integrated at different sites on the chromosome, and a ctrA P1 mutant, we demonstrate that
      transcription of the P1 promoter is repressed by DNA methylation. Moreover moving the native
      ctrA gene to a position near the chromosomal terminus, which delays the conversion of the ctrA
      promoter from the fully to the hemimethylated state until late in the cell cycle, inhibited
      ctrA P1 transcription, and altered the time of accumulation of the CtrA protein and the size
      distribution of swarmer cells. Together, these results show that CcrM-catalyzed methylation
      adds another layer of control to the regulation of ctrA expression.
AU  - Reisenauer A
AU  - Shapiro L
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 2002 21: 4969-4977.

PMID- 137900
VI  - 252
DP  - 1977
TI  - Purification and properties of the P15 specific restriction endonuclease from Escherichia coli.
PG  - 451-456
AB  - The specific restriction endonuclease of the Escherichia coli plasmid, P15, has
      been purified to apparent homogeneity by a procedure that includes
      DNA-cellulose chromatography as well as a new endonuclease assay.
      Sedimentation on glycerol gradients showed two peaks of activity with values of
      11.3 S and 15.7 S.  The highly purified enzyme requires ATP and Mg2+ for
      activity and is stimulated by S-adenosylmethionine.  A methylase activity is
      observed in the course of the endonucleolytic reaction which protects some of
      the DNA sites from cleavage.
AU  - Reiser J
AU  - Yuan R
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1977 252: 451-456.

PMID- Not included in PubMed...
VI  - 31
DP  - 1975
TI  - A new cleavage assay for restriction endonucleases.
PG  - 745
AB  - Four different assays have recently been used for restriction enzymes.  Both
      sucrose gradient and gel electrophoresis assays do not give quantitative values
      whereas transfection is very time consuming.  The standard filter-binding assay
      is based on the formation of an enzyme-DNA complex which can then be trapped on
      nitrocellulose filters.  However, the restriction endonucleases from E. coli
      (P1) and E. coli (15) do not show such binding, and a new cleavage assay that
      was quick and quantitative had to be developed.  The basis for the assay is the
      observation of Saucier and Wang (Biochem. 12, 2755, 1973) that circular lambda
      DNA binds to nitrocellulose filters under specified conditions, whereas linear
      lambda DNA will pass through.  For the cleavage assay linear lambda DNA is
      circularized to form hydrogen-bonded circles (Hershey circles).  The circles
      are then exposed to the enzyme in a complete reaction mixture; the reaction is
      stopped by SDS and filtered rapidly through nitrocellulose filters without any
      subsequent washing.  The filters are dried and counted in a liquid
      scintillation counter.  The assay is specific (as checked with modified DNA and
      dependence on cofactors), linear and quantitative.  It has been used
      successfully in the purification of the restriction endonucleases from E. coli
      (P1) and E. coli (15).
AU  - Reiser J
AU  - Yuan R
PT  - Journal Article
TA  - Experientia
JT  - Experientia
SO  - Experientia 1975 31: 745.

PMID- Not carried by PubMed...
VI  - 13
DP  - 1995
TI  - Complete nucleotide sequence of the Porphyra purpurea chloroplast genome.
PG  - 333-335
AB  - The complete nucleotide sequence of the chloroplast genome of the red alga Porphyra purpurea
      has been determined (accession number = U38804).  The circular genome is 191,028 bp in length
      and encodes approximately 250 genes.
AU  - Reith M
AU  - Munholland J
PT  - Journal Article
TA  - Plant Mol. Biol. Rep.
JT  - Plant Mol. Biol. Rep.
SO  - Plant Mol. Biol. Rep. 1995 13: 333-335.

PMID- 12787669
VI  - 329
DP  - 2003
TI  - Catalytic mechanism of DNA-(cytosine-C5)-methyltransferases revisited: covalent intermediate formation is not essential for methyl group transfer by the murine Dnmt3a enzyme.
PG  - 675-684
AB  - Co-transfections of reporter plasmids and plasmids encoding the catalytic domain of the murine
      Dnmt3a DNA methyltransferase lead to inhibition of
      reporter gene expression. As Dnmt3a mutants with C-->A and E-->A exchanges
      in the conserved PCQ and ENV motifs in the catalytic center of the enzyme
      also cause repression, we checked for their catalytic activity in vitro.
      Surprisingly, the activity of the cysteine variant and of the
      corresponding full-length Dnmt3a variant is only two to sixfold reduced
      with respect to wild-type Dnmt3a. In contrast, enzyme variants carrying
      E-->A, E-->D or E-->Q exchanges of the ENV glutamate are catalytically
      almost inactive, demonstrating that this residue has a central function in
      catalysis. Since the glutamic acid residue contacts the flipped base, its
      main function could be to hold the target base at a position that supports
      methyl group transfer. Whereas wild-type Dnmt3a and the ENV variants form
      covalent complexes with 5-fluorocytidine modified DNA, the PCN variant
      does not. Therefore, covalent complex formation is not essential in the
      reaction mechanism of Dnmt3a. We propose that correct positioning of the
      flipped base and the cofactor and binding to the transition state of
      methyl group transfer are the most important roles of the Dnmt3a enzyme in
      the catalytic cycle of methyl group transfer.
AU  - Reither S
AU  - Li F
AU  - Gowher H
AU  - Jeltsch A
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2003 329: 675-684.

PMID- 22535929
VI  - 194
DP  - 2012
TI  - Sequencing of K60, Type Strain of the Major Plant Pathogen Ralstonia solanacearum.
PG  - 2742-2743
AB  - Ralstonia solanacearum is a widespread and destructive plant pathogen. We present the genome
      of the type strain, K60 (phylotype IIA, sequevar 7). Sequevar 7
      strains cause ongoing tomato bacterial wilt outbreaks in the southeastern United
      States. K60 generally resembles R. solanacearum CFBP2957, a Caribbean tomato
      isolate, but has almost 360 unique genes.
AU  - Remenant B
AU  - Babujee L
AU  - Lajus A
AU  - Medigue C
AU  - Prior P
AU  - Allen C
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2742-2743.

PMID- 27738030
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Carnobacterium divergens V41, a Bacteriocin-Producing Strain.
PG  - e01109-16
AB  - In this study, we present the draft genome sequence of Carnobacterium divergens V41. This
      strain was previously reported as producing divercin V41, a bacteriocin
      of interest for food biopreservation. Its genome revealed also the presence of a
      gene cluster putatively involved in polyketide production, which is unique in
      lactic acid bacteria.
AU  - Remenant B
AU  - Borges F
AU  - Cailliez-Grimal C
AU  - Revol-Junelles AM
AU  - Marche L
AU  - Lajus A
AU  - Medigue C
AU  - Pilet MF
AU  - Prevost H
AU  - Zagorec M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01109-16.

PMID- 20550686
VI  - 11
DP  - 2010
TI  - Genomes of three tomato pathogens within the Ralstonia solanacearum species complex reveal significant evolutionary divergence.
PG  - 379
AB  - ABSTRACT: BACKGROUND: The Ralstonia solanacearum species complex includes
      thousands of strains pathogenic to an unusually wide range of plant
      species. These globally dispersed and heterogeneous strains cause
      bacterial wilt diseases, which have major socio-economic impacts.
      Pathogenicity is an ancestral trait in R. solanacearum and strains with
      high genetic variation can be subdivided into four phylotypes, correlating
      to isolates from Asia (phylotype I), the Americas (phylotype IIA and IIB),
      Africa (phylotype III) and Indonesia (phylotype IV). Comparison of genome
      sequences strains representative of this phylogenetic diversity can help
      determine which traits allow this bacterium to be such a pathogen of so
      many different plant species and how the bacteria survive in many
      different habitats. RESULTS: The genomes of three tomato bacterial wilt
      pathogens, CFBP2957 (Phy. IIA), CMR15 (phy. III) and PSI07 (phy. IV) were
      sequenced and manually annotated. These genomes were compared with those
      of three previously sequenced R. solanacearum strains: GMI1000 (tomato,
      phy. I), IPO1609 (potato, phy. IIB), and Molk2 (banana, phy. IIB). The
      major genomic features (size, G+C content, number of genes) were conserved
      across all of the six sequenced strains. Despite relatively high genetic
      distances (calculated from average nucleotide identity) and many genomic
      rearrangements, more than 60% of the genes of the megaplasmid and 70% of
      those on the chromosome are syntenic. The three new genomic sequences
      revealed the presence of several previously unknown traits, probably
      acquired by horizontal transfers, within the genomes of R. solanacearum,
      including a type IV secretion system, a rhi-type anti-mitotic toxin and
      two small plasmids. Genes involved in virulence appear to be evolving at a
      faster rate than the genome as a whole. CONCLUSIONS: Comparative analysis
      of genome sequences and gene content confirmed the differentiation of R.
      solanacearum species complex strains into four phylotypes. Genetic
      distances between strains, in conjunction with CGH analysis of a larger
      set of strains, revealed differences great enough to consider
      reclassification of the R. solanacearum species complex into three
      species. The data are still too fragmentary to link genomic classification
      and phenotypes, but these new genome sequences identify a pan-genome more
      representative of the diversity in the R. solanancearum species complex.
AU  - Remenant B
AU  - Coupat-Goutaland B
AU  - Guidot A
AU  - Cellier G
AU  - Wicker E
AU  - Allen C
AU  - Fegan M
AU  - Pruvost O
AU  - Elbaz M
AU  - Calteau A
AU  - Salvignol G
AU  - Mornico D
AU  - Mangenot S
AU  - Barbe V
AU  - Medigue C
AU  - Prior P
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2010 11: 379.

PMID- 21931687
VI  - 6
DP  - 2011
TI  - Phylotype IV strains of Ralstonia solanacearum, R. syzygii and the blood disease bacterium form a single genomic species despite their divergent life-styles.
PG  - e24356
AB  - 
AU  - Remenant B
AU  - de Cambiaire JC
AU  - Cellier G
AU  - Jacobs JM
AU  - Mangenot S
AU  - Barbe V
AU  - Lajus A
AU  - Vallenet D
AU  - Medigue C
AU  - Fegan M
AU  - Allen C
AU  - Prior P
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2011 6: e24356.

PMID- 23472227
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Phyllosphere Model Bacterium Pantoea agglomerans 299R.
PG  - e00036-13
AB  - Bacteria belonging to the genus are common colonizers of plant leaf surfaces. Here, we present
      the draft genome sequence of 299R, a phyllosphere isolate that
      has become a model strain for studying the ecology of plant leaf-associated
      bacterial commensals.
AU  - Remus-Emsermann MN
AU  - Kim EB
AU  - Marco ML
AU  - Tecon R
AU  - Leveau JH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00036-13.

PMID- 28300228
VI  - 11
DP  - 2016
TI  - Complete genome sequence of Pseudomonas citronellolis P3B5, a candidate for microbial phyllo-remediation of hydrocarbon-contaminated sites.
PG  - 75
AB  - Pseudomonas citronellolis is a Gram negative, motile gammaproteobacterium belonging to the
      order Pseudomonadales and the family Pseudomonadaceae. We
      isolated strain P3B5 from the phyllosphere of basil plants (Ocimum basilicum L.).
      Here we describe the physiology of this microorganism, its full genome sequence,
      and detailed annotation. The 6.95 Mbp genome contains 6071 predicted protein
      coding sequences and 96 RNA coding sequences. P. citronellolis has been the
      subject of many studies including the investigation of long-chain aliphatic
      compounds and terpene degradation. Plant leaves are covered by long-chain
      aliphates making up a waxy layer that is associated with the leaf cuticle. In
      addition, basil leaves are known to contain high amounts of terpenoid substances,
      hinting to a potential nutrient niche that might be exploited by P.
      citronellolis. Furthermore, the isolated strain exhibited resistance to several
      antibiotics. To evaluate the potential of this strain as source of transferable
      antibiotic resistance genes on raw consumed herbs we therefore investigated if
      those resistances are encoded on mobile genetic elements. The availability of the
      genome will be helpful for comparative genomics of the phylogenetically broad
      pseudomonads, in particular with the sequence of the P. citronellolis type strain
      PRJDB205 not yet publicly available. The genome is discussed with respect to a
      phyllosphere related lifestyle, aliphate and terpenoid degradation, and
      antibiotic resistance.
AU  - Remus-Emsermann MN
AU  - Schmid M
AU  - Gekenidis MT
AU  - Pelludat C
AU  - Frey JE
AU  - Ahrens CH
AU  - Drissner D
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 75.

PMID- 26159532
VI  - 3
DP  - 2015
TI  - Genome Sequence of Arthrobacter sp. YC-RL1, an Aromatic Compound-Degrading Bacterium.
PG  - e00749-15
AB  - We report the 4.04-Mb draft genome sequence of Arthrobacter sp. YC-RL1, an aromatic
      compound-degrading bacterium. YC-RL1 could degrade a wide range of
      aromatic compounds, including naphthaline, 1,2,3,4-tetrachlorobenzene, fluorene,
      4-nitrophenol, bisphenol A, biphenyl, and p-xylene. The genome sequence of YC-RL1
      will promote the investigation of the biodegradation of aromatic compounds.
AU  - Ren L
AU  - Shi Y
AU  - Jia Y
AU  - Yan Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00749-15.

PMID- 3027691
VI  - 22
DP  - 1986
TI  - Biosynthesis of restriction endonuclease SalGI and optimal conditions of its purification.
PG  - 736-741
AB  - The effect of the growing phase of Streptomyces albus G. and the components of
      the culture medium on the biosynthesis of restriction endonuclease SalGI was
      studied.  The conditions of DNA sedimentation with streptomycin sulfate and
      polyethylenimine and separation of proteins with ammonium sulfate were
      investigated as well.  A maximal quantity of the enzyme was observed in the
      cells in 18-20 h of cultivation in flasks on a shaker.  The optimal
      concentrations of the medium components (g/l) were found by mathematical
      methods of the experiment planning:  glucose - 19,0; peptone - 5.2;
      K2HPO4.3H2O-5.0.  The optimal concentrations for DNA sedimentation with
      streptomycin sulfate and polyethylenimine were found to be 1.8-2.0% and
      0.2-0.3%, respectively.  The optimal concentration of ammonium sulfate for
      protein separation is 70% of saturation.
AU  - Ren LS
AU  - Oreshkin EN
AU  - Grachyov YP
PT  - Journal Article
TA  - Prikl. Biokhim. Mikrobiol.
JT  - Prikl. Biokhim. Mikrobiol.
SO  - Prikl. Biokhim. Mikrobiol. 1986 22: 736-741.

PMID- 12712204
VI  - 422
DP  - 2003
TI  - Unique physiological and pathogenic features of Leptospira interrogans revealed by whole-genome sequencing.
PG  - 888
AB  - Leptospirosis is a widely spread disease of global concern. Infection causes flu-like episodes
      with frequent severe renal and hepatic damage,
      such as haemorrhage and jaundice. In more severe cases, massive pulmonary
      haemorrhages, including fatal sudden haemoptysis, can occur. Here we
      report the complete genomic sequence of a representative virulent serovar
      type strain (Lai) of Leptospira interrogans serogroup Icterohaemorrhagiae
      consisting of a 4.33-megabase large chromosome and a 359-kilobase small
      chromosome, with a total of 4,768 predicted genes. In terms of the genetic
      determinants of physiological characteristics, the facultatively parasitic
      L. interrogans differs extensively from two other strictly parasitic
      pathogenic spirochaetes, Treponema pallidum and Borrelia burgdorferi,
      although similarities exist in the genes that govern their unique
      morphological features. A comprehensive analysis of the L. interrogans
      genes for chemotaxis/motility and lipopolysaccharide synthesis provides a
      basis for in-depth studies of virulence and pathogenesis. The discovery of
      a series of genes possibly related to adhesion, invasion and the
      haematological changes that characterize leptospirosis has provided clues
      about how an environmental organism might evolve into an important human
      pathogen.
AU  - Ren S-X et al
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2003 422: 888.

PMID- 24970825
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Enterotoxigenic Escherichia coli Strain W25K.
PG  - e00593-14
AB  - Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrheal disease in  humans and
      newly weaned pigs. Here, we report the draft genome sequence of ETEC
      strain W25K, which causes diarrhea in piglets.
AU  - Ren W
AU  - Liu G
AU  - Yin J
AU  - Chen S
AU  - Li T
AU  - Kong X
AU  - Peng Y
AU  - Yin Y
AU  - Hardwidge PR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00593-14.

PMID- 20207761
VI  - 192
DP  - 2010
TI  - Complete genome sequence of Enterobacter cloacae subsp. cloacae type strain ATCC 13047.
PG  - 2463-2464
AB  - Enterobacter cloacae is an important nosocomial pathogen. Here, we report the completion of
      the genome sequence of E. cloacae ATCC 13047, the type
      strain of E. cloacae subsp. cloacae. Multiple sets of virulence
      determinant and heavy-metal resistance genes have been found in the
      genome. To the best of our knowledge, this is the first complete genome
      sequence of the E. cloacae species.
AU  - Ren Y
AU  - Ren Y
AU  - Zhou Z
AU  - Guo X
AU  - Li Y
AU  - Feng L
AU  - Wang L
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 2463-2464.

PMID- 2181400
VI  - 18
DP  - 1990
TI  - Cloning, characterization, and expression in Escherichia coli of the gene coding for the CpG DNA methylase from Spiroplasma sp. strain MQ1(M.SssI) .
PG  - 1145-1152
AB  - We describe here the cloning, characterization and expression in E. coli of the
      gene coding for a DNA methylase from Spiroplasma sp. strain MQ1 (M.SssI).  This
      enzyme methylates completely and exclusively CpG sequences.  The Spiroplasma
      gene was transcribed in E. coli using its own promoter.  Translation of the
      entire message required the use of an opal suppressor, suggesting that UGA
      triplets code for tryptophan in Spiroplasma.  Sequence analysis of the gene
      revealed several UGA triplets, in a 1158 bp long open reading frame.  The
      deduced amino acid sequence revealed in M.SssI all common domains
      characteristic of bacterial cytosine DNA methylases.  The putative sequence
      recognition domain of M.SssI showed no obvious similarities with that of the
      mouse DNA methylase, in spite of their common sequence specificity.  The cloned
      enzyme methylated exclusively CpG sequences both in vivo and in vitro.  In
      contrast to the mammalian enzyme which is primarily a maintenance methylase,
      M.SssI displayed de novo methylase activity, characteristic of prokaryotic
      cytosine DNA methylases.
AU  - Renbaum P
AU  - Abrahamove D
AU  - Fainsod A
AU  - Wilson GG
AU  - Rottem S
AU  - Razin A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 1145-1152.

PMID- 7731043
VI  - 248
DP  - 1995
TI  - Footprint analysis of M.SssI and M.HhaI methyltransferases reveals extensive interactions with the substrate DNA backbone.
PG  - 19-26
AB  - The interactions of the CpG methyltransferases M.SssI and M.HhaI (GCGC) with substrate DNA
      were investigated using three different footprinting techniques. The two structurally related
      enzymes displayed similar specific and non-specific contacts with DNA while bound to their
      target sequences. DNase I footprinting implicated a region of 18 to 21 base-pairs with which
      these enzymes interact. Dimethylsulfate protection experiments mostly revealed specific base
      interactions; each enzyme was shown to interact predominantly with bases at its recognition
      site in the major groove. However, hydroxyl radical footprints demonstrated extensive
      interactions with the sugar-phosphate backbone on both strands of the DNA substrate. Both
      enzymes protected a 16 nucleotide region, in a staggered fashion, covering 9 to 10 nucleotides
      on each strand. The protected regions, extending for almost a full turn of DNA on each strand,
      were offset by 6 to 7 nucleotides in the 5' direction, placing both regions on the same face
      of the double helix, bracketing the major groove. The results suggest that these
      methyltransferases straddle the major groove from the backbone, but protrude into the groove
      only to specifically interact with their recognition sites. The sequence-independent
      interactions observed on the sugar-phosphate backbone may explain the ability of the enzymes
      to recognize a small sequence, as well as their processive mode of action.
AU  - Renbaum P
AU  - Razin A
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1995 248: 19-26.

PMID- 1446743
VI  - 313
DP  - 1992
TI  - Mode of action of the Spiroplasma CpG methylase M.SssI.
PG  - 243-247
AB  - The cytosine DNA methylase from the wall-less prokaryote, Spiroplasma strain MQ1 (M.SssI)
      methylates completely and exclusively CpG-containing sequences, thus showing sequence
      specificity which is similar to that of mammalian DNA methylases. M.SssI is shown here to
      methylate duplex DNA processively as judged by kinetic analysis of methylated intermediates.
      The cytosine DNA methylases. M.HpaII and M.HhaI from other prokaryotic organisms, appear to
      methylate in a non-processive manner or with a very low degree of processivity. The
      Spiroplasma enzyme interacts with duplex DNA irrespective of the presence of CpG sequences in
      the substrate DNA. The enzyme proceeds along a CpG-containing DNA substrate molecule
      methylating one strand of DNA at a time.
AU  - Renbaum P
AU  - Razin A
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1992 313: 243-247.

PMID- 7607487
VI  - 157
DP  - 1995
TI  - Interaction of M.SssI and M.HhaI with single-base mismatched oligodeoxynucleotide duplexes.
PG  - 177-179
AB  - As part of an attempt to elucidate the mode of interaction of the CpG methyltransferase M.SssI
      with its substrate, we have prepared a series of double-stranded oligodeoxyribonucleotides
      containing one mismatch in the CpG recognition site.  The mismatched duplexes were used to
      analyze the binding capabilities and enzymatic activity of M.SssI and M.HhaI (recognizes
      GCGC).  We demonstrate here that M.SssI binds specifically to substrates containing either a
      C/A or G/T mismatch in the recognition sequence, i.e., 5'-GCGC/CACG-5' or 5'-GCGC/CGTG-5',
      respectively.  The enzyme also shows significant enzymatic activity with these mismatched
      substrates.  These results suggest that site recognition and methylation of M.SssI take place
      on the same strand.  M.HhaI bound and methylated the C/A mismatch very efficiently, but
      recognition of the G/T mismatch was scarcely detectable.
AU  - Renbaum P
AU  - Razin A
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 177-179.

PMID- 14752164
VI  - 303
DP  - 2004
TI  - A predator unmasked: life cycle of Bdellovibrio bacteriovorus from a genomic perspective.
PG  - 689-692
AB  - Predatory bacteria remain molecularly enigmatic, despite their presence in
      many microbial communities. Here we report the complete genome of
      Bdellovibrio bacteriovorus HD100, a predatory Gram-negative bacterium that
      invades and consumes other Gram-negative bacteria. Its surprisingly large
      genome shows no evidence of recent gene transfer from its prey. A plethora
      of paralogous gene families coding for enzymes, such as hydrolases and
      transporters, are used throughout the life cycle of B. bacteriovorus for
      prey entry, prey killing, and the uptake of complex molecules.
AU  - Rendulic S
AU  - Jagtap P
AU  - Rosinus A
AU  - Eppinger M
AU  - Baar C
AU  - Lanz C
AU  - Keller H
AU  - Lambert C
AU  - Evans KJ
AU  - Goesmann A
AU  - Meyer F
AU  - Sockett RE
AU  - Schuster SC
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2004 303: 689-692.

PMID- 18079367
VI  - 319
DP  - 2008
TI  - The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants.
PG  - 64-69
AB  - We report the draft genome sequence of the model moss Physcomitrella patens and compare its
      features with those of flowering plants, from which it is separated
      by more than 400 million years, and unicellular aquatic algae. This comparison
      reveals genomic changes concomitant with the evolutionary movement to land,
      including a general increase in gene family complexity; loss of genes associated
      with aquatic environments (e.g., flagellar arms); acquisition of genes for
      tolerating terrestrial stresses (e.g., variation in temperature and water
      availability); and the development of the auxin and abscisic acid signaling
      pathways for coordinating multicellular growth and dehydration response. The
      Physcomitrella genome provides a resource for phylogenetic inferences about gene
      function and for experimental analysis of plant processes through this plant's
      unique facility for reverse genetics.
AU  - Rensing SA et al
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2008 319: 64-69.

PMID- 25013134
VI  - 2
DP  - 2014
TI  - First Whole-Genome Sequence of a Clinical Isolate of Multidrug-Resistant Mycobacterium bovis BCG.
PG  - e00611-14
AB  - The attenuated BCG strain of Mycobacterium bovis is widely used as a vaccine against
      tuberculosis. However, in rare cases, it can be pathogenic to humans.
      Here, we report the first draft of a whole-genome sequence of a
      multidrug-resistant clinical isolate of M. bovis BCG.
AU  - Renvoise A
AU  - Pang S
AU  - Bernard C
AU  - Brossier F
AU  - Veziris N
AU  - Capton E
AU  - Jarlier V
AU  - Sougakoff W
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00611-14.

PMID- 29122869
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Streptococcus thermophilus Strain B59671, Which Naturally Produces the Broad-Spectrum Bacteriocin Thermophilin 110.
PG  - e01213-17
AB  - Streptococcus thermophilus strain B59671 is a Gram-positive lactic acid bacterium that
      naturally produces a broad-spectrum bacteriocin, thermophilin 110, and is
      capable of producing gamma-aminobutyric acid (GABA). The complete genome sequence
      for this strain contains 1,821,173 nucleotides, 1,936 predicted genes, and an
      average G+C content of 39.1%.
AU  - Renye JA Jr
AU  - Needleman DS
AU  - Somkuti GA
AU  - Steinberg DH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01213-17.

PMID- 
VI  - 
DP  - 1994
TI  - Structural and functional organization of the genes of the EcoRII restriction-modification system.
PG  - 1-22
AB  - 
AU  - Repik AV
PT  - Journal Article
TA  - Ph.D. Thesis, Russian Academy of Sciences
JT  - Ph.D. Thesis, Russian Academy of Sciences
SO  - Ph.D. Thesis, Russian Academy of Sciences 1994 : 1-22.

PMID- Not included in PubMed...
VI  - 33
DP  - 1997
TI  - MspR91, a new isoschizomer of ScrFI restriction endonuclease from Micrococcus species.
PG  - 284-286
AB  - MspR91 restriction endonuclease was isolated from Micrococcus species identified by screening
      soil bacteria for site-specific endonucleases.  The enzyme recognizes and cleaves the
      palindromic sequence 5'-CC/NGG-3'.
AU  - Repin VE
AU  - Andreeva IS
AU  - Kileva EV
AU  - Shevchenko AV
AU  - Abdurashitov MA
AU  - Repin MV
AU  - Degtyarev SK
PT  - Journal Article
TA  - Prikl. Biokhim. Mikrobiol.
JT  - Prikl. Biokhim. Mikrobiol.
SO  - Prikl. Biokhim. Mikrobiol. 1997 33: 284-286.

PMID- 8494562
VI  - 19
DP  - 1993
TI  - Bse118I, an isoschizomer of the Cfr10I restriction endonuclease from Bacillus coagulans.
PG  - 406-409
AB  - The recognition sequence and cleavage point for Bse118I restriction endonuclease have been
      determined as (5') R^CCGGY.
AU  - Repin VE
AU  - Babkin IV
AU  - Tereshchenko TA
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1993 19: 406-409.

PMID- 1667028
VI  - 11
DP  - 1991
TI  - Search of restriction endonuclease producers with required specificity.
PG  - 20-22
AB  - Six site-specific restriction endonucleases were isolated from Bacillus
      thuringiensis strains chosen from 58 strains sought purposefully for the
      production of restriction enzymes.  All six strains produce isoschizomers of
      Sau3AI.
AU  - Repin VE
AU  - Burtseva LI
AU  - Burlak VA
AU  - Trusova SI
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1991 11: 20-22.

PMID- 8494563
VI  - 4
DP  - 1993
TI  - Bco116I, An isoschizomer of Ksp632I from Bacillus coagulans.
PG  - 410-413
AB  - The recognition sequence and cleavage point of restriction endonuclease Bco116I have been
      determined as (5') CTCTTC (1/4).
AU  - Repin VE
AU  - Chizhikov VE
AU  - Tereshchenko TA
AU  - Lebedev LR
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1993 4: 410-413.

PMID- 1317567
VI  - 28
DP  - 1992
TI  - Comparison of express-methods used for the detection of restriction endonucleases in microorganisms.
PG  - 152-155
AB  - The sensitivity of several express-methods used for the detection of bacterial endonucleases
      was compared. The most sensitive method is that employing Triton X-100.
AU  - Repin VE
AU  - Degtyarev SK
PT  - Journal Article
TA  - Prikl. Biokhim. Mikrobiol.
JT  - Prikl. Biokhim. Mikrobiol.
SO  - Prikl. Biokhim. Mikrobiol. 1992 28: 152-155.

PMID- 
VI  - 0
DP  - 1998
TI  - The producers of restriction endonucleases from natural microbe isolates and the development on this basis of enzyme production technologies.
PG  - 18-27
AB  - The screening of natural bacterial strains isolated from various ecological niches in order to
      discover site specific nucleases has been carried out using different modifications of the
      express method for detection of restriction endonucleases in bacterial colonies.  More than 60
      easy to grow strains belonging to different bacterial taxa and promising for practical use
      were obtained.  Some approaches to increase the strain efficiency as well as the purification
      schemes to produce highly pure preparations of restriction endonuclease were suggested.
AU  - Repin VE
AU  - Lebedev LR
AU  - Andreeva IS
AU  - Puchkova LI
AU  - Zernov YP
AU  - Serov GD
AU  - Tereshchenko TA
AU  - Aphinogenova GN
AU  - Pustoshilova NM
PT  - Journal Article
TA  - Biotekhnologiya
JT  - Biotekhnologiya
SO  - Biotekhnologiya 1998 0: 18-27.

PMID- 7607519
VI  - 157
DP  - 1995
TI  - New restriction endonucleases from thermophilic soil bacteria.
PG  - 321-322
AB  - Using the most effective rapid method for the detection of restriction endonucleases (ENases)
      in microorganisms, 32 thermophilic producers have been isolated.  All strains belong to the
      genus Bacillus.  Thermostable isoschizomers of ENases, such as AvaI, BbvI, BbvII, BclI, BsaBI,
      BsiYI, BsrI, BstEII, BstNI, Cfr10I, ClaI, FspI, HaeIII, HpaII, Ksp632I and SfeI, were
      isolated.
AU  - Repin VE
AU  - Lebedev LR
AU  - Puchkova L
AU  - Serov GD
AU  - Tereschenko T
AU  - Chizikov VE
AU  - Andreeva I
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 321-322.

PMID- Not carried by PubMed...
VI  - 15
DP  - 1989
TI  - The cultivation of Bacillus species 21, producer of restriction endonuclease Bse21I.
PG  - 108-111
AB  - The effect of the components of the culture medium, temperature of cultivation
      and the growing phase of Bacillus species 21 on the yield of the restrictase
      activity of this microorganism was studied.  A maximal quantity of the enzyme
      per 1 g cells was observed at the beginning of the stationary phase of growth.
      Using mathematical methods for planning experiments allowed us to raise the
      Bse21I yield more than 8-fold.
AU  - Repin VE
AU  - Polshina SV
AU  - Bozhko NA
AU  - Degtyarev SK
PT  - Journal Article
TA  - Izv. Sib. Otd. Akad. Nauk SSSR
JT  - Izv. Sib. Otd. Akad. Nauk SSSR
SO  - Izv. Sib. Otd. Akad. Nauk SSSR 1989 15: 108-111.

PMID- Not carried by PubMed...
VI  - 14
DP  - 1988
TI  - Search of soil microorganisms for production of restriction endonucleases.
PG  - 110-113
AB  - A search of soil microorganisms for the production of restriction endonucleases
      was carried out.  Three strains belonging to species of Bacillus subtilis,
      Bacillus megaterium and Aeromonas punctata were found and identified.  The
      strains' restrictases were shown to be isoschizomers of ClaI and Sau3AI.  The
      optimal conditions for cultivation of Bacillus subtilis 15 to increase enzyme
      outcome were established.
AU  - Repin VE
AU  - Prichodko EA
AU  - Degtyarev SK
PT  - Journal Article
TA  - Izv. Sib. Otd. Akad. Nauk SSSR
JT  - Izv. Sib. Otd. Akad. Nauk SSSR
SO  - Izv. Sib. Otd. Akad. Nauk SSSR 1988 14: 110-113.

PMID- 10369693
VI  - 45
DP  - 1999
TI  - HpyNI is the first restriction endonuclease isolated from Helicobacter pylori.
PG  - A6
AB  - Restriction-modification systems serve as a biological tool to ensure relative stability of
      genetic material of the microbe, degrading alien DNA penetrated into bacterial cell.  The aim
      of the study was to isolate and characterize restriction endonucleases of H. pylori.  H.
      pylori strain was isolated from the gastric mucosa of duodenal ulcer patient.  The strain had
      typical morphological and biochemical properties of H. pylori and was highly resistant to
      metronidazole.  To study site-specificity viral and plasmid DNA's were used: T7, lambda, and
      pBR322.  MsrR9I and Bst38I restrictases were utilized as standard.  The given strain of H.
      pylori showed nuclease activity, and endonuclease obtained was called HpyNI according to the
      generally accepted nomenclature.  The enzyme restricted standard substrate DNAs with the site
      specific to base sequence 5'-CCNGG-3'.  Additional hydrolysis with Bst38I could not yield
      novel fragments.  However, hydrolysis with HpyNI and MsrR9I showed complete homogeneity.  Thus
      HpyNI proved to be an isoschizomer of ScrFI, in which this recognition site was first
      described. Similar site specific endonucleases are widely represented in various microbial
      taxons.  Horizontal transfer occurs between genomes of various bacteria, and restriction may
      play a part in this process.  H. pylori is evolutionarily close to Escherichia coli and the
      latter showed the greatest number of ScrFI isoschizomers, thus one could not exclude the
      exchange of genes between these two bacteria.
AU  - Repin VE
AU  - Puchkova LI
AU  - Ananko GG
AU  - Reshetnikov OV
AU  - Kurilovich SA
PT  - Journal Article
TA  - Gut
JT  - Gut
SO  - Gut 1999 45: A6.

PMID- 8643035
VI  - 64
DP  - 1995
TI  - Luminescent bacteria as producers of specific restriction endonucleases.
PG  - 751-755
AB  - Luminescent bacteria isolated from the waters of the Black Sea and the Indian and Pacific
      Oceans were tested for the presence of restriction endonucleases.  Restriction sites were
      determined for 12 of the 19 restriction enzyme producers revealed.  The enzymes were
      identified as isoschizomers of AflII, BanI, HaeIII, PstI, Sau3AI, and Sau96I.  Possible
      participation of the restriction and modification enzymes in the interaction of bacterial
      symbionts with the animal macrosymbiont is discussed.
AU  - Repin VE
AU  - Puchkova LI
AU  - Rodicheva EK
AU  - Vydryakova GA
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 1995 64: 751-755.

PMID- Not included in PubMed...
VI  - 33
DP  - 1997
TI  - Restriction endonucleases from symbiotic luminous bacteria.
PG  - 152-155
AB  - Marine luminous bacteria from the Black Sea and the Indian and Pacific Oceans were assayed for
      restriction endonucleases.  Nineteen producers of restriction endonucleases were found; the
      recognition sites were determined for 13 identified restriction endonucleases.  The identified
      enzymes were isoschizomers of AflII, BanI, HaeIII, NarI, PstI, Sau3AI, or Sau96I restriction
      endonucleases.  The role of restriction-modification enzymes in the symbiotic relationships
      between bacteria and their hosts was suggested.
AU  - Repin VE
AU  - Puchkova LI
AU  - Rodicheva EK
AU  - Vydryakova GA
PT  - Journal Article
TA  - Prikl. Biokhim. Mikrobiol.
JT  - Prikl. Biokhim. Mikrobiol.
SO  - Prikl. Biokhim. Mikrobiol. 1997 33: 152-155.

PMID- Not carried by PubMed...
VI  - 42
DP  - 1989
TI  - Aerobic spore-forming bacteria as producers of restriction endonucleases.
PG  - 969-972
AB  - From 58 strains of aerobic sporeforming bacteria studied, including
      their thermophilic forms, 5 strains have restrictase activity.  All
      restrictases
      produced by these strains are isoschizomers of known restrictases
      characteristic
      of bacilli.  For the forst time specific restrictase producers have been
      indicated, which reveal the order of hexanucleotides.
AU  - Repin VE
AU  - Rechkunova NI
AU  - Degtyarev SK
AU  - Hachaturyan AA
AU  - Afrikyan EK
PT  - Journal Article
TA  - Biol. J. Armenia
JT  - Biol. J. Armenia
SO  - Biol. J. Armenia 1989 42: 969-972.

PMID- 8391262
VI  - 19
DP  - 1993
TI  - New restriction endonucleases from thermophilic bacteria of the genus Bacillus.
PG  - 583-585
AB  - Restriction endonucleases have been isolated from 26 thermophilic strains of the Bacillus
      genus, their recognition sequences were determined, and for 15 of them cleavage sites
      identified. The enzymes proved to be isoschizomers of known endonucleases BstNI, EarI, HaeIII,
      HpaII, Cfr10I, BsiYI, BclI, BbvII, BbvI, BstEII, BsaBI, BsrI, FspI, ClaI, SfeI.
AU  - Repin VE
AU  - Serov GD
AU  - Puchkova LI
AU  - Tereshenko TA
AU  - Lebedev LR
AU  - Chigikov VE
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1993 19: 583-585.

PMID- Not included in PubMed...
VI  - 110
DP  - 1990
TI  - Occurrence and function of restriction endonucleases (A Review).
PG  - 34-47
AB  - Modern nomenclature and classification of restriction endonucleases and related
      topics are discussed.  Particular emphasis is placed on the distribution of
      restriction enzymes among various taxons of microorganisms.  The possible
      functional role of restriction enzymes in vivo and their evolution within
      bacteria is discussed.  Basic methods for screening for type II enzymes are
      described with a rationale for the use of rapid methods for analyzing large
      numbers of bacterial strains.  Research perspectives in this branch of
      molecular biology are presented.
AU  - Repin VE
AU  - Shelkunov SN
PT  - Journal Article
TA  - Usp. Sovrem. Biol.
JT  - Usp. Sovrem. Biol.
SO  - Usp. Sovrem. Biol. 1990 110: 34-47.

PMID- 
VI  - 0
DP  - 1989
TI  - Screening microorganisms isolated from air for restriction endonuclease producers.
PG  - 14-17
AB  - None
AU  - Repin VE
AU  - Shilyayeva OH
PT  - Journal Article
TA  - Microbiological investigations in Western Siberia
JT  - Microbiological investigations in Western Siberia
SO  - Microbiological investigations in Western Siberia 1989 0: 14-17.

PMID- 15292156
VI  - 186
DP  - 2004
TI  - Complete genomic nucleotide sequence of the temperate bacteriophage Aaphi23 of Actinobacillus actinomycetemcomitans.
PG  - 5523-5528
AB  - The entire double-stranded DNA genome of the Actinobacillus actinomycetemcomitans
      bacteriophage AaPhi23 was sequenced. Linear DNA
      contained in the phage particles is circularly permuted and terminally
      redundant. Therefore, the physical map of the phage genome is circular.
      Its size is 43,033 bp with an overall molar G+C content of 42.5 mol%.
      Sixty-six potential open reading frames (ORFs) were identified,
      including an ORF resulting from a translational frameshift. A putative
      function could be assigned to 23 of them. Twenty-three other ORFs share
      homologies only with hypothetical proteins present in several bacteria
      or bacteriophages, and 20 ORFs seem to be specific for phage AaPhi23.
      The organization of the phage genome and several genetic functions
      share extensive similarities to that of the lambdoid phages. However,
      AaPhi23 encodes a DNA adenine methylase, and the DNA packaging strategy
      is more closely related to the P22 system. The attachment sites of
      AaPhi23 (attP) and several A. actinomycetemcomitans hosts (attB) are 49
      bp long.
AU  - Resch G
AU  - Kulik EM
AU  - Dietrich FS
AU  - Meyer E
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2004 186: 5523-5528.

PMID- 28963226
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Xanthomonas arboricola pv. juglandis J303, Isolated from Infected Walnut Trees in Southern Chile.
PG  - e01085-17
AB  - Here, we report the draft genome sequence of Xanthomonas arboricola pv. juglandis J303,
      isolated from infected walnut trees in southern Chile. The size of the
      genome is 5,066,424 bp with a G+C content of 65.4%. X. arboricola pv. juglandis
      J303 has several genes related to virulence, antibiotic resistance, and copper
      resistance.
AU  - Retamales J
AU  - Segovia C
AU  - Alvarado R
AU  - Nunez P
AU  - Santander J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01085-17.

PMID- 27257210
VI  - 4
DP  - 2016
TI  - Complete Genome Sequences of Lytic Bacteriophages of Xanthomonas arboricola pv. juglandis.
PG  - e00336-16
AB  - Three bacteriophages, f20-Xaj, f29-Xaj, and f30-Xaj, with lytic activity against  Xanthomonas
      arboricola pv. juglandis were isolated from walnut trees (VIII Bio
      Bio Region, Chile). These lytic bacteriophages have double-stranded DNA (dsDNA)
      genomes of 43,851 bp, 41,865 bp, and 44,262 bp, respectively. These are the first
      described bacteriophages with lytic activity against X. arboricola pv. juglandis
      that can be utilized as biocontrol agents.
AU  - Retamales J
AU  - Vasquez I
AU  - Santos L
AU  - Segovia C
AU  - Ayala M
AU  - Alvarado R
AU  - Nunez P
AU  - Santander J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00336-16.

PMID- 25767229
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Bacillus subtilis subsp. subtilis Strain 3NA.
PG  - e00084-15
AB  - Bacillus subtilis 3NA reaches high cell densities during fed-batch fermentation and is an
      interesting target for further optimization as a production strain.
      Here, we announce the full genome of B. subtilis 3NA. The presence of specific
      Bacillus subtilis 168 and W23 genetic features suggests that 3NA is a hybrid of
      these strains.
AU  - Reuss DR
AU  - Schuldes J
AU  - Daniel R
AU  - Altenbuchner J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00084-15.

PMID- 27469946
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Bacillus subtilis subsp. subtilis Strain 6.
PG  - e00759-16
AB  - Bacillus subtilis 6 is a genome-reduced strain that was cured from six prophages  and AT-rich
      islands. This strain is of great interest for biotechnological
      applications. Here, we announce the full-genome sequence of this strain.
      Interestingly, the conjugative element ICEBs1 has most likely undergone
      self-excision in B. subtilis 6.
AU  - Reuss DR
AU  - Thurmer A
AU  - Daniel R
AU  - Quax WJ
AU  - Stulke J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00759-16.

PMID- 6252708
VI  - 20
DP  - 1980
TI  - Protection of foreign DNA against host-controlled restriction in bacterial cells.  II. Protection of pSF2124 plasmid by the gene function of bacteriophages T3 and T7.
PG  - 345-354
AB  - When restriction-active Escherichia coli cells (r+p1m+p1) are transformed
      with the pSF2124 plasmid, a common vector in experimental gene transfer, the efficiency
      of transformation (e.o.t.) is lowered by 2 orders of magnitude compared with restriction-
      negative (r-p1m-p1 or r-p1m+p1) recipient cells due to restriction of the pSF2124 DNA by
      endoR.EcoP1.  Preinfection of r+p1m+p1 recipient cells with pSF2124 attains the same
      high value as that of r-m- cells.  The specific role of the ocr+ gene function was
      demonstrated by the use of ocr- mutants (T3/R7, T7/D111): Preinfection with such phage
      mutants does not increase the e.o.t. of r+p1m+p1 cells.  An unspecific e.o.t. alteration of
      restriction-negative (r-m-) recipient cells by ocr+ or ocr- phages was excluded.  The ocr+
      gene function can be exploited to protect pSF2124 against DNA restriction.  The recipient
      cells survive the process of phage preinfection and transformation and stably replicate
      themselves as well as the plasmid DNA.
AU  - Reuter M
AU  - Kruger DH
AU  - Scholz D
AU  - Rosenthal HA
PT  - Journal Article
TA  - Z. Allg. Mikrobiol.
JT  - Z. Allg. Mikrobiol.
SO  - Z. Allg. Mikrobiol. 1980 20: 345-354.

PMID- 9525936
VI  - 273
DP  - 1998
TI  - Cooperative binding properties of restriction endonuclease EcoRII with DNA recognition sites.
PG  - 8294-8300
AB  - EcoRII is a member of the expanding group of type IIe restriction endonucleases that share the
      distinguishing feature of requiring cooperativity between two recognition sites in their
      substrate DNA.  To determine the stoichiometry of the active NDA-enzyme complex and the mode
      of cooperative interaction, we have investigated the dependence of EcoRII cleavage on the
      concentration of EcoRII dimers.  Maximal restriction was observed at dimer/site ratios of 0.25
      and 0.5.  The molecular weight of the DNA-enzyme complex eluted from a gel filtration column
      also corresponds to a dimeric enzyme structure bound to two substrate sites.  We conclude that
      one EcoRII dimer is sufficient to interact cooperatively with two DNA recognition sites.  A
      Lac repressor "barrier" bound between two normally reactive EcoRII sites did not inhibit
      restriction endonuclease activity, indicating that cooperativity between EcoRII sites is
      achieved by bending or looping of the intervening DNA stretch.  Comparative cleavage of linear
      substrates with differently spaced interacting sites revealed an inverse correlation between
      cleavage rate and site distance.  At the optimal distance of one helical turn, EcoRII cleavage
      is independent of the orientation of the recognition sequence in the DNA double strand.
AU  - Reuter M
AU  - Kupper D
AU  - Meisel A
AU  - Schroeder C
AU  - Kruger DH
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1998 273: 8294-8300.

PMID- 8385888
VI  - 209
DP  - 1993
TI  - Use of specific oligonucleotide duplexes to stimulate cleavage of refractory DNA sites by restriction endonucleases.
PG  - 232-237
AB  - There are numerous restriction endonuclease (ENases) which are known never to achieve total
      cleavage of certain unmethylated target DNAs. In addition to EcoRII we found seven ENasese
      (AtuBI, Cfr9I, Eco57I, Ksp6321, NaeI, NarI, and SauBMKI) that were stimulated by
      oligodeoxyribonucleotide (oligo) duplexes containing enzyme-specific recognition sequences to
      cut the target DNAs much more efficiently and in most cases even to completion. These enzymes
      are class-II and class-IIS ENases isolated from different bacterial species and possess a
      varying number of specific sites in the refractory DNA substrates. For DNA analysis and
      large-scale preparation of certain restriction fragments where complete digestions are
      essential we recommend taking into account the fact that various ENases can be activiated by
      specific oligo duplexes to drive restriction digestions to completion.
AU  - Reuter M
AU  - Kupper D
AU  - Pein CD
AU  - Petrusyte M
AU  - Siksnys V
AU  - Frey B
AU  - Kruger DH
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 1993 209: 232-237.

PMID- 
VI  - 14
DP  - 2004
TI  - Structure and function of Type IIE restriction endonucleases or: From a plasmid that restricts phage replication to a new molecular DNA recognition mechanism.
PG  - 261-295
AB  - Restriction endonucleases and DNA methyltransferases are encoded by chromosomal, plasmid, or
      viral genes.  In eubacteria as well as in archaea, they often form biologically active DNA
      restriction-modification systems.  The first R-M systems, discovered by reversible growth
      reduction of bacterial viruses, were found to be encoded by chromosomal genes in Escherichia
      coli K-12, Escherichia coli B, and Salmonella typhimurium.  Besides the prophage P1 and the
      related plasmid p15 also naturally occurring drug resistance plasmids (R factors) of the fi-
      (fertility inhibition-minus) type have been shown to restrict and modify infecting
      bacteriophage or trans-conjugated plasmid DNAs in vivo.  The first R-factor controlled R-M
      systems, called EcoRI and EcoRII today, have been defined by those phenotypical properties.
      Endonucleolysis and cytosine methylation, respectively, have been proposed as the molecular
      mechanisms of EcoRII-specific restriction and modification.  EcoRII was among the very first
      R-M enzymes for which the DNA substrate site was identified.  The REase EcoRII recognizes the
      sequence 5'-CC(A/T)GG which exhibits a twofold rotational symmetry with a dyad axis
      corresponding to the central A-T pair.  EcoRII cleaves the phosphodiester bond at the 5' end
      of the first cytosine of the unmethylated sequence.
AU  - Reuter M
AU  - Muecke M
AU  - Krueger DH
PT  - Journal Article
TA  - Nucleic Acids Mol. Biol.
JT  - Nucleic Acids Mol. Biol.
SO  - Nucleic Acids Mol. Biol. 2004 14: 261-295.

PMID- 1979301
VI  - 95
DP  - 1990
TI  - An improved method for the detection of Dcm methylation in DNA molecules.
PG  - 161-162
AB  - The intrinsic insensitivity of EcoRII recognition sites in RF DNAs of phage M13 and vector
      M13mp18 towards this restriction endonuclease can be overcome by adding site-specific
      oligodeoxyribonucleotide duplexes to the restriction sample. Since Dcm- DNA but not Dcm+
      -methylated DNA becomes susceptible under these conditions, this procedure constitutes an
      improvement of the Dcm methylation assay.
AU  - Reuter M
AU  - Pein C-D
AU  - Butkus V
AU  - Kruger DH
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1990 95: 161-162.

PMID- 9988771
VI  - 274
DP  - 1999
TI  - Regions of endonuclease EcoRII involved in DNA target recognition identified by membrane-bound peptide repertoires.
PG  - 5213-5221
AB  - Target sequence-specific DNA binding regions of the restriction endonuclease EcoRII were
      identified by screening a membrane-bound EcoRII-derived peptide scan with an EcoRII
      recognition site (CCWGG) oligonucleotide duplex.  Dodecapeptides overlapping by nine amino
      acids and representing the complete protein were prepared by spot synthesis.  Two separate DNA
      binding regions, amino acids 88-102 and amino acids 256-273, which share the consensus motif
      KXRXXK, emerged.  Screening 570 single substitution analogues obtained by exchanging every
      residue of both binding sites for all other amino acids demonstrated that replacing basic
      residues in the consensus motifs significantly reduced DNA binding.  EcoRII mutant enzymes
      generated by substituting alanine or glutamic acid for the consensus lysine residues in DNA
      binding site I expressed attentuated DNA binding, whereas corresponding substitutions in DNA
      binding site II caused impaired cleavage, but enzyme secondary structure was unaffected.
      Furthermore, Glu96, which is part of a potential catalytic motif and also locates to DNA
      binding site I, was demonstrated to be critical for DNA cleavage and binding.  Homology
      studies of DNA binding site II revealed strong local homology to SsoII (recognition sequence,
      CCNGG) and patterns of sequence conservation, suggesting the existence of functionally related
      DNA binding sites in diverse restriction endonucleases with recognition sequences containing
      terminal C:G or G:C pairs.
AU  - Reuter M
AU  - Schneider-Mergener J
AU  - Kupper D
AU  - Meisel A
AU  - Mackeldanz P
AU  - Kruger DH
AU  - Schroeder C
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1999 274: 5213-5221.

PMID- Not carried by PubMed...
VI  - 24
DP  - 1986
TI  - Evidence for a specific inhibitor protein of DNA methyltransferases.
PG  - 323-325
AB  - The ocr protein encoded by the bacterial virus T7 is the first known inhibitor protein which
      blocks DNA methyltransferases specifically. It inhibits the methyl transfer to DNA conferred
      by the methylase M.EcoK, however, it is not active against the methylases M.dam and M.EcoRII.
AU  - Reuter VM
AU  - Bogdarina IG
AU  - Kruger DH
PT  - Journal Article
TA  - Biol. Rundsch.
JT  - Biol. Rundsch.
SO  - Biol. Rundsch. 1986 24: 323-325.

PMID- 11944347
VI  - 64
DP  - 2002
TI  - Bsu5044I - Isoschisomer of endonuclease restriction AsuI.
PG  - 57-59
AB  - Endonuclease of restriction of type II has been found in Bacillus subtilis B-5044 during
      testing of endophytic strains of cotton plants bacilli.  The restrictase Bsu5044I hydrolysed
      DNA of M13mp18 phage in 4 sites; pUC19 DNA in 5 sites; pBR322 in 15 sites.  There were a lot
      of sites restriction in DNAs of phages T7 and lambda.  A comparison of electrophoretical
      divisions of Bsu5044I and Cfr13I fragments of phages and plasmid DNAs showed their identity.
      Thus, the found restrictase Bsu5044I is an isoschisomer of AsuI.
AU  - Reva OM
AU  - Lukyanchuk VV
AU  - Polishchuk LV
PT  - Journal Article
TA  - Mikrobiol. Zh.
JT  - Mikrobiol. Zh.
SO  - Mikrobiol. Zh. 2002 64: 57-59.

PMID- Not carried by PubMed...
VI  - 0
DP  - 1983
TI  - DNA Modification:  Glucosylation.
PG  - 156-165
AB  - None
AU  - Revel HR
PT  - Journal Article
TA  - Bacteriophage T4
JT  - Bacteriophage T4
SO  - Bacteriophage T4 1983 0: 156-165.

PMID- 4290282
VI  - 31
DP  - 1967
TI  - Restriction of nonglucosylated T-even bacteriophage: properties of permissive mutants of Escherichia coli B and K12.
PG  - 688-701
AB  - Mutants of Escherichia coli B and K12 which are permissive for either nonglucosylated
      T6 alone or for all the nonglucosylated T-even bacteriophages have been isolated
      after mutagenesis with nitrosoguanidine. The fully permissive mutants of B, derived
      in a single step, require vitamin Bl, whereas those of K12, obtained in two steps, have
      no novel nutritional requirements. Extracts of related permissive and reskicting
      bacteria show no differences in the levels or specificities of their endonuclease I and
      exonuclease III activities. Strain KlZ-1100, an endonuclease-deficient strain, restricts
      all nonglucosylated T-even bacteriophages. Spheroplasts of restrict.ing bacteria
      restrict ?r particles of the nonglucosylated T-even phages.
AU  - Revel HR
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1967 31: 688-701.

PMID- 4897044
VI  - 39
DP  - 1969
TI  - Restriction of nonglucosylated T-even bacteriophages by prophage P1.
PG  - 1-17
AB  - Glucosyl transferase (gt) mutants of all the T-even bacteriophages, with less
      than 3% of the normal complement of glucose on their DNA, fall into two groups
      with respect to restriction by prophage P1.  Mutants of the first group, called
      rp1, are restricted by P1 prophage irrespective of the nature of the hosts on
      which the phage has grown; mutants of the second group, called rcp1, are
      restricted by P1 only if they have grown on a permissive host lacking
      UDPG-PPase.  Mutant prophages P1 r-m+ and P1 r-m-, which do not restrict
      unmodified lambda phage, also fail to restrict gt rp1 or rcp1 phage.  The gt
      mutants grown on P1 r-m+ lysogens are not modified.  Single-step mutants of gt
      phage, called up1, which are insensitive to P1 restriction have been isolated
      from T1gt rp1 and T4gt rp1, but not from T6gt rp1.  The up1 mutation does not
      arise from loss or gain of a diffusible function and probably represents an
      alteration in a site on the DNA recognized by the P1 restricting enzyme.  The
      rp1 site maps outside the gt genes.  Both gt rp1 and gt up1 phages are
      restricted by the resistance transfer factor N1.
AU  - Revel HR
AU  - Georgopoulos CP
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1969 39: 1-17.

PMID- 4937994
VI  - 45
DP  - 1971
TI  - Mutants of T2gt with altered DNA methylase activity:  relation to restriction by prophage P1.
PG  - 484-495
AB  - Glucosyl transferase (gt) mutants of T-even phages of a class called rp1 are restricted by
      prophage P1. Unrestricted mutants up1, derived from T2gt rp1, have hypermethylated DNA. From
      up1 one obtains in turn uRp1 mutants, which lack methyl groups on their DNA. Phage up1 is
      dominant to either rp1 or uRp1 phage in mixed infections. The uRp1 mutations map close to and
      on either side of the up1 mutation suggesting that both classes of mutation affect a single
      gene. Analysis of DNA methylase activity in crude extracts of Sh infected with T2 or its
      various gt derivatives reveals that the phage methylase induced by up1 phage differs in
      specificity from the methylase of wild-type phage. The uRp1 phage fail to induce any methylase
      activity.
AU  - Revel HR
AU  - Hattman SM
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1971 45: 484-495.

PMID- 4950809
VI  - 4
DP  - 1970
TI  - DNA-glucosylation in T-even phage:  Genetic determination and role in phage-host interaction.
PG  - 177-192
AB  - Host-controlled modification phenomena.  The term "host-controlled
      modification" covers a number of phenomena, first discovered in work on
      bacteriophage:  a phage may become unable to infect successfully a given host
      strain because of having previously grown in a different host.  Analysis of
      this phenomenon in its most common form, especially with Escherichia coli and
      phages lambda and fd, has revealed that these "restrictions" in host range are
      due to changes in the DNA molecules that made them susceptible to a limited
      endonucleolytic attack upon entering the "restricting" bacterial host.  The
      attack occurs at specific "sites," presumably specific nucleotide sequences, in
      the DNA molecules, and is accompanied in vivo by partial exonucleolytic
      solubilization of the DNA fragments.  The term "modification" refers to the
      fact that DNA produced in a given host strain is not restricted when it enters
      cells of that same strain.  Modification consists of a specific methylation of
      some base(s), adenine or cytosine, which renders the sites insensitive to the
      specific restriction.  Because restriction can affect sites in the bacterial
      DNA, it is not surprising that ability to restrict and ability to modify a
      given site are usually associated in a given strain.  In fact, the restriction
      and modification activities in a given E. coli strain are determined by a group
      of three adjacent genes, r,m, and s, which together constitute the hs (host
      specificity) system.  The r and m genes specify the restricting and modifying
      functions.  The s gene determines the specificity of the phenomenon, presumably
      by specifying a component common to a restricting and a modifying enzyme, which
      recognizes the target sequence in the DNA: the m enzyme methylates the target
      sequence if it is inside the cell; the r enzyme breaks it if it enters
      unmethylated from the outside.  Both hs modification and restriction require
      S-adenosyl methionine (SAM), as a methyl donor in modification  and also as a
      cofactor in restriction.  Methylation of DNA generates 6-methyl-aminopurine
      (6-MAP) from adenine residues and 5-methylcytosine (MC) from cytosine.  Mutants
      r- do not restrict; mutants s- neither restrict nor modify.  Mutations m- are
      found only together with r- mutations; it has been suggested that in an r+m-
      bacterium there would be a suicidal attack on the bacterial DNA by the r+
      function.  Besides its own hs system, which may be present or absent in a given
      strain, a bacterium may exhibit other restriction systems due to episomes or
      plasmids such as prophages or "resistance" factors.
AU  - Revel HR
AU  - Luria SE
PT  - Journal Article
TA  - Annu. Rev. Genet.
JT  - Annu. Rev. Genet.
SO  - Annu. Rev. Genet. 1970 4: 177-192.

PMID- 23105049
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of a Variant of Campylobacter jejuni NCTC 11168.
PG  - 6298-6299
AB  - Campylobacter jejuni NCTC 11168 is widely used in research, but at least two variants have
      been reported. The available genome was sequenced from a variant
      which later showed a different phenotype and gene expression profile. Here we
      present the complete genome sequence of a second variant of C. jejuni NCTC 11168.
AU  - Revez J
AU  - Schott T
AU  - Rossi M
AU  - Hanninen ML
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6298-6299.

PMID- 2841156
VI  - 235
DP  - 1988
TI  - AsnI:  a novel class II restriction endonuclease from Arthrobacter sp., strain N-CM, recognizing 5'-AT/TAAT-3'.
PG  - 241-246
AB  - A new class II restriction endonuclease, AsnI, with a novel sequence
      specificity was isolated from the Gram-positive eubacterium Arthrobacter
      species, strain N-CM.  AsnI recognizes the unambiguously defined palindromic
      hexanucleotide  5'-AT^TAAT-3' 3'-TAAT^TA-5' consisting of A- and T-residues.
      The novel enzyme in the presence of Mg2+ cleaves specifically both strands as
      indicated by the arrows.  The staggered cuts generate 5'-protruding ends with
      single-stranded 5'-TA-3' dinucleotide extensions.  The novel enzyme may be a
      useful tool for cloning experiments by complementation of the few enzymes such
      as PstI and PvuI cutting only once in the Ampr-gene of plasmids pBR322 and
      pBR328.
AU  - Rexer BU
AU  - Jarsch M
AU  - Sagmeister C
AU  - Gluck B
AU  - Berger G
AU  - Kessler C
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1988 235: 241-246.

PMID- 27151786
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of the Larvicidal Bacterium Lysinibacillus sphaericus Strain OT4b.25.
PG  - e00257-16
AB  - Lysinibacillus sphaericus OT4b.25 is a native Colombian strain isolated from coleopteran
      larvae in an oak forest near Bogota D.C.; this strain has shown high
      levels of pathogenic activity against Culex quinquefasciatus larvae in laboratory
      assays compared to that of other members of the same species. Using Pacific
      Biosciences sequencing technology, we propose a chromosomal contig of 4,665,775
      bp that, according to comparative analysis, is highly similar to that of
      reference strain L. sphaericus C3-41.
AU  - Rey A
AU  - Silva-Quintero L
AU  - Dussan J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00257-16.

PMID- 
VI  - 5
DP  - 2004
TI  - Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species.
PG  - R77
AB  - Bacillus licheniformis is a Gram-positive, spore-forming soil
      bacterium that is used in the biotechnology industry to manufacture
      enzymes, antibiotics, biochemicals and consumer products. This species is
      closely related to the well studied model organism Bacillus subtilis, and
      produces an assortment of extracellular enzymes that may contribute to
      nutrient cycling in nature.  We determined the complete nucleotide sequence
      of the B. licheniformis ATCC 14580 genome which comprises a circular
      chromosome of 4,222,336 base-pairs (bp) containing 4,208 predicted
      protein-coding genes with an average size of 873 bp, seven rRNA operons,
      and 72 tRNA genes. The B. licheniformis chromosome contains large regions
      that are colinear with the genomes of B. subtilis and Bacillus halodurans,
      and approximately 80% of the predicted B. licheniformis coding sequences
      have B. subtilis orthologs.  Despite the unmistakable organizational
      similarities between the B. licheniformis and B. subtilis genomes, there
      are notable differences in the numbers and locations of prophages,
      transposable elements and a number of extracellular enzymes and secondary
      metabolic pathway operons that distinguish these species. Differences
      include a region of more than 80 kilobases (kb) that comprises a cluster of
      polyketide synthase genes and a second operon of 38 kb encoding plipastatin
      synthase enzymes that are absent in the B. licheniformis genome. The
      availability of a completed genome sequence for B. licheniformis should
      facilitate the design and construction of improved industrial strains and
      allow for comparative genomics and evolutionary studies within this group
      of Bacillaceae.
AU  - Rey MW et al
PT  - Journal Article
TA  - Genome Biology
JT  - Genome Biology
SO  - Genome Biology 2004 5: R77.

PMID- 29567733
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Endophytic Isolates of Klebsiella variicola and Klebsiella pneumoniae Obtained from the Same Sugarcane Plant.
PG  - e00147-18
AB  - Endophytic Klebsiella variicola KvMx2 and Klebsiella pneumoniae KpMx1 isolates obtained from
      the same sugarcane stem were used for whole-genome sequencing. The
      genomes revealed clear differences in essential genes for plant growth,
      development, and detoxification, as well as nitrogen fixation, catalases,
      cellulases, and shared virulence factors described in the K. pneumoniae pathogen.
AU  - Reyna-Flores F
AU  - Barrios-Camacho H
AU  - Dantan-Gonzalez E
AU  - Ramirez-Trujillo JA
AU  - Lozano ABLF
AU  - Rodriguez-Medina N
AU  - Garza-Ramos U
AU  - Suarez-Rodriguez R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00147-18.

PMID- 18445019
VI  - 6
DP  - 2008
TI  - Electron microscopy encounters with unusual thermophiles helps direct genomic analysis of Aciduliprofundum boonei.
PG  - 331-336
AB  - Terry Beveridge's enthusiasm about the ingenuity of microorganisms has stimulated many new
      avenues of microbial research. One example where Terry's observations helped direct the
      scientific process was in the analysis of the draft genome of the thermoacidophilic archaeum,
      Aciduliprofundum boonei. This deep-sea vent heterotroph ferments peptides as its primary
      metabolic pathway, using numerous enzymes encoding for proteolytic or peptidolytic activities.
      An almost complete modified Embden-Meyerhof-Parnas pathway operates in the gluconeogenic
      direction. Terry was particularly intrigued by the S-layer and flagellum of A. boonei.
      Although only putative genes for the S-layer protein could be identified, several genes
      encoding for glycosyl transferases were located in the draft genome that could glycosylate the
      S-layer proteins and protect the proteins from the acidic environment. Furthermore, A. boonei
      possesses a unique organization to its flagellum genes and may represent a third
      organizational type within the Archaea.
AU  - Reysenbach A-L
AU  - Flores GE
PT  - Journal Article
TA  - Geobiology
JT  - Geobiology
SO  - Geobiology 2008 6: 331-336.

PMID- 29472320
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of a Novel Thermofilum sp. Strain from a New Zealand Hot Spring Enrichment Culture.
PG  - e00005-18
AB  - A draft genome of a new Thermofilum sp. strain was obtained from an enrichment culture
      metagenome. Like its relatives, Thermofilum sp. strain NZ13 is adapted to
      organic-rich thermal environments and has to depend on other organisms and the
      environment for some key amino acids, purines, and cofactors.
AU  - Reysenbach AL
AU  - Donaho JA
AU  - Hinsch TM
AU  - Kelley JF
AU  - Kouba K
AU  - Podar M
AU  - Stott MB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00005-18.

PMID- 29545298
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of a Dictyoglomus sp. from an Enrichment Culture of a New Zealand Geothermal Spring.
PG  - e00150-18
AB  - A draft genome of a novel Dictyoglomus sp., NZ13-RE01, was obtained from a New Zealand hot
      spring enrichment culture. The 1,927,012-bp genome is similar in both
      size and G+C content to other Dictyoglomus spp. Like its relatives, Dictyoglomus
      sp. NZ13-RE01 encodes many genes involved in complex carbohydrate metabolism.
AU  - Reysenbach AL
AU  - Donaho JA
AU  - Kelley JF
AU  - St. John E
AU  - Turner C
AU  - Podar M
AU  - Stott MB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00150-18.

PMID- 19136599
VI  - 191
DP  - 2009
TI  - Complete and draft genome sequences of six members of the Aquificales.
PG  - 1992-1993
AB  - The Aquificales are widespread in marine and terrestrial hydrothermal
      environments. Here, we report the complete and draft genome sequences of
      six new members of the Aquificales: two marine species, Persephonella
      marina strain EX-H1 and Hydrogenivirga strain 128-5-R1 (from the East
      Pacific Rise, 9 degrees 50.3'N, 104 degrees 17.5'W, and the Eastern Lau
      Spreading Center, 176 degrees 11.5'W, 20 degrees 45.8'S, respectively),
      and four terrestrial isolates, Sulfurihydrogenibium azorense strain
      Az-Fu1, Sulfurihydrogenibium yellowstonense strain SS-5, and
      Sulfurihydrogenibium strain Y03AOP1 (from Furnas, Azores, Portugal, and
      Calcite Springs and Obsidian Pool in Yellowstone National Park, United
      States, respectively), and the only thermoacidophilic isolate,
      Hydrogenobaculum strain Y04AAS1 (from a stream adjacent to Obsidian Pool).
      Significant differences among the different species exist that include
      nitrogen metabolism, hydrogen utilization, chemotaxis, and signal
      transduction, providing insights into their ecological niche adaptations.
AU  - Reysenbach AL
AU  - Hamamura N
AU  - Podar M
AU  - Griffiths E
AU  - Ferreira S
AU  - Hochstein R
AU  - Heidelberg J
AU  - Johnson J
AU  - Mead D
AU  - Pohorille A
AU  - Sarmiento M
AU  - Schweighofer K
AU  - Seshadri R
AU  - Voytek MA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2009 191: 1992-1993.

PMID- 25999567
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of a Papaverine-Degrading, Gram-positive Arthrobacter sp.,  Isolated from Soil Near Hohenheim, Germany.
PG  - e00422-15
AB  - We present the 4.8-Mb draft genome of a soil bacterium identified as Arthrobacter sp. This
      Gram-positive soil bacterium is able to use the aromatic compound
      papaverine as sole carbon source and will be examined for novel oxygenases.
AU  - Reznicek O
AU  - Facey SJ
AU  - Hauer B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00422-15.

PMID- 25977422
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Phenylobacterium immobile Strain E (DSM 1986), Isolated  from Uncontaminated Soil in Ecuador.
PG  - e00420-15
AB  - We report the draft genome sequence of 3.3 Mb and the sequence (19.2 kb) of a natural plasmid
      isolated from Phenylobacterium immobile strain E (DSM 1986), able
      to degrade xenobiotic compounds as the sole carbon source. The sequences reveal a
      large number of novel Rieske nonheme iron aromatic ring-hydroxylating oxygenases
      (RHOs).
AU  - Reznicek O
AU  - Luesken F
AU  - Facey SJ
AU  - Hauer B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00420-15.

PMID- 26656489
VI  - 44
DP  - 2015
TI  - Natural C-independent expression of restriction endonuclease in a C protein-associated restriction-modification system.
PG  - 2646-2660
AB  - Restriction-modification (R-M) systems are highly prevalent among bacteria and archaea, and
      appear to play crucial roles in modulating horizontal gene transfer and protection against
      phage. There is much to learn about these diverse enzymes systems, especially their
      regulation. Type II R-M systems specify two independent enzymes: a restriction endonuclease
      (REase) and protective DNA methyltransferase (MTase). Their activities need to be finely
      balanced in vivo. Some R-M systems rely on specialized transcription factors called C
      (controller) proteins. These proteins play a vital role in the temporal regulation of R-M gene
      expression, and function to indirectly modulate the horizontal transfer of their genes across
      the species. We report novel regulation of a C-responsive R-M system that involves a C protein
      of a poorly-studied structural class - C.Csp231I. Here, the C and REase genes share a
      bicistronic transcript, and some of the transcriptional auto-control features seen in other
      C-regulated R-M systems are conserved. However, separate tandem promoters drive most
      transcription of the REase gene, a distinctive property not seen in other tested C-linked R-M
      systems. Further, C protein only partially controls REase expression, yet plays a role in
      system stability and propagation. Consequently, high REase activity was observed after
      deletion of the entire C gene, and cells bearing the DeltaC R-M system were outcompeted in
      mixed culture assays by those with the WT R-M system. Overall, our data reveal unexpected
      regulatory variation among R-M systems.
AU  - Rezulak M
AU  - Borsuk I
AU  - Mruk I
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2015 44: 2646-2660.

PMID- 27811108
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Lactobacillus animalis Strain P38 and Lactobacillus reuteri Strain P43 Isolated from Chicken Cecum.
PG  - e01229-16
AB  - Here, we present the genome sequence of Lactobacillus animalis strain P38 and Lactobacillus
      reuteri strain P43, both isolated from the cecum content of a
      4-week old chicken fed a diet supplemented with the prebiotic
      beta(1-4)galacto-oligosaccharide (GOS). These indigenous Lactobacillus isolates
      are potential probiotic organisms for poultry.
AU  - Rezvani M
AU  - Mendoza M
AU  - Koci MD
AU  - Daron C
AU  - Levy J
AU  - Hassan HM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01229-16.

PMID- 27811103
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Lactobacillus crispatus C25 Isolated from Chicken Cecum.
PG  - e01223-16
AB  - Lactic acid bacteria are important members of the gut microbiota of humans and animals. Here,
      we present the genome sequence of Lactobacillus crispatus strain
      C25, originally isolated from the cecum of 4-week-old chicken fed a standard
      diet. This isolate represents a potential probiotic strain for poultry.
AU  - Rezvani M
AU  - Mendoza M
AU  - Koci MD
AU  - Daron C
AU  - Levy J
AU  - Hassan HM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01223-16.

PMID- 26514763
VI  - 3
DP  - 2015
TI  - Genome Sequence of the Deep-Sea Bacterium Idiomarina abyssalis KMM 227T.
PG  - e01256-15
AB  - Idiomarina abyssalis KMM 227(T) is an aerobic flagellar gammaproteobacterium found at a depth
      of 4,000 to 5,000 m below sea level in the Pacific Ocean. This
      paper presents a draft genome sequence for I. abyssalis KMM 227(T), with a
      predicted composition of 2,684,812 bp (47.15% G+C content) and 2,611 genes, of
      which 2,508 were predicted coding sequences.
AU  - Rheaume BA
AU  - Mithoefer S
AU  - MacLea KS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01256-15.

PMID- 11932749
VI  - 416
DP  - 2002
TI  - DNMT1 and DNMT3b cooperate to silence genes in human cancer cells.
PG  - 552-556
AB  - Inactivation of tumour suppressor genes is central to the development of all common forms of
      human cancer. This inactivation often results from epigenetic silencing associated with
      hypermethylation rather than intragenic mutations. In human cells, the mechanisms underlying
      locus-specific or global methylation patterns remain unclear. The prototypic DNA
      methyltransferase, Dnmt1, accounts for most methylation in mouse cells, but human cancer cells
      lacking DNMT1 retain significant genomic methylation and associated gene silencing. We
      disrupted the human DNMT3b gene in a colorectal cancer cell line. This deletion reduced global
      DNA methylation by less than 3%. Surprisingly, however, genetic disruption of both DNMT1 and
      DNMT3b nearly eliminated methyltransferase activity, and reduced genomic DNA methylation by
      greater than 95%. These marked changes resulted in demethylation of repeated sequences, loss
      of insulin-like growth factor II (IGF2) imprinting, abrogation of silencing of the tumour
      suppressor gene p16INK4a, and growth suppression. Here we demonstrate that two enzymes
      cooperatively maintain DNA methylation and gene silencing in human cancer cells, and provide
      compelling evidence that such methylation is essential for optimal neoplastic proliferation.
AU  - Rhee I
AU  - Bachman KE
AU  - Park BH
AU  - Jair K-W
AU  - Yen R-WC
AU  - Schuebel KE
AU  - Cui H
AU  - Feinberg AP
AU  - Lengauer C
AU  - Kinzler KW
AU  - Baylin SB
AU  - Vogelstein B
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2002 416: 552-556.

PMID- 10801130
VI  - 404
DP  - 2000
TI  - CpG methylation is maintained in human cancer cells lacking DNMT1.
PG  - 1003-1007
AB  - Hypermethylation is associated with the silencing of tumour susceptibility genes in several
      forms of cancer; however, the mechanisms responsible for this aberrant methylation are poorly
      understood. The prototypic DNA methyltransferase, DNMT1, has been widely assumed to be
      responsible for most of the methylation of the human genome, including the abnormal
      methylation found in cancers. To test this hypothesis, we disrupted the DNMT1 gene through
      homologous recombination in human colorectal carcinoma cells. Here we show that cells lacking
      DNMT1 exhibited markedly decreased cellular DNA methyltransferase activity, but there was only
      a 20% decrease in overall genomic methylation. Although juxtacentromeric satellites became
      significantly demethylated, most of the loci that we analysed, including the tumour suppressor
      gene p16INK4a, remained fully methylated and silenced. These results indicate that DNMT1 has
      an unsuspected degree of regional specificity in human cells and that methylating activities
      other than DNMT1 can maintain the methylation of most of the genome.
AU  - Rhee I
AU  - Jair KW
AU  - Yen RW
AU  - Lengauer C
AU  - Herman JG
AU  - Kinzler KW
AU  - Vogelstein B
AU  - Baylin SB
AU  - Schuebel KE
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2000 404: 1003-1007.

PMID- 9232030
VI  - 55
DP  - 1997
TI  - Influence of the medium composition and plasmid combination on the growth of recombinant Escherichia coli JM109 and on the production of the fusion protein EcoRI::SPA.
PG  - 69-83
AB  - Plasmid-free and plasmid-harboring E. coli JM109 strains were investigated in shaken flasks,
      stirred tanks in batch and continuous operation.  The shaken flask cultivations were performed
      in M9 minimal medium and in media with various protein supplements.  The host hardly grows on
      M9 minimal medium as opposed to the plasmid-harboring cells, which grow well on this medium.
      All of the investigated cells propagate well on protein-containing media.  The influence of
      the combinations of repressor plasmid pRK248cI, the protection plasmid EcoR4 and the
      production plasmid pMTC48 were determined on the initial specific growth rate of the E. coli
      JM109 without gene expression, on the yield coefficient of cell growth, acetate concentration
      and acetate yield coefficient in the yeast extract-containing (HM) medium.  The influence of
      various media on the induction of the gene expression were evaluated.  In cultivation media
      with protein supplement, the growth rate and yield coefficient increased.  The variation of
      the volumetric and specific beta-lactamase activities with the cultivation time were
      determined in a stirred tank reactor in HM medium.  With increasing dilution rate the process
      performance decreased.  Simple relationships exist between the substrate uptake rate and the
      specific growth rate of the continuous cultivated cells in M9 and HM media.  The influence of
      the dilution rate on the cell mass concentration, colony forming units, acetate formation,
      yield coefficients of growth and acetate formation, substrate uptake rate, CO2 production
      rate, ammonium formation rate and beta-lactamase activity in M9 and HM media were determined
      as well.  Carbon balances of the batch and continuous cultivations indicated high carbon
      recoveries.  On account of the higher growth rate of plasmid-harboring cells than that of the
      plasmid-free cells, the behavior of the investigated plasmid-free and plasmid-harboring E.
      coli JM109 cells deviates from the published properties of other plasmid-free and
      plasmid-harboring E. coli cells.
AU  - Rhee JI
AU  - Bode J
AU  - Diaz-Ricci JC
AU  - Poock D
AU  - Weigel B
AU  - Kretzmer G
AU  - Schugerl K
PT  - Journal Article
TA  - J. Biotechnol.
JT  - J. Biotechnol.
SO  - J. Biotechnol. 1997 55: 69-83.

PMID- 
VI  - 19
DP  - 1998
TI  - Mathematical simulation of the growth of a three plasmid harboring Escherichia coli JM109 strain and the production of the fusion protein EcoRI::SPA with a four-compartment model.
PG  - 261-267
AB  - In the previous papers the process variables of plasmid-free, one-, two- and three-plasmid
      harboring E. coli JM109 cells were investigated in batch and continuous cultivation as a
      function of the medium composition, plasmid content, dilution rate and cultivation
      (generation) time.  In the present paper the growth of the recombinant E. coli JM109 [pEcoR4,
      pRK248cI, pMTC48] and the production of the fusion protein EcoRI::SPA are simulated by using a
      four-compartment model, consisting of the active cell components (ribosomes, mRNA, tRNA, and
      others) (A), the structure forming materials and chromosomal DNA (Z), the plasmid-DNA (G) and
      the recombinant enzyme protein (E).  At the first time, all of the three plasmids: the
      production plasmid (Gp), the repressor plasmid (Gr) and the protection plasmid (Gs) are taken
      into account in the plasmid DNA-compartment of the model.  The calculated and measured courses
      of the cell mass, the concentrations of glucose and acetate, and the products as well as the
      particular plasmids agree well.
AU  - Rhee JI
AU  - Schuegerl K
PT  - Journal Article
TA  - Bioprocess Eng.
JT  - Bioprocess Eng.
SO  - Bioprocess Eng. 1998 19: 261-267.

PMID- 22675583
VI  - 5
DP  - 2011
TI  - Complete genome sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1.
PG  - 331-340
AB  - Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 oC and pH 5.0 and
      fer-ments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of
      this spo-rogenic lactic acid bacterium to grow at 50-55 oC and pH 5.0 makes this organism an
      attrac-tive microbial biocatalyst for production of optically pure lactic acid at industrial
      scale not only from glucose derived from cellulose but also from xylose, a major constituent
      of hemi-cellulose. This bacterium is also considered as a potential probiotic. Complete genome
      se-quence of a representative strain, B. coagulans strain 36D1, is presented and discussed.
AU  - Rhee MS
AU  - Moritz BE
AU  - Xie G
AU  - Glavina-del-Rio T
AU  - Dalin E
AU  - Tice H
AU  - Bruce D
AU  - Goodwin L
AU  - Chertkov O
AU  - Brettin T
AU  - Han C
AU  - Detter C
AU  - Pitluck S
AU  - Land ML
AU  - Patel M
AU  - Ou M
AU  - Harbrucker R
AU  - Ingram LO
AU  - Shanmugam KT
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 5: 331-340.

PMID- 
VI  - 0
DP  - 2002
TI  - Determination of cleavage sites of restriction endonuclease FmuI to plasmid pUB110 DNA.
PG  - 50-53
AB  - We cleave the plasmid pUB110 DNA with FmuI and some restriction endonucleases and map the
      restriction sites according to the cleavage fragments.  The restriction endonuclease, FmuI
      acts on 6 cleavage sites in the plasmid pUB110 DNA.
AU  - Ri S
AU  - Ra SR
PT  - Journal Article
TA  - Choson Minjujuui Inmin Konghwaguk Kwahagwon Tongbo
JT  - Choson Minjujuui Inmin Konghwaguk Kwahagwon Tongbo
SO  - Choson Minjujuui Inmin Konghwaguk Kwahagwon Tongbo 2002 0: 50-53.

PMID- Not carried by PubMed...
VI  - 19
DP  - 1987
TI  - Molecular mechanism of host controlled restriction and modification in Haemophilus influenzae 1.  Isolation of a restriction positive mutant.
PG  - 393-405
AB  - Wild type Haemophilus influenzae strain Rd has been mutagenized by acridine
      orange treatment to produce a mutant MB69 which has cell division time,
      transforming ability and radiosensitivity similar to that of the parent, but
      does not allow normal growth of Haemophilus phage.  The mutant is sensitive to
      adsorption of phage HP1c1 at similar levels as the parent strain.  However,
      after entry into the host, phage HP1c1 DNA is specifically degraded into
      discrete fragments of molecular sizes about one fifth of the parent phage DNA
      estimated at 4.5 x 10/6 daltons.  Evidence is presented to support the
      suggestion that the isolated mutant is restriction positive.
AU  - Riazuddin S
AU  - Athar A
AU  - Sohail A
AU  - Ahmed Z
PT  - Journal Article
TA  - Pak. J. Zool.
JT  - Pak. J. Zool.
SO  - Pak. J. Zool. 1987 19: 393-405.

PMID- Not carried by PubMed...
VI  - 30
DP  - 1987
TI  - Presence of new TypeII specificity restriction enzymes in local bacteria.
PG  - 819-824
AB  - Eight bacterial strains isolated from local environments have been screened for
      the presence of new Type II restriction enzymes by analyzing lambda DNA
      fragments resulting from protein DNA interactions.  Partially purified protein
      extracts of two of these strains, namely Pseudomonas aeruginosa A and
      Citrobacter freundii A4 contain endonuclease activities which have been highly
      purified by a combination of gel filtration, ion exchange and affinity
      chromatography.  The identity of the new enzymes, designated as PaeAI and
      CfrA4I, have been confirmed by analyses of incised lambda, PhiX174RFI, pBR322,
      adeno-2 and M13 mp 19 RFI DNA substrates as truly Type II restriction enzymes.
      The isolated enzymes, by analogy with known enzymes, seem to recognize CCGCGG
      and CTGCAG base sequences respectively.
AU  - Riazuddin S
AU  - Sohail A
AU  - Maqbool T
AU  - Khan E
AU  - Mushtaq R
PT  - Journal Article
TA  - Pak. J. Sci. Ind. Res.
JT  - Pak. J. Sci. Ind. Res.
SO  - Pak. J. Sci. Ind. Res. 1987 30: 819-824.

PMID- 22829535
VI  - 22
DP  - 2012
TI  - Finished bacterial genomes from shotgun sequence data.
PG  - 2270-2277
AB  - Exceptionally accurate genome reference sequences have proven to be of great
      value to microbial researchers. Thus, to date, about 1800 bacterial genome
      assemblies have been "finished" at great expense with the aid of manual
      laboratory and computational processes that typically iterate over a period of
      months or even years. By applying a new laboratory design and new assembly
      algorithm to 16 samples, we demonstrate that assemblies exceeding finished
      quality can be obtained from whole-genome shotgun data and automated computation.
      Cost and time requirements are thus dramatically reduced.
AU  - Ribeiro FJ
AU  - Przybylski D
AU  - Yin S
AU  - Sharpe T
AU  - Gnerre S
AU  - Abouelleil A
AU  - Berlin AM
AU  - Montmayeur A
AU  - Shea TP
AU  - Walker BJ
AU  - Young SK
AU  - Russ C
AU  - Nusbaum C
AU  - Maccallum I
AU  - Jaffe DB
PT  - Journal Article
TA  - Genome Res.
JT  - Genome Res.
SO  - Genome Res. 2012 22: 2270-2277.

PMID- 26383667
VI  - 3
DP  - 2015
TI  - Genome Sequence of Rhizobium ecuadorense Strain CNPSo 671T, an Indigenous N2-Fixing Symbiont of the Ecuadorian Common Bean (Phaseolus vulgaris L.) Genetic  Pool.
PG  - e01058-15
AB  - Rhizobium ecuadorense CNPSo 671(T) was isolated from a common bean nodule in Ecuador. The
      draft genome brings novelty about indigenous rhizobial species in centers of genetic diversity
      of the legume.
AU  - Ribeiro RA
AU  - Delamuta JR
AU  - Gomes DF
AU  - Souza RC
AU  - Chueire LM
AU  - Hungria M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01058-15.

PMID- 28883142
VI  - 5
DP  - 2017
TI  - Genome Sequence of Bradyrhizobium mercantei Strain SEMIA 6399T, Isolated from Nodules of Deguelia costata in Brazil.
PG  - e00943-17
AB  - SEMIA 6399T is the type strain of Bradyrhizobium mercantei, a nitrogen-fixing symbiont of
      Deguelia costata Its draft genome contains 8,842,857 bp with 8,246
      predicted coding sequences (CDS), several related to amino acids and derivatives
      and to stress tolerance, with an emphasis on oxidative stress, in addition to
      symbiotic genes.
AU  - Ribeiro RA
AU  - Helene LCF
AU  - Delamuta JRM
AU  - Hungria M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00943-17.

PMID- 27979939
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Blautia faecis Strain Marseille-P328, Isolated from the  Human Ascending Colon.
PG  - e01383-16
AB  - Blautia faecis strain Marseille P328 was isolated from the ascending colon of a French
      patient. We sequenced the 4.45-Mb genome of the strain and compared it
      with that of other species of the Blautia genus.
AU  - Ricaboni D
AU  - Mailhe M
AU  - Labas N
AU  - Vitton V
AU  - Raoult D
AU  - Million M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01383-16.

PMID- 10460177
VI  - 38
DP  - 1999
TI  - Thermodynamic, spectroscopic, and equilibrium binding studies of DNA sequence context effects in six 22-base pair deoxyoligonucleotides.
PG  - 11197-11208
AB  - Effects of different end sequences on stability, circular dichroism spectra (CD), and enzyme
      binding properties were investigated for six 22-base pair, non-self-complementary duplex DNA
      oligomers. The center sequences of these deoxyoligonucleotides have 8-14 base pairs in common
      and are flanked on both sides by sequences differing in context and A-T content.
      Temperature-induced melting transitions monitored by differential scanning calorimetry (DSC)
      and ultraviolet absorbance were measured for the six duplexes in buffered 115 mM Na(+)
      solutions. Values of the melting transition enthalpy, DeltaH(cal), and entropy, DeltaS(cal),
      were obtained directly from DSC experiments. Melting transition parameters, DeltaH(vH) and
      DeltaS(vH), were also estimated from van't Hoff analysis of optical melting curves collected
      as a function of DNA concentration, assuming a two-state melting transition. Melting free
      energies (20 degrees C) of the six DNAs evaluated from DSC experiments ranged from -18.7 to
      -32.7 kcal/mol. van't Hoff estimates of the free energies ranged from -18.5 to -48.0
      kcal/mol. With either method, the trends in free energy as a function of sequence were
      identical. Equilibrium binding by BamHI restriction endonuclease to the 22-base pair DNAs was
      also investigated. The central eight base pairs of all six molecules, 5'-A-GGATCC-A-3',
      contained a BamHI recognition sequence bounded by A-T base pairs. Magnesium free binding
      assays were performed by titering BamHI against a constant concentration of each of the
      deoxyoligonucleotide substrates and analyzing reaction products by gel retardation. Binding
      isotherms of the total amount of bound DNA versus protein concentration were constructed which
      provided semiquantitative estimates of the equilibrium dissociation constants for dissociation
      of BamHI from the six DNA oligomers. Dissociation constants ranged from 0.5 x 10(-)(9) to 12.0
      x 10(-)(9) M with corresponding binding free energies of -12.5 to -10.6 (+/-0. 1) kcal/mol. An
      inverse relationship is found when binding and stability are compared.
AU  - Riccelli PV
AU  - Vallone PM
AU  - Kashin I
AU  - Faldasz BD
AU  - Lane MJ
AU  - Benight AS
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1999 38: 11197-11208.

PMID- Not carried by PubMed...
VI  - 72
DP  - 1997
TI  - Investigations of DNA context effects: influences of flanking sequence stability on site specific binding of BamHI restriction enzyme to duplex DNA oligomers.
PG  - A95
AB  - Binding of BamHI restriction enzyme was investigated for short DNA duplex oligomer substrates
      containing the cognate site 5'-GGATCC-3' flanked on both sides by sequences of different A-T
      or G-C composition.  Binding reactions were conducted in buffer containing 10 mM CaCl2 and
      analyzed by gel-shift assays.  While cleavage activity of the enzyme was eliminated under
      these conditions, site specific binding was retained.  For each DNA substrate, binding
      isotherms were constructed and equilibrium binding constants evaluated.  Binding constants
      greater than 10^9 M-1 were observed and found to vary at least 10-fold as a function of
      flanking sequence.  Significantly higher binding of BamHI was observed for duplex substrates
      containing A-T flanking sequences.  Optical melting curves of the DNAs were also measured in
      the binding buffer.  From these results, the thermodynamic stabilities of the DNA substrates
      were evaluated.  Comparisons of the results of the binding assays with those of the melting
      analysis revealed an inverse correlation between flanking sequence stability and binding
      affinity of BamHI suggesting stability of flanking DNA context may comprise a significant
      component of DNA recognition by site-specific binding agents.
AU  - Riccelli PV
AU  - Vallone PM
AU  - Lane MJ
AU  - Benight AS
PT  - Journal Article
TA  - J. Biophys.
JT  - J. Biophys.
SO  - J. Biophys. 1997 72: A95.

PMID- 23405320
VI  - 1
DP  - 2013
TI  - Genome Sequences of Two Lactococcus garvieae Strains Isolated from Meat.
PG  - e00018-12
AB  - Lactococcus garvieae is an important fish pathogen and an emerging opportunistic  human
      pathogen, as well as a component of natural microbiota in dairy and meat products. We present
      the first report of genome sequences of L. garvieae I113 and Tac2 strains isolated from a meat
      source.
AU  - Ricci G
AU  - Ferrario C
AU  - Borgo F
AU  - Eraclio G
AU  - Fortina MG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00018-12.

PMID- 22328751
VI  - 194
DP  - 2012
TI  - Genome Sequences of Lactococcus garvieae TB25, Isolated from Italian Cheese, and  Lactococcus garvieae LG9, Isolated from Italian Rainbow Trout.
PG  - 1249-1250
AB  - Lactococcus garvieae is a fish pathogen and an emerging zoonotic opportunistic pathogen as
      well as a component of natural microbiota in dairy products. Here, we
      present the first report of a genome sequence of L. garvieae TB25, isolated from
      a dairy source, and that of L. garvieae LG9, isolated from rainbow trout.
AU  - Ricci G
AU  - Ferrario C
AU  - Borgo F
AU  - Rollando A
AU  - Fortina MG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1249-1250.

PMID- 27587821
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Clostridium difficile Belonging to Ribotype 018 and Sequence Type 17.
PG  - e00907-16
AB  - Clostridium difficile, belonging to ribotype 018 (RT018), is one of the most prevalent
      genotypes circulating in hospital settings in Italy. Here, we report
      the draft genome of C. difficile CD8-15 belonging to RT018, isolated from a
      patient with fatal C. difficile-associated infection.
AU  - Riccobono E
AU  - Di Pilato V
AU  - Della MN
AU  - Meini S
AU  - Ciraolo F
AU  - Torricelli F
AU  - Rossolini GM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00907-16.

PMID- 27471578
VI  - 11
DP  - 2016
TI  - Complete genome of Nitrosospira briensis C-128, an ammonia-oxidizing bacterium from agricultural soil.
PG  - 46
AB  - Nitrosospira briensis C-128 is an ammonia-oxidizing bacterium isolated from an acid
      agricultural soil. N. briensis C-128 was sequenced with PacBio RS
      technologies at the DOE-Joint Genome Institute through their Community Science
      Program (2010). The high-quality finished genome contains one chromosome of 3.21
      Mb and no plasmids. We identified 3073 gene models, 3018 of which are protein
      coding. The two-way average nucleotide identity between the chromosomes of
      Nitrosospira multiformis ATCC 25196 and Nitrosospira briensis C-128 was found to
      be 77.2 %. Multiple copies of modules encoding chemolithotrophic metabolism were
      identified in their genomic context. The gene inventory supports
      chemolithotrophic metabolism with implications for function in soil environments.
AU  - Rice MC et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 46.

PMID- 28302769
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Nitrosomonas cryotolerans ATCC 49181, a Phylogenetically Distinct Ammonia-Oxidizing Bacterium Isolated from Arctic  Waters.
PG  - e00011-17
AB  - Nitrosomonas cryotolerans ATCC 49181 is a cold-tolerant marine ammonia-oxidizing  bacterium
      isolated from seawater collected in the Gulf of Alaska. The
      high-quality complete genome contains a 2.87-Mbp chromosome and a 56.6-kbp
      plasmid. Chemolithoautotrophic modules encoding ammonia oxidation and CO2
      fixation were identified.
AU  - Rice MC et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00011-17.

PMID- 10931930
VI  - 28
DP  - 2000
TI  - Recognition of native DNA methylation by the PvuII restriction endonuclease.
PG  - 3143-3150
AB  - Recognizing the methylation status of specific DNA sequences is central to the function of
      many systems in eukaryotes and prokaryotes. Restriction-modification systems have to
      distinguish between 'self' and 'non-self' DNA and depend on the inability of restriction
      endonucleases to cleave their DNA substrates when the DNA is appropriately methylated. These
      endonucleases thus provide a model system for studying the recognition of DNA methylation by
      proteins. We have characterized the interaction of R.PvuII with DNA containing the
      physiologically relevant N4-methylcytosine modification. R.PvuII binds (N4m)C-modified DNA
      and cleaves it very slowly. Methylated strands in hemimethylated duplexes were cleaved at a
      higher rate than in fully methylated duplexes, in parallel with a higher binding affinity for
      hemimethylated DNA. The co-crystal structures of R.PvuII-DNA, together with a mutagenesis
      study, have implicated specific amino acids in recognition of the methylatable base; one of
      these is His84. We report that replacing His84 with Ala reduced the rate of cleavage of
      unmodified DNA but, in contrast, slightly increased the cleavage of (N4m)C-modified DNA.
AU  - Rice MR
AU  - Blumenthal RM
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2000 28: 3143-3150.

PMID- 7720955
VI  - 9
DP  - 1995
TI  - The PvuII (CAGCTG) endonuclease binds to and cleaves CAG5mCTG sites.
PG  - A1400
AB  - The PvuII restriction modification system recognizes the sequence CAGCTG. Cleavage by the
      restriction endonuclease (R.PvuII) occurs between the central bases, leaving blunt ends. The
      PvuII methylase modifies the internal cytosine residue at the N4 position, but the sequence
      CAG5mCTG has also been reported to be protected from cleavage by R.PvuII. Our evidence
      suggests that cleavage of this sequence does in fact occur. This conclusion is based on the
      following criteria. First, a cell expressing M.AluI, which generates AG5mCT, cannot be stably
      transformed with R.PvuII, indicating that the protection provided by M.AluI is incomplete.
      Second, a synthetic oligonucleotide with 5-methylcytosine substituted from the internal
      cytosine is bound by R.PvuII in gel mobility shift assays. Third, the same methylated
      oligonucleotide is slowly cleaved by R.PvuII (but not at all by R.AluI). These results are
      consistent with the recently-determined structure of R.PvuII-DNA cocrystals.
AU  - Rice MR
AU  - Calvin-Koons MD
AU  - Blumenthal RM
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1995 9: A1400.

PMID- 9927736
VI  - 27
DP  - 1999
TI  - Substrate recognition by the PvuII endonuclease: binding and cleavage of CAG5mCTG sites.
PG  - 1032-1038
AB  - The PvuII restriction endonuclease (R.PvuII) cleaves CAG/CTG sequences as indicated, leaving
      blunt ends.  Its cognate methyltransferase generates N4-methylcytosine, yielding CAGN4mCTG,
      though the mechanism by which this prevents cleavage by R.PvuII is unknown.  The heterologous
      5-methylcytosine methylation CAG5mCTG has also been reported to prevent cleavage by R.PvuII
      and this has been used in some cloning methods.  Since this heterologous methylation occurs at
      the native methylated base, it can provide insights into the detection of DNA methylation by
      R.PvuII.  We found that the cloned gene for R.PvuII could not stably transform cells protected
      only by M.AluI (AG5mCT) and then determined that R.PvuII cleaves CAG5mCTG in vitro, even when
      both strands are methylated.  DNase I footprint analysis and competition experiments reveal
      that R.PvuII binds to CAG5mCTG specifically, though with reduced affinity relative to the
      unmethylated sequence.  These results provide biochemical support for the published structures
      of R.PvuII complexed with DNA containing CAGCTG and CAG5-iodoCTG and support a model for how
      methylation interferes with DNA cleavage by this enzyme.
AU  - Rice MR
AU  - Koons MD
AU  - Blumenthal RM
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1999 27: 1032-1038.

PMID- 28232425
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of Six Copper-Resistant Xanthomonas Strains Causing Bacterial Spot of Solaneous Plants, Belonging to X. gardneri, X. euvesicatoria,  and X. vesicatoria, Using Long-Read Technology.
PG  - e01693-16
AB  - Xanthomonas vesicatoria, Xanthomonas euvesicatoria, and Xanthomonas gardneri cause bacterial
      spot disease. Copper has been applied since the 1920s as part of
      integrated management programs. The first copper-resistant strains were reported
      some decades later. Here, we fully sequenced six Xanthomonas strains pathogenic
      to tomato and/or pepper and having a copper-resistant phenotype.
AU  - Richard D
AU  - Boyer C
AU  - Lefeuvre P
AU  - Canteros BI
AU  - Beni-Madhu S
AU  - Portier P
AU  - Pruvost O
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01693-16.

PMID- 27979933
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of a Copper-Resistant Bacterium from the Citrus Phyllosphere, Stenotrophomonas sp. Strain LM091, Obtained Using Long-Read  Technology.
PG  - e01327-16
AB  - The Stenotrophomonas genus shows great adaptive potential including resistance to multiple
      antimicrobials, opportunistic pathogenicity, and production of numerous
      secondary metabolites. Using long-read technology, we report the sequence of a
      plant-associated Stenotrophomonas strain originating from the citrus phyllosphere
      that displays a copper resistance phenotype.
AU  - Richard D
AU  - Boyer C
AU  - Lefeuvre P
AU  - Pruvost O
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01327-16.

PMID- 28336584
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of Six Copper-Resistant Xanthomonas citri pv. citri Strains Causing Asiatic Citrus Canker, Obtained Using Long-Read Technology.
PG  - e00010-17
AB  - The gammaproteobacterium Xanthomonas citri pv. citri causes Asiatic citrus canker. Pathotype A
      strains have a broad host range, which includes most
      commercial citrus species, and they cause important economic losses worldwide.
      Control often relies on frequent copper sprays. We present here the complete
      genomes of six X. citri pv. citri copper-resistant strains.
AU  - Richard D
AU  - Boyer C
AU  - Verniere C
AU  - Canteros BI
AU  - Lefeuvre P
AU  - Pruvost O
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00010-17.

PMID- 3269388
VI  - 134
DP  - 1988
TI  - Restriction endonucleases in Clostridium pasteurianum ATCC 6013 and Clostridium thermohydrosulfuricum DSM568.
PG  - 3151-3157
AB  - A small collection of Clostridia were surveyed for type II restriction endonucleases. Enzymes
      were detected in two organisms. Clostridium pasteurianum ATCC 6013 contains an isoschizomer of
      ThaI (FnuDII) [5'-CGCG-3'] and preliminary evidence suggests that cleavage generates
      blunt-ended fragments. Clostridium thermohydrosulfuricum DSM568 contains an isoschizomer of
      MboI (Sau3A) [5'-GATC-3'], that is inactive on dam methylated substrates. The DNA of this
      latter organism shows dam methylation.
AU  - Richards DF
AU  - Linnett PE
AU  - Oultram JD
AU  - Young M
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1988 134: 3151-3157.

PMID- 25523764
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence for the Shellfish Pathogen Vibrio coralliilyticus RE98 Isolated from a Shellfish Hatchery.
PG  - e01253-14
AB  - Vibrio coralliilyticus is a pathogen of corals and larval shellfish. Publications on strain
      RE98 list it as a Vibrio tubiashii; however, whole genome sequencing
      confirms RE98 as V. coralliilyticus containing a total of 6,037,824 bp consisting
      of two chromosomes (3,420,228 and 1,917,482 bp) and two megaplasmids (380,714 and
      319,400 bp).
AU  - Richards GP
AU  - Bono JL
AU  - Watson MA
AU  - Needleman DS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01253-14.

PMID- 28818891
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Pseudoalteromonas piscicida Strain DE2-B, a Bacterium with Broad Inhibitory Activity toward Human and Fish Pathogens.
PG  - e00752-17
AB  - Pseudoalteromonas piscicida strain DE2-B is a halophilic bacterium which has broad inhibitory
      activity toward vibrios and other human and fish pathogens. We
      report the first closed genome sequence for this species, which consists of two
      chromosomes (4,128,210 and 1,188,838 bp). Annotation revealed multiple genes
      encoding proteases with potential antibacterial properties.
AU  - Richards GP
AU  - Needleman DS
AU  - Watson MA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00752-17.

PMID- 25523763
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of the Larval Shellfish Pathogen Vibrio tubiashii Type Strain ATCC 19109.
PG  - e01252-14
AB  - Vibrio tubiashii is a larval shellfish pathogen. Here, we report the first closed genome
      sequence for this species (ATCC type strain 19109), which consists of two
      chromosomes (3,294,490 and 1,766,582 bp), two megaplasmids (251,408 and 122,808
      bp), and two plasmids (57,076 and 47,973 bp).
AU  - Richards GP
AU  - Needleman DS
AU  - Watson MA
AU  - Bono JL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01252-14.

PMID- 21536150
VI  - 11
DP  - 2011
TI  - Comparative genomics and the role of lateral gene transfer in the evolution of bovine adapted Streptococcus agalactiae.
PG  - 1263-1275
AB  - In addition to causing severe invasive infections in humans, Streptococcus
      agalactiae, or group B Streptococcus (GBS), is also a major cause of bovine
      mastitis. Here we provide the first genome sequence for S. agalactiae isolated
      from a cow diagnosed with clinical mastitis (strain FSL S3-026). Comparison to
      eight S. agalactiae genomes obtained from human disease isolates revealed 183
      genes specific to the bovine strain. Subsequent polymerase chain reaction (PCR)
      screening for the presence/absence of a subset of these loci in additional bovine
      and human strains revealed strong differentiation between the two groups (Fisher
      exact test: p<0.0001). The majority of the bovine strain-specific genes (
      approximately 85%) clustered tightly into eight genomic islands, suggesting these
      genes were acquired through lateral gene transfer (LGT). This bovine GBS also
      contained an unusually high proportion of insertion sequences (4.3% of the total
      genome), suggesting frequent genomic rearrangement. Comparison to other
      mastitis-causing species of bacteria provided strong evidence for two cases of
      interspecies LGT within the shared bovine environment: bovine S. agalactiae with
      Streptococcus uberis (nisin U operon) and Streptococcus dysgalactiae subsp.
      dysgalactiae (lactose operon). We also found evidence for LGT, involving the
      salivaricin operon, between the bovine S. agalactiae strain and either
      Streptococcus pyogenes or Streptococcus salivarius. Our findings provide insight
      into mechanisms facilitating environmental adaptation and acquisition of
      potential virulence factors, while highlighting both the key role LGT has played
      in the recent evolution of the bovine S. agalactiae strain, and the importance of
      LGT among pathogens within a shared environment.
AU  - Richards VP
AU  - Lang P
AU  - Pavinski-Bitar PD
AU  - Lefebure T
AU  - Schukken YH
AU  - Zadoks RN
AU  - Stanhope MJ
PT  - Journal Article
TA  - Infect. Genet. Evol.
JT  - Infect. Genet. Evol.
SO  - Infect. Genet. Evol. 2011 11: 1263-1275.

PMID- 10521079
VI  - 134
DP  - 1999
TI  - Role of DNA methylation in the regulation of cell function.
PG  - 333-340
AB  - The methylation of DNA helps stabilize chromatin in an inactive configuration and inhibits
      gene transcription. This mechanism of gene regulation is involved in essential genetic events
      including differentiation, genomic imprinting, and X chromosome inactivation. The alteration
      of methylation patterns can result in abnormal gene expression, with significant pathologic
      effects including carcinogenesis, autoimmunity, and some of the changes in gene expression
      associated with aging. The mechanisms establishing, maintaining, and modifying methylation
      patterns in normal and pathologic states are only now becoming understood, as are the
      mechanisms relating DNA methylation to gene expression and chromosome inactivation. Further
      characterization of these mechanisms holds promise for delaying or preventing the changes in
      methylation patterns that contribute to cancer, autoimmunity, and aging.
AU  - Richardson B
AU  - Yung R
PT  - Journal Article
TA  - J. Lab. Clin. Med.
JT  - J. Lab. Clin. Med.
SO  - J. Lab. Clin. Med. 1999 134: 333-340.

PMID- 10443442
VI  - 113
DP  - 1999
TI  - Chromosomal double strand breaks induced in mammalian cells by expression of I-SceI endonuclease.
PG  - 453-463
AB  - Until recently, investigators interested in analyzing the repair of chromosomal double-strand
      breaks in mammalian cells have been limited by the inability to introduce defined DSBs within
      the genome.  Traditional methods of introducing breaks have included irradiation or the
      introduction of restriction enzymes; however, both of these methods cause multiple lesions at
      different chromosomal loci.  Many of these types of studies have relied on cytogenetics for
      the detection of gross genomic changes owing to misrepair at these damaged sites.
AU  - Richardson C
AU  - Elliott B
AU  - Jasin M
PT  - Journal Article
TA  - Methods Mol. Biol.
JT  - Methods Mol. Biol.
SO  - Methods Mol. Biol. 1999 113: 453-463.

PMID- 21478351
VI  - 193
DP  - 2011
TI  - Genome sequences of Salmonella enterica serovar Typhimurium, Choleraesuis, Dublin and Gallinarum strains of highly defined virulence in  food-producing animals.
PG  - 3162-3163
AB  - Salmonella enterica is an animal and zoonotic pathogen of worldwide importance and may be
      classified into serovars differing in virulence and
      host range. We sequenced and annotated the genomes of serovar Typhimurium,
      Choleraesuis, Dublin and Gallinarum strains of defined virulence in each
      of three food-producing animal hosts. This provides valuable measures of
      intra-serovar diversity and opportunities to formally link genotypes to
      phenotypes in target animals.
AU  - Richardson EJ
AU  - Limaye B
AU  - Inamdar H
AU  - Datta A
AU  - Manjari KS
AU  - Pullinger GD
AU  - Thomson NR
AU  - Joshi RR
AU  - Watson M
AU  - Stevens MP
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3162-3163.

PMID- 1645973
VI  - 4
DP  - 1991
TI  - Alterations in DNA-restriction enzyme interactions by O4-alkyldeoxythymidines.
PG  - 162-168
AB  - O4-Alkyldeoxythymidines have been extensively studied for their ability to cause mutations and
      to induce cancer.  Since these adducts can change DNA conformation, they may also have a more
      immediate effect of altering DNA-protein interactions.  To address this issue, the effects of
      these adducts on restriction enzyme activity were examined.  Oligodeoxyribonucleosides
      containing O4-ethyldeoxythymidine (O4-EtdT) or O4-methyldeoxythymidine (O4-MedT) at a unique
      site within the sequence 5'-GAATGGATCCTAATGAGATC-3' were constructed by automated DNA
      synthesis.  This sequence contains the recognition site for various restriction enzymes.
      These oligomers were annealed to various complementary strands and digested with restriction
      enzymes:  BamHI or BstI (GGATCC); Sau3A, NdeII, or MboI (GATC); DpnI (GmATC); and BstYI, MflI,
      or XhoII (PuGATCPy).  Analysis of the digests demonstrated that the presence of either O4-EtdT
      or O4-MedT abolished the ability of XhoII, MboI, MflI, or NdeII to cut at the restriction
      site.  DpnI failed to cut any of the oligomers.  BamHI, Sau3A, BstI, and BstYI exhibited
      alterations in cutting specificity depending upon the oligomers used.  These results
      demonstrated that O4-alkyldeoxythymidine adducts alter DNA-restriction enzyme interactions in
      a protein- and sequence-dependent manner.  Because of the importance of natural methylation in
      genetic regulation it is possible that aberrant methylation in the form of DNA adducts could
      also alter protein-DNA interactions in cells exposed to DNA-modifying agents.
AU  - Richardson FC
AU  - Richardson KK
PT  - Journal Article
TA  - Mol. Carcinog.
JT  - Mol. Carcinog.
SO  - Mol. Carcinog. 1991 4: 162-168.

PMID- 1579470
VI  - 20
DP  - 1992
TI  - Synthesis and restriction enzyme analysis of oligodeoxyribonucleotides containing the anti-cancer drug 2', 2'-difluoro-2'-deoxycytidine.
PG  - 1763-1768
AB  - The anti-cancer drug 2',2'-difluoro-2'-deoxycytidine (dFdC) is internally incorporated into
      DNA in vitro. To determine the effects of this incorporation on DNA structure and function,
      the beta-cyanoethyl phosphoramidite of dFdC was synthesized and oligodeoxyribonucleotides
      containing dFdC were made using automated solid phase DNA synthesis techniques. Extension of
      the coupling time was required to achieve high coupling efficiency, suggesting a significant
      reduction in the rate of phosphotriester formation. Insertion of dFdC 5' into the recognition
      sequence of restriction enzymes HpaII and KpnI reduced the rate of cutting by 4% and 14% over
      60 minutes. This reduction is similar to the effects seen with arabinofuranosylcytidine
      (ara-C) but small compared to the reductions caused by base analogues and phosphothioates.
      Insertion of dFdC into the BamHI recognition sequence, but not 5' to the cut site, did not
      alter the rate of cutting/recognition. The presence of a single dFdC reduced the Tm's of
      oligomers by 2-4C, depending on sequence and location. These results demonstrate that, once
      incorporated into DNA, dFdC does not greatly alter recognition between DNA and restriction
      enzymes; however, it does significantly alter duplex stability.
AU  - Richardson FC
AU  - Richardson KK
AU  - Kroin JS
AU  - Hertel LW
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 1763-1768.

PMID- 17449609
VI  - 189
DP  - 2007
TI  - Comparative genome analysis of four magnetotactic bacteria reveals a complex set of group-specific genes implicated in magnetosome biomineralization and function.
PG  - 4899-4910
AB  - Magnetotactic bacteria (MTB) are a heterogeneous group of aquatic
      prokaryotes with a unique intracellular organelle, the magnetosome, which
      orients the cell along magnetic field lines. Magnetotaxis is a complex
      phenotype, which depends on the coordinate synthesis of magnetosomes and
      the ability to swim and orient along the direction caused by the
      interaction with the Earth's magnetic field. Although a number of putative
      magnetotaxis genes were recently identified within a conserved genomic
      magnetosome island (MAI) of several MTB, their functions have remained
      mostly unknown, and it was speculated that additional genes located
      outside the MAI might be involved in magnetosome formation and
      magnetotaxis. In order to identify genes specifically associated with the
      magnetotactic phenotype, we conducted comparisons between four sequenced
      magnetotactic Alphaproteobacteria including the nearly complete genome of
      Magnetospirillum gryphiswaldense strain MSR-1, the complete genome of
      Magnetospirillum magneticum strain AMB-1, the complete genome of the
      magnetic coccus MC-1, and the comparative-ready preliminary genome
      assembly of Magnetospirillum magnetotacticum strain MS-1 against an
      in-house database comprising 426 complete bacterial and archaeal genome
      sequences. A magnetobacterial core genome of about 891 genes was found
      shared by all four MTB. In addition to a set of approximately 152
      genus-specific genes shared by the three Magnetospirillum strains, we
      identified 28 genes as group specific, i.e., which occur in all four
      analyzed MTB but exhibit no (MTB-specific genes) or only remote
      (MTB-related genes) similarity to any genes from nonmagnetotactic
      organisms and which besides various novel genes include nearly all mam and
      mms genes previously shown to control magnetosome formation. The
      MTB-specific and MTB-related genes to a large extent display synteny,
      partially encode previously unrecognized magnetosome membrane proteins,
      and are either located within (18 genes) or outside (10 genes) the MAI of
      M. gryphiswaldense. These genes, which represent less than 1% of the 4,268
      open reading frames of the MSR-1 genome, as yet are mostly of unknown
      functions but are likely to be specifically involved in magnetotaxis and,
      thus, represent prime targets for future experimental analysis.
AU  - Richter M
AU  - Kube M
AU  - Bazylinski DA
AU  - Lombardot T
AU  - Glockner FO
AU  - Reinhardt R
AU  - Schuler D
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2007 189: 4899-4910.

PMID- 27063562
VI  - 586
DP  - 2016
TI  - PacBio SMRT assembly of a complex multi-replicon genome reveals chlorocatechol degradative operon in a region of genome plasticity.
PG  - 239-247
AB  - We have sequenced a Burkholderia genome that contains multiple replicons and large repetitive
      elements that would make it inherently difficult to assemble by short read sequencing
      technologies. We illustrate how the integrated long read correction algorithms implemented
      through the PacBio Single Molecule Real-Time (SMRT) sequencing technology successfully
      provided a de novo assembly that is a reasonable estimate of both the gene content and genome
      organization without making any further modifications. This assembly is comparable to related
      organisms assembled by more labour intensive methods. Our assembled genome revealed regions of
      genome plasticity for further investigation, one of which harbours a chlorocatechol
      degradative operon highly homologous to those previously identified on globally ubiquitous
      plasmids. In an ideal world, this assembly would still require experimental validation to
      confirm gene order and copy number of repeated elements. However, we submit that particularly
      in instances where a polished genome is not the primary goal of the sequencing project, PacBio
      SMRT sequencing provides a financially viable option for generating a biologically relevant
      genome estimate that can be utilized by other researchers for comparative studies.
AU  - Ricker N
AU  - Shen SY
AU  - Goordial J
AU  - Jin S
AU  - Fulthorpe RR
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 2016 586: 239-247.

PMID- 28619799
VI  - 5
DP  - 2017
TI  - Genome Sequence of Weissella cibaria DmW_103, Isolated from Wild Drosophila.
PG  - e00512-17
AB  - Lactic acid bacteria are commonly associated with Drosophila spp. Here, we report on the
      isolation of a strain of Weissella cibaria and the sequencing, assembly,
      and annotation of its genome. A total of 35 contigs were generated, with 2,349
      coding sequences found.
AU  - Ricks NJ
AU  - Carroll C
AU  - Walters A
AU  - Newell PD
AU  - Chaston JM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00512-17.

PMID- 8015614
VI  - 370
DP  - 1994
TI  - No limits on restriction.
PG  - 78
AB  - The structure of the endonuclease R.PvuII in the absence and presence of its recognition site
      indicates how the interaction with DNA might proceed.
AU  - Riddihough G
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1994 370: 78.

PMID- 29435100
VI  - 13
DP  - 2018
TI  - Complete genome sequence of Pseudomonas alcaliphila JAB1 (=DSM 26533), a versatile degrader of organic pollutants.
PG  - 3
AB  - In this study, following its isolation from contaminated soil, the genomic sequence of
      Pseudomonas alcaliphila strain JAB1 (=DSM 26533), a
      biphenyl-degrading bacterium, is reported and analyzed in relation to its
      extensive degradative capabilities. The P. alcaliphila JAB1 genome (GenBank
      accession no. CP016162) consists of a single 5.34 Mbp-long chromosome with a GC
      content of 62.5%. Gene function was assigned to 3816 of the 4908 predicted genes.
      The genome harbors a bph gene cluster, permitting degradation of biphenyl and
      many congeners of polychlorinated biphenyls (PCBs), a ben gene cluster, enabling
      benzoate and its derivatives to be degraded, and phe gene cluster, which permits
      phenol degradation. In addition, P. alcaliphila JAB1 is capable of
      cometabolically degrading cis-1,2-dichloroethylene (cDCE) when grown on phenol.
      The strain carries both catechol and protocatechuate branches of the
      beta-ketoadipate pathway, which is used to funnel the pollutants to the central
      metabolism. Furthermore, we propose that clustering of MALDI-TOF MS spectra with
      closest phylogenetic relatives should be used when taxonomically classifying the
      isolated bacterium; this, together with 16S rRNA gene sequence and chemotaxonomic
      data analyses, enables more precise identification of the culture at the species
      level.
AU  - Ridl J
AU  - Suman J
AU  - Fraraccio S
AU  - Hradilova M
AU  - Strejcek M
AU  - Cajthaml T
AU  - Zubrova A
AU  - Macek T
AU  - Strnad H
AU  - Uhlik O
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2018 13: 3.

PMID- 24501625
VI  - 8
DP  - 2013
TI  - Genome sequence of the Leisingera aquimarina type strain (DSM 24565(T)), a member of the marine Roseobacter clade rich in extrachromosomal elements.
PG  - 389-402
AB  - Leisingera aquimarina Vandecandelaere et al. 2008 is a member of the genomically  well
      characterized Roseobacter clade within the family Rhodobacteraceae.
      Representatives of the marine Roseobacter clade are metabolically versatile and
      involved in carbon fixation and biogeochemical processes. They form a
      physiologically heterogeneous group, found predominantly in coastal or polar
      waters, especially in symbiosis with algae, in microbial mats, in sediments or
      associated with invertebrates. Here we describe the features of L. aquimarina DSM
      24565(T) together with the permanent-draft genome sequence and annotation. The
      5,344,253 bp long genome consists of one chromosome and an unusually high number
      of seven extrachromosomal elements and contains 5,129 protein-coding and 89 RNA
      genes. It was sequenced as part of the DOE Joint Genome Institute Community
      Sequencing Program 2010 and of the activities of the Transregional Collaborative
      Research Centre 51 funded by the German Research Foundation (DFG).
AU  - Riedel T et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 389-402.

PMID- 23450211
VI  - 7
DP  - 2012
TI  - Genome sequence of the orange-pigmented seawater bacterium Owenweeksia hongkongensis type strain (UST20020801(T)).
PG  - 120-130
AB  - Lau . 2005 is the sole member of the monospecific genus in the family a poorly characterized
      family at the genome level thus far. This family comprises seven
      genera within the class . Family members are known to be psychrotolerant,
      rod-shaped and orange pigmented (beta-carotene), typical for . For growth,
      seawater and complex organic nutrients are necessary. The genome of UST20020801
      is only the second genome of a member of the family whose sequence has been
      deciphered. Here we describe the features of this organism, together with the
      complete genome sequence and annotation. The 4,000,057 bp long chromosome with
      its 3,518 protein-coding and 45 RNA genes is a part of the project.
AU  - Riedel T et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 7: 120-130.

PMID- 23450183
VI  - 7
DP  - 2012
TI  - Genome sequence of the Antarctic rhodopsins-containing flavobacterium Gillisia limnaea type strain (R-8282(T)).
PG  - 107-119
AB  - Van Trappen et al. 2004 is the type species of the genus , which is a member of the well
      characterized family . The genome of R-8282 is the first sequenced
      genome (permanent draft) from a type strain of the genus . Here we describe the
      features of this organism, together with the permanent-draft genome sequence and
      annotation. The 3,966,857 bp long chromosome (two scaffolds) with its 3,569
      protein-coding and 51 RNA genes is a part of the of and project.
AU  - Riedel T et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 7: 107-119.

PMID- 25858846
VI  - 3
DP  - 2015
TI  - Genome Resequencing of the Virulent and Multidrug-Resistant Reference Strain Clostridium difficile 630.
PG  - e00276-15
AB  - We resequenced the complete genome of the virulent and multidrug-resistant pathogen
      Clostridium difficile strain 630. A combination of single-molecule
      real-time and Illumina sequencing technology revealed the presence of an
      additional rRNA gene cluster, additional tRNAs, and the absence of a transposon
      in comparison to the published and reannotated genome sequence.
AU  - Riedel T
AU  - Bunk B
AU  - Thurmer A
AU  - Sproer C
AU  - Brzuszkiewicz E
AU  - Abt B
AU  - Gronow S
AU  - Liesegang H
AU  - Daniel R
AU  - Overmann J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00276-15.

PMID- 26450746
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of the Clostridium difficile Type Strain DSM 1296T.
PG  - e01186-15
AB  - In this study, we sequenced the complete genome of the Clostridium difficile type strain DSM
      1296(T). A combination of single-molecule real-time (SMRT) and Illumina sequencing technology
      revealed the presence of one chromosome and two extrachromosomal elements, the bacteriophage
      phiCDIF1296T and a putative plasmid-like structure harboring genes of another bacteriophage.
AU  - Riedel T
AU  - Bunk B
AU  - Wittmann J
AU  - Thurmer A
AU  - Sproer C
AU  - Gronow S
AU  - Liesegang H
AU  - Daniel R
AU  - Overmann J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01186-15.

PMID- 25197467
VI  - 9
DP  - 2014
TI  - Complete genome sequence of the bacteriochlorophyll a-containing Roseibacterium elongatum type strain (DSM 19469(T)), a representative of the Roseobacter group  isolated from Australian coast sand.
PG  - 840-854
AB  - Roseibacterium elongatum Suzuki et al. 2006 is a pink-pigmented and bacteriochlorophyll
      a-producing representative of the Roseobacter group within
      the alphaproteobacterial family Rhodobacteraceae. Representatives of the marine
      'Roseobacter group' were found to be abundant in the ocean and play an important
      role in global and biogeochemical processes. In the present study we describe the
      features of R. elongatum strain OCh 323(T) together with its genome sequence and
      annotation. The 3,555,102 bp long genome consists of one circular chromosome with
      no extrachromosomal elements and is one of the smallest known Roseobacter
      genomes. It contains 3,540 protein-coding genes and 59 RNA genes. Genome analysis
      revealed the presence of a photosynthetic gene cluster, which putatively enables
      a photoheterotrophic lifestyle. Gene sequences associated with quorum sensing,
      motility, surface attachment, and thiosulfate and carbon monoxide oxidation could
      be detected. The genome was sequenced as part of the activities of the
      Transregional Collaborative Research Centre 51 (TRR51) funded by the German
      Research Foundation (DFG).
AU  - Riedel T
AU  - Fiebig A
AU  - Goker M
AU  - Klenk HP
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 840-854.

PMID- 25197468
VI  - 9
DP  - 2014
TI  - Genome sequence of the Wenxinia marina type strain (DSM 24838(T)), a representative of the Roseobacter group isolated from oilfield sediments.
PG  - 855-865
AB  - Wenxinia marina Ying et al. 2007 is the type species of the genus Wenxinia, a representative
      of the Roseobacter group within the alphaproteobacterial family
      Rhodobacteraceae, isolated from oilfield sediments of the South China Sea. This
      family was shown to harbor the most abundant bacteria especially from coastal and
      polar waters, but was also found in microbial mats, sediments and attached to
      different kind of surfaces. Here we describe the features of W. marina strain
      HY34(T) together with the genome sequence and annotation of strain DSM 24838(T)
      and novel aspects of its phenotype. The 4,181,754 bp containing genome sequence
      encodes 4,047 protein-coding genes and 59 RNA genes. The genome of W. marina DSM
      24838(T) was sequenced as part of the activities of the Genomic Encyclopedia of
      Type Strains, Phase I: the one thousand microbial genomes (KMG) project funded by
      the DoE and the Transregional Collaborative Research Centre 51 (TRR51) funded by
      the German Research Foundation (DFG).
AU  - Riedel T
AU  - Fiebig A
AU  - Han J
AU  - Huntemann M
AU  - Spring S
AU  - Petersen J
AU  - Ivanova NN
AU  - Markowitz V
AU  - Woyke T
AU  - Goker M
AU  - Kyrpides NC
AU  - Klenk HP
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 855-865.

PMID- 24501650
VI  - 9
DP  - 2013
TI  - Genome sequence of the Litoreibacter arenae type strain (DSM 19593(T)), a member  of the Roseobacter clade isolated from sea sand.
PG  - 117-127
AB  - Litoreibacter arenae Kim et al. 2012 is a member of the genomically well-characterized
      Rhodobacteraceae clade within the Roseobacter clade.
      Representatives of this clade are known to be metabolically versatile and
      involved in marine carbon-producing and biogeochemical processes. They form a
      physiologically heterogeneous group of Alphaproteobacteria and were mostly found
      in coastal or polar waters, especially in symbiosis with algae, in microbial
      mats, in sediments or together with invertebrates and vertebrates. Here we
      describe the features of L. arenae DSM 19593(T), including novel aspects of its
      phenotype, together with the draft genome sequence and annotation. The 3,690,113
      bp long genome consists of 17 scaffolds with 3,601 protein-coding and 56 RNA
      genes. This genome was sequenced as part of the activities of the Transregional
      Collaborative Research Centre 51 funded by the German Research Foundation (DFG).
AU  - Riedel T
AU  - Fiebig A
AU  - Petersen J
AU  - Gronow S
AU  - Kyrpides NC
AU  - Goker M
AU  - Klenk HP
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 9: 117-127.

PMID- 25197472
VI  - 9
DP  - 2014
TI  - Genome sequence of the pink to light reddish-pigmented Rubellimicrobium mesophilum type strain (DSM 19309(T)), a representative of the Roseobacter group   isolated from soil, and emended description of the species.
PG  - 902-913
AB  - Rubellimicrobium mesophilum Dastager et al. 2008 is a mesophilic and light reddish-pigmented
      representative of the Roseobacter group within the
      alphaproteobacterial family Rhodobacteraceae. Representatives of the Roseobacter
      group play an important role in the marine biogeochemical cycles and were found
      in a broad variety of marine environments associated with algal blooms, different
      kinds of sediments, and surfaces of invertebrates and vertebrates. Roseobacters
      were shown to be widely distributed, especially within the total bacterial
      community found in coastal waters, as well as in mixed water layers of the open
      ocean. Here we describe the features of R. mesophilum strain MSL-20(T) together
      with its genome sequence and annotation generated from a culture of DSM 19309(T).
      The 4,927,676 bp genome sequence consists of one chromosome and probably one
      extrachromosomal element. It contains 5,082 protein-coding genes and 56 RNA
      genes. As previously reported, the G+C content is significantly different from
      the actual genome sequence-based G+C content and as the type strain tests
      positively for oxidase, the species description is emended accordingly. The
      genome was sequenced as part of the activities of the Transregional Collaborative
      Research Centre 51 (TRR51) funded by the German Research Foundation (DFG).
AU  - Riedel T
AU  - Spring S
AU  - Fiebig A
AU  - Petersen J
AU  - Goker M
AU  - Klenk HP
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 902-913.

PMID- 25197501
VI  - 9
DP  - 2014
TI  - Genome sequence of the exopolysaccharide-producing Salipiger mucosus type strain  (DSM 16094(T)), a moderately halophilic member of the Roseobacter clade.
PG  - 1333-1345
AB  - Salipiger mucosus Martinez-Canovas et al. 2004 is the type species of the genus Salipiger, a
      moderately halophilic and exopolysaccharide-producing representative
      of the Roseobacter lineage within the alphaproteobacterial family
      Rhodobacteraceae. Members of this family were shown to be the most abundant
      bacteria especially in coastal and polar waters, but were also found in microbial
      mats and sediments. Here we describe the features of the S. mucosus strain DSM
      16094(T) together with its genome sequence and annotation. The 5,689,389-bp
      genome sequence consists of one chromosome and several extrachromosomal elements.
      It contains 5,650 protein-coding genes and 95 RNA genes. The genome of S. mucosus
      DSM 16094(T) was sequenced as part of the activities of the Transregional
      Collaborative Research Center 51 (TRR51) funded by the German Research Foundation
      (DFG).
AU  - Riedel T
AU  - Spring S
AU  - Fiebig A
AU  - Petersen J
AU  - Kyrpides NC
AU  - Goker M
AU  - Klenk HP
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 1333-1345.

PMID- 26203330
VI  - 10
DP  - 2015
TI  - Genome sequence of the Roseovarius mucosus type strain (DSM 17069(T)), a bacteriochlorophyll a-containing representative of the marine Roseobacter group  isolated from the dinoflagellate Alexandrium ostenfeldii.
PG  - 17
AB  - Roseovarius mucosus Biebl et al. 2005 is a bacteriochlorophyll a-producing representative of
      the marine Roseobacter group within the alphaproteobacterial
      family Rhodobacteraceae, which was isolated from the dinoflagellate Alexandrium
      ostenfeldii. The marine Roseobacter group was found to be abundant in the ocean
      and plays an important role for global and biogeochemical processes. Here we
      describe the features of the R. mucosus strain DFL-24(T) together with its genome
      sequence and annotation generated from a culture of DSM 17069(T). The 4,247,724
      bp containing genome sequence encodes 4,194 protein-coding genes and 57 RNA
      genes. In addition to the presence of four plasmids, genome analysis revealed the
      presence of genes associated with host colonization, DMSP utilization,
      cytotoxins, and quorum sensing that could play a role in the interrelationship of
      R. mucosus with the dinoflagellate A. ostenfeldii and other marine organisms.
      Furthermore, the genome encodes genes associated with mixotrophic growth, where
      both reduced inorganic compounds for lithotrophic growth and a photoheterotrophic
      lifestyle using light as additional energy source could be used.
AU  - Riedel T
AU  - Spring S
AU  - Fiebig A
AU  - Scheuner C
AU  - Petersen J
AU  - Goker M
AU  - Klenk HP
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 17.

PMID- 28619474
VI  - 307
DP  - 2017
TI  - High metabolic versatility of different toxigenic and non-toxigenic Clostridioides difficile isolates.
PG  - 311-320
AB  - Clostridioides difficile (formerly Clostridium difficile) is a major nosocomial
      pathogen with an increasing number of community-acquired infections causing
      symptoms from mild diarrhea to life-threatening colitis. The pathogenicity of C.
      difficile is considered to be mainly associated with the production of
      genome-encoded toxins A and B. In addition, some strains also encode and express
      the binary toxin CDT. However; a large number of non-toxigenic C. difficile
      strains have been isolated from the human gut and the environment. In this study,
      we characterized the growth behavior, motility and fermentation product formation
      of 17 different C. difficile isolates comprising five different major genomic
      clades and five different toxin inventories in relation to the C. difficile model
      strains 630Deltaerm and R20291. Within 33 determined fermentation products, we
      identified two yet undescribed products (5-methylhexanoate and
      4-(methylthio)-butanoate) of C. difficile. Our data revealed major differences in
      the fermentation products obtained after growth in a medium containing casamino
      acids and glucose as carbon and energy source. While the metabolism of branched
      chain amino acids remained comparable in all isolates, the aromatic amino acid
      uptake and metabolism and the central carbon metabolism-associated fermentation
      pathways varied strongly between the isolates. The patterns obtained followed
      neither the classification of the clades nor the ribotyping patterns nor the
      toxin distribution. As the toxin formation is strongly connected to the
      metabolism, our data allow an improved differentiation of C. difficile strains.
      The observed metabolic flexibility provides the optimal basis for the adaption in
      the course of infection and to changing conditions in different environments
      including the human gut.
AU  - Riedel T
AU  - Wetzel D
AU  - Hofmann JD
AU  - Plorin SP
AU  - Dannheim H
AU  - Berges M
AU  - Zimmermann O
AU  - Bunk B
AU  - Schober I
AU  - Sproer C
AU  - Liesegang H
AU  - Jahn D
AU  - Overmann J
AU  - Gross U
AU  - Neumann-Schaal M
PT  - Journal Article
TA  - Int. J. Med. Microbiol.
JT  - Int. J. Med. Microbiol.
SO  - Int. J. Med. Microbiol. 2017 307: 311-320.

PMID- 8371990
VI  - 21
DP  - 1993
TI  - Restriction endonuclease AlwNI is blocked by overlapping Dcm methylation.
PG  - 4148
AB  - Many restriction enzymes are unable to cleave DNA if their recognition sequence contains
      methylated residues. The two sequence-specific methylases present in most laboratory strains
      of Escherichia coli are the Dam methylase, which methylates the N6 position of A within the
      sequence GATC, and the Dcm methylase, which methylates the C5 position of the internal C
      residue with the sequence CC(A/T)GG. During the construction of derivatives of plasmid
      pCHG-3122, which contains three recognition sites for the restriction endonuclease AlwNI, we
      observed that one of the sites was only poorly cleaved when the plasmid DNA was isolated from
      E. coli strain DH5-alpha. Inspection of the sequences flanking the three AlwNI recognition
      sites showed that one of them located inside the LacZ fragment (ant position 2145) overlapped
      with a recognition site for Dcm Methylase (see Table 1).
AU  - Rieger A
AU  - Nassal M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 4148.

PMID- 28522729
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Two Streptococcus pneumoniae Serotype 19A Sequence Type 226 Clinical Isolates from Hungary, Hu17 with High-Level Beta-Lactam Resistance and Hu15 of a Penicillin-Sensitive Phenotype.
PG  - e00401-17
AB  - The draft genome sequences of two multiple-antibiotic-resistant Streptococcus pneumoniae
      isolates from Hungary, Hu15 and Hu17, are reported here. Strain Hu15
      is penicillin susceptible, whereas Hu17 is a high-level-penicillin-resistant
      strain. Both isolates belong to the serotype 19A sequence type 226, a
      single-locus variant (in the ddl locus) of the Hungary19A-6 clone.
AU  - Rieger M
AU  - Denapaite D
AU  - Bruckner R
AU  - Maurer P
AU  - Hakenbeck R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00401-17.

PMID- 18037438
VI  - 375
DP  - 2008
TI  - Restriction Endonuclease Inhibitor IPI* of Bacteriophage T4: A Novel Structure for a Dedicated Target.
PG  - 720-734
AB  - Phage T4 protects its DNA from the two-gene-encoded gmrS/gmrD (glucose-modified
      hydroxymethylcytosine restriction endonuclease) CT of
      pathogenic Escherichia coli, CT596, by injecting several hundred copies of
      the 76-amino-acid-residue nuclease inhibitor, IPI*, into the infected
      host. Here, the three-dimensional solution structure of mature IPI* is
      reported as determined by nuclear magnetic resonance techniques using 1290
      experimental nuclear Overhauser effect and dipolar coupling constraints (
      approximately 17 constraints per residue). Close examination of this
      oblate-shaped protein structure reveals a novel fold consisting of two
      small beta-sheets (beta1: B1 and B2; beta2: B3-B5) flanked at the N- and
      C-termini by alpha-helices (H1 and H2). Such a fold is very compact in
      shape and allows ejection of IPI* through the narrow 30-A portal and tail
      tube apertures of the virion without unfolding. Structural and dynamic
      measurements identify an exposed hydrophobic knob that is a putative
      gmrS/gmrD-binding site. A single gene from the uropathogenic E. coli
      UT189, which codes for a gmrS/gmrD-like UT fusion enzyme (with
      approximately 90% identity to the heterodimeric CT enzyme), has evolved
      IPI* inhibitor immunity. Analysis of the gmrS/gmrD restriction
      endonuclease enzyme family and its IPI* family phage antagonists reveals
      an evolutionary pathway that has elaborated a surprisingly diverse and
      specifically fitted set of coevolving attack and defense structures.
AU  - Rifat D
AU  - Wright NT
AU  - Varney KM
AU  - Weber DJ
AU  - Black LW
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2008 375: 720-734.

PMID- 12900540
VI  - 99
DP  - 2002
TI  - X chromosome inactivation, differentiation, and DNA methylation revisited, with a tribute to Susumu Ohno.
PG  - 17-24
AB  - X chromosome inactivation and DNA methylation are reviewed, with emphasis on the contributions
      of Susumu Ohno and the predictions made
      in my 1975 paper (Riggs, 1975) in which I proposed the "maintenance
      methylase" model for somatic inheritance of methylation patterns and
      suggested that DNA methylation would be involved in mammalian X
      chromosome inactivation and development. The maintenance methylase
      model is discussed and updated to consider methylation patterns in cell
      populations that have occasional, stochastic methylation changes by de
      novo methylation or demethylation, either active or passive. The "way
      station" model for the spread of X inactivation by LINE- 1 elements is
      also considered, and some recent results from my laboratory are briefly
      reviewed.
AU  - Riggs AD
PT  - Journal Article
TA  - Cytogenet. Genome Res.
JT  - Cytogenet. Genome Res.
SO  - Cytogenet. Genome Res. 2002 99: 17-24.

PMID- 25908150
VI  - 3
DP  - 2015
TI  - Draft genome sequence of a novel culturable marine chroococcalean cyanobacterium  from the South atlantic ocean.
PG  - e00384-15
AB  - The novel chroococcalean cyanobacterium strain CENA595 was isolated from the deep chlorophyll
      maximum layer of the continental shelf of the South Atlantic Ocean.
      Here, we report the draft genome sequence for this strain, consisting of 60
      contigs containing a total of 5,265,703 bp and 3,276 putative protein-coding
      genes.
AU  - Rigonato J
AU  - Alvarenga DO
AU  - Branco LH
AU  - Varani AM
AU  - Brandini FP
AU  - Fiore MF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00384-15.

PMID- 29069349
VI  - 9
DP  - 2017
TI  - Legionella becoming a mutualist: adaptive processes shaping the genome of symbiont in the louse Polyplax serrata.
PG  - 2946-2957
AB  - Legionellaceae are intracellular bacteria known as important human pathogens. In
      the environment, they are mainly found in biofilms associated with amoebas. In
      contrast to the gammaproteobacterial family Enterobacteriaceae, which established
      a broad spectrum of symbioses with many insect taxa, the only instance of
      legionella-like symbiont has been reported from lice of the genus Polyplax. Here,
      we sequenced the complete genome of this symbiont and compared its main
      characteristics to other Legionella species and insect symbionts. Based on
      rigorous multigene phylogenetic analyses, we confirm this bacterium as a member
      of the genus Legionella and propose the name Candidatus Legionella polyplacis,
      sp.n. We show that the genome of Ca. Legionella polyplacis underwent massive
      degeneration, including considerable size reduction (529.746 bp, 484 protein
      coding genes) and a severe decrease in GC content (23%). We identify several
      possible constraints underlying the evolution of this bacterium. On one hand, Ca.
      Legionella polyplacis and the louse symbionts Riesia and Puchtella experienced
      convergent evolution, perhaps due to adaptation to similar hosts. On the other
      hand, some metabolic differences are likely to reflect different phylogenetic
      positions of the symbionts and hence availability of particular metabolic
      function in the ancestor. This is exemplified by different arrangements of
      thiamine metabolism in Ca. Legionella polyplacis and Riesia. Finally, horizontal
      gene transfer is shown to play a significant role in the adaptive and
      diversification process. Particularly, we show that Ca. L. polyplacis
      horizontally acquired a complete biotin operon (bioADCHFB) that likely assisted
      this bacterium when becoming an obligate mutualist.
AU  - Rihova J
AU  - Novakova E
AU  - Husnik F
AU  - Hypsa V
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2017 9: 2946-2957.

PMID- 21465086
VI  - 156
DP  - 2011
TI  - The genomes and comparative genomics of Lactobacillus delbrueckii phages.
PG  - 1217-1233
AB  - Lactobacillus delbrueckii phages are a great source of genetic diversity.
      Here, the genome sequences of Lb. delbrueckii phages LL-Ku, c5 and JCL1032
      were analyzed in detail, and the genetic diversity of Lb. delbrueckii
      phages belonging to different taxonomic groups was explored. The lytic
      isometric group b phages LL-Ku (31,080 bp) and c5 (31,841 bp) showed a
      minimum nucleotide sequence identity of 90% over about three-fourths of
      their genomes. The genomic locations of their lysis modules were unique,
      and the genomes featured several putative overlapping transcription units
      of genes. LL-Ku and c5 virions displayed peptidoglycan hydrolytic activity
      associated with a ~36-kDa protein similar in size to the endolysin.
      Unexpectedly, the 49,433-bp genome of the prolate phage JCL1032
      (temperate, group c) revealed a conserved gene order within its structural
      genes. Lb. delbrueckii phages representing groups a (a phage LL-H), b and
      c possessed only limited protein sequence homology. Genomic comparison of
      LL-Ku and c5 suggested that diversification of Lb. delbrueckii phages is
      mainly due to insertions, deletions and recombination. For the first time,
      the complete genome sequences of group b and c Lb. delbrueckii phages are
      reported.
AU  - Riipinen KA
AU  - Forsman P
AU  - Alatossava T
PT  - Journal Article
TA  - Arch. Virol.
JT  - Arch. Virol.
SO  - Arch. Virol. 2011 156: 1217-1233.

PMID- 28450512
VI  - 5
DP  - 2017
TI  - Genome Sequence of 'Candidatus Carsonella ruddii' Strain BC, a Nutritional Endosymbiont of Bactericera cockerelli.
PG  - e00236-17
AB  - Here, we report the genome of 'Candidatus Carsonella ruddii' strain BC, a nutritional
      endosymbiont of the tomato psyllid Bactericera cockerelli The
      173,802-bp genome contains 198 protein-coding genes, with a G+C content of 14.8%.
AU  - Riley AB
AU  - Kim D
AU  - Hansen AK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00236-17.

PMID- 27795289
VI  - 4
DP  - 2016
TI  - Complete Genome Sequences of Three Important Methicillin-Resistant Clinical Isolates of Staphylococcus pseudintermedius.
PG  - e01194-16
AB  - We report the first complete genome sequences of three predominant clones (ST68,  ST71, and
      ST84) of methicillin-resistant Staphylococcus pseudintermedius in North
      America. All strains were isolated from canine infections and have different
      SCCmec elements and antibiotic resistance gene patterns.
AU  - Riley MC
AU  - Perreten V
AU  - Bemis DA
AU  - Kania SA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01194-16.

PMID- 23929465
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Helicobacter fennelliae Strain MRY12-0050, Isolated from a Bacteremia Patient.
PG  - e00512-13
AB  - Helicobacter fennelliae, a human enterohepatic pathogen, causes bacteremia and colitis. We
      isolated H. fennelliae strain MRY12-0050 from a female patient; this
      strain was isolated from 2 other patients from the same hospital during the same
      period, suggesting human-to-human transmission. This is the first report of an H.
      fennelliae genome sequence.
AU  - Rimbara E
AU  - Matsui M
AU  - Mori S
AU  - Suzuki S
AU  - Suzuki M
AU  - Kim H
AU  - Sekizuka T
AU  - Kuroda M
AU  - Shibayama K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00512-13.

PMID- 
VI  - 1
DP  - 2005
TI  - Saturation mutagenesis of Thr862, the amino acid essential for substrate specificity of Eco57I restriction endonuclease.
PG  - 11-14
AB  - Type IIG restriction endonuclease Eco57I cleaves DNA 16/14 nucleotides away from the
      asymmetric recognition sequence 5'-CTGAAG.  The enzyme also possesses methyltransferase
      activity that modifies the second A base within the 5'-CTGAAG strand of the target duplex
      (underlined).  In previous studies, Eco57I mutants with altered substrate specificity
      5'-CTGRAG were isolated.  These mutant enzymes have Asn or Ser instead of Thr in the 862th
      position of the protein.  In order to evaluate the impact of T862 on the substrate
      specificity, it was changed to the other 17 amino acids.  The in vivo cleavage activity and
      substrate specificity of the resulting mutant enzymes was examined (i) by testing lethality of
      the mutants to the host cells in the absence or presence of Eco57I (specificity 5'-CTGAAG) and
      GsuI (specificity 5'-CTGGAG) methyltransferases, and (ii) by testing the ability of the
      mutants to induce SOS DNA repair response in the absence or presence of protecting
      methyltransferases.  The results indicate that mutants T862G, T862C and, probably, T862A and
      T862D could display altered substrate specificity.  The recognition sequence of T862F, H, K,
      L, Q, M and Y mutants was the same as that of the wild type enzyme.  The remaining
      substitutions rendered the enzyme catalytically inactive.
AU  - Rimseliene R
AU  - Janulaitis A
PT  - Journal Article
TA  - Biologija
JT  - Biologija
SO  - Biologija 2005 1: 11-14.

PMID- 11124947
VI  - 276
DP  - 2001
TI  - Mutational analysis of two putative catalytic motifs of the Type IV restriction endonuclease Eco57I.
PG  - 10492-10497
AB  - The role of two sequence motifs (SM) as putative cleavage catalytic centers (77)PD(X13)EAK (SM
      I) and (811)PD(X20)DQK (SM II) of type IV restriction endonuclease Eco57I was studied by
      site-directed mutational analysis. Substitutions within SM I; D78N, D78A, D78K, and E92Q
      reduced cleavage activity of Eco57I to a level undetectable both in vivo and in vitro.
      Residual endonucleolytic activity of the E92Q mutant was detected only when the Mg(2+) in the
      standard reaction mixture was replaced with Mn(2+). The mutants D78N and E92Q retained the
      ability to interact with DNA specifically. The mutants also retained DNA methylation activity
      of Eco57I. The properties of the SM I mutants indicate that Asp(78) and Glu(92) residues are
      essential for cleavage activity of the Eco57I, suggesting that the sequence motif
      (77)PD(X13)EAK represents the cleavage active site of this endonuclease. Eco57I mutants
      containing single amino acid substitutions within SM II (D812A, D833N, D833A) revealed only a
      small or moderate decrease of cleavage activity as compared with wild-type Eco57I, indicating
      that the SM II motif does not represent the catalytic center of Eco57I. The results, taken
      together, allow us to conclude that the Eco57I restriction endonuclease has one catalytic
      center for cleavage of DNA.
AU  - Rimseliene R
AU  - Janulaitis A
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2001 276: 10492-10497.

PMID- 12628245
VI  - 327
DP  - 2003
TI  - Engineering of restriction endonucleases: using methylation activity of the bifunctional endonuclease Eco571 to select the mutant with a novel sequence specificity.
PG  - 383-391
AB  - Type II restriction endonucleases (REs) are widely used tools in molecular biology,
      biotechnology and diagnostics. Efforts to generate new
      specificities by structure-guided design and random mutagenesis have been
      unsuccessful so far. We have developed a new procedure called the
      methylation activity-based selection (MABS) for generating REs with a new
      specificity. MABS uses a unique property of bifunctional type II REs to
      methylate DNA targets they recognize. The procedure includes three steps:
      (1) conversion of a bifunctional RE into a monofunctional DNA-modifying
      enzyme by cleavage center disruption; (2) mutagenesis and selection of
      mutants with altered DNA modification specificity based on their ability
      to protect predetermined DNA targets; (3) reconstitution of the cleavage
      center's wild-type structure. The efficiency of the MABS technique was
      demonstrated by altering the sequence specificity of the bifunctional RE
      Eco57I from 5'-CTGAAG to 5'-CTGRAG, and thus generating the mutant
      restriction endonuclease (and DNA methyltransferase) of a specificity not
      known before. This study provides evidence that MABS is a promising
      technique for generation of REs with new specificities.
AU  - Rimseliene R
AU  - Maneliene Z
AU  - Lubys A
AU  - Janulaitis A
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2003 327: 383-391.

PMID- Not carried by PubMed...
VI  - 1
DP  - 1997
TI  - Site-directed mutagenesis of type IV restriction endonuclease Eco57I.
PG  - 31-33
AB  - Amino acid sequence analysis of type IV restriction endonuclease Eco57I revealed two sequence
      motifs 77PDX13EXK and 811PDX20 DXK as putative catalytic sites.  We have used a site-directed
      mutational analysis of these regions in order, to determine their role in catalysis.
      Catalytic properties of the mutants were studied in vivo and in vitro.  The replacement of D78
      and E92, respectively, by mutations N78, A78, K78, Q92, resulted in the complete loss of
      cleavage activity.  The D833N mutant cleaves DNA with reduced rate.  The activity of the D812A
      mutant seems to be the same as that of the wild type R. Eco57I.  The results suggest that
      amino acids D87 and E92 are essential for cleavage activity of the Eco57I restriction
      endonuclease, and the sequence motif 77PDX13EXK is a catalytic center of the enzyme.
AU  - Rimseliene R
AU  - Timinskas A
PT  - Journal Article
TA  - Biologija
JT  - Biologija
SO  - Biologija 1997 1: 31-33.

PMID- 
VI  - 2
DP  - 1998
TI  - Cloning the PaeI restriction-modification system in Escherichia coli.
PG  - 77-78
AB  - PaeI, type II restriction-modification system from bacterium Pseudomonas aeruginosa,
      recognizes DNA sequence 5'-CGATCG-3'.  The PaeI methyltransferase (Mtase)-encoding gene,
      paeIM, was cloned into Escherichia coli using biochemical Mtase selection method.  According
      to the results of Southern-blot analysis, chromosomal map of Pseudomonas aeruginosa was
      generated localizing the paeIM gene and flanking regions.  The paeIR gene was cloned as a 2.1
      kb Eco47III DNA fragment into pBR322 vector.  In order to increase the PaeI restriction
      endonuclease expression and yield in E. coli, the paeIR gene was subcloned into multicopy
      plasmid pIC-19H.  80000 units of R.PaeI per gram of wet-weight cells were produced, approx. 20
      times more than were produced by P. aeruginosa.
AU  - Rimseliene R
AU  - Vaisvila R
PT  - Journal Article
TA  - Biologija
JT  - Biologija
SO  - Biologija 1998 2: 77-78.

PMID- 7607493
VI  - 157
DP  - 1995
TI  - The eco72IC gene specifies a trans-acting factor which influences expression of both DNA methyltransferase and endonuclease from the Eco72I restriction-modification system.
PG  - 217-219
AB  - Eco72I from Escherichia coli RFL72 is a type-II restriction-modification (R-M) system
      recognizing and cleaving the sequence 5'-CAC/GTG-3'.  The R-M genes are transcribed
      divergently and between the two genes is a small open reading frame codirectional to the R
      gene.  This small ORF acts both to stimulate ENase expression and to depress DNA
      methyltransferase synthesis.  The activity of beta-Gal produced from the eco72IM::lacZ
      translational fusion increased ten-fold, and eco72IR::lacZ translational fusion beta-Gal
      activity decreased 130-fold when eco72IC was inactivated by a frameshift mutation.  Analysis
      of nucleotide sequences of R-M systems, containing C genes, revealed a 5'-ACCTTATAGTC-3'
      consensus sequence upstream from the regulatory genes in all six analysed R-M systems.  This
      sequence, named the C-box, may play the role of an operator sequence.
AU  - Rimseliene R
AU  - Vaisvila R
AU  - Janulaitis A
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 217-219.

PMID- 8224900
VI  - 133
DP  - 1993
TI  - Cloning, purification and characterization of the BseCI DNA methyltransferase from Bacillus stearothermophilus.
PG  - 91-94
AB  - The gene (bseCIM) encoding the BseCI DNA methyltransferase (MTase; M.BseCI) from a Bacillus
      stearothermophilus species was cloned and expressed in Escherichia coli using plasmid vector
      pBR322. Selection of transformants carrying bseCIM was based on resistance of the modified
      plasmid to cleavage by BseCI. The MTase was purified to homogeneity and further characterized.
      Its size as determined by sodium dodecyl sulfate-polyacrylamide-gel electrophoresis and size
      exclusion chromatography was 68 kDa, suggesting that the MTase exists as a monomer. When phage
      lambda DNA was used as a substrate, the optimum temperature for MTase activity was determined
      to be 50-55 degrees C and optimum pH approx 7.4. M.BseCI is inhibited by concentrations of
      NaCl and KCl greater than 50 mM, and it does not require Mg2+ for activity. Finally, M.BseCI
      methylates the 3' adenine residue in the sequence, 5'ATCGAT 3', similarly to its
      isoschizomer M.ClaI.
AU  - Rina M
AU  - Bouriotis V
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1993 133: 91-94.

PMID- 1691485
VI  - 18
DP  - 1990
TI  - Isolation and identification of restriction endonuclease BsiSI.
PG  - 1654
AB  - None
AU  - Rina M
AU  - Bouriotis V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 1654.

PMID- 9332385
VI  - 197
DP  - 1997
TI  - Cloning and characterization of the gene encoding PspPI methyltransferase from the Antarctic psychrotroph Psychrobacter sp. strain TA137.
PG  - 353-360
AB  - The gene (pspPIM) encoding the PspPI DNA methyltransferase (MTase) associated with the PspPI
      restriction-modification system (5'-GGNCC-3') of Psychrobacter species TA137 has been cloned
      and expressed in E. coli, and its nucleotide sequence has been determined.  The coding region
      was 1248 nt in length and capable of specifying a 46,826-Da protein of 416 amino acids.  The
      predicted sequence of the MTase protein displays ten sequence motifs characteristic of all
      prokaryotic m5C-MTases and shows the highest similarity to other MTases that methylate the
      GGNCC sequence, namely M.Eco47II and M.Sau96I.  All three MTases methylate the internal
      cytosine within their recognition sequence.  Sequence similarities between M.PspPI and its
      isospecific M.Eco47II and M.Sau96I as well as with four other m5C-MTases that methylate the
      related GGWCC sequence, namely M.SinI, M.HgiCII, M.HgiBI, M.HgiEI have been also found within
      the variable region of these proteins.  On the basis of structural information from M.HhaI and
      M.HaeIII, several M.PspPI residues that are expected to interact with DNA can be predicted.
      Furthermore, an organization of the variable region of m5C-MTases into two segments exhibiting
      a pattern of conserved residues and a considerable degree of structural homologies is
      described.
AU  - Rina M
AU  - Caufrier F
AU  - Markaki M
AU  - Mavromatis K
AU  - Kokkinidis M
AU  - Bouriotis V
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1997 197: 353-360.

PMID- 2326209
VI  - 18
DP  - 1990
TI  - Isolation and identification of restriction endonuclease BsiKI.
PG  - 1655
AB  - None
AU  - Rina M
AU  - Clark D
AU  - Bouriotis V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 1655.

PMID- 1579477
VI  - 20
DP  - 1992
TI  - Isolation and identification of restriction endonuclease BseCl.
PG  - 1807
AB  - BseCI, an isoschizomer of ClaI has been purified from Bacillus species. BseCI recognizes the
      sequence 5' ...ATCGAT ...3' and cleaves between T and C. The enzyme was purified using the
      following chromatographic steps: 1. Phosphocellulose, 2. Heparin-Sepharose, 3. DEAE-cellulose.
AU  - Rina M
AU  - Dialektakis D
AU  - Clark D
AU  - Pagomenou M
AU  - Bouriotis V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 1807.

PMID- 1956803
VI  - 19
DP  - 1991
TI  - Isolation and identification of restriction endonuclease SgrBI.
PG  - 6342
AB  - SgrBI, an isoschizomer of SacII has been purified from Streptomyces griseus.
      SgrBI recognises the palindromic sequence 5'...CCGCGG...3' generating
      3'-protruding GC-dinucleotides.
AU  - Rina M
AU  - Karagouni A
AU  - Pagomenou M
AU  - Bouriotis V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 6342.

PMID- 1956802
VI  - 19
DP  - 1991
TI  - Isolation and identification of restriction endonuclease SseAI.
PG  - 6341
AB  - SseAI, an isoschizomer of NarI, has been purified from Streptomyces species.
      SseAI recognises the palindromic sequence 5'...GGCGCC...3' and cleaves between
      the second G and C.
AU  - Rina M
AU  - Karagouni A
AU  - Pagomenou M
AU  - Tsigos I
AU  - Bouriotis V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 6341.

PMID- 7959066
VI  - 150
DP  - 1994
TI  - Sequence of the cloned bseCIM gene: M.BseCI reveals high homology to M.BanIII.
PG  - 71-73
AB  - The bseCIM gene, encoding M.BseCI methyltransferase (MTase) from a Bacillus stearothermophilus
      strain, has been previously cloned and expressed in Escherichia coli. The nucleotide (nt)
      sequence of a 2357-bp BspMII-EcoRI fragment encoding bseCIM has now been determined. The
      sequence predicts a MTase of 579 amino acids (aa), 66.7 kDa. Comparison of the deduced aa
      sequence of M.BseCI with sequences of various MTases revealed a significant homology to
      m6A-MTases, especially to its isoschizomer M.BanIII from Bacillus aneurinolyticus.
AU  - Rina M
AU  - Markaki M
AU  - Bouriotis V
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1994 150: 71-73.

PMID- 2146592
VI  - 18
DP  - 1990
TI  - Isolation and identification of restriction endonuclease BssAI.
PG  - 6161
AB  - None
AU  - Rina M
AU  - Stratidakis I
AU  - Bouriotis V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 6161.

PMID- 1653952
VI  - 19
DP  - 1991
TI  - Isolation and identification of restriction endonuclease BseBI.
PG  - 4776
AB  - BseBI, an isoschizomer of BstNI has been purified from Bacillus
      stearothermophilus species.  BseBI recognises the sequence 5'...CCWGG...3' (W=A
      or T) and cleaves between C and W.
AU  - Rina M
AU  - Tsigos I
AU  - Karagouni A
AU  - Pagomenou M
AU  - Bouriotis V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 4776.

PMID- 1579478
VI  - 20
DP  - 1992
TI  - Isolation and identification of restriction endonuclease SseBI.
PG  - 1808
AB  - SseBI, an isoschizomer of StuI has been purified from Streptomyces species. SseBI recognizes
      the sequence 5' ... AGGCCT ...3' and cleaves between G and C. The enzyme was purified using
      the following chromatographic steps: 1. Blue Sepharose F3GA, 2. Heparin-Sepharose.
AU  - Rina M
AU  - Tzanodaskalaki M
AU  - Karagouni A
AU  - Pagomenou M
AU  - Bouriotis V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 1808.

PMID- 1579476
VI  - 20
DP  - 1992
TI  - Isolation and identification of restriction endonuclease MspCI.
PG  - 1806
AB  - MspCI, an isoschizomer of AflII, has been purified from Micrococcus species. MspCI recognizes
      the sequence 5' ...CTTAAG ...3' and cleaves between C and T. The enzyme was purified using
      the following chromatographic steps: 1. Blue Sepharose F3GA; 2. Heparin-Sepharose; 3. DEAE
      Sepharose.
AU  - Rina M
AU  - Tzanodaskalaki M
AU  - Karagouni A
AU  - Pagomenou M
AU  - Bouriotis V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 1806.

PMID- 
VI  - 0
DP  - 1986
TI  - Entry of a procaryotic endonuclease into the nucleus of Saccharomyces cerevisiae.
PG  - 395-413
AB  - Recent experiment have documented the existence of amino acid sequences, acting
      as nuclear signal sequences, that result in the accumulation of proteins in the
      nucleus.  In this paper, the issue of whether or not a protein must possess a
      nuclear signal in order to enter the nucleus is examined.  For these
      experiments, a plasmid capable of expressing EcoRI endonuclease in the yeast
      Saccharomyces cerevisiae has been constructed and transformed into several
      yeast strains.  Two results demonstrate that this bacterial protein can enter
      the yeast nucleus:  First, yeast cells expressing the endonuclease gene die
      with kinetics that are proportional to the capacity of the strain to repair
      double stranded breaks in nuclear DNA.  Secondly, the nuclear DNA contains
      extensive double stranded breaks at EcoRI sites and only at EcoRI sites.
      Therefore, there is no apparent requirement for a protein to contain a complex
      nuclear localization signal in order to enter the nucleus.  Additional
      experiments demonstrate that in-frame fusion of an open reading frame to the 5'
      end of the endonuclease structural gene results in synthesis of a hybrid
      protein that retains endonucleolytic activity.  Mutants of the endonuclease are
      described that allow the activity of the enzyme to be modulated independently
      of its synthesis.
AU  - Rine J
AU  - Barnes G
PT  - Journal Article
TA  - Yeast Cell Biology
JT  - Yeast Cell Biology
SO  - Yeast Cell Biology 1986 0: 395-413.

PMID- 
VI  - 381640
DP  - 2018
TI  - Resolving the complex Bordetella pertussis genome using barcoded nanopore sequencing.
PG  - 0
AB  - The genome of Bordetella pertussis is complex, with high GC content and many repeats, each
      longer than 1,000 bp. Short-read DNA sequencing is unable to resolve the structure of the
      genome; however, long-read sequencing offers the opportunity to produce single-contig B.
      pertussis assemblies using sequencing reads which are longer than the repetitive sections. We
      used an R9.4 MinION flow cell and barcoding to sequence five B. pertussis strains in a single
      sequencing run. We then trialled combinations of the many nanopore-user-community-built
      long-read analysis tools to establish the current optimal assembly pipeline for B. pertussis
      genome sequences. Our best long-read-only assemblies were produced by Canu read correction
      followed by assembly with Flye and polishing with Nanopolish, whilst the best hybrids (using
      nanopore and Illumina reads together) were produced by Canu correction followed by Unicycler.
      This pipeline produced closed genome sequences for four strains, revealing inter-strain
      genomic rearrangement. However, read mapping to the Tohama I reference genome suggests that
      the remaining strain contains an ultra-long duplicated region (over 100 kbp), which was not
      resolved by our pipeline. We have therefore demonstrated the ability to resolve the structure
      of several B. pertussis strains per single barcoded nanopore flow cell, but the genomes with
      highest complexity (e.g. very large duplicated regions) remain only partially resolved using
      the standard library preparation and will require an alternative library preparation method.
      For full strain characterisation, we recommend hybrid assembly of long and short reads
      together; for comparison of genome arrangement, assembly using long reads alone is sufficient.
AU  - Ring N
AU  - Abrahams J
AU  - Jain M
AU  - Olsen H
AU  - Preston A
AU  - Bagby S
PT  - Journal Article
TA  - bioRxiv
JT  - bioRxiv
SO  - bioRxiv 2018 381640: 0.

PMID- 1584789
VI  - 89
DP  - 1992
TI  - The Escherichia coli chromosome contains specific, unmethylated dam and dcm sites.
PG  - 4539-4543
AB  - The Escherichia coli chromosome encodes two methylases, dam and dcm, which recognize the
      sequences GATC and CC(A/T)GG, respectively. Specific dam and dcm sites on the E. coli
      chromosome were found to be unmethylated in vivo by using pulsed-field gel electrophoresis
      experiments scanning megabase regions of DNA. Some sites were totally unmethylated. The dam
      sites display variable methylation depending on the local sequence, and, in general, their
      methylation shows complex modulation by growth conditions and growth rate, suggesting multiple
      protection mechanisms. Sites resistant to complete dam or dcm methylation appear to be
      distributed throughout the chromosome. These unusual sites may identify regions of the
      chromosome with interesting biological functions.
AU  - Ringquist S
AU  - Smith CL
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1992 89: 4539-4543.

PMID- 23851394
VI  - 499
DP  - 2013
TI  - Insights into the phylogeny and coding potential of microbial dark matter.
PG  - 431-437
AB  - Genome sequencing enhances our understanding of the biological world by providing
      blueprints for the evolutionary and functional diversity that shapes the
      biosphere. However, microbial genomes that are currently available are of limited
      phylogenetic breadth, owing to our historical inability to cultivate most
      microorganisms in the laboratory. We apply single-cell genomics to target and
      sequence 201 uncultivated archaeal and bacterial cells from nine diverse habitats
      belonging to 29 major mostly uncharted branches of the tree of life, so-called
      'microbial dark matter'. With this additional genomic information, we are able to
      resolve many intra- and inter-phylum-level relationships and to propose two new
      superphyla. We uncover unexpected metabolic features that extend our
      understanding of biology and challenge established boundaries between the three
      domains of life. These include a novel amino acid use for the opal stop codon, an
      archaeal-type purine synthesis in Bacteria and complete sigma factors in Archaea
      similar to those in Bacteria. The single-cell genomes also served to
      phylogenetically anchor up to 20% of metagenomic reads in some habitats,
      facilitating organism-level interpretation of ecosystem function. This study
      greatly expands the genomic representation of the tree of life and provides a
      systematic step towards a better understanding of biological evolution on our
      planet.
AU  - Rinke C et al
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2013 499: 431-437.

PMID- 3028800
VI  - 163
DP  - 1987
TI  - Influence of N6-methylation of residue A(5) on the conformational behaviour of d(C-C-G-A-A-T-T-C-G-G) in solution studied by 1H-NMR spectroscopy 1. The duplex form.
PG  - 275-286
AB  - One- and two-dimensional NMR studies at 300 MHz and 500 MHz were carried out on
      the two oligonucleotides d(C-C-G-A-A-T-T-C-G-G) and d(C-C-G-A-m6A-T-T-C-G-G) in
      aqueous solution.  NMR spectra was observed at 10 mM sample concentration over
      the temperature range 273-368 K.  Assignments are given of the base, H1', H2',
      H2", H3' and of some H4' resonances, based upon a combination of
      two-dimensional correlation spectra (COSY) and two-dimensional nuclear
      Overhauser effect spectra (NOESY); imino-proton resonances were assigned with
      the aid of a two-dimensional NOE experiment.  Chemical shift vs temperature
      profiles were constructed in order to gain insight into the influence of
      N6-methylation of residue A(5) on the temperature-dependent conformational
      behaviour of the decamer and to determine thermodynamic parameters for the
      duplex-to-coil tranasition.  The NOESY spectra, the imino-proton spectra and
      the shift profiles of the two compounds, under conditions where each forms a
      B-DNA-type duplex, are very similar.  This is taken to indicate that the
      influence of N6-methylation of residue A(5) on the local structure of the
      duplex must be small.  However, the temperature dependence of the
      (non-)exchangeable proton resonances of the two compounds reveals that
      methylation slows down the duplex- single-strand exchange.  Furthermore, a
      thermodynamic analysis of the two compounds indicates that N6-methylation
      slightly decreases the stability of the duplex relative to the monomeric forms
      (Tm is reduced from 332 K down to 325 K at 10 mM sample concentration).
      Proton-proton couplings were obtained by means of one-dimensional and
      two-dimensional NMR experiments and were used in a conformational analysis of
      the sugar ring of each residue of the two compounds in the duplex form.  The
      analysis indicated that all sugar rings display conformational flexibility in
      the intact duplex:  population S-type sugar conformation ranges from 70% to
      100%. A more refined analysis of the sugar rings of the parent compound
      revealed a sequence-dependent variation of the sugar geometry.  This variation
      does not follow well the trend predicted by the Calladine/Dickerson Sigma3-sum
      rule [Dickerson, R.E.(1983).  J. Mol. Biol. 166, 419-441; Calladine, C.R.
      (1982) J. Mol. Biol. 161, 343-352}; moreover the actual variations appear to be
      smaller in solution than those expected on the basis of known X-ray structures.
AU  - Rinkel LJ
AU  - van der Marel GA
AU  - van Boom JH
AU  - Altona C
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1987 163: 275-286.

PMID- 26893410
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Shewanella sp. Strain P1-14-1, a Bacterial Inducer of Settlement and Morphogenesis in Larvae of the Marine Hydroid Hydractinia  echinata.
PG  - e00003-16
AB  - The assembly and annotation of the draft genome sequence of Shewanella sp. strain P1-14-1 are
      reported here to investigate the genes responsible for interkingdom
      interactions, secondary metabolite production, and microbial electrogenesis.
AU  - Rischer M
AU  - Klassen JL
AU  - Wolf T
AU  - Guo H
AU  - Shelest E
AU  - Clardy J
AU  - Beemelmanns C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00003-16.

PMID- 4375200
VI  - 89
DP  - 1974
TI  - Action of Escherichia coli P1 restriction endonuclease on Simian Virus 40 DNA.
PG  - 517-544
AB  - The P1 restriction endonuclease prepared from a P1 lysogen of Escherichia coli makes one
      double-strand break in simian virus (SV40) DNA.  In the presence of cofactors
      S-adenosylmethionine and ATP the enzyme cleaves 70% of the closed circular SV40 DNA molecules
      once to produce unit-length linear molecules and renders the remaining 30% resistant to
      further cleavage.  No molecules were found by electron microscopy or by gel electrophoresis
      that were cleaved more than once.  It would appear that the double-strand break is made by two
      nearly simultaneous single-strand breaks, since no circular DNA molecules containing one
      single-strand break were found as intermediates during the cleavage reaction.  The EcoP1
      endonuclease-cleaved linear SV40 DNA molecules are not cleaved at a unique site, as shown by
      the generation of about 65% circular molecules after denaturation and renaturation.  These
      EcoP1 endonuclease-cleaved, renatured circular molecules are resistant to further cleavage by
      EcoP1 endonuclease.  The EcoP1 endonuclease cleavage sites on SV40 DNA were mapped relative to
      the partial denaturation map and to the EcoRI and HpaII restriction endonuclease cleavage
      sites.  These maps suggest there are a minimum of four unique but widely space cleavage sites
      at 0.09, 0.19, 0.52, and 0.66 SV40 units relative to the EcoRI site.  The frequency of
      cleavage at any particular site differs from that at another site.  If S-adenosylmethionine is
      omitted from the enzyme reaction mix, SV40 DNA is cleaved into several fragments.  An average
      of 4.6 +/- 1 methyl groups are transferred to SV40 DNA from S-adenosylmethionine during the
      course of a normal reaction containing the cofactors.  Under conditions which optimize this
      methylation, 7 +/- 1 methyl groups can be transferred to DNA.  This methylation protects most
      of the molecules from further cleavage.  he methyl groups were mapped relative to the
      Hemophilus influenzae restriction endonuclease fragments.  The A fragment receives three to
      four methyl groups and the B and G fragments each receive one to two methyl groups.  These
      fragments correspond to those in which cleavage sites are located.
AU  - Risser R
AU  - Hopkins N
AU  - Davis RW
AU  - Delius H
AU  - Mulder C
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1974 89: 517-544.

PMID- 2842672
VI  - 194
DP  - 1988
TI  - A mutation in the DNA adenine methylase gene (dam) of Salmonella typhimurium decreases susceptibility to 9-aminoacridine-induced frameshift mutagenesis.
PG  - 131-141
AB  - A mutant of Salmonella typhimurium with a reduced response to mutation
      induction by 9-aminoacridine (9AA) has been isolated.  The mutation (dam-2) is
      located in the DNA adenine methylase gene.  The dam-2 mutant strain exhibits a
      level of sensitivity to 2-aminopurine (2AP) intermediate between that of the
      dam+ and the DNA adenine methylation-deficit dam-1 strain, and 2AP sensitivity
      was reversed by introduction of a mutH mutation or of the plasmid pMQ148 (which
      carries a functional Escherichia coli dam+ gene).  However, the dam-2 strain is
      not grossly defective in DNA adenine methylase activity.  Whole cell DNA
      appears full methylated at -GATC- sites.  The levels of 9AA required to induce
      equivalent levels of frameshift mutagenesis in the dam-2 strain were
      approximately 2-fold higher than for the dam+ strain.  Introduction of pMQ148
      dam+ reduced the level of 9AA required for induction of frameshift mutations
      4-fold in the dam-2 strain and 2-fold in the dam+ strain.  The dam-2 mutation
      had no effect on the levels of ICR191 required for induction of frameshift
      mutations, but introduction of pMQ148 reduced the ICR191-induced mutagenesis
      2-fold.  The dam+/pMQ148, dam-2/pMQ148 and dam-1/pMQ148 strains showed
      identical dose-response curves for both 9AA and ICR191.  These results are
      consistent with a slightly reduced (dam-2) or increased (pMQ148) rate of
      methylation at the replication fork.  The 2AP sensitivity of the dam-2 strain
      cannot be simply explained.  Furthermore, addition of methionine to the assay
      medium reverses the 2AP sensitivity of the dam-2 strain, but has no effect on
      9AA mutagenesis.
AU  - Ritchie L
AU  - Podger DM
AU  - Hall RM
PT  - Journal Article
TA  - Mutat. Res.
JT  - Mutat. Res.
SO  - Mutat. Res. 1988 194: 131-141.

PMID- 3522556
VI  - 167
DP  - 1986
TI  - Mutant of Salmonella typhimurium LT2 deficient in DNA adenine methylation.
PG  - 420-422
AB  - A mutant of Salmonella typhimurium LT2 deficient in methylation of the adenine residues in the
      sequence 5'-GATC-3' was isolated.  The mutation (dam-1) was linked to the cysG locus, and
      the properties of the mutant were similar to those of Escherichia coli dam mutants.  Reversion
      of the hisC3076 frameshift marker by 9-aminoacridine was substantially enhanced by the dam-1
      mutation, implying a direct role for adenine methylation in the prevention of frameshift
      mutation induction.
AU  - Ritchie LJ
AU  - Hall RM
AU  - Podger DM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1986 167: 420-422.

PMID- 2155857
VI  - 86
DP  - 1990
TI  - DNA methylation in Neisseria gonorrhoeae and other Neisseriae.
PG  - 103-106
AB  - It has been reported in the literature that Neisseria gonorrhoeae DNA is modified by the
      methyltransferases (MTases) M.NgoI, M.NgoII, and M.NgoIII, as well as three other cytosine
      MTases and one adenine MTase, even if the corresponding restriction endonucleases are not
      present.  We envisioned the possibility of cloning one of the N. gonorrhoeae MTase-encoding
      genes for use as a species-specific DNA probe.  We therefore undertook a survey of methylation
      patterns of several clinical isolates of N. gonorrhoeae and N. meningitidis as well as ATCC
      strains of other Neisseriae.  We found, from digestion patterns with isoschizomers, one N.
      gonorrhoeae strain that lacked M.NgoII and two that lacked M.NgoIII.  All N. meningitidis
      strains (save one) were resistant to digestion with NlaIV thus possessing an MTase like NgoV,
      and one was resistant to SstII, thus having an NgoIII-like MTase.  None were resistant to
      isoschizomers of NgoI, NgoIII and NgoIV.  Some other Neisseriae had an MTase with NlaIV (NgoV)
      specificity, but none had NgoI, NgoIV, NgoII or NgoIII specificity, except for the
      Branhamella-like N. caviae-ovis group and N. lactamica where these specificities were present
      in at least one strain of this group.  Therefore, among the Neisseriae other than N. caviae
      only M.NgoI is N. gonorrhoeae-specific.
      [ The enzyme called NgoI in this abstract has been renamed NgoWI, Jan/1998. ]
      [ The enzyme called NgoII in this abstract has been renamed NgoCII, Jan/1998. ]
      [ The enzyme called NgoIII in this abstract has been renamed NgoKIII, Jan/1998. ]
AU  - Ritchot N
AU  - Roy PH
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1990 86: 103-106.

PMID- 18640997
VI  - 59
DP  - 2008
TI  - Isolation and expression analysis of genes encoding MET, CMT, and DRM methyltransferases in oil palm (Elaeis guineensis Jacq.) in relation to the mantled somaclonal variation.
PG  - 3271-3281
AB  - In oil palm (Elaeis guineensis Jacq.), 5% of somatic embryo-derived regenerants show homeotic
      changes during floral development, involving
      an apparent feminization of male parts in flowers of both sexes, called
      the 'mantled' phenotype. This variant phenotype is associated with a
      reduction in the level of global DNA methylation. To explore possible
      relationships between DNA methylation level and accumulation of
      DNA-(cytosine-5) methyltransferase (DNMT) transcripts, the full-length
      coding sequences corresponding to three different DNMT families in oil
      palm, namely the MET, CMT, and DRM classes, have been isolated and
      characterized. The corresponding genes were designated as EgMET1,
      EgCMT1, and EgDRM1, and encode predicted polypeptides of 1543, 925, and
      591 amino acid residues, respectively. Expression of oil palm DNMTs was
      compared between normal and variant calli and in florescence tissues
      using quantitative reverse-transcription PCR. A consistent increase in
      transcript levels of EgMET1 and EgCMT1 was found in variant
      fast-growing calli relative to nodular-compact calli. Nodular-compact
      calli give rise to about 5% of abnormal regenerants whereas
      fast-growing calli generate 95% of 'mantled' palms in their clonal
      offspring and were previously demonstrated as having markedly
      hypomethylated DNA. In immature abnormal in florescences only EgMET1
      transcript levels were increased, while no changes in relative
      abundance of the EgCMT1 or EgDRM1 transcripts were observed.
AU  - Rival A
AU  - Jaligot E
AU  - Beule T
AU  - Finnegan EJ
PT  - Journal Article
TA  - J. Exp. Bot.
JT  - J. Exp. Bot.
SO  - J. Exp. Bot. 2008 59: 3271-3281.

PMID- 25059863
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of the Model Rhizosphere Strain Azospirillum brasilense  Az39, Successfully Applied in Agriculture.
PG  - e00683-14
AB  - We present the complete genome sequence of Azospirillum brasilense Az39, isolated from wheat
      roots in the central region of Argentina and used as inoculant in
      extensive and intensive agriculture during the last four decades. The genome
      consists of 7.39 Mb, distributed in six replicons: one chromosome, three
      chromids, and two plasmids.
AU  - Rivera D
AU  - Revale S
AU  - Molina R
AU  - Gualpa J
AU  - Puente M
AU  - Maroniche G
AU  - Paris G
AU  - Baker D
AU  - Clavijo B
AU  - McLay K
AU  - Spaepen S
AU  - Perticari A
AU  - Vazquez M
AU  - Wisniewski-Dye F
AU  - Watkins C
AU  - Martinez-Abarca F
AU  - Vanderleyden J
AU  - Cassan F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00683-14.

PMID- 25377708
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Leuconostoc mesenteroides P45 Isolated from Pulque, a Traditional Mexican Alcoholic Fermented Beverage.
PG  - e01130-14
AB  - Leuconostoc mesenteroides P45 was isolated from the traditional Mexican pulque beverage. We
      report its draft genome sequence, assembled in 6 contigs consisting
      of 1,874,188 bp and no plasmids. Genome annotation predicted a total of 1,800
      genes, 1,687 coding sequences, 52 pseudogenes, 9 rRNAs, 51 tRNAs, 1 noncoding
      RNA, and 44 frameshifted genes.
AU  - Riveros-Mckay F
AU  - Campos I
AU  - Giles-Gomez M
AU  - Bolivar F
AU  - Escalante A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01130-14.

PMID- 25780504
VI  - 9
DP  - 2014
TI  - An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3.
PG  - 11
AB  - When the genome of Ruegeria pomeroyi DSS-3 was published in 2004, it represented  the first
      sequence from a heterotrophic marine bacterium. Over the last ten
      years, the strain has become a valuable model for understanding the cycling of
      sulfur and carbon in the ocean. To ensure that this genome remains useful, we
      have updated 69 genes to incorporate functional annotations based on new
      experimental data, and improved the identification of 120 protein-coding regions
      based on proteomic and transcriptomic data. We review the progress made in
      understanding the biology of R. pomeroyi DSS-3 and list the changes made to the
      genome.
AU  - Rivers AR
AU  - Smith CB
AU  - Moran MA
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 11.

PMID- 28705960
VI  - 5
DP  - 2017
TI  - Draft Whole-Genome Assemblies of Drug-Resistant Clinical Isolates of Klebsiella pneumoniae from the Philippines.
PG  - e00475-17
AB  - Here, we report the draft assemblies of 11 clinical isolates of Klebsiella pneumoniae that are
      resistant to cephalosporins, carbapenems, and/or colistin.
      The assemblies ranged from 5.37 Mbp to 5.70 Mbp in size. Several plasmid
      sequences were present, and resistance genes spanning multiple classes of
      antibiotics were predicted.
AU  - Roa MB
AU  - Liles VR
AU  - Torres BC
AU  - Klinzing DC
AU  - Lagamayo E
AU  - Navoa-Ng J
AU  - Daroy MLG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00475-17.

PMID- 21256016
VI  - 21
DP  - 2011
TI  - Redox-Responsive Zinc Finger Fidelity Switch in Homing Endonuclease and  Intron Promiscuity in Oxidative Stress.
PG  - 243-248
AB  - It is well understood how mobile introns home to allelic sites, but how
      they are stimulated to transpose to ectopic locations on an
      evolutionary timescale is unclear [1]. Here we show that a group I
      intron can move to degenerate sites under oxidizing conditions. The
      phage T4 td intron endonuclease, I-Tevl, is responsible for this
      infidelity. We demonstrate that I-Tevl, which promotes mobility and is
      subject to autorepression [2] and translational control [3], is also
      regulated posttranslationally by a redox mechanism. Redox regulation is
      exercised by a zinc finger (ZF) in a linker that connects the catalytic
      domain of I-Tevl to the DNA binding domain. Four cysteines coordinate
      Zn2+ in the ZF, which ensures that I-Tevl cleaves its DNA substrate at
      a fixed distance, 23-25 nucleotides upstream of the intron insertion
      site [4]. We show that the fidelity of I-Tevl cleavage is controlled by
      redox-responsive Zn2+ cycling. When the ZF is mutated, or after
      exposure of the wild-type I-Tevl to H2O2, intron homing to degenerate
      sites is increased, likely because of indiscriminate DNA cleavage.
      These results suggest a mechanism for rapid intron dispersal, joining
      recent descriptions of the activation of biomolecular processes by
      oxidative stress through cysteine chemistry [5, 6].
AU  - Robbins JB
AU  - Smith D
AU  - Belfort M
PT  - Journal Article
TA  - Curr. Biol.
JT  - Curr. Biol.
SO  - Curr. Biol. 2011 21: 243-248.

PMID- 17289754
VI  - 35
DP  - 2007
TI  - Homing endonuclease I-TevIII: dimerization as a means to a double-strand break.
PG  - 1589-1600
AB  - Homing endonucleases are unusual enzymes, capable of recognizing lengthy DNA sequences and
      cleaving site-specifically within genomes. Many homing
      endonucleases are encoded within group I introns, and such enzymes promote
      the mobility reactions of these introns. Phage T4 has three group I
      introns, within the td, nrdB and nrdD genes. The td and nrdD introns are
      mobile, whereas the nrdB intron is not. Phage RB3 is a close relative of
      T4 and has a lengthier nrdB intron. Here, we describe I-TevIII, the H-N-H
      endonuclease encoded by the RB3 nrdB intron. In contrast to previous
      reports, we demonstrate that this intron is mobile, and that this mobility
      is dependent on I-TevIII, which generates 2-nt 3' extensions. The enzyme
      has a distinct catalytic domain, which contains the H-N-H motif, and
      DNA-binding domain, which contains two zinc fingers required for
      interaction with the DNA substrate. Most importantly, I-TevIII, unlike the
      H-N-H endonucleases described so far, makes a double-strand break on the
      DNA homing site by acting as a dimer. Through deletion analysis, the
      dimerization interface was mapped to the DNA-binding domain. The unusual
      propensity of I-TevIII to dimerize to achieve cleavage of both DNA strands
      underscores the versatility of the H-N-H enzyme family.
AU  - Robbins JB
AU  - Stapleton M
AU  - Stanger MJ
AU  - Smith D
AU  - Dansereau JT
AU  - Derbyshire V
AU  - Belfort M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2007 35: 1589-1600.

PMID- 27587819
VI  - 4
DP  - 2016
TI  - High-Quality Draft Genome Sequences of Two Xanthomonas Pathotype Strains Infecting Aroid Plants.
PG  - e00902-16
AB  - We present here the draft genome sequences of bacterial pathogens of the Araceae  family,
      Xanthomonas axonopodis pv. dieffenbachiae LMG 695 and Xanthomonas
      campestris pv. syngonii LMG 9055, differing in host range. A comparison between
      genome sequences will help understand the mechanisms involved in tissue
      specificity and adaptation to host plants.
AU  - Robene I
AU  - Bolot S
AU  - Pruvost O
AU  - Arlat M
AU  - Noel LD
AU  - Carrere S
AU  - Jacques MA
AU  - Koebnik R
AU  - Gagnevin L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00902-16.

PMID- 27856584
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Robinsoniella peoriensis 6600698, a Confounder of Clostridium difficile Diagnosis.
PG  - e01275-16
AB  - Robinsoniella peoriensis is a Gram-positive, strictly anaerobic, spore-forming, rod-shaped
      organism. Here, we report the draft genome of R. peoriensis 6600698,
      initially classified as Clostridium difficile due to growth on selective agar, a
      fecal gdh PCR-positive result, and clinical symptoms. R. peoriensis is a
      potential confounder of C. difficile diagnosis.
AU  - Roberts CH
AU  - Shaw HA
AU  - Ferguson N
AU  - Holland M
AU  - Wren BW
AU  - Stabler RA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01275-16.

PMID- 3000598
VI  - 43
DP  - 1985
TI  - IS10 transposition is regulated by DNA adenine methylation.
PG  - 117-130
AB  - We show that dam- mutants are a major class of E. coli mutants with increased IS10 activity.
      IS10 has two dam methylation sites, one within the transposase
      promoter and one within the inner terminus where transposase presumably binds.
      Absence of methylation results in increased activity of both promoter and
      terminus, and completely accounts for increased transposition in dam- strains.
      Transposition of Tn903 and Tn5 are also increased in dam- strains, probably for
      analogous reasons. Transposition is also increased when IS10 is hemimethylated.
      One hemimethylated species is much more active than the other and is estimated to
      be at least 1000 times more active than a fully methylated element. Evidence is
      presented that the promoter and inner terminus of IS10 are coordinately activated
      in a dam-dependent fashion, presumably because they are hemimethylated at the
      same time. Thus, in dam+ strains, IS10 will transpose preferentially when DNA is
      hemimethylated. We suggest specifically that IS10 transposition may
      preferentially occur immediately after passage of a chromosomal replication fork.
AU  - Roberts D
AU  - Hoopes BC
AU  - McClure WR
AU  - Kleckner N
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1985 43: 117-130.

PMID- 23910724
VI  - 280
DP  - 2013
TI  - Mutations of the domain forming the dimeric interface of the ArdA protein affect dimerization and antimodification activity but not antirestriction activity.
PG  - 4903-4914
AB  - ArdA antirestriction proteins are encoded by genes present in many conjugative plasmids and
      transposons within bacterial genomes. Antirestriction is the ability to prevent cleavage of
      foreign incoming DNA by restriction-modification (RM) systems. Antimodification, the ability
      to inhibit modification by the RM system, can also be observed with some antirestriction
      proteins. As these mobile genetic elements can transfer antibiotic resistance genes, the ArdA
      proteins assist their spread. The consequenc of antirestriction is therefore the enhanced
      dissemination of mobile genetic elements. ArdA proteins cause antirestriction by mimicking the
      DNA structure bound by TypeI RM enzymes. The crystal structure of ArdA showed it to be a
      dimeric protein with a highly elongated curved cylindrical shape [McMahon SA etal. (2009)
      Nucleic Acids Res 37, 4887-4897]. Each monomer has three domains covered with negatively
      charged side chains and a very small interface with the other monomer. We investigated the
      role of the domain forming the dimer interface for ArdA activity via site-directed
      mutagenesis. The antirestriction activity of ArdA was maintained when up to seven mutations
      per monomer were made or the interface was disrupted such that the protein could only exist as
      a monomer. The antimodification activity of ArdA was lost upon mutation of this domain. The
      ability of the monomeric form of ArdA to function in antirestriction suggests, first, that it
      can bind independently to the restriction subunit or the modificat ion subunits of the RM
      enzyme, and second, that the many ArdA homologues with long amino acid extensions, present in
      sequence databases, may be active in antirestriction.Structured digital abstract ArdA and ArdA
      bind by molecular sieving (1, 2) ArdA and ArdA bind by cosedimentation in solution (1, 2)
AU  - Roberts GA
AU  - Chen K
AU  - Bower EKM
AU  - Madrzak J
AU  - Woods A
AU  - Barker AM
AU  - Cooper LP
AU  - White JH
AU  - Blakely GW
AU  - Manfield I
AU  - Dryden DTF
PT  - Journal Article
TA  - FEBS J.
JT  - FEBS J.
SO  - FEBS J. 2013 280: 4903-4914.

PMID- 23002145
VI  - 40
DP  - 2012
TI  - Removal of a frameshift between the hsdM and hsdS genes of the EcoKI Type IA DNA  restriction and modification system produces a new type of system and links the  different families of Type I systems.
PG  - 10916-10924
AB  - The EcoKI DNA methyltransferase is a trimeric protein comprised of two modification subunits
      (M) and one sequence specificity subunit (S). This enzyme
      forms the core of the EcoKI restriction/modification (RM) enzyme. The 3' end of
      the gene encoding the M subunit overlaps by 1 nt the start of the gene for the S
      subunit. Translation from the two different open reading frames is
      translationally coupled. Mutagenesis to remove the frameshift and fuse the two
      subunits together produces a functional RM enzyme in vivo with the same
      properties as the natural EcoKI system. The fusion protein can be purified and
      forms an active restriction enzyme upon addition of restriction subunits and of
      additional M subunit. The Type I RM systems are grouped into families, IA to IE,
      defined by complementation, hybridization and sequence similarity. The fusion
      protein forms an evolutionary intermediate form lying between the Type IA family
      of RM enzymes and the Type IB family of RM enzymes which have the frameshift
      located at a different part of the gene sequence.
AU  - Roberts GA
AU  - Chen K
AU  - Cooper LP
AU  - White JH
AU  - Blakely GW
AU  - Dryden DT
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: 10916-10924.

PMID- 21685455
VI  - 39
DP  - 2011
TI  - An investigation of the structural requirements for ATP hydrolysis and DNA cleavage by the EcoKI Type I DNA restriction and modification enzyme.
PG  - 7667-7676
AB  - Type I DNA restriction/modification systems are oligomeric enzymes capable of switching
      between a methyltransferase function on hemimethylated host
      DNA and an endonuclease function on unmethylated foreign DNA. They have
      long been believed to not turnover as endonucleases with the enzyme
      becoming inactive after cleavage. Cleavage is preceded and followed by
      extensive ATP hydrolysis and DNA translocation. A role for dissociation of
      subunits to allow their reuse has been proposed for the EcoR124I enzyme.
      The EcoKI enzyme is a stable assembly in the absence of DNA, so recycling
      was thought impossible. Here, we demonstrate that EcoKI becomes unstable
      on long unmethylated DNA; reuse of the methyltransferase subunits is
      possible so that restriction proceeds until the restriction subunits have
      been depleted. We observed that RecBCD exonuclease halts restriction and
      does not assist recycling. We examined the DNA structure required to
      initiate ATP hydrolysis by EcoKI and find that a 21-bp duplex with
      single-stranded extensions of 12 bases on either side of the target
      sequence is sufficient to support hydrolysis. Lastly, we discuss whether
      turnover is an evolutionary requirement for restriction, show that the ATP
      hydrolysis is not deleterious to the host cell and discuss how foreign DNA
      occasionally becomes fully methylated by these systems.
AU  - Roberts GA
AU  - Cooper LP
AU  - White JH
AU  - Su TJ
AU  - Zipprich JT
AU  - Geary P
AU  - Kennedy C
AU  - Dryden DT
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2011 39: 7667-7676.

PMID- 23771140
VI  - 41
DP  - 2013
TI  - Impact of target site distribution for Type I restriction enzymes on the evolution of methicillin-resistant Staphylococcus aureus (MRSA) populations.
PG  - 7472-7484
AB  - A limited number of Methicillin-resistant Staphylococcus aureus (MRSA) clones are responsible
      for MRSA infections worldwide, and those of different lineages carry
      unique Type I restriction-modification (RM) variants. We have identified the
      specific DNA sequence targets for the dominant MRSA lineages CC1, CC5, CC8 and
      ST239. We experimentally demonstrate that this RM system is sufficient to block
      horizontal gene transfer between clinically important MRSA, confirming the
      bioinformatic evidence that each lineage is evolving independently. Target sites
      are distributed randomly in S. aureus genomes, except in a set of large
      conjugative plasmids encoding resistance genes that show evidence of spreading
      between two successful MRSA lineages. This analysis of the identification and
      distribution of target sites explains evolutionary patterns in a pathogenic
      bacterium. We show that a lack of specific target sites enables plasmids to evade
      the Type I RM system thereby contributing to the evolution of increasingly
      resistant community and hospital MRSA.
AU  - Roberts GA
AU  - Houston PJ
AU  - White JH
AU  - Chen K
AU  - Stephanou AS
AU  - Cooper LP
AU  - Dryden DT
AU  - Lindsay JA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2013 41: 7472-7484.

PMID- 22684506
VI  - 40
DP  - 2012
TI  - Exploring the DNA mimicry of the Ocr protein of phage T7.
PG  - 8129-8143
AB  - DNA mimic proteins have evolved to control DNA-binding proteins by competing with the target
      DNA for binding to the protein. The Ocr protein of bacteriophage T7 is
      the most studied DNA mimic and functions to block the DNA-binding groove of Type
      I DNA restriction/modification enzymes. This binding prevents the enzyme from
      cleaving invading phage DNA. Each 116 amino acid monomer of the Ocr dimer has an
      unusual amino acid composition with 34 negatively charged side chains but only 6
      positively charged side chains. Extensive mutagenesis of the charges of Ocr
      revealed a regression of Ocr activity from wild-type activity to partial activity
      then to variants inactive in antirestriction but deleterious for cell viability
      and lastly to totally inactive variants with no deleterious effect on cell
      viability. Throughout the mutagenesis the Ocr mutant proteins retained their
      folding. Our results show that the extreme bias in charged amino acids is not
      necessary for antirestriction activity but that less charged variants can affect
      cell viability by leading to restriction proficient but modification deficient
      cell phenotypes.
AU  - Roberts GA
AU  - Stephanou AS
AU  - Kanwar N
AU  - Dawson A
AU  - Cooper LP
AU  - Chen K
AU  - Nutley M
AU  - Cooper A
AU  - Blakely GW
AU  - Dryden DT
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: 8129-8143.

PMID- 14972552
VI  - 318
DP  - 2004
TI  - The genome and proteome of coliphage T1.
PG  - 245-266
AB  - The genome of enterobacterial phage T1 has been sequenced, revealing that
      its 50.7-kb terminally redundant, circularly permuted sequence contains
      48,836 bp of nonredundant nucleotides. Seventy-seven open reading frames
      (ORFs) were identified, with a high percentage of small genes located at
      the termini of the genomes displaying no homology to existing phage or
      prophage proteins. Of the genes showing homologs (47%), we identified
      those involved in host DNA degradation (three endonucleases) and T1
      replication (DNA helicase, primase, and single-stranded DNA-binding
      proteins) and recombination (RecE and Erf homologs). While the tail genes
      showed homology to those from temperate coliphage N15, the capsid
      biosynthetic genes were unique. Phage proteins were resolved by 2D gel
      electrophoresis, and mass spectrometry was used to identify several of the
      spots including the major head, portal, and tail proteins, thus verifying
      the annotation.
AU  - Roberts MD
AU  - Martin NL
AU  - Kropinski AM
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 2004 318: 245-266.

PMID- 
VI  - 0
DP  - 2008
TI  - Restriction and modification enzymes and their recognition sequences.
PG  - 215-216
AB  - 
AU  - Roberts RJ
PT  - Journal Article
TA  - Life Illuminated
JT  - Life Illuminated
SO  - Life Illuminated 2008 0: 215-216.

PMID- 
VI  - 
DP  - 1998
TI  - Restriction enzymes.
PG  - 379-397
AB  - A summary of the properties of the commercially available Type II restriction enzymes,
      including digestion conditions. The information in this list is taken from Roberts, R.J. and
      Macelis, D. (1996) 24, 223-235 plus updates from REBASE, the restriction enzyme database (URL
      - http://www.neb.com/rebase).
AU  - Roberts RJ
PT  - Journal Article
TA  - Molecular Genetic Analysis of Populations: A Practical Approach
JT  - Molecular Genetic Analysis of Populations: A Practical Approach
SO  - Molecular Genetic Analysis of Populations: A Practical Approach 1998 : 379-397.

PMID- 
VI  - 0
DP  - 1985
TI  - Restriction enzymes.
PG  - 203-210
AB  - Restriction enzymes are endodeoxyribonucleases that recognise short, specific
      sequences within DNA molecules and then catalyse double-strand cleavage of the
      DNA.  Three distinct classes of restriction enzymes are known:  Type I, Type
      II, Type III.  In this Appendix, restriction enzymes and their isoschizomers
      are listed alphabetically by prototype.  Their availability from three major
      commercial sources is indicated, as are the buffer conditions recommended by
      the manufacturer.  It should be noted that for most restriction enzymes, their
      activity varies little over a wide range of ionic strength and pH, and the
      values listed in general have not rigorously been shown to be optimal.  The
      information in this list is taken from Roberts, R.J. Nucleic Acids Res. (1984)
      12, r167-r204, and the New England Biolabs catalogue (1984 edition).
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acid Hybridisation: A Practical Approach
JT  - Nucleic Acid Hybridisation: A Practical Approach
SO  - Nucleic Acid Hybridisation: A Practical Approach 1985 0: 203-210.

PMID- 
VI  - 0
DP  - 1992
TI  - Restriction enzymes.
PG  - 281-296
AB  - Restriction enzymes are endodeoxyribonucleases that recognize short, specific
      sequences within DNA molecules and then catalyse double-strand cleavage of the
      DNA.  Three distinct classes of restriction enzymes are known: (a) Type I
      enzymes (b) Type II enzymes (c) Type III enzymes.  In this Appendix restriction
      enzymes and their isoschizomers are listed alphabetically by prototype.  Their
      availability from three major commercial sources is indicated, as are the
      buffer conditions recommended by the manufacturer.  It should be noted that for
      most restriction enzymes, their activity varies little over a wide range of
      ionic strength and pH, and the values listed in general have not rigorously
      been shown to be optimal.  The information in this list is taken from Roberts,
      R.J., Nucleic Acids Res. (1984), 12, r167=t204, and the New England Biolabs
      catalogue (1991 edition).
AU  - Roberts RJ
PT  - Journal Article
TA  - Molecular Genetic Analysis of Populations: A Practical Approach
JT  - Molecular Genetic Analysis of Populations: A Practical Approach
SO  - Molecular Genetic Analysis of Populations: A Practical Approach 1992 0: 281-296.

PMID- 
VI  - 0
DP  - 1978
TI  - Restriction endonucleases.
PG  - 5-9
AB  - None
AU  - Roberts RJ
PT  - Journal Article
TA  - Microbiology-1982
JT  - Microbiology-1982
SO  - Microbiology-1982 1978 0: 5-9.

PMID- 
VI  - 6
DP  - 1984
TI  - Restriction endonucleases, DNA sequencing and computers.
PG  - 305-316
AB  - Among the 250 TypeII restriction endonucleases now characterized, there are
      more than 70 different specificities and yet there is no indication that the
      range of specificities is exhausted.  Indeed, there is good reason to believe
      that hundreds, if not thousands, of different specificities would be found if a
      diligent search were carried out.  One reason for this speculation is
      illustrated in Table 1, which shows the range of sequence patterns with which
      different Type II restriction endonucleases interact.  Among the simple
      symmetric hexanucleotide sequences designated here as Class A, almost half of
      the possible sequence patterns are already represented by well-characterized
      enzymes.  There is no reason to believe that a similar number of enzymes will
      not be found for the other patterns in Classes B through F.  Similarly, it
      seems likely that enzymes recognizing degenerate patterns, like HgiAI and AccI,
      are not the sole representatives of the class.  Within the last year alone,
      five new classes (C,D,F,N., and O) were added to this list.
AU  - Roberts RJ
PT  - Journal Article
TA  - In Physics and Contemporary Needs
JT  - In Physics and Contemporary Needs
SO  - In Physics and Contemporary Needs 1984 6: 305-316.

PMID- 
VI  - 0
DP  - 1982
TI  - Restriction endonucleases.
PG  - 311-340
AB  - None
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleases
JT  - Nucleases
SO  - Nucleases 1982 0: 311-340.

PMID- 
VI  - 0
DP  - 1977
TI  - The role of restriction endonucleases in genetic engineering.
PG  - 21-32
AB  - The class II restriction endonucleases have played a key role in the
      development of recombinant DNA technology although, of the many enzymes now
      available, only EcoRI and HindIII have been used extensively.  This chapter
      describes some of the newly discovered restriction endonucleases which seem to
      provide alternative possibilities for genetic engineering and suggests schemes
      whereby the specificity of the nucleases can be exploited in the creation of
      new recombinant genomes.
AU  - Roberts RJ
PT  - Journal Article
TA  - In: Recombinant Molecules: Impact on Science Society
JT  - In: Recombinant Molecules: Impact on Science Society
SO  - In: Recombinant Molecules: Impact on Science Society 1977 0: 21-32.

PMID- 
VI  - 0
DP  - 1976
TI  - Restriction and modification enzymes and their recognition sequences.
PG  - 532-534
AB  - None
AU  - Roberts RJ
PT  - Journal Article
TA  - In Handbook of Biochemistry and Molecular Biology
JT  - In Handbook of Biochemistry and Molecular Biology
SO  - In Handbook of Biochemistry and Molecular Biology 1976 0: 532-534.

PMID- 
VI  - 0
DP  - 1977
TI  - Restriction and modification enzymes and their recognition sequences.
PG  - 757-768
AB  - None
AU  - Roberts RJ
PT  - Journal Article
TA  - DNA Insertion Elements, Plasmids, and Episomes.
JT  - DNA Insertion Elements, Plasmids, and Episomes.
SO  - DNA Insertion Elements, Plasmids, and Episomes. 1977 0: 757-768.

PMID- 
VI  - 166
DP  - 2000
TI  - Analysis of Restriction Modification systems from whole genome sequences.
PG  - A37
AB  - Until recently all of the 3200 restriction enzymes known to man had been found by obtaining
      bacteria from culture collections or environ-mental samples and assaying them biochemically
      and genetically.  During the last 15 years, many of these Restriction-Modification (RM)
      systems have been cloned and sequenced and it is now possible to use quite so-phisticated
      search algorithms to screen new DNA sequences for the presence of DNA methyltransferase genes.
      Experience among known systems has shown that restriction enzyme genes always lie close to
      their cognate methyltransferase genes.  Analysis of the bacterial and archaeal genome
      sequences shows that methyltransferase genes are more common than one would have expected on
      the basis of previous biochemical screening.  Frequently, they clearly form part of an RM
      system, because the adjacent open reading frames show similarity to known restriction enzyme
      genes.  Very often, though, the adjacent open reading frames have no homologs in GenBank and
      become candidates either for restriction enzymes with novel specificities or for new examples
      of previously uncloned specificities. We are developing methods to allow these candidate genes
      quickly to be tested biochemically. Initial results are promising and it seems clear that
      screening DNA sequence databases and websites will be a very productive method to find
      restriction enzymes with new specificities.
AU  - Roberts RJ
PT  - Journal Article
TA  - Abstracts AAAS Ann. Mtg.
JT  - Abstracts AAAS Ann. Mtg.
SO  - Abstracts AAAS Ann. Mtg. 2000 166: A37.

PMID- 
VI  - 280
DP  - 2013
TI  - Hans Krebs Lecture Bacterial methylomes.
PG  - 0
AB  - Bacterial DNA methyltransferases are best known as orphan enzymes such as the Dam methylase of
      E. coli or as components of restriction-modification systems.  Until recently, rigorously
      determining the specificity of MTases has been a tedious process.  When they were components
      of Type II restriction systems it has been assumed that the MTases would have the same
      specificity as the cognate restriction enzyme.  For Type I and Type III RM systems specificity
      determination was rarely attempted.  With the advent of SMRT sequencing from Pacific
      Biosciences this situation has changed dramatically.  Now it has become very simple to
      determine MTase recognition sequences both for individual MTases cloned in plasmids and also
      for whole bacterial genomes.  This offers new insights into the functioning of bacteria and
      has led to the discovery of several novel MTases with unexpected properties.
AU  - Roberts RJ
PT  - Journal Article
TA  - FEBS J.
JT  - FEBS J.
SO  - FEBS J. 2013 280: 0.

PMID- 15840723
VI  - 102
DP  - 2005
TI  - How restriction enzymes became the workhorses of molecular biology.
PG  - 5905-5908
AB  - Restriction enzymes have proved to be invaluable for the physical mapping of DNA. They offer
      unparalleled opportunities for diagnosing DNA sequence content and are used in fields as
      disparate as criminal forensics and basic research. In fact, without restriction enzymes, the
      biotechnology industry would certainly not have flourished as it has. The first experiments
      demonstrating the utility of restriction enzymes were carried out by Danna and Nathans and
      reported in 1971. This pioneering study set the stage for the modern practice of molecular
      biology in which restriction enzymes are ubiquitous tools, although they are often taken for
      granted.
AU  - Roberts RJ
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2005 102: 5905-5908.

PMID- 7833450
VI  - 14
DP  - 1994
TI  - An amazing distortion in DNA induced by a methyltransferase.
PG  - 103-117
AB  - republication of the Nobel lecture
AU  - Roberts RJ
PT  - Journal Article
TA  - Biosci. Rep.
JT  - Biosci. Rep.
SO  - Biosci. Rep. 1994 14: 103-117.

PMID- Not carried by PubMed...
VI  - 33
DP  - 1994
TI  - An amazing distortion in DNA induced by a methyltransferase (Nobel lecture).
PG  - 1222-1228
AB  - 
AU  - Roberts RJ
PT  - Journal Article
TA  - Angew. Chem. Int. Ed. Engl.
JT  - Angew. Chem. Int. Ed. Engl.
SO  - Angew. Chem. Int. Ed. Engl. 1994 33: 1222-1228.

PMID- 6246329
VI  - 65
DP  - 1980
TI  - Directory of restriction endonucleases.
PG  - 1-15
AB  - This article is intended to serve as a directory to the restriction endonucleases which have
      not been characterized.  All endonucleases which cleave DNA at a specific sequence have been
      considered to be restriction enzymes, although in most cases there is no direct genetic
      evidence for the presence of a host-controlled restriction-modification system.  Certain
      strains are omitted from the table to save space.  Thus the many different Staphylococcus
      aureus isolates which contain an isoschizomer of Sau3A are not listed individually.  Similarly
      the many strains of gliding bacteria (orders: Myxobacterales and Cytophagales) which showed
      evidence of specific endonucleases during a large-scale screening are still rather poorly
      characterized.  Within the table the source of each microorganism is given either as an
      individual or a National Culture Collection.  The enzymes are named in accordance with the
      proposal of Smith and Nathans.  When two enzymes recognize the same sequence (i.e., are
      isoschizomers), the prototype (i.e., the first example isolated) is indicated in parentheses
      in column 3 of the table.  The recognition sequences (column 4 of the table) are abbreviated
      so that only one strand, reading 5'-3', is indicated and the point of cleavage, when known,
      is indicated by an arrow.  When two bases appear in parentheses, either one may appear at that
      position within the recognition sequence.  Where known, the base modified by the corresponding
      methylase is indicated by an asterisk.  A* is N6-methyladenosine; C* is 5-methylcytosine.  The
      frequency of cleavage (columns five to eight) is experimentally determined for bacteriophage
      lambda and adenovirus-2 DNAs, but represents the computer-derived values from the published
      sequences of SV40 and PhiX174 DNAs.  When more than one reference appears (column 9 of the
      table), the first contains the purification procedure for the restriction enzyme, the second
      concerns its recognition sequence, the third contains the purification procedure for the
      methylase, and the fourth describes its recognition sequence.  In some cases two references
      appear in one of these categories when two independent groups have reached similar
      conclusions.
AU  - Roberts RJ
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1980 65: 1-15.

PMID- 232216
VI  - 68
DP  - 1979
TI  - Directory of restriction endonucleases.
PG  - 27-41
AB  - Table I is intended to serve as a directory to the restriction endonucleases
      that have now been characterized.  In forming the list, all endonucleases that
      cleave DNA at a specific sequence have been considered restriction enzymes,
      although in most cases there is no direct genetic evidence for the presence of
      a host-controlled restriction-modification system.  Certain strains have been
      omitted from this list to save space.  Thus the many different Staphylococcus
      aureus isolates containing an isoschizomer of Sau3A are not listed
      individually.  Similarly the numerous strains of gliding bacteria (orders
      Myxobacterales and Cytophagales) that showed evidence of specific endonucleases
      during a large-scale screening are still rather poorly characterized.  Within
      Table I the source of each microorganism is given either as an individual or a
      national culture collection.  The enzymes are named in accordance with the
      proposal of Smith and Nathans.
AU  - Roberts RJ
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1979 68: 27-41.

PMID- 340964
VI  - 271
DP  - 1978
TI  - Restriction endonucleases:  a new role in vivo?
PG  - 502
AB  - Few enzymes have been exploited as thoroughly as the bacterial restriction
      enzymes.  In recent years they have been instrumental in dramatic advances in
      DNA sequence analysis, genetic engineering, and studies of gene structure.
AU  - Roberts RJ
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1978 271: 502.

PMID- 360075
VI  - 275
DP  - 1978
TI  - The Nobel Prizewinners 1978: Medicine.
PG  - 689-690
AB  - The restriction endonucleases, which have become so familiar to the molecular
      biologist, have finally come of age with the award of this year's Nobel Prize
      in Physiology and Medicine to Dr. Werner Arber of the University of Basel and
      to Drs. Daniel Nathans and Hamilton O. Smith of Johns Hopkins University.  They
      each played a critical but separate role in drawing attention to these
      bacterial enzymes which dominate so much present research.
AU  - Roberts RJ
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1978 275: 689-690.

PMID- 6280143
VI  - 10
DP  - 1982
TI  - Restriction and modification enzymes and their recognition sequences.
PG  - r117-r144
AB  - Since the last compilation of restriction endonucleases, 97 new entries have been added,
      including 17 new specificities. Most notable among the new specificities is AhaIII (TTTAAA),
      which is the first restriction enzyme to recognize only A/T base pairs. Other valuable new
      specificities are ApaI (GGGCCC), AflII (CTTAAG), CfrI (PYGGCCPu), EcoRV (GATATC), FokI
      (GGATG), HgiJII (GPuGCPyC), MluI (ACGCGT), NdeI (CATATG), NaeI (GCCGGC), NarI (GGCGCC), NcoI
      (CCATGG), NruI (TCGCGA), NspBII (GCC/GGC), NspCI (PuCATGPy), ScrFI (CCNGG) and XmnI
      (GAA[N]4TTC). Two entries have been removed, RruI and RruII, because the strain producing them
      has been lost. Fortunately an isoschizomer of RruI has been found. This is ScaI (AGTACT).
      Among the 355 enzymes listed, there are a minimum of 85 different specificities.
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1982 10: r117-r144.

PMID- 6243774
VI  - 8
DP  - 1980
TI  - Restriction and modification enzymes and their recognition sequences.
PG  - r63-r80
AB  - Since the last compilation of restriction endonucleases, more than 30 Type II
      restriction endonucleases have been discovered, including some valuable new
      specificities.  These include AcyI (GPuCGPyC), DdeI (CTNAG), Fnu4HI (GCNGC),
      RsaI (GTAC), SphI (GCAGTC), and XmaIII (CGGCCG).  In addition, a number of new
      isoschizomers have been discovered and further information about the
      recognition sequences of some old entries is now available.  AvaX is renamed
      AvaIII.
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1980 8: r63-r80.

PMID- 2159140
VI  - 18
DP  - 1990
TI  - Restriction enzymes and their isoschizomers.
PG  - 2331-2365
AB  - A review
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 2331-2365.

PMID- 6328451
VI  - 12
DP  - 1984
TI  - Restriction and modification enzymes and their recognition sequences.
PG  - r167-r204
AB  - Since the last compilation of restriction endonucleases, 80 new entries have
      been added, including 12 new specificities.  These are Cfr101 (PuCCGGPy),
      Eco47III (AGCGCT), EcoA (GAG(N)7GTCA), MaeI (CTAG), MaeII (ACGT), MaeIII
      (GTNAC), NlaIII (CATG), NlaIV (GGNNCC), NotI (GCGGCCGC), SnaBI (TACGTA), ScaI
      (AGTACT) and SfiI (GGCCNNNNNGGCC).  NotI and SfiI are the first example of Type
      II enzymes that recognize octanucleotide sequences.  In addition to these two
      new sequence patterns, one additional new sequence pattern is recognized by
      NlaIV.  The first example of unusual methylation is provided in the BcnI system
      where the methylase protects by the formation of N4-methylcytosine.  Among the
      475 enzymes listed, there are a minimum of 103 different specificities.  New
      entries, together with new information about recognition sequences, are
      indicated (@).  In forming this list, all endonucleases cleaving DNA at a
      specific sequence have been considered to be restriction enzymes, although in
      most cases there is no direct genetic evidence for the presence of a
      restriction-modification system.  These endonucleases are named in accordance
      with the proposal of Smith and Nathans.  Within the table, the source of each
      microorganism is given either as an individual or a National Culture
      Collection.  If further information is required, it can be found either in the
      first reference which, in each case, refer to the purification procedure for
      the restriction enzyme, or from the individuals who have provided their
      unpublished results.  Where more than one reference appears, the second
      concerns the recognition sequence for the restriction enzyme, the third
      describes the purification procedure for the methylase and the fourth describes
      the recognition sequence of the methylase.  In some cases, several references
      appear in one of these categories when independent groups have reached similar
      conclusions.
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1984 12: r167-r204.

PMID- Not carried by PubMed...
VI  - 0
DP  - 1981
TI  - Restriction endonucleases, DNA sequencing, and computers.
PG  - 621-634
AB  - Among the 250 Type II restriction endonucleases now characterized, there are
      more than 70 different specificities and yet there is no indication that the
      range of specificities is exhausted.  Indeed, there is good reason to believe
      that hundreds, if not thousands, of different specificities would be found if a
      diligent search were carried out.
AU  - Roberts RJ
PT  - Journal Article
TA  - Developmental Biology Using Purified Genes
JT  - Developmental Biology Using Purified Genes
SO  - Developmental Biology Using Purified Genes 1981 0: 621-634.

PMID- 6245015
VI  - 8
DP  - 1980
TI  - Restriction and modification enzymes and their recognition sequences.
PG  - 329-343
AB  - Since the last compilation of restriction endonucleases, more than 30 type II
      restriction endonucleases have been discovered, including some with valuable
      new specificities.  These include AcyI (GPuCGPyC), AsuII (TTCGAA), DdeI
      (CTNAG), Fnu4HI (GCNGC), RsaI (GTAC), SphI (GCATGC) and XmaIII (CGGCCG).  In
      addition, a number of new isoschizomers have been discovered and further
      information about the recognition sequences of some old entries is now
      available.  AvaX is renamed AvaIII.  In forming this list, all endonucleases
      cleaving DNA at a specific sequence have been considered to be restriction
      enzymes although, in most cases, there is no direct genetic evidence for the
      presence of a restriction modification system.
AU  - Roberts RJ
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1980 8: 329-343.

PMID- 6259615
VI  - 9
DP  - 1981
TI  - Restriction and modification enzymes and their recognition sequences.
PG  - r75-r96
AB  - Since the last compilation of Type II restriction endonucleases, more than 45 new enzymes have
      been discovered. Among the valuable new specificities are GdiI and its isoschizomer StuI
      (AGGCCT), GdiII (PyGGCCG), HgiEII (ACC[N]6GGT), RruI (AGTACT), Tth111I and its isoschizomers
      TtrI and TteI (GACNNNGTC), and Tth111II (CAAPuCA). The new enzyme NciI (CC[G/C]GG) turns out
      to be an isoschizomer of CauII whose recognition has recently been determined. The recognition
      sequences of SnaI (GTATAC) and SauI (CDTNAGG) have also been newly determined. Among the 258
      enzymes listed, there are at least 69 different specificities. New entries, together with new
      information about recognition sequences, are indicated. .
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1981 9: r75-r96.

PMID- 369952
VI  - 4
DP  - 1978
TI  - Restriction and modification enzymes and their recognition sequences.
PG  - 183-193
AB  - During the last few years many bacterial strains have been examined for the
      presence of Type II restriction endonucleases and a large number of these
      enzymes have now been characterized.  Much of the information available has
      never been formally published.  While this reflects the lengthy time which can
      elapse between discovery and publication, increasingly it results from the fact
      that a newly discovered endonuclease is an isoschizomer of a more familiar one.
      Thtus, unless the new source offers some advantage, there is a natural trend
      to avoid formal publication.  To some extent, review articles fill this gap;
      however, they quickly become outdated.  The present compilation is an attempt
      to extend current awareness of the enzymes now available.
AU  - Roberts RJ
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1978 4: 183-193.

PMID- 3033611
VI  - 15
DP  - 1987
TI  - Restriction enzymes and their isoschizomers.
PG  - r189-r217
AB  - Since the last compilation of restriction enzymes, 251 new entries have been
      added including 21 new specificities.  With the growing size of this database
      and the recognition that the most widespread use of the information is as a
      database for computer programs predicting restriction enzyme cleavage patterns,
      a new format has been adopted.  This new format is intended to contain the
      minimal amount of information required by a computer program.  It should be
      noted that only enzymes for which the recognition sequence is known are
      included.
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1987 15: r189-r217.

PMID- 2851532
VI  - 5
DP  - 1987
TI  - Restriction and modification enzymes and their recognition sequence.
PG  - 1-49
AB  - Since the last published compilation of restriction endonucleases 130 new
      enzymes have been discovered, including many new specificities.  Especially
      noteworthy are the enzymes NotI (GCGGGCCGC) and SfiI (GGCCNNNNNGGCC) which are
      the first Type II enzymes to recognize octanucleotide sequences.  They have the
      useful property of cutting DNA sufficiently infrequently so that their sites
      provide useful landmarks for mapping bacterial genomes and eukaryotic
      chromosomes.  Among the 645 enzymes listed there are now a minimum of 137
      different specificities.  In forming this list all endonucleases cleaving DNA
      at a specific sequence have been considered to be restriction enzymes, although
      in most cases there is no direct genetic evidence for the presenece of a
      restriction-modification system.  These endonucleases are named in accordance
      with the proposal of Smith and Nathans.  Within the table the source of each
      microorganism is given either as an individual or a national culture
      collection.  If further information is required it can be found either in the
      first reference which in each case refers to the purification procedure for the
      restriction enzyme, or from the individuals who have provided their unpublished
      results.  Where more than one reference appears, the second concerns the
      recognition sequence for the restriction enzyme, the third describes the
      purification procedure for the methylase and the fourth describes the
      recognition sequence of the methylase.  In some cases, several references
      appear in one of these categories when independent groups have reached similar
      conclusions.
AU  - Roberts RJ
PT  - Journal Article
TA  - Gene Amplif. Anal.
JT  - Gene Amplif. Anal.
SO  - Gene Amplif. Anal. 1987 5: 1-49.

PMID- 2541417
VI  - 17
DP  - 1989
TI  - Restriction enzymes and their isoschizomers.
PG  - r347-r387
AB  - Since the last compilation of restriction enzymes (1), 156 new entries have
      been added including 12 new specificities.  With the growing size of this
      database and the recognition that the most widespread use of the information is
      as a database for computer programs predicting restriction enzyme cleavage
      patterns, the new format has been continued.  This format is intended to
      contain the minimal amount of information required by a computer program.  It
      should be noted that only enzymes for which the recognition sequence is known
      are included.  This new list is shown in the first Table, while an alphabetical
      listing of all Type II enzymes is presented in the second Table.  A copy of the
      restriction enzyme data base in its previous format (2), including enzymes of
      unknown recognition sequence, will be available upon request.  It should also
      be noted that an alternative compilation of these enzymes has recently been
      produced (3).
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: r347-r387.

PMID- 6306557
VI  - 11
DP  - 1983
TI  - Restriction and modification enzymes and their recognition sequences.
PG  - r135-r167
AB  - Since the last compilation of restriction endonucleases, 43 new entries have
      been added, including 6 new specificities.  These are AatII (GACGTC), AflIII
      (ACPuPyGT), BinI (GGATC), EcopDXI (ATCA(N)^ATTC), NspBII (C(A/C)GC(T/G)G and
      SduI (G(G/A/T)GC(C/A/T)C).  EcopDXI is the first example of a Type I enzyme
      that recognizes an octanucleotide sequence.  Both NspBII and SduI recognize
      sequence patterns that have not been described before.
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1983 11: r135-r167.

PMID- 2987885
VI  - 13
DP  - 1985
TI  - Restriction and modification enzymes and their recognition sequences.
PG  - r165-r200
AB  - Since the last compilation of restriction endonucleases forty-nine new entries
      have been added, including nine new specificities, these are DraII (PuGGNCCPy),
      DraIII (CACNNNGTG), EcoD (TTA(N)7GTCPy), EspI (GCTNAGC), NheI (GCTAGC), RsrII
      (CGG(A/T)CCG), StyI (CC(A/T)(A/T)GG), SspI (AATATT) and SpeI (ACTAGT).  In
      addition, the enzyme Asp718 is an interesting isoschizomer of KpnI.  It cleaves
      the recognition sequence to leave a 5' terminal extension instead of the 3'
      terminal extension left by KpnI.
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1985 13: r165-r200.

PMID- 2835753
VI  - 16
DP  - 1988
TI  - Restriction enzymes and their isoschizomers.
PG  - r271-r313
AB  - Since the last compilation of restriction enzymes, 156 new entries have been
      added including 12 new specificities.  With the growing size of this database
      and the recognition that the most widespread use of the information is as a
      database for computer programs predicting restriction enzyme cleavage patterns,
      the new format has been continued.  This format is intended to contain the
      minimal amount of information required by a computer program.  It should be
      noted that only enzymes for which the recognition sequence is known are
      included.  This new list is shown in the first Table, while an alphabetical
      listing of all Type II enzymes is presented in the second Table.  A copy of the
      restriction enzyme data base in its previous format, including enzymes of
      unknown recognition sequence, will be available upon request.  It should also
      be noted that an alternative compilation of these enzymes has recently been
      produced.  The database shown in these Tables is available online through the
      BIONET computer resource.  A version corresponding to the printed text is
      located in the file <ROBERTS>RESTRICT.NAR several alternative versions are
      available and are documented in <ROBERTS>RESTRICT.DOC  In forming this list,
      all endonucleases cleaving DNA at a specific sequence have been considered to
      be restriction enzymes, although in most cases there is no direct genetic
      evidence for the presence of a restriction-modification system.  The
      endonucleases are named in accordance with the proposal of Smith and Nathans.
      Several enzymes appear in this list with revised names.  These revisions were
      made to avoid confusion with existing enzymes or to increase the uniformity of
      the names.  In each case the name changes were made with the approval of the
      appropriate authors.
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1988 16: r271-r313.

PMID- 795607
VI  - 4
DP  - 1976
TI  - Restriction endonucleases.
PG  - 123-164
AB  - This review provides a comprehensive account of the current status of the biology and
      biochemistry of restriction endonucleases. Both Class I and Class II restriction endonucleases
      will be considered. However, emphasis will be placed on the Class II group, which recognizes
      and cleaves a specific duplex DNA sequence. Their occurrence, purification, and
      characterization is discussed in detail. The characterization includes physical mapping
      information and determination of recognition sequences. In addition to detailed discussions of
      the biochemical properties of the enzymes, considerable attention is paid to the uses of these
      enzymes as tools for research in molecular biology. These uses include physical mapping of
      genomes and their transcripts, genetic analysis (marker rescue, etc.), DNA sequence analysis,
      analysis of complex genomes, and genetic engineering. Specific examples of each use are
      outlined. Practical aspects of both the isolation and use of the restriction endonucleases
      form the major theme of this review.
AU  - Roberts RJ
PT  - Journal Article
TA  - CRC Crit. Rev. Biochem.
JT  - CRC Crit. Rev. Biochem.
SO  - CRC Crit. Rev. Biochem. 1976 4: 123-164.

PMID- 
VI  - 14
DP  - 2004
TI  - A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases, and their genes.
PG  - 1-18
AB  - There are three main groups of restriction endonucleases (REases) called Types I, II, and III.
      Since 1973, REases and DNA methyltransferases (MTases) have been named based on an original
      suggestion by Smith and Nathans.  They proposed that the enzyme names should begin with a
      three-letter acronym in which the first letter was the first letter of the genus from which
      the enzyme was isolated and the next two letters were the first two letters of the species
      name.  Extra letters or numbers could be added to indicate individual strains or serotypes.
      Thus, the enzyme HindII was one of four enzymes isolated from Haemophilus influenzae serotype
      d.  The first three letters of the name were italicized.  Later, a formal proposition for
      naming the genes encoding REases and MTases was adopted.  When there were only a handful of
      enzymes known, these schemes were very useful, but as more enzymes have been found, often from
      different genera and species with names whose three-letter acronyms would be identical,
      considerable laxity in naming conventions has appeared.  In addition, we now know that each
      major type of enzyme can contain subtypes.  This especially applies to the Type II enzymes, of
      which more than 3500 have been characterized.  In this paper we revisit the naming conventions
      and outline an updated scheme that incorporates current knowledge about the complexities of
      these enzymes.  We describe a set of naming conventions for REases and their associated
      MTases.  Since the homing endonucleases have been named in an analogous fashion, we proposed
      that similar guidelines be applied to that group of enzymes.  Finally, it is important to
      realize that the aim of this document is to provide a nomenclature for these enzymes, not to
      provide a rigorous classification.
AU  - Roberts RJ et al
PT  - Journal Article
TA  - Nucleic Acids Mol. Biol.
JT  - Nucleic Acids Mol. Biol.
SO  - Nucleic Acids Mol. Biol. 2004 14: 1-18.

PMID- 12654995
VI  - 31
DP  - 2003
TI  - A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes.
PG  - 1805-1812
AB  - A nomenclature is described for restriction endonucleases, DNA methyltransferases, homing
      endonucleases and related genes and gene
      products. It provides explicit categories for the many different Type II
      enzymes now identified and provides a system for naming the putative genes
      found by sequence analysis of microbial genomes.
AU  - Roberts RJ et al
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2003 31: 1805-1812.

PMID- 171410
VI  - 91
DP  - 1975
TI  - A second specific endonuclease from Haemophilus aegyptius.
PG  - 121-123
AB  - A second restriction-like endonuclease has been partially purified from
      Haemophilus aegyptius.  This enzyme cleaves bacteriophage lambda DNA and
      adenovirus 2 DNA at many sites, but cleaves simian virus 40 DNA at only one
      site.
AU  - Roberts RJ
AU  - Breitmeyer JB
AU  - Tabachnik NF
AU  - Myers PA
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1975 91: 121-123.

PMID- 9759487
VI  - 67
DP  - 1998
TI  - Base flipping.
PG  - 181-198
AB  - Base flipping is the phenomenon whereby a base in normal B-DNA is swung completely out of the
      helix into an extrahelical position.  It was discovered in 1994 when the first co-crystal
      structure was reported for a cytosine-5 DNA methyltransferase binding to DNA.  Since then it
      has been shown to occur in many systems where enzymes need access to a DNA base to perform
      chemistry on it.  Many DNA glycosylases that remove abnormal bases from DNA use this
      mechanism.  This review describes systems known to use base flipping as well as many systems
      where it is likely to occur but has not yet been rigorously demonstrated.  The mechanism and
      evolution of base flipping are also discussed.  A review.
AU  - Roberts RJ
AU  - Cheng X
PT  - Journal Article
TA  - Annu. Rev. Biochem.
JT  - Annu. Rev. Biochem.
SO  - Annu. Rev. Biochem. 1998 67: 181-198.

PMID- 
VI  - 0
DP  - 1993
TI  - Type II restriction enzymes.
PG  - 35-88
AB  - 

          I. Introduction and history

         II. Recognition sequences and cleavage properties

                  A. Type IIs enzymes

                  B. Degenerate recognition sequences

                  C. Unusual type II enzymes

                  D. Determination of cleavage sites

                  E. Effects of methylation

                  F. Single-stranded DNA cleavage

        III. Genes and their organization

                  A. Cloning

                  B. Genetic location

                  C. Sequences

         IV. DNA Binding

                  A. Enzymes that bind specifically to their recognition sites

                  B. Enzymes that fail to bind specifically to their recognition sites

                  C. Transfer to recognition sites

          V. DNA Cleavage

                  A. Plasmid substrates

                  B. Oligonucleotide substrates

                  C. Specificity

         VI. Crystallography

                  A. Protein structures

                  B. DNA structures

                  C. DNA-protein interfaces

        VII. Phosphodiester hydrolysis

       VIII. DNA recognition functions

                  A. Altered enzymes

                  B. Altered substrates

                  C. Coupling recognition to catalysis

         IX. Evolution

          X. Conclusions and future prospects

      

AU  - Roberts RJ
AU  - Halford SE
PT  - Journal Article
TA  - Nucleases
JT  - Nucleases
SO  - Nucleases 1993 0: 35-88.

PMID- 
VI  - 0
DP  - 1993
TI  - The restriction enzymes.
PG  - 439-444
AB  - 
AU  - Roberts RJ
AU  - Macelis D
PT  - Journal Article
TA  - Nucleases
JT  - Nucleases
SO  - Nucleases 1993 0: 439-444.

PMID- 1317958
VI  - 20
DP  - 1992
TI  - Restriction enzymes and their isoschizomers.
PG  - 2167-2180
AB  - The restriction enzyme database, REBASE, contains information about restriction enzymes and
      their associated methylases. Since the last description of the contents of REBASE, 204 new
      entries have been added including 5 new Type II enzymes and 4 new Type I enzymes. A complete
      list of these new enzymes can be found in Table I. A total of 2103 restriction enzymes are now
      known and include 17 different Type I specificities, 179 different Type II specificities and 4
      different Type III specificities. Table II contains a listing of all prototype restriction
      enzymes (Types I, II and III), together with their commercially available isoschizomers and
      neoschizomers that cleave at a position different from their prototype.
AU  - Roberts RJ
AU  - Macelis D
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 2167-2180.

PMID- 8392714
VI  - 21
DP  - 1993
TI  - REBASE-restriction enzymes and methylases.
PG  - 3125-3137
AB  - The restriction enzyme database, REBASE, is a collection of information about restriction
      enzymes and methylases. Since the last description of the contents of REBASE (1), 265 new
      entries have been added including 8 new Type II enzymes: AclI, AA^CGTT; Bce83I, CTTGAG
      (16/14); BscGI, CCCGT; BseRI, GAGGAG (10/8); Bsp1407I, T^GTACA; BspLU11I, A^CATGT; BsrDI,
      GCAATG (2/0) and SexAI A^CCWGGT. A complete list of these new enzymes can be found in Table I.
      A total of 2393 restriction enzymes is now known including 17 different Type I specificities,
      188 different Type II specificities and 4 different Type II specificities. Table II contains a
      listing of all prototype restriction enzymes (Types I, II and III), together with their
      commercially available isoschizomers and neoschizomers that cleave at a position different
      from their prototype.
AU  - Roberts RJ
AU  - Macelis D
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 3125-3137.

PMID- 7937073
VI  - 22
DP  - 1994
TI  - REBASE - restriction enzymes and methylases.
PG  - 3628-3639
AB  - REBASE is a comprehensive database of information about restriction enzymes and their
      associated methylases, including their recognition and cleavage sites and their commercial
      availability. Information from REBASE is available via monthly electronic mailings as well as
      via WAIS and anonymous ftp. Specialized files are available that can be used directly by many
      software packages.
AU  - Roberts RJ
AU  - Macelis D
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1994 22: 3628-3639.

PMID- 8594587
VI  - 24
DP  - 1996
TI  - REBASE--restriction enzymes and methylases.
PG  - 223-235
AB  - REBASE is a comprehensive database of information about restriction enzymes and their
      associated methylases, including their recognition and cleavage sites and their commercial
      availability.  Information from REBASE is available via monthly electronic mailings as well as
      via WAIS, anonymouse ftp and through the World Wide Web (htp://www.neb.com/rebase).
      Specialized files are available that can be used directly by many software packages.
AU  - Roberts RJ
AU  - Macelis D
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1996 24: 223-235.

PMID- 9399870
VI  - 26
DP  - 1998
TI  - REBASE - restriction enzymes and methylases.
PG  - 338-350
AB  - REBASE is a comprehensive database of information about restriction enzymes and their
      associated methylases, including their recognition and cleavage sites and their commercial
      availability. Also included is a listing of homing endonucleases. Information from REBASE is
      available via monthly electronic mailings as well as via anonymous ftp and through the World
      Wide Web. The REBASE web site, http://www.neb.com/rebase , is where we maintain a web page for
      every enzyme, reference and supplier. Additionally, there is a search facility, help and NEWS
      pages, and a complete description of our various services. Specialized files are available
      that can be used directly by many software packages.
AU  - Roberts RJ
AU  - Macelis D
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1998 26: 338-350.

PMID- 11125108
VI  - 29
DP  - 2001
TI  - REBASE-restriction enzymes and methylases.
PG  - 268-269
AB  - REBASE contains comprehensive information about restriction enzymes, DNA methylases and
      related proteins such as nicking enzymes, specificity subunits and control proteins.
      It contains published and unpublished references, recognition and cleavage sites,
      isoschizomers, commercial availability, methylation sensitivity, crystal data and
      sequence data. Homing endonucleases are also included. Most recently, extensive
      information about the methylation sensitivity of restriction enzymes has been added
      and a new feature contains complete analyses of the putative restriction systems in
      the sequenced bacterial and archaeal genomes. The data is distributed via email,
      ftp (ftp.neb.com) and the Web (http://rebase.neb.com).
AU  - Roberts RJ
AU  - Macelis D
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2001 29: 268-269.

PMID- 10592256
VI  - 28
DP  - 2000
TI  - REBASE - restriction enzymes and methylases.
PG  - 306-307
AB  - REBASE is a comprehensive database of information about restriction enzymes and related
      proteins. It contains published and unpublished references, recognition and cleavage sites,
      isoschizomers, commercial availability, methylation sensitivity, crystal and sequence data.
      DNA methyltransferases, homing endonucleases, nicking enzymes, specificity subunits and
      control proteins are also included. Most recently, putative DNA methyltransferases and
      restriction enzymes, as predicted from analysis of genomic sequences, are also listed. The
      data is distributed via Email, ftp (ftp.neb.com), and the Web (http://rebase.neb.com).
AU  - Roberts RJ
AU  - Macelis D
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2000 28: 306-307.

PMID- 1645876
VI  - 19
DP  - 1991
TI  - Restriction enzymes and their isoschizomers.
PG  - 2077-2109
AB  - A review of all known restriction enzymes and a description of the REBASE
      database.
AU  - Roberts RJ
AU  - Macelis D
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 2077-2109.

PMID- 9016548
VI  - 25
DP  - 1997
TI  - REBASE-restriction enzymes and methylases.
PG  - 248-262
AB  - REBASE is a comprehensive database of information about restriction enzymes and their
      associated methylases, including their recognition and cleavage sites and their commercial
      availability.  Information from REBASE is available via monthly electronic mailings as well as
      via anonymous ftp, WAIS/gopher and through the World Wide Web (http://www.neb.com/rebase).
      Specialized files are available that can be used directly by many software packages.
AU  - Roberts RJ
AU  - Macelis D
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1997 25: 248-262.

PMID- 9847213
VI  - 27
DP  - 1999
TI  - REBASE-restriction enzymes and methylases.
PG  - 312-313
AB  - REBASE is a comprehensive database of information about restriction enzymes and their
      associated methylases, including their recognition and cleavage sites and their commercial
      availability.  Also included is a listing of homing endonucleases.  Information from REBASE is
      distributed via monthly electronic mailings as well as through anonymous ftp and the World
      Wide Web.  The REBASE web site (http://www.neb.com/rebase) contains a web page for every
      enzyme, reference and supplier.  Additionally, there is a search facility, help and NEWS
      pages, and a complete description of our various services.  Specialized files are available
      that can be used directly by many software packages.
AU  - Roberts RJ
AU  - Macelis D
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1999 27: 312-313.

PMID- 1085372
VI  - 103
DP  - 1976
TI  - A specific endonuclease from Haemophilus haemolyticus.
PG  - 199-208
AB  - A restriction-like endonuclease, HhaI, has been partially purified from
      Haemophilus haemolyticus.  This enzyme cleaves bacteriophage lambda DNA and
      adenovirus-2 DNA at many sites, and cleaves simian virus 40 DNA at only two
      sites.  It recognizes the sequence 5'-G-C-G-^C-3' 3'-C-^G-C-G-5' and cuts at
      the sites indicated by the arrows.
AU  - Roberts RJ
AU  - Myers PA
AU  - Morrison A
AU  - Murray K
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1976 103: 199-208.

PMID- 1271462
VI  - 102
DP  - 1976
TI  - A specific endonuclease from Arthrobacter luteus.
PG  - 157-165
AB  - A new restriction-like endonuclease, AluI, has been partially purified from Arthrobacter
      luteus. This enzyme cleaves bacteriophage lambda DNA, adenovirus-2 DNA and simian virus 40 DNA
      at may sites including all sites cleaved by the endonuclease HindIII from Haemophilus
      influenzae serotype d. Radioactive oligonucleotides in pancreatic DNAase digests of
      (5'-32P)-labelled fragments of phage lambda DNA relased by the action of AluI had the 5'
      terminal sequence pC-T-N-. The enzyme recognizes the tetranucleotide sequence
      3'-T-C-^-G-A-5' 5'-A-G-^C-T-3' and cleaves it at the position marked by the arrows.
AU  - Roberts RJ
AU  - Myers PA
AU  - Morrison A
AU  - Murray K
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1976 102: 157-165.

PMID- 19846593
VI  - 38
DP  - 2010
TI  - REBASE--a database for DNA restriction and modification: enzymes, genes and genomes.
PG  - D234-D236
AB  - REBASE is a comprehensive database of information about restriction enzymes, DNA
      methyltransferases and related proteins involved in the
      biological process of restriction-modification (R-M). It contains fully
      referenced information about recognition and cleavage sites,
      isoschizomers, neoschizomers, commercial availability, methylation
      sensitivity, crystal and sequence data. Experimentally characterized
      homing endonucleases are also included. The fastest growing segment of
      REBASE contains the putative R-M systems found in the sequence databases.
      Comprehensive descriptions of the R-M content of all fully sequenced
      genomes are available including summary schematics. The contents of REBASE
      may be browsed from the web (http://rebase.neb.com) and selected
      compilations can be downloaded by ftp (ftp.neb.com). Additionally, monthly
      updates can be requested via email.
AU  - Roberts RJ
AU  - Vincze T
AU  - Posfai J
AU  - Macelis D
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2010 38: D234-D236.

PMID- 15608184
VI  - 33
DP  - 2005
TI  - REBASE - Restriction enzymes and DNA methyltransferases.
PG  - D230-D232
AB  - REBASE is a comprehensive database of information about restriction enzymes, DNA
      methyltransferases and related proteins involved in restriction-modification.  It contains
      both published and unpublished work with information about recognition and cleavage sites,
      isoschizomers, commercial availability, crystal and sequence data.  Experimentally
      characterized homing endonucleases are also included.  Additionally, REBASE contains complete
      and up-to-date information about the methylation sensitivity of restriction endonucleases.  An
      extensive analysis is included of the restriction-modification systems that are predicted to
      be present in the sequenced bacterial and archaeal genomes from GenBank.  The contents of
      REBASE are available by browsing from the web (http://rebase.neb.com/rebase/rebase.html) and
      through selected compilations by ftp (ftp.neb.com) and as monthly updates that can be
      requested via email.
AU  - Roberts RJ
AU  - Vincze T
AU  - Posfai J
AU  - Macelis D
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2005 33: D230-D232.

PMID- 17202163
VI  - 35
DP  - 2007
TI  - REBASE--enzymes and genes for DNA restriction and modification.
PG  - D269-D270
AB  - REBASE is a comprehensive database of information about restriction enzymes, DNA
      methyltransferases and related proteins involved in the biological process of
      restriction-modification. It contains fully referenced information about recognition and
      cleavage sites, isoschizomers, neoschizomers, commercial availability, methylation
      sensitivity, crystal and sequence data. Experimentally characterized homing endonucleases are
      also included. All newly sequenced genomes are analyzed for the presence of putative
      restriction systems and these data are included within the REBASE. The contents or REBASE may
      be browsed from the web (http://rebase.neb.com/rebase/rebase.ftp.html) and selected
      compilations can be downloaded by ftp (ftp.neb.com). Additionally, monthly updates can be
      requested via email.
AU  - Roberts RJ
AU  - Vincze T
AU  - Posfai J
AU  - Macelis D
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2007 35: D269-D270.

PMID- 25378308
VI  - 43
DP  - 2015
TI  - REBASE-a database for DNA restriction and modification: enzymes, genes and genomes.
PG  - D298-D299
AB  - REBASE is a comprehensive and fully curated database of information about the components of
      restriction-modification (RM) systems. It contains fully referenced
      information about recognition and cleavage sites for both restriction enzymes and
      methyltransferases as well as commercial availability, methylation sensitivity,
      crystal and sequence data. All genomes that are completely sequenced are analyzed
      for RM system components, and with the advent of PacBio sequencing, the
      recognition sequences of DNA methyltransferases (MTases) are appearing rapidly.
      Thus, Type I and Type III systems can now be characterized in terms of
      recognition specificity merely by DNA sequencing. The contents of REBASE may be
      browsed from the web http://rebase.neb.com and selected compilations can be
      downloaded by FTP (ftp.neb.com). Monthly updates are also available via email.
AU  - Roberts RJ
AU  - Vincze T
AU  - Posfai J
AU  - Macelis D
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2015 43: D298-D299.

PMID- 12520038
VI  - 31
DP  - 2003
TI  - REBASE: restriction enzymes and methyltransferases.
PG  - 418-420
AB  - REBASE contains comprehensive information about restriction enzymes, DNA methyltransferases
      and related proteins such as nicking enzymes,
      specificity subunits and control proteins. It contains published and
      unpublished references, recognition and cleavage sites, isoschizomers,
      commercial availability, crystal and sequence data. Homing endonucleases
      are also included. REBASE contains the most complete and up-to-date
      information about the methylation sensitivity of restriction
      endonucleases. In addition, there is extensive information about the known
      and putative restriction-modification (R-M) systems in more than 100
      sequenced bacterial and archaeal genomes. The data is available on the web
      (http://rebase.neb.com/rebase/rebase.html), through ftp (ftp.neb.com) and
      as monthly updates via email.
AU  - Roberts RJ
AU  - Vincze T
AU  - Posfai J
AU  - Macelis D
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2003 31: 418-420.

PMID- 834250
VI  - 265
DP  - 1977
TI  - Recognition sequence of specific endonuclease BamHI from Bacillus amyloliquefaciens H.
PG  - 82-84
AB  - Many specific endonucleases (restriction endonucleases) have been isolated and
      recognition sequences have been determined for a number of them.  The isolation
      of a new specific endonuclease, BamHI, from Bacillus amyloliquefaciens H has
      recently been described.  We have determined the recognition sequence of BamHI
      and find that it cleaves the two-fold rotationallly symmetric sequence
      5'-G-^G-A-T-C-C-3' 3'-C-C-T-A-G-^G-5' at the positions indicated by the arrows
      generating fragments with cohesive termini.
AU  - Roberts RJ
AU  - Wilson GA
AU  - Young FE
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1977 265: 82-84.

PMID- 15313181
VI  - 322
DP  - 2004
TI  - Effects of chromatin structure on the enzymatic and DNA binding functions of DNA methyltransferases DNMT1 and Dnmt3a in vitro.
PG  - 110-118
AB  - DNA methylation is an epigenetic modification of the genome critical for numerous processes,
      including transcriptional repression and
      maintenance of chromatin structure. Recent studies have revealed
      connections between DNA methylation and other epigenetic modifications
      such as ATP-dependent chromatin remodeling. It remains unclear,
      however, exactly how chromatin and epigenetic chromatin modifications
      affect the biological properties of the DNA methyltransferases (DNMT1,
      DNMT3A, and DNMT3B). Using a highly purified system and the 5S rDNA
      gene as free DNA or assembled into a mononucleosome, we have compared
      the effects of chromatin structure on DNMT1 and Dnmt3a. The catalytic
      efficiency for both enzymes decreased on the mononucleosome, similar
      to8-fold for DNMT1 and 17-fold for Dnmt3a. DNMT1 and Dnmt3a bound to
      DNA and mononucleosomal substrates in gel shift experiments with
      approximately equal affinity and in a cooperative manner. We also show
      that DNMT1 interacts with hSNF2H chromatin remodeling enzyme and that
      DNMT1 binds mononucleosomes with higher affinity in the presence of
      hSNF2H. These findings raise interesting implications about the
      interactions of mammalian DNA methyltransferases with chromatin and
      provide the first evidence that a chromatin remodeling enzyme can alter
      the biological properties of a DNMT.
AU  - Robertson AK
AU  - Geiman TM
AU  - Sankpal UT
AU  - Hager GL
AU  - Robertson KD
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 2004 322: 110-118.

PMID- 10852881
VI  - 182
DP  - 2000
TI  - The Brucella abortus CcrM DNA methyltransferase is essential for viability, and its overexpression attenuates intracellular replication in murine macrophages.
PG  - 3482-3489
AB  - The CcrM DNA methyltransferase of the alpha-proteobacteria catalyzes the methylation of the
      adenine in the sequence GAnTC.  Like Dam in the enterobacteria, CcrM plays a regulatory role
      in Caulobacter crescentus and Rhizobium meliloti.  CcrM is essential for viability in both of
      these organisms, and we show here that it is also essential in Brucella abortus.  Further,
      increased copy number of the ccrM gene results in striking changes in B. abortus morphology,
      DNA replication, and growth in murine macrophages.  We generated strains that carry ccrM
      either on a low-copy-number plasmid (strain GR131) or on a moderate-copy-number plasmid
      (strain GR132).  Strain GR131 has wild-type morphology and chromosome number, as assessed by
      flow cytometry.  In contrast, strain GR132 has abnormal branched morphology, suggesting
      aberrant cell division, and increased chromosome number.  Although these strains exhibit
      different morphologies and DNA content, the replication of both strains in macrophages is
      attenuated.  These data imply that the reduction in survival in host cells is not due solely
      to a cell division defect but is due to additional functions of CcrM.  Because CcrM is
      essential in B. abortus and increased ccrM copy number attentuates survival in host cells, we
      propose that CcrM is an appropriate target for new antibiotics.
AU  - Robertson GT
AU  - Reisenauer A
AU  - Wright R
AU  - Jensen RB
AU  - Jensen A
AU  - Shapiro L
AU  - Roop RM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2000 182: 3482-3489.

PMID- 29371368
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of an Escherichia coli O121:H19 Strain from an Outbreak  in Canada Associated with Flour.
PG  - e01561-17
AB  - Here, we present the first complete genome sequence of an Escherichia coli non-O157
      Shiga-toxin producing isolate, 16-9255, from serotype O121:H19. This
      strain is notable as a clinical case recovered from a recent Canadian
      flour-associated outbreak event.
AU  - Robertson J
AU  - Lin J
AU  - Levett PN
AU  - Nadon C
AU  - Nash J
AU  - Berry C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01561-17.

PMID- 29348347
VI  - 6
DP  - 2018
TI  - Completed Genome Sequences of Strains from 36 Serotypes of Salmonella.
PG  - e01472-17
AB  - We report here the completed closed genome sequences of strains representing 36 serotypes of
      Salmonella These genome sequences will provide useful references for
      understanding the genetic variation between serotypes, particularly as references
      for mapping of raw reads or to create assemblies of higher quality, as well as to
      aid in studies of comparative genomics of Salmonella.
AU  - Robertson J
AU  - Yoshida C
AU  - Gurnik S
AU  - Nash JHE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01472-17.

PMID- 
VI  - 133
DP  - 2003
TI  - DNA methyltransferase function and regulation.
PG  - 3845S
AB  - DNA methylation is an epigenetic modification of the genome catalyzed by a group of 3 DNA
      methyltransferases: DNMT1, 3A, and 3B.  Methyl groups are not randomly distributed in
      mammalian cells but rather are compartmentalized in repetitive DNA, heterochromatic regions,
      and parasitic elements.  Other regions of the genome, such as CpG island promoters, are almost
      always unmethylated.  Given the minimal sequence requirements of the DNMTs (CpG), it is likely
      that they are directed to sequences that are to be methylated by interactions with other
      proteins, particularly chromatin-associated factors.  This compartmentalization is essential
      because genetic knockouts of the DNMTs lead to embryonic lethality, and reversal of the normal
      DNA methylation patterns is a hallmark of the most transformed cells.
AU  - Robertson K
PT  - Journal Article
TA  - J. Nutr.
JT  - J. Nutr.
SO  - J. Nutr. 2003 133: 3845S.

PMID- 11420731
VI  - 20
DP  - 2001
TI  - DNA methylation, methyltransferases, and cancer.
PG  - 3139-3155
AB  - The field of epigenetics has recently moved to the forefront of studies relating to diverse
      processes such as transcriptional regulation, chromatin structure, genome integrity, and
      tumorigenesis. Recent work has revealed how DNA methylation and chromatin structure are linked
      at the molecular level and how methylation anomalies play a direct causal role in
      tumorigenesis and genetic disease. Much new information has also come to light regarding the
      cellular methylation machinery, known as the DNA methyltransferases, in terms of their roles
      in mammalian development and the types of proteins they are known to interact with. This
      information has forced a new view for the role of DNA methyltransferases. Rather than enzymes
      that act in isolation to copy methylation patterns after replication, the types of
      interactions discovered thus far indicate that DNA methyltransferases may be components of
      larger complexes actively involved in transcriptional control and chromatin structure
      modulation. These new findings will likely enhance our understanding of the myriad roles of
      DNA methylation in disease as well as point the way to novel therapies to prevent or repair
      these defects.
AU  - Robertson KD
PT  - Journal Article
TA  - Oncogene
JT  - Oncogene
SO  - Oncogene 2001 20: 3139-3155.

PMID- 10888886
VI  - 25
DP  - 2000
TI  - DNMT1 forms a complex with Rb, E2F1 and HDAC1 and represses transcription from E2F-responsive promoters.
PG  - 338-342
AB  - Methylation of CpG islands is associated with transcriptional silencing and the formation of
      nuclease-resistant chromatin structures enriched in hypoacetylated histones.
      Methyl-CpG-binding proteins, such as MeCP2, provide a link between methylated DNA and
      hypoacetylated histones by recruiting histone deacetylase, but the mechanisms establishing the
      methylation patterns themselves are unknown. Whether DNA methylation is always causal for the
      assembly of repressive chromatin or whether features of transcriptionally silent chromatin
      might target methyltransferase remains unresolved. Mammalian DNA methyltransferases show
      little sequence specificity in vitro, yet methylation can be targeted in vivo within
      chromosomes to repetitive elements, centromeres and imprinted loci. This targeting is
      frequently disrupted in tumour cells, resulting in the improper silencing of tumour-suppressor
      genes associated with CpG islands. Here we show that the predominant mammalian DNA
      methyltransferase, DNMT1, co-purifies with the retinoblastoma (Rb) tumour suppressor gene
      product, E2F1, and HDAC1 and that DNMT1 cooperates with Rb to repress transcription from
      promoters containing E2F-binding sites. These results establish a link between DNA
      methylation, histone deacetylase and sequence-specific DNA binding activity, as well as a
      growth-regulatory pathway that is disrupted in nearly all cancer cells.
AU  - Robertson KD
AU  - Ait-Si-Ali S
AU  - Yokochi T
AU  - Wade PA
AU  - Jones PL
AU  - Wolffe AP
PT  - Journal Article
TA  - Nat. Genet.
JT  - Nat. Genet.
SO  - Nat. Genet. 2000 25: 338-342.

PMID- 10688866
VI  - 21
DP  - 2000
TI  - DNA methylation: past, present and future directions.
PG  - 461-467
AB  - DNA methylation, or the covalent addition of a methyl group to cytosine within the context of
      the CpG dinucleotide, has profound effects on the mammalian genome. These effects include
      transcriptional repression via inhibition of transcription factor binding or the recruitment
      of
      methyl-binding proteins and their associated chromatin remodeling factors, X chromosome
      activation, imprinting and the suppression of parasitic DNA sequences. DNA methylation is also
      essential for proper embryonic development; however, its presence can add an additional burden
      to the genome. Normal methylation patterns are frequently disrupted in tumor cells with global
      hypomethylation accompanying region-specific hypermethylation. When these hypermethylation
      events occur within the promoter of a tumor suppressor gene they will silence the gene and
      provide the cell with a growth advantage in a manner akin to deletions or mutations. Recent
      work indicating that DNA methylation is an important player in both DNA repair and genome
      stability as well as the discovery of a new family of DNA methyltransferases makes now a very
      exciting period for the methylation field. This review will highlight the major findings in
      the methylation field over the past 20 years then summarize the most important and interesting
      future directions the field is likely to take in the next millennium.
AU  - Robertson KD
AU  - Jones PA
PT  - Journal Article
TA  - Carcinogenesis
JT  - Carcinogenesis
SO  - Carcinogenesis 2000 21: 461-467.

PMID- 10773079
VI  - 28
DP  - 2000
TI  - Differential mRNA expression of the human DNA methyltransferases (DNMTs) 1, 3a and 3b during the G0/G1 to S phase transition in normal and tumor cells.
PG  - 2108-2113
AB  - DNA methylation is essential for mammalian development, X-chromosome inactivation, and
      imprinting yet aberrant methylation patterns are one of the most common features of
      transformed cells. One of the proposed causes for these defects in the methylation machinery
      is overexpression of one or more of the three known catalytically active DNA
      methyltransferases (DNMTs) 1, 3a and 3b, yet there are clearly examples in which
      overexpression is minimal or non-existent but global methylation anomalies persist. An
      alternative mechanism which could give rise to global methylation errors is the improper
      expression of one or more of the DNMTs during the cell cycle. To begin to study the latter
      possibility we examined the expression of the mRNAs for DNMT1, 3a and 3b during the cell cycle
      of normal and transformed cells. We found that DNMT1 and 3b levels were significantly
      downregulated in G0/G1 while DNMT3a mRNA levels were less sensitive to cell cycle
      alterations and were maintained at a slightly higher level in tumor lines compared to normal
      cell strains. Enzymatic activity assays revealed a similar decrease in the overall methylation
      capacity of the cells during G0/G1 arrest and again revealed that a tumor cell line
      maintained a higher methylation capacity during arrest than a normal cell strain. These
      results reveal a new level of control exerted over the cellular DNA methylation machinery, the
      loss of which provides an alternative mechanism for the genesis of the aberrant methylation
      patterns observed in tumor cells.
AU  - Robertson KD
AU  - Keyomarsi K
AU  - Gonzales FA
AU  - Velicescu M
AU  - Jones PA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2000 28: 2108-2113.

PMID- 10325416
VI  - 27
DP  - 1999
TI  - The human DNA methyltransferases 1, 3a and 3b: coordinate mRNA expression in normal tissues and overexpression in tumors.
PG  - 2291-2298
AB  - DNA methylation in mammals is required for embryonic development, X chromosome inactivation
      and imprinting.  Previous studies have shown that methylation patterns become abnormal in
      malignant cells and may contribute to tumorigenesis by improper de novo methylation and
      silencing of the promoters for growth-regulatory genes.  RNA and protein levels of the DNA
      methyltransferase DNMT1 have been shown to be elevated in tumors, however murine stem cells
      lacking Dnmt1 are still able to de novo methylate viral DNA.  The recent cloning of a new
      family of DNA methyltransferases (Dmnt3a and Dmnt3b) in mouse which methylate hemimethylated
      and unmethylated templates with equal efficiencies make them candidates for the long sought de
      novo methyltransferases.  We have investigated the expression of human DNMT1, 3a and 3b and
      found widespread, coordinate expression of all three transcripts in most normal tissues.
      Chromosomal mapping placed DNMT3a on chromosome 2p23 and DNMT3b on chromosome 20q11.2.
      Significant overexpression of DNMT3b was seen in tumors while DNMT1 and DNMT3a were only
      modestly overexpressed and with lower frequency.  Lastly, several novel alternatively spliced
      forms of DNMT3b, which may have altered enzymatic activity, were found to be expressed in a
      tissue-specific manner.
AU  - Robertson KD
AU  - Uzvolgyi E
AU  - Liang G
AU  - Talmadge C
AU  - Sumegi J
AU  - Gonzales FA
AU  - Jones PA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1999 27: 2291-2298.

PMID- 11262868
VI  - 1
DP  - 2000
TI  - DNA methylation in health and disease.
PG  - 11-19
AB  - DNA methylation has recently moved to centre stage in the aetiology of human
      neurodevelopmental syndromes such as the fragile X, ICF and Rett syndromes.  These diseases
      result from the misregulation of genes that occurs with the loss of appropriate epigenetic
      controls during neuronal development.  Recent advances have connected DNA methylation to
      chromatin-remodelling enzymes, and understanding this link will be central to the design of
      new therapeutic tools.
AU  - Robertson KD
AU  - Wolffe AP
PT  - Journal Article
TA  - Genetics
JT  - Genetics
SO  - Genetics 2000 1: 11-19.

PMID- 8298050
VI  - 66
DP  - 1994
TI  - Mediation of molecular recognition in protein-DNA complexes by bound water: a mechanism for "star activity" of restriction endonucleases.
PG  - A34
AB  - For many restriction endonucleases such as EcoRI, accurate protein-DNA recognition is
      disrupted by changes in buffer composition, leading to an unexplained loss of specificity
      termed "star activity". We have found that the extent of cleavage by EcoRI at non-canonical
      sites is strongly correlated with the osmotic pressure in the reaction. This relationship is
      unique to osmotic pressure, and is independent of other physical or chemical properties of the
      osmolyte. An analogous correlation between osmotic pressure and star activity is observed for
      other restriction enzymes including PvuII and BamHI. Specificity for cleavage at canonical
      sites is restored by the application of hydrostatic pressure to counteract the effects of
      osmotic pressure. Elevated osmotic pressures induce a fundamental change in the selectivity of
      EcoRI -- at 100 atm osmotic pressure the rate of cleavage at the canonical site actually
      decreases, whereas the rate of cleavage at "star" sites increases. The alteration of
      specificity accompanying release of water clearly implicates one or more water molecules in
      mediating accurate recognition of specific sequences of DNA by the enzyme. The change in
      selectivity is manifested in both the association and catalytic steps of the reaction. Under
      standard conditions, water may participate as a general mediator for sequence specific
      recognition of DNA by restriction enzymes and other DNA-binding proteins.
AU  - Robinson CR
AU  - Sligar SG
PT  - Journal Article
TA  - Biophys. J.
JT  - Biophys. J.
SO  - Biophys. J. 1994 66: A34.

PMID- 9482860
VI  - 95
DP  - 1998
TI  - Changes in solvation during DNA binding and cleavage are critical to altered specificity of the EcoRI endonuclease.
PG  - 2186-2191
AB  - Restriction endonucleases such as EcoRI bind and cleave DNA with great specificity and
      represent a paradigm for protein-DNA interactions and molecular recognition.  Using osmotic
      pressure to induce water release, we demonstrate the participation of bound waters in the
      sequence discrimination of substrate DNA by EcoRI.  Changes in solvation can play a critical
      role in directing sequence-specific DNA binding by EcoRI and are also crucial in assisting
      site discrimination during catalysis.  By measuring the volume change for complex formation,
      we show that at the cognate sequence (GAATTC) EcoRI binding releases about 70 fewer water
      molecules than binding at an alternate DNA sequence (TAATTC), which differs by a single base
      pair.  EcoRI complexation with nonspecific DNA releases substantially less water than either
      of these specific complexes.  In cognate substrates (GAATTC) kcat decreases as osmotic
      pressure is increased, indicating that binding of about 30 water molecules accompanies the
      cleavage reaction.  For the alternate substrate (TAATTC), release of about 40 water molecules
      accompanies the reaction, indicated by a dramatic acceleration of the rate when osmotic
      pressure is raised.  These large differences in solvation effects demonstrate that water
      molecules can be key players in the molecular recognition process during both association and
      catalytic phases of the EcoRI reaction, acting to change the specificity of the enzyme.  For
      both the protein-DNA complex and the transition state, there may be substantial conformational
      differences between cognate and alternate sites, accompanied by significant alterations in
      hydration and solvent accessibility.
AU  - Robinson CR
AU  - Sligar SG
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1998 95: 2186-2191.

PMID- 7909343
VI  - 18C
DP  - 1994
TI  - Mediation of molecular recognition in protein-DNA complexes by bound water: a mechanism for "star activity" of restriction endonucleases.
PG  - 138
AB  - For many restriction endonucleases such as EcoRI, accurate protein-DNA recognition is
      disrupted by changes in buffer composition, leading to an unexplained loss of specificity
      termed "star activity". We have found that the extent of cleavage by EcoRI at non-canonical
      sites is strongly correlated with the osmotic pressure in the reaction. This relationship is
      unique to osmotic pressure, and is independent of other physical or chemical properties of the
      osmolyte. An analogous correlation between osmotic pressure and star activity is observed for
      other restriction enzymes including PvuII and BamHI. For EcoRI, specificity for cleavage at
      the canonical site is restored by the application of hydrostatic pressure to counteract the
      effects of osmotic pressure. Elevated osmotic pressures induce a fundamental change in the
      selectivity of EcoRI -- at 100 atm osmotic pressure the rate of cleavage at the canonical sie
      actually decreases, whereas the rate of cleavage at "star" sites increases. The alteration of
      specificity accompanying release of water clearly implicates one or more water molecules in
      mediating accurate recognition of specific sequences of DNA by the enzyme. The change in
      selectivity is manifested in both the association and catalytic steps of the reaction. Under
      standard conditions, water may participate as a general mediator for sequence specific
      recognition of DNA by restriction enzymes and other DNA-binding proteins.
AU  - Robinson CR
AU  - Sligar SG
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1994 18C: 138.

PMID- 8230215
VI  - 234
DP  - 1993
TI  - Molecular recognition mediated by bound water. A mechanism for star activity of the restriction endonuclease EcoRI.
PG  - 302-306
AB  - Many restriction endonucleases such as EcoRI lose some specificity for their recognition
      sequence under certain buffer conditions. The cause of this disruption of accurate protein-DNA
      recognition has never been explained. By cleaving DNA with EcoRI in the presence of several
      osmolytes, we show that the extent of this EcoRI "star activity" depends strongly upon osmotic
      pressure. The loss of specificity accompanying decreased water activity implies a role for one
      or more water molecules in recognition of specific sequences of DNA. Water mediation may
      constitute a general motif for sequence-specific DNA recognition by restriction enzymes and
      other DNA-binding proteins.
AU  - Robinson CR
AU  - Sligar SG
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1993 234: 302-306.

PMID- 8142380
VI  - 33
DP  - 1994
TI  - Hydrostatic pressure reverses osmotic pressure effects on the specificity of EcoRI-DNA interactions.
PG  - 3787-3793
AB  - To characterize the role of water in protein-DNA interactions, we have studied the specificity
      of the EcoRI restriction endonuclease as a function of osmotic and hydrostatic pressure. The
      extent of cleavage by the enzyme at noncanonical ("star") sites is shown to depend uniquely
      upon the osmotic pressure in the reaction as controlled by the addition of a wide variety of
      neutral solutes. Alteration of cleavage specificity ("EcoRI* activity") is not uniformly
      correlated with any other colligative solvent property such as dielectric constant, viscosity,
      or water concentration. The application of hydrostatic pressure reverses the effects of
      osmotic pressure, restoring the natural selectivity of the enzyme for its canonical site
      GAATTC. This combination of observations provides compelling evidence that the site-specific
      recognition of canonical site DNA by EcoRI is mediated by discretely bound water molecules and
      that the release of these waters induces a fundamental change in the specificity of the
      interaction, leading to cleavage at alternative sites. This comprehensive analysis of solvent
      effects facilitates the unambiguous identification of structurally and functionally specific
      waters involved in macromolecular recognition events.
AU  - Robinson CR
AU  - Sligar SG
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1994 33: 3787-3793.

PMID- 7724581
VI  - 92
DP  - 1995
TI  - Heterogeneity in molecular recognition by restriction endonucleases: Osmotic and hydrostatic pressure effects on BamHI, PvuII, and EcoRV specificity.
PG  - 3444-3448
AB  - The cleavage specificity of the PvuII and BamHI restriction endonucleases is found to be
      dramatically reduced at elevated osmotic pressure. Relaxation in specificity of these
      otherwise highly accurate and specific enzymes, previously termed "star activity", is uniquely
      correlated with osmotic pressure between 0 and 100 atmospheres. No other colligative solvent
      property exhibits a uniform correlation with star activity for all of the compounds tested.
      Application of hydrostatic pressure counteracts the effects of osmotic pressure and restores
      the natural selectivity of the enzymes for their canonical recognition sequences. These
      results indicate that water solvation plays an important role in the site-specific recognition
      of DNA by many restriction enzymes. Osmotic pressure did not induce an analogous effect on the
      specificity of the EcoRV endonuclease, implying that selective hydration effects do not
      participate in DNA recognition in this system. Hydrostatic pressure was found to have little
      effect on the star activity induced by changes in ionic strength, pH, or divalent cation,
      suggesting that distinct mechanisms may exist for these observed alterations in specificity.
      Recent evidence has indicated that BamHI and EcoRI share similar structural motifs, while
      PvuII and EcoRV belong to a different structural family. Evidently, the use of hydration water
      to assist in site-specific recognition is a motif neither limited to nor defined by structural
      families.
AU  - Robinson CR
AU  - Sligar SG
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1995 92: 3444-3448.

PMID- 
VI  - 
DP  - 2001
TI  - Restriction endonucleases.
PG  - 225-266
AB  - Molecular biologists routinely use restriction enzymes as key reagents for a variety of
      applications including genomic mapping, restriction fragment length polymorphism (RFLP)
      analysis, DNA sequencing, and a host of recombinant DNA methodologies.  Few would argue that
      these enzymes are not indispensable tools for the variety of techniques used in the
      manipulation of DNA, but like many common tools that are easy to use, they are not always
      applied as efficiently and effectively as possible.  This chapter focuses on the biochemical
      attributes and requirements of restriction enzymes and delivers strategies to optimize their
      use in simple and complex reactions.
AU  - Robinson D
AU  - Walsh PR
AU  - Bonventre JA
PT  - Journal Article
TA  - Molecular biology problem solver.
JT  - Molecular biology problem solver.
SO  - Molecular biology problem solver. 2001 : 225-266.

PMID- 27688326
VI  - 4
DP  - 2016
TI  - Genome Sequences of 15 Gardnerella vaginalis Strains Isolated from the Vaginas of Women with and without Bacterial Vaginosis.
PG  - e00879-16
AB  - Gardnerella vaginalis is a predominant species in bacterial vaginosis, a dysbiosis of the
      vagina that is associated with adverse health outcomes,
      including preterm birth. Here, we present the draft genome sequences of 15
      Gardnerella vaginalis strains (now available through BEI Resources) isolated from
      women with and without bacterial vaginosis.
AU  - Robinson LS
AU  - Perry J
AU  - Lek S
AU  - Wollam A
AU  - Sodergren E
AU  - Weinstock G
AU  - Lewis WG
AU  - Lewis AL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00879-16.

PMID- 16188402
VI  - 252
DP  - 2005
TI  - A dam mutant of Yersinia pestis is attenuated and induces protection against plague.
PG  - 251-256
AB  - We have constructed a dam mutant of Yersinia pestis GB. In BALB/c mice inoculated
      subcutaneously, the median lethal dose of the mutant was at least 2000-fold
      higher than the wild type. Mice inoculated with sub-lethal doses of the mutant
      were protected against a subsequent challenge with virulent Y. pestis. The effect
      of dam inactivation on gene expression was examined using a DNA microarray, which
      revealed increased expression of a number of genes associated with the SOS
      response. These results confirm the key role of Dam in the regulation of
      virulence, and its potential role as a target for the generation of attenuated
      strains of pathogenic bacteria.
AU  - Robinson VL
AU  - Oyston PC
AU  - Titball RW
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2005 252: 251-256.

PMID- 26061173
VI  - 10
DP  - 2015
TI  - Azotobacter Genomes: The Genome of Azotobacter chroococcum NCIMB 8003 (ATCC 4412).
PG  - E0127997
AB  - The genome of the soil-dwelling heterotrophic N2-fixing Gram-negative bacterium
      Azotobacter chroococcum NCIMB 8003 (ATCC 4412) (Ac-8003) has been determined. It
      consists of 7 circular replicons totalling 5,192,291 bp comprising a circular
      chromosome of 4,591,803 bp and six plasmids pAcX50a, b, c, d, e, f of 10,435 bp,
      13,852, 62,783, 69,713, 132,724, and 311,724 bp respectively. The chromosome has
      a G+C content of 66.27% and the six plasmids have G+C contents of 58.1, 55.3,
      56.7, 59.2, 61.9, and 62.6% respectively. The methylome has also been determined
      and 5 methylation motifs have been identified. The genome also contains a very
      high number of transposase/inactivated transposase genes from at least 12 of the
      17 recognised insertion sequence families. The Ac-8003 genome has been compared
      with that of Azotobacter vinelandii ATCC BAA-1303 (Av-DJ), a derivative of strain
      O, the only other member of the Azotobacteraceae determined so far which has a
      single chromosome of 5,365,318 bp and no plasmids. The chromosomes show
      significant stretches of synteny throughout but also reveal a history of many
      deletion/insertion events. The Ac-8003 genome encodes 4628 predicted
      protein-encoding genes of which 568 (12.2%) are plasmid borne. 3048 (65%) of
      these show > 85% identity to the 5050 protein-encoding genes identified in Av-DJ,
      and of these 99 are plasmid-borne. The core biosynthetic and metabolic pathways
      and macromolecular architectures and machineries of these organisms appear
      largely conserved including genes for CO-dehydrogenase, formate dehydrogenase and
      a soluble NiFe-hydrogenase. The genetic bases for many of the detailed phenotypic
      differences reported for these organisms have also been identified. Also many
      other potential phenotypic differences have been uncovered. Properties endowed by
      the plasmids are described including the presence of an entire aerobic corrin
      synthesis pathway in pAcX50f and the presence of genes for retro-conjugation in
      pAcX50c. All these findings are related to the potentially different
      environmental niches from which these organisms were isolated and to emerging
      theories about how microbes contribute to their communities.
AU  - Robson RL
AU  - Jones R
AU  - Robson RM
AU  - Schwartz A
AU  - Richardson TH
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2015 10: E0127997.

PMID- 12917642
VI  - 424
DP  - 2003
TI  - Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation.
PG  - 1042-1047
AB  - The marine unicellular cyanobacterium Prochlorococcus is the smallest-known oxygen-evolving
      autotroph. It numerically dominates the
      phytoplankton in the tropical and subtropical oceans, and is responsible
      for a significant fraction of global photosynthesis. Here we compare the
      genomes of two Prochlorococcus strains that span the largest evolutionary
      distance within the Prochlorococcus lineage and that have different
      minimum, maximum and optimal light intensities for growth. The
      high-light-adapted ecotype has the smallest genome (1,657,990 base pairs,
      1,716 genes) of any known oxygenic phototroph, whereas the genome of its
      low-light-adapted counterpart is significantly larger, at 2,410,873 base
      pairs (2,275 genes). The comparative architectures of these two strains
      reveal dynamic genomes that are constantly changing in response to myriad
      selection pressures. Although the two strains have 1,350 genes in common,
      a significant number are not shared, and these have been differentially
      retained from the common ancestor, or acquired through duplication or
      lateral transfer. Some of these genes have obvious roles in determining
      the relative fitness of the ecotypes in response to key environmental
      variables, and hence in regulating their distribution and abundance in the
      oceans.
AU  - Rocap G et al
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2003 424: 1042-1047.

PMID- 11381024
VI  - 11
DP  - 2001
TI  - Evolutionary role of restriction/modification systems as revealed by comparative genome analysis.
PG  - 946-958
AB  - Type II restriction modification systems (RMSs) have been regarded either as defense tools or
      as molecular parasites of bacteria. We extensively analyzed their evolutionary role from the
      study of their impact in the complete genomes of 26 bacteria and 35 phages in terms of
      palindrome avoidance. This analysis reveals that palindrome avoidance is not universally
      spread among bacterial species and that it does not correlate with taxonomic proximity.
      Palindrome avoidance is also not universal among bacteriophage, even when their hosts code for
      RMSs, and depends strongly on the genetic material of the phage. Interestingly, palindrome
      avoidance is intimately correlated with the infective behavior of the phage. We observe that
      the degree of palindrome and restriction site avoidance is significantly and consistently less
      important in phages than in their bacterial hosts. This result brings to the fore a larger
      selective load for palindrome and restriction site avoidance on the bacterial hosts than on
      their infecting phages. It is then consistent with a view where type II RMSs are considered as
      parasites possibly at the verge of mutualism. As a consequence, RMSs constitute a nontrivial
      third player in the host-parasite relationship between bacteria and phages.
AU  - Rocha EP
AU  - Danchin A
AU  - Viari A
PT  - Journal Article
TA  - Genome Res.
JT  - Genome Res.
SO  - Genome Res. 2001 11: 946-958.

PMID- 11972343
VI  - 30
DP  - 2002
TI  - Genomic repeats, genome plasticity and the dynamics of Mycoplasma evolution.
PG  - 2031-2042
AB  - Mycoplasmas evolved by a drastic reduction in genome size, but their genomes contain numerous
      repeated sequences with important roles in their evolution. We have established a
      bioinformatic strategy to detect the major recombination hot-spots in the genomes of
      Mycoplasma pneumoniae, Mycoplasma genitalium, Ureaplasma urealyticum and Mycoplasma pulmonis.
      This allowed the identification of large numbers of potentially variable regions, as well as a
      comparison of the relative recombination potentials of different genomic regions. Different
      trends are perceptible among mycoplasmas, probably due to different functional and structural
      constraints. The largest potential for illegitimate recombination in M. pulmonis is found at
      the vsa locus and its comparison in two different strains reveals numerous changes since
      divergence. On the other hand, the main M. pneumoniae and M. genitalium adhesins rely on large
      distant repeats and, hence, homologous recombination for variation. However, the relation
      between the existence of repeats and antigenic variation is not necessarily straightforward,
      since repeats of P1 adhesin were found to be anti-correlated with epitopes recognized by
      patient antibodies. These different strategies have important consequences for the structures
      of genomes, since large distant repeats correlate well with the major chromosomal
      rearrangements. Probably to avoid such events, mycoplasmas strongly avoid inverse repeats, in
      comparison to co-oriented repeats.
AU  - Rocha EPC
AU  - Blanchard A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2002 30: 2031-2042.

PMID- 26941131
VI  - 4
DP  - 2016
TI  - Genome Sequence of a Mycoplasma meleagridis Field Strain.
PG  - e00017-16
AB  - Mycoplasma meleagridis is a major cause of disease and economic loss in turkeys.  Here, we
      report the genome sequence of an M. meleagridis field strain, which
      enlarges the knowledge about this bacterium and helps the identification of
      possible coding sequences for drug resistance genes and specific antigens.
AU  - Rocha TS
AU  - Bertolotti L
AU  - Catania S
AU  - Pourquier P
AU  - Rosati S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00017-16.

PMID- 4000933
VI  - 13
DP  - 1985
TI  - The chloroplast ribosomal intron of Chlamydomonas reinhardii codes for a polypeptide related to mitochondrial maturases.
PG  - 975-984
AB  - The sequences of the 888bp chloroplast ribosomal intron and of the flanking 23S rRNA gene
      regions of Chlamydomonas reinhardii have been established. The intron can be folded with a
      secondary structure which is typical of group I introns of fungal mitochondrial genes. It
      contains a 489bp open reading frame encoding a potential polypeptide that is related to
      mitochondrial maturases.
AU  - Rochaix JD
AU  - Rahire M
AU  - Michel F
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1985 13: 975-984.

PMID- 28232446
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Flavobacteriumpsychrophilum Strain OSU THCO2-90, Used for Functional Genetic Analysis.
PG  - e01665-16
AB  - We report here the complete annotated genome sequence of Flavobacterium psychrophilum OSU
      THCO2-90, isolated from Coho salmon (Oncorhynchus kisutch) in
      Oregon. The genome consists of a circular chromosome with 2,343 predicted open
      reading frames. This strain has proved to be a valuable tool for functional
      genomics.
AU  - Rochat T
AU  - Barbier P
AU  - Nicolas P
AU  - Loux V
AU  - Perez-Pascual D
AU  - Guijarro JA
AU  - Bernardet JF
AU  - Duchaud E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01665-16.

PMID- 28963207
VI  - 5
DP  - 2017
TI  - Full Sequencing and Genomic Analysis of Three emm75 Group A Streptococcus Strains Recovered in the Course of an Epidemiological Shift in French Brittany.
PG  - e00957-17
AB  - While the incidence and invasiveness of type emm75 group A Streptococcus (GAS) infections
      increased in French Brittany during 2013, we sequenced and analyzed
      the genomes of three independent strains isolated in 2009, 2012, and 2014,
      respectively. In this short-term evolution, genomic analysis evidenced mainly the
      integration of new phages encoding virulence factors.
AU  - Rochefort A
AU  - Boukthir S
AU  - Moullec S
AU  - Meygret A
AU  - Adnani Y
AU  - Lavenier D
AU  - Faili A
AU  - Kayal S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00957-17.

PMID- 9393436
VI  - 256
DP  - 1997
TI  - Transposon-like structure of a new plasmid-encoded restriction-modification system in Rhizobium leguminosarum VF39SM.
PG  - 387-396
AB  - Total DNA isolated from Rhizobium leguminosarum VF39SM cells is resistant to cleavage by the
      restriction endonuclease PstI.  Plasmid curing and transfer studies localized this phenotype
      to pRleVF39b, the second smallest of six plasmids found in this bacterium.  In vitro selection
      for vector modification was employed to isolate a presumptive methylase gene (M.Rle39BI) from
      a plasmid gene library.  Total and plasmid DNAs isolated from E. coli containing M.RleBI were
      resistant to digestion by PstI.  Sequence data suggested that a putative restriction
      endonuclease (R.Rle39BI) was also encoded on the same fragment.  The two genes were flanked by
      identical copies of a putative insertion sequence, which was also present in several copies
      elsewhere in the VF39SM genome.  The presence of this element in other strains examined
      suggested that this element is indeed an insertion sequence.  The differences in G/C content
      between the DNA coding for the R/M system and that of the IS element suggest that this DNA
      region may have been acquired by horizontal transfer.
AU  - Rochepeau P
AU  - Selinger LB
AU  - Hynes MF
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1997 256: 387-396.

PMID- 23074188
VI  - 40
DP  - 2012
TI  - Evolutionary transitions to new DNA methyltransferases through target site expansion and shrinkage.
PG  - 11627-11637
AB  - DNA-binding and modifying proteins show high specificity but also exhibit a certain level of
      promiscuity. Such latent promiscuous activities comprise the
      starting points for new protein functions, but this hypothesis presents a
      paradox: a new activity can only evolve if it already exists. How then, do novel
      activities evolve? DNA methyltransferases, for example, are highly divergent in
      their target sites, but how transitions toward novel sites occur remains unknown.
      We performed laboratory evolution of the DNA methyltransferase M.HaeIII. We found
      that new target sites emerged primarily through expansion of the original site,
      GGCC, and the subsequent shrinkage of evolved expanded sites. Variants evolved
      for sites that are promiscuously methylated by M.HaeIII [GG((A)/(T))CC and
      GGCGCC] carried mutations in 'gate-keeper' residues. They could thereby methylate
      novel target sites such as GCGC and GGATCC that were neither selected for nor
      present in M.HaeIII. These 'generalist' intermediates were further evolved to
      obtain variants with novel target specificities. Our results demonstrate the ease
      by which new DNA-binding and modifying specificities evolve and the mechanism by
      which they occur at both the protein and DNA levels.
AU  - Rockah-Shmuel L
AU  - Tawfik DS
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: 11627-11637.

PMID- 26274323
VI  - 11
DP  - 2015
TI  - Systematic Mapping of Protein Mutational Space by Prolonged Drift Reveals the Deleterious Effects of Seemingly Neutral Mutations.
PG  - e1004421
AB  - Systematic mappings of the effects of protein mutations are becoming increasingly popular.
      Unexpectedly, these experiments often find that proteins are tolerant to
      most amino acid substitutions, including substitutions in positions that are
      highly conserved in nature. To obtain a more realistic distribution of the
      effects of protein mutations, we applied a laboratory drift comprising 17 rounds
      of random mutagenesis and selection of M.HaeIII, a DNA methyltransferase. During
      this drift, multiple mutations gradually accumulated. Deep sequencing of the
      drifted gene ensembles allowed determination of the relative effects of all
      possible single nucleotide mutations. Despite being averaged across many
      different genetic backgrounds, about 67% of all nonsynonymous, missense mutations
      were evidently deleterious, and an additional 16% were likely to be deleterious.
      In the early generations, the frequency of most deleterious mutations remained
      high. However, by the 17th generation, their frequency was consistently reduced,
      and those remaining were accepted alongside compensatory mutations. The tolerance
      to mutations measured in this laboratory drift correlated with sequence exchanges
      seen in M.HaeIII's natural orthologs. The biophysical constraints dictating
      purging in nature and in this laboratory drift also seemed to overlap. Our
      experiment therefore provides an improved method for measuring the effects of
      protein mutations that more closely replicates the natural evolutionary forces,
      and thereby a more realistic view of the mutational space of proteins.
AU  - Rockah-Shmuel L
AU  - Toth-Petroczy A
AU  - Tawfik DS
PT  - Journal Article
TA  - PLOS Comp. Biol.
JT  - PLOS Comp. Biol.
SO  - PLOS Comp. Biol. 2015 11: e1004421.

PMID- 14572033
VI  - 75
DP  - 2003
TI  - Continuous monitoring of a restriction enzyme digest of DNA on a microchip with automated capillary sample introduction.
PG  - 3704-3711
AB  - Continuous analysis of a DNA restriction enzyme digest on a microfabricated device is
      demonstrated with minimal intervention and
      enhanced time resolution. A 62-base-pair fragment of dsDNA containing a
      KpnI site was used to demonstrate this process. A capillary was used to
      transfer sample from a single reaction mix to a microfabricated chip with
      parallel separation lanes. The 6-carboxyfluorescein-labeled DNA fragments
      were detected with a CCD camera as they separated in the lanes, which were
      filled with linear polyacrylamide. The products of the restriction enzyme
      digest were monitored for up to 60 min at an average sampling rate of 1
      injection/46 s, with consecutive injections as short as 1 injection/14 s.
      The digest was injected directly into the chip, eliminating the need for
      any sample-handling steps after addition of the enzyme to the reaction
      mix. The effects of temperature and restriction enzyme concentration were
      briefly examined, as well. This work shows the potential of this method to
      provide valuable information about the process of restriction enzyme
      cleavage.
AU  - Roddy ES
AU  - Price M
AU  - Ewing AG
PT  - Journal Article
TA  - Anal. Chem.
JT  - Anal. Chem.
SO  - Anal. Chem. 2003 75: 3704-3711.

PMID- 1847988
VI  - 225
DP  - 1991
TI  - Isolation and genetic structure of IS112, an insertion sequence responsible for the inactivation of the SalI restriction-modification system of Streptomyces albus G.
PG  - 142-147
AB  - IS112 is a transposable element identified in Streptomyces albus G by its
      frequent mutagenic insertion into the genes for the SalI
      restriction-modification system.  IS112 is present in several copies in the
      genome of S. albus G.  Homologous sequences were detected in other Streptomyces
      strains.  Sequence analysis revealed that IS112 has a length of 883 bp with a
      GC content of 67.4%.  The copy that was isolated contained imperfect inverted
      repeats (16/20 match) at its ends and was flanked by a 2 bp duplication at the
      target site, which was located within the gene (salIR) for the SalI
      endonuclease.  A long open reading frame (ORF) encoding a putative polypeptide
      of 256-253 amino acids spans almost the entire sequence.  Significant homology
      was detected between this polypeptide and that corresponding to ORFB of IS493,
      an insertion sequence recently isolated from Streptomyces lividans 66.
AU  - Rodicio MR
AU  - Alvarez MA
AU  - Chater KF
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1991 225: 142-147.

PMID- Not included in PubMed...
VI  - 213
DP  - 1988
TI  - Cloning and expression of the SalI restriction-modification genes of Streptomyces albus G.
PG  - 346-353
AB  - The Streptomyces albus G genes (salR and salM) for the class II restriction
      enzyme SalI (SalGI) and its cognate modification enzyme were cloned in
      Streptomyces lividans 66.  Selection was initially for the salR gene.  From a
      library of S. albus G DNA in the high copy number plasmid pIJ486 several clones
      of S. lividans were obtained that were resistant to phage PhiC31 unmodified at
      the many SalI sites in its DNA, but were sensitive to modified phages last
      propagated on a restriction-deficient, modification- proficient mutant of S.
      albus G.  SalI activity was detected in cell-free extracts of the clones,
      though only at levels comparable with that in S. albus G.  Five different
      recombinant plasmids were isolated, with inserts of 5.6, 5.7, 8.9, 10 and 18.9
      kb that contained a common region of 4.5 kb.  These plasmids could not be
      digested by SalI, although the vector has four recognition sites for this
      enzyme, indicating that the salM gene was also cloned and expressed.
      Subcloning experiments in S. lividans indicated the approximate location of
      salR and salM, and in Escherichia coli led to detectable expression of salM but
      not of salR.  A variety of previously isolated S. albus G mutants affected in
      aspects of SalI-specific restriction and modification were complemented by the
      cloned DNA; they included a mutant temperature-sensitive for growth apparently
      because of a mutation in salM.  Southern blotting showed that DNA homologous to
      the cloned sal genes was present in Xanthomonas and Rhodococcus strains, but
      not detectably in Herpetosiphon strains, all of which produce SalI
      isoschizomers.
AU  - Rodicio MR
AU  - Chater KF
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1988 213: 346-353.

PMID- 3074016
VI  - 74
DP  - 1988
TI  - The SalI (SalGI) restriction-modification system of Streptomyces albus G.
PG  - 39-42
AB  - The salIR and salM genes of Streptomyces albus G specify the SalGI (SalI)
      restriction enzyme and its cognate methyltransferase, respectively.  These
      enzymes are responsible for restriction and modification of bacteriophages.
      Some phages carry genes that interfere with SalI-specific modification.  The
      sal genes have been cloned in a Streptomyces host-vector system.  Use of the
      cloned DNA as a hybridization probe reveals that sal mutants frequently arise
      from transposition of a DNA segment of approx. 1 kb into the sal genes.  Some,
      but not all, other bacteria that produce SalGI isoschizomers contain nucleotide
      sequences that hybridize with sal DNA.
AU  - Rodicio MR
AU  - Chater KF
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 39-42.

PMID- 7828868
VI  - 151
DP  - 1994
TI  - Organization and sequence of the SalI restriction-modification system.
PG  - 167-172
AB  - The organization and nucleotide (nt) sequences were determined for the genes encoding the SalI
      restriction and modification (R-M) system (recognition sequence 5'-GTCGAC-3') from
      Streptomyces albus G. The system comprises two genes, salIR, coding for the restriction
      endonuclease (ENase, R.SalI; probably 315 amino acids (aa), a predicted Mr of 35,305; product,
      GTCGAC) and salIM, coding for the methyltransferase (MTase, M.SalI; probably 587 aa, a
      predicted Mr of 64,943; product, GRCGm6AC). The genes are adjacent, they have the same
      orientation, and they occur in the order salIR then SalIM. R.SalI contains a putative
      magnesium-binding motif similar to those at the active sites of R.EcoRI and R.EcoRV, but
      otherwise it bears little aa sequence similarity to other ENases. M.SalI is a member of the
      m6A-gamma class of MTases. In aa sequence it resembles M.AccI, another m5A-gamma-MTase whose
      recognition sequence includes the SalI recognition sequence as a subset.
AU  - Rodicio MR
AU  - Quinton-Jager T
AU  - Moran LS
AU  - Slatko BE
AU  - Wilson GG
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1994 151: 167-172.

PMID- 28280021
VI  - 5
DP  - 2017
TI  - Whole-Genome Shotgun Sequencing of Cephalosporin-Resistant Salmonella enterica Serovar Typhi.
PG  - e01639-16
AB  - Typhoid is one of the leading causes of mortality in developing countries. Here,  we report
      the draft genome sequences of four Salmonella enterica serovar Typhi
      strains isolated from bloodstream infections in a tertiary care hospital. The
      sequence data indicate genomes of ~4.5 Mb for all isolates, with one plasmid in
      each.
AU  - Rodrigues C
AU  - Kapil A
AU  - Sharma A
AU  - Devanga RNK
AU  - Inbanathan FY
AU  - Veeraraghavan B
AU  - Kang G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01639-16.

PMID- 26941155
VI  - 4
DP  - 2016
TI  - Draft Genome of Rhodococcus rhodochrous TRN7, Isolated from the Coast of Trindade Island, Brazil.
PG  - e01707-15
AB  - Here, we present a draft genome and annotation of Rhodococcus rhodochrous TRN7, isolated from
      Trindade Island, Brazil, which will provide genetic data to benefit
      the understanding of its metabolism.
AU  - Rodrigues EM
AU  - Pylro VS
AU  - Dobbler PT
AU  - Victoria F
AU  - Roesch LF
AU  - Totola MR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01707-15.

PMID- 29519836
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Labrenzia sp. Strain EL143, a Coral-Associated Alphaproteobacterium with Versatile Symbiotic Living Capability and Strong  Halogen Degradation Potential.
PG  - e00132-18
AB  - We report here the genome sequence of Labrenzia sp. EL143, an alphaproteobacterium isolated
      from the gorgonian coral Eunicella labiata that
      possesses various genes involved in halogen and aromatic compound degradation, as
      well as polyketide synthesis. The strain also maintains multiple genes that
      confer resistance to toxic compounds such as heavy metals and antibiotics.
AU  - Rodrigues GN
AU  - Lago-Leston A
AU  - Costa R
AU  - Keller-Costa T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00132-18.

PMID- Not carried by PubMed...
VI  - 12
DP  - 1995
TI  - Cloning and expression of genes coding for Haemophilus influenzae Rf restriction and modification enzymes.  Purification of the recombinant endonuclease.
PG  - 156-159
AB  - The genes coding for HinfI restriction and modification enzymes were cloned from the
      Haemophilus influenzae Rf strain using pUC18 plasmid as vector.  To select the genes from the
      library, the classical modification phenotype selection was used.  When introduced into
      Escherichia coli HB101 strain, the recombinant plasmid pERHinf4 was able to direct the
      expression of the restriction phenotype.  The crude extracts from the transformed E. coli
      contained roughly twice the amount of restrictase expressed by the natural source.  A
      purification procedure for the restrictase is described which when applied to the recombinant
      enzyme, renders a preparation free of contaminant exonucleases and phosphatases.  The overall
      recovery of the purification procedure was about 33% of the total activity.
AU  - Rodriguez A
AU  - Lleonart R
AU  - Martinez AS
AU  - Ryes G
AU  - Gonzalez E
AU  - Brito JE
PT  - Journal Article
TA  - Biotecnol. Apl.
JT  - Biotecnol. Apl.
SO  - Biotecnol. Apl. 1995 12: 156-159.

PMID- 25931600
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of the Clinical Beijing-Like Strain Mycobacterium tuberculosis 323 Using the PacBio Real-Time Sequencing Platform.
PG  - e00371-15
AB  - We report here the whole-genome sequence of the multidrug-resistant Beijing-like  strain
      Mycobacterium tuberculosis 323, isolated from a 15-year-old female patient
      who died shortly after the initiation of second-line drug treatment. This strain
      is representative of the Beijing-like isolates from Colombia, where this lineage
      is becoming a public health concern.
AU  - Rodriguez JG
AU  - Pino C
AU  - Tauch A
AU  - Murcia MI
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00371-15.

PMID- 8385889
VI  - 209
DP  - 1993
TI  - Polyphosphate present in DNA preparations from Filamentous fungal species of Colletotrichum inhibits restriction endonucleases and other enzymes.
PG  - 291-297
AB  - During the development of a procedure for the isolation of total genomic DNA from filamentous
      fungi (Rodriguez, R.J., and Yoder, O.C., Exp. Myco. 15, 232-242, 1991) a cell fraction was
      isolated which inhibited the digestion of DNA by restriction enzymes. After elimination of
      DNA, RNA, proteins, and lipids, the active compund was purified by gel filtration to yield a
      single fraction capable of complete inhibition of restriction enzyme activity. The inhibitor
      did not absorb uv light above 220 nm, and was resistant to alkali and acid at 25 degrees C and
      to temperatures as high as 100 degrees C. More extensive analyses demonstrated that the
      inhibitor was also capable of inhibiting T4 DNA ligase and TaqI DNA polymerase, but not DNase
      or RNase. Chemical analyses indicated that the inhibitor was devoid of carbohydrates, protein,
      lipids and nucleic acids but rich in phosphorus. A combination of nuclear magnetic resonance,
      metachromatic shift of toluidine blue, and gel filtration indicated that the inhibitor was a
      polyphosphate (polyP) containing approximately 60 phosphate molecules. The mechanism of
      inhibition appeared to involve complexing of polyP to the enzymatic proteins. All species of
      Colletotrichum analyzed produced polyP equivalent in chain length and concentration. A
      modification to the original DNA extraction procedure is described which eliminates polyP and
      reduces the time necessary to obtain DNA of sufficient purity for restriction enzyme digestion
      and TaqI polymerase amplification.
AU  - Rodriguez RJ
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 1993 209: 291-297.

PMID- 20113962
VI  - 20
DP  - 2010
TI  - Comparative functional genomics of mammalian DNA methyltransferases.
PG  - 243-255
AB  - DNA methylation involves biochemical modification of DNA by addition of methyl groups onto CpG
      dinucleotides, and this epigenetic mechanism
      regulates gene expression in disease and development. Mammalian DNA
      methyltransferases, DNMT (DNMT1, DNMT3A and DNMT3B), together with the
      accessory protein DNMT3L establish specific DNA methylation patterns in
      the genome during gametogenesis, embryogenesis and somatic tissue
      development. The present study addresses the structural and functional
      conservation of the DNMT in humans, mice and cattle and the patterns of
      mRNA abundance of the different enzymes during embryogenesis to improve
      understanding of epigenetic regulation in early development. The
      findings showed a high degree of structural and functional conservation
      among the human, mouse, and bovine DNMT. The results also showed
      similar patterns of transcript abundance for all of the proteins at
      different stages of early embryo development. Remarkably, all of the
      DNMT with an important role in DNA methylation (DNMT1, DNMT3A, DNMT3B,
      and DNMT3L) show a greater degree of structural similarity between
      human and bovine than that between human and mouse. These results have
      important implications for the selection of an appropriate model for
      study of DNA methylation during early development in humans.
AU  - Rodriguez-Osorio N
AU  - Wang HF
AU  - Rupinski J
AU  - Bridges SM
AU  - Memili E
PT  - Journal Article
TA  - Reprod. Biomed. Online
JT  - Reprod. Biomed. Online
SO  - Reprod. Biomed. Online 2010 20: 243-255.

PMID- 20370821
VI  - 12
DP  - 2010
TI  - Annotation and overview of the Pseudomonas savastanoi pv. savastanoi NCPPB 3335 draft genome reveals the virulence gene complement of a tumour-inducing pathogen of woody hosts.
PG  - 1604-1620
AB  - Pseudomonas savastanoi pv. savastanoi is a tumour-inducing pathogen of Olea
      europaea L. causing olive knot disease. Bioinformatic analysis of the draft
      genome sequence of strain NCPPB 3335, which encodes 5232 predicted coding genes
      on a total length of 5856 998 bp and a 57.12% G + C, revealed a large degree of
      conservation with Pseudomonas syringae pv. phaseolicola 1448A and P. syringae pv.
      tabaci 11528. However, NCPPB 3335 contains twelve variable genomic regions, which
      are absent in all previously sequenced P. syringae strains. Various features that
      could contribute to the ability of this strain to survive in a woody host were
      identified, including broad catabolic and transport capabilities for degrading
      plant-derived aromatic compounds, the duplication of sequences related to the
      biosynthesis of the phytohormone indoleacetic acid (iaaM, iaaH) and its amino
      acid conjugate indoleacetic acid-lysine (iaaL gene), and the repertoire of
      strain-specific putative type III secretion system effectors. Access to this
      seventh genome sequence belonging to the 'P. syringae complex' allowed us to
      identify 73 predicted coding genes that are NCPPB 3335-specific. Results shown
      here provide the basis for detailed functional analysis of a tumour-inducing
      pathogen of woody hosts and for the study of specific adaptations of a P.
      savastanoi pathovar.
AU  - Rodriguez-Palenzuela P et al
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2010 12: 1604-1620.

PMID- 25384481
VI  - 197
DP  - 2014
TI  - EcoKI Type I Restriction-Modification System in Escherichia coli Affect, but is Not an Absolute Barrier for, Conjugation.
PG  - 337-342
AB  - The rapid evolution of bacteria is crucial to their survival, and is among other  things
      caused by exchange, transfer and uptake of DNA. Conjugation is one of the
      main mechanisms by which bacteria share their DNA, and is thought to be
      controlled by varied bacterial immune systems. Contradictory results, based on
      phenotypical studies, have been presented on Restriction-Modification systems as
      a barrier for conjugation and other means of uptake of exogenous DNA. In this
      study, we show that inactivation of the R.EcoKI restriction enzyme in strain
      Escherichia coli K-12 strain MG1655 increases the conjugational transfer of
      plasmid pOLA52, which carriers two EcoKI recognition sites. Interestingly, the
      results were not absolute, and uptake of un-methylated pOLA52 was still observed
      in the wild-type strain (with intact hsdR gene), but with a reduction of 85%
      compared to the mutant recipient having a disrupted hsdR gene. This leads to the
      conclusion that EcoKI Restriction-Modification affects the uptake of DNA by
      conjugation, but is not a major barrier for plasmid transfer.
AU  - Roer L
AU  - Aarestrup FM
AU  - Hasman H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2014 197: 337-342.

PMID- 27822532
VI  - 1
DP  - 2016
TI  - Is the Evolution of Salmonella enterica subsp. enterica Linked to Restriction-Modification Systems?
PG  - e00009-16
AB  - Salmonella enterica subsp. enterica bacteria are highly diverse foodborne pathogens that are
      subdivided into more than 1,500 serovars. The diversity is
      believed to result from mutational evolution, as well as intra- and interspecies
      recombination that potentially could be influenced by restriction-modification
      (RM) systems. The aim of this study was to investigate whether RM systems were
      linked to the evolution of Salmonella enterica subsp. enterica. The study
      included 221 Salmonella enterica genomes, of which 68 were de novo sequenced and
      153 were public available genomes from ENA. The data set covered 97 different
      serovars of Salmonella enterica subsp. enterica and an additional five genomes
      from four other Salmonella subspecies as an outgroup for constructing the
      phylogenetic trees. The phylogenetic trees were constructed based on multiple
      alignment of core genes, as well as the presence or absence of pangenes. The
      topology of the trees was compared to the presence of RM systems, antimicrobial
      resistance (AMR) genes, Salmonella pathogenicity islands (SPIs), and plasmid
      replicons. We did not observe any correlation between evolution and the RM
      systems in S. enterica subsp. enterica. However, sublineage correlations and
      serovar-specific patterns were observed. Additionally, we conclude that plasmid
      replicons, SPIs, and AMR were all better correlated to serovars than to RM
      systems. This study suggests a limited influence of RM systems on the evolution
      of Salmonella enterica subsp. enterica, which could be due to the conjugational
      mode of horizontal gene transfer in Salmonella. Thus, we conclude that other
      factors must be involved in shaping the evolution of bacteria. IMPORTANCE The
      evolution of bacterial pathogens, their plasticity and ability to rapidly change
      and adapt to new surroundings are crucial for understanding the epidemiology and
      public health. With the application of genomics, it became clear that horizontal
      gene transfer played a key role in evolution. To understand the evolution and
      diversification of pathogens, we need to understand the processes that drive the
      horizontal gene transfer. Restriction-modification systems are thought to cause
      rearrangements within the chromosome, as well as act as a barrier to horizontal
      gene transfer. However, here we show that the correlation between
      restriction-modification systems and evolution in other bacterial species does
      not apply to Salmonella enterica subsp. enterica. In summary, from this work, we
      conclude that other mechanisms might be involved in controlling and shaping the
      evolution of Salmonella enterica subsp. enterica.
AU  - Roer L
AU  - Hendriksen RS
AU  - Leekitcharoenphon P
AU  - Lukjancenko O
AU  - Kaas RS
AU  - Hasman H
AU  - Aarestrup FM
PT  - Journal Article
TA  - mSystems
JT  - mSystems
SO  - mSystems 2016 1: e00009-16.

PMID- 28546491
VI  - 5
DP  - 2017
TI  - Genome Sequence of Acinetobacter lactucae OTEC-02, Isolated from Hydrocarbon-Contaminated Soil.
PG  - e00400-17
AB  - Acinetobacter lactucae OTEC-02 was isolated from hydrocarbon-contaminated soils.  Whole-genome
      sequence analysis was performed to learn more about the strain's
      ability to degrade different types of recalcitrant toxic monoaromatic
      hydrocarbons. The genome of this bacterium revealed its genomic properties and
      versatile metabolic features, as well as a complete prophage.
AU  - Rogel-Hernandez MA
AU  - Guerrero G
AU  - Rincon-Molina CI
AU  - Ruiz-Valdiviezo VM
AU  - Cisneros-Perez C
AU  - Castanon-Gonzalez JH
AU  - Lopez-Lopez A
AU  - Martinez-Romero E
AU  - Rincon-Rosales R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00400-17.

PMID- 15527412
VI  - 69
DP  - 2004
TI  - Plasmid pRARE as a vector for cloning to construct a superproducer of the site-specific nickase N.BspD6I.
PG  - 1123-1127
AB  - The gene of methylase M.SccL1I that protects DNA against hydrolysis with the nickase N.BspD6I
      was inserted into plasmid pRARE carrying
      genes of tRNA, which are rare in E. coli. The insertion of the gene
      sscML1I into pRARE was reasoned by incompatibility of pRARE and the
      plasmid carrying the gene sscML1I, because both plasmids contained the
      same ori-site. Upon transformation of E. coli TOP10F' cells with both
      the recombinant plasmid pRARE/MSsc and the expression vector pET28b
      containing the nickase gene bspD6IN under the phage T7 promoter, a
      strain of E. coli was obtained which produced 7(.)10(5) units of the
      nickase N.BspD6I per 1 g wet biomass, and this yield was two orders of
      magnitude higher than the yield of the enzyme from the strain free of
      pRARE/MSsc.
AU  - Rogulin EA
AU  - Perevyazova TA
AU  - Zheleznaya LA
AU  - Matvienko NI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 2004 69: 1123-1127.

PMID- 21036996
VI  - 193
DP  - 2010
TI  - Complete Genome Sequencing of A Carbon Monooxide Utilizing Acetogen, Eubacterium limosum KIST612.
PG  - 307-308
AB  - Eubacterium limosum KIST612 is an anaerobic acetogenic bacterium that uses CO as a sole
      carbon/energy source and produces acetate, butyrate and
      ethanol. To evaluate its potential as a syngas microbial catalyst, we have
      sequenced the complete 4.3 Mb genome of E. limosum KIST612.
AU  - Roh H
AU  - Ko HJ
AU  - Kim D
AU  - Choi DG
AU  - Park S
AU  - Kim S
AU  - Chang IS
AU  - Choi IG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 193: 307-308.

PMID- 21551311
VI  - 193
DP  - 2011
TI  - Genome Sequence of the Abyssomicin- and Proximicin-Producing Marine Actinomycete Verrucosispora maris AB-18-032.
PG  - 3391-3392
AB  - Verrucosispora maris AB-18-032 is a marine actinomycete that produces atrop-abyssomicin C and
      proximicin A, both of which have novel structures
      and modes of action. In order to understand the biosynthesis of these
      compounds, to identify further biosynthetic potential and to facilitate
      rational improvement of secondary metabolite titers, we have sequenced the
      complete 6.7 Mb genome of Verrucosispora maris AB-18-032.
AU  - Roh H
AU  - Uguru GC
AU  - Ko HJ
AU  - Kim S
AU  - Kim BY
AU  - Goodfellow M
AU  - Bull AT
AU  - Kim KH
AU  - Bibb MJ
AU  - Choi IG
AU  - Stach JE
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3391-3392.

PMID- 22535948
VI  - 194
DP  - 2012
TI  - Genome Sequence of Vibrio sp. Strain EJY3, an Agarolytic Marine Bacterium Metabolizing 3,6-Anhydro-L-Galactose as a Sole Carbon Source.
PG  - 2773-2774
AB  - The metabolic fate of 3,6-anhydro-l-galactose (l-AHG) is unknown in the global marine carbon
      cycle. Vibrio sp. strain EJY3 is an agarolytic marine bacterium
      that can utilize l-AHG as a sole carbon source. To elucidate the metabolic
      pathways of l-AHG, we have sequenced the complete genome of Vibrio sp. strain
      EJY3.
AU  - Roh H
AU  - Yun EJ
AU  - Lee S
AU  - Ko HJ
AU  - Kim S
AU  - Kim BY
AU  - Song H
AU  - Lim KI
AU  - Kim KH
AU  - Choi IG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2773-2774.

PMID- 20601480
VI  - 192
DP  - 2010
TI  - Complete Genome Sequence of Halalkalicoccus jeotgali B3T, an Extremely Halophilic Archaeon.
PG  - 4528-4529
AB  - Halalkalicoccus jeotgali B3(T), isolated from salt-fermented seafood from Korea, is an
      extremely halophilic archaeon belonging to the family
      Halobacteriaceae. Here, we present the complete genome sequence of the
      type strain Hac. jeotgali B3(T) (3,698,650 bp, with a G+C content of
      62.5%), which consists of one chromosome and six plasmids. This is the
      first complete genome sequence of the Halalkalicoccus species.
AU  - Roh SW
AU  - Nam YD
AU  - Nam SH
AU  - Choi SH
AU  - Park HS
AU  - Bae JW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 4528-4529.

PMID- 26450717
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Campylobacter fetus MMM01, Isolated from a Chronic Kidney Disease Patient with Sepsis.
PG  - e01055-15
AB  - Campylobacter fetus is a Gram-negative bacterium that has caused several cases of human and
      animal disease. Here, we report the draft genome sequence of C. fetus MMM01, isolated from the
      blood of a 60-year-old patient with type II diabetes and chronic kidney disease. The sequence
      has a total length of 1,740,393 bp and an average G+C content of 33.1%. The availability of
      the draft genome sequence of C. fetus MMM01 isolated from a case of chronic kidney disease
      will contribute to a better understanding of the pathophysiological mechanisms of this
      organism.
AU  - Rohit A
AU  - Kumar BK
AU  - Deekshit VK
AU  - Rai P
AU  - Kumar RV
AU  - Jayaprakash J
AU  - Madhushankara B
AU  - Karunasagar I
AU  - Karunasagar I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01055-15.

PMID- 17000723
VI  - 74
DP  - 2006
TI  - Potential source of Francisella tularensis live vaccine strain attenuation determined by genome comparison.
PG  - 6895-6906
AB  - Francisella tularensis is a bacterial pathogen that causes the zoonotic
      disease tularemia and is important to biodefense. Currently, the only
      vaccine known to confer protection against tularemia is a specific live
      vaccine strain (designated LVS) derived from a virulent isolate of
      Francisella tularensis subsp. holarctica. The origin and source of
      attenuation of this strain are not known. To assist with the design of a
      defined live vaccine strain, we sought to determine the genetic basis of
      the attenuation of LVS. This analysis relied primarily on the comparison
      between the genome of LVS and Francisella tularensis holarctica strain
      FSC200, which differ by only 0.08% of their nucleotide sequences. Under
      the assumption that the attenuation was due to a loss of function(s), only
      coding regions were examined in this comparison. To complement this
      analysis, the coding regions of two slightly more distantly related
      Francisella tularensis strains were also compared against the LVS coding
      regions. Thirty-five genes show unique sequence variations predicted to
      alter the protein sequence in LVS compared to the other Francisella
      tularensis strains. Due to these polymorphisms, the functions of 15 of
      these genes are very likely lost or impaired. Seven of these genes were
      demonstrated to be under stronger selective constraints, suggesting that
      they are the most probable to be the source of LVS attenuation and useful
      for a newly defined vaccine.
AU  - Rohmer L
AU  - Brittnacher M
AU  - Svensson K
AU  - Buckley D
AU  - Haugen E
AU  - Zhou Y
AU  - Chang J
AU  - Levy R
AU  - Hayden H
AU  - Forsman M
AU  - Olson M
AU  - Johansson A
AU  - Kaul R
AU  - Miller SI
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2006 74: 6895-6906.

PMID- 1802038
VI  - 2
DP  - 1991
TI  - Use of the DNA fragments generated by a restriction enzyme (Bcg I) for the construction of overlapping clone libraries.
PG  - 65-67
AB  - The human genome contains at intervals the sequence recognized by the
      restriction endonuclease BcgI.  We propose to take advantage of the presence of
      this sequence for the construction of overlapping clone libraries.  The
      proposal holds for any other genome in which there are similar projects of
      physical mapping and sequencing.
AU  - Roizes G
AU  - Charlieu J-P
AU  - Marcais B
AU  - Bellis M
PT  - Journal Article
TA  - DNA Seq.
JT  - DNA Seq.
SO  - DNA Seq. 1991 2: 65-67.

PMID- 225204
VI  - 104
DP  - 1979
TI  - A new specific endonuclease from Anabaena variabilis.
PG  - 39-44
AB  - A large number of site-specific endonucleases have been isolated from Anabaena
      variabilis and we now describe a third from this organism, AvaIII, which cuts
      SV40 DNA three times.  From the positions of these breaks on the physical map
      of SV40, the DNA sequence recognised by the enzyme can be deduced.  It has not
      yet been possible to separate this enzyme from AvaI.
AU  - Roizes G
AU  - Nardeux PC
AU  - Monier R
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1979 104: 39-44.

PMID- 478298
VI  - 6
DP  - 1979
TI  - A new site-specific endonuclease showing phenotypical crypticity in a tumorigenic strain of Agrobacterium tumefaciens.
PG  - 43-50
AB  - AtuBVI, an endonuclease showing new site-specificity, has been isolated from
      the tumorigenic strain IIBV7 of Agrobacterium tumefaciens, and is undetectable
      in the non-tumorigenic sister strain IIBNV6.  AtuBVI degrades IIBV7 DNA in
      vitro and should, therefore, be regarded as being phenotypically cryptic in the
      bacterial cell; it also shows anomalous behavior under certain incubation
      conditions.  These properties point to a possible role for this enzyme in the
      insertion of exogenous Ti-plasmid DNA into plant tissues during tumorigenesis.
AU  - Roizes G
AU  - Pages M
AU  - Lecou C
AU  - Patillon M
AU  - Kovoor A
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1979 6: 43-50.

PMID- 913578
VI  - 82
DP  - 1977
TI  - A restriction endonuclease from Agrobacterium tumefaciens.
PG  - 69-70
AB  - The tumorous growth of plant tissues known as Crowngall is induced by certain
      strains of Agrobacterium tumefaciens (Smith and Townsend, Conn.) and there is
      considerable evidence that foreign DNA is integrated in the genome of the
      transformed host cell.  A specific endonuclease of the bacterium could then
      conceivably play a role in the insertion process.  In this letter we describe
      the isolation of a sequence-specific endonuclease from a tumorigenic strain,
      B6, of Agrobacterium tumefaciens.  The recognition site as well as the
      modification specificity of this enzyme, named AtuI, are shown to be identical
      to those of a known restriction enzyme, EcoRI.
AU  - Roizes G
AU  - Patillon M
AU  - Kovoor A
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1977 82: 69-70.

PMID- 24970824
VI  - 2
DP  - 2014
TI  - Genome Sequence of Streptomyces olindensis DAUFPE 5622, Producer of the Antitumoral Anthracycline Cosmomycin D.
PG  - e00541-14
AB  - Streptomyces olindensis DAUFPE 5622, which was isolated from a Brazilian soil sample, produces
      the antitumor anthracycline cosmomycin D. The genome sequence is
      9.4 Mb in length, with a G+C content of 71%. Thirty-four putative secondary
      metabolite biosynthetic gene clusters were identified, including the cosmomycin D
      cluster.
AU  - Rojas JD
AU  - Starcevic A
AU  - Baranasic D
AU  - Ferreira-Torres MA
AU  - Contreras CA
AU  - Garrido LM
AU  - Araujo WL
AU  - de Souza RF
AU  - Zucko J
AU  - Hranueli D
AU  - Long PF
AU  - Cullum J
AU  - Padilla G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00541-14.

PMID- 26159530
VI  - 3
DP  - 2015
TI  - Genome Sequence of Vibrio VPAP30, Isolated from an Episode of Massive Mortality of Reared Larvae of the Scallop Argopecten purpuratus.
PG  - e00745-15
AB  - We report here the 5.167-Mbp draft genome sequence of Vibrio VPAP30, isolated from an
      Argopecten purpuratus larval culture. Vibrio VPAP30 is the etiological
      agent of a vibriosis outbreak causing a complete collapse of a larval culture of
      the scallop A. purpuratus, which occurred in a commercial hatchery in Chile.
AU  - Rojas R
AU  - Miranda CD
AU  - Romero J
AU  - Asenjo F
AU  - Valderrama K
AU  - Segovia C
AU  - Ugalde JA
AU  - Santander J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00745-15.

PMID- 23516222
VI  - 1
DP  - 2013
TI  - Genome Sequences of Avian Pathogenic Escherichia coli Strains Isolated from Brazilian Commercial Poultry.
PG  - e0011013
AB  - Avian pathogenic Escherichia coli (APEC) infections are responsible for significant losses in
      the poultry industry worldwide. The disease might present
      as different local infections or as septicemia. Here, we present the draft genome
      sequences of three Brazilian APEC strains isolated from different kinds of
      infections. The availability of these APEC genome sequences is important for
      gaining a thorough understanding of the genomic features of E. coli, particularly
      those of this pathotype.
AU  - Rojas TC
AU  - Maluta RP
AU  - Parizzi LP
AU  - Koenigkan LV
AU  - Yang J
AU  - Yu J
AU  - Pereira GA
AU  - Dias-da-Silveira W
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0011013.

PMID- 22582380
VI  - 194
DP  - 2012
TI  - Draft Genome of a Brazilian Avian-Pathogenic Escherichia coli Strain and In Silico Characterization of Virulence-Related Genes.
PG  - 3023
AB  - Avian-pathogenic Escherichia coli (APEC) strains cause extraintestinal diseases in avian
      species. Here, we present the draft genome of an APEC strain (SCI-07) from Brazil that was
      isolated from skin lesions (gelatinous edema) on the head and periorbital tissues of a laying
      hen with swollen head syndrome.
AU  - Rojas TC
AU  - Parizzi LP
AU  - Tiba MR
AU  - Chen L
AU  - Pereira GA
AU  - Sangal V
AU  - Yang J
AU  - Yu J
AU  - Dias-da-Silveira W
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3023.

PMID- 29255574
VI  - 12
DP  - 2017
TI  - Draft genome of Paraburkholderia caballeronis TNe-841(T), a free-living, nitrogen-fixing, tomato plant-associated bacterium.
PG  - 80
AB  - 10.1601/nm.26956 caballeronis is a plant-associated bacterium. Strain TNe-841(T)  was isolated
      from the rhizosphere of tomato (Solanum lycopersicum L. var.
      lycopersicum) growing in Nepantla Mexico State. Initially this bacterium was
      found to effectively nodulate Phaseolus vulgaris L. However, from an analysis of
      the genome of strain TNe-841(T) and from repeat inoculation experiments, we found
      that this strain did not nodulate bean and also lacked nodulation genes,
      suggesting that the genes were lost. The genome consists of 7,115,141 bp with a G
      + C content of 67.01%. The sequence includes 6251 protein-coding genes and 87 RNA
      genes.
AU  - Rojas-Rojas FU et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 80.

PMID- 27660789
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Heavy Metal-Resistant Cupriavidus alkaliphilus ASC-732T, Isolated from Agave Rhizosphere in the Northeast of Mexico.
PG  - e01013-16
AB  - Cupriavidus alkaliphilus ASC-732(T) was isolated from the rhizosphere of agave plant growing
      in alkaline soils in San Carlos, Tamaulipas, Mexico. The species is
      able to grow in the presence of arsenic, zinc, and copper. The genome sequence of
      strain ASC-732(T) is 6,125,055 bp with 5,586 genes and an average G+C content of
      67.81%.
AU  - Rojas-Rojas FU
AU  - Huntemann M
AU  - Clum A
AU  - Pillay M
AU  - Palaniappan K
AU  - Varghese N
AU  - Mikhailova N
AU  - Stamatis D
AU  - Reddy TB
AU  - Markowitz V
AU  - Ivanova N
AU  - Kyrpides N
AU  - Woyke T
AU  - Shapiro N
AU  - Ibarra JA
AU  - Estrada-de LSP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01013-16.

PMID- 22887676
VI  - 194
DP  - 2012
TI  - Genome Sequence of Bartonella birtlesii, a Bacterium Isolated from Small Rodents  of the Genus Apodemus.
PG  - 4779
AB  - Bartonella birtlesii is a facultative intracellular bacterium isolated from the blood of small
      mammals of the genus Apodemus. The present study reports the draft
      genome of Bartonella birtlesii strain IBS 135(T) (CIP 106691(T)).
AU  - Rolain JM
AU  - Vayssier-Taussat M
AU  - Gimenez G
AU  - Robert C
AU  - Fournier PE
AU  - Raoult D
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4779.

PMID- 1873344
VI  - 56
DP  - 1991
TI  - Effects of Sphingomyelin and its enzymatic hydrolysis products on heterologous methylation of calf thymus DNA by cytosine-DNA methyltransferase EcoRII.
PG  - 295-300
AB  - It was found that sphingomyelin and its enzymatic hydrolysis products, choline
      and sphingosine, influence the degree of DNA methylation in the reaction of
      heterologous methylation by methylase EcoRII in vitro.  Sphingomyelin was found
      to be able to activate (by 20%), sphingosine and choline inhibit methylation.
      Phosphatidylcholine had no effect on DNA methylation in an in vitro system.
      The role of lipids in the regulation of gene expression during enzymatic
      modification (methylation) of DNA is discussed.
AU  - Romanenko EB
AU  - Pushkareva MY
AU  - Alessenko AV
AU  - Vanyushin BF
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1991 56: 295-300.

PMID- 17223787
VI  - 71
DP  - 2006
TI  - DNA-methyltransferase SsoII as a bifunctional protein: Features of the interaction with the promoter region of SsoII restriction-modification genes.
PG  - 1341-1349
AB  - DNA duplexes bearing an aldehyde group at the 2'-position of the sugar moiety were used for
      affinity modification of (cytosine-5)-DNA
      methyltransferase SsoII. It is shown that lysine residues of M.SsoII
      N-terminal region are located in proximity to DNA sugar-phosphate
      backbone of a regulatory sequence of promoter region of SsoII
      restriction-modification enzyme coding genes. The ability of the two
      M.SsoII subunits to interact with DNA regulatory sequence has been
      demonstrated by affinity modification using DNA duplexes with two
      2'-aldehyde groups. Changes in nucleotide sequence of one half of the
      regulatory region prevented cross-linking of the second M.SsoII
      subunit. The results on sequential affinity modification of M.SsoII by
      two types of modified DNA ligands (i.e. by 2'-aldehyde-containing and
      phosphoryldisulfide-containing) have demonstrated the possibility of
      covalent attachment of the protein to two different DNA recognition
      sites: regulatory sequence and methylation site.
AU  - Romanenkov AS
AU  - Kisil OV
AU  - Zatsepin TS
AU  - Yamskova OV
AU  - Karyagina AS
AU  - Metelev VG
AU  - Oretskaya TS
AU  - Kubareva EA
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 2006 71: 1341-1349.

PMID- 28684570
VI  - 5
DP  - 2017
TI  - Whole-Genome Shotgun Sequence of Salmonella bongori, First Isolated in Northwestern Italy.
PG  - e00560-17
AB  - This study describes the whole-genome shotgun sequence of Salmonella bongori 48:z35:-,
      originally isolated from a 1-year-old symptomatic patient in northwest
      Italy, a typically nonendemic area. The draft genome sequence contained 4.56 Mbp
      and the G+C content was 51.27%.
AU  - Romano A
AU  - Bellio A
AU  - Macori G
AU  - Cotter PD
AU  - Bianchi DM
AU  - Gallina S
AU  - Decastelli L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00560-17.

PMID- 23405290
VI  - 1
DP  - 2013
TI  - Genome Sequence of Lactobacillus saerimneri 30a (Formerly Lactobacillus sp. Strain 30a), a Reference Lactic Acid Bacterium Strain Producing Biogenic Amines.
PG  - e00097-12
AB  - Lactobacillus sp. strain 30a (Lactobacillus saerimneri) produces the biogenic amines
      histamine, putrescine, and cadaverine by decarboxylating their amino acid
      precursors. We report its draft genome sequence (1,634,278 bases, 42.6% G+C
      content) and the principal findings from its annotation, which might shed light
      onto the enzymatic machineries that are involved in its production of biogenic
      amines.
AU  - Romano A
AU  - Trip H
AU  - Campbell-Sills H
AU  - Bouchez O
AU  - Sherman D
AU  - Lolkema JS
AU  - Lucas PM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00097-12.

PMID- 1338116
VI  - 54
DP  - 1992
TI  - Screening for restriction endonucleases in methane-oxidizing bacteria.
PG  - 32-39
AB  - 51 methane-oxidizing bacterial strains such as Methylomonas methanica, M.rubra, Methylococcus
      capsulatus, M. thermophilus, M. luteus, M. ucrainicus, M. whittenburyi, Methylosinus
      trichosporium, M. sporium, Methylocystis parvus isolated from various ecological niches and
      geographical regions of the Ukraine and also the strains received from R. Whittenbury and Y.
      Heyer were screened for restriction endonucleases. Type II restriction endonucleases were
      detected in IMV B-3112 (=12 b), IMV B-3027 (=26), IMV B-3019 (=9 c), IMV B-3017 (=17 c). IMV
      B-3226 (=26 v). IMV B-3033 (=Y), IMV B-3100 (=100) and IMV B-3494 (=IE494). The results
      obtained were indicative of a relatively high frequency of occurrence of restriction enzymes
      in methane-oxidizing bacteria. There were KpnI (Asp718I) restriction endonuclease
      isoschizomers in crude extracts of IMV B-3112, B-3017, B-3019, B-3027 isolated from
      fresh-water silt as well as in IMV B-3226 strain isolated from waste-water silt. Although
      these isolates had been previously considered as atypical strains of M. ucrainicus, more
      detailed study of their properties allowed placing them with Methylovarius luteus
      (=Methylococcus luteus). IMV B-3494 strain was identified as Methylococcus capsulatus. Strain
      IMV B-3033 had earlier been allocated to Methylovarius whittenburyi (=Methylococcus
      whittenburyi). Specificity of restriction endonucleases of this strain was not tested.
      Therefore, for the first time restriction endonucleases were detected in methane-oxidizing
      bacteria. 8 strains (3 species) among 51 strains (13 species) were found to produce
      restriction endonucleases displaying three different types of specificity at least. Producers
      of restriction endonucleases having KpnI (Asp718I) specificity were isolated from different
      water and silt samples of the Dnieper flood-land more than 20 years ago.
AU  - Romanovskaya VA
AU  - Alexeyev MF
AU  - Gunkovskaya NV
AU  - Stolyar SM
AU  - Shatohina ES
AU  - Malashenko YR
PT  - Journal Article
TA  - Mikrobiol. Zh.
JT  - Mikrobiol. Zh.
SO  - Mikrobiol. Zh. 1992 54: 32-39.

PMID- 29496827
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Escherichia albertii Strain 1551-2, a Potential Extracellular and Intracellular Pathogen.
PG  - e00075-18
AB  - Escherichia albertii has recently been recognized as an emerging human and bird enteric
      pathogen. Here, we report the complete chromosome sequence of a clinical
      isolate of E. albertii strain 1551-2, which may provide information about the
      pathogenic potential of this new species and the mechanisms of evolution of
      Escherichia species.
AU  - Romao FT
AU  - Hernandes RT
AU  - Ooka T
AU  - Hayashi T
AU  - Sperandio V
AU  - Gomes TAT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00075-18.

PMID- Not included in PubMed...
VI  - 136
DP  - 1990
TI  - Abortive phage infection and restriction/modification activities directed by pTR2030 determinants are enhanced by recombination with conjugal elements in lactococci.
PG  - 1817-1824
AB  - The recombinant plasmid pTK6 is composed of a 13.6 kb fragment from pTR2030
      encoding phage resistance determinants for restriction/modification (R+/M+) and
      abortive phage infection (Hsp+) cloned into shuttle vector pSA3 (erythromycin
      resistance, Emr).  Conjugal matings were performed to mobilize pTK6-encoded
      markers from Lactococcus lactis subsp. lactis MMS362 and MG1363.  Emr
      transconjugants were recovered at 10-6 per input donor and harboured pTK6 or
      recombinant plasmids not found in either parental strain.  The recombinant
      plasmids (pTRK78 and pTRK79) encoded Emr, Hsp+ and R+/M+, and transferred at
      high frequency in second-round matings.  Mobilization of pTK6 from the
      otherwise plasmid-free donor, L. lactis MG1363, confirmed the presence of a
      conjugal element in this strain.  Phage resistance in transconjugants
      containing pTRK78 and pTRK79 was markedly enhanced over a pTK6-directed Hsp+
      and R+/M+.  In L. lactis LM2345 transconjugants, a reduction in plaque size was
      accompanied by a significant decrease in the efficiency of plaquing for phages
      c2 (10-2 to 10-6) and p2(<10-9).  L. lactis NCK203 transconjugants containing
      pTRK78 or pTRK79 exhibited an additional 100-1000-fold reduction in the
      plaquing efficiency of Phi48 (10-4 to 10-5) over pTK6 imposed restriction
      (10-2).  Increased resistance to phage was a consequence of the physical
      interaction of pTR2030-derived sequences on pTK6 with a conjugal element
      resident in the donor strains.
AU  - Romero DA
AU  - Klaenhammer TR
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1990 136: 1817-1824.

PMID- 10049392
VI  - 181
DP  - 1999
TI  - Complete sequence of a 184-kilobase catabolic plasmid from Sphingomonas aromaticivorans F199.
PG  - 1585-1602
AB  - The complete 184,457-bp sequence of the aromatic catabolic plasmid, pNL1,
      from Sphingomonas aromaticivorans F199 has been determined.  A total of 186 open
      reading frames are predicted to encode proteins, of which 79 are likely directly
      associated with catabolism or transport of aromatic compounds.  Genes that encode
      enzymes associated with the degradation of biphenyl, naphthalene, m-xylene, and p-
      cresol are predicted to be distributed among 15 gene clusters.  The unusual coclustering
      of genes associated with different pathways appears to have evolved in response to
      similarities in biochemical mechanisms required for the degradation of intermediates in
      different pathways.  A putative efflux pump and several hypothetical membrane-
      associated proteins were identified and predicted to be involved in the transport of
      aromatic compounds and/or intermediates in catabolism across the cell wall.  Several
      genes associated with integration and recombination, including two group II intron-
      associated maturases, were identified in the replication region, suggesting that pNL1 is
      able to undergo integration and excision events with the chromosome and/or other
      portions of the plasmid.  Conjugative transfer of pNL1 to another Sphingomonas sp. was
      demonstrated, and genes associated with this function were found in two large clusters.
      Approximately one-third of the ORFs (59 of them) have no obvious homology to known
      genes.
AU  - Romine MF
AU  - Stillwell LC
AU  - Wong K-K
AU  - Thurston SJ
AU  - Sisk EC
AU  - Sensen C
AU  - Gaasterland T
AU  - Fredrickson JK
AU  - Saffer JD
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1999 181: 1585-1602.

PMID- 25573925
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Sphingomonas sp. Strain Ant20, Isolated from Oil-Contaminated Soil on Ross Island, Antarctica.
PG  - e01309-14
AB  - Here, we present the draft genome of Sphingomonas sp. strain Ant20, isolated from oil-polluted
      soil near Scott Base, Ross Island, Antarctica. The genome of this
      aromatic hydrocarbon-degrading bacterium provides valuable information on the
      microbially mediated biodegradation of aromatic compounds in cold-climate
      systems.
AU  - Ronca S
AU  - Frossard A
AU  - Guerrero LD
AU  - Makhalanyane TP
AU  - Aislabie JM
AU  - Cowan DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01309-14.

PMID- 27491996
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Two Avian Pathogenic Escherichia coli Strains of Clinical Importance, E44 and E51.
PG  - e00768-16
AB  - Avian pathogenic Escherichia coli strains have remarkable impacts on animal welfare and the
      production economy in the poultry industry worldwide. Here, we
      present the draft genomes of two isolates from chickens (E44 and E51) obtained
      from field outbreaks and subsequently investigated for their potential for use in
      autogenous vaccines for broiler breeders.
AU  - Ronco T
AU  - Stegger M
AU  - Andersen PS
AU  - Pedersen K
AU  - Li L
AU  - Thofner IC
AU  - Olsen RH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00768-16.

PMID- 28596409
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of a Sequence Type 398 Methicillin-Resistant Staphylococcus aureus Isolate from a Danish Dairy Cow with Mastitis.
PG  - e00492-17
AB  - Livestock-associated (LA) methicillin-resistant Staphylococcus aureus (MRSA) strains of
      sequence type 398 (ST398) colonize both humans and various livestock
      species. In 2016, an ST398 LA-MRSA isolate (Sa52) was collected from a Danish
      dairy cow with mastitis, and here, we report the draft genome sequence of strain
      Sa52.
AU  - Ronco T
AU  - Stegger M
AU  - Pedersen K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00492-17.

PMID- 26993463
VI  - 194
DP  - 2016
TI  - Structural basis for recognition of histone H3K36me3 nucleosome by human de novo  DNA methyltransferases 3A and 3B.
PG  - 357-367
AB  - DNA methylation is an important epigenetic modification involved in chromatin organization and
      gene expression. The function of DNA methylation depends on cell
      context and is correlated with histone modification patterns. In particular,
      trimethylation of Lys36 on histone H3 tail (H3K36me3) is associated with DNA
      methylation and elongation phase of transcription. PWWP domains of the de novo
      DNA methyltransferases DNMT3A and DNMT3B read this epigenetic mark to guide DNA
      methylation. Here we report the first crystal structure of the DNMT3B PWWP
      domain-H3K36me3 complex. Based on this structure, we propose a model of the
      DNMT3A PWWP domain-H3K36me3 complex and build a model of DNMT3A (PWWP-ADD-CD) in
      a nucleosomal context. The trimethylated side chain of Lys36 (H3K36me3) is
      inserted into an aromatic cage similar to the 'Royal' superfamily domains known
      to bind methylated histones. A key interaction between trimethylated Lys36 and a
      conserved water molecule stabilized by Ser270 explains the lack of affinity of
      mutated DNMT3B (S270P) for the H3K36me3 epigenetic mark in the ICF
      (Immunodeficiency, Centromeric instability and Facial abnormalities) syndrome.
      The model of the DNMT3A-DNMT3L heterotetramer in complex with a dinucleosome
      highlights the mechanism for recognition of nucleosome by DNMT3s and explains the
      periodicity of de novo DNA methylation.
AU  - Rondelet G
AU  - Dal Maso T
AU  - Willems L
AU  - Wouters J
PT  - Journal Article
TA  - J. Struct. Biol.
JT  - J. Struct. Biol.
SO  - J. Struct. Biol. 2016 194: 357-367.

PMID- 28795598
VI  - 9
DP  - 2017
TI  - Inhibition studies of DNA methyltransferases by maleimide derivatives of RG108 as non-nucleoside inhibitors.
PG  - 1465-1481
AB  - AIM: DNA methyltransferases (DNMTs) are important drug targets for epigenetic therapy of
      cancer. Nowadays, non-nucleoside DNMT inhibitors are in development to
      address high toxicity of nucleoside analogs. However, these compounds still have
      low activity in cancer cells and mode of action of these compounds remains
      unclear. MATERIALS and METHODS: In this work, we studied maleimide derivatives of
      RG108 by biochemical, structural and computational approaches to highlight their
      inhibition mechanism on DNMTs. RESULTS: Findings demonstrated a correlation
      between cytotoxicity on mesothelioma cells of these compounds and their
      inhibitory potency against DNMTs. Noncovalent and covalent docking studies,
      supported by crystallographic (apo structure of M.HhaI) and differential scanning
      fluorimetry assays, provided detailed insights into their mode of action and
      revealed essential residues for the stabilization of such compounds inside DNMTs.
      [Formula: see text].
AU  - Rondelet G
AU  - Fleury L
AU  - Faux C
AU  - Masson V
AU  - Dubois J
AU  - Arimondo PB
AU  - Willems L
AU  - Wouters J
PT  - Journal Article
TA  - Future Med Chem
JT  - Future Med Chem
SO  - Future Med Chem 2017 9: 1465-1481.

PMID- 22247526
VI  - 194
DP  - 2012
TI  - Draft Genome Sequences of the Pseudomonas fluorescens Biocontrol Strains Wayne1R and Wood1R.
PG  - 724-725
AB  - Pseudomonas fluorescens strains Wayne1R and Wood1R have proven capacities to improve plant
      health. Here we report the draft genome sequences and
      automatic annotations of both strains. Genome comparisons reveal
      similarities with P. fluorescens strain Pf-5, reveal the novelty of
      Wood1R, and indicate some genes that may be related to biocontrol.
AU  - Rong X
AU  - Baysal GF
AU  - Meulia T
AU  - McSpadden GBB
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 724-725.

PMID- 22247532
VI  - 194
DP  - 2012
TI  - Draft Genome Sequences of the Biocontrol Bacterium Mitsuaria sp. Strain H24L5A.
PG  - 734-735
AB  - Mitsuaria sp. strain H24L5A is a plant-associated bacterium with proven capacities to suppress
      plant pathogens. Here, we report the draft genome
      sequences and automatic annotation of H24L5A. Comparative genomic analysis
      indicates H24L5A's similarity to the Leptothrix and Methylibium species,
      as well as several genes potentially contributing to its biocontrol
      activities.
AU  - Rong X
AU  - Gurel FB
AU  - Meulia T
AU  - McSpadden GBB
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 734-735.

PMID- 25838480
VI  - 3
DP  - 2015
TI  - Draft Whole-Genome Sequences of 14 Vibrio parahaemolyticus Clinical Isolates with an Ambiguous K Serogroup.
PG  - e00217-15
AB  - Vibrio parahaemolyticus is a bacterial pathogen responsible for mild to severe
      gastroenteritis, wound infections, and septicemia resulting from the ingestion or
      handling of raw or undercooked contaminated seafood. Here, we report the draft
      whole-genome sequences and annotations of 14 Canadian V. parahaemolyticus
      clinical isolates that were serologically identified as K group II using
      polyvalent antisera but were not specifically K serogrouped using monovalent
      antisera.
AU  - Ronholm J
AU  - Petronella N
AU  - Kenwell R
AU  - Banerjee S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00217-15.

PMID- 27660774
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Two Salmonella enterica Strains Isolated from Sprouted  Chia and Flax Seed Powders.
PG  - e00963-16
AB  - A 2014 foodborne salmonellosis outbreak in Canada and the United States implicated, for the
      first time, sprouted chia seed powder as the vehicle of
      transmission. Here, we report the draft whole genome sequences of two Salmonella
      enterica strains isolated from sprouted powders related to the aforementioned
      outbreak.
AU  - Ronholm J
AU  - Petronella N
AU  - Tamber S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00963-16.

PMID- 27660773
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of 11 Salmonella enterica Strains with Variable Levels of  Barotolerance.
PG  - e00952-16
AB  - The diversity of the genus Salmonella is reflected in the physiological adaptations used by
      its members in response to stressors such as high pressure.
      Here we report the draft whole genome sequences of 11 Salmonella enterica
      strains, five sensitive strains and six demonstrating high levels of pressure
      resistance.
AU  - Ronholm J
AU  - Petronella N
AU  - Tamber S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00952-16.

PMID- 2041758
VI  - 19
DP  - 1991
TI  - RmaI, a type II restriction endonuclease from Rhodothermus marinus which recognizes 5' CTAG 3'.
PG  - 2789
AB  - RmaI, an isoschizomer of MaeI has been isolated from Rhodothermus marinus. RmaI recognizes the
      palindromic sequence 5'-CTAG-3'.  Like its isoschizomer RmaI cleaves the sequence, C/TAG,
      generating 5'-protruding TA-dinucleotides. The recognition sequence of RmaI was determined
      using double digestions on pBR322- and phiX174 DNAs (figure 1, lanes 2-6 and 8-12).  The
      cleavage patterns obtained were compared with computer-derived mapping data.  The data
      predicts the sequence 5'-CTAG-3'.  The sequence was also tested by digesting Lambda- and
      M13mp18 DNAs with RmaI (figure 1, lanes 13 and 14).  The fragments obtained matched the
      computer predicted fragments that would be produced when cleaving at 5'-CTAG-3'.  RmaI has
      the following number of recognition sites on these commonly used DNAs: pUC19, pBR322, phiX174,
      SV40, M13mp18, T7, Lambda and Adeno2.  The cleavage site of RmaI was determined by cleavage of
      primed synthesis reaction.  M13mp19 DNA containing the recognition site of RmaI was used as a
      template.  Using an M13 sequencing primer the DNA was sequenced according to Sanger et al.  In
      addition to the four standard reactions a fifth reaction was performed which was extended
      through the RmaI recognition site. The reaction was terminated by heat treatment and the
      product was cleaved with RmaI.  The cleaved product was divided in two.  The addition of
      Klenow to one part resulted in a band migrating with the A-band (figure 2, lane +).  The
      cleaved product (figure 2, lane -) migrated with the C-band.  Thus, the cleavage site for RmaI
      is:
      5'-C/TA-G-3'
      3'-G-AT/C-5'.
AU  - Ronka J
AU  - Hjorleifsdottir S
AU  - Tenkanen T
AU  - Pitkanen K
AU  - Mattila P
AU  - Kristjansson JK
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 2789.

PMID- 28160295
VI  - 40
DP  - 2017
TI  - Comparative assessment of Vibrio virulence in marine fish larvae.
PG  - 1373-1385
AB  - Vibrionaceae infections are a major obstacle for marine larviculture; however,
      little is known about virulence differences of Vibrio strains. The virulence of
      Vibrio strains, mostly isolated from vibriosis outbreaks in farmed fish, was
      tested in larval challenge trials with cod (Gadus morhua), turbot (Scophthalmus
      maximus) and halibut (Hippoglossus hippoglossus) using a multiwell dish assays
      with single-egg/larvae cultures. The strains differed significantly in virulence
      as some caused a high mortality of larva reaching 100% mortality after a few
      days, while others had no or only marginal effects on survival. Some Vibrio
      strains were pathogenic in all of the larva species, while some caused disease
      only in one of the species. Twenty-nine of the Vibrio anguillarum strains
      increased the mortality of larvae from at least one fish species; however,
      pathogenicity of the strains differed markedly. Other Vibrio species had no or
      less pronounced effects on larval mortalities. Iron uptake has been related to V.
      anguillarum virulence; however, the presence or absence of the plasmid pJM1
      encoding anguibactin did not correlate with virulence. The genomes of V.
      anguillarum were compared (D. Castillo, P.W. D'Alvise, M. Middelboe and L. Gram,
      unpublished data) and most of the high-virulent strains had acquired virulence
      genes from other pathogenic Vibrio.
AU  - Ronneseth A
AU  - Castillo D
AU  - D'Alvise P
AU  - Tonnesen O
AU  - Haugland G
AU  - Grotkjaer T
AU  - Engell-Sorensen K
AU  - Norremark L
AU  - Bergh O
AU  - Wergeland HI
AU  - Gram L
PT  - Journal Article
TA  - J. Fish Dis.
JT  - J. Fish Dis.
SO  - J. Fish Dis. 2017 40: 1373-1385.

PMID- 26205857
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Cellulolytic and Xylanolytic Thermophile Clostridium clariflavum Strain 4-2a.
PG  - e00797-15
AB  - Clostridium clariflavum strain 4-2a, a novel strain isolated from a thermophilic  biocompost
      pile, has demonstrated an extensive capability to utilize both
      cellulose and hemicellulose under thermophilic anaerobic conditions. Here, we
      report the draft genome of this strain.
AU  - Rooney EA et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00797-15.

PMID- 25953163
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Biocontrol Strain Pseudomonas fluorescens LBUM223.
PG  - e00443-15
AB  - Pseudomonas fluorescens LBUM223 is a plant growth-promoting rhizobacterium (PGPR) with
      biocontrol activity against various plant pathogens. It produces the
      antimicrobial metabolite phenazine-1-carboxylic acid, which is involved in the
      biocontrol of Streptomyces scabies, the causal agent of common scab of potato.
      Here, we report the complete genome sequence of P. fluorescens LBUM223.
AU  - Roquigny R
AU  - Arseneault T
AU  - Gadkar VJ
AU  - Novinscak A
AU  - Joly DL
AU  - Filion M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00443-15.

PMID- 28082495
VI  - 5
DP  - 2017
TI  - Genome Sequence of Christensenella minuta DSM 22607T.
PG  - e01451-16
AB  - Obesity influences and is influenced by the human gut microbiome. Here, we present the genome
      of Christensenella minuta, a highly heritable bacterial
      species which has been found to be strongly associated with obesity through an
      unknown biological mechanism. This novel genome provides a valuable resource for
      future obesity therapeutic studies.
AU  - Rosa BA
AU  - Hallsworth-Pepin K
AU  - Martin J
AU  - Wollam A
AU  - Mitreva M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01451-16.

PMID- 383999
VI  - 129
DP  - 1979
TI  - Electron microscopic studies of the mechanism of action of the restriction endonuclease of Escherichia coli B.
PG  - 619-635
AB  - Reaction intermediates and products formed by the restriction endonuclease of Escherichia coli
      B with fd replicative form DNA substrates containing recognition sites in known positions and
      orientations have been characterized by electron microscopy.  After exposure of these
      substrates to enzyme, loops of duplex DNA were frequently observed, usually at or near the
      termini.  Analysis of the size and structure of the loops observed with various DNA substrates
      suggests that the enzyme binds initially to the recognition site then remains bound to the DNA
      in the region of this site while tracking towards a site of cleavage.  Tracking appears to
      occur only on the 5' side of the asymmetric recognition sequence, 5' . . .
      T-G-A-(N)8-T-G-C-T . . . 3'; however, the location of the cleavage sites appears to be
      random, at least within certain limits of distance from the recognition site.  Enzyme-DNA
      complexes remain intact even after the double-strand cleavage is completed, and this complex
      acts as a potent ATPase with no obvious function.  This latter reaction might represent an
      artifactual uncoupling of ATP hydrolysis from the tracking of the enzyme along the DNA;
      alternatively, it might indicate an in vivo function for the enzyme of which we are unaware.
AU  - Rosamond J
AU  - Endlich B
AU  - Linn S
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1979 129: 619-635.

PMID- 27417845
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Seven Bacterial Strains Isolated from a Polymicrobial Culture of Coccolith-Bearing (C-Type) Emiliania huxleyi M217.
PG  - e00673-16
AB  - Strains of Rhodobacteraceae, Sphingomonadales, Alteromonadales, and Bacteroidetes were
      isolated from a polymicrobial culture of the coccolith-forming (C-type)
      haptophyte Emiliania huxleyi strain M217. The genomes encode genes for the
      production of algal growth factors and the consumption of their hosts' metabolic
      by-products, suggesting that the polymicrobial culture harbors many symbiotic
      interactions.
AU  - Rosana AR
AU  - Orata FD
AU  - Xu Y
AU  - Simkus DN
AU  - Bramucci AR
AU  - Boucher Y
AU  - Case RJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00673-16.

PMID- 25999575
VI  - 3
DP  - 2015
TI  - Draft genome sequences of clostridium strains native to Colombia with the potential to produce solvents.
PG  - e00486-15
AB  - Genomes from four Clostridium sp. strains considered to be mesophilic anaerobic bacteria,
      isolated from crop soil in Colombia, with a strong potential to produce
      alcohols like 1,3-propanediol, were analyzed. We present the draft genome of
      these strains, which will be useful for developing genetic engineering
      strategies.
AU  - Rosas-Morales JP
AU  - Perez-Mancilla X
AU  - Lopez-Kleine L
AU  - Montoya CD
AU  - Riano-Pachon DM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00486-15.

PMID- 12083790
VI  - 295
DP  - 2002
TI  - Importance of phosphate contacts for sequence recognition by EcoRI restriction enzyme.
PG  - 198-205
AB  - We have studied the importance of charge and hydrogen-bonding potential of the phosphodiester
      backbone for binding and cleavage by EcoRI restriction endonuclease.  We used 12-mer
      oligodeoxynucleotide substrates with single substitutions of phosphates by chiral
      methylphosphonates at each position of the recognition sequence -pGpApApTpTpCp-.  Binding was
      moderately reduced between 4- and 400-fold more or less equally for the RP and SP-analogues
      mainly caused by missing charge interaction.  The range of cleavage effects was much wider.
      Four substrates were not cleaved at all.  At both flanking positions and in the purine half of
      the sequence up to the central position, cleavage was more impaired than binding and
      differences between RP and SP diastereomers were more pronounced.  These effects are easily
      interpreted by direct phosphate contacts seen in the crystal structure.  For the effects of
      substitutions in the pyrimidine half of the recognition sequence, more indirect effects have
      to be discussed.
AU  - Rosati O
AU  - Srivastava TK
AU  - Katti SB
AU  - Alves J
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 2002 295: 198-205.

PMID- 9512532
VI  - 26
DP  - 1998
TI  - Consensus-degenerate hybrid oligonucleotide primers for amplification of distantly related sequences.
PG  - 1628-1635
AB  - We describe a new primer design strategy for PCR amplification of unknown targets that are
      related to multiply-aligned protein sequences.  Each primer consists of a short 3' degenerate
      core region and a longer 5' consensus clamp region. Only 3-4 highly conserved amino acid
      residues are necessary for design of the core, which is stabilized by the clamp during
      annealing to template molecules.  During later rounds of amplification, the non-degenerate
      clamp permits stable annealing to product molecules.  We demonstrate the practical utility of
      this hybrid primer method by detection of diverse reverse transcriptase-like genes in a human
      genome, and by detection of C5 DNA methyltransferase homologs in various plant DNAs.  In each
      case, amplified products were sufficiently pure to be cloned without gel fractionation.  This
      Consensus-Degenerate Hybrid Oligonucleotide Primer strategy has been implemented as a computer
      program that is accessible over the World Wide Web (http://blocks.fhcrc.org/codehop.html) and
      is directly linked from the BlockMaker multiple sequence alignment site for hybrid primer
      prediction beginning with a set of related protein sequences.
AU  - Rose TM
AU  - Schultz ER
AU  - Henikoff JG
AU  - Pietrokovski S
AU  - McCallum CM
AU  - Henikoff S
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1998 26: 1628-1635.

PMID- 16971456
VI  - 34
DP  - 2006
TI  - Homing endonuclease I-CreI derivatives with novel DNA target specificities - mutant homing enzyme via mutagenesis for DNA cleavage and gene therapy.
PG  - 4791-4800
AB  - Homing endonucleases are highly specific enzymes, capable of recognizing and cleaving unique
      DNA sequences in complex genomes. Since such DNA
      cleavage events can result in targeted allele-inactivation and/or
      allele-replacement in vivo, the ability to engineer homing endonucleases
      matched to specific DNA sequences of interest would enable powerful and
      precise genome manipulations. We have taken a step-wise genetic approach
      in analyzing individual homing endonuclease I-CreI protein/DNA contacts,
      and describe here novel interactions at four distinct target site
      positions. Crystal structures of two mutant endonucleases reveal the
      molecular interactions responsible for their altered DNA target
      specificities. We also combine novel contacts to create an endonuclease
      with the predicted target specificity. These studies provide important
      insights into engineering homing endonucleases with novel target
      specificities, as well as into the evolution of DNA recognition by this
      fascinating family of proteins.
AU  - Rosen LE
AU  - Morrison HA
AU  - Masri S
AU  - Brown MJ
AU  - Springstubb B
AU  - Sussman D
AU  - Stoddard BL
AU  - Seligman LM
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2006 34: 4791-4800.

PMID- 231683
VI  - 135
DP  - 1979
TI  - Survey and mapping of restriction endonuclease cleavage sites in bacteriophage T7 DNA.
PG  - 907-915
AB  - A survey of restriction endonucleases having different cleavage specificities
      has identified 10 that do not cut wild-type bacteriophage T7 DNA, 11 that cut
      at six or fewer sites, four that cut at 18 to 45 sites, and 12 that cut at more
      than 50 sites.  All the cleavage sites for the 13 enzymes that cut a 26 or
      fewer sites have been mapped.  Cleavage sites for each of the 10 enzymes that
      do not cut T7 DNA would be expected to occur an average of 9 to 10 times in a
      random nucleotide sequence the length of T7 DNA.  A possible explanation for
      the lack of any cleavage sites for these enzymes might be that T7 encounters
      enzymes having these specificities in natural hosts, and that the sites have
      been eliminated from T7 DNA by natural selection.  Five restriction
      endonucleases were found to cut within the terminal repetition of T7 DNA; one
      of these, KpnI, cuts at only three additional sites in the T7 DNA molecule.
      The length of the terminal repetition was estimated by two independent means to
      be approximately 155 to 160 base-pairs.
AU  - Rosenberg AH
AU  - Simon MN
AU  - Studier FW
AU  - Roberts RJ
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1979 135: 907-915.

PMID- Not included in PubMed...
VI  - 0
DP  - 1987
TI  - Development of a Protein Design Strategy for EcoRI Endonuclease.
PG  - 237-250
AB  - The 3 angstrom structure of a co-crystalline recognition complex between EcoRI
      endonuclease and the cognate oligonucleotide TCGCGAATTCGCG has been solved.
      Each subunit of the endonuclease is organized into a domain with a/b
      architecture.  The b-sheet consists of anti-parallel and parallel motifs.  The
      amino acid residues which interact directly with the DNA to perform the
      hydrolysis are located primarily in the anti-parallel motif, while those which
      form sequence specific hydrogen bonds with the bases are found in the parallel
      motif.  The hydrolytic active site is located in a cleft which is not fully
      assembled in this structure (which was obtained in the absence of magnesium).
      The DNA conformation departs significantly from those which have been observed
      in crystals containing pure DNA; suggesting that the altered conformation has
      been stabilized by the enzyme.  The conformations seen only upon protein
      binding are termed neo-conformations to distinguish them from those which are
      intrinsically stable in the absence of protein.  The determinants of sequence
      specificity include "modular" interactions based on the crossover
      alpha-helices, i.e., those which connect the b-strands of the parallel segment
      of the principal B-sheet.  They are pointing into the major groove of the DNA
      and amino acid side chains at the amino ends of these helices form bidentate
      hydrogen bonding interactions with the bases.  The inner recognition module
      consists of two symmetry-related alpha-helices which recognize the inner
      tetranucleotide (AATT), while the two symmetry-equivalent outer recognition
      modules are single alpha-helices which recognize the GC base pairs.
AU  - Rosenberg J
AU  - Wang B
AU  - Frederick C
AU  - Reich N
AU  - Greene P
AU  - Grable J
AU  - McClarin J
PT  - Journal Article
TA  - Protein Eng.
JT  - Protein Eng.
SO  - Protein Eng. 1987 0: 237-250.

PMID- Not included in PubMed...
VI  - 1
DP  - 1991
TI  - Structure and function of restriction endonucleases.
PG  - 104-113
AB  - The past year has seen significant advances in our understanding of the
      structure and function of restriction endonucleases.  The highlights include a
      revised chain tracing for EcoRI endonuclease from Escherichia coli, structures
      soon to be reported for E. coli EcoRV endonuclease and significant advances in
      the biochemistry and molecular genetics of both enzymes.
AU  - Rosenberg JM
PT  - Journal Article
TA  - Curr. Opin. Struct. Biol.
JT  - Curr. Opin. Struct. Biol.
SO  - Curr. Opin. Struct. Biol. 1991 1: 104-113.

PMID- 6765637
VI  - 1
DP  - 1981
TI  - The structure and function of the EcoRI restriction endonuclease.
PG  - 131-164
AB  - *

        I. DNA mapping

       II. X-ray diffraction analysis of EcoRI endonuclease crystals

      III. DNA binding properties of EcoRI methylase and endonuclease

       IV. Degeneracies in restriction recognition sequences

      

AU  - Rosenberg JM
AU  - Boyer HW
AU  - Greene P
PT  - Journal Article
TA  - Gene Amplif. Anal.
JT  - Gene Amplif. Anal.
SO  - Gene Amplif. Anal. 1981 1: 131-164.

PMID- 682193
VI  - 122
DP  - 1978
TI  - Preliminary X-ray diffraction analysis of crystalline EcoRI endonuclease.
PG  - 241-245
AB  - EcoRI endonuclease crystallizes in space group C2 with unit cell parameters a =
      209 angstroms, b = 129 angstroms, c = 50 angstroms and B = 98.4o.  Four 29,000
      molecular weight subunits per asymmetric unit would give a reasonable Vm value
      of 2.87 cubic angstroms/dalton.  EcoRI endonuclease is the first protein which
      recognizes a specific sequence of bases in DNA to be crystallized in a form
      suitable for high resolution structure analysis.
AU  - Rosenberg JM
AU  - Dickerson RE
AU  - Greene PJ
AU  - Boyer HW
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1978 122: 241-245.

PMID- 6299667
VI  - 1
DP  - 1982
TI  - EcoRI* specificity and hydrogen bonding.
PG  - 117-124
AB  - Under standard conditions, EcoRI endonuclease uniquely recognizes the inverted
      repeat GAATTC.  However, this specificity breaks down under non-standard
      conditions into what has been termed EcoRI* specificity, wherein many other
      sequences are recognized.  We show here that the hydrolysis rates at all known
      EcoRI* sites can be summarized by the hierarchies: G > > A > T > > C at the
      first position, A > > [G,C] > > T at the second and third position, and the
      corresponding complements at the last three positions.  This is consistent with
      a recognition model which assumes that there are two specific hydrogen bonds
      per base pair under standard conditions.  One or more of these are randomly
      replaced by water under EcoRI* conditions and the position of a sequence within
      the appropriate bonds are common recognition features that can be identified by
      examining the DNA.  The recognition points thereby identified for EcoRI all
      fall within the major groove of the DNA.
AU  - Rosenberg JM
AU  - Greene P
PT  - Journal Article
TA  - DNA
JT  - DNA
SO  - DNA 1982 1: 117-124.

PMID- 3856713
VI  - 9B
DP  - 1985
TI  - Structure of DNA-EcoRI endonuclease complex at 3 angstroms resolution.
PG  - 101
AB  - The 3 angstrom structure of a co-crystalline recognition complex between EcoRI
      endonuclease and the oligonucleotide TCGCGAATTCGCG will be reported.  The DNA
      and the protein share a common (crystallographic) two-fold axis of rotational
      symmetry, as expected from the intrinsic symmetry of the recognition site
      (GAATTC).  The DNA conformation within the complex is different from that found
      in the absence of protein suggesting that the set of conformational states
      which are accessable to protein-free DNA is expanded by the binding of sequence
      specific proteins.  These include the torsional neo-1 kink which widens the
      major groove by unwinding the DNA by approximately 25o thereby facilitating
      contact between the edges of the purine bases and amino acid side chains.  A
      second (neo-2) kink is located three base-pairs away which also facilitates
      access of protein to DNA and/or has a role in the hydrolytic mechanism of this
      enzyme.  A five stranded a/b structure forms the foundation of each
      endonuclease subunit with the strands of beta-sheet and the alpha-helices
      oriented approximately perpendicular to the average DNA helix axis.
      Polypeptide loops at the carboxy edge of the beta-sheet form a cleft which
      contains the segment of DNA backbone spanning the scissile bond.  (DNA
      hydrolysis was inhibited via omission of Mg+2).  The cleft is complementary to
      one strand of double helical DNA and its shape determined by the intrinsic
      twist of b-sheet.  This novel feature suggests that DNA and protein are
      intrinsically complementary at fundamental level.  Sequence specificity is
      determined by "modular" interactions.  One large symmetric module recognizes
      the inner tetranucleotide (AATT while two additional symmetry-equivalent
      modules recognizes the outer base pairs.  The inner module consists of two
      symmetry equivalent alpha-helices which project from the a/b units.  Lysine and
      glutamic acid side chains at the ends of the alpha-helices hydrogen bond to the
      adenine residues thereby determining the specificity for the inner
      tetranucleotide.  The outer module is formed by a separate segment of the
      polypeptide chain containing an arginine side chain which hydrogen bonds to
      guanine.
AU  - Rosenberg JM
AU  - McClarin J
AU  - Grable J
AU  - Frederick C
AU  - Samudzi C
AU  - Jen-Jacobson L
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1985 9B: 101.

PMID- 3505899
VI  - 5
DP  - 1987
TI  - Structure and function of the EcoRI restriction endonuclease.
PG  - 119-145
AB  - The highly specific recognition of the double-stranded sequence d(GAATTC) by
      EcoRI endonuclease offers compelling advantages as a system for investigating
      sequence specific recognition of DNA.  It is a small protein (31,065 daltons,
      276 amino acids) of known sequence which forms highly stable catalytically
      active dimers in solution.  The enzyme hydrolyzes the phosphodiester bond
      between the guanylic and adenylic acid residues resulting in a 5'-phosphate.
      The reaction proceeds with inversion of configuration at the reactive
      phosphorus, implying that there is an odd number of chemical events during the
      hydrolysis.  The simplest interpretation of this observation is that the enzyme
      does not form a covalent intermediate with the DNA.  Although EcoRI
      endonuclease requires Mg2+ for phosphodiester bond hydrolysis, it binds
      specifically to its cognate hexanucleotide in the absence of Mg2+ with a
      dissociation constant on the order of 10-11 M-1.  The enzyme also binds DNA in
      a nonspecific manner ie., at sites other than GAATTC; this does not result in
      hydrolysis of the DNA.  It has been postulated that the nonspecific complex
      enhances the rate of formation of formation of the specific complex by
      facilitated diffusion along the DNA.  Both the EcoRI endonuclease and the EcoRI
      methylase recognize the same hexanucleotide; however, the latter methylates the
      central adenine residues of both strands at the exocyclic N-6 amino group.
      When either one or both groups is methtylated the endonuclease no longer
      cleaves the DNA.  Thus, EcoRI endonuclease not only discriminates between its
      hexanucleotide and all other hexanucleotides, it also discriminates between
      different methtylation states of the same hexanucleotide.  Cocrystals of DNA
      and protein that diffract to high resolution are required for a full
      understanding of sequence specificity in the EcoRI system.  We have obtained
      cocrystals and determined their structure.  Here we report the structure of the
      recognition complex including interactions involved in sequence specificity.
AU  - Rosenberg JM
AU  - McClarin JA
AU  - Frederick CA
AU  - Grable J
AU  - Boyer HW
AU  - Greene PJ
PT  - Journal Article
TA  - Gene Amplif. Anal.
JT  - Gene Amplif. Anal.
SO  - Gene Amplif. Anal. 1987 5: 119-145.

PMID- Not carried by PubMed...
VI  - 0
DP  - 1987
TI  - The structure and function of EcoRI endonuclease.
PG  - 11-43
AB  - The 3 angstrom structure of a co-crystalline recognition complex between EcoRI
      endonuclease and the cognate oligonucleotide TCGCGAATTCGCG has been solved by
      the ISIR method using a platinum isomorphous derivative.  Each subunit of the
      endonuclease is organized into an a/b domain based on a five stranded
      beta-sheet and an extension, called the "arm" which wraps around the DNA.  The
      primary beta-sheet consists of anti-parallel and parallel motifs which contain
      the sites of DNA strand scission and sequence specific recognition,
      respectively.  The hydrolytic active site is located in a cleft which binds the
      DNA backbone in the vicinity of the scissile bond.  The DNA conformation
      departs significantly from those which have been observed in crystals
      containing pure DNA; suggesting that the altered conformation has been
      stabilized by the enzyme.  The conformations seen only upon protein binding are
      termed neo-conformations to distinguish them from those which are intrinsically
      stable in the absence of protein.  Sequence specificity is determined by
      "modular" interactions based on the crossover alpha-helices, i.e., those which
      connect the beta-strands of the parallel segment of the principal beta-sheet.
      They are pointing into the major groove of the DNA and amino acid side chains
      at the amino ends of these helices form bidentate interactions with the bases.
      The inner recognition module consists of two symmetry-related alpha-helices
      which recognize the inner tetranucleotide (AATT), while the two
      symmetry-equivalent outer recognition modules are single alpha-helices wihch
      recognize the GC base pairs.
AU  - Rosenberg JM
AU  - McClarin JA
AU  - Frederick CA
AU  - Wang B-C
AU  - Boyer HW
AU  - Grable J
AU  - Greene P
PT  - Journal Article
TA  - Biological Organization: Macromolecular Interactions at High Resolution.
JT  - Biological Organization: Macromolecular Interactions at High Resolution.
SO  - Biological Organization: Macromolecular Interactions at High Resolution. 1987 0: 11-43.

PMID- Not carried by PubMed...
VI  - 26B
DP  - 1986
TI  - The 3 angstrom structure of a DNA-EcoRI endonuclease recognition complex.
PG  - 147-157
AB  - The 3 angstrom structure of a co-crystalline recognition complex between EcoRI
      endonuclease and the cognate oligonucleotide TCGCGAATTCGCG has been solved by
      the ISIR method using a platinum isomorphous derivative.  Each subunit of the
      endonuclease is organized into an a/b domain based on a five stranded
      beta-sheet and an extension, called the "arm", which wraps around the DNA.  The
      primary beta-sheet consists of anti-parallel and parallel sub-domains which
      contain the sites of DNA strand scission and sequence specific recognition,
      respectively.  The hydrolytic active site is located in a cleft which binds the
      DNA backbone in the vicinity of the scissile bond.  The DNA conformation
      departs significantly from those which have been observed in crystals
      containing pure DNA; suggesting that the altered conformation has been
      stabilized by the enzyme.  The conformations seen only upon protein binding are
      termed neo-conformations to distinguish them from those which are intrinsically
      stable in the absence of protein.  Sequence specificity is determined by
      "modular" interactions based on the crossover alpha-helices, i.e., those which
      connect the beta-strands of the parallel segment of the principal beta-sheet.
      They are pointing into the major groove of the DNA and amino acid side chains
      at the amino ends of these helices form bidentate interactions with the bases.
      The inner recognition module consists of two symmetry-related alpha-helices
      which recognize the inner tetranucleotide (AATT), while the two
      symmetry-equivalent outer recognition modules are single alpha-helices which
      recognize the GC base pairs.
AU  - Rosenberg JM
AU  - McClarin JA
AU  - Frederick CA
AU  - Wang B-C
AU  - Boyer HW
AU  - Greene P
PT  - Journal Article
TA  - Chem. Scr.
JT  - Chem. Scr.
SO  - Chem. Scr. 1986 26B: 147-157.

PMID- 
VI  - 0
DP  - 1987
TI  - Structure of the DNA-EcoRI endonuclease recognition complex.
PG  - 255-259
AB  - The 3 angstrom structure of the co-crystalline recognition complex between
      EcoRI endonuclease and the cognate oligonucleotide TCGCGAATTCGCG has been
      solved by the ISIR method using a platinum isomorphous derivative.  Refinement
      is in progress.  The endonuclease-DNA recognition complex consists of a
      distorted double helix and a protein dimer composed of identical subunits
      related by a two-fold axis of rotational symmetry.  The distortions of the DNA
      are induced by the binding of the protein.  They are concentrated into separate
      features which are localized disruptions of the double helical symmetry.  These
      disruptions appear to have structural consequences which propagate over long
      distances through the DNA via twisting and perhaps bending effects.  They are
      therefore referred to as neo-kinks.  The Type-I neo-kink spans the central
      two-fold symmetry axis of the complex and it introduces a net unwinding of 25
      degrees into the DNA.  This increases the separation of the DNA backbones
      across the major groove thereby facilitating access by the protein to the base
      edges, which are at the floor of the groove.  The Type-I neo-kink also realigns
      adjacent adenine residues within the central AATT tetranucleotide so as to
      create the detailed geometry necessary for amino acid side chains to bridge
      across these purines.
AU  - Rosenberg JM
AU  - McClarin JA
AU  - Frederick CA
AU  - Wang B-C
AU  - Grable J
AU  - Boyer HW
AU  - Greene P
PT  - Journal Article
TA  - Structure, Dynamics and Function of Biomolecules
JT  - Structure, Dynamics and Function of Biomolecules
SO  - Structure, Dynamics and Function of Biomolecules 1987 0: 255-259.

PMID- Not included in PubMed...
VI  - 12
DP  - 1987
TI  - Structure and recognition mechanism of EcoRI endonuclease.
PG  - 395-398
AB  - The structure of a complex between EcoRI endonuclease and a cognate
      oligonucleotide shows that sequence specificity is mediated by 12 protein-DNA
      hydrogen bonds.  These interactions discriminate the EcoRI recognition site
      from all other sequences because any base substitution would rupture at least
      one of these hydrogen bonds.
AU  - Rosenberg JM
AU  - McClarin JA
AU  - Frederick CA
AU  - Wang B-C
AU  - Grable J
AU  - Boyer HW
AU  - Greene P
PT  - Journal Article
TA  - Trends Biochem. Sci.
JT  - Trends Biochem. Sci.
SO  - Trends Biochem. Sci. 1987 12: 395-398.

PMID- 3005116
VI  - 39
DP  - 1985
TI  - EcoK restriction during in vitro packaging of coliphage lambda DNA.
PG  - 313-315
AB  - The K restriction system of Escherichia coli works in vitro [Meselson and Yuan,
      Nature 217 (1968) 1110-1114].  E. coli C lacks the K restriction system.  I
      show that in vitro packaging in standard E. coli K-12-derived systems effects a
      loss of plaque-former output from K-unmodified lambda DNA relative to
      K-modified lambda DNA when compared with packaging in the E. coli C-derived
      system of Rosenberg et al. [Gene 38 (1985) 165-175].  I conclude that the EcoK
      restriction system is active in standard in vitro packaging systems.  EcoK
      restriction during in vitro packaging could specifically depress recovery of
      some lambdaand cosmid clones of eukaryotic DNA or any other DNA not modified
      for EcoK restriction.
AU  - Rosenberg SM
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1985 39: 313-315.

PMID- 19060169
VI  - 75
DP  - 2009
TI  - Genome analysis of the meat starter culture bacterium Staphylococcus carnosus TM300.
PG  - 811-822
AB  - The Staphylococcus carnosus genome has the highest GC content of all
      sequenced staphylococcal genomes, with 34.6%, and therefore represents a
      species that is set apart from S. aureus, S. epidermidis, S.
      saprophyticus, and S. haemolyticus. With only 2.56 Mbp, the genome belongs
      to a family of smaller staphylococcal genomes, and the ori and ter regions
      are asymmetrically arranged with the replichores I (1.05 Mbp) and II (1.5
      Mbp). The events leading up to this asymmetry probably occurred not that
      long ago in evolution, as there was not enough time to approach the
      natural tendency of a physical balance. Unlike the genomes of pathogenic
      species, the TM300 genome does not contain mobile elements such as
      plasmids, insertion sequences, transposons, or STAR elements; also, the
      number of repeat sequences is markedly decreased, suggesting a
      comparatively high stability of the genome. While most S. aureus genomes
      contain several prophages and genomic islands, the TM300 genome contains
      only one prophage, PhiTM300, and one genomic island, nuSCA1, which is
      characterized by a mosaic structure mainly composed of species-specific
      genes. Most of the metabolic core pathways are present in the genome. Some
      open reading frames are truncated, which reflects the nutrient-rich
      environment of the meat starter culture, making some functions
      dispensable. The genome is well equipped with all functions necessary for
      the starter culture, such as nitrate/nitrite reduction, various sugar
      degradation pathways, two catalases, and nine osmoprotection systems. The
      genome lacks most of the toxins typical of S. aureus as well as genes
      involved in biofilm formation, underscoring the nonpathogenic status.
AU  - Rosenstein R
AU  - Nerz C
AU  - Biswas L
AU  - Resch A
AU  - Raddatz G
AU  - Schuster SC
AU  - Gotz F
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2009 75: 811-822.

PMID- 21326336
VI  - 5
DP  - 2011
TI  - RNA-seq reveals cooperative metabolic interactions between two termite-gut spirochete species in co-culture.
PG  - 1133-1142
AB  - The hindguts of wood-feeding termites typically contain hundreds of
      microbial species. Together with their insect host, these gut microbes
      degrade lignocellulose into usable catabolites. Although past research
      revealed many facets of the stepwise flow of metabolites in this scheme,
      not much is known about the breadth of interactions occurring between
      termite-gut microbes. Most of these microbes are thought to depend on, and
      to have co-speciated with, their host and each other for millions of
      years. In this study, we explored the interactions of two spirochetes
      previously isolated from the very same termite species. As hydrogen (H(2))
      is the central free intermediate in termite-gut lignocellulose digestion,
      we focused on interactions between two closely related termite-gut
      spirochetes possessing complementary H(2) physiologies: one produces H(2),
      while the other consumes it. In vitro, these two Treponema species
      markedly enhanced each other's growth. RNA sequencing resolved the
      transcriptomes of these two closely related organisms, revealing that
      co-cultivation causes comprehensive changes in global gene expression. The
      expression of well over a 100 genes in each species was changed >twofold,
      with over a dozen changed >10-fold. Several changes implicating
      synergistic cross-feeding of known metabolites were validated in vitro.
      Additionally, certain activities beneficial to the host were
      preferentially expressed during consortial growth. However, the majority
      of changes in gene expression are not yet understandable, but indicate a
      broad, comprehensive and mutualistic interaction between these closely
      related, co-resident gut symbionts. The results suggest that staggeringly
      intricate networks of metabolic and gene interactions drive lignocellulose
      degradation and co-evolution of termite gut microbiota.
AU  - Rosenthal AZ
AU  - Matson EG
AU  - Eldar A
AU  - Leadbetter JR
PT  - Journal Article
TA  - ISME J.
JT  - ISME J.
SO  - ISME J. 2011 5: 1133-1142.

PMID- 22815447
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Treponema sp. Strain JC4, a Novel Spirochete Isolated from the Bovine Rumen.
PG  - 4130
AB  - Morphologically and biochemically diverse members of the Treponema genus are present in the
      gastrointestinal tract of ruminants, yet very little is understood
      about their functional importance to this microbiome. Here we describe the
      annotated draft genome sequence of Treponema sp. strain JC4, a novel spirochete
      isolated from a bovine rumen sample.
AU  - Rosewarne CP
AU  - Cheung JL
AU  - Smith WJ
AU  - Evans PN
AU  - Tomkins NW
AU  - Denman SE
AU  - O'Cuiv P
AU  - Morrison M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4130.

PMID- 23405323
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Clostridium sp. Maddingley, Isolated from Coal-Seam Gas  Formation Water.
PG  - e00081-12
AB  - Clostridium sp. Maddingley was isolated as an axenic culture from a brown coal-seam formation
      water sample collected from Victoria, Australia. It lacks the solventogenesis genes found in
      closely related clostridial strains. Metabolic reconstructions suggest that volatile fatty
      acids are the main fermentation end products.
AU  - Rosewarne CP
AU  - Greenfield P
AU  - Li D
AU  - Tran-Dinh N
AU  - Bradbury MI
AU  - Midgley DJ
AU  - Hendry P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00081-12.

PMID- 23405289
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Methanobacterium sp. Maddingley, Reconstructed from Metagenomic Sequencing of a Methanogenic Microbial Consortium Enriched from  Coal-Seam Gas Formation Water.
PG  - e00082-12
AB  - The draft genome of Methanobacterium sp. Maddingley was reconstructed from metagenomic
      sequencing of a methanogenic microbial consortium enriched from coal-seam gas formation water.
      It is a hydrogenotrophic methanogen predicted to grow using hydrogen and carbon dioxide.
AU  - Rosewarne CP
AU  - Greenfield P
AU  - Li D
AU  - Tran-Dinh N
AU  - Midgley DJ
AU  - Hendry P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00082-12.

PMID- 23586779
VI  - 14
DP  - 2013
TI  - Reductive evolution in Streptococcus agalactiae and the emergence of a host adapted lineage.
PG  - 252
AB  - BACKGROUND: During host specialization, inactivation of genes whose function is
      no more required is favored by changes in selective constraints and evolutionary
      bottlenecks. The Gram positive bacteria Streptococcus agalactiae (also called
      GBS), responsible for septicemia and meningitis in neonates also emerged during
      the seventies as a cause of severe epidemics in fish farms. To decipher the
      genetic basis for the emergence of these highly virulent GBS strains and of their
      adaptation to fish, we have analyzed the genomic sequence of seven strains
      isolated from fish and other poikilotherms. RESULTS: Comparative analysis shows
      that the two groups of GBS strains responsible for fish epidemic diseases are
      only distantly related. While strains belonging to the clonal complex 7 cannot be
      distinguished from their human CC7 counterparts according to their gene content,
      strains belonging to the ST260-261 types probably diverged a long time ago. In
      this lineage, specialization to the fish host was correlated with a massive gene
      inactivation and broad changes in gene expression. We took advantage of the low
      level of sequence divergence between GBS strains and of the emergence of
      sublineages to reconstruct the different steps involved in this process.
      Non-homologous recombination was found to have played a major role in the genome
      erosion. CONCLUSIONS: Our results show that the early phase of genome reduction
      during host specialization mostly involves accumulation of small and likely
      reversible indels, followed by a second evolutionary step marked by a higher
      frequency of large deletions.
AU  - Rosinski-Chupin I
AU  - Sauvage E
AU  - Mairey B
AU  - Mangenot S
AU  - Ma L
AU  - Da Cunha V
AU  - Rusniok C
AU  - Bouchier C
AU  - Barbe V
AU  - Glaser P
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2013 14: 252.

PMID- 15186419
VI  - 52
DP  - 2004
TI  - The Mycoplasma fermentans prophage phiMFV1: genome organization, mobility and variable expression of an encoded surface protein.
PG  - 1703-1720
AB  - The approximately 16 kb genome of the Mycoplasma fermentans phiMFV1 prophage is described, and
      its mobility, replication and effect on the
      mycoplasma surface phenotype are demonstrated. In various M. fermentans
      strains, phiMFV1 was either absent or integrated at diverse (and sometimes
      multiple) chromosomal sites, each marked by a conserved TTTTTA target
      sequence that is duplicated upon integration. Precise excision,
      replication of an extrachromosomal form and loss of phiMFV1 from the
      mycoplasmal genome were documented in a series of clonal derivatives of M.
      fermentans propagated in culture. Of 18 open reading frames (ORFs) encoded
      by phiMFV1, most can be ascribed functions related to phage biology,
      whereas one encodes a unique coiled-coil membrane surface protein, Mem,
      that was confirmed to be expressed in propagating populations of M.
      fermentans. With the exception of Mem and other minor ORFs, the striking
      similarity between the deduced proteomes of phiMFV1 and the recently
      described phiMAV1 of arthritogenic strains of Mycoplasma arthritidis,
      along with the prominent gene synteny between these elements, provides the
      taxonomic basis for a new family of prophage. Their coding features are
      consistent with long-term residence in mycoplasma genomes and the
      divergence of species within a phylogenetic clade of mycoplasmas. The
      unique Mem protein expressed from phiMFV1 and the unique hypothetical
      surface lipoproteins encoded by phiMAV1 and phiMFV1 also suggest that
      prophage-associated genes may provide specific, selectable phenotypic
      traits during co-evolution of mycoplasma species with their respective
      mammalian hosts. Retention of these labile prophage elements in organisms
      with such drastically reduced genome sizes implies a significant role in
      adaptation and survival.
AU  - Roske K
AU  - Calcutt MJ
AU  - Wise KS
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2004 52: 1703-1720.

PMID- 27469962
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Photobacterium sp. Strain J15, Isolated from Seawater of Southwestern Johor, Malaysia.
PG  - e00739-16
AB  - Here, we report the genome sequences of Photobacterium sp. strain J15, isolated from seawater
      in Johor, Malaysia, with the ability to produce lipase and
      asparaginase. The PacBio genome sequence analysis of Photobacterium sp. strain
      J15 generated revealed its potential in producing enzymes with different
      catalytic functions.
AU  - Roslan NN
AU  - Sabri S
AU  - Oslan SN
AU  - Baharum SN
AU  - Leow TC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00739-16.

PMID- 29146857
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequence of Salmonella enterica subsp. enterica Serovar Typhimurium  Strain UPM 260, Isolated from a Broiler Chicken in Perak, Malaysia.
PG  - e01272-17
AB  - Salmonella enterica subsp. enterica serovar Typhimurium is one of several well-categorized
      Salmonella serotypes recognized globally. Here, we report the
      whole-genome sequence of S Typhimurium strain UPM 260, isolated from a broiler
      chicken.
AU  - Roslan NS
AU  - Jabeen S
AU  - Mat IN
AU  - Omar AR
AU  - Bejo MH
AU  - Ideris A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01272-17.

PMID- 4610987
VI  - 52
DP  - 1973
TI  - Modification-deficient mutants of bacteriophage Pl.  I. Restriction by Pl cryptic lysogens.
PG  - 213-222
AB  - The Pl restriction-modification system is responsible for the inefficient
      plating of c2 and c3 mutants of bacteriophage Pl on Pl cryptic lysogens.  Pl
      cryptic is a defective prophage which does not express Pl immunity but which
      does express Pl modification and restriction.  The rare c2 or c3 phage which do
      grow on the Pl cryptic lysogens [abbreviated (Plcry)], lose their ability to do
      so after growth on a nonlysogenic host.  Temperature-sensitive c2 mutants grown
      on a nonlysogenic host at the permissive temperature plate efficiently on
      (Plcry).  If grown at a nonpermissive temperature, however, the c2 ts mutants
      plate inefficiently on (Plcry).  Plr-m+, a nonrestricting P1 phage, plates
      efficiently on (Plcry), but Plr-m-, which neither restricts nor modifies,
      plates inefficiently on (Plcry).  These results are explained as follows:  Pl
      DNA is itself a substrate for the Pl directed modification-restriction system.
      Normally, during lytic growth, Pl DNA is modified.  However, Plr-m-, c2, and c3
      mutants are modification-defective.  Thus, when their unmodified DNA enters
      (Plcry), it is subject to Pl restriction.  Direct evidence for this hypothesis
      was obtained from experiments in which the abilitiy of Pl phage to modify
      lambda was studied.  Plr-m-, c2 and c3 mutants cannot modify lambda whereas Pl
      wild type and Plr-m+ are able to do so.  Furthermore, c2 and c3 mutants can
      complement each other to express Pl modification.  Plr-m- is not complemented
      by either c2 or c3 mutants.  It is concluded that c2 and c3 are two cistrons
      required for P1 modification.  Plr-m- may be missing, or unable to transcribe,
      the c2 and c3 genes.
AU  - Rosner JL
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1973 52: 213-222.

PMID- 27811112
VI  - 4
DP  - 2016
TI  - Metagenome-Assembled Genome Sequence of Pseudomonas stutzeri Strain CO183 Isolated from a Coalbed Methane Well.
PG  - e01237-16
AB  - A near-complete Pseudomonas stutzeri draft genome was extracted from a coalbed metagenome. The
      draft genome described herein provides insight into the
      functional pathways encoded by this bacterium and its potential role in coalbed
      methane environments.
AU  - Ross DE
AU  - Gulliver D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01237-16.

PMID- 27795237
VI  - 4
DP  - 2016
TI  - Reconstruction of a Nearly Complete Pseudomonas Draft Genome Sequence from a Coalbed Methane-Produced Water Metagenome.
PG  - e01024-16
AB  - The draft genome sequence of Pseudomonas stutzeri strain K35 was separated from a metagenome
      derived from a produced water microbial community of a coalbed methane
      well. The genome encodes a complete nitrogen fixation pathway and the upper and
      lower naphthalene degradation pathways.
AU  - Ross DE
AU  - Gulliver D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01024-16.

PMID- 28883141
VI  - 5
DP  - 2017
TI  - Metagenome-Assembled Genome Sequences of Acetobacterium sp. Strain MES1 and Desulfovibrio sp. Strain MES5 from a Cathode-Associated Acetogenic Microbial  Community.
PG  - e00938-17
AB  - Draft genome sequences of Acetobacterium sp. strain MES1 and Desulfovibrio sp. strain MES5
      were obtained from the metagenome of a cathode-associated community
      enriched within a microbial electrosynthesis system (MES). The draft genome
      sequences provide insight into the functional potential of these microorganisms
      within an MES and a foundation for future comparative analyses.
AU  - Ross DE
AU  - Marshall CW
AU  - May HD
AU  - Norman RS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00938-17.

PMID- 25593246
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Sulfurospirillum sp. Strain MES, Reconstructed from the  Metagenome of a Microbial Electrosynthesis System.
PG  - e01336-14
AB  - A draft genome of Sulfurospirillum sp. strain MES was isolated through taxonomic  binning of a
      metagenome sequenced from a microbial electrosynthesis system (MES)
      actively producing acetate and hydrogen. The genome contains the nosZDFLY genes,
      which are involved in nitrous oxide reduction, suggesting the potential role of
      this strain in denitrification.
AU  - Ross DE
AU  - Marshall CW
AU  - May HD
AU  - Norman RS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01336-14.

PMID- 2165387
VI  - 114
DP  - 1990
TI  - Restriction enzymes.
PG  - 906
AB  - None
AU  - Ross DW
PT  - Journal Article
TA  - Arch. Pathol. Lab. Med.
JT  - Arch. Pathol. Lab. Med.
SO  - Arch. Pathol. Lab. Med. 1990 114: 906.

PMID- 2833428
VI  - 61
DP  - 1987
TI  - Characterization of the Escherichia coli modified cytosine restriction (mcrB) gene.
PG  - 277-289
AB  - The McrB restriction system of Escherichia coli K-12 is responsible for the
      inactivation of 5-methylcytosine-containing DNA.  The mcrB mutation of E. coli
      strain K802 was complemented by hybrid plasmid pUC9-14 which consists of a
      5.5-kb BglII-EcoRI fragment from the E. coli K-12 chromosome cloned in pUC9
      (Ross and Braymer, 1987).  The limits of the mcrB gene within the 5.5-kb insert
      were defined by deletion portions of the fragment and assaying for McrB
      restriction of M. AluI-methylated DNA.   A 51-kDa polypeptide was identified as
      the mcrB gene product based on an analysis of maxicell-labeled polypeptides
      from pUC9-14 and deletion derivatives of this plasmid.  Deletion analyses and
      transcription initiation assays enabled us to determine the direction of
      transcription and translation of mcrB.  Transcription initiates approx. 710 bp
      beyond the end of the hsdS gene, and proceeds in the same direction as the
      transcription of the hsdR, hsdM, and hsdS genes, which is clockwise on the
      conventional E. coli map.
AU  - Ross TK
AU  - Achberger EC
AU  - Braymer HD
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1987 61: 277-289.

PMID- 2649480
VI  - 171
DP  - 1989
TI  - Nucleotide sequence of the McrB region of Escherichia coli K-12 and evidence for two independent translational initiation sites at the mcrB locus.
PG  - 1974-1981
AB  - The McrB restriction system of Escherichia coli K-12 is responsible for the
      biological inactivation of foreign DNA that contains 5-methylcytosine residues.
      Within the McrB region of the chromosome is the mcrB gene, which encodes a
      protein of 51 kilodaltons (kDa), and the mcrC gene, the product of which is 39
      kDa.  The nucleotide sequence of a 2695-base-pair segment encompassing the McrB
      region was determined.  The deduced amino acid sequence was used to identify
      two open reading frames specifying peptides of 455 and 348 amino acids,
      corresponding to the products of the mcrB and mcrC genes, respectively.  A
      single-nucleotide overlap was found to exist between the termination codon of
      the mcrB gene and the proposed initiation codon of the mcrC gene.  The presence
      of an additional peptide of 33 kDa in strains containing various recombinant
      plasmids with portions of the McrB region has been reported by Ross et al.  The
      analysis of frameshift and deletion mutants of one such hybrid plasmid,
      pRAB-13, provided evidence for a second translational initiation site within
      the McrB open reading frame.  The proposed start codon for translation of the
      33-kDa peptide lies 481 nucleotides downstream from the initation codon for the
      51-kDa mcrB gene product.  The 33-kDa peptide may play a regulatory role in the
      McrB restriction of DNA containing 5-methylcytosine.
AU  - Ross TK
AU  - Achberger EC
AU  - Braymer HD
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1989 171: 1974-1981.

PMID- 2664457
VI  - 216
DP  - 1989
TI  - Identification of a second polypeptide required for McrB restriction of 5-methylcytosine-containing DNA in Escherichia coli K12.
PG  - 402-407
AB  - The McrB restriction system in Escherichia coli K12 causes sequence-specific
      recognition and inactivation of DNA containing 5-methylcytosine residues.  We
      have previously located the mcrB gene near hsdS at 99 min on the E. coli
      chromosome and demonstrated that it encodes a 51 kDa polypeptide required for
      restriction of M.AluI methylated (A-G-5mC-T) DNA.  We show here, by analysis of
      maxicell protein synthesis of various cloned fragments from the mcrB region,
      that a second protein of approximately 39 kDa is also required for
      McrB-directed restriction.  The new gene, designated mcrC, is adjacent to mcrB
      and located distally to hsdS.  The McrB phenotype has been correlated
      previously with restriction of 5-hydroxy-methylcytosine (HMC)-containing T-even
      phage DNA that lacks the normal glucose modification of HMC, formally
      designated RglB (for restriction of glucoseless phage).  This report reveals a
      difference between the previously correlated McrB and RglB restriction systems:
      while both require the mcrB gene product only the McrB system requires the
      newly identified mcrC-encoded 39-kDa polypeptide.
AU  - Ross TK
AU  - Achberger EC
AU  - Braymer HD
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1989 216: 402-407.

PMID- 3031021
VI  - 169
DP  - 1987
TI  - Localization of a genetic region involved in McrB restriction by Escherichia coli K-12.
PG  - 1757-1759
AB  - A 5,500-base-pairs BglII-EcoRI fragment proximal to the hsd genes of
      Escherichia coli K-12 has been cloned in the plasmid vector pUC9.  The
      resultant hybrid plasmid was shown to complement the mcrR mutation of E. coli
      K802.  The presence of the hybrid plasmid in strain K802 caused an 18.3-fold
      drop in transformation efficiency with AluI-methylated pACYC184 relative to
      unmethylated pACYC184.  These results indicate that the cloned DNA is involved
      in the McrB system of restriction of 5-methylcytosine DNA.
AU  - Ross TK
AU  - Braymer HD
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1987 169: 1757-1759.

PMID- 9336981
VI  - 13
DP  - 1997
TI  - Stabilization of the restriction enzyme EcoRI dried with Trehalose and other selected glass-forming solutes.
PG  - 609-616
AB  - The stabilization of the restriction enzyme EcoRI by its incorporation into aqueous
      glass-forming carbohydrate or polymer solutions, followed by vacuum-drying to low moisture,
      has been studied.  Glass-forming solutes included trehalose, sucrose, lactose, maltose,
      raffinose, maltodextrin, DE 10, and poly(vinylpyrrolidone) (molecular weight 40,000, PVP).
      Among the solutes examined, trehalose and sucrose protected the enzyme most effectively during
      storage at 37 and 45 C.  The restriction enzyme dried with trehalose or sucrose maintained its
      activity without detectable loss for at least 20 days at 37 C and 12 days at 45 C.  In
      contrast, the activity of the enzyme dried with maltodextrin or PVP was reduced during vacuum
      desiccation and also it decreased remarkably during storage at the same temperatures.  Stored
      (37/45 C) vacuum-dried trehalose and sucrose systems were either a dense paste or a very
      viscous syrup, and this indicated that they were not glassy.  Moreover, no relationship was
      found between the glass transition temperatures (Tg) of the pure added solute and enzyme
      protection during storage, since, e.g., sucrose which has significantly lower Tg values
      protected the enzyme much better than either maltose, lactose, maltodextrin, or PVP.  The
      trisaccharide raffinose offered good protection of enzyme activity, and its role as a novel
      excipient matrix for labile enzyme stabilization deserves further investigation.  The
      stability of enzyme EcoRI was rapidly lost when the vacuum-dried trehalose and sucrose systems
      were humidified to 58% relative humidity and stored at 45 C, and this was attributed to
      disaccharide crystallization.
AU  - Rossi S
AU  - Buera MP
AU  - Moreno S
AU  - Chirife J
PT  - Journal Article
TA  - Biotechnol. Prog.
JT  - Biotechnol. Prog.
SO  - Biotechnol. Prog. 1997 13: 609-616.

PMID- 9888358
VI  - 73
DP  - 1998
TI  - The effects of enzyme inactivation and incubation buffer on digestion in situ with restriction endonucleases.
PG  - 325-328
AB  - Previous studies have shown that components of the incubation reaction other than the
      restriction endonucleases in an in situ restriction enzyme digest of chromosomes may induce
      G-like banding patterns.  To determine whether factors other than DNA base composition play a
      role in determining restriction enzyme induced bands, we investigated the effect of reaction
      buffers alone or in the presence of heat inactivated enzymes.  Our results show that enzymes
      such as AluI, RsaI and MspI become inactivated during 3-24 hr incubations at 37 C and that
      reaction buffers alone failed to produce G-like bands when inactive endonucleases were
      included.
AU  - Rossino R
AU  - Gosalvez J
AU  - Mezzanotte R
PT  - Journal Article
TA  - Biotech. Histochem.
JT  - Biotech. Histochem.
SO  - Biotech. Histochem. 1998 73: 325-328.

PMID- 1079804
VI  - 123
DP  - 1975
TI  - Methylase Activities from Haemophilus influenzae that protect Haemophilus parainfluenzae Transforming Deoxyribonucleic Acid from Inactivation by Haemophilus influenzae Endonuclease R.
PG  - 287-293
AB  - Specific methylases that have the properties of deoxyribonucleic acid (DNA)
      modification enzymes have been isolated from Haemophilus influenzae strain Rd.
      Two activities (methylase IIa and methylase III) were found to protect
      transforming DNA of H. parainfluenzae from the action of H. influenzae
      restriction enzymes.  To determine the specificity of the protection, a
      procedure based on biological activity was developed for the separation and
      purification of the restriction endonucleases from H. influenzae strain Rd.
      Two endonuclease R activities presumably corresponding to HindII and HindIII
      (P.H. Roy and H.O. Smith, 1973; H.O. Smith and K.W. Wilcox, 1970) were
      characterized by differences in their chromatographic properties, ability to
      attack T7 DNA, and inactivation of the transforming activity of different
      markers of H. parainfluenzae DNA.  One endonuclease R enzyme (HindII) attacked
      T7 DNA and was found to inactivate the dalacin resistance marker (<0.01%
      activity remaining) with only a slight effect on the streptomycin resistance
      marker (83% activity remaining).  Methylase IIa treatment protected 40% of the
      dalacin resistance marker of H. parainfluenzae DNA from inactivation by HindII.
      The other restriction activity (HindIII) was inert towards T7 DNA and
      inactivated the streptomycin resistance marker of H. parainfluenzae DNA (<0.01%
      activity remaining) without any effect on the dalacin resistance marker.  The
      methylation of H. parainfluenzae DNA accomplished by methylase III protected
      60% of the transforming activity of the streptomycin resistance marker of H.
      parainfluenzae DNA from the action of HindIII.
AU  - Roszczyk E
AU  - Goodgal S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1975 123: 287-293.

PMID- 9651316
VI  - 273
DP  - 1998
TI  - Functional roles of conserved amino acid residues in DNA methyltransferases investigated by site-directed mutagenesis of the EcoRV adenine-M6-methyltransferase.
PG  - 17333-17342
AB  - All DNA methyltransferases have similar catalytic domains containing nine blocks of conserved
      amino acid residues.  We have investigated by site-directed mutagenesis the function of 17
      conserved residues in the EcoRV alpha-adenine-N6-DNA methyltransferase.  The structure of this
      class of MTases has been predicted recently.  The variants were characterized with respect to
      their catalytic activities and their abilities to bind to DNA and the S-adenosylmethionine
      cofactor.  Amino acids located in motifs X, I, and II are shown to be involved in AdoMet
      binding (Lys16, Glu37, Phe39, and Asp58).  Some of the mutants defective in AdoMet binding are
      also impaired in DNA binding, suggesting allosteric interactions between the AdoMet and DNA
      binding site.  Asp78 (motif III), which was supposed to form a hydrogen bond to the AdoMet on
      the basis of the structure predictions, turned out not to be important for AdoMet binding,
      suggesting that motif III has not been identified correctly.  R128A and N130A, having
      mutations in the putative DNA binding domain, are unable to bind to DNA.  Residues located in
      motifs IV, V, VI, and VIII are involved in catalysis (Asp193, Tyr196, Asp211, Ser229, Trp231,
      and Tyr258), some of them presumably in binding the flipped target base, because mutations at
      these residues fail to significantly interfere with DNA and AdoMet binding but strongly reduce
      catalysis. Our results are in substantial agreement with the structure prediction for EcoRV
      alpha-adenine-N6-methyltransferase and x-ray structures of other MTases.
AU  - Roth M
AU  - Helm-Kruse S
AU  - Friedrich T
AU  - Jeltsch A
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1998 273: 17333-17342.

PMID- 10782999
VI  - 381
DP  - 2000
TI  - Biotin-Avidin microplate assay for the quantitative analysis of enzymatic methylation of DNA by DNA methyltransferases.
PG  - 269-272
AB  - An assay is described to measure methylation of biotinylated oligonucleotide substrates by DNA
      methyltransferases using [methyl-3H]-AdoMet.  After the methylation reaction the
      oligonucleotides are immobilized on an avidin-coated microplate.  The incorporation of [3H]
      into the DNA is quenched by addition of unlabeled AdoMet to the binding buffer.  Unreacted
      AdoMet and enzyme are removed by washing.  To release the radioactivity incorporated into the
      DNA, the wells are incubated with a non-specific endonuclease and the radioactivity determined
      by liquid scintillation counting.  As an example, we have studied methylation of DNA by the
      EcoRV DNA methyltransferase.  The reaction progress curves measured with this assay are linear
      with respect to time.  Methylation rates linearly increase with enzyme concentration.  The
      rates are comparable to results obtained with the same enzyme using a different assay.  The
      biotin-avidin assay is inexpensive, convenient, quantitative, fast and well suited to process
      many samples in parallel.  The accuracy of the assay is high, allowing to reproduce results
      within +-10%. The assay is very sensitive as demonstrated by the detection of incorporation of
      0.8 fmol methyl groups into the DNA. Under the experimental conditions, this corresponds to
      methylation of only 0.03% of all target sites of the substrate.  Using this assay, the DNA
      methylation activity of some M.EcoRV variants could be detected that was not visible by other
      in vitro methylation assays.
AU  - Roth M
AU  - Jeltsch A
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 2000 381: 269-272.

PMID- 11470870
VI  - 29
DP  - 2001
TI  - Changing the target base specificity of the EcoRV DNA methyltransferase by rational de novo protein-design.
PG  - 3137-3144
AB  - The EcoRV DNA-(adenine-N(6))-methyltransferase (M.EcoRV) specifically modifies the first
      adenine residue within GATATC sequences. During catalysis, the enzyme flips its target base
      out of the DNA helix and binds it into a target base-binding pocket, which is formed in part
      by Lys16 and Tyr196. A cytosine residue is accepted by wild-type M.EcoRV as a substrate at a
      31-fold reduced efficiency with respect to the k(cat)/K(M) values if it is located in a CT
      mismatch substrate (GCTATC/GATATC). Cytosine residues positioned in a CG base pair
      (GCTATC/GATAGC) are modified at much more reduced rates, because flipping out the target base
      is much more difficult in this case. We intended to change the target base specificity of
      M.EcoRV from adenine-N(6) to cytosine-N(4). To this end we generated, purified and
      characterized 15 variants of the enzyme, containing single, double and triple amino acid
      exchanges following different design approaches. One concept was to reduce the size of the
      target base-binding pocket by site-directed mutagenesis. The K16R variant showed an altered
      specificity, with a 22-fold preference for cytosine as the target base in a mismatch
      substrate. This corresponds to a 680-fold change in specificity, which was accompanied by only
      a small loss in catalytic activity with the cytosine substrate. The K16R/Y196W variant no
      longer methylated adenine residues at all and its activity towards cytosine was reduced only
      17-fold. Therefore, we have changed the target base specificity of M.EcoRV from adenine to
      cytosine by rational protein design. Because there are no natural paragons for the variants
      described here, a change of the target base specificity of a DNA interacting enzyme was
      possible by rational de novo design of its active site.
AU  - Roth M
AU  - Jeltsch A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2001 29: 3137-3144.

PMID- 28705964
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Seven Streptococcus agalactiae Strains Isolated from Camelus dromedarius at the Horn of Africa.
PG  - e00525-17
AB  - We present draft whole-genome sequences of seven Streptococcus agalactiae strains isolated
      from Camelus dromedarius in Kenya and Somalia. These data are an
      extension to the group B Streptococcus (GBS) pangenome and might provide more
      insight into the underlying mechanisms of pathogenicity and antibiotic resistance
      of camel GBS.
AU  - Rothen J
AU  - Schindler T
AU  - Pothier JF
AU  - Younan M
AU  - Certa U
AU  - Daubenberger C
AU  - Pfluger V
AU  - Jores J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00525-17.

PMID- 29519846
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Listeria monocytogenes Strain MR310, Isolated from a  Pastured-Flock Poultry Farm System.
PG  - e00171-18
AB  - Investigation of Listeria monocytogenes transmission from environmental sources associated
      with pasture-raised chickens to poultry products is needed to
      determine ways to prevent potential foodborne illness. Here, we report the
      complete genome sequence of Listeria monocytogenes MR310, one of the isolates
      from a pastured-flock poultry management system.
AU  - Rothrock MJ Jr
AU  - Fan P
AU  - Jeong KC
AU  - Kim SA
AU  - Ricke SC
AU  - Park SH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00171-18.

PMID- 23042999
VI  - 194
DP  - 2012
TI  - Genome of Enterobacteriophage Lula/phi80 and Insights into Its Ability To Spread in the Laboratory Environment.
PG  - 6802-6817
AB  - The novel temperate bacteriophage Lula, contaminating laboratory Escherichia coli
      strains, turned out to be the well-known lambdoid phage phi80. Our previous
      studies revealed that two characteristics of Lula/phi80 facilitate its spread in
      the laboratory environment: cryptic lysogen productivity and stealthy
      infectivity. To understand the genetics/genomics behind these traits, we
      sequenced and annotated the Lula/phi80 genome, encountering an E. coli-toxic gene
      revealed as a gap in the sequencing contig and analyzing a few genes in more
      detail. Lula/phi80's genome layout copies that of lambda, yet homology with other
      lambdoid phages is mostly limited to the capsid genes. Lula/phi80's DNA is
      resistant to cutting with several restriction enzymes, suggesting DNA
      modification, but deletion of the phage's damL gene, coding for DNA adenine
      methylase, did not make DNA cuttable. The damL mutation of Lula/phi80 also did
      not change the phage titer in lysogen cultures, whereas the host dam mutation did
      increase it almost 100-fold. Since the high phage titer in cultures of Lula/phi80
      lysogens is apparently in response to endogenous DNA damage, we deleted the only
      Lula/phi80 SOS-controlled gene, dinL. We found that dinL mutant lysogens release
      fewer phage in response to endogenous DNA damage but are unchanged in their
      response to external DNA damage. The toxic gene of Lula/phi80, gamL, encodes an
      inhibitor of the host ATP-dependent exonucleases, RecBCD and SbcCD. Its own
      antidote, agt, apparently encoding a modifier protein, was found nearby.
      Interestingly, Lula/phi80 lysogens are recD and sbcCD phenocopies, so GamL and
      Agt are part of lysogenic conversion.
AU  - Rotman E
AU  - Kouzminova E
AU  - Plunkett G III
AU  - Kuzminov A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6802-6817.

PMID- 25700419
VI  - 3
DP  - 2015
TI  - Closed Genome Sequence of Clostridium pasteurianum ATCC 6013.
PG  - e01596-14
AB  - We report here the closed genome of Clostridium pasteurianum ATCC 6013, a saccharolytic,
      nitrogen-fixing, and spore-forming Gram-positive obligate anaerobe. The organism is of
      biotechnological interest due to the production of solvents (butanol and 1,3-propanediol) but
      can be associated with food spoilage.  The genome comprises a total of 4,351,223 bp.
AU  - Rotta C
AU  - Poehlein A
AU  - Schwarz K
AU  - McClure P
AU  - Daniel R
AU  - Minton NP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01596-14.

PMID- 7969147
VI  - 14
DP  - 1994
TI  - Introduction of double-strand breaks into the genome of mouse cells by expression of a rare-cutting endonuclease.
PG  - 8096-8106
AB  - To maintain genomic integrity, double-strand breaks (DSBs) in chromosomal DNA must be
      repaired. In mammalian systems, the analysis of the repair of chromosomal DSBs has been
      limited by the inability to introduce well-defined DSBs in genomic DNA. In this study, we
      created specific DSBs in mouse chromosomes for the first time, using an expression system for
      a rare-cutting endonuclease, I-SceI. A genetic assay has been devised to monitor the repair of
      DSBs, whereby cleavage sites for I-SceI have been integrated into the mouse genome in two
      tandem neomycin phosphotransferase genes. We find that cleavage of the I-SceI sites is very
      efficient, with at least 12% of stably transfected cells having at least one cleavage event
      and, of these, more than 70% have undergone cleavage at both I-SceI sites. Cleavage of both
      sites in a fraction of clones deletes 3.8 kb of intervening chromosomal sequences. We find
      that the DSBs are repaired by both homologous and nonhomologous mechanisms. Nonhomologous
      repair events frequently result in small deletions after rejoining of the two DNA ends. Some
      of these appear to occur by simple blunt-ended ligation, whereas several others may occur
      through annealing of short regions of terminal homology. The DSBs are apparently
      recombinogenic, stimulating gene targeting of a homologous fragment by more than 2 orders of
      magnitude. Whereas gene-targeted clones are nearly undetectable without endonuclease
      expression, they represent approximately 10% of cells transfected with the I-SceI expression
      vector. Gene targeted clones are of two major types, those that occur by two-sided homologous
      recombination with the homologous fragment and those that occur by one-sided homologous
      recombination. Our results are expected to impact a number of areas in the study of mammalian
      genome dynamics, including the analysis of the repair of DSBs and homologous recombination
      and, potentially, molecular genetic analyses of mammalian genomes.
AU  - Rouet P
AU  - Smih F
AU  - Jasin M
PT  - Journal Article
TA  - Mol. Cell. Biol.
JT  - Mol. Cell. Biol.
SO  - Mol. Cell. Biol. 1994 14: 8096-8106.

PMID- 8016116
VI  - 91
DP  - 1994
TI  - Expression of a site-specific endonuclease stimulates homologous recombination in mammalian cells.
PG  - 6064-6068
AB  - Double-strand breaks introduced into DNA in vivo have been shown to enhance homologous
      recombination in a variety of chromosomal and extrachromosomal loci in Saccharomyces
      cerevisiae. To introduce double-strand breaks in DNA at defined locations in mammalian cells,
      we have constructed a mammalian expression vector for a modified form of I-SceI, a yeast
      mitochondrial intron-encoded endonuclease with an 18-bp recognition sequence. Expression of
      the modified I-SceI endonuclease in COS1 cells results in cleavage of model recombination
      substrates and enhanced extrachromosomal recombination, as assayed by chloramphenicol
      acetyltransferase activity and Southern blot analysis. Constitutive expression of the
      endonuclease in mouse 3T3 cells is not lethal, possibly due to either the lack of I-SceI sites
      in the genome or sufficient repair of them. Expression of an endonuclease with such a long
      recognition sequence will provide a powerful approach to studying a number of molecular
      processes in mammalian cells, including homologous recombination.
AU  - Rouet P
AU  - Smith F
AU  - Jasin M
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1994 91: 6064-6068.

PMID- 7829490
VI  - 270
DP  - 1995
TI  - Regulation of the DNA methyltransferase by the Ras-AP-1 signaling pathway.
PG  - 1595-1601
AB  - Using deletion analysis and site-specific mutagenesis to map the 5' regulatory region of the
      DNA methyltransferase (MeTase) gene, we show that a 106-bp sequence (at -1744 to -1650)
      bearing three AP-1 sites is responsible for induction of DNA MeTase promoter activity. Using
      transient cotransfection chloramphenicol acetyltransferase assays in P19 cells, we show that
      the DNA MeTase promoter is induced by c-Jun or Ha-Ras but not by a dominant negative mutant of
      Jun, 99. The activation of the DNA MeTase promoter by Jun is inhibited in a ligand dependent
      manner by the glucocorticoid receptor. Stable expression of Ha-Ras in P19 cells results in
      induction of transcription of the DNA MeTase mRNA as determined by nuclear run-on assays and
      the steady state levels of DNA MeTase mRNA as determined by an RNase protection assay. These
      experiments establish a potential molecular link between nodal cellular signaling pathways and
      the control of expression of the DNA MeTase gene. This provides us with a possible molecular
      explanation for the hyperactivation of DNA MeTase in many cancer cells and suggests that DNA
      MeTase is one possible downstream effector of Ras.
AU  - Rouleau J
AU  - MacLeod AR
AU  - Szyf M
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1995 270: 1595-1601.

PMID- 1392082
VI  - 3
DP  - 1992
TI  - Regulation of the mouse DNA methyltransferase by signal transduction pathways.
PG  - A25
AB  - A hallmark of DNA methylation in vertebrates is the fact that only a fraction of the CpG
      sequences is methylated (60-80%) and that nonmethylated cytosines are distributed in a
      nonrandom fashion, generating a pattern of methylation that is gene and tissue specific. DNA
      methylation is catalyzed by the DNA methyltransferase enzyme (DNA MeTase). We have previously
      hypothesized that regulated changes in the level of DNA MeTase gene expression might be an
      important mechanism through which DNA methylation patterns are generated(Szyf et al., J. Biol.
      Chem. 266, 10027-10030, 1991). If this is true the DNA MeTase gene should be responsive to
      cellular signal transduction pathways that are involved in cellular differentiation. Sequence
      analysis of the promoter region revealed several potential binding sites for transcript factor
      complexes (AP-1, GRE and E-boxes) that might be involved in the regulation of the DNA MeTase
      gene expression by different signal transduction pathways (Rouleau et al., J. Biol. Chem.,
      267, 7368-7377. 1992). To test this hypothesis we cotransfected P19 cells with a chimeric
      construct containing 2.3 kb sequences from the 5' region of the DNA MeTase fused to
      CAT(pMetCAT+) with fos and jun. DNA MeTase gene promoter activity was induced 60-fold by fos
      and jun but not by a mutant of jun lacking the DNA binding domain. This induction was
      inhibited by deletion of the 7 AP-1 sites in the 5' region of the DNA MeTase. Gel retardation
      assays demonstated the formation of an AP-1 complex with an AP-1 binding site in the promoter
      region. Induction of DNA MeTase transcripton by fos and jun was inhibited by the human
      glucocorticoid receptor while expression of the receptor per se had no effect on DNA MeTase
      activity. The DNA MeTase is responsive also to the myogenesis regulator MyoD which expression
      results in a 20 fold induction of the DNA MeTase gene. This work suggests for the first time a
      molecular link between extracellular signals and possible changes in the covalent structure of
      the genome.
AU  - Rouleau J
AU  - Szyf M
PT  - Journal Article
TA  - Mol. Biol. Cell
JT  - Mol. Biol. Cell
SO  - Mol. Biol. Cell 1992 3: A25.

PMID- 1559980
VI  - 267
DP  - 1992
TI  - The mouse DNA methyltransferase 5'-region .
PG  - 7368-7377
AB  - We have cloned and characterized 5'-flanking sequences of the DNA methyltransferase (MeTase)
      gene. DNA MeTase gene transcription is initiated at a few discrete sites: 343 and 90 base
      pairs upstream of the translation initiation site as determined by RNase protection and primer
      extension assays. The promoter sequences that regulate expression of DNA MeTase, as defined by
      chloramphenicol acetyltransferase assays, reside between position - 171 and the transcription
      start site. The promoter of DNA MeTase does not contain TATAA or CAAT boxes and is unusual
      because it does not contain the CG-rich elements characteristic of TATAA-less housekeeping
      genes. The 5'-flanking region of DNA MeTase contains AP-1, AP-2 and glucocorticoid response
      elements, suggesting possible regulation by cellular transduction pathways. The base
      composition of the DNA MeTase promoter is markedly different from that of other housekeeping
      genes. Whereas most housekeeping genes are characterized by CG-rich areas in their
      5'-flanking regions, the TG dinucleotide is over-represented in DNA MeTase 5'-flanking
      sequences, including a perfect tandem repeat of T/G between positions -685 and -650. DNA
      methylation patterns play an important role in the developmental regulation of gene expression
      in vertebrates. DNA MeTase activity is probably regulated to maintain this pattern of
      methylation. We suggest that the DNA MeTase promoter represents a new class of housekeeping
      gene promoters that was designed to ensure high fidelity regulation of gene expression.
AU  - Rouleau J
AU  - Tanigawa G
AU  - Szyf M
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1992 267: 7368-7377.

PMID- 25428974
VI  - 2
DP  - 2014
TI  - Kingella kingae KK247, an Atypical Pulsed-Field Gel Electrophoresis Clone A Strain.
PG  - e01228-14
AB  - Kingella kingae strain KK247 was isolated from an adult Israeli patient with endocarditis. It
      belongs to pulsed-field gel electrophoresis clone A, has a
      2,113,021-bp genome, a 15,507-bp plasmid that carries genes encoding
      beta-lactamases, and possesses 45 transposases, compared to the 5 detected in
      other K. kingae strains.
AU  - Rouli L
AU  - Robert C
AU  - Raoult D
AU  - Yagupsky P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01228-14.

PMID- 23209205
VI  - 194
DP  - 2012
TI  - Genome Sequence of Coxiella burnetii 109, a Doxycycline-Resistant Clinical Isolate.
PG  - 6939
AB  - Coxiella burnetii 109, with a 2.03-Mb genome, is a doxycycline-resistant human isolate that
      was isolated from the cardiac valve of a German male patient with Q
      fever endocarditis who died during the course of the treatment due to the
      bacterium's resistance to doxycycline. This new genome can be useful for future
      comparative genomic or Q fever studies.
AU  - Rouli L
AU  - Rolain JM
AU  - El Filali A
AU  - Robert C
AU  - Raoult D
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6939.

PMID- 4901831
VI  - 195
DP  - 1969
TI  - The Escherichia coli B restriction endonuclease.
PG  - 219-229
AB  - 1.  The restriction endonuclease of Escherichia coli B has been purified
      1000-fold from crude extracts. 2.  It has been found to be similar to the K12
      and PI restriction endonucleases, i.e., it requires ATP,
      S-adenosyl-L-methionine and Mg2+ and unmodified DNA for enzymatic activity and
      has an estimated large molecular weight (approx. 300,000 daltons). 3.  It
      introduces a limited number of double strand scissions in unmodified lambda vir
      DNA, Escherichia coli chromosomal DNA and probably one double strand scission
      per fd replicative form DNA.  The double strand scission in the unmodified fd
      replicative form DNA occurs by a two-step mechanism. 4.  Replicative form DNA
      generated from an fd mutant which is only restricted by Escherichia coli B by a
      factor of 1.10-2 (versus 1.10-4 for wild type fd) is also a substrate for the B
      restriction endonuclease.  Cosedimentation of the endonuclease-treated wild
      type and mutant replicative form DNA results in qualitatively identical
      patterns of DNA distribution.
AU  - Roulland-Dussoix D
AU  - Boyer HW
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1969 195: 219-229.

PMID- Not carried by PubMed...
VI  - 69
DP  - 1969
TI  - B Restriction endonuclease of Escherichia coli.
PG  - 46
AB  - We have purified the B restriction endonuclease by a factor of 1,500 from a
      crude extract of E. coli.  The enzyme preparation is free of detectable
      exonuclease and nonspecific endonuclease activities under conditions optimum
      for the restriction endonuclease activity.  The B restriction endonuclease
      activity has an absolute requirement for SAM, ATP, Mg++ and unmodified duplex
      DNA (i.e. DNA originating in a strain without B modification).  The enzyme
      produces a limited number of double strand scissions in unmodified lambda++,
      lambda vir,  fd RF, colE1 and E. coli DNA.  The double strand scission is made
      by two proximal single strand scissions.  The molecular weight of the enzyme
      has been estimated at about 140,000 daltlons.  With the exception of substrate
      specificity, the B restriction endonuclease appears to be similar to the K
      restriction endonuclease.  We have found that the B restriction endonuclease
      produces a linear molecule from the fd RF with an estimated molecular weight of
      2.8 x 10/6 daltons and sediments a little slower than the nicked RF molecules
      (ratio =  1.14).  We conclude that there is one double strand scission per RF
      molecule and have used this as a substrate to study the kinetics of the
      reaction.  RF, prepared from a mutant fd which is restricted in vivo 100-fold
      less than WT fd, is attacked at a rate less than one-half that of the WT RF.
AU  - Roulland-Dussoix D
AU  - Boyer HW
PT  - Journal Article
TA  - Bacteriol. Proc.
JT  - Bacteriol. Proc.
SO  - Bacteriol. Proc. 1969 69: 46.

PMID- 
VI  - 0
DP  - 1975
TI  - R Factor-Controlled Restriction and Modification of Deoxyribonucleic Acid.
PG  - 187-198
AB  - The restriction and modification of deoxyribonucleic acid (DNA) appear to be
      quite prevalent in bacteria although by no means ubiquitous.  In Escherichia
      coli strains alone, there appear to be over six different restriction and
      modification systems in terms of enzymatic specificity.  In E. coli strains,
      the enzymes responsible for the restriction and modification of DNA are
      genetically controlled by chromosomal, plasmid, or viral genes.  At least in
      some cases, it is clear that the restriction endonuclease and modification
      methylase of a given "host specificity" interact with the same substrate, a
      specific sequence of nucleotide base pairs.  This sequence defines the host
      specificity of a bacterial cell which possesses a set of restriction and
      modification enzymes. Naturally occurring bacterial strains or strains
      constructed in the laboratory can be demonstrated to have several sets of
      restriction and modification enzymes.
AU  - Roulland-Dussoix D
AU  - Yoshimori R
AU  - Greene P
AU  - Betlach M
AU  - Goodman HM
AU  - Boyer HW
PT  - Journal Article
TA  - Microbiology-1974
JT  - Microbiology-1974
SO  - Microbiology-1974 1975 0: 187-198.

PMID- 10888872
VI  - 25
DP  - 2000
TI  - DNMT1 binds HDAC2 and a new co-repressor, DMAP1, to form a complex at replication foci.
PG  - 269-277
AB  - DNA methylation can contribute to transcriptional silencing through several transcriptionally
      repressive complexes, which include methyl-CpG binding domain proteins (MBDs) and histone
      deacetylases (HDACs).  We show here that the chief enzyme that maintains mammalian DNA
      methylation, DNMT1, can also establish a repressive transcription complex. The non-catalytic
      amino terminus of DNMT1 binds to HDAC2 and a new protein, DMAP1 (for DNMT1 associated
      protein), and can mediate transcriptional repression. DMAP1 has intrinsic transcription
      repressive activity, and binds to the transcriptional co-repressor TSG101. DMAP1 is targeted
      to replication foci through interaction with the far N terminus of DNMT1 throughout S phase,
      whereas HDAC2 joins DNMT1 and DMAP1 only during late S phase, providing a platform for how
      histones may become deacetylated in heterochromatin following replication. Thus, DNMT1 not
      only maintains DNA methylation, but also may directly target, in a heritable manner,
      transcriptionally repressive chromatin to the genome during DNA replication.
AU  - Rountree MR
AU  - Bachman KE
AU  - Baylin SB
PT  - Journal Article
TA  - Nat. Genet.
JT  - Nat. Genet.
SO  - Nat. Genet. 2000 25: 269-277.

PMID- 13376869
VI  - 15
DP  - 1956
TI  - Variations in a related series of staphylococcal bacteriophages.
PG  - 266-279
AB  - Stocks of staphylococcal phage 47C (serological group A) contained some group B
      phage.  This was found to have originated in a lysogenic staphylococcus
      previously used to propagate phage 47C and which had subsequently lost its
      lysogenicity.  The lysogenic phage was thus perpetuated in the phage stocks as
      a lytic phage.  The characters of the two phages are described.  When they
      lysogenized five different strains of staphylococci changes in typing pattern
      were produced.  There was evidence which indicated that, in the prophage state,
      the two phages occupy different sites and that there is no cross-immunity
      between them.  The propagation of the phages in different hosts resulted in
      changes in their host range.  A virulent mutant of the B prophage was induced
      by the application of a variety of phages to the strain carrying it.
AU  - Rountree PM
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1956 15: 266-279.

PMID- 
VI  - 52
DP  - 2000
TI  - Restriction enzymes in native bacteria of Nicaragua.
PG  - 10-18
AB  - Advances in genetic engineering and molecular biology have led to the utilization of bacteria
      in the biotechnology industry.  In this study, restriction enzymes present in bacteria
      collected from aqueous medium in Nicaragua have been identified and classified.  Restriction
      activity was found in 25% of the total of bacteria analyzed.  The process of purification of
      bacterial protein extracts with Sau96I and PvuII activities is discussed.  This work is a
      result of an effort to implement modern biotechnological methods of research in Nicaragua.
AU  - Roustan-Espinosa I
AU  - Guerrero D
AU  - Flores E
AU  - Huete-Perez J
PT  - Journal Article
TA  - Revista Univ. Centroamer.
JT  - Revista Univ. Centroamer.
SO  - Revista Univ. Centroamer. 2000 52: 10-18.

PMID- 25614564
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Alkaliphilic Exiguobacterium sp. Strain HUD, Isolated from a Polymicrobial Consortia.
PG  - e01451-14
AB  - An alkaliphilic microorganism from the genus Exiguobacterium, Exiguobacterium sp. strain HUD
      was isolated from a fermentative, methanogenic polymicrobial microcosm
      operating at pH 10. The draft genome shows the presence of genes encoding for the
      metabolism of a range of carbohydrates under both aerobic and anaerobic
      conditions.
AU  - Rout SP
AU  - Rai A
AU  - Humphreys PN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01451-14.

PMID- 23407462
VI  - 7
DP  - 2012
TI  - Non-contiguous finished genome sequence and description of Kurthia massiliensis sp. nov.
PG  - 221-232
AB  - Kurthia massiliensis strain JC30(T) sp. nov. is the type strain of K. massiliensis sp. nov., a
      new species within the genus Kurthia. This strain, whose
      genome is described here, was isolated from the fecal flora of a healthy patient.
      K. massiliensis is a Gram-positive aerobic rod. Here we describe the features of
      this organism, together with the complete genome sequence and annotation. The
      3,199,090 bp long genome contains 3,240 protein-coding genes and 86 RNA genes,
      including between 3 and 4 rRNA genes.
AU  - Roux V
AU  - El Karkouri K
AU  - Lagier JC
AU  - Robert C
AU  - Raoult D
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 7: 221-232.

PMID- 25197500
VI  - 9
DP  - 2014
TI  - Non-contiguous finished genome sequence and description of Kurthia senegalensis sp. nov.
PG  - 1321-1332
AB  - Kurthia senegalensis strain JC8E(T) sp. nov. is the type strain of K. senegalensis sp. nov., a
      new species within the genus Kurthia. This strain, whose
      genome is described here, was isolated from the fecal flora of a healthy patient.
      K. senegalensis is an aerobic rod. Here we describe the features of this
      organism, together with the complete genome sequence and annotation. The
      2,975,103 bp long genome contains 2,889 protein-coding genes and 83 RNA genes,
      including between 4 and 6 rRNA genes.
AU  - Roux V
AU  - Lagier JC
AU  - Gorlas A
AU  - Robert C
AU  - Raoult D
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 1321-1332.

PMID- 24976893
VI  - 9
DP  - 2013
TI  - Non-contiguous finished genome sequence and description of Oceanobacillus massiliensis sp. nov.
PG  - 370-384
AB  - Oceanobacillus massiliensis strain N'Diop(T) sp. nov. is the type strain of O. massiliensis
      sp. nov., a new species within the genus Oceanobacillus. This
      strain, whose genome is described here, was isolated from the fecal flora of a
      healthy patient. O. massiliensis is an aerobic rod. Here we describe the features
      of this organism, together with the complete genome sequence and annotation. The
      3,532,675 bp long genome contains 3,519 protein-coding genes and 72 RNA genes,
      including between 6 and 8 rRNA operons.
AU  - Roux V
AU  - Million M
AU  - Robert C
AU  - Magne A
AU  - Raoult D
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 9: 370-384.

PMID- 22933754
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Actinomyces massiliensis Strain 4401292T.
PG  - 5121
AB  - A draft genome sequence of Actinomyces massiliensis, an anaerobic bacterium isolated from a
      patient's blood culture, is described here. CRISPR-associated
      proteins, insertion sequences, and toxin-antitoxin loci were found on the genome.
AU  - Roux V
AU  - Robert C
AU  - Gimenez G
AU  - Gharbi R
AU  - Raoult D
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5121.

PMID- 22933772
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Brevibacterium massiliense Strain 541308T.
PG  - 5151-5152
AB  - A draft genome sequence of Brevibacterium massiliense, an aerobic bacterium isolated from a
      human ankle discharge, is described here. CRISPR-associated
      proteins were found to be encoded in the genome, and analysis of transport
      proteins was performed.
AU  - Roux V
AU  - Robert C
AU  - Gimenez G
AU  - Raoult D
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5151-5152.

PMID- 23209235
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Staphylococcus massiliensis Strain 5402776T.
PG  - 6984-6985
AB  - A draft genome sequence of Staphylococcus massiliensis, Gram-positive cocci isolated from a
      human brain abscess sample, is described here. One clustered
      regularly interspaced short palindromic repeat, three transposases, six putative
      transposases, and one potential provirus were characterized.
AU  - Roux V
AU  - Robert C
AU  - Gimenez G
AU  - Raoult D
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6984-6985.

PMID- 24976891
VI  - 9
DP  - 2013
TI  - Non-contiguous finished genome sequence of Phocaeicola abscessus type strain 7401987(T.).
PG  - 351-358
AB  - Phocaeicola abscessus strain 7401987(T) is the sole member of the genus Phocaeicola. This
      bacterium is Gram-negative, non-spore-forming, coccoid to
      rod-shaped and motile by lophotrichous flagella. It was isolated from a human
      brain abscess sample. In this work, we describe a set of features of this
      organism, together with the complete genome sequence and annotation. The
      2,530,616 bp long genome contains 2,090 protein-coding genes and 54 RNA genes,
      including 4 rRNA operons.
AU  - Roux V
AU  - Robert C
AU  - Raoult D
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 9: 351-358.

PMID- 25197502
VI  - 9
DP  - 2014
TI  - Non-contiguous finished genome sequence of Prevotella timonensis type strain 4401737(T.).
PG  - 1346-1353
AB  - Prevotella timonensis strain 4401737(T) is a member of the genus Prevotella, which contains
      anaerobic Gram-negative bacteria. It was isolated from a human
      breast abscess. In this work, we describe a set of features of this organism,
      together with the complete genome sequence and annotation. The 3,169,464 bp long
      genome contains 2,746 protein-coding genes and 56 RNA genes, including 3 or 4
      rRNA operons.
AU  - Roux V
AU  - Robert C
AU  - Raoult D
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 1346-1353.

PMID- 25197476
VI  - 9
DP  - 2014
TI  - Non-contiguous finished genome sequence of Corynebacterium timonense type strain  5401744(T.).
PG  - 948-955
AB  - Corynebacterium timonense strain 5401744(T) is a member of the genus Corynebacterium which
      contains Gram-positive bacteria with a high G+C content. It
      was isolated from the blood of a patient with endocarditis. In this work, we
      describe a set of features of this organism, together with the complete genome
      sequence and annotation. The 2,553,575 bp long genome contains 2,401
      protein-coding genes and 55 RNA genes, including between 5 and 6 rRNA operons.
AU  - Roux V
AU  - Robert C
AU  - Raoult D
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 948-955.

PMID- 1628840
VI  - 116
DP  - 1992
TI  - 'Stop-codon-specific' restriction endonucleases: their use in mapping and gene manipulation.
PG  - 21-26
AB  - Certain restriction endonucleases recognize target sequences that contain the stop triplet TAG
      and are commonly either 4 or 6 bp in length. Interestingly, these restriction targets do not
      occur at the frequency expected on the basis of base composition and size. For example, the
      tetranucleotide MaeI recognition sequence (CTAG) occurs considerably less commonly (5-8 fold)
      in the genome of Escherichia coli (and many other eubacteria) than expected from
      mononucleotide frequencies. This surprising rarity is particularly evident in protein-encoding
      genes and is largely dictated by codon usage. Thus, amber (TAG) nonsense mutations frequently
      give rise to novel MaeI (CTAG) sites which are unique within a translated region. Such
      amber/MaeI sites, whether arising spontaneously or created in vitro by site-directed
      mutagensis, act as a useful physical marker for the presence of the nonsense mutation and are
      a convenient startpoint for a range of diverse procedures. These features provide a useful
      supplement to protein engineering methods which use nonsense suppression to mediate amino acid
      replacements.
AU  - Rowland GC
AU  - Lim PP
AU  - Glass RE
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1992 116: 21-26.

PMID- 27387281
VI  - 44
DP  - 2016
TI  - Perpetuating the homing endonuclease life cycle: identification of mutations that modulate and change I-TevI cleavage preference.
PG  - 7350-7359
AB  - Homing endonucleases are sequence-tolerant DNA endonucleases that act as mobile genetic
      elements. The ability of homing endonucleases to cleave substrates with
      multiple nucleotide substitutions suggests a high degree of adaptability in that
      changing or modulating cleavage preference would require relatively few amino
      acid substitutions. Here, using directed evolution experiments with the GIY-YIG
      homing endonuclease I-TevI that targets the thymidylate synthase gene of phage
      T4, we readily isolated variants that dramatically broadened I-TevI cleavage
      preference, as well as variants that fine-tuned cleavage preference. By combining
      substitutions, we observed an approximately 10 000-fold improvement in cleavage
      on some substrates not cleaved by the wild-type enzyme, correlating with a
      decrease in readout of information content at the cleavage site. Strikingly, we
      were able to change the cleavage preference of I-TevI to that of the isoschizomer
      I-BmoI which targets a different cleavage site in the thymidylate synthase gene,
      recapitulating the evolution of cleavage preference in this family of homing
      endonucleases. Our results define a strategy to isolate GIY-YIG nuclease domains
      with distinct cleavage preferences, and provide insight into how homing
      endonucleases may escape a dead-end life cycle in a population of saturated
      target sites by promoting transposition to different target sites.
AU  - Roy AC
AU  - Wilson GG
AU  - Edgell DR
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2016 44: 7350-7359.

PMID- 23405324
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Pseudomonas aeruginosa Strain N002, Isolated from Crude  Oil-Contaminated Soil from Geleky, Assam, India.
PG  - e00104-12
AB  - Here, we report the draft genome sequence of crude oil-degrading Pseudomonas aeruginosa strain
      N002, isolated from a crude oil-polluted soil sample from
      Geleky, Assam, India. Multiple genes potentially involved in crude oil
      degradation were identified.
AU  - Roy AS
AU  - Baruah R
AU  - Gogoi D
AU  - Borah M
AU  - Singh AK
AU  - Deka BHP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00104-12.

PMID- 8528138
VI  - 36
DP  - 1995
TI  - Bam HI cleaves the self complementary dodecamer d-CGCGGAGCCGCG, before the two G's and possibly binds in the DNA major groove.
PG  - 759-770
AB  - Oligodeoxynucleotides with GT or GA mispairs within the Bam HI recognition sequence (GGATCC),
      have been prepared. Binding and cleavage of the native
      vis a vis the mismatch substrates by Bam HI are analysed. UV melting
      curves and CD spectra of the oligomers suggest a double stranded B-DNA
      conformation. The enzyme Bam HI binds with varying affinities to the
      oligomers except the one with the GT wobble base pair. Bam HI cleaves the
      cognate sequence, GGATCC, between the two Guanines but cleaves GGAGCC
      before the guanines. The unusual cleavage is due to a local distortion in
      the DNA structure. Kinetic analysis of the cleavage reactions using the
      35S labeled hexadecamers, d-ATGGCGGATCCGCCAT and d-ATGGCGGAGCCGCCAT, as
      substrates gives Km values 11.08 nM and 1.16 nM with corresponding Kcat of
      11.04 and 0.62 min-1 respectively. The results are consistent with the
      binding of Bam HI in the major groove.
AU  - Roy KB
AU  - Vrushank D
PT  - Journal Article
TA  - Biochem. Mol. Biol. Int.
JT  - Biochem. Mol. Biol. Int.
SO  - Biochem. Mol. Biol. Int. 1995 36: 759-770.

PMID- 7978240
VI  - 220
DP  - 1994
TI  - Use of isotope-dilution phenomenon to advantage in the determination of kinetic constants Km and Kcat for BamHI restriction endonuclease: an empirical and interative approach.
PG  - 160-164
AB  - An assay using a very small amount of 35S-labeled deoxyoligonucleotide as a substrate for the
      determination of Km and Kcat for the restriction enzyme BamHI is described. Two synthetic
      deoxyoligonucleotides, ATGGCGGATCCGC and ATGGCGGAGCCGC, containing the cognate and a mismatch
      BamHI sequence, respectively, were labeled by an end-filling reaction using the Klenow
      fragment of DNA polymerase and [35S]dATP to generate the labeled self-complementary
      substrates. The dependence of BamHI hydrolysis on substrate concentration was investigated
      using mixtures of a fixed amount of radiolabeled substrate and varying amounts of cold-labeled
      substrate over a wide range. The apparent competitive inhibition observed due to the
      phenomenon of carrier dilution was analytically corrected by an empirical as well as an
      iterative approach to give Km values comparable to those reported in the literature. We have
      found that the values obtained using the empirical formula are very close to the precise
      values obtained through iteration. Our procedure has used isotopic dilution to advantage to
      make the assay less expensive and can be applied effectively to any enzyme-substrate reaction
      in which the substrate and the product have radioactive labels. The method would be especially
      useful for a rapid analysis and comparison of kinetic constants of various mutant enzymes or
      substrates.
AU  - Roy KB
AU  - Vrushank D
AU  - Jayaram B
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 1994 220: 160-164.

PMID- 4544320
VI  - 81
DP  - 1973
TI  - DNA methylases of Hemophilus influenzae Rd.  II. Partial recognition site base sequences.
PG  - 445-459
AB  - A small percentage of the adenine bases in Hemophilus influenzae strain Rd DNA
      are methylated in the 6-amino position.  The methyl groups are introduced
      specifically by at least four different DNA methylases (I, II, III and IV).  A
      method is described for determining the 3' and 5' nearest-neighbor bases to
      methylated adenine so as to reveal the specificity of each methylase.
      Tritium-labeled methyl groups are introduced into the DNA.  The DNA is then
      digested to dinucleotides using the Bacillus subtilis phage SP3 DNase, followed
      by removal of the terminal 5'-phosphoryl group with phosphatase to produce
      dinucleoside monophosphates.  These are analyzed by Aminex A25 (Bio-Rad)
      chromatography.  Dinucleoside monophosphate species containing the 3' neighbor
      or the 5' neighbor are resolved so that a trinucleotide is determined that
      contains the centrally placed methylated adenine.  H. influenzae Rd DNA
      contains seven dinucleoside monophosphate species, about 80% representing GpmA
      and mApT in approximately equal amount.  DNA methylases I, II, III and IV
      introduce methyl groups into sequences containing the trinucleotides CpmApC,
      PupmApC, NpmApA and GpmApT, respectively.  The sequence methylated by DNA
      methylase II is consistent with the recognition site determined by Kelly &
      Smith (1970) for the H. influenzae restriction enzyme, endonuclease R.
AU  - Roy PH
AU  - Smith HO
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1973 81: 445-459.

PMID- 4591672
VI  - 81
DP  - 1973
TI  - DNA methylases of Hemophilus influenzae Rd I.  Purification and properties.
PG  - 427-444
AB  - Hemophilus influenzae strain Rd DNA contains small amounts of 5-methylcytosine
      (0.012%) and significantly greater amounts of N-6-methyladenine (0.34%).  Four
      DNA adenine methylases have been identified and purified from crude extracts of
      H. influenzae Rd by means of phosphocellulose chromatography.  Each of the four
      enzymes requires S-adenosyl-L-methionine as a methyl group donor and each
      differs in its ability to methylate various DNAs in vitro.  DNA methylase I is
      related to the genetically described modification-restriction system in H.
      influenzae Rd, and is presumably the modification enzyme for that system.  DNA
      methylase II introduces approximately 130 methyl groups into a phage T7 DNA
      molecule and protects T7 DNA from the H. influenzae Rd restriction enzyme,
      endonuclease R, described by Smith & Wilcox (1970).  These findings indicate
      that DNA methylase II is the modification enzyme corresponding to endonuclease
      R.  A third modification-restriction system, which does not affect T7 DNA, has
      been detected in H. influenzae Rd.  DNA methylase III is apparently the
      modification enzyme for this system.  The biological function of DNA methylase
      IV remains unknown.
AU  - Roy PH
AU  - Smith HO
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1973 81: 427-444.

PMID- 20107499
VI  - 5
DP  - 2010
TI  - Complete genome sequence of the multiresistant taxonomic outlier Pseudomonas aeruginosa PA7.
PG  - e8842
AB  - Pseudomonas aeruginosa PA7 is a non-respiratory human isolate from Argentina that is
      multiresistant to antibiotics. We first sequenced gyrA,
      gyrB, parC, parE, ampC, ampR, and several housekeeping genes and found
      that PA7 is a taxonomic outlier. We report here the complete sequence of
      the 6,588,339 bp genome, which has only about 95% overall identity to
      other strains. PA7 has multiple novel genomic islands and a total of 51
      occupied regions of genomic plasticity. These islands include antibiotic
      resistance genes, parts of transposons, prophages, and a pKLC102-related
      island. Several PA7 genes not present in PAO1 or PA14 are putative
      orthologues of other Pseudomonas spp. and Ralstonia spp. genes. PA7
      appears to be closely related to the known taxonomic outlier DSM1128
      (ATCC9027). PA7 lacks several virulence factors, notably the entire TTSS
      region corresponding to PA1690-PA1725 of PAO1. It has neither exoS nor
      exoU and lacks toxA, exoT, and exoY. PA7 is serotype O12 and pyoverdin
      type II. Preliminary proteomic studies indicate numerous differences with
      PAO1, some of which are probably a consequence of a frameshift mutation in
      the mvfR quorum sensing regulatory gene.
AU  - Roy PH
AU  - Tetu SG
AU  - Larouche A
AU  - Elbourne L
AU  - Tremblay S
AU  - Ren Q
AU  - Dodson R
AU  - Harkins D
AU  - Shay R
AU  - Watkins K
AU  - Mahamoud Y
AU  - Paulsen IT
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2010 5: e8842.

PMID- 25301651
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the First Isolate of Extensively Drug-Resistant Mycobacterium tuberculosis in Ireland.
PG  - e01002-14
AB  - Extensive drug resistance is an emerging threat to the control of tuberculosis (TB) worldwide,
      even in countries with low TB incidence. We report the draft
      whole-genome sequence of the first reported extensively drug-resistant TB
      (XDR-TB) strain isolated in Ireland (a low-incidence setting) and describe a
      number of single-nucleotide variations that correlate with its XDR phenotype.
AU  - Roycroft E
AU  - Mac AM
AU  - O'Toole RF
AU  - Fitzgibbon M
AU  - Rogers TR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01002-14.

PMID- 25477412
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Anoxybacillus flavithermus Strain 25, Isolated from the  Garga Hot Spring in the Barguzin Valley, Baikal Region, Russian Federation.
PG  - e01258-14
AB  - Anoxybacillus flavithermus strain 25 was isolated from a sediment sample from the Garga hot
      spring in the Barguzin Valley, Baikal Region, Russian Federation (54
      degrees 19'3.72'N, 110 degrees 59'38.4'E). The sequenced and annotated genome
      is 2,838,680 bp and encodes 3,009 genes.
AU  - Rozanov AS
AU  - Bryanskaya AV
AU  - Kotenko AV
AU  - Malup TK
AU  - Peltek SE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01258-14.

PMID- 26044423
VI  - 3
DP  - 2015
TI  - Draft genome sequence of a halorubrum h3 strain isolated from the burlinskoye salt lake (altai krai, Russia).
PG  - e00566-15
AB  - A Halorubrum H3 strain was isolated from a water and silt sample from Burlinskoye Lake (Altai
      Krai, Russia, 53 degrees 8'19'N 78 degrees 24'27'E). According to
      16S rRNA sequences, this strain is most closely related to Halorubrum
      saccharovorum. The completely sequenced and annotated genome is 3,282,373 bp and
      contains 3,237 genes.
AU  - Rozanov AS
AU  - Bryanskaya AV
AU  - Malup TK
AU  - Kotenko AV
AU  - Peltek SE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00566-15.

PMID- 29437110
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Bacillus altitudinis Strain KU-skv2(2), Isolated from a  Microbial Mat on an Anthropogenic Pipe from Caldera Uzon (Kamchatka, Russia).
PG  - e01572-17
AB  - Bacillus altitudinis strain KU-skv2(2) was isolated from a microbial mat on an anthropogenic
      pipe from Caldera Uzon (Kamchatka, Russia, 54 degrees 30'0.23'N,
      160 degrees 0'15.18'E). The sequenced and annotated genome is 3,739,340 bp in
      size and encodes 3,929 genes.
AU  - Rozanov AS
AU  - Korzhuk AV
AU  - Shipova AA
AU  - Bryanskaya AV
AU  - Peltek SE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01572-17.

PMID- 25414504
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Geobacillus stearothermophilus Strains 22 and 53, Isolated from the Garga Hot Spring in the Barguzin River Valley of the Russian  Federation.
PG  - e01205-14
AB  - Geobacillus stearothermophilus strains 22 and 53 were isolated from sediment samples isolated
      from the Garga hot spring (72 degrees C) located in the valley
      of the river Barguzin (the Baikal region, Russian Federation) (54 degrees
      19'3.72'N, 110 degrees 59'38.4'E).
AU  - Rozanov AS
AU  - Logacheva MD
AU  - Peltek SE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01205-14.

PMID- 29439042
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Bacillus altitudinis Strain KL4, Isolated from Bottom Sediments in Lake Krotovaya Lyaga (Novosibirsk Region, Russia).
PG  - e01494-17
AB  - The Bacillus altitudinis strain KL4 was isolated from bottom sediments in Lake Krotovaya Lyaga
      (Novosibirsk Region, Russia, 53.7 degrees N, 77.9 degrees E). The
      sequenced and annotated genome is 3,738,419 bp long and carries 3,909 genes.
AU  - Rozanov AS
AU  - Shipova AA
AU  - Bryanskaya AV
AU  - Tekutieva LA
AU  - Son OM
AU  - Peltek SE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01494-17.

PMID- 9099856
VI  - 188
DP  - 1997
TI  - Overexpression of BsoBI restriction endonuclease in E. coli, purification of the recombinant BsoBI, and identification of catalytic residues of BsoBI by random mutagenesis.
PG  - 35-39
AB  - BsoBI is a type II restriction enzyme found in Bacillus stearothermophilus JN209 that
      recognizes the symmetric sequence 5'-CYCGRG-3' (Y=C or T; R=A or G) and cleaves between the
      first and second base to generate a four-base 5' extension.  The cloning and sequencing of
      BsoBI restriction-modification system has been described by Ruan et al.  Here we report the
      overexpression of the BsoBI restriction endonuclease gene in E. coli by insertion of the
      endonuclease gene into an expression vector pRRS.  The recombinant BsoBI was purified to
      homogeneity and its N-terminus sequence was determined.  It has the same N-terminal aa
      sequence as the native enzyme.  The constitutive expression of BsoBI from pRRS is lethal to E.
      coli in the absence of the cognate methylase.  The BsoBIR gene was mutagenized with either
      hydroxylamine or by error-prone polymerase chain reaction in vitro and transferred into E.
      coli via plasmid vectors in the absence of the cognate methylase.  Surviving transformants
      were selected that carry BsoBI variants which lost endonuclease activity.  DNA sequencing of
      the mutant alleles revealed that G123, D124, D212, D246, E252 and H253 are important residues
      for enzymatic activity.  An electrophoretic mobility shift assay was used to identify
      binding-proficient and cleavage-deficient variants.  Seven variants I95M&D124Y, G123R, D212N,
      K207R&D212V, D246N, D246G and E252K can still bind DNA despite the loss of cleavage activity.
      Thus, residues D124, D212, D246 and E252 may be located near or within the catalytic center,
      and are likely involved in metal ion binding.
AU  - Ruan H
AU  - Lunnen KD
AU  - Pelletier JJ
AU  - Xu S-Y
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1997 188: 35-39.

PMID- 8917312
VI  - 252
DP  - 1996
TI  - Cloning and sequence comparison of AvaI and BsoBI restriction-modification systems.
PG  - 695-699
AB  - AvaI and BsoBI restriction endonucleases are isoschizomers which recognize the symmetric
      sequence 5'CYCGRG3' and cleave between the first C and second Y to generate a four-base 5'
      extension.  The AvaI restriction endonuclease gene (avaIR) and methylase gene (avaIM) were
      cloned into Escherichia coli by the methylase selection method.  The BsoBI restriction
      endonuclease gene (bsoBIM) were cloned by the "endo-blue" method (SOS induction assay), and
      the remainder of bsoBIM was cloned by inverse PCR.  The nucleotide sequences of the two
      restriction-modification (RM) systems were determined.  Comparisons of the predicted amino
      acid sequences indicated that AvaI and BsoBI endonucleases share 55% identity, whereas the two
      methylases share 41% identity.  Although the two systems show similarity in protein sequence,
      their gene organization differs.  The avaIM gene precedes avaIR in the AvaI RM system, while
      the bsoBIR gene is located upstream of bsoBIM in the BsoBI RM system.  Both AvaI and BsoBI
      methylases contain  motifs conserved among the N4 cytosine methylases.
AU  - Ruan H
AU  - Lunnen KD
AU  - Scott ME
AU  - Moran LS
AU  - Slatko BE
AU  - Pelletier JJ
AU  - Hess EJ
AU  - Benner J
AU  - Wilson GG
AU  - Xu S-Y
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1996 252: 695-699.

PMID- 17521723
VI  - 58
DP  - 2007
TI  - Sequence analysis and characterizations of two novel plasmids isolated from Thermus sp. 4C.
PG  - 84-87
AB  - Two novel plasmids, named pS4C and pL4C, were isolated from the thermophilic bacterium Thermus
      sp. 4C. The pS4C with a length of 5015bp
      and 58.25% of G+C content, contains 9 putative open reading frames (ORFs).
      The larger plasmid, pL4C, consisting of 21,248bp, has a G+C content of
      68.60% and 34 putative ORFs. Both plasmids encode their own replication
      protein. The ORF 22 of pL4C and the ORF 4 of pS4C encode proteins with
      high sequence similarities to integrase (97%) and transposase (97%),
      respectively, which are both involved in DNA rearrangement and exchange.
      Furthermore, sequence analysis of pL4C also showed that several
      plasmid-encoded genes may be involved in DNA modification and repair, such
      as DNA G:T-mismatch repair endonuclease and micrococcal nuclease-like
      protein. These proteins may be involved in raising the repair efficiency
      and other minor editing needs. Interestingly, the elimination of plasmids
      significantly lowered the growth temperature of Thermus sp. 4C. Few
      reports dealing with the DNA repair enzymes on the plasmid from Thermus
      strains were published so far.
AU  - Ruan L
AU  - Xu X
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 2007 58: 84-87.

PMID- 24435864
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Kurthia huakuii LAM0618T, an Organic-Pollutant-Degrading Strain Isolated from Biogas Slurry.
PG  - e01158-13
AB  - Kurthia huakuii LAM0618(T) is a facultative anaerobic pollutant-degrading bacterium isolated
      from biogas slurry. An analysis of the draft genome sequence
      of LAM0618(T) reveals a genome size of 3,585,165 bp, with a mean G+C content of
      39.1%. The genome contains 3,560 coding sequences and 112 tRNA and 33 rRNA genes.
AU  - Ruan Z
AU  - Wang Y
AU  - Song J
AU  - Zhai Y
AU  - Zhang C
AU  - Chen C
AU  - Li Y
AU  - Zhao B
AU  - Zhao B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01158-13.

PMID- 197493
VI  - 4
DP  - 1977
TI  - Relaxed circular SV40 DNA as cleavage intermediate of two restriction endonucleases.
PG  - 1803-1813
AB  - We have determined the mode of cleavage of superhelical SV40 DNA (Form I) by
      restriction endonucleases EcoRI and HpaII at 37C.  By analysis with agarose gel
      electrophoresis and direct examination with dark field electron microscopy, we
      found that a large amount of the single-nicked circular DNA (FormII) was
      produced before the linear SV40 DNA (Form III) appeared.  Thus, both
      restriction enzymes cleave only one strand of the superhelical DNA first.  The
      second cleavage on the complementary strand occurred after a lag period.  The
      first order rate constant for the second cleavage by EcoRI endonuclease was
      determined and a kinetic reaction scheme for both enzymes is proposed.
AU  - Ruben G
AU  - Spielman P
AU  - Tu C-PD
AU  - Jay E
AU  - Siegel B
AU  - Wu R
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1977 4: 1803-1813.

PMID- 211492
VI  - 5
DP  - 1978
TI  - Substrate dependence of the mechanism of EcoRI endonuclease.
PG  - 2991-2997
AB  - The mechanism of EcoRI endonuclease is substrate dependent.  At 37C,
      dissociation of the enzyme-Form II DNA intermediates of ColE1 ENA and
      bacteriophage G4 RFI DNA is negligible.  Therefore, both DNA strands within the
      EcoRI sequence are cleaved during a single binding event.  However, double
      strand cleavage of SV40 DNA occurs without dissociation of the enzyme in only
      75% of the catalytic events.  This mechanistic difference presumably reflects
      sequence differences about the EcoRI sites of these DNA's.
AU  - Rubin RA
AU  - Modrich P
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1978 5: 2991-2997.

PMID- 332688
VI  - 252
DP  - 1977
TI  - EcoRI methylase physical and catalytic properties of the homogeneous enzyme.
PG  - 7265-7272
AB  - Escherichia coli RI methylase has been isolated by a procedure which is suitable for large
      scale use and which yields enzyme with a specific activity 10-fold higher than previous
      methods.  The purified methylase is homogeneous as judged by polyacrylamide gel
      electrophoresis, isoelectric focusing, and analytical sedimentation.  The methylase is a basic
      protein composed of a single polypeptide chain of molecular weight 39,000, the stable form in
      solution being a 3.0 S monomer.  No aggregation has been observed at concentrations up to 0.3
      mg/ml in the temperature range of 4-30C, and the presence of S-adenosyl-L-methionine is
      without effect.  Catalytic studies have demonstrated that the enzyme functions as a monomer.
      Initial rates of methyl transfer are first order in methylase concentration, and the enzyme
      obeys Michaelis-Menten kinetics with respect to both substrates.  At 37C, the Km for the EcoRI
      site of ColE1 DNA is 1.3 nM, that for S-adenosyl-L-methionine is 0.26 microm, and the turnover
      number is three methyl transfers per min.  The mechanism of methyl transfer to unmodified DNA
      is also consistent with the functional form of the enzyme being a monomer.  The enzyme
      transfers methyl groups to the EcoRI sequence one at a time and dissociates from the DNA prior
      to any subsequent catalytic events.  Furthermore, the kinetic parameters for addition of a
      second methyl group to a site which is already methylated on one strand are not more favorable
      than those for addition of the first.  These properties of the methylase are in marked
      contrast to those of the endonuclease (Modrich, P., and Zabel, D. (1976) J. Biol. Chem. 251,
      5866-5874).  Thus, we suggest that the two proteins interact with their common recognition
      sequence in different ways.
AU  - Rubin RA
AU  - Modrich P
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1977 252: 7265-7272.

PMID- 6246382
VI  - 65
DP  - 1980
TI  - Purification and properties of EcoRI endonuclease.
PG  - 96-104
AB  - The Escherichia coli RI (EcoRI) DNA restriction and modification enzymes
      recognize a common twofold symmetrical hexanucleotide sequence in duplex DNA.
      d(pG^pApA*pTpTpCp) d(pCpTpTpA*pAp^Gp) EcoRI restriction endonuclease cleaves
      the DNA duplex within this sequence (see arrows in above sequence), while the
      modification enzyme methylates the two adenine residues adjacent to the axis of
      symmetry (asterisks) to yield 6-methylaminopurine.  The presence of one
      6-methylaminopurine residue within this sequence is sufficient to block single-
      or double-stranded cleavage by the endonuclease.  EcoRI endonuclease has been
      extensively used as a reagent for the preparation of recombinant molecules.  In
      addition, the EcoRI enzymes are biochemically simple and hence provide an ideal
      system for study of sequence-specific DNA-protein interaction.  We describe
      here a convenient method for isolation of large quantities of the endonuclease,
      a rapid assay procedure for quantitation of specific endonucleolytic activity,
      as well as physical and catalytic properties of the homogeneous protein.
AU  - Rubin RA
AU  - Modrich P
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1980 65: 96-104.

PMID- 6257702
VI  - 256
DP  - 1981
TI  - Partial NH2- and C00H-Terminal Sequence Analyses of EcoRI DNA Restriction and Modification Enzymes.
PG  - 2140-2142
AB  - NH2- and C00H-terminal amino acid sequences of the EcoRI restriction and modification enzymes
      have been determined.  The results allow localization of the coding regions within the DNA
      segment which controls activity of both enzymes.  Processing of the endonuclease is limited to
      removal of NH2-terminal formylmethionine whereas, in the case of the methylase, formylMet-Ala
      is removed.
AU  - Rubin RA
AU  - Modrich P
AU  - Vanaman TC
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1981 256: 2140-2142.

PMID- 15703294
VI  - 102
DP  - 2005
TI  - Complete genome sequence of Vibrio fischeri: A symbiotic bacterium with pathogenic congeners.
PG  - 3004-3009
AB  - Vibrio fischeri belongs to the Vibrionaceae, a large family of marine gamma-proteobacteria
      that includes several dozen species known to engage in a diversity of beneficial or pathogenic
      interactions with animal tissue. Among the small number of pathogenic Vibrio species that
      cause human diseases are Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus, the
      only members of the Vibrionaceae that have had their genome sequences reported. Nonpathogenic
      members of the genus Vibrio, including a number of beneficial symbionts, make up the majority
      of the Vibrionaceae, but none of these species has been similarly examined. Here we report the
      genome sequence of V. fischeri ES114, which enters into a mutualistic symbiosis in the light
      organ of the bobtail squid, Euprymna scolopes. Analysis of this sequence has revealed
      surprising parallels with V. cholerae and other pathogens.
AU  - Ruby EG
AU  - Urbanowski M
AU  - Campbell J
AU  - Dunn A
AU  - Faini M
AU  - Gunsalus R
AU  - Lostroh P
AU  - Lupp C
AU  - McCann J
AU  - Millikan D
AU  - Schaefer A
AU  - Stabb E
AU  - Stevens A
AU  - Visick K
AU  - Whistler C
AU  - Greenberg EP
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2005 102: 3004-3009.

PMID- 25197436
VI  - 9
DP  - 2014
TI  - Genome sequence of the squalene-degrading bacterium Corynebacterium terpenotabidum type strain Y-11(T) (= DSM 44721(T)).
PG  - 505-513
AB  - Corynebacterium terpenotabidum Takeuchi et. al 1999 is a member of the genus Corynebacterium,
      which contains Gram-positive and non-spore forming bacteria with
      a high G+C content. C. terpenotabidum was isolated from soil based on its ability
      to degrade squalene and belongs to the aerobic and non-hemolytic Corynebacteria.
      It displays tolerance to salts (up to 8%) and is related to Corynebacterium
      variabile involved in cheese ripening. As this is a type strain of
      Corynebacterium, this project describing the 2.75 Mbp long chromosome with its
      2,369 protein-coding and 72 RNA genes will aid the G enomic E ncyclopedia of
      Bacteria and Archaea project.
AU  - Ruckert C
AU  - Albersmeier A
AU  - Al-Dilaimi A
AU  - Bednarz H
AU  - Niehaus K
AU  - Szczepanowski R
AU  - Kalinowski J
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 505-513.

PMID- 23408721
VI  - 7
DP  - 2012
TI  - Genome sequence of the halotolerant bacterium Corynebacterium halotolerans type strain YIM 70093(T) (= DSM 44683(T)).
PG  - 284-293
AB  - Corynebacterium halotolerans Chen et al. 2004 is a member of the genus
      Corynebacterium which contains Gram-positive bacteria with a high G+C content. C.
      halotolerans, isolated from a saline soil, belongs to the non-lipophilic,
      non-pathogenic corynebacteria. It displays a high tolerance to salts (up to 25%)
      and is related to the pathogenic corynebacteria C. freneyi and C. xerosis. As
      this is a type strain in a subgroup of Corynebacterium without complete genome
      sequences, this project describing the 3.14 Mbp long chromosome and the 86.2 kbp
      plasmid pCha1 with their 2,865 protein-coding and 65 RNA genes will aid the
      Genomic Encyclopedia ofBacteria andArchaea project.
AU  - Ruckert C
AU  - Albersmeier A
AU  - Al-Dilaimi A
AU  - Niehaus K
AU  - Szczepanowski R
AU  - Kalinowski J
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 7: 284-293.

PMID- 26021938
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Corynebacterium camporealensis DSM 44610, Isolated from the Milk of a Manchega Sheep with Subclinical Mastitis.
PG  - e00572-15
AB  - Corynebacterium camporealensis has been isolated in pure culture from milk samples of dairy
      sheep affected by subclinical mastitis. The complete genome
      sequence of the type strain DSM 44610, recovered from milk of a Manchega sheep,
      comprises 2,451,810 bp with a mean G+C content of 59.41% and 2,249 protein-coding
      genes.
AU  - Ruckert C
AU  - Albersmeier A
AU  - Winkler A
AU  - Tauch A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00572-15.

PMID- 26021937
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Corynebacterium kutscheri DSM 20755, a Corynebacterial Type Strain with Remarkably Low G+C Content of Chromosomal DNA.
PG  - e00571-15
AB  - The complete genome sequence of the type strain Corynebacterium kutscheri DSM 20755 comprises
      2,354,065 bp and 2,047 protein-coding genes. The mean G+C content
      of the chromosomal DNA is 46.46%, which is the lowest value detected so far in a
      member of the genus Corynebacterium.
AU  - Ruckert C
AU  - Albersmeier A
AU  - Winkler A
AU  - Tauch A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00571-15.

PMID- 26294641
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of the Type Strain Corynebacterium epidermidicanis DSM 45586, Isolated from the Skin of a Dog Suffering from Pruritus.
PG  - e00959-15
AB  - The complete genome sequence of Corynebacterium epidermidicanis DSM 45586 comprises 2,692,072
      bp with 58.06% G+C content. The annotation revealed 2,466
      protein-coding regions, including genes for surface-anchored proteins with Cna
      B-type or bacterial Ig-like domains and for an adhesive SpaABC-type pilus with
      similarity to fimbrial subunits of Corynebacterium resistens DSM 45100.
AU  - Ruckert C
AU  - Eimer J
AU  - Winkler A
AU  - Tauch A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00959-15.

PMID- 26358597
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of the Type Strain Corynebacterium mustelae DSM 45274, Isolated from Various Tissues of a Male Ferret with Lethal Sepsis.
PG  - e01012-15
AB  - The complete genome of Corynebacterium mustelae DSM 45274 comprises 3,474,226 bp  and 3,188
      genes. Prominent niche and virulence factors are SpaBCA- and SpaDEF-type pili with similarity
      to pilus proteins of Corynebacterium resistens and Corynebacterium urealyticum and an
      immunomodulatory EndoS-like endoglycosidase probably catalyzing the removal of distinct
      glycans from IgG antibodies.
AU  - Ruckert C
AU  - Eimer J
AU  - Winkler A
AU  - Tauch A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01012-15.

PMID- 24407645
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Streptomyces roseochromogenes subsp. oscitans DS 12.976, Producer of the Aminocoumarin Antibiotic Clorobiocin.
PG  - e01147-13
AB  - Streptomyces roseochromogenes subsp. oscitans DS 12.976 is the producer of the
      gyrase-inhibiting aminocoumarin antibiotic clorobiocin. Here, we present a draft
      genome sequence of this strain, in which we identified the clorobiocin gene
      cluster as well as an unusually high number (43) of further putative secondary
      metabolite clusters.
AU  - Ruckert C
AU  - Kalinowski J
AU  - Heide L
AU  - Apel AK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01147-13.

PMID- 26227591
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of the Type Strain Corynebacterium testudinoris DSM 44614, Recovered from Necrotic Lesions in the Mouth of a Tortoise.
PG  - e00784-15
AB  - The complete genome sequence of the type strain Corynebacterium testudinoris DSM  44614 from
      the mouth of a tortoise comprises 2,721,226 bp with a mean G+C content
      of 63.14%. The automatic annotation of the genome sequence revealed 4 rRNA
      operons, 51 tRNA genes, 7 other RNA genes, and 2,561 protein-coding regions.
AU  - Ruckert C
AU  - Kriete M
AU  - Jaenicke S
AU  - Winkler A
AU  - Tauch A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00784-15.

PMID- 26227590
VI  - 3
DP  - 2015
TI  - Virulence Factor Genes Detected in the Complete Genome Sequence of Corynebacterium uterequi DSM 45634, Isolated from the Uterus of a Maiden Mare.
PG  - e00783-15
AB  - The complete genome sequence of the type strain Corynebacterium uterequi DSM 45634 from an
      equine urogenital tract specimen comprises 2,419,437 bp and 2,163
      protein-coding genes. Candidate virulence factors are homologs of DIP0733,
      DIP1281, and DIP1621 from Corynebacterium diphtheriae and of sialidase precursors
      from Trueperella pyogenes and Chlamydia trachomatis.
AU  - Ruckert C
AU  - Kriete M
AU  - Jaenicke S
AU  - Winkler A
AU  - Tauch A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00783-15.

PMID- 23045504
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Bacillus anthracis UR-1, Isolated from a German Heroin User.
PG  - 5997-5998
AB  - We report the draft genome sequence of Bacillus anthracis UR-1, isolated from a fatal case of
      injectional anthrax in a German heroin user. Analysis of the genome
      sequence of strain UR-1 may aid in describing phylogenetic relationships between
      virulent heroin-associated isolates of B. anthracis isolated in the United
      Kingdom, Germany, and other European countries.
AU  - Ruckert C
AU  - Licht K
AU  - Kalinowski J
AU  - Espirito SC
AU  - Antwerpen M
AU  - Hanczaruk M
AU  - Reischl U
AU  - Holzmann T
AU  - Gessner A
AU  - Tiemann C
AU  - Grass G
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5997-5998.

PMID- 21262282
VI  - 155
DP  - 2011
TI  - Genome sequence of B. amyloliquefaciens type strain DSM7T reveals differences to plant-associated B. amyloliquefaciens FZB42.
PG  - 78-85
AB  - The complete genome sequence of Bacillus amyloliquefaciens type strain DSM7T is presented. A
      comparative
      analysis between the genome sequences of the plant associated strain FZB42 (Chen et al., 2007)
      with the genome of B. amyloliquefaciens DSM7T revealed obvious differences in the variable
      part of the
      genomes, whilst the core genomes were found to be very similar. The strains FZB42 and DSM7T
      have in
      common 3345 genes (CDS) in their core genomes; whilst 547 and 344 CDS were found to be unique
      in
      DSM7T and FZB42, respectively. The core genome shared by both strains exhibited 97.89%
      identity on
      amino acid level. The number of genes representing the core genome of the strains FZB42,
      DSM7T, and
      Bacillus subtilis DSM10T was calculated as being 3098 and their identity was 92.25%. The
      3,980,199 bp
      genome of DSM7T contains numerous genomic islands (GI) detected by different methods. Many of
      them
      were located in vicinity of tRNA, glnA, and glmS gene copies. In contrast to FZB42, but
      similar to B. subtilis
      DSM10T, the GI were enriched in prophage sequences and often harbored transposases, integrases
      and recombinases. Compared to FZB42, B. amyloliquefaciens DSM7T possessed a reduced potential
      to
      non-ribosomally synthesize secondary metabolites with antibacterial and/or antifungal action.
      B. amyloliquefaciens
      DSM7T did not produce the polyketides difficidin and macrolactin and was impaired in its
      ability to produce lipopeptides other than surfactin. Differences established within the
      variable part of
      the genomes, justify our proposal to discriminate the plant-associated ecotype represented by
      FZB42
      from the group of type strain related B. amyloliquefaciens soil bacteria.
AU  - Rueckert C
AU  - Blom J
AU  - Chen XH
AU  - Reva O
AU  - Borriss R
PT  - Journal Article
TA  - J. Biotechnol.
JT  - J. Biotechnol.
SO  - J. Biotechnol. 2011 155: 78-85.

PMID- 11029001
VI  - 407
DP  - 2000
TI  - The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum.
PG  - 508-513
AB  - Thermoplasma acidophilum is a thermoacidophilic archaeon that thrives at 59 C and pH2, which
      was isolated from self-heating coal refuse piles and solfatara fields.  Species of the genus
      Thermoplasma do not possess a rigid cell wall, but are only delimited by a plasma membrane.
      Many macromolecular assemblies from Thermoplasma, primarily proteases and chaperones, have
      been pivotal in elucidating the structure and function of their more complex eukaryotic
      homologues.  Our interest in protein folding and degradation led us to seek a more complete
      representation of the proteins involved in these pathways by determining the genome sequence
      of the organism.  Here we have sequenced the 1,564,905-base-pair genome in just 7,855
      sequencing reactions by using a new strategy.  The 1,509 open reading frames identify
      Thermoplasma as a typical euryarchaeon with a substantial complement of bacteria-related
      genes; however, evidence indicates that there has been much lateral gene transfer between
      Thermoplasma and Sulfolobus solfataricus, a phylogenetically distance crenarchaeon inhabiting
      the same environment.  At least 252 open reading frames, including a complete protein
      degradation pathway and various transport proteins, resemble Sulfolobus proteins most closely.
AU  - Ruepp A
AU  - Graml W
AU  - Santos-Martinez M-L
AU  - Koretke KK
AU  - Volker C
AU  - Mewes HW
AU  - Frishman D
AU  - Stocker S
AU  - Lupas AN
AU  - Baumeister W
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2000 407: 508-513.

PMID- 21685288
VI  - 193
DP  - 2011
TI  - Genome Sequence of the Curdlan-Producing Agrobacterium sp. Strain ATCC 31749.
PG  - 4294-4295
AB  - Agrobacterium sp. ATCC 31749 is an industrial strain for the commercial production of curdlan,
      an important exopolysaccharide with food and
      medical applications. Here we report the genome sequence of the
      curdlan-producing strain ATCC 31749. Genome sequencing is the first step
      toward the understanding of regulation of curdlan biosynthesis.
AU  - Ruffing AM
AU  - Castro-Melchor M
AU  - Hu WS
AU  - Chen RR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4294-4295.

PMID- 28854875
VI  - 18
DP  - 2017
TI  - Xanthomonas adaptation to common bean is associated with horizontal transfers of genes encoding TAL effectors.
PG  - 670
AB  - BACKGROUND: Common bacterial blight is a devastating bacterial disease of common
      bean (Phaseolus vulgaris) caused by Xanthomonas citri pv. fuscans and Xanthomonas
      phaseoli pv. phaseoli. These phylogenetically distant strains are able to cause
      similar symptoms on common bean, suggesting that they have acquired common
      genetic determinants of adaptation to common bean. Transcription Activator-Like
      (TAL) effectors are bacterial type III effectors that are able to induce the
      expression of host genes to promote infection or resistance. Their capacity to
      bind to a specific host DNA sequence suggests that they are potential candidates
      for host adaption. RESULTS: To study the diversity of tal genes from Xanthomonas
      strains responsible for common bacterial blight of bean, whole genome sequences
      of 17 strains representing the diversity of X. citri pv. fuscans and X. phaseoli
      pv. phaseoli were obtained by single molecule real time sequencing. Analysis of
      these genomes revealed the existence of four tal genes named tal23A, tal20F,
      tal18G and tal18H, respectively. While tal20F and tal18G were chromosomic, tal23A
      and tal18H were carried on plasmids and shared between phylogenetically distant
      strains, therefore suggesting recent horizontal transfers of these genes between
      X. citri pv. fuscans and X. phaseoli pv. phaseoli strains. Strikingly, tal23A was
      present in all strains studied, suggesting that it played an important role in
      adaptation to common bean. In silico predictions of TAL effectors targets in the
      common bean genome suggested that TAL effectors shared by X. citri pv. fuscans
      and X. phaseoli pv. phaseoli strains target the promoters of genes of similar
      functions. This could be a trace of convergent evolution among TAL effectors from
      different phylogenetic groups, and comforts the hypothesis that TAL effectors
      have been implied in the adaptation to common bean. CONCLUSIONS: Altogether, our
      results favour a model where plasmidic TAL effectors are able to contribute to
      host adaptation by being horizontally transferred between distant lineages.
AU  - Ruh M
AU  - Briand M
AU  - Bonneau S
AU  - Jacques MA
AU  - Chen NWG
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2017 18: 670.

PMID- 28883134
VI  - 5
DP  - 2017
TI  - First Complete Genome Sequences of Xanthomonas citri pv. vignicola Strains CFBP7111, CFBP7112, and CFBP7113 Obtained Using Long-Read Technology.
PG  - e00813-17
AB  - Xanthomonas citri pv. vignicola strains cause bacterial blight of the legume crop cowpea. We
      report whole-genome sequences of three X. citri pv. vignicola strains
      obtained using PacBio single-molecule real-time sequencing. Such genomic data
      provide new information on pathogenicity factors, such as transcription
      activator-like effectors.
AU  - Ruh M
AU  - Briand M
AU  - Bonneau S
AU  - Jacques MA
AU  - Chen NWG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00813-17.

PMID- 28751394
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Pseudomonas viridiflava CFBP 1590, Isolated from Diseased Cherry in France.
PG  - e00662-17
AB  - Pseudomonas viridiflava causes foliar and stem necrosis, as well as stem and root rot on a
      wide range of plants. We report here the first complete genome of a P.
      viridiflava strain, isolated from diseased tissue of a cherry tree.
AU  - Ruinelli M
AU  - Blom J
AU  - Pothier JF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00662-17.

PMID- 26184950
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Pseudomonas frederiksbergensis SI8, a Psychrotrophic Aromatic-Degrading Bacterium.
PG  - e00811-15
AB  - Pseudomonas frederiksbergensis strain SI8 is a psychrotrophic bacterium capable of efficient
      aerobic degradation of aromatic hydrocarbons. The draft genome of P.
      frederiksbergensis SI8 is 6.57 Mb in size, with 5,904 coding sequences and 60.5%
      G+C content. The isopropylbenzene (cumene) degradation pathway is predicted to be
      present in P. frederiksbergensis SI8.
AU  - Ruiz ON
AU  - Brown LM
AU  - Striebich RC
AU  - Mueller SS
AU  - Gunasekera TS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00811-15.

PMID- 8349541
VI  - 175
DP  - 1993
TI  - Isolation and characterization of an Escherichia coli strain with a high frequency of C-to-T mutations at 5-methylcytosines.
PG  - 4985-4989
AB  - We used a genetic selection system to isolate a strain of Escherichia coli with a high
      frequency of C-to-T transition mutations at the second C of the sequence CCAGG. Cytosines in
      other sequences do not mutate to thymine at a high frequency in this strain, and the
      frequencies of other base substitution mutations are not increased to the same extent. The
      gene responsible for the mutator phenotype has been mapped to 43 min on the E. coli
      chromosome. Several lines of evidence indicate that this gene is distinct from the very short
      patch repair gene vsr.
AU  - Ruiz SM
AU  - Letourneau S
AU  - Cupples CG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1993 175: 4985-4989.

PMID- 7805889
VI  - 357
DP  - 1995
TI  - Selective inhibition of cytosine-DNA methylases by polyamines.
PG  - 192-196
AB  - We have advanced the hypothesis that polyamines affect DNA methylation and thus promote the
      expression of developmentally controlled genes. We demonstrate that the activity of
      cytosine-DNA methyltransferases HpaII, HhaI, HaeIII and SssI is inhibited by physiological
      concentrations of polyamines. On the other hand, activity of the adenine-DNA methyltransferase
      EcoRI, and restriction enzymes HpaII, HhaI, HaeIII and EcoRI, is insensitive to polyamine
      concentrations up to 40 mM. Our results indicate that the effect of polyamines on cytosine-DNA
      methyltransferases is rather selective and suggest a possible mode of action in vivo.
AU  - Ruiz-Herrera J
AU  - Ruiz-Medrano R
AU  - Dominguez A
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1995 357: 192-196.

PMID- 29146860
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of a Novel Nonnodulating Rhizobium Species Isolated from Agave americana L. Rhizosphere.
PG  - e01280-17
AB  - We report here the complete genome sequence of Rhizobium sp. strain ACO-34A, isolated from
      Agave americana L. rhizosphere. No common nod genes were found, but
      there were nif genes for nitrogen fixing. A low average nucleotide identity to
      reported species supports its designation as a novel Rhizobium species that has a
      complete ribosomal operon in a plasmid.
AU  - Ruiz-Valdiviezo VM
AU  - Rogel-Hernandez MA
AU  - Guerrero G
AU  - Rincon-Molina CI
AU  - Garcia-Perez LG
AU  - Gutierrez-Miceli FA
AU  - Villalobos-Maldonado JJ
AU  - Lopez-Lopez A
AU  - Martinez-Romero E
AU  - Rincon-Rosales R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01280-17.

PMID- 27469968
VI  - 4
DP  - 2016
TI  - Genome Sequence of Bacillus anthracis Strain Tangail-1 from Bangladesh.
PG  - e00748-16
AB  - Soil was collected in July 2013 at a site where a cow infected with anthrax had been the month
      before. Selective culturing yielded Bacillus anthracis strain
      Tangail-1. Here, we report the draft genome sequence of this Bacillus anthracis
      isolate that belongs to the canonical A.Br.001/002 clade.
AU  - Rume FI
AU  - Antwerpen M
AU  - Braun P
AU  - Biswas PK
AU  - Yasmin M
AU  - Grass G
AU  - Ahsan CR
AU  - Hanczaruk M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00748-16.

PMID- 21317333
VI  - 193
DP  - 2011
TI  - Draft Genome Sequences of Six Escherichia coli Isolates from the Stepwise Model of Emergence of Escherichia coli O157:H7.
PG  - 2058-2059
AB  - Enterohemorrhagic Escherichia coli (EHEC) of serotype O157:H7 has been implicated in
      food-borne illnesses worldwide. An evolutionary model was
      proposed in which the highly pathogenic EHEC O157:H7 serotype arose from
      its ancestor, enteropathogenic E. coli (EPEC) O55:H7 (sorbitol fermenting
      [SOR(+)] and beta-glucuronidase positive [GUD(+)]), through sequential
      gain of virulence, phenotypic traits, and serotype change. Here we report
      six draft genomes of strains belonging to this evolutionary model: two
      EPEC O55:H7 (SOR(+) GUD(+)) strains, two nonmotile EHEC O157:H(-) strains
      (SOR(+) GUD(+)) containing plasmid pSFO157, one EHEC O157:H7 (SOR(-)
      GUD(+)) strain, and one O157:H7 strain containing plasmid pSFO157 (SOR(+)
      GUD(+)).
AU  - Rump LV
AU  - Strain EA
AU  - Cao G
AU  - Allard MW
AU  - Fischer M
AU  - Brown EW
AU  - Gonzalez-Escalona N
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 2058-2059.

PMID- 1461722
VI  - 20
DP  - 1992
TI  - Characterization of the self-splicing products of a mobile intron from the nuclear rDNA of Physarum polycephalum.
PG  - 5899-5906
AB  - We have characterized the splicing products formed in vitro from RNA derived from the mobile
      group I intron in the nuclear rDNA of Physarum polycephalum, Pp LSU 3. This intron is a close
      relative of the well known Tetrahymena intron Tt LSU 1, being inserted at exactly the same
      position in the rDNA and sharing about 90% sequence identity with Tt LSU 1 in the conserved
      elements characteristic of the catalytic core of all group I introns. However, Pp LSU 3
      differs from Tt LSU 1 in that it encodes a site-specific endonuclease, which mediates the
      homing of the intron to unoccupied target sites. The endonuclease, I-Ppo, would appear to be a
      unique example of a protein encoded by an RNA polymerase I transcript. To gain clues to the
      splicing products formed in vivo, and to the nature of the messenger RNA for I-Ppo, we
      subjected Pp LSU 3 RNA to standard self-splicing conditions in vitro, and then analyzed the
      products by size, by northern blotting, and by primer extension. The results show two novel
      features. First, in addition to the expected 5' splice site, there is an alternative 5'
      splice site in the upstream exon, just preceding the first codon of the I-Ppo open reading
      frame. Second, at the position corresponding to the major circularization site in Tt LSU 1
      there is an internal processing site, leading to the efficient separation of two halves of the
      excised intron, the 5' half encoding I-Ppo and 3' half containing the ribozyme.
      Surprisingly, this cleavage appears not to be due to circularization followed by the
      hydrolytic opening of the circle, but rather to G addition. The formation of these products in
      vitro suggests how the messenger RNA for the I-Ppo endonuclease may be generated in vivo.
AU  - Ruoff B
AU  - Johansen S
AU  - Vogt VM
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 5899-5906.

PMID- 28143787
VI  - 23
DP  - 2017
TI  - Clonal or not clonal? Investigating hospital outbreaks of KPC-producing Klebsiella pneumoniae with whole-genome sequencing.
PG  - 470475
AB  - OBJECTIVES: Whole-genome sequencing (WGS) is a promising tool for identifying
      transmission pathways in outbreaks caused by multidrug-resistant bacteria.
      However, it is uncertain how the data produced by WGS can be best integrated into
      epidemiologic investigations. METHODS: We tested various genomic analyses to
      identify clonal groups in two distinct outbreaks of Klebsiella pneumoniae
      carbapenemase-producing K. pneumoniae that occurred in Switzerland in 2013 and
      2015. In blinded fashion, we sequenced 12 strains involved in the two outbreaks,
      respectively, and six that were epidemiologically unrelated. We analysed genomic
      commonalities from conserved genes to plasmid-borne antibiotic resistance genes
      (ARGs) and contrasted these results with available epidemiologic evidence.
      RESULTS: Using WGS, blinded analysts correctly identified the two clusters of
      strains from the two outbreaks. Nonetheless, the 2015 index strain was found to
      be slightly different (1-3 single nucleotide variants) from the strains recovered
      from secondary cases, likely because prior long-term carriage (3 years) by the
      index patient allowed for genetic mutations over time. Also, we observed
      occasional loss of ARG-bearing plasmidic fragments in outbreak-causing strains.
      CONCLUSIONS: Retrospective WGS analysis was successful in identifying clonal
      groups in both outbreaks. Still, data should be analysed with caution in cases of
      previous long-term carriage of the studied bacteria.
AU  - Ruppe E
AU  - Olearo F
AU  - Pires D
AU  - Baud D
AU  - Renzi G
AU  - Cherkaoui A
AU  - Goldenberger D
AU  - Huttner A
AU  - Francois P
AU  - Harbarth S
AU  - Schrenzel J
PT  - Journal Article
TA  - Clin. Microbiol. Infect.
JT  - Clin. Microbiol. Infect.
SO  - Clin. Microbiol. Infect. 2017 23: 470475.

PMID- 17355176
VI  - 5
DP  - 2007
TI  - The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific.
PG  - e77
AB  - The world's oceans contain a complex mixture of micro-organisms that are for the most part,
      uncharacterized both genetically and biochemically. We report here a metagenomic study of the
      marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as
      part of the Sorcerer II Global Ocean Sampling expedition. These samples, collected across a
      several-thousand km transect from the North Atlantic through the Panama Canal and ending in
      the South Pacific yielded an extensive dataset consisting of 7.7 million sequencing reads (6.3
      billion bp). Though a few major microbial clades dominate the planktonic marine niche, the
      dataset contains great diversity with 85% of the assembled sequence and 57% of the unassembled
      data being unique at a 98% sequence identity cutoff. Using the metadata associated with each
      sample and sequencing library, we developed new comparative genomic and assembly methods. One
      comparative genomic method, termed "fragment recruitment," addressed questions of genome
      structure, evolution, and taxonomic or phylogenetic diversity, as well as the biochemical
      diversity of genes and gene families. A second method, termed "extreme assembly," made
      possible the assembly and reconstruction of large segments of abundant but clearly nonclonal
      organisms. Within all abundant populations analyzed, we found extensive intra-ribotype
      diversity in several forms: (1) extensive sequence variation within orthologous regions
      throughout a given genome; despite coverage of individual ribotypes approaching 500-fold, most
      individual sequencing reads are unique; (2) numerous changes in gene content some with direct
      adaptive implications; and (3) hypervariable genomic islands that are too variable to
      assemble. The intra-ribotype diversity is organized into genetically isolated populations that
      have overlapping but independent distributions, implying distinct environmental preference. We
      present novel methods for measuring the genomic similarity between metagenomic samples and
      show how they may be grouped into several community types. Specific functional adaptations can
      be identified both within individual ribotypes and across the entire community, including
      proteorhodopsin spectral tuning and the presence or absence of the phosphate-binding gene
      PstS.
AU  - Rusch DB et al
PT  - Journal Article
TA  - PLoS Biology
JT  - PLoS Biology
SO  - PLoS Biology 2007 5: e77.

PMID- 23405308
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of a Single Cell of SAR86 Clade Subgroup IIIa.
PG  - e00030-12
AB  - SAR86 denotes a 16S clade of gammaproteobacteria that are ubiquitous in ocean surface waters.
      So far, SAR86 is resistant to cultivation; thus, little is known about the genome contents or
      physiology of this clade. Recently, four partial genome sequences for SAR86 subclades I and II
      were published. Here, we present the draft genome sequence of a single cell from SAR86
      subgroup IIIa isolated from coastal waters in San Diego, CA.
AU  - Rusch DB
AU  - Lombardo MJ
AU  - Yee-Greenbaum J
AU  - Novotny M
AU  - Brinkac LM
AU  - Lasken RS
AU  - Dupont CL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00030-12.

PMID- 28860258
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of the Pathogenic Vibrio vulnificus Type Strain ATCC 27562.
PG  - e00907-17
AB  - Vibrio vulnificus has the highest death rate and economic burden per case of any  foodborne
      pathogen in the United States. A complete genome sequence of the type
      strain promotes comparative analyses with other clinical and environmental
      isolates, improving our understanding of this important human pathogen and
      successful environmental organism.
AU  - Rusch DB
AU  - Rowe-Magnus DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00907-17.

PMID- 10725539
VI  - 78
DP  - 2000
TI  - A fluorescence based non-radioactive electrophoretic mobility shift assay.
PG  - 163-170
AB  - Electrophoretic mobility shift assay (EMSA) or gel shift assay is one of the most powerful
      methods for studying protein-DNA interactions. Typically,
      32P-labeled DNA probes containing the sequence bound by the protein of interest are used in
      EMSA (rEMSA). Although rEMSA is sensitive and practicable, it relies on the
      handling of hazardous radioisotopes, and does not easily allow quantification. We developed a
      non-radioactive procedure using fluorescence (Cyano dye Cy5) labeled
      oligodeoxynucleotide duplexes as specific probes (fEMSA) and an automatic DNA sequencer for
      analysis. Testing different DNA-binding proteins (restriction endonuclease
      EcoRII, transcription factor NFkappaB and it's subunit p50) the results in fEMSA and rEMSA
      are similar in regard to quality, reproducibility, and sensitivity. fEMSA allows
      a semiquantitative screening of large amounts of samples for specific DNA binding activities
      and is, therefore, a high throughput technology for semiquantitative analysis of
      DNA-protein interaction.
AU  - Ruscher K
AU  - Reuter M
AU  - Kupper D
AU  - Trendelenburg G
AU  - Dirnagl U
AU  - Meisel A
PT  - Journal Article
TA  - J. Biotechnol.
JT  - J. Biotechnol.
SO  - J. Biotechnol. 2000 78: 163-170.

PMID- 25977430
VI  - 3
DP  - 2015
TI  - Genome Sequence of Bacillus thuringiensis Strain Btm27, an Egyptian Isolate Highly Toxic to Cotton Leafworm.
PG  - e00446-15
AB  - Bacillus thuringiensis is a potent microbial control agent against insect pests.  Here, we
      present the draft genome of the Egyptian strain Btm27 that shows high
      toxicity toward the cotton leafworm. The genome contains three insecticidal genes
      cry1Ac9, cry2Ab1, and vip3V that have been implicated in conferring toxicity
      toward lepidoptera.
AU  - Rusconi B
AU  - Chen Y
AU  - Koenig SS
AU  - El-Helow ER
AU  - Eppinger M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00446-15.

PMID- 6765643
VI  - 1
DP  - 1981
TI  - Purification of the sequence-specific endonuclease PalI.
PG  - 239-242
AB  - *

        I. Growth of cells

       II. Purification of PalI

      III. Physical and chemical properties of the enzyme

       IV. Purification of other enzymes

      

AU  - Rushizky GW
PT  - Journal Article
TA  - Gene Amplif. Anal.
JT  - Gene Amplif. Anal.
SO  - Gene Amplif. Anal. 1981 1: 239-242.

PMID- 26689194
VI  - 16
DP  - 2015
TI  - Lifespan of restriction-modification systems critically affects avoidance of their recognition sites in host genomes.
PG  - 1084
AB  - BACKGROUND: Avoidance of palindromic recognition sites of Type II restriction-modification
      (R-M) systems was shown for many R-M systems in dozens
      of prokaryotic genomes. However the phenomenon has not been investigated
      systematically for all presently available genomes and annotated R-M systems. We
      have studied all known recognition sites in thousands of prokaryotic genomes and
      found factors that influence their avoidance. RESULTS: Only Type II R-M systems
      consisting of independently acting endonuclease and methyltransferase (called
      'orthodox' here) cause avoidance of their sites, both palindromic and asymmetric,
      in corresponding prokaryotic genomes; the avoidance takes place for ~ 50 % of
      1774 studied cases. It is known that prokaryotes can acquire and lose R-M
      systems. Thus it is possible to talk about the lifespan of an R-M system in a
      genome. We have shown that the recognition site avoidance correlates with the
      lifespan of R-M systems. The sites of orthodox R-M systems that are encoded in
      host genomes for a long time are avoided more often (up to 100 % in certain
      cohorts) than the sites of recently acquired ones. We also found cases of site
      avoidance in absence of the corresponding R-M systems in the genome. An analysis
      of closely related bacteria shows that such avoidance can be a trace of lost R-M
      systems. Sites of Type I, IIcapital ES, Cyrillic/G, IIM, III, and IV R-M systems
      are not avoided in vast majority of cases. CONCLUSIONS: The avoidance of orthodox
      Type II R-M system recognition sites in prokaryotic genomes is a widespread
      phenomenon. Presence of an R-M system without an underrepresentation of its site
      may indicate that the R-M system was acquired recently. At the same time, a
      significant underrepresentation of a site may be a sign of presence of the
      corresponding R-M system in this organism or in its ancestors for a long time.
      The drastic difference between site avoidance for orthodox Type II R-M systems
      and R-M systems of other types can be explained by a higher rate of specificity
      changes or a less self-toxicity of the latter.
AU  - Rusinov I
AU  - Ershova A
AU  - Karyagina A
AU  - Spirin S
AU  - Alexeevski A
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2015 16: 1084.

PMID- 22362745
VI  - 40
DP  - 2012
TI  - DNA looping by FokI: the impact of synapse geometry on loop topology at varied site orientations.
PG  - 4977-4987
AB  - Most restriction endonucleases, including FokI, interact with two copies of their recognition
      sequence before cutting DNA. On DNA with two sites they act in cis
      looping out the intervening DNA. While many restriction enzymes operate
      symmetrically at palindromic sites, FokI acts asymmetrically at a non-palindromic
      site. The directionality of its sequence means that two FokI sites can be bridged
      in either parallel or anti-parallel alignments. Here we show by biochemical and
      single-molecule biophysical methods that FokI aligns two recognition sites on
      separate DNA molecules in parallel and that the parallel arrangement holds for
      sites in the same DNA regardless of whether they are in inverted or repeated
      orientations. The parallel arrangement dictates the topology of the loop trapped
      between sites in cis: the loop from inverted sites has a simple 180 degrees bend,
      while that with repeated sites has a convoluted 360 degrees turn. The ability of
      FokI to act at asymmetric sites thus enabled us to identify the synapse geometry
      for sites in trans and in cis, which in turn revealed the relationship between
      synapse geometry and loop topology.
AU  - Rusling DA
AU  - Laurens N
AU  - Pernstich C
AU  - Wuite GJ
AU  - Halford SE
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: 4977-4987.

PMID- 10982881
VI  - 28
DP  - 2000
TI  - Examination of the DNA substrate selectivity of DNA cytosine methyltransferases using mass tagging.
PG  - 3594-3599
AB  - The biological significance of cytosine methylation is as yet incompletely understood, but
      substantial and growing evidence strongly suggests that perturbation of methylation patterns,
      resulting from the infidelity of DNA cytosine methyltransferase, is an important component of
      the development of human cancer. We have developed a novel in vitro assay that allows us to
      quantitatively determine the DNA substrate preferences of cytosine methylases. This approach,
      which we call mass tagging, involves the labeling of target cytosine residues in synthetic DNA
      duplexes with stable isotopes, such as (15)N. Methylation is then measured by the formation of
      5-methylcytosine (5mC) by gas chromatography/mass spectrometry. The DNA substrate selectivity
      is determined from the mass spectrum of the product 5mC. With the non-symmetrical duplex DNA
      substrate examined in this study we find that the bacterial methyltransferase HpaII (duplex
      DNA recognition sequence CCGG) methylates the one methylatable cytosine of each strand
      similarly. Introduction of an A-C mispair at the methylation site shifts methylation
      exclusively to the mispaired cytosine residue. In direct competition assays with HpaII
      methylase we observe that the mispaired substrate is methylated more extensively than the
      fully complementary, normal substrate, although both have one HpaII methylation site. Through
      the use of this approach we will be able to learn more about the mechanisms by which
      methylation patterns can become altered.
AU  - Rusmintratip V
AU  - Riggs AD
AU  - Sowers LC
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2000 28: 3594-3599.

PMID- 20139183
VI  - 192
DP  - 2010
TI  - Genome Sequence of Streptococcus gallolyticus: Insights into Its Adaptation to the Bovine Rumen and Its Ability To Cause Endocarditis.
PG  - 2266-2276
AB  - Streptococcus gallolyticus (formerly known as Streptococcus bovis biotype I) is an increasing
      cause of endocarditis among streptococci and
      frequently associated with colon cancer. S. gallolyticus is part of the
      rumen flora but also a cause of disease in ruminants as well as in birds.
      Here we report the complete nucleotide sequence of strain UCN34,
      responsible for endocarditis in a patient also suffering from colon
      cancer. Analysis of the 2,239 proteins encoded by its 2,350-kb-long genome
      revealed unique features among streptococci, probably related to its
      adaptation to the rumen environment and its capacity to cause
      endocarditis. S. gallolyticus has the capacity to use a broad range of
      carbohydrates of plant origin, in particular to degrade polysaccharides
      derived from the plant cell wall. Its genome encodes a large repertoire of
      transporters and catalytic activities, like tannase, phenolic compounds
      decarboxylase, and bile salt hydrolase, that should contribute to the
      detoxification of the gut environment. Furthermore, S. gallolyticus
      synthesizes all 20 amino acids and more vitamins than any other sequenced
      Streptococcus species. Many of the genes encoding these specific functions
      were likely acquired by lateral gene transfer from other bacterial species
      present in the rumen. The surface properties of strain UCN34 may also
      contribute to its virulence. A polysaccharide capsule might be implicated
      in resistance to innate immunity defenses, and glucan mucopolysaccharides,
      three types of pili, and collagen binding proteins may play a role in
      adhesion to tissues in the course of endocarditis.
AU  - Rusniok C
AU  - Couve E
AU  - Da Cunha V
AU  - El Gana R
AU  - Zidane N
AU  - Bouchier C
AU  - Poyart C
AU  - Leclercq R
AU  - Trieu-Cuot P
AU  - Glaser P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 2266-2276.

PMID- 24812224
VI  - 2
DP  - 2014
TI  - Genome Sequence of Salmonella enterica subsp. enterica Strain Durban.
PG  - e00399-14
AB  - We report the genome sequence of Salmonella enterica subsp. enterica strain Durban, isolated
      from a patient with salmonellosis and typhoid fever. The strain
      is closely related to S. enterica subsp. enterica strain P125109 but differs in
      loss of the SE20 prophage and acquisition of a prophage similar to ELPhiS.
AU  - Russell DA
AU  - Bowman CA
AU  - Hatfull GF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00399-14.

PMID- 27688316
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Gordonia terrae 3612.
PG  - e01058-16
AB  - Here, we report the complete genome sequence of Gordonia terrae 3612, also known  by the
      strain designations ATCC 25594, NRRL B-16283, and NBRC 100016. The genome
      sequence reveals it to be free of prophage and clustered regularly interspaced
      short palindromic repeats (CRISPRs), and it is an effective host for the
      isolation and characterization of Gordonia bacteriophages.
AU  - Russell DA
AU  - Guerrero BCA
AU  - Garlena RA
AU  - Hatfull GF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01058-16.

PMID- 27013048
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Arthrobacter sp. ATCC 21022, a Host for Bacteriophage Discovery.
PG  - e00168-16
AB  - We report the complete genome sequence ofArthrobactersp. ATCC 21022, a strain maintained by
      ATCC and a commonly used host for bacteriophage isolation and
      genomic analysis. The strain is prophage-free and CRISPR-free but codes for two
      predicted restriction-modification systems.
AU  - Russell DA
AU  - Hatfull GF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00168-16.

PMID- 18297739
VI  - 237
DP  - 2008
TI  - Alternative splicing and expression analysis of bovine DNA methyltransferase 1.
PG  - 1051-1059
AB  - Methylation of specific CG residues in the mammalian genome results in tissue-specific
      patterns of gene expression, which are critical for
      cell differentiation. Embryos that fail to establish and maintain
      proper DNA methylation patterns show severe developmental abnormalities
      as is the case of DNA methyltransferase 1 (Dnmt1) -deficient embryos.
      Dnmt1 is the main maintenance methyltransferase in the mouse and its
      expression is regulated by a splicing mechanism that dictates the
      expression of stage-specific isoforms. Little is known about Dnmt1
      expression in the cow and isoforms of Dnmt1 are yet unknown in this
      species. Here we demonstrate that the previously described bovine Dnmt1
      transcript is ubiquitously expressed in embryos and fetal tissue. In
      addition, we report the identification of a splice variant of the
      bovine Dnmt1, which shows a ubiquitous expression pattern. This new
      transcript was detected using 5'RACE and genomic mapping and its
      expression pattern was shown to be consistent with a tissue-specific
      mode of regulation. Furthermore, our analysis shows that the expression
      of an oocyte-specific isoform of Dnmt1 is unlikely to occur in cattle.
      The newly reported isoform of Dnmt1 was demonstrated to be, similarly
      to Dnmt1a, polyadenylated and if translated possess the functional
      domains necessary for maintenance and de novo methyltransferase
      activity.
AU  - Russell DF
AU  - Betts DH
PT  - Journal Article
TA  - Dev. Dyn.
JT  - Dev. Dyn.
SO  - Dev. Dyn. 2008 237: 1051-1059.

PMID- 2659593
VI  - 264
DP  - 1989
TI  - The detection of extremely rare DNA modifications.
PG  - 10787-10794
AB  - DNA methylation in Escherichia coli plays a role in many key cellular processes, including DNA
      replication, repair, restriction, and transcription. However, several mutant bacterial strains
      exist which are deficient in DNA methylase activities. Thus, it has been suggested that
      methylation produced by the dam (DNA adenine methylase) gene is required for the viability of
      E. coli and that dam- strains still produce low levels of methylation. Current experimental
      methods are not sensitive enough to detect a few potentially essential methylated sites per
      genome. Here we describe a method for the detection of N6-methyladenine at specific sites with
      a sensitivity of one site in more than 10 megabases. We show that methylation produced by both
      the dam and hsd (EcoK) genes is not required for the growth of E. coli and identify the site
      of EcoK modification. Minor adaptations of the technique should enable the identification of
      other rare DNA modifications.
AU  - Russell DW
AU  - Hirata RK
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1989 264: 10787-10794.

PMID- 3304662
VI  - 50
DP  - 1987
TI  - Hemimethylation prevents DNA replication in E. coli.
PG  - 1071-1079
AB  - The DNA adenine methylase of E. coli methylates adenines at GATC sequences. Strains deficient
      in this methylase are transformed poorly by methylated plasmids that depend on either the
      pBR322 or the chromosomal origins for replication. We show here that hemimethylated plasmids
      also transform dam- bacteria poorly but that unmethylated plasmids transform them at high
      frequencies. Hemimethylated daughter molecules accumulate after the transformation of dam-
      strains by fully methylated plasmids, suggesting that hemimethylation prevents DNA
      replication. We also show that plasmids purified from dam+ bacteria are hemimethylated at
      certain sites. These results can explain why newly formed daughter molecules are not
      substrates for an immediate reinitiation of DNA replication in wild-type E. coli.
AU  - Russell DW
AU  - Zinder ND
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1987 50: 1071-1079.

PMID- 23516199
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Hypervirulent Klebsiella pneumoniae Strain hvKP1, Isolated in Buffalo, New York.
PG  - e0006513
AB  - Hypervirulent variants of Klebsiella pneumoniae have been primarily reported in the Asian
      Pacific Rim, but they are spreading across the globe. We report the
      sequence of K. pneumoniae strain hvKP1, which caused liver-splenic abscesses in
      an otherwise healthy 24-year-old from Buffalo, NY, which will assist in
      determining why these variants are more pathogenic than 'classic' K. pneumoniae
      strains.
AU  - Russo TA
AU  - Gill SR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0006513.

PMID- 936829
VI  - 234
DP  - 1976
TI  - Restriction and modification of typing phages by an R factor in S. typhi.
PG  - 491-501
AB  - We have investigated the qualities of one R factor 552 discovered on a strain of S. typhi
      resistant to A, C, S, T, non-typable, isolated from stool cultures; from the same patient,
      before starting the treatment we isolated, from his blood sample, the strain S. typhi 221,
      sensitive to A, C, T, degraded phage-type Vi A.  Factor R 552 fi- when infecting strains of S.
      typhi Vi A and of A degraded 221- leads to the conversion of the respective phage-types into
      non-typable ones, as a result of the restricting and modifying effect on phage ViA and on the
      derivatives resulting from it.  Derivative R 552-1 as a resistance marker to ampicillin has a
      restrictive effect on the phage of S. panama A 47 too.  Not taking into account possible
      causes such as spontaneous mutation, lysogeny, and adsorption of phages, we reach the
      conclusion that R factor 552, through its restrictive effect, is the only cause responsible
      for the existence in the same patient of two strains of S. typhi different from the point of
      view of phage-type antibiotype.
AU  - Rusu V
AU  - Dorobat-Baron O
AU  - Cosman M
AU  - Lazaroae D
PT  - Journal Article
TA  - Zentralbl. Bakteriol. [Orig. A]
JT  - Zentralbl. Bakteriol. [Orig. A]
SO  - Zentralbl. Bakteriol. [Orig. A] 1976 234: 491-501.

PMID- Not carried by PubMed...
VI  - 57
DP  - 1997
TI  - Molecular studies of restriction genes in enteric bacteria.
PG  - 4210
AB  - Bacterial cells contain various restriction-modification systems to protect themselves from
      incoming foreign DNA.  Most bacteria have at least one such system.  In this study, the
      restriction genes and the location of the genes on the chromosome were examined in three
      enteric bacteria, Salmonella typhimurium LT2, Klebsiella pneumoniae GM 236, and Klebsiella
      pneumoniae M5a1.  The 98 minute region of the Salmonella typhimurium LT2 chromosome comprises
      at least two R-M systems.  From genetic data this region was previously thought to be only one
      minute in length but was found to be larger than two minutes using a physical mapping
      technique, pulsed field gel electrophoresis.  The KpnAI and KpnBI R-M systems were recognized
      in K. pneumoniae strain M5a1 and GM236, respectively.  A macro-restriction map of Klebsiella
      pneumoniae GM236 was constructed in this study using PFGE and Southern hybridization.  The
      genome was digested with three rare cutting restriction enzymes (BlnI, I-CeuI, and XbaI).  The
      estimated size of the GM236 genome was 4,582 (+/-80) kb, in accordance with the range of other
      enteric bacteria.  The partial digest of I-CeuI allowed a tentative ordering of the eight
      fragments on a circular map.  The map was remarkably similar to the map of Escherichia coli
      and S. typhimurium with the exception of two fragments.  I-CeuI cuts the GM236 chromosome in
      eight fragments whereas it cuts E. coli and Salmonella genomes in seven.  This suggests a
      possible duplication of the ribosomal cluster in the GM236 strain.  The constructed map,
      although tentative, has permitted the mapping of hsdRKpnBI, a restriction gene located on a
      322 kb BlnI fragment and also on a 40 kb XbaI fragment.  In this study, hsdRKpnAI, another
      restriction gene recognized in K. pneumoniae M5a1, was subcloned and sequenced.  The DNA
      sequence of 4.5 kb was determined and only one open reading frame of 3,305 base pairs was
      considered as the coding region for the HsdRKpnAI polypeptide.  The nucleotide sequence of the
      hsdRKpnAI gene showed no significant similarity to any other sequences in the GenBank
      database.  However, the deduced amino acid sequence showed a moderate degree of homology (26%)
      with EcoR124II (former EcoR124/3I), a type IC restriction enzyme and KpnBI.  After alignment
      of the three proteins, seven helicase motifs, typical of type I and III restriction enzymes,
      were found.  This similarity between the three proteins and other current evidence show that
      KpnAI and KpnBI are probably the first type I restriction endonucleases recognized in K.
      pneumoniae.
AU  - Rutebuka OB
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1997 57: 4210.

PMID- Not carried by PubMed...
VI  - 95
DP  - 1995
TI  - DNA sequence analysis of the KpnAI restriction gene of Klebsiella pneumoniae M5a1.
PG  - 522
AB  - We have recently cloned the restriction genes of the KpnAI and KpnBI restriction-modification
      systems of K. pneumoniae strains M5aI and GM236 and have reported the nucleotide and deduced
      amino acid sequence of the KpnBI gene.  We have now sequenced and analyzed a 4.5 kb
      Sau3AI/BamHI restriction fragment of the KpnAI clone, pNLA2, which expresses restriction
      activity in r-KpnAI m+KpnAI mutants.  From the DNA sequence, we deduce an open reading frame
      (ORF) of 3.3 kb (nucleotides 1156 to 4458) that appears to encode an HsdR polypeptide.
      However, the ORF does not show any nucleotide sequence similarity with other genes that are
      available from the PC/Gene GenBank.  In spite of the lack of nucleotide sequence similarity,
      the deduced amino acid sequence shows a high degree of homology with EcoR124/3, a type IC
      restriction enzyme, and the KpnBI polypeptide.  The KpnAI restriction endonuclease, like other
      type I and type III endonuclease, also contains sequence motifs characteristic of
      superfamily-II helicases which may be involved in DNA unwinding at the cleavage site.  Our
      data suggests that the KpnAI system is most likely to be a type I restriction-modification
      system.
AU  - Rutebuka OB
AU  - Lee NS
AU  - Ryu J
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1995 95: 522.

PMID- 24971497
VI  - 118
DP  - 2014
TI  - Restriction Enzyme Ecl18kI-Induced DNA Looping Dynamics by Single-Molecule FRET.
PG  - 8575-8582
AB  - Many type II restriction endonucleases require binding of two copies of a recognition site for
      efficient DNA cleavage. Simultaneous interaction of the enzyme with two DNA sites results in
      DNA loop formation. It was demonstrated with the tethered particle motion technique that such
      looping is a dynamic process where a DNA loop is repeatedly formed and disrupted. Here we use
      a better and in the context of protein-induced DNA looping virtually unexploited strategy of
      single-molecule Forster resonance energy transfer of surface immobilized biomolecules to
      quantitatively study the dynamics of Ecl18kI endonuclease-induced DNA looping and determine
      the rate constants of loop formation and disruption. We show that two DNA-bound Ecl18kI dimers
      efficiently form a bridging tetramer looping out intervening DNA with a rate that is only a
      few orders of magnitude lower than the diffusion limited rate. On the other hand, the
      existence of Ecl18kI tetramer is only transient, and the loop is rapidly disrupted within
      about 1 s.
AU  - Rutkauskas D
AU  - Petkelyte M
AU  - Naujalis P
AU  - Sasnauskas G
AU  - Tamulaitis G
AU  - Zaremba M
AU  - Siksnys V
PT  - Journal Article
TA  - J. Phys. Chem. B
JT  - J. Phys. Chem. B
SO  - J. Phys. Chem. B 2014 118: 8575-8582.

PMID- 7607518
VI  - 157
DP  - 1995
TI  - SacNI, an isoschizomer of BanII isolated from Streptomyces achromogenes recognizes the 5'-GRGCY/C sequence.
PG  - 319-320
AB  - SacNI, an isoschizomer of the restriction endonuclease, BanII, has been isolated from
      Streptomyces achromogenes N-J-H.  SacNI recognizes the palindromic sequence, 5'-GRGCY/C, and
      cleaves within the recognition sequence, generating a 3' protruding RGCY end (where R=A or G,
      and Y=C or G).
AU  - Rutkowska SM
AU  - Skowron PM
AU  - Bielawski K
AU  - Podhajska AJ
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 319-320.

PMID- 7607517
VI  - 157
DP  - 1995
TI  - Purification and characterization of the restriction endonuclease AvcI from Actinomyces cristalomycini.
PG  - 317-318
AB  - The restriction endonuclease AvcI, an isoschizomer of Sau96I was purified from Actinomyces
      cristalomycini.  AvcI recognizes a 5-bp palindromic sequence, 5'-G/GNCC and cleaves it after
      the first G residue producing a 3-nucleotide 5'-overhang.
AU  - Rutkowska SM
AU  - Skowron PM
AU  - Podhajska AJ
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 317-318.

PMID- 1095148
VI  - 131
DP  - 1975
TI  - Recent Advances in Microbial Genetics.
PG  - 284-289
AB  - Evolution depends on genetic diversity, and the genetic information contained
      within double-stranded deoxyribonucleic acid (DNA) of bacterial cells can be
      altered by mutation or by recombination.  Mutations include changes in genes
      that occur naturally or are brought about experimentally by agents such as
      chemicals or by ionizing radiation.  In contrast, recombination results from an
      interaction between one micro-organism with another distinct and separate
      micro-organism.  Recombination provides a rapid method for producing changes in
      genotype and is generally confined to a sexual process in higher animals.  The
      prokaryotic unicellular bacterium differs from eukaryotic animal and plant
      cells in that it possesses a single, circular, closed chromosome.  A variety of
      different recombination mechanisms have been discovered in bacteria; these
      include the entry of naked DNA into bacterial cells (a process called
      transformation), the transfer of genetic information incorporated in
      bacteriophages (termed transduction), and a sexual process involving transfer
      of genetic material between bacterial cells in close apposition (called
      conjugation).  Studies of these mechanisms have led to a deeper understanding
      of the molecular basis of gene action and are well described (see Hayes, 1968).
      Recent advances in our knowledge of nucleic acids have led to the creation in
      the laboratory of new combinations of genetic material.  This has been achieved
      by splicing together DNA from entirely different sources to form hybrid
      molecules that are less likely to occur during evolutionary processes.  This
      review is confined to a discussion of these techniques which have caused so
      much public disquiet.
AU  - Rutter JM
PT  - Journal Article
TA  - Br. Vet. J.
JT  - Br. Vet. J.
SO  - Br. Vet. J. 1975 131: 284-289.

PMID- 10037813
VI  - 27
DP  - 1999
TI  - Characterization of a CACAG pentanucleotide repeat in Pasteurella haemolytica and its possible role in modulation of a novel type III restriction-modification system.
PG  - 1505-1511
AB  - In a previous study, a recombinant plasmid that contains a CACAG pentanucleotide repeat was
      isolated from a Pasteurella haemolytica A1 library.  Southern hybridization analysis using a
      (CACAG)5 probe indicated the presence of two loci that contain the pentanucleotide repeats on
      the genome of P. haemolytica A1. Additional hybridization analyses against genomic DNA from
      related microorganisms indicated that the repeats are only present in P. haemolytica and
      Pasteurella trehalosi T3.  The various serotypes of P. haemolytica were found to have either
      one or two of the CACAG repeat-containing loci.  Examination of the locus designated Rpt2 by
      PCR and sequence analysis indicated that the number of CACAG repeats could change upon serial
      subculture which most likely occurs as a result of DNA slipped-strand mispairing.  A plasmid
      carrying the Rpt2 locus was isolated and characterized.  Sequence analysis indicated that the
      CACAG repeats are contained within the 5'-end of a gene that showed homology to mod genes of
      type III restriction-modification systems.  A second open reading frame downstream was
      identified which showed homology to res genes of type III restriction-modification systems.
      Both the modification and restriction proteins could be expressed and polypeptides of the
      expected sizes were detected by SDS-PAGE.  Restriction activity could also be detected in
      crude cytoplasmic extracts of Escherichia coli strains carrying the mod and res genes on
      recombinant plasmids.
AU  - Ryan KA
AU  - Lo YC
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1999 27: 1505-1511.

PMID- 25593248
VI  - 3
DP  - 2015
TI  - Genome Sequence of the Heteropolysaccharide-Producing Strain Lactobacillus mucosae DPC 6426.
PG  - e01350-14
AB  - Exopolysaccharide-synthesizing Lactobacillus mucosae DPC 6426 is a heterofermentative strain,
      which has demonstrated cholesterol-lowering properties
      in an animal model of lipid-driven atherosclerosis. The genome revealed a
      plethora of homologues linked to carbohydrate metabolism and mucin binding.
AU  - Ryan PM
AU  - Guinane CM
AU  - London LE
AU  - Kelleher PR
AU  - Fitzgerald GF
AU  - Caplice NM
AU  - Ross RP
AU  - Stanton C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01350-14.

PMID- 23121719
VI  - 280
DP  - 2013
TI  - DNA methyltransferase SsoII: a balance between DNA methylation and transcription repression.
PG  - 127
AB  - Restriction-modification systems serve as primitive immune systems protecting bacterial cells
      from phage infection.  R-M system SsoII from Shigella sonnei consists of a DNA
      methyltransferase and a restriction endonuclease.  M.SsoII methylates C5 atom of the second
      cytosine in the sequence 5'-CCNGG-3' (N=A, C, G or T) in dsDNA while R.SsoII cleaves this
      site in case it remains unmethylated.  Since phage DNA is not methylated, R.SsoII hydrolyzes
      it and protects the host cell.  In case the endonuclease activity exceeds the
      methyltransferase activity, the host cell DNA can be cleaved as well.  Therefore, M. SsoII and
      R.SsoII expression should be strictly coordinated.  This coordination is provided by M.SsoII
      itself: it represses transcription of its own gene and stimulates transcription of the R.SsoII
      gene via binding to the regulatory site which is located in the promoter region of the R-M
      system SsoII.  Surpringly, M.SsoII forms a much more stable complex with the regulatory site
      than with the methylation site.  Moreover, M.SsoII binding with the former one prevents its
      binding with the latter one.  Does M.SsoII still methylate DNA?  We show that (i) M.SsoII
      association rate with the methylation site is higher than that for the regulatory site; (ii)
      amount of the methylation sites in a bacterial cell is on average 10,000 times higher than
      amount of the regulatory sites.  Both these factors direct M.SsoII to the DNA methylation.
      M.SsoII has an extremely high affinity to the regulatory site (Kd < nM, i.e. effective binding
      even when there are only two regulatory sites per cell).  We conclude that the plasmid-encoded
      R-M system SsoII is naturally adjusted for acting at low concentrations.  Therefore, this
      system is not a great burden for a cell and has spread among different species and genders of
      Enterobacteriaceae.
AU  - Ryazanova A
AU  - Migur A
AU  - Norkin M
AU  - Timofeyeva N
AU  - Fedorova O
AU  - Kubareva E
PT  - Journal Article
TA  - FEBS J.
JT  - FEBS J.
SO  - FEBS J. 2013 280: 127.

PMID- 
VI  - 0
DP  - 2012
TI  - Diverse domains of (cytosine-5)-DNA methyltransferases: Structural and functional characterization.
PG  - 29-69
AB  - (Cytosine-5)-DNA methyltransferases (C5-DNA MTases) are enzymes which catalyze methyl group
      transfer from S-adenosyl-L-methionine to C5 atom of cytosine residue in DNA.  As a result,
      AdoMet is converted into S-adenosyl-L-homocysteine.  The recognition sites of C5-DNA MTases
      are usually short palindromic sequences (2-6 bp) in double-stranded DNA.  One or both DNA
      strands can be methylated.  The introduced methyl group is localized in the major groove of
      the DNA double helix and thus does not disrupt Watson-Crick interactions.
AU  - Ryazanova AY
AU  - Abrosimova LA
AU  - Oretskaya TS
AU  - Kubareva EA
PT  - Journal Article
TA  - Methylation - from DNA, RNa and histones to diseases and treatment
JT  - Methylation - from DNA, RNa and histones to diseases and treatment
SO  - Methylation - from DNA, RNa and histones to diseases and treatment 2012 0: 29-69.

PMID- 21274469
VI  - 136
DP  - 2011
TI  - The study of the interaction of (cytosine-5)-DNA methyltransferase SsoII with DNA by acoustic method.
PG  - 1227-1233
AB  - The interaction of (cytosine-5)-DNA methyltransferase SsoII (M. SsoII) with double-stranded
      DNA was studied by means of thickness shear mode
      acoustic method (TSM) and gel electrophoresis. M. SsoII recognizes in
      double-stranded DNA the methylation site 5'-CCNGG-3' (N = A, C, G, T)
      and methylates the inner cytosine residue. M. SsoII also acts as a
      transcription factor via binding to the regulatory site
      5'-AGGACAAATTGTCCT-3' in the promoter region of SsoII
      restriction-modification system. We designed three 60-mer biotinylated
      DNA duplexes: with the methylation site (60met), with the regulatory
      site (60reg), and without a specific binding site (60oct). A strong
      binding of M. SsoII with each one of the studied DNA immobilized on the
      TSM transducer has been shown. The equilibrium dissociation constants,
      K-D, of the M. SsoII-DNA complexes decreased in the order 60oct > 60reg
      > 60met, suggesting a higher stability of M. SsoII-60met complex in
      comparison with the others. The association rate constant, k(a), was
      also higher for 60met, while similar values were obtained for 60reg and
      60oct. The difference in the kinetic parameters for 60met and 60reg
      suggested a possible way of coordination between the two M. SsoII
      functions in a cell.
AU  - Ryazanova AY
AU  - Kubareva EA
AU  - Grman I
AU  - Lavrova NV
AU  - Ryazanova EM
AU  - Oretskaya TS
AU  - Hianik T
PT  - Journal Article
TA  - Analyst
JT  - Analyst
SO  - Analyst 2011 136: 1227-1233.

PMID- 21090246
VI  - 44
DP  - 2010
TI  - Secondary structure of SsoII-like (Cytosine-5)-DNA methyltransferases N-terminal region determined by Circular dichroism spectroscopy.
PG  - 911-921
AB  - (Cytosine-5)-DNA methyltransferase SsoII (M.SsoII) has a long N-terminal region (1-71
      residues) preceding the sequence with conservative motifs, which are characteristic for all
      DNA methyltrans-ferases of such kind. The presence of this region provides M.SsoII capability
      to act as a transcription regulator in SsoII restriction-modification system. To perform its
      regulatory function, M.SsoII binds specifically to a 15-mer inverted repeat in the promoter
      region of SsoII restriction-modification system genes. In the present work, properties of the
      protein Delta(72-379)M.Ecl18kI are studied, which is a deletion mutant of the SsoII-like
      DNA-methyltransferase M.Ecl18kI and is homologous to M.SsoII N-terminal region.
      Delta(72-379)M.Ecl18kI capability to bind specifically a DNA duplex containing the regulatory
      site is demonstrated. However, such a binding takes place only in the presence of high protein
      excess relative to DNA, which could indicate an altered structure in the deletion mutant in
      comparison with the full-length M.SsoII. Circular dichroism spectroscopy demonstrated that
      Delta(72-379)M.Ecl18kI has a strongly pronounced secondary structure and contains 32%
      alpha-helices and 20% beta-strands. Amino acid sequences alignment of M.SsoII N-terminal
      region and transcription factors of known spatial structure is made. An assumption is made how
      alpha-helices and beta-strands are arranged in M.SsoII N-terminal region.
AU  - Ryazanova AY
AU  - Molochkov NV
AU  - Abrosimova LA
AU  - Alexeevsky AV
AU  - Karyagina AS
AU  - Protsenko AS
AU  - Friedhoff P
AU  - Oretskaya TS
AU  - Kubareva EA
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2010 44: 911-921.

PMID- 21888553
VI  - 30
DP  - 2011
TI  - Crosslinking of (cytosine-5)-DNA methyltransferase SsoII and its complexes with specific DNA duplexes provides an insight into their structures.
PG  - 632-650
AB  - (Cytosine-5)-DNA methyltransferase SsoII (M.SsoII) functions as a methyltransferase and also
      as a transcription factor Chemical and photochemical crosslinking was used for exploring the
      structure of M.SsoII-DNA complexes and M.SsoII in the absence of DNA. Photocrosslinking with
      4-(N-maleimido)benzophenone demonstrated that in the M.SsoII complex with DNA containing the
      regulatory site, the M.SsoII region responsible for methylation was bound to DNA flanking the
      regulatory site, which contained no methylation sequence. This required high flexibility of
      the linker connecting the M.SsoII N-terminal domain and the M.SsoII region responsible for
      methylation. The flexibility was demonstrated by crosslinking with bis-maleimidoethane and
      1,11-bis-maleimidotetraethyleneglycol.
AU  - Ryazanova AY
AU  - Winkler I
AU  - Friedhoff P
AU  - Viryasov MB
AU  - Oretskaya TS
AU  - Kubareval EA
PT  - Journal Article
TA  - Nucleosides Nucleotides Nucleic Acids
JT  - Nucleosides Nucleotides Nucleic Acids
SO  - Nucleosides Nucleotides Nucleic Acids 2011 30: 632-650.

PMID- 25767224
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Paenibacillus polymyxa Strain Sb3-1, a Soilborne Bacterium with Antagonistic Activity toward Plant Pathogens.
PG  - e00052-15
AB  - The genome of Paenibacillus polymyxa Sb3-1, a strain that shows antagonistic activities
      against pathogenic fungi and bacteria, consists of one 5.6-Mb circular
      chromosome and two plasmids of 223 kb and 8 kb. The genome reveals several genes
      that potentially contribute to its antagonistic and plant growth promotion
      activity.
AU  - Rybakova D
AU  - Wetzlinger U
AU  - Muller H
AU  - Berg G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00052-15.

PMID- 
VI  - 
DP  - 2006
TI  - Biochemical characterization of the Escherichia coli very short patch repair pathway and its coordination with methyltransferase repair of  O6-methylguanine.
PG  - 1-273
AB  - The E. coli Very Short Patch Repair (VSPR) system corrects T:G mismatches that arise through
      Dcm-mediated methylation and subsequent deamination of the underlined cytosine residue in the
      palindromic sequence 5'-CCWGG-3' (W is an adenine or thymine). Vsr initiates VSPR by
      producing a single stranded nick on the 5' side of the mismatched T. The MutS and MutL
      mismatch recognition proteins stimulate this activity, as cells lacking either of these
      proteins display diminished VSPR. Genetic studies also indicate that Pol I is responsible for
      removing and replacing a short tract of nucleotides downstream of the incision site and that
      DNA Ligase seals the nick to complete the repair event. However, until now, biochemical
      investigation of the repair steps downstream of Vsr incision have been lacking.  Herein, we
      describe two novel in vitro assays used to probe the biochemical events of VSPR. The first was
      used to verify the reconstitution of VSPR using purified E. coli Vsr, Pol I, and DNA Ligase
      enzymes, while the second was used to measure the distribution of VSPR patch sizes in whole
      cell extracts. By monitoring the loss of radiosignal from a series of substrates that
      contained the label at prescribed distances downstream of the T:G mismatch, we were able to
      determine that VSPR patches are distributed around 2 to 4 deoxynucleotides in length.
      Interestingly, under certain reaction conditions, the addition of DNA Ligase improved the
      efficiency of repair initiation by Vsr, suggesting that VSPR may be optimal in the context of
      a multi-protein complex.  Lastly, we investigated the effect of VSPR proteins on
      methyltransferase (MTase) repair of O6-methylguanine (6mG). MTase repair of O6mG opposite T
      results in a G:T mismatch that must be further processed to yield the native G:C base pairing.
      The G:T mismatch is therefore an intersection of the two pathways and led us to hypothesize
      that MTase and VSPR proteins might interact. Indeed, cells lacking the functions of MutS,
      MutL, or Vsr proteins displayed decreased MTase repair in vivo, revealing a previously unknown
      interaction. The cooperation between proteins of these two repair systems may shed light on
      the biological significance of the VSPR system.
AU  - Rye PT
PT  - Journal Article
TA  - Ph.D. Thesis, MIT, USA
JT  - Ph.D. Thesis, MIT, USA
SO  - Ph.D. Thesis, MIT, USA 2006 : 1-273.

PMID- Not carried by PubMed...
VI  - 22
DP  - 1989
TI  - A new restriction endonuclease, Bsp1894I, from Bacillus sphaericus 1894.
PG  - 444-447
AB  - A new restriction endonuclease, Bsp1894I, has been isolated from Bacillus
      sphaericus 1894 (KCTC 1188), and its catalytic properties have been studied.
      This enzyme recognizes the DNA sequence 5'-G^GNCC-3' and cleaves at the site as
      indicated by the arrow.  Bsp1894I is an isoschizomer of AsuI, Sau96I, and
      Cfr13I.  It shows maximum activity at a pH range between 6 and 7 in the
      presence of 10 mM MgCl2.  The optimum reaction temperature for Bsp1894I is 42C.
      Unlike its isoschizomers, Bsp1894I does not require NaCl for optimum activity.
AU  - Ryu CJ
AU  - Lee CH
AU  - Yoo OJ
PT  - Journal Article
TA  - Korean Biochem. J.
JT  - Korean Biochem. J.
SO  - Korean Biochem. J. 1989 22: 444-447.

PMID- Not carried by PubMed...
VI  - 0
DP  - 1998
TI  - Establishment of the KpnAI R-M system of Klebsiella pneumoniae requires prior host modification.
PG  - 288
AB  - Type I restriction-modification systems have been classified into 4 families: IA, IB, IC and
      newly identified ID.  They consist of 3 consecutive genes, hsdR, hsdM and hsdS which encode
      for subunits R(restriction), M(modification) and S(specificity), respectively.  When entire
      R-M genes were transferred to bacteria, without corresponding modification, through either
      conjugation, transduction or transformation, the expression of restriction enzymes are somehow
      regulated that the R-M genes can be established without degrading recipient DNA.  The basis of
      the mechanism of "establishment" still remains to be elucidated.  We have recently cloned R
      and MS genes separately for Klebsiella pneumoniae KpnAI R-M system.  In the present project,
      the "establishment" of the KpnAI system was studied by using plasmid transformation as a gene
      transfer system.  All the three (R, M and S) genes were combined and cloned into pUC18.  When
      the entire system was transferred into recipient (E. coli DH5a), no Amp-resistant
      transformants were obtained.  However, when the recipient cells were modified with a
      modification proficient plasmid, many transformants were obtained.  This result is in sharp
      contrast with other known type I enzymes where the entire system is transferred without
      killing the recipient.  Thus, the KpnAI R-M enzymes seems to be the first example of the type
      I R-M system which requires prior methylation of the chromosome before their establishments.
AU  - Ryu J
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1998 0: 288.

PMID- Not carried by PubMed...
VI  - 97
DP  - 1997
TI  - The restriction enzyme KpnAI of Klebsiella pneumoniae is a new member of the type ID family.
PG  - 285
AB  - We have described the KpnAI restriction and modification system in Klebsiella pneumoniae M5a1.
      The restriction gene (hsdR, 3.3 kb) was cloned into pBR322 and the DNA was sequenced.  In this
      project, the corresponding modification genes were identified in the 5' flanking region of
      the hsdR gene and cloned into pUC19.  The DNA sequence reveals two open reading frames that
      are designated hsdM (1.6kb) and hsdS (1.3kb).  These two genes form a single transcriptional
      unit and their coding sequences overlap by five nucleotides.  Thus the KpnAI R-M system
      consists of three genes in the order of hsdM, hsdS and hsdR and organized into two
      transcriptional units.  These features are typical to the type I restriction enzymes. Homology
      studies reveal that the predicted R, M and S peptides share 97%, 98% and 58% homology,
      respectively, with the corresponding peptides of the StySBLI restriction enzyme, a prototype
      of the type ID family recently identified in Salmonella blegdam.  These high homologies
      indicate that the KpnAI restriction enzyme is another member of the type ID family. The KpnAI
      enzyme is the first type I restriction enzyme identified in Klebsiella species.
AU  - Ryu J
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1997 97: 285.

PMID- 18562466
VI  - 36
DP  - 2008
TI  - Quick identification of Type I restriction enzyme isoschizomers using newly developed pTypeI and reference plasmids.
PG  - e81
AB  - Although DNA-recognition sequences are among the most important characteristics of restriction
      enzymes and their corresponding methylases,
      determination of the recognition sequence of a Type-I restriction enzyme
      is a complicated procedure. To facilitate this process we have previously
      developed plasmid R-M tests and the computer program RM search. To
      specifically identify Type-I isoschizomers, we engineered a pUC19
      derivative plasmid, pTypeI, which contains all of the 27 Type-I
      recognition sequences in a 248-bp DNA fragment. Furthermore, a series of
      27 plasmids (designated 'reference plasmids'), each containing a unique
      Type-I recognition sequence, were also constructed using pMECA, a
      derivative of pUC vectors. In this study, we tried those vectors on 108
      clinical E. coli strains and found that 48 strains produced isoschizomers
      of Type I enzymes. A detailed study of 26 strains using these 'reference
      plasmids' revealed that they produce seven different isoschizomers of the
      prototypes: EcoAI, EcoBI, EcoKI, Eco377I, Eco646I, Eco777I and Eco826I.
      One strain EC1344 produces two Type I enzymes (EcoKI and Eco377I).
AU  - Ryu J
AU  - Rowsell E
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2008 36: e81.

PMID- 3056913
VI  - 170
DP  - 1988
TI  - Complementation and hybridization evidence for additional families of Type I DNA restriction and modification genes in Salmonella serotypes.
PG  - 5785-5788
AB  - Of eight Salmonella, serB-linked hsd genes for the restriction and modification
      of DNA transferred to Escherichia coli/Salmonella hybrids, only two-those with
      SM and ST (S. muenchen and S. thompson, respectively) specificities - may have
      weakly complemented rSB- and non complemented rK-.  An A-specific DNA probe
      failed to hybridize to HindIII-restricted fragments of each of the hybrids, but
      an SB (S. typhimurium)-specific probe hybridized to DNA from the hybrid with ST
      specificity.  These results indicate that additional families of the type I hsd
      genes may exist.
AU  - Ryu J-I
AU  - Rajadas PT
AU  - Bullas LR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1988 170: 5785-5788.

PMID- 30533921
VI  - 7
DP  - 2018
TI  - Draft Genome Sequence of Mycobacterium parafortuitum Strain P7335.
PG  - e00950-18
AB  - Mycobacterium parafortuitum is a rapidly growing nontuberculous mycobacterium, initially
      isolated from soil in Japan. The 6,175,772-bp draft genome sequence of
      M. parafortuitum strain P7335 exhibits a G+C content of 68.4%, 5,783
      protein-coding genes, and 66 predicted RNA genes, including 59 tRNA genes, 6 rRNA
      operons, and 1 transfer-messenger RNA.
AU  - Saad J
AU  - Levasseur A
AU  - Drancourt M
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e00950-18.

PMID- 9530521
VI  - 44
DP  - 1998
TI  - Studies on the heterologous expression of BstVI restriction endonuclease in Escherichia coli.
PG  - 391-397
AB  - Bacterial restriction and modification systems must be regulated to avoid self-restriction.
      It is generally accepted that cognate DNA methyltransferases normally protect both, the
      host's chromosome and extrachromosomal elements from the activity of their endonuclease
      counterparts.  When the bstVIRm genes from Bacillus stearothermophilusV were subcloned into
      Escherichia coli, several clones exhibiting a r+m- phenotype were found.  The present work was
      undertaken to analyze the possibility that mechanisms other than DNA methylation could account
      for the viability of these cells.  No evidence was found for an inhibitory agent or
      endonuclease compartmentation.  In vivo experiments showed that lambda phage multiplication
      was poorly restricted by the heterologous enzyme.  The restricting activity against the
      incoming phage increased however when phage adsortion was performed at higher temperatures.
      Analogous experiments in which a DNA-repair deficient strain was used as a host for the
      thermophilic R-M system suggested, to some extent, the participation of the repair machinery
      in the viability of r-m- clones.
AU  - Saavedra C
AU  - Gonzalez E
AU  - Vasquez C
PT  - Journal Article
TA  - Biochem. Mol. Biol. Int.
JT  - Biochem. Mol. Biol. Int.
SO  - Biochem. Mol. Biol. Int. 1998 44: 391-397.

PMID- 10429188
VI  - 263
DP  - 1999
TI  - Structural studies of the BstVI restriction-modification proteins by fluorescence spectroscopy.
PG  - 65-70
AB  - Structural studies of the proteins of the BstVI restriction-modification system of Bacillus
      stearothermophilus V were carried out using intrinsic fluorescence techniques. The exposure
      and environments of their tryptophanyl residues were determined using collisional quenchers.
      Quenching of BstVI endonuclease by iodide suggested a heterogeneous class of tryptophan
      residues, while the results obtained with M.BstVI methylase were consistent with a rather
      exposed tryptophan population. A comparison of the quenching efficiencies at 20 degrees C and
      55 or 60 degrees C showed that their structures are more flexible and open at the temperature
      at which they exhibit maximal activity. The endonuclease reached its active conformation only
      after 1 h of incubation at 60 degrees C. Fluorescence changes were observed upon Mn2+ and Mg2+
      binding, with Kd values in the range 3-5 microM.  The binding of S-adenosyl-L-methionine to
      the methylase produced conformational changes, which were consistent with binding to a single
      site of Kd 550 and 680 microM at 20 degrees C and 55 degrees C, respectively. Quenching
      experiments with iodide showed that the presence of S-adenosyl-L-methionine leads to different
      conformational states at 20 degrees C and 55 degrees C.  These results were interpreted in
      terms of differences in the structural characteristics of these restriction-modification
      proteins as well as in terms of differences in the conformational states that these enzymes
      exhibit at 20 degrees C and at the temperature at which they are most active.
AU  - Saavedra C
AU  - Vasquez C
AU  - Encinas MV
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1999 263: 65-70.

PMID- 26966208
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Lactobacillus plantarum CRL1506, an Immunomodulatory Strain Isolated from Goat Milk.
PG  - e00108-16
AB  - This report describes a draft genome sequence of Lactobacillus plantarum CRL1506, a probiotic
      strain with immunomodulatory properties isolated from goat milk. The
      reads generated by a whole-genome shotgun (WGS) strategy on an Illumina MiSeq
      sequencer were assembled into contigs with a total size of 3,228,096 bp. The
      draft genome sequence of L. plantarum CRL1506 will be useful for further studies
      of specific genetic features of this strain and for understanding the mechanisms
      of its immunobiotic properties.
AU  - Saavedra L
AU  - Hebert EM
AU  - Albarracin L
AU  - Salva S
AU  - Alvarez S
AU  - Kitazawa H
AU  - Villena J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00108-16.

PMID- 28209815
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequence of a Colombian Acinetobacter baumannii Strain, a Coproducer of OXA-72 and OXA-255-Like Carbapenemases.
PG  - e01558-16
AB  - Colombian Acinetobacter baumannii strain ST920 was isolated from the sputum of a  68-year-old
      male patient. This isolate possessed blaOXA-72 and blaOXA-255-like
      genes. The assembled genome contained 4,104,098 pb and 38.79% G+C content. This
      is the first case reported of the coproduction (blaOXA-72 and blaOXA-255-like) of
      carbapenem-hydrolyzing class D beta-lactamases (CHDLs) in Acinetobacter
      baumannii.
AU  - Saavedra SY
AU  - Prada-Cardozo D
AU  - Rincon V
AU  - Perez-Cardona H
AU  - Hidalgo AM
AU  - Gonzalez MN
AU  - Reguero MT
AU  - Valenzuela-de-Silva EM
AU  - Mantilla JR
AU  - Falquet L
AU  - Barreto-Hernandez E
AU  - Duarte C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01558-16.

PMID- 28106148
VI  - 7
DP  - 2017
TI  - Complete-genome sequencing elucidates outbreak dynamics of CA-MRSA USA300 (ST8-spa t008) in an academic hospital of Paramaribo, Republic of Suriname.
PG  - 41050
AB  - We report the investigation of an outbreak situation of methicillin-resistant
      Staphylococcus aureus (MRSA) that occurred at the Academic Hospital Paramaribo
      (AZP) in the Republic of Suriname from April to May 2013. We performed whole
      genome sequencing with complete gap closure for chromosomes and plasmids on all
      isolates. The outbreak involved 12 patients and 1 healthcare worker/nurse at the
      AZP. In total 24 isolates were investigated. spa typing, genome-wide single
      nucleotide polymorphism (SNP) analysis, ad hoc whole genome multilocus sequence
      typing (wgMLST), stable core genome MLST (cgMLST) and in silico PFGE were used to
      determine phylogenetic relatedness and to identify transmission. Whole-genome
      sequencing (WGS) showed that all isolates were members of genomic variants of the
      North American USA300 clone. However, WGS revealed a heterogeneous population
      structure of USA300 circulating at the AZP. We observed up to 8 SNPs or up to 5
      alleles of difference by wgMLST when the isolates were recovered from different
      body sites of the same patient or if direct transmission between patients was
      most likely. This work describes the usefulness of complete genome sequencing of
      bacterial chromosomes and plasmids providing an unprecedented level of detail
      during outbreak investigations not being visible by using conventional typing
      methods.
AU  - Sabat AJ
AU  - Hermelijn SM
AU  - Akkerboom V
AU  - Juliana A
AU  - Degener JE
AU  - Grundmann H
AU  - Friedrich AW
PT  - Journal Article
TA  - Sci. Rep.
JT  - Sci. Rep.
SO  - Sci. Rep. 2017 7: 41050.

PMID- 24002094
VI  - 57
DP  - 2013
TI  - Novel Organization of the Arginine Catabolic Mobile Element and Staphylococcal Cassette Chromosome mec Composite Island and Its Horizontal Transfer between Distinct Staphylococcus aureus Genotypes.
PG  - 5774-5777
AB  - In this study, 425 methicillin-resistant Staphylococcus aureus (MRSA) isolates
      recovered in the Dutch-German Euregio were investigated for the presence of the
      arginine catabolic mobile element (ACME). Sequence analysis by whole-genome
      sequencing revealed an entirely new organization of the ACME-staphylococcal
      cassette chromosome mec composite island (SCCmec-CI), with truncated ACME type II
      located downstream of SCCmec. An identical nucleotide sequence of ACME-SCCmec-CI
      was found in two distinct MRSA lineages (t064-ST8 and t002-ST5), which has not
      been reported previously in S. aureus.
AU  - Sabat AJ
AU  - Kock R
AU  - Akkerboom V
AU  - Hendrix R
AU  - Skov RL
AU  - Becker K
AU  - Friedrich AW
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2013 57: 5774-5777.

PMID- 26198147
VI  - 70
DP  - 2015
TI  - Whole-genome analysis of an oxacillin-susceptible CC80 mecA-positive Staphylococcus aureus clinical isolate: insights into the mechanisms of cryptic methicillin resistance.
PG  - 2956-2964
AB  - OBJECTIVES: The mec and bla systems, among other genetic factors, are critical in regulating
      the expression of methicillin resistance in Staphylococcus aureus. We examined by WGS a
      naturally occurring oxacillin-susceptible mecA-positive S. aureus isolate to identify the
      mechanism conferring oxacillin susceptibility.
      METHODS: The mecA-positive oxacillin-susceptible S. aureus isolate GR2 (penicillin and
      oxacillin MICs 0.094 and 1 mg/L, respectively), belonging to clonal complex 80, was
      characterized. DNA fragment libraries were sequenced on Roche 454 and Illumina MiSeq
      sequencers and de novo assembly of the genome was generated using SeqMan NGen software.
      Plasmid curing was conducted by SDS treatment. Expression of mecA was quantified without/with
      beta-lactam pressure.
      RESULTS: The genome of GR2 consisted of a 2 792 802 bp chromosome and plasmids pGR2A (28 895
      bp) and pGR2B (2473 bp). GR2 carried SCCmec type IV, with a truncated/non-functional mecR1
      gene and no mecI. A single copy of the bla system, with an organization unique for S. aureus,
      was found, harboured by plasmid pGR2A. Particularly, the blaZ gene was orientated like its
      regulatory genes, blaI and blaR1, and a gene encoding transposase IS66 was integrated between
      blaZ and the regulatory genes deleting the 5'-end of blaR1; blaI, encoding blaZ/mecA
      repressor, was intact. After plasmid loss, GR2 became penicillin and oxacillin resistant (MICs
      0.5 and 6 mg/L, respectively).
      CONCLUSIONS: We can conclude that after exposure to beta-lactams, the non-functional BlaR1
      does not cleave the mecA repressor BlaI, derepression does not occur and mecA is not
      efficiently expressed. Removal of the bla system after curing of pGR2A allows constitutive
      expression of mecA, resulting in oxacillin and penicillin resistance.
AU  - Sabat AJ
AU  - Pournaras S
AU  - Akkerboom V
AU  - Tsakris A
AU  - Grundmann H
AU  - Friedrich AW
PT  - Journal Article
TA  - J. Antimicrob. Chemother.
JT  - J. Antimicrob. Chemother.
SO  - J. Antimicrob. Chemother. 2015 70: 2956-2964.

PMID- 15305915
VI  - 6
DP  - 2004
TI  - Different SAR86 subgroups harbour divergent proteorhodopsins.
PG  - 903-910
AB  - Proteorhodopsins (PRs), bacterial photoactive proton pumps, were originally detected in the
      uncultured marine gamma-proteobacterial SAR86
      group. PRs are now known to occur in both the gamma and alpha marine
      proteobacterial lineages. Recent environmental shotgun sequence analysis
      in the Sargasso Sea has added yet more diversity, and a potentially
      broader taxonomic distribution, to the PR family. Much remains to be
      learned, however, about within-taxon PR variability and the broader
      organismal distribution of different PR types. We report here genomic
      analyses of large genome fragments from different subgroups of the SAR86
      lineage, recovered from naturally occurring bacterioplankton populations
      in coastal Red Sea and open ocean Pacific waters. Sequence comparisons
      were performed on large bacterial artificial chromosomes (BACs) bearing
      both rRNA and PR genes, derived from different SAR86 subgroups. Our
      analyses indicated the presence of different PR sequence types within the
      same SAR86 rRNA subgroup. The data suggested that the distribution of
      particular PR types does not necessarily parallel the phylogenetic
      relationship inferred from highly conserved genes such as rRNA. Further
      analyses of the genomic regions flanking PR also revealed a potential
      pathway for the biosynthesis of retinal, the PR chromophore that is
      required to generate the functionally active photoprotein. Finally,
      comparison of our results with recently reported Sargasso Sea
      environmental shotgun sequence assemblies demonstrated the utility of BAC
      clones for interpreting environmental shotgun sequence data, much of which
      is represented in short contigs that have an overall low depth of
      coverage.
AU  - Sabehi G
AU  - Beja O
AU  - Suzuki MT
AU  - Preston CM
AU  - DeLong EF
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2004 6: 903-910.

PMID- 7541838
VI  - 250
DP  - 1995
TI  - An extended -10 promoter alone directs transcription of the DpnII operon of Streptococcus pneumoniae.
PG  - 144-155
AB  - The genetic cassette encoding the DpnII restriction-modification system of Streptococcus
      pneumoniae gave transcription products of approximately 2.7 and 1.8 kilobases. The larger,
      mRNA1, covered both of the methylase genes, dpnM and dpnA, and the endonuclease gene dpnB; the
      smaller, mRNA2, covered only the dpnA and dpnB genes. Transcription of mRNA1 was shown to
      begin at the translation start site for dpnM, thereby producing an mRNA without any apparent
      ribosome-binding site for translation of the DpnM methylase. The promoter for mRNA1 was shown
      by base substitution and deletion analysis to consist of an extended -10 site, TaTGgTATAAT,
      with no required -35 site. A possible promoter further upstream with close matches to a -35
      site and a nonextended -10 site was not used. A survey of 36 proven and putative promoters
      used by S. pneumoniae revealed that 61% of them contained the full -10 extension, although,
      other than the dpmM promoter, they matched at a -35 site, as well. It appears that, unlike
      those found in Escherchia coli, S. pneumoniae promoters frequently require an extended -10
      site, and such a site can function naturally without a -35 site.
AU  - Sabelnikov AG
AU  - Greenberg B
AU  - Lacks SA
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1995 250: 144-155.

PMID- 25999552
VI  - 3
DP  - 2015
TI  - Draft genome sequences of 18 oral streptococcus strains that encode amylase-binding proteins.
PG  - e00510-15
AB  - A number of commensal oral streptococcal species produce a heterogeneous group of proteins
      that mediate binding of salivary alpha-amylase. This interaction likely
      influences streptococcal colonization of the oral cavity. Here, we present draft
      genome sequences of several strains of oral streptococcal species that bind human
      salivary amylase.
AU  - Sabharwal A
AU  - Liao YC
AU  - Lin HH
AU  - Haase EM
AU  - Scannapieco FA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00510-15.

PMID- 26968884
VI  - 71
DP  - 2016
TI  - Whole-genome typing and characterization of blaVIM19-harbouring ST383 Klebsiella pneumoniae by PFGE, whole-genome mapping and WGS.
PG  - 1501-1509
AB  - OBJECTIVES: We utilized whole-genome mapping (WGM) and WGS to characterize 12 clinical
      carbapenem-resistant Klebsiella pneumoniae strains (TGH1-TGH12). METHODS: All strains were
      screened for carbapenemase genes by PCR, and typed by MLST, PFGE (XbaI) and WGM (AflII)
      (OpGen, USA). WGS (Illumina) was performed on TGH8 and TGH10. Reads were de novo assembled and
      annotated [SPAdes, Rapid Annotation Subsystem Technology (RAST)]. Contigs were aligned
      directly, and after in silico AflII restriction, with corresponding WGMs (MapSolver, OpGen;
      BioNumerics, Applied Maths). RESULTS: All 12 strains were ST383. Of the 12 strains, 11 were
      carbapenem resistant, 7 harboured blaKPC-2 and 11 harboured blaVIM-19. Varying the parameters
      for assigning WGM clusters showed that these were comparable to STs and to the eight PFGE
      types or subtypes (difference of three or more bands). A 95% similarity coefficient assigned
      all 12 WGMs to a single cluster, whereas a 99% similarity coefficient (or >/=10
      unmatched-fragment difference) assigned the 12 WGMs to eight (sub)clusters. Based on a
      difference of three or more bands between PFGE profiles, the Simpson's diversity indices
      (SDIs) of WGM (0.94, Jackknife pseudo-values CI: 0.883-0.996) and PFGE (0.93, Jackknife
      pseudo-values CI: 0.828-1.000) were similar (P = 0.649). However, the discriminatory power of
      WGM was significantly higher (SDI: 0.94, Jackknife pseudo-values CI: 0.883-0.996) than that of
      PFGE profiles typed on a difference of seven or more bands (SDI: 0.53, Jackknife pseudo-values
      CI: 0.212-0.849) (P = 0.007). CONCLUSIONS: This study demonstrates the application of WGM to
      understanding the epidemiology of hospital-associated K. pneumoniae. Utilizing a combination
      of WGM and WGS, we also present here the first longitudinal genomic characterization of the
      highly dynamic carbapenem-resistant ST383 K. pneumoniae clone that is rapidly gaining
      importance in Europe.
AU  - Sabirova JS
AU  - Xavier BB
AU  - Coppens J
AU  - Zarkotou O
AU  - Lammens C
AU  - Janssens L
AU  - Burggrave R
AU  - Wagner T
AU  - Goossens H
AU  - Malhotra-Kumar S
PT  - Journal Article
TA  - J. Antimicrob. Chemother.
JT  - J. Antimicrob. Chemother.
SO  - J. Antimicrob. Chemother. 2016 71: 1501-1509.

PMID- 24970829
VI  - 2
DP  - 2014
TI  - Complete Genome Sequences of Two Prolific Biofilm-Forming Staphylococcus aureus Isolates Belonging to USA300 and EMRSA-15 Clonal Lineages.
PG  - e00610-14
AB  - Methicillin-resistant Staphylococcus aureus (MRSA) causes serious infections that are even
      more difficult to treat when associated with a biofilm phenotype that
      facilitates evasion of the host immune system and antibiotics. As a first step
      toward understanding the mechanisms underlying biofilm formation, we sequenced
      the genomes of two prolific biofilm-forming strains belonging to the two most
      important globally disseminated clonal lineages, USA300 and EMRSA-15.
AU  - Sabirova JS
AU  - Xavier BB
AU  - Hernalsteens JP
AU  - De Greve H
AU  - Ieven M
AU  - Goossens H
AU  - Malhotra-Kumar S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00610-14.

PMID- 29903820
VI  - 6
DP  - 2018
TI  - Complete Genome Sequences of Three Campylobacter jejuni Phage-Propagating Strains.
PG  - e00514-18
AB  - Bacteriophage therapy can potentially reduce Campylobacter jejuni numbers in livestock, but it
      requires a detailed understanding of phage-host interactions.
      C. jejuni strains readily infected by certain phages are designated as
      phage-propagating strains. Here, we report the complete genome sequences of three
      such strains, NCTC 12660, NCTC 12661, and NCTC 12664.
AU  - Sacher JC
AU  - Yee E
AU  - Szymanski CM
AU  - Miller WG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00514-18.

PMID- 29903819
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Campylobacter jejuni Strain 12567, a Livestock-Associated Clade Representative.
PG  - e00513-18
AB  - We report here the complete genome sequence of Campylobacter jejuni strain 12567, a member of
      a C. jejuni livestock-associated clade that expresses glycoconjugates
      associated with improved gastrointestinal tract persistence.
AU  - Sacher JC
AU  - Yee E
AU  - Szymanski CM
AU  - Miller WG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00513-18.

PMID- 4348308
VI  - 51
DP  - 1973
TI  - Studies of SV40 DNA. IV.  Cleavage of SV40 DNA by restriction endonuclease from Hemophilus parainfluenzae.
PG  - 517-520
AB  - None
AU  - Sack GH Jr
AU  - Nathans D
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1973 51: 517-520.

PMID- 9016683
VI  - 24
DP  - 1996
TI  - Rapid analysis of DNA methylation using new restriction enzyme sites created by bisulfite modification.
PG  - 5058-5059
AB  - Bisulfite converts non-methylated cytosine in DNA to uracil leaving 5-methylcytosine
      unaltered.  Here, predicted changes in restriction enzyme sites following reaction of genomic
      DNA with bisulfite and amplification of the product by the polymerase chain reaction (PCR)
      were used to assess the methylation of CpG sites.  This procedure differs from conventional
      DNA methylation analysis by methylation-sensitive restriction enzymes because it does not rely
      on an absence of cleavage to detect methylated sites, the two strands of DNA produce different
      restriction enzyme sites and may be differentially analyzed, and closely related sequences may
      be separately analyzed by using specific PCR primers.
AU  - Sadri R
AU  - Hornsby PJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1996 24: 5058-5059.

PMID- 12675801
VI  - 48
DP  - 2003
TI  - Multiplication of a restriction-modification gene complex.
PG  - 417-427
AB  - Previous works have suggested that some gene complexes encoding a restriction (R) enzyme and a
      cognate modification (M) enzyme may behave as
      selfish mobile genetic elements. RM gene complexes, which destroy
      'non-self' elements marked by the absence of proper methylation, are often
      associated with mobile genetic elements and are involved in various genome
      rearrangements. Here, we found amplification of a restriction-modification
      gene complex. BamHI gene complex inserted into the Bacillus chromosome
      showed resistance to replacement by a homologous stretch of DNA. Some
      cells became transformed with the donor without losing BamHI. In most of
      these transformants, multiple copies of BamHI and the donor allele were
      arranged as tandem repeats. When a clone carrying one copy of each allele
      was propagated, extensive amplification of BamHI and the donor unit was
      observed in a manner dependent on restriction enzyme gene. This suggests
      that restriction cutting of the genome participates in the amplification.
      Visualization by fluorescent in situ hybridization revealed that the
      amplification occurred in single cells in a burst-like fashion that is
      reminiscent of induction of provirus replication. The multiplication
      ability in a bacterium with natural capacity for DNA release, uptake and
      transformation will be discussed in relation to spreading of RM gene
      -complexes.
AU  - Sadykov M
AU  - Asami Y
AU  - Niki H
AU  - Handa N
AU  - Itaya M
AU  - Tanokura M
AU  - Kobayashi I
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2003 48: 417-427.

PMID- 11680490
VI  - 483
DP  - 2001
TI  - Selfish maintenance and amplification of BamHI restriction modification gene complex on Bacillus subtilis chromosome.
PG  - S159
AB  - It has been shown that some type II RM (restriction modification) gene complexes on a plasmid
      resist replacement by an incompatible plasmid through post-segregational host killing.  Here
      we present experimental evidence for selfish maintenance of BamHI RM gene complex on Bacillus
      subtilis chromosome.  pBR322 derivatives carrying BamHI restriction +/- modification gene
      complex and neomycin resistance gene were inserted into B. subtilis chromosome.  We then tried
      to replace them by a homologous stretch of DNA that contains spectinomycin resistance gene by
      natural transformation.  The efficiency of apparent replacement was several fold less, and the
      resulting transformant colonies were smaller in the r+ cells than in the r- cells.  Moreover,
      some of these clones were able to grow on media containing both spectinomycin and neomycin.
      By PCR, we found that some of these clones retained the recipient RM gene complex and neomycin
      phosphotransferase gene as well as the donor spectinomycin resistance gene.  Southern analysis
      of chromosomal DNA provided supporting evidence.  Moreover, by Southern analyses and DNA
      sequencing we found genome rearrangements, i.e. "amplicon" structures with different level of
      amplification.  Possible mechanisms of gene amplification will be discussed.
AU  - Sadykov M
AU  - Handa N
AU  - Asami Y
AU  - Tanokura M
AU  - Itaya M
AU  - Kobayashi I
PT  - Journal Article
TA  - Mutat. Res.
JT  - Mutat. Res.
SO  - Mutat. Res. 2001 483: S159.

PMID- 29449380
VI  - 6
DP  - 2018
TI  - Annotated Genome Sequences of 16 Lineage 4 Mycobacterium tuberculosis Strains from Guatemala.
PG  - e00024-18
AB  - Whole-genome sequencing has resulted in new insights into the phylogeography of Mycobacterium
      tuberculosis However, only limited genomic data are available from
      M. tuberculosis strains in Guatemala. Here we report 16 complete genomes of
      clinical strains belonging to the Euro-American lineage 4, the most common
      lineage found in Guatemala and Central America.
AU  - Saelens JW
AU  - Lau-Bonilla D
AU  - Moller A
AU  - Xet-Mull AM
AU  - Medina N
AU  - Guzman B
AU  - Calderon M
AU  - Herrera R
AU  - Stout JE
AU  - Arathoon E
AU  - Samayoa B
AU  - Tobin DM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00024-18.

PMID- 18037886
VI  - 39
DP  - 2007
TI  - Genomic analysis of Bartonella identifies type IV secretion systems as host adaptability factors.
PG  - 1469-1476
AB  - The bacterial genus Bartonella comprises 21 pathogens causing characteristic intraerythrocytic
      infections. Bartonella bacilliformis is a
      severe pathogen representing an ancestral lineage, whereas the other
      species are benign pathogens that evolved by radial speciation. Here, we
      have used comparative and functional genomics to infer pathogenicity genes
      specific to the radiating lineage, and we suggest that these genes may
      have facilitated adaptation to the host environment. We determined the
      complete genome sequence of Bartonella tribocorum by shotgun sequencing
      and functionally identified 97 pathogenicity genes by signature-tagged
      mutagenesis. Eighty-one pathogenicity genes belong to the core genome
      (1,097 genes) of the radiating lineage inferred from genome comparison of
      B. tribocorum, Bartonella henselae and Bartonella quintana. Sixty-six
      pathogenicity genes are present in B. bacilliformis, and one has been lost
      by deletion. The 14 pathogenicity genes specific for the radiating lineage
      encode two laterally acquired type IV secretion systems, suggesting that
      these systems have a role in host adaptability.
AU  - Saenz HL
AU  - Engel P
AU  - Stoeckli MC
AU  - Lanz C
AU  - Raddatz G
AU  - Vayssier-Taussat M
AU  - Birtles R
AU  - Schuster SC
AU  - Dehio C
PT  - Journal Article
TA  - Nat. Genet.
JT  - Nat. Genet.
SO  - Nat. Genet. 2007 39: 1469-1476.

PMID- 26472823
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Acinetobacter parvus CM11, Acinetobacter radioresistens CM38, and Stenotrophomonas maltophilia BR12, Isolated from Murine Proximal Colonic Tissue.
PG  - e01089-15
AB  - Here, we report three genome sequences of bacteria isolated from murine proximal  colonic
      tissue and identified as Acinetobacter parvus CM11, Acinetobacter radioresistens CM38, and
      Stenotrophomonas maltophilia BR12.
AU  - Saffarian A
AU  - Mulet C
AU  - Naito T
AU  - Bouchier C
AU  - Tichit M
AU  - Ma L
AU  - Grompone G
AU  - Sansonetti PJ
AU  - Pedron T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01089-15.

PMID- 27979948
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Delftia tsuruhatensis CM13 Isolated from Murine Proximal Colonic Tissue.
PG  - e01398-16
AB  - We report here the complete genome sequence of Delftia tsuruhatensis CM13, isolated from
      murine proximal colonic tissue. The genome assembly using PacBio
      single-molecule real-time sequencing resulted in a single scaffold of 7.19 Mb.
AU  - Saffarian A
AU  - Mulet C
AU  - Tournebize R
AU  - Naito T
AU  - Sansonetti PJ
AU  - Pedron T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01398-16.

PMID- 24407646
VI  - 2
DP  - 2014
TI  - Draft genome sequence of atrazine-utilizing bacteria isolated from Indian agricultural soil.
PG  - e01149-13
AB  - We report the draft genome sequences of two tropical bacterial isolates capable of degrading
      the herbicide atrazine. Alcaligenes sp. strain EGD-AK7 and
      Arthrobacter sp. strain AK-YN10 were isolated from Indian agricultural soil in
      which sugarcane is grown, with a reported history of atrazine use. EGD-AK7 has
      the atzABCDEF genes and AK-YN10 has the trzN and atzBC genes for atrazine
      degradation.
AU  - Sagarkar S
AU  - Bhardwaj P
AU  - Yadav TC
AU  - Qureshi A
AU  - Khardenavis A
AU  - Purohit HJ
AU  - Kapley A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01149-13.

PMID- 7630713
VI  - 23
DP  - 1995
TI  - Sse8387I, a useful eight base cutter for mammalian genome analysis (influence of methylation on the activity of Sse8387I).
PG  - 2367-2370
AB  - To develop restriction enzymes that are useful for genome analysis, we previously performed
      screening and isolated Sse8387I from Streptomyces sp. strain 8387. Sse8387I is a restriction
      enzyme that recognizes 5'-CCTGCA/GG-3' and cleaves DNA at the site shown by the diagonal.
      The present study evaluated the effects of methylation that is important when Sse8387I is used
      for genome analysis. Sse8387I lost cleavage activity after methylation of adenine or
      methylation of cytosine at any site in the recognition sequence. However, the recognition
      sequence of Sse8387I contains no CG sequence, which is the mammalian methylation sequence. In
      addition, we evaluated the effects of methylation of CG at sites other than the recognition
      sequence. The cleavage activity of Sse8387I was maintained even when CG sequences were present
      immediately before or after, or near the recognition sequence, and cytosine was methylated.
      These results suggest that CG methylation does not affect the cleavage activity of Sse8387I.
      Therefore, Sse8387I seems to be very useful for mammalian genome analysis.
AU  - Sagawa H
AU  - Ohshima A
AU  - Kato I
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1995 23: 2367-2370.

PMID- 1741262
VI  - 20
DP  - 1992
TI  - Isolation and identification of restriction endonuclease Aor51HI from Acidiphilium organovorum 51H.
PG  - 365
AB  - Aor5HI, a type II restriction endonuclease, has been isolated from Acidiphilium
      organovorum 51H, an isoschizomer of Eco47III, recognizes the palindromic six
      base sequence 5'-AGCGCT-3', and cleaves the center of recognition sequence
      giving the blunted end.
AU  - Sagawa H
AU  - Takagi M
AU  - Nomura Y
AU  - Inagaki K
AU  - Tano T
AU  - Kishimato N
AU  - Kotani H
AU  - Nakajima K
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 365.

PMID- 1098145
VI  - 189
DP  - 1975
TI  - Selective Silencing of eukaryotic DNA.
PG  - 426-433
AB  - A molecular basis is proposed for programmed inactivation or loss of eukaryotic
      DNA.
AU  - Sager R
AU  - Kitchin R
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1975 189: 426-433.

PMID- 4506760
VI  - 69
DP  - 1972
TI  - Molecular basis of maternal inheritance.
PG  - 2410-2413
AB  - The mechanism of preferential transmission (i.e., maternal inheritance) of
      cytoplasmic genes was investigated with chloroplast DNA of Chlamydomonas as a
      model system.  The behavior of nuclear and chloroplast DNAs were compared in
      the sexual cycle; DNAs from male and female parents were distinguished by
      labeling with 14N- or 15NH4Cl and then by making the crosses: 14N (female) X
      15N (male) and the reciprocal.  Chloroplast DNAs from the two parents followed
      different paths in the zygote, but nuclear DNAs showed no differences.
      Chloroplast DNA from the female parent persists in the zygote, but undergoes a
      density shift of 0.003-0.005 g/cm3 to a lighter buoyant density, whereas that
      from the male disappears soon after zygote formation.  The possibility is
      discussed that a modification-restriction system may be involved.
AU  - Sager R
AU  - Lane D
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1972 69: 2410-2413.

PMID- 26564055
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Thermus scotoductus Strain K1, Isolated from a Geothermal Spring in Karvachar, Nagorno Karabakh.
PG  - e01346-15
AB  - The 2,379,636-bp draft genome sequence of Thermus scotoductus strain K1, isolated from
      geothermal spring outlet located in the Karvachar region in Nagorno Karabakh
      is presented. Strain K1 shares about 80% genome sequence similarity with T.
      scotoductus strain SA-01, recovered from a deep gold mine in South Africa.
AU  - Saghatelyan A
AU  - Poghosyan L
AU  - Panosyan H
AU  - Birkeland NK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01346-15.

PMID- 2837377
VI  - 298
DP  - 1988
TI  - Selectivity of DNA methylase BspRI.
PG  - 1266-1268
AB  - None
AU  - Sagitov VR
AU  - Aleksandrov AA
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1988 298: 1266-1268.

PMID- 29519837
VI  - 6
DP  - 2018
TI  - Genome Sequence of Bacillus halotolerans Strain MS50-18A with Antifungal Activity against Phytopathogens, Isolated from Saline Soil in San Luis Potosi, Mexico.
PG  - e00135-18
AB  - Bacillus halotolerans strain MS50-18A, isolated from saline soil, possesses antifungal
      activity toward root rot causal phytopathogens and has friendly
      interactions with the chili pepper plant. The draft genome sequence is 4.06 Mb in
      length and contains 4,215 genes. Genes related to glycine/betaine uptake and
      bacilysin biosynthesis are present, supporting its saline stress tolerance and
      antifungal activity.
AU  - Sagredo-Beltran J
AU  - De La Cruz-Rodriguez Y
AU  - Alvarado-Rodriguez M
AU  - Vega-Arreguin J
AU  - Rodriguez-Guerra R
AU  - Alvarado-Gutierrez A
AU  - Fraire-Velazquez S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00135-18.

PMID- 10684923
VI  - 28
DP  - 2000
TI  - Intronic GIY-YIUG endonuclease gene in the mitochondrial genome of Podospora curvicolla: evidence for mobility.
PG  - 1299-1306
AB  - Endonuclease genes encoded in invasive introns are themselves supposed to be mobile elements
      which, during evolution, have colonized pre-existing introns converting them into invasive
      elements.  This hypothesis is supported by numerous data concerning the LAGLI-DADG subclass of
      intronic endonucleases. Less is known about the GIY-YIG ORFs which constitute another family
      of endonucleases. In this paper we describe the presence of one optional GIY-YIG ORF in the
      second intron of the mitochondrial cytochrome b gene in the fungus Podospora curvicolla. We
      show that this GIY-YIG ORF is efficiently transferred from an ORF-containing intron to an
      ORF-less allele. We also show that the products of both the GIY-YIG ORF and the non-canonical
      LAGLI-DADG-GIY-YIG ORF, which is generated by its integration, have endonuclease activities
      which recognize and cut the insertion site of the optional sequence. This constitutes the
      first direct evidence for potential mobility of an intronic GIY-YIG endonuclease. We discuss
      the role that such a mobile sequence could have played during evolution.
AU  - Saguez C
AU  - Lecellier G
AU  - Koll F
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2000 28: 1299-1306.

PMID- 29122862
VI  - 5
DP  - 2017
TI  - Genome Sequences of Mycobacteriophages Findley, Hurricane, and TBond007.
PG  - e01123-17
AB  - We report here the genome sequences of three newly isolated phages that infect Mycobacterium
      smegmatis mc(2)155. Phages Findley, Hurricane, and TBond007 were
      discovered in geographically distinct locations and are related to cluster K
      mycobacteriophages, with Findley being similar to subcluster K2 phages and
      Hurricane and TBond007 being similar to subcluster K3 phages.
AU  - Saha S et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01123-17.

PMID- 9628345
VI  - 379
DP  - 1998
TI  - Functional analysis of conserved motifs in type III restriction-modification enzymes.
PG  - 511-517
AB  - EcoP1I and EcoP15I are members of type III restriction-modification enzymes.  EcoPI and
      EcoP15I DNA methyltransferases transfer a methyl group from S-adenosyl-L-methionine to the N6
      position of the second adenine residues in their recognition sequences, 5'-AGACC-3' and
      5'-CAGCAG-3' respectively.  We have altered various residues in two highly conserved
      sequences, FxGxG (motif I) and DPPY (motif IV) in these proteins by site-directed mutagenesis.
      Using a mixture of in vivo and in vitro assays, our results on the mutational analysis of
      these methyltransferases demonstrate the universal role of motif I in AdoMet binding and a
      role for motif IV in catalysis.  All six cysteine residues in EcoP15I DNA methyltransferase
      have been substituted with serine and the role of cysteine residues in EcoP15I DNA
      methyltransferase catalyzed reaction assessed.  The Res subunits of type III restriction
      enzymes share a distant sequence similarity with and contain the motifs characteristic of the
      DEAD box proteins.  We have carried out site-directed mutagenesis of the conserved residues in
      two of the helicase motifs of the EcoP1I restriction enzyme in order to investigate the role
      of motifs in DNA cleavage by this enzyme.  Our findings indicate that certain conserved
      residues in these motifs are involved in ATP hydrolysis while the other residues are involved
      in coupling restriction of DNA to ATP hydrolysis.  Taken collectively, these results form the
      basis for a detailed structure-function analysis of EcoP1I and EcoP15I restriction enzymes.
AU  - Saha S
AU  - Ahmad I
AU  - Reddy YVR
AU  - Krishnamurthy V
AU  - Rao DN
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1998 379: 511-517.

PMID- 7723013
VI  - 247
DP  - 1995
TI  - ATP hydrolysis is required for DNA cleavage by EcoPI restriction enzyme.
PG  - 559-567
AB  - The type III restriction endonuclease EcoPI, coded by bacteriophage P1, cleaves unmodified DNA
      in the presence of ATP and magnesium ions. We show that purified EcoPI restriction enzyme
      fails to cleave DNA in the presence of non-hydrolyzable ATP analogs. More importantly, this
      study demonstrates that EcoPI restriction enzyme has an inherent ATPase activity, and ATP
      hydrolysis is necessary for DNA cleavage. Furthermore, we show that the progress curve of the
      reaction with EcoPI restriction enzyme exhibits a lag which is dependent on the enzyme
      concentration. Kinetic analysis of the progress curves of the reaction suggest slow
      transitions that can occur during the reaction, characteristic of hysteretic enzymes. The role
      of ATP in the cleavage mechanism of type III restriction enzymes is discussed.
AU  - Saha S
AU  - Rao DN
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1995 247: 559-567.

PMID- 9199404
VI  - 269
DP  - 1997
TI  - Mutations in the Res subunit of the EcoPI restriction enzyme that affect ATP-dependent reactions.
PG  - 342-354
AB  - The Res subunits of the type III restriction-modification enzymes share a statistically
      significant amino acid sequence similarity with several RNA and DNA helicases of the so-called
      DEAD family.  It was postulated that in type III restriction enzymes a DNA helicase activity
      may be required for local unwinding at the cleavage site.  The members of this family share
      seven conserved motifs, all of which are found in the Res subunit of the type III restriction
      enzymes.  To determine the contribution, if any, of these motifs in DNA cleavage by EcoPI, a
      type III restriction enzyme, we have made changes in motifs I and II.  While mutations in
      motif I (GTGKT) clearly affected ATP hydrolysis and resulted in loss of DNA cleavage activity,
      mutation in motif II (DEPH) significantly decreased ATP hydrolysis but had no effect on DNA
      cleavage.  The double mutant R.EcoPIK90R-H229K showed no significant ATPase or DNA restriction
      activity though ATP binding was not affected.  These results imply that there are at least two
      ATPase reaction centers in EcoPI restriction enzyme.  Motif I appears to be involved in
      coupling DNA restriction to ATP hydrolysis.  Our results indicate that EcoPI restriction
      enzyme does not have a strand separation activity.  We suggest that these motifs play a role
      in the ATP-dependent translocation that has been proposed to occur in the type III restriction
      enzymes.
AU  - Saha S
AU  - Rao DN
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1997 269: 342-354.

PMID- 29545292
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of the Environmental Burkholderia pseudomallei Sequence  Type 131 Isolate MSHR1435, Associated with a Chronic Melioidosis Infection.
PG  - e00072-18
AB  - The Burkholderia pseudomallei isolate MSHR1435 is a fully virulent environmental  sequence
      type 131 (ST131) isolate that is epidemiologically associated with a
      17.5-year chronic melioidosis infection. The completed genome will serve as a
      reference for studies of environmental ecology, virulence, and chronic B.
      pseudomallei infections.
AU  - Sahl JW
AU  - Mayo M
AU  - Price EP
AU  - Sarovich DS
AU  - Kaestli M
AU  - Pearson T
AU  - Williamson CHD
AU  - Nottingham R
AU  - Sheridan K
AU  - Wagner DM
AU  - Currie BJ
AU  - Keim P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00072-18.

PMID- 23704173
VI  - 1
DP  - 2013
TI  - Genome Sequence of Burkholderia pseudomallei NCTC 13392.
PG  - e00183-13
AB  - Here, we describe the draft genome sequence of Burkholderia pseudomallei NCTC 13392. This
      isolate has been distributed as K96243, but distinct genomic
      differences have been identified. The genomic sequence of this isolate will
      provide the genomic context for previously conducted functional studies.
AU  - Sahl JW
AU  - Stone JK
AU  - Gelhaus HC
AU  - Warren RL
AU  - Cruttwell CJ
AU  - Funnell SG
AU  - Keim P
AU  - Tuanyok A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00183-13.

PMID- 27516523
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Serratia marcescens U36365, a Green Pigment-Producing Strain Isolated from a Patient with Urinary Tract Infection.
PG  - e00837-16
AB  - Serratia marcescens is an emerging nosocomial pathogen associated with urinary and respiratory
      tract infections. In this study, we determined the genome of a
      green pigment-producing clinical strain, U36365, isolated from a hospital in
      Southern India. De novo assembly of PacBio long-read sequencing indicates that
      the U36365 genome consists of a chromosome of 5.12 Mbps and no plasmids.
AU  - Sahni RD
AU  - Amalanathan R
AU  - Devanga RNK
AU  - Mathai J
AU  - Veeraraghavan B
AU  - Biswas I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00837-16.

PMID- 15289832
VI  - 12
DP  - 2004
TI  - Inhibition of DNA methyltransferase by antisense oligodeoxynucleotide modifies cell characteristics in gastric cancer cell lines.
PG  - 527-531
AB  - DNA (cytosine-5-)-methyltransferase 1 (DNMT1) plays an important role in the maintenance of
      DNA methylation patterns via complicated networks
      including signaling pathways and transcriptional factors, relating to
      cell differentiation or carcinogenesis. In the present study, we
      designed an antisense oligodeoxynucleotide of DNMT1 (AS/MT: 5'-CGGTAC
      GCGCCGGCATCT-3') and demonstrated successful inhibition of DNMT1
      expression by AS/MT at the protein level, using gastric cancer cell
      lines in vitro. E-cadherin protein expression was increased, and both
      cyclin D1 and PCNA were decreased by AS/MT treatment. AS/MT also
      induced suppression of cell growth as determined by BrDU uptake
      incorporation, in a dose-dependent manner, suggesting specificity of
      AS/MT. Simultaneously, morphological alterations were observed in both
      TMK-1 and MKN-45 cells after 24 h incubation with 2 muM of AS/MT. The
      cells changed shape from their original forms to dispersed,
      fibroblast-like cells with neurite-like processes, accompanied by an
      increased adhesive potential of the cells. An in vivo model of
      peritoneal dissemination using the nude mouse system showed an
      increased malignant potential of AS/MT treated TMK-1 cells as
      demonstrated by a greater number of peritoneal tumor nodules in the
      AS/MT as compared to the NS/MT treated group, 34.8+/-4.3 vs. 22.4+/-3.0
      nodules, respectively (p=0.0039). The total wet tumor weight in the
      AS/MT group (350+/-47.4 g) was significantly greater than that in the
      NS/MT group (248+/-41.5 g) (p=0.0065). In conclusion, the inhibition of
      DNA methylation by DNMT1 by an antisense oligodeoxynucleotide
      influences cell morphology and adhesion, as well as cell growth in
      gastric cancer cells in vitro. Moreover, these alterations in the
      characteristics of cancer cells resulted in an increased ability to
      attach onto the peritoneum in the nude mouse system in vivo, suggesting
      that strict clinical guidelines will be necessary to utilize such a DNA
      methylation inhibitor, since it does not always mean a therapeutic
      antitumor strategy.
AU  - Saikawa Y
AU  - Kubota T
AU  - Maeda S
AU  - Otani Y
AU  - Kumai K
AU  - Kitajima M
PT  - Journal Article
TA  - Oncol. Rep.
JT  - Oncol. Rep.
SO  - Oncol. Rep. 2004 12: 527-531.

PMID- 29606600
VI  - 308
DP  - 2018
TI  - Growth advantage of Escherichia coli O104:H4 strains on 5-N-acetyl-9-O-acetyl neuraminic acid as a carbon source is dependent on heterogeneous phage-Borne nanS-p esterases.
PG  - 459-468
AB  - Enterohemorrhagic E. coli (EHEC) are serious bacterial pathogens which are able
      to cause a hemorrhagic colitis or the life-threatening hemolytic-uremic syndrome
      (HUS) in humans. EHEC strains can carry different numbers of phage-borne nanS-p
      alleles that are responsible for acetic acid release from mucin from bovine
      submaxillary gland and 5-N-acetyl-9-O-acetyl neuraminic acid (Neu5,9Ac2), a
      carbohydrate present in mucin. Thus, Neu5,9Ac2 can be transformed to 5-N-acetyl
      neuraminic acid, an energy source used by E. coli strains. We hypothesize that
      these NanS-p proteins are involved in competitive growth of EHEC in the
      gastrointestinal tract of humans and animals. The aim of the current study was to
      demonstrate and characterize the nanS-p alleles of the 2011 E. coli O104:H4
      outbreak strain LB226692 and analyze whether the presence of multiple nanS-p
      alleles in the LB226692 genome causes a competitive growth advantage over a
      commensal E. coli strain. We detected and characterized five heterogeneous
      phage-borne nanS-p alleles in the genome of E. coli O104:H4 outbreak strain
      LB226692 by in silico analysis of its genome. Furthermore, successive deletion of
      all nanS-p alleles, subsequent complementation with recombinant NanS-p13-His, and
      in vitro co-culturing experiments with the commensal E. coli strain AMC 198 were
      conducted. We could show that nanS-p genes of E. coli O104:H4 are responsible for
      growth inhibition of strain AMC 198, when Neu5,9Ac2 was used as sole carbon
      source in co-culture. The results of this study let us suggest that multiple
      nanS-p alleles may confer a growth advantage by outcompeting other E. coli
      strains in Neu5,9Ac2 rich environments, such as mucus in animal and human gut.
AU  - Saile N
AU  - Schwarz L
AU  - Eissenberger K
AU  - Klumpp J
AU  - Fricke FW
AU  - Schmidt H
PT  - Journal Article
TA  - Int. J. Med. Microbiol.
JT  - Int. J. Med. Microbiol.
SO  - Int. J. Med. Microbiol. 2018 308: 459-468.

PMID- 27474715
VI  - 82
DP  - 2016
TI  - In Silico and Functional Analysis of Prophage-Encoded 5-N-Acetyl-9-O-Acetyl Neuraminic Acid Esterases of E. coli O157:H7 Strain EDL933.
PG  - 5940-5950
AB  - (ORFs) in its genome which are highly homologous to the chromosomal nanS gene. The latter is
      part of the nanCMS operon,
      which is present in most E. coli strains and encodes an esterase which is responsible for the
      monodeacetylation of 5-N-acetyl-9-
      O-acetyl neuraminic acid (Neu5,9Ac2). Whereas one prophage-borne ORF (z1466) has been
      characterized in previous studies,
      the functions of the other nanS-homologous ORFs are unknown. In the current study, the
      nanS-homologous ORFs of EDL933
      were initially studied in silico. Due to their homology to the chromosomal nanS gene and their
      location in prophage genomes,
      we designated them nanS-p and numbered the different nanS-p alleles consecutively from 1 to
      10. The two alleles nanS-p2 and
      nanS-p4 were selected for production of recombinant proteins, their enzymatic activities were
      investigated, and differences in
      their temperature optima were found. Furthermore, a function of these enzymes in substrate
      utilization could be demonstrated
      using an E. coli C600nanS mutant in a growth medium with Neu5,9Ac2 as the carbon source and
      supplementation with the
      different recombinant NanS-p proteins. Moreover, generation of sequential deletions of all
      nanS-p alleles in strain EDL933 and
      subsequent growth experiments demonstrated a gene dose effect on the utilization of Neu5,9Ac2.
      Since Neu5,9Ac2 is an important
      component of human and animal gut mucus and since the nutrient availability in the large
      intestine is limited, we hypothesize
      that the presence of multiple Neu5,9Ac2 esterases provides them a nutrient supply under
      certain conditions in the large intestine,
      even if particular prophages are lost.
AU  - Saile N
AU  - Voigt A
AU  - Kessler S
AU  - Stressler T
AU  - Klumpp J
AU  - Fischer L
AU  - Schmidt H
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2016 82: 5940-5950.

PMID- 6255295
VI  - 180
DP  - 1980
TI  - The hsd (host specificity) genes of E. coli K12.
PG  - 35-46
AB  - The hsd genes of E. coli K12 have been cloned in phage lambda by a combination
      of in vitro and in vivo techniques.  Three genes, whose products are required
      for K-specific restriction and modification, have been identified by
      complementation tests as hsdR, M, and S.  The order of these closely linked
      genes was established as R, M, S by analysis of the DNA of genetically
      characterised deletion derivatives of lambda hsd phages.  The three genes are
      transcribed in the same direction but not necessarily as a single operon.
      Genetic evidence identifies two promoters, one from which transcription of hsdM
      and S is initiated and a second for the hsdR gene.  The hsdR gene codes for a
      polypeptide of molecular weight ~130,000; hsdM for one of 62-65,000 and the
      hsdS gene was associated with two polypeptides of approximately 50000.
      Circumstantial evidence suggest that one of these two polypeptides may be a
      degradation, or processed, derivative of the other.  The hsdS polypeptide of E.
      coli B has a slightly higher mobility in an SDS-polyacrylamide gel than does
      that of E. coli K12.  A probe comprising most of the hsdR gene and all of the
      hsdM and S genes of E. coli K12 shares extensive homology with the DNA of E.
      coli B but none with that of E. coli C.
AU  - Sain B
AU  - Murray NE
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1980 180: 35-46.

PMID- 27340078
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Acetobacter malorum CECT 7742, a Strain Isolated from Strawberry Vinegar.
PG  - e00620-16
AB  - The present article reports the draft genome sequence of the strain Acetobacter malorum CECT
      7742, an acetic acid bacterium isolated from strawberry vinegar.
      This species is characterized by the production of d-gluconic acid from
      d-glucose, which it further metabolizes to keto-d-gluconic acids.
AU  - Sainz F
AU  - Mas A
AU  - Torija MJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00620-16.

PMID- 27365351
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Gluconobacter cerinus CECT 9110 and Gluconobacter japonicus CECT 8443, Acetic Acid Bacteria Isolated from Grape Must.
PG  - e00621-16
AB  - We report here the draft genome sequences of Gluconobacter cerinus strain CECT9110 and
      Gluconobacter japonicus CECT8443, acetic acid bacteria isolated from grape must. Gluconobacter
      species are well known for their ability to oxidize sugar alcohols into the corresponding
      acids. Our objective was to select strains  to oxidize effectively d-glucose.
AU  - Sainz F
AU  - Mas A
AU  - Torija MJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00621-16.

PMID- 23472224
VI  - 1
DP  - 2013
TI  - Genome Sequence of Lawsonia intracellularis Strain N343, Isolated from a Sow with Hemorrhagic Proliferative Enteropathy.
PG  - e00027-13
AB  - is the etiological agent of proliferative enteropathy (PE), causing mild or acute hemorrhagic
      diarrhea in infected animals. Here we report the genome sequence of
      strain N343, isolated from a sow that died of hemorrhagic PE. N343 contains 24
      single nucleotide polymorphisms and 90 indels compared to the reference strain
      PHE/MN1-00.
AU  - Sait M
AU  - Aitchison K
AU  - Wheelhouse N
AU  - Wilson K
AU  - Lainson FA
AU  - Longbottom D
AU  - Smith DG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00027-13.

PMID- 107390
VI  - 170
DP  - 1979
TI  - Mapping of genes determining nonpermissiveness and host-specific restriction to bacteriophages in Bacillus subtilis Marburg.
PG  - 117-122
AB  - Bacillus subtilis Marburg is nonpermissive for the multiplication of
      bacteriophages SP10 and uNR2.  A permissive mutant was derived from the Marburg
      strain, and the genetic determinants of nonpermissiveness were analyzed by PBS1
      transduction.  The simultaneous presence of two genes as mutant alleles, nonA
      and nonB, was necessary for permissiveness.  The gene nonA is linked very
      closely to rfm (cotransfer: 90%); nonB is located between dal and purB
      (cotransfer of nonB and purB6: 48%).  The genetic determinant of host-specific
      restriction intrinsic to the Marburg strain (hsrM) was found to be identical or
      very closely linked to nonB.  The segregation of nonB and hsrM has never been
      observed in the course of transduction analysis.  The mutation, hsrM1,
      diminishes the restriction activity, but not the host-controlled modifiction.
AU  - Saito H
AU  - Shibata T
AU  - Ando T
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1979 170: 117-122.

PMID- 26988057
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Aggregatibacter actinomycetemcomitans Serotype g Strain NUM4039 (JCM 30399).
PG  - e00158-16
AB  - Aggregatibacter actinomycetemcomitans is considered to be a major etiological agent of
      aggressive periodontitis and includes serotype a to g strains. We herein
      report the first complete genome sequence of A. actinomycetemcomitans serotype g
      strain NUM4039. The genome is 2,382,853 bp in length with a G+C content of
      44.34%.
AU  - Saito M
AU  - Hirasawa M
AU  - Kuwahara N
AU  - Okada T
AU  - Umezawa K
AU  - Kobayashi T
AU  - Okamoto M
AU  - Naito M
AU  - Hirasawa M
AU  - Takada K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00158-16.

PMID- 16287978
VI  - 102
DP  - 2005
TI  - The genome sequence of Clostridium botulinum type C neurotoxin-converting phage and the molecular mechanisms of unstable lysogeny.
PG  - 17472-17477
AB  - Botulinum neurotoxins (BoNTXs) produced by Clostridium botulinum are among
      the most poisonous substances known. Of the seven types of BoNTXs, genes
      for type C1 and D toxins (BoNTX/C1 and D) are carried by bacteriophages.
      The gene for exoenzyme C3 also resides on these phages. Here, we present
      the complete genome sequence of c-st, a representative of
      BoNTX/C1-converting phages. The genome is a linear double-stranded DNA of
      185,682 bp with 404-bp terminal direct repeats, the largest known
      temperate phage genome. We identified 198 potential protein-coding
      regions, including the genes for production of BoNTX/C1 and exoenzyme C3.
      Very exceptionally, as a viable bacteriophage, a number of insertion
      sequences were found on the c-st genome. By analyzing the molecular
      structure of the c-st genome in lysogens, we also found that it exists as
      a circular plasmid prophage. These features account for the unstable
      lysogeny of BoNTX phages, which has historically been called
      "pseudolysogeny." The PCR scanning analysis of other BoNTX/C1 and D phages
      based on the c-st sequence further revealed that BoNTX phages comprise a
      divergent phage family, probably generated by exchanging genomic segments
      among BoNTX phages and their relatives.
AU  - Sakaguchi Y
AU  - Hayashi T
AU  - Kurokawa K
AU  - Nakayama K
AU  - Oshima K
AU  - Fujinaga Y
AU  - Ohnishi M
AU  - Ohtsubo E
AU  - Hattori M
AU  - Oguma K
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2005 102: 17472-17477.

PMID- 24459252
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Clostridium botulinum Type B Strain Osaka05, Isolated from an Infant Patient with Botulism in Japan.
PG  - e01010-13
AB  - Clostridium botulinum strain Osaka05, which has been isolated from an infant patient with
      botulism in Japan, is the first strain producing botulinum
      neurotoxin subtype B6. Here, we report the draft genome sequence of C. botulinum
      Osaka05.
AU  - Sakaguchi Y
AU  - Hosomi K
AU  - Uchiyama J
AU  - Ogura Y
AU  - Umeda K
AU  - Sakaguchi M
AU  - Kohda T
AU  - Mukamoto M
AU  - Misawa N
AU  - Matsuzaki S
AU  - Hayashi T
AU  - Kozaki S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01010-13.

PMID- 27660784
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Marine Sponge Symbiont Pseudoalteromonas luteoviolacea IPB1, Isolated from Hilo, Hawaii.
PG  - e01002-16
AB  - We report here the 6.0-Mb draft genome assembly of Pseudoalteromonas luteoviolacea strain IPB1
      that was isolated from the Hawaiian marine sponge
      Iotrochota protea Genome mining complemented with bioassay studies will elucidate
      secondary metabolite biosynthetic pathways and will help explain the ecological
      interaction between host sponge and microorganism.
AU  - Sakai-Kawada FE
AU  - Yakym CJ
AU  - Helmkampf M
AU  - Hagiwara K
AU  - Ip CG
AU  - Antonio BJ
AU  - Armstrong E
AU  - Ulloa WJ
AU  - Awaya JD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01002-16.

PMID- 29930067
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Lawsonibacter asaccharolyticus JCM 32166(T), a Butyrate-Producing Bacterium, Isolated from Human Feces.
PG  - e00563-18
AB  - Here, we report the draft genome sequence of Lawsonibacter asaccharolyticus JCM 32166(T), a
      butyrate-producing bacterium, isolated from human feces. The genomic
      analysis reveals genes for butyrate synthesis and will facilitate the study on
      the role of this strain in the human gut.
AU  - Sakamoto M
AU  - Ikeyama N
AU  - Yuki M
AU  - Ohkuma M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00563-18.

PMID- 30533935
VI  - 7
DP  - 2018
TI  - Draft Genome Sequence of Faecalimonas umbilicata JCM 30896(T), an Acetate-Producing Bacterium Isolated from Human Feces.
PG  - e01091-18
AB  - Here, we report the draft genome sequence of Faecalimonas umbilicata JCM 30896(T), an
      acetate-producing bacterium isolated from human feces. The genomic
      analysis reveals genes for acetate and vitamin B12 synthesis and will facilitate
      the study of the role of this strain in the human gut.
AU  - Sakamoto M
AU  - Ikeyama N
AU  - Yuki M
AU  - Ohkuma M
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e01091-18.

PMID- 26380636
VI  - 10
DP  - 2015
TI  - High quality draft genome sequence of Bacteroides barnesiae type strain BL2(T) (DSM 18169(T)) from chicken caecum.
PG  - 48
AB  - Bacteroides barnesiae Lan et al. 2006 is a species of the genus Bacteroides, which belongs to
      the family Bacteroidaceae. Strain BL2(T) is of interest because  it was isolated from the gut
      of a chicken and the growing awareness that the anaerobic microbiota of the caecum is of
      benefit for the host and may impact poultry farming. The 3,621,509 bp long genome with its
      3,059 protein-coding and 97 RNA genes is a part of the Genomic Encyclopedia of Type Strains,
      Phase I: the  one thousand microbial genomes (KMG) project.
AU  - Sakamoto M
AU  - Lapidus AL
AU  - Han J
AU  - Trong S
AU  - Haynes M
AU  - Reddy TB
AU  - Mikhailova N
AU  - Huntemann M
AU  - Pati A
AU  - Ivanova NN
AU  - Pukall R
AU  - Markowitz VM
AU  - Woyke T
AU  - Klenk HP
AU  - Kyrpides NC
AU  - Ohkuma M
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 48.

PMID- 24482517
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Three Strains of Bacteroides pyogenes Isolated from a Cat and Swine.
PG  - e01242-13
AB  - Here, we report the draft genome sequences of Bacteroides pyogenes JCM 6294(T), JCM 6292, and
      JCM 10003, which were isolated from a cat and swine and were
      recently classified into a single species, B. pyogenes. Comparative analyses of
      these genomes revealed the diversification of B. pyogenes strains isolated from
      different animals.
AU  - Sakamoto M
AU  - Oshima K
AU  - Suda W
AU  - Kitamura K
AU  - Iida T
AU  - Hattori M
AU  - Ohkuma M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01242-13.

PMID- 23887912
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences of Porphyromonas crevioricanis JCM 15906T and Porphyromonas cansulci JCM 13913T Isolated from a Canine Oral Cavity.
PG  - e00483-13
AB  - Here, we report the draft genome sequences of Porphyromonas crevioricanis JCM 15906(T) and
      Porphyromonas cansulci JCM 13913(T), which were isolated from a
      canine oral cavity and were recently united under the single species P.
      crevioricanis. These two genome sequences are very similar, and yet a high degree
      of genome rearrangements is observed.
AU  - Sakamoto M
AU  - Tanaka N
AU  - Shiwa Y
AU  - Yoshikawa H
AU  - Ohkuma M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00483-13.

PMID- 26494666
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Bradyrhizobium japonicum Is-1, Which Is Incompatible with Rj2 Genotype Soybeans.
PG  - e01219-15
AB  - We report the draft genome sequence of Bradyrhizobium japonicum Is-1, which is incompatible
      with Rj2 genotype soybeans. The estimated genome size of this strain is 8.9 Mb. Genome
      sequence information of this strain will help to identify a causal gene for this
      incompatibility.
AU  - Sakata T
AU  - Kanesaki Y
AU  - Yoshikawa H
AU  - Tsurumaru H
AU  - Yamakawa T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01219-15.

PMID- 26494661
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Thiostrepton-Producing Streptomyces azureus ATCC 14921.
PG  - e01183-15
AB  - Streptomyces azureus ATCC 14921 belongs to the Streptomyces cyaneus cluster and is known to be
      a thiostrepton producer. Here, we report a draft genome sequence for this strain, consisting
      of 350 contigs containing a total of 8,790,525 bp, 8,164 predicted coding sequences, and a G+C
      content of 70.9%.
AU  - Sakihara K
AU  - Maeda J
AU  - Tashiro K
AU  - Fujino Y
AU  - Kuhara S
AU  - Ohshima T
AU  - Ogata S
AU  - Doi K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01183-15.

PMID- 30498561
VI  - 13
DP  - 2018
TI  - The draft genome sequence of 'Nitrospira lenta' strain BS10, a nitrite oxidizing  bacterium isolated from activated sludge.
PG  - 32
AB  - The genus Nitrospira is considered to be the most widespread and abundant group of
      nitrite-oxidizing bacteria in many natural and man-made ecosystems. However,
      the ecophysiological versatility within this phylogenetic group remains highly
      understudied, mainly due to the lack of pure cultures and genomic data. To
      further expand our understanding of this biotechnologically important genus, we
      analyzed the high quality draft genome of 'Nitrospira lenta' strain BS10, a
      sublineage II Nitrospira that was isolated from a municipal wastewater treatment
      plant in Hamburg, Germany. The genome of 'N. lenta' has a size of 3,756,190 bp
      and contains 3968 genomic objects, of which 3907 are predicted protein-coding
      sequences. Thorough genome annotation allowed the reconstruction of the 'N.
      lenta' core metabolism for energy conservation and carbon fixation. Comparative
      analyses indicated that most metabolic features are shared with N. moscoviensis
      and 'N. defluvii', despite their ecological niche differentiation and
      phylogenetic distance. In conclusion, the genome of 'N. lenta' provides important
      insights into the genomic diversity of the genus Nitrospira and provides a
      foundation for future comparative genomic studies that will generate a better
      understanding of the nitrification process.
AU  - Sakoula D
AU  - Nowka B
AU  - Spieck E
AU  - Daims H
AU  - Lucker S
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2018 13: 32.

PMID- 28034857
VI  - 4
DP  - 2016
TI  - Draft Whole-Genome Sequence of the Alkaliphilic Alishewanella aestuarii Strain HH-ZS, Isolated from Historical Lime Kiln Waste-Contaminated Soil.
PG  - e01447-16
AB  - Here, we present the whole-genome sequence of an environmental Gram-negative Alishewanella
      aestuarii strain (HH-ZS), isolated from the hyperalkaline
      contaminated soil of a historical lime kiln in Buxton, United Kingdom.
AU  - Salah ZB
AU  - Rout SP
AU  - Humphreys PN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01447-16.

PMID- Not carried by PubMed...
VI  - 96
DP  - 1994
TI  - In vivo modulation of the EcoK restriction endonuclease.
PG  - 357-358
AB  - Recently, we have found a novel type of restriction alleviation (RA) which occurs in strains
      carrying recB alone or recB in combination with additional mutations (recBC sbcBC, recBC sbcBC
      recJ, recBC sbcBC recF, recBC sucBC recA).  It occurs in the absence of UV irraditation and
      depends on the presence of the commonly used plasmids (such as pACYC184).  It is, however,
      independent of the host and phage recombination systems.  The mechanism of this type of RA is
      unknown.  Therefore, it was interesting to see whether UV-induced RA and plasmid-mediated RA
      have a common mechanism.  For this purpose, we measured the efficiency of plating of
      unmodified lambda on three sets of UV-irradiated bacteria: 1. E. coli JC7623 recB21 recC22
      sbcB15 sbcC201 carrying the plasmid pACYC184 and, as a control, plasmid-free derivative; 2. E.
      coli N2281 rec B21 recC22 sbcB15 sbcC201 recA13 carrying pACYC184 and its plasmid-free
      derivative.  3. E. coli AB1157 (wild type) carrying pACYC184 and its plasmid-free derivative.
AU  - Salaj-Smic E
AU  - Donjerkovic D
AU  - Trgovcevic Z
PT  - Journal Article
TA  - Periodicum Biologorum
JT  - Periodicum Biologorum
SO  - Periodicum Biologorum 1994 96: 357-358.

PMID- 9068628
VI  - 179
DP  - 1997
TI  - Modulation of EcoKI restriction in vivo: Role of the lambda gam protein and plasmid metabolism.
PG  - 1852-1856
AB  - Two novel types of alleviation of DNA restriction by the EcoKI restriction endonuclease are
      described.  The first type depends on the presence of the gam gene product (Gam protein) of
      bacteriophage lambda.  The efficiency of plating of unmodified phage lambda is greatly
      increased when the restricting Escherichia coli K-12 host carries a gam+ plasmid.  The effect
      is particularly striking in wild-type strains and, to a lesser extent, in the presence of sbcC
      and recA mutations.  In all cases, Gam-dependent alleviation of restriction requires active
      recBCD genes of the host and recombination (red) genes of the infecting phage.  The enhanced
      capacity of Gam-expressing cells to repair DNA strand breaks might account for this
      phenomenon.  The second type is caused by the presence of a plasmid in a restricting host
      lacking RecBCD enzyme.  Commonly used plasmids such as the cloning vector pACYC184  can
      produce such an effect in strains carrying recB single mutations or in recBC sbcBC strains.
      Plasmid-mediated restriction alleviation in recBC sbcBC strains is independent of the host
      RecF, RecJ, and RecA proteins and phage recombination functions.  The presence of plasmids can
      also relieve restriction in recD strains.  This effect depends, however, on the RecA function
      in the host.  The molecular mechanism of the plasmid-mediated restriction alleviation remains
      unclear.
AU  - Salaj-Smic E
AU  - Marsic N
AU  - Trgovcevic Z
AU  - Lloyd RG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1997 179: 1852-1856.

PMID- 11121067
VI  - 97
DP  - 2000
TI  - A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains.
PG  - 14668-14673
AB  - Helicobacter pylori colonizes the stomach of half of the world's population, causing a wide
      spectrum of disease ranging from
      asymptomatic gastritis to ulcers to gastric cancer. Although the basis
      for these diverse clinical outcomes is not understood, more severe
      disease is associated with strains harboring a pathogenicity island. To
      characterize the genetic diversity of more and less virulent strains,
      we examined the genomic content of 15 H. pylori clinical isolates by
      using a whole genome H. pylori DNA microarray. We found that a full 22%
      of H. pylori genes are dispensable in one or more strains, thus
      defining a minimal functional core of 1281 H. pylori genes. While the
      core genes encode most metabolic and cellular processes, the
      strain-specific genes include genes unique to H. pylori, restriction
      modification genes, transposases, and genes encoding cell surface
      proteins, which may aid the bacteria under specific circumstances
      during their long-term infection of genetically diverse hosts. We
      observed distinct patterns of the strain-specific gene distribution
      along the chromosome, which may result from different mechanisms of
      gene acquisition and loss. Among the strain-specific genes, we have
      found a class of candidate virulence genes identified by their
      coinheritance with the pathogenicity island.
AU  - Salama N
AU  - Guillemin K
AU  - McDaniel TK
AU  - Sherlock G
AU  - Tompkins L
AU  - Falkow S
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2000 97: 14668-14673.

PMID- 17337568
VI  - 189
DP  - 2007
TI  - Genetic analysis of Helicobacter pylori strain populations colonizing the stomach at different times postinfection.
PG  - 3834-3845
AB  - Genetic diversity of the human gastric pathogen Helicobacter pylori in an
      individual host has been observed; whether this diversity represents
      diversification of a founding strain or a mixed infection with distinct
      strain populations is not clear. To examine this issue, we analyzed
      multiple single-colony isolates from two to four separate stomach biopsies
      of eight adult and four pediatric patients from a high-incidence Mexican
      population. Eleven of the 12 patients contained isolates with identical
      random amplified polymorphic DNA, amplified fragment length polymorphism,
      and vacA allele molecular footprints, whereas a single adult patient had
      two distinct profiles. Comparative genomic hybridization using
      whole-genome microarrays (array CGH) revealed variation in 24 to 67 genes
      in isolates from patients with similar molecular footprints. The one
      patient with distinct profiles contained two strain populations differing
      at 113 gene loci, including the cag pathogenicity island virulence genes.
      The two strain populations in this single host had different spatial
      distributions in the stomach and exhibited very limited genetic exchange.
      The total genetic divergence and pairwise genetic divergence between
      isolates from adults and isolates from children were not statistically
      different. We also analyzed isolates obtained 15 and 90 days after
      experimental infection of humans and found no evidence of genetic
      divergence, indicating that transmission to a new host does not induce
      rapid genetic changes in the bacterial population in the human stomach.
      Our data suggest that humans are infected with a population of closely
      related strains that vary at a small number of gene loci, that this
      population of strains may already be present when an infection is
      acquired, and that even during superinfection genetic exchange among
      distinct strains is rare.
AU  - Salama NR
AU  - Gonzalez-Valencia G
AU  - Deatherage B
AU  - Aviles-Jimenez F
AU  - Atherton JC
AU  - Graham DY
AU  - Torres J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2007 189: 3834-3845.

PMID- 11823852
VI  - 415
DP  - 2002
TI  - Genome sequence of the plant pathogen Ralstonia solanacearum.
PG  - 497-502
AB  - Ralstonia solanacearum is a devastating, soil-borne plant pathogen with a global distribution
      and an unusually wide host range. It is a model system for the dissection of molecular
      determinants governing pathogenicity. We present here the complete genome sequence and its
      analysis of strain GMI1000. The 5.8-megabase (Mb) genome is organized into two replicons: a
      3.7-Mb chromosome and a 2.1-Mb megaplasmid. Both replicons have a mosaic structure providing
      evidence for the acquisition of genes through horizontal gene transfer. Regions containing
      genetically mobile elements associated with the percentage of G+C bias may have an important
      function in genome evolution. The genome encodes many proteins potentially associated with a
      role in pathogenicity. In particular, many putative attachment factors were identified. The
      complete repertoire of type III secreted effector proteins can be studied. Over 40 candidates
      were identified. Comparison with other genomes suggests that bacterial plant pathogens and
      animal pathogens harbour distinct arrays of specialized type III-dependent effectors.
AU  - Salanoubat M et al
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2002 415: 497-502.

PMID- 15073292
VI  - 150
DP  - 2004
TI  - The diversity within an expanded and redefined repertoire of phase-variable genes in Helicobacter pylori.
PG  - 817-830
AB  - Phase variation is a common mechanism used by pathogenic bacteria to generate intra-strain
      diversity that is important in niche adaptation and is strongly associated with virulence
      determinants.  Previous analyses of the complete sequences of the Helicobacter pylori strains
      26695 and J99 have identified 36 putative phase-variable genes among the two genomes through
      their association with homopolymeric tracts and dinucleotide repeats.  Here a comparative
      analysis of the two genomes is reported and an updated and expanded list of 46 candidate
      phase-variable genes in H. pylori is described.  These have been systematically investigated
      by PCR and sequencing for the presence of the genes, and the presence and variability in
      length of the repeats in strains 26695 and J99 and in a collection of unrelated H. pylori
      strains representative of the main global subdivisions recently suggested.  This provides
      supportive evidence for the phase variability of 30 of the 46 candidates.  Other differences
      in this subset of genes were observed (i) in the repeats, which can be present or absent among
      the strains, or stabilized in different strains and (ii) in the gene-complements of the
      strains.  Differences between genes were not consistently correlated with the geographic
      population distribution of the strains.  This study extends and provides new evidence for
      variation of this type in H. pylori, and of the high degree of diversity of the repertoire of
      genes which display phase-variable switching within individual strains.
AU  - Salauen L
AU  - Linz B
AU  - Suerbaum S
AU  - Saunders NJ
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2004 150: 817-830.

PMID- 29880597
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Listeria monocytogenes DFPST0073, Isolated from Imported Mexican Soft Cheese.
PG  - e00496-18
AB  - The genome of Listeria monocytogenes strain DFPST0073, isolated from imported fresh Mexican
      soft cheese in 2003, was sequenced using the Illumina MiSeq
      platform. Reads were assembled using SPAdes, and genome annotation was performed
      using the NCBI Prokaryotic Genome Annotation Pipeline.
AU  - Salazar JK
AU  - Gonsalves LJ
AU  - Schill KM
AU  - Sanchez LM
AU  - Anderson N
AU  - Keller SE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00496-18.

PMID- 28232434
VI  - 5
DP  - 2017
TI  - Genome Sequence of Enterotoxigenic Escherichia coli Strain FMU073332.
PG  - e01600-16
AB  - Enterotoxigenic Escherichia coli (ETEC) is an important cause of bacterial diarrheal illness,
      affecting practically every population worldwide, and was
      estimated to cause 120,800 deaths in 2010. Here, we report the genome sequence of
      ETEC strain FMU073332, isolated from a 25-month-old girl from Tlaltizapan,
      Morelos, Mexico.
AU  - Saldana-Ahuactzi Z
AU  - Cruz-Cordova A
AU  - Rodea GE
AU  - Porta H
AU  - Navarro-Ocana A
AU  - Eslava-Campos C
AU  - Cevallos MA
AU  - Xicohtencatl-Cortes J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01600-16.

PMID- 10413481
VI  - 38
DP  - 1999
TI  - RNA and protein catalysis in group II intron splicing and mobility reactions using purified components.
PG  - 9069-9083
AB  - Group II introns encode proteins with reverse transcriptase activity. These proteins also
      promote RNA splicing (maturase activity) and then, with the excised intron, form a
      site-specific DNA endonuclease that promotes intron mobility by reverse splicing into DNA
      followed by target DNA-primed reverse transcription. Here, we used an Escherichia coli
      expression system for the Lactococcus lactis group II intron Ll.LtrB to show that the
      intron-encoded protein (LtrA) alone is sufficient for maturase activity, and that RNP
      particles containing only the LtrA protein and excised intron RNA have site-specific DNA
      endonuclease and target DNA-primed reverse transcriptase activity. Detailed analysis of the
      splicing reaction indicates that LtrA is an intron-specific splicing factor that binds to
      unspliced precursor RNA with a K(d) of </=0.12 pM at 30 degrees C. This binding occurs in a
      rapid bimolecular reaction, which is followed by a slower step, presumably an RNA
      conformational change, required for splicing to occur. Our results constitute the first
      biochemical analysis of protein-dependent splicing of a group II intron and demonstrate that a
      single intron-encoded protein can interact with the intron RNA to carry out a coordinated
      series of reactions leading to splicing and mobility.
AU  - Saldanha R
AU  - Chen B
AU  - Wank H
AU  - Matsuura M
AU  - Edwards J
AU  - Lambowitz AM
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1999 38: 9069-9083.

PMID- 29976603
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Three Salmonella enterica Serovar 4,[5],12:i:- Strains  and One S. enterica Serovar Typhimurium Strain, Isolated in Brazil.
PG  - e00488-18
AB  - Draft genomes of three Salmonella enterica 4,[5],12:i:- (STi) strains isolated from human
      infections were obtained using Illumina sequencing. They were negative
      for the fljBA operon but positive for hin, and k-mer analyses revealed their
      identity as S. enterica 4,[5],12:i:- 08-1736 and S Typhimurium. A draft S
      Typhimurium sequence is described for comparison.
AU  - Sales AIL
AU  - Milanez GP
AU  - Nascimento LC
AU  - do Carmo CP
AU  - da Costa FLP
AU  - Pereira GAG
AU  - Martinez R
AU  - Brocchi M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00488-18.

PMID- 21725009
VI  - 193
DP  - 2011
TI  - Genome sequence of 1,4-dioxane degrading Pseudonocardia dioxanivorans strain CB1190.
PG  - 4549-4550
AB  - Pseudonocardia dioxanivorans CB1190 is the first bacterium reported to be capable of growth on
      the environmental contaminant 1,4-dioxane, and the
      first member of the genus Pseudonocardia for which there is an annotated
      genome sequence. Preliminary analysis of the genome (chromosome and three
      plasmids) indicates that strain CB1190 possesses several multicomponent
      monooxygenases that could be involved in the aerobic degradation of
      1,4-dioxane and other environmental contaminants.
AU  - Sales CM
AU  - Mahendra S
AU  - Grostern A
AU  - Parales RE
AU  - Goodwin L
AU  - Woyke T
AU  - Nolan M
AU  - Lapidus A
AU  - Chertkov O
AU  - Ovchinnikova G
AU  - Szcyrba A
AU  - Alvarez-Cohen L
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4549-4550.

PMID- 28883130
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of a Pseudomonas aeruginosa NA04 Bacterium Isolated from an Entomopathogenic Nematode.
PG  - e00746-17
AB  - We report the draft genome sequence of Gram-negative bacterium Pseudomonas aeruginosa NA04,
      isolated from the entomopathogenic nematode Heterorhabditis
      indica MOR03. The draft genome consists of 54 contigs, a length of 6.37 Mb, and a
      G+C content 66.49%.
AU  - Salgado-Morales R
AU  - Rivera-Gomez N
AU  - Lozano-Aguirre BLF
AU  - Hernandez-Mendoza A
AU  - Dantan-Gonzalez E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00746-17.

PMID- 28860237
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Photorhabdus luminescens HIM3 Isolated from an Entomopathogenic Nematode in Agricultural Soils.
PG  - e00745-17
AB  - In this work, we report the draft genome sequence of Photorhabdus luminescens strain HIM3, a
      symbiotic bacterium associated with the entomopathogenic nematode
      Heterorhabditis indica MOR03, isolated from soil sugarcane in Yautepec, Morelos,
      Mexico. These bacteria have a G+C content of 42.6% and genome size of 5.47 Mb.
AU  - Salgado-Morales R
AU  - Rivera-Gomez N
AU  - Martinez-Ocampo F
AU  - Lozano-Aguirre BLF
AU  - Hernandez-Mendoza A
AU  - Dantan-Gonzalez E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00745-17.

PMID- 25373147
VI  - 25
DP  - 2014
TI  - Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains.
PG  - 119-128
AB  - Large-scale bacterial genome sequencing efforts to date have provided limited information on
      the most prevalent category of disease: sporadically acquired infections caused by common
      pathogenic bacteria. Here, we performed whole-genome sequencing and de novo assembly of 312
      blood- or urine-derived isolates of extraintestinal pathogenic (ExPEC) Escherichia coli, a
      common agent of sepsis and community-acquired urinary tract infections, obtained during the
      course of routine clinical care at a single institution. We find that ExPEC E. coli are highly
      genomically heterogeneous, consistent with pan-genome analyses encompassing the larger
      species. Investigation of differential virulence factor content and antibiotic resistance
      phenotypes reveals markedly different profiles among lineages and among strains infecting
      different body sites. We use high-resolution molecular epidemiology to explore the dynamics of
      infections at the level of individual patients, including identification of possible
      person-to-person transmission. Notably, a limited number of discrete lineages caused the
      majority of bloodstream infections, including one subclone (ST131-H30) responsible for 28% of
      bacteremic E. coli infections over a 3-yr period. We additionally use a microbial
      genome-wide-association study (GWAS) approach to identify individual genes responsible for
      antibiotic resistance, successfully recovering known genes but notably not identifying any
      novel factors. We anticipate that in the near future, whole-genome sequencing of
      microorganisms associated with clinical disease will become routine. Our study reveals what
      kind of information can be obtained from sequencing clinical isolates on a large scale, even
      well-characterized organisms such as E. coli, and provides insight into how this information
      might be utilized in a healthcare setting.
AU  - Salipante SJ
AU  - Roach DJ
AU  - Kitzman JO
AU  - Snyder MW
AU  - Stackhouse B
AU  - Butler-Wu SM
AU  - Lee C
AU  - Cookson BT
AU  - Shendure J
PT  - Journal Article
TA  - Genome Res.
JT  - Genome Res.
SO  - Genome Res. 2014 25: 119-128.

PMID- 25395647
VI  - 2
DP  - 2014
TI  - The Draft Genome Sequence of Sphingomonas sp. Strain FukuSWIS1, Obtained from Acidic Lake Grosse Fuchskuhle, Indicates Photoheterotrophy and a Potential for  Humic Matter Degradation.
PG  - e01183-14
AB  - Sphingomonas spp. are Alphaproteobacteria considered to be versatile bacteria that can utilize
      a variety of natural substrates available in terrestrial and
      aquatic systems. Sphingomonas sp. strain FukuSWIS1 was isolated from the
      eutrophic and acidic freshwater Lake Grosse Fuchskuhle in northeastern Germany.
      The strain has a genome size of 3.89 Mb, possesses a set of photosynthetic genes,
      and expresses photopigment BChl a under oxic conditions. Thus, this strain
      belongs to the aerobic anoxygenic phototrophic (AAP) bacteria, which are most
      likely involved in humic matter degradation as indicated by the presence of
      organic compound mineralizing genes.
AU  - Salka I
AU  - Srivastava A
AU  - Allgaier M
AU  - Grossart HP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01183-14.

PMID- 27014417
VI  - 11
DP  - 2016
TI  - Insights into the single cell draft genome of 'Candidatus Achromatium palustre'.
PG  - 28
AB  - 'Candidatus Achromatium palustre' was recently described as the first marine representative
      of the Achromatium spp. in the Thiotrichaceae - a sister lineage
      to the Chromatiaceae in the Gammaproteobacteria. Achromatium spp. belong to the
      group of large sulfur bacteria as they can grow to nearly 100 mum in size and
      store elemental sulfur (S(0)) intracellularly. As a unique feature, Achromatium
      spp. can accumulate colloidal calcite (CaCO3) inclusions in great amounts.
      Currently, both process and function of calcite accumulation in bacteria is
      unknown, and all Achromatium spp. are uncultured. Recently, three single-cell
      draft genomes of Achromatium spp. from a brackish mineral spring were published,
      and here we present the first draft genome of a single 'Candidatus Achromatium
      palustre' cell collected in the sediments of the Sippewissett Salt Marsh, Cape
      Cod, MA. Our draft dataset consists of 3.6 Mbp, has a G + C content of 38.1 % and
      is nearly complete (83 %). The next closest relative to the Achromatium spp.
      genomes is Thiorhodovibrio sp. 907 of the family Chromatiaceae, containing
      phototrophic sulfide-oxidizing bacteria.
AU  - Salman V
AU  - Berben T
AU  - Bowers RM
AU  - Woyke T
AU  - Teske A
AU  - Angert ER
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 28.

PMID- 29567740
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of the Live Attenuated Vaccine Strain Brucella melitensis Rev.1.
PG  - e00175-18
AB  - Live attenuated vaccines are essential elements in control programs for the prevention of
      brucellosis. Here, we report the whole-genome sequence of the
      original Elberg Brucella melitensis Rev.1 vaccine strain, passage 101 (1970).
      Commercial lines of the original strain have been successfully used in small
      ruminants worldwide.
AU  - Salmon-Divon M
AU  - Banai M
AU  - Bardenstein S
AU  - Blum SE
AU  - Kornspan D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00175-18.

PMID- 28385841
VI  - 5
DP  - 2017
TI  - Genome Sequences of Two Naphthalene-Degrading Strains of Pseudomonas balearica, Isolated from Polluted Marine Sediment and from an Oil Refinery Site.
PG  - e00116-17
AB  - The genome sequences of Pseudomonas balearica strains LS401 (CCUG 66666) and st101 (CCUG
      66667) have been determined. The strains were isolated as naphthalene
      degraders from polluted marine sediment and from a sample from an oil refinery
      site, respectively. These genomes provide essential data about the biodegradation
      capabilities and the ecological implications of P. balearica.
AU  - Salva-Serra F
AU  - Jakobsson HE
AU  - Busquets A
AU  - Gomila M
AU  - Jaen-Luchoro D
AU  - Segui C
AU  - Aliaga-Lozano F
AU  - Garcia-Valdes E
AU  - Lalucat J
AU  - Moore ER
AU  - Bennasar-Figueras A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00116-17.

PMID- 27013051
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Streptococcus gordonii Type Strain CCUG 33482T.
PG  - e00175-16
AB  - Streptococcus gordoniitype strain CCUG 33482(T)is a member of theStreptococcus mitisgroup,
      isolated from a case of subacute bacterial endocarditis. Here, we
      report the draft genome sequence ofS. gordoniiCCUG 33482(T), composed of 41
      contigs of a total size of 2.15 Mb with 2,061 annotated coding sequences.
AU  - Salva-Serra F
AU  - Jakobsson HE
AU  - Thorell K
AU  - Gonzales-Siles L
AU  - Hallback ET
AU  - Jaen-Luchoro D
AU  - Boulund F
AU  - Sikora P
AU  - Karlsson R
AU  - Svensson L
AU  - Bennasar A
AU  - Engstrand L
AU  - Kristiansson E
AU  - Moore ER
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00175-16.

PMID- 24503999
VI  - 2
DP  - 2014
TI  - First draft genome sequence of a member of the genus planomicrobium, isolated from the chandra river, India.
PG  - e01259-13
AB  - We report the first draft genome sequence of a member of the genus Planomicrobium, isolated
      from a soil sample from the Chandra River, located in
      the cold deserts of Himachal Pradesh, India. The draft genome assembly for
      Planomicrobium glaciei strain CHR43 has a size of 3,900,800 bp with a G+C content
      of 46.97%.
AU  - Salwan R
AU  - Swarnkar MK
AU  - Singh AK
AU  - Kasana RC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01259-13.

PMID- 18452608
VI  - 9
DP  - 2008
TI  - Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A.
PG  - 204
AB  - BACKGROUND: Xanthomonas oryzae pv. oryzae causes bacterial blight of rice (Oryza sativa L.), a
      major disease that constrains production of this
      staple crop in many parts of the world. We report here on the complete
      genome sequence of strain PXO99A and its comparison to two previously
      sequenced strains, KACC10331 and MAFF311018, which are highly similar to
      one another. RESULTS: The PXO99A genome is a single circular chromosome of
      5,240,075 bp, considerably longer than the genomes of the other strains
      (4,941,439 bp and 4,940,217 bp, respectively), and it contains 5083
      protein-coding genes, including 87 not found in KACC10331 or MAFF311018.
      PXO99A contains a greater number of virulence-associated transcription
      activator-like effector genes and has at least ten major chromosomal
      rearrangements relative to KACC10331 and MAFF311018. PXO99A contains
      numerous copies of diverse insertion sequence elements, members of which
      are associated with 7 out of 10 of the major rearrangements. A
      rapidly-evolving CRISPR (clustered regularly interspersed short
      palindromic repeats) region contains evidence of dozens of phage
      infections unique to the PXO99A lineage. PXO99A also contains a unique,
      near-perfect tandem repeat of 212 kilobases close to the replication
      terminus. CONCLUSION: Our results provide striking evidence of genome
      plasticity and rapid evolution within Xanthomonas oryzae pv. oryzae. The
      comparisons point to sources of genomic variation and candidates for
      strain-specific adaptations of this pathogen that help to explain the
      extraordinary diversity of Xanthomonas oryzae pv. oryzae genotypes and
      races that have been isolated from around the world.
AU  - Salzberg SL et al
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2008 9: 204.

PMID- 29051257
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Halophilic Hahella sp. Strain CCB-MM4, Isolated from Matang Mangrove Forest in Perak, Malaysia.
PG  - e01147-17
AB  - Hahella sp. strain CCB-MM4 is a halophilic bacterium isolated from estuarine mangrove
      sediment. The genome sequence of Hahella sp. CCB-MM4 provides insights
      into exopolysaccharide biosynthesis and the lifestyle of the bacterium thriving
      in a saline mangrove environment.
AU  - Sam KK
AU  - Lau NS
AU  - Furusawa G
AU  - Amirul AA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01147-17.

PMID- 11243793
VI  - 306
DP  - 2001
TI  - Catalytic efficiency and sequence selectivity of a restriction endonuclease modulated by a distal manganese ion binding site.
PG  - 851-861
AB  - Crystal structures of EcoRV endonuclease bound in a ternary complex with cognate duplex DNA
      and manganese ions have previously revealed an Mn2+-binding site located between the enzyme
      and the DNA outside of the dyad-symmetric GATATC recognition sequence. In each of the two
      enzyme subunits, this metal ion bridges between a distal phosphate group of the DNA and the
      imidazole ring of His71. The new metal-binding site is specific to Mn2+ and is not occupied in
      ternary cocrystal structures with either Mg2+ or Ca2+. Characterization of the H71A and H71Q
      mutants of EcoRV now demonstrates that these distal Mn2+ sites significantly modulate activity
      toward both cognate and non-cognate DNA substrates. Single-turnover and steady-state kinetic
      analyses show that removal of the distal site in the mutant enzymes increases Mn2+-dependent
      cleavage rates of specific substrates by tenfold. Conversely, the enhancement of non-cognate
      cleavage at GTTATC sequences by Mn2+ is significantly attenuated in the mutants. As a
      consequence, under Mn2+ conditions Eco RV-H71A and EcoRV-H71Q are 100 to 700-fold more
      specific than the wild-type enzyme for cognate DNA relative to the GTTATC non-cognate site.
      These data reveal a strong dependence of DNA cleavage efficiency upon metal ion-mediated
      interactions located some 20 ? distant from the scissile phosphodiester linkages.  They also
      show that discrimination of cognate versus non-cognate DNA sequences by EcoRV depends in part
      on contacts with the sugar-phosphate backbone outside of the target site.
AU  - Sam MD
AU  - Horton NC
AU  - Nissan TA
AU  - Perona JJ
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2001 306: 851-861.

PMID- 
VI  - 121
DP  - 1999
TI  - Mn2+-dependent catalysis by restriction enzymes: Pre-steady-state analysis of EcoRV endonuclease reveals burst kinetics and the origins of reduced activity.
PG  - 1444-1447
AB  - The origins of divalent metal-dependent catalytic properties in phosphoryl transfer by EcoRV
      endonuclease have been investigated by transient kinetic methods.  Pre-steady-state
      measurements on short oligodeoxynucleotide substrates reveal a burst of product formation for
      both Mg2+- and Mn2+-catalyzed DNA cleavage reactions, indicating that for each metal ion the
      product release step is partially or completely rate-limiting.  However, the steepness of the
      burst is far greater for Mn2+ reactions, and analysis of the steady-state portions of the
      reaction profiles shows that the overall rate is 6-fold slower in the presence of this
      cofactor.  The strongly rate-limiting product release step in Mn2+ reactions may arise from
      the higher intrinsic affinity of this metal ion for phosphates.  Single-turnover experiments
      carried out with enzyme in molar excess over DNA were also used to isolate the chemical step
      of the reaction.  In contrast to the slower steady-state rates, both these measurements and
      the pre-steady-state reaction bursts show that the bond-breaking and bond-making steps are
      significantly better catalyzed by Mn2+.  This supports models for catalysis deduced from X-ray
      crystal structures of the enzyme-substrate DNA complex, in which a divalent metal ion is
      directly ligated to the pro-Sp oxygen of the scissile group.
AU  - Sam MD
AU  - Perona JJ
PT  - Journal Article
TA  - J. Am. Chem. Soc.
JT  - J. Am. Chem. Soc.
SO  - J. Am. Chem. Soc. 1999 121: 1444-1447.

PMID- 10350476
VI  - 38
DP  - 1999
TI  - Catalytic roles of divalent metal ions in phosphoryl transfer by EcoRV endonuclease.
PG  - 6576-6586
AB  - The rate constant for the phosphoryl transfer step in site-specific DNA cleavage by EcoRV
      endonuclease has been determined as a function of pH and identity of the required divalent
      metal ion cofactor, for both wild-type and T93A mutant enzymes. These measurements show
      bell-shaped pH-rate curves for each enzyme in the presence of Mg2+ as a cofactor, indicating
      general base catalysis for the nucleophilic attack of hydroxide ion on the scissile phosphate,
      and general acid catalysis for protonation of the leaving 3'-O anion. The kinetic data
      support a model for phosphoryl transfer based on wild-type and T93A cocrystal structures, in
      which the ionizations of two distinct metal-ligated waters respectively generate the attacking
      hydroxide ion and the proton for donation to the leaving group. The model concurs with recent
      observations of two metal ions bound in the active sites of the type II restriction
      endonucleases BamHI and BglI, suggesting the possibility of a similar catalytic mechanism
      functioning in many or all members of this enzyme family.
AU  - Sam MD
AU  - Perona JJ
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1999 38: 6576-6586.

PMID- 27795282
VI  - 4
DP  - 2016
TI  - High-Quality Draft Genome Sequence of an Endophytic Pseudomonas viridiflava Strain with Herbicidal Properties against Its Host, the Weed Lepidium draba L.
PG  - e01170-16
AB  - Here, we report the draft genome sequence of Pseudomonas viridiflava strain CDRTc14 a
      pectinolytic bacterium showing herbicidal activity, isolated from the
      root of Lepidium draba L. growing as a weed in an Austrian vineyard. The
      availability of this genome sequence allows us to investigate the genetic basis
      of plant-microbe interactions.
AU  - Samad A
AU  - Trognitz F
AU  - Antonielli L
AU  - Compant S
AU  - Sessitsch A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01170-16.

PMID- 25953162
VI  - 3
DP  - 2015
TI  - Genome Sequence of Rhodococcus sp. Strain PML026, a Trehalolipid Biosurfactant Producer and Biodegrader of Oil and Alkanes.
PG  - e00433-15
AB  - Rhodococcus sp. strain PML026 produces an array of trehalolipid biosurfactant compounds in
      order to utilize hydrophobic carbon sources, such as oils and
      alkanes. Here, we report the high-quality draft genome sequence of this strain,
      which has a total length of 5,168,404 bp containing 4,835 protein-coding
      sequences, 12 rRNAs, and 45 tRNAs.
AU  - Sambles CM
AU  - White DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00433-15.

PMID- 7695650
VI  - 20
DP  - 1994
TI  - Isolation, purification and characterization of new site-specific endonucleases BciBI and BciBII produced by Bacillus circulans.
PG  - 1327-1333
AB  - New site-specific endonucleases BciBI and BciBII have been detected in Bacillus circulans. The
      enzymes were purified by fractionation of cell-free extract with polyethylene imine and
      ammonium sulphate (40-80% of saturation) followed by chromatography on DEAE-sepharose,
      blue-sepharose and phosphocellulose. The endonucleases BciBI and BciBII were separated only at
      the final step of the purification -- by chromatography on the phosphocellulose column. The
      yields of BciBI and BciBII were 600 and 10,000 U/g of cells. It was found that restriction
      endonucleases BciBI and BciBII are isoschizomers of ClaI and BstNI, respectively.
AU  - Samko OT
AU  - Kalugin AA
AU  - Eldarov MA
AU  - Karpychev IV
AU  - Anikeitcheva NV
AU  - Khoroshutina EB
AU  - Skryabin KG
AU  - Librik GI
AU  - Sokolov NN
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1994 20: 1327-1333.

PMID- 24709259
VI  - 58
DP  - 2014
TI  - Detection of OXA-370, an OXA-48-Related Class D beta-Lactamase, in Enterobacter hormaechei from Brazil.
PG  - 3566-3567
AB  - The class D B-lactamase OXA-48 (1) and its variants have emerged as important determinants of
      carbapenem resistance in Enterobacteriaceae, representing a public health concern in some
      countries (2-4). The objective of this study was to report a new OXA-48 variant.
AU  - Sampaio JL
AU  - Ribeiro VB
AU  - Campos JC
AU  - Rozales FP
AU  - Magagnin CM
AU  - Falci DR
AU  - da Silva RC
AU  - Dalarosa MG
AU  - Luz DI
AU  - Vieira FJ
AU  - Antochevis LC
AU  - Barth AL
AU  - Zavascki AP
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2014 58: 3566-3567.

PMID- Not carried by PubMed...
VI  - 95
DP  - 1995
TI  - A DNA cytosine methyltransferase-like gene in Streptococcal conjugative transposon, Tn5252.
PG  - 511
AB  - Tn5252, a 47 kb element, belongs to a distinct class of conjugative transposons mediating
      multiple antibiotic resistance in Streptococci.  To determine the physical structure of the
      element, fragments of transposon DNA were cloned into Escherichia coli.  However, a 3.27 kb
      EcoRI segment of DNA carrying the right junction region could not be cloned on several of the
      commonly used high copy E. coli plasmid vectors, even though portions of this DNA segment
      could be independently cloned.  Using these the DNA sequence of this region was obtained and
      was found to carry an open reading frame (ORF6).  Genbank analysis of the predicted amino acid
      sequence of ORF6 detected extensive homology to a number of prokaryotic cytosine
      methyltransferases.  To investigate the possible role of the cytosine methyltransferase-like
      gene in the conjugative transposition of Tn5252, insertion mutagenesis of this locus was
      carried out using the E. coli plasmid, pVA891.  Blot hybridization experiments confirmed the
      intended insertion mutation.  The newly created strain would be used as a donor in
      filter-mating experiments to determine the transferability of the element carrying the
      mutation.  Also we have cloned the 3.27 kb EcoRI fragment carrying the ORF6 in a Streptococcal
      plasmid, pLS1, which would be used in complementation experiments.
AU  - Sampath J
AU  - Vijayakumar MN
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1995 95: 511.

PMID- 9473447
VI  - 39
DP  - 1998
TI  - Identification of a DNA cytosine methyltransferase gene in conjugative transposon Tn5252.
PG  - 63-76
AB  - The nucleotide sequence of the 3.5-kb right junction fragment of the streptococcal conjugative
      transposon Tn5252 was obtained.  The DNA fragment was found to carry four putative genes one
      of which displayed a high degree of similarity to prokaryotic 5C-cytosine methyltransferases
      carrying multiple sequence specificities.  No cognate endonuclease gene was detected in the
      sequenced DNA.  Purified methylase polypeptide synthesized in a T7 promoter-controlled
      overexpression system was found to lack methylase activity while the cell extracts of host
      cells containing the recombinant plasmid carrying the methylase gene were active.  In vivo
      mutations in the methylase gene did not seem to affect the transferability of the element.
AU  - Sampath J
AU  - Vijayakumar MN
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 1998 39: 63-76.

PMID- 11923356
VI  - 40
DP  - 2002
TI  - Genetic and phenotypic differences between Legionella pneumophila strains.
PG  - 1352-1362
AB  - Legionnaires' disease is a potentially lethal pneumonia that is primarily due to infection by
      the species Legionella pneumophila, although more than 40 other species are known. Certain L.
      pneumophila subgroups, particularly serogroup 1, are associated with the majority of the
      epidemics. The genetic bases for these differences in virulence have not been determined.
      Three strains, AA100, JR32, and Lp01, have been used in many molecular pathogenesis studies of
      L. pneumophila. We found genetic differences between these strains by PCR and Southern
      analyses that may be related to their ability to cause disease. We also examined the
      distribution of these genetic loci in clinical and environmental isolates of Legionella and
      found a correlation between the presence of two of these loci, rtxA and lvh, and the ability
      to cause disease in humans. Examination of the interactions of these strains with host cells
      suggested that they differ in important phenotypic characteristics including adherence, entry,
      and intracellular replication. Furthermore, in the mouse model of infection they display
      differing levels of replication in lungs. These studies emphasize the importance of further
      investigation into the genetic makeup of these strains, which is likely to lead to the
      identification of additional factors involved in Legionella pathogenesis.
AU  - Samrakandi MM
AU  - Cirillo SLG
AU  - Ridenour DA
AU  - Bermudez LE
AU  - Cirillo JD
PT  - Journal Article
TA  - J. Clin. Microbiol.
JT  - J. Clin. Microbiol.
SO  - J. Clin. Microbiol. 2002 40: 1352-1362.

PMID- 23813728
VI  - 195
DP  - 2013
TI  - Effect of the abortive infection mechanism and type III toxin/antitoxin system AbiQ on the lytic cycle of Lactococcus lactis phages.
PG  - 3947-3956
AB  - To survive in phage-containing environments, bacteria have evolved an array of
      anti-phage systems. Similarly, phages have overcome these hurdles through various
      means. Here, we investigated how phages are able to circumvent the Lactococcus
      lactis AbiQ system, a type III toxin-antitoxin with antiviral activities.
      Lactococcal phage-escaping mutants were obtained in the laboratory and their
      genome sequenced. Three unrelated genes of unknown function were mutated in
      derivatives of three distinct lactococcal siphophages: orf38 of phage P008, m1 of
      phage bIL170, and e19 of phage c2. One-step growth curve experiments revealed
      that the phage mutations had a fitness cost while transcriptional analyses showed
      that AbiQ modified the early-expressed phage mRNAs profile. The L. lactis AbiQ
      system was also transferred into E. coli MG1655 and tested against several
      coliphages. While AbiQ was efficient against phages T4 (Myoviridae) and T5
      (Siphoviridae), escaping mutants of only phage 2 (Myoviridae) could be isolated.
      Genome sequencing revealed a mutation in gene orf210, a putative DNA polymerase.
      Taken altogether, different phages genes or genes products are targeted or
      involved in AbiQ phenotype. Moreover, this antiviral system is active against
      various phages families infecting Gram-positive and Gram-negative bacteria. A
      model for the mode of action of AbiQ is proposed.
AU  - Samson JE
AU  - Belanger M
AU  - Moineau S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2013 195: 3947-3956.

PMID- 23979432
VI  - 11
DP  - 2013
TI  - Revenge of the phages: defeating bacterial defences.
PG  - 675-687
AB  - Bacteria and their viral predators (bacteriophages) are locked in a constant battle. In order
      to proliferate in phage-rich environments, bacteria have an impressive arsenal of defence
      mechanisms, and in response, phages have evolved counter-strategies to evade these antiviral
      systems. In this Review, we describe the various tactics that are used by phages to overcome
      bacterial resistance mechanisms, including adsorption inhibition, restriction-modification,
      CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated
      proteins) systems and abortive infection. Furthermore, we consider how these observations have
      enhanced our knowledge of phage biology, evolution and phage-host interactions.
AU  - Samson JE
AU  - Magadan AH
AU  - Sabri M
AU  - Moineau S
PT  - Journal Article
TA  - Nat. Rev. Microbiol.
JT  - Nat. Rev. Microbiol.
SO  - Nat. Rev. Microbiol. 2013 11: 675-687.

PMID- 20802084
VI  - 76
DP  - 2010
TI  - Characterization of Lactococcus lactis phage 949 and comparison with other lactococcal phages.
PG  - 6843-6852
AB  - The virulent Lactococcus lactis phage 949 was isolated in 1975 from cheese
      whey in New Zealand. This phage is a member of the Siphoviridae family and
      of a rare lactococcal phage group that bears its name (949 group). It has
      an icosahedral capsid (79-nm diameter) and a very long noncontractile tail
      (length, 500 nm; width, 12 nm). It infected 7 of 59 tested L. lactis
      strains, a somewhat expanded host range for a rare lactococcal phage. The
      abortive phage infection defense mechanisms AbiQ and AbiT strongly
      inhibited the multiplication of phage 949, but AbiK and AbiV did not. Its
      double-stranded DNA (dsDNA) genome of 114,768 bp is, to date, the largest
      among lactococcal phages. Its GC content was calculated at 32.7%, which is
      the lowest reported for a lactococcal phage. Its 154 open reading frames
      (ORFs) share limited identity with database sequences. In addition,
      terminal redundancy was observed as well as the presence of six tRNAs, one
      group I intron, and putative recombinases. SDS-PAGE coupled with mass
      spectrometry identified 13 structural proteins. The genomes of the members
      of the 10 currently known L. lactis phage groups were used to construct a
      proteomic tree. Each L. lactis phage group separated into distinct genetic
      clusters, validating the current classification scheme. Of note, members
      of the polythetic P335 groups were clearly separated into subgroups.
AU  - Samson JE
AU  - Moineau S
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2010 76: 6843-6852.

PMID- 17563350
VI  - 104
DP  - 2007
TI  - Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut.
PG  - 10643-10648
AB  - The human gut is home to trillions of microbes, thousands of bacterial phylotypes, as well as
      hydrogen-consuming methanogenic archaea. Studies in
      gnotobiotic mice indicate that Methanobrevibacter smithii, the dominant
      archaeon in the human gut ecosystem, affects the specificity and
      efficiency of bacterial digestion of dietary polysaccharides, thereby
      influencing host calorie harvest and adiposity. Metagenomic studies of the
      gut microbial communities of genetically obese mice and their lean
      littermates have shown that the former contain an enhanced representation
      of genes involved in polysaccharide degradation, possess more archaea, and
      exhibit a greater capacity to promote adiposity when transplanted into
      germ-free recipients. These findings have led to the hypothesis that M.
      smithii may be a therapeutic target for reducing energy harvest in obese
      humans. To explore this possibility, we have sequenced its 1,853,160-bp
      genome and compared it to other human gut-associated M. smithii strains
      and other Archaea. We have also examined M. smithii's transcriptome and
      metabolome in gnotobiotic mice that do or do not harbor Bacteroides
      thetaiotaomicron, a prominent saccharolytic bacterial member of our gut
      microbiota. Our results indicate that M. smithii is well equipped to
      persist in the distal intestine through (i) production of surface glycans
      resembling those found in the gut mucosa, (ii) regulated expression of
      adhesin-like proteins, (iii) consumption of a variety of fermentation
      products produced by saccharolytic bacteria, and (iv) effective
      competition for nitrogenous nutrient pools. These findings provide a
      framework for designing strategies to change the representation and/or
      properties of M. smithii in the human gut microbiota.
AU  - Samuel BS
AU  - Hansen EE
AU  - Manchester JK
AU  - Coutinho PM
AU  - Henrissat B
AU  - Fulton R
AU  - Latreille P
AU  - Kim K
AU  - Wilson RK
AU  - Gordon JI
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2007 104: 10643-10648.

PMID- 16456032
VI  - 34
DP  - 2006
TI  - Engineering a rare-cutting restriction enzyme: genetic screening and selection of NotI variants.
PG  - 796-805
AB  - Restriction endonucleases (REases) with 8-base specificity are rare specimens in nature. NotI
      from Nocardia otitidis-caviarum (recognition
      sequence 5'-GCGGCCGC-3') has been cloned, thus allowing for mutagenesis
      and screening for enzymes with altered 8-base recognition and cleavage
      activity. Variants possessing altered specificity have been isolated by
      the application of two genetic methods. In step 1, variant E156K was
      isolated by its ability to induce DNA-damage in an indicator strain
      expressing M.EagI (to protect 5'-NCGGCCGN-3' sites). In step 2, the E156K
      allele was mutagenized with the objective of increasing enzyme activity
      towards the alternative substrate site: 5'-GCTGCCGC-3'. In this procedure,
      clones of interest were selected by their ability to eliminate a
      conditionally toxic substrate vector and induce the SOS response. Thus,
      specific DNA cleavage was linked to cell survival. The secondary
      substitutions M91V, F157C and V348M were each found to have a positive
      effect on specific activity when paired with E156K. For example, variant
      M91V/E156K cleaves 5'-GCTGCCGC-3' with a specific activity of 8.2 x 10(4)
      U/mg, a 32-fold increase over variant E156K. A comprehensive analysis
      indicates that the cleavage specificity of M91V/E156K is relaxed to a
      small set of 8 bp substrates while retaining activity towards the NotI
      sequence.
AU  - Samuelson JC
AU  - Morgan RD
AU  - Benner JS
AU  - Claus TE
AU  - Packard SL
AU  - Xu SY
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2006 34: 796-805.

PMID- 12054862
VI  - 319
DP  - 2002
TI  - Directed evolution of restriction endonuclease BstYI to achieve increased substrate specificity.
PG  - 673-683
AB  - Restriction endonucleases have proven to be especially resistant to engineering altered
      substrate specificity, in part, due to the requirement of a cognate DNA methyltransferase for
      cellular DNA protection. The thermophilic restriction endonuclease BstYI recognizes and
      cleaves all hexanucleotide sequences described by 5'-RGATCY-3' (where R=A or G and Y=C or
      T). The recognition of a degenerate sequence is a relatively common feature of the more than
      3000 characterized restriction endonucleases. However, very little is known concerning
      substrate recognition by such an enzyme. Our objective was to investigate the substrate
      specificity of BstYI by attempting to increase the specificity to recognition of only AGATCT.
      By a novel genetic selection/screening process, two BstYI variants were isolated with a
      preference for AGATCT cleavage. A fundamental element of the selection process is modification
      of the Escherichia coli host genomic DNA by the BglII N4-cytosine methyltransferase to protect
      AGATCT sites. The amino acid substitutions resulting in a partial change of specificity were
      identified and combined into one superior variant designated NN1. BstYI variant NN1 displays a
      12-fold preference for cleavage of AGATCT over AGATCC or GGATCT. Moreover, cleavage of the
      GGATCC sequence is no longer detected. This study provides further evidence that laboratory
      evolution strategies offer a powerful alternative to structure-guided protein design.
AU  - Samuelson JC
AU  - Xu S-Y
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2002 319: 673-683.

PMID- 15247348
VI  - 32
DP  - 2004
TI  - The isolation of strand-specific nicking endonucleases from a randomized SapI expression library.
PG  - 3661-3671
AB  - The Type IIS restriction endonuclease SapI recognizes the DNA sequence 5'-GCTCTTC-3' (top
      strand by convention) and cleaves downstream (N1/N4) indicating top- and bottom-strand
      spacing, respectively. The asymmetric nature of DNA recognition presented the possibility that
      one, if not two, nicking variants might be created from SapI. To explore this possibility, two
      parallel selection procedures were designed to isolate either top-strand nicking or
      bottom-strand nicking variants from a randomly mutated SapI expression library. These
      procedures take advantage of a SapI substrate site designed into the expression plasmid, which
      allows for in vitro selection of plasmid clones possessing a site-specific and strand-specific
      nick. A procedure designed to isolate bottom-strand nicking enzymes yielded Nb.SapI-1
      containing a critical R420I substitution near the end of the protein. The top-strand procedure
      yielded several SapI variants with a distinct preference for top-strand cleavage. Mutations
      present within the selected clones were segregated to confirm a top-strand nicking phenotype
      for single variants Q240R, E250K, G271R or K273R. The nature of the amino acid substitutions
      found in the selected variants provides evidence that SapI may possess two active sites per
      monomer. This work presents a framework for establishing the mechanism of SapI DNA cleavage.
AU  - Samuelson JC
AU  - Zhu Z
AU  - Xu S-y
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2004 32: 3661-3671.

PMID- 21914891
VI  - 193
DP  - 2011
TI  - Draft Genome Sequence of the Electricigen Acidiphilium sp. Strain PM (DSM 24941).
PG  - 5585-5586
AB  - Acidiphilium sp. strain PM (DSM 24941) was isolated from Rio Tinto's acidic, heavy metal-rich
      waters. Voltammetry experiments revealed that
      this strain is capable of electricity production even under aerobic
      conditions. Here we report the draft genome sequence of Acidiphilium sp.
      PM and a preliminary genome analysis that reveals a versatile respiratory
      metabolism.
AU  - San Martin-Uriz P
AU  - Gomez MJ
AU  - Arcas A
AU  - Bargiela R
AU  - Amils R
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5585-5586.

PMID- 28705977
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Two Mycobacterium bovis Strains Isolated from Beef Cattle in Paraguay.
PG  - e00616-17
AB  - This work reports the draft genome sequences of the Mycobacterium bovis strains M1009 and
      M1010, isolated from the lymph nodes of two infected cows on a beef
      farm in Paraguay. Comparative genomics between these strains and other regional
      strains may provide more insights regarding M. bovis epidemiology in South
      America.
AU  - Sanabria L
AU  - Lagrave L
AU  - Nishibe C
AU  - Ribas ACA
AU  - Zumarraga MJ
AU  - Almeida NF
AU  - Araujo FR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00616-17.

PMID- 11159979
VI  - 69
DP  - 2001
TI  - Gene discovery through genomic sequencing of Brucella abortus.
PG  - 865-868
AB  - Brucella abortus is the etiological agent of brucellosis, a disease that
      affects bovines and human. We generated DNA random sequences from the
      genome of B. abortus strain 2308 in order to characterize molecular
      targets that might be useful for developing immunological or
      chemotherapeutic strategies against this pathogen. The partial sequencing
      of 1,899 clones allowed the identification of 1,199 genomic sequence
      surveys (GSSs) with high homology (BLAST expect value < 10(-5)) to
      sequences deposited in the GenBank databases. Among them, 925 represent
      putative novel genes for the Brucella genus. Out of 925 nonredundant GSSs,
      470 were classified in 15 categories based on cellular function. Seven
      hundred GSSs showed no significant database matches and remain available
      for further studies in order to identify their function. A high number of
      GSSs with homology to Agrobacterium tumefaciens and Rhizobium meliloti
      proteins were observed, thus confirming their close phylogenetic
      relationship. Among them, several GSSs showed high similarity with genes
      related to nodule nitrogen fixation, synthesis of nod factors, nodulation
      protein symbiotic plasmid, and nodule bacteroid differentiation. We have
      also identified several B. abortus homologs of virulence and pathogenesis
      genes from other pathogens, including a homolog to both the Shda gene from
      Salmonella enterica serovar Typhimurium and the AidA-1 gene from
      Escherichia coli. Other GSSs displayed significant homologies to genes
      encoding components of the type III and type IV secretion machineries,
      suggesting that Brucella might also have an active type III secretion
      machinery.
AU  - Sanchez DO
AU  - Zandomeni RO
AU  - Cravero S
AU  - Verdun RE
AU  - Pierrou E
AU  - Faccio P
AU  - Diaz G
AU  - Lanzavecchia S
AU  - Aguero F
AU  - Frasch ACC
AU  - Andersson SGE
AU  - Rosetti OL
AU  - Grau O
AU  - Ugalde RA
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2001 69: 865-868.

PMID- 2998580
VI  - 31
DP  - 1985
TI  - Restriction-modification systems in Streptomyces antibioticus.
PG  - 942-946
AB  - Several restriction systems were detected in different strains of Streptomyces
      antibioticus by using actinophages as biological indicators. Adsorption of
      phages to the bacteria, together with the study of the efficiency of plating
      gave an initial indication of restriction in three strains. The alternation of
      efficiency of plating values obtained from restricting and nonrestricting
      hosts, detected among the different strains tested. Two specific endonucleases
      with a possible role in restriction were detected in strains ATCC 11891 and ETH
      7451, respectively.
AU  - Sanchez J
AU  - Barbes C
AU  - Hernandez A
AU  - de los Reyes-Gavilan CG
AU  - Hardisson C
PT  - Journal Article
TA  - Can. J. Microbiol.
JT  - Can. J. Microbiol.
SO  - Can. J. Microbiol. 1985 31: 942-946.

PMID- 
VI  - 9
DP  - 2018
TI  - Genomic Diversity in the Endosymbiotic Bacterium Rhizobium leguminosarum.
PG  - E60
AB  - Rhizobium leguminosarum bv. viciae is a soil -proteobacterium that establishes a diazotrophic
      symbiosis with different legumes of the Fabeae tribe. The number of genome sequences from
      rhizobial strains available in public databases is constantly increasing, although complete,
      fully annotated
      genome structures from rhizobial genomes are scarce. In this work, we report and analyse the
      complete genome of R. leguminosarum bv. viciae UPM791. Whole genome sequencing can provide new
      insights into the genetic features contributing to symbiotically relevant processes such as
      bacterial
      adaptation to the rhizosphere, mechanisms for efficient competition with other bacteria, and
      the ability to establish a complex signalling dialogue with legumes, to enter the root without
      triggering plant defenses, and, ultimately, to fix nitrogen within the host. Comparison of the
      complete genome sequences of two strains of R. leguminosarum bv. viciae, 3841 and UPM791,
      highlights the existence of different symbiotic plasmids and a common core chromosome.
      Specific genomic traits, such as plasmid content or a distinctive regulation, define
      differential physiological capabilities of these endosymbionts. Among them, strain UPM791
      presents unique adaptations for recycling the hydrogen generated in the nitrogen fixation
      process.
AU  - Sanchez-Canizares C
AU  - Jorrin B
AU  - Duran D
AU  - Nadendla S
AU  - Albareda M
AU  - Rubio-Sanz L
AU  - Lanza M
AU  - Gonzalez-Guerrero M
AU  - Prieto R
AU  - Brito B
AU  - Giglio M
AU  - Rey L
AU  - Ruiz-Argueso T
AU  - Palacios JM
AU  - Imperial J
PT  - Journal Article
TA  - Genes (Basel)
JT  - Genes (Basel)
SO  - Genes (Basel) 2018 9: E60.

PMID- 28774976
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Stenotrophomonas bentonitica BII-R7T, a Selenite-Reducing Bacterium Isolated from Spanish Bentonites.
PG  - e00719-17
AB  - The Gram-negative bacterium Stenotrophomonas bentonitica BII-R7T was isolated from bentonite
      formations. Like other species within the genus Stenotrophomonas,
      strain BII-R7T possesses high tolerance to numerous heavy metals, suggesting
      potential for bioremediation purposes. The draft genome sequence reported here
      comprises 4.37 Mb with a G+C content of 66.5% and 3,796 predicted protein-coding
      sequences.
AU  - Sanchez-Castro I
AU  - Bakkali M
AU  - Merroun ML
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00719-17.

PMID- 29146845
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of 23 Salmonella enterica Strains Isolated from Cattle in  Ibadan, Nigeria, Representing 21 Salmonella Serovars.
PG  - e01128-17
AB  - To provide a better understanding of the diversity of Salmonella enterica, we report the
      assembled genome sequences of 23 Salmonella enterica strains isolated from fecal samples of
      cattle in Nigeria comprising 21 different Salmonella serovars.
AU  - Sanchez-Leon M
AU  - Fashae K
AU  - Kastanis G
AU  - Allard M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01128-17.

PMID- 23516210
VI  - 1
DP  - 2013
TI  - Draft Genome of the Marine Gammaproteobacterium Halomonas titanicae.
PG  - e0008313
AB  - Halomonas titanicae strain BH1 is a heterotrophic, aerobic marine bacterium which was isolated
      from rusticles of the RMS Titanic wreck. Here we report the draft
      genome sequence of this halophilic gammaproteobacterium.
AU  - Sanchez-Porro C
AU  - de la Haba RR
AU  - Cruz-Hernandez N
AU  - Gonzalez JM
AU  - Reyes-Guirao C
AU  - Navarro-Sampedro L
AU  - Carballo M
AU  - Ventosa A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0008313.

PMID- 25818841
VI  - 25
DP  - 2015
TI  - DNA methylation in bacteria: from the methyl group to the methylome.
PG  - 9-16
AB  - Formation of C(5)-methyl-cytosine, N(4)-methyl-cytosine, and N(6)-methyl-adenine  in bacterial
      genomes is postreplicative, and occurs at specific targets. Base methylation can modulate the
      interaction of DNA-binding proteins with their cognate sites, and controls chromosome
      replication, correction of DNA mismatches, cell cycle-coupled transcription, and formation of
      epigenetic lineages by phase variation. During four decades, the roles of DNA methylation in
      bacterial physiology have been investigated by analyzing the contribution of individual methyl
      groups or small methyl group clusters to the control of DNA-protein interactions. Nowadays,
      single-molecule real-time sequencing can analyze the DNA methylation of the entire genome (the
      'methylome'). Bacterial methylomes provide a wealth of information on the methylation marks
      present in bacterial genomes, and may open a new era in bacterial epigenomics.
AU  - Sanchez-Romero MA
AU  - Cota I
AU  - Casadesus J
PT  - Journal Article
TA  - Curr. Opin. Microbiol.
JT  - Curr. Opin. Microbiol.
SO  - Curr. Opin. Microbiol. 2015 25: 9-16.

PMID- 25291767
VI  - 2
DP  - 2014
TI  - Genome Sequences of Two Nondomesticated Bacillus subtilis Strains Able To Form Thick Biofilms on Submerged Surfaces.
PG  - e00946-14
AB  - Genomes of two nondomesticated strains of Bacillus subtilis subspecies subtilis,  NDmed and
      NDfood, have been sequenced. Both strains form very thick and spatially
      complex biofilms on submerged surfaces. Moreover, biofilms of the NDmed isolate
      were shown to be highly resistant to antimicrobials action.
AU  - Sanchez-Vizuete P
AU  - Tanaka K
AU  - Bridier A
AU  - Shirae Y
AU  - Yoshida K
AU  - Bouchez T
AU  - Aymerich S
AU  - Briandet R
AU  - Le Coq D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00946-14.

PMID- 18502523
VI  - 74
DP  - 2008
TI  - Construction of a high-efficiency shuttle vector for Histophilus somni.
PG  - 106-109
AB  - The genetic manipulation of Histophilus somni is limited due to its high-fidelity
      restriction-modification system. The broad host-range
      shuttle plasmid pLS88 is capable of transforming some strains of H.
      somni, but is an inefficient vector. We have constructed an improved
      version of pLS88, pNS3K, that transforms H. somni strain 2336 100-fold
      more efficiently than its predecessor. The transformation efficiency
      was further increased when pNS3K was isolated from H. somni and
      retransformed into the same strain. As proof of principle, the
      lipooligosaccharide biosynthesis gene lob-2A was cloned into pNS3K and
      expressed in H. somni strain 129Pt, which lacks this gene. Thus, pNS3K
      is a useful shuttle vector for H. somni and a potential vector for
      genetic manipulation of this bacterium.
AU  - Sandal I
AU  - Seleem MN
AU  - Elswaifi SF
AU  - Sriranganathan N
AU  - Inzana TJ
PT  - Journal Article
TA  - J. Microbiol. Methods
JT  - J. Microbiol. Methods
SO  - J. Microbiol. Methods 2008 74: 106-109.

PMID- 21990049
VI  - 67
DP  - 2012
TI  - Transfer of an Escherichia coli ST131 multiresistance cassette has created a Klebsiella pneumoniae-specific plasmid associated with a major nosocomial outbreak.
PG  - 74-83
AB  - ObjectivesTo characterize the complete sequence, horizontal spread and
      stability of the CTX-M-15-encoding multiresistance plasmid of a Klebsiella
      pneumoniae strain involved in a large nosocomial outbreak.MethodsThe 220
      kbp plasmid pUUH239.2 was completely sequenced using 454 technology. The
      conjugational host range, conjugation frequencies, plasmid stability and
      fitness cost of plasmid carriage were studied in vitro. Conjugational
      spread during the outbreak was assessed retrospectively by multiplex PCR
      screening, restriction fragment length polymorphism and
      PFGE.ResultsPlasmid pUUH239.2 encodes resistance to beta-lactams
      (bla(CTX-M-15), bla(TEM-1) and bla(OXA-1)), aminoglycosides
      [aac-(6')-1b-cr and aadA2], tetracyclines [tet(A) and tetR], trimethoprim
      (dhfrXII), sulphonamides (sul1), quaternary ammonium compounds
      (qacEDelta1), macrolides [mph(A)-mxr-mphR(A)] and heavy metal ions
      (silver, copper and arsenic). The plasmid consists of a backbone, highly
      similar to the K. pneumoniae plasmid pKPN3, and a 41 kbp resistance
      region, highly similar to the resistance regions of plasmids pEK499 and
      pC15-1a previously isolated from Escherichia coli strains belonging to the
      outbreak lineage ST131 (where ST stands for sequence type). The pUUH239.2
      plasmid is stable in K. pneumoniae but unstable in E. coli and confers a
      fitness cost when introduced into a naive host cell. Transfer of pUUH239.2
      from the outbreak K. pneumoniae clone to the E. coli of the patients'
      intestinal floras has occurred on multiple occasions during the
      outbreak.ConclusionsThe plasmid pUUH239.2 is a composite of the pKPN3 K.
      pneumoniae plasmid backbone and the bla(CTX-M-15)-encoding multiresistance
      cassette associated with the internationally recognized outbreak strain E.
      coli ST131. The resulting plasmid differs in stability between K.
      pneumoniae and E. coli, and this has probably limited the spread of this
      plasmid during the outbreak.
AU  - Sandegren L
AU  - Linkevicius M
AU  - Lytsy B
AU  - Melhus A
AU  - Andersson DI
PT  - Journal Article
TA  - J. Antimicrob. Chemother.
JT  - J. Antimicrob. Chemother.
SO  - J. Antimicrob. Chemother. 2012 67: 74-83.

PMID- 16257983
VI  - 33
DP  - 2005
TI  - SegH and Hef: two novel homing endonucleases whose genes replace the mobC and mobE genes in several T4-related phages.
PG  - 6203-6213
AB  - T4 contains two groups of genes with similarity to homing endonucleases, the seg-genes ((s)
      over bar imilarity to (e) over bar
      ndonucleases encoded by (g) over bar roup I introns) containing GIY-YIG
      motifs and the mob-genes (similarity to mobile endonucleases)
      containing H-N-H motifs. The four seg-genes characterized to date
      encode homing endonucleases with cleavage sites close to their
      respective gene loci while none of the mob-genes have been shown to
      cleave DNA. Of 18 phages screened, only T4 was found to have mobC while
      mobE genes were found in five additional phages. Interestingly, three
      phages encoded a seg-like gene (hereby called segH) with a GIY-YIG
      motif in place of mobC. An additional phage has an unrelated gene
      called hef ((h) over bar oming (e) over bar ndonuclease-like (f) over
      bar unction) in place of the mobE gene. The gene products of both novel
      genes displayed homing endonuclease activity with cleavage site
      specificity close to their respective genes. In contrast to intron
      encoded homing endonucleases, both SegH and Hef can cleave their own
      DNA as well as DNA from phages without the genes. Both segH and mobE
      (and most likely hef) can home between phages in mixed infections. We
      discuss why it might be a selective advantage for phage freestanding
      homing endonucleases to cleave both HEG-containing and HEG-less
      genomes.
AU  - Sandegren L
AU  - Nord D
AU  - Sjoberg BM
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2005 33: 6203-6213.

PMID- 15026408
VI  - 279
DP  - 2004
TI  - Distribution, sequence homology, and homing of group I introns among T-even-like bacteriophages: evidence for recent transfer of old introns.
PG  - 22218-22227
AB  - Self-splicing group I introns are being found in an increasing number of bacteriophages. Most
      introns contain an open reading frame coding for a homing endonuclease that confers mobility
      to both the intron and the homing endonuclease gene (HEG). The frequent occurrence of
      intron/HEG has raised questions whether group I introns are spread via horizontal transfer
      between phage populations. We have determined complete sequences for the known group I introns
      among T-even-like bacteriophages together with sequences of the intron-containing genes td,
      nrdB, and nrdD from phages with and without introns. A previously uncharacterized phage
      isolate, U5, is shown to contain all three introns, the only phage besides T4 found with a
      "full set" of these introns. Sequence analysis of td and nrdB genes from intron-containing and
      intronless phages provides evidence that recent horizontal transmission of introns has
      occurred among the phages. The fact that several of the HEGs have suffered deletions rendering
      them non-functional implies that the homing endonucleases are of no selective advantage to the
      phage and are rapidly degenerating and probably dependent upon frequent horizontal
      transmissions for maintenance within the phage populations. Several of the introns can home to
      closely related intronless phages during mixed infections. However, the efficiency of homing
      varies and is dependent on homology in regions flanking the intron insertion site. The
      occurrence of optional genes flanking the respective intron-containing gene can strongly
      affect the efficiency of homing. These findings give further insight into the mechanisms of
      propagation and evolution of group I introns among the T-even-like bacteriophages.
AU  - Sandegren L
AU  - Sjoberg BM
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2004 279: 22218-22227.

PMID- 19223323
VI  - 37
DP  - 2009
TI  - Targeting individual subunits of the FokI restriction endonuclease to specific DNA strands.
PG  - 2105-2115
AB  - Many restriction endonucleases are dimers that act symmetrically at palindromic DNA sequences,
      with each active site cutting one strand. In
      contrast, FokI acts asymmetrically at a non-palindromic sequence, cutting
      'top' and 'bottom' strands 9 and 13 nucleotides downstream of the site.
      FokI is a monomeric protein with one active site and a single monomer
      covers the entire recognition sequence. To cut both strands, the monomer
      at the site recruits a second monomer from solution, but it is not yet
      known which DNA strand is cut by the monomer bound to the site and which
      by the recruited monomer. In this work, mutants of FokI were used to show
      that the monomer bound to the site made the distal cut in the bottom
      strand, whilst the recruited monomer made in parallel the proximal cut in
      the top strand. Procedures were also established to direct FokI activity,
      either preferentially to the bottom strand or exclusively to the top
      strand. The latter extends the range of enzymes for nicking specified
      strands at specific sequences, and may facilitate further applications of
      FokI in gene targeting.
AU  - Sanders KL
AU  - Catto LE
AU  - Bellamy SR
AU  - Halford SE
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: 2105-2115.

PMID- 3139060
VI  - 70
DP  - 1988
TI  - Phage resistance in lactic acid bacteria.
PG  - 411-422
AB  - The interactions between lactic acid bacteria and their phages are commercially
      significant.  Current research has focused on the elucidation of the mechanisms
      and genetics of phage resistance.  Phage resistance genes have been linked to
      plasmid DNA for Streptococcus lactis and Streptococcus cremoris, and
      preliminary studies suggest the operation of mechanisms such as the prevention
      of phage adsorption, restriction/modification, and abortive infection.  Some
      phage resistance plasmids can be conjugally transferred, providing a means of
      dissemination among phage-sensitive strains for the construction of
      phage-resistant starter cultures.
AU  - Sanders ME
PT  - Journal Article
TA  - Biochimie
JT  - Biochimie
SO  - Biochimie 1988 70: 411-422.

PMID- 16345908
VI  - 42
DP  - 1981
TI  - Evidence for plasmid linkage of restriction and modification in Streptococcus cremoris KH.
PG  - 944-950
AB  - Restriction and modification have been demonstrated in Streptococcus cremoris
      KH cells when infected by Streptococcus lactis C2 phage (designated c2) at an
      efficiency of plating of 2 X 10-7.  The growth of c2 phage through KH cells
      produces modified progeny phage capable of unrestricted growth on KH cells.
      The ability of single-colony isolates of S. cremoris KH cultures to restrict
      and modify c2 phage was found to be variable.  From 2 to 6.5% of colonies
      isolated were partially deficient in restrictive capacity, permitting a greater
      plaquing ability by c2 phage of 1.8 to 2.9 log cycles.  No completely
      restrictionless mutants were isolated from 1,000 colonies examined.  Mutants
      were shown to be deficient in both restriction and modification capabilities of
      the same specificity.  The frequent occurrence of a genotypic change that
      resulted in the loss of both restriction and modification capacities indicated
      the involvement of plasmid deoxyribonucleic acid in genetically determining
      this specific restriction and modification system.  S. cremoris KH was found to
      harbor 11 plasmid molecules, with molecular weights (X10-6) estimated to be 50,
      41, 24, 18, 10, 7.4, 3.3, 3.0, 2.8, 2.5, and 1.5.  Of the 27 mutants examined,
      25 were missing the 10-megadalton plasmid.  This consistent plasmid difference
      among the majority of mutants isolated supports the involvement of this plasmid
      in restriction and modification.  Plasmid linkage of restriction and
      modification systems provides a genetic mechanism for the rapid development of
      phage-sensitive starter cultures due to the inherent instability of
      extrachromosomal elements.
AU  - Sanders ME
AU  - Klaenhammer TR
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1981 42: 944-950.

PMID- 16346553
VI  - 47
DP  - 1984
TI  - Phage resistance in a phage-insensitive strain of Streptococcus lactis:  temperature-dependent phage development and host-controlled phage replication.
PG  - 979-985
AB  - Streptococcus lactis ME2 is a dairy starter strain that is insensitive to a
      variety of phage, including Phi18.  The efficiency of plating of Phi18 on ME2
      and N1 could be increased from <1 X 10-9 to 5.0 X 10-2 and from 7.6 X 10-7 to
      2.1 X 10-2, respectively, when the host strains were subcultured at 40C before
      plating the phage and the phage assay plates were incubated at 40C.
      Host-dependent replication was demonstrated in N1 at 30C and in N1 and ME2 at
      40C, suggesting the operation of a temperature-sensitive restriction and
      modification system in MER2 and N1.  The increased sensitivity of ME2 and N1 to
      Phi18 at 40C was also demonstrated by lysis of broth cultures and increased
      plaque size.  ME2 grown at 40C showed an increased ability to adsorb Phi18,
      indicating a second target for temperature-dependent phage sensitivity in ME2.
      Challenge of N1 with a Phi18 preparation that had been previously modified for
      growth on N1 indicated that at 40C phage development was characterized by a
      shorter latent period and larger burst size than at 30C.  The evidence
      presented suggests that the high degree of phage insensitivity expressed by ME2
      consists of a variety of temperature-sensitive mechanisms, including (i) the
      prevention of phage adsorption, (ii) host-controlled restriction of phage, and
      (iii) suppression of phage development.  At 30C these factors appear to act
      cooperatively to prevent the successful emergence of lytic phage active against
      S. lactis ME2.
AU  - Sanders ME
AU  - Klaenhammer TR
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1984 47: 979-985.

PMID- 16345629
VI  - 40
DP  - 1980
TI  - Restriction and modification in group N streptococci: Effect of heat on development of modified lytic bacteriophage.
PG  - 500-506
AB  - The appearance of lytic bacteriophage against newly introduced starter strains used during
      commercial cheese manufacture occurs rapidly, and their origin is not well understood.  In
      this study, members of the group N streptococci were examined for the presence of
      bacteriophage restriction and modification systems.  Two streptococcal phages from
      Streptococcus cremoris TR and Streptococcus lactis C2 (phage designations tr and c2) showed
      restricted lytic development on S. cremoris 799 and KH, respectively.  Efficiency of plaquing
      was 1.9 x 10^-7 for tr plaqued on 799 and 2.1 x 10^-7 for c2 plaqued on KH.  After passage
      through the restrictive hosts, these phages demonstrated high  lytic ability for formerly
      restrictive hosts.  Stress of the restrictive host strains at temperatures of 40 to 50oC
      resulted in a significant increase in the efficiency of plaquing of restricted bacteriophages.
      Elevated temperatures are encountered during commercial cheese manufacture.  The results
      suggested that the temporary loss of host restriction activity with the resulting modification
      of nonspecific bacteriophage may contribute directly to the appearance of lytic phage against
      new starter strains.
AU  - Sanders ME
AU  - Klaenhammer TR
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1980 40: 500-506.

PMID- 16346419
VI  - 46
DP  - 1983
TI  - Characterization of phage-sensitive mutants from a phage-insensitive strain of Streptococcus lactis: Evidence for a plasmid determinant that prevents phage adsorption.
PG  - 1125-1133
AB  - A phage-insensitive strain of Streptococcus lactis, designated ME2, was used as a prototype
      strain for the study of mechanisms and genetics of phage resistance in the lactic
      streptococci.  Mutants sensitive to a Streptococcus cremoris phage, Phi18, were isolated at a
      level of 17% from cultures of ME2 after sequential transfer at 30oC.  Phage-sensitive mutants
      of ME2 were not fully permissive to Phi18.  The efficiency of plating of Phi18 on the mutants
      was 5 x 10^-7 as compared with <10^-0 for Phi18 on ME2.  Further characterization of the
      mutants showed that they efficiently adsorbed Phi18 at levels of >99.8%, whereas ME2 adsorbed
      only 20 to 40% of Phi18.  These results suggest that increased phage susceptibility of the
      mutants may result from the loss of a mechanism that inhibits phage adsorption.  Moreover, the
      high frequency of spontaneous mutation in ME2 indicates the involvement of an unstable genetic
      determinant in this phage defense mechanism.  ME2 was shown to possess 13 plasmids ranging in
      size from 1.6 to 34 megadaltons.  Of 40 mutants examined that had increased efficiencies of
      plating, all were missing a 30-megadalton plasmid, pME0030.  These data suggest that pME0030
      codes for a function that prevents phage adsorption.  Further phenotypic characterization of
      the phage-sensitive mutants showed that some mutants were deficient in the ability to ferment
      lactose and hydrolyze milk proteins.  However, the Lac+ and Prt+ phenotype segregated
      independently of the phage-sensitivity phenotype.  One phage-sensitive adsorption mutant,
      designated N1, was tested for susceptibility to 14 different phages.  N1 showed increased
      capacity to adsorb 4 and to replicate 2 of these 14 phages, thereby indicating a phage
      resistance mechanism in ME2 that generalizes to phage interactions other than the specific
      o18-ME2 phage-host interaction.  These data provide evidence for a unique plasmid-linked phage
      defense mechanism in phage-insensitive strains of lactic streptococci.
AU  - Sanders ME
AU  - Klaenhammer TR
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1983 46: 1125-1133.

PMID- Not included in PubMed...
VI  - 73
DP  - 1990
TI  - Cloning of phage resistance genes from Lactococcus lactis ssp. cremoris KH.
PG  - 2044-2053
AB  - A 17.5-kb plasmid conferring restriction and modification-type phage resistance
      in Lactococcus lactis ssp. cremoris KH was transformed into Lactococcus lactis
      LM0230 and cloned onto an origin of replication-deficient vector directly into
      L. lactis.  Expression of phage resistance was seen in L. lactis but not in E.
      coli.  A restriction map was generated of the cloned plasmid, and the region
      encoding phage resistance was localized by insertional inactivation and
      deletion analysis.
AU  - Sanders ME
AU  - Shultz JW
PT  - Journal Article
TA  - J. Dairy Sci.
JT  - J. Dairy Sci.
SO  - J. Dairy Sci. 1990 73: 2044-2053.

PMID- 26798087
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Serratia marcescens SmUNAM836, a Nonpigmented Multidrug-Resistant Strain Isolated from a Mexican Patient with Obstructive  Pulmonary Disease.
PG  - e01417-15
AB  - Serratia marcescens SmUNAM836 is a multidrug-resistant clinical strain isolated in Mexico City
      from a patient with chronic obstructive pulmonary disease. Its
      complete genome sequence was determined using PacBio RS II SMRT technology,
      consisting of a 5.2-Mb chromosome and a 26.3-kb plasmid, encoding multiple
      resistance determinants and virulence factors.
AU  - Sandner-Miranda L
AU  - Vinuesa P
AU  - Soberon-Chavez G
AU  - Morales-Espinosa R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01417-15.

PMID- 26705421
VI  - 8
DP  - 2015
TI  - Whole-genome sequence of an evolved Clostridium pasteurianum strain reveals Spo0A deficiency responsible for increased butanol production and superior growth.
PG  - 227
AB  - BACKGROUND: Biodiesel production results in crude glycerol waste from the transesterification
      of fatty acids (10 % w/w). The solventogenic Clostridium
      pasteurianum, an anaerobic Firmicute, can produce butanol from glycerol as the
      sole carbon source. Coupling butanol fermentation with biodiesel production can
      improve the overall economic viability of biofuels. However, crude glycerol
      contains growth-inhibiting byproducts which reduce feedstock consumption and
      solvent production. RESULTS: To obtain a strain with improved characteristics, a
      random mutagenesis and directed evolution selection technique was used. A
      wild-type C. pasteurianum (ATCC 6013) culture was chemically mutagenized, and the
      resulting population underwent 10 days of selection in increasing concentrations
      of crude glycerol (80-150 g/L). The best-performing mutant (M150B) showed a 91 %
      increase in butanol production in 100 g/L crude glycerol compared to the
      wild-type strain, as well as increased growth rate, a higher final optical
      density, and less production of the side product PDO (1,3-propanediol). Wild-type
      and M150B strains were sequenced via Single Molecule Real-Time (SMRT) sequencing.
      Mutations introduced to the M150B genome were identified by sequence comparison
      to the wild-type and published closed sequences. A major mutation (a deletion) in
      the gene of the master transcriptional regulator of sporulation, Spo0A, was
      identified. A spo0A single gene knockout strain was constructed using a
      double--crossover genome-editing method. The Spo0A-deficient strain showed
      similar tolerance to crude glycerol as the evolved mutant strain M150B.
      Methylation patterns on genomic DNA identified by SMRT sequencing were used to
      transform plasmid DNA to overcome the native C. pasteurianum restriction
      endonuclease. CONCLUSIONS: Solvent production in the absence of Spo0A shows C.
      pasteurianum differs in solvent-production regulation compared to other
      solventogenic Clostridium. Growth-associated butanol production shows C.
      pasteurianum to be an attractive option for further engineering as it may prove a
      better candidate for butanol production through continuous fermentation.
AU  - Sandoval NR
AU  - Venkataramanan KP
AU  - Groth TS
AU  - Papoutsakis ET
PT  - Journal Article
TA  - Biotechnol. Biofuels.
JT  - Biotechnol. Biofuels.
SO  - Biotechnol. Biofuels. 2015 8: 227.

PMID- 1975563
VI  - 26
DP  - 1990
TI  - A computer program to assist in the choice of restriction endonucleases for use in DNA analysis.
PG  - 39-52
AB  - Type II restriction endonucleases cleave double stranded DNA molecules at sites characterized
      by one or more sets of nucleotide pairs sequences. These digestions are essential in such
      procedures as DNA cloning, DNA sequencing and restriction fragment length polymorphism (RFLP)
      analyses. A large number of enzymes with different sequence specificities are available. To
      date, most choices of restriction endonucleases have been made by trial and error. A computer
      program, REDI, has been developed that predicts the ability of a particular restriction enzyme
      to detect mutations. Characteristics of both the restriction endonuclease used and the DNA
      being cut are incorporated as variables in the program. The program was tested using mouse
      mitochondrial DNA (mtDNA) and bacteriophage lambda DNA because these have been sequenced and
      are well characterized. REDI was strongly correlated (rs = +0.862, n = 11, P less than 0.001)
      with mouse mtDNA RFLP detected by Ferris et al. [1] (Genetics, 105 (1983) 681-721). Even
      though predictions may be altered by a non-random association of nucleotides, which varies
      among DNA molecules, the predictions increase the probability of selecting the most efficient
      enzymes for use in the analysis of a particular DNA molecule.
AU  - Sands TW
AU  - Petras ML
AU  - Van Wijngaarden J
PT  - Journal Article
TA  - Int. J. Biomed. Comput.
JT  - Int. J. Biomed. Comput.
SO  - Int. J. Biomed. Comput. 1990 26: 39-52.

PMID- 26452736
VI  - 16
DP  - 2015
TI  - Adherence and invasive properties of Corynebacterium diphtheriae strains correlates with the predicted membrane-associated and secreted proteome.
PG  - 765
AB  - BACKGROUND: Non-toxigenic Corynebacterium diphtheriae strains are emerging as a
      major cause of severe pharyngitis and tonsillitis as well as invasive diseases
      such as endocarditis, septic arthritis, splenic abscesses and osteomyelitis. C.
      diphtheriae strains have been reported to vary in their ability to adhere and
      invade different cell lines. To identify the genetic basis of variation in the
      degrees of pathogenicity, we sequenced the genomes of four strains of C.
      diphtheriae (ISS 3319, ISS 4060, ISS 4746 and ISS 4749) that are well
      characterised in terms of their ability to adhere and invade mammalian cells.
      RESULTS: Comparative analyses of 20 C. diphtheriae genome sequences, including 16
      publicly available genomes, revealed a pan-genome comprising 3,989 protein coding
      sequences that include 1,625 core genes and 2,364 accessory genes. Most of the
      genomic variation between these strains relates to uncharacterised genes encoding
      hypothetical proteins or transposases. Further analyses of protein sequences
      using an array of bioinformatic tools predicted most of the accessory proteome to
      be located in the cytoplasm. The membrane-associated and secreted proteins are
      generally involved in adhesion and virulence characteristics. The genes encoding
      membrane-associated proteins, especially the number and organisation of the pilus
      gene clusters (spa) including the number of genes encoding surface proteins with
      LPXTG motifs differed between different strains. Other variations were among the
      genes encoding extracellular proteins, especially substrate binding proteins of
      different functional classes of ABC transport systems and 'non-classical'
      secreted proteins. CONCLUSIONS: The structure and organisation of the spa gene
      clusters correlates with differences in the ability of C. diphtheriae strains to
      adhere and invade the host cells. Furthermore, differences in the number of genes
      encoding membrane-associated proteins, e.g., additional proteins with LPXTG
      motifs could also result in variation in the adhesive properties between
      different strains. The variation in the secreted proteome may be associated with
      the degree of pathogenesis. While the role of the 'non-classical' secretome in
      virulence remains unclear, differences in the substrate binding proteins of
      various ABC transport systems and cytoplasmic proteins potentially suggest strain
      variation in nutritional requirements or a differential ability to utilize
      various carbon sources.
AU  - Sangal V
AU  - Blom J
AU  - Sutcliffe IC
AU  - von Hunolstein C
AU  - Burkovski A
AU  - Hoskisson PA
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2015 16: 765.

PMID- 24200588
VI  - 21
DP  - 2014
TI  - A lack of genetic basis for biovar differentiation in clinically important Corynebacterium diphtheriae from whole genome sequencing.
PG  - 54-57
AB  - The differentiation of clinically important Corynebacterium diphtheriae into
      specific biovars is complex and phylogenetically unclear. Comparative genomic
      analyses of 17 strains indicate that the division of C. diphtheriae into
      different biovars does not correlate with the variation in the gene content in
      the relevant metabolic categories that are potentially involved in the biovar
      discrimination. The biochemical separation is also not supported by phylogenetic
      analyses, suggesting molecular methods of typing C. diphtheriae strains should be
      adopted much more widely.
AU  - Sangal V
AU  - Burkovski A
AU  - Hunt AC
AU  - Edwards B
AU  - Blom J
AU  - Hoskisson PA
PT  - Journal Article
TA  - Infect. Genet. Evol.
JT  - Infect. Genet. Evol.
SO  - Infect. Genet. Evol. 2014 21: 54-57.

PMID- 22887653
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Corynebacterium diphtheriae Biovar Intermedius NCTC 5011.
PG  - 4738
AB  - We report an annotated draft genome of the human pathogen Corynebacterium diphtheriae bv.
      intermedius NCTC 5011. This strain is the first C. diphtheriae
      bv. intermedius strain to be sequenced, and our results provide a useful
      comparison to the other primary disease-causing biovars, C. diphtheriae bv.
      gravis and C. diphtheriae bv. mitis. The sequence has been deposited at
      DDBJ/EMBL/GenBank with the accession number AJVH01000000.
AU  - Sangal V
AU  - Tucker NP
AU  - Burkovski A
AU  - Hoskisson PA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4738.

PMID- 22628502
VI  - 194
DP  - 2012
TI  - The Draft Genome Sequence of Corynebacterium diphtheriae bv. mitis NCTC 3529 Reveals Significant Diversity between the Primary Disease-Causing Biovars.
PG  - 3269
AB  - We report the draft genome of the human pathogen Corynebacterium diphtheriae bv.  mitis NCTC
      3529. This is the first C. diphtheriae bv. mitis strain to be
      sequenced and reveals significant differences from the other primary biovar, C.
      diphtheriae bv. gravis.
AU  - Sangal V
AU  - Tucker NP
AU  - Burkovski A
AU  - Hoskisson PA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3269.

PMID- 24407635
VI  - 2
DP  - 2014
TI  - Genome Sequence of Escherichia coli O157:H7 Strain 2886-75, Associated with the First Reported Case of Human Infection in the United States.
PG  - e01120-13
AB  - First identified in 1982 as a human pathogen, enterohemorrhagic Escherichia coli  of the
      O157:H7 serotype is a major cause of food-borne acquired human infections.
      Here, we report the genome sequence of the first known strain of this serotype
      isolated in the United States.
AU  - Sanjar F et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01120-13.

PMID- 27389262
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequence of Multidrug-Resistant Pseudomonas aeruginosa Strain BAMCPA07-48, Isolated from a Combat Injury Wound.
PG  - e00547-16
AB  - We report here the complete genome sequence of Pseudomonas aeruginosa strain BAMCPA07-48,
      isolated from a combat injury wound. The closed genome sequence of
      this isolate is a valuable resource for pathogenome characterization of P.
      aeruginosa associated with wounds, which will aid in the development of a
      higher-resolution phylogenomic framework for molecular-guided
      pathogen-surveillance.
AU  - Sanjar F
AU  - Karna SL
AU  - Chen T
AU  - Chen P
AU  - Abercrombie JJ
AU  - Leung KP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00547-16.

PMID- 29954890
VI  - 6
DP  - 2018
TI  - Draft Genome Assemblages of 10 Xanthomonas vasicola pv. zeae Strains, Pathogens Causing Leaf Streak Disease of Maize in South Africa.
PG  - e00532-18
AB  - Maize bacterial leaf streak disease has spread across maize crops in South Africa and
      therefore potentially poses a threat to maize production and food security.
      Until recently, this pathogen was identified as a Xanthomonas campestris
      pathovar, whereas our South African genomes seem to be more divergent and create
      their own subclade.
AU  - Sanko TJ
AU  - Kraemer AS
AU  - Niemann N
AU  - Gupta AK
AU  - Flett BC
AU  - Mienie C
AU  - Bezuidenhout CC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00532-18.

PMID- 12060679
VI  - 30
DP  - 2002
TI  - Mutational analysis of conserved residues in HhaI DNA methyltransferase.
PG  - 2628-2638
AB  - HhaI DNA methyltransferase belongs to the C5-cytosine methyltransferase family, which is
      characterized by the presence of a set of highly conserved amino acids and motifs present in
      an invariant order. HhaI DNA methyltransferase has been subjected to a lot of biochemical and
      crystallographic studies. A number of issues, especially the role of the conserved amino acids
      in the methyltransferase activity, have not been addressed. Using sequence comparison and
      structural data, a structure-guided mutagenesis approach was undertaken, to assess the role of
      conserved amino acids in catalysis. Site-directed mutagenesis was performed on amino acids
      involved in cofactor S-adenosyl-L-methionine (AdoMet) binding (Phe18, Trp41, Asp60 and
      Leu100). Characterization of these mutants, by in vitro /in vivo restriction assays and
      DNA/AdoMet binding studies, indicated that most of the residues present in the AdoMet-binding
      pocket were not absolutely essential. This study implies plasticity in the recognition of
      cofactor by HhaI DNA methyltransferase.
AU  - Sankpal UT
AU  - Rao DN
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2002 30: 2628-2638.

PMID- 12139442
VI  - 37
DP  - 2002
TI  - Structure, function, and mechanism of HhaI DNA methyltransferases.
PG  - 167-197
AB  - A vast amount of literature has accumulated on the characterization of DNA methyltransferases.
      The HhaI DNA methyltransferase, a C5-cytosine methyltransferase, has been the subject of
      investigation for the last 2 decades. Biochemical and kinetic characterization have led to an
      understanding of the catalytic and kinetic mechanism of the methyltransfer reaction. The HhaI
      methyltransferase has also been subjected to extensive structural analysis, with the
      availability of 12 structures with or without a cofactor and a variety of DNA substrates. The
      mechanism of base flipping, first described for the HhaI methyltransferase, is conserved among
      all DNA methyltransferases and is also found to occur in numerous DNA repair enzymes. Studies
      with other methyltransferase reveal a significant structural and functional similarity among
      different types of methyltransferases. This review aims to summarize the available information
      on the HhaI DNA methyltransferase.
AU  - Sankpal UT
AU  - Rao DN
PT  - Journal Article
TA  - Crit. Rev. Biochem. Mol. Biol.
JT  - Crit. Rev. Biochem. Mol. Biol.
SO  - Crit. Rev. Biochem. Mol. Biol. 2002 37: 167-197.

PMID- 29748412
VI  - 6
DP  - 2018
TI  - Genome Sequence of the Symbiotic Type Strain Mesorhizobium helmanticense CSLC115N Isolated from Lotus corniculatus Nodules.
PG  - e00412-18
AB  - Mesorhizobium helmanticense is a novel species that was isolated from root nodules of Lotus
      corniculatus grown in an alfisol soil from Carbajosa de la
      Sagrada, a Mediterranean region in the province of Salamanca in northwest Spain.
      The whole-genome sequence of the type strain M. helmanticense CSLC115N is
      reported in this study.
AU  - Sannazzaro AI
AU  - Torres TGA
AU  - Caballero M
AU  - Dip D
AU  - Pistorio M
AU  - Estrella MJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00412-18.

PMID- 29026451
VI  - 12
DP  - 2017
TI  - Genomic insights into the thiamin metabolism of Paenibacillus thiaminolyticus NRRL B-4156 and P. apiarius NRRL B-23460.
PG  - 59
AB  - Paenibacillus thiaminolyticus is the model organism for studying thiaminase I, an enigmatic
      extracellular enzyme. Originally isolated from the feces of clinical
      patients suffering from thiamin deficiency, P. thiaminolyticus has been
      implicated in thiamin deficiencies in humans and other animals due to its ability
      to produce this thiamin-degrading enzyme. Its close relative, P. apiarius, also
      produces thiaminase I and was originally isolated from dead honeybee larvae,
      though it has not been reported to be a honeybee pathogen. We generated draft
      genomes of the type strains of both species, P. thiaminolyticus NRRL B-4156 and
      P. apiarius NRRL B-23460, to deeply explore potential routes of thiamin
      metabolism. We discovered that the thiaminase I gene is located in a highly
      conserved operon with thiamin biosynthesis and salvage genes, as well as genes
      involved in the biosynthesis of the antibiotic bacimethrin. Based on metabolic
      pathway predictions, P. apiarius NRRL B-23460 has the genomic capacity to
      synthesize thiamin de novo using a pathway that is rarely seen in bacteria, but
      P. thiaminolyticus NRRL B-4156 is a thiamin auxotroph. Both genomes encode
      importers for thiamin and the pyrimidine moiety of thiamin, as well as enzymes to
      synthesize thiamin from pyrimidine and thiazole.
AU  - Sannino D
AU  - Angert ER
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 59.

PMID- 7371644
VI  - 105
DP  - 1980
TI  - Deoxyribonucleic acid methyltransferase from the eukaryote, Chlamydomonas reinhardi.
PG  - 471-480
AB  - DNA methyltransferase was purified 310-fold from a green alga. Chlamydomonas reinhardi
      vegetative cells. The native enzyme of molecular weight 55000-58000 catalyzed the transfer of
      methyl groups from S-adenosylmethionine to the 5 position of cytosine in DNA. Native DNA
      accepted methyl groups 10-fold more than did denatured DNA. The sequence specificity analysis
      of methylated deoxycytidine in vitro revealed that the enzyme introduces methyl groups
      preferentially into sequences containing 5'd(T-mC-R)3'. Kinetic anlaysis of the reaction
      indicated that the enzyme obeys a random sequential mechanism. The extent of saturation with
      methyl groups depends upon the species from which the DNA was obtained. Kinetic analysis of
      the reaction catalyzes by RNA polymerase II has indicated that DNA methylation decreases the
      rate of initiation of RNA synthesis, but does not affect the rate of RNA chain elongation.
AU  - Sano H
AU  - Sager R
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1980 105: 471-480.

PMID- 29326204
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Brevibacillusreuszeri Strain NIT02, Isolated from a Laundered Rental Cloth Hot Towel.
PG  - e01353-17
AB  - Brevibacillus reuszeri is a Gram-positive spore-forming bacterium. Here, we present the draft
      genome sequence of Brevibacillus reuszeri strain NIT02, which
      was isolated from a laundered rental cloth hot towel.
AU  - Sano KI
AU  - Anraku A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01353-17.

PMID- 
VI  - 272
DP  - 2005
TI  - Codes in the codons: codon-amino acid complementarity revealed in the structures of restriction enzyme - DNA complexes.
PG  - 100
AB  - In the early years after the elucidation of the DNA structure, there was controversy about
      whether there was any chemical rationale underlying the genetic code. In 1967, Carl Woese
      proposed that there was stereochemical affinity between amino acids and the base sequences
      that code for them. The alternative hypothesis proposed by Crick among others, that the exact
      genetic code was largely accidental, became largely accepted by the molecular biology
      community. We have now constructed a "periodic table" linking the chemical properties of the
      amino acids and the sequences of their associated codons. The amino acid table showed
      significant periodicity and indicated the importance of the central base in determining the
      chemical properties of amino acids. This adds support to Woese' original hypothesis. If this
      stereochemical and structural affinity were true, we would expect interactions between amino
      acids and their associated codons to be favoured in DNA-protein complexes. We originally
      tested this hypothesis using known structures of restriction enzyme - DNA complexes. We found
      that, not only were cleavage-site like base sequences found disproportionately often in the
      DNA sequences of restriction enzymes, but that, in the complex structures, the amino acids
      coded by those site-like sequences were found close to the restriction sites themselves. The
      average distance between the closest atoms in the codon and amino acid was significantly
      lowest when the amino acid involved was positively charged. We now update this work to include
      restriction enzyme - DNA complexes that have entered the PDB since December 2003.
AU  - Sansom CE
AU  - Biro JC
AU  - Benyo B
AU  - Benyo Z
PT  - Journal Article
TA  - FEBS J.
JT  - FEBS J.
SO  - FEBS J. 2005 272: 100.

PMID- 12959402
VI  - 9
DP  - 2003
TI  - The novel conjugative transposon tn1207.3 carries the macrolide efflux gene mef(A) in Streptococcus pyogenes.
PG  - 243-247
AB  - The macrolide efflux gene mef(A) of the Streptococcus pyogenes clinical strain 2812A was found
      to be carried by a 52-kb chromosomal genetic
      element that could be transferred by conjugation to the chromosome of
      other streptococcal species. The characteristics of this genetic element
      are typical of conjugative transposons and was named Tn1207.3. The size of
      Tn1207.3 was established by pulsed-field gel electrophoresis (PFGE), and
      DNA sequencing analysis showed that the 7,244 bp at the left end of
      Tn1207.3 were identical to those of the pneumococcal Tn1207.1 element.
      Tn1207.3-like genetic elements were found to be inserted at a single
      specific chromosomal site in 12 different clinical isolates S. pyogenes
      exhibiting the M phenotype of resistance to macrolides and carrying the
      mef(A) gene. Tn1207.3 was transferred from S. pyogenes 2812A to
      Streptococcus pneumoniae, and sequence analysis carried out on six
      independent transconjugants showed that insertion of Tn1207.3 in the
      pneumococcal genome always occurred at a single specific site as in
      Tn1207.1. Using MF2, a representative S. pneumoniae transconjugant, as a
      donor, Tn1207.3 was transferred again by conjugation to S. pyogenes and
      Streptococcus gordonii. The previously described nonconjugative element
      Tn1207.1 of S. pneumoniae appears to be a defective element, part of a
      longer conjugative transposon that carries mef(A) and is found in clinical
      isolates of S. pyogenes.
AU  - Santagati M
AU  - Iannelli F
AU  - Cascone C
AU  - Campanile F
AU  - Oggioni MR
AU  - Stefani S
AU  - Pozzi G
PT  - Journal Article
TA  - Microb. Drug Resist.
JT  - Microb. Drug Resist.
SO  - Microb. Drug Resist. 2003 9: 243-247.

PMID- 28751391
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of Eight Rhizobium Symbionts Associated with Common Bean (Phaseolus vulgaris).
PG  - e00645-17
AB  - We present here the high-quality complete genome sequences of eight strains of
      Rhizobium-nodulating Phaseolus vulgaris Comparative analyses showed that some of
      them belonged to different genomic and evolutionary lineages with common
      symbiotic properties. Two novel symbiotic plasmids (pSyms) with P. vulgaris
      specificity are reported here.
AU  - Santamaria RI
AU  - Bustos P
AU  - Perez-Carrascal OM
AU  - Miranda-Sanchez F
AU  - Vinuesa P
AU  - Martinez-Flores I
AU  - Juarez S
AU  - Lozano L
AU  - Martinez-Romero E
AU  - Cevallos MA
AU  - Romero D
AU  - Davila G
AU  - Ormeno-Orrillo E
AU  - Gonzalez V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00645-17.

PMID- 26586881
VI  - 3
DP  - 2015
TI  - High-Quality Draft Genome Sequence of Bacillus amyloliquefaciens Strain 629, an Endophyte from Theobroma cacao.
PG  - e01325-15
AB  - Bacillus amyloliquefaciens strain 629 is an endophyte isolated from Theobroma cacao L. Here,
      we report the draft genome sequence (3.9 Mb) of B.
      amyloliquefaciens strain 629 containing 16 contigs (3,903,367 bp), 3,912 coding
      sequences, and an average 46.5% G+C content.
AU  - SantAnna BM
AU  - Marbach PP
AU  - Rojas-Herrera M
AU  - De Souza JT
AU  - Roque MR
AU  - Queiroz AT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01325-15.

PMID- 11483893
VI  - 7
DP  - 2001
TI  - Analysis of alpha-crystallin chaperone function using restriction enzymes and citrate synthase.
PG  - 172-177
AB  - PURPOSE: To compare the abilities of [alpha]A-crystallin, [alpha]B-crystallin, and
      mini-[alpha]A-crystallin (a synthetic peptide
      chaperone representing the functional unit of [alpha]A-crystallin) to
      protect against heat-induced inactivation of citrate synthase (CS) and
      restriction enzymes, SmaI and NdeI. METHODS: Restriction enzymes, SmaI and
      NdeI were heated at different temperatures in the presence of various
      amounts of molecular chaperones and tested for their ability to cleave
      plasmid DNA. The aggregation of CS was measured at 43 degrees C while the
      loss in activity was monitored at 37 degrees C in the presence of various
      crystallins. RESULTS: Restriction enzyme activities were protected by the
      crystallin subunits up to 37 degrees C for SmaI and 43 degrees C for NdeI.
      However, the mini-[alpha]A-crystallin was unable to protect endonuclease
      activity. The crystallin subunits and the peptide chaperone were able to
      suppress thermal aggregation of CS at 43 degrees C, but failed to
      stabilize its activity at 37 degrees C. CONCLUSIONS: The ability of
      [alpha]-crystallin subunits to stabilize denaturing proteins varies from
      enzyme to enzyme as evidenced by the inactivation of CS and protection of
      SmaI and NdeI activity in the presence of [alpha]-crystallin subunits.
      Additionally, our results show that there could be more than one site in
      [alpha]A-crystallin responsible for its chaperone-like action. By addition
      of crystallin subunits to restriction enzymes prior to or during storage,
      transport, or assay would maintain or improve their activity thereby
      decreasing their cost.
AU  - Santhoshkumar P
AU  - Sharma KK
PT  - Journal Article
TA  - Mol. Vis.
JT  - Mol. Vis.
SO  - Mol. Vis. 2001 7: 172-177.

PMID- 6205762
VI  - 33
DP  - 1983
TI  - On the mechanism of inhibition of DNA-cytosine methyltransferases by cytosine analogs.
PG  - 9-10
AB  - In recent years 5-methylcytosine residues in DNA have been implicated to have an important
      role in the control of eucaryotic gene expression (see Razin and Riggs, Science 210, 604-610,
      1980). Consequently, there has been much interest in cytosine analogs such as 5-azacytosine
      (5-azaC) and 5-fluorocytosine (5-fluoro-C), which, when incorporated into DNA, inhibit
      methylation and profoundly affect gene expression and differentiation (see Taylor and Jones,
      JBM 162, 679-692, 1982). The degree of hypomethylation far exceeds the levels of such analogs
      in DNA and is not simply a result of their inability to serve as methyl acceptors. It is now
      clear that DNAs containing low levels of these analogs are potent inhibitors of DNA-cytosine
      methyltansferase (DCMT), but the mechanism of inhibition is unresolved. In this report, we
      review pertinent literature and formulate a proposal for the molecular mechanism by which DCMT
      is inhibited bly DNA containing 5-aza-C or 5-fluoro-C. A similar mechanism explains how small
      amounts of 5-aza-C or 5-fluoro-C in tRNA cause specific loss of tRNA-cytosine
      methyltransferase activity (Lu et al., Biochem. Pharmacol. 28, 489-495, 1979; Lu and
      Randerath, Cancer Res. 40, 2701-2705, 1980).
AU  - Santi DV
AU  - Garrett CE
AU  - Barr PJ
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1983 33: 9-10.

PMID- 6209710
VI  - 81
DP  - 1984
TI  - Covalent bond formation between a DNA-cytosine methyltransferase and DNA containing 5-azacytosine.
PG  - 6993-6997
AB  - DNA containing 5-azacytosine (azaC) has previously been shown to be a
      potent inhibitor of DNA-cytosine methyltransferases.  In this report, we describe
      experiments which demonstrate that azaC-DNA forms a covalent complex with HpaII
      methylase, a bacterial enzyme that methylates the internal C of C-C-G-G sequences.  The
      complex does not undergo detectable dissociation over at least 3 days and is stable to
      denaturation with NaDodSO4.  After extensive digestion of the complex with DNase and
      phosphodiesterase, gel filtration gave the methylase bound to approximately one equivalent
      of azaC; the digested complex had an apparent molecular weight similar to that of the native
      enzyme.  Although prior treatment of azaC-DNA with HpaII endonuclease had only a slight
      effect on binding of the methylase, treatment with MspI endonuclease, which also cleaves
      at C-C-G-G sequences, resulted in a significant reduction in binding; this indicates that
      azaC residues in the recognition sequence of HpaII are an important component in the
      covalent interaction of the methylase.  However, since there was residual binding it is
      possible that azaC residues elsewhere in DNA also covalently bind to the methylase.  These
      results provide an explanation of why azaC-DNA is such a potent inhibitor of cytosine
      methyltransferases and how the incorporation of such low levels of azaC into DNA can
      result in dramatic decreases in the methylation of cytosine.  Finally, consideration of the
      probable catalytic mechanism of cytosine methylases and the chemical properties of azaC
      suggests that the inhibition is, at least in part, an active-site directed process and permits
      a
      proposal for the structure of the covalent complex.
AU  - Santi DV
AU  - Norment A
AU  - Garrett CE
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1984 81: 6993-6997.

PMID- 23754393
VI  - 110
DP  - 2013
TI  - The genome of Phaeocystis globosa virus PgV-16T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes.
PG  - 10800-10805
AB  - Large dsDNA viruses are involved in the population control of many
      globally distributed species of eukaryotic phytoplankton and have
      a prominent role in bloomtermination. The genus Phaeocystis (Haptophyta,
      Prymnesiophyceae) includes several high-biomass-forming
      phytoplankton species, such as Phaeocystis globosa, the blooms of
      which occur mostly in the coastal zone of the North Atlantic and the
      North Sea. Here,we report the 459,984-bp-long genomesequence of
      P. globosa virus strain PgV-16T, encoding 434 proteins and eight
      tRNAs and, thus, the largest fully sequenced genome to date among
      viruses infecting algae. Surprisingly, PgV-16T exhibits no phylogenetic
      affinity with other viruses infecting microalgae (e.g., phycodnaviruses),
      including those infecting Emiliania huxleyi, another
      ubiquitous bloom-forming haptophyte. Rather, PgV-16T belongs to
      anemerging clade (theMegaviridae) clustering the viruses endowed
      with the largest known genomes, including Megavirus, Mimivirus
      (both infecting acanthamoeba), and a virus infecting the marine
      microflagellate grazer Cafeteria roenbergensis. Seventy-five percent
      of the best matches of PgV-16T-predicted proteins correspond to
      two viruses [Organic Lake phycodnavirus (OLPV)1 and OLPV2] from
      a hypersaline lake in Antarctica (Organic Lake), the hosts of which
      are unknown. As for OLPVs and other Megaviridae, the PgV-16T
      sequence data revealed the presence of a virophage-like genome.
      However, no virophage particle was detected in infected P. globosa
      cultures. The presence of many genes found only in Megaviridae in
      its genome and the presence of an associated virophage strongly
      suggest that PgV-16T shares a common ancestry with the largest
      known dsDNA viruses, the host range ofwhich already encompasses
      the earliest diverging branches of domain Eukarya.
AU  - Santini S
AU  - Jeudi S
AU  - Bartoli J
AU  - Poirot O
AU  - Lescot-David M
AU  - Barbe V
AU  - Wommack EK
AU  - Abergel C
AU  - Brussaard C
AU  - Claverie J-M
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2013 110: 10800-10805.

PMID- 23469336
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Chromate-Resistant and Biofilm-Producing Strain Pseudomonas alcaliphila 34.
PG  - e00125-12
AB  - We report the draft genome sequence of 34, a Cr(VI)-hyperresistant and biofilm-producing
      bacterium that might be used for the bioremediation of
      chromate-polluted soils. The genome sequence might be helpful in exploring the
      mechanisms involved in chromium resistance and biofilm formation.
AU  - Santopolo L
AU  - Marchi E
AU  - Decorosi F
AU  - Galardini M
AU  - Brilli M
AU  - Giovannetti L
AU  - Viti C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00125-12.

PMID- 25587132
VI  - 112
DP  - 2015
TI  - Genomic and proteomic characterization of Candidatus Nitrosopelagicus brevis: an ammonia-oxidizing archaeon from the open ocean.
PG  - 1173-1178
AB  - Thaumarchaeota are among the most abundant microbial cells in the
      ocean, but difficulty in cultivating marine Thaumarchaeota has
      hindered investigation into the physiological and evolutionary basis
      of their success. We report here a closed genome assembled from
      a highly enriched culture of the ammonia-oxidizing pelagic thaumarchaeon
      CN25, originating from the open ocean. The CN25
      genome exhibits strong evidence of genome streamlining, including
      a 1.23-Mbp genome, a high coding density, and a low number of
      paralogous genes. Proteomic analysis recovered nearly 70% of the
      predicted proteins encoded by the genome, demonstrating that
      a high fraction of the genome is translated. In contrast to other
      minimal marine microbes that acquire, rather than synthesize,
      cofactors, CN25 encodes and expresses near-complete biosynthetic
      pathways for multiple vitamins. Metagenomic fragment recruitment
      indicated the presence of DNA sequences >90% identical to the CN25
      genome throughout the oligotrophic ocean. We propose the provisional
      name "Candidatus Nitrosopelagicus brevis" str. CN25 for this
      minimalist marine thaumarchaeon and suggest it as a potentialmodel
      system for understanding archaeal adaptation to the open ocean.
AU  - Santoro AE
AU  - Dupont CL
AU  - Richter RA
AU  - Craig MT
AU  - Carini P
AU  - McIlvin MR
AU  - Yang Y
AU  - Orsi W
AU  - Moran D
AU  - Saito M
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2015 112: 1173-1178.

PMID- 21936946
VI  - 42
DP  - 2011
TI  - Genome of Mycoplasma haemofelis, unraveling its strategies for survival and persistence.
PG  - 102
AB  - Mycoplasma haemofelis is a mycoplasmal pathogen (hemoplasma) that attaches to the host's
      erythrocytes. Distributed worldwide, it has a
      significant impact on the health of cats causing acute disease and,
      despite treatment, establishing chronic infection. It might also have a
      role as a zoonotic agent, especially in immunocompromised patients.
      Whole genome sequencing and analyses of M. haemofelis strain Ohio2 was
      undertaken as a step toward understanding its survival and persistence.
      Metabolic pathways are reduced, relying on the host to supply many of
      the nutrients and metabolites needed for survival. M. haemofelis must
      import glucose for ATP generation and ribose derivates for RNA/DNA
      synthesis. Hypoxanthine, adenine, guanine, uracil and CMP are scavenged
      from the environment to support purine and pyrimidine synthesis. In
      addition, nicotinamide, amino acids and any vitamins needed for growth,
      must be acquired from its environment. The core proteome of M.
      haemofelis contains an abundance of paralogous gene families,
      corresponding to 70.6% of all the CDSs. This 'paralog pool' is a rich
      source of different antigenic epitopes that can be varied to elude the
      host's immune system and establish chronic infection. M. haemofelis
      also appears to be capable of phase variation, which is particularly
      relevant to the cyclic bacteremia and persistence, characteristics of
      the infection in the cat. The data generated herein should be of great
      use for understanding the mechanisms of M. haemofelis infection.
      Further, it will provide new insights into its pathogenicity and clues
      needed to formulate media to support the in vitro cultivation of M.
      haemofelis.
AU  - Santos AP
AU  - Guimaraes AMS
AU  - do Nascimento NC
AU  - SanMiguel PJ
AU  - Martin SW
AU  - Messick JB
PT  - Journal Article
TA  - Vet. Res.
JT  - Vet. Res.
SO  - Vet. Res. 2011 42: 102.

PMID- 20561021
VI  - 12
DP  - 2010
TI  - The metavirome of a hypersaline environment.
PG  - 2965-2976
AB  - Hypersaline environments harbour the highest number of virus-like
      particles reported for planktonic systems. However, very little is known
      about the genomic diversity of these virus assemblages since most of the
      knowledge on halophages is based on the analysis of a few isolates
      infecting strains of hyperhalophilic Archaea that may not be
      representatives of the natural microbiota. Here, we report the
      characterization, through a metagenomic approach, of the viral assemblage
      inhabiting a crystallizer pond (CR30) from a multi-pond solar saltern in
      Santa Pola (SE Spain). A total of 1.35 Mbp were cloned that yielded a
      total of 620 kb sequenced viral DNA. The metavirome was highly diverse and
      different from virus communities of marine and other aquatic environments
      although it showed some similarities with metaviromes from high-salt ponds
      in solar salterns in San Diego (SW USA), indicating some common traits
      between high-salt viromes. A high degree of diversity was found in the
      halophages as revealed by the presence of 2479 polymorphic nucleotides.
      Dinucleotide frequency analysis of the CR30 metavirome showed a good
      correlation with GC content and enabled the establishment of different
      groups, and even the assignment of their putative hosts: the archaeon
      Haloquadratum walsbyi and the bacterium Salinibacter ruber.
AU  - Santos F
AU  - Yarza P
AU  - Parro V
AU  - Briones C
AU  - Anton J
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2010 12: 2965-2976.

PMID- 27563042
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the Aureocin A53-Producing Strain Staphylococcus aureus  A53.
PG  - e00858-16
AB  - Here, we present the 2,658,363-bp draft genome sequence of the aureocin A53-producing strain
      Staphylococcus aureus A53. This genome information may
      contribute to the optimal and rational exploitation of aureocin A53 as an
      antimicrobial agent and to its production in large scale.
AU  - Santos OC
AU  - Duarte AF
AU  - Albano RM
AU  - Bastos MC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00858-16.

PMID- 26358601
VI  - 3
DP  - 2015
TI  - Genome Sequence of Streptomyces caatingaensis CMAA 1322, a New Abiotic Stress-Tolerant Actinomycete Isolated from Dried Lake Bed Sediment in the Brazilian Caatinga Biome.
PG  - e01020-15
AB  - The genome sequence of the first Streptomyces species isolated from the Brazilian Caatinga is
      reported here. Genes related to environmental stress tolerance were prevalent and included
      many secondary metabolic gene clusters.
AU  - Santos SN
AU  - Gacesa R
AU  - Taketani RG
AU  - Long PF
AU  - Melo IS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01020-15.

PMID- 26021916
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Bacillus sp. Strain CMAA 1185, a Cellullolytic Bacterium Isolated from Stain House Lake, Antarctic Peninsula.
PG  - e00436-15
AB  - The aim of this study was to report the genome sequence of the cellulolytic Bacillus sp.
      strain CMAA 1185, isolated from Stain House Lake, Antarctica.
AU  - Santos SN
AU  - Kavamura VN
AU  - Taketani RG
AU  - Vasconcellos RL
AU  - Zucchi TD
AU  - Melo IS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00436-15.

PMID- 25814603
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Pedobacter sp. Strain NL19, a Producer of Potent Antibacterial Compounds.
PG  - e00184-15
AB  - Here, we report the draft genome sequence of Pedobacter sp. strain NL19. The genome has 5.99
      Mbp and a G+C content of 39.0%. NL19 was isolated from sludge
      from an abandoned uranium mine in the north of Portugal, and it produces potent
      antibacterials against Gram-positive and Gram-negative bacteria.
AU  - Santos T
AU  - Cruz A
AU  - Caetano T
AU  - Covas C
AU  - Mendo S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00184-15.

PMID- 23144402
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of 'Candidatus Portiera aleyrodidarum' BT-QVLC, an Obligate Symbiont That Supplies Amino Acids and Carotenoids to Bemisia tabaci.
PG  - 6654-6655
AB  - The genome of 'Candidatus Portiera aleyrodidarum,' the primary endosymbiont of the whitefly
      Bemisia tabaci (Mediterranean species), is reported. It presents a
      reduced genome (357 kb) encoding the capability to synthetize, or participate in
      the synthesis of, several amino acids and carotenoids, being the first insect
      endosymbiont capable of supplying carotenoids.
AU  - Santos-Garcia D
AU  - Farnier PA
AU  - Beitia F
AU  - Zchori-Fein E
AU  - Vavre F
AU  - Mouton L
AU  - Moya A
AU  - Latorre A
AU  - Silva FJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6654-6655.

PMID- 10816123
VI  - 28
DP  - 2000
TI  - The cytotoxic effect of DNA methyltransferase I over-expression is mediated by the N-terminal.
PG  - A182
AB  - DNA methyltransferase 1, the essential enzyme maintaining DNA methylation patterns in
      mammalian cells, contains a 500 amino acid catalytic domain and an N-terminal 1200 amino acid
      complex regulatory domain determining specificity and intracellular localization.
      Overexpression of the enzyme in somatic cells is very difficult, even more of the
      oocyte-specific form lacking the first 120 amino acids.  To elucidate the underlying causes,
      the mouse and human cDNAs encoding this form were transfected into mouse F9 cells and various
      human cell lines.  Few cell clones were obtained which contained rearranged cDNAs after two
      weeks, but the number of transfected cells was not notably diminished up to 3 days.
      Surprisingly, deletion of the catalytic domain did not obliterate cytotoxicity; rather a 150
      amino acid subdomain containing the PCNA-binding site and an NLS was found to be sufficient.
      Mutation of the PCNA-binding sequence abolished cytotoxicity.  Thus, DNMT1 overexpression
      causes a slow-acting cytotoxic effect via binding to PCNA, possibly by interfering with DNA
      replication.  DNMT1 may be a multifunctional enzyme important beyond DNA methylation.
AU  - Santourlidis S
AU  - Schulz WA
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 2000 28: A182.

PMID- 28473390
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Lactobacillus reuteri CECT8605.
PG  - e00297-17
AB  - Lactobacillus reuteri CECT8605 has shown potential probiotic properties in both in vitro and
      in vivo assays. Besides its beneficial characteristics, general
      aspects concerning genetic stability and safety for human consumption have been
      studied. Its genome sequence has been a useful tool to support preliminary
      conclusions based on empirical observations.
AU  - Sanudo AI
AU  - Olivares MM
AU  - Banuelos O
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00297-17.

PMID- 12524290
VI  - 84
DP  - 2003
TI  - Thermodynamic and kinetic basis of promiscuity in mutant EcoRI endonucleases.
PG  - 367a
AB  - We have used fluorescence-quenching measurements to characterize the partitioning of a variety
      of indolyl-labeled phospho- and sphingolipids
      between gel or liquid-ordered and liquid-disordered lipid domains in
      several types of lipid bilayers where such domains coexist. In both
      cholesterol-free and cholesterol-containing lipid mixtures, sphingolipids
      with diverse polar headgroups (ranging from sphingomyelin and
      monoglycosylceramides to ganglioside GM1) show a net preference for
      partitioning into ordered domains, which varies modestly in magnitude with
      varying headgroup structure. The affinities of different sphingolipids for
      ordered lipid domains do not vary in a consistent manner with the size or
      other simple structural properties of the polar headgroup, such that for
      example ganglioside GM1 partitions between ordered and disordered lipid
      domains in a manner very similar to sphingomyelin. Ceramide exhibits a
      dramatically higher affinity for ordered lipid domains in both
      cholesterol-free and cholesterol-containing bilayers than do other
      sphingolipids. Our findings suggest that sphingolipids with a variety of
      headgroup structures will be enriched by substantial factors in
      liquid-ordered versus liquid-disordered regions of membranes, in a manner
      that is only modestly dependent on the nature of the polar headgroup.
      Ceramide is predicted to show a very strong enrichment in such domains,
      supporting previous suggestions that ceramide-mediated signaling may be
      compartmentalized to liquid-ordered (raft and raft-related) domains in the
      plasma membrane.
AU  - Sapienza P
AU  - Kurpiewski M
AU  - Jen-Jacobson L
PT  - Journal Article
TA  - Biophys. J.
JT  - Biophys. J.
SO  - Biophys. J. 2003 84: 367a.

PMID- 15811370
VI  - 348
DP  - 2005
TI  - Thermodynamic and kinetic basis for the relaxed DNA sequence specificity of "promiscuous" mutant EcoRI endonucleases.
PG  - 307-324
AB  - Promiscuous mutant EcoRI endonucleases produce lethal to sublethal effects because they cleave
      Escherichia coli DNA despite the presence of the EcoRI methylase. Three promiscuous mutant
      forms, Ala138Thr, Glu192Lys and His114Tyr, have been characterized with respect to their
      binding affinities and first-order cleavage rate constants towards the three classes of DNA
      sites: specific, miscognate (EcoRI*) and non-specific. We have made the unanticipated and
      counterintuitive observations that the mutant restriction endonucleases that exhibit relaxed
      specificity in vivo nevertheless bind more tightly than the wild-type enzyme to the specific
      recognition sequence in vitro, and show even greater preference for binding to the cognate
      GAATTC site over miscognate sites. Binding preference for EcoRI* over non-specific DNA is also
      improved. The first-order cleavage rate constants of the mutant enzymes are normal for the
      cognate site GAATTC, but are greater than those of the wild-type enzyme at EcoRI* sites. Thus,
      the mutant enzymes use two mechanisms to partially bypass the multiple fail-safe mechanisms
      that protect against cleavage of genomic DNA in cells carrying the wild-type EcoRI
      restriction-modification system: (a) binding to EcoRI* sites is more probable than for
      wild-type enzyme because non-specific DNA is less effective as a competitive inhibitor; (b)
      the combination of increased affinity and elevated cleavage rate constants at EcoRI* sites
      makes double-strand cleavage of these sites a more probable outcome than it is for the
      wild-type enzyme. Semi-quantitative estimates of rates of EcoRI* site cleavage in vivo,
      predicted using the binding and cleavage constants measured in vitro, are in accord with the
      observed lethal phenotypes associated with the three mutations.
AU  - Sapienza PJ
AU  - Dela-Torre CA
AU  - McCoy WH
AU  - Jana SV
AU  - Jen-Jacobson L
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2005 348: 307-324.

PMID- 17997963
VI  - 15
DP  - 2007
TI  - Structural and Thermodynamic Basis for Enhanced DNA Binding by a Promiscuous Mutant EcoRI Endonuclease.
PG  - 1368-1382
AB  - Promiscuous mutant EcoRI endonucleases bind to the canonical site GAATTC more tightly than
      does the wild-type endonuclease, yet cleave variant
      (EcoRI( *)) sites more rapidly than does wild-type. The crystal structure
      of the A138T promiscuous mutant homodimer in complex with a GAATTC site is
      nearly identical to that of the wild-type complex, except that the Thr138
      side chains make packing interactions with bases in the 5'-flanking
      regions outside the recognition hexanucleotide while excluding two bound
      water molecules seen in the wild-type complex. Molecular dynamics
      simulations confirm exclusion of these waters. The structure and
      simulations suggest possible reasons why binding of the A138T protein to
      the GAATTC site has DeltaS degrees more favorable and DeltaH degrees less
      favorable than for wild-type endonuclease binding. The interactions of
      Thr138 with flanking bases may permit A138T, unlike wild-type enzyme, to
      form complexes with EcoRI( *) sites that structurally resemble the
      specific wild-type complex with GAATTC.
AU  - Sapienza PJ
AU  - Rosenberg JM
AU  - Jen-Jacobson L
PT  - Journal Article
TA  - Structure
JT  - Structure
SO  - Structure 2007 15: 1368-1382.

PMID- 29519839
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Methylobacterium sp. Strain V23, Isolated from Accretion Ice of the Antarctic Subglacial Lake Vostok.
PG  - e00145-18
AB  - Here, we report the draft genome sequence of Methylobacterium sp. strain V23, a bacterium
      isolated from accretion ice of the subglacial Lake Vostok (3,592 meters
      below the surface). This genome makes possible the study of ancient and
      psychrophilic genes and proteins from a subglacial environment isolated from the
      surface for at least 15 million years.
AU  - Sapp A
AU  - Huguet-Tapia JC
AU  - Sanchez-Lamas M
AU  - Antelo GT
AU  - Primo ED
AU  - Rinaldi J
AU  - Klinke S
AU  - Goldbaum FA
AU  - Bonomi HR
AU  - Christner BC
AU  - Otero LH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00145-18.

PMID- 
VI  - 
DP  - 2008
TI  - Investigation of type IIS restriction endonuclease BfiI domain organization by using a new random gene dissection approach.
PG  - 1-42
AB  - Conclusions
      1. The genes of BfiI restriction-modification system were cloned. The system
      comprises two cytosine-N4-methyltransferases and a restriction endonuclease.
      2. A new method for investigation of protein domain organization, Random
      Gene Dissection, was proposed. The interdomain region of the chosen model protein, FokI REase,
      was determined using the new method, and it was in perfect agreement with the linker region
      predicted from the tertiary structure of FokI.
      3. Interdomain region of BfiI REase was determined by Random Gene
      Dissection method.
      4. Indirect data (induction of SOS response, toxicity) indicate that the
      N-terminal domain of BfiI acts as a nuclease.
      5. The DNA binding assay using purified C-terminal domain of BfiI indicates
      that it is responsible for target recognition.
      6. The complementary fragments of FokI and BfiI were isolated using Random
      Gene Dissection. Therefore the Random Gene Dissection method can be
      used not only for identification of interdomain regions, but also for isolation of
      complementing fragments of proteins.
AU  - Sapranauskas R
PT  - Journal Article
TA  - Ph.D. Thesis, Vilnius University
JT  - Ph.D. Thesis, Vilnius University
SO  - Ph.D. Thesis, Vilnius University 2008 : 1-42.

PMID- 16206911
VI  - 39
DP  - 2005
TI  - Random gene dissection: a tool for the investigation of protein structural organization.
PG  - 395-402
AB  - To investigate the domain structure of proteins and the function of individual domains,
      proteins are usually subjected to limited proteolysis, followed by isolation of protein
      fragments and determination of their functions.  We have developed an approach we call random
      gene dissection for the identification of functional protein domains and their interdomain
      regions as well as their in vivo complementing fragments.  The approach was tested on a
      two-domain protein, the type IIS restriction endonuclease BfiI.  The collection of BfiI
      insertional mutants was screened for those that are endonucleolytically active and thus induce
      the SOS DNA repair response.  Sixteen isolated mutants of the wild-type specificity contained
      insertions that were dispersed in a relatively large region of the target recognition domain.
      They split the gene into two complementing parts that separately were unable to induce the SOS
      DNA repair response.  In contrast, all 19 mutants of relaxed specificity contained the
      cassette inserted into a very narrow interdomain region that connects BfiI domains responsible
      for DNA recognition and for cleavage.  As expected, only the N-terminal fragment of BfiI was
      required to induce SOS response.  Our results demonstrate that RGD can be used as a general
      method to identify complementing fragments and functional domains in enzymes.
AU  - Sapranauskas R
AU  - Lubys A
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 2005 39: 395-402.

PMID- 10880511
VI  - 275
DP  - 2000
TI  - Novel subtype of type IIs restriction enzymes. BfiI endonuclease exhibits similarities to the EDTA-resistant nuclease Nuc of Salmonella typhimurium.
PG  - 30878-30885
AB  - The type IIs restriction enzyme BfiI recognizes the non-palindromic nucleotide sequence
      5'-ACTGGG-3' and cleaves complementary DNA strands 5/4 nucleotides downstream of the
      recognition sequence. The genes coding for the BfiI restriction-modification (R-M) system were
      cloned/sequenced and biochemical characterization of the BfiI restriction enzyme was
      performed. The BfiI R-M system contained three proteins: two N4-methylcytosine
      methyltransferases and a restriction enzyme. Sequencing of bisulfite-treated methylated DNA
      indicated that each methyltransferase modifies cytosines on opposite strands of the
      recognition sequence.  The N-terminal part of the BfiI restriction enzyme amino acid sequence
      revealed intriguing similarities to an EDTA-resistant nuclease of Salmonella typhimurium.
      Biochemical analyses demonstrated that BfiI, like the nuclease of S. typhimurium, cleaves DNA
      in the absence of Mg(2+) ions and hydrolyzes an artificial substrate bis(p-nitrophenyl)
      phosphate. However, unlike the nonspecific S. typhimurium nuclease, BfiI restriction enzyme
      cleaves DNA specifically. We propose that the DNA-binding specificity of BfiI stems from the
      C-terminal part of the protein. The catalytic N-terminal subdomain of BfiI radically differs
      from that of type II restriction enzymes and is presumably similar to the EDTA-resistant
      nonspecific nuclease of S. typhimurium; therefore, BfiI did not require metal ions for
      catalysis. We suggest that BfiI represents a novel subclass of type IIs restriction enzymes
      that differs from the archetypal FokI endonuclease by the fold of its cleavage domain, the
      domain location, and reaction mechanism.
AU  - Sapranauskas R
AU  - Sasnauskas G
AU  - Lagunavicius A
AU  - Vilkaitis G
AU  - Lubys A
AU  - Siksnys V
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2000 275: 30878-30885.

PMID- 24652977
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of a Multidrug-Resistant Acinetobacter baumannii PKAB07 Clinical Strain from India Belonging to Sequence Type 195.
PG  - e00184-14
AB  - Acinetobacter baumannii has emerged as one of the most common nosocomial pathogens and is
      considered to be a significant threat to public health
      worldwide. Here, we present the draft genome sequence of a multidrug-resistant
      clinical strain of A. baumannii PKAB07 isolated from a wound infection in India
      during 2011 to 2012.
AU  - Saranathan R
AU  - Tomar A
AU  - Sudhakar P
AU  - Arunkumar KP
AU  - Prashanth K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00184-14.

PMID- 15562004
VI  - 32
DP  - 2004
TI  - Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily.
PG  - 6129-6135
AB  - The restriction endonuclease (REase) R.KpnI is an orthodox Type IIP enzyme, which binds to DNA
      in the absence of metal ions and cleaves the DNA sequence 5'-GGTAC^C-3' in the presence of
      Mg2+ as shown generating 3' four base overhangs. Bioinformatics analysis reveals that R.KpnI
      contains a beta-beta-alpha-Me-finger fold, which is characteristic of many HNH-superfamily
      endonucleases, including homing endonuclease I-HmuI, structure-specific T4 endonuclease VII,
      colicin E9, sequence non-specific Serratia nuclease and sequence-specific homing endonuclease
      I-PpoI. According to our homology model of R.KpnI, D148, H149 and Q175 correspond to the
      critical D, H and N or H residues of the HNH nucleases. Substitutions of these three conserved
      residues lead to the loss of the DNA cleavage activity by R.KpnI, confirming their importance.
      The mutant Q175E fails to bind DNA at the standard conditions, although the DNA binding and
      cleavage can be rescued at pH 6.0, indicating a role for Q175 in DNA binding and cleavage. Our
      study provides the first experimental evidence for a Type IIP REase that does not belong to
      the PD...D/EXK superfamily of nucleases, instead is a member of the HNH superfamily.
AU  - Saravanan M
AU  - Bujnicki JM
AU  - Cymerman IA
AU  - Rao DN
AU  - Nagaraja V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2004 32: 6129-6135.

PMID- 
VI  - 85
DP  - 2003
TI  - A new type II restriction endonuclease, OfoI from nonheterocystous cynobacterium Oscillatoria foreaui.
PG  - 188-190
AB  - Although restriction enzymes are widely distributed in nature, many bacterial genera are yet
      to be explored for the presence of this important class of enzymes.  We have purified and
      characterized a new type II restriction endonuclease, OfoI from a nonheterocyst cyanobacterium
      Oscillatoria foreaui.  The recognition sequence has been determined by primer extension
      analysis.  The purified enzyme OfoI recognizes and cleaves the palindromic hexanucleotide
      5'-C/YCGRG-3', generating 5'-protruding ends.
AU  - Saravanan M
AU  - Elango K
AU  - Chandrashekaran S
AU  - Anand N
AU  - Nagaraja V
PT  - Journal Article
TA  - Curr. Sci.
JT  - Curr. Sci.
SO  - Curr. Sci. 2003 85: 188-190.

PMID- 17785455
VI  - 282
DP  - 2007
TI  - Dual role for Zn2+ in maintaining structural integrity and inducing DNA sequence specificity in a promiscuous endonuclease.
PG  - 32320-32326
AB  - We describe two uncommon roles for Zn2+ in enzyme KpnI restriction endonuclease (REase). Among
      all of the REases studied, KpnI REase is unique in its DNA binding and cleavage
      characteristics. The enzyme is a poor discriminator of DNA sequences, cleaving DNA in a
      promiscuous manner in the presence of Mg2+. Unlike most Type II REases, the active site of the
      enzyme comprises an HNH motif, which can accommodate Mg2+, Mn2+, or Ca2+. Among these metal
      ions, Mg2+ and Mn2+ induce promiscuous cleavage by the enzyme, whereas Ca2+-bound enzyme
      exhibits site-specific cleavage. Examination of the sequence of the protein revealed the
      presence of a zinc finger CCCH motif rarely found in proteins of prokaryotic origin. The zinc
      binding motif tightly coordinates zinc to provide a rigid structural framework for the enzyme
      needed for its function. In addition to this structural scaffold, another atom of zinc binds
      to the active site to induce high fidelity cleavage and suppress the Mg2+- and Mn2+-mediated
      promiscuous behavior of the enzyme. This is the first demonstration of distinct structural and
      catalytic roles for zinc in an enzyme, suggesting the distinct origin of KpnI REase.
AU  - Saravanan M
AU  - Vasu K
AU  - Ghosh S
AU  - Nagaraja V
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2007 282: 32320-32326.

PMID- 17430971
VI  - 35
DP  - 2007
TI  - R.KpnI, an HNH superfamily REase, exhibits differential discrimination at non-canonical sequences in the presence of Ca2+ and Mg2+.
PG  - 2777-2786
AB  - KpnI REase recognizes palindromic sequence, GGTAC downward arrowC, and forms complex in the
      absence of divalent metal ions, but requires the ions for DNA cleavage. Unlike most other
      REases, R.KpnI shows promiscuous DNA cleavage in the presence of Mg(2+). Surprisingly, Ca(2+)
      suppresses the Mg(2+)-mediated promiscuous activity and induces high fidelity cleavage. To
      further analyze these unique features of the enzyme, we have carried out DNA binding and
      kinetic analysis. The metal ions which exhibit disparate pattern of DNA cleavage have no role
      in DNA recognition. The enzyme binds to both canonical and non-canonical DNA with comparable
      affinity irrespective of the metal ions used. Further, Ca(2+)-imparted exquisite specificity
      of the enzyme is at the level of DNA cleavage and not at the binding step. With the canonical
      oligonucleotides, the cleavage rate of the enzyme was comparable for both Mg(2+)- and
      Mn(2+)-mediated reactions and was about three times slower with Ca(2+). The enzyme
      discriminates non-canonical sequences poorly from the canonical sequence in Mg(2+)-mediated
      reactions unlike any other Type II REases, accounting for the promiscuous behavior. R.KpnI,
      thus displays properties akin to that of typical Type II REases and also endonucleases with
      degenerate specificity in its DNA recognition and cleavage properties.
AU  - Saravanan M
AU  - Vasu K
AU  - Kanakaraj R
AU  - Rao DN
AU  - Nagaraja V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2007 35: 2777-2786.

PMID- 18647833
VI  - 105
DP  - 2008
TI  - Evolution of sequence specificity in a restriction endonuclease by a point mutation.
PG  - 10344-10347
AB  - Restriction endonucleases (REases) protect bacteria from invading foreign DNAs and are endowed
      with exquisite sequence specificity. REases have
      originated from the ancestral proteins and evolved new sequence
      specificities by genetic recombination, gene duplication, replication
      slippage, and transpositional events. They are also speculated to have
      evolved from nonspecific endonucleases, attaining a high degree of
      sequence specificity through point mutations. We describe here an example
      of generation of exquisitely site-specific REase from a highly-promiscuous
      one by a single point mutation.
AU  - Saravanan M
AU  - Vasu K
AU  - Nagaraja V
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2008 105: 10344-10347.

PMID- 1848651
VI  - 225
DP  - 1991
TI  - A new specific DNA endonuclease activity in yeast mitochondria.
PG  - 340-341
AB  - Two group I intron-encoded proteins from the yeast mitochondrial genome have already been
      shown to have a specific DNA endonuclease activity. This activity mediates intron insertion by
      cleaving the DNA sequence corresponding to the splice junction of an intronless strain. We
      have discovered in mitochondrial extracts from the yeast strain 777-3A a new DNA endonuclease
      activity which cleaves the fused exon A3-exon A4 junction sequence of the COXI gene.
AU  - Sargueil B
AU  - Delahodde A
AU  - Hatat D
AU  - Tian GL
AU  - Lazowska J
AU  - Jacq C
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1991 225: 340-341.

PMID- 2216759
VI  - 18
DP  - 1990
TI  - In vivo and in vitro analyses of an intron-encoded DNA endonuclease from yeast mitochondria.  Recognition site by site-directed mutagenesis.
PG  - 5659-5665
AB  - The pal 4 nuclease (termed I-Sce II) is encoded in the group I aI 4 intron of the COX I gene
      of Saccharomyces cerevisiae. It introduces a specific double-strand break at the junction of
      the two exons A4-A5 and thus mediates the insertion of the intron into an intronless strain.
      To define the sequence recognized by pal 4 we introduced 35 single mutations in its target
      sequence and examined their cleavage properties either in vivo in E. coli (when different
      forms of the paI 4 proteins were artificially produced) or in vitro with mitochondrial
      extracts of a mutant yeast strain blocked in the splicing of the aI 4 intron. We also detected
      the pal 4 DNA endonuclease activity in extracts of the wild type strain. The results suggest
      that 6 to 9 noncontiguous bases in the 17 base-pair region examined are necessary for pal 4
      nuclease to bind and cleave its recognition site. We observed that the pal 4 nuclease
      specificity can be significantly different with the different forms of the protein thus
      explaining why only some forms are highly toxic in E. coli. This study shows that pal 4
      recognition site is a complex phenomenon and this might have evolutionary implications on the
      transfer properties of the intron.
AU  - Sargueil B
AU  - Hatat D
AU  - Delahodde A
AU  - Jacq C
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 5659-5665.

PMID- 21573076
VI  - 6
DP  - 2011
TI  - Wolbachia Prophage DNA Adenine Methyltransferase Genes in Different Drosophila-Wolbachia Associations.
PG  - e19708
AB  - Wolbachia is an obligatory intracellular bacterium which often manipulates the reproduction of
      its insect and isopod hosts. In
      contrast, Wolbachia is an essential symbiont in filarial nematodes.
      Lately, Wolbachia has been implicated in genomic imprinting of host DNA
      through cytosine methylation. The importance of DNA methylation in cell
      fate and biology calls for in depth studing of putative
      methylation-related genes. We present a molecular and phylogenetic
      analysis of a putative DNA adenine methyltransferase encoded by a
      prophage in the Wolbachia genome. Two slightly different copies of the
      gene, met1 and met2, exhibit a different distribution over various
      Wolbachia strains. The met2 gene is present in the majority of strains,
      in wAu, however, it contains a frameshift caused by a 2 bp deletion.
      Phylogenetic analysis of the met2 DNA sequences suggests a long
      association of the gene with the Wolbachia host strains. In addition,
      our analysis provides evidence for previously unnoticed multiple
      infections, the detection of which is critical for the molecular
      elucidation of modification and/or rescue mechanism of cytoplasmic
      incompatibility.
AU  - Saridaki A
AU  - Sapountzis P
AU  - Harris HL
AU  - Batista PD
AU  - Biliske JA
AU  - Pavlikaki H
AU  - Oehler S
AU  - Savakis C
AU  - Braig HR
AU  - Bourtzis K
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2011 6: e19708.

PMID- 21914888
VI  - 193
DP  - 2011
TI  - Draft Genome Sequence of Nesterenkonia sp. Strain F, Isolated From Aran-Bidgol Salt Lake in Iran.
PG  - 5580
AB  - The draft genome of the aerobic, Gram-positive, halophilic chemoorganotroph Nesterenkonia sp.
      strain F consists of a 2,812,133-bp
      chromosome. This study is the first to report the shotgun-sequenced draft
      genome of a member of the genus Nesterenkonia.
AU  - Sarikhan S
AU  - Azarbaijani R
AU  - Yeganeh LP
AU  - Fazeli AS
AU  - Amoozegar MA
AU  - Salekdeh GH
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5580.

PMID- 30533939
VI  - 7
DP  - 2018
TI  - First Genome Sequence of Pasteurella multocida Type B Strain BAUTB2, a Major Pathogen Responsible for Mortality of Bovines in Bangladesh.
PG  - e00901-18
AB  - Here, we report the first genome sequence of Pasteurella multocida BAUTB2 isolated from a
      buffalo that died from hemorrhagic septicemia in Rajshahi,
      Bangladesh. Using Illumina HiSeq technology, the BAUTB2 genome length was
      determined to be 2,439,149 bp, with 40.8% GC content, 2,307 coding sequences
      (CDS), 6 rRNAs, 51 tRNAs, and 4 noncoding RNAs (ncRNAs).
AU  - Sarker MSA
AU  - Rahman MT
AU  - Mahmud MM
AU  - Tagliamonte MS
AU  - Chowdhury SMZH
AU  - Islam MR
AU  - Rahman MB
AU  - El Zowalaty ME
AU  - Nazir KHMNH
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e00901-18.

PMID- 2994650
VI  - 131
DP  - 1985
TI  - Conformational Microheterogeniety in a DNA Double Helix:  Structure of Restriction Endonuclease BamHI Recognition Site.
PG  - 269-276
AB  - Structural studies using 500 MHz 1H NMR spectroscopy on BamHI recognition site
      d(GGATCC)2 in solution at 19C is reported.  The resonances from the sugar ring
      and base protons have been assigned from the 2D-COSY and NOESY spectra.
      Analyses of the NOESY cross-peaks between the base protons H8/H6 and sugar
      protons H2'/H2", H3' reveal that the nucleotide units G2, A3 and C6 adopt
      (C3'-endo, x = 200o-220o) conformation while G1, T4 and C5 exhibit (C2'-endo,
      x= 240o-260o) conformation.  NMR data clearly suggest that the two strands of
      d(GGATCC)2 are conformationally equivalent and there is a structural two-fold
      between the two A-T pairs.  The above information and the NOESY data are used
      to generate a structural model of d(GGATCC)2.  The important features are: (i)
      G1-G2 stack, the site of cleavage, shows an alternation in sugar pucker i.e.
      C2'-endo, C3'-endo as in a B-A junction, (ii) G2-A3 stack adopts a mini A-DNA,
      both the sugars being C3'-endo, (iii) A3-T4 stack, the site of two-fold,
      displays an A-B junction with alternation in sugar pucker as C3'-endo,
      C2'-endo, (iv) T4-C5 stack adopts a mini B-DNA both the sugars being C2'-endo
      and (v) C5-C6 stack exhibits a B-A junction with C2'-endo, C3'-endo sugar
      puckers.  Thus, our studies demonstrate that conformational microheterogeniety
      with a structural two fold, is present in the BamHI recognition site.
AU  - Sarma MH
AU  - Dhingra MM
AU  - Gupta G
AU  - Sarma RH
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1985 131: 269-276.

PMID- 19717610
VI  - 191
DP  - 2009
TI  - Dam methylation controls O-antigen chain length in Salmonella enterica serovar enteritidis by regulating the expression of Wzz protein.
PG  - 6694-6700
AB  - We reported previously that a Salmonella enterica serovar Enteritidis dam mutant  expressing a
      truncated Dam protein does not agglutinate in the presence of
      specific antibodies against O9 polysaccharide. Here we investigate the
      participation of Dam in lipopolysaccharide (LPS) synthesis in Salmonella. The LPS
      O-antigen profiles of a dam null mutant (SEDeltadam) and the Salmonella serovar
      Enteritidis parental strain were examined by using electrophoresis and silver
      staining. Compared to the parental strain, SEDeltadam produced LPS with shorter
      O-antigen polysaccharide chains. Since Wzz is responsible for the chain length
      distribution of the O antigen, we investigated whether Dam methylation is
      involved in regulating wzz expression. Densitometry analysis showed that the
      amount of Wzz produced by SEDeltadam is threefold lower than the amount of Wzz
      produced by the parental strain. Concomitantly, the activity of the wzz promoter
      in SEDeltadam was reduced nearly 50% in logarithmic phase and 25% in stationary
      phase. These results were further confirmed by reverse transcription-PCR showing
      that wzz gene expression was threefold lower in the dam mutant than in the
      parental strain. Our results demonstrate that wzz gene expression is
      downregulated in a dam mutant, indicating that Dam methylation activates
      expression of this gene. This work indicates that wzz is a new target regulated
      by Dam methylation and demonstrates that DNA methylation not only affects the
      production of bacterial surface proteins but also the production of surface
      polysaccharides.
AU  - Sarnacki SH
AU  - Marolda CL
AU  - Noto LM
AU  - Giacomodonato MN
AU  - Valvano MA
AU  - Cerquetti MC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2009 191: 6694-6700.

PMID- 24224063
VI  - 8
DP  - 2013
TI  - The Role of the Methyltransferase Domain of Bifunctional Restriction Enzyme RM.BpuSI in Cleavage Activity.
PG  - e80967
AB  - Restriction enzyme (REase) RM.BpuSI can be described as a Type IIS/C/G REase for its cleavage
      site outside of the recognition sequence (Type IIS), bifunctional polypeptide possessing both
      methyltransferase (MTase) and endonuclease activities (Type IIC) and endonuclease activity
      stimulated by S-adenosyl-L-methionine (SAM) (Type IIG). The stimulatory effect of SAM on
      cleavage activity presents a major paradox: a co-factor of the MTase activity that renders the
      substrate unsusceptible to cleavage enhan es the cleavage activity. Here we show that the RM.
      BpuSI MTase activity modifies both cleavage substrate and product only when they are
      unmethylated. The MTase activity is, however, much lower than that of M1. BpuSI and is thought
      not to be the major MTase for host DNA protection. SAM and sinefungin (SIN) increase the V-max
      of the RM. BpuSI cleavage activity with a proportional change in Km, suggesting the presence
      of an energetically more favorable pathway is taken. We further showed that RM. BpuSI under
      goes substantial conformational changes in the presence of Ca2+, SIN, cleavage substrate
      and/or product. Distinct conformers are inferred as the pre-cleavage/cleavage state (in the
      presence of Ca2+, substrate or both) and MTase state (in the presence of SIN and substrate,
      SIN and product or product alone). Interestingly, RM. BpuSI adopts a unique conformation when
      only SIN is present. This SIN-bound state is inferred as a branch point for cleavage and MTase
      activity and an intermediate to an energetically  favorable pathway for cleavage, probably
      through increasing the binding affinity of the substrate to the enzyme under cleavage
      conditions. Mutation of a SAM-binding residue resulted in altered conformational changes in
      the presence of substrate or Ca2+ and eliminated cleavage activity. The present study
      underscores the role of the MTase domain as facilitator of efficient cleavage activity for RM.
      BpuSI.
AU  - Sarrade-Loucheur A
AU  - Xu SY
AU  - Chan SH
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2013 8: e80967.

PMID- 21190666
VI  - 100
DP  - 2011
TI  - In the Arms of EcoRI - probing the Binding Specificity of the Restriction Endonuclease Using Electron Spin Resonance.
PG  - 144a-145a
AB  - Pulsed electron spin resonance (ESR) was used to probe the binding specificity of EcoRI, a
      restriction endonuclease that binds to and cleaves a six base pair sequence of DNA. EcoRI
      binds to the specific sequence GAATTC with an affinity that is 50,000-90,000-fold greater than
      that of a miscognate site that differs by only one base pair. Low binding affinity is also
      exhibited at non-specific binding sites which differ from the specific sequence by two or more
      base pairs.  Distance measurements were performed on several spin labeled EcoRI mutants when
      bound to specific, miscognate, and non-specific sequences of DNA using Double
      Electron-Electron Resonance. These distances demonstrated that on average the arms of EcoRI,
      thought to play a major role in binding specificity, are similarly positioned. Additionally,
      noncognate (miscognate and non-specific) complexes demonstrated broader distance distributions
      indicating that the flexibility
      of the arms is greater in these complexes. Room temperature continuous
      wave (CW) experiments were also performed on the EcoRI mutant complexes at both X-band and
      W-band to probe the arm region dynamics. Higher sensitivity
      to the fast motional dynamics of the spin label at W-band resolved differences in two of the
      EcoRI complexes that were not apparent in the X-band CW spectra. Molecular dynamics (MD)
      simulations were performed on the
      spin-label-modified specific EcoRI-DNA crystal structure to model the average
      nitroxide orientation. Disparity in average distance as well as distribution indicates a need
      for further sampling of the spin label in silico. This work is supported by NSF.
AU  - Sarver J
AU  - Stone K
AU  - Townsend J
AU  - Sapienza P
AU  - Jen-Jacobson L
AU  - Saxena S
PT  - Journal Article
TA  - Biophys. J.
JT  - Biophys. J.
SO  - Biophys. J. 2011 100: 144a-145a.

PMID- 25103762
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Rodent Opportunistic Pathogen Pasteurella pneumotropica ATCC 35149T.
PG  - e00771-14
AB  - Pasteurella pneumotropica is an opportunistic pathogen in rodents that is commonly isolated
      from upper respiratory tracts in laboratory rodents. Here, we
      report the draft genome sequence of the P. pneumotropica type strain ATCC 35149,
      which was first isolated and characterized as biotype Jawetz.
AU  - Sasaki H
AU  - Ishikawa H
AU  - Asano R
AU  - Ueshiba H
AU  - Matsumoto T
AU  - Boot R
AU  - Kawamoto E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00771-14.

PMID- Not included in PubMed...
VI  - 49
DP  - 1985
TI  - Purification, properties and recognition sequence of site-specific restriction endonuclease from Gluconobacter cerinus IFO 3285.
PG  - 3017-3022
AB  - A type II restriction endonuclease designated as GceCLI, was purified from
      cells of Gluconobacter cerinus IFO 3285.  The purified enzyme was found to be
      homogeneous on polyacrylamide gel disc electrophoresis.  The enzyme worked best
      at 37C and pH 7.5 and required 7mm MgCl2 and 100 mm NaCl.  The purified enzyme
      was stable when preincubated over a pH range of 7.5 to 9.5 for 12 hr at 4C and
      a temperature range of 37 to 40C for 5 min at pH 7.5.  The enzyme was shown to
      cleave lambda, PhiX174 RF, SV40, pBR322, M13 mp7 RF and Ad2 DNAs at 4, 1,0,0,0
      and 25 or more sites, respectively, and to recognize the DNA sequence of
      5'-C-C-G-G-3' and to cut between C and G on the right side of the sequence,
      being an isoschizomer of SacII of Streptomyces achromogenes ATCC 12767.
AU  - Sasaki J
AU  - Murakami M
AU  - Yamada Y
PT  - Journal Article
TA  - Agric. Biol. Chem.
JT  - Agric. Biol. Chem.
SO  - Agric. Biol. Chem. 1985 49: 3017-3022.

PMID- Not included in PubMed...
VI  - 48
DP  - 1984
TI  - Purification, properties and recognition sequence of site-specific restriction endonuclease from Acetobacter liquefaciens AJ 2881.
PG  - 3027-3034
AB  - A type II restriction endonuclease, designated as AliAJI, was purified from
      cells of Acetobacter liquefaciens AJ 2881 by combined column chromatography on
      heparin-Sepharose CL-6B, DEAE-Sepharose CL-6B and blue Sepharose CL-6B.  The
      purified enzyme was homogeneous on polyacrylamide gel disc electrophoresis, and
      the enzyme preparation was free from other nuclease activities, as judged by
      constancy of lambda DNA-digest electrophoretic patterns after prolonged
      incubation fro 24 hr.  The enzyme was optimally active at 37C at pH 7.5,
      required neither sodium chloride nor ammonium sulfate, both of which rather
      inhibited enzyme activity at high concentration (100 and 75 mM, respectively),
      and cleaved lambda, PhiX174 RF, SV40, pBR322, M13 mp7RF and Ad2 DNAs at 18, 1,
      2, 1, 1 and 25 more sites, respectively.  The recognition sequence of the
      enzyme on DNA molecules was determined to be 5'-C-T-G-C-A-G-3', and the enzyme
      was found to cut between A and G in the sequence, being an isoschizomer of the
      endonuclease of Providencia stuartii 164 (PstI).
AU  - Sasaki J
AU  - Yamada Y
PT  - Journal Article
TA  - Agric. Biol. Chem.
JT  - Agric. Biol. Chem.
SO  - Agric. Biol. Chem. 1984 48: 3027-3034.

PMID- 16332782
VI  - 71
DP  - 2005
TI  - Purification of cytochrome P450 and ferredoxin, involved in bisphenol A degradation, from Sphingomonas sp. strain AO1.
PG  - 8024-8030
AB  - In a previous study (M. Sasaki, J. Maki, K. Oshiman, Y. Matsumura, and T.
      Tsuchido, Biodegradation 16:449-459, 2005), the cytochrome P450 monooxygenase
      system was shown to be involved in bisphenol A (BPA) degradation by Sphingomonas
      sp. strain AO1. In the present investigation, we purified the components of this
      monooxygenase, cytochrome P450 (P450bisd), ferredoxin (Fd(bisd)), and ferredoxin
      reductase (Red(bisd)). We demonstrated that P450bisd and Fd(bisd) are homodimeric
      proteins with molecular masses of 102.3 and 19.1 kDa, respectively, by gel
      filtration chromatography analysis. Spectroscopic analysis of Fd(bisd) revealed
      the presence of a putidaredoxin-type [2Fe-2S] cluster. P450(bisd), in the
      presence of Fd(bisd), Red(bisd), and NADH, was able to convert BPA. The K(m) and
      kcat values for BPA degradation were 85 +/- 4.7 microM and 3.9 +/- 0.04 min(-1),
      respectively. NADPH, spinach ferredoxin, and spinach ferredoxin reductase
      resulted in weak monooxygenase activity. These results indicated that the
      electron transport system of P450bisd might exhibit strict specificity. Two BPA
      degradation products of the P450(bisd) system were detected by high-performance
      liquid chromatography analysis and were thought to be
      1,2-bis(4-hydroxyphenyl)-2-propanol and 2,2-bis(4-hydroxyphenyl)-1-propanol based
      on mass spectrometry-mass spectrometry analysis. This is the first report
      demonstrating that the cytochrome P450 monooxygenase system in bacteria is
      involved in BPA degradation.
AU  - Sasaki M
AU  - Akahira A
AU  - Oshiman K
AU  - Tsuchido T
AU  - Matsumura Y
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2005 71: 8024-8030.

PMID- 26514766
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Methicillin-Resistant Staphylococcus schleiferi Strain TSCC54 of Canine Origin.
PG  - e01268-15
AB  - We report a complete genome sequence of the methicillin-resistant Staphylococcus  schleiferi
      strain TSCC54, isolated from the skin of a dog in Tokyo, Japan.
AU  - Sasaki T
AU  - Tsubakishita S
AU  - Kuwahara-Arai K
AU  - Matsuo M
AU  - Lu YJ
AU  - Tanaka Y
AU  - Hiramatsu K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01268-15.

PMID- 12466555
VI  - 30
DP  - 2002
TI  - The complete genomic sequence of Mycoplasma penetrans, an intracellular bacterial pathogen in humans.
PG  - 5293-5300
AB  - The complete genomic sequence of an intracellular bacterial pathogen, Mycoplasma penetrans
      HF-2 strain, was determined. The HF-2 genome consists of a 1 358 633 bp single circular
      chromosome containing 1038 predicted coding sequences (CDSs), one set of rRNA genes and 30
      tRNA genes. Among the 1038 CDSs, 264 predicted proteins are common to the Mycoplasmataceae
      sequenced thus far and 463 are M.penetrans specific. The genome contains the two-component
      system but lacks the essential cellular gene, uridine kinase. The relatively large genome of
      M.penetrans HF-2 among mycoplasma species may be accounted for by both its rich core proteome
      and the presence of a number of paralog families corresponding to 25.4% of all CDSs. The
      largest paralog family is the p35 family, which encodes surface lipoproteins including the
      major antigen, P35. A total of 44 genes for p35 and p35 homologs were identified and 30 of
      them form one large cluster in the chromosome. The genetic tree of p35 paralogs suggests the
      occurrence of dynamic chromosomal rearrangement in paralog formation during evolution. Thus,
      M.penetrans HF-2 may have acquired diverse repertoires of antigenic variation-related genes to
      allow its persistent infection in humans.
AU  - Sasaki Y
AU  - Ishikawa J
AU  - Yamashita A
AU  - Oshima K
AU  - Kenri T
AU  - Furuya K
AU  - Yoshino C
AU  - Horino A
AU  - Shiba T
AU  - Sasaki T
AU  - Hattori M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2002 30: 5293-5300.

PMID- 17267608
VI  - 104
DP  - 2007
TI  - Site-specific DNA transesterification catalyzed by a restriction enzyme.
PG  - 2115-2120
AB  - Most restriction endonucleases use Mg2+ to hydrolyze phosphodiester bonds at specific DNA
      sites. We show here that Bfil, a
      metal-independent restriction enzyme from the phospholipase D
      superfamily, catalyzes both DNA hydrolysis and transesterification
      reactions at its recognition site. In the presence of alcohols such as
      ethanol or glycerol, it attaches the alcohol covalently to the 5'
      terminus of the cleaved DNA. Under certain conditions, the terminal
      3'-OH of one DNA strand can attack the target phosphodiester bond in
      the other strand to create a DNA hairpin. Transesterification reactions
      on DNA with phosphorothioate linkages at the target bond proceed with
      retention of stereoconfiguration at the phosphorus, indicating,
      uniquely for a restriction enzyme, a two-step mechanism. We propose
      that Bfil first makes a covalent enzyme-DNA intermediate, and then it
      resolves it by a nucleophilic attack of water or an alcohol, to yield
      hydrolysis or transesterification products, respectively.
AU  - Sasnauskas G
AU  - Connolly BA
AU  - Halford SE
AU  - Siksnys V
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2007 104: 2115-2120.

PMID- 18515343
VI  - 36
DP  - 2008
TI  - Template-directed addition of nucleosides to DNA by the BfiI restriction enzyme.
PG  - 3969-3977
AB  - Restriction endonucleases catalyse DNA cleavage at specific sites. The BfiI endonuclease cuts
      DNA to give staggered ends with 1-nt 3'-extensions.
      We show here that BfiI can also fill in the staggered ends: while cleaving
      DNA, it can add a 2'-deoxynucleoside to the reaction product to yield
      directly a blunt-ended DNA. We propose that nucleoside incorporation
      proceeds through a two-step reaction, in which BfiI first cleaves the DNA
      to make a covalent enzyme-DNA intermediate and then resolves it by a
      nucleophilic attack of the 3'-hydroxyl group of the incoming nucleoside,
      to yield a transesterification product. We demonstrate that base pairing
      of the incoming nucleoside with the protruding DNA end serves as a
      template for the incorporation and governs the yield of the elongated
      product. The efficiency of the template-directed process has been
      exploited by using BfiI for the site-specific modification of DNA
      5'-termini with an amino group using a 5'-amino-5'-deoxythymidine.
AU  - Sasnauskas G
AU  - Connolly BA
AU  - Halford SE
AU  - Siksnys V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2008 36: 3969-3977.

PMID- 12750473
VI  - 100
DP  - 2003
TI  - How the BfiI restriction enzyme uses one active site to cut two DNA strands.
PG  - 6410-6415
AB  - Unlike other restriction enzymes, BfiI functions without metal ions. It recognizes an
      asymmetric DNA sequence, 5'-ACTGGG-3', and cuts top and
      bottom strands at fixed positions downstream of this sequence. Many
      restriction enzymes are dimers of identical subunits, with one active site
      for each DNA strand. Others, like FokI, dimerize transiently during
      catalysis. BfiI is also a dimer but it has only one active site, at the
      dimer interface. We show here that BfiI remains a dimer as it makes
      double-strand breaks in DNA and that its single active site acts
      sequentially, first on the bottom and then the top strand. Hence, after
      cutting the bottom strand, a rearrangement of either the protein and/or
      the DNA in the BfiI-DNA complex must switch the active site to the top
      strand. Low pH values selectively block top-strand cleavage, converting
      BfiI into a nicking enzyme that cleaves only the bottom strand. The switch
      to the top strand may depend on the ionization of the cleaved 5' phosphate
      in the bottom strand. BfiI thus uses a mechanism for making double-strand
      breaks that is novel among restriction enzymes.
AU  - Sasnauskas G
AU  - Halford SE
AU  - Siksnys V
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2003 100: 6410-6415.

PMID- 10194315
VI  - 38
DP  - 1999
TI  - Plasmid DNA cleavage by MunI restriction enzyme: Single-turnover and steady-state kinetic analysis.
PG  - 4028-4036
AB  - Mutational analysis has previously indicated that D83 and E98 residues are essential for DNA
      cleavage activity and presumably chelate a Mg2+ ion at the active site of MunI restriction
      enzyme. In the absence of metal ions, protonation of an ionizable residue with a pKa > 7.0,
      most likely one of the active site carboxylates, controls the DNA binding specificity of MunI.
      Thus, competition between H+ and Mg2+ binding at the active site of MunI presumably plays an
      important role in catalysis/binding. In the present study we have identified elementary steps
      and intermediates in the reaction pathway of plasmid DNA cleavage by MunI and elucidated the
      effect of pH and Mg2+ ions on the individual steps of the DNA cleavage reaction. The kinetic
      analysis indicated that the multiple-turnover rate of plasmid cleavage by MunI is limited by
      product release     throughout the pH range 6.0-9.3. Quenched-flow experiments revealed that
      open circle DNA is an obligatory intermediate in the reaction pathway. Under optimal reaction
      conditions, open circle DNA remains bound to the MunI; however it is released into the
      solution at low [MgCl2]. Rate constants for the phosphodiester bond hydrolysis of the first
      (k1) and second (k2) strand of plasmid DNA at pH 7.0 and 10 mM MgCl2 more than 100-fold exceed
      the kcat value which is limited by product dissociation. The analysis of the pH and [Mg2+]
      dependences of k1 and k2 revealed that both H+ and Mg2+ ions compete for the binding to the
      same residue at the active site of MunI. Thus, the decreased rate of phosphodiester hydrolysis
      by MunI at pH < 7.0 may be due to the reduction of affinity for the Mg2+ binding at the active
      site. Kinetic analysis of DNA cleavage by MunI yielded estimates for the
      association-dissociation rate constants of enzyme-substrate complex and demonstrated the
      decreased stability of the MunI-DNA complex at pH values above 8.0.
AU  - Sasnauskas G
AU  - Jeltsch A
AU  - Pingoud A
AU  - Siksnys V
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1999 38: 4028-4036.

PMID- 21771860
VI  - 39
DP  - 2011
TI  - Target site cleavage by the monomeric restriction enzyme BcnI requires translocation to a random DNA sequence and a switch in enzyme orientation.
PG  - 8844-8856
AB  - Endonucleases that generate double-strand breaks in DNA often possess two identical subunits
      related by rotational symmetry, arranged so that the
      active sites from each subunit act on opposite DNA strands. In contrast to
      many endonucleases, Type IIP restriction enzyme BcnI, which recognizes the
      pseudopalindromic sequence 5'-CCSGG-3' (where S stands for C or G) and
      cuts both DNA strands after the second C, is a monomer and possesses a
      single catalytic center. We show here that to generate a double-strand
      break BcnI nicks one DNA strand, switches its orientation on DNA to match
      the polarity of the second strand and then cuts the phosphodiester bond on
      the second DNA strand. Surprisingly, we find that an enzyme flip required
      for the second DNA strand cleavage occurs without an excursion into bulk
      solution, as the same BcnI molecule acts processively on both DNA strands.
      We provide evidence that after cleavage of the first DNA strand, BcnI
      remains associated with the nicked intermediate and relocates to the
      opposite strand by a short range diffusive hopping on DNA.
AU  - Sasnauskas G
AU  - Kostiuk G
AU  - Tamulaitis G
AU  - Siksnys V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2011 39: 8844-8856.

PMID- 28934493
VI  - 45
DP  - 2017
TI  - UbaLAI is a monomeric Type IIE restriction enzyme.
PG  - 9583-9594
AB  - Type II restriction endonucleases (REases) form a large and highly diverse group  of enzymes.
      Even REases specific for a common recognition site often vary in
      their oligomeric structure, domain organization and DNA cleavage mechanisms. Here
      we report biochemical and structural characterization of the monomeric
      restriction endonuclease UbaLAI, specific for the pseudosymmetric DNA sequence
      5'-CC/WGG-3' (where W = A/T, and '/' marks the cleavage position). We present a
      1.6 A co-crystal structure of UbaLAI N-terminal domain (UbaLAI-N) and show that
      it resembles the B3-family domain of EcoRII specific for the 5'-CCWGG-3'
      sequence. We also find that UbaLAI C-terminal domain (UbaLAI-C) is closely
      related to the monomeric REase MvaI, another enzyme specific for the 5'-CCWGG-3'
      sequence. Kinetic studies of UbaLAI revealed that it requires two recognition
      sites for optimal activity, and, like other type IIE enzymes, uses one copy of a
      recognition site to stimulate cleavage of a second copy. We propose that during
      the reaction UbaLAI-N acts as a handle that tethers the monomeric UbaLAI-C domain
      to the DNA, thereby helping UbaLAI-C to perform two sequential DNA nicking
      reactions on the second recognition site during a single DNA-binding event. A
      similar reaction mechanism may be characteristic to other monomeric two-domain
      REases.
AU  - Sasnauskas G
AU  - Tamulaitiene G
AU  - Tamulaitis G
AU  - Calyseva J
AU  - Laime M
AU  - Rimseliene R
AU  - Lubys A
AU  - Siksnys V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2017 45: 9583-9594.

PMID- 26001968
VI  - 43
DP  - 2015
TI  - Structure-guided sequence specificity engineering of the modification-dependent restriction endonuclease LpnPI.
PG  - 6144-6155
AB  - The eukaryotic Set and Ring Associated (SRA) domains and structurally similar DNA recognition
      domains of prokaryotic cytosine modification-dependent restriction
      endonucleases recognize methylated, hydroxymethylated or glucosylated cytosine in
      various sequence contexts. Here, we report the apo-structure of the N-terminal
      SRA-like domain of the cytosine modification-dependent restriction enzyme LpnPI
      that recognizes modified cytosine in the 5'-C(mC)DG-3' target sequence (where mC
      is 5-methylcytosine or 5-hydroxymethylcytosine and D = A/T/G). Structure-guided
      mutational analysis revealed LpnPI residues involved in base-specific
      interactions and demonstrated binding site plasticity that allowed limited target
      sequence degeneracy. Furthermore, modular exchange of the LpnPI specificity loops
      by structural equivalents of related enzymes AspBHI and SgrTI altered sequence
      specificity of LpnPI. Taken together, our results pave the way for specificity
      engineering of the cytosine modification-dependent restriction enzymes.
AU  - Sasnauskas G
AU  - Zagorskaite E
AU  - Kauneckaite K
AU  - Tamulaitiene G
AU  - Siksnys V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2015 43: 6144-6155.

PMID- 20047964
VI  - 38
DP  - 2010
TI  - A novel mechanism for the scission of double-stranded DNA: BfiI cuts both 3'-5' and 5'-3' strands by rotating a single active site.
PG  - 2399-2410
AB  - Metal-dependent nucleases that generate double-strand breaks in DNA often possess two
      symmetrically-equivalent subunits, arranged so that the active
      sites from each subunit act on opposite DNA strands. Restriction
      endonuclease BfiI belongs to the phospholipase D (PLD) superfamily and
      does not require metal ions for DNA cleavage. It exists as a dimer but has
      at its subunit interface a single active site that acts sequentially on
      both DNA strands. The active site contains two identical histidines
      related by 2-fold symmetry, one from each subunit. This symmetrical
      arrangement raises two questions: first, what is the role and the
      contribution to catalysis of each His residue; secondly, how does a
      nuclease with a single active site cut two DNA strands of opposite
      polarities to generate a double-strand break. In this study, the roles of
      active-site histidines in catalysis were dissected by analysing
      heterodimeric variants of BfiI lacking the histidine in one subunit. These
      variants revealed a novel mechanism for the scission of double-stranded
      DNA, one that requires a single active site to not only switch between
      strands but also to switch its orientation on the DNA.
AU  - Sasnauskas G
AU  - Zakrys L
AU  - Zaremba M
AU  - Cosstick R
AU  - Gaynor JW
AU  - Halford SE
AU  - Siksnys V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2010 38: 2399-2410.

PMID- 22461548
VI  - 194
DP  - 2012
TI  - Genome Sequence of Staphylococcus aureus VC40, a Vancomycin- and Daptomycin-Resistant Strain, To Study the Genetics of Development of Resistance  to Currently Applied Last-Resort Antibiotics.
PG  - 2107-2108
AB  - The increasing emergence of multidrug-resistant Staphylococcus aureus is a problem of global
      importance. Here, we report the genome of S. aureus VC40, which
      is resistant to the last-resort antibiotics vancomycin and daptomycin. Its genome
      sequence will allow insights into the mechanisms that convey full resistance to
      these compounds.
AU  - Sass P
AU  - Berscheid A
AU  - Jansen A
AU  - Oedenkoven M
AU  - Szekat C
AU  - Strittmatter A
AU  - Gottschalk G
AU  - Bierbaum G
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2107-2108.

PMID- 23950133
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Manhattan Strain 111113, from an Outbreak of Human Infections in Northern Italy.
PG  - e00632-13
AB  - We announce the draft genome sequence of Salmonella enterica subsp. enterica serovar Manhattan
      strain 111113, isolated from a patient during an outbreak in
      northern Italy. The genome, which was obtained with Illumina MiSeq technology, is
      composed of 21 contigs for a total of 4,684,342 bp, with a G+C content of 52.17%.
AU  - Sassera D
AU  - Gaiarsa S
AU  - Scaltriti E
AU  - Morganti M
AU  - Bandi C
AU  - Casadei G
AU  - Pongolini S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00632-13.

PMID- 23599297
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Stenotrophomonas maltophilia Strain EPM1, Found in Association with a Culture of the Human Parasite Giardia duodenalis.
PG  - e00182-13
AB  - We report the draft genome sequence of the Stenotrophomonas maltophilia strain EPM1, found in
      association with a culture of Giardia duodenalis. The draft genome
      sequence of S. maltophilia strain EPM1, obtained with Roche 454 GS-FLX Titanium
      technology, is composed of 19 contigs totaling 4,785,869 bp, with a G+C content
      of 66.37%.
AU  - Sassera D
AU  - Leardini I
AU  - Villa L
AU  - Comandatore F
AU  - Carta C
AU  - Almeida A
AU  - do Ceu SM
AU  - Gaiarsa S
AU  - Marone P
AU  - Pozio E
AU  - Caccio SM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00182-13.

PMID- 21690562
VI  - 28
DP  - 2011
TI  - Phylogenomic evidence for the presence of a flagellum and cbb3 oxidase in the free-living mitochondrial ancestor.
PG  - 3285-3296
AB  - The initiation of the intracellular symbiosis that would give rise to
      mitochondria and eukaryotes was a major event in the history of life on
      earth. Hypotheses to explain eukaryogenesis fall into two broad and
      competing categories: those proposing that the host was a phagocytotic
      proto-eukaryote that preyed upon the free-living mitochondrial ancestor
      (hereafter FMA) and those proposing that the host was an archaebacterium
      that engaged in syntrophy with the FMA. Of key importance to these
      hypotheses are whether the FMA was motile or non-motile, and the
      atmospheric conditions under which the FMA thrived. Reconstructions of the
      FMA based on genome content of Rickettsiales representatives - generally
      considered to be the closest living relatives of mitochondria - indicate
      that it was non-motile and aerobic. We have sequenced the genome of
      Candidatus Midichloria mitochondrii, a novel and phylogenetically
      divergent member of the Rickettsiales. We found that it possesses unique
      gene sets found in no other Rickettsiales, including 26 genes associated
      with flagellar assembly, and a cbb(3)-type cytochrome oxidase.
      Phylogenomic analyses show that these genes were inherited in a vertical
      fashion from an ancestral alpha-proteobacterium, and indicate that the FMA
      possessed a flagellum, and could undergo oxidative phosphorylation under
      both aerobic and microoxic conditions. These results indicate that the FMA
      played a more active and potentially parasitic role in eukaryogenesis than
      currently appreciated, and provide an explanation for how the symbiosis
      could have evolved under low levels of oxygen.
AU  - Sassera D
AU  - Lo N
AU  - Epis S
AU  - D'Auria G
AU  - Montagna M
AU  - Comandatore F
AU  - Horner D
AU  - Pereto J
AU  - Luciano AM
AU  - Franciosi F
AU  - Ferri E
AU  - Crotti E
AU  - Bazzocchi C
AU  - Daffonchio D
AU  - Sacchi L
AU  - Moya A
AU  - Latorre A
AU  - Bandi C
PT  - Journal Article
TA  - Mol. Biol. Evol.
JT  - Mol. Biol. Evol.
SO  - Mol. Biol. Evol. 2011 28: 3285-3296.

PMID- 24874681
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Mycobacterium triplex DSM 44626.
PG  - e00499-14
AB  - We announce the draft genome sequence of Mycobacterium triplex strain DSM 44626,  a
      nontuberculosis species responsible for opportunistic infections. The genome
      described here is composed of 6,382,840 bp, with a G+C content of 66.57%, and
      contains 5,988 protein-coding genes and 81 RNA genes.
AU  - Sassi M
AU  - Croce O
AU  - Robert C
AU  - Raoult D
AU  - Drancourt M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00499-14.

PMID- 25169861
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Staphylococcus aureus subsp. aureus Strain HG003, an NCTC8325 Derivative.
PG  - e00855-14
AB  - We report the draft genome sequence of a Staphylococcus aureus NCTC8325 derivative, strain
      HG003. HG003 contains functional global regulators rsbU and
      tcaR and is therefore considered as a reference for studies of regulation and
      virulence. The genome is composed of 2,797,898 bp and will be essential for
      subsequent RNAseq analysis.
AU  - Sassi M
AU  - Felden B
AU  - Augagneur Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00855-14.

PMID- 23950116
VI  - 1
DP  - 2013
TI  - Noncontiguous Genome Sequence of Mycobacterium septicum Strain DSM 44393T.
PG  - e00574-13
AB  - The rapidly growing Mycobacterium septicum rarely causes pulmonary infections. We report here
      the draft genome sequence of M. septicum strain DSM 44393(T),
      isolated from catheter-related bacteremia and initially identified as a member of
      Mycobacterium fortuitum.
AU  - Sassi M
AU  - Robert C
AU  - Raoult D
AU  - Drancourt M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00574-13.

PMID- 23991261
VI  - 8
DP  - 2013
TI  - Non-contiguous genome sequence of Mycobacterium simiae strain DSM 44165(T.).
PG  - 306-317
AB  - Mycobacterium simiae is a non-tuberculosis mycobacterium causing pulmonary infections in both
      immunocompetent and imunocompromized patients. We announce the
      draft genome sequence of M. simiae DSM 44165(T). The 5,782,968-bp long genome
      with 65.15% GC content (one chromosome, no plasmid) contains 5,727 open reading
      frames (33% with unknown function and 11 ORFs sizing more than 5000 -bp), three
      rRNA operons, 52 tRNA, one 66-bp tmRNA matching with tmRNA tags from
      Mycobacterium avium, Mycobacterium tuberculosis, Mycobacterium bovis,
      Mycobacterium microti, Mycobacterium marinum, and Mycobacterium africanum and 389
      DNA repetitive sequences. Comparing ORFs and size distribution between M. simiae
      and five other Mycobacterium species M. simiae clustered with M. abscessus and M.
      smegmatis. A 40-kb prophage was predicted in addition to two prophage-like
      elements, 7-kb and 18-kb in size, but no mycobacteriophage was seen after the
      observation of 10(6) M. simiae cells. Fifteen putative CRISPRs were found. Three
      genes were predicted to encode resistance to aminoglycosides, betalactams and
      macrolide-lincosamide-streptogramin B. A total of 163 CAZYmes were annotated. M.
      simiae contains ESX-1 to ESX-5 genes encoding for a type-VII secretion system.
      Availability of the genome sequence may help depict the unique properties of this
      environmental, opportunistic pathogen.
AU  - Sassi M
AU  - Robert C
AU  - Raoult D
AU  - Drancourt M
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 306-317.

PMID- 25676774
VI  - 3
DP  - 2015
TI  - Genome Sequence of the Clinical Isolate Staphylococcus aureus subsp. aureus Strain UAMS-1.
PG  - e01584-14
AB  - We report here the draft genome sequence of Staphylococcus aureus subsp. aureus strain UAMS-1.
      UAMS-1 is a virulent oxacillin-susceptible clinical isolate. Its
      genome is composed of 2,763,963 bp and will be useful for further gene expression
      analysis using RNA sequencing (RNA-seq) technology.
AU  - Sassi M
AU  - Sharma D
AU  - Brinsmade SR
AU  - Felden B
AU  - Augagneur Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01584-14.

PMID- 29074668
VI  - 5
DP  - 2017
TI  - Draft Whole-Genome Sequence of Psychrotrophic Arthrobacter sp. Strain 7749, Isolated from Antarctic Marine Sediments with Applications in Enantioselective  Alcohol Oxidation.
PG  - e01197-17
AB  - Here, we report the 4.12-Mb draft genome sequence of Arthrobacter sp. strain 7749, isolated
      from marine sediment samples of the Antarctic Peninsula, using
      enriched medium with (RS)-1-(4-phenyl)-ethanol as a carbon source. This genome
      sequence will provide relevant information for applications in enantioselective
      alcohol oxidation to improve industrial catalytic processes.
AU  - Sastre DE
AU  - Santos LP
AU  - Kagohara E
AU  - Andrade LH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01197-17.

PMID- 26656597
VI  - 10
DP  - 2015
TI  - DNA Methylation Assessed by SMRT Sequencing Is Linked to Mutations in Neisseria meningitidis Isolates.
PG  - e0144612
AB  - The Gram-negative bacterium Neisseria meningitidis features extensive genetic variability. To
      present, proposed virulence genotypes are also detected in
      isolates from asymptomatic carriers, indicating more complex mechanisms
      underlying variable colonization modes of N. meningitidis. We applied the Single
      Molecule, Real-Time (SMRT) sequencing method from Pacific Biosciences to assess
      the genome-wide DNA modification profiles of two genetically related N.
      meningitidis strains, both of serogroup A. The resulting DNA methylomes revealed
      clear divergences, represented by the detection of shared and of strain-specific
      DNA methylation target motifs. The positional distribution of these methylated
      target sites within the genomic sequences displayed clear biases, which suggest a
      functional role of DNA methylation related to the regulation of genes. DNA
      methylation in N. meningitidis has a likely underestimated potential for
      variability, as evidenced by a careful analysis of the ORF status of a panel of
      confirmed and predicted DNA methyltransferase genes in an extended collection of
      N. meningitidis strains of serogroup A. Based on high coverage short sequence
      reads, we find phase variability as a major contributor to the variability in DNA
      methylation. Taking into account the phase variable loci, the inferred functional
      status of DNA methyltransferase genes matched the observed methylation profiles.
      Towards an elucidation of presently incompletely characterized functional
      consequences of DNA methylation in N. meningitidis, we reveal a prominent
      colocalization of methylated bases with Single Nucleotide Polymorphisms (SNPs)
      detected within our genomic sequence collection. As a novel observation we report
      increased mutability also at 6mA methylated nucleotides, complementing mutational
      hotspots previously described at 5mC methylated nucleotides. These findings
      suggest a more diverse role of DNA methylation and Restriction-Modification (RM)
      systems in the evolution of prokaryotic genomes.
AU  - Sater MR
AU  - Lamelas A
AU  - Wang G
AU  - Clark TA
AU  - Roltgen K
AU  - Mane S
AU  - Korlach J
AU  - Pluschke G
AU  - Schmid CD
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2015 10: e0144612.

PMID- 28839031
VI  - 5
DP  - 2017
TI  - Complete Sequence of a Staphylococcus aureus Clonal Complex 81 Strain, the Dominant Lineage in Food Poisoning Outbreaks in Japan.
PG  - e00853-17
AB  - Staphylococcus aureus No. 10 is an isolate from a staphylococcal food poisoning outbreak in
      Japan, classified as clonal complex 81 subtype 1. It preferentially
      produces larger quantities of staphylococcal enterotoxin A (SEA) and
      staphylococcal enterotoxin H (SEH) in foods and media. Here, we report the
      complete annotated genome sequence of the chromosome and a plasmid.
AU  - Sato'o Y
AU  - Hisatsune J
AU  - Hirakawa H
AU  - Ono HK
AU  - Omoe K
AU  - Sugai M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00853-17.

PMID- 1369309
VI  - 54
DP  - 1990
TI  - Purification of restriction endonuclease from Acetobacter aceti IFO 3281 (AatII) and its properties.
PG  - 3319-3325
AB  - The restriction endonuclease AatII was purified from cell-free extracts of
      Acetobacter aceti IFO 3281 by streptomycin treatment, ammonium sulfate
      fractionation, combined column chromatographies on DEAE-Toyopearl 650S,
      heparin-Sepharose CL-6B and DEAE-Sepharose CL-6B and FPLC on Mono Q and on
      Superose 12 (gel filtration).  The purified enzyme was homogeneous on
      SDS-polyacrylamide gel disk electrophoresis.  The relative molecular mass of
      the purified enzyme was 190,000 daltons by gel filtration.  The
      SDS-polyacrylamide gel disk electrophoresis gave the relative molecular mass of
      47,500 daltons.  These data indicated that the purified, native enzyme is a
      tetramer (190,000 daltons) composed of four 47,500-dalton subunits.  The
      isoelectric point of the enzyme was 6.0.  The purified enzyme was intensely
      activated by manganese ion (50-fold increase or more when compared with
      magnesium ion).  The enzyme worked best at 37C and pH 8.5 in a reaction mixture
      (50 microliters) containing 1.0 micrograms lambda DNA, 10 mM Tris-HCI, 7 mM
      2-mercaptoethanol, 7 mM MnCl2 and 50 mM NaCl.  The enzyme recognizes the same
      palindromic hexanucleotide sequence 5'-GACGTC-3', cuts between T and C and
      produces a 3'-tetranucleotide extension in the presence of MnCl2, as it does in
      the presence of MgCl2.
AU  - Sato H
AU  - Suzuki T
AU  - Yamada Y
PT  - Journal Article
TA  - Agric. Biol. Chem.
JT  - Agric. Biol. Chem.
SO  - Agric. Biol. Chem. 1990 54: 3319-3325.

PMID- Not included in PubMed...
VI  - 36
DP  - 1990
TI  - The restriction endonuclease AatI from Acetobacter aceti IFO 3281, an isoschizomer of StuI, has a dimeric structure.
PG  - 273-277
AB  - The restriction endonuclease AatI, an isoschizomer of the StuI endonuclease,
      was first reported in Acetobacter aceti IFO 3281 by Sugisaki et al.  However, a
      detailed enzymatic study has not been done as yet regarding the AatI
      endonuclease.  During the course of our studies on acetic acid bacteria, we
      purified the AatI endonuclease to a homogeneous state and found that the enzyme
      has a dimeric structure.  This paper describes the purification and properties
      of the AatI endonuclease.
AU  - Sato H
AU  - Yamada Y
PT  - Journal Article
TA  - J. Gen. Appl. Microbiol.
JT  - J. Gen. Appl. Microbiol.
SO  - J. Gen. Appl. Microbiol. 1990 36: 273-277.

PMID- 265518
VI  - 74
DP  - 1977
TI  - A thermostable sequence-specific endonuclease from Thermus aquaticus.
PG  - 542-546
AB  - A sequence-specific endonuclease, TaqI, of novel specificity has been partially purified from
      an extreme thermophile, Thermus aquaticus.  The enzyme cleaves bacteriophage lambda DNA at
      many (>30) sites and bacteriophage PhiX174 RF DNA at 10 sites.  The enzyme is active at
      temperatures up to 79C.  The cleavage sites on PhiX174 RF DNA have been mapped.  The sequence
      recognized and cleaved by TaqI has been shown to be the symmetrical tetranucleotide:
      5' T-^C-G-A 3'
      3' A-G-C-^T 5'.
AU  - Sato S
AU  - Hutchison CA III
AU  - Harris JI
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1977 74: 542-546.

PMID- 6448253
VI  - 88
DP  - 1980
TI  - A DNA methylase from Thermus thermophilus HB8.
PG  - 737-747
AB  - A DNA methylase was purified in a homogeneous state from an extremely
      thermophilic bacterium, Thermus thermophilus HB8, by chromatography on,
      successively, phosphocellulose, CM-cellulose, and haparin-Sepharose.  The
      molecular weight of the enzyme was determined to be about 44,000 by gel
      filtration on a Sephadex G-100 column and 41,000 by SDS-polyacrylamide gel
      electrophoresis, and these findings suggest a single polypeptide enzyme.  The
      enzyme develops maximum activity around pH 7.4 and at 70C.  Enzymatic activity
      is completely inhibited by 0.2M NaCl or 2 mM HgCl2.  The enzyme transfers
      methyl groups from S-adenosyl-L-methionine to a double stranded DNA.  The sole
      product of the reaction was identified as N-6-methyl adenine after hydrolysis
      of the DNA with formic acid.  The enzyme kinetics obey the Michaelis-Menten
      equation and Km values for S-adenosylmethionine and lambda phage DNA were
      determined to be 0.8 microM and 10 microgram/ml, respectively.  The enzyme does
      not transfer methyl groups to TthHB8I endonuclease digested DNA as well as the
      host (T. thermophilus HB8) DNA.  The number of methyl groups of the fully
      methylated PhiX174 RF DNA was about twice as many as TthHB8I endonuclease sites
      on the DNA.  The distribution of the methyl groups of PhiX174 RF DNA among the
      HaeIII  fragments was the same as that of TthHB8I endonuclease sites,
      suggesting that this DNA methylase is the other component of the
      modification-restriction system including TthHB8I endonuclease.  The enzyme
      probably recognizes the sequence, 5'-TCGA-3', in a double stranded DNA and
      probably methylates adenine in the above sequence.
AU  - Sato S
AU  - Nakazawa K
AU  - Shinomiya T
PT  - Journal Article
TA  - J. Biochem. (Tokyo)
JT  - J. Biochem. (Tokyo)
SO  - J. Biochem. (Tokyo) 1980 88: 737-747.

PMID- 730757
VI  - 84
DP  - 1978
TI  - An isoschizomer of TaqI from Thermus thermophilus HB8.
PG  - 1319-1321
AB  - A site-specific endonuclease has been isolated from Thermus thermophilus HB8
      and named TthHB81.  It recognizes the same sequences as TaqI from Thermus
      aquaticus TY-1 does.  The amount of Tth HB81 in the cells was comparable to
      that of TaqI.  T. thermophilus HB8 has an advantage over T. aquaticus YT-1 for
      preparation of a TaqI-like enzyme since it is easier to obtain T. thermophilus
      HB8 cells in quantity.
AU  - Sato S
AU  - Shinomiya T
PT  - Journal Article
TA  - J. Biochem. (Tokyo)
JT  - J. Biochem. (Tokyo)
SO  - J. Biochem. (Tokyo) 1978 84: 1319-1321.

PMID- 23887908
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Gluconobacter frateurii NBRC 103465, a Glyceric Acid-Producing Strain.
PG  - e00369-13
AB  - Gluconobacter frateurii strain NBRC 103465 can efficiently produce glyceric acid  (GA) from
      raw glycerol feedstock derived from biodiesel fuel production
      processes. Here, we report the 3.4-Mb draft genome sequence of G. frateurii NBRC
      103465. The draft genome sequence can be applied to examine the enzymes and
      electron transport system involved in GA production.
AU  - Sato S
AU  - Umemura M
AU  - Koike H
AU  - Habe H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00369-13.

PMID- 29097473
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Multidrug-Resistant Streptococcus pneumoniae Serotype 19F Isolated from an Invasive Infection in Sapporo, Japan.
PG  - e01239-17
AB  - Invasive infection of multidrug-resistant Streptococcus pneumoniae is a serious clinical
      concern. Here, we report the complete genome sequence of a
      multidrug-resistant S. pneumoniae serotype 19F strain isolated from a patient
      with an invasive infection in Sapporo, Japan.
AU  - Sato T
AU  - Ohkoshi Y
AU  - Wada T
AU  - Fukushima Y
AU  - Murabayashi H
AU  - Takakuwa Y
AU  - Nishiyama K
AU  - Shiraishi T
AU  - Nakajima C
AU  - Suzuki Y
AU  - Yokota SI
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01239-17.

PMID- 12813092
VI  - 185
DP  - 2003
TI  - Genome analysis of a novel Shiga toxin 1 (Stx1)-converting phage which is closely related to Stx2-converting phages but not to other Stx1-converting phages.
PG  - 3966-3971
AB  - Two Stx-converting phages, designated Stx1 phi and Stx2 phi-II, were isolated from an
      Escherichia coli O157:H7 strain, Morioka V526, and their
      entire nucleotide sequences were determined. The genomes of both phages
      were similar except for the stx gene-flanking regions. Comparing these
      phages to other known Stx-converting phages, we concluded that Stx1 phi is
      a novel Stx1-converting phage closely related to Stx2-converting phages so
      far reported.
AU  - Sato T
AU  - Shimizu T
AU  - Watarai M
AU  - Kobayashi M
AU  - Kano S
AU  - Hamabata T
AU  - Takeda Y
AU  - Yamasaki S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2003 185: 3966-3971.

PMID- 27491978
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Burkholderia stabilis LA20W, a Trehalose Producer That Uses Levulinic Acid as a Substrate.
PG  - e00795-16
AB  - Burkholderia stabilis LA20W produces trehalose using levulinic acid (LA) as a substrate. Here,
      we report the 7.97-Mb draft genome sequence of B. stabilis
      LA20W, which will be useful in investigations of the enzymes involved in LA
      metabolism and the mechanism of LA-induced trehalose production.
AU  - Sato Y
AU  - Koike H
AU  - Kondo S
AU  - Hori T
AU  - Kanno M
AU  - Kimura N
AU  - Morita T
AU  - Kirimura K
AU  - Habe H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00795-16.

PMID- 29496828
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of the Radioresistant Bacterium Deinococcus aerius TR0125,  Isolated from the High Atmosphere above Japan.
PG  - e00080-18
AB  - Deinococcus aerius strain TR0125 is a bacterium isolated from the high atmosphere above Japan
      that shows strong resistance to desiccation, UV-C, and gamma
      radiation. Here, we report the draft genome sequence of D. aerius (4.5 Mb), which
      may provide useful genetic information supporting its biochemical features.
AU  - Satoh K
AU  - Arai H
AU  - Sanzen T
AU  - Kawaguchi Y
AU  - Hayashi H
AU  - Yokobori SI
AU  - Yamagishi A
AU  - Oono Y
AU  - Narumi I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00080-18.

PMID- 26868384
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the Radioresistant Bacterium Deinococcus grandis, Isolated from Freshwater Fish in Japan.
PG  - e01631-15
AB  - Deinococcus grandis is a radioresistant bacterium isolated from freshwater fish in Japan. Here
      we reported the draft genome sequence of D. grandis (4.1 Mb),
      which will be useful for elucidating the common principles of radioresistance in
      Deinococcus species through the comparative analysis of genomic sequences.
AU  - Satoh K
AU  - Onodera T
AU  - Omoso K
AU  - Takeda-Yano K
AU  - Katayama T
AU  - Oono Y
AU  - Narumi I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01631-15.

PMID- 26272567
VI  - 3
DP  - 2015
TI  - Complete Genome Sequences of Low-Passage Virulent and High-Passage Avirulent Variants of Pathogenic Leptospira interrogans Serovar Manilae Strain UP-MMC-NIID,  Originally Isolated from a Patient with Severe Leptospirosis, Determined Using  PacBio Single-.
PG  - e00882-15
AB  - Here, we report the complete genome sequences of low-passage virulent and high-passage
      avirulent variants of pathogenic Leptospira interrogans serovar
      Manilae strain UP-MMC-NIID, a major causative agent of leptospirosis. While there
      were no major differences between the genome sequences, the levels of base
      modifications were higher in the avirulent variant.
AU  - Satou K
AU  - Shimoji M
AU  - Tamotsu H
AU  - Juan A
AU  - Ashimine N
AU  - Shinzato M
AU  - Toma C
AU  - Nohara T
AU  - Shiroma A
AU  - Nakano K
AU  - Teruya K
AU  - Terabayashi Y
AU  - Ohki S
AU  - Koizumi N
AU  - Okano S
AU  - Suzuki T
AU  - Hirano T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00882-15.

PMID- 24744331
VI  - 2
DP  - 2014
TI  - Complete Genome Sequences of Eight Helicobacter pylori Strains with Different Virulence Factor Genotypes and Methylation Profiles, Isolated from Patients with Diverse Gastrointestinal Diseases on Okinawa Island, Japan.
PG  - e00286-14
AB  - We report the complete genome sequences of eight Helicobacter pylori strains isolated from
      patients with gastrointestinal diseases in Okinawa, Japan.
      Whole-genome sequencing and DNA methylation detection were performed using the PacBio
      platform. De novo assembly determined a single, complete contig for each strain. Furthermore,
      methylation analysis identified virulence factor genotype-dependent motifs.
AU  - Satou K
AU  - Shiroma A
AU  - Teruya K
AU  - Shimoji M
AU  - Nakano K
AU  - Juan A
AU  - Tamotsu H
AU  - Terabayashi Y
AU  - Aoyama M
AU  - Teruya M
AU  - Suzuki R
AU  - Matsuda M
AU  - Sekine A
AU  - Kinjo N
AU  - Kinjo F
AU  - Yamaoka Y
AU  - Hirano T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00286-14.

PMID- 21304654
VI  - 1
DP  - 2009
TI  - Complete genome sequence of Eggerthella lenta type strain (IPP VPI 0255).
PG  - 174-182
AB  - Eggerthella lenta (Eggerth 1935) Wade et al. 1999, emended Wurdemann et al. 2009  is the type
      species of the genus Eggerthella, which belongs to the
      actinobacterial family Coriobacteriaceae. E. lenta is a Gram-positive,
      non-motile, non-sporulating pathogenic bacterium that can cause severe
      bacteremia. The strain described in this study has been isolated from a rectal
      tumor in 1935. Here we describe the features of this organism, together with the
      complete genome sequence, and annotation. This is the first complete genome
      sequence of the genus Eggerthella, and the 3,632,260 bp long single replicon
      genome with its 3123 protein-coding and 58 RNA genes is part of the Genomic
      Encyclopedia of Bacteria and Archaea project.
AU  - Saunders E et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2009 1: 174-182.

PMID- 21304683
VI  - 2
DP  - 2010
TI  - Complete genome sequence of Haloterrigena turkmenica type strain (4k).
PG  - 107-116
AB  - Haloterrigena turkmenica (Zvyagintseva and Tarasov 1987) Ventosa et al. 1999, comb. nov. is
      the type species of the genus Haloterrigena in the euryarchaeal
      family Halobacteriaceae. It is of phylogenetic interest because of the yet
      unclear position of the genera Haloterrigena and Natrinema within the
      Halobacteriaceae, which created some taxonomic problems historically. H.
      turkmenica, was isolated from sulfate saline soil in Turkmenistan, is a
      relatively fast growing, chemoorganotrophic, carotenoid-containing, extreme
      halophile, requiring at least 2 M NaCl for growth. Here we describe the features
      of this organism, together with the complete genome sequence, and annotation.
      This is the first complete genome sequence of the genus Haloterrigena, but the
      eighth genome sequence from a member of the family Halobacteriaceae. The
      5,440,782 bp genome (including six plasmids) with its 5,287 protein-coding and 63
      RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Saunders E et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 2: 107-116.

PMID- 12480877
VI  - 148
DP  - 2002
TI  - The minimal mobile element.
PG  - 3756-3760
AB  - Horizontal transfer of genes is an integral component of bacterial evolution and is
      particularly associated with processes related to environmental adaptation and virulence.  The
      association of many host adaptive and virulence genes with mobile genetic elements such as
      transposases and bacteriophages rejects this.  Presumably the association of the gene
      conferring some competitive advantage for the recipient strain facilitates the dissemination
      of the mobile element.  The presence of larger elements such as pathogenicity islands or
      islands of horizontal transfer is also characteristic of some bacterial species.  However,
      analysis of complete bacterial genomes suggests a previously unrecognized mechanism of
      mobilization that utilizes natural transformation and homologous recombination, and that is
      independent of transposases and other mobilization mechanisms.
AU  - Saunders N
AU  - Snyder L
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2002 148: 3756-3760.

PMID- 10931317
VI  - 37
DP  - 2000
TI  - Repeat-associated phase variable genes in the complete genome sequence of Neisseria meningitidis strain MC58.
PG  - 207-215
AB  - Phase variation, mediated through variation in the length of simple sequence repeats, is
      recognized as an important mechanism for
      controlling the expression of factors involved in bacterial virulence.
      Phase variation is associated with most of the currently recognized
      virulence determinants of Neisseria meningitidis. Based upon the
      complete genome sequence of the N. meningitidis serogroup B strain
      MC58, we have identified tracts of potentially unstable simple sequence
      repeats and their potential functional significance determined on the
      basis of sequence context. Of the 65 potentially phase variable genes
      identified, only 13 were previously recognized. Comparison with the
      sequences from the other two pathogenic Neisseria sequencing projects
      shows differences in the length of the repeats in 36 of the 65 genes
      identified, including 25 of those not previously known to be phase
      variable. Six genes that did not have differences in the length of the
      repeat instead had polymorphisms such that the gene would not be
      expected to be phase variable in at least one of the other strains. A
      further 12 candidates did not have homologues in either of the other
      two genome sequences. The large proportion of these genes that are
      associated with frameshifts and with differences in repeat length
      between the neisserial genome sequences is further corroborative
      evidence that they are phase variable. The number of potentially phase
      variable genes is substantially greater than for any other species
      studied to date, and would allow N. meningitidis to generate a very
      large repertoire of phenotypes through expression of these genes in
      different combinations. Novel phase variable candidates identified in
      the strain MC58 genome sequence include a spectrum of genes encoding
      glycosyltransferases, toxin related products, and metabolic activities
      as well as several restriction/modification and bacteriocin-related
      genes and a number of open reading frames (ORFs) for which the function
      is currently unknown. This suggests that the potential role of phase
      variation in mediating bacterium-host interactions is much greater than
      has been appreciated to date. Analysis of the distribution of
      homopolymeric tract lengths indicates that this species has
      sequence-specific mutational biases that favour the instability of
      sequences associated with phase variation.
AU  - Saunders NJ
AU  - Jeffries AC
AU  - Peden PF
AU  - Hood DW
AU  - Tettelin H
AU  - Rappuoli R
AU  - Moxon ER
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2000 37: 207-215.

PMID- 9570395
VI  - 27
DP  - 1998
TI  - Simple sequence repeats in the Helicobacter pylori genome.
PG  - 1091-1098
AB  - We describe an integrated system for the analysis of DNA sequence motifs within complete
      bacterial genome sequences.  This system is based around ACeDB, a genome database with an
      integrated graphical user interface; we identify and display motifs in the context of genetic,
      sequence and bibliographic data.  Tomb et al. (1997) previously reported the identification of
      contingency genes in Helicobacter pylori through their association with homopolymeric tracts
      and dinucleotide repeats.  With this as a starting point, we validated the system by a search
      for this type of repeat and used the contextual information to assess the likelihood that they
      mediate phase variation in the associated open reading frames.  We found all of the repeats
      previously described, and identified 27 putative phase-variable genes (including 17 previously
      described).  These could be divided into three groups: lipopolysaccharide biosynthesis,
      cell-surface-associated proteins and DNA restriction/modification systems.  Five of the
      putative genes did not have obvious homologues in any of the public domain sequence databases.
      The reading frame of some ORFs was disrupted by the presence of the repeats, including the
      alpha(1-2) fucosyltransferase gene, necessary for the synthesis of the Lewis Y epitope.  An
      additional benefit of this approach is that the results of each search can be analyzed further
      and compared with those from other genomes.  This revealed that H. pylori has an unusually
      high frequency of homopurine:homopyrimidine repeats suggesting mechanistic biases that favor
      their presence and instability.
AU  - Saunders NJ
AU  - Peden JF
AU  - Hood DW
AU  - Moxon ER
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1998 27: 1091-1098.

PMID- 11058140
VI  - 28
DP  - 2000
TI  - The Thy Pol-2 intein of Thermococcus hydrothermalis is an isoschizomer of PI-TliI and PI-TfuII endonucleases.
PG  - 4391-4396
AB  - Thy Pol-2 intein, from Thermococcus hydrothermalis, belongs to the same allelic family as
      TliPol-2 (PI-TliI), Tfu Pol-2 (PI-TfuII) and TspTY Pol-3 mini-intein, all inserted at the
      pol-c site of archaeal DNA polymerase genes. This new intein was cloned, expressed in
      Escherichia coli and purified. The intein is a specific endonuclease (PI-ThyI) which cleaves
      the inteinless sequence of the ThyDNA pol gene.  Moreover, PI-TliI, PI-TfuII and PI-ThyI are
      very similar endonucleases which cleave DNA in the same optimal conditions at 70 degrees C
      yielding similar 3'-hydroxyl overhangs of 4 bp and the reaction is subject to product
      inhibition. The three enzymes are able to cleave the three DNA sequences spanning the pol-c
      site and a 24 bp consensus cleavage site was defined for the three isoschizomers. However, the
      exact size of the minimal cleavage site depends both on the substrate sequence and the
      endonuclease. The inability of the isoschizomers to cleave the inteinless DNA polymerase gene
      from Pyrococcus spp. KOD is due to point substitutions on the 5' side of the pol-c site,
      suggesting that the absence of inteins of this allelic family in DNA polymerase genes from
      Pyrococcus spp. can be linked to small differences in the target site sequence.
AU  - Saves I
AU  - Eleaume H
AU  - Dietrich J
AU  - Masson J-M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2000 28: 4391-4396.

PMID- 12364594
VI  - 30
DP  - 2002
TI  - Investigating the endonuclease activity of four Pyrococcus abyssi inteins.
PG  - 4158-4165
AB  - Among the 14 inteins of the Pyrococcus abyssi genome, 10 harbour the LAGLIDADG motifs of
      dodecapeptide endonucleases.  Four of these were cloned, expressed in Escherichia coli and
      purified to assay their potential endonuclease activity.  PabRIR1-2 and PabRIR1-3 are specific
      endonucleases, named PI-PabI and PI-PabII, respectively, cleaving the sequence spanning their
      homing site.  This is consistent with their size and with the relative positions and sequences
      of their endonuclease motifs.  However, PI-PabI is 10-fold more active than PI-PabII and a
      discrepancy of the DNA recognition and cleavage mechanisms was observed between the two
      inteins.  In particular, analysis of the DNA cleavage reactions by MALDI-TOF highlighted that
      while the cleavage of DNA by PI-PabI consists of two steps corresponding to the cleavage of
      each DNA strand, PI-PabII processes the two DNA strands simultaneously.  Furthermore, the two
      inteins interact differently with DNA.  In addition, we did not detect any endonuclease
      activity for PabLon and PabRIR1-1.  deletions in the intein sequences and mutations in the
      putative endonuclease motifs probably abolish this activity.  Hence, inteins from the same
      archaebacteria, even if contained in the same host protein, did not evolve uniformly and are
      presumably at different stages of the invasion cycle.
AU  - Saves I
AU  - Morlot C
AU  - Thion L
AU  - Rolland J-L
AU  - Dietrich J
AU  - Masson J-M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2002 30: 4158-4165.

PMID- 10644683
VI  - 275
DP  - 2000
TI  - Inteins of Thermococcus fumicolans DNA Polymerase Are Endonucleases with Distinct Enzymatic Behaviors.
PG  - 2335-2341
AB  - The DNA polymerase gene of Thermococcus fumicolans harbors two intein genes. Both inteins have
      been produced in Escherichia coli and purified either as naturally spliced products from the
      expression of the complete DNA polymerase gene or directly from the cloned inteins genes. Both
      recombinant inteins exhibit endonuclease activity, with an optimal temperature of 70 degrees
      C. The Tfu pol-1 intein, which belongs to the Psp KOD pol-1 allelic family, recognizes and
      cleaves a minimal sequence of 16 base pairs (bp) on supercoiled DNA with either Mn(2+) or
      Mg(2+) as cofactor. It cleaves linear DNA only with Mn(2+) and requires a 19-bp minimal
      recognition sequence. The Tfu pol-2 intein, which belongs to the Tli pol-2 allelic family, is
      a highly active homing endonuclease using Mg(2+) as cofactor. Its minimal recognition and
      cleavage site is 21 bp long either on linear or circular DNA substrates. Its endonuclease
      activity is strongly inhibited by the 3' digestion product, which remains bound to the enzyme
      after the cleavage reaction. According to current nomenclature, these endonucleases were named
      PI-TfuI and PI-TfuII. These two inteins thus exhibit different requirements for metal cofactor
      and substrate topology as well as different mechanism of action.
AU  - Saves I
AU  - Ozanne V
AU  - Dietrich J
AU  - Masson JM
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2000 275: 2335-2341.

PMID- 11691918
VI  - 29
DP  - 2001
TI  - Identification of the first eubacterial endonuclease coded by an intein allele in the pps1 gene of mycobacteria.
PG  - 4310-4318
AB  - A survey of a vast range of mycobacterial strains led us to discover a new Pps1 intein allele
      in Mycobacterium gastri which differs from those of Mycobacterium tuberculosis and
      Mycobacterium leprae in both its sequence and insertion site. While little is known about
      Pps1, except that it belongs to the YC24 family of ABC transporters, we show that, unlike the
      other inteins described so far from Eubacteria, the MgaPps1 intein possesses a specific
      endonuclease activity. The intein is the first eubacterial intein to be characterised as an
      endonuclease. Like other intein endonucleases, its minimal sequence for recognition and
      cleavage is quite large, with 22 bp spanning the Pps1-c site. The fact that an active
      endonuclease is found among the mycobacterial inteins supports the concept of a cyclical model
      of invasion by horizontal transfer of these genes, followed by degeneration and loss until a
      new invasion event, thus explaining their long-term persistence in closely related eubacterial
      species.
AU  - Saves I
AU  - Westrelin F
AU  - Daffe M
AU  - Masson J-M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2001 29: 4310-4318.

PMID- 23469338
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of a Clinical Strain of Yersinia enterocolitica (IP10393) of Bioserotype 4/O:3 from France.
PG  - e00150-12
AB  - We sequenced the genome of a clinical isolate of (IP10393) from France. This strain belongs to
      bioserotype 4/O:3, which is the most common pathogenic subgroup
      worldwide. The draft genome has a size of 4,463,212 bp and a G+C content of
      47.0%, and it is predicted to contain 4,181 coding sequences.
AU  - Savin C
AU  - Frangeul L
AU  - Ma L
AU  - Bouchier C
AU  - Moszer I
AU  - Carniel E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00150-12.

PMID- 22675601
VI  - 6
DP  - 2012
TI  - Complete genome sequencing and analysis of Saprospira grandis str. Lewin, a predatory marine bacterium.
PG  - 84-93
AB  - Saprospira grandis is a coastal marine bacterium that can capture and prey upon other marine
      bacteria using a mechanism known as 'ixotrophy'. Here, we present
      the complete genome sequence of Saprospira grandis str. Lewin isolated from La
      Jolla beach in San Diego, California. The complete genome sequence comprises a
      chromosome of 4.35 Mbp and a plasmid of 54.9 Kbp. Genome analysis revealed
      incomplete pathways for the biosynthesis of nine essential amino acids but
      presence of a large number of peptidases. The genome encodes multiple copies of
      sensor globin-coupled rsbR genes thought to be essential for stress response and
      the presence of such sensor globins in Bacteroidetes is unprecedented. A total of
      429 spacer sequences within the three CRISPR repeat regions were identified in
      the genome and this number is the largest among all the Bacteroidetes sequenced
      to date.
AU  - Saw JH
AU  - Yuryev A
AU  - Kanbe M
AU  - Hou S
AU  - Young AG
AU  - Aizawa S
AU  - Alam M
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 6: 84-93.

PMID- 24194836
VI  - 8
DP  - 2013
TI  - Cultivation and Complete Genome Sequencing of Gloeobacter kilaueensis sp. nov., from a Lava Cave in Kilauea Caldera, Hawai'i.
PG  - e76376
AB  - The ancestor of Gloeobacter violaceus PCC 7421T is believed to have diverged from that of all
      known cyanobacteria before
      the evolution of thylakoid membranes and plant plastids. The long and largely independent
      evolutionary history of G.
      violaceus presents an organism retaining ancestral features of early oxygenic photoautotrophs,
      and in whom cyanobacteria
      evolution can be investigated. No other Gloeobacter species has been described since the genus
      was established in 1974
      (Rippka et al., Arch Microbiol 100:435). Gloeobacter affiliated ribosomal gene sequences have
      been reported in
      environmental DNA libraries, but only the type strain's genome has been sequenced. However,
      we report here the
      cultivation of a new Gloeobacter species, G. kilaueensis JS1T, from an epilithic biofilm in a
      lava cave in Ky'lauea Caldera,
      Hawai'i. The strain's genome was sequenced from an enriched culture resembling a
      low-complexity metagenomic sample,
      using 9 kb paired-end 454 pyrosequences and 400 bp paired-end Illumina reads. The JS1T and G.
      violaceus PCC 7421T
      genomes have little gene synteny despite sharing 2842 orthologous genes; comparing the genomes
      shows they do not
      belong to the same species. Our results support establishing a new species to accommodate
      JS1T, for which we propose the
      name Gloeobacter kilaueensis sp. nov. Strain JS1T has been deposited in the American Type
      Culture Collection (BAA-2537),
      the Scottish Marine Institute's Culture Collection of Algae and Protozoa (CCAP 1431/1), and
      the Belgian Coordinated
      Collections of Microorganisms (ULC0316). The G. kilaueensis holotype has been deposited in the
      Algal Collection of the US
      National Herbarium (US# 217948). The JS1T genome sequence has been deposited in GenBank under
      accession number
      CP003587. The G+C content of the genome is 60.54 mol%. The complete genome sequence of G.
      kilaueensis JS1T may
      further understanding of cyanobacteria evolution, and the shift from anoxygenic to oxygenic
      photosynthesis.
AU  - Saw JHW
AU  - Schatz M
AU  - Brown MV
AU  - Kunkel DD
AU  - Foster JS
AU  - Shick H
AU  - Christensen S
AU  - Hou S
AU  - Wan X
AU  - Donachie SP
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2013 8: e76376.

PMID- 16338412
VI  - 13
DP  - 2005
TI  - Crystal structure of the restriction-modification system control element C.BclI and mapping of its binding site.
PG  - 1837-1847
AB  - Protection from DNA invasion is afforded by restriction-modification systems in many bacteria.
      The efficiency of protection depends crucially on the relative expression levels of
      restriction versus methytransferase genes. This regulation is provided by a controller
      protein, named C protein. Studies of the Bcll system in E. coli suggest that C.Bcll functions
      as a negative regulator for M.Bcll expression, implying that it plays a role in defense
      against foreign DNA during virus infection. C.Bcll binds (Kd = 14.3 nM) to a 2-fold symmetric
      C box DNA sequence that overlaps with the putative -35 promoter region upstream of the bcllM
      and bcllC genes. The C.Bcll fold comprises five alpha helices: two helices form a
      helix-turn-helix motif, and the remaining three helices form the extensive dimer interface.
      The C.Bcll-DNA model proposed suggests that DNA bending might play an important role in gene
      regulation, and that Glu27 and Asp31 in C.Bcll might function critically in the regulation.
AU  - Sawaya MR
AU  - Zhu Z
AU  - Mersha F
AU  - Chan S-h
AU  - Dabur R
AU  - Xu S-y
AU  - Balendiran GK
PT  - Journal Article
TA  - Structure
JT  - Structure
SO  - Structure 2005 13: 1837-1847.

PMID- 24994803
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Rifamycin Producer Amycolatopsis rifamycinica DSM 46095.
PG  - e00662-14
AB  - Amycolatopsis rifamycinica DSM 46095 is an actinobacterium that produces rifamycin SV, an
      antibiotic used against Mycobacterium tuberculosis. Here, we
      present the draft genome of DSM 46095, which harbors a novel rifamycin polyketide
      biosynthetic gene cluster (rif PKS) that differed by 10% in nucleotide sequence
      from the already reported rif PKS cluster of Amycolatopsis mediterranei S699.
AU  - Saxena A
AU  - Kumari R
AU  - Mukherjee U
AU  - Singh P
AU  - Lal R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00662-14.

PMID- 24029761
VI  - 1
DP  - 2013
TI  - Genome Sequence of Novosphingobium lindaniclasticum LE124T, Isolated from a Hexachlorocyclohexane Dumpsite.
PG  - e00715-13
AB  - Novosphingobium lindaniclasticum LE124(T) is a hexachlorocyclohexane (HCH)-degrading bacterium
      isolated from a high-dosage-point HCH dumpsite (450 mg
      HCH/g soil) located in Lucknow, India (27 degrees 00'N and 81 degrees 09'E).
      Here, we present the annotated draft genome sequence of strain LE124(T), which
      has an estimated size of 4.86 Mb and is comprised of 4,566 coding sequences.
AU  - Saxena A
AU  - Nayyar N
AU  - Sangwan N
AU  - Kumari R
AU  - Khurana JP
AU  - Lal R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00715-13.

PMID- 18596144
VI  - 46
DP  - 2008
TI  - Genetic Classification of Severe Early Childhood Caries Using Subtracted DNA Fragments from Streptococcus mutans.
PG  - 2868-2873
AB  - Streptococcus mutans is one of several members of the oral indigenous
      biota linked with severe early childhood caries (S-ECC). Because most
      humans harbor S. mutans, but not all manifest disease, it has been
      proposed that the strains of S. mutans associated with S-ECC are
      genetically distinct from those found in caries-free (CF) children. The
      objective of this study was to identify common DNA fragments from S.
      mutans present in S-ECC but not in CF children. Using suppressive
      subtractive hybridization, we found a number of DNA fragments (biomarkers)
      present in 88 to 95% of the S-ECC S. mutans strains but not in CF S.
      mutans strains. We then applied machine learning techniques including
      support vector machines and neural networks to identify the biomarkers
      with the most predictive power for disease status, achieving a 92%
      accurate classification of the strains as either S-ECC or CF associated.
      The presence of these gene fragments in 90 to 100% of the 26 S-ECC
      isolates tested suggested their possible functional role in the
      pathogenesis of S. mutans associated with dental caries.
AU  - Saxena D
AU  - Caufield PW
AU  - Li Y
AU  - Brown S
AU  - Song J
AU  - Norman R
PT  - Journal Article
TA  - J. Clin. Microbiol.
JT  - J. Clin. Microbiol.
SO  - J. Clin. Microbiol. 2008 46: 2868-2873.

PMID- 26586874
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Gulbenkiania mobilis Strain MB1, a Sulfur-Metabolizing Thermophile Isolated from a Hot Spring in Central India.
PG  - e01295-15
AB  - This paper reports the draft genome sequence of the proteobacterium Gulbenkiania  mobilis
      strain MB1, a sulfur-metabolizing thermophile isolated from a hot spring
      located in Pachmarhi, India. This study reports the first draft genome sequence
      of any species from the genus Gulbenkiania.
AU  - Saxena R
AU  - Chaudhary N
AU  - Dhakan DB
AU  - Sharma VK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01295-15.

PMID- 28408674
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Mycobacterium sp. MS1601, a Bacterium Performing Selective Oxidation of Polyols.
PG  - e00156-17
AB  - Corynebacterium sp. (ATCC 21245) is reclassified here as Mycobacterium sp. MS1601 based on 16S
      rRNA gene and complete-genome sequence analysis. It is able to
      oxidize branched polyols to corresponding hydroxycarboxylic acids. The total size
      of the genome sequence was 6,829,132 bp, including one circular chromosome of
      6,407,860 bp.
AU  - Sayed M
AU  - Sayed WF
AU  - Hatti-Kaul R
AU  - Pyo SH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00156-17.

PMID- 2555795
VI  - 17
DP  - 1989
TI  - Inhibition of restriction endonuclease hydrolysis by phosphorothioate-containing DNA.
PG  - 9495
AB  - None
AU  - Sayers JR
AU  - Olsen DB
AU  - Eckstein F
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 9495.

PMID- 2830594
VI  - 16
DP  - 1988
TI  - Strand specific cleavage of phosphorothioate-containing DNA by reaction with restriction endonucleases in the presence of ethidium bromide.
PG  - 803-813
AB  - A method for achieving strand specific nicking of DNA has been developed.
      Phosphorothioate groups were incorporated enzymatically into the (-) strand of
      M13 RF IV DNA.  When such DNA is reacted with restriction endonucleases in the
      presence of ethidium bromide, nicked DNA (RF II) is produced.  All of the
      restriction enzymes tested linearised phosphorothioate-containing DNA in the
      absence of this dye.  The strand specificity of the reaction was investigated
      by employing the ethidium bromide mediated nicking reaction in the
      phosphorothioate-based oligonucleotide-directed mutagenesis method.  The
      mutational efficiences obtained were in the region of 64-89%, indicating that
      these restriction enzymes hydrolyse the phosphodiester bond at the cleavage
      site of the unsubstituted (+) strand.
AU  - Sayers JR
AU  - Schmidt W
AU  - Wendeler A
AU  - Eckstein F
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1988 16: 803-813.

PMID- 29449399
VI  - 6
DP  - 2018
TI  - Genome Sequences of 12 Pseudomonas lundensis Strains Isolated from the Lungs of Humans.
PG  - e01461-17
AB  - We report here the first complete genome sequence of a human Pseudomonas lundensis isolate,
      strain AU1044, and the draft genomes of 11 other clinical P.
      lundensis strains, isolated from the lungs of cystic fibrosis patients. The
      genome of strain AU1044 is 4.81 Mb and encodes seven 16S rRNAs.
AU  - Scales BS
AU  - Erb-Downward JR
AU  - Falkowski NR
AU  - LiPuma JJ
AU  - Huffnagle GB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01461-17.

PMID- 25635025
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Seven Pseudomonas fluorescens Subclade III Strains Isolated from Cystic Fibrosis Patients.
PG  - e01285-14
AB  - We report here the first draft genome sequences of Pseudomonas fluorescens strains that have
      been isolated from humans. The seven assembled draft genomes
      contained an average of 60.1% G+C content, were an average genomic size of 6.3
      Mbp, and mapped by multilocus sequence analysis to subclade III.
AU  - Scales BS
AU  - Erb-Downward JR
AU  - Huffnagle IM
AU  - LiPuma JJ
AU  - Huffnagle GB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01285-14.

PMID- 26227600
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Five Pseudomonas fluorescens Subclade I and II Strains, Isolated from Human Respiratory Samples.
PG  - e00837-15
AB  - We report the draft genomes of five Pseudomonas fluorescens strains, isolated from clinical
      samples. Phylogenetic analysis places three in subclade I and two
      in subclade II of the P. fluorescens species complex. The average G+C content and
      genomic size are 63% and 7.1 Mbp (subclade I) and 59.6% and 6.14 Mbp (subclade
      II), respectively.
AU  - Scales BS
AU  - Erb-Downward JR
AU  - LiPuma JJ
AU  - Huffnagle GB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00837-15.

PMID- 17720189
VI  - 372
DP  - 2007
TI  - Coevolution of a Homing Endonuclease and Its Host Target Sequence.
PG  - 1305-1319
AB  - We have determined the specificity profile of the homing endonuclease I-AniI and compared it
      to the conservation of its host gene. Homing
      endonucleases are encoded within intervening sequences such as group I
      introns. They initiate the transfer of such elements by cleaving cognate
      alleles lacking the intron, leading to their transfer via homologous
      recombination. Each structural homing endonuclease family has arrived at
      an appropriate balance of specificity and fidelity that avoids toxicity
      while maximizing target recognition and invasiveness. I-AniI recognizes a
      strongly conserved target sequence in a host gene encoding apocytochrome B
      and has fine-tuned its specificity to correlate with wobble versus
      nonwobble positions across that sequence and to the amount of degeneracy
      inherent in individual codons. The physiological target site in the host
      gene is not the optimal substrate for recognition and cleavage: at least
      one target variant identified during a screen is bound more tightly and
      cleaved more rapidly. This is a result of the periodic cycle of intron
      homing, which at any time can present nonoptimal combinations of
      endonuclease specificity and insertion site sequences in a biological
      host.
AU  - Scalley-Kim M
AU  - McConnell-Smith A
AU  - Stoddard BL
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2007 372: 1305-1319.

PMID- 2587239
VI  - 17
DP  - 1989
TI  - Isolation and identification of restriction endonuclease BshGI.
PG  - 8883
AB  - None
AU  - Scarpelis G
AU  - Moissidou A
AU  - Rina M
AU  - Bouriotis V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 8883.

PMID- 11024175
VI  - 28
DP  - 2000
TI  - Structure of RsrI methyltransferase, a member of the N6-adenine beta class of DNA methyltransferases.
PG  - 3950-3961
AB  - DNA methylation is important in cellular, developmental and disease processes, as well as in
      bacterial restriction-modification systems. Methylation of DNA at the amino groups of cytosine
      and adenine is a common mode of protection against restriction endonucleases afforded by the
      bacterial methyltransferases.  The first structure of an N6-adenine methyltransferase
      belonging to the beta class of bacterial methyltransferases is described here. The structure
      of M.RsrI from Rhodobacter sphaeroides, which methylates the second adenine of the GAATTC
      sequence, was determined to 1.75 A resolution using X-ray crystallography. Like other
      methyltransferases, the enzyme contains the methylase fold and has well-defined substrate
      binding pockets. The catalytic core most closely resembles the PvuII methyltransferase, a
      cytosine amino methyltransferase of the same beta group. The larger nucleotide binding pocket
      observed in M.RsrI is expected because it methylates adenine. However, the most striking
      difference between the RsrI methyltransferase and the other bacterial enzymes is the structure
      of the putative DNA target recognition domain, which is formed in part by two helices on an
      extended arm of the protein on the face of the enzyme opposite the active site. This
      observation suggests that a dramatic conformational change or oligomerization may take place
      during DNA binding and methylation.
AU  - Scavetta RD
AU  - Thomas CB
AU  - Walsh MA
AU  - Szegedi S
AU  - Joachimiak A
AU  - Gumport RI
AU  - Churchill MEA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2000 28: 3950-3961.

PMID- 8082176
VI  - 25
DP  - 1994
TI  - A mitochondrial group-I intron in fission yeast encodes a maturase and is mobile in crosses.
PG  - 336-341
AB  - The open reading frame in the first intron of the mitochondrial gene encoding subunit I of
      cytochrome c oxidase encodes a maturase and stimulates homologous recombination in Escherichia
      coli.  In this paper, we demonstrate that this intron is mobile in crosses, indicating that it
      also encodes an endonuclease.  This is the first report on an intron which possesses mobility
      and acts as a maturase.
AU  - Schaefer B
AU  - Wilde B
AU  - Massardo DR
AU  - Manna F
AU  - Del Giudice L
AU  - Wolf K
PT  - Journal Article
TA  - Curr. Genet.
JT  - Curr. Genet.
SO  - Curr. Genet. 1994 25: 336-341.

PMID- 8682220
VI  - 10
DP  - 1996
TI  - A new class IIS zinc finger restriction enzyme with specificity for SP1 binding sites.
PG  - A1241
AB  - A new restriction endonuclease (Sp1ase) was constructed by fusing the DNA-cleavage domain of
      the restriction endonuclease FokI in frame with the zinc-finger DNA-binding domain of the
      transcription factor Sp1.  This construct was shown to selectively digest plasmid DNA carrying
      consensus Sp1 sites.  Splase was also shown to selectively digest plasmid DNA carrying the
      HIV-1 LTR.  Sp1ase is a genetically engineered restriction enzyme conveying specificity for
      Sp1 binding sites.  The site-specific phosphodiesterase activity of Sp1ase has been
      characterized and shown to have more specific cleavage of one strand of DNA than the other.
      Sp1ase recognizes a ten base-pair DNA sequence and hydrolyzes phosphodiester bonds upstream of
      the binding sequence.  The binding specificity of Sp1ase makes this a rare cutter
      restriction enzyme which could be valuable in creating large DNA fragments for genome
      sequencing projects.  This result presents the opportunity to creat other restriction enzymes
      by altering the binding specificity of the zinc finger recognition helix.
AU  - Schaeffer CJ
AU  - Huang B
AU  - Tsai M-D
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1996 10: A1241.

PMID- 5167101
VI  - 22
DP  - 1971
TI  - Staphylococcus epidermidis BV:  Antibiotic resistance patterns, physiological characteristics, and bacteriophage susceptibility.
PG  - 693-699
AB  - Staphylococcus epidermidis BV is a group of mannitol-fermenting
      coagulase-negative staphylococci characterized by multiple antibiotic
      resistance, very similar biochemical characteristics, and phage susceptibility.
      Clinical isolates belonging to this group are resistant to most antibiotics
      tested, including oxacillin, lincomycin, and novobiocin.  The only antibiotic
      to which all tested strains are sensitive is vancomycin.  Common biochemical
      traits of the tested S. epidermidis BV strains include fermentation of
      trehalose and ribose, phospho-b-glucosidase activity, growth on synthetic
      medium with amino acids as carbon source, and lack of deoxyribonuclease,
      phosphatase, lipase, and gelatinase activity.  Some of these characteristics
      appear more frequently in mannitol-positive control strains than in
      mannitol-negative strains.  S. epidermidis  BV strains carry lysogenic phages
      with a host range restricted to this group.  These phages allow the
      differentiation of individual strains.
AU  - Schaefler S
PT  - Journal Article
TA  - Appl. Microbiol.
JT  - Appl. Microbiol.
SO  - Appl. Microbiol. 1971 22: 693-699.

PMID- 7961503
VI  - 176
DP  - 1994
TI  - Cloning and characterization of a DNA region encoding a stress-sensitive restriction system from Corynebacterium glutamicum ATCC 13032 and analysis of its role in intergeneric conjugation with Escherichia coli.
PG  - 7309-7319
AB  - RP4-mediated transfer of mobilizable plasmids in intergeneric conjugation of Escherichia coli
      donors with Corynebacterium glutamicum ATCC 13032 is severely affected by a restriction system
      in the recipient that can be inactivated by a variety of exogenous stress factors. In this
      study a rapid test procedure based on intergeneric conjugal plasmid transfer that permitted
      the distinction between restriction-negative and restriction-positive C. glutamicum clones was
      developed. By using this procedure, clones of the restriction-deficient mutant strain C.
      glutamicum RM3 harboring a plasmid library of the wild-type chromosome were checked for their
      restriction properties. A complemented clone with a restriction-positive phenotype was
      isolated and found to contain a plasmid with a 7-kb insertion originating from the wild-type
      chromosome. This plasmid, termed pRES806, is able to complement the restriction-deficient
      phenotype of different C. glutamicum mutants. Sequence analysis revealed the presence of two
      open reading frames (orf1 and orf2) on the complementing DNA fragment. The region comprising
      orf1 and orf2 displayed a strikingly low G+C content and was present exclusively in C.
      glutamicum strains. Gene disruption experiments with the wild type proved that orf1 is
      essential for complementation, but inactivation of orf2 also resulted in a small but
      significant increase in fertility. These results were confirmed by infection assays with the
      bacteriophage CL31 from Corynebacterium lilium ATCC 15990.
AU  - Schafer A
AU  - Schwarzer A
AU  - Kalinowski J
AU  - Puhler A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1994 176: 7309-7319.

PMID- 9426239
VI  - 203
DP  - 1997
TI  - The Corynebacterium glutamicum cglIM gene encoding a 5-cytosine methyltransferase enzyme confers a specific DNA methylation pattern in an McrBC-deficient Escherichia coli strain.
PG  - 95-101
AB  - The cglIM gene of the coryneform soil bacterium Corynebacterium glutamicum ATCC 13032 has been
      cloned and characterized.  The coding region comprises 1092 nucleotides and specifies a
      protein of 363 amino acid residues with a deduced Mr of 40,700.  The amino acid sequence
      showed striking similarities to methyltransferase enzymes generating 5-methylcytosine
      residues, especially to M.NgoVII from Neisseria gonorrhoeae recognizing the sequence GCSGC.
      The cglIM gene is organized in an unusual operon which contains, in addition, two genes
      encoding stress-sensitive restriction enzymes.  Using PCR techniques the entire gene including
      the promoter region was amplified from the wild-type chromosome and cloned in Escherichia
      coli.  Expression of the cglIM gene in E. coli under the control of its own promoter conferred
      the C. glutamicum-specific methylation pattern to co-resident shuttle plasmids and led to a
      260-fold increase in the transformation rate of C. glutamicum.  In addition, the methylation
      pattern produced by this methyltransferase enzyme is responsible for the sensitivity of DNA
      from C. glutamicum to the modified cytosine restriction system of E. coli.
AU  - Schafer A
AU  - Tauch A
AU  - Droste N
AU  - Puhler A
AU  - Kalinowski J
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1997 203: 95-101.

PMID- 9651494
VI  - 214
DP  - 1998
TI  - Mosaic structure of the cox2 gene in the petite negative yeast Schizosaccharomyces pombe: a group II intron is inserted at the same location as the otherwise unrelated group II introns in the mitochondria of higher plants.
PG  - 101-112
AB  - In contrast to homologous genes in other fungal mitochondrial genomes, the gene encoding
      subunit 2 of cytochrome oxidase (cox2) in several Schizosaccharomyces pombe strains contains a
      large group II intron. Its 2436 nucleotides can be folded into a typical group II intron
      secondary structure, possessing all the expected sequence motifs for subgroup IIA1 (Michel et
      al., 1989).  This intron is remarkable for the following reasons: (i) Five nucleotide changes
      were observed compared with the continuous form of the cox2 gene in the reference strain 50 at
      the 3'-exon sequence, but not in the 5'-exon. (ii) One of these changes occurred at the
      splice point leading to a serine instead of a threonine residue in the deduced cox2
      polypeptide. In all cases, the alterations resulted in the replacement of more frequently used
      codons by rare ones. (iii) Although the intron is able to undergo splicing, the sequence
      motifs thought to be necessary for interaction between the 5'-exon and the intron during the
      splicing process (the EBS1/IBS1 as well as the EBS2/IBS2 pairings) are unusual. (iv) The
      intron is inserted at the same location in the cox2 gene as the otherwise unrelated intron
      from higher plants.
AU  - Schafer B
AU  - Kaulich K
AU  - Wolf K
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1998 214: 101-112.

PMID- 28174620
VI  - 12
DP  - 2017
TI  - Complete genome sequence of Thermus brockianus GE-1 reveals key enzymes of xylan/xylose metabolism.
PG  - 22
AB  - Thermus brockianus strain GE-1 is a thermophilic, Gram-negative, rod-shaped and non-motile
      bacterium that was isolated from the Geysir geothermal area, Iceland.
      Like other thermophiles, Thermus species are often used as model organisms to
      understand the mechanism of action of extremozymes, especially focusing on their
      heat-activity and thermostability. Genome-specific features of T. brockianus GE-1
      and their properties further help to explain processes of the adaption of
      extremophiles at elevated temperatures. Here we analyze the first whole genome
      sequence of T. brockianus strain GE-1. Insights of the genome sequence and the
      methodologies that were applied during de novo assembly and annotation are given
      in detail. The finished genome shows a phred quality value of QV50. The complete
      genome size is 2.38 Mb, comprising the chromosome (2,035,182 bp), the megaplasmid
      pTB1 (342,792 bp) and the smaller plasmid pTB2 (10,299 bp). Gene prediction
      revealed 2,511 genes in total, including 2,458 protein-encoding genes, 53 RNA and
      66 pseudo genes. A unique genomic region on megaplasmid pTB1 was identified
      encoding key enzymes for xylan depolymerization and xylose metabolism. This is in
      agreement with the growth experiments in which xylan is utilized as sole source
      of carbon. Accordingly, we identified sequences encoding the xylanase Xyn10, an
      endoglucanase, the membrane ABC sugar transporter XylH, the xylose-binding
      protein XylF, the xylose isomerase XylA catalyzing the first step of xylose
      metabolism and the xylulokinase XylB, responsible for the second step of xylose
      metabolism. Our data indicate that an ancestor of T. brockianus obtained the
      ability to use xylose as alternative carbon source by horizontal gene transfer.
AU  - Schafers C
AU  - Blank S
AU  - Wiebusch S
AU  - Elleuche S
AU  - Antranikian G
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 22.

PMID- 24501635
VI  - 8
DP  - 2013
TI  - Genome sequence of the marine bacterium Corynebacterium maris type strain Coryn-1(T) (= DSM 45190(T)).
PG  - 516-524
AB  - Corynebacterium maris Coryn-1(T) Ben-Dov et al. 2009 is a member of the genus Corynebacterium
      which contains Gram-positive, non-spore forming bacteria with a
      high G+C content. C. maris was isolated from the mucus of the Scleractinian coral
      Fungia granulosa and belongs to the aerobic and non-haemolytic corynebacteria. It
      displays tolerance to salts (up to 10%) and is related to the soil bacterium
      Corynebacterium halotolerans. As this is a type strain in a subgroup of
      Corynebacterium without complete genome sequences, this project, describing the
      2.78 Mbp long chromosome and the 45.97 kbp plasmid pCmaris1, with their 2,584
      protein-coding and 67 RNA genes, will aid the G enomic E ncyclopedia of Bacteria
      and Archaea project.
AU  - Schaffert L
AU  - Albersmeier A
AU  - Bednarz H
AU  - Niehaus K
AU  - Kalinowski J
AU  - Ruckert C
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 516-524.

PMID- 28031775
VI  - 11
DP  - 2016
TI  - Complete genome sequence of the actinomycete Actinoalloteichus hymeniacidonis type strain HPA 177T isolated from a marine sponge.
PG  - 91
AB  - Actinoalloteichus hymeniacidonis HPA 177T is a Gram-positive, strictly aerobic, black pigment
      producing and spore-forming actinomycete, which forms branching
      vegetative hyphae and was isolated from the marine sponge Hymeniacidon perlevis.
      Actinomycete bacteria are prolific producers of secondary metabolites, some of
      which have been developed into anti-microbial, anti-tumor and immunosuppressive
      drugs currently used in human therapy. Considering this and the growing interest
      in natural products as sources of new drugs, actinomycete bacteria from the
      hitherto poorly explored marine environments may represent promising sources for
      drug discovery. As A. hymeniacidonis, isolated from the marine sponge, is a type
      strain of the recently described and rare genus Actinoalloteichus, knowledge of
      the complete genome sequence enables genome analyses to identify genetic loci for
      novel bioactive compounds. This project, describing the 6.31 Mbp long chromosome,
      with its 5346 protein-coding and 73 RNA genes, will aid the Genomic Encyclopedia
      of Bacteria and Archaea project.
AU  - Schaffert L
AU  - Albersmeier A
AU  - Winkler A
AU  - Kalinowski J
AU  - Zotchev SB
AU  - Ruckert C
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 91.

PMID- 8367285
VI  - 21
DP  - 1993
TI  - I-SceIII an intron-encoded DNA endonuclease from yeast mitochondria. Asymmetrical DNA binding properties and cleavage reaction.
PG  - 3683-3689
AB  - We have previously discovered the new intron-encoded endonuclease I-SceIII by expressing, in
      E.coli, the ORF contained in the third intron of the yeast mitochondrial COX I gene. In this
      work, we analyzed the in vitro properties of partially purified I-SceIII and found that it is
      a very specific DNA endonuclease, tolerating relatively few base changes in its 20 base pair
      long target site. I-SceIII should be a useful molecular tool to analyze the structure of large
      genomes. Interestingly, I-SceIII is the first P1-P2 DNA endonuclease for which DNA binding
      properties could be analyzed by band-shift experiments. Clearly, the cleavage products
      corresponding to the upstream A3 exon and to the downstream A4 exon could compete with the
      substrate A3-A4 in forming a DNA-protein complex. However, the A3 exon competes more
      efficiently than the downstream A4 product. The cleavage of the two DNA strands is also
      asymmetric; the top strand (non-transcribed strand) is cleaved faster than the bottom strand,
      a property found under various experimental conditions. These findings sugest that this
      intron-encoded DNA endonuclease may have a role in the RNA splicing process of the intron.
AU  - Schapira M
AU  - Desdouets C
AU  - Jacq C
AU  - Perea J
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 3683-3689.

PMID- 9696758
VI  - 180
DP  - 1998
TI  - The cyanobacterium Synechocystis sp. strain PCC 6803 expresses a DNA methyltransferase specific for the recognition sequence of the restriction endonuclease PvuI.
PG  - 4116-4122
AB  - By use of restriction endonucleases, the DNA of the cyanobacterium Synechocystis sp. strain
      PCC 6803 was analyzed for DNA-specific methylation.  Three different recognition sites of
      methyltransferases, a dam-like site including N6-methyladenosine and two other sites with
      methylcytosine, were identified, whereas no activities of restriction endonucleases could be
      detected in this strain.  Slr0214, a Synechocystis gene encoding a putative methyltransferase
      that shows significant similarities to C5-methylcytosine-synthesizing enzymes, was amplified
      by PCR and cloned for further characterization.  Mutations in slr0214 were generated by the
      insertion of an aphII gene cassette.  Analyses of chromosomal DNAs of such mutants
      demonstrated that the methylation pattern was changed.  The recognition sequence of the
      methyltransferase was identified as 5'-CGATCG-3', corresponding to the recognition sequence
      of PvuI.  The specific methyltransferase activity was significantly reduced in protein
      extracts obtained from mutant cells.  Mutation of slr0214 also led to changed growth
      characteristics of the cells compared to wild-type cells.  These alterations led to the
      conclusion that the methyltransferase Slr0214 might play a regulatory role in Synechocystis.
      The Slr0214 protein was also overexpressed in Escherichia coli, and the purified protein
      demonstrated methyltransferase activity and specificity for PvuI recognition sequences in
      vitro.  We propose the designation SynMI (Synechocystis methyltransferase I) for the
      slr0214-encoded enzyme.
AU  - Scharnagl M
AU  - Richter S
AU  - Hagemann M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1998 180: 4116-4122.

PMID- Not included in PubMed...
VI  - 372
DP  - 1991
TI  - Cloning of the methyltransferase gene from Arabidopsis thaliana.
PG  - 742-743
AB  - DNA methylation is a widespread modification in eucaryotic cells and thought to be envolved in
      gene regulation.  Recently we showed that in vitro methylation of transgenes was inherited in
      tobacco plants and led to gene inactivation.  In plants DNA methylation differs from that in
      animal cells in respect to a much higher amount of 5-methylcytosine content of the DNA and to
      an altered sequence specificity of the methyltransferase (Mtase).  Cytosines in CpG and CpNpG
      sequences were methylated in plant DNA whereas only 5mCpG can be found in animal DNA.
      Furthermore it was shown that wheat Mtase had a preference for endogenous double stranded DNA
      as substrate and a lower molecular mass distinguishes it from the mammalian enzyme.  Little is
      known about the structure and regulation of eucaryotic Mtases, especially from plants and only
      from mouse cells the corresponding cDNA had been cloned and sequenced.  To characterize the
      Mtase gene from Arabidopsis a genomic library from nuclear DNA was established in EMBL3 and
      screened with heterologous probes encoding the cDNA of mouse Mtase (gift from T. Bestor).
      Several clones which hybridized under low stringent conditions were isolated and part of the
      DNA sequence was determined.  We found significant homology to the mouse Mtase cDNA on
      nucleotide and on amino acid level.  Furthermore this region is part of a conserved domain of
      cytosine Mtases not only from eucaryotic but also from bacterial and phage origin.  Using the
      cloned fragments as probes for hybridization experiments to each other and to total
      Arabidopsis DNA we identified at least 3 different sequences which are related but not totally
      homologous.  However they all hybridize to the mouse Mtase cDNA.  We conclude therefore that
      Arabidopsis Mtase is encoded by a gene family.
AU  - Scheidt G
AU  - Graessmann A
AU  - Weber H
PT  - Journal Article
TA  - Biol. Chem. Hoppe Seyler
JT  - Biol. Chem. Hoppe Seyler
SO  - Biol. Chem. Hoppe Seyler 1991 372: 742-743.

PMID- 8152926
VI  - 22
DP  - 1994
TI  - Are there two DNA methyltransferase gene families in plant cells?  A new potential methyltransferase gene isolated from an Arabidopsis thaliana genomic library.
PG  - 953-958
AB  - Using the 1kb 3' terminal DNA fragment of the mouse methyltransferase cDNA as a probe and low
      stringent hybridisation conditions, a new potential methyltransferase (MTase) gene family was
      isolated from an Arabidopsis thaliana genomic DNA library. One clone (MTase-11), which gave
      the strongest signal at the Northern blot, was entirely sequenced (11483 bp) and further
      characterised. Under consideration of the likely open reading frames and our preliminary cDNA
      experiments we propose that the clone 11 gene encodes for an ~90 kD protein. As deduced from
      the DNA sequence this protein contains all conserved sequence motifs specific for the 5m
      cytosine MTases. MTase-11 gene expression was demonstrable in callus and during germination
      but not in one month old plants or in leaves.
AU  - Scheidt G
AU  - Weber H
AU  - Graessmann M
AU  - Graessmann A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1994 22: 953-958.

PMID- 2066944
VI  - 18
DP  - 1991
TI  - Procainamide inhibits DNA methyltransferase in a human T cell line.
PG  - 530-534
AB  - Procainamide, a widely used antiarrythmic, causes DNA hypomethylation in the
      human T cell line Jurkat, but the mechanism is unknown.  We report that
      procainamide inhibits the DNA methyltransferase catalyzed transfer of methyl
      groups from S-adenosylmethionine to DNA, but has no effect on other known
      regulators of DNA methylation.  Our results suggest that procainamide could
      inhibit cellular DNA methylation by inhibiting DNA methyltransferase activity.
AU  - Scheinbart LS
AU  - Johnson MA
AU  - Gross LA
AU  - Edelstein SR
AU  - Richardson BC
PT  - Journal Article
TA  - J. Rheumatol.
JT  - J. Rheumatol.
SO  - J. Rheumatol. 1991 18: 530-534.

PMID- 4897045
VI  - 39
DP  - 1969
TI  - The mechanism of restriction of bacteriophage lambda in Escherichia coli strains: Demonstration of an in vivo requirement for S-adenosylmethionine.
PG  - 66-73
AB  - Restriction of phage lambda by certain Escherichia coli strains involves the degradation of
      the phage DNA in strains with a host-controlled modification system different from the one
      carried by the restricted phage.  By infecting the restricting host strain with phage T3,
      prior to infection with phage lambda, it was possible to inactivate the capacity of host cells
      to restrict phage lambda.  We have shown that this inactivation is specifically due to the
      production, in these T3-infected host cells, of an enzyme which cleaves S-adenosylmethionine.
      Since SAM is necessary for methylation reactions, it follows from these observations that
      methylation of the restricted lambda DNA might be required to make it susceptible to the
      host-controlled restriction system.  Several E. coli strains have a host-controlled
      restriction system, e.g., E. coli K12 and E. coli B, but also prophage P1 controls such a
      system.  Our results show that both the E. coli K12 and B restriction systems require SAM for
      activity.  The P1 restriction system, however, does not appear to have such a requirement.
AU  - Schell J
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1969 39: 66-73.

PMID- Not included in PubMed...
VI  - 45
DP  - 1966
TI  - The effect of heat on host-controlled restriction of phage lambda in Escherichia coli K(P1).
PG  - 61-72
AB  - The growth of phage lambda.C (i.e. phage lambda grown in Escherichia coli C) in
      E. coli K lysogenized by phage P1 is normally restricted so that the efficiency
      of plating of phage lambda.C on K(P1) compared to C is about 10-7.  When K(P1)
      bacteria are heated before infection with phage lambda.C this restriction may
      be decreased as much as a million-fold.  The time of exposure to elevated
      temperature (49C and above) required to achieve this increase in e.o.p. of
      phage lambda.C decreased with increasing temperature up to temperatures which
      began to inhibit the capacity of bacteria to grow phage.  Heated K(P1) bacteria
      recovered their ability to restrict phage lambda.C following the resumption of
      growth at 37C.  Part of this recovery can be inhibited by chloramphenicol.  A
      more dramatic recovery of restriction is observed when heated K(P1) bacteria
      are resuspended in hypertonic media.  Experiments are described which indicate
      that phage lambda.C is restricted at an early step after adsorption and that,
      if phage escapes this restriction, it can grow in heated bacteria subsequently
      converted into restricting hosts by resuspension in hypertonic media.
AU  - Schell J
AU  - Glover SW
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1966 45: 61-72.

PMID- 5326494
VI  - 7
DP  - 1966
TI  - The effect of various physiological conditions on host-controlled restriction in Escherichia coli K (P1).
PG  - 273-276
AB  - Growth of K(P1) bacteria under conditions which lead to a reduction in the level of nucleases
      also leads to a reduction in their ability to restrict the growth of lambda.C.  Experiments
      designed to estimate the time after adsorption at which restriction takes place indicate that
      phage DNA is probably restricted by a nuclease while passing through the periplasm.
AU  - Schell J
AU  - Glover SW
PT  - Journal Article
TA  - Genet. Res.
JT  - Genet. Res.
SO  - Genet. Res. 1966 7: 273-276.

PMID- 4956496
VI  - 7
DP  - 1966
TI  - On the localization of a factor responsible for host-controlled restriction in Escherichia coli K(P1).
PG  - 277-279
AB  - Recent experiments indicate that an essential step in the restriction of phage lambda.C by E.
      coli K(P1) bacteria may involve an enzyme located on the surface of the cells, and a
      surface-localized nuclease has been implicated in the restriction of non-glucosylated T4 DNA
      by E. coli B.  Neu & Heppel have shown that several enzymes, alkaline phosphatase, latent
      RNase, 5'-nucleotidase, acid phosphatase, cyclic phosphodiesterase and an RNA inhibited DNase
      can be partly or completely released by E. coli cells during spheroplast formation.  These
      authors also reported that surface-localized enzymes can also be released by EDTA treatment
      followed by washing at 4 C.  The results reported in this paper show that the restriction of
      phage lambda.C by K(P1) cells is markedly reduced when the cells are treated with EDTA and
      washed several times with cold distilled water.
AU  - Schell J
AU  - Glover SW
PT  - Journal Article
TA  - Genet. Res.
JT  - Genet. Res.
SO  - Genet. Res. 1966 7: 277-279.

PMID- Not included in PubMed...
VI  - 4
DP  - 1963
TI  - The restriction of phage T3 by certain strains of Escherichia coli.
PG  - 483-484
AB  - The efficiency of plating (e.o.p.) of phage T3 is equal on the E. coli strains
      B and C, and also on most F- strains of K12 (afterwards called K).  However, in
      strains of K which carry the F episome its e.o.p. is greatly reduced.  On most
      F+ strains of K its e.o.p. is about 10-5.  The phages which do multiply in the
      F+ bacteria are not modified; they still have an e.o.p. of 10-5 when replated
      on the same host.  The actual fraction of cells which accept T3 phages is
      approximately 10-2, and these cells yield a small burst of unmodified T3.  It
      seems to be this combination of restriction coupled with a small burst which
      defines the level of the e.o.p. and produces the typical small plaques which
      are observed on F+ strains.  As a result of screening a large number of male
      and female strains of K two striking exceptions were found to the observation
      stated above.  The F+ strain W1485 was found to plate efficiently, while some
      F- derivatives of 58-161 plate T3 with a low e.o.p.  In an effort to elucidate
      this situation a series of conjugation experiments was performed to establish
      the relationship between F and T3 restriction.  The results of these
      experiments are presented in Table 1.
AU  - Schell J
AU  - Glover SW
AU  - Stacey KA
AU  - Broda PMA
AU  - Symonds N
PT  - Journal Article
TA  - Genet. Res.
JT  - Genet. Res.
SO  - Genet. Res. 1963 4: 483-484.

PMID- 12381787
VI  - 99
DP  - 2002
TI  - The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract.
PG  - 14422-14427
AB  - Bifidobacteria are Gram-positive prokaryotes that naturally colonize the human
      gastrointestinal tract (GIT) and vagina. Although not numerically dominant in the complex
      intestinal microflora, they are considered as key commensals that promote a healthy GIT. We
      determined the 2.26-Mb genome sequence of an infant-derived strain of Bifidobacterium longum,
      and identified 1,730 possible coding sequences organized in a 60%-GC circular chromosome.
      Bioinformatic analysis revealed several physiological traits that could partially explain the
      successful adaptation of this bacteria to the colon. An unexpectedly large number of the
      predicted proteins appeared to be specialized for catabolism of a variety of oligosaccharides,
      some possibly released by rare or novel glycosyl hydrolases acting on "nondigestible" plant
      polymers or host-derived glycoproteins and glycoconjugates. This ability to scavenge from a
      large variety of nutrients likely contributes to the competitiveness and persistence of
      bifidobacteria in the colon. Many genes for oligosaccharide metabolism were found in
      self-regulated modules that appear to have arisen in part from gene duplication or horizontal
      acquisition. Complete pathways for all amino acids, nucleotides, and some key vitamins were
      identified; however, routes for Asp and Cys were atypical. More importantly, genome analysis
      provided insights into the reciprocal interactions of bifidobacteria with their hosts. We
      identified polypeptides that showed homology to most major proteins needed for production of
      glycoprotein-binding fimbriae, structures that could possibly be important for adhesion and
      persistence in the GIT. We also found a eukaryotic-type serine protease inhibitor (serpin)
      possibly involved in the reported immunomodulatory activity of bifidobacteria.
AU  - Schell MA
AU  - Karmirantzou M
AU  - Snel B
AU  - Vilanova D
AU  - Berger B
AU  - Pessi G
AU  - Zwahlen MC
AU  - Desiere F
AU  - Bork P
AU  - Delley M
AU  - Prodmore RD
AU  - Arigoni F
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2002 99: 14422-14427.

PMID- 7580999
VI  - 36
DP  - 1995
TI  - The accessibility of thiophosphorylated groups in DNA fragments to the enzymatic activity of ligases and restriction endonuclease BbsI.
PG  - 1037-1043
AB  - The aim of this paper was to test the possibility to ligate and hydrolyse DNA
      sequences containing thiomodified ends and bonds.  T4 DNA ligase was shown to ligate DNA
      fragments regardless of whether it contains phosphorylated or thiophosphorylated 5'-ends.  But
      the cleavage of an internally thiomodified phosphodiester bond was found to be totally
      inhibited
      when using the nonpalindromic restrictase BbsI.  The special properties of this restriction
      endonuclease should allow the development of an oriented cloning strategy when combined with
      T4 ligase and a thiophosphorylation of DNA fragments.
AU  - Schenk JA
AU  - Heymann S
AU  - Micheel B
PT  - Journal Article
TA  - Biochem. Mol. Biol. Int.
JT  - Biochem. Mol. Biol. Int.
SO  - Biochem. Mol. Biol. Int. 1995 36: 1037-1043.

PMID- 17576694
VI  - 35
DP  - 2007
TI  - Dynamics of Dnmt1 interaction with the replication machinery and its role in postreplicative maintenance of DNA methylation.
PG  - 4301-4312
AB  - Postreplicative maintenance of genomic methylation patterns was proposed to depend largely on
      the binding of DNA methyltransferase 1 (Dnmt1) to PCNA, a core component of the replication
      machinery. We investigated how
      the slow and discontinuous DNA methylation could be mechanistically linked
      with fast and processive DNA replication. Using photobleaching and
      quantitative live cell imaging we show that Dnmt1 binding to PCNA is
      highly dynamic. Activity measurements of a PCNA-binding-deficient mutant
      with an enzyme-trapping assay in living cells showed that this interaction
      accounts for a 2-fold increase in methylation efficiency. Expression of
      this mutant in mouse dnmt1(-/-) embryonic stem (ES) cells restored CpG
      island methylation. Thus association of Dnmt1 with the replication
      machinery enhances methylation efficiency, but is not strictly required
      for maintaining global methylation. The transient nature of this
      interaction accommodates the different kinetics of DNA replication and
      methylation while contributing to faithful propagation of epigenetic
      information.
AU  - Schermelleh L
AU  - Haemmer A
AU  - Spada F
AU  - Rosing N
AU  - Meilinger D
AU  - Rothbauer U
AU  - Cristina CM
AU  - Leonhardt H
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2007 35: 4301-4312.

PMID- 16179921
VI  - 2
DP  - 2005
TI  - Trapped in action: direct visualization of DNA methyltransferase activity in living cells.
PG  - 751-756
AB  - DNA methyltransferases have a central role in the complex regulatory network of epigenetic
      modifications controlling gene expression in
      mammalian cells. To study the regulation of DNA methylation in living
      cells, we developed a trapping assay using transiently expressed
      fluorescent DNA methyltransferase 1 (Dnmt1) fusions and mechanism-based
      inhibitors 5-azacytidine (5-aza-C) or 5-aza-2'-deoxycytidine (5-aza-dC).
      These nucleotide analogs are incorporated into the newly synthesized DNA
      at nuclear replication sites and cause irreversible immobilization, that
      is, trapping of Dnmt1 fusions at these sites. We measured trapping by
      either fluorescence bleaching assays or photoactivation of
      photoactivatable green fluorescent protein fused to Dnmt1 (paGFP-Dnmt1) in
      mouse and human cells; mutations affecting the catalytic center of Dnmt1
      prevented trapping. This trapping assay monitors kinetic properties and
      activity-dependent immobilization of DNA methyltransferases in their
      native environment, and makes it possible to directly compare mutations
      and inhibitors that affect regulation and catalytic activity of DNA
      methyltransferases in single living cells.
AU  - Schermelleh L
AU  - Spada F
AU  - Easwaran HP
AU  - Zolghadr K
AU  - Margot JB
AU  - Cardoso MC
AU  - Leonhardt H
PT  - Journal Article
TA  - Nat. Methods
JT  - Nat. Methods
SO  - Nat. Methods 2005 2: 751-756.

PMID- 10899825
VI  - 2
DP  - 2000
TI  - Oligonucleotide scanning of native mRNAs in extracts predicts intracellular ribozyme efficiency: ribozyme-mediated reduction of the murine DNA methyltransferase.
PG  - 26-38
AB  - Modulation of gene expression by catalytic RNA requires accessible ribozyme cleavage sites in
      the target mRNA, and accessibility is determined by the secondary and tertiary structure of
      the target RNA, as affected by its interactions with cellular proteins. As we previously
      reported, an oligonucleotide-scanning approach using antisense oligonucleotides can be used to
      determine RNA accessibility in cell extracts. To test whether this method can be used to
      improve selection of ribozyme target sites, we designed ribozymes corresponding to the sites
      identified by oligonucleotide scanning and have evaluated their catalytic activities, first in
      cell extracts and then in transduced cell lines. As a target we used the mRNA of murine DNA
      (cytosine-5)-methyltransferase 1 (MTase). For intracellular studies, the ribozyme genes were
      inserted downstream of a Pol III tRNAVAL promoter, which in turn was cloned in the U3 region
      of a retroviral vector. We find that the efficiency of the ribozymes both in cell extracts and
      in vivo corresponds with the relative effectiveness predicted by the oligonucleotide-scanning
      assay. The best ribozyme causes a 70-80% reduction in the MTase mRNA levels in NIH 3T3 cells
      that are stably transduced with the retroviral constructs. This reduction in mRNA levels is
      accompanied by a small decrease in the methylation of repetitive intercisternal A particle DNA
      elements. Ribozyme expression also increased several-fold the reactivation frequency of a
      methylation-silenced green fluorescent protein (GFP) transgene. Both the reduction in
      methylation and reactivation of GFP were roughly equivalent to the effects obtained by
      treating NIH 3T3 cells with 2.5 mM 5-azacytidine, which gives an effect of about 10% of
      maximum. These results confirm the validity of the cell extract approach for ribozyme site
      selection and provide a potentially useful ribozyme for future study of DNA methyltransferase
      function.
AU  - Scherr M
AU  - Reed M
AU  - Huang CF
AU  - Riggs AD
AU  - Rossi JJ
PT  - Journal Article
TA  - Mol. Ther.
JT  - Mol. Ther.
SO  - Mol. Ther. 2000 2: 26-38.

PMID- 3312202
VI  - 262
DP  - 1987
TI  - Identification, purification and characterization of Escherichia coli virus T1 DNA methyltransferase.
PG  - 15225-15231
AB  - An Escherichia coli virus T1-induced DNA methyltransferase was identified by
      activity gel analysis in homogenates of infected E. coli
      DNA-adenine-methylation-deficient strains.  Although the Mr of this protein
      (31,000) is in the same range as that of the E. coli DNA adenine
      methyltransferase, the two proteins are not closely related; the E. coli dam
      gene does not hybridize with T1 DNA. Selective conditions for measurement of
      the T1 activity were developed, and the enzyme was purified to functional
      homogeneity, as shown by activity analysis in polyacrylamide gels.
      Requirements for optimal activity of the viral enzyme were determined to be pH
      6.9, ionic strengths below 0.1 M KCl, and a temperature between 40 and 43C.
      The Km for S-adenosyl-L-methionine is 4.9 microM.  The purified T1 DNA
      methyltransferase is capable of methylating adenine in 5'-GATC-3' sites in
      vitro.
AU  - Scherzer E
AU  - Auer B
AU  - Schweiger M
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1987 262: 15225-15231.

PMID- 25780503
VI  - 9
DP  - 2014
TI  - Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305(T)),  phylogenomic analysis and reclassification of Planctomycetes including the  descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen.   nov. and emen.
PG  - 10
AB  - Planctomyces brasiliensis Schlesner 1990 belongs to the order Planctomycetales, which differs
      from other bacterial taxa by several distinctive features such as
      internal cell compartmentalization, multiplication by forming buds directly from
      the spherical, ovoid or pear-shaped mother cell and a cell wall consisting of a
      proteinaceous layer rather than a peptidoglycan layer. The first strains of P.
      brasiliensis, including the type strain IFAM 1448(T), were isolated from a water
      sample of Lagoa Vermelha, a salt pit near Rio de Janeiro, Brasil. This is the
      second completed genome sequence of a type strain of the genus Planctomyces to be
      published and the sixth type strain genome sequence from the family
      Planctomycetaceae. The 6,006,602 bp long genome with its 4,811 protein-coding and
      54 RNA genes is a part of the G enomic E ncyclopedia of Bacteria and Archaea
      project. Phylogenomic analyses indicate that the classification within the
      Planctomycetaceae is partially in conflict with its evolutionary history, as the
      positioning of Schlesneria renders the genus Planctomyces paraphyletic. A
      re-analysis of published fatty-acid measurements also does not support the
      current arrangement of the two genera. A quantitative comparison of phylogenetic
      and phenotypic aspects indicates that the three Planctomyces species with type
      strains available in public culture collections should be placed in separate
      genera. Thus the genera Gimesia, Planctopirus and Rubinisphaera are proposed to
      accommodate P. maris, P. limnophilus and P. brasiliensis, respectively.
      Pronounced differences between the reported G + C content of Gemmata
      obscuriglobus, Singulisphaera acidiphila and Zavarzinella formosa and G + C
      content calculated from their genome sequences call for emendation of their
      species descriptions. In addition to other features, the range of G + C values
      reported for the genera within the Planctomycetaceae indicates that the
      descriptions of the family and the order should be emended.
AU  - Scheuner C et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 10.

PMID- 
VI  - 14
DP  - 2004
TI  - Two of a kind: BamHI and BglII.
PG  - 215-236
AB  - Among the more than 3500 Type II restriction endonucleases identified to date, fourteen have
      been structurally characterized so far, including EcoRI, EcoRV, BamHI, PvuII, FokI, Cfr10I,
      BglI, BglII, BsoBI, NaeI, NgoMIV, Bse634I (an isoschizomer of Cfr10I), MunI, and HincII.  All
      except Cfr10I and Bse634I have been found to be bound to their cognate DNA sites.  Despite the
      lack of sequence homology, all REases consist of a central beta-sheet that is flanked by
      alpha-helices on both sides.  Interestingly, a similar alpha/beta core is also present in
      other DNA-acting enzymes such as lambda-exonuclease, MutH, Vsr endonuclease, and TnsA from the
      Tn7 transposase.  In the common core only three beta-strands are absolutely conserved, two of
      these strands contain the amino acid residues directly involved in catalysis.  The similarity
      at the tertiary structure level is strongest between endonucleases that share a similar
      cleavatge pattern, such as between BamHI and EcoRI which cleave DNA to leave four-base 5'
      overhangs, or between EcoRV and PvuII which cleave DNA to produce blunt ends.  An exception is
      BglI that has a similar fold as EcoRV and PvuII but cleaves DNA to leave 3' overhangs.
      Overall, the similarity reflects constraints in positioning of the active sites: 17-19 A apart
      to produce four-base 5' overhangs and ~2A apart to produce blunt ends.  The active sites
      occur at one end of the central beta-sheet and contain at least three superimposable residues
      that are critical for catalysis.  Two of these residues are acidic, while the third residue is
      usually a lysine, except in BamHI, which has a glutamate and in BglII which has a glutamine.
AU  - Scheuring-Vanamee E
AU  - Viadiu H
AU  - Lukacs CM
AU  - Aggarwal AK
PT  - Journal Article
TA  - Nucleic Acids Mol. Biol.
JT  - Nucleic Acids Mol. Biol.
SO  - Nucleic Acids Mol. Biol. 2004 14: 215-236.

PMID- 26067957
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Raoultella terrigena R1Gly, a Diazotrophic Endophyte.
PG  - e00607-15
AB  - Raoultella terrigena R1Gly is a diazotrophic endophyte isolated from surface-sterilized roots
      of Nicotiana tabacum. The whole-genome sequence was
      obtained to investigate the endophytic characteristics of this organism at the
      genetic level, as well as to compare this strain with its close relatives. To our
      knowledge, this is the first genome obtained from the Raoultella terrigena
      species and only the third genome from the Raoultella genus, after Raoultella
      ornitholytic and Raoultella planticola. This genome will provide a foundation for
      further comparative genomic, metagenomic, and functional studies of this genus.
AU  - Schicklberger M
AU  - Shapiro N
AU  - Loque D
AU  - Woyke T
AU  - Chakraborty R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00607-15.

PMID- 22135304
VI  - 40
DP  - 2012
TI  - A novel zinc-finger nuclease platform with a sequence-specific cleavage module.
PG  - 2623-2638
AB  - Zinc-finger nucleases (ZFNs) typically consist of three to four zinc fingers (ZFs) and the
      non-specific DNA-cleavage domain of the restriction endonuclease FokI. In this configuration,
      the ZFs constitute the binding module and the FokI domain the cleavage module. Whereas new
      binding modules, e.g. TALE sequences, have been considered as alternatives to ZFs, no efforts
      have been undertaken so far to replace the catalytic domain of FokI as the cleavage module in
      ZFNs. Here, we have fused a three ZF array to the restriction endonuclease PvuII to generate
      an alternative ZFN. While PvuII adds an extra element of specificity when combined with ZFs,
      ZF-PvuII constructs must be designed such that only PvuII sites with adjacent ZF-binding sites
      are cleaved. To achieve this, we introduced amino acid substitutions into PvuII that alter
      K(m) and k(cat) and increase fidelity. The optimized ZF-PvuII fusion constructs cleave DNA at
      addressed sites with a >1000-fold preference over unaddressed PvuII sites in vitro as well as
      in cellula. In contrast to the 'analogous' ZF-FokI nucleases, neither excess of enzyme over
      substrate nor prolonged incubation times induced unaddressed cleavage in vitro. These results
      present the ZF-PvuII platform as a valid alternative to conventional ZFNs.
AU  - Schierling B
AU  - Dannemann N
AU  - Gabsalilow L
AU  - Wende W
AU  - Cathomen T
AU  - Pingoud A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: 2623-2638.

PMID- 
VI  - 276
DP  - 2009
TI  - Development of a 'photoswitchable' restriction endonuclease.
PG  - 291
AB  - The engineering of proteins in order to obtain light-responsive characteristics is in focus of
      photochemical research, because of the possibility to regulate protein function quickly and
      reversibly, which is difficult to achieve by other means. As a proof of principle for
      promising applications in future, we tried to generate a restriction endonuclease that can be
      turned on and off by irradiation with light, using the single chain (sc) variant of the
      restriction enzyme PvuII. 'Photoswitchable' proteins have been produced using azobenzene
      crosslinkers that can be isomerized between the trans- and cis-state and vice versa by
      illumination at specific wavelengths or by thermal relaxation from the cis- to the more stable
      trans-state. Up to now, a 7-fold higher activity could be obtained with a variant of scPvuII
      modified by two intramolecular crosslinks with 4,4'- azobenzene-dimaleimide in the cis
      configuration than in the trans configuration. Switching was shown to be fully reversible. The
      higher activity of the scPvuII variant with the azobenzene group in the cis state was shown to
      be due to an increase mainly in Vmax.
AU  - Schierling B
AU  - Noel AJ
AU  - Thi LH
AU  - Wende W
AU  - Pingoud A
PT  - Journal Article
TA  - FEBS J.
JT  - FEBS J.
SO  - FEBS J. 2009 276: 291.

PMID- 20080559
VI  - 107
DP  - 2010
TI  - Controlling the enzymatic activity of a restriction enzyme by light.
PG  - 1361-1366
AB  - For many applications it would be desirable to be able to control the activity of proteins by
      using an external signal. In the present study, we have explored the possibility of modulating
      the activity of a restriction
      enzyme with light. By cross-linking two suitably located cysteine residues
      with a bifunctional azobenzene derivative, which can adopt a cis- or
      trans-configuration when illuminated by UV or blue light, respectively,
      enzymatic activity can be controlled in a reversible manner. To determine
      which residues when cross-linked show the largest 'photoswitch effect,'
      i.e., difference in activity when illuminated with UV vs. blue light, > 30
      variants of a single-chain version of the restriction endonuclease PvuII
      were produced, modified with azobenzene, and tested for DNA cleavage
      activity. In general, introducing single cross-links in the enzyme leads
      to only small effects, whereas with multiple cross-links and additional
      mutations larger effects are observed. Some of the modified variants,
      which carry the cross-links close to the catalytic center, can be
      modulated in their DNA cleavage activity by a factor of up to 16 by
      illumination with UV (azobenzene in cis) and blue light (azobenzene in
      trans), respectively. The change in activity is achieved in seconds, is
      fully reversible, and, in the case analyzed, is due to a change in V(max)
      rather than K(m).
AU  - Schierling B
AU  - Noel AJ
AU  - Wende W
AU  - Hien LT
AU  - Volkov E
AU  - Kubareva E
AU  - Oretskaya T
AU  - Kokkinidis M
AU  - Rompp A
AU  - Spengler B
AU  - Pingoud A
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2010 107: 1361-1366.

PMID- 22613569
VI  - 586
DP  - 2012
TI  - Redesigning the single-chain variant of the restriction endonuclease PvuII by circular permutation.
PG  - 1736-1741
AB  - The restriction endonuclease PvuII has been introduced as a sequence-specific cleavage module
      in highly-specific nucleases for gene
      targeting. Here, a structural reorganization of the single-chain
      variant of PvuII (scPvuII) was performed by circular permutation as a
      proof-of-concept in order to find out whether the relocated, new
      termini next to structural elements important for DNA recognition and
      catalysis could be used for the fusion with other regulatory protein
      domains. Three circularly permuted variants of scPvuII were obtained
      that all maintain the specific endonucleolytic activity of scPvuII.
AU  - Schierling B
AU  - Wende W
AU  - Pingoud A
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 2012 586: 1736-1741.

PMID- 1881899
VI  - 88
DP  - 1991
TI  - Integration of DNA fragments by illegitimate recombination in Saccharomyces cerevisiae.
PG  - 7585-7589
AB  - DNA fragments (generated by BamHI treatment) with no homology to the yeast genome were
      transformed into Saccharomyces cerevisiae. When the fragments were transformed in the presence
      of the BamHI enzyme, they integrated into genomic BamHI sites. When the fragments were
      transformed in the absence of the enzyme, they integrated into genomic G-A-T-C sites. Since
      the G-A-T-C sequence is present at the ends of BamHI fragments, this result indicates that
      four base pairs of homology are sufficient for some types of mitotic recombination.
AU  - Schiestl RH
AU  - Petes TD
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1991 88: 7585-7589.

PMID- 20546576
VI  - 11
DP  - 2010
TI  - Whole genome analysis of a livestock-associated methicillin-resistant Staphylococcus aureus ST398 isolate from a case of human endocarditis.
PG  - 376
AB  - BACKGROUND: Recently, a new livestock-associated methicillin-resistant Staphylococcus aureus
      (MRSA) Sequence Type 398 (ST398) isolate has emerged
      worldwide. Although there have been reports of invasive disease in humans, MRSA
      ST398 colonization is much more common in livestock and demonstrates especially
      high prevalence rates in pigs and calves. The aim of this study was to compare
      the genome sequence of an ST398 MRSA isolate with other S. aureus genomes in
      order to identify genetic traits that may explain the success of this particular
      lineage. Therefore, we determined the whole genome sequence of S0385, an MRSA
      ST398 isolate from a human case of endocarditis. RESULTS: The entire genome
      sequence of S0385 demonstrated considerable accessory genome content differences
      relative to other S. aureus genomes. Several mobile genetic elements that confer
      antibiotic resistance were identified, including a novel composite of an type V
AU  - Schijffelen MJ
AU  - Boel CH
AU  - van Strijp JA
AU  - Fluit AC
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2010 11: 376.

PMID- 
VI  - 6
DP  - 1984
TI  - Screening for and characterizing restriction endonucleases.
PG  - 117-140
AB  - The ability to cleave DNA at specific sequences is the fundamental technology
      which was responsible for the rapid development of genetic engineering.  The
      type II restriction endonucleases are the enzymes which enable scientists to
      cleave DNA at specific sequences.  In 1974, Richard Roberts distributed a list
      of 30 restriction endonucleases.  Eighteen of these recognized unique
      sequences; the remainder were isoschizomers, enzymes from different bacterial
      sources that recognize the same sequence.  Presently the list contains 398
      restriction endonucleases, 91 of which are unique.  The increased number of
      restriction endonucleases available now has allowed greater flexibility and
      versatility in experimental strategies and design.  Continuing the search for
      and identifying new restriction endonucleases will further reduce the
      limitations and permit more precision in genetic engineering.  This chapter
      describes a method for screening bacterial cells for the presence of type II
      restriction endonucleases, and procedures for characterizing these restriction
      endonucleases with respect to recognition sequence and site of cleavage.  The
      recognition sequence is defined here as the nucleotide sequence which is
      required for cleavage.  The site of cleavage is defined as the position of the
      cleavage with relation to the recognition sequence.  For example, the
      recognition sequence for EcoRI is GAATTC.  The site of cleavage is between the
      G and A residues which produces a four base 5' extension (GAATTC).
AU  - Schildkraut I
PT  - Journal Article
TA  - Genet. Eng. (N Y)
JT  - Genet. Eng. (N Y)
SO  - Genet. Eng. (N Y) 1984 6: 117-140.

PMID- 6329909
VI  - 27
DP  - 1984
TI  - The cleavage site for the restriction endonuclease EcoRV is 5'-GAT^ATC-3'.
PG  - 327-329
AB  - The cleavage site for the restriction endonuclease EcoRV has been found to be
      5'-GAT^ATC-3', rather than 5'-GATAT^C-3' as reported earlier by Kholmina et al.
      (Dokl. Akad. Nauk. SSSR 253 (1980) 495-497).
AU  - Schildkraut I
AU  - Banner CDB
AU  - Rhodes CS
AU  - Parekh S
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1984 27: 327-329.

PMID- 3037499
VI  - 15
DP  - 1987
TI  - The cleavage site for the restriction endonucleases BanI and HgiCI is 5' ...G^GPyPuCC ...3'.
PG  - 5492
AB  - We have determined the cleavage site for the restriction endonucleases BanI and
      HgiC 1 to be identical.  Both cleaving the sequence 5'... G^GPyPuCC ...3'
      leaving a 4 base 5' extension.  This is in contrast to Kroger et al, who
      reported the cleavage for HgiCI as 5' ...^GGPyPuCC...3' leaving a 6 base 5'
      extension.
AU  - Schildkraut I
AU  - Lynch J
AU  - Morgan R
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1987 15: 5492.

PMID- 22334601
VI  - 67
DP  - 2012
TI  - Detection of qnr genes among Escherichia coli isolates of animal origin and complete sequence of the conjugative qnrB19-carrying plasmid pQNR2078.
PG  - 1099-1102
AB  - OBJECTIVES: The aims of this study were to identify qnr genes among
      quinolone-resistant Escherichia coli isolates from defined disease conditions of
      companion and farm animals obtained in the BfT-GermVet study, and to gain insight
      into their localization and the organization of the qnr gene regions. METHODS:
      The qnr genes were detected by PCR and confirmed by sequencing. qnr-positive
      isolates were checked for mutations in DNA gyrase and topoisomerase IV genes by
      PCR and sequencing of the quinolone resistance-determining regions. Multilocus
      sequence typing (MLST) was performed for the qnr-positive E. coli isolates.
      Plasmids harbouring qnr genes were transferred by conjugation into E. coli
      recipients, subjected to PCR-based replicon typing and plasmid-MLST, and one
      qnrB19-carrying plasmid was sequenced completely. RESULTS: Only 2 of 417 E. coli
      isolates investigated carried qnr genes. Both isolates originated from horses and
      showed MLST type ST86. They harboured conjugative qnrB19-carrying plasmids, which
      proved to be indistinguishable by restriction analysis, belonged to
      incompatibility group IncN, showed plasmid-MLST type ST8 and did not carry other
      resistance genes. The qnrB19 gene was flanked by copies of the insertion sequence
      IS26. One of these plasmids, pQNR2078, was sequenced completely and had a size of
      42 379 bp. Except for the resistance gene region, plasmid pQNR2078 closely
      resembled the bla(CTX-M-65)-carrying plasmid pKC396 from E. coli. CONCLUSIONS:
      qnr genes were rarely detected among E. coli from animals in the BfT-GermVet
      study. The qnrB19 gene was detected on conjugative plasmids, with IS26 being
      likely involved in the mobility of qnrB19.
AU  - Schink AK
AU  - Kadlec K
AU  - Schwarz S
PT  - Journal Article
TA  - J. Antimicrob. Chemother.
JT  - J. Antimicrob. Chemother.
SO  - J. Antimicrob. Chemother. 2012 67: 1099-1102.

PMID- Not included in PubMed...
VI  - 37
DP  - 1986
TI  - A site-specific endonuclease activity in Halobacterium halobium.
PG  - 325-329
AB  - In Halobacterium halobium and some related strains, a site-specific
      endonuclease activity was found.  This activity requires 3 M NaCl and 5-10 mM
      Mg2+ ions for function.  The 3 cleavage sites in plasmid pBR322 were mapped,
      but no homology between these sites was found.  H. halobium DNA is resistant to
      cleavage, which may be due to a modification of the DNA.  The behaviour of the
      endonuclease can be explained by the presence of a Type I or Type III-like
      restriction-modification system.
AU  - Schinzel R
AU  - Burger KJ
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1986 37: 325-329.

PMID- 
VI  - 101
DP  - 2001
TI  - Bacteriophage resistance in Streptococcus thermophilus.
PG  - 476
AB  - Thermophilic lactic acid bacteria are frequently used as starter cultures for the industrial
      preparation of yoghurt or cheese.
      Bacteriophage attack of these starter cultures has been described as
      the main reason for fermentation failures. Natural phage resistance
      mechanisms of bacteria include restriction/modification (R/M) systems,
      enzyme complexes, that modify host DNA by methylation and degrade
      unmodified incoming DNA. Type 1 R/M systems are encoded by three genes,
      named hsdR, hsdM and hsdS. A complex of all three proteins, R, M and S,
      is needed for degradation of unmodified DNA, whereas DNA modification
      only requires the M and S subunits. The hsdM and hsdS genes are located
      on the same operon, whereas the hsdR gene is usually transcribed from
      its own promoter. A type I R/M system was identified on the genome of
      S. thermophilus 4134, a phage resistant industrial strain used for the
      production of yoghurt. The organization of the three genes is unusual,
      in that they appear to be located on the same operon. The hsdR and hsdM
      genes show high sequence identity to the corresponding genes of plasmid
      located type 1 R/M systems from Lactococcos lactis or S. thermophilus,
      suggesting a gene transfer event from a mobile genetic element into the
      genome of S. thermophilus 4134.
AU  - Schirawski J
AU  - van Sinderen D
AU  - Fitzgerald G
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 2001 101: 476.

PMID- 16536454
VI  - 17
DP  - 2006
TI  - Synthesis and in vitro evaluation of biotinylated RG108: a high affinity compound for studying binding interactions with human DNA  methyltransferases.
PG  - 261-266
AB  - Small-molecule inhibitors of DNA methyltransferases such as RG108 represent promising
      candidates for cancer drug development. We report the
      synthesis and in vitro analysis of a biotinylated RG108 conjugate,
      2-(1,3-dioxo-1,3-dihydro-isoindol-2-yl)-3-(5-[3-[5-(2-oxo-hexahydro-thieno
      [3,4-d]imidazol-4-yl)pentanoylamino]propoxy]-1H-indol-3-yl)propionic acid
      (bio-RG108), for the evaluation of interactions with DNA methyltransferase
      enzymes. The structural design of the chemically modified inhibitor was
      aided by molecular modeling, which suggested the possibility for extensive
      chemical modifications at the 5-position of the tryptophan moiety in
      RG108. The inhibitory activity of the corresponding derivative was
      confirmed in a cell-free biochemical assay, where bio-RG108 showed an
      undiminished inhibition of DNA methyltransferase activity (IC50 = 40 nM).
      Bio-RG108 therefore represents a suitable bioconjugate for the elucidation
      of inhibitory mechanisms and for the affinity purification of
      RG108-associated proteins.
AU  - Schirrmacher E
AU  - Beck C
AU  - Brueckner B
AU  - Schmitges F
AU  - Siedlecki P
AU  - Bartenstein P
AU  - Lyko F
AU  - Schirrmacher R
PT  - Journal Article
TA  - Bioconjugate Chem.
JT  - Bioconjugate Chem.
SO  - Bioconjugate Chem. 2006 17: 261-266.

PMID- 12657791
VI  - 59
DP  - 2003
TI  - Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of HP1352, a putative DNA methyltransferase  in Helicobacter pylori.
PG  - 719-720
AB  - The putative methyltransferase gene HP1352 from Helicobacter pylori strain 26695 was
      heterologously expressed in Escherichia coli. The 359-amino-acid
      gene product was purified and crystallized. The crystals belong to space
      group I2(1)2(1)2(1) and show diffraction to at least 2.5 A resolution. The
      unit-cell parameters are a = 69.6, b = 86.6, c = 140.0 A. A greater than
      90% complete native data set has been collected and structure
      determination using the molecular-replacement method is ongoing.
AU  - Schirwitz K
AU  - Lundin A
AU  - Skoglund A
AU  - Krabbe M
AU  - Engstrand L
AU  - Enroth C
PT  - Journal Article
TA  - Acta Crystallogr. D Biol. Crystallogr.
JT  - Acta Crystallogr. D Biol. Crystallogr.
SO  - Acta Crystallogr. D Biol. Crystallogr. 2003 59: 719-720.

PMID- 4371329
VI  - 120
DP  - 1974
TI  - Mutants of the N-3 R-Factor conditionally defective in hspII modification and deoxyribonucleic acid-cytosine methylase activity.
PG  - 234-239
AB  - The N-3 resistance (R) factor specifies a deoxyribonucleic acid (DNA)-cytosine
      methylase and a DNA restriction-modification (hspII) system.  We have isolated
      three independent mutants that are conditionally defective in their ability to
      modify bacteriophage lambda and to methylate DNA-cytosine residues.  The ratio
      of 5-methylcytosine to N6-methyladenine in bacterial DNA and in the DNA of
      phages lambda and fd was determined after labeling with [methyl-3H]methionine
      at various growth temperatures.  Although the ability of the wild-type N-3
      factor to modify phage lambda and to methylate DNA-cytosine residues was
      unaffected with increasing temperature, two of the mutants exhibited a parallel
      loss in modification and cytosine methylation ability.  The ability of the
      third mutant to carry out these functions was dependent on the presence or
      absence of an amber suppressor mutation in the host genome.  These results
      offer further support for the notion that hspII modification is mediated by a
      DNA-cytosine methylase.  Evidence is also presented that the modification
      methylase is responsible for the in vivo methylation of phage fd DNA (which is
      not subject to hspII restriction in vivo).
AU  - Schlagman S
AU  - Hattman S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1974 120: 234-239.

PMID- 770462
VI  - 126
DP  - 1976
TI  - In vivo methylation by Escherichia coli K-12 mec+ Deoxyribonucleic Acid-cytosine methylase protects against in vitro cleavage by the RII restriction endonuclease (R.EcoRII).
PG  - 990-996
AB  - We have analyzed the susceptibility of the deoxyribonucleic acid (DNA) of phage
      fd replicative form (RF) and of Escherichia coli to in vitro cleavage by
      purified RII restriction endonuclease (R.EcoRII).  The results are summarized
      as follows:  (i) fd.mec- RFI, isolated from infected E. coli K-12 mec- bacteria
      (a mutant strain lacking DNA-cytosine methylase activity), is cleaved into at
      least two fragments, whereas fd.mec+ RFI, isolated from the parental mec+
      strain, is not cleaved.  (ii) E. coli mec- DNA is extensively degraded, whereas
      E. coli mec+ DNA is resistant to cleavage.  We conclude that the E. coli mec+
      DNA-cytosine methylase acts as an RII modification enzyme.
AU  - Schlagman S
AU  - Hattman S
AU  - May MS
AU  - Berger L
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1976 126: 990-996.

PMID- 2685754
VI  - 17
DP  - 1989
TI  - The bacteriophage T2 and T4 DNA-[N6-adenine] methyltransferase (Dam) sequence specificities are not identical.
PG  - 9101-9112
AB  - Bacteriophages T2 and T4 encode DNA-[N6-adenine] methyltransferases (Dam) which differ from
      each other by only three amino acids. The canonical recognition sequence for these enzymes in
      both cytosine and 5-hydroxymethylcytosine-containing DNA is GATC; at a lower efficiency they
      also recognize some non-canonical sites in sequences derived from GAY (where Y is cytosine or
      thymine). We found that T4 Dam fails to methylate certain GATA and GATT sequences which are
      methylated by T2 Dam. This indicates that T2 Dam and T4 Dam do not have identical sequence
      specificities. We analyzed DNA sequence data files obtained from GenBank, containing bout 30%
      of the T4 genome, to estimate the overall frequency of occurrence of GATC, as well as
      non-canonical sites derived from GAY. The observed N6methyladenine (m6A) content of T4 DNA,
      methylated exclusively at GATC (by Escherichia coli Dam), was found to be in good agreeement
      with this estimate. Although GATC is fully methylated in virion DNA, only a small percentage
      of the non-canonical sequences are methylated.
AU  - Schlagman SL
AU  - Hattman S
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 9101-9112.

PMID- 6307815
VI  - 22
DP  - 1983
TI  - Molecular cloning of a functional dam+ gene coding for phage T4 DNA adenine methylase.
PG  - 139-156
AB  - Phages T2 and T4 induce synthesis of a DNA-adenine methylase which is coded for
      by a phage gene, dam+. These enzymes methylate adenine residues in specific
      sequences which include G-A-T-C, the methylation site of the host Escherichia
      coli dam+ methylase.  Methylation of G-A-T-C to G-m6A-T-C protects the site
      against cleavage by the MboI restriction nuclease.  We have taken advantage of
      this property to enrich and screen for transformants which contain a cloned,
      functional T4 dam+ gene.  These recombinant molecules consist of a 1.85-kb
      HindIII fragment inserted into the plasmid pBR322; both orientations of the
      fragment express the methylase gene, suggesting that transcription is from a T4
      promoter.  We have tested the 1.85-kb insert for sensitivity to a variety of
      restriction nucleases and have found single sites for EcoRI, BalI, XbaI, and at
      least two sites for BstNI (EcoRII).  The relative positions of these
      restriction sites have also been determined.  Physical mapping was carried out
      by Southern blot hybridization with 32P-labeled (nick-translated clone) probe.
      These experiments showed that the insert corresponds to a HindIII fragment
      located on the physical map of T4 between positions 16.2 and 18.1 kb from the
      T4rIIA-rIIB junction.  E. coli dam- possesses several phenotypic differences
      from the wild-type dam+ parent, including an increased sensitivity to
      2-aminopurine (2-AP).  We found that T4 dam+ clones could relieve dam- cells of
      their increased sensitivity to 2-AP.
AU  - Schlagman SL
AU  - Hattman S
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1983 22: 139-156.

PMID- 3512529
VI  - 165
DP  - 1986
TI  - Direct role of the Escherichia coli Dam DNA methyltransferase in methylation-directed mismatch repair.
PG  - 896-900
AB  - The T4 dam+ gene has been cloned (S. L. Schlagman and S. Hattman, Gene 22:139-156, 1983) and
      transferred into an Escherichia coli dam-host. In this host, the T4 Dam DNA methyltransferase
      methylates mainly, if not exclusively, the sequence 5'-GATC-3'; this sequence specificity is
      the same as that of the E. coli Dam enzyme. Expression of the cloned T4 dam+ gene suppresses
      almost all the phenotypic traits associated with E. coli dam mutants, with the exception of
      hypermutability. In wild-type hosts, 20- to 500-fold overproduction of the E. coli Dam
      methylase by plasmids containing the cloned E. coli dam+ gene results in a hypermutability
      phenotype (G.E. Herman and P. Modrich, J. Bacteriol. 145:644-646, 1981; M.G. Marinus, A.
      Poteete, and J.A. Arraj, Gene 28:123-125, 1984). In contrast, the same high level of T4 Dam
      methylase activity, produced by plasmids containing the cloned T4 dam+ gene, does not result
      in hypermutability. To account for these results we propose that the E. coli Dam methylase may
      be directly involved in the process of methylation-instructed mismatch repair and that the T4
      Dam methylase is unable to substitute for the E. coli enzyme.
AU  - Schlagman SL
AU  - Hattman S
AU  - Marinus MG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1986 165: 896-900.

PMID- 3072268
VI  - 73
DP  - 1988
TI  - The DNA [adenine-N6]methyltransferase (Dam) of bacteriophage T4.
PG  - 517-530
AB  - A functional bacteriophage T4 dam+ gene, which specifies a DNA [adenine-N6]
      methyltransferase (Dam), was cloned on a 1.8-kb HindIII fragment [Schlagman and
      Hattman, Gene 22 (1983) 139-156].  Sequence analysis [McDonald and Mosig, EMBO
      J. 3(1984) 2863-2871] revealed two overlapping in-phase open reading frames
      (ORFs).  The 5' proximal ORF initiates translation at an AUG and encodes a
      30-kDA polypeptide, whereas the downstream ORF initiates translation at a GUG
      and encodes a 26-kDa polypeptide.  Analysis of BAL 31 deletions in our original
      dam+ clone has verified that at least one of these overlapping ORFs, in fact,
      encodes T4 Dam.  To investigate where T4 Dam translation is initiated, we have
      constructed plasmids in which a tac or lambda pL promoter is placed 5' to
      either the longer ORF or just the shorter ORF.  Only clones which contain a
      promoter in front of the longer ORF produce active T4 Dam.  This indicates that
      the 26-kDa polypeptide alone cannot be T4 Dam.  Additional experiments suggest
      that only the 30-kDa polypeptide is required for enzyme activity and that the
      shorter ORF is not translated in plasmid-carrying cells.  We also present
      evidence that T4 Dam is capable of methylating 5'-GATC-3', GATm5C, and GAThmC
      sequences; non-canonical sites (e.g., GACC) are also methylated, but much less
      efficiently.
AU  - Schlagman SL
AU  - Miner Z
AU  - Feher Z
AU  - Hattman S
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 73: 517-530.

PMID- 22675581
VI  - 5
DP  - 2011
TI  - Complete genome sequence of Parvibaculum lavamentivorans type strain (DS-1(T)).
PG  - 298-310
AB  - Parvibaculum lavamentivorans DS-1(T) is the type species of the novel genus Parvibaculum in
      the novel family Rhodobiaceae (formerly Phyllobacteriaceae) of
      the order Rhizobiales of Alphaproteobacteria. Strain DS-1(T) is a non-pigmented,
      aerobic, heterotrophic bacterium and represents the first tier member of
      environmentally important bacterial communities that catalyze the complete
      degradation of synthetic laundry surfactants. Here we describe the features of
      this organism, together with the complete genome sequence and annotation. The
      3,914,745 bp long genome with its predicted 3,654 protein coding genes is the
      first completed genome sequence of the genus Parvibaculum, and the first genome
      sequence of a representative of the family Rhodobiaceae.
AU  - Schleheck D
AU  - Weiss M
AU  - Pitluck S
AU  - Bruce D
AU  - Land ML
AU  - Han S
AU  - Saunders E
AU  - Tapia R
AU  - Detter C
AU  - Brettin T
AU  - Han J
AU  - Woyke T
AU  - Goodwin L
AU  - Pennacchio L
AU  - Nolan M
AU  - Cook AM
AU  - Kjelleberg S
AU  - Thomas T
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 5: 298-310.

PMID- 6246341
VI  - 65
DP  - 1980
TI  - Assaying of organisms for the presence of restriction endonucleases.
PG  - 19-23
AB  - The utility of sequence-specific endonucleases recommends their use in a wide variety of
      applications.  Typically a potential user is faced with the problem of determining which of
      the large number of enzymes already known will cleave in acceptable locations.  Thus an easy,
      uniform, and rapid scheme for partial purification of these enzymes would greatly assist the
      initial screening.  A purification step fulfilling these requirements could also be of value
      as a first step when pure enzyme is required or of use in searching for new varieties of
      endonuclease.  Dextran-polyethylene glycol phase partition meets the requirements of speed and
      convenience.  Here it is shown that adjustment of the salt concentration during the phase
      partition step allows separation of most of the interfering nuclease activities in the crude
      extracts of many strains containing site-specific nucleases.
AU  - Schleif R
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1980 65: 19-23.

PMID- 22723795
VI  - 3
DP  - 2012
TI  - Metagenomic analysis of ammonia oxidizing archaea affiliated with the soil group.
PG  - 208
AB  - Ammonia-oxidising archaea (AOA) have recently been recognized as a significant component of
      many microbial communities and represent one of the most abundant prokaryotic groups in the
      biosphere. However, only few AOA have been successfully cultivated so far and information on
      the physiology and genomic content remains scarce. We have performed a metagenomic analysis to
      extend the knowledge of the AOA affiliated with group I.1b that is widespread in terrestrial
      habitats and of which no genome sequences has been described yet. A fosmid library was
      generated from samples of a radioactive thermal cave (46oC) in the Austrian Central Alps in
      which AOA had been found as a major part of the microbial community. Out of sixteen fosmids
      that possessed either an amoA or 16S rRNA gene affiliating with AOA, five were fully
      sequenced, four of which grouped with the soil/I.1b (Nitrososphaera-) lineage and one with
      marine/I.1a (Nitrosopumilus-) lineage. Phylogenetic analyses of amoBC and an associated
      conserved gene were congruent with earlier analyses based on amoA and 16S rRNA genes and
      supported the separation of the soil and marine group. Several putative genes that did not
      have homologues in  currently available marine thaumarchaeota genomes indicated that AOA of
      the soil group contain specific genes that are distinct from their marine relatives. Potential
      cis regulatory elements around conserved promoter motifs found upstream of the amo genes in
      sequenced (meta-) genomes differed in marine and soil group AOA. On one fosmid, a group of
      genes including amoA and amoB were flanked by identical transposable insertion sequences,
      indicating that amoAB could potentially be co-mobilized in the form of a composite transposon.
      This might be one of the mechanisms that caused the greater variation in gene order compared
      to genomes in the marine counterparts. Our findings highlight the genetic diversity within the
      two major and widespread lineages of thaumarchaeota.
AU  - Schleper C
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2012 3: 208.

PMID- 9748430
VI  - 180
DP  - 1998
TI  - Genomic analysis reveals chromosomal variation in natural populations of the uncultured psychrophilic archaeon Cenarchaeum symbiosum.
PG  - 5003-5009
AB  - Molecular phylogenetic surveys have recently revealed an ecologically widespread crenarchaeal
      group that inhabits cold and temperate terrestrial and marine environments.  To date these
      organisms have resisted isolation in pure culture, and so their phenotypic and genotypic
      characteristics remain largely unknown.  To characterize these archaea, and to extend
      methodological approaches for characterizing uncultivated microorganisms, we initiated genomic
      analyses of the nonthermophilic crenarchaeote Cenarchaeum symbiosum found living in
      association with a marine sponge, Axinella mexicana.  Complex DNA libraries derived from the
      host-symbiont population yielded several large clones containing the ribosomal operon from C.
      symbiosum.  Unexpectedly, cloning and sequence analysis revealed the presence of two closely
      related variants that were consistently found in the majority of host individuals analyzed.
      Homologous regions from the two variants were sequenced and compared in detail.  The variants
      exhibit >99.2% sequence identity in both small- and large-subunit rRNA genes and they contain
      homologous protein-encoding genes in identical order and orientation over a 28-kbp overlapping
      region.  Our study not only indicates the potential for characterizing uncultivated
      prokaryotes by genome sequencing but also identifies the primary complication inherent in the
      approach: the widespread genomic microheterogeneity in naturally occurring prokaryotic
      populations.
AU  - Schleper C
AU  - DeLong EF
AU  - Preston CM
AU  - Feldman RA
AU  - Wu K-Y
AU  - Swanson RV
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1998 180: 5003-5009.

PMID- 17483268
VI  - 73
DP  - 2007
TI  - Possible Origins of CTnBST, a Conjugative Transposon Found Recently in a Human Colonic Bacteroides Strain.
PG  - 4226-4233
AB  - A previous survey of Bacteroides isolates suggested that the ermB gene
      entered Bacteroides spp. recently. Previously, ermB had been found almost
      exclusively in gram-positive bacteria. In one Bacteroides strain, ermB was
      located on 100-kb conjugative transposon (CTn) CTnBST. To assess the
      possible origin of this CTn, we obtained the full DNA sequence of CTnBST
      and used this information to investigate its possible origins. Over
      one-half of CTnBST had high sequence identity to a putative CTn found in
      the genome of Bacteroides fragilis YCH46. This included the ends of the
      CTn and genes involved in integration, transfer, and excision. However,
      the region around the ermB gene contained genes that appeared to originate
      from gram-positive organisms. In particular, a 7-kb segment containing the
      ermB gene was 100% identical to an ermB region found in the genome of the
      gram-positive bacterium Arcanobacterium pyogenes. A screen of Bacteroides
      isolates whose DNA cross-hybridized with a CTnBST probe revealed that
      several isolates did not carry the 7-kb region, implying that the
      acquisition of this region may be more recent than the acquisition of the
      entire CTnBST element by Bacteroides spp. We have also identified other
      Bacteroides isolates that carry a slightly modified 7-kb region but have
      no other traces of CTnBST. Thus, it is possible that this 7-kb region
      could itself be part of a mobile element that has inserted in a
      Bacteroides CTn. Our results show that CTnBST is a hybrid element which
      has acquired a portion of its coding region from gram-positive bacteria
      but which may originally have come from Bacteroides spp. or some related
      species.
AU  - Schlesinger DJ
AU  - Shoemaker NB
AU  - Salyers AA
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2007 73: 4226-4233.

PMID- 
VI  - 
DP  - 2006
TI  - Structure, localization/regulation and interaction-partners of the Dam-Methyltransferase of Escherichia coli.
PG  - 1-161
AB  - 
AU  - Schlickenrieder M
PT  - Journal Article
TA  - Ph.D. Thesis, Germany
JT  - Ph.D. Thesis, Germany
SO  - Ph.D. Thesis, Germany 2006 : 1-161.

PMID- 8995524
VI  - 265
DP  - 1997
TI  - Differential binding of S-adenosylmethionine, S-adenosylhomocysteine and sinefungin to the adenine-specific DNA methyltransferase M.TaqI.
PG  - 56-67
AB  - The crystal structures of the binary complexes of the DNA methyltransferase M.TaqI with the
      inhibitor Sinefungin and the reaction product S-adenosyl-L-homocysteine were determined, both
      at 2.6 A resolution.  Structural comparison of these binary complexes with the complex formed
      by M.TaqI and the cofactor S-adenosyl-L-methionine suggests that the key element for molecular
      recognition of these ligands is the binding of their adenosine part in a pocket, and
      discrimination between cofactor, reaction product and inhibitor is mediated by different
      conformations of these molecules; the methionine part of S-adenosyl-L-methionine is located in
      the binding cleft, whereas the amino acid moieties of Sinefungin and S-adenosyl-l-homocysteine
      are in a different orientation and interact with the active site amino acid residues
      105NPPY108.  Dissociation constants for the complexes of M.TaqI with the three ligands were
      determined spectrofluorometrically.  Sinefungin binds more strongly than
      S-adenosyl-L-homocysteine or S-adenosyl-L-methionine, with KD=0.34 microM, 2.4 microM and 2.0
      microM, respectively.
AU  - Schluckebier G
AU  - Kozak M
AU  - Bleimling N
AU  - Weinhold E
AU  - Saenger W
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1997 265: 56-67.

PMID- 7669263
VI  - 12
DP  - 1995
TI  - Structure and function of the adenine specific DNA methyltransferase M.TaqI.
PG  - A206
AB  - Methylation of DNA bases is frequently employed by most living organisms to enhance the
      informational content of DNA.  DNA methyltransferases (MTases) transfer a methyl group from
      the cofactor S-adenosyl-methionine (AdoMet) to either adenine N6, cytosine N4 (N-MTases) or
      cytosine C5 (C-MTases) in a specific DNA sequence.  AdoMet is thereby converted to
      S-adenosyl-homocysteine (AdoHcy), and a proton is released.  In procaryotes, DNA MTases are
      usually part of restriction/modification systems (R/M system), which consist typically of an
      endonuclease (ENase) and a DNA MTase with the same recognition sequence.  The ENase cleaves
      unmethylated double stranded DNA, e.g. of invading viruses.  The cognate MTase methylates the
      host's DNA making it insusceptable against cleavage.  In eucaryotes DNA methylation plays a
      role in such different phenomena as cell differentiation, genomic imprinting and
      carcinogenesis.  We determined the first crystal structure of an N-MTase from the R/M system I
      of Thermus aquaticus (M.TaqI) in complex with its cofactor AdoMet at a resolution of 2.4
      Angstroms.  It shows alpha/beta-folding of the enzyme into two domains of roughly equal size.
      Both domains are oriented towards each other such that they form a cleft which is studded
      with positively charged amino acid residues and is sufficiently wide to accommodate B-DNA.
      The N-terminal domain binds AdoMet and contains all amino acid residues which are conserved
      throughout all DNA MTases.  As with probably all AdoMet dependent MTases the cofactor is bound
      at an alpha-beta-alpha-fold which resembles the Rossmann-fold of dinucleotide binding
      proteins.  The C-terminal domain functions in DNA binding and molecular recognition of the DNA
      substrate.  Additionally, crystals of the enzyme complexed with the reaction product AdoHcy
      and the competitive inhibitor Sinefungin were grown.  The X-Ray structures show the same
      overall folding of the polypeptide chain as with the M.TaqI-AdoMet complex.  Small, but
      distinctive differences in the binding of the small molecules provide insight into the
      molecular recognition of the cofactor.
AU  - Schluckebier G
AU  - Labahn J
AU  - Granzin J
AU  - Saenger W
PT  - Journal Article
TA  - J. Biomol. Struct. Dyn.
JT  - J. Biomol. Struct. Dyn.
SO  - J. Biomol. Struct. Dyn. 1995 12: A206.

PMID- 9628329
VI  - 379
DP  - 1998
TI  - M.TaqI: Possible catalysis via cation-pi interactions in N-specific DNA methyltransferases.
PG  - 389-400
AB  - The adenine-specific DNA methyltransferase M.TaqI transfers a methyl group from
      S-adenosylmethionine to N6 of the adenine residue in the DNA sequence 5'-TCGA-3'.  In the
      crystal structure of M.TaqI in complex with S-adenosylmethionine the enzyme is folded into two
      domains: An N-terminal catalytic domain, whose fold is conserved among S-adenosylmethionine
      dependent methyltransferases, and a DNA recognition domain which possesses a unique fold.  In
      the active site, two aromatic residues, Tyr 108 and Phe 196, are postulated to bind the
      flipped-out target DNA adenine which becomes methylated.  By lowering the energy of the
      positively charged transition state via cationic-pi interactions, these two residues probably
      hold a key role in catalysis.
AU  - Schluckebier G
AU  - Labahn J
AU  - Granzin J
AU  - Saenger W
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1998 379: 389-400.

PMID- 7607476
VI  - 157
DP  - 1995
TI  - A model for DNA binding and enzyme action derived from crystallographic studies of the TaqI N6-adenine-methyltransferase.
PG  - 131-134
AB  - The crystal structures of the DNA-N6-adenine-methyltransferase M.TaqI, in complexes with the
      cofactor S-adenosyl-L-methionine (AdoMet) and the competitive inhibitor sinefungin (Sf) show
      identical folding of the polypeptide chains into two domains.  The N-terminal domain carries
      the cofactor-binding site, the C-terminal domain is thought to be implicated in
      sequence-specific DNA binding.  Model building of the M.TaqI-DNA complex suggests that the
      adenine to be methylated swings out of the double helix as found previously in the
      cytosine-C5-MTase HhaI DNA co-crystal structure.  A torsion of the methionine moiety of the
      cofactor is required to bring the methyl group within reach of the swung-out base and allow
      methyl group transfer.
AU  - Schluckebier G
AU  - Labahn J
AU  - Granzin J
AU  - Schildkraut I
AU  - Saenger W
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 131-134.

PMID- 7897657
VI  - 247
DP  - 1995
TI  - Universal catalytic domain structure of AdoMet-dependent methyltransferases.
PG  - 16-20
AB  - The DNA methyltransferases, M.HhaI and M.TaqI, and catechol O-methyl-transferase (COMT)
      catalyze the transfer of a methyl group from the cofactor S-adenosyl-L-methionine (AdoMet) to
      carbon-5 of cytosine, to nitrogen-6 of adenine, and to a hydroxyl group of catechol,
      respectively. The catalytic domains of the bilobal proteins, M.HhaI and M.TaqI, and the entire
      single domain of COMT have similar folding with an alpha/beta structure containing a mixed
      central beta-sheet. The functional residues are located in equivalent regions at the carboxyl
      ends of the parallel beta-strands. The cofactor binding sites are almost identical and the
      essential catalytic amino acids coincide. The comparable protein folding and the existence of
      equivalent amino acids in similar secondary and tertiary positions indicate that many (if not
      all) AdoMet-dependent methyltransferases have a common catalytic domain structure. This
      permits tertiary structure prediction of other DNA, RNA, protein, and small-molecule
      AdoMet-dependent methyltransferases from their amino acid sequences.
AU  - Schluckebier G
AU  - O'Gara M
AU  - Saenger W
AU  - Cheng X
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1995 247: 16-20.

PMID- 16122561
VI  - 54
DP  - 2005
TI  - Plasmid pB8 is closely related to the prototype IncP-1beta plasmid R751 but transfers poorly to Escherichia coli and carries a new transposon encoding a small multidrug resistance efflux protein.
PG  - 135-148
AB  - The IncP-1beta plasmid pB8, which confers resistance to amoxicillin,
      spectinomycin, streptomycin, and sulfonamides, was previously isolated
      from a sewage treatment plant. It was found to possess abnormal
      conjugative transfer properties, i.e., transfer to Escherichia coli by
      conjugation or electroporation could not be detected. We showed in this
      study that plasmid pB8 is transferable to E. coli by conjugation, but only
      at low frequencies and under specific experimental conditions, a
      phenomenon that is very unusual for IncP-1 plasmids. Determination of the
      complete 57,198bp pB8 nucleotide sequence revealed that the backbone of
      the plasmid consists of a complete set of IncP-1beta-specific genes for
      replication initiation, conjugative plasmid transfer, stable inheritance,
      and plasmid control with an organisation identical to that of the
      prototype IncP-1beta plasmid R751. All of the minor differences in the pB8
      backbone sequence compared to that of R751 were also found in other
      IncP-1beta plasmids known to transfer to and replicate in E. coli.
      Plasmids pB8 and R751 can be distinguished with respect to their accessory
      genetic elements. First, the pB8 region downstream of the replication
      initiation gene trfA contains two transposable elements one of which is
      similar to Tn5501. The latter transposon encodes a putative
      post-segregational-killing system and the small multidrug resistance (SMR)
      protein QacF, mediating quaternary ammonium compound resistance. The
      accessory genes in this region are not responsible for the poor plasmid
      transfer to E. coli since a pB8 deletion derivative devoid of all genes in
      that region showed the same conjugative transfer properties as pB8. A
      Tn5090/Tn402 derivative carrying a class 1 integron is located between the
      conjugative transfer modules. The Tn5090/Tn402 integration-sites are
      exactly identical on pB8 and R751 but in contrast to R751 the pB8 element
      carries the resistance gene cassettes oxa-2 for amoxicillin resistance and
      aadA4 for streptomycin/spectinomycin resistance, the integron-specific
      conserved segment consisting of the genes qacEDelta1, sul1, and orf5, and
      a truncated tni transposition module (tniAB). Although future work will
      have to determine the molecular basis for the poor transfer of pB8 to E.
      coli, our findings demonstrate that the host-range of typical IncP-1
      plasmids may be less broad than expected.
AU  - Schluter A
AU  - Heuer H
AU  - Szczepanowski R
AU  - Poler SM
AU  - Schneiker S
AU  - Puhler A
AU  - Top EM
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 2005 54: 135-148.

PMID- 19376903
VI  - 75
DP  - 2009
TI  - Rhizobium sp. NGR234 possesses a remarkable number of secretion systems.
PG  - 4035-4045
AB  - Rhizobium sp. NGR234 is a unique alpha-proteobacterium (Order -
      Rhizobiales) that forms nitrogen-fixing nodules with more legumes than any
      other micro-symbiont. Here we report that the 3.93 Mbp chromosome
      (cNGR234) encodes most functions required for cellular growth. Few
      essential functions are encoded on the 2.43 Mbp mega-plasmid (pNGR234b)
      and none are present on the second 0.54 Mbp symbiotic plasmid (pNGR234a).
      Amongst many striking features, the 6.9 Mbp genome encodes more different
      secretion systems than any other known rhizobia and probably most known
      bacteria. Altogether 132 genes and proteins are linked to secretory
      processes. Secretion systems identified include general and export
      pathways (GSP
AU  - Schmeisser C et al
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2009 75: 4035-4045.

PMID- 2355390
VI  - 32
DP  - 1990
TI  - Bacteriophages in Helicobacter (Campylobacter) pylori.
PG  - 101-104
AB  - Bacteriophages in different stages of maturation were found in thin sections of a clinical
      isolate of Helicobacter (Campylobacter) pylori. Mature phage heads measured 70 x 60 nm and the
      tail at least 120 nm. Lysogeny was maintained during subculture on blood agar for more than 3
      months after isolation from a gastric biopsy.
AU  - Schmid EN
AU  - von Recklinghausen G
AU  - Ansorg R
PT  - Journal Article
TA  - J. Med. Microbiol.
JT  - J. Med. Microbiol.
SO  - J. Med. Microbiol. 1990 32: 101-104.

PMID- 27789631
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the Xanthan Producer Xanthomonas campestris LMG 8031.
PG  - e01069-16
AB  - Here, we report the draft genome sequence of Xanthomonas campestris LMG 8031, for which nearly
      no genetic information is available, despite its good
      xanthan-producing properties. We performed an Illumina-based sequencing approach
      of LMG 8031. The genome revealed a 5.0-Mb chromosome having 4,434 coding
      sequences and a G+C content of 65%.
AU  - Schmid J
AU  - Huptas C
AU  - Wenning M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01069-16.

PMID- 24970826
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Kozakia baliensis SR-745, the First Sequenced Kozakia Strain from the Family Acetobacteraceae.
PG  - e00594-14
AB  - Kozakia baliensis belongs to the family Acetobacteraceae and was described for the first time
      in 2002. These acetic acid bacteria are able to produce acetic
      acid from various carbon sources and 2- and 5-keto-d-gluconate from glucose. The
      novel K. baliensis strain SR-745 was isolated from a pineapple fruit bought in a
      German supermarket. The strain produces large amounts of organic acids when grown
      on glucose-containing medium and accepts also glycerol, fructose, mannitol, and
      sucrose as a C source. When grown under light and high-oxygen conditions in
      submerged culture, the production of a pink pigment is observed after 72 h.
AU  - Schmid J
AU  - Koenig S
AU  - Pick A
AU  - Steffler F
AU  - Yoshida S
AU  - Miyamoto K
AU  - Sieber V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00594-14.

PMID- 6324124
VI  - 12
DP  - 1984
TI  - Three new restriction endonucleases MaeI, MaeII and MaeIII from Methanococcus aeolicus.
PG  - 2619-2628
AB  - Three type II restriction endonucleases, MaeI, MaeII and MaeIII, with novel
      site specificities have been isolated and purified form the archaebacterium
      Methanococcus aeolicus PL-15/H.  The recognition sequences of these enzymes are
      C^T A G   (MaeI)  A^C G T   (MaeII) ^G T N A C  (MaeIII)  with the sites of
      cleavage as indicated by the arrows.  The sequences were confirmed by
      restriction and computer analyses on sequenced DNA's of plasmid pBR322,
      bacteriophage lambda and PhiX174 and virus SV40.
AU  - Schmid K
AU  - Thomm M
AU  - Laminet A
AU  - Laue FG
AU  - Kessler C
AU  - Stetter KO
AU  - Schmitt R
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1984 12: 2619-2628.

PMID- 232591
VI  - 19
DP  - 1979
TI  - Studies on the substrate specificity of the DNA methylase activity from Escherichia coli K-12.
PG  - 489-495
AB  - A partially purified extract of DNA methylases from E. coli K-12 containing DNA-adenine as
      well as DNA-cytosine methylase activities has been examined with respect to different DNA
      species as substrates.  The results show that the natural content of 6-MAP in the applied DNA
      represses the DNA-adenine methylase activity.  On the other hand, 5-MC, already present in the
      substrate does not influence the activity of the DNA-cytosine methylase.  DNA from Micrococcus
      radiodurans, which is completely free of methylated bases served as a comparison.  Since
      netropsin preferentially binds to AT-rich regions of DNA, the influence of this oligopeptide
      antibiotic on the methylation of DNA was investigated.  As expected the antibiotic
      predominantly inhibits adenine methylation of DNA.  The degree of inhibition depends on the
      molar ratio of netropsin to DNA phosphate.
AU  - Schmidt A
AU  - Reinert H
AU  - Venner H
AU  - Bieber J
PT  - Journal Article
TA  - Z. Allg. Mikrobiol.
JT  - Z. Allg. Mikrobiol.
SO  - Z. Allg. Mikrobiol. 1979 19: 489-495.

PMID- 17977734
VI  - 16
DP  - 2008
TI  - Sequence-specific methyltransferase-induced labelling (SMILing) of plasmid DNA for studying cell transfection.
PG  - 40-48
AB  - Plasmid DNA (pUC19 and pBR322) was sequence-specifically, covalently labelled with Cy3
      fluorophores using a newly synthesised
      N-adenosylaziridine cofactor and the DNA methyltransferase M.TaqI. The
      fluorescently labelled plasmids were used for transfection of mammalian
      cells and their intracellular distribution was visualised by
      epifluorescence and confocal fluorescence microscopy. Although these
      prokaryotic plasmids do not contain nuclear import sequences,
      translocation into the nuclei was observed.
AU  - Schmidt FH-G
AU  - Hueben M
AU  - Gider B
AU  - Renault F
AU  - Teulade-Fichou M-P
AU  - Weinhold E
PT  - Journal Article
TA  - Bioorg. Med. Chem.
JT  - Bioorg. Med. Chem.
SO  - Bioorg. Med. Chem. 2008 16: 40-48.

PMID- 28572305
VI  - 5
DP  - 2017
TI  - Genome Sequence of Escherichia coli E28, a Multidrug-Resistant Strain Isolated from a Chicken Carcass, and Its Spontaneously Inducible Prophage.
PG  - e00348-17
AB  - In this study, we sequenced the complete genome of the multidrug-resistant Escherichia coli
      strain E28, which was used as an indicator strain for phage
      therapy in vivo We used a combination of single-molecule real-time and Illumina
      sequencing technology to reveal the presence of a spontaneously inducible
      prophage.
AU  - Schmidt I
AU  - Riedel T
AU  - Schober I
AU  - Bunk B
AU  - Sproer C
AU  - Bierbrodt A
AU  - Lehnherr H
AU  - Wittmann J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00348-17.

PMID- Not included in PubMed...
VI  - 372
DP  - 1991
TI  - Enzyme - substrate investigation of dcm methylase.
PG  - 748
AB  - To investigate the enzyme-substrate complex of the dcm methylase we synthesized
      5-fluoro-2'-deoxycytidine as a substrate analogue. The synthesis was successful by selective
      amination of 5-fluoro-2'-deoxyuridine. 5-fluoro-2'-deoxycytidine has not been incorporated
      into oligonucleotides chemically. The direct usage of 5-fluoro-2'-deoxycytidine for
      oligonucleotide synthesis is made difficult due to the increased acid and alkaline sensitivity
      of this monomer. As an alternative we investigated the incorporation of
      4-methylmercapto-5-fluoro-2'-deoxyuridine and the subsequently amination of the 4' position.
      In principal it is possible to incorporate the 4' methylmercapto derivative into
      oligonucleotides using the phosporamidite method. However, during the oxidation step we
      observed a partial conversion into 5-fluoro-2'deoxyuridine. Under the assumption that only
      the 5-fluoro-2'-deoxycytidine-containing oligonucleotide will be recognized as a substrate we
      used the oligonucleotide mixture for our first experiments.
AU  - Schmidt S
AU  - Cech D
AU  - Fritz H-J
PT  - Journal Article
TA  - Biol. Chem. Hoppe Seyler
JT  - Biol. Chem. Hoppe Seyler
SO  - Biol. Chem. Hoppe Seyler 1991 372: 748.

PMID- 25792065
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of the Persistent Listeria monocytogenes Strain R479a.
PG  - e00150-15
AB  - The complete genome sequence of the persistent Listeria monocytogenes strain R479a isolated
      from smoked salmon in Denmark and belonging to lineage II, serovar
      1/2a, and multilocus sequence type 8 (ST8) is presented here.
AU  - Schmitz-Esser S
AU  - Gram L
AU  - Wagner M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00150-15.

PMID- 9628328
VI  - 379
DP  - 1998
TI  - Involvement of DNA methylation in human carcinogenesis.
PG  - 377-388
AB  - It is now generally accepted that the presence of 5-methylcytosine in human DNA has both a
      genetic and an epigenetic effect on cellular development, differentiation and transformation.
      First, 5mC is more unstable than its unmethylated counterpart cytosine.  Hydrolytic
      deamination of 5mC leads to a G/T mismatch and subsequently, if unrepaired, to a C-T
      transition mutation.  Sites of DNA methylation are mutational hotspots in many human tumors.
      Second, DNA methylation of promoter regions is often correlated with the down regulation of
      the corresponding gene.  Both of these effects have fundamental consequences for basic
      functions of the cell like cellular differentiation, the development of cancer and possibly
      other diseases, and on the evolutionary process.  Recent hypotheses also propose a role for
      methylation in the process of aging.  In this review we will describe recent findings and
      hypotheses about the function of 5mC in DNA with the focus on its involvement in human
      carcinogenesis.
AU  - Schmutte C
AU  - Jones PA
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1998 379: 377-388.

PMID- 20075913
VI  - 463
DP  - 2010
TI  - Genome sequence of the palaeopolyploid soybean.
PG  - 178-183
AB  - Soybean (Glycine max) is one of the most important crop plants for seed protein and oil
      content, and for its capacity to fix atmospheric nitrogen through
      symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by
      a whole-genome shotgun approach and integrated it with physical and high-density
      genetic maps to create a chromosome-scale draft sequence assembly. We predict
      46,430 protein-coding genes, 70% more than Arabidopsis and similar to the poplar
      genome which, like soybean, is an ancient polyploid (palaeopolyploid). About 78%
      of the predicted genes occur in chromosome ends, which comprise less than
      one-half of the genome but account for nearly all of the genetic recombination.
      Genome duplications occurred at approximately 59 and 13 million years ago,
      resulting in a highly duplicated genome with nearly 75% of the genes present in
      multiple copies. The two duplication events were followed by gene diversification
      and loss, and numerous chromosome rearrangements. An accurate soybean genome
      sequence will facilitate the identification of the genetic basis of many soybean
      traits, and accelerate the creation of improved soybean varieties.
AU  - Schmutz J et al
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2010 463: 178-183.

PMID- 4891753
VI  - 3
DP  - 1969
TI  - Mutant of PhiX174 accessible to host-controlled modification.
PG  - 541-542
AB  - Host-controlled modification has been shown to occur with several bacteriophage
      strains carrying their genetic information on a single-stranded
      deoxyribonucleic acid (DNA) molecule.  All these bacteriophage strains (fd, fl,
      M13, F12) are related inasmuch as their particles are rod shaped, contain
      single-stranded DNA molecules of comparable size, and infect only male
      bacteria.  Other single-stranded DNA phages unrelated to this group, such as
      PhiX174 and S13, are unable to infect cells of Escherichia coli K-12 and B, so
      that their sensitivity to K- and B- host specificity cannot be investigated
      directly.  However, using spheroplasts of E. coli and infecting them with
      PhiX174 DNA molecules, Benzinger showed that PhiX174 DNA is not restricted by
      B- or Pl host specificity.  Lack of restriction of PhiX174 and the related
      phage S13 by P1-host specificity has also been shown by Eskridge, Weinfeld, and
      Paigen by using the host pair E. coli C and C (P1).  In the experiments
      presented here, hybrids were selected from crosses with E. coli C and B (rB+
      mB+), and C and K-12 (rK+ mK+), sensitive to infection by PhiX174 and carrying
      the genes responsible for B- and K-host specificity, respectively.  With these
      hybrids, E. coli BC and KC, respectively, it is shown that wild-type PhiX174 is
      not susceptible to modification and restriction controlled by the genes
      responsible for lambda DNA modification and restriction.  The findings
      concerning B-host specificity thus confirm the results of Benzinger.  However,
      a PhiX174 mutant was isolated which is accessible to restriction and
      modification in the hybrid E. coli BC.
AU  - Schnegg B
AU  - Hofschneider PH
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1969 3: 541-542.

PMID- 2180941
VI  - 265
DP  - 1990
TI  - Primary structure of a DNA (N6-Adenine)-methyltransferase from Escherichia coli virus T1.
PG  - 6086-6091
AB  - Escherichia coli virus T1 encodes a DNA (N6-adenine)-methyltransferase (M.T1)
      with the same sequence specificity as the E. coli DNA
      (N6-adenine)-methyltransferase (M.Eco dam).  This enzyme was purified to
      homogeneity and a partial amino acid sequence determined.  Oligonucleotides
      were constructed and used not only as probes to map the gene on the T1 genome,
      but also as primers in sequencing reactions to establish the nucleotide
      sequence of the M.T1 locus by primer extension.  These data represent the first
      analysis of the genomic organization of bacterial virus T1 on a molecular
      level.  Significant homology to E. coli consensus transcription and
      translation-initiation signals suggest that the gene for M.T1 is most probably
      under control of its own promoter.  It may be transcribed as a polycistronic
      mRNA, together with a downstream open reading frame which codes for a
      polypeptide containing 83 amino acids (HP 83).  Both the deduced primary and
      the secondary structure of the M.T1 were compared to those of other known DNA
      methyltransferases, especially those recognizing the sequence, GATC; there is
      little similarity of the T1 enzyme to the other members of this family.
AU  - Schneider-Scherzer E
AU  - Auer B
AU  - de Groot EJ
AU  - Schweiger M
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1990 265: 6086-6091.

PMID- 3228491
VI  - 369
DP  - 1988
TI  - Identification, purification, characterization and sequencing of DNA-methyltransferase from E. coli virus T1.
PG  - 910
AB  - Immediately after infection E. coli virus T1 induces a DNA-methyltransferase,
      which methylates the GATC-sites at adenine in vivo and in vitro.  The activity
      is associated with a protein of MW 31,000 and can be visualized by activity
      analysis in polyacrylamide gels.  Assay conditions were developed which permit
      selective measurement of the T1 activity in the presence of E. coli
      DNA-methyltransferases.
AU  - Schneider-Scherzer E
AU  - Auer B
AU  - Schweiger M
PT  - Journal Article
TA  - Biol. Chem. Hoppe Seyler
JT  - Biol. Chem. Hoppe Seyler
SO  - Biol. Chem. Hoppe Seyler 1988 369: 910.

PMID- 17965706
VI  - 25
DP  - 2007
TI  - Complete genome sequence of the myxobacterium Sorangium cellulosum.
PG  - 1281-1289
AB  - The genus Sorangium synthesizes approximately half of the secondary metabolites isolated from
      myxobacteria, including the anti-cancer
      metabolite epothilone. We report the complete genome sequence of the model
      Sorangium strain S. cellulosum So ce56, which produces several natural
      products and has morphological and physiological properties typical of the
      genus. The circular genome, comprising 13,033,779 base pairs, is the
      largest bacterial genome sequenced to date. No global synteny with the
      genome of Myxococcus xanthus is apparent, revealing an unanticipated level
      of divergence between these myxobacteria. A large percentage of the genome
      is devoted to regulation, particularly post-translational phosphorylation,
      which probably supports the strain's complex, social lifestyle. This
      regulatory network includes the highest number of eukaryotic protein
      kinase-like kinases discovered in any organism. Seventeen secondary
      metabolite loci are encoded in the genome, as well as many enzymes with
      potential utility in industry.
AU  - Schneiker S et al
PT  - Journal Article
TA  - Nat. Biotechnol.
JT  - Nat. Biotechnol.
SO  - Nat. Biotechnol. 2007 25: 1281-1289.

PMID- 21396969
VI  - 155
DP  - 2011
TI  - The complete genome sequence of the dominant Sinorhizobium meliloti field isolate SM11 extends the S. meliloti pan-genome.
PG  - 20-33
AB  - Isolates of the symbiotic nitrogen-fixing species Sinorhizobium meliloti usually contain a
      chromosome and two large megaplasmids encoding functions that are absolutely required for the
      specific interaction of the microsymbiont with corresponding host plants leading to an
      effective symbiosis. The complete genome sequence, including the megaplasmids pSmeSM11c
      (related to pSymA) and pSmeSM11d (related to pSymB), was established for the dominant,
      indigenous S. meliloti strain SM11 that had been isolated during a long-term field release
      experiment with genetically modified S. meliloti strains. The chromosome, the largest replicon
      of S. meliloti SM11, is 3,908,022bp in size and codes for 3785 predicted protein coding
      sequences. The size of megaplasmid pSmeSM11c is 1,633,319bp and it contains 1760 predicted
      protein coding sequences whereas megaplasmid pSmeSM11d is 1,632,395bp in size and comprises
      1548 predicted coding sequences. The gene content of the SM11 chromosome is quite similar to
      that of the reference strain S. meliloti Rm1021. Comparison of pSmeSM11c to pSymA of the
      reference strain revealed that many gene regions of these replicons are variable, supporting
      the assessment that pSymA is a major hot-spot for intra-specific differentiation. Plasmids
      pSymA and pSmeSM11c both encode unique genes. Large gene regions of pSmeSM11c are closely
      related to corresponding parts of Sinorhizobium medicae WSM419 plasmids. Moreover, pSmeSM11c
      encodes further novel gene regions, e.g. additional plasmid survival genes (partition,
      mobilisation and conjugative transfer genes), acdS encoding 1-aminocyclopropane-1-carboxylate
      deaminase involved in modulation of the phytohormone ethylene level and genes having predicted
      functions in degradative capabilities, stress response, amino acid metabolism and associated
      pathways. In contrast to Rm1021 pSymA and pSmeSM11c, megaplasmid pSymB of strain Rm1021 and
      pSmeSM11d are highly conserved showing extensive synteny with only few rearrangements. Most
      remarkably, pSmeSM11b contains a new gene cluster predicted to be involved in polysaccharide
      biosynthesis. Compilation of the S. meliloti SM11 genome sequence contributes to an extension
      of the S. meliloti pan-genome.
AU  - Schneiker-Bekel S
AU  - Wibberg D
AU  - Bekel T
AU  - Blom J
AU  - Linke B
AU  - Neuweger H
AU  - Stiens M
AU  - Vorholter FJ
AU  - Weidner S
AU  - Goesmann A
AU  - Puhler A
AU  - Schluter A
PT  - Journal Article
TA  - J. Biotechnol.
JT  - J. Biotechnol.
SO  - J. Biotechnol. 2011 155: 20-33.

PMID- 2831507
VI  - 16
DP  - 1988
TI  - Cleavage by EcoO109I and DraII is inhibited by overlapping dcm methylation.
PG  - 1623
AB  - We have recently determined the nucleotide sequence of the bgl operon of E. coli. Sequence
      analysis revealed the presence of two recognition sites for restriction endonuclease EcoO109I
      and its isoschizomer DraII. Both enzymes recognize and cut the sequence RG'GNCCY. However,
      digestion of plasmid pFDX733 containing the entire operon with either enzyme resulted in only
      linearization (Fig. 1, lanes 1 and 3). We noted that the resistant site overlaps with a dcm
      methylation site (CmCT/AGG). The sequence at this site is GGGGCCTGG. When we isolated plasmid
      pFDX733 from a Dcm- host, the DNA was efficiently cut with both enzymes at both positions
      (Fig. 1, lanes 2 and 4). We conclude that enzymes EcoO109I and DraII are sensitive to
      overlapping dcm methylation at their recognition sites.
AU  - Schnetz K
AU  - Rak B
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1988 16: 1623.

PMID- 28546480
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Streptomyces phaeoluteigriseus DSM41896.
PG  - e00371-17
AB  - The draft genome for the type strain Streptomyces phaeoluteigriseus DSM41896 (ISP 5182) is
      reported. It was classified as a member of the Streptomyces
      violaceusniger clade; however, a polyphasic study showed it was a separate
      species based on its distinct spore morphology and 16S rRNA sequence. The genome
      sequence confirms it as a separate species.
AU  - Schniete JK
AU  - Salih TS
AU  - Algora-Gallardo L
AU  - Santos T
AU  - Filgueira-Martinez S
AU  - Herron PR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00371-17.

PMID- 21296965
VI  - 193
DP  - 2011
TI  - Whole-Genome Sequence of the Transformable Neisseria meningitidis Serogroup A Strain WUE2594.
PG  - 2064-2065
AB  - Serogroup A meningococci are a leading cause of bacterial meningitis in children and young
      adults worldwide. However, the genetic basis of
      serogroup A strains' virulence and their epidemiological properties remain
      poorly understood. Therefore, we sequenced the complete genome of the
      transformable Neisseria meningitidis serogroup A strain WUE2594.
AU  - Schoen C
AU  - Weber-Lehmann J
AU  - Blom J
AU  - Joseph B
AU  - Goesmann A
AU  - Strittmatter A
AU  - Frosch M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 2064-2065.

PMID- Not carried by PubMed...
VI  - 42
DP  - 1993
TI  - A Practical Guide to DNA Methylation.
PG  - 22-27
AB  - Most problems attributable to DNA methylation fall into one of two categories: inability to
      cut DNA with restriction enzymes; inability to obtain transformants. This article contains
      background information that explains why these problems ocur in cloning, followed by
      troubleshooting tips that will help you determine if methylation is the problem and if so, how
      to solve it. A final Section describes common eukaryotic methylation patterns and how to use
      this information to your advantage. DNA methylation refers to the covalent modification of DNA
      by transfer of a methyl group from S-adenosylmethionine to one of a few possible sites on
      cyosine or adenine. The molecular biologist will primarily encounter m5C methylation of
      cytosine and m6N methylation of adenine (Figure 1). The guidelines in this article, however,
      also apply to other types of methylation such as m4C methylation of cytosine and m4C
      hydroxymethylation of cytosine (1).
AU  - Schoenfeld T
PT  - Journal Article
TA  - Promega Notes
JT  - Promega Notes
SO  - Promega Notes 1993 42: 22-27.

PMID- 1727392
VI  - 6
DP  - 1992
TI  - Bca77I: A restriction enzyme from Bacillus caldolyticus cleaving the novel hexanucleotide (A/T)^CCGG(A/T) .
PG  - A77
AB  - I describe a restriction enzyme, Bca77I, derived from the intermediate
      thermophile, Bacillus caldolyticus (Promega strain 77).  The cognate sequence
      for this restriction enzyme is the degenerate hexanucleotide, (A/T)CCGG(A/T)
      and the cleavage site is 5' of the external cytosine.  The methylation
      sensitivity of the endonuclease was examined.  Methylation of the external
      cytosine (m5C) completely blocks restriction by Bca77I; methylation of the
      internal cytosine (5mC) only decreases marginally the rate of cleavage.  It is
      expected that Bca77I will be a valuable tool for the molecular biologist.
AU  - Schoenfeld T
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1992 6: A77.

PMID- Not included in PubMed...
VI  - 61
DP  - 1992
TI  - Bca77I: A restriction enzyme from Bacillus caldolyticus cleaving the novel hexanucleotide (A/T)^CCGG(A/T) .
PG  - A77
AB  - I describe a restriction enzyme, Bca77I, derived from the intermediate
      thermophile, Bacillus caldolyticus (Promega strain 77).  The cognate sequence
      for this restriction enzyme is the degenerate hexanucleotide, (A/T)CCGG(A/T)
      and the cleavage site is 5' of the external cytosine.  The methylation
      sensitivity of the endonuclease was examined.  Methylation of the external
      cytosine (5mC) completely blocks restriction by Bca77I; methylation of the
      internal cytosine (5mC) only decreases marginally the rate of cleavage.  It is
      expected that Bca77I will be a valuable tool for the molecular biologist.
AU  - Schoenfeld T
PT  - Journal Article
TA  - Biophys. J.
JT  - Biophys. J.
SO  - Biophys. J. 1992 61: A77.

PMID- 1547950
VI  - 111
DP  - 1992
TI  - Bst71I: an isoschizomer of the type-IIS restriction enzyme, BbvI, recognizing the GCAGC(8/12) site.
PG  - 141-142
AB  - A new type-IIS restriction enzyme, Bst71I, with the specificity 5'-GCAGC(N)8
      CGTCG(N)12
      was isolated from Bacillus stearothermophilus (Promega No. 71).  This enzyme
      is an isoschizomer of BbvI with somewhat improved characteristics for use by
      molecular biologists.
AU  - Schoenfeld T
AU  - Fiandt M
AU  - Schink M
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1992 111: 141-142.

PMID- 1644318
VI  - 117
DP  - 1992
TI  - Bca771: a new type-II restriction endonuclease from Bacillus caldolyticus cutting at the (A/T)^CCGG(A/T) site.
PG  - 99-101
AB  - We describe a new restriction enzyme recognizing a degenerate hexanucleotide sequence and
      cleaving the 5'-W^CCGGW site (W = A or T). This enzyme cuts with high efficiency all four
      permutations of this sequence; ACCGGA (TCCGGT on the opposite stand), ACCGGT and TCCGGA.
      Methylation of the external cytosine completely blocks restriction while methylation of the
      internal cytosine only decreases the rate of restriction activity.
AU  - Schoenfeld T
AU  - King KB
AU  - Schink M
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1992 117: 99-101.

PMID- 2787022
VI  - 17
DP  - 1989
TI  - Purification and characterization of an isoschizomer of AsuII from Clostridium sporogenes.
PG  - 4417
AB  - A new type II restriction enzyme, Csp45I, was isolated from Clostridium
      sporogenes and characterized.  Digestion of a standard substrate and sequencing
      confirmed that both the recognition sequence and the cut site, TT/CGAA, were
      the same as those of AsuII and BstBI.
AU  - Schoenfeld T
AU  - Mead DA
AU  - Fiandt M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 4417.

PMID- 23608703
VI  - 30
DP  - 2013
TI  - Lateral gene transfer of Family A DNA polymerases between thermophilic viruses, Aquificae, and Apicomplexa.
PG  - 1653-1664
AB  - Bioinformatics and functional screens identified a group of Family A-type DNA
      Polymerase (polA) genes encoded by viruses inhabiting circumneutral and alkaline
      hot springs in Yellowstone National Park and the US Great Basin. The proteins
      encoded by these viral polA genes (PolAs) shared no significant sequence
      similarity with any known viral proteins but were remarkably similar to PolAs
      encoded by two of three families of the bacterial phylum Aquificae and by several
      apicoplast-targeted PolA-like proteins found in the eukaryotic phylum
      Apicomplexa, which includes the obligate parasites Plasmodium, Babesia, and
      Toxoplasma. The viral gene products share signature elements previously
      associated only with Aquificae and Apicomplexa PolA-like proteins and were
      similar to proteins encoded by prophage elements of a variety of otherwise
      unrelated Bacteria, each of which additionally encoded a prototypical bacterial
      PolA. Unique among known viral DNA polymerases, the viral PolA proteins of this
      study share with the Apicomplexa proteins large amino-terminal domains with
      putative helicase/primase elements but low primary sequence similarity. The
      genomic context and distribution, phylogeny, and biochemistry of these PolA
      proteins suggest that thermophilic viruses transferred polA genes to the
      Apicomplexa, likely through secondary endosymbiosis of a virus-infected
      proto-apicoplast, and to the common ancestor of two of three Aquificae families,
      where they displaced the orthologous cellular polA gene. On the basis of
      biochemical activity, gene structure, and sequence similarity, we speculate that
      the xenologous viral-type polA genes may have functions associated with
      diversity-generating recombination in both Bacteria and Apicomplexa.
AU  - Schoenfeld TW
AU  - Murugapiran S
AU  - Dodsworth JA
AU  - Floyd S
AU  - Lodes M
AU  - Mead DA
AU  - Hedlund BP
PT  - Journal Article
TA  - Mol. Biol. Evol.
JT  - Mol. Biol. Evol.
SO  - Mol. Biol. Evol. 2013 30: 1653-1664.

PMID- 
VI  - 28
DP  - 2000
TI  - Identification of the catalytic centres of the homing endonuclease PI-SceI by site-directed mutagenesis.
PG  - A332
AB  - The homing endonuclease PI-SceI from Saccharomyces cerevisiae is composed of two domains:
      Domain I is responsible for protein splicing and specific DNA binding and domain II harbours
      the endonuclease function which mediates the mobility of the gene of PI-SceI by introducing a
      double strand break into an allele that lacks it.  Cellular repair leads to the integration of
      the sequence into this allele.  It was unknown whether the DNA cleavage is due to one
      catalytic centre cleaving both DNA strands or two active sites each cleaving one strand.  To
      solve this problem we exchanged amino acids in the vicinity of D218 and D326 of the
      characteristic LAGLIDADG motifs which were already shown to be essential.  The amino acids
      chosen for mutagenesis were selected based on a structural comparison with the homodimeric
      enzyme I-CreI.  Results of experiments with substrates with a nick in the cleavage position
      are taken as evidence for the existence of two catalytic sites: The variant D229N cleaves a
      substrate with a nick in the top strand whereas a substrate with a nick in the bottom strand
      is hardly cleaved.  T341N displays an opposite behavior, i.e. prefers to cleave a DNA
      substrate nicked in the bottom strand.  Taking together all our results, including
      characterization of PI-SceI with respect to DNA binding and cleavage, leads to this model of
      DNA strand cleavage: PI-SceI contains two catalytic centres.  In catalytic centre I D218 and
      D229 coordinate the metal ion and induce the cleavage of the top strand.  This is the rate
      limiting step of cleavage.  The cleavage of the bottom strand is done by active site II
      containing D326 as metal ion binding site.  Intriguingly, the mutants D229N and T341N which
      are almost inactive in cleaving double stranded DNA can do so when crosslinked to the
      substrate.  This could be interpreted to mean that crosslinking fixes the enzyme-substrate
      complex in a conformation resembling the transition state, similarly as observed with EcoRV.
AU  - Schoettler S
AU  - Christ F
AU  - Pingoud V
AU  - Wende W
AU  - Pingoud A
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 2000 28: A332.

PMID- 11123916
VI  - 39
DP  - 2000
TI  - Identification of Asp218 and Asp326 as the principal Mg2+ binding ligands of the homing endonuclease PI-SceI.
PG  - 15895-15900
AB  - The monomeric homing endonuclease PI-SceI harbors two catalytic centers which cooperate in the
      cleavage of the two strands of its extended
      recognition sequence. Structural and biochemical data suggest that
      catalytic center I contains Asp218, Asp229, and Lys403, while catalytic
      center II contains Asp326, Thr341, and Lys301. The analogy with I-CreI,
      for which the cocrystal structure with the DNA substrate has been
      determined, suggests that Asp218 and Asp229 in catalytic center I and
      Asp326 and Thr341 in catalytic center II serve as ligands for Mg2+, the
      essential divalent metal ion cofactor which can be replaced by Mn2+ in
      vitro. We have carried out a mutational analysis of these presumptive
      Mg2+ ligands. The variants carrying an alanine or asparagine
      substitution bind DNA, but (with the exception of the D229N variant)
      are inactive in DNA cleavage in the presence of Mg2+, demonstrating
      that these residues are important for cleavage. Our finding that the
      PI-SceI variants carrying single cysteine substitutions at these
      positions are inactive in the presence of the oxophilic Mg2+ but active
      in the presence of the thiophilic Mn2+ suggests that the amino acid
      residues at these positions are involved in cofactor binding. From the
      fact that in the presence of Mn2+ the D218C and D326C variants are even
      more active than the wild-type enzyme, it is concluded that Asp218 and
      Asp326 are the principal Mg2+ ligands of PI-SceI. On the basis of these
      findings and the available structural information, a model for the
      composition of the two Mg2+ binding sites of PI-SceI is proposed.
AU  - Schoettler S
AU  - Wende W
AU  - Pingoud V
AU  - Pingoud A
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2000 39: 15895-15900.

PMID- 27602182
VI  - 11
DP  - 2016
TI  - Near complete genome sequence of the animal feed probiotic, Bacillus amyloliquefaciens H57.
PG  - 60
AB  - Bacillus amyloliquefaciens H57 is a bacterium isolated from lucerne for its ability to prevent
      feed spoilage. Further interest developed when ruminants fed
      with H57-inoculated hay showed increased weight gain and nitrogen retention
      relative to controls, suggesting a probiotic effect. The near complete genome of
      H57 is ~3.96 Mb comprising 16 contigs. Within the genome there are 3,836 protein
      coding genes, an estimated sixteen rRNA genes and 69 tRNA genes. H57 has the
      potential to synthesise four different lipopeptides and four polyketide
      compounds, which are known antimicrobials. This antimicrobial capacity may
      facilitate the observed probiotic effect.
AU  - Schofield BJ
AU  - Skarshewski A
AU  - Lachner N
AU  - Ouwerkerk D
AU  - Klieve AV
AU  - Dart P
AU  - Hugenholtz P
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 60.

PMID- 16321955
VI  - 187
DP  - 2005
TI  - The genome of bacteriophage K1F, a T7-like phage that has acquired the ability to replicate on K1 strains of Escherichia coli.
PG  - 8499-8503
AB  - Bacteriophage K1F specifically infects Escherichia coli strains that
      produce the K1 polysaccharide capsule. Like several other K1
      capsule-specific phages, K1F encodes an endo-neuraminidase (endosialidase)
      that is part of the tail structure which allows the phage to recognize and
      degrade the polysaccharide capsule. The complete nucleotide sequence of
      the K1F genome reveals that it is closely related to bacteriophage T7 in
      both genome organization and sequence similarity. The most striking
      difference between the two phages is that K1F encodes the endosialidase in
      the analogous position to the T7 tail fiber gene. This is in contrast with
      bacteriophage K1-5, another K1-specific phage, which encodes a very
      similar endosialidase which is part of a tail gene \"module\" at the end of
      the phage genome. It appears that diverse phages have acquired
      endosialidase genes by horizontal gene transfer and that these genes or
      gene products have adapted to different genome and virion architectures.
AU  - Scholl D
AU  - Merril C
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2005 187: 8499-8503.

PMID- 6282712
VI  - 17
DP  - 1982
TI  - Modification of EcoRI restriction sites by Cauloacter vibrioides.
PG  - 163-166
AB  - A comparison of EcoRI digestion profiles of plasmid RP1 isolated from
      Caulobacter vibrioides WS48 and Escherichia coli CSH29 demonstrated that EcoRI
      sites were modified by WS48.
AU  - Scholl DR
AU  - Patterson RB Jr
AU  - Jollick JD
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1982 17: 163-166.

PMID- 3003104
VI  - 261
DP  - 1986
TI  - Polypeptide sequences involved in the cleavage of DNA by the restriction endonuclease EcoRI.
PG  - 2228-2234
AB  - We have prepared a variety of fragments of the restriction endonuclease EcoRI
      by partial or total CNBr or acid cleavage of the protein.  These fragments were
      isolated by preparatvie polyacrylamide gel electrophoresis in the presence of
      sodium dodecyl sulfate.  They were analyzed in a qualitative manner for
      phosphodiesterase activity.  Antibodies against these fragments were elicited
      in rats and tested for binding to native EcoRI in an enzyme-linked immunoassay.
      We conclude from these experiments that the DNA binding site of EcoRI is
      located in the COOH-terminal half of the molecule, close to and probably
      comprising amino acid residues 137 to 157.  This conclusion is reinforced by
      the observation that this sequence shows homology to the sequences of the
      recognition helix of other gene-regulatory proteins.
AU  - Scholtissek S
AU  - Pingoud A
AU  - Maass G
AU  - Zabeau M
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1986 261: 2228-2234.

PMID- 6315538
VI  - 24
DP  - 1983
TI  - The nucleotide sequence of the HhaII restriction and modification genes from Haemophilus haemolyticus.
PG  - 227-236
AB  - We have determined the nucleotide squence of a cloned 1710-bp segment of Haemophilus
      haemolyticus DNA which contains the HhaII restriction (r) and modification (m) genes. The m
      gene is 513 bp in length and the r gene is 681 bp in length. Both are in the same reading
      frame, being separated by a 21-bp region. A ribosome-binding site is identified in front of
      each gene, but no Haemophilus promoter is apparent on the cloned fragment. Transcription
      originates from a plasmid promoter and proceeds in the direction m to r.
AU  - Schoner B
AU  - Kelly S
AU  - Smith HO
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1983 24: 227-236.

PMID- 28495778
VI  - 5
DP  - 2017
TI  - Draft Genome of the Heterotrophic Iron-Oxidizing Bacterium 'Acidibacillus ferroxidans' Huett2, Isolated from a Mine Drainage Ditch in Freiberg, Germany.
PG  - e00323-17
AB  - Here, we communicate the draft genome of 'Acidibacillus ferrooxidans' Huett2, a novel strain
      of an acidophilic, heterotrophic, iron-oxidizing bacterium belonging
      to the phylum Firmicutes It was isolated from a water drainage system of a former
      minefield in Freiberg, Germany.
AU  - Schopf S
AU  - Ullrich SR
AU  - Heine T
AU  - Schlomann M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00323-17.

PMID- 22933768
VI  - 194
DP  - 2012
TI  - Genome Sequence of a Neisseria meningitidis Capsule Null Locus Strain from the Clonal Complex of Sequence Type 198.
PG  - 5144-5145
AB  - Neisseria meningitidis is a commensal and accidental pathogen exclusively of humans. Although
      the production of polysaccharide capsules is considered to be
      essential for meningococcal virulence, there have been reports of constitutively
      unencapsulated strains causing invasive meningococcal disease (IMD). Here we
      report the genome sequence of a capsule null locus (cnl) strain of sequence type
      198 (ST-198), which is found in half of the reported cases of IMD caused by cnl
      meningococcal strains.
AU  - Schork S
AU  - Schluter A
AU  - Blom J
AU  - Schneiker-Bekel S
AU  - Puhler A
AU  - Goesmann A
AU  - Frosch M
AU  - Schoen C
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5144-5145.

PMID- 21705603
VI  - 193
DP  - 2011
TI  - Genome sequence of Helicobacter bizzozeronii strain CIII-1, an isolate from human gastric mucosa.
PG  - 4565-4566
AB  - The canine-adapted Helicobacter bizzozeronii is the only non-pylori Helicobacter species
      isolated from human gastric biopsies. Here we present
      the genome sequence of the strain CIII-1 isolated from a 45 year-old
      female patient with severe gastric symptoms. This is the first genome
      sequence of non-pylori gastric Helicobacter isolated from human gastritis.
AU  - Schott T
AU  - Rossi M
AU  - Hanninen ML
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4565-4566.

PMID- 9851708
VI  - 258
DP  - 1998
TI  - Protein engineering of the restriction endonuclease EcoRV: structure-guided design of enzyme variants that recognize the base pairs flanking the recognition site.
PG  - 184-191
AB  - We generated variants of the restriction endonuclease EcoRV that discriminate between
      recognition sites with different flanking sequences.  This was achieved by designing new
      contacts to the bases in the major groove of the DNA preceding and following the EcoRV
      recognition site.  We selected Ala181 as the starting point for the extension of the site
      specificity of EcoRV because, according to the structure of the specific EcoRV DNA complex,
      this residue is involved in a water mediated contact with the bases flanking the recognition
      sequence on the 5' side.  A substitution of this alanine residue by other amino acid residues
      changes the protein-DNA interface in this region and potentially creates new contacts, such
      that EcoRV variants could have an extended specificity, i.e. a greater selectivity for EcoRV
      sites within a particular sequence context.  EcoRV variants with naturally occurring amino
      acid residues at position 181 were produced and their selectivity analyzed with
      oligodeoxynucleotide and plasmid substrates that differ only in the base pairs immediately
      flanking the EcoRV site.  Some variants, having amino acid residues with long or bulky side
      chains at position 181 showed altered preferences for the base pairs flanking the recognition
      sequence with oligodeoxynucleotide substrates without losing their catalytic efficiency.  One
      variant, A181K, is able to discriminate between purine and pyrimidine bases on the 5' side of
      the recognition sequence, probably by means of a new hydrogen bond to the N7 of the purine
      base.  Another variant, A181E, strongly prefers a thymine base on the 5' side of the
      recognition sequence, presumably due to a hydrogen bond formed between the protonated glutamic
      acid residue and the 04 of thymine.
AU  - Schottler S
AU  - Wenz C
AU  - Lanio T
AU  - Jeltsch A
AU  - Pingoud A
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1998 258: 184-191.

PMID- 9440532
VI  - 180
DP  - 1998
TI  - A type IC restriction-modification system in Lactococcus lactis.
PG  - 407-411
AB  - Three genes coding for the endonuclease, methylase, and specificity subunits of a type I
      restriction-modification (RM) system in the Lactococcus lactis plasmid pIL2614 have been
      characterized.  Plasmid location, sequence homologies, and inactivation studies indicated that
      this R-M system is most probably of type IC.
AU  - Schouler C
AU  - Clier F
AU  - Luisa A
AU  - Lerayer L
AU  - Ehrlich SD
AU  - Chopin M-C
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1998 180: 407-411.

PMID- 9593305
VI  - 28
DP  - 1998
TI  - Combinational variation of restriction modification specificities in Lactococcus lactis.
PG  - 169-178
AB  - Three genes coding for a type I R-M system related to the class C enzymes have been identified
      on the chromosome of Lactococcus lactis strain IL1403.  In addition, plasmids were found that
      encode only the HsdS subunit that directs R-M specificity.  The presence of these plasmids in
      IL1403 conferred a new R-M phenotype on the host, indicating that the plasmid-encoded HsdS is
      able to interact with the chromosomally encoded HsdR and hsdM subunits.  Such combinational
      variation of type I R-M systems may facilitate the evolution of their specificity and thus
      reinforce bacterial resistance against invasive foreign unmethylated DNA.
AU  - Schouler C
AU  - Gautier M
AU  - Ehrlich SD
AU  - Chopin M-C
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1998 28: 169-178.

PMID- 25278542
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Oyster Larval Probiotic Bacterium Vibrio sp. Strain  OY15.
PG  - e01006-14
AB  - We report the draft genome sequence of Vibrio sp. strain OY15, a Gram-negative marine
      bacterium isolated from an oyster (Crassostrea virginica) digestive tract
      and shown to possess probiotic activity. The availability of this genome sequence
      will facilitate the study of the mechanisms of probiotic activity as well as
      virulence capacity.
AU  - Schreier HJ
AU  - Schott EJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01006-14.

PMID- 25237023
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Shellfish Bacterial Pathogen Vibrio sp. Strain B183.
PG  - e00914-14
AB  - We report the draft genome sequence of Vibrio sp. strain B183, a Gram-negative marine
      bacterium isolated from shellfish that causes mortality in larval
      mariculture. The availability of this genome sequence will facilitate the study
      of its virulence mechanisms and add to our knowledge of Vibrio sp. diversity and
      evolution.
AU  - Schreier HJ
AU  - Schott EJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00914-14.

PMID- 27540074
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Rheinheimera sp. Strain SA_1 Isolated from Iron Backwash Sludge in Germany.
PG  - e00853-16
AB  - Rheinheimera sp. strain SA_1 is an iron-depositing bacterium for which we report  a draft
      genome sequence. Strain SA_1 was isolated from iron backwash sludge of a
      waterworks in Germany. The Illumina MiSeq technique was used to sequence the
      genome of the strain.
AU  - Schroder J
AU  - Braun B
AU  - Liere K
AU  - Szewzyk U
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00853-16.

PMID- 22843578
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Corynebacterium bovis DSM 20582, Which Causes Clinical Mastitis in Dairy Cows.
PG  - 4437
AB  - Bovine mastitis represents the most economically important disease in dairy cows  and can be
      caused by Corynebacterium bovis, a commensal in the bovine udder. The
      draft genome sequence provides insights into the adaptation of this bacterium to
      the bovine habitat and its lipolytic capabilities to utilize components of cow's
      milk.
AU  - Schroder J
AU  - Glaub A
AU  - Schneider J
AU  - Trost E
AU  - Tauch A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4437.

PMID- 22524407
VI  - 13
DP  - 2012
TI  - Complete genome sequence, lifestyle, and multi-drug resistance of the human pathogen Corynebacterium resistens DSM 45100 isolated from blood samples of a leukemia patient.
PG  - 141
AB  - BACKGROUND: Corynebacterium resistens was initially recovered from human
      infections and recognized as a new coryneform species that is highly resistant to
      antimicrobial agents. Bacteremia associated with this organism in
      immunocompromised patients was rapidly fatal as standard minocycline therapies
      failed. C. resistens DSM 45100 was isolated from a blood culture of samples taken
      from a patient with acute myelocytic leukemia. The complete genome sequence of C.
      resistens DSM 45100 was determined by pyrosequencing to identify genes
      contributing to multi-drug resistance, virulence, and the lipophilic lifestyle of
      this newly described human pathogen. RESULTS: The genome of C. resistens DSM
      45100 consists of a circular chromosome of 2,601,311 bp in size and the 28,312-bp
      plasmid pJA144188. Metabolic analysis showed that the genome of C. resistens DSM
      45100 lacks genes for typical sugar uptake systems, anaplerotic functions, and a
      fatty acid synthase, explaining the strict lipophilic lifestyle of this species.
      The genome encodes a broad spectrum of enzymes ensuring the availability of
      exogenous fatty acids for growth, including predicted virulence factors that
      probably contribute to fatty acid metabolism by damaging host tissue. C.
      resistens DSM 45100 is able to use external L-histidine as a combined carbon and
      nitrogen source, presumably as a result of adaptation to the hitherto unknown
      habitat on the human skin. Plasmid pJA144188 harbors several genes contributing
      to antibiotic resistance of C. resistens DSM 45100, including a tetracycline
      resistance region of the Tet W type known from Lactobacillus reuteri and
      Streptococcus suis. The tet(W) gene of pJA144188 was cloned in Corynebacterium
      glutamicum and was shown to confer high levels of resistance to tetracycline,
      doxycycline, and minocycline in vitro. CONCLUSIONS: The detected gene repertoire
      of C. resistens DSM 45100 provides insights into the lipophilic lifestyle and
      virulence functions of this newly recognized pathogen. Plasmid pJA144188 revealed
      a modular architecture of gene regions that contribute to the multi-drug
      resistance of C. resistens DSM 45100. The tet(W) gene encoding a ribosomal
      protection protein is reported here for the first time in corynebacteria. Cloning
      of the tet(W) gene mediated resistance to second generation tetracyclines in C.
      glutamicum, indicating that it might be responsible for the failure of
      minocycline therapies in patients with C. resistens bacteremia.
AU  - Schroder J
AU  - Maus I
AU  - Meyer K
AU  - Wordemann S
AU  - Blom J
AU  - Jaenicke S
AU  - Schneider J
AU  - Trost E
AU  - Tauch A
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2012 13: 141.

PMID- 3023202
VI  - 45
DP  - 1986
TI  - Unusual occurrence of EcoP1 and EcoP15 recognition sites and counterselection of type II methylation and restriction sequences in bacteriophage T7 DNA.
PG  - 77-86
AB  - Selected and counterselected oligodeoxynucleotide sequences were identified in the total
      sequence of bacteriophage T7 DNA using a statistical criterion derived for a probability model
      of the Markov chain type. All extremely rare tetra- and pentadeoxynucleotides are (or contain)
      recognition sequences for the Escherichia coli DNA methylases dam or dcm. Most of the 37
      hexadeoxynucleotides absent from T7 DNA are recognition sequences for type II
      modification/restriction enzymes of E. coli or related species.  In contrast
      to most restriction sites counterselected during evolution, the EcoP1 site GGTCT
      occurs 126 times in the T7 genome, and phage T7 replication is severly repressed in
      P1-lysogenic host cells. We demonstrate that the frequency of the EcoP1 site is determined by
      that of the overlapping recognition sites for T7 primase, an essential phage enzyme. The
      recognition site of a type III enzyme, EcoP15, is also not counterselected. In T7 DNA all 36
      EcoP15 sites are arranged in such a manner that the sequence CAGCAG is confined to the H
      strand, the complementary sequence CTGCTG to the L strand. This "strand bias" is highly
      significant and, therefore, very probably selected. A functional relational between this
      strand bias and the refractive behaviour of phage T7 to EcoP15 restriction is suspected.
AU  - Schroeder C
AU  - Jurkschat H
AU  - Meisel A
AU  - Reich JG
AU  - Kruger D
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1986 45: 77-86.

PMID- 6378191
VI  - 43
DP  - 1984
TI  - DNA methylation of T3 virus ocr+ and ocr- strains in Escherichia coli cells harbouring the EcoK DNA host specificity system.
PG  - K1-K5
AB  - The influence of the T3 gene functions ocr+ and sam+ on the extent of phage DNA
      methylation in Escherichia coli K12 cells was studied by determining the
      proportion of 6-methylaminopurine to adenine in the purified DNA of T3
      wild-type, sam- and ocr-sam phage strains.  We demonstrate that the DNA of T3
      ocr-sam- mutants carries 12 methyl groups as a result of the action of the
      host-specificity methylase EcoK.  In contrast to this the DNA of ocr+ strains
      is not EcoK-specifically methylated.
AU  - Schroeder C
AU  - Reuter M
AU  - Kruger DH
PT  - Journal Article
TA  - Biomed. Biochim. Acta
JT  - Biomed. Biochim. Acta
SO  - Biomed. Biochim. Acta 1984 43: K1-K5.

PMID- 19054537
VI  - 384
DP  - 2009
TI  - Genomic analysis of the smallest giant virus--Feldmannia sp. virus 158.
PG  - 223-232
AB  - Genomic analysis of Feldmannia sp. virus 158, the second phaeovirus to be sequenced in hits
      entirety, provides further evidence that large double-stranded DNA viruses share similar
      evolutionary pressures as cellular organisms.  Reductive evolution is clearly evident within
      the phaeoviruses which occurred via several routes: the loss of genes from an ancestral virus
      core genome most likely through genetic drift; and as a result of relatively large
      recombination events that caused wholesale loss of genes.  The entire genome is 154,641 bp in
      lenth and has 150 predicted coding sequences of which 87% have amino acid sequence
      similarities to other algal virus coding sequences within the family Phycodnavirdae.
      Significant similarities were found, for thirty eight coding sequences (25%), to genes in gene
      databanks that are known to be involved in processes that include DNA replication, DNA
      methylation, signal transduction, viral integration and transposition, and protein-protein
      interactions.  Unsurprisingly, the greatest similarity was observed between the two known
      viruses that infect Feldmannia, indicating the taxonomic linkage of these two viruses with
      their hosts.  Moreover, comparative analysis of phycodnaviral genomic sequences revealed the
      smallest set of core genes (10 out of a possible 31) required to make a functional
      nucleocytoplasmic large dsDNA virus.
AU  - Schroeder DC
AU  - Park Y
AU  - Yoon HM
AU  - Lee YS
AU  - Kang SW
AU  - Meints RH
AU  - Ivey RG
AU  - Choi TJ
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 2009 384: 223-232.

PMID- 24356846
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Bacillus subtilis Strain PY79.
PG  - e01085-13
AB  - Bacillus subtilis is a Gram-positive soil-dwelling and endospore-forming bacterium in the
      phylum Firmicutes. B. subtilis strain PY79 is a prototrophic
      laboratory strain that has been highly used for studying a wide variety of
      cellular pathways. Here, we announce the complete whole-genome sequence of B.
      subtilis PY79.
AU  - Schroeder JW
AU  - Simmons LA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01085-13.

PMID- 
VI  - 61
DP  - 2000
TI  - Structure-function studies of lima bean trypsin inhibitor and EcoRII methyltransferase.
PG  - 3052-B
AB  - Lima bean trypsin inhibitor studies.  The crystal structure of a stable trypsin inhibitor from
      lima bean was determined to 2.5 Angstrom resolution.  The space group is cubic, I213 with
      a=110.67 A.  Native Lima Bean Trypsin Inhibitor (LBTI) crystals diffract x-rays to 1.65
      Angstrom resolution and yield data that are 93.99% complete.  LBTI has a unique property in
      that it is thermally stable to the extent that it can be boiled for ten minutes without
      destroying its activity.  This protein also shows a high degree of homology with protease
      inhibitors of the Bowman-Birk class: it contains 79 amino acid residues, including 14
      cysteines.  Thus, the structure was determined by first building a homology model of LBTI
      using adzuki bean trypsin inhibitor and of the molecular replacement method using the
      homology-modeled LBTI as a search model.  In this study, the three-dimensional structure of
      LBTI is presented and discussed.  Methyltransferase studies.  DNA methylation is believed to
      be an important mechanism for DNA recognition, transcription regulation and DNA replication in
      bacteria, plants and animals.  EcoRII methyltransferase (M.EcoRII) is a cytosine-C5 DNA
      methylating enzyme.  A model of its three-dimensional structure is proposed on the basis of
      homology modeling.  Crystal structures of two members of the same family of enzymes, HaeIII
      and HhaI methyltransferases (M.HaeIII and M.HhaI respectively), were used as template
      molecules.  Molecular dynamics calculations were used to ensure sampling of conformationally
      stable structures.  The final model has good geometry.  The DNA and cofactor binding residues
      are in expected positions to form proper interactions.  M.EcoRIII is 147 amino acids longer
      than the template molecules, and hence the model contains several loops that are significantly
      longer than those in M.HaeIII and M.HhaI.  The model provides a framework for interpretation
      and designing site-directed mutants that have a potential to improve crystallization
      experiments of this enzyme, and other similar enzymes.
AU  - Schroeder SG
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 2000 61: 3052-B.

PMID- 9543000
VI  - 10
DP  - 1997
TI  - Structural studies of EcoRII methylase: exploring similarities among methylases.
PG  - 1385-1393
AB  - EcoRII methyltransferase is a cytosine-C5 DNA methylating enzyme.  A model of its
      three-dimensional structure is proposed on the basis of homology modeling.  Crystal structures
      of two members of the same family of enzymes, HaeIII and HhaI methyltransferases (M.HaeIII and
      M.HhaI respectively), were used as template molecules.  Molecular dynamics was used to ensure
      sampling of conformationally stable structures.  The final model has good geometry.  The DNA
      and cofactor binding residues are in expected positions and form proper interactions.
      M.EcoRII is 147 amino acids longer than the template molecules, and hence the model contains
      several loops that are significantly longer than those in M.HaeIII and M.HhaI.  The model
      provides a framework for interpretation and designing site-directed mutants that have a
      potential to improve crystallization experiments of this enzyme, and possibly other similar
      enzymes.
AU  - Schroeder SG
AU  - Samudzi CT
PT  - Journal Article
TA  - Protein Eng.
JT  - Protein Eng.
SO  - Protein Eng. 1997 10: 1385-1393.

PMID- 26718035
VI  - 24
DP  - 2006
TI  - Protein Methyltransferases: Their Distribution Among the Five Structural Classes of AdoMet-Dependent Methyltransferases.
PG  - 3-28
AB  - S-adenosyl-L-methionine (AdoMet) dependent methyltransferases (MTases) are involved in
      biosynthesis, signal transduction, protein repair,
      chromatin regulation, and gene silencing. Five different structural
      folds (designated I through V) have been described that bind AdoMet and
      catalyze methyltransfer to diverse substrates, although the great
      majority of known MTases have the Class I fold. Even within a
      particular MTase class the amino-acid sequence similarity can be as low
      as 10%. Thus, the structural and catalytic requirements for
      methyltransfer from AdoMet appear to be remarkably flexible. MTases
      that act on protein substrates have been found to date among three of
      the five structural classes (I, the classical fold; III, the corrin
      MTase fold; and V, the SET fold).'There are many paths to the top of
      the mountain, but the view is always the same.'-Chinese proverb The
      Columbia World of Quotations, New York, Columbia University Press, 1996
AU  - Schubert HL
AU  - Blumenthal RM
AU  - Cheng X
PT  - Journal Article
TA  - Enzymes
JT  - Enzymes
SO  - Enzymes 2006 24: 3-28.

PMID- 12826405
VI  - 28
DP  - 2003
TI  - Many paths to methyltransfer: a chronicle of convergence.
PG  - 329-335
AB  - S-adenosyl-L-methionine (AdoMet) dependent methyltransferases (MTases) are involved in
      biosynthesis, signal transduction, protein repair, chromatin
      regulation and gene silencing. Five different structural folds (I-V) have
      been described that bind AdoMet and catalyze methyltransfer to diverse
      substrates, although the great majority of known MTases have the Class I
      fold. Even within a particular MTase class the amino-acid sequence
      similarity can be as low as 10%. Thus, the structural and catalytic
      requirements for methyltransfer from AdoMet appear to be remarkably
      flexible.
AU  - Schubert HL
AU  - Blumenthal RM
AU  - Cheng X
PT  - Journal Article
TA  - Trends Biochem. Sci.
JT  - Trends Biochem. Sci.
SO  - Trends Biochem. Sci. 2003 28: 329-335.

PMID- 12741815
VI  - 42
DP  - 2003
TI  - Structures along the catalytic pathway of PrmC/HemK, an N(5)-glutamine AdoMet-dependent methyltransferase.
PG  - 5592-5599
AB  - Posttranslational methylation of release factors on the glutamine residue of a conserved GGQ
      motif is required for efficient termination of protein
      synthesis. This methylation is performed by an N(5)-glutamine
      methyltransferase called PrmC/HemK, whose crystal structure we report here
      at 2.2 A resolution. The electron density at the active site appears to
      contain a mixture of the substrates, S-adenosyl-L-methionine (AdoMet) and
      glutamine, and the products, S-adenosyl-L-homocysteine (AdoHcy) and
      N(5)-methylglutamine. The C-terminal domain of PrmC adopts the canonical
      AdoMet-dependent methyltransferase fold and shares structural similarity
      with the nucleotide N-methyltransferases in the active site, including use
      of a conserved (D/N)PPY motif to select and position the glutamine
      substrate. Residues of the PrmC (197)NPPY(200) motif form hydrogen bonds
      that position the planar Gln side chain such that the lone-pair electrons
      on the nitrogen nucleophile are oriented toward the methyl group of
      AdoMet. In the product complex, the methyl group remains pointing toward
      the sulfur, consistent with either an sp(3)-hybridized, positively charged
      Gln nitrogen, or a neutral sp(2)-hybridized nitrogen in a strained
      conformation. Due to steric overlap within the active site, proton loss
      and formation of the neutral planar methylamide product are likely to
      occur during or after product release. These structures, therefore,
      represent intermediates along the catalytic pathway of PrmC and show how
      the (D/N)PPY motif can be used to select a wide variety substrates.
AU  - Schubert HL
AU  - Phillips JD
AU  - Hill CP
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2003 42: 5592-5599.

PMID- 24926042
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Bacillus cereus Sensu Lato Bacteriophage Bcp1.
PG  - e00334-14
AB  - Bacillus cereus sensu lato organisms are an ecologically diverse group that includes etiologic
      agents of food poisoning, periodontal disease, and anthrax.
      The recently identified Bcp1 bacteriophage infects B. cereus sensu lato and is
      being developed as a therapeutic decontamination agent and diagnostic
      countermeasure. We announce the complete genome sequence of Bcp1.
AU  - Schuch R
AU  - Pelzek AJ
AU  - Fazzini MM
AU  - Nelson DC
AU  - Fischetti VA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00334-14.

PMID- 
VI  - 0
DP  - 1992
TI  - Comparison of different reactor designs and performances.
PG  - 232-235
AB  - *

      In the chemical industry, the production costs are mainly influenced by chemical and other

      running expenditures. The same holds true for the manufacturing of biotechnological bulk

      products. In contrast to the high-added-value products, the costs of product separation and

      purification are low compared to the product formation costs.

      	

      In the case of production with aerobic microorganisms, the key factors are the costs for

      chemicals (mainly substrate) and energy (including aeration and cooling). The reactor costs

      are relatively unimportant. Therefore, for the selection of suitable reactors, not only their

      volumetric peformance (e.g., volumetric productivity), but their specific performance with

      respect to the key parameters (chemicals, energy) are decisive.

      

      According to industrial practice, the medium composition has a much larger effect on the

      process performance than on the reactor type, upon which, however, the optimal medium

      composition depends, at least for filamentous molds.

      

      Comparison of reactors and their performances can be carried out on different levels, i.e.,

      with regard to

         - the oxygen transfer rate and efficiency,

         - the cell mass productivity and efficiency,

         - the metabolite or enzyme productivity.

      

      The efficiency can be related to the substrate or energy consumption.

      

AU  - Schugerl K
PT  - Journal Article
TA  - Proc. Ninth Int. Biotech. Symp. Expo.
JT  - Proc. Ninth Int. Biotech. Symp. Expo.
SO  - Proc. Ninth Int. Biotech. Symp. Expo. 1992 0: 232-235.

PMID- 22843606
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of the Broad-Host-Range Strain Sinorhizobium fredii USDA257.
PG  - 4483
AB  - Here we announce the complete genome sequence of the symbiotic and nitrogen-fixing bacterium
      Sinorhizobium fredii USDA257. The genome shares a high
      degree of sequence similarity with the closely related broad-host-range strains
      S. fredii NGR234 and HH103. Most strikingly, the USDA257 genome encodes a wealth
      of secretory systems.
AU  - Schuldes J
AU  - Rodriguez OM
AU  - Schmeisser C
AU  - Krishnan HB
AU  - Daniel R
AU  - Streit WR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4483.

PMID- 25798594
VI  - 10
DP  - 2015
TI  - Complete Genome Sequence of Borrelia afzelii K78 and Comparative Genome Analysis.
PG  - E0120548
AB  - The main Borrelia species causing Lyme borreliosis in Europe and Asia are
      Borrelia afzelii, B. garinii, B. burgdorferi and B. bavariensis. This is in
      contrast to the United States, where infections are exclusively caused by B.
      burgdorferi. Until to date the genome sequences of four B. afzelii strains, of
      which only two include the numerous plasmids, are available. In order to further
      assess the genetic diversity of B. afzelii, the most common species in Europe,
      responsible for the large variety of clinical manifestations of Lyme borreliosis,
      we have determined the full genome sequence of the B. afzelii strain K78, a
      clinical isolate from Austria. The K78 genome contains a linear chromosome
      (905,949 bp) and 13 plasmids (8 linear and 5 circular) together presenting 1,309
      open reading frames of which 496 are located on plasmids. With the exception of
      lp28-8, all linear replicons in their full length including their telomeres have
      been sequenced. The comparison with the genomes of the four other B. afzelii
      strains, ACA-1, PKo, HLJ01 and Tom3107, as well as the one of B. burgdorferi
      strain B31, confirmed a high degree of conservation within the linear chromosome
      of B. afzelii, whereas plasmid encoded genes showed a much larger diversity.
      Since some plasmids present in B. burgdorferi are missing in the B. afzelii
      genomes, the corresponding virulence factors of B. burgdorferi are found in B.
      afzelii on other unrelated plasmids. In addition, we have identified a species
      specific region in the circular plasmid, cp26, which could be used for species
      determination. Different non-coding RNAs have been located on the B. afzelii K78
      genome, which have not previously been annotated in any of the published Borrelia
      genomes.
AU  - Schuler W
AU  - Bunikis I
AU  - Weber-Lehman J
AU  - Comstedt P
AU  - Kutschan-Bunikis S
AU  - Stanek G
AU  - Huber J
AU  - Meinke A
AU  - Bergstrom S
AU  - Lundberg U
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2015 10: E0120548.

PMID- 28729273
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Microbacterium sp. Strain LEMMJ01, Isolated from Antarctic Ornithogenic Soil.
PG  - e00672-17
AB  - We report here the 3,637,012-bp draft genome sequence of Microbacterium sp. strain LEMMJ01,
      isolated from ornithogenic soil from King George Island,
      Antarctica. The total number of genes presented in the draft genome sequence was
      3,553, and the total number of coding sequences was 3,497. In addition, genes
      related to the production of terpene and carotenoids were revealed.
AU  - Schultz J
AU  - de Souza YAP
AU  - Mansur MCPPR
AU  - Vermelho AB
AU  - da Mota FF
AU  - Rosado AS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00672-17.

PMID- 2833815
VI  - 240
DP  - 1988
TI  - The interplay between chemistry and biology in the design of enzymatic catalysts.
PG  - 426-433
AB  - Chemists and biologist are focusing considerable effort on the development of
      efficient, highly selective catalysts for the synthesis or modification of
      complex molecules.  Two approaches are described here, the generation of
      catalytic antibodies and hybrid enzymes, which exploit the binding and
      catalytic machinery of nature in catalyst design.  Characterization of these
      systems is providing additional insight into the mechanisms of molecular
      recognition and catalysis which may, in turn, lead to the design of tailor-made
      catalysts for applications in chemistry, biology and medicine.
AU  - Schultz PG
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1988 240: 426-433.

PMID- 6417654
VI  - 80
DP  - 1983
TI  - Sequence-specific double-strand cleavage of DNA by penta-N-methylpyrrolecarboxamide-EDTA.Fe(II).
PG  - 6834-6837
AB  - In the presence of O2 and 5 mM dithiothreitol,
      penta-N-methylpyrrolecarboxamide-EDTA.Fe(II) [P5E.Fe(II)] at 0.5 microM cleaves
      pBR322 plasmid DNA (50 microM in base pairs) on opposite strands to afford
      discrete DNA fragments as analyzed by agarose gel electrophoresis.
      High-resolution denaturing gel electrophoresis of a 32P-end-labeled
      517-base-pair restriction fragment containing a major cleavage site reveals
      that P5E.Fe(II) cleaves 3-5 base pairs contiguous to a 6-base-pair sequence,
      5'-T-T-T-T-T-A-3' (4,323-4,328 base pairs).  The major binding orientation of
      the pentapeptide occurs with the amino terminus at the adenine side of this
      sequence.  In the presence of 5 mM dithiothreitol, 0.01 microM P5E.Fe(II)
      converts form I pBR322 DNA at 022 microM plasmid (1.0 mM in base pairs) to 40%
      form II, indicating the cleavage reaction is catalytic, turning over a minimum
      of nine times.  This synthetic molecule achieves double-strand cleavage of DNA
      (pH 7.9, 25C) at the 6-base-pair recognition level and may provide an approach
      to the design of "artificial restriction enzymes".
AU  - Schultz PG
AU  - Dervan PB
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1983 80: 6834-6837.

PMID- 27103729
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a Novel Marine Bacterium, Paraglaciecola sp. Strain S66, with Hydrolytic Activity against Seaweed Polysaccharides.
PG  - e00304-16
AB  - A novel agarolytic gammaproteobacterium, ITALIC! Paraglaciecolasp. S66, was isolated from
      marine samples of eelgrass ( ITALIC! Zosterasp.) and sequenced. The
      draft genome contains a large number of enzyme-encoding genes with predicted
      function against several complex polysaccharides found in the cell walls of
      algae.
AU  - Schultz-Johansen M
AU  - Glaring MA
AU  - Bech PK
AU  - Stougaard P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00304-16.

PMID- 9822618
VI  - 17
DP  - 1998
TI  - Crosslinking the EcoRV restriction endonuclease across the DNA-binding site reveals transient intermediates and conformational changes of the enzyme during DNA binding and catalytic turnover.
PG  - 6757-6766
AB  - EcoRV completely encircles bound DNA with two loops, forming the entry and exit gate for the
      DNA substrate.  These loops were crosslinked generating CL-EcoRV which binds and releases
      linear DNA only slowly, because threading linear DNA into and out of the DNA-binding
      'tunnel' of CL-EcoRV is not very effective.  If the crosslinking reaction is carried out
      with a circular bound DNA, CL-EcoRV is hyperactive towards the trapped substrate which is
      cleaved very quickly but not very accurately.  CL-EcoRV also binds to, but does not cleave,
      circular DNA when added from the outside, because it cannot enter the active site.  Based on
      these results a two-step binding model is proposed for EcoRV: initial DNMA binding occurs at
      the outer side of the loops before the gate opens and then the DNA is transferred to the
      catalytic center.
AU  - Schulze C
AU  - Jeltsch A
AU  - Franke I
AU  - Urbanke C
AU  - Pingoud A
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1998 17: 6757-6766.

PMID- 8632477
VI  - 257
DP  - 1996
TI  - M.BssHII, a multispecific cytosine-C5-DNA-methyltransferase with unusual target recognizing properties.
PG  - 949-959
AB  - A new multispecific cytosine-C5-DNA-methyltransferase (C5-MTase), M.BssHII,
      was identified in Bacillus stearothermophilus H3.  The M.BssHII gene was cloned and sequenced.
      The amino acid sequence deduced shows the characteristic building plan of a C5-MTase.  By
      sequencing bisulfite-treated DNA methylated by M.BssHII and by restriction enzyme analysis, we
      defined the following methylation targets of M.BssHII: ACGCGT/CCGCGG (Mlu/SacII),
      PuGCGCPy (HaeII), PuCCGGPy (Cfr10I) and GCGCGC (BssHII).  The relative location of the
      specificity determinants in the C5-MTase was derived from the analysis of M.BssHII derivatives
      carrying deletions within the variable region V and chimeric C5-MTases constructed between
      M.BssHII and the related monospecific enzyme M.Phi3TII.  Four of the M.BssHII specificities
      (MluI, SacII, Cfr10I and BssHII) could be associated with amino acid segments within the
      variable region V.  The determinant for HaeII activity had to be assigned to sequences
      defining
      the enzyme core, the first example of a C5-MTase in which a sequence-specific methylation
      potential is mediated by structures outside of the variable region.  Another intriguing result
      came
      from the analysis of one particular chimera made between M.BssHII and M.Phi3TII.  This
      construct showed a relaxation of the methylation capacity, both with respect to the target
      recognized and the targeting of methylation within this sequence.
AU  - Schumann J
AU  - Walter J
AU  - Willert J
AU  - Wild C
AU  - Koch D
AU  - Trautner TA
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1996 257: 949-959.

PMID- 7607466
VI  - 157
DP  - 1995
TI  - M.BssHII: a new multispecific C5-DNA-methyltransferase.
PG  - 103-104
AB  - M.BssHII is a new multispecific C5-DNA-methyltransferase recognizing five different targets.
      As the enzyme has been isolated from a thermophilic Bacillus, the protein should show enhanced
      intrinsic thermostability and therefore be a promising candidate for crystallizing a
      multispecific MTase.
AU  - Schumann J
AU  - Willert J
AU  - Wild C
AU  - Waler J
AU  - Trautner TA
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 103-104.

PMID- 26966195
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Rheinheimera sp. F8, a Biofilm-Forming Strain Which Produces Large Amounts of Extracellular DNA.
PG  - e00082-16
AB  - Rheinheimera sp. strain F8 is a biofilm-forming gammaproteobacterium that has been found to
      produce large amounts of filamentous extracellular DNA. Here, we
      announce the de novo assembly of its genome. It is estimated to be 4,464,511 bp
      in length, with 3,970 protein-coding sequences and 92 RNA-coding sequences.
AU  - Schuster AK
AU  - Szewzyk U
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00082-16.

PMID- 3006334
VI  - 150
DP  - 1986
TI  - Characterization of viruses infecting a eukaryotic chlorella-like green alga.
PG  - 170-177
AB  - Nineteen plaque-forming viruses of the unicellular, eukaryotic Chlorella-like
      green alga, strain NC64A, were isolated from the various geographic regions in
      the United States and characterized.  Like the previously described virus,
      PBCV-1, all of the new viruses were large polyhedrons, sensitive to chloroform,
      and contained large dsDNA genomes of ca.  300 kbp.  All of the viral DNAs
      contained 5-methyldeoxycytidine which varied from 0.1 to 47% of the
      deoxycytidine.  In addition, 10 of the viral DNAs contained
      N6-methyldeoxyadenosine which varied from 8.1 to 37% of the deoxyadenosine.
      These viruses, along with 11 previously described viruses which replicate in
      the same Chlorella host, were grouped into 11 classes based on at least one of
      the following properties:  plaque size, reaction with PBCV-1 antiserum, or the
      nature and abundance of methylated bases in their genomic DNA.
AU  - Schuster AM
AU  - Burbank DE
AU  - Meister B
AU  - Skrdla MP
AU  - Meints RH
AU  - Hattman S
AU  - Swinton D
AU  - Van Etten JL
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1986 150: 170-177.

PMID- 20935092
VI  - 193
DP  - 2011
TI  - Whole-Genome Sequences of Thirteen Isolates of Borrelia burgdorferi.
PG  - 1018-1020
AB  - Borrelia burgdorferi is a causative agent of Lyme disease in North America and Eurasia. The
      first complete genome sequence of B. burgdorferi strain 31, available for more than a decade,
      has assisted research on the
      pathogenesis of Lyme disease. Because a single genome sequence is not
      sufficient to understand the relationship between genotypic and geographic
      variation and disease phenotype, we determined the whole-genome sequences
      of 13 additional B. burgdorferi isolates that span the range of natural
      variation. These sequences should allow improved understanding of
      pathogenesis and provide a foundation for novel detection, diagnosis, and
      prevention strategies.
AU  - Schutzer SE
AU  - Fraser-Liggett CM
AU  - Casjens SR
AU  - Qiu WG
AU  - Dunn JJ
AU  - Mongodin EF
AU  - Luft BJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 1018-1020.

PMID- 22207749
VI  - 194
DP  - 2012
TI  - Whole-Genome Sequences of Borrelia bissettii, Borrelia valaisiana, and Borrelia spielmanii.
PG  - 545-546
AB  - It has been known for decades that human Lyme disease is caused by the three spirochete
      species Borrelia burgdorferi, Borrelia afzelii, and
      Borrelia garinii. Recently, Borrelia valaisiana, Borrelia spielmanii, and
      Borrelia bissettii have been associated with Lyme disease. We report the
      complete genome sequences of B. valaisiana VS116, B. spielmanii A14S, and
      B. bissettii DN127.
AU  - Schutzer SE
AU  - Fraser-Liggett CM
AU  - Qiu WG
AU  - Kraiczy P
AU  - Mongodin EF
AU  - Dunn JJ
AU  - Luft BJ
AU  - Casjens SR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 545-546.

PMID- 26337887
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of a Metronidazole-Resistant Gardnerella vaginalis Isolate.
PG  - e00992-15
AB  - We report the draft genome sequence of a Gardnerella vaginalis strain (3549624) isolated from
      a vaginal specimen. G. vaginalis is associated with bacterial vaginosis, the most common cause
      of vaginal discharge, which is often treated with metronidazole. This isolate is highly
      resistant to metronidazole (MIC, 500 microg/ml) and may be useful for comparative genomic
      studies to determine the molecular basis of metronidazole resistance in this species.
AU  - Schuyler JA
AU  - Chadwick SG
AU  - Mordechai E
AU  - Adelson ME
AU  - Gygax SE
AU  - Hilbert DW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00992-15.

PMID- 26564054
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of a Metronidazole-Resistant Derivative of Gardnerella vaginalis Strain ATCC 14019.
PG  - e01345-15
AB  - We report the genome sequence of a metronidazole-resistant derivative of Gardnerella vaginalis
      ATCC 14019. This strain was obtained after serial selection
      to increase the MIC from 4 to >/=500 microg/ml. Two coding changes, in genes
      encoding a response regulator and an NAD(+) synthetase, arose during selection.
AU  - Schuyler JA
AU  - Mordechai E
AU  - Adelson ME
AU  - Gygax SE
AU  - Hilbert DW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01345-15.

PMID- 26337886
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of a Metronidazole-Susceptible Atopobium vaginae Isolate.
PG  - e00991-15
AB  - We report the draft genome sequence of a vaginal isolate of Atopobium vaginae vaginae (strain
      44061), an organism linked to bacterial vaginosis (BV), the most  common gynecological
      infection in the United States. This species is often highly resistant to metronidazole, which
      is a front-line therapy for BV. Strain 44061 is a metronidazole-susceptible isolate (MIC, 16
      microg/ml), and its genome sequence  will be useful for comparative studies to elucidate the
      molecular basis of metronidazole resistance in this species.
AU  - Schuyler JA
AU  - Mordechai E
AU  - Adelson ME
AU  - Gygax SE
AU  - Hilbert DW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00991-15.

PMID- 3000892
VI  - 39
DP  - 1985
TI  - Restriction endonucleases in Azospirillum.
PG  - 113-116
AB  - Azospirillum brasilense, A. amazonense, and A. lipoferum strains were screened
      for restriction endonucleases using phage lambda DNA.  The extract of A.
      brasilense 29711 cleaved lambda DNA into specific fragments.  It was concluded
      that this strain possesses a class II restriction endonuclease which was named
      AbrI.  AbrI has a single recognition site on lambda DNA at position of approx.
      33500 bp. AbrI was characterized as an isoschizomer of XhoI, which cuts lambda
      DNA at 33498 bp and cleaves double-stranded DNA at the sequence 5'-C^TCGAG-3'.
      From other Azospirilla strains only A. amazonense QRZ42 extracts (AamI
      activity) cleaved DNA into specific fragments under certain conditions.
AU  - Schwabe G
AU  - Posseckert G
AU  - Klingmuller W
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1985 39: 113-116.

PMID- 12948488
VI  - 332
DP  - 2003
TI  - Complete nucleotide sequence of pHG1: a Ralstonia eutropha H16 megaplasmid encoding key enzymes of H(2)-based ithoautotrophy and anaerobiosis.
PG  - 369-383
AB  - The self-transmissible megaplasmid pHG1 carries essential genetic information for the
      facultatively lithoautotrophic and facultatively
      anaerobic lifestyles of its host, the Gram-negative soil bacterium
      Ralstonia eutropha H16. We have determined the complete nucleotide
      sequence of pHG1. This megaplasmid is 452,156 bp in size and carries 429
      potential genes. Groups of functionally related genes form loose clusters
      flanked by mobile elements. The largest functional group consists of
      lithoautotrophy-related genes. These include a set of 41 genes for the
      biosynthesis of the three previously identified hydrogenases and of a
      fourth, novel hydrogenase. Another large cluster carries the genetic
      information for denitrification. In addition to a dissimilatory nitrate
      reductase, both specific and global regulators were identified. Also
      located in the denitrification region is a set of genes for cytochrome c
      biosynthesis. Determinants for several enzymes involved in the
      mineralization of aromatic compounds were found. The genes for conjugative
      plasmid transfer predict that R.eutropha forms two types of pili. One of
      them is related to the type IV pili of pathogenic enterobacteria. pHG1
      also carries an extensive "junkyard" region encompassing 17 remnants of
      mobile elements and 22 partial or intact genes for phage-type integrase.
      Among the mobile elements is a novel member of the IS5 family, in which
      the transposase gene is interrupted by a group II intron.
AU  - Schwartz E
AU  - Henne A
AU  - Cramm R
AU  - Eitinger T
AU  - Friedrich B
AU  - Gottschalk G
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2003 332: 369-383.

PMID- 23599494
VI  - 340
DP  - 2013
TI  - The helicase-like domains of type III restriction enzymes trigger long-range diffusion along DNA.
PG  - 353-356
AB  - Helicases are ubiquitous adenosine triphosphatases (ATPases) with widespread roles in genome
      metabolism.  Here, we report a previously undescribed functionality for ATPases with
      helicase-like domains; namely, that ATP hydrolysis can trigger ATP-independent long-range
      protein diffusion on DNA in one dimension (1D).  Specifically, using single-molecule
      fluorescence microscopy we show that the Type III restriction enzyme EcoP15I uses its ATPase
      to switch into a distinct structural state that diffuses on DNA over long distances and long
      times.  The switching occurs only upon binding to the target site and requires hydrolysis of
      ~30 ATPs.  We define the mechanism for these enzymes and show how ATPase activity is involved
      in DNA target site verification and 1D signaling, roles that are common in DNA metabolism: for
      example, in nucleotide excision and mismatch repair.
AU  - Schwarz FW
AU  - Toth J
AU  - van Aelst K
AU  - Cui G
AU  - Clausing S
AU  - Szczelkun MD
AU  - Seidel R
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2013 340: 353-356.

PMID- 
VI  - 100
DP  - 2011
TI  - Type III Restriction Enzymes Use 1D Diffusion to Communicate the Relative Orientation of their Distant Target Sites.
PG  - 191
AB  - Type III restriction enzymes sense that relative orientation of their distant target sites and
      cleave DNA only if at least two of them are situated in an inverted repeat.  The communication
      process is strictly dependent on ATP hydrolysis catalyzed by their superfamily 2 helicase
      domains.  Given the similarity to Type I restriction enzymes, which couple ATP hydrolysis to
      directed motion on DNA, unidirectional loop translocation that may partially be accommpanied
      by 3D diffusive looping has  been the suggested communication mechanism for Type III enzymes.
      Based on magnetic tweezers single-molecule cleavage experiments and ATPase measurements we
      suggest an alternative inter-site communication mechanism using 1D diffusion along the DNA
      contour.  In order to verify this hypothesis we directly visualize the motion of quantum-dot
      labeled Type III restriction enzymes along DNA.  For this we use a setup that combines
      magnetic tweezers with total internal reflection fluorescence microscopy.  The enzymes undergo
      a fast diffusive motion along DNA capable of scanning kbp distances per second.  We also find
      that the affinity of the enzymes to non-specific and specific DNA is regulated by the presence
      of ATP suggesting that ATP hydrolysis acts as a trigger for diffusion.  Thus, Type III
      restricotn enzymes are the first DNa-mopdifying enzymes which communicate target site
      orientations over long distances via 1D diffusion.
AU  - Schwarz FW
AU  - Toth J
AU  - van Aelst K
AU  - Cui G
AU  - Szczelkun MD
AU  - Seidel R
PT  - Journal Article
TA  - Biophys. J.
JT  - Biophys. J.
SO  - Biophys. J. 2011 100: 191.

PMID- 21724613
VI  - 39
DP  - 2011
TI  - DNA cleavage site selection by Type III restriction enzymes provides evidence for head-on protein collisions following 1D bidirectional motion.
PG  - 8042-8051
AB  - DNA cleavage by the Type III Restriction-Modification enzymes requires communication in 1D
      between two distant indirectly-repeated recognitions
      sites, yet results in non-specific dsDNA cleavage close to only one of the
      two sites. To test a recently proposed ATP-triggered DNA sliding model, we
      addressed why one site is selected over another during cleavage. We
      examined the relative cleavage of a pair of identical sites on DNA
      substrates with different distances to a free or protein blocked end, and
      on a DNA substrate using different relative concentrations of protein.
      Under these conditions a bias can be induced in the cleavage of one site
      over the other. Monte-Carlo simulations based on the sliding model
      reproduce the experimentally observed behaviour. This suggests that
      cleavage site selection simply reflects the dynamics of the preceding
      stochastic enzyme events that are consistent with bidirectional motion in
      1D and DNA cleavage following head-on protein collision.
AU  - Schwarz FW
AU  - van Aelst K
AU  - Toth J
AU  - Seidel R
AU  - Szczelkun MD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2011 39: 8042-8051.

PMID- 28963203
VI  - 5
DP  - 2017
TI  - Complete Draft Genome Sequence of Escherichia coli KRX, a Strain for Efficient Cloning and High-Yield Expression of Proteins under Control of the T7 RNA  Polymerase.
PG  - e00933-17
AB  - Escherichia coli KRX is a strain offering both a high transformation efficiency and the
      possibility to produce the target protein to high yields in one host,
      avoiding additional cloning steps. Here, the draft genome sequence of E. coli KRX
      is presented and provides the genetic basis for additional biotechnological
      applications.
AU  - Schwarzhans JP
AU  - Wibberg D
AU  - Winkler A
AU  - Kalinowski J
AU  - Friehs K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00933-17.

PMID- 3588691
VI  - 45
DP  - 1987
TI  - Analysis of the inhibition of restriction endonuclease cleavage by UV damage.
PG  - 76s
AB  - It has been shown that thymine dimers in the recognition sequence of a
      restriction endonuclease inhibit cleavage of the substrate.  Quantitative gel
      electrophoresis analysis allows evaluation of the extent to which cleavage is
      inhibited at different sites in the same DNA.  Since the recognition sequence
      is the same at all sites, any differences in sensitivity to cleavage must
      result from differences in the base sequences near the recognition sites.  We
      have observed different amounts of cleavage inhibition for the EcoRI sites in
      lambda DNA.  The amount of inhibition is correlated with the probability of
      dimer formation within 10 bases on either side of the cleavage site.
      Endonucleases BamHI, EcoRI and HaeII were found to be insensitive to damage by
      254 nm UV.  DNA complexed with EcoRI was protected from UV damage by the bound
      protein.
AU  - Schweikart KM
AU  - Ribeiro E
AU  - Larcom LL
PT  - Journal Article
TA  - Photochem. Photobiol.
JT  - Photochem. Photobiol.
SO  - Photochem. Photobiol. 1987 45: 76s.

PMID- 28272476
VI  - 7
DP  - 2017
TI  - Novel methicillin resistance gene mecD in clinical Macrococcus caseolyticus strains from bovine and canine sources.
PG  - 43797
AB  - Methicillin-resistant Macrococcus caseolyticus strains from bovine and canine
      origins were found to carry a novel mecD gene conferring resistance to all
      classes of beta-lactams including anti-MRSA cephalosporins. Association of
      beta-lactam resistance with mecD was demonstrated by gene expression in S. aureus
      and deletion of the mecD-containing island in M. caseolyticus. The mecD gene was
      located either on an 18,134-bp M. caseolyticus resistance island (McRImecD-1) or
      a 16,188-bp McRImecD-2. Both islands were integrated at the 3' end of the rpsI
      gene, carried the mecD operon (mecD-mecR1m-mecIm), and genes for an integrase of
      the tyrosine recombinase family and a putative virulence-associated protein
      (virE). Apart from the mecD operon, that shared 66% overall nucleotide identity
      with the mecB operon, McRImecD islands were unrelated to any mecB-carrying
      elements or staphylococcal cassette chromosome mec. Only McRImecD-1 that is
      delimitated at both ends by direct repeats was capable of circular excision. The
      recombined excision pattern suggests site-specific activity of the integrase and
      allowed identification of a putative core attachment site. Detection of
      rpsI-associated integrases in Bacillus and S. aureus reveals a potential for
      broad-host range dissemination of the novel methicillin resistance gene mecD.
AU  - Schwendener S
AU  - Cotting K
AU  - Perreten V
PT  - Journal Article
TA  - Sci. Rep.
JT  - Sci. Rep.
SO  - Sci. Rep. 2017 7: 43797.

PMID- 20849449
VI  - 13
DP  - 2011
TI  - A blueprint of ectoine metabolism from the genome of the Industrial producer Halomonas elongata DSM 2581(T).
PG  - 1973-1994
AB  - The halophilic g-proteobacterium Halomonas elongata DSM 2581T thrives at high salinity by
      synthesizing and accumulating the compatible solute ectoine.  Ectoine levels are highly
      regulated according to external salt levels but the overall picture of its metabolism and
      control is not well understood. Apart from its critical role in cell adaptation to halophilic
      environments, ectoine can be used as a stabilizer for enzymes and as a cell protectant in skin
      and health care applications and is thus produced annually on a scale of tons in an industrial
      process using H. elongata as producer strain. This paper presents the complete genome sequence
      of H. elongata (4 061 296 bp) and includes experiments and analysis identifying and
      characterizing the entire ectoine metabolism, including a newly discovered pathway for ectoine
      degradation and its cyclic connection to ectoine synthesis.  The degradation of ectoine (doe)
      proceeds via hydrolysis of ectoine (DoeA) to Na-acetyl-L-2,4-diaminobutyric acid, followed by
      deacetylation to diaminobutyric acid (DoeB). In H. elongata, diaminobutyric acid can either
      flow off to aspartate or re-enter the ectoine synthesis pathway, forming a cycle of ectoine
      synthesis and degradation. Genome comparison revealed that the ectoine degradation pathway
      exists predominantly in non-halophilic bacteria unable to synthesize ectoine. Based on the
      resulting genetic and biochemical data, a metabolic flux model of ectoine metabolism was
      derived that can be used to understand the way H. elongata survives under varying salt
      stresses and that provides a basis for a model-driven improvement of industrial ectoine
      production.
AU  - Schwibbert K
AU  - Marin-Sanguino A
AU  - Bagyan I
AU  - Heidrich G
AU  - Lentzen G
AU  - Seitz H
AU  - Rampp M
AU  - Schuster SC
AU  - Klenk H-P
AU  - Pfeiffer F
AU  - Oesterhelt D
AU  - Kunte HJ
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2011 13: 1973-1994.

PMID- Not included in PubMed...
VI  - 18
DP  - 1964
TI  - Host-controlled modification of Rhizobium bacteriophage.
PG  - 333-343
AB  - Host-controlled phenotypic variation of host specificity was observed with two
      rhizobiophage strains, OL1 and OL5, following growth on six strains of
      Rhizobium leguminosarum and R. trifolii.  The six hosts could be assigned to
      four groups, each group representing a different pattern of host specificity.
      Initial adaptation of OL5 to hosts L2, L7, and L25 appeared to involve
      mutation, although replication in cells of these hosts generally involved
      additional phenotypic restriction.  Restricted and unrestricted forms of a
      phage did not differ significantly in their ability to adsorb to several hosts.
      One-step analysis of the L25-specific form of OL5 grown in L25 cells indicated
      a low average burst size of approximately one unrestricted plaque-forming unit
      in a small proportion of cells which were able to produce infective centres on
      L4.  One-cycle analysis of L4-specific OL5 modified by growth in L25 confirmed
      the phenotypic nature of phage variation in this phage-host system, and
      indicated that specificity for L4 was not replicated in L25.
AU  - Schwinghamer EA
PT  - Journal Article
TA  - Aust. J. Biol. Sci.
JT  - Aust. J. Biol. Sci.
SO  - Aust. J. Biol. Sci. 1964 18: 333-343.

PMID- 17965162
VI  - 190
DP  - 2008
TI  - Broad-host-range Yersinia phage PY100: genome sequence, proteome analysis of virions, and DNA packaging strategy.
PG  - 332-342
AB  - PY100 is a lytic bacteriophage with a broad host range within the genus
      Yersinia. The phage forms plaques on strains of the three human pathogenic
      species Yersinia enterocolitica, Y. pseudotuberculosis, and Y. pestis at
      37 degrees C. PY100 was isolated from farm manure and intended to be used
      in phage therapy trials. PY100 has an icosahedral capsid containing
      double-stranded DNA and a contractile tail. The genome consists of 50,291
      bp and is predicted to contain 93 open reading frames (ORFs). PY100 gene
      products were found to be homologous to the capsid proteins and proteins
      involved in DNA metabolism of the enterobacterial phage T1; PY100 tail
      proteins possess homologies to putative tail proteins of phage AaPhi23 of
      Actinobacillus actinomycetemcomitans. In a proteome analysis of virion
      particles, 15 proteins of the head and tail structures were identified by
      mass spectrometry. The putative gene product of ORF2 of PY100 shows
      significant homology to the gene 3 product (small terminase subunit) of
      Salmonella phage P22 that is involved in packaging of the concatemeric
      phage DNA. The packaging mechanism of PY100 was analyzed by hybridization
      and sequence analysis of DNA isolated from virion particles. Newly
      replicated PY100 DNA is cut initially at a pac recognition site, which is
      located in the coding region of ORF2.
AU  - Schwudke D
AU  - Ergin A
AU  - Michael K
AU  - Volkmar S
AU  - Appel B
AU  - Knabner D
AU  - Konietzny A
AU  - Strauch E
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2008 190: 332-342.

PMID- 23409263
VI  - 1
DP  - 2013
TI  - Genome of a Gut Strain of Bacillus subtilis.
PG  - e00184-12
AB  - Bacillus subtilis is a Gram-positive, rod-shaped, spore-forming bacterium. We present the
      genome sequence of an undomesticated strain, BSP1, isolated from
      poultry. The sequence of the BSP1 genome supports the view that B. subtilis has a
      biphasic lifestyle, cycling between the soil and the animal gastrointestinal
      tract, and it provides molecular-level insight into the adaptation of B. subtilis
      to life under laboratory conditions.
AU  - Schyns G
AU  - Serra CR
AU  - Lapointe T
AU  - Pereira-Leal JB
AU  - Potot S
AU  - Fickers P
AU  - Perkins JB
AU  - Wyss M
AU  - Henriques AO
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00184-12.

PMID- 4570925
VI  - 11
DP  - 1973
TI  - Mapping of new Escherichia coli K and 15 restriction sites on specific fragments of bacteriophage PhiX174 DNA.
PG  - 378-385
AB  - We have isolated several new PhiX174 mutants which contain sites sensitive to
      restriction by Escherichia coli.  One contains an E. coli 15 restriction site
      and three are double mutants containing an E. coli K site as well as the E.
      coli 15 site.  The replicative form (RF) DNA of one of the mutants containing a
      K site has been shown to be restricted in spheroplasts of a K-12 strain.  The
      infectivity of this RF, but not wild-type RF, has also been shown to be
      inactivated by an E. coli K extract and by purified K restriction enzyme in
      vitro.  The product of the RF treated with purified K restriction enzyme in
      vitro is a full length linear molecule.  The mutant sites have also been
      localized to specific regions of the PhiX174 genome by a fragment mapping
      technique, making use of specific fragments of PhiX174 RF DNA obtained by
      digestion with a specific endonuclease.
AU  - Sclair M
AU  - Edgell MH
AU  - Hutchison CA
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1973 11: 378-385.

PMID- 24389641
VI  - 46
DP  - 2014
TI  - Regulation of protein stability of DNA methyltransferase 1 by post-translational modifications.
PG  - 199-203
AB  - DNA methylation is an important epigenetic mechanism that ensures correct gene expression and
      maintains genetic stability. DNA methyltransferase 1 (DNMT1) is the primary enzyme that
      maintains DNA methylation during replication. Dysregulation of DNMT1 is implicated in a
      variety of diseases. DNMT1 protein stability is regulated via various post-translational
      modifications, such as acetylation and ubiquitination, but also through protein-protein
      interactions. These mechanisms ensure DNMT1 is properly activated during the correct time of
      the cell cycle and at correct genomic loci, as well as in response to appropriate
      extracellular cues. Further understanding of these regulatory mechanisms may help to design
      novel therapeutic approaches for human diseases.
AU  - Scott A
AU  - Song J
AU  - Ewing R
AU  - Wang Z
PT  - Journal Article
TA  - Acta Biochim. Biophys. Sin.
JT  - Acta Biochim. Biophys. Sin.
SO  - Acta Biochim. Biophys. Sin. 2014 46: 199-203.

PMID- 17105352
VI  - 4
DP  - 2006
TI  - The Genome of Deep-Sea Vent Chemolithoautotroph Thiomicrospira crunogena XCL-2.
PG  - e383
AB  - Presented here is the complete genome sequence of Thiomicrospira crunogena XCL-2,
      representative of ubiquitous chemolithoautotrophic sulfur-oxidizing
      bacteria isolated from deep-sea hydrothermal vents. This
      gammaproteobacterium has a single chromosome (2,427,734 base pairs), and
      its genome illustrates many of the adaptations that have enabled it to
      thrive at vents globally. It has 14 methyl-accepting chemotaxis protein
      genes, including four that may assist in positioning it in the redoxcline.
      A relative abundance of coding sequences (CDSs) encoding regulatory
      proteins likely control the expression of genes encoding carboxysomes,
      multiple dissolved inorganic nitrogen and phosphate transporters, as well
      as a phosphonate operon, which provide this species with a variety of
      options for acquiring these substrates from the environment. Thiom.
      crunogena XCL-2 is unusual among obligate sulfur-oxidizing bacteria in
      relying on the Sox system for the oxidation of reduced sulfur compounds.
      The genome has characteristics consistent with an obligately
      chemolithoautotrophic lifestyle, including few transporters predicted to
      have organic allocrits, and Calvin-Benson-Bassham cycle CDSs scattered
      throughout the genome.
AU  - Scott KM et al
PT  - Journal Article
TA  - PLoS Biology
JT  - PLoS Biology
SO  - PLoS Biology 2006 4: e383.

PMID- 21925113
VI  - 10
DP  - 2011
TI  - The genome of th17 cell-inducing segmented filamentous bacteria reveals extensive auxotrophy and adaptations to the intestinal environment.
PG  - 260-272
AB  - Perturbations of the composition of the symbiotic intestinal microbiota can have
      profound consequences for host metabolism and immunity. In mice, segmented
      filamentous bacteria (SFB) direct the accumulation of potentially proinflammatory
      Th17 cells in the intestinal lamina propria. We present the genome sequence of
      SFB isolated from monocolonized mice, which classifies SFB phylogenetically as a
      unique member of Clostridiales with a highly reduced genome. Annotation analysis
      demonstrates that SFB depend on their environment for amino acids and essential
      nutrients and may utilize host and dietary glycans for carbon, nitrogen, and
      energy. Comparative analyses reveal that SFB are functionally related to members
      of the genus Clostridium and several pathogenic or commensal "minimal" genera,
      including Finegoldia, Mycoplasma, Borrelia, and Phytoplasma. However, SFB are
      functionally distinct from all 1200 examined genomes, indicating a gene
      complement representing biology relatively unique to their role as a gut
      commensal closely tied to host metabolism and immunity.
AU  - Sczesnak A
AU  - Segata N
AU  - Qin X
AU  - Gevers D
AU  - Petrosino JF
AU  - Huttenhower C
AU  - Littman DR
AU  - Ivanov II
PT  - Journal Article
TA  - Cell Host Microbe
JT  - Cell Host Microbe
SO  - Cell Host Microbe 2011 10: 260-272.

PMID- 16120967
VI  - 33
DP  - 2005
TI  - Characterization of the Type III restriction endonuclease PstII from Providencia stuartii.
PG  - 4775-4787
AB  - A new Type III restriction endonuclease designated PstII has been purified from Providencia
      stuartii. PstII recognizes the hexanucleotide sequence 5'-CTGATG(N)(25-26/27-28)-3'.
      Endonuclease activity requires a substrate with two copies of the recognition site in
      head-to-head repeat and is dependent on a low level of ATP hydrolysis ( approximately 40
      ATP/site/min). Cleavage occurs at just one of the two sites and results in a staggered cut
      25-26 nt downstream of the top strand sequence to generate a two base 5'-protruding end.
      Methylation of the site occurs on one strand only at the first adenine of 5'-CATCAG-3'.
      Therefore, PstII has characteristic Type III restriction enzyme activity as exemplified by
      EcoPI or EcoP15I. Moreover, sequence asymmetry of the PstII recognition site in the T7 genome
      acts as an historical imprint of Type III restriction activity in vivo. In contrast to other
      Type I and III enzymes, PstII has a more relaxed nucleotide specificity and can cut DNA with
      GTP and CTP (but not UTP). We also demonstrate that PstII and EcoP15I cannot interact and
      cleave a DNA substrate suggesting that Type III enzymes must make specific protein-protein
      contacts to activate endonuclease activity.
AU  - Sears A
AU  - Peakman LJ
AU  - Wilson GG
AU  - Szczelkun MD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2005 33: 4775-4787.

PMID- 16120968
VI  - 33
DP  - 2005
TI  - Subunit assembly modulates the activities of the Type III restriction-modification enzyme PstII in vitro.
PG  - 4788-4796
AB  - We demonstrate that, like other Type III restriction endonuclease, PstII does not turnover
      such that a DNA substrate is only fully cleaved at a
      Res2Mod2-to-site ratio of approximately 1:1. However, unlike other Type
      III enzymes, the cleavage rate profiles varied with protein concentration:
      using 5 nM DNA and 25 nM PstII, approximately half of the DNA was cut at a
      fast rate while the remainder was cut 24 times more slowly; in comparison,
      with 100 nM PstII cleavage occurs at a single fast rate. The inclusion of
      the methyl donor S-adenosyl methionine does not alter the rates with 100
      nM PstII but with 25 nM PstII the reaction stopped after completion of the
      initial fast cleavage phase owing to methylation. Concentration-dependent
      rates were also observed in methylation assays: at 100 nM PstII, a single
      slow rate was measured while at lower PstII concentrations both fast and
      slow rates were measured. We propose a model in which the intact Res2Mod2
      complex favoured at high PstII concentrations is a fast endonuclease/slow
      methyltransferase while the various subassemblies which coexist at lower
      concentrations are fast methyltransferases. A potential role for
      disassembly in control of restriction activity in vivo is discussed.
AU  - Sears A
AU  - Szczelkun MD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2005 33: 4788-4796.

PMID- 8836187
VI  - 24
DP  - 1996
TI  - BaeI, another unusual BcgI-like restriction endonuclease.
PG  - 3590-3592
AB  - BcgI and BcgI-like restriction endonucleases have a very distinct characteristic which causes
      them to differ from the other classified restriction enzymes; they all cleave double-stranded
      DNA specifically on both sides of the recognition sites.  Here we report a new BcgI-like
      restriction endonuclease, BaeI, isolated from Bacillus sphaericus.  Like BcgI, BaeI also
      cleaves double-stranded DNA on both strands upstream and downstream of its recognition
      sequence (10/15)ACNNNNGTAYC(12/7).  There are two dominant polypeptides in the final
      preparation of BaeI with molecular masses of ~80 and 55 kDa.  Both are slightly larger than
      the two BcgI subunits.  BaeI requires both Mg2+ and AdoMet to cleave DNA.  Accompanying
      bilateral cleavage activity, the heteromeric BaeI also has an N6-adenine methyltransferase
      activity which modifies the symmetrically located adenines within its recognition sequence.
AU  - Sears LE
AU  - Zhou B
AU  - Aliotta JM
AU  - Morgan RD
AU  - Kong H
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1996 24: 3590-3592.

PMID- 16804543
VI  - 38
DP  - 2006
TI  - The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome.
PG  - 779-786
AB  - We determined the complete genome sequence of Clostridium difficile strain 630, a virulent and
      multidrug-resistant strain. Our analysis indicates
      that a large proportion (11%) of the genome consists of mobile genetic
      elements, mainly in the form of conjugative transposons. These mobile
      elements are putatively responsible for the acquisition by C. difficile of
      an extensive array of genes involved in antimicrobial resistance,
      virulence, host interaction and the production of surface structures. The
      metabolic capabilities encoded in the genome show multiple adaptations for
      survival and growth within the gut environment. The extreme genome
      variability was confirmed by whole-genome microarray analysis; it may
      reflect the organism's niche in the gut and should provide information on
      the evolution of virulence in this organism.
AU  - Sebaihia M et al
PT  - Journal Article
TA  - Nat. Genet.
JT  - Nat. Genet.
SO  - Nat. Genet. 2006 38: 779-786.

PMID- 16885469
VI  - 188
DP  - 2006
TI  - Comparison of the genome sequence of the poultry pathogen Bordetella avium with those of B. bronchiseptica, B. pertussis, and B. parapertussis reveals extensive diversity in surface structures associated with host interaction.
PG  - 6002-6015
AB  - Bordetella avium is a pathogen of poultry and is phylogenetically distinct from Bordetella
      bronchiseptica, Bordetella pertussis, and Bordetella parapertussis, which are other species in
      the Bordetella genus that infect mammals. In order to understand the evolutionary relatedness
      of Bordetella species and further the understanding of pathogenesis, we obtained the complete
      genome sequence of B. avium strain 197N, a pathogenic strain that has been extensively
      studied. With 3,732,255 base pairs of DNA and 3,417 predicted coding sequences, it has the
      smallest genome and gene complement of the sequenced bordetellae. In this study, the presence
      or absence of previously reported virulence factors from B. avium was confirmed, and the
      genetic bases for growth characteristics were elucidated. Over 1,100 genes present in B. avium
      but not in B. bronchiseptica were identified, and most were predicted to encode surface or
      secreted proteins that are likely to define an organism adapted to the avian rather than the
      mammalian respiratory tracts. These include genes coding for the synthesis of a polysaccharide
      capsule, hemagglutinins, a type I secretion system adjacent to two very large genes for
      secreted proteins, and unique genes for both lipopolysaccharide and fimbrial biogenesis. Three
      apparently complete prophages are also present. The BvgAS virulence regulatory system appears
      to have polymorphisms at a poly(C) tract that is involved in phase variation in other
      bordetellae. A number of putative iron-regulated outer membrane proteins were predicted from
      the sequence, and this regulation was confirmed experimentally for five of these.
AU  - Sebaihia M et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2006 188: 6002-6015.

PMID- 17519437
VI  - 17
DP  - 2007
TI  - Genome sequence of a proteolytic (Group I) Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes.
PG  - 1082-1092
AB  - Clostridium botulinum is a heterogeneous Gram-positive species that comprises four genetically
      and physiologically distinct groups of bacteria that share the
      ability to produce botulinum neurotoxin, the most poisonous toxin known to man,
      and the causative agent of botulism, a severe disease of humans and animals. We
      report here the complete genome sequence of a representative of Group I
      (proteolytic) C. botulinum (strain Hall A, ATCC 3502). The genome consists of a
      chromosome (3,886,916 bp) and a plasmid (16,344 bp), which carry 3650 and 19
      predicted genes, respectively. Consistent with the proteolytic phenotype of this
      strain, the genome harbors a large number of genes encoding secreted proteases
      and enzymes involved in uptake and metabolism of amino acids. The genome also
      reveals a hitherto unknown ability of C. botulinum to degrade chitin. There is a
      significant lack of recently acquired DNA, indicating a stable genomic content,
      in strong contrast to the fluid genome of Clostridium difficile, which can form
      longer-term relationships with its host. Overall, the genome indicates that C.
      botulinum is adapted to a saprophytic lifestyle both in soil and aquatic
      environments. This pathogen relies on its toxin to rapidly kill a wide range of
      prey species, and to gain access to nutrient sources, it releases a large number
      of extracellular enzymes to soften and destroy rotting or decayed tissues.
AU  - Sebaihia M et al
PT  - Journal Article
TA  - Genome Res.
JT  - Genome Res.
SO  - Genome Res. 2007 17: 1082-1092.

PMID- 20118253
VI  - 192
DP  - 2010
TI  - Complete Genome Sequence Of The Plant Pathogen Erwinia amylovora Strain ATCC 49946.
PG  - 2020-2021
AB  - Erwinia amylovora causes the economically important disease fire blight that affects rosaceous
      plants, especially pear and apple. Here we report the complete genome sequence and annotation
      of strain ATCC 49946. The analysis of the sequence and its comparison with sequenced genomes
      of closely related enterobacteria revealed signs of pathoadaptation to rosaceous hosts.
AU  - Sebaihia M
AU  - Bocsanczy AM
AU  - Biehl BS
AU  - Quail MA
AU  - Perna NT
AU  - Glasner JD
AU  - Declerck GA
AU  - Cartinhour S
AU  - Schneider DJ
AU  - Bentley SD
AU  - Parkhill J
AU  - Beer SV
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 2020-2021.

PMID- Not carried by PubMed...
VI  - 48
DP  - 1992
TI  - Bacteriophages of Streptococcus-salivarius ssp thermophilus: Characterization of hereditary relationships and determination of virus-host interaction.
PG  - 25-29
AB  - Problems due to bacteriophage infection are widespread in all dairy fermentations. Since the
      pioneering work of Whitehead and Cox, numerous studies in the past 50 years have led to a
      higher degree in the control of starter activity. However, most of the research in this area
      focussed on bacteriophages of mesophilic streptococci, which are now characterized quite well
      down to the genomic level. On the other hand very little is known about the phages of
      thermophilic streptococci. Up to now these viruses were mainly characterized on the basis of
      ultrastructure and their host range. Problems like the frequency of temperate phages and the
      risk of lysogenic strains in fermentation, as well as the spontaneous change of some host
      strains in their sensitivity to bacteriophages or phage-defense mechanisms of Streptococcus
      salivarius ssp. thermophilus are as poorly understood as the genome of the bacteriophage, but
      demand a solution in order to isolate or construct stable phage-resistant starter cultures for
      the dairy industry.
AU  - Sebastiani H
AU  - Jager H
PT  - Journal Article
TA  - Milchwissenschaft
JT  - Milchwissenschaft
SO  - Milchwissenschaft 1992 48: 25-29.

PMID- 8098386
VI  - 17D
DP  - 1993
TI  - Effect of restriction endonucleases on HIV infection.
PG  - 76
AB  - HIV RNA undergoes obligatory reverse transcription to a dsDNA form in the cytoplasm of
      infected cells. This step is critical for the establishment of infection. However, no
      treatment has yet been devised to target the dsDNA. If the dsDNA form of the virus could be
      destroyed before translocating to the nucleus and integrating into the host genome, then
      perhaps amplifiation of the virus within the organism might be prevented and disease
      progression halted. Bacterial cells possess DNA site-specific restriction-modification systems
      that provide protection from viral infections. The type II restriction endonucleases recognize
      a particular sequence in DNA and cleave the DNA in the vicinity of that sequence. We
      investigated whether the type II restriction endonucleases could modify the course of HIV
      infection in human PBL. Studies performed to date indicate that enzymes known to cleave the
      dsDNA form of the virus inhibit the development of RT activity in cultures of infected human
      PBL whereas a control enzyme which lacks a restriction site on HIV dsDNA fails to inhibit
      virus replication. The replication kinetics were delayed and the absolute RT level achieved in
      the treated cultures was reduced. Additionally, morphologic changes associated with infection,
      such as syncytia formation, were significantly delayed. Of critical importance, the
      restriction endonucleases do not appear to damage host cell DNA as shown by their failure to
      inhibit proliferation of activated human PBL in vitro. Thus, type II restriction endonucleases
      may prove useful in the study and treatment of HIV infection.
AU  - Sechler JMG
AU  - Clouse KA
AU  - Strebel K
AU  - Weih KA
AU  - Rosenberg AS
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1993 17D: 76.

PMID- 28904741
VI  - 12
DP  - 2017
TI  - Complete genome of Arthrobacter alpinus strain R3.8, bioremediation potential unraveled with genomic analysis.
PG  - 52
AB  - Arthrobacter alpinus R3.8 is a psychrotolerant bacterial strain isolated from a soil sample
      obtained at Rothera Point, Adelaide Island, close to the Antarctic
      Peninsula. Strain R3.8 was sequenced in order to help discover potential cold
      active enzymes with biotechnological applications. Genome analysis identified
      various cold adaptation genes including some coding for anti-freeze proteins and
      cold-shock proteins, genes involved in bioremediation of xenobiotic compounds
      including naphthalene, and genes with chitinolytic and N-acetylglucosamine
      utilization properties and also plant-growth-influencing properties. In this
      genome report, we present a complete genome sequence of A. alpinus strain R3.8
      and its annotation data, which will facilitate exploitation of potential novel
      cold-active enzymes.
AU  - See-Too WS
AU  - Ee R
AU  - Lim YL
AU  - Convey P
AU  - Pearce DA
AU  - Mohidin TBM
AU  - Yin WF
AU  - Chan KG
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 52.

PMID- 2227451
VI  - 94
DP  - 1990
TI  - Cloning, expression and characterization of the Sau3AI restriction and modification genes in Staphylococcus carnosus TM300.
PG  - 37-43
AB  - The genes encoding the restriction enzyme (ENase) and modification enzyme
      (MTase) of Staphylococcus aureus 3A (recognition sequence 5'-GATC-3') have been
      cloned in Staphylococcus carnosus TM300 using the vector pCA44.  Clones
      carrying both genes were isolated from DNA libraries prepared with MboI +
      BamHI.  The DNA region encoding M.Sau3AI was subcloned on a 3.66-kb EcoRV
      fragment in vector pT181mcs.  Plasmids purified from the clones were resistant
      to digestion with Sau3AI, indicating that the sau3AIM gene was expressed and
      the product was functional in S. carnosus.  Cell lysates of clones with both
      activities encoded on plasmid pSEM7, cut DNA with the same pattern as Sau3AI,
      showing that the sau3AIR gene was also expressed and the ENase was functional
      in S. carnosus.  Sequence analysis shows that both genes are transcribed in the
      same direction and encode polypeptides with calculated Mrs of 56477 for
      R.Sau3AI and 47300 for M.Sau3AI.  Efforts to clone one or both genes in
      Escherichia coli have so far failed.
AU  - Seeber S
AU  - Kessler C
AU  - Gotz F
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1990 94: 37-43.

PMID- 21304168
VI  - 2
DP  - 2011
TI  - Evidence of a Dominant Lineage of Vibrio cholerae-Specific Lytic Bacteriophages Shed by Cholera Patients over a 10-Year Period in Dhaka, Bangladesh.
PG  - e00334-10
AB  - ABSTRACT Lytic bacteriophages are hypothesized to contribute to the seasonality and duration
      of cholera epidemics in Bangladesh. However, the bacteriophages contributing to this
      phenomenon have yet to be characterized at a molecular genetic level. In this study, we
      isolated and sequenced the genomes of 15 bacteriophages from stool samples from cholera
      patients spanning a 10-year surveillance period in Dhaka, Bangladesh. Our results indicate
      that a single novel bacteriophage type, designated ICP1 (for the International Centre for
      Diarrhoeal Disease Research, Bangladesh cholera phage 1) is present in all stool samples from
      cholera patients, while two other bacteriophage types, one novel (ICP2) and one T7-like
      (ICP3), are transient. ICP1 is a member of the Myoviridae family and has a 126-kilobase genome
      comprising 230 open reading frames. Comparative sequence analysis of ICP1 and related isolates
      from this time period indicates a high level of genetic conservation. The ubiquitous presence
      of ICP1 in cholera patients and the finding that the O1 antigen of lipopolysaccharide (LPS)
      serves as the ICP1 receptor suggest that ICP1 is extremely well adapted to predation of
      human-pathogenic V. cholerae O1. IMPORTANCE The severe diarrheal disease cholera is caused by
      the bacterium Vibrio cholerae, which can be transmitted to humans from the aquatic
      environment. Factors that affect V. cholerae in the environment can impact the occurrence of
      cholera outbreaks; one of these factors is thought to be the presence of bacterial viruses, or
      bacteriophages. Bacteriophages that prey on V. cholerae in the environment, and potentially in
      humans, have not been extensively genetically characterized. Here, we isolated and sequenced
      the genomes of bacteriophages from cholera patient stool samples collected over a 10-year
      period in Dhaka, Bangladesh, a region that suffers from regular cholera outbreaks. We describe
      a unique bacteriophage present in all samples, infer its evolution by sequencing multiple
      isolates from different patients over time, and identify the host receptor that shows that the
      bacteriophage specifically predates the serogroup of V. cholerae responsible for the majority
      of disease occurrences.
AU  - Seed KD
AU  - Bodi KL
AU  - Kropinski AM
AU  - Ackermann HW
AU  - Calderwood SB
AU  - Qadri F
AU  - Camilli A
PT  - Journal Article
TA  - MBio
JT  - MBio
SO  - MBio 2011 2: e00334-10.

PMID- 16140471
VI  - 251
DP  - 2005
TI  - Isolation and characterization of bacteriophages of the Burkholderia cepacia complex.
PG  - 273-280
AB  - The Burkholderia cepacia complex consists of nine phenotypically similar
      but genotypically distinct beta-proteobacteria that are metabolically
      diverse and highly antibiotic resistant. Because of this exceptional
      intrinsic antibiotic resistance, infections with B. cepacia complex
      members are difficult to treat clinically and new alternative therapies
      are required. One strategy that holds some promise is the use of naturally
      occurring antibacterial bacteriophages that could potentially bind to and
      lyse B. cepacia complex cells in vivo. Towards that end, we used
      enrichment techniques to isolate lytic and lysogenic bacteriophages
      specific to the B. cepacia complex. The newly isolated bacteriophages were
      characterized by host range analysis, electron microscopy, genome
      restriction analysis, and partial DNA sequencing. These isolates include a
      bacteriophage with one of the broadest host ranges yet identified for any
      bacteriophage specific to the B. cepacia complex, and the first
      description of bacteriophages capable of lysing B. ambifaria.
AU  - Seed KD
AU  - Dennis JJ
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2005 251: 273-280.

PMID- 18218779
VI  - 105
DP  - 2008
TI  - The genome of Clostridium kluyveri, a strict anaerobe with unique metabolic features.
PG  - 2128-2133
AB  - Clostridium kluyveri is unique among the clostridia; it grows anaerobically on ethanol and
      acetate as sole energy sources. Fermentation products are butyrate, caproate, and H(2). We
      report here the genome sequence of C. kluyveri, which revealed new insights into the metabolic
      capabilities of this well studied organism. A membrane-bound energy-converting NADH:ferredoxin
      oxidoreductase (RnfCDGEAB) and a cytoplasmic butyryl-CoA dehydrogenase complex (Bcd/EtfAB)
      coupling the reduction of crotonyl-CoA to butyryl-CoA with the reduction of ferredoxin
      represent a new energy-conserving module in anaerobes. The genes for NAD-dependent ethanol
      dehydrogenase and NAD(P)-dependent acetaldehyde dehydrogenase are located next to genes for
      microcompartment proteins, suggesting that the two enzymes, which are isolated together in a
      macromolecular complex, form a carboxysome-like structure. Unique for a strict anaerobe, C.
      kluyveri harbors three sets of genes predicted to encode for polyketide/nonribosomal peptide
      synthetase hybrides and one set for a nonribosomal peptide synthetase. The latter is predicted
      to catalyze the synthesis of a new siderophore, which is formed under iron-deficient growth
      conditions.
AU  - Seedorf H
AU  - Fricke WF
AU  - Veith B
AU  - Bruggemann H
AU  - Liesegang H
AU  - Strittmatter A
AU  - Miethke M
AU  - Buckel W
AU  - Hinderberger J
AU  - Li F
AU  - Hagemeier C
AU  - Thauer RK
AU  - Gottschalk G
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2008 105: 2128-2133.

PMID- 10708382
VI  - 146
DP  - 2000
TI  - Molecular characterization of the lactococcal plasmid pCIS3: natural stacking of specificity subunits of a type I restriction/modification system in a single lactococcal strain.
PG  - 435-443
AB  - A 6.1 kb plasmid from the Lactococcus lactis subsp. cremoris strain UC509.9. named pCIS3, was
      found to mediate a restriction/modification
      (RIM) phenotype, Nucleotide sequence analysis of pCIS3 revealed the
      presence of an hsdS gene, typical of type I R/M systems, The presence
      of this plasmid resulted in a 10(4)-fold reduction in the efficiency of
      plating (e.o.p.) of unmodified phage. In addition to the hsdS gene of
      pCIS3, two more hsd5 genes were identified in strain UC509.9, one
      located on the chromosome downstream of a gene highly homologous to
      hsdM genes and a third on the smallest (4 kb) plasmid, named pCIS1. The
      replication region of pCIS3 was highly similar to that of a large
      family of lactococcal theta replicons, In addition, pCIS3 was found to
      encode a member of the CorA family of magnesium transporters.
AU  - Seegers JFML
AU  - van Sinderen D
AU  - Fitzgerald GF
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2000 146: 435-443.

PMID- 3008089
VI  - 14
DP  - 1986
TI  - Palindromic oligonucleotides containing 7-deaza-2'-deoxyguanosine: solid-phase synthesis of d[(p)GG*AATTCC] octamers and recognition by the endodeoxyribonuclease EcoRI.
PG  - 2319-2332
AB  - Octadeoxynucleotides with the sequence d[(p)GG*AATTCC] have been prepared by
      solid-phase synthesis employing regular and base-modified phosphoramidites.
      These oligomers which contain an isosterically altred recognition sequence of
      the endodeoxyribonuclease EcoRI form duplexes under appropriate salt
      conditions.  Since G* can represent 7-deaza-2'-deoxyguanosine the oligomers
      were used as probes to study their cleavage by the endodeoxyribonuclease EcoRI.
      The enzymatic hydrolysis of the modified octamer was strongly decreased
      compared to the regular DNA-fragment.  This shows that quanine N-7 located at
      the cleavage site is important for the recognition process by the enzyme.  The
      residual enzymatic activity is discussed on the basis of reduced specificity
      towards the recognition fragment.  The fact that this cleavage occurs already
      under regular conditions indicates that the process described here bases on an
      intrinsic property of the oligomer and is different from the star activity.
AU  - Seela F
AU  - Driller H
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1986 14: 2319-2332.

PMID- 3040084
VI  - 26
DP  - 1987
TI  - Palindromic  octa-  and  dodecanucleotides containing 2'-deoxytubercidin: synthesis,  hairpin formation, and recognition by the endodeoxyribonuclease EcoRI.
PG  - 2232-2238
AB  - Octa- and dodecanucleotides containing 2'-deoxytubericidin within the
      endodeoxyribonuclease   EcoRI  recognition  fragment  d(GAATTC)  have  been
      prepared  by  solid-phase synthesis. Whereas octamers as well as dodecamers
      with  a  "random"  flanking region formed duplexes in aqueous solution, the
      dodecamer  d(CGCGAATTCGCG)  and  isosterically  modified  oligomers thereof
      showed  a  strong tendency of hairpin formation. Due to this, cleavage with the
      endodeoxyribonuclease EcoRI was strongly decreased.  In contrast,
      d(GTAGAATTCTAC) was easily cleaved by the enzyme. Single replacement of one of
      the  dA  residues by 2'-deoxytubercidin within the recognition sequence
      decreased   the   cleavage   velocity  but  retained  specificity.  Twofold
      modification  prevents cleavage of the oligomer. This implies that both N-7
      purine  nitrogens  are  proton acceptor sites for the endodeoxyribonuclease
      EcoRI.
AU  - Seela F
AU  - Kehne A
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1987 26: 2232-2238.

PMID- 1738604
VI  - 20
DP  - 1992
TI  - 7-Deazapurine containing DNA: efficiency of c7GdTP, c7AdTP and c7IdTP incorporation during PCR-amplification and protection from endodeoxyribonuclease hydrolysis.
PG  - 55-61
AB  - The enzymatic synthesis of 7-deazapurine nucleoside containing DNA (501 bp) is performed by
      PCR-amplification (Taq polymerase) using a pUC18 plasmid DNA as template and the triphosphates
      of 7-deaza-2'-deoxyguanosine (c7Gd), -adenosine (c7Ad) and -inosine (c7Id). c7GdTP can fully
      replace dGTP resulting in a completely modified DNA-fragment of defined size and sequence. The
      other two 7-deazapurine triphosphates (c7AdTP) and (c7IdTP) require the presence of the parent
      purine 2-deoxyribonucleotides. In purine/7-deazapurine nucleotide mixtures Taq polymerase
      prefers purine over 7-deazapurine nucleotides but accepts c7GdTP much better than c7AdTP or
      c7IdTP. As incorporation of 7-deazapurine nucleotides represents a modification of the major
      groove of DNA it can be used to probe DNA/protein interaction. Regioselective phosphodiester
      hydrolysis of the modified DNA-fragments was studied with 28 endodeoxyribonucleases. c7Gd is
      able to protect the DNA from the phosphodiester hydrolysis in more than 20 cases, only a few
      enzymes (MaeIII, RsaI, HindIII, PvuII or TaqI) do still hydrolyze the modified DNA. c7Ad
      protects DNA less efficiently, as this DNA could only be modified in part. The absence of N-7
      as potential binding position or a geometric distortion of the recognition duplex caused by
      the 7-deazapurine base can account for protection of hydrolysis.
AU  - Seela F
AU  - Roling A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 55-61.

PMID- 1062791
VI  - 73
DP  - 1976
TI  - Sequence-specific recognition of double helical nucleic acids by proteins.
PG  - 804-808
AB  - The base pairs in double helical nucleic acids have been compared to see how
      they can be recognized by proteins.  We conclude that a single hydrogen bond is
      inadequate for uniquely identifying any particular base pair, as this leads to
      numerous degeneracies.  However, using two hydrogen bonds, fidelity of base
      pair recognition may be achieved.  We propose specific amino-acid side chain
      interactions involving two hydrogen bonds as a component of the recognition
      system for base pairs.  In the major groove we suggest that asparagine or
      glutamine binds to adenine of the base pair, or arginine binds to guanine.  In
      the minor groove, we suggest an interaction between asparagine or glutamine
      with guanine of the base pair.  We also discuss the role that ions and other
      amino-acid side chains may play in recognition interactions.
AU  - Seeman NC
AU  - Rosenberg JM
AU  - Rich A
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1976 73: 804-808.

PMID- 28935734
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Two Strains of a Newly Described Species, Sphingobacterium cellulitidis.
PG  - e00956-17
AB  - The draft genome sequences of two strains of a newly described species, Sphingobacterium
      cellulitidis, have been determined. The type strain originated
      from cellulitis of a toe of a patient and the other strain from the environment.
      The sequences will provide the reference genomes of the new Sphingobacterium
      species.
AU  - Seemann T
AU  - Bulach DM
AU  - Carter G
AU  - Albert MJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00956-17.

PMID- 26089408
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the First Human Isolate of the Ruminant Pathogen Mycoplasma capricolum subsp. capricolum.
PG  - e00583-15
AB  - Mycoplasma capricolum subsp. capricolum is a well-known pathogen of small ruminants. A recent
      human case of septicemia involving this agent raised the
      question of its potential pathogenicity to humans. We present the first draft
      genome sequence of a human Mycoplasma capricolum subsp. capricolum isolate.
AU  - Seersholm FV
AU  - Fischer A
AU  - Heller M
AU  - Jores J
AU  - Sachse K
AU  - Mourier T
AU  - Hansen AJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00583-15.

PMID- 23704188
VI  - 1
DP  - 2013
TI  - Genome Sequence of Pseudomonas aeruginosa PA45, a Highly Virulent Strain Isolated from a Patient with Bloodstream Infection.
PG  - e00289-13
AB  - Pseudomonas aeruginosa is a ubiquitous opportunistic pathogen causing a broad range of
      infections in humans. We provide the draft genome sequence of the
      recently identified and highly virulent P. aeruginosa PA45 strain. Its 6.6-Mb
      genome contains 6,822 genes, including an unparalleled number of virulence genes,
      which might explain its aggressive phenotype.
AU  - Segata N
AU  - Ballarini A
AU  - Jousson O
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00289-13.

PMID- 29046740
VI  - 12
DP  - 2017
TI  - Draft genome sequence and characterization of commensal Escherichia coli strain BG1 isolated from bovine gastro-intestinal tract.
PG  - 61
AB  - Escherichia coli is the most abundant facultative anaerobic bacteria in the gastro-intestinal
      tract of mammals but can be responsible for intestinal
      infection due to acquisition of virulence factors. Genomes of pathogenic E. coli
      strains are widely described whereas those of bovine commensal E. coli strains
      are very scarce. Here, we report the genome sequence, annotation, and features of
      the commensal E. coli BG1 isolated from the gastro-intestinal tract of cattle.
      Whole genome sequencing analysis showed that BG1 has a chromosome of 4,782,107 bp
      coding for 4465 proteins and 97 RNAs. E. coli BG1 belonged to the serotype
      O159:H21, was classified in the phylogroup B1 and possessed the genetic
      information encoding 'virulence factors' such as adherence systems, iron
      acquisition and flagella synthesis. A total of 12 adherence systems were detected
      reflecting the potential ability of BG1 to colonize different segments of the
      bovine gastro-intestinal tract. E. coli BG1 is unable to assimilate ethanolamine
      that confers a nutritional advantage to some pathogenic E. coli in the bovine
      gastro-intestinal tract. Genome analysis revealed the presence of i) 34 amino
      acids change due to non-synonymous SNPs among the genes encoding ethanolamine
      transport and assimilation, and ii) an additional predicted alpha helix inserted
      in cobalamin adenosyltransferase, a key enzyme required for ethanolamine
      assimilation. These modifications could explain the incapacity of BG1 to use
      ethanolamine. The BG1 genome can now be used as a reference (control strain) for
      subsequent evolution and comparative studies.
AU  - Segura A
AU  - Auffret P
AU  - Klopp C
AU  - Bertin Y
AU  - Forano E
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 61.

PMID- 25845594
VI  - 43
DP  - 2015
TI  - Specificity of the ModA11, ModA12 and ModD1 epigenetic regulator N6-adenine DNA methyltransferases of Neisseria meningitidis.
PG  - 4150-4162
AB  - Phase variation (random ON/OFF switching) of gene expression is a common feature  of
      host-adapted pathogenic bacteria. Phase variably expressed N(6)-adenine DNA
      methyltransferases (Mod) alter global methylation patterns resulting in changes
      in gene expression. These systems constitute phase variable regulons called
      phasevarions. Neisseria meningitidis phasevarions regulate genes including
      virulence factors and vaccine candidates, and alter phenotypes including
      antibiotic resistance. The target site recognized by these Type III N(6)-adenine
      DNA methyltransferases is not known. Single molecule, real-time (SMRT) methylome
      analysis was used to identify the recognition site for three key N. meningitidis
      methyltransferases: ModA11 (exemplified by M.NmeMC58I) (5'-CGY M6A: G-3'), ModA12
      (exemplified by M.Nme77I, M.Nme18I and M.Nme579II) (5'-AC M6A: CC-3') and ModD1
      (exemplified by M.Nme579I) (5'-CC M6A: GC-3'). Restriction inhibition assays and
      mutagenesis confirmed the SMRT methylome analysis. The ModA11 site is complex and
      atypical and is dependent on the type of pyrimidine at the central position, in
      combination with the bases flanking the core recognition sequence 5'-CGY M6A:
      G-3'. The observed efficiency of methylation in the modA11 strain (MC58) genome
      ranged from 4.6% at 5'-GCGC M6A: GG-3' sites, to 100% at 5'-ACGT M6A: GG-3'
      sites. Analysis of the distribution of modified sites in the respective genomes
      shows many cases of association with intergenic regions of genes with altered
      expression due to phasevarion switching.
AU  - Seib KL
AU  - Jen FE
AU  - Tan A
AU  - Scott AL
AU  - Kumar R
AU  - Power PM
AU  - Chen LT
AU  - Wu HJ
AU  - Wang AH
AU  - Hill DM
AU  - Luyten YA
AU  - Morgan RD
AU  - Roberts RJ
AU  - Maiden MC
AU  - Boitano M
AU  - Clark TA
AU  - Korlach J
AU  - Rao DN
AU  - Jennings MP
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2015 43: 4150-4162.

PMID- 11821238
VI  - 32
DP  - 2002
TI  - Phase variable restriction-modification systems in Moraxella catarrhalis.
PG  - 159-165
AB  - A repetitive DNA motif was used as a marker to identify novel genes in the mucosal pathogen
      Moraxella catarrhalis. There is a high prevalence of such repetitive motifs in virulence genes
      that display phase variable expression. Two repeat containing loci were identified using a
      digoxigenin-labelled 5'-(CAAC)(6)-3' oligonucleotide probe. The repeats are located in the
      methylase components of two distinct type III restriction-modification (R-M) systems. We
      suggest that the phase variable nature of these R-M systems indicates that they have an
      important role in the biology of M. catarrhalis.
AU  - Seib KL
AU  - Peak IR
AU  - Jennings MP
PT  - Journal Article
TA  - FEMS Immunol. Med. Microbiol.
JT  - FEMS Immunol. Med. Microbiol.
SO  - FEMS Immunol. Med. Microbiol. 2002 32: 159-165.

PMID- 21680891
VI  - 25
DP  - 2011
TI  - A novel epigenetic regulator associated with the hypervirulent Neisseria meningitidis clonal complex 41/44.
PG  - 3622-3633
AB  - Neisseria meningitidis is a major cause of septicemia and meningitis. The hypervirulent clonal
      complex 41/44 (cc41/44) has emerged as the predominant cause
      of serogroup B meningococcal disease, having been responsible for recent
      outbreaks and epidemics worldwide. However, the meningococcal factors that enable
      transition from asymptomatic carriage to rapidly progressing disease are poorly
      understood. Here we describe a novel phase-variable DNA methyltransferase, ModD,
      which was identified in the genome sequence of a New Zealand epidemic isolate.
      Investigation of the distribution of modD in the wider meningococcal population,
      by PCR and sequence analysis of genetically diverse N. meningitidis strains,
      revealed the presence of modD in 20/27 strains in cc41/44, but in only 2/47
      strains from other clonal complexes, indicating a significant association of modD
      with cc41/44 (Fisher's exact P value=3x10(-10)). The modD gene contains
      5'-ACCGA-3' repeats that mediate phase variation, leading to reversible on/off
      switching of modD expression. Microarray analysis of modD-on/off variants
      revealed that ModD regulates expression of multiple genes involved in
      colonization, infection, and protection against host defenses, with increased
      catalase expression in the modD-on variant conferring increased resistance to
      oxidative stress. The modulation of gene expression via the ModD phase-variable
      regulon (phasevarion), and its significant association with the cc41/44, suggest
      a role in the fitness and/or pathogenesis of strains belonging to the cc41/44.
AU  - Seib KL
AU  - Pigozzi E
AU  - Muzzi A
AU  - Gawthorne JA
AU  - Delany I
AU  - Jennings MP
AU  - Rappuoli R
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 2011 25: 3622-3633.

PMID- 18388857
VI  - 27
DP  - 2008
TI  - Motor step size and ATP coupling efficiency of the dsDNA translocase EcoR124I.
PG  - 1388-1398
AB  - The Type I restriction-modification enzyme EcoR124I is an archetypical helicase-based dsDNA
      translocase that moves unidirectionally along the
      30-50 strand of intact duplex DNA. Using a combination of ensemble and
      single-molecule measurements, we provide estimates of two
      physicochemical constants that are fundamental to a full description of
      motor protein activity-the ATP coupling efficiency (the number of ATP
      consumed per base pair) and the step size (the number of base pairs
      transported per motor step). Our data indicate that EcoR124I makes
      small steps along the DNA of 1 bp in length with 1 ATP consumed per
      step, but with some uncoupling of the ATPase and translocase cycles
      occurring so that the average number of ATP consumed per base pair
      slightly exceeds unity. Our observations form a framework for
      understanding energy coupling in a great many other motors that
      translocate along dsDNA rather than ssDNA.
AU  - Seidel R
AU  - Bloom JG
AU  - Dekker C
AU  - Szczelkun MD
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 2008 27: 1388-1398.

PMID- 24013420
VI  - 12
DP  - 2013
TI  - Switching roles for a helicase.
PG  - 3125-3126
AB  - Helicases are widespread enzymes that share a core RecA fold and characteristic amino acid
      motifs which together form an ATP binding/hydrolysis site.  For the classical helicases (i.e.,
      those which confirm to the family name), ATP-binding provides energy to drive the separation
      of polynucleotide duplexes into single strands.  There are also many enzymes which on the
      basis of structure and motifs appear to be helicases, but which fulfill alternative functions
      without the necessity for strand separation.  These include nucleo-protein remodeling,
      long-range motion along dsDNA and molecular signaling.  The activities and mechanisms of these
      enzymes, often termed "helicase-like" or "pseudo-helicases", are not well understood.  Recent
      studies that try to elucidate the full repertoire of helicase activity provide more and more
      surprises for their numerous roles in genome metabolism.
AU  - Seidel R
AU  - Szczelkun MD
PT  - Journal Article
TA  - Cell Cycle
JT  - Cell Cycle
SO  - Cell Cycle 2013 12: 3125-3126.

PMID- 
VI  - 86
DP  - 2004
TI  - Translocation of type I restriction endonuclease EcoR124I along DNA measured with magnetic tweezers.
PG  - 316a
AB  - Type I restriction enzymes belong to the machinery of bacteria that protects them against
      invasion by viruses. After sequence specific
      binding to viral DNA they translocate up to several thousands of bp and
      induce DNA cleavage remote from the recognition site. Using magnetic
      tweezers, we measured the translocation process of this enzyme. A
      magnetic particle is used to stretch DNA in an applied magnetic field.
      By tracking the displacement of the particle, translocation activity
      can be recorded in real time. We found that the enzyme is moving with a
      constant speed as fast as 550+30 bp/s. By varying the applied force
      the translocation velocity, the maximum translocated distance as well
      as the time between translocation events, could be measured as a
      function of the load exerted to the tethered DNA molecule.
AU  - Seidel R
AU  - van der Scheer C
AU  - van Noort J
AU  - Firman K
AU  - Dekker C
PT  - Journal Article
TA  - Biophys. J.
JT  - Biophys. J.
SO  - Biophys. J. 2004 86: 316a.

PMID- 15300241
VI  - 11
DP  - 2004
TI  - Real-time observation of DNA translocation by the type I restriction modification enzyme EcoR124I.
PG  - 838-843
AB  - Type I restriction enzymes bind sequence-specifically to unmodified DNA and subsequently pull
      the adjacent DNA toward themselves. Cleavage then
      occurs remotely from the recognition site. The mechanism by which these
      members of the superfamily 2 (SF2) of helicases translocate DNA is
      largely unknown. We report the first single-molecule study of DNA
      translocation by the type I restriction enzyme EcoR124I.
      Mechanochemical parameters such as the translocation rate and
      processivity, and their dependence on force and ATP concentration, are
      presented. We show that the two motor subunits of EcoR124I work
      independently. By using torsionally constrained DNA molecules, we found
      that the enzyme tracks along the helical pitch of the DNA molecule.
      This assay may be directly applicable to investigating the tracking of
      other DNA-translocating motors along their DNA templates.
AU  - Seidel R
AU  - van Noort J
AU  - van der Scheer C
AU  - Bloom JGP
AU  - Dekker NH
AU  - Dutta CF
AU  - Blundell A
AU  - Robinson T
AU  - Firman K
AU  - Dekker C
PT  - Journal Article
TA  - Nat. Struct. Mol. Biol.
JT  - Nat. Struct. Mol. Biol.
SO  - Nat. Struct. Mol. Biol. 2004 11: 838-843.

PMID- 21685285
VI  - 193
DP  - 2011
TI  - Draft Genome Sequence of Streptomyces Strain S4, a Symbiont of the Leaf-Cutting Ant Acromyrmex octospinosus.
PG  - 4270-4271
AB  - Streptomyces spp. are common symbionts of the leaf-cutting ant species Acromyrmex
      octospinosus, which feeds on basidiomycete fungus leaf matter
      and harvests the lipid- and carbohydrate-rich gongylidia as a food source.
      A. octospinosus and other ant genera use antifungal compounds produced by
      Streptomyces spp. and other actinomycetes in order to help defend their
      fungal gardens from parasitic fungi. Herein, we report the draft genome
      sequence of Streptomyces strain S4, an antifungal-producing symbiont of A.
      octospinosus.
AU  - Seipke RF
AU  - Crossman L
AU  - Drou N
AU  - Heavens D
AU  - Bibb MJ
AU  - Caccamo M
AU  - Hutchings MI
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4270-4271.

PMID- 
VI  - 7
DP  - 2008
TI  - A design and feasibility study of reactions comprising DNA molecular machine that walks autonomously by using a restriction enzyme.
PG  - 303-315
AB  - In this paper, we propose an autonomous molecular walking machine using DNA. This molecular
      machine follows a track of DNA equipped with many single-strand DNA stators arranged in a
      certain pattern. The molecular machine achieves autonomous walk by using a restriction enzyme
      as source of power. With a proposed machine we can control its moving direction and we can
      easily extend walking patterns in two or three dimensions. Combination of multiple legs and
      ssDNA stators can control the walking pattern. We designed and performed a series of
      feasibility study with computer simulation
      and molecular biology experiments.
AU  - Sekiguchi H
AU  - Komiya K
AU  - Kiga D
AU  - Yamamura M
PT  - Journal Article
TA  - Nat. Comput.
JT  - Nat. Comput.
SO  - Nat. Comput. 2008 7: 303-315.

PMID- 16423019
VI  - 8
DP  - 2006
TI  - Sequence analysis of three plasmids harboured in Rhodococcus erythropolis strain PR4.
PG  - 334-346
AB  - Rhodococcus erythropolis strain PR4 has been isolated as an alkane-degrading bacterium. The
      strain harbours one linear plasmid, pREL1
      (271 577 bp) and two circular plasmids, pREC1 (104 014 bp) and pREC2 (3637
      bp), all with some sequence similarities to other Rhodococcus plasmids.
      For pREL1, pREC1 and pREC2, 298, 102 and 3 open reading frames,
      respectively, were predicted. Linear plasmid pREL1 has several regions
      homologous to plasmid pBD2 found in R. erythropolis BD2. Sequence analysis
      of pREL1 and pBD2 identified common metal-resistance genes on both, but
      pREL1 also encodes alkane-degradation genes not found on pBD2, with enzyme
      constituents some of which are quite different from those of other
      organisms. The alkane hydroxylase consisted of a cytochrome P450
      monooxygenase, a 2Fe-2S ferredoxin, and a ferredoxin reductase. The
      ferredoxin reductase amino acid sequence resembles the AlkT (rubredoxin
      reductase) sequence. A zinc-containing alcohol dehydrogenase further
      oxydizes alkanols, alkane oxidation products catalysed by alkane
      hydroxylase. Of the circular plasmids, the pREC1 sequence is partially
      similar to the sequence of pREAT701, the virulence plasmid found in
      Rhodococcus equi. pREC1 has no pREAT701 virulence genes and encodes genes
      for beta-oxidation of fatty acids. Thus, joint actions of enzymes encoded
      by pREL1 and pREC1 may enable efficient mineralization of alkanes.
AU  - Sekine M
AU  - Tanikawa S
AU  - Omata S
AU  - Saito M
AU  - Fujisawa T
AU  - Tsukatani N
AU  - Tajima T
AU  - Sekigawa T
AU  - Kosugi H
AU  - Matsuo Y
AU  - Nishiko R
AU  - Imamura K
AU  - Ito M
AU  - Narita H
AU  - Tago S
AU  - Fujita N
AU  - Harayama S
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2006 8: 334-346.

PMID- 11514530
VI  - 183
DP  - 2001
TI  - Distribution of the SsuDAT1I restriction-modification system among different serotypes of Streptococcus suis.
PG  - 5436-5440
AB  - The SsuDAT1I restriction-modification (R-M) system, which contains two methyltransferases and
      two restriction endonucleases with recognition sequence 5'-GATC-3', was first found in a
      field isolate of Streptococcus suis serotype 2. Isoschizomers of the R-M system were found in
      the same locus between purH and purD in a field isolate of serotype 1/2 and the reference
      strains of serotypes 3, 7, 23, and 26 among 29 strains of different serotypes examined in this
      study. The R-M gene sequences in serotypes 1/2, 3, 7, and 23 were very similar to those of
      SsuDAT1I, whereas those in serotype 26 were less similar. These results indicate intraspecies
      recombination among them and genetic divergence through their evolution.
AU  - Sekizaki T
AU  - Osaki M
AU  - Takamatsu D
AU  - Shimoji Y
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2001 183: 5436-5440.

PMID- 11133943
VI  - 183
DP  - 2001
TI  - Evidence for horizontal transfer of SsuDAT1I restriction-modification genes to the Streptococcus suis genome.
PG  - 500-511
AB  - Different strains of Streptococcus suis serotypes 1 and 2 isolated from pigs either contained
      a restriction-modification (R-M) system or lacked it. The R-M system was an isoschizomer of
      Streptococcus pneumoniae DpnII, which recognizes the nucleotide sequence 5'-GATC-3'. The
      nucleotide sequencing of the genes encoding the R-M system in S. suis DAT1, designated
      SsuDAT1I, showed that the SsuDAT1I gene region contained two methyltransferase genes,
      designated ssuMA and ssuMB, as does the DpnII system. The deduced amino acid sequences of
      M.SsuMA and M.SsuMB showed 70 and 90% identity to M.DpnII and M.DpnA, respectively. However,
      the SsuDAT1I system contained two isoschizomeric restriction endonuclease genes, designated
      ssuRA and ssuRB. The deduced amino acid sequence of R.SsuRA was 49% identical to that of
      R.DpnII, and R.SsuRB was 72% identical to R.LlaDCHI of Lactococcus lactis subsp. cremoris
      DCH-4. The four SsuDAT1I genes overlapped and were bounded by purine biosynthetic gene
      clusters in the following gene order: purF-purM-purN-purH-ssuMA-ssuMB-ssuRA-ssuRB-purD-purE.
      The G+C content of the SsuDAT1I gene region (34.1%) was lower than that of the pur region
      (48.9%), suggesting horizontal transfer of the SsuDAT1I system. No transposable element or
      long-repeat sequence was found in the flanking regions. The SsuDAT1I genes were functional by
      themselves, as they were individually expressed in Escherichia coli. Comparison of the
      sequences between strains with and without the R-M system showed that only the region from 53
      bp upstream of ssuMA to 5 bp downstream of ssuRB was inserted in the intergenic sequence
      between purH and purD and that the insertion target site was not the recognition site of
      SsuDAT1I. No notable substitutions or insertions could be found, and the structures were
      conserved among all the strains. These results suggest that the SsuDAT1I system could have
      been integrated into the S. suis chromosome by an illegitimate recombination mechanism.
AU  - Sekizaki T
AU  - Otani Y
AU  - Osaki M
AU  - Takamatsu D
AU  - Shimoji Y
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2001 183: 500-511.

PMID- 15659665
VI  - 187
DP  - 2005
TI  - Different foreign genes incidentally integrated into the same locus of the Streptococcus suis genome.
PG  - 872-883
AB  - Some strains of Streptococcus suis possess a type II restriction-modification (RM) system,
      whose genes are thought to be
      inserted into the genome between purH and purD from a foreign source by
      illegitimate recombination. In this study, we characterized the purHD
      locus of the S. suis genomes of 28 serotype reference strains by DNA
      sequencing. Four strains contained the RM genes in the locus, as
      described before, whereas 11 strains possessed other genetic regions of
      seven classes. The genetic regions contained a single gene or multiple
      genes that were either unknown or similar to hypothetical genes of
      other bacteria. The mutually exclusive localization of the genetic
      regions with the atypical G+C contents indicated that these regions
      were also acquired from foreign sources. No transposable element or
      long-repeat sequence was found in the neighboring regions. An alignment
      of the nucleotide sequences, including the RM gene regions, suggested
      that the foreign regions were integrated by illegitimate recombination
      via short stretches of nucleotide identity. By using a thermosensitive
      suicide plasmid, the RM genes were experimentally introduced into an S.
      suis strain that did not contain any foreign genes in that locus.
      Integration of the plasmid into the S. suis genome did not occur in the
      purHD locus but occurred at various chromosomal loci, where there were
      2 to 10 bp of nucleotide identity between the chromosome and the
      plasmid. These results suggest that various foreign genes described
      here were incidentally integrated into the same locus of the S. suis
      genome.
AU  - Sekizaki T
AU  - Takamatsu D
AU  - Osaki M
AU  - Shimoji Y
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2005 187: 872-883.

PMID- 25503461
VI  - 9
DP  - 2014
TI  - Complete genome sequence and comparative genomic analysis of Mycobacterium massiliense JCM 15300 in the Mycobacterium abscessus group reveal a conserved genomic island MmGI-1 related to putative lipid metabolism.
PG  - e114848
AB  - Mycobacterium abscessus group subsp., such as M. massiliense, M. abscessus sensu stricto and
      M. bolletii, are an environmental organism found in soil, water and other ecological niches,
      and have been isolated from respiratory tract infection, skin and soft tissue infection,
      postoperative infection of cosmetic surgery. To determine the unique genetic feature of M.
      massiliense, we sequenced the complete genome of M. massiliense type strain JCM 15300
      (corresponding to CCUG 48898). Comparative genomic analysis was performed among Mycobacterium
      spp. and among M. abscessus group subspp., showing that additional sz-oxidation-related genes
      and, notably, the mammalian cell entry (mce) operon were located on a genomic island, M.
      massiliense Genomic Island 1 (MmGI-1), in M. massiliense. In addition, putative anaerobic
      respiration system-related genes and additional mycolic acid cyclopropane synthetase-related
      genes were found uniquely in M. massiliense. Japanese isolates of M. massiliense also
      frequently possess the MmGI-1 (14/44, approximately 32%) and three unique conserved regions
      (26/44; approximately 60%, 34/44; approximately 77% and 40/44; approximately 91%), as well as
      isolates of other countries (Malaysia, France, United Kingdom and United States). The
      well-conserved genomic island MmGI-1 may play an important role in high growth potential with
      additional lipid metabolism, extra factors for survival in the environment or synthesis of
      complex membrane-associated lipids. ORFs on MmGI-1 showed similarities to ORFs of
      phylogenetically distant M. avium complex (MAC), suggesting that horizontal gene transfer or
      genetic recombination events might have occurred within MmGI-1 among M. massiliense and MAC.
AU  - Sekizuka T
AU  - Kai M
AU  - Nakanaga K
AU  - Nakata N
AU  - Kazumi Y
AU  - Maeda S
AU  - Makino M
AU  - Hoshino Y
AU  - Kuroda M
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2014 9: e114848.

PMID- 28424528
VI  - 7
DP  - 2017
TI  - Elucidation of quantitative structural diversity of remarkable rearrangement regions, shufflons, in IncI2 plasmids.
PG  - 928
AB  - A multiple DNA inversion system, the shufflon, exists in incompatibility (Inc) I1 and I2
      plasmids. The shufflon generates variants of the PilV protein, a minor component of the thin
      pilus. The shufflon is one of the most difficult regions for de novo genome assembly because
      of its structural diversity even in an isolated bacterial clone. We determined complete genome
      sequences, including those of IncI2 plasmids carrying mcr-1, of three Escherichia coli strains
      using single-molecule, real-time (SMRT) sequencing and Illumina sequencing. The sequences
      assembled using only SMRT sequencing contained misassembled regions in the shufflon. A hybrid
      analysis using SMRT and Illumina sequencing resolved the misassembled region and revealed that
      the three IncI2 plasmids, excluding the shufflon region, were highly conserved. Moreover, the
      abundance ratio of whole-shufflon structures could be determined by quantitative structural
      variation analysis of the SMRT data, suggesting that a remarkable heterogeneity of
      whole-shufflon structural variations exists in IncI2 plasmids. These findings indicate that
      remarkable rearrangement regions should be validated using both long-read and short-read
      sequencing data and that the structural variation of PilV in the shufflon might be closely
      related to phenotypic heterogeneity of plasmid-mediated transconjugation involved in
      horizontal gene transfer even in bacterial clonal populations.
AU  - Sekizuka T
AU  - Kawanishi M
AU  - Ohnishi M
AU  - Shima A
AU  - Kato K
AU  - Yamashita A
AU  - Matsui M
AU  - Suzuki S
AU  - Kuroda M
PT  - Journal Article
TA  - Sci. Rep.
JT  - Sci. Rep.
SO  - Sci. Rep. 2017 7: 928.

PMID- 25059867
VI  - 2
DP  - 2014
TI  - Whole-Genome Sequence of CMY-2 beta-Lactamase-Producing Salmonella enterica Serovar Typhimurium Strain L-3553.
PG  - e00711-14
AB  - Salmonella enterica serovar Typhimurium pulsed-field gel electrophoresis cluster  VII has been
      isolated from cattle populations in Japan since the mid-2000s. Some
      cluster VII isolates exhibited extended-spectrum cephalosporin resistance defined
      by the blaCMY-2 gene located in a chromosomal genomic island, GI-VII-6. We
      determined the whole-genome sequence of strain L-3553 as the reference strain.
AU  - Sekizuka T
AU  - Lee K
AU  - Kuroda M
AU  - Kusumoto M
AU  - Iwata T
AU  - Uchida I
AU  - Tanaka K
AU  - Tamamura Y
AU  - Akiba M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00711-14.

PMID- 21966500
VI  - 6
DP  - 2011
TI  - Complete sequencing of the blaNDM-1-positive IncA/C plasmid from Escherichia coli ST38 isolate suggests a possible origin from plant pathogens.
PG  - e25334
AB  - The complete sequence of the plasmid pNDM-1_Dok01 carrying New Delhi metallo-b-lactamase
      (NDM-1) was determined
      by whole genome shotgun sequencing using Escherichia coli strain NDM-1_Dok01 (multilocus
      sequence typing type: ST38)
      and the transconjugant E. coli DH10B. The plasmid is an IncA/C incompatibility type composed
      of 225 predicted coding
      sequences in 195.5 kb and partially shares a sequence with blaCMY-2-positive IncA/C plasmids
      such as E. coli AR060302
      pAR060302 (166.5 kb) and Salmonella enterica serovar Newport pSN254 (176.4 kb). The blaNDM-1
      gene in pNDM-1_Dok01 is
      terminally flanked by two IS903 elements that are distinct from those of the other
      characterized NDM-1 plasmids,
      suggesting that the blaNDM-1 gene has been broadly transposed, together with various mobile
      elements, as a cassette gene.
      The chaperonin groES and groEL genes were identified in the blaNDM-1-related composite
      transposon, and phylogenetic
      analysis and guanine-cytosine content (GC) percentage showed similarities to the homologs of
      plant pathogens such as
      Pseudoxanthomonas and Xanthomonas spp., implying that plant pathogens are the potential source
      of the blaNDM-1 gene.
      The complete sequence of pNDM-1_Dok01 suggests that the blaNDM-1 gene was acquired by a novel
      composite transposon
      on an extensively disseminated IncA/C plasmid and transferred to the E. coli ST38 isolate.
AU  - Sekizuka T
AU  - Matsui M
AU  - Yamane K
AU  - Takeuchi F
AU  - Ohnishi M
AU  - Hishinuma A
AU  - Arakawa Y
AU  - Kuroda M
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2011 6: e25334.

PMID- 22583953
VI  - 12
DP  - 2012
TI  - Corynebacterium ulcerans 0102 carries the gene encoding diphtheria toxin on a prophage different from the C. diphtheriae NCTC 13129 prophage.
PG  - 72
AB  - ABSTRACT: BACKGROUND: Corynebacterium ulcerans can cause a diphtheria-like
      illness, especially when the bacterium is lysogenized with a tox gene-carrying
      bacteriophage that produces diphtheria toxin. Acquisition of toxigenicity upon
      phage lysogenization is a common feature of C. ulcerans and C. diphtheriae.
      However, because of a lack of C. ulcerans genome information, a detailed
      comparison of prophages has not been possible between these two clinically
      important and closely related bacterial species. RESULTS: We determined the whole
      genome sequence of the toxigenic C. ulcerans 0102 isolated in Japan.The genomic
      sequence showed a striking similarity with that of Corynebacterium
      pseudotuberculosis and, to a lesser extent, with that of C. diphtheriae. The 0102
      genome contained three distinct prophages. One of these, PhiCULC0102-I, was a
      tox-positive prophage containing genes in the same structural order as for
      tox-positive C. diphtheriae prophages. However, the primary structures of the
      individual genes involved in the phage machinery showed little homology between
      the two counterparts. CONCLUSION: Taken together, these results suggest that the
      tox-positive prophage in this strain of C. ulcerans has a distinct origin from
      that of C. diphtheriae NCTC 13129.
AU  - Sekizuka T
AU  - Yamamoto A
AU  - Komiya T
AU  - Kenri T
AU  - Takeuchi F
AU  - Shibayama K
AU  - Takahashi M
AU  - Kuroda M
AU  - Iwaki M
PT  - Journal Article
TA  - BMC Microbiol.
JT  - BMC Microbiol.
SO  - BMC Microbiol. 2012 12: 72.

PMID- 1741276
VI  - 20
DP  - 1992
TI  - Purification and properties of the MboII, a class-IIS restriction endonuclease.
PG  - 433-438
AB  - After five purification steps a homogeneous preparation of endonuclease MboII was obtained,
      and several properties of the enzyme were determined. MboII is a monomer, with Mr under native
      and denaturing conditions being 47 - 49,000 Da. Endonuclease MboII is a basic protein (pl 8.3)
      which remains active when Mg2+ is replaced by Mn2+, Co2+, Ca2+, or Fe2+. MboII exhibits a star
      activity in the presence of some of the following reagents or ions: DMSO, glycerol, ethanol
      (and Co2+ or Mn2+ at pH 6). MboII does not bend DNA and is heat sensitive, losing activity
      after 15 min at 50C.
AU  - Sektas M
AU  - Kaczorowski T
AU  - Podhajska AJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 433-438.

PMID- 7607488
VI  - 157
DP  - 1995
TI  - Interaction of the MboII restriction endonuclease with DNA.
PG  - 181-185
AB  - The binding of the MboII restriction endonuclease (R.MboII; ENase) to DNA containing its
      recognition site was investigated using a mobility shift assay.  R.MboII forms specific,
      stable and immunodetectable complexes with its canonical target sequence.  The association
      constant (a) of R.MboII was calculated to be 2.89 x 10/9M, and is about 10/4-fold higher than
      the Ka value for non-specific binding.  Based on results obtained after sedimentation of the
      R.MboII-DNA complex in a glycerol gradient and measurement of the retardation of the complexes
      in polyacrylamide gels, we conclude that specific binding to the canonical sequence involves
      a monomer of R.MboII.  DNase I footprinting has shown that the enzyme covers 16 nucleotides of
      DNA on the 5'-GAAGA-3' strand.
AU  - Sektas M
AU  - Kaczorowski T
AU  - Podhajska AJ
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 181-185.

PMID- 19033196
VI  - 105
DP  - 2008
TI  - The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome.
PG  - 18964-18969
AB  - Following birth, the breast-fed infant gastrointestinal tract is rapidly colonized by a
      microbial consortium often dominated by bifidobacteria.
      Accordingly, the complete genome sequence of Bifidobacterium longum subsp.
      infantis ATCC15697 reflects a competitive nutrient-utilization strategy
      targeting milk-borne molecules which lack a nutritive value to the
      neonate. Several chromosomal loci reflect potential adaptation to the
      infant host including a 43 kbp cluster encoding catabolic genes,
      extracellular solute binding proteins and permeases predicted to be active
      on milk oligosaccharides. An examination of in vivo metabolism has
      detected the hallmarks of milk oligosaccharide utilization via the central
      fermentative pathway using metabolomic and proteomic approaches. Finally,
      conservation of gene clusters in multiple isolates corroborates the
      genomic mechanism underlying milk utilization for this infant-associated
      phylotype.
AU  - Sela DA
AU  - Chapman J
AU  - Adeuya A
AU  - Kim JH
AU  - Chen F
AU  - Whitehead TR
AU  - Lapidus A
AU  - Rokhsar DS
AU  - Lebrilla CB
AU  - German JB
AU  - Price NP
AU  - Richardson PM
AU  - Mills DA
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2008 105: 18964-18969.

PMID- Not included in PubMed...
VI  - 376
DP  - 1995
TI  - Altering the substrate specificity of the restriction endonuclease EcoRV.
PG  - S152
AB  - The type II restriction endonuclease EcoRV recognizes and cleaves the DNA sequence GAT/ATC. By
      simultaneous exchange of several amino acids of the DNA recognition loop we want to generate
      mutant enzymes that no longer cleave the cognate site but related ones, preferably those for
      which at present no restriction enzyme is described or even commercially available. In our
      approach, a large pool of EcoRV-mutants is generated by random mutagenesis and after an in
      vivo selection, mutants with the desired specificity are selected.  At present, the work
      concentrates on establishing a suitable screening system: a catalytically inactive EcoRV
      mutant is used as a repressor for a toxic gene product, i.e. the restriction endonuclease
      EcoRI.  Cells expressing EcoRI that are not protected by the corresponding methyltransferase
      have a probability for survival that is 1:10^6.  An exchange of the operator sequence upstream
      of the toxic gene, i.e. from GATATC to TATATA, should allow for a positive screening for
      EcoRV-mutants that bind to the new sequence and thereby repress the expression of the toxic
      gene.  In a subsequent step, the catalytic activity of the EcoRV mutant has to be restored by
      site-directed mutagenesis.  Alternatively, we try to identify EcoRV mutants with altered
      specificity directly.  For this purpose, an E. coli strain is used that induces the lac operon
      upon DNA damage.  After UV irradiation or expression of a restriction enzyme in the absence of
      the corresponding methylase, these cells grow to blue colonies on X-Gal agar plates. If the
      cells are protected against cleavage at GATATC sites by the EcoRV methylase, the colonies are
      white.  In contrast, EcoRV mutants with an altered specificity can cleave DNA in vivo even in
      the presence of the methylase, and cells expressing such a variant will give blue colonies on
      X-Gal agar.
AU  - Selent U
AU  - Pingoud A
PT  - Journal Article
TA  - Biol. Chem. Hoppe Seyler
JT  - Biol. Chem. Hoppe Seyler
SO  - Biol. Chem. Hoppe Seyler 1995 376: S152.

PMID- 1591242
VI  - 31
DP  - 1992
TI  - A site-directed mutagenesis study to identify amino acid residues involved in the catalytic function of the restriction endonuclease EcoRV.
PG  - 4808-4815
AB  - We have used site-directed mutagenesis of the EcoRV restriction endonuclease to change amino
      acid side chains that have been shown crystallographically to be in close proximity to the
      scissile phosphodiester bond of the DNA substrate. DNA cleavage assays of the resulting mutant
      proteins indicate that the larges effects on nucleolytic activity result from substitution of
      Asp74, Asp90, and Lys92. We suggest on the basis of structural information, mutagenesis data,
      and analogies with other nucleases that Asp74 and Asp90 might be involved in Mg2+ binding
      and/or catalysis and that Lys92 probably stabilizes the pentacovalent phosphorus in the
      transition state. These amino acids are part of a sequence motif, Pro-Asp...Asp/Glu-X-Lys,
      which is also present in EcoRI. In both enzymes, it is located in a structurally similar
      context near the scissile phosphodiester bond. A preliminary mutational analysis with EcoRI
      indicates that this sequence motif is of similar functional importance for EcoRI and EcoRV. On
      the basis of these results, a proposal is made for the mechanism of DNA cleavage by EcoRV and
      EcoRI.
AU  - Selent U
AU  - Ruter T
AU  - Kohler E
AU  - Liedtke M
AU  - Thielking V
AU  - Alves J
AU  - Oelgeschlager T
AU  - Wolfes H
AU  - Peters F
AU  - Pingoud A
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1992 31: 4808-4815.

PMID- 12202772
VI  - 30
DP  - 2002
TI  - Mutations altering the cleavage specificity of a homing endonuclease.
PG  - 3870-3879
AB  - The homing endonuclease I-CreI recognizes and cleaves a particular 22 bp DNA sequence. The
      crystal structure of I-CreI bound to homing site DNA has previously been determined, leading
      to a number of predictions about specific protein-DNA contacts. We test these predictions by
      analyzing a set of endonuclease mutants and a complementary set of homing site mutants. We
      find evidence that all structurally predicted I-CreI/DNA contacts contribute to DNA
      recognition and show that these contacts differ greatly in terms of their relative importance.
      We also describe the isolation of a collection of altered specificity I-CreI derivatives. The
      in vitro DNA-binding and cleavage properties of two such endonucleases demonstrate that our
      genetic approach is effective in identifying homing endonucleases that recognize and cleave
      novel target sequences.
AU  - Seligman LM
AU  - Chisholm KM
AU  - Chevalier BS
AU  - Chadsey MS
AU  - Edwards ST
AU  - Savage JH
AU  - Veillet AL
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2002 30: 3870-3879.

PMID- 2977770
VI  - 74
DP  - 1988
TI  - DNA methylation and control of genome organization in Neurospora crassa.
PG  - 109-111
AB  - Why are 5S rRNA genes dispersed in the genome of Neurospora, instead of tandemly arranged as
      in most organisms? A likely answer to this question came from studying an exceptional pair of
      adjacent Neurospora 5S genes, or pseudogenes, designated zeta and eta. The zeta-eta region
      consists of a diverged direct tandem duplication of a 0.8-kb segment including a 5S rRNA gene.
      Sequence comparisons of the zeta and eta 5S rRNA regions with each other and with other 5S
      regions suggested that the approx. 15% divergence between the zeta and eta 'duplicate'
      segments resulted exclusively from CG to TA mutations. Unlike other 5S rRNA regions examined,
      the zeta-eta region is heavily methylated. Thus it seemed likely that these transition
      mutations arose by deamination of mC residues. In the course of exploring the basis for the
      extraordinarily heavy methylation in the zeta-eta region, we discovered a novel genetic
      process that accounts for the methylation and provides a probable explanation for why 5S rRNA
      genes are generally dispersed in Neurospora.
AU  - Selker EU
AU  - Cambareri EB
AU  - Garrett PW
AU  - Haack KR
AU  - Jensen BC
AU  - Shabtach E
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 109-111.

PMID- 12189210
VI  - 99
DP  - 2002
TI  - Induction and maintenance of nonsymmetrical DNA methylation in Neurospora.
PG  - 16485-16490
AB  - One can imagine a variety of mechanisms that should result in self-perpetuating biological
      states. It is generally assumed that cytosine methylation is propagated in eukaryotes by
      enzymes that specifically methylate hemimethylated symmetrical sites (e.g., (5')CpG/GpC(5')
      or (5')CpNpG/GpNpC(5')). Although there is wide support for this model, we and others have
      found examples of methylation that must be propagated by a different mechanism. Most
      methylated regions of the Neurospora genome that have been examined are products of
      repeat-induced point mutation, a premeiotic genome defense system that litters duplicated
      sequences with C.G to T.A mutations and typically leaves them methylated at remaining
      cytosines. In general, such relics of repeat-induced point mutation are capable of triggering
      methylation de novo. Nevertheless, some reflect a mechanism that can propagate heterogeneous
      methylation at nonsymmetrical sites. We propose that de novo and maintenance methylation are
      manifestations of a single mechanism in Neurospora, catalyzed by the DIM-2 DNA
      methyltransferase. The action of DIM-2 is controlled by the DIM-5 histone H3 Lys-9
      methyltransferase, which in turn is influenced by other modifications of histone H3. DNA
      methylation indirectly recruits histone deacetylases, providing the framework of a
      self-reinforcing system that could result in propagation of DNA methylation and the associated
      silenced chromatin state.
AU  - Selker EU
AU  - Freitag M
AU  - Kothe GO
AU  - Margolin BS
AU  - Rountree MR
AU  - Allis CD
AU  - Tamaru H
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2002 99: 16485-16490.

PMID- 8259516
VI  - 262
DP  - 1993
TI  - Dense nonsymmetrical DNA methylation resulting from repeat-induced point mutation in Neurospora.
PG  - 1724-1728
AB  - Cytosine methylation has been implicated in epigenetic control of gene expression in animals,
      plants and fungi. It has been assumed that all methylation in eukaryotes is at symmetrical
      sequences such as CpG/GpC, because this can explain perpetuation of methylation states. Here
      the bisulfite genomic sequencing method was used to examine methylation in DNA from a
      Neurospora gene exposed to repeat-induced point mutation. 5-Methylcytosine was not limited to
      symmetrical sites and individual molecules showed different patterns and amounts of
      modification. The methylation extended beyond the mutated region and even beyond the edge of
      the duplicated segment.
AU  - Selker EU
AU  - Fritz DY
AU  - Singer MJ
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1993 262: 1724-1728.

PMID- 12712205
VI  - 422
DP  - 2003
TI  - The methylated component of the Neurospora crassa genome.
PG  - 893-897
AB  - Cytosine methylation is common, but not ubiquitous, in eukaryotes. Mammals and the fungus
      Neurospora crassa have about 2-3% of cytosines methylated.
      In mammals, methylation is almost exclusively in the under-represented CpG
      dinucleotides, and most CpGs are methylated whereas in Neurospora,
      methylation is not preferentially in CpG dinucleotides and the bulk of the
      genome is unmethylated. DNA methylation is essential in mammals but is
      dispensable in Neurospora, making this simple eukaryote a favoured
      organism in which to study methylation. Recent studies indicate that DNA
      methylation in Neurospora depends on one DNA methyltransferase, DIM-2
      (ref. 6), directed by a histone H3 methyltransferase, DIM-5 (ref. 7), but
      little is known about its cellular and evolutionary functions. As only
      four methylated sequences have been reported previously in N. crassa, we
      used methyl-binding-domain agarose chromatography to isolate the
      methylated component of the genome. DNA sequence analysis shows that the
      methylated component of the genome consists almost exclusively of relics
      of transposons that were subject to repeat-induced point mutation--a
      genome defence system that mutates duplicated sequences.
AU  - Selker EU
AU  - Tountas NA
AU  - Cross SH
AU  - Margolin BS
AU  - Murphy JG
AU  - Bird AP
AU  - Freitag M
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2003 422: 893-897.

PMID- 9159929
VI  - 14
DP  - 1997
TI  - Intron open reading frames as mobile elements and evolution of a group I intron.
PG  - 518-526
AB  - Group I introns are proposed to have become mobile following the acquisition of open reading
      frames (ORFs) that encode highly specific DNA endonucleases. This proposal implies that intron
      ORFs could behave as autonomously mobile entities. This was supported by abundant
      circumstantial evidence but no experiment of ORF transfer from an ORF-containing intron to its
      ORF-less counterpart has been described. In this paper we present such experiments, which
      demonstrate the efficient mobility of the mitochondrial nad1-i4-orf1 between two Podospora
      strains. The homing of this mobile ORF was accompanied by a bidirectional co-conversion that
      did not systematically involve the whole intron sequence. Orf1 acquisition would be the most
      recent step in the evolution of the nad1-i4 intron, which has resulted in many strains of
      Podospora having an intron with two ORFs (biorfic) and four splicing pathways. We show that
      two of the splicing events that operate in this biorfic intron, as evidenced by PCR
      experiments, are generated by a 5'-alternative splice site, which is most probably a remnant
      of the monoorfic ancestral form of the intron. We propose a sequential evolution model that is
      consistent with the four organizations of the corresponding nad1 locus that we found among
      various species of the Pyrenomycete family; these organizations consist of no intron, an
      intron alone, a monoorfic intron, and a biorfic intron.
AU  - Sellem CH
AU  - Belcour L
PT  - Journal Article
TA  - Mol. Biol. Evol.
JT  - Mol. Biol. Evol.
SO  - Mol. Biol. Evol. 1997 14: 518-526.

PMID- 1594457
VI  - 20
DP  - 1992
TI  - Bsp423I, a novel isoschizomer of BbvI from Bacillus recognizing 5'-GCAGC-3'.
PG  - 2377
AB  - We have isolated Bsp423I, a novel class-II restriction endonuclease from Bacillus species
      recognizing the palindromic sequence 5'-GCAGC-3' generating 5'-protruding tetranucleotides
      within the sequence complementary to 5'-GCAGC(N)8-3'. With respect to its isoschizomer BbvI
      it can be isolated in higher purity and stability. From the mapping and sequencing data the
      specificity of Bsp423I is concluded as: 5'-GCAGC(N)8/-3' 3'-CGTCG(N)12/-5'.
AU  - Sellmann E
AU  - Knoblich I-M
AU  - Kaluza K
AU  - Frey B
AU  - Schmitz GG
AU  - Westermann P
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 2377.

PMID- Not included in PubMed...
VI  - 64
DP  - 1993
TI  - Studies on DNA modification in Oscillatoria sp. MKU 178.
PG  - 49-50
AB  - Cyanobacterial DNA are generally believed to be resistant to restriction by endonucleases due
      to extensive modification of the DNA. We report here the absence of a dam-mediated
      modification in a cyanobacterium, Oscillatoria sp. MKU 178.
AU  - Selvakumar KS
AU  - Shanmugasundaram S
PT  - Journal Article
TA  - Curr. Sci.
JT  - Curr. Sci.
SO  - Curr. Sci. 1993 64: 49-50.

PMID- 12367517
VI  - 322
DP  - 2002
TI  - Specificity of Protein-DNA Recognition Revealed by Structure-based Potentials: Symmetric/Asymmetric and Cognate/Non-cognate Binding.
PG  - 907
AB  - Asymmetric binding of protein homodimers to DNA, which has been observed in a number of
      protein-DNA complexes, leads to subtle structural differences between the two subunits. Such
      structural differences are frequently observed when the subunits form cognate and non-cognate
      protein-DNA complexes, respectively. Analysis of these structural effects on binding
      specificity should provide insight into the mechanism of protein-DNA recognition. We
      previously derived empirical potential functions for specific nucleotide base-amino acid
      interactions from statistical analyses of the structures of many protein-DNA complexes and
      used a combinatorial threading procedure to evaluate the fitness of the DNA sequences
      involved. We then introduced Z-scores to measure the specificity with which proteins bind to
      DNA within complexes, as compared to random DNA sequences. Here, we examined in detail the
      structural effects of asymmetric and cognate/non-cognate binding on specificity. Marked
      differences in the specificity of DNA binding were observed for the two subunits of lambda
      repressor, the glucocorticoid receptor, and for transcription factors containing a Zn(2)Cys(6)
      binuclear cluster domain, which are known to bind asymmetrically to DNA. Moreover, the
      differences in the specificity with which BamHI and EcoRV endonucleases bind to their cognate
      and non-cognate DNA sequences were clearly detected using this approach; indeed, analysis of
      EcoRV binding enabled us to show the cooperative effect of sequence and structure on binding
      specificity. The present results demonstrate the utility of this approach when examining the
      structure-specificity relationship in protein-DNA recognition, as subtle structural
      differences in symmetric/asymmetric and cognate/non-cognate binding were clearly shown to
      cause marked differences in specificity. This method can also be used as a tool for checking
      new structures of protein-DNA complexes for their specificity.
AU  - Selvaraj S
AU  - Kono H
AU  - Sarai A
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2002 322: 907.

PMID- 16332697
VI  - 33
DP  - 2005
TI  - Transcription regulation of the EcoRV restriction-modification system.
PG  - 6942-6951
AB  - When a plasmid containing restriction-modification (R-M) genes enters a naive host, unmodified
      host DNA can be destroyed by restriction endonuclease. Therefore, expression of R-M genes must
      be regulated to ensure that enough methyltransferase is produced and that host DNA is
      methylated before the endonuclease synthesis begins. In several R-M systems, specialized
      Control (C) proteins coordinate expression of the R and the M genes. C proteins bind to DNA
      sequences called C-boxes and activate expression of their cognate R genes and inhibit the M
      gene expression, however the mechanisms remain undefined. Here, we studied the regulation of
      gene expression in the C protein-dependent EcoRV system. We map the divergent EcoRV M and R
      gene promoters and we define the site of C protein-binding that is sufficient for activation
      of the EcoRV R transcription.
AU  - Semenova E
AU  - Minakhin L
AU  - Bogdanova E
AU  - Nagornykh M
AU  - Vasilov A
AU  - Heyduk T
AU  - Solonin A
AU  - Zakharova M
AU  - Severinov K
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2005 33: 6942-6951.

PMID- 23908298
VI  - 1
DP  - 2013
TI  - Genome Sequence of Porcine Escherichia coli Strain IMT8073, an Atypical Enteropathogenic E. coli Strain Isolated from a Piglet with Diarrhea.
PG  - e00573-13
AB  - Escherichia coli is a highly diverse bacterial species, with atypical enteropathogenic E. coli
      (aEPEC) causing intestinal disease in both human and
      animal hosts. Here, we report the first complete genome sequence of an aEPEC
      strain of sequence type ST794 and serotype Ont:H7, isolated from a diseased
      piglet.
AU  - Semmler T
AU  - Eichhorn I
AU  - Bethe A
AU  - Bauerfeind R
AU  - Pickard D
AU  - Kingsley RA
AU  - Dougan G
AU  - Wieler LH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00573-13.

PMID- 23516220
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Frankia sp. Strain QA3, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodule of Alnus nitida.
PG  - e0010313
AB  - Members of the actinomycete genus Frankia form a nitrogen-fixing symbiosis with 8 different
      families of actinorhizal plants. We report a high-quality draft genome
      sequence for Frankia sp. strain QA3, a nitrogen-fixing actinobacterium isolated
      from root nodules of Alnus nitida.
AU  - Sen A et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0010313.

PMID- 22936717
VI  - 30
DP  - 2012
TI  - Inferring the Evolutionary History of IncP-1 Plasmids Despite Incongruence among Backbone Gene Trees.
PG  - 154-166
AB  - Plasmids of the incompatibility group IncP-1 can transfer and replicate in many
      genera of the Proteobacteria. They are composed of backbone genes that encode a
      variety of essential functions as well as accessory genes that have implications
      for human health and environmental remediation. While it is well understood that
      the accessory genes are transferred horizontally between plasmids, recent studies
      have also provided examples of recombination in the backbone genes of IncP-1
      plasmids. As a consequence, phylogeny estimation based on backbone genes is
      expected to produce conflicting gene tree topologies. The main goal of this study
      was therefore to infer the evolutionary history of IncP-1 plasmids in the
      presence of both vertical and horizontal gene transfer. This was achieved by
      quantifying the incongruence among gene trees and attributing it to known causes
      such as, a) phylogenetic uncertainty, b) coalescent stochasticity, and c)
      horizontal inheritance. Topologies of gene trees exhibited more incongruence than
      could be attributed to phylogenetic uncertainty alone. Species-tree estimation
      using a Bayesian framework that takes coalescent stochasticity into account was
      well supported, but it differed slightly from the maximum likelihood tree
      estimated by concatenation of backbone genes. After removal of the gene that
      demonstrated a signal of intergroup recombination, the concatenated tree was
      congruent with the species-tree estimate, which itself was robust to
      inclusion/exclusion of the recombinant gene. Thus, in spite of horizontal gene
      exchange both within and among IncP-1 subgroups, the backbone genome of these
      IncP-1 plasmids retains a detectable vertical evolutionary history.
AU  - Sen D
AU  - Brown CJ
AU  - Top EM
AU  - Sullivan J
PT  - Journal Article
TA  - Mol. Biol. Evol.
JT  - Mol. Biol. Evol.
SO  - Mol. Biol. Evol. 2012 30: 154-166.

PMID- 25744984
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Terrestrial Cyanobacterium Scytonema millei VB511283, Isolated from Eastern India.
PG  - e00009-15
AB  - We report here the draft genome sequence of Scytonema millei VB511283, a cyanobacterium
      isolated from biofilms on the exterior of stone monuments in
      Santiniketan, eastern India. The draft genome is 11,627,246 bp long (11.63 Mb),
      with 118 scaffolds. About 9,011 protein-coding genes, 117 tRNAs, and 12 rRNAs are
      predicted from this assembly.
AU  - Sen D
AU  - Chandrababunaidu MM
AU  - Singh D
AU  - Sanghi N
AU  - Ghorai A
AU  - Mishra GP
AU  - Madduluri M
AU  - Adhikary SP
AU  - Tripathy S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00009-15.

PMID- 21948829
VI  - 77
DP  - 2011
TI  - Broad-Host-Range Plasmids from Agricultural Soils Have IncP-1 Backbones with Diverse Accessory Genes.
PG  - 7975-7983
AB  - Broad-host-range plasmids are known to spread genes between distinct phylogenetic
      groups of bacteria. These genes often code for resistances to antibiotics and
      heavy metals or degradation of pollutants. Although some broad-host-range
      plasmids have been extensively studied, their evolutionary history and genetic
      diversity remain largely unknown. The goal of this study was to analyze and
      compare the genomes of 12 broad-host-range plasmids that were previously isolated
      from Norwegian soils by exogenous plasmid isolation and that encode mercury
      resistance. Complete nucleotide sequencing followed by phylogenetic analyses
      based on the relaxase gene traI showed that all the plasmids belong to one of two
      subgroups (beta and epsilon) of the well-studied incompatibility group IncP-1. A
      diverse array of accessory genes was found to be involved in resistance to
      antimicrobials (streptomycin, spectinomycin, and sulfonamides), degradation of
      herbicides (2,4-dichlorophenoxyacetic acid and 2,4-dichlorophenoxypropionic
      acid), and a putative new catabolic pathway. Intramolecular transposition of
      insertion sequences followed by deletion was found to contribute to the diversity
      of some of these plasmids. The previous observation that the insertion sites of a
      Tn501-related element are identical in four IncP-1beta plasmids (pJP4, pB10,
      R906, and R772) was further extended to three more IncP-1beta plasmids (pAKD15,
      pAKD18, and pAKD29). We proposed a hypothesis for the evolution of these
      Tn501-bearing IncP-1beta plasmids that predicts recent diversification followed
      by worldwide spread. Our study increases the available collection of complete
      IncP-1 plasmid genome sequences by 50% and will aid future studies to enhance our
      understanding of the evolution and function of this important plasmid family.
AU  - Sen D
AU  - Van der Auwera GA
AU  - Rogers LM
AU  - Thomas CM
AU  - Brown CJ
AU  - Top EM
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2011 77: 7975-7983.

PMID- 10512804
VI  - 77
DP  - 1999
TI  - Free energy calculations and molecular dynamics simulations of wild-type and variants of the DNA-EcoRI complex.
PG  - 1801-1810
AB  - Molecular dynamics simulations and free energy calculations of the wild-type EcoRI-DNA complex
      and several variants have been performed in aqueous solvent. In general, the theoretical
      estimations of the free energy differences (DeltaDeltaA) qualitatively agree well with the
      corresponding experimental data. The modifications which were experimentally found unfavorable
      compared to the wild-type complex were also found to be so in theoretical estimates. The
      mutant where the amino group of the base Ade(6) was replaced by a hydrogen atom eliminating
      one H-bond between the DNA and the protein, was experimentally found to be more stable than
      the wild-type complex. It was speculated that the modification also caused a structural
      relaxation in the DNA making DeltaDeltaA favorable. Our theoretical estimate yields a positive
      DeltaDeltaA in this case, but the difference is small, and no significant local structural
      relaxation was observed. The major H-bonds between the DNA and the protein in the wild-type
      complex are found to be maintained in the different mutants although the specific and
      non-specific interaction energies between the interacting the DNA bases and the protein
      residues are different in different mutants. The interaction pattern of the other nearby
      nucleotides are significantly influenced by each modification. Thus, the alteration of the
      non-specific interactions may also play an indirect role in determining the specificity of the
      complex. The interaction of the Gua(4) of the DNA with the protein is found to be most
      sensitive to any alteration in the recognition site. Because Gua(4) is the nucleotide closest
      to the scissile bond, this extra sensitivity seems to play an important role in altering the
      functional activity of the complex.
AU  - Sen S
AU  - Nilsson L
PT  - Journal Article
TA  - Biophys. J.
JT  - Biophys. J.
SO  - Biophys. J. 1999 77: 1801-1810.

PMID- 10512803
VI  - 77
DP  - 1999
TI  - Structure, interaction, dynamics and solvent effects on the DNA-EcoRI complex in aqueous solution from molecular dynamics simulation.
PG  - 1782-1800
AB  - A 0.7-ns molecular dynamics simulation of the DNA-EcoRI complex in a 7.0-A solvent shell
      indicated a stable behavior of the system. No significant evaporation or smearing of the
      solvent's outer boundary occurred. The structure and the intermolecular interactions were
      found to be well maintained during the simulation. The interaction pattern in the simulation
      was found to be very similar to that in the crystal structure. Most of the specific
      interactions between the DNA and the protein were found to be enhanced in the simulation
      compared to that in the crystal structure as a result of improved interaction geometry. The
      nonspecific interactions were found to be stronger than the specific ones. The specific
      interactions between the N7 atoms of Gua(4) or Ade(5) or Ade(6) and the protein were found to
      be present over almost the entire time of the simulation, whereas hydrogen bonds involving the
      amino groups of the Ade(5) and Ade(6) with the protein were found to be relatively weaker,
      with lower probability and shorter lifetime. The time evolution of the root mean square
      deviations of the DNA and the protein were highly correlated even at the later part of the
      simulation, showing the tight binding between them. Several long-lived water bridges were
      found between the DNA backbone atoms and the protein and also between the two protein
      monomers, which increased the overall stability of the complex. The two protein monomers were
      found to interact strongly with each other. The energy of the DNA kink deformation was
      estimated as approximately 31 kcal/mol.
AU  - Sen S
AU  - Nilsson L
PT  - Journal Article
TA  - Biophys. J.
JT  - Biophys. J.
SO  - Biophys. J. 1999 77: 1782-1800.

PMID- 27660791
VI  - 4
DP  - 2016
TI  - Genome Sequence of the Arsenic-Resistant Haladaptatus sp. Strain R4 Isolated from Ramnagar, West Bengal, India.
PG  - e01017-16
AB  - Here, we present the draft genome of Haladaptatus sp. strain R4, a halophilic archaea that
      produces an orange-pink pigment and is capable of growing in a wide
      salinity range. The genome assembly shows genes for arsenic resistance,
      siderophore production, trehalose and glycine betaine biosynthesis, uptake and
      transporters of sodium, potassium, and chloride ions.
AU  - Sen U
AU  - Mukherjee T
AU  - Bose S
AU  - Roy C
AU  - Rameez MJ
AU  - Ghosh W
AU  - Mukhopadhyay SK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01017-16.

PMID- 17389927
VI  - 3
DP  - 2007
TI  - Structural stability and endonuclease activity of a PI-SceI GFP-fusion protein.
PG  - 205-211
AB  - Homing endonucleases are site-specific and rare cutting endonucleases often encoded by intron
      or intein containing genes. They lead to the
      rapid spread of the genetic element that hosts them by a process termed
      'homing'; and ultimately the allele containing the element will be
      fixed in the population.
      PI-SceI, an endonuclease encoded as a protein insert or intein
      within the yeast V-ATPase catalytic subunit encoding gene (vma1), is
      among the best characterized homing endonucleases. The structures of
      the Sce VMA1 intein and of the intein bound to its target site are
      known. Extensive biochemical studies performed on the PI-SceI enzyme
      provide information useful to recognize critical amino acids involved
      in self-splicing and endonuclease functions of the protein. Here we
      describe an insertion of the Green Fluorescence Protein (GFP) into a
      loop which is located between the endonuclease and splicing domains of
      the Sce VMA1 intein. The GFP is functional and the additional GFP
      domain does not prevent intein excision and endonuclease activity.
      However, the endonuclease activity of the newly engineered protein was
      different from the wild-type protein in that it required the presence
      of Mn2+ and not Mg2+ metal cations for activity.
AU  - Senejani AG
AU  - Gogarten JP
PT  - Journal Article
TA  - Int. J. Biol. Sci.
JT  - Int. J. Biol. Sci.
SO  - Int. J. Biol. Sci. 2007 3: 205-211.

PMID- 8747667
VI  - 19
DP  - 1995
TI  - Oligonucleotide activation of the type IIe restriction enzyme NaeI for digestion of refractory sites.
PG  - 990-993
AB  - Certain restriction endonucleases previously shown to exhibit DNA site preferences have a
      two-site DNA cleavage mechanism.  These type IIe restriction endonucleases include NaeI, NarI,
      EcoRII, HpaII and SacII.  Because of this two-site mechanism, it is often difficult or
      impossible to achieve complete digestion of DNA subsrtrate.  Inasmuch as these enzymes are
      commonly used in molecular biology, a method for enzyme activation to provide complete DNA
      digestion is useful.  We have commercialized such a method for NaeI using a double-stranded
      oligonucleotide containing a modified NaeI recognition sequence.  Cleavage of resistant sites
      requires the presence of a DNA sequence that is more cleavable to bind the activator site.
      The regions flanking the recognition site on our NaeI oligonucleotide cause it to serve as
      this more cleavable sequence.  This activates the enzyme to cleave the resistant sequence in
      the catalytic site, while the oligonucleotide modification does not allow the activator to be
      depleted during the reaction.  Turbo NaeI provides for rapid digestion of sites previously
      found difficult or impossible to completely cleave and does not interfere with subsequent
      molecular biology techniques that might be performed downstream on the substrate DNA, such as
      ligation, end-labeling or nick translation.
AU  - Senesac JH
AU  - Allen JR
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 1995 19: 990-993.

PMID- 9187772
VI  - 22
DP  - 1997
TI  - Application of oligonucleotide activation to restriction endonuclease NarI.
PG  - 1166-1168
AB  - Restriction endonuclease NarI cleaves DNA using a two-site mechanism, placing it in the type
      IIe class of restriction endonucleases.  Although these enzymes have very useful recognition
      sequences, the two-site mechanism limits the practical application.  Site preferences often
      cause incomplete substrate digestion.  Oligonucleotide activation of NarI eliminates
      incomplete digestions, making it possible to use NarI restriction sites in many common
      molecular biology techniques.  A modified oligonucleotide was chosen for optimal activation of
      restriction endonuclease NarI.  This oligonucleotide was demonstrated to allow complete
      digestion in many commonly used substrates.
AU  - Senesac JH
AU  - Romanin JK
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 1997 22: 1166-1168.

PMID- 29976609
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Bioactive Strain Streptomyces sp. SMS_SU21, Isolated from Soil Sediment of the Sundarbans Mangrove Ecosystem.
PG  - e00614-18
AB  - Streptomyces sp. SMS_SU21 possesses strong antimicrobial activity and antioxidant potential.
      This strain was isolated from the Sundarbans mangrove ecosystem, and
      its draft genome comprises 7,449,420 bp with 6,680 open reading frames. Genome
      analysis of strain SMS_SU21 provides insight into its secondary metabolite
      arsenal and reveals the gene clusters putatively responsible for its bioactive
      potential.
AU  - Sengupta S
AU  - Pramanik A
AU  - Basak P
AU  - Bhattacharyya M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00614-18.

PMID- 27908999
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a Multiresistant Bovine Isolate of Staphylococcus lentus from Tanzania.
PG  - e01345-16
AB  - We report here the draft genome sequence of a Staphylococcus lentus isolate, 050AP, collected
      in Tanzania from a swab of healthy bovine perineum. The draft
      genome sequence contained 2.72 Mbp and 2,750 coding sequences with a G+C content
      of 31.7%.
AU  - Seni J
AU  - Mshana SE
AU  - Msigwa F
AU  - Matee M
AU  - Mazigo H
AU  - Parkhill J
AU  - Holmes MA
AU  - Paterson GK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01345-16.

PMID- 24285646
VI  - 1
DP  - 2013
TI  - Genome Sequence of Rickettsia gravesii, Isolated from Western Australian Ticks.
PG  - e00975-13
AB  - Rickettsia gravesii is a new Rickettsia species closely related to the human pathogen
      Rickettsia massiliae. Here, we describe the genome sequence of R.
      gravesii strain BWI-1, isolated from Amblyomma triguttatum triguttatum ticks
      collected from humans on Barrow Island, Western Australia.
AU  - Sentausa E
AU  - Abdad MY
AU  - Robert C
AU  - Stenos J
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00975-13.

PMID- 25189579
VI  - 2
DP  - 2014
TI  - Genome Sequence of Rickettsia tamurae, a Recently Detected Human Pathogen in Japan.
PG  - e00838-14
AB  - Rickettsia tamurae is a member of the spotted fever group rickettsiae, which was  reported in
      2011 to cause human infections in Japan. We report the draft genome
      sequence of R. tamurae strain AT-1(T), isolated from Amblyomma testudinarium
      ticks.
AU  - Sentausa E
AU  - El Karkouri K
AU  - Michelle C
AU  - Caputo A
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00838-14.

PMID- 25059861
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Rickettsia aeschlimannii, Associated with Hyalomma marginatum Ticks.
PG  - e00666-14
AB  - Rickettsia aeschlimannii is a tick-associated human pathogen. We report here the  draft genome
      of R. aeschlimannii strain MC16, isolated from Hyalomma marginatum
      marginatum ticks collected in Morocco.
AU  - Sentausa E
AU  - El Karkouri K
AU  - Michelle C
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00666-14.

PMID- 25377719
VI  - 2
DP  - 2014
TI  - Genome Sequence of Rickettsia hoogstraalii, a Geographically Widely Distributed Tick-Associated Bacterium.
PG  - e01171-14
AB  - Rickettsia hoogstraalii is a tick-associated member of the spotted fever group rickettsiae
      that is geographically widely distributed. We report here the draft
      genome of R. hoogstraalii strain Croatica(T) (=DSM 22243 = UTMB 00003), which was
      isolated from Haemaphysalis sulcata ticks collected in Croatia.
AU  - Sentausa E
AU  - El Karkouri K
AU  - Nguyen TT
AU  - Caputo A
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01171-14.

PMID- 22887666
VI  - 194
DP  - 2012
TI  - Genome Sequence of Rickettsia conorii subsp. caspia, the Agent of Astrakhan Fever.
PG  - 4763-4764
AB  - Rickettsia conorii subsp. caspia is the agent of Astrakhan fever, a spotted fever group
      rickettsiosis endemic to Astrakhan, Russia. The present study reports the
      draft genome of Rickettsia conorii subsp. caspia strain A-167.
AU  - Sentausa E
AU  - El Karkouri K
AU  - Robert C
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4763-4764.

PMID- 22628514
VI  - 194
DP  - 2012
TI  - Genome Sequence of Rickettsia conorii subsp. indica, the Agent of Indian Tick Typhus.
PG  - 3288-3289
AB  - Rickettsia conorii subsp. indica is the agent of Indian tick typhus. The present  study
      reports the draft genome of Rickettsia conorii subsp. indica strain ITTR
      (ATCC VR-597).
AU  - Sentausa E
AU  - El Karkouri K
AU  - Robert C
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3288-3289.

PMID- 22933760
VI  - 194
DP  - 2012
TI  - Genome Sequence of Rickettsia conorii subsp. israelensis, the Agent of Israeli Spotted Fever.
PG  - 5130-5131
AB  - Rickettsia conorii subsp. israelensis is the agent of Israeli spotted fever. The  present
      study reports the draft genome of Rickettsia conorii subsp. israelensis
      strain ISTT CDC1, isolated from a Rhipicephalus sanguineus tick collected in
      Israel.
AU  - Sentausa E
AU  - El Karkouri K
AU  - Robert C
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5130-5131.

PMID- 22493192
VI  - 194
DP  - 2012
TI  - Sequence and Annotation of Rickettsia sibirica sibirica Genome.
PG  - 2377
AB  - Rickettsia sibirica sibirica is the causative agent of Siberian or North Asian tick typhus, a
      tick-borne rickettsiosis known to exist in Siberia and eastern
      China. Here we present the draft genome of Rickettsia sibirica sibirica strain
      BJ-90 isolated from Dermacentor sinicus ticks collected in Beijing, China.
AU  - Sentausa E
AU  - El Karkouri K
AU  - Robert C
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2377.

PMID- 22493199
VI  - 194
DP  - 2012
TI  - Genome Sequence of 'Rickettsia sibirica subsp. mongolitimonae'.
PG  - 2389-2390
AB  - 'Rickettsia sibirica subsp. mongolitimonae' is the agent of lymphangitis-associated
      rickettsiosis, an emerging human disease that has been
      diagnosed in Europe and Africa. The present study reports the draft genome of
      Rickettsia sibirica subsp. mongolitimonae strain HA-91.
AU  - Sentausa E
AU  - El Karkouri K
AU  - Robert C
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2389-2390.

PMID- Not included in PubMed...
VI  - 98
DP  - 1989
TI  - In situ methylation of insect chromosomes with methylase HpaII.
PG  - 105-108
AB  - A method of in situ DNA methylation with the prokaryotic methylase HpaII has
      been developed on fixed mitotic and meiotic chromosomes of the insect species
      Baetica ustulata.  Incorporation of methyl groups into the chromosomal DNA is
      revealed by autoradiography using a laelled substrate and by its ability to
      prevent endonuclease digestion.  The method allows direct visualization of
      clusters of methylatable CCGG sites.  The distribution of these clusters in the
      chromosome complement of Baetica shows two separate domains of heterochromatic
      DNA which differ in their methylation patterns.  Each is distributed at
      equivalent locations in both homologus and nonhomologus chromosomes.  The
      existence of two compartments, one methylated and the other unmethylated, in
      the heterochromatic DNA could be interpreted as a remnant of the ancestral
      echinoderm-like pattern of methylation.
AU  - Sentis C
AU  - Santos J
AU  - Fernandez-Piqueras J
PT  - Journal Article
TA  - Chromosoma
JT  - Chromosoma
SO  - Chromosoma 1989 98: 105-108.

PMID- Not carried by PubMed...
VI  - 25
DP  - 1992
TI  - Studies on the role of arginyl residue in EcoRI methylase.
PG  - 54-59
AB  - Treatment of EcoRI methylase with phenylglyoxal resulted in time and concentration dependent
      enzyme inactivation. The reaction followed pseudo first-order kinetics until 90 to 95% of the
      enzyme had been inactivated, and prolonged incubation with phenylglyoxal resulted in complete
      inactivation. Second order rate constant (K) for the inactivation of EcoRI methylase by
      phenylglyoxal was 666 M-1 min-1. The slope determined from the plot of log (100/t1/2) against
      log (phenylglyoxal) indicated that the reaction of 1 molecule of phenylglyoxal reagent in
      necessary for inactivation of each active site in EcoRI methylase. Preincubation with pUC19 or
      S-adenosylmethionine as substrates decreased significantly the rate of inactivation by
      phenylglyoxal. By nitrocellulose binding assay, phenylglyoxal was observed to reduce DNA
      binding capacity of the enzyme more rapidly than S-adenosylmethionine. Furthermore, DNA
      binding capacity of the enzyme was preserved when the enzyme was preincubated with pUC19 DNA.
      The cumulative results suggest that arginyl residue plays a very important role as a DNA
      binding residue in EcoRI methylase.
AU  - Seo JH
AU  - Cho YD
PT  - Journal Article
TA  - Korean Biochem. J.
JT  - Korean Biochem. J.
SO  - Korean Biochem. J. 1992 25: 54-59.

PMID- Not carried by PubMed...
VI  - 24
DP  - 1991
TI  - Studies on the role of cysteinyl residue in EcoRI methylase.
PG  - 193-199
AB  - The chemical modification of cysteinyl residue of EcoRI methylase by NEM and
      DACM resulted in the loss of the enzyme activity following pseudo first order
      kinetics.  Second order rate constants (K) for the inactivation of EcoRI
      methylase by NEM and DACM were 685 M-1.min-1 and  99960 M-1.min-1,
      respectively.  The reaction orders with respect to NEM and DACM were determined
      from plot of log (100/t1/2) against log (NEM) and log (DACM).  When the data
      are plotted as indicated above, slopes of 0.95 and 1.25 are obtained,
      suggesting that inactivation is the result of the reaction of one cysteinyl
      residue per active site of EcoRI methylase.  The inactivation of EcoRI
      methylase by DTNB was reversed upon addition of excess 2-mercaptoethanol.  When
      the enzyme solution was preincubated with the substrates, the inactivation of
      the enzyme by NEM and DACM was protected.  Furtheremore, loss of SAM binding
      capacity of EcoRI methylase was detected by nitrocellulose filter binding
      assay.  Based on the data, we suggest that cysteinyl residue of EcoRI methylase
      plays a very important role as a SAM binding residue.
AU  - Seo JH
AU  - Cho YD
PT  - Journal Article
TA  - Korean Biochem. J.
JT  - Korean Biochem. J.
SO  - Korean Biochem. J. 1991 24: 193-199.

PMID- 21478339
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Burkholderia gladioli BSR3.
PG  - 3149
AB  - We report the complete genome sequence of Burkholderia gladioli BSR3 isolated from a diseased
      rice sheath in Korea.
AU  - Seo YS
AU  - Lim JY
AU  - Choi BS
AU  - Kim H
AU  - Goo E
AU  - Lee B
AU  - Lim JS
AU  - Choi IY
AU  - Moon JS
AU  - Kim J
AU  - Hwang I
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3149.

PMID- 25943361
VI  - 16
DP  - 2015
TI  - Comparative genome analysis of rice-pathogenic Burkholderia provides insight into capacity to adapt to different environments and hosts.
PG  - 349
AB  - BACKGROUND: In addition to human and animal diseases, bacteria of the genus
      Burkholderia can cause plant diseases. The representative species of
      rice-pathogenic Burkholderia are Burkholderia glumae, B. gladioli, and B.
      plantarii, which primarily cause grain rot, sheath rot, and seedling blight,
      respectively, resulting in severe reductions in rice production. Though
      Burkholderia rice pathogens cause problems in rice-growing countries,
      comprehensive studies of these rice-pathogenic species aiming to control
      Burkholderia-mediated diseases are only in the early stages. RESULTS: We first
      sequenced the complete genome of B. plantarii ATCC 43733T. Second, we conducted
      comparative analysis of the newly sequenced B. plantarii ATCC 43733T genome with
      eleven complete or draft genomes of B. glumae and B. gladioli strains.
      Furthermore, we compared the genome of three rice Burkholderia pathogens with
      those of other Burkholderia species such as those found in environmental habitats
      and those known as animal/human pathogens. These B. glumae, B. gladioli, and B.
      plantarii strains have unique genes involved in toxoflavin or tropolone toxin
      production and the clustered regularly interspaced short palindromic repeats
      (CRISPR)-mediated bacterial immune system. Although the genome of B. plantarii
      ATCC 43733T has many common features with those of B. glumae and B. gladioli,
      this B. plantarii strain has several unique features, including quorum sensing
      and CRISPR/CRISPR-associated protein (Cas) systems. CONCLUSIONS: The complete
      genome sequence of B. plantarii ATCC 43733T and publicly available genomes of B.
      glumae BGR1 and B. gladioli BSR3 enabled comprehensive comparative genome
      analyses among three rice-pathogenic Burkholderia species responsible for tissue
      rotting and seedling blight. Our results suggest that B. glumae has evolved
      rapidly, or has undergone rapid genome rearrangements or deletions, in response
      to the hosts. It also, clarifies the unique features of rice pathogenic
      Burkholderia species relative to other animal and human Burkholderia species.
AU  - Seo YS
AU  - Lim JY
AU  - Park J
AU  - Kim S
AU  - Lee HH
AU  - Cheong H
AU  - Kim SM
AU  - Moon JS
AU  - Hwang I
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2015 16: 349.

PMID- 20137899
VI  - 35
DP  - 2010
TI  - Complete nucleotide sequence of the fosfomycin resistance transposon Tn2921.
PG  - 413-414
AB  - Fosfomycin is a cell wall-active antibiotic introduced into clinical practice around 1970.
      Despite its broad spectrum of activity and good pharmacological properties, its use has been
      somewhat hampered by the high number of spontaneous resistant mutants isolated following
      antibiotic challenge in many bacterial pathogens, most of them carrying chromosomal mutations
      impairing drug transport.
AU  - Seoane A
AU  - Sangari FJ
AU  - Lobo JM
PT  - Journal Article
TA  - Int. J. Antimicrob. Agents
JT  - Int. J. Antimicrob. Agents
SO  - Int. J. Antimicrob. Agents 2010 35: 413-414.

PMID- 27904456
VI  - 32
DP  - 2016
TI  - Methylome Analysis of Two Xanthomonas spp. Using Single-Molecule Real-Time Sequencing.
PG  - 500-507
AB  - Single-molecule real-time (SMRT) sequencing allows identification of methylated DNA bases and
      methylation patterns/motifs at the genome level. Using SMRT
      sequencing, diverse bacterial methylomes including those of Helicobacter pylori,
      Lactobacillus spp., and Escherichia coli have been determined, and previously
      unreported DNA methylation motifs have been identified. However, the methylomes
      of Xanthomonas species, which belong to the most important plant pathogenic
      bacterial genus, have not been documented. Here, we report the methylomes of
      Xanthomonas axonopodis pv. glycines (Xag) strain 8ra and X. campestris pv.
      vesicatoria (Xcv) strain 85-10. We identified N(6)-methyladenine (6mA) and
      N(4)-methylcytosine (4mC) modification in both genomes. In addition, we assigned
      putative DNA methylation motifs including previously unreported methylation
      motifs via REBASE and MotifMaker, and compared methylation patterns in both
      species. Although Xag and Xcv belong to the same genus, their methylation
      patterns were dramatically different. The number of 4mC DNA bases in Xag (66,682)
      was significantly higher (29 fold) than in Xcv (2,321). In contrast, the number
      of 6mA DNA bases (4,147) in Xag was comparable to the number in Xcv (5,491).
      Strikingly, there were no common or shared motifs in the 10 most frequently
      methylated motifs of both strains, indicating they possess unique species- or
      strain-specific methylation motifs. Among the 20 most frequent motifs from both
      strains, for 9 motifs at least 1% of the methylated bases were located in
      putative promoter regions. Methylome analysis by SMRT sequencing technology is
      the first step toward understanding the biology and functions of DNA methylation
      in this genus.
AU  - Seong HJ
AU  - Park HJ
AU  - Hong E
AU  - Lee SC
AU  - Sul WJ
AU  - Han SW
PT  - Journal Article
TA  - Plant Pathol. J.
JT  - Plant Pathol. J.
SO  - Plant Pathol. J. 2016 32: 500-507.

PMID- 1314207
VI  - 113
DP  - 1992
TI  - The yeast mitochondrial intron aI5a: associated endonuclease activity and in vivo mobility.
PG  - 1-8
AB  - By analyzing crosses between yeast strains carrying different combinations of mitochondrial
      (mt) introns, we have shown that the aI5a intron is mobile in vivo. Furthermore, we have
      observed that the mobility of intron aI5a is affected by both the nuclear and mt genotypes. We
      have also detected a restriction endonuclease (ENase) activity that cleaves intronless mt
      genomes close to the aI5a intron insertion site and thus might be involved in intron mobility.
      Furthermore, similar to other ENases encoded by mobile mt introns of yeast, the ENase
      generates a cut with a four-base 3'-OH overhang. Thus, intron aI5a represents a
      characteristic member of the family of mobile group-I introns.
AU  - Seraphin B
AU  - Faye G
AU  - Hatat D
AU  - Jacq C
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1992 113: 1-8.

PMID- 2987871
VI  - 13
DP  - 1985
TI  - A mitochondrial reading frame which may code for a maturase-like protein in Saccharomyces cerevisiae.
PG  - 3005-3014
AB  - In S. cerevisiae, the large oxi3/oli2 mitochondrial transcript contains
      the products of the oxi3, aap1 and oli2 genes and an unassigned reading
      frame, RF3. In the work presented here, we have completed the nucleotide
      sequence of RF3. We have shown that RF3 is composed of four fairly large
      ORFs which overlap within GC rich sequences. Furthermore, a shift of +1
      base was found between each pair of consecutive reading frames. We discuss
      how these frameshifts could be removed to produce a 500 aminoacid long
      protein containing the two well conserved P1 and P2 oligopeptide sequences
      featuring several mitochondrial intron reading frames, suggesting,
      thereby, a RNA-maturase-like activity for the putative RF3 protein. In
      addition, we suggest that the insertion of GC clusters in a gene could
      provide a novel way of regulating its expression.
AU  - Seraphin B
AU  - Simon M
AU  - Faye G
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1985 13: 3005-3014.

PMID- 25237022
VI  - 2
DP  - 2014
TI  - Draft Whole-Genome Sequence of Serratia marcescens Strain MCB, Associated with Oscheius sp. MCB (Nematoda: Rhabditidae) Isolated from South Africa.
PG  - e00911-14
AB  - Here we report on the draft genome sequence of Serratia marcescens strain MCB associated with
      Oscheius sp. MCB (Nematoda: Rhabditidae) isolated from South
      African soil. S. marcescens strain MCB has 5,304,212-bp genome size with 4,877
      genes and a G+C content of 59.1%.
AU  - Serepa MH
AU  - Gray VM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00911-14.

PMID- 20007596
VI  - 38
DP  - 2010
TI  - The structure of the KlcA and ArdB proteins reveals a novel fold and antirestriction activity against Type I DNA restriction systems in vivo  but not in vitro.
PG  - 1723-1737
AB  - Plasmids, conjugative transposons and phage frequently encode anti-restriction proteins to
      enhance their chances of entering a new
      bacterial host that is highly likely to contain a Type I DNA restriction
      and modification (RM) system. The RM system usually destroys the invading
      DNA. Some of the anti-restriction proteins are DNA mimics and bind to the
      RM enzyme to prevent it binding to DNA. In this article, we characterize
      ArdB anti-restriction proteins and their close homologues, the KlcA
      proteins from a range of mobile genetic elements; including an ArdB
      encoded on a pathogenicity island from uropathogenic Escherichia coli and
      a KlcA from an IncP-1b plasmid, pBP136 isolated from Bordetella pertussis.
      We show that all the ArdB and KlcA act as anti-restriction proteins and
      inhibit the four main families of Type I RM systems in vivo, but fail to
      block the restriction endonuclease activity of the archetypal Type I RM
      enzyme, EcoKI, in vitro indicating that the action of ArdB is indirect and
      very different from that of the DNA mimics. We also present the structure
      determined by NMR spectroscopy of the pBP136 KlcA protein. The structure
      shows a novel protein fold and it is clearly not a DNA structural mimic.
AU  - Serfiotis-Mitsa D
AU  - Herbert AP
AU  - Roberts GA
AU  - Soares DC
AU  - White JH
AU  - Blakely GW
AU  - Uhrin D
AU  - Dryden DT
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2010 38: 1723-1737.

PMID- 18838147
VI  - 383
DP  - 2008
TI  - The Orf18 Gene Product from Conjugative Transposon Tn916 Is an ArdA Antirestriction Protein that Inhibits Type I DNA Restriction-Modification  Systems.
PG  - 970-981
AB  - Gene orf18, which is situated within the intercellular transposition region of the conjugative
      transposon Tn916 from the bacterial pathogen Enterococcus faecalis, encodes a putative ArdA
      (alleviation of restriction of DNA A) protein. Conjugative transposons are generally resistant
      to DNA restriction upon transfer to a new host. ArdA from Tn916 may be responsible for the
      apparent immunity of the transposon to DNA restriction and modification (R/M) systems and for
      ensuring that the transposon has a broad host range. The orf18 gene was engineered for
      overexpression in Escherichia coli, and the recombinant ArdA protein was purified to
      homogeneity. The protein appears to exist as a dimer at nanomolar concentrations but can form
      larger assemblies at micromolar concentrations. R/M assays revealed that ArdA can efficiently
      inhibit R/M by all four major classes of Type I R/M enzymes both in vivo and in vitro. These
      R/M systems are present in over 50% of sequenced prokaryotic genomes. Our results suggest that
      ArdA can overcome the restriction barrier following conjugation and so helps increase the
      spread of antibiotic resistance genes by horizontal gene transfer.
AU  - Serfiotis-Mitsa D
AU  - Roberts GA
AU  - Cooper LP
AU  - White JH
AU  - Nutley M
AU  - Cooper A
AU  - Blakely GW
AU  - Dryden DT
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2008 383: 970-981.

PMID- 11042490
VI  - 65
DP  - 2000
TI  - A study of the Asp110-Glu112 region of EcoRII restriction endonuclease by site-directed mutagenesis.
PG  - 1006-1010
AB  - Site-directed mutagenesis of the ecoRII gene has been used to search for the active site of
      the EcoRII restriction endonuclease. Plasmids
      with point mutations in ecoRII gene resulting in substitutions of amino
      acid residues in the Asp110-Glu112 region of the EcoRII endonuclease
      (Asp110 --> Lys, Asn, Thr, Val, or Ile; Pro111 --> Arg, His, Ala, or
      Leu; Glu112 --> Lys, Gin, or Asp) have been constructed. When expressed
      in E. coli, ail these plasmids displayed EcoRII endonuclease activity,
      We also constructed a plasmid containing a mutant ecoRII gene with
      deletion of the sequence coding the Gln109-Pro111 region of the
      protein. This mutant protein had no EcoRII endonuclease activity. The
      data suggest that Asp110, Pro111, and Glu112 residues do not
      participate in the formation of the EcoRII active site. However, this
      region seems to be relevant for the formation of the tertiary structure
      of the EcoRII endonuclease.
AU  - Sergeev VN
AU  - Chalov SE
AU  - Drutsa VL
AU  - Gromova ES
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2000 65: 1006-1010.

PMID- 29674535
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of 20 Salmonella enterica subsp. enterica Serovar Typhimurium Strains Isolated from Swine in Santa Catarina, Brazil.
PG  - e00232-18
AB  - Salmonellosis is a disease with a high incidence worldwide, and Salmonella enterica subsp.
      enterica serovar Typhimurium is one of the most clinically
      important serovars. We report here the draft genome sequences of 20 S.
      Typhimurium strains isolated from swine in Santa Catarina, Brazil. These draft
      genomes will improve our understanding of S. Typhimurium in Brazil.
AU  - Seribelli AA
AU  - Frazao MR
AU  - Gonzales JC
AU  - Cao G
AU  - Leon MS
AU  - Kich JD
AU  - Allard MW
AU  - Falcao JP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00232-18.

PMID- 28770028
VI  - 12
DP  - 2017
TI  - First draft genome sequence of a strain from the genus Fusibacter isolated from Salar de Ascotan in Northern Chile.
PG  - 43
AB  - Fusibacter sp. 3D3 (ATCC BAA-2418) is an arsenate-reducing halotolerant strain within the
      Firmicutes phylum, isolated from the Salar de Ascotan, a hypersaline
      salt flat in Northern Chile. This high-Andean closed basin is an athalassohaline
      environment located at the bottom of a tectonic basin surrounded by mountain
      range, including some active volcanoes. This landscape can be an advantageous
      system to explore the effect of salinity on microorganisms that mediate
      biogeochemical reactions. Since 2000, microbial reduction of arsenic has been
      evidenced in the system, and the phylogenetic analysis of the original community
      plus the culture enrichments has revealed the predominance of Firmicutes phylum.
      Here, we describe the first whole draft genome sequence of an arsenic-reducing
      strain belonging to the Fusibacter genus showing the highest 16S rRNA gene
      sequence similarity (98%) with Fusibacter sp. strain Vns02. The draft genome
      consists of 57 contigs with 5,111,250 bp and an average G + C content of 37.6%.
      Out of 4780 total genes predicted, 4700 genes code for proteins and 80 genes for
      RNAs. Insights from the genome sequence and some microbiological features of the
      strain 3D3 are available under Bioproject accession PRJDB4973 and Biosample
      SAMD00055724. The release of the genome sequence of this strain could contribute
      to the understanding of the arsenic biogeochemistry in extreme environments.
AU  - Serrano AE
AU  - Escudero LV
AU  - Tebes-Cayo C
AU  - Acosta M
AU  - Encalada O
AU  - Fernandez-Moroso S
AU  - Demergasso C
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 43.

PMID- 29051252
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Vibrio sp. Strain V1B Isolated from the Gut Microflora of the Scallop Argopecten purpuratus.
PG  - e01130-17
AB  - A new Vibrio strain, V1B, was isolated from the intestinal tract of the scallop Argopecten
      purpuratus Strain V1B is closely related to the species Vibrio
      inhibens BFLP-10, which has been characterized as showing antagonistic activity
      against pathogenic Vibrio sp. We report here the draft genome of the isolated
      Vibrio sp. strain V1B.
AU  - Serrano W
AU  - Tarazona UI
AU  - Olaechea RM
AU  - Friedrich MW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01130-17.

PMID- 29773630
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of a New Vibrio Strain with the Potential To Produce Bacteriocin-Like Inhibitory Substances, Isolated from the Gut Microflora of  Scallop (Argopecten purpuratus).
PG  - e00419-18
AB  - A new Vibrio strain, V7A, was isolated from the intestinal tract of the Peruvian  scallop
      (Argopecten purpuratus). Strain V7A clusters within the Mediterranei
      clade of the genus Vibrio and has the potential to produce bacteriocin-like
      inhibitory substances (BLIS). Here, we report the draft genome sequence of Vibrio
      mediterranei strain V7A.
AU  - Serrano W
AU  - Tarazona UI
AU  - Olaechea RM
AU  - Friedrich MW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00419-18.

PMID- Not carried by PubMed...
VI  - 1
DP  - 1997
TI  - Fluorescence studies of the DNA base flipping induced by a cytosine-5 methyltransferase.
PG  - 9-12
AB  - A novel fluorescence-based method for detecting and studying DNA base flipping in enzyme-DNA
      complexes is described.  The target cytosine for the DNA methyltransferase HhaI (GCGC) was
      replaced by a fluorescent base, 2-aminopurine.  Constistent with the extrahelical trapping of
      the target base, a 90-fold increase in the fluorescence intensity was observed upon binding of
      M. HhaI to a 37-mer duplex substrate.  Similar substitutions of bases adjacent to the target
      cytosine result in a relatively small change.  Stopped-flow fluorescence experiments under
      non-catalytic conditions allowed to monitor the course of base-flipping directly.  Kinetic
      analysis shows that the site-specific binding of the enzyme is a diffusion-controlled process,
      while the subsequent flipping motion is achieved in 1 millisecond, or faster.  Other classes
      of enzymes suspected to employ the base flipping in their mechanisms can be investigated with
      this method.
AU  - Serva S
AU  - Klimasauskas S
AU  - Weinhold E
PT  - Journal Article
TA  - Biologija
JT  - Biologija
SO  - Biologija 1997 1: 9-12.

PMID- Not carried by PubMed...
VI  - 0
DP  - 1996
TI  - High-level expression of MvaI DNA methyltransferase.
PG  - 48-50
AB  - Construction of a high level expression system for the DNA-(cytosine-N4)-methyltransferase
      M.MvaI is described.  The entire M.MvaI coding region was introduced as a 1511bp Alw44I-BpiI
      fragment into the high expression vector pPR594E9.  The resultant plasmid (pPR-MvaIM7) was
      expressed in the E. coli strain GM119 by induction with IPTG.  In the induced cells,
      catalytically active M.MvaI was produced at a level of about 10% of their total protein.  The
      enzyme was purified to apparent homogeneity by a four-column chromatographic procedure in a
      yield of about 0.2 mg of pure enzyme per 1g of cell paste.  The molecular weight and the amino
      terminal sequence of the protein agrees with that predicted from the DNA sequence.
AU  - Serva S
AU  - Velyvis R
AU  - Lazareviciute L
AU  - Klimasauskas S
PT  - Journal Article
TA  - Biologija
JT  - Biologija
SO  - Biologija 1996 0: 48-50.

PMID- 
VI  - 2000
DP  - 2000
TI  - Stopped-flow fluorescence studies of DNA base flipping by HhaI methyltransferase.
PG  - A468
AB  - Rotation of a nucleotide out of the DNA helix (base flipping) has been first observed for the
      HhaI methyltransferase followed by numerous other DNA modification and repair enzymes.  M.HhaI
      catalyzes transfer of a methyl group from cofactor S-adenosyl-L-methionine onto the C5
      position of the first cytosine in the target sequence GCGC.  In this study, stopped-flow and
      rapid-quench techniques were employed in combination with fluorescence detection for kinetic
      characterization of individual steps on the reaction pathway of M.HhaI.  Selective labeling of
      the DNA substrate was achieved by synthetic incorporation of 2-aminopurine at the target
      position which showed a dramatic increase in fluorescence signal upon transition of the base
      from the stacked to an extrahelical position.  Association, dissociation and single-turnover
      experimental setups permitted the direct determination of microscopic rate constants for DNA
      binding, flipping of the target base, methyl group transfer and release of methylated DNA.  We
      demonstrate here that the target sites on short DNA duplexes are predominantly located via a
      diffusion-collision pathway and the subsequent base flipping is nearly instantaneous (<1 ms)
      for the G-2AP mismatch.  We show for the first time that the chemical methyl transfer step
      (0.15 s-1) is faster than the steady-state turnover (0.02 s-1) and directly confirm that decay
      of the ternary product complex (methylated DNA-M.HhaI-AdoHcy) is rate-limiting in the
      catalytic cycle.  Global fitting and simulation analysis in conjunction with structural data
      suggest detailed catalytic mechanisms for DNA base flipping and catalysis by DNA cytosine-5
      methyltransferases.
AU  - Serva S
AU  - Weinhold E
AU  - Klimasauskas S
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 2000 2000: A468.

PMID- 9671807
VI  - 26
DP  - 1998
TI  - Chemical display of thymine residues flipped out by DNA methyltransferases.
PG  - 3473-3479
AB  - The DNA cytosine-C5 methyltransferase M.HhaI flips its target base out of the DNA helix during
      interaction with the substrate sequence GCGC.  Binary and ternary complexes between M.HhaI and
      hemimethylated DNA duplexes were used to examine the suitability of four chemical methods to
      detect flipped-out bases in protein-DNA complexes.  These methods probe the structural
      peculiarities of pyrimidine bases in DNA.  We find that in cases when the target cytosine is
      replaced with thymine (GTGC), KMnO4 proved an efficient probe for positive display of
      flipped-out thymines.  The generality of this procedure was further verified by examining a
      DNA adenine-N6 methyltransferase, M.TaqI, in which case an enhanced reactivity of thymine
      replacing the target adenine (TCGT) in the recognition sequence TCGA was also observed.  Our
      results support the proposed base-flipping mechanism for adenine methyltransferases, and offer
      a convenient laboratory tool for detection of flipped-out thymines in protein-DNA complexes.
AU  - Serva S
AU  - Weinhold E
AU  - Roberts RJ
AU  - Klimasauskas S
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1998 26: 3473-3479.

PMID- 23405365
VI  - 1
DP  - 2013
TI  - Genome Sequence of the Acidophilic Bacterium Acidocella sp. Strain MX-AZ02.
PG  - e00041-12
AB  - Here, we report the draft genome sequence of Acidocella sp. strain MX-AZ02, an acidophilic and
      heterotrophic alphaproteobacterium isolated from a geothermal lake in western Mexico.
AU  - Servin-Garciduenas LE
AU  - Garrett RA
AU  - Amils R
AU  - Martinez-Romero E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00041-12.

PMID- 24604657
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Sulfolobales Archaeon AZ1, Obtained through Metagenomic Analysis of a Mexican Hot Spring.
PG  - e00164-14
AB  - The Sulfolobales archaea have been found inhabiting acidic hot springs all over the world.
      Here, we report the 1.798-Mbp draft genome sequence of the
      thermoacidophilic Sulfolobales archaeon AZ1, reconstructed from the metagenome of
      a Mexican hot spring. Sequence-based comparisons revealed that the Sulfolobales
      archaeon AZ1 represents a novel candidate genus.
AU  - Servin-Garciduenas LE
AU  - Martinez-Romero E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00164-14.

PMID- 23618716
VI  - 1
DP  - 2013
TI  - Genome sequence of a novel archaeal fusellovirus assembled from the metagenome of a mexican hot spring.
PG  - e00164-13
AB  - The consensus genome sequence of a new member of the family Fuselloviridae designated as SMF1
      (Sulfolobales Mexican fusellovirus 1) is presented. The
      complete circular genome was recovered from a metagenomic study of a Mexican hot
      spring. SMF1 exhibits an exceptional coding strand bias and a reduced set of
      fuselloviral core genes.
AU  - Servin-Garciduenas LE
AU  - Peng X
AU  - Garrett RA
AU  - Martinez-Romero E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00164-13.

PMID- 23105056
VI  - 194
DP  - 2012
TI  - Genome Sequence of Rhizobium sp. Strain CCGE510, a Symbiont Isolated from Nodules of the Endangered Wild Bean Phaseolus albescens.
PG  - 6310-6311
AB  - We present the genome sequence of Rhizobium sp. strain CCGE510, a nitrogen fixing bacterium
      taxonomically affiliated with the R. leguminosarum-R. etli group,
      isolated from wild Phaseolus albescens nodules grown in native pine forests in
      western Mexico. P. albescens is an endangered bean species phylogenetically
      related to P. vulgaris. In spite of the close host relatedness, Rhizobium sp.
      CCGE510 does not establish an efficient symbiosis with P. vulgaris. This is the
      first genome of a Rhizobium symbiont from a Phaseolus species other than P.
      vulgaris, and it will provide valuable new insights about symbiont-host
      specificity.
AU  - Servin-Garciduenas LE
AU  - Rogel MA
AU  - Ormeno-Orrillo E
AU  - Delgado-Salinas A
AU  - Martinez-Romero J
AU  - Sanchez F
AU  - Martinez-Romero E
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6310-6311.

PMID- 26988045
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Bradyrhizobium sp. Strain CCGE-LA001, Isolated from Field Nodules of the Enigmatic Wild Bean Phaseolus microcarpus.
PG  - e00126-16
AB  - We present the complete genome sequence of Bradyrhizobium sp. strain CCGE-LA001,  a
      nitrogen-fixing bacterium isolated from nodules of Phaseolus microcarpus.
      Strain CCGE-LA001 represents the first sequenced bradyrhizobial strain obtained
      from a wild Phaseolus sp. Its genome revealed a large and novel symbiotic island.
AU  - Servin-Garciduenas LE
AU  - Rogel MA
AU  - Ormeno-Orrillo E
AU  - Zayas-Del MA
AU  - Sanchez F
AU  - Martinez-Romero E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00126-16.

PMID- 24604647
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Commensalibacter papalotli MX01, a Symbiont Identified from the Guts of Overwintering Monarch Butterflies.
PG  - e00128-14
AB  - We report the draft genome sequence of Commensalibacter papalotli strain MX01, isolated from
      the intestines of an overwintering monarch butterfly. The
      2,332,652-bp AT-biased genome of C. papalotli MX01 is the smallest genome for a
      member of the Acetobacteraceae family and provides the first evidence of plasmids
      in Commensalibacter.
AU  - Servin-Garciduenas LE
AU  - Sanchez-Quinto A
AU  - Martinez-Romero E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00128-14.

PMID- 2011502
VI  - 19
DP  - 1991
TI  - The commercially available restriction enzyme BspHI is blocked by overlapping methylation.
PG  - 183
AB  - This report shows that BspHI is sensitive to dam methylation
AU  - Servos S
AU  - Silva C
AU  - Dougan G
AU  - Charles IG
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 183.

PMID- 29553575
VI  - 36
DP  - 2018
TI  - Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection.
PG  - 359-367
AB  - Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible
      plant polysaccharides into nutrients used for growth. Understanding
      the functions carried out by the rumen microbiota is important for reducing
      greenhouse gas production by ruminants and for developing biofuels from
      lignocellulose. We present 410 cultured bacteria and archaea, together with their
      reference genomes, representing every cultivated rumen-associated archaeal and
      bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid
      production and methanogenesis pathways, and assign specific taxa to functions. A
      total of 336 organisms were present in available rumen metagenomic data sets, and
      134 were present in human gut microbiome data sets. Comparison with the human
      microbiome revealed rumen-specific enrichment for genes encoding de novo
      synthesis of vitamin B12, ongoing evolution by gene loss and potential vertical
      inheritance of the rumen microbiome based on underrepresentation of markers of
      environmental stress. We estimate that our Hungate genome resource represents
      approximately 75% of the genus-level bacterial and archaeal taxa present in the
      rumen.
AU  - Seshadri R et al
PT  - Journal Article
TA  - Nat. Biotechnol.
JT  - Nat. Biotechnol.
SO  - Nat. Biotechnol. 2018 36: 359-367.

PMID- 15637277
VI  - 307
DP  - 2005
TI  - Genome sequence of the PCE-Dechlorinating bacterium Dehalococcoides ethenogenes.
PG  - 105-108
AB  - Dehalococcoides ethenogenes is the only bacterium known to reductively dechlorinate the
      groundwater pollutants, tetrachloroethene (PCE) and trichloroethene, to ethene. Its
      1,469,720-base pair chromosome contains large dynamic duplicated regions and integrated
      elements. Genes encoding 17 putative reductive dehalogenases, nearly all of which were
      adjacent to genes for transcription regulators, and five hydrogenase complexes were
      identified. These findings, plus a limited repertoire of other metabolic modes, indicate that
      D. ethenogenes is highly evolved to utilize halogenated organic compounds and H2.
      Diversification of reductive dehalogenase functions appears to have been mediated by recent
      genetic exchange and amplification. Genome analysis provides insights into the organism's
      complex nutrient requirements and suggests that an ancestor was a nitrogen-fixing autotroph.
AU  - Seshadri R et al
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2005 307: 105-108.

PMID- 16980456
VI  - 188
DP  - 2006
TI  - Genome Sequence of Aeromonas hydrophila ATCC 7966T: Jack of All Trades.
PG  - 8272-8282
AB  - The complete genome of Aeromonas hydrophila ATCC 7966(T) was sequenced. Aeromonas, a
      ubiquitous waterborne bacterium, has been placed by the
      Environmental Protection Agency on the Contaminant Candidate List because
      of its potential to cause human disease. The 4.7-Mb genome of this
      emerging pathogen shows a physiologically adroit organism with broad
      metabolic capabilities and considerable virulence potential. A large array
      of virulence genes, including some identified in clinical isolates of
      Aeromonas spp. or Vibrio spp., may confer upon this organism the ability
      to infect a wide range of hosts. However, two recognized virulence
      markers, a type III secretion system and a lateral flagellum, that are
      reported in other A. hydrophila strains are not identified in the
      sequenced isolate, ATCC 7966(T). Given the ubiquity and free-living
      lifestyle of this organism, there is relatively little evidence of
      fluidity in terms of mobile elements in the genome of this particular
      strain. Notable aspects of the metabolic repertoire of A. hydrophila
      include dissimilatory sulfate reduction and resistance mechanisms (such as
      thiopurine reductase, arsenate reductase, and phosphonate degradation
      enzymes) against toxic compounds encountered in polluted waters. These
      enzymes may have bioremediative as well as industrial potential. Thus, the
      A. hydrophila genome sequence provides valuable insights into its ability
      to flourish in both aquatic and host environments.
AU  - Seshadri R
AU  - Joseph SW
AU  - Chopra AK
AU  - Sha J
AU  - Shaw J
AU  - Graf J
AU  - Haft D
AU  - Wu M
AU  - Ren Q
AU  - Rosovitz MJ
AU  - Madupu R
AU  - Tallon L
AU  - Kim M
AU  - Jin S
AU  - Vuong H
AU  - Stine OC
AU  - Ali A
AU  - Horneman AJ
AU  - Heidelberg JF
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2006 188: 8272-8282.

PMID- 17342207
VI  - 2
DP  - 2007
TI  - An assessment of the role of DNA adenine methyltransferase on gene expression regulation in E coli.
PG  - e273
AB  - N6-Adenine methylation is an important epigenetic signal, which regulates various processes,
      such as DNA replication and repair and transcription. In gamma-proteobacteria, Dam is a
      stand-alone enzyme that methylates GATC sites, which are non-randomly distributed in the
      genome. Some of these overlap with transcription factor binding sites. This work describes a
      global computational analysis of a published Dam knockout microarray alongside other publicly
      available data to throw insights into the extent to which Dam regulates transcription by
      interfering with protein binding. The results indicate that DNA methylation by DAM may not
      globally affect gene transcription by physically blocking access of transcription factors to
      binding sites. Down-regulation of Dam during stationary phase correlates with the activity of
      TFs whose binding sites are enriched for GATC sites.
AU  - Seshasayee AS
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2007 2: e273.

PMID- 22573173
VI  - 40
DP  - 2012
TI  - Context-dependent conservation of DNA methyltransferases in bacteria.
PG  - 7066-7073
AB  - DNA methytransferases (MTs) in bacteria are best understood in the context of
      restriction-modification (R-M) systems, which act as bacterial immune systems
      against incoming DNA including phages, but have also been described as selfish
      elements. But several orphan MTs, which are not associated with any restriction
      enzyme, have also been characterized and may protect against parasitism by R-M
      systems. The occurrence of MTs in these two contexts, namely as part of R-M
      systems or as orphans, is poorly understood. Here we report the results of a
      comparative genomic survey of DNA MTs across approximately 1000 bacterial
      genomes. We show that orphan MTs overwhelm R-M systems in their occurrence. In
      general, R-M MTs are poorly conserved, whereas orphans are nearly as conserved
      within a genus as any average gene. However, oligonucleotide usage and
      conservation patterns across genera suggest that both forms of MTs might have
      been horizontally acquired. We suggest that many orphan MTs might be
      'degradation' products of R-M systems, based on the properties of orphan MTs
      encoded adjacent to highly diverged REs. In addition, several fully degraded R-M
      systems exist in which both the MT and the RE are highly divergent from their
      corresponding reference R-M pair. Despite their sporadic occurrence, conserved
      R-M systems are present in strength in two highly transformable genera, in which
      they may contribute to selection against integration of foreign DNA.
AU  - Seshasayee AS
AU  - Singh P
AU  - Krishna S
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: 7066-7073.

PMID- 10369689
VI  - 18
DP  - 1999
TI  - M.PhiBssHII, a novel cytosine-C5-DNA-methyltransferase with target-recognizing domains at separated locations of the enzyme.
PG  - 3502-3508
AB  - In all cytosine-C5-DNA-methyltransferases (MTases) from prokaryotes and eukaryotes, remarkably
      conserved amino acid sequence elements responsible for general enzymatic functions are
      arranged in the same canonical order. In addition, one variable region, which includes the
      target-recognizing domain(s) (TRDs) characteristic for each enzyme, has been localized in one
      region between the same blocks of these conserved elements. This conservation in the order of
      conserved and variable sequences suggests stringent structural constraints in the primary
      structure to obtain the correct folding of the enzymes. Here we report the characterization of
      a new type of a multispecific MTase, M.PhiBssHII, which is expressed as two isoforms. Isoform
      I is an entirely novel type of MTase which has, in addition to the TRDs at the conventional
      location, one TRD located at a non-canonical position at its N-terminus. Isoform II is
      represented by the same MTase, but without the N-terminal TRD. The N-terminal TRD provides
      HaeII methylation specificity to isoform I. The TRD is fully functional when engineered into
      either the conventional variable region of M.PhiBssHII or the related monospecific M.Phi3TII
      MTase. The implications of this structural plasticity with respect to the evolution of MTases
      are discussed.
AU  - Sethmann S
AU  - Ceglowski P
AU  - Willert J
AU  - Iwanicka-Nowicka R
AU  - Trautner TA
AU  - Walter J
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1999 18: 3502-3508.

PMID- 19597163
VI  - 26
DP  - 2009
TI  - Genes within genes: multiple LAGLIDADG homing endonucleases target the ribosomal protein S3 gene encoded within an rnl group I intron of  Ophiostoma and related taxa.
PG  - 2299-2315
AB  - In some ascomycete fungi, ribosomal protein S3 (Rps3) is encoded within a group I intron
      (mL2449) that is inserted in the U11 region of the
      mitochondrial large subunit rDNA (rnl) gene. Previous characterization of
      the mL2449 intron in strains of Ophiostoma novo-ulmi subspecies americana
      (Dutch Elm Disease) revealed a complex genes-within-genes arrangement
      whereby a LAGLIDADG homing endonuclease gene (HEG) is inserted into the
      RPS3 gene near the 3' terminus, creating a hybrid Rps3-LAGLIDADG fusion
      protein. Here, we examined 119 additional strains of Ophiostoma and
      related taxa representing 85 different species by a polymerase chain
      reaction- based survey and detected both short (approximately 1.6 kb) and
      long (>2.2 kb) versions of the mL2449 intron in 88 and 31 strains,
      respectively. Among the long versions encountered, 21 were sequenced,
      revealing the presence of either intact or degenerated HEG-coding regions
      inserted within the RPS3 gene. Surprisingly, we identified two new HEG
      insertion sites in RPS3; one near the original C-terminal insertion site
      and one near the N-terminus of RPS3. In all instances, the HEGs are fused
      in-frame with the RPS3-coding sequences to create fusion proteins.
      However, comparative sequence analysis showed that upon insertion, the
      HEGs displaced a portion of the RPS3-coding region. Remarkably, the
      displaced RPS3-coding segments are duplicated and fused in-frame to the 3'
      end of RPS3, restoring a full-length RPS3 gene. We cloned and expressed
      the LAGLIDADG portion of two Rps3-HEG fusions, and showed that I-OnuI and
      I-LtrI generate 4 nucleotide (nt), 3' overhangs, and cleave at or 1 nt
      upstream of the HEG insertion site, respectively. Collectively, our data
      indicate that RPS3 genes are a refuge for distinct types of LAGLIDADG HEGs
      that are defined by the presence of duplicated segments of the host gene
      that restore the RPS3 gene, thus minimizing the impact of the HEG
      insertion on Rps3 function.
AU  - Sethuraman J
AU  - Majer A
AU  - Friedrich NC
AU  - Edgell DR
AU  - Hausner G
PT  - Journal Article
TA  - Mol. Biol. Evol.
JT  - Mol. Biol. Evol.
SO  - Mol. Biol. Evol. 2009 26: 2299-2315.

PMID- 19429624
VI  - 191
DP  - 2009
TI  - Genome sequence of Azotobacter vinelandii, an obligate aerobe specialized to support diverse anaerobic metabolic processes.
PG  - 4534-4545
AB  - Azotobacter vinelandii is a soil bacterium related to the Pseudomonas genus that fixes
      nitrogen under aerobic conditions while simultaneously
      protecting nitrogenase from oxygen damage. In response to carbon
      availability, this organism undergoes a simple differentiation process to
      form cysts that are resistant to drought and other physical and chemical
      agents. Here we report the complete genome sequence of A. vinelandii DJ,
      which has a single circular genome of 5,365,318 bp. In order to reconcile
      an obligate aerobic lifestyle with exquisitely oxygen-sensitive processes,
      A. vinelandii is specialized in terms of its complement of respiratory
      proteins. It is able to produce alginate, a polymer that further protects
      the organism from excess exogenous oxygen, and it has multiple
      duplications of alginate modification genes, which may alter alginate
      composition in response to oxygen availability. The genome analysis
      identified the chromosomal locations of the genes coding for the three
      known oxygen-sensitive nitrogenases, as well as genes coding for other
      oxygen-sensitive enzymes, such as carbon monoxide dehydrogenase and
      formate dehydrogenase. These findings offer new prospects for the wider
      application of A. vinelandii as a host for the production and
      characterization of oxygen-sensitive proteins.
AU  - Setubal JC et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2009 191: 4534-4545.

PMID- 6306590
VI  - 11
DP  - 1983
TI  - A new restriction endonuclease from Acetobacter pasteurianus.
PG  - 4409-4415
AB  - A restriction endonuclease, ApaI, has been partially purified from Acetobacter
      pasteurianus.  This enzyme cleaves bacteriophage lambda DNA and Simian virus 40
      DNA at one site, adenovirus-2 DNA at more than nine sites, but it does not
      cleave PhiX174 DNA nor plasmid pBR322 DNA.  This enzyme recognizes the
      sequence5' GGGCC^C 3' 3' C^CGGG 5'and cuts at the sites indicated by the
      arrows.
AU  - Seurinck J
AU  - Van de Voorde A
AU  - Van Montagu M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1983 11: 4409-4415.

PMID- 29567731
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of 12 Dry-Heat-Resistant Bacillus Strains Isolated from the Cleanrooms Where the Viking Spacecraft Were Assembled.
PG  - e00094-18
AB  - Spore-forming microorganisms are of concern for forward contamination because they can survive
      harsh interplanetary travel. Here, we report the draft genome
      sequences of 12 spore-forming strains isolated from the Manned Spacecraft
      Operations Building (MSOB) and the Vehicle Assembly Building (VAB) in Cape
      Canaveral, FL, where the Viking spacecraft were assembled.
AU  - Seuylemezian A
AU  - Cooper K
AU  - Schubert W
AU  - Vaishampayan P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00094-18.

PMID- 28860236
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Solibacillus kalamii, Isolated from an Air Filter Aboard the International Space Station.
PG  - e00696-17
AB  - We report here the draft genome of Solibacillus kalamii ISSFR-015, isolated from  a
      high-energy particulate arrestance filter aboard the International Space
      Station. The draft genome sequence of this strain contains 3,809,180 bp with an
      estimated G+C content of 38.61%.
AU  - Seuylemezian A
AU  - Singh NK
AU  - Vaishampayan P
AU  - Venkateswaran K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00696-17.

PMID- 29439046
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Acinetobacter and Bacillus Strains Isolated from Spacecraft-Associated Surfaces.
PG  - e01554-17
AB  - We report here the draft genome sequences of four strains isolated from spacecraft-associated
      surfaces exhibiting increased resistance to stressors such
      as UV radiation and exposure to H2O2 The draft genomes of strains 1P01SC(T),
      FO-92(T), 50v1, and 2P01AA had sizes of 5,500,894 bp, 4,699,376 bp, 3,174,402 bp,
      and 4,328,804 bp, respectively.
AU  - Seuylemezian A
AU  - Vaishampayan P
AU  - Cooper K
AU  - Venkateswaran K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01554-17.

PMID- 30533937
VI  - 7
DP  - 2018
TI  - Whole-Genome Sequences of Two Pseudomonas fluorescens Strains Isolated from Roots of Tomato and Cucumber Plants.
PG  - e00974-18
AB  - Pseudomonas fluorescens strain EC1 was isolated from Cucumis sativus (cucumber) roots, and P.
      fluorescens SC1 was isolated from Solanum lycopersicum (tomato)
      roots. The P. fluorescens SC1 genome has a total sequence length of 6,157,842 bp,
      and the P. fluorescens EC1 genome has a total sequence length of 6,125,428 bp.
AU  - Sevigny JL
AU  - LaJoie J
AU  - Shehata S
AU  - Christensen E
AU  - Cornfield S
AU  - Koziol L
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e00974-18.

PMID- 8003045
VI  - 20
DP  - 1994
TI  - Affinity modification of restriction-endonuclease EcoRII by DNA duplex containing a monosubstituted pyrophosphate internucleotide bond.
PG  - 413-419
AB  - An oligonucleotide duplex with an active monosubstituted pyrophosphate bond within the
      recognition site of the EcoRII restriction endonuclease was cross-linked to this enzyme with a
      yield of 10-15%. The cross-linking specificity was proved by the absence of the cross-linking
      to a DNA duplex with the same modification but without the EcoRII recognition site as well as
      by unmodified EcoRII substrate's inhibition of the cross-linking.
AU  - Shabarova ZA
AU  - Sheflyan GY
AU  - Kuznetsova SA
AU  - Kubareva EA
AU  - Sysoev ON
AU  - Ivanovskaya MG
AU  - Gromova ES
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1994 20: 413-419.

PMID- 28104662
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of Three Cupriavidus Strains Isolated from Various Malaysian Environments.
PG  - e01498-16
AB  - Cupriavidus sp. USMAA1020, USMAA2-4, and USMAHM13 are capable of producing
      polyhydroxyalkanoate (PHA). This biopolymer is an alternative solution to
      synthetic plastics, whereby polyhydroxyalkanoate synthase is the key enzyme
      involved in PHA biosynthesis. Here, we report the complete genomes of three
      Cupriavidus sp. strains: USMAA1020, USMAA2-4, and USMAHM13.
AU  - Shafie NA
AU  - Lau NS
AU  - Ramachandran H
AU  - Amirul AA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01498-16.

PMID- 26067950
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Paenibacillus sp. Strain DMB20, Isolated from Alang Ship-Breaking Yard, Which Harbors Genes for Xenobiotic Degradation.
PG  - e00554-15
AB  - Paenibacillus sp. strain DMB20, in cometabolism with other Proteobacteria and Firmicutes,
      exhibits azoreduction of textile dyes. Here, we report the draft
      genome sequence of this bacterium, consisting of 6,647,181 bp with 7,668 coding
      sequences (CDSs). The data presented highlight multiple sets of functional genes
      associated with xenobiotic compound degradation.
AU  - Shah B
AU  - Jain K
AU  - Patel N
AU  - Pandit R
AU  - Patel A
AU  - Joshi CG
AU  - Madamwar D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00554-15.

PMID- 29650582
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of 12 Clinical and Environmental Methicillin-Resistant Staphylococcus pseudintermedius Strains Isolated from a Veterinary Teaching  Hospital in Washington State.
PG  - e00290-18
AB  - Methicillin-resistant Staphylococcus pseudintermedius (MRSP) is a globally emergent
      multidrug-resistant pathogen of dogs associated with nosocomial
      transmission in dogs and with potential zoonotic impacts. Here, we report the
      draft whole-genome sequences of 12 hospital-associated MRSP strains and their
      resistance genotypes and phenotypes.
AU  - Shah DH
AU  - Jones LP
AU  - Paul N
AU  - Davis MA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00290-18.

PMID- 29496839
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of a Ciprofloxacin-Resistant Salmonella enterica subsp.  enterica Serovar Kentucky Sequence Type 198 Strain, PU131, Isolated from a Human Patient in Washington State.
PG  - e00125-18
AB  - Strains of the ciprofloxacin-resistant (Cip(r)) Salmonella enterica subsp. enterica serovar
      Kentucky sequence type 198 (ST198) have rapidly and extensively
      disseminated globally to become a major food safety and public health concern.
      Here, we report the complete genome sequence of a Cip(r)S. Kentucky ST198 strain,
      PU131, isolated from a human patient in Washington State (USA).
AU  - Shah DH
AU  - Paul NC
AU  - Guard J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00125-18.

PMID- 18023966
VI  - 158
DP  - 2007
TI  - In vivo restriction endonuclease activity of the Anabaena PCC 7120 XisA protein in Escherichia coli.
PG  - 679-684
AB  - Anabaena PCC 7120 genome contains three elements, which get excised out during late stages of
      heterocyst differentiation by a site-specific
      recombination process. The XisA protein, which excises the nifD
      element, shows sequence homology with the integrase family of tyrosine
      recombinase. The 11 by target site of XisA CGGAGTAATCC contains a 3 bp
      inverted repeat. Here, we report restriction endonuclease activity of
      XisA by specific loss of plasmids containing single or double target
      sites. The pMX25 plasmid containing two tat-get sites demonstrated
      endonuclease activity proportional to excision frequency. Different
      plasmid substrates containing one base pair mutation in the inverted
      repeat of the target site were monitored for endonuclease activity.
      Mutation of A4C retained endonuclease activity, while other
      modifications lost endonuclease activity. The presence of an additional
      copy of the target site enhanced endonuclease activity. These results
      suggest that the XisA protein could be an IIE type of restriction
      endonuclease in addition to being a recombinase. (C) 2007 Elsevier
      Masson SAS. All rights reserved.
AU  - Shah GR
AU  - Karunakaran R
AU  - Kumar GN
PT  - Journal Article
TA  - Res. Microbiol.
JT  - Res. Microbiol.
SO  - Res. Microbiol. 2007 158: 679-684.

PMID- 25635022
VI  - 3
DP  - 2015
TI  - Draft Whole-Genome Sequence of Bacillus altitudinis Strain B-388, a Producer of Extracellular RNase.
PG  - e01502-14
AB  - Here, we present a draft genome sequence of Bacillus altitudinis strain B-388, including a
      putative plasmid. The strain was isolated from the intestine of
      Indian meal moth, a common pest of stored grains, and it is characterized by the
      production of extracellular RNase, similar to binase, which is of interest for
      comparative studies and biotechnology.
AU  - Shah MR
AU  - Ulyanova V
AU  - Malanin S
AU  - Dudkina E
AU  - Vershinina V
AU  - Ilinskaya O
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01502-14.

PMID- 24158552
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences of Bordetella hinzii and Bordetella trematum.
PG  - e00838-13
AB  - Bordetella hinzii colonizes the respiratory tracts of poultry but can also infect
      immunocompromised humans. Bordetella trematum, however, only infects humans,
      causing ear and wound infections. Here, we present the first draft genome
      sequences of strains B. hinzii ATCC 51730 and B. trematum CCUG 13902.
AU  - Shah NR
AU  - Moksa M
AU  - Novikov A
AU  - Perry MB
AU  - Hirst M
AU  - Caroff M
AU  - Fernandez RC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00838-13.

PMID- 26494660
VI  - 3
DP  - 2015
TI  - Genome Sequence of 'Candidatus Thioglobus autotrophica' Strain EF1, a Chemoautotroph from the SUP05 Clade of Marine Gammaproteobacteria.
PG  - e01156-15
AB  - Chemoautotrophic marine bacteria from the SUP05 clade of marine gammaproteobacteria often
      dominate low-oxygen waters in upwelling regions, fjords, and hydrothermal systems. Here, we
      announce the complete genome sequence  of 'Candidatus Thioglobus autotrophica' strain EF1,
      the first cultured chemoautotrophic representative from the SUP05 clade.
AU  - Shah V
AU  - Morris RM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01156-15.

PMID- 21994930
VI  - 193
DP  - 2011
TI  - Whole-Genome Sequence of Streptococcus pseudopneumoniae Isolate IS7493.
PG  - 6102-6103
AB  - Streptococcus pseudopneumoniae is a member of the viridans group streptococci (VGS) whose
      pathogenic significance is unclear. We announce
      the complete genome sequence of S. pseudopneumoniae IS7493. The genome
      sequence will assist in the characterization of this new organism and
      facilitate the development of accurate diagnostic assays to distinguish it
      from Streptococcus pneumoniae and Streptococcus mitis.
AU  - Shahinas D
AU  - Tamber GS
AU  - Arya G
AU  - Wong A
AU  - Lau R
AU  - Jamieson F
AU  - Ma JH
AU  - Alexander DC
AU  - Low DE
AU  - Pillai DR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6102-6103.

PMID- 18578505
VI  - 47
DP  - 2008
TI  - C-13 relaxation studies of the DNA target sequence for HhaI methyltransferase reveal unique motional properties.
PG  - 7617-7625
AB  - The goal of this work was to examine if sequence-dependent conformational flexibility in DNA
      plays a role in base extrusion, a
      common conformational change induced by many DNA-modifying enzymes. We
      studied the dynamics of the double-stranded DNA target of the HhaI
      methyltransferase by recording an extensive set of C-13 NMR relaxation
      parameters. We observe that the cytidine furanose rings experience fast
      (picosecond to nanosecond) motions that are not present in other
      nucleotides; the methylation site experiences particularly high
      mobility. We also observe that the bases of guanosine and cytidine
      residues within the HhaI recognition sequence GCGC experience motions
      on a much slower (1-100 mu s) time scale. We compare these observations
      with previous solution and solid-state NMR studies of the EcoRI
      nuclease target sequence, and solid-state NMR studies of a similar HhaI
      target construct. While an increased mobility of cytidine furanose
      rings compared to those of other nucleotides is observed for both
      sequences, the slower motions are only observed in the HhaI target DNA.
      We propose that this inherent flexibility lowers the energetic barriers
      that must occur when the DNA binds to the HhaI methyltransferase and
      for extrusion of the cytidine prior to its methylation.
AU  - Shajani Z
AU  - Varani G
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2008 47: 7617-7625.

PMID- 22548694
VI  - 12
DP  - 2012
TI  - Clonal complexes and virulence factors of Staphylococcus aureus from several cities in India.
PG  - 64
AB  - BACKGROUND: Diseases from Staphylococcus aureus are a major problem in Indian
      hospitals and recent studies point to infiltration of community associated
      methicillin resistant S. aureus (CA-MRSA) into hospitals. Although CA-MRSA are
      genetically different from nosocomial MRSA, the distinction between the two
      groups is blurring as CA-MRSA are showing multidrug resistance and are endemic in
      many hospitals. Our survey of samples collected from Indian hospitals between
      2004 and 2006 had shown mainly hospital associated methicillin resistant
      Staphylococcus aureus (HA-MRSA) carrying staphylococcal cassette chromosome mec
      (SCCmec) type III and IIIA. But S. aureus isolates collected from 2007 onwards
      from community and hospital settings in India have shown SCCmec type IV and V
      cassettes while several variations of type IV SCCmec cassettes from IVa to IVj
      have been found in other parts of the world. In the present study, we have
      collected nasal swabs from rural and urban healthy carriers and pus, blood etc
      from in patients from hospitals to study the distribution of SCCmec elements and
      sequence types (STs) in the community and hospital environment. We performed
      molecular characterization of all the isolates to determine their lineage and
      microarray of select isolates from each sequence type to analyze their toxins,
      virulence and immune-evasion factors. RESULTS: Molecular analyses of 68 S. aureus
      isolates from in and around Bengaluru and three other Indian cities have been
      carried out. The chosen isolates fall into fifteen STs with all major clonal
      complexes (CC) present along with some minor ones. The dominant MRSA clones are
      ST22 and ST772 among healthy carriers and patients. We are reporting three novel
      clones, two methicillin sensitive S. aureus (MSSA) isolates belonging to ST291
      (related to ST398 which is live stock associated), and two MRSA clones, ST1208
      (CC8), and ST672 as emerging clones in this study for the first time. Sixty nine
      percent of isolates carry Panton- Valentine Leucocidin genes (PVL) along with
      many other toxins. There is more diversity of STs among methicillin sensitive S.
      aureus than resistant ones. Microarray analysis of isolates belonging to
      different STs gives an insight into major toxins, virulence factors, adhesion and
      immune evasion factors present among the isolates in various parts of India.
      CONCLUSIONS: S. aureus isolates reported in this study belong to a highly diverse
      group of STs and CC and we are reporting several new STs which have not been
      reported earlier along with factors influencing virulence and host pathogen
      interactions.
AU  - Shambat S
AU  - Nadig S
AU  - Prabhakara S
AU  - Bes M
AU  - Etienne J
AU  - Arakere G
PT  - Journal Article
TA  - BMC Microbiol.
JT  - BMC Microbiol.
SO  - BMC Microbiol. 2012 12: 64.

PMID- 27635006
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Four Novel Thermal- and Alkaline-Tolerant Egyptian Rhizobium Strains Nodulating Berseem Clover.
PG  - e00988-16
AB  - Four Rhizobium strains were isolated from berseem clover in Egypt. The symbiotically
      effective, salt-tolerant, strain Rhiz950 was identified as new
      species, Rhizobium aegypticaum sv. trifolii (USDA 7124(T)). The other three
      thermal- and pH-tolerant strains were identified as Rhizobium bangladeshense sv.
      trifolii, the type strain is USDA 7125(T).
AU  - Shamseldin A
AU  - Nelson MS
AU  - Staley C
AU  - Guhlin J
AU  - Sadowsky MJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00988-16.

PMID- 24604650
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Agar-Degrading Bacterium Catenovulum sp. Strain DS-2, Isolated from Intestines of Haliotis diversicolor.
PG  - e00144-14
AB  - Catenovulum sp. strain DS-2, isolated from intestines of Haliotis diversicolor, is able to
      degrade agar and produce agaro-oligosaccharides. Here, we report the
      draft genome sequence of Catenovulum sp. strain DS-2.
AU  - Shan D
AU  - Li X
AU  - Gu Z
AU  - Wei G
AU  - Gao Z
AU  - Shao Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00144-14.

PMID- 24604651
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Carrageenan-Degrading Bacterium Cellulophaga sp. Strain KL-A, Isolated from Decaying Marine Algae.
PG  - e00145-14
AB  - Cellulophaga sp. strain KL-A, isolated from decaying marine algae, is able to degrade
      iota-carrageenan. Here, we report the draft genome sequence of
      Cellulophaga sp. strain KL-A.
AU  - Shan D
AU  - Ying J
AU  - Li X
AU  - Gao Z
AU  - Wei G
AU  - Shao Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00145-14.

PMID- 28912322
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Streptomyces sp. XY006, an Endophyte Isolated from Tea (Camellia sinensis).
PG  - e00971-17
AB  - Streptomyces sp. XY006 is an endophytic bacterium isolated from the young leaf material of the
      tea plant (Camellia sinensis). The draft genome consists of 8.2
      Mb and encodes 7,415 putative open reading frames. This strain is found to
      contain a high capacity for the production of natural products.
AU  - Shan W
AU  - Liu H
AU  - Zhou Y
AU  - Yu X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00971-17.

PMID- 24356823
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Ralstonia solanacearum Race 4 Biovar 4 Strain SD54.
PG  - e00890-13
AB  - Ralstonia solanacearum is an important etiological agent that can cause serious bacterial wilt
      in a very wide range of potential host plants, including ginger.
      Here, we report the complete genome sequence of R. solanacearum SD54, a race 4
      biovar 4 (R4B4) strain from a diseased ginger plant in China.
AU  - Shan W
AU  - Yang X
AU  - Ma W
AU  - Yang Y
AU  - Guo X
AU  - Guo J
AU  - Zheng H
AU  - Li G
AU  - Xie B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00890-13.

PMID- 25494783
VI  - 141
DP  - 2014
TI  - Hydration properties of natural and synthetic DNA sequences with methylated adenine or cytosine bases in the R.DpnI target and BDNF promoter studied by molecular dynamics simulations.
PG  - 22D512
AB  - Adenine and cytosine methylation are two important epigenetic modifications of DNA sequences
      at the levels of the genome and transcriptome. To characterize the differential roles of
      methylating adenine or cytosine with respect to their hydration properties, we performed
      conventional MD simulations and free energy perturbation calculations for two particular DNA
      sequences, namely the brain-derived neurotrophic factor (BDNF) promoter and the R.DpnI-bound
      DNA that are known to undergo methylation of C5-methyl cytosine and N6-methyl adenine,
      respectively. We found that a single methylated cytosine has a clearly favorable hydration
      free energy over cytosine since the attached methyl group has a slightly polar character. In
      contrast, capping the strongly polar N6 of adenine with a methyl group gives a slightly
      unfavorable contribution to its free energy of solvation. Performing the same demethylation in
      the context of a DNA double-strand gave quite similar results for the more solvent-accessible
      cytosine but much more unfavorable results for the rather buried adenine. Interestingly, the
      same demethylation reactions are far more unfavorable when performed in the context of the
      opposite (BDNF or R.DpnI target) sequence. This suggests a natural preference for methylation
      in a specific sequence context. In addition, free energy calculations for demethylating
      adenine or cytosine in the context of B-DNA vs. Z-DNA suggest that the conformational B-Z
      transition of DNA transition is rather a property of cytosine methylated sequences but is not
      preferable for the adenine-methylated sequences investigated here.
AU  - Shanak S
AU  - Helms V
PT  - Journal Article
TA  - J. Chem. Phys.
JT  - J. Chem. Phys.
SO  - J. Chem. Phys. 2014 141: 22D512.

PMID- 24407652
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Asaia sp. Strain SF2.1, an Important Member of the Microbiome of Anopheles Mosquitoes.
PG  - e01202-13
AB  - Asaia spp. are abundant members of the microbiota of Anopheles mosquitoes, the principle
      vectors of malaria. Here, we report the draft genome sequence of Asaia
      sp. strain SF2.1. This strain is under development as a platform to deliver
      antimalarial peptides and proteins to adult female Anopheles mosquitoes.
AU  - Shane JL
AU  - Bongio NJ
AU  - Favia G
AU  - Lampe DJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01202-13.

PMID- 29674561
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of the Heavy-Metal-Tolerant Endophytic Type Strain of Salinicola tamaricis.
PG  - e00358-18
AB  - The first complete genome sequence of a recently described Salinicola tamaricis species was
      determined for the strain F01(T) (=CCTCC AB 2015304(T) =KCTC
      42855(T)). The strain was isolated from the leaves of wetland plant Tamarix
      chinensis Lour and shows a high tolerance to heavy metals, such as manganese,
      nickel, lead, and copper ions.
AU  - Shang N
AU  - Zhu Q
AU  - Dai M
AU  - Zhao G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00358-18.

PMID- 24211387
VI  - 534
DP  - 2014
TI  - Restriction enzyme cutting site distribution regularity for DNA looping technology.
PG  - 222-228
AB  - The restriction enzyme cutting site distribution regularity and looping conditions were
      studied systematically. We obtained the restriction enzyme
      cutting site distributions of 13 commonly used restriction enzymes in 5 model
      organism genomes through two novel self-compiled software programs. All of the
      average distances between two adjacent restriction sites fell sharply with
      increasing statistic intervals, and most fragments were 0-499bp. A shorter DNA
      fragment resulted in a lower looping rate, which was also directly proportional
      to the DNA concentration. When the length was more than 500bp, the concentration
      did not affect the looping rate. Therefore, the best known fragment length was
      longer than 500bp, and did not contain the restriction enzyme cutting sites which
      would be used for digestion. In order to make the looping efficiencies reach
      nearly 100%, 4-5 single cohesive end systems were recommended to digest the
      genome separately.
AU  - Shang Y
AU  - Zhang N
AU  - Zhu P
AU  - Luo Y
AU  - Huang K
AU  - Tian W
AU  - Xu W
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 2014 534: 222-228.

PMID- 27932638
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Three Hypervirulent Carbapenem-Resistant Klebsiella pneumoniae Isolates from Bacteremia.
PG  - e01081-16
AB  - Hypervirulent Klebsiella pneumoniae strains have been increasingly reported worldwide, and
      there is emergence of carbapenem resistance among them. Here, we
      report the genome sequences of three carbapenem-resistant hypervirulent K.
      pneumoniae isolates isolated from bacteremic patients at a tertiary-care center
      in South India.
AU  - Shankar C
AU  - Nabarro LE
AU  - Devanga RNK
AU  - Muthuirulandi SDP
AU  - Daniel JL
AU  - Doss CGP
AU  - Veeraraghavan B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01081-16.

PMID- 27834717
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of an Extended-Spectrum-beta-Lactamase-Positive Hypervirulent Klebsiella pneumoniae Strain with Novel Sequence Type 2318 Isolated  from a Neonate.
PG  - e01273-16
AB  - Antimicrobial resistance among hypervirulent Klebsiella pneumoniae is increasingly reported.
      Here, we report the draft genome sequence of a
      hypervirulent K. pneumoniae strain isolated from a neonate with sepsis belonging
      to novel sequence type 2318 (ST2318).
AU  - Shankar C
AU  - Santhanam S
AU  - Kumar M
AU  - Gupta V
AU  - Devanga RNK
AU  - Veeraraghavan B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01273-16.

PMID- 30533897
VI  - 7
DP  - 2018
TI  - Genome Sequence of a Moderately Halophilic Bacillus cereus Strain, TS2, Isolated  from Saltern Sediments.
PG  - e00873-18
AB  - We report the 5.3-Mbp genome sequence of Bacillus cereus strain TS2, which was isolated from
      the sediments of a solar saltern in southern India. Genome analysis
      of B. cereus TS2, a salt-resistant strain, will improve our understanding of how
      B. cereus, a food pathogen, responds to hyperosmotic stress.
AU  - Shankar M
AU  - Mageswari A
AU  - Suganthi C
AU  - Gunasekaran P
AU  - Gothandam KM
AU  - Karthikeyan S
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e00873-18.

PMID- 22843603
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Plant Growth-Promoting Bacterium Enterobacter cloacae GS1.
PG  - 4479
AB  - Here, we present the genome sequence of Enterobacter cloacae GS1. This strain proficiently
      colonizes rice roots and promotes plant growth by improving plant
      nutrition. Analyses of the E. cloacae GS1 genome will throw light on the genetic
      factors involved in root colonization, growth promotion, and ecological success
      of this rhizobacterium.
AU  - Shankar M
AU  - Ponraj P
AU  - Ilakiam D
AU  - Rajendhran J
AU  - Gunasekaran P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4479.

PMID- 8370536
VI  - 131
DP  - 1993
TI  - Purification and characterization of restriction endonuclease MgoI from Mycobacterium gordonae.
PG  - 153-154
AB  - A restriction endonuclease, MgoI an isoschizomer of Sau3AI, was purified from Mycobacterium
      gordonae TRC1318. As compared to Sau3AI, the yield of MgoI was seven-eight fold higher, the
      enzyme was four times more stable at 37C, and in addition, had optimal activity over a much
      broader range of salt concentrations.
AU  - Shankar S
AU  - Tyagi AK
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1993 131: 153-154.

PMID- 8406034
VI  - 132
DP  - 1993
TI  - MchAI and MchAII, two class-II restriction endonucleases from Mycobacterium chelonei.
PG  - 119-123
AB  - We have purified and characterized two class-II restriction endonucleases from the saprophyte
      Mycobacterium chelonei AMB 82. MchAI was an isoschizomer of NotI recognizing and cleaving at
      5'-GC/GGCCGC. MchAI did not require Triton X-100 for activity and was fully active at
      concentrations over 10-200 mM KCl and MgCl2. MchAII was an isoschizomer of HaeIII recognizing
      and cleaving at 5'-GG/CC. MchAII was active in 10 mM and was inactive at KCl concentrations
      lower than 250 mM.
AU  - Shankar S
AU  - Tyagi AK
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1993 132: 119-123.

PMID- 1614878
VI  - 20
DP  - 1992
TI  - MhaAI, a novel isoschizomer of PstI from Mycobacterium habana recognizing 5'-CTGCA/G-3'.
PG  - 2891
AB  - We have isolated a novel class II restriction endonuclease, MhaAI, from Mycobacterium habana
      strain 206 which recognizes the sequence 5'-CTGCA/G-3' and generates 3' protruding
      fragments. Unlike its isoschizomer PstI, MhaAI did not exhibit star activity even at glycerol
      concentrations as high as 35% and at units/ug DNA ratios greater than 300. MhaAI was fully
      active in low salt (10 mM Tris pH 8.0, 10 mM MgCl2) in comparison to PstI, which requires NaCl
      at a concentration of 50-100 mM for optimal activity. MhaAI was also found equally active in
      10 to 200 mM concentration range of KCl as well as MgCl2. The enzyme, however, was inhibited
      by NaCl concentrations greater than 50 mM.
AU  - Shankar S
AU  - Tyagi AK
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 2891.

PMID- 1614877
VI  - 20
DP  - 1992
TI  - MfoAI, a novel isoschizomer of HaeIII from Mycobacterium fortuitum recognizing 5'-GG/CC-3' .
PG  - 2890
AB  - We have isolated a novel class II restriction endonuclease, MfoAI, from Mycobacterium
      fortuitum TMC 1529 which recognizes the sequence 5'-GG/CC-3' generating blunt ended
      fragments. MfoAI was found to have a very high affinity for phosphocellulose and eluted late
      at a concentration of 1.8 M KCl. This permitted very rapid purification of the enzyme
      completely free from non-specific nucleases. In contrast to the situation in Haemophilus
      aegyptius which has HaeIII and HaeII, MfoAI was found to be the only activity associated with
      M. fortuitum TMC 1529, suggesting this organism to be a better source for this enzyme. In
      addition, the activity of MfoAI was independent of salt concentration and purified MfoAI was
      equally active in 10-200 mM concentrations of KCl, MgCl2 and NaCl and in the wide pH range of
      7.4-11.0.
AU  - Shankar S
AU  - Tyagi AK
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 2890.

PMID- 1322684
VI  - 12
DP  - 1992
TI  - Silmut: A Computer Program for the Identification of Regions Suitable for Silent Mutagenesis to Introduce Restriction Enzyme Recognition Sequences.
PG  - 882-884
AB  - We describe a set of IBM-compatible computer programs designed to selectively identify the
      potential sites for silent mutagenesis within a target DNA sequence. This program is based on
      a novel strategy of identifying amino acid motifs compatible with each restriction site
      (BioTechniques 12:382-384m 1991). The programs can be used to identify the suitability for the
      introduction of any 6-base nucleic acid sequences, such as restriction enzyme sites in
      cassette mutagenesis strategies. The Table program generates a table of multiple amino acid
      motifs for each restriction enzyme, obtained by translating each unique recognition sequence
      in all three reading frames. The Silmut program which utilizes the features of Table, will
      further identify the presence of a match betwen any amino acid motif of each restriction
      enzyme and the input target sequence. Minor manipulations of the database files will enable
      the individual researcher to identify the potential for introduction of any 6-base sequences
      by silent mutagenesis.
AU  - Shankarappa B
AU  - Vijayananda K
AU  - Ehrlich G
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 1992 12: 882-884.

PMID- 25195760
VI  - 70
DP  - 2014
TI  - Structural basis for the substrate selectivity of PvuRts1I, a 5-hydroxymethylcytosine DNA restriction endonuclease.
PG  - 2477-2486
AB  - 5-Hydroxymethylation is a curious modification of cytosine that was discovered some decades
      ago, but its functional role in eukaryotes still awaits elucidation. 5-Hydroxymethylcytosine
      is an epigenetic marker that is crucial for multiple biological processes. The profile is
      altered under certain disease conditions such as cancer, Huntington's disease and
      Alzheimer's disease. Using the DNA-modification-dependent restriction endonuclease AbaSI
      coupled with sequencing (Aba-seq), the hydroxymethylome can be deciphered at the resolution of
      individual bases. The method is based on the enzymatic properties of AbaSI, a member of the
      PvuRts1I family of endonucleases. PvuRts1I is a modification-dependent endonuclease with high
      selectivity for 5-hydroxymethylcytosine over 5-methylcytosine and cytosine. In this study, the
      crystal structure of PvuRts1I was determined in order to understand and improve the substrate
      selectivity. A nuclease domain and an SRA-like domain are located at the N- and C-termini,
      respectively. Through comparison with other SRA-domain structures, the SRA-like domain was
      proposed to be the 5-hmC recognition module. Several mutants of PvuRts1I with enzymatic
      activity restricted to 5-hydroxymethylcytosine only were generated based on the structural
      analysis, and these enzyme variants are appropriate for separating the hydroxymethylome from
      the wider methylome.
AU  - Shao C
AU  - Wang C
AU  - Zang J
PT  - Journal Article
TA  - Acta Crystallogr. D Biol. Crystallogr.
JT  - Acta Crystallogr. D Biol. Crystallogr.
SO  - Acta Crystallogr. D Biol. Crystallogr. 2014 70: 2477-2486.

PMID- 8620003
VI  - 35
DP  - 1996
TI  - Protein splicing: Evidence for an N-O acyl rearrangement as the initial step in the splicing process.
PG  - 3810-3815
AB  - Protein splicing involves the self-catalyzed formation of a branched
      intermediate, which then resolves into the excised intervening sequence and the spliced
      protein.  A possible mechanism for branched intemediate formation is an N-O
      rearrangement of the peptide bond involving the amino group of the conserved
      serine/cysteine residue at the upstream splice junction to yield a linear peptide ester
      intermediate.  This possibility was examined using an in vitro splicing system involving the
      intervening sequence from the DNA polymerase of the extremely thermophilic archeon,
      Pyrococcus sp. GB-D.  Because thioesters react much more rapidly with nitrogen
      nucleophiles at neutral pH than do oxygen esters, protein-splicing precursors in which the
      serine residue of interest was replaced by cysteine were constructed and purified.  In the
      presence of 0.25M hydroxylamine or 0.1M ethylene diamine at pH 6 or higher, these
      constructs underwent rapid cleavage at the upstream splice junction, consistent with the
      aminolysis of a thioester.  The site of hydroxylaminolysis was identified by analysis of the
      C-terminus of the polypeptide cleavage products.  Comparison of the C-terminal peptide
      hydroxamate with the synthetic peptide hydroxamates with respect to chromatographic
      mobility, colorimetric assay, amino acid composition, and high-resolution mass
      spectrometry showed that the hydroxylamine-sensitive site in the splicing precursor was the
      peptide bond adjacent to the serine residue at the upstream splice junction.  These results
      provide evidence that the peptide bond at the upstream splice junction can undergo a self-
      catalyzed N-O or N-S acyl rearrangement to yield a linear polypeptide ester intermediate
      and suggest that this kind of rearrangement constitutes the first step in protein splicing.
AU  - Shao Y
AU  - Xu M-Q
AU  - Paulus H
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1996 35: 3810-3815.

PMID- 7662664
VI  - 34
DP  - 1995
TI  - Protein splicing: characterization of the aminosuccinimide residue at the carboxyl terminus of the excised intervening sequence.
PG  - 10844-10850
AB  - Protein splicing is a self-catalyzed, posttranslational process which
      converts a precursor polypeptide into two new proteins by the excision of an internal
      polypeptide segment and the ligation of the flanking polypeptides.  Evidence has been
      presented that protein splicing involves a branched intermediate, which is resolved into the
      two protein products by the cyclization of an asparagine residue to aminosuccinimide.  This
      report describes the chemical synthesis of a peptide with a C-terminal aminosuccinimide
      residue, corresponding to the putative C-terminus of the excised intervening sequence
      (intein) derived from the thermostable DNA polymerase of Pyrococcus species GB-D.  The
      synthetic aminosuccinimide peptide was compared with the C-terminal cyanogen bromide
      peptide of the excised intein and found to be indistinguishable in terms of its
      chromatographic properties, high-resolution mass spectrum, and colorimetric assay
      involving reaction with hydroxylamine.  This establishes definitively that protein splicing is
      accompanied by the cyclization of asparagine to yield an aminosuccinimide residue at the C-
      terminus of the excised intein and that this unusual residue is therefore a natural
      constituent
      of spliced proteins.  The effects of pH and temperature on the stability of the synthetic
      aminosuccinimide peptide are described.  The stability of the C-terminal aminosuccinimide
      decreased with increasing pH, similar to the internal aminosuccinimide residues that occur
      in many proteins as intermediates in protein deamidation, but the C-terminal
      aminosuccinimide was 5-10 times more stable than internal aminosuccinimides, with a half-
      life of about 80 h at 25oC and pH 7.4, accounting for its relative ease of isolation.
AU  - Shao Y
AU  - Xu M-Q
AU  - Paulus H
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1995 34: 10844-10850.

PMID- 26044415
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Erwinia tracheiphila, an Economically Important Bacterial Pathogen of Cucurbits.
PG  - e00482-15
AB  - Erwinia tracheiphila is one of the most economically important pathogens of cucumbers, melons,
      squashes, pumpkins, and gourds in the northeastern and
      midwestern United States, yet its molecular pathology remains uninvestigated.
      Here, we report the first draft genome sequence of an E. tracheiphila strain
      isolated from an infected wild gourd (Cucurbita pepo subsp. texana) plant. The
      genome assembly consists of 7 contigs and includes a putative plasmid and at
      least 20 phage and prophage elements.
AU  - Shapiro LR
AU  - Scully ED
AU  - Roberts D
AU  - Straub TJ
AU  - Geib SM
AU  - Park J
AU  - Stephenson AG
AU  - Salaau RE
AU  - Liu Q
AU  - Beattie G
AU  - Gleason M
AU  - De Moraes CM
AU  - Mescher MC
AU  - Fleischer SG
AU  - Kolter R
AU  - Pierce N
AU  - Zhaxybayeva O
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00482-15.

PMID- 1472114
VI  - 18
DP  - 1992
TI  - Site-specific endonuclease BstM6I from the natural isolate Bacillus stearothermophilus M6.
PG  - 1186-1189
AB  - A site-specific endonuclease activity was found in extracts of Bacillus stearothermophilus M6
      isolated from molasses. The functionally pure enzyme designated as BstM6I was obtained by
      consecutive chromatographies on blue sepharose, hydroxyapatite, and heparin-sepharose. The
      endonuclease recognizes the nucleotide sequence CC^WGG in double-stranded DNA and cleaves it
      as indicated by the arrow to give one-nucleotide 5'-protruding ends. Consequently, the
      site-specific endonuclease BstM6I is an isoschizomer of BstNI.
AU  - Shapovalova NI
AU  - Ivanov LY
AU  - Matvienko NI
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1992 18: 1186-1189.

PMID- 8284231
VI  - 21
DP  - 1993
TI  - BspKT6I, a new site-specific endonuclease which cleaves the GATC site producing two nucleotide 5'-protruding ends.
PG  - 5794
AB  - A new class II restriction endonuclease BspKT6I was isolated from soil thermophilic bacteria
      Bacillus species KT6. The enzyme was purified by chromatography on blue-agarose,
      heparin-Sepharose and hydroxylapatite. Digestion of T7 DNA has revealed that the enzyme is an
      isoschizomer of Sau3AI. Cleavage points were determined by the primed-synthesis reaction using
      M13mp18 DNA. The cleavage product resulted in a band that comigrated with G (Fig 1). Upon
      addition of the DNA-polymerase, a band appeared two nucleotides higher. These results indicate
      that the enzyme recognizes the palindromic sequence G^ATC and cleaves it as indicated creating
      two nucleotide 5'-extensions. It is the first isomer of Sau3AI producing such ends. The DNA
      fragments produced by this enzyme can be ligated with PvuI-produced DNA fragments. BspKT6I is
      sensitive to dam-methylation. It does not cleave pBR322 isolated from the E. coli dam+ strain
      and results in almost complete digestion of pBR322 isolated from the dam-strain (Fig. 2). The
      optimal reaction buffer is 10 mM Tris-HCl (ph 7.5), 10 mM MgCl2.
AU  - Shapovalova NI
AU  - Zheleznaja LA
AU  - Matvienko NI
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 5794.

PMID- 7873680
VI  - 59
DP  - 1994
TI  - New site-specific endonuclease and methylase from the thermophilic strain Bacillus species KT6.
PG  - 1730-1738
AB  - The site-specific endonuclease R.BspKT6I and the cognate site-specific methylase M.BspKT6I
      were isolated to functionally pure state from the thermophilic strain Bacillus species KT6 by
      Sephadex G-100 gel filtration followed by chromatography on heparin-Sepharose and
      hydroxyapatite. Endonuclease BspKT6I is not an isoschizomer, but an isomer of Sau3AI and MboI.
      It recognizes the GAT/C sequence and cleaves it as shown by arrow, and, in distinction to
      Sau3AI and MboI, produces a protruding 3' dinucleotide. The cleavage of the site is inhibited
      by dam methylation. The sticky ends resulting from BspKT6I cleavage are identical and
      complementary to those formed after PvuI cleavage. The methylase isolated from B. species KT6
      protects the DNA from subsequent cleavage by BspKT6I. The methylated base is adenine.
AU  - Shapovalova NI
AU  - Zheleznaya LA
AU  - Matvienko NI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1994 59: 1730-1738.

PMID- 8018770
VI  - 59
DP  - 1994
TI  - A new site-specific endonuclease BspKT5I.
PG  - 485-493
AB  - A new site-specific endonuclease (BspKT5I) has been isolated from the thermophilic soil
      bacterium Bacillus KT5 by chromatography on Blue agarose, hydroxyapatite, and
      heparin-Sepharose; it is free from interfering impurities. On double-stranded DNA, BspKT5I
      recognizes the sequence 5'-CTGAAG16N^/3'-GACTTC14N^ and cleaves the DNA at the recognition
      site indicated by the arrows to form 3'-protruding dinucleotide termini. The isolated
      endonuclease is an isoschizomer of Eco57I. However, unlike Eco57I, it is not stimulated by
      S-adenosylmethionine (SAM) and thus belongs to subclass IIS and not to class IV, as Eco57I.
      Furthermore, endonuclease BspKT5I, in contrast to Eco57I, has no methylase activity.
AU  - Shapovalova NI
AU  - Zheleznaya LA
AU  - Matvienko NN
AU  - Matvienko NI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1994 59: 485-493.

PMID- 11087417
VI  - 39
DP  - 2000
TI  - Reviving a dead enzyme: cytosine deaminations promoted by an inactive DNA methyltransferase and an S-adenosylmethionine analogue.
PG  - 14611-14616
AB  - The enzymes that transfer a methyl group to C5 of cytosine within specific sequences (C5
      Mtases) deaminate the target cytosine to uracil if the methyl donor S-adenosylmethionine (SAM)
      is omitted from the reaction.  Recently, it was shown that cytosine deamination caused by C5
      Mtases M.HpaII, M.SssI and M.MspI is enhanced in the presence of several analogues of SAM, and
      a mechanism for this analogue-promoted deamination was proposed. According to this mechanism,
      the analogues protonate C5 of the target cytosine, creating a dihydrocytosine intermediate
      that is susceptible to deamination. We show here that one of these analogues,
      5'-aminoadenosine (AA), enhances cytosine deamination by the Mtase M. EcoRII, but it does so
      without enhancing protonation of C5. Further, we show that uracil is an intermediate in the
      mutational pathway and propose an alternate mechanism for the analogue-promoted deamination.
      The new mechanism involves a facilitated water attack at C4 but does not require attack at C6
      by the enzyme. The latter feature of the mechanism was tested by using M.EcoRII mutants
      defective in the nucleophilic attack at C6 in the deamination assay. We find that although
      these proteins are defective in methyl transfer and cytosine deamination, they cause cytosine
      deaminations in the presence of AA in the reaction. Our results point to a possible connection
      between the catalytic mechanism of C5 Mtases and of enzymes that transfer methyl groups to
      N(4) of cytosine. Further, they provide an unusual example where a coenzyme activates an
      otherwise "dead" enzyme to perform catalysis by a new reaction pathway.
AU  - Sharath AN
AU  - Weinhold E
AU  - Bhagwat AS
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2000 39: 14611-14616.

PMID- 26988058
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of 'Halomonas chromatireducens' Strain AGD 8-3, a Haloalkaliphilic Chromate- and Selenite-Reducing Gammaproteobacterium.
PG  - e00160-16
AB  - Here, we report the complete genome sequence (3.97 Mb) of 'Halomonas chromatireducens' AGD
      8-3, a denitrifying bacterium capable of chromate and
      selenite reduction under extreme haloalkaline conditions. This strain was
      isolated from soda solonchak soils of the Kulunda steppe, Russian Federation.
AU  - Sharko FS
AU  - Shapovalova AA
AU  - Tsygankova SV
AU  - Komova AV
AU  - Boulygina ES
AU  - Teslyuk AB
AU  - Gotovtsev PM
AU  - Namsaraev ZB
AU  - Khijniak TV
AU  - Nedoluzhko AV
AU  - Vasilov RG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00160-16.

PMID- 3705506
VI  - 32
DP  - 1986
TI  - Effect of various conditions on stability of DNA-methylases from cells of Mycobacterium smegmatis butyricum.
PG  - 125-129
AB  - DNA-methylases from M. sm. butyricum, produced by means of isoelectrofocusing, were
      characterized by slow spontaneous variations in the activity with amplitude of 75-80% under
      conditions of storage in glycerol at -10 C.  Effect of various conditions on stabilization of
      activity of adenine methylases M.Mbu4,2 and M.Mbu7,2 was studied.  Alterations in the
      enzymatic activity were not found in presence of substances applied usually to stabilize the
      enzymes, blood serum albumin and cations of two valent metals as the values of the alterations
      occurred in the ranges of the enzyme activity variations.
AU  - Sharkova EV
AU  - Nikolskaya II
AU  - Shomodi P
AU  - Feldesh I
AU  - Debov SS
PT  - Journal Article
TA  - Vopr. Med. Khim.
JT  - Vopr. Med. Khim.
SO  - Vopr. Med. Khim. 1986 32: 125-129.

PMID- 6597662
VI  - 30
DP  - 1984
TI  - Isolation and fractionation of DNA-methylases from Mycobacterium butyricum.
PG  - 72-76
AB  - Properties of total preparation of methylases from M. butyricum strain were
      studied using various methods of column chromatography.  Distinct heterogeneity
      of the methylase preparation was demonstrated by gel filtration, anion exchange
      chromatography on diethyl aminoethyl cellulose and affinity chromatography on
      Sepharose blue.  Several methylases, dissimilar both in physico-chemical
      properties and in their specificity to nitrogenous bases, were found in M.
      butyricum cells.  In the strain studied methylases of adenine and cytosine were
      found, which were responsible for biosynthesis of 6-methyladenine and
      5-methylcytosine in the acceptor DNA at the ratio 9:1.
AU  - Sharkova EV
AU  - Nikolskaya II
AU  - Shomodi P
AU  - Feldesh I
AU  - Debov SS
PT  - Journal Article
TA  - Vopr. Med. Khim.
JT  - Vopr. Med. Khim.
SO  - Vopr. Med. Khim. 1984 30: 72-76.

PMID- 25301656
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Cellulosimicrobium sp. Strain MM, Isolated from Arsenic-Rich Microbial Mats of a Himalayan Hot Spring.
PG  - e01020-14
AB  - Microbial mats situated at the Manikaran hot springs (>95 degrees C) are characterized by
      their high arsenic content (140 ppb), qualifying as a stressed
      niche. Here, we report the annotated draft genome (3.85 Mb) of Cellulosimicrobium
      sp. strain MM, isolated from these microbial mats, consisting of 3,718 coding
      sequences, with an average % G+C of 74.4%.
AU  - Sharma A
AU  - Hira P
AU  - Shakarad M
AU  - Lal R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01020-14.

PMID- 24504000
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Kocuria palustris PEL.
PG  - e01261-13
AB  - We report the 2.9-Mb draft genome sequence of an actinobacterium, Kocuria palustris PEL, of
      the family Micrococcaceae.
AU  - Sharma G
AU  - Khatri I
AU  - Subramanian S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01261-13.

PMID- 27358428
VI  - 8
DP  - 2016
TI  - Complete Genome of the Starch-Degrading Myxobacteria Sandaracinus amylolyticus DSM 53668T.
PG  - 2520-2529
AB  - Myxobacteria are members of delta-proteobacteria and are typified by large genomes,
      well-coordinated social behavior, gliding motility, and
      starvation-induced fruiting body formation. Here, we report the 10.33 Mb whole
      genome of a starch-degrading myxobacterium Sandaracinus amylolyticus DSM 53668(T)
      that encodes 8,962 proteins, 56 tRNA, and two rRNA operons. Phylogenetic
      analysis, in silico DNA-DNA hybridization and average nucleotide identity reveal
      its divergence from other myxobacterial species and support its taxonomic
      characterization into a separate family Sandaracinaceae, within the suborder
      Sorangiineae. Sequence similarity searches using the Carbohydrate-active enzymes
      (CAZyme) database help identify the enzyme repertoire of S. amylolyticus involved
      in starch, agar, chitin, and cellulose degradation. We identified 16
      alpha-amylases and two gamma-amylases in the S. amylolyticus genome that likely
      play a role in starch degradation. While many of the amylases are seen conserved
      in other delta-proteobacteria, we notice several novel amylases acquired via
      horizontal transfer from members belonging to phylum Deinococcus-Thermus,
      Acidobacteria, and Cyanobacteria. No agar degrading enzyme(s) were identified in
      the S. amylolyticus genome. Interestingly, several putative beta-glucosidases and
      endoglucanases proteins involved in cellulose degradation were identified.
      However, the absence of cellobiohydrolases/exoglucanases corroborates with the
      lack of cellulose degradation by this bacteria.
AU  - Sharma G
AU  - Khatri I
AU  - Subramanian S
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2016 8: 2520-2529.

PMID- 1631169
VI  - 89
DP  - 1992
TI  - Identification of a family of bacteriophage T4 genes encoding proteins similar to those present in group I introns of fungi and phage.
PG  - 6658-6662
AB  - The bacteriophage T4 segA gene lies in a genetically unmapped region between the gene betagt
      (beta-glucosyltransferase) and uvsX (recombination protein) and encodes a protein of 221 amino
      acids. We have found that the first 100 amino acids of the SegA protein are highly similar to
      the N termini of four other predicted T4 proteins, also of unknown function. Together these
      five proteins, SegA-E (similar to endonucleases of group I introns), contain regions of
      similarity to the endonuclease I-TevI, which is encoded by the mobile group I intron of the T4
      td gene, and to putative endonucleases of group I introns present in the mitochondria of
      Neurospora crassa, Podospora anserina, and Saccharomyces douglasii. Intron-encoded
      endonucleases are required for the movement (homing) of the intron DNA into an intronless
      gene, cutting at or near the site of intron insertion. Our in vitro assays indicate that SegA,
      like I-TevI, is a Mg2+-dependent DNA endonuclease that has preferred sites for cutting. Unlike
      the I-TevI gene, however, there is no evidence that segA (or the other seg genes) resides
      within introns. Thus, it is possible that segA encodes an endonuclease that is involved in the
      movement of the endonuclease-encoding DNA rather than in the homing of an intron.
AU  - Sharma M
AU  - Ellis RL
AU  - Hinton DM
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1992 89: 6658-6662.

PMID- 7961394
VI  - 176
DP  - 1994
TI  - Purification and characterization of the SegA protein of bacteriophage T4, an endonuclease related to proteins encoded by group I introns.
PG  - 6439-6448
AB  - Although not encoded by an intron, the bacteriophage T4 SegA protein shares common amino acid
      motifs with a family of proteins found within mobile group I introns present in fungi and
      phage.  Each of these intron-encoded proteins is thought to initiate the homing of its own
      intron by cleaving the intronless DNA at or near the site of insertion.  Previously, we have
      found that SegA also cleaves DNA.  In this report, we have purfied the SegA protein and
      characterized this endonuclease activity extensively.  SegA protein cleaved circular and
      linear plasmids, DNA containing unmodified cytosine, and wild-type T4 DNA containing
      hydromethylated, glucosylated cytosines.  In all cases, certain sites on the DNA were highly
      preferred for cleavage, but with increasing protein concentration or time of incubation,
      cleavage occurred at many sites.  SegA cleaving activity was stimulated by the presence of ATP
      or ATPgammaS.  Sequence analysis of three highly preferred cleavage sites did not reveal a
      simple consensus sequence, suggesting that even among highly preferred sites, SegA tolerates
      many different sequences.  A T4 segA amber mutant that we constructed had no phenotype, and
      PCR analyses indicated that several T-even-related phages lack the segA gene.  Taken together,
      our results show that SegA is an endonuclease with a hierarchy of site specificity, and these
      results are consistent with the insertion of SegA DNA into the T4 genome some time after the
      divergence of the closely related T-even phages.
AU  - Sharma M
AU  - Hinton DM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1994 176: 6439-6448.

PMID- 
VI  - 31
DP  - 2003
TI  - Demonstration of the principles of restriction endonuclease cleavage reactions using thermostable BflI from Anoxybacillus flavithermus.
PG  - 392-396
AB  - Restriction enzymes are basic tools in recombinant DNA technology. To shape the molecular
      biology experiments, the students must know how to
      work with these molecular scissors. Here, we describe an integrated set
      of experiments, introduced in the "Advances in Molecular Biology and
      Biotechnology" postgraduate course, which covers the important aspects
      about restriction endonucleases: preparation of cell-lysate, one-column
      partial-purification, assay, effect of temperature, buffers, Mg2+ ions
      and glycerol on activity, and quality control of two-column partially
      purified enzyme. Examples of study questions, which help students
      understand the theoretical basis of the experiments, have been given.
AU  - Sharma P
AU  - D'Souza DR
AU  - Bhandari D
AU  - Parashar V
AU  - Capalash N
PT  - Journal Article
TA  - Biochem. Mol. Biol. Educ.
JT  - Biochem. Mol. Biol. Educ.
SO  - Biochem. Mol. Biol. Educ. 2003 31: 392-396.

PMID- 22887680
VI  - 194
DP  - 2012
TI  - Genome Sequence of Microbacterium yannicii, a Bacterium Isolated from a Cystic Fibrosis Patient.
PG  - 4785
AB  - Microbacterium yannicii is a Gram-positive, aerobic, yellow-pigmented, rod-shaped, nonmotile,
      oxidase-negative, and catalase-positive bacterium isolated
      on Columbia colistin-nalidixic acid (CNA) agar with 5% sheep blood from the
      sputum of a cystic fibrosis patient. The present study reports the draft genome
      of a Microbacterium yannicii strain.
AU  - Sharma P
AU  - Diene SM
AU  - Gimenez G
AU  - Robert C
AU  - Rolain JM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4785.

PMID- 28983000
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence Analysis of Multidrug-Resistant Escherichia coli Strains Isolated in 2013 from Humans and Chickens in Nigeria.
PG  - e01073-17
AB  - Here, we present the draft genome sequences of nine multidrug-resistant Escherichia coli
      strains isolated from humans (n = 6) and chicken carcasses (n =
      3) from Lagos, Nigeria, in 2013. Multiple extended-spectrum beta-lactamase (ESBL)
      genes were identified in these isolates.
AU  - Sharma P
AU  - Gupta SK
AU  - Adenipekun EO
AU  - Barrett JB
AU  - Hiott LM
AU  - Woodley TA
AU  - Iwalokun BA
AU  - Oyedeji KS
AU  - Oluwadun A
AU  - Ramadan H
AU  - Frye JG
AU  - Jackson CR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01073-17.

PMID- 29146833
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Eight Streptogramin-Resistant Enterococcus Species Isolated from Animal and Environmental Sources in the United States.
PG  - e01287-17
AB  - Here, we present the draft genome sequences of eight streptogramin-resistant Enterococcus
      species isolated from animals and an environmental source in the
      United States from 2001 to 2004. Antimicrobial resistance genes were identified
      conferring resistance to the macrolide-lincosamide-streptogramins,
      aminoglycosides, tetracyclines, beta-lactams, and glycopeptides.
AU  - Sharma P
AU  - Gupta SK
AU  - Barrett JB
AU  - Hiott LM
AU  - House SL
AU  - Woodley TA
AU  - Frye JG
AU  - Jackson CR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01287-17.

PMID- 29545289
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Five Novel Ochrobactrum spp. Isolated from Different Avian Hosts in Nigeria.
PG  - e00063-18
AB  - Here, we present the draft genome sequences of five multidrug-resistant novel Ochrobactrum
      species strains isolated from a pigeon, a duck, and chickens from
      Nigeria in 2009.
AU  - Sharma P
AU  - Killmaster LF
AU  - Volkening JD
AU  - Cardenas-Garcia S
AU  - Shittu I
AU  - Meseko CA
AU  - Sulaiman LK
AU  - Joannis TM
AU  - Miller PJ
AU  - Afonso CL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00063-18.

PMID- 29650578
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Three Ochrobactrum spp. Isolated from Different Avian Hosts in Pakistan.
PG  - e00269-18
AB  - Here, we present the draft genome sequences of three Ochrobactrum sp. strains with
      multidrug-resistant properties, isolated in 2015 from a pigeon and two
      chickens in Pakistan.
AU  - Sharma P
AU  - Killmaster LF
AU  - Volkening JD
AU  - Cardenas-Garcia S
AU  - Wajid A
AU  - Rehmani SF
AU  - Basharat A
AU  - Miller PJ
AU  - Afonso CL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00269-18.

PMID- 26294628
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of a Staphylococcus aureus Strain Isolated from a Cow with  Clinical Mastitis.
PG  - e00914-15
AB  - We report here the draft genome of Staphylococcus aureus causing clinical mastitis in a cow
      from India. It is a major causative agent of mastitis and,
      further, livestock-associated strains are emerging as a potential threat to
      public health, thereby warranting studies to understand the genome of this deadly
      pathogen.
AU  - Sharma P
AU  - Reddy DP
AU  - Kumar PA
AU  - Gadicherla R
AU  - George N
AU  - Bhandari V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00914-15.

PMID- 22804681
VI  - 58
DP  - 2012
TI  - Kinetics of medium-chain-length polyhydroxyalkanoate production by a novel isolate of Pseudomonas putida LS46.
PG  - 982-989
AB  - Six bacteria that synthesize medium-chain-length polyhydroxyalkanoates (mcl-PHAs)
      were isolated from sewage sludge and hog barn wash and identified as strains of
      Pseudomonas and Comamonas by 16S rDNA gene sequencing. One isolate, Pseudomonas
      putida LS46, showed good PHA production (22% of cell dry mass) in glucose medium,
      and it was selected for further studies. While it is closely related to other P.
      putida strains (F1, KT2440, BIRD-1, GB-1, S16, and W619), P. putida LS46 was
      genetically distinct from these other strains on the basis of nucleotide sequence
      analysis of the cpn60 gene hypervariable region. PHA production was detected as
      early as 12 h in both nitrogen-limited and nitrogen-excess conditions. The
      increase in PHA production after 48 h was higher in nitrogen-limited cultures
      than in nitrogen-excess cultures. Pseudomonas putida LS46 produced mcl-PHAs when
      cultured with glucose, glycerol, or C(6)-C(14) saturated fatty acids as carbon
      sources, and mcl-PHAs accounted for 56% of the cell dry mass when cells were
      batch cultured in medium containing 20 mmol/L octanoate. Although
      3-hydroxydecanoate was the major mcl-PHA monomer (58.1-68.8 mol%) in P. putida
      LS46 cultured in glucose medium, 3-hydroxyoctanoate was the major monomer
      produced in octanoate medium (88 mol%).
AU  - Sharma PK
AU  - Fu J
AU  - Cicek N
AU  - Sparling R
AU  - Levin DB
PT  - Journal Article
TA  - Can. J. Microbiol.
JT  - Can. J. Microbiol.
SO  - Can. J. Microbiol. 2012 58: 982-989.

PMID- 23599293
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Medium-Chain-Length Polyhydroxyalkanoate-Producing Pseudomonas putida Strain LS46.
PG  - e00151-13
AB  - We describe the draft genome sequence of Pseudomonas putida strain LS46, a novel  isolate that
      synthesizes medium-chain-length polyhydroxyalkanoates. The draft
      genome of P. putida LS46 consists of approximately 5.86 million bp, with a G+C
      content of 61.69%. A total of 5,316 annotated genes and 5,219 coding sequences
      (CDS) were identified.
AU  - Sharma PK
AU  - Fu J
AU  - Zhang X
AU  - Fristensky BW
AU  - Davenport K
AU  - Chain PS
AU  - Sparling R
AU  - Levin DB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00151-13.

PMID- 19788421
VI  - 276
DP  - 2009
TI  - Rice cytosine DNA methyltransferases - gene expression profiling during reproductive development and abiotic stress.
PG  - 6301-6311
AB  - DNA methylation affects important developmental processes in both plants and animals. The
      process of methylation of cytosines at C-5 is
      catalysed by DNA methyltransferases (MTases), which are highly
      conserved, both structurally and functionally, in eukaryotes. In this
      study, we identified and characterized cytosine DNA MTase genes that
      are activated with the onset of reproductive development in rice. The
      rice genome (Oryza sativa L. subsp. japonica) encodes a total of 10
      genes that contain the highly conserved MTase catalytic domain. These
      genes have been categorized into subfamilies on the basis of
      phylogenetic relationships. A microarray-based gene expression profile
      of all 10 MTases during 22 stages/tissues that included 14 stages of
      reproductive development and five vegetative tissues together with
      three stresses, cold, salt and dehydration stress, revealed specific
      windows of MTase activity during panicle and seed development. The
      expression of six methylases was specifically/preferentially
      upregulated with the initiation of floral organs. Significantly, one of
      the MTases was also activated in young seedlings in response to cold
      and salt stress. The molecular studies presented here suggest a greater
      role for these proteins and the epigenetic process in affecting genome
      activity during reproductive development and stress than was previously
      anticipated.
AU  - Sharma R
AU  - Singh RKM
AU  - Malik G
AU  - Deveshwar P
AU  - Tyagi AK
AU  - Kapoor S
AU  - Kapoor M
PT  - Journal Article
TA  - FEBS J.
JT  - FEBS J.
SO  - FEBS J. 2009 276: 6301-6311.

PMID- 22493202
VI  - 194
DP  - 2012
TI  - Genome Sequence of Xanthomonas axonopodis pv. punicae Strain LMG 859.
PG  - 2395
AB  - We report the 4.94-Mb genome sequence of Xanthomonas axonopodis pv. punicae strain LMG 859,
      the causal agent of bacterial leaf blight disease in pomegranate.
      The draft genome will aid in comparative genomics, epidemiological studies, and
      quarantine of this devastating phytopathogen.
AU  - Sharma V
AU  - Midha S
AU  - Ranjan M
AU  - Pinnaka AK
AU  - Patil PB
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2395.

PMID- 22328768
VI  - 194
DP  - 2012
TI  - Genome Sequence of Brevibacillus laterosporus Strain GI-9.
PG  - 1279
AB  - We report the 5.18-Mb genome sequence of Brevibacillus laterosporus strain GI-9,  isolated
      from a subsurface soil sample during a screen for novel strains
      producing antimicrobial compounds. The draft genome of this strain will aid in
      biotechnological exploitation and comparative genomics of Brevibacillus
      laterosporus strains.
AU  - Sharma V
AU  - Singh PK
AU  - Midha S
AU  - Ranjan M
AU  - Korpole S
AU  - Patil PB
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1279.

PMID- 15702925
VI  - 22
DP  - 2005
TI  - Residues distal from the active site that alter enzyme function in M.HhaI DNA cytosine methyltransferase.
PG  - 533-543
AB  - Ten M.HhaI residues were replaced with alanine to probe the importance of distal protein
      elements to substrate/cofactor binding, methyl
      transfer, and product release. The substitutions, ranging from 6-20 A
      from the active site were evaluated by thermodynamic analysis, AdoMet
      DNA pre-steady and steady-state kinetics, to obtain K-d(AdoMet),
      K-d(DNA), k(cat)/K-m(DNA), k(cat), and k(methyltransfer) values. For
      the wild-type M.Hhal, product release steps dominate catalytic turnover
      while the 4-fold faster internal microscopic constant kmethyltransfer
      presents an upper limit. The methyl transfer reaction has
      Delta H and Delta S values of 10.3
      kcal/mol and 29.4 cal/(mol K), respectively, consistent with a
      compressed transition state similar to that observed in the gas phase.
      Although the ten mutants remained largely unperturbed in methyl
      transfer, long-range effects influencing substrate/cofactor binding and
      product release were observed. Positive enhancements were seen in
      Asp(73)Ala, which showed a 25-fold improvement in AdoMet affinity and
      in Val(282)Ala, which showed a 4-fold improvement in catalytic
      turnover. Based on an analysis of the positional probability within the
      C-5-cytosine DNA methyltransferase family we propose that certain
      conserved distal residues may be important in mediating long-range
      effects.
AU  - Sharma V
AU  - Youngblood B
AU  - Reich N
PT  - Journal Article
TA  - J. Biomol. Struct. Dyn.
JT  - J. Biomol. Struct. Dyn.
SO  - J. Biomol. Struct. Dyn. 2005 22: 533-543.

PMID- 27979932
VI  - 4
DP  - 2016
TI  - Complete Genome Sequences of Curli-Negative and Curli-Positive Isolates of Foodborne Escherichia coli O157:H7 Strain 86-24.
PG  - e01323-16
AB  - Escherichia coli O157:H7 strain 86-24 does not produce curli fimbriae, but gives  rise to
      curli-positive isolates at a variable frequency. Here, we report the
      complete genome sequences of curli-negative and curli-positive isolates of strain
      86-24.
AU  - Sharma VK
AU  - Bayles DO
AU  - Alt DP
AU  - Looft T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01323-16.

PMID- 29540638
VI  - 33
DP  - 2018
TI  - Comparative Genomic Insights into Endofungal Lifestyles of Two Bacterial Endosymbionts, Mycoavidus cysteinexigens and Burkholderia rhizoxinica.
PG  - 66-76
AB  - Endohyphal bacteria (EHB), dwelling within fungal hyphae, markedly affect the
      growth and metabolic potential of their hosts. To date, two EHB belonging to the
      family Burkholderiaceae have been isolated and characterized as new taxa,
      Burkholderia rhizoxinica (HKI 454(T)) and Mycoavidus cysteinexigens (B1-EB(T)),
      in Japan. Metagenome sequencing was recently reported for Mortierella elongata
      AG77 together with its endosymbiont M. cysteinexigens (Mc-AG77) from a
      soil/litter sample in the USA. In the present study, we elucidated the complete
      genome sequence of B1-EB(T) and compared it with those of Mc-AG77 and HKI 454(T).
      The genomes of B1-EB(T) and Mc-AG77 contained a higher level of prophage
      sequences and were markedly smaller than that of HKI 454(T). Although the
      B1-EB(T) and Mc-AG77 genomes lacked the chitinolytic enzyme genes responsible for
      invasion into fungal cells, they contained several predicted toxin-antitoxin
      systems including an insecticidal toxin complex and PIN domain imposing an
      addiction-like mechanism essential for endohyphal growth control during host
      colonization. Despite the different host fungi, the alignment of amino acid
      sequences showed that the HKI 454(T) genome consisted of 1,265 (32.6%) and 1,221
      (31.5%) orthologous coding sequences (CDSs) with those of B1-EB(T) and Mc-AG77,
      respectively. This comparative study of three phylogenetically associated
      endosymbionts has provided insights into their origin and evolution, and suggests
      the later bacterial invasion and adaptation of B1-EB(T) to its host metabolism.
AU  - Sharmin D
AU  - Guo Y
AU  - Nishizawa T
AU  - Ohshima S
AU  - Sato Y
AU  - Takashima Y
AU  - Narisawa K
AU  - Ohta H
PT  - Journal Article
TA  - Microbes Environ.
JT  - Microbes Environ.
SO  - Microbes Environ. 2018 33: 66-76.

PMID- 26067976
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Moderately Halophilic Methanotroph Methylohalobius crimeensis Strain 10Ki.
PG  - e00644-15
AB  - Methylohalobius crimeensis strain 10Ki is a moderately halophilic aerobic methanotroph
      isolated from a hypersaline lake in the Crimean Peninsula, Ukraine.  This organism has the
      highest salt tolerance of any cultured methanotroph. Here, we present a draft genome sequence
      of this bacterium.
AU  - Sharp CE et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00644-15.

PMID- 4354250
VI  - 12
DP  - 1973
TI  - Detection of two restriction endonuclease activities in Haemophilus parainfluenzae using analytical agarose-ethidium bromide electrophoresis.
PG  - 3055-3063
AB  - A rapid assay for restriction enzymes has been developed using electrophoresis
      of DNA through 1.4% agarose gels in the presence of 0.5 microgram/ml of
      ethidium bromide.  The method eliminates lengthy staining and destaining
      procedures and resolves species of DNA which are less than 7 Mdaltons.  As
      little as 0.05 microgram of DNA can easily be detected by direct examination of
      the gels in ultraviolet light.  Using this technique, we have identified two
      different restricting activities in extracts of Haemophilus parainfluenzae.
      The two activities have different chromatographic properties on
      phosphocellulose and Bio-Gel A-0.5m, and they attack SV40 DNA at different
      sites.  One activity (HpaII) cleaves SV40 DNA at a single position situated
      0.38 fractional genome length from the insertion point of SV40 sequences into
      the adenovirus SV40 hybrid Ad2++ND1.  The other activity (HpaI) cleaves SV40
      DNA at three sites which appear to coincide with 3 of the 11 cleavage points
      attacked by a restriction system isolated from H. influenzae strain Rd.
AU  - Sharp PA
AU  - Sugden B
AU  - Sambrook J
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1973 12: 3055-3063.

PMID- 2832688
VI  - 3
DP  - 1986
TI  - Molecular evolution of bacteriophages: Evidence of selection against the recognition sites of host restriction enzymes.
PG  - 75-83
AB  - Restriction enzymes produced by bacteria serve as a defense against invading
      bacteriophages, and so phages without other protection would be expected to
      undergo selection to eliminate recognition sites for these enzymes from their
      genomes.  The observed frequencies of all restriction sites in the genomes of
      all completely sequenced DNA phages (T7, lambda, PhiX174, G4, M13, fl, fd, and
      IKe) have been compared to expected frequencies derived from trinucleotide
      frequencies.  Attention was focused on 6-base palindromes since they comprise
      the typical recognition sites for type II restriction enzymes.  All of these
      coliphages, with the exception of lambda and G4, exhibit significant avoidance
      of the particular sequences that are enterobacterial restriction sites.  As
      expected, the sequenced fraction of the genome of Phi29, a Bacillus subtilis
      phage, lacks Bacillus restriction sites.  By contrast, the RNA phage MS2,
      several viruses that infect eukaryotes (EBV, adenovirus, papilloma, and SV40),
      and three mitochondrial genomes (human, mouse and cow) were found not to lack
      restriction sites.  Because the particular palindromes avoided correspond
      closely with the recognition sites for host enzymes and because other viruses
      and small genomes do not show this avoidance, it is concluded that the effect
      indeed results from natural selection.
AU  - Sharp PM
PT  - Journal Article
TA  - Mol. Biol. Evol.
JT  - Mol. Biol. Evol.
SO  - Mol. Biol. Evol. 1986 3: 75-83.

PMID- 1409708
VI  - 89
DP  - 1992
TI  - Roles of selection and recombination in the evolution of type I restriction-modification systems in enterobacteria.
PG  - 9836-9840
AB  - Restriction-modification systems can protect bacteria against viral infection. Sequences of
      the hsdM gene, encoding one of the three subunits of type I restriction-modification systems,
      have been determined for four strains of enterobacteria. Comparison with the known sequences
      of EcoKI and EcoR124I indicated that all are homologous, though they fall into three families
      (exemplified by EcoKI, EcoAI, and EcoR124I), the first two of which are apparently allelic.
      The extent of amino acid sequence identity between EcoKI and EcoAI is so low that the genes
      encoding them might be better termed pseudoalleles; this almost cerainly reflects genetic
      exchange among highly divergent species. Within the EcoKI family the ratio of intra- to
      interspecific divergence is very high. The extent of divergence between the genes from
      Escherichia coli K-12 and Salmonella typhimurium LT2 is similar to that for other genes with
      the same level of codon usage bias. In contrast, intraspecific divergence (between E. coli
      strains B and K-12) is extremely high and may reflect the action of frequency-dependent
      selection mediated by bacteriophages. There is also evidence of lateral transfer of a short
      sequence between E. coli and S. typhimurium.
AU  - Sharp PM
AU  - Kelleher JE
AU  - Daniel AS
AU  - Cowan GM
AU  - Murray NE
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1992 89: 9836-9840.

PMID- 27071032
VI  - 11
DP  - 2016
TI  - CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites.
PG  - e0152404
AB  - High-throughput sequencing continues to produce an immense volume of information  that is
      processed and assembled into mature sequence data. Data analysis tools
      are urgently needed that leverage the embedded DNA sequence polymorphisms and
      consequent changes to restriction sites or sequence motifs in a high-throughput
      manner to enable biological experimentation. CisSERS was developed as a
      standalone open source tool to analyze sequence datasets and provide biologists
      with individual or comparative genome organization information in terms of
      presence and frequency of patterns or motifs such as restriction enzymes.
      Predicted agarose gel visualization of the custom analyses results was also
      integrated to enhance the usefulness of the software. CisSERS offers several
      novel functionalities, such as handling of large and multiple datasets in
      parallel, multiple restriction enzyme site detection and custom motif detection
      features, which are seamlessly integrated with real time agarose gel
      visualization. Using a simple fasta-formatted file as input, CisSERS utilizes the
      REBASE enzyme database. Results from CisSERS enable the user to make decisions
      for designing genotyping by sequencing experiments, reduced representation
      sequencing, 3'UTR sequencing, and cleaved amplified polymorphic sequence (CAPS)
      molecular markers for large sample sets. CisSERS is a java based graphical user
      interface built around a perl backbone. Several of the applications of CisSERS
      including CAPS molecular marker development were successfully validated using
      wet-lab experimentation. Here, we present the tool CisSERS and results from
      in-silico and corresponding wet-lab analyses demonstrating that CisSERS is a
      technology platform solution that facilitates efficient data utilization in
      genomics and genetics studies.
AU  - Sharpe RM
AU  - Koepke T
AU  - Harper A
AU  - Grimes J
AU  - Galli M
AU  - Satoh-Cruz M
AU  - Kalyanaraman A
AU  - Evans K
AU  - Kramer D
AU  - Dhingra A
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2016 11: e0152404.

PMID- 2046552
VI  - 5
DP  - 1991
TI  - Transcriptional analysis of the restriction and modification genes of bacteriophage P1.
PG  - 685-694
AB  - Bacteriophage P1 res and mod genes encode the restriction and modification
      polypeptides of the Type III restriction enzyme EcoPI.  Northern blot analysis
      using res- and mod-specific probes revealed the presence of two separate
      transcripts in strains harbouring the EcoPI restriction and modification genes.
      Furthermore, by constructing a series of fusions with a promoterless lacZ
      gene, we show that both the res and mod genes are transcribed from separate
      promoters.  A more detailed investigation of the mod promoter region revealed
      two promoters located some 70 and 140 bp upstream from the translational start
      codon.  In addition, another pair of promoters and a further separate promoter
      are located more than 500 bp upstream from this start codon.  Two short open
      reading frames are located between these distal and proximal promoter clusters.
      Transcription of the res gene is initiated from within the mod open reading
      frame from two adjacent promoters.  In addition a functional promoter is
      located on the antisense strand close to the res promoter region.  The
      relationship between the transcription units of the res and mod genes is
      discussed.
AU  - Sharrocks AD
AU  - Hornby DP
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1991 5: 685-694.

PMID- Not carried by PubMed...
VI  - 91
DP  - 1991
TI  - Isolation and characterization of thermophilic restriction endonucleases.
PG  - 199
AB  - Restriction endonucleases BsiBI, BsiEI, BsiGI, BsiUI and BsiYI were isolated from thermophilic
      Bacillus spp. BsiBI, BsiEI and BsiUI were purified by using a DEAE sephacel column and a
      heparin sepharose column, while BsiYI was followed by a FPLC mono Q column. Unpurified BsiGI
      was used. Recognition sites of these enzymes were found by means of single and double
      digestions on different DNA of known sequences. The cleavage sites were determined according
      to FEMS Microbiol. Lett. 66:153-156 (1990). BsiGI and BsiUI were found to recognize TCCGGA and
      CCWGG respectively. The recognition and cleavage sites of the other three enzymes are: BsiBI:
      GATNN^NNATC; BsiEI: CGRY^CG and BsiYI: CCNNNNN^NNATC. These enzymes worked well at 55C. BsiBI
      and BsiUI were sensitive to dam and dcm methylation respectively. The optimal ionic strength
      for BsiEI and BsiYI was medium salt buffer, while that for BsiBI, BsiGI and BsiUI was high
      salt buffer. During the characterization of BsiYI, we found that a G nucleotide is missed at
      position 1227 of pACYC177 recorded in GenBank. This error also occurs in pACYC184 and p15A.
AU  - Shaw PC
AU  - Clark DR
AU  - Kam KM
AU  - Mok YK
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1991 91: 199.

PMID- 8224898
VI  - 133
DP  - 1993
TI  - XcmI as a universal restriction enzyme for single-stranded DNA.
PG  - 85-89
AB  - Single-stranded DNA can be cleaved into defined fragments at any predetermined site by
      interaction with a specially designed oligodeoxyribonucleotide (oligo) adaptor and the
      class-IIN restriction endonuclease, XcmI. The oligo adaptor has the structure
      (CCANNNNNNNNNTGG
       GGTNNNNNNNNNACC). Upon hybridization to the target DNA through the central 9-nucleotide
      region and with the addition of XcmI, the template DNA is specifically cleaved to near
      completion. Hairpin structures on the template close to the hybridization site reduce the
      efficacy of cleavage.
AU  - Shaw PC
AU  - Mok YK
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1993 133: 85-89.

PMID- 
VI  - 229
DP  - 2005
TI  - Structure-activity relationship study of (-)-epicatechin analogues as DNA methyltransferase inhibitors.
PG  - U186-U187
AB  - Hypermethylation of DNA cPG islands is an important epigenetic mechanism for aberrant gene
      silencing in cancer.  Although nucleoside analogue inhibitors of DNA methyltransferases can
      reverse abnormal DNA hypermethylation in cancer cells, their clinical utility is limited due
      to side effects.  The development of nonnucleoside DNMTs that lack systemic toxicity is a
      promising approach to targeting epigenetic mechanisms for cancer therapy.  (-)-Epicatechin
      analogues extracted from green tea inhibit DNMT.  Among them, EGCG and ECG exhibit inhibitory
      activity with IC50 values of 20-30 uM.  Our objective is to synthesize (-)-epicatechin
      scaffold, a series of derivaties have been synthesized and screened for activity in an in
      vitro recombinant DNMT assay system.  Lead compounds with potent inhibitory activity will
      subsequently be evaluated in cancer cell-based models of viability, apoptosis and DNA
      methylation status.
AU  - Shaw YJ
AU  - Chen CS
PT  - Journal Article
TA  - ACS Abstracts
JT  - ACS Abstracts
SO  - ACS Abstracts 2005 229: U186-U187.

PMID- 11427726
VI  - 98
DP  - 2001
TI  - The complete genome of the crenarchaeon Sulfolobus solfataricus P2.
PG  - 7835-7840
AB  - The genome of the crenarchaeon Sulfolobus solfataricus P2 contains 2,992,245 bp on a single
      chromosome and encodes 2,977 proteins and many RNAs. One-third of the encoded proteins have no
      detectable homologs in other sequenced genomes. Moreover, 40% appear to be archaeal-specific,
      and only 12% and 2.3% are shared exclusively with bacteria and eukarya, respectively. The
      genome shows a high level of plasticity with 200 diverse insertion sequence elements, many
      putative nonautonomous mobile elements, and evidence of integrase-mediated insertion events.
      There are also long clusters of regularly spaced tandem repeats. Different transfer systems
      are used for the uptake of inorganic and organic solutes, and a wealth of intracellular and
      extracellular proteases, sugar, and sulfur metabolizing enzymes are encoded, as well as
      enzymes of the central metabolic pathways and motility proteins. The major metabolic electron
      carrier is not NADH as in bacteria and eukarya but probably ferredoxin. The essential
      components required for DNA replication, DNA repair and recombination, the cell cycle,
      transcriptional initiation and translation, but not DNA folding, show a strong eukaryal
      character with many archaeal-specific features. The results illustrate major differences
      between crenarchaea and euryarchaea, especially for their DNA replication mechanism and cell
      cycle processes and their translational apparatus.
AU  - She Q et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2001 98: 7835-7840.

PMID- 26430032
VI  - 3
DP  - 2015
TI  - Genome Sequencing of Ralstonia solanacearum Race 4, Biovar 4, and Phylotype I, Strain YC45, Isolated from Rhizoma kaempferiae in Southern China.
PG  - e01110-15
AB  - Ralstonia solanacearum is an important phytopathogen that attacks over 400 plant  species,
      including Zingiberaceae plants. Here, we report the complete genome sequence of strain YC45,
      which was isolated from Rhizoma kaempferiae in southern  China.
AU  - She X
AU  - Tang Y
AU  - He Z
AU  - Lan G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01110-15.

PMID- 8843433
VI  - 21
DP  - 1996
TI  - Splicing of a group II intron in a functional transfer gene of Lactococcus lactis.
PG  - 45-53
AB  - A chromosomally located sex factor that controls conjugation in Lactococcus lactis 712 has
      been cloned and sequenced, leading to the discovery of an open reading frame with homology to
      the maturases of group II self-splicing introns.  Reverse transcriptase polymerase chain
      reaction amplification was used to demonstrate that the intron was spliced out of mRNA in
      vivo, and sequence analysis revealed the site of splicing.  The intron was inserted within a
      sex-factor gene which encodes a protein with homology to proteins involved in rolling-circle
      DNA replication.  Gene-disruption experiments were used to demonstrate that this mobA gene was
      essential for sex-factor transfer and this suggests that intron splicing is a necessary part
      of the conjugation process.  The sequence of the intron was modelled to produce a secondary
      structure that exhibited several features characteristic of the IIA subgroup.  Here we report
      the characterization of a new group II intron in the Gram-positive bacterium L. lactis and
      demonstrate for the first time in bacteria both splicing in vivo and an active role for the
      gene carrying the intron.
AU  - Shearman C
AU  - Godon J-J
AU  - Gasson M
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1996 21: 45-53.

PMID- 9815163
VI  - 9
DP  - 1998
TI  - Conformational transition of restriction endonuclease MvaI-substrate complex under the influence of Mg2+ probed by DNA-protein linking studies.
PG  - 703-707
AB  - The method of protein affinity modification by DNA analogues was used to study the
      characteristic features of restriction endonuclease MvaI interaction with DNA.
      Oligonucleotide duplexes containing a monosubstituted pyrophosphate internucleotide bond were
      used for cross-linking to the enzyme.  The conditions of the reaction of MvaI endonuclease
      with these reagents were investigated.  On the basis of data obtained, the model of successive
      inclusion of two Mg2+ ions into an MvaI endonuclease-substrate complex was proposed and
      confirmed by the kinetic scheme of the process.
AU  - Sheflyan GY
AU  - Kubareva EA
AU  - Gromova ES
AU  - Shabarova ZA
PT  - Journal Article
TA  - Bioconjugate Chem.
JT  - Bioconjugate Chem.
SO  - Bioconjugate Chem. 1998 9: 703-707.

PMID- 8268318
VI  - 58
DP  - 1993
TI  - Hydrolysis of 5-fluorodeoxycytidine-containing DNA duplexes using restriction endonucleases.
PG  - 1806-1811
AB  - Cleavage by restriction endonucleases MvaI and EcoRII of DNA duplexes, in which the internal
      deoxycytidine in one of the strands of the recognition site is substituted for
      5-fluorodeoxycytidine, has been studied. It has been found that the modified strands of these
      duplexes are cleaved by endonuclease MvaI with a greater efficiency than the intact ones.
      Endonuclease EcoRII does not practically cleave such substrate analogs. The UV absorbance
      spectra of 5-fluorodeoxycytidine and the 14-member oligodeoxyribonucleotide with modification
      in the middle of the strand have been measured. A hypothesis has been put forward about the
      structural features of 5-fluorodeoxycytidine-containing DNA duplexes.
AU  - Sheflyan GY
AU  - Kubareva EA
AU  - Gromova ES
AU  - Shabarova ZA
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1993 58: 1806-1811.

PMID- 8706883
VI  - 390
DP  - 1996
TI  - Cross-linking of SsoII restriction endonuclease to cognate and non-cognate DNAs.
PG  - 307-310
AB  - Specific and non-specific interactions of SsoII restriction endonuclease (R.SsoII) were probed
      by the method of covalent attachment to modified DNA containing an active monosubstituted
      pyrophosphate internucleotide bond instead of a phosphodiester one.  R.SsoII with six
      N-terminal His residues was shown to be cross-linked to duplexes with this type of
      modification, either containing or not the recognition sequence.  Competition experiments with
      covalent attachment of R.SsoII to activated DNAs demonstrated the similar affinity of the
      enzyme to cognate and noncognate DNAs in the absence of cofactor, Mg2+ ions.
AU  - Sheflyan GY
AU  - Kubareva EA
AU  - Kuznetsova SA
AU  - Karyagina AS
AU  - Nikolskaya II
AU  - Gromova ES
AU  - Shabarova ZA
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1996 390: 307-310.

PMID- 7607489
VI  - 157
DP  - 1995
TI  - Chemical cross-linking of MvaI and EcoRII enzymes to DNA duplexes containing monosubstituted pyrophosphate internucleotide bond.
PG  - 187-190
AB  - DNA duplexes containing a monosubstituted pyrophosphate internucleotide group, instead of a
      phosphodiester bond, were used as cross-linking reagents for the affinity modification of the
      restriction endonucleases EcoRII and MvaI (R.EcoRII and R.MvaI).  An active group was
      introduced into the enzyme's recognition site or between the recognition site and flanking
      sequence.  The substrate properties of such DNA duplexes were determined.  Cross-linking
      specificity was demonstrated by competition experiments with unmodified substrate, as well as
      by the absence of cross-linking to an active duplex lacking a recognition site.  It was shown
      that the nucleophilicity of the buffer solution and the presence of the enzyme cofactor Mg2+
      dramatically affected the cross-linking yield.
AU  - Sheflyan GY
AU  - Kubareva EA
AU  - Volkov EM
AU  - Oretskaya TS
AU  - Gromova ES
AU  - Shabarova ZA
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 187-190.

PMID- Not carried by PubMed...
VI  - 34
DP  - 1993
TI  - Interaction of restriction endonuclease MvaI with synthetic DNA duplexes.
PG  - 516-520
AB  - 
AU  - Sheflyan GY
AU  - Tashlitskii VN
AU  - Kubareva EA
PT  - Journal Article
TA  - Vestn. Mosk. Univ.
JT  - Vestn. Mosk. Univ.
SO  - Vestn. Mosk. Univ. 1993 34: 516-520.

PMID- 24051318
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences of Helicobacter pylori Strains Isolated from Regions of Low and High Gastric Cancer Risk in Colombia.
PG  - e00736-13
AB  - The draft genome sequences of six Colombian Helicobacter pylori strains are presented. These
      strains were isolated from patients from regions of high and low
      gastric cancer risk in Colombia and were characterized by multilocus sequence
      typing. The data provide insights into differences between H. pylori strains of
      different phylogeographic origins.
AU  - Sheh A
AU  - Piazuelo MB
AU  - Wilson KT
AU  - Correa P
AU  - Fox JG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00736-13.

PMID- 25428971
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Eight Enterohepatic Helicobacter Species Isolated from  Both Laboratory and Wild Rodents.
PG  - e01218-14
AB  - The draft genome sequences of eight enterohepatic Helicobacter species, H. muridarum, H.
      trogontum, H. typhlonius, and five unnamed helicobacters, are
      presented here. Using laboratory mice pervasively infected with helicobacters, we
      characterized the presence of known virulence factors.
AU  - Sheh A
AU  - Shen Z
AU  - Fox JG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01218-14.

PMID- 29074670
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Desulfovibrio desulfuricans Strain G11, a Model Sulfate-Reducing, Hydrogenotrophic, and Syntrophic Partner Organism.
PG  - e01207-17
AB  - Here, we report the draft genome of the Gram-negative, sulfate-reducing bacterium
      Desulfovibrio desulfuricans strain G11. Isolated from a rumen fluid enrichment,
      this culture has been a model syntrophic partner due to its metabolic
      flexibility. The assembly yielded a single circular chromosome of 3,414,943 bp
      and a 57% G+C content.
AU  - Sheik CS
AU  - Sieber JR
AU  - Badalamenti JP
AU  - Carden K
AU  - Olson A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01207-17.

PMID- 9925782
VI  - 285
DP  - 1999
TI  - Mechanism of inhibition of DNA (cytosine C5)-methyltransferases by oligodeoxyribonucleotides containing 5,6-dihydro-5-azacytosine.
PG  - 2021-2034
AB  - A key step in the predicted mechanism of enzymatic transfer of methyl groups from
      S-adenosyl-L-methionine to cytosine residues in DNA is the transient formation of a
      dihydrocytosine intermediate covalently linked to cysteine in the active site of a DNA
      (cytosine C5)-methyltransferase.  Crystallographic analysis of complexes formed by HhaI
      methyltransferase, AdoMet and a target oligodeoxyribonucleotide containing 5-fluorocytosine
      confirmed the existence of this dihydrocytosine intermediate.  Based on the premise that
      5,6-dihydro-5-azacytosine, a cytosine analog with an sp3-hybridized carbon (CH2) at position 6
      and an NH group at position 5, could mimic the non-aromatic character of the cytosine ring in
      this transition state, we synthesized a series of synthetic substrates for DNA C5-MTase
      containing DZCyt.  Substitution of DZCyt for target cytosines in C-G dinucleotides of
      single-stranded or double-stranded oligodeoxyribonucleotide substrates led to complete
      inhibition of methylation by murine DNA C5-MTase.  Substitution of DZCyt for the target
      cytosine in G-C-G-C sites in double-stranded oligodeoxyribonucleotides had a similar effect on
      methylation by M.HhaI.  Oligodeoxyribonucleotides containing DZCyt formed a tight but
      reversible complex with M.HhaI, and were consistently more potent as inhibitors of DNA
      methylation than oligodeoxyribonucleotides identical in sequence containing 5-fluorocytosine.
      Crystallographic analysis of a ternary complex involving M.HhaI, S-adenosyl-L-homocysteine and
      a double-stranded 13-mer oligodeoxyribonucleotide containing DZCyt at the target position
      showed that the analog is flipped out of the DNA helix in the same manner as cytosine,
      5-methylcytosine, and 5-fluorocytosine.  However, no formation of a covalent bond was detected
      between the sulfur atom of the catalytic site nucleophile, cysteine 81, and the pyrimidine C6
      carbon.  These results indicate that DZCyt can occupy the active site of M.HhaI as a
      transition state mimic and, because of the high degree of affinity of its interaction with the
      enzyme, it can act as a potent inhibitor of methylation.
AU  - Sheikhnejad G
AU  - Brank A
AU  - Christman JK
AU  - Goddard A
AU  - Alvarez E
AU  - Ford H Jr
AU  - Marquez VE
AU  - Marasco CJ
AU  - Sufrin JR
AU  - O'Gara M
AU  - Cheng X
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1999 285: 2021-2034.

PMID- Not included in PubMed...
VI  - 46
DP  - 1992
TI  - Comparison of substrate specificity of mammalian and bacterial CpG DNA methyltransferases (MTases).
PG  - 24
AB  - Methylation of C residues at specific sites in DNA of higher eukaryotes appears to play a role
      in regulating gene expression during development and diferentiation. Silencing genes by
      methylation can in part explain genomic imprinting and alterations in patterns of methylation
      during the early stages of carcinogenesis may account for some changes in gene expression in
      tumor cells. Although the distribution of 5mC in mammalian DNA is tissue- and
      species-specific, little is known about MTases role in establishing specific patterns of
      methylation. Mammalian DNA (mDNA) MTase is most active in methylating C residues in
      hemi-methylated CpG sites and prefers substrates with high GC content and multiple CpGs approx
      15 residues apart.  To more fully characterize the specificity of mDNA MTase, we analyzed
      its activity with a variety of defined DNA substrates and compared it with a bacterial MTase,
      SssI, which is reported to act on hemi-methylated CpG sites with equal efficency. Using
      defined unmethylated single (ss)- and double stranded (ds)-DNAs as substrates, we find that:1)
      the initial rate of methylation of both ss-and ds-DNA-by SssI and mDNA MTase is influenced by
      sequence, often in opposite ways; 2) depending on sequence, SssI may be more active on ds-
      than ss-DNA. Activity of mDNA MTase with ss-DNA is highly variable and dependent on sequence
      but is always low with unmethylated ds-DNA. Using 5mC-substituted substrates, we find that
      hemi-methylation either has no effect or inhibits activity of SssI but always activates mDNA
      MTase. mDNA MTase is most active with hemi-methylated ds-DNA ans ss-DNA with 5mC near the
      5'-end. These results demonstrate that although both MTases catalyze the same reaction,
      methylation of C residues in CpG dinucleotides, they have quite different specificities. This
      should be considered when these enzymes are used to quantitate hypomethylation at CpG sites in
      DNA resulting from exposure of mammalian cells or tissues to conditions or agents that affect
      DNA methylation. Finally, our findings suggest that 5mC residues in specific sequences in
      ss-DNA may serve to activate de novo methylation in mammalian cells allowing alteration of
      existing methylation patterns.
AU  - Sheikhnejad G
AU  - Marasco C
AU  - Sufrin J
AU  - Christman JK
PT  - Journal Article
TA  - Biomed. Pharmacother.
JT  - Biomed. Pharmacother.
SO  - Biomed. Pharmacother. 1992 46: 24.

PMID- 23853579
VI  - 9
DP  - 2013
TI  - DNA methylation impacts gene expression and ensures hypoxic survival of Mycobacterium tuberculosis.
PG  - e1003419
AB  - DNA methylation regulates gene expression in many organisms. In eukaryotes, DNA methylation is
      associated with gene repression, while it exerts both activating
      and repressive effects in the Proteobacteria through largely locus-specific
      mechanisms. Here, we identify a critical DNA methyltransferase in M.
      tuberculosis, which we term MamA. MamA creates N(6)-methyladenine in a six base
      pair recognition sequence present in approximately 2,000 copies on each strand of
      the genome. Loss of MamA reduces the expression of a number of genes. Each has a
      MamA site located at a conserved position relative to the sigma factor -10
      binding site and transcriptional start site, suggesting that MamA modulates their
      expression through a shared, not locus-specific, mechanism. While strains lacking
      MamA grow normally in vitro, they are attenuated in hypoxic conditions,
      suggesting that methylation promotes survival in discrete host microenvironments.
      Interestingly, we demonstrate strikingly different patterns of DNA
      methyltransferase activity in different lineages of M. tuberculosis, which have
      been associated with preferences for distinct host environments and different
      disease courses in humans. Thus, MamA is the major functional adenine
      methyltransferase in M. tuberculosis strains of the Euro-American lineage while
      strains of the Beijing lineage harbor a point mutation that largely inactivates
      MamA but possess a second functional DNA methyltransferase. Our results indicate
      that MamA influences gene expression in M. tuberculosis and plays an important
      but strain-specific role in fitness during hypoxia.
AU  - Shell SS
AU  - Prestwich EG
AU  - Baek SH
AU  - Shah RR
AU  - Sassetti CM
AU  - Dedon PC
AU  - Fortune SM
PT  - Journal Article
TA  - PLoS Pathog.
JT  - PLoS Pathog.
SO  - PLoS Pathog. 2013 9: e1003419.

PMID- 8682220
VI  - 10
DP  - 1996
TI  - Ability of cytosine methyltransferases to bind substrates containing mismatches is not sufficient for causing C to T mutations.
PG  - A965
AB  - Hydrolytic deamination of cytosine to uracil and of 5-methylcytosine to thymine create
      mismatches, which - if unrepaired - can cause C to T mutations.  It was found that cytosine
      methyltransferases (C5 Mtases) M.HhaI and M.HpaII bind tightly to these mismatches suggesting
      that the C5 Mtases may prevent repair of U:G and T:G mismatches by competing with mismatch
      correction systems.  To test this, we studied the binding of WT M.EcoRII and its mutant in
      which active site cysteine was replaced with serine (C186S) to oligonucleotide duplexes
      containing U:G or T:G mismatches.  We found that C186S mutant binds more tightly to duplexes
      containing mismatches than the wild type enzyme.  The tightness of binding to the mismatched
      duplexes was generally comparable to that with the cognate sequence.  In contrast, when the
      ability of the C186S mutant to promote C to T mutations was tested using a genetic reversion
      system, we found that the magnitude of reversion caused by the WT M.EcoRII was about 50 fold
      higher than that caused by the C186S mutant.  This shows that the ability of C5 Mtases to bind
      U:G or T:G mismatch containing duplexes is not sufficient to promote C to T mutations.
AU  - Sheluho D
AU  - Khariwala S
AU  - Yebra MJ
AU  - Bhagwat AS
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1996 10: A965.

PMID- 9230899
VI  - 255
DP  - 1997
TI  - Lack of correlation between binding of EcoRII methyltransferase to DNA duplexes containing mismatches and the promotion of C to T mutations.
PG  - 54-59
AB  - The cytosine methyltransferases (MTases) M.HhaI and M.HpaII bind substrates in which the
      target cytosine is replaced by uracil or thymine, i.e. DNA containing a U:G or a T:G mismatch.
      We have extended this observation to the EcoRII MTase (M.EcoRII) and determined the apparent
      Kd for binding.  Using a genetic assay we have also tested the possibility that MTase binding
      to U:G mismatches may interfere with repair of the mismatches and promote C:G to T:A
      mutations.  We have compared two mutants of M.EcoRII that are defective for catalysis by the
      wild-type enzyme for their ability to bind DNA containing U:G or T:G mismatches and for their
      ability to promote C to T mutations.  We find that although all three proteins are able to
      bind DNAs with mismatches, only the wild-type enzyme promotes C:G to T:A mutations in vivo.
      Therefore, the ability of M.EcoRII to bind U:G mismatched duplexes is not sufficient for their
      mutagenic action in cells.
AU  - Sheluho D
AU  - Yebra MJ
AU  - Shariwala SS
AU  - Bhagwat AS
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1997 255: 54-59.

PMID- 9294199
VI  - 94
DP  - 1997
TI  - Structure of the imprinted mouse Snrpn gene and establishment of its parental-specific methylation pattern.
PG  - 10267-10272
AB  - The mouse Snrpn gene encodes the Smn protein, which is involved in RNA splicing.  The gene
      maps to a region in the central part of chromosome 7 that is syntenic to the
      Prader-Willi/Angelman syndromes region on human chromosome 15q11-q13.  The mouse gene, like
      its human counterpart, is imprinted and paternally expressed, primarily in brain and heart.
      We provide here a detailed description of the structural features and differential methylation
      pattern of the gene.  We have identified a maternally methylated region at the 5' end (DMR1),
      which correlates inversely with the Snrpn paternal expression.  We also describe a region at
      the 3' end of the gene (DMR1), which correlates inversely with the Snrpn paternal expression.
      We also describe a region at the 3' end of the gene (DMR2) that is preferentially methylated
      on the paternal allele.  Analysis of Snrpn mRNA levels in a methylase-deficient mouse embryo
      revealed that maternal methylation of DMR1 may play a role in silencing the maternal allele.
      Yet both regions, DMR1 and DMR2, inherit the parental-specific methylation profile from the
      gametes.  This methylation pattern is erased in 12.5 days postcoitum primordial germ cells and
      reestablished during gametogenesis.  DMR1 is remethylated during oogenesis, whereas DMR2 is
      remethylated during spermatogenesis.  Once established, these methylation patterns are
      transmitted to the embryo and maintained, protected from methylation changes during
      embryogenesis and cell differentiation.  Transfections of DMR1 and DMR2 into embryonic stem
      cells and injection into pronuclei of fertilized eggs reveal that embryonic cells lack the
      capacity to establish anew the differential methylation pattern of Snrpn.  That all PWS
      patients lack DMR1, together with the overall high resemblance of the mouse gene to the human
      SNRPN, offers an excellent experimental tool to study the regional control of this imprinted
      chromosomal domain.
AU  - Shemer R
AU  - Birger Y
AU  - Riggs AD
AU  - Razin A
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1997 94: 10267-10272.

PMID- 
VI  - 0
DP  - 1996
TI  - Establishment of imprinted methylation patterns during development.
PG  - 215-229
AB  - Genomic imprinting is a classic example of epigenetic control of gene expression in mammals.
      It represents a process that marks the parental origin of certain genes, resulting in their
      allele-specific expression.  Imprinting, which is implicated in the inequality of the maternal
      and paternal genomes in mammals, results in the developmental failure of isoparental embryos
      to develop properly.  An imbalance of specific parental chromosomes in the embryo or aberrant
      expression of the imprinted genes results in a number of genetic disorders in man and may also
      contribute to tumor development.  Several model explanations have been proposed for the
      evolutionary acquisition of genomic imprinting as a developmental control mechanism in
      mammals.  One of these models suggests that imprinting might have evolved in mammals because
      of the conflicting "interests" of maternal and paternal genes within the embryo.  This model
      proposes that paternally expressed genes promote embryonic growth, whereas maternal genes act
      to restrain the use of maternal resources.  A suitable example that corroborates this argument
      is the paternally expressed Igf2 gene and its counterpart, maternally expressed receptor
      (Igf2r).  The different contribution to the embryonic phenotype of paternal and maternal genes
      had in fact been demonstrated in parthenogenetic and androgenetic embryos.  Although the
      development of extraembryonic tissues in parthenogenetic embryos harboring two copies of the
      maternal genome is impaired, the development of the embryo proper is normal.  In contrast, the
      embryo proper in androgenones carrying two copies of the paternal genome does not develop
      properly whereas extraembryonic tissues develop normally.
AU  - Shemer R
AU  - Razin A
PT  - Journal Article
TA  - Epigenetic Mechanisms of Gene Regulation
JT  - Epigenetic Mechanisms of Gene Regulation
SO  - Epigenetic Mechanisms of Gene Regulation 1996 0: 215-229.

PMID- 24009113
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Alicyclobacillus acidoterrestris Strain ATCC 49025.
PG  - e00638-13
AB  - Alicyclobacillus acidoterrestris is a spore-forming Gram-positive, thermo-acidophilic,
      nonpathogenic bacterium which contaminates commercial
      pasteurized fruit juices. The draft genome sequence for A. acidoterrestris strain
      ATCC 49025 is reported here, providing genetic data relevant to the successful
      adaptation and survival of this strain in its ecological niche.
AU  - Shemesh M
AU  - Pasvolsky R
AU  - Sela N
AU  - Green SJ
AU  - Zakin V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00638-13.

PMID- 20541511
VI  - 18
DP  - 2010
TI  - Unusual target site disruption by the rare-cutting HNH restriction endonuclease PacI.
PG  - 734-743
AB  - The crystal structure of the rare-cutting HNH restriction endonuclease PacI in complex with
      its eightbase-pair target recognition sequence 50-TTAATT AA-30 has been determined to 1.9 Ao
      resolution. The enzyme forms an extended homodimer, with each subunit containing two
      zinc-bound motifs surrounding a bba-metal catalytic site. The latter is unusual in that a
      tyrosine residue likely initiates strand cleavage. PacI dramatically distorts its target
      sequence from Watson-Crick duplex DNA base pairing, with every base separated from its
      original partner. Two bases on each strand are unpaired, four are engaged in noncanonical A:A
      and T:T base pairs, and the remaining two bases are matched with new Watson-Crick partners.
      This represents a highly unusual DNA binding mechanism for a restriction endonuclease, and
      implies that initial recognition of the target site might involve significantly different
      contacts from those visualized in the DNA-bound cocrystal structures.
AU  - Shen BW
AU  - Heiter DF
AU  - Chan SH
AU  - Wang H
AU  - Xu SY
AU  - Morgan RD
AU  - Wilson GG
AU  - Stoddard BL
PT  - Journal Article
TA  - Structure
JT  - Structure
SO  - Structure 2010 18: 734-743.

PMID- 26705195
VI  - 428
DP  - 2016
TI  - The Structural Basis of Asymmetry in DNA Binding and Cleavage as Exhibited by the I-SmaMI LAGLIDADG Meganuclease.
PG  - 206-220
AB  - LAGLIDADG homing endonucleases ('meganucleases') are highly specific DNA cleaving enzymes
      that are used for genome engineering. Like other enzymes that act on DNA
      targets, meganucleases often display binding affinities and cleavage activities
      that are dominated by one protein domain. To decipher the underlying mechanism of
      asymmetric DNA recognition and catalysis, we identified and characterized a new
      monomeric meganuclease (I-SmaMI), which belongs to a superfamily of homologous
      enzymes that recognize divergent DNA sequences. We solved a series of crystal
      structures of the enzyme-DNA complex representing a progression of sequential
      reaction states, and we compared the structural rearrangements and surface
      potential distributions within each protein domain against their relative
      contribution to binding affinity. We then determined the effects of equivalent
      point mutations in each of the two enzyme active sites to determine whether
      asymmetry in DNA recognition is translated into corresponding asymmetry in DNA
      cleavage activity. These experiments demonstrate the structural basis for
      'dominance' by one protein domain over the other and provide insights into this
      enzyme's conformational switch from a nonspecific search mode to a more specific
      recognition mode.
AU  - Shen BW
AU  - Lambert A
AU  - Walker BC
AU  - Stoddard BL
AU  - Kaiser BK
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2016 428: 206-220.

PMID- 15313606
VI  - 342
DP  - 2004
TI  - DNA binding and cleavage by the HNH homing endonuclease I-HmuI.
PG  - 43-56
AB  - The structure of I-HmuI, which represents the last family of homing endonucleases without a
      defining crystallographic structure, has been
      determined in complex with its DNA target. A series of diverse protein
      structural domains and motifs, contacting sequential stretches of
      nucleotide bases, are distributed along the DNA target. I-HmuI contains
      an N-terminal domain with a DNA-binding surface found in the I-PpoI
      homing endonuclease and an associated HNH/N active site found in the
      bacterial colicins, and a C-terminal DNA-binding domain previously
      observed in the I-TevI homing endonuclease. The combination and
      exchange of these features between protein families indicates that the
      genetic mobility associated with homing endonucleases extends to the
      level of independent structural domains. I-HmuI provides an unambiguous
      structural connection between the His-Cys box endonucleases and the
      bacterial colicins, supporting the hypothesis that these enzymes
      diverged from a common ancestral nuclease.
AU  - Shen BW
AU  - Landthaler M
AU  - Shub DA
AU  - Stoddard BL
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2004 342: 43-56.

PMID- 21724614
VI  - 39
DP  - 2011
TI  - Characterization and crystal structure of the type IIG restriction endonuclease RM.BpuSI.
PG  - 8223-8236
AB  - A type IIG restriction endonuclease, RM.BpuSI from Bacillus pumilus, has been characterized
      and its X-ray crystal structure determined at 2.35A
      resolution. The enzyme is comprised of an array of 5-folded domains that
      couple the enzyme's N-terminal endonuclease domain to its C-terminal
      target recognition and methylation activities. The REase domain contains a
      PD-x(15)-ExK motif, is closely superimposable against the FokI
      endonuclease domain, and coordinates a single metal ion. A helical bundle
      domain connects the endonuclease and methyltransferase (MTase) domains.
      The MTase domain is similar to the N6-adenine MTase M.TaqI, while the
      target recognition domain (TRD or specificity domain) resembles a
      truncated S subunit of Type I R-M system. A final structural domain, that
      may form additional DNA contacts, interrupts the TRD. DNA binding and
      cleavage must involve large movements of the endonuclease and TRD domains,
      that are probably tightly coordinated and coupled to target site
      methylation status.
AU  - Shen BW
AU  - Xu D
AU  - Chan SH
AU  - Zheng Y
AU  - Zhu Z
AU  - Xu SY
AU  - Stoddard BL
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2011 39: 8223-8236.

PMID- 1473145
VI  - 71
DP  - 1992
TI  - High frequency mutagenesis by a DNA methyltransferase.
PG  - 1073-1080
AB  - HpaII methylase (M. HpaII), an example of a DNA(cytosine-5)-methyltransferase, was found to
      induce directly a high frequency of C to U transition mutations in double-stranded DNA. A
      mutant pSV2-neo plasmid, constructed with an inactivating T to C transition mutation creating
      a CCGG site, was incubated with M.HpaII in the absence of S-adenosylmethionine (SAM). This
      caused an approximately 104-fold increase in the rate of reversion when the mutant neo plasmid
      was transformed into bacteria lacking uracil-DNA glycosylase. The mutation frequency was very
      sensitive to SAM concentration and was reduced to background when the concentration of the
      methyl donor exceeded 300 nM. The data support current models for the formation of a covalent
      complex between the methyltransferase and cytosine. They also suggest that the occurrence of
      muational hot spots at CpG sites may not always be due to spontaneous deamination of
      5-methylcytosine, but might also be initiated by enzymatic deamination of cytosine and proceed
      through a C to U to T pathway.
AU  - Shen J
AU  - Rideout WM III
AU  - Jones PA
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1992 71: 1073-1080.

PMID- 8152929
VI  - 22
DP  - 1994
TI  - The rate of hydrolytic deamination of 5-methylctyosine in double-stranded DNA.
PG  - 972-976
AB  - The modified base, 5-methylcytosine, constitutes approximately 1% of human DNA, but sites
      containing 5-methylcytosine account for at least 30% of all germline and somatic point
      mutations. A genetic assay with a sensitivity of 1 in 10/7, based on reversion to neomycin
      resistance of a mutant pSV2-neo plasmid, was utilized to determine and compare the deamination
      rates of 5-methylcytosine and cytosine in double-stranded DNA for the first time. The rate
      constants for spontaneous hydrolytic deamination of 5-methylcytosine and cytosine in
      double-stranded DNA at 37 C were 5.8x10/-13 s/-1 and 2.6 x 10/-13 s/-1, respectively. These
      rates are more than sufficient to explain the observed frequency of mutation at sites
      containing 5-methylcytosine and emphasize the importance of hydrolytic deamination as a major
      source of human mutations.
AU  - Shen J
AU  - Rideout WM III
AU  - Jones PA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1994 22: 972-976.

PMID- 7501446
VI  - 23
DP  - 1995
TI  - A mutant HpaII methyltransferase functions as a mutator enzyme.
PG  - 4275-4282
AB  - DNA (cytosine-5)-methyltransferases can cause deamination of cytosine when the cofactor
      S-adenosylmethionine (AdoMet) is limiting and thus function as sequence-specific C-U mutator
      enzymes.  Here we explored whether mutations causing inactivation of the cofactor binding
      activity of the HpaII methyltransferase, thus mimicking conditions of limiting AdoMet
      concentration, could convert a DNA methyltransferase to a C-U mutator enzyme.  We created two
      mutator enzymes from the HpaII methyltransferase (F38S and G40D) which both showed enhanced
      cytosine deamination activities in vitro and in vivo.  Interestingly, the G:U mispairs
      generated by these enzymes were not repaired completely in bacteria equipped with uracil-DNA
      glycosylase-initiated repair machinery, giving rise to a potent mutator phenotype.  This is
      the first report showing the creation of mutator enzymes from a DNA methyltransferase and the
      demonstration of their mutagenicity in living cells.
AU  - Shen J-C
AU  - Zingg J-M
AU  - Yang AS
AU  - Schmutte C
AU  - Jones PA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1995 23: 4275-4282.

PMID- 16926421
VI  - 74
DP  - 2006
TI  - Extensive genomic plasticity in Pseudomonas aeruginosa revealed by identification and distribution studies of novel genes among clinical isolates.
PG  - 5272-5283
AB  - The distributed genome hypothesis (DGH) states that each strain within a
      bacterial species receives a unique distribution of genes from a
      population-based supragenome that is many times larger than the genome of
      any given strain. The observations that natural infecting populations are
      often polyclonal and that most chronic bacterial pathogens have highly
      developed mechanisms for horizontal gene transfer suggested the DGH and
      provided the means and the mechanisms to explain how chronic infections
      persist in the face of a mammalian host's adaptive defense mechanisms.
      Having previously established the validity of the DGH for obligate
      pathogens, we wished to evaluate its applicability to an opportunistic
      bacterial pathogen. This was accomplished by construction and analysis of
      a highly redundant pooled genomic library containing approximately 216,000
      functional clones that was constructed from 12 low-passage clinical
      isolates of Pseudomonas aeruginosa, 6 otorrheic isolates and 6 from other
      body sites. Sequence analysis of 3,214 randomly picked clones (mean insert
      size, approximately 1.4 kb) from this library demonstrated that 348
      (10.8%) of the clones were unique with respect to all genomic sequences of
      the P. aeruginosa prototype strain, PAO1. Hypothetical translations of the
      open reading frames within these unique sequences demonstrated protein
      homologies to a number of bacterial virulence factors and other proteins
      not previously identified in P. aeruginosa. PCR and reverse
      transcription-PCR-based assays were performed to analyze the distribution
      and expression patterns of a 70-open reading frame subset of these
      sequences among 11 of the clinical strains. These sequences were unevenly
      distributed among the clinical isolates, with nearly half (34/70) of the
      novel sequences being present in only one or two of the individual
      strains. Expression profiling revealed that a vast majority of these
      sequences are expressed, strongly suggesting they encode functional
      proteins.
AU  - Shen K et al
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2006 74: 5272-5283.

PMID- 20507910
VI  - 38
DP  - 2010
TI  - A single amino acid substitution confers enhanced methylation activity of mammalian Dnmt3b on chromatin DNA.
PG  - 6054-6064
AB  - Dnmt3a and Dnmt3b are paralogous enzymes responsible for de novo DNA methylation but with
      distinguished biological functions. In mice,
      disruption of Dnmt3b but not Dnmt3a causes global DNA hypomethylation,
      especially in repetitive sequences, which comprise the large majority of
      methylated DNA in the genome. By measuring DNA methylation activity of
      Dnmt3a and Dnmt3b homologues from five species, we found that mammalian
      Dnmt3b possessed significantly higher methylation activity on chromatin
      DNA than Dnmt3a and non-mammalian Dnmt3b. Sequence comparison and
      mutagenesis experiments identified a single amino acid substitution
      (I662N) in mammalian Dnmt3b as being crucial for its high chromatin DNA
      methylation activity. Further mechanistic studies demonstrated this
      substitution markedly enhanced the binding of Dnmt3b to nucleosomes and
      hence increased the chromatin DNA methylation activity. Moreover, this
      substitution was crucial for Dnmt3b to efficiently methylate repetitive
      sequences, which increased dramatically in mammalian genomes. Consistent
      with our observation that Dnmt3b evolved more rapidly than Dnmt3a during
      the emergence of mammals, these results demonstrated that the I662N
      substitution in mammalian Dnmt3b conferred enhanced chromatin DNA
      methylation activity and contributed to functional adaptation in the
      epigenetic system.
AU  - Shen L
AU  - Gao G
AU  - Zhang Y
AU  - Zhang H
AU  - Ye Z
AU  - Huang S
AU  - Huang J
AU  - Kang J
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2010 38: 6054-6064.

PMID- 18812424
VI  - 62
DP  - 2008
TI  - Complete nucleotide sequence of pKP96, a 67 850 bp multiresistance plasmid encoding qnrA1, aac(6')-Ib-cr and blaCTX-M-24 from Klebsiella pneumoniae.
PG  - 1252-1256
AB  - OBJECTIVES: The multiresistance plasmid pKP96 from Klebsiella pneumoniae
      was sequenced completely and analysed concerning its genetic environment
      and distributing of antimicrobial resistance genes. METHODS: The complete
      sequence of the plasmid was determined using a whole-genome shotgun
      approach. MICs of 13 antimicrobial agents were determined using Etests. A
      conjugation experiment was performed in liquid medium. RESULTS: pKP96 is a
      circularly closed 67 850 bp multiresistance plasmid with an IncN
      incompatibility group. Seventy putative genes were identified according to
      the annotation of the finished sequence. The backbone region of the
      plasmid, comprising the conjugal transfer and plasmid replication regions,
      showed 91% identity to the IncN plasmid R46. Several mobile elements were
      found to be inserted into pKP96 together with antimicrobial resistance
      genes, including qnrA1, aac(6')-Ib-cr and bla(CTX-M-24). CONCLUSIONS:
      Plasmid pKP96 is a chimera that has acquired its multiple antimicrobial
      resistance determinants horizontally from different sources. It may have
      evolved from an ancestor plasmid similar to R46 through the stepwise
      events of integration or recombination.
AU  - Shen P
AU  - Jiang Y
AU  - Zhou Z
AU  - Zhang J
AU  - Yu Y
AU  - Li L
PT  - Journal Article
TA  - J. Antimicrob. Chemother.
JT  - J. Antimicrob. Chemother.
SO  - J. Antimicrob. Chemother. 2008 62: 1252-1256.

PMID- 6262907
VI  - 23
DP  - 1980
TI  - Restriction endonucleases from three strains of Haemophilus influenzae.
PG  - 1435-1442
AB  - The restriction endonucleases, Hin P1I, Hin S1I and Hin S2I are isolated from
      three strains of Haemophilus influenzae respectively.  By polymin P treatment,
      ammonium sulphage precipitation and column chromatography on phosphocellulose
      and on heparin-Sepharose, Hin P1I is partially purified.  No contaminating
      deoxyribonuclease activities have been detected in this purified enzyme
      preparation.  The face that the digestion patterns of Hin P1I and HhaI on phage
      lambda, plasmids ColE1 and pBR 322 DNAs are identical indicates that they are
      isoschizomers but their splitting sites are different.  The banding patterns of
      Hin S1I and Hin S2I are also the same as that of HhaI.
AU  - Shen S
AU  - Li Q
AU  - Yan P
AU  - Zhou B
AU  - Ye S
AU  - Lu Y
AU  - Wang D
PT  - Journal Article
TA  - Sci. Sin.
JT  - Sci. Sin.
SO  - Sci. Sin. 1980 23: 1435-1442.

PMID- 27795290
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Spiroplasma helicoides TABS-2T (DSM 22551), a Bacterium Isolated from a Horsefly (Tabanus abactor).
PG  - e01201-16
AB  - Spiroplasma helicoides TABS-2T (DSM 22551) was isolated from the gut of a horsefly (Tabanus
      abactor) collected near Ardmore, Oklahoma, USA, in 1987. Here,
      we report the complete genome sequence of this bacterium to facilitate the
      investigation of its biology and the comparative genomics among Spiroplasma
      species.
AU  - Shen WY
AU  - Lo WS
AU  - Lai YC
AU  - Kuo CH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01201-16.

PMID- 22328763
VI  - 194
DP  - 2012
TI  - Genome Sequence of Pseudomonas chlororaphis GP72, a Root-Colonizing Biocontrol Strain.
PG  - 1269-1270
AB  - Pseudomonas chlororaphis GP72 is a root-colonizing biocontrol strain isolated from a green
      pepper rhizosphere. It can produce several secondary metabolites to
      suppress phytopathogens. Here we present a 6.6-Mb assembly of its genome, which
      is the first genome sequence of the P. chlororaphis group and may provide
      insights into its antifungal activities.
AU  - Shen X
AU  - Chen M
AU  - Hu H
AU  - Wang W
AU  - Peng H
AU  - Xu P
AU  - Zhang X
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1269-1270.

PMID- 20453098
VI  - 192
DP  - 2010
TI  - Complete Genome Sequences of Yersinia pestis from Natural Foci in China.
PG  - 3551-3552
AB  - Yersinia pestis, the causative agent of plague, is a deadly bacterium that affects humans.
      Strain D106004 was isolated from a new plague focus in
      Yulong County, China, in 2006. To gain insights into the epidemic origin,
      we have sequenced the genomes of D106004 and strains Z176003 and D182038,
      isolated from neighboring regions.
AU  - Shen X
AU  - Wang Q
AU  - Xia L
AU  - Zhu X
AU  - Zhang Z
AU  - Liang Y
AU  - Cai H
AU  - Zhang E
AU  - Wei J
AU  - Chen C
AU  - Song Z
AU  - Zhang H
AU  - Yu D
AU  - Hai R
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 3551-3552.

PMID- 25212613
VI  - 2
DP  - 2014
TI  - Draft genome sequences of six enterohepatic helicobacter species isolated from humans and one from rhesus macaques.
PG  - e00857-14
AB  - Draft genome sequences of seven enterohepatic Helicobacter species, H. bilis, H.  canadensis,
      H. canis, H. cinaedi, H. winghamensis, H. pullorum, and H. macacae,
      are presented. These isolates were obtained from clinical patients and a nonhuman
      primate. Due to potential zoonotic risks, we characterized antibiotic resistance
      markers and Helicobacter virulence factors.
AU  - Shen Z
AU  - Sheh A
AU  - Young SK
AU  - Abouelliel A
AU  - Ward DV
AU  - Earl AM
AU  - Fox JG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00857-14.

PMID- 16081699
VI  - 309
DP  - 2005
TI  - Accurate multiplex polony sequencing of an evolved bacterial genome.
PG  - 1728-1732
AB  - We describe a DNA sequencing technology in which a commonly available, inexpensive
      epifluorescence microscope is converted to rapid
      nonelectrophoretic DNA sequencing automation. We apply this technology to
      resequence an evolved strain of Escherichia coli at less than one error
      per million consensus bases. A cell-free, mate-paired library provided
      single DNA molecules that were amplified in parallel to 1-micrometer beads
      by emulsion polymerase chain reaction. Millions of beads were immobilized
      in a polyacrylamide gel and subjected to automated cycles of sequencing by
      ligation and four-color imaging. Cost per base was roughly one-ninth as
      much as that of conventional sequencing. Our protocols were implemented
      with off-the-shelf instrumentation and reagents.
AU  - Shendure J
AU  - Porreca GJ
AU  - Reppas NB
AU  - Lin X
AU  - McCutcheon JP
AU  - Rosenbaum AM
AU  - Wang MD
AU  - Zhang K
AU  - Mitra RD
AU  - Church GM
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2005 309: 1728-1732.

PMID- 24786959
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Gluconobacter oxydans Strain DSM 2003, an Important  Biocatalyst for Industrial Use.
PG  - e00417-14
AB  - Gluconobacter oxydans strain DSM 2003 can efficiently produce some industrially important
      building blocks, such as (R)-lactic acid and (R)-2-hydroxybutyric acid.
      Here, we present a 2.94-Mb assembly of its genome sequence, which might provide
      further insights into the molecular mechanism of its biocatalysis in order to
      further improve its biotechnological applications.
AU  - Sheng B
AU  - Ni J
AU  - Gao C
AU  - Ma C
AU  - Xu P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00417-14.

PMID- 29449403
VI  - 6
DP  - 2018
TI  - High-Quality Complete Genome Sequences of Three Bovine Shiga Toxin-Producing Escherichia coli O177:H- (fliCH25) Isolates Harboring Virulent stx2 and Multiple   Plasmids.
PG  - e01592-17
AB  - Shiga toxin-producing Escherichia coli (STEC) bacteria are zoonotic pathogens. We report here
      the high-quality complete genome sequences of three STEC O177:H-
      (fliCH25) strains, SMN152SH1, SMN013SH2, and SMN197SH3. The assembled genomes
      consisted of one optical map-verified circular chromosome for each strain, plus
      two plasmids for SMN013SH2 and three plasmids for SMN152SH1 and SMN197SH3,
      respectively.
AU  - Sheng H
AU  - Duan M
AU  - Hunter SS
AU  - Minnich SA
AU  - Settles ML
AU  - New DD
AU  - Chase JR
AU  - Fagnan MW
AU  - Hovde CJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01592-17.

PMID- 27688322
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Geobacillus thermoglucosidasius NCIMB 11955, the Progenitor of a Bioethanol Production Strain.
PG  - e01065-16
AB  - The industrially important thermophile Geobacillus thermoglucosidasius has the potential to
      produce chemicals and fuels from biomass-derived sugar feedstocks.
      Here, we present the genome sequence of strain NCIMB 11955, the progenitor of an
      ethanologenic industrial strain, revealing 11 single-nucleotide polymorphisms and
      2 indels compared to strain DSM 2542 and two novel plasmids.
AU  - Sheng L
AU  - Zhang Y
AU  - Minton NP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01065-16.

PMID- 3012472
VI  - 14
DP  - 1986
TI  - Hydrolysis by restriction endonucleases at their DNA recognition sequences substituted with mismatched base pairs.
PG  - 4407-4420
AB  - Restriction endonucleases were tested for their ability to catalyze the
      cleavage of mismatch-containing recognition sites in DNA.  These mismatched
      base pairs were T.G, U.G, or A.C in covalently closed, circular heteroduplexes
      prepared by in vitro extension of chemically synthesized oligonucleotide
      primers annealed to a bacteriophage M13-derived viral DNA.  None of the
      restriction enzymes was able to completely cleave the mismatch-containing
      recognition sites under standard conditions.  However, three of them, SmaI,
      SalI, and SstI, catalyzed partial digestion leading to an accumulation of DNA
      singly nicked at the mismatched recognition site.  The ability of SmaI and SstI
      to partially cleave at a mismatch was shown to depend on the nature and
      position of the mismatch within the corresponding recognition site.  In
      contrast, little or no digestion was obtained with AccI, HincII, HindIII, and
      KpnI at mismatch-containing sites.  Therefore, in some cases a transition-type
      substitution in only one strand of a recognition site inhibits restriction
      endonuclease-catalyzed digestion at that site although in others partial
      digestion occurs.
AU  - Shenoy S
AU  - Daigle K
AU  - Ehrlich KC
AU  - Gehrke CW
AU  - Ehrlich M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1986 14: 4407-4420.

PMID- 22081385
VI  - 194
DP  - 2012
TI  - Genome sequences and phylogenetic analysis of K88- and F18-positive porcine enterotoxigenic Escherichia coli.
PG  - 395-405
AB  - Porcine enterotoxigenic Escherichia coli (ETEC) continues to result in major morbidity and
      mortality in the swine industry via postweaning diarrhea. The key
      virulence factors of ETEC strains, their serotypes, and their fimbrial components
      have been well studied. However, most studies to date have focused on
      plasmid-encoded traits related to colonization and toxin production, and the
      chromosomal backgrounds of these strains have been largely understudied. Here, we
      generated the genomic sequences of K88-positive and F18-positive porcine ETEC
      strains and examined the phylogenetic distribution of clinical porcine ETEC
      strains and their plasmid-associated genetic content. The genomes of porcine ETEC
      strains UMNK88 and UMNF18 were both found to contain remarkable plasmid
      complements containing known virulence factors, potential novel virulence
      factors, and antimicrobial resistance-associated elements. The chromosomes of
      these strains also possessed several unique genomic islands containing
      hypothetical genes with similarity to classical virulence factors, although
      phage-associated genomic islands dominated the accessory genomes of these
      strains. Phylogenetic analysis of 78 clinical isolates associated with neonatal
      and porcine diarrhea revealed that a limited subset of porcine ETEC lineages
      exist that generally contain common toxin and fimbrial profiles, with many of the
      isolates belonging to the ST10, ST23, and ST169 multilocus sequencing types.
      These lineages were generally distinct from existing human ETEC database
      isolates. Overall, most porcine ETEC strains appear to have emerged from a
      limited subset of E. coli lineages that either have an increased propensity to
      carry plasmid-encoded virulence factors or have the appropriate ETEC core genome
      required for virulence.
AU  - Shepard SM
AU  - Danzeisen JL
AU  - Isaacson RE
AU  - Seemann T
AU  - Achtman M
AU  - Johnson TJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 395-405.

PMID- 23405326
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Bacillus thuringiensis Strain 407 Cry-.
PG  - e00158-12
AB  - Bacillus thuringiensis is an insect pathogen that has been used widely as a biopesticide.
      Here, we report the genome sequence of strain 407 Cry-, which is
      used to study the genetic determinants of pathogenicity. The genome consists of a
      5.5-Mb chromosome and nine plasmids, including a novel 502-kb megaplasmid.
AU  - Sheppard AE
AU  - Poehlein A
AU  - Rosenstiel P
AU  - Liesegang H
AU  - Schulenburg H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00158-12.

PMID- 26823590
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of KPC-Producing Klebsiella pneumoniae Strain CAV1193.
PG  - e01649-15
AB  - Carbapenem resistance in Klebsiella pneumoniae, frequently conferred by the blaKPC gene, is a
      major public health threat. We sequenced a blaKPC-containing
      strain of K. pneumoniae belonging to the emergent lineage ST941, in order to
      better understand the evolution of blaKPC within this species.
AU  - Sheppard AE
AU  - Stoesser N
AU  - Sebra R
AU  - Kasarskis A
AU  - Deikus G
AU  - Anson L
AU  - Walker AS
AU  - Peto TE
AU  - Crook DW
AU  - Mathers AJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01649-15.

PMID- 10773089
VI  - 28
DP  - 2000
TI  - The complete DNA sequence and analysis of R27, a large IncHI plasmid from Salmonella typhi that is temperature sensitive for transfer.
PG  - 2177-2186
AB  - Salmonella typhi, the causative agent of typhoid fever, annually infects 16 million people and
      kills 600,000 world wide. Plasmid-encoded multiple drug resistance in S. typhi is always
      encoded by plasmids of incompatibility group H (IncH). The complete DNA sequence of the large
      temperature-sensitive conjugative plasmid R27, the prototype for the IncHI1 family of
      plasmids, has been compiled and analyzed. This 180 kb plasmid contains 210 open reading frames
      (ORFs), of which 14 have been previously identified and 56 exhibit similarity to other plasmid
      and prokaryotic ORFs. A number of insertion elements were found, including the full Tn 10
      transposon, which carries tetracycline resistance genes. Two transfer regions, Tra1 and Tra2,
      are present, which are separated by a minimum of 64 kb. Homologs of the DNA-binding proteins
      TlpA and H-NS that act as temperature-regulated repressors in other systems have been located
      in R27. Sequence analysis of transfer and replication regions supports a mosaic-like structure
      for R27. The genes responsible for conjugation and plasmid maintenance have been identified
      and mechanisms responsible for thermosensitive transfer are discussed.
AU  - Sherburne CK
AU  - Lawley TD
AU  - Gilmour MW
AU  - Blattner FR
AU  - Burland V
AU  - Grotbeck E
AU  - Rose DJ
AU  - Taylor DE
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2000 28: 2177-2186.

PMID- 3034245
VI  - 144
DP  - 1987
TI  - Two dimensional NMR studies on the solution structure of d-CTCGAGCTCGAG.
PG  - 26-34
AB  - Two dimensional (2D) FT-NMR investigations have been carried out on the
      self-complementary dodecanucleotide d-CTCGAGCTCGAG, which has cleavage sites
      for the restriction enzyme XhoI (between C and T).  The central TCG portion is
      also known to show a preference for DNAase activity.  Complete resonance
      assignments have been obtained for the non-exchangeable sugar and base protons
      of the oligonucleotide.  Information regarding sugar geometries, glycosidic
      torsion angles and other structural parameters has been obtained from the
      relative intensities of the cross peaks in the COSY and NOESY spectra.  The
      results indicate that deoxyribose rings of C1 and C7 adopt a conformation
      different from the remaining sugars in the double helical oligonucleotide.  The
      Central TCG portion also exhibits variations in the backbone structure.  The
      base stacking in the double helix shows interesting sequence dependent effects
      suggesting that the sequence effects are not localised to nearest neighbours
      but extended over longer stretches.
AU  - Sheth A
AU  - Ravikumar M
AU  - Hosur RV
AU  - Govil G
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1987 144: 26-34.

PMID- 26380642
VI  - 10
DP  - 2015
TI  - Complete genome sequence of the phenanthrene-degrading soil bacterium Delftia acidovorans Cs1-4.
PG  - 55
AB  - Polycyclic aromatic hydrocarbons (PAH) are ubiquitous environmental pollutants and microbial
      biodegradation is an important means of remediation of PAH-contaminated soil. Delftia
      acidovorans Cs1-4 (formerly Delftia sp. Cs1-4) was isolated by using phenanthrene as the sole
      carbon source from PAH contaminated soil in Wisconsin. Its full genome sequence was determined
      to gain insights into  a mechanisms underlying biodegradation of PAH. Three genomic libraries
      were constructed and sequenced: an Illumina GAii shotgun library (916,416,493 reads),  a 454
      Titanium standard library (770,171 reads) and one paired-end 454 library (average insert size
      of 8 kb, 508,092 reads). The initial assembly contained 40 contigs in two scaffolds. The 454
      Titanium standard data and the 454 paired end data were assembled together and the consensus
      sequences were computationally shredded into 2 kb overlapping shreds. Illumina sequencing data
      was assembled, and the consensus sequence was computationally shredded into 1.5 kb overlapping
      shreds. Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer
      walks. A total of 182 additional reactions were needed to close gaps and to raise the quality
      of the finished sequence. The final assembly is based on 253.3 Mb of 454 draft data (averaging
      38.4 X coverage) and 590.2 Mb of Illumina draft data (averaging 89.4 X coverage). The genome
      of strain Cs1-4 consists of a single circular chromosome of 6,685,842 bp (66.7 %G+C)
      containing 6,028 predicted genes; 5,931 of these genes were protein-encoding and 4,425 gene
      products were assigned to a putative function. Genes encoding phenanthrene degradation were
      localized to a 232 kb genomic island (termed the phn island), which contained near its 3' end
      a bacteriophage P4-like integrase, an enzyme often associated with chromosomal integration of
      mobile genetic elements. Other biodegradation pathways reconstructed from the genome sequence
      included: benzoate (by the acetyl-CoA pathway), styrene, nicotinic acid (by the maleamate
      pathway) and the pesticides Dicamba and Fenitrothion. Determination of the complete genome
      sequence of D. acidovorans Cs1-4 has provided new insights the microbial mechanisms of PAH
      biodegradation that may shape the process in the environment.
AU  - Shetty AR et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 55.

PMID- 28963222
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Biofilm-Forming and Non-Biofilm-Forming Nontyphoidal Salmonella enterica Serovars.
PG  - e01061-17
AB  - The genetic basis for biofilm formation among nontyphoidal salmonellae (NTS) remains poorly
      understood. This draft genome submission provides initial insights
      on the genetic differences between biofilm-forming and non-biofilm-forming
      clinical and environmental NTS serovars.
AU  - Shetty D
AU  - Grigoryan AA
AU  - Alshalchi S
AU  - Withana GN
AU  - Roy J
AU  - Lawrence JR
AU  - Vidovic S
AU  - Korber DR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01061-17.

PMID- 23661481
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Methylophaga lonarensis MPLT, a Haloalkaliphilic (Non-Methane-Utilizing) Methylotroph.
PG  - e00202-13
AB  - Methylophaga lonarensis strain MPL(T) is a haloalkaliphilic methylotroph isolated from Lonar
      Lake, a saline and alkaline lake in Maharashtra, India. Strain MPL(T)
      utilizes methanol as its sole carbon and energy source. Here, we present the
      draft genome sequence of M. lonarensis MPL(T) (VKM B-2684(T) = MCC 1002(T)).
AU  - Shetty SA
AU  - Marathe NP
AU  - Munot H
AU  - Antony CP
AU  - Dhotre DP
AU  - Murrell JC
AU  - Shouche YS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00202-13.

PMID- 29074659
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Eubacterium hallii Strain L2-7.
PG  - e01167-17
AB  - The complete genome sequence of Eubacterium hallii strain L2-7 is reported here.  This
      intestinal strain produces butyrate from glucose as well as lactate when
      acetate is provided in the growth medium. In addition, strain L2-7 has been shown
      to improve insulin sensitivity in db/db mice, indicating its application
      potential.
AU  - Shetty SA
AU  - Ritari J
AU  - Paulin L
AU  - Smidt H
AU  - De Vos WM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01167-17.

PMID- 29437093
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of 42 Helicobacter pylori Isolates from Rural Regions of South India.
PG  - e01486-17
AB  - Helicobacter pylori is a successful human gastric pathogen that is associated with the
      development of gastric cancer. The draft genome sequences of 42 H.
      pylori clinical strains isolated from South Indian rural populations will provide
      further insights into the evolution and genetic makeup of Indian H. pylori
      strains.
AU  - Shetty V
AU  - Lamichhane B
AU  - Chua EG
AU  - Ballal M
AU  - Tay CY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01486-17.

PMID- 16246913
VI  - 33
DP  - 2005
TI  - Transgene-induced CCWGG methylation does not alter CG methylation patterning in human kidney cells.
PG  - 6124-6136
AB  - Several reports suggest that C(m)CWGG methylation tends not to co-exist with (m)CG methylation
      in human cells. We have asked whether or not
      methylation at CCWGG sites can influence CG methylation. DNA from cells
      expressing an M.EcoRII-GFP fusion was actively methylated at CCWGG sites.
      CG methylation as measured by R.HpaII/R.MspI ratios was unchanged in cells
      expressing the transgene. Cloned representatives of C(m)CWGG methylated
      DNA often contained, or were adjacent to an ALU repeat, suggesting that
      M.EcoRII-GFP actively methylated gene-rich R-band DNA. The transgenic
      methyltransferase applied C(m)CWGG methylation to a representative human
      promoter that was heavily methylated at CG dinucleotides (the SERPINB5
      promoter) and to a representative promoter that was essentially
      unmethylated at CG dinucleotides (the APC promoter). In each case, the CG
      methylation pattern remained in its original state, unchanged by the
      presence of neighboring C(m)CWGG sites. Q-PCR measurements showed that RNA
      expression from the APC gene was not significantly altered by the presence
      of C(m)CWGG in its promoter. Kinetic studies suggested that an adjacent
      C(m)CWGG methylation site influences neither the maintenance nor the de
      novo methylation activities of purified human Dnmt1. We conclude that
      C(m)CWGG methylation does not exert a significant effect on CG methylation
      in human kidney cells.
AU  - Shevchuk T
AU  - Kretzner L
AU  - Munson K
AU  - Axume J
AU  - Clark J
AU  - Dyachenko OV
AU  - Caudill M
AU  - Buryanov Y
AU  - Smith SS
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2005 33: 6124-6136.

PMID- 10578468
VI  - 25
DP  - 1999
TI  - DNA methyltransferase-based assay for the cytosine methylation level in the DNA sequence CCWGG.
PG  - 630-633
AB  - An assay for the cytosine methylation level in the eukaryotic DNA CCWGG sequence is proposed.
      The method is based on the ability of DNA methylase BstNI to methylate DNA containing in a
      CCWGG site a nonmodified or 5-methylated cytosine to yield N4-methyl- or
      N4,5-dimethylcytosine, respectively.
AU  - Shevchuk TV
AU  - Buryanov YI
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1999 25: 630-633.

PMID- 
VI  - 48
DP  - 2001
TI  - The effect of the gene encoding EcoRII DNA methyltransferase on the phenotype of transgenic tumor cell lines of Nicotiana tabacum and the  methylation level of CpNpG sequences in their genome.
PG  - 478-482
AB  - Several tumor cell lines were obtained by transforming Nicotiana tabacum plants with the
      recombinant Ti plasmid comprising the gene
      encoding EcoRII DNA methyltransferase (M.EcoRII) and subjected to
      analysis. The transformed lines differed in their morphology, growth
      dependence on hormones, and nopaline-synthesizing capacity. Southern
      blot-hybridization showed that the M.EcoRII gene was present in the
      cells of all transformed lines. However, genome analysis using
      polymerase chain reaction with the oligonucleotide primers recognizing
      5'-ends of the M.EcoRII gene did not exhibit the full-length copies of
      the gene. Lower methylation of CpNpG sequences characteristic of all
      transformed cells could result from the disturbance of one of several
      plant DNA methyltransferase genes following its homologous
      recombination with the M.EcoRII gene.
AU  - Shevchuk TV
AU  - Zakharchenko NS
AU  - Dyachenko OV
AU  - Buryanov YI
PT  - Journal Article
TA  - Russ. J. Plant Physiol.
JT  - Russ. J. Plant Physiol.
SO  - Russ. J. Plant Physiol. 2001 48: 478-482.

PMID- 24136850
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Rhodococcus erythropolis DN1, a Crude Oil Biodegrader.
PG  - e00846-13
AB  - We report the 6,548-Mb genome sequence of Rhodococcus erythropolis strain DN1, isolated from
      the oil-contaminated soil in the Karagandy region of Kazakhstan.
      The draft genome sequence of strain DN1 might provide new insights into the
      genetic mechanisms of crude oil biodegradation.
AU  - Shevtsov A
AU  - Tarlykov P
AU  - Zholdybayeva E
AU  - Momynkulov D
AU  - Sarsenova A
AU  - Moldagulova N
AU  - Momynaliev K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00846-13.

PMID- 24371203
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Live Vaccine Strain Brucella abortus 82.
PG  - e01101-13
AB  - Vaccination is a crucial part of the brucellosis eradication programs worldwide.  A live
      vaccine strain of Brucella abortus 82 has been successfully used for the
      vaccination of cattle against brucellosis in the former Soviet republics for the
      last 39 years. Here, we report the genome sequence of Brucella abortus 82.
AU  - Shevtsov A
AU  - Tarlykov P
AU  - Zholdybayeva E
AU  - Shevtsova E
AU  - Momynkulov D
AU  - Sytnik I
AU  - Karibaev T
AU  - Chsherbakov A
AU  - Momynaliev K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01101-13.

PMID- 20630106
VI  - 7
DP  - 2010
TI  - Complete genome sequence of a Megalocytivirus (family Iridoviridae) associated with turbot mortality in China.
PG  - 159
AB  - ABSTRACT: BACKGROUND: Turbot reddish body iridovirus (TRBIV) causes
      serious systemic diseases with high mortality in the cultured turbot,
      Scophthalmus maximus. We here sequenced and analyzed the complete genome
      of TRBIV, which was identified in Shandong province, China. RESULTS: The
      genome of TRBIV is a linear double-stranded DNA of 110,104 base pairs,
      comprising 55% G + C. Total 115 open reading frames were identified,
      encoding polypeptides ranging from 40 to 1168 amino acids. Amino acid
      sequences analysis revealed that 39 of the 115 potential gene products of
      TRBIV show significant homology to other iridovirus proteins. Phylogenetic
      analysis of conserved genes indicated that TRBIV is closely related to
      infectious spleen and kidney necrosis virus (ISKNV), rock bream iridovirus
      (RBIV), orange-spotted grouper iridovirus (OSGIV), and large yellow
      croaker iridovirus (LYCIV). The results indicated that TRBIV belongs to
      the genus Megalocytivirus (family Iridoviridae). CONCLUSIONS: The
      determination of the genome of TRBIV will provide useful information for
      comparative study of Megalocytivirus and developing strategies to control
      outbreaks of TRBIV-induced disease.
AU  - Shi CY
AU  - Jia KT
AU  - Yang B
AU  - Huang J
PT  - Journal Article
TA  - Virol. J.
JT  - Virol. J.
SO  - Virol. J. 2010 7: 159.

PMID- 11530011
VI  - 130
DP  - 2001
TI  - Xenopus Eggs Express an Identical DNA Methyltransferase, Dnmt1, to Somatic Cells.
PG  - 359-366
AB  - In mouse, an oocyte-specific short isoform of DNA methyltransferase-1 (Dnmt1) lacking amino
      terminal 118 amino acid residues exists and plays a crucial role in maintaining the
      methylation state of imprinted genes during early embryogenesis [Howell et al. (2001) Cell
      104, 829-838]. To address the question of whether or not Xenopus oocyte expresses such a short
      isoform, we raised monoclonal antibodies against the amino-terminal portion of Xenopus Dnmt1.
      Two of the isolated monoclonal antibodies, 3C6 and 4A8, were determined to recognize (1-32)
      and (115-126) of Xenopus Dnmt1, respectively. The amounts of Dnmt1 in Xenopus eggs were
      determined to be similar, 10.0 2.5, 8.0 0.8, and 8.2 0.2 ng per egg with monoclonal antibodies
      3C6 and 4A8, and polyclonal antibodies, respectively. This indicated that Dnmt1 in Xenopus
      mature eggs had an identical amino-terminal sequence to the amino acid sequence deduced from
      the cDNA. Together with the fact that Dnmt1 in A6 cells immuno-reacted with all the monoclonal
      antibodies isolated and with the polyclonal antibodies, we concluded that Dnmt1 expressed in
      Xenopus mature eggs possesses an identical amino-terminal sequence to that in somatic cells.
      Immuno-purified Xenopus Dnmt1 in mature eggs showed similar specific activity to that in
      proliferating A6 cells and that of mouse recombinant Dnmt1.
AU  - Shi L
AU  - Suetake I
AU  - Kawakami T
AU  - Aimoto S
AU  - Tajima S
PT  - Journal Article
TA  - J. Biochem. (Tokyo)
JT  - J. Biochem. (Tokyo)
SO  - J. Biochem. (Tokyo) 2001 130: 359-366.

PMID- 24122235
VI  - 14
DP  - 2014
TI  - The identification of the nitrate assimilation related genes in the novel Bacillus megaterium NCT-2 accounts for its ability to use nitrate as its only source of nitrogen.
PG  - 219-227
AB  - Bacillus megaterium NCT-2 is a novel bacterium that can utilize nitrate as its
      only nitrogen source for growth.The nitrate assimilation related genes that are
      involved in this process would be expected to be crucial. However, little is
      known about the genomic background of this bacterium,let alone the sequences of
      the nitrate assimilation related genes. In order to further investigate the
      nitrate assimilation function of the NCT-2, genome sequencing was performed.After
      obtaining the fine map of the NCT-2 genome, which was submitted to the NCBI
      GenBank (AHTF00000000), the sequences of the nitrate assimilation related genes
      (the nitrate reductase electron transfer subunit nasB and the nitrate reductase
      catalytic subunit nasC, the nitrite reductase [NAD(P)H]large subunit nasD and the
      nitrite reductase [NAD(P)H] small subunit nasE, and the glutamine synthetase
      glnA) were identified.Multiple alignments were performed to find out the sequence
      identities of the nitrate assimilation related genes to that of their similar
      species. Through KEGG signaling mapping search, the nitrate assimilation related
      genes were revealed to be located in the nitrogen metabolism signaling pathway.
      The putative 3D protein structures of these genes were modeled by SWISS MODEL,
      and shown to be highly similar to the nitrate assimilation related genes in the
      PDB database. Finally, the sequence validity of the nitrate assimilation related
      genes was verified by PCR with specifically designed primers.
AU  - Shi W
AU  - Lu W
AU  - Liu Q
AU  - Zhi Y
AU  - Zhou P
PT  - Journal Article
TA  - Funct. Integr. Genomics
JT  - Funct. Integr. Genomics
SO  - Funct. Integr. Genomics 2014 14: 219-227.

PMID- 22965101
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Thermostable-Agarase-Producing Marine Bacterium Catenovulum agarivorans YM01T, Which Reveals the Presence of a Series of  Agarase-Encoding Genes.
PG  - 5484
AB  - Marine bacterium Catenovulum agarivorans YM01(T) can produce highly thermostable  agarases.
      The draft genome of YM01(T) is about 5.36 Mb and harbors approximately
      4,913 genes, including 15 agarase (2 alpha-agarase and 13 beta-agarase)-encoding
      genes, which will provide references to functional characterization of various
      agarases from marine bacteria.
AU  - Shi X
AU  - Yu M
AU  - Yan S
AU  - Dong S
AU  - Zhang XH
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5484.

PMID- 24675851
VI  - 2
DP  - 2014
TI  - Genome Sequence of Proteus mirabilis Clinical Isolate C05028.
PG  - e00167-14
AB  - Genomic DNA of Proteus mirabilis C05028 was sequenced by an Illumina HiSeq platform and was
      assembled to 39 scaffolds with a total length of 3.8 Mb. Next,
      open reading frames (ORFs) were identified and were annotated by the KEGG, COG,
      and NR databases. Finally, we found special virulence factors only existing in P.
      mirabilis C05028.
AU  - Shi X
AU  - Zhu Y
AU  - Li Y
AU  - Jiang M
AU  - Lin Y
AU  - Qiu Y
AU  - Chen Q
AU  - Yuan Y
AU  - Ni P
AU  - Hu Q
AU  - Huang S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00167-14.

PMID- 26337884
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Streptococcus thermophilus MN-BM-A02, a Rare Strain with a High Acid-Producing Rate and Low Post-Acidification Ability.
PG  - e00979-15
AB  - Streptococcus thermophilus MN-BM-A02 was originally isolated from a traditional fermented
      dairy product in China. The characteristics of this bacterium are its high acid-producing rate
      and low post-acidification. This study presents the genome sequence of MN-BM-A02. Its complete
      genome comprises 2,025 genes and 1,850,434 nucleotides with an average G+C content of 39%.
AU  - Shi Y
AU  - Chen Y
AU  - Li Z
AU  - Yang L
AU  - Chen W
AU  - Mu Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00979-15.

PMID- 30528016
VI  - 76
DP  - 2019
TI  - Genetic characterization and potential molecular dissemination mechanism of tet (31) gene in Aeromonas caviae from an oxytetracycline wastewater treatment system.
PG  - 259-266
AB  - Recently, the rarely reported tet(31) tetracycline resistance determinant was commonly
      found in Aeromonas salmonicida, Gallibacterium anatis, and Oblitimonas alkaliphila isolated
      from farming animals and related environment. However, its distribution in other bacteria
      and potential molecular dissemination mechanism in environment are still unknown. The
      purpose of this study was to investigate the potential mechanism underlying dissemination
      of tet(31) by analysing the tet(31)-carrying fragments in A. caviae strains isolated from an
      aerobic biofilm reactor treating oxytetracycline bearing wastewater. Twenty-three A. caviae
      strains were screened for the tet(31) gene by polymerase chain reaction (PCR). Three strains
      (two harbouring tet(31), one not) were subjected to whole genome sequencing using
      the PacBio RSII platform. Seventeen A. caviae strains carried the tet(31) gene and exhibited
      high resistance levels to oxytetracycline with minimum inhibitory concentrations (MICs)
      ranging from 256 to 512 mg/L. tet(31) was comprised of the transposon Tn6432 on the
      chromosome of A. caviae, and Tn6432 was also found in 15 additional tet(31)-positive
      A. caviae isolates by PCR. More important, Tn6432 was located on an integrative conjugative
      element (ICE)-like element, which could mediate the dissemination of the tet(31)-carrying
      transposon Tn6432 between bacteria. Comparative analysis demonstrated that Tn6432
      homologs with the structure ISCR2-kphzF-tetR(31)-tet(31)-kglmM-sul2 were also carried by
      A. salmonicida, G. anatis, and O. alkaliphila, suggesting that this transposon can be
      transferred
      between species and even genera. This work provides the first report on the identification of
      the tet(31) gene in A. caviae, and will be helpful in exploring the dissemination mechanisms
      of tet(31) in water environment.
AU  - Shi Y
AU  - Tian Z
AU  - Leclercq SO
AU  - Zhang H
AU  - Yang M
AU  - Zhang Y
PT  - Journal Article
TA  - J. Environ. Sci. (China)
JT  - J. Environ. Sci. (China)
SO  - J. Environ. Sci. (China) 2019 76: 259-266.

PMID- 25814604
VI  - 3
DP  - 2015
TI  - Genome Sequence of Organophosphorus Pesticide-Degrading Bacterium Pseudomonas stutzeri Strain YC-YH1.
PG  - e00192-15
AB  - Pseudomonas stutzeri strain YC-YH1, isolated from pesticide-polluted soil, efficiently
      degrades organophosphorus pesticides (OPPs) such as chlorpyrifos,
      parathion-methyl, triazophos, and parathion. Here, we report the genome sequence
      (4.83 Mb) of P. stutzeri YC-YH1 to facilitate further investigation of the
      OPP-degrading mechanism.
AU  - Shi YH
AU  - Ren L
AU  - Jia Y
AU  - Yan YC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00192-15.

PMID- 29622609
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Salmonella enterica Serovar Enteritidis and Kentucky Isolates from Retail Poultry Sources.
PG  - e00193-18
AB  - The draft genome sequences of four Salmonella enterica serovar Enteritidis and Kentucky
      isolates were evaluated for biofilm formation and antibiotic resistance.
      The Salmonella serovar Kentucky strains CFS84 and CFS85 and Salmonella serovar
      Enteritidis strains CFS86 and CFS87 were isolated from retail poultry sources in
      Arkansas.
AU  - Shi Z
AU  - Kaldhone PR
AU  - Khajanchi BK
AU  - Foley SL
AU  - Ricke SC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00193-18.

PMID- 182257
VI  - 442
DP  - 1976
TI  - The restriction endonucleases in Bacillus amyloliquefaciens N strain.  Substrate specificities.
PG  - 184-196
AB  - Two species of restriction endonuclease were isolated by gel filtration and
      DEAE-cellulose chromatography from a cell-free extract of Bacillus
      amyloliquefaciens (B. subtilis) N strain; a lower molecular weight endonuclease
      (endonuclease R.BamNI) and a higher molecular-weight one (endonuclease
      R.BamNx).  Both of them required only Mg2+ for their activities.  Endonuclease
      R.BamNx introduced a larger number of site-specific scissions in Escheria coli
      phage lambda DNA than endonuclease R.BamNI did.  Endonuclease R.BamNx cleaved
      Bacillus phage Phi105C DNA at the specific sites which are classified into two
      groups: one type of sites is modified by B. amyloliquefaciens H strain in vivo
      while the other is not affected.  It was also active on DNAs of E. coli phage
      T7, lambda dvl, Simian virus 40 (SV40) and colicinogenic factor ColEI and was
      inactive on DNAs of Bacillus phages Phi29 and M2.  Endonuclease R.BamNi cleaved
      DNA in the same nucleotide sequences as endonuclease R.BamHI isolated from H
      strain by Wilson and Young.  This endonuclease was active on DNAs of phage
      lambda, lambda dvl and SV40, and was inactive of phages Phi105C, Phi29, M2 and
      T7, and ColEI DNA.
AU  - Shibata T
AU  - Ando T
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1976 442: 184-196.

PMID- 807794
VI  - 138
DP  - 1975
TI  - In vitro Modification and Restriction of Phage Phi105C DNA with Bacillus subtilis N Cell-free Extract.
PG  - 269-279
AB  - The enzymes involved in host-controlled modification and restriction by
      Bacillus subtilis strain N were detected in cell-free extracts.  In the
      presence of Mg2+, the N-specific endonuclease cleaved unmodified DNA but did
      not attack Phi105C.N DNA carrying N-specific modification.  The restriction
      endonuclease required neither SAM nor ATP for its activity.  The N-specific
      modification enzyme was active only in the presence of SAM, indicating that
      modification in this system is a methylation of DNA.
AU  - Shibata T
AU  - Ando T
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1975 138: 269-279.

PMID- 4215952
VI  - 131
DP  - 1974
TI  - Host controlled modification and restriction in Bacillus subtilis.
PG  - 275-280
AB  - The host controlled modification and restriction was found in Bacillus subtilis
      Marburg 168, Bacillus subtilis (B. amyloliquefaciens) N and H, by use of a
      clear plaque mutant of temperate phage Phi105 (Phi105C).  This phenomenon of
      "modification and restriction" was similar to that found in Escherichia coli,
      Haemophilus influenzae and other micro-organisms.  Phi105 carrying Marburg 168
      specific modification (Phi105C.168) plated on B. subtilis N and H with an
      efficiency of 10-5 and 10-2, respectively.  Phi105C carrying the modification
      endowed by B. subtilis N (Phi105C.N) had an efficiency of plating on B.
      subtilis 168 of 4 x 10-2 and was not restricted by B. subtilis H.  Phi105C
      carrying H specific modification (Phi105C.H) plated on B. subtilis 168 and N
      with an efficiency of 10-1-10-2 and 10-5, respectively.  Modification type of
      Phi105C was determined by the last host strain and was not genetic behavior of
      the phage.  Efficiencies of plating of Bacillus phages Phi29 and SPP1 were not
      affected by the modification and restriction described in the ent paper.
AU  - Shibata T
AU  - Ando T
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1974 131: 275-280.

PMID- Not included in PubMed...
VI  - 42
DP  - 1978
TI  - Simultaneous preparation of a DNA ligase and restriction endonucleases from Bacillus amyloliquefaciens N.
PG  - 1613-1615
AB  - None
AU  - Shibata T
AU  - Hayase E
AU  - Ando T
PT  - Journal Article
TA  - Agric. Biol. Chem.
JT  - Agric. Biol. Chem.
SO  - Agric. Biol. Chem. 1978 42: 1613-1615.

PMID- 
VI  - 0
DP  - 1982
TI  - Genetic study of restriction endonucleases in Bacillus subtilis.
PG  - 71-74
AB  - During this decade, research has revealed that various microorganisms have a
      type of intracellular endodeoxyribonuclease that recognizes specific nucleotide
      sequences in double-stranded DNA and introduces double-stranded scissions at or
      near those sequences.  These endonucleases are called site-specific
      endonucleases or type II restriction endonucleases, although only a few of them
      have been proven to be involved in restriction and modification of genetically
      foreign entities invading into a cell.  Therefore, this type of endonuclease
      might have other biological roles in living cells, such as recombination.  In
      Bacillus subtilis, restriction and modification of phages were not known until
      1974, when Trautner et al. and we found, independently, that strains of B.
      subtilis, including the 168 strain, exhibited restriction and modification of
      phages SPP1 or Phi105C.  We then found that 13 of 40 B. subtilis strains
      (including B. amyloliquefaciens) and 11 strains of other Bacillus species have
      site-specific endonucleases.  As an initial step in elucidating the biological
      roles of site-specific endonucleases, we analyzed the genes for such
      endonucleases.
AU  - Shibata T
AU  - Ikawa S
AU  - Ando T
PT  - Journal Article
TA  - Microbiology-1982
JT  - Microbiology-1982
SO  - Microbiology-1982 1982 0: 71-74.

PMID- 824277
VI  - 128
DP  - 1976
TI  - Site-specific Deoxyribonucleases in Bacillus subtilis and other Bacillus strains.
PG  - 473-476
AB  - We systematically studied site-specific deoxyribonucleases in Bacillus strains
      and detected deoxyribonuclease activities in 20 of 62 strains tested.
AU  - Shibata T
AU  - Ikawa S
AU  - Kim C
AU  - Ando T
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1976 128: 473-476.

PMID- 110786
VI  - 139
DP  - 1979
TI  - Introduction of host-controlled modification and restriction systems of Bacillus subtilis IAM1247 into Bacillus subtilis 168.
PG  - 308-310
AB  - Bacillus subtilis IAM1247 had two modification and restriction systems
      (Bsu12471 and Bsu1247II), the former producing an isoschizomer of PstI
      endonuclease.  A transformant clone was isolated which had Bsu 168, BsuR, and
      Bsu12471 systems coexisting within a genome.
AU  - Shibata T
AU  - Ikawa S
AU  - Komatsu Y
AU  - Ando T
AU  - Saito H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1979 139: 308-310.

PMID- 8165303
VI  - 39
DP  - 1994
TI  - Genetic recombination and site-specific endonucleases in mitochondria.
PG  - 589-600
AB  - 
AU  - Shibata T
AU  - Morishima N
PT  - Journal Article
TA  - Tanpakushitsu Kakusan Koso
JT  - Tanpakushitsu Kakusan Koso
SO  - Tanpakushitsu Kakusan Koso 1994 39: 589-600.

PMID- 8095080
VI  - 17C
DP  - 1993
TI  - A mitochondrial multi-site specific endonuclease, endo SceI of Saccharomyces cerevisiae.
PG  - 154
AB  - There are two classes of sequence specific endonucleases active on double-stranded DNA in
      eukaryotic cells. Endonucleases in one class exhibit very strict site-specificity which allows
      to cut DNA at any one (or a few) sites among the whole genome. These endonucleases have been
      shown to initiate site-specific genetic recombination in vivo including "intron homing".
      Endonucleases in the other class introduce a number of double-stranded breaks in various
      double-stranded DNA like bacterial restriction endonucleases. Until now, three endonucleases
      were biochemically or genetically identified to belong to the latter class; i.e. Endo.SceI and
      Endo.SceII of Saccharomyces cerevisiae, and Endo.SuvI from Saccharomyces uvarum (S.
      carlsbergensis). The active form of Endo.SceII is a heterodimer of 75kDa- and 50kDa- subunits
      and localized in mitochondria. Endo.SceI and Endo.SuvI contain the 50kDa subunit, and each of
      them is a product of the allele of a mitochondrial gene (ENS2). The difference in sequence
      specificity between Endo.SceI and Endo.SuvI is caused by the substitution of two amino acids.
      The cutting sites of Endo.SceI have complex features and the cutting creates staggered ends
      with 4 bases protruding at the 3' ends. These are common featues of all sequence-specific
      endonucleases from yeast. Another common feature is the presence of two clusters of partially
      conserved 12 amino acid sequences. We looked at events around a genetic marker (Oli') which
      was located at ca 200 bps from a cutting site for Endo.SceI in a mitochondrial gene, oli2. The
      site was shown to be partially cleaved in vivo in mitotic cells having active Endo.SceI. We
      found mating-dependent introduction of a double-stranded break at the cutting site in the oli2
      gene in a haploid lacking Endo.ScII upon the mating with a partner having active Endo.SceI. At
      the same time, we observed polarized gene conversion at oli2 locus. The disparity in
      conversion depends on the presence of active Endo.SceI in a parent and the difference in the
      sensitivity of the cutting sites to Endo.SceI between parental strains. Endo.SceI cuts
      mitochondrial DNA at more than 30 sites in vitro and we detected in vivo cutting at the
      cutting sites for Enco.SceI other than that in oli2 in haploid or diploid cells having active
      Endo.SceI. These results suggest that the recombination induced by Endo.SceI is probably
      homologous rather than site-specific recombination. The subunit structure and the mechanism to
      protect genomic DNA from complete cleavage by the endonuclease are different between Endo.SceI
      and endonucleases of the other class. The 75kDa-subunit of Endo.SceI is HSP70, which is
      involved in the import of protein into mitochondria. This suggests a regulatory role for the
      larger subunit of Endo.SceI in vivo. Although Endo.SceI is dispensable, we found another
      site-specific endonuclease from S. cerevisiae lacking a gene for Endo.SceI (Ohta K., Nicolas,
      A., Keszenman-Pereyra, D. and T.S.). Thus, mitochondria have multiple species of site-specific
      endonucleases and the endonucleases or the recombination induced by them plays a basic role in
      this organelle.
AU  - Shibata T
AU  - Morishima N
AU  - Nakagawa K
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1993 17C: 154.

PMID- 7625280
VI  - 31
DP  - 1995
TI  - Multi-site-specific endonucleases and the initiation of homologous genetic recombination in yeast.
PG  - 77-91
AB  - The notion that homologous recombination is a regulated biological process is not a familiar
      one.  In yeasts, homologous recombination and most site-specific ones are initiated by
      site-specific double-stranded breaks that are introduced within cis-acting elements for the
      recombination.  On the other hand, yeasts have a group of site-specific endonucleases
      (multi-site-specific endonucleases) that have a number of cleavage sites on each DNA.  One of
      them, Endo.SceI of S. cerevisiae, was shown to introduce double-stranded breaks at a number of
      well-defined sites on the mitochondrial DNA in vivo.  An Endo.SceI-induced double-stranded
      break was demonstrated to induce homologous recombination in mitochondria.  Like the case of
      homologous recombination of nuclear chromosomes, the double-stranded break induces gene
      conversion of both genetic markers flanking and in the proximity of the cleavage site, and the
      cleaved DNA acts as a recipient of genetic information from the uncleaved partner DNA.  The 70
      kDa-heat-shock protein (HSP70)-subunit of Endo.SceI and a general role of the HSP70 in the
      regulation of protein-folding suggest the regulation of nucleolytic activity of Endo.SceI and
      a general role of the HSP70 in the regulation of protein-folding suggest the regulation of
      nucleolytic activity of Endo.SceI.
AU  - Shibata T
AU  - Nakagawa K-I
AU  - Morishima N
PT  - Journal Article
TA  - Adv. Biophys.
JT  - Adv. Biophys.
SO  - Adv. Biophys. 1995 31: 77-91.

PMID- 6088501
VI  - 259
DP  - 1984
TI  - On the nucleotide sequence recognized by a eukaryotic site-specific endonuclease, Endo.SceI from yeast.
PG  - 10499-10506
AB  - Endo.SceI which is isolated from cells of Saccharomyces cerevisiae is a
      eukaryotic site-specific endonuclease active on double-stranded DNA.  At each
      cleavage site, Endo.SceI cuts only a defined phosphodiester bond in each strand
      of the double helix.  We compared nucleotide sequences around five cleavage
      sites for Endo.SceI using a computer.  We could not find any common specific
      sequence consisting of five base pairs or more among them.  However, we found a
      26-base pair consensus sequence which included 15 conserved nucleotides,
      allowing any of the five sequences to include a few nucleotides deviated from
      the consensus sequence.  The consensus sequence is
      5'-CAn*PYnnAnnCYYGTTnnnPnYnnYA-3', where P, Y, n, and * denote purine,
      pyrimidine, any nucleotide, and the center of the cleavage site, respectively.
      The numbers of sites at which the consensus sequence appears in pBR322 DNA,
      PhiX174 replicative form DNA, fd replicative form DNA, or SV40 DNA are close to
      those of the cleavage sites for Endo.SceI.  We found that a 33-base pair
      fragment was efficiently cut at the defined phosphodiester bonds by Endo.SceI.
      This 33-base pair fragment included 25 base pairs out of the 26-base pair
      consensus sequence.  The fragments in which a part of the consensus sequence
      was missing were not cut by Endo.SceI.  These observations suggest that the
      consensus sequence described above is the major characteristic around the
      cleavage sites recognized by Endo.SceI and that the mode of recognition of
      cleavage sites by Endo.SceI is different from that by restriction
      endonucleases.  We found homology between the consensus sequence for Endo.SceI
      and the sequences around the cleavage sites for two other site-specific
      endonucleases of S. cerevisiae: Endo.SceII and YZ-Endo which is involved in
      mating type switching.
AU  - Shibata T
AU  - Watabe H
AU  - Kaneko T
AU  - Iino T
AU  - Ando T
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1984 259: 10499-10506.

PMID- 23833137
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Burkholderia sp. Strain RPE64, Bacterial Symbiont of  the Bean Bug Riptortus pedestris.
PG  - e00441-13
AB  - We isolated Burkholderia symbiont strain RPE64 from the bean bug Riptortus pedestris. Analysis
      of the complete 6.96-Mb genome, which consists of three
      chromosomes and two plasmids, will facilitate further understanding of
      insect-microbe symbiosis and the development of pest-control technologies.
AU  - Shibata TF
AU  - Maeda T
AU  - Nikoh N
AU  - Yamaguchi K
AU  - Oshima K
AU  - Hattori M
AU  - Nishiyama T
AU  - Hasebe M
AU  - Fukatsu T
AU  - Kikuchi Y
AU  - Shigenobu S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00441-13.

PMID- 17897676
VI  - 373
DP  - 2007
TI  - AdoMet-dependent Methyl-transfer: Glu(119) Is Essential for DNA C5-Cytosine Methyltransferase M.HhaI.
PG  - 1157-1168
AB  - The role of Glu119 in S-adenosyl-l-methionine-dependent DNA methyltransferase M.HhaI-catalyzed
      DNA methylation was studied. Glu119
      belongs to the highly conserved Glu/Asn/Val motif found in all DNA
      C5-cytosine methyltransferases, and its importance for M.HhaI function
      remains untested. We show that formation of the covalent intermediate
      between Cys81 and the target cytosine requires Glu119, since conversion to
      Ala, Asp or Gln lowers the rate of methyl transfer 10(2)-10(6) fold.
      Further, unlike the wild-type M.HhaI, these mutants are not trapped by the
      substrate in which the target cytosine is replaced with the
      mechanism-based inhibitor 5-fluorocytosine. The DNA binding affinity for
      the Glu119Asp mutant is decreased 10(3)-fold. Thus, the ability of the
      enzyme to stabilize the extrahelical cytosine is coupled directly to tight
      DNA binding. The structures of the ternary protein/DNA/AdoHcy complexes
      for both the Glu119Ala and Glu119Gln mutants (2.70 A and 2.75 A,
      respectively) show that the flipped base is positioned nearly identically
      with that observed in the wild-type M.HhaI complex. A single water
      molecule in the Glu119Ala structure between Ala119 and the extrahelical
      cytosine N3 is lacking in the Glu119Gln and wild-type M.HhaI structures,
      and most likely accounts for this mutant's partial activity. Glu119 has
      essential roles in activating the target cytosine for nucleophilic attack
      and contributes to tight DNA binding.
AU  - Shieh FK
AU  - Reich NO
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2007 373: 1157-1168.

PMID- 16926025
VI  - 362
DP  - 2006
TI  - The Role of Arg165 Towards Base Flipping, Base Stabilization and Catalysis in M.HhaI.
PG  - 516-527
AB  - Arg165 forms part of a previously identified base flipping motif in the bacterial DNA cytosine
      methyltransferase, M.HhaI. Replacement of Arg165
      with Ala has no detectable effect on either DNA or AdoMet affinity, yet
      causes the base flipping and restacking transitions to be decreased
      approximately 16 and 190-fold respectively, thus confirming the importance
      of this motif. However, these kinetic changes cannot account for the
      mutant's observed 10(5)-fold decreased catalytic rate. The mutant
      enzyme/cognate DNA cocrystal structure (2.79 A resolution) shows the
      target cytosine to be positioned approximately 30 degrees into the major
      groove, which is consistent with a major groove pathway for nucleotide
      flipping. The pyrimidine-sugar chi angle is rotated to approximately +171
      degrees , from a range of -95 degrees to -120 degrees in B DNA, and -77
      degrees in the WT M.HhaI complex. Thus, Arg165 is important for
      maintaining the cytosine positioned for nucleophilic attack by Cys81. The
      cytosine sugar pucker is in the C2'-endo-C3'-exo (South conformation), in
      contrast to the previously reported C3'-endo (North conformation)
      described for the original 2.70 A resolution cocrystal structure of the WT
      M.HhaI/DNA complex. We determined a high resolution structure of the WT
      M.HhaI/DNA complex (1.96 A) to better determine the sugar pucker. This new
      structure is similar to the original, lower resolution WT M.HhaI complex,
      but shows that the sugar pucker is O4'-endo (East conformation),
      intermediate between the South and North conformers. In summary, Arg165
      plays significant roles in base flipping, cytosine positioning, and
      catalysis. Furthermore, the previously proposed M.HhaI-mediated changes in
      sugar pucker may not be an important contributor to the base flipping
      mechanism. These results provide insights into the base flipping and
      catalytic mechanisms for bacterial and eukaryotic DNA methyltransferases.
AU  - Shieh FK
AU  - Youngblood B
AU  - Reich NO
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2006 362: 516-527.

PMID- 2158687
VI  - 176
DP  - 1990
TI  - Cloning and sequencing the cytosine methyltransferase gene M. CviJI from Chlorella virus IL-3A.
PG  - 16-24
AB  - The Chlorella virus IL-3A gene encoding the DNA methyltransferase M.CviJI,
      which methylates the internal cytosine in (G/A)GC(T/C/G) sequences, was cloned
      and expressed in Escherichia coli.  The region containing the M.CviJI gene was
      sequenced and a single open reading frame of 1101 bp was identified that could
      code for a polypeptide of 367 amino acids with a predicted molecular weight of
      41,864.  M.CviJI contained regions of amino acids which were similar to
      bacterial cytosine methyltransferases.  Eighteen other Chlorella viruses, of 36
      tested, contained DNA sequences which hybridized to the M.CviJI gene; DNA from
      some, but not all, of these 18 viruses also contained 5-methylcytosine in
      (G/A)GC(T/C/G) sequences.
AU  - Shields SL
AU  - Burbank DE
AU  - Grabherr R
AU  - Van Etten JL
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1990 176: 16-24.

PMID- 2467142
VI  - 13D
DP  - 1989
TI  - Molecular cloning and characterization of the gene encoding the cytosine methyltransferase.
PG  - 214
AB  - The gene encoding the DNA methyltransferase, M.CviJI from Chlorella virus IL-3A
      was cloned in pUC19 and expressed in E. coli RR1.  Recombinant plasmid
      pIL-3A.22.8 containing a 3.6 kbp KpnI/Sau3A restriction fragment encoding
      M.CviJI methylates the internal cytosine in PuGCPy sequences or a subset of
      PuGCPy sequences in vivo.  Methylation of these sequences by M.CviJI prevents
      digestion of pIL-3A.22.8 by restriction endonucleases sensitive to cytosine
      methylation in PuGCPy recognition sequences.  Transposon Tn5 mutagenesis
      localized the M.CviJI functional domain on pIL-3A.22.8.  Restriction fragments
      from the HpaI restriction site, 185 bp from the termini of the terminal repeat
      of Tn5, to the SalI and KpnI restriction site of pIL-3A.22.8 polylinker were
      isolated from individual Tn5 mutants.  These restriction fragments containing
      the functional domain and flanking sequences were subcloned in single stranded
      sequencing vectors M13mp18 and M13mp19 for nucleotide sequencing.  The amino
      acid sequence deduced from M.CviJI nucleotide sequence was compared to the
      amino acid sequence of 5-methylcytosine methyltransferases from prokaryotes to
      determine potentially shared protein domains.  The M.CviJI gene was not
      essential for IL-3A replication since a M.CviJI deletion mutant also replicated
      in Chlorella.
AU  - Shields SL
AU  - Burbank DE
AU  - Van Etten JL
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1989 13D: 214.

PMID- 24526639
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Rhodococcus rhodochrous Strain ATCC 21198.
PG  - e00054-14
AB  - Rhodococcus rhodochrous is a Gram-positive red-pigmented bacterium commonly found in the soil.
      The draft genome sequence for R. rhodochrous strain ATCC 21198 is presented here to provide
      genetic data for a better understanding of its lipid-accumulating capabilities.
AU  - Shields-Menard SA
AU  - Brown SD
AU  - Klingeman DM
AU  - Indest K
AU  - Hancock D
AU  - Wewalwela JJ
AU  - French WT
AU  - Donaldson JR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00054-14.

PMID- 
VI  - 62
DP  - 2002
TI  - Characterization and inhibition of an essential adenine DNA methyltransferase from Caulobacter crescentus.
PG  - 3185-3186
AB  - Genetic evidence has established that DNA methylation provides an obligatory signal for the
      proper progression through the Caulobacter crescentus cell cycle.  The enzyme responsible for
      catalyzing this reaction is a cell-cycle regulated adenine DNA methyltransferase (CcrM).  CcrM
      activity is tightly restricted to predivisional cells by a delicate coordination between
      transcription and proteolytic elimination by a Lon-mediated pathway.  Further underscoring the
      importance of this enzyme is the observation that CcrM is essential for C. crescentus
      viability and that it is only the second known DNA methyltransferase that lacks a cognate
      restriction endonuclease.  To further our understanding of the regulatory role played by CcrM,
      we sought to investigate the biophysical and biochemical properties of this enzyme.
      Equilibrium ultracentrifugation, velocity ultracentrifugation, and chemical crosslinking
      reveal that CcrM is dimeric at physiological concentrations.  However, surface plasmon
      resonance experiments evince that CcrM binds as a monomer to DNA containing the CcrM canonical
      methylation sequence, GANTC.  Collectively, these findings suggest that CcrM dimerization
      serves to stabilize CcrM from premature in vivo proteolysis.  The recently sequenced C.
      crescentus genome unveiled the presence of 4,496 CcrM methylation sites.  Following
      semiconservative DNA replication, CcrM must methylate a total of 8,992 sites on the two
      resulting copies of the genome within the strict temporal constraints of the predivisional
      cells.  Using defined, synthetic substrates that contain multiple methylation sites, CcrM
      processively methylates DNA over a minimum distance of 82 base pairs.  Moreover, CcrM is
      capable of methylating GANTC clusters with no apparent effect on methylation efficiency.
      Despite slow kinetic rate constants, these experiments demonstrate that CcrM is kinetically
      competent to support full genomic methylation within the enforced activity interval.
      Homologues of CcrM are found throughout the alpha-subdivision of proteobacteria.  Many of the
      members of this group are pathogens.  The observation that CcrM activity is essential for
      cellular viability in all of these microorganisms, coupled with the absence of adenine methyl
      modification in eukaryotic species, has implicated CcrM as a target for antimicrobial drug
      design.  Efforts to identify and characterize potential inhibitors are discussed with an
      emphasis on a panel of diphenyl borinic esters.
AU  - Shier VK
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 2002 62: 3185-3186.

PMID- 11278726
VI  - 276
DP  - 2001
TI  - Identification of the active oligomeric state of an essential adenine DNA methyltransferase from Caulobacter crescentus.
PG  - 14744-14751
AB  - Caulobacter crescentus contains one of the two known prokaryotic DNA methyltransferases that
      lacks a cognate endonuclease. This endogenous cell cycle regulated adenine DNA
      methyltransferase (CcrM) is essential for C. crescentus cellular viability. DNA methylation
      catalyzed by CcrM provides an obligatory signal for the proper progression through the cell
      cycle. To further our understanding of the regulatory role played by CcrM, we sought to
      investigate its biophysical properties. In this paper we employed equilibrium
      ultracentrifugation, velocity ultracentrifugation, and chemical cross-linking to show that
      CcrM is dimeric at physiological concentrations. However, surface plasmon resonance
      experiments in the presence of S-adenosyl-homocysteine evince that CcrM binds as a monomer to
      a defined hemi-methylated DNA substrate containing the canonical methylation sequence, GANTC.
      Initial velocity experiments demonstrate that dimerization of CcrM does not affect DNA
      methylation. Collectively, these findings suggest that CcrM is active as a monomer and
      provides a possible in vivo role for dimerization as a means to stabilize CcrM from premature
      catabolism.
AU  - Shier VK
AU  - Hancey CJ
AU  - Benkovic SJ
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2001 276: 14744-14751.

PMID- 
VI  - 
DP  - 2009
TI  - Developing DNA probes to trap DNA cytosine-5 methyltransferases involved in promoter hypermethylation in cancer.
PG  - 1-90
AB  - A major limitation to making significant advances in diagnosing and treating cancer is that we
      do not have a thorough understanding of the mechanisms leading to abnormal DNA methylation in
      cancer cells. Although there is a plethora of information on genes that are hypermethylated in
      cancer cells, we rarely know which DNA cytosine-5 methyltransferase (DNMTs) and what complex
      is involved in methylating particular promoters in cancer cells. I developed two types of DNA
      probes, a diazirine and a disulfide based, which can be incorporated at specific positions of
      oligonucleotides that have potential to trap DNMTs and their cofactors at a particular
      promoter. A diazirine photophore was introduced into either the major or minor groove of DNA
      via a convertible nucleoside methodology. The resulting DNA probes efficiently cross-linked
      with two different proteins studied as examples, the E. coli DNA adenine methyltransferase
      (EcoDam) and the human 06-alkylguanine-DNA alkyltransferase (hAGT). Efficient cross-linking of
      diazirine can be utilized to trap proteins from cell extracts. Taking advantage of DNMTs'
      invariant active site Cys and their base flipping property, a new disulfide-based DNA probe,
      l'-methylenedisulfide deoxyribose, which can efficiently cross-link Haemophilus haemolyticus
      methylase (M. Hhal) and Spiroplasma sp. Methylase (M. SssI) was also developed. Compared to
      commercially available 5-FdC, the new probe cross-links DNMTs quickly. Using a disulfide
      tether on the N4 position of cytosine, catalytic domain of DNMT3A (DNMT3 AC) has been
      crosslinked to DNA in high efficiency. Such a high cross-linking yield of DNMT3AC holds great
      promise in identifying DNMTs and their cofactors that act on particular promoters, as well as
      in structurally characterizing the DNMT3 AC-DNA complex.
AU  - Shigdel UK
PT  - Journal Article
TA  - Ph.D. Thesis, Univ. of Chicago
JT  - Ph.D. Thesis, Univ. of Chicago
SO  - Ph.D. Thesis, Univ. of Chicago 2009 : 1-90.

PMID- 19108695
VI  - 130
DP  - 2008
TI  - A New 1'-Methylenedisulfide Deoxyribose that Forms an Efficient Cross-Link to DNA Cytosine-5 Methyltransferase (DNMT).
PG  - 17634-17635
AB  - Although only four bases, adenine, guanine, cytosine, and thymine,
      encode all genetic information in DNA, there is a heritable "fifth" base,
      5-methylcytosine, which can induce epigenetic changes that alter
      chromatin structures. Methylation at the 5-position of cytosine in a
      CpG dinucleotide is catalyzed by a conserved group of proteins called
      DNA cytosine-5 methyltransferases (DNMTs) by using S-adenosylmethionine
      (SAM) as the cofactor (Figure 1A). This modification has
      a profound effect on gene expression. Many cancer cells are characterized
      by abnormal DNA methylation. Repetitive DNA sequences and
      some genes are hypomethylated and transcriptionally active, whereas
      many genes are hypermethylated and transcriptionally inactive.1
      Inhibition of human DNMTs has been shown to be an effective strategy
      to treat various cancers.
AU  - Shigdel UK
AU  - He C
PT  - Journal Article
TA  - J. Am. Chem. Soc.
JT  - J. Am. Chem. Soc.
SO  - J. Am. Chem. Soc. 2008 130: 17634-17635.

PMID- 22078906
VI  - 72
DP  - 2012
TI  - Emergence in Japan of an imipenem-susceptible, meropenem-resistant Klebsiella pneumoniae carrying blaIMP-6.
PG  - 109-112
AB  - We identified 5 Klebsiella pneumoniae isolates showing high resistance to
      beta-lactams except imipenem and designated them ISMRK (imipenem-susceptible but
      meropenem-resistant Klebsiella). They carried the bla(IMP-6) and bla(CTX-M-2) on
      a self-transmissible plasmid. ISMRK may be falsely categorized as susceptible to
      carbapenems if imipenem is used to screen carbapenem resistance.
AU  - Shigemoto N
AU  - Kuwahara R
AU  - Kayama S
AU  - Shimizu W
AU  - Onodera M
AU  - Yokozaki M
AU  - Hisatsune J
AU  - Kato F
AU  - Ohge H
AU  - Sugai M
PT  - Journal Article
TA  - Diagn. Microbiol. Infect. Dis.
JT  - Diagn. Microbiol. Infect. Dis.
SO  - Diagn. Microbiol. Infect. Dis. 2012 72: 109-112.

PMID- 10993077
VI  - 407
DP  - 2000
TI  - Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS.
PG  - 81-86
AB  - Almost all aphid species (Homoptera, Insecta) have 60-80 huge cells called bacteriocytes,
      within which are round-shaped bacteria that are designated Buchnera. These bacteria are
      maternally transmitted to eggs and embryos through host generations, and the mutualism between
      the host and the bacteria is so obligate that neither can reproduce independently. Buchnera is
      a close relative of Escherichia coli, but it contains more than 100 genomic copies per cell,
      and its genome size is only a seventh of that of E. coli. Here we report the complete genome
      sequence of Buchnera sp. strain APS, which is composed of one 640,681-base-pair chromosome and
      two small plasmids. There are genes for the biosyntheses of amino acids essential for the
      hosts in the genome, but those for non-essential amino acids are missing, indicating
      complementarity and syntrophy between the host and the symbiont. In addition, Buchnera lacks
      genes for the biosynthesis of cell-surface components, including lipopolysaccharides and
      phospholipids, regulator genes and genes involved in defense of the cell. These results
      indicate that Buchnera is completely symbiotic and viable only in its limited niche, the
      bacteriocyte.
AU  - Shigenobu S
AU  - Watanabe H
AU  - Hattori M
AU  - Sakaki Y
AU  - Ishikawa H
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2000 407: 81-86.

PMID- 23277585
VI  - 110
DP  - 2013
TI  - Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing.
PG  - 1053-1058
AB  - The cyanobacterial phylum encompasses oxygenic photosynthetic prokaryotes of a
      great breadth of morphologies and ecologies; they play key roles in global carbon
      and nitrogen cycles. The chloroplasts of all photosynthetic eukaryotes can trace
      their ancestry to cyanobacteria. Cyanobacteria also attract considerable interest
      as platforms for "green" biotechnology and biofuels. To explore the molecular
      basis of their different phenotypes and biochemical capabilities, we sequenced
      the genomes of 54 phylogenetically and phenotypically diverse cyanobacterial
      strains. Comparison of cyanobacterial genomes reveals the molecular basis for
      many aspects of cyanobacterial ecophysiological diversity, as well as the
      convergence of complex morphologies without the acquisition of novel proteins.
      This phylum-wide study highlights the benefits of diversity-driven genome
      sequencing, identifying more than 21,000 cyanobacterial proteins with no
      detectable similarity to known proteins, and foregrounds the diversity of
      light-harvesting proteins and gene clusters for secondary metabolite
      biosynthesis. Additionally, our results provide insight into the distribution of
      genes of cyanobacterial origin in eukaryotic nuclear genomes. Moreover, this
      study doubles both the amount and the phylogenetic diversity of cyanobacterial
      genome sequence data. Given the exponentially growing number of sequenced
      genomes, this diversity-driven study demonstrates the perspective gained by
      comparing disparate yet related genomes in a phylum-wide context and the insights
      that are gained from it.
AU  - Shih PM et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2013 110: 1053-1058.

PMID- 
VI  - 1
DP  - 2010
TI  - Identification of a restriction endonuclease (SacC1) from Saccharomyces cerevisiae.
PG  - 127-135
AB  - palindromic sequence 5'CTCGAC3' cleaving both DNA strands upstream and downstream of its
      recognition sequence and makes a staggered cut at the distance of five bases from the
      recognition sequence on the upper strand and at the seventh base on the complementary strand.
      It shares similar
      characteristics with Sac I from Streptomyces achromogenes as well as Sst1 from Streptomyces
      Stanford and Psp124B1 from Pseudomonas species. It has been purified by ammonium sulphate
      precipitation, dialysis, and gel filtration using phosphocellulose, DEAE-cellulose and
      Sephadex G-100
      with an optimal pH range (7.5-8.5), active at 37oC and dependent on Mg+2 or Mn2+ which
      increases its activity by 4- and 2-folds, respectively, while other cations decrease its
      activity to some extents.  Cleavage on both sides of the recognition sequence is
      characteristic of Type IIB systems but all IIB
      enzymes studied so far have been found to recognize discontinuous sites and a distinctive
      subunit/domain organization that is not present in the SacC1 enzyme. There are similarities
      between SacC1 and other homing endonucleases belonging to the LAGLIDADG family such as a
      requirement for Mg2+ (or Mn2+) for cleavage to take place, optimal activity at alkaline pH and
      stimulation of the reaction by moderate concentrations of the monovalent cation.
AU  - Shikara M
PT  - Journal Article
TA  - J. Yeast Fungal Res.
JT  - J. Yeast Fungal Res.
SO  - J. Yeast Fungal Res. 2010 1: 127-135.

PMID- 
VI  - 1
DP  - 2010
TI  - A specific inhibitory protein to a restriction enzyme from Saccharomyces cerevisiae.
PG  - 174-182
AB  - A specific protein inhibitor for the restriction enzyme (SacC1) has been purified from
      Saccharomyces
      cerevisiae approximately 21,000 fold and its inhibitory properties have been characterized.
      The
      isoelectric points (pI) of SacCI and its inhibitor are 9.0 and 5.22, respectively. The
      molecular weight of
      SacC1, the inhibitor and SacC1-inhibitor complex were estimated by gel filtration on a
      Sephadex G-100
      column to be 64,000, 32,000 and 85,000, respectively. The inhibitor protein inhibits SacC1
      catalytic
      activities efficiently, but has no effect on other restriction enzymes tested. Inhibition does
      not occur
      unless SacC1 enzyme is exposed to the inhibitor protein prior to the reaction of the enzyme
      with DNA.
      The inhibitory activity is independent of temperature. The inhibition increased linearly with
      the addition
      of inhibitor to various amounts of SacC1, up to 85% inhibition. The slope of inhibition was
      constant
      irrespective of the initial amount of SacC1 and Ki value of 3.45 x 10-12 was obtained. The
      inhibitor
      interacts strongly with SacC1 and this interaction could increase the stability of the
      complex, possibly
      manifesting itself as SacC1 decreases in the dissociation rate due to the electrostatic
      attraction between
      the two groups or the stability may increase by potentially stronger electrostatic
      interaction. The
      conformational specificity between SacC1 and its inhibitor seems to be essential for their
      interaction.
      The extremely strong affinity of the inhibitor to SacC1 is remarkable and stronger than the
      affinity of
      several restriction enzymes.
AU  - Shikara M
PT  - Journal Article
TA  - J. Yeast Fungal Res.
JT  - J. Yeast Fungal Res.
SO  - J. Yeast Fungal Res. 2010 1: 174-182.

PMID- 9592151
VI  - 26
DP  - 1998
TI  - DNA-methyltransferase SsoII interaction with own promoter region binding site.
PG  - 2659-2664
AB  - The investigation of SsoII DNA-methyltransferase interaction with the intergenic region of
      SsoII restriction-modification system was carried out.  Seven guanine residues protected by
      M.SsoII from methylation with dimethylsulfate and thus probably involved in enzyme-DNA
      recognition were identified.  Six of them are located symmetrically within the 15 bp inverted
      repeat inside the SsoII promoter region.  The crosslinking of SsoII methyltransferase with DNA
      duplexes containing 5-bromo-2'-deoxyuridine instead of thymidine was performed.  The
      crosslinked products were obtained in all cases, thus proving that tested thymines were in
      proximity with enzyme.  The ability to produce the crosslinked products in one case was
      2-5-fold higher than in other ones.  This allowed us to imply that the thymine residue in this
      position of the inverted repeat could be in contact with M.SsoII.  Based on the experimental
      data, two symmetrical 4 bp clusters (GGAC), which could be involved in the interaction with
      M.SsoII in the DNA-protein complex, were identified.  The model of M.SsoII interaction with
      its own promoter was proposed.
AU  - Shilov I
AU  - Tashlitsky V
AU  - Khodoun M
AU  - Vasilev S
AU  - Alekseev Y
AU  - Kuzubov A
AU  - Kubareva E
AU  - Karyagina A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1998 26: 2659-2664.

PMID- 26893435
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Flavobacterium psychrophilum Strain KTEN-1510 with Genotype A/G-C, Isolated from an Ayu (Plecoglossus altivelis altivelis) in the  Kagami River, Kochi, Japan.
PG  - e01762-15
AB  - In this paper, we describe the draft genome sequence of Flavobacterium psychrophilum strain
      KTEN-1510, with genotype A/G-C. This strain was isolated in
      October 2015 from the gills of an ayu (Plecoglossus altivelis altivelis) in the
      upper Kagami River in central Kochi Prefecture on Shikoku Island, Japan.
AU  - Shimizu M
AU  - Goda H
AU  - Yamasaki K
AU  - Oshima S
AU  - Ohnishi K
AU  - Osaki Y
AU  - Kataoka S
AU  - Imajoh M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01762-15.

PMID- 11792842
VI  - 99
DP  - 2002
TI  - Complete genome sequence of Clostridium perfringens, an anaerobic flesh-eater.
PG  - 996-1001
AB  - Clostridium perfringens is a Gram-positive anaerobic spore-forming bacterium that causes
      life-threatening gas gangrene and mild
      enterotoxaemia in humans, although it colonizes as normal intestinal flora of humans and
      animals. The organism is known to produce a
      variety of toxins and enzymes that are responsible for the severe myonecrotic lesions. Here we
      report the complete 3,031,430-bp sequence
      of C. perfringens strain 13 that comprises 2,660 protein coding regions and 10 rRNA genes,
      showing pronounced low overall G + C
      content (28.6%). The genome contains typical anaerobic fermentation enzymes leading to gas
      production but no enzymes for the
      tricarboxylic acid cycle or respiratory chain. Various saccharolytic enzymes were found, but
      many enzymes for amino acid biosynthesis were
      lacking in the genome. Twenty genes were newly identified as putative virulence factors of C.
      perfringens, and we found a total of five
      hyaluronidase genes that will also contribute to virulence. The genome analysis also proved an
      efficient method for finding four members of
      the two-component VirR/VirS regulon that coordinately regulates the pathogenicity of C.
      perfringens. Clearly, C. perfringens obtains
      various essential materials from the host by producing several degradative enzymes and toxins,
      resulting in massive destruction of the host
      tissues.
AU  - Shimizu T
AU  - Ohtani K
AU  - Hirakawa H
AU  - Ohshima K
AU  - Yamashita A
AU  - Shiba T
AU  - Ogasawara N
AU  - Hattori M
AU  - Kuhara S
AU  - Hayashi H
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2002 99: 996-1001.

PMID- 24018670
VI  - 77
DP  - 2013
TI  - Genomic Features of Lactococcus lactis IO-1, a Lactic Acid Bacterium That Utilizes Xylose and Produces High Levels of L-Lactic Acid.
PG  - 1804-1808
AB  - Lactococcus lactis IO-1 (JCM7638) produces L-lactic acid predominantly when grown at high
      xylose concentrations, and its utilization is highly desired in the green plastics industry.
      Therefore it is worthwhile studying its genomic traits. In this study, we focused on (i) genes
      of possible horizontal transfer derivation (prophages, the nisin-sucrose transposon, and
      several restriction-modification systems), and (ii) genes for the synthetic pathways of amino
      acids and vitamins in the IO-1 genome. In v ew of the results of this analysis, we consider
      their meanings in strain IO-1.
AU  - Shimizu-Kadota M
AU  - Kato H
AU  - Shiwa Y
AU  - Oshima K
AU  - Machii M
AU  - Araya-Kojima T
AU  - Zendo T
AU  - Hattori M
AU  - Sonomoto K
AU  - Yoshikawa H
PT  - Journal Article
TA  - Biosci. Biotechnol. Biochem.
JT  - Biosci. Biotechnol. Biochem.
SO  - Biosci. Biotechnol. Biochem. 2013 77: 1804-1808.

PMID- Not included in PubMed...
VI  - 53
DP  - 1989
TI  - M.HhaI-methylated DNA is resistant to cleavage by R.BbeI.
PG  - 2841-2842
AB  - Shows that BbeI can cleave GGCG5mCC, GGCGC5mC, but not GG5mCGCC.
AU  - Shimizu-Kadota M
AU  - Shibahara-Sone H
PT  - Journal Article
TA  - Agric. Biol. Chem.
JT  - Agric. Biol. Chem.
SO  - Agric. Biol. Chem. 1989 53: 2841-2842.

PMID- 15937923
VI  - 233
DP  - 2005
TI  - Identification of a gene required for de novo DNA methylation of the zebrafish no tail gene.
PG  - 1509-1516
AB  - The zebrafish no tail gene (ntl) is indispensable for tail and notochord development. We have
      shown previously that ntl is de novo methylated
      during early embryogenesis. To find the gene that de novo methylates ntl
      and understand the meaning of this methylation, we cloned seven genes that
      encode the conserved catalytic domain of methyltransferases. We found that
      injection of antisense morpholino oligonucleotides against one of them,
      termed dnmt7, into eggs significantly reduced the level of ntl
      methylation, although no apparent phenotype was induced by the injection.
      Inhibition of Dnmt7 activity did not change the level of genome-wide
      methylation nor did it affect de novo methylation of injected plasmid DNA,
      indicating that Dnmt7 specifically methylates ntl in the genome.
AU  - Shimoda N
AU  - Yamakoshi K
AU  - Miyake A
AU  - Takeda H
PT  - Journal Article
TA  - Dev. Dyn.
JT  - Dev. Dyn.
SO  - Dev. Dyn. 2005 233: 1509-1516.

PMID- 27795235
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequence of the Nitrogen-Fixing Symbiotic Rhizobium Mesorhizobium loti Strain TONO.
PG  - e01016-16
AB  - Mesorhizobium loti is the nitrogen-fixing microsymbiont for legumes of the genus  Lotus Here,
      we report the whole-genome sequence of a Mesorhizobium loti strain,
      TONO, which is used as a symbiont for the model legume Lotus japonicus The
      whole-genome sequence of the strain TONO will be a solid platform for comparative
      genomics analyses and for the identification of genes responsible for the
      symbiotic properties of Mesorhizobium species.
AU  - Shimoda Y
AU  - Hirakawa H
AU  - Sato S
AU  - Saeki K
AU  - Hayashi M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01016-16.

PMID- 26089421
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Comamonas sp. Strain E6 (NBRC 107749), a Degrader of Phthalate Isomers through the Protocatechuate 4,5-Cleavage Pathway.
PG  - e00643-15
AB  - Comamonas sp. strain E6 can degrade o-phthalate, terephthalate, and isophthalate  via the
      protocatechuate 4,5-cleavage pathway. Here, we report the draft genome
      sequence of E6 in order to provide insights into its mechanisms in o-phthalate
      catabolism and its potential use for biotechnological applications.
AU  - Shimodaira J
AU  - Kamimura N
AU  - Hosoyama A
AU  - Yamazoe A
AU  - Fujita N
AU  - Masai E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00643-15.

PMID- 27340052
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Comamonas thiooxydans Strain PHE2-6 (NBRC 110656), a Chlorinated-Ethene-Degrading Bacterium.
PG  - e00487-16
AB  - Comamonas thiooxydans strain PHE2-6 (NBRC 110656), which was isolated from a
      trichloroethene-contaminated site in Japan, utilizes phenol as a sole source of
      carbon and cometabolizes cis- and trans-dichloroethenes. We report here the draft
      genome sequence of this strain, containing 5,309,680 bp, with 60.6% G+C content.
AU  - Shimodaira J
AU  - Yonezuka K
AU  - Tabata M
AU  - Nagase S
AU  - Kasai D
AU  - Hosoyama A
AU  - Yamazoe A
AU  - Fujita N
AU  - Fukuda M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00487-16.

PMID- Not included in PubMed...
VI  - 44
DP  - 1980
TI  - Site-specific endonucleases in Streptomyces strains.
PG  - 1665-1666
AB  - A large number of class II restriction endonucleases have now been isolated
      from various microorganisms.  Since their discovery they have become invaluable
      tools in researches of physical mapping DNA sequencing and gene cloning.  Only
      four Streptomyces strains have been reported to produce restriction-like
      endonucleases; Streptomyces achromogenes (SacI, SacII, and SacIII), S. albus G
      (SalI and SalII), and S. lavendulae (SlaI).  The first two strains produce
      exactly identical enzymes.  In this communication, we report the results of
      survey of restriction-like endonucleases among Streptomyces strains.
AU  - Shimotsu H
AU  - Takahashi H
AU  - Saito H
PT  - Journal Article
TA  - Agric. Biol. Chem.
JT  - Agric. Biol. Chem.
SO  - Agric. Biol. Chem. 1980 44: 1665-1666.

PMID- 6260571
VI  - 11
DP  - 1980
TI  - A new site-specific endonuclease StuI from Streptomyces tubercidicus.
PG  - 219-225
AB  - A new sequence-specific endonuclease, StuI, produced by Streptomyces
      tubercidicus KCC S-0054, was identified and partially purified.  StuI
      recognizes the hexanucleotide "palindromic" sequence:
      5'-AGG^CCT-3'
      3'-TCC^GGA-5'  and cleaves it at the middle, producing blunt ends.
AU  - Shimotsu H
AU  - Takahashi H
AU  - Saito H
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1980 11: 219-225.

PMID- 28385852
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of a Coastal Cyanobacterium, Synechococcus sp. Strain NIES-970.
PG  - e00139-17
AB  - Members of the cyanobacterial genus Synechococcus are abundant in marine environments. To
      better understand the genomic diversity of marine Synechococcus
      spp., we determined the complete genome sequence of a coastal cyanobacterium,
      Synechococcus sp. NIES-970. The genome had a size of 3.1 Mb, consisting of one
      chromosome and four plasmids.
AU  - Shimura Y
AU  - Hirose Y
AU  - Misawa N
AU  - Wakazuki S
AU  - Fujisawa T
AU  - Nakamura Y
AU  - Kanesaki Y
AU  - Yamaguchi H
AU  - Kawachi M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00139-17.

PMID- 23851651
VI  - 159
DP  - 2014
TI  - Complete genome sequence of marine bacterium Pseudoalteromonas phenolica bacteriophage TW1.
PG  - 159-162
AB  - For molecular study of marine bacteria Pseudoalteromonas phenolica using
      bacteriophage, a novel bacteriophage, TW1, belonging to the family Siphoviridae,
      was isolated, and its genome was completely sequenced and analyzed. The phage TW1
      genome consists of 39,940-bp-length double-stranded DNA with a GC content of
      40.19 %, and it was predicted to have 62 open reading frames (ORFs), which were
      classified into functional groups, including phage structure, packaging, DNA
      metabolism, regulation, and additional function. The phage life style prediction
      using PHACTS showed that it may be a temperate phage. However, genes related to
      lysogeny and host lysis were not detected in the phage TW1 genome, indicating
      that annotation information about P. phenolica phages in the genome databases may
      not be sufficient for the functional prediction of their encoded proteins. This
      is the first report of a P. phenolica-infecting phage, and this phage genome
      study will provide useful information for further molecular research on P.
      phenolica and its phage, as well as their interactions.
AU  - Shin H
AU  - Lee JH
AU  - Ahn CS
AU  - Ryu S
AU  - Cho BC
PT  - Journal Article
TA  - Arch. Virol.
JT  - Arch. Virol.
SO  - Arch. Virol. 2014 159: 159-162.

PMID- 22843579
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of the Opportunistic Food-Borne Pathogen Cronobacter sakazakii ES15.
PG  - 4438-4439
AB  - Cronobacter sakazakii is an emerging pathogen associated with several outbreaks of food-borne
      illness in premature infants. To characterize its physiology and
      pathogenicity at the molecular level, C. sakazakii ES15 was isolated and its
      genome was completely sequenced and analyzed. Here, the results are announced and
      major findings from its annotation data are reported.
AU  - Shin H
AU  - Lee JH
AU  - Choi Y
AU  - Ryu S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4438-4439.

PMID- 22570242
VI  - 86
DP  - 2012
TI  - Complete Genome Sequence of Cronobacter sakazakii Bacteriophage CR3.
PG  - 6367-6368
AB  - Due to the high risk of Cronobacter sakazakii infection in infants fed powdered
      milk formula and the emergence of antibiotic-resistant strains, an alternative
      biocontrol agent using bacteriophage is needed to control this pathogen. To
      further the development of such an agent, the C. sakazakii-targeting
      bacteriophage CR3 was isolated and its genome was completely sequenced. Here, we
      announce the genomic analysis results of the largest C. sakazakii phage known to
      date and report the major findings from the genome annotation.
AU  - Shin H
AU  - Lee JH
AU  - Kim Y
AU  - Ryu S
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 2012 86: 6367-6368.

PMID- 22205721
VI  - 86
DP  - 2012
TI  - Complete Genome Sequence of Salmonella enterica Serovar Typhimurium Bacteriophage SPN1S.
PG  - 1284-1285
AB  - To understand the interaction between the host of pathogenic Salmonella enterica
      serovar Typhimurium and its bacteriophage, we isolated the bacteriophage SPN1S.
      It is a lysogenic phage in the Podoviridae family and uses the O-antigen of
      lipopolysaccharides (LPS) as a host receptor. Comparative genomic analysis of
      phage SPN1S and the S. enterica serovar Anatum-specific phage epsilon15 revealed
      different host specificities, probably due to the low homology of host
      specificity-related genes. Here we report the complete circular genome sequence
      of S. Typhimurium-specific bacteriophage SPN1S and show the results of our
      analysis.
AU  - Shin H
AU  - Lee JH
AU  - Lim JA
AU  - Kim H
AU  - Ryu S
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 2012 86: 1284-1285.

PMID- 24257316
VI  - 69
DP  - 2013
TI  - Single origin of three plasmids bearing blaCTX-M-15 from different Klebsiella pneumoniae clones.
PG  - 969-972
AB  - OBJECTIVES: To determine and compare the complete nucleotide sequences of plasmids carrying
      blaCTX-M-15 from three different Klebsiella pneumoniae clones.
      METHODS: IncFII-type plasmids pKP02022, pKP09085 and pKP007 were extracted from three K.
      pneumoniae strains. These strains belong to sequence types (STs) ST15,
      ST48 and ST23, respectively, and were isolated in Korea. Plasmids were sequenced using the 454
      Genome Sequencer FLX system. RESULTS: The three plasmids, pKP02022
      (203577 bp), pKP09085 (213019 bp) and pKP007 (246 176 bp), all exhibited a very similar
      structure, with a pKPN3-like backbone and a resistance region including blaOXA-1,
      aac(6')-Ib-cr and cat genes as well as blaCTX-M-15. They were also very similar to pUUH239.2,
      previously isolated in Sweden. Iron (III) uptake-related genes were found in pKP007 from the
      ST23 strain, which has been reported to be associated with liver abscesses. The resistance
      region contained several insertion sequences, such as IS26, which may play an important role
      in structural rearrangements of plasmids. CONCLUSIONS: The very similar structure of the three
      plasmids, extracted from different clones, suggests that the spread of CTX-M-producing K.
      pneumoniae isolates might result from the horizontal transfer of plasmids and subsequent
      integration and recombination.
AU  - Shin J
AU  - Soo-Ko K
PT  - Journal Article
TA  - J. Antimicrob. Chemother.
JT  - J. Antimicrob. Chemother.
SO  - J. Antimicrob. Chemother. 2013 69: 969-972.

PMID- 27084942
VI  - 44
DP  - 2016
TI  - Horizontal transfer of DNA methylation patterns into bacterial chromosomes.
PG  - 460-471
AB  - Horizontal gene transfer (HGT) is the non-inherited acquisition of novel DNA sequences. HGT is
      common and important in bacteria because it enables the rapid generation of new phenotypes
      such as antibiotic resistance. Here we show that in vivo and in vitro DNA methylation patterns
      can be horizontally transferred into bacterial chromosomes to program cell phenotypes. The
      experiments were performed using a synthetic system in Escherichia coli where different DNA
      methylation patterns within the cis-regulatory sequence of the agn43 gene turn on or off a
      fluorescent reporter (CFP). With this system we demonstrated that DNA methylation patterns not
      only accompany the horizontal transfer of genes into the bacterial cytoplasm but can be
      transferred into chromosomes by: (i) bacteriophage P1 transduction; and (ii) transformation of
      extracellular synthetic DNA. We also modified the experimental system by replacing CFP with
      the SgrS small RNA, which regulates glucose and methyl alpha-D-glucoside uptake, and showed
      that horizontally acquired DNA methylation patterns can increase or decrease cell fitness.
      That is, horizontally acquired DNA methylation patterns can result in the selection for and
      against cells that have HGT. Findings from these proof-of-concept experiments have
      applications in synthetic biology and potentially broad implications for bacterial adaptation
      and evolution.
AU  - Shin JE
AU  - Lin C
AU  - Lim HN
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2016 44: 460-471.

PMID- 21685278
VI  - 193
DP  - 2011
TI  - Genome Sequence of Corynebacterium nuruki S6-4T, Isolated from Alcohol Fermentation Starter.
PG  - 4257
AB  - Corynebacterium nuruki S6-4(T), isolated from Korean alcohol fermentation starter, is a
      strictly aerobic, nonmotile, Gram-positive, and rod-shaped
      bacterium belonging to the genus Corynebacterium and the actinomycete
      group. We report here the draft genome sequence of C. nuruki strain
      S6-4(T) (3,106,595 bp, with a G+C content of 69.5%).
AU  - Shin NR
AU  - Whon TW
AU  - Roh SW
AU  - Kim MS
AU  - Jung MJ
AU  - Lee J
AU  - Bae JW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4257.

PMID- 22374946
VI  - 194
DP  - 2012
TI  - Genome Sequence of Sphingomonas sp. Strain PAMC 26605, Isolated from Arctic Lichen (Ochrolechia sp.).
PG  - 1607
AB  - The endosymbiotic bacterium Sphingomonas sp. strain PAMC 26605 was isolated from  Arctic
      lichens (Ochrolechia sp.) on the Svalbard Islands. Here we report the
      draft genome sequence of this strain, which could provide further insights into
      the symbiotic mechanism of lichens in extreme environments.
AU  - Shin SC
AU  - Ahn DH
AU  - Lee JK
AU  - Kim SJ
AU  - Hong SG
AU  - Kim EH
AU  - Park H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1607.

PMID- 22493208
VI  - 194
DP  - 2012
TI  - Genome Sequence of a Salinibacterium sp. Isolated from Antarctic Soil.
PG  - 2404
AB  - The draft genome of Salinibacterium sp. PAMC 21357, isolated from permafrost soil of
      Antarctica, was determined. Here we present a 3.1-Mb draft genome sequence of
      Salinibacterium sp. that could provide further insight into the genetic
      determination of its cold-adaptive properties.
AU  - Shin SC
AU  - Kim SJ
AU  - Ahn DH
AU  - Lee JK
AU  - Lee H
AU  - Lee J
AU  - Hong SG
AU  - Lee YM
AU  - Park H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2404.

PMID- 22408244
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Sphingomonas echinoides ATCC 14820.
PG  - 1843
AB  - Sphingomonas is a Gram-negative, yellow-pigmented, chemoheterotrophic, strictly aerobic
      bacterium. The bacterium is known to be metabolically versatile and can
      utilize a wide range of natural compounds as well as some types of environmental
      contaminants, such as creosote, polychlorinated biphenyls, etc. Here, we report
      the draft genome sequence of Sphingomonas echinoides ATCC 14820, which will
      provide additional information to enhance our understanding of metabolic
      versatility of Sphingomonas.
AU  - Shin SC
AU  - Kim SJ
AU  - Ahn-do H
AU  - Lee JK
AU  - Park H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1843.

PMID- 22408245
VI  - 194
DP  - 2012
TI  - Genome Sequence of Pseudomonas sp. Strain PAMC 25886, Isolated from Alpine Glacial Cryoconite.
PG  - 1844
AB  - Pseudomonas spp. have shown characteristics of efficiently metabolizing environmental
      pollutants and also producing exopolysaccharides known as biofilms.
      Here we present the draft genome sequence of Pseudomonas sp. strain PAMC 25886,
      which was isolated from glacier cryoconite in the Alps mountain permafrost region
      and which may provide further insight into biodegradative and/or
      biofilm-producing mechanisms in a cold environment.
AU  - Shin SC
AU  - Kim SJ
AU  - Hong SG
AU  - Ahn-do H
AU  - Lee YM
AU  - Lee H
AU  - Lee J
AU  - Park H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1844.

PMID- 22535926
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of the 2,3-Butanediol-Producing Klebsiella pneumoniae Strain KCTC 2242.
PG  - 2736-2737
AB  - Here we report the full genome sequence of Klebsiella pneumoniae KCTC 2242,consisting of a
      5.26-Mb chromosome (57.6% GC%; 5,035 genes [4,923 encoding
      known proteins, 112 RNA genes]) and a 202-kb plasmid (50.2% GC%; 229 genes [229
      encoding known proteins]).
AU  - Shin SH
AU  - Kim S
AU  - Kim JY
AU  - Lee S
AU  - Um Y
AU  - Oh MK
AU  - Kim YR
AU  - Lee J
AU  - Yang KS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2736-2737.

PMID- 22493189
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Klebsiella oxytoca KCTC 1686, Used in Production of 2,3-Butanediol.
PG  - 2371-2372
AB  - Here we report the full genome sequence of Klebsiella oxytoca KCTC 1686, which is used in
      production of 2,3-butanediol. The KCTC 1686 strain contains 5,974,109 bp
      with G+C content of 56.05 mol% and contains 5,488 protein-coding genes and 110
      structural RNAs.
AU  - Shin SH
AU  - Kim S
AU  - Kim JY
AU  - Lee S
AU  - Um Y
AU  - Oh MK
AU  - Kim YR
AU  - Lee J
AU  - Yang KS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2371-2372.

PMID- 22493190
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Enterobacter aerogenes KCTC 2190.
PG  - 2373-2374
AB  - This is the first complete genome sequence of the Enterobacter aerogenes species. Here we
      present the genome sequence of E. aerogenes KCTC 2190, which contains
      5,280,350 bp with a G + C content of 54.8 mol%, 4,912 protein-coding genes, and
      109 structural RNAs.
AU  - Shin SH
AU  - Kim S
AU  - Kim JY
AU  - Lee S
AU  - Um Y
AU  - Oh MK
AU  - Kim YR
AU  - Lee J
AU  - Yang KS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2373-2374.

PMID- 22328761
VI  - 194
DP  - 2012
TI  - Genome Sequence of Paenibacillus terrae HPL-003, a Xylanase-Producing Bacterium Isolated from Soil Found in Forest Residue.
PG  - 1266
AB  - This article reports on the full genome sequence of Paenibacillus terrae HPL-003, which is a
      Gram-positive, endospore-forming, xylanase-producing bacterium
      isolated from soil found in forest residue on Gara Mountain. The strain HPL-003
      contains 6,083,395 bp with a G+C content of 46.77 mol%, 2,633 protein-coding
      genes, and 117 structural RNAs.
AU  - Shin SH
AU  - Kim S
AU  - Kim JY
AU  - Song HY
AU  - Cho SJ
AU  - Kim DR
AU  - Lee KI
AU  - Lim HK
AU  - Park NJ
AU  - Hwang IT
AU  - Yang KS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1266.

PMID- 23814034
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Raoultella ornithinolytica Strain B6, a 2,3-Butanediol-Producing Bacterium Isolated from Oil-Contaminated Soil.
PG  - e00395-13
AB  - Here we report the full genome sequence of Raoultella ornithinolytica strain B6,  a
      Gram-negative aerobic bacillus belonging to the family Enterobacteriaceae. This
      2,3-butanediol-producing bacterium was isolated from oil-contaminated soil on
      Backwoon Mountain in South Korea. Strain B6 contains 5,398,151 bp with 4,909
      protein-coding genes, 104 structural RNAs, and 55.88% G+C content.
AU  - Shin SH
AU  - Um Y
AU  - Beak JH
AU  - Kim S
AU  - Lee S
AU  - Oh MK
AU  - Kim YR
AU  - Lee J
AU  - Yang KS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00395-13.

PMID- 25584140
VI  - 9
DP  - 2014
TI  - Non-contiguous finished genome sequence and description of the gliding bacterium  Flavobacterium seoulense sp. nov.
PG  - 34
AB  - Flavobacterium seoulense strain EM1321(T) is the type strain of Flavobacterium seoulense sp.
      nov., a proposed novel species within the genus Flavobacterium.
      This strain is a Gram-reaction-negative, aerobic, rod-shaped bacterium isolated
      from stream water in Bukhansan National Park, Seoul. This organism is motile by
      gliding. Here, we describe the features of Flavobacterium seoulense EM1321(T),
      together with its genome sequence and annotation. The genome comprised 3,792,640
      bp, with 3,230 protein-coding genes and 52 RNA genes.
AU  - Shin SK
AU  - Goo H
AU  - Cho YJ
AU  - Kwon S
AU  - Yong D
AU  - Yi H
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 34.

PMID- 29700157
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of the First South Korean Clinical Isolate of Burkholderia  pseudomallei, H0901.
PG  - e00336-18
AB  - We report here the draft genome sequence of Burkholderia pseudomallei H0901. This strain was
      isolated in 2003 from the first melioidosis patient in South Korea.
AU  - Shin YW
AU  - Choi MM
AU  - Chun JH
AU  - Yu JY
AU  - Kim DW
AU  - Rhie GE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00336-18.

PMID- 27609910
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Kosakonia sacchari Strain BO-1, an Endophytic Diazotroph Isolated from a Sweet Potato.
PG  - e00868-16
AB  - The complete genome sequence of the endophytic diazotroph Kosakonia sacchari, isolated from a
      sweet potato, was analyzed. The 4,902,106-bp genome with 53.7%
      G+C content comprises 4,638 open reading frames, including nif genes, 84 tRNAs,
      and seven complete rRNAs in a circular chromosome.
AU  - Shinjo R
AU  - Uesaka K
AU  - Ihara K
AU  - Loshakova K
AU  - Mizuno Y
AU  - Yano K
AU  - Tanaka A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00868-16.

PMID- 6255411
VI  - 8
DP  - 1980
TI  - A second site specific endonuclease from Thermus thermophilus 111, Tth111II.
PG  - 3275-3285
AB  - A second site specific endonuclease with novel specificity has been purified
      from Thermus thermophilus strain 111 and named Tth111II.  the enzyme is active
      at temperature up to 80C and requires Mg2+ for endonuclease activity.  Tth111II
      cleaves PhiX174 RFDNA into 11 fragments and lambda DNA into more than 25
      fragments.  From the 5' -terminal sequences of Tth111II fragments of PhiX174
      RFDNA determined by the two dimensional homochromatography and the survey on
      nucleotide sequence PhiX174 RFDNA, it was concluded that Tth111II recognizes
      the DNA sequence 5'CAAPuCA(N)11 ^ 3' 3'GTTPyGT(N)9 ^ 5' and cleaves the sites
      as indicated by the arrows.
AU  - Shinomiya T
AU  - Kobayashi M
AU  - Sato S
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1980 8: 3275-3285.

PMID- 6265880
VI  - SS8
DP  - 1980
TI  - A second site specific endonuclease from Thermus thermophilus 111, Tth111II.
PG  - S181-S184
AB  - A second site specific endonuclease with a novel specificity has been isolated
      from Thermus thermophilus strain 111 and named Tth111II.  The enzyme is active
      at temperature up to 80C and requires Mg2+ or Mn2+ for activity.  Tth111II
      cleaves PhiX174 RF into 11 fragments.  From the analysis of 5' terminal
      sequences of the PhiX 174 RF DNA fragments produced by Tth111II action, it was
      concluded that Tth111II recognized the DNA sequence 5'CAAPuCA(N)11^3'
      3'GTTPyGT(N)9^5' and cleaved the sites as indicated by arrows.
AU  - Shinomiya T
AU  - Kobayashi M
AU  - Sato S
PT  - Journal Article
TA  - Nucleic Acids Symp. Ser.
JT  - Nucleic Acids Symp. Ser.
SO  - Nucleic Acids Symp. Ser. 1980 SS8: S181-S184.

PMID- 6298191
VI  - 92
DP  - 1982
TI  - A new aspect of a restriction endonuclease Tth111I.  It has a degenerated specificity (Tth111I*).
PG  - 1823-1832
AB  - We previously reported that Thermus thermophilus 111 contained two restriction
      enzymes, Tth111I and Tth111II.  The former does not cleave PhiX174 RFDNA and
      the latter does.  We have now found another endonuclease activity able to
      cleave PhiX174 RFDNA in the cell extract of T. thermophilus 111.
AU  - Shinomiya T
AU  - Kobayashi M
AU  - Sato S
AU  - Uchida T
PT  - Journal Article
TA  - J. Biochem. (Tokyo)
JT  - J. Biochem. (Tokyo)
SO  - J. Biochem. (Tokyo) 1982 92: 1823-1832.

PMID- 6243779
VI  - 8
DP  - 1980
TI  - A site specific endonuclease from Thermus thermophilus 111, Tth111I.
PG  - 43-56
AB  - A site specific endonuclease with novel specificity has been isolated from
      Thermus thermophilus strain 111 and named Tth111I.  Tth111I cleaves lambda DNA
      into three fragments of 23.5, 25.7 and 50.8% of the total length, and ColE1 DNA
      into two fragments of nearly equal length.  The sequences around Tth111I
      cleavage sites of ColE1 and lambda DNA were determined by the Maxam and Gilbert
      method and the two dimensional mapping method.  The results suggest that
      Tth111I recognizes the DNA sequence 5'-TGACN^NNGTC-3' 3'-ACTGNN^NCAG-5' site as
      indicated by the arrows.  Assuming that the first T.A pair in the sequence can
      be replaced for any base pair, the Tth111I recognition sequence has the
      symmetry with the two-fold axis as most type II restriction endonucleases do.
AU  - Shinomiya T
AU  - Sato S
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1980 8: 43-56.

PMID- 23887915
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of the Carbazole Degrader Pseudomonas resinovorans Strain CA10 (NBRC 106553).
PG  - e00488-13
AB  - Pseudomonas resinovorans strain CA10 can grow on carbazole as its sole carbon and nitrogen
      source. Here, we report the complete nucleotide sequence of the CA10
      genome (a 6,285,863-bp chromosome and a 198,965-bp plasmid). CA10 carries a
      larger number of genes that are potentially responsible for aromatic hydrocarbon
      metabolism than do other previously sequenced Pseudomonas spp.
AU  - Shintani M
AU  - Hosoyama A
AU  - Ohji S
AU  - Tsuchikane K
AU  - Takarada H
AU  - Yamazoe A
AU  - Fujita N
AU  - Nojiri H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00488-13.

PMID- 24459274
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of the Thermophilic Polychlorinated Biphenyl Degrader Geobacillus sp. Strain JF8 (NBRC 109937).
PG  - e01213-13
AB  - Geobacillus sp. strain JF8 (NBRC 109937) utilizes biphenyl and naphthalene as sole carbon
      sources and degrades polychlorinated biphenyl (PCB) at 60 degrees C.
      Here, we report the complete nucleotide sequence of the JF8 genome (a
      3,446,630-bp chromosome and a 39,678-bp plasmid). JF8 has the smallest genome
      among the known PCB degraders.
AU  - Shintani M
AU  - Ohtsubo Y
AU  - Fukuda K
AU  - Hosoyama A
AU  - Ohji S
AU  - Yamazoe A
AU  - Fujita N
AU  - Nagata Y
AU  - Tsuda M
AU  - Hatta T
AU  - Kimbara K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01213-13.

PMID- 10871362
VI  - 28
DP  - 2000
TI  - Comparison of whole genome sequences of Chlamydia pneumoniae J138 from Japan and CWL029 from USA.
PG  - 2311-2314
AB  - Chlamydia pneumoniae is a widespread pathogen of humans causing pneumonia and bronchitis.
      There are many reports of an association between C. pneumoniae infection and atherosclerosis.
      We determined the whole genome sequence of C. pneumoniae strain J138 isolated in Japan in 1994
      and compared it with the sequence of strain CWL029 isolated in the USA before 1987.  The J138
      circular chromosome consists of 1,226,565 nt (40.7% G&C) with 1072 likely protein-coding genes
      that is 3665 nt shorter than the CWL029 genome.  Plasmids, phage- or transposon-like sequences
      were not identified.  The overall genomic organization, gene order and predicted proteomes of
      the two strains are very similar, suggesting a high level of structural and functional
      conservation between the two unrelated isolates.  The most conspicuous differences in the J138
      genome relative to the CWL029 genome are the absence of five DNA segments, ranging in size
      from 89 to 1649 nt, and the presence of three DNA segments, ranging from 27 to 84 nt.  The
      complex organization of these 'different zones' may be attributable to a unique system of
      recombination.
AU  - Shirai M
AU  - Hirakawa H
AU  - Kimoto M
AU  - Tabuchi M
AU  - Kishi F
AU  - Ouchi K
AU  - Shiba T
AU  - Ishii K
AU  - Hattori M
AU  - Kuhara S
AU  - Nakazawa T
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2000 28: 2311-2314.

PMID- 23563565
VI  - 77
DP  - 2013
TI  - The AplI Restriction-Modification System in an Edible Cyanobacterium, Arthrospira (Spirulina) platensis NIES-39, Recognizes the Nucleotide Sequence 5'-CTGCAG-3'.
PG  - 782-788
AB  - The degradation of foreign DNAs by restriction enzymes in an edible cyanobacterium,
      Arthrospira platensis, is a potential barrier for gene-transfer experiments in this
      economically valuable organism. We overproduced in Escherichia coli the proteins involved in a
      putative restriction-modification system of A. platensis NIES-39. The protein produced from
      the putative type II restriction enzyme gene NIES39_K04640 exhibited an endonuclease activity
      that cleaved DNA within the sequence 5'-CTGCAG-3' between the A at the fifth position and
      the G at the sixth position. We designated this enzyme AplI. The protein from the adjacent
      gene NIES39_K04650, which encodes a putative DNA (cytosine-5-)-methyltransferase, rendered DNA
      molecules resistant to AplI by modifying the C at the fourth position (but not the C at the
      first position) in the recognition sequence. This modification enzyme, M.AplI, should be
      useful for converting DNA molecules into AplI-resistant forms for use in gene-transfer
      experiments. A summary of restriction enzymes in various Arthrospira strains is also presented
      in this paper.
AU  - Shiraishi H
AU  - Tabuse Y
PT  - Journal Article
TA  - Biosci. Biotechnol. Biochem.
JT  - Biosci. Biotechnol. Biochem.
SO  - Biosci. Biotechnol. Biochem. 2013 77: 782-788.

PMID- 23637617
VI  - 9
DP  - 2013
TI  - Mouse Oocyte Methylomes at Base Resolution Reveal Genome-Wide Accumulation of Non-CpG Methylation and Role of DNA Methyltransferases.
PG  - e1003439
AB  - DNA methylation is an epigenetic modification that plays a crucial role in normal mammalian
      development, retrotransposon silencing, and
      cellular reprogramming. Although methylation mainly occurs on the
      cytosine in a CG site, non-CG methylation is prevalent in pluripotent
      stem cells, brain, and oocytes. We previously identified non-CG
      methylation in several CG-rich regions in mouse germinal vesicle
      oocytes (GVOs), but the overall distribution of non-CG methylation and
      the enzymes responsible for this modification are unknown. Using
      amplification-free whole-genome bisulfite sequencing, which can be used
      with minute amounts of DNA, we constructed the base-resolution
      methylome maps of GVOs, non-growing oocytes (NGOs), and mutant GVOs
      lacking the DNA methyltransferase Dnmt1, Dnmt3a, Dnmt3b, or Dnmt3L. We
      found that nearly two-thirds of all methylcytosines occur in a non-CG
      context in GVOs. The distribution of non-CG methylation closely
      resembled that of CG methylation throughout the genome and showed clear
      enrichment in gene bodies. Compared to NGOs, GVOs were over four times
      more methylated at non-CG sites, indicating that non-CG methylation
      accumulates during oocyte growth. Lack of Dnmt3a or Dnmt3L resulted in
      a global reduction in both CG and non-CG methylation, showing that
      non-CG methylation depends on the Dnmt3a-Dnmt3L complex. Dnmt3b was
      dispensable. Of note, lack of Dnmt1 resulted in a slight decrease in CG
      methylation, suggesting that this maintenance enzyme plays a role in
      non-dividing oocytes. Dnmt1 may act on CG sites that remain
      hemimethylated in the de novo methylation process. Our results provide
      a basis for understanding the mechanisms and significance of non-CG
      methylation in mammalian oocytes.
AU  - Shirane K
AU  - Toh H
AU  - Kobayashi H
AU  - Miura F
AU  - Chiba H
AU  - Ito T
AU  - Kono T
AU  - Sasaki H
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2013 9: e1003439.

PMID- 27417842
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequence of Filimonas lacunae, a Bacterium of the Family Chitinophagaceae Characterized by Marked Colony Growth under a High-CO2  Atmosphere.
PG  - e00667-16
AB  - We report here the genome sequence of Filimonas lacunae, a bacterium of the family
      Chitinophagaceae characterized by high-CO2-dependent growth. The 7.81-Mb
      circular genome harbors many genes involved in carbohydrate degradation and
      related genetic regulation, suggesting the role of the bacterium as a
      carbohydrate degrader in diverse environments.
AU  - Shiratori-Takano H
AU  - Takano H
AU  - Ueda K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00667-16.

PMID- 26184947
VI  - 3
DP  - 2015
TI  - First Complete Genome Sequences of Staphylococcus aureus subsp. aureus Rosenbach  1884 (DSM 20231T), Determined by PacBio Single-Molecule Real-Time Technology.
PG  - e00800-15
AB  - The first complete genome sequences of Staphylococcus aureus subsp. aureus Rosenbach 1884
      strain DSM 20231(T), the type strain of the bacterium causing
      staphylococcal disease, were determined using PacBio RS II. The sequences
      represent the chromosome (2,755,072 bp long; G+C content, 32.86%) and a plasmid
      (27,490 bp long; G+C content, 30.69%).
AU  - Shiroma A
AU  - Terabayashi Y
AU  - Nakano K
AU  - Shimoji M
AU  - Tamotsu H
AU  - Ashimine N
AU  - Ohki S
AU  - Shinzato M
AU  - Teruya K
AU  - Satou K
AU  - Hirano T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00800-15.

PMID- 29650577
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of New Genomospecies 'Candidatus Pectobacterium maceratum' Strains, Which Cause Soft Rot in Plants.
PG  - e00260-18
AB  - Investigation of collections of phytopathogenic bacteria has revealed some strains distinct
      from known Pectobacterium spp. We report here the draft genome
      sequences of five such strains, isolated during the period of 1947 to 2012. Based
      on comparative genomics, we propose a new candidate genomospecies of the genus
      Pectobacterium, 'Candidatus Pectobacterium maceratum.'
AU  - Shirshikov FV
AU  - Korzhenkov AA
AU  - Miroshnikov KK
AU  - Kabanova AP
AU  - Barannik AP
AU  - Ignatov AN
AU  - Miroshnikov KA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00260-18.

PMID- 9312422
VI  - 62
DP  - 1997
TI  - Three site-specific endonucleases from Thermophilic strain Bacillus species LA are isoschizomers of HhaI, AsuII, and HindIII.
PG  - 280-290
AB  - Screening of thermophilic bacterial strains revealed a strain containing three site-specific
      endonucleases: BspLAI, BspLAII, and BspLAIII.  These endonucleases were purified to functional
      purity by sequential chromatography.  Recognition sites, DNA cleavage sites, and some
      properties of the endonucleases were determined.  BspLAI recognizes the sequence 5'-GCG/C-3'
      on the DNA molecule and is an isoschizomer of endonuclease HhaI.  BspLAII recognizes the
      sequence 5'-TT/CGAA-3' and is an isoschizomer of AsuII.  BspLAIII recognizes site
      5'-A/AGCTT-3' and is an isoschizomer of endonuclease HindIII.  All the three enzymes exhibit
      maximal activity at 55oC.  The optimal buffer is MRB, pH 7.4.  They retain activity on storage
      for 3 weeks at room temperature and thus are highly stable.
AU  - Shiryaev SA
AU  - Zheleznaya LA
AU  - Matvienko NI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1997 62: 280-290.

PMID- 10810186
VI  - 65
DP  - 2000
TI  - Two new site-specific endonucleases from Staphylococcus species strain D5.
PG  - 553-561
AB  - Staphylococcus species strain D5 containing two site-specific endonucleases, SspD5I and
      SspD5II, was found during screening of a bacterial strain collection from soil. These
      endonucleases
      were purified to functional homogeneity by sequential chromatography. Site-specific
      endonuclease SspD5I recognizes the sequence 5'-GGTGA(8N/8N)^3' on DNA. Unlike HphI, it
      cleaves DNA at a distance of 8 nucleotides from the recognition sequence on both chains
      producing blunt-end DNA fragments, while endonuclease HphI cleaves DNA forming mononucleotide
      3'-OH protruding ends. Thus, endonuclease SspD5I is a new type II site-specific endonuclease
      and a neoschizomer of endonuclease HphI. The advantage of this new endonuclease is that the
      blunt-end DNA products of this enzyme can be inserted without additional treatment into vector
      DNAs cleaved with endonucleases yielding DNA blunt-ends. Endonuclease SspD5II recognizes the
      site
      5'-ATGCA^T-3' and thus is an isoschizomer of endonuclease NsiI. The molecular
      mass of SspD5I is about 35 kD and that of SspD5II is 40 kD. The enzymes exhibit maximal
      activity at 37 C. The optimal buffer for the reaction is HRB (10 mM Tris-HCl, pH 7.5,
      10 mM MgCl2, 100 mM NaCl, and 1 mM dithiothreitol).
AU  - Shiryaev SA
AU  - Zheleznyakova EN
AU  - Matvienko NN
AU  - Zheleznaya LA
AU  - Matvienko NI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 2000 65: 553-561.

PMID- 178910
VI  - 18
DP  - 1976
TI  - Restriction endonuclease from Haemophilus gallinarum (HgaI) cleaves polyoma DNA at four locations.
PG  - 793-798
AB  - A restriction endonuclease obtained from Haemophilus gallinarum (HgaI) cleaves
      polyoma DNA at four specific sites.  Using the EcoRI, HindIII, and HpaII
      endonuclease restriction sites as reference, the four HgaI cleavage sites were
      mapped at 0.02, 0.14, 0.27, and 0.48 fractional lengths, clockwise, from the
      single EcoRI cleavage site.
AU  - Shishido K
AU  - Berg P
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1976 18: 793-798.

PMID- 28933529
VI  - 12
DP  - 2017
TI  - Simultaneous Production of Anabaenopeptins and Namalides by the Cyanobacterium Nostoc sp. CENA543.
PG  - 2746-2755
AB  - Anabaenopeptins are a diverse group of cyclic peptides, which contain an unusual
      ureido linkage. Namalides are shorter structural homologues of anabaenopeptins,
      which also contain an ureido linkage. The biosynthetic origins of namalides are
      unknown despite a strong resemblance to anabaenopeptins. Here, we show the
      cyanobacterium Nostoc sp. CENA543 strain producing new (nostamide B-E (2, 4, 5,
      and 6)) and known variants of anabaenopeptins (schizopeptin 791 (1) and
      anabaenopeptin 807 (3)). Surprisingly, Nostoc sp. CENA543 also produced namalide
      B (8) and the new namalides D (7), E (9), and F (10) in similar amounts to
      anabaenopeptins. Analysis of the complete Nostoc sp. CENA543 genome sequence
      indicates that both anabaenopeptins and namalides are produced by the same
      biosynthetic pathway through module skipping during biosynthesis. This unique
      process involves the skipping of two modules present in different nonribosomal
      peptide synthetases during the namalide biosynthesis. This skipping is an
      efficient mechanism since both anabaenopeptins and namalides are synthesized in
      similar amounts by Nostoc sp. CENA543. Consequently, gene skipping may be used to
      increase and possibly broaden the chemical diversity of related peptides produced
      by a single biosynthetic gene cluster. Genome mining demonstrated that the
      anabaenopeptin gene clusters are widespread in cyanobacteria and can also be
      found in tectomicrobia bacteria.
AU  - Shishido TK
AU  - Jokela J
AU  - Fewer DP
AU  - Wahlsten M
AU  - Fiore MF
AU  - Sivonen K
PT  - Journal Article
TA  - ACS Chem. Biol.
JT  - ACS Chem. Biol.
SO  - ACS Chem. Biol. 2017 12: 2746-2755.

PMID- 23766407
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Arthrobacter gangotriensis Strain Lz1yT, Isolated from a Penguin Rookery Soil Sample Collected in Antarctica, near the Indian Station  Dakshin Gangotri.
PG  - e00347-13
AB  - We report here the 4.3-Mb genome of Arthrobacter gangotriensis strain Lz1y(T), isolated from a
      penguin rookery soil sample collected in Antarctica, near the
      Indian station Dakshin Gangotri.
AU  - Shivaji S
AU  - Ara S
AU  - Bandi S
AU  - Singh A
AU  - Kumar PA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00347-13.

PMID- 23766406
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Bhargavaea cecembensis Strain DSE10T, Isolated from a Deep-Sea Sediment Sample Collected at a Depth of 5,904 m from the  Chagos-Laccadive Ridge System in the Indian Ocean.
PG  - e00346-13
AB  - Here, we report the 3.2-Mbp draft genome sequence of Bhargavaea cecembensis strain DSE10(T),
      isolated from a sediment sample collected from the
      Chagos-Laccadive ridge system in the Indian Ocean at a depth of 5,904 m.
AU  - Shivaji S
AU  - Ara S
AU  - Begum Z
AU  - Ruth M
AU  - Singh A
AU  - Kumar PA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00346-13.

PMID- 23682146
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Cesiribacter andamanensis Strain AMV16T, Isolated from a Soil Sample from a Mud Volcano in the Andaman Islands, India.
PG  - e00240-13
AB  - Here we report the 4.75-Mb genome of Cesiribacter andamanensis strain AMV16(T), isolated from
      a soil sample from a mud volcano in the Andaman Islands, India.
AU  - Shivaji S
AU  - Ara S
AU  - Begum Z
AU  - Srinivas TN
AU  - Singh A
AU  - Kumar PA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00240-13.

PMID- 23846277
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Arcticibacter svalbardensis Strain MN12-7T, a Member of  the Family Sphingobacteriaceae Isolated from an Arctic Soil Sample.
PG  - e00484-13
AB  - The 4.69-Mb genome sequence of Arcticibacter svalbardensis strain MN12-7(T), isolated from an
      Arctic soil sample, is reported.
AU  - Shivaji S
AU  - Ara S
AU  - Prasad S
AU  - Manasa BP
AU  - Begum Z
AU  - Singh A
AU  - Kumar PA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00484-13.

PMID- 23950138
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Cyclobacterium qasimii Strain M12-11BT, Isolated from Arctic Marine Sediment.
PG  - e00642-13
AB  - A 6.29-Mb genome sequence of Cyclobacterium qasimii strain M12-11B(T), isolated from an Arctic
      marine sediment sample, is reported.
AU  - Shivaji S
AU  - Ara S
AU  - Singh A
AU  - Kumar PA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00642-13.

PMID- 23144386
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Cecembia lonarensis Strain LW9T, Isolated from Lonar Lake, a Haloalkaline Lake in India.
PG  - 6631
AB  - The draft genome sequence (4.84 Mb) of Cecembia lonarensis strain LW9(T), isolated from a
      water sample (4.5-m depth) from Lonar Lake, a meteorite-created
      haloalkaline lake in India, is reported. The enzymes produced by these
      microorganisms need to be stable under alkaline conditions prevailing in its
      habitat. Such enzymes would be of immense importance for enzymatic processes
      operating at high pH.
AU  - Shivaji S
AU  - Ara S
AU  - Singh A
AU  - Pinnaka AK
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6631.

PMID- 23144382
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Bacillus isronensis Strain B3W22, Isolated from the Upper Atmosphere.
PG  - 6624-6625
AB  - We report the 4.0-Mb genome sequence of Bacillus isronensis strain B3W22 isolated from air
      collected at an altitude ranging from 27 to 30 km above the city of
      Hyderabad, in India. This genome sequence will contribute to the objective of
      determining the microbial diversity of the upper atmosphere.
AU  - Shivaji S
AU  - Ara S
AU  - Singh SK
AU  - Bandi S
AU  - Singh A
AU  - Pinnaka AK
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6624-6625.

PMID- 7541760
VI  - 157
DP  - 1995
TI  - Expression of the mcrA gene of Escherichia coli is regulated post-transcriptionally, possibly by sequestration of the Shine-Dalgarno region.
PG  - 201-207
AB  - The polypeptides encoded by the mcrA gene were analysed using a T7 expression system.  Cloned
      fragments of 1.6 and 1.0 kb displayed an McrA+/RglA+ phenotype and directed synthesis of a
      31-kDa polypeptide.  A derivative of these clones altered at an internal HindIII site
      displayed an McrA+/RglA- phenotype and directed production of a 23-kDa polypeptide.  A
      construct carrying the 1.0-kb mcrA insert yielded a single 1.3-kb transcript.  The mcrA
      transcript was found to start from C, G, T and G, namely the fourth, fifth, sixth and seventh
      nucleotides (nt), respectively, downstream from the last nt of the putative -10 region.  Two
      mcrA transcriptional/translational fusions were made in the pT7-7 expression vector and the
      protein encoded by these constructs were analysed.  Regulation of mcrA expression was studied
      by quantitative Northern anlaysis of RNA from various mcrA clones.  Together with a computer
      analysis of the translation initiation region in these mRNAs, the results suggest that the
      expression of mcrA may be regulated at the translational level.
AU  - Shivapriya R
AU  - Prasad R
AU  - Narayanan IL
AU  - Krishnaswamy S
AU  - Dharmalingam K
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 201-207.

PMID- 25931593
VI  - 3
DP  - 2015
TI  - Genome Sequences of Three Strains of Lactobacillus paracasei of Different Origins and with Different Cholate Sensitivities.
PG  - e00178-15
AB  - We report here the draft genome sequences of three strains of Lactobacillus paracasei (NRIC
      0644, NRIC 1781, and NRIC 1917) isolated from different sources.
      The three genomes range from 2.95 to 3.15 Mb with a G+C content of 46% and
      contain approximately 2,700 protein coding sequences.
AU  - Shiwa Y
AU  - Atarashi H
AU  - Tanaka N
AU  - Okada S
AU  - Yoshikawa H
AU  - Endo A
AU  - Miyaji T
AU  - Nakagawa J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00178-15.

PMID- 23682142
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences of Two Pairs of Human Intestinal Bifidobacterium longum subsp. longum Strains, 44B and 1-6B and 35B and 2-2B, Consecutively Isolated from  Two Children after a 5-Year Time Period.
PG  - e00234-13
AB  - We report the genome sequences of four isolates of a human gut symbiont, Bifidobacterium
      longum. Strains 44B and 35B were isolated from two 1-year-old
      infants, while 1-6B and 2-2B were isolated from the same children 5 years later.
      The sequences permit investigations of factors enabling long-term colonization of
      bifidobacteria.
AU  - Shkoporov AN
AU  - Efimov BA
AU  - Khokhlova EV
AU  - Chaplin AV
AU  - Kafarskaya LI
AU  - Durkin AS
AU  - McCorrison J
AU  - Torralba M
AU  - Gillis M
AU  - Sutton G
AU  - Weibel DB
AU  - Nelson KE
AU  - Smeianov VV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00234-13.

PMID- 11875970
VI  - 28
DP  - 2002
TI  - A comparative structure-function analysis and molecular mechanism of action of endonucleases from Serratia marcescens and Physarum  polycephalum.
PG  - 23-31
AB  - Structural and functional characteristics were compared for wild-type nuclease from Serratia
      marcescens, which belongs to the family of DNA/RNA nonspecific endonucleases, its mutational
      forms, and the nuclease I-PpoI from Physarum polycephalum, which is a representative of the
      Cys-His box-containing subgroup of the superfamily of extremely specific intron-encoded homing
      DNases. Despite the lack of sequence homology and the overall different topology of the
      Serratia marcescens and I-PpoI nucleases, their active sites have a remarkable structural
      similarity. Both of them have a unique magnesium atom in the active site, which is a part of
      the coordinately bonded water-magnesium complex involved in their catalytic acts. In the
      enzyme-substrate complexes, the Mg2+ ion is chelated by an Asp residue, coordinates two oxygen
      atoms of DNA, and stabilizes the transition state of the phosphate anion and 3'-OH group of
      the leaving nucleotide. A new mechanism of the phosphodiester bond cleavage, which is common
      for the Serratia marcescens and I-PpoI nucleases and differs from the known functioning
      mechanism of the restriction and homing endonucleases, was proposed. It presumes a His residue
      as a general base for the activation of a non-cluster water molecule at the nucleophilic in
      line displacement of the 3'-leaving group. A strained metalloenzyme-substrate complex is
      formed during hydrolysis and relaxes to the initial state after the reaction.
AU  - Shlyapnikov SV
AU  - Lunin VV
AU  - Blagova EV
AU  - Abaturov LV
AU  - Perbandt M
AU  - Betzel C
AU  - Mikhailov AM
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 2002 28: 23-31.

PMID- 21321201
VI  - 108
DP  - 2011
TI  - DNA methyltransferase 1, cytosine methylation, and cytosine hydroxymethylation in mammalian mitochondria.
PG  - 3630-3635
AB  - Mitochondrial DNA (mtDNA) has been reported to contain 5-methylcytosine (5mC) at CpG
      dinucleotides, as in the nuclear genome, but neither the
      mechanism generating mtDNA methylation nor its functional significance
      is known. We now report the presence of 5-hydroxymethylcytosine (5hmC)
      as well as 5mC in mammalian mtDNA, suggesting that previous studies
      underestimated the level of cytosine modification in this genome. DNA
      methyltransferase 1 (DNMT1) translocates to the mitochondria, driven by
      a mitochondrial targeting sequence located immediately upstream of the
      commonly accepted translational start site. This targeting sequence is
      conserved across mammals, and the encoded peptide directs a
      heterologous protein to the mitochondria. DNMT1 is the only member of
      the three known catalytically active DNA methyltransferases targeted to
      the mitochondrion. Mitochondrial DNMT1 (mtDNMT1) binds to mtDNA,
      proving the presence of mtDNMT1 in the mitochondrial matrix. mtDNMT1
      expression is up-regulated by NRF1 and PGC1 alpha, transcription
      factors that activate expression of nuclear-encoded mitochondrial genes
      in response to hypoxia, and by loss of p53, a tumor suppressor known to
      regulate mitochondrial metabolism. Altered mtDNMT1 expression
      asymmetrically affects expression of transcripts from the heavy and
      light strands of mtDNA. Hence, mtDNMT1 appears to be responsible for
      mtDNA cytosine methylation, from which 5hmC is presumed to be derived,
      and its expression is controlled by factors that regulate mitochondrial
      function.
AU  - Shock LS
AU  - Thakkar PV
AU  - Peterson EJ
AU  - Moran RG
AU  - Taylor SM
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2011 108: 3630-3635.

PMID- 26089434
VI  - 3
DP  - 2015
TI  - Genome Sequence of the Soil Bacterium Janthinobacterium sp. KBS0711.
PG  - e00689-15
AB  - We present a draft genome of Janthinobacterium sp. KBS0711 that was isolated from agricultural
      soil. The genome provides insight into the ecological strategies of
      this bacterium in free-living and host-associated environments.
AU  - Shoemaker WR
AU  - Muscarella ME
AU  - Lennon JT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00689-15.

PMID- 24115541
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Brucella melitensis Strain ADMAS-G1, Isolated from Placental Fluids of an Aborted Goat.
PG  - e00809-13
AB  - Here, we report the draft genome sequence and annotation of the Brucella melitensis strain
      designated ADMAS-G1, isolated from placental fluids of an
      aborted goat. The length of the genome is 3,284,982 bp, with a 57.3% GC content.
      A total of 3,325 protein-coding genes and 63 RNA genes were predicted.
AU  - Shome R
AU  - Krithiga N
AU  - Muttannagouda RB
AU  - Veeregowda BM
AU  - Swati S
AU  - Shome BR
AU  - Vishnu U
AU  - Sankarasubramanian J
AU  - Sridhar J
AU  - Gunasekaran P
AU  - Rahman H
AU  - Rajendhran J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00809-13.

PMID- 25146137
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Brucella abortus S99: Designated Antigenic Smooth Reference Strain Used in Diagnostic Tests in India.
PG  - e00824-14
AB  - Brucella abortus strain S99 is widely used for the preparation of colored, plain, recombinant
      and smooth lipopolysaccharide antigens for the preparation of
      Brucella diagnostic kits. The genome of this strain was sequenced and the length
      of the genome was 3,253,175 bp, with 57.2% G+C content. A total of 3,365 protein
      coding genes and 53 RNA genes were predicted.
AU  - Shome R
AU  - Krithiga N
AU  - Padmashree BS
AU  - Sankarasubramanian J
AU  - Vishnu US
AU  - Sridhar J
AU  - Gunasekaran P
AU  - Rajendhran J
AU  - Rahman H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00824-14.

PMID- 15855533
VI  - 49
DP  - 2005
TI  - Seven Novel Variants of the Staphylococcal Chromosomal Cassette mec in Methicillin-Resistant Staphylococcus aureus Isolates from Ireland.
PG  - 2070-2083
AB  - Methicillin-resistant Staphylococcus aureus (MRSA) isolates recovered in
      Irish hospitals between 1971 and 2002 were characterized using multilocus
      sequence typing (MLST) (n = 130) and SCCmec typing (n = 172). Where
      atypical SCCmec typing results were obtained, PCR amplification of entire
      SCCmec elements, analysis of amplimer mobility, and nucleotide sequencing
      were undertaken. MLST revealed that 129/130 isolates had the same
      genotypes as internationally spread MRSA clones, including ST239, ST247,
      ST250, ST5, ST22, ST36, and ST8. A novel genotype, ST496, was identified
      in one isolate. Half of the isolates (86/172) had SCCmec type I, IA, II,
      III, or IV. The remaining 86 isolates harbored novel SCCmec variants in
      three distinct genetic backgrounds: (i) 74/86 had genotype ST8 and either
      one of five novel SCCmec II (IIA, IIB, IIC, IID, and IIE) or one of two
      novel SCCmec IV (IVE and IVF) variants; (ii) 3/86 had genotype ST239 and a
      novel SCCmec III variant; (iii) 9/86 had a novel SCCmec I variant
      associated with ST250. SCCmec IVE and IVF were similar to SCCmec IVc and
      IVb, respectively, but differed in the region downstream of mecA. The five
      SCCmec II variants were similar to SCCmec IVb in the region upstream of
      the ccr complex but otherwise were similar to SCCmec II, except for the
      following regions: SCCmec IIA and IID had a novel mec complex, A.4 (Delta
      mecI-IS1182-Delta mecI-mecR1-mecA-IS431mec); SCCmec IIC and IIE had a
      novel mec complex, A.3 (IS1182-Delta mecI-mecR1-mecA-IS431mec); SCCmec IID
      and IIE lacked pUB110; SCCmec IIC and IIE lacked a region of DNA between
      Tn554 and the mec complex; and SCCmec IIB lacked Tn554. This study has
      demonstrated a hitherto-undescribed degree of diversity within SCCmec.
AU  - Shore A
AU  - Rossney AS
AU  - Keane CT
AU  - Enright MC
AU  - Coleman DC
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2005 49: 2070-2083.

PMID- 18852274
VI  - 52
DP  - 2008
TI  - Detection of staphylococcal cassette chromosome mec-associated DNA segments in multiresistant methicillin-susceptible Staphylococcus aureus  (MSSA) and identification of Staphylococcus epidermidis ccrAB4 in both  methicillin-resistant S. aureus and MSSA.
PG  - 4407-4419
AB  - Methicillin-susceptible Staphylococcus aureus (MSSA) can arise from methicillin-resistant S.
      aureus (MRSA) following partial or complete
      excision of staphylococcal cassette chromosome mec (SCCmec). This study
      investigated whether multiresistant MSSA isolates from Irish hospitals,
      where MRSA has been endemic for decades, harbor SCCmec DNA. Twenty-five
      multiresistant MSSA isolates recovered between 2002 and 2006 were tested
      for SCCmec DNA by PCR and were genotyped by multilocus sequence typing and
      spa typing. All isolates lacked mecA. Three isolates (12%) harbored SCCmec
      DNA; two of these (genotype ST8/t190) harbored a 26-kb SCCmec IID
      (II.3.1.2) remnant that lacked part of mecI and all of mecR1, mecA, and
      IS431; the third isolate (ST8/t3209) harbored the SCCmec region from dcs
      to orfX. All three isolates were detected as MRSA using the BD GeneOhm and
      Cepheid's Xpert MRSA real-time PCR assays. Six isolates (ST8/t190, n = 4;
      ST5/t088, n = 2), including both isolates with the SCCmec IID remnant,
      harbored ccrAB4 with 100% identity to ccrAB4 from the Staphylococcus
      epidermidis composite island SCC-CI. This ccrAB4 gene was also identified
      in 23 MRSA isolates representative of ST8/t190-MRSA with variant SCCmec II
      subtypes IIA to IIE, which predominated previously in Irish hospitals.
      ccrAB4 was located 5,549 bp upstream of the left SCCmec junction in both
      the MRSA and MSSA isolates with SCCmec elements and remnants and 5,549 bp
      upstream of orfX in the four MSSA isolates with ccrAB4 only on an SCC-CI
      homologous region. This is the first description of a large SCCmec remnant
      with ccr and partial mec genes in MSSA and of the S. epidermidis SCC-CI
      and ccrAB4 genes in S. aureus.
AU  - Shore AC
AU  - Rossney AS
AU  - O'Connell B
AU  - Herra CM
AU  - Sullivan DJ
AU  - Humphreys H
AU  - Coleman DC
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2008 52: 4407-4419.

PMID- 11563955
VI  - 66
DP  - 2001
TI  - Putative DNA-(amino)methyltransferases in eucaryotes.
PG  - 753-762
AB  - By computer analysis of the known data bases, we have established that the open reading frames
      (ORF) coding for proteins that possess high degree of homology with procaryotic
      DNA-(amino)methyltransferases are present in the genomes of Leishmania major, Saccharomyces
      cerevisiae, Schizosaccharomyces pombe, Arabidopsis thaliana, Drosophila melanogaster,
      Caenorhabditis elegans, and Homo sapiens. Conservative motifs typical for bacterial
      DNA-(amino)methyltransferases are detected in the amino acid sequences of these putative
      proteins. The ORF of all putative eucaryotic DNA-(amino)methyltransferases found are encoded
      in nuclear DNA. In mitochondrial genomes including a few fully sequenced higher plant mtDNA,
      nucleotide sequences significantly homologous to genes of procaryotic
      DNA-(amino)methyltransferases are not found. Thus, ORF homologous to bacterial adenine
      DNA-methyltransferases are present in nuclei of protozoa, yeasts, insects, nematodes,
      vertebrates, higher plants, and other eucaryotes. A special search for corresponding proteins
      and, in particular, adenine DNA-methyltransferases in these organisms and a study of their
      functions are quite promising.
AU  - Shorning BY
AU  - Vanyushin BF
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 2001 66: 753-762.

PMID- 2158074
VI  - 18
DP  - 1990
TI  - Probing of unusual DNA structures in topologically constrained form V DNA: use of restriction enzymes as structural probes.
PG  - 267-275
AB  - The ability of DNA sequences to adopt unusual structures under superhelical
      torsional stress has been studied.  Sequences that are forced to adopt an
      unusual conformation in topologically constrained pBR322 form V DNA (Lk=0) were
      mapped using restriction enzymes as probes.  Restriction enzymes such as BamHI,
      PstI, AvaI and HindIII could not cleave their recognition sequences.  The
      removal of topological constraint relieved this inhibition.  The influence of
      neighbouring sequences on the ability of a given sequence to adopt an unusual
      DNA structure, presumbly a left handed Z conformation, was studied through
      single hit analysis.  Using multiple cut restriction enzymes such as NarI and
      FspI, it could be shown that under identical topological strain, the extent of
      structural alteration is greatly influenced by the neighbouring sequences.  In
      light of the variety of sequences and locations that could be mapped to adopt
      non-B conformation in pBR322 form V DNA, restriction enzymes appear as
      potential structural probes for natural DNA sequences.
AU  - Shouche YS
AU  - Ramesh N
AU  - Brahmachari SK
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 267-275.

PMID- 28770027
VI  - 12
DP  - 2017
TI  - The genome of the cotton bacterial blight pathogen Xanthomonas citri pv. malvacearum strain MSCT1.
PG  - 42
AB  - Xanthomonas citri pv. malvacearum is a major pathogen of cotton, Gossypium hirsutum L.. In
      this study we report the complete genome of the X. citri pv.
      malvacearum strain MSCT1 assembled from long read DNA sequencing technology. The
      MSCT1 genome is the first X. citri pv. malvacearum genome with complete coding
      regions for X. citri pv. malvacearum transcriptional activator-like effectors. In
      addition functional and structural annotations are presented in this study that
      will provide a foundation for future pathogenesis studies with MSCT1.
AU  - Showmaker KC
AU  - Arick MAII
AU  - Hsu CY
AU  - Martin BE
AU  - Wang X
AU  - Jia J
AU  - Wubben MJ
AU  - Nichols RL
AU  - Allen TW
AU  - Peterson DG
AU  - Lu SE
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 42.

PMID- 19170728
VI  - 11
DP  - 2008
TI  - Transcriptional activity of paddy soil bacterial communities.
PG  - 960-970
AB  - Summary Bulk mRNA was used to explore the transcriptional activity of bacterial communities in
      oxic versus anoxic paddy soil. Two microbial cDNA
      libraries were constructed from composite samples using semi-randomly
      primed RT-PCR. cDNAs averaged 500-600 bp in length and were treated as
      expressed sequence tags (ESTs). Clustering analysis of 805 random cDNAs
      resulted in 179 and 155 different ESTs for the oxic and anoxic zones
      respectively. Using an E-value threshold of e(-10), a total of 218
      different ESTs could be assigned by blastx, while 116 ESTs were predicted
      novel. Both the proportion and significance of the EST assignments
      increased with cDNA length. Taxonomic assignment was more powerful in
      discriminating between the aerobic and anaerobic bacterial communities
      than functional inference, as most ESTs in both oxygen zones were putative
      indicators of similar housekeeping functions, in particular ABC-type
      transporters. A few ESTs were putative indicators for community function
      in a biogeochemical context, such as beta-oxidation of long-chain fatty
      acids specifically in the oxic zone. Expressed sequence tags assigned to
      Alpha- and Betaproteobacteria were predominantly found in the oxic zone,
      while those affiliated with Deltaproteobacteria were more frequently
      detected in the anoxic zone. At the genus level, multiple assignments to
      Bradyrhizobium and Geobacter were unique to the oxic and anoxic zones
      respectively. The phylum-level affiliations of 93 16S rRNA sequences
      corresponded well with two taxonomically distinct EST patterns. Expressed
      sequence tags affiliated with Acidobacteria and Chloroflexi were
      frequently detected in both oxygen zones. In summary, the soil
      metatranscriptome is accessible for global analysis and such studies have
      great potential in elucidating the taxonomic and functional status of soil
      bacterial communities, but study significance depends on the number and
      length of cDNAs being randomly analysed.
AU  - Shrestha PM
AU  - Kube M
AU  - Reinhardt R
AU  - Liesack W
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2008 11: 960-970.

PMID- 18319611
VI  - 25
DP  - 2008
TI  - Genetic organization of the hrp genes cluster in Erwinia pyrifoliae and characterization of HR active domains in HrpNEp protein by mutational analysis.
PG  - 30-42
AB  - The disease-specific (dsp) region and the hypersensitive response and
      pathogenicity (hrp) genes, including the hrpW, hrpNEp, and hrpC operons
      have previously been sequenced in Erwinia pyrifoliae WT3 [Shrestha et al.
      (2005a)]. In this study, the remaining hrp genes, including the hrpC,
      hrpA, hrpS, hrpXY, hrpL and hrpJ operons, were determined. The hrp genes
      cluster (ca. 38 kb) was comprised of eight transcriptional units and
      contained nine hrc (hrp conserved) genes. The genetic organization of the
      hrp/hrc genes and their orientation for the transcriptions were also
      similar to and collinear with those of E. amylovora, showing > or = 80%
      homologies. However, ORFU1 and ORFU2 of unknown functions, present between
      the hrpA and hrpS operons of E. amylovora, were absent in E. pyrifoliae.
      To determine the HR active domains, several proteins were prepared from
      truncated fragments of the N-terminal and the C-terminal regions of
      HrpN(Ep) protein of E. pyrifoliae. The proteins prepared from the
      N-terminal region elicited HR, but not from those of the C-terminal region
      indicating that HR active domains are located in only N-terminal region of
      the HrpN(Ep) protein. Two synthetic oligopeptides produced HR on tobacco
      confirming presence of two HR active domains in the HrpN(Ep). The HR
      positive N-terminal fragment (HN delta C187) was further narrowed down by
      deleting C-terminal amino acids and internal amino acids to investigate
      whether amino acid insertion region have role in faster and stronger HR
      activity in HrpN(Ep) than HrpN(Ea). The HrpN(Ep) mutant proteins HN delta
      C187 (D1AIR), HN delta C187 (D2AIR) and HN delta C187 (DM41) retained
      similar HR activation to that of wild-type HrpN(Ep). However, the HrpN(Ep)
      mutant protein HN delta C187 (D3AIR) lacking third amino acid insertion
      region (102 to 113 aa) reduced HR when compared to that of wild-type
      HrpN(Ep). Reduction in HR elicitation could not be observed when single
      amino acids at different positions were substituted at third amino acids
      insertion region. But, substitution of amino acids at L103R, L106K and
      L110R showed reduction in HR activity on tobacco suggesting their
      importance in activation of HR faster in the HrpN(Ep) although it requires
      further detailed analysis.
AU  - Shrestha R
AU  - Park DH
AU  - Cho JM
AU  - Cho S
AU  - Wilson C
AU  - Hwang I
AU  - Hur JH
AU  - Lim CK
PT  - Journal Article
TA  - Mol. Cells
JT  - Mol. Cells
SO  - Mol. Cells 2008 25: 30-42.

PMID- 28839021
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of 10 Environmental Pseudomonas aeruginosa Strains Isolated from Soils, Sediments, and Waters.
PG  - e00804-17
AB  - Pseudomonas aeruginosa is an important opportunistic pathogen that has the ability to grow in
      a range of environmental niches. Here, we report the draft
      genome sequences of 10 environmental strains of the bacterium isolated from
      soils, sediments, and waters in various locations in North America and South
      Africa.
AU  - Shrestha SD
AU  - Guttman DS
AU  - Perron GG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00804-17.

PMID- 28818887
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Escherichia coli O104 Strains of Bovine and Human Origin.
PG  - e00630-17
AB  - Cattle harbor and shed in their feces several Escherichia coli O104 serotypes. All O104
      strains examined were intimin negative and belonged to the B1
      phylogroup, and some were Shiga toxigenic. We report here the genome sequences of
      bovine O104:H7 (n = 5), O104:H23 (n = 2), O104:H8 (n = 1), and O104:H12 (n = 1)
      isolates and human clinical isolates of O104:H7 (n = 5).
AU  - Shridhar PB
AU  - Patel IR
AU  - Gangiredla J
AU  - Mammel MK
AU  - Noll L
AU  - Shi X
AU  - Bai J
AU  - Elkins CA
AU  - Strockbine N
AU  - Nagaraja TG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00630-17.

PMID- 24435872
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Sterol-Transforming Mycobacterium neoaurum Strain VKM Ac-1815D.
PG  - e01177-13
AB  - Mycobacterium neoaurum strain VKM Ac-1815D produces 4-androstene-3,17-dione as a  major
      compound from phytosterols. Here, we report the complete genome sequence of
      the strain. The genome consists of a single circular 5,438,190-bp chromosome,
      with a G+C content of 66.88%, containing 5,318 putative open reading frames
      (ORFs), 46 tRNAs, and 6 rRNAs. Arrays of cholesterol metabolism genes are
      randomly clustered throughout the chromosome.
AU  - Shtratnikova VY
AU  - Bragin EY
AU  - Dovbnya DV
AU  - Pekov YA
AU  - Schelkunov MI
AU  - Strizhov N
AU  - Ivashina TV
AU  - Ashapkin VV
AU  - Donova MV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01177-13.

PMID- 25635031
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Mycobacterium sp. Strain VKM Ac-1817D, Capable of Producing 9alpha-Hydroxy-androst-4-ene-3,17-dione from Phytosterol.
PG  - e01447-14
AB  - Mycobacterium sp. strain VKM Ac-1817D is capable of converting phytosterol into 9alpha-hydroxy
      androst-4-ene-3,17-dione (9-OH-AD), which is a valuable
      intermediate for the steroid pharmaceutical industry. Here, a complete genome
      sequence of the strain is reported. The genome consists of a single circular
      6,324,222-bp chromosome with a G+C content of 66.2% and encodes approximately
      6,000 CDSs, 54 tRNAs, and 6 rRNAs.
AU  - Shtratnikova VY
AU  - Schelkunov MI
AU  - Dovbnya DV
AU  - Pekov YA
AU  - Bragin EY
AU  - Ashapkin VV
AU  - Donova MV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01447-14.

PMID- 25573942
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Steroid-Transforming Nocardioides simplex VKM Ac-2033D.
PG  - e01406-14
AB  - Nocardioides simplex VKM Ac-2033D is an effective microbial catalyst for 3-ketosteroid
      1(2)-dehydrogenation, and it is capable of effective reduction of
      carbonyl groups at C-17 and C-20, hydrolysis of acetylated steroids, and
      utilization of natural sterols. Here, the complete genome sequence is reported.
      An array of genes related to steroid metabolic pathways have been identified.
AU  - Shtratnikova VY
AU  - Schelkunov MI
AU  - Pekov YA
AU  - Fokina VV
AU  - Logacheva MD
AU  - Sokolov SL
AU  - Bragin EY
AU  - Ashapkin VV
AU  - Donova MV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01406-14.

PMID- 21642450
VI  - 193
DP  - 2011
TI  - Genome Sequence of the Repetitive-Sequence-Rich Mycoplasma fermentans Strain M64.
PG  - 4302-4303
AB  - Mycoplasma fermentans is a microorganism commonly found in the genitourinary and respiratory
      tracts of healthy individuals and AIDS
      patients. The complete genome of the repetitive-sequence-rich M.
      fermentans strain M64 is reported here. Comparative genomics analysis
      revealed dramatic differences in genome size between this strain and the
      recently completely sequenced JER strain.
AU  - Shu HW
AU  - Liu TT
AU  - Chan HI
AU  - Liu YM
AU  - Wu KM
AU  - Shu HY
AU  - Tsai SF
AU  - Hsiao KJ
AU  - Hu WS
AU  - Ng WV
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4302-4303.

PMID- 1330319
VI  - 71
DP  - 1992
TI  - Protein introns: A new home for endonucleases.
PG  - 183-186
AB  - An underlying principle of the classical era of molecular biology--that RNA is an exact copy
      of information in one of the DNA strands--was shattered forever with the discovery of RNA
      splicing. Although at first introns could be considered an aberration of eukaryotes and their
      viruses, self-splicing RNAs were soon discovered in mitochondrial, chloroplastic, nuclear,
      bacteriophage, and bacterial genes. Additional modes of gene organization and expression
      continue to emerge with no end in sight. Over the past several years we have witnessed the
      discovery of programmed ribosomal frameshifting and hopping, trans-splicing, RNA editing, and
      cotranslational suppression of nonsense codons. The latest of these surprises is protein
      splicing: the excision of an internal segment of a polypeptide and religation of the flanking
      regions to create a functional protein. The evidence for protein splicing rests on data from
      three genes: VMA1/TFP1, which encodes a subunit of yeast vacuolar ATPase, the gene encoding
      DNA polymerase of the archaen thermophile Thermococcus litoralis (with two "introns"), and the
      recA gene of Mycobacterium tuberculosis. Although the number of examples is small, there is
      one from each of the three major phylogenetic divisions, so the phenomenon may be very widely
      distributed. Phylogenetic distance notwithstanding, these phenomena are remarkably similar:
      findings in each system have foreshadowed similar results in the others. Therefore, although
      specific citations are given, a summary of data from all three systems will be presented.
AU  - Shub DA
AU  - Goodrich-Blair H
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1992 71: 183-186.

PMID- 7817395
VI  - 19
DP  - 1994
TI  - Amino acid sequence motif of group I intron endonucleases is conserved in open reading frames of group II introns.
PG  - 402-404
AB  - Both group I and group II intron RNAs are capable of self splicing, with cleavage-ligation
      proceeding by concerted transesterification reactions. Although they tend to be localized to
      the same cellular compartments (mitochondria and chloroplasts), these two categories of
      self-splicing RNAs bear no features that would indicate a common evolutionary origin. Recent
      attempts to ascribe similarities to the intermolecular structures formed in nuclear
      spliceosomes and the intramolecular structures in group I and group II introns underscore the
      current interest in determining the evolutionary origins and interactions of these
      self-splicing intron classes.
AU  - Shub DA
AU  - Goodrich-Blair H
PT  - Journal Article
TA  - Trends Biochem. Sci.
JT  - Trends Biochem. Sci.
SO  - Trends Biochem. Sci. 1994 19: 402-404.

PMID- 3422485
VI  - 85
DP  - 1988
TI  - Structural conservation among three homologous introns of bacteriophage T4 and the group I introns of eukaryotes.
PG  - 1151-1155
AB  - Three group I introns of bacteriophage T4 have been compared with respect to their sequence
      and structural properties. The introns include the td intervening sequence, as well as the two
      newly described introns in the nrdB and sunY genes of T4. The T4 introns are very closely
      related, containing phylogenetically conserved sequence elements that allow them to be folded
      into a core structure that is characteristic of eukaryotic group IA introns. Similarities
      extend outward to the exon sequences surrounding the three introns. All three introns contain
      open reading frames (ORFs). Although the intron ORFs are not homologous and occur at different
      positions, all three ORFs are looped-out of the structure models, with only the 3' ends of
      each of the ORFs extending into the secondary structure. This arrangement invites interesting
      speculations on the regulation of splicing by translation. The high degree of similarity
      between the T4 introns and the eukaryotic group I introns must reflect a common ancestry,
      resulting either from vertical acquisition of a primordial RNA element or from horizontal
      transfer.
AU  - Shub DA
AU  - Gott JM
AU  - Xu MQ
AU  - Lang BF
AU  - Michel F
AU  - Tomashewski J
AU  - Pedersen-Lane J
AU  - Belfort M
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1988 85: 1151-1155.

PMID- 2841063
VI  - 52
DP  - 1987
TI  - A family of autocatalytic group I introns in bacteriophage T4.
PG  - 193-200
AB  - The first intron to be discovered in a prokaryotic mRNA was found in the td gene of
      bacteriophage T4.  The presence of an intron in this gene, which encodes thymidylate synthase,
      was detected by sequence comparisons at the DNA and protein levels.  Thus, a stop codon was
      encountered in the DNA sequence before the end of the protein-coding sequence.  Subsequent
      experimentation revealed that the intron in the td gene was excised autocatalytically from
      precursor RNA.  The splicing mechanism resembled that used by group I introns of eukaryotes: a
      series of transesterification reactions triggered by nucleophilic attack by guanosine (or GTP)
      at the 5' splice site.  The primary intron excision product was linear, containing a noncoded
      G at the 5' end.  Although the discovery of an intron in phage T4 was entirely unexpected, it
      encouraged us (in collaboration with M. Belfort) to look for additional group I introns in the
      T4 genome.  Further examples would permit sequence and structural comparisons that might lend
      insight into their evolutionary origin.  Additionally, we hoped that their locations within
      the T4 genome would infer a possible regulatory function in prokaryotic gene expression.  We
      took advantage of the fact that, since G is added to the 5' end of the intron, autocatalytic
      group I introns could be specifically labeled in vitro for use as probes for DNA blotting
      experiments.  If group I introns were in more than just the td gene, multiple RNA species
      would be labeled when total RNA is extracted from T4-infected cells and incubated with
      [a-32P]GTP in vitro.  When used as a probe for a Southern blot of T4 DNA, this RNA should
      hybridize to several DNA bands.
AU  - Shub DA
AU  - Xu M-Q
AU  - Gott JM
AU  - Zeeh A
AU  - Wilson LD
PT  - Journal Article
TA  - Cold Spring Harb. Symp. Quant. Biol.
JT  - Cold Spring Harb. Symp. Quant. Biol.
SO  - Cold Spring Harb. Symp. Quant. Biol. 1987 52: 193-200.

PMID- 1870977
VI  - 19
DP  - 1991
TI  - Purification of BsuE methyltransferase and its application in genome mapping.
PG  - 4233-4239
AB  - We have used a combination of BsuE methyltransferase (M.BsuEII) and NotI
      restriction enzyme to cut genomic DNA at a subset of NotI sites.  The
      usefulness of this system is shown in a re-examination of the restriction map
      of the human MHC.  Combinations of methylases and restriction enzymes can be
      used to generate cuts at different frequencies in genomic DNA, such that they
      generate ends complementary to NotI ends, and can be used in conjunction with
      NotI linking clones in chromosome jumping experiments.  These enzyme
      combinations have the potential to produce cutting sites in genomic DNA spaced
      at intervals favorable for extensive mapping, fragment enrichment, and cloning
      efforts.
AU  - Shukla H
AU  - Kobayashi Y
AU  - Arenstorf H
AU  - Yasukochi Y
AU  - Weissman SM
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 4233-4239.

PMID- 4610408
VI  - 252
DP  - 1974
TI  - Model for wandering restriction enzymes.
PG  - 76-78
AB  - None
AU  - Shulman MJ
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1974 252: 76-78.

PMID- 26337885
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Rhodococcus ruber Strain P25, an Active Polychlorinated  Biphenyl Degrader.
PG  - e00990-15
AB  - We report the 5,728,255-bp draft genome sequence of Rhodococcus ruber P25, isolated from a
      soil polluted with halogenated aromatic compounds in the city of  Perm, Russia. The strain
      degrades polychlorinated biphenyls and a broad range of  aromatic compounds. It possesses
      genes that mediate the degradation of biphenyls/polychlorinated biphenyls, naphthalene, and
      monoaromatic compounds.
AU  - Shumkova ES
AU  - Olsson BE
AU  - Kudryavtseva AV
AU  - Plotnikova EG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00990-15.

PMID- 25953188
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Mycobacterium tuberculosis Strain E186hv of Beijing B0/W Lineage with Reduced Virulence.
PG  - e00403-15
AB  - We report a draft genome sequence of Mycobacterium tuberculosis strain E186hv, belonging to
      the Beijing B0/W lineage and isolated from a patient from Kurgan,
      Russia. This clinical isolate showed a reduced virulence phenotype unusual for
      this lineage and resistance to isoniazid, rifampin, ethambutol, pyrazinamide, and
      ofloxacin. We analyzed single nucleotide polymorphisms (SNPs) associated with
      virulence.
AU  - Shur KV
AU  - Klimina KM
AU  - Zakharevich NV
AU  - Maslov DA
AU  - Bekker OB
AU  - Zaychikova MV
AU  - Kamaev EY
AU  - Kravchenko MA
AU  - Skornyakov SN
AU  - Zhang Y
AU  - Danilenko VN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00403-15.

PMID- 25908133
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequences of Eight Campylobacter jejuni Isolates from Wild Birds.
PG  - e00315-15
AB  - We present here the draft genome sequences of 8 Campylobacter jejuni strains isolated from
      wild birds. The strains were initially isolated from swabs taken
      from resident wild birds in the Tokachi area of Japan. The genome sizes range
      from 1.65 to 1.77 Mbp.
AU  - Shyaka A
AU  - Kusumoto A
AU  - Asakura H
AU  - Kawamoto K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00315-15.

PMID- 14744977
VI  - 32
DP  - 2004
TI  - Cassette-like variation of restriction enzyme genes in Escherichia coli C and relatives.
PG  - 522-534
AB  - A surprising result of comparative bacterial genomics has been the large amount of DNA found
      to be present in one strain but not in another of the same species. We examine in detail one
      location where gene content varies extensively, the restriction cluster in Escherichia coli.
      This region is designated the Immigration Control Region (ICR) for the density and variability
      of restriction functions found there. To better define the boundaries of this variable locus,
      we determined the sequence of the region from a restrictionless strain, E.coli C. Here we
      compare the 13.7 kb E.coli C sequence spanning the site of the ICR with corresponding
      sequences from five E.coli strains and Salmonella typhimurium LT2. To discuss this variation,
      we adopt the term 'framework' to refer to genes that are stable components of genomes within
      related lineages, while 'migratory' genes are transient inhabitants of the genome.
      Strikingly, seven different migratory DNA segments, encoding different sets of genes and gene
      fragments, alternatively occupy a single well-defined location in the seven strains examined.
      The flanking framework genes, yjiS and yjiA, display approximately normal patterns of
      conservation. The patterns observed are consistent with the action of a site-specific
      recombinase. Since no nearby gene codes for a likely recombinase of known families, such a
      recombinase must be of a new family or unlinked.
AU  - Sibley MH
AU  - Raleigh EA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2004 32: 522-534.

PMID- 29192078
VI  - 5
DP  - 2017
TI  - Genome Sequence of Bacillus velezensis S141, a New Strain of Plant Growth-Promoting Rhizobacterium Isolated from Soybean Rhizosphere.
PG  - e01312-17
AB  - Bacillus velezensis strain S141 is a plant growth-promoting rhizobacterium
      isolated from soybean (Glycine max) rhizosphere that enhances soybean growth,
      nodulation, and N2 fixation efficiency by coinoculation with Bradyrhizobium
      diazoefficiens USDA110. The S141 genome was identified to comprise a
      3,974,582-bp-long circular DNA sequence encoding at least 3,817 proteins.
AU  - Sibponkrung S
AU  - Kondo T
AU  - Tanaka K
AU  - Tittabutr P
AU  - Boonkerd N
AU  - Teaumroong N
AU  - Yoshida KI
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01312-17.

PMID- 28183751
VI  - 5
DP  - 2017
TI  - Genome Sequences of Human and Livestock Isolates of Brucella melitensis and Brucella abortus from the Country of Georgia.
PG  - e01518-16
AB  - Brucellosis, which is among the most widespread global zoonotic diseases, is endemic in the
      nation of Georgia and causes substantial human morbidity and
      economic loss. Here, we report whole-genome sequences of three Brucella
      melitensis and seven Brucella abortus isolates from cattle, sheep, and humans
      that represent genetic groups discovered in Georgia.
AU  - Sidamonidze K
AU  - Hang J
AU  - Yang Y
AU  - Dzavashvili G
AU  - Zhgenti E
AU  - Trapaidze N
AU  - Imnadze P
AU  - Nikolich MP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01518-16.

PMID- 22768368
VI  - 6
DP  - 2012
TI  - Complete genome sequence of Dehalogenimonas lykanthroporepellens type strain (BL-DC-9(T)) and comparison to 'Dehalococcoides' strains.
PG  - 251-264
AB  - Dehalogenimonas lykanthroporepellens is the type species of the genus Dehalogenimonas, which
      belongs to a deeply branching lineage within the phylum
      Chloroflexi. This strictly anaerobic, mesophilic, non spore-forming,
      Gram-negative staining bacterium was first isolated from chlorinated solvent
      contaminated groundwater at a Superfund site located near Baton Rouge, Louisiana,
      USA. D. lykanthroporepellens was of interest for genome sequencing for two
      reasons: (a) an unusual ability to couple growth with reductive dechlorination of
      environmentally important polychlorinated aliphatic alkanes and (b) a
      phylogenetic position that is distant from previously sequenced bacteria. The
      1,686,510 bp circular chromosome of strain BL-DC-9(T) contains 1,720 predicted
      protein coding genes, 47 tRNA genes, a single large subunit rRNA (23S-5S) locus,
      and a single, orphan, small subunit rRNA (16S) locus.
AU  - Siddaramappa S et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 6: 251-264.

PMID- 21914898
VI  - 193
DP  - 2011
TI  - Genome of a Novel Isolate of Paracoccus denitrificans Capable of Degrading N,N-Dimethylformamide.
PG  - 5598-5599
AB  - The bacterial genus Paracoccus is comprised of metabolically versatile organisms having
      diverse degradative capabilities and potential industrial
      and environmental applications for bioremediation in particular. We report
      a de novo-assembled sequence and annotation of the genome of a novel
      isolate of Paracoccus denitrificans originally sourced from coal mine
      tailings in India. The isolate was capable of utilizing
      N,N-dimethylformamide (DMF) as a source of carbon and nitrogen and
      therefore holds potential for bioremediation and mineralization of
      industrial pollutants. The genome sequence and biological circuitry
      revealed thereupon will be invaluable in understanding the metabolic
      capabilities, functioning, and evolution of this important bacterial
      organism.
AU  - Siddavattam D
AU  - Karegoudar TB
AU  - Mudde SK
AU  - Kumar N
AU  - Baddam R
AU  - Avasthi TS
AU  - Ahmed N
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5598-5599.

PMID- 28572322
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Escherichia coli Strain M8, Isolated from ob/ob Mice.
PG  - e00449-17
AB  - Escherichia coli is one of the common inhabitants of the mammalian gastrointestinal track. We
      isolated a strain from an ob/ob mouse and performed
      whole-genome sequencing, which yielded a chromosome of ~5.1 Mb and three plasmids
      of ~160 kb, ~6 kb, and ~4 kb.
AU  - Siddharth J
AU  - Membrez M
AU  - Chakrabarti A
AU  - Betrisey B
AU  - Chou CJ
AU  - Parkinson SJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00449-17.

PMID- 21481189
VI  - 278
DP  - 2011
TI  - Auto-methylation of the mouse DNA-(cytosine C5)-methyltransferase Dnmt3a at its active site cysteine residue.
PG  - 2055-2063
AB  - The Dnmt3a DNA methyltransferase is responsible for establishing DNA methylation patterns
      during mammalian development. We show here that
      the mouse Dnmt3a DNA methyltransferase is able to transfer the methyl
      group from S-adenosyl-L-methionine (AdoMet) to a cysteine residue in
      its catalytic center. This reaction is irreversible and relatively
      slow. The yield of auto-methylation is increased by addition of Dnmt3L,
      which functions as a stimulator of Dnmt3a and enhances its AdoMet
      binding. Auto-methylation was observed in binary Dnmt3a AdoMet
      complexes. In the presence of CpG containing dsDNA, which is the
      natural substrate for Dnmt3a, the transfer of the methyl group from
      AdoMet to the flipped target base was preferred and auto-methylation
      was not detected. Therefore, this reaction might constitute a
      regulatory mechanism which could inactivate unused DNA
      methyltransferases in the cell, or it could simply be an aberrant side
      reaction caused by the high methyl group transfer potential of AdoMet.
AU  - Siddique A
AU  - Jurkowska RZ
AU  - Jurkowski TP
AU  - Jeltsch A
PT  - Journal Article
TA  - FEBS J.
JT  - FEBS J.
SO  - FEBS J. 2011 278: 2055-2063.

PMID- 26494669
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Enteropathogenic Bacterium Campylobacter jejuni Strain cj255.
PG  - e01223-15
AB  - The enteropathogen Campylobacter jejuni is a global health disaster, being one of the leading
      causes of bacterial gastroenteritis. Here, we present the draft genome sequence of C. jejuni
      strain cj255, isolated from a chicken source in Islamabad, Pakistan. The draft genome sequence
      will aid in epidemiological studies and quarantine of this broad-host-range pathogen.
AU  - Siddiqui FM
AU  - Ibrahim M
AU  - Noureen N
AU  - Noreen Z
AU  - Titball RW
AU  - Champion OL
AU  - Wren BW
AU  - Studholme D
AU  - Bokhari H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01223-15.

PMID- 25291768
VI  - 2
DP  - 2014
TI  - Genome Sequence of Porphyromonas gingivalis Strain HG66 (DSM 28984).
PG  - e00947-14
AB  - Porphyromonas gingivalis is considered a major etiologic agent in adult periodontitis.
      Gingipains are among its most important virulence factors, but
      their release is unique in strain HG66. We present the genome sequence of HG66
      with a single contig of 2,441,680 bp and a G+C content of 48.1%.
AU  - Siddiqui H
AU  - Yoder-Himes DR
AU  - Mizgalska D
AU  - Nguyen KA
AU  - Potempa J
AU  - Olsen I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00947-14.

PMID- 24903880
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Geobacillus thermopakistaniensis Strain MAS1.
PG  - e00559-14
AB  - Geobacillus thermopakistaniensis strain MAS1 was isolated from a hot spring located in the
      Northern Areas of Pakistan. The draft genome sequence was 3.5 Mb
      and identified a number of genes of potential industrial importance, including
      genes encoding glycoside hydrolases, pullulanase, amylopullulanase, glycosidase,
      and alcohol dehydrogenases.
AU  - Siddiqui MA
AU  - Rashid N
AU  - Ayyampalayam S
AU  - Whitman WB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00559-14.

PMID- 26430027
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Burkholderia pseudomallei and Staphylococcus aureus, Isolated from a Patient with Chronic Rhinosinusitis.
PG  - e01075-15
AB  - Here, we report the draft genome sequences of Burkholderia pseudomallei and Staphylococcus
      aureus causing chronic rhinosinusitis. Whole-genome sequencing determined the B. pseudomallei
      as sequence type (ST) 1381 and the S. aureus as ST8. B. pseudomallei possessed the blaOXA-59
      gene. This study illustrates the potential emergence of B. pseudomallei in cases of chronic
      rhinosinusitis.
AU  - Sidjabat HE
AU  - Cottrell K
AU  - Cervin A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01075-15.

PMID- 26769934
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the Oral Commensal Streptococcus oralis 89a with Interference Activity against Respiratory Pathogens.
PG  - e01546-15
AB  - We report the draft genome sequence of the oral commensal Streptococcus oralis 89a isolated
      from the throat of a healthy child during a streptococcal
      tonsillitis outbreak in Umea, Sweden. S. oralis 89a was known to have
      interference activity against respiratory pathogens in which the colicin V was
      the potential bacteriocin-encoding gene.
AU  - Sidjabat HE
AU  - Grahn HE
AU  - Cervin A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01546-15.

PMID- 26316639
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Two IMP-4-Producing Escherichia coli Sequence Type 131  Isolates in Australia.
PG  - e00983-15
AB  - We report the draft genome sequences of two unrelated cases of Escherichia coli sequence type
      131 (ST131) possessing the carbapenemase gene blaIMP-4. The E. coli ST131 SN5 isolate also
      possessed blaSHV-12 and plasmid-mediated quinolone-resistance genes. Wider dissemination of
      blaIMP-4 may occur due to the  blaIMP-4-carrying L/M or HI2 plasmids among E. coli ST131
      isolates.
AU  - Sidjabat HE
AU  - Robson J
AU  - Paterson DL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00983-15.

PMID- 
VI  - 26
DP  - 2009
TI  - Specific versus Nonspecific DNA Binding of the Restriction Endonuclease EcoRV Measured by Self-Cleavage Assay.
PG  - 896-897
AB  - 
AU  - Sidorova N
AU  - Muradymov S
AU  - Rau DC
PT  - Journal Article
TA  - J. Biomol. Struct. Dyn.
JT  - J. Biomol. Struct. Dyn.
SO  - J. Biomol. Struct. Dyn. 2009 26: 896-897.

PMID- 
VI  - 14
DP  - 2004
TI  - The role of water in the EcoRI-DNA binding.
PG  - 319-337
AB  - In many respects, Type II restriction endonucleases are prototypical DNA-binding proteins.  In
      order to avoid catastrophic consequences for the cell, however, these enzymes must be far more
      stringent in recognition of their target sequences and subsequent DNA cleavage than other
      specific sequence recognition proteins that regulate gene activity.  In contrast to E. coli
      Lac and lambda Cro repressors, for example, that show gradually decreasing binding energies as
      the recognition sequence is changed, many restriction nucleases are exquisitely specific.
      EcoRI will bind to its recognition sequence, GAATTC, with an association equilibrium constant
      Ka,sp ~10^11 M-1 and to a completely nonspecific sequence with Ka,nonsp ~10^7 M-1.  A change
      of even a single base pair is sufficient to decrease the binding constant at least by 10^3,
      bringing it within a factor ~10 or less of nonspecific binding.
AU  - Sidorova N
AU  - Rau DC
PT  - Journal Article
TA  - Nucleic Acids Mol. Biol.
JT  - Nucleic Acids Mol. Biol.
SO  - Nucleic Acids Mol. Biol. 2004 14: 319-337.

PMID- 
VI  - 272
DP  - 2005
TI  - A novel self-cleavage assay for measuring DNA binding of restriction endonucleases.
PG  - 565
AB  - DNA-protein interactions can be analyzed by methods based on physical separation of complexes
      from free DNA fragments (gel mobility shift and filter binding assays) or by techniques
      probing DNA-protein equilibrium directly in a solution (e.g. fluorescence and calorimetry).
      These later techniques require larger amounts of materials and do not provide enough
      sensitivity for measuring equilibrium association constants in the range 10^9-10^12 M-1. Both
      gel mobility shift and filter binding assays that can measure these large binding constants,
      however, have been criticized for the danger of disrupting equilibrium by physically
      separating DNA-protein complexes from free species. We have developed a novel self-cleavage or
      self-footprinting assay that uses the nuclease activity of restriction endonucleases to
      measure sensitively their specific binding to DNA. At sufficiently high concentrations of
      neutral osmolytes cleavage reaction can be triggered at only those DNA fragments with bound
      enzyme. Under these conditions the fraction of specific DNA fragment cleaved reliably reflects
      the fraction of DNA initially bound to the enzyme. The self-cleavage assay allows measurement
      of binding equilibrium and kinetics directly in solution avoiding the intrinsic problems of
      gel mobility shift and filter binding assays while providing the same sensitivity level. We
      compare here the self-cleavage and gel mobility shift assays applied to the dissociation
      kinetics and binding equilibrium of two restriction endonucleases, EcoRI and BamHI. The
      technique can be used, in principle, for any protein possessing DNA cleavage activity if its
      interactions with DNA are sensitive to osmotic stress.
AU  - Sidorova NY
AU  - Muradymov S
AU  - Rau DC
PT  - Journal Article
TA  - FEBS J.
JT  - FEBS J.
SO  - FEBS J. 2005 272: 565.

PMID- 17008319
VI  - 281
DP  - 2006
TI  - Differences in hydration coupled to specific and nonspecific competitive binding and to specific DNA binding of the restriction endonuclease BamHI.
PG  - 35656-35666
AB  - Using the osmotic stress technique together with a self-cleavage assay we measure directly
      differences in sequestered water between specific
      and nonspecific DNA-BamHI complexes as well as the numbers of water
      molecules released coupled to specific complex formation. The
      difference between specific and nonspecific binding free energy of the
      BamHI scales linearly with solute osmolal concentration for seven
      neutral solutes used to set water activity. The observed osmotic
      dependence indicates that the nonspecific DNA-BamHI complex sequesters
      some 120-150 more water molecules than the specific complex. The weak
      sensitivity of the difference in number of waters to the solute
      identity suggests that these waters are sterically inaccessible to
      solutes. This result is in close agreement with differences in the
      structures determined by x-ray crystallography. We demonstrate
      additionally that when the same solutes that were used in competition
      experiments are used to probe changes accompanying the binding of free
      BamHI to its specific DNA sequence, the measured number of water
      molecules released in the binding process is strikingly
      solute-dependent ( with up to 10-fold difference between solutes). This
      result is expected for reactions resulting in a large change in a
      surface exposed.
AU  - Sidorova NY
AU  - Muradymov S
AU  - Rau DC
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2006 281: 35656-35666.

PMID- 21624054
VI  - 278
DP  - 2011
TI  - Solution parameters modulating DNA binding specificity of the restriction endonuclease EcoRV.
PG  - 2713-2727
AB  - The DNA binding stringency of restriction endonucleases is crucial for their proper function.
      The X-ray structures of the specific and
      non-cognate complexes of the restriction nuclease EcoRV are
      considerably different suggesting significant differences in the
      hydration and binding free energies. Nonetheless, the majority of
      studies performed at pH 7.5, optimal for enzymatic activity, have found
      a < 10-fold difference between EcoRV binding constants to the specific
      and nonspecific sequences in the absence of divalent ions. We used a
      recently developed self-cleavage assay to measure EcoRV-DNA competitive
      binding and to evaluate the influence of water activity, pH and salt
      concentration on the binding stringency of the enzyme in the absence of
      divalent ions. We find the enzyme can readily distinguish specific and
      nonspecific sequences. The relative specific-nonspecific binding
      constant increases strongly with increasing neutral solute
      concentration and with decreasing pH. The difference in number of
      associated waters between specific and nonspecific DNA-EcoRV complexes
      is consistent with the differences in the crystal structures. Despite
      the large pH dependence of the sequence specificity, the osmotic
      pressure dependence indicates little change in structure with pH. The
      large osmotic pressure dependence means that measurement of protein-DNA
      specificity in dilute solution cannot be directly applied to binding in
      the crowded environment of the cell. In addition to divalent ions,
      water activity and pH are key parameters that strongly modulate binding
      specificity of EcoRV.
AU  - Sidorova NY
AU  - Muradymov S
AU  - Rau DC
PT  - Journal Article
TA  - FEBS J.
JT  - FEBS J.
SO  - FEBS J. 2011 278: 2713-2727.

PMID- 
VI  - 100
DP  - 2011
TI  - Unusual DNA-Binding Kinetics of the Restriction Endonuclease EcoRV.
PG  - 72
AB  - We have applied a self-cleavage assay, developed previously by us, to measure
      EcoRV-DNA binding in solution. Self-cleavage assay monitors only enzymatically
      competent complexes of the endonuclease. This technique does not have
      the limitations of more commonly used gel mobility shift assay while providing
      the same level of sensitivity.Wefound that the EcoRV has quite unusual kinetics
      of specific complex formation in the absence of divalent ions that was not reported
      previously. A significant fraction of the total enzyme, ~ 45%, forms enzymatically
      competent complexes unusually slowly, especially at pH 7.6. This
      novel result can be explained by a very slow transition between two conformations
      of the free enzyme in solution. The equilibrium distribution of the slowly
      and quickly associating protein structures and their exchange kinetics may depend
      on many parameters including pH, salt, osmolytes, and divalent cations.
      The observation of at least two kinetics components in association indicates
      that EcoRV is an allosteric protein with at least two conformations. Allosterism
      is now recognized as important concept for DNA-protein complexes, offering an
      additional level of control over binding and activity. We are continuing our investigation
      into the EcoRV structures responsible for the different kinetic classes
      of association.
AU  - Sidorova NY
AU  - Muradymov SR
AU  - Royal RM
AU  - Rau DC
PT  - Journal Article
TA  - Biophys. J.
JT  - Biophys. J.
SO  - Biophys. J. 2011 100: 72.

PMID- 
VI  - 78
DP  - 2000
TI  - Self-footprint of the restriction endonuclease EcoRI.
PG  - 299A
AB  - The dissociation rate of the EcoRI-DNA specific complex is strongly linked to water activity.
      In the presence of osmolytes (betaine, sucrose, methyl glucoside, t-butanol, etc.) stability
      of the specific EcoRI-DNA complex increases dramatically.  Osmotic stress technique offers a
      practical way of manipulating dissociation rates controllably and to measure complex
      properties on an experimentally convenient time scale.  It has been shown recently that
      osmotic stress also slows down cleavage reaction of the EcoRI at its specific sequence.  We
      believe this effect is at least partly due to the slowing of the EcoRI dissociation from the
      product of the cleavage reaction.  Using osmotic stress technique we have developed a method
      for using the nuclease activity of EcoRI to measure sensitively its specific binding.  We show
      using gel shift assay that only those sites on DNA initially occupied by protein immediately
      prior to adding Mg2+ are apparently cleaved.  The level of specific DNA fragment cleavage
      remains constant for as long as 40 min.  This self-footprint assay allows measurement of EcoRI
      binding equilibrium and kinetics avoiding intrinsic gel-shift and filter-binding assay
      problems.  There is the possibility of using such a technique for any protein possessing DNA
      cleavage activity given that its interactions with DNA are sensitive to osmotic stress.
AU  - Sidorova NY
AU  - Rau DC
PT  - Journal Article
TA  - Biophys. J.
JT  - Biophys. J.
SO  - Biophys. J. 2000 78: 299A.

PMID- 11453689
VI  - 310
DP  - 2001
TI  - Linkage of EcoRI dissociation from its specific DNA recognition site to water activity, salt concentration, and pH: separating their roles in specific and non-specific binding.
PG  - 801-816
AB  - We have measured the dependencies of both the dissociation rate of specifically bound EcoRI
      endonuclease and the ratio of non-specific and specific association constants on water
      activity, salt concentration, and pH in order to distinguish the contributions of these
      solution components to specific and non-specific binding. For proteins such as EcoRI that
      locate their specific recognition site efficiently by diffusing along non-specific DNA, the
      specific site dissociation rate can be separated into two steps: an equilibrium between
      non-specific and specific binding of the enzyme to DNA, and the dissociation of
      non-specifically bound protein. We demonstrated previously that the osmotic dependence of the
      dissociation rate is dominated by the equilibrium between specific and non-specific binding
      that is independent of the osmolyte nature. The remaining osmotic sensitivity linked to the
      dissociation of non-specifically bound protein depends significantly on the particular
      osmolyte used, indicating a change in solute-accessible surface area. In contrast, the
      dissociation of non-specifically bound enzyme accounts for almost all the pH and
      salt-dependencies. We observed virtually no pH-dependence of the equilibrium between specific
      and non-specific binding measured by the competition assay. The observed weak salt-sensitivity
      of the ratio of specific and non-specific association constants is consistent with an osmotic,
      rather than electrostatic, action. The seeming lack of a dependence on viscosity suggests the
      rate-limiting step in dissociation of non-specifically bound protein is a discrete
      conformational change rather than a general diffusion of the protein away from the DNA.
AU  - Sidorova NY
AU  - Rau DC
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2001 310: 801-816.

PMID- 8901570
VI  - 93
DP  - 1996
TI  - Differences in water release for the binding of EcoRI to specific and nonspecific DNA sequences.
PG  - 12272-12277
AB  - The free energy difference between complexes of the restriction nuclease EcoRI with
      nonspecific DNA and with the enzyme's recognition sequence is linearly dependent on the water
      chemical potential of the solution, set using several very different solutes, ranging from
      glycine and glycerol to triethylene glycol and sucrose.  This osmotic dependence indicates
      that the nonspecific complex sequesters some 110 waters more than the specific complex with
      the recognition sequence.  The insensitivity of the difference in number of waters released to
      the solute identity further indicates that this water is sequestered in a space that is
      sterically inaccessible to solutes, most likely at the protein-DNA interface of the
      nonspecific complex.  Calculations based on the structure of the specific complex suggest that
      the apposing DNA and protein surfaces in the nonspecific complex retain approximately a full
      hydration layer of water.
AU  - Sidorova NY
AU  - Rau DC
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1996 93: 12272-12277.

PMID- 10496418
VI  - 17
DP  - 1999
TI  - Removing water from an EcoRI-noncognate DNA complex with osmotic stress.
PG  - 19-31
AB  - We recently showed that a nonspecific complex of the restriction nuclease EcoRI with poly
      (dI-dC) sequesters significantly more water at the protein-DNA interface than the complex with
      the specific recognition sequence. The nonspecific complex seems to retain almost a full
      hydration layer at the interface. We now find that at low osmotic pressures a complex of the
      restriction nuclease EcoRI with a DNA sequence that differs by only one base pair from the
      recognition site (a 'star' sequence) sequesters about 70 waters more than the specific one,
      a value virtually indistinguishable from nonspecific DNA. Unlike complexes with oligo (dI-dC)
      or with a sequence that differs by two base pairs from the recognition sequence, however, much
      of the water in the 'star' sequence complex is removed at high osmotic pressures. The energy
      of removing this water can be calculated simply from the osmotic pressure work done on the
      complex. The ability to measure not only the changes in water sequestered by DNA-protein
      complexes for different sequences, but also the work necessary to remove this water is a
      potentially powerful new tool for coupling inferred structural changes and thermodynamics.
AU  - Sidorova NY
AU  - Rau DC
PT  - Journal Article
TA  - J. Biomol. Struct. Dyn.
JT  - J. Biomol. Struct. Dyn.
SO  - J. Biomol. Struct. Dyn. 1999 17: 19-31.

PMID- 10738198
VI  - 53
DP  - 2000
TI  - The dissociation rate of the EcoRI-DNA-specific complex is linked to water activity.
PG  - 363-368
AB  - In many respects, the dissociation rate constant of a DNA-protein or protein-protein complex
      is as important a physical parameter as the equilibrium constant.  The regulation of most
      cellular activities and developmental control are dynamic rather than static processes.  With
      many techniques, the successful physiochemical characterization of a complex depends
      ciritically on the lifetime of the complex during isolation or measurement.  With present
      technologies, the very powerful, single molecule methods used for mapping the kinetic barriers
      of complex dissociation reactions require lifetimes on the order of minutes.  We report here
      that the dissociation rate of the specific complex between the restriction nuclease EcoRI and
      its recognition DNA sequence is strongly dependent on water activity (in addition to its known
      dependence on salt activity).  This observation means that the dissociation rate of complexes
      in the crowded conditions found within cells cannot be straightforwardly predicted from dilute
      solution measurements, even though salt, temperature, and pH conditions are fixed to those
      found in vivo.  In addition, these results suggest a practical method to extend the lifetime
      of "weak" complexes sufficiently to perform biophysical and biochemical characterizations.
AU  - Sidorova NY
AU  - Rau DC
PT  - Journal Article
TA  - Biopolymers
JT  - Biopolymers
SO  - Biopolymers 2000 53: 363-368.

PMID- 22003381
VI  - 6
DP  - 2011
TI  - The Complete Genome Sequence of Thermoproteus tenax: A Physiologically Versatile Member of the Crenarchaeota.
PG  - E24222
AB  - Here, we report on the complete genome sequence of the hyperthermophilic
      Crenarchaeum Thermoproteus tenax (strain Kra1, DSM 2078(T)) a type strain
      of the crenarchaeotal order Thermoproteales. Its circular 1.84-megabase
      genome harbors no extrachromosomal elements and 2,051 open reading frames
      are identified, covering 90.6% of the complete sequence, which represents
      a high coding density. Derived from the gene content, T. tenax is a
      representative member of the Crenarchaeota. The organism is strictly
      anaerobic and sulfur-dependent with optimal growth at 86 degrees C and pH
      5.6. One particular feature is the great metabolic versatility, which is
      not accompanied by a distinct increase of genome size or information
      density as compared to other Crenarchaeota. T. tenax is able to grow
      chemolithoautotrophically (CO/H) as well as chemoorganoheterotrophically
      in presence of various organic substrates. All pathways for synthesizing
      the 20 proteinogenic amino acids are present. In addition, two presumably
      complete gene sets for NADH:quinone oxidoreductase (complex I) were
      identified in the genome and there is evidence that either NADH or reduced
      ferredoxin might serve as electron donor. Beside the typical archaeal
      AA-ATP synthase, a membrane-bound pyrophosphatase is found, which might
      contribute to energy conservation. Surprisingly, all genes required for
      dissimilatory sulfate reduction are present, which is confirmed by growth
      experiments. Mentionable is furthermore, the presence of two proteins
      (ParA family ATPase, actin-like protein) that might be involved in cell
      division in Thermoproteales, where the ESCRT system is absent, and of
      genes involved in genetic competence (DprA, ComF) that is so far unique
      within Archaea.
AU  - Siebers B
AU  - Zaparty M
AU  - Raddatz G
AU  - Tjaden B
AU  - Albers SV
AU  - Bell SD
AU  - Blombach F
AU  - Kletzin A
AU  - Kyrpides N
AU  - Lanz C
AU  - Plagens A
AU  - Rampp M
AU  - Rosinus A
AU  - von Jan M
AU  - Makarova KS
AU  - Klenk HP
AU  - Schuster SC
AU  - Hensel R
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2011 6: E24222.

PMID- 12804601
VI  - 306
DP  - 2003
TI  - Establishment and functional validation of a structural homology model for human DNA methyltransferase 1.
PG  - 558-563
AB  - Changes in DNA methylation patterns play an important role in tumorigenesis. The DNA
      methyltransferase 1 (DNMT1) protein represents a
      major DNA methyltransferase activity in human cells and is therefore a
      prominent target for experimental cancer therapies. However, there are
      only few available inhibitors and their high toxicity and low specificity
      have so far precluded their broad use in chemotherapy. Based on the strong
      conservation of catalytic DNA methyltransferase domains we have used a
      homology modeling approach to determine the three-dimensional structure of
      the DNMT1 catalytic domain. Our results suggest an overall structural
      conservation with other DNA methyltransferases but also indicate local
      conformational differences. To prove the validity of our model we used it
      as a template to design a novel derivative of the known DNA
      methyltransferase inhibitor 5-azacytidine. The resulting compound
      (N4-fluoroacetyl-5-azacytidine) functioned as an efficient inhibitor of
      DNA methylation in human tumor cell lines and also provides novel
      opportunities for pharmacological applications.
AU  - Siedlecki P
AU  - Boy RG
AU  - Comagic S
AU  - Schirrmacher R
AU  - Wiessler M
AU  - Zielenkiewicz P
AU  - Suhai S
AU  - Lyko F
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 2003 306: 558-563.

PMID- 16420053
VI  - 49
DP  - 2006
TI  - Discovery of two novel, small-molecule inhibitors of DNA methylation.
PG  - 678-683
AB  - DNA methyltransferases are promising targets for cancer therapy. In many cancer cells
      promoters of tumor suppressor genes are hypermethylated,
      which results in gene inactivation. It has been shown that DNA
      methyltransferase inhibitors can suppress tumor growth and have
      significant therapeutic value. However, the established inhibitors are
      limited in their application due to their substantial cytotoxicity. To
      discover novel compounds for the inhibition of human DNA
      methyltransferases, we have screened a set of small molecules available
      from the NCI database. Using a 3-dimensional model of the human DNA
      methyltransferase 1 and a modified docking and scoring procedure, we have
      identified a small list of molecules with high affinities for the active
      site of the enzyme. The two highest scoring structures were found to
      inhibit DNA methyltransferase activity in vitro and in vivo. The newly
      discovered inhibitors validate our screening procedure and also provide a
      useful basis for further rational drug development.
AU  - Siedlecki P
AU  - Boy RG
AU  - Musch T
AU  - Brueckner B
AU  - Suhai S
AU  - Lyko F
AU  - Zielenkiewicz P
PT  - Journal Article
TA  - J. Med. Chem.
JT  - J. Med. Chem.
SO  - J. Med. Chem. 2006 49: 678-683.

PMID- 20473607
VI  - 87
DP  - 2010
TI  - I-SceI endonuclease: a new tool for DNA repair studies and genetic manipulations in streptomycetes.
PG  - 1525-1532
AB  - Actinomycetes are Gram-positive bacteria with a complex life cycle. They
      produce many pharmaceutically relevant secondary metabolites, including
      antibiotics and anticancer drugs. However, there is a limited number of
      biotechnological applications available as opposed to genetic model
      organisms like Bacillus subtilis or Escherichia coli. We report here a
      system for the functional expression of a synthetic gene encoding the
      I-SceI homing endonuclease in several streptomycetes. Using the synthetic
      sce(a) gene, we were able to create controlled genomic DNA double-strand
      breaks. A mutagenesis system, based on the homing endonuclease I-SceI, has
      been developed to construct targeted, non-polar, unmarked gene mutations
      in Streptomyces sp. Tu6071. In addition, we have shown that homologous
      recombination is a major pathway in streptomycetes to repair an
      I-SceI-generated DNA double-strand break. This novel I-SceI-based tool
      will be useful in fundamental studies on the repair mechanism of DNA
      double-strand breaks and for a variety of biotechnological applications.
AU  - Siegl T
AU  - Petzke L
AU  - Welle E
AU  - Luzhetskyy A
PT  - Journal Article
TA  - Appl. Microbiol. Biotechnol.
JT  - Appl. Microbiol. Biotechnol.
SO  - Appl. Microbiol. Biotechnol. 2010 87: 1525-1532.

PMID- 18065616
VI  - 74
DP  - 2008
TI  - Genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans.
PG  - 1145-1156
AB  - Sulfur-oxidizing epsilonproteobacteria are common in a variety of
      sulfidogenic environments. These autotrophic and mixotrophic
      sulfur-oxidizing bacteria are believed to contribute substantially to the
      oxidative portion of the global sulfur cycle. In order to better
      understand the ecology and roles of sulfur-oxidizing
      epsilonproteobacteria, in particular those of the widespread genus
      Sulfurimonas, in biogeochemical cycles, the genome of Sulfurimonas
      denitrificans DSM1251 was sequenced. This genome has many features,
      including a larger size (2.2 Mbp), that suggest a greater degree of
      metabolic versatility or responsiveness to the environment than seen for
      most of the other sequenced epsilonproteobacteria. A branched electron
      transport chain is apparent, with genes encoding complexes for the
      oxidation of hydrogen, reduced sulfur compounds, and formate and the
      reduction of nitrate and oxygen. Genes are present for a complete,
      autotrophic reductive citric acid cycle. Many genes are present that could
      facilitate growth in the spatially and temporally heterogeneous sediment
      habitat from where Sulfurimonas denitrificans was originally isolated.
      Many resistance-nodulation-development family transporter genes (10 total)
      are present; of these, several are predicted to encode heavy metal efflux
      transporters. An elaborate arsenal of sensory and regulatory
      protein-encoding genes is in place, as are genes necessary to prevent and
      respond to oxidative stress.
AU  - Sievert SM
AU  - Scott KM
AU  - Klotz MG
AU  - Chain PS
AU  - Hauser LJ
AU  - Hemp J
AU  - Hugler M
AU  - Land M
AU  - Lapidus A
AU  - Larimer FW
AU  - Lucas S
AU  - Malfatti SA
AU  - Meyer F
AU  - Paulsen IT
AU  - Ren Q
AU  - Simon J
AU  - USF GC
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2008 74: 1145-1156.

PMID- 
VI  - 
DP  - 1982
TI  - Determination of the specific recognition sequence of the restriction enzyme Rlu-1I from Rhizobium lupini.
PG  - 1-109
AB  - This is the enzyme RluI.
AU  - Sievert U
PT  - Journal Article
TA  - Ph.D. Thesis, Erlangen University, W. Germany
JT  - Ph.D. Thesis, Erlangen University, W. Germany
SO  - Ph.D. Thesis, Erlangen University, W. Germany 1982 : 1-109.

PMID- 20348266
VI  - 192
DP  - 2010
TI  - Complete genome sequence of Lactococcus lactis subsp. lactis KF147, a plant-associated lactic acid bacterium.
PG  - 2649-2650
AB  - Lactococcus lactis is a lactic acid bacterium used in the production of many fermented dairy
      products. We report the complete genome sequence of
      L. lactis subsp. lactis KF147, a nondairy strain isolated from mung bean
      sprouts. The circular chromosome of 2,598,144 bp, the largest among the
      sequenced lactococcal strains, encodes many properties related to
      adaptation to the plant environment.
AU  - Siezen RJ
AU  - Bayjanov J
AU  - Renckens B
AU  - Wels M
AU  - van Hijum SA
AU  - Molenaar D
AU  - van Hylckama VJE
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 2649-2650.

PMID- 
VI  - 194
DP  - 2011
TI  - Complete resequencing and reannotation of the Lactobacillus plantarum WCFS1 genome.
PG  - 195-196
AB  - There is growing interest in the beneficial effects of Lactobacillus plantarum on human
      health. The genome of L. plantarum WCFS1, first sequenced in 2001, was resequenced using
      Solexa technology. We identified 116 nucleotide corrections and improved function prediction
      for nearly 1,200 proteins, with a focus on metabolic functions and cell surface-associated
      proteins.
AU  - Siezen RJ
AU  - Francke C
AU  - Renckens B
AU  - Boekhorst J
AU  - Wels M
AU  - Kleerebezem M
AU  - van Hijum SAFT
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 194: 195-196.

PMID- 16332824
VI  - 71
DP  - 2005
TI  - Complete Sequences of Four Plasmids of Lactococcus lactis subsp. cremoris SK11 Reveal Extensive Adaptation to the Dairy Environment.
PG  - 8371-8382
AB  - Lactococcus lactis strains are known to carry plasmids encoding industrially important traits.
      L. lactis subsp. cremoris SK11 is widely used by the dairy industry in cheese making. Its
      complete plasmid complement was sequenced and found to contain the plasmids pSK11A (10,372
      bp), pSK11B (13,332 bp), pSK11L (47,165 bp), and pSK11P (75,814 bp). Six highly homologous
      repB-containing replicons were found, all belonging to the family of lactococcal theta-type
      replicons. Twenty-three complete insertion sequence elements segment the plasmids into
      numerous modules, many of which can be identified as functional units or containing
      functionally related genes. Plasmid-encoded functions previously known to reside on L. lactis
      SK11 plasmids were now mapped in detail, e.g., lactose utilization (lacR-lacABCDFEGX), the
      proteolytic system (prtM-prtP, pepO, pepF), and the oligopeptide permease system (oppDFBCA).
      Newly identified plasmid-encoded functions could facilitate the uptake of various cations,
      while the pabA and pabB genes could be essential for folate biosynthesis. A competitive
      advantage could be obtained by using the putative flavin adenine dinucleotide-dependent
      d-lactate dehydrogenase and oxalate:formate antiporter for enhanced ATP synthesis, while the
      activity of the predicted alpha-acetolactate decarboxylase may contribute to the formation of
      an additional electron sink. Various stress response proteins are plasmid encoded, which could
      enhance strain robustness. A substantial number of these "adaptation" genes have not been
      described before on L. lactis plasmids. Moreover, several genes were identified for the first
      time in L. lactis, possibly reflecting horizontal gene transfer.
AU  - Siezen RJ
AU  - Renckens B
AU  - van Swam I
AU  - Peters S
AU  - van Kranenburg R
AU  - Kleerebezem M
AU  - de Vos WM
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2005 71: 8371-8382.

PMID- 18039825
VI  - 74
DP  - 2008
TI  - Genome-scale genotype-phenotype matching of two Lactococcus lactis isolates from plants identifies mechanisms of adaptation to the plant niche.
PG  - 424-436
AB  - Lactococcus lactis is a primary constituent of many starter cultures used for the
      manufacturing of fermented dairy products, but the species
      also occurs in various nondairy niches such as (fermented) plant
      material. Three genome sequences of L. lactis dairy strains (IL-1403,
      SK11, and MG1363) are publicly available. An extensive molecular and
      phenotypic diversity analysis was now performed on two L. lactis plant
      isolates. Diagnostic sequencing of their genomes resulted in over 2.5
      Mb of sequence for each strain. A high synteny was found with the
      genome of L. lactis IL-1403, which was used as a template for contig
      mapping and locating deletions and insertions in the plant L. lactis
      genomes. Numerous genes were identified that do not have homologs in
      the published genome sequences of dairy L. lactis strains. Adaptation
      to growth on substrates derived from plant cell walls is evident from
      the presence of gene sets for the degradation of complex plant polymers
      such as xylan, arabinan, glucans, and fructans but also for the uptake
      and conversion of typical plant cell wall degradation products such as
      alpha-galactosides, P-glucosides, arabinose, xylose, galacturonate,
      glucuronate, and gluconate. Further niche-specific differences are
      found in genes for defense (nisin biosynthesis), stress response
      (nonribosomal peptide synthesis and various transporters), and
      exopolysaccharide biosynthesis, as well as the expected differences in
      various mobile elements such as prophages, plasmids,
      restrictionmodification systems, and insertion sequence elements. Many
      of these genes were identified for the first time in Lactococcus
      lactis. In most cases good correspondence was found with the phenotypic
      characteristics of these two strains.
AU  - Siezen RJ
AU  - Starrenburg MJC
AU  - Boekhorst J
AU  - Renckens B
AU  - Molenaar D
AU  - van Hylckama-Vlieg JET
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2008 74: 424-436.

PMID- 
VI  - 8
DP  - 2012
TI  - AFM protein-protein interactions within the EcoR124I molecular motor.
PG  - 6358-6363
AB  - Dynamic Force Spectroscopy (DFS), an Atomic Force Microscopy (AFM) technique, has been used to
      investigate the interaction between the
      HsdR subunit and the core methylase (MTase) of the Type I
      Restriction-Modification (R-M) enzyme EcoR124I. Such systems are of
      interest in bionanotechnology owing to their ability to translocate
      DNA, thus acting as molecular motors. Forces between a glutathione
      S-transferase (GST)-HsdR(PrrI) motor subunit attached to an AFM tip
      using a polyethylene gycol linker and the core MTase on poly-L-lysine
      pre-treated mica were measured at different loading rates. In the
      absence of an applied force, the position of energy barrier x(diss),
      bond dissociation rate k(diss)(0) and lifetime of the bond tau(0) were
      calculated to be 1.35 +/- 0.17 nm, 0.16 s(-1) and 6.3 s, respectively.
      The k(diss)(0) value was a little lower than that obtained from
      magnetic tweezers (0.4 s(-1)), suggesting that the thermodynamic
      equilibrium may be affected by the presence of DNA. This work
      demonstrates that kinetic data concerning protein-protein interactions
      between subunits within Type I R-M enzymes are accessible via AFM. Such
      information is important for structure elucidation and the development
      of nanodevices.
AU  - Sikora AE
AU  - Smith JR
AU  - Campbell SA
AU  - Firman K
PT  - Journal Article
TA  - Soft Matter
JT  - Soft Matter
SO  - Soft Matter 2012 8: 6358-6363.

PMID- 21304697
VI  - 2
DP  - 2010
TI  - Complete genome sequence of Sulfurospirillum deleyianum type strain (5175).
PG  - 149-157
AB  - Sulfurospirillum deleyianum Schumacher et al. 1993 is the type species of the genus
      Sulfurospirillum. S. deleyianum is a model organism for studying sulfur
      reduction and dissimilatory nitrate reduction as an energy source for growth.
      Also, it is a prominent model organism for studying the structural and functional
      characteristics of cytochrome c nitrite reductase. Here, we describe the features
      of this organism, together with the complete genome sequence and annotation. This
      is the first completed genome sequence of the genus Sulfurospirillum. The
      2,306,351 bp long genome with its 2,291 protein-coding and 52 RNA genes is part
      of the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Sikorski J et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 2: 149-157.

PMID- 21304703
VI  - 2
DP  - 2010
TI  - Complete genome sequence of Segniliparus rotundus type strain (CDC 1076).
PG  - 203-211
AB  - Segniliparus rotundus Butler 2005 is the type species of the genus Segniliparus,  which is
      currently the only genus in the corynebacterial family Segniliparaceae.
      This family is of large interest because of a novel late-emerging genus-specific
      mycolate pattern. The type strain has been isolated from human sputum and is
      probably an opportunistic pathogen. Here we describe the features of this
      organism, together with the complete genome sequence and annotation. This is the
      first completed genome sequence of the family Segniliparaceae. The 3,157,527 bp
      long genome with its 3,081 protein-coding and 52 RNA genes is part of the Genomic
      Encyclopedia of Bacteria and Archaea project.
AU  - Sikorski J et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 2: 203-211.

PMID- 21304690
VI  - 3
DP  - 2010
TI  - Complete genome sequence of Meiothermus silvanus type strain (VI-R2).
PG  - 37-46
AB  - Meiothermus silvanus (Tenreiro et al. 1995) Nobre et al. 1996 belongs to a thermophilic genus
      whose members share relatively low degrees of 16S rRNA gene
      sequence similarity. Meiothermus constitutes an evolutionary lineage separate
      from members of the genus Thermus, from which they can generally be distinguished
      by their slightly lower temperature optima. M. silvanus is of special interest as
      it causes colored biofilms in the paper making industry and may thus be of
      economic importance as a biofouler. This is the second completed genome sequence
      of a member of the genus Meiothermus and only the third genome sequence to be
      published from a member of the family Thermaceae. The 3,721,669 bp long genome
      with its 3,667 protein-coding and 55 RNA genes is a part of the Genomic
      Encyclopedia of Bacteria and Archaea project.
AU  - Sikorski J et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 3: 37-46.

PMID- 21304692
VI  - 3
DP  - 2010
TI  - Complete genome sequence of Acetohalobium arabaticum type strain (Z-7288).
PG  - 57-65
AB  - Acetohalobium arabaticum Zhilina and Zavarzin 1990 is of special interest because of its
      physiology and its participation in the anaerobic C(1)-trophic chain in
      hypersaline environments. This is the first completed genome sequence of the
      family Halobacteroidaceae and only the second genome sequence in the order
      Halanaerobiales. The 2,469,596 bp long genome with its 2,353 protein-coding and
      90 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea
      project.
AU  - Sikorski J et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 3: 57-65.

PMID- 21304749
VI  - 3
DP  - 2010
TI  - Complete genome sequence of Sulfurimonas autotrophica type strain (OK10).
PG  - 194-202
AB  - Sulfurimonas autotrophica Inagaki et al. 2003 is the type species of the genus Sulfurimonas.
      This genus is of interest because of its significant contribution
      to the global sulfur cycle as it oxidizes sulfur compounds to sulfate and by its
      apparent habitation of deep-sea hydrothermal and marine sulfidic environments as
      potential ecological niche. Here we describe the features of this organism,
      together with the complete genome sequence and annotation. This is the second
      complete genome sequence of the genus Sulfurimonas and the 15(th) genome in the
      family Helicobacteraceae. The 2,153,198 bp long genome with its 2,165
      protein-coding and 55 RNA genes is part of the Genomic Encyclopedia of Bacteria
      and Archaea project.
AU  - Sikorski J et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 3: 194-202.

PMID- 21304735
VI  - 3
DP  - 2010
TI  - Complete genome sequence of Ilyobacter polytropus type strain (CuHbu1).
PG  - 304-314
AB  - Ilyobacter polytropus Stieb and Schink 1984 is the type species of the genus Ilyobacter, which
      belongs to the fusobacterial family Fusobacteriaceae. The
      species is of interest because its members are able to ferment quite a number of
      sugars and organic acids. I. polytropus has a broad versatility in using various
      fermentation pathways. Also, its members do not degrade poly-beta-hydroxybutyrate
      but only the monomeric 3-hydroxybutyrate. This is the first completed genome
      sequence of a member of the genus Ilyobacter and the second sequence from the
      family Fusobacteriaceae. The 3,132,314 bp long genome with its 2,934
      protein-coding and 108 RNA genes consists of two chromosomes (2 and 1 Mbp long)
      and one plasmid, and is a part of the Genomic Encyclopedia of Bacteria and
      Archaea project.
AU  - Sikorski J et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 3: 304-314.

PMID- 21886860
VI  - 4
DP  - 2011
TI  - Complete genome sequence of Mahella australiensis type strain (50-1 BON).
PG  - 331-341
AB  - Mahella australiensis Bonilla Salinas et al. 2004 is the type species of the genus Mahella,
      which belongs to the family Thermoanaerobacteraceae. The species
      is of interest because it differs from other known anaerobic spore-forming
      bacteria in its G+C content, and in certain phenotypic traits, such as carbon
      source utilization and relationship to temperature. Moreover, it has been
      discussed that this species might be an indigenous member of petroleum and oil
      reservoirs. This is the first completed genome sequence of a member of the genus
      Mahella and the ninth completed type strain genome sequence from the family
      Thermoanaerobacteraceae. The 3,135,972 bp long genome with its 2,974
      protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria
      and Archaea project.
AU  - Sikorski J et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 4: 331-341.

PMID- 
VI  - 14
DP  - 2004
TI  - Structure and function of the tetrameric restriction enzymes.
PG  - 237-259
AB  - Type II restriction endonucleases recognize specific DNA sequences, typically 4-8 bp in
      length, and cleave phosphodiester bonds in the presence of Mg2+, within or close to their
      recognition sites.  Around 3500 species, from variety of bacteria with nearly 240 differing
      specificities, have now been characterized.  Most of the sequences recognized by Type II
      restriction endonucleases are palindromic, i.e. possess a twofold rotational axis of symmetry.
      On the basis of this observation, Kelly and Smith proposed the first model for the interaction
      of these restriction enzymes with DNA.  According to their model, recognition of the
      palindromic DNA sequence is achieved by two identical protein subunits related by a twofold
      axis of symmetry.  Each subunit faces the same nucleotide sequence on the opposite DNA strand
      and contains one active site.  Symmetrical nicking of opposite DNA strands by both monomers
      within a homodimer generates the double-strand break.  Hence, the symmetry of the recognition
      sequence implies the oligomeric state of the restriction enzyme.
AU  - Siksnys V
AU  - Grazulis S
AU  - Huber R
PT  - Journal Article
TA  - Nucleic Acids Mol. Biol.
JT  - Nucleic Acids Mol. Biol.
SO  - Nucleic Acids Mol. Biol. 2004 14: 237-259.

PMID- 8223580
VI  - 217
DP  - 1993
TI  - Catalytic and binding properties of restriction endonuclease Cfr9I.
PG  - 411-419
AB  - The Cfr9I restriction endonuclease recognizes and cleaves the duplex DNA sequence C^CCGG. The
      binding of restriction endonuclease Cfr9I to DNA was examined in the absence of Mg2+ using
      gel-mobility-shift and nitrocellulose-filter-binding assays. It was shown that restriction
      endonuclease Cfr9I bound DNA fragments either containing or lacking the canonical recognition
      sequence with equal affinity. These results suggest that the specificity of restriction
      endonuclease Cfr9I is expressed during the catalytic step. The cleavage of supercoiled pUC18
      DNA by restriction endonuclease Cfr9I showed that at low concentrations of MgCl2, only with
      open-circular DNA, nicks appeared in one strand at the recognition sequence, while the
      cleavage of the second strand was very slow. At these conditions the supercoiled DNA was
      converted to open-circular and linear forms simultaneously rather than consecutively. It was
      shown that open-circular DNA was a poor substrate for restriction endonuclease Cfr9I. These
      results suggested that both Mg2+ and intact recognition sequence are required to drive the
      enzyme into the correct conformation to ensure DNA cleavage.
AU  - Siksnys V
AU  - Pleckaityte M
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1993 217: 411-419.

PMID- 1332782
VI  - 1160
DP  - 1992
TI  - Role of the reactive cysteine residue in restriction endonuclese Cfr9I.
PG  - 199-205
AB  - Chemical modification studies were performed to elucidate the role of Cys-residues in the
      catalysis/binding of restriction endonuclease Cfr9I. Incubation of restriction endonuclease
      Cfr9I with N-ethylmaleimide (NEM), iodoacetate, 5-5'-dithiobis (2-nitrobenzoic acids) at pH
      7.5 led to a complete loss of the catalytic activity. However, no enzyme inactivation was
      detectable after modification of the enzyme with iodoacetamide and methyl
      methanethiosulfonate. Complete protection of the enzyme against inactivation by NEM was
      observed in the presence of substrate implying that Cys-residues may be lcoated at or in the
      vicinity of the active site of enzyme. Direct substrate-binding studies of native and modified
      restriction endonuclease Cfr9I using a gel-mobility shift assay indicated that the
      modification of the enzyme by NEM was hindered by substrate binding. A single Cys-residue was
      modified during the titration of the enzyme with DTNB with concomitant loss of the catalytic
      activity. The pH-dependence of inactivation of Cfr9I by NEM revealed the modification of the
      residue with a pKa value of 8.9 +/- 0.2. The dependence of the reaction rate of substrate
      hydrolysis by Cfr9I versus pH revealed two essential residues with pKa values of 6.3 +/- 0.15
      and 8.7 +/- 0.15, respectively. The evidence presented suggests that the restriction
      endonuclease Cfr9I contains a reactive sulfhydryl residue which is non-essential for
      catalysis, but is located at or near the substrate binding site.
AU  - Siksnys V
AU  - Pleckaityte M
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1992 1160: 199-205.

PMID- 10518946
VI  - 291
DP  - 1999
TI  - The Cfr10I restriction enzyme is functional as a tetramer.
PG  - 1105-1118
AB  - It is thought that most of the type II restriction endonucleases interact with DNA as
      homodimers. Cfr10I is a typical type II restriction enzyme that recognises the 5'-Pu^CCGGPy
      sequence and cleaves it as indicated by the arrow.  Gel-filtration and analytical
      ultracentrifugation data presented here indicate that Cfr10I is a homotetramer in isolation.
      Only the SfiI restriction enzyme that recognises the long interrupted recognition sequence
      5'-GGCCNNNNNGGCC has been previously reported to operate as a tetramer however, its structure
      is unknown. Analysis of Cfr10I crystals revealed that a single molecule in the asymmetric unit
      is repeated by D2 symmetry to form a tetramer. To determine whether the packing of the Cfr10I
      in the crystal reflects the quaternary structure of the protein in solution, the tryptophan
      W220 residue located at the putative dimer-dimer interface was mutated to alanine, and the
      structural and functional consequences of the substitution were analysed. Equilibrium
      sedimentation experiments revealed that, in contrast to the wild-type Cfr10I, the W220A mutant
      exists in solution predominantly as a dimer. In addition, the tetramer seems to be a
      catalytically important form of Cfr10I, since the DNA cleavage activity of the W220A mutant is
      < 0.1% of that of the wild-type enzyme. Further, analysis of plasmid DNA cleavage suggests
      that the Cfr10I tetramer is able to interact with two copies of the recognition sequence,
      located on the same DNA molecule. Indeed, electron microscopy studies demonstrated that two
      distant recognition sites are brought together through the DNA looping induced by the
      simultaneous binding of the Cfr10I tetramer to both sites. These data are consistent with the
      tetramer being a functionally important form of Cfr10I.
AU  - Siksnys V
AU  - Skirgaila R
AU  - Sasnauskas G
AU  - Urbanke C
AU  - Cherny D
AU  - Grazulis S
AU  - Huber R
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1999 291: 1105-1118.

PMID- 
VI  - 275
DP  - 2008
TI  - How do restriction enzymes acquire specificities for different target sites?
PG  - 10
AB  - Restriction enzymes recognize 4-8 bp DNA sequences and cut at their target site with exquisite
      specificity.  Many orthodox restriction endonucleases interacting with symmetric recognition
      sites achieve sequence specificity making direct nucleobase-amino acid contacts with their
      target sites.  Ecl18kI and EcoRII-C/PspGI restriction enzymes recognize interrupted
      pentanucleotide sites CCNGG and CCWGG, respectively.  Structural studies demonstrate that
      Ecl18kI/EcoRII-C/PspGI and the NgoMIV restriction enzyme specific for the non-interrupted
      GCCGGC site share striking structural similarities and interact identically with the
      symmetrical CC:GG half-sites.  It turned out that Ecl18kI specific for the CCNGG and
      EcoRII-C/PspGI specific for the CCWGG site flip central nucleotides from DNA double helix to
      interact with the conserved CC:GG parts of their target sequences and achieve cleavage.
      However, Ecl18kI and EcoRII-C/PspGI accept different base pairs at the center, raising a
      question whether the base pair strength/stability or a direct readout of the flipped out bases
      determine the differences in specificity.  Using a combination of the X-ray structural
      analysis and biochemical methods we show that EcoRII-C/PspGI achieve the specificity for the
      CCWGG sequence by a double check mechanism by probing both the stability of the central base
      pair and identity of the flipped out base in the pocket.
AU  - Siksnys V
AU  - Tamulaitis G
AU  - Zaremba M
AU  - Szczepanowski R
AU  - Bochtler M
PT  - Journal Article
TA  - FEBS J.
JT  - FEBS J.
SO  - FEBS J. 2008 275: 10.

PMID- 7607515
VI  - 157
DP  - 1995
TI  - Sequence similarity among type-II restriction endonucleases, related by their recognized 6-bp target and tetranucleotide-overhang cleavage.
PG  - 311-314
AB  - The type-II restriction endonucleases (ENases) EcoRI (recognition sequence G/AATTC), RsrI
      (G/AATTC), XcyI (C/CCGGG), Cfr9I (C/CCGGG) and MunI (C/AATTG), all cleave hexanucleotide
      palindromic sequences, leaving tetranucleotide 5'-overhangs.  Two regions of similarity that
      appear in the same order and relative position were identified among the amino-acid sequences
      of ENases.  These regions map to the structural elements of EcoRI involved in the building of
      the catalytic site and in interactions with the central nucleotides of the recognized
      sequence.  We propose that these ENases might all share a similar structural organization of
      the active site and structural motifs involved in interactions with specific DNA recognition
      sequences.
AU  - Siksnys V
AU  - Timinskas A
AU  - Klimasauskas S
AU  - Butkus V
AU  - Janulaitis A
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 311-314.

PMID- 8181741
VI  - 142
DP  - 1994
TI  - CAATTG-specific restriction-modification munI genes from Mycoplasma: sequence similarities between R.MunI and R.EcoRI.
PG  - 1-8
AB  - The genes coding for the MunI restriction-modification (R-M) system, which recognize the
      sequence 5'-CAATTG, have been cloned and expressed in Escherichia coli, and their nucleotide
      sequences have been determined. The restriction endonuclease (ENase: R.MunI) is encoded by an
      open reading frame (ORF) of 606 bp, and a 699-bp ORF codes for the methyltransferase (MTase).
      The two genes are transcribed divergently from a 355-bp region. The gene encoding the ENase is
      preceded by a short co-linear ORF of 222 bp. The deduced amino acid (aa) sequence of this
      short ORF (SORF) closely resembles the sequences of a family of regulatory proteins that are
      associated with other type-II R-M systems. Comparative analysis of the deduced aa sequence of
      R.MunI revealed several regions of similarity to the EcoRI and RsrI ENases that recognize the
      GAATTC sequence. The similar mode of interaction of MunI, EcoRI and RsrI with the
      tetranucleotide AATT, common to the recognition sequences of these ENases, was suggested.
AU  - Siksnys V
AU  - Zareckaja N
AU  - Vaisvila R
AU  - Timinskas A
AU  - Stakenas P
AU  - Butkus V
AU  - Janulaitis A
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1994 142: 1-8.

PMID- 21410225
VI  - 50
DP  - 2011
TI  - Photocaged Variants of the MunI and PvuII Restriction Enzymes.
PG  - 2800-2807
AB  - Regulation of proteins by light is a new and promising strategy for the external control of
      biological processes. In this study, we demonstrate
      the ability to regulate the catalytic activity of the MunI and PvuII
      restriction endonucleases with light. We used two different approaches
      to attach a photoremovable caging compound, 2-nitrobenzyl bromide
      (NBB), to functionally important regions of the two enzymes. First, we
      covalently attached a caging molecule at the dimer interface of Muni to
      generate an inactive monomer. Second, we attached NBB at the DNA
      binding site of the single-chain variant of PvuII (scPvuII) to prevent
      binding and cleavage of the DNA substrate. Upon removal of the caging
      group by UV irradiation, nearly 50% of the catalytic activity of Muni
      and 80% of the catalytic activity of PvuII could be restored.
AU  - Silanskas A
AU  - Foss M
AU  - Wende W
AU  - Urbanke C
AU  - Lagunavicius A
AU  - Pingoud A
AU  - Siksnys V
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2011 50: 2800-2807.

PMID- 22236287
VI  - 23
DP  - 2012
TI  - Catalytic Activity Control of Restriction Endonuclease-Triplex Forming Oligonucleotide Conjugates.
PG  - 203-211
AB  - 
AU  - Silanskas A
AU  - Zaremba M
AU  - Sasnauskas G
AU  - Siksnys V
PT  - Journal Article
TA  - Bioconjugate Chem.
JT  - Bioconjugate Chem.
SO  - Bioconjugate Chem. 2012 23: 203-211.

PMID- 3074017
VI  - 74
DP  - 1988
TI  - Cloning, purification and characterization of the M.NdeI methyltransferase from Neisseria denitrificans.
PG  - 43-44
AB  - Meeting Abstract
AU  - Silber KR
AU  - Polisson C
AU  - Rees PA
AU  - Benner JS
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 43-44.

PMID- 8384141
VI  - 133
DP  - 1993
TI  - Heteroduplex strand-specificity in restriction-stimulated recombination by the RecE pathway of Escherichia coli.
PG  - 439-448
AB  - The RecE recombination pathway is active in Escherichia coli recB recC sbcA mutants. To
      isolate and characterize products and intermediates of RecE-mediated, break-induced,
      intramolecular recombination, we infected recB recC sbcA mutants, expressing EcoRI
      endonuclease, with chimeric gamma phages that allow EcoRI-mediated release of cloned linear
      recombination substrates. Substrates with direct terminal repeats recombined to yield a
      circular product with one copy of the repeated sequence. Some recombinations were
      heteroallelic for the recombining markers. Markers distant to the break were recovered in the
      circular product at a higher frequency than markers close to the break. To examine the
      heteroduplex structures that may have yielded the heteroallelic recombinants, non-replicative
      substrates were employed. Some of the nonreplicative recombination products contained
      heteroduplexes, with a strong bias for paired strands ending 3' at the break. This strand
      bias in heteroduplex formation is consistent with recombination models that postulate
      homologous pairing of protruding 3' single-stranded ends.
AU  - Silberstein Z
AU  - Shalit M
AU  - Cohen A
PT  - Journal Article
TA  - Genetics
JT  - Genetics
SO  - Genetics 1993 133: 439-448.

PMID- 25792066
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Pseudomonas aeruginosa Mucoid Strain FRD1, Isolated from a Cystic Fibrosis Patient.
PG  - e00153-15
AB  - We announce here the complete genome sequence of the Pseudomonas aeruginosa mucoid strain
      FRD1, isolated from the sputum of a cystic fibrosis patient. The
      complete genome of P. aeruginosa FRD1 is 6,712,339 bp. This genome will allow
      comparative genomics to be used to identify genes associated with virulence,
      especially those involved in chronic pulmonary infections.
AU  - Silo-Suh LA
AU  - Suh SJ
AU  - Ohman DE
AU  - Wozniak DJ
AU  - Pridgeon JW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00153-15.

PMID- 21037006
VI  - 193
DP  - 2010
TI  - Complete Genome Sequence of Corynebacterium pseudotuberculosis I-19, strain isolated from Israel Bovine mastitis.
PG  - 323-324
AB  - This work portrays a report on complete and annotated genome sequence of Corynebacterium
      pseudotuberculosis I-19 isolated from an Israel dairy cow
      with sever clinical mastitis. To present the whole-genome sequence, de
      novo assembly approach using 33 million short (25 bp) mate paired SOLiD
      reads only was applied. More so, the automatic, functional and manual
      annotation was attained with the use of several algorithms in a multi-step
      process.
AU  - Silva A et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 193: 323-324.

PMID- 23144408
VI  - 194
DP  - 2012
TI  - Complete genome sequence of Corynebacterium pseudotuberculosis Cp31, isolated from an Egyptian buffalo.
PG  - 6663-6664
AB  - Corynebacterium pseudotuberculosis is of major veterinary importance because it
      affects many animal species, causing economically significant livestock diseases
      and losses. Therefore, the genomic sequencing of various lines of this organism,
      isolated from different hosts, will aid in the development of diagnostic methods
      and new prevention and treatment strategies and improve our knowledge of the
      biology of this microorganism. In this study, we present the genome of C.
      pseudotuberculosis Cp31, isolated from a buffalo in Egypt.
AU  - Silva A et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6663-6664.

PMID- 24407640
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Corynebacterium ulcerans FRC58, Isolated from the Bronchitic Aspiration of a Patient in France.
PG  - e01132-13
AB  - Corynebacterium ulcerans is a bacterial species with high importance because it causes
      infections in animals and, rarely, in humans. Its virulence mechanisms
      remain unclear. The current study describes the draft genome of C. ulcerans
      FRC58, which was isolated from the bronchitic aspiration of a patient in France.
AU  - Silva AS
AU  - Barauna RA
AU  - de Sa PC
AU  - das Gracas DA
AU  - Carneiro AR
AU  - Thouvenin M
AU  - Azevedo V
AU  - Badell E
AU  - Guiso N
AU  - da Silva AL
AU  - Ramos RT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01132-13.

PMID- 28280012
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Pseudoalteromonas sp. Strain PAB 2.2 Isolated from Abrolhos Bank (Brazil).
PG  - e00016-17
AB  - We present here the draft genome sequence of Pseudoalteromonas sp. strain PAB 2.2, isolated
      from water of Parcel de Abrolhos coral reef (17 degrees 57'32.7';
      38 degrees 30'20.3'), on Abrolhos Bank, at a depth of 12 m. The assembly
      consists of 4,434,635 bp and contains 40 contigs, with a G+C content of 41.60%.
AU  - Silva BS
AU  - Nobrega MS
AU  - Leomil L
AU  - Tschoeke DA
AU  - Garcia GD
AU  - Dias G
AU  - Thompson CC
AU  - Thompson FL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00016-17.

PMID- 26564044
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of a Human-Invasive Salmonella enterica Serovar Typhimurium Strain of the Emerging Sequence Type 213 Harboring a Multidrug  Resistance IncA/C Plasmid and a blaCMY-2-Carrying IncF Plasmid.
PG  - e01323-15
AB  - Salmonella enterica subsp. enterica serovar Typhimurium strain 33676 was isolated in Mexico
      City, Mexico, from a patient with a systemic infection, and its
      complete genome sequence was determined using PacBio single-molecule real-time
      technology. Strain 33676 harbors an IncF plasmid carrying the extended-spectrum
      cephalosporin gene blaCMY-2 and a multidrug resistance IncA/C plasmid.
AU  - Silva C
AU  - Calva E
AU  - Calva JJ
AU  - Wiesner M
AU  - Fernandez-Mora M
AU  - Puente JL
AU  - Vinuesa P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01323-15.

PMID- 27081133
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Salmonella enterica Serovar Typhimurium Strain SO2 (Sequence Type 302) Isolated from an Asymptomatic Child in Mexico.
PG  - e00253-16
AB  - The complete genome sequence ofSalmonella entericaserovar Typhimurium strain SO2, isolated
      from an asymptomatic child in Mexico, was determined using PacBio
      single-molecule real-time technology. Strain SO2 has six complete chromosomal
      prophages, namely, ST104, Gifsy-2, ST64B, Gifsy-1, ELPhiS, and FSL SP-004, and
      carries aSalmonellavirulence plasmid.
AU  - Silva C
AU  - Calva E
AU  - Puente JL
AU  - Zaidi MB
AU  - Vinuesa P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00253-16.

PMID- 27081132
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Salmonella enterica Serovar Typhimurium Strain YU15 (Sequence Type 19) Harboring the Salmonella Genomic Island 1 and Virulence  Plasmid pSTV.
PG  - e00252-16
AB  - The complete genome ofSalmonella entericasubsp.entericaserovar Typhimurium sequence type 19
      (ST19) strain YU15, isolated in Yucatan, Mexico, from a human
      baby stool culture, was determined using PacBio technology. The chromosome
      contains five intact prophages and theSalmonellagenomic island 1 (SGI1). This
      strain carries theSalmonellavirulence plasmid pSTV.
AU  - Silva C
AU  - Calva E
AU  - Puente JL
AU  - Zaidi MB
AU  - Vinuesa P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00252-16.

PMID- 22083712
VI  - 80
DP  - 2012
TI  - Infection of Mice by Salmonella enterica Serovar Enteritidis Involves Additional Genes That Are Absent in the Genome of Serovar Typhimurium.
PG  - 839-849
AB  - Salmonella enterica serovar Enteritidis causes a systemic, typhoid-like infection in newly
      hatched poultry and mice. In the present study, a
      library of 54,000 transposon mutants of S. Enteritidis phage type 4
      (PT4) strain P125109 was screened for mutants deficient in the in vivo
      colonization of the BALB/c mouse model using a microarray-based
      negative-selection screening. Mutants in genes known to contribute to
      systemic infection (e.g., Salmonella pathogenicity island 2 [SPI-2],
      aro, rfa, rfb, phoP, and phoQ) and enteric infection (e.g., SPI-1 and
      SPI-5) in this and other Salmonella serovars displayed colonization
      defects in our assay. In addition, a strong attenuation was observed
      for mutants in genes and genomic islands that are not present in S.
      Typhimurium or in most other Salmonella serovars. These genes include a
      type I restriction/modification system (SEN4290 to SEN4292), the peg
      fimbrial operon (SEN2144A to SEN2145B), a putative pathogenicity island
      (SEN1970 to SEN1999), and a type VI secretion system remnant SEN1001,
      encoding a hypothetical protein containing a lysin motif (LysM) domain
      associated with peptidoglycan binding. Proliferation defects for
      mutants in these individual genes and in exemplar genes for each of
      these clusters were confirmed in competitive infections with wild-type
      S. Enteritidis. A Delta SEN1001 mutant was defective for survival
      within RAW264.7 murine macrophages in vitro. Complementation assays
      directly linked the SEN1001 gene to phenotypes observed in vivo and in
      vitro. The genes identified here may perform novel virulence functions
      not characterized in previous Salmonella models.
AU  - Silva CA
AU  - Blondel CJ
AU  - Quezada CP
AU  - Porwollik S
AU  - Andrews-Polymenis HL
AU  - Toro CS
AU  - Zaldivar M
AU  - Contreras I
AU  - McClelland M
AU  - Santiviago CA
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2012 80: 839-849.

PMID- 26893417
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Staphylococcus aureus Strains Isolated from Subclinical Bovine Mastitis in Brazil.
PG  - e01594-15
AB  - Here, we present the draft genome sequences of four Staphylococcus aureus strains isolated
      from mastitic milk collected from animals with subclinical
      manifestations. Three of them were typed as sequence type 126 (ST126), a genotype
      with no genome sequence available. ST126 is found in several herds of southern
      Brazil and is described as a bovine pathogen strongly associated with milk around
      the world.
AU  - Silva DM
AU  - da Silva MP
AU  - Vidigal PM
AU  - Barcelos RM
AU  - Klein RC
AU  - Aguilar AP
AU  - Fabres-Klein MH
AU  - Oliveira G
AU  - Ribon AO
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01594-15.

PMID- 15190132
VI  - 32
DP  - 2004
TI  - Analysis of the LAGLIDADG interface of the monomeric homing endonuclease I-DmoI.
PG  - 3156-3168
AB  - The general structural fold of the LAGLIDADG endonuclease family consists of two similar
      alpha/beta domains (alpha beta beta alpha beta beta alpha) that assemble either as homodimers
      or monomers with the domains related by pseudo-two-fold symmetry. At the center of this
      symmetry is the closely packed LAGLIDADG two-helix bundle that forms the main inter- or
      intra-molecular contact region between the domains of single- or double-motif proteins,
      respectively. In this work, we further examine the role of the LAGLIDADG residues involved in
      the helix?helix interaction. The interchangeability of the LAGLIDADG helix interaction was
      explored by grafting interfacial residues from the homodimeric I-CreI into the corresponding
      positions in the monomeric I-DmoI. The resulting LAGLIDADG exchange mutant is partially
      active, preferring to nick dsDNA rather than making the customary double-strand break. A
      series of partial revertants within the mutated LAGLIDADG region are shown to restore cleavage
      activity to varying degrees resulting in one I-DmoI mutant that is more active than wild-type
      I-DmoI. The phenotype of some of these mutants was reconciled on the basis of similarity to
      the GxxxG helix interaction found in transmembrane proteins. Additionally, a split variant of
      I-DmoI was created, demonstrating that the LAGLIDADG helices of I-DmoI are capable of forming
      and maintaining the protein?protein interface in trans to create an active heterodimer.
AU  - Silva GH
AU  - Belfort M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2004 32: 3156-3168.

PMID- 16872628
VI  - 361
DP  - 2006
TI  - From monomeric to homodimeric endonucleases and back: Engineering novel specificity of LAGLIDADG enzymes.
PG  - 744-754
AB  - Monomeric homing endonucleases of the LAGLIDADG family recognize DNA in a bipartite manner,
      reflecting the underlying structural assembly of two protein domains (A and B) related by
      pseudo 2-fold symmetry. This architecture allows for changes in DNA specificity via the
      distinct combination of these half-site domains. The key to engineering such hybrid proteins
      lies in the LAGLIDADG two-helix bundle that forms both the domain interface and the
      endonuclease active site. In this study, we utilize domain A of the monomeric I-DmoI to
      demonstrate the feasibility of generating functional homodimeric endonucleases that recognize
      palindromic DNA sequences derived from the original, non-palindromic target. Wild-type I-DmoI
      domain A is capable of forming a homodimer (H-DmoA) that binds tightly to, but does not cleave
      efficiently, its anticipated DNA target. Partial restoration of DNA cleavage ability was
      obtained by re-engineering the LAGLIDADG dimerization interface (H-DmoC). Upon fusing two
      copies of H-DmoC via a short peptide linker, a novel, site-specific DNA endonuclease was
      created (H-DmoC2). Like I-DmoI, H-DmoC2 is thermostable and cleaves the new target DNA to
      generate the predicted 4 nt 3'-OH overhangs but, unlike I-DmoI, H-DmoC2 retains stringent
      cleavage specificity when substituting Mn(2+) for Mg(2+) as co-factor. This novel endonuclease
      allows speculation regarding specificity of monomeric LAGLIDADG proteins, while it supports
      the evolutionary genesis of these proteins by a gene duplication event.
AU  - Silva GH
AU  - Belfort M
AU  - Wende W
AU  - Pingoud A
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2006 361: 744-754.

PMID- 10047486
VI  - 286
DP  - 1999
TI  - Crystal structure of the thermostable archaeal intron-encoded endonuclease I-DmoI.
PG  - 1123-1136
AB  - I-DmoI is a 22 kDa endonuclease encoded by an intron in the 23 S rRNA gene of the
      hyperthermophilic archaeon Desulfurococcus mobilis.  The structure of I-DmoI has been
      determined to 2.2 A resolution using multi-wave-length anomalous diffraction techniques.
      I-DmoI, a protein of the LAGLIDADG motif family, represents the first structure of a
      freestanding endonuclease with two LALIDADG motifs, and the first of a thermostable homing
      endonuclease.  I-DmoI consists of two similar alpha/beta domains (alpha beta beta alpha beta
      beta alpha) related by pseudo 2-fold symmetry.  The LAGLIDADG motifs are located at the
      carboxy-terminal end of the first alpha-helix of each domain.  These helices form a two-helix
      bundle at the interface between the domains and are perpendicular to a saddle-shaped DNA
      binding surface, formed by two four-stranded antiparallel beta-sheets. Despite substantially
      different sequences, the overall fold of I-DmoI is similar to that of two other LAGLIDADG
      proteins for which the structures are known, I-CreI and the endonuclease domain of PI-SceI.
      The three structures differ most in the loops connecting the beta-strands, relating to the
      respective DNA target site sizes and geometries.  In addition, the absence of conserved
      residues surrounding the active site, other than those within the LAGLIDADG motif, is of
      mechanistic importance.  Finally, the carboxy-terminal domain of I-DmoI is smaller and has a
      more irregular fold than the amino-terminal domain, which is more similar to I-CreI, a
      symmetric homodimeric endonuclease.  This is reversed compared to PI-SceI, where the
      amino-terminal domain is more similar to carboxy-terminal domain of I-DmoI and to I-CreI, with
      interesting evolutionary implications.
AU  - Silva GH
AU  - Dalgaard JZ
AU  - Belfort M
AU  - Van Roey P
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1999 286: 1123-1136.

PMID- 28428305
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Plasmid-Free Lactococcus lactis subsp. lactis Strain LMG 19460.
PG  - e00210-17
AB  - We report here the draft genome sequence of the plasmid-free Lactococcus lactis subsp. lactis
      strain LMG 19460. This strain has potential application for a
      cost-effective production of food-grade plasmid DNA to use in DNA vaccines,
      produce recombinant proteins, and be used as a mucosal delivery vehicle of
      therapeutic molecules.
AU  - Silva IN
AU  - Duarte S
AU  - Moreira LM
AU  - Monteiro GA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00210-17.

PMID- 25676757
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Two Burkholderia multivorans Sequential Isolates from a Chronic Lung Infection of a Cystic Fibrosis Patient.
PG  - e01531-14
AB  - Burkholderia multivorans belongs to the Burkholderia cepacia complex, which comprises
      opportunistic pathogens infecting cystic fibrosis (CF) patients. Here,
      we report the genome sequences and annotations of two sequential B. multivorans
      clinical isolates (D2095 and D2214) displaying different traits. The differences
      in the genomic contents of these isolates may provide clues regarding the
      evolution of B. multivorans within the airways of a CF patient.
AU  - Silva IN
AU  - Santos PM
AU  - Moreira LM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01531-14.

PMID- 29496842
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Sphingorhabdus sp. Strain EL138, a Metabolically Versatile Alphaproteobacterium Isolated from the Gorgonian Coral Eunicella labiata.
PG  - e00142-18
AB  - Here, we report the draft genome sequence of Sphingorhabdus sp. strain EL138, an
      alphaproteobacterium that shows potential to degrade polycyclic aromatic
      compounds and to cope with various heavy metals and antibiotics. Moreover, the
      strain, isolated from the gorgonian coral Eunicella labiata, possesses several
      genes involved in the biosynthesis of polyphosphates, polyketides, and
      terpenoids.
AU  - Silva SG
AU  - Lago-Leston A
AU  - Costa R
AU  - Keller-Costa T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00142-18.

PMID- 29437111
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Xanthomonas citri pv. anacardii Strain IBSBF2579 from Brazil.
PG  - e01574-17
AB  - The bacterium Xanthomonas citri pv. anacardii is the agent of angular leaf spot of the cashew
      tree (Anacardium occidentale L.). The complete genome sequencing of the strain IBSBF2579 was
      done on an Illumina HiSeq 2500 platform. The de novo assembly of the X. citri pv. anacardii
      strain IBSBF2579 genome yielded 133 contigs, with a size of 5,329,247 bp and a G+C content of
      64.03%. The prediction was performed by GeneMarkS and the automatic annotation by Rapid
      Annotations using Subsystems Technology (RAST), with 4,406 identified genes.
AU  - Silva-Junior WJ
AU  - Farias ARG
AU  - Lima NB
AU  - Benko-Iseppon AM
AU  - Aburjaile F
AU  - Balbino VQ
AU  - Falcao RM
AU  - Leitao PJSS
AU  - Sousa-Paula LC
AU  - Mariano RLR
AU  - Souza EB
AU  - Gama MAS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01574-17.

PMID- 25466623
VI  - 109
DP  - 2014
TI  - The draft genome sequence of multidrug-resistant Pseudomonas aeruginosa strain CCBH4851, a nosocomial isolate belonging to clone SP (ST277) that is prevalent in Brazil.
PG  - 1086-1087
AB  - The high occurrence of nosocomial multidrug-resistant (MDR) microorganisms is
      considered a global health problem. Here, we report the draft genome sequence of
      a MDR Pseudomonas aeruginosa strain isolated in Brazil that belongs to the
      endemic clone ST277. The genome encodes important resistance determinant genes
      and consists of 6.7 Mb with a G+C content of 66.86% and 6,347 predicted coding
      regions including 60 RNAs.
AU  - Silveira M
AU  - Albano R
AU  - Asensi M
AU  - Assef AP
PT  - Journal Article
TA  - Memorias do Instituto Oswaldo Cruz
JT  - Memorias do Instituto Oswaldo Cruz
SO  - Memorias do Instituto Oswaldo Cruz 2014 109: 1086-1087.

PMID- 15297930
VI  - 49
DP  - 2004
TI  - Characterization of the DNA adenine 5 '-GATC-3 ' methylase HpyIIIM from Helicobacter pylori.
PG  - 47-54
AB  - The effect of inactivation of the 5'-GATC-3' methylase HpyIIIM in Helicobacter pylori (H.
      pylori) on mismatch repair, adherence, and in
      vitro fitness was examined. Chromosomal DNA from 90 H. pylori strains
      was isolated, and restriction enzyme digestion indicated all strains
      examined possess HpyIIIM. Wild-type H. pylori and a strain with an
      inactive HpyIIIM were found to have rifampicin mutation frequencies of
      2.93 x 10(-7) and 1.05 x 10(-7) (P > 0.05), respectively, indicating
      that HpyIIIM does not appear to be important in mismatch repair.
      Adherence of H. pylori in an in vitro model cell system was also
      unaffected by inactivation of HpyIIIM. Inactivation of HpyIIIM did not
      result in a decrease in fitness, as determined by liquid in vitro
      competition experiments.
AU  - Simala-Grant JL
AU  - Lam E
AU  - Keelan M
AU  - Taylor DE
PT  - Journal Article
TA  - Curr. Microbiol.
JT  - Curr. Microbiol.
SO  - Curr. Microbiol. 2004 49: 47-54.

PMID- Not included in PubMed...
VI  - 41
DP  - 1986
TI  - Properties and recognition sequence of site-specific endonuclease from Streptomyces aureofaciens.
PG  - 357-365
AB  - A type II restriction endonuclease Sau3239I was purified from Streptomyces
      aureofaciens 3239.  The recognition sequence for the enzyme was determined 5' -
      C ^ T C G A G - 3' 3' - G A G C T ^ C - 5' 	and cleaved at the position
      indicated by the arrows, producing a tetranucleotide 5'-terminal extension.
      Therefore Sau 3239I endonuclease is an isoschizomer of XhoI endonuclease.	The
      contribution of the type II restriction enzymes to recombinant DNA technology
      has stimulated extensive search for these enzymes which have been isolated from
      a great variety of bacteria, including the actinomycetes {Streptomyces
      aureofaciens IKA 18/4} is SauI {Timko et al., 1981}.  Another specific
      restriction endonuclease was found in the chlortetracycline {CTC} producing
      prototrophic strain of Streptomyces aureofaciens CCM 3239 {Gasperik et al.,
      1983}.  We report here this endonuclease designated as Sau 3239I which was
      isolated from this strain.  The isolation procedure and determination of the
      recognition sequence are described.
AU  - Simbochova G
AU  - Timko J
AU  - Zelinkova E
AU  - Zelinka J
PT  - Journal Article
TA  - Biologia (Bratisl)
JT  - Biologia (Bratisl)
SO  - Biologia (Bratisl) 1986 41: 357-365.

PMID- Not included in PubMed...
VI  - 42
DP  - 1987
TI  - Some physical and chemical properties of site-specific endonuclease Sau3239I from Streptomyces aureofaciens.
PG  - 1129-1136
AB  - Sau3239I was isolated and purified from Streptomyces aureofaciens CCM 3239. The
      substrate specificity and the cleavage site of this enzyme is 5' - C^TCGAG - 3'
      and thus it is an isoschizomer of XhoI (Simbochova et al., 1986).  Some of its
      physical properties and substrate specificity are described.
AU  - Simbochova G
AU  - Timko J
AU  - Zelinkova E
AU  - Zelinka J
PT  - Journal Article
TA  - Biologia (Bratisl)
JT  - Biologia (Bratisl)
SO  - Biologia (Bratisl) 1987 42: 1129-1136.

PMID- 7698656
VI  - 155
DP  - 1995
TI  - SanDI, a new type-II restriction endonuclease that recognizes 5'-GG/GWCCC-3'.
PG  - 129-130
AB  - A new restriction endonuclease (ENase), SanDI, has been isolated from an unidentified species
      of Streptomyces. SanDI recognizes the 7-bp interrupted palindrome 5'-GG/GWCCC-3' (W=A or T)
      and cleaves double-stranded DNA after the second G in the sequence, producing 3-nt long 5'
      protruding ends. SanDI is a rare-cutting ENase and should therefore be useful for megabase
      mapping and vector constructions.
AU  - Simcox TG
AU  - Fabian L
AU  - Kretz K
AU  - Hedden V
AU  - Simcox MEC
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 155: 129-130.

PMID- 1756971
VI  - 109
DP  - 1991
TI  - SrfI, a new type-II restriction endonuclease that recognizes the octanucleotide sequence,.
PG  - 121-123
AB  - A new restriction endonuclease, SrfI, has been isolated from an unidentified
      species of Streptomyces.  SrfI recognizes the 8-bp palindrome, 5'-GCCCGGGC and
      cleaves double-stranded DNA after the third C in the sequence, producing blunt
      ends.  SrfI is a rare-cutting enzyme and should therefore be useful for
      megabase mapping.
AU  - Simcox TG
AU  - Marsh SJ
AU  - Gross EA
AU  - Lernhardt W
AU  - Davis S
AU  - Simcox MEC
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1991 109: 121-123.

PMID- 4562392
VI  - 112
DP  - 1972
TI  - Degradation of bacteriophage lambda deoxyribonucleic acid after restriction by Escherichia coli K-12.
PG  - 161-169
AB  - Wild-type bacteria which restrict the deoxyribonucleic acid (DNA) of infecting
      phage when the phage do not carry the proper host modification rapidly degrade
      that restricted DNA to acid-soluble products.  The purified restriction enzyme
      acts as an endonuclease in vitro to cleave restrictable DNA and does not
      further degrade the DNA fragment products.  We have examined mutants of
      Escherichia coli K-12 which lack various nucleases in order to determine which
      nucleases are involved in the rapid acid solubilization in vivo of unmodified
      lambda DNA following restriction.  Bacteria which are wild type, recA-, or
      polA1- degrade about 50% of the unmodified phage DNA within 10 min of
      infection, with little subsequent degradation.  Mutants which are recB- or
      recC- degrade unmodified DNA very slowly, solubilizing about 15% of the DNA by
      10 min after infection.  Two classes of phenotypic revertants of recB-/C-
      mutants were also tested.  Bacteria which are sbcA- restrict poorly and do not
      degrade much of the restricted DNA.  Bacteria which are sbcB- restrict
      normally.  This mutation does not appear to affect degradation of restricted
      phage DNA in recB-/C- mutants, but such degradation is decreased in recB+/C+
      bacteria.  The presence of a functional lambda exonuclease gene is not required
      for degradation after restriction.
AU  - Simmon VF
AU  - Lederberg S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1972 112: 161-169.

PMID- 23412845
VI  - 159
DP  - 2013
TI  - Type 1 and type 2 strains of Mycoplasma pneumoniae form different biofilms.
PG  - 737-747
AB  - Several mycoplasma species have been shown to form biofilms that confer resistance to
      antimicrobials and which may affect the host immune system, thus making treatment and
      eradication of the pathogens difficult. The present study shows that the biofilms formed by
      two strains of the human pathogen Mycoplasma pneumoniae differ quantitatively and
      qualitatively. Compared with strain UAB PO1, strain M129 grows well but forms biofilms that
      are less robust, with towers that are less smooth at the margins. A polysaccharide containing
      N-acetylglucosamine is secreted by M129 into the culture medium but found in tight association
      with the cells of UAB PO1. The polysaccharide may have a role in biofilm formation,
      contributing to differences in virulence, chronicity and treatment outcome between strains of
      M. pneumoniae. The UAB PO1 genome was found to be that of a type 2 strain of M. pneumoniae,
      whereas M129 is type 1. Examination of other M.
      pneumoniae isolates suggests that the robustness of the biofilm correlates with the strain
      type.
AU  - Simmons WL
AU  - Daubenspeck JM
AU  - Osborne JD
AU  - Balish MF
AU  - Waites KB
AU  - Dybvig K
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2013 159: 737-747.

PMID- 22492928
VI  - 86
DP  - 2012
TI  - Genome of Klebsiella sp.-Infecting Bacteriophage vB_KleM_RaK2.
PG  - 5406
AB  - Despite the fact that multidrug-resistant Klebsiella sp. strains emerge rapidly
      (Xu J, et al., Adv. Mater. Res. 268-270:1954-1956, 2011) and bacteriophages have
      been reported to be useful in controlling these bacteria (Kumari S, Harjai K,
      Chhibber S, J. Med. Microbiol. 60:205-210, 2011), the complete genome sequences
      of only five Klebsiella phages (four siphoviruses and one myovirus) can be found
      in databases. In this paper, we report on the complete genome sequence of
      Klebsiella sp.-infecting bacteriophage vB_KleM_RaK2. With a genome size of
      345,809 bp, this is the second largest myovirus and the largest Klebsiella phage
      sequenced to date. This phage differs substantially from other myoviruses since
      411 out of 534 vB_KleM_RaK2 open reading frames have no known functions and lack
      any reliable database matches. Comparative analysis of the genome sequence of
      vB_KleM_RaK2 suggests that this phage forms a distinct phylogenetic branch within
      the family Myoviridae of tailed bacteriophages.
AU  - Simoliunas E
AU  - Kaliniene L
AU  - Truncaite L
AU  - Klausa V
AU  - Zajanckauskaite A
AU  - Meskys R
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 2012 86: 5406.

PMID- 673848
VI  - 5
DP  - 1978
TI  - DNA-methylase from regenerating rat liver: purification and characterisation.
PG  - 2153-2167
AB  - DNA methylase has been purified 660-fold from nuclei from regenerating rat liver. The enzyme
      is able to methylate single stranded (ss) and double stranded (ds) DNA, the only reaction
      product being 5-methylcytosine. Previously unmethylated double stranded DNA from prokaryotes
      (M. luteus) as well as from eukaryotes (Ascaris suis) can serve as substrates. The synthetic
      copolymers (dG-dC)n. (dC-dG)n and (dG,dC)n are also methylated. While SV40 DNA is almost not
      methylated, PM2 DNA is a good substrate even in the supercoiled form. The enzyme methylates 1
      in 17 bases in heterologous M. luteus DNA, but only 1 in 590 in homologous rat liver DNA. The
      high methylation level of M. luteus DNA, an analysis of the methylated pyrimidine isostichs
      and a preliminary dinucleotide analysis suggest that all the CpGs in a DNA can be methylated.
AU  - Simon D
AU  - Grunert F
AU  - Acken UV
AU  - Doring HP
AU  - Kroger H
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1978 5: 2153-2167.

PMID- 11491304
VI  - 309
DP  - 2001
TI  - Covalent joining of the subunits of a homodimeric type II restriction endonuclease: single-chain PvuII endonuclease.
PG  - 89-97
AB  - The PvuII restriction endonuclease has been converted from its natural homodimeric form into a
      single polypeptide chain by tandemly linking
      the two subunits through a short peptide Linker. The arrangement of the
      single-chain PvuII (sc PvuII) is (2-157)-GlySerGlyGly-(2-157), where
      (2-157) represents the amino acid residues of the enzyme subunit and
      Gly-SerGlyGly is the peptide linker. By introducing the corresponding
      tandem gene into Escherichia coli, PvuII endonuclease activity could
      be detected in functional in vivo assays. The sc enzyme was expressed
      at high level as a soluble protein. The purified enzyme was shown to
      have the molecular mass expected for the designed sc protein. Based on
      the DNA cleavage patterns obtained with different substrates, the
      cleavage specificity of the sc PvuII is indistinguishable from that of
      the wild-type (wt) enzyme. The sc enzyme binds specifically to the
      cognate DNA site under non-catalytic conditions, in the presence of
      Ca2+, with the expected 1:1 stoichiometry. Under standard catalytic
      conditions, the sc enzyme cleaves simultaneously the two DNA strands in
      a concerted manner. Steady-state kinetic parameters of DNA cleavage by
      the sc and wt PvuII showed that the sc enzyme is a potent, but somewhat
      less efficient catalyst; the k(cat)/K-M values are 1.11 x 10^9 and
      3.50 x 10^9 min^-1 M^-1 for the sc and wt enzyme, respectively. The
      activity decrease is due to the lower turnover number and to the lower
      substrate affinity. The sc arrangement provides a facile route to
      obtain asymmetrically modified heterodimeric enzymes.
AU  - Simoncsits A
AU  - Tjornhammar ML
AU  - Rasko T
AU  - Kiss A
AU  - Pongor S
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2001 309: 89-97.

PMID- 25260590
VI  - 42
DP  - 2014
TI  - ClpXP protease targets long-lived DNA translocation states of a helicase-like motor to cause restriction alleviation.
PG  - 12082-12091
AB  - We investigated how Escherichia coli ClpXP targets the helicase-nuclease (HsdR) subunit of the
      bacterial Type I restriction-modification enzyme EcoKI during restriction alleviation (RA). RA
      is a temporary reduction in endonuclease activity that occurs when Type I enzymes bind
      unmodified recognition sites on the host genome. These conditions arise upon acquisition of a
      new system by a naive host, upon generation of new sites by genome rearrangement/mutation or
      during homologous recombination between hemimethylated DNA. Using recombinant DNA and proteins
      in vitro, we demonstrate that ClpXP targets EcoKI HsdR during dsDNA translocation on circular
      DNA but not on linear DNA. Protein roadblocks did not activate HsdR proteolysis. We suggest
      that DNA translocation lifetime, which is elevated on circular DNA relative to linear DNA, is
      important to RA. To identify the ClpX degradation tag (degron) in HsdR, we used bioinformatics
      and biochemical assays to design N- and C-terminal mutations that were analysed in vitro and
      in vivo. None of the mutants produced a phenotype consistent with loss of the degron,
      suggesting an as-yet-unidentified recognition pathway. We note that an EcoKI nuclease mutant
      still produces cell death in a clpx- strain, consistent with DNA damage induced by unregulated
      motor activity.
AU  - Simons M
AU  - Diffin FM
AU  - Szczelkun MD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2014 42: 12082-12091.

PMID- 21712244
VI  - 39
DP  - 2011
TI  - Recycling of protein subunits during DNA translocation and cleavage by Type I restriction-modification enzymes.
PG  - 7656-7666
AB  - The Type I restriction-modification enzymes comprise three protein subunits; HsdS and HsdM
      that form a methyltransferase (MTase) and HsdR
      that associates with the MTase and catalyses Adenosine-5'-triphosphate
      (ATP)-dependent DNA translocation and cleavage. Here, we examine whether
      the MTase and HsdR components can 'turnover' in vitro, i.e. whether they
      can catalyse translocation and cleavage events on one DNA molecule,
      dissociate and then re-bind a second DNA molecule. Translocation
      termination by both EcoKI and EcoR124I leads to HsdR dissociation from
      linear DNA but not from circular DNA. Following DNA cleavage, the HsdR
      subunits appear unable to dissociate even though the DNA is linear,
      suggesting a tight interaction with the cleaved product. The MTases of
      EcoKI and EcoAI can dissociate from DNA following either translocation or
      cleavage and can initiate reactions on new DNA molecules as long as free
      HsdR molecules are available. In contrast, the MTase of EcoR124I does not
      turnover and additional cleavage of circular DNA is not observed by
      inclusion of RecBCD, a helicase-nuclease that degrades the linear DNA
      product resulting from Type I cleavage. Roles for Type I restriction
      endonuclease subunit dynamics in restriction alleviation in the cell are
      discussed.
AU  - Simons M
AU  - Szczelkun MD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2011 39: 7656-7666.

PMID- 10910347
VI  - 406
DP  - 2000
TI  - The genome sequence fo the plant pathogen Xylella fastidiosa.
PG  - 151-157
AB  - Xylella fastidiosa is a fastidious, xylem-limited bacterium that causes a range of
      economically important plant diseases.  Here we report the complete genome sequence of X.
      fastidiosa clone 9a5c, which causes citrus variegated chlorosis-a serious disease of orange
      trees.  The genome comprises a 52.7% GC-rich 2,679,305-base-pair circular chromosome and two
      plasmids of 51,158 bp and 1,285 bp.  We can assign putative functions to 47% of the 2,904
      predicted coding regions.  Efficient metabolic functions are predicted, with sugars as the
      principal energy and carbon source, supporting existence in the nutrient-poor xylem sap.  The
      mechanisms associated with pathogenicity and virulence involve toxins, antibiotics and ion
      sequestration systems, as well as bacterium-bacterium and bacterium-host interactions mediated
      by a range of proteins.  Orthologues of some of these proteins have only been identified in
      animal and human pathogens; their presence in X. fastidiosa indicates that the molecular basis
      for bacterial pathogenicity is both conserved and independent of host.  At least 83 genes are
      bacteriophage-derived and include virulence-associated genes from other bacteria, providing
      direct evidence of phage-mediated horizontal gene transfer.
AU  - Simpson AJ et al
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2000 406: 151-157.

PMID- 28218898
VI  - 14
DP  - 2017
TI  - Detecting DNA cytosine methylation using nanopore sequencing.
PG  - 407-410
AB  - In nanopore sequencing devices, electrolytic current signals are sensitive to base
      modifications, such as 5-methylcytosine (5-mC). Here we quantified the
      strength of this effect for the Oxford Nanopore Technologies MinION sequencer. By
      using synthetically methylated DNA, we were able to train a hidden Markov model
      to distinguish 5-mC from unmethylated cytosine. We applied our method to sequence
      the methylome of human DNA, without requiring special steps for library
      preparation.
AU  - Simpson JT
AU  - Workman RE
AU  - Zuzarte PC
AU  - David M
AU  - Dursi LJ
AU  - Timp W
PT  - Journal Article
TA  - Nat. Methods
JT  - Nat. Methods
SO  - Nat. Methods 2017 14: 407-410.

PMID- 21304632
VI  - 1
DP  - 2009
TI  - Complete genome sequence of Kytococcus sedentarius type strain (541).
PG  - 12-20
AB  - Kytococcus sedentarius (ZoBell and Upham 1944) Stackebrandt et al. 1995 is the type strain of
      the species, and is of phylogenetic interest because of its
      location in the Dermacoccaceae, a poorly studied family within the
      actinobacterial suborder Micrococcineae. Kytococcus sedentarius is known for the
      production of oligoketide antibiotics as well as for its role as an opportunistic
      pathogen causing valve endocarditis, hemorrhagic pneumonia, and pitted
      keratolysis. It is strictly aerobic and can only grow when several amino acids
      are provided in the medium. The strain described in this report is a free-living,
      nonmotile, Gram-positive bacterium, originally isolated from a marine
      environment. Here we describe the features of this organism, together with the
      complete genome sequence, and annotation. This is the first complete genome
      sequence of a member of the family Dermacoccaceae and the 2,785,024 bp long
      single replicon genome with its 2639 protein-coding and 64 RNA genes is part of
      the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Sims D et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2009 1: 12-20.

PMID- 3014571
VI  - 41
DP  - 1986
TI  - Inhibition of bacterial DNA-dependent RNA polymerases and restriction endonuclease by UV-absorbing components from Propolis.
PG  - 131-132
AB  - Several UV-absorbing substances inhibiting the DNA-dependent RNA polymerases of
      Escherichia coli and Streptomyces aureofaciens, as well as the restriction
      endonuclease EcoRI have been isolated from the water-soluble extract of
      Propolis by two-dimensional paper chromatography.  The inhibition of bacterial
      RNA-polymerases by the components of Propolis was probably due to the loss of
      their ability to bind to DNA.  The general characteristic of the UV-absorbing
      component of Propolis with the most pronounced inhibitory effect upon
      transcription in vitro is described.
AU  - Simuth J
AU  - Trnovsky J
AU  - Jelokova J
PT  - Journal Article
TA  - Pharmazie
JT  - Pharmazie
SO  - Pharmazie 1986 41: 131-132.

PMID- 8289838
VI  - 0
DP  - 1993
TI  - Class II restriction-modification systems in Enterobacter cloacae.
PG  - 10-13
AB  - Various clinical strains of Enterobacter cloacae have been examined for the presence of
      site-specific endonuclease activities. Type II restriction endonucleases have been isolated
      from 6 strains. Recognition sequences for all of these enzymes have been determined and the
      cleavage sites were identified for two of them. The enzymes proved to be isoschizomers of
      EcoRII and PstI. Restriction endonucleases Ecl2zI and Ecl37kI recognize the nucleotide
      sequences CTGCA/G and are true isoschizomers of PstI. The genes for Ecl54kI and Ecl57kI
      restriction modification systems (isoschizomers of EcoRII) were found to be located on the
      IncN group of plasmids, whereas the genes for Ecl2zI and Ecl699kI seem to be located on the
      chromosomes of the host cells.
AU  - Sineva EV
AU  - Zakharova GG
AU  - Tarutina ZE
AU  - Kravetz AN
AU  - Solonin AS
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1993 0: 10-13.

PMID- Not included in PubMed...
VI  - 73
DP  - 1990
TI  - Plasmid-induced abortive infection in Lactococci: a review.
PG  - 2239-2251
AB  - The longevity of mesophilic lactococci in dairy fermentations depends to a large extent on
      whether or not the strains carry effective phage-resistance mechanisms.  Among the different
      systems that exist in lactococci, abortive infection is highly significant because it is the
      cell's strongest defense against the phages that most often disrupt cheese making.
      Phage-resistant strains that carry plasmids encoding abortive defenses have already been
      constructed using genetic strategies.  These strains have been used successfully in commercial
      cheese making since 1986.  Still, our knowledge of the molecular mechanisms underlying
      abortive infection and the means through which it retards phage development is limited.  This
      review addresses abortive infection in lactococci relative to similar phenomena in other
      bacteria.  Further understanding of the abortive infection process should accelerate genetic
      efforts to strengthen this phage defense as well as facilitate efforts to combine it with
      other mechanisms in the construction of specialized strains that are insensitive to attack by
      phage.
AU  - Sing WD
AU  - Klaenhammer TR
PT  - Journal Article
TA  - J. Dairy Sci.
JT  - J. Dairy Sci.
SO  - J. Dairy Sci. 1990 73: 2239-2251.

PMID- Not included in PubMed...
VI  - 136
DP  - 1990
TI  - Characteristics of phage abortion conferred in lactococci by the conjugal plasmid pTR2030.
PG  - 1807-1815
AB  - The effect of pTR2030 on phage DNA injection, transfection, release of progeny phage, and cell
      death was evaluated for a number of lactococcal phages. Infection by prolate phage c2 and
      small isometric phage p2 of derivatives of Lactococcus lactis LM2301 with or without pTR2030,
      and infection by small isometric phage phi31 of derivatives of L. lactis NCK202 with or
      without pTR2030 was studied. Phage DNA injection was not affected by pTR2030 when examined
      using blender-resistant-complex assays with 32P-labelled DNA or by observaton of phage
      labelled with the fluorescent dye 4',6-diamidino-2-phenylindole(DAPI). Successful
      transfection of hosts bearing pTR2030 indicated that the plasmid did not retard passage of
      naked phage DNA across the membrane. Infective-centre assays were used to determine whether
      progeny were released from phage-infected pTR2030 hosts that do not support plaque formation
      by small isometric phages. In all cases, pTR2030 reduced the number of infected hosts which
      generated viable phage. When progeny were released, the phage burst size was reduced. The data
      confirmed that pTR2030 interferes with development of prolate and small isometric phages in a
      similar manner via a classical abortive infection mechanism.
AU  - Sing WD
AU  - Klaenhammer TR
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1990 136: 1807-1815.

PMID- Not carried by PubMed...
VI  - 88
DP  - 1988
TI  - Characterization of a recombinant plasmid, pTRK12, encoding restriction/modification and proteolytic activities in lactic streptococci.
PG  - 147
AB  - Restriction and modification (R+/M+) activities are widely distributed in
      lactic streptococci and often associated with plasmid DNA.  A
      lactose-fermenting (Lac+) transconjugant (designated Streptococcus lactis
      NCK40) was isolated from matings between S. cremoris TDM1 and a plasmid-free
      recipient.  NCK40 contained a plasmid approximating 100 kb (pTRK11) that
      correlated with Lac+ and conjugal transfer ability (Tra+) and a 13 kb plasmid
      (pTRK10) which was linked to proteolytic activity (Prt+).  S. lactis NCK40
      exhibited phage restriction and modification; the efficiency of plaquing (EOP)
      for phage c2 was 10-3.  Two types of Lac- derivatives of NCK40, both cured of
      pTRK11, were isolated.  One exhibited R-/M- Prt+ and contained pTRK10.  The
      second type was R+/M+ Prt+ and contained a new 30 kb plasmid (pTRK12).  pTRK10
      and pTRK11 were not detected in the R+/M+ Prt+ variant.  Restriction analyses
      demonstrated that pTRK12 (R+/M+ Prt+) contained all detectable regions of
      pTRK10 (Prt+).  Hybridization experiments using a 32P-pTRK11 probe identified
      regions of pTRK12 that originated from the 100 kb plasmid, pTRK11.  These data
      demonstrated that formation of a new 30 kb plasmid encoding R+/M+ and Prt+ was
      the result of recombination events between pTRK10 and pTRK11 occurring upon
      destabilization of Lac+.
AU  - Sing WD
AU  - Klaenhammer TR
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1988 88: 147.

PMID- Not included in PubMed...
VI  - 74
DP  - 1991
TI  - Characterization of restriction-modification plasmids from Lactococcus lactis ssp. cremoris and their effects when combined with pTR2030.
PG  - 1133-1144
AB  - Three different restriction-modification plasmids (pTRK12, pTRK30, pTRK317)
      were isolated from an industrial starter strain, Lactococcus lactis ssp.
      cremoris TDM1.  A lactose-fermenting transconjugant, Lactococcus lactis ssp.
      lactis NCK40, was isolated from matings between L. lactis ssp. cremoris TDM1
      and a plasmid-free recipient.  The NCK40 transmissible plasmid (pTRK11)
      encoding for restriction modification and a 13.5-kb plasmid (pTRK10) encoding
      proteolytic activity.  Following isolation of lactose-negative derivatives from
      NCK40, a 30.5-kb plasmid, pTRK12, was identified that encoded proteolytic and
      restriction-modification of the identical specificity as pTRK11.  Restriction
      analyses and hybridization experiments indicated that pTRK12 contained
      sequences from pTRK11 and all of pTRK10.  Cotransformation of total plasmid DNA
      from L. lactis ssp. cremoris TDM1 with vector pVS2 identified two other
      restriction-modification plasmids, pTRK30 (28.0 kb) and pTRK317 (15.5 kb).
      Efficiencies of plaquing from phage c2 on restriction-modification
      transconjugants and transformants was 10/2 to 10/4.  The specificity of
      restriction-modification activities conferred by each of the three plasmids was
      different.  When the abortive infection plasmid pTR2030 was combined with
      pTRK30, both phage inhibition phenotypes were expressed.  However, when pTR2030
      was combined with pTRK12, the abortive infection phenotype was not fully
      expressed.  Significant cell death occurred when abortive infection cells
      containing only pTR2030 were infected with phage.  Combining the
      restriction-modification system of pTRK30 with pTR2030 significantly improved
      cell survival following phage infection.  Operation of restriction-modification
      systems in conjunction with the abortive defense mechanism maximized cell
      survival.  The data suggest that cell death is minimized when the lytic cycle
      is halted by restriction before abortive infection responses induce phage
      abortion and kill the cell.
AU  - Sing WD
AU  - Klaenhammer TR
PT  - Journal Article
TA  - J. Dairy Sci.
JT  - J. Dairy Sci.
SO  - J. Dairy Sci. 1991 74: 1133-1144.

PMID- 16347085
VI  - 51
DP  - 1986
TI  - Conjugal transfer of bacteriophage resistance determinants on pTR2030 into Streptococcus cremoris strains.
PG  - 1264-1271
AB  - Agar surface conjugal matings were used to introduce heat-sensitive phage
      resistance (hsp+) determinants carried on the conjugal plasmid pTR2030 into
      Streptococcus cremoris KH, HP, 924, and TDM1.  Lactose-fermenting (Lac+)
      transconjugants were selected from matings of Lac- variants of S. cremoris KH,
      HP, 924, and TDM1 with Streptococcus lactis ME2 or a high-frequency donor, S.
      lactis T-EK1 (pTR1040, Lac+; pTR2030, Hsp+).  For all of the S. cremoris
      strains examined, select Lac+ transconjugants were completely resistant to
      plaquing by their homologous lytic phages.  In all cases the plaquing
      efficiencies were less than 10-9.  Acquisition of a 30-megadalton plasmid
      (pTR2030) in the S. cremoris phage-resistant transconjugants was demonstrated
      by direct plasmid analysis, by hybridization with 32P-labeled probes, or by
      conugal transfer of pTR2030 out of the phage-resistant transconjugants into a
      plasmid-cured recipient, S. lactis LM2302.  Acid production, coagulation
      ability, and proteolytic activity of phage-resistant transconjugants in milk
      were comparable to those of their phage-sensitive parents.  Further, S.
      cremoris phage-resistant transconjugants were not attacked by phage in starter
      culture activity tests, which included a 40C incubation period.  The results
      demonstrated that phage resistance determinants on pTR2030 could be conjugally
      transferred to a variety of S. cremoris strains and confer resistance to phage
      under conditions encountered during cheese manufacture.  Phage-resistant
      transconjugants of S. cremoris M43 and HP were also constructed without the use
      of antibiotic markers to select conjugal recipients from mating mixtures.
AU  - Sing WD
AU  - Klaenhammer TR
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1986 51: 1264-1271.

PMID- 16348864
VI  - 59
DP  - 1993
TI  - A strategy for rotation of different bacteriophage defenses in a lactococcal single-strain started culture system.
PG  - 365-372
AB  - A new strategy for starter culture rotations was developed for a series of phage-resistant
      clones genetically derived from a single strain of Lactococcus lactis subsp. lactis.
      Phage-resistant derivatives carrying different defense systems were constructed via
      conjugatiion with various plasmids encoding abortive infection (Abi/Hsp) and/or restriction
      and modification (R/M) systems of different specificity. The plasmids included pTR2030 (Hsp+
      R+/M+),pTN20 (Abi+ R+/M+), pTRK11 (R+/M+), and pTRK68 (R+/M+). Selected phage-resistant
      transconjugants or transformants were evaluated in different rotation sequences through cycles
      of the Heap-Lawrence starter culture activity test in milk contaminated with phage and when
      from the previous cycle. When used in consecutive sequences, derivative strains carrying the
      R/M systems encoded by pTN20, pTRK11, and pTRK68 retarded phage development when the initial
      levels of phage contamination were below 102 PFU/ml but not when levels were increased to 103
      PFU/ml. Use of a derivative bearing pTR2030 (Hsp+ R+/M+) at the beginning of the rotation
      prevented phage development, even when the inital levels of phage contamination were high (106
      PFU/ml). Alternating the type and specificity of R/M and Abi defenses through the rotation
      prevented phage proliferation and in some cases eliminated contaminting phages. A model
      rotation sequence for the phage defense rotation strategy was developed and performed
      sucessfully over nine cycles of the Heap-Lawrence starter culture activity test in the
      presence of high-titer commercial phage composites. This phage defense rotation strategy is
      designed to protect a highly specilized Lactococcus strain from phage attack during continuous
      and extended use in the dairy industry.
AU  - Sing WD
AU  - Klaenhammer TR
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1993 59: 365-372.

PMID- 23105054
VI  - 194
DP  - 2012
TI  - Genome Sequence of Nitratireductor aquibiodomus Strain RA22.
PG  - 6307
AB  - The genus Nitratireductor represents nitrate-reducing bacteria from the family
      Phyllobacteriaceae. Here we report the draft genome sequence of Nitratireductor
      aquibiodomus strain RA22, which contains 4,592,790 bp, with a G+C content of
      61.30%, and has 4,241 protein coding genes.
AU  - Singh A
AU  - Jangir PK
AU  - Kumari C
AU  - Sharma R
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6307.

PMID- 23868132
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Indibacter alkaliphilus Strain LW1T, Isolated from Lonar Lake, a Haloalkaline Lake in the Buldana District of Maharashtra, India.
PG  - e00513-13
AB  - We report the 5.0-Mb genome sequence of Indibacter alkaliphilus strain LW1(T), isolated from a
      haloalkaline crater lake in the Buldana district, Maharashtra,
      India.
AU  - Singh A
AU  - Kumar JP
AU  - Sharma R
AU  - Singh A
AU  - Kumar PA
AU  - Shivaji S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00513-13.

PMID- 25059877
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Lutibaculum baratangense Strain AMV1T, Isolated from a Mud Volcano in Andamans, India.
PG  - e00735-14
AB  - The 4.3-Mb genome of Lutibaculum baratangense strain AMV1(T), isolated from a soil sample
      collected from a mud volcano in Andamans, India, is reported. The
      draft genome of strain Lutibaculum baratangense AMV1(T) consists of 4,300,776 bp
      with a G+C content of 66.93 mol% and 4,198 predicted coding regions, including 56
      RNAs.
AU  - Singh A
AU  - Sreenivas A
AU  - Sathyanarayana RG
AU  - Pinnaka AK
AU  - Shivaji S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00735-14.

PMID- 18665914
VI  - 56
DP  - 2008
TI  - Cooperative activity of DNA methyltransferases for maintenance of symmetrical and non-symmetrical cytosine methylation in Arabidopsis thaliana.
PG  - 814-823
AB  - Maintenance of cytosine methylation in plants is controlled by three DNA methyltransferases.
      MET1 maintains CG methylation, and DRM1/2 and
      CMT3 act redundantly to enforce non-CG methylation. RPS, a repetitive
      hypermethylated DNA fragment from Petunia hybrida, attracts DNA
      methylation when transferred into Petunia or other species. In
      Arabidopsis thaliana, which does not contain any RPS homologues, RPS
      transgenes are efficiently methylated in all sequence contexts. To test
      which DNA methylation pathways regulate RPS methylation, we examined
      maintenance of RPS methylation in various mutant backgrounds.
      Surprisingly, CG methylation was lost in a drm1/2/cmt3 mutant, and
      non-CG methylation was almost completely eliminated in a met1 mutant.
      An unusual cooperative activity of all three DNA methyltransferases is
      therefore required for maintenance of both CG and non-CG methylation in
      RPS. Other unusual features of RPS methylation are the independence of
      its non-CG methylation from the RNA-directed DNA methylation (RdDM)
      pathway and the exceptional maintenance of methylation at a CC(m)TGG
      site in some epigenetic mutants. This is indicative of activity of a
      methylation system in plants that may have evolved from the DCM
      methylation system that controls CC(m)WGG methylation in bacteria. Our
      data suggest that strict separation of CG and non-CG methylation
      pathways does not apply to all target regions, and that caution is
      required in generalizing methylation data obtained for individual
      genomic regions.
AU  - Singh A
AU  - Zubko E
AU  - Meyer P
PT  - Journal Article
TA  - Plant J.
JT  - Plant J.
SO  - Plant J. 2008 56: 814-823.

PMID- 17602219
VI  - 76
DP  - 2007
TI  - Selective loss of lin genes from hexachlorocyclohexane-degrading Pseudomonas aeruginosa ITRC-5 under different growth conditions.
PG  - 895-901
AB  - The chlorinated insecticide a-hexachlorocyclohexane
      (a-HCH) is sequentially metabolized by the
      products of linA, linB, linC, linD, linE, and linF genes to
      a-ketoadipate, which is subsequently mineralized. Two or
      more copies of these genes are present in the bacterium
      Pseudomonas aeruginosa ITRC-5 that was isolated earlier
      by selective enrichment on technical-HCH. At least one
      copy of linA, linB, linC, linD, and possibly linE is lost from
      ITRC-5 upon its growth on a-HCH. All the lin genes,
      however, are lost when the bacterium was grown in Luria-
      Bertani (LB) medium. The loss of lin genes is accompanied
      with the loss/rearrangement of insertion sequence IS6100
      genes. Concomitant to the loss of lin genes, the degradation
      of HCH-isomers by "a-HCH grown cells" is slower, when
      compared with "technical-HCH grown cells", and is
      completely lost by "LB-grown cells". The selective loss
      of lin genes during different growth conditions has not been
      reported before and is expected to help in understanding the
      dynamism of degradative genes.
AU  - Singh AK
AU  - Chaudhary P
AU  - Macwan AS
AU  - Diwedi UN
AU  - Kumar A
PT  - Journal Article
TA  - Appl. Microbiol. Biotechnol.
JT  - Appl. Microbiol. Biotechnol.
SO  - Appl. Microbiol. Biotechnol. 2007 76: 895-901.

PMID- 29097480
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Hydrocarbon-Degrading Bacterium Acinetobacter pittii Strain ABC Isolated from Noonmati Refinery, Assam, India.
PG  - e01264-17
AB  - We report here the 3.84-Mb draft genome sequence of hydrocarbon-degrading Acinetobacter pittii
      strain ABC isolated from oil-contaminated soil in Guwahati,
      India. The genome sequence contains 3,602 coding sequences and a G+C content of
      38.83%. This is the first report of the genome sequence of an Acinetobacter
      pittii from an oil-contaminated environment.
AU  - Singh AK
AU  - Chettri B
AU  - Ghosh A
AU  - Chikara SK
AU  - Tripathi T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01264-17.

PMID- 29122880
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Novosphingobium panipatense Strain P5:ABC, Isolated from Hydrocarbon-Contaminated Soil from Noonmati Refinery, Assam, India.
PG  - e01265-17
AB  - Novosphingobium panipatense P5:ABC is a hydrocarbon-degrading bacterium isolated  from
      petroleum-contaminated soil. Here, we present the 5.74-Mb draft genome
      sequence with 5,206 genes and an average G+C content of 64.7%. The genomic
      information will improve our understanding of the diversity of N. panipatense and
      the mechanisms of microbe-based hydrocarbon degradation.
AU  - Singh AK
AU  - Chettri B
AU  - Ghosh A
AU  - Chikara SK
AU  - Tripathi T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01265-17.

PMID- 27034497
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Mycobacterium fortuitum Isolated from Murine Brain.
PG  - e00191-16
AB  - Mycobacterium fortuitumsubsp.fortuitumATCC 6841 is a type and standard laboratory testing
      quality control strain. We report here the completed draft genome
      sequence for a strain isolated from the brains ofM. fortuitum-infected mice.
AU  - Singh AK
AU  - Karaulia P
AU  - Chopra S
AU  - Dasgupta A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00191-16.

PMID- 24029763
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Sphingobium quisquiliarum Strain P25T, a Novel Hexachlorocyclohexane (HCH)-Degrading Bacterium Isolated from an HCH Dumpsite.
PG  - e00717-13
AB  - Here, we report the draft genome sequence (4.2 Mb) of Sphingobium quisquiliarum strain P25(T),
      a natural lin (genes involved in degradation of hexachlorocyclohexane [HCH] isomers) variant
      genotype, isolated from a heavily contaminated (450 mg HCH/g of soil) HCH dumpsite.
AU  - Singh AK
AU  - Sangwan N
AU  - Sharma A
AU  - Gupta V
AU  - Khurana JP
AU  - Lal R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00717-13.

PMID- 25745001
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Cyanobacterium Hassallia byssoidea Strain VB512170, Isolated from Monuments in India.
PG  - e00064-15
AB  - The draft genome assembly of Hassallia byssoidea strain VB512170 with a genome size of ~13 Mb
      and 10,183 protein-coding genes in 62 scaffolds is reported here
      for the first time. This is a terrestrial hydrophobic cyanobacterium isolated
      from monuments in India. We report several copies of luciferase and antibiotic
      genes in this organism.
AU  - Singh D
AU  - Chandrababunaidu MM
AU  - Panda A
AU  - Sen D
AU  - Bhattacharyya S
AU  - Adhikary SP
AU  - Tripathy S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00064-15.

PMID- 25953161
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Brucella abortus Virulent Strain 544.
PG  - e00419-15
AB  - Here, we present the draft genome sequence and annotation of Brucella abortus virulent strain
      544. The genome of this strain is 3,289,405 bp long, with 57.2%
      G+C content. A total of 3,259 protein-coding genes and 60 RNA genes were
      predicted.
AU  - Singh DK
AU  - Kumar A
AU  - Tiwari AK
AU  - Sankarasubramanian J
AU  - Vishnu US
AU  - Sridhar J
AU  - Gunasekaran P
AU  - Rajendhran J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00419-15.

PMID- 
VI  - 76
DP  - 2004
TI  - Abasic site stabilization by aromatic DNA base surrogates: High-affinity binding to a base-flipping DNA-methyltransferase.
PG  - 1563-1570
AB  - DNA-methyltransferases catalyze the sequence-specific transfer of the methyl group of
      S-adenosylmethionine to target bases in genomic DNA.
      For gaining access to their target embedded within a double-helical
      structure, DNA-methyltransferases (DNA-MTases) rotate the target base
      out of the DNA helix. This base-flipping leads to the formation of an
      apparent abasic site. MTases such as cytosine-specific M.HhaI and
      M.HaeIII and also the repair enzyme uracil DNA glycosylase (UDG)
      insert amino acid side chains into the opened space and/or rearrange
      base-pairing. The adenine-specific DNA MTase M.TaqI binds without
      amino acid insertion. This binding mode allows for a substitution of
      the orphaned thymine with larger DNA base surrogates without steric
      interference by inserted amino acid side chains. DNA containing
      pyrenyl, naphthyl, acenaphthyl, and biphenyl residues was tested in
      M.TaqI binding studies. The synthesis of DNA building blocks required
      the formation of a C-glycosidic bond, which was established by using
      protected 1-chloro-2-deoxyribose as glycosyl donor and organocuprates
      as glycosyl acceptors. It is shown that all of the base surrogates
      enhanced the binding affinity to M.TaqI. Incorporation of pyrene
      increased the binding affinity by a factor of 400. Interestingly, there
      is a correlation between the observed order of dissociation constants
      and the ability of a base surrogate to stabilize abasic sites in model
      duplexes.
AU  - Singh I
AU  - Beuck C
AU  - Bhattacharya A
AU  - Hecker W
AU  - Parmar VS
AU  - Weinhold E
AU  - Seitz O
PT  - Journal Article
TA  - Pure Appl. Chem.
JT  - Pure Appl. Chem.
SO  - Pure Appl. Chem. 2004 76: 1563-1570.

PMID- 1737615
VI  - 6
DP  - 1992
TI  - Active genes in budding yeast display enhanced in vivo accessibility to foreign DNA methylases: a novel in vivo probe for chromatin structure of yeast.
PG  - 186-196
AB  - Unlike higher eukaryotes, where an inverse correlation has been generally
      observed between gene expression and methylation of CpG sites, the budding
      yeast Saccharomyces cerevisiae lacks DNA methylation.  Gene regulatory
      mechanisms can function independently of DNA methylation in yeast, and yeast
      strains expressing foreign DNA methylases that modify adenine and CpG residues
      have been found to be viable.  We have used such strains to determine whether
      the transcriptional status of genes can influence the level of their DNA
      methylation in vivo.  Several genes were tested, for example, GAL1, -7, and
      -10, PHO5, HMRa and HML alpha, and STE2 and STE3.  Surprisingly, we found that
      all the genes displayed several fold more methylation in the expressed state as
      compared to the repressed state.  This procedure serves as a novel in vivo
      probe for the chromatin structure of yeast and potentially for higher
      eukaryotes.
AU  - Singh J
AU  - Klar AJS
PT  - Journal Article
TA  - Genes Dev.
JT  - Genes Dev.
SO  - Genes Dev. 1992 6: 186-196.

PMID- 26564052
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of the Drug-Naive Classical Staphylococcus aureus Strain FDA209P.
PG  - e01343-15
AB  - We report the complete genome sequence of the methicillin-sensitive Staphylococcus aureus
      (MSSA) strain FDA209P (ATCC 6538P and NCTC 7447).
AU  - Singh M
AU  - Sasaki T
AU  - Matsuo M
AU  - Morimoto Y
AU  - Aiba Y
AU  - Hiramatsu K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01343-15.

PMID- 7669263
VI  - 12
DP  - 1995
TI  - Inhibitory effects of a GC-sequence- and minor groove-binding Hoechst 33258 analogue on DNA cleavage by selected restriction endonucleases.
PG  - A220
AB  - In continuance of our research efforts in the area of employing the important features of
      ligand-DNA molecular recognition in expanding the design and development of minor groove
      binding class of compounds, we recently reported a bis(pyridoimidazole) analogue of Hoechst
      33258 and demonstrated its preference for selective binding to a GC-rich sequence.  Such
      compounds offer an approach to the experimental manipulation of sequence-specific protein-DNA
      interactions.  A convenient way to test this hypothesis is to look for the effects on the
      DNA-cleavage activity of restriction enzymes with recognition sites that are comparable in
      size and nature to the ligand binding sites.  We have observed distinct inhibitory effects of
      the bis(pyridoimidazole) compound on the cleavage of EcoRI-linearized pBR322 DNA in individual
      agarose gel electrophoresis assays by three selected endonucleases, MscI (at 5'-TGGCCA),
      NruI (at 5'TCGCGA), and FspI (at 5'-TGCGCA).  The extent to which this minor groove binding
      ligand provides protection of the GC-rich sites towards restriction cleavage can be ranked, in
      qualitative terms, as TGGCCA >> TCGCGA > TGCGCA.  It is important to recognize that the
      restriction enzymes are widely believed to interact through the major groove of their cognate
      DNA sequences and the observed effects presumably arise from changes in the helix conformation
      brought about by the minor groove binding ligand.
AU  - Singh MP
AU  - Lown JW
PT  - Journal Article
TA  - J. Biomol. Struct. Dyn.
JT  - J. Biomol. Struct. Dyn.
SO  - J. Biomol. Struct. Dyn. 1995 12: A220.

PMID- 19322801
VI  - 4
DP  - 2009
TI  - Molecular Modeling and Molecular Dynamics Studies of Hydralazine with Human DNA Methyltransferase 1.
PG  - 792-799
AB  - DNA methyltransferases (DNMTs) are a family of enzymes that methylate DNA at the C5 position
      of cytosine residues and their inhibition is a
      promising strategy for the treatment of various developmental and
      proliferative diseases, particularly cancers. In the present study, a
      binding model for hydralazine, with a validated homology model of human
      DNMT, was developed by the use of automated molecular docking and
      molecular dynamics simulations. The docking protocol was validated by
      predicting the binding mode of 2'-deoxycytidine, 5-azacytidine, and
      5-aza-2'-deoxycytidine. The inhibitory activity of hydralazine toward
      DNMT may be rationalized at the molecular level by similar interactions
      within the binding pocket (e.g., by a similar pharmacophore) as
      established by substrate-like deoxycytidine analogues. These
      interactions involve a complex network of hydrogen bonds with arginine
      and glutamic acid residues that also play a major role in the mechanism
      of DNA methylation. Despite the different scaffolds of other
      non-nucleoside DNMT inhibitors such as procaine and procainamide, the
      current modeling work reveals that these drugs exhibit similar
      interactions within the DNMT1 binding site. These findings are valuable
      in guiding the rational design and virtual screening of novel DNMT
      inhibitors.
AU  - Singh N
AU  - Duenas-Gonzalez A
AU  - Lyko F
AU  - Medina-Franco JL
PT  - Journal Article
TA  - ChemMedChem
JT  - ChemMedChem
SO  - ChemMedChem 2009 4: 792-799.

PMID- 28572310
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Thermophiles Isolated from Yates Shaft, a Deep-Subsurface Environment.
PG  - e00405-17
AB  - The whole-genome sequences of seven thermophiles that could grow at >55 degrees C, but not at
      37 degrees C, were generated. These thermophilic bacteria will play
      a useful role as model microorganisms, and analyzing their genomes will help to
      understand the observed production of novel bioactive compounds, including
      thermozymes and macromolecules.
AU  - Singh NK
AU  - Carlson C
AU  - Sani RK
AU  - Venkateswaran K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00405-17.

PMID- 23558533
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Acinetobacter baumannii Strain MSP4-16.
PG  - e0013713
AB  - We report the 4.0-Mb draft genome sequence of Acinetobacter baumannii strain MSP4-16, isolated
      from a mangrove soil sample from Parangipettai (11 degrees
      30'N, 79 degrees 47'E), Tamil Nadu, India. The draft genome sequence of strain
      MSP4-16 consists of 3,944,542 bp, with a G+C content of 39%, 5,387 protein coding
      genes, and 69 RNAs.
AU  - Singh NK
AU  - Kumar S
AU  - Raghava GP
AU  - Mayilraj S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0013713.

PMID- 11371159
VI  - 309
DP  - 2001
TI  - Interaction of a group II intron ribonucleoprotein endonuclease with its DNA target site investigated by DNA footprinting and modification interference.
PG  - 361-386
AB  - Group II intron mobility occurs by a target DNA-primed reverse transcription mechanism in
      which the intron RNA reverse splices directly into one strand of a double-stranded DNA target
      site, while the intron-encoded protein cleaves the opposite strand and uses it as a primer to
      reverse transcribe the inserted intron RNA. The group II intron endonuclease, which mediates
      this process, is an RNP particle that contains the intron-encoded protein and the excised
      intron RNA and uses both cooperatively to recognize DNA target sequences. Here, we analyzed
      the interaction of the Lactococcus lactis Ll.LtrB group II intron endonuclease with its DNA
      target site by DNA footprinting and modification-interference approaches. In agreement with
      previous mutagenesis experiments showing a relatively large target site, DNase I protection
      extends from position -25 to +19 from the intron-insertion site on the top strand and from -28
      to +16 on the bottom strand. Our results suggest that the protein first recognizes a small
      number of specific bases in the distal 5'-exon region of the DNA target site via major-groove
      interactions. These base interactions together with additional phosphodiester-backbone
      interactions along one face of the helix promote DNA unwinding, enabling the intron RNA to
      base-pair to DNA top-strand positions -12 to +3 for reverse splicing. Notably, DNA unwinding
      extends to at least position +6, somewhat beyond the region that base-pairs with the intron
      RNA, but is not dependent on interaction of the conserved endonuclease domain with the 3'
      exon. Bottom-strand cleavage occurs after reverse splicing and requires recognition of a small
      number of additional bases in the 3' exon, the most critical being T+5 in the now
      single-stranded downstream region of the target site. Our results provide the first detailed
      view of the interaction of a group II intron endonuclease with its DNA target site. Copyright
      2001 Academic Press.
AU  - Singh NN
AU  - Lambowitz AM
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2001 309: 361-386.

PMID- 26950320
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of an Invasive Streptococcus agalactiae Isolate Lacking Pigmentation.
PG  - e00015-16
AB  - This report provides the whole-genome sequence of Streptococcus agalactiae isolate GB00037
      isolated from a newborn in Calgary, Canada. This serotype V
      isolate is unique because it lacks pigment production previously shown to be
      critical for S. agalactiae virulence.
AU  - Singh P
AU  - Aronoff DM
AU  - Davies HD
AU  - Manning SD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00015-16.

PMID- 28408669
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Permafrost Bacterium Nesterenkonia sp. Strain PF2B19, Revealing a Cold Adaptation Strategy and Diverse Biotechnological Potential.
PG  - e00133-17
AB  - Nesterenkonia sp. strain PF2B19, a psychrophilic bacterium, was isolated from 44,800-year-old
      permafrost. The draft genome sequence of this strain revealed the
      presence of genes involved in the production of cold active enzymes, carotenoid
      biosynthesis, fatty acid biosynthesis, and resistance to heavy metals. These
      results show the immense potential of the strain.
AU  - Singh P
AU  - Kapse N
AU  - Roy U
AU  - Singh SM
AU  - Dhakephalkar PK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00133-17.

PMID- 25125653
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Rifamycin Derivatives Producing Amycolatopsis mediterranei Strain DSM 46096/S955.
PG  - e00837-14
AB  - Amycolatopsis mediterranei DSM 46096 produces antibiotics of the rifamycin family,
      27-demethoxy-27-hydroxyrifamycin B,
      25-desacetyl-27-demethoxy-27-hydroxyrifamycin, and
      27-demethoxy-27-hydroxyrifamycin SV, which are effective against Gram-negative
      bacteria. Here, we present the draft genome of A. mediterranei 46096 (approx.
      10.2 Mbp) having 104 contigs with a GC content of 71.3% and 9,382 coding
      sequences.
AU  - Singh P
AU  - Kumari R
AU  - Mukherjee U
AU  - Saxena A
AU  - Sood U
AU  - Lal R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00837-14.

PMID- 26450735
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of a Diarrheagenic Morganella morganii Isolate.
PG  - e01165-15
AB  - This is a report of the whole-genome draft sequence of a diarrheagenic Morganella morganii
      isolate from a patient in Michigan, USA. This genome represents an important addition to the
      limited number of pathogenic M. morganii genomes available.
AU  - Singh P
AU  - Mosci R
AU  - Rudrik JT
AU  - Manning SD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01165-15.

PMID- 23045509
VI  - 194
DP  - 2012
TI  - Whole-Genome Shotgun Sequencing of a Colonizing Multilocus Sequence Type 17 Streptococcus agalactiae Strain.
PG  - 6005
AB  - This report highlights the whole-genome shotgun draft sequence for a Streptococcus agalactiae
      strain representing multilocus sequence type (ST) 17,
      isolated from a colonized woman at 8 weeks postpartum. This sequence represents
      an important addition to the published genomes and will promote comparative
      genomic studies of S. agalactiae recovered from diverse sources.
AU  - Singh P
AU  - Springman AC
AU  - Davies HD
AU  - Manning SD
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6005.

PMID- 19937653
VI  - 19
DP  - 2010
TI  - Mutational analysis of active-site residues in the Mycobacterium leprae RecA intein, a LAGLIDADG homing endonuclease: Asp(122) and Asp(193) are  crucial to the double-stranded DNA cleavage activity whereas Asp(218) is not.
PG  - 111-123
AB  - Mycobacterium leprae recA harbors an in-frame insertion sequence that encodes an intein homing
      endonuclease (PI-MleI). Most inteins (intein
      endonucleases) possess two conserved LAGLIDADG (DOD) motifs at their
      active center. A common feature of LAGLIDADG-type homing endonucleases
      is that they recognize and cleave the same or very similar DNA
      sequences. However, PI-MleI is distinctive from other members of the
      family of LAGLIDADG-type HEases for its modular structure with
      functionally separable domains for DNA-binding and cleavage, each with
      distinct sequence preferences. Sequence alignment analyses of PI-MleI
      revealed three putative LAGLIDADG motifs; however, there is conflicting
      bioinformatics data in regard to their identity and specific location
      within the intein polypeptide. To resolve this conflict and to
      determine the active-site residues essential for DNA target site
      recognition and double-stranded DNA cleavage, we performed
      site-directed mutagenesis of presumptive catalytic residues in the
      LAGLIDADG motifs. Analysis of target DNA recognition and kinetic
      parameters of the wild-type PI-MleI and its variants disclosed that the
      two amino acid residues, Asp(122) (in Block C) and Asp(193) (in
      functional Block E), are crucial to the double-stranded DNA
      endonuclease activity, whereas Asp(218) (in pseudo-Block E) is not.
      However, despite the reduced catalytic activity, the PI-MleI variants,
      like the wild-type PI-MleI, generated a footprint of the same length
      around the insertion site. The D122T variant showed significantly
      reduced catalytic activity, and D122A and D193A mutations although
      failed to affect their DNA-binding affinities, but abolished the
      double-stranded DNA cleavage activity. On the other hand, D122C variant
      showed approximately twofold higher double-stranded DNA cleavage
      activity, compared with the wild-type PI-MleI. These results provide
      compelling evidence that Asp(122) and Asp(193) in DOD motif I and II,
      respectively, are bona fide active-site residues essential for DNA
      cleavage activity. The implications of these results are discussed in
      this report.
AU  - Singh P
AU  - Tripathi P
AU  - Muniyappa K
PT  - Journal Article
TA  - Protein Sci.
JT  - Protein Sci.
SO  - Protein Sci. 2010 19: 111-123.

PMID- 19605345
VI  - 284
DP  - 2009
TI  - Characterization of Mycobacterium leprae RecA Intein, a LAGLIDADG Homing Endonuclease, Reveals a Unique Mode of DNA Binding, Helical Distortion, and Cleavage Compared with a Canonical LAGLIDADG Homing Endonuclease.
PG  - 25912-25928
AB  - Mycobacterium leprae, which has undergone reductive evolution leaving behind a minimal set of
      essential genes, has retained intervening
      sequences in four of its genes implicating a vital role for them in the
      survival of the leprosy bacillus. A single in-frame intervening
      sequence has been found embedded within its recA gene. Comparison of
      the M. leprae recA intervening sequence with the known intervening
      sequences indicated that it has the consensus amino acid sequence
      necessary for being a LAGLIDADG-type homing endonuclease. In light of
      massive gene decay and function loss in the leprosy bacillus, we sought
      to investigate whether its recA intervening sequence encodes a
      catalytically active homing endonuclease. Here we show that the
      purified M. leprae RecA intein (PI-MleI) binds to cognate DNA and
      displays endonuclease activity in the presence of alternative divalent
      cations, Mg2+ or Mn2+. A combination of approaches, including four
      complementary footprinting assays such as DNase I,
      copper-phenanthroline, methylation protection, and KMnO4, enhancement
      of 2-aminopurine fluorescence, and mapping of the cleavage site
      revealed that PI-MleI binds to cognate DNA flanking its insertion site,
      induces helical distortion at the cleavage site, and generates two
      staggered double strand breaks. Taken together, these results implicate
      that PI-MleI possesses a modular structure with separate domains for
      DNA target recognition and cleavage, each with distinct sequence
      preferences. From a biological standpoint, it is tempting to speculate
      that our findings have implications for understanding the evolution of
      the LAGLIDADG family of homing endonucleases.
AU  - Singh P
AU  - Tripathi P
AU  - Silva GH
AU  - Pingoud A
AU  - Muniyappa K
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2009 284: 25912-25928.

PMID- 26021931
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of an Evolved Thermotoga maritima Isolate.
PG  - e00557-15
AB  - Thermotoga maritima is a hyperthermophilic bacterium with a small genome (1.86 Mbp). Genome
      resequencing of Tma200, a derivative produced by experimental
      microbial evolution, revealed the occurrence of deletions and substitution
      mutations. Their identification contributes to a better understanding of genome
      instability in this organism.
AU  - Singh R
AU  - Gradnigo J
AU  - White D
AU  - Lipzen A
AU  - Martin J
AU  - Schackwitz W
AU  - Moriyama E
AU  - Blum P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00557-15.

PMID- 27570579
VI  - 11
DP  - 2016
TI  - First high quality draft genome sequence of a plant growth promoting and cold active enzyme producing psychrotrophic Arthrobacter agilis strain L77.
PG  - 54
AB  - Arthrobacter agilis strain L77, is a plant growth promoting and cold active hydrolytic enzymes
      producing psychrotrophic bacterium, isolated from Pangong
      Lake, a subglacial lake in north western Himalayas, India. Genome analysis
      revealed metabolic versatility with genes involved in metabolism and cold shock
      adaptation, utilization and biosynthesis of diverse structural and storage
      polysaccharides such as plant based carbon polymers. The genome of Arthrobacter
      agilis strain L77 consists of 3,608,439 bp (3.60 Mb) of a circular chromosome.
      The genome comprises of 3316 protein coding genes and 74 RNA genes, 725
      hypothetical proteins, 25 pseudo-genes and 1404 unique genes.
AU  - Singh RN
AU  - Gaba S
AU  - Yadav AN
AU  - Gaur P
AU  - Gulati S
AU  - Kaushik R
AU  - Saxena AK
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 54.

PMID- 12051838
VI  - 318
DP  - 2002
TI  - Binding of a group II intron-encoded reverse transcriptase/maturase to its high affinity intron RNA binding site involves sequence-specific recognition and autoregulates translation.
PG  - 287-303
AB  - Mobile group II introns encode reverse transcriptases that bind specifically to the intron
      RNAs to promote both intron mobility and RNA splicing (maturase activity). Previous studies
      with the Lactococcus lactis Ll.LtrB intron suggested a model in which the intron-encoded
      protein (LtrA) binds first to a primary high-affinity binding site in intron subdomain DIVa,
      an idiosyncratic structure at the beginning of the LtrA coding sequence, and then makes
      additional contacts with conserved regions of the intron to fold the RNA into the
      catalytically active structure. Here, we analyzed the DIVa binding site by iterative in vitro
      selection and in vitro mutagenesis. Our results show that LtrA binds to a small region at the
      distal end of DIVa that contains the ribosome-binding site and initiation codon of the LtrA
      open reading frame. The critical elements are in a small stem-loop structure emanating from a
      purine-rich internal loop, with both sequence and structure playing a role in LtrA
      recognition. The ribosome-binding site falls squarely within the LtrA-binding region and is
      sequestered directly by the binding of LtrA or by stabilization of the small stem-loop or
      both. Finally, by using LacZ fusions in Escherichia coli, we show that the binding of LtrA to
      DIVa down-regulates translation. This mode of regulation limits accumulation of the
      potentially deleterious intron-encoded protein and may facilitate splicing by halting ribosome
      entry into the intron. The recognition of the DIVa loop-stem-loop structure accounts, in part,
      for the intron specificity of group II intron maturases and has parallels in
      template-recognition mechanisms used by other reverse transcriptases.
AU  - Singh RN
AU  - Saldanha RJ
AU  - D'Souza LM
AU  - Lambowitz AM
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2002 318: 287-303.

PMID- 29903817
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Cloacibacterium normanense IMET F, a Microalgal Growth-Promoting Bacterium, and Aeromonas jandaei IMET J, a Microalgal  Growth-Inhibiting Bacterium.
PG  - e00503-18
AB  - We report here the whole-genome sequencing results of two bacterial isolates, Aeromonas
      jandaei IMET J and Cloacibacterium normanense IMET F, that inhibit
      (possibly due to denitrifying gene clusters) and promote (possibly due to an
      ammonification system), respectively, the growth of the microalgal strains
      Scenedesmus HTB1 and Chlorella vulgaris 1807.
AU  - Singh SK
AU  - Major SR
AU  - Cai H
AU  - Chen F
AU  - Hill RT
AU  - Li Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00503-18.

PMID- 23469332
VI  - 1
DP  - 2013
TI  - Genome Sequence of the 'Indian Bison Type' Biotype of Mycobacterium avium subsp.  paratuberculosis Strain S5.
PG  - e00005-13
AB  - We report the 4.79-Mb genome sequence of the 'Indian Bison Type' biotype of subsp. strain
      S5, isolated from a terminally sick Jamunapari goat at the CIRG
      (Central Institute for Research on Goats) farm in India. This draft genome will
      help in studying novelties of this biotype, which is widely distributed in
      animals and human beings in India.
AU  - Singh SV
AU  - Kumar N
AU  - Singh SN
AU  - Bhattacharya T
AU  - Sohal JS
AU  - Singh PK
AU  - Singh AV
AU  - Singh B
AU  - Chaubey KK
AU  - Gupta S
AU  - Sharma N
AU  - Kumar S
AU  - Raghava GP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00005-13.

PMID- 19537161
VI  - 9
DP  - 2009
TI  - In silico Analysis of Evolutionary Patterns in Restriction Endonucleases.
PG  - 45-53
AB  - Restriction endonucleases represent one of the best studied examples of DNA binding proteins.
      Type II restriction endonucleases recognize short
      sequences of foreign DNA and cleave the target on both strands with
      remarkable sequence specificity. Type II restriction endonucleases are
      part of restriction modification systems. Restriction modification
      systems occur ubiquitously among bacteria and archaea. Restriction
      endonucleases are indispensable tools in molecular biology and
      biotechnology. They are important model system for specific
      protein-nucleic acid interactions and also serve as good example for
      investigating structural, functional and evolutionary relationships
      among various biomolecules. The interaction between restriction
      endonucleases and their recognition sequences plays a crucial role in
      biochemical activities like catalytic site/metal binding, DNA repair
      and recombination etc. We study various patterns in restriction
      endonucleases type II and analyzed their structural, functional and
      evolutionary role. Our studies support X-ray crystallographic studies,
      arguing for divergence and molecular evolution. Conservation patterns
      of the nuclease superfamily have also been analyzed by estimating
      site-specific evolutionary rates for the analyzed structures related to
      respective chains in this study.
AU  - Singh TR
AU  - Pardasani KR
PT  - Journal Article
TA  - In Silico Biology
JT  - In Silico Biology
SO  - In Silico Biology 2009 9: 45-53.

PMID- 28663295
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of a Multidrug-Resistant Serratia marcescens Strain, Isolated from a Patient with Peritoneal Cancer in South Africa.
PG  - e00580-17
AB  - We report here the draft genome sequence of Serratia marcescens ML2637, isolated  from a South
      African pediatric patient in the intensive care unit with peritoneal
      cancer. The genome comprised 5,718,350 bp, with a 59.1% G+C content. There were
      5,594 predicted genes, including 5,301 protein-coding genes, 199 pseudogenes, and
      94 RNA genes.
AU  - Singh-Moodley A
AU  - Perovic O
AU  - Mtshali S
AU  - Ismail A
AU  - Allam M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00580-17.

PMID- 28385832
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Two Clinical Isolates of Burkholderia mallei Obtained from Nasal Swabs of Glanderous Equines in India.
PG  - e00063-17
AB  - Burkholderia mallei is a Gram-negative coccobacillus which causes glanders-a fatal disease of
      equines that may occasionally be transmitted to humans. Several
      cases of outbreaks have been reported from India since 2006. This paper presents
      draft genome sequences of two B. mallei strains isolated from equines affected by
      glanders in India.
AU  - Singha H
AU  - Malik P
AU  - Saini S
AU  - Khurana SK
AU  - Elschner MC
AU  - Mertens K
AU  - Barth SA
AU  - Tripathi BN
AU  - Singh RK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00063-17.

PMID- 29217795
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Pseudomonas fragi Strain DBC, Which Has the Ability To Degrade High-Molecular-Weight Polyaromatic Hydrocarbons.
PG  - e01347-17
AB  - Pseudomonas fragi strain DBC was isolated from crude oil-contaminated soil. The genome of P.
      fragi DBC is comprised of 5,072,304 bp with 54.09% GC content. Genes
      for degradation of polyaromatic hydrocarbons were found in the genome, in
      addition to genetic elements for related physiological functions such as
      chemotaxis, detoxification, and quorum sensing.
AU  - Singha LP
AU  - Kotoky R
AU  - Pandey P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01347-17.

PMID- 25858839
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of a Novel Bacterium within the Family Rhodocyclaceae That Degrades Polycyclic Aromatic Hydrocarbons.
PG  - e00251-15
AB  - A polycyclic aromatic hydrocarbon-degrading bacterium designated strain Ca6, a member of the
      family Rhodocyclaceae and a representative of the uncharacterized
      pyrene group 1 (PG1), was isolated and its genome sequenced. The presence of
      several genes suspected to be associated with PG1 was confirmed, and additional
      genes for aromatic compound metabolism were detected.
AU  - Singleton DR
AU  - Dickey AN
AU  - Scholl EH
AU  - Wright FA
AU  - Aitken MD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00251-15.

PMID- 27795254
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of a Bacterium Representing a Deep Uncultivated Lineage  within the Gammaproteobacteria Associated with the Degradation of Polycyclic  Aromatic Hydrocarbons.
PG  - e01086-16
AB  - The bacterial strain TR3.2, representing a novel deeply branching lineage within  the
      Gammaproteobacteria, was isolated and its genome sequenced. This isolate is
      the first cultivated representative of the previously described 'Pyrene Group 2'
      (PG2) and represents a variety of environmental sequences primarily associated
      with petrochemical contamination and aromatic hydrocarbon degradation.
AU  - Singleton DR
AU  - Dickey AN
AU  - Scholl EH
AU  - Wright FA
AU  - Aitken MD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01086-16.

PMID- 8660613
VI  - 238
DP  - 1996
TI  - Engineering DNA and protein chimeras utilizing coding sequences of restriction sites.
PG  - 205-208
AB  - Various engineering strategies have been employed so far to generate chimeric proteins for the
      purpose of structure-function studies.  None of these methods, except splicing by overlap
      extension (SOE)3, however, can be considered as providing a general methodology for generating
      chimeras.  SOE is a powerful technique considering its simplicity and versatility.  One
      limitation of the SOE procedure, however, is the difficulty in amplification when the chimera
      is large.  In the present report, we describe a procedure for generating chimeras by altering
      the codon sequences of one amino acid pair of the seven around the junction using the PCR
      technique.  The altered nucleotide sequence of the amino acid pair creates a restriction site
      that is utilized for formation of the desired chimera.  This procedure, like the SOE method,
      eliminates the need for single-stranded template and viral vector intermediates, and thus does
      not require a cloning and screening step.  However, in engineering relatively long chimeras,
      the described procedure is more advantageous because this method amplifies smaller fragments.
      The present technique is simple and 100% efficient.
AU  - Sinha D
AU  - Bakhshi MR
AU  - Vora RK
AU  - Kirby EP
AU  - Budzynski AZ
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 1996 238: 205-208.

PMID- 24972799
VI  - 20
DP  - 2014
TI  - Interdomain communication in the endonuclease/motor subunit of type I restriction-modification enzyme EcoR124I.
PG  - 2334
AB  - Restriction-modification systems protect bacteria from foreign DNA. Type I
      restriction-modification enzymes are multifunctional heteromeric complexes with DNA-cleavage
      and ATP-dependent DNA translocation activities located on endonuclease/motor subunit HsdR. The
      recent structure of the first intact motor subunit of the type I restriction enzyme from
      plasmid EcoR124I suggested a mechanism by which stalled translocation triggers DNA cleavage
      via a lysine residue on the endonuclease domain that contacts ATP bound between the two
      helicase domains. In the present work, molecular dynamics simulations are used to explore this
      proposal. Molecular dynamics simulations suggest that the Lys-ATP contact alternates with a
      contact with a nearby loop housing the conserved QxxxY motif that had been implicated in DNA
      cleavage. This model is tested here using in vivo and in vitro experiments. The results
      indicate how local interactions are transduced to domain motions within the endonuclease/motor
      subunit.
AU  - Sinha D
AU  - Shamayeva K
AU  - Ramasubramani V
AU  - Reha D
AU  - Bialevich V
AU  - Khabiri M
AU  - Guzanova A
AU  - Milbar N
AU  - Weiserova M
AU  - Csefalvay E
AU  - Carey J
AU  - Ettrich R
PT  - Journal Article
TA  - J. Mol. Model.
JT  - J. Mol. Model.
SO  - J. Mol. Model. 2014 20: 2334.

PMID- 28280030
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Idiomarina sp. Strain 5.13, a Highly Stress-Resistant Bacterium Isolated from the Southwest Indian Ridge.
PG  - e01747-16
AB  - Idiomarina sp. strain 5.13, able to produce biopolymer and exopolysaccharide, was isolated
      from a sediment sample collected from the Southwest Indian Ridge, Indian
      Ocean. Analysis of its draft genome sequence provides insights into its
      remarkable stress tolerance and offers the genetic basis for harnessing the
      biotechnological potential of this strain.
AU  - Sinha RK
AU  - Krishnan KP
AU  - Kurian PJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01747-16.

PMID- 23472225
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Wolbachia Endosymbiont of Drosophila suzukii.
PG  - e00032-13
AB  - is one of the most successful and abundant symbiotic bacteria in nature, infecting more than
      40% of the terrestrial arthropod species. Here we report the
      draft genome sequence of a novel strain named 'Suzi' that was retrieved from the
      genome sequencing of its host, the invasive pest .
AU  - Siozios S
AU  - Cestaro A
AU  - Kaur R
AU  - Pertot I
AU  - Rota-Stabelli O
AU  - Anfora G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00032-13.

PMID- 28153907
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Acholeplasma laidlawii, a Common Contaminant of Cell Cultures.
PG  - e01578-16
AB  - Mollicutes are important cell culture contaminants which may eventually affect the results of
      biological assays or affect their interpretation. Acholeplasma
      laidlawii is one of the most frequent contaminants of cell cultures. Here, we
      report the complete genome sequence of A. laidlawii strain MDBK/IPV, recovered
      from Madin-Darby bovine kidney (MDBK) cells.
AU  - Siqueira FM
AU  - Cibulski SP
AU  - Teixeira TF
AU  - Mayer FQ
AU  - Roehe PM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01578-16.

PMID- 23497205
VI  - 14
DP  - 2013
TI  - New insights on the biology of swine respiratory tract mycoplasmas from a comparative genome analysis.
PG  - 175
AB  - BACKGROUND: Mycoplasma hyopneumoniae, Mycoplasma flocculare and Mycoplasma
      hyorhinis live in swine respiratory tracts. M. flocculare, a commensal bacterium,
      is genetically closely related to M. hyopneumoniae, the causative agent of
      enzootic porcine pneumonia. M. hyorhinis is also pathogenic, causing
      polyserositis and arthritis. In this work, we present the genome sequences of M.
      flocculare and M. hyopneumoniae strain 7422, and we compare these genomes with
      the genomes of other M. hyoponeumoniae strain and to the a M. hyorhinis genome.
      These analyses were performed to identify possible characteristics that may help
      to explain the different behaviors of these species in swine respiratory tracts.
      RESULTS: The overall genome organization of three species was analyzed, revealing
      that the ORF clusters (OCs) differ considerably and that inversions and
      rearrangements are common. Although M. flocculare and M. hyopneumoniae display a
      high degree of similarity with respect to the gene content, only some genomic
      regions display considerable synteny. Genes encoding proteins that may be
      involved in host-cell adhesion in M. hyopneumoniae and M. flocculare display
      differences in genomic structure and organization. Some genes encoding adhesins
      of the P97 family are absent in M. flocculare and some contain sequence
      differences or lack of domains that are considered to be important for adhesion
      to host cells. The phylogenetic relationship of the three species was confirmed
      by a phylogenomic approach. The set of genes involved in metabolism, especially
      in the uptake of precursors for nucleic acids synthesis and nucleotide
      metabolism, display some differences in copy number and the presence/absence in
      the three species. CONCLUSIONS: The comparative analyses of three mycoplasma
      species that inhabit the swine respiratory tract facilitated the identification
      of some characteristics that may be related to their different behaviors. M.
      hyopneumoniae and M. flocculare display many differences that may help to explain
      why one species is pathogenic and the other is considered to be commensal.
      However, it was not possible to identify specific virulence determinant factors
      that could explain the differences in the pathogenicity of the analyzed species.
      The M. hyorhinis genome contains differences in some components involved in
      metabolism and evasion of the host's immune system that may contribute to its
      growth aggressiveness. Several horizontal gene transfer events were identified.
      The phylogenomic analysis places M. hyopneumoniae, M. flocculare and M. hyorhinis
      in the hyopneumoniae clade.
AU  - Siqueira FM
AU  - Thompson CE
AU  - Virginio VG
AU  - Gonchoroski T
AU  - Reolon L
AU  - Almeida LG
AU  - da Fonseca MM
AU  - de Souza R
AU  - Prosdocimi F
AU  - Schrank IS
AU  - Ferreira HB
AU  - de Vasconcelos AT
AU  - Zaha A
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2013 14: 175.

PMID- 22461558
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Pattern-Forming Social Bacterium Paenibacillus dendritiformis C454 Chiral Morphotype.
PG  - 2127-2128
AB  - Paenibacillus dendritiformis is a Gram-positive, soil-dwelling, spore-forming social
      microorganism. An intriguing collective faculty of this strain is
      manifested by its ability to switch between different morphotypes, such as the
      branching (T) and the chiral (C) morphotypes. Here we report the 6.3-Mb draft
      genome sequence of the P. dendritiformis C454 chiral morphotype.
AU  - Sirota-Madi A
AU  - Olender T
AU  - Helman Y
AU  - Brainis I
AU  - Finkelshtein A
AU  - Roth D
AU  - Hagai E
AU  - Leshkowitz D
AU  - Brodsky L
AU  - Galatenko V
AU  - Nikolaev V
AU  - Gutnick DL
AU  - Lancet D
AU  - Ben-Jacob E
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2127-2128.

PMID- 21167037
VI  - 11
DP  - 2010
TI  - Genome sequence of the pattern forming Paenibacillus vortex bacterium reveals potential for thriving in complex environments.
PG  - 710
AB  - BACKGROUND: The pattern-forming bacterium Paenibacillus vortex is notable for its
      advanced social behavior, which is reflected in development of colonies with
      highly intricate architectures. Prior to this study, only two other Paenibacillus
      species (Paenibacillus sp. JDR-2 and Paenibacillus larvae) have been sequenced.
      However, no genomic data is available on the Paenibacillus species with
      pattern-forming and complex social motility. Here we report the de novo genome
      sequence of this Gram-positive, soil-dwelling, sporulating bacterium. RESULTS:
      The complete P. vortex genome was sequenced by a hybrid approach using 454 Life
      Sciences and Illumina, achieving a total of 289x coverage, with 99.8% sequence
      identity between the two methods. The sequencing results were validated using a
      custom designed Agilent microarray expression chip which represented the coding
      and the non-coding regions. Analysis of the P. vortex genome revealed 6,437 open
      reading frames (ORFs) and 73 non-coding RNA genes. Comparative genomic analysis
      with 500 complete bacterial genomes revealed exceptionally high number of
      two-component system (TCS) genes, transcription factors (TFs), transport and
      defense related genes. Additionally, we have identified genes involved in the
      production of antimicrobial compounds and extracellular degrading enzymes.
      CONCLUSIONS: These findings suggest that P. vortex has advanced faculties to
      perceive and react to a wide range of signaling molecules and environmental
      conditions, which could be associated with its ability to reconfigure and
      replicate complex colony architectures. Additionally, P. vortex is likely to
      serve as a rich source of genes important for agricultural, medical and
      industrial applications and it has the potential to advance the study of social
      microbiology within Gram-positive bacteria.
AU  - Sirota-Madi A
AU  - Olender T
AU  - Helman Y
AU  - Ingham C
AU  - Brainis I
AU  - Roth D
AU  - Hagi E
AU  - Brodsky L
AU  - Leshkowitz D
AU  - Galatenko V
AU  - Nikolaev V
AU  - Mugasimangalam RC
AU  - Bransburg-Zabary S
AU  - Gutnick DL
AU  - Lancet D
AU  - Ben-Jacob E
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2010 11: 710.

PMID- 
VI  - 274
DP  - 2007
TI  - Study of DNA translocation by EcoR124I type I RM enzyme.
PG  - 305
AB  - EcoR124I, Type I restriction-modification enzyme, is multifunctional, hetero-oligomeric enzyme
      complex, able of ATP hydrolysis coupled to DNA translocation, the 1-D motion along the DNA
      lattice. These activities are conferred by superfamily 2 (SF2) helicase motifs in the HsdR
      subunit, however, the helicase motifs are not involved in DNA unwinding.
      For studying DNA translocation activity of this enzyme, we prevented in vitro experiments to
      be hampered by cleavage of DNA substrates by making substitutions of the conserved amino acid
      residues in endonuclease motif D-X13-14-E-X-K of the HsdR subunit, responsible for restriction
      activity of the enzyme(the substitutions made: D151A, E165A, E165D, E165H and K167A). Mutant
      HsdR subunits were purified and endonucleases reconstituted from the wt methylase and
      individual mutant HsdR subunits were analysed in vitro. DNA translocation activity and ATPase
      activity of these mutants were analysed using a combination of bulk stopped-flow experiments
      and single-molecule magnetic tweezers technique. The cleavage mutants of the EcoR124I enzyme
      showed initiation and translocation rates similar to wild-type. However, ATPase activity of
      the mutants was lower than of the wt enzyme. These results open new questions about HsdR
      structure and its conformation in the subunit assembly. Only the K167A mutant had DNA
      translocation and ATPase activity comparable to the wild type, which could be used as a useful
      model for further investigation of the mechanism of DNA translocation of SF2 helicases.
AU  - Sisakova E
AU  - Seidel R
AU  - Szczelkun M
AU  - Weiserova M
PT  - Journal Article
TA  - FEBS J.
JT  - FEBS J.
SO  - FEBS J. 2007 274: 305.

PMID- 18511464
VI  - 36
DP  - 2008
TI  - A RecB-family nuclease motif in the Type I restriction endonuclease EcoR124I.
PG  - 3939-3949
AB  - The Type I restriction-modification enzyme EcoR124I is an ATP-dependent endonuclease that uses
      dsDNA translocation to locate and cleave distant
      non-specific DNA sites. Bioinformatic analysis of the HsdR subunits of
      EcoR124I and related Type I enzymes showed that in addition to the
      principal PD-(E/D)xK Motifs, I, II and III, a QxxxY motif is also present
      that is characteristic of RecB-family nucleases. The QxxxY motif resides
      immediately C-terminal to Motif III within a region of predicted
      alpha-helix. Using mutagenesis, we examined the role of the Q and Y
      residues in DNA binding, translocation and cleavage. Roles for the QxxxY
      motif in coordinating the catalytic residues or in stabilizing the
      nuclease domain on the DNA are discussed.
AU  - Sisakova E
AU  - Stanley LK
AU  - Weiserova M
AU  - Szczelkun MD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2008 36: 3939-3949.

PMID- 23222132
VI  - 41
DP  - 2013
TI  - The Type ISP Restriction-Modification enzymes LlaBIII and LlaGI use a translocation-collision mechanism to cleave non-specific DNA distant from their  recognition sites.
PG  - 1071-1080
AB  - The Type ISP Restriction-Modification (RM) enzyme LlaBIII is encoded on plasmid pJW566 and can
      protect Lactococcus lactis strains against bacteriophage
      infections in milk fermentations. It is a single polypeptide RM enzyme comprising
      Mrr endonuclease, DNA helicase, adenine methyltransferase and target-recognition
      domains. LlaBIII shares >95% amino acid sequence homology across its first three
      protein domains with the Type ISP enzyme LlaGI. Here, we determine the
      recognition sequence of LlaBIII (5'-TnAGCC-3', where the adenine complementary to
      the underlined base is methylated), and characterize its enzyme activities.
      LlaBIII shares key enzymatic features with LlaGI; namely, adenosine
      triphosphate-dependent DNA translocation ( approximately 309 bp/s at 25 degrees
      C) and a requirement for DNA cleavage of two recognition sites in an inverted
      head-to-head repeat. However, LlaBIII requires K(+) ions to prevent non-specific
      DNA cleavage, conditions which affect the translocation and cleavage properties
      of LlaGI. By identifying the locations of the non-specific dsDNA breaks
      introduced by LlaGI or LlaBIII under different buffer conditions, we validate
      that the Type ISP RM enzymes use a common translocation-collision mechanism to
      trigger endonuclease activity. In their favoured in vitro buffer, both LlaGI and
      LlaBIII produce a normal distribution of random cleavage loci centred midway
      between the sites. In contrast, LlaGI in K(+) ions produces a far more
      distributive cleavage profile.
AU  - Sisakova E
AU  - van Aelst K
AU  - Diffin FM
AU  - Szczelkun MD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2013 41: 1071-1080.

PMID- 
VI  - 272
DP  - 2005
TI  - Mutagenic analysis of the HsdR motor subunit of type IC restriction modification enzyme EcoR124I.
PG  - 336
AB  - Enzyme EcoR124I belongs to the IC family of restriction modification enzymes, intelligent
      molecular motors. It is able to detect the methylation status of its DNA target sequence and
      respond with alternative activities, methylation or translocation of DNA. While bound to its
      target site, it translocates DNA towards itself simultaneously in both directions (500bp/sec).
      It uses the free energy associated with ATP hydrolysis to translocate DNA so that DNA cleavage
      occurs remote from the asymmetric recognition site. The enzyme EcoR124I is a multifunctional,
      multi-subunit enzyme, composed of three different subunits, which are encoded by the genes
      hsdR, hsdM and hsdS. Products of all three genes are required for DNA cleavage, producing the
      endonuclease. HsdR subunit is a multifunctional motor protein, which has been shown to possess
      ATPase, helicase and restriction activity. To provide a fully functional molecular motor,
      which can never cleave DNA, the amino acid motif X, the active site of the endonuclease domain
      of the HsdR subunit, was subjected to site-directed mutagenesis. The complementation analysis
      proved that the substitutions D151A, E165A, E165D, E165H, K167A in the HsdR subunit fully
      removed the restriction activity in vivo of the EcoR124I enzyme. The mutant subunits were
      separately overproduced, purified and mixed with purified methylase to reconstitute the
      EcoR124I endonuclease in vitro. As a substrate for DNA cleavage in vitro we used the plasmid
      pCFD30 containing a single site for EcoR124I. The test of restriction activity showed that
      reconstituted endonucleases were not able to cleave covalently closed plasmid DNA to linear
      DNA in contrast to the wild-type enzyme.
AU  - Sisakova E
AU  - Weiserova M
PT  - Journal Article
TA  - FEBS J.
JT  - FEBS J.
SO  - FEBS J. 2005 272: 336.

PMID- 18952104
VI  - 384
DP  - 2008
TI  - The Interrelationship of Helicase and Nuclease Domains during DNA Translocation by the Molecular Motor EcoR124I.
PG  - 1273-1286
AB  - The type I restriction-modification enzyme EcoR124I comprises three subunits with the
      stoichiometry HsdR(2)/HsdM(2)/HsdS(1). The HsdR subunits
      are archetypical examples of the fusion between nuclease and helicase
      domains into a single polypeptide, a linkage that is found in a great many
      other DNA processing enzymes. To explore the interrelationship between
      these physically linked domains, we examined the DNA translocation
      properties of EcoR124I complexes in which the HsdR subunits had been
      mutated in the RecB-like nuclease motif II or III. We found that nuclease
      mutations can have multiple effects on DNA translocation despite being
      distinct from the helicase domain. In addition to reductions in DNA
      cleavage activity, we also observed decreased translocation and ATPase
      rates, different enzyme populations with different characteristic
      translocation rates, a tendency to stall during initiation and altered
      HsdR turnover dynamics. The significance of these observations to our
      understanding of domain interactions in molecular machines is discussed.
AU  - Sisakova E
AU  - Weiserova M
AU  - Dekker C
AU  - Seidel R
AU  - Szczelkun MD
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2008 384: 1273-1286.

PMID- 14715260
VI  - 314
DP  - 2004
TI  - Single-stranded DNA binding and methylation by EcoP1I DNA methyltransferase.
PG  - 159-165
AB  - EcoP1I methyltransferase (M.EcoP1I) belongs to the type III restriction-modification system
      encoded by prophage PI that infects
      Escherichia coli. Binding of M.EcoP1I to double-stranded DNA and
      single-stranded DNA has been characterized. Binding to both single- and
      double-stranded DNA could be competed out by unlabeled single-stranded
      DNA. Metal ions did not influence DNA binding. Interestingly, M.EcoP1I
      was able to methylate single-stranded DNA. Kinetic parameters were
      determined for single and double-stranded DNA methylation. This feature
      of the enzyme probably functions in protecting the phage genome from
      restriction by type III restriction enzymes and thus could be
      considered as an anti-restriction system. This study describing in
      vitro methylation of single-stranded DNA by the type III
      methyltransferase EcoP1I allows understanding of the mechanism of
      action of these enzymes and also their role in the biology of
      single-stranded phages.
AU  - Sistla S
AU  - Krishnamurthy V
AU  - Rao DN
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 2004 314: 159-165.

PMID- 15121719
VI  - 39
DP  - 2004
TI  - S-adenosyl-L-methionine-dependent restriction enzyme.
PG  - 1-19
AB  - Restriction-modification (R-M) enzymes are classified into type I, II, III, and IV, based on
      their recognition sequence, subunit composition,
      cleavage position, and cofactor requirements. While the role of
      S-Adenosyl-L-methionine (AdoMet) as the methyl group donor in the
      methylation reaction is undisputed, its requirement in DNA cleavage
      reaction has been subject to intense study. AdoMet is a prerequisite
      for the DNA cleavage by most type I enzymes known so far, with the
      exception of R.EcoR124I. A number of new type 11 restriction enzymes
      belonging to the type IIB and IIG family were found to show AdoMet
      dependence for their cleavage reaction. The type III enzymes have been
      found to require AdoMet for their restriction function. AdoMet
      functions as an allosteric effector of the DNA cleavage reaction and
      has been shown to bring about conformational changes in the protein
      upon binding.
AU  - Sistla S
AU  - Rao DN
PT  - Journal Article
TA  - Crit. Rev. Biochem. Mol. Biol.
JT  - Crit. Rev. Biochem. Mol. Biol.
SO  - Crit. Rev. Biochem. Mol. Biol. 2004 39: 1-19.

PMID- 26438860
VI  - 112
DP  - 2015
TI  - Variable genetic architectures produce virtually identical molecules in bacterial symbionts of fungus-growing ants.
PG  - 13150-13154
AB  - Objectives: The mec and bla systems, among other genetic factors, are critical in regulating
      the expression of methicillin resistance in Staphylococcus aureus. We examined by WGS a
      naturally occurring oxacillin-susceptible mecA-positive S. aureus isolate to identify the
      mechanism conferring oxacillin susceptibility.
      Methods: The mecA-positive oxacillin-susceptible S. aureus isolate GR2 (penicillin and
      oxacillin MICs 0.094 and
      1 mg/L, respectively), belonging to clonal complex 80,was characterized. DNA fragment
      libraries were sequenced on Roche 454 and Illumina MiSeq sequencers and de novo assembly of
      the genome was generated using SeqMan NGen software. Plasmid curing was conducted by SDS
      treatment. Expression of mecA was quantified without/with b-lactam pressure.
      Results: The genome of GR2 consisted of a 2792802 bp chromosome and plasmids pGR2A (28895 bp)
      and pGR2B (2473 bp). GR2 carried SCCmec type IV, with a truncated/non-functional mecR1 gene
      and no mecI. A single copy of the bla system, with an organization unique for S. aureus, was
      found, harboured by plasmid pGR2A. Particularly, the blaZ gene was orientated like its
      regulatory genes, blaI and blaR1, and a gene encoding transposase IS66 was integrated between
      blaZ and the regulatory genes deleting the 5-end of blaR1; blaI,
      encoding blaZ/mecA repressor, was intact. After plasmid loss, GR2 became penicillin and
      oxacillin resistant (MICs 0.5 and 6 mg/L, respectively).
      Conclusions: We can conclude that after exposure to b-lactams, the non-functional BlaR1 does
      not cleave the mecA repressor BlaI, derepression does not occur and mecA is not efficiently
      expressed. Removal of the bla system
      after curing of pGR2A allows constitutive expression of mecA, resulting in oxacillin and
      penicillin resistance.
AU  - Sit CS
AU  - Van Arnam EB
AU  - Ramadhar TR
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2015 112: 13150-13154.

PMID- 24478765
VI  - 5
DP  - 2014
TI  - Helicobacter pylori DNA methyltransferases and the epigenetic field effect in cancerization.
PG  - 115
AB  - Helicobacter pylori, a Gram-negative, microaerophilic bacterium, has co-existed with human
      beings as a prominent member of their gastric microbiota for approximately 105 years.  It
      infects approximately half the world's population, and most infected individuals are
      asymptomatic, but histologically exhibit superficial gastritis.  Only a minority of infected
      individuals develop gastric or duodenal ulcers that necessitate treatment.  Prolonged
      inflammation caused by chronic (often lifelong) infection predisposes a small fraction of
      infected individuals to develop gastric adenocarcinoma or lymphoma of the mucosa-associated
      lymphoid tissue (MALT lymphoma).  Unfortunately, the prognosis for cases of gastric cancer is
      very poor, with 5-year survival rates being lower than 15%.
AU  - Sitaraman R
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2014 5: 115.

PMID- 
VI  - 0
DP  - 2002
TI  - Restriction-modification systems and chromosomal rearrangements in mycoplasmas.
PG  - 371-390
AB  - The restriction-modification (R-M) systems are so named because of their ability to degrade
      foreign DNA (restrict viral infection) and to methylate (modify) unmethylated and
      hemimethylated DNA.  They were discovered as genetic elements that determined the
      susceptibility of E. coli and S. typhimurium to phage infection in a strain-dependent manner,
      with bacteriophage plaquing efficiency being reduced upon infection of a heterologous host
      strain.  At the time of writing, 3154 R-M enzymes, many with overlapping DNA recognition
      specificities, have been catalogued in the restriction enzyme database (REBASE).  R-M systems
      are ubiquitous and arose early in prokaryotic evolution.
AU  - Sitaraman R
AU  - Dybvig K
PT  - Journal Article
TA  - Mol. Biol. Pathog. Mycoplasmas
JT  - Mol. Biol. Pathog. Mycoplasmas
SO  - Mol. Biol. Pathog. Mycoplasmas 2002 0: 371-390.

PMID- 
VI  - 101
DP  - 2001
TI  - Functional analysis of a unique site-specific recombinase from Mycoplasma pulmonis.
PG  - 388
AB  - Mycoplasma pulmonis has been shown to undergo high-frequency phase variation at different loci
      within its genome - the two paralogous hsd
      (host specificity determinant) loci that encode type I restriction and
      modification (R-M) systems, and the vsa (variable surface antigen)
      locus that encodes surface lipoproteins. Analyses of the hsd and vsa
      gene loci have shown that they are organized as site-specific
      invertible elements. Recently, the genome of M. pulmonis strain UAB
      CTIP has been completely sequenced. Based on sequence homology, an open
      reading frame near the vsa locus was predicted to encode a
      site-specific recombinase. This is the only known site-specific
      recombinase identified in Mollicutes that is not part of a viral and/or
      transposable element. To test the functionality and sequence
      specificity of the predicted recombinase, two assay systems have been
      designed in an E. coli background using information about the regions
      of the hsd and vsa genes that are actually involved in site-specific
      recombination. Two copies of the relevant hsd (or vsa) regions were
      cloned in opposite orientation into plasmid vectors. E. coli harboring
      these "reporter" plasmids were then transformed with a compatible
      plasmid containing the putative recombinase gene. The clones so
      obtained were screened by PCR for inversion at the hsd- or vsa-derived
      inverted repeats. The resulting amplicons corresponding to DNA
      inversions were also sequenced, further verifying the occurrence of the
      predicted inversions. This work proves that the putative recombinase is
      functional and catalyzes site-specific inversions of the hsd- and
      vsa-derived sequences that are known to undergo inversions in M.
      pulmonis. The use of a single enzyme to catalyze DNA inversions at
      different genetic loci is consistent with the observed genetic economy
      of mycoplasmas. In view of the sequence differences between the sites
      of inversion at the vsa and hsd loci, experiments to determine the
      minimal sequence requirements for site-specific recombination are in
      progress.
AU  - Sitaraman R
AU  - Dybvig K
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 2001 101: 388.

PMID- 9383194
VI  - 26
DP  - 1997
TI  - The hsd loci of Mycoplasma pulmonis: organization, rearrangements and expression of genes.
PG  - 109-120
AB  - Two paralogous, site-specific invertible loci, designated hsd1 and hsd2, have been identified
      in the Mycoplasma pulmonis genome.  They encode putative type I restriction and modification
      systems with maximum sequence homology to the type IC family, which includes EcoR124II and
      EcoDXXI.  Each locus encodes an endonuclease subunit, a methylase subunit and two DNA
      specificity subunits.  The gene organization at each locus is such that hsdR and hsdM are
      flanked by two hsdS genes.  Within each locus, one of the hsdS genes, hsdR and hsdM, is
      encoded in tandem by the same DNA strand, while the second hsdS gene is encoded by the
      complementary strand but without overlap with the other three hsd genes.  The hsdR and hsdM
      sequences of one locus are almost identical to their counterparts in the other.  The four hsdS
      genes (two per locus) are highly homologous at their 5' ends and also share sequence
      similarities in the 3' ends of their corresponding coding regions.  Owing to the disposition
      of and sequence similarities among the hsdS genes, they form inverted repeats at each locus.
      Analysis by polymerase chain reaction has shown that both loci behave as site-specific DNA
      invertible elements with multiple inversion sites, termed 'vipareetus', occurring within the
      hsdS genes.  The inversions lead to a reassortment of hsdS sequences, generating an array of
      recombinant genes that probably encode S subunits possessing alternative DNA-binding
      specificities.  Sequence information obtained from the analysis of hsd2 transcripts by 5'
      RACE indicates that inversion induces the transcription of alternative hsdS genes by the
      relocation of coding sequences downstream of a promoter and ribosome-binding sites situated at
      one end of each locus.
AU  - Sitaraman R
AU  - Dybvig K
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1997 26: 109-120.

PMID- 22178763
VI  - 494
DP  - 2012
TI  - Methylation-dependent DNA restriction in Bacillus anthracis.
PG  - 44-50
AB  - Bacillus anthracis, the causative agent of anthrax, is poorly transformed with DNA that is
      methylated on adenine or cytosine. Here we characterize
      three genetic loci encoding type IV methylation-dependent restriction
      enzymes that target DNA containing C5-methylcytosine (m5C). Strains in
      which these genes were inactivated, either singly or collectively, showed
      increased transformation by methylated DNA. Additionally, a triple mutant
      with an ~30-kb genomic deletion could be transformed by DNA obtained from
      Dam(+)Dcm(+)E. coli, although at a low frequency of ~10(-3)
      transformants/10(6)cfu. This strain of B. anthracis can potentially serve
      as a preferred host for shuttle vectors that express recombinant proteins,
      including proteins to be used in vaccines. The gene(s) responsible for the
      restriction of m6A-containing DNA in B. anthracis remain unidentified, and
      we suggest that poor transformation by such DNA could in part be a
      consequence of the inefficient replication of hemimethylated DNA in B.
      anthracis.
AU  - Sitaraman R
AU  - Leppla SH
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 2012 494: 44-50.

PMID- 13678957
VI  - 28
DP  - 2003
TI  - New types of conserved sequence domains in DNA-binding regions of homing endonucleases.
PG  - 473-477
AB  - We have identified four new types of short conserved sequence domains in homing endonucleases
      and related proteins. These domains are modular,
      appearing in various combinations. One domain includes a motif known by
      structure as a novel sequence-specific DNA-binding helix. Sequence
      similarity shows two other domains to be new types of helix-turn-helix
      DNA-binding domains. We term the new domains nuclease-associated modular
      DNA-binding domains (NUMODs).
AU  - Sitbon E
AU  - Pietrokovski S
PT  - Journal Article
TA  - Trends Biochem. Sci.
JT  - Trends Biochem. Sci.
SO  - Trends Biochem. Sci. 2003 28: 473-477.

PMID- 29122867
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of a Methicillin-Resistant Sequence Type 39 Staphylococcal  Isolate Obtained from Seafood.
PG  - e01193-17
AB  - The draft genome sequence of a methicillin-resistant Staphylococcus aureus (MRSA) sequence
      type 39 (ST 39) isolate obtained from the dried ribbonfish of Gujarat,
      India, is reported here. Staphylococcus-specific genes were present in this MRSA
      isolate. The whole-genome sequence of this strain contains 2,693 protein-coding
      genes and 70 RNAs within the 2.82-Mb genome.
AU  - Sivaraman GK
AU  - Vanik D
AU  - Visnuvinayagam S
AU  - Prasad MM
AU  - Murugadas V
AU  - Nadella RK
AU  - Ravishankar CN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01193-17.

PMID- 28839017
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of a Methicillin-Resistant Staphylococcus aureus Isolate (Sequence Type 1) from Seafood.
PG  - e00776-17
AB  - The draft genome sequence of a methicillin-resistant Staphylococcus aureus (MRSA) isolate
      (sequence type 1 [ST 1]) from the salted dried ribbonfish from Gujarat,
      India, is reported here. Staphylococcus genus-specific genes were present in this
      MRSA isolate. The whole-genome sequence of this strain contains 2,797
      protein-coding genes and 80 RNAs within the 2.85-Mb genome.
AU  - Sivaraman GK
AU  - Vanik D
AU  - Visnuvinayagam S
AU  - Prasad MM
AU  - Ravishankar CN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00776-17.

PMID- 22610857
VI  - 40
DP  - 2012
TI  - Crystal structure and mechanism of action of the N6-methyladenine-dependent type  IIM restriction endonuclease R.DpnI.
PG  - 7563-7572
AB  - DNA methylation-dependent restriction enzymes have many applications in genetic engineering
      and in the analysis of the epigenetic state of eukaryotic genomes.
      Nevertheless, high-resolution structures have not yet been reported, and
      therefore mechanisms of DNA methylation-dependent cleavage are not understood.
      Here, we present a biochemical analysis and high-resolution DNA co-crystal
      structure of the N(6)-methyladenine (m6A)-dependent restriction enzyme R.DpnI.
      Our data show that R.DpnI consists of an N-terminal catalytic PD-(D/E)XK domain
      and a C-terminal winged helix (wH) domain. Surprisingly, both domains bind DNA in
      a sequence- and methylation-sensitive manner. The crystal contains R.DpnI with
      fully methylated target DNA bound to the wH domain, but distant from the
      catalytic domain. Independent readout of DNA sequence and methylation by the two
      domains might contribute to R.DpnI specificity or could help the monomeric enzyme
      to cut the second strand after introducing a nick.
AU  - Siwek W
AU  - Czapinska H
AU  - Bochtler M
AU  - Bujnicki JM
AU  - Skowronek K
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: 7563-7572.

PMID- Not included in PubMed...
VI  - 8
DP  - 1982
TI  - Inhibition of the restriction of DNA by endonucleases in the presence of Actinomycin D, Distamycin A, and their analogs.
PG  - 470-477
AB  - The cleavage of phage lambda cI857s7 by the restriction endonucleases EcoRI and
      SmaI in the presence of actinomycin D, distamycin A, and the distamycin analog
      distamine, and also of polyfunctional ligands -- distaccins -- has been
      studied.  Distamine suppresses the cleavage of phage lambda DNA by endonuclease
      EcoRI in the same way as distamycin A.  Actinomycin D selectively blocks the
      action of endonucleases SmaI and EcoRI; in the latter case the cleavage of only
      one recognition site is suppressed.  In the inhibition of the action of
      endonuclease EcoRI simultaneously by two ligands, actinomycin D and distamycin
      A or actinomycin D and distamine, "additivity" of their action on the
      recognition site present at the point of contact of the EcoRI fragments E and F
      was detected.  When DNA was cleaved by endonuclease SmaI in the presence of
      these ligands no "additivity" was revealed.  In this case, a rise in the degree
      of cleavage of the DNA at the points of contact of the SmaI fragments A and B,
      and D and C, as compared with the action of actinomycin D alone, was observed.
      Distaccins are nonspecific inhibitors of the cleavage of DNA under the
      influence of the enzymes EcoRI and SmaI; distaccin-O protects the sections of
      the recognition of endonuclease SmaI and does not block the action of
      endonuclease EcoRI.
AU  - Sizova IA
AU  - Glibin EN
AU  - Ginzburg OF
AU  - Tereshin IM
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1982 8: 470-477.

PMID- 26221418
VI  - 10
DP  - 2015
TI  - High-quality draft genome sequences of five anaerobic oral bacteria and description of Peptoanaerobacter stomatis gen. nov., sp. nov., a new member of  the family Peptostreptococcaceae.
PG  - 37
AB  - Here we report a summary classification and the features of five anaerobic oral bacteria from
      the family Peptostreptococcaceae. Bacterial strains were isolated
      from human subgingival plaque. Strains ACC19a, CM2, CM5, and OBRC8 represent the
      first known cultivable members of 'yet uncultured' human oral taxon 081; strain
      AS15 belongs to 'cultivable' human oral taxon 377. Based on 16S rRNA gene
      sequence comparisons, strains ACC19a, CM2, CM5, and OBRC8 are distantly related
      to Eubacterium yurii subs. yurii and Filifactor alocis, with 93.2 - 94.4 % and
      85.5 % of sequence identity, respectively. The genomes of strains ACC19a, CM2,
      CM5, OBRC8 and AS15 are 2,541,543; 2,312,592; 2,594,242; 2,553,276; and 2,654,638
      bp long. The genomes are comprised of 2277, 1973, 2325, 2277, and 2308
      protein-coding genes and 54, 57, 54, 36, and 28 RNA genes, respectively. Based on
      the distinct characteristics presented here, we suggest that strains ACC19a, CM2,
      CM5, and OBRC8 represent a novel genus and species within the family
      Peptostreptococcaceae, for which we propose the name Peptoanaerobacter stomatis
      gen. nov., sp. nov. The type strain is strain ACC19a(T) (=HM-483(T); =DSM
      28705(T); =ATCC BAA-2665(T)).
AU  - Sizova MV
AU  - Chilaka A
AU  - Earl AM
AU  - Doerfert SN
AU  - Muller PA
AU  - Torralba M
AU  - McCorrison JM
AU  - Durkin AS
AU  - Nelson KE
AU  - Epstein SS
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 37.

PMID- 25428973
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Francisella endociliophora Strain FSC1006, Isolated from a Laboratory Culture of the Marine Ciliate Euplotes raikovi.
PG  - e01227-14
AB  - A strain of Francisella endociliophora was isolated from a laboratory culture of  the marine
      ciliate Euplotes raikovi. Here, we report the complete genome sequence
      of the bacterial strain FSC1006 (Francisella Strain Collection, Swedish Defence
      Research Agency, Umea, Sweden).
AU  - Sjodin A
AU  - Ohrman C
AU  - Backman S
AU  - Larkeryd A
AU  - Granberg M
AU  - Lundmark E
AU  - Karlsson E
AU  - Nilsson E
AU  - Vallesi A
AU  - Tellgren-Roth C
AU  - Stenberg P
AU  - Thelaus J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01227-14.

PMID- 22099122
VI  - 17
DP  - 2011
TI  - Drug-Resistance Mechanisms in Vibrio cholerae O1 Outbreak Strain, Haiti, 2010.
PG  - 2151-2154
AB  - To increase understanding of drug-resistant Vibrio cholerae, we studied selected
      molecular mechanisms of antimicrobial drug resistance in the 2010 Haiti V.
      cholerae outbreak strain. Most resistance resulted from acquired genes located on
      an integrating conjugative element showing high homology to an integrating
      conjugative element identified in a V. cholerae isolate from India.
AU  - Sjolund-Karlsson M
AU  - Reimer A
AU  - Folster JP
AU  - Walker M
AU  - Dahourou G
AU  - Batra DG
AU  - Martin I
AU  - Joyce K
AU  - Parsons MB
AU  - Boncy J
AU  - Whichard JM
AU  - Gilmour MW
PT  - Journal Article
TA  - Emerg. Infect. Dis.
JT  - Emerg. Infect. Dis.
SO  - Emerg. Infect. Dis. 2011 17: 2151-2154.

PMID- 147865
VI  - 133
DP  - 1978
TI  - Biological characteristics of a Type I restriction-modification system in Staphylococcus aureus.
PG  - 1144-1149
AB  - Two restriction-modification systems, S1 and S2, are present in Staphylococcus aureus RN450
      (S. Iordanescu and M. Surdeanu, J. Gen. Microbiol., 96:277-281,1976).  System S2 affects phage
      multiplication after both infection and transfection.  Unmodified plasmid and chromosomal DNAs
      are also not expressed following transduction and transformation into a restrictive host.
      Restricted phages are, however, capable of conferring phage-mediated competence, although the
      state of competence does not affect the restriction-modification system. The restricting
      activity of system S2 is inactivated by heat treatment of the cells.  An enzymatic activity
      that restricts unmodified phage DNA in the presence of ATP, Mg2+, and S-adenosylmethionine was
      recovered from cell-free extracts of a strain RN450 derivative.
AU  - Sjostrom JE
AU  - Lofdahl S
AU  - Philipson L
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1978 133: 1144-1149.

PMID- 21486474
VI  - 12
DP  - 2011
TI  - Clostridium botulinum group III: a group with dual identity shaped by plasmids, phages and mobile elements.
PG  - 185
AB  - ABSTRACT: BACKGROUND: Clostridium botulinum strains can be divided into
      four physiological groups that are sufficiently diverged to be considered
      as separate species. We here presentHere we present the first complete
      genome of a C. botulinum strain from physiological group III, causing
      animal botulism. We also compare the sequence to three new draft genomes
      from the same physiological group. RESULTS: The 2.77 Mb chromosome was
      highly conserved between the isolates and also closely related to that of
      C. novyi. However, the sequence was very different from the human C.
      botulinum group genomes. Replication-directed translocations were rare and
      conservation of synteny was high. The largest difference between C.
      botulinum group III isolates occurred within their surprisingly large
      plasmidomes and in the pattern of mobile elements insertions. Five
      plasmids, constituting 13.5% of the total genetic material, were present
      in the completed genome. Interestingly, the set of plasmids differed
      compared to other isolates. The largest plasmid, the botulinum- neurotoxin
      carrying prophage, was conserved to at a level similar to that of the
      chromosome while the medium-sized plasmids seemed to be undergoing faster
      genetic drift. These plasmids also contained more mobile elements than
      other replicons. Several toxins and resistance genes were identified, many
      of which were located on the plasmids. CONCLUSIONS: The completion of the
      genome of C. botulinum group III has revealed it to be a genome withof
      dual identity. It belongs to the pathogenic species C. botulinum, but as a
      genotypic species it should also include C. novyi and C. haemolyticum. The
      genotypic species share a conserved chromosomal core that can be
      transformed into various pathogenic variants by modulation of the highly
      plastic plasmidome.
AU  - Skarin H
AU  - Hafstrom T
AU  - Westerberg J
AU  - Segerman B
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2011 12: 185.

PMID- 159204
VI  - 15
DP  - 1979
TI  - Specificity of modification-restriction of bacteriophages P1 and lambda in strains of Escherichia coli K-12 controlled by the R124 plasmid.
PG  - 1719-1723
AB  - The specificities of restriction of bacteriophages P1 and lambda controlled by
      R plasmids in Escherichia coli have been investigated.  The isogenic strains
      harbouring the plasmids pAS26 coding for restriction endonuclease R.EcoRI, R245
      coding for restriction endonuclease R.EcoRII and R124 have been investigated in
      the present work.  Modification-restriction controlled by R124 has been found
      to differ in specificity from those controlled by R245 and pAS26.  Frequencies
      of restriction of bacteriophages P1vir and lambdavir specified by R124 plasmid
      differ from the frequencies in the strains harbouring pAS26 and R245 plasmids
      as well.  The difference is due to the specificity of restriction-modification
      controlled by R124.  The data obtained are consistent with the determination of
      R124 specified restriction-modification activity as a novel one designated
      R.EcoRIII.
AU  - Skavronskaya AG
AU  - Aleshkin GI
AU  - Demkin VV
PT  - Journal Article
TA  - Genetika
JT  - Genetika
SO  - Genetika 1979 15: 1719-1723.

PMID- 21625595
VI  - 6
DP  - 2011
TI  - Phage Encoded H-NS: A Potential Achilles Heel in the Bacterial Defence System.
PG  - e20095
AB  - The relationship between phage and their microbial hosts is difficult to elucidate in complex
      natural ecosystems. Engineered systems performing
      enhanced biological phosphorus removal (EBPR), offer stable, lower
      complexity communities for studying phage-host interactions. Here,
      metagenomic data from an EBPR reactor dominated by Candidatus
      Accumulibacter phosphatis (CAP), led to the recovery of three complete and
      six partial phage genomes. Heat-stable nucleoid structuring (H-NS)
      protein, a global transcriptional repressor in bacteria, was identified in
      one of the complete phage genomes (EPV1), and was most similar to a
      homolog in CAP. We infer that EPV1 is a CAP-specific phage and has the
      potential to repress up to 6% of host genes based on the presence of
      putative H-NS binding sites in the CAP genome. These genes include CRISPR
      associated proteins and a Type III restriction-modification system, which
      are key host defense mechanisms against phage infection. Further, EPV1 was
      the only member of the phage community found in an EBPR microbial
      metagenome collected seven months prior. We propose that EPV1 laterally
      acquired H-NS from CAP providing it with a means to reduce bacterial
      defenses, a selective advantage over other phage in the EBPR system. Phage
      encoded H-NS could constitute a previously unrecognized weapon in the
      phage-host arms race.
AU  - Skennerton CT
AU  - Angly FE
AU  - Breitbart M
AU  - Bragg L
AU  - He S
AU  - McMahon KD
AU  - Hugenholtz P
AU  - Tyson GW
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2011 6: e20095.

PMID- 9642051
VI  - 279
DP  - 1998
TI  - Structure-based redesign of the catalytic/metal binding site of Cfr10I restriction endonuclease reveals importance of spatial rather than sequence conservation of active centre residues.
PG  - 473-481
AB  - According to the crystal structure of Cfr10I restriction endonuclease the acidic residues
      D134, E71 and E204 are clustered together and presumably chelate metal ion(s) at the active
      site.  Indeed, investigation of the DNA cleavage properties of substitutional mutants of
      Cfr10I D134A, E71Q, E71A and E204Q reveals that D134, E71 and E204 residues are essential for
      cleavage activity, supporting their active site function.  Structural comparison indicates
      that the D134 residue of Cfr10I spatially overlaps with aspartate residues D91 and D74, from
      the invariant active site motifs 90PD(X19)EAK and 73 PD(X15)DIK of EcoRI and EcoRV,
      respectively.  However, structural studies in conjunction with mutational analyses suggest
      that the sequence motif 133PD(X55)K(X13)E corresponds to the active site of Cfr10I, but
      differs from the canonical active site motifs of EcoRI and EcoRV.  According to the crystal
      structure of Cfr10I the serine S188 residue from the 188SVK sequence motif is a spatial
      equivalent of the acidic residue from the (E/D)XK-part of the active site motif, which is
      conserved between EcoRI and EcoRV.  Site-directed mutagenesis experiments of Cfr10I, however,
      revealed that S188 was not so important for catalysis while the E204 residue located 2.8A away
      indeed was essential for cleavage, suggesting that the glutamate E204 rather than the S188
      residue contributes to the metal binding site in Cfr10I.  In addition, model-building studies
      suggest that mutual interchange of the E204 and S188 residues should lead only to minor
      positional differences of the carboxylate residues of glutamate side-chains.  The double
      mutant S188E/E204S was therefore prepared by site-directed mutagenesis where the active site
      motif 133 PD(X55)K(X13)E of Cfr10I was changed to a canonical motif 133PD(X53)EVK, which is
      similar to that of EcoRI and EcoRV.  Interestingly, the double mutant S188E/E204S of Cfr10I
      with redesigned active site structure, exhibited 10% of Wt cleavage activity in a lambda DNA
      cleavage assay.  Thus, structure guided redesign of the catalytic/metal binding site of
      Cfr10I, provides novel experimental evidence to suggest that spatial rather than sequence
      conservation plays the dominant role in the formation of restriction enzyme active sites.
AU  - Skirgaila R
AU  - Grazulis S
AU  - Bozic D
AU  - Huber R
AU  - Siksnys V
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1998 279: 473-481.

PMID- 9628363
VI  - 379
DP  - 1998
TI  - Ca2+-ions stimulate DNA binding specificity of Cfr10I restriction enzyme.
PG  - 595-598
AB  - The Cfr10I restriction enzyme recognizes the degenerate hexanucleotide sequence
      5'-Pu/CCGGPy-3' and cleaves it as indicated.  DNA binding studies of Cfr10I endonuclease
      were performed using gel mobility shift assay.  Analysis of Cfr10I binding to DAN revealed
      that in the absence of metal ions Cfr10I binds to DNA containing or lacking the recognition
      sequence with similar low affinity.  Addition of Ca2+ to the binding specificity of Cfr10I.
AU  - Skirgaila R
AU  - Siksnys V
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1998 379: 595-598.

PMID- 3009478
VI  - 261
DP  - 1986
TI  - An endonuclease from Chlamydomonas reinhardtii that cleaves the sequence TATA.
PG  - 6806-6810
AB  - An endodeoxyribonuclease, designated CreI, was purified 16,000-fold from
      zygotes of the eukaryote Chlamydomonas reinhardtii.  CreI preferentially
      attacks the sequence TATA producing double stsrand breaks with
      3'-phosphomonoester and 5'-hydroxyl termini.  The endonuclease has an Mr =
      27,000 and requires Ca2+ at pH 7.5 for optimal activity.
AU  - Sklar R
AU  - Altman D
AU  - Sager R
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1986 261: 6806-6810.

PMID- 17921292
VI  - 189
DP  - 2007
TI  - Functional analysis of the M.HpyAIV DNA methyltransferase of Helicobacter pylori.
PG  - 8914-8921
AB  - A large number of genes encoding restriction-modification (R-M) systems are found in the
      genome of the human pathogen Helicobacter pylori. R-M
      genes comprise approximately 10% of the strain-specific genes, but the
      relevance of having such an abundance of these genes is not clear. The
      type II methyltransferase (MTase) M.HpyAIV, which recognizes GANTC sites,
      was present in 60% of the H. pylori strains analyzed, whereof 69% were
      resistant to restriction enzyme digestion, which indicated the presence of
      an active MTase. H. pylori strains with an inactive M.HpyAIV phenotype
      contained deletions in regions of homopolymers within the gene, which
      resulted in premature translational stops, suggesting that M.HpyAIV may be
      subjected to phase variation by a slipped-strand mechanism. An M.HpyAIV
      gene mutant was constructed by insertional mutagenesis, and this mutant
      showed the same viability and ability to induce interleukin-8 in
      epithelial cells as the wild type in vitro but had, as expected, lost the
      ability to protect its self-DNA from digestion by a cognate restriction
      enzyme. The M.HpyAIV from H. pylori strain 26695 was overexpressed in
      Escherichia coli, and the protein was purified and was able to bind to DNA
      and protect GANTC sites from digestion in vitro. A bioinformatic analysis
      of the number of GANTC sites located in predicted regulatory regions of H.
      pylori strains 26695 and J99 resulted in a number of candidate genes.
      katA, a selected candidate gene, was further analyzed by quantitative
      real-time reverse transcription-PCR and shown to be significantly
      down-regulated in the M.HpyAIV gene mutant compared to the wild-type
      strain. This demonstrates the influence of M.HpyAIV methylation in gene
      expression.
AU  - Skoglund A
AU  - Bjorkholm B
AU  - Nilsson C
AU  - Andersson AF
AU  - Jernberg C
AU  - Schirwitz K
AU  - Enroth C
AU  - Krabbe M
AU  - Engstrand L
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2007 189: 8914-8921.

PMID- 
VI  - 8
DP  - 2003
TI  - Are hsdS-subunits in restriction-modification systems involved in Helicobacter pylori virulence?
PG  - 492
AB  - Few regulatory genes are present in the H. pylori genome, but there is an abundance of genes
      homologous to restriction-modification systems, that may play a role in gene regulation.  Each
      strain has its own unique set of R-M genes.  In a recent study, the presence of hsdS genes
      (specificity subunits of type I R-M systems) in clinical isolates was associated with
      induction of a more robust host response in gnotobiotic transgenic mice.  We aim to study hsdS
      genes and their involvement in virulence.  By PCR-amplification, two hsdS genes were detected
      in 100% of the isolates, however, the amplified products had variable sizes.  We have
      sequenced one hsdS locus in nine clinical isolates.  The sequenced locus reveal large
      variations between the strains, but there were also conserved regions.  One of the conserved
      domain is known as the target recognition domain.  We have constructed insertion mutants in
      type I hsdS and hsdM (modification subunit of type I systems) genes: jhp0726, HP0790, HP0462
      and HP0463.  Preliminary results indicate that one of the mutant strains (HP0462::km) has
      reduced growth compared with the wild-type strain.  Strains deficient in hsdS and hsdM genes
      do not show altered ability to induce IL-8 production in AGS-cells.  The effects of
      inactivation of the hsdS genes on global gene expression are now being investigated using a
      whole-genome microarray.  To investigate the involvement of hsdS genes in virulence, the
      host-response of mutant compared with wild-type strains will be studied in germfree mice.
AU  - Skoglund A
AU  - Bjorkholm B
AU  - Nilsson C
AU  - Krabbe M
AU  - Engstrand L
PT  - Journal Article
TA  - Helicobacter
JT  - Helicobacter
SO  - Helicobacter 2003 8: 492.

PMID- 14506783
VI  - 293
DP  - 2003
TI  - Are hsdS-subunits in restriction-modification systems involved in Helicobacter pylori virulence?
PG  - 125
AB  - Few regulatory genes are present in the H. pylori genome, but there is an abundance of genes
      homologous to restriction-modification systems, that may play a role in gene regulation.  Each
      strain has its own unique set of R-M genes.  In a recent study, the presence of hsdS genes
      (specifically subunits of type I R-M systems) in clinical isolates was associated with
      induction of a more robust host response in gnotobiotic transgenic mice.  We aim to study hsdS
      genes and their involvement in virulence.  By PCR-amplification, two hsdS genes were detected
      in 100% of the isolates, however the amplified products had variable sizes.  We have sequenced
      one hsdS locus in 9 clinical isolates.  The sequenced locus reveals large variations between
      the strains, but there were also conserved regions.  One of the conserved domains is known as
      the target recognition domain.  We have constructed insertion mutants in type I hsdS and hsdM
      (modification subunit of type I systems) genes: jhp0726, HP0790, HP0462 and HP0463.
      Preliminary results indicate that one of the mutant strains (HP0462::km) has reduced growth
      compared to the wild-type strain.  Strains deficient in hsdS and hsdM genes do not show
      altered ability to induce IL-8 production in AGS-cells.  The effects of inactivation of the
      hsdS genes on global gene expression are now being investigated using a whole-genome
      microarray.  To investigate the involvement of hsdS genes in virulence, the host-response of
      mutant compared to wild-type strains will be studied in germfree mice.
AU  - Skoglund A
AU  - Bjorkholm B
AU  - Nilsson C
AU  - Krabbe M
AU  - Engstrand L
PT  - Journal Article
TA  - Int. J. Med. Microbiol.
JT  - Int. J. Med. Microbiol.
SO  - Int. J. Med. Microbiol. 2003 293: 125.

PMID- 11697346
VI  - 291S
DP  - 2001
TI  - DNA methyltransferases in Helicobacter pylori.
PG  - 94-95
AB  - DNA methyltransferases are enzymes that modify specific sequences in DNA.  In bacteria, this
      modification is important as protection of "self" DNA in restriction-modification systems and
      in cellular processes such as DNA repair, control of cell division and regulation of virulence
      genes.  We are interested in the role of multiple methyltransferases in H. pylori.  To
      determine the distribution of methyltransferase genes in DNA prepared from clinical isolates
      of H. pylori, oligonucleotide pairs directed towards conserved regions of 18 MT genes were
      used in PCR.  The PCR reaction for four genes, HPO260, HPO263, HPO478 and HPO910, were present
      in all the DNA isolates tested, whereas other MT genes were only present in a subset of the
      strains.  We are now proceeding to inactivate these and four additional MT genes in H. pylori
      strain 26695 by insertion of a Kanamycin cassette (aphA) from Campylobacter coli into the MT
      reading frame to determine the phenotypical effect of loss of the MT activity.  The first of
      our inactivation constructs, HP0483 (not conserved in clinical isolates) was interrupted
      without any obvious effect on the growth of the mutant as compared with wild-type bacteria.
      This indicates that the restriction enzyme encoded downstream of the MT gene was not expressed
      under the conditions used, since that likely would have resulted in degradation of the
      chromosomal DNA in the mutant.  We will continue to analyze this and other MT mutants for
      their phenotype.  We are also interested in gene regulation and we will investigate whether
      these MT genes are regulated by environmental stimuli.
AU  - Skoglund A
AU  - Engstrand L
AU  - Krabbe ME
PT  - Journal Article
TA  - Int. J. Med. Microbiol.
JT  - Int. J. Med. Microbiol.
SO  - Int. J. Med. Microbiol. 2001 291S: 94-95.

PMID- 2187744
VI  - 88
DP  - 1990
TI  - Construction of an efficient overproducer clone of HinfI restriction endonuclease using the polymerase chain reaction.
PG  - 1-5
AB  - We describe the use of the polymerase chain reaction (PCR) technique to alter
      transcriptional and translational signals surrounding a gene so as to achieve
      overexpression in Escherichia coli.  By changing the ribosome-binding site
      sequence preceding the hinfIR gene to match the consensus E. coli signal and by
      adding a transcription terminator sequence immediately following the gene, the
      yield of HinfI was increased about tenfold over that obtained from the natural
      Haemophilus influenzae signals.  The addition of the positive retroregulator
      stem-loop sequence derived from the crystal protein-encoding gene of Bacillus
      thuringiensis downstream from the hinfIR gene further increased yields by
      twofold to a level of 13% of the total cellular protein.
AU  - Skoglund CM
AU  - Smith HO
AU  - Chandrasegaran S
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1990 88: 1-5.

PMID- 772170
VI  - 31
DP  - 1976
TI  - Effects of the phage P1 restriction system on Coliphage PhiW: Degradation and complex formation of phage PhiW DNA.
PG  - 9-20
AB  - Growth of phages PhiW and T7 was restricted in Escherichia coli lysogenic for phage P1.  Only
      a fraction of the infected cells gave burst of phages.  Cells permitting phage growth gave
      normal burst size.  Host strains carrying P1 mutants with defective endonuclease gave no
      restriction of phages T7 and Phi3, the latter a host-range mutant of PhiW.  Degradation but
      not modification of parental phage DNA could be demonstrated.  Although no DNA, RNA or protein
      was synthesized in PhiW infected P1 lysogenic cells, the parental phage DNA was found in
      increasingly larger complexes during the course of infection.  At early times after infection,
      parental phage DNA was found to sediment about twice as fast as mature phage DNA.  At later
      times during the infection the parental phage DNA was recovered as a very rapidly sedimenting
      material.  Such material was also found in alkaline sucrose gradient centrifugation after
      treatment of the cell extract with sodium dodecyl sulphate, pronase digestion and phenol
      extractions.
AU  - Skogman GS
AU  - Bjork GR
PT  - Journal Article
TA  - J. Gen. Virol.
JT  - J. Gen. Virol.
SO  - J. Gen. Virol. 1976 31: 9-20.

PMID- 3036382
VI  - 62
DP  - 1987
TI  - Assessment of DNA binding of platinum-radio-sensitizer complexes by inhibition of restriction enzymes.
PG  - 117-129
AB  - A simple and rapid method has been used to compare the binding of platinum
      complexes to DNA, in a relatively qualitative manner.  A compound bound at or
      near the restriction site inhibits enzymatic cleavage of DNA; inhibition of
      BamHI and EcoRI activity by complexes was assessed in this study using
      linearized pSV2-gpt plasmid.  Our particular interest was in DNA binding by
      complexes of platinum (Pt) with known organic radiosensitizers (RS), to
      determine whether the Pt was able to target the RS to the DNA. Although the
      Pt-RS complexes investiaged themselves have moderate radiosensitizing ability
      (like the inorganic complexes, cis- or trans-diamminedichloroplatinum(II), c-
      or t-DDP) none of the Pt-RS inhibit to the same extent as c- or t-DDP.
      However, there appears to be some correlation between enhanced
      radiosensitization by Pt-RS over Pt(RS), with the degree of Pt binding (as
      assessed by our assay).  Our results using isolated DNA suggest that not all
      complexes bind well (e.g. Pt with two RS ligands), but that in certain cases
      (e.g. Pt with only one RS), it is possible to target the drug to the DNA.  An
      ammine or amine ligand may be required in order to target a radiosensitizer to
      DNA using platinum.
AU  - Skov KA
AU  - Adomat H
AU  - Konway DC
AU  - Farrell NP
PT  - Journal Article
TA  - Chem. Biol. Interact.
JT  - Chem. Biol. Interact.
SO  - Chem. Biol. Interact. 1987 62: 117-129.

PMID- 8166773
VI  - 125
DP  - 1993
TI  - Atypical DNA-binding properties of class-IIS restriction endonucleases:evidence for recognition of the cognate sequence by a FokI monomer.
PG  - 1-10
AB  - The DNA-binding properties of the FokI restriction endonuclease were studied using the
      gel-mobility-shift assay. Specific recognition of the cognate sequence and cleavage of DNA are
      distinguishable functions and can be separated. FokI binds to its recognition site
      predominantly as a monomer. At high concentrations, FokI exhibits a cooperative recognition
      sequence-dependent aggregation. In 20 mM KCl/10 mM Tris-HCl buffer, the binding constant of
      FokI to its cognate site is 6.0-7.9 x 10/8 per mol and is lower than the values for most
      gene-regulatory proteins. FokI binding is 600-1500 times weaker to non-cognate double-stranded
      DNA than to the GGATG site, and 30,000 times weaker to single-stranded DNA or tRNA. The method
      of Bading [Nucleic Acids Res. 16 (1988) 5241-5248], used for determining the stoichometry of
      protein bound to DNA by gel-mobility-shift assay, is extended.
AU  - Skowron P
AU  - Kaczorowski T
AU  - Tucholski J
AU  - Podhajska AJ
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1993 125: 1-10.

PMID- 28911108
VI  - 45
DP  - 2017
TI  - The third restriction-modification system from Thermus aquaticus YT-1: solving the riddle of two TaqII specificities.
PG  - 9005-9018
AB  - Two restriction modification systems have been previously discovered in Thermus aquaticus
      YT-1.  TaqI is a 263-amino acid (aa) Type IIP restriction enzyme that recognizes and cleaves
      within the symmetric sequence 5-TCGA-3. TaqII, in contrast, is a 1105-aa Type IIC
      restriction-and-modification enzyme, one of a family of Thermus homologs. TaqII was originally
      reported to recognize two different asymmetric sequences: 5-GACCGA-3 and 5-CACCCA-3. We
      previously cloned the taqIIRM gene, purified the recombinant protein from Escherichia coli,
      and showed that TaqII recognizes the 5-GACCGA-3 sequence only. Here, we report the discovery,
      isolation, and characterization of TaqIII, the third RM system from T. aquaticus YT-1. TaqIII
      is a 1101-aa Type IIC/IIL enzyme and recognizes the 5-CACCCA-3 sequence previously attributed
      to TaqII. The cleavage site is 11/9 nucleotides downstream of the A residue. The enzyme
      exhibits striking biochemical similarity to TaqII. The 93% identity between their aa sequences
      suggests that they have a common evolutionary origin. The genes are located on two separate
      plasmids, and are probably paralogs or pseudoparalogs. Putative positions and aa that specify
      DNA recognition were identified and recognition motifs for 6 uncharacterized Thermus-family
      enzymes were predicted.
AU  - Skowron PM
AU  - Anton BP
AU  - Czajkowska E
AU  - Zebrowska J
AU  - Sulecka E
AU  - Krefft D
AU  - Jezewska-Frackowiak J
AU  - Zolnierkiewicz O
AU  - Witkowska M
AU  - Morgan RD
AU  - Wilson GG
AU  - Fomenkov A
AU  - Roberts RJ
AU  - Zylicz-Stachula A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2017 45: 9005-9018.

PMID- 12853651
VI  - 31
DP  - 2003
TI  - A new Thermus sp. class-IIS enzyme sub-family: isolation of a "twin" endonuclease TspDTI with a novel specificity 5'-ATGAA(N11/9)-3', related to TspGWI, TaqII and Tth111II.
PG  - e74
AB  - The TspDTI restriction endonuclease, which shows a novel recognition specificity
      5'-ATGAA(N(11/9))-3', was isolated from Thermus sp. DT. TspDTI
      appears to be a 'twin' of restriction endonuclease TspGWI from Thermus sp.
      GW, as we have previously reported. TspGWI was isolated from the same
      location as TspDTI, it recognizes a related sequence 5'-ACGGA(N(11/9))-3'
      and has conserved cleavage positions. Both enzymes resemble two other
      class-IIS endonucleases from Thermus sp.: TaqII and Tth111II. N-terminal
      amino acid sequences of TspGWI tryptic peptides exhibit 88.9-100%
      similarity to the TaqII sequence. All four enzymes were purified to
      homogeneity; their polypeptide sizes (114.5-122 kDa) make them the largest
      class-IIS restriction endonucleases known to date. The existence of a
      Thermus sp. sub-family of class-IIS restriction endonucleases of a common
      origin is herein proposed.
AU  - Skowron PM
AU  - Majewski J
AU  - Zylicz-Stachula A
AU  - Rutkowska SM
AU  - Jaworowska I
AU  - Harasimowicz-Slowinska RI
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2003 31: e74.

PMID- 7607522
VI  - 157
DP  - 1995
TI  - Cloning and applications of the two/three-base restriction endonuclease R.CviJI from IL-3A virus-infected Chlorella.
PG  - 37-41
AB  - The gene (cviJIR) encoding the two/three-base R.CviJI eukaryotic restriction endonuclease
      (ENase) from IL-3A virus-infected Chlorella was cloned into Escherichia coli.  A high
      frequency of DNA cleavage by R.CviJI required overexpression of the gene encoding the M.CviJI
      methyltransferase prior to cloning the gene for the ENase.  Both genes were sequenced and
      their organization was determined to be in head-to-tail order.  The open reading frame coding
      for R.CviJI can potentially translate a 41.4-kDa protein; however, in the E. coli host, a
      truncated version of the enzyme is produced (32.5 kDa).  The recombinant ENase does not
      exhibit ATP-induced 'star' activity (R.CviJI cleaves at RGCY, while R.CviJI* also cleaves at
      RGCR and YGCY, but not at YGCR), as is characteristic for native R.CviJI.  The very high
      frequency of DNA cleavage by R.CviJI* was exploited in the development of a quasi-random
      shotgun library method.  R.CviJI*-generated oligodeoxyribonucleotides were applied to improve
      certain molecular biology applications, i.e., DNA labeling, detection, high-resolution
      restriction mapping, amplification and epitope mapping.
AU  - Skowron PM
AU  - Swaminathan N
AU  - McMaster K
AU  - George D
AU  - Van Etten JL
AU  - Mead DA
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 37-41.

PMID- 23919831
VI  - 14
DP  - 2013
TI  - Three-stage biochemical selection: cloning of prototype class IIS/IIC/IIG restriction endonuclease-methyltransferase TsoI from the thermophile Thermus scotoductus.
PG  - 17
AB  - BACKGROUND: In continuing our research into the new family of bifunctional restriction
      endonucleases (REases), we describe the cloning of the tsoIRM gene.
      Currently, the family includes six thermostable enzymes: TaqII, Tth111II,
      TthHB27I, TspGWI, TspDTI, TsoI, isolated from various Thermus sp. and two
      thermolabile enzymes: RpaI and CchII, isolated from mesophilic bacteria
      Rhodopseudomonas palustris and Chlorobium chlorochromatii, respectively. The
      enzymes have several properties in common. They are large proteins (molecular
      size app. 120 kDa), coded by fused genes, with the REase and methyltransferase
      (MTase) in a single polypeptide, where both activities are affected by
      S-adenosylmethionine (SAM). They recognize similar asymmetric cognate sites and
      cleave at a distance of 11/9 nt from the recognition site. Thus far, we have
      cloned and characterised TaqII, Tth111II, TthHB27I, TspGWI and TspDTI. RESULTS:
      TsoI REase, which originate from thermophilic Thermus scotoductus RFL4 (T.
      scotoductus), was cloned in Escherichia coli (E. coli) using two rounds of
      biochemical selection of the T. scotoductus genomic library for the TsoI
      methylation phenotype. DNA sequencing of restriction-resistant clones revealed
      the common open reading frame (ORF) of 3348 bp, coding for a large polypeptide of
      1116 aminoacid (aa) residues, which exhibited a high level of similarity to
      Tth111II (50% identity, 60% similarity). The ORF was PCR-amplified, subcloned
      into a pET21 derivative under the control of a T7 promoter and was subjected to
      the third round of biochemical selection in order to isolate error-free clones.
      Induction experiments resulted in synthesis of an app. 125 kDa protein,
      exhibiting TsoI-specific DNA cleavage. Also, the wild-type (wt) protein was
      purified and reaction optima were determined. CONCLUSIONS: Previously we
      identified and cloned the Thermus family RM genes using a specially developed
      method based on partial proteolysis of thermostable REases. In the case of TsoI
      the classic biochemical selection method was successful, probably because of the
      substantially lower optimal reaction temperature of TsoI (app. 10-15 degrees C).
      That allowed for sufficient MTase activity in vivo in recombinant E. coli.
      Interestingly, TsoI originates from bacteria with a high optimum growth
      temperature of 67 degrees C, which indicates that not all bacterial enzymes match
      an organism's thermophilic nature, and yet remain functional cell components.
      Besides basic research advances, the cloning and characterisation of the new
      prototype REase from the Thermus sp. family enzymes is also of practical
      importance in gene manipulation technology, as it extends the range of available
      DNA cleavage specificities.
AU  - Skowron PM
AU  - Vitkute J
AU  - Ramanauskaite D
AU  - Mitkaite G
AU  - Jezewska-Frackowiak J
AU  - Zebrowska J
AU  - Zylicz-Stachula A
AU  - Lubys A
PT  - Journal Article
TA  - BMC Mol. Biol.
JT  - BMC Mol. Biol.
SO  - BMC Mol. Biol. 2013 14: 17.

PMID- 22735699
VI  - 40
DP  - 2012
TI  - Rational engineering of sequence specificity in R.MwoI restriction endonuclease.
PG  - 8579-8592
AB  - R.MwoI is a Type II restriction endonucleases enzyme (REase), which specifically  recognizes a
      palindromic interrupted DNA sequence 5'-GCNNNNNNNGC-3' (where N
      indicates any nucleotide), and hydrolyzes the phosphodiester bond in the DNA
      between the 7th and 8th base in both strands. R.MwoI exhibits remote sequence
      similarity to R.BglI, a REase with known structure, which recognizes an
      interrupted palindromic target 5'-GCCNNNNNGGC-3'. A homology model of R.MwoI in
      complex with DNA was constructed and used to predict functionally important amino
      acid residues that were subsequently targeted by mutagenesis. The model, together
      with the supporting experimental data, revealed regions important for recognition
      of the common bases in DNA sequences recognized by R.BglI and R.MwoI. Based on
      the bioinformatics analysis, we designed substitutions of the S310 residue in
      R.MwoI to arginine or glutamic acid, which led to enzyme variants with altered
      sequence selectivity compared with the wild-type enzyme. The S310R variant of
      R.MwoI preferred the 5'-GCCNNNNNGGC-3' sequence as a target, similarly to R.BglI,
      whereas the S310E variant preferentially cleaved a subset of the MwoI sites,
      depending on the identity of the 3rd and 9th nucleotide residues. Our results
      represent a case study of a REase sequence specificity alteration by a single
      amino acid substitution, based on a theoretical model in the absence of a crystal
      structure.
AU  - Skowronek K
AU  - Boniecki MJ
AU  - Kluge B
AU  - Bujnicki JM
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: 8579-8592.

PMID- 16498623
VI  - 63
DP  - 2006
TI  - Theoretical model of restriction endonuclease HpaI in complex with DNA, predicted by fold recognition and validated by site-directed mutagenesis.
PG  - 1059-1068
AB  - Type II restriction enzymes are commercially important deoxyribonucleases and very attractive
      targets for protein engineering
      of new specificities. At the same time they are a very challenging test
      bed for protein structure prediction methods. Typically, enzymes that
      recognize different sequences show little or no amino acid sequence
      similarity to each other and to other proteins. Based on
      crystallographic analyses that revealed the same PD-(D/E)XK fold for
      more than a dozen case studies, they were nevertheless considered to be
      related until the combination of bioinformatics and mutational analyses
      has demonstrated that some of these proteins belong to other, unrelated
      folds PLD, HNH, and GIY-YIG. As a part of a large-scale project aiming
      at identification of a three-dimensional fold for all type II REases
      with known sequences (currently similar to 1000 proteins), we carried
      out preliminary structure prediction and selected candidates for
      experimental validation. Here, we present the analysis of Hpal REase,
      an ORFan with no detectable homologs, for which we detected a
      structural template by protein fold recognition, constructed a model
      using the FRankenstein monster approach and identified a number of
      residues important for the DNA binding and catalysis. These predictions
      were confirmed by site-directed mutagenesis and in vitro analysis of
      the mutant proteins. The experimentally validated model of Hpal will
      serve as a low-resolution structural platform for evolutionary
      considerations in the subgroup of blunt-cutting REases with different
      specificities. The research protocol developed in the course of this
      work represents a streamlined version of the previously used techniques
      and can be used in a high-throughput fashion to build and validate
      models for other enzymes, especially ORFans that exhibit no sequence
      similarity to any other protein in the database.
AU  - Skowronek KJ
AU  - Kosinski J
AU  - Bujnicki JM
PT  - Journal Article
TA  - Proteins
JT  - Proteins
SO  - Proteins 2006 63: 1059-1068.

PMID- 2842668
VI  - 0
DP  - 1988
TI  - Restriction endonucleases from Bifidobacteria.
PG  - 15-16
AB  - The site specific restriction endonucleases were found in four strains among
      the twelve strains of anaerobic bacteria of the genus Bifidobacterium.  Two of
      the restriction endonucleases studied, BadI from B. adolescentis LVA1 and BbfI
      from B. bifidum LVA3, are isoschizomers of XhoI and recognize the nucleotide
      sequence CTCGAG.  The restriction endonucleases Bbf7411I from B. bifidum 7411
      and Bla7920I from B. lactentis 7920 recognize and hydrolyze the nucleotide
      sequence TCCGGA having a specificity analogous to that of the restriction
      endonuclease CauB3I.  Like CauB3I, these restriction endonucleases are unable
      to hydrolyze DNA if the adenine residues in the recognition site are
      methylated.
AU  - Skrypina NA
AU  - Kramarov VM
AU  - Lyannaya AM
AU  - Smolyaninov VV
AU  - Goncharova GI
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1988 0: 15-16.

PMID- 2550978
VI  - 21
DP  - 1989
TI  - The EcoDXXI restriction and modification system: cloning the genes and homology to Type I restriction and modification systems.
PG  - 195-204
AB  - The Escherichia coli plasmid pDXX1 codes for a type I restriction and
      modification system, EcoDXXI.  A 15.5-kb BamHI fragment from pDXX1 has been
      cloned and contains the hsdR, hsdM, and hsdS genes that encode the EcoDXX1
      system.  The EcoDXX1 hsd genes can complement the gene products of the EcoR124
      and EcoR124/3 hsd systems, but not those of EcoK and EcoB.  Hybridization
      experiments using EcoDXX1 hsd genes as a probe demonstrate homology between
      EcoDXX1 and EcoK or EcoB systems.
AU  - Skrzypek E
AU  - Piekarowicz A
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 1989 21: 195-204.

PMID- 29301889
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Pseudomonas putida UV4 and UV4/95, Toluene Dioxygenase-Expressing Producers of cis-1,2-Dihydrodiols.
PG  - e01419-17
AB  - Here, we present draft genome sequences of Pseudomonas putida strains UV4 and UV4/95, which
      demonstrate an ability to conduct a wide range of industrially
      important biotransformations of arenes, alkenes, and phenols.
AU  - Skvortsov T
AU  - Hoering P
AU  - Arkhipova K
AU  - Whitehead RC
AU  - Boyd DR
AU  - Allen CCR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01419-17.

PMID- 28450525
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of 'Candidatus Synechococcus spongiarum,' Cyanobacterial Symbionts of the Mediterranean Sponge Aplysina aerophoba.
PG  - e00268-17
AB  - We report here four draft genome sequences belonging to clade F of the cyanobacterium
      'Candidatus Synechococcus spongiarum' of the marine sponge
      Aplysina aerophoba, which were collected from two nearby locations in the
      northern Adriatic Sea. The sequences provide the basis for within-clade
      comparisons between members of this widespread group of cyanobacterial sponge
      symbionts.
AU  - Slaby BM
AU  - Hentschel U
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00268-17.

PMID- 10447688
VI  - 264
DP  - 1999
TI  - Feedback regulation of DNA methyltransferase gene expression by methylation.
PG  - 191-199
AB  - This paper tests the hypothesis that expression of the DNA methyltransferase, dnmt1, gene is
      regulated by a methylation-sensitive DNA element. Methylation of DNA is an attractive system
      for feedback regulation of DNA methyltransferase as the final product of the reaction,
      methylated DNA, can regulate gene expression in cis. We show that an AP-1-dependent regulatory
      element of dnmt1 is heavily methylated in most somatic tissues and in the mouse embryonal cell
      line, P19, and completely unmethylated in a mouse adrenal carcinoma cell line, Y1. dnmt1 is
      highly over expressed in Y1 relative to P19 cell lines. Global inhibition of DNA methylation
      in P19 cells by 5-azadeoxycytidine results in demethylation of the AP-1 regulatory region and
      induction of dnmt1 expression in P19cells, but not Y1 cells.  We propose that this regulatory
      region of dnmt1 acts as a sensor of the DNA methylation capacity of the cell. These results
      provide an explanation for the documented coexistence of global hypomethylation and high
      levels of DNA methyltransferase activity in many cancer cells and for the carcinogenic effect
      of hypomethylating diets.
AU  - Slack A
AU  - Cervoni N
AU  - Pinard M
AU  - Szyf M
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1999 264: 191-199.

PMID- 2822609
VI  - 23
DP  - 1987
TI  - Endonuclease from Acholeplasma laidlawii strain JA1 associated with in vivo restriction of DNA containing 5-methylcytosine.
PG  - 423-426
AB  - Transfection of Acholeplasma laidlawii strain JA1 with viral DNAs that have
      been sequence-specifically methylated in vitro has led us to previously
      postulate that JA1 cells contain an enzyme which cleaves only DNA containing
      5-methylcytosine, regardless of the nucleotide sequence containing that base.
      In this paper we show that an endonuclease activity is present in extracts from
      JA1 cells but not in extracts from a restriction deficient variant of JA1.  The
      partially purified enzyme cleaves to only DNA containing 5-methylcytosine, but
      also DNA containing no methylated bases.  We discuss why this endonuclease
      activity may not have the same in vitro specificity as would be expected from
      in vivo experiments.
AU  - Sladek TL
AU  - Maniloff J
PT  - Journal Article
TA  - Isr. J. Med. Sci.
JT  - Isr. J. Med. Sci.
SO  - Isr. J. Med. Sci. 1987 23: 423-426.

PMID- 3001023
VI  - 165
DP  - 1986
TI  - Mycoplasma restriction: identification of a new type of restriction specificity for DNA containing 5-methylcytosine.
PG  - 219-225
AB  - Mycoplasma bacteriophage L51 single-stranded DNA and L2 double-stranded DNA are
      host cell modified and restricted when they transfect Acholeplasma laidlawii
      JA1 and K2 cells.  The L51 genome has a single restriction endonuclease MboI
      site (recognition sequence GATC), which contains 5-methylcytosine when the DNA
      is isolated from L51 phage grown in K2 cells but is unmethylated when the DNA
      is from phage grown in JA1 cells.  This GATC sequence is nonessential, since an
      L51 mutant in which the MboI site was deleted was still viable.  DNA from this
      deletion mutant phage was not restricted during transfection of either strain
      K2 or containing the sequence GAT 5-methylcytosine.  We conclude that K2 cells
      have a restriction system specific for DNA containing the sequence GATC and
      protect their DNA by methylating cytosine in this sequence.  In contrast, JA1
      cells (which contain no methylated DNA bases) have a newly discovered type of
      restriction-modification system.  From results of studies of the restriction of
      specifically methylated DNAs, we conclude that JA1 cells restrict DNA
      containing 5-methylcytosine, regardless of the nucleotide sequence containing
      5-methylcytosine.  This is the first report of a DNA restriction activity
      specific for a single (methylated) base.  Modification in this system is the
      absence of cytosine methylating activity.  A restriction-deficient variant of
      strain JA1, which retains the JA1 modification phenotype, was isolated,
      indicating that JA1 cells have a gene product with restriction specificity for
      DNA containing 5-methylcytosine.
AU  - Sladek TL
AU  - Nowak JA
AU  - Maniloff J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1986 165: 219-225.

PMID- 22646482
VI  - 13
DP  - 2012
TI  - Complementation between inactive fragments of SssI DNA methyltransferase.
PG  - 17
AB  - Background: Silencing mammalian genes by targeted DNA (cytosine-5) methylation of selected CG
      sites in the genome would be a powerful technique to analyze epigenomic information and to
      study the roles of DNA methylation in physiological and pathological states. A promising
      approach of targeted DNA methylation is based on the ability of split fragments of a monomeric
      DNA methyltransferase (C5-MTase) to associate and form active enzyme. A few C5-MTases of
      different specificities have been shown to possess the ability of fragment complementation,
      but a demonstration of this phenomenon for a C5-MTase, which has CG specificity and thus can
      be targeted to methylate any CG site, has been lacking. The purpose of this study was to test
      whether the CG-specific prokaryotic C5-MTase M.SssI shows the phenomenon of fragment
      complementation.
      Results: We show that truncated inactive N-terminal fragments of M.SssI can assemble with
      truncated inactive C-terminal fragments to form active enzyme in vivo when produced in the
      same E. coli cell. Overlapping and non-overlapping fragments as well as fragments containing
      short appended foreign sequences had complementation capacity. In optimal combinations
      C-terminal fragments started between conserved motif VIII and the predicted target recognizing
      domain of M.SssI. DNA methyltransferase activity in crude extracts of cells with the best
      complementing fragment pairs was ~ 4 per cent of the activity of cells producing the full
      length enzyme.  Fusions of two N-terminal and two C-terminal fragments to 21.6 kDa zinc finger
      domains only slightly reduced complementation ability of the fragments.
      Conclusions: The CG-specific DNA methyltransferase M.SssI shows the phenomenon of fragment
      complementation in vivo in E. coli. Fusion of the split fragments to six unit zinc finger
      domains does not substantially interfere with the formation of active enzyme. These
      observations and the large number of complementing fragment combinations representing a wide
      range of MTase activity offer the possibility to develop M.SssI into a programmable DNA
      ethyltransferase of high specificity.
AU  - Slaska-Kiss K
AU  - Timar E
AU  - Kiss A
PT  - Journal Article
TA  - BMC Mol. Biol.
JT  - BMC Mol. Biol.
SO  - BMC Mol. Biol. 2012 13: 17.

PMID- 19251847
VI  - 8
DP  - 2009
TI  - Genome Sequences of Three Agrobacterium Biovars Help Elucidate the Evolution of Multi-Chromosome Genomes in Bacteria.
PG  - 2501-2511
AB  - The family Rhizobiaceae contains plant-associated bacteria with critical roles in ecology and
      agriculture. Within this family, many Rhizobium and
      Sinorhizobium strains are nitrogen-fixing plant mutualists, while many
      strains designated as Agrobacterium are plant pathogens. These contrasting
      lifestyles are primarily dependent on the transmissible plasmids each
      strain harbors. Members of Rhizobiaceae also have diverse genome
      architectures that include single chromosomes, multiple chromosomes, and
      plasmids of various sizes. Agrobacterium strains have been divided into
      three Biovars, based on physiological and biochemical properties. The
      genome of a Biovar I strain, A. tumefaciens C58, has been previously
      sequenced. In this study the genomes of the Biovar II strain A.
      radiobacter K84, a commercially available biological control strain that
      inhibits certain pathogenic agrobacteria, and the Biovar III strain A.
      vitis S4, a narrow host range strain that infects grapes and invokes a
      hypersensitive response on non-host plants, were fully sequenced and
      annotated. Comparison with other sequenced members of the
      alpha-proteobacteria provides new data on evolution of multi-partite
      bacterial genomes. Primary chromosomes show extensive conservation of both
      gene content and order. In contrast, secondary chromosomes share smaller
      percentages of genes, and conserved gene order is restricted to short
      blocks. We propose that secondary chromosomes originated from an ancestral
      plasmid to which genes have been transferred from a progenitor primary
      chromosome. Similar patterns are observed in select beta- and
      gamma-proteobacteria species. Together these results define the evolution
      of chromosome architecture and gene content among the Rhizobiaceae and
      support a generalized mechanism for second chromosome formation among
      bacteria.
AU  - Slater SC et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2009 8: 2501-2511.

PMID- 2827113
VI  - 15
DP  - 1987
TI  - Cloning, sequencing and expression of the TaqI restriction-modification system.
PG  - 9781-9796
AB  - The TaqI modification and restriction genes (recognition sequence TCGA) have
      been cloned in E. coli and their DNA sequences have been determined.  Both
      proteins were characterized and the N-terminal sequence of the endonuclease was
      determined.  The genes have the same transcriptional orientation with the
      methylase gene 5' to the endonuclease gene.  The methylase gene is 1089 bp in
      length (363 amino acids, 40,575 daltons); the endonuclease gene is 702 bp in
      length (234 amino acis, 27,523 daltons); they are separated by 132 bp.  Both
      methylase and endonuclease activity can be detected in cell extracts.  The
      clones fully modify the vector and chromosomal DNA but they fail to restrict
      infecting phage.  Clones carrying only the restriction gene are viable even in
      the absence of modification.  The restriction gene contains 7 TaqI sites; the
      modification gene contains none.  This asymmetric distribution of sites could
      be important in the regulation of the expression of the endonuclease gene.
AU  - Slatko BE
AU  - Benner JS
AU  - Jager-Quinton T
AU  - Moran LS
AU  - Simcox TG
AU  - VanCott EM
AU  - Wilson GG
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1987 15: 9781-9796.

PMID- 3248732
VI  - 74
DP  - 1988
TI  - Cloning and analysis of the HaeIII and HaeII methyltransferase genes.
PG  - 45-50
AB  - The HaeIII methyltransferase (MTase) gene from Haemophilus aegyptius
      (recognition sequence: 5'-GGCC-3') was cloned into Escherichia coli in the
      plasmid vector pBR322.  The gene was isolated on a single EcoRI fragment and on
      a single HindIII fragment.  Clones carrying additional adjacent fragments were
      found to code also for the HaeII restriction endonuclease and HaeII
      modification MTase (recognition sequence:  5'-PuGCGCPy-3').  The sequence of
      the HaeIII modification gene was determined.  The inferred amino acid sequence
      of the protein was found to share extensive similarity with other sequenced
      m5C-MTases.  The central non-conserved region of the M.HaeIII MTase, thought to
      form the nucleotide sequence-specificity domain, is almost identical to that of
      the M.BsuRI, M.BspRI and M.NgoPII MTases, which also recognize the sequence
      5'-GGCC-3'.
AU  - Slatko BE
AU  - Croft R
AU  - Moran LS
AU  - Wilson GG
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 45-50.

PMID- 18203449
VI  - 2
DP  - 2007
TI  - Dual restriction enzyme digest of cationic-gold-coated DNA scaffolds.
PG  - 821-825
AB  - DNA strands coated with AuNPs were cleaved by restriction enzymes while in solution or on a
      surface. Enzymatic activity was verified by gel
      electrophoresis prior to surface analysis. Cleavage results suggest
      that enzymes can recognize the AuNP-coated strands while on the
      surfaces, though specificity in digestion has not yet been verified.
      Development allows for advances in site specific localization of
      components using biological media.
AU  - Slavin JWJ
AU  - Ivanisevic A
PT  - Journal Article
TA  - Int. J. Nanomedicine
JT  - Int. J. Nanomedicine
SO  - Int. J. Nanomedicine 2007 2: 821-825.

PMID- 11930014
VI  - 99
DP  - 2002
TI  - The complete genome of the hyperthermophile Methanopyrus kandleri AV19 and monophyly of Archaeal methanogens.
PG  - 4644-4649
AB  - We have determined the complete 1,694,969-nt sequence of the GC-rich genome of Methanopyrus
      kandleri by using a whole direct genome sequencing approach. This approach is based on
      unlinking of genomic DNA with the ThermoFidelase version of M. kandleri topoisomerase V and
      cycle sequencing directed by 2'-modified oligonucleotides (Fimers).
      Sequencing redundancy (3.3x) was sufficient to assemble the genome with less than one error
      per 40 kb. Using a combination of sequence database searches and coding potential prediction,
      1,692 protein-coding genes and 39 genes for
      structural RNAs were identified. M. kandleri proteins show an unusually high content of
      negatively charged amino acids, which might be an adaptation to the high intracellular
      salinity. Previous phylogenetic analysis of 16S RNA suggested that M. kandleri belonged to a
      very deep branch, close to the root of the archaeal tree. However, genome comparisons indicate
      that, in both trees constructed using concatenated alignments of ribosomal proteins and trees
      based on gene content, M.
      kandleri consistently groups with other archaeal methanogens. M. kandleri shares the set of
      genes implicated in
      methanogenesis and, in part, its operon organization with Methanococcus jannaschii and
      Methanothermobacter
      thermoautotrophicum. These findings indicate that archaeal methanogens are monophyletic. A
      distinctive feature of M.
      kandleri is the paucity of proteins involved in signaling and regulation of gene expression.
      Also, M. kandleri appears to
      have fewer genes acquired via lateral transfer than other archaea. These features might
      reflect the extreme habitat of this
      organism. Full author list: Slesarev,A.I., Mezhevaya,K.V., Makarova,K.S., Polushin,N.N.,
      Shcherbinina,O.V., Shakhova,V.V., Belova,G.I., Aravind,L., Natale,D.A., Rogozin,I.B.,
      Tatusov,R.L., Wolf,Y.I., Stetter,K.O., Malykh,A.G., Koonin,E.V., Kozyavkin,S.A.
AU  - Slesarev AI
AU  - Mezhevaya KV
AU  - Makarova KS
AU  - Polushin NN
AU  - Shcherbinina OV
AU  - Shakhova VV
AU  - Belova GI
AU  - Aravind L
AU  - Natale DA
AU  - Rogozin IB
AU  - Tatusov RL
AU  - Wolf YI
AU  - Stetter KO
AU  - Malykh AG
AU  - Koonin EV
AU  - Kozyavkin SA
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2002 99: 4644-4649.

PMID- 18511120
VI  - 60
DP  - 2008
TI  - Complete sequence of Enterococcus faecium pVEF3 and the detection of an omega-epsilon-zeta toxin-antitoxin module and an ABC transporter.
PG  - 75-85
AB  - Glycopeptide resistant Enterococcus faecium (GREF) persists on Norwegian
      poultry farms despite the ban on the growth promoter avoparcin. The
      biological basis for long-term persistence of avoparcin resistance is not
      fully understood. This study presents the complete DNA sequence of the E.
      faecium R-plasmid pVEF3 and functional studies of some plasmid-encoded
      traits (a toxin-antitoxin (TA) system and an ABC transporter) that may be
      of importance for plasmid persistence. The pVEF3 (63.1 kbp), isolated from
      an E. faecium strain of poultry origin sampled in Norway in 1999, has 71
      coding sequences including the vanA avoparcin/vancomycin resistance
      encoding gene cluster. pVEF3 encodes the TA system omega-epsilon-zeta, and
      plasmid stability tests and transcription analysis show that
      omega-epsilon-zeta is functional in Enterococcus faecalis OGIX, although
      with decreasing effect over time. The predicted ABC transporter was not
      found to confer reduced susceptibility to any of the 28 substances tested.
      The TA system identified in the pVEF-type plasmids may contribute to vanA
      plasmid persistence on Norwegian poultry farms. However, size and
      compositional heterogeneity among E. faecium vanA plasmids suggest that
      additional plasmid maintenance systems in combination with host specific
      factors and frequent horizontal gene transfer and rearrangement causes the
      observed plasmid composition and distribution patterns.
AU  - Sletvold H
AU  - Johnsen PJ
AU  - Hamre I
AU  - Simonsen GS
AU  - Sundsfjord A
AU  - Nielsen KM
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 2008 60: 75-85.

PMID- 22821013
VI  - 29
DP  - 2012
TI  - Genome reduction and co-evolution between the primary and secondary bacterial symbionts of psyllids.
PG  - 3781-3792
AB  - Genome reduction in obligately intracellular bacteria is one of the most
      well-established patterns in the field of molecular evolution. In the extreme,
      many sap-feeding insects harbor nutritional symbionts with genomes that are so
      reduced that it is not clear how they perform basic cellular functions. For
      example, the primary symbiont of psyllids (Carsonella) maintains one of the
      smallest and most AT-rich bacterial genomes ever identified and has surprisingly
      lost many genes that are thought to be essential for its role in provisioning its
      host with amino acids. However, our understanding of this extreme case of genome
      reduction is limited, as genomic data for Carsonella are available from only a
      single host species, and little is known about the functional role of "secondary"
      bacterial symbionts in psyllids. To address these limitations, we analyzed
      complete Carsonella genomes from pairs of congeneric hosts in three divergent
      genera within the Psyllidae (Ctenarytaina, Heteropsylla, and Pachypsylla) as well
      as complete secondary symbiont genomes from two of these host species
      (Ctenarytaina eucalypti and Heteropsylla cubana). Although the Carsonella genomes
      are generally conserved in size, structure, and GC content and exhibit
      genome-wide signatures of purifying selection, we found that gene loss has
      remained active since the divergence of the host species and had a particularly
      large impact on the amino acid biosynthesis pathways that define the symbiotic
      role of Carsonella. In some cases, the presence of additional bacterial symbionts
      may compensate for gene loss in Carsonella, as functional gene content indicates
      a high degree of metabolic complementarity between co-occurring symbionts. The
      genomes of the secondary symbionts also show signatures of long-term evolution as
      vertically transmitted, intracellular bacteria, including more extensive genome
      reduction than typically observed in facultative symbionts. Therefore, a history
      of co-evolution with secondary bacterial symbionts can partially explain the
      ongoing genome reduction in Carsonella. However, the absence of these secondary
      symbionts in other host lineages indicates that the relationships are dynamic and
      that other mechanisms, such as changes in host diet or functional coordination
      with the host genome, must also be at play.
AU  - Sloan DB
AU  - Moran NA
PT  - Journal Article
TA  - Mol. Biol. Evol.
JT  - Mol. Biol. Evol.
SO  - Mol. Biol. Evol. 2012 29: 3781-3792.

PMID- 4570605
VI  - 113
DP  - 1973
TI  - Host specificity of Salmonella typhimurium deoxyribonucleic acid restriction and modification.
PG  - 724-726
AB  - The restriction and modification genes of Salmonella typhimurium which lie near
      the thr locus were transferred to a restrictionless mutant of Escherichia coli.
      These genes were found to be allelic to the E. coli K, B, and A restriction
      and modification genes.  E. coli recombinants with the restriction and
      modfication host specificity of S. typhimurium restricted phage lambda that had
      been modified by each of the seven known host specificities of E. coli at an
      efficiency of plating levels of abobut 10-2.  Phage lambda modified with the S.
      typhimurium host specificity was restricted by six of the seven E. coli host
      specificiteis but not by the RII (fi- R-factor controlled) host specificity.
      It is proposed that the restriction and modification enzymes of this S.
      typhimurium host specificity have two substrates, one of which is a substrate
      for the RII host specificity enzymes.
AU  - Slocum H
AU  - Boyer HW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1973 113: 724-726.

PMID- Not included in PubMed...
VI  - 29
DP  - 1971
TI  - In vitro restriction of DNA.  Demonstration that the DNA of mutant phage are resistant to attack by restriction endonuclease.
PG  - 405
AB  - Various bacterial systems (Escherichia coli, Hemophilus, and others)
      demonstrate a mechanism for rejecting non-homologous DNA, i.e., DNA which
      originates in a cell of a different strain.  This host-controlled restriction,
      more specifically degradation, is brought about by a 2-step enzymatic mechanism
      involving an endonuclease which introduces a limited number of double-strand
      scissions at 2 specific sites (a site being a sequence of nucleotide base
      pairs) on a DNA molecule.  The endonuclease does not recognize or introduce
      double-strand scissions at these sites if there has been a prior methylation of
      1 or 2 bases in the site (known as host-controlled modification of DNA).  The
      modification methylase and restriction endonuclease recognize the same
      substrate by virtue of the 2 enzymes having a common subunit which recognizes
      the sequence of base pairs.  Small circular phage DNA have 2 sites recognized
      by the endonuclease and methylase per molecule.  The biologic effect of the
      restriction endonuclease is to abort the lytic cycle of the phage.  That is,
      only 1 in 10,000 phage infected are successful.  Phage mutants can be obtained
      that have successful lytic cycles of 1 in 100.  I recombined 2 independent
      mutants to obtain a phage totally resistant to the endonuclease, i.e., a
      probability of 1.0 that the lytic cycle takes place.  In vitro, the single
      mutants are degraded to intact linear molecules, whereas the recombinant is
      completely resistant to degradation, meaning no single strand breaks are made
      at either mutant site.  The results can be interpreted on the basis of the
      substrate being a sequence of base pairs with 2-fold dimensional symmetry.
AU  - Slocum HC
PT  - Journal Article
TA  - Tex. Rep. Biol. Med.
JT  - Tex. Rep. Biol. Med.
SO  - Tex. Rep. Biol. Med. 1971 29: 405.

PMID- 29437115
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Legionella sainthelensi Isolated from a Patient with  Legionnaires' Disease.
PG  - e01588-17
AB  - Legionella sainthelensi is an aquatic environmental bacterium that in humans can  cause
      Legionnaires' disease (LD), an often severe form of pneumonia. Here, we
      report the first complete genome of a L. sainthelensi clinical isolate obtained
      in 2001 from a patient with LD in Canterbury, New Zealand.
AU  - Slow S
AU  - Anderson T
AU  - Biggs P
AU  - Kennedy M
AU  - Murdoch D
AU  - Cree S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01588-17.

PMID- 28619815
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of a Legionella longbeachae Serogroup 1 Strain Isolated  from a Patient with Legionnaires' Disease.
PG  - e00564-17
AB  - Legionella longbeachae serogroup 1, predominantly found in soil and composted plant material,
      causes the majority of cases of Legionnaires' disease (LD) in New
      Zealand. Here, we report the complete genome sequence of an L. longbeachae
      serogroup 1 (sg1) isolate derived from a patient hospitalized with LD in
      Christchurch, New Zealand.
AU  - Slow S
AU  - Anderson T
AU  - Miller J
AU  - Singh S
AU  - Murdoch D
AU  - Biggs PJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00564-17.

PMID- 21655244
VI  - 6
DP  - 2011
TI  - Complete Genome Sequence of Treponema paraluiscuniculi, Strain Cuniculi A: The Loss of Infectivity to Humans Is Associated with Genome Decay.
PG  - e20415
AB  - Treponema paraluiscuniculi is the causative agent of rabbit venereal spirochetosis. It is not
      infectious to humans, although its
      genome structure is very closely related to other pathogenic Treponema species including
      Treponema pallidum subspecies pallidum, the etiological agent of syphilis. In this study, the
      genome sequence of Treponema paraluiscuniculi, strain Cuniculi A, was determined by a
      combination of several high-throughput sequencing strategies. Whereas the overall size
      (1,133,390 bp), arrangement, and gene content of the Cuniculi A genome closely resembled those
      of the T. pallidum genome, the T. paraluiscuniculi genome contained a markedly higher number
      of pseudogenes and gene fragments (51). In addition to pseudogenes, 33 divergent genes were
      also found in the T. paraluiscuniculi genome. A set of 32 (out of 84) affected genes encoded
      proteins of known or predicted function in the Nichols genome. These proteins included
      virulence factors, gene regulators and components of DNA repair and recombination. The
      majority (52 or 61.9%) of the Cuniculi A
      pseudogenes and divergent genes were of unknown function. Our results indicate that T.
      paraluiscuniculi has evolved from a T. pallidum-like ancestor and adapted to a specialized
      host-associated niche (rabbits) during loss of infectivity to humans. The genes that are
      inactivated or altered in T. paraluiscuniculi are candidates for virulence factors important
      in the infectivity and pathogenesis of T. pallidum subspecies.
AU  - Smajs D
AU  - Zobanikova M
AU  - Strouhal M
AU  - Cejkova D
AU  - Dugan-Rocha S
AU  - Pospisilova P
AU  - Norris SJ
AU  - Albert T
AU  - Qin X
AU  - Hallsworth-Pepin K
AU  - Buhay C
AU  - Muzny DM
AU  - Chen L
AU  - Gibbs RA
AU  - Weinstock GM
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2011 6: e20415.

PMID- 25838488
VI  - 3
DP  - 2015
TI  - Genome Sequence of Magnetospirillum magnetotacticum Strain MS-1.
PG  - e00233-15
AB  - Here, we report the genome sequence of Magnetospirillum magnetotacticum strain MS-1, which
      consists of of 36 contigs and 4,136 protein-coding genes.
AU  - Smalley MD
AU  - Marinov GK
AU  - Bertani LE
AU  - DeSalvo G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00233-15.

PMID- 23405321
VI  - 1
DP  - 2013
TI  - Genome Sequence of Helicobacter heilmannii Sensu Stricto ASB1 Isolated from the Gastric Mucosa of a Kitten with Severe Gastritis.
PG  - e00033-12
AB  - Here we report the genome sequence of Helicobacter heilmannii sensu stricto ASB1  isolated
      from the gastric mucosa of a kitten with severe gastritis. Helicobacter heilmannii sensu
      stricto has also been associated with gastric disease in humans. Availability of this genome
      sequence will contribute to the identification of genes involved in the pathogen's virulence
      and carcinogenic properties.
AU  - Smet A
AU  - Van Nieuwerburgh F
AU  - Ledesma J
AU  - Flahou B
AU  - Deforce D
AU  - Ducatelle R
AU  - Haesebrouck F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00033-12.

PMID- 20585456
VI  - 5
DP  - 2010
TI  - Complete nucleotide sequence of CTX-M-15-plasmids from clinical Escherichia coli isolates: insertional events of transposons and insertion sequences.
PG  - E11202
AB  - BACKGROUND: CTX-M-producing Escherichia coli strains are regarded as major
      global pathogens. METHODOLOGY/PRINCIPAL FINDINGS: The nucleotide sequence
      of three plasmids (pEC_B24: 73801-bp; pEC_L8: 118525-bp and pEC_L46:
      144871-bp) from Escherichia coli isolates obtained from patients with
      urinary tract infections and one plasmid (pEC_Bactec: 92970-bp) from an
      Escherichia coli strain isolated from the joint of a horse with arthritis
      were determined. Plasmid pEC_Bactec belongs to the IncI1 group and carries
      two resistance genes: bla(TEM-1) and bla(CTX-M-15). It shares more than
      90% homology with a previously published bla(CTX-M)-plasmid from E. coli
      of human origin. Plasmid pEC_B24 belongs to the IncFII group whereas
      plasmids pEC_L8 and pEC_L46 represent a fusion of two replicons of type
      FII and FIA. On the pEC_B24 backbone, two resistance genes, bla(TEM-1) and
      bla(CTX-M-15), were found. Six resistance genes, bla(TEM-1),
      bla(CTX-M-15), bla(OXA-1), aac6'-lb-cr, tetA and catB4, were detected on
      the pEC_L8 backbone. The same antimicrobial drug resistance genes, with
      the exception of tetA, were also identified on the pEC_L46 backbone.
      Genome analysis of all 4 plasmids studied provides evidence of a seemingly
      frequent transposition event of the bla(CTX-M-15)-ISEcp1 element. This
      element seems to have a preferred insertion site at the tnpA gene of a
      bla(TEM)-carrying Tn3-like transposon, the latter itself being inserted by
      a transposition event. The IS26-composite transposon, which contains the
      bla(OXA-1), aac6'-lb-cr and catB4 genes, was inserted into plasmids pEC_L8
      and pEC_L46 by homologous recombination rather than a transposition event.
      Results obtained for pEC_L46 indicated that IS26 also plays an important
      role in structural rearrangements of the plasmid backbone and seems to
      facilitate the mobilisation of fragments from other plasmids. CONCLUSIONS:
      Collectively, these data suggests that IS26 together with ISEcp1 could
      play a critical role in the evolution of diverse multiresistant plasmids
      found in clinical Enterobacteriaceae.
AU  - Smet A
AU  - Van Nieuwerburgh F
AU  - Vandekerckhove TT
AU  - Martel A
AU  - Deforce D
AU  - Butaye P
AU  - Haesebrouck F
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2010 5: E11202.

PMID- 24874670
VI  - 2
DP  - 2014
TI  - Draft Whole-Genome Sequence of a New Variant of Vibrio cholerae O1 El Tor Strain  Isolated from a Cholera Patient in Russia.
PG  - e00432-14
AB  - Draft whole-genome sequencing of the Vibrio cholerae capital O, Cyrillic1 El Tor  clinical
      strain L3226, isolated in Moscow in 2010, was carried out. Various
      mutations in the virulence-associated mobile elements were determined in its
      genome that differentiated this strain from the reference V. cholerae capital O,
      Cyrillic1 El Tor strain N16961.
AU  - Smirnova NI
AU  - Cherkasov AV
AU  - Krasnov YM
AU  - Agafonov DA
AU  - Kutyrev VV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00432-14.

PMID- 28232438
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequencing of Vibrio cholerae O1 El Tor Strains Isolated in Ukraine  (2011) and Russia (2014).
PG  - e01640-16
AB  - Here, we present the draft whole-genome sequence of Vibrio cholerae O1 El Tor strains 76 and
      M3265/80, isolated in Mariupol, Ukraine, and Moscow, Russia. The
      presence of various mutations detected in virulence-associated mobile elements
      indicates high genetic similarity of the strains reported here with new highly
      virulent variants of the cholera agent V. cholerae.
AU  - Smirnova NI
AU  - Krasnov YM
AU  - Agafonova EY
AU  - Shchelkanova EY
AU  - Alkhova ZV
AU  - Kutyrev VV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01640-16.

PMID- 17182629
VI  - 35
DP  - 2007
TI  - Specific targeting of cytosine methylation to DNA sequences in vivo.
PG  - 740-754
AB  - Development of methods that will allow exogenous imposition of inheritable gene-specific
      methylation patterns has potential application in both
      therapeutics and in basic research. An ongoing approach is the use of
      targeted DNA methyltransferases, which consist of a fusion between
      gene-targeted zinc-finger proteins and prokaryotic DNA cytosine
      methyltransferases. These enzymes however have so far demonstrated
      significant and unacceptable levels of non-targeted methylation. We now
      report the development of second-generation targeted methyltransferase
      enzymes comprising enhanced zinc-finger arrays coupled to
      methyltransferase mutants that are functionally dominated by their
      zinc-finger component. Both in vitro plasmid methylation studies and a
      novel bacterial assay reveal a high degree of target-specific methylation
      by these enzymes. Furthermore, we demonstrate for the first time transient
      expression of targeted cytosine methyltransferase in mammalian cells
      resulting in the specific methylation of a chromosomal locus. Importantly,
      the resultant methylation pattern is inherited through successive cell
      divisions.
AU  - Smith AE
AU  - Ford KG
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2007 35: 740-754.

PMID- 28935743
VI  - 5
DP  - 2017
TI  - Genome Sequence for Shiga Toxin-Producing Escherichia coli O26:H11, Associated with a Cluster of Hemolytic-Uremic Syndrome Cases in South Africa, 2017.
PG  - e00989-17
AB  - Shiga toxin-producing Escherichia coli (STEC) strains are primarily foodborne pathogens that
      may cause diarrheal outbreaks and are associated with severe
      complications, specifically hemolytic-uremic syndrome (HUS). We report here
      genome sequence data for STEC O26:H11, which is associated with a cluster of
      cases of HUS, a rarely described syndrome in South Africa.
AU  - Smith AM
AU  - Bosco KJ
AU  - Nicol MP
AU  - Kleynhans J
AU  - McCulloch M
AU  - Duze ST
AU  - Ismail A
AU  - Allam M
AU  - Tau NP
AU  - Keddy KH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00989-17.

PMID- 27056221
VI  - 4
DP  - 2016
TI  - Genome Sequences for a Cluster of Human Isolates of Listeria monocytogenes Identified in South Africa in 2015.
PG  - e00200-16
AB  - Listeria monocytogenesis a Gram-positive bacterium with a ubiquitous presence in  the
      environment. There is growing concern about the increasing prevalence ofL.
      monocytogenesassociated with food-borne outbreaks. Here we report genome
      sequences for a cluster of human isolates ofL. monocytogenesidentified in South
      Africa in 2015.
AU  - Smith AM
AU  - Naicker P
AU  - Bamford C
AU  - Shuping L
AU  - McCarthy KM
AU  - Sooka A
AU  - Smouse SL
AU  - Tau N
AU  - Keddy KH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00200-16.

PMID- 24903873
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of the Highly Transformable Pseudomonas stutzeri Strain  28a24.
PG  - e00543-14
AB  - Here, we report the complete genome sequence for an isolate of Pseudomonas stutzeri that is
      highly competent for natural transformation. This sequence
      enables insights into the genetic basis of natural transformation rate variations
      and provides an additional data point for genomic comparisons across a ubiquitous
      and highly diverse bacterial species.
AU  - Smith BA
AU  - Dougherty KM
AU  - Baltrus DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00543-14.

PMID- 29437109
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Lysinibacillus fusiformis Strain Juneja, a Laboratory-Derived Pathogen of Drosophila melanogaster.
PG  - e01571-17
AB  - Drosophila melanogaster is a model for the study of innate immunity, yet we have  limited
      knowledge of its natural pathogens. In this study, we sequenced the
      genome of Lysinibacillus fusiformis strain Juneja, isolated from laboratory fly
      stocks. As a Gram-positive bacterium with unique peptidoglycans, this strain may
      provide a new model for pathogen recognition.
AU  - Smith BR
AU  - Unckless RL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01571-17.

PMID- 2096397
VI  - 24
DP  - 1990
TI  - Plasmid transformation of Bacteroides spp. by electroporation.
PG  - 100-109
AB  - Transformation of Bacterioides spp. with a variety of plasmid DNAs was accomplished using
      electroporation. The standard transformation assay system used to deduce the optimal
      electroporation parameters employed a 50-to 100-fold concentrated cell suspension of
      mid-logarithmic phase Bacterioides fragilis strain 638 and the 5.4-kb clindamycin resistance
      (Ccr) vector pBI191. A variety of electroporation buffers were used successfully in
      transformation experiments but of these 1 mM MgCl2 in 10% glycerol was superior. The
      incorporation of MgCl2 was essential for optimum viability prior to electroporation and for
      optimum transformation. Transformants were routinely obtained using 5-ms pulses over a range
      of field strengths from 5 to 12.5 kV/cm, with a maximum of >1000000/ug DNA at 12.5 kV/cm. The
      number of transformants increased linearly with respect to DNA concentration over the range
      0.01-2 ug tested. Recovery of transformants required an expression period of up to 2.5 h
      following exposure to the electric field. This period, however, was dependent on the
      antibiotic resistance marker used for selection of transformants, with a significantly shorter
      incubation required when chloramphenicol rather than clindamycin was used in the selective
      medium. The effect of the DNA source of transformation was tested using the shuttle vector
      pFD288. Plasmid DNA isolated from Bacteriodes uniformis, Bacteroides ovatus, or Bacteroides
      thetaiotaomicron transformed B. fragilis 638 at frequencies 7.5 to 12.5 fold less than those
      observed for controls with homologous DNA. Further reductions were seen with Escherichia coli
      purified pFD288, which transformed at 1000-fold lower frequencies. Finally, using homologous
      pFD288 or pBI191 isolated from strain 638, several strains of B. fragilis, B. uniformis, and
      B. ovatus were transformed successfully without modification of the standard assay system. Two
      strains each of B. thetaiotaomicron and Baceriodes ruminicola were not transformed using the
      methods described here.
AU  - Smith CJ
AU  - Parker A
AU  - Rogers MB
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 1990 24: 100-109.

PMID- 24201193
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Antibiotic-Producing Epiphytic Isolate Pantoea ananatis BRT175.
PG  - e00902-13
AB  - Pantoea is a member of the Enterobacteriaceae, whose members have been shown to produce novel
      antibiotics. Here, we report the 4.8-Mb genome sequence of Pantoea
      ananatis strain BRT175, an epiphytic isolate from strawberries that produces an
      antibiotic that is effective against the fire blight pathogen, Erwinia amylovora.
AU  - Smith DD
AU  - Kirzinger MW
AU  - Stavrinides J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00902-13.

PMID- 24179115
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Antibiotic-Producing Cystic Fibrosis Isolate Pantoea agglomerans Tx10.
PG  - e00904-13
AB  - Pantoea agglomerans is an enteric bacterium that is capable of causing both plant and human
      disease. Here, we report the genome sequence of a cystic fibrosis
      isolate, P. agglomerans Tx10, which produces an antibiotic that is effective
      against Staphylococcus aureus.
AU  - Smith DD
AU  - Kirzinger MW
AU  - Stavrinides J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00904-13.

PMID- 
VI  - 6326
DP  - 2006
TI  - DNA looping and cleavage by restriction enzymes studied by manipulation of single DNA molecules with optical tweezers.
PG  - 1-13
AB  - Looping and cleavage of single DNA molecules by the two-site restriction endonuclease Sau3AI
      were measured with optical tweezers.  A DNA template containing many recognition sites was
      used, permitting loop sizes from ~10 to 10,000 basepairs.  At high enzyme concentration
      cleavage events were detected within 5 seconds and nearly all molecules were cleaved within 5
      minutes.  Activity decreased ~10-fold as the DNA tension was increased from 0.03 to 0.7 pN.
      Substituting Ca2+ for Mg2+ blocked cleavage, permitting measurement of stable loops.  At low
      tension, the initial rates of cleavage and looping were similar (~0.025 s-1 at 0.1 pN),
      suggesting that looping is rate limiting.  Short loops formed more rapidly than long loops.
      The optimum size decreased from ~250 to 45 bp and the average number of loops (in 1 minute)
      from 4.2 to 0.75 as tension was increased from 0.03 to 0.7 pN.  No looping was detected at 5
      pN.  These findings are in qualitative agreement with recent theoretical predictions
      considering only DNA mechanics, but we observed weaker suppression with tension and smaller
      loop sizes.  Our results suggest that the span and elasticity of the protein complex and
      protein-induced DNA bending and wrapping play an important role.
AU  - Smith DE
AU  - Gemmen GJ
AU  - Millin R
PT  - Journal Article
TA  - Proc. SPIE-Int. Soc. Opt. Eng.
JT  - Proc. SPIE-Int. Soc. Opt. Eng.
SO  - Proc. SPIE-Int. Soc. Opt. Eng. 2006 6326: 1-13.

PMID- 768923
VI  - 3
DP  - 1976
TI  - The isolation and partial characterization of a new restriction endonuclease from Providencia stuartii.
PG  - 343-353
AB  - We describe the isolation of a new class 2 restriction endonuclease from
      Providencia stuartii 164.  Using the procedure of osmotic shock treatment, we
      have partially purified this enzyme (PstI) and have begun preliminary work to
      characterize its specificity and requirements.  PstI requires Mg++ as the only
      cofactor and produces more than 18 cleavages in wild type lambda.  We have
      determined the location of 7 of these cleavages by the use of deletion and
      insertion mutants of lambda.
AU  - Smith DI
AU  - Blattner FR
AU  - Davies J
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1976 3: 343-353.

PMID- 3029699
VI  - 15
DP  - 1987
TI  - Overabundance of rare-cutting restriction endonuclease sites in the human genome.
PG  - 1173-1184
AB  - A human chromosome 3-specific cosmid library was constructed from a somatic
      cell hybrid containing human chromosome 3 as its only human component.  This
      library was screened to identify 230 human recombinants which contained an
      average insert size of 37 kilobases.  DNA prepared from 54 of these cosmids,
      representing 2000 kilobases of human DNA, was then tested for restriction
      endonuclease sites for EcoRI, HindIII, KpnI, XhoI, and DraI, as well as those
      of the rare-cutting restriction endonucleases NotI, SfiI, NruI, MluI, SacII,
      and BssHII.  Sites for the latter enzymes were much more abundant than would be
      expected from theoretical calculations, reflecting non-random clustering of
      these sites.  This has important implications for the use of these enzymes in
      the construction of physical maps of chromosomes.  Some individual cosmids
      contained large numbers of rare sites, offering an alternative means of
      physically mapping chromosomes based upon identifying clusters of rare
      restriction sites.  These clusters appear to be spaced an average of 1000 kb
      apart.
AU  - Smith DI
AU  - Golembieski W
AU  - Gilbert JD
AU  - Kizyma L
AU  - Miller OJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1987 15: 1173-1184.

PMID- 8713843
VI  - 58
DP  - 1996
TI  - Restriction endonuclease digestion of DNA..
PG  - 11-15
AB  - The ability to cleave DNA at specific sites is one of the cornerstones of today's methods of
      DNA manipulation.  Restriction endonucleases are bacterial enzymes that cleave duplex DNA at
      specific target sequences with the production of defined fragments.  These enzymes can be
      purchased from the many manufacturers of biotechnology products.  The nomenclature of enzymes
      is based on a simple system, proposed by Smith and Nathans.  The name of the enzyme (such as
      BamHI, EcoRI, and so on) tells us about the origin of the enzyme, but does not give us any
      information about the specificity of cleavage.  This has to be determined for each individual
      enzyme.  The recognition site for most of the commonly used enzymes is a short palindromic
      sequence, usually either 4, 5, or 6 bp in length, such as AGCT (for AluI), GAATTC (for EcoRI),
      and so on.  Each enzyme cuts the palindrome at a particular site, and two different enzymes
      may have the same recognition sequence, but cleave the DNA at different points within that
      sequence.  The cleavage sites fall into three different categories, either flush (or blunt) in
      which the recognition site is cut in the middle, or with either 5'- or 3'-overhangs, in
      which case unpaired bases will be produced on both ends of the fragment.  For a comprehensive
      review of restriction endonucleases, see Fuchs and Blakesley.
AU  - Smith DR
PT  - Journal Article
TA  - Methods Mol. Biol.
JT  - Methods Mol. Biol.
SO  - Methods Mol. Biol. 1996 58: 11-15.

PMID- 9371463
VI  - 179
DP  - 1997
TI  - Complete genome sequence of Methanobacterium thermoautotrophicum delta H: functional analysis and comparative genomics.
PG  - 7135-7155
AB  - The complete 1,751,377-bp sequence of the genome of the thermophilic archaeon Methanobacterium
      thermoautotrophicum deltaH has been determined by a whole-genome shotgun sequencing approach.
      A total of 1,855 open reading frames have been identified that appear to encode polypeptides,
      844 (46%) of which have been assigned putative functions based on their similarities to
      database sequences with assigned functions.  A total of 514 (28%) of the ORF-encoded
      polypeptides are related to sequences with unknown functions, and 496 (27%) have little or no
      homology to sequences in public databases.  Comparisons with Eucarya-, Bacteria-, and
      Archaea-specific databases reveal that 1,013 of the putative gene products (54%) are most
      similar to polypeptide sequences described previously for other organisms in the domain
      Archaea.  Comparisons with the Methanococcus jannaschii genome data underlie the extensive
      divergence that has occurred between these two methanogens; only 352 (19%) of M.
      thermoautotrophicum ORFs encode sequences that are >50% identical to M. jannaschii
      polypeptides, and there is little conservation in the relative locations of orthologous genes.
      When the M. thermoautotrophicum ORFs are compared to sequences from only the eucaryal and
      bacterial domains, 786 (42%) are more similar to bacterial sequences and 241 (13%) are more
      similar to eucaryal sequences.  The bacterial domain-like gene products include the majority
      of those predicted to be involved in cofactor and small molecule biosyntheses, intermediary
      metabolism, transport, nitrogen fixation, regulatory functions, and interactions with the
      environment.  Most proteins predicted to be involved in DNA metabolism, transcription, and
      translation are more similar to eucaryal sequences.  Gene structure and organization have
      features that are typical of the Bacteria, including genes that encode polypeptides closely
      related to eucaryal proteins.  There are 24 polypeptides that could form two-component sensor
      kinase-response regulator systems and homologs of the bacterial Hsp70-response proteins DnaK
      and DnaJ, which are notably absent in M. jannaschii.  DNA replication initiation and
      chromosome packaging in M. thermoautotrophicum are predictd to have eucaryal features, based
      on the presence of two Cdc6 homologs and three histones; however, the presence of an ftsZ gene
      indicates a bacterial type of cell division initiation.  The DNA polymerases include an
      X-family repair type and an unusual archaeal B type formed by two separate polypeptides.  The
      DNA-dependent RNA polymerase subunits A', A", B', B" and H are encoded in a typical archaeal
      RNAP operon, although a second A' subunit-encoding gene is present at a remote location.
      There are two rRNA operons, and 39 tRNA genes are dispersed around the genome, although most
      of these occur in clusters.  Three of the tRNA genes have introns, including the tRNAPro (GGG)
      gene, which contains a second intron at an unprecedented location.  There is no
      selenocysteinyl-tRNA gene nor evidence for classically organized IS elements, prophages, or
      plasmids.  The genome contains one intein and two extended repeats (3.6 and 8.6 kb) that are
      members of a family with 18 representatives in the M. jannaschii genome.
AU  - Smith DR et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1997 179: 7135-7155.

PMID- 1461739
VI  - 20
DP  - 1992
TI  - In vivo specificity of EcoRI DNA methyltransferase.
PG  - 6091-6096
AB  - The EcoRI adenine DNA methyltransferase forms part of a bacterial restriction/modification
      system; the methyltransferase modifies the second adenine within the canonical site GAATTC,
      thereby preventing the EcoRI endonuclease from cleaving this site. We show that five
      noncanonical EcoRI sites (TAATTC, CAATTC, GTATTC, GGATTC and GAGTTC) are not methylated in
      vivo under conditons when the canonical site is methylated. Only when the methyltransferase is
      overxpressed is partial in vivo methylation of the five sites detected. Our results suggest
      that the methyltransferase does not protect host DNA against potential endonuclease-mediated
      cleavage at noncanonical sites. Our related in vitro analysis of the methyltransferase reveals
      a low level of sequence-discrimination. We propose that the high in vivo specificity may be
      due to the active removal of methylated sequences by DNA repair enzymes (J. Bacteriology
      (1987), 169 3243-3250).
AU  - Smith DW
AU  - Crowder SW
AU  - Reich NO
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 6091-6096.

PMID- 29798915
VI  - 6
DP  - 2018
TI  - Genome Sequence of Geothermobacter sp. Strain HR-1, an Iron Reducer from the Lo'ihi Seamount, Hawai'i.
PG  - e00339-18
AB  - Geothermobacter sp. strain HR-1 was isolated from the Lo'ihi Seamount vent system in the
      Pacific Ocean at a depth of 1,000 m. Reported here is its 3.84-Mb genome
      sequence.
AU  - Smith H
AU  - Abuyen K
AU  - Tremblay J
AU  - Savalia P
AU  - Perez-Rodriguez I
AU  - Emerson D
AU  - Tully B
AU  - Amend J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00339-18.

PMID- 24265494
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence and Description of Janthinobacterium sp. Strain CG3, a Psychrotolerant Antarctic Supraglacial Stream Bacterium.
PG  - e00960-13
AB  - Here we present the draft genome sequence of Janthinobacterium sp. strain CG3, a
      psychrotolerant non-violacein-producing bacterium that was isolated from the
      Cotton Glacier supraglacial stream. The genome sequence of this organism will
      provide insight as to the mechanisms necessary for bacteria to survive in
      UV-stressed icy environments.
AU  - Smith H
AU  - Akiyama T
AU  - Foreman C
AU  - Franklin M
AU  - Woyke T
AU  - Teshima H
AU  - Davenport K
AU  - Daligault H
AU  - Erkkila T
AU  - Goodwin L
AU  - Gu W
AU  - Xu Y
AU  - Chain P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00960-13.

PMID- 26823573
VI  - 4
DP  - 2016
TI  - Genome Sequence of Janthinobacterium sp. CG23_2, a Violacein-Producing Isolate from an Antarctic Supraglacial Stream.
PG  - e01468-15
AB  - Here, we present the draft genome sequence for the violacein-producing Janthinobacterium sp.
      CG23_2 isolated from an Antarctic supraglacial stream. The
      genome is ~7.85 Mb, with a G+C content of 63.5%. The genome includes 7,247
      candidate protein coding genes, which may provide insight into UV tolerance
      mechanisms.
AU  - Smith HJ
AU  - Foreman CM
AU  - Akiyama T
AU  - Franklin MJ
AU  - Devitt NP
AU  - Ramaraj T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01468-15.

PMID- 25477404
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of a Metabolically Diverse Antarctic Supraglacial Stream Organism, Polaromonas sp. Strain CG9_12, Determined Using Pacific Biosciences  Single-Molecule Real-Time Sequencing Technology.
PG  - e01242-14
AB  - Polaromonas species are found in a diversity of environments and are particularly common in
      icy ecosystems. Polaromonas sp. strain CG9_12 is an aerobic,
      Gram-negative, catalase-positive, white-pigmented bacterium of the Proteobacteria
      phylum. Here, we present the draft genome sequence of Polaromonas sp. strain
      CG9_12, isolated from an Antarctic supraglacial stream.
AU  - Smith HJ
AU  - Foreman CM
AU  - Ramaraj T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01242-14.

PMID- Not carried by PubMed...
VI  - 5
DP  - 1976
TI  - Restriction endonucleases as enzymatic tools for DNA analysis and genetic manipulation.
PG  - 313-319
AB  - Living cells contain a variety of nucleases capable of cleaving the
      phosphodiester bonds of nucleic acid chains.  These are generally of two kinds:
      exonucleases that act at chain termini to release nucleotides or
      oligonucleotides, and endonucleases that cleave at internal bonds.  Many
      endonucleases act randomly, cleaving each phosphodiester bond with about equal
      probability regardless of the local base sequence.  Several years ago a new
      class of DNA nucleases that cleave both strands of double-stranded DNA at sites
      of specific base sequence, four to six bases in length, was discovered in
      bacteria.  These endonucleases are called restriction enzymes because they are
      components of bacterial restriction-modification (R-M) systems that determine a
      host-specific DNA immunity mechanism.  Each R-M system consists of a
      restriction endonuclease and a modification methylase of similar site
      specificity.  The modification enzyme methylates sites in the host chromosome
      to protect against cleavage by their restriction endonuclease.  However,
      improperly methylated foreign DNA entering the cell, for example, by virus
      infection, will be cleaved and subsequently degraded to nucleotides by cellular
      exonucleases.  Since their discovery, restriction endonucleases have been
      widely exploited as new tools for DNA analysis because of their ability to
      cleave DNA molecules at only a few sites to produce specific DNA fragments.
      Restriction fragments from a given DNA molecule may be ordered into a physical
      map that can serve as a framework for location of genetic functions and for
      nucleotide sequence analysis.  The possibilities of using restriction
      endonucleases for genetic manipulation have aroused great interest.  Novel
      kinds of recombinant DNA molecules can be constructed by rearranging DNA
      fragments within a chromosome or by joining fragments from one species to those
      of another to form hybrid chromosomes.  Fragments bearing specific genes may be
      joined to self-replicating viral or plasmid chromosomes and isolated by
      molecular cloning in suitable host bacteria.  The recombinant plasmid or virus
      DNAs often exist as multiple copies intracellularly, thus providing large
      quantities of the inserted DNA fragments for sequence analysis and studies of
      gene organization and function.  In many cases, products of inserted genes,
      such as specific enzymes, are obtained in high yield.  In a brief 3 to 4 years,
      a whole new recombinant DNA technology has arisen that has many important
      potential commercial as well as research applications. This review will briefly
      cover properties of restriction endonucleases and their major applications.
      Comprehensive reviews have been written by Arber and Nathans and Smith.
AU  - Smith HO
PT  - Journal Article
TA  - PAABS Revista
JT  - PAABS Revista
SO  - PAABS Revista 1976 5: 313-319.

PMID- 377492
VI  - 205
DP  - 1979
TI  - Nucleotide sequence specificity of restriction endonucleases.
PG  - 455-462
AB  - In the past 7 to 8 years we have witnessed the development of a new DNA
      technology that has fundamentally altered our approach to modern genetics.  The
      basic ingredients of this new technology are the cleavage site-specific
      restriction enzymes: a special class of bacterial endonucleases that can
      recognize specific nucleotide sequenceas in duplex DNA and produce
      double-stranded cleavages.  A collection of these enzymes, each with its own
      particular sequence specificity, can be used to cleave DNA molecules into
      unique sets of fragments for DNA sequencing, chromosome analysis, gene
      isolation, and construction of recombinant DNA.  The latter, together with the
      concept of molecular cloning, has given birth to the new field of genetic
      engineering, and from this many new and exciting medical and research
      applications are expected.  My own role in these developments occurred
      primarily in the period of 1968 to 1970 when my colleagues and I made the
      chance discovery of the first of the cleavage site-specific restriction
      enzymes.  I now briefly present this work in historical context because it
      leads naturally into the main part of my lecture, describing our present
      knowledge of restriction and modification enzymes.  Although many applications
      have been reviewed, I should like to describe in some detail the use of these
      enzymes as model systems for studying sequence-specific interactions of protein
      and DNA, which is one of the major research interests in my laboratory.
AU  - Smith HO
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1979 205: 455-462.

PMID- Not included in PubMed...
VI  - 7
DP  - 1974
TI  - Restriction endonuclease from Hemophilus influenzae Rd.
PG  - 71-85
AB  - A growing number of molecular biologists are turning to restriction enzymes as
      tools for analysis of DNA molecules and chromosomal DNA.  Restriction enzymes
      are site-specific endonucleases that can be isolated from various strains of
      bacteria.  They are capable of recognizing particular base sequences within
      native DNA molecules and producing double-strand cleavage.  Thus viral genomes
      or other DNA molecules may be cleaved in a highly specific and reproducible
      manner into a number of double-stranded fragments.  These are useful for
      localization of genetic functions, DNA base sequencing, and a number of other
      purposes.  This article describes the purification of restriction enzyme from
      H. influenzae Rd.  The procedure is similar to that reported by Smith and
      Wilcox but incorporates modifications which facilitate assay and large scale
      purification.
AU  - Smith HO
PT  - Journal Article
TA  - Methods Mol. Biol.
JT  - Methods Mol. Biol.
SO  - Methods Mol. Biol. 1974 7: 71-85.

PMID- 1689055
VI  - 87
DP  - 1990
TI  - Finding sequence motifs in groups of functionally related proteins.
PG  - 826-830
AB  - We have developed a method for rapidly finding patterns of conserved amino acid
      residues (motifs) in groups of functionally related proteins.  All 3-amino acid
      patterns in a group of proteins of the type aa1 d1 aa2 d2 aa3, where d1 and d2
      are distances that can be varied in a range up to 24 residues, are accumulated
      into an array.  Segments of the proteins are aligned on each other by a scoring
      method that obtains an average relatedness value for all the amino acids in
      each column of the aligned sequence block based on the Dayhoff relatedness odds
      matrix.  The automated method successfully finds and displays nearly all of the
      sequence motifs that have been previously reported to occur in 33 reverse
      transcriptases, 18 DNA integrases, and 30 DNA methyltransferases.
AU  - Smith HO
AU  - Annau TM
AU  - Chandrasegaran S
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1990 87: 826-830.

PMID- 787937
VI  - 9
DP  - 1976
TI  - A simple method for DNA restriction site mapping.
PG  - 2387-2399
AB  - When a DNA molecule, enzymatically labelled with 32P at one end, is partially
      digested with a restriction enzyme labelled DNA fragments are obtained which
      form an overlapping series of molecules, all with a common labelled terminus.
      A restriction map can then be constructed from an analysis of the size
      distribution of these molecules.  This technique has been used for the
      restriction site mapping of cloned histone DNA (h22) where as many as 35
      cleavage sites may be accurately determined in a single experiment.
AU  - Smith HO
AU  - Birnstiel ML
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1976 9: 2387-2399.

PMID- 
VI  - 0
DP  - 1984
TI  - Methylases of the type II restriction-modification systems.
PG  - 39-71
AB  - Most bacteria contain a small fraction (0.5-2%) of methylated cytosine or
      adenine bases in their chromosomes.  Some of this methylation apparently plays
      a role in directing mismatch repair systems to the correct strands in newly
      replicated DNA.  However, in many bacterial strains, a substantial fraction can
      be identified with host-specific restriction-modification (RM) systems.  These
      ubiquitous systems play an important biological role in protecting bacteria
      against viral infections.  Each system has two functional components: 1) a
      restriction endonuclease capable of recognizing sequence-specific sites in DNA
      and producing double-stranded cleavage; and 2) a modification enzyme
      recognizing the same DNA sites as the restriction enzyme and protecting them by
      modification.  So far, all modifications found are either 5-methylcytosine or
      6-methyladenine.  The modification enzymes are methyltransferases, and AdoMet
      appears to be the exclusively methyl group donor.  (For reviews, see Arber,
      1974; Modrich, 1979; Smith, 1979; Modrich and Roberts, 1982).
AU  - Smith HO
AU  - Kelly SV
PT  - Journal Article
TA  - DNA Methylation. Biochemistry and Biological Significance.
JT  - DNA Methylation. Biochemistry and Biological Significance.
SO  - DNA Methylation. Biochemistry and Biological Significance. 1984 0: 39-71.

PMID- 4368687
VI  - 29
DP  - 1974
TI  - Enzymatic methods for sequence analysis applied to DNA restriction and methylation sites.
PG  - 282-294
AB  - Restriction enzymes are site-specific endonucleases produced by various
      bacteria, bacterial plasmids, and viruses.  In those cases where they produce
      double-stranded cleavage of DNA within their recognition sites, sequence
      analysis of the site is equivalent to determination of the 5'- and 3'-terminal
      bases of the restricted DNA.  We have developed special enzymatic methods for
      limited analysis of this type.  In addition, every host that produces a
      restriction endonuclease also produces a companion DNA modification enzyme,
      usually a methylase, with identical or similar site recognition.  This enzyme
      serves to modify and protect the restriction sites of the host chromosome.  In
      the second section of this chapter we describe a procedure for partial analysis
      of methylation sites.
AU  - Smith HO
AU  - Kelly TJ
AU  - Roy PH
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1974 29: 282-294.

PMID- 6246330
VI  - 65
DP  - 1980
TI  - Purification and properties of HindII and HindIII endonucleases from Haemophilus influenzae Rd.
PG  - 104-108
AB  - Haemophilus influenzae Rd is the source for two restriction endonucleases,
      HindII and HindIII, that may be separated and purified using conventional ion
      exchange chromatography media.  The basic steps in the procedure are removal of
      nucleic acids from the cell extract, separation of the two activities by
      DEAE-cellulose chromatography, and chromatography of each activity on
      phosphocellulose as a combined purification and concentration step.
AU  - Smith HO
AU  - Marley GM
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1980 65: 104-108.

PMID- 4588280
VI  - 81
DP  - 1973
TI  - A suggested nomenclature for bacterial host modification and restriction systems and their enzymes.
PG  - 419-423
AB  - In the proposed nomenclature restriction-modification systems are named
      according to host organism and strain.  Different R-M+ systems in a single host
      are designated by Roman numerals.  Restriction nucleases and modification
      methylases are given the general names endonuclase R and methylase M, followed
      by their R-M system name.
AU  - Smith HO
AU  - Nathans D
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1973 81: 419-423.

PMID- 5312500
VI  - 51
DP  - 1970
TI  - A restriction enzyme from Hemophilus influenzae. I. Purification and general properties.
PG  - 379-391
AB  - Extracts of Hemophilus influenzae strain Rd contain an endonuclease activity
      which produces a rapid decrease in the specific viscosity of a variety of
      foreign native DNA's; the specific viscosity of H. influenzae DNA is not
      altered under the same conditions.  This "restriction" endonuclease activity
      has been purified approximately 200-fold.  The purified enzyme contains no
      detectable exo- or endonucleolytic activity against H. influenzae DNA.
      However, with native phage T7 DNA as substrate, it produces about 40
      double-strand 5'-phosphoryl, 3'-hydroxyl cleavages.  The limit product has an
      average length of about 1000 nucleotide pairs and contains no single-strand
      breaks.  The enzyme is inactive on denatured DNA and it requires no special
      co-factors other than magnesium ions.
AU  - Smith HO
AU  - Wilcox KW
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1970 51: 379-391.

PMID- 765764
VI  - 143
DP  - 1976
TI  - Characterisation of plasmids coding for the restriction endonuclease EcoRI.
PG  - 319-325
AB  - The properties of two plasmids coding for the CcoRI restriction and modification enzymes are
      described. Both plasmids are non
      auto-transferring (NTP) but can be mobilised by transfer factors. Strains
      carrying NTP13 produce colicin E1 and the EcoRI enzymes. This plasmid has
      a molecular weight of 6 X 10(6) daltons and is present as approximately 12
      copies per chromosome. The second plasmid, NTP14, was detected after
      mobilisation of the EcoRI plasmid with the R factor RI-19. NTP14 codes for
      ampicillin resistance, synthesis of the EcoRI enzymes and colicin E1. The
      molecular weight of NTP14 is 10.7 X 10(6) daltons and there are about 14
      copies per chromosome. DNA-DNA reassociation experiments were performed to
      determine the interrelationships of NTP13, NTP14, ColE1 and the R factor
      R1-19. NTP13 and NTP14 continue to replicate when cellular protein
      synthesis is inhibited by the addition of chloramphenicol.
AU  - Smith HR
AU  - Humphreys GO
AU  - Willshaw GA
AU  - Anderson ES
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1976 143: 319-325.

PMID- Not carried by PubMed...
VI  - 29
DP  - 1968
TI  - The restriction of T2 bacteriophage by Escherichia coli, strain W.
PG  - 9292B
AB  - This thesis presents studies on the restriction of T2 bacteriophage infection
      by Escherichia coli strain W, a bacterial strain lysogenic for a prophage which
      is related to bacteriophage P2.
AU  - Smith HS
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1968 29: 9292B.

PMID- 9862996
VI  - 27
DP  - 1999
TI  - A detailed study of the substrate specificity of a chimeric restriction enzyme.
PG  - 674-681
AB  - Recently, the crystal structure of the designed zinc finger protein, deltaQNK, bound to a
      preferred DNA sequence was reported.  We have converted deltaQNK into a novel site-specific
      endonuclease by linking it to the FokI cleavage domain (FN).  The substrate specificity and
      DNA cleavage properties of the resulting chimeric restriction enzyme (deltaQNK-FN) were
      investigated, and the binding affinities of deltaQNK and deltaQNK-FN for various DNA
      substrates were determined.  Substrates that are bound by deltaQNK with high affinity are the
      same as those that are cleaved efficiently by deltaQNK-FN.  The binding of deltaQNK-FN to each
      substrate was ~2-fold weaker than that for deltaQNK.  Thus, the fusion of the FokI cleavage
      domain to the zinc finger motif does not change the DNA sequence specificity of the zinc
      finger protein and does not change its binding affinity significantly.
AU  - Smith J
AU  - Berg JM
AU  - Chandrasegaran S
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1999 27: 674-681.

PMID- 10954606
VI  - 28
DP  - 2000
TI  - Requirements for double-strand cleavage by chimeric restriction enzymes with zinc finger DNA-recognition domains.
PG  - 3361-3369
AB  - This study concerns chimeric restriction enzymes that are hybrids between a zinc finger
      DNA-binding domain and the non-specific DNA-cleavage domain from the natural restriction
      enzyme FokI. Because of the flexibility of DNA recognition by zinc fingers, these enzymes are
      potential tools for cleaving DNA at arbitrarily selected sequences. Efficient double-strand
      cleavage by the chimeric nucleases requires two binding sites in close proximity. When cuts
      were mapped on the DNA strands, it was found that they occur in pairs separated by
      approximately 4 bp with a 5' overhang, as for native FokI. Furthermore, amino acid changes
      in the dimer interface of the cleavage domain abolished activity. These results reflect a
      requirement for dimerization of the cleavage domain. The dependence of cleavage efficiency on
      the distance between two inverted binding sites was determined and both upper and lower limits
      were defined. Two different zinc finger combinations binding to non-identical sites also
      supported specific cleavage. Molecular modeling was employed to gain insight into the precise
      location of the cut sites. These results define requirements for effective targets of chimeric
      nucleases and will guide the design of novel specificities for directed DNA cleavage in vitro
      and in vivo.
AU  - Smith J
AU  - Bibikova M
AU  - Whitby FG
AU  - Reddy AR
AU  - Chandrasegaran S
AU  - Carroll D
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2000 28: 3361-3369.

PMID- 17130168
VI  - 34
DP  - 2006
TI  - A combinatorial approach to create artificial homing endonucleases cleaving chosen sequences.
PG  - e149
AB  - Meganucleases, or homing endonucleases (HEs) are sequence-specific endonucleases with large
      (>14 bp) cleavage sites that can be used to
      induce efficient homologous gene targeting in cultured cells and plants.
      These findings have opened novel perspectives for genome engineering in a
      wide range of fields, including gene therapy. However, the number of
      identified HEs does not match the diversity of genomic sequences, and the
      probability of finding a homing site in a chosen gene is extremely low.
      Therefore, the design of artificial endonucleases with chosen
      specificities is under intense investigation. In this report, we describe
      the first artificial HEs whose specificity has been entirely redesigned to
      cleave a naturally occurring sequence. First, hundreds of novel
      endonucleases with locally altered substrate specificity were derived from
      I-CreI, a Chlamydomonas reinhardti protein belonging to the LAGLIDADG
      family of HEs. Second, distinct DNA-binding subdomains were identified
      within the protein. Third, we used these findings to assemble four sets of
      mutations into heterodimeric endonucleases cleaving a model target or a
      sequence from the human RAG1 gene. These results demonstrate that the
      plasticity of LAGLIDADG endonucleases allows extensive engineering, and
      provide a general method to create novel endonucleases with tailored
      specificities.
AU  - Smith J
AU  - Grizot S
AU  - Arnould S
AU  - Duclert A
AU  - Epinat JC
AU  - Prieto PC
AU  - Redondo P
AU  - Blanco FJ
AU  - Bravo J
AU  - Montoya G
AU  - Paques F
AU  - Duchateau P
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2006 34: e149.

PMID- 4552762
VI  - 63
DP  - 1972
TI  - Host specificity of DNA by Escherichia coli. XIV.  The role of nucleotide methylation in in vivo B-specific modification.
PG  - 1-8
AB  - N-6-methyladenine is the only methylated base detected in bacteriophage fd DNA.
      Its frequency is (1) host dependent: fd grown on a strain providing B-specific
      modification to DNA carries twice as many methyl moieties in its DNA as phage
      grown on a non-modifying host; and (2) dependent on the number of sites with
      affinity for B-specific restriction: the DNA of a B-restriction insensitive
      double mutant of fd is only half as much methylated after growth on B as its
      wild type parent.  These results permit one to correlate methylation of
      specifically located adenines with B-specific modification.  Quantitative
      measurements suggest that one N-6-methyladenine is carried per B-host
      specificity site on the modified, single stranded fd DNA.  Wild-type fd has two
      such sites.  The biological function assigned to methylation brought about by
      B-specific modification is the protection of the DNA from its destruction by
      restriction endonuclese R.B.
AU  - Smith JD
AU  - Arber W
AU  - Kuhnlein U
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1972 63: 1-8.

PMID- 24994804
VI  - 2
DP  - 2014
TI  - Complete Genome Sequences of Bacillus subtilis subsp. subtilis Laboratory Strains JH642 (AG174) and AG1839.
PG  - e00663-14
AB  - The Gram-positive bacterium Bacillus subtilis is widely used for studies of cellular and
      molecular processes. We announce the complete genomic sequences of
      strain AG174, our stock of the commonly used strain JH642, and strain AG1839, a
      derivative that contains a mutation in the replication initiation gene dnaB and a
      linked Tn917.
AU  - Smith JL
AU  - Goldberg JM
AU  - Grossman AD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00663-14.

PMID- 762109
VI  - 254
DP  - 1979
TI  - Purification and characterization of the sequence-specific endonuclease BamHI.
PG  - 1003-1006
AB  - The specific endonuclease BamHI from Bacillus amyloliquefaciens (RUB 500) has
      been purified to apparent homogeneity.  Two active forms of the enzyme
      corresponding to the dimeric and tetrameric forms have been isolated.  On
      sodium dodecyl sulfate-polyacrylamide gel electrophoresis, the enzyme
      dissociated into Mr = 22,000 _+ 500 subunits.  BamHI has a broad pH optimum on
      the alkaline side and requires Mg2+ which can be partially replaced by Mn2+.
      The enzyme catalysis appears to be governed by a two-step mechanism.
AU  - Smith LA
AU  - Chirikjian JG
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1979 254: 1003-1006.

PMID- 9628344
VI  - 379
DP  - 1998
TI  - Expression and characterization of the N-terminal fragment of the hsdS subunit of M.EcoR124I.
PG  - 505-509
AB  - The type IC modification methyltransferase M.EcoR124I is a trimeric enzyme of 162 kDa
      consisting of two copies of the modification subunit, HsdM, and a single DNA specificity
      subunit, HsdS.  Studies to date have been largely restricted to the HsdM subunit or the intact
      methyltransferase, since the HsdS subunit is insoluble when expressed independently of HsdM.
      Using PCR, we have cloned and expressed 13 fragments of the gene for the hsdS subunit,
      including the sequences encoding each of the variable and conserved domains and various
      combinations of these.  Only two of these fragments were found to be soluble, an 8.6 kDa
      fragment (S11) comprising the central conserved domain and a 25 kDa N-terminal fragment (S3)
      containing the N-terminal variable domain and the central conserved domain.  Analysis of the
      larger of these fragments by gel retardation shows that the protein binds DNA in the presence
      of HsdM at a subunit stoichiometry of 1:1.  Gel filtration and CD spectroscopy indicate that
      the protein is monomeric and predominantly alpha-helical.
AU  - Smith MA
AU  - Mernagh DR
AU  - Kneale GG
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1998 379: 505-509.

PMID- 11724530
VI  - 314
DP  - 2001
TI  - Domain structure and subunit interactions in the type I DNA methyltransferase M.EcoR124I.
PG  - 41-50
AB  - The type IC DNA methyltransferase M.EcoR124I is a trimeric enzyme of 162 kDa consisting of two
      modification subunits, HsdM, and a single specificity subunit, HsdS. Studies have been largely
      restricted to the HsdM subunit or to the intact methyltransferase since the HsdS subunit is
      insoluble when over-expressed independently of HsdM. Two soluble fragments of the HsdS subunit
      have been cloned, expressed and purified; a 25 kDa N-terminal fragment (S3) comprising the
      N-terminal target recognition domain together with the central conserved domain, and an 8.6
      kDa fragment (S11) comprising the central conserved domain alone.  Analytical
      ultracentrifugation shows that the S3 subunit exists principally as a dimer of 50 kDa. Gel
      retardation and competition assays show that both S3 and S11 are able to bind to HsdM, each
      with a subunit stoichiometry of 1:1. The tetrameric complex (S3/HsdM)(2) is required for
      effective DNA binding. Cooperative binding is observed and at low enzyme concentration, the
      multisubunit complex dissociates, leading to a loss of DNA binding activity. The (S3/HsdM)(2)
      complex is able to bind to both the EcoR124I DNA recognition sequence GAAN(6)RTCG and a
      symmetrical DNA sequence GAAN(7)TTC, but has a 30-fold higher affinity binding for the latter
      DNA sequence. Exonuclease III footprinting of the (S3/HsdM)(2) -DNA complex indicates that 29
      nucleotides are protected on each strand, corresponding to a region 8 bp on both the 3' and
      5' sides of the recognition sequence bound by the (S3/HsdM)(2) complex.
AU  - Smith MA
AU  - Read CM
AU  - Kneale GG
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2001 314: 41-50.

PMID- 1454536
VI  - 20
DP  - 1992
TI  - Cloning and characterization of genes for the PvuI restriction and modification system.
PG  - 5743-5747
AB  - The genes encoding the endonuclease and the methylase of the PvuI restriction and modification
      system were cloned in E.coli and characterized. The genes were adjacent in tandem orientation
      spanning a distance of 2200 bases. The PvuI endonuclease was a single polypeptide with a
      calculated molecular weight of 27,950 daltons. The endonuclease was easily detectable when the
      gene was expressed from its endogenous promotor and present on a low copy plasmid, but
      expression was considerably enhanced when the endonuclease gene was placed under the control
      of a strong promotor on a high copy plasmid. The methylase did not completely protect plasmid
      DNA from R.PvuI digeston unitl the methylase gene was placed under lac promotor control in a
      multicopy plasmid. In the absence of the M.PvuI methylase, expression of the R.PvuI
      endonuclease from the lac promotor on a multicopy plasmid was not lethal to wild type E.coli,
      but was lethal in a temperature-sensitive ligase mutant at the non-permissive temperature.
      Moreover, induction of the R.PvuI endonuclease under lambda pL promotor control resulted in
      complete digestion of the E. coli chromosome by R.PvuI.
AU  - Smith MD
AU  - Longo M
AU  - Gerard GF
AU  - Chatterjee DK
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 5743-5747.

PMID- 15659696
VI  - 187
DP  - 2005
TI  - DNA methylation in lysogens of pathogenic Burkholderia spp. requires prophage induction and is restricted to excised phage DNA.
PG  - 1196-1200
AB  - Burkholderia mallei-specific phage  E125 encodes DNA methyltransferases in both the lysogenic
      and replication modules within its genome. Characterization of DNA methylation in recombinant
      systems, specifically in  E125 lysogenic strains of B. mallei and Burkholderia thailandensis,
      revealed that, upon induction, cytosine methylation was targeted specifically to the phage
      episome but not the phage provirus or the host chromosome.
AU  - Smith MJ
AU  - Jeddeloh JA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2005 187: 1196-1200.

PMID- 29326203
VI  - 6
DP  - 2018
TI  - High-Quality Whole-Genome Sequences for 21 Enterotoxigenic Escherichia coli Strains Generated with PacBio Sequencing.
PG  - e01311-17
AB  - Enterotoxigenic Escherichia coli (ETEC) is an important diarrheagenic pathogen. We report here
      the high-quality whole-genome sequences of 21 ETEC strains
      isolated from patients in the United States, international diarrheal surveillance
      studies, and cruise ship outbreaks.
AU  - Smith P
AU  - Lindsey RL
AU  - Rowe LA
AU  - Batra D
AU  - Stripling D
AU  - Garcia-Toledo L
AU  - Drapeau D
AU  - Knipe K
AU  - Strockbine N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01311-17.

PMID- 19808936
VI  - 37
DP  - 2009
TI  - DNA cleavage and methylation specificity of the single polypeptide restriction-modification enzyme LlaGI.
PG  - 7206-7218
AB  - LlaGI is a single polypeptide restriction-modification enzyme encoded on the
      naturally-occurring plasmid pEW104 isolated from Lactococcus lactis
      ssp. cremoris W10. Bioinformatics analysis suggests that the enzyme
      contains domains characteristic of an mrr endonuclease, a superfamily 2
      DNA helicase and a gamma-family adenine methyltransferase. LlaGI was
      expressed and purified from a recombinant clone and its properties
      characterised. An asymmetric recognition sequence was identified,
      5'-CTnGAyG-3' (where n is A, G, C or T and y is C or T). Methylation of
      the recognition site occurred on only one strand (the non-degenerate dA
      residue of 5'-CrTCnAG-3' being methylated at the N6 position). Double
      strand DNA breaks at distant, random sites were only observed when two
      head-to-head oriented, unmethylated copies of the site were present;
      single sites or pairs in tail-to-tail or head-to-tail repeat only
      supported a DNA nicking activity. dsDNA nuclease activity was dependent
      upon the presence of ATP or dATP. Our results are consistent with a
      directional long-range communication mechanism that is necessitated by the
      partial site methylation. In the accompanying manuscript [Smith et al.
      (2009) The single polypeptide restriction-modification enzyme LlaGI is a
      self-contained molecular motor that translocates DNA loops], we
      demonstrate that this communication is via 1-dimensional DNA loop
      translocation. On the basis of this data and that in the third
      accompanying manuscript [Smith et al. (2009) An Mrr-family nuclease motif
      in the single polypeptide restriction-modification enzyme LlaGI], we
      propose that LlaGI is the prototype of a new sub-classification of
      Restriction-Modification enzymes, named Type I SP (for Single
      Polypeptide).
AU  - Smith RM
AU  - Diffin FM
AU  - Savery NJ
AU  - Josephsen J
AU  - Szczelkun MD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: 7206-7218.

PMID- 23147004
VI  - 41
DP  - 2012
TI  - Organization of the BcgI restriction-modification protein for the transfer of one methyl group to DNA.
PG  - 405-417
AB  - The Type IIB restriction-modification protein BcgI contains A and B subunits in a 2:1 ratio: A
      has the active sites for both endonuclease and methyltransferase
      functions while B recognizes the DNA. Like almost all Type IIB systems, BcgI
      needs two unmethylated sites for nuclease activity; it cuts both sites upstream
      and downstream of the recognition sequence, hydrolyzing eight phosphodiester
      bonds in a single synaptic complex. This complex may incorporate four A(2)B
      protomers to give the eight catalytic centres (one per A subunit) needed to cut
      all eight bonds. The BcgI recognition sequence contains one adenine in each
      strand that can be N(6)-methylated. Although most DNA methyltransferases operate
      at both unmethylated and hemi-methylated sites, BcgI methyltransferase is only
      effective at hemi-methylated sites, where the nuclease component is inactive.
      Unlike the nuclease, the methyltransferase acts at solitary sites, functioning
      catalytically rather than stoichiometrically. Though it transfers one methyl
      group at a time, presumably through a single A subunit, BcgI methyltransferase
      can be activated by adding extra A subunits, either individually or as part of
      A(2)B protomers, which indicates that it requires an assembly containing at least
      two A(2)B units.
AU  - Smith RM
AU  - Jacklin AJ
AU  - Marshall JJ
AU  - Sobott F
AU  - Halford SE
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 41: 405-417.

PMID- 19783815
VI  - 37
DP  - 2009
TI  - The single polypeptide restriction-modification enzyme LlaGI is a self-contained molecular motor that translocates DNA loops.
PG  - 7219-7230
AB  - To cleave DNA, the single polypeptide restriction-modification enzyme LlaGI must communicate
      between a pair of indirectly repeated recognition
      sites. We demonstrate that this communication occurs by a 1-dimensional
      route, namely unidirectional dsDNA loop translocation rightward of the
      specific recognition sequence 5'-CTnGAyG-3' as written (where n is either
      A, G, C or T and y is either C or T). Motion across thousands of base
      pairs is catalysed by the helicase domain and requires the hydrolysis of
      1.5-2 ATP per base pair. DNA loop extrusion is accompanied by changes in
      DNA twist consistent with the motor following the helical pitch of the
      polynucleotide track. LlaGI is therefore an example of a polypeptide that
      is a completely self-contained, multi-functional molecular machine.
AU  - Smith RM
AU  - Josephsen J
AU  - Szczelkun MD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: 7219-7230.

PMID- 19793866
VI  - 37
DP  - 2009
TI  - An Mrr-family nuclease motif in the single polypeptide restriction-modification enzyme LlaGI.
PG  - 7231-7238
AB  - Bioinformatic analysis of the putative nuclease domain of the single polypeptide
      restriction-modification enzyme LlaGI reveals amino acid
      motifs characteristic of the Escherichia coli methylated DNA-specific Mrr
      endonuclease. Using mutagenesis, we examined the role of the conserved
      residues in both DNA translocation and cleavage. Mutations in those
      residues predicted to play a role in DNA hydrolysis produced enzymes that
      could translocate on DNA but were either unable to cleave the
      polynucleotide track or had reduced nuclease activity. Cleavage by LlaGI
      is not targeted to methylated DNA, suggesting that the conserved motifs in
      the Mrr domain are a conventional sub-family of the PD-(D/E)XK superfamily
      of DNA nucleases.
AU  - Smith RM
AU  - Josephsen J
AU  - Szczelkun MD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: 7231-7238.

PMID- 23147005
VI  - 41
DP  - 2012
TI  - Organization of the BcgI restriction-modification protein for the cleavage of eight phosphodiester bonds in DNA.
PG  - 391-404
AB  - Type IIB restriction-modification systems, such as BcgI, feature a single protein with both
      endonuclease and methyltransferase activities. Type IIB nucleases
      require two recognition sites and cut both strands on both sides of their
      unmodified sites. BcgI cuts all eight target phosphodiester bonds before
      dissociation. The BcgI protein contains A and B polypeptides in a 2:1 ratio: A
      has one catalytic centre for each activity; B recognizes the DNA. We show here
      that BcgI is organized as A(2)B protomers, with B at its centre, but that these
      protomers self-associate to assemblies containing several A(2)B units. Moreover,
      like the well known FokI nuclease, BcgI bound to its site has to recruit
      additional protomers before it can cut DNA. DNA-bound BcgI can alternatively be
      activated by excess A subunits, much like the activation of FokI by its catalytic
      domain. Eight A subunits, each with one centre for nuclease activity, are
      presumably needed to cut the eight bonds cleaved by BcgI. Its nuclease reaction
      may thus involve two A(2)B units, each bound to a recognition site, with two more
      A(2)B units bridging the complexes by protein-protein interactions between the
      nuclease domains.
AU  - Smith RM
AU  - Marshall JJ
AU  - Jacklin AJ
AU  - Retter SE
AU  - Halford SE
AU  - Sobott F
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 41: 391-404.

PMID- 24634443
VI  - 42
DP  - 2014
TI  - TstI, a Type II restriction-modification protein with DNA recognition, cleavage and methylation functions in a single polypeptide.
PG  - 5809-5822
AB  - Type II restriction-modification systems cleave and methylate DNA at specific sequences.
      However, the Type IIB systems look more like Type I than conventional Type II schemes as they
      employ the same protein for both restriction and modification and for DNA recognition. Several
      Type IIB proteins, including the archetype BcgI, are assemblies of two polypeptides: one with
      endonuclease and methyltransferase roles, another for DNA recognition. Conversely, some IIB
      proteins express all three functions from separate segments of a single polypeptide. This
      study analysed one such single-chain protein, TstI. Comparison with BcgI showed that the one-
      and the two-polypeptide systems differ markedly. Unlike the heterologous assembly of BcgI,
      TstI forms a homotetramer. The tetramer bridges two recognition sites before eventually
      cutting the DNA in both strands on both sides of the sites, but at each site the first
      double-strand break is made long before the second. In contrast, BcgI cuts all eight target
      bonds at two sites in a single step. TstI also differs from BcgI in either methylating or
      cleaving unmodified sites at similar rates. The site may thus be modified before TstI can make
      the second double-strand break. TstI MTase acts best at hemi-methylated sites.
AU  - Smith RM
AU  - Pernstich C
AU  - Halford SE
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2014 42: 5809-5822.

PMID- 25614576
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Sphingobacterium sp. Strain ML3W, Isolated from Wings of Myotis lucifugus Infected with White Nose Syndrome.
PG  - e01477-14
AB  - Sphingobacterium sp. strain ML3W was isolated from the wing of a bat infected with white nose
      syndrome. We report the complete 5.33-Mb genome sequence of
      Sphingobacterium sp. strain ML3W, obtained using Pacific Biosciences technology.
      Being the second complete Sphingobacterium sequence, this will increase knowledge
      of the genus.
AU  - Smith SA
AU  - Krasucki SP
AU  - McDowell JV
AU  - Balke VL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01477-14.

PMID- 
VI  - 11
DP  - 2000
TI  - Inhibition of human DNA (cytosine-5) methyltransferase by the 451nt RNA component of human telomerase.
PG  - 438a-439a
AB  - A link between telomerase expression and chromosome stability has been recognized for some
      time, and links between chromosome instability and cytosine methylation have recently been
      firmly established.  Most research indicates that the local hypermethylation and global
      hypomethylation associated with tumorigenesis are markers of chromosome instability, which in
      turn is a hallmark of tumor progression.  The enzymes that apply methylation patterns to DNA
      [DNA (cytosine-5) methyltransferases], are known to show a strong preference for DNA sequences
      capable of adopting multiple secondary structures.  Sequences of this type are present at
      sites that are often prone to clastic mutation (e.g. triplet repeat sequences that expand and
      become methylated in fragile X-linked mental retardation).  These findings, coupled with
      reports that methyltransferase mutations induce clastic mutation, suggest that
      methyltransferases may play a role in the recognition and repair of clastogenic damage in
      organisms that must incorporate sequences prone to secondary structure formation into their
      genomes.  The preference for sequences that adopt secondary structure exhibited by these
      enzymes, extends to RNA.  RNA:DNA hybrids can bind to methyltransferase but are not methylated
      on either strand.  The 451 nt human temomerase RNA (hTR) adopts secondary structures that bind
      to the human placental enzyme and inhibit its action with an inhibition constant in the nM
      range.  Given the widely observed elevation of h TR levels in human cancers, and the
      mechanistic similarities between dyskerin, (a putative pseudouracil synthase involved in hTR
      processing), and the DNA methyltransferase, these data raise the possibility that DNA
      methyltransferase may form a complex with hTR-RNA during tumorigenesis, protecting hTRRNA from
      degradation and promoting chromosome instability by blocking the normal action of DNA
      methyltransferase.
AU  - Smith SS
PT  - Journal Article
TA  - Mol. Biol. Cell
JT  - Mol. Biol. Cell
SO  - Mol. Biol. Cell 2000 11: 438a-439a.

PMID- 
VI  - 6
DP  - 2000
TI  - Conformation space and the emergence of new functions for eukaryotic DNA (cytosine-5) methyltransferases.
PG  - S11
AB  - The existence of a link correlating CpG methylation with gene silencing as seen in mammalian
      gene imprinting, X-chromosome inactivation, and the repression of viral genomes and L1
      elements now seems quite plausible.  The evidence suggests that methylation in certain regions
      of a gene can provide one of the signals necessary for the regional assembly of
      heterochromatin.  On the other hand, work with histone deacetylase inhibitors suggests that
      methylation is not one of the primary controls on transcription because reactivation does not
      require demethylation.  DNA (cytosine-5)methyltransferases, the enzymes that apply methylation
      patterns are known to show a strong preference for DNA sequences from regions with high
      conformation space (i.e. sequences capable of adopting multiple secondary structures).  Such
      sequences are present at sites that are often prone to clastic mutation (e.g. triplet repeat
      sequences that expand in fragile X-linked mental retardation).  Moreover, lesions in
      methyltransferase genes have been shown to promote clastic mutation.  These findings suggest
      that methyltransferases play an additional role in the recognition and repair of clastogenic
      damage in organisms that must incorporate sequences with high conformation spaces into their
      genomes.  Such organisms may use stalled methyltransferase proteins as a cue in the repair of
      inactive chromatin domains containing high conformation-space sequences.  The preference for
      high conformation-space sequences exhibited by these enzymes extends to RNA.  RNA:DNA hybrids
      can bind to methyltransferase but are not methylated on either strand.  Short RNA sequences
      from the Xist gene and the 451nt human telomerase RNA (hTR) adopt secondary structures that
      bind to the human placental enzyme and inhibit its action.  Given the widely observed
      elevation of hTR levels in human cancers, and the mechanistic similarities between dyskerin, a
      putative pseudouracil synthase, and the DNA methyltransferase, the data raise the possibility
      that a DNA methyltransferase-hTR complex may form during tumorigenesis, protecting hTR from
      degradation and promoting chromosome instability by blocking the normal action of DNA
      methyltransferase.  These findings suggest that the elevation of hTR levels in prostate cancer
      cells that we have observed in expressed prostatic secretion may be partially responsible for
      the disruptions in methylation patterning and chromosomal instability that have been noted in
      these tumor specimens.
AU  - Smith SS
PT  - Journal Article
TA  - Int. J. Mol. Med.
JT  - Int. J. Mol. Med.
SO  - Int. J. Mol. Med. 2000 6: S11.

PMID- 10964556
VI  - 302
DP  - 2000
TI  - Gilbert's conjecture: The search for DNA (cytosine-5) demethylases and the emergence of new functions for eukaryotic DNA (cytosine-5) methyltransferases.
PG  - 1-7
AB  - In 1985 Walter Gilbert challenged members of the DNA methylation community assembled at a
      National Institutes of Health meeting organized by Giulio Cantoni and Ahron Razin with the
      following words: "The most exciting aspect about the methyl groups on DNA is the thought that
      they might provide a locally inherited change in a DNA structure. However, for that to be
      interesting, those changes have to be different in different cells. Furthermore, the
      alterations in methylation have to be freely imposable and have to be maintained. It is not
      yet clear that all these properties are true. So I don't think one will find that methylation
      ever is one of the primary, top-level controls on gene expression." In essence, Gilbert's
      conjecture, that DNA methylation is not one of the top-level controls on gene expression,
      assumes that evidence in favor of both of its testable propositions will not be obtained.
      Evidence for the first proposition, that alterations in methylation status associated with
      gene-expression states have to be maintained, was already available in 1985 and has been
      strengthened by a number of very recent experiments. However, the extensive effort to obtain
      evidence for the second proposition, that alterations in methylation status be freely
      imposable, has not been successful in its original intent. The effort has, on the other hand,
      resulted in the emergence of new functions for 5-methylcytosine and the cytosine
      methyltransferases in eukaryotic DNA repair, recombination and chromosome stability.
AU  - Smith SS
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2000 302: 1-7.

PMID- 9852213
VI  - 1
DP  - 1998
TI  - Stalling of DNA methyltransferase in chromosome stability and chromosome remodelling (Review).
PG  - 147-156
AB  - As a consequence of their mechanism of action, DNA (cytosine-5) methyltransferases from both
      prokaryotes and eukaryotes necessarily recognize mispaired bases in unusual DNA structures as
      catalytic transition-state analogs.  A review of the available data suggests that the enzymes
      are designed to stall at these sites because they are unable to release substrates or products
      that are fixed in a conformation resembling the transition state.  The enzymes can operate by
      a two-step process in which they first methylate extrahelical cytosines satisfying their
      recognition requirements and subsequently stall at the site of methylation.  On RNA and
      DNA-RNA hybrids they may operate by a similar one-step process in which they stall at
      transition-state analogs without methylating cytosine moieties.  These natural capacities
      suggest that the enzymes may physically participate in stable nucleoprotein assemblies formed
      as components of normal chromatin structure or as intermediates in the repair of unusual
      structures.  The methyltransferases, themselves, may physically participate in chromosome
      remodelling as part of a mechanism of inactivation or imprinting by stabilizing RNA-DNA
      hybrids or RNA-RNA secondary structure involving cis-acting untranslated RNAs like the product
      of the Xist gene.  Methyltransferase may physically participate in the repair of certain
      unusual structures by serving as a nucleation point.  The affinity for secondary structure in
      nucleic acids may account for the spreading of DNA methylation patterns.  Titration of host
      methyltransferase by RNA-DNA hybrids and RNA secondary structure formed during retroviral
      replication in certain tumorigenic retroviruses, like MMTV, may account for global
      hypomethylation observed in retrovirally transformed cells.  In a similar fashion, titration
      of methyltransferase by secondary structures associated with chromosome instability may
      account for global hypomethylation observed in association with local hypermethylation in
      tumorigenesis.
AU  - Smith SS
PT  - Journal Article
TA  - Int. J. Mol. Med.
JT  - Int. J. Mol. Med.
SO  - Int. J. Mol. Med. 1998 1: 147-156.

PMID- 7863011
VI  - 49
DP  - 1994
TI  - Biological implications of the mechanism of action of human DNA (cytosine-5)methyltransferase.
PG  - 65-111
AB  - I. Mechanism of action of the human DNA (cytosine-5)methyltransferase
      A.  Sequence of catalytic events
      B.  sp2-sp3 energetics and stereochemistry at C-6 and C-5 of cytosine
      C.  Conformational change in the enzyme--DNA complex
      D.  Potential for proton-mediated hydrolytic deamination
      II.  Selectivity of human DNA methyltransferases
      A.  De Novo methylation
      B.  Methyl-directed methylation
      C.  Structurally induced methylation
      D.  The three-nucleotide recognition motif
      E.  Enzyme--DNA interaction at the asymmetric DNA-binding site
      III.  Biological implications of the mechanism
      A.  Specificity of human DNA methylation
      B.  Pattern formation as the key to the function of vertebrate DNA methylation
      C.  Key elements of pattern formation are demonstrated by the phenomenon of concerted
      modification
      D.  Enzymology of pattern formation mechanisms
      E.  Enzymology of disturbances in patterning produced by DNA damage
      F.  Deamination at C-G dinucleotides
      IV.  Conclusions
      References
AU  - Smith SS
PT  - Journal Article
TA  - Prog. Nucleic Acid Res. Mol. Biol.
JT  - Prog. Nucleic Acid Res. Mol. Biol.
SO  - Prog. Nucleic Acid Res. Mol. Biol. 1994 49: 65-111.

PMID- 9168963
VI  - 234
DP  - 1997
TI  - Stalling of human methyltransferase at single-strand conformers from the Huntington's locus.
PG  - 73-78
AB  - We describe evidence for a sequence of events in which the human DNA (cytosine-5)
      methyltransferase first methylates spontaneous single-stranded conformers and then stalls at
      the methylated site to produce a complex with the conformationally unusual DNA.  This property
      of the enzyme is a result of its ability to respond to a general loss of symmetry at its CG
      recognition site.  The data suggest that DNA methyltransferase, itself, may physically
      participate in biological processes that distinguish between DNA that is in the normal
      Watson-Crick paired conformation and DNA that is conformationally unusual (e.g. a hairpin loop
      or misassembled replication intermediate).  The in vitro methylation of spontaneous SSCs from
      the Huntington's locus illustrates the phenomenon.
AU  - Smith SS
AU  - Baker DJ
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1997 234: 73-78.

PMID- 10487516
VI  - 26
DP  - 1999
TI  - DNA methylation in eukaryotic chromosome stability revisited: DNA methyltransferase in the management of DNA conformation space.
PG  - 1-9
AB  - A previous working hypothesis on the role of DNA methylation in eukaryotic stability presented
      enzymological data suggesting the DNA methylation has evolved as a biological response to the
      formation of unusual DNA structures.  That evidence suggested that human DNA methyltransferase
      is uniquely suited to participate in a repair system that functions to suppress unusual DNA
      structures.  The evolution of this repair system was suggested to be a prerequisite for the
      incorporation of dynamic sequences into the genome, because such sequences are particularly
      prone to the formation of unusual DNA structures that promote clastic mutagenesis.  In the
      intervening period, considerable evidence has accumulated in support of this proposal.  Here,
      we extend the previous working hypothesis in light of the current experimental data to give a
      more detailed picture of the role of DNA methylation in eukaryotic chromosome stability.
AU  - Smith SS
AU  - Crocitto L
PT  - Journal Article
TA  - Mol. Carcinog.
JT  - Mol. Carcinog.
SO  - Mol. Carcinog. 1999 26: 1-9.

PMID- 3658670
VI  - 15
DP  - 1987
TI  - Human DNA (cytosine-5)methyltransferase selectively methylates duplex DNA containing mispairs.
PG  - 6899-6916
AB  - The presence of the C-C mispair in a defined duplex oligodeoxynucleotide enhanced its capacity
      to serve as a substrate for highly purified human DNA methyltransferase. Analysis of tritiated
      reaction products showed that the C-C mispair acted as a "methylation acceptor" in that it was
      itself rapidly methylated. The m5C-G base pair also enhanced the capacity of the
      oligodeoxynucleotide to serve as a substrate for the enzyme. However, this complementary base
      pair was found to act as a "methylation director". That is, the presence of the m5C in one
      strand induced the enzyme to rapidly methylate at the cytosine residue on the opposite strand
      in an adjacent C-G base pair.
AU  - Smith SS
AU  - Hardy TA
AU  - Baker DJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1987 15: 6899-6916.

PMID- 1988679
VI  - 217
DP  - 1991
TI  - Recognition of unusual DNA structures by human DNA (cytosine-5) methyltransferase.
PG  - 39-51
AB  - The symmetry of the responses of the human DNA (cytosine-5) methyltransferase
      to alternative placements of 5-methylcytosine in model oligodeoxynucleotide
      duplexes containing unusual structures has been examined.  The results of these
      experiments more clearly define the DNA recognition specificity of the enzyme.
      A simple three-nucleotide recognition motif within the CG dinucleotide pair can
      be identified in each enzymatically methylated duplex.  The data can be
      summarized by numbering the four nucleotides in the dinucleotide pair thus: 1
      4 / 2   3  With reference to this numbering scheme, position 1 can be occupied
      by cytosine or 5-methylcytosine; position 2 can be occupied by guanosine or
      inosine; position 3, the site of enzymatic methylation, can be occupied only by
      cytosine; and position 4 can be occupied by guanosine, inosine,
      O6-methylguanosine, cytosine, adenosine, an abasic site, or the 3' hydroxyl
      group at the end of a gapped molecule.  Replacing the guanosine normally found
      at position 4 with any of the moieties introduces unusual (non-Watson-Crick)
      pairing at position 3 and generally enhances methylation of the cytosine at
      that site.  The exceptional facility of the enzyme in actively methylating
      unusual DNA structures suggests that the evolution of the DNA
      methyltransferase, and perhaps DNA methylation itself may be linked to the
      biological occurrence of unusual DNA structures.
AU  - Smith SS
AU  - Kan JLC
AU  - Baker DJ
AU  - Kaplan BE
AU  - Dembek P
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1991 217: 39-51.

PMID- 1584813
VI  - 89
DP  - 1992
TI  - Mechanism of human methyl-directed DNA methyltransferase and the fidelity of cytosine methylation.
PG  - 4744-4748
AB  - The properties of the methyl-directed DNA (cytosine-5)-methyltransferase (EC2.1.1.37) suggest
      that it is the enzyme that maintains patterns of methylation in the human genome. Proposals
      for the enzyme's mechanism of action suggest that 5-methyldeoxycytidine is produced from
      deoxycytidine via a dihydrocytosine intermediate. We have used an oligodeoxynucleotide
      containing 5-fluorodeoxycytidine as a suicide substrate to capture the enzyme and the
      dihydrocytosine intermediate. Gel retardation experiments demonstrate the formation of the
      expected covalent complex between duplex DNA containing 5-fluorodeoxycytidine and the human
      enzyme. Formation of the complex was dependent upon the presence of the methyl donor
      S-adenosylmethionine, suggesting that it comprises an enzyme-linked 5-substituted
      dihydrocytosine moiety in DNA. Dihydrocytosine derivatives are extremely labile toward
      hydrolytic deamination in aqueous solution. Because C-to-T transition mutations are especially
      prevalent at CG sites in human DNA, we have used high-performance liquid chromatography to
      search for thymidine that might be generated by hydrolysis during the methyl transfer
      reaction. Despite the potential for deamination inherent in the formation of the intermediate,
      the methyltransferase did not produce detectable amounts of thymidine. The data suggest that
      the ability of the human methyltransferase to preserve genetic information when copying a
      methylation pattern (i.e., its fidelity) is comparable to the ability of a mammalian DNA
      polymerase to preserve genetic information when copying a DNA sequence. Thus the high
      frequency of C-to-T transitions at CG sites in human DNA does not appear to be due to the
      normal enzymatic maintenance of methylation patterns.
AU  - Smith SS
AU  - Kaplan BE
AU  - Sowers LC
AU  - Newman EM
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1992 89: 4744-4748.

PMID- 7486847
VI  - 15
DP  - 1995
TI  - DNA methyltransferases in the recognition and repair of hairpin loops lacking precise Watson-Crick homology.
PG  - 1671
AB  - Sequences from codon-12 of the c-Ha-ras gene, the trinucleotide repeat region of the FMR-1
      gene and the trinucleotide repeat region of the HuntingtonM-Us disease gene spontaneously form
      hairpin loops under physiological conditions even though these loops lack precise Watson-Crick
      homology.  The formation of loops of this type during replication may provide a new driving
      force for genetic damage during carcinogenesis and the expression of genetic diseases.  The
      exceptional capacity of the human methyltransferase to recognize these loops is a consequence
      of its mechanism of action which requires that it unstack the cytosine ring from the DNA helix
      as it activates the ring for methylation by nucleophilic attack at C6.  The rate of
      methylation is enhanced by the capacity of mispairs (e.g. C.C., C.C+ or A+.C mispairs) in the
      stems of such loops to serve as transition state analogs for the catalysis.  These findings
      suggest that the mechanisms by which methyl groups and chromosomal abnormalities accumulate in
      the c-Ha-ras region of chromosome 11 during carcinogenesis and at the FMR-1 locus during
      repeat expansion involve structurally-induced de novo methylation at sites undergoing local
      conformational change.  Models for the participation of methyltransferases in the recognition
      and repair of looped structures suggest that they might serve to mark looped structures for
      repair.  Cycles of loop formation and repair are expected to produce spreading of de novo
      methylation in the vicinity of affected genes.  Asymmetrically methylated duplexes produced by
      repair of the looped structures would be rapidly converted to symmetrically methylated
      duplexes through the methyl-directed activity of the human methyltransferase.
AU  - Smith SS
AU  - Kho MR
AU  - Baker DJ
PT  - Journal Article
TA  - Anticancer Res.
JT  - Anticancer Res.
SO  - Anticancer Res. 1995 15: 1671.

PMID- 7720955
VI  - 9
DP  - 1995
TI  - Recognition of telomere-like structures from the human C-Ha-Ras gene and the trinucleotide repeat of the FMR-1 gene of fragile X by human DNA methyltransferase.
PG  - A1324
AB  - Telomere-like hairprins from the c-Ha-ras gene and from the FMR-1 gene are exceptional
      substrates for human DNA(cytosine-5)methyltransferases. This is a consequence of the mechanism
      of action of these enzymes which requires that a group at the active site carry out
      nucleophilic attack of an unstacked-cytosine ring in DNA. Thus the rate of methylation is
      enhanced by the capacity of mispairs like C.C or C.C+ found on telomere-like loops formed in
      C-rich DNA strands to serve as transition state analogs for the catalysis. These findings
      suggest that the mechanisms by which methyl groups and chromosomal abnormalities accumulate at
      the FMR-1 locus during repeat expansion in fragile X syndrome and in the c-Ha-ras region of
      chromosome 11 during carcinogenesis may involve structurally-induced de novo methylation at
      sites undergoing local conformational change. Possible roles for cytosine methylation in loop
      repair and trinucleotide repeat expansion will be discussed.
AU  - Smith SS
AU  - Laayoun A
AU  - Baker DJ
AU  - Kho MR
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1995 9: A1324.

PMID- 1731943
VI  - 31
DP  - 1992
TI  - Recognition of foldback DNA by the human DNA (Cytosine-5-)-methyltransferase.
PG  - 850-854
AB  - In order to specifiy the recognition requirements of the human DNA
      (cytosine-5-)-methyltransferase, two isomeric 48mers were synthesized so as to
      link a long block of DNA with a shorter complementary block of DNA through a
      tether consisting of five thymidine residues.  These isomeric foldback
      molecules, differing only in the location of the 5-methyldeoxycytosine, were
      shown to be unimolecular, to contain a region of duplex DNA, and to contain a
      region of single-stranded DNA.  When used as substrates for the DNA
      methyltransferase, only one of the isomers was methylated.  A comparison of the
      structures of the two isomers allows us to begin to define the potential sites
      of interaction between the enzyme and the three nucleotides forming a
      structural motif consisting of 5-methyldeoxycytosine, its base-paired
      deoxyguanosine, and a deoxycytosine 5' to the paired deoxyguanosine.
AU  - Smith SS
AU  - Lingeman RG
AU  - Kaplan BE
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1992 31: 850-854.

PMID- Not carried by PubMed...
VI  - 16
DP  - 1988
TI  - Restriction enzyme searches using the word processing software:  LOCOSCRIPT.
PG  - 224-226
AB  - One of the most important routine applications of computers in biochemistry and
      molecular biology is the determination of restriction enzyme sites.  In our
      laboratory, we routinely carry out restriction enzyme searches on the
      University's Vax System, using the Staden Molecular Biology software.
      Dedicated molecular biology software, however, can be expensive, and is
      frequently difficult to obtain for the computer system which happens to be
      available, while for those involved in introducing a genetic
      engineering/biotechnology component into the life science courses offered by
      colleges of further education and schools, the purchase of software may prove a
      major hurdle.  Even when the systems and software are available, competition
      from colleagues for terminals can mean constant frustration and delay to the
      biochemist wanting to do a simple restriction enzyme search which is well
      within the capacity of the cheapest PCW.  We now describe a rapid and reliable
      method of performing restriction enzyme searches and other molecular biology
      functions using the word processing software LOCOSCRIPT included with the
      Amstrad PCWQ 8256.  At a total cost for the complete system - computer,
      monitor, dot matrix printer and LOCOSCRIPT - of 299 Pounds plus VAT, this
      brings restriction enzyme searches and similar functions within the range of
      all educational institutes and research labs, and even of the individual
      scientist or teacher, many of whom already possess and use the system as a word
      processor.
AU  - Smith T
PT  - Journal Article
TA  - Biochemical Education
JT  - Biochemical Education
SO  - Biochemical Education 1988 16: 224-226.

PMID- 3350238
VI  - 2
DP  - 1988
TI  - Aurintricarboxylic acid inhibition of restriction endonuclease is not recognition site-specific.
PG  - A589
AB  - Aurintricarboxylic acid (ATA) has been previously shown to inhibit nucleases,
      including restriction endonucleases.  The discovery of restriction
      endonucleases which do not require guanine or cytosine bases within the
      recognition sequence provides an opportunity to determine whether or not the
      presence of these bases is required for inhibition by ATA.  In addition to the
      endonuclease DraI, which does not contain guanine-cytosine (GC) base pairs
      within the recognition sequence, two other restriction enzymes were included as
      controls.  These endonucleases were HaeIII, which has a recognition site
      without adenine-thymine (AT) base pairs, and HindIII, which contains both AT
      and GC base pairs within the recognition sequence.  ATA was included in
      restriction digests with the above endonucleases.  Following termination of the
      reactions, DNA fragments were separated by agarose gel electrophoresis.  The
      results indicate that inhibition by ATA does not require a specific base pair
      within the recognition sequence.
AU  - Smith TJ
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1988 2: A589.

PMID- 18060065
VI  - 2
DP  - 2007
TI  - Analysis of the Neurotoxin Complex Genes in Clostridium botulinum A1-A4 and B1 Strains: BoNT/A3, /Ba4 and /B1 Clusters Are Located within  Plasmids.
PG  - e1271
AB  - BACKGROUND: Clostridium botulinum and related clostridial species express extremely potent
      neurotoxins known as botulinum neurotoxins (BoNTs) that
      cause long-lasting, potentially fatal intoxications in humans and other
      mammals. The amino acid variation within the BoNT is used to categorize
      the species into seven immunologically distinct BoNT serotypes (A-G) which
      are further divided into subtypes. The BoNTs are located within two
      generally conserved gene arrangements known as botulinum progenitor
      complexes which encode toxin-associated proteins involved in toxin
      stability and expression. METHODOLOGY/PRINCIPAL FINDINGS: Because serotype
      A and B strains are responsible for the vast majority of human botulism
      cases worldwide, the location, arrangement and sequences of genes from
      eight different toxin complexes representing four different BoNT/A
      subtypes (BoNT/A1-Ba4) and one BoNT/B1 strain were examined. The bivalent
      Ba4 strain contained both the BoNT/A4 and BoNT/bvB toxin clusters. The
      arrangements of the BoNT/A3 and BoNT/A4 subtypes differed from the BoNT/A1
      strains and were similar to those of BoNT/A2. However, unlike the BoNT/A2
      subtype, the toxin complex genes of BoNT/A3 and BoNT/A4 were found within
      large plasmids and not within the chromosome. In the Ba4 strain, both BoNT
      toxin clusters (A4 and bivalent B) were located within the same 270 kb
      plasmid, separated by 97 kb. Complete genomic sequencing of the BoNT/B1
      strain also revealed that its toxin complex genes were located within a
      149 kb plasmid and the BoNT/A3 complex is within a 267 kb plasmid.
      CONCLUSIONS/SIGNIFICANCE: Despite their size differences and the BoNT
      genes they contain, the three plasmids containing these toxin cluster
      genes share significant sequence identity. The presence of partial
      insertion sequence (IS) elements, evidence of recombination/gene
      duplication events, and the discovery of the BoNT/A3, BoNT/Ba4 and BoNT/B1
      toxin complex genes within plasmids illustrate the different mechanisms by
      which these genes move among diverse genetic backgrounds of C. botulinum.
AU  - Smith TJ
AU  - Hill KK
AU  - Foley BT
AU  - Detter JC
AU  - Munk AC
AU  - Bruce DC
AU  - Doggett NA
AU  - Smith LA
AU  - Marks JD
AU  - Xie G
AU  - Brettin TS
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2007 2: e1271.

PMID- 25489752
VI  - 30
DP  - 2014
TI  - Genomic sequences of six botulinum neurotoxin-producing strains representing three clostridial species illustrate the mobility and diversity of botulinum neurotoxin genes.
PG  - 102-113
AB  - The whole genomes for six botulinum neurotoxin-producing clostridial strains were sequenced to
      provide references for under-represented toxin types, bivalent strains or unusual toxin
      complexes associated with a bont gene. The strains include three Clostridium botulinum Group I
      strains (CDC 297, CDC 1436, and Prevot 594), a Group II C. botulinum strain (Eklund 202F), a
      Group IV Clostridium argentinense strain (CDC 2741), and a Group V Clostridium baratii strain
      (Sullivan). Comparisons of the Group I genomic sequences revealed close relationships and
      conservation of toxin gene locations with previously published Group I C. botulinum genomes.
      The bont/F6 gene of strain Eklund 202F was determined to be a chimeric toxin gene composed of
      bont/F1 and bont/F2. The serotype G strain CDC 2741 remained unfinished in 20 contigs with the
      bont/G located within a 1.15Mb contig, indicating a possible chromosomal location for this
      toxin gene. Within the genome of C. baratii Sullivan strain, direct repeats of IS1182
      insertion sequence (IS) elements were identified flanking the bont/F7 toxin complex that may
      be the mechanism of bont insertion into C. baratii.
      Highlights of the six strains are described and release of their genomic sequences will allow
      further study of unusual neurotoxin-producing clostridial strains.
AU  - Smith TJ
AU  - Hill KK
AU  - Xie G
AU  - Foley BT
AU  - Williamson CH
AU  - Foster JT
AU  - Johnson SL
AU  - Chertkov O
AU  - Teshima H
AU  - Gibbons HS
AU  - Johnsky LA
AU  - Karavis MA
AU  - Smith LA
PT  - Journal Article
TA  - Infect. Genet. Evol.
JT  - Infect. Genet. Evol.
SO  - Infect. Genet. Evol. 2014 30: 102-113.

PMID- 24459281
VI  - 2
DP  - 2014
TI  - Whole-Genome Sequencing of Erwinia amylovora Strains from Mexico Detects Single Nucleotide Polymorphisms in rpsL Conferring Streptomycin Resistance and in the  avrRpt2 Effector Altering Host Interactions.
PG  - e01229-13
AB  - We report draft genome sequences of three Mexican Erwinia amylovora strains. A novel plasmid,
      pEA78, was identified. Comparative genomics revealed an rpsL
      chromosomal mutation conferring high-level streptomycin resistance in two
      strains. In the effector gene avrRpt2, a single nucleotide polymorphism was
      detected that overcomes fire blight disease resistance in Malus x robusta 5.
AU  - Smits TH
AU  - Guerrero-Prieto VM
AU  - Hernandez-Escarcega G
AU  - Blom J
AU  - Goesmann A
AU  - Rezzonico F
AU  - Duffy B
AU  - Stockwell VO
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01229-13.

PMID- 26067963
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of the Cyanogenic Phosphate-Solubilizing Pseudomonas sp. Strain CCOS 191, a Close Relative of Pseudomonas mosselii.
PG  - e00616-15
AB  - We sequenced the complete genome of the isolate Pseudomonas sp. CCOS 191. This strain is able
      to dissolve phosphate minerals and form cyanide. The genome
      sequence is used to establish the phylogenetic relationship of this species.
AU  - Smits TH
AU  - Pothier JF
AU  - Ruinelli M
AU  - Blom J
AU  - Frasson D
AU  - Koechli C
AU  - Fabbri C
AU  - Brandl H
AU  - Duffy B
AU  - Sievers M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00616-15.

PMID- 26659685
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Commercial Biocontrol Strain Pantoea agglomerans P10c.
PG  - e01448-15
AB  - We report here the draft genome sequence of the biocontrol strain Pantoea agglomerans P10c,
      composed of a draft chromosome and two plasmids: the 559-kb
      large Pantoea plasmid 1 (pPag3) and a 182-kb plasmid (pPag1). A genomic island
      containing pantocin A biosynthesis genes was identified.
AU  - Smits TH
AU  - Rezzonico F
AU  - Blom J
AU  - Goesmann A
AU  - Abelli A
AU  - Kron MR
AU  - Vanneste JL
AU  - Duffy B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01448-15.

PMID- 20952567
VI  - 192
DP  - 2010
TI  - Genome Sequence of the Biocontrol Agent Pantoea vagans Strain C9-1.
PG  - 6486-6487
AB  - Pantoea vagans is a Gram-negative enterobacterial plant epiphyte of a broad range of plants.
      Here we report the 4.89-Mb genome sequence of P.
      vagans strain C9-1 (formerly Pantoea agglomerans), which is commercially
      registered for biological control of fire blight, a disease of pear and
      apple trees caused by Erwinia amylovora.
AU  - Smits TH
AU  - Rezzonico F
AU  - Kamber T
AU  - Goesmann A
AU  - Ishimaru CA
AU  - Stockwell VO
AU  - Frey JE
AU  - Duffy B
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 6486-6487.

PMID- 11917108
VI  - 99
DP  - 2002
TI  - Genome sequence and comparative microarray analysis of serotype M18 group A Streptococcus strains associated with acute rheumatic fever outbreaks.
PG  - 4668-4673
AB  - Acute rheumatic fever (ARF), a sequelae of group A Streptococcus (GAS) infection, is the most
      common cause of preventable childhood heart disease worldwide. The molecular basis of ARF and
      the subsequent rheumatic heart disease are poorly understood. Serotype M18 GAS strains have
      been associated for decades with ARF outbreaks in the U.S. As a first step toward gaining new
      insight into ARF pathogenesis, we sequenced the genome of strain MGAS8232, a serotype M18
      organism isolated from a patient with ARF. The genome is a circular chromosome of 1,895,017
      bp, and it shares 1.7 Mb of closely related genetic material with strain SF370 (a sequenced
      serotype M1 strain). Strain MGAS8232 has 178 ORFs absent in SF370. Phages, phage-like
      elements, and insertion sequences are the major sources of variation between the genomes. The
      genomes of strain MGAS8232 and SF370 encode many of the same proven or putative virulence
      factors. Importantly, strain MGAS8232 has genes encoding many additional secreted proteins
      involved in human-GAS interactions, including streptococcal pyrogenic exotoxin A (scarlet
      fever toxin) and two uncharacterized pyrogenic exotoxin homologues, all phage-associated. DNA
      microarray analysis of 36 serotype M18 strains from diverse localities showed that most
      regions of variation were phages or phage-like elements. Two epidemics of ARF occurring 12
      years apart in Salt Lake City, UT, were caused by serotype M18 strains that were genetically
      identical, or nearly so. Our analysis provides a critical foundation for accelerated research
      into ARF pathogenesis and a molecular framework to study the plasticity of GAS genomes.
AU  - Smoot JC
AU  - Barbian KD
AU  - Van Gompel JJ
AU  - Smoot LM
AU  - Chaussee MS
AU  - Sylva GL
AU  - Sturdevant DE
AU  - Ricklefs SM
AU  - Porcella SF
AU  - Parkins LD
AU  - Beres SB
AU  - Campbell DS
AU  - Smith TM
AU  - Zhang Q
AU  - Kapur V
AU  - Daly JA
AU  - Veasy LG
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2002 99: 4668-4673.

PMID- 6255419
VI  - 8
DP  - 1980
TI  - The 5'-cytosine in CCGG is methylated in two eukaryotic DNAs and MspI is sensitive to methylation at this site.
PG  - 3829-3840
AB  - Novikoff rat hepatoma and bovine liver DNAs were digested with MspI or HpaII. Restriction
      fragments were end-labeled using [a-32P]-dCTP and the Klenow fragment of E. coli DNA
      polymerase I and then digested to 2'-deoxyribonucleoside-3'-monophosphates using micrococcal
      nuclease and spleen phosphodiesterase. Mononucleotides were separated by two-dimensional thin
      layer chromatography, localized by radioautography, and the [32P]-label quantitated by
      scintillation spectrometry. This method, based on known specificities of MspI and HpaII, shows
      that CCGG, CMGG, and MCGG (M refers to 5-methylcytosine) occur at frequencies of 89.6%, 1.4%,
      and 9.0%, respectively, in the rat DNA and at 41.6%, 48.3%, and 10.0%, respectively, in the
      ovine DNA. [32P] recovery in 3'-5-MedCMP from end-labeled MspI digests was negligible
      compared to recovery from HpaII digests. Hence, MspI is sensitive to methylation at the 5'
      cytosine in the sequence CCGG.
AU  - Sneider TW
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1980 8: 3829-3840.

PMID- 22914622
VI  - 4
DP  - 2012
TI  - Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing.
PG  - 148RA116
AB  - The Gram-negative bacteria Klebsiella pneumoniae is a major cause of nosocomial
      infections, primarily among immunocompromised patients. The emergence of strains
      resistant to carbapenems has left few treatment options, making infection
      containment critical. In 2011, the U.S. National Institutes of Health Clinical
      Center experienced an outbreak of carbapenem-resistant K. pneumoniae that
      affected 18 patients, 11 of whom died. Whole-genome sequencing was performed on
      K. pneumoniae isolates to gain insight into why the outbreak progressed despite
      early implementation of infection control procedures. Integrated genomic and
      epidemiological analysis traced the outbreak to three independent transmissions
      from a single patient who was discharged 3 weeks before the next case became
      clinically apparent. Additional genomic comparisons provided evidence for
      unexpected transmission routes, with subsequent mining of epidemiological data
      pointing to possible explanations for these transmissions. Our analysis
      demonstrates that integration of genomic and epidemiological data can yield
      actionable insights and facilitate the control of nosocomial transmission.
AU  - Snitkin ES
AU  - Zelazny AM
AU  - Thomas PJ
AU  - Stock F
AU  - Henderson DK
AU  - Palmore TN
AU  - Segre JA
PT  - Journal Article
TA  - Sci. Transl. Med.
JT  - Sci. Transl. Med.
SO  - Sci. Transl. Med. 2012 4: 148RA116.

PMID- 26159528
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Pragia fontium 24613, an Environmental Bacterium from the Family Enterobacteriaceae.
PG  - e00740-15
AB  - The complete genome sequence of Pragia fontium 24613 was determined using PacBio  RSII, Roche
      454, and SOLiD sequencing. A total of 3,579 genes were predicted,
      including 3,338 protein-coding sequences and 146 pseudogenes. This is the first
      whole-genome sequence of a strain belonging to the environmental genera of the
      family Enterobacteriaceae.
AU  - Snopkova K
AU  - Sedlar K
AU  - Bosak J
AU  - Chaloupkova E
AU  - Provaznik I
AU  - Smajs D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00740-15.

PMID- 6321170
VI  - 138
DP  - 1984
TI  - Supercoiling and the mechanism of restriction endonucleases.
PG  - 275-280
AB  - 1. We have used topoisomerase I in the presence of netropsin and ethidium
      bromide to generate DNA molecules of varying superhelical density.  2.
      Digestion by endonuclease EcoRI is sensitive to supercoiling, being maximal for
      the relaxed form.  Endonucleases AvaI and BamHI, by contrast, are relatively
      unaffected.  3. The results are interpreted in terms of the base composition of
      the DNA in the vicinity of these sites. dA + dT-rich regions are more
      susceptible to deformation than are dG + dC-rich ones.  4. Analysis of the
      rates of disappearance of linear molecules confirms a two-step mechanism for
      EcoRI cleavage but suggests that BamHI and AvaI cleave both strands
      simultaneously.
AU  - Snounou G
AU  - Malcolm ADB
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1984 138: 275-280.

PMID- 11494868
VI  - 340
DP  - 2001
TI  - Locating cobalt-binding sites on DNA using restriction endonucleases.
PG  - 519-528
AB  - The interactions of simple metal complexes with DNA have been widely studied.  The interaction
      specificities of these molecules range from simple outside binding, such as observed with
      [Co(NH3)6]3+, to covalent binding as observed with Pt(NH3)2Cl2, to reactions involving DNA
      oxidative cleavage through Fenton or related chemistries.  One important feature of such
      interactions, especially those leading to covalent binding, is the sequence specificity of the
      reaction.  It has been well established that platination of DNA by Pt(NH3)2Cl2 is highly
      sequence specific with a preferential reaction at -GG- sites, although reactions involving
      -GA- and -GC- sites have also been noted.  Reaction at an isolated -GG- or -GA- site results
      in an intrastrand cross-link composed of a pur(N7)-Pt-pur(N7) linkage, whereas the reaction at
      a -GC- site results in an interstrand cross-link with the same type of linkage.  The sequence
      specificity of these and related reactions is due to the accessibility to N7 of purines,
      located in the major groove of the DNA, and to the nucleophilicity of N7, particularly that of
      guanine bases.
AU  - Snow AM
AU  - Sheardy RD
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 2001 340: 519-528.

PMID- 23201561
VI  - 167
DP  - 2013
TI  - Genome sequence of Corynebacterium pseudotuberculosis biovar equi strain 258 and prediction of antigenic targets to improve biotechnological vaccine production.
PG  - 135-141
AB  - Corynebacterium pseudotuberculosis is the causative agent of several veterinary
      diseases in a broad range of economically important hosts, which can vary from
      caseous lymphadenitis in sheep and goats (biovar ovis) to ulcerative lymphangitis
      in cattle and horses (biovar equi). Existing vaccines against C.
      pseudotuberculosis are mainly intended for small ruminants and, even in these
      hosts, they still present remarkable limitations. In this study, we present the
      complete genome sequence of C. pseudotuberculosis biovar equi strain 258,
      isolated from a horse with ulcerative lymphangitis. The genome has a total size
      of 2,314,404 bp and contains 2088 predicted protein-coding regions. Using in
      silico analysis, eleven pathogenicity islands were detected in the genome
      sequence of C. pseudotuberculosis 258. The application of a reverse vaccinology
      strategy identified 49 putative antigenic proteins, which can be used as
      candidate vaccine targets in future works.
AU  - Soares SC et al
PT  - Journal Article
TA  - J. Biotechnol.
JT  - J. Biotechnol.
SO  - J. Biotechnol. 2013 167: 135-141.

PMID- 21705591
VI  - 193
DP  - 2011
TI  - Draft Genome Sequences of Two Pseudomonas aeruginosa Clinical Isolates with Different Antibiotic Susceptibilities.
PG  - 5573
AB  - Pseudomonas aeruginosa is a primary cause of opportunistic infections. We have sequenced and
      annotated the genomes of two P. aeruginosa clinical
      isolates evidencing different antibiotic susceptibilities. Registered
      differences in the composition of their accessory genomes may provide
      clues on P. aeruginosa strategies to thrive in different environments like
      infection loci.
AU  - Soares-Castro P
AU  - Marques D
AU  - Demyanchuk S
AU  - Faustino A
AU  - Santos PM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5573.

PMID- 23405299
VI  - 1
DP  - 2013
TI  - Towards the Description of the Genome Catalogue of Pseudomonas sp. Strain M1.
PG  - e00146-12
AB  - Pseudomonas sp. strain M1 is a soil isolate with remarkable biotechnological potential. The
      genome of Pseudomonas sp. M1 was sequenced using both 454 and
      Illumina technologies. A customized genome assembly pipeline was used to
      reconstruct its genome sequence to a single scaffold.
AU  - Soares-Castro P
AU  - Santos PM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00146-12.

PMID- 4130596
VI  - 17
DP  - 1973
TI  - Symmetry in protein-nucleic acid interaction and its genetic implications.
PG  - 411-490
AB  - Symmetry principles are known to play a fundamental role in biological
      organization, governing the assembly of macromolecular subunits into viruses,
      membranes, oligomeric globular and fibrous proteins, and cellular organelles
      (Crick and Watson, 1956; Caspar and Klug, 1962; Monod et al., 1965; for an
      excellent review, see Engstrom and Strandberg, 1968).  Thus, for example, small
      spherical viruses utilize icosahedral symmetry in their construction, identical
      protein subunits being used to form large protein shells in which each subunit
      has, as nearly as possible, the same local environment (Caspar and Klug, 1962;
      Finch and Klug, 1966; Klug and Finch, 1968; Finch et al., 1970; for a review,
      see Klug et al., 1966).
AU  - Sobell HM
PT  - Journal Article
TA  - Adv. Genet.
JT  - Adv. Genet.
SO  - Adv. Genet. 1973 17: 411-490.

PMID- Not included in PubMed...
VI  - 376
DP  - 1995
TI  - Mapping of the functional regions of the EcoRV methyltransferase by random mutagenesis and screening for inactive mutants.
PG  - S155
AB  - To examine the structure and the mechanism of the EcoRV DNA methyltransferase several mutants
      were produced by random mutagenesis and selection for inactive mutants.  Until now, 11
      catalytically inactive single mutants were found: P8L; V20A; F115S; S121P; F139L; F172S;
      C192R; D193G; E212G; W231R and F249V.  Two of the mutant proteins (F139L and F249V) were not
      expressed in the cell, although the promotor sequence was intact, suggesting that these
      proteins are misfolded and rapidly degraded.  For further characterization the other mutant
      enzymes were purified by affinity-chromatography.  It turned out, that all proteins except
      wild type and the W231R mutant were insoluble suggestive of structural alterations caused by
      the mutations.  Whereas the purified wild type enzyme has a specific activity of 1.3 x 10^6
      U/mg, W231R is catalytically inactive in vitro.  Currently, the DNA- and
      S-adenosylmethionine-binding properties of the mutants are investigated.
AU  - Sobotta T
AU  - Pingoud A
AU  - Jeltsch A
PT  - Journal Article
TA  - Biol. Chem. Hoppe Seyler
JT  - Biol. Chem. Hoppe Seyler
SO  - Biol. Chem. Hoppe Seyler 1995 376: S155.

PMID- 21409633
VI  - 12
DP  - 1992
TI  - Methyltransferases as tools to alter the specificity of restriction endonucleases.
PG  - 159-172
AB  - Pulsed-field gel electrophoresis (PFGE) has allowed the resolution of very large DNA fragments
      from any organism. To apply PFGE to practical problems such as genetic mapping and map-based
      gene cloning, it is necessary to specifically generate large DNA fragments that can then be
      separated by PFGE. Ideally, restriction enzymes would exist that could generate DNA fragments
      of desired sizes. Other factors being equal, and supposing that DNA sequences were random,
      then enzymes with larger target sequences should produce larger DNA fragments. In practice, no
      restriction enzymes are known to have larger than 8-bp-long target sites and, of course, DNA
      sequences are not random. These realities severely limit the observed sizes of DNA fragments
      produced by restriction enzymes acting on genomic DNA particularly in the case of eukaryotic
      genomes, which are large and complex. This chapter describes enzymatic strategies to generate
      large DNA fragments and statistical tools that can aid researchers in choosing the restriction
      enzymes that are most likely to generate large fragments in the genome in question, if a
      sequence data base can be investigated.
AU  - Sobral BWS
AU  - McClelland M
PT  - Journal Article
TA  - Methods Mol. Biol.
JT  - Methods Mol. Biol.
SO  - Methods Mol. Biol. 1992 12: 159-172.

PMID- 28336606
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Chromobacterium aquaticum CC-SEYA-1, a Nonpigmented Member of the Genus Chromobacterium.
PG  - e01661-16
AB  - Chromobacterium aquaticum CC-SEYA-1T, isolated from a spring in Taiwan, shares many
      characteristics with other members of the genus but also contains auxin
      biosynthesis genes and does not produce the pigment violacein. Chromobacterium
      sp. 49, isolated from Brazil, is identified here as C. aquaticum, indicating that
      this is a cosmopolitan species.
AU  - Soby SD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01661-16.

PMID- 28336604
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Chromobacterium pseudoviolaceum LMG 3953T, an Enigmatic  Member of the Genus Chromobacterium.
PG  - e01632-16
AB  - Chromobacterium pseudoviolaceum LMG 3953T was separated from Chromobacterium violaceum in
      2009, but little is known of its origin or environmental role. Here,
      the genome of LMG 3953T was sequenced to understand the evolution of the genus
      Chromobacterium It is not clear from this sequence that C. pseudoviolaceum is
      taxonomically distinct from C. violaceum.
AU  - Soby SD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01632-16.

PMID- 25814611
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Clostridium tyrobutyricum Strain DIVETGP, Isolated from  Cow's Milk for Grana Padano Production.
PG  - e00213-15
AB  - We announce the draft genome sequence of Clostridium tyrobutyricum strain DIVETGP. This strain
      was isolated from cow's milk used for Grana Padano cheese
      production. The genome was obtained using Illumina HiSeq technology and comprises
      45 contigs for 3,018,999 bp, with a G+C content of 30.8%.
AU  - Soggiu A
AU  - Piras C
AU  - Gaiarsa S
AU  - Bendixen E
AU  - Panitz F
AU  - Bendixen C
AU  - Sassera D
AU  - Brasca M
AU  - Bonizzi L
AU  - Roncada P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00213-15.

PMID- 23012275
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Halomonas smyrnensis AAD6T.
PG  - 5690-5691
AB  - Halomonas smyrnensis AAD6(T) is a Gram-negative, aerobic, exopolysaccharide-producing, and
      moderately halophilic bacterium that produces
      levan, a fructose homopolymer with many potential uses in various industries. We
      report the draft genome sequence of H. smyrnensis AAD6(T), which will accelerate
      research on the rational design and optimization of microbial levan production.
AU  - Sogutcu E
AU  - Emrence Z
AU  - Arikan M
AU  - Cakiris A
AU  - Abaci N
AU  - Oner ET
AU  - Ustek D
AU  - Arga KY
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5690-5691.

PMID- 29301879
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Photobacterium leiognathi Strain JS01.
PG  - e01396-17
AB  - Photobacterium leiognathi is a bioluminescent symbiont of fish of the Leiognathidae family.
      Here, we present the full-genome sequence of P. leiognathi
      strain JS01, a strain isolated from a nonluminescent Loligo sp. squid of
      Singaporean origin. No finished genome sequence of this species is currently
      publicly available.
AU  - Soh JYK
AU  - Russell CW
AU  - Fenlon SN
AU  - Chen SL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01396-17.

PMID- 7607495
VI  - 157
DP  - 1995
TI  - Purification and characterization of C.BamHI, a regulator of the BamHI restriction-modification system.
PG  - 227-228
AB  - The bamHIC gene, controlling the BamHI restriction-modification (R-M) system can functionally
      be replaced by providing pvuIIC or smaIC in trans.  C.BamHI, the protein product encoded by
      bamHIC, has been purified and shown to bind a 345-bp DNA fragment within the BamHI R-M system.
AU  - Sohail A
AU  - Ives CL
AU  - Brooks JE
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 227-228.

PMID- 2198248
VI  - 172
DP  - 1990
TI  - A gene required for very short patch repair in Escherichia coli is adjacent to the DNA cytosine methylase gene.
PG  - 4214-4221
AB  - Deamination of 5-methylcytosine in DNA results in T/G mismatches. If unrepaired, these
      mismatches can lead to C-to-T transition mutations. The very short patch (VSP) repair process
      in Escherichia coli counteracts the mutagenic process by repairing the mismatches in favor of
      the G-containing strand. Previously we have shown that a plasmid containing an 11-kilobase
      fragment from the E. coli chromosome can complement a chromosomal mutation defective in both
      cytosine methylation and VSP repair. We have now mapped the regions essential for the two
      phenotypes. In the process, we have constructed plasmids that complement the chromosomal
      mutation for methylation, but not for repair, and vice versa. The genes responsible for these
      phenotypes have been identified by DNA sequence analysis. The gene essential for cytosine
      methylation, dcm, is predicted to code for a 473-amino-acid protein and is not required for
      VSP repair. It is similar to other DNA cytosine methylases and shares extensive sequence
      similarity with its isoschizomer, EcoRII methylase. The segment of DNA essential for VSP
      repair contains a gene that should code for a 156-amino-acid protein. This gene, named vsr, is
      not essential for DNA methylation. Remarkably, the 5' end of this gene appears to overlap the
      3' end of dcm. The two genes appear to be transcribed from a common promoter but are in
      different translational registers. This gene arrangement may assure that Vsr is produced along
      with Dcm and may minimize the mutagenic effects of cytosine methylation.
AU  - Sohail A
AU  - Lieb M
AU  - Dar M
AU  - Bhagwat AS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1990 172: 4214-4221.

PMID- Not carried by PubMed...
VI  - 19
DP  - 1987
TI  - Discovery of two new Type II restriction enzymes.
PG  - 371-391
AB  - Eight bacterial strains isolated from local environments have been screened for
      the presence of new restriction enzymes judging from the analysis of 1.4%
      agarose gel patterns of different DNA substrates.  Partially purified protein
      extracts of two of these strains, namely Pseudomonas ovalis and Enterobacter
      agglomerans exhibit the presence of Type II restriction endonucleases.  The new
      enzymes have been highly purified by a combination of gel filtration, ion
      exchange and affinity chromatography and are designated as PovI and EagI,
      respectively.  The identity of the new enzymes have been further confirmed by
      DNA double digest analysis with a variety of substrate DNAs which yielded no
      extra fragment.  This enzyme has been renamed EagMI to avoid confusion with the
      previous EagI.
AU  - Sohail A
AU  - Mushtaq R
AU  - Khan E
AU  - Maqbool T
AU  - Riazuddin S
PT  - Journal Article
TA  - Pak. J. Zool.
JT  - Pak. J. Zool.
SO  - Pak. J. Zool. 1987 19: 371-391.

PMID- 22740663
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Pseudomonas syringae Pathovar Syringae Strain FF5, Causal Agent of Stem Tip Dieback Disease on Ornamental Pear.
PG  - 3733-3734
AB  - Pseudomonas syringae FF5 causes stem tip dieback disease on ornamental pear (Pyrus
      calleryana). Its genome encodes a complete type III secretion system
      (T3SS) and HopAC1, HopM1, AvrE1, HopI1, HopAA1, HopJ1, HopAH2, HopAH1, HopAG1,
      and HopAZ1. Lacking detectable homologues of other T3SS effectors, it may encode
      novel, undiscovered effectors.
AU  - Sohn KH
AU  - Jones JD
AU  - Studholme DJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3733-3734.

PMID- 7756931
VI  - 2
DP  - 1995
TI  - Search, isolation and study of restrictases.
PG  - 47-51
AB  - New Class II restrictases were searched in over 800 microorganisms by using a highly sensitive
      toluene micro technique developed in the laboratory. This enabled site-specific endonuclease
      activity to be revealed in 72 strains. Thirty-two new restriction endonucleases were
      identified, which were highly purified and contained no impurities of nonspecific nucleases,
      phosphatases. Many of them (LpII, PaeI, PaeBI, ApiI, CsiAI, BavAI, BavAIII, BbvAI, etc.) are
      of interest for use in molecular genetic studies. Corynebacterium species cells were used to
      isolate a new super coarse hissing restrictase CsiBI that recognizes the 8-nucleotide site
      GCGGCCGC (the isoschizomer NotI) and a fine tool for obtaining enlarged fragments of pro- and
      eukaryotic genome.
AU  - Sokolov NN
PT  - Journal Article
TA  - Vestn. Akad. Med. Nauk SSSR
JT  - Vestn. Akad. Med. Nauk SSSR
SO  - Vestn. Akad. Med. Nauk SSSR 1995 2: 47-51.

PMID- 2546070
VI  - 0
DP  - 1989
TI  - Current approaches to the search of new restriction endonucleases.
PG  - 3-7
AB  - The main methodological approaches to the search for new restriction
      endonucleases are reviewed.  These methods include obtaining acellular extracts
      by ultrasonic disintegration of microbial cells, osmotic shock effects, the
      effects of organic solvents, mechanical disruption of bacterial cells, biphasic
      division after Albertson and others.  The resolving power of any method
      discussed depends mainly on the level of restriction endonuclease activity, the
      presence of nonspecific endonucleases in the biomass, the presence of
      exonucleases and the taxonomy of the microorganisms used.
AU  - Sokolov NN
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1989 0: 3-7.

PMID- 1963673
VI  - 0
DP  - 1990
TI  - Restriction endonucleases: Isolation methods and schemes.
PG  - 1-6
AB  - The great successes achieved in the last 10-15 years in the field of recombinant DNA
      technology have been largely due to the practical use of site-specific endonucleases (class II
      restriction endonucleases; EC 3.1.23.X).  We must agree with the opinion of F. Yang, who
      believes that one of the major discoveries that determined the course of development of
      genetic engineering was the discovery of restriction enzymes by S. Luria and M. Human.  The
      enormous interest in restriction endonucleases as research tools is due, on one hand, to their
      unique properites - their ability to form sticky ends on DNA fragments, the variety of
      recognizable nucleotide sequences, and the positions of the points of cleavage of the
      recognition sites.  On the other hand, restriction enodnucleases, which possess extremely high
      specificity with respect to the DNA nucleotide sequences that they recognize and hydrolyze,
      represent a splendid model for the study of the important general biological problems of
      nucleic-protein recognition.  Considering the great interest in restriction endonucleases
      among biochemists, molecular biologists, and specialists in allied fields, it is advisable to
      examine the basic methodological approaches and the most widespread schemes of isolation of
      these enzymes, to assess the difficulties and problems standing in the way of the production
      of purified restriction endonuclease preparations.
AU  - Sokolov NN
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1990 0: 1-6.

PMID- 2849847
VI  - 9
DP  - 1988
TI  - Search of strains producing new restriction endonucleases.
PG  - 86-89
AB  - The search for restriction endonucleases in 154 strains belonging to 104
      species of 32 genera of microorganisms has been carried out by the method of
      rapid toluene assay.  In 10 strains the activity of endonucleases specifically
      fragmenting the DNA of phage lambda in the presence of Mg2+ ions has been
      detected.  Restriction enzymes PaeI and PaeII found in two Pseudomonas
      aeruginosa strains have been identified as the true isoschizomers of
      restriction endonucleases SphI and SmaI respectively.  The results of the
      screening of restriction enzyme-producing strains indicate that the production
      of restriction enzymes is widespread among microorganisms of the genus
      Bacillus.
AU  - Sokolov NN
AU  - Anikeitcheva NV
AU  - Fitsner AB
AU  - Samko OT
AU  - Khoroshutina EB
AU  - Kalugin AA
PT  - Journal Article
TA  - Zh. Mikrobiol. Epidemiol. Immunobiol.
JT  - Zh. Mikrobiol. Epidemiol. Immunobiol.
SO  - Zh. Mikrobiol. Epidemiol. Immunobiol. 1988 9: 86-89.

PMID- 1326276
VI  - 18
DP  - 1992
TI  - Site-specific endonuclease BbvBI from Bacillus brevis.
PG  - 47-51
AB  - A new restriction endonuclease BbvBI free from contaminating non-specific nucleases and
      phosphatases was isolated from the Bacillus brevis cells. The enzyme was purified by
      fractionating the sonicated cell-free extract in a two-phase PEG/dextran system and subsequent
      chromatographies on DEAE-sepharose, blue sepharose and heparin sepharose. The endonuclease
      BbvBI displayed the maximal activity at 45 degrees C, pH between 8.0 and 8.5, MgCl2
      concentration in the range of 5-10 mM and at the low ionic strength. It is shown that the
      enzyme cleaves the sequence G^GYPC'C, with the preferential cleavage of GGTACC and GGACC site
      as compared with GGTGCC and GGCGCC. Thus, the restriction endonuclease BbvBI is a true
      isoschizomer of nuclease BanI.
AU  - Sokolov NN
AU  - Eldarov MA
AU  - Anikeitcheva NV
AU  - Karpychev IV
AU  - Samko OT
AU  - Fitzner AB
AU  - Kalugin AA
AU  - Choroshoutina EB
AU  - Skryabin KG
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1992 18: 47-51.

PMID- 1839653
VI  - 17
DP  - 1991
TI  - BcoAI, a new site-specific endonuclease from Bacillus coagulans.
PG  - 1188-1192
AB  - A new site-specific endonuclease was detected in toluene lysates of Bacillus
      coagulans AUCM B-732 and designated as BcoAI.  The enzyme was purified by
      fractionation of the cell-free extract in the two-phase PEG/dextran system
      followed by chromatography on DEAE-sepharose and phosphocellulose and shown to
      be free of nonspecific nucleases and phosphatases.  BcoAI has three cleavage
      sites on lambda DNA, but does not cleave SV40, pBR322 and pUC19 DNA.  BcoAI
      recognizes the sequence 5'CAC^GTG3' on double-stranded DNA and cleaves it as
      indicated by the arrow to yield blunt-ended DNA fragments.  Thus, BcoAI is a
      true isoschizomer of PmaCI from Pseudomonas maltophila C.
AU  - Sokolov NN
AU  - Eldarov MA
AU  - Anikeitcheva NV
AU  - Karpychev IV
AU  - Samko OT
AU  - Fitzner AB
AU  - Kalugin AA
AU  - Choroshoutina EB
AU  - Skryabin KG
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1991 17: 1188-1192.

PMID- 9556203
VI  - 44
DP  - 1998
TI  - Isolation and characterization of CspBI, a novel NotI isoschizomer from Corynebacterium species B recognizing 5'-GC/GGCCGC-3'.
PG  - 433-441
AB  - Sixty-seven bacterial strains were surveyed for the presence of type II restriction
      endonucleases, especially concerning super-rare-cutting enzymes.  Fourteen strains were found
      to contain specific enzymes.  One of them CspBI from Corynebacterium species B was purified
      and characterized as an isoschizomer of NotI, which recognizes the palindromic octanucleotide
      sequence 5'-GC/GGCCGC-3' and cleaves at the position shown by the arrow.  A comparison
      between the cleavage patterns on different DNA's, obtained with partially purified
      endonucleases from other detected producers including some strains of Corynebacterium,
      Cellulomonas, and Rhizobium has shown that these enzymes do not belong to super-rare-cutting
      restriction enodnucleases.
AU  - Sokolov NN
AU  - Eldarov MA
AU  - Rina M
AU  - Korolev SV
AU  - Markaki M
AU  - Kalugin AA
AU  - Omelyanuk NM
AU  - Skryabin KG
AU  - Bouriotis V
PT  - Journal Article
TA  - Biochem. Mol. Biol. Int.
JT  - Biochem. Mol. Biol. Int.
SO  - Biochem. Mol. Biol. Int. 1998 44: 433-441.

PMID- 2993850
VI  - 10
DP  - 1985
TI  - A site-specific endonuclease from Pseudomonas aeruginosa.
PG  - 159-161
AB  - PaeI, a new restriction endonuclease from Pseudomonas aeruginosa clinical
      strain was isolated and chracterized.  It recognizes and cleaves the sequence
      5'-GCATG^C-3' generating DNA fragments with 3'-tetranucleotide sticky ends.
      DNAs of pBR322, SV40 and bacteriophage lambda have one, two and six PaeI
      recognition sites, respectively.Seventy-two strains of Pseudomonas,
      Clostridium, Escherichia coli, Shigella, Proteus and Saccharomyces were
      screened for the presence of site-specific endonucleases.  Here we describe the
      PaeI restriction enzyme found in Pseudomonas aeruginosa; other data will be
      published elsewhere.Earlier Hinkle and Miller isolated from P. aeruginosa a
      PaeR7 restriction endonuclease recognizing and cleaving a sequence
      5'-C^TCGAG-3'.  Sequence analysis of DNAs cleaved by PaeI shows that the enzyme
      is the isoschizomer of SphI.
AU  - Sokolov NN
AU  - Fitsner AB
AU  - Anikeitcheva NV
AU  - Choroshoutina YB
AU  - Samko OT
AU  - Kolosha VO
AU  - Fodor I
AU  - Votrin II
PT  - Journal Article
TA  - Mol. Biol. Rep.
JT  - Mol. Biol. Rep.
SO  - Mol. Biol. Rep. 1985 10: 159-161.

PMID- 3026511
VI  - 102
DP  - 1986
TI  - Effect of thio-specific reagent on Pseudomonas aeruginosa PaeI and PaeII restriction endonuclease activity.
PG  - 695-697
AB  - Because of their unique properties class II restriction endonucleases are
      widely used in research in molecular biology and genetic engineering.  By now
      more than 400 restriction endonucleases have been described, their
      physicochemical and catalytic properties and the structure of many of these
      enzymes have been reasonably well studied and techniques have been developed
      for seeking them in microorganisms and isolating them.  However, there is
      hardly any information in the literature on sulfhydryl groups of restriction
      endonucleases and their role in interaction with the DNA substrate.  The only
      exception is an investigation of the sensitivity of 11 restriction
      endonucleases to the action of alkylating and mercury compounds.
AU  - Sokolov NN
AU  - Fitsner AB
AU  - Anikeitcheva NV
AU  - Khoroshutina EB
AU  - Samko OT
PT  - Journal Article
TA  - Biull. Eksp. Biol. Med.
JT  - Biull. Eksp. Biol. Med.
SO  - Biull. Eksp. Biol. Med. 1986 102: 695-697.

PMID- Not carried by PubMed...
VI  - 3
DP  - 1987
TI  - Pseudomonas aeruginosa restrictases:  Physico-chemical properties, substrate specificity, prospects of application.
PG  - 578-585
AB  - The optimal conditions of the reaction catalyzed by restrictases PaeI and PaeII
      (the optimum of pH, temperature, effects of divalent cations) were studied.
      The activity of restrictase PaeII is dependent on the K+ ions.  The molecular
      mass of restrictases PaeI and PaeII is approximately 150 and 130 kD,
      respectively.  On the base of data on the substrate specificity and the
      structure of the recognition site, it was determined, that restrictases PaeI
      and PaeII are isoschizomers of restrictases SphI and SmaI, correspondingly.
AU  - Sokolov NN
AU  - Fitsner AB
AU  - Anikeitcheva NV
AU  - Samko OT
AU  - Khoroshutina EB
AU  - Kolosha VO
AU  - Fodor II
PT  - Journal Article
TA  - Biotekhnologiya
JT  - Biotekhnologiya
SO  - Biotekhnologiya 1987 3: 578-585.

PMID- 2629242
VI  - 6
DP  - 1989
TI  - Role of bivalent cations in endonucleolysis of DNA catalyzed by restrictases.
PG  - 66-69
AB  - Electrophoretic analysis of products obtained after hydrolysis of phage lambda
      DNA by means of restrictase PaeI was carried out after preincubation of DNA or
      the enzyme with Mg2+ as well as after preincubation of DNA simultaneously with
      the enzyme and the subsequent addition of the required components into the
      experimental samples.  The analysis showed that Mg2+ ions were apparently not
      required for the enzyme-substrate complex formation and caused destabilization
      of the complex.  Restrictase PaeI was active when Mg2+ was substituted by Mn2+,
      Ca2+, Zn2+, Co2+ but not by Cd2+, Cu2+ or Ni2+.  Experiments with
      o-phenanthroline showed that Zn2+ cations are important for the catalytic
      activity of restrictase PaeI.  Possible functions of Zn2+ in protein-nucleic
      acids recognition are discussed.
AU  - Sokolov NN
AU  - Fitsner AB
AU  - Anikeycheva NV
AU  - Kovalenko NA
PT  - Journal Article
TA  - Vopr. Med. Khim.
JT  - Vopr. Med. Khim.
SO  - Vopr. Med. Khim. 1989 6: 66-69.

PMID- 6320927
VI  - 97
DP  - 1984
TI  - Determination of restriction endonuclease activity in Toluene lysates of bacterial cells.
PG  - 163-165
AB  - By now more than 350 restriction endonucleases have been described in the
      literature and they are widely used in molecular biology and in bioengineering
      research.  Selection of strains producing restriction endonucleases with a view
      to finding new and unique restriction enzymes is continuously in progress.  For
      this reason there is an urgent need for quick and reliable ways of determining
      restriction endonuclease activity in bacterial cells.  The method generally
      used to estimate restriction endonuclease activity in bacterial cells involves
      disintegration of the cells with ultrasound followed by high-speed
      centrifugation in order to obtain a cell-free extract.  An essential
      shortcoming of this method is that the extracts contain activity of nonspecific
      endo- and exonucleases, in the presence of whose action it is not always
      possible to reveal specific activity of restriction endonucleases.  For
      instance, according to data in the literature, activity of only three of the 16
      restriction endonucleases studied can be found in unpurified extracts.
AU  - Sokolov NN
AU  - Fitsner AB
AU  - Khoroshutina EB
AU  - Kheislere MY
PT  - Journal Article
TA  - Biull. Eksp. Biol. Med.
JT  - Biull. Eksp. Biol. Med.
SO  - Biull. Eksp. Biol. Med. 1984 97: 163-165.

PMID- 2111602
VI  - 36
DP  - 1990
TI  - Effect of monovalent cations on activity of site-specific endonuclease PaeII.
PG  - 65-67
AB  - The activity of restrictase PaeII, contrary to known Type II restriction
      enzymes (except of true isoschizomer SmaI), depended absolutely on monovalent
      cations.  This pattern is atypical for Type II restrictases.  At the same time,
      restrictase PaeII was able to hydrolyze DNA as a substrate in the absence of
      exogenous Mg2+, if the incubation mixture contained cations K+, Rb+, Cs+ and
      NH4+ but not Na+ or Li+.  Mg2+ was found to activate the enzyme in the presence
      of monovalent cations.  Based on the protective effect of K+ against
      inactivation of restrictase PaeII by means of thiol-affecting reagents and high
      temperature as well as on stabilization of the enzyme by KCl during storage,
      monovalent cations appear to participate in formation of protein molecular
      structure, which is optimal for catalytic effect and resistant to inactivation.
AU  - Sokolov NN
AU  - Fitsner AB
AU  - Samko OT
AU  - Khoroshutina EB
AU  - Kalugin AA
PT  - Journal Article
TA  - Vopr. Med. Khim.
JT  - Vopr. Med. Khim.
SO  - Vopr. Med. Khim. 1990 36: 65-67.

PMID- 1614884
VI  - 20
DP  - 1992
TI  - BavAI, a restriction endonuclease from Bacillus alvei.
PG  - 2897
AB  - A restriction endonuclease BavAI, free of contaminating nuclease activity was isolated from
      Bacillus alvei strain 675 using column chromatography on DEAE cellulose and Blue Sepharose
      CL-6B. Optimal conditions for BavAI digestion were determined at 30C in a buffer containing 10
      mM MgCl2, 30 mM KCl at pH 7.5-8.3. The yield of the enzyme from 10 grams of wet cells was
      22,000 units. The enzyme cleaves lambda phage DNA at 15 sites, Ad-2 DNA at 24 sites and
      plasmid pBR322 DNA at a unique site. The single cleavage site of BavAI on pBR322 DNA was
      mapped by standard double digestion analysis to approximately position 2000. From these data
      we deduced that the restriction enzyme cuts at PvuII sites. This was confirmed by comparing
      patterns of lambda DNA digests obtained with BavAI, PvuII and BavAI + PvuII simultaneously.
AU  - Sokolov NN
AU  - Fitzner AB
AU  - Eldarov MA
AU  - Anikeicheva NB
AU  - Kalugin AA
AU  - Samko OT
AU  - Khoroshoutina EB
AU  - Fodor I
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 2897.

PMID- Not carried by PubMed...
VI  - 12
DP  - 1984
TI  - A systematic method to isolate restriction endonucleases.
PG  - 54-62
AB  - None
AU  - Sokolov NN
AU  - Kheislere MY
AU  - Alexandrova SS
AU  - Zildere AM
AU  - Ansberga SE
PT  - Journal Article
TA  - Izv. Akad. Nauk Latv. SSR
JT  - Izv. Akad. Nauk Latv. SSR
SO  - Izv. Akad. Nauk Latv. SSR 1984 12: 54-62.

PMID- 3025709
VI  - 0
DP  - 1986
TI  - New specific endonucleases PaeI and PaeII from Pseudomonas aeruginosa.
PG  - 24-26
AB  - Specific endonuclease activities have been found in two Pseudomonas aeruginosa
      strains.  Isolation and purification of enzymes and determining their specific
      activities have permitted one to find out that PaeI is an isoshizomer of SphI
      and digests the sequence 5'-GCATG^C-3'.  Another isolated enzyme PaeII is an
      isoschizomer of SmaI and cleaves DNA in a fragment 5'-CCC^GGG-3'.  The use of
      PaeI and PaeII enzymes in genetical engineering and their advantages are
      discussed.
AU  - Sokolov NN
AU  - Kolosha VO
AU  - Fitsner AB
AU  - Anikeitcheva NV
AU  - Khoroshutina EB
AU  - Samko OT
AU  - Fodor I
AU  - Votrin II
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1986 0: 24-26.

PMID- 9611761
VI  - 9
DP  - 1998
TI  - New site-specific endonucleases from Brevibacterium species.
PG  - 35-38
AB  - New site-specific endonucleases BecAI and BecAII have been detected in Brevibacterium species
      A.  Endonuclease BecAII free from contaminating nonspecific endonucleases, exonucleases, and
      phosphatases was isolated by column chromatography on phosphocellulose, heparin sepharose, and
      DNA cellulose.  It recognizes and cleaves the 5'-GG/CC-3' sequence and is a true
      isoschizomer of HaeIII restriction enzyme.  The other restriction endonuclease, BecAI, cleaves
      Ad2 DNA at least by 2 sites but not the DNA of phage lambda, T7, SV40, PhiX174, and plasmids
      pBR322 and pUC19.  The substrate specificity of BecAI indicates its appurtenance to the super
      rare restriction endonucleases.
AU  - Sokolov NN
AU  - Korolev SV
AU  - Rina M
AU  - Eldarov MA
AU  - Gervaziev YV
AU  - Skryabin KG
AU  - Bouriotis V
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1998 9: 35-38.

PMID- 2285421
VI  - 16
DP  - 1990
TI  - Site-specific endonucleases LplI and AagI.
PG  - 1040-1044
AB  - New site-specific endonucleases LplI and AagI have been isolated from the
      Lactobacillus plantarum and Achromobacter agile cells, respectively.  The
      enzymes' purification stages included treatment of cell-free extracts with
      polyethylenimine, fractionation in a two-phase system by Albertsson's method,
      chromatography on blue Sepharose and DEAE-cellulose.  The results of cleavage
      of a 5'-32P-labelled oligodeoxynucleotide duplex by restriction endonucleases
      LplI and AagI indicate that these enzymes recognize and cut the sequence
      AT^CGAT, being therefore true isoschizomers of the ClaI restriction
      endonuclease from Caryophanon latum.  The L. plantarum strain has 400 fold more
      endonuclease production as compared with the ClaI producer and is preferred for
      preparative isolation of LplI.
AU  - Sokolov NN
AU  - Maneliene ZP
AU  - Butkus VV
AU  - Fitzner AB
AU  - Khoroshutina EB
AU  - Kalugin AA
AU  - Janulaitis A
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1990 16: 1040-1044.

PMID- 7695651
VI  - 20
DP  - 1994
TI  - New site-specific endonucleases from Bacillus strains.
PG  - 1334-1341
AB  - In a search for new restriction endonucleases type II, among forty bacterial strains of the
      Bacillus genus two strains producing site-specific endonucleases have been found.
      Endonucleases BbvAIII and BspFI, isolated from B. brevis BLM B-677 and B. species F, are shown
      to be true isoschizomers of BspMII (Kpn2I) and Sau3AI, respectively.
AU  - Sokolov NN
AU  - Samko OT
AU  - Anikeitcheva NV
AU  - Kalugin AA
AU  - Khoroshutina EB
AU  - Plutalov OV
AU  - Birikh KR
AU  - Berlin YA
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1994 20: 1334-1341.

PMID- 95843
VI  - 15
DP  - 1979
TI  - Restriction endonucleases as an instrument in comparative biochemical studies.
PG  - 8-21
AB  - 
AU  - Sokolov NN
AU  - Votrin II
PT  - Journal Article
TA  - Zh. Evol. Biokhim. Fiziol.
JT  - Zh. Evol. Biokhim. Fiziol.
SO  - Zh. Evol. Biokhim. Fiziol. 1979 15: 8-21.

PMID- 656508
VI  - 43
DP  - 1978
TI  - Isolation and certain properties of restriction endonuclease from Bacillus amyloliquefaciens.
PG  - 865-871
AB  - A partially purified preparation of the restriction endonuclease BamHI was
      isolated from cells of Bacillus amyloliquefaciens.  The proposed method of
      purification of restriction enzyme BamHI is a modification of the method
      described by Wilson and Young.  Decomposition of the cells with ultrasound,
      treatment with streptomycin sulfate, fractionation with ammonium sulfate,
      chromatography on DEAE-cellulose and hydroxyapatite, and rechromatography on
      DEAE-cellulose were used for the isolation and purification of the enzyme.  The
      restriction enzyme BamHI splits the linear double-stranded DNA molecule of
      phage lambda into six fragments.  The enzyme is stable to storage in ice in
      sodium or potassium phosphate buffer with beta-mercaptoethanol (10 mM) for
      1.5-2 months.
AU  - Sokolov NN
AU  - Votrin II
AU  - Fitsner AB
AU  - Anikeitcheva NV
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1978 43: 865-871.

PMID- 19380375
VI  - 37
DP  - 2009
TI  - Crystal structure of the {beta}{beta}{alpha}-Me type II restriction endonuclease Hpy99I with target DNA.
PG  - 3799-3810
AB  - The betabetaalpha-Me restriction endonuclease (REase) Hpy99I recognizes the CGWCG target
      sequence and cleaves it with unusual stagger (five
      nucleotide 5'-recessed ends). Here we present the crystal structure of the
      specific complex of the dimeric enzyme with DNA. The Hpy99I protomer
      consists of an antiparallel beta-barrel and two beta4alpha2 repeats. Each
      repeat coordinates a structural zinc ion with four cysteine thiolates in
      two CXXC motifs. The betabetaalpha-Me region of the second beta4alpha2
      repeat holds the catalytic metal ion (or its sodium surrogate) via Asp148
      and Asn165 and activates a water molecule with the general base His149. In
      the specific complex, Hpy99I forms a ring-like structure around the DNA
      that contacts DNA bases on the major and minor groove sides via the first
      and second beta4alpha2 repeats, respectively. Hpy99I interacts with the
      central base pair of the recognition sequence only on the minor groove
      side, where A:T resembles T:A and G:C is similar to C:G. The Hpy99I-DNA
      co-crystal structure provides the first detailed illustration of the
      betabetaalpha-Me site in REases and complements structural information on
      the use of this active site motif in other groups of endonucleases such as
      homing endonucleases (e.g. I-PpoI) and Holliday junction resolvases (e.g.
      T4 endonuclease VII).
AU  - Sokolowska M
AU  - Czapinska H
AU  - Bochtler M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: 3799-3810.

PMID- 20935048
VI  - 39
DP  - 2011
TI  - Hpy188I-DNA pre- and post-cleavage complexes--snapshots of the GIY-YIG nuclease mediated catalysis.
PG  - 1554-1564
AB  - The GIY-YIG nuclease domain is present in all kingdoms of life and has diverse functions. It
      is found in the eukaryotic flap endonuclease and
      Holliday junction resolvase Slx1-Slx4, the prokaryotic nucleotide excision
      repair proteins UvrC and Cho, and in proteins of 'selfish' genetic
      elements. Here we present the structures of the ternary pre- and
      post-cleavage complexes of the type II GIY-YIG restriction endonuclease
      Hpy188I with DNA and a surrogate or catalytic metal ion, respectively. Our
      structures suggest that GIY-YIG nucleases catalyze DNA hydrolysis by a
      single substitution reaction. They are consistent with a previous proposal
      that a tyrosine residue (which we expect to occur in its phenolate form)
      acts as a general base for the attacking water molecule. In contrast to
      the earlier proposal, our data identify the general base with the GIY and
      not the YIG tyrosine. A conserved glutamate residue (Glu149 provided in
      trans in Hpy188I) anchors a single metal cation in the active site. This
      metal ion contacts the phosphate proS oxygen atom and the leaving group
      3'-oxygen atom, presumably to facilitate its departure. Taken together,
      our data reveal striking analogy in the absence of homology between
      GIY-YIG and betabetaalpha-Me nucleases.
AU  - Sokolowska M
AU  - Czapinska H
AU  - Bochtler M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2011 39: 1554-1564.

PMID- 17445830
VI  - 369
DP  - 2007
TI  - Monomeric Restriction Endonuclease BcnI in the Apo Form and in an Asymmetric Complex with Target DNA.
PG  - 722-734
AB  - Restriction endonuclease BcnI cleaves duplex DNA containing the sequence CC/SGG (S stands for
      C or G, / designates a cleavage position) to generate
      staggered products with single nucleotide 5'-overhangs. Here, we show that
      BcnI functions as a monomer that interacts with its target DNA in 1:1
      molar ratio and report crystal structures of BcnI in the absence and in
      the presence of DNA. In the complex with DNA, BcnI makes specific contacts
      with all five bases of the target sequence and not just with a half-site,
      as the protomer of a typical dimeric restriction endonuclease. Our data
      are inconsistent with BcnI dimerization and suggest that the enzyme
      introduces double-strand breaks by sequentially nicking individual DNA
      strands, although this remains to be confirmed by kinetic experiments.
      BcnI is remotely similar to the DNA repair protein MutH and shares
      approximately 20% sequence identity with the restriction endonuclease
      MvaI, which is specific for the related sequence CC/WGG (W stands for A or
      T). As expected, BcnI is structurally similar to MvaI and recognizes
      conserved bases in the target sequence similarly but not identically. BcnI
      has a unique machinery for the recognition of the central base-pair.
AU  - Sokolowska M
AU  - Kaus-Drobek M
AU  - Czapinska H
AU  - Tamulaitis G
AU  - Szczepanowski RH
AU  - Urbanke C
AU  - Siksnys V
AU  - Bochtler M
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2007 369: 722-734.

PMID- 17568994
VI  - 64
DP  - 2007
TI  - Restriction endonucleases that resemble a component of the bacterial DNA repair machinery.
PG  - 2351-2357
AB  - It has long been known that most Type II restriction endonucleases share a conserved core fold
      and similar active-sites. The same core folding motif is also present in the MutH protein, a
      component of the bacterial DNA mismatch repair machinery. In contrast to most Type II
      restriction endonucleases, which assemble into functional dimers and catalyze double-strand
      breaks, MutH is a monomer and nicks hemimethylated DNA. Recent biochemical and
      crystallographic studies demonstrate that the restriction enzymes BcnI and MvaI share many
      additional features with MutH-like proteins, but not with most other restriction
      endonucleases. The structurally similar monomers all recognize approximately symmetric target
      sequences asymmetrically. Differential sensitivities to slight substrate asymmetries, which
      could be altered by protein engineering, determine whether the enzymes catalyze only
      single-strand nicks or double-strand breaks.
AU  - Sokolowska M
AU  - Kaus-Drobeka M
AU  - Czapinska H
AU  - Tamulaitis G
AU  - Siksnys V
AU  - Bochtler M
PT  - Journal Article
TA  - Cell. Mol. Life Sci.
JT  - Cell. Mol. Life Sci.
SO  - Cell. Mol. Life Sci. 2007 64: 2351-2357.

PMID- 2323549
VI  - 67
DP  - 1990
TI  - Isolation and characterization of a type II restriction endonuclease from Streptococcus thermophilus.
PG  - 261-266
AB  - A type II restriction endonuclease Sth134I was isolated from Streptococcus
      thermophilus strain 134.  The enzyme is an isoschizomer of HpaII. The
      restriction endonuclease is most active at Mg(II) >5 mM; in the pH range of
      7.5-8; temperature of 50-55C; and (KCl) or (NaCl) below 100 mM.  Double
      digestion and ligation experiments experiments showed that Sth134I apparently
      recognized and cleaves DNA at the sequence CCGG to produce two-base,
      5'-protruding ends.
AU  - Solaiman DKY
AU  - Somkuti GA
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1990 67: 261-266.

PMID- Not included in PubMed...
VI  - 80
DP  - 1991
TI  - A type II restriction endonuclease of Streptococcus thermophilus ST117.
PG  - 75-80
AB  - Streptococcus thermophilus strain 117 produces a type II restriction
      endonuclease designated as Sth117I.  This enzyme was isolated from cell
      extracts by membrane filtration and ammonium sulfate fractionation.  Anion
      exchange chromatography on DE52 yielded an enzyme preparation free of
      nonspecific nucleases.  The optimal reaction conditions for Sth117I are: (1)
      [MgCl2] > 5 mM; (2) pH range of 6.5-7; (3) incubation temperature between 37
      and 50C; and (4) [NaCl] or [KCl] < 50 mM.  The results of single- and
      double-digestion experiments indicated that the Sth117I was an isoschizomer of
      BstNI and EcoRII with the recognition sequence of 5'-CCWGG-3'.  The cleavage
      site of Sth117I was identified as 5'-CC^WGG-3' by 5'-end analysis.  This was
      supported by the results of ligation experiments with Sth117I-restricted DNAs
      and the BstNI- or EcoRII-generated fragments.
AU  - Solaiman DKY
AU  - Somkuti GA
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1991 80: 75-80.

PMID- 11991637
VI  - 8
DP  - 2002
TI  - A novel mechanism for protein-assisted group I intron splicing.
PG  - 412-425
AB  - Previously it was shown that the Aspergillus nidulans (A.n.) mitochondrial COB intron
      maturase, I-AniI, facilitates splicing of the
      COB intron in vitro. In this study, we apply kinetic analysis of
      binding and splicing along with RNA deletion analysis to gain insight
      into the mechanism of I-AniI facilitated splicing. Our results are
      consistent with I-AniI and A.n. COB pre-RNA forming a specific but
      labile encounter complex that is resolved into the native,
      splicing-competent complex. Significantly, kinetic analysis of splicing
      shows that the resolution step is rate limiting for splicing. RNA
      deletion studies show that I-Anil requires most of the A.n. COB intron
      for binding suggesting that the integrity of the I-AniI-binding site
      depends on overall RNA tertiary structure. These results, taken
      together with the observation that A.n. COB intron lacks significant
      stable tertiary structure in the absence of protein, support a model in
      which I-AniI preassociates with an unfolded COB intron via a "labile"
      interaction that facilitates correct folding of the intron catalytic
      core, perhaps by resolving misfolded RNAs or narrowing the number of
      conformations sampled by the intron during its search for native
      structure. The active intron conformation is then "locked in" by
      specific binding of I-AniI to its intron interaction site.
AU  - Solem A
AU  - Chatterjee P
AU  - Caprara MG
PT  - Journal Article
TA  - RNA
JT  - RNA
SO  - RNA 2002 8: 412-425.

PMID- 18350140
VI  - 3
DP  - 2008
TI  - Klebsiella pneumoniae multiresistance plasmid pMET1: similarity with the Yersinia pestis plasmid pCRY and integrative conjugative elements.
PG  - E1800
AB  - BACKGROUND: Dissemination of antimicrobial resistance genes has become an important public
      health and biodefense threat. Plasmids are important contributors to the rapid acquisition of
      antibiotic resistance by pathogenic bacteria. PRINCIPAL FINDINGS: The nucleotide sequence of
      the Klebsiella pneumoniae multiresistance plasmid pMET1 comprises 41,723 bp and includes
      Tn1331.2, a transposon that carries the bla(TEM-1) gene and a perfect duplication of a 3-kbp
      region including the aac(6')-Ib, aadA1, and bla(OXA-9) genes. The replication region of pMET1
      has been identified. Replication is independent of DNA polymerase I, and the replication
      region is highly related to that of the cryptic Yersinia pestis 91001 plasmid pCRY. The
      potential partition region has the general organization known as the parFG locus. The
      self-transmissible pMET1 plasmid includes a type IV secretion system consisting of proteins
      that make up the mating pair formation complex (Mpf) and the DNA transfer (Dtr) system. The
      Mpf is highly related to those in the plasmid pCRY, the mobilizable high-pathogenicity island
      from E. coli ECOR31 (HPI(ECOR31)), which has been proposed to be an integrative conjugative
      element (ICE) progenitor of high-pathogenicity islands in other Enterobacteriaceae including
      Yersinia species, and ICE(Kp1), an ICE found in a K. pneumoniae strain causing primary liver
      abscess. The Dtr MobB and MobC proteins are highly related to those of pCRY, but the
      endonuclease is related to that of plasmid pK245 and has no significant homology with the
      protein of similar function in pCRY. The region upstream of mobB includes the putative oriT
      and shares 90% identity with the same region in the HPI(ECOR31). CONCLUSIONS: The comparative
      analyses of pMET1 with pCRY, HPI(ECOR31), and ICE(Kp1 )show a very active rate of genetic
      exchanges between Enterobacteriaceae including Yersinia species, which represents a high
      public health and biodefense threat due to transfer of multiple resistance genes to pathogenic
      Yersinia strains.
AU  - Soler-Bistue AJ
AU  - Birshan D
AU  - Tomaras AP
AU  - Dandekar M
AU  - Tran T
AU  - Newmark J
AU  - Bui D
AU  - Gupta N
AU  - Hernandez K
AU  - Sarno R
AU  - Zorreguieta A
AU  - Actis LA
AU  - Tolmasky ME
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2008 3: E1800.

PMID- 16896525
VI  - 10
DP  - 2006
TI  - Characterisation of the novel restriction endonuclease SuiI from Sulfolobus islandicus.
PG  - 629-634
AB  - A restriction endonuclease activity from Sulfolobus islandicus REN2H1 was purified by
      phosphocellulose and cation exchange chromatography.
      The enzyme cuts DNA at the recognition site GCwGC as could be shown by
      restriction analysis of plasmids and short synthetic duplex DNA. The
      cleavage occurs after the first guanosine base and is inhibited by
      5-methylcytosine methylation. The restriction activity is
      salt-sensitive and has an optimal activity around 70 degrees C.
AU  - Sollner S
AU  - Berkner S
AU  - Lipps G
PT  - Journal Article
TA  - Extremophiles
JT  - Extremophiles
SO  - Extremophiles 2006 10: 629-634.

PMID- 2227395
VI  - 26
DP  - 1990
TI  - Cloning of genes for restriction-modification system Sfl2aI from Shigella flexneri 2a.
PG  - 1126-1128
AB  - The Sfl2aI system of restriction-modification (RM) was revealed in the cells of
      Shigella flexneri encoded by pKMR114 plasmid belonging to the IncN
      incompatibility group.  The genes for the Sf12aI RM system were cloned.  The
      system was ascribed to the enzymes of the EcoRII specificity, as shown by in
      vivo and in vitro experiments.  Restriction analysis of these genes' region and
      antigenic properties of the Sfl2aI endonuclease pointed to significant
      differences between this and the EcoRII RM system.
AU  - Solodukhina LI
AU  - Korotayev AI
AU  - Solonin AS
AU  - Kuzmin NP
PT  - Journal Article
TA  - Genetika
JT  - Genetika
SO  - Genetika 1990 26: 1126-1128.

PMID- 2599373
VI  - 25
DP  - 1989
TI  - Type II restriction-modification systems from Shigella strains.
PG  - 1571-1577
AB  - Two restriction-modification systems specified by two plasmids have been
      discovered in clinical species of Shigella.  The plasmids are designated
      pKMR114 and pKMR115.  Both are of 60800 bp and belong to the IncN
      incompatibility group.  The EcoRI, EcoRV, HindIII restriction patterns of both
      plasmid DNAs are identical.  As shown by the efficiency of plating of
      bacteriophage lambdavir on the strains harbouring plasmids encoding EcoRI,
      EcoRII, EcoRIII, EcoRIV, EcoRV systems and plasmids studied, the new plasmids
      control synthesis of enzymes with the specificity of EcoRII.  The main
      distinctive feature of pKMR114 is the ability to decrease the efficiency of
      plating of bacteriophage T4 having glycosylated DNA.
AU  - Solodukhina LI
AU  - Manuvakhova MS
AU  - Korotayev AI
PT  - Journal Article
TA  - Genetika
JT  - Genetika
SO  - Genetika 1989 25: 1571-1577.

PMID- 713886
VI  - 47
DP  - 1978
TI  - On the phenomenon of restriction and modification of temperate phages for the lysogenic Streptomyces hygroscopicus culture.
PG  - 956-959
AB  - Temperate phages were isolated from the lysogenic culture of Streptomyces hygroscopicus 0485
      in the indicator cultures of S. hygroscopicus 0477 and S. levoris 1331.  The phages were found
      to be identical in the morphology of particles and serological properties.  The phenomenon of
      cross limitation, by the culture of S. hygroscopicus 0477, of the phage growing on the culture
      of S. levoris 1331, and vice versa, was established.  At the same time, the phages were shown
      to be modified by the host cell.
AU  - Solovyeva NY
AU  - Rautenstein YI
PT  - Journal Article
TA  - Mikrobiologiia
JT  - Mikrobiologiia
SO  - Mikrobiologiia 1978 47: 956-959.

PMID- 7402131
VI  - 49
DP  - 1980
TI  - On the restriction and modification of actinophages by the cultures of Streptomyces hygroscopicus and Streptomyces levoris.
PG  - 512-515
AB  - The capability for restriction and modification was studied in the cultures of Streptomyces
      hygroscopicus 0477 and Streptomyces levoris 1331, 2340, 2144 toward the active against them
      temperate phages and three polyphages.  All these cultures were found to be capable of the
      restriction and modification of the temperate phage.  Certain differences in restriction and
      modification were established between S. levoris 1331 and the two other cultures of this
      species.  The culture 1331 could modify the temperate phage only with respect to itself rather
      than the two other cultures.  The phage growing on culture 1331 was restricted not only by
      culture 0477, but also by the strains of S. levoris 2340 and 2144.  At the same time, the
      phage growing on the strains 2340 and 2144 gave the identical effectiveness of inoculation on
      any of these cultures, as well as on the culture 1331, and was restricted to the same degree
      by the culture 0477.  One of the examined polyphages 14/3 was not restricted by any of the
      tested cultures. Two other polyphages SH4 and p4 were restricted only by the culture 2144.
      However, the modification by this culture was not observed.  Among the studied cultures of S.
      levoris, the culture 2144 was most capable of the restriction.
AU  - Solovyeva NY
AU  - Rautenstein YI
PT  - Journal Article
TA  - Mikrobiologiia
JT  - Mikrobiologiia
SO  - Mikrobiologiia 1980 49: 512-515.

PMID- 11136134
VI  - 42
DP  - 2001
TI  - Molecular properties of Streptococcus thermophilus plasmid pER35 encoding a restriction modification system.
PG  - 122-128
AB  - Bacteriophage attack on lactic fermentation bacteria (LFB) is costly to the dairy industry
      because it results in product loss. One mechanism
      used by LFB to protect themselves from bacteriophage attack is
      restriction of foreign DNA. Three plasmids, pER16, pER35, and pER36,
      from three different strains of the thermotolerant dairy fermentation
      bacterium Streptococcus thermophilus were sequenced. One of these
      plasmids, pER35, isolated from S. thermophilus ST135, encoded a type IC
      restriction-modification (R-M) system very similar to those encoded on
      plasmids pIL2614 in Lactococcus lactis subsp. lactis and pND861 in
      Lactococcus lactis biovar diacetylactis. The high degree of identity
      between the R-M systems encoded on pER35, pIL2614, and pND861 indicated
      the potential for horizontal transfer of these genes between different
      species of lactic fermentation bacteria. Similar to the functional R-M
      system encoded on pIL2614 that protects the mesophilic L. lactis subsp.
      lactis against phage attack, the R-M system on pER35 most likely
      functions in the same role in S. thermophilus ST135. The plasmid pER16
      was found to encode the specificity subunit of the R-M system, but not
      the R or M subunits. In addition, all three plasmids encoded proteins
      that are present on other S. thermophilus plasmids, including a protein
      for rolling-circle replication (RepA) and a low-molecular-weight stress
      protein (Hsp). The presence of a complete R-M system encoded on a
      plasmid in S. thermophilus, a species that often lacks plasmids, is
      novel and may be beneficial for protecting S. thermophilus from
      bacteriophage attack under dairy fermentation conditions.
AU  - Solow BT
AU  - Somkuti GA
PT  - Journal Article
TA  - Curr. Microbiol.
JT  - Curr. Microbiol.
SO  - Curr. Microbiol. 2001 42: 122-128.

PMID- 29599162
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Escherichia coli KL53.
PG  - e00220-18
AB  - Here, we report the draft genome sequence of a clinical isolate of the
      uropathogenic strain Escherichia coli KL53. A total of 5,083,632 bp was de novo
      assembled into 170 contigs containing 89 RNAs and 5,034 protein-coding genes.
      Remarkable is the presence of the tellurite resistance (ter) operon on a plasmid.
AU  - Soltys K
AU  - Vavrova S
AU  - Budis J
AU  - Palkova L
AU  - Minarik G
AU  - Grones J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00220-18.

PMID- 3029675
VI  - 15
DP  - 1987
TI  - Nucleotide sequence and expression of the gene encoding the EcoRII modification enzyme.
PG  - 313-332
AB  - The gene coding for the EcoRII modification enzyme has been cloned and the
      nucleotide sequence of 1933 base pairs containing the gene has been determined.
      The gene codes for a protein of 477 amino acids.  Two transcriptional start
      sites have been mapped by S1 mapping.  One deletion that removes 34 N-terminal
      amino acids was found to have partial enzyme activity.  Comparison of the
      EcoRII methylase sequence with other cytosine methylases revealed several
      domains of partial homology among all cytosine methylases.  Cloning the gene in
      multicopy pUC vectors increased the expression by 6-18 fold.  A 40 fold
      overproduction of the EcoRII methylase was obtained by cloning the gene in the
      expression vector carrying the lambda PL promoter.
AU  - Som S
AU  - Bhagwat AS
AU  - Friedman S
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1987 15: 313-332.

PMID- 9006057
VI  - 179
DP  - 1997
TI  - Characterization of the intergenic region which regulates the MspI restriction-modification system.
PG  - 964-967
AB  - The 110-bp intergenic region between mspIM and mspIR, the genes encoding the MspI modification
      (M.MspI) and restriction (R.MspI) enzymes, respectively, was fused, in both orientations, with
      lacZ.  Expression of a single-copy mspIM-lacZ fusion is more than 400-fold stronger than
      expression of an mspIR-lacZ fusion.  M.MspI in trans represses expression of the mspIM-lacZ
      fusion by binding to the DNA but does not affect expression of the mspIRlacZ fusion.
      Transcription start sites of the genes were identified, and a set of nonoverlapping promoters
      was assigned.  DNase I footprinting showed that M.MspI binds to a site within the intergenic
      region that includes only the mspIM regulatory elements.
AU  - Som S
AU  - Friedman S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1997 179: 964-967.

PMID- 7523398
VI  - 269
DP  - 1994
TI  - Inhibition of transcription in vitro by binding of DNA(cytosine-5)-methylases to DNA templates containing cytosine analogs.
PG  - 25986-25991
AB  - DNA(cytosine-5)-methylases form tight complexes at their methylation sites when the target
      cytosine residue is substituted by analogs such as 5-azacytosine or 5-fluorocytosine. To test
      whether such complexes can block RNA transcription in vitro, template DNA-containing
      methylation sites were prepared, in which cytosine residues in either the (+)- or (-)-strand
      were substituted by the analogs. Such templates, irrespective of the strand in which
      substitution was made, could effectively block the elongation of RNA at specific sites when
      complexed with EcoRII methylase. The protein-DNA complex probably prevents the unwinding of
      the template strands or might directly present itself as a steric block to the advancing RNA
      polymerase. RNA synthesis was also inhibited at specific sites due to complex formation
      between azacytosine-containing DNA and two other methylases, HhaI and HpaII. The 3' ends of
      the interrupted transcripts were mapped and were found to lie within 13-14, 13, and 23
      nucleotides of the binding sites on the (-)-strand for HhaI, HpaII, and EcoRII methylases,
      respectively. Exonuclease III footprinting revealed that the boundaries of the complexed
      methylases, HhaI, HpaII, and EcoRII, on the (-)-strand were within 2-3, 1-2, and 9-10
      nucleotides, respectively, of the last nucleotide copied by the RNA polymerase.
AU  - Som S
AU  - Friedman S
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1994 269: 25986-25991.

PMID- 7693455
VI  - 12
DP  - 1993
TI  - Autogenous regulation of the EcoRII methylase gene at the transcriptional level: effect of 5-azacytidine.
PG  - 4297-4303
AB  - mRNA of the EcoRII methylase (M.EcoRII), a type II modification enzyme, was induced when
      Escherichia coli carrying a cloned M.EcoRII gene was exposed to the bacteriocidal drug
      5-azacytidine. Induction occurred only when transcription was initiated from its own promoter.
      When the 5' promoter sequences were deleted or replaced with the lac promoter sequences, no
      induction occurred. The induction was independent of the template DNA level, but the presence
      of an intact M.EcoRII protein was a requirement. The drug is incorporated into DNA which then
      inhibits M.EcoRII by binding tightly to the enzyme. A deletion within the M.EcoRII coding
      region caused a marked increase in the basal level of mRNA transcribed from the M.EcoRII
      promoter, but no induction occurred upon 5-azacytidine treatment. The level could be reduced
      to normal by M.EcoRII in trans. In vitro, the enzyme bound to the sequence upstream of the
      transcription start sites and inhibited the initiation of transcription. These experiments
      indicate that expression of the M.EcoRII gene was autogenously regulated at the
      transcriptional level. Similar regulation is also noted in another DNA (cytosine-5) methylase,
      M.MspI.
AU  - Som S
AU  - Friedman S
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1993 12: 4297-4303.

PMID- 7816624
VI  - 22
DP  - 1994
TI  - Regulation of EcoRII methyltransferase: effect of mutations on gene expression and in vitro binding to the promoter region.
PG  - 5347-5353
AB  - EcoRII methyltransferase (M.EcoRII) which methylates the second C in the sequence CCWGG
      (W=A/T) is autogenously regulated by binding to the 5' regulatory region of its gene. DNase I
      footprinting experiments demonstrated that purified M.EcoRII protected a 47-49 bp region of
      DNA immediately upstream of the ecoRIIM coding region. We have studied this interaction with
      mutants of the enzyme, in vitro by DNA binding and in vivo by investigating the repression in
      trans of expression of beta-galactosidase from an ecoRIIM-lacZ operon fusion. Two
      catalytically active mutants failed to repress expression of the fusion whereas catalytically
      inactive mutants had repressor activity. However, with one of the catalytically inactive
      mutants, C186S, in which the catalytic Cys was replaced with Ser, and which bound unmethylated
      CCWGG sequences, repression could only be demonstrated when those sequences in cellular DNA
      were methylated by supplying a cloned dcm gene in trans. In vitro binding of the DNA fragment
      containing the ecoRIIIM regulatory region was detected only with the mutants that showed
      repressor activity, including C186S. Results indicate that down-regulation of the gene in vivo
      and binding to the promoter in vitro are not dependent on the catalytic properties of
      M.EcoRII. Mobility shift experiments with C186S also revealed that it could bind either the
      promoter or unmethylated CCWGG sites, but not both. We conclude that the concentration of
      unmethylated CCWGG sites controls expression from the ecoRIIM promoter.
AU  - Som S
AU  - Friedman S
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1994 22: 5347-5353.

PMID- 3350238
VI  - 2
DP  - 1988
TI  - Photolabeling of the EcoRII DNA methylase with S-adenosyl-L-methionine.
PG  - A567
AB  - Ultraviolet irradiation of EcoRII methylase enzyme in the presence of its
      substrate, S-adenosyl-L-methionine (SAM), results in the formation of a stable
      enzyme-substrate adduct.  Although the extent of photolabeling is low (1-2%),
      it is specific for the enzyme.  Heat inactivated enzyme or proteins for which
      SAM is not a substrate undergo negligible adduct formation upon uv irradiation.
      Formation of the enzyme-substrate adduct can be demonstrated by
      SDS-polyacrylamide gel electrophoresis after irradiation of the enzyme in the
      presence of either [3H]-methyl or [35S] labeled SAM.  At a concentration of 30
      micrograms the SAM analogues S-adenosyl-L-homocysteine (Ki=0.83 micrograms) and
      sinefungin (Ki=4.3 micrograms) are effective inhibitors of photolabeling
      whereas S-adenosyl-D-homocysteine (Ki=46 micrograms) is a poor inhibitor.
      These experiments indicate that SAM becomes covalently bound at the catalytic
      SAM binding site.  Studies in which the SAM-photolabeled methylase has been
      chemically cleaved at selective sites indicate that binding occurs at a
      localized region of the protein.
AU  - Som S
AU  - Friedman S
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1988 2: A567.

PMID- 2323503
VI  - 4
DP  - 1990
TI  - Identification of a highly conserved domain in the EcoRII DNA methylase that can be photolabeled with S-adenosylmethionine.
PG  - A1839
AB  - DNA methyltransferases can be specifically labeled with either [3H]-methyl or
      [35S] S-adenosylmethionine (AdoMet) upon uv irradiation (Som and Friedman, J.
      Biol. Chem., 1990, in press).  The labeling is believed to occur at the AdoMet
      binding site.  With the purpose of localizing the AdoMet binding site of one
      such enzyme, the EcoRII methylase (EcoRIIM), we cleaved [3H]-AdoMet labeled
      EcoRIIM by chemical and enzyme-catalyzed reactions and isolated the
      radiolabeled peptides by SDS-PAGE and by HPLC.  Amino-terminal sequencing of
      all such fragments localized a common region where 75-80% of labeling occurred.
      This region includes a highly conserved core sequence present in all the
      cytosine methylases.  One such fragment was further digested with chymotrypsin
      and the amino acid analysis of the resulting radioactive peptide was consistent
      with the sequence AGFP(C)QPFSL.  However, the cysteine residue could not be
      identified as carboxymethylcysteine.  This PC bond was found to be completely
      protected from a cleavage reaction that specifically cleaves the peptide bond
      N-terminal to a cysteine residue.  These results suggest that the cysteine
      residue is modified by the labeling reaction and is probably located at or
      close to the AdoMet binding site.
AU  - Som S
AU  - Friedman S
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1990 4: A1839.

PMID- 1993667
VI  - 266
DP  - 1991
TI  - Identification of a highly conserved domain in the EcoRII methyltransferase which can be photolabeled with S-adenosyl-L-[methyl-3H] methionine.
PG  - 2937-2945
AB  - DNA methyltransferases can be photolabeled with S-adenosyl-L-methionine
      (AdoMet).  Specific incorporation of radioactivity has been demonstrated after
      photolabeling with either [methyl-3H]AdoMet or [35S]AdoMet (Som, S., and
      Friedman, S. (1990) J. Biol. Chem. 265, 4278-4283).  The labeling is believed
      to occur at the AdoMet binding site.  With the purpose of localizing the site
      responsible for [methyl-3H]AdoMet photolabeling, we cleaved the labeled EcoRII
      methyltransferase by chemical and enzymatic reactions and isolated the
      radiolabeled peptides by sodium dodecylsulfate-polyacrylamide gel
      electrophoresis and high pressure liquid chromatography.  The labeled peptides
      were identified by amino-terminal sequencing.  A common region was localized
      which accounted for 65-70% of the total label.  This region includes a highly
      conserved core sequence present in all DNA (cytosine 5)-methyltransferases.
      One such fragment was digested further with chymotrypsin, and amino acid
      analysis of the resulting 3H-labeled peptide was consistent with the sequence
      Ala-Gly-Phe-Pro-(Cys)-Gln-Pro-Phe-Ser-Leu.  However, the cysteine residue was
      not recovered as carboxymethylcysteine.  The Pro-Cys bond was found to be
      protected from cleavage at cysteine residues after cyanylation.  These results
      suggest that the cysteine residue is modified by the labeling reaction.  The
      chymotryptic fragment was hydrolyzed enzymatically to single amino acids, and
      the labeled amino acid was identified as S-methylcytsteine by thin layer
      chromatography.  These results indicate that the cysteine residue is located at
      or close to the AdoMet binding site of EcoRII methyltransferase.
AU  - Som S
AU  - Friedman S
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1991 266: 2937-2945.

PMID- 2407734
VI  - 265
DP  - 1990
TI  - Direct photolabeling of the EcoRII methyltransferase with S-Adenosyl-L-methionine.
PG  - 4278-4283
AB  - Ultraviolet irradiation of EcoRII methyltransferase in the presence of its substrate,
      S-adenosyl-L-methionine (AdoMet), results in the formation of a stable enzyme-substrate
      adduct. This adduct can be demonstrated by sodium dodecyl sulfate-polyacrylamide gel
      electrophoresis after irradiation of the enzyme in the presence of either [methyl-3H]AdoMet or
      [35S]AdoMet. The extent of photolabeling is low. Under optimal conditions 4.5 pmol of
      [3H]AdoMet is incorporated into 100 pmol of enzyme. Use of the 8-azido derivative of AdoMet as
      the photolabeling substrate increases the incorporation by approximately 2-fold. However, this
      adduct, unlike the one formed with AdoMet, is not stable when treated with thiol reagents or
      precipitated with trichloracetic acid. A catalytically active conformation of the enzyme is
      needed for AdoMet photolabeling. Heat-inactivated enzyme or proteins for which AdoMet is not a
      substrate or cofactor do not undergo adduct formation. Two other methyltransferases, MspI and
      dam methylases are also shown to form adducts with AdoMet upon UV irradiation. The binding
      constant of the EcoRII methyltransferase for AdoMet determined with the photolabeling reaction
      is 11 microM, which is similar to the binding constant of 9 microM previously reported
      (Freidman, S. (1986) Nucleic Acids Res. 14, 4543-4556). The AdoMet analogs
      S-adenosyl-L-homocysteine (Ki=0.83 microM) and sinefungin (Ki=4.3 microM) are effective
      inhibitors of photolabeling, whereas S-adenosyl-D-homocysteine (Ki=46 microM) is a poor
      inhibitor. These experiments indicate that AdoMet becomes covalently bound at the
      AdoMet-binding site on the enzyme molecule. The EcoRII methyltransferase-AdoMet adduct is very
      stable and could be used to identify the AdoMet-binding site on DNA methyltransferases.
AU  - Som S
AU  - Friedman S
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1990 265: 4278-4283.

PMID- Not carried by PubMed...
VI  - 91
DP  - 1991
TI  - Insertion and deletion mutants in the presumed target recognition domain of the EcoRII DNA methylase.
PG  - A436
AB  - In order to understand the function of various core domains of
      DNA(cytosine-5)-methyltransferases (Mtases) and to locate the target
      recognition domain (TRD), we prepared insertion and deletion mutants of the
      EcoRII methylase.  Insertion of 4 amino acids between residues 107-108, 117-118
      and 186-187 resulted in total loss of catalytic activity.  These insertion are
      either within or near the motifs conserved in all Mtases.  Ten other mutants
      with insertions placed in variable regions of the methylase retained activity.
      In an attempt to prepare mutants with random internal deletions within the
      variable region (residues 295-407) believed to contain the TRD, we randomly
      fused N- and C-terminal segments deleted for part or all of the variable
      region.  Two catalytically active mutants have a deletion of 5 to 7 amino
      acids.  Forty-five active isolates were found to have duplications ranging from
      a few to more than 100 amino acids.  The duplications occurred within the
      entire 400 bp region.  These results indicate that unlike the N-terminal
      variable region which can be deleted with retention of enzyme activity, this
      internal region, although variable in length in different Mtases, cannot accept
      large deletions with retention of activity.
AU  - Som S
AU  - Yang LF
AU  - Friedman S
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1991 91: A436.

PMID- 374993
VI  - 168
DP  - 1979
TI  - Nucleotide sequence of the recognition site of the B-specific restriction modification system in E. coli.
PG  - 331-335
AB  - Two sB mutations in the genome of bacteriophage fd were located by sequence analysis in the fd
      sequence at positions 971 and 6341.  Base changes at or close to these positions in phage M13
      and in phage f1 am 124 also correlate with a loss of sensitivity to B restriction.  From the
      sequence homology between the sequences at the two sB sites the recognition signal for the E.
      coli B restriction/modification enzyme is predicted to be:  5' TGA---8N---TGCT 3' 3'
      ACT---8N---ACGA 5'.
AU  - Sommer R
AU  - Schaller H
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1979 168: 331-335.

PMID- 21524909
VI  - 21
DP  - 2011
TI  - Detection of 5-hydroxymethylcytosine in a combined glycosylation restriction analysis (CGRA) using restriction enzyme Taq(alpha)I.
PG  - 5075-5077
AB  - 5-Hydroxymethylcytosine (5-hmC) is a newly discovered DNA base in mammalian cells that is
      believed to be another important epigenetic
      modification. Here we report the use of a methylation-insensitive
      restriction enzyme Taq(alpha)I coupled with selective chemical labeling
      of 5-hmC in a combined glycosylation restriction analysis (CGRA) to
      detect 5-hmC in TCGA sequences. This method, differentiates fully
      versus hemi-hydroxymethylated cytosine in the CpG dinucleotide, adds a
      new tool to facilitate biological studies of 5-hmC.
AU  - Song CX
AU  - Yu M
AU  - Dai Q
AU  - He C
PT  - Journal Article
TA  - Bioorg. Med. Chem. Lett.
JT  - Bioorg. Med. Chem. Lett.
SO  - Bioorg. Med. Chem. Lett. 2011 21: 5075-5077.

PMID- 19402659
VI  - 3
DP  - 2009
TI  - A Simple, Universal Colorimetric Assay for Endonuclease/Methyltransferase Activity and Inhibition Based on an  Enzyme-Responsive Nanoparticle System.
PG  - 1183-1189
AB  - An enzyme responsive nanoparticle system that uses a DNA-gold nanoparticle (AuNP) assembly as
      the substrate has been developed for
      the simple, sensitive, and universal monitoring of restriction
      endonucleases in real time. This new assay takes advantage of the
      palindromic recognition sequence of the restriction nucleases and the
      unique optical properties of AuNPs and is simpler than the procedure
      previously described by by Xu et al. (Angew. Chem. Int. Ed. Engl. 2007,
      46, 3468-3470). Because it involves only one type of ssDNA modified
      AuNPs, this assay can be directed toward most of the endonucleases by
      simply changing the recognition sequence found within the linker DNA.
      In addition, the endonuclease activity could be quantitatively analyzed
      by the value of the reciprocal of hydrolysis half time (t(1/2)(-1).
      Furthermore, our new design could also be applied to the assay of
      methyltransferase activity since the methylation of DNA inhibits its
      cleavage by the corresponding restriction endonuclease, and thus, this
      new methodology can be easily adapted to high-throughput screening of
      methyltransferase inhibitors.
AU  - Song GT
AU  - Chen CE
AU  - Ren JS
AU  - Qu XG
PT  - Journal Article
TA  - ACS NANO
JT  - ACS NANO
SO  - ACS NANO 2009 3: 1183-1189.

PMID- 21163962
VI  - 331
DP  - 2011
TI  - Structure of DNMT1-DNA complex reveals a role for autoinhibition in maintenance DNA methylation.
PG  - 1036-1040
AB  - Maintenance of genomic methylation patterns is mediated primarily by DNA methyltransferase-1
      (DNMT1). We have solved structures of mouse and human
      DNMT1 composed of CXXC, tandem bromo-adjacent homology (BAH1/2), and
      methyltransferase domains bound to DNA-containing unmethylated CpG sites.
      The CXXC specifically binds to unmethylated CpG dinucleotide and positions
      the CXXC-BAH1 linker between the DNA and the active site of DNMT1,
      preventing de novo methylation. In addition, a loop projecting from BAH2
      interacts with the target recognition domain (TRD) of the
      methyltransferase, stabilizing the TRD in a retracted position and
      preventing it from inserting into the DNA major groove. Our studies
      identify an autoinhibitory mechanism, in which unmethylated CpG
      dinucleotides are occluded from the active site to ensure that only
      hemimethylated CpG dinucleotides undergo methylation.
AU  - Song J
AU  - Rechkoblit O
AU  - Bestor TH
AU  - Patel DJ
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2011 331: 1036-1040.

PMID- 22323818
VI  - 335
DP  - 2012
TI  - Structure-based mechanistic insights into DNMT1-mediated maintenance DNA methylation.
PG  - 709-712
AB  - DNMT1, the major maintenance DNA methyltransferase in animals, helps to regulate  gene
      expression, genome imprinting, and X-chromosome inactivation. We report on
      the crystal structure of a productive covalent mouse DNMT1(731-1602)-DNA complex
      containing a central hemimethylated CpG site. The methyl group of methylcytosine
      is positioned within a shallow hydrophobic concave surface, whereas the cytosine
      on the target strand is looped out and covalently anchored within the catalytic
      pocket. The DNA is distorted at the hemimethylated CpG step, with side chains
      from catalytic and recognition loops inserting through both grooves to fill an
      intercalation-type cavity associated with a dual base flip-out on partner
      strands. Structural and biochemical data establish how a combination of active
      and autoinhibitory mechanisms ensures the high fidelity of DNMT1-mediated
      maintenance DNA methylation.
AU  - Song J
AU  - Teplova M
AU  - Ishibe-Murakami S
AU  - Patel DJ
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2012 335: 709-712.

PMID- 27587820
VI  - 4
DP  - 2016
TI  - Genome Sequence of Porphyrobacter dokdonensis DSW-74T, Isolated from Seawater off Dokdo in the East Sea (Sea of Korea).
PG  - e00903-16
AB  - Porphyrobacter dokdonensis strain DSW-74, isolated from seawater off of Dokdo, Republic of
      Korea, is a member of the family Erythrobacteraceae In this study,
      the genome sequence of DSW-74 was determined using the Illumina HiSeq 2000
      platform and assembled into 11 contigs. Its genome is approximately 3.0 Mb with a
      G+C content of 64.8%, in which 2,875 protein-coding sequences and 47 RNA genes
      were predicted.
AU  - Song JY
AU  - Hong J
AU  - Kwak MJ
AU  - Kwon SK
AU  - Kim JF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00903-16.

PMID- 20889745
VI  - 192
DP  - 2010
TI  - Draft Genome Sequence of Streptomyces clavuligerus NRRL 3585, a Producer of Diverse Secondary Metabolites.
PG  - 6317-6318
AB  - Streptomyces clavuligerus is an important industrial strain that produces a number of
      antibiotics, including clavulanic acid and cephamycin C. A
      high-quality draft genome sequence of the S. clavuligerus NRRL 3585 strain
      was produced by employing a hybrid approach that involved Sanger
      sequencing, Roche/454 pyrosequencing, optical mapping, and partial
      finishing. Its genome, comprising four linear replicons, one chromosome,
      and four plasmids, carries numerous sets of genes involved in the
      biosynthesis of secondary metabolites, including a variety of antibiotics.
AU  - Song JY
AU  - Jeong H
AU  - Yu DS
AU  - Fischbach MA
AU  - Park HS
AU  - Kim JJ
AU  - Seo JS
AU  - Jensen SE
AU  - Oh TK
AU  - Lee KJ
AU  - Kim JF
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 6317-6318.

PMID- 22740679
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Plant Growth-Promoting Rhizobacterium Bacillus sp. Strain  JS.
PG  - 3760-3761
AB  - Volatile and nonvolatile compounds emitted from the plant growth-promoting rhizobacterium
      Bacillus sp. strain JS enhance the growth of tobacco and lettuce.
      Here, we report the high-quality genome sequence of this bacterium. Its 4.1-Mb
      genome reveals a number of genes whose products are possibly involved in
      promotion of plant growth or antibiosis.
AU  - Song JY
AU  - Kim HA
AU  - Kim JS
AU  - Kim SY
AU  - Jeong H
AU  - Kang SG
AU  - Kim BK
AU  - Kwon SK
AU  - Lee CH
AU  - Yu DS
AU  - Kim BS
AU  - Kim SH
AU  - Kwon SY
AU  - Kim JF
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3760-3761.

PMID- 23144399
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of the Antifungal-Producing Plant-Benefiting Bacterium Burkholderia pyrrocinia CH-67.
PG  - 6649-6650
AB  - Burkholderia pyrrocinia CH-67 was isolated from forest soil as a biocontrol agent to be
      utilized in agriculture. Here, we report the 8.05-Mb draft genome sequence
      of this bacterium. Its genome contains genes involved in biosynthesis of
      secondary metabolites and plant growth promotion, which may contribute to
      probiotic effects on plants.
AU  - Song JY
AU  - Kwak MJ
AU  - Lee KY
AU  - Kong HG
AU  - Kim BK
AU  - Kwon SK
AU  - Lee SW
AU  - Kim JF
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6649-6650.

PMID- 22740673
VI  - 194
DP  - 2012
TI  - Genome Sequence of Enterohemorrhagic Escherichia coli NCCP15658.
PG  - 3749-3750
AB  - Enterohemorrhagic Escherichia coli causes severe food-borne disease in the guts of humans and
      animals. Here, we report the high-quality draft genome sequence of
      E. coli NCCP15658 isolated from a patient in the Republic of Korea. Its genome
      size was determined to be 5.46 Mb, and its genomic features, including genes
      encoding virulence factors, were analyzed.
AU  - Song JY
AU  - Yoo RH
AU  - Jang SY
AU  - Seong WK
AU  - Kim SY
AU  - Jeong H
AU  - Kang SG
AU  - Kim BK
AU  - Kwon SK
AU  - Lee CH
AU  - Yu DS
AU  - Park MS
AU  - Cho SH
AU  - Kim JF
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3749-3750.

PMID- 23682144
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Marinobacter sp. BSs20148.
PG  - e00236-13
AB  - Marinobacter sp. BSs20148 was isolated from marine sediment collected from the Arctic Ocean at
      a water depth of 3,800 m. Here we report the complete genome
      sequence of Marinobacter sp. BSs20148. This genomic information will facilitate
      the study of the physiological metabolism, ecological roles, and evolution of the
      Marinobacter species.
AU  - Song L
AU  - Ren L
AU  - Li X
AU  - Yu D
AU  - Yu Y
AU  - Wang X
AU  - Liu G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00236-13.

PMID- 26472827
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Burkholderia pseudomallei Strain 350105, Isolated in Hainan, China, in 1976.
PG  - e01162-15
AB  - Burkholderia pseudomallei is the etiological agent of the potentially fatal disease
      melioidosis. Here, we report the draft genome sequence of a virulent water isolate obtained
      from the Hainan Province of China in 1976, B. pseudomallei strain 350105.
AU  - Song L
AU  - Yu Y
AU  - Feng L
AU  - He J
AU  - Wang T
AU  - Zhu H
AU  - Duan Q
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01162-15.

PMID- 26679594
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Francisella tularensis Strain 410108 from Tibet, China.
PG  - e01489-15
AB  - Francisella tularensis is the etiological agent of the potentially fatal disease  tularemia.
      Here, we report the draft genome sequence of a virulent human isolate
      from Tibet, China in 1962, F. tularensis strain 410108, an intermediate-genotype
      strain of F. tularensis subsp. holarctica between biovar japonica and
      non-japonica strains in the world.
AU  - Song L
AU  - Yu Y
AU  - Feng L
AU  - Wang T
AU  - He J
AU  - Zhu H
AU  - Duan Q
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01489-15.

PMID- 23887917
VI  - 1
DP  - 2013
TI  - Genome Sequence of Bacillus subtilis SPZ1, an Evolved Strain for Higher Uptake Rate of Tributyrin.
PG  - e00511-13
AB  - The lipase-producing strain Bacillus subtilis SPZ1 is isolated from the medium by tributyrin
      as the sole carbon source. Here, we present a 4.13-Mb assembly of its
      genome sequence, which may provide various kinds of useful information related to
      Bacillus spp., such as mechanisms and control of the substrate uptake and protein
      secretion pathways.
AU  - Song P
AU  - Xu X
AU  - Jiang L
AU  - Zhang R
AU  - Wang J
AU  - Xu Q
AU  - Li S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00511-13.

PMID- 23144428
VI  - 194
DP  - 2012
TI  - Genome Sequence of Stenotrophomonas maltophilia S028, an Isolate Harboring the AmpR-L2 Resistance Module.
PG  - 6696
AB  - Multidrug-resistant Stenotrophomonas maltophilia has emerged as an important cause of
      nosocomial infections, which is attributable mainly to the production of
      diverse beta-lactamases by S. maltophilia. The L2 beta-lactamase mediated by the
      AmpR-L2 module is the most represented lactamase. Here, we announce the genome
      sequence of S028, an isolate harboring the AmpR-L2 module.
AU  - Song S
AU  - Yuan X
AU  - Liu S
AU  - Zhang N
AU  - Wang Y
AU  - Ke Y
AU  - Xu J
AU  - Huang L
AU  - Chen Z
AU  - Li Y
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6696.

PMID- 9666477
VI  - 8
DP  - 1998
TI  - XspI, a new Type II restriction endonuclease from a Xanthomonas species.
PG  - 370-373
AB  - A new Type II restriction endonuclease, XspI, was purified 11-fold in seven steps to
      homogeneity from Xanthomonas sp. strain YK1 grown aerobically in Luria broth.  The final
      specific activity of the purified enzyme was 3890 micrograms of lambda DNA digested per h per
      mg of protein.  The molecular weight of the native enzyme was determined to be 54,000.  Sodium
      dodecyl sulfate-gel electrophoresis revealed two identical subunits of molecular weight
      29,000.  The purified enzyme was most active at 37 C in the presence of 100 mM KCl and 5 mM
      MgCl2 under pH range from 7.5 to 8.0.  The enzyme was stable at least for 1 h at 37 C, but was
      inactivated after 20 min at 65 C.  XspI recognized the tetranucleotide sequence, 5'-CTAG-3',
      and cleaved it between C and T, like its isoschizomers MaeI and BfaI.  The ability of the
      source organism to grow aerobically, together with the heat inactivation of the enzyme,
      confers practical advantages upon XspI over its known isoschizomers.
AU  - Song T
AU  - Kang BS
AU  - Kim YM
PT  - Journal Article
TA  - Mol. Cells
JT  - Mol. Cells
SO  - Mol. Cells 1998 8: 370-373.

PMID- 27587804
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Mycobacterium avium, Isolated from Commercial Domestic Pekin Ducks (Anas platyrhynchos domestica), Determined Using PacBio  Single-Molecule Real-Time Technology.
PG  - e00769-16
AB  - Mycobacterium avium is an important pathogenic bacterium in birds and has never,  to our
      knowledge, reported to be isolated from domestic ducks. We present here
      the complete genome sequence of a virulent strain of Mycobacterium avium,
      isolated from domestic Pekin ducks for the first time, which was determined by
      PacBio single-molecule real-time technology.
AU  - Song XH
AU  - Chen HX
AU  - Zhou WS
AU  - Wang JB
AU  - Liu MF
AU  - Wang MS
AU  - Cheng AC
AU  - Jia RY
AU  - Chen S
AU  - Sun KF
AU  - Yang Q
AU  - Wu Y
AU  - Chen XY
AU  - Zhu DK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00769-16.

PMID- 27151800
VI  - 4
DP  - 2016
TI  - Genome Sequence of Riemerella anatipestifer Strain RCAD0122, a Multidrug-Resistant Isolate from Ducks.
PG  - e00332-16
AB  - Riemerella anatipestifer is an important pathogenic bacterium in waterfowl and other avian
      species. We present here the genome sequence of R. anatipestifer
      RCAD0122, a multidrug-resistant strain isolated from infected ducks. The isolate
      contains at least nine types of antibiotic resistance-associated genes.
AU  - Song XH
AU  - Zhou WS
AU  - Wang JB
AU  - Liu MF
AU  - Wang MS
AU  - Cheng AC
AU  - Jia RY
AU  - Chen S
AU  - Sun KF
AU  - Yang Q
AU  - Wu Y
AU  - Chen XY
AU  - Zhu DK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00332-16.

PMID- 25676768
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Chemolithoautotrophic Acetogenic Butanol-Producing Eubacterium limosum ATCC 8486.
PG  - e01564-14
AB  - Eubacterium limosum ATCC 8486 is an anaerobic chemolithoautotrophic acetogenic bacterium that
      converts and transforms syngas and isoflavonoids to butanol and
      phytoestrogens, respectively. Here, we report the draft genome sequence of the E.
      limosum ATCC 8486 (4.37 Mb) strain and its annotation information, including
      syngas fermentation and denitrification metabolic pathways.
AU  - Song Y
AU  - Cho BK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01564-14.

PMID- 25931594
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Clostridium aceticum DSM 1496, a Potential Butanol Producer through Syngas Fermentation.
PG  - e00258-15
AB  - Clostridium aceticum DSM 1496 is a Gram-negative anaerobic chemolithoautotrophic  acetogenic
      bacterium that is capable of producing commodity chemicals from syngas
      fermentation. In this study, we report the draft genome sequence of the C.
      aceticum DSM 1496 strain (4.16 Mb) to elucidate the syngas fermentation metabolic
      pathway.
AU  - Song Y
AU  - Hwang S
AU  - Cho BK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00258-15.

PMID- 24831152
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Clostridium scatologenes ATCC 25775, a Chemolithoautotrophic Acetogenic Bacterium Producing 3-Methylindole and  4-Methylphenol.
PG  - e00459-14
AB  - Clostridium scatologenes ATCC 25775 is a strictly anaerobic and chemolithoautotrophic
      acetogenic bacterium that converts syngas into multi-carbon
      compounds such as acetate, indole, 3-methylindole, and 4-methylphenol. Here we
      report the draft genome sequence of C. scatologenes ATCC 25775 (7.3 Mbp) to
      elucidate its metabolic pathway for syngas fermentation.
AU  - Song Y
AU  - Jeong Y
AU  - Shin HS
AU  - Cho BK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00459-14.

PMID- 2834695
VI  - 16
DP  - 1988
TI  - DNA cleavage by AatI and StuI is sensitive to Escherichia coli dcm methylation.
PG  - 2718
AB  - While attempting to subclone the StuI - EcoNI fragment of pRIF 309+ we found that the AGGCCT
      site was not cleaved by StuI or its isoschizomer AatI. Upon examination of the DNA sequence it
      became evident that this site overlapped an E. coli dcm methylation site CC(T/)AGG, ie.
      AGGCCTGG, which when methylated could be resistant to cleavage. To test this proposition we
      prepared pRIF 309+ in the dcm- E. coli strain GM 2929 kindly supplied by Dr. B. Bachmann. As
      can be seen in Fig. 1 pRIF 309+ prepared from a dcm- host is cleaved by StuI. An identical
      result was obtained with AatI.
AU  - Song Y-H
AU  - Rueter T
AU  - Geiger R
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1988 16: 2718.

PMID- 25657276
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequence of Listeria monocytogenes Strains from Clinical and Environmental Samples from Varanasi, India.
PG  - e01496-14
AB  - We present here the whole-genome sequences of Listeria monocytogenes from Ganges  River water,
      agricultural soil, and human clinical samples from Varanasi, India,
      which will be used for a comparative analysis.
AU  - Soni DK
AU  - Singh KM
AU  - Ghosh A
AU  - Chikara SK
AU  - Joshi CG
AU  - Dubey SK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01496-14.

PMID- 26404610
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Methicillin-Sensitive Staphylococcus aureus ATCC 29213.
PG  - e01095-15
AB  - Staphylococcus aureus subsp. aureus ATCC 29213 is one of the most commonly used strains in
      drug discovery research and for quality control. We report the completed draft genome sequence
      for the strain.
AU  - Soni I
AU  - Chakrapani H
AU  - Chopra S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01095-15.

PMID- 27552638
VI  - 11
DP  - 2017
TI  - Global occurrence and heterogeneity of the Roseobacter-clade species Ruegeria mobilis.
PG  - 569-583
AB  - Tropodithietic acid (TDA)-producing Ruegeria mobilis strains of the Roseobacter clade have
      primarily been isolated from marine aquaculture and have probiotic
      potential due to inhibition of fish pathogens. We hypothesized that TDA producers
      with additional novel features are present in the oceanic environment. We
      isolated 42 TDA-producing R. mobilis strains during a global marine research
      cruise. While highly similar on the 16S ribosomal RNA gene level (99-100%
      identity), the strains separated into four sub-clusters in a multilocus sequence
      analysis. They were further differentiated to the strain level by average
      nucleotide identity using pairwise genome comparison. The four sub-clusters could
      not be associated with a specific environmental niche, however, correlated with
      the pattern of sub-typing using co-isolated phages, the number of prophages in
      the genomes and the distribution in ocean provinces. Major genomic differences
      within the sub-clusters include prophages and toxin-antitoxin systems. In
      general, the genome of R. mobilis revealed adaptation to a particle-associated
      life style and querying TARA ocean data confirmed that R. mobilis is more
      abundant in the particle-associated fraction than in the free-living fraction
      occurring in 40% and 6% of the samples, respectively. Our data and the TARA data,
      although lacking sufficient data from the polar regions, demonstrate that R.
      mobilis is a globally distributed marine bacterial species found primarily in the
      upper open oceans. It has preserved key phenotypic behaviors such as the
      production of TDA, but contains diverse sub-clusters, which could provide new
      capabilities for utilization in aquaculture.
AU  - Sonnenschein EC
AU  - Nielsen KF
AU  - D'Alvise P
AU  - Porsby CH
AU  - Melchiorsen J
AU  - Heilmann J
AU  - Kalatzis PG
AU  - Lopez-Perez M
AU  - Bunk B
AU  - Sproer C
AU  - Middelboe M
AU  - Gram L
PT  - Journal Article
TA  - ISME J.
JT  - ISME J.
SO  - ISME J. 2017 11: 569-583.

PMID- 28984543
VI  - 67
DP  - 2017
TI  - Phaeobacter piscinae sp. nov., a novel species of the roseobacter group and potential aquaculture probiont.
PG  - 4559-4564
AB  - Four heterotrophic, antimicrobial, motile, marine bacterial strains, 27-4T, 8-1, M6-4.2 and
      S26, were isolated from aquaculture units in Spain, Denmark and Greece. All four strains
      produced the antibiotic compound tropodithietic acid, which is a key molecule in their
      antagonism against fish pathogenic bacteria. Cells of the strains were Gram-reaction-negative,
      rod-shaped and formed star-shaped aggregates in liquid culture and brown-coloured colonies on
      marine agar. The predominant cellular fatty acids were C18 : 1!7c, C16 : 0, C11 methyl C18 :
      1!7c and C16 : 0 2-OH, and the polar lipids comprised phosphatidylglycerol,
      diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an aminolipid, a
      phospholipid
      and an unidentified lipid. The strains grew optimally at 3133 C. Growth was observed at a salt
      concentration between 0.5 and 56%NaCl with an optimum at 23 %. The pH range for growth of the
      strains was from pH 6 to 88.5 with an optimum at pH 7. Based on 16S rRNA gene sequence
      analysis, the strains are affiliated with the genus Phaeobacter. The genome sequences of the
      strains have a DNA G+C content of 60.1% and share an average nucleotide identity (ANI) of more
      than 95%.  The four strains are distinct from the type strains of the closely related species
      Phaeobacter gallaeciensis and Phaeobacter
      inhibens based on an ANI of 90.591.7 and 89.690.4 %, respectively, and an in silico DNADNA
      hybridization relatedness of 43.946.9 and 39.841.9 %, respectively. On the basis of
      phylogenetic analyses as well as phenotypic and chemotaxonomic properties, the isolates are
      considered to represent a novel species, for which the name Phaeobacter piscinae sp. nov. is
      proposed. The type strain is 27-4T (=DSM 103509T=LMG 29708T).
AU  - Sonnenschein EC
AU  - Phippen CBW
AU  - Nielsen KF
AU  - Mateiu RV
AU  - Melchiorsen J
AU  - Gram L
AU  - Overmann J
AU  - Freese HM
PT  - Journal Article
TA  - Int. J. Syst. Evol. Microbiol.
JT  - Int. J. Syst. Evol. Microbiol.
SO  - Int. J. Syst. Evol. Microbiol. 2017 67: 4559-4564.

PMID- 26494681
VI  - 3
DP  - 2015
TI  - Draft Whole-Genome Sequence of Xenorhabdus sp. Strain GDc328, Isolated from the Indigenous South African Nematode Host Steinernema khoisanae.
PG  - e01239-15
AB  - Here, we describe the draft genome sequence of Xenorhabdus sp. GDc328, an endosymbiont of the
      native South African entomopathogenic nematode host, Steinernema khoisanae. The total genome
      size of the bacteria is 4.09 Mb. The genome comprises a total of 3,608 genes with a molecular
      G+C content of 44.64%.
AU  - Soobramoney LA
AU  - Featherston J
AU  - Gray VM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01239-15.

PMID- 
VI  - 
DP  - 1995
TI  - Host restriction-modification as related to gene transfer in the nitrogen-fixing cyanobacterium, Cyanothece sp.
PG  - 1-132
AB  - Cyanothece sp. strain BH68K (ATCC 51142) is a marine unicellular
      cyanobacterium capable of oxygenic photosynthesis and aerobic nitrogen fixation in a
      single cell without undergoing morphological differentiation.  In order to develop a gene
      transfer system for this organism, shuttle vectors are required that are capable of
      replication
      in E. coli and Cyanothece sp.  Therefore, the plasmids of several clonal isolates have been
      characterized.  Each Cyanothece isolate contains three or four plasmids ranging in size from
      4.8 kb to 40 kb.  A small 4.8 kb plasmid (pSE480), from the clonal isolate Cyanothece sp.
      strain BH68F, has been subcloned and restriction mapped.  Ten restriction sites have been
      mapped, five of which are unique and are suitable for further subcloning.  Shuttle vectors
      derived from pSE480 were used in an attempt to transfer genes by natural competency and
      electroporation.  Lack of transformation prompted the analysis of Cyanothece sp. strain
      BH68K for restriction barriers.  Cell wash supernatants revealed a cell wall-associated
      nuclease that exhibited non-site-specific degradation of covalently- closed circular and
      linear double-stranded DNA molecules, including Cyanothece sp. strain BH68K
      chromosomal DNA.  The nuclease also degraded Cyanothece sp. total RNA and phage
      M13mp18 ssDNA.  Cyanothece sp. strain BH68K cell extracts contain three type II
      restriction endonucleases, designated Csp68KI, Csp68KII, and Csp68KIII.  Csp68KI is
      an isoschizomer of AvaII and recognizes the nucleotide sequence 5'-G/GWCC-3' (W=A or
      T).  Cleavage occurred between the guanosine nucleotides producing 3-bp 5' overhang
      ends. Csp68KII is an isoschizomer of AsuII and restricts DNA at the recognition sequence
      5'-TT/CGAA-3'.  Cleavage occurred between thymine and cytosine producing 2-bp 5'
      overhang ends.  The third restriction endonuclease, Csp68KIII, is an isoschizomer of
      AvaIII and restricts DNA at the recognition sequence 5'- ATGCA/T-3'.  Cleavage occurred
      between the 3' adenosine and thymine nucleotides producing 4- bp 3' overhang ends.  The
      methylase genes M.Csp68KI, M.Csp68KIV and M.Csp68KV have been cloned from
      plasmid libraries of Cyanothece sp. strain BH68K.  The last two methylases inhibit
      restriction by the four-base, site-specific enzymes MspI and HaeIII, respectively. Cloned
      methylase genes from host restriction-modification systems can be used to construct helper
      plasmids that methylate shuttle vectors prior to gene transfer.
AU  - Soper BW
PT  - Journal Article
TA  - Ph.D. Thesis, State University of New York, Binghamton, USA
JT  - Ph.D. Thesis, State University of New York, Binghamton, USA
SO  - Ph.D. Thesis, State University of New York, Binghamton, USA 1995 : 1-132.

PMID- Not carried by PubMed...
VI  - 56
DP  - 1996
TI  - Host restriction-modification as related to gene transfer in the nitrogen-fixing cyanobacterium, cyanothece sp.
PG  - 3585B
AB  - Cyanothece sp. strain BH68K (ATCC 51142) is a marine unicellular cyanobacterium capable of
      oxygenic photosynthesis and aerobic nitrogen fixation in a single cell without undergoing
      morphological differentiation.  In order to develop a gene transfer system for this organism,
      shuttle vectors are required that are capable of replication in E. coli and Cyanothece sp.
      Therefore, the plasmids of several clonal isolates have been characterized.  Each Cyanothece
      isolate contains three or four plasmids ranging in size from 4.8 kb to 40 kb.  A small 4.8 kb
      plasmid (pSE480), from the clonal isolate Cyanothece sp. strain BH68F, has been subcloned and
      restriction mapped.  Ten restriction sites have been mapped, five of which are unique and are
      suitable for further subcloning.  Shuttle vectors derived from pSE480 were used in attempt to
      transfer genes by natural competency and electroporation.  Lack of transformation prompted the
      analysis of Cyanothece sp. strain BH68K for restriction barriers.  Cell wash supernatants
      revealed a cell wall-associated nuclease that exhibited non-site-specific degradation of
      covalently-closed circular and linear double-stranded DNA molecules, including Cyanothece sp.
      strain BH68K cell extracts contain three type II restriction endonucleases, designated
      Csp68KI, Csp68KII, and Csp68KIII.  Csp68KI is an isoschizomer of AvaII and recognizes the
      nucleotide sequence 5'-G/GWCC-3' (W=A or T).  Cleavage occurred between the guanosine
      nucleotides producing 3-bp 5' overhang ends.  Csp68KII is an isoschizomer of AsuII and
      restricts DNA at the recognition sequence 5'-TT/CGAA-3'.  Cleavage occurred between thymine
      and cytosine producing 2-bp 5' overhang ends.  The third restriction endonuclease, Csp68KIII,
      is an isoschizomer of AvaIII and restricts DNA at the recognition sequence 5'-ATGCA/T-3'.
      Cleavage occurred between the 3' adenosine and thymine nucleotides producing 4-bp 3'
      overhang ends.  The methylase genes M.Csp68KI, M.Csp68KIV and M.Csp68KV have been cloned from
      plasmid libraries of Cyanothece sp. strain BH68K.  The last two methylases inhibit restriction
      by the four-base, site-specific enzymes MspI and HaeIII, respectively.  Cloned methylase genes
      from host restriction-modification systems can be used to construct helper plasmids that
      methylate shuttle vectors prior to gene transfer.
AU  - Soper BW
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1996 56: 3585B.

PMID- 9701642
VI  - 6
DP  - 1998
TI  - Restriction-modification systems in the marine, aerobic, nitrogen-fixing unicellular cyanobacterium Cyanothece sp. ATCC 51142.
PG  - 183-185
AB  - Cyanothece sp. ATCC 51142 possesses six host restriction-modification systems (HRMS), and
      these HRMS were designated as Csp68KI to Csp68KVI.  So far, four restriction enzymes have been
      characterized biochemically, and the other two were deduced based on the cloning of
      corresponding DNA methyltransferase genes M. Csp68KIV and M.Csp68KV from the Cyanothece
      genome.  Csp68KI, Csp68KII, Csp68KIII, Csp68KIV, Csp68KV, and Csp68KVI are isoschizomers of
      AvaII, AsuII, AvaIII, MspI, HaeIII, and FnuDII, respectively.  The cleavage specificities for
      Csp68KI, Csp68KII, Csp68KIII, and Csp68KVI were characterized.  The Cyanothece restriction
      enzymes showed different temperature and salt requirements for their optimal activity.  For
      example, the restriction enzyme Csp68KII functions optimally at 50 C and Csp68KIII requires
      higher salt for its activity.
AU  - Soper BW
AU  - Hollister WR
AU  - Reddy KJ
PT  - Journal Article
TA  - J. Mar. Biotechnol.
JT  - J. Mar. Biotechnol.
SO  - J. Mar. Biotechnol. 1998 6: 183-185.

PMID- 8660373
VI  - 223
DP  - 1996
TI  - Characterization of additional host restriction-modification systems in the unicellular cyanobacterium Cyanothece sp.
PG  - 24-30
AB  - In order to develop a gene transfer system for the unicellular diazotrophic cyanobacterium
      Cyanothece sp. strain BH68K, this organism has been further investigated for the presence of
      additional host restriction-modification enzymes other than Csp68KI, previously reported for
      Cyanothece sp.  Analysis of cell extracts by phosphocellulose and Mono Q fast protein liquid
      chromatography (FPLC) has led to the identification of three new restriction endonucleases.
      These enzymes have been designated Csp68KII, Csp68KIII, and Csp68KVI.  Csp68KII is an
      isoschizomer of AsuII and restricts DNA at the recognition sequence 5'-TT/CGAA-3'.  Cleavage
      occurred between thymine and cytosine producing 2 bp 5' overhang ends.  The third restriction
      enodnuclease, Csp68KII, is an isoschizomer of AvaIII and restricts DNA at the recognition
      sequence 5'-ATGCA/T-3'.  Cleavage occurred between the 3' adenosine and thymine nucleotides
      producing 4 bp 3' overhang ends.  The fourth enzyme identified, Csp68KVI, recognizes CGCG and
      cleaves this sequence between the internal guanine and cytosine nucleotides producing blunt
      ends.
AU  - Soper BW
AU  - Hollister WR
AU  - Reddy KJ
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1996 223: 24-30.

PMID- 8071241
VI  - 176
DP  - 1994
TI  - Identification of a nuclease and host restriction-modification in the unicellular, aerobic nitrogen-fixing cyanobacterium Cyanothece sp.
PG  - 5565-5570
AB  - In the process of developing a gene transfer system for the marine, unicellular,
      nitrogen-fixing cyanobacterium Cyanothece sp. strain BH68K, two major restriction barriers
      have been identified. A cell wall-associated nuclease exhibited non-site-specific degradation
      of covalently closed circular and linear double-stranded DNA molecules, including Cyanothece
      sp. strain BH68K chromosomal DNA. The nuclease is easily released from intact cells by using
      water or buffer containing Triton X-100. Nuclease activity was undetectable in cell extracts
      prepared from water-washed cells. Comparison of the restriction endonuclease susceptibility of
      Cyanothece sp. strain BH68K DNA to that of Anabaena sp. strain PCC 7120 revealed that these
      organisms have a nearly identical pattern of restriction and therefore may contain similar
      systems for DNA methylation. Restriction by DpnI, MboI, and Sau3AI indicated the presence of
      adenine methylation. Cyanothece sp. strain BH68KI was easily detected in cell extracts without
      extensive purification. Csp68KI is an isoschizomer of AvaII and recognizes the nucleotide
      sequence 5'-GG(A/T)CC-3'. Cleavage occurs between the guanosine nucleotides producing 3-bp
      5' overhang ends.
AU  - Soper BW
AU  - Reddy KJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1994 176: 5565-5570.

PMID- 25614568
VI  - 3
DP  - 2015
TI  - Full-Length Genome Sequence of Type M/emm83 Group A Streptococcus pyogenes Strain STAB1101, Isolated from Clustered Cases in Brittany.
PG  - e01459-14
AB  - Here, we announce the complete annotated genome sequence of a Streptococcus pyogenes M/emm83
      strain, STAB1101, isolated from clustered cases in homeless
      persons in Brittany (France). The genome is composed of 1,709,790 bp, with a G+C
      content of 38.4% and 1,550 identified coding sequences (CDS), and it harbors a
      Tn916-like transposon.
AU  - Soriano N
AU  - Vincent P
AU  - Auger G
AU  - Cariou ME
AU  - Moullec S
AU  - Lagente V
AU  - Ygout JF
AU  - Kayal S
AU  - Faili A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01459-14.

PMID- 25169855
VI  - 2
DP  - 2014
TI  - Closed Genome Sequence of Noninvasive Streptococcus pyogenes M/emm3 Strain STAB902.
PG  - e00792-14
AB  - We report a closed genome sequence of group A Streptococcus genotype emm3 (GAS M/emm3) strain
      STAB902, isolated from a superficial pyodermatitis. The genome is
      composed of 1,892,124 bp, 6 integrated prophages, and has 1,858 identified coding
      sequences (CDSs). It has been fitted with the two available invasive GAS M/emm3
      strains.
AU  - Soriano N
AU  - Vincent P
AU  - Moullec S
AU  - Meygret A
AU  - Lagente V
AU  - Kayal S
AU  - Faili A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00792-14.

PMID- 25414498
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Streptococcus pyogenes M/emm44 Strain STAB901, Isolated in a Clonal Outbreak in French Brittany.
PG  - e01174-14
AB  - We report the complete genome sequence of an invasive isolate of Streptococcus pyogenes
      M/emm44, belonging to a clonal outbreak that occurred in French
      Brittany. The genome is composed of 1,795,608 bp, with a GC content of 38.5%, has
      1,358 identified coding sequences (CDSs), and harbors a novel Tn916-like
      transposon (Tn6253).
AU  - Soriano N
AU  - Vincent P
AU  - Piau C
AU  - Moullec S
AU  - Gautier P
AU  - Lagente V
AU  - Faili A
AU  - Kayal S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01174-14.

PMID- 25978546
VI  - 10
DP  - 2016
TI  - Elemental sulfur and acetate can support life of a novel strictly anaerobic haloarchaeon.
PG  - 240-252
AB  - Archaea domain is comprised of many versatile taxa that often colonize extreme habitats. Here,
      we report the discovery of strictly anaerobic extremely halophilic euryarchaeon, capable of
      obtaining energy by dissimilatory reduction of elemental sulfur using acetate as the only
      electron donor and forming sulfide and CO2 as the only products. This type of respiration has
      never been observed in hypersaline anoxic habitats and is the first example of such metabolic
      capability in the entire Archaea domain. We isolated and cultivated these unusual organisms,
      selecting one representative strain, HSR2, for detailed characterization. Our studies
      including physiological tests, genome sequencing, gene expression, metabolomics and
      [14C]-bicarbonate assimilation assays revealed that HSR2 oxidized acetate completely via the
      tricarboxylic acid cycle. Anabolic assimilation of acetate occurred via activated glyoxylate
      bypass and anaplerotic carboxylation. HSR2 possessed sulfurtransferase and an array of
      membrane-bound polysulfide reductase genes, all of which were expressed during the growth. Our
      findings suggest the biogeochemical contribution of haloarchaea in hypersaline anoxic
      environments must be reconsidered.
AU  - Sorokin DY
AU  - Kublanov IV
AU  - Gavrilov SN
AU  - Rojo D
AU  - Roman P
AU  - Golyshin PN
AU  - Slepak VZ
AU  - Smedile F
AU  - Ferrer M
AU  - Messina E
AU  - La Cono V
AU  - Yakimov MM
PT  - Journal Article
TA  - ISME J.
JT  - ISME J.
SO  - ISME J. 2016 10: 240-252.

PMID- 22763649
VI  - 6
DP  - 2012
TI  - Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi.
PG  - 2245-2256
AB  - Nitrite-oxidizing bacteria (NOB) catalyze the second step of nitrification, a
      major process of the biogeochemical nitrogen cycle, but the recognized diversity
      of this guild is surprisingly low and only two bacterial phyla contain known NOB.
      Here, we report on the discovery of a chemolithoautotrophic nitrite oxidizer that
      belongs to the widespread phylum Chloroflexi not previously known to contain any
      nitrifying organism. This organism, named Nitrolancetus hollandicus, was isolated
      from a nitrifying reactor. Its tolerance to a broad temperature range (25-63
      degrees C) and low affinity for nitrite (K(s)=1 mM), a complex layered cell
      envelope that stains Gram positive, and uncommon membrane lipids composed of
      1,2-diols distinguish N. hollandicus from all other known nitrite oxidizers. N.
      hollandicus grows on nitrite and CO(2), and is able to use formate as a source of
      energy and carbon. Genome sequencing and analysis of N. hollandicus revealed the
      presence of all genes required for CO(2) fixation by the Calvin cycle and a
      nitrite oxidoreductase (NXR) similar to the NXR forms of the proteobacterial
      nitrite oxidizers, Nitrobacter and Nitrococcus. Comparative genomic analysis of
      the nxr loci unexpectedly indicated functionally important lateral gene transfer
      events between Nitrolancetus and other NOB carrying a cytoplasmic NXR, suggesting
      that horizontal transfer of the NXR module was a major driver for the spread of
      the capability to gain energy from nitrite oxidation during bacterial evolution.
      The surprising discovery of N. hollandicus significantly extends the known
      diversity of nitrifying organisms and likely will have implications for future
      research on nitrification in natural and engineered ecosystems.
AU  - Sorokin DY
AU  - Lucker S
AU  - Vejmelkova D
AU  - Kostrikina NA
AU  - Kleerebezem R
AU  - Rijpstra WI
AU  - Damste JS
AU  - Le Paslier D
AU  - Muyzer G
AU  - Wagner M
AU  - van Loosdrecht MC
AU  - Daims H
PT  - Journal Article
TA  - ISME J.
JT  - ISME J.
SO  - ISME J. 2012 6: 2245-2256.

PMID- 28106880
VI  - 11
DP  - 2017
TI  - Discovery of anaerobic lithoheterotrophic haloarchaea, ubiquitous in hypersaline habitats.
PG  - 1245-1260
AB  - Hypersaline anoxic habitats harbour numerous novel uncultured archaea whose
      metabolic and ecological roles remain to be elucidated. Until recently, it was
      believed that energy generation via dissimilatory reduction of sulfur compounds
      is not functional at salt saturation conditions. Recent discovery of the strictly
      anaerobic acetotrophic Halanaeroarchaeum compels to change both this assumption
      and the traditional view on haloarchaea as aerobic heterotrophs. Here we report
      on isolation and characterization of a novel group of strictly anaerobic
      lithoheterotrophic haloarchaea, which we propose to classify as a new genus
      Halodesulfurarchaeum. Members of this previously unknown physiological group are
      capable of utilising formate or hydrogen as electron donors and elemental sulfur,
      thiosulfate or dimethylsulfoxide as electron acceptors. Using genome-wide
      proteomic analysis we have detected the full set of enzymes required for
      anaerobic respiration and analysed their substrate-specific expression. Such
      advanced metabolic plasticity and type of respiration, never seen before in
      haloarchaea, empower the wide distribution of Halodesulfurarchaeum in hypersaline
      inland lakes, solar salterns, lagoons and deep submarine anoxic brines. The
      discovery of this novel functional group of sulfur-respiring haloarchaea
      strengthens the evidence of their possible role in biogeochemical sulfur cycling
      linked to the terminal anaerobic carbon mineralisation in so far overlooked
      hypersaline anoxic habitats.
AU  - Sorokin DY
AU  - Messina E
AU  - Smedile F
AU  - Roman P
AU  - Damste JSS
AU  - Ciordia S
AU  - Mena MC
AU  - Ferrer M
AU  - Golyshin PN
AU  - Kublanov IV
AU  - Samarov NI
AU  - Toshchakov SV
AU  - La Cono V
AU  - Yakimov MM
PT  - Journal Article
TA  - ISME J.
JT  - ISME J.
SO  - ISME J. 2017 11: 1245-1260.

PMID- 20827598
VI  - 674
DP  - 2010
TI  - Large-Scale Identification and Analysis of C-Proteins<BOOK> Computational Biology of Transcription Factor Binding.
PG  - 269-282
AB  - The restriction-modification system is a toxin antitoxin mechanism of bacterial cells to
      resist phage attacks. High efficiency comes at a
      price of high maintenance costs: (1) a host cell dies whenever it loses
      restriction-modification genes and (2) whenever a plasmid with
      restriction-modification genes enters a naive cell, modification enzyme
      (methylase) has to be expressed prior to the synthesis of the
      restriction enzyme (restrictase) or the cell dies. These phenomena
      imply a sophisticated regulatory mechanism. During the evolution
      several such mechanisms were developed, of which one relies on a
      special C(control)protein, a short autoregulatory protein containing an
      HTH-domain. Given the extreme diversity among restriction-modification
      systems, one could expect that C-proteins had evolved into several
      groups that might differ in autoregulatory binding sites architecture.
      However, only a few C-proteins (and the corresponding binding sites)
      were known before this study. Bioinformatics studies applied to
      C-proteins and their binding sites were limited to groups of well-known
      C-proteins and lacked systematic analysis. In this work, the authors
      use bioinformatics techniques to discover 201 C-protein genes with
      predicted autoregulatory binding sites. The systematic analysis of the
      predicted sites allowed for the discovery of 10 structural classes of
      binding sites.
AU  - Sorokin V
AU  - Severinov K
AU  - Gelfand MS
PT  - Journal Article
TA  - Methods Mol. Biol.
JT  - Methods Mol. Biol.
SO  - Methods Mol. Biol. 2010 674: 269-282.

PMID- 19056824
VI  - 37
DP  - 2009
TI  - Systematic prediction of control proteins and their DNA binding sites.
PG  - 441-451
AB  - We present here the results of a systematic bioinformatics analysis of control (C) proteins, a
      class of DNA-binding regulators that control
      time-delayed transcription of their own genes as well as restriction
      endonuclease genes in many type II restriction-modification systems.
      More than 290 C protein homologs were identified and DNA-binding sites
      for 70 of new and previously known C proteins were predicted by a
      combination of phylogenetic footprinting and motif searches in DNA
      upstream of C protein genes. Additional analysis revealed that a large
      proportion of C protein genes are translated from leaderless RNA, which
      may contribute to time-delayed nature of genetic switches operated by
      these proteins. Analysis of genetic contexts of newly identified C
      protein genes revealed that they are not exclusively associated with
      restriction-modification genes; numerous instances of associations with
      genes originating from mobile genetic elements were observed. These
      instances might be vestiges of ancient horizontal transfers and
      indicate that during evolution ancestral restriction-modification
      system genes were the sites of mobile elements insertions.
AU  - Sorokin V
AU  - Severinov K
AU  - Gelfand MS
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: 441-451.

PMID- 1964711
VI  - 52
DP  - 1990
TI  - Restriction endonucleases from the genus Bacillus.
PG  - 8-11
AB  - Production regularities of site-specific endonucleases by aerobic spore-forming bacteria,
      isolated from different ecological sources, have been studied. It is shown that more than 1/3
      of all the cultures studied produce site-specific endonucleases. A dependence of the frequency
      of occurrence of bacterial producers on the ecological niche of their separation has been
      noticed. The data on production of species-specific restrictases have been obtained which can
      serve as additional characteristics for the differentiation of close species of Bacilli.
AU  - Sorokulova IB
AU  - Kramarov VM
AU  - Reznik SR
AU  - Smirnov VV
PT  - Journal Article
TA  - Mikrobiol. Zh.
JT  - Mikrobiol. Zh.
SO  - Mikrobiol. Zh. 1990 52: 8-11.

PMID- 14757241
VI  - 230
DP  - 2004
TI  - Identification of novel virulence-associated loci in uropathogenic Escherichia coli by suppression subtractive hybridization.
PG  - 203-208
AB  - To identify novel virulence-associated genes in uropathogenic Escherichia coli (UPEC) strains,
      a suppression subtractive hybridization strategy was applied to genomic DNA of four clinical
      UPEC isolates from patients suffering from cystitis or pyelonephritis. The genomic DNA of four
      isolates (tester strains) was subtracted from the DNA of two different driver strains, the
      well characterized UPEC strain CFT073 and the non-pathogenic E. coli K-12 strain MG1655. We
      determined the sequence of 172 tester strain-specific DNA fragments, 86 of which revealed only
      low or no homology to nucleotide sequences of public databases. We further determined the
      virulence association of the 86 novel DNA fragments using each DNA fragment as a probe in
      Southern hybridizations of a reference strain collection consisting of 60 extraintestinal
      pathogenic E. coli isolates, and 40 non-virulent E. coli strains from stool samples. From
      this, 19 novel DNA fragments were demonstrated to be significantly associated with virulent
      strains and thus may represent new virulence traits. Our results support the idea of a
      considerable genetic variability among UPEC strains and suggest that novel genomic
      determinants might contribute to virulence of UPEC.
AU  - Sorsa LJ
AU  - Dufke S
AU  - Schubert S
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2004 230: 203-208.

PMID- 24459268
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Microbispora sp. Strain ATCC-PTA-5024, Producing the Lantibiotic NAI-107.
PG  - e01198-13
AB  - We report the draft genome sequence of Microbispora sp. strain ATCC-PTA-5024, a soil isolate
      that produces NAI-107, a new lantibiotic with the potential to treat
      life-threatening infections caused by multidrug-resistant Gram-positive
      pathogens. The draft genome of strain Microbispora sp. ATCC-PTA-5024 consists of
      8,543,819 bp, with a 71.2% G+C content and 7,860 protein-coding genes.
AU  - Sosio M
AU  - Gallo G
AU  - Pozzi R
AU  - Serina S
AU  - Monciardini P
AU  - Bera A
AU  - Stegmann E
AU  - Weber T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01198-13.

PMID- 3020510
VI  - 14
DP  - 1986
TI  - Methylation and restriction endonuclease cleavage of linear Z-DNA in the presence of hexamminecobalt (III) ions.
PG  - 7237-7252
AB  - These studies employed the synthetic linear DNA, poly dGdC, in the B and cobalt
      hexammine chloride (Co)-induced Z form to determine the effect of conformation
      on protein-DNA interactions.  The rate of the reaction of the restriction
      endonucleases, HhaI and CfoI, are reduced with Z DNA as compared to B DNA.  The
      ability of both restriction endonucleases to react with an aggregate form of Z
      DNA (Z* DNA) is found to depend upon how the Z* DNA is formed.  When Z* DNA is
      induced by low concentrations of Co (50 microM), the endonucleases remain
      active.  In the presence of 100 microM Co, which causes increased aggregation,
      the endonucleases are inactive.  The HhaI DNA methyltransferase reacts at equal
      rates with the B, Z and low cobalt Z* form.  these results are significantly
      different than those observed with Z form dGdC tracts inserted into circular
      DNA molecules.
AU  - Soslau G
AU  - Parker J
AU  - Nelson JW
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1986 14: 7237-7252.

PMID- 6312980
VI  - 115
DP  - 1983
TI  - Selective inhibition of restriction endonuclease cleavage by DNA intercalators.
PG  - 484-491
AB  - The preferred dye binding sites and the microenvironment of known nucleotide sequences within
      mitochondrial and plasmid pBR322 DNA was probed in a gross fashion with restriction
      endonucleases.  The intercalating dyes, ethidium bromide and propidium iodide, do not inhibit
      a given restriction endonuclease equally at all of the restriction sites within a DNA
      molecule.  The selective inhibition may be explained, in part, by the potential B to Z
      conformation transition of DNA flanking the restriction site and by preferred dye binding
      sites.  Propidium iodide was found to be a more potent inhibitor than ethidium bromide and the
      inhibition is independent of the type of cut made by the enzyme.
AU  - Soslau G
AU  - Pirollo K
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1983 115: 484-491.

PMID- 
VI  - 0
DP  - 1991
TI  - Determination of substrate specificity of restriction endonuclease Mlu113I.
PG  - 66-67
AB  - The recognition sequence and cleavage point of restriction endonuclease Mlu113I have been
      determined as 5'GG/CGCC.
AU  - Sosnovtsev SV
AU  - Dedkov VS
AU  - Rechkunova NI
AU  - Zernov IP
AU  - Degtyarev SK
PT  - Journal Article
TA  - Sib. Biol. J.
JT  - Sib. Biol. J.
SO  - Sib. Biol. J. 1991 0: 66-67.

PMID- 27034492
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Mycobacterium bovis Strain BCG-1 (Russia).
PG  - e00182-16
AB  - Mycobacterium bovisBCG (Bacille Calmette-Guerin) is a vaccine strain used for protection
      against tuberculosis. Here, we announce the complete genome sequence
      ofM. bovisstrain BCG-1 (Russia). Extensive use of this strain necessitates the
      study of its genome stability by comparative analysis.
AU  - Sotnikova EA
AU  - Shitikov EA
AU  - Malakhova MV
AU  - Kostryukova ES
AU  - Ilina EN
AU  - Atrasheuskaya AV
AU  - Ignatyev GM
AU  - Vinokurova NV
AU  - Gorbachyov VY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00182-16.

PMID- 16517630
VI  - 72
DP  - 2006
TI  - Using DNA microarrays to identify library-independent markers for bacterial source tracking.
PG  - 1843-1851
AB  - Bacterial source tracking is used to apportion fecal pollution among
      putative sources. Within this context, library-independent markers are
      genetic or phenotypic traits that can be used to identify the host origin
      without a need for library-dependent classification functions. The
      objective of this project was to use mixed-genome Enterococcus microarrays
      to identify library-independent markers. Separate shotgun libraries were
      prepared for five host groups (cow, dog, elk/deer, human, and waterfowl),
      using genomic DNAs (gDNAs) from ca. 50 Enterococcus isolates for each
      library. Microarrays were constructed (864 probes per library), and 385
      comparative genomic hybridizations were used to identify putative markers.
      PCR assays were used to screen 95 markers against gDNAs from isolates from
      known sources collected throughout the United States. This validation
      process narrowed the selection to 15 markers, with 7 having no recognized
      homologues and the remaining markers being related to genes involved in
      metabolic pathways and DNA replication. In most cases, each marker was
      exclusive to one of four Enterococcus species (Enterococcus casseliflavus,
      E. faecalis, E. hirae, or E. mundtii). Eight markers were highly specific
      to either cattle, humans, or elk/deer, while the remaining seven markers
      were positive for various combinations of hosts other than humans. Based
      on microarray hybridization data, the prevalence of host-specific markers
      ranged from 2% to 45% of isolates collected from their respective hosts. A
      20-fold difference in prevalence could present challenges for the
      interpretation of library-independent markers.
AU  - Soule M
AU  - Kuhn E
AU  - Loge F
AU  - Gay J
AU  - Call DR
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2006 72: 1843-1851.

PMID- 11606594
VI  - 277
DP  - 2002
TI  - DNA Binding and Recognition by the IIs Restriction Endonuclease MboII.
PG  - 887-895
AB  - The type IIs restriction endonuclease MboII recognizes nonsymmetrical GAAGA sites, cutting 8
      (top strand) and 7 (bottom strand) bases to the right. Gel retardation showed that MboII bound
      specifically to GAAGA sequences, producing two distinct complexes each containing one MboII
      and one DNA molecule. Interference analysis indicated that the initial species formed, named
      complex 1, comprised an interaction between the enzyme and the GAAGA target. Complex 2
      involved interaction of the protein with both the GAAGA and the cutting sites. Only in the
      presence of divalent metal ions such as Ca(2+) is the conversion of complex 1 to 2 rapid.
      Additionally, a very retarded complex was seen with Ca(2+), possibly a (MboII)(2)-(DNA)(2)
      complex. Plasmids containing a single GAAGA site were hydrolyzed slowly by MboII. Plasmids
      containing two sites were cut far more rapidly, suggesting that the enzyme requires two
      recognition sites in the same DNA molecule for efficient hydrolysis. MboII appears to have a
      mechanism similar to the best characterized type IIs enzyme, FokI. Both enzymes initially bind
      DNA as monomers, followed by dimerization to give an (enzyme)(2)-(DNA)(2) complex.
      Dimerization is efficient only when the two target sites are located in the same DNA molecule
      and requires divalent metal ions.
AU  - Soundararajan M
AU  - Chang Z
AU  - Morgan RD
AU  - Heslop P
AU  - Connolly BA
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2002 277: 887-895.

PMID- 26184935
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Corynebacterium pseudotuberculosis Strain 12C.
PG  - e00759-15
AB  - We present here the complete genome sequence of Corynebacterium pseudotuberculosis strain 12C,
      isolated from a sheep abscess in the Brazil. The
      sequencing was performed with the Ion Torrent Personal Genome Machine (PGM)
      system, a fragment library, and a coverage of ~48-fold. The genome presented is a
      circular chromosome with 2,337,451 bp in length, 2,119 coding sequences, 12
      rRNAs, 49 tRNAs, and a G+C content of 52.83%.
AU  - Sousa TJ
AU  - Mariano D
AU  - Parise D
AU  - Parise M
AU  - Viana MV
AU  - Guimaraes LC
AU  - Benevides LJ
AU  - Rocha F
AU  - Bagano P
AU  - Ramos R
AU  - Silva A
AU  - Figueiredo H
AU  - Almeida S
AU  - Azevedo V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00759-15.

PMID- 26586896
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Amikacin- and Kanamycin-Resistant Mycobacterium tuberculosis MT433 without rrs and eis Mutations.
PG  - e01363-15
AB  - We announce the draft genome sequence of amikacin- and kanamycin-resistant Mycobacterium
      tuberculosis MT433, which has been previously described as the
      strain carrying an unknown resistance mechanism.
AU  - Sowajassatakul A
AU  - Coker OO
AU  - Prammananan T
AU  - Chaiprasert A
AU  - Phunpruch S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01363-15.

PMID- 
VI  - 0
DP  - 1995
TI  - Restriction-modification systems of methanogenic Archaea.
PG  - 505-506
AB  - Several type II restriction endonucleases have been isolated from methanogenic Archaea.  MaeI
      is the predominant restriction endonuclease isolated from Methanococcus aeolicus; MaeII and
      MaeIII appear in lower concentrations.  MaeI and MaeII recognize unique palindromic
      tetranucleotide sequences, and MaeIII recognizes a unique palindromic pentanucleotide
      sequence.  All three endonucleases produce 5' protruding ends.  MvnI from Methanococcus
      vanielii recognizes a tetranucleotide sequence and is an isoschizomer of the
      blunt-end-generating endonucleases ThaI and FnuDII.  All four methanogen endonucleases are
      available commercially.  Four endonuclease-methyltransferase systems have been identified.
      MwoI endonuclease (R.MwoI) and methyltransferase (M.MwoI) isolated from Methanobacterium
      wolfei are thermophilic (optimum activity 65oC) and recognize a unique sequence.  R.MwoI
      yields three nucleotide 3'-terminal extensions; M.MwoI is hypothesized to methylate C
      residues.  Both genes have been cloned and expressed at low levels in Escherichia coli.
      Plasmid-encoded R.MthI from Methanobacterium thermoautotrophicum is an isoschizomer of
      blunt-end-generating NgoPII.  Deduced amino acid sequence of R.MthTI is highly similar to that
      of R.NgoII, and M.MthTI has high sequence similarity to M.NgoPII and M.HaeIII.
      Plasmid-encoded MthFI and MthZI from M. thermoautotrophicum are isoschizomers of each other
      and of MaeI.  The restriction endonuclease and methyltransferase recognize a palindromic
      tetranucleotide.  The deduced amino acid sequence of M.MthZI shows significant similarity to
      that of m4C-MTases.  The occurrence of three restriction-modification systems that recognize
      CTAG within the methanogenic Archaea and reports that the CTAG sequence in DNA from species of
      halophilic Archaea is refractory to digestion by CTAG-specific XbaI, SpeI, and NheI suggest
      that CTAG-specific restriction-modification systems are more characteristic in the Archaea
      than in the Bacteria.  Continued characterization of restriction-modification systems in the
      methanogenic Archaea will be important for determining the compatibility of strains and DNA in
      the development of effective transgenic systems among archaeal species.
AU  - Sowers KR
PT  - Journal Article
TA  - Archaea: Methanogens: A laboratory manual.
JT  - Archaea: Methanogens: A laboratory manual.
SO  - Archaea: Methanogens: A laboratory manual. 1995 0: 505-506.

PMID- 2854812
VI  - 74
DP  - 1988
TI  - Molecular cloning and identification of protein products of rglB locus of Escherichia coli.
PG  - 51-52
AB  - Meeting Abstract
AU  - Sozhamannan S
AU  - Dharmalingam K
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 51-52.

PMID- 16859735
VI  - 46
DP  - 2006
TI  - Regulation of DNA methyltransferase 1.
PG  - 224-234
AB  - Although essentially all cells of a mammalian organism contain the same genetic information
      they may differ dramatically in form and function.  This cellular differentiation is
      established during development by cascades of transcription factors driving the expression of
      cell-type specific sets of genes.  These cell type specific gene expression patterns are
      established, maintained and changed in conjunction with epigenetic mechanisms including DNA
      methylation, histone modification and chromatin structure.  The most tangible epigenetic mark
      is DNA methylation, a postreplicative modification, which in vertebrates is mainly catalyzed
      by DNA methyltransferases (Dnmts: EC 2.1.1.37) 1, 3a and 3b at palindromic CpG sites.  The DNA
      methylation pattern changes along with cellular differentiation and is generally inversely
      correlated with transcriptional activity.  Over the past decade, several functional links
      between DNA methylation, histone modification, chromatin structure and transcriptional
      regulation have been discovered.  In mammalian cells Dnmt1 is the major and ubiquitously
      expressed Dnmt.  By direct and indirect interactions Dnmt1 plays a central role in the
      epigenetic networks controlling gene expression in development and disease.  We will outline
      results and open questions concerning the regulation of Dnmt1 and dicuss novel approaches to
      study Dnmts in living cells.
AU  - Spada F
AU  - Rothbauer U
AU  - Zolghadr K
AU  - Schermelleh L
AU  - Leonhardt H
PT  - Journal Article
TA  - Adv. Enzyme Regul.
JT  - Adv. Enzyme Regul.
SO  - Adv. Enzyme Regul. 2006 46: 224-234.

PMID- 23057602
VI  - 14
DP  - 2012
TI  - The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: Insights into metabolic versatility and environmental adaptations.
PG  - 3122-3145
AB  - The cohort of the ammonia-oxidizing archaea
      (AOA) of the phylum Thaumarchaeota is a diverse,
      widespread and functionally important group of
      microorganisms in many ecosystems. However, our
      understanding of their biology is still very rudimentary
      in part because all available genome sequences
      of this phylum are from members of the Nitrosopumilus
      cluster. Here we report on the complete
      genome sequence of Candidatus Nitrososphaera
      gargensis obtained from an enrichment culture, representing
      a different evolutionary lineage of AOA frequently found in high numbers in many terrestrial
      environments. With its 2.83 Mb the genome is much
      larger than that of other AOA. The presence of
      a high number of (active) IS elements/transposases,
      genomic islands, gene duplications and a complete
      CRISPR/Cas defence system testifies to its dynamic
      evolution consistent with low degree of synteny
      with other thaumarchaeal genomes. As expected,
      the repertoire of conserved enzymes proposed to be
      required for archaeal ammonia oxidation is encoded
      by N. gargensis, but it can also use urea and possibly
      cyanate as alternative ammonia sources. Furthermore,
      its carbon metabolism is more flexible at the
      central pyruvate switch point, encompasses the
      ability to take up small organic compounds and
      might even include an oxidative pentose phosphate
      pathway. Furthermore, we show that thaumarchaeota
      produce cofactor F420 as well as polyhydroxyalkanoates.
      Lateral gene transfer from bacteria and
      euryarchaeota has contributed to the metabolic
      versatility of N. gargensis. This organisms is well
      adapted to its niche in a heavy metal-containing
      thermal spring by encoding a multitude of heavy
      metal resistance genes, chaperones and mannosylglycerate
      as compatible solute and has the genetic
      ability to respond to environmental changes by signal
      transduction via a large number of two-component
      systems, by chemotaxis and flagella-mediated
      motility and possibly even by gas vacuole formation.
      These findings extend our understanding of thaumarchaeal
      evolution and physiology and offer many testable
      hypotheses for future experimental research on
      these nitrifiers.
AU  - Spang A et al
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2012 14: 3122-3145.

PMID- 25945739
VI  - 521
DP  - 2015
TI  - Complex archaea that bridge the gap between prokaryotes and eukaryotes.
PG  - 173-179
AB  - The origin of the eukaryotic cell remains one of the most contentious puzzles in  modern
      biology. Recent studies have provided support for the emergence of the
      eukaryotic host cell from within the archaeal domain of life, but the identity
      and nature of the putative archaeal ancestor remain a subject of debate. Here we
      describe the discovery of 'Lokiarchaeota', a novel candidate archaeal phylum,
      which forms a monophyletic group with eukaryotes in phylogenomic analyses, and
      whose genomes encode an expanded repertoire of eukaryotic signature proteins that
      are suggestive of sophisticated membrane remodelling capabilities. Our results
      provide strong support for hypotheses in which the eukaryotic host evolved from a
      bona fide archaeon, and demonstrate that many components that underpin
      eukaryote-specific features were already present in that ancestor. This provided
      the host with a rich genomic 'starter-kit' to support the increase in the
      cellular and genomic complexity that is characteristic of eukaryotes.
AU  - Spang A
AU  - Saw JH
AU  - Jorgensen SL
AU  - Zaremba-Niedzwiedzka K
AU  - Martijn J
AU  - Lind AE
AU  - van Eijk R
AU  - Schleper C
AU  - Guy L
AU  - Ettema TJ
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2015 521: 173-179.

PMID- Not carried by PubMed...
VI  - 83
DP  - 1983
TI  - Restriction endonuclease activities of Neisseria meningitidis.
PG  - 214
AB  - Restriction endonuclease activities present in different strains of Neisseria
      meningitidis were studied.  Enzymes from cell free sonicates were partially
      purified by Blue-2 cross linked agarose (Sigma) column chromatography.
      Restriction enzyme activity was eluted by 0.5 M NaCl in Tris-HCl buffer pH 7.6.
      Excess NaCl was dialyzed out against Tris-HCl buffer pH 7.6.  Restriction
      enzyme activity from different strains was assayed by 0.8% agarose slab gel
      electrophoresis.  Enzyme preparations from three different strains (DRES-W34,
      M1011 and DRES-30) gave three distinct restriction endonuclease (NmeI, NmeIII
      and NmeIV) activities.  Using a linear gradient of NaCl (from 0.0 to 0.5 M),
      two restriction endonuclease activities NmeI and NmeII present in DRES-W34 were
      separated into two distinct peaks.  These two enzyme activities were eluted at
      0.15 M NaCl and 0.25 NaCl respectively.  NmeI and NmeII gave 18 and 28 cleavage
      fragments when incubated with lambda DNA.  NmeII did not cleave SV-40 and
      PhiX174 DNA.  Restriction endonuclease NmeI was further characterized.  It was
      inhibited by 0.4 M NaCl but did require MgCl2 for its enzyme activity.  MgCl2
      at concentration above 0.02 M inhibited its enzyme activity completely.  NmeI
      activity was abolished completely after 30 min of incubation at 65C.  NmeI, II
      and III were quite stable when stored at -70C but NmeIV lost its activity.
AU  - Sparling R
AU  - Bhatti AR
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1983 83: 214.

PMID- 6099459
VI  - 41
DP  - 1984
TI  - NmeI, a restriction endonuclease from Neisseria meningitidis.
PG  - 73-79
AB  - A restriction endonuclease, NmeI, present in Neisseria meningitidis was
      partially purified by passing through a blue 2-cross linked agarose column, no
      contaminating nucleases remained detectable.  This enzyme cleaved phage lambda,
      adenovirus type 2 and PhiX174 DNA but did not cleave SV40 DNA.  It had an
      absolute requirement for Mg2+ for its activity and was inhibited by high
      concentrations of NaCl or MgCl2.  NmeI activity was completely abolished after
      1 h of incubation at 65C.  S-adenosyl-L-methionine and ATP had no effect on its
      activity suggesting that NmeI is a type II restriction endonuclease enzyme.  It
      is the first report of a restriction enzyme present in N. meningitidis.
AU  - Sparling R
AU  - Bhatti AR
PT  - Journal Article
TA  - Microbios
JT  - Microbios
SO  - Microbios 1984 41: 73-79.

PMID- 23788549
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Aeromonas molluscorum Strain 848TT, Isolated from Bivalve Molluscs.
PG  - e00382-13
AB  - We report here the draft genome sequence of Aeromonas molluscorum 848T, the type  strain of
      this Aeromonas species, which was isolated from wedge shells (Donax
      trunculus) obtained from a retail market in Barcelona, Spain, in 1997.
AU  - Spataro N
AU  - Farfan M
AU  - Albarral V
AU  - Sanglas A
AU  - Loren JG
AU  - Fuste MC
AU  - Bosch E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00382-13.

PMID- 10769743
VI  - 28
DP  - 2000
TI  - Efficient DNA subcloning through selective restriction endonuclease digestion.
PG  - 660-662
AB  - Described here is a selective restriction endonuclease digestion method that eliminates the
      electrophoresis step that is usually used during the subcloning of new DNA sequences into
      typical E. coli-based plasmids. The method increases yield while decreasing laboratory
      resource and time utilization. By using donor and acceptor sequences that contain unique
      restriction sites found only outside of the intended recombination sequences, the initial
      digestion products can be directly combined without electrophoresis if the ligation step is
      followed by a selective digestion using the unique restriction enzymes before transformation.
      This system is based on the several order of magnitude decrease in transformation efficiency
      of linearized compared to circular plasmids. As an example, this method was used to obtain
      recombinants between a 3.6 kb acceptor plasmid and 3.0 kb insert following one ligation
      reaction after the failure of nine standard reactions using similar amounts of input DNA. It
      is particularly applicable to situations in which low subcloning efficiencies are expected.
      The technique can be extended to a large percentage of planned recombinations by using
      nonidentical compatible cohesive or blunt-ended fragments, or site-directed mutagenesis.
AU  - Spear MA
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 2000 28: 660-662.

PMID- 24459271
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Enterococcus faecalis Strain PF3, Isolated from Adelie Penguin Feces from Antarctica.
PG  - e01209-13
AB  - Enterococcus faecalis is one of the leading causes of nosocomial infections and is a common
      commensal organism in humans and other animals. In this study, we
      report a draft genome sequence for the E. faecalis strain PF3, isolated from
      Adelie penguin feces collected from Warriner Island, Antarctica.
AU  - Spence RJ
AU  - Pavasovic A
AU  - Smith JJ
AU  - Prentis PJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01209-13.

PMID- 12562802
VI  - 185
DP  - 2003
TI  - Whole-genome sequence variation among multiple isolates of Pseudomonas aeruginosa.
PG  - 1316-1325
AB  - Whole-genome shotgun sequencing was used to study the sequence variation
      of three Pseudomonas aeruginosa isolates, two from clonal infections of
      cystic fibrosis patients and one from an aquatic environment, relative to
      the genomic sequence of reference strain PAO1. The majority of the PAO1
      genome is represented in these strains; however, at least three prominent
      islands of PAO1-specific sequence are apparent. Conversely, approximately
      10% of the sequencing reads derived from each isolate fail to align with
      the PAO1 backbone. While average sequence variation among all strains is
      roughly 0.5%, regions of pronounced differences were evident in
      whole-genome scans of nucleotide diversity. We analyzed two such divergent
      loci, the pyoverdine and O-antigen biosynthesis regions, by complete
      resequencing. A thorough analysis of isolates collected over time from one
      of the cystic fibrosis patients revealed independent mutations resulting
      in the loss of O-antigen synthesis alternating with a mucoid phenotype.
      Overall, we conclude that most of the PAO1 genome represents a core P.
      aeruginosa backbone sequence while the strains addressed in this study
      possess additional genetic material that accounts for at least 10% of
      their genomes. Approximately half of these additional sequences are novel.
AU  - Spencer DH
AU  - Kas A
AU  - Smith EE
AU  - Raymond CK
AU  - Sims EH
AU  - Hastings M
AU  - Burns JL
AU  - Kaul R
AU  - Olsen MV
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2003 185: 1316-1325.

PMID- 25573945
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Anammox Bacterium 'Candidatus Scalindua brodae,' Obtained Using Differential Coverage Binning of Sequencing Data from Two Reactor   Enrichments.
PG  - e01415-14
AB  - We present the draft genome of anammox bacterium 'Candidatus Scalindua brodae,' which at 282
      contigs is a major improvement over the highly fragmented genome
      assembly of related species 'Ca. Scalindua profunda' (1,580 contigs) which was
      previously published.
AU  - Speth DR
AU  - Russ L
AU  - Kartal B
AU  - Op den Camp HJ
AU  - Dutilh BE
AU  - Jetten MS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01415-14.

PMID- 16698548
VI  - 14
DP  - 2006
TI  - The Structure of I-CeuI Homing Endonuclease: Evolving Asymmetric DNA Recognition from a Symmetric Protein Scaffold.
PG  - 869-880
AB  - Homing endonucleases are highly specific catalysts of DNA strand breaks, leading to the
      transfer of mobile intervening sequences containing the
      endonuclease ORF. We have determined the structure and DNA recognition
      behavior of I-CeuI, a homodimeric LAGLIDADG endonuclease from
      Chlamydomonas eugametos. This symmetric endonuclease displays unique
      structural elaborations on its core enzyme fold, and it preferentially
      cleaves a highly asymmetric target site. This latter property represents
      an early step, prior to gene fusion, in the generation of asymmetric DNA
      binding platforms from homodimeric ancestors. The divergence of the
      sequence, structure, and target recognition behavior of homing
      endonucleases, as illustrated by this study, leads to the invasion of
      novel genomic sites by mobile introns during evolution.
AU  - Spiegel PC
AU  - Chevalier B
AU  - Sussman D
AU  - Turmel M
AU  - Lemieux C
AU  - Stoddard BL
PT  - Journal Article
TA  - Structure
JT  - Structure
SO  - Structure 2006 14: 869-880.

PMID- 3141151
VI  - 177
DP  - 1988
TI  - Structure of mouse DNA (cytosine-5-)-methyltransferase.
PG  - 29-34
AB  - DNA (cytosine-5-)-methyltransferase was purified as a single polypeptide (190
      kDa by SDS-PAGE) from mouse P815 mastocytoma cells.  This enzyme transfers
      methyl groups to unmethylated as well as to hemimethylated DNA sites with a
      strong preference for the hemimethylated substrate.  A structural analysis of
      the isolated enzyme by electron microscopical techniques was undertaken.  On
      the basis of the results obtained, we propose a model for the enzyme structure.
      This model describes the enzyme as a hemielliptical globular structure with
      dimensions of 5.4-6.7 nm for the height h and 10.3-10.8 nm for the diameter d,
      respectively; this globular structure bears a small appendix at the flat side.
      A molecular mass of 235-250 kDa is calculated from the measured dimensions.
      Limited trypsin digestion of the enzyme led to a 160-kDa fragment which
      preserved the gross morphology of the original material.  The possible
      structure function relationships are discussed.
AU  - Spiess E
AU  - Tomassetti A
AU  - Hernaiz-Driever P
AU  - Pfeifer GP
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1988 177: 29-34.

PMID- 27738041
VI  - 4
DP  - 2016
TI  - Complete Genome Sequences of Bordetella flabilis, Bordetella bronchialis, and 'Bordetella pseudohinzii'.
PG  - e01132-16
AB  - We report here the complete genome sequences of Bordetella flabilis and Bordetella bronchialis
      recovered from cultures of individuals with cystic
      fibrosis (CF), and 'Bordetella pseudohinzii' recovered from a CF mouse model.
AU  - Spilker T
AU  - Darrah R
AU  - LiPuma JJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01132-16.

PMID- 27103710
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of 63 Pseudomonas aeruginosa Isolates Recovered from Cystic Fibrosis Sputum.
PG  - e00231-16
AB  - Here, we report the draft genome sequences of 63 ITALIC! Pseudomonas aeruginosaisolates,
      recovered in culture of sputum from 15 individuals with
      cystic fibrosis (CF) receiving care in a single CF care center over a 13-year
      period. These sequences add value to studies of within-host evolution of
      bacterial pathogens during chronic infection.
AU  - Spilker T
AU  - LiPuma JJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00231-16.

PMID- 26634766
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Marine Pathogen Vibrio coralliilyticus RE22.
PG  - e01432-15
AB  - Vibrio coralliilyticus RE22 is a causative agent of vibriosis in larval bivalves. We report
      here the draft genome sequence of V. coralliilyticus RE22 and describe
      additional virulence factors that may provide insight into its mechanism of
      pathogenicity.
AU  - Spinard E
AU  - Kessner L
AU  - Gomez-Chiarri M
AU  - Rowley DC
AU  - Nelson DR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01432-15.

PMID- 27469949
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the Emerging Bivalve Pathogen Vibrio tubiashii subsp. europaeus.
PG  - e00625-16
AB  - Vibrio tubiashii subsp. europaeus is a bivalve pathogen isolated during episodes  of mortality
      affecting larval cultures in different shellfish hatcheries. Here,
      we announce the draft genome sequence of the type strain PP-638 and describe
      potential virulence factors, which may provide insight into the mechanism of
      pathogenicity.
AU  - Spinard EJ
AU  - Dubert J
AU  - Nelson DR
AU  - Gomez-Chiarri M
AU  - Barja JL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00625-16.

PMID- 2174670
VI  - 114
DP  - 1990
TI  - Restriction enzymes.  To the Editor.
PG  - 1190
AB  - In his article on restriction enzymes in the Archives, Dr. Ross omits the important effects of
      methylation on the activity of restriction enzymes.  The ability of a restriction endonuclease
      to cleave and inactivate invading bacteriophage DNA without destroying the bacterial
      chromosome depends on the presence within the cell of a corresponding modification methylase
      that recognizes the same DNA sequence and methylates either an adenine or a cytosine, thus
      rendering the sequence resistant to cleavage.  It is the methylation of restriction sites
      present on the chromosome, not the absence of such sites (as suggested in the article), that
      enables restriction-modification systems to distinguish "self" from "non- self" DNA;
      bacteriophage DNA that has been modified by the EcoRI methylase is also resistant to the
      action of the EcoRI endonuclease.
AU  - Spitzer ED
PT  - Journal Article
TA  - Arch. Pathol. Lab. Med.
JT  - Arch. Pathol. Lab. Med.
SO  - Arch. Pathol. Lab. Med. 1990 114: 1190.

PMID- 110588
VI  - 95
DP  - 1979
TI  - Colivirus-T3-coded S-adenosylmethionine hydrolase.
PG  - 227-233
AB  - Bacteriophage T3 induces an enzyme activity which hydrolyzes
      S-adenosylmethionine.  This S-adenosylmethionine hydrolase is interesting, not
      only because of its unique activity, but also because the protein has to
      overcome host restriction.  S-adenosylmethionine hydrolase was purified to
      homogeneity using affinity chromatography on S-adenosylhomocysteine-Sepharose.
      The enzyme occurs in two forms, A and B.  Form A consists of the viral peptide
      chain only; its native and subunit molecular weight is 17,000.  Form B
      contains, in addition, a host subunit with a molecular weight of 49,000.  The
      host subunit does not modifiy S-adenosylmethionine cleavage in vitro and no
      apparent relationship to the host-restriction system could be detected.
AU  - Spoerel N
AU  - Herrlich P
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1979 95: 227-233.

PMID- 763348
VI  - 278
DP  - 1979
TI  - A novel bacteriophage defence mechanism: the anti-restriction protein.
PG  - 30-34
AB  - Bacteriophage T3 and T7 protect their DNA from restriction by producing, as the
      earliest detectable phage functions, anti-restriction proteins.  Although the
      two phage proteins differ in their chromatographic and antigenic properties,
      they act by the same mechanism: the anti-restriction proteins inhibit E. coli
      K12 restriction endonuclease by direct interaction.
AU  - Spoerel N
AU  - Herrlich P
AU  - Bickle TA
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1979 278: 30-34.

PMID- 24675860
VI  - 2
DP  - 2014
TI  - Genome Sequence of Yersinia similis Y228T, a Member of the Yersinia pseudotuberculosis Complex.
PG  - e00216-14
AB  - We report here on the genome sequence of Yersinia similis 228(T) isolated in Germany. The
      genome has a size of 4.9 Mb and a G+C content of 47% and is
      predicted to contain 4,135 coding sequences. Annotation of the 60,687-bp
      extrachromosomal element predicted 67 coding sequences and a G+C content of
      47.8%.
AU  - Sprague LD
AU  - Neubauer H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00216-14.

PMID- 26383649
VI  - 3
DP  - 2015
TI  - De Novo Genome Sequence of Yersinia aleksiciae Y159T.
PG  - e01066-15
AB  - We report here on the genome sequence of Yersinia aleksiciae Y159(T), isolated in Finland in
      1981. The genome has a size of 4 Mb, a G+C content of 49%, and is predicted to contain 3,423
      coding sequences.
AU  - Sprague LD
AU  - Neubauer H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01066-15.

PMID- 28408677
VI  - 5
DP  - 2017
TI  - Genome Sequence of Pasteurella multocida Razi 0002 of Avian Origin.
PG  - e00161-17
AB  - We report here on the genome sequence of Pasteurella multocida Razi 0002 of avian origin,
      isolated in Iran. The genome has a size of 2,289,036 bp, a G+C content of
      40.3%, and is predicted to contain 2,079 coding sequences.
AU  - Sprague LD
AU  - Tadayon K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00161-17.

PMID- 28153892
VI  - 5
DP  - 2017
TI  - Genome Sequence of Pasteurella multocida Strain Razi_Pm0001.
PG  - e01532-16
AB  - We report here the genome sequence of Pasteurella multocida Razi_Pm0001 from bovine origin,
      isolated in Iran in 1936. The genome has a size of 2,360,663 bp, a
      G+C content of 40.4%, and is predicted to contain 2,052 coding sequences.
AU  - Sprague LD
AU  - Tadayon K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01532-16.

PMID- 23408247
VI  - 7
DP  - 2012
TI  - Complete genome sequence of the sulfate-reducing firmicute Desulfotomaculum ruminis type strain (DL(T)).
PG  - 304-319
AB  - Desulfotomaculum ruminis Campbell and Postgate 1965 is a member of the large genus
      Desulfotomaculum which contains 30 species and is contained in the family
      Peptococcaceae. This species is of interest because it represents one of the few
      sulfate-reducing bacteria that have been isolated from the rumen. Here we
      describe the features of D. ruminis together with the complete genome sequence
      and annotation. The 3,969,014 bp long chromosome with a total of 3,901
      protein-coding and 85 RNA genes is the second completed genome sequence of a type
      strain of the genus Desulfotomaculum to be published, and was sequenced as part
      of the DOE Joint Genome Institute Community Sequencing Program 2009.
AU  - Spring S et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 7: 304-319.

PMID- 21304664
VI  - 1
DP  - 2009
TI  - Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575).
PG  - 242-253
AB  - Desulfotomaculum acetoxidans Widdel and Pfennig 1977 was one of the first sulfate-reducing
      bacteria known to grow with acetate as sole energy and carbon
      source. It is able to oxidize substrates completely to carbon dioxide with
      sulfate as the electron acceptor, which is reduced to hydrogen sulfide. All
      available data about this species are based on strain 5575(T), isolated from
      piggery waste in Germany. Here we describe the features of this organism,
      together with the complete genome sequence and annotation. This is the first
      completed genome sequence of a Desulfotomaculum species with validly published
      name. The 4,545,624 bp long single replicon genome with its 4370 protein-coding
      and 100 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea
      project.
AU  - Spring S et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2009 1: 242-253.

PMID- 21304676
VI  - 2
DP  - 2010
TI  - Complete genome sequence of Desulfohalobium retbaense type strain (HR(100)).
PG  - 38-48
AB  - Desulfohalobium retbaense (Ollivier et al. 1991) is the type species of the polyphyletic genus
      Desulfohalobium, which comprises, at the time of writing, two
      species and represents the family Desulfohalobiaceae within the
      Deltaproteobacteria. D. retbaense is a moderately halophilic sulfate-reducing
      bacterium, which can utilize H(2) and a limited range of organic substrates,
      which are incompletely oxidized to acetate and CO(2), for growth. The type strain
      HR(100) (T) was isolated from sediments of the hypersaline Retba Lake in Senegal.
      Here we describe the features of this organism, together with the complete genome
      sequence and annotation. This is the first completed genome sequence of a member
      of the family Desulfohalobiaceae. The 2,909,567 bp genome (one chromosome and a
      45,263 bp plasmid) with its 2,552 protein-coding and 57 RNA genes is a part of
      the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Spring S et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 2: 38-48.

PMID- 21304709
VI  - 2
DP  - 2010
TI  - Complete genome sequence of Thermosphaera aggregans type strain (M11TL).
PG  - 245-259
AB  - Thermosphaera aggregans Huber et al. 1998 is the type species of the genus Thermosphaera,
      which comprises at the time of writing only one species. This
      species represents archaea with a hyperthermophilic, heterotrophic, strictly
      anaerobic and fermentative phenotype. The type strain M11TL(T) was isolated from
      a water-sediment sample of a hot terrestrial spring (Obsidian Pool, Yellowstone
      National Park, Wyoming). Here we describe the features of this organism, together
      with the complete genome sequence and annotation. The 1,316,595 bp long single
      replicon genome with its 1,410 protein-coding and 47 RNA genes is a part of the
      Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Spring S et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 2: 245-259.

PMID- 27300277
VI  - 10
DP  - 2016
TI  - Characterization of the first cultured representative of Verrucomicrobia subdivision 5 indicates the proposal of a novel phylum.
PG  - 2801-2816
AB  - The recently isolated strain L21-Fru-ABT represents moderately halophilic,
      obligately anaerobic and saccharolytic bacteria that thrive in the suboxic
      transition zones of hypersaline microbial mats. Phylogenetic analyses based on
      16S rRNA genes, RpoB proteins and gene content indicated that strain L21-Fru-ABT
      represents a novel species and genus affiliated with a distinct phylum-level
      lineage originally designated Verrucomicrobia subdivision 5. A survey of
      environmental 16S rRNA gene sequences revealed that members of this newly
      recognized phylum are wide-spread and ecologically important in various anoxic
      environments ranging from hypersaline sediments to wastewater and the intestine
      of animals. Characteristic phenotypic traits of the novel strain included the
      formation of extracellular polymeric substances, a Gram-negative cell wall
      containing peptidoglycan and the absence of odd-numbered cellular fatty acids.
      Unusual metabolic features deduced from analysis of the genome sequence were the
      production of sucrose as osmoprotectant, an atypical glycolytic pathway lacking
      pyruvate kinase and the synthesis of isoprenoids via mevalonate. On the basis of
      the analyses of phenotypic, genomic and environmental data, it is proposed that
      strain L21-Fru-ABT and related bacteria are specifically adapted to the
      utilization of sulfated glycopolymers produced in microbial mats or biofilms.
AU  - Spring S
AU  - Bunk B
AU  - Sproer C
AU  - Schumann P
AU  - Rohde M
AU  - Tindall BJ
AU  - Klenk HP
PT  - Journal Article
TA  - ISME J.
JT  - ISME J.
SO  - ISME J. 2016 10: 2801-2816.

PMID- 25414506
VI  - 2
DP  - 2014
TI  - Genome Sequence of Gammaproteobacterial Pseudohaliea rubra Type Strain DSM 19751, Isolated from Coastal Seawater of the Mediterranean Sea.
PG  - e01208-14
AB  - Pseudohaliea rubra strain DSM 19751T is an aerobic marine gammaproteobacterium that was
      isolated from surface coastal seawater of the Mediterranean Sea. Here,
      we present its genome sequence and annotation. Genome analysis revealed the
      presence of genes involved in the synthesis of bacteriochlorophyll-a and the
      reserve compound glycogen.
AU  - Spring S
AU  - Fiebig A
AU  - Riedel T
AU  - Goker M
AU  - Klenk HP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01208-14.

PMID- 20966086
VI  - 157
DP  - 2011
TI  - Variation in a surface-exposed region of the Mycoplasma pneumoniae P40 protein as a consequence of homologous DNA recombination between RepMP5  elements.
PG  - 473-483
AB  - Mycoplasma pneumoniae is a human pathogen that causes a range of respiratory tract infections.
      The first step in infection is adherence of
      the bacteria to the respiratory epithelium. This step is mediated by a
      specialized organelle, which contains several proteins (cytadhesins) that
      have an important function in adherence. Two of these cytadhesins, P40 and
      P90, represent the proteolytic products from a single
AU  - Spuesens EB
AU  - van de Kreeke N
AU  - Estevao S
AU  - Hoogenboezem T
AU  - Sluijter M
AU  - Hartwig NG
AU  - van Rossum AM
AU  - Vink C
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2011 157: 473-483.

PMID- 12888347
VI  - 331
DP  - 2003
TI  - Structural and Biochemical Characterization of a New Mg2+ Binding Site Near Tyr94 in the Restriction Endonuclease PvuII.
PG  - 395-406
AB  - We have determined the crystal structure of the PvuII endonuclease in the presence of Mg(2+).
      According to the structural data, divalent metal ion
      binding in the PvuII subunits is highly asymmetric. The PvuII-Mg(2+)
      complex has two distinct metal ion binding sites, one in each monomer. One
      site is formed by the catalytic residues Asp58 and Glu68, and has
      extensive similarities to a catalytically important site found in all
      structurally examined restriction endonucleases. The other binding site is
      located in the other monomer, in the immediate vicinity of the hydroxyl
      group of Tyr94; it has no analogy to metal ion binding sites found so far
      in restriction endonucleases. To assign the number of metal ions involved
      and to better understand the role of Mg(2+) binding to Tyr94 for the
      function of PvuII, we have exchanged Tyr94 by Phe and characterized the
      metal ion dependence of DNA cleavage of wild-type PvuII and the Y94F
      variant. Wild-type PvuII cleaves both strands of the DNA in a concerted
      reaction. Mg(2+) binding, as measured by the Mg(2+) dependence of DNA
      cleavage, occurs with a Hill coefficient of 4, meaning that at least two
      metal ions are bound to each subunit in a cooperative fashion upon
      formation of the active complex. Quenched-flow experiments show that DNA
      cleavage occurs about tenfold faster if Mg(2+) is pre-incubated with
      enzyme or DNA than if preformed enzyme-DNA complexes are mixed with
      Mg(2+). These results show that Mg(2+) cannot easily enter the active
      center of the preformed enzyme-DNA complex, but that for fast cleavage the
      metal ions must already be bound to the apoenzyme and carried with the
      enzyme into the enzyme-DNA complex. The Y94F variant, in contrast to
      wild-type PvuII, does not cleave DNA in a concerted manner and metal ion
      binding occurs with a Hill coefficient of 1. These results indicate that
      removal of the Mg(2+) binding site at Tyr94 completely disrupts the
      cooperativity in DNA cleavage. Moreover, in quenched-flow experiments Y94F
      cleaves DNA about ten times more slowly than wild-type PvuII, regardless
      of the order of mixing. From these results we conclude that wild-type
      PvuII cleaves DNA in a fast and concerted reaction, because the Mg(2+)
      required for catalysis are already bound at the enzyme, one of them at
      Tyr94. We suggest that this Mg(2+) is shifted to the active center during
      binding of a specific DNA substrate. These results, for the first time,
      shed light on the pathway by which metal ions as essential cofactors enter
      the catalytic center of restriction endonucleases.
AU  - Spyridaki A
AU  - Matzen C
AU  - Lanio T
AU  - Jeltsch A
AU  - Simoncsits A
AU  - Athanasiadis A
AU  - Scheuring-Vanamee E
AU  - Kokkinidis M
AU  - Pingoud A
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2003 331: 395-406.

PMID- 25278517
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of a Psychrophilic Bacterium, Sphingomonas antarcticum, Isolated from the Soils of Schirmacher Oasis, Antarctica.
PG  - e00696-14
AB  - We report the 4.5-Mbp genome sequences of Sphingobacterium antarcticum 4BY, a psychrophilic
      bacterium isolated from the soils of Schirmacher Oasis, Antarctica.
      The draft genome of S. antarcticum strain 4BY consists of 4,566,318 bp with 40.4%
      G+C content, 4,234 protein coding genes, and 52 RNAs.
AU  - Sreenivas A
AU  - Sathyanarayana RG
AU  - Shivaji S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00696-14.

PMID- 19390608
VI  - 5
DP  - 2009
TI  - Phasevarions Mediate Random Switching of Gene Expression in Pathogenic Neisseria.
PG  - e1000400
AB  - Many host-adapted bacterial pathogens contain DNA methyltransferases (mod genes) that are
      subject to phase-variable expression
      (high-frequency reversible ON/OFF switching of gene expression). In
      Haemophilus influenzae, the random switching of the modA gene controls
      expression of a phase-variable regulon of genes (a phasevarion), via
      differential methylation of the genome in the modA ON and OFF states.
      Phase-variable mod genes are also present in Neisseria meningitidis and
      Neisseria gonorrhoeae, suggesting that phasevarions may occur in these
      important human pathogens. Phylogenetic studies on phase-variable mod
      genes associated with type III restriction modification (R-M) systems
      revealed that these organisms have two distinct mod genes-modA and
      modB. There are also distinct alleles of modA (abundant: modA11, 12,
      13; minor: modA4, 15, 18) and modB (modB1, 2). These alleles differ
      only in their DNA recognition domain. ModA11 was only found in N.
      meningitidis and modA13 only in N. gonorrhoeae. The recognition site
      for the modA13 methyltransferase in N. gonorrhoeae strain FA1090 was
      identified as 5'-AGAAA-3'. Mutant strains lacking the modA11, 12 or 13
      genes were made in N. meningitidis and N. gonorrhoeae and their
      phenotype analyzed in comparison to a corresponding mod ON wild-type
      strain. Microarray analysis revealed that in all three modA alleles
      multiple genes were either upregulated or downregulated, some of which
      were virulence-associated. For example, in N. meningitidis MC58
      (modA11), differentially expressed genes included those encoding the
      candidate vaccine antigens lactoferrin binding proteins A and B.
      Functional studies using N. gonorrhoeae FA1090 and the clinical isolate
      O1G1370 confirmed that modA13 ON and OFF strains have distinct
      phenotypes in antimicrobial resistance, in a primary human cervical
      epithelial cell model of infection, and in biofilm formation. This
      study, in conjunction with our previous work in H. influenzae,
      indicates that phasevarions may be a common strategy used by
      host-adapted bacterial pathogens to randomly switch between
      differentiated cell types.
AU  - Srikhanta YN
AU  - Dowideit SJ
AU  - Edwards JL
AU  - Falsetta ML
AU  - Wu HJ
AU  - Harrison OB
AU  - Fox KL
AU  - Seib KL
AU  - Maguire TL
AU  - Wang AHJ
AU  - Maiden MC
AU  - Grimmond SM
AU  - Apicella MA
AU  - Jennings MP
PT  - Journal Article
TA  - PLoS Pathog.
JT  - PLoS Pathog.
SO  - PLoS Pathog. 2009 5: e1000400.

PMID- 20140025
VI  - 8
DP  - 2010
TI  - The phasevarion: phase variation of type III DNA methyltransferases controls coordinated switching in multiple genes.
PG  - 196-206
AB  - In several host-adapted pathogens, phase variation has been found to occur in genes that
      encode methyltransferases associated with type III restriction-modification systems. It was
      recently shown that in the human pathogens Haemophilus influenzae, Neisseria gonorrhoeae and
      Neisseria meningitidis phase variation of a type III DNA methyltransferase, encoded by members
      of the mod gene family, regulates the expression of multiple genes. This novel genetic system
      has been termed the 'phasevarion' (phase-variable regulon). The wide distribution of
      phase-variable mod family genes indicates that this may be a common strategy used by
      host-adapted bacterial pathogens to randomly switch between distinct cell types.
AU  - Srikhanta YN
AU  - Fox KL
AU  - Jennings MP
PT  - Journal Article
TA  - Nat. Rev. Microbiol.
JT  - Nat. Rev. Microbiol.
SO  - Nat. Rev. Microbiol. 2010 8: 196-206.

PMID- 28947652
VI  - 85
DP  - 2017
TI  - Phasevarion-Regulated Virulence in the Emerging Pediatric Pathogen Kingella kingae.
PG  - e00319-17
AB  - Kingella kingae is a common etiological agent of pediatric osteoarticular infections. While
      current research has expanded our understanding of K. kingae
      pathogenesis, there is a paucity of knowledge about host-pathogen interactions
      and virulence gene regulation. Many host-adapted bacterial pathogens contain
      phase variable DNA methyltransferases (mod genes), which can control expression
      of a regulon of genes (phasevarion) through differential methylation of the
      genome. Here, we identify a phase variable type III mod gene in K. kingae,
      suggesting that phasevarions operate in this pathogen. Phylogenetic studies
      revealed that there are two active modK alleles in K. kingae Proteomic analysis
      of secreted and surface-associated proteins, quantitative PCR, and a heat shock
      assay comparing the wild-type modK1 ON (i.e., in frame for expression) strain to
      a modK1 OFF (i.e., out of frame) strain revealed three virulence-associated genes
      under ModK1 control. These include the K. kingae toxin rtxA and the heat shock
      genes groEL and dnaK Cytokine expression analysis showed that the interleukin-8
      (IL-8), IL-1beta, and tumor necrosis factor responses of THP-1 macrophages were
      lower in the modK1 ON strain than in the modK1::kan mutant. This suggests that
      the ModK1 phasevarion influences the host inflammatory response and provides the
      first evidence of this phase variable epigenetic mechanism of gene regulation in
      K. kingae.
AU  - Srikhanta YN
AU  - Fung KY
AU  - Pollock GL
AU  - Bennett-Wood V
AU  - Howden BP
AU  - Hartland EL
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2017 85: e00319-17.

PMID- 29170397
VI  - 7
DP  - 2017
TI  - Methylomic and phenotypic analysis of the ModH5 phasevarion of Helicobacter pylori.
PG  - 16140
AB  - The Helicobacter pylori phase variable gene modH, typified by gene HP1522 in strain 26695,
      encodes a N(6)-adenosine type III DNA methyltransferase. Our
      previous studies identified multiple strain-specific modH variants (modH1 -
      modH19) and showed that phase variation of modH5 in H. pylori P12 influenced
      expression of motility-associated genes and outer membrane protein gene hopG.
      However, the ModH5 DNA recognition motif and the mechanism by which ModH5
      controls gene expression were unknown. Here, using comparative single molecule
      real-time sequencing, we identify the DNA site methylated by ModH5 as
      5'-G(m6)ACC-3'. This motif is vastly underrepresented in H. pylori genomes, but
      overrepresented in a number of virulence genes, including motility-associated
      genes, and outer membrane protein genes. Motility and the number of flagella of
      H. pylori P12 wild-type were significantly higher than that of isogenic modH5 OFF
      or DeltamodH5 mutants, indicating that phase variable switching of modH5
      expression plays a role in regulating H. pylori motility phenotypes. Using the
      flagellin A (flaA) gene as a model, we show that ModH5 modulates flaA promoter
      activity in a GACC methylation-dependent manner. These findings provide novel
      insights into the role of ModH5 in gene regulation and how it mediates epigenetic
      regulation of H. pylori motility.
AU  - Srikhanta YN
AU  - Gorrell RJ
AU  - Power PM
AU  - Tsyganov K
AU  - Boitano M
AU  - Clark TA
AU  - Korlach J
AU  - Hartland EL
AU  - Jennings MP
AU  - Kwok T
PT  - Journal Article
TA  - Sci. Rep.
JT  - Sci. Rep.
SO  - Sci. Rep. 2017 7: 16140.

PMID- 22162751
VI  - 6
DP  - 2011
TI  - Phasevarion Mediated Epigenetic Gene Regulation in Helicobacter pylori.
PG  - e27569
AB  - Many host-adapted bacterial pathogens contain DNA methyltransferases (mod genes) that are
      subject to phase-variable expression
      (high-frequency reversible ON/OFF switching of gene expression). In
      Haemophilus influenzae and pathogenic Neisseria, the random switching
      of the modA gene, associated with a phase-variable type III restriction
      modification (R-M) system, controls expression of a phase-variable
      regulon of genes (a 'phasevarion'), via differential methylation of
      the genome in the modA ON and OFF states. Phase-variable type III R-M
      systems are also found in Helicobacter pylori, suggesting that
      phasevarions may also exist in this key human pathogen. Phylogenetic
      studies on the phase-variable type III modH gene revealed that there
      are 17 distinct alleles in H. pylori, which differ only in their DNA
      recognition domain. One of the most commonly found alleles was modH5
      (16% of isolates). Microarray analysis comparing the wild-type P12modH5
      ON strain to a P12 Delta modH5 mutant revealed that six genes were
      either up-or down-regulated, and some were virulence-associated. These
      included flaA, which encodes a flagella protein important in motility
      and hopG, an outer membrane protein essential for colonization and
      associated with gastric cancer. This study provides the first evidence
      of this epigenetic mechanism of gene expression in H. pylori.
      Characterisation of H. pylori modH phasevarions to define stable
      immunological targets will be essential for vaccine development and may
      also contribute to understanding H. pylori pathogenesis.
AU  - Srikhanta YN
AU  - Gorrell RJ
AU  - Steen JA
AU  - Gawthorne JA
AU  - Kwok T
AU  - Grimmond SM
AU  - Robins-Browne RM
AU  - Jennings MP
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2011 6: e27569.

PMID- 15802471
VI  - 102
DP  - 2005
TI  - The phasevarion: a genetic system controlling coordinated, random switching of expression of multiple genes.
PG  - 5547-5551
AB  - Several host-adapted bacterial pathogens contain methyltransferases associated with type III
      restriction-modification (R-M) systems that are
      subject to reversible, high-frequency on/off switching of expression
      (phase variation). To investigate the role of phase-variable expression of
      R-M systems, we made a mutant strain lacking the methyltransferase (mod)
      associated with a type III R-M system of Haemophilus influenzae and
      analyzed its phenotype. By microarray analysis, we identified a number of
      genes that were either up- or down-regulated in the mod mutant strain.
      This system reports the coordinated random switching of a set of genes in
      a bacterial pathogen and may represent a widely used mechanism.
AU  - Srikhanta YN
AU  - Maguire TL
AU  - Stacey KJ
AU  - Grimmond SM
AU  - Jennings MP
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2005 102: 5547-5551.

PMID- 
VI  - 66
DP  - 2005
TI  - Construction of a marker-free DNA adenine methylase (Dam) mutant of Burkholderia pseudomallei.
PG  - 550
AB  - Burkholderia pseudomallei is the causative agent of melioidosis, a severe disease of humans
      and animals.  Presently no vaccine exists to protect against meliodosis.  It has recently been
      shown that DNA adenine methylase mutants of Salmonella enterica serovar Typhimurium are
      markedly attenuated but highly effective as live vaccines against Salmonella infection of mice
      and chickens.  To determine if this observation could be extended to B. pseudomallei, a
      marker-free Dam mutant of B. pseudomallei was constructed and characterized.  The deletion has
      been fully defined at the molecular level with no foreign DNA or drug resistance gene remain
      in the B. pseudomallei mutant strain.  The dam mutant of B. pseudomallei was constructed by
      using in vitro directed mutagenesis.  The first step, the B. pseudomallei dam gene was
      PCR-amplified and the PCR product was digested with SmaI/SalI and ligated into pUC18.  The
      ligated products were introduced into E.coli DH5a by electroporation and one clone with the
      predicted insert size was selected and designated pPHE157.  The cloned gene was sequenced and
      found 100% identity with that of the published sequence.  The next step, the 175 bp StyI/EagI
      fragment located within the dam gene in pPHE157 was deleted to yield pPHE158.  The SmaI/SalI
      fragment containing the Delta-dam was cloned into pEG19Tc replacement vector containing the
      counterselectable sacB marker and transferred from E. coli PHE122-1 to B. pseudomallei
      wild-type strain by conjugation method.  One desired dam mutants of B. pseudomallei designated
      PHB 136 was positively identified on the basis of sucrose tolerance on sucrose containing
      media.  The phenotype of this dam mutant strain was confirmed by its sensitivity to the
      2-aminopurine and by restriction analysis using MboI endonuclease, which recognize and cleaves
      DNA at non-methylated GATC sequences.  The genotype of the dam mutant was further confirmed by
      PCR and Southern blot analysis.  Studies aimed to determine the attenuation level and vaccine
      efficacy in a mouse model of this dam mutant are underway.
AU  - Srilunchang M
AU  - Homchampa P
AU  - Proungvitaya T
AU  - Wongratanacheewin S
PT  - Journal Article
TA  - Tissue Antigens
JT  - Tissue Antigens
SO  - Tissue Antigens 2005 66: 550.

PMID- 25053786
VI  - 5
DP  - 2014
TI  - vanG element insertions within a conserved chromosomal site conferring vancomycin resistance to Streptococcus agalactiae and Streptococcus anginosus.
PG  - E01386-E01314
AB  - Three vancomycin-resistant streptococcal strains carrying vanG elements (two
      invasive Streptococcus agalactiae isolates [GBS-NY and GBS-NM, both serotype II
      and multilocus sequence type 22] and one Streptococcus anginosus [Sa]) were
      examined. The 45,585-bp elements found within Sa and GBS-NY were nearly identical
      (together designated vanG-1) and shared near-identity over an ~15-kb overlap with
      a previously described vanG element from Enterococcus faecalis. Unexpectedly,
      vanG-1 shared much less homology with the 49,321-bp vanG-2 element from GBS-NM,
      with widely different levels (50% to 99%) of sequence identity shared among 44
      related open reading frames. Immediately adjacent to both vanG-1 and vanG-2 were
      44,670-bp and 44,680-bp integrative conjugative element (ICE)-like sequences,
      designated ICE-r, that were nearly identical in the two group B streptococcal
      (GBS) strains. The dual vanG and ICE-r elements from both GBS strains were
      inserted at the same position, between bases 1328 and 1329, within the identical
      RNA methyltransferase (rumA) genes. A GenBank search revealed that although most
      GBS strains contained insertions within this specific site, only sequence type 22
      (ST22) GBS strains contained highly related ICE-r derivatives. The vanG-1 element
      in Sa was also inserted within this position corresponding to its rumA homolog
      adjacent to an ICE-r derivative. vanG-1 insertions were previously reported
      within the same relative position in the E. faecalis rumA homolog. An ICE-r
      sequence perfectly conserved with respect to its counterpart in GBS-NY was
      apparent within the same site of the rumA homolog of a Streptococcus dysgalactiae
      subsp. equisimilis strain. Additionally, homologous vanG-like elements within the
      conserved rumA target site were evident in Roseburia intestinalis. Importance:
      These three streptococcal strains represent the first known vancomycin-resistant
      strains of their species. The collective observations made from these strains
      reveal a specific hot spot for insertional elements that is conserved between
      streptococci and different Gram-positive species. The two GBS strains potentially
      represent a GBS lineage that is predisposed to insertion of vanG elements.
AU  - Srinivasan V
AU  - Metcalf BJ
AU  - Knipe KM
AU  - Ouattara M
AU  - McGee L
AU  - Shewmaker PL
AU  - Glennen A
AU  - Nichols M
AU  - Harris C
AU  - Brimmage M
AU  - Ostrowsky B
AU  - Park CJ
AU  - Schrag SJ
AU  - Frace MA
AU  - Sammons SA
AU  - Beall B
PT  - Journal Article
TA  - MBio
JT  - MBio
SO  - MBio 2014 5: E01386-E01314.

PMID- 23929469
VI  - 1
DP  - 2013
TI  - Genome Sequence of Staphylococcus massiliensis Strain S46, Isolated from the Surface of Healthy Human Skin.
PG  - e00553-13
AB  - Staphylococcus massiliensis strain S46 was isolated from the surface of healthy human skin.
      Here, we report the draft genome sequence of S. massiliensis S46
      (2,447,110 bp, with a G+C content of 36.3%).
AU  - Srivastav R
AU  - Singh A
AU  - Jangir PK
AU  - Kumari C
AU  - Muduli S
AU  - Sharma R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00553-13.

PMID- 6795184
VI  - 148
DP  - 1981
TI  - Deoxyribonucleic acid methylation in mycobacteria.
PG  - 716-719
AB  - Deoxyribonucleic acid modification in six strains of mycobacteria was investigated. The
      presence of 5-methylcytosine in the virulent strain
      Mycobacterium tuberculosis H37Rv and its absence in the avirulent strain M.
      tuberculosis H37Ra and other saprophytic, fast-growing mycobacteria appear to be
      the salient features. However, deoxyribonucleic acid from M. smegmatis SN2
      lysogenized with the temperature phage I3 showed the presence of
      5-methylcytosine. All of the strains had N6-methyladenine.
AU  - Srivastava R
AU  - Gopinathan KP
AU  - Ramakrishnan T
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1981 148: 716-719.

PMID- 
VI  - 3
DP  - 2003
TI  - Expression of a mitochondrially targeted restriction endonuclease in skeletal muscle causes a mitochondrial myopathy.
PG  - 158-159
AB  - 
AU  - Srivastava S
AU  - Moraes CT
PT  - Journal Article
TA  - Mitochondrion
JT  - Mitochondrion
SO  - Mitochondrion 2003 3: 158-159.

PMID- 11751691
VI  - 10
DP  - 2001
TI  - Manipulating mitochondrial DNA heteroplasmy by a mitochondrially targeted restriction endonuclease.
PG  - 3093-3099
AB  - Mutations in the mitochondrial DNA (mtDNA) can cause a variety of human diseases. In most
      cases, such mutations are heteroplasmic (i.e. mutated
      and wild-type mtDNA coexist) and a small percentage of wild-type
      sequences can have a strong protective effect against a metabolic
      defect. Because a genetic approach to correct mtDNA mutations is not
      currently available, the ability to modulate heteroplasmy would have a
      major impact in the phenotype of many patients with mitochondrial
      disorders. We show here that a restriction endonuclease targeted to
      mitochondria has this ability. A mitochondrially targeted PstI degraded
      mtDNA harboring PstI sites, in some cases leading to a complete loss of
      mitochondrial genomes. Recombination between DNA ends released by PstI
      was not observed. When expressed in a heteroplasmic rodent cell line,
      containing one mtDNA haplotype with two sites for PstI and another
      haplotype having none, the mitochondrial PstI caused a significant
      shift in heteroplasmy, with an accumulation of the mtDNA haplotype
      lacking PstI sites. These experiments provide proof of the principle
      that restriction endonucleases are feasible tools for genetic therapy
      of a sub-group of mitochondrial disorders. Although this approach is
      limited by the presence of mutation-specific restriction sites,
      patients with neuropathy, ataxia and retinitis pigmentosa (NARP) could
      benefit from it, as the T8399G mutation creates a unique restriction
      site that is not present in wild-type human mitochondrial DNA.
AU  - Srivastava S
AU  - Moraes CT
PT  - Journal Article
TA  - Hum. Mol. Genet.
JT  - Hum. Mol. Genet.
SO  - Hum. Mol. Genet. 2001 10: 3093-3099.

PMID- 29122874
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequences of Variants of Bacillus anthracis Sterne and Their Toxin Gene Deletion Mutants.
PG  - e01231-17
AB  - Here, we report the draft genome sequences of three laboratory variants of Bacillus anthracis
      Sterne and their double (Deltalef Deltacya) and triple
      (Deltapag Deltalef Deltacya) toxin gene deletion derivatives.
AU  - Staab A
AU  - Plaut RD
AU  - Pratt C
AU  - Lovett SP
AU  - Wiley MR
AU  - Biggs TD
AU  - Bernhards RC
AU  - Beck LC
AU  - Palacios GF
AU  - Stibitz S
AU  - Jones KL
AU  - Goodwin BG
AU  - Smith MA
AU  - Sozhamannan S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01231-17.

PMID- 23405351
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences of Pseudomonas fluorescens BS2 and Pusillimonas noertemannii BS8, Soil Bacteria That Cooperate To Degrade the  Poly-gamma-d-Glutamic Acid Anthrax Capsule.
PG  - e00057-12
AB  - A mixed culture of Pseudomonas fluorescens BS2 and Pusillimonas noertemannii BS8  degraded
      poly-gamma-d-glutamic acid; when the 2 strains were cultured separately, no hydrolytic
      activity was apparent. Here we report the draft genome sequences of both soil isolates.
AU  - Stabler RA
AU  - Negus D
AU  - Pain A
AU  - Taylor PW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00057-12.

PMID- 5317919
VI  - 21
DP  - 1965
TI  - Intracellular modification of nucleic acids.
PG  - 211-216
AB  - None
AU  - Stacey KA
PT  - Journal Article
TA  - Br. Med. Bull.
JT  - Br. Med. Bull.
SO  - Br. Med. Bull. 1965 21: 211-216.

PMID- 23961308
VI  - 8
DP  - 2013
TI  - Complete genome sequence of Coriobacterium glomerans type strain (PW2(T)) from the midgut of Pyrrhocoris apterus L. (red soldier bug).
PG  - 15-25
AB  - Coriobacterium glomerans Haas and Konig 1988, is the only species of the genus Coriobacterium,
      family Coriobacteriaceae, order Coriobacteriales, phylum
      Actinobacteria. The bacterium thrives as an endosymbiont of pyrrhocorid bugs,
      i.e. the red fire bug Pyrrhocoris apterus L. The rationale for sequencing the
      genome of strain PW2(T) is its endosymbiotic life style which is rare among
      members of Actinobacteria. Here we describe the features of this symbiont,
      together with the complete genome sequence and its annotation. This is the first
      complete genome sequence of a member of the genus Coriobacterium and the sixth
      member of the order Coriobacteriales for which complete genome sequences are now
      available. The 2,115,681 bp long single replicon genome with its 1,804
      protein-coding and 54 RNA genes is part of the G enomic E ncyclopedia of Bacteria
      and Archaea project.
AU  - Stackebrandt E et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 15-25.

PMID- 23991255
VI  - 8
DP  - 2013
TI  - Genome sequence of the free-living aerobic spirochete Turneriella parva type strain (H(T)), and emendation of the species Turneriella parva.
PG  - 228-238
AB  - Turneriella parva Levett et al. 2005 is the only species of the genus Turneriella which was
      established as a result of the reclassification of Leptospira parva
      Hovind-Hougen et al. 1982. Together with Leptonema and Leptospira, Turneriella
      constitutes the family Leptospiraceae, within the order Spirochaetales. Here we
      describe the features of this free-living aerobic spirochete together with the
      complete genome sequence and annotation. This is the first complete genome
      sequence of a member of the genus Turneriella and the 13(th) member of the family
      Leptospiraceae for which a complete or draft genome sequence is now available.
      The 4,409,302 bp long genome with its 4,169 protein-coding and 45 RNA genes is
      part of the G enomic E ncyclopedia of Bacteria and Archaea project.
AU  - Stackebrandt E et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 228-238.

PMID- 23961310
VI  - 8
DP  - 2013
TI  - High-quality-draft genome sequence of the yellow-pigmented flavobacterium Joostella marina type strain (En5(T)).
PG  - 37-46
AB  - At present, Joostella marina Quan et al. 2008 is the sole species with a validly  published
      name in the genus Joostella, family Flavobacteriacae, phylum
      Bacteriodetes. It is a yellow-pigmented, aerobic, marine organism about which
      little has been reported other than the chemotaxonomic features required for
      initial taxonomic description. The genome of J. marina strain En5(T) complements
      a list of 16 Flavobacteriaceae strains for which complete genomes and draft
      genomes are currently available. Here we describe the features of this bacterium,
      together with the complete genome sequence, and annotation. This is the first
      member of the genus Joostella for which a complete genome sequence becomes
      available. The 4,508,243 bp long single replicon genome with its 3,944
      protein-coding and 60 RNA genes is part of the G enomic E ncyclopedia of Bacteria
      and Archaea project.
AU  - Stackebrandt E et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 37-46.

PMID- 8299969
VI  - 137
DP  - 1993
TI  - Purification and characterisation of the restriction endonuclease ItaI from Ilyobacter tartaricus recognizing 5'-GC^NGC-3'.
PG  - 347-348
AB  - ItaI, an isoschizomer of the subclass IIW [Kessler and Manta, Gene 92 (1990) 1-248]
      restriction endonuclease (ENase), Fnu4HI [Leung et al., Nucleic Acids Res. 6 (1979) 17-25],
      has been isolated from Ilyobacter tartaricus. The ENase has the five-base palindromic
      recognition sequence, 5'GC^NGC-3'. It cleaves behind the second nucleotide and produces a
      one--nt 5' overhang.
AU  - Stadtler P
AU  - von Strandmann RP
AU  - Walter T
AU  - Frey B
AU  - Auer H
AU  - Hengstenberg W
AU  - Schmitz G
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1993 137: 347-348.

PMID- 27908987
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Three Clinical Isolates of Tannerella forsythia Isolated from Subgingival Plaque from Periodontitis Patients in the United  States.
PG  - e01286-16
AB  - We report the genome sequences of three clinical isolates of Tannerella forsythia from the
      subgingival plaque of periodontitis patients attending clinics at the
      School of Dental Medicine, University at Buffalo. The availability of these
      genome sequences will aid the understanding of the pathogenesis of periodontitis.
AU  - Stafford GP
AU  - Chaudhuri RR
AU  - Haraszthy V
AU  - Friedrich V
AU  - Schaffer C
AU  - Ruscitto A
AU  - Honma K
AU  - Sharma A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01286-16.

PMID- 22815448
VI  - 194
DP  - 2012
TI  - Complete Genome Sequences of Probiotic Strains Bifidobacterium animalis subsp. lactis B420 and Bi-07.
PG  - 4131-4132
AB  - We present the complete genomes of Bifidobacterium animalis subsp. lactis B420 and Bi-07.
      Comparative genomic analysis with the type strain DSMZ10140 revealed
      40 to 55 single nucleotide polymorphisms (SNPs) and an indel in a clustered
      regularly interspaced short palindromic repeat (CRISPR) locus. These genetic
      differences provide a molecular basis for strain typing within the two main
      phylogenetic groups of this monomorphic species.
AU  - Stahl B
AU  - Barrangou R
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4131-4132.

PMID- 23788546
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Probiotic Strain Lactobacillus acidophilus La-14.
PG  - e00376-13
AB  - We present the 1,991,830-bp complete genome sequence of Lactobacillus acidophilus strain La-14
      (SD-5212). Comparative genomic analysis revealed 99.98% similarity
      overall to the L. acidophilus NCFM genome. Globally, 111 single nucleotide
      polymorphisms (SNPs) (95 SNPs, 16 indels) were observed throughout the genome.
      Also, a 416-bp deletion in the LA14_1146 sugar ABC transporter was identified.
AU  - Stahl B
AU  - Barrangou R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00376-13.

PMID- 8650239
VI  - 93
DP  - 1996
TI  - Introduction of asymmetry in the naturally symmetric restriction endonuclease EcoRV to investigate intersubunit communication in the homodimeric protein.
PG  - 6175-6180
AB  - Type II restriction endonucleases are dimers of two identical subunits that together form one
      binding site for the double-stranded DNA substrate.  Cleavage within the palindromic
      recognition site occurs in the two strands of the duplex in a concerted manner, due to the
      action of two catalytic centers, one per subunit.  To investigate how the two identical
      subunits of the restriction endonuclease EcoRV cooperate in binding and cleaving their
      substrate, heterodimeric versions of EcoRV with different amino acid substitutions in the two
      subunits were constructed.  For this purpose, the ecorV gene was fused to the coding region
      for the glutathione-binding domain of the glutathione S-transferase and a His6-tag,
      respectively.  Upon cotransformation of Escherichia coli cells with both gene fusions stable
      homo- and heterodimers of the EcoRV variants are produced, which can be separated and purified
      to homogeneity by affinity chromatography over Ni-nitrilotriacetic acid and glutathione
      columns.  A steady-state kinetic analysis shows that the activity of a heterodimeric variant
      with one inactive catalytic center is decreased by 2-fold, demonstrating that the two
      catalytic centers operate independently from each other.  In contrast, heterodimeric variants
      with a defect in one DNA-binding site have a 30- to 50-fold lower activity, indicating that
      the two subunits of EcoRV cooperate in the recognition of the palindromic DNA sequence.  By
      combining a subunit with an inactive catalytic center with a subunit with a defect in the
      DNA-binding site, EcoRV heterodimers were produced that only nick DNA specifically within the
      EcoRV recognition sequence.
AU  - Stahl F
AU  - Wende W
AU  - Jeltsch A
AU  - Pingoud A
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1996 93: 6175-6180.

PMID- 9628339
VI  - 379
DP  - 1998
TI  - The mechanism of DNA cleavage by the type II restriction enzyme EcoRV: Asp36 is not directly involved in DNA cleavage but serves to couple indirect readout to catalysis.
PG  - 467-473
AB  - Three different mechanisms have been proposed to describe DNA cleavage by the type II
      restriction endonuclease EcoRV, which differ in the number and function of metal ions directly
      involved in catalysis and the different roles assigned to amino acid residues in the active
      sites and a phosphate group of the substrate.  There are only four acidic amino acid residues
      close to the scissile bond: the essential Asp74 and Asp90, the non-essential Glu45, and Asp36.
      We show here that Asp36 can be exchanged for alanine, with only minor effects on the cleavage
      rate of the nearby phosphodiester bond, excluding that Asp36 could be directly involved in
      catalysis.  Hence, the two versions of the two-metal-ion mechanism are not compatible with the
      experimental data, because too few ligands for two metal ions are present near the active site
      of EcoRV.  Our result, thus, supports the one-metal-ion mechanism for EcoRV.  We suggest that
      Asp36 has an allosteric effect by which specific contacts between one strand of the DNA and
      one subunit of the enzyme trigger the activation of one catalytic center.  Given the similar
      structures of the active sites of EcoRV, EcoRI, BamHI, PvuII and FokI, as well as the
      occurrence of a characteristic catalytic motif in several other restriction enzymes, we
      conclude that these enzymes most likely share a similar mechanism of DNA cleavage, whose
      characteristic feature is the involvement of only one Mg2+ ion in catalysis.
AU  - Stahl F
AU  - Wende W
AU  - Jeltsch A
AU  - Pingoud A
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1998 379: 467-473.

PMID- 9548954
VI  - 37
DP  - 1998
TI  - Intra- vs intersubunit communication in the homodimeric restriction enzyme EcoRV: Thr37 and Lys38 involved in indirect readout are only important for the catalytic activity of their own subunit.
PG  - 5682-5688
AB  - EcoRV is a dimer of two identical subunits which together form one binding site for the
      double-stranded DNA substrate.  Concerted cleavage of both strands of the duplex requires
      intersubunit communication to synchronize the two catalytic centers of EcoRV.  Here we address
      the question of how contacts to the DNA backbone trigger conformational changes which lead to
      the activation of both catalytic centers.  The structure of the specific EcoRV-DNA complex
      shows that a region including amino acids Thr37 and Lys38 is involved in interactions with the
      DNA backbone and is a candidate for intersubunit communication.  Homodimeric EcoRV T37A and
      K38A variants have a 1000-fold reduced catalytic activity.  To examine whether Thr37 and Lys38
      of one subunit affect the catalytic center in the same subunit and/or in the other subunit, we
      have produced heterodimeric variants containing a Thr37-Ala or Lys38-Ala substitution in one
      subunit combined with a wild type subunit or with a subunit which contains an amino acid
      substitution (Asp90-Ala) in the active site (D90A/T37A and D90A/K38A).  Cleavage experiments
      with supercoiled pAT153 show that wt/T37A and wt/K38A preferentially nick the DNA.  A
      steady-state kinetic analysis of the cleavage of an oligodeoxynucleotide substrate shows that
      the activity of wt/T37A and wt/K38A is half of that of wild type EcoRV, whereas D90A/T37A and
      D90A/K38A are almost inactive.  These results demonstrate that Thr37 and Lys38 affect
      primarily the catalytic center in their own subunit and that both subunits of EcoRV can be
      activated independently of each other.  We suggest that Thr37 and Lys38 control the catalytic
      activity of the active site in their own subunit by positioning a-helix B.
AU  - Stahl F
AU  - Wende W
AU  - Wenz C
AU  - Jeltsch A
AU  - Pingoud A
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1998 37: 5682-5688.

PMID- 1406610
VI  - 26
DP  - 1992
TI  - MunI mycoplasmic restriction-modification system and its possible role in pathogenesis.
PG  - 546-557
AB  - A restriction-modification system named R-M MunI, isolated from Friend's murine
      erythroleukemia cells, was purified and characterized. This site-specific endonuclease
      recognizes and cleaves the 5'-C'AATTG nucleotide sequence and is an isoschizomer of the MfeI
      restrictase from Mycoplasma fermentans. Site-specific methylation modifies the second adenine
      residue in the same sequence (5'-CAm6ATTG). It was shown that this enzyme system is from a
      Mycoplasma that contaminates the cell line. The Mycoplasma's DNA hybridizes with
      species-specific probes for M. fermentans and Mycoplasma arginini. The possible role of
      mycoplasmic restriction-modification enzymes in the pathogenesis of aquired immune deficiency
      syndrome is discussed.
AU  - Stakenas PS
AU  - Zaretskaya NM
AU  - Maneliene ZP
AU  - Mauricas MM
AU  - Butkus VV
AU  - Yanulaitis AA
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1992 26: 546-557.

PMID- 27284129
VI  - 4
DP  - 2016
TI  - Complete Genome and Plasmid Sequences for Rhodococcus fascians D188 and Draft Sequences for Rhodococcus Isolates PBTS 1 and PBTS 2.
PG  - e00495-16
AB  - Rhodococcus fascians, a phytopathogen that alters plant development, inflicts significant
      losses in plant production around the world. We report here the
      complete genome sequence of R. fascians D188, a well-characterized model isolate,
      and Rhodococcus species PBTS (pistachio bushy top syndrome) 1 and 2, which were
      shown to be responsible for a disease outbreak in pistachios.
AU  - Stamler RA
AU  - Vereecke D
AU  - Zhang Y
AU  - Schilkey F
AU  - Devitt N
AU  - Randall JJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00495-16.

PMID- 9345771
VI  - 155
DP  - 1997
TI  - Identification and characterization of a Treponema pallidum subsp. pallidum gene encoding a DNA adenine methyltransferase.
PG  - 115-119
AB  - The nucleotide sequence of a DNA adenine methyltransferase gene from Treponema pallidum has
      been determined.  Southern blot analysis of T. pallidum chromosomal DNA indicated that this
      gene is present as a single copy.  The dam gene encodes a 303 amino acid protein whose deduced
      sequence has significant homology with DNA (N6-adenine) methyltransferases.  T. pallidum Dam
      can be assigned to group alpha DNA amino methyltransferases based on the order of nine
      conserved motifs that are present in the protein.  Digests of T. pallidum chromosomal DNA
      performed with isoschizomer restriction endonucleases (Sau3AI, DpnI, and MboI) confirmed the
      presence of methylated adenine residues in GATC sequences (Dam+ phenotype).
AU  - Stamm LV
AU  - Greene SR
AU  - Barnes NY
AU  - Bergen HL
AU  - Hardham JM
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1997 155: 115-119.

PMID- 2467142
VI  - 13D
DP  - 1989
TI  - A convenient assay for DNA methyltransferase.
PG  - 226
AB  - Assaying DNA methylase by measuring transfer of tritium from the 5 position of
      DNA cytosine to water rather than labelled methyl transfer from S-adenosyl
      methionine to DNA cuts post-incubation procedures from hours to minutes.  The
      methodology and validating data obtained in our laboratory will be presented.
AU  - Stampeggioni E
AU  - Palitti F
AU  - Carotti D
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1989 13D: 226.

PMID- 25212621
VI  - 2
DP  - 2014
TI  - Draft genome of a novel chlorobi member assembled by tetranucleotide binning of a hot spring metagenome.
PG  - e00897-14
AB  - The genome of a member of the phylum Chlorobi was assembled from a shotgun metagenomic
      sequence of a hot spring in Mammoth Lakes, CA. This organism appears
      to be a novel, aerobic, photosynthetic Chlorobi member, expanding the knowledge
      of this underrepresented phylum.
AU  - Stamps BW
AU  - Corsetti FA
AU  - Spear JR
AU  - Stevenson BS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00897-14.

PMID- 24926055
VI  - 2
DP  - 2014
TI  - Genome Sequence of Thermoanaerobaculum aquaticum MP-01T, the First Cultivated Member of Acidobacteria Subdivision 23, Isolated from a Hot Spring.
PG  - e00570-14
AB  - Thermoanaerobaculum aquaticum MP-01(T) is currently the only cultivated and described member
      of Acidobacteria subdivision 23. Here, we report the genome
      sequence for this novel microorganism that was isolated from a hot spring.
AU  - Stamps BW
AU  - Losey NA
AU  - Lawson PA
AU  - Stevenson BS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00570-14.

PMID- 29496829
VI  - 6
DP  - 2018
TI  - Finished Genome Sequence of a Polyurethane-Degrading Pseudomonas Isolate.
PG  - e00084-18
AB  - Pseudomonas sp. strain WP001 is a laboratory isolate capable of polyurethane polymer
      degradation and harbors a predicted lipase precursor gene. The genome of
      strain WP001 is 6.15 Mb in size and is composed of seven scaffolds with a G+C
      content of 60.54%. Strain WP001 is closely related to Pseudomonas fluorescens
      based on ribosomal DNA comparisons.
AU  - Stamps BW
AU  - Zingarelli S
AU  - Hung CS
AU  - Drake CA
AU  - Varaljay VA
AU  - Stevenson BS
AU  - Crookes-Goodson WJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00084-18.

PMID- 3027536
VI  - 20
DP  - 1986
TI  - Netropsin, distamycin A, bis-netropsins as selective inhibitors of the effect of restrictases and DNaseI.
PG  - 1614-1624
AB  - The influence was investigated of netropsin, a number of bis-netropsins, and
      distamycin A on hydrolysis of DNA fragments by restrictases.  In parallel to
      inhibition of hydrolysis, binding sites were determined for ligands on the same
      DNA fragments according to shielding from partial hydrolysis by DNaseI
      (footprinting).  Combined analysis of ligand binding sites with their capacity
      for inhibition of hydrolysis led to the following conclusions.  1) Inhibition
      of the effect of restrictases by these ligands is associated with formation of
      a complex of ligand with the recognition site on DNA.  Experimental results
      obtained permit definition of the zone required for overlapping of the site of
      restrictase recognition and the binding site of ligand at +/- nucleotides from
      the axis of symmetry of the site of restrictase recognition.  The overlapping
      of the site occupied by one molecule of ligand with the restrictase recognition
      site is not an adequate condition for complete inhibition of hydrolysis.  2)
      Based on known specificity of netropsin for a nucleotide sequence, the
      restrictase recognition sites can be predicted at which inhibition of
      hydrolysis of DNA by restrictases will be observed.  3)  Netropsin and
      bis-netropsins display differing specificities and can be used for selective
      inhibition of restrictases at different recognition sites.
AU  - Stanchev BS
AU  - Grokhovskii SL
AU  - Khorlin AA
AU  - Gottikh BP
AU  - Zhuze AL
AU  - Skamrov AV
AU  - Bibilashvili RS
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1986 20: 1614-1624.

PMID- 11296229
VI  - 20
DP  - 2001
TI  - Loss of the maintenance methyltransferase, xDnmt1, induces apoptosis in Xenopus embryos.
PG  - 1963-1973
AB  - DNA methylation is necessary for normal embryogenesis in animals. Here we show that loss of
      the maintenance methyltransferase, xDnmt1p, triggers an apoptotic response during Xenopus
      development, which accounts for the loss of specific cell populations in hypomethylated
      embryos. Hypomethylation-induced apoptosis is accompanied by a stabilization in xp53 protein
      levels after the mid-blastula transition. Ectopic expression of HPV-E6, which promotes xp53
      degradation, prevents cell death, implying that the apoptotic signal is mediated by xp53. In
      addition, inhibition of caspase activation by overexpression of Bcl-2 results in the
      development of cellular masses that resemble embryonic blastomas. Embryonic tissue explant
      experiments suggest that hypomethylation alters the developmental potential of early embryo
      cells and that apoptosis is triggered by differentiation. Our results imply that loss of DNA
      methylation in differentiated somatic cells provides a signal via p53 that activates cell
      death pathways.
AU  - Stancheva I
AU  - Hensey C
AU  - Meehan RR
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 2001 20: 1963-1973.

PMID- 10562566
VI  - 18
DP  - 1999
TI  - Asymmetry of Dam remethylation on the leading and lagging arms of plasmid replicative intermediates.
PG  - 6542-6551
AB  - In Escherichia coli, adenine methylation at the sequence GATC allows coupling of cellular
      processes to chromosome replication and the cell cycle. The transient presence of
      hemimethylated DNA after replication facilitates post-replicative mismatch repair, induces
      transcription of some genes and allows transposition of mobile elements. We were interested in
      estimating the half-life of hemimethylated DNA behind the replication fork in plasmid
      molecules and in determining whether Dam methyltransferase restores N6 adenine methylation
      simultaneously on both replicative arms. We show that remethylation takes place asynchronously
      on the leading and lagging daughter strands shortly after replication. On the leading arm the
      fully methylated adenine is restored ~2000 bp (corresponding to 2 s) behind the replication
      fork, while remethylation takes twice as long (at 3500-4000 bp or ~3.5-4 s) on the lagging
      replicative arm. This observation suggests that Dam remethylation of the lagging arm requires
      ligated Okazaki fragments.
AU  - Stancheva I
AU  - Koller T
AU  - Sogo JM
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1999 18: 6542-6551.

PMID- 10673503
VI  - 14
DP  - 2000
TI  - Transient depletion of xDnmt1 leads to premature gene activation in Xenopus embryos.
PG  - 313-327
AB  - In Xenopus laevis zygotic transcription begins at the midblastula
      transition (MBT). Prior to this the genome is organized into chromatin
      that facilitates rapid cycles of DNA replication but not transcription.
      Here we demonstrate that DNA methylation contributes to the overall
      transcriptional silencing before MBT. Transient depletion of the maternal
      DNA methyltransferase (xDnmt1) by anti sense RNA during cleavage stages is
      associated with a decrease in the genomic 5-methyl-cytosine content and
      leads to the activation of zygotic transcription approximately two cell
      cycles earlier than normal. Hypomethylation allows the early expression of
      mesodermal marker genes such as Xbra, Cerberus, and Otx2, which are
      subsequently down-regulated during gastrulation of the xDnmt1-depleted
      embryos. The temporal switch in gene expression may account for the
      appearance of body plan defects that we observe. Loss of xDnmt1 can be
      rescued by the coinjection of mouse or human Dnmt1 protein. These results
      demonstrate that DNA methylation has a role in the regulation of
      immediately early genes in Xenopus at MBT.
AU  - Stancheva I
AU  - Meehan RR
PT  - Journal Article
TA  - Genes Dev.
JT  - Genes Dev.
SO  - Genes Dev. 2000 14: 313-327.

PMID- 10329129
VI  - 288
DP  - 1999
TI  - DNA cleavage by the EcoRV restriction endonuclease: pH dependence and proton transfers in catalysis.
PG  - 105-116
AB  - To characterize the pH dependence of phosphodiester hydrolysis by the EcoRV endonuclease in
      the presence of Mn2+, single turnover reactions on a 12 bp DNA substrate were examined by
      stopped-flow and quench-flow methods between pH 6.0 and 8.5.  At each pH value, the apparent
      rate constants for phosphodiester hydrolysis increased hyperbolically with the concentration
      of MnCl2, thus allowing values to be determined for the intrinsic rate constant at saturation
      with Mn2+ and the equilibrium dissociation constant for Mn2+.  The equilibrium constants
      showed no systematic variation across the pH range tested, while the rate constants increased
      steeply with increasing pH up to an asymptote above pH 7.5.  At low pH conditions, the
      gradient of a plot of log (rate constant) against pH approached a value of 2.  DNA cleavage by
      EcoRV thus requires the de-protonation of two acidic groups.  To determine whether aspartate
      36 is one of the groups, mutants of EcoRV were made with other amino acid residues at position
      36.  Glutamate caused a partial loss of activity, while all other replacements gave near-zero
      activities.  In contrast to wild-type EcoRV, the mutant with glutamate required the
      de-protonation of only one acidic group for DNA cleavage.  A mechanism for EcoRV is proposed
      in which the water molecule that hydrolyses the phosphodiester bond is de-protonated by two
      Bronsted bases, probably the ionized forms of aspartate 36 and glutamate 45.
AU  - Stanford NP
AU  - Halford SE
AU  - Baldwin GS
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1999 288: 105-116.

PMID- 11101527
VI  - 19
DP  - 2000
TI  - One- and three-dimensional pathways for proteins to reach specific DNA sites.
PG  - 6546-6557
AB  - Proteins that interact with specific DNA sites bind to DNA at random and then translocate to
      the target site. This may occur by one-dimensional diffusion along the DNA, or through
      three-dimensional space via multiple dissociation/re-associations. To distinguish these
      routes, reactions of the EcoRV endonuclease were studied on substrates with two EcoRV sites
      separated by varied distances. The fraction of encounters between the DNA and the protein that
      resulted in the processive cleavage of both sites decreased as the length of intervening DNA
      was increased, but not in the manner demanded for one-dimensional diffusion. The variation in
      processivity with inter-site spacing shows instead that protein moves from one site to another
      through three-dimensional space, by successive dissociation/re-associations, though each
      re-association to a new site is followed by a search of the DNA immediately adjacent to that
      site.  Although DNA-binding proteins are usually thought to find their target sites by
      one-dimensional pathways, three-dimensional routes may be more common than previously
      anticipated.
AU  - Stanford NP
AU  - Szczelkun MD
AU  - Marko JF
AU  - Halford SE
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 2000 19: 6546-6557.

PMID- Not carried by PubMed...
VI  - 0
DP  - 1996
TI  - Bpu10I restriction endonuclease is composed of two nonidentical subunits.
PG  - 51-53
AB  - The genes of the Bpu10I restriction-modification (RM) system have been cloned and sequenced.
      Nucleotide sequence analysis revealed four major open reading frames oriented tandemly.
      Comparison of amino acid sequences, subcloning and deletion mapping experiments have been
      applied to investigate all ORFs mentioned. ORFI and ORFII correspond to two
      m5C-methyltransferases.  Four conserved aa blocks including the EXK motif, which is known to
      be involved in the active center formation of restriction endonucleases, were detected by
      comparing aa sequences of ORFIII with ORFIV.  It was demonstrated that the dsDNA could be
      hydrolysed specifically only in the presence of both ORFIII and ORFIV intact, indicating that
      Bpu10I Enase is composed from two heterosubunits.
AU  - Stankevicius K
AU  - Lubys A
AU  - Timinskas A
AU  - Janulaitis A
PT  - Journal Article
TA  - Biologija
JT  - Biologija
SO  - Biologija 1996 0: 51-53.

PMID- 9461472
VI  - 26
DP  - 1998
TI  - Cloning and analysis of the four genes coding for Bpu10I restriction-modification enzymes.
PG  - 1084-1091
AB  - The Bpu10I R-M system from Bacillus pumilus 10, which recognizes the asymmetric 5'-CCTNAGC
      sequence, has been cloned, sequenced and expressed in Escherichia coli.  The system comprises
      four adjacent, similarly oriented genes encoding two m5C MTases and two subunits of Bpu10I
      ENase (34.5 and 34 kDa).  Both Bpu10IR genes either in cis or trans are needed for the
      manifestation of R.Bpu10I activity.  Subunits of R.Bpu10I, purified to apparent homogeneity,
      are both required for cleavage activity. This heterosubunit structure distinguishes the Bpu10I
      restriction endonuclease from all other type II restriction enzymes described previously.  The
      subunits reveal 25% amino acid identity.  Significant similarity was also identified between a
      43 amino acid region of R.DdeI and one of the regions of higher identity shared between the
      Bpu10I subunits, a region that could possibly include the catalytic/Mg2+ binding center.  The
      similarity between Bpu10I and DdeI Mtases is not limited to the conserved motifs typical for
      m5C MTases.  It extends into the variable region that lies between CMs VIII and IX.
      Duplication of a progenitor gene, encoding an enzyme recognizing a symmetric nucleotide
      sequence, followed by concerted divergent evolution, may provide a possible scenario leading
      to the emergence of the Bpu10I ENase, which recognizes an overall asymmetric sequence and
      cleaves within it symmetrically.
AU  - Stankevicius K
AU  - Lubys A
AU  - Timinskas A
AU  - Vaitkevicius D
AU  - Janulaitis A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1998 26: 1084-1091.

PMID- 7607524
VI  - 157
DP  - 1995
TI  - Cloning and characterization of the unusual restriction-modification system comprising two restriction endonucleases and one methyltransferase.
PG  - 49-53
AB  - An Escherichia coli RFL47 DNA fragment containing the Eco47IR and Eco47II
      restriction-modification (R-M) system has been cloned and sequenced.  A clone carrying this
      system has been selected by its ability to restrict phage lambda in vivo.  The sequence of
      5360 bp was determined, and its analysis revealed three major open reading frames (ORF)
      corresponding to two restriction endonucleases (ENases) and one DNA methyltransferase (MTase):
      R.Eco47II (239 amino acids (aa)), R.Eco47I (230 aa) and M.Eco47II (417 aa).  The M.Eco47II
      aa  sequence possesses all conserved domains typical for m5C MTases and its variable region
      has a  high homology with M.Sau96I and M.SinI.  The ORF harboring a predicted helix-turn-helix
      motif  upstream from the eco47IR gene has been found.  No sequence resembling the eco47IM
      gene has been detected in the complete fragment sequenced, although disrupted ORF, possibly
      corresponding to the transposase-encoding gene, has been found in the intergenic area between
      eco47IIM and eco47IR.  No homology was found between the ENases; however, both revealed
      homology with their isoschizomers, R.SinI and R.Sau96I.
AU  - Stankevicius K
AU  - Povilionis P
AU  - Lubys A
AU  - Menkevicius S
AU  - Janulaitis A
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 49-53.

PMID- Not carried by PubMed...
VI  - 0
DP  - 1996
TI  - Expression autoregulation of the Eco47II methyltransferase gene.
PG  - 54-56
AB  - Amino acid sequence analysis revealed a strong helix-turn-helix motif in the N-terminus of the
      M.Eco47II, with a standard deviation of 7.1.  The autoregulatory mechanism of the expression
      of the eco47IIM gene has been proved by using the lacZ fusion technique.  We have demonstrated
      that the HTH motif of M.Eco47II is necessary for the repression of the M.Eco47II promoter but
      not for the methylation of the DNA target.  Mutation in the catalytic center of M.Eco47II
      strongly reduces the methylation function, but has no effect on repression.
AU  - Stankevicius K
AU  - Timinskas A
PT  - Journal Article
TA  - Biologija
JT  - Biologija
SO  - Biologija 1996 0: 54-56.

PMID- 10620678
VI  - 182
DP  - 2000
TI  - Identification of four loci isolated from two Streptococcus thermophilus phage genomes responsible for mediating bacteriophage resistance.
PG  - 271-277
AB  - Sequence data derived from the Streptococcus thermophilus phages phiO1205 and phi7201
      indicated that each of these phages contains a distinct DNA
      region dedicated to replication. Southern blotting experiments showed that
      phages infecting S. thermophilus may be divided into at least two groups,
      each containing the presumptive replication functions of either
AU  - Stanley E
AU  - Walsh L
AU  - van der Zwet A
AU  - Fitzgerald GF
AU  - van Sinderen D
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2000 182: 271-277.

PMID- 16642041
VI  - 25
DP  - 2006
TI  - When a helicase is not a helicase: dsDNA tracking by the motor protein EcoR124l.
PG  - 2230-2239
AB  - Using a combination of single molecule and bulk solution measurements, we have examined the
      DNA translocation activity of a helicase, the Type
      I restriction modification enzyme EcoR124I. We find that EcoR124I can
      translocate past covalent interstrand crosslinks, inconsistent with an
      obligatory unwinding mechanism. Instead, translocation of the intact
      dsDNA occurs principally via contacts to the sugar-phosphate backbone
      and bases of the 30 - 50 strand; contacts to the 50 - 30 strand are not
      essential for motion but do play a key role in stabilising the motor on
      the DNA. A model for dsDNA translocation is presented that could be
      applicable to a wide range of other enzyme complexes that are also
      labelled as helicases but which do not have actual unwinding activity.
AU  - Stanley LK
AU  - Seidel R
AU  - van der Scheer C
AU  - Dekker NH
AU  - Szczelkun MD
AU  - Dekker C
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 2006 25: 2230-2239.

PMID- 16936313
VI  - 34
DP  - 2006
TI  - Direct and random routing of a molecular motor protein at a DNA junction.
PG  - 4387-4394
AB  - With the aim of investigating how motor proteins negotiate DNA nanostructures, we produced
      test circuits based on recombination
      intermediates in which 1D translocation across a Holliday junction (HJ)
      could be assessed by subsequent triplex displacement signals on each
      DNA arm. Using the EcoR124I restriction-modification enzyme, a 3'-5'
      double-strand DNA (dsDNA) translocase, we could show that the motor
      will tend to follow its translocated strand across a junction.
      Nonetheless, as the frequency of junction bypass events increases, the
      motor will occasionally jump tracks.
AU  - Stanley LK
AU  - Szczelkun MD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2006 34: 4387-4394.

PMID- 27856596
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Cyanobacterium sp. Strain IPPAS B-1200 with a Unique Fatty Acid Composition.
PG  - e01306-16
AB  - Here, we report the draft genome of Cyanobacterium sp. IPPAS strain B-1200, isolated from Lake
      Balkhash, Kazakhstan, and characterized by the unique fatty
      acid composition of its membrane lipids, which are enriched with myristic and
      myristoleic acids. The approximate genome size is 3.4 Mb, and the predicted
      number of coding sequences is 3,119.
AU  - Starikov AY
AU  - Usserbaeva AA
AU  - Sinetova MA
AU  - Sarsekeyeva FK
AU  - Zayadan BK
AU  - Ustinova VV
AU  - Kupriyanova EV
AU  - Los DA
AU  - Mironov KS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01306-16.

PMID- 18326675
VI  - 74
DP  - 2008
TI  - Complete genome sequence of Nitrobacter hamburgensis X14 and comparative genomic analysis of species within the genus Nitrobactei.
PG  - 2852-2863
AB  - The alphaproteobacterium Nitrobacter hamburgensis X14 is a gram-negative facultative
      chemolithoautotroph that conserves energy
      from the oxidation of nitrite to nitrate. Sequencing and analysis of
      the Nitrobacter hamburgensis X14 genome revealed four replicons
      comprised of one chromosome (4.4 Mbp) and three plasmids (294, 188, and
      121 kbp). Over 20% of the genome is composed of pseudogenes and
      paralogs. Whole-genome comparisons were conducted between N.
      hamburgensis and the finished and draft genome sequences of Nitrobacter
      winogradskyi and Nitrobacter sp. strain Nb-311A, respectively. Most of
      the plasmid-borne genes were unique to N. hamburgensis and encode a
      variety of functions (central metabolism, energy conservation,
      conjugation, and heavy metal resistance), yet similar to 21 kb of a
      similar to 28-kb "autotrophic" island on the largest plasmid was
      conserved in the chromosomes of Nitrobacter winogradskyi Nb-255 and
      Nitrobacter sp. strain Nb-311A. The N. hamburgensis chromosome also
      harbors many unique genes, including those for heme-copper oxidases,
      cytochrome b(561), and putative pathways for the catabolism of
      aromatic, organic, and one-carbon compounds, which help verify and
      extend its mixotrophic potential. A Nitrobacter "subcore" genome was
      also constructed by removing homologs found in strains of the closest
      evolutionary relatives, Bradyrhizobium japonicum and Rhodapseudomonas
      palustris. Among the Nitrobacter subcore inventory (116 genes), copies
      of genes or gene clusters for nitrite oxidoreductase (NXR), cytochromes
      associated with a dissimilatory nitrite reductase (NirK), PII-like
      regulators, and polysaccharide formation were identified. Many of the
      subcore genes have diverged significantly from, or have origins
      outside, the alphaproteobacterial lineage and may indicate some of the
      unique genetic requirements for nitrite oxidation in Nitrobacter.
AU  - Starkenburg SR
AU  - Larimer FW
AU  - Stein LY
AU  - Klotz MG
AU  - Chain PSG
AU  - Sayavedra-Soto LA
AU  - Poret-Peterson AT
AU  - Gentry ME
AU  - Arp DJ
AU  - Ward B
AU  - Bottomley PJ
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2008 74: 2852-2863.

PMID- 21705610
VI  - 193
DP  - 2011
TI  - Genome of the Cyanobacterium Microcoleus vaginatus FGP-2, a Photosynthetic Ecosystem Engineer of Arid Land Soil Biocrusts Worldwide.
PG  - 4569-4570
AB  - The filamentous cyanobacterium, Microcoleus vaginatus, is found in arid land soils worldwide.
      The genome of M. vaginatus strain FGP-2 allows exploration of genes involved in
      photosynthesis, desiccation tolerance, alkane production, and other features contributing to
      this organism's ability function as a major component of biological soil crusts in arid
      lands.
AU  - Starkenburg SR
AU  - Reitenga KG
AU  - Freitas T
AU  - Johnson S
AU  - Chain PS
AU  - Garcia-Pichel F
AU  - Kuske CR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4569-4570.

PMID- 24675859
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Cytophaga fermentans JCM 21142T, a Facultative Anaerobe  Isolated from Marine Mud.
PG  - e00206-14
AB  - Cytophaga fermentans strain JCM 21142(T) is a marine-dwelling facultative anaerobe. The draft
      genome sequence of this strain revealed its diverse
      chemoorganotrophic potential, which makes it capable of metabolizing various
      polysaccharide substrates. The genome data will facilitate further studies on its
      taxonomic reclassification, its metabolism, and the mechanisms pertaining to
      bacterial gliding.
AU  - Starns D
AU  - Oshima K
AU  - Suda W
AU  - Iino T
AU  - Yuki M
AU  - Inoue J
AU  - Kitamura K
AU  - Iida T
AU  - Darby A
AU  - Hattori M
AU  - Ohkuma M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00206-14.

PMID- 28751392
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Rathayibacter sp. Strain VKM Ac-2630 Isolated from Leaf  Gall Induced by the Knapweed Nematode Mesoanguina picridis on Acroptilon repens.
PG  - e00650-17
AB  - A draft genome sequence of Rathayibacter sp. strain VKM Ac-2630 was derived using Ion Torrent
      sequencing technology. The genome size of this strain is 3.88 Mb,
      with an average G+C content of 72.0%. Genomic evidence of an aerobic mode of
      respiration and a heterotrophic lifestyle of this bacterium was obtained.
AU  - Starodumova IP
AU  - Tarlachkov SV
AU  - Prisyazhnaya NV
AU  - Dorofeeva LV
AU  - Ariskina EV
AU  - Chizhov VN
AU  - Subbotin SA
AU  - Evtushenko LI
AU  - Vasilenko OV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00650-17.

PMID- 25375929
VI  - 8
DP  - 2014
TI  - Whole Genome Sequence of the Treponema pallidum subsp. endemicum Strain Bosnia A: The Genome Is Related to Yaws Treponemes but Contains Few Loci Similar to Syphilis Treponemes.
PG  - E3261
AB  - BACKGROUND: T. pallidum subsp. endemicum (TEN) is the causative agent of bejel
      (also known as endemic syphilis). Clinical symptoms of syphilis and bejel are
      overlapping and the epidemiological context is important for correct diagnosis of
      both diseases. In contrast to syphilis, caused by T. pallidum subsp. pallidum
      (TPA), TEN infections are usually spread by direct contact or contaminated
      utensils rather than by sexual contact. Bejel is most often seen in western
      Africa and in the Middle East. The strain Bosnia A was isolated in 1950 in
      Bosnia, southern Europe. METHODOLOGY/PRINCIPAL FINDINGS: The complete genome of
      the Bosnia A strain was amplified and sequenced using the pooled segment genome
      sequencing (PSGS) method and a combination of three next-generation sequencing
      techniques (SOLiD, Roche 454, and Illumina). Using this approach, a total
      combined average genome coverage of 513x was achieved. The size of the Bosnia A
      genome was found to be 1,137,653 bp, i.e. 1.6-2.8 kbp shorter than any previously
      published genomes of uncultivable pathogenic treponemes. Conserved gene synteny
      was found in the Bosnia A genome compared to other sequenced syphilis and yaws
      treponemes. The TEN Bosnia A genome was distinct but very similar to the genome
      of yaws-causing T. pallidum subsp. pertenue (TPE) strains. Interestingly, the TEN
      Bosnia A genome was found to contain several sequences, which so far, have been
      uniquely identified only in syphilis treponemes. CONCLUSIONS/SIGNIFICANCE: The
      genome of TEN Bosnia A contains several sequences thought to be unique to TPA
      strains; these sequences very likely represent remnants of recombination events
      during the evolution of TEN treponemes. This finding emphasizes a possible role
      of repeated horizontal gene transfer between treponemal subspecies in shaping the
      Bosnia A genome.
AU  - Staudova B
AU  - Strouhal M
AU  - Zobanikova M
AU  - Cejkova D
AU  - Fulton LL
AU  - Chen L
AU  - Giacani L
AU  - Centurion-Lara A
AU  - Bruisten SM
AU  - Sodergren E
AU  - Weinstock GM
AU  - Smajs D
PT  - Journal Article
TA  - PLoS Neglected Trop. Dis.
JT  - PLoS Neglected Trop. Dis.
SO  - PLoS Neglected Trop. Dis. 2014 8: E3261.

PMID- 12923100
VI  - 185
DP  - 2003
TI  - Complete nucleotide sequence and genetic organization of the 210-Kilobase linear plasmid of Rhodococcus erythropolis BD2.
PG  - 5269-5274
AB  - The complete nucleotide sequence of the linear plasmid pBD2 from Rhodococcus erythropolis BD2
      comprises 210,205 bp. Sequence analyses of
      pBD2 revealed 212 putative open reading frames (ORFs), 97 of which had an
      annotatable function. These ORFs could be assigned to six functional
      groups: plasmid replication and maintenance, transport and
      metalloresistance, catabolism, transposition, regulation, and protein
      modification. Many of the transposon-related sequences were found to flank
      the isopropylbenzene pathway genes. This finding together with the
      significant sequence similarities of the ipb genes to genes of the linear
      plasmid-encoded biphenyl pathway in other rhodococci suggests that the ipb
      genes were acquired via transposition events and subsequently distributed
      among the rhodococci via horizontal transfer.
AU  - Stecker C
AU  - Johann A
AU  - Herzberg C
AU  - Averhoff B
AU  - Gottschalk G
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2003 185: 5269-5274.

PMID- 22638584
VI  - 40
DP  - 2012
TI  - Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily.
PG  - 7016-7045
AB  - Proteins belonging to PD-(D/E)XK phosphodiesterases constitute a functionally diverse
      superfamily with representatives involved in replication, restriction, DNA repair and
      tRNA-intron splicing. Their malfunction in humans triggers severe diseases, such as Fanconi
      anemia and Xeroderma pigmentosum. To date there have been several attempts to identify and
      classify new PD-(D/E)KK phosphodiesterases using remote homology detection methods. Such
      efforts are complicated, because the superfamily exhibits extreme sequence and structural
      divergence. Using advanced homology detection methods supported with superfamily-wide domain
      architecture and horizontal gene transfer analyses, we provide a comprehensive
      reclassification of proteins containing a PD-(D/E)XK domain. The PD-(D/E)XK phosphodiesterases
      span over 21 900 proteins, which can be classified into 121 groups of various families. Eleven
      of them, including DUF4420, DUF3883, DUF4263, COG5482, COG1395, Tsp45I, HaeII, Eco47II, ScaI,
      HpaII and Replic_Relax, are newly assigned to the PD-(D/E)XK superfamily. Some groups of
      PD-(D/E)XK proteins are present in all domains of life, whereas others occur within small
      numbers of organisms. We observed multiple horizontal gene transfers even between human
      pathogenic bacteria or from Prokaryota to Eukaryota. Uncommon domain arrangements greatly
      elaborate the PD-(D/E)XK world. These include domain architectures suggesting regulatory roles
      in Eukaryotes, like stress sensing and cell-cycle regulation. Our results may inspire further
      experimental studies aimed at identification of exact biological functions, specific
      substrates and molecular mechanisms of reactions performed by these highly diverse proteins.
AU  - Steczkiewicz K
AU  - Muszewska A
AU  - Knizewski L
AU  - Rychlewski L
AU  - Ginalski K
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: 7016-7045.

PMID- 21602330
VI  - 193
DP  - 2011
TI  - Genome sequence of lineage III Listeria monocytogenes strain HCC23.
PG  - 3679-3680
AB  - More than 98% of reported human listeriosis cases are caused by Listeria monocytogenes
      serotypes within lineages I and II. Serotypes within lineage
      III (4a and 4c) are commonly isolated from environmental and food
      specimens. We report the first complete genome sequence of a lineage III
      isolate, HCC23, which will be used for comparative analysis.
AU  - Steele CL
AU  - Donaldson JR
AU  - Paul D
AU  - Banes MM
AU  - Arick T
AU  - Bridges SM
AU  - Lawrence ML
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3679-3680.

PMID- 3002270
VI  - 50
DP  - 1985
TI  - Streptococcus cremoris M12R transconjugants carrying the conjugal plasmid pTR2030 are insensitive to attack by lytic bacteriophages.
PG  - 851-858
AB  - Conjugal transfer of lactose-fermenting ability (Lac+), nisin resistance (Nisr), and phage
      resistance (Hsp+) was demonstrated in mating between Streptococcus lactis ME2 (donor) and
      Streptococcus cremoris M43a (recipient), a derivative of M12R. Transconjugants were detected
      by transfer of Lac+ and were found to exhibit Nisr and harbor a 40-megadalton plasmid
      (pTR1040). Fifty-six percent of Lac+ transconjugants were resistant to the S. cremoris M12R
      lytic phage. Efficiency of plaquing for phage m12r.M12 on a phage-resistant transconjugant,
      T2r-M43a, was <4.3 x 10 -10. Five additional phages which were virulent for S. cremoris M12R
      and isolated from industrial sources failed to plaque on S. cremoris T2r-M43a. Mating
      experiments with T2r-M43a revealed that phage resistance was accompanied by high-frequency
      conjugation ability (Tra+) and the appearance of both pTR1040 and pTR2030 encoding Lac+ Nisr
      and Tra+ Hsp+, respectively, in transconjugants of S. lactis mLM2302. Phage-sensitive Lac+
      transconjugants of S. cremoris M43a. Unlike the S. lactis LM2302 transconjugant carrying
      pTR2030, resistance of T2r-M43a to phage was not affective at high temperatures (35 to 40 deg.
      C) or destabilized in repeated transfers through a starter culture activity test. These
      results demonstrated that phage resistance conferred by pTR2030 in the S. cremoris
      transconjugant was effective against industrially significant phages under fermentation
      conditions normally encountered during cheese manufacture.
AU  - Steenson LR
AU  - Klaenhammer TR
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1985 50: 851-858.

PMID- 3537034
VI  - 69
DP  - 1986
TI  - Plasmid heterogeneity in Streptococcus cremoris M12R:  effects on proteolytic activity and host-dependent phage replication.
PG  - 2227-2236
AB  - Examination of single colony isolates from a culture of Streptococcus cremoris
      M12R revealed a high degree of variability in plasmid deoxyribonucleic acid
      composition.  Fifty percent of the M12R population displayed proteolytic
      activity and harbored a 13-Mdalton plasmid (pLR2013).  This plasmid was not
      present in proteinase-deficient variants isolated from the culture, which
      provided correlative evidence for linkage of proteinase activity to pLR2013.
      Four percent of the M12R population demonstrated resistance to phage m12r.M12.
      This resistance was identified by restriction and modification activities
      against m12r.M12 phage, which was dependent on the presence of a 20-Md plasmid,
      pLR1020.  Loss of restriction and modification activities was observed upon
      curing of pLR1020.  In conjugal mating studies with Streptococcus lactis ME2,
      transfer frequency of lactose-fermenting ability to a restriction and
      modification-deficient variant of M12R was 100-fold higher than to a variant
      exhibiting restriction and modification activities.  The data provided evidence
      for restriction and modification activities in select S. cremoris M12R variants
      that are linked to pLR1020 and restrict both the plaquing ability of phage and
      efficiency of plasmid transfer by conjugation.
AU  - Steenson LR
AU  - Klaenhammer TR
PT  - Journal Article
TA  - J. Dairy Sci.
JT  - J. Dairy Sci.
SO  - J. Dairy Sci. 1986 69: 2227-2236.

PMID- 2014170
VI  - 19
DP  - 1991
TI  - Molecular cloning and characterization of the gene encoding the adenine methyltransferase M.CviRI from Chlorella virus XZ-6E.
PG  - 307-311
AB  - The gene encoding the DNA methyltransferase M.CviRI from Chlorella virus XZ-6E
      was cloned and expressed in Escherichia coli.  M.CviRI methylates adenine in
      TGCA sequences.  DNA containing the M.CviRI gene was sequenced and a single
      open reading frame of 1137 bp was identified which could code for a polypeptide
      of 379 amino acids with a predicted molecular weight of 42,814.  Comparison of
      the M.CviRI predicted amino acid sequence with another Chlorella virus and 14
      bacterial adenine methyltransferases revealed extensive similarity to the other
      Chlorella virus enzyme.
AU  - Stefan C
AU  - Xia Y
AU  - Van Etten JL
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 307-311.

PMID- Not carried by PubMed...
VI  - 3
DP  - 1987
TI  - Search for the modification-restriction systems.
PG  - 128-131
AB  - The DNA modification-restriction systems have been studied for their presence
      in 19 Agrobacteria strains, including the virulent ones with Ti-plasmids of
      various classes, the avirulent octopine and nopaline strain derivatives
      obtained by curing the Agrobacteria virulent strains from Ti-plasmids as well
      as natural isolates of avirulent Agrobacteria.  It is shown that the presence
      of the DNA modification-restriction system with EcoRII specificity is a
      characteristic feature of the Agrobacteria octopine strains and of their cured
      avirulent derivatives.  The Agrobacteria nopaline strains, their cured
      avirulent derivatives, and most of the Agrobacteria natural avirulent strains
      contain the DNA modification-restriction systems different from EcoRII.  The
      chromosomal nature of these characters is shown.
AU  - Stefanishina TV
AU  - Bogdarina IG
AU  - Buryanov YI
PT  - Journal Article
TA  - Biopol. Kletka
JT  - Biopol. Kletka
SO  - Biopol. Kletka 1987 3: 128-131.

PMID- 26941145
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Lactobacillus casei DPC6800, an Isolate with the Potential to Diversify Flavor in Cheese.
PG  - e00063-16
AB  - Lactobacillus casei is a nonstarter lactic acid bacterium commonly present in various types of
      cheeses. It is believed that strains of this species have a
      significant impact on the development of cheese flavor. The draft genome sequence
      of L. casei DPC6800, isolated from a semi-hard Dutch cheese, is reported.
AU  - Stefanovic E
AU  - Casey A
AU  - Cotter P
AU  - Cavanagh D
AU  - Fitzgerald G
AU  - McAuliffe O
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00063-16.

PMID- 28729270
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Three Lactobacillusparacasei Strains, Members of the Nonstarter Microbiota of Mature Cheddar Cheese.
PG  - e00655-17
AB  - Lactobacillus paracasei strains are common members of the nonstarter microbiota present in
      various types of cheeses. The draft genome sequences of three strains
      isolated from mature cheddar cheeses are reported here.
AU  - Stefanovic E
AU  - Fitzgerald G
AU  - McAuliffe O
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00655-17.

PMID- 29340007
VI  - 13
DP  - 2018
TI  - Genomic insights into Mycobacterium simiae human colonization.
PG  - 1
AB  - Mycobacterium simiae (Karassova V, Weissfeiler J, Kraszanay E, Acta Microbiol Acad Sci Hung
      12:275-82, 1965) is a slow-growing nontuberculous Mycobacterium
      species found in environmental niches, and recently evidenced as an opportunistic
      Human pathogen. We report here the genome of a clinical isolate of M. simiae
      (MsiGto) obtained from a patient in Guanajuato, Mexico. With a size of 6,684,413
      bp, the genomic sequence of strain MsiGto is the largest of the three M. simiae
      genomes reported to date. Gene prediction revealed 6409 CDSs in total, including
      6354 protein-coding genes and 52 RNA genes. Comparative genomic analysis
      identified shared features between strain MsiGto and the other two reported M.
      simiae genomes, as well as unique genes. Our data reveals that M. simiae MsiGto
      harbors virulence-related genes, such as arcD, ESAT-6, and those belonging to the
      antigen 85 complex and mce clusters, which may explain its successful transition
      to the human host. We expect the genome information of strain MsiGto will provide
      a better understanding of infective mechanisms and virulence of this emergent
      pathogen.
AU  - Steffani-Vallejo JL
AU  - Brunck ME
AU  - Acosta-Cruz EY
AU  - Montiel R
AU  - Barona-Gomez F
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2018 13: 1.

PMID- 28818899
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Sphingobacterium sp. CZ-UAM, Isolated from a Methanotrophic Consortium.
PG  - e00792-17
AB  - Sphingobacterium sp. CZ-UAM was isolated from a methanotrophic consortium in mineral medium
      using methane as the only carbon source. A draft genome of 5.84 Mb
      with a 40.77% G+C content is reported here. This genome sequence will allow the
      investigation of potential methanotrophy in this isolated strain.
AU  - Steffani-Vallejo JL
AU  - Zuniga C
AU  - Cruz-Morales P
AU  - Lozano L
AU  - Morales M
AU  - Licona-Cassani C
AU  - Revah S
AU  - Utrilla J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00792-17.

PMID- 23887918
VI  - 1
DP  - 2013
TI  - Genome Sequence of Staphylococcus aureus Strain CA-347, a USA600 Methicillin-Resistant Isolate.
PG  - e00517-13
AB  - The Staphylococcus aureus clonal lineage CC45 is a predominant colonizer of healthy
      individuals in northern Europe and constitutes a highly basal cluster of
      the S. aureus population. Here, we report the complete genome sequence of S.
      aureus strain CA-347 (NRS648), a representative of the methicillin-resistant
      USA600 clone predominantly found in the United States.
AU  - Stegger M
AU  - Driebe EM
AU  - Roe C
AU  - Lemmer D
AU  - Bowers JR
AU  - Engelthaler DM
AU  - Keim P
AU  - Andersen PS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00517-13.

PMID- 21123532
VI  - 49
DP  - 2011
TI  - Rapid PCR Detection of Staphylococcus aureus Clonal Complex 398 by Targeting the Restriction-Modification System Carrying sau1-hsdS1.
PG  - 732-734
AB  - A PCR targeting sau1-hsdS1 was developed for rapid detection of Staphylococcus aureus clonal
      complex 398 (CC398). High sensitivity
      (100%) and specificity (100%) were shown by evaluating the test on a
      large strain collection (n = 1,307). We recommend this test for
      accurate, rapid, and inexpensive diagnosis of methicillin-resistant S.
      aureus (MRSA) CC398 in hospitals and on farms.
AU  - Stegger M
AU  - Lindsay JA
AU  - Moodley A
AU  - Skov R
AU  - Broens EM
AU  - Guardabassi L
PT  - Journal Article
TA  - J. Clin. Microbiol.
JT  - J. Clin. Microbiol.
SO  - J. Clin. Microbiol. 2011 49: 732-734.

PMID- 22374956
VI  - 194
DP  - 2012
TI  - Genome Sequence of Staphylococcus aureus Strain 11819-97, an ST80-IV European Community-Acquired Methicillin-Resistant Isolate.
PG  - 1625-1626
AB  - The European methicillin-resistant Staphylococcus aureus (MRSA) clone ST80-IV has historically
      dominated community-associated infections in major parts of Europe
      and is a lineage strongly linked to skin and soft tissue infections. Here, we
      report the genome sequence of an ST80-IV representative, 11819-97, isolated from
      a skin infection in Denmark in 1997.
AU  - Stegger M
AU  - Price LB
AU  - Larsen AR
AU  - Gillece JD
AU  - Waters AE
AU  - Skov R
AU  - Andersen PS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1625-1626.

PMID- 2158077
VI  - 18
DP  - 1990
TI  - Ligation-mediated PCR improves the sensitivity of methylation analysis by restriction enzymes and detection of specific DNA strand breaks.
PG  - 1435-1439
AB  - DNA methylation at specific sites is most frequently studied by use of
      methylation-sensitive restriction endonucleases and Southern blotting.  We
      report here that the sensitivity of this method can be increased
      several-hundred-fold by applying a ligation-mediated polymerase chain reaction
      (LM-PCR) procedure followign enzyme treatment.  DNA is cleaved simultaneously
      with two restriction enzymes, one sensitive and one insensitive to methylation.
      After cleavage, a gene-specific oligonucleotide primer is used for primer
      extension, followed by linker ligation and then conventional PCR.  Using this
      technique, we demonstrate that DNA from 100 cells (about 0.6 ng) can be
      prepared and qualitatively analyzed for methylation at sites in an X-linked CpG
      island, and 50 ng of DNA can be analyzed quantitatively.  A site 23 bp
      downstream of the major transcription start site of human phosphoglycerate
      kinase-1 (PGK-1) is 52 +/- 7 percent methylated in DNA from female blood and
      greater than 98 percent unmethylated in DNA from male blood or HeLa cells.
      This method detects quantitatively specific breaks in either double stranded or
      single stranded DNA.  Thus new assays for enzymes and DNA structure can be
      devised.
AU  - Steigerwald SD
AU  - Pfeifer GP
AU  - Riggs AD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 1435-1439.

PMID- 1321116
VI  - 174
DP  - 1992
TI  - Construction of a Neisseria gonorrhoeae MS11 derivative deficient in NgoMI restriction and modification.
PG  - 4899-4906
AB  - We have cloned from Neisseria gonorrhoeae MS11 the gene encoding a methylase that modifies the
      sequence GCCGGC. The corresponding restriction enzyme was also encoded by this clone. Sequence
      analysis demonstrated that the methylase shares sequence similarities with other cytosine
      methylases, but the sequence organization of M.NgoMI is different from that seen for other
      cytosine methylases. A deletion was introduced into the chromosome of N. gonorrhoeae MS11 to
      produce strain MUG701, a strain that is inactivated in both the methylase and the restriction
      genes. Although this strain no longer methylated its DNA at the NgoMI recognition sequence,
      cells were viable and had no other significant phenotypic changes. Transformation data
      indicated that MS11 does not produce enough restriction activity to block plasmid
      transformation in the gonococcus, even though restriction activity could be demonstrated in E.
      coli containing the cloned gene.
      [ The enzyme called NgoMI in this abstract has been renamed NgoMIV, Jan/1998. ]
AU  - Stein DC
AU  - Chien R
AU  - Seifert SH
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1992 174: 4899-4906.

PMID- 2826333
VI  - 56
DP  - 1988
TI  - Restriction of plasmid DNA during transformation but not conjugation in Neisseria gonorrhoeae.
PG  - 112-116
AB  - Neisseria gonorrhoeae strains WR302 and PGH3-2 were characterized with respect to their
      restriction-modification phenotype.  WR302 DNA was cleaved by HaeIII, indicating the lack of
      methylation at the GGCC sequence.  PGH3-2 produced NgoSI (an isoschizomer of NgoII).  WR302
      produced a restriction enzyme with a recognition sequence different from that of NgoI, NgoII,
      or NgoIII.  Plasmid pFT180 isolated from WR302 was unable to transform PGH3-2, whereas plasmid
      pFT180 isolated from PGH3-2 was able to transform PGH3-2 at a very high frequency.  When
      plasmid pFT180 isolated from WR302 isolated from WR302 was methylated in vitro with methylase
      M.HaeIII, this plasmid was able to transform PGH3-2.  NgoSI was able to restrict WR302 DNA in
      vitro, whereas it was incapable of restricting PGH3-2 DNA in vitro.  When the
      self-transmissible R factor pFT6 was mobilized from WR302 to PGH3-2 by conjugation, a
      1-order-of-magnitude difference in transfer frequencies was observed, as compared with an
      isogenic cross.  The data indicate that host-mediated restriction can prevent the gonococcus
      from acquiring DNA via transformation but not via conjugation.
      [ The enzyme called NgoSI in this abstract has been renamed NgoSII, Jan/1998. ]
AU  - Stein DC
AU  - Gregoire S
AU  - Piekarowicz A
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 1988 56: 112-116.

PMID- 9628358
VI  - 379
DP  - 1998
TI  - Sequence similarities between the genes encoding the S.NgoI and HaeII restriction/modification systems.
PG  - 575-578
AB  - The DNA sequence encoding the S.NgoI restriction/modification system was identified from a
      gene bank made from Neisseria gonorrhoaea strain WR302 by identifying recombinant plasmids
      that induced the reporter system in a methylase detection strain AP1-200-9 and were resistant
      to digestion with NgoI.  The DNA sequence was determined from one of these (pUCP30).  M.NgoI
      is a protein of 315aa with a predicted MW of 35,296 Da and R.NgoI is a protein of 350aa with a
      predicted MW of 40,650 Da.  The termination codon of M.NgoI overlapped the start codon of
      R.NgoI.  The same strategy was used to clone the R/M system encoding HaeII from Haemophilus
      aegyptius strain ATCC 11116.  The DNA sequence from one clone representing this class (pAP704)
      was determined.  HaeII methylase is a protein of 318aa with a predicted MW of 35,669 Da and
      R.HaeII contains 352aa with a predicted MW of 40,800 Da.  Aa alignments between the two
      methylases indicated that they were 74.3% identical and 79% similar. DNA sequence alignments
      revealed 68% identity.  An aa alignment between the two restriction enzymes indicated that
      they were 60% identical and 68% similar.  DNA sequence alignments revealed 61% identity.  The
      DNA sequences flanking these two systems were identified and used to determine the genomic
      organization of the two systems.  The S.NgoI genes were found between two genes, one with high
      homology to GTP binding proteins of unknown function and one with homology to genes involved
      in tRNA synthetase synthesis.  The HaeII R/M genes were located between two genes, mucF and
      mucE.  The DNA sequence of the HaeII R/M system was compared to the genomic DNA sequence of H.
      influenzae Rd. Although the DNA sequences flanking the HaeII system were >99% identical to
      contiguous DNA fragments found in the genome of H. influenzae Rd, no homology was seen with
      the DNA sequences encoding the HaeII R/M system, indicating that it is not found in this
      strain.  Given the vast difference in the GC content of S.NgoI and HaeII, their apparent
      insertion into polycistronic operons, and their difference in codon usage when compared to the
      species from which they were isolated, the data suggest that these R/M systems originated in
      an organism other than Neisseria or Haemophilus.
AU  - Stein DC
AU  - Gunn JS
AU  - Piekarowicz A
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1998 379: 575-578.

PMID- 7607490
VI  - 157
DP  - 1995
TI  - Restriction and modification systems of Neisseria gonorrhoeae.
PG  - 19-22
AB  - An individual strain of Neisseria gonorrhoeae may produce up to 16 different DNA
      methyltransferases (MTases).  We have used a novel cloning system that is able to detect MTase
      clones in the absence of direct selection to identify 14 different MTase clones.  Initial
      characterization of these clones indicates that at least seven of these MTases are linked to
      restriction endonuclease (ENase) systems.  Six of these systems have been characterized by DNA
      sequence analysis, and the open reading frames encoding each of these systems have been
      identified.  The recognition sequences for the cloned systems have the following
      specificities: S.NgoI, RGCGCY; S.NgoII, GGCC; S.NgoIV, GCCGCC; S.NgoV, GGNNCC; S.NgoVII,
      GCSGC; S.NgoVIIIA, GGTGA; and S.NgoVIIIC, TCACC.  Of those systems that have been cloned,
      NgoI-NgoVII are typical type II R-M systems, with each encoding a DNA MTase that methylates
      cytosine in position 5.  NgoVIII is a type IIS system, containing an ENase and two different
      MTases.  One of these is a cytosine MTase (NgoVIIIC) and the other is an adenine MTase
      (NgoVIIIA).  Although most of our clones encodes both the ENase and the MTase, none of the six
      R-M systems are genetically linked on the chromosome.
AU  - Stein DC
AU  - Gunn JS
AU  - Radlinska M
AU  - Piekarowicz A
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 19-22.

PMID- 21441518
VI  - 193
DP  - 2011
TI  - Genome sequence of the methanotrophic Alphaproteobacterium, Methylocystis sp. Rockwell (ATCC 49242).
PG  - 2668-2669
AB  - Methylocystis sp. strain Rockwell (ATCC 49242) is an aerobic methane-oxidizing
      Alphaproteobacterium isolated from an aquifer in southern California. Unlike most
      methanotrophs in the Methylocystaceae family, this strain has a single pmo operon encoding
      particulate methane monooxygenase but no evidence of the genes encoding soluble methane
      monooxygenase. This is the first reported genome sequence of a member of the Methylocystis
      species of the Methylocystaceae family in the order Rhizobiales.
AU  - Stein LY et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 2668-2669.

PMID- 20952571
VI  - 192
DP  - 2010
TI  - Genome Sequence of the Obligate Methanotroph Methylosinus trichosporium Strain OB3b.
PG  - 6497-6498
AB  - Methylosinus trichosporium OB3b (for 'oddball' strain 3b) is an obligate aerobic
      methane-oxidizing alphaproteobacterium that was originally
      isolated in 1970 by Roger Whittenbury and colleagues. This strain has
      since been used extensively to elucidate the structure and function of
      several key enzymes of methane oxidation, including both particulate and
      soluble methane monooxygenase (sMMO) and the extracellular copper chelator
      methanobactin. In particular, the catalytic properties of soluble methane
      monooxygenase from M. trichosporium OB3b have been well characterized in
      context with biodegradation of recalcitrant hydrocarbons, such as
      trichloroethylene. The sequence of the M. trichosporium OB3b genome is the
      first reported from a member of the Methylocystaceae family in the order
      Rhizobiales.
AU  - Stein LY et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 6497-6498.

PMID- 20061480
VI  - 192
DP  - 2010
TI  - The complete genome sequence of L. seeligeri, a non-pathogenic member of the genus Listeria.
PG  - 1473-1474
AB  - We report the complete and annotated genome sequence of the non-pathogenic L. seeligeri
      SLCC3954 serovar 1/2b type strain harboring the smallest completely sequenced genome of the
      genus Listeria.
AU  - Steinweg C
AU  - Kuenne CT
AU  - Billion A
AU  - Mraheil MA
AU  - Domann E
AU  - Ghai R
AU  - Barbuddhe SB
AU  - Karst U
AU  - Goesmann A
AU  - Puhler A
AU  - Weisshaar B
AU  - Wehland J
AU  - Lampidis R
AU  - Kreft J
AU  - Goebel W
AU  - Chakraborty T
AU  - Hain T
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 1473-1474.

PMID- 2204954
VI  - 23
DP  - 1990
TI  - Structural studies of protein-nucleic acid interaction:  the source of sequence-specific binding.
PG  - 205-280
AB  - 1. Introduction and overview
      2. Principles of sequence-specific nucleic-acid recognition
      2.1 The problem that is set: what is being recognized?
      2.2 Role of the major groove in DNA recognition
      2.3 Role of nucleic acid bendability
      2.4 Role of water molecules in sequence recognition
      2.5 Role of the minor groove in DNA and RNA recognition
      3. DNA-binding structure motifs
      3.1 Helix-turn-helix
      3.2 Zinc fingers
      3.3 Helices of the dinucleotide fold
      3.4 other motifs
      4. Similarities and differences in RNA and DNA recognition
      5. Sequence-specific DNA-binding proteins
      5.1 Repressors and activators
      5.1.1 Lac operon regulation
      (a) E. coli catabolite gene activator protein (CAP)
      (b) E. coli lac repressor protein
      5.1.2 Structural studies of the bacterial phage repressors
      (a) 434 Repressor fragment complexed with DNA
      (b) Lambda cro
      (c) Lambda cI repressor fragment
      5.1.3 E. coli Trp repressor
      5.1.4 E. coli Met repressor
      5.1.5 Zinc-containing DNA-binding domains (zinc fingers) TFIIIA
      5.2 Restriction endonuclease - E. coli EcoRI
      5.3 Site-specific recombination-Gamma Delta Resolvase
      6. Sequence-independent DNA-binding proteins
      6.1 Klenow fragment of E. coli DNA Polymerase I
      6.2 Bovine pancreatic DNase I
      6.3 E. coli Hu protein
      7. Sequence-specific RNA-binding proteins
      7.1 E. coli glutaminyl-tRNA synthetase complexed with tRNA
      8. Conclusions and prospects
      9. Acknowledgements
      10. References
AU  - Steitz TA
PT  - Journal Article
TA  - Q. Rev. Biophys.
JT  - Q. Rev. Biophys.
SO  - Q. Rev. Biophys. 1990 23: 205-280.

PMID- 25428976
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Thalassotalea sp. Strain ND16A Isolated from Eastern Mediterranean Sea Water Collected from a Depth of 1,055 Meters.
PG  - e01231-14
AB  - Thalassotalea sp. strain ND16A belongs to the family Colwelliaceae and was isolated from
      eastern Mediterranean Sea water at a depth of 1,055 m. Members of
      Colwelliaceae are ubiquitous marine heterotrophs. Here, we report the draft
      genome sequence of Thalassotalea sp. strain ND16A, a member of the newly
      described genus Thalassotalea.
AU  - Stelling SC
AU  - Techtmann SM
AU  - Utturkar SM
AU  - Alshibli NK
AU  - Brown SD
AU  - Hazen TC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01231-14.

PMID- 
VI  - 74
DP  - 2010
TI  - Plasmids of Xylella fastidiosa mulberry-infecting strains share extensive sequence identity and gene complement with pVEIS01 from the earthworm symbiont Verminephrobacter eiseniae.
PG  - 238-245
AB  - A ~25 kbp plasmid was present in each of four Californian strains of Xylella fastidiosa from
      mulberry affected with leaf scorch disease.  Fragments of each plasmid were cloned into
      Escherichia coli, sequenced, and assembled into circular contigs of 25,105 bp (pXF-RIV11 and
      pXF-RIV16) or 24,372 bp (pXF-RIV19 and pXF-RIV25).  The four plasmids shared >99.8% sequence
      identity, excluding a 732 bp insertion common to pXF-RIV11 and pXF-RIV16.  BLAST searches
      identified seven regions (totaling 19,252 bp) sharing greater than or equal to 75% nucleotide
      sequence identity with pVEI201, a 31 kbp plasmid from the earthworm symbiont Verminephrobacter
      eiseniae.  Using pXF-RIV11 as a query in BLASTX searches, putative functions of
      plasmid-encoded open reading frames were identified.  Fourteen ORFs were associated with DNA
      transfer (Type IV secretion), four with plasmid stability (plasmid toxin/anti-toxin
      addiction), one with protein export (Type II secretion), one with plasmid DNA replication
      initiation (trfA), and the remaining ORFs associated with other or unknown functions.  The
      putative origin of DNA replication (oriV) was located adjacent to the trfA ORF and was similar
      in structure to that of plasmids belonging to the incP-1 incompatibility group.  E. coli
      plasmids bearing fragments of pXF-RIV11 and the nptII gene as a selectable marker were tested
      for replication in X. fastidiosa strain Temecula1.  Only fragments bearing oriV and trfA were
      competent for replication in X. fastidiosa.  Collectively, these results indicate that
      mulberry strains of X. fastidiosa harbor plasmids encoding genes associated with DNA transfer
      and plasmid stability not previously identified on the chromosome of sequenced X. fastidiosa
      strains and that ancestors of distantly related bacterial species occupying different niches
      appear to have exchanged genetic material.
AU  - Stenger DC
AU  - Lee MW
AU  - Rogers EE
AU  - Chen J
PT  - Journal Article
TA  - Physiol. Mol. Plant Pathol.
JT  - Physiol. Mol. Plant Pathol.
SO  - Physiol. Mol. Plant Pathol. 2010 74: 238-245.

PMID- 28963221
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Marinobacter vinifirmus Type Strain FB1.
PG  - e01058-17
AB  - The gammaproteobacterium Marinobacter vinifirmus is associated with moderately saline
      environments and is often found in marine ecosystems. Here, we report the
      draft genome sequence of M. vinifirmus type strain FB1 (3.8 Mbp, 3,588 predicted
      genes). The presented sequence will improve our understanding of the taxonomy and
      evolution of the genus Marinobacter.
AU  - Stepanov VG
AU  - Roberts DJ
AU  - Fox GE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01058-17.

PMID- 24762934
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Deinococcus phoenicis, a Novel Strain Isolated during the Phoenix Lander Spacecraft Assembly.
PG  - e00301-14
AB  - Deinococcus phoenicis strain 1P10ME(T) is a radiation- and desiccation-resistant  bacterium
      isolated from a cleanroom facility where the Phoenix Lander spacecraft was assembled. In order
      to facilitate investigations of the nature of the extreme resistance of D. phoenicis to
      bactericidal factors, a draft genome sequence of D. phoenicis was determined.
AU  - Stepanov VG
AU  - Vaishampayan P
AU  - Venkateswaran K
AU  - Fox GE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00301-14.

PMID- 26798109
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Marinobacter sp. Strain P4B1, an Electrogenic Perchlorate-Reducing Strain Isolated from a Long-Term Mixed Enrichment Culture of  Marine Bacteria.
PG  - e01617-15
AB  - The perchlorate-reducing strain Marinobacter sp. strain P4B1 was isolated from a  long-term
      perchlorate-degrading enrichment culture seeded with marine sediment.
      The draft genome of Marinobacter sp. P4B1 is comprised of the bacterial
      chromosome (3.60 Mbp, G+C 58.51%, 3,269 predicted genes) and its associated
      plasmid pMARS01 (0.14 Mbp, G+C 52.95%, 165 predicted genes).
AU  - Stepanov VG
AU  - Xiao Y
AU  - Lopez AJ
AU  - Roberts DJ
AU  - Fox GE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01617-15.

PMID- 24309739
VI  - 1
DP  - 2013
TI  - Genome Sequence of Enterobacter turicensis Strain 610/05 (LMG 23731), Isolated from Fruit Powder.
PG  - e00996-13
AB  - We report the draft genome sequence of Enterobacter turicensis strain 610/05 (LMG 23731),
      isolated from fruit powder. The draft genome has a size of 4,182,790 bp
      and a G+C% content of 58.0.
AU  - Stephan R
AU  - Grim CJ
AU  - Gopinath GR
AU  - Mammel MK
AU  - Sathyamoorthy V
AU  - Trach LH
AU  - Chase HR
AU  - Fanning S
AU  - Tall BD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00996-13.

PMID- 21037008
VI  - 193
DP  - 2010
TI  - Complete Genome Sequence of Cronobacter turicensis LMG 23827, a foodborne pathogen causing deaths in neonates.
PG  - 309-310
AB  - Here we report the complete and annotated genome sequence of Cronobacter turicensis, an
      opportunistic foodborne pathogen, which is known as rare but important causes of
      live-threatening neonatal infections. Among all proteins of C. turicensis, 223 have been
      annotated as virulence and disease-related proteins.
AU  - Stephan R
AU  - Lehner A
AU  - Tischler P
AU  - Rattei T
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 193: 309-310.

PMID- 19523474
VI  - 391
DP  - 2009
TI  - Dissection of the DNA mimicry of the bacteriophage T7 Ocr protein using chemical modification.
PG  - 565-576
AB  - The homodimeric Ocr (overcome classical restriction) protein of bacteriophage T7 is a
      molecular mimic of double-stranded DNA and a highly
      effective competitive inhibitor of the bacterial type I
      restriction/modification system. The surface of Ocr is replete with acidic
      residues that mimic the phosphate backbone of DNA. In addition, Ocr also
      mimics the overall dimensions of a bent 24-bp DNA molecule. In this study,
      we attempted to delineate these two mechanisms of DNA mimicry by
      chemically modifying the negative charges on the Ocr surface. Our analysis
      reveals that removal of about 46% of the carboxylate groups per Ocr
      monomer results in an approximately 50-fold reduction in binding affinity
      for a methyltransferase from a model type I restriction/modification
      system. The reduced affinity between Ocr with this degree of modification
      and the methyltransferase is comparable with the affinity of DNA for the
      methyltransferase. Additional modification to remove approximately 86% of
      the carboxylate groups further reduces its binding affinity, although the
      modified Ocr still binds to the methyltransferase via a mechanism
      attributable to the shape mimicry of a bent DNA molecule. Our results show
      that the electrostatic mimicry of Ocr increases the binding affinity for
      its target enzyme by up to approximately 800-fold.
AU  - Stephanou AS
AU  - Roberts GA
AU  - Cooper LP
AU  - Clarke DJ
AU  - Thomson AR
AU  - MacKay CL
AU  - Nutley M
AU  - Cooper A
AU  - Dryden DT
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2009 391: 565-576.

PMID- 19013430
VI  - 378
DP  - 2009
TI  - A mutational analysis of DNA mimicry by ocr, the gene 0.3 antirestriction protein of bacteriophage T7.
PG  - 129-132
AB  - The ocr protein of bacteriophage T7 is a structural and electrostatic mimic of approximately
      24 base pairs of double-stranded B-form DNA. As
      such, it inhibits all Type I restriction and modification (R/M) enzymes
      by blocking their DNA binding grooves and inactivates them. This allows
      the infection of the bacterial cell by T7 to proceed unhindered by the
      action of the R/M defence system. We have mutated aspartate and
      glutamate residues on the surface of ocr to investigate their
      contribution to the tight binding between the EcoKI Type I R/M enzyme
      and ocr. Contrary to expectations, all of the single and double site
      mutations of ocr constructed were active as anti-R/M proteins in vivo
      and in vitro indicating that the mimicry of DNA by ocr is very
      resistant to change.
AU  - Stephanou AS
AU  - Roberts GA
AU  - Tock MR
AU  - Pritchard EH
AU  - Turkington R
AU  - Nutley M
AU  - Cooper A
AU  - Dryden DTF
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 2009 378: 129-132.

PMID- 26294626
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of a Community-Associated Methicillin-Resistant Panton-Valentine Leukocidin-Positive Staphylococcus aureus Sequence Type 30  Isolate from a Pediatric Patient with a Lung Infection in Brazil.
PG  - e00907-15
AB  - The sequence of methicillin-resistant Staphylococcus aureus strain B6 (sequence type 30
      [ST30], spa type t433, staphylococcal chromosomal cassette mec element
      [SCCmec] type IVc, Panton-Valentine leukocidin [PVL] positive), isolated from a
      pediatric patient with a lung infection in Niteroi, Rio de Janeiro, Brazil, is
      described here. The draft genome sequence includes a 2.8-Mb chromosome,
      accompanied by a 20-kb plasmid containing blaZ and two small cryptic plasmids.
AU  - Stephens C
AU  - Cho PJ
AU  - Afonso-de-Araujo V
AU  - Gomes IM
AU  - de Azevedo-Sias SM
AU  - Araujo CCA
AU  - Riley LW
AU  - Aguiar-Alves F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00907-15.

PMID- 8577742
VI  - 93
DP  - 1996
TI  - A cell cycle-regulated bacterial DNA methyltransferase is essential for viability.
PG  - 1210-1214
AB  - The CcrM adenine DNA methyltransferase, which specifically modifies GANTC sequences, is
      necessary for viability in Caulobacter crescentus.  To our knowledge, this is the first
      example of an essential prokaryotic DNA methyltransferase that is not part of a DNA
      restriction/modification system.  Homologs of CcrM are widespread in the a subdivision of the
      Proteobacteria, suggesting that methylation at GANTC sites may have important functions in
      other members of this diverse group as well.  Temporal control of DNA methylation state has an
      important role in Caulobacter development, and we show that this organism utilizes an unusual
      mechanism for control of remethylation of newly replicated DNA.  CcrM is synthesized de novo
      late in the cell cycle, coincident with full methylation of the chromosome, and is then
      subjected to proteolysis prior to cell division.
AU  - Stephens C
AU  - Reisenauer A
AU  - Wright R
AU  - Shapiro L
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1996 93: 1210-1214.

PMID- Not carried by PubMed...
VI  - 94
DP  - 1994
TI  - A common regulatory system controls transcription of flagellar genes and an essential DNA methyltransferase in Caulobacter.
PG  - 203
AB  - Our lab has recently isolated an essential Caulobacter gene (ccrM) encoding a DNA
      methyltransferase which modifies DNA in a cell-cycle dependent manner.  ccrM transcription,
      and CcrM methylation activity, occur only in the predivisional cell as chromosomal replication
      is nearing completion.  Proper temporal control of CcrM activity is crucial, as constitutive
      expression of ccrM results in defects in cell morphology and timing of chromosomal
      replication.  We are thus interested in understanding the control of ccrM transcription.  The
      functional ccrM promoter region was defined by deletion analysis, and the start site of
      transcription was determined.  Immediately upstream of the start site is a sequence with
      striking similarity to the consensus promoter for Caulobacter Class II flagellar genes, which
      are also activated in the predivisional cell.  The RNA polymerase species recognizing these
      promoters is not yet known.  Mutations in bases conserved between the ccrM and Class II
      promoters greatly reduce ccrM transcription.  In addition, ccrM and Class II promoters are
      rapidly repressed when DNA synthesis is inhibited.  It is proposed, therefore, that ccrM is
      transcribed by the same factors used for Class II flagellar genes.  Deletion analysis
      indicated that 20 bp downstream of the transcription start site was also required for ccrM
      promoter activity.  This region contains a 10 bp inverted repeat containing two CcrM
      methylation sites.  Roles for this sequence, and perhaps its methylation state, in promoter
      activation are being examined.
AU  - Stephens C
AU  - Shapiro L
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1994 94: 203.

PMID- Not carried by PubMed...
VI  - 95
DP  - 1995
TI  - An essential DNA methyltransferase in Caulobacter crescentus.
PG  - 330
AB  - In the dimorphic bacterium Caulobacter crescentus, methylation of GAnTC sites in newly
      replicated DNA only occurs late in the cell cycle, shortly before cell division.  The
      Caulobacter ccM gene, which encodes the DNA methyltransferase (M.CcrII) responsible for
      methylation of GAnTC sites, is transcribed only in the predivisional cell.  We have found that
      ccrM expression depends on a promoter homologous to that used by Caulobacter Class II
      flagellar genes, demonstrating that the system controlling the flagellar genetic hierarchy
      also regulates other genes in the predivisional cell.  Antibodies generated to M.CcrII were
      used to show that this protein is highly unstable, and M.CcrII levels during the cell cycle
      are tightly linked to transcription of ccrM.  Temporal regulation of methylation by M.CcrII is
      necessary for normal development, as strains which express ccrM throughout the cell cycle,
      and which therefore have continuously fully methylated DNA, exhibit abnormalities in control
      of DNA replication and cell division.  We have used gene replacement experiments to
      demonstrate that the ccrM gene is essential for growth and viability.  ccrM is to our
      knowledge the first essential prokaryotic DNA methyltransferase.  To further examine the
      function of M.CcrII in Caulobacter growth and development, we have constructed strains in
      which ccrM expression can be controlled exogeneously.  We are examining the pysiological
      consequences of blocking methylation completely, and of inducing methylation at inappropriate
      times in the cell cycle.
AU  - Stephens C
AU  - Shapiro L
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1995 95: 330.

PMID- 26543109
VI  - 3
DP  - 2015
TI  - Complete Genome Sequences of Four Escherichia coli ST95 Isolates from Bloodstream Infections.
PG  - e01241-15
AB  - Finished genome sequences are presented for four Escherichia coli strains isolated from
      bloodstream infections at San Francisco General Hospital. These
      strains provide reference sequences for four major fimH-identified sublineages
      within the multilocus sequence type (MLST) ST95 group, and provide insights into
      pathogenicity and differential antimicrobial susceptibility within this group.
AU  - Stephens CM
AU  - Skerker JM
AU  - Sekhon MS
AU  - Arkin AP
AU  - Riley LW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01241-15.

PMID- 7896686
VI  - 177
DP  - 1995
TI  - Coordinate cell cycle control of a Caulobacter DNA methyltransferase and the flagellar genetic hierarchy.
PG  - 1662-1669
AB  - The expression of the Caulobacter ccrM gene and the activity of its product, the M.CcrII DNA
      methyltransferase, are limited to a discrete portion of the cell cycle. Temporal control of
      DNA methylation has been shown to be critical for normal development in the dimorphic
      Caulobacter life cycle. To understand the mechanism by which ccrM expression is regulated
      during the cell cycle, we have identified and characterized the ccrM promoter region. We have
      found that it belongs to an unusual promoter family used by several Caulobacter class II
      flagellar genes. The expression of these class II genes initiates assembly of the flagellum
      just prior to activation of the ccrM promoter in the predivisional cell. Mutational analysis
      of two M.CcrII methylation sites located 3' to the ccrM promoter suggests that methylation
      might influence the temporally controlled inactivation of ccrM transcription. An additional
      parallel between the ccrM and class II flagellar promoters is that their transcription
      responds to a cell cycle DNA replication checkpoint. We propose that a common regulatory
      system coordinates the expression of functionally diverse genes during the Caulobacter cell
      cycle.
AU  - Stephens CM
AU  - Zweiger G
AU  - Shapiro L
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1995 177: 1662-1669.

PMID- 6276358
VI  - 149
DP  - 1982
TI  - Partial purification and cleavage specificity of a site-specific endonuclease, SciNI, isolated from Spiroplasma citri.
PG  - 508-514
AB  - A site-specific endonuclease, SciNI, has been partially purified from the plant
      pathogen Spiroplasma citri.  The enzyme recognizes the sequence 5'-G-C-G-C-3'
      and cleaves between the first G and C.  3'-C-G-C-G-5' SciNI is an isoschizomer
      of HhaI, but generates DNA fragments with 5' rather than 3' single-stranded
      protrusions.
AU  - Stephens MA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1982 149: 508-514.

PMID- 9784136
VI  - 282
DP  - 1998
TI  - Genome Sequence of an Obligate Intracellular Pathogen of Humans: Chlamydia trachomatis.
PG  - 754-759
AB  - Analysis of the 1,042,519-base pair Chlamydia trachomatis genome revealed unexpected features
      related to the complex biology of chlamydiae. Although chlamydiae lack many biosynthetic
      capabilities, they retain functions for performing key steps and interconversions of
      metabolites obtained from their mammalian host cells. Numerous potential virulence-associated
      proteins also were characterized. Several eukaryotic chromatin-associated domain proteins were
      identified, suggesting a eukaryotic-like mechanism for chlamydial nucleoid condensation and
      decondensation. The phylogenetic mosaic of chlamydial genes, including a large number of genes
      with phylogenetic origins from eukaryotes, implies a complex evolution for adaptation to
      obligate intracellular parasitism.  [ Comment in: Science 1998 Oct 23;282(5389):638-9 ]
AU  - Stephens RS
AU  - Kalman S
AU  - Lammel CJ
AU  - Fan J
AU  - Marathe R
AU  - Aravind L
AU  - Mitchell WP
AU  - Olinger L
AU  - Tatusov RL
AU  - Zhao Q
AU  - Koonin EV
AU  - Davis RW
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1998 282: 754-759.

PMID- 2695392
VI  - 85
DP  - 1989
TI  - Comparison of the nucleotide and amino acid sequences of the RsrI and EcoRI restriction endonucleases.
PG  - 1-13
AB  - The RsrI endonuclease, a type-II restriction endonuclease (ENase) found in
      Rhodobacter sphaeroides, is an isoschizomer of the EcoRI ENase.  A clone
      containing an 11-kb BamHI fragment was isolated from an R. sphaeroides genomic
      DNA library by hybridization with synthetic oligodeoxyribonucleotide probes
      based on the N-terminal amino acid (aa) sequence of RsrI.  Extracts of E. coli
      containing a subclone of the 11-kb fragment display RsrI activity.  Nucleotide
      sequence analysis reveals an 831-bp open reading frame encoding a polypeptide
      of 277 aa.  A 50% identity exists within a 266-aa overlap between the deduced
      aa sequences of RsrI and EcoRI.  Regions of 75-100% aa sequence identity
      correspond to key structural and functional regions of EcoRI.  The type-II
      ENases have many common properties, and a common origin might have been
      expected.  Nevertheless, this is the first demonstration of aa sequence
      similarity between ENases produced by different organisms.
AU  - Stephenson FH
AU  - Ballard BT
AU  - Boyer HW
AU  - Rosenberg JM
AU  - Greene PJ
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1989 85: 1-13.

PMID- 2602165
VI  - 17
DP  - 1989
TI  - Nucleotide sequence of the gene encoding the RsrI methyltransferase.
PG  - 10503
AB  - None
AU  - Stephenson FH
AU  - Greene PJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 10503.

PMID- 28104660
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Methane-Oxidizing Bacterium 'Candidatus Methylomonas sp. LWB' Isolated from Movile Cave.
PG  - e01491-16
AB  - We describe the draft genome sequence of 'Candidatus Methylomonas sp. LWB' isolated from
      Movile Cave microbial mat samples. The genome contains both the
      soluble and particular methane monooxygenase; however, one of the putative
      particulate methane monooxygenase gene clusters is ordered pmoABC rather than in
      the canonical gene arrangement of pmoCAB.
AU  - Stephenson J
AU  - Kumaresan D
AU  - Hillebrand-Voiculescu AM
AU  - Brooks E
AU  - Whiteley AS
AU  - Murrell JC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01491-16.

PMID- 10373580
VI  - 27
DP  - 1999
TI  - BseSI, a restriction endonuclease from Bacillus stearothermophilus Jo 10-553, which recognizes the novel hexanucleotide sequence 5'-G(G/T)GC(A/C)/C-3'.
PG  - 2644-2645
AB  - A new restriction endonuclease BseSI has been isolated from Bacillus stearothermophilus
      Jo10-553. BseSI recognizes a degenerate hexanucleotide sequence 5'-G(G/T)GC(A/C)^C-3' and
      cleaves DNA to produce 3'-protruding tetranucleotide ends.
AU  - Steponaviciene D
AU  - Maneliene Z
AU  - Petrusyte M
AU  - Janulaitis A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1999 27: 2644-2645.

PMID- 20979102
VI  - 33
DP  - 2011
TI  - The phage-host arms race: Shaping the evolution of microbes.
PG  - 43-51
AB  - Bacteria, the most abundant organisms on the planet, are outnumbered by a factor of 10 to 1 by
      phages that infect them. Faced with the rapid evolution and turnover of phage particles,
      bacteria have evolved various mechanisms to evade phage infection and killing, leading to an
      evolutionary arms race. The extensive co-evolution of both phage and host has resulted in
      considerable diversity on the part of both bacterial and phage defensive and offensive
      strategies. Here, we discuss the unique and common features of phage resistance mechanisms and
      their role in global biodiversity. The commonalities between defense mechanisms suggest
      avenues for the discovery of novel forms of these mechanisms based on their evolutionary
      traits.
AU  - Stern A
AU  - Sorek R
PT  - Journal Article
TA  - Bioessays
JT  - Bioessays
SO  - Bioessays 2011 33: 43-51.

PMID- 2995323
VI  - 164
DP  - 1985
TI  - Evidence that adenine methylation influences DNA-protein interactions in Escherichia coli.
PG  - 490-493
AB  - In this review, most of the information presented will be derived from studies
      with Escherichia coli K-12 (E. coli) and its related bacteriophages, simply
      because more is known about methylation in these organisms than in any other.
      The two methylated bases that have been detected in E. coli are 6-methyladenine
      (6-meAde) and 5-methylcytosine.  Since little is known about the biological
      function of 6-methylcytosine, I will deal exclusively here with the studies on
      6-meAde.
AU  - Sternberg N
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1985 164: 490-493.

PMID- 2236019
VI  - 87
DP  - 1990
TI  - Cleavage of the bacteriophage P1 packaging site (pac) is regulated by adenine methylation.
PG  - 8070-8074
AB  - The packaging of bacteriophage P1 DNA is initiated when the phage packaging
      site (pac) is recognized and cleaved and continues until the phage head is
      full.  We have previously shown that pac is a 162-base-pair segment of P1 DNA
      that contains seven DNA adenine methyltransferase methylation sites (5'-GATC).
      We show here that cleavage of pac is methylation sensitive.  Both in vivo and
      in vitro experiments indicate that methylated pac is cleavable, whereas
      unmethylated pac is not.  Moreover, DNA isolated from P1 phage and containing
      an uncut pac site was a poor substrate for in vitro cleavage until it was
      methylated by the Escherichia coli DNA adenine methyltransferase.  Comparison
      of that uncut pac DNA with other viral DNA fragments by digestion with
      methylation-sensitive restriction enzymes indicated that the uncut pac DNA was
      preferentially undermethylated.  In contrast, virion DNA containing a cut pac
      site was not undermethylated.  We believe these results indicate that pac
      cleavage is regulated by adenine methylation during the phage lytic cycle.
AU  - Sternberg N
AU  - Coulby J
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1990 87: 8070-8074.

PMID- 4746493
VI  - 182
DP  - 1973
TI  - Conformation of N6-methyladenine, a base involved in DNA modification:restriction processes.
PG  - 833-834
AB  - Crystal structures of N6,N9-dimethyladenine and N6-methyladenine hydrochloride
      were determined from three-dimensional x-ray diffraction data.  The bases
      assume a conformation in which the N(6)-methyl group blocks one of the
      hydrogen-bonding sites normally used by adenine to form Watson-Crick pairs with
      thymine in double-helical DNA.  When in this conformation, N6-methyladenine
      residues might alter the secondary structure of DNA, thereby preventing the
      scission of modified DNA's by restriction enzymes.
AU  - Sternglanz H
AU  - Bugg CE
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1973 182: 833-834.

PMID- 14760742
VI  - 5
DP  - 2004
TI  - Chimeras of the homing endonuclease PI-Scel and the homologous Candida tropicalis Intein: A study to explore the possibility of exchanging  DNA-binding modules to obtain highly specific endonucleases with  altered specificity.
PG  - 206-213
AB  - Homing endonucleases are extremely specific endodeoxyribonucleases. In vivo, these enzymes
      confer mobility on their genes by inducing a very
      specific double-strand cut in cognate alleles that lack the cooling
      sequence for the homing endonuclease; the cellular repair of the
      double-strand break with the endonuclease-containing allele as a
      template leads to integration of the endonuclease gene, completing the
      homing process. As a result of their extreme sequence specificity
      homing endonucleases are promising tools for genome engineering, For
      this, purpose, it is desirable to design enzymes with defined new
      specificities. To analyse which DNA-binding elements are potential
      candidates for use in the design of enzymes with modified or even new
      specificity, we produced several chimeric proteins derived from the
      Saccharomyces cerevisiae VMA1 intein (PI-SceI) and the related Candida
      tropicalis VMA1 intein. Although the mature Candida intein is devoid of
      endonucleolytic activity the exchange of two DNA-binding modules of
      PI-Scel with the homologous elements from the Candida intein results in
      an active endonuclease. The low sequence homology in these modules
      indicates that different protein - DNA contacts are responsible for the
      recognition of related DNA sequences. This flexibility in DNA
      recognition should, in principle, allow endonucleases to be produced
      with new specificities useful for genome engineering.
AU  - Steuer S
AU  - Pingoud V
AU  - Pingoud A
AU  - Wende W
PT  - Journal Article
TA  - Chembiochem
JT  - Chembiochem
SO  - Chembiochem 2004 5: 206-213.

PMID- 25502681
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Gephyronic Acid Producer Cystobacter violaceus Strain Cb vi76.
PG  - e01299-14
AB  - A draft genome sequence of Cystobacter violaceus strain Cb vi76, which produces the eukaryotic
      protein synthesis inhibitor gephyronic acid, has been obtained.
      The genome contains numerous predicted secondary metabolite clusters, including
      the gephyronic acid biosynthetic pathway. This genome will contribute to the
      investigation of secondary metabolism in other Cystobacter strains.
AU  - Stevens DC
AU  - Young J
AU  - Carmichael R
AU  - Tan J
AU  - Taylor RE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01299-14.

PMID- 23804401
VI  - 23
DP  - 2013
TI  - Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods.
PG  - 1541-1553
AB  - Recent advancements in sequencing-based DNA methylation profiling methods provide an
      unprecedented opportunity to map complete DNA
      methylomes. These include whole-genome bisulfite sequencing (WGBS,
      MethyiC-seq, or BS-seq), reduced-representation bisulfite sequencing
      (RRBS), and enrichment-based methods such as MeDIP-seq, MBD-seq, and
      MRE-seq. These methods yield largely comparable results but differ
      significantly in extent of genomic CpG coverage, resolution,
      quantitative accuracy, and cost, at least while using current
      algorithms to interrogate the data. None of these existing methods
      provides single-CpG resolution, comprehensive genome-wide coverage, and
      cost feasibility for a typical laboratory. We introduce methylCRF, a
      novel conditional random fields based algorithm that integrates
      methylated DNA immunoprecipitation (MeDIP-seq) and
      methylation-sensitive restriction enzyme (MRE-seq) sequencing data to
      predict DNA methylation levels at single-CpG resolution. Our method is
      a combined computational and experimental strategy to produce DNA
      methylomes of all 28 million CpGs in the human genome for a fraction
      (<10%) of the cost of whole-genome bisulfite sequencing methods.
      methylCRF was benchmarked for accuracy against Infinium arrays, RRBS,
      WGBS sequencing, and locus-specific bisulfite sequencing performed on
      the same human embryonic stem cell line. methylCRF transformation of
      MeDIP-seq/MRE-seq was equivalent to a biological replicate of WGBS in
      quantification, coverage, and resolution. We used conventional
      bisulfite conversion, PCR, cloning, and sequencing to validate loci
      where our predictions do not agree with whole-genome bisulfite data,
      and in 11 out of 12 cases, methylCRF predictions of methylation level
      agree better with validated results than does whole-genome bisulfite
      sequencing. Therefore, methylCRF transformation of MeDIP-seq/MRE-seq
      data provides an accurate, inexpensive, and widely accessible strategy
      to create full DNA methylomes.
AU  - Stevens M
AU  - Cheng JB
AU  - Li D
AU  - Xie M
AU  - Hong C
AU  - Maire CL
AU  - Ligon KL
AU  - Hirst M
AU  - Marra MA
AU  - Costello JF
AU  - Wang T
PT  - Journal Article
TA  - Genome Res.
JT  - Genome Res.
SO  - Genome Res. 2013 23: 1541-1553.

PMID- 28126942
VI  - 5
DP  - 2017
TI  - Complete and Assembled Genome Sequence of Vagococcus teuberi DSM 21459T, a Novel  Species Isolated from Fermented Cow Milk in Mali.
PG  - e01514-16
AB  - The genome of Vagococcus teuberi DSM 21459T, a strain isolated from Malian fermented milk, was
      sequenced using single-molecule real-time sequencing. The
      genome of V. teuberi DSM 21459T is the first sequenced genome of this novel
      species and the second genome among the genus Vagococcus.
AU  - Stevens MJ
AU  - Inglin RC
AU  - Meile L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01514-16.

PMID- 26139727
VI  - 3
DP  - 2015
TI  - Complete and Assembled Genome Sequence of Staphylococcus aureus RKI4, a Food-Poisoning Strain Exhibiting a Novel S. aureus Pathogenicity Island Carrying seb.
PG  - e00769-15
AB  - The genome of Staphylococcus aureus RKI4, a strain isolated from feces of a patient in a case
      of staphylococcal food poisoning, was sequenced using combined
      Illumina and single-molecule real-time sequencing. Hierarchical assembly of the
      genome resulted in a 2,725,654-bp chromosome and a 17,905-bp mobile genetic
      element.
AU  - Stevens MJ
AU  - Stephan R
AU  - Johler S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00769-15.

PMID- 28057751
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Staphylococcus aureus 1608, a Strain That Caused Toxic Mastitis in Twin Cows.
PG  - e01438-16
AB  - Staphylococcus aureus 1608 is a strain that caused a lethal mastitis in cows. Here, the draft
      genome sequence of the strain is presented.
AU  - Stevens MJ
AU  - Stephan R
AU  - Johler S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01438-16.

PMID- 28818903
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Staphylococcus aureus S681, a Tetracycline-Sensitive Livestock-Associated Methicillin-Resistant Clonal Complex 398 Strain.
PG  - e00805-17
AB  - We present the draft genome sequence of an atypical tetracycline-susceptible
      livestock-associated methicillin-resistant Staphylococcus aureus (MRSA) strain.
      It contains 2,817,340 bp and 2,858 coding sequences, including 6 rRNA operons, 56
      tRNAs, and 4 noncoding RNA (ncRNA) genes. The strain harbors a tet(M) gene, but
      15 point mutations in amino acids are present that likely impair the
      functionality of TetM.
AU  - Stevens MJA
AU  - Stephan R
AU  - Johler S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00805-17.

PMID- 29567735
VI  - 6
DP  - 2018
TI  - Complete and Assembled Genome Sequence of Salmonella enterica subsp. enterica Serotype Senftenberg N17-509, a Strain Lacking Salmonella Pathogen Island 1.
PG  - e00156-18
AB  - The genome of Salmonella enterica subsp. enterica serotype Senftenberg N17-509, a strain
      isolated from desiccated coconut, was sequenced using single-molecule
      real-time sequencing. It consists of a 5.1-Mbp chromosome and a 29-kb linear
      plasmid.
AU  - Stevens MJA
AU  - Zurfluh K
AU  - Althaus D
AU  - Corti S
AU  - Lehner A
AU  - Stephan R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00156-18.

PMID- 29567736
VI  - 6
DP  - 2018
TI  - Complete and Assembled Genome Sequences of Pantoea calida DSM 22759(T) and Pantoea gaviniae DSM 22758(T).
PG  - e00157-18
AB  - The genomes of Pantoea calida DSM 22759(T) and Pantoea gaviniae DSM 22758(T) were sequenced
      using single-molecule real-time sequencing. They consist of a 4.3-Mbp
      chromosome containing 4,092 genes, of which 3,977 encode proteins, and a 4.5-Mbp
      chromosome containing 4,236 genes, of which 4,120 encode proteins, respectively.
AU  - Stevens MJA
AU  - Zurfluh K
AU  - Stephan R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00157-18.

PMID- 28302775
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Bacillus licheniformis VSD4, a Diesel Fuel-Degrading and Plant Growth-Promoting Phyllospheric Bacterium.
PG  - e00027-17
AB  - We report here the 4.19-Mb draft genome sequence of Bacillus licheniformis VSD4,  a
      Gram-positive bacterium of the Bacillaceae family, isolated from leaves of
      Hedera helix growing at a high-traffic city center in Belgium. Knowledge about
      its genome will help to evaluate its potential as an inoculant in
      phylloremediation applications.
AU  - Stevens V
AU  - Thijs S
AU  - McAmmond B
AU  - Langill T
AU  - Van Hamme J
AU  - Weyens N
AU  - Vangronsveld J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00027-17.

PMID- 28232452
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Rhodococcus erythropolis VSD3, a Diesel Fuel-Degrading and Plant Growth-Promoting Bacterium Isolated from Hedera helix Leaves.
PG  - e01680-16
AB  - We report here the 6.55-Mb draft genome sequence of Rhodococcus erythropolis VSD3, a
      Gram-positive bacterium of the Nocardiaceae family, isolated from leaves
      of Hedera helix growing at a high-traffic city center in Belgium. The exploration
      of its genome will contribute to the assessment of its application as an
      inoculant in phylloremediation approaches.
AU  - Stevens V
AU  - Thijs S
AU  - McAmmond B
AU  - Langill T
AU  - Van Hamme J
AU  - Weyens N
AU  - Vangronsveld J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01680-16.

PMID- 21651822
VI  - 8
DP  - 2011
TI  - Analysis of a viral metagenomic library from 200 m depth in Monterey Bay, California constructed by direct shotgun cloning.
PG  - 287
AB  - ABSTRACT: BACKGROUND: Viruses have a profound influence on both the
      ecology and evolution of marine plankton, but the genetic diversity of
      viral assemblages, particularly those in deeper ocean waters, remains
      poorly described. Here we report on the construction and analysis of a
      viral metagenome prepared from below the euphotic zone in a temperate,
      eutrophic bay of coastal California. METHODS: We purified viruses from
      approximately one cubic meter of seawater collected from 200m depth in
      Monterey Bay, CA. DNA was extracted from the virus fraction, sheared, and
      cloned with no prior amplification into a plasmid vector and propagated in
      E. coli to produce the MBv200m library. Random clones were sequenced by
      the Sanger method. Sequences were assembled then compared to sequences in
      GenBank and to other viral metagenomic libraries using BLAST analyses.
      RESULTS: Only 26% of the 881 sequences remaining after assembly had
      significant (E </= 0.001) BLAST hits to sequences in the GenBank nr
      database, with most being matches to bacteria (15%) and viruses (8%). When
      BLAST analysis included environmental sequences, 74% of sequences in the
      MBv200m library had a significant match. Most of these hits (70%) were to
      microbial metagenome sequences and only 0.7% were to sequences from viral
      metagenomes. Of the 121 sequences with a significant hit to a known virus,
      94% matched bacteriophages (Families Podo-, Sipho-, and Myoviridae) and 6%
      matched viruses of eukaryotes in the Family Phycodnaviridae (5 sequences)
      or the Mimivirus (2 sequences). The largest percentages of hits to viral
      genes of known function were to those involved in DNA modification (25%)
      or structural genes (17%). Based on reciprocal BLAST analyses, the MBv200m
      library appeared to be most similar to viral metagenomes from two other
      bays and least similar to a viral metagenome from the Arctic Ocean.
      CONCLUSIONS: Direct cloning of DNA from diverse marine viruses was
      feasible and resulted in a distribution of virus types and functional
      genes at depth that differed in detail, but were broadly similar to those
      found in surface marine waters. Targeted viral analyses are useful for
      identifying those components of the greater marine metagenome that
      circulate in the subcellular size fraction.
AU  - Steward GF
AU  - Preston CM
PT  - Journal Article
TA  - Virol. J.
JT  - Virol. J.
SO  - Virol. J. 2011 8: 287.

PMID- 10954592
VI  - 28
DP  - 2000
TI  - Expression of ZmMET1, a gene encoding a DNA methyltransferase from maize, is associated not only with DNA replication in actively proliferating cells, but also with altered DNA methylation status in cold-stressed quiescent cells.
PG  - 3250-3259
AB  - A cDNA fragment encoding part of a DNA methyltransferase was isolated from maize. The putative
      amino acid sequence identically matched that deduced from a genomic sequence in the database
      (accession no. AF063403), and the corresponding gene was designated as ZmMET1. Bacterially
      expressed ZmMET1 actively methylated DNA in vitro. Transcripts of ZmMET1 could be shown to
      exclusively accumulate in actively proliferating cells of the meristems of mesocotyls and root
      apices, suggesting ZmMET1 expression to be associated with DNA replication. This was confirmed
      by simultaneous decrease of transcripts of ZmMET1 and histone H3, a marker for DNA
      replication, in seedlings exposed to wounding, desiccation and salinity, all of which suppress
      cell division. Cold stress also depressed both transcripts in root tissues. In contrast,
      however, accumulation of ZmMET1 transcripts in shoot mesocotyls was not affected by cold
      stress, whereas those for H3 sharply decreased. Such a differential accumulation of ZmMET1
      transcripts was consistent with ZmMET1 protein levels as revealed by western blotting.
      Expression of ZmMET1 is thus coexistent, but not completely dependent on DNA replication.
      Southern hybridization analysis with a methylation-sensitive restriction enzyme revealed that
      cold treatment induced demethylation of DNA in the Ac/Ds transposon region, but not in other
      genes, and that such demethylation primarily occurred in roots. These results suggested that
      the methylation level was decreased selectively by cold treatment, and that ZmMET1 may, at
      least partly, prevent such demethylation.
AU  - Steward N
AU  - Kusano T
AU  - Sano H
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2000 28: 3250-3259.

PMID- 7731231
VI  - 19A
DP  - 1995
TI  - The mechanism of action of the McrBC restriction enzyme of E. coli K-12.
PG  - 118
AB  - As more restriction systems are characterised, their properties are being found to be more
      diverse and the traditional three classes of restriction enzymes (Types I, II and III) are
      becoming inadequate for classification. McrBC is one enzyme which fails to fit neatly into any
      of the three classes. Like enzymes of classes I and III it is a multi-subunit enzyme
      (consisting of 2 proteins, McrB and McrC) which requires two "half-sites" on the DNA for
      cleavage. However, unlike the enzymes so far described in these classes, McrBC recognises only
      methylated DNA, requiring at least one methylated C in each half-site, which is of the form
      5'-RmC-3'. Unusually, the half-sites can be symmetric or asymmetric as the DNA will be
      cleaved irrespective of which strand(s) the methylated Cs are on. Qualitatively, then, McrBC
      can recognise the half-sites in an orientation-independent manner. However, using synthetic
      oligos with the methylated bases in various configurations, we have shown that the efficiency
      of cleavage varies with the configuration of the methylated Cs.
      Spacing requirements for the half-sites were further investigated using a series of plasmids
      which contain only two McrBC half-sites, flanking a polylinker into which were inserted DNA
      fragments of various sizes, we have also found that cleavage efficiency depends on the spacing
      between the half-sites. Maximal cleavage occurs with a spacing of approximately 40-80bp, but
      cleavage can occur, less efficiently, with spacing of up to and including 1.2kb but not 3kb.
      The DNA is cleaved neither at a single position close to the recognition site like Type III
      enzymes, nor at a site very distant from the recognition site as with Type I enzymes, but
      rather at multiple positions close to only one half-site in each molecule, with no apparent
      preference for one half-site over the other.
      As McrBC shows no sequence similarity to other restriction enzymes (this is the case for
      many restriction enzymes) a clue as to its evolution may be obtained by elucidation of its
      mechanism of action. It is again similar to enzymes of Types I and III in requiring a
      nucleotide for cleavage but differs in its requirement for GTP rather than ATP. By gel
      retardation assays using synthetic oligos containing two appropriately-methylated and
      appropriately-spaced McrBC half-sites, we have shown that GTP is required for the initial
      binding of McrBC to DNA but it remains to be determined whether GTP is further required to
      allow communication between half-sites by McrBC as is true for ATP in the case of Type I and
      Type III enzymes.
AU  - Stewart F
AU  - Dila D
AU  - Raleigh E
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1995 19A: 118.

PMID- 10788324
VI  - 298
DP  - 2000
TI  - Methyl-specific DNA binding by McrBC, a modification-dependent restriction enzyme.
PG  - 611-622
AB  - McrBC, a GTP-requiring, modification-dependent endonuclease of Escherichia coli K-12,
      specifically recognizes DNA sites of the form 5' R(m)C 3'. DNA cleavage normally requires
      translocation-mediated coordination between two such recognition elements at distinct sites.
      We have investigated assembly of the cleavage-competent complex with gel-shift and DNase I
      footprint analysis. In the gel-shift system, McrB(L) binding resulted in a fast-migrating
      specific shifted band, in a manner requiring both GTP and Mg(2+). The binding was specific for
      methylated DNA and responded to local sequence changes in the same way that cleavage does.
      Single-stranded DNA competed for McrB(L)-binding in a modification and sequence-specific
      fashion. A supershifted species was formed in the presence of McrC and GTPgammaS. DNase I
      footprint analysis showed modest cooperativity in binding to two sites, and a two-site
      substrate displayed protection in non-specific spacer DNA in addition to the recognition
      elements. The addition of McrC did not affect the footprint obtained. We propose that McrC
      effects a conformational change in the complex rather than a reorganization of the DNA:protein
      interface.
AU  - Stewart FJ
AU  - Panne D
AU  - Bickle TA
AU  - Raleigh EA
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2000 298: 611-622.

PMID- 9628366
VI  - 379
DP  - 1998
TI  - Dependence of McrBC cleavage on distance between recognition elements.
PG  - 611-616
AB  - DNA cleavage by the modification-dependent restriction enzyme McrBC requires the presence of
      two suitably modified recognition elements appropriately spaced in the substrate.  To
      characterize the spacing requirement in more detail, we have constructed a plasmid with a
      single McrBC cleavage site, in which the distance between recognition elements could be
      systematically varied while preserving the local sequence surrounding the recognition
      elements.  Optimal separation between elements was 55-103 base pairs, with detectable cleavage
      observed at spacing of 32 bp to 2 kb; no cleavage was seen with spacing of 22 bp or less or
      with 3 kb between elements.  Changing the spacing by 4 basepairs within the optimal range has
      little effect on the efficiency of cleavage, suggesting that the recognition elements need not
      lie on the same face of the DNA helix.
AU  - Stewart FJ
AU  - Raleigh EA
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1998 379: 611-616.

PMID- 24167005
VI  - 71
DP  - 2014
TI  - Draft genomes of 12 host-adapted and environmental isolates of Pseudomonas aeruginosa and their positions in the core genome phylogeny.
PG  - 20-25
AB  - Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen particularly associated with
      the inherited disease cystic fibrosis (CF). Pseudomonas aeruginosa is well known to have a
      large and adaptable genome that enables it to colonise a wide range of ecological niches.
      Here, we have used a comparative genomics approach to identify changes that occur during
      infection of the CF lung.
      We used the mucoid phenotype as an obvious marker of host adaptation and compared these
      genomes to analyse SNPs, indels and islands within near-isogenic pairs. To commence the
      correction of the natural bias towards clinical isolates in genomics studies and to widen our
      understanding of the genomic diversity of P. aeruginosa, we included four environmental
      isolates in our analysis. Our data suggest that genome plasticity plays an important role in
      chronic infection and that the strains sequenced in this study are representative of the two
      major phylogenetic groups as determined by core genome SNP analysis.
AU  - Stewart L
AU  - Ford A
AU  - Sangal V
AU  - Jeukens J
AU  - Boyle B
AU  - Kukavica-Ibrulj I
AU  - Caim S
AU  - Crossman L
AU  - Hoskisson PA
AU  - Levesque R
AU  - Tucker NP
PT  - Journal Article
TA  - Pathog Dis.
JT  - Pathog Dis.
SO  - Pathog Dis. 2014 71: 20-25.

PMID- 21227987
VI  - 49
DP  - 2011
TI  - Genetic characterization indicates that a specific subpopulation of Pseudomonas aeruginosa is associated with keratitis infections.
PG  - 993-1003
AB  - Pseudomonas aeruginosa is a common opportunistic bacterial pathogen that causes a
      variety of infections in humans. Populations of P. aeruginosa are dominated by
      common clones that can be isolated from diverse clinical and environmental
      sources. To determine whether specific clones are associated with corneal
      infection, we used a portable genotyping microarray system to analyze a set of 63
      P. aeruginosa isolates from patients with corneal ulcers (keratitis). We then
      used population analysis to compare the keratitis isolates to a wider collection
      of P. aeruginosa from various nonocular sources. We identified various markers in
      a subpopulation of P. aeruginosa associated with keratitis that were in strong
      disequilibrium with the wider P. aeruginosa population, including oriC, exoU,
      katN, unmodified flagellin, and the carriage of common genomic islands. The
      genome sequencing of a keratitis isolate (39016; representing the dominant
      serotype O11), which was associated with a prolonged clinical healing time,
      revealed several genomic islands and prophages within the accessory genome. The
      PCR amplification screening of all 63 keratitis isolates, however, provided
      little evidence for the shared carriage of specific prophages or genomic islands
      between serotypes. P. aeruginosa twitching motility, due to type IV pili, is
      implicated in corneal virulence. We demonstrated that 46% of the O11 keratitis
      isolates, including 39016, carry a distinctive pilA, encoding the pilin of type
      IV pili. Thus, the keratitis isolates were associated with specific
      characteristics, indicating that a subpopulation of P. aeruginosa is adapted to
      cause corneal infection.
AU  - Stewart RM
AU  - Wiehlmann L
AU  - Ashelford KE
AU  - Preston SJ
AU  - Frimmersdorf E
AU  - Campbell BJ
AU  - Neal TJ
AU  - Hall N
AU  - Tuft S
AU  - Kaye SB
AU  - Winstanley C
PT  - Journal Article
TA  - J. Clin. Microbiol.
JT  - J. Clin. Microbiol.
SO  - J. Clin. Microbiol. 2011 49: 993-1003.

PMID- 29491851
VI  - 9
DP  - 2018
TI  - Pantoea ananatis Genetic Diversity Analysis Reveals Limited Genomic Diversity as  Well as Accessory Genes Correlated with Onion Pathogenicity.
PG  - 184
AB  - Pantoea ananatis is a member of the family Enterobacteriaceae and an enigmatic plant pathogen
      with a broad host range. Although P. ananatis strains can be
      aggressive on onion causing foliar necrosis and onion center rot, previous
      genomic analysis has shown that P. ananatis lacks the primary virulence secretion
      systems associated with other plant pathogens. We assessed a collection of fifty
      P. ananatis strains collected from Georgia over three decades to determine
      genetic factors that correlated with onion pathogenic potential. Previous genetic
      analysis studies have compared strains isolated from different hosts with varying
      diseases potential and isolation sources. Strains varied greatly in their
      pathogenic potential and aggressiveness on different cultivated Allium species
      like onion, leek, shallot, and chive. Using multi-locus sequence analysis (MLSA)
      and repetitive extragenic palindrome repeat (rep)-PCR techniques, we did not
      observe any correlation between onion pathogenic potential and genetic diversity
      among strains. Whole genome sequencing and pan-genomic analysis of a sub-set of
      10 strains aided in the identification of a novel series of genetic regions,
      likely plasmid borne, and correlating with onion pathogenicity observed on single
      contigs of the genetic assemblies. We named these loci Onion Virulence Regions
      (OVR) A-D. The OVR loci contain genes involved in redox regulation as well as
      pectate lyase and rhamnogalacturonase genes. Previous studies have not identified
      distinct genetic loci or plasmids correlating with onion foliar pathogenicity or
      pathogenicity on a single host pathosystem. The lack of focus on a single host
      system for this phytopathgenic disease necessitates the pan-genomic analysis
      performed in this study.
AU  - Stice SP
AU  - Stumpf SD
AU  - Gitaitis RD
AU  - Kvitko BH
AU  - Dutta B
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2018 9: 184.

PMID- 18562031
VI  - 136
DP  - 2008
TI  - Comparative genomic hybridisation and ultrafast pyrosequencing revealed remarkable differences between the Sinorhizobium meliloti genomes of the model strain Rm1021 and the field isolate SM11.
PG  - 31-37
AB  - Genomic variation between the Sinorhizobium meliloti model strain Rm1021 and the field isolate
      SM11 was assessed by using the genome-wide
      S. meliloti Rm1021 Sm6k-oligonucleotide microarray in a comparative
      genomic hybridisation experiment. Several gene clusters present in the
      Rm1021 genome are missing in the SM11 genome. In detail, three missing
      gene clusters were identified for the chromosome, five for megaplasmid
      pSymA and two for megaplasmid pSymB. To confirm these hybridisation
      results, the draft genome sequence of the S. meliloti field isolate
      SM11 was established by 454-pyrosequencing. Three sequencing runs on
      the ultrafast Genome Sequencer 20 System yielded 112.5 million bases.
      These could be assembled into 905 larger contigs resulting in a nearly
      15-fold coverage of the 7.1 Mb SM11 genome. The missing gene regions
      identified by comparative genomic hybridisation could be confirmed by
      the results of the 454-sequencing project. An in-depth analysis of
      these gene regions resulted in the following findings: (i) a complete
      type I restriction/modification system encoded by a composite
      transposon is absent in the chromosome of strain SM11. (ii) Most of the
      Rm1021 denitrification genes and the complete siderophore biosynthesis
      operon were found to be missing on SM11 megaplasmid pSymA. (iii) S.
      meliloti SM11 megaplasmid pSymB lacks a complete cell surface
      carbohydrate synthesis gene cluster. (iv) Several genes that are absent
      in the SM11 genome could be assigned to insertion sequences and
      transposons.
AU  - Stiens M
AU  - Becker A
AU  - Bekel T
AU  - Godde V
AU  - Goesmann A
AU  - Niehaus K
AU  - Schneiker-Bekel S
AU  - Selbitschka W
AU  - Weidner S
AU  - Schluter A
AU  - Puhler A
PT  - Journal Article
TA  - J. Biotechnol.
JT  - J. Biotechnol.
SO  - J. Biotechnol. 2008 136: 31-37.

PMID- 17466030
VI  - 271
DP  - 2007
TI  - Sequence analysis of the 181-kb accessory plasmid pSmeSM11b, isolated from a dominant Sinorhizobium meliloti strain identified during a long-term field release experiment.
PG  - 297-309
AB  - The 181 251 bp accessory plasmid pSmeSM11b of Sinorhizobium meliloti
      strain SM11, belonging to a dominant indigenous S. meliloti subpopulation
      identified during a long-term field release experiment, was sequenced.
      This plasmid has 166 coding sequences (CDSs), 42% of which encode proteins
      with homology to proteins of known function. Plasmid pSmeSM11b is a member
      of the repABC replicon family and contains a large gene region coding for
      a conjugation system similar to that of other self-transmissible plasmids
      in Rhizobium and Agrobacterium. Another pSmeSM11b gene region, possibly
      involved in sugar metabolism and polysaccharide catabolism, resembled a
      region of S. meliloti 1021 megaplasmid pSymB and in the genome of
      Sinorhizobium medicae WSM419. Another module of plasmid pSmeSM11b encodes
      proteins similar to those of the nitrogen-fixing actinomycete Frankia
      CcI3, and which are likely to be involved in the synthesis of a secondary
      metabolite. Several ORFs of pSmeSM11b were predicted to play a role in
      nonribosomal peptide synthesis. Plasmid pSmeSM11b has many mobile genetic
      elements, which contribute to the mosaic composition of the plasmid.
AU  - Stiens M
AU  - Schneiker S
AU  - Puhler A
AU  - Schluter A
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2007 271: 297-309.

PMID- 24205358
VI  - 8
DP  - 2013
TI  - Cytosine-to-Uracil Deamination by SssI DNA Methyltransferase.
PG  - e79003
AB  - The prokaryotic DNA(cytosine-5)methyltransferase M. SssI shares the specificity of eukaryotic
      DNA methyltransferases (CG) and is an important model and experimental tool in the study of
      eukaryotic DNA methylation. Previously, M. SssI was shown to be able to catalyze deamination
      of the target cytosine to uracil if the methyl donor S-adenosyl-methionine (SAM) was missing
      from the reaction. To test whether this side-activity of the enzyme can be used to distinguish
      between unmethylated and C5-methylate cytosines in CG dinucleotides, we re-investigated, using
      a sensitive genetic reversion assay, the cytosine deaminase activity of M. SssI. Confirming
      previous results we showed that M. SssI can deaminate cytosine to uracil in a slow reaction in
      the absence of SAM and that the rate of this reaction can be increased by the SAM analogue
      5'-amino-5'-deoxyadenosine. We could not detect M. SssI-catalyzed deamination of
      C5-methylcytosine (C-m5). We found conditions where the rate of M. SssI mediated C-to-U deamin
      ation was at least 100-fold higher than the rate of C-m5-to-T conversion. Although this
      difference in reactivities suggests that the enzyme could be used to identify C5-methylated
      cytosines in the epigenetically important CG dinucleotides, the rate of M. SssI mediated
      cytosine deamination is too low to become an enzymatic alternative to the bisulfite reaction.
      Amino acid replacements in the presumed SAM binding pocket of M. SssI (F17S and G19D) resulted
      in greatly reduced methyltransferase activity. The G1 9D variant showed cytosine deaminase
      activity in E. coli, at physiological SAM concentrations. Interestingly, the C-to-U deaminase
      activity was also detectable in an E. coli ung(+) host proficient in uracil excision repair.
AU  - Stier I
AU  - Kiss A
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2013 8: e79003.

PMID- 20693529
VI  - 38
DP  - 2010
TI  - The Type II restriction endonuclease MvaI has dual specificity.
PG  - 8231-8238
AB  - The MvaI restriction endonuclease cuts 5'-CC downward arrowAGG-3'/5'-CC upward arrowTGG-3'
      sites as indicated by the arrows. N4-methylation of the
      inner cytosines (C(m4)CAGG/C(m4)CTGG) protects the site against MvaI
      cleavage. Here, we show that MvaI nicks the G-strand of the related
      sequence (CCGGG/CCCGG, BcnI site) if the inner cytosines are
      C5-methylated: C(m5)C downward arrowGGG/CC(m5)CGG. At M.SssI-methylated
      SmaI sites, where two oppositely oriented methylated BcnI sites partially
      overlap, double-nicking leads to double-strand cleavage (CC(m5)C downward
      arrowGGG/CC(m5)C upward arrowGGG) generating fragments with blunt ends.
      The double-strand cleavage rate and the stringency of substrate site
      recognition is lower at the methylation-dependent site than at the
      canonical target site. MvaI is the first restriction endonuclease shown to
      possess, besides the 'normal' activity on its unmethylated recognition
      site, also a methylation-directed activity on a different sequence.
AU  - Stier I
AU  - Kiss A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2010 38: 8231-8238.

PMID- 29146841
VI  - 5
DP  - 2017
TI  - Draft Whole-Genome Sequences of 18 Flavobacterium spp.
PG  - e00865-17
AB  - We report here the draft whole-genome sequences for 18 Flavobacterium species type strains
      that have historically been associated with fish gill disease.
AU  - Stine CB
AU  - Li C
AU  - Crosby TC
AU  - Hasbrouck NR
AU  - Lam C
AU  - Tadesse DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00865-17.

PMID- 29773627
VI  - 6
DP  - 2018
TI  - Draft Whole-Genome Sequences of Chryseobacterium piscicola and Chryseobacterium shigense.
PG  - e00413-18
AB  - We report the draft whole-genome sequences for Chryseobacterium piscicola and Chryseobacterium
      shigense type strains, bacteria that have been associated with
      fish gill disease.
AU  - Stine CB
AU  - Li C
AU  - Crosby TC
AU  - Hasbrouck NR
AU  - Lam C
AU  - Tadesse DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00413-18.

PMID- 18403782
VI  - 18
DP  - 2008
TI  - Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis.
PG  - 729-741
AB  - Mycobacterium marinum, a ubiquitous pathogen of fish and amphibia, is a near relative of
      Mycobacterium tuberculosis, the etiologic agent of
      tuberculosis in humans. The genome of the M strain of M. marinum comprises
      a 6,636,827-bp circular chromosome with 5424 CDS, 10 prophages, and a
      23-kb mercury-resistance plasmid. Prominent features are the very large
      number of genes (57) encoding polyketide synthases (PKSs) and nonribosomal
      peptide synthases (NRPSs) and the most extensive repertoire yet reported
      of the mycobacteria-restricted PE and PPE proteins, and related-ESX
      secretion systems. Some of the NRPS genes comprise a novel family and seem
      to have been acquired horizontally. M. marinum is used widely as a model
      organism to study M. tuberculosis pathogenesis, and genome comparisons
      confirmed the close genetic relationship between these two species, as
      they share 3000 orthologs with an average amino acid identity of 85%.
      Comparisons with the more distantly related Mycobacterium avium subspecies
      paratuberculosis and Mycobacterium smegmatis reveal how an ancestral
      generalist mycobacterium evolved into M. tuberculosis and M. marinum. M.
      tuberculosis has undergone genome downsizing and extensive lateral gene
      transfer to become a specialized pathogen of humans and other primates
      without retaining an environmental niche. M. marinum has maintained a
      large genome so as to retain the capacity for environmental survival while
      becoming a broad host range pathogen that produces disease strikingly
      similar to M. tuberculosis. The work described herein provides a
      foundation for using M. marinum to better understand the determinants of
      pathogenesis of tuberculosis.
AU  - Stinear TP et al
PT  - Journal Article
TA  - Genome Res.
JT  - Genome Res.
SO  - Genome Res. 2008 18: 729-741.

PMID- 25931597
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Isolate Staphylococcus aureus LHSKBClinical, Isolated from an Infected Hip.
PG  - e00336-15
AB  - We report here the genome sequence of a clinical isolate of Staphylococcus aureus from an
      orthopedic infection. Phenotypically diverse Staphylococcus aureus
      strains are associated with orthopedic infections and subsequent implant failure,
      and some are highly resistant to antibiotics. This genome sequence will support
      further analyses of strains causing orthopedic infections.
AU  - Stipetic LH
AU  - Hamilton G
AU  - Dalby MJ
AU  - Davies RL
AU  - Meek RM
AU  - Ramage G
AU  - Smith DG
AU  - Burgess KE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00336-15.

PMID- 233289
VI  - 45
DP  - 1979
TI  - The sensitivity of phage DNA and plasmid DNA for a restriction enzyme from Staphylococcus aureus.
PG  - 19-23
AB  - In Staphylococcus aureus transduction of different tetracycline and chloramphenicol plasmids
      with a group I III modification was possible to group I and III strains.  Group II strains,
      containing a restriction endonuclease, had a restriction both for the phage and the plasmids:
      two restriction-deficient group II strains were good acceptors for these plasmids.
AU  - Stobberingh EE
AU  - Meijers JA
AU  - Van Kats-Renaud JH
PT  - Journal Article
TA  - Antonie Van Leeuwenhoek
JT  - Antonie Van Leeuwenhoek
SO  - Antonie Van Leeuwenhoek 1979 45: 19-23.

PMID- 885840
VI  - 131
DP  - 1977
TI  - Occurrence of a Class II Restriction Endonuclease in Staphylococcus aureus.
PG  - 645-649
AB  - The occurrence of class II restriction endonucleases (enzymes that both
      recognize and cleave a specific nucleotide sequence in deoxyribonucleic acid
      (DNA) in Staphyloccus aureus has been investigated by analysis of crude
      extracts obtained from different propagating strains of the International Phage
      Typing System.  Of the four main groups of strains in the International System,
      only extracts of group II strains were found to contain class II restriction
      endonucleases.  The identical cleavage patterns obtained by incubation of
      different DNAs with cell extracts of group II strains suggest that these
      enzymes all recognize and cleave the same nucleotide sequence.  This
      recognition site has been determined to be 5'-G-A-T-C-3' 3'-C-T-A-G-5' for the
      prototype of these enzymes, Sau3AI (J. Sussenbach et al., Nucl. Acids Res. 3:
      3192-3202, 1976).  Evidence is presented that the classification of group II
      strains is based on restriction modification and is correlated with the
      presence of a class II restriction endonuclease that recognizes and cleaves the
      above sequence.
AU  - Stobberingh EE
AU  - Schiphof R
AU  - Sussenbach JS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1977 131: 645-649.

PMID- 141491
VI  - 99
DP  - 1977
TI  - Restriction-deficient mutants of Staphylococcus aureus.
PG  - 359-367
AB  - A series of restriction-deficient mutants was isolated from non-lysogenic strains of
      Staphylococcus aureus belonging to phage groups I and II.  Some mutants were sensitive to all
      phages tested.  With one possible exception, all the mutants were unaffected in their
      modification systems.  The breakdown of DNA of phages, restricted in the parental strains, was
      reduced in both the mutants that were tested.  The restriction in propagating strain 3A could
      be transduced to its restriction-deficient mutant.  The transduction efficiency increased
      after ultraviolet irradiation of the transducing phage suggesting that the gene for
      restriction is present on the bacterial chromosome.
AU  - Stobberingh EE
AU  - Winkler KC
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1977 99: 359-367.

PMID- 20545861
VI  - 78
DP  - 2010
TI  - Social networking between mobile introns and their host genes.
PG  - 1-4
AB  - P>Homing endonucleases have long been known as the orchestrators of intron mobility. However,
      the extent of their influence on the intron
      and its genetic and cellular environment is still being elucidated. The
      accompanying paper emphasizes the importance of temporal control of
      endonuclease expression on splicing, expression of the host gene and
      cellular metabolism, while it raises questions to guide future inquiry.
AU  - Stoddard B
AU  - Belfort M
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2010 78: 1-4.

PMID- 16336743
VI  - 38
DP  - 2005
TI  - Homing endonuclease structure and function.
PG  - 49-95
AB  - Homing endonucleases are encoded by open reading frames that are embedded within group I,
      group II and archaeal introns, as well as inteins (intervening sequences that are spliced and
      excised post-translationally). These enzymes initiate transfer of those elements (and
      themselves) by generating strand breaks in cognate alleles that lack the intervening sequence,
      as well as in additional ectopic sites that broaden the range of intron and intein mobility.
      Homing endonucleases can be divided into several unique families that are remarkable in
      several respects: they display extremely high DNA-binding specificities which arise from long
      DNA target sites (14-40 bp), they are tolerant of a variety of sequence variations in these
      sites, and they display disparate DNA cleavage mechanisms. A significant number of homing
      endonucleases also act as maturases (highly specific cofactors for the RNA splicing reactions
      of their cognate introns). Of the known homing group I endonuclease families, two (HNH and
      His-Cys box enzymes) appear to be diverged from a common ancestral nuclease. While crystal
      structures of several representatives of the LAGLIDADG endonuclease family have been
      determined, only structures of single members of the HNH (I-HmuI), His-Cys box (I-PpoI) and
      GIY-YIG (I-TevI) families have been elucidated. These studies provide an important source of
      information for structure-function relationships in those families, and are the centerpiece of
      this review. Finally, homing endonucleases are significant targets for redesign and selection
      experiments, in hopes of generating novel DNA binding and cutting reagents for a variety of
      genomic applications.
AU  - Stoddard BL
PT  - Journal Article
TA  - Q. Rev. Biophys.
JT  - Q. Rev. Biophys.
SO  - Q. Rev. Biophys. 2005 38: 49-95.

PMID- 21220111
VI  - 19
DP  - 2011
TI  - Homing endonucleases: from microbial genetic invaders to reagents for targeted DNA modification.
PG  - 7-15
AB  - Homing endonucleases are microbial DNA-cleaving enzymes that mobilize their own reading frames
      by generating double strand breaks at specific genomic invasion sites. These proteins display
      an economy of size, and yet recognize long DNA sequences (typically 20 to 30 base pairs). They
      exhibit a wide range of fidelity at individual nucleotide positions in a manner that is
      strongly influenced by host constraints on the coding sequence of the targeted gene. The
      activity of these proteins leads to site-specific recombination events that can result in the
      insertion, deletion, mutation, or correction of DNA sequences. Over the past fifteen years,
      the crystal structures of representatives from several homing endonuclease families have been
      solved, and methods have been described to create variants of these enzymes that cleave novel
      DNA targets. Engineered homing endonucleases proteins are now being used to generate targeted
      genomic modifications for a variety of biotech and medical applications.
AU  - Stoddard BL
PT  - Journal Article
TA  - Structure
JT  - Structure
SO  - Structure 2011 19: 7-15.

PMID- 
VI  - 27
DP  - 1999
TI  - The structure, function, and convergent evolution of intron-encoded homing endonucleases.
PG  - A39
AB  - The homing endonucleases are a diverse family of proteins encoded by open reading frames in
      genetically mobile, self-splicing introns.  Similar endonucleases have also been identified as
      optional, independently folded domains in self-splicing protein introns, termed 'inteins'.
      These comparatively small enzymes share the ability to recognize and cleave long DNA sites of
      20 to 40 bp, and promote the lateral transfer of their host intron or intein to these sites by
      a targeted transposition.  These proteins also display flexibility of site-recognition, and
      are capable of tolerating changes at any position in the target DNA site.  Our laboratory has
      determined the structure of representative members of two families of homing endonucleases,
      both unbound and complexed to their DNA targets: I-CreI (a LAGLIDADG endonuclease) and I-PpoI
      (a his-cys box endonuclease).  The structures both demonstrate an impressive ability of these
      proteins to adopt an economical, elongated fold and to form a DNA complex with sub-saturating
      atomic contacts across the full length of the homing site.  The co-crystal structures indicate
      that the enzymes probably follow two very different structural mechanisms for phosphodiester
      hydrolysis.
AU  - Stoddard BL
AU  - Jurica M
AU  - Heath P
AU  - Flick K
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 1999 27: A39.

PMID- 
VI  - 3
DP  - 2008
TI  - Advances in engineering homing endonucleases for gene targeting: ten years after structures.
PG  - 135-167
AB  - Homing endonucleases are highly site-specific endonucleases that induce homologous
      recombination or gene conversion in vivo by cleaving long (typically >18bp) DNA target sites.
      Homing endonucleases are under development as tools for targeted genetic engineering
      applications, ranging from therapeutic gene correction to metabolic and population
      engineering.  The first structures of homing endonucleases were reported 10 years ago.  Since
      that time, representative structures from each of the known families of homing endonucleases
      have been determined, and the corresponding details of their mechanisms of DNA recognition and
      cleavage have been elucidated.  Using this information, the LAGLIDADG homing endonuclease
      family has been identified as the most tractable for further modification by structure-based
      selection and/or engineering approaches.  Most recently, successful redesign of the I-CreI
      endonuclease has led to the development of reagents that recognize and act on genes associated
      with monogenic diseases, including the human RAG1 and XPC genes.  These studies demonstrate
      the feasibility of using engineered homing endonucleases to promote efficient and target
      site-specific modification of chromosomal loci.  Current studies are rapidly improving the
      throughput and efficiency of homing endonuclease design and selection, and aim to optimize the
      specificity and activity of the resulting endonucleases for targeted genomic applications in
      medicine and biotechnology.
AU  - Stoddard BL
AU  - Scharenberg AM
AU  - Monnat RJ Jr
PT  - Journal Article
TA  - Prog. Gene Ther.
JT  - Prog. Gene Ther.
SO  - Prog. Gene Ther. 2008 3: 135-167.

PMID- 24906440
VI  - 33
DP  - 2014
TI  - Characterization of the staphylococcal cassette chromosome mec insertion site in 108 isolates lacking the mecA gene and identified as methicillin-resistant Staphylococcus aureus by the Xpert MRSA assay.
PG  - 1967-1971
AB  - During a 3-year period, 848 patients were detected as carriers of
      methicillin-resistant Staphylococcus aureus (MRSA) by the Xpert MRSA assay
      (Cepheid). Among them, 108 patients (12.7 %) were colonized with strains showing
      methicillin-susceptible phenotypes and absence of the mecA gene, despite being
      positive with the rapid polymerase chain reaction (PCR) assay. DNA sequences of
      the staphylococcal cassette chromosome mec (SCCmec) insertion site of these
      "false-positive" strains was determined by direct sequencing of the genomic DNA.
      More than half (53.7 %) of the strains had DNA sequences unrelated to either SCC
      or SCCmec and one-third had DNA sequences related to non-mec SCC. Only 10.2 % of
      the strains carried sequences related to SCCmec, suggesting that a sequence
      containing the mecA gene was lost from an SCCmec. These findings differ from the
      general idea that all methicillin-susceptible S. aureus having positive Xpert
      MRSA assay results are essentially MRSA that lost the mecA gene.
AU  - Stojanov M
AU  - Blanc DS
PT  - Journal Article
TA  - Eur. J. Clin. Microbiol. Infect. Dis.
JT  - Eur. J. Clin. Microbiol. Infect. Dis.
SO  - Eur. J. Clin. Microbiol. Infect. Dis. 2014 33: 1967-1971.

PMID- 16885440
VI  - 188
DP  - 2006
TI  - Class 1 Integrons Potentially Predating the Association with Tn402-Like Transposition Genes Are Present in a Sediment Microbial Community.
PG  - 5722-5730
AB  - Integrons are genetic elements that contribute to lateral gene transfer in bacteria as a
      consequence of possessing a site-specific recombination system. This system facilitates the
      spread of genes when they are part of mobile cassettes. Most integrons are contained within
      chromosomes and are confined to specific bacterial lineages. However, this is not the case for
      class 1 integrons, which were the first to be identified and are one of the single biggest
      contributors to multidrug-resistant nosocomial infections, carrying resistance to many
      antibiotics in diverse pathogens on a global scale. The rapid spread of class 1 integrons in
      the last 60 years is partly a result of their association with a specific suite of
      transposition functions, which has facilitated their recruitment by plasmids and other
      transposons. The widespread use of antibiotics has acted as a positive selection pressure for
      bacteria, especially pathogens, which harbor class 1 integrons and their associated antibiotic
      resistance genes. Here, we have isolated bacteria from soil and sediment in the absence of
      antibiotic selection. Class 1 integrons were recovered from four different bacterial species
      not known to be human pathogens or commensals. All four integrons lacked the transposition
      genes previously considered to be a characteristic of this class. At least two of these
      integrons were located on a chromosome, and none of them possessed antibiotic resistance
      genes. We conclude that novel class 1 integrons are present in a sediment environment in
      various bacteria of the beta-proteobacterial class. These data suggest that the dispersal of
      this class may have begun before the "antibiotic era."
AU  - Stokes HW
AU  - Nesbo CL
AU  - Holley M
AU  - Bahl MI
AU  - Gillings MR
AU  - Boucher Y
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2006 188: 5722-5730.

PMID- 23833130
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of the Thermophilic and Facultatively Chemolithoautotrophic Sulfate Reducer Archaeoglobus sulfaticallidus Strain  PM70-1T.
PG  - e00406-13
AB  - Dissimilatory sulfate-reducing archaea of the genus Archaeoglobus display divergent
      preferences in the use of energy sources and electron acceptors. Here
      we present the complete genome sequence of the thermophilic Archaeoglobus
      sulfaticallidus strain PM70-1(T), which distinctly couples chemolithoautotrophic
      growth on H2/CO2 to sulfate reduction in addition to heterotrophic growth.
AU  - Stokke R
AU  - Hocking WP
AU  - Steinsbu BO
AU  - Steen IH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00406-13.

PMID- 7695837
VI  - 375
DP  - 1994
TI  - Genes for DNA cytosine methyltransferases and structural proteins, expressed during lytic growth by the phage Phi-H of the archaebacterium Halobacterium salinarium.
PG  - 747-757
AB  - Lytic genes and transcription from the Halobacterium salinarium phage phi-H were studied.
      Genes for three structural proteins were located to the left arm of the linear phage genome.
      The right arm was shown to encode three DNA cytosine methyltransferases, the first such
      sequences reported from an archaebacterium. One cytosine methyltransferase is of the
      N(4)-methyltransferase type. The other two open reading frames (ORFs) seem to be parts of the
      same gene, which has been split by a recombination event. This gene product is of the
      C5-methyltransferase type. The methyltransferase genes are the first phi-H genes detected
      showing high homology to eubacterial proteins. Five of the six described gene products have a
      higher proportion of acidic over basic amino acid residues, a common characteristic of
      halobacterial proteins. Lytic phi-H transcription was shown to produce three RNA species, two
      shorter species encoding the methyltransferase genes and one large species transcribed from
      both the right and the left phage arm and subsequently being processed upstream of the region
      encoding the structural proteins.
AU  - Stolt P
AU  - Grampp B
AU  - Zillig W
PT  - Journal Article
TA  - Biol. Chem. Hoppe Seyler
JT  - Biol. Chem. Hoppe Seyler
SO  - Biol. Chem. Hoppe Seyler 1994 375: 747-757.

PMID- 24482507
VI  - 2
DP  - 2014
TI  - Genome Sequence of the Thermophilic Cyanobacterium Thermosynechococcus sp. Strain NK55a.
PG  - e01060-13
AB  - The genome of the unicellular cyanobacterium Thermosynechococcus sp. strain NK55a, isolated
      from the Nakabusa hot spring, Nagano Prefecture, Japan, comprises
      a single, circular, 2.5-Mb chromosome. The genome is predicted to contain 2,358
      protein-encoding genes, including genes for all typical cyanobacterial
      photosynthetic and metabolic functions. No genes encoding hydrogenases or
      nitrogenase were identified.
AU  - Stolyar S
AU  - Liu Z
AU  - Thiel V
AU  - Tomsho LP
AU  - Pinel N
AU  - Nelson WC
AU  - Lindemann SR
AU  - Romine MF
AU  - Haruta S
AU  - Schuster SC
AU  - Bryant DA
AU  - Fredrickson JK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01060-13.

PMID- 23969058
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of the Encephalomyelitic Burkholderia pseudomallei Strain MSHR305.
PG  - e00656-13
AB  - We describe the complete genome sequence of Burkholderia pseudomallei MSHR305, a  clinical
      isolate taken from a fatal encephalomyelitis case, a rare form of
      melioidosis. This sequence will be used for comparisons to identify the genes
      that are involved in neurological cases.
AU  - Stone JK
AU  - Johnson SL
AU  - Bruce DC
AU  - Detter JC
AU  - Mayo M
AU  - Currie BJ
AU  - Gelhaus HC
AU  - Keim P
AU  - Tuanyok A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00656-13.

PMID- 25767226
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Clostridium tyrobutyricum Strains FAM22552 and FAM22553, Isolated from Swiss Semihard Red-Smear Cheese.
PG  - e00078-15
AB  - Clostridium tyrobutyricum is the main microorganism responsible for late blowing  defect in
      cheeses. Here, we present the draft genome sequences of two C.
      tyrobutyricum strains isolated from a Swiss semihard red-smear cheese. The two
      draft genomes comprise 3.05 and 3.08 Mbp and contain 3,030 and 3,089 putative
      coding sequences, respectively.
AU  - Storari M
AU  - Wuthrich D
AU  - Bruggmann R
AU  - Berthoud H
AU  - Arias-Roth E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00078-15.

PMID- 28865135
VI  - 13
DP  - 2018
TI  - Designing Randomized DNA Sequences Free of Restriction Enzyme Recognition Sites.
PG  - 
AB  - DNA libraries containing random 'barcodes' complicate synthetic biology workflows that
      utilize restriction enzymes since restriction sites can appear inside some
      barcodes. By removing bases at particular sites in the barcodes, it is possible
      to create semi-random pools of barcodes that do not contain any restriction
      sites. The challenge is to remove as few bases as possible to maximize the number
      of sequences in the pool while ensuring all sequences are free of restriction
      sites. The authors present CutFree, a computational approach to create pools of
      random DNA barcodes that lack a pre-defined set of restriction sites. The
      resulting pools can be inexpensively produced en masse with standard DNA
      synthesis techniques. CutFree is experimentally validated by blocking digestion
      of pools of barcodes designed to frequently contain restriction sites. Using
      CutFree, a pool of 1.3 billion barcodes that are free from recognition sites for
      182 commercially available restriction enzymes is designed. CutFree is available
      as a software package and an online tool (http://jensenlab.net/tools).
AU  - Storm AJ
AU  - Jensen PA
PT  - Journal Article
TA  - Biotechnol. J.
JT  - Biotechnol. J.
SO  - Biotechnol. J. 2018 13: .

PMID- 10984043
VI  - 406
DP  - 2000
TI  - Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen.
PG  - 959-964
AB  - Pseudomonas aeruginosa is a ubiquitous environmental bacterium that is one of the top three
      causes of opportunistic human infections. A major factor in its prominence as a pathogen is
      its intrinsic resistance to antibiotics and disinfectants. Here we report the complete
      sequence of P. aeruginosa strain PAO1. At 6.3 million base pairs, this is the largest
      bacterial genome sequenced, and the sequence provides insights into the basis of the
      versatility and intrinsic drug resistance of P. aeruginosa. Consistent with its larger genome
      size and environmental adaptability, P. aeruginosa contains the highest proportion of
      regulatory genes observed for a bacterial genome and a large number of genes involved in the
      catabolism, transport and efflux of organic compounds as well as four potential chemotaxis
      systems. We propose that the size and complexity of the P. aeruginosa genome reflect an
      evolutionary adaptation permitting it to thrive in diverse environments and resist the effects
      of a variety of antimicrobial substances.
AU  - Stover CK et al
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2000 406: 959-964.

PMID- 8473307
VI  - 268
DP  - 1993
TI  - Determination of the DNA bend angle induced by the restriction endonuclease EcoRV in the presence of Mg2++.
PG  - 8645-8650
AB  - We have used the method of Zinkel and Crothers (1990, Biopolymers 29: 29-38) to determine the
      degree of bending induced by the binding of the restriction endonuclease EcoRV to its
      recognition sequence (-GATATC-). A set of four calibration DNA fragments was constructed that
      contained zero, two, four, or six phased A-tracts in their centers and an EcoRV site at the
      5'-end to account for the electrophoretic influence of the bound protein. The mobilities of
      these calibration molecules complexed with EcoRV were compared to that of a test DNA
      containing a central EcoRV site also complexed with EcoRV. The EcoRV-induced bend angle was
      found to be 44 +/- 4. These experiments were performed with a catalytically inactive EcoRV
      mutant that still binds DNA specifically in the presence of Mg2+. In the absence of Mg2+,
      which is necessary for specific binding, there is no difference in the mobilities of the
      fragments with a peripheral or a central EcoRV site complexed with EcoRV, indicating that
      nonspecific binding on average does not lead to measurable DNA bending.
AU  - Stover T
AU  - Kohler E
AU  - Fagin U
AU  - Wende W
AU  - Wolfes H
AU  - Pingoud A
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1993 268: 8645-8650.

PMID- 
VI  - 194
DP  - 2011
TI  - Draft genome sequence of Novosphingobium nitrogenifigens Y88T.
PG  - 201
AB  - Novosphingobium nitrogenifigens was originally isolated from pulp and paper mill wastewater, a
      low-nitrogen, high-carbon environment.  N. nitrogenifigens is the first known nitrogen-fixing,
      polyhydroxyalkanoate-accumulating sphingomonad, and we report the annotated draft genome
      sequence of the type strain Y88T here.
AU  - Strabala TJ
AU  - Macdonald L
AU  - Liu V
AU  - Smit A-M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 194: 201.

PMID- 24982175
VI  - 111
DP  - 2014
TI  - Metagenomic scaffolds enable combinatorial lignin transformation.
PG  - 10143-10148
AB  - Engineering the microbial transformation of lignocellulosic biomass is essential
      to developing modern biorefining processes that alleviate reliance on
      petroleum-derived energy and chemicals. Many current bioprocess streams depend on
      the genetic tractability of Escherichia coli with a primary emphasis on
      engineering cellulose/hemicellulose catabolism, small molecule production, and
      resistance to product inhibition. Conversely, bioprocess streams for lignin
      transformation remain embryonic, with relatively few environmental strains or
      enzymes implicated. Here we develop a biosensor responsive to monoaromatic lignin
      transformation products compatible with functional screening in E. coli. We use
      this biosensor to retrieve metagenomic scaffolds sourced from coal bed bacterial
      communities conferring an array of lignin transformation phenotypes that
      synergize in combination. Transposon mutagenesis and comparative sequence
      analysis of active clones identified genes encoding six functional classes
      mediating lignin transformation phenotypes that appear to be rearrayed in nature
      via horizontal gene transfer. Lignin transformation activity was then
      demonstrated for one of the predicted gene products encoding a multicopper
      oxidase to validate the screen. These results illuminate cellular and
      community-wide networks acting on aromatic polymers and expand the toolkit for
      engineering recombinant lignin transformation based on ecological design
      principles.
AU  - Strachan CR
AU  - Singh R
AU  - VanInsberghe D
AU  - Ievdokymenko K
AU  - Budwill K
AU  - Mohn WW
AU  - Eltis LD
AU  - Hallam SJ
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2014 111: 10143-10148.

PMID- 27257194
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Mycobacterium kansasii Strains 1010001454, 1010001458,  1010001468, 1010001493, 1010001495, and 1010001469, Isolated from Environmental  Sources.
PG  - e00456-16
AB  - Mycobacterium kansasii belongs to the nontuberculous mycobacteria (NTM) and causes
      opportunistic infections with both pulmonary and extrapulmonary
      manifestations. Here, we report the draft genome sequences of six environmental
      M. kansasii strains, designated 1010001495 (type I), 1010001469 (type II),
      1010001468 (type III), 1010001458 (type IV), 1010001454 (type V), and 1010001493
      (type V), originally isolated in five different European countries.
AU  - Strapagiel D
AU  - Borowka P
AU  - Marciniak B
AU  - Bakula Z
AU  - van Ingen J
AU  - Safianowska A
AU  - Brzostek A
AU  - Dziadek J
AU  - Jagielski T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00456-16.

PMID- 12036419
VI  - 11
DP  - 2002
TI  - Epigenetic cancer therapies: DNA methyltransferase inhibitors.
PG  - 747-754
AB  - Human cancers frequently show altered patterns of DNA methylation, particularly at CpG
      islands.  These CpG islands are sequences of DNA rich in CpG dinucleotides and are often found
      close to gene promoters.  Methylation within islands has been shown to be associated with
      transcriptional repression of the linked gene.  Genes involved in all facets of tumour
      development and progression can become methylated and epigenetically silenced.  Re-expression
      of such silenced genes can lead to suppression of tumour growth or sensitisation to anticancer
      therapies.  Agents that can reverse DNA methylation include nucleoside and non-nucleoside
      inhibitors of DNA methyltransferase.  Such agents are now undergoing preclinical evaluation
      and clinical trials in cancer patients.
AU  - Strathdee G
AU  - Brown R
PT  - Journal Article
TA  - Expert Opin. Invest. Drugs
JT  - Expert Opin. Invest. Drugs
SO  - Expert Opin. Invest. Drugs 2002 11: 747-754.

PMID- 14523116
VI  - 149
DP  - 2003
TI  - A cryptic plasmid of Yersinia enterocolitica encodes a conjugative transfer system related to the regions of CloDF13 Mob and IncX Pil.
PG  - 2829-2845
AB  - Yersinia enterocolitica 29930 (biotype 1A; O : 7,8), the producing strain of the
      phage-tail-like bacteriocin enterocoliticin, possesses a
      plasmid-encoded conjugative type IV transfer system. The genes of the
      conjugative system were found by screening of a cosmid library constructed
      from total DNA of strain 29930. The cosmid Cos100 consists of the vector
      SuperCos1 and an insert DNA of 40 303 bp derived from a cryptic plasmid of
      strain 29930. The conjugative transfer system consists of genes encoding a
      DNA transfer and replication system (Dtr) with close relationship to the
      mob region of the mobilizable plasmid CloDF13 and a gene cluster encoding
      a mating pair formation system (Mpf) closely related to the Mpf system of
      the IncX plasmid R6K. However, a gene encoding a homologue of TaxB, the
      coupling protein of the IncX system, is missing. The whole transfer region
      has a size of approximately 17 kb. The recombinant plasmid Cos100 was
      shown to be transferable between Escherichia coli and Yersinia with
      transfer frequencies up to 0.1 transconjugants per donor. Mutations
      generated by inserting a tetracycline cassette into putative tri genes
      yielded a transfer-deficient phenotype. Conjugative transfer of the
      cryptic plasmid could not be demonstrated in the original host Y.
      enterocolitica 29930. However, a kanamycin-resistance-conferring
      derivative of the plasmid was successfully introduced into E. coli K-12 by
      transformation and was shown to be self-transmissible. Furthermore,
      Southern blot hybridization and PCR experiments were carried out to
      elucidate the distribution of the conjugative transfer system in YERSINIA:
      In total, six Y. enterocolitica biotype 1A strains harbouring closely
      related systems on endogenous plasmids were identified.
AU  - Strauch E
AU  - Goelz G
AU  - Knabner D
AU  - Konietzny A
AU  - Lanka E
AU  - Appel B
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2003 149: 2829-2845.

PMID- 18824528
VI  - 76
DP  - 2008
TI  - Bacteriophage 2851 is a prototype phage for dissemination of the Shiga toxin variant gene 2c in Escherichia coli O157:H7.
PG  - 5466-5477
AB  - The production of Shiga toxin (Stx) (verocytotoxin) is a major virulence
      factor of Escherichia coli O157:H7 strains (Shiga toxin-producing E. coli
      [STEC] O157). Two types of Shiga toxins, designated Stx1 and Stx2, are
      produced in STEC O157. Variants of the Stx2 type (Stx2, Stx2c) are
      associated with high virulences of these strains for humans. A
      bacteriophage designated 2851 from a human STEC O157 encoding the Stx2c
      variant was described previously. Nucleotide sequence analysis of the
      phage 2851 genome revealed 75 predicted coding sequences and indicated a
      mosaic structure typical for lambdoid phages. Analyses of free phages and
      K-12 phage 2851 lysogens revealed that upon excision from the bacterial
      chromosome, the loss of a phage-encoded IS629 element leads to fusion of
      phage antA and antB genes, with the generation of a recombined antAB gene
      encoding a strong antirepressor. In wild-type E. coli O157 as well as in
      K-12 strains, phage 2851 was found to be integrated in the sbcB locus.
      Additionally, phage 2851 carries an open reading frame which encodes an
      OspB-like type III effector similar to that found in Shigella spp.
      Investigation of 39 stx(2c) E. coli O157 strains revealed that all except
      1 were positive for most phage 2851-specific genes and possessed a
      prophage with the same border sequences integrated into the sbcB locus.
      Phage 2851-specific sequences were absent from most stx(2c)-negative E.
      coli O157 strains, and we suggest that phage 2851-like phages contributed
      significantly to the dissemination of the Stx2c variant toxin within this
      group of E. coli.
AU  - Strauch E
AU  - Hammerl JA
AU  - Konietzny A
AU  - Schneiker-Bekel S
AU  - Arnold W
AU  - Goesmann A
AU  - Puhler A
AU  - Beutin L
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2008 76: 5466-5477.

PMID- 7592498
VI  - 177
DP  - 1995
TI  - Delineation of AbrB-binding sites on the Bacillus subtilis spoOH, kinB, ftsAZ, and pbpE promoters and use of a derived homology to identify a previously unsuspected binding site in the bsuB1 methylase promoter.
PG  - 6999-7002
AB  - DNase I footprinting experiments showed that AbrB binds to the regulatory regions of the
      spoOH, kinB, ftsAZ, and pbpE genes.  A conserved motif was found in these and other
      AbrB-binding sites.  A search for Bacillus subtilis DNA sequences containing this motif led to
      the prediction that AbrB would bind to the promoter controlling the bsuB1 methylase gene.
      DNase I footprinting experiments confirmed this prediction.
AU  - Strauch MA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1995 177: 6999-7002.

PMID- 12477932
VI  - 99
DP  - 2002
TI  - Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.
PG  - 16899-16903
AB  - The National Institutes of Health Mammalian Gene Collection (MGC) Program is a
      multiinstitutional effort to identify and sequence a cDNA clone
      containing a complete ORF for each human and mouse gene. ESTs were
      generated from libraries enriched for full-length cDNAs and analyzed to
      identify candidate full-ORF clones, which then were sequenced to high
      accuracy. The MGC has currently sequenced and verified the full ORF for a
      nonredundant set of >9,000 human and >6,000 mouse genes. Candidate
      full-ORF clones for an additional 7,800 human and 3,500 mouse genes also
      have been identified. All MGC sequences and clones are available without
      restriction through public databases and clone distribution networks (see
      http:mgc.nci.nih.gov).
AU  - Strausberg RL et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2002 99: 16899-16903.

PMID- 6265320
VI  - 12
DP  - 1980
TI  - Single-strand and double-strand cleavage at half-modified and fully modified recognition sites for the restriction nucleases Sau3A and TaqI.
PG  - 267-275
AB  - The influence of cytosine methylation on the cleavage of DNA by the restriction
      nucleases Sau3A and TaqI has been investigated.  Bovine satellite DNA fragments
      containing a GATCGA sequence, i.e. a Sau3A site overlapping with a TaqI site
      have been used in this study.  The methylation of these fragments has been
      determined by sequence analysis.  It has been found that a TaqI site (TCGA)
      methylated at cytosine in both DNA strands is still sensitive to double-strand
      cleavage.  A Sau3A site (GATC), however, is rendered resistant to double-strand
      cleavage by methylation of a single cytosine.  Fragments containing the
      "half-modified" Sau3A site are nicked in the unmethylated DNA strand.  It has
      been shown by sequence analysis of nicked DNA that the single-strand break
      occurs at the same position which is cleaved in unmodified DNA.
AU  - Streeck RE
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1980 12: 267-275.

PMID- 19724127
VI  - F65
DP  - 2009
TI  - Overexpression, purification and preliminary X-ray diffraction analysis of the controller protein C.Csp231I from Citrobacter sp RFL231.
PG  - 898-901
AB  - Restriction-modification controller proteins play an essential role in regulating the temporal
      expression of restriction-modification genes.
      The controller protein C.Csp231I represents a new class of controller
      proteins. The gene was sublconed to allow overexpression in Escherichia
      coli. The protein was purified to homogeneity and crystallized using
      the hanging-drop vapour-diffusion method. The crystals diffracted to
      2.0 angstrom resolution and belonged to space group P2(1). An
      electrophoretic mobility-shift assay provided evidence of strong
      binding of C.Csp231I to a sequence located upstream of the csp231IC
      start codon.
AU  - Streeter SD
AU  - McGeehan JE
AU  - Kneale GG
PT  - Journal Article
TA  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
JT  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
SO  - Acta Crystallogr. F Struct. Biol. Cryst. Commun. 2009 F65: 898-901.

PMID- 15590905
VI  - 32
DP  - 2004
TI  - DNA footprinting and biophysical characterization of the controller protein C.AhdI suggests the basis of a genetic switch.
PG  - 6445-6453
AB  - We have cloned and expressed the ahdIC gene of the AhdI restriction-modification system and
      have purified the resulting controller (C) protein to homogeneity. The protein sequence shows
      a HTH motif typical of that found in many transcriptional regulators. C.AhdI is found to form
      a homodimer of 16.7 kDa; sedimentation equilibrium experiments show that the dimer dissociates
      into monomers at low concentration, with a dissociation constant of 2.5 microM. DNase I and
      Exo III footprinting were used to determine the C.AhdI DNA-binding site, which is found
      approximately 30 bp upstream of the ahdIC operon. The intact homodimer binds cooperatively to
      a 35 bp fragment of DNA containing the C-protein binding site with a dissociation constant of
      5-6 nM, as judged both by gel retardation analysis and by surface plasmon resonance, although
      in practice the affinity for DNA is dominated by protein dimerization as DNA binding by the
      monomer is negligible. The location of the C-operator upstream of both ahdIC and ahdIR
      suggests that C.AhdI may act as a positive regulator of the expression of both genes, and
      could act as a molecular switch that is critically dependent on the K(d) for the monomer-dimer
      equilibrium. Moreover, the structure and location of the C.AhdI binding site with respect to
      the putative -35 box preceding the C-gene suggests a possible mechanism for autoregulation of
      C.AhdI expression.
AU  - Streeter SD
AU  - Papapanagiotou I
AU  - McGeehan JE
AU  - Kneale GG
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2004 32: 6445-6453.

PMID- 3029955
VI  - 157
DP  - 1987
TI  - Expression and proteolytic processing of the darA antirestriction gene product of bacteriophage P1.
PG  - 167-171
AB  - The darA gene coding for one of the two bacteriophage P1 antirestriction functions is
      expressed late after infection or induction.  The protein is made as a high-molecular-weight
      soluble precursor.  This is proteolytically cleaved to the mature form, which is a structural
      component of the phage head.  Defective mutants of the phage have been found in which the
      synthesis of gpdarA is normal but processing does not take place.  These mutations all map to
      the same region of the P1 genome and we propose that they lie in the structural gene for the
      processing protease.
AU  - Streiff MB
AU  - Iida S
AU  - Bickle TA
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1987 157: 167-171.

PMID- 8654989
VI  - 172
DP  - 1996
TI  - Novel specific endonuclease activity recognizing a 10-bp sequence.
PG  - 47-48
AB  - We report here the generation of a novel restriction endonuclease (Enase) activity
      with the 10-bp recognition sequence,
      5'-GmATnnnGmA/-TCnnnA-TC-3'
      3'-C-TAnnnC-T/mAGnnnTmAG-5'.
      This specificity could be achieved by first methylating a substrate DNA with M.MamI in vivo,
      followed by in vitro R.DpnI restriction.
AU  - Striebel H-M
AU  - Kessler C
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1996 172: 47-48.

PMID- 2401411
VI  - 91
DP  - 1990
TI  - MamI, a novel class-II restriction endonuclease from Microbacterium ammoniaphilum recognizing 5'-GATNN^NNATC-3'.
PG  - 95-100
AB  - A new site-specific class-II restriction endonuclease, MamI, has been discovered in the
      nonsporulating Gram-positive Microbacterium ammoniaphilum. MamI recognition sequence and
      cleavage positions were deduced using experimental and computer-assisted mapping and
      sequencing approaches. MamI cleavage specificity corresponds to: 5'-GATNN^NNATC-3'
      3'-CTANN^NNTAG-5'. The novel 43-kD enzyme recognizes a palindromic hexanucleotide
      interrupted by four ambiguous nucleotides. MamI cleavage positions are both located in the
      center of the recognition sequence resulting in blunt-ended fragments after cleavage in the
      presence of Mg2+ ions. MamI is inhibited by N6-methyladenine residues. In case of overlapping
      sequences of MamI and Escherichia coli-coded DNA modification methyltransferase M.EcodamI
      (5'-GmATC-3'), cleavage of DNA isolated from E. coli wild-type cells will be inhibited. By
      applying incubation conditions forcing star activity, relaxation of MamI sequence specificity
      is observed (MamI*).
AU  - Striebel H-M
AU  - Schmitz GG
AU  - Kaluza K
AU  - Jarsch M
AU  - Kessler C
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1990 91: 95-100.

PMID- 8654988
VI  - 172
DP  - 1996
TI  - Cloning and characterization of the MamI restriction-modification system from Microbacterium ammoniaphilum in Escherichia coli.
PG  - 41-46
AB  - The genes encoding a class-IIN restriction-modification (R-M) system (MamI,
      sequence specificity 5'-GATnn/nnATC-3' / 3'-CTAnn/nnTAG-5' from Microbacterium
      ammoniaphilum have been cloned in Escherichia coli.  The vector used for cloning was plasmid
      pUC18 modified by the inclusion of three MamI recognition sites.  Recombinant clones
      containing
      the mamIM gene in its genomic context became fully methylated in vivo and remained completely
      resistant against digestion with the R.MamI restriction enodnuclease (Enase).  Determination
      of the
      nucleotide (nt) sequence revealed three open reading frames with lengths of 1089 bp (ORF1),
      276
      bp (ORFc) and 927 bp (ORF2).  On the basis of expression and deletion experiments, the 1089-bp
      ORF1 was assigned to mamIM encoding the M.MamI DNA methyltransferase (Mtase).  By amino
      acid sequencing of the N terminus of R.MamI and comparison of the deduced nt sequence with
      ORF2, the 927-bp ORF2 was idenified as the mamIR gene encoding R.MamI.  The 276-bp Orfc,
      located between mamIR and mamIM, is part of the DNA sequence downstream from mamIM
      shown to be necessary for controlled mamIM expression.
AU  - Striebel H-M
AU  - Seeber S
AU  - Jarsch M
AU  - Kessler C
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1996 172: 41-46.

PMID- 3025706
VI  - 5
DP  - 1985
TI  - Plasmid recombination stimulated by restriction endonuclease EcoRI in vivo: specificity of recombinant plasmid formation in RecA cells of Escherichia coli.
PG  - 13-19
AB  - The restriction endonuclease EcoRI dependent recombination of compatible plasmids has been
      studied in RecA cells of Escherichia coli.  Plasmid RP4 and the isogenic ColE1 type plasmids
      pSA14 or pSA25, differing in restriction-modification RM EcoRI genes, have been used to study
      this type of recombination.  EcoRI dependent recombination of plasmids is demonstrated in RecA
      cells and, thus, is independent of general system of homologous recombination.  The classes of
      recombinant plasmids isolated from RecA cells differ from the classes isolated from wild type
      cells.  Levels of tetracyclin resistance conferred by plasmid RP4 are shown to be dependent on
      the alleles of recA+ gene, being extremely low in RecA cells.  This property is demonstrated
      to be useful for obtaining the multicopy recombinant plasmids resulting from EcoRI dependent
      recombination in RecA cells of Escherichia coli.
AU  - Strikhanov SN
AU  - Aleshkin GI
AU  - Skavronskaya AG
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1985 5: 13-19.

PMID- 23679073
VI  - 14
DP  - 2013
TI  - Genomic and physiological variability within Group II (non-proteolytic) Clostridium botulinum.
PG  - 333
AB  - BACKGROUND: Clostridium botulinum is a group of four physiologically and
      phylogenetically distinct bacteria that produce botulinum neurotoxin. While
      studies have characterised variability between strains of Group I (proteolytic)
      C. botulinum, the genetic and physiological variability and relationships between
      strains within Group II (non-proteolytic) C. botulinum are not well understood.
      In this study the genome of Group II strain C. botulinum Eklund 17B (NRP) was
      sequenced and used to construct a whole genome DNA microarray. This was used in a
      comparative genomic indexing study to compare the relatedness of 43 strains of
      Group II C. botulinum (14 type B, 24 type E and 5 type F). These results were
      compared with characteristics determined from physiological tests. RESULTS: Whole
      genome indexing showed that strains of Group II C. botulinum isolated from a wide
      variety of environments over more than 75 years clustered together indicating the
      genetic background of Group II C. botulinum is stable. Further analysis showed
      that strains forming type B or type F toxin are closely related with only toxin
      cluster genes targets being unique to either type. Strains producing type E toxin
      formed a separate subset. Carbohydrate fermentation tests supported the
      observation that type B and F strains form a separate subset to type E strains.
      All the type F strains and most of type B strains produced acid from amylopectin,
      amylose and glycogen whereas type E strains did not. However, these two subsets
      did not differ strongly in minimum growth temperature or maximum NaCl
      concentration for growth. No relationship was found between tellurite resistance
      and toxin type despite all the tested type B and type F strains carrying tehB,
      while the sequence was absent or diverged in all type E strains. CONCLUSIONS:
      Although Group II C. botulinum form a tight genetic group, genomic and
      physiological analysis indicates there are two distinct subsets within this
      group. All type B strains and type F strains are in one subset and all type E
      strains in the other.
AU  - Stringer SC
AU  - Carter AT
AU  - Webb MD
AU  - Wachnicka E
AU  - Crossman LC
AU  - Sebaihia M
AU  - Peck MW
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2013 14: 333.

PMID- 19187283
VI  - 11
DP  - 2009
TI  - Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide.
PG  - 1038-1055
AB  - Summary Sulfate-reducing bacteria (SRB) belonging to the metabolically
      versatile Desulfobacteriaceae are abundant in marine sediments and
      contribute to the global carbon cycle by complete oxidation of organic
      compounds. Desulfobacterium autotrophicum HRM2 is the first member of this
      ecophysiologically important group with a now available genome sequence.
      With 5.6 megabasepairs (Mbp) the genome of Db. autotrophicum HRM2 is about
      2 Mbp larger than the sequenced genomes of other sulfate reducers (SRB). A
      high number of genome plasticity elements (> 100 transposon-related
      genes), several regions of GC discontinuity and a high number of
      repetitive elements (132 paralogous genes Mbp(-1)) point to a different
      genome evolution when comparing with Desulfovibrio spp. The metabolic
      versatility of Db. autotrophicum HRM2 is reflected in the presence of
      genes for the degradation of a variety of organic compounds including
      long-chain fatty acids and for the Wood-Ljungdahl pathway, which enables
      the organism to completely oxidize acetyl-CoA to CO(2) but also to grow
      chemolithoautotrophically. The presence of more than 250 proteins of the
      sensory/regulatory protein families should enable Db. autotrophicum HRM2
      to efficiently adapt to changing environmental conditions. Genes encoding
      periplasmic or cytoplasmic hydrogenases and formate dehydrogenases have
      been detected as well as genes for the transmembrane TpII-c(3), Hme and
      Rnf complexes. Genes for subunits A, B, C and D as well as for the
      proposed novel subunits L and F of the heterodisulfide reductases are
      present. This enzyme is involved in energy conservation in methanoarchaea
      and it is speculated that it exhibits a similar function in the process of
      dissimilatory sulfate reduction in Db. autotrophicum HRM2.
AU  - Strittmatter AW et al
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2009 11: 1038-1055.

PMID- 20418398
VI  - 192
DP  - 2010
TI  - Complete Genome Sequence of the Photosynthetic Purple Nonsulfur Bacterium Rhodobacter capsulatus SB 1003.
PG  - 3545-3546
AB  - Rhodobacter capsulatus SB 1003 belongs to the group of purple nonsulfur bacteria. Its genome
      consists of a 3.7-Mb chromosome and a 133-kb plasmid.
      The genome encodes genes for photosynthesis, nitrogen fixation,
      utilization of xenobiotic organic substrates, and synthesis of
      polyhydroxyalkanoates. These features made it a favorite research tool for
      studying these processes. Here we report its complete genome sequence.
AU  - Strnad H
AU  - Lapidus A
AU  - Paces J
AU  - Ulbrich P
AU  - Vlcek C
AU  - Paces V
AU  - Haselkorn R
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 3545-3546.

PMID- 24652983
VI  - 2
DP  - 2014
TI  - Genome Sequence of Rhodococcus erythropolis Strain CCM2595, a Phenol Derivative-Degrading Bacterium.
PG  - e00208-14
AB  - We announce the completion of the genome sequence of a phenol derivative-degrading bacterium,
      Rhodococcus erythropolis strain CCM2595. This
      bacterium is interesting in the context of bioremediation for its capability to
      degrade phenol, catechol, resorcinol, hydroxybenzoate, hydroquinone,
      p-chlorophenol, p-nitrophenol, pyrimidines, and sterols.
AU  - Strnad H
AU  - Patek M
AU  - Fousek J
AU  - Szokol J
AU  - Ulbrich P
AU  - Nesvera J
AU  - Paces V
AU  - Vlcek C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00208-14.

PMID- 21097610
VI  - 193
DP  - 2010
TI  - Complete Genome Sequence of the Haloaromatic Acids-degrading Bacterium Achromobacter xylosoxidans A8.
PG  - 791-792
AB  - Achromobacter xylosoxidans strain A8 was isolated from soil contaminated with polychlorinated
      biphenyls. It can use 2-chlorobenzoate and
      2,5-dichlorobenzoate as sole sources of carbon and energy. This property
      makes it a good starting microorganism for further development towards a
      bioremediation tool. The genome of A. xylosoxidans consists of a 7-Mb
      chromosome and two large plasmids (98 kb, 248 kb). Besides genes for
      utilization of xenobiotic organic substrates it encodes genes associated
      with pathogenesis, toxin production and resistance. Here we report its
      complete genome sequence.
AU  - Strnad H
AU  - Ridl J
AU  - Paces J
AU  - Kolar M
AU  - Vlcek C
AU  - Paces V
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 193: 791-792.

PMID- 1836279
VI  - 254
DP  - 1991
TI  - Site-specific cleavage of human chromosome 4 mediated by triple-helix formation.
PG  - 1639-1642
AB  - Direct physical isolation of specific DNA segments from the human genome is a
      necessary goal in human genetics.  For testing whether triple-helix mediated
      enzymatic cleavage can liberate a specific segment of a human chromosome, the
      tip of human chromosome 4, which contains the entire candidate region for the
      Huntington's disease gene, was chosen as a target.  A 16-base pyrimidine
      oligodeoxyribonucleotide was able to locate a 16-base pair purine target site
      within more than 10 gigabase pairs of genomic DNA and mediate the exact
      enzymatic cleavage at that site in more than 80 percent yield.  The recognition
      motif is sufficiently generalizable that most cosmids should contain a sequence
      targetable by triple-helix formation.  This method may facilitate the
      orchestrated dissection of human chromosomes from normal and affected
      individuals into megabase sized fragments and facilitate the isolation of
      candidate gene loci.
AU  - Strobel SA
AU  - Doucette-Stamm LA
AU  - Riba L
AU  - Housman DE
AU  - Dervan PB
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1991 254: 1639-1642.

PMID- 22958348
VI  - 13
DP  - 2012
TI  - Complete genome sequence of Saccharothrix espanaensis DSM 44229T and comparison to the other completely sequenced Pseudonocardiaceae.
PG  - 465
AB  - ABSTRACT: BACKGROUND: The genus Saccharothrix is a representative of the family
      Pseudonocardiaceae, known to include producer strains of a wide variety of potent
      antibiotics. Saccharothrix espanaensis produces both saccharomicins A and B of
      the promising new class of heptadecaglycoside antibiotics, active against both
      bacteria and yeast. RESULTS: To better assess its capabilities, the complete
      genome sequence of S. espanaensis was established. With a size of 9,360,653 bp,
      coding for 8,501 genes, it stands alongside other Pseudonocardiaceae with large
      genomes. Besides a predicted core genome of 810 genes shared in the family, S.
      espanaensis has a large number of accessory genes: 2,967 singletons when compared
      to the family, of which 1,292 have no clear orthologs in the RefSeq database. The
      genome analysis revealed the presence of 26 biosynthetic gene clusters
      potentially encoding secondary metabolites. Among them, the cluster coding for
      the saccharomicins could be identified. CONCLUSION: S. espanaensis is the first
      completely sequenced species of the genus Saccharothrix. The genome discloses the
      cluster responsible for the biosynthesis of the saccharomicins, the largest
      oligosaccharide antibiotic currently identified. Moreover, the genome revealed 25
      additional putative secondary metabolite gene clusters further suggesting the
      strain's potential for natural product synthesis.
AU  - Strobel T
AU  - Al-Dilaimi A
AU  - Blom J
AU  - Gessner A
AU  - Kalinowski J
AU  - Luzhetska M
AU  - Puhler A
AU  - Szczepanowski R
AU  - Bechthold A
AU  - Ruckert C
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2012 13: 465.

PMID- 6209609
VI  - 12
DP  - 1984
TI  - Methylation of either cytosine in the recognition sequence CGCG inhibits ThaI cleavage of DNA.
PG  - 8073-8083
AB  - ThaI (CGCG) sites which overlap HhaI (GCGC) sites in PhiX174 and pBR322 DNA
      were methylated in vitro with HhaI methylase and S-adenosylmethionine to yield
      CGmCG, mCGmCG (5-methylcytosine, mC).  Methylation of either cytosine in the
      ThaI recognition sequence rendered the DNA resistant to ThaI cleavage.  Rat
      pituitary cell genomic DNA was digested with ThaI or 2 other known
      methylation-sensitive enzymes, AvaI or XhoI.  After electrophoresis and
      ethidium bromide staining of the DNA, all 3 enzymes showed the infrequent DNA
      cleavage characteristic of methylation-sensitive enzymes.  Comparison of
      pituitary growth hormone (GH) genes bearing strain-specific degrees of
      methylation showed the less methylated gene to be more frequently cut by either
      AvaI or ThaI.  ThaI resistant sites in GH genes were cleaved by ThaI after
      exposing cells to 5-azacytidine, an inhibitor of DNA methylation.  We conclude
      that ThaI is a useful restriction enzyme for the analysis of mC at CGCG
      sequences in eukaryotic DNA.
AU  - Strobl JS
AU  - Thompson EB
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1984 12: 8073-8083.

PMID- 16598256
VI  - 440
DP  - 2006
TI  - Deciphering the evolution and metabolism of an anammox bacterium from a community genome.
PG  - 790-794
AB  - Anaerobic ammonium oxidation (anammox) has become a main focus in
      oceanography and wastewater treatment.  It is also the nitrogen cycle's
      major remaining biochemical enigma.  Among its features, the occurrence of
      hydrazine as a free intermediate of catabolism, the biosynthesis of
      ladderane lipids and the role of cytoplasm differentiation are unique in
      biology.  Here we use environmental genomics - the reconstruction of
      genomic data directly from the environment - to assemble the genome of the
      uncultured anammox bacterium Kuenenia stuttgartiensis from a complex
      bioreactor community.  The genome data illuminate the evolutionary history
      of the Planctomycetes and allow us to expose the genetic blueprint of the
      organism's special properties.  Most significantly, we identified candidate
      genes responsible for ladderane biosynthesis and biological hydrazine
      metabolism, and discovered unexpected metabolic versatility.
AU  - Strous M et al
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2006 440: 790-794.

PMID- 2297565
VI  - 57
DP  - 1990
TI  - Structural studies of the BamHI restriction enzyme.
PG  - 68
AB  - Type II restriction enzymes are ideal for studying protein-DNA interactions
      because of their high sequence specificity and striking variety.  Large,
      well-ordered BamHI crystals, diffracting to 2.3 angstrom, were obtained from
      PEG solutions.  These crystals occur in two forms:  monoclinic (space group C2,
      unit cell constants: a=76.24 angstrom, b=46.0 angstrom, c=69.4 angstrom and
      beta=110.5 degrees) and orthorhombic (space group C222/1, unit cell constants:
      a=46.7 angstrom, b=76.6 angstrom and c=143.6 angstrom).  In both crystal forms
      there is one protein monomer per asymmetric unit.  Currently, we are searching
      for heavy atom derivatives of the enzyme.  We are also attempting
      cocrystallization of the enzyme with a 12-bp DNA fragment containing the BamHI
      recognition site (5'-GGATCC-3').  We have recently obtained large, plate-like
      crystals, which we are exploring for the presence of DNA by X-ray and
      biochemical methods.
AU  - Strzelecka T
AU  - Dorner L
AU  - Schildkraut I
AU  - Aggarawal A
PT  - Journal Article
TA  - Biophys. J.
JT  - Biophys. J.
SO  - Biophys. J. 1990 57: 68.

PMID- 8201623
VI  - 239
DP  - 1994
TI  - Crystallization and preliminary X-ray analysis of restriction endonuclease BamHI-DNA complex.
PG  - 430-432
AB  - Restriction endonuclease BamHI from Bacillus amyloliquefaciens has been co-crystallized with a
      12 bp DNA fragment that encompasses its recognition site. The co-crystals diffract to at least
      1.95 A resolution and belong to space group P212121. The unit cell parameters are a=108.8 A,
      b=81.9 A, c=68.8 A, consistent with one complex in the crystallographic asymmetric unit. The
      direction of the DNA appears to be along the b axis. In order to achieve end to end stacking
      of DNA, the complex must lie on the screw axis along b. A self-rotation function has
      determined the directions of the non-crystallographic 2-fold axes.
AU  - Strzelecka T
AU  - Newman M
AU  - Dorner LF
AU  - Knott R
AU  - Schildkraut I
AU  - Aggarwal AK
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1994 239: 430-432.

PMID- 20169071
VI  - 5
DP  - 2010
TI  - The smallest known genomes of multicellular and toxic cyanobacteria: comparison, minimal gene sets for linked traits and the evolutionary implications.
PG  - E9235
AB  - Cyanobacterial morphology is diverse, ranging from unicellular spheres or
      rods to multicellular structures such as colonies and filaments.
      Multicellular species represent an evolutionary strategy to differentiate
      and compartmentalize certain metabolic functions for reproduction and
      nitrogen (N(2)) fixation into specialized cell types (e.g. akinetes,
      heterocysts and diazocytes). Only a few filamentous, differentiated
      cyanobacterial species, with genome sizes over 5 Mb, have been sequenced.
      We sequenced the genomes of two strains of closely related filamentous
      cyanobacterial species to yield further insights into the molecular basis
      of the traits of N(2) fixation, filament formation and cell
      differentiation. Cylindrospermopsis raciborskii CS-505 is a
      cylindrospermopsin-producing strain from Australia, whereas Raphidiopsis
      brookii D9 from Brazil synthesizes neurotoxins associated with paralytic
      shellfish poisoning (PSP). Despite their different morphology, toxin
      composition and disjunct geographical distribution, these strains form a
      monophyletic group. With genome sizes of approximately 3.9 (CS-505) and
      3.2 (D9) Mb, these are the smallest genomes described for free-living
      filamentous cyanobacteria. We observed remarkable gene order conservation
      (synteny) between these genomes despite the difference in repetitive
      element content, which accounts for most of the genome size difference
      between them. We show here that the strains share a specific set of 2539
      genes with >90% average nucleotide identity. The fact that the CS-505 and
      D9 genomes are small and streamlined compared to those of other
      filamentous cyanobacterial species and the lack of the ability for
      heterocyst formation in strain D9 allowed us to define a core set of genes
      responsible for each trait in filamentous species. We presume that in
      strain D9 the ability to form proper heterocysts was secondarily lost
      together with N(2) fixation capacity. Further comparisons to all available
      cyanobacterial genomes covering almost the entire evolutionary branch
      revealed a common minimal gene set for each of these cyanobacterial
      traits.
AU  - Stucken K
AU  - John U
AU  - Cembella A
AU  - Murillo AA
AU  - Soto-Liebe K
AU  - Fuentes-Valdes JJ
AU  - Friedel M
AU  - Plominsky AM
AU  - Vasquez M
AU  - Glockner G
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2010 5: E9235.

PMID- 24510140
VI  - 46
DP  - 2013
TI  - Cyanobacterial defense mechanisms against foreign DNA transfer and their impact on genetic engineering.
PG  - 373-382
AB  - Cyanobacteria display a large diversity of cellular forms ranging from unicellular to complex
      multicellular filaments or aggregates. Species in the group present a wide range of metabolic
      characteristics including the fixation of atmospheric nitrogen, resistance to extreme
      environments, production of hydrogen, secondary metabolites and exopolysaccharides. These
      characteristics led to the growing interest in cyanobacteria across the fields of ecology,
      evolution, cell biology and biotechnology. The nu ber of available cyanobacterial genome
      sequences has increased considerably in recent years, with more than 140 fully sequenced
      genomes to date. Genetic engineering of cyanobacteria is widely applied to the model
      unicellular strains Synechocystis sp. PCC 6803 and Synechococcus elongatus PCC 7942. However
      the establishment of transformation protocols in many other cyanobacterial strains is
      challenging. One obstacle to the development of these novel model organisms is that many
      species have doubling times of 48 h or more, much longer than the bacterial models E. coli or
      B. subtilis. Furthermore, cyanobacterial defense mechanisms against foreign DNA pose a
      physical and biochemical barrier to DNA insertion in most strains. Here we review the various
      barriers to DNA uptake in the context of lateral gene transfer among microbes and the various
      mechanisms for DNA acquisition within the prokaryotic domain. Understanding the cyanobacterial
      defense mechanisms is expected to assist in the development and establishment of novel
      transformation protocols that are specifically suitable for this group.
AU  - Stucken K
AU  - Koch R
AU  - Dagan T
PT  - Journal Article
TA  - Biol. Res.
JT  - Biol. Res.
SO  - Biol. Res. 2013 46: 373-382.

PMID- 2251125
VI  - 18
DP  - 1990
TI  - Statistical analysis of nucleotide sequences.
PG  - 6641-6647
AB  - In order to scan nucleic acid databases for potentially relevant but as yet
      unknown signals, we have developed an improved statistical model for pattern
      analysis of nucleic acid sequences by modifying previous methods based on
      Markov chains.  We demonstrate the importance of selecting the appropriate
      parameters in order for the method to function at all.  The model allows the
      simultaneous analysis of several short sequences with unequal base frequencies
      and Markov order k+0 as is usually the case in databases.  As a test of these
      modifications, we show that in E. coli sequences there is a bias against
      palindromic hexamers which correspond to known restriction enzyme recognition
      sites.
AU  - Stuckle EE
AU  - Emmrich C
AU  - Grob U
AU  - Nielsen PJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 6641-6647.

PMID- 24710305
VI  - 2
DP  - 2011
TI  - Draft Genome Sequences of Xanthomonas sacchari and Two Banana-Associated Xanthomonads Reveal Insights into the Xanthomonas Group 1 Clade.
PG  - 1050-1065
AB  - We present draft genome sequences for three strains of Xanthomonas species, each of which was
      associated with banana plants (Musa species) but is not closely related to the previously
      sequenced banana-pathogen Xanthomonas campestris pathovar musacearum. Strain NCPPB4393 had
      been deposited as Xanthomonas campestris pathovar musacearum but in fact falls within the
      species Xanthomonas sacchari. Strain NCPPB1132 is more distantly related to Xanthomonas
      sacchari whilst strain NCPPB 1131 grouped in a distinct species-level clade related to X.
      sacchari, along with strains from ginger, rice, cotton and sugarcane. These three newly
      sequenced strains share many genomic features with the previously sequenced Xanthomonas
      albilineans, for example possessing an unsual metE allele and lacking the Hrp type III
      secretion system. However, they are distinct from Xanthomonas albilineans in many respects,
      for example showing little evidence of genome reduction. They also lack the SPI-1 type III
      secretion system found in Xanthomonas albilineans. Unlike X. albilineans, all three strains
      possess a gum gene cluster. The data reported here provide the first genome-wide survey of
      non-Hrp Xanthomonas species other than Xanthomonas albilineans, which is an atypical member of
      this group. We hope that the availability of complete sequence data for this group of
      organisms is the first step towards understanding their interactions with plants and
      identifying potential virulence factors.
AU  - Studholme DJ
AU  - Wasukira A
AU  - Paszkiewicz K
AU  - Aritua V
AU  - Thwaites R
AU  - Smith J
AU  - Grant M
PT  - Journal Article
TA  - Genes (Basel)
JT  - Genes (Basel)
SO  - Genes (Basel) 2011 2: 1050-1065.

PMID- 1095770
VI  - 94
DP  - 1975
TI  - Gene 0.3 of Bacteriophage T7 Acts to Overcome the DNA Restriction System of the Host.
PG  - 283-295
AB  - Wild-type bacteriophage T7 is not subject to restriction by the Escherichia
      coli B and K restriction systems, but T7 mutants that are susceptible to such
      restriction have been isolated.  These mutants are all defective in gene 0.3,
      the first T7 gene to be expressed after infection.  The gene 0.3 protein
      apparently acts to prevent modification as well as restriction, suggesting that
      it may interact with a component of the host restriction-modification system
      that is required for both processes.  Mutants in which gene 0.3 is completely
      deleted are only partially modified by growth on hosts with an active
      restriction-modification system, presumably because the conditions of T7
      infection overload the modifying capacity of the cells.  This is in contrast to
      phages such as lambda that are completely modified during growth.  Since gene
      0.3 is not essential for growth in non-restricting hosts, it has been possible
      to isolate deletions which extend to the left of gene 0.3 into the region where
      E. coli RNA polymerase initiates the synthesis of T7 early RNA.  Two of the
      three strong initiators from which E. coli RNA polymerase transcribes the early
      region can be deleted.  In the course of searching for T7 mutants that are
      unable to overcome restriction, it was discovered that mutants defective in
      gene 2 are able to plate on E. coli C with essentially normal efficiency, and
      most gene 7 mutants are able to plate on both C and K strains.  It has not been
      determined why genes 2 and 7 seem to be needed for growth in some E. coli
      strains but not in others.
AU  - Studier FW
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1975 94: 283-295.

PMID- 2838843
VI  - 85
DP  - 1988
TI  - Model for how type I restriction enzymes select cleavage sites in DNA.
PG  - 4677-4681
AB  - Under appropriate conditions, digestion of phage T7 DNA by the type I
      restriction enzyme EcoK produces an orderly progression of discrete DNA
      fragments.  All details of the fragmentation pattern can be explained on the
      basis of the known properties of type I enzymes, together with two further
      assumptions:  (i) in the ATP-stimulated translocation reaction, the enzyme
      bound at the recognition sequence translocates DNA toward itself from both
      direction simultaneously; and (ii) when translocation causes neighboring
      enzymes to meet, they cut the DNA between them.  The kinetics of digestion at
      37C indicates that the rate of translocation of DNA from each side of a bound
      enzyme is about 200 base pairs per second, and the cuts are completed within
      15-25 sec of the time neighboring enzymes meet.  The resulting DNA fragments
      each contain a single recognition site with an enzyme (or subunit) remaining
      bound to it.  At high enzyme concentrations, such fragments can be further
      degraded, apparently by cooperation between the specifically bound and excess
      enzymes.  This model is consistent with a substantial body of previous work on
      the nuclease activity of EcoB and EcoK, and it explains in a simple way how
      cleavage sites are selected.
AU  - Studier FW
AU  - Bandyopadhyay PK
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1988 85: 4677-4681.

PMID- 781304
VI  - 19
DP  - 1976
TI  - SAMase gene of bacteriophage T3 is responsible for overcoming host restriction.
PG  - 136-145
AB  - Deletion and point mutants of T3 have been isolated and used to show that the
      early region of T3 DNA is organized in the same way as that of T7 DNA.
      Homologous early RNAs and proteins of the two phages have been identified by
      electrophoresis on polyacrylamide gels in the presence of sodium dodecyl
      sulfate.  Both phages have five early mRNA's, numbered 0.3, 0.7, 1,1.1, and 1.3
      from left to right, although no T3 protein that corresponds to the 1.1 protein
      of T7 has yet been identified.  In general, corresponding early RNAs and
      proteins of the two phages migrate differently on gels, indicating that they
      differ in molecular weight and/or conformation.  In both T7 and T3, gene 0.3 is
      responsible for overcoming the DNA restriction system of the host, gene 0.7
      specifies a protein kinase, gene 1 specifies a phage-specific RNA polymerase,
      and gene 1.3 specifies a polynucleotide ligase.  The 0.3 protein of T3 is
      responsible for the S-adenosylmethionine cleaving activity (SAMase) induced
      after T3 (but not T7) infection.  However, cleaving of S-adenosylmethionine
      does not appear to be the primary mechanism by which T3 overcomes host
      restriction, since at least one mutant of T3 has lost the SAMase activity
      without losing the ability to overcome host restriction.
AU  - Studier FW
AU  - Movva NR
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1976 19: 136-145.

PMID- 24874675
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Lactobacillus animalis 381-IL-28.
PG  - e00478-14
AB  - Lactobacillus animalis 381-IL-28 is an integral component of a multistrain commercial culture
      with food biopreservative and pathogen biocontrol
      functionality. A draft sequence of the L. animalis 381-IL-28 genome is described
      in this paper.
AU  - Sturino JM
AU  - Rajendran M
AU  - Altermann E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00478-14.

PMID- 23788534
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Pediocin-Encoding Biopreservative and Biocontrol Strain Pediococcus acidilactici D3.
PG  - e00208-13
AB  - We describe a draft genome sequence for Pediococcus acidilactici strain D3, a component of
      multistrain commercial cultures with biopreservative and biocontrol
      properties in food-based applications. Strain D3 encodes at least one
      antimicrobial peptide, pediocin AMPd3. The AMPd3-encoding operon exhibits high
      sequence similarity to the archetype pediocin, PA-1, encoded by P. acidilactici
      PAC 1.0.
AU  - Sturino JM
AU  - Rajendran M
AU  - Altermann E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00208-13.

PMID- 22207746
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Leucobacter chromiiresistens, an Extremely Chromium-Tolerant Strain.
PG  - 540-541
AB  - Here we present the draft genome of Leucobacter chromiiresistens. This is the first genome
      sequence of an organism belonging to the genus
      Leucobacter. L. chromiiresistens was sequenced due to its capability to
      tolerate up to 300 mM Cr(VI) in the medium, which is so far a unique
      feature for microorganisms.
AU  - Sturm G
AU  - Buchta K
AU  - Kurz T
AU  - Rensing SA
AU  - Gescher J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 540-541.

PMID- 2657665
VI  - 17
DP  - 1989
TI  - DNA cleavage by restriction endonucleases PflMI is inhibited in recognition sites modified by dcm methylation.
PG  - 3615
AB  - None
AU  - Sturm RA
AU  - Yaciuk P
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 3615.

PMID- 11679734
VI  - 57
DP  - 2001
TI  - Crystallization and preliminary X-ray analysis of ocr, the product of gene 0.3 of bacteriophage T7.
PG  - 1652-1654
AB  - Ocr, the product of gene 0.3 of bacteriophage T7, prevents the action of restriction
      endonucleases of the host bacteria. The amino-acid sequence of
      ocr has less than 20% similarity to any protein of known three-dimensional
      structure. Ocr has been crystallized in a number of different crystal
      forms and X-ray data for the seleno-L-methionine-substituted form has been
      collected to a resolution of 1.8 A. The presence of caesium was found to
      be required for good crystal growth. Anomalous X-ray data was used to
      identify possible positions for Se and Cs atoms in the unit cell.
AU  - Sturrock SS
AU  - Dryden DT
AU  - Atanasiu C
AU  - Dornan J
AU  - Bruce S
AU  - Cronshaw A
AU  - Taylor P
AU  - Walkinshaw MD
PT  - Journal Article
TA  - Acta Crystallogr. D Biol. Crystallogr.
JT  - Acta Crystallogr. D Biol. Crystallogr.
SO  - Acta Crystallogr. D Biol. Crystallogr. 2001 57: 1652-1654.

PMID- 9254696
VI  - 25
DP  - 1997
TI  - A prediction of the amino acids and structures involved in DNA recognition by type I DNA restriction and modification enzymes.
PG  - 3408-3414
AB  - The S subunits of type I DNA restriction/modification enzymes are responsible for recognizing
      the DNA target sequence for the enzyme.  They contain two domains of approximately 150 amino
      acids, each of which is responsible for recognizing one half of the bipartite asymmetric
      target.  In the absence of any known tertiary structure for type I enzymes or recognizable DNA
      recognition motifs in the highly variable amino acid sequences of the S subunits, it has
      previously not been possible to predict which amino acids are responsible for sequence
      recognition.  Using a combination of sequence alignment and secondary structure prediction
      methods to analyze the sequences of S subunits, we predict that all of the 51 known target
      recognition domains have the same tertiary structure.  Furthermore, this structure is similar
      to the structure of the TRD of the C5-cytosine methyltransferase, HhaI, which recognizes its
      DNA target via interactions with two short polypeptide loops and a beta strand.  Our results
      predict the location of these sequence recognition structures within the TRDs of all type I S
      subunits.
AU  - Sturrock SS
AU  - Dryden DTF
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1997 25: 3408-3414.

PMID- 185196
VI  - 128
DP  - 1976
TI  - Restriction Enzymes Do Not Play a Significant Role in Haemophilus Homospecific or Heterospecific Transformation.
PG  - 212-220
AB  - Competent Haemophilus influenzae Rd recipients, either as phage HP1 restricting
      (r+) or nonrestricting (r-) nonlysogens or defective lysogens, were exposed to
      deoxyribonucleic acids from various wild-type phage HP1 lysogenic H. influenzae
      serotype strains (non-encapsulated derivatives of serotypes alpha, beta, c, d,
      and e), to DNA from lysogenic Haemophilus parahaemolyticus, and to DNA from
      modified and nonmodified phage HP1.  Transformation of antibiotic resistance
      markers and of prophage markers in homospecific crosses was observed to be
      unaffected by the recipient restriction phenotype, whereas the transfection
      response was much reduced in r+ recipients.  Heterospecific transformation of
      prophage markers was reduced by only 80 to 90%, whereas antibiotic resistance
      marker transformation was 1,000 to 10,000 times lower.  Heterospecific
      transfection was at least 100 times lower than homospecific transfection in
      both r+ and r- recipients.  The general conclusion is that neither class I nor
      class II restriction enzymes affect significantly the transformation efficiency
      in homospecific and heterospecific crosses.  The efficiency of heterospecific
      transformation may depend mainly on the deoxyribonucleic acid homology in the
      genetic marker region.
AU  - Stuy JH
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1976 128: 212-220.

PMID- 21952544
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Type Strain Campylobacter fetus subsp. venerealis NCTC 10354T.
PG  - 5871-5872
AB  - Campylobacter fetus subsp. venerealis is the etiologic agent of bovine genital
      campylobacteriosis, a sexually transmitted disease of cattle that
      is of worldwide importance. The complete sequencing and annotation of the
      genome of the type strain C. fetus subsp. venerealis NCTC 10354(T) are
      reported.
AU  - Stynen AP et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5871-5872.

PMID- 9569625
VI  - 43
DP  - 1998
TI  - Lack of surface receptors not restriction-modification system determines F4 phage resistance in Streptococcus bovis II/1.
PG  - 35-38
AB  - The resistance of Streptococcus bovis strain II/1, the producer of SbvI restriction
      endonuclease, to F4 phage infection was demonstrated by the double-agar-layer method.  Despite
      the presence of restriction endonuclease SbvI which can cleave F4 phage DNA to numerous
      fragments in vitro, the evidence that adsorption inhibition is the most important defense
      mechanism in phage resistance of S. bovis II/1 strain was obtained by adhesion experiments in
      vivo.  Electron microscopy of phage-host mixtures showed many phage particles on the bacterial
      surface of phage-sensitive S. bovis 47/3 control strain in comparison with no phage particles
      seen on S. bovis II/1 (phage-resistant) strain surface.
AU  - Styriak I
AU  - Pristas P
AU  - Javorsky P
PT  - Journal Article
TA  - Folia Microbiol. (Praha)
JT  - Folia Microbiol. (Praha)
SO  - Folia Microbiol. (Praha) 1998 43: 35-38.

PMID- 24652975
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Xylella fastidiosa Pear Leaf Scorch Strain in Taiwan.
PG  - e00166-14
AB  - The draft genome sequence of Xylella fastidiosa pear leaf scorch strain PLS229, isolated from
      the pear cultivar Hengshan (Pyrus pyrifolia) in Taiwan, is reported
      here. The bacterium has a genome size of 2,733,013 bp, with a G+C content of
      53.1%. The PLS229 genome was annotated and has 3,259 open reading frames and 50
      RNA genes.
AU  - Su CC
AU  - Deng WL
AU  - Jan FJ
AU  - Chang CJ
AU  - Huang H
AU  - Chen J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00166-14.

PMID- 22038964
VI  - 193
DP  - 2011
TI  - Genome Sequence of Bacillus pumilus S-1, an Efficient Isoeugenol-Utilizing Producer for Natural Vanillin.
PG  - 6400-6401
AB  - Bacillus pumilus S-1 is an efficient isoeugenol-utilizing producer of natural vanillin. The
      genome of B. pumilus S-1 contains the epoxide
      hydrolase and six candidate monooxygenases that make it possible to
      explore the mechanism involved in conversion of isoenguenol to vanillin in
      the B. pumilus strain.
AU  - Su F
AU  - Hua D
AU  - Zhang Z
AU  - Wang X
AU  - Tang H
AU  - Tao F
AU  - Tai C
AU  - Wu Q
AU  - Wu G
AU  - Xu P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6400-6401.

PMID- 23105047
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Thermophile Bacillus coagulans Hammer, the Type Strain of  the Species.
PG  - 6294-6295
AB  - Here we announce a 3.0-Mb assembly of the Bacillus coagulans Hammer strain, which is the type
      strain of the species within the genus Bacillus. Genomic analyses
      based on the sequence may provide insights into the phylogeny of the species and
      help to elucidate characteristics of the poorly studied strains of Bacillus
      coagulans.
AU  - Su F
AU  - Tao F
AU  - Tang H
AU  - Xu P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6294-6295.

PMID- 22038963
VI  - 193
DP  - 2011
TI  - Genome Sequence of the Thermophilic Strain Bacillus coagulans XZL4, an Efficient Pentose-Utilizing Producer of Chemicals.
PG  - 6398-6399
AB  - Bacillus coagulans XZL4 is an efficient pentose-utilizing producer of important platform
      compounds, such as l-lactic acid, 2,3-butanediol, and
      acetoin. Here we present a 2.8-Mb assembly of its genome. Simple and
      efficient carbohydrate metabolism systems, especially the
      transketolase/transaldolase pathway, make it possible to convert pentose
      sugars to products at high levels.
AU  - Su F
AU  - Xu K
AU  - Zhao B
AU  - Tai C
AU  - Tao F
AU  - Tang H
AU  - Xu P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6398-6399.

PMID- 21705584
VI  - 193
DP  - 2011
TI  - Genome Sequence of the Thermophilic Strain Bacillus coagulans 2-6, an Efficient Producer of High-Optical-Purity L-Lactic Acid.
PG  - 4563-4564
AB  - Bacillus coagulans 2-6 is an efficient producer of lactic acid. The genome of B. coagulans 2-6
      owns the smallest genome size among the members of genus Bacillus known to date. The
      frameshift mutation at the start of D-lactate dehydrogenase might be responsible for the
      production of high optical purity L-lactic-acid.
AU  - Su F
AU  - Yu B
AU  - Sun J
AU  - Ou HY
AU  - Zhao B
AU  - Wang L
AU  - Qin J
AU  - Tang H
AU  - Tao F
AU  - Jarek M
AU  - Scharfe M
AU  - Ma C
AU  - Ma Y
AU  - Xu P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4563-4564.

PMID- 24903872
VI  - 2
DP  - 2014
TI  - Genome Sequence of a Promising Hydrogen-Producing Facultative Anaerobic Bacterium, Brevundimonas naejangsanensis Strain B1.
PG  - e00542-14
AB  - Brevundimonas naejangsanensis strain B1 is a newly isolated, facultative anaerobic bacterium
      capable of producing hydrogen with high efficiency. Here, we
      present a 2.94-Mb assembly of the genome sequence of strain B1, which may provide
      further insights into the molecular mechanism of hydrogen production from
      bioresource.
AU  - Su H
AU  - Zhang T
AU  - Bao M
AU  - Jiang Y
AU  - Wang Y
AU  - Tan T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00542-14.

PMID- 23209248
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of a Novel Bacterial Strain, LSJC7, Belonging to the Family Enterobacteriaceae with Dual Resistance to Arsenic and Tetracycline.
PG  - 7005-7006
AB  - Strain LSJC7, with dual resistance to arsenic and tetracycline, was isolated from an antimony
      tailing in China. Its 16S rRNA gene sequence has the highest
      similarity to that of Enterobacter cloacae subsp. dissolvens LMG 2683(T)
      (97.02%). Here we present the approximately 4.6-Mbp draft genome sequence of
      strain LSJC7.
AU  - Su J
AU  - Ye J
AU  - Zhu Y
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 7005-7006.

PMID- 24407625
VI  - 2
DP  - 2014
TI  - Genome Sequence of Bacillus cereus Strain LCT-BC235, Carried by the Shenzhou VIII Spacecraft.
PG  - e00665-13
AB  - In order to explore the effect of space environments on Bacillus cereus, we determined the
      draft genome sequence of a B. cereus strain, LCT-BC235, which was
      isolated after space flight.
AU  - Su L
AU  - Wang T
AU  - Zhou L
AU  - Wu C
AU  - Guo Y
AU  - Chang D
AU  - Liu Y
AU  - Jiang X
AU  - Yin S
AU  - Liu C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00665-13.

PMID- 22689237
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Bacillus cereus Strain LCT-BC244.
PG  - 3549
AB  - Bacillus cereus is a prevalent, soil-dwelling, Gram-positive bacterium. Some strains are
      harmful to humans and cause food-borne illness, while other strains
      can be beneficial as probiotics for animals. To gain insight into the bacterial
      genetic determinants, we report the genome sequence of a strain, LCT-BC244, which
      was isolated from CGMCC 1.230.
AU  - Su L
AU  - Zhou T
AU  - Zhou L
AU  - Fang X
AU  - Li T
AU  - Wang J
AU  - Guo Y
AU  - Chang D
AU  - Wang Y
AU  - Li D
AU  - Liu C
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3549.

PMID- 9925601
VI  - 65
DP  - 1999
TI  - LlaFI, a type III restriction and modification system in Lactococcus lactis.
PG  - 686-693
AB  - We describe a type III restriction and modification system, LlaFI, in Lactococcus lactis.
      LlaFI is encoded by a 12-kb native plasmid, pND801, harbored in L. lactis LL42-1.  Sequencing
      revealed two adjacent open reading frames.  One ORF encodes a 680-amino-acid polypeptide, and
      this ORF is followed by a second ORF which encodes an 873-amino-acid polypeptide.  The two
      ORFs appear to be organized in an operon.  A homology search revealed that the two ORFs
      exhibited significant similarity to type III restriction and modification subunits.  The
      complete amino acid sequence of the Mod subunit of LlaFI was aligned with the amino acid
      sequences of four previously described type III methyltransferases.  Both the N-terminal
      regions and the C-terminal regions of the Mod proteins are conserved, while the central
      regions are more variable.  An S-adenosyl methionine binding motif (present in all adenine
      methyltransferases) was found in the N-terminal region of the Mod protein.  The seven
      conserved helicase motifs found in the previously described type III R/M systems were found at
      the same relative positions in the LlaFI Res sequence, LlaFI has cofactor requirements for
      activity that are characteristic of the previously described type III enzymes.  ATP and Mg2+
      are required for endonucleolytic activity; however, the activity is not strictly dependent on
      the presence of Ado-Met but is stimulated by it.  To our knowledge, this is the first type III
      R/M system that has been characterized not just in lactic acid bacteria but also in
      gram-positive bacteria.
AU  - Su P
AU  - Im H
AU  - Hsieh H
AU  - Kanga S
AU  - Dunn NW
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1999 65: 686-693.

PMID- 
VI  - 20
DP  - 1998
TI  - Additive effects of two different plasmid-linked restriction and modification systems in Lactococcus.
PG  - 515-518
AB  - Two plasmids, pND801 and pND802, encoding different restriction and modification systems were
      isolated from Lactococcus lactis ssp. lactis LL42-1 and Lactococcus lactis ssp. cremoris
      LC14-1, respectively.  PND802 contained one SphI restriction enzyme site and the whole plasmid
      was cloned into the SphI site of the streptococcal/E. coli shuttle vector pSA3 generating the
      plasmid pND803.  PND803 was stably maintained in L. lactis MG1363 harboring pND801.  The
      combination of the two R/M systems within L. lactis MG1363 resulted in an additive resistance
      towards both isometric phage and prolate phage.
AU  - Su P
AU  - Ng A
AU  - Kennelly V
AU  - Costello M
AU  - Harvey M
AU  - Dunn N
PT  - Journal Article
TA  - Biotechnol. Lett.
JT  - Biotechnol. Lett.
SO  - Biotechnol. Lett. 1998 20: 515-518.

PMID- 15107490
VI  - 32
DP  - 2004
TI  - Unusual 2-aminopurine fluorescence from a complex of DNA and the EcoKI methyltransferase.
PG  - 2223-2230
AB  - The methyltransferase, M.EcoKI, recognizes the DNA sequence 5'-AACNNNNNNGTGC-3' and
      methylates adenine at the underlined positions. DNA methylation has been shown by
      crystallography to occur via a base flipping mechanism and is believed to be a general
      mechanism for all methyltransferases. If no structure is available, the fluorescence of
      2-aminopurine is often used as a signal for base flipping as it shows enhanced fluorescence
      when its environment is perturbed. We find that 2-aminopurine gives enhanced fluorescence
      emission not only when it is placed at the M.EcoKI methylation sites but also at a location
      adjacent to the target adenine. Thus it appears that 2-aminopurine fluorescence intensity is
      not a clear indicator of base flipping but is a more general measure of DNA distortion. Upon
      addition of the cofactor S-adenosyl-methionine to the M.EcoKI:DNA complex, the 2-aminopurine
      fluorescence changes to that of a new species showing excitation at 345 nm and emission at 450
      nm. This change requires a fully active enzyme, the correct cofactor and the 2-aminopurine
      located at the methylation site. However, the new fluorescent species is not a covalently
      modified form of 2-aminopurine and we suggest that it represents a hitherto undetected
      physicochemical form of 2-aminopurine.
AU  - Su T-J
AU  - Connolly BA
AU  - Darlington C
AU  - Mallin R
AU  - Dryden DTF
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2004 32: 2223-2230.

PMID- 15942026
VI  - 33
DP  - 2005
TI  - DNA bending by M.EcoKI methyltransferase is coupled to nucleotide flipping.
PG  - 3235-3244
AB  - The maintenance methyltransferase M.EcoKI recognizes the bipartite DNA sequence
      5'-AACNNNNNNGTGC-3', where N is any nucleotide. M.EcoKI preferentially methylates a sequence
      already containing a methylated adenine at or complementary to the underlined bases in the
      sequence. We find that the introduction of a single-stranded gap in the middle of the
      non-specific spacer, of up to 4 nt in length, does not reduce the binding affinity of M.EcoKI
      despite the removal of non-sequence-specific contacts between the protein and the DNA
      phosphate backbone. Surprisingly, binding affinity is enhanced in a manner predicted by simple
      polymer models of DNA flexibility. However, the activity of the enzyme declines to zero once
      the single-stranded region reaches 4 nt in length. This indicates that the recognition of
      methylation of the DNA is communicated between the two methylation targets not only through
      the protein structure but also through the DNA structure. Furthermore, methylation recognition
      requires base flipping in which the bases targeted for methylation are swung out of the DNA
      helix into the enzyme. By using 2-aminopurine fluorescence as the base flipping probe we find
      that, although flipping occurs for the intact duplex, no flipping is observed upon
      introduction of a gap. Our data and polymer model indicate that M.EcoKI bends the non-specific
      spacer and that the energy stored in a double-stranded bend is utilized to force or flip out
      the bases. This energy is not stored in gapped duplexes. In this way, M.EcoKI can determine
      the methylation status of two adenine bases separated by a considerable distance in
      double-stranded DNA and select the required enzymatic response.
AU  - Su T-J
AU  - Tock MR
AU  - Egelhaaf SU
AU  - Poon WCK
AU  - Dryden DTF
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2005 33: 3235-3244.

PMID- 28428307
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Three Listeria monocytogenes Isolates from Foods in China.
PG  - e00220-17
AB  - Listeria monocytogenes is a foodborne pathogen of global concern because of the high mortality
      rate among patients. The draft genome sequences of three L.
      monocytogenes strains isolated from foods are reported here. The availability of
      these genomes should provide useful information on the genomic diversity of L.
      monocytogenes isolated from foods in China.
AU  - Su X
AU  - Cao G
AU  - Kuang D
AU  - Zhang J
AU  - Chen Y
AU  - Allard M
AU  - Brown E
AU  - Shi X
AU  - Meng J
AU  - Xu X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00220-17.

PMID- 24092777
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Encapsulated Haemophilus influenzae Type f KR494, an  Invasive Isolate That Caused Necrotizing Myositis.
PG  - e00470-13
AB  - Haemophilus influenzae serotype f (Hif) is an etiologic agent of bacterial invasive disease.
      Here, we report the first annotated genome sequence of the Hif
      strain KR494, which was isolated from a patient suffering from sepsis and
      necrotizing myositis. The genome sequence will increase the understanding of Hif
      pathogenesis.
AU  - Su YC
AU  - Horhold F
AU  - Singh B
AU  - Riesbeck K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00470-13.

PMID- 23868133
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Enterococcus faecium Strain CRL 1879, Isolated from a Northwestern Argentinian Artisanal Cheese.
PG  - e00514-13
AB  - We report the draft genome sequence of the bacteriocin producer Enterococcus faecium strain
      CRL 1879, isolated from a northwestern Argentinian artisanal
      cheese. The draft genome sequence is composed of 73 contigs for 2,886,747 bp,
      with 3,140 protein-coding genes. Six biosynthetic clusters for bacteriocin class
      II production were found. Typical virulence determinants, which have relevance in
      food safety, were not present.
AU  - Suarez NE
AU  - Saavedra L
AU  - Slozilova I
AU  - Bonacina J
AU  - Demnerova K
AU  - Sesma F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00514-13.

PMID- 19640327
VI  - 76
DP  - 2009
TI  - Evidence for the presence of restriction/modification systems in Lactobacillus delbrueckii.
PG  - 433-440
AB  - The bacteriophages Cb1/204 and Cb1/342 were obtained by induction from the commercial strain
      Lactobacillus delbrueckii subsp. lactis Cb1, and
      propagated on Lactobacillus delbrueckii subsp. lactis 204 (Lb.l 204)
      and Lactobacillus delbrueckii subsp. bulgaricus 342 (Lb.b 342),
      respectively. By cross sensitivity, it was possible to detect a delay
      in the lysis of Lb.l 204 with Cb1/342 phage, while the adsorption rate
      was high (99-5%). Modified and unmodified phages were isolated using
      phage Cb1/342 and strain Lb.l 204. The EOP (Efficiency of Plaquing)
      values for the four phages (Cb1/204, Cb1/342, Cb1/342 modified and
      Cb1/342 unmodified) suggested that an R/M system modified the original
      temperate phage, and the Bg/II-DNA restriction patterns of these phages
      might point out the presence of a Type II R/M system. Also, the
      existence of a Type I R/M system was demonstrated by PCR and nucleotide
      sequence, being the percentages of alignment homology with Type I R/M
      systems reported previously higher than 95%. In this study it was
      possible to demonstrate that the native phage resistant mechanisms and
      the occurrence of prophages in commercial host strains, contribute
      strongly to diversify the phage population in a factory environment.
AU  - Suarez V
AU  - Zago M
AU  - Giraffa G
AU  - Reinheimer J
AU  - Quiberoni A
PT  - Journal Article
TA  - J. Dairy Res.
JT  - J. Dairy Res.
SO  - J. Dairy Res. 2009 76: 433-440.

PMID- 18976830
VI  - 128
DP  - 2008
TI  - Phage-resistance linked to cell heterogeneity in the commercial strain Lactobacillus delbrueckii subsp lactis Ab1.
PG  - 401-405
AB  - The aim of this work was to study the relationship between the cell morphological
      heterogeneity and the phage-resistance in the commercial
      strain Lactobacillus delbrueckii subsp. lactis Ab1. Two morphological
      variants (named C and T) were isolated from this strain.
      Phage-resistant derivatives were isolated from them and the percentage
      of occurrence of confirmed phage-resistant cells was 0.001% of the
      total cellular population. Within these phage-resistant cell
      derivatives there were T (3 out of 4 total isolates) and C (1 out of 4
      total isolates) variants. The study of some technological properties
      (e.g. proteolytic and acidifying activities) demonstrated that most of
      phage-resistant derivatives were not as good as the parental strain.
      However. for one derivative (a T variant), the technological properties
      Were better than those of the parental strain. On the other hand, it
      was possible to determinate that the system of phage-resistance in the
      T variants was interference in adsorption step, with adsorption rates <
      15%. For the C variant derivative it was possible to demonstrate the
      presence of a restriction/modification system and, moreover, to
      determinate that this system could be Type 1R/M.
AU  - Suarez VB
AU  - Maciel N
AU  - Guglielmotti D
AU  - Zago M
AU  - Giraffa G
AU  - Reinheimer J
PT  - Journal Article
TA  - Int. J. Food Microbiol.
JT  - Int. J. Food Microbiol.
SO  - Int. J. Food Microbiol. 2008 128: 401-405.

PMID- 22965089
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Citreicella aestuarii Strain 357, a Member of the Roseobacter Clade Isolated without Xenobiotic Pressure from a Petroleum-Polluted    Beach.
PG  - 5464-5465
AB  - Citreicella aestuarii 357 is a member of the Roseobacter clade that was isolated  without
      xenobiotic pressure from an oil-polluted sand sample from the Galician
      coast (Spain). Its genome sequence suggests an organoheterotrophic metabolism,
      including a wide catabolic potential for aromatic hydrocarbons.
AU  - Suarez-Suarez LY
AU  - Brunet-Galmes I
AU  - Pina-Villalonga JM
AU  - Christie-Oleza JA
AU  - Pena A
AU  - Bennasar A
AU  - Armengaud J
AU  - Nogales B
AU  - Bosch R
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5464-5465.

PMID- 18814946
VI  - 138
DP  - 2008
TI  - Resolution of the EcoRII restriction endonuclease-DNA complex structure in solution using fluorescence spectroscopy.
PG  - 107-114
AB  - The X-ray structure for the type HE EcoRII restriction endonuclease has been resolved (X.E.
      Zhou, Y. Wang, M. Reuter, M. Mucke, D.H. Kruger,
      EJ. Meehan and L. Chen. Crystal structure of type HE restriction
      enclonuclease EcoRII reveals an autoinhibition mechanism by a novel
      effector-binding fold. J. Mol. Biol. 335 (2004) 307319.1, but the
      structure of the R.EcoRII-DNA complex is still unknown. The aim of this
      article was to examine the structure of the pre-reactive R.EcoRII-DNA
      complex in solution by fluorescence spectroscopy. The structure for the
      R.EcoRII-DNA complex was resolved by determining the fluorescence
      resonance energy transfer (FRET) between two fluorescent dyes,
      covalently attached near the EcoRII recognition sites, that were
      located at opposite ends of a lengthy two-site DNA molecule. Analysis
      of the FRET data from the two-site DNA revealed a likely model for the
      arrangement of the two EcoRII recognition sites relative to each other
      in the R.EcoRII-DNA complex in the presence of Ca2+ ions. According to
      this model, the R.EcoRII binds the two-site DNA and forms a DNA loop in
      which the EcoRII recognition sites are 20 +/- 10 A distant to each
      other and situated at an angle of 70 +/- 10 degrees.
AU  - Subach F
AU  - Kirsanova O
AU  - Liquier J
AU  - Gromova ES
PT  - Journal Article
TA  - Biophys. Chem.
JT  - Biophys. Chem.
SO  - Biophys. Chem. 2008 138: 107-114.

PMID- 
VI  - 78
DP  - 2008
TI  - Investigation of restriction endonuclease EcoRII complex with DNA in solution by FTIR spectroscopy.
PG  - 1103-1109
AB  - The X-ray structure of type IIE EcoRII restriction endonuclease has been solved but the
      structure of the R.EcoRII-DNA complex is still unknown. We report here on the structure of the
      pre-reactive R.EcoRII-DNA-Ca2+ complex in solution examined by FTIR spectroscopy. The
      secondary structure of R.EcoRII as well as the structure of the target DNA in the
      R.EcoRII-DNA-Ca2+ complex was characterized. It was shown that the R.EcoRII-DNA-Ca2+ complex
      formation is accompanied by changes in the spectrum of both DNA bases and DNA sugar-phosphate
      backbone that suggest contacts of the enzyme with different groups of atoms in DNA. The change
      of the R.EcoRII secondary structure in the R.EcoRII-DNA-Ca2+ complex is also observed.
AU  - Subach FV
AU  - Liquier J
AU  - Gromova ES
PT  - Journal Article
TA  - Russ. J. Gen. Chem.
JT  - Russ. J. Gen. Chem.
SO  - Russ. J. Gen. Chem. 2008 78: 1103-1109.

PMID- 14743537
VI  - 29
DP  - 2003
TI  - The preparation of DNA duplexes containing internucleotide phosphorothioate groups in various positions of the recognition site for the EcoRII restriction endonuclease.
PG  - 623-631
AB  - Twenty-four 12-mer DNA duplexes, each containing a chiral phosphorothioate group successively
      replacing one of the internucleotide phosphate groups
      either in the EcoRII recognition site (5'CCA/TGG) or near to it, were
      obtained for studying the interaction of the restriction endonuclease
      EcoRII with internucleotide DNA phosphates. Twelve of the 12-mer
      oligonucleotides were synthesized as Rp and Sp diastereomeric mixtures.
      Six of them were separated by reversed-phase HPLC using various buffers.
      Homogeneous diastereomers of the other oligonucleotides were obtained by
      enzymatic ligation of the Rp and Sp diastereomers of 5- to 7-mer
      oligonucleotides preliminarily separated by HPLC with the corresponding
      short oligonucleotides on a complementary DNA template. The English
      version of the paper: Russian Journal of Bioorganic Chemistry, 2003, vol.
      29, no. 6; see also http://www.maik.ru.
AU  - Subach FV
AU  - Muller S
AU  - Tashlitsky VN
AU  - Petrauskene OV
AU  - Gromova ES
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 2003 29: 623-631.

PMID- 16681387
VI  - 45
DP  - 2006
TI  - Impact of benzo[a] pyrene-2 '-deoxyguanosine lesions on methylation of DNA by SssI and HhaI DNA methyltransferases.
PG  - 6142-6159
AB  - DNA damage caused by the binding of the tumorigen 7R, 8S-diol 9S, 10R-epoxide (B[a]PDE), a
      metabolite of bezo[a] pyrene, to guanine in
      CpG dinucleotide sequences could affect DNA methylation and, thus,
      represent a potential epigenetic mechanism of chemical carcinogenesis.
      In this work, we investigated the impact of stereoisomeric (+)- and
      (-)- trans-anti-B[a]P-N-2-dG adducts (B+ and B-) on DNA methylation by
      prokaryotic DNA methyltransferases M. SssI and M. HhaI. These two
      methyltransferases recognize (C) under bar pG and G (C) under bar GC
      sequences, respectively, and transfer a methyl group to the C5 atom of
      cytosine (C). A series of 18-mer unmethylated or hemimethylated
      oligodeoxynucleotide duplexes containing trans-anti-B[a]P-N-2-dG
      adducts was generated. The B+ or B- residues were introduced either 5 '
      or 3 ' adjacent or opposite to the target 2 '-deoxycytidines. The B[a]
      PDE lesions practically produced no effect on M. SssI binding to DNA
      but reduced M. HhaI binding by 1-2 orders of magnitude. In most cases,
      the benzo[ a] pyrenyl residues decreased the methylation efficiency of
      hemimethylated and unmethylated DNA by M. SssI and M. HhaI. An absence
      of the methylation of hemimethylated duplexes was observed when either
      the (+)- or the (-)-trans-anti-B[a]P-N-2-dG adduct was positioned 5 '
      to the target dC. The effects observed may be related to the minor
      groove conformation of the bulky benzo[a]pyrenyl residue and to a
      perturbation of the normal contacts of the methyltransferase catalytic
      loop with the B[a]PDE-modified DNA. Our results indicate that a
      trans-anti-B[a] P-N-2-dG lesion flanking a target dC in the CpG
      dinucleotide sequence on its 5 '- side has a greater adverse impact on
      methylation than the same lesion when it is 3 ' adjacent or opposite to
      the target dC.
AU  - Subach OM
AU  - Baskunov VB
AU  - Darii MV
AU  - Maltseva DV
AU  - Alexandrov DA
AU  - Kirsanova OV
AU  - Kolbanovskiy A
AU  - Kolbanovskiy M
AU  - Johnson F
AU  - Bonala R
AU  - Geacintov NE
AU  - Gromova ES
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2006 45: 6142-6159.

PMID- 15182354
VI  - 271
DP  - 2004
TI  - 2-Pyrimidinone as a probe for studying the EcoRII DNA methyltransferase-substrate interaction.
PG  - 2391-2399
AB  - EcoRII DNA methyltransferase (M.EcoRII) recognizes the 5'...CC*T/AGG...3' DNA sequence and
      catalyzes the transfer of the
      methyl group from S-adenosyl-L-methionine to the C5 position of the
      inner cytosine residue (C*). Here, we study the mechanism of inhibition
      of M.EcoRII by DNA containing 2-pyrimidinone, a cytosine analogue
      lacking an NH2 group at the C4 position of the pyrimidine ring. Also,
      DNA containing 2-pyrimidinone was used for probing contacts of M.EcoRII
      with functional groups of pyrimidine bases of the recognition sequence.
      2-Pyrimidinone was incorporated into the 5'...CCT/AGG...3' sequence
      replacing the target and nontarget cytosine and central thymine
      residues. Study of the DNA stability using thermal denaturation of
      2-pyrimidinone containing duplexes pointed to the influence of the
      bases adjacent to 2-pyrimidinone and to a greater destabilizing
      influence of 2-pyrimidinone substitution for thymine than that for
      cytosine. Binding of M.EcoRII to 2-pyrimidinone containing DNA and
      methylation of these DNA demonstrate that the amino group of the outer
      cytosine in the EcoRII recognition sequence is not involved in the
      DNA-M.EcoRII interaction. It is probable that there are contacts
      between the functional groups of the central thymine exposed in the
      major groove and M.EcoRII. 2-Pyrimidinone replacing the target cytosine
      in the EcoRII recognition sequence forms covalent adducts with
      M.EcoRII. In the absence of the cofactor S-adenosyl-L-methionine,
      proton transfer to the C5 position of 2-pyrimidinone occurs and in the
      presence of S-adenosyl-L-methionine, methyl transfer to the C5 position
      of 2-pyrimidinone occurs.
AU  - Subach OM
AU  - Khoroshaev AV
AU  - Gerasimov DN
AU  - Baskunov VB
AU  - Shchyolkina AK
AU  - Gromova ES
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 2004 271: 2391-2399.

PMID- 17388812
VI  - 274
DP  - 2007
TI  - The stereochemistry of benzo(a)pyrene-2'-deoxyguanosine adducts affects DNA methylation by SssI and HhaI DNA methyltransferases.
PG  - 2121-2134
AB  - The biologically most significant genotoxic metabolite of the environmental pollutant
      benzo[a]pyrene (B[a]P), (+)-7R,8S-diol 9S,10R-epoxide, reacts chemically with guanine in DNA,
      resulting in the predominent formation of (+)-trans-B[a]P-N2-dG and, to a lesser extent,
      (+)-cis-B[a]P-N2-dG adducts.  Here, we compare the effects of the adduct stereochemistry and
      conformation on the methylation of cytosine catalyzed by two purified prokaryotic DNA
      methyltransferases, SssI and HhaI, with the lesions positioned within or adjacent to their CG
      and GCGC recognition sites, respectively.  The fluorescence properties of the pyrenyl residues
      of the (+)-cis-B[a]aP-N2-dG and (+)-trans-B[a]P-N2-dG adducts in complexes with MTases are
      enhanced, but to different extents, indicating that aromatic B[a]P residues are positioned in
      different microenvironments in the DNA-protein complexes.  We have previously shown that the
      (+)-trans-isomeric adduct inhibits both the binding and methylating efficiencies (kcat) of
      both MTases.  Here we show that the stereoisomeric (+)-cis-B[a]P-N2-dG lesion has only a
      minimal effect on the binding of these MTases and on kcat.  The minor-groove (+)-trans adduct
      interferes with the formation of the normal DNA minor-groove contacts with the catalytic loop
      of the MTases.  However, the intercalated base-displaced (+)-cis adduct does not interfere
      with the minor-groove DNA-catalytic loop contacts, allowing near-normal binding of the MTases
      and undiminished kcat values.
AU  - Subach OM
AU  - Maltseva DV
AU  - Shastry A
AU  - Kolbanovskiy A
AU  - Klimasauskas S
AU  - Geacintov NE
AU  - Gromova ES
PT  - Journal Article
TA  - FEBS J.
JT  - FEBS J.
SO  - FEBS J. 2007 274: 2121-2134.

PMID- 25977424
VI  - 3
DP  - 2015
TI  - Draft Whole-Genome Sequence of Lactobacillus fermentum LfQi6, Derived from the Human Microbiome.
PG  - e00423-15
AB  - We report a 2.21-Mbp draft whole-genome sequence of Lactobacillus fermentum Qi6 (LfQi6). This
      strain demonstrates activity against pathogenic biofilms, enhances
      the skin barrier, and upregulates innate immune defenses. The genome sequence
      information of this strain will help to identify molecules that hold promise for
      the discovery of novel therapeutics for dermatological disorders.
AU  - Subhadra B
AU  - Krier J
AU  - Hofstee K
AU  - Monsul N
AU  - Berkes E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00423-15.

PMID- 2684015
VI  - 275
DP  - 1989
TI  - On the inhibition of deoxycytidylate hydroxymethylase by 5-fluoro-2'-deoxycytidine 5'-monophosphate .
PG  - 11-15
AB  - Studies were performed to determine whether 5-fluoro-2'-deoxycytidine 5'-monophosphate
      (FdCMP) is an inhibitor of deoxycytidylate hydroxymethylase and whether it could form an
      isolable covalent complex with the enzyme and the cofactor, 5,10-methylenetetrahydrofolate.
      The results showed that although FdCMP is a competitive inhibitor of dCMP hydroxymethylase, it
      does not cause time-dependent inhibition of the enzyme in the presence of cofactor. Further,
      although uv difference spectral evidence was found for a FdCMP-cofactor-enzyme complex, the
      complex was not sufficiently stable to isolate on nitrocellulose filters. We conclude that
      FdCMP is not a mechanism-based inhibitor of dCMP hydroxymethylase.
AU  - Subramaniam R
AU  - Wang Y
AU  - Mathews CK
AU  - Santi DV
PT  - Journal Article
TA  - Arch. Biochem. Biophys.
JT  - Arch. Biochem. Biophys.
SO  - Arch. Biochem. Biophys. 1989 275: 11-15.

PMID- 29326211
VI  - 6
DP  - 2018
TI  - Draft Whole-Genome Sequence of Deinococcus sp. UR1, a Putative Novel Species Isolated from an External Stainless Steel Surface in the Canadian Prairies.
PG  - e01407-17
AB  - Deinococcus sp. strain UR1, a resilient bacterium isolated from the surface of a  stainless
      steel sign located on the University of Regina campus in Saskatchewan,
      Canada, was sequenced to 56-fold coverage to produce 73 contigs with a consensus
      length of 4,472,838 bp and a G+C content of 69.37%.
AU  - Suchan DM
AU  - Steve JJ
AU  - Pierce AJ
AU  - Olshefsky SC
AU  - Kirzinger MWB
AU  - Perry BJ
AU  - Cameron ADS
AU  - Yost CK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01407-17.

PMID- 3533162
VI  - 51
DP  - 1986
TI  - Study of the conditions of activation and stabilization of Shigella sonnei 47 DNA methylases in the process of fractionation, purification, and during storage.
PG  - 1369-1376
AB  - A comparative investigation was made of the factors of activation and
      conditions of stabilization of partially purified and individual fractions of
      DNA methylases of the strain Shigella sonnei 47.  The influence of the
      temperature system, glycerin, albumin, protease inhibitors, divalent ions, as
      well as the conditions of storage at the value of the isoelectric point of the
      protein on the activity of the enzymes of methylation was studied.  It was
      shown that the effects of activating factors and levels of stabilization differ
      appreciably, depending on the degree of purification and the composition of the
      enzyme preparations  It was established that glycerin is ineffective as a
      stabilizing agent.  It was shown that of all the divalent cations studied the
      only activator universal for the methylases of Shigella sonnei 47 is Ca2+ ions.
      A pronounced stabilizing effect of albumin on the activity of these DNA
      methylases was demonstrated.  With the exception of one enzymatic fraction, the
      protease inhibitors have virtually no effect on the level of methylating
      activity of the preparations.  The phenomenon of spontaneous fluctuations of
      the methylating activity of Shigella sonnei 47 enzyme preparations during
      storage is described.
AU  - Suchkov SV
AU  - Lopatina NG
AU  - Arutyunyan EE
AU  - Nikolskaya II
AU  - Debov SS
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1986 51: 1369-1376.

PMID- 6353752
VI  - 29
DP  - 1983
TI  - Isoelectrofocusing of DNA-methylases from Shigella sonnei 47.
PG  - 117-122
AB  - Fractionation of bacterial methylases was studied by means of the isoelectrofocusing
      technique.  The method exhibited high accuracy, efficiency and reproducibility in studies of
      methylases from Shigella sonnei 47.  High column capacity and distinct focusing effect
      increased the experimental advantages of work with various amounts of protein as compared with
      ion exchange chromatography.  By means of the isoelectrofocusing technique three methylases
      were detected in the strain S. sonnei 47, which were dissimilar in their isoelectric points at
      pH 6.5, 8.4 and 9.8.  These findings indicate the heterogeneous pattern of enzyme methylation
      in the strain studied.  Complete removing of endogenous DNA was the main precondition for
      correct fractionation of methylases by means of the isoelectrofocusing technique.  A procedure
      is described for purification of S. sonnei 47 methylases from traces of endogenous DNA by
      affinity chromatography on heparin-Sepharose.
AU  - Suchkov SV
AU  - Nikolskaya II
AU  - Debov SS
PT  - Journal Article
TA  - Vopr. Med. Khim.
JT  - Vopr. Med. Khim.
SO  - Vopr. Med. Khim. 1983 29: 117-122.

PMID- 3904838
VI  - 50
DP  - 1985
TI  - Fractionation and purification of DNA-methylases of Shigella sonnei 47 cells.
PG  - 1797-1804
AB  - Possible applications of various column chromatography techniques and isoelectrofocusing for
      the study of DNA-methylases of Shigella sonnei 47 cells were analyzed.  A simple, rapid and
      convenient procedure based on the use of cation-exchange chromatography was developed for
      obtaining a highly active total preparation of methylases.  Affinity chromatography on
      heparin-Sepharose was shown to be a promising approach for separating methylases according to
      their specificity towards nitrogenous bases.  Isoelectrofocusing was used to identify in
      Shigella sonnei 47 cells six individual methylating enzymes differing in their pI values.
      Under the stipulation that Shigella sonnei 47 DNA-methylases show a tendency to aggregate in
      the course of fractionation, column chromatography is of little or no use in isolating and
      purifying individual methylating enzymes of the given strain.  The advantages of the
      isoelectrofocusing technique and its utility in the study of different molecular forms of
      site-specific enzymes are discussed.
AU  - Suchkov SV
AU  - Nikolskaya II
AU  - Debov SS
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1985 50: 1797-1804.

PMID- 7922330
VI  - 4
DP  - 1994
TI  - Flip out and modify.
PG  - 252-255
AB  - The crystal structure of a complex between a methyltransferase and DNA shows that, remarkably,
      the target cytosine base is swung out of the double helix and located next to the enzyme's
      S-adenosyl-L-homocysteine cofactor.
AU  - Suck D
PT  - Journal Article
TA  - Curr. Biol.
JT  - Curr. Biol.
SO  - Curr. Biol. 1994 4: 252-255.

PMID- 15185747
VI  - 56
DP  - 2004
TI  - Detection of glycosylase, endonuclease and methyltransferase enzyme activities using immobilized oligonucleotides.
PG  - 139-143
AB  - A novel rapid assay for detection of DNA glycosylase, restriction endonuclease, and DNA
      methyltransferase enzyme activities is presented.
      The assay is based on enzyme-dependent label release (in the case of
      glycosylase and endonuclease), or non-release (in the case of
      methyltransferase) into solution from end-labeled DNA immobilized on a
      solid support (CPG or Tenta Gel S-NH2). The assay has been validated
      for monitoring activity of repair enzyme uracil-DNA glycosylase,
      restriction endonucleases SsoII, MvaI and EcoRII and (cytosine-5)-DNA
      methyltransferase SsoII. Two types of labels have been tested and found
      compatible with the assay: radioactive (32P) and fluorescent
      (rhodamine B and fluorescein). The enzyme activity is estimated as a
      ratio of the label released into solution to the total amount of the
      label. Use of fluorescent labeling facilitates detection while use of
      solid phase-immobilized substrates facilitates product separation,
      improved assay sensitivity, and increases throughput of assay. Proposed
      technique provides an estimate of enzyme activity but not its specific
      activity. Thus, the assay will most valuable in the applications where
      rapid estimation of enzyme activity is necessary.
AU  - Sudina A
AU  - Volkov E
AU  - Oretskaya T
AU  - Naryshkin N
AU  - Ivanovskaya M
AU  - Kubareva E
PT  - Journal Article
TA  - Life
JT  - Life
SO  - Life 2004 56: 139-143.

PMID- 16212552
VI  - 70
DP  - 2005
TI  - Affinity modification of the restriction endonuclease SsoII by 2'-aldehyde-containing double stranded DNAs.
PG  - 1137-1144
AB  - Properties of 2'-aldehyde-containing double stranded DNAs (dsDNAs) have been studied for the
      first time as substrate analogs of the restriction endonuclease SsoII. These reactive
      oligonucleotides were successfully cross-linked to the restriction endonuclease SsoII by
      reductive amination, and conditions for DNA-protein conjugate trypsinolysis followed by the
      oligonucleotide-peptide conjugate purification were optimized. Use of MALDI-TOF mass
      spectrometry revealed that covalent linkage forms between the sugar moiety of the central
      pyrimidine nucleoside of the SsoII recognition site and Lys173 of the enzyme. The latter is
      probably involved in initial steps of enzyme-substrate recognition during dsDNA readout.
AU  - Sudina AE
AU  - Zatsepin TS
AU  - Pingoud V
AU  - Pingoud A
AU  - Oretskaya TS
AU  - Kubareva EA
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2005 70: 1137-1144.

PMID- 21914885
VI  - 193
DP  - 2011
TI  - Complete Genome of the Cellulolytic Ruminal Bacterium Ruminococcus albus 7.
PG  - 5574-5575
AB  - Ruminococcus albus 7 is a highly cellulolytic ruminal bacterium that is a member of the phylum
      Firmicutes. Here, we describe the complete genome of
      this microbe. This genome will be useful for rumen microbiology and
      cellulosome biology and in biofuel production, as one of its major
      fermentation products is ethanol.
AU  - Suen G et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5574-5575.

PMID- 25792061
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Polychlorinated Biphenyl-Degrading Bacterium Cupriavidus basilensis KF708 (NBRC 110671) Isolated from Biphenyl-Contaminated  Soil.
PG  - e00143-15
AB  - We report the draft genome sequence of Cupriavidus basilensis KF708 (NBRC 110671), which
      utilizes biphenyl as a sole carbon source and degrades
      polychlorinated biphenyls (PCBs). The KF708 strain possesses genes for biphenyl
      catabolism and other genes involved in various aromatic compounds.
AU  - Suenaga H
AU  - Yamazoe A
AU  - Hosoyama A
AU  - Kimura N
AU  - Hirose J
AU  - Watanabe T
AU  - Fujihara H
AU  - Futagami T
AU  - Goto M
AU  - Furukawa K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00143-15.

PMID- 25792060
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Polychlorinated Biphenyl-Degrading Bacterium Pseudomonas putida KF703 (NBRC 110666) Isolated from Biphenyl-Contaminated Soil.
PG  - e00142-15
AB  - Pseudomonas putida KF703 (NBRC 110666) utilizes biphenyl as a sole source of carbon and
      degrades polychlorinated biphenyls (PCBs). Here, we report the draft
      genome sequence of the KF703 strain, which provides insight into the molecular
      mechanisms of adaptation to an environment polluted by aromatic compounds.
AU  - Suenaga H
AU  - Yamazoe A
AU  - Hosoyama A
AU  - Kimura N
AU  - Hirose J
AU  - Watanabe T
AU  - Fujihara H
AU  - Futagami T
AU  - Goto M
AU  - Furukawa K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00142-15.

PMID- 28209826
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of the Polychlorinated Biphenyl-Degrading Bacterium Pseudomonas putida KF715 (NBRC 110667) Isolated from Biphenyl-Contaminated Soil.
PG  - e01624-16
AB  - Pseudomonas putida KF715 (NBRC 110667) utilizes biphenyl as a sole source of carbon and
      degrades polychlorinated biphenyls (PCBs). Here, we report a complete
      genome sequence of the KF715 strain, which comprises a circular chromosome and
      four plasmids. Biphenyl catabolic genes were located on the largest plasmid,
      pKF715A.
AU  - Suenaga H
AU  - Yamazoe A
AU  - Hosoyama A
AU  - Kimura N
AU  - Hirose J
AU  - Watanabe T
AU  - Fujihara H
AU  - Futagami T
AU  - Goto M
AU  - Furukawa K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01624-16.

PMID- 29773628
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Azospira sp. Strain I13, a Nitrous Oxide-Reducing Bacterium Harboring Clade II Type nosZ.
PG  - e00414-18
AB  - We report here a draft genome sequence of Azospira sp. strain I13 in the class
      Betaproteobacteria, a facultative anaerobic bacterium responsible for nitrous
      oxide (N2O) reduction. Deciphering this genome would pave the way for the use of
      Azospira sp. strain I13 to facilitate N2O consumption in a nitrogen-removing
      bioreactor emitting N2O.
AU  - Suenaga T
AU  - Aoyagi T
AU  - Hosomi M
AU  - Hori T
AU  - Terada A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00414-18.

PMID- 12810954
VI  - 100
DP  - 2003
TI  - The complete genome sequence of the carcinogenic bacterium Helicobacter hepaticus.
PG  - 7901-7906
AB  - Helicobacter hepaticus causes chronic hepatitis and liver cancer in mice. It is the prototype
      enterohepatic Helicobacter species and a close
      relative of Helicobacter pylori, also a recognized carcinogen. Here we
      report the complete genome sequence of H. hepaticus ATCC51449. H.
      hepaticus has a circular chromosome of 1,799,146 base pairs, predicted to
      encode 1,875 proteins. A total of 938, 953, and 821 proteins have
      orthologs in H. pylori, Campylobacter jejuni, and both pathogens,
      respectively. H. hepaticus lacks orthologs of most known H. pylori
      virulence factors, including adhesins, the VacA cytotoxin, and almost all
      cag pathogenicity island proteins, but has orthologs of the C. jejuni
      adhesin PEB1 and the cytolethal distending toxin (CDT). The genome
      contains a 71-kb genomic island (HHGI1) and several genomic islets whose
      G+C content differs from the rest of the genome. HHGI1 encodes three basic
      components of a type IV secretion system and other virulence protein
      homologs, suggesting a role of HHGI1 in pathogenicity. The genomic
      variability of H. hepaticus was assessed by comparing the genomes of 12 H.
      hepaticus strains with the sequenced genome by microarray hybridization.
      Although five strains, including all those known to have caused liver
      disease, were indistinguishable from ATCC51449, other strains lacked
      between 85 and 229 genes, including large parts of HHGI1, demonstrating
      extensive variation of genome content within the species.
AU  - Suerbaum S et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2003 100: 7901-7906.

PMID- 17046852
VI  - 140
DP  - 2006
TI  - The amino-terminus of mouse DNA methyltransferase 1 forms an independent domain and binds to DNA with the sequence involving PCNA binding motif.
PG  - 763-776
AB  - DNA methylation patterns in genome are maintained during replication by a DNA
      methyltransferase Dnmt1. Mouse Dnmt1 is a 180 kDa protein
      comprising the N-terminal regulatory domain, which covers 2/3 of the
      molecule, and the rest C-terminal catalytic domain. In the present
      study, we demonstrated that the limited digestion of full-length Dnmt1
      with different proteases produced a common N-terminal fragment, which
      migrated along with Dnmt1 (1-248) in SDS-polyacrylamide gel
      electrophoresis. Digestion of the N-terminal domains larger than Dnmt1
      (1-248) with chymotrypsin again produced the fragment identical to the
      size of Dnmt1 (1-248). These results indicate that the N-terminal
      domain of 1-248 forms an independent domain. This N-terminal domain
      showed DNA binding activity, and the responsible sequence was narrowed
      to the 79 amino acid residues involving the proliferating cell nuclear
      antigen (PCNA) binding motif. The DNA binding activity did not
      distinguish between DNA methylated and non-methylated states, but
      preferred to bind to the minor groove of AT-rich sequence. The DNA
      binding activity of the N-terminal domain competed with the PCNA
      binding. We propose that DNA binding activity of the N-terminal domain
      contributes to the localization of Dnmt1 to AT-rich sequence such as
      Line 1, satellite, and the promoter of tissue-specific silent genes.
AU  - Suetake I
AU  - Hayata D
AU  - Tajima S
PT  - Journal Article
TA  - J. Biochem. (Tokyo)
JT  - J. Biochem. (Tokyo)
SO  - J. Biochem. (Tokyo) 2006 140: 763-776.

PMID- 21510846
VI  - 437
DP  - 2011
TI  - Characterization of DNA-binding activity in the N-terminal domain of the DNA methyltransferase Dnmt3a.
PG  - 141-148
AB  - 
AU  - Suetake I
AU  - Mishima Y
AU  - Kimura H
AU  - Lee Y-H
AU  - Goto Y
AU  - Takeshima H
AU  - Ikegami T
AU  - Tajima S
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 2011 437: 141-148.

PMID- 12869530
VI  - 133
DP  - 2003
TI  - Distinct enzymatic properties of recombinant mouse DNA methyltransferases Dnmt3a and Dnmt3b.
PG  - 737-744
AB  - Recombinant mouse Dnmt3a and Dnmt3b were expressed in sf9 cells and purified to near
      homogeneity. The purified Dnmt3a and Dnmt3b gave specific
      activities of 1.8 +/- 0.3 and 1.3 +/- 0.1 mol/h/mol enzyme towards
      poly(dGdC)-poly(dGdC), respectively, which were the highest among those
      reported. Dnmt3a or Dnmt3b showed similar K(m) values towards
      poly(dIdC)-poly(dIdC) and poly(dGdC)-poly(dGdC). The K(m) values for
      S-adenosyl-L-methionine were not affected by the methyl-group acceptors,
      poly(dI-dC)-poly(dIdC) and poly(dG-dC)-poly(dGdC). The results indicate
      that the enzymes are de novo-type DNA methyltransferases. Dnmt3a and
      Dnmt3b activities were inhibited by Mn(2+) and Ni(2+) and showed broad pH
      optima around neutral pH. Both enzymes were susceptible to sodium ions,
      which inhibited their activity at around physiological ionic strength.
      However, Dnmt3a was fully active at physiological potassium concentration,
      but Dnmt3b was not. Using designed oligonucleotides for the analysis of
      cytosine methylation, we demonstrated that, in addition to CpG, Dnmt3a
      methylated CpA but not CpT and CpC, and that Dnmt3b methylated CpA and CpT
      but scarcely CpC. The relative activity of Dnmt3b towards nonCpG sequences
      was higher than that of Dnmt3a. These differences in enzymatic properties
      of Dnmt3a and Dnmt3b may contribute to the distinct functions of these
      enzymes in vivo.
AU  - Suetake I
AU  - Miyazaki J
AU  - Murakami C
AU  - Takeshima H
AU  - Tajima S
PT  - Journal Article
TA  - J. Biochem. (Tokyo)
JT  - J. Biochem. (Tokyo)
SO  - J. Biochem. (Tokyo) 2003 133: 737-744.

PMID- 11482456
VI  - 26
DP  - 2001
TI  - Proliferation stage-dependent expression of DNA methyltransferase (Dnmt1) in mouse small intestine.
PG  - 79-86
AB  - In cultured cells, the maintenance-type DNA methyltransferase (Dnmt1) is highly expressed
      during the proliferation stage. In the present
      study, we detected significant expression of Dnmt1 protein in the
      nuclear fraction of mouse small intestine. From its mobility in SDS
      polyacrylamide gel electrophoresis and the specific antibodies against
      the somatic cell-type Dnmt1, Dnmt1 was determined as a somatic cell
      type. Immunofluorescence study revealed that the Dnmt1 was highly
      expressed in the proliferating stem cells in crypts, and was localized
      in the nuclei. The present results indicate that the expression of
      Dnmt1 in vivo is also under the control of cell proliferation as in
      cultured cells.
AU  - Suetake I
AU  - Shi LH
AU  - Watanabe D
AU  - Nakamura M
AU  - Tajima S
PT  - Journal Article
TA  - Cell Struct. Funct.
JT  - Cell Struct. Funct.
SO  - Cell Struct. Funct. 2001 26: 79-86.

PMID- 15105426
VI  - 279
DP  - 2004
TI  - DNMT3L stimulates the DNA methylation activity of Dnmt3a and Dnmt3b through a direct interaction.
PG  - 27816-27823
AB  - In mammals, the resetting of DNA methylation patterns in early embryos and germ cells is
      crucial for development. Two DNA methyltransferases, Dnmt3a and Dnmt3b, are responsible for
      the creation of DNA methylation patterns. Dnmt3L, a member of the Dnmt3 family, has been
      reported to be necessary for maternal methylation imprinting, possibly by interacting with
      Dnmt3a and/or Dnmt3b (Hata et al., Development 129, 1983-1993, 2002). In the present study,
      the effect of DNMT3L, a human homologue of Dnmt3L, on the DNA methylation activity of mouse
      Dnmt3a and Dnmt3b was examined in vitro. DNMT3L enhanced the DNA methylation activity of
      Dnmt3a and Dnmt3b about 1.5-3 fold in a dose-dependent manner, but not that of Dnmt1. Although
      the extents of stimulation were different, a stimulatory effect on the DNA methylation
      activity was observed for all the substrate DNA sequences examined, such as those of the
      maternally methylated SNRPN and Lit-1 imprinting genes, the paternally methylated H19
      imprinting gene, the CpG island of the myoD gene, the 5S ribosomal RNA gene, an artificial 28
      bp DNA, poly(dGdC)-poly(dGdC), and poly(dIdC)-poly(dIdC). DNMT3L could not bind to DNA but
      could to Dnmt3a and Dnmt3b, indicating that the stimulatory effect of DNMT3L on the DNA
      methylation activity may not be due to the guiding of Dnmt3a and Dnmt3b to the targeting DNA
      sequence, but may comprise a direct effect on their catalytic activity. The carboxyl-terminal
      half of DNMT3L was found to be responsible for the enhancement of the enzyme activity.
AU  - Suetake I
AU  - Shinozaki F
AU  - Miyagawa J
AU  - Takeshima H
AU  - Tajima S
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2004 279: 27816-27823.

PMID- 25720680
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Acinetobacter calcoaceticus Strain P23, a Plant Growth-Promoting Bacterium of Duckweed.
PG  - e00026-15
AB  - Acinetobacter calcoaceticus strain P23 is a plant growth-promoting bacterium, which was
      isolated from the surface of duckweed. We report here the draft genome  sequence of strain
      P23. The genome data will serve as a valuable reference for understanding the molecular
      mechanism of plant growth promotion in aquatic plants.
AU  - Sugawara M
AU  - Hosoyama A
AU  - Yamazoe A
AU  - Morikawa M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00026-15.

PMID- 28254989
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Bradyrhizobium diazoefficiens USDA 122, a Nitrogen-Fixing Soybean Symbiont.
PG  - e01743-16
AB  - We report the complete genome sequence of Bradyrhizobium diazoefficiens USDA 122, a
      nitrogen-fixing soybean symbiont. The genome consists of a 9.1 Mb circular
      chromosome, and 8,551 coding sequences (CDSs) were predicted on the genome. The
      sequence will provide insight into the evolution of rhizobial genome, and the
      symbiotic compatibility with host plants.
AU  - Sugawara M
AU  - Tsukui T
AU  - Kaneko T
AU  - Ohtsubo Y
AU  - Sato S
AU  - Nagata Y
AU  - Tsuda M
AU  - Mitsui H
AU  - Minamisawa K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01743-16.

PMID- 
VI  - 12
DP  - 2017
TI  - Genetic characterization of blaNDM plasmids in carbapenem-resistant Escherichia coli isolated in Myanmar.
PG  - e184720
AB  - The bacterial enzyme New Delhi metallo- and #946;-lactamase hydrolyzes almost all  and
      #946;-lactam antibiotics,
      including carbapenems, which are drugs of last resort for severe bacterial infections.
      The spread of carbapenem-resistant Enterobacteriaceae that carry the New Delhi metallo-
      and #946;-lactamase gene, blaNDM, poses a serious threat to public health. In this study, we
      genetically
      characterized eight carbapenem-resistant Escherichia coli isolates from a tertiary care
      hospital in Yangon, Myanmar. The eight isolates belonged to five multilocus-sequence
      types and harbored multiple antimicrobial-resistance genes, resulting in resistance against
      nearly all of the antimicrobial agents tested, except colistin and fosfomycin. Nine plasmids
      harboring blaNDM genes were identified from these isolates. Multiple blaNDM genes were
      found in the distinct Inc-replicon types of the following plasmids: an IncA/C2 plasmid
      harboring
      blaNDM-1 (n = 1), IncX3 plasmids harboring blaNDM-4 (n = 2) or blaNDM-7 (n = 1), IncFII
      plasmids harboring blaNDM-4 (n = 1) or blaNDM-5 (n = 3), and a multireplicon F plasmid
      harboring
      blaNDM-5 (n = 1). Comparative analysis highlighted the diversity of the blaNDM-harboring
      plasmids and their distinct characteristics, which depended on plasmid replicon types. The
      results indicate circulation of phylogenetically distinct strains of carbapenem-resistant
      E. coli with various plasmids harboring blaNDM genes in the hospital.
AU  - Sugawara Y
AU  - Akeda Y
AU  - Sakamoto N
AU  - Takeuchi D
AU  - Motooka D
AU  - Nakamura S
AU  - Hagiya H
AU  - Yamamoto N
AU  - Nishi I
AU  - Yoshida H
AU  - Okada K
AU  - Zin KN
AU  - Aye MM
AU  - Tomono K
AU  - Hamada S
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2017 12: e184720.

PMID- 1190452
VI  - 68
DP  - 1975
TI  - Agarose slab-gel electrophoresis equipment.
PG  - 36-46
AB  - Simple slab-gel molds which utilize the electrophoresis apparatus described by
      F.W. Studier (J. Mol. Biol. 79, 237 (1973)) have been designed for pouring and
      running agarose slab-gels.  Analytical gels in which many samples are run
      simultaneously facilitate the assay of many enzymes which lead to physical
      changes in DNA, whereas the preparative gels allow the separation of large
      quantities (1-20 mg) of DNA fragments.
AU  - Sugden B
AU  - DeTroy B
AU  - Roberts RJ
AU  - Sambrook J
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 1975 68: 36-46.

PMID- 29674550
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of a Shewanella halifaxensis Strain Isolated from the Intestine of Marine Red Seabream (Pagrus major), Which Includes an Integrative  Conjugative Element with Macrolide Resistance Genes.
PG  - e00297-18
AB  - Shewanella halifaxensis strain 6JANF4-E-4 was isolated from the intestine of a red seabream
      (Pagrus major). Here, we report the draft genome sequence of this
      bacterium, which includes an integrative conjugative element of the SXT/R391
      family, where the macrolide resistance determinants mef(C) and mph(G) exist.
AU  - Sugimoto Y
AU  - Maruyama F
AU  - Suzuki S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00297-18.

PMID- 631561
VI  - 3
DP  - 1978
TI  - Recognition sequence of a restriction endonuclease from Haemophilus gallinarum.
PG  - 17-28
AB  - From a comparison of the sequences in and around the cleavage sites of
      restriction endonuclease HgaI isolated from Haemophilus gallinarum, the
      recognition sequence and cleavage site of this enzyme was deduced as below:
      (5')-----N^pN-N-N-N-N-N-N-N-N-N-G-C-G-T-C-N-----(3')
      (3')-----N-N-N-N-N-Np^N-N-N-N-N-C-G-C-A-G-N-----(5') This enzyme recognizes a
      specific but asymmetric penta-nucleotide sequence, GCGTC, and introduces
      staggered cleavages at appointed positions away from the recognition sequence,
      generating protruding 5'-ends of five nucleotides.  The sequences surrounding
      the cleavage sites bear no obvious relation to one another.
AU  - Sugisaki H
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1978 3: 17-28.

PMID- Not included in PubMed...
VI  - 71
DP  - 1993
TI  - Nucleotide sequence of the gene of HgaI restriction endonuclease.
PG  - 338-342
AB  - 
AU  - Sugisaki H
PT  - Journal Article
TA  - Bull. Inst. Chem. Res. Kyoto Univ.
JT  - Bull. Inst. Chem. Res. Kyoto Univ.
SO  - Bull. Inst. Chem. Res. Kyoto Univ. 1993 71: 338-342.

PMID- 6282705
VI  - 16
DP  - 1981
TI  - New restriction endonucleases from Flavobacterium okeanokoites (FokI) and Micrococcus luteus (MluI).
PG  - 73-78
AB  - Two new restriction endonucleases have been isolated from Flavobacterium
      okeanokoites IFO12536 and Micrococcus luteus IFO12992 and named FokI and MluI,
      respectively.  Based on analysis of the sequences around the restriction sites,
      the recognition sequences and cleavage sites of these endonucleases were
      deduced as below: FokI:	(5')--N-G-G-A-T-G-N-N-N-N-N-N-N-N-N^pN-N-N-N--N--(3')
      	(3')--N-C-C-T-A-C-N-N-N-N-N-N-N-N-N--N-N-N-Np^N--(5') and
      MluI:	(5')--N-A^pC-G-C-G--T-N--(3') 	(3')--N-T  G-C-G-Cp^A-N--(5') 	MluI
      introduces double-strand cleavages at unique sequences that are completely
      two-fold rotationally symmetric like most type II restriction endonucleases.
      FokI belongs to a class of restriction endonucleases that recognize specific
      but asymmetric nucleotide sequences and introduce staggered cleavages at
      appointed positions away from the recognition sequences.
AU  - Sugisaki H
AU  - Kanazawa S
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1981 16: 73-78.

PMID- 2647724
VI  - 264
DP  - 1989
TI  - The FokI restriction-modification system.  II. Presence of two domains in FokI methylase responsible for modification of different DNA strands.
PG  - 5757-5761
AB  - Based on the previous findings that the FokI methylase (MFokI) consists of 647
      amino acid residues and contains two copies of the segment specific for adenine
      methylase, Asp-Pro-Pro-Tyr, at amino acid positions 218-221 and 548-551, the
      role of these copies in the methylation reaction was investigated by
      introduction of a mutation into each segment.  The MFokI gene was inserted into
      M13 vectors, and the Asp residues in the two segments were converted to Gly and
      Ala by oligonucleotide-directed mutagenesis.  The wild-type and mutant genes
      were recloned into an expression vector, from which gene products were
      purified.  A short DNA fragment carrying the FokI recognition site was treated
      with each of these enzymes, and after separation of the two strands by duplex
      formation with M13 viral DNAs carrying the respective strands, the presence or
      absence of modification was judged from susceptibility to FokI endonuclease.
      The results of analysis showed that different strands were modified in an
      asymmetric way by the introduction of mutations into one of the two segments,
      and that the segments at the N-terminal and C-terminal moieties participated in
      modification of the strands carrying 5'-GGATG-3' and 3'-CCTAC-5', respectively.
      We concluded that MFokI contained two functional domains each of which was
      responsible for modification of different strands in the target DNA.
AU  - Sugisaki H
AU  - Kita K
AU  - Takanami M
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1989 264: 5757-5761.

PMID- 6292849
VI  - 10
DP  - 1982
TI  - New restriction endonucleases from Acetobacter aceti and Bacillus aneurinolyticus.
PG  - 5747-5752
AB  - *

      Two restriction endonucleases with new sequence specificities have been

      isolated from Acetobacter aceti IFO 3281 and Bacillus aneurinolyticus IAM 1077

      and named AatII and BanII, respectively.  Based on analysis of the sequences

      around the restriction sites, the recognition sequences and cleavage sites of

      these endonucleases were deduced as below:

      

       AatII:  (5') ---N-G- A-C-G-T^pC-N---  (3')

               (3') ---N-Cp^T-G-C-A- G-N---  (5')

      

       BanII:  (5') --N-G -Pu-G-C-Py^pC-N--  (3')

               (3') --N-Cp^Py-C-G-Pu- G-N--  (5')

      

AU  - Sugisaki H
AU  - Maekawa Y
AU  - Kanazawa S
AU  - Takanami M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1982 10: 5747-5752.

PMID- Not included in PubMed...
VI  - 60
DP  - 1982
TI  - Screening of type II restriction endonucleases.  I.  Isolation and characterization of enzymes from fifteen bacterial strains.
PG  - 328-335
AB  - One hundred and forty-seven bacterial strains were surveyed for the presence of
      type II restriction endonucleases, and eighteen species of enzymes were
      successfully isolated from fifteen strains in which enzyme activities were
      identified.  Based on analysis of the restriction patterns generated from viral
      and plasmid DNAs and of the sequences around the cleavage-sites, four of
      enzymes named AatII, BanII, FokII and MluI were found to have new
      specificities.  The remaining fourteen enzymes, named AatI, AtuIAMI, BanIII,
      BprI, EcoICRI, GglI, GinI, MauI, PaiI, PanI, PflI, PpuI, and SpaI, were
      isoschizomers of known enzymes.
AU  - Sugisaki H
AU  - Maekawa Y
AU  - Kanazawa S
AU  - Takanami M
PT  - Journal Article
TA  - Bull. Inst. Chem. Res. Kyoto Univ.
JT  - Bull. Inst. Chem. Res. Kyoto Univ.
SO  - Bull. Inst. Chem. Res. Kyoto Univ. 1982 60: 328-335.

PMID- 4357389
VI  - 246
DP  - 1973
TI  - DNA Sequence restricted by restriction endonuclease AP from Haemophilus aphirophilus.
PG  - 138-140
AB  - Many bacterial strains contain strain-specific restriction endonucleases which
      degrade foreign DNA at a limited number of sites.  The site-specific action of
      these enzymes is thought to be a consequence of their ability to recognise
      specific nucleotide sequences.  Such sequences restricted by endonuclease R
      (endoR) from Haemophilus influenzae Rd and RI endonuclease (endo RI) from
      Escherichia coli carrying R factor have been determined.  In our laboratory,
      several species of similar enzymes have been isolated from different
      Haemophilus strains.  Different enzymes seem to have different cleavage site
      specificities, since each enzyme produces different sizes of fragments from
      bacteriophage DNA.  We analysed the terminal nucleotide sequences of fragments
      produced from fd RF-I (doubly closed replicative form) DNA and T3 DNA by
      cleavage with one of the Haemophilus enzymes, endonuclease AP (endo AP)
      isolated from H. aphirophilus, and found that this enzyme cleaved DNA at a
      sequence of four nucleotide pairs with a two-fold rotational symmetry.
AU  - Sugisaki H
AU  - Takanami M
PT  - Journal Article
TA  - Nature New Biol.
JT  - Nature New Biol.
SO  - Nature New Biol. 1973 246: 138-140.

PMID- 1856224
VI  - 266
DP  - 1991
TI  - The HgaI restriction-modification system contains two cytosine methylase genes responsible for modification of different DNA strands.
PG  - 13952-13957
AB  - A DNA fragment of about 3.4 kilobase pairs that expressed the HgaI modification activity was
      cloned from the chromosomal DNA of Haemophilus gallinarum, and its nucleotide sequence was
      determined. Two open reading frames (ORF) which could code for structurally similar proteins
      were identified in the upstream and middle regions and a truncated ORF in the downstream
      region in the same orientation. When the respective ORF's were separately cloned, the clones
      carrying the upstream and middle ORF's both expressed the modification activity, indicating
      that the two genes are involved in modification of the HgaI restriction modification system.
      In order to determine the sites of modification precisely, the respective genes were recloned
      into an expression vector, from which gene products were purified. A short DNA fragment
      carrying the HgaI recognition site was treated with each of these enzymes, and after
      separation of the two strands by duplex formation with M13 viral DNAs carrying the respective
      strands, the presence or absence of modification was judged from susceptibility to HgaI
      endonuclease. The results of analysis showed that different strands were modified in an
      asymmetric way by each gene product. Analysis of the species and positions of modified bases
      by the Maxam-Gilbert method further demonstrated that the gene products from the upstream and
      middle ORF's participated in methylation of the inter cytosine residues of the strands
      carrying 3'-CTGCG-5' and 5'-GACGC-3', respectively. We concluded that the HgaI
      modification system consisted of two cytosine methylase genes responsible for modification of
      different strands in the target DNA.
AU  - Sugisaki H
AU  - Yamamoto K
AU  - Takanami M
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1991 266: 13952-13957.

PMID- 29954904
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Two Edwardsiella piscicida Strains, JF1307 and JF1411,  Isolated from Diseased Olive Flounder (Paralichthys olivaceus) Cultured in Japan.
PG  - e00600-18
AB  - Edwardsiella piscicida strains JF1307 and JF1411 were isolated from cultured olive flounder
      that were diagnosed as being infected with edwardsiellosis. The
      draft genome sequences of the two isolates comprise 3,882,000 bp and 3,827,424 bp
      with G+C contents of 59.5% and 59.6%, respectively.
AU  - Sugiura H
AU  - Monno S
AU  - Yamashita H
AU  - Kato Y
AU  - Imajoh M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00600-18.

PMID- 24723714
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Methicillin-Resistant Staphylococcus aureus KT/Y21, a Sequence Type 772 (ST772) Strain Isolated from a Pediatric Blood Sample in Terengganu, Malaysia.
PG  - e00271-14
AB  - Here, we report the draft genome sequence of a methicillin-resistant Staphylococcus aureus
      (MRSA) strain, KT/Y21, isolated from a blood sample of a pediatric patient. This strain
      belongs to sequence type 772 (ST772), harbors the staphylococcal cassette chromosome mec
      element (SCCmec) type V, and is positive for the Panton-Valentine leukocidin (PVL) pathogenic
      determinant.
AU  - Suhaili Z
AU  - Lean SS
AU  - Yahya A
AU  - Mohd DMN
AU  - Ali AM
AU  - Yeo CC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00271-14.

PMID- 24336372
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Streptococcus pneumoniae Strain A026, a Clinical Multidrug-Resistant Isolate Carrying Tn2010.
PG  - e01034-13
AB  - Streptococcus pneumoniae is a primary cause of bacterial infection in humans. Here, we present
      the complete genome sequence of S. pneumoniae strain A026, which
      is a multidrug-resistant strain isolated from cerebrospinal fluid.
AU  - Sui Z
AU  - Zhou W
AU  - Yao K
AU  - Liu L
AU  - Zhang G
AU  - Yang Y
AU  - Feng J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01034-13.

PMID- 18433771
VI  - 378
DP  - 2008
TI  - The recognition domain of the BpuJI restriction endonuclease in complex with cognate DNA at 1.3-A resolution.
PG  - 1084-1093
AB  - Type IIS restriction endonucleases recognize asymmetric DNA sequences and cleave both DNA
      strands at fixed positions downstream of the recognition
      site. The restriction endonuclease BpuJI recognizes the asymmetric
      sequence 5'-CCCGT; however, it cuts at multiple sites in the vicinity of
      the target sequence. BpuJI consists of two physically separate domains,
      with catalytic and dimerization functions in the C-terminal domain and DNA
      recognition functions in the N-terminal domain. Here we report the crystal
      structure of the BpuJI recognition domain bound to cognate DNA at 1.3-A
      resolution. This region folds into two winged-helix subdomains, D1 and D2,
      interspaced by the DL subdomain. The D1 and D2 subdomains of BpuJI share
      structural similarity with the similar subdomains of the FokI DNA-binding
      domain; however, their orientations in protein-DNA complexes are
      different. Recognition of the 5'-CCCGT target sequence is achieved by
      BpuJI through the major groove contacts of amino acid residues located on
      both the helix-turn-helix motifs and the N-terminal arm. The role of these
      interactions in DNA recognition is also corroborated by mutational
      analysis.
AU  - Sukackaite R
AU  - Grazulis S
AU  - Bochtler M
AU  - Siksnys V
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2008 378: 1084-1093.

PMID- 22570415
VI  - 40
DP  - 2012
TI  - The recognition domain of the methyl-specific endonuclease McrBC flips out 5-methylcytosine.
PG  - 7552-7562
AB  - DNA cytosine methylation is a widespread epigenetic mark.  Biological effects of DNA
      methylation are mediated by the proteins that preferentially bind to 5-methylcytosine (5mC) in
      different sequence contexts.  Until now two different structural mechanisms have been
      established for 5mC recognition in eukaryotes; however, it is still unknown how discrimination
      of the 5mC modification is achieved in prokaryotes.  Here we report the crystal structure of
      the N-terminal DNA-binding domain (McrB-N) of the methyl-specific endonuclease McrBC from
      Escherichia coli.  The McrB-N protein shows a novel DNA-binding fold adapted for
      5-mC-recognition.  In the McrB-N structure in complex with methylated DNA, the 5mC base is
      flipped out from the DNA duplex and positioned within a binding pocket.  Base flipping
      elegantly explains why McrBC system restricts only T4-even phages impaired in glycosylation
      [Luria, S.E. and Human, M.L. (1952) A nonhereditary, host-induced variation of bacterial
      viruses.  J. Bacteriol., 64, 557-569]: flipped out 5-hydroxymethylcytosine is accommodated in
      the binding pocket but there is no room for the glycosylated base.  The mechanism for 5mC
      recognition employed by McrB-N is highly reminiscent of that for eukaryotic SRA domains,
      despite the differences in their protein folds.
AU  - Sukackaite R
AU  - Grazulis S
AU  - Tamulaitis G
AU  - Siksnys V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: 7552-7562.

PMID- 17392342
VI  - 35
DP  - 2007
TI  - Restriction endonuclease BpuJI specific for the 5'-CCCGT sequence is related to the archaeal Holliday junction resolvase family.
PG  - 2377-2389
AB  - Type IIS restriction endonucleases (REases) recognize asymmetric DNA sequences and cleave both
      DNA strands at fixed positions downstream of the
      recognition site. REase BpuJI recognizes the asymmetric sequence 5'-CCCGT,
      however it cuts at multiple sites in the vicinity of the target sequence.
      We show that BpuJI is a dimer, which has two DNA binding surfaces and
      displays optimal catalytic activity when bound to two recognition sites.
      BpuJI is cleaved by chymotrypsin into an N-terminal domain (NTD), which
      lacks catalytic activity but binds specifically to the recognition
      sequence as a monomer, and a C-terminal domain (CTD), which forms a dimer
      with non-specific nuclease activity. Fold recognition approach reveals
      that the CTD of BpuJI is structurally related to archaeal Holliday
      junction resolvases (AHJR). We demonstrate that the isolated catalytic CTD
      of BpuJI possesses end-directed nuclease activity and preferentially cuts
      3 nt from the 3'-terminus of blunt-ended DNA. The nuclease activity of the
      CTD is repressed in the apo-enzyme and becomes activated upon specific DNA
      binding by the NTDs. This leads to a complicated pattern of specific DNA
      cleavage in the vicinity of the target site. Bioinformatics analysis
      identifies the AHJR-like domain in the putative Type III enzymes and
      functionally uncharacterized proteins.
AU  - Sukackaite R
AU  - Lagunavicius A
AU  - Stankevicius K
AU  - Urbanke C
AU  - Venclovas C
AU  - Siksnys V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2007 35: 2377-2389.

PMID- 25593252
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Cyanobacterium Aphanizomenon flos-aquae Strain 2012/KM1/D3, Isolated from the Curonian Lagoon (Baltic Sea).
PG  - e01392-14
AB  - We report here the de novo genome assembly of a cyanobacterium, Aphanizomenon flos-aquae
      strain 2012/KM1/D3, a harmful bloom-forming species in temperate
      aquatic ecosystems. The genome is 5.7 Mb with a G+C content of 38.2%, and it is
      enriched mostly with genes involved in amino acid and carbohydrate metabolism.
AU  - Sulcius S
AU  - Alzbutas G
AU  - Kvederaviciute K
AU  - Koreiviene J
AU  - Zakrys L
AU  - Lubys A
AU  - Paskauskas R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01392-14.

PMID- 26566420
VI  - 10
DP  - 2015
TI  - High-quality draft genome sequence of a new phytase-producing microorganism Pantoea sp. 3.5.1.
PG  - 95
AB  - Strain 3.5.1 was isolated from soils of the Republic of Tatarstan, Russia, on the basis of
      presence of a high phytate-degrading activity. Strains with such
      activities attract special interest because of its potential use as feed
      additives and natural manures. Strain 3.5.1 harbors a 99 % 16S rRNA nucleotide
      sequence similarity to different Pantoea species (P. vagans, P. ananatis, P.
      agglomerans, P. anthophila and Pantoea sp.) and exhibits unique biochemical
      properties that do not allow strain identification up to species. Moreover, the
      strain 3.5.1 shows a low ANI and MALDI-TOF Mass Spectrometry scores. Thus, it is
      likely that the strain 3.5.1 represents a new Pantoea species. Here, we present
      the genome sequence of Pantoea sp. strain 3.5.1. The 4,964,649 bp draft genome
      consists of 23 contigs with 4,556 protein-coding and 143 RNA genes. Genome
      sequencing and annotation revealed two phytase genes and putative regulatory
      genes controlling its activity.
AU  - Suleimanova AD
AU  - Toymentseva AA
AU  - Boulygina EA
AU  - Kazakov SV
AU  - Mardanova AM
AU  - Balaban NP
AU  - Sharipova MR
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 95.

PMID- 12003951
VI  - 184
DP  - 2002
TI  - Comparative sequence analysis of the symbiosis island of Mesorhizobium loti strain R7A.
PG  - 3086-3095
AB  - The Mesorhizobium loti strain R7A symbiosis island is a 502-kb
      chromosomally integrated element which transfers to nonsymbiotic
      mesorhizobia in the environment, converting them to Lotus symbionts. It
      integrates into a phenylalanine tRNA gene in a process mediated by a
      P4-type integrase encoded at the left end of the element. We have
      determined the nucleotide sequence of the island and compared its deduced
      genetic complement with that reported for the 611-kb putative symbiosis
      island of M. loti strain MAFF303099. The two islands share 248 kb of DNA,
      with multiple deletions and insertions of up to 168 kb interrupting highly
      conserved colinear DNA regions in the two strains. The shared DNA regions
      contain all the genes likely to be required for Nod factor synthesis,
      nitrogen fixation, and island transfer. Transfer genes include a trb
      operon and a cluster of potential tra genes which are also present on the
      strain MAFF303099 plasmid pMLb. The island lacks plasmid replication
      genes, suggesting that it is a site-specific conjugative transposon. The
      R7A island encodes a type IV secretion system with strong similarity to
      the vir pilus from Agrobacterium tumefaciens that is deleted from
      MAFF303099, which in turn encodes a type III secretion system not found on
      the R7A island. The 414 genes on the R7A island also include putative
      regulatory genes, transport genes, and an array of metabolic genes. Most
      of the unique hypothetical genes on the R7A island are strain-specific and
      clustered, suggesting that they may represent other acquired genetic
      elements rather than symbiotically relevant DNA.
AU  - Sullivan JT
AU  - Trzebiatowski JR
AU  - Cruickshank RW
AU  - Gouzy J
AU  - Brown SD
AU  - Elliot RM
AU  - Fleetwood DJ
AU  - McCallum NG
AU  - Rossbach U
AU  - Stuart GS
AU  - Weaver JE
AU  - Webby RJ
AU  - de Bruijn FJ
AU  - Ronson CW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2002 184: 3086-3095.

PMID- Not included in PubMed...
VI  - 44
DP  - 1987
TI  - Characterization of DNA restriction and modification activities in Neisseria species.
PG  - 389-393
AB  - Type II restriction endonuclease activities detected in various Neisseria
      species were characterized for sequence specificity and precise site of
      cleavage.  NsiCI isolated from N. sicca C351 cleaves the sequence 5'-GAT^ATC-3'
      (EcoRV isoschizomer); NmeCI from N. meningitidis C114 and NphI from N.
      pharyngis C245 cleave 5'-N^GATCN-3' (MboI isoschizomers); NgoPII and NgoPIII
      from N. gonorrhoeae P9-2 cleave at 5'-GG^CC-3' (HaeIII isoschizomer) and
      5'-CC^GCGG-3' (SacII isoschizomer), respectively.  Chromosomal DNA isolated
      from these strains and two other N. meningitidis strains (which lacked
      detectable endonuclease activities), was found to be refractive to cleavage by
      various restriction enzymes, implying the presence of methylase activities
      additional to those required for protection against the cellular endonucleases.
      [Note .. the printed abstract was wrong and is corrected here]
AU  - Sullivan KM
AU  - Macdonald HJ
AU  - Saunders JR
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1987 44: 389-393.

PMID- 
VI  - 0
DP  - 1988
TI  - Determination of the endonuclease and methylase content of Neisseria gonorrhoeae strain P9 and the cloning therefrom of two functional methylase genes.
PG  - 329-334
AB  - Neisseria gonorrhoeae strain P9 possesses five DNA cytosine methyltransferases designated
      M.NgoPI (M.HaeII isoschizomer), M.NgoPII (M.HaeIII), M.NgoPIII (M.SacII), M.NgoPIV (M.NaeI)
      and M.NgoPV.  Two corresponding endonuclease activities, NgoPII (GGCC) and NgoPIII (CCGCGG)
      were also detected.  Recombinant plasmids harbouring functional M.NgoPI (PuGCGCPy) and
      M.NgoPII methyltransferases were isolated by restriction of an amplified gene library with the
      appropriate endonuclease.  After transformation of E. coli RR1, plasmid DNA from individual
      transformants was analysed for protection against HaeII or HaeIII respectively to obtain
      clones carrying the methylase genes.  It was noted that certain E. coli strains, notably DH1
      could not be transformed by plasmids containing the functional M.NgoPI or M.NgoPII genes.
AU  - Sullivan KM
AU  - Saunders JR
PT  - Journal Article
TA  - Gonococci and Meningococci
JT  - Gonococci and Meningococci
SO  - Gonococci and Meningococci 1988 0: 329-334.

PMID- 2837733
VI  - 16
DP  - 1988
TI  - Sequence analysis of the NgoPII methyltransferase gene from Neisseria gonorrhoeae P9:  homologies with other enzymes recognizing the sequence 5'-GGCC-3'.
PG  - 4369-4387
AB  - Recombinant plasmids harbouring the functional M.NgoPII methyltransferase (specificity
      5'-GGCC-3') were isolated from amplified gene libraries of gonococcal chromosomal DNA cloned
      in pBR322 and in Escherichia coli RR1.  The M.NgoPII gene was localized by sub-cloning and the
      nucleotide sequence of a cloned 1.6 kb segment of Neisseria gonorrhoeae DNA harbouring the
      methylase gene was determined.  This data, coupled with sub-cloning experiments and in vitro
      transcription-translation studies, indicates a theoretical size of 38.5 kd for the methylase
      protein.  The predicted amino acid sequence of the methylase contains significant regions of
      homology with the projected sequences of other cytosine-modifying methylases, upon which the
      activity of these enzymes is likely to depend.
AU  - Sullivan KM
AU  - Saunders JR
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1988 16: 4369-4387.

PMID- 2501649
VI  - 216
DP  - 1989
TI  - Nucleotide sequence and genetic organization of the NgoPII restriction-modification system of Neisseria gonorrhoeae.
PG  - 380-387
AB  - The NgoPII restriction endonuclease, which recognizes the sequences 5'-GG^CC-3', differs
      from its isoschizomer HaeIII in being sensitive to methylation at the external cytosine
      residue.  The entire nucleotide sequence of a cloned 3.3 kb segment of Neisseria gonorrhoeae
      strain P9 chromosomal DNA which harbours the NgoPII restriction-modification system has been
      determined. This data, coupled with sub-cloning experiments, indicates that the restriction
      endonuclease (R.NgoPII) and modification (M.NgoPII) genes are transcribed from separate
      promoters but are arranged in tandem, with the R.NgoPII gene being located on the 5' side of
      the M.NgoPII gene.  Unlike all previously reported restriction systems the 3' end of the
      endonuclease open reading frame overlaps the 5' end of the methylase open reading frame by 8
      codons.  This overlap may have implications for the regulation of the NgoPII
      restriction-modification system.
AU  - Sullivan KM
AU  - Saunders JR
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1989 216: 380-387.

PMID- 20662890
VI  - 12
DP  - 2010
TI  - Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments.
PG  - 3035-3056
AB  - T4-like myoviruses are ubiquitous, and their genes are among the most
      abundant documented in ocean systems. Here we compare 26 T4-like genomes,
      including 10 from non-cyanobacterial myoviruses, and 16 from marine
      cyanobacterial myoviruses (cyanophages) isolated on diverse
      Prochlorococcus or Synechococcus hosts. A core genome of 38 virion
      construction and DNA replication genes was observed in all 26 genomes,
      with 32 and 25 additional genes shared among the non-cyanophage and
      cyanophage subsets, respectively. These hierarchical cores are highly
      syntenic across the genomes, and sampled to saturation. The 25 cyanophage
      core genes include six previously described genes with putative functions
      (psbA, mazG, phoH, hsp20, hli03, cobS), a hypothetical protein with a
      potential phytanoyl-CoA dioxygenase domain, two virion structural genes,
      and 16 hypothetical genes. Beyond previously described cyanophage-encoded
      photosynthesis and phosphate stress genes, we observed core genes that may
      play a role in nitrogen metabolism during infection through modulation of
      2-oxoglutarate. Patterns among non-core genes that may drive niche
      diversification revealed that phosphorus-related gene content reflects
      source waters rather than host strain used for isolation, and that carbon
      metabolism genes appear associated with putative mobile elements. As well,
      phages isolated on Synechococcus had higher genome-wide %G+C and often
      contained different gene subsets (e.g. petE, zwf, gnd, prnA, cpeT) than
      those isolated on Prochlorococcus. However, no clear diagnostic genes
      emerged to distinguish these phage groups, suggesting blurred boundaries
      possibly due to cross-infection. Finally, genome-wide comparisons of both
      diverse and closely related, co-isolated genomes provide a locus-to-locus
      variability metric that will prove valuable for interpreting metagenomic
      data sets.
AU  - Sullivan MB et al
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2010 12: 3035-3056.

PMID- 15828858
VI  - 3
DP  - 2005
TI  - Three prochlorococcus cyanophage genomes: signature features and ecological interpretations.
PG  - E144
AB  - The oceanic cyanobacteria Prochlorococcus are globally important,
      ecologically diverse primary producers. It is thought that their viruses
      (phages) mediate population sizes and affect the evolutionary trajectories
      of their hosts. Here we present an analysis of genomes from three
      Prochlorococcus phages: a podovirus and two myoviruses. The morphology,
      overall genome features, and gene content of these phages suggest that
      they are quite similar to T7-like (P-SSP7) and T4-like (P-SSM2 and P-SSM4)
      phages. Using the existing phage taxonomic framework as a guideline, we
      examined genome sequences to establish "core" genes for each phage group.
      We found the podovirus contained 15 of 26 core T7-like genes and the two
      myoviruses contained 43 and 42 of 75 core T4-like genes. In addition to
      these core genes, each genome contains a significant number of
      "cyanobacterial" genes, i.e., genes with significant best BLAST hits to
      genes found in cyanobacteria. Some of these, we speculate, represent
      "signature" cyanophage genes. For example, all three phage genomes contain
      photosynthetic genes (psbA, hliP) that are thought to help maintain host
      photosynthetic activity during infection, as well as an aldolase family
      gene (talC) that could facilitate alternative routes of carbon metabolism
      during infection. The podovirus genome also contains an integrase gene
      (int) and other features that suggest it is capable of integrating into
      its host. If indeed it is, this would be unprecedented among cultured
      T7-like phages or marine cyanophages and would have significant
      evolutionary and ecological implications for phage and host. Further, both
      myoviruses contain phosphate-inducible genes (phoH and pstS) that are
      likely to be important for phage and host responses to phosphate stress, a
      commonly limiting nutrient in marine systems. Thus, these marine
      cyanophages appear to be variations of two well-known phages-T7 and T4-but
      contain genes that, if functional, reflect adaptations for infection of
      photosynthetic hosts in low-nutrient oceanic environments.
AU  - Sullivan MB
AU  - Coleman ML
AU  - Weigele P
AU  - Rohwer F
AU  - Chisholm SW
PT  - Journal Article
TA  - PLoS Biology
JT  - PLoS Biology
SO  - PLoS Biology 2005 3: E144.

PMID- 29051249
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Serotype III Streptococcus agalactiae Sequence Type 17 Strain 874391.
PG  - e01107-17
AB  - Here we report the complete genome sequence of Streptococcus agalactiae strain 874391. This
      serotype III isolate is a member of the hypervirulent sequence type
      17 (ST-17) lineage that causes a disproportionate number of cases of invasive
      disease in humans and mammals. A brief historical context of the strain is
      discussed.
AU  - Sullivan MJ
AU  - Forde BM
AU  - Prince DW
AU  - Ipe DS
AU  - Ben Zakour NL
AU  - Davies MR
AU  - Dougan G
AU  - Beatson SA
AU  - Ulett GC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01107-17.

PMID- 24009111
VI  - 1
DP  - 2013
TI  - The Complete Genome Sequence of Proteus mirabilis Strain BB2000 Reveals Differences from the P. mirabilis Reference Strain.
PG  - e00024-13
AB  - We announce the complete genome sequence for Proteus mirabilis strain BB2000, a model system
      for self recognition. This opportunistic pathogen contains a single,
      circular chromosome (3,846,754 bp). Comparisons between this genome and that of
      strain HI4320 reveal genetic variations corresponding to previously unknown
      physiological and self-recognition differences.
AU  - Sullivan NL
AU  - Septer AN
AU  - Fields AT
AU  - Wenren LM
AU  - Gibbs KA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00024-13.

PMID- Not carried by PubMed...
VI  - 15
DP  - 1995
TI  - Super restriction enzymes for future biotechnology.
PG  - 19-25
AB  - 
AU  - Sumaoka J
AU  - Komiyama M
PT  - Journal Article
TA  - Kino Zairyo
JT  - Kino Zairyo
SO  - Kino Zairyo 1995 15: 19-25.

PMID- 16088826
VI  - 192
DP  - 2005
TI  - Evolutionary origin and emergence of a highly successful clone of serotype M1 group A Streptococcus involved multiple horizontal gene transfer   events.
PG  - 771-782
AB  - To better understand the molecular events involved in the origin of new pathogenic bacteria,
      we studied the evolution of a highly virulent clone
      of serotype M1 group A Streptococcus (GAS). Genomic, DNA-DNA microarray,
      and single-nucleotide polymorphism analyses indicated that this clone
      evolved through a series of horizontal gene transfer events that involved
      (1) the acquisition of prophages encoding streptococcal pyrogenic exotoxin
      A and extracellular DNases and (2) the reciprocal recombination of a 36-kb
      chromosomal region encoding the extracellular toxins NAD(+)-glycohydrolase
      (NADase) and streptolysin O (SLO). These gene transfer events were
      associated with significantly increased production of SLO and NADase.
      Virtual identity in the 36-kb region present in contemporary serotype M1
      and M12 isolates suggests that a serotype M12 strain served as the donor
      of this region. Multiple horizontal gene transfer events were a crucial
      factor in the evolutionary origin and emergence of a very abundant
      contemporary clone of serotype M1 GAS.
AU  - Sumby P
AU  - Porcella SF
AU  - Madrigal AG
AU  - Barbian KD
AU  - Virtaneva K
AU  - Ricklefs SM
AU  - Sturdevant DE
AU  - Graham MR
AU  - Vuopio-Varkila J
AU  - Hoe NP
AU  - Musser JM
PT  - Journal Article
TA  - J. Infect. Dis.
JT  - J. Infect. Dis.
SO  - J. Infect. Dis. 2005 192: 771-782.

PMID- 12867465
VI  - 185
DP  - 2003
TI  - Phase variation in the phage growth limitation system of Streptomyces coelicolor  A3(2).
PG  - 4558-4563
AB  - The phase-variable phage growth limitation (Pgl) system of Streptomyces coelicolor A3(2) is an
      unusual bacteriophage resistance mechanism that confers
      protection against the temperate phage phiC31 and homoimmune relatives. Pgl is
      subject to phase variation, and data presented here show that this is at least
      partially due to expansion and contraction of a polyguanine tract present within
      the putative adenine-specific DNA methyltransferase gene, pglX. Furthermore, the
      pglX paralogue SC6G9.02, here renamed pglS, was shown to be able to interfere
      with the Pgl phenotype, suggesting that PglS could provide an alternative
      activity to that conferred by PglX.
AU  - Sumby P
AU  - Smith MC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2003 185: 4558-4563.

PMID- 11972785
VI  - 44
DP  - 2002
TI  - Genetics of the phage growth limitation (Pgl) system of Streptomyces coelicolor A3(2).
PG  - 489-500
AB  - The phage growth limitation (Pgl) system, encoded by Streptomyces coelicolor A3(2), confers
      protection against the temperate bacteriophage
      phiC31 and its homoimmune relatives. The Pgl phenotype is characterized by
      the ability of Pgl+ hosts to support a phage burst on initial infection
      but subsequent cycles are severely attenuated. Previously, two adjacent
      genes pglY and pglZ were shown to be required for Pgl. It had been shown
      by Southern blotting that Streptomyces lividans, a close relative of S.
      coelicolor and naturally Pgl-, does not contain homologues of pglYZ and
      that introduction of pglYZ into S. lividans is not sufficient to confer a
      Pgl+ phenotype. Moreover, the mechanism of the Pgl+<--> Pgl- phase
      variation associated with this phenotype is also not understood. Here we
      describe two novel genes, pglW and pglX, that were shown to be part of
      this system by complementation of Pgl- mutants and by insertional
      mutagenesis. pglW encodes a 169 kDa protein that includes putative motifs
      for both serine/threonine protein kinase activity and DNA binding. pglX
      encodes a 136 kDa protein with putative adenine-specific DNA
      methyltransferase activity. pglW and pglX have overlapping stop-start
      codons suggesting transcriptional and translational coupling. S1 mapping
      of transcripts initiating up-stream of pglW indicated that, like pglYZ,
      pglWX is expressed in uninfected cultures. A homologue of pglX with 76%
      amino acid identity was identified in S. coelicolor, and insertional
      mutagenesis indicated that this gene was not required for the Pgl+
      phenotype. Southern blots indicated that S. lividans does not contain
      homologues of pglW or pglX. A plasmid encoding pglWXYZ was able to confer
      the Pgl+ phenotype to S. lividans implying that these four genes
      constitute the whole system.
AU  - Sumby P
AU  - Smith MC
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2002 44: 489-500.

PMID- 194592
VI  - 1
DP  - 1977
TI  - A rapid procedure for purification of EcoRI endonuclease.
PG  - 78-85
AB  - A convenient and rapid procedure has been developed to purify restriction
      endonuclease EcoRI.  The method involves sonication of cells at low ionic
      strength, precipitation of the endonuclease with Polymin P (a
      polyethyleneimine), elution of the enzyme from the Polymin P precipitate,
      ammonium sulfate precipitation and chromatography on phosphocellulose.  The
      purified restriction endonuclease is free of exonuclease and other
      endonucleases.
AU  - Sumegi J
AU  - Breedveld D
AU  - Hosenlopp P
AU  - Chambon P
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1977 1: 78-85.

PMID- 16352842
VI  - 188
DP  - 2006
TI  - Divergence and mosaicism among virulent soil phages of the Burkholderia cepacia complex.
PG  - 255-268
AB  - We have determined the genomic sequences of four virulent myophages, Bcep1, Bcep43, BcepB1A,
      and Bcep781, whose hosts are soil isolates of the
      Burkholderia cepacia complex. Despite temporal and spatial separations
      between initial isolations, three of the phages (Bcep1, Bcep43, and
      Bcep781, designated the Bcep781 group) exhibit 87% to 99% sequence
      identity to one another and most coding region differences are due to
      synonymous nucleotide substitutions, a hallmark of neutral genetic drift.
      Phage BcepB1A has a very different genome organization but is clearly a
      mosaic with respect to many of the genes of the Bcep781 group, as is a
      defective prophage element in Photorhabdus luminescens. Functions were
      assigned to 27 out of 71 predicted genes of Bcep1 despite extreme sequence
      divergence. Using a lambda repressor fusion technique, 10 Bcep781-encoded
      proteins were identified for their ability to support homotypic
      interactions. While head and tail morphogenesis genes have retained
      canonical gene order despite extreme sequence divergence, genes involved
      in DNA metabolism and host lysis are not organized as in other phages.
      This unusual genome arrangement may contribute to the ability of the
      Bcep781-like phages to maintain a unified genomic type. However, the
      Bcep781 group phages can also engage in lateral gene transfer events with
      otherwise unrelated phages, a process that contributes to the
      broader-scale genomic mosaicism prevalent among the tailed phages.
AU  - Summer EJ
AU  - Gonzalez CF
AU  - Bomer M
AU  - Carlile T
AU  - Embry A
AU  - Kucherka AM
AU  - Lee J
AU  - Mebane L
AU  - Morrison WC
AU  - Mark L
AU  - King MD
AU  - LiPuma JJ
AU  - Vidaver AK
AU  - Young R
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2006 188: 255-268.

PMID- 3763408
VI  - 14
DP  - 1986
TI  - Alkyl phosphotriester modified oligodeoxyribonucleotides.  VI. NMR and UV spectroscopic studies of ethyl phosphotriester (Et) modified Rp-Rp and Sp-Sp duplexes, {d[GGAA(Et)TTCC]}2.
PG  - 7421-7436
AB  - 1H NMR chemical shift assignments for the title compounds were made for all but
      a few H5' and H5" signals using two-dimensional nuclear Overhauser effect
      (2D-NOE) data, which was also used for the first time to assign absolute
      configuration at phosphorus.  The chemical shifts were, in general, similar to
      those reported [Broido, M.S., et al. (1985) Eur. J. Biochem. 150, 117-128] for
      the B-like conformation of the unmodified, parent duplex, {d(GGAATTCC)]2.
      Differences in chemical shifts for corresponding protons were mostly localized
      to the AA(Et)TT region, and showed some stereochemical dependence.  Unambiguous
      assignment of the phosphotriester 31P signals was achieved in a novel way using
      selective insensitive nucleus enhancement by polarization transfer (selective
      INEPT) NMR.  The Rp-Rp duplex melted ca. 11C lower than either the Sp-Sp or
      parent duplexes, as evidenced by Tm and variable temperature 1H/31P NMR
      measurements.  The 2D-NOE data for the Rp-Rp duplex suggested possible steric
      interactions between the ethyl group and the H3' of the flanking A residue.  At
      low ionic strength, the Sp-Sp and parent duplexes had similar stability but at
      high ionic strength the Sp-Sp duplex was less stable.
AU  - Summers MF
AU  - Powell C
AU  - Egan W
AU  - Byrd RA
AU  - Wilson WD
AU  - Zon G
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1986 14: 7421-7436.

PMID- 27034489
VI  - 4
DP  - 2016
TI  - Genome Sequences of Five Nonvirulent Listeria monocytogenes Serovar 4 Strains.
PG  - e00179-16
AB  - We present the complete genome sequences of five nonpathogenicListeria monocytogenesserovar 4
      strains: WSLC 1018 (4e), 1019 (4c), 1020 (4a), 1033 (4d),
      and 1047 (4d). These sequences may help to uncover genes involved in the
      synthesis of the serovar antigens-phenotypic determinants of virulence deemed
      clinically relevant.
AU  - Sumrall E
AU  - Klumpp J
AU  - Shen Y
AU  - Loessner MJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00179-16.

PMID- 27257213
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Geobacter anodireducens SD-1T, a Salt-Tolerant Exoelectrogenic Microbe in Bioelectrochemical Systems.
PG  - e00415-16
AB  - Strain SD-1 is the type strain of the species Geobacter anodireducens, which was  originally
      isolated from a microbial fuel cell reactor in the United States. The
      characteristic of this bacterium is its high electrochemical activity. Here, we
      report the fully assembled genome and plasmid sequence of G. anodireducens
      SD-1(T).
AU  - Sun D
AU  - Cheng S
AU  - Wang A
AU  - Huang F
AU  - Liu W
AU  - Xia X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00415-16.

PMID- 
VI  - 114
DP  - 2017
TI  - Identification of a Pseudomonas putida as biocontrol agent for tomato bacterial wilt disease.
PG  - 45-50
AB  - A bacterial isolate, A1, was collected from the rhizosphere soil of cultivated peanuts. Based
      on its 16 S rRNA sequence, this isolate was identified as a Pseudomonas putida strain. On
      minimal medium supplemented with
      diverse nutrient substrates, the P. putida A1 strain could use fructose and fructosan,
      trehalose, and inositol as sole carbon resources. The ability of these four carbon resources,
      as well as leaf and root exudates, to stimulate cell migration in a chemotaxis assay was
      investigated. P. putida A1 was labelled with GFP to study colonization on the root surface;
      this strain was found to aggregate around wound sites. In addition to forming biofilms in
      vitro, A1 showed antimicrobial activity against several plant pathogenic bacteria, including
      Ralstonia solanacearum, Xanthomonas oryzae pv. oryzae, X. o. pv. oryzicola, and X. citri
      subsp. citri. In evaluations of biocontrol potential of tomato bacterial wilt, this isolate
      delayed the appearance of wilt symptoms for 4 days and reduced wilt disease severity. Overall,
      our results indicate that P. putida A1 could be an effective biocontrol agent for plant
      soil-borne diseases.
AU  - Sun D
AU  - Zhuo T
AU  - Hu X
AU  - Fan X
AU  - Zou H
PT  - Journal Article
TA  - Biol. Control
JT  - Biol. Control
SO  - Biol. Control 2017 114: 45-50.

PMID- Not carried by PubMed...
VI  - 21
DP  - 1988
TI  - Purification and characterization of a restriction endonuclease ZanI from Zymomonas anaerobia.
PG  - 419-422
AB  - We described the purification and characterization of a sequence restriction endonuclease,
      ZanI, found from Zymomonas anaerobia (NCI B8227). The purified enzyme is essentially
      homogeneous and the subunit molecular weight is 30,000+/- 1,000 as judged by 10%
      polyacrylamide gel electrophoresis containing 0.1% SDS. The recognition sequence and the
      cleavage site (indicated by the arrow) were determined to be 5'-CC^(AT) GG-3', the same
      sequence as recognized by BstNI and EcoRII. ZanI endonuclease is able to cleave dcm-methylated
      DNA and is maximally active at 37C.
AU  - Sun DK
AU  - Yoo OJ
PT  - Journal Article
TA  - Korean Biochem. J.
JT  - Korean Biochem. J.
SO  - Korean Biochem. J. 1988 21: 419-422.

PMID- 27658354
VI  - 6
DP  - 2016
TI  - Genetic characterization of two fully sequenced multi-drug resistant plasmids pP10164-2 and pP10164-3 from Leclercia adecarboxylata.
PG  - 33982
AB  - We previously reported the complete sequence of the resistance plasmid
      pP10164-NDM, harboring blaNDM (conferring carbapenem resistance) and bleMBL
      (conferring bleomycin resistance), which is recovered from a clinical Leclercia
      adecarboxylata isolate P10164 from China. This follow-up work disclosed that
      there were still two multidrug-resistant (MDR) plasmids pP10164-2 and pP10164-3
      coexisting in this strain. pP10164-2 and pP10164-3 were completely sequenced and
      shown to carry a wealth of resistance genes, which encoded the resistance to at
      least 10 classes of antibiotics (beta-lactams. macrolides, quinolones,
      aminoglycosides, tetracyclines, amphenicols, quaternary ammonium compounds,
      sulphonamides, trimethoprim, and rifampicin) and 7 kinds of heavy mental
      (mercury, silver, copper, nickel, chromate, arsenic, and tellurium). All of these
      antibiotic resistance genes are associated with mobile elements such as
      transposons, integrons, and insertion sequence-based transposable units,
      constituting a total of three novel MDR regions, two in pP10164-2 and the other
      one in pP10164-3. Coexistence of three resistance plasmids pP10164-NDM, pP10164-2
      and pP10164-3 makes L. adecarboxylata P10164 tend to become extensively
      drug-resistant.
AU  - Sun F
AU  - Zhou D
AU  - Sun Q
AU  - Luo W
AU  - Tong Y
AU  - Zhang D
AU  - Wang Q
AU  - Feng W
AU  - Chen W
AU  - Fan Y
AU  - Xia P
PT  - Journal Article
TA  - Sci. Rep.
JT  - Sci. Rep.
SO  - Sci. Rep. 2016 6: 33982.

PMID- 26679251
VI  - 71
DP  - 2016
TI  - Genetic characterization of a novel blaDIM-2-carrying megaplasmid p12969-DIM from clinical Pseudomonas putida.
PG  - 909-912
AB  - OBJECTIVES: To characterize a blaDIM-2-carrying 409 kb megaplasmid p12969-DIM of
      Pseudomonas putida 12969 from a patient with pneumonia in China. METHODS: The
      complete nucleotide sequence of p12969-DIM was determined with a paired-end
      library and a mate-pair library using next-generation sequencing technology.
      RESULTS: blaDIM-2, a close blaDIM-1 variant, was identified in p12969-DIM. DIM-2
      differs from DIM-1 by two amino acid substitutions Ser119Leu and Ser209Pro. The
      p12969-DIM backbone is highly similar to pOZ176, but the IncP-2-type
      stability/replication/conjugal transfer system in the pOZ176 backbone is absent
      from p12969-DIM. The p12969-DIM accessory regions, a 45.7 kb MDR and a novel
      insertion sequence, ISPpu23, are almost entirely distinct from pOZ176. The MDR
      region contains a novel Tn21-subgroup transposon Tn6286 inserted with two class 1
      integrons, In1225 and In1226; a Tn5503-family transposon-like element inserted
      with a strAB locus; and a novel Tn21-subgroup transposon-like element inserted
      with a class 1 integron, In1224. The three integrons carry blaDIM-2 as well as a
      number of additional genes conferring resistance to quinolones, aminoglycosides,
      chloramphenicol, florfenicol, trimethoprim, streptomycin, quaternary ammonium
      compounds and sulphonamides. p12969-DIM has two distinct replication/stability
      systems, repA/parAB-parB2 of an unknown incompatibility group in the backbone and
      repABC/mazFE of the IncQ2 group in the MDR region. CONCLUSIONS: The MDR region of
      p12969-DIM harbours many resistance genes as well as a second
      replication/stability system. This article is the first report of a fully
      sequenced blaDIM-carrying plasmid.
AU  - Sun F
AU  - Zhou D
AU  - Wang Q
AU  - Feng J
AU  - Feng W
AU  - Luo W
AU  - Liu Y
AU  - Qiu X
AU  - Yin Z
AU  - Xia P
PT  - Journal Article
TA  - J. Antimicrob. Chemother.
JT  - J. Antimicrob. Chemother.
SO  - J. Antimicrob. Chemother. 2016 71: 909-912.

PMID- 26112786
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Elizabethkingia meningoseptica, Isolated from a T-Cell Non-Hodgkin's Lymphoma Patient.
PG  - e00673-15
AB  - An Elizabethkingia meningoseptica infection was detected at the end stage of a patient with
      T-cell non-Hodgkin's lymphoma. The complete genome of this isolated
      strain, FMS-007, was generated in one contig with a total size of 3,938,967 bp. A
      preliminary screening indicated that the genome contains drug resistance genes to
      aminoglycosides and beta-lactams. A clustered regularly interspaced short
      palindromic repeats (CRISPR)/CRISPR-associated proteins (CRISPR/Cas) system with
      16 direct repeats and 15 spacers was identified.
AU  - Sun G
AU  - Wang L
AU  - Bao C
AU  - Li T
AU  - Ma L
AU  - Chen L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00673-15.

PMID- 21304732
VI  - 3
DP  - 2010
TI  - Complete genome sequence of Desulfarculus baarsii type strain (2st14).
PG  - 276-284
AB  - Desulfarculus baarsii (Widdel 1981) Kuever et al. 2006 is the type and only species of the
      genus Desulfarculus, which represents the family Desulfarculaceae
      and the order Desulfarculales. This species is a mesophilic sulfate-reducing
      bacterium with the capability to oxidize acetate and fatty acids of up to 18
      carbon atoms completely to CO(2). The acetyl-CoA/CODH (Wood-Ljungdahl) pathway is
      used by this species for the complete oxidation of carbon sources and autotrophic
      growth on formate. The type strain 2st14(T) was isolated from a ditch sediment
      collected near the University of Konstanz, Germany. This is the first completed
      genome sequence of a member of the order Desulfarculales. The 3,655,731 bp long
      single replicon genome with its 3,303 protein-coding and 52 RNA genes is a part
      of the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Sun H et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 3: 276-284.

PMID- 21304737
VI  - 3
DP  - 2010
TI  - Complete genome sequence of Nocardiopsis dassonvillei type strain (IMRU 509).
PG  - 325-336
AB  - Nocardiopsis dassonvillei (Brocq-Rousseau 1904) Meyer 1976 is the type species of the genus
      Nocardiopsis, which in turn is the type genus of the family
      Nocardiopsaceae. This species is of interest because of its ecological
      versatility. Members of N. dassonvillei have been isolated from a large variety
      of natural habitats such as soil and marine sediments, from different plant and
      animal materials as well as from human patients. Moreover, representatives of the
      genus Nocardiopsis participate actively in biopolymer degradation. This is the
      first complete genome sequence in the family Nocardiopsaceae. Here we describe
      the features of this organism, together with the complete genome sequence and
      annotation. The 6,543,312 bp long genome consist of a 5.77 Mbp chromosome and a
      0.78 Mbp plasmid and with its 5,570 protein-coding and 77 RNA genes is a part of
      the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Sun H et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 3: 325-336.

PMID- 
VI  - 116
DP  - 1998
TI  - Molecular cloning of the PsaA and PsaB genes for the core proteins of photosystem I from the thermophilic cyanobacterium Mastigocladus Iaminosus (Accession No. AF038558).
PG  - 1192
AB  - 
AU  - Sun J
AU  - He Z
AU  - Nechushtai R
AU  - Chitnis PR
PT  - Journal Article
TA  - Plant Physiol.
JT  - Plant Physiol.
SO  - Plant Physiol. 1998 116: 1192.

PMID- 
VI  - 82
DP  - 2002
TI  - The restriction enzyme BamHI is poised for sliding along DNA in a model of the nonspecific complex.
PG  - 463a
AB  - The mechanism by which DNA-binding proteins find their specific binding sites is unclear.  To
      understand how the protein reaches its cognate site within a long piece of DNA, the crystal
      structures of the nonspecific and the specific BamHI-DNA complexes were used as templates to
      study the electrostatic interactions and possible sliding pathways.  A model is proposed for
      the initial nonspecific binding of BamHI to a long stretch of B-form DNA, in which BamHI and
      DNA adopt an orientation different from that in the crystal structures.  This arrangement of a
      nonspecific complex is supported by the salt-dependence of the interaction, which is in good
      agreement with experimental results if calculated in this model, but not in the crystal
      structure.  The electrostatic interaction calculated for different orientations of BamHI
      relative to DNA appears to be sufficient to steer the protein to this favorable configuration
      parallel to the DNA axis.  The results are independent of DNA sequence, so that BamHI could
      bind equally to any site along DNA thus enabling it to slide.  The calculations suggest that
      the DNA helical structure could affect the pathway of sliding: the preference for sliding
      along the DNA helix pitch stems from the ~2.5kcal/mol energy barrier that opposes sliding
      along one face of DNA.
AU  - Sun J
AU  - Weinstein H
PT  - Journal Article
TA  - Biophys. J.
JT  - Biophys. J.
SO  - Biophys. J. 2002 82: 463a.

PMID- 25635009
VI  - 3
DP  - 2015
TI  - Draft genome sequence of a rhodococcus strain isolated from tannery wastewater treatment sludge.
PG  - e01463-14
AB  - Rhodococcus sp. Chr-9 can degrade pyridine in the presence of chromate. Its draft genome
      sequence revealed that strain Chr-9 harbors sets of genes for resistance
      to heavy metals such as lead, mercury, arsenate, and cobalt, as well as three
      different gene clusters for metabolizing aromatic compounds, such as phenol,
      benzoate, and 4-nitrophenol.
AU  - Sun JQ
AU  - Xu L
AU  - Wang LJ
AU  - Wu XL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01463-14.

PMID- 19781866
VI  - 141
DP  - 2010
TI  - DNA adenine methylase is involved in the pathogenesis of Edwardsiella tarda.
PG  - 149-154
AB  - Edwardsiella tarda is a serious aquaculture pathogen that can infect many Cultured fish
      species. The aim of this study was to investigate
      the potential importance of DNA adenine methylase (Dam) in E. tarda
      pathogenesis. The E. tardo dam gene (dam(Et)) was cloned from a
      pathogenic strain, TXD1, isolated from diseased fish. Dam(Et) shares
      high (70.2%) sequence identity with the Dam proteins of Yersinia
      enterocolitica and several other bacterial species. Recombinant Dam(Et)
      is able to complement a dam-deficient Escherichia coli strain and
      methylate the genomic DNA. Attenuation of dam(Et) expression by
      antisense RNA interference had no apparent effect on the growth of
      TXD1, but caused significant attenuation of overall bacterial virulence
      and altered several stress responses including spontaneous mutation,
      recovering from UV radiation and H2O2 exposure, binding to host mucus,
      and dissemination in host blood and liver. In addition, attenuation of
      dam(Et) expression increased luxS expression and AI-2 activities in E.
      tarda. These results indicate that Dam(Et) is a virulence determinant
      and plays a role in the pathogenesis of TXD1, and that temporal
      expression of dam(Et), is essential for optimal bacterial infection.
AU  - Sun K
AU  - Jiao XD
AU  - Zhang M
AU  - Sun L
PT  - Journal Article
TA  - Vet. Microbiol.
JT  - Vet. Microbiol.
SO  - Vet. Microbiol. 2010 141: 149-154.

PMID- Not carried by PubMed...
VI  - 19
DP  - 1989
TI  - Kinetic studies on cleavage of adenovirus type 5 DNA by restriction endonuclease EcoRI.
PG  - 71-76
AB  - The two EcoRI restriction sites on Adenovirus Type 5 DNA have been affirmed and relative
      lengths of EcoRI digest products of Ad5 DNA are 77%, 7%, 16% for the fragment A, C, B
      respectively. The kinetic of cleavage of Ad5 DNA by EcoRI was studied using quantitative
      evaluation of the ethidium bromide fluorescence of DNA fragments separated on agarose gel. The
      overall rate constants of cleavage at different EcoRI site have been determined. The rate
      constants for two cleavage sites depend on the enzyme concentration and reaction temperature.
      Thermodynamic studies have shed light on the importance of the nucleotide sequences around the
      restriction sites, which modulate the activation barriers for the cleavage process itself.
AU  - Sun L
PT  - Journal Article
TA  - Xibei Daxue Xuebao
JT  - Xibei Daxue Xuebao
SO  - Xibei Daxue Xuebao 1989 19: 71-76.

PMID- 29159508
VI  - 293
DP  - 2018
TI  - Comparative genomics and transcriptome analysis of Lactobacillus rhamnosus ATCC 11443 and the mutant strain SCT-10-10-60 with enhanced L-lactic acid production capacity.
PG  - 265-276
AB  - Mechanisms for high L-lactic acid production remain unclear in many bacteria.
      Lactobacillus rhamnosus SCT-10-10-60 was previously obtained from L. rhamnosus
      ATCC 11443 via mutagenesis and showed improved L-lactic acid production. In this
      study, the genomes of strains SCT-10-10-60 and ATCC 11443 were sequenced. Both
      genomes are a circular chromosome, 2.99 Mb in length with a GC content of
      approximately 46.8%. Eight split genes were identified in strain SCT-10-10-60,
      including two LytR family transcriptional regulators, two Rex redox-sensing
      transcriptional repressors, and four ABC transporters. In total, 60 significantly
      up-regulated genes (log2fold-change >/= 2) and 39 significantly down-regulated
      genes (log2fold-change </= - 2) were identified by a transcriptome comparison
      between strains SCT-10-10-60 and ATCC 11443. KEGG pathway enrichment analysis
      revealed that "pyruvate metabolism" was significantly different (P < 0.05)
      between the two strains. The split genes and the differentially expressed genes
      involved in the "pyruvate metabolism" pathway are probably responsible for the
      increased L-lactic acid production by SCT-10-10-60. The genome and transcriptome
      sequencing information and comparison of SCT-10-10-60 with ATCC 11443 provide
      insights into the anabolism of L-lactic acid and a reference for improving
      L-lactic acid production using genetic engineering.
AU  - Sun L
AU  - Lu Z
AU  - Li J
AU  - Sun F
AU  - Huang R
PT  - Journal Article
TA  - Mol. Genet. Genomics
JT  - Mol. Genet. Genomics
SO  - Mol. Genet. Genomics 2018 293: 265-276.

PMID- 27789641
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the Cellulolytic Strain Clostridium sp. Bc-iso-3 Isolated from an Industrial-Scale Anaerobic Digester.
PG  - e01188-16
AB  - Clostridium sp. Bc-iso-3 is a cellulolytic strain isolated from a Swedish industrial-scale
      biogas digester. Here, we present the draft genome sequence of
      this strain, which consists of four contigs with a total length of 4,327,139 bp
      and an average coverage of 312.97x.
AU  - Sun L
AU  - Schnurer A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01188-16.

PMID- 23209212
VI  - 194
DP  - 2012
TI  - Genome Sequence of Clostridium tunisiense TJ, Isolated from Drain Sediment from a Pesticide Factory.
PG  - 6950-6951
AB  - Clostridium tunisiense is a Gram-positive, obligate anaerobe that was first isolated in an
      anaerobic evironment under eutrophication. Here we report the
      first genome sequence of the Clostridium tunisiense TJ isolated from drain
      sediment of a pesticide factory in Tianjin, China. The genome is of great
      importance for both basic and application research.
AU  - Sun L
AU  - Wang Y
AU  - Yu C
AU  - Zhao Y
AU  - Gan Y
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6950-6951.

PMID- Not carried by PubMed...
VI  - 20
DP  - 1990
TI  - Initial studies on chemical modification of several amino acid residues of the restriction endonuclease XhoI.
PG  - 65-71
AB  - The restriction endonuclease XhoI can be inactivated by some specific protein
      inhibitors.  XhoI is sensitive not only to sulfhydryl reagents but also to
      reagents that modify lysine and arginine residues.  Inactivation of the enzyme
      obeyed pseudo-first-order kinetics and resulted in complete elimination of
      catalysis.  Lambda DNA as substrate is strongly protected against inactivation
      by the reagents.  These data suggest that XhoI has essential lysine and/or
      arginine residues and SH groups which are crucial to the enzymatic activity.
AU  - Sun L
AU  - Yin J
PT  - Journal Article
TA  - Xibei Daxue Xuebao
JT  - Xibei Daxue Xuebao
SO  - Xibei Daxue Xuebao 1990 20: 65-71.

PMID- Not carried by PubMed...
VI  - 21
DP  - 1989
TI  - The influence of DNA conformation and base composition flanking recognition sites on the cleavage rate of restriction.
PG  - 456-460
AB  - The relations between the nucleotide sequences adjacent to the recognition sites and the
      cleavage rate of DNA with restriction endonucleases were investigated.  Our data indicate that
      the recognition sites flanked by the A-T rich sequences are cleaved faster than those flanked
      by G-C rich sequences regardless of the DNA conformation.
AU  - Sun L-K
AU  - Hong R
PT  - Journal Article
TA  - Acta Biochim. Biophys. Sin.
JT  - Acta Biochim. Biophys. Sin.
SO  - Acta Biochim. Biophys. Sin. 1989 21: 456-460.

PMID- Not carried by PubMed...
VI  - 6
DP  - 1990
TI  - Kinetics and thermodynamics of specific and non-specific interactions between BglI restriction endonuclease and pBR322-DNA.
PG  - 334-338
AB  - Cleavage of pBR322-DNA by BglI was studied at different temperatures and various incubation
      times. Kinetic constants and thermodynamic parameters of the reaction were evaluated.  The
      similarity between linear and circular DNA in specific and non-specific interaction with
      the restriction endonuclease has been demonstrated by their kinetic constants and
      thermodynamic parameters. The specific binding is about 2 orders of magnitude stronger than
      non-specific binding. Ks is more dependent on temperature then KN. Complex formation is
      weakened with increasing temperature. The values of enthalpy and entropy show that both
      specific and non-specific binding need no activation energy and the "disorder" of the molecule
      is decreased with binding. The key element that limits the cleavage rate is Kc.  From
      the experimental results, it is evident that the recognition site adjacent to the A-T
      rich sequences has a low activation energy for cleavage and can be cleaved fast. This is
      probably due to the fact that the sequences adjacent to the recognition site may regulate the
      activation threshold of the cleavage.
AU  - Sun L-K
AU  - Ruan H
PT  - Journal Article
TA  - Chinese Biochem. J.
JT  - Chinese Biochem. J.
SO  - Chinese Biochem. J. 1990 6: 334-338.

PMID- Not carried by PubMed...
VI  - 4
DP  - 1988
TI  - Calculation of cleavage rates of restriction endonuclease on circular DNA.
PG  - 64-66
AB  - In this paper, we have deduced a set of equations to calculate the cleavage rates of
      restriction endonucleases on circular DNA by mathematical and physiochemical methods. They are
      important to study the kinetics and modification of restriction endonucleases.
AU  - Sun L-K
AU  - Wang X
AU  - Hong R
PT  - Journal Article
TA  - Acta Biophys. Sinica
JT  - Acta Biophys. Sinica
SO  - Acta Biophys. Sinica 1988 4: 64-66.

PMID- 29192072
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Bacillus velezensis L-1, Which Has Antagonistic Activity against Pear Diseases.
PG  - e01271-17
AB  - Bacillus velezensis L-1 is an effective biocontrol agent against pear diseases. Here, we
      report the complete genome sequence of B. velezensis L-1 in which
      clusters related to the biosynthesis of secondary metabolites were predicted.
      This genome provides insights into the possible biocontrol mechanisms and
      furthers application of this specific bacterium.
AU  - Sun P
AU  - Cui J
AU  - Jia X
AU  - Wang W
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01271-17.

PMID- 29371344
VI  - 6
DP  - 2018
TI  - Whole-Genome Sequence of Mycoplasma bovis Strain Ningxia-1.
PG  - e01367-17
AB  - A genome sequence of the Mycoplasma bovis Ningxia-1 strain was tested by Pacific  Biosciences
      (PacBio) single-molecule real-time (SMRT) sequencing technology. The
      strain was isolated from a lesioned calf lung in 2013 in Pengyang, Ningxia,
      China. The single circular chromosome of 1,033,629 bp shows differences between
      complete Mycoplasma bovis genome in insertion-like sequences (ISs), integrative
      conjugative elements (ICEs), lipoproteins (LPs), variable surface lipoproteins
      (VSPs), pathogenicity islands (PAIs), etc.
AU  - Sun P
AU  - Luo H
AU  - Zhang X
AU  - Xu J
AU  - Guo Y
AU  - He S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01367-17.

PMID- 23414301
VI  - 13
DP  - 2013
TI  - Isolation and genomic characterization of SfI, a serotype-converting bacteriophage of Shigella flexneri.
PG  - 39
AB  - ABSTRACT: BACKGROUND: All Shigella flexneri serotypes except serotype 6 share a
      common O-antigen tetrasaccharide backbone and nearly all variation between
      serotypes are due to glucosyl and/or O-acetyl modifications of the common O units
      mediated by glycosyltransferases encoded by serotype-converting bacteriophages.
      Several S. flexneri serotype-converting phages including SfV, SfX, Sf6 and SfII
      have been isolated and characterized. However, S. flexneri serotype-converting
      phage SfI which encodes a type I modification of serotype 1 (1a, 1b, 1c and 1d)
      had not yet been characterized. RESULTS: The SfI phage was induced and purified
      from a S. flexneri serotype 1a clinical strain 019. Electron microscopy showed
      that the SfI phage has a hexagonal head and a long contractile tail,
      characteristic of the members of Myoviridae family. SfI can convert serotype Y to
      serotype 1a and serotype X to serotype 1d, but cannot convert 10 other S.
      flexneri serotypes (1a, 1b, 2a, 2b, 3a, 3b, 4a, 4b, 5a, Xv) tested, suggesting
      that SfI has a narrow host range. Similar to other S. flexneri
      serotype-converting phages, SfI integrates into the tRNA-thrW gene adjacent to
      proA of the host chromosome when lysogenized. The complete sequence of the SfI
      genome was 38,389 bp, encoding 66 open reading frames and two tRNA genes. Phage
      SfI shares significant homology with S. flexneri phage SfV, Escherichia coli
      prophage e14 and lambda, and is classified into the lambdoid phage family. SfI
      was found to use a cos mechanism for DNA packaging similar to that of phage SfV.
      CONCLUSIONS: SfI contains features of lambdoid phages and is closely related to
      S. flexneri phage SfV, E. coli prophage e14 and lambda. The characterization of
      SfI enhances our understanding of serotype conversion of S. flexneri.
AU  - Sun Q
AU  - Lan R
AU  - Wang Y
AU  - Wang J
AU  - Wang Y
AU  - Li P
AU  - Du P
AU  - Xu J
PT  - Journal Article
TA  - BMC Microbiol.
JT  - BMC Microbiol.
SO  - BMC Microbiol. 2013 13: 39.

PMID- 22965078
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Yersinia pestis Strain 2501, an Isolate from the Great Gerbil Plague Focus in Xinjiang, China.
PG  - 5447-5448
AB  - We deciphered the genome of Yersinia pestis strain 2501, isolated from the Junggar Basin, a
      newly discovered great gerbil plague focus in Xinjiang, China.
      The total length of assembly was 4,597,322 bp, and 4,265 coding sequences were
      predicted within the genome. It is the first Y. pestis genome from this plague
      focus.
AU  - Sun S
AU  - Yang X
AU  - Yuan Y
AU  - Dai X
AU  - Yan Y
AU  - Cao H
AU  - Luo T
AU  - Guo R
AU  - Wang X
AU  - Song Y
AU  - Yang R
AU  - Zhang Y
AU  - Cui Y
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5447-5448.

PMID- 27492002
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Streptomyces sp. F-3.
PG  - e00780-16
AB  - Streptomyces sp. F-3 is a kind of thermophilic Streptomyces strain that can produce
      cellulolytic enzymes and diverse secondary metabolites. Here, we report
      the complete genome of this organism, whose genome length is 5,303,958 bp,
      containing 6,041 protein-coding genes, 69 tRNA operons, and three rRNA operons.
AU  - Sun X
AU  - Meng J
AU  - Liu S
AU  - Zhang H
AU  - Wang L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00780-16.

PMID- 26316633
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Dysgonomonas macrotermitis Strain JCM 19375T, Isolated from the Gut of a Termite.
PG  - e00963-15
AB  - Here, we report the draft genome sequence of Dysgonomonas macrotermitis strain JCM 19375(T),
      which was isolated from the hindgut of a fungus-growing termite, Macrotermes barneyi. The
      genome information reveals the role of this strain in lignocellulose degradation and
      adaptation to the gut environment.
AU  - Sun X
AU  - Yang Y
AU  - Zhang N
AU  - Shen Y
AU  - Ni J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00963-15.

PMID- 27198035
VI  - 4
DP  - 2016
TI  - Genome Sequence of Enterococcus pernyi, a Pathogenic Bacterium for the Chinese Oak Silkworm, Antheraea pernyi.
PG  - e01764-15
AB  - We report the draft genome assembly of Enterococcus pernyi The genome sequence is 3.09 Mb in
      length with a G+C content of 38.35%. It covers 3,153 genes with an
      average length of 854 bp, and contains 65 tRNAs, 13 small RNAs, and 18 rRNAs.
      Moreover, it contains 9 genomic islands with an average length of 14,058 bp and 3
      prophages with an average length of 37,430 bp.
AU  - Sun Y
AU  - Li X
AU  - Wang G
AU  - Wang Y
AU  - Jiang Y
AU  - Liu Y
AU  - Yu Z
AU  - Qin L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01764-15.

PMID- 23599286
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of an Acinetobacter Strain Harboring the NDM-1 Gene.
PG  - e00023-12
AB  - The NDM-1 gene is a significant public health concern. Acinetobacter is one of the most
      prevalent opportunistic pathogens causing recent nosocomial infections
      with NDM-1, and drug-resistant strains pose serious threats to public health
      worldwide. Herein, we present the genomic sequence of Acinetobacter calcoaceticus
      subsp. anitratus XM1570, a multidrug-resistant isolate that carries the blaNDM-1
      gene.
AU  - Sun Y
AU  - Song Y
AU  - Song H
AU  - Liu J
AU  - Wang P
AU  - Qiu S
AU  - Chen S
AU  - Zhu L
AU  - Ji X
AU  - Wang Z
AU  - Liu N
AU  - Xia L
AU  - Chen W
AU  - Feng S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00023-12.

PMID- 28428834
VI  - 12
DP  - 2017
TI  - Genome sequencing and analysis of Ralstonia solanacearum phylotype I strains FJAT-91, FJAT-452 and FJAT-462 isolated from tomato, eggplant, and chili pepper in China.
PG  - 29
AB  - Ralstonia solanacearum is an extremely destructive pathogen able to cause disease in a wide
      range of host plants. Here we report the draft genome sequences of the
      strains FJAT-91, FJAT-452 and FJAT-462, isolated from tomato, eggplant, and chili
      pepper, respectively, in China. In addition to the genome annotation, we
      performed a search for type-III secreted effectors in these strains, providing a
      detailed annotation of their presence and distinctive features compared to the
      effector repertoire of the reference phylotype I strain (GMI1000). In this
      analysis, we found that each strain has a unique effector repertoire, encoding
      both strain-specific effector variants and variations shared among all three
      strains. Our study, based on strains isolated from different hosts within the
      same geographical location, provides insight into effector repertoires sufficient
      to cause disease in different hosts, and may contribute to the identification of
      host specificity determinants for R. solanacearum.
AU  - Sun Y
AU  - Wang K
AU  - Caceres-Moreno C
AU  - Jia W
AU  - Chen A
AU  - Zhang H
AU  - Liu R
AU  - Macho AP
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 29.

PMID- 26415554
VI  - 6
DP  - 2015
TI  - Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera.
PG  - 8322
AB  - Lactobacilli are a diverse group of species that occupy diverse nutrient-rich
      niches associated with humans, animals, plants and food. They are used widely in
      biotechnology and food preservation, and are being explored as therapeutics.
      Exploiting lactobacilli has been complicated by metabolic diversity, unclear
      species identity and uncertain relationships between them and other commercially
      important lactic acid bacteria. The capacity for biotransformations catalysed by
      lactobacilli is an untapped biotechnology resource. Here we report the genome
      sequences of 213 Lactobacillus strains and associated genera, and their encoded
      genetic catalogue for modifying carbohydrates and proteins. In addition, we
      describe broad and diverse presence of novel CRISPR-Cas immune systems in
      lactobacilli that may be exploited for genome editing. We rationalize the
      phylogenomic distribution of host interaction factors and bacteriocins that
      affect their natural and industrial environments, and mechanisms to withstand
      stress during technological processes. We present a robust phylogenomic framework
      of existing species and for classifying new species.
AU  - Sun Z et al
PT  - Journal Article
TA  - Nat. Commun.
JT  - Nat. Commun.
SO  - Nat. Commun. 2015 6: 8322.

PMID- 20511504
VI  - 192
DP  - 2010
TI  - Complete genome sequence of probiotic Bifidobacterium animalis subsp. lactis strain V9.
PG  - 4080-4081
AB  - Bifidobacterium animalis subsp. lactis strain V9 is a Chinese commercial bifidobacteria with
      several probiotic functions. It was isolated from a healthy Mongolian child in China. We
      present here the complete genome sequence of V9 and compared it to 3 other published genomes
      of B. animalis subsp. lactis strains. The result indicates the lack of polymorphism among
      strains of this subspecies of different continent origins.
AU  - Sun Z
AU  - Chen X
AU  - Wang J
AU  - Gao P
AU  - Zhou Z
AU  - Ren Y
AU  - Sun T
AU  - Wang L
AU  - Meng H
AU  - Chen W
AU  - Zhang H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 4080-4081.

PMID- 21515763
VI  - 193
DP  - 2011
TI  - Complete genome sequence of Lactobacillus delbrueckii subsp. bulgaricus strain ND02.
PG  - 3426-3427
AB  - Lactobacillus delbrueckii subsp. bulgaricus strain ND02 is a Chinese commercial dairy starter
      used for the manufacture of yoghurt. It was
      isolated from the naturally fermented yak milk in Qinghai, China. Here, we
      report the main genome features of ND02 and several differences with two
      other published genomes of Lactobacillus delbrueckii subsp. bulgaricus
      strains.
AU  - Sun Z
AU  - Chen X
AU  - Wang J
AU  - Zhao W
AU  - Shao Y
AU  - Guo Z
AU  - Zhang X
AU  - Zhou Z
AU  - Sun T
AU  - Wang L
AU  - Meng H
AU  - Zhang H
AU  - Chen W
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3426-3427.

PMID- 21131489
VI  - 193
DP  - 2010
TI  - Complete genome sequence of Streptococcus thermophilus strain ND03.
PG  - 793-794
AB  - Streptococcus thermophilus strain ND03 is a Chinese commercial dairy starter used for the
      manufacture of yoghurt. It was isolated from the naturally fermented yak milk in Qinghai,
      China. We present here the complete genome sequence of ND03 and compared it to 3 other
      published genomes of Streptococcus thermophilus strains.
AU  - Sun Z
AU  - Chen X
AU  - Wang J
AU  - Zhao W
AU  - Shao Y
AU  - Wu L
AU  - Zhou Z
AU  - Sun T
AU  - Wang L
AU  - Meng H
AU  - Zhang H
AU  - Chen W
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 193: 793-794.

PMID- 26564038
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Bacillus amyloliquefaciens XK-4-1, a Plant Growth-Promoting Endophyte with Antifungal Activity.
PG  - e01306-15
AB  - Here, we report the draft genome sequence of a bacterial plant-growth-promoting endophyte,
      Bacillus amyloliquefaciens XK-4-1, which consists of one circular
      chromosome of 3,941,805 bp with 3,702 coding sequences (CDSs). The data presented
      highlight multiple sets of functional genes associated with its plant-beneficial
      characteristics.
AU  - Sun Z
AU  - Hsiang T
AU  - Zhou Y
AU  - Zhou J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01306-15.

PMID- 23352666
VI  - 3
DP  - 2013
TI  - High-Resolution Enzymatic Mapping of Genomic 5-Hydroxymethylcytosine in Mouse Embryonic Stem Cells.
PG  - 567-576
AB  - We describe the use of a unique DNA-modification-dependent restriction endonuclease AbaSI
      coupled with sequencing (Aba-seq) to map
      high-resolution hydroxymethylome of mouse E14 embryonic stem cells. The
      specificity of AbaSI enables sensitive detection of
      5-hydroxymethylcytosine (5hmC) at low-occupancy regions. Bioinformatic
      analysis suggests 5hmCs in genic regions closely follow the 5mC
      distribution. 5hmC is generally depleted in CpG islands and only
      enriched in a small set of repetitive elements. A regularly spaced and
      oscillating 5hmC pattern was observed at the binding sites of CTCF.
      5hmC is enriched at the poised enhancers with the monomethylated
      histone H3 lysine 4 (H3K4me1) marks, but not at the active enhancers
      with the acetylated histone H3 lysine 27 (H3K27Ac) marks. Non-CG
      hydroxymethylation appears to be prevalent in the mitochondrial genome.
      We propose that some amounts of transiently stable 5hmCs may indicate a
      poised epigenetic state or demethylation intermediate, whereas others
      may suggest a locally accessible chromosomal environment for the TET
      enzymatic apparatus.
AU  - Sun ZY
AU  - Terragni J
AU  - Borgaro JG
AU  - Liu YW
AU  - Yu L
AU  - Guan SX
AU  - Wang H
AU  - Sun DP
AU  - Cheng XD
AU  - Zhu ZY
AU  - Pradhan S
AU  - Zheng Y
PT  - Journal Article
TA  - Cell Rep.
JT  - Cell Rep.
SO  - Cell Rep. 2013 3: 567-576.

PMID- 23105083
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Halotolerant Staphylococcus sp. Strain OJ82, Isolated from Korean Traditional Salt-Fermented Seafood.
PG  - 6353-6354
AB  - Staphylococcus sp. strain OJ82 was isolated from a Korean traditional fermented squid seafood,
      ojingeo-jeotgal. Staphylococcus sp. OJ82 could grow and show
      extracellular protease and beta-galactosidase activities in the presence of
      extremely high saline (20%). Here, we report the genome sequence of
      Staphylococcus sp. OJ82.
AU  - Sung JS
AU  - Chun J
AU  - Choi S
AU  - Park W
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6353-6354.

PMID- 26358609
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of a vanA-Type Vancomycin-Resistant Reference Strain, Enterococcus faecium ATCC 51559.
PG  - e01053-15
AB  - Vancomycin-resistant Enterococcus faecium has emerged as a multidrug-resistant pathogen in
      hospital settings. Here, we present the draft genome sequence of a high-level
      vancomycin-resistant strain, E. faecium ATCC 51559, which is employed  as a standard
      laboratory vanA genotype-positive control strain for clinical and laboratory studies.
AU  - Sung K
AU  - Khan S
AU  - Marasa B
AU  - Min S
AU  - Kweon O
AU  - Mohamed N
AU  - Cerniglia C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01053-15.

PMID- 26679597
VI  - 3
DP  - 2015
TI  - Genomic Sequence of a Clinical Vancomycin-Resistant Reference Strain, Enterococcus faecalis ATCC 51299.
PG  - e01495-15
AB  - In this paper, we present a draft genome sequence of a quality control reference  strain,
      Enterococcus faecalis ATCC 51299 (multilocus sequencing type [MLST] ST6),
      which is sensitive to teicoplanin but resistant to vancomycin. It is used in an
      agar screening test for streptomycin, gentamicin, and vancomycin resistance and
      the resistance marker vanB.
AU  - Sung K
AU  - Khan S
AU  - Marasa B
AU  - Min S
AU  - Kweon O
AU  - Nawaz M
AU  - Cerniglia C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01495-15.

PMID- 27198011
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Mycobacterium tuberculosis Clinical Isolate Spoligotype SIT745/EAI1-MYS.
PG  - e00323-16
AB  - Mycobacterium tuberculosis is known to cause pulmonary and extrapulmonary tuberculosis. This
      organism showed special phylogeographical specificity. Here,
      we report the complete genome sequence of M. tuberculosis clinical isolate
      spoligotype SIT745/EAI1-MYS, which was isolated from a Malaysian tuberculosis
      patient.
AU  - Suraiya S
AU  - Semail N
AU  - Ismail MF
AU  - Abdullah JM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00323-16.

PMID- 9590162
VI  - 93
DP  - 1998
TI  - Imprinting and the initiation of gene silencing in the germ line.
PG  - 309-312
AB  - Inheritance of genes in active or repressed states requires appropriate chromosomal
      modifications and DNA methylation.  Imprinting of a determined state into the chromatin
      structure therefore constitutes a memory of all developmental decisions taken within
      individual cells.  Genomic or gametic imprinting is however a unique manifestation of such
      epigenetic inheritance in which expression of certain genes is governed by their parental
      origin, from generation to generation.  Some of these genes show expression after paternal
      inheritance while others are expressed only when inherited from the maternal germ line.  The
      most striking feature of imprinted genes therefore is that the active and inactive parental
      alleles coexist within individual cells.  Over 20 imprinted genes have so far been identified.
      Parental genomes are functionally nonequivalent during development because of the differential
      expression of imprinted genes. A review.
AU  - Surani MA
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1998 93: 309-312.

PMID- Not carried by PubMed...
VI  - 57
DP  - 1997
TI  - Facilitated diffusion of the EcoRI DNA methyltransferase under both catalytic and noncatalytic conditions and the potential of Z DNA disrupt protein translocation on DNA.
PG  - 5631B-5632B
AB  - Previous experiments in our lab have suggested that the EcoRI DNA methyltransferase might
      utilize one-dimensional facilitated diffusion to locate its specific binding site on a DNA
      substrate.  In the current study, initial experiments to characterize this phenomenon with
      regard to the methyltransferase focus on the contribution of nonspecific DNA to enzyme
      efficiency (kcat/Km).  This parameter increases 4-fold as DNA length increases from 14 to 429
      basepairs and increases 2-fold as the distance from the site to the nearest end is increased
      from 29 to 378 basepairs.  No changes in kcat/Km result from further increases in either case.
      A facilitated diffusion mechanism is proposed in which the methyltransferase scans an average
      of <400 base pairs prior to dissociation from a DNA molecule.  The methyltransferase was found
      to methylate two sites on a single DNA molecule in a distributive rather than a processive
      manner, suggesting that the enzyme dissociates from the DNA prior to release of the reaction
      product S-adenosylhomocysteine.  A direct competition experiment with the EcoRI endonuclease
      shows the methyltransferase to be slightly more efficient at specific site location and
      catalysis.  A rationale for the role of facilitated diffusion in this type II
      restriction-modification system is proposed.  In addition, the contribution of nonspecific DNA
      to binding parameters (d, koff, and kon) was determined for the methyltransferase under
      noncatalytic conditions.  An increase in DNA size from 14 to 775 base pairs causes a 20-fold
      decrease in Kd, while koff remains constant over the same range.  The calculated kon increases
      with longer substrates, consistent with a facilitated diffusion mechanism.  However, the
      combined results deviate from the model developed to describe facilitated diffusion.  Our
      results were successfully simulated using numerical integration of a kinetic scheme invoking
      protein dissociation via the ends of DNA.  Consistent with this scheme, the methyltransferase
      dissociates more slowly from a circularized DNA molecule than from the identical linearized
      form.  The final set of experiments is an attempt to determine the effect of Z DNA on the
      ability of proteins to translocate on DNA.  Z DNA formation in a linear substrate is confirmed
      with Z DNA-specific antibody binding and preliminary results with the EcoRI endonuclease
      suggest that Z DNA decreases the rate of DNA cleavage by 2- to 3-fold.  However, subsequent
      experiments with more highly purified endonuclease do not support this conclusion.  Z DNA
      cannot be detected in the linear substrates with chemical modification techniques, so the
      assay was modified to use the methyltransferase and a supercoiled DNA substrate.  Although
      there is an observable effect on kcat and Km in the supercoiled substrate, control experiments
      make an assignment of this effect to the presence of Z DNA unclear.
AU  - Surby MA
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1997 57: 5631B-5632B.

PMID- 1727392
VI  - 6
DP  - 1992
TI  - The role of nonspecific DNA in the site location kinetics of the EcoRI DNA methyltransferase.
PG  - A356
AB  - The EcoRI DNA methyltransferase is an extremely efficient enzyme, with a
      kcat/Km of 4.1 X 10/8 s-1M-1 for plasmid DNA.  Its kcat/Km decreases to 0.51 X
      10/8 s-1M-1 when a 14 basepair synthetic oligonucleotide is used as a
      substrate.  A possible explanation for these observations is that the methylase
      utilizes facilitated diffusion along nonspecific DNA as a mechanism for site
      location.  This was first tested using a processivity assay developed for the
      EcoRI endonuclease (J. Biol. Chem., Oct. 25, 1985, 260 (24) pp 13130-13137).
      In contrast to our results with the endonuclease, no processive methylation was
      observed with this assay.  The role of facilitated diffusion in initial site
      location was then investigated by kinetic analysis of restriction fragments
      ranging in size from 4363 to 108 basepairs, all of which contained a single
      EcoRI site.  There were no differences observed in the rate of methyl group
      incorporation for the various substrates.  This leads us to conclude that the
      specificity enhancement observed for the plasmid DNA is due either to
      nonspecific sequences <108 basepairs away from the canonical site of the DNA
      substrate or to some other phenomenon (e.g. flanking sequence differences).
AU  - Surby MA
AU  - Reich NO
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1992 6: A356.

PMID- Not included in PubMed...
VI  - 31
DP  - 1992
TI  - The role of nonspecific DNA in the site-location kinetics of the EcoRI DNA methyltransferase.
PG  - 2208
AB  - The EcoRI DNA methyltransferase is an extremely efficient enzyme, with a
      kcat/Km of 4.1 x 10/8 S-1M-1 for plasmid DNA.  Its kcat/Km decreases to 0.51 x
      10.8 S-1 M-1 when a 14-base-pair synthetic oligonucleotide is used as a
      substrate.  Canonical site flanking sequence differences between the plasmid
      and the 14-bp oligonucleotide were shown to have no effect on kcat/Km.  A
      possible explanation for these observations is that the methylase utilizes
      facilitated diffusion along nonspecific DNA as a mechanism for site location.
      This was first tested using a processivity assay developed for the EcoRI
      endonuclease [(1985) J. Biol. Chem. 260 (24), 13130-13137].  In contrast to our
      results with the endonuclease, no processive methylation was observed with this
      assay.  The role of facilitated diffusion in initial site location was then
      investigated by kinetic analysis of restriction fragments ranging in size from
      4363 to 108 bp, all of which contained a single EcoRI site.  There were no
      differences observed in the rate of methyl group incorporation for various
      substrates.  This leads us to conclude that the specificity enhancement
      observed for the plasmid DNA is due to nonspecific sequences <108 bp away from
      the canonical site of the DNA substrate.
AU  - Surby MA
AU  - Reich NO
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1992 31: 2208.

PMID- 8652562
VI  - 35
DP  - 1996
TI  - Facilitated diffusion of the EcoRI DNA methyltransferase is described by a novel mechanism.
PG  - 2209-2217
AB  - The contribution of nonspecific DNA to binding parameters (Kd, koff, and kon) was determined
      for the EcoRI DNA methyltransferase under noncatalytic conditions.  An increase in DNA size
      from 14 to 775 base pairs causes a 20-fold decrease in Kd, while koff remains constant over
      the same range.  The calculated kon increases with longer substrates, consistent with a
      facilitated diffusion mechanism.  However, the combined results deviate from the model
      developed to describe facilitated diffusion.  Our results were successfully simulated using
      numerical integration of a kinetic scheme invoking protein dissociation via the ends of DNA.
      Consistent with this scheme, the methyltransferase dissociates more slowly from a circularized
      DNA molecule than from the identical linearized form.  The simulation strategy correctly
      models our data with the methyltransferase and should be generally useful for routine modeling
      of facilitated diffusion involving protein-DNA systems.
AU  - Surby MA
AU  - Reich NO
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1996 35: 2209-2217.

PMID- 8652561
VI  - 35
DP  - 1996
TI  - Contribution of facilitated diffusion and processive catalysis to enzyme efficiency: Implications for the EcoRI restriction-modification system.
PG  - 2201-2208
AB  - The contribution of nonspecific DNA to enzyme efficiency (kcat/Km) is described for a
      sequence-specific DNA-modifying enzyme.  Our investigation focuses on the EcoRI DNA
      methyltransferase which transfers a methyl group from the cofactor S-adenosylmethionine to the
      second adenine in the double-stranded DNA sequence GAATTC.  kcat/Km increases 4-fold as DNA
      length increases from 14 to 429 base pairs and increases 2-fold as the distance from the site
      to the nearest end is increased from 29 to 378 base pairs.  No changes in kcat/Km result from
      further increases in either case.  A facilitated diffusion mechanism is proposed in which the
      methyltransferase scans an average of <400 base pairs prior to dissociation from a DNA
      molecule.  The methyltransferase was found to methylate two sites on a single DNA molecule in
      a distributive rather than a processive manner, suggesting that the enzyme dissociates from
      the DNA prior to release of the reaction product S-adenosylhomocysteine.  A direct competition
      experiment with the EcoRI endonuclease shows the methyltransferase to be slightly more
      efficient at specific site location and catalysis.  A rationale for the role of facilitated
      diffusion in this type II restriction-modification system is proposed.
AU  - Surby MA
AU  - Reich NO
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1996 35: 2201-2208.

PMID- Not carried by PubMed...
VI  - 203
DP  - 1992
TI  - The role of nonspecific DNA in the site-location kinetics of the EcoRI DNA methyltransferase.
PG  - 110-BIOL
AB  - The EcoRI DNA methyltransferase is an extremely efficient enzyme, with a kcat/Km of 4.1 x 10/8
      S-1M-1 for plasmid DNA. Its kcat/Km decreases to 0.51 x 10/8 S-1M-1 when a 14 basepair
      synthetic oligonucleotide is used as a substrate. Cannonical site flanking sequence
      differences between the plasmid and the 14 basepair oligonucleotide were shown to have no
      effect on kcat/Km. A possible explanation for these observations is that the methylase
      utilizes facilitated diffusion along nonspecific DNA as a mechanism for site location. This
      was first tested using a processivity assay developed for the EcoRI endonuclease (J. Biol.
      Chem., Oct. 25,1985, 260 (24), pp 13130-13137). In contrast to our results with the
      endonuclease, no processive methylation was observed with this assay. The role of facilitated
      diffusion in initial site location was then investigated by kinetic analysis of restriction
      fragments ranging in size from 4363 to 108 basepairs, all of which contained a single EcoRI
      site. There were no differences observed in the rate of methyl group incorporation for the
      various substrates. This leads us to conclude that the specificity enhancement observed for
      the plasmid DNA is due to nonspecific sequences <108 basepairs aways from the canonical site
      of the DNA substrate.
AU  - Surby MA
AU  - Reich NO
PT  - Journal Article
TA  - ACS Abstracts
JT  - ACS Abstracts
SO  - ACS Abstracts 1992 203: 110-BIOL.

PMID- 3001318
VI  - 186
DP  - 1985
TI  - EcoA:  The first member of a new family of Type I restriction modification systems - Gene organization and enzymatic activities.
PG  - 77-85
AB  - The characterization of the EcoA restriction-modification enzymes from
      Escherichia coli 15T- is described.  The reactions catalysed by these enzymes
      are very similar to those catalysed by the classical type I restriction and
      modification enzymes, a family of genetically related proteins.  The detailed
      mechanisms, particularly for DNA modification, differ.  The genetic and
      transcriptional organizations are also very similar to those of the classical
      systems, despite the fact that EcoA is not allelic to the others.  We
      demonstrate that the expression of the EcoA genes is controlled following
      conjugative transfer to other strains in such a way that no lethality is
      observed, probably because the reciptient chromosome is completely modified
      before restriction activity is expressed.
AU  - Suri B
AU  - Bickle TA
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1985 186: 77-85.

PMID- 6325094
VI  - 108
DP  - 1984
TI  - Bacterial DNA modification.
PG  - 1-9
AB  - As first proposed by Arber (1965), DNA restriction/modification systems (R/M
      systems) are mediated by endonucleases and DNA methylases that recognize the
      same DNA sequences.  The endonuclease recognizes its specific sequence as a
      signal to cleave the DNA unless the sequence has been previously methylated by
      the modification enzyme.  Chromosomal DNA from cells harboring the R/M system
      is normally methylated, and is thus not a substrate for the restriction enzyme.
      Foreign DNA lacking the specific methylation pattern and introduced into the
      cell by phase infection, conjugation, or transformation is the only known
      natural substrate for restriction.  R/M systems can therefore be considered
      primitive prokaryotic analogues of the eukaryotic immune system.  A vast body
      of literature on the genetics and biochemistry of R/M systems has accumulated
      since they were first investigated 20 years ago (Arber and Dussoix 1962), and
      it is now clear that R/M systems can be conveniently classified into three
      types (Boyer 1971; Kauc and Piekarowicz 1978; Nathans and Smith 1975).  The
      most complicated of these are the type-I systems, which are mediated by
      complex, multifunctional enzymes and which were the first proteins shown to
      recognize specific DNA sequences.  The restriction enzymes EcoK and EcoB from
      the Escherichia coli strains K12 and B are the two prototypes, and are still
      the only ones to have been studied in detail.
AU  - Suri B
AU  - Nagaraja V
AU  - Bickle TA
PT  - Journal Article
TA  - Curr. Top. Microbiol. Immunol.
JT  - Curr. Top. Microbiol. Immunol.
SO  - Curr. Top. Microbiol. Immunol. 1984 108: 1-9.

PMID- 6325176
VI  - 3
DP  - 1984
TI  - The EcoA restriction and modification system of Escherichia coli 15T-: enzyme structure and DNA recognition sequence.
PG  - 575-579
AB  - The EcoA restriction enzyme from Escherichia coli 15T- has been isolated.  It
      proves to be an unusual enzyme, clearly related functionally to the classical
      type I restriction enzymes.  The basic enzyme is a two subunit modification
      methylase.  Another protein species can be purified which by itself has not
      enzymatic activities but which converts the modification methylase to an ATP
      and S-adenosylmethionine-dependent restriction endonuclease.  The DNA
      recognition sequence of EcoA has an overall structure that is very similar to
      previously determined type I sequences.  It is:
      5'-GAGNNNNNNNGTCA-3'3'-CTCNNNNNNNCAGT-5'where N can be any nucleotide.
      Modification methylates the adenosyl residue in the specific trinucleotide and
      the adenosyl residue in the lower strand of the specific tetranucleotide.
AU  - Suri B
AU  - Shepherd JCW
AU  - Bickle TA
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1984 3: 575-579.

PMID- 29326225
VI  - 6
DP  - 2018
TI  - Genomic Insights into Biofilm-Forming Enterococcus faecalis SK460 Isolated from a Chronic Diabetic Ulcer Patient.
PG  - e01463-17
AB  - Enterococcus faecalis is recognized as one of the leading pathogens causing nosocomial
      infections. Here we report a draft genome sequence of Enterococcus
      faecalis SK460, isolated from a chronic diabetic foot ulcer patient. This strain
      exhibits various biofilm-associated genes, virulence genes, and
      antibiotic-resistance genes related to aminoglycoside, macrolide, and
      tetracycline resistance.
AU  - Suryaletha K
AU  - Narendrakumar L
AU  - John J
AU  - Reghunathan D
AU  - Prasannakumar M
AU  - Thomas S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01463-17.

PMID- 28163824
VI  - 12
DP  - 2017
TI  - Draft genome sequence of Lactobacillus plantarum strains E2C2 and E2C5 isolated from human stool culture.
PG  - 15
AB  - Probiotic Lactobacillus species offer various health benefits, thus have been employed in
      treatment and prevention of various diseases. Due to the differences
      in the isolation source and the site of action, most of the lactobacilli tested
      in-vitro for probiotics properties fail to extend similar effects in-vivo.
      Consequently, the search of autochthonous, efficacious and probably population
      specific probiotics is a high priority in the probiotics research. In this
      regards, whole genome sequencing of as many Lactobacillus as possible will help
      to deepen our understanding of biology and their health effects. Here, we provide
      the genomic insights of two coherent oxalic acid tolerant Lactobacillus species
      (E2C2 and E2C5) isolated from two different healthy human gut flora. These two
      isolates were found to have higher tolerance towards oxalic acid (300 mM sodium
      oxalate). The draft genome of strain E2C2 consists of 3,603,563 bp with 3289
      protein-coding genes, 94 RNA genes, and 43.99% GC content, while E2C5 contained
      3,615,168 bp, 3293 coding genes (93.4% of the total genes), 95 RNA genes and
      43.97% GC content. Based on 16S rRNA gene sequence analysis followed by in silico
      DNA-DNA hybridization studies, both the strains were identified as Lactobacillus
      plantarum belonging to family Lactobacillaceae within the phylum Firmicutes. Both
      the strains were genomically identical, sharing 99.99% CDS that showed 112 SNPs.
      Both the strains also exhibited deconjugation activity for the bile salts while
      genome analysis revealed that the L. plantarum strains E2C2 and E2C5 also have
      the ability to produce vitamins, biotin, alpha- and beta- glucosidase suggesting
      potential probiotic activities of the isolates. The description presented here is
      based on the draft genomes of strains E2C2 and E2C5 which are submitted to
      GenBank under the accession numbers LSST00000000.1 and LTCD00000000.1,
      respectively.
AU  - Suryavanshi MV
AU  - Paul D
AU  - Doijad SP
AU  - Bhute SS
AU  - Hingamire TB
AU  - Gune RP
AU  - Shouche YS
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 15.

PMID- 23012283
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Desulfurococcus fermentans, a Hyperthermophilic Cellulolytic Crenarchaeon Isolated from a Freshwater Hot Spring in Kamchatka,  Russia.
PG  - 5703-5704
AB  - Desulfurococcus fermentans is the first known cellulolytic archaeon. This hyperthermophilic
      and strictly anaerobic crenarchaeon produces hydrogen from
      fermentation of various carbohydrates and peptides without inhibition by
      accumulating hydrogen. The complete genome sequence reported here suggested that
      D. fermentans employs membrane-bound hydrogenases and novel glycohydrolases for
      hydrogen production from cellulose.
AU  - Susanti D et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5703-5704.

PMID- 28408663
VI  - 5
DP  - 2017
TI  - Permanent Draft Genome Sequence of Desulfurococcus amylolyticus Strain Z-533T, a  Peptide and Starch Degrader Isolated from Thermal Springs in the Kamchatka  Peninsula and Kunashir Island, Russia.
PG  - e00078-17
AB  - Desulfurococcus amylolyticus Z-533T, a hyperthermophilic crenarcheon, ferments peptide and
      starch, generating acetate, isobutyrate, isovalerate, CO2, and
      hydrogen. Unlike D. amylolyticus Z-1312, it cannot use cellulose and is inhibited
      by hydrogen. The reported draft genome sequence of D. amylolyticus Z-533T will
      help to understand the molecular basis for these differences.
AU  - Susanti D
AU  - Johnson EF
AU  - Lapidus A
AU  - Han J
AU  - Reddy TB
AU  - Mukherjee S
AU  - Pillay M
AU  - Perevalova AA
AU  - Ivanova NN
AU  - Woyke T
AU  - Kyrpides NC
AU  - Mukhopadhyay B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00078-17.

PMID- 26767090
VI  - 11
DP  - 2016
TI  - Permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161,  a thermoacidophilic sulfur-reducing crenarchaeon isolated from acidic hot springs  of Hveravellir, Iceland.
PG  - 3
AB  - This report presents the permanent draft genome sequence of Desulfurococcus mobilis type
      strain DSM 2161, an obligate anaerobic hyperthermophilic
      crenarchaeon that was isolated from acidic hot springs in Hveravellir, Iceland.
      D. mobilis utilizes peptides as carbon and energy sources and reduces elemental
      sulfur to H2S. A metabolic construction derived from the draft genome identified
      putative pathways for peptide degradation and sulfur respiration in this
      archaeon. Existence of several hydrogenase genes in the genome supported previous
      findings that H2 is produced during the growth of D. mobilis in the absence of
      sulfur. Interestingly, genes encoding glucose transport and utilization systems
      also exist in the D. mobilis genome though this archaeon does not utilize
      carbohydrate for growth. The draft genome of D. mobilis provides an additional
      mean for comparative genomic analysis of desulfurococci. In addition, our
      analysis on the Average Nucleotide Identity between D. mobilis and
      Desulfurococcus mucosus suggested that these two desulfurococci are two different
      strains of the same species.
AU  - Susanti D
AU  - Johnson EF
AU  - Lapidus A
AU  - Han J
AU  - Reddy TB
AU  - Pilay M
AU  - Ivanova NN
AU  - Markowitz VM
AU  - Woyke T
AU  - Kyrpides NC
AU  - Mukhopadhyay B
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 3.

PMID- 1005115
VI  - 3
DP  - 1976
TI  - A restriction endonuclease from Staphylococcus aureus.
PG  - 3193-3202
AB  - A specific endonuclease, Sau3AI, has been partially purified from
      Staphylococcus aureus strain 3A by DEAE-cellulose chromatography.  The enzyme
      cleaves adenovirus type 5 DNA many times, SV40 DNA eight times but does not
      cleave double-stranded PhiX174 DNA.  It recognizes the sequence 5' ^-G-A-T-C-
      3' 3'  -C-T-A-G-^ 5'  and cleaves as indicated by the arrows.  Evidence is
      presented that this enzyme plays a role in the biological
      restriction-modification system of Staphylococcus aureus strain 3A.
AU  - Sussenbach JS
AU  - Monfoort CH
AU  - Schiphof R
AU  - Stobberingh EE
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1976 3: 3193-3202.

PMID- 652518
VI  - 5
DP  - 1978
TI  - A second site-specific restriction endonuclease from Staphylococcus aureus.
PG  - 1153-1163
AB  - A site-specific restriction endonuclease has been isolated from Staphylococcus
      aureus PS 96.  This enzyme, Sau96I, recognizes the DNA sequence
      5'--G-^G-N-C-C--3' 3'--C-C-N-G-^G--5' and cleaves as indicated by the arrows.
      The enzyme cleaves adenovirus type 5 and lambda DNA many times, SV40 DNA 10
      times and PhiX174 RF DNA 2 times.  Evidence is presented that the enzyme is
      involved in biological restriction-modification.
AU  - Sussenbach JS
AU  - Steenbergh PH
AU  - Rost JA
AU  - van Leeuwen WJ
AU  - van Embden JDA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1978 5: 1153-1163.

PMID- 15313605
VI  - 342
DP  - 2004
TI  - Isolation and characterization of new homing endonuclease specificities at individual target site positions.
PG  - 31-41
AB  - Homing endonucleases are highly specific DNA endonucleases, encoded within mobile introns or
      inteins, that induce targeted recombination,
      double-strand repair and gene conversion of their cognate target sites.
      Due to their biological function and high level of target specificity,
      these enzymes are under intense investigation as tools for gene
      targeting. These studies require that naturally occurring enzymes be
      redesigned to recognize novel target sites. Here, we report studies in
      which the homodimeric LAGLIDADG homing endonuclease I-CreI is altered
      at individual side-chains corresponding to contact points to distinct
      base-pairs in its target site. The resulting enzyme constructs drive
      specific elimination of selected DNA targets in vivo and display
      shifted specificities of DNA binding and cleavage in vitro. Crystal
      structures of two of these constructs demonstrate that substitution of
      individual side-chain/DNA contact patterns can occur with almost no
      structural deformation or rearrangement of the surrounding complex,
      facilitating an isolated, modular redesign strategy for homing
      endonuclease activity and specificity.
AU  - Sussman D
AU  - Chadsey M
AU  - Fauce S
AU  - Engel A
AU  - Bruett A
AU  - Monnat R
AU  - Stoddard BL
AU  - Seligman LM
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2004 342: 31-41.

PMID- 24009120
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Thermotoga maritima A7A Reconstructed from Metagenomic Sequencing Analysis of a Hydrocarbon Reservoir in the Bass Strait, Australia.
PG  - e00688-13
AB  - The draft genome sequence of Thermotoga maritima A7A was obtained from a metagenomic assembly
      obtained from a high-temperature hydrocarbon reservoir in
      the Gippsland Basin, Australia. The organism is predicted to be a motile anaerobe
      with an array of catabolic enzymes for the degradation of numerous carbohydrates.
AU  - Sutcliffe B
AU  - Midgley DJ
AU  - Rosewarne CP
AU  - Greenfield P
AU  - Li D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00688-13.

PMID- 97636
VI  - 5
DP  - 1978
TI  - The cleavage site of the restriction endonuclease AvaII.
PG  - 2313-2319
AB  - We have determined that the type II restriction enzyme AvaII, isolated from
      Anabaena variabilis, recognizes and cuts the sequence 5' - G^GTCC - 3' 3' -
      CCAG^G - 5' The eight AvaII sites of pBR322 have been mapped, as well as a
      unique site for AvaI.
AU  - Sutcliffe JG
AU  - Church GM
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1978 5: 2313-2319.

PMID- 1317461
VI  - 225
DP  - 1992
TI  - McrBC:  a multisubunit GTP-dependent restriction endonuclease.
PG  - 327-358
AB  - McrBC-mediated restriction of modified DNA has been studied extensively by genetic methods,
      but little is known of its molecular action. We have used overproducing plasmid constructs to
      facilitate purification of the McrB L and McrC proteins, and report preliminary
      characterization of the activity of the complex. Both proteins are required for cleavage of
      appropriately modified DNA in vitro, in a reaction absolutely dependent on GTP. ATP inhibits
      the reaction. The sequence and modification requirements for cleavage of the substrate reflect
      those seen in vivo. The position of cleavage was examined at the nucleotide level, revealing
      that cleavage occurs at multiple positions in a small region. Based upon these observations,
      and upon cleavage of model oligonucleotide substrates, it is proposed that the recognition
      site for this enzyme consists of the motif RmC(N40-80) RmC, with cleavage occurring at
      multiple positions on both strands between the modified C residues. In subunit composition,
      cofactor requirement, and relation between cleavage and recognition site, McrBC does not fit
      into any of the classes (types I to IV) of restriction enzyme so far described.
AU  - Sutherland E
AU  - Coe L
AU  - Raleigh EA
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1992 225: 327-358.

PMID- 28183760
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of the Acetylene-Fermenting Pelobacter sp. Strain SFB93.
PG  - e01573-16
AB  - Acetylene fermentation is a rare metabolism that was previously reported as being unique to
      Pelobacter acetylenicus Here, we report the genome sequence of
      Pelobacter sp. strain SFB93, an acetylene-fermenting bacterium isolated from
      sediments collected in San Francisco Bay, CA.
AU  - Sutton JM
AU  - Baesman SM
AU  - Fierst JL
AU  - Poret-Peterson AT
AU  - Oremland RS
AU  - Dunlap DS
AU  - Akob DM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01573-16.

PMID- 28183759
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of Two Acetylene-Fermenting Pelobacter acetylenicus Strains.
PG  - e01572-16
AB  - Acetylene fermentation is a rare metabolism that was serendipitously discovered during
      C2H2-block assays of N2O reductase. Here, we report the genome sequences
      of two type strains of acetylene-fermenting Pelobacter acetylenicus, the
      freshwater bacterium DSM 3246 and the estuarine bacterium DSM 3247.
AU  - Sutton JM
AU  - Baesman SM
AU  - Fierst JL
AU  - Poret-Peterson AT
AU  - Oremland RS
AU  - Dunlap DS
AU  - Akob DM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01572-16.

PMID- 28935732
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of emm111 Type Streptococcus pyogenes Strain GUR, with  Antitumor Activity, and Its Derivative Strain GURSA1 with an Inactivated emm  Gene.
PG  - e00939-17
AB  - We present here the complete genome sequence of Streptococcus pyogenes type emm111 strain GUR,
      a throat isolate from a scarlet fever patient, which has been
      used to treat cancer patients in the former Soviet Union. We also present the
      complete genome sequence of its derivative strain GURSA1 with an inactivated emm
      gene.
AU  - Suvorova MA
AU  - Tsapieva AN
AU  - Bak EG
AU  - Chereshnev VA
AU  - Kiseleva EP
AU  - Suvorov AN
AU  - Arumugam M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00939-17.

PMID- 
VI  - 16
DP  - 2016
TI  - Construction of a Streptococcus strain mutant in the M protein gene.
PG  - 235-236
AB  - 
AU  - Suvorova MA
AU  - Tsapieva AN
AU  - Duplik NV
AU  - Kramskoy TA
AU  - Grabovskaya KB
AU  - Kiseleva EP
AU  - Chereshnev VA
AU  - Suvorov AN
PT  - Journal Article
TA  - Med. Akad. Z.
JT  - Med. Akad. Z.
SO  - Med. Akad. Z. 2016 16: 235-236.

PMID- 
VI  - 0
DP  - 2012
TI  - Host-mimicking strategies in DNA methylation for improved bacterial transformation.
PG  - 219-236
AB  - In 1928, Griffith reported that soluble substances from virulent pneumococcal cells
      transformed non-virulent pneumococcus to virulent forms.  This substance has now been
      demonstrated to be DNA.  This is considered to be the first report on genetic transformation
      of bacteria by exogenous DNA.  Subsequently, natural competence of Bacillus subtilis was
      reported in 1958 by Young and Spizizen.  They also demonstrated genetic transformation of
      natural competent B. subtilis cells using exogenous DNA.  It was in 1970 that genetic
      transformation of Escherichia coli using chemically competent cells was reported.  Thus,
      genetic transformation of common bacterial models was established at an early stage in the
      development of bacteriology.  The alternative view is that bacterial models such as B.
      subtilis and E. coli have become the mainstay of this field because of high transformation
      ability.  Genetic transformation techniques remain important for studying numerous bacteria
      and for the advancement of bacteriology, biochemistry, applied microbiology, and microbial
      biotechnology.  Moreover, recent developments in the search for new bacteria and genome
      sequencing have provided numerous effective bacteria that are useful for biological studies
      and industrial applications.  With these developments, there is a greater demand for
      establishing genetic transformation methods for more bacteria.
AU  - Suzuki H
PT  - Journal Article
TA  - Methylation - from DNA, RNa and histones to diseases and treatment
JT  - Methylation - from DNA, RNa and histones to diseases and treatment
SO  - Methylation - from DNA, RNa and histones to diseases and treatment 2012 0: 219-236.

PMID- 26543129
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Caedibacter varicaedens, a Kappa Killer Endosymbiont Bacterium of the Ciliate Paramecium biaurelia.
PG  - e01310-15
AB  - Caedibacter varicaedens is a kappa killer endosymbiont bacterium of the ciliate Paramecium
      biaurelia. Here, we present the draft genome sequence of C.
      varicaedens.
AU  - Suzuki H
AU  - Dapper AL
AU  - Jackson CE
AU  - Lee H
AU  - Pejaver V
AU  - Doak TG
AU  - Lynch M
AU  - Preer JR Jr
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01310-15.

PMID- 21282711
VI  - 3
DP  - 2011
TI  - Comparative Genomic Analysis of the Streptococcus dysgalactiae Species Group: Gene Content, Molecular Adaptation, and Promoter Evolution.
PG  - 168-185
AB  - Comparative genomics of closely related bacterial species with different
      pathogenesis and host preference can provide a means of identifying the specifics
      of adaptive differences. Streptococcus dysgalactiae (SD) is comprised of two
      subspecies: S. dysgalactiae subsp. equisimilis is both a human commensal organism
      and a human pathogen, and S. dysgalactiae subsp. dysgalactiae is strictly an
      animal pathogen. Here, we present complete genome sequences for both taxa, with
      analyses involving other species of Streptococcus but focusing on adaptation in
      the SD species group. We found little evidence for enrichment in biochemical
      categories of genes carried by each SD strain, however, differences in the
      virulence gene repertoire were apparent. Some of the differences could be
      ascribed to prophage and integrative conjugative elements. We identified
      approximately 9% of the nonrecombinant core genome to be under positive
      selection, some of which involved known virulence factors in other bacteria.
      Analyses of proteomes by pooling data across genes, by biochemical category,
      clade, or branch, provided evidence for increased rates of evolution in several
      gene categories, as well as external branches of the tree. Promoters were
      primarily evolving under purifying selection but with certain categories of genes
      evolving faster. Many of these fast-evolving categories were the same as those
      associated with rapid evolution in proteins. Overall, these results suggest that
      adaptation to changing environments and new hosts in the SD species group has
      involved the acquisition of key virulence genes along with selection of
      orthologous protein-coding loci and operon promoters.
AU  - Suzuki H
AU  - Lefebure T
AU  - Hubisz MJ
AU  - Pavinski-Bitar P
AU  - Lang P
AU  - Siepel A
AU  - Stanhope MJ
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2011 3: 168-185.

PMID- 21791952
VI  - 21
DP  - 2011
TI  - Improvement of transformation efficiency by strategic circumvention of restriction barriers in Streptomyces griseus.
PG  - 675-678
AB  - DNA methylation in Streptomyces griseus IFO 13350 was analyzed by high-performance liquid
      chromatographic analysis and bisulfite-based analysis to
      reveal two methylation sites, 5'-GC5mCGGC-3' and 5'-GAG5mCTC-3'. The methylation
      was reconstituted in Escherichia coli by simultaneous expression of S. griseus
      SGR4675 and S. achromogenes M.SacI. The E. coli cells produced plasmids that
      mimicked the methylation profile of S. griseus DNA, which was readily introduced
      into S. griseus. The results of this study raise the possibility of a promising
      approach to establish efficient transformation in several streptomycetes.
AU  - Suzuki H
AU  - Takahashi S
AU  - Osada H
AU  - Yoshida K
PT  - Journal Article
TA  - J. Microbiol. Biotechnol.
JT  - J. Microbiol. Biotechnol.
SO  - J. Microbiol. Biotechnol. 2011 21: 675-678.

PMID- 22814504
VI  - 22
DP  - 2012
TI  - Genetic Transformation of Geobacillus kaustophilus HTA426 by Conjugative Transfer of Host-Mimicking Plasmids.
PG  - 1279-1287
AB  - We established an efficient transformation method for thermophile Geobacillus kaustophilus
      HTA426 using conjugative transfer from
      Escherichia coli of host-mimicking plasmids that imitate DNA
      methylation of strain HTA426 to circumvent its DNA restriction
      barriers. Two conjugative plasmids, pSTE33T and pUCG18T, capable of
      shuttling between E. coli and Geobacillus spp., were constructed. The
      plasmids were first introduced into E. coli BR408, which expressed one
      inherent DNA methylase gene (dam) and two heterologous methylase genes
      from strain HTA426 (GK1380-GK1381 and GK0343-GK0344). The plasmids were
      then directly transferred from E. coli cells to strain HTA426 by
      conjugative transfer using pUB307 or pRK2013 as a helper plasmid.
      pUCG18T was introduced very efficiently (transfer efficiency,
      10(-5)-10(-3) recipient(-1)). pSTE33T showed lower efficiency
      (10(-7)-10(-6) recipient(-1)) but had a high copy number and high
      segregational stability. Methylase genes in the donor substantially
      affected the transfer efficiency, demonstrating that the host-mimicking
      strategy contributes to efficient transformation. The transformation
      method, along with the two distinguishing plasmids, increases the
      potential of G kaustophilus HTA426 as a thermophilic host to be used in
      various applications and as a model for biological studies of this
      genus. Our results also demonstrate that conjugative transfer is a
      promising approach for introducing exogenous DNA into thermophiles.
AU  - Suzuki H
AU  - Yoshida K
PT  - Journal Article
TA  - J. Microbiol. Biotechnol.
JT  - J. Microbiol. Biotechnol.
SO  - J. Microbiol. Biotechnol. 2012 22: 1279-1287.

PMID- 27660772
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Pseudomonas sp. LAB-08 Isolated from Trichloroethene-Contaminated Aquifer Soil.
PG  - e00948-16
AB  - Pseudomonas sp. LAB-08 was isolated from a phenol-fed bioreactor constructed with contaminated
      aquifer soil as the inoculum. Strain LAB-08 utilized phenol as a
      sole carbon and energy source. Here, we report the genome sequence and annotation
      of Pseudomonas sp. LAB-08.
AU  - Suzuki K
AU  - Aziz FA
AU  - Inuzuka Y
AU  - Tashiro Y
AU  - Futamata H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00948-16.

PMID- 8598534
VI  - 9
DP  - 1995
TI  - DMI-1, A new DNA methyltransferase inhibitor produced by Streptomyces sp. strain No. 560.
PG  - 243-252
AB  - A new inhibitor of DNA methyltransferase named DMI-1 has been discovered in
      the culture filtrate of Streptomyces sp. strain No. 560.  DMI-1 was purified by extraction
      with
      ethyl acetate followed by Diaion HP-20SS and silica gel column chromatography.  The structure
      of
      DMI-1 was determined to be 8-methylpentadecanoic acid (C16H32O2).  DMI-1 is a novel inhibitor
      of methyltransferase isolated from microorganisms and is structurally different from
      sinefungin
      and A9145C which are structural analogs of S-adenosylmethionine (methyl donor).  DMI-1 was a
      strong inhibitor of N6-methyladenine-DNA methyltransferase (M.EcoRI, EC2.1.1.72) in a
      noncompetitive manner and its inhibition depended on the pH and temperature in the assay
      media.
AU  - Suzuki K
AU  - Nagao K
AU  - Tokunaga J
AU  - Hirosawa M
AU  - Tsubone H
AU  - Uyeda M
PT  - Journal Article
TA  - J. Enzym. Inhib.
JT  - J. Enzym. Inhib.
SO  - J. Enzym. Inhib. 1995 9: 243-252.

PMID- 8872747
VI  - 10
DP  - 1996
TI  - Inhibition of DNA methyltransferase by microbial inhibitors and fatty acids.
PG  - 271-280
AB  - Streptomyces sp. strain No. 560 produces four kinds of DNA methyltransferase inhibitors in the
      culture filtrate.  One of them, DMI-4 was distinguished from DMI-1, -2 and -3 previously
      reported with respect to certain properties.  DMI-4 is considered to be a triglyceride
      consisting of the fatty acids anteisopentadecanoic acid (C15:0), isopalmitic acid (C16:0) and
      isostearic acid (C18:0) from the results of gas chromatography analysis.  Since DMI-4 contains
      three molecules of fatty acid, and the previously reported DMI-1, 8-methylpentadecanoic acid,
      is analogous to a fatty acid, the inhibitory activity of various fatty acids and their methyl
      esters has been examined against EcoRI DNA methyltransferase (M.EcoRI).  Oleic acid (C18:1)
      was found to be a potent inhibitor of M.EcoRI.  The inhibitory activity of oleic acid was
      shown to be pH- and temperature-dependent and inhibited M.EcoRI in a noncompetitive manner
      with respect to DNA or S-adenosylmethionine (SAM).  The number of carbon atoms and double
      bonds in the fatty acid molecule affected the inhibitory activity, but their methyl esters
      were not inhibitors.  Our results suggest that the length of the carbon chain, the number of
      double bonds and the presence of a carboxyl group and branched methyl group in the fatty acid
      molecule may play an important role in the inhibition of DNA methyltransferase.
AU  - Suzuki K
AU  - Nagao K
AU  - Tokunaga J
AU  - Katayama N
AU  - Uyeda M
PT  - Journal Article
TA  - J. Enzym. Inhib.
JT  - J. Enzym. Inhib.
SO  - J. Enzym. Inhib. 1996 10: 271-280.

PMID- 23868126
VI  - 1
DP  - 2013
TI  - Genome Sequences of Multidrug-Resistant Acinetobacter baumannii Strains from Nosocomial Outbreaks in Japan.
PG  - e00476-13
AB  - Acinetobacter baumannii has emerged worldwide as an important nosocomial pathogen in medical
      institutions. Here, we present the draft genome sequences of A.
      baumannii strains MRY09-0642, MRY10-0558, and MRY12-0277 that were isolated from
      nosocomial outbreaks in Japan between 2008 and 2012 and that are resistant to
      antimicrobial agents, including carbapenems, fluoroquinolones, and
      aminoglycosides.
AU  - Suzuki M
AU  - Matsui M
AU  - Suzuki S
AU  - Rimbara E
AU  - Asai S
AU  - Miyachi H
AU  - Takata T
AU  - Hiraki Y
AU  - Kawano F
AU  - Shibayama K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00476-13.

PMID- 25953190
VI  - 3
DP  - 2015
TI  - Genome Sequence of a Carbapenem-Resistant Strain of Ralstonia mannitolilytica.
PG  - e00405-15
AB  - Ralstonia mannitolilytica, a Gram-negative aerobic bacterium, is an opportunistic human
      pathogen that is becoming more common in cases of nosocomial infections. We
      report for the first time the whole-genome sequence analysis of R.
      mannitolilytica strain MRY14-0246, which carries the intrinsic
      OXA-443/OXA-22-like and OXA-444/OXA-60-like beta-lactamase genes and is resistant
      to meropenem.
AU  - Suzuki M
AU  - Nishio H
AU  - Asagoe K
AU  - Kida K
AU  - Suzuki S
AU  - Matsui M
AU  - Shibayama K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00405-15.

PMID- 24179116
VI  - 1
DP  - 2013
TI  - Genome Sequence of a Strain of the Human Pathogenic Bacterium Pseudomonas alcaligenes That Caused Bloodstream Infection.
PG  - e00919-13
AB  - Pseudomonas alcaligenes, a Gram-negative aerobic bacterium, is a rare opportunistic human
      pathogen. Here, we report the whole-genome sequence of P.
      alcaligenes strain MRY13-0052, which was isolated from a bloodstream infection in
      a medical institution in Japan and is resistant to antimicrobial agents,
      including broad-spectrum cephalosporins and monobactams.
AU  - Suzuki M
AU  - Suzuki S
AU  - Matsui M
AU  - Hiraki Y
AU  - Kawano F
AU  - Shibayama K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00919-13.

PMID- 15933044
VI  - 71
DP  - 2005
TI  - Large-scale engineering of the Corynebacterium glutamicum genome.
PG  - 3369-3372
AB  - The engineering of Corynebacterium glutamicum is important for enhanced production of
      biochemicals. To construct an improved C. glutamicum genome,
      we developed a precise genome excision method based on the Cre/loxP
      recombination system and successfully deleted 11 distinct genomic regions
      identified by comparative analysis of C. glutamicum genomes. Despite the
      loss of several predicted open reading frames, the mutant cells exhibited
      normal growth under standard laboratory conditions. With a total of 250 kb
      (7.5% of the genome), the 11 genomic regions were loaded with cryptic
      prophages, transposons, and genes of unknown function which were
      dispensable for cell growth, indicating recent horizontal acquisitions to
      the genome. This provides an interesting background for functional genomic
      studies and can be used in the improvement of cell traits.
AU  - Suzuki N
AU  - Okayama S
AU  - Nonaka H
AU  - Tsuge Y
AU  - Inui M
AU  - Yukawa H
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2005 71: 3369-3372.

PMID- 17720818
VI  - 73
DP  - 2007
TI  - Rhizobial factors required for stem nodule maturation and maintenance in Sesbania rostrata-Azorhizobium caulinodans ORS571 symbiosis.
PG  - 6650-6659
AB  - The molecular and physiological mechanisms behind the maturation and maintenance of
      N(2)-fixing nodules during development of symbiosis between
      rhizobia and legumes still remain unclear, although the early events of
      symbiosis are relatively well understood. Azorhizobium caulinodans ORS571
      is a microsymbiont of the tropical legume Sesbania rostrata, forming
      N(2)-fixing nodules not only on the roots but also on the stems. In this
      study, 10,080 transposon-inserted mutants of A. caulinodans ORS571 were
      individually inoculated onto the stems of S. rostrata, and those mutants
      that induced ineffective stem nodules, as displayed by halted development
      at various stages, were selected. From repeated observations on stem
      nodulation, 108 Tn5 mutants were selected and categorized into seven
      nodulation types based on size and N(2) fixation activity. Tn5 insertions
      of some mutants were found in the well-known nodulation, nitrogen
      fixation, and symbiosis-related genes, such as nod, nif, and fix,
      respectively, lipopolysaccharide synthesis-related genes, C(4)
      metabolism-related genes, and so on. However, other genes have not been
      reported to have roles in legume-rhizobium symbiosis. The list of newly
      identified symbiosis-related genes will present clues to aid in
      understanding the maturation and maintenance mechanisms of nodules.
AU  - Suzuki S
AU  - Aono T
AU  - Lee KB
AU  - Suzuki T
AU  - Liu CT
AU  - Miwa H
AU  - Wakao S
AU  - Iki T
AU  - Oyaizu H
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2007 73: 6650-6659.

PMID- 24845058
VI  - 5
DP  - 2014
TI  - Physiological and genomic features of highly-alkaliphilic hydrogen-utilizing Betaproteobacteria from a continental serpentinizing site.
PG  - 3900
AB  - Serpentinization, or the aqueous alteration of ultramafic rocks, results in challenging
      environments for life in continental sites due to the combination of extremely high pH, low
      salinity and lack of obvious electron acceptors and carbon sources.  Nevertheless, certain
      Betaproteobacteria have been frequently observed in such environments.  Here we describe
      physiological and genomic features of three related Betaprobacterial strains isolated from
      highly alkaline (pH 11.6) serpentinizing springs at The Cedars, California.  All three strains
      are obligate alkaliphiles with an optimum for growth at pH 11 and are capable of autotrophic
      growth with hydrogen, calcium carbonate and oxygen.  The three strains exhibit differences,
      however, regarding the utilization of organic carbon and electron acceptors.  Their global
      distribution and physiological, genomic and transcriptomic characteristics indicate that the
      strains are adapted to the alkaline and calcium-rich environments represented by the
      terrestrial serpentinizing ecosystems.  We propose placing these strains in a new genus
      'Serpentinomonas'.
AU  - Suzuki S
AU  - Kuenen JG
AU  - Schipper K
AU  - van der Velde S
AU  - Ishii S
AU  - Wu A
AU  - Sorokin DY
AU  - Tenney A
AU  - Meng XY
AU  - Morrill PL
AU  - Kamagata Y
AU  - Muyzer G
AU  - Nealson KH
PT  - Journal Article
TA  - Nat. Commun.
JT  - Nat. Commun.
SO  - Nat. Commun. 2014 5: 3900.

PMID- 28473379
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Brevundimonas sp. Strain SH203, Producing Cellouronate (beta-1,4-Linked Polyglucuronate) Lyase.
PG  - e00262-17
AB  - In this study, we report the draft genome sequence of Brevundimonas sp. strain SH203, which
      was previously isolated from natural soil and has the ability to
      degrade beta-1,4-polygluculonate (cellouronate). This genomic information may
      provide new insight into the mechanisms by which cellouronate is degraded.
AU  - Suzuki T
AU  - Kikuchi M
AU  - Konno N
AU  - Habu N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00262-17.

PMID- 1369358
VI  - 55
DP  - 1991
TI  - A restriction endonuclease (DpaI) from Deleya pacifica IAM 14115, a marine bacterium, an isoschizomer of ScaI.
PG  - 2647-2649
AB  - The marine bacteria have been considered to be important, but unused, uncommon
      and unknown resources in the fields of applied and industrial microbiology.  In
      previous papers, we reported a new restriction endonuclease, designated AgeI,
      from Agrobacterium gelatinovorum Ahrens 1968 IAM 12617, a marine bacterium.
      During the course of our screenings, we have found another marine bacterium to
      produce a restriction endonuclease (DpaI, isoschizomer of ScaI) in a large
      amount within the cells and the enzyme to have unique physiochemical
      properties.
AU  - Suzuki T
AU  - Sato Y
AU  - Yamada Y
AU  - Akagawa-Matsushita M
AU  - Yamasato K
PT  - Journal Article
TA  - Agric. Biol. Chem.
JT  - Agric. Biol. Chem.
SO  - Agric. Biol. Chem. 1991 55: 2647-2649.

PMID- 8987585
VI  - 60
DP  - 1996
TI  - Cloning and nucleotide sequence of ApaLI restriction-modification system from Acetobacter pasteurianus IFO 13753.
PG  - 1401-1405
AB  - The ApaLI restriction-modification system from Acetobacter pasteurianus IFO 13753 recognizes
      the nucleotide sequence GTGCAC.  The gene coding for the ApaLI methylase (M.ApaLI) was cloned
      into Escherichia coli DH5aMCR, and the nucleotide sequence of the gene was analyzed.  The
      M.ApaLI gene coded for a protein of 429 amino acid residues (molecular mass, 46,554 daltons).
      The ApaLI restriction endonuclease (R.ApaLI) gene was analyzed by inverse polymerase chain
      reaction.  The R.ApaLI gene coded for a protein of 375 amino acid residues (molecular mass,
      42,143 daltons).  The two genes had the same orientation separated by two base pairs.  The
      deduced amino acid sequence of M.ApaLI shows significant similarities to the family of
      cytosine-5 methylases.  However, the deduced amino acid sequence of R.ApaLI did not have as
      much relatedness in the nucleotide sequence, when compared with those of the other restriction
      endonucleases already reported.
AU  - Suzuki T
AU  - Sugimoto E
AU  - Tahara Y
AU  - Yamada Y
PT  - Journal Article
TA  - Biosci. Biotechnol. Biochem.
JT  - Biosci. Biotechnol. Biochem.
SO  - Biosci. Biotechnol. Biochem. 1996 60: 1401-1405.

PMID- 8901102
VI  - 60
DP  - 1996
TI  - Cloning and nucleotide sequence of the AgeI methylase gene from Agrobacterium gelatinovorum IAM 12617, a marine bacterium.
PG  - 444-447
AB  - The AgeI restriction-modification system from a marine bacterium, Agrobacterium
      gelatinovorum IAM 12617, recognizes the nucleotide sequence ACCGGT.  The gene coding for
      the AgeI methylase (M.AgeI) was cloned into Escherichia coli DH5 alphaMCR, and the
      nucleotides of the gene were sequenced.  The M.AgeI gene coded for a protein of 429 amino acid
      residues (molecular mass, 47,358 daltons).  The deduced amino acid sequence of M.AgeI was
      compared with those of other methylases and showed that there are high degrees of similarity
      in
      some cytosine-5-methylases.
AU  - Suzuki T
AU  - Sugimoto E
AU  - Tahara Y
AU  - Yamada Y
PT  - Journal Article
TA  - Biosci. Biotechnol. Biochem.
JT  - Biosci. Biotechnol. Biochem.
SO  - Biosci. Biotechnol. Biochem. 1996 60: 444-447.

PMID- 21815100
VI  - 765
DP  - 2011
TI  - Plasmid Artificial Modification: A Novel Method for Efficient DNA Transfer into Bacteria.
PG  - 309-326
AB  - Bacterial transformation is an essential component of many molecular biological techniques,
      but bacterial restriction-modification (R-M)
      systems can preclude the efficient introduction of shuttle vector
      plasmids into target bacterial cells. Whole-genome DNA sequences have
      recently been published for a variety of bacteria. Using homology and
      motif analyses, putative R-M genes can be identified from genome
      sequences. Introducing DNA methyltransferase genes into Escherichia
      coli cells causes subsequently transformed plasmids to be modified by
      these enzymes.We propose a new method, designated Plasmid Artificial
      Modification (PAM). A PAM plasmid encoding the modification enzymes
      expressed by the target bacterial host is transformed into E. coli (PAM
      host). Propagation of a shuttle vector from the PAM host to the target
      bacterium ensures that the plasmid will be modified such that it is
      protected from restriction endonuclease digestion in the target
      bacterium. The result will be a higher transformation efficiency.Here,
      we describe the use of PAM and electroporation to transform
      Bifidobacterium adolescentis ATCC15703. By introducing two genes
      encoding modification enzymes, we improved transformation efficiency
      10(5)-fold.
AU  - Suzuki T
AU  - Yasui K
PT  - Journal Article
TA  - Methods Mol. Biol.
JT  - Methods Mol. Biol.
SO  - Methods Mol. Biol. 2011 765: 309-326.

PMID- 22208198
VI  - 101
DP  - 2011
TI  - Visual Analysis of Concerted Cleavage by Type IIF Restriction Enzyme SfiI in Subsecond Time Region.
PG  - 2992-2998
AB  - Many DNA regulatory factors require communication between distantly separated DNA sites for
      their activity.  The type IIF restriction enzyme SfiI is often used as a model system of site
      communication.  Here, we used fast-scanning atomic force microscopy to monitor the DNA
      cleavage process with SfiI and the changes in the single SfiI-DNA complex in the presence of
      either Mg2+ or Ca2+ at a scan rate of 1-2 fps.  The increased time resolution allowed us to
      visualize the concerted cleavage of the protein at two cognate sites.  The four termini
      generated by the cleavage were released in a multistep manner.  The high temporal resolution
      enabled us to visualize the translocation of a DNA strand on a looped complex and
      intersegmental transfer of the SfiI protein in which swapping of the site is performed without
      protein dissociation.  On the basis of our results, we propose that the SfiI tetramer can
      remain bound to one of the sites even after cleavage, allowing the other site on the DNA
      molecule to fill the empty DNA-binding cleft by combining a one-dimensional diffusion-mediated
      sliding and a segment transfer mechanism.
AU  - Suzuki Y
AU  - Gilmore JL
AU  - Yoshimura SH
AU  - Henderson RM
AU  - Lyubchenko YL
AU  - Takeyasu K
PT  - Journal Article
TA  - Biophys. J.
JT  - Biophys. J.
SO  - Biophys. J. 2011 101: 2992-2998.

PMID- 23723396
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of an Escherichia coli O157:H43 Strain Isolated from Cattle.
PG  - e00263-13
AB  - Here we report the draft genome sequence of an Escherichia coli O157:H43 strain,  designated
      T22, with an atypical virulence gene profile and isolated from healthy
      cattle. T22 produces cytolethal distending toxin V (CDT-V) and belongs to
      phylogenetic group B1 and sequence type 155 (ST155).
AU  - Svab D
AU  - Horvath B
AU  - Szucs A
AU  - Maroti G
AU  - Toth I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00263-13.

PMID- 16417459
VI  - 70
DP  - 2005
TI  - Location of the bases modified by M.BcoKIA and M.BcoKIB methylases in the sequence 5'-CTCTTC-3'/5'-GAAGAG-3'.
PG  - 1363-1366
AB  - The strain Bacillus coagulans K contains two DNA-methyltransferases, M.BcoKIA and M.BcoKIB,
      which recognize the sequence 5'-CTCTTC-3'/5'-GAAGAG-3' and possess N4-methylcytosine and
      N6-methyladenine specificities, respectively.  A special construct containing the recognition
      site of BcoKI and sits of four IIS restriction endonucleases (IIS restriction endonuclease
      cassette) was designed to locate the nucleotides modified by the methylases.  The modified
      bases were determined as: 5'm4CTCTTC-3'/5'-GAAGAm6G-3'.
AU  - Svadbina IV
AU  - Matvienko NN
AU  - Zheleznaya LA
AU  - Matvienko NI
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2005 70: 1363-1366.

PMID- 
VI  - 69
DP  - 2004
TI  - Isolation and characterization of site-specific DNA- methyltransferases from Bacillus coagulans K.
PG  - 372-379
AB  - Two site-specific DNA methyltransferases, M.BcoKIA and M.BcoKIB, were isolated from the
      thermophilic strain Bacillus coagulans K. Each of the methylases protects the recognition site
      5'-CTCTTC-3'/5'-GAAGAG-3' from cleavage with the cognate restriction endonuclease BcoKI.
      It is shown that M.BcoKIB is an N6-adenine specific methylase and M.BcoKIA is an N4-cytosine
      specific methylase. According to bisulfite mapping, M.BcoKIA methylates the first cytosine in
      the sequence 5'-CTCTTC-3'.
AU  - Svadbina IV
AU  - Zelinskaya NV
AU  - Kovalevskaya NP
AU  - Zheleznaya LA
AU  - Matvienko NI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 2004 69: 372-379.

PMID- 12765526
VI  - 68
DP  - 2003
TI  - Bacillus species LU4 is an effective producer of thermostable site-specific endonuclease BspLU4I, an isoschizomer of AvaI.
PG  - 429-435
AB  - The site-specific endonuclease BspLU4I was discovered in the thermophilic Bacillus species LU4
      strain and purified to functionally pure state by
      chromatography on blue agarose, hydroxyapatite HTP, and heparin-Sepharose
      columns. Analysis of cleavage patterns of different DNAs with known
      nucleotide sequences demonstrated that the enzyme recognizes the CPyCGPuG
      site on the DNA. Cleavage points in the sequence were determined with the
      elongated primer method. It was shown that the endonuclease is an
      isoschizomer of AvaI. The final yield of the enzyme is 2.25.10(6) units
      per g wet biomass.
AU  - Svadbina IV
AU  - Zheleznyakova EN
AU  - Zheleznaya LA
AU  - Matvienko NI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 2003 68: 429-435.

PMID- 15996102
VI  - 44
DP  - 2005
TI  - DNA cytosine C-5 methyltransferase Dnmt1: Catalysis-dependent release of allosteric inhibition.
PG  - 9472-9485
AB  - We followed the cytosine C-5 exchange reaction with Dnmt1 to characterize its preference for
      different DNA substrates, its
      allosteric regulation, and to provide a basis for comparison with the
      bacterial enzymes. We determined that the methyl transfer is
      rate-limiting, and steps up to and including the cysteine-cytosine
      covalent intermediate are in rapid equilibrium. Changes in these rapid
      equilibrium steps account for many of the previously described features
      of Dnmt1 catalysis and specificity including faster reactions with
      premethylated DNA versus unmethylated DNA, faster reactions with DNA in
      which guanine is replaced with inosine [poly(dC-dG) vs poly(dI-dC)],
      and 10-100-fold slower catalytic rates with Dnmt1 relative to the
      bacterial enzyme M.HhaI. Dnmt1 interactions with the guanine within the
      CpG recognition site can prevent the premature release of the target
      base and solvent access to the active site that could lead to mutagenic
      deamination. Our results suggest that the beta-elimination step
      following methyl transfer is not mediated by free solvent. Dnmt1 shows
      a kinetic lag in product formation and allosteric inhibition with
      unmethylated DNA that is not observed with premethylated DNA. Thus, we
      suggest the enzyme undergoes a slow relief from allosteric inhibition
      upon initiation of catalysis on unmethylated DNA. Notably, this relief
      from allosteric inhibition is not caused by self-activation through the
      initial methylation reaction, as the same effect is observed during the
      cytosine C5 exchange reaction in the absence of AdoMet. We describe
      limitations in the Michaelis-Menten kinetic analysis of Dnmt1 and
      suggest alternative approaches.
AU  - Svedruzic AM
AU  - Reich NO
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2005 44: 9472-9485.

PMID- 18220765
VI  - 15
DP  - 2008
TI  - Mammalian cytosine DNA methyltransferase Dnmt1: Enzymatic mechanism, novel mechanism-based inhibitors, and RNA-directed DNA methylation.
PG  - 92-106
AB  - This is a review of the enzymatic mechanism of DNA methyltransferase Dnmt1 and analysis of its
      implications on regulation of DNA methylation
      in mammalian cells and design of novel mechanism-based inhibitors. The
      methylation reaction by Dnmt1 has different phases that depend on DNA
      substrate and allosteric regulation. Consequently, depending on the
      phase, the differences in catalytic rates between unmethylated and
      pre-methylated DNA can vary between 30-40 fold, 3-6 fold or only 1
      fold. The allosteric site and the active site can bind different
      molecules. Allosteric activity depends on DNA sequence, methylation
      pattern and DNA structure (single stranded vs. double stranded). Dnmt1
      binds poly(ADP-ribose) and some RNA molecules. The results on kinetic
      preferences, allosteric activity and binding preference of Dnmt1 are
      combined together in one comprehensive model mechanism that can address
      regulation of DNA methylation in cells; namely, inhibition of DNA
      methylation by poly(ADP-ribose), RNA-directed DNA methylation by
      methylated and unmethylated non-coding RNA molecules, and transient
      interactions between Dnmt1 and genomic DNA. Analysis of reaction
      intermediates showed that equilibrium between base-flipping and
      base-restacking events can be the key mechanism in control of enzymatic
      activity. The two events have equal but opposite effect on accumulation
      of early reaction intermediates and methylation rates. The accumulation
      of early reaction intermediates can be exploited to improve the current
      inhibitors of Dnmt1 and achieve inhibition without toxic modifications
      in genomic DNA.
      [1,2-dihydropyrimidin-2-one]-5-methylene-(methylsulfonium)-adenosyl is
      described as the lead compound.
AU  - Svedruzic ZM
PT  - Journal Article
TA  - Curr. Med. Chem.
JT  - Curr. Med. Chem.
SO  - Curr. Med. Chem. 2008 15: 92-106.

PMID- 
VI  - 223
DP  - 2002
TI  - Enzymatic properties of mouse cytosine DNA methyltransferase DNMT1.
PG  - C75
AB  - DNA methylation is a gene control and chromatin organization mechanism that has been
      associated with oncogene activation, mutagenic cytosine deamination, cell cycle changes,
      retrovirus silencing, cell differentiation, and aging. This work evaluates the main catalytic
      features of Dnmt1, the principal methyltransferase in eukaryotic cells.  Pre-steady state and
      steady state kinetics were used together with solvent kinetic isotope effect and pH studies to
      analyze catalytic preference for pre-methylated DNA, enzyme processivity on its DNA substrate,
      allosteric regulation and likelihood of mutagenic deamination. The preference for
      pre-methylated DNA is due to a faster target base attack, faster methyl transfer and faster
      acid base catalysis that is likely to come from a specific conformational change in the active
      site. Unlike its bacterial counterparts, Dnmt1 can recognize DNA as pre-methylated even when
      5mC is one out of fifteen cytosines, however the enzyme is not self activated early in the
      methylation reaction on unmethylated DNA. A novel analysis of processivity rate constants
      showed that the processivity of Dnmt1 depends on the substrate and can be regulated through
      the allosteric site. The extent of allosteric regulation depends on catalytic activity, DNA
      sequence and the methylation status. DNA binding at the allosteric site inhibits catalytic
      action of Dnmt1 and initiates DNA release from its active site. Interaction between Dnmt1 and
      proliferating cell nuclear antigen (PCNA) facilitates the on rate for the substrate DNA, and
      has no effect on enzyme processivity. Analogues of S-Adenosylmethionine and solvent kinetic
      isotope effect studies showed that enzyme mediated mutagenesis and cytosine deamination are
      due to enzymes inability to protect its reactive intermediates. Mutagenesis is likely in
      catalytic action by mammalian and bacterial cytosine methyltransferases, however mammalian
      enzyme is 200 times less likely to be mutagenic in the absence of the cofactor. Presented
      studies give enzymatic insights to biology of DNA methylation and show novel methods to study
      C5 pyrimidine methyltransferases.
AU  - Svedruzic ZM
AU  - Reich NO
PT  - Journal Article
TA  - ACS Abstracts
JT  - ACS Abstracts
SO  - ACS Abstracts 2002 223: C75.

PMID- 16274244
VI  - 44
DP  - 2005
TI  - Mechanism of allosteric regulation of Dnmt1's processivity.
PG  - 14977-14988
AB  - We have analyzed the relationship between the allosteric regulation and processive catalysis
      of DNA methyltransferase 1 (Dnmt1). Processivity is
      described quantitatively in terms of turnover rate, DNA dissociation rate,
      and processivity probability. Our results provide further evidence that
      the active site and the allosteric sites on Dnmt1 can bind DNA
      independently. Dnmt1's processive catalysis on unmethylated DNA is
      partially inhibited when the allosteric site binds unmethylated DNA and
      fully inhibited when the allosteric site binds a single-stranded
      oligonucleotide inhibitor. The partial inhibition by unmethylated DNA is
      caused by a decrease in the turnover rate and an increase in the substrate
      DNA dissociation rate. Processive catalysis with premethylated DNA is not
      affected if the allosteric site is exposed to premethylated DNA but is
      fully inhibited if the allosteric site binds unmethylated DNA or
      poly(dA-dT). In sum, the occupancy of the allosteric site modulates the
      enzyme's commitment to catalysis, which reflects the nature of the
      substrate and the DNA bound at the allosteric site. Our in vitro results
      are consistent with the possibility that the processive action of Dnmt1
      may be regulated in vivo by specific regulatory nucleic acids such as DNA,
      RNA, or poly(ADP-ribose).
AU  - Svedruzic ZM
AU  - Reich NO
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2005 44: 14977-14988.

PMID- 21725021
VI  - 193
DP  - 2011
TI  - Genome Sequence of the Arctic Methanotroph Methylobacter tundripaludum SV96.
PG  - 6418-6419
AB  - Methylobacter tundripaludum SV96(T) (ATCC BAA-1195) is a psychrotolerant aerobic
      methane-oxidizing gammaproteobacterium (Methylococcales,
      Methylococcaceae) living in High Arctic wetland soil. The strain was
      isolated from soil harvested in July 1996 close to the settlement
      Ny-Alesund, Svalbard, Norway (78 degrees 56'N, 11 degrees 53'E), and
      described as a novel species in 2006. The genome includes pmo and pxm
      operons encoding copper membrane monooxygenases (Cu-MMOs), genes required
      for nitrogen fixation, and the nirS gene implicated in dissimilatory
      nitrite reduction to NO but no identifiable inventory for further
      processing of nitrogen oxides. These genome data provide the basis to
      investigate M. tundripaludum SV96, identified as a major player in the
      biogeochemistry of Arctic environments.
AU  - Svenning MM et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6418-6419.

PMID- 25792039
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Francisella guangzhouensis Strain 08HL01032T, Isolated from Air-Conditioning Systems in China.
PG  - e00024-15
AB  - We present the complete genome sequence of Francisella guangzhouensis strain 08HL01032(T),
      which consists of one chromosome (1,658,482 bp) and one plasmid
      (3,045 bp) with G+C contents of 32.0% and 28.7%, respectively.
AU  - Svensson D
AU  - Ohrman C
AU  - Backman S
AU  - Karlsson E
AU  - Nilsson E
AU  - Bystrom M
AU  - Larkeryd A
AU  - Myrtennas K
AU  - Stenberg P
AU  - Qu PH
AU  - Trygg J
AU  - Scholz HC
AU  - Forsman M
AU  - Sjodin A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00024-15.

PMID- 11729191
VI  - 277
DP  - 2002
TI  - Water-assisted dual mode cofactor recognition by HhaI DNA methyltransferase.
PG  - 4042-4049
AB  - Energetically competent binary recognition of the cofactor S-adenosyl-L-methionine (AdoMet)
      and the product S-adenosyl-L-homocysteine (AdoHcy) by the DNA (cytosine C-5) methyltransferase
      (M.HhaI) is demonstrated herein. Titration calorimetry reveals a dual mode, involving a
      primary dominant exothermic reaction followed by a weaker endothermic one, for the recognition
      of AdoMet and AdoHcy by M.HhaI. Conservation of the bimodal recognition in W41I and W41Y
      mutants of M.HhaI excludes the cation-Pi interaction between the methylsulfonium group of
      AdoMet and the Pi face of the Trp(41) indole ring from a role in its origin. Small magnitude
      of temperature-independent heat capacity changes upon AdoMet or AdoHcy binding by M.HhaI
      preclude appreciable conformational alterations in the reacting species. Coupled
      osmotic-calorimetric analyses of AdoMet and AdoHcy binding by M.HhaI indicate that a net
      uptake of nearly eight and 10 water molecules, respectively, assists their primary
      recognition. A change in water activity at constant temperature and pH is sufficient to
      engender and conserve enthalpy-entropy compensation, consistent with a true osmotic effect.
      The results implicate solvent reorganization in providing the major contribution to the origin
      of this isoequilibrium phenomenon in AdoMet and AdoHcy recognition by M.HhaI. The observations
      provide unequivocal evidence for the binding of AdoMet as well as AdoHcy to M.HhaI in solution
      state. Isotope partitioning analysis and preincubation studies favor a random mechanism for
      M.HhaI-catalyzed reaction. Taken together, the results clearly resolve the issue of cofactor
      recognition by free M.HhaI, specifically in the absence of DNA, leading to the formation of an
      energetically and catalytically competent binary complex.
AU  - Swaminathan CP
AU  - Sankpal UT
AU  - Rao DN
AU  - Surolia A
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2002 277: 4042-4049.

PMID- 8190639
VI  - 22
DP  - 1994
TI  - Restriction generated oligonucleotides utilizing the two base recognition endonuclease CviJI.
PG  - 1470-1475
AB  - The conversion of an anonymous DNA sample into numerous oligonucleotides is enzymatically
      feasible using an unusual restriction endonuclease, CviJI. Depending on reaction conditions,
      CviJI is capable of digesting DNA at a two or three base recognition sequence. CviJI normally
      cleaves RGCY sites between the G and C to leave blunt ends. Under 'relaxed' conditions CviJI
      cleaves RGCY, and RGCR/YGCY, but not YGCR sites. In theory, CviJI* restriction of pUC19 (2686
      bp) should produce 157 fragments, 75% of which are smaller than 20 bp. Instead, 96% of the
      CviJI* fragments were 18-56 bp long and none of the fragments generates sequence specific
      oligonucleotides homologous for the cognate template. The enzymatic conversion of anonymous
      DNA into sequence specific oligomers has implications for several conventional and novel
      molecular biology procedures.
AU  - Swaminathan N
AU  - George D
AU  - McMaster K
AU  - Szablewski J
AU  - Van Etten JL
AU  - Mead DA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1994 22: 1470-1475.

PMID- 8692682
VI  - 24
DP  - 1996
TI  - Molecular cloning of the three base restriction endonuclease R.CviJI from eukaryotic Chlorella virus IL-3A.
PG  - 2463-2469
AB  - R.CviJI is unique among site-specific restriction endonucleases in that its activity can be
      modulated to recognize either a two or three base sequence.  Normally R.CviJI cleaves RGCY
      sites between the G and C to leave blunt ends.  In the presence of ATP, R.CviJI cleaves RGCN
      and YGCY sites, but not YGCR sites.  The gene encoding R.CviJI was cloned from the eukaryotic
      Chlorella virus IL-3A and expressed in Escherichia coli.  The primary E. coli cviJIR gene
      product is a 278 amino acid protein initiated from a GTG codon, rather than the expected 358
      amino acid protein, displays the normal restriction activity but not the R.CviJI* activity of
      the native enzyme.  Nine restriction and modification proteins which recognize a central GC or
      CG sequence share short regions of identity with R.CviJI amino acids 144-235, suggesting that
      this region is the recognition and/or catalytic domain.
AU  - Swaminathan N
AU  - Mead DA
AU  - McMaster K
AU  - George D
AU  - Van Etten JL
AU  - Skowron PM
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1996 24: 2463-2469.

PMID- 28619804
VI  - 5
DP  - 2017
TI  - Permanent Draft Genome Sequence for Frankia sp. Strain Cc1.17, a Nitrogen-Fixing  Actinobacterium Isolated from Root Nodules of Colletia cruciata.
PG  - e00530-17
AB  - Frankia sp. strain Cc1.17 is a member of the Frankia lineage 3, the organisms of  which are
      able to reinfect plants of the Eleagnaceae, Rhamnaceae, and Myricaceae
      families and the genera Gynmnostoma and Alnus Here, we report the 8.4-Mbp draft
      genome sequence, with a G+C content of 72.14% and 6,721 candidate protein-coding
      genes.
AU  - Swanson E
AU  - Oshone R
AU  - Nouioui I
AU  - Abebe-Akele F
AU  - Simpson S
AU  - Morris K
AU  - Thomas WK
AU  - Sen A
AU  - Ghodhbane-Gtari F
AU  - Gtari M
AU  - Tisa LS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00530-17.

PMID- 26722013
VI  - 3
DP  - 2015
TI  - Permanent Draft Genome Sequence of Frankia sp. Strain AvcI1, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Alnus viridis subsp. crispa  Grown in Canada.
PG  - e01511-15
AB  - Frankia strain AvcI1, isolated from root nodules of Alnus viridis subsp. crispa,  is a member
      of Frankia lineage Ia, which is able to reinfect plants of the
      Betulaceae and Myricaceae families. Here, we report a 7.7-Mbp draft genome
      sequence with a G+C content of 72.41% and 6,470 candidate protein-encoding genes.
AU  - Swanson E
AU  - Oshone R
AU  - Simpson S
AU  - Morris K
AU  - Abebe-Akele F
AU  - Thomas WK
AU  - Tisa LS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01511-15.

PMID- 26679592
VI  - 3
DP  - 2015
TI  - Permanent Draft Genome Sequence of Frankia sp. Strain ACN1ag, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Alnus glutinosa.
PG  - e01483-15
AB  - Frankia strain ACN1(ag) is a member of Frankia lineage Ia, which are able to re-infect plants
      of the Betulaceae and Myricaceae families. Here, we report a
      7.5-Mbp draft genome sequence with a G+C content of 72.35% and 5,687 candidate
      protein-encoding genes.
AU  - Swanson E
AU  - Oshone R
AU  - Simpson S
AU  - Morris K
AU  - Abebe-Akele F
AU  - Thomas WK
AU  - Tisa LS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01483-15.

PMID- 17986450
VI  - 36
DP  - 2008
TI  - The Arabidopsis Information Resource (TAIR): gene structure and function annotation.
PG  - D1009-D1014
AB  - The Arabidopsis Information Resource (TAIR, http://arabidopsis.org) is the model organism
      database for the fully sequenced and intensively studied
      model plant Arabidopsis thaliana. Data in TAIR is derived in large part
      from manual curation of the Arabidopsis research literature and direct
      submissions from the research community. New developments at TAIR include
      the addition of the GBrowse genome viewer to the TAIR site, a redesigned
      home page, navigation structure and portal pages to make the site more
      intuitive and easier to use, the launch of several TAIR web services and a
      new genome annotation release (TAIR7) in April 2007. A combination of
      manual and computational methods were used to generate this release, which
      contains 27,029 protein-coding genes, 3889 pseudogenes or transposable
      elements and 1123 ncRNAs (32,041 genes in all, 37,019 gene models). A
      total of 681 new genes and 1002 new splice variants were added. Overall,
      10,098 loci (one-third of all loci from the previous TAIR6 release) were
      updated for the TAIR7 release.
AU  - Swarbreck D
AU  - Wilks C
AU  - Lamesch P
AU  - Berardini TZ
AU  - Garcia-Hernandez M
AU  - Foerster H
AU  - Li D
AU  - Meyer T
AU  - Muller R
AU  - Ploetz L
AU  - Radenbaugh A
AU  - Singh S
AU  - Swing V
AU  - Tissier C
AU  - Zhang P
AU  - Huala E
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2008 36: D1009-D1014.

PMID- 25414495
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Psychrotrophic Acinetobacter sp. Strain MN12 (MTCC 10786), Which Produces a Low-Temperature-Active and Alkaline-Stable Peptidase.
PG  - e01167-14
AB  - We report here the draft genome sequence of Acinetobacter sp. strain MN12 (MTCC 10786), which
      is a psychrotrophic bacterium that produces an extracellular
      low-temperature-active and alkaline-stable peptidase. The draft genome assembly
      of Acinetobacter sp. MN12 has a size of 4.31 Mbp, with a G+C content of 40.75%.
AU  - Swarnkar MK
AU  - Salwan R
AU  - Kasana RC
AU  - Singh AK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01167-14.

PMID- Not included in PubMed...
VI  - 31
DP  - 1992
TI  - Construction of a mechanism-based inhibitor for EcoRI DNA methyltransferase.
PG  - 2206
AB  - Our results using N-ethylmaleimide modification suggest that cysteine 223 is
      critical for the EcoRI DNA methyltransferase catalyzed methylation of the
      second adenine in the GAATTC recognition sequence.  A plausible catalytic
      mechanism involving this cysteine is shown below: A key feature is the
      formation of a methylase-DNA covalent intermediate.  We are testing this
      mechanism by incorporating a 6-chloropurine riboside into the DNA substrate.
      This substituted analogue is proposed to act as a mechanism-based or active
      site directed inactivator due to the excellent leaving group potential of the
      6-chloro moiety.  We are submitting this analogue to inactivation analysis and
      isolating the peptide sequence attached to the DNA to determine the reactive
      residue in the catalytic site of EcoRI DNA methyltransferase.
AU  - Sweetnam KR
AU  - Reich NO
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1992 31: 2206.

PMID- Not carried by PubMed...
VI  - 203
DP  - 1992
TI  - Construction of a mechanism-based inhibitor for EcoRI DNA methyltransferase.
PG  - 102-BIOL
AB  - Our results using N-ethyl maleimide modification suggest that cysteine 223 is critical for the
      EcoRI DNA methyltransferase catalyzed methylation of the second adenine in the GAATTC
      recognition sequence. A plausible catalytic mechanism involving this cysteine is shown below:
      a key feature is the formation of a methylase-DNA covalent intermediate. We are testing this
      mechanism by incorporating a 6-chloropurine riboside into the DNA substrate. This substituted
      analog is proposed to act as a mechanism based or active site directed inactivator due to the
      excellent leaving group potential of the 6-chloro moiety. We are submitting this analog to
      inactivation analysis and isolating the peptide sequence attached to the DNA to determine the
      reactive residue in the catalytic site of EcoRI DNA methyltransferase.
AU  - Sweetnam KR
AU  - Reich NO
PT  - Journal Article
TA  - ACS Abstracts
JT  - ACS Abstracts
SO  - ACS Abstracts 1992 203: 102-BIOL.

PMID- 18252824
VI  - 105
DP  - 2008
TI  - Niche adaptation and genome expansion in the chlorophyll d-producing cyanobacterium Acaryochloris marina.
PG  - 2005-2010
AB  - Acaryochloris marina is a unique cyanobacterium that is able to produce chlorophyll d as its
      primary photosynthetic pigment and thus efficiently
      use far-red light for photosynthesis. Acaryochloris species have been
      isolated from marine environments in association with other oxygenic
      phototrophs, which may have driven the niche-filling introduction of
      chlorophyll d. To investigate these unique adaptations, we have sequenced
      the complete genome of A. marina. The DNA content of A. marina is composed
      of 8.3 million base pairs, which is among the largest bacterial genomes
      sequenced thus far. This large array of genomic data is distributed into
      nine single-copy plasmids that code for >25% of the putative ORFs. Heavy
      duplication of genes related to DNA repair and recombination (primarily
      recA) and transposable elements could account for genetic mobility and
      genome expansion. We discuss points of interest for the biosynthesis of
      the unusual pigments chlorophyll d and alpha-carotene and genes
      responsible for previously studied phycobilin aggregates. Our analysis
      also reveals that A. marina carries a unique complement of genes for these
      phycobiliproteins in relation to those coding for antenna proteins related
      to those in Prochlorococcus species. The global replacement of major
      photosynthetic pigments appears to have incurred only minimal
      specializations in reaction center proteins to accommodate these alternate
      pigments. These features clearly show that the genus Acaryochloris is a
      fitting candidate for understanding genome expansion, gene acquisition,
      ecological adaptation, and photosystem modification in the cyanobacteria.
AU  - Swingley WD et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2008 105: 2005-2010.

PMID- 17098896
VI  - 189
DP  - 2007
TI  - The complete genome sequence of Roseobacter denitrificans reveals a mixotrophic rather than photosynthetic metabolism.
PG  - 683-690
AB  - Purple aerobic anoxygenic phototrophs (AAPs) are the only organisms known to capture light
      energy to enhance growth only in the presence of oxygen
      but do not produce oxygen. The highly adaptive AAPs compose more than 10%
      of the microbial community in some euphotic upper ocean waters and are
      potentially major contributors to the fixation of the greenhouse gas CO2.
      We present the complete genomic sequence and feature analysis of the AAP
      Roseobacter denitrificans, which reveal clues to its physiology. The
      genome lacks genes that code for known photosynthetic carbon fixation
      pathways, and most notably missing are genes for the Calvin cycle enzymes
      ribulose bisphosphate carboxylase (RuBisCO) and phosphoribulokinase.
      Phylogenetic evidence implies that this absence could be due to a gene
      loss from a RuBisCO-containing alpha-proteobacterial ancestor. We describe
      the potential importance of mixotrophic rather than autotrophic CO2
      fixation pathways in these organisms and suggest that these pathways
      function to fix CO2 for the formation of cellular components but do not
      permit autotrophic growth. While some genes that code for the
      redox-dependent regulation of photosynthetic machinery are present, many
      light sensors and transcriptional regulatory motifs found in purple
      photosynthetic bacteria are absent.
AU  - Swingley WD
AU  - Sadekar S
AU  - Mastrian SD
AU  - Matthies HJ
AU  - Hao J
AU  - Ramos H
AU  - Acharya CR
AU  - Conrad AL
AU  - Taylor HL
AU  - Dejesa LC
AU  - Shah MK
AU  - O'huallachain ME
AU  - Lince MT
AU  - Blankenship RE
AU  - Beatty JT
AU  - Touchman JW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2007 189: 683-690.

PMID- 2987032
VI  - 184
DP  - 1985
TI  - Replacement of the deoxycytidine residues in Rhizobium bacteriophage RL38JI DNA.
PG  - 294-298
AB  - Rhizobium phage RL38JI DNA is resistant to cleavage by a variety of restriction
      endonucleases, and is only partially sensitive to digestion by pancreatic DNase
      I or by micrococcal nuclease.  We have found that a mixture of DNase I, P1
      nuclease, and bacterial alkaline phosphatase will quantitatively digest RL38JI
      DNA to deoxyribonucleosides.  HPLC analysis revealed that dCyd is nearly
      totally absent among these digestion products, while dGuo, dAdo, and Thd are
      readily detected.  Three additional peaks are always present; their retention
      properties correspond to no known modified deoxyribonucleosides.  Thus it
      appears that dCyd is replaced in phage RL38JI DNA by as many as 3 different
      modified residues.
AU  - Swinton D
AU  - Hattman S
AU  - Benzinger R
AU  - Buchanan-Wollaston V
AU  - Beringer J
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1985 184: 294-298.

PMID- 6369315
VI  - 80
DP  - 1983
TI  - Purification and characterization of the unusual deoxynucleoside, alpha-N-(9-beta-D-2'-deoxyribofuranosylpurin-t-yl) glycinamide, specified by the phage Mu modification function.
PG  - 7400-7404
AB  - Bacteriophage Mu encodes a protein that modifies ~15% of DNA adenine residues
      to a new and unusual form.  Modified DNA was enzymatically digested to
      deoxynucleosides, and the products were fractionated by HPLC.  A modified
      adenine nucleoside, designated dA'/x, was purified and its molecular structure
      was established by mass spectrometry.  We show that dA'/x is
      alpha-N-(9-beta-D-2'-deoxyribofuranosylpurin-t-yl)-glycinamide.  The dA'/x
      obtained from DNA was indistinguishable from the synthetic product with respect
      to its chromatographic behavior (HPLC and gas chromatography) and mass
      spectrum.  Acid hydrolysis degrades dA'/x to produce N6-carboxymethyladenine;
      this compound corresponds to the base Ax observed in earlier studies.
AU  - Swinton D
AU  - Hattman S
AU  - Crain PF
AU  - Cheng C-S
AU  - Smith DL
AU  - McCloskey JA
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1983 80: 7400-7404.

PMID- 21952543
VI  - 193
DP  - 2011
TI  - Genome Sequence of Thermotoga sp. Strain RQ2, a Hyperthermophilic Bacterium Isolated from a Geothermally Heated Region of the Seafloor near  Ribeira Quente, the Azores.
PG  - 5869-5870
AB  - Thermotoga sp. strain RQ2 is probably a strain of Thermotoga maritima. Its complete genome
      sequence allows for an examination of the extent and
      consequences of gene flow within Thermotoga species and strains.
      Thermotoga sp. RQ2 differs from T. maritima in its genes involved in
      myo-inositol metabolism. Its genome also encodes an apparent fructose
      phosphotransferase system (PTS) sugar transporter. This operon is also
      found in Thermotoga naphthophila strain RKU-10 but no other Thermotogales.
      These are the first reported PTS transporters in the Thermotogales.
AU  - Swithers KS et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5869-5870.

PMID- 21914881
VI  - 193
DP  - 2011
TI  - Genome Sequence of Kosmotoga olearia Strain TBF 19.5.1, a Thermophilic Bacterium with a Wide Growth Temperature Range, Isolated from the Troll B  Oil Platform in the North Sea.
PG  - 5566-5567
AB  - Kosmotoga olearia strain TBF 19.5.1 is a member of the Thermotogales that grows best at 65
      degrees C and very well even at 37 degrees C. Information
      about this organism is important for understanding the evolution of
      mesophiles from thermophiles. Its genome sequence reveals extensive gene
      gains and a large content of mobile genetic elements. It also contains
      putative hydrogenase genes that have no homologs in the other member of
      the Thermotogales.
AU  - Swithers KS
AU  - Dipippo JL
AU  - Bruce DC
AU  - Detter C
AU  - Tapia R
AU  - Han S
AU  - Goodwin LA
AU  - Han J
AU  - Woyke T
AU  - Pitluck S
AU  - Pennacchio L
AU  - Nolan M
AU  - Mikhailova N
AU  - Land ML
AU  - Nesbo CL
AU  - Gogarten JP
AU  - Noll KM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5566-5567.

PMID- 25977437
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Nonmarine Agarolytic Bacterium Cellvibrio sp. OA-2007.
PG  - e00468-15
AB  - Cellvibrio sp. OA-2007 is a Gram-negative, aerobic, and agarolytic bacterium isolated from
      activated sludge. We present the draft genome sequence of strain
      OA-2007, composed of 97 contigs, totaling 4,595,379 bp in size, and containing
      4,094 open reading frames, with a G+C content of 47.71%.
AU  - Syazni YM
AU  - Kasuu M
AU  - Nakasaki K
AU  - Ariga O
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00468-15.

PMID- Not included in PubMed...
VI  - 825
DP  - 1985
TI  - A site-specific endonuclease from Caulobacter crescentus CB-13: restriction endonuclease CcrI.
PG  - 236-243
AB  - A site-specific restriction endonuclease (CcrI) has been identified from
      Caulobacter crescentus CB-13.  This enzyme has been purified to homogeneity and
      the cleavage patterns with various DNAs and sequence data show that CcrI
      recognizes the same sequence as the XhoI restriction endonuclease
      (5'-C^T-C-G-A-G-3').  CcrI has an absolute requirement for magnesium ions with
      an optimum concentration of 4 mM.  The enzyme is optimally active at pH 8.0 and
      is stable up to 70C.  CcrI has a molecular weight of 65300 and exists as a
      monomer in its native state.  Most of the physical characteristics observed for
      CcrI were similar to those observed for XhoI.  Kinetic studies on CcrI and XhoI
      suggest that the enzymes with lambda DNA in the same manner, however with
      PhiX-174 RF DNA, CcrI has a greater affinity for the supercoiled molecule than
      XhoI.
AU  - Syddall R
AU  - Stachow C
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1985 825: 236-243.

PMID- 25814588
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Sanguibacteroides justesenii, gen. nov., sp. nov., Strains OUH 308042T (= ATCC BAA-2681T) and OUH 334697 (= ATCC BAA-2682), Isolated  from Blood Cultures from Two Different Patients.
PG  - e00005-15
AB  - We announce here the draft genome sequences of Sanguibacteroides justesenii, gen. nov., sp.
      nov., strains OUH 308042(T) (= DSM 28342(T) = ATCC BAA-2681(T)) and OUH
      334697 (= DSM 28341 = ATCC BAA-2682), isolated from blood cultures from two
      different patients and composed of 51 and 39 contigs for totals of 3,385,516 and
      3,410,672 bp, respectively.
AU  - Sydenham TV
AU  - Hasman H
AU  - Justesen US
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00005-15.

PMID- 24407628
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of the Novel Giant Pseudomonas Phage PaBG.
PG  - e00929-13
AB  - The novel giant Pseudomonas aeruginosa bacteriophage PaBG was isolated from a water sample of
      the ultrafreshwater Lake Baikal. We report the complete genome
      sequence of this Myoviridae bacteriophage, comprising 258,139 bp of
      double-stranded DNA containing 308 predicted open reading frames.
AU  - Sykilinda NN
AU  - Bondar AA
AU  - Gorshkova AS
AU  - Kurochkina LP
AU  - Kulikov EE
AU  - Shneider MM
AU  - Kadykov VA
AU  - Solovjeva NV
AU  - Kabilov MR
AU  - Mesyanzhinov VV
AU  - Vlassov VV
AU  - Drukker VV
AU  - Miroshnikov KA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00929-13.

PMID- 26221420
VI  - 10
DP  - 2015
TI  - Draft genome sequence of Methylibium sp. strain T29, a novel fuel oxygenate-degrading bacterial isolate from Hungary.
PG  - 39
AB  - Methylibium sp. strain T29 was isolated from a gasoline-contaminated aquifer and  proved to
      have excellent capabilities in degrading some common fuel oxygenates
      like methyl tert-butyl ether, tert-amyl methyl ether and tert-butyl alcohol along
      with other organic compounds. Here, we report the draft genome sequence of M. sp.
      strain T29 together with the description of the genome properties and its
      annotation. The draft genome consists of 608 contigs with a total size of
      4,449,424 bp and an average coverage of 150x. The genome exhibits an average G +
      C content of 68.7 %, and contains 4754 protein coding and 52 RNA genes, including
      48 tRNA genes. 71 % of the protein coding genes could be assigned to COG
      (Clusters of Orthologous Groups) categories. A formerly unknown circular plasmid
      designated as pT29A was isolated and sequenced separately and found to be 86,856
      bp long.
AU  - Szabo Z
AU  - Gyula P
AU  - Robotka H
AU  - Bato E
AU  - Galik B
AU  - Pach P
AU  - Pekker P
AU  - Papp I
AU  - Bihari Z
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 39.

PMID- 16144727
VI  - 121
DP  - 2006
TI  - In vitro expression of the restriction endonucleases LlaMI and ScrFI isolated from Lactococcus lactis M19 and UC503.
PG  - 144-153
AB  - A new restriction endonuclease LlaMI has been characterized in Lactococcus lactis subsp.
      cremoris M19. LlaMI recognizes the sequence 5'-CCNGG-3' and cuts after the second cytosine.
      This restriction endonuclease is related to commercially available ScrFI but not identical to
      it. Comparative analysis of the predicted amino acid sequences of LlaMI and ScrFI indicates
      five non-conservative amino acid changes between these two restriction enzymes. These two
      enzymes were expressed in vitro as histidine-tagged fusion proteins. LlaMI was shown to be
      more sensitive to high salt concentration than ScrFI. Southern blotting and hybridization
      analysis indicate that the gene for LlaMI R/M system is chromosomally encoded.
AU  - Szatmari G
AU  - Hua NM
AU  - Vzdornov D
AU  - Daigle F
AU  - Smoragiewicz W
AU  - Mamet-Bratley MD
AU  - Karska-Wysocki B
PT  - Journal Article
TA  - J. Biotechnol.
JT  - J. Biotechnol.
SO  - J. Biotechnol. 2006 121: 144-153.

PMID- 12471895
VI  - 35
DP  - 2000
TI  - How do proteins move along DNA?  Lessons from type-I and type-III restriction endonucleases.
PG  - 131-143
AB  - A fundamental requirement of nearly every genetic event, including DNA replication,
      transcription, cleavage and repair, is the protein-mediated communication between distance DNA
      sites.  Four general mechanisms for this 'action at a distance' were described by Adzuma and
      Mizuuchi and are illustrated in Figure 1.  The first three models, DNA sliding, DNA hopping
      and DNA looping, are driven passively by random thermal fluctuations of the protein or DNA,
      with significant consequences for the efficiency of the reactions.  In DNA sliding, a protein
      bound to non-specific DNA diffuses either leftwards or rightwards without dissociating,
      altering the DNA-binding register by 1 bp.  By confining diffusion to one dimension, the
      probability of finding a second site or protein is increased.  However, the number of physical
      steps needed to move between two DNA loci by linear diffusion has a square power dependence on
      the distance between those sites; for instance, travelling 1000 bp takes 1 x 10^6 steps, which
      in turn requires a linear diffusion rate at least 1 x 10^6 times faster than the DNA
      dissociation rate.  Generally, DNA-binding proteins associate transiently with non-specific
      sequences and DNA sliding would only be feasible over quite short distances, less than 100 bp.
      In DNA hopping, a protein physically releases DNA, diffuses in three dimensions and randomly
      rebinds the same DNA molecule at an alternative site.  The DNA acts as a binding 'reservoir'
      - given enough time, one protein could sample every available binding locus.
      Three-dimensional diffusion on a random coil has a square-root power dependence on the
      distance between target sites, but because sampling is non-linear, sites may be overlooked and
      the protein could even diffuse away from the DNA altogether.  In DNA looping, a protein
      remains bound to a specific DNA sequence whilst segmental diffusion of the polynucleotide
      brings distant DNA sites (and any bound proteins) into close proximity.  In general, the
      tethering of two proteins on to the same DNA molecule increases the probability of
      protein-protein interactions.  However, the probability of juxtaposition decreases as the
      distance between the sites increases, an effect that is particularly marked on linear DNA.
      DNA-looping events are less likely over distances greater than ~1000 bp without the
      cooperation of accessory factors, such as DNA-bending proteins.
AU  - Szczelkun MD
PT  - Journal Article
TA  - Essays Biochem.
JT  - Essays Biochem.
SO  - Essays Biochem. 2000 35: 131-143.

PMID- 11827554
VI  - 41
DP  - 2002
TI  - Kinetic models of translocation, head-on collision, and DNA cleavage by type I restriction endonucleases.
PG  - 2067-2074
AB  - Digestion of linear DNA by type I restriction endonucleases is generally activated following
      the head-on collision of two
      translocating enzymes. However, the resulting distributions of cleavage
      loci along the DNA vary with different enzymes; in some cases, cleavage
      is located in a discrete region midway between a pair of recognition
      sites while in other cases cleavage is broadly distributed and occurs
      at nearly every intervening locus. Statistical models for DNA
      translocation, collision, and cleavage are described that can account
      for these observations and that are generally applicable to other
      DNA-based motor proteins. If translocation is processive (stepping
      forward is significantly more likely than DNA dissociation), then the
      linear distribution of an ensemble of proteins can be described simply
      using a Poisson relationship. The pattern of cleavage sites resulting
      from collision between two processive type I enzymes over a distance d
      can then be described by a binomial distribution with a standard
      deviation 0.5.d(1/2). Alternatively, if translocation is nonprocessive
      (stepping forward or dissociating become equally likely events), the
      linear distribution is described by a continuum of populated states and
      is thus extended. Comparisons of model data to the kinetics of DNA
      translocation and cleavage discount the nonprocessive model. Instead,
      the observed differences between enzymes are due to asynchronous events
      that occur upon collision. Therefore, type I restriction enzymes can be
      described as having processive DNA translocation but, in some cases,
      nonprocessive DNA cleavage.
AU  - Szczelkun MD
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2002 41: 2067-2074.

PMID- 23161014
VI  - 767
DP  - 2013
TI  - Roles for Helicases as ATP-Dependent Molecular Switches.
PG  - 225-244
AB  - On the basis of the familial name, a 'helicase' might be expected to have an enzymatic
      activity that unwinds duplex polynucleotides to form single strands. A more encompassing
      taxonomy that captures alternative enzymatic roles has defined helicases as a sub-class of
      molecular motors that move directionally and processively along nucleic acids, the so-called
      'translocases'. However, even this definition may be limiting in capturing the full scope of
      helicase mechanism and activity. Discussed here is another, alternative view of helicases-as
      machines which couple NTP-binding and hydrolysis to changes in protein conformation to resolve
      stable nucleoprotein assembly states. This 'molecular switch' role differs from the
      classical view of helicases as molecular motors in that only a single catalytic NTPase cycle
      may be involved. This is illustrated using results obtained with the DEAD-box family of RNA
      helicases and with a model bacterial system, the ATP-dependent Type III
      restriction-modification enzymes. Further examples are discussed and illustrate the
      wide-ranging examples of molecular switches in genome metabolism.
AU  - Szczelkun MD
PT  - Journal Article
TA  - Adv. Exp. Med. Biol.
JT  - Adv. Exp. Med. Biol.
SO  - Adv. Exp. Med. Biol. 2013 767: 225-244.

PMID- 21428945
VI  - 39
DP  - 2011
TI  - Translocation, switching and gating: potential roles for ATP in long-range communication on DNA by Type III restriction endonucleases.
PG  - 589-594
AB  - To cleave DNA, the Type III RM (restriction-modification) enzymes must communicate the
      relative orientation of two recognition sequences, which may be separated by many thousands of
      base pairs. This long-range interaction requires ATP hydrolysis by a helicase domain, and both
      active (DNA translocation) and passive (DNA sliding) modes of motion along DNA have been
      proposed. Potential roles for ATP binding and hydrolysis by the helicase domains are
      discussed, with a focus on bipartite ATPases that act as molecular switches.
AU  - Szczelkun MD
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 2011 39: 589-594.

PMID- 7662656
VI  - 34
DP  - 1995
TI  - Sequence-specific binding of DNA by the EcoRV restriction and modification enzymes with nucleic acid and cofactor analogues.
PG  - 10724-10733
AB  - The DNA-binding properties of the EcoRV restriction endonuclease and modification
      methyltransferase with their recognition sequence (GATATC) were analyzed using the
      electrophoretic band-shift assay.  It has previously been observed that the endonuclease does
      not bind specifically to GATATC sequences in the absence of the essential cofactor Mg2+.  To
      investigate any possible roles for Mg2+ in promoting specific DNA binding, a set of
      hydrolysis-resistant oligonucleotide substrates were synthesized that contained either
      phosphate (phosphorothioate, 3'-S-phosphorothiolate), sugar (4'-thiothymidine), or base
      (7-deaza-2'-deoxyadenosine) modifications.  However, it was found that none of these were
      specifically bound by the endonuclease in either the absence or the presence of Mg2+.  In
      contrast, the methylase bound to GATATC sequences much more strongly than to nonspecific
      sites, and it was possible to observe the formation of enzyme-DNA complexes by gel
      retardation.  Binding to GATATC sequences was increased by the addition of sinefungin, a
      nonreactive analogue of the essential cofactor S-adenosyl-L-methionine (AdoMet).  Presumably
      this also occurs with AdoMet although methylation and turnover prevented its direct
      observation.  In the presence of sinefungin the strongest binding was observed with
      hemimethylated EcoRV sequences (Kd=11-13 nM), and unmethylated DNA was bound less well
      (Kd=46nM).  Specific, albeit weaker binding was also seen with the dimethylated product
      (Kd=143 nM).  A difference in electrophoretic mobility was observed between enzyme-substrate
      and enzyme-product complexes suggestive of structural differences between them.  The Kapp
      value found for sinefungin, with the hemimethylated EcoRV sequence, was 10.9 mM.
AU  - Szczelkun MD
AU  - Connolly BA
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1995 34: 10724-10733.

PMID- 8947056
VI  - 15
DP  - 1996
TI  - Repercussions of DNA tracking by the type IC restriction endonuclease EcoR124I on linear, circular and catenated substrates.
PG  - 6335-6347
AB  - Type I restriction endonucleases such as EcoR124I cleave DNA at undefined loci, distant from
      their recognition sequences, by a mechanism that involves the enzyme tracking along the DNA
      between recognition and cleavage sites.  This mechanism was examined on plasmids that carried
      recognition sites for EcoR124I and recombination sites for resolvase, the latter to create DNA
      catenanes.  Supercoiled substrates with either one or two restriction sites were linearized by
      EcoR124I at similar rates, although the two-site molecule underwent further cleavage more
      readily than the one-site DNA.  The catenane from the plasmid with one EcoR124I site, carrying
      the site on the smaller of the two rings, was cleaved by EcoR124I exclusively in the small
      ring, and this underwent multiple cleavage akin to the two-site plasmid.  Linear substrates
      derived from the plasmids were cleaved by EcoR124I at very slow rates.  The communication
      between recognition and cleavage sites therefore cannot stem from random looping.  Instead, it
      must follow the DNA contour between the sites.  On a circular DNA, the translocation of
      non-specific DNA past the specifically bound protein should increase negative supercoiling in
      one domain and decrease it in the other.  The ensuing topological barrier may be the trigger
      for DNA cleavage.
AU  - Szczelkun MD
AU  - Dillingham MS
AU  - Janscak P
AU  - Firman K
AU  - Halford SE
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1996 15: 6335-6347.

PMID- 20298192
VI  - 38
DP  - 2010
TI  - Maintaining a sense of direction during long-range communication on DNA.
PG  - 404-409
AB  - Many biological processes rely on the interaction of proteins with multiple DNA sites
      separated by thousands of base pairs. These
      long-range communication events can be driven by both the thermal
      motions of proteins and DNA, and directional protein motions that are
      rectified by ATP hydrolysis. The present review describes conflicting
      experiments that have sought to explain how the ATP-dependent Type Ill
      restriction-modification enzymes can cut DNA with two sites in an
      inverted repeat, but not DNA with two sites in direct repeat. We
      suggest that an ATPase activity may not automatically indicate a DNA
      translocase, but can alternatively indicate a molecular switch that
      triggers communication by thermally driven DNA sliding. The generality
      of this mechanism to other ATP-dependent communication processes such
      as mismatch repair is also discussed.
AU  - Szczelkun MD
AU  - Friedhoff P
AU  - Seidel R
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 2010 38: 404-409.

PMID- 
VI  - 0
DP  - 2001
TI  - Restriction Endonuclease.
PG  - 1693-1696
AB  - The term 'restriction enzyme' was first coined more than 30 years ago, following the classic
      observation that phage grown on one bacterial species would grow poorly on another strain of
      the same species; the phage were 'restricted' in their host range.  The restriction activity
      was dependent on an endonuclease which cleaves double-stranded DNA upon binding a specific
      sequence of nucleotides (the recognition site).  However, transfer of a methyl group from the
      donor S-adenosylmethionine to a particular base on one or both strands of the recognition site
      prevents cleavage.  This modification is catalyzed by a methyltransferase activity.  The host
      DNA can therefore be protected from self-digestion, even during semiconservative replication
      when one strand is temporally unmodified.  Conversely, any invasive DNA is unlikely to carry
      the correct pattern of methylated bases, and will be a target for cleavage.  The presence in
      parallel of endonuclease and methyltransferase activities produces a bacterial equivalent of
      an immune system, capable of distinguishing self from foreign DNA.  Probably as a consequence
      of this custodial role, restriction endonucleases are widespread in nature, appearing in every
      bacterial generus examined.
AU  - Szczelkun MD
AU  - Halford SE
PT  - Journal Article
TA  - Encyclopaedia of Genetics
JT  - Encyclopaedia of Genetics
SO  - Encyclopaedia of Genetics 2001 0: 1693-1696.

PMID- 8635479
VI  - 15
DP  - 1996
TI  - Recombination by resolvase to analyse DNA communications by the SfiI restriction endonuclease.
PG  - 1460-1469
AB  - The SfiI endonuclease differs from other type II restriction enzymes by cleaving DNA
      concertedly at two copies of its recognition site, its optimal activity being with two sites
      on the same DNA molecule.  The nature of this communication event between distant DNA sites
      was analysed on plasmids with recognition sites for SfiI interspersed with recombination sites
      for resolvase.  These were converted by resolvase to catenanes carrying one SfiI site on each
      ring.  The catenanes were cleaved by SfiI almost as readily as a single ring with two sites,
      in contrast to the slow reactions on DNA rings with one SfiI site.  Interactions between SfiI
      sites on the same DNA therefore cannot follow the DNA contour and, instead, must stem from
      their physical proximity.  In buffer lacking Mg2+, where SfiI is inactive while resolvase is
      active, the addition of SfiI to a plasmid with target sites for both proteins blocked
      recombination by resolvase, due to the restriction enzyme bridging its sites and thus
      isolating the sites for resolvase into separate loops.  The extent of DNA looping by SfiI
      matched its extent of DNA cleavage in the presence of Mg2+.
AU  - Szczelkun MD
AU  - Halford SE
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1996 15: 1460-1469.

PMID- 9300058
VI  - 271
DP  - 1997
TI  - Selection of non-specific DNA cleavage sites by the type IC restriction endonuclease EcoR124I.
PG  - 112-123
AB  - The type IC restriction endonuclease EcoR124I binds specifically to its recognition sequence
      but subsequently translocates non-specific DNA past the complex in an ATP-dependent mechanism.
      The enzyme thus has the potential to cleave DNA at loci distant from the recognition site.  We
      have scrutinized the link between translocation and cleavage on linear and circular DNA
      substrates.  On linear DNA carrying two recognition sites, the majority of cleavages at loci
      distant from the recognition site occurred between the two sites, regardless of the inter-site
      distance or relative orientations.  On circular DNA carrying one site, distant cleavages
      occurred throughout the DNA but an equivalent linear molecule underwent considerably fewer
      cleavages at distant loci.  These results agree with published models for DNA tracking.
      However, on every molecule investigated, discrete cleavage sites were also observed within
      +/-250bp of the recognition sites.  The localized cleavages were not confined to particular
      DNA sequences and were independent of DNA topology.  We propose a model to account for both
      distant and localized cleavage events.  The conformation of the DNA loop extruded during
      tracking may result in two DNA segments being held in proximity to the restriction moiety on
      the protein, one close to the EcoR124I site and another distant from the site: cleavage may
      occur in either segment.  Alternatively, the cutting of DNA close to recogniton sites may be
      the result of multiple nicks being generated in the expanding loop before any extensive
      translocation.
AU  - Szczelkun MD
AU  - Janscak P
AU  - Firman K
AU  - Halford SE
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1997 271: 112-123.

PMID- 7662657
VI  - 34
DP  - 1995
TI  - Probing the protein-DNA interface of the EcoRV modification methyltransferase bound to its recognition sequence, GATATC.
PG  - 10734-10743
AB  - The DNA contacts produced between the EcoRV modification methyltransferase and its recognition
      sequence, GATATC, have been determined.  The enzyme's general location in a
      methylase/DNA/sinefungin ternary complex was evaluated by protection from exonuclease III
      digestion.  Important phosphate contacts were resolved using N-ethyl-N-nitrosourea ethylation
      interference footprinting.  Methylation protection and interference using dimethyl sulfate
      were employed to assess significant contacts to purinic bases.  The protein-DNA interface was
      further probed using oligodeoxynucleotides containing base analogues within the GATATC
      sequence.  Most of the experiments were carried out using hemimethylated sequences, i.e.,
      having 6-methyladenosine at the methylation site in one of the strands.  The momomeric
      methylase was found to bind to the DNA in two different orientations for the methylation of
      each strand.  The enzyme approaches the DNA, predominantly from one "side", and makes most of
      its contacts in the major groove.  In either of the two binding events contacts are made to
      the four phosphates NpNpNpGpA and the three bases GAT (where GAT represents the 5' half of
      the GATATC site) on both DNA strands.  The phosphates and bases in the 3' ATC half are much
      less important.  Although the contacts made to the equivalent locations on each strand are
      similar, they display a slight but consistent change dependent on which strand contains the
      6-methyldeoxyadenosine.  This strand variation shows completely reciprocal behavior, switching
      around exactly, depending entirely on the methylated deoxyadenosine location.  It is this
      that provides evidence for the two binding modes.  The results obtained are discussed in terms
      of possible models for the protein-DNA interface.
AU  - Szczelkun MD
AU  - Jones H
AU  - Connolly BA
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1995 34: 10734-10743.

PMID- 16879432
VI  - 6
DP  - 2006
TI  - In vivo analysis of the relationships between the splicing and homing activities of a group I intron-encoded I-ScaI/bi2-maturase of  Saccharomyces capensis produced in the yeast cytoplasm.
PG  - 823-835
AB  - The I-ScaI/bi2-maturase of Saccharomyces capensis acts as a specific homing endonuclease
      promoting intron homing, and as a maturase
      promoting intron splicing. Using the universal code equivalent of the
      mitochondrial gene encoding the I-ScaI/bi2-maturase, a number of
      truncated forms of the synthetic gene were constructed, shortened on
      either side, as were several mutated alleles of the protein. The
      shortest translation product that fully retains both activities in vivo
      corresponds to 228 codons of the C-terminal region of the bi2
      intron-encoded protein, whereas proteins resulting from more extensive
      deletions either at the N-terminus or at the C-terminus (up to 73 and
      four residues, respectively) were able to complement wholly the lack of
      endogenous maturase, but all lost the endonuclease activity. Similarly,
      all introduced mutations completely abolished the I-ScaI activity while
      some mutant proteins retained substantial splicing function.
      Immunodetection experiments demonstrated that different cytoplasmically
      translated forms of the I-ScaI/bi2-maturase protein were imported into
      mitochondria and correctly processed. They appeared to be tightly
      associated with mitochondrial membranes. Homology modelling of the
      I-ScaI/bi2-maturase protein allowed us to relate both enzymatic
      activities to elements of enzyme structure.
AU  - Szczepanek T
AU  - Gora M
AU  - Monteilhet C
AU  - Wysocka M
AU  - Lazowska J
AU  - Golik P
PT  - Journal Article
TA  - FEMS Yeast Res.
JT  - FEMS Yeast Res.
SO  - FEMS Yeast Res. 2006 6: 823-835.

PMID- 11016843
VI  - 264
DP  - 2000
TI  - Critical base substitutions that affect the splicing and/or homing activities of the group I intron bi2 of yeast mitochondria.
PG  - 137-144
AB  - The second intron (bi2) of the cyt b gene from related Saccharomyces species has an
      extraordinarily conserved sequence and can have
      different functions in wild-type cells. The protein encoded by the S.
      cerevisiae intron functions as a maturase to promote intron splicing,
      while the homologous S. capensis intron encodes a bifunctional protein
      that acts both as a maturase and as a homing endonuclease (I-ScaI)
      promoting intron mobility. The protein encoded by intron bi2 belongs to
      a large gene family characterized by the presence of two conserved
      LAGLIDADG motifs (P1 and P2). In this study, we analysed a set of
      splicing-deficient mutants of the S. cerevisiae intron bi2 that carry
      non-directed mutations affecting the maturase activity, and a set of
      directed missense mutations introduced into the bifunctional protein
      encoded by the S. capensis intron. Analysis of these mutations has
      allowed identification of the residues in the conserved P1 and P2
      motifs which are crucial for splicing and homing activities. Moreover,
      several mutations which are located in the C-terminal part of the
      protein have been found to affect both functions.
AU  - Szczepanek T
AU  - Jamoussi K
AU  - Lazowska J
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 2000 264: 137-144.

PMID- 8670880
VI  - 15
DP  - 1996
TI  - Replacement of two non-adjacent amino acids in the S. cerevisiae bi2 intron-encoded RNA maturase is sufficient to gain a homing-endonuclease activity.
PG  - 3758-3767
AB  - Two homologous group I introns, the second intron of the cyt b gene, from related
      Saccharomyces species differ in their mobility.  The S. capensis intron is mobile and encodes
      the I-ScaI endonuclease promoting intron homing, whilst the homologous S. cerevisiae intron is
      not mobile, but functions as an RNA maturase promoting splicing. These two intron-encoded
      proteins differ by only four amino acid substitutions.  Taking advantage of the remarkable
      similarity of the two intron open reading frames and using biolistic transformation of
      mitochondria, we show that the replacement of only two non- adjacent residues in the S.
      cerevisiae maturase carboxy-terminal sequence is sufficient to induce a homing-endonuclease
      activity without losing the splicing function.  Also, we demonstrate that these two activities
      reside in the S. capensis bi2-encoded protein which functions in both splicing and intron
      mobility in the wild-type cells.  These results provide new insight into our understanding of
      the activity and the evolution of group I intron- encoded proteins.
AU  - Szczepanek T
AU  - Lazowska J
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1996 15: 3758-3767.

PMID- 8112577
VI  - 139
DP  - 1994
TI  - Two homologous introns from related Saccharomyces species differ in their mobility.
PG  - 1-7
AB  - We have studied gene conversion initiated by the ai3 intron of the Saccharomyces cerevisiae
      mitochondrial COX1 gene and its homologous intron (S.cap.ai1) from Saccharomyces capensis.
      The approach used involved the measurement of intron transmission amongst the progeny of
      crosses between constructed recipient and donor strains.  We found that the S. cerevisiae ai3
      intron is extremely active as a donor in gene conversion, whereas its homologous S. capensis
      intron is not.  We have established the sequence of S.cap.ai1 and compared its open reading
      frame with that of I-SceIII encoded by the homologous S. cerevisiae intron.  The two
      protein-coding intron sequences are almost identical, except that the S. capensis ORF contains
      an in-frame stop codon.  This finding provides a strong indication that the 3' part of the S.
      cerevisiae intron ORF encoding I-SceIII (which should not be translated in the S. capensis
      intron) must be critical for function of mtDNA endonucleases to mediate intron mobility.
AU  - Szczepanek T
AU  - Macadre C
AU  - Meunier B
AU  - Lazowska J
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1994 139: 1-7.

PMID- 21115076
VI  - 155
DP  - 2011
TI  - Sequencing and comparative analysis of IncP-1alpha antibiotic resistance plasmids reveal a highly conserved backbone and differences within accessory regions.
PG  - 95-103
AB  - In spite of the importance of IncP-1 plasmids in horizontal gene transfer
      among bacteria, in particular antibiotic resistance spread, so far only
      three plasmids from the subgroup IncP-1alpha have been completely
      sequenced. In this study we doubled this number. The three IncP-1alpha
      plasmids pB5, pB11 and pSP21 were isolated from bacteria of two different
      sewage treatment plants and sequenced by a combination of next-generation
      and capillary sequencing technologies. A comparative analysis including
      the previously analysed IncP-1alpha plasmids RK2, pTB11 and pBS228
      revealed a highly conserved plasmid backbone (at least 99.9% DNA sequence
      identity) comprising 54 core genes loaded with different accessory
      elements. The accessory elements of the plasmid pB5 constitute a class 1
      integron interrupting the parC gene and an IS6100 copy inserted into the
      integron. In addition, the tetracycline resistance genes tetAR and the
      ISTB11-like element are located between the klc operon and the trfA-ssb
      operon. Plasmid pB11 is loaded with a Tn5053-like mercury resistance
      transposon between the parCBA and parDE operons and contains tetAR that
      are identical to those identified in plasmid pB5 and the insertion
      sequence ISSP21. Plasmid pSP21 harbours an ISPa7 element in a Tn402
      transposon including a class 1 integron between the partitioning genes
      parCBA and parDE. The IS-element ISSP21 (99.89% DNA sequence identity to
      ISSP21 from pB11), inserted downstream of the tetR gene and a copy of
      ISTB11 (identical to ISTB11 on pTB11) inserted between the genes pncA and
      pinR. On all three plasmids the accessory genes are almost always located
      between the backbone modules confirming the importance of the backbone
      functions for plasmid maintenance. The striking backbone conservation
      among the six completely sequenced IncP-1alpha plasmids is in contrast to
      the much higher diversity within the IncP-1beta subgroup.
AU  - Szczepanowski R
AU  - Eikmeyer F
AU  - Harfmann J
AU  - Blom J
AU  - Rogers LM
AU  - Brown CJ
AU  - Top EM
AU  - Schluter A
PT  - Journal Article
TA  - J. Biotechnol.
JT  - J. Biotechnol.
SO  - J. Biotechnol. 2011 155: 95-103.

PMID- 18829716
VI  - 36
DP  - 2008
TI  - Central base pair flipping and discrimination by PspGI.
PG  - 6109-6117
AB  - PspGI is a representative of a group of restriction endonucleases that recognize a pentameric
      sequence related to CCNGG. Unlike the previously
      investigated Ecl18kI, which does not have any specificity for the central
      base pair, PspGI prefers A/T over G/C in its target site. Here, we present
      a structure of PspGI with target DNA at 1.7 A resolution. In this
      structure, the bases at the center of the recognition sequence are
      extruded from the DNA and flipped into pockets of PspGI. The flipped
      thymine is in the usual anti conformation, but the flipped adenine takes
      the normally unfavorable syn conformation. The results of this and the
      accompanying manuscript attribute the preference for A/T pairs over G/C
      pairs in the flipping position to the intrinsically lower penalty for
      flipping A/T pairs and to selection of the PspGI pockets against guanine
      and cytosine. Our data show that flipping can contribute to the
      discrimination between normal bases. This adds a new role to base flipping
      in addition to its well-known function in base modification and DNA damage
      repair.
AU  - Szczepanowski RH
AU  - Carpenter MA
AU  - Czapinska H
AU  - Zaremba M
AU  - Tamulaitis G
AU  - Siksnys V
AU  - Bhagwat AS
AU  - Bochtler M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2008 36: 6109-6117.

PMID- 17603476
VI  - 25
DP  - 2007
TI  - Structure-based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases.
PG  - 786-793
AB  - Artificial endonucleases consisting of a FokI cleavage domain tethered to engineered
      zinc-finger DNA-binding proteins have proven useful for
      stimulating homologous recombination in a variety of cell types. Because
      the catalytic domain of zinc-finger nucleases (ZFNs) must dimerize to
      become active, two subunits are typically assembled as heterodimers at the
      cleavage site. The use of ZFNs is often associated with significant
      cytotoxicity, presumably due to cleavage at off-target sites. Here we
      describe a structure-based approach to reducing off-target cleavage. Using
      in silico protein modeling and energy calculations, we increased the
      specificity of target site cleavage by preventing homodimerization and
      lowering the dimerization energy. Cell-based recombination assays
      confirmed that the modified ZFNs were as active as the original ZFNs but
      elicit significantly less genotoxicity. The improved safety profile may
      facilitate therapeutic application of the ZFN technology.
AU  - Szczepek M
AU  - Brondani V
AU  - Buchel J
AU  - Serrano L
AU  - Segal DJ
AU  - Cathomen T
PT  - Journal Article
TA  - Nat. Biotechnol.
JT  - Nat. Biotechnol.
SO  - Nat. Biotechnol. 2007 25: 786-793.

PMID- 19400796
VI  - 72
DP  - 2009
TI  - Molecular analysis of restriction endonuclease EcoRII from Escherichia coli reveals precise regulation of its enzymatic activity by autoinhibition.
PG  - 1011-1021
AB  - Bacterial restriction endonuclease EcoRII requires two recognition sites to cleave DNA.
      Proteolysis of EcoRII revealed the existence of
      two stable domains, EcoRII-N and EcoRII-C. Reduction of the enzyme to
      its C-terminal domain, EcoRII-C, unleashed the enzyme activity; this
      truncated form no longer needed two recognition sites and cleaved DNA
      much more efficiently than EcoRII wild-type. The crystal structure of
      EcoRII showed that probably the N-terminal domain sterically occludes
      the catalytic site, thus apparently controlling the cleavage activity.
      Based on these data, EcoRII was the first restriction endonuclease for
      which an autoinhibition mechanism as regulatory strategy was proposed.
      In this study, we probed this assumption and searched for the
      inhibitory element that mediates autoinhibition. Here we show that
      repression of EcoRII-C is achieved by addition of the inhibitory domain
      EcoRII-N or by single soluble peptides thereof in trans. Moreover, we
      perturbed contacts between the N- and the C-terminal domain of EcoRII
      by site-directed mutagenesis and proved that beta-strand B1 and
      alpha-helix H2 are essential for autoinhibition; deletion of either
      secondary structural element completely relieved EcoRII autoinhibition.
      This potent regulation principle that keeps EcoRII enzyme activity
      controlled might protect bacteria against suicidal restriction of rare
      unmodified recognition sites in the cellular genome.
AU  - Szczepek M
AU  - Mackeldanz P
AU  - Moncke-Buchner E
AU  - Alves J
AU  - Kruger DH
AU  - Reuter M
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2009 72: 1011-1021.

PMID- 24651469
VI  - 10
DP  - 2014
TI  - Probabilistic approach to predicting substrate specificity of methyltransferases.
PG  - e1003514
AB  - We present a general probabilistic framework for predicting the substrate specificity of
      enzymes. We designed this approach to be easily applicable to
      different organisms and enzymes. Therefore, our predictive models do not rely on
      species-specific properties and use mostly sequence-derived data. Maximum
      Likelihood optimization is used to fine-tune model parameters and the Akaike
      Information Criterion is employed to overcome the issue of correlated variables.
      As a proof-of-principle, we apply our approach to predicting general substrate
      specificity of yeast methyltransferases (MTases). As input, we use several
      physico-chemical and biological properties of MTases: structural fold,
      isoelectric point, expression pattern and cellular localization. Our method
      accurately predicts whether a yeast MTase methylates a protein, RNA or another
      molecule. Among our experimentally tested predictions, 89% were confirmed,
      including the surprising prediction that YOR021C is the first known MTase with a
      SPOUT fold that methylates a substrate other than RNA (protein). Our approach not
      only allows for highly accurate prediction of functional specificity of MTases,
      but also provides insight into general rules governing MTase substrate
      specificity.
AU  - Szczepinska T
AU  - Kutner J
AU  - Kopczynski M
AU  - Pawlowski K
AU  - Dziembowski A
AU  - Kudlicki A
AU  - Ginalski K
AU  - Rowicka M
PT  - Journal Article
TA  - PLOS Comp. Biol.
JT  - PLOS Comp. Biol.
SO  - PLOS Comp. Biol. 2014 10: e1003514.

PMID- 21638680
VI  - 34
DP  - 2006
TI  - Two restriction endonucleases.
PG  - 228-229
AB  - Terms to be familiar with before you start to solve the test: restriction endonucleases;
      palindromic sequences; blunt ends; cohesive
      ("sticky") ends; in vitro DNA synthesis; radioactive nucleotide
      precursors; template-primer complexes; DNA ligation.|
AU  - Szeberenyi J
PT  - Journal Article
TA  - Biochem. Mol. Biol. Educ.
JT  - Biochem. Mol. Biol. Educ.
SO  - Biochem. Mol. Biol. Educ. 2006 34: 228-229.

PMID- 11024177
VI  - 28
DP  - 2000
TI  - DNA binding properties in vivo and target recognition domain sequence alignment analyses of wild-type and mutant RsrI [N6-adenine] DNA methyltransferases.
PG  - 3972-3981
AB  - A genetic selection method, the P22 challenge-phage assay, was used to characterize DNA
      binding in vivo by the prokaryotic beta class [N6-adenine] DNA methyltransferase M.RsrI.
      M.RsrI mutants with altered binding affinities in vivo were isolated. Unlike the wild-type
      enzyme, a catalytically compromised mutant, M.RsrI (L72P), demonstrated site-specific DNA
      binding in vivo. The L72P mutation is located near the highly conserved catalytic motif IV,
      DPPY (residues 65-68). A double mutant, M.RsrI (L72P/D173A), showed less binding in vivo than
      did M.RsrI (L72P). Thus, introduction of the D173A mutation deleteriously affected DNA
      binding. D173 is located in the putative target recognition domain (TRD) of the enzyme.
      Sequence alignment analyses of several beta class MTases revealed a TRD sequence element that
      contains the D173 residue. Phylogenetic analysis suggested that divergence in the amino acid
      sequences of these methyltransferases correlated with differences in their DNA target
      recognition sequences. Furthermore, MTases of other classes (alpha and gamma) having the same
      DNA recognition sequence as the beta class MTases share related regions of amino acid
      sequences in their TRDs.
AU  - Szegedi SS
AU  - Gumport RI
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2000 28: 3972-3981.

PMID- 9806752
VI  - 12
DP  - 1998
TI  - A novel scheme for the purification of wildtype and mutant RsrI DNA methyltransferases (MTases).
PG  - A1437
AB  - RsrI DNA MTase (M.RsrI) is an S-adenosylmethionine-dependent enzyme that recognizes the duplex
      DNA sequence 5-GAATTC-3 and methylates the central adenine at the N6 position.  M.RsrI is
      isocatalytic but not homologous with M.EcoRI.  These two proteins show only 15.6% amino acid
      identity.  Our laboratory has purified M.RsrI and is generating M.RsrI mutants as part of an
      effort to understand how the two dissimilar proteins perform the same catalytic function.  A
      simpler method for purifying the wild-type M.RsrI has been developed, reducing the
      purification steps from six to two.  The isolation of wild-type M.RsrI to >90% purity from
      8.0g of E. coli cells paste yields approximately 7.5 mg of protein.  This amount represents a
      >4-fold increase in the yield of protein as compared to our previous purification method.  A
      mutant, M.RsrI (L72P), is currently being purified in a similar manner.  This mutant was
      generated by random PCR mutagenesis and isolated using the in vivo DNA binding assay, the
      bacteriophage P22 challenge-phage assay.  Wild-type M.RsrI is toxic and shows no DNA binding
      in the assay.  M.RsrI (L72P), on the other hand, is non-toxic and gives reproducible binding.
      Catalytic assays of >70% pure M.RsrI (L72P) have shown that it retains weak catalytic
      activity.  This mutation lies close to the highly conserved catalytic motif "DPPY", and may
      affect catalysis and/or AdoMet binding.  We will generate more M.RsrI for attempts at
      crystallization, and will purify M.RsrI (L72P) and other mutants recently generated by
      site-directed PCR mutagenesis.
AU  - Szegedi SS
AU  - Ma Z
AU  - Gumport RI
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1998 12: A1437.

PMID- 
VI  - 13
DP  - 1999
TI  - Characterization of the DNA binding and kinetic properties of wild-type Rsr[N6-adenine] methyltransferase (M.RsrI).
PG  - A1367
AB  - M.RsrI recognizes the DNA sequence GAATTC and catalyzes the transfer of a methyl group from
      S-adenosylmethionine to the exocyclic amino group of the central adenine to form GamATTC and
      S-adenosylhomocysteine.  Our research focuses on the characterization for the DNA binding,
      catalytic and structural properties of M.RsrI.  First the wild-type protein was purified to
      >95% homogeneity using a simplified procedure involving two chromatographic steps.  Gel-shift
      assays of the protein were then performed on 1 or 5 nM canonical unmethylated, hemimethylated,
      and dimethylated, or control (CTTAAG) 25-mer DNA duplexes in the presence of sinefungin, a
      potent inhibitory analogue of AdoMet.  The following KD values obtained: hemimethylated, 3-7
      nM; unmethylated, 30nM; and dimethylated and control, > 2500 nM.  Some pre-steady state
      kinetic parameters of M.RsrI have been determined.  Upon the addition of enzyme pre-incubated
      with radiolabeled AdoMet, M.RsrI shows a "burst" of methylated product formation equivalent to
      the enzyme concentration in the presence of excess hemimethylated 14-mer DNA and radiolabeled
      AdoMet.  This is followed by a slower step that represents the catalytic turnover (kcat).  The
      dissociation constants for AdoMet (8.4 microM), AdoHcy (3.5 microM), and sinefungin (4.6
      microM) have been determined for M.RsrI using an intrinsic tryptophan fluorescence quenching
      assay.
AU  - Szegedi SS
AU  - Reich NO
AU  - Gumport RI
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1999 13: A1367.

PMID- 11024176
VI  - 28
DP  - 2000
TI  - Substrate binding in vitro and kinetics of RsrI [N6-adenine] DNA methyltransferase.
PG  - 3962-3971
AB  - RsrI [N6-adenine] DNA methyltransferase (M.RsrI), which recognizes GAATTC and is a member of a
      restriction-modification system in Rhodobacter sphaeroides, was purified to >95% homogeneity
      using a simplified procedure involving two ion exchange chromatographic steps. Electrophoretic
      gel retardation assays with purified M.RsrI were performed on unmethylated, hemimethylated,
      dimethylated or non-specific target DNA duplexes (25 bp) in the presence of sinefungin, a
      potent inhibitory analog of AdoMet. M.RsrI binding was affected by the methylation status of
      the DNA substrate and was enhanced by the presence of the cofactor analog. M.RsrI bound DNA
      substrates in the presence of sinefungin with decreasing affinities: hemimethylated >
      unmethylated > dimethylated >> non-specific DNA. Gel retardation studies with DNA substrates
      containing an abasic site substituted for the target adenine DNA provided evidence consistent
      with M.RsrI extruding the target base from the duplex. Consistent with such base flipping, an
      approximately 1.7-fold fluorescence intensity increase was observed upon stoichiometric
      addition of M.RsrI to hemimethylated DNA containing the fluorescent analog 2-aminopurine in
      place of the target adenine. Pre-steady-state kinetic and isotope-partitioning experiments
      revealed that the enzyme displays burst kinetics, confirmed the catalytic competence of the
      M.RsrI-AdoMet complex and eliminated the possibility of an ordered mechanism where DNA is
      required to bind first. The equilibrium dissociation constants for AdoMet, AdoHcy and
      sinefungin were determined using an intrinsic tryptophan fluorescence-quenching assay.
AU  - Szegedi SS
AU  - Reich NO
AU  - Gumport RI
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2000 28: 3962-3971.

PMID- 18635051
VI  - 111
DP  - 1981
TI  - Phage-induced development of a site-specific endonuclease in Anacystis nidulans, a cyanobacterium.
PG  - 1-10
AB  - Anacystis nidulans infected by cyanophage AS-1 produces a site-specific endonuclease cleaving
      double-stranded DNA, as judged from the gel electrophoretic analysis of the reaction products
      and the determination of the terminal nucleotide at the 5'-end of the fragments.  The enzyme
      was purified to near electrophoretic homogeneity.  It has a molecular weight of 40,000 +/-
      4,000.  Only Mg2+ ions are required for enzyme activity.  Limit digestion was not obtained
      even after extensive digestion of substrate DNA with large amounts of the purified enzyme.
      This suggests that the endonuclease splits the substrate at more than one nucleotide sequence
      with a different efficiency for each sequence.  The following observations suggest that the
      endonuclease takes part in the breakdown of host DNA in the infected cell: purified host DNA
      is degraded by, while cyanophage AS-1 DNA is protected against, the enzyme, and the appearance
      of the endonuclease during the lytic cycle coincides with the onset of intensive degradation
      of host DNA.
AU  - Szekeres M
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1981 111: 1-10.

PMID- 2820801
VI  - 222
DP  - 1987
TI  - Cleavage and sequence recognition of 2,6-diaminopurine-containing DNA by site-specific endonucleases.
PG  - 89-94
AB  - The susceptibility of 2,6-diaminopurine (DAP)-containing bacteriophage DNA to
      several restriction and other endonucleases was examined.  With the only
      exception of TaqI, these enzymes did not accept the modified base as a
      substitute for adenine.  The phage DNA was extensively fragmented by the
      restriction endonucleases which recognized only G and C-containing sites.
      5'-terminal analysis of the MspI and SmaI fragments revealed that d(DAP-T)
      basepairs can be mistaken by some enzymes for d(G-C) pairs.
AU  - Szekeres M
AU  - Matveyev AV
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1987 222: 89-94.

PMID- 6299728
VI  - 131
DP  - 1983
TI  - Evidence for a restriction/modification-like system in Anacystis nidulans infected by cyanophage AS-1.
PG  - 137-141
AB  - Anacystis nidulans infected by AS-1 cyanophage contains an endonuclease (AS-1
      endonuclease) which splits host DNA but not AS-1 phage DNA [Szekeres, M. (1981)
      Virology, 111, 1-10].  AS-1 phage DNA proved to be resistant not only to AS-1
      endonuclease but also to a number of restriction endonucleases the recognition
      sites of which contain a central dG-dC dinucleotide.  Since an unmodified
      5'dG-dC dinucleotide was shown to be present at the sites at which DNA is
      cleaved by AS-1 endonuclease, the results suggest that the sites attacked
      preferentially by the AS-1 endonuclease are specifically protected on the AS-1
      DNA molecule.  The modification of AS-1 DNA was shown to occur specifically in
      infected Anacystis because AS-1 DNA fragments which are normally resistant to
      AS-1 endonuclease became susceptible to this enzyme if inserted into pBR322
      plasmid and cloned in Escherichia coli.  AS-1 DNA was shown to contain about 5%
      of a modified nucleotide which was not 5-methyldeoxycytidylic acid.  Results
      presented and our earlier data suggest that in Anacystis infected by AS-1
      phage, a restriction/modification-like system operates which is able to
      elimminate 'unwanted' (host) DNA selectively.
AU  - Szekeres M
AU  - Szmidt AE
AU  - Torok I
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1983 131: 137-141.

PMID- 21778233
VI  - 286
DP  - 2011
TI  - Mining Endonuclease Cleavage Determinants in Genomic Sequence Data.
PG  - 32617-32627
AB  - Homing endonucleases have great potential as tools for targeted gene therapy and gene
      correction, but identifying variants of these enzymes
      capable of cleaving specific DNA targets of interest is necessary
      before the widespread use of such technologies is possible. We
      identified homologues of the LAGLIDADG homing endonuclease I-AniI and
      their putative target insertion sites by BLAST searches followed by
      examination of the sequences of the flanking genomic regions. Amino
      acid substitutions in these homologues that were located close to the
      target site DNA, and thus potentially conferring differences in target
      specificity, were grafted onto the I-AniI scaffold. Many of these
      grafts exhibited novel and unexpected specificities. These findings
      show that the information present in genomic data can be exploited for
      endonuclease specificity redesign.
AU  - Szeto MD
AU  - Boissel SJS
AU  - Baker D
AU  - Thyme SB
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2011 286: 32617-32627.

PMID- 8269964
VI  - 218
DP  - 1993
TI  - Kinetic characterization of the EcaI methyltransferase.
PG  - 727-733
AB  - A kinetic analysis of the EcaI adenine-N6-specific methyltransferase (MTase) is presented. The
      enzyme catalyzes the transfer of a methyl group from S-adenosyl-L-methionine (AdoMet) to the
      adenine of the GGTNACC sequence with a random rapid-equilibrium mechanism. Experiments with a
      synthetic, 14-bp DNA substrate suggest that recognition of the specific site of DNA occurs
      after the binding of AdoMet. Proton concentration does not affect the dissociation constant of
      AdoMet while Vm and the dissociation constant of DNA show a maximum around pH 8. Increasing
      the amount of S-adenosyl-L-homocysteine decreases the inhibitory effect of methylated DNA
      which proves the active role of AdoMet in site recognition. Experiments with hemimethylated
      DNA show that the methylase binds the double-stranded DNA asymmetrically.
AU  - Szilak L
AU  - Der A
AU  - Deak F
AU  - Venetianer P
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1993 218: 727-733.

PMID- 8065896
VI  - 22
DP  - 1994
TI  - Self-methylation of BspRI DNA-methyltransferase.
PG  - 2876-2881
AB  - The DNA (cytosine-5)-methyltransferase (m5C-MTase) M.BspRI is able to accept the methyl group
      from the methyl donor S-adenosyl-L-methionine (AdoMet) in the absence of DNA. Transfer of the
      methyl group to the enzyme is a slow reaction relative to DNA methylation. Self-methylation is
      dependent on the native conformation of the enzyme and is inhibited by
      S-adenosyl-L-homocysteine, DNA and sulfhydryl reagents. Amino acid sequencing of proteolytic
      peptides obtained from M.BspRI, which had been methylated with [methyl-3H]AdoMet, and thin
      layer chromatography of the modified amino acid identified two cysteines, Cys156 and Cys181
      that bind the methyl group in the form of S-methylcysteine. One of the acceptor residues,
      Cys156 is the highly conserved cysteine which plays the role of the catalytic nucleophile of
      m5C-MTases.
AU  - Szilak L
AU  - Finta C
AU  - Patthy A
AU  - Venetianer P
AU  - Kiss A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1994 22: 2876-2881.

PMID- 7607467
VI  - 157
DP  - 1995
TI  - Self-methylation of the M.BspRI methyltransferase.
PG  - 105
AB  - In the absence of DNA substrate, the DNA methyltransferase (MTase) M.BspRI can methylate
      itself using the methyl donor S-adenosyl-L-methionine (AdoMet).  The methyl group is
      transferred to two Cys residues of the MTase.
AU  - Szilak L
AU  - Finta C
AU  - Patthy A
AU  - Venetianer P
AU  - Kiss A
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 105.

PMID- 2204026
VI  - 18
DP  - 1990
TI  - Cloning and nucleotide sequence of the genes coding for the Sau96I restriction and modification enzymes.
PG  - 4659-4664
AB  - The genes coding for the GGNCC specific Sau96I restriction and modification
      enzymes were cloned and expressed in E. coli.  The DNA sequence predicts a 430
      amino acid protein (Mr: 49,252) for the methyltransferase and a 261 amino acid
      protein (Mr: 30,486) for the endonuclease.  No protein sequence similarity was
      detected between the Sau96I methyltransferase and endonuclease.  The
      methyltransferase contains the sequence elements characteristic for m5C
      methyltransferases.  In addition to this, M.Sau96I shows similarity, also in
      the variable region with one m5C-methyltransferase (M.SinI) which has closely
      related recognition specificity (GGA/TCC).  M.Sau96I methylates the internal
      cytosine within the GGNCC recognition sequence.  The Sau96I endonuclease
      appears to act as a monomer.
AU  - Szilak L
AU  - Venetianer P
AU  - Kiss A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 4659-4664.

PMID- 1396713
VI  - 209
DP  - 1992
TI  - Purification and biochemical characterization of the EcaI DNA methyltransferase.
PG  - 391-397
AB  - The EcaI GGTNACC-specific DNA-adenine modification methyltransferase has been purufied to
      apparent homogeneity. The active form of the DNA methyltransferase is a single polypeptide.
      The enzyme has a pH optimum at pH 8.0 and a temperature optimum at 25oC. EcaI DNA
      methyltransferase transfers one methyl group to the adenine of the recognition site in a
      single binding event. The Km was 170 nM for DNA and 1.8 microM for the methyl donor
      S-adenosylmethionine. Methylated DNA is a competitive inhibitor with respect to DNA (Ki-3.5
      nM). The other product of the DNA-methylation reaction, S-adenosylhomocysteine was found to be
      a competitive inhibitor with respect to S-adenosylmethionine (Ki= 2.7 uM). The
      S-adenosylmethionine analog sinefungin was shown to be a very strong inhibitor (Ki = 3.5 nM)
      of the DNA methyltransferase reaction.
AU  - Szilak L
AU  - Venetianer P
AU  - Kiss A
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1992 209: 391-397.

PMID- 3198418
VI  - 61
DP  - 1988
TI  - The characterization and cloning of the NotI restriction-modification system.
PG  - 308
AB  - NotI, a Type II restriction-modification system from the actinomycete Nocardia
      otitidis-caviarum, recognizes the sequence GCGGCCGC.  We are currently purifying and
      characterizing the proteins of this system.  The endonuclease, which cleaves at GC^GGCCGC, has
      been sized by gel filtration and estimated to be approximately 85,000 daltons.  The NotI
      methylase protein has been partially purified and we are in the process of determining its
      size as well as the site and type (N-4 or C-5) of modification it provides.  The N. otitidis
      genomic DNA has been purified and analyzed by HPLC analysis for base composition and for the
      presence of modified bases.  Two approaches are being used to clone the NotI system.  First
      genomic libraries constructed in E. coli are being selected for methylase expression.  Second,
      genomic libraries will also be made and selected in Streptomyces lividans.  In addition to
      selection for methylase expression, we also will be selecting the libraries with phage.  This
      approach has been successfully used in cloning the SalI restriction-modification system.
AU  - Sznyter LA
AU  - Brooks JE
PT  - Journal Article
TA  - Heredity
JT  - Heredity
SO  - Heredity 1988 61: 308.

PMID- 3266860
VI  - 74
DP  - 1988
TI  - The characterization and cloning of the EagI restriction-modification system.
PG  - 53
AB  - Meeting Abstract
AU  - Sznyter LA
AU  - Brooks JE
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 53.

PMID- Not carried by PubMed...
VI  - 89
DP  - 1989
TI  - The cloning and characterization of the EagI restriction-modification system.
PG  - 180
AB  - EagI is a Type II restriction-modification system from the gram-negative
      enteric bacterium Enterobacter agglomerans.  It recognizes the sequence CGGCCG
      with the endonuclease cleaving at C^GGCCG.  The genomic DNA from this organism
      has been purified and analyzed by HPLC analysis for base composition and for
      the presence of modified bases.  The EagI system has been cloned on a 2.9 kb
      PstI fragment in pLSN3 (a pBR322 derivative containing three NotI sites) by
      selection with the NotI endonuclease.  The 2.9kb PstI fragment was then cloned
      into pUC19 in both orientations.  On this higher copy plasmid, an increase of
      endonuclease activity was found in the crude extracts.  The level of increase
      is dependent on orientation.  These clones are currently being characterized.
      We have explored the Mcr phenotype of the most active EagI containing clone and
      find that it is highly restricted by mcrB.  The boundaries of the genes have
      been assigned by deletion subcloning and Tn5 mutagenesis.  The protein products
      of the EagI system are also being characterized.  The endonuclease has been
      purified and sized by gel filtration.  EagI is estimated to be approximately
      78,000 daltons.  The EagI methylase protein has been purified and the size as
      well as site and type (N-4 or C-5) of modification it provides is being
      determined.
AU  - Sznyter LA
AU  - Marcus AM
AU  - Brooks JE
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1989 89: 180.

PMID- 2823226
VI  - 15
DP  - 1987
TI  - Nucleotide sequence of the DdeI restriction-modification system and characterization of the methylase protein.
PG  - 8249-8266
AB  - The DdeI restriction-modification system was previously cloned and has been
      maintained in E. coli on two separate and compatible plasmids.  The nucleotide
      sequence of the endonuclease and methylase genes has now been determined; it
      predicts proteins of 240 amino acids, Mr=27,808, and 415 amino acids,
      Mr=47,081, respectively.  Inspection of the DNA sequence shows that the 3' end
      of the methylase gene had been deleted during cloning.  The clone containing
      the complete methylase gene was made and compared to that containing the
      truncated gene; only clones containing the truncated form support the
      endonuclease gene in E. coli.  Bal-31 deletion studies show that methylase
      expression in the Dde clones is also dependent upon orientation of the gene
      with respect to pBR322.  The truncated and complete forms of the methylase
      protein were purified and compared; the truncated form appears to be more
      stable and active in vitro.  Finally, comparison of the deduced amino acid
      sequence of M.DdeI with that of other known cytosine methylases shows
      significant regions of homology.
AU  - Sznyter LA
AU  - Slatko B
AU  - Moran L
AU  - O'Donnell KH
AU  - Brooks JE
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1987 15: 8249-8266.

PMID- 
VI  - 0
DP  - 1989
TI  - Cloning and characterization of the SphI restriction-modification system from S. phaeochromogenes.
PG  - 361
AB  - SphI, a Type II restriction-modification system from the actinomycete Streptomyces
      phaeochromogenes, recognizes the sequence GCATGC.  The endonuclease cleaves at GCATG/C leaving
      a 3' four base overhang.  A 5.4kb insert carrying the methylase gene has been cloned into the
      PstI site of pBR322 and expressed in E. coli at a low level as evidenced by incomplete
      modification of chromosomal DNA and lack of modification of phage DNA in vivo.  The clone has
      no endonuclease activity.  The plasmid has been extensively mapped; Tn-5 insertion mutagenesis
      is being used to locate the methylase gene.  The fragment is also being positioned by Southern
      hybridization onto the S. phaeochromogenes chromosome.  Attempts will be made to clone and
      express the complete system in Streptomyces.
AU  - Sznyter LA
AU  - Vaccaro CM
AU  - Jager-Quinton T
AU  - Wilson G
AU  - Brooks JE
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1989 0: 361.

PMID- 6254840
VI  - 10
DP  - 1980
TI  - Cloning the modification methylase gene of Bacillus sphaericus R in Escherichia coli.
PG  - 219-225
AB  - The gene coding for the sequence-specific modification methylase methM - BspI
      of Bacillus sphaericus R has been cloned in Escherichia coli by means of
      plasmid pBR322.  The selection was based on the expression of the cloned gene
      which rendered the recombinant plasmid resistant to BspI restriction
      endonuclease cleavage.  The gene is carried by a 9 kb BamHI fragment and by a
      smaller 2.5 kb EcoRI fragment derived from the BamHI fragment.  The
      Bsp-specific methylase level was found to be higher in the recombinant clones
      than in the parental strain.  The methylase gene is probably located on the
      Bacillus sphaericus chromosome, and not on a plasmid known to be carried by
      this strain.  The recombinant clones do not exhibit any BspI restriction
      endonuclease activity.
AU  - Szomolanyi I
AU  - Kiss A
AU  - Venetianer P
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1980 10: 219-225.

PMID- 21378122
VI  - 39
DP  - 2011
TI  - Characterization of PvuRts1I endonuclease as a tool to investigate genomic 5-hydroxymethylcytosine.
PG  - 5149-5156
AB  - In mammalian genomes a sixth base, 5-hydroxymethylcytosine ((hm)C), is generated by enzymatic
      oxidation of 5-methylcytosine ((m)C). This
      discovery has raised fundamental questions about the functional relevance
      of (hm)C in mammalian genomes. Due to their very similar chemical
      structure, discrimination of the rare (hm)C against the far more abundant
      (m)C is technically challenging and to date no methods for direct
      sequencing of (hm)C have been reported. Here, we report on a purified
      recombinant endonuclease, PvuRts1I, which selectively cleaves
      (hm)C-containing sequences. We determined the consensus cleavage site of
      PvuRts1I as (hm)CN(11-12)/N(9-10)G and show first data on its potential to
      interrogate (hm)C patterns in mammalian genomes.
AU  - Szwagierczak A
AU  - Brachmann A
AU  - Schmidt CS
AU  - Bultmann S
AU  - Leonhardt H
AU  - Spada F
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2011 39: 5149-5156.

PMID- 
VI  - 0
DP  - 1991
TI  - Modifying specificities of restriction enzymes.
PG  - 371-376
AB  - For the last five years, our laboratory has been studying various aspects of
      controlled cleavage of DNA, both for (1) the 50 bp-10 kb range of
      single-stranded (ss) and double-stranded (ds) DNA fragments, plasmids or
      phages, and (2) for very large genomes of bacteria, yeast and higher
      eukaryotes.  We are using commerical restriction enzymes (ENases) either (i) of
      the class-IIS variety (ENase-IIS) (Szybalski, 1985), where the recognition site
      on the DNA for the ENase is separated by several base pairs from the cleavage
      site, together with an adapter oligodeoxynucleotide (oligo), or (ii) various
      combinations of a particular ENase, its cognate methyltransferase (MTase) and
      DNA-binding protein whose binding site contains the corresponding ENase/MTase
      recognition site.  The ENase-IIS enzymes were used either for precise cutting
      (Podhajska and Szybalski, 1985) or for precise trimming of DNA (Hasan et al,
      1986), whereas the MTase/ENase/DNA-binding protein combination was used for
      very rare cuts in large genomes (Koob et al., 1968; Grimes et al., 1990; Koob
      and Szybalski, 1990).
AU  - Szybalski W
PT  - Journal Article
TA  - Biotechnology: Bridging Research and Applications
JT  - Biotechnology: Bridging Research and Applications
SO  - Biotechnology: Bridging Research and Applications 1991 0: 371-376.

PMID- 3007286
VI  - 40
DP  - 1985
TI  - Universal restriction endonucleases: designing novel cleavage specificities by combining adapter oligodeoxynucleotide and enzyme moieties.
PG  - 169-173
AB  - Class IIS restriction endonucleases cleave double-stranded (ds) DNA at precise
      distances from their recognition sequences.  A method is proposed which
      utilizes this separation between the recognition site and the cut site to allow
      a class IIS enzyme, e.g., FokI, to cleave practically any predetermined
      sequence by combining the enzyme with a properly designed oligodeoxynucleotide
      adapter.  Such an adapter is constructed from the constant recognition site
      domain (a hairpin containing the ds sequence, e.g., G/C G/C A/T T/A G/C for
      FokI) and a variable, single-stranded (ss) domain complementary to the ss
      sequence to be cleaved (at 9 and 13 nucleotides on the paired strands from the
      recognition sequence in the exampled of FokI).  The ss sequence designated to
      be cleaved could be provided by ss phage DNA (e.g., M13), gapped ds plasmids,
      or supercoiled ds plasmids that were alkali denatured and rapidly neutralized.
      Combination of all three components, namely the class IIS enzyme, the ssDNA
      target sequence, and the complementing adapter, would result in target DNA
      cleavage at the specific predetermined site.  The target ss DNA could be
      converted to the precisely cleaved ds DNA by DNA polymerase, utilizing the
      adapter oligodeoxynucleotide as primer.  This novel procedure represents the
      first example of changing enzyme specificity by synthetic design.  A
      practically unlimited assortment of new restriction specificities could be
      produced.  The method should have many specific and general applications when
      its numerous ramification are exploited.
AU  - Szybalski W
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1985 40: 169-173.

PMID- 3266859
VI  - 74
DP  - 1988
TI  - Nomenclature for bacterial genes coding for class-II restriction endonucleases and modification methyltransferases.
PG  - 279-280
AB  - A proposed nomenclature for restriction enzyme and methylase genes.
AU  - Szybalski W
AU  - Blumenthal RM
AU  - Brooks JE
AU  - Hattman S
AU  - Raleigh EA
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 279-280.

PMID- 2055464
VI  - 100
DP  - 1991
TI  - Class-IIS restriction enzymes - a review.
PG  - 13-26
AB  - Class-IIS restriction enzymes (ENases-IIS) interact with two discrete sites on
      double-stranded DNA: the recognition site, which is 4-7 bp long, and the
      cleavage site, usually 1-20 bp away from the recognition site.  The recognition
      sequences of ENases-IIS are totally (or partially) asymmetric and all of the
      characterized ENases-IIS are monomeric.  A total of 35 ENases-IIS are described
      (80, if all isoschizomers are taken into consideration) together with ten
      related ENases (class IIT), and 15 cognate methyltransferases (MTases-IIS).
      The physical, chemical, and molecular properties of the ENases-IIS and
      MTases-IIS are reviewed and many unique applications of this class of enzymes
      are described, including: precise trimming of DNA; retrieval of cloned
      fragments; gene assembly; use as a universal restriction enzyme; cleavage of
      single-stranded DNA; detection of point mutations; tandem amplification;
      printing-amplification reaction; and localization of methylated bases.
AU  - Szybalski W
AU  - Kim SC
AU  - Hasan N
AU  - Podhajska AJ
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1991 100: 13-26.

PMID- 744485
VI  - 4
DP  - 1978
TI  - Nobel prizes and restriction enzymes.
PG  - 181-182
AB  - We have two reasons to rejoice in the wise choices made by the Nobel Committee in 1978.  The
      discovery of the restriction enzymes and their application in genetic mapping, a main topic of
      our journal, were selected for this award, and one of our Editors, Dr. Hamilton O. Smith, was
      honored as one of the three recipients.
AU  - Szybalski W
AU  - Skalka A
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1978 4: 181-182.

PMID- 9770119
VI  - 17
DP  - 1998
TI  - Targeting DNA methyltransferase in cancer.
PG  - 219-231
AB  - DNA methyltransferase is an enzyme responsible for generating and maintaining DNA methylation
      patterns.  DNA methylation patterns control different genome functions, thus they are an
      important component of the epigenetic information.  It has been recently postulated that DNA
      methyltransferase plays an important role in oncogenesis and that it is a candidate target for
      anticancer therapy.  This commentary discusses the possible mechanisms through which DNA
      methyltransferase participates in oncogenesis and the rationale for targeting it in cancer.
AU  - Szyf M
PT  - Journal Article
TA  - Cancer Metastasis Rev.
JT  - Cancer Metastasis Rev.
SO  - Cancer Metastasis Rev. 1998 17: 219-231.

PMID- 7940985
VI  - 15
DP  - 1994
TI  - DNA methylation properties: consequences for pharmacology.
PG  - 233-238
AB  - DNA methylation plays an important role in controlling the profile of gene expression of
      mammalian cells. The hypothesis presented in this article is that DNA methylation patterns are
      determined by an interplay between the level of DNA methyltransferase and demethylase
      activities and site-specific signals. The expression of the DNA methyltransferase gene is
      regulated with the proliferative state of the cell and it is upregulated by cellular oncogenic
      pathways, resulting in hypermethylation and repression of tumour-suppressing loci. DNA
      methyltransferase inhibitors would inhibit the excessive activity of DNA methyltransferase in
      cancer cells and induce the original cellular programme of tumour suppression. They can also
      be used to turn on alternative programmes of gene expression. Specific DNA methyltransferase
      antagonists might provide us with therapeutic agents directed at a nodal point of regulation
      of genetic information.
AU  - Szyf M
PT  - Journal Article
TA  - Trends Pharmacol. Sci.
JT  - Trends Pharmacol. Sci.
SO  - Trends Pharmacol. Sci. 1994 15: 233-238.

PMID- 11282571
VI  - 6
DP  - 2001
TI  - The role of DNA methyltransferase 1 in growth control.
PG  - D599-D609
AB  - Vertebrate DNA contains in addition to the four bases comprising the genetic information a
      modified base, 5-methylcytosine that plays an important role in the epigenome. The methylated
      bases form a pattern of methylation that is cell specific and is faithfully inherited during
      cell division. The enzyme DNA methyltransferase 1 DNMT1 is responsible for copying the DNA
      methylation pattern but other de novo methyltransferase as well as demethylases might also be
      involved. Multiple mechanisms are in place to ensure the coordinate inheritance of the DNA
      methylation pattern with DNA replication. There is a bilateral relationship between the cell
      cycle and DNMT1. The expression of DNMT1 is tightly regulated with the cell cycle while the
      expression of DNMT1 can affect the cell cycle. DNMT1 protein might regulate cell cycle events
      by mechanisms that are independent of its DNA methylation activity through its multiple
      protein-protein interactions. The unique position of DNMT1 in the cell cycle is consistent
      with the hypothesis that it plays an important role in cancer.
AU  - Szyf M
PT  - Journal Article
TA  - Front. Biosci.
JT  - Front. Biosci.
SO  - Front. Biosci. 2001 6: D599-D609.

PMID- 14744498
VI  - 6
DP  - 2003
TI  - DNA methylation and cancer therapy.
PG  - 341-353
AB  - Vertebrate DNA is modified by methyl moieties at the 5'-position of cytosine rings residing
      in the di-nucleotide sequence CpG. Approximately
      80% of CpG dinucleotide sequences are methylated. The pattern of
      distribution of methylated CGs is cell-type specific and correlates with
      gene expression programming and chromatin structure. Three kinds of
      seemingly contradictory aberrations in DNA methylation are observed in
      cancer, global hypomethylation, and regional hypermethylation and
      deregulated level of expression of DNA methyltransferases. It was
      previously proposed that the DNA methylation machinery is a candidate
      target for anticancer therapy. Inhibition of hypermethylation was the
      first therapeutic target. However, recent data suggests that inhibition of
      DNA methylation might have untoward effects such as induction of genes
      involved in metastasis. This review discusses the relative role of the
      three levels of alteration in the DNA methylation in cancer, proposes a
      unified hypothesis on the relative roles of increased DNA
      methyltransferase as well as the coexistence of hypo -and hyper-
      methylation in cancer and its possible implications on anticancer therapy.
AU  - Szyf M
PT  - Journal Article
TA  - Drug Resistance Updates
JT  - Drug Resistance Updates
SO  - Drug Resistance Updates 2003 6: 341-353.

PMID- 11475533
VI  - 1
DP  - 2000
TI  - The DNA methylation machinery as a therapeutic target.
PG  - 101-118
AB  - Pharmacology and therapeutics have traditionally focused on altering the activity of specific
      proteins that play an important physiological role either to counteract disease processes or
      to achieve changes in physiology that are of benefit to the patient.  The explosion in our
      understanding of gene expression programs opens up new horizons for pharmacological
      intervention.  Key processes reversibly controlling genetic programs are attractive drug
      targets.  DNA methylation is a fundamental feature of genomes and the control of their
      function and is therefore a candidate for pharmacological manipulation that might have
      important therapeutic advantage.  This review argues that DNA methylation plays an important
      role in the control of genomic processes, suggests how the DNA methylation machinery is
      involved in cancer, identifies the enzymatic processes that are a target for drug
      intervention, proposes potential therapeutic utilities for agents that manipulate the DNA
      methylation machinery and discusses novel drugs that target the DNA methylation machinery.
AU  - Szyf M
PT  - Journal Article
TA  - Curr. Drug Targets
JT  - Curr. Drug Targets
SO  - Curr. Drug Targets 2000 1: 101-118.

PMID- 6233606
VI  - 81
DP  - 1984
TI  - DNA methylation pattern is determined by the intracellular level of the methylase.
PG  - 3278-3282
AB  - Extrachromosomal plasmid DNA is transiently undermethylated in Escherichia coli during
      amplification in the presence of chloramphenicol. In addition, undermethylation of phage
      lambda DNA was observed after thermal induction of a lambda cI857 lysogen while the integrated
      lambda phage DNA was found to be fully methylated. these methylation pattern changes occur
      under conditions (extensive replication) in which the intracellular methylase level becomes
      limiting. In an E. coli strain that harbors a plasmid that carries the dam methylase gene and
      therefore overproduces dam methylase, there is no undermethylation of dam sites in either of
      the extrachromosomal DNAs. The sites that are methylated by the mec methylase in both plasmid
      and lambda phage DNAs were undermethylated in the dam overproducer as well. These results
      indicate that the intracellular level of the E. coli methylase determines the DNA methylation
      pattern.
AU  - Szyf M
AU  - Avraham-Haetzni K
AU  - Reifman A
AU  - Shlomai J
AU  - Kaplan F
AU  - Oppenheim A
AU  - Razin A
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1984 81: 3278-3282.

PMID- 
VI  - 1
DP  - 1998
TI  - Oligonucleotides as inhibitors of DNA methyltransferase: novel antitumor drugs.
PG  - 93-101
AB  - DNA MeTase is now emerging as an important new therapeutic target.  The recent understanding
      of its critical role in development of cancer leads us to propose that modulation of this
      enzyme will be of therapeutic value.  The hairpin oligonucleotide inhibitors discussed in this
      review are, to our knowledge, the first representatives of novel DNA MeTase inhibitors that
      are bona fide substrate analogs.  They also constitute a new example of the use of DNA as
      antagonists of natural ligands of nuclear proteins.
AU  - Szyf M
AU  - Bigey P
PT  - Journal Article
TA  - Curr. Res. Mol. Ther.
JT  - Curr. Res. Mol. Ther.
SO  - Curr. Res. Mol. Ther. 1998 1: 93-101.

PMID- 6296768
VI  - 10
DP  - 1982
TI  - Studies on the biological role of DNA methylation:  V. The pattern of E. coli DNA methylation.
PG  - 7247-7259
AB  - The distribution of the methylatable sites GATC and CCA/TGG was studied by analyzing the
      molecular average size of restriction fragments of E. coli DNA. Both sites were found to be
      randomly distributed, reflecting a random pattern of methylation. The methylation pattern of
      specific sequences such as the origin of replication and rRNA genes has been studied in wild
      type E. coli and a methylation deficient (dam- dcm-) mutant. These sequences were found to be
      methylated in wild type cells and unmethylated in the mutant indicating that there is no
      effect of the state of methylation of these sequences on their expression. Analysis of the
      state of methylation of GATC sites in newly replicating DNA using the restriction enzyme DpnI
      (cleaves only when both strands are methylated) revealed no detectable hemimethylated DNA
      suggesting that methylation occurs at the replication fork. Taking together the results
      presented here and previously published data, we arrive at the conclusion that the most likely
      function of E. coli DNA methylations is probably in preventing nuclease activity.
AU  - Szyf M
AU  - Gruenbaum Y
AU  - Urieli-Shoval S
AU  - Razin A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1982 10: 7247-7259.

PMID- 10911912
VI  - 910
DP  - 2000
TI  - How does DNA methyltransferase cause oncogenic transformation?
PG  - 156-174
AB  - Global hypomethylation of genes and repetitive sequences, as well as hypermethylation of
      certain genes known to be involved in tumor suppression, are observed concurrently in cancer
      cells. Aberrant expression of DNA methyltransferase 1 (dnmt1) is a downstream effector of
      multiple tumorigenic pathways, and several data suggest that dnmt1 plays a causal role in
      these pathways. These data raise two critical questions: Why does ectopic expression of dnmt1
      transform cells? and How can global hypomethylation exist in a cell that bears high levels of
      DNMT1 activity? It is proposed that DNMT1 induces cellular transformation by a mechanism that
      does not involve DNA methylation and that the low level of methylation in cancer cells is a
      result of induction of a DNA demethylase in these cells. Both DNMT1 and the demethylase play a
      causal role in cellular transformation and are candidate anticancer targets.
AU  - Szyf M
AU  - Knox DJ
AU  - Milutinovic S
AU  - Slack AD
AU  - Araujo FD
PT  - Journal Article
TA  - Ann. NY Acad. Sci.
JT  - Ann. NY Acad. Sci.
SO  - Ann. NY Acad. Sci. 2000 910: 156-174.

PMID- 3536887
VI  - 168
DP  - 1986
TI  - Biological role of DNA methylation:  sequence-specific single-strand breaks associated with hypomethylation of GATC sites in Escherichia coli DNA.
PG  - 1487-1490
AB  - The effect of methylation of GATC sites in Escherichia coli DNA on the formation of
      single-strand breaks was studied with dam+, dam mutant, and Dam-overproducer strains.
      Single-strand breaks have been observed in dam mutant cells predominantly at TpT and, to a
      lesser extent, at CpC. In dam mutant cells harboring pTP166 (a plasmid containing the dam
      gene), no such nicks were observed.
AU  - Szyf M
AU  - Meisels E
AU  - Razin A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1986 168: 1487-1490.

PMID- Not carried by PubMed...
VI  - 37
DP  - 1996
TI  - Antisense oligonucleotides directed against DNA methyltransferase inhibit tumorigenesis.
PG  - 353
AB  - We have previously shown that DNA methyltransferase is a downstream
      effector
      of the Ras oncogenic signaling pathway.  To test the hypothesis that inhibition of DNA
      MeTase
      could reverse tumorigenesis and to test the possibility  that DNA MeTase could serve as an
      anticancer target, we have treated a number of human and mouse cancer cell lines with
      antisense
      phosphorothioate modified oligonucleotides directed at the translation initiation region of
      either
      human or mouse DNA MeTase mRNA as well as control oligonucleotides.  The cell lines
      tested
      were Y1, a mouse adrenocortical cell carcinoma, NCI-H596, a human lung
      adenosquamous
      carcinoma, NCI-H496, a lung small cell carcinoma nd SF126 a human glioma.  The
      antisense
      oligonucleotides inhibited DNA MeTase mRNA, DNA MeTase activity as well as DNA
      methylation in a dose dependent manner (0.1-20 uM).  Focus formation in soft agar was
      dramatically inhibited by DNA MeTase antisense oligonucleotides.  Tumor formation in
      nude mice
      (the NCI-H446 line) was inhibited when the cells expressed an exogenously introduced
      antisense
      DNA MeTase RNA whereas control cells formed tumors.  Injection of DNA MeTase
      antisense
      oligonucleotides (ip) (0.55-30 mg/kg every 48 hours) delayed tumor formation by NCI-
      H446 cells
      in nude mice and by Y1 cells in syngeneic LAF-1 mice.  These studies support the
      hypothesis that
      inhibition of DNA MeTase could reverse tumorigenesis and that DNA MeTase is a target
      for
      anticancer therapy.
AU  - Szyf M
AU  - Ramchandani S
AU  - MacLeod R
AU  - Croteau S
AU  - von Hofe E
PT  - Journal Article
TA  - Proc. Amer. Assoc. Cancer Res.
JT  - Proc. Amer. Assoc. Cancer Res.
SO  - Proc. Amer. Assoc. Cancer Res. 1996 37: 353.

PMID- Not carried by PubMed...
VI  - 4
DP  - 1993
TI  - Mammalian cells contain a general (CpG) DNA demethylating activity.
PG  - 74a
AB  - A hallmark of vertebrate DNA is the fact that a significant fraction of the cytosines in the
      dinucleotide sequence CpG is methylated generating a pattern of methylation that is site and
      tissue specific. The pattern of methylation is formed during development by de novo
      methylation and demethylation processes. The biochemical mechanisms that are responsible for
      demethylation are unclear. To address the question whether mammalian cells contain a general
      activity that can remove methyl groups from CpG sequences, we transfected an in vitro
      methylated SK plasmid (wih SS1 methylase) into a mouse embryonal teratocarcinoma cell line and
      analyzed the state of methylation of the transfected demethylation between one and two days
      after transfection as judged by a HpaII/MspI analysis of the transfected DNA. All HpaII sites
      were demethylated suggesting that the demethylase activity exhibits limited specificity under
      these conditions. However, demethylation of areas that contain a low density of CpG sequences
      is inefficient relative to that of CpG dense regions. The demethylase activity is limiting in
      embryonal cells as determined by a dose response curve. Demethylase activity is not restricted
      to embryonal cells and demethylation of plasmid DNA was observed in 10T1/2 and C2 cell lines.
      Previous publications have suggested that demethylation involves a base excision repair
      process rather than an active removal of methyl groups. To address this question we developed
      an in vitro assay for demethylation. Using this assay we show that demethylation of methylated
      SK plasmid DNA by a P19 nuclear extract does not require the presence of dNTPs or dCTP. This
      implies that demethylation involves an active removal of methyl groups from DNA. Our results
      demonstrate that parallel to the general DNA methylase activity, mammalian cells contain a
      general DNA demethylase activity. We suggest that the specificity of demethylation during the
      developmental process is determined by factors that limit the accessibility of DNA to the DNA
      demethylase machinery.
AU  - Szyf M
AU  - Theberge J
PT  - Journal Article
TA  - Mol. Biol. Cell
JT  - Mol. Biol. Cell
SO  - Mol. Biol. Cell 1993 4: 74a.

PMID- 10857920
VI  - 78
DP  - 2000
TI  - Metalloporphyrin mediated DNA cleavage by a low concentration of HaeIII restriction enzyme.
PG  - 383-389
AB  - The plasmid DNA scission by the restriction enzyme HaeIII was investigated in the presence of
      tetrakis(1-methylpyridinium-4-yl)porphyrin (H2TMPyP) and its manganese(III), iron(III),
      nickel(II), cobalt(III) and zinc(II) derivatives. The effect of metalloporphyrins on plasmid
      DNA cleavage was ascertained by gel electrophoresis. UV-Vis absorption spectroscopy and
      circular dichroism (CD) spectroscopy. In the absence of the metalloporphyrins, plasmid DNA
      scission did not occur in the presence of a low concentration of HaeIII (0.2 units microL(-1))
      at 37 degrees C after 1 h incubation. However, DNA cleavage occurred in the presence of the
      metalloporphyrins and HaeIII (0.2 units microL(-1)) at 37 degrees C after 1 h incubation. Gel
      electrophoresis results indicate the catalytic effect of metalloporphyrins (Mn(III)-,
      Fe(III)-, Co(III)- and Zn(II)TMPyP) by binding to both DNA and the enzyme through
      electrostatic interaction, which was confirmed by the change in UV-Vis and CD spectra. A
      mechanism for the enhanced DNA cleavage is proposed.
AU  - Tabata M
AU  - Nakajima K
AU  - Nyarko E
PT  - Journal Article
TA  - J. Inorg. Biochem.
JT  - J. Inorg. Biochem.
SO  - J. Inorg. Biochem. 2000 78: 383-389.

PMID- 27056231
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of a gamma-Hexachlorocyclohexane Degrader, Sphingobium sp. Strain TKS, Isolated from a gamma-Hexachlorocyclohexane-Degrading Microbial  Community.
PG  - e00247-16
AB  - Here, we report the complete genome sequence of a gamma-hexachlorocyclohexane (gamma-HCH)
      degrader,Sphingobiumsp. strain TKS, which was isolated from a
      gamma-HCH-degrading microbial community. The genome of TKS consists of two
      chromosomes and nine plasmids. Thelingenes for conversion of gamma-HCH to
      beta-ketoadipate are dispersed on chromosome 1 and three out of the nine
      plasmids.
AU  - Tabata M
AU  - Ohhata S
AU  - Kawasumi T
AU  - Nikawadori Y
AU  - Kishida K
AU  - Sato T
AU  - Ohtsubo Y
AU  - Tsuda M
AU  - Nagata Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00247-16.

PMID- 27056230
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of a gamma-Hexachlorocyclohexane-Degrading Bacterium, Sphingobium sp. Strain MI1205.
PG  - e00246-16
AB  - Here, we report the complete genome sequence of a gamma-hexachlorocyclohexane
      (gamma-HCH)-degrading bacterium,Sphingobiumsp. strain MI1205. The genome of
      MI1205 consists of two chromosomes and four plasmids with sizes of 33 to 292 kb.
      All thelingenes for gamma-HCH metabolism are dispersed on the four plasmids.
AU  - Tabata M
AU  - Ohhata S
AU  - Nikawadori Y
AU  - Sato T
AU  - Kishida K
AU  - Ohtsubo Y
AU  - Tsuda M
AU  - Nagata Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00246-16.

PMID- 23682148
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of the gamma-Hexachlorocyclohexane-Degrading Bacterium Sphingomonas sp. Strain MM-1.
PG  - e00247-13
AB  - gamma-Hexachlorocyclohexane (gamma-HCH) is a man-made chlorinated insecticide that has caused
      serious environmental problems. Here, we report the complete
      genome sequence of the gamma-HCH-degrading bacterium Sphingomonas sp. strain
      MM-1, which consists of one chromosome and five plasmids. All the specific lin
      genes that are almost identical to those of Sphingobium japonicum UT26 for the
      conversion of gamma-HCH to beta-ketoadipate are dispersed on four out of the five
      plasmids.
AU  - Tabata M
AU  - Ohtsubo Y
AU  - Ohhata S
AU  - Tsuda M
AU  - Nagata Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00247-13.

PMID- 29459649
VI  - 8
DP  - 2018
TI  - Evolving Bacterial Fitness with an Expanded Genetic Code.
PG  - 3288
AB  - Since the fixation of the genetic code, evolution has largely been confined to 20
      proteinogenic amino acids. The development of orthogonal translation systems that
      allow for the codon-specific incorporation of noncanonical amino acids may
      provide a means to expand the code, but these translation systems cannot be
      simply superimposed on cells that have spent billions of years optimizing their
      genomes with the canonical code. We have therefore carried out directed evolution
      experiments with an orthogonal translation system that inserts 3-nitro-L-tyrosine
      across from amber codons, creating a 21 amino acid genetic code in which the
      amber stop codon ambiguously encodes either 3-nitro-L-tyrosine or stop. The 21
      amino acid code is enforced through the inclusion of an addicted, essential gene,
      a beta-lactamase dependent upon 3-nitro-L-tyrosine incorporation. After 2000
      generations of directed evolution, the fitness deficit of the original strain was
      largely repaired through mutations that limited the toxicity of the noncanonical.
      While the evolved lineages had not resolved the ambiguous coding of the amber
      codon, the improvements in fitness allowed new amber codons to populate protein
      coding sequences.
AU  - Tack DS
AU  - Cole AC
AU  - Shroff R
AU  - Morrow BR
AU  - Ellington AD
PT  - Journal Article
TA  - Sci. Rep.
JT  - Sci. Rep.
SO  - Sci. Rep. 2018 8: 3288.

PMID- 28153910
VI  - 5
DP  - 2017
TI  - Genome Sequence of Lactobacillus paracasei Strain LC-Ikematsu, Isolated from a Pineapple in Okinawa, Japan.
PG  - e01583-16
AB  - The draft genome sequence of Lactobacillus paracasei strain LC-Ikematsu, isolated from a
      pineapple in Okinawa, was determined. The total length of the 87 contigs
      was 3.08 Mb with a G+C content of 46.2% and 2,946 coding sequences. The genome
      analysis revealed its biosynthetic ability of 11 amino acids.
AU  - Tada I
AU  - Saitoh S
AU  - Aoyama H
AU  - Shinzato N
AU  - Yamamoto N
AU  - Arita M
AU  - Ikematsu S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01583-16.

PMID- 22038962
VI  - 193
DP  - 2011
TI  - Genome Sequence of Multidrug-Resistant Pseudomonas aeruginosa NCGM1179.
PG  - 6397
AB  - We report the annotated genome sequence of multidrug-resistant Pseudomonas aeruginosa strain
      NCGM1179, which is highly resistant to carbapenems,
      aminoglycosides, and fluoroquinolones and is emerging at medical
      facilities in Japan.
AU  - Tada T
AU  - Kitao T
AU  - Miyoshi-Akiyama T
AU  - Kirikae T
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6397.

PMID- 29301885
VI  - 6
DP  - 2018
TI  - Complete Genome Sequences of 14 Salmonella enterica Serovar Enteritidis Strains Recovered from Human Clinical Cases between 1949 and 1995 in the United States.
PG  - e01406-17
AB  - Salmonella enterica serovar Enteritidis is one of the most commonly isolated foodborne
      pathogens and is transmitted primarily to humans through consumption of
      contaminated poultry and poultry products. We are reporting completely closed
      genome and plasmid sequences of historical S Enteritidis isolates recovered from
      humans between 1949 and 1995 in the United States.
AU  - Tadesse DA
AU  - Hoffmann M
AU  - Sarria S
AU  - Lam C
AU  - Brown E
AU  - Allard M
AU  - McDermott PF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01406-17.

PMID- 22275106
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Brucella suis VBI22, Isolated from Bovine Milk.
PG  - 910
AB  - Brucella suis is the causative agent of swine brucellosis and is known to be able to infect
      several different hosts, including cattle, dogs, and
      horses, without causing disease symptoms. Here we report the complete
      genome sequence of Brucella suis VBI22, which was isolated from raw milk
      from an infected cow.
AU  - Tae H
AU  - Shallom S
AU  - Settlage R
AU  - Hawkins GN
AU  - Adams LG
AU  - Garner HR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 910.

PMID- 22038969
VI  - 193
DP  - 2011
TI  - Revised Genome Sequence of Brucella suis 1330.
PG  - 6410
AB  - Brucella suis is a causative agent of porcine brucellosis. We report the resequencing of the
      original sample upon which the published sequence of
      Brucella suis 1330 is based and describe the differences between the
      published assembly and our assembly at 12 loci.
AU  - Tae H
AU  - Shallom S
AU  - Settlage R
AU  - Preston D
AU  - Adams LG
AU  - Garner HR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6410.

PMID- Not included in PubMed...
VI  - 56
DP  - 1988
TI  - Purification and properties of a site-specific restriction endonuclease AaaI from Acetobacter aceti subsp. aceti No. 1023.
PG  - 161-166
AB  - A type II restriction endonuclease, named AaaI, was purified from Acetobacter
      aceti subsp. aceti No. 1023.  The optimum pH and temperature were determined to
      be 8.5 and 37C, respectively.  The enzyme activity was stimulated by the
      addition of either NaCl or KCl and their optimum concentrations were 100 mM for
      both cations.  AaaI recognized the hexanucleotide sequence
      5'-C^GGCCG-3'/GCCGG^C and cleaved it at the positions indicated by the arrows.
      AaaI is an isoschizomer of XmaIII from Xanthomonas malvacearum and Eco52I from
      Escherichia coli.
AU  - Tagami H
AU  - Tayama K
AU  - Tohyama T
AU  - Fukaya M
AU  - Okumura H
AU  - Kawamura Y
AU  - Horinouchi S
AU  - Beppu T
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1988 56: 161-166.

PMID- 23929491
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Clostridium sp. Strain DL-VIII, a Novel Solventogenic Clostridium Species Isolated from Anaerobic Sludge.
PG  - e00605-13
AB  - We report the genome sequence of Clostridium sp. strain DL-VIII, a novel Gram-positive,
      endospore-forming, solventogenic bacterium isolated from activated
      anaerobic sludge of a wastewater treatment plant. Aside from a complete sol
      operon, the 6,477,357-bp genome of DL-VIII reveals genes for several unique
      enzymes with applications in lignocellulose degradation, including two phenolic
      acid decarboxylases.
AU  - Taghavi S
AU  - Izquierdo JA
AU  - van der Lelie D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00605-13.

PMID- 27660783
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a Cardiobacterium hominis Strain Isolated from Blood Cultures of a Patient with Infective Endocarditis.
PG  - e00999-16
AB  - Cardiobacterium hominis is a well-known commensal bacterium of the oral cavity and an agent of
      infective endocarditis in humans. Here, we provide a draft genome
      sequence of a pathogenic strain isolated from blood cultures of a patient with
      infectious endocarditis.
AU  - Tagini F
AU  - Pillonel T
AU  - Asner S
AU  - Prod'hom G
AU  - Greub G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00999-16.

PMID- 23868129
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Moderately Halophilic Gammaproteobacterium Halomonas anticariensis FP35T.
PG  - e00497-13
AB  - Halomonas anticariensis strain FP35(T) is a moderately halophilic bacterium isolated from a
      soil sample taken from Fuente de Piedra, a saline wetland in the
      province of Malaga (Spain), which produces an exopolysaccharide and
      quorum-sensing signaling molecules of the type N-acylhomoserine lactone. We
      report here the draft genome sequence of this gammaproteobacterium.
AU  - Tahrioui A
AU  - Quesada E
AU  - Llamas I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00497-13.

PMID- 29496837
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of a New Zealand Isolate of the Bovine Pathogen Streptococcus uberis.
PG  - e00119-18
AB  - Streptococcus uberis forms part of the native microbiota of cattle and is able to
      opportunistically infect the mammary gland; as such, it is a leading cause of
      bovine mastitis globally. Here, we report the complete genome sequence of S.
      uberis NZ01, isolated in New Zealand from a cow with a clinical case of bovine
      mastitis.
AU  - Taiaroa G
AU  - Harbison-Price N
AU  - Ferguson SA
AU  - Carter GP
AU  - Williamson DA
AU  - Macknight RC
AU  - Cook GM
AU  - Heikal A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00119-18.

PMID- 24970828
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Entomopathogenic Serratia liquefaciens Strain FK01.
PG  - e00609-14
AB  - In the present study, we determined the draft genome sequence of the entomopathogenic
      bacterium Serratia liquefaciens FK01, which is highly virulent
      to the silkworm. The draft genome is ~5.28 Mb in size, and the G+C content is
      55.8%.
AU  - Taira E
AU  - Iiyama K
AU  - Mon H
AU  - Mori K
AU  - Akasaka T
AU  - Tashiro K
AU  - Yasunaga-Aoki C
AU  - Lee JM
AU  - Kusakabe T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00609-14.

PMID- 29439056
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of the Nonheterocystous Cyanobacterium Pseudanabaena sp. ABRG5-3.
PG  - e01608-17
AB  - We report here the complete sequences of the main genome (4.8 Mb) and seven plasmids of the
      semifilamentous, nonheterocystous cyanobacterium Pseudanabaena
      sp. ABRG5-3, a strain isolated from a pond in Japan. These data are expected to
      enhance our understanding of the Pseudanabaena subclade near the root of
      cyanobacterial diversity.
AU  - Tajima N
AU  - Kanesaki Y
AU  - Sato S
AU  - Yoshikawa H
AU  - Maruyama F
AU  - Kurokawa K
AU  - Ohta H
AU  - Nishizawa T
AU  - Asayama M
AU  - Sato N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01608-17.

PMID- 
VI  - 35
DP  - 2003
TI  - DNA methyltransferase and DNA methylation.
PG  - 936-948
AB  - 
AU  - Tajima S
PT  - Journal Article
TA  - Gendai Iryo
JT  - Gendai Iryo
SO  - Gendai Iryo 2003 35: 936-948.

PMID- 8586618
VI  - 117
DP  - 1995
TI  - Isolation and expression of a chicken DNA methyltransferase cDNA.
PG  - 1050-1057
AB  - A 0.5 kb fragment of chicken DNA methyltransferase cDNA was PCR-amplified using a set of
      degenerate primers.  A clone harboring a 5 kb insert was isolated from a cDNA library by
      screening with the PCR-amplified cDNA fragment as a probe.  The elucidated nucleotide sequence
      gave a 4,614 nucleotide open reading frame, and the predicted protein was highly homologous to
      the mouse and human DNA methyltransferases, especially in  the amino acid sequence of the
      catalytic domain in the carboxyl-terminal region.  The cysteine-rich region and Lys-Gly repeat
      first found in the mouse sequence were also conserved in chicken.  However, about 250 amino
      acid residues in the amino-terminal portion of chicken DNA methyltransferase diverged from the
      amino-terminus of the mouse or human sequence.  Northern blot analysis showed that the message
      of chicken DNA methyltransferase was expressed at high levels in the testis, in the lung and
      in Marek's virus-transformed chicken T-lymphoma cells.  Expression of the chicken DNA
      methyltransferase is COS1 cells demonstrated that the enzyme is a so-called maintenance type
      methylase.  When poly(dG-dC)-poly(dG-dC) was used as the methyl acceptor, to provide a measure
      of de novo methylase activity, the Km value for S-adenosyl-L-methionine was about 5 microM,
      which was 10 times higher than that when poly(dI-dC)-poly(dI-dC) was used.  The affinity of
      DNA methyltransferase for S-adenosyl L-methionine in catalyzing de novo-type methylation
      activity  was lower than that in catalyzing maintenance-type activity, though it was still
      high enough for the enzyme to work as a de novo-type methylase under physiological conditions.
AU  - Tajima S
AU  - Tsuda H
AU  - Wakabayashi N
AU  - Asano A
AU  - Mizuno S
AU  - Nishimori K
PT  - Journal Article
TA  - J. Biochem. (Tokyo)
JT  - J. Biochem. (Tokyo)
SO  - J. Biochem. (Tokyo) 1995 117: 1050-1057.

PMID- 24976887
VI  - 9
DP  - 2013
TI  - Genome sequence of Ensifer sp. TW10; a Tephrosia wallichii (Biyani) microsymbiont native to the Indian Thar Desert.
PG  - 304-314
AB  - Ensifer sp. TW10 is a novel N2-fixing bacterium isolated from a root nodule of the perennial
      legume Tephrosia wallichii Graham (known locally as Biyani) found
      in the Great Indian (or Thar) desert, a large arid region in the northwestern
      part of the Indian subcontinent. Strain TW10 is a Gram-negative, rod shaped,
      aerobic, motile, non-spore forming, species of root nodule bacteria (RNB) that
      promiscuously nodulates legumes in Thar Desert alkaline soil. It is fast growing,
      acid-producing, and tolerates up to 2% NaCl and capable of growth at 40(o)C. In
      this report we describe for the first time the primary features of this Thar
      Desert soil saprophyte together with genome sequence information and annotation.
      The 6,802,256 bp genome has a GC content of 62% and is arranged into 57 scaffolds
      containing 6,470 protein-coding genes, 73 RNA genes and a single rRNA operon.
      This genome is one of 100 RNB genomes sequenced as part of the DOE Joint Genome
      Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria
      (GEBA-RNB) project.
AU  - Tak N et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 9: 304-314.

PMID- 26769944
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Streptococcus orisasini SH06, Isolated from a Healthy Thoroughbred Gastrointestinal Tract.
PG  - e01566-15
AB  - Streptococcus orisasini SH06 was isolated from a healthy thoroughbred gastrointestinal tract.
      Here, we report the draft genome sequence of this
      organism. This paper is the first published report of the genomic sequence of S.
      orisasini.
AU  - Takagi M
AU  - Nakano A
AU  - Toh H
AU  - Oshima K
AU  - Arakawa K
AU  - Nakajima F
AU  - Tashiro K
AU  - Kikusui T
AU  - Yanagida F
AU  - Morita H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01566-15.

PMID- 9361436
VI  - 63
DP  - 1997
TI  - Characterization of DNA polymerase from Pyrococcus sp. strain KOD1 and its application to PCR.
PG  - 4504-4510
AB  - The DNA polymerase gene from the archaeon Pyrococcus sp. strain KOD1 (DOD DNA polymerase)
      contains a long open reading frame of 5,013 bases that encodes 1,671 amino acid residues.
      Similarity analysis revealed that the DNA polymerase contained a putative 3'-5' exonuclease
      activity and two in-frame intervening sequences of 1,080 bp (360 amino acids; KOD pol
      intein-1) and 1,611 bp (537 amino acids; KOD pol intein-2), which are located in the middle of
      regions conserved among eukaryotic and archaeal a-like DNA polymerases.  The mature form of
      the DNA polymerase gene was expressed in Escherichia coli, and the recombinant enzyme was
      purified and characterized.  3'-5' exonuclease activity was confirmed, and although KOD DNA
      polymerase's optimum temperature (75 C) and mutation frequency (3.5 x 10^-3) were similar to
      those of a DNA polymerase from Pyrococcus furiosus (Pfu DNA polymerase), the KOD DNA
      polymerase exhibited an extension rate (100 to 130 nucleotides/s) 5 times higher than those of
      Pfu DNA polymerase.  These characteristics enabled the KOD DNA polymerase to perform a more
      accurate PCR in a shorter reaction time.
AU  - Takagi M
AU  - Nishioka M
AU  - Kakihara H
AU  - Kitabayashi M
AU  - Inoue H
AU  - Kawakami B
AU  - Oka M
AU  - Imanaka T
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1997 63: 4504-4510.

PMID- 2998344
VI  - 231
DP  - 1985
TI  - A new site-specific endonuclease, ScaI, from Streptomyces caespitosus.
PG  - 229-232
AB  - A new site-specific endonuclease has been isolated from Streptomyces
      caespitosus and named ScaI.  Based on analysis of sequences around the
      restriction sites in pBR322 and pBR325, the recognition sequence of ScaI
      endonuclease was deduced to be a new hexanucleotide 5'-AGTACT-3'.  The cleavage
      site was determined by comparing the ScaI-cleaved roduct of a primer-extended
      M13mp18-SCA DNA, which contains an AGTACT sequence, with dideoxy chain
      terminator ladders of the same DNA.  ScaI was found to cleave the recognition
      sequence between the internal T and A, leaving flush ends to the cleaved
      fragments.
AU  - Takahashi H
AU  - Kojima H
AU  - Saito H
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 1985 231: 229-232.

PMID- Not included in PubMed...
VI  - 24
DP  - 1978
TI  - Viable T4 bacteriophage containing cytosine-substituted DNA (T4dC phage).  I.  Behavior towards the restriction-modification systems of Escherichia coli and derivation of a new T4 phage strain (T4dC) having the complete T4 genome.
PG  - 297-306
AB  - A multiple mutant of bacteriophage T4, which had been proved to contain
      cytosine-substituted DNA, was grown in a suppressor-containing or
      non-containing (supo) strain of Escherichia coli B or K12, and the progeny
      phage obtained was grown on test strains carrying various restriction systems.
      As a result, the growth of this phage was found to be subject to the rK, rB,
      and rP1 restriction systems.  Two T4 strains, named UNF-r1 and UNF-r+1,
      sensitive to the rK, rB, and rP1 restriction systems, were newly derived by the
      genetic cross and mutagenesis.  The former had the unf-39 mutation instead of
      the alc-8 mutation, the latter had the rII+ region and the unf-39 mutation,
      besides the amE51 (gene 56; dCTPase), denA (endonuclease II), and denB
      (endonuclease IV) mutations.  It was demonstrated that UNF-r+1 DNA possessed a
      SalI recognition site in the rII-denB region which was deleted in UNF-r1 DNA.
AU  - Takahashi H
AU  - Saito H
AU  - Ikeda Y
PT  - Journal Article
TA  - J. Gen. Appl. Microbiol.
JT  - J. Gen. Appl. Microbiol.
SO  - J. Gen. Appl. Microbiol. 1978 24: 297-306.

PMID- 21763721
VI  - 66
DP  - 2011
TI  - The genome sequence of the incompatibility group Igamma plasmid R621a: Evolution of IncI plasmids.
PG  - 112-121
AB  - We present the complete genome sequence of the tetracycline resistance plasmid R621a isolated
      from Salmonella typhimurium, which belongs to the incompatibility group Igamma. In the
      93,185bp circular double-stranded R621a genome, 96 complete ORFs are predicted. In addition,
      one and six different kinds of proteins are produced by translational reinitiation and
      shufflon multiple inversions, respectively. The genome consists of four regions: replication,
      leading, transfer, and miscellaneous regions. The R621a genome is similar to those of IncI1
      plasmids such as R64 and ColIb-P9 and particularly to those of pEK204 and pEC_Bactec. Three
      major differences including inc, parAB, and excA regions were noted between R621a and
      prototype IncI1 plasmids. Seven nucleotide replacements and one nucleotide deletion in the
      putative Inc RNA sequence are found between R621a and IncI1 plasmids irrespective of close
      similarity in the other parts of the rep system. The sequences of R621a parAB and excA genes
      are significantly different from those of R64 and ColIb-P9, while those of R621a parAB and
      excA genes exhibit close similarity to those of pEK204 and pEC_Bactec, respectively. The R621a
      genome is suggested to be formed by acquiring parAB and excA genes from pEK204 and pEC_Bactec
      genomes, respectively, and then novel inc function by the mutations. The insertions in the
      R621a, pEK204, and pEC_Bactec genomes are flanked by direct repeats, suggesting that
      insertions accompanied by long target duplications have also played an important role in the
      evolution of IncI plasmids.
AU  - Takahashi H
AU  - Shao M
AU  - Furuya N
AU  - Komano T
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 2011 66: 112-121.

PMID- 428725
VI  - 5
DP  - 1979
TI  - A new site-specific endonuclease from Streptomyces lavendulae (SlaI) .
PG  - 9-18
AB  - A new restriction-like endonuclease, SlaI, was found and partially purified
      from Streptomyces lavendulae ATCC8664.  This endonuclease cleaved bacteriophage
      lambda DNA at only one site, and cytosine-substituted bacteriophage T4 DNA at
      16 sites.  The recognition sequence was determined by using SlaI fragments of
      cytosine-substituted bacteriophage T4 DNA.  The hexanucleotide recognized by
      SlaI endonuclease was 5'-C^T-C-G-A-G-3' 3'-G-A-G-C-A^C-5' with the sites of
      cleavage as indicated by the arrows.  Therefore, SlaI endonuclease was an
      isoschizomer of XhoI endonuclease.
AU  - Takahashi H
AU  - Shimizu M
AU  - Saito H
AU  - Ikeda Y
AU  - Sugisaki H
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1979 5: 9-18.

PMID- 8931334
VI  - 145
DP  - 1996
TI  - Restriction barrier composed of an extracellular nuclease and restriction endonuclease in the unicellular cyanobacterium Microcystis sp.
PG  - 107-111
AB  - The unicellular cyanobacterium Microcystis aeruginosa K-81 has two types of restriction
      barrier, an extracellular nuclease and sequence-specific endonucleases.  The nuclease was
      detected in the culture supernatant and it was easily released from the cells by washing with
      water or buffer containing Triton X-100.  This nuclease was identified as a polypeptide of
      about 28 kDa that digested covalently closed circular and linear double-stranded DNAs,
      including chromosomal DNA from M. aeruginosa K-81.  Among another 13 Microcystis strains
      examined, 3 produced an extracellular nuclease.  Furthermore, M. aeruginosa K-81 contained two
      sequence-specific endonucleases, MaeK81I and MaeK81II, which were isoschizomers of SplI and
      Sau96I, respectively.
AU  - Takahashi I
AU  - Hayano D
AU  - Asayama M
AU  - Masahiro F
AU  - Watahiki M
AU  - Shirai M
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1996 145: 107-111.

PMID- 6279580
VI  - 90
DP  - 1981
TI  - Molecular multiplicity of nuclease TT1 from Thermus thermophilus HB8.
PG  - 1521-1527
AB  - Purified nuclease TT1 from Thermus thermophilus HB8 has multimolecular weight
      forms, each of which is composed of three different subunits, a (10.8 x 104), b
      (7.8 x 104), and c (4.1 x 104).  The molecular weight of this enzyme were
      estimated by gel filtration, polyacrylamide gel electrophoresis and equilibrium
      sedimentation.  It was found that most of the enzyme has a molecular weight of
      about 22 x 104 being a monomer having the subunit composition of abc.  The
      remaining part of the enzyme has larger molecular weights and is considered to
      be size-isomers of abc.  The alpha-helical content, 5.5-6.5%, and the
      b-structure, about 28% were estimated from the CD spectrum at 4C.
AU  - Takahashi M
AU  - Kobayashi M
AU  - Uchida T
PT  - Journal Article
TA  - J. Biochem. (Tokyo)
JT  - J. Biochem. (Tokyo)
SO  - J. Biochem. (Tokyo) 1981 90: 1521-1527.

PMID- 12399478
VI  - 184
DP  - 2002
TI  - A DNA methyltransferase can protect the genome from postdisturbance attack by a restriction-modification gene complex.
PG  - 6100-6108
AB  - In prokaryotic genomes, some DNA methyltransferases form a restriction-modification gene
      complex, but some others are present by themselves. Dcm gene product, one of these orphan
      methyltransferases found in Escherichia coli and related bacteria, methylates DNA to generate
      5'-CmCWGG just as some of its eukaryotic homologues do. Vsr mismatch repair function of an
      adjacent gene prevents C-to-T mutagenesis enhanced by this methylation but promotes other
      types of mutation and likely has affected genome evolution. The reason for the existence of
      the dcm-vsr gene pair has been unclear. Earlier we found that several restriction-modification
      gene complexes behave selfishly in that their loss from a cell leads to cell killing through
      restriction attack on the genome. There is also increasing evidence for their potential
      mobility. EcoRII restriction-modification gene complex recognizes the same sequence as Dcm,
      and its methyltransferase is phylogenetically related to Dcm. In the present work, we found
      that stabilization of maintenance of a plasmid by linkage of EcoRII gene complex, likely
      through postsegregational cell killing, is diminished by dcm function. Disturbance of EcoRII
      restriction-modification gene complex led to extensive chromosome degradation and severe loss
      of cell viability. This cell killing was partially suppressed by chromosomal dcm and
      completely abolished by dcm expressed from a plasmid. Dcm, therefore, can play the role of a
      'molecular vaccine' by defending the genome against parasitism by a restriction-modification
      gene complex.
AU  - Takahashi N
AU  - Naito Y
AU  - Handa N
AU  - Kobayashi I
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2002 184: 6100-6108.

PMID- 21305031
VI  - 6
DP  - 2011
TI  - IS-Linked Movement of a Restriction-Modification System.
PG  - e16554
AB  - Potential mobility of restriction-modification systems has been suggested by
      evolutionary/bioinformatic analysis of prokaryotic
      genomes. Here we demonstrate in vivo movement of a
      restriction-modification system within a genome under a laboratory
      condition. After blocking replication of a temperature-sensitive
      plasmid carrying a PaeR7I restriction-modification system in
      Escherichia coli cells, the plasmid was found integrated into the
      chromosome of the surviving cells. Sequence analysis revealed that, in
      the majority of products, the restriction-modification system was
      linked to chromosomal insertion sequences (ISs). Three types of
      products were: (I) apparent co-integration of the plasmid and the
      chromosome at a chromosomal IS1 or IS5 copy (24/28 analyzed); (II) de
      novo insertion of IS1 with the entire plasmid except for a 1-3 bp
      terminal deletion (2/28); and (III) reciprocal crossing-over between
      the plasmid and the chromosome involving 1-3 bp of sequence identity
      (2/28). An R-negative mutation apparently decreased the efficiency of
      successful integration by two orders of magnitude. Reconstruction
      experiments demonstrated that the restriction-dependence was mainly due
      to selection against cells without proper integration: their growth was
      inhibited by the restriction enzyme action. These results demonstrate
      collaboration of a mobile element and a restriction-modification system
      for successful joint migration. This collaboration may have promoted
      the spread and, therefore, the long-term persistence of these complexes
      and restriction-modification systems in a wide range of prokaryotes.
AU  - Takahashi N
AU  - Ohashi S
AU  - Sadykov MR
AU  - Mizutani-Ui Y
AU  - Kobayashi I
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2011 6: e16554.

PMID- 12903110
VI  - 2
DP  - 2002
TI  - Direct monitoring of EcoRII restriction enzyme reactions on a 27MHz quartz-crystal microbalance.
PG  - 71-72
AB  - EcoRII is a type IIE restriction endonuclease characterized by a highly cooperative reaction
      mechanism that depends on simultaneous binding of the dimeric enzyme molecule to two copies of
      its recognition site.  Gaining insights about reaction property of EcoRII binding to its
      recognition site and effect of divalent metal ion on DNA cleavage process, a DNA-immobilized
      quartz crystal microbalance, which enables real-time monitoring both the binding of enzyme and
      the cleavage reaction on DNA strands as mass changes, was utilized.
AU  - Takahashi S
AU  - Matsuno H
AU  - Furusawa H
AU  - Okahata Y
PT  - Journal Article
TA  - Nucleic Acids Res. Suppl.
JT  - Nucleic Acids Res. Suppl.
SO  - Nucleic Acids Res. Suppl. 2002 2: 71-72.

PMID- 18367450
VI  - 283
DP  - 2008
TI  - Direct monitoring of allosteric recognition of type IIE restriction endonuclease EcoRII.
PG  - 15023-15030
AB  - EcoRII is a homodimer with two domains consisting of a DNA-binding N terminus and a catalytic
      C terminus and recognizes two specific
      sequences on DNA. It shows a relatively complicated cleavage reaction
      in bulk solution. After binding to either recognition site, EcoRII
      cleaves the other recognition site of the same DNA (cis-binding) strand
      and/or the recognition site of the other DNA (trans-binding) strand.
      Although it is difficult to separate these two reactions in bulk
      solution, we could simply obtain the binding and cleavage kinetics of
      only the cis-binding by following the frequency (mass) changes of a
      DNA-immobilized quartz-crystal microbalance (QCM) responding to the
      addition of EcoRII in aqueous solution. We obtained the maximum binding
      amounts (Delta m(max)) the dissociation constants (K-d), the binding
      and dissociation rate constants (k(on) and k(off)), and the catalytic
      cleavage reaction rate constants (k(cat)) for wildtype EcoRII, the
      N-terminal-truncated form (EcoRII N-domain), and the mutant derivatives
      in its C-terminal domain (K263A and R330A). It was determined from the
      kinetic analyses that the N-domain, which covers the catalytic C-domain
      in the absence of DNA, preferentially binds to the one DNA recognition
      site while transforming EcoRII into an active form allosterically, and
      then the secondary C-domain binds to and cleaves the other recognition
      site of the DNA strand.
AU  - Takahashi S
AU  - Matsuno H
AU  - Furusawa H
AU  - Okahata Y
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2008 283: 15023-15030.

PMID- 
VI  - JB12
DP  - 2008
TI  - Detection of DNA methylation using methylation sensitive restriction enzyme.
PG  - 62-68
AB  - 
AU  - Takai D
PT  - Journal Article
TA  - Jikken Igaku Bessatsu
JT  - Jikken Igaku Bessatsu
SO  - Jikken Igaku Bessatsu 2008 JB12: 62-68.

PMID- 10584021
VI  - 65
DP  - 1999
TI  - Molecular phylogenetic analysis of archaeal intron-containing genes coding for rRNA obtained from a deep-subsurface geothermal water pool.
PG  - 5586-5589
AB  - Molecular phylogenetic analysis of a naturally occurring microbial community in a
      deep-subsurface geothermal environment indicated that the phylogenetic diversity of the
      microbial population in the environment was extremely limited and that only hyperthermophilic
      archaeal members closely related to Pyrobaculum were present. All archaeal ribosomal DNA
      sequences contained intron-like sequences, some of which had open reading frames with repeated
      homing-endonuclease motifs. The sequence similarity analysis and the phylogenetic analysis of
      these homing endonucleases suggested the possible phylogenetic relationship among archaeal
      rRNA-encoded homing endonucleases.
AU  - Takai K
AU  - Horikoshi K
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1999 65: 5586-5589.

PMID- 11058132
VI  - 28
DP  - 2000
TI  - Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis.
PG  - 4317-4331
AB  - The 4,202,353 bp genome of the alkaliphilic bacterium Bacillus halodurans C-125 contains 4066
      predicted protein coding sequences (CDSs), 2141 (52.7%) of which have functional assignments,
      1182 (29%) of which are conserved CDSs with unknown function and 743 (18. 3%) of which have no
      match to any protein database.  Among the total CDSs, 8.8% match sequences of proteins found
      only in Bacillus subtilis and 66.7% are widely conserved in comparison with the proteins of
      various organisms, including B. subtilis. The B. halodurans genome contains 112 transposase
      genes, indicating that transposases have played an important evolutionary role in horizontal
      gene transfer and also in internal genetic rearrangement in the genome. Strain C-125 lacks
      some of the necessary genes for competence, such as comS, srfA and rapC, supporting the fact
      that competence has not been demonstrated experimentally in C-125. There is no paralog of
      tupA, encoding teichuronopeptide, which contributes to alkaliphily, in the C-125 genome and an
      ortholog of tupA cannot be found in the B. subtilis genome. Out of 11 sigma factors which
      belong to the extracytoplasmic function family, 10 are unique to B. halodurans, suggesting
      that they may have a role in the special mechanism of adaptation to an alkaline environment.
AU  - Takami H
AU  - Nakasone K
AU  - Takaki Y
AU  - Maeno G
AU  - Sasaki R
AU  - Masui N
AU  - Fuji F
AU  - Hirama C
AU  - Nakamura Y
AU  - Ogasawara N
AU  - Kuhara S
AU  - Horikoshi K
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2000 28: 4317-4331.

PMID- 15576355
VI  - 32
DP  - 2004
TI  - Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus.
PG  - 6292-6303
AB  - We present herein the first complete genome sequence of a thermophilic Bacillus-related
      species, Geobacillus kaustophilus HTA426, which is composed of a 3.54 Mb chromosome and a 47.9
      kb plasmid, along with a comparative analysis with five other mesophilic bacillar genomes.
      Upon orthologous grouping of the six bacillar sequenced genomes, it was found that 1257 common
      orthologous groups composed of 1308 genes (37%) are shared by all the bacilli, whereas 839
      genes (24%) in the G.kaustophilus genome were found to be unique to that species. We were able
      to find the first prokaryotic sperm protamine P1 homolog, polyamine synthase, polyamine ABC
      transporter and RNA methylase in the 839 unique genes; these may contribute to thermophily by
      stabilizing the nucleic acids. Contrasting results were obtained from the principal component
      analysis (PCA) of the amino acid composition and synonymous codon usage for highlighting the
      thermophilic signature of the G. kaustophilus genome. Only in the PCA of the amino acid
      composition were the Bacillus-related species located near, but were distinguishable from, the
      borderline distinguishing thermophiles from mesophiles on the second principal axis. Further
      analysis revealed some asymmetric amino acid substitutions between the thermophiles and the
      mesophiles, which are possibly associated with the thermoadaptation of the organism.
AU  - Takami H
AU  - Takaki Y
AU  - Chee G-J
AU  - Nishi S
AU  - Shimamura S
AU  - Suzuki H
AU  - Matsui S
AU  - Uchiyama I
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2004 32: 6292-6303.

PMID- 12235376
VI  - 30
DP  - 2002
TI  - Genome sequence of Oceanobacillus iheyensis isolated from the Iheya Ridge and its unexpected adaptive capabilities to extreme environments.
PG  - 3927-3935
AB  - Oceanobacillus iheyensis HTE831 is an alkaliphilic and extremely halotolerant Bacillus-related
      species isolated from deep-sea sediment. We present here the complete genome sequence of
      HTE831 along with analyses of genes required for adaptation to highly alkaline and saline
      environments. The genome consists of 3.6 Mb, encoding many proteins potentially associated
      with roles in regulation of intracellular osmotic pressure and pH homeostasis. The candidate
      genes involved in alkaliphily were determined based on comparative analysis with three
      Bacillus species and two other Gram-positive species. Comparison with the genomes of other
      major Gram-positive bacterial species suggests that the backbone of the genus Bacillus is
      composed of approximately 350 genes. This second genome sequence of an alkaliphilic
      Bacillus-related species will be useful in understanding life in highly alkaline environments
      and microbial diversity within the ubiquitous bacilli.
AU  - Takami H
AU  - Takaki Y
AU  - Uchiyama I
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2002 30: 3927-3935.

PMID- 21914871
VI  - 193
DP  - 2011
TI  - Genome Sequences of Two Stress-Tolerant Campylobacter jejuni Poultry Strains, 305 and DFVF1099.
PG  - 5546-5547
AB  - Campylobacter jejuni is a food-borne pathogen with a high prevalence in poultry meat, which in
      fresh unfrozen condition is the major source of
      campylobacteriosis. C. jejuni strains DFVF1099 and 305 are considered
      tolerant to several environmental stresses (T. Birk et al., J. Food Prot.
      73:258-265, 2010; S. L. On et al., Int. J. Med. Microbiol. 296:353-363,
      2006). Here, we report the genome sequences of C. jejuni 305 and DFVF1099,
      a turkey and a chicken isolate, respectively.
AU  - Takamiya M
AU  - Ozen A
AU  - Rasmussen M
AU  - Alter T
AU  - Gilbert T
AU  - Ussery DW
AU  - Knochel S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5546-5547.

PMID- 21677848
VI  - 4
DP  - 2011
TI  - Genome Sequence of Campylobacter jejuni strain 327, a strain isolated from a turkey slaughterhouse.
PG  - 113-122
AB  - Campylobacter is one of the leading causes of food-borne gastroenteritis
      and has a high prevalence in poultry. Campylobacter jejuni subsp. jejuni
      327 is a subspecies of the genus Campylobacter of the family
      Campylobacteraceae in the phylum Proteobacteria. The microaerophilic,
      spiral shaped, catalase positive bacterium obtains energy from the
      metabolism of amino acids and Krebs cycle intermediates. Strain 327 was
      isolated from a turkey slaughter production line and is considered
      environmentally sensitive to food processing (cold, heat, drying) and
      storage conditions. The 327 whole genome shotgun sequence of 1,618,613 bp
      long consists of 1,740 protein-coding genes, 46 tRNA genes and 3 rRNA
      operons. A protein based BLAST analysis places the turkey isolate 327
      close to the human clinical strain 81116 (NCTC 11828).
AU  - Takamiya M
AU  - Ozen A
AU  - Rasmussen M
AU  - Alter T
AU  - Gilbert T
AU  - Ussery DW
AU  - Knochel S
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 4: 113-122.

PMID- 4542920
VI  - 34
DP  - 1973
TI  - Specific cleavage of coliphage fd DNA by five different restriction endonucleases from Haemophilus genus.
PG  - 318-322
AB  - None
AU  - Takanami M
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1973 34: 318-322.

PMID- Not included in PubMed...
VI  - 7
DP  - 1974
TI  - Restriction endonucleases AP, GA, and H-1 from three Haemophilus strains.
PG  - 113-133
AB  - None
AU  - Takanami M
PT  - Journal Article
TA  - Methods Mol. Biol.
JT  - Methods Mol. Biol.
SO  - Methods Mol. Biol. 1974 7: 113-133.

PMID- 11946929
VI  - 29
DP  - 1973
TI  - Cleavage site specificity of an endonuclease prepared from Haemophilus influenzae strain H-1.
PG  - 267-270
AB  - None
AU  - Takanami M
AU  - Kojo H
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1973 29: 267-270.

PMID- 1080205
VI  - 95
DP  - 1975
TI  - Studies on Bacteriophage fd DNA I.  A Cleavage Map of the fd Genome.
PG  - 21-31
AB  - In order to construct a physical map of the bacteriophage fd genome, the doubly
      closed replicative form (RFI) DNA of phage fd was cleaved into unique fragments
      by four different restriction endonucleases (Hap, Hga, HinH and Hind) prepared
      from Haemophilus strains H. aphirophilus, H. gallinarum, H. influenzae H-I and
      H. influenzae Rd, respectively.  As Hind cleaved RFI DNA at a single site, this
      site was used as a reference point for mapping.  HinH cleaved RFI DNA at three
      sites, Hga at six sites and Hap at 13 sites, respectively.  The 5'-termini of
      the fragments produced by either HinH or Hga were labelled with 32P in the
      polynucleotide kinase reaction.  The labelled fragments were separated and
      further cleaved by other enzymes.  The re-digestion products of partially
      digested fragments were also analysed.  On the basis of these data and
      estimates of the size of each fragment, a cleavage map of the phage fd genome
      was constructed.
AU  - Takanami M
AU  - Okamoto T
AU  - Sugimoto K
AU  - Sugisaki H
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1975 95: 21-31.

PMID- 28183761
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Ichthyobacterium seriolicida JBKA-6T, Isolated from Yellowtail (Seriola quinqueradiata) Affected by Bacterial Hemolytic Jaundice.
PG  - e01574-16
AB  - Ichthyobacterium seriolicida is a fish bacterial pathogen that causes hemolytic jaundice in
      farmed yellowtail in Japan. To understand more about the
      characteristics of this bacterium, we determined its complete genome sequence.
      Two hemolysin genes which may be important for its pathogenicity were identified
      in the I. seriolicida genome.
AU  - Takano T
AU  - Nakamura Y
AU  - Matsuyama T
AU  - Sakai T
AU  - Shigenobu Y
AU  - Sugaya T
AU  - Yasuike M
AU  - Fujiwara A
AU  - Kondo H
AU  - Hirono I
AU  - Fukuda Y
AU  - Nakayasu C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01574-16.

PMID- 1980198
VI  - 7
DP  - 1990
TI  - Restriction enzyme from Lactobacillus fermentum.
PG  - 64
AB  - Restriction-modification is important in phage resistance. However, little is known about
      restriction enzymes of lactic acid bacteria. We have found that Lactobacillus fermentum CP-34
      has apparent site-specific endonuclease activity, purified and studied the characteristics of
      the enzyme.
AU  - Takano T
AU  - Ochi A
AU  - Yamamoto N
PT  - Journal Article
TA  - FEMS Microbiol. Rev.
JT  - FEMS Microbiol. Rev.
SO  - FEMS Microbiol. Rev. 1990 7: 64.

PMID- 4867907
VI  - 34
DP  - 1968
TI  - Mechanism of host-controlled restriction of bacteriophage lambda by R factors in Escherichia coli K12.
PG  - 290-302
AB  - In the host-controlled modification of phage lambda by fi- R factors, N-3 and
      R-15, the infectivity of the unmodified lambda DNA was specifically destroyed
      by the sonicated extracts from the restrictive, endonuclease I-less (endo
      I-less) mutant of Escherichia coli K12 carrying N-3 or R-15, to a greater
      extent than by the sonicates from the nonrestrictive, endo I-less bacteria.  In
      the control experiments, the lambda DNA modified by N-3 was inactivated to much
      lesser extents both by the sonicates from the restrictive, endo I-less bacteria
      and by those from the nonrestrictive, endo I-less bacteria.  In all these
      systems of reactions, the phage DNA was hardly degraded into acid-soluble
      forms.  The host specifically inactivated, unmodified lambda DNA, however, was
      split fragmentally as was shown by the patterns of zone sedimentation, but the
      modified lambda DNA was not.  The activity which destroys the infectivity of
      the unmodified lambda DNA resided totally in the spheroplasts of the
      restrictive bacteria.
AU  - Takano T
AU  - Watanabe T
AU  - Fukasawa T
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1968 34: 290-302.

PMID- 5339542
VI  - 25
DP  - 1966
TI  - Specific inactivation of infectious lambda DNA by sonicates of restrictive bacteria with R factors.
PG  - 192-204
AB  - In the studies on the host-controlled modification (Arber, 1965a) of
      bacteriophage lambda, certain aspects of two fundamental functions of host
      bacteria have been elucidated:  Modification is a function by which viral DNA
      is subjected to some chemical alterations (Arber, 1965b).  Restriction is
      another function which recognizes the modification pattern or the host
      specificity and serves to restrict the phage mutliplication depending on the
      host specificity (Arber and Dussoix, 1962).  Analogous experiments are now
      under way in the system of P1-controlled restriction in our laboratories.
AU  - Takano T
AU  - Watanabe T
AU  - Fukasawa T
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1966 25: 192-204.

PMID- 18408034
VI  - 190
DP  - 2008
TI  - Complete genome sequence of the soil actinomycete Kocuria rhizophila.
PG  - 4139-4146
AB  - The soil actinomycete Kocuria rhizophila belongs to the suborder Micrococcineae, a divergent
      bacterial group for which only a limited
      amount of genomic information is currently available. K. rhizophila is
      also important in industrial applications; e.g., it is commonly used as a
      standard quality control strain for antimicrobial susceptibility testing.
      Sequencing and annotation of the genome of K. rhizophila DC2201 (NBRC
      103217) revealed a single circular chromosome (2,697,540 bp; G+C content
      of 71.16%) containing 2,357 predicted protein-coding genes. Most of the
      predicted proteins (87.7%) were orthologous to actinobacterial proteins,
      and the genome showed fairly good conservation of synteny with
      taxonomically related actinobacterial genomes. On the other hand, the
      genome seems to encode much smaller numbers of proteins necessary for
      secondary metabolism (one each of nonribosomal peptide synthetase and type
      III polyketide synthase), transcriptional regulation, and lateral gene
      transfer, reflecting the small genome size. The presence of probable
      metabolic pathways for the transformation of phenolic compounds generated
      from the decomposition of plant materials, and the presence of a large
      number of genes associated with membrane transport, particularly amino
      acid transporters and drug efflux pumps, may contribute to the organism's
      utilization of root exudates, as well as the tolerance to various organic
      compounds.
AU  - Takarada H
AU  - Sekine M
AU  - Kosugi H
AU  - Matsuo Y
AU  - Fujisawa T
AU  - Omata S
AU  - Kishi E
AU  - Shimizu A
AU  - Tsukatani N
AU  - Tanikawa S
AU  - Fujita N
AU  - Harayama S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2008 190: 4139-4146.

PMID- 7706218
VI  - 116
DP  - 1994
TI  - Two forms of restriction enzyme HindIII.
PG  - 1281-1286
AB  - Restriction endonuclease HindIII was purified from Haemophilus influenzae Rd. Two active
      fractions, P1 and P2, were obtained in phosphocellulose chromatography. HindIII could be
      purified completely from the first fraction, P1, by subsequent DEAE-cellulose chromatography.
      The second fraction, P2, showed HindIII activity higher than that of P1, though it was still
      contaminated with some minor proteins. The HindIII in the P2 fraction showed differences in
      stability, binding to substrate DNA, electrophoretic mobility, etc., from the HindIII in the
      P1 fraction. It is likely that there are two forms of HindIII in the bacterial cell. The
      endonuclease HindIII in the P2 fraction was finally purified by DNA-cellulose chromatography,
      though considerable loss of enzymatic activity resulted. Upon infection of the cells with
      phage T4, the P2 fraction in phosphocellulose chromatography almost disappeared. The presence
      of two forms of HindIII may be related to bacterial defense against viral infection.
AU  - Takasaki Y
PT  - Journal Article
TA  - J. Biochem. (Tokyo)
JT  - J. Biochem. (Tokyo)
SO  - J. Biochem. (Tokyo) 1994 116: 1281-1286.

PMID- Not included in PubMed...
VI  - 60
DP  - 1996
TI  - Alternation of two forms of restriction endonuclease HindIII.
PG  - 396-400
AB  - Two forms of the restriction enzyme HindIII were alternated with each other under
      some physiological or biochemical conditions.  Addition of a low amount of phage T7 to the
      culture of HindIII-producing Haemophilus influenzae Rd, resulted in appearance of some amounts
      of the P2 fraction of HindIII, which was eluted with a high concentration of KCl from a
      phosphocellulose column.  Higher amounts of T7 caused a decrease of the P2 fraction; finally
      the
      alternative P1 fraction of HindIII, which was eluted with a lower concentration of KCl,
      remained
      exclusively.  Addition of disaccharides such as maltose and trehalose to the bacterial
      extract,
      yielded more P2, although the disaccharides inhibited this enzyme.  Urea showed an interesting
      distribution of these two forms of HindIII.  Phosphocellulose chromatography in the presence
      of
      2M urea generated a broad peak of HindIII activity.  Addition of 4M urea, on the contrary,
      showed
      only one active peak of this enzyme.  The HindIII could be purified by the following DEAE-
      cellulose chromatography.  The results indicate the presence of only one kind of HindIII
      molecule,
      which was alternated between free and bound forms, and a certain kind of factor that would
      equilibrate these two forms.
AU  - Takasaki Y
PT  - Journal Article
TA  - Biosci. Biotechnol. Biochem.
JT  - Biosci. Biotechnol. Biochem.
SO  - Biosci. Biotechnol. Biochem. 1996 60: 396-400.

PMID- 24058473
VI  - 8
DP  - 2013
TI  - Efficient TALEN construction for Bombyx mori gene targeting.
PG  - E73458
AB  - Engineered nucleases are artificial enzymes able to introduce double stranded
      breaks at desired genomic locations. The double stranded breaks start the
      error-prone repair process of non-homologous end-joining (NHEJ), which eventually
      leads to the induction of mutations at target sites. We showed earlier that ZFNs
      and TALENs are able to induce NHEJ mutations in the B. mori genome. In order to
      optimize our mutagenesis protocol, we modified one of the reported truncated
      TALEN scaffolds and optimized it for use in the B. mori embryo. We also
      established a novel B. mori somatic cell assay suitable for the preselection of
      highly efficient TALENs directly in the B. mori model system. We compared the
      efficiency of several TALEN pairs based on three different frameworks using the
      BmBLOS2 gene. The new active TALENs show one order of magnitude higher efficiency
      than those we used previously. We confirmed the utility of our improved protocol
      by mutagenesis of the autosomal gene, red egg (Bm-re) and showed that it allows
      obtaining homozygous mutants in G1. Our procedure minimizes the chance of failure
      in B. mori gene targeting experiments.
AU  - Takasu Y
AU  - Sajwan S
AU  - Daimon T
AU  - Osanai-Futahashi M
AU  - Uchino K
AU  - Sezutsu H
AU  - Tamura T
AU  - Zurovec M
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2013 8: E73458.

PMID- 12034832
VI  - 30
DP  - 2002
TI  - Phenotypic and genotypic variation in methylases involved in type II restriction-modification systems in Helicobacter pylori.
PG  - 2444-2452
AB  - To determine relationships between Helicobacter pylori geographical origin and type II
      methylase activity, we examined 122 strains from various locations around the world for
      methylase expression. Most geographic regions possessed at least one strain resistant to
      digestion by each of 14 restriction endonucleases studied. Across all of the strains studied,
      the average number of active methylases was 8.2 +/- 1.9 with no significant variation between
      the major geographic regions. Although seven pairs of isolates showed the same susceptibility
      patterns, their cagA/vacA status differed, and the remaining 108 strains each possessed unique
      patterns of susceptibility. From a single clonal group, 15 of 18 strains showed identical
      patterns of resistance, but diverged with respect to M.MboII activity. All of the methylases
      studied were present in all major human population groupings, suggesting that their horizontal
      acquisition pre-dated the separation of these populations. For the hpyV and hpyAIV
      restriction-modification systems, an in-depth analysis of genotype, indicating extensive
      diversity of cassette size and chromosomal locations regardless of the susceptibility
      phenotype, points toward substantial strain-specific selection involving these loci.
AU  - Takata T
AU  - Aras R
AU  - Tavakoli D
AU  - Ando T
AU  - Olivares AZ
AU  - Blaser MJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2002 30: 2444-2452.

PMID- 
VI  - 102
DP  - 2002
TI  - The gene product of Campylobacter jejuni gene Cj0208 is a DNA methyltransferase with specificity for GAATTC.
PG  - 164
AB  - To understand the mechanisms of DNA methylation in Campylobacter jejuni, we examined the
      genetic and phenotypic properties of a putative
      adenine methyltransferase gene, Cj0208. This gene encodes a 364-amino
      acid protein and was present in all 11 C. jejuni strains tested. A
      BLAST search using the Cj208 amino acid sequence revealed that the
      putative protein was most closely related to CATG-recognizing adenine
      DNA methyltransferases, including M. HpyI of Helicobacter pylori.
      However, phylogenetic analysis (using PAUP 4.0b2) revealed that Cj0208
      was closely related to M. Sse9I, which recognizes AATT, and that it's
      next closest relative is M. EcoRI, which recognizes GAATTC. DNA
      isolated from C. jejuni strains was shown to be resistant to digestion
      by EcoRI and susceptible to restriction enzymes recognizing AATT
      (TSP509I), and CATG (NlaIII). After cloning Cj0208 from C. jejuni
      strain 11168, overexpression in an Escherichia coli strain lacking
      endogenous methyltransferases rendered DNA from these cells resistant
      to EcoRI digestion. This suggests that Cj0208 is a methyltransferase
      with specificity for GAATTC. A dot blot assay using antibodies that
      react specifically with DNA containing m6A or m4C modifications
      identified Cj0208 as an m6A methyltransferase. An isogenic Cj0208
      mutant was susceptible to EcoRI, confirming the role of this methylase
      in protecting GAATTC sites. We conclude that Cj0208 encodes a DNA
      methyltransferase with m6A activity and specificity for GAATTC. The
      resistance of C. jejuni strains to EcoRI digestion suggests that this
      gene is well-conserved.
AU  - Takata T
AU  - Wassenaar TM
AU  - Xu Q
AU  - Blaser MJ
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 2002 102: 164.

PMID- 25477402
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Marine Flavobacterium Jejuia pallidilutea Strain 11shimoA1 and Pigmentation Mutants.
PG  - e01236-14
AB  - Here, we present the draft genome sequence of a novel carotenoid 2'-isopentenylsaproxanthin
      producer, Jejuia pallidilutea strain 11shimoA1,
      isolated from the surface of seaweed in Japan, and the ethyl
      methanesulfonate-induced pigmentation mutants. This genomic information will help
      to not only elucidate the 2'-isopentenylsaproxanthin biosynthetic pathway but
      also understand the evolution of flavobacteria.
AU  - Takatani N
AU  - Nakanishi M
AU  - Meirelles P
AU  - Mino S
AU  - Suda W
AU  - Oshima K
AU  - Hattori M
AU  - Ohkuma M
AU  - Hosokawa M
AU  - Miyashita K
AU  - Thompson FL
AU  - Niwa A
AU  - Sawabe T
AU  - Sawabe T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01236-14.

PMID- 25395640
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Marine Flavobacterium Algibacter lectus Strains SS8 and NR4.
PG  - e01168-14
AB  - Here, we present the draft genome sequences of a zeaxanthin-producing flavobacterium,
      Algibacter lectus strains SS8 and NR4, isolated from coastal
      sediment and rock surfaces in Hakodate, Japan, respectively. This genomic
      information represents the first Algibacter genome sequences, which will help us
      to elucidate the biology and evolution of Flavobacteriaceae bacteria.
AU  - Takatani N
AU  - Nakanishi M
AU  - Meirelles P
AU  - Mino S
AU  - Suda W
AU  - Oshima K
AU  - Hattori M
AU  - Ohkuma M
AU  - Hosokawa M
AU  - Miyashita K
AU  - Thompson FL
AU  - Niwa A
AU  - Sawabe T
AU  - Sawabe T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01168-14.

PMID- 28450506
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Nylon Oligomer-Degrading Bacterium Arthrobacter sp.  Strain KI72.
PG  - e00217-17
AB  - We report here the 4.6-Mb genome sequence of a nylon oligomer-degrading bacterium,
      Arthrobacter sp. strain KI72. The draft genome sequence of strain KI72
      consists of 4,568,574 bp, with a G+C content of 63.47%, 4,372 coding sequences
      (CDSs), 54 tRNAs, and six rRNAs.
AU  - Takehara I
AU  - Kato DI
AU  - Takeo M
AU  - Negoro S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00217-17.

PMID- 22887669
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Bacillus cereus NC7401, Which Produces High Levels of the Emetic Toxin Cereulide.
PG  - 4767-4768
AB  - We report the complete and annotated genome sequence of Bacillus cereus NC7401, a
      representative of the strain group that causes emetic-type food poisoning. The
      emetic toxin, cereulide, is produced by a nonribosomal protein synthesis (NRPS)
      system that is encoded by a gene cluster on a large resident plasmid, pNCcld.
AU  - Takeno A
AU  - Okamoto A
AU  - Tori K
AU  - Oshima K
AU  - Hirakawa H
AU  - Toh H
AU  - Agata N
AU  - Yamada K
AU  - Ogasawara N
AU  - Hayashi T
AU  - Shimizu T
AU  - Kuhara S
AU  - Hattori M
AU  - Ohta M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4767-4768.

PMID- 18823905
VI  - 383
DP  - 2008
TI  - Mouse Dnmt3a Preferentially Methylates Linker DNA and Is Inhibited by Histone H1.
PG  - 810-821
AB  - In mammals, DNA methylation is crucial for embryonic development and germ cell
      differentiation. The DNA methylation patterns are created by de novo-type DNA
      methyltransferases (Dnmts) 3a and 3b. Dnmt3a is crucial for global methylation, including that
      of imprinted genes in germ cells. In eukaryotic nuclei, genomic DNA is packaged into
      multinucleosomes with linker histone H1, which binds to core nucleosomes, simultaneously
      making contacts in the linker DNA that separates adjacent nucleosomes. In the present study,
      we prepared oligonucleosomes from HeLa nuclei with or without linker histone H1 and used them
      as a substrate for Dnmt3a. Removal of histone H1 enhanced the DNA methylation activity.
      Furthermore, Dnmt3a preferentially methylated the linker between the two nucleosome core
      regions of reconstituted dinucleosomes, and the binding of histone H1 inhibited the DNA
      methylation activity of Dnmt3a towards the linker DNA. Since an identical amount of histone H1
      did not inhibit the activity towards naked DNA, the inhibitory effect of histone H1 was not on
      the Dnmt3a catalytic activity but on its preferential location in the linker DNA of the
      dinucleosomes. The central globular domain and C-terminal tail of the histone H1 molecule were
      indispensable for inhibition of the DNA methylation activity of Dnmt3a. We propose that the
      binding and release of histone H1 from the linker portion of chromatin may regulate the local
      DNA methylation of the genome by Dnmt3a, which is expressed ubiquitously in somatic cells in
      vivo.
AU  - Takeshima H
AU  - Suetake I
AU  - Tajima S
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2008 383: 810-821.

PMID- 24948758
VI  - 2
DP  - 2014
TI  - Whole-Genome Sequence of Burkholderia sp. Strain RPE67, a Bacterial Gut Symbiont  of the Bean Bug Riptortus pedestris.
PG  - e00556-14
AB  - Burkholderia sp. strain RPE67 is a bacterial symbiont isolated from a field-collected bean
      bug, Riptortus pedestris. To understand the genetic basis of
      the insect-microbe symbiosis, we performed whole-genome sequencing of the
      Burkholderia strain, revealing an 8.69-Mb genome consisting of three chromosomes
      and three plasmids.
AU  - Takeshita K
AU  - Shibata TF
AU  - Nikoh N
AU  - Nishiyama T
AU  - Hasebe M
AU  - Fukatsu T
AU  - Shigenobu S
AU  - Kikuchi Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00556-14.

PMID- 21518897
VI  - 108
DP  - 2011
TI  - Structural insight into maintenance methylation by mouse DNA methyltransferase 1 (Dnmt1).
PG  - 9055-9059
AB  - Methylation of cytosine in DNA plays a crucial role in development through inheritable gene
      silencing. The DNA methyltransferase Dnmt1 is responsible for the propagation of methylation
      patterns to the next generation via its preferential methylation of hemimethylated CpG sites
      in the genome; however, how Dnmt1 maintains methylation patterns is not fully understood. Here
      we report the crystal structure of the large fragment (291-1620) of mouse Dnmt1 and its
      complexes with cofactor S-adenosyl-L-methionine and its product S-adenosyl-L-homocystein.
      Notably, in the absence of DNA, the N-terminal domain responsible for targeting Dnmt1 to
      replication foci is inserted into the DNA-binding pocket, indicating that this domain must be
      removed for methylation to occur. Upon binding of S-adenosyl-L-methionine, the catalytic
      cysteine residue undergoes a conformation transition to a catalytically competent position.
      For the recognition of hemimethylated DNA, Dnmt1 is expected to utilize a target recognition
      domain that overhangs the putative DNA-binding pocket. Taking into considerations the recent
      report of a shorter fragment structure of Dnmt1 that the CXXC motif positions itself in the
      catalytic pocket and prevents aberrant de novo methylation, we propose that maintenance
      methylation is a multistep process accompanied by structural changes.
AU  - Takeshita K
AU  - Suetake I
AU  - Yamashita E
AU  - Suga M
AU  - Narita H
AU  - Nakagawa A
AU  - Tajima S
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2011 108: 9055-9059.

PMID- 16237012
VI  - 187
DP  - 2005
TI  - Whole-genome sequencing of Staphylococcus haemolyticus uncovers the extreme plasticity of its genome and the evolution of Human-colonizing   Staphylococcal species.
PG  - 7292-7308
AB  - Staphylococcus haemolyticus is an opportunistic bacterial pathogen that colonizes human skin
      and is remarkable for its highly antibiotic-resistant
      phenotype. We determined the complete genome sequence of S.haemolyticus to
      better understand its pathogenicity and evolutionary relatedness to the
      other staphylococcal species. A large proportion of the open reading
      frames in the genomes of S.haemolyticus, Staphylococcus aureus, and
      Staphylococcus epidermidis were conserved in their sequence and order on
      the chromosome. We identified a region of the bacterial chromosome just
      downstream of the origin of replication that showed little homology among
      the species but was conserved among strains within a species. This novel
      region, designated the "oriC environ," likely contributes to the evolution
      and differentiation of the staphylococcal species, since it was enriched
      for species-specific nonessential genes that contribute to the biological
      features of each staphylococcal species. A comparative analysis of the
      genomes of S.haemolyticus, S.aureus, and S.epidermidis elucidated
      differences in their biological and genetic characteristics and pathogenic
      potentials. We identified as many as 82 insertion sequences in the
      S.haemolyticus chromosome that probably mediated frequent genomic
      rearrangements, resulting in phenotypic diversification of the strain.
      Such rearrangements could have brought genomic plasticity to this species
      and contributed to its acquisition of antibiotic resistance.
AU  - Takeuchi F
AU  - Watanabe S
AU  - Baba T
AU  - Yuzawa H
AU  - Ito T
AU  - Morimoto Y
AU  - Kuroda M
AU  - Cui L
AU  - Takahashi M
AU  - Ankai A
AU  - Baba S
AU  - Fukui S
AU  - Lee JC
AU  - Hiramatsu K
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2005 187: 7292-7308.

PMID- 
VI  - 102
DP  - 2002
TI  - Quantitative detection of expression of the Helicobacter pylori methyltransferase-encoding gene hpyIM in vivo and in vitro.
PG  - 242
AB  - Helicobacter pylori are highly diverse bacteria that persist in the human stomach and induce
      chronic gastritis for the virtual lifetime of
      their hosts, a process that increases risk for peptic ulceration,
      gastric adenocarcinoma, and gastric lymphoma. Despite a high degree of
      genetic diversity, particularly among restriction-modification systems,
      hpyIM which encodes a DNA adenine methyltransferase is highly conserved
      among all H. pylori strains. Because of this high level of
      conservation, we sought to determine whether levels of hpyIM expression
      within colonized human mucosa correlated with disease status or mucosal
      injury and whether there was a relationship between levels of
      expression in vivo and in vitro. PCR-light and slot blot hybridizations
      were used to quantitate hypIM transcripts in gastric tissue or in
      broth-grown cells and quantities were normalized to levels of H. pylori
      16s rRNA. Among 41 clinical biopsies, levels of hpyIM transcripts
      varied dramatically and were not related to disease outcome or severity
      of inflammation. Four strains isolated from biopsies were selected for
      more detailed in vitro studies, and for each strain, levels of hpyIM
      were higher during log-phase growth compared with stationary phase. For
      three of the four strains, levels of hypIM transcripts were lower in
      vitro than in vivo. Since bacterial contact with host cells regulates
      gene expression in other organisms, we next sought to determine if
      adherence of H. pylori to gastric epithelial cells resulted in hpyIM
      expression patterns that more closely reflected levels observed in
      vivo. hpyIM transcript levels after two hours of adherence were not
      related to levels identified within inflamed tissue, suggesting that
      events independent from isolated bacterial:epithelial cell contact may
      regulate hpyIM expression in vivo.
AU  - Takeuchi H
AU  - Donahue JP
AU  - Krishna U
AU  - Miller GG
AU  - Peek RM Jr
AU  - Israel DA
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 2002 102: 242.

PMID- 12355374
VI  - 186
DP  - 2002
TI  - Characterization of expression of a functionally conserved Helicobacter pylori methyltransferase-encoding gene within inflamed mucosa and  during in vitro growth.
PG  - 1186-1189
AB  - Methylation of bacterial DNA can regulate microbial growth and virulence. Expression of hpyIM,
      a conserved methyltransferase of the
      gastric pathogen Helicobacter pylori, was quantitated in gastric biopsy
      specimens from 41 H. pylori-infected patients and during growth in
      vitro, by quantitative reverse transcriptase-polymerase chain reaction
      and/or RNA slot-blot analysis, to determine whether levels of
      transcription were associated with pathologic outcome, as based on both
      severity of gastritis and inflammatory cytokine levels, or were
      regulated by bacterial growth phase. The effects that hpyIM
      inactivation has on bacterial morphology were determined by electron
      microscopy. Expression of hpyIM varied dramatically within colonized
      gastric tissue, and levels were not related to either colonization
      density, severity of inflammation, mucosal IL-8 concentrations, or
      clinical disease. In vitro, hpyIM expression was higher during
      log-phase growth and was required for normal bacterial morphology,
      suggesting that hpyIM expression may be growth-phase regulated within
      the gastric niche.
AU  - Takeuchi H
AU  - Israel DA
AU  - Miller GG
AU  - Donahue JP
AU  - Krishna U
AU  - Gaus K
AU  - Peek RM
PT  - Journal Article
TA  - J. Infect. Dis.
JT  - J. Infect. Dis.
SO  - J. Infect. Dis. 2002 186: 1186-1189.

PMID- 24695768
VI  - 9
DP  - 2014
TI  - Complete Genome Sequence of the Biocontrol Strain Pseudomonas protegens Cab57 Discovered in Japan Reveals Strain-Specific Diversity of This Species.
PG  - E93683
AB  - The biocontrol strain Pseudomonas sp. Cab57 was isolated from the rhizosphere of
      shepherd's purse growing in a field in Hokkaido by screening the antibiotic
      producers. The whole genome sequence of this strain was obtained by paired-end
      and whole-genome shotgun sequencing, and the gaps between the contigs were closed
      using gap-spanning PCR products. The P. sp. Cab57 genome is organized into a
      single circular chromosome with 6,827,892 bp, 63.3% G+C content, and 6,186
      predicted protein-coding sequences. Based on 16S rRNA gene analysis and whole
      genome analysis, strain Cab57 was identified as P. protegens. As reported in P.
      protegens CHA0 and Pf-5, four gene clusters (phl, prn, plt, and hcn) encoding the
      typical antibiotic metabolites and the reported genes associated with Gac/Rsm
      signal transduction pathway of these strains are fully conserved in the Cab57
      genome. Actually strain Cab57 exhibited typical Gac/Rsm activities and antibiotic
      production, and these activities were enhanced by knocking out the retS gene (for
      a sensor kinase acting as an antagonist of GacS). Two large segments (79 and 115
      kb) lacking in the Cab57 genome, as compared with the Pf-5 genome, accounted for
      the majority of the difference (247 kb) between these genomes. One of these
      segments was the complete rhizoxin analog biosynthesis gene cluster (ca. 79 kb)
      and another one was the 115-kb mobile genomic island. A whole genome comparison
      of those relative strains revealed that each strain has unique gene clusters
      involved in metabolism such as nitrite/nitrate assimilation, which was identified
      in the Cab57 genome. These findings suggest that P. protegens is a ubiquitous
      bacterium that controls its biocontrol traits while building up strain-specific
      genomic repertoires for the biosynthesis of secondary metabolites and niche
      adaptation.
AU  - Takeuchi K
AU  - Noda N
AU  - Someya N
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2014 9: E93683.

PMID- 19103658
VI  - 37
DP  - 2009
TI  - Optimization of in vivo activity of a bifunctional homing endonuclease and maturase reverses evolutionary degradation.
PG  - 877-890
AB  - The LAGLIDADG homing endonuclease (LHE) I-AniI has adopted an extremely efficient secondary
      RNA splicing activity that is beneficial to its host,
      balanced against inefficient DNA cleavage. A selection experiment
      identified point mutations in the enzyme that act synergistically to
      improve endonuclease activity. The amino-acid substitutions increase
      target affinity, alter the thermal cleavage profile and significantly
      increase targeted recombination in transfected cells. The RNA splicing
      activity is not affected by these mutations. The improvement in DNA
      cleavage activity is largely focused on one of the enzyme's two active
      sites, corresponding to a rearrangement of a lysine residue hypothesized
      to act as a general base. Most of the constructs isolated in the screen
      contain one or more mutations that revert an amino-acid identity to a
      residue found in one or more close homologues of I-AniI. This implies that
      mutations that have previously reduced the endonuclease activity of I-AniI
      are identified and reversed, sometimes in combination with additional
      'artificial' mutations, to optimize its in vivo activity.
AU  - Takeuchi R
AU  - Certo M
AU  - Caprara MG
AU  - Scharenberg AM
AU  - Stoddard BL
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: 877-890.

PMID- 25408403
VI  - 1239
DP  - 2015
TI  - Engineering of Customized Meganucleases via In Vitro Compartmentalization and In Cellulo Optimization.
PG  - 105-132
AB  - LAGLIDADG homing endonucleases (also referred to as 'meganucleases') are compact DNA
      cleaving enzymes that specifically recognize long target sequences (approximately 20 base
      pairs), and thus serve as useful tools for therapeutic genome engineering. While stand-alone
      meganucleases are sufficiently active to introduce targeted genome modification, they can be
      fused to additional sequence-specific DNA binding domains in order to improve their
      performance in target cells. In this chapter, we describe an approach to retarget
      meganucleases to DNA targets of interest (such as sequences found in genes and cis regulatory
      regions), which is feasible in an academic laboratory environment. A combination of two
      selection systems, in vitro compartmentalization and two-plasmid cleavage assay in bacteria,
      allow for efficient engineering of meganucleases that specifically cleave a wide variety of
      DNA sequences.
AU  - Takeuchi R
AU  - Choi M
AU  - Stoddard BL
PT  - Journal Article
TA  - Methods Mol. Biol.
JT  - Methods Mol. Biol.
SO  - Methods Mol. Biol. 2015 1239: 105-132.

PMID- 21784983
VI  - 108
DP  - 2011
TI  - Tapping natural reservoirs of homing endonucleases for targeted gene modification.
PG  - 13077-13082
AB  - Homing endonucleases mobilize their own genes by generating double-strand breaks at individual
      target sites within potential host DNA. Because of their high specificity, these proteins are
      used for 'genome editing' in higher eukaryotes. However, alteration of homing endonuclease
      specificity is quite challenging. Here we describe the identification and phylogenetic
      analysis of over 200 naturally occurring LAGLIDADG homing endonucleases (LHEs). Biochemical
      and structural characterization of endonucleases from one clade within the phylogenetic tree
      demonstrates strong conservation of protein structure contrasted against highly diverged DNA
      target sites and indicates that a significant fraction of these proteins are sufficiently
      stable and active to serve as engineering scaffolds. This information was exploited to create
      a targeting enzyme to disrupt the endogenous monoamine oxidase B gene in human cells. The
      ubiquitous presence and diversity of LHEs described in this study may facilitate the creation
      of many tailored nucleases for genome editing.
AU  - Takeuchi R
AU  - Lambert AR
AU  - Mak AN
AU  - Jacoby K
AU  - Dickson RJ
AU  - Gloor GB
AU  - Scharenberg AM
AU  - Edgell DR
AU  - Stoddard BL
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2011 108: 13077-13082.

PMID- 12749863
VI  - 286
DP  - 2003
TI  - Effects of cadmium on DNA-(cytosine-5) methyltransferase activity and DNA methylation status during cadmium-induced cellular transformation.
PG  - 355-365
AB  - Cadmium is a human carcinogen that likely acts via epigenetic mechanisms. Since DNA
      methylation alterations represent an important epigenetic event
      linked to cancer, the effect of cadmium on DNA methyltransferase (MeTase)
      activity was examined using in vitro (TRL1215 rat liver cells) and ex vivo
      (M.SssI DNA MeTase) systems. Cadmium effectively inhibited DNA MeTases in
      a manner that was noncompetitive with respect to substrate (DNA),
      indicating an interaction with the DNA binding domain rather than the
      active site. Based on these results, the effects of prolonged cadmium
      exposure on DNA MeTase and genomic DNA methylation in TRL1215 cells were
      studied. After 1 week of exposure to 0-2.5 microM cadmium, DNA MeTase
      activity was reduced (up to 40%) in a concentration-dependent fashion,
      while genomic DNA methylation showed slight but significant reductions at
      the two highest concentrations. After 10 weeks of exposure, the cells
      exhibited indications of transformation, including hyperproliferation,
      increased invasiveness, and decreased serum dependence. Unexpectedly,
      these cadmium-transformed cells exhibited significant increases in DNA
      methylation and DNA MeTase activity. These results indicate that, while
      cadmium is an effective inhibitor of DNA MeTase and initially induces DNA
      hypomethylation, prolonged exposure results in DNA hypermethylation and
      enhanced DNA MeTase activity.
AU  - Takiguchi M
AU  - Achanzar WE
AU  - Qu W
AU  - Li G
AU  - Waalkes MP
PT  - Journal Article
TA  - Exp. Cell Res.
JT  - Exp. Cell Res.
SO  - Exp. Cell Res. 2003 286: 355-365.

PMID- 1776964
VI  - 17
DP  - 1991
TI  - Oligodeoxynucleotides, containing 6-O-alkylated guanine segments recognized by HaeIII restriction endonuclease.
PG  - 806-808
AB  - A series of self-complementary decadeoxynucleotides containing a native or modified HaeIII
      site GGCC (with one or both guanine residues 6-0-cetylated) have been synthesized by the
      phosphotriester approach.  The nonmodified decanucleotide is normally digested with snake
      venom phosphodiesterase as well as with HaeIII and BspI restriction endonucleases, whereas the
      bulky 6-O-alkyl substitutent strongly inhibits the VPDE hydrolysis and completely prevents
      digestion with the endonucleases.
AU  - Taktakishvili MO
AU  - Tabdzhun A
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1991 17: 806-808.

PMID- 27516496
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Micromonospora sp. Strain HK10, Isolated from Kaziranga  National Park, India.
PG  - e00559-15
AB  - We report the 6.92-Mbp genome sequence of Micromonospora sp. HK10, isolated from  soil samples
      collected from Kaziranga National Park, Assam, India. The full
      genome of strain Micromonospora sp. strain HK10 consists of 6,911,179 bp with
      73.39% GC content, 6,196 protein-coding genes, and 86 RNAs.
AU  - Talukdar M
AU  - Das D
AU  - Borah C
AU  - Deka-Boruah HP
AU  - Bora TC
AU  - Singh AK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00559-15.

PMID- 29599159
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of the First New Delhi Metallo-beta-Lactamase (NDM-1)-Producing Escherichia coli Strain Isolated in Peru.
PG  - e00199-18
AB  - We present here the draft genome sequence of the first New Delhi metallo-beta-lactamase
      (NDM-1)-producing Escherichia coli strain, belonging to
      sequence type 155 (ST155), isolated in Peru. Assembly of this draft genome
      resulted in 5,061,184 bp, revealing a clinically significant resistome for
      beta-lactams, aminoglycosides, tetracyclines, phenicols, sulfonamides,
      trimethoprim, and fluoroquinolones.
AU  - Tamariz J
AU  - Llanos C
AU  - Seas C
AU  - Montenegro P
AU  - Lagos J
AU  - Fernandes MR
AU  - Cerdeira L
AU  - Lincopan N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00199-18.

PMID- 11713521
VI  - 414
DP  - 2001
TI  - A histone H3 methyltransferase controls DNA methylation in Neurospora crassa.
PG  - 277-283
AB  - DNA methylation is involved in epigenetic processes such as X-chromosome inactivation,
      imprinting and silencing of transposons. We have demonstrated previously that dim-2 encodes a
      DNA methyltransferase that is responsible for all known cytosine methylation in Neurospora
      crassa. Here we report that another Neurospora gene, dim-5, is required for DNA methylation,
      as well as for normal growth and full fertility. We mapped dim-5 and identified it by
      transformation with a candidate gene. The mutant has a nonsense mutation in a SET domain of a
      gene related to histone methyltransferases that are involved in heterochromatin formation in
      other organisms.  Transformation of a wild-type strain with a segment of dim-5 reactivated a
      silenced hph gene, apparently by 'quelling' of dim-5. We demonstrate that recombinant DIM-5
      protein specifically methylates histone H3 and that replacement of lysine 9 in histone H3 with
      either a leucine or an arginine phenocopies the dim-5 mutation. We conclude that DNA
      methylation depends on histone methylation.
AU  - Tamaru H
AU  - Selker EU
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2001 414: 277-283.

PMID- 19948806
VI  - 192
DP  - 2010
TI  - Genome Sequence of the Cellulosome-Producing Mesophilic Organism Clostridium cellulovorans 743B.
PG  - 901-902
AB  - Clostridium cellulovorans 743B was isolated from a wood chip pile and is an anaerobic and
      mesophilic spore-forming bacterium. This organism
      degrades native substrates in soft biomass such as corn fiber and rice
      straw efficiently by producing an extracellular enzyme complex called the
      cellulosome. Here we report the genome sequence of C. cellulovorans 743B.
AU  - Tamaru Y
AU  - Miyake H
AU  - Kuroda K
AU  - Nakanishi A
AU  - Kawade Y
AU  - Yamamoto K
AU  - Uemura M
AU  - Fujita Y
AU  - Doi RH
AU  - Ueda M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 901-902.

PMID- 20601475
VI  - 192
DP  - 2010
TI  - Complete Genome Sequence of Beijerinckia indica subsp. indica.
PG  - 4532-4533
AB  - Beijerinckia indica subsp. indica is an aerobic, acidophilic, exopolysaccharide-producing,
      N2-fixing soil bacterium. It is a generalist
      chemoorganotroph that is phylogenetically closely related to facultative
      and obligate methanotrophs of the genera Methylocella and Methylocapsa.
      Here we report the full genome sequence of this bacterium.
AU  - Tamas I
AU  - Dedysh SN
AU  - Liesack W
AU  - Stott MB
AU  - Alam M
AU  - Murrell JC
AU  - Dunfield PF
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 4532-4533.

PMID- 12089438
VI  - 296
DP  - 2002
TI  - 50 million years of genomic stasis in endosymbiotic bacteria.
PG  - 2376-2379
AB  - Comparison of two fully sequenced genomes of Buchnera aphidicola, the obligate endosymbionts
      of aphids, reveals the most extreme genome stability to date: no chromosome rearrangements or
      gene acquisitions have occurred in the past 50 to 70 million years, despite substantial
      sequence evolution and the inactivation and loss of individual genes. In contrast, the genomes
      of their closest free-living relatives, Escherichia coli and Salmonella spp., are more than
      2000-fold more labile in content and gene order. The genomic stasis of B. aphidicola, likely
      attributable to the loss of phages, repeated sequences, and recA, indicates that B. aphidicola
      is no longer a source of ecological innovation for its hosts.
AU  - Tamas I
AU  - Klasson L
AU  - Canback B
AU  - Naslund AK
AU  - Eriksson A-S
AU  - Wernegreen JJ
AU  - Sandstrom JP
AU  - Moran NA
AU  - Andersson SGE
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2002 296: 2376-2379.

PMID- 26272568
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence and Annotation of Phyllosphere-Persisting Salmonella enterica subsp. enterica Serovar Livingstone Strain CKY-S4, Isolated from an  Urban Lake in Regina, Canada.
PG  - e00884-15
AB  - Here, we report the first draft genome sequence of Salmonella enterica subsp. enterica serovar
      Livingstone. This S. Livingstone strain CKY-S4 displayed biofilm
      formation and cellulose production and could persist on lettuce. This genome may
      help the study of mechanisms by which enteric pathogens colonize food crops.
AU  - Tambalo DD
AU  - Perry BJ
AU  - Fitzgerald SF
AU  - Cameron AD
AU  - Yost CK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00884-15.

PMID- 26159537
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Clavibacter michiganensis subsp. nebraskensis Strain DOAB 397, Isolated from an Infected Field Corn Plant in Manitoba, Canada.
PG  - e00768-15
AB  - In 2014, the pathogen Clavibacter michiganensis subsp. nebraskensis was isolated  from
      symptomatic corn leaves in Manitoba, Canada. We report the draft genome
      sequence of C. michiganensis subsp. nebraskensis DOAB 397, consisting of 3.059 Mb
      with 73.0% G+C content, 2,922 predicted protein-coding sequences, 45 tRNAs, 3
      rRNAs, and 37 pseudogenes.
AU  - Tambong JT
AU  - Xu R
AU  - Adam Z
AU  - Cott M
AU  - Rose K
AU  - Reid LM
AU  - Daayf F
AU  - Briere S
AU  - Bilodeau GJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00768-15.

PMID- 25838484
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Enterotoxigenic Escherichia coli Strain E24377A, Obtained from a Tribal Drinking Water Source in India.
PG  - e00225-15
AB  - Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrheal disease in  humans and
      animals. Its dissemination can occur through water sources
      contaminated by it. Here, we report for the first time the draft genome sequence
      of ETEC strain E24377A, obtained from a tribal drinking water source in India.
AU  - Tamhankar AJ
AU  - Nerkar SS
AU  - Khadake PP
AU  - Akolkar DB
AU  - Apurwa SR
AU  - Deshpande U
AU  - Khedkar SU
AU  - Stalsby-Lundborg C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00225-15.

PMID- 15134658
VI  - 1698
DP  - 2004
TI  - Crystallization and preliminary crystallographic studies of a bifunctional restriction endonuclease Eco57I.
PG  - 251-254
AB  - Restriction endonuclease Eco57I from Escherichia coli recognizes asymmetric DNA sequence
      5'-CTGAAG and has both restriction (DNA cleavage a short distance away from the recognition
      site) and modification (methylation) activities residing in a single polypeptide chain. Single
      crystals of wild-type Eco57I ternary complexes with double-stranded DNA and sinefungin, a
      stimulator of endonuclease activity, were obtained by the vapor diffusion technique and
      characterized crystallographically for different variants of the DNA component. The best data
      for the complex with 25-mer DNA were collected to 4.2-A resolution at 100 K using synchrotron
      radiation. The crystals are orthorhombic, space group P2(1)2(1)2, with a=164.3, b=293.0,
      c=71.1 A, and contain two to four copies of the protein in the asymmetric unit.
AU  - Tamulaitiene G
AU  - Grazulis S
AU  - Janulaitis A
AU  - Janowski R
AU  - Bujacz G
AU  - Jaskolski M
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 2004 1698: 251-254.

PMID- 16962970
VI  - 14
DP  - 2006
TI  - The crystal structure of the rare-cutting restriction enzyme SdaI reveals unexpected domain architecture.
PG  - 1389-1400
AB  - Rare-cutting restriction enzymes are important tools in genome analysis.  We report here the
      crystal structure of SdaI restriction endonuclease, which is specific for the 8 bp sequence
      CCTGCA/GG ("/" designates the cleavage site).  Unlike orthodox Type IIP enzymes, which are
      single domain proteins, the SdaI monomer is composed of two structural domains.  The N domain
      contains a classical winged helix-turn-helix (wHTH) DNA binding motif, while the C domain
      shows a typical restriction endonuclease fold.  The active site of SdaI is located within the
      C domain and represents a variant of the canonical PD-(D/E)XK motif.  SdaI determinants of
      sequence specificity are clustered on the recognition helix of the wHTH motif at the N domain.
      The modular architecture of SdaI, wherein one domain mediates DNA binding while the other
      domain is predicted to catalyze hydrolysis, distinguishes SdaI from previously characterized
      restriction enzymes interacting with symmetric recognition sequences.
AU  - Tamulaitiene G
AU  - Jakubauskas A
AU  - Urbanke C
AU  - Huber R
AU  - Grazulis S
AU  - Siksnys V
PT  - Journal Article
TA  - Structure
JT  - Structure
SO  - Structure 2006 14: 1389-1400.

PMID- 28039325
VI  - 45
DP  - 2017
TI  - Restriction endonuclease AgeI is a monomer which dimerizes to cleave DNA.
PG  - 3547-3558
AB  - Although all Type II restriction endonucleases catalyze phosphodiester bond hydrolysis within
      or close to their DNA target sites, they form different
      oligomeric assemblies ranging from monomers, dimers, tetramers to higher order
      oligomers to generate a double strand break in DNA. Type IIP restriction
      endonuclease AgeI recognizes a palindromic sequence 5-A/CCGGT-3 and cuts it ('/'
      denotes the cleavage site) producing staggered DNA ends. Here, we present crystal
      structures of AgeI in apo and DNA-bound forms. The structure of AgeI is similar
      to the restriction enzymes that share in their target sites a conserved CCGG
      tetranucleotide and a cleavage pattern. Structure analysis and biochemical data
      indicate, that AgeI is a monomer in the apo-form both in the crystal and in
      solution, however, it binds and cleaves the palindromic target site as a dimer.
      DNA cleavage mechanism of AgeI is novel among Type IIP restriction endonucleases.
AU  - Tamulaitiene G
AU  - Jovaisaite V
AU  - Tamulaitis G
AU  - Songailiene I
AU  - Manakova E
AU  - Zaremba M
AU  - Grazulis S
AU  - Xu SY
AU  - Siksnys V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2017 45: 3547-3558.

PMID- 18400171
VI  - 16
DP  - 2008
TI  - NotI Is Not Boring.
PG  - 497-498
AB  - Crystal structures of the restriction endonuclease NotI in free and DNA bound forms, presented
      in this issue of Structure (Lambert et al., 2008), provide a unique insight into the
      structural details of 8 base pair  sequence recognition by the restriction enzyme.
AU  - Tamulaitiene G
AU  - Siksnys V
PT  - Journal Article
TA  - Structure
JT  - Structure
SO  - Structure 2008 16: 497-498.

PMID- 25429979
VI  - 42
DP  - 2014
TI  - Crystal structure of the R-protein of the multisubunit ATP-dependent restriction  endonuclease NgoAVII.
PG  - 14022-14030
AB  - The restriction endonuclease (REase) NgoAVII is composed of two proteins, R.NgoAVII and
      N.NgoAVII, and shares features of both Type II restriction enzymes and Type I/III
      ATP-dependent restriction enzymes (see accompanying paper Zaremba et al., 2014). Here we
      present crystal structures of the R.NgoAVII apo-protein and the R.NgoAVII C-terminal domain
      bound to a specific DNA. R.NgoAVII is composed of two domains: an N-terminal nucleolytic PLD
      domain; and a C-terminal B3-like DNA-binding domain identified previously in BfiI and EcoRII
      REases, and in plant transcription factors. Structural comparison of the B3-like domains of
      R.NgoAVII, EcoRII, BfiI and the plant transcription factors revealed a conserved DNA-binding
      surface comprised of N- and C-arms that together grip the DNA. The C-arms of R.NgoAVII,
      EcoRII, BfiI and plant B3 domains are similar in size, but the R.NgoAVII N-arm which makes the
      majority of the contacts to the target site is much longer. The overall structures of
      R.NgoAVII and BfiI are similar; however, whilst BfiI has stand-alone catalytic activity,
      R.NgoAVII requires an auxiliary cognate N.NgoAVII protein and ATP hydrolysis in order to
      cleave DNA at the target site. The structures we present will help formulate future
      experiments to explore the molecular mechanisms of intersubunit crosstalk that control DNA
      cleavage by R.NgoAVII and related endonucleases.
AU  - Tamulaitiene G
AU  - Silanskas A
AU  - Grazulis S
AU  - Zaremba M
AU  - Siksnys V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2014 42: 14022-14030.

PMID- 
VI  - 0
DP  - 2000
TI  - DNA bending induced by MunI restriction endonuclease.
PG  - 11-15
AB  - Bending of DNA induced by the specific binding of the restriction endonuclease MunI has been
      investigated by the empirical method of Thompson and Landy and the method of calibrated
      standards.  The R.MunI induced bending angles were found to be 42o +/- 4o at pH 6.5 and 56o
      +/1 4o at pH 8.3 in the presence of Ca2+ ions.  Similar values of DNA bending angles were
      obtained in the complexes of active site mutants D83A and E98A with specific DNA under the
      same conditions.  Results of bending experiments support the assumption that elimination of
      electrostatic repulsion between charged carboxylates and phosphate oxygens by protonation of
      the active site carboxylate residue(s), their replacement to alanine or neutralization by Ca2+
      binding yields similar DNA-protein complexes.
AU  - Tamulaitis G
AU  - Lagunavicius A
PT  - Journal Article
TA  - Biologija
JT  - Biologija
SO  - Biologija 2000 0: 11-15.

PMID- 16497303
VI  - 580
DP  - 2006
TI  - Biochemical and mutational analysis of EcoRII functional domains reveals evolutionary links between restriction enzymes.
PG  - 1665-1671
AB  - The archetypal Type BE restriction endonuclease EcoRII is a dimer that has a modular
      structure. DNA binding studies indicate that the isolated
      C-terminal domain dimer has an interface that binds a single cognate
      DNA molecule whereas the N-terminal domain is a monomer that also binds
      a single copy of cognate DNA. Hence, the full-length EcoRII contains
      three putative DNA binding interfaces: one at the C-terminal domain
      dimer and two at each of the N-terminal domains. Mutational analysis
      indicates that the C-terminal domain shares conserved active site
      architecture and DNA binding elements with the tetrameric restriction
      enzyme NgoMIV. Data provided here suggest possible evolutionary
      relationships between different subfamilies of restriction enzymes.
AU  - Tamulaitis G
AU  - Mucke M
AU  - Siksnys V
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 2006 580: 1665-1671.

PMID- 26240380
VI  - 43
DP  - 2015
TI  - Functional significance of protein assemblies predicted by the crystal structure  of the restriction endonuclease BsaWI.
PG  - 8100-8110
AB  - Type II restriction endonuclease BsaWI recognizes a degenerated sequence 5'-W/CCGGW-3' (W
      stands for A or T, '/' denotes the cleavage site). It belongs to
      a large family of restriction enzymes that contain a conserved CCGG
      tetranucleotide in their target sites. These enzymes are arranged as dimers or
      tetramers, and require binding of one, two or three DNA targets for their optimal
      catalytic activity. Here, we present a crystal structure and biochemical
      characterization of the restriction endonuclease BsaWI. BsaWI is arranged as an
      'open' configuration dimer and binds a single DNA copy through a minor groove
      contacts. In the crystal primary BsaWI dimers form an indefinite linear chain via
      the C-terminal domain contacts implying possible higher order aggregates. We show
      that in solution BsaWI protein exists in a dimer-tetramer-oligomer equilibrium,
      but in the presence of specific DNA forms a tetramer bound to two target sites.
      Site-directed mutagenesis and kinetic experiments show that BsaWI is active as a
      tetramer and requires two target sites for optimal activity. We propose BsaWI
      mechanism that shares common features both with dimeric Ecl18kI/SgrAI and bona
      fide tetrameric NgoMIV/SfiI enzymes.
AU  - Tamulaitis G
AU  - Rutkauskas M
AU  - Zaremba M
AU  - Grazulis S
AU  - Tamulaitiene G
AU  - Siksnys V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2015 43: 8100-8110.

PMID- 16529772
VI  - 358
DP  - 2006
TI  - Simultaneous Binding of Three Recognition Sites is Necessary for a Concerted Plasmid DNA Cleavage by EcoRII Restriction Endonuclease.
PG  - 406-419
AB  - According to the current paradigm type IIE restriction endonucleases are homodimeric proteins
      that simultaneously bind to two recognition sites but
      cleave DNA at only one site per turnover: the other site acts as an
      allosteric locus, activating the enzyme to cleave DNA at the first.
      Structural and biochemical analysis of the archetypal type IIE restriction
      enzyme EcoRII suggests that it has three possible DNA binding interfaces
      enabling simultaneous binding of three recognition sites. To test if
      putative synapsis of three binding sites has any functional significance,
      we have studied EcoRII cleavage of plasmids containing a single, two and
      three recognition sites under both single turnover and steady state
      conditions. EcoRII displays distinct reaction patterns on different
      substrates: (i) it shows virtually no activity on a single site plasmid;
      (ii) it yields open-circular DNA form nicked at one strand as an
      obligatory intermediate acting on a two-site plasmid; (iii) it cleaves
      concertedly both DNA strands at a single site during a single turnover on
      a three site plasmid to yield linear DNA. Cognate oligonucleotide added in
      trans increases the reaction velocity and changes the reaction pattern for
      the EcoRII cleavage of one and two-site plasmids but has little effect on
      the three-site plasmid. Taken together the data indicate that EcoRII
      requires simultaneous binding of three rather than two recognition sites
      in cis to achieve concerted DNA cleavage at a single site. We show that
      the orthodox type IIP enzyme PspGI which is an isoschisomer of EcoRII,
      cleaves different plasmid substrates with equal rates. Data provided here
      indicate that type IIE restriction enzymes EcoRII and NaeI follow
      different mechanisms. We propose that other type IIE restriction enzymes
      may employ the mechanism suggested here for EcoRII.
AU  - Tamulaitis G
AU  - Sasnauskas G
AU  - Mucke M
AU  - Siksnys V
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2006 358: 406-419.

PMID- 11997010
VI  - 518
DP  - 2002
TI  - Alternative arrangements of catalytic residues at the active sites of restriction enzymes.
PG  - 17-22
AB  - A catalytic sequence motif PDX10-30(E/D)XK is found in many restriction enzymes. On the basis
      of sequence similarities and mapping of the conserved residues to the crystal structure of
      NgoMIV we suggest that residues D160, K182, R186, R188 and E195 contribute to the
      catalytic/DNA binding site of the Ecl18kI restriction endonuclease. Mutational analysis
      confirms the functional significance of the conserved residues of Ecl18kI. Therefore, we
      conclude that the active site motif 159VDX21KX12E of Ecl18kI differs from the canonical
      PDX10-30(E/D)XK motif characteristic for most of the restriction enzymes. Moreover, we propose
      that two subfamilies of endonucleases Ecl18kI/PspGI/EcoRII and Cfr10I/Bse634I/NgoMIV,
      specific, respectively, for CCNGG/CCWGG and RCCGGY/GCCGGC sites, share conserved active site
      architecture and DNA binding elements.
AU  - Tamulaitis G
AU  - Solonin AS
AU  - Siksnys V
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 2002 518: 17-22.

PMID- 18820295
VI  - 36
DP  - 2008
TI  - How PspGI, catalytic domain of EcoRII and Ecl18kI acquire specificities for different DNA targets.
PG  - 6101-6108
AB  - Restriction endonucleases Ecl18kI and PspGI/catalytic domain of EcoRII recognize CCNGG and
      CCWGG sequences (W stands for A or T), respectively.
      The enzymes are structurally similar, interact identically with the
      palindromic CC:GG parts of their recognition sequences and flip the
      nucleotides at their centers. Specificity for the central nucleotides
      could be influenced by the strength/stability of the base pair to be
      disrupted and/or by direct interactions of the enzymes with the flipped
      bases. Here, we address the importance of these contributions. We
      demonstrate that wt Ecl18kI cleaves oligoduplexes containing canonical,
      mismatched and abasic sites in the central position of its target sequence
      CCNGG with equal efficiencies. In contrast, substitutions in the binding
      pocket for the extrahelical base alter the Ecl18kI preference for the
      target site: the W61Y mutant prefers only certain mismatched substrates,
      and the W61A variant cuts exclusively at abasic sites, suggesting that
      pocket interactions play a major role in base discrimination. PspGI and
      catalytic domain of EcoRII probe the stability of the central base pair
      and the identity of the flipped bases in the pockets. This 'double check'
      mechanism explains their extraordinary specificity for an A/T pair in the
      flipping position.
AU  - Tamulaitis G
AU  - Zaremba M
AU  - Szczepanowski RH
AU  - Bochtler M
AU  - Siksnys V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2008 36: 6101-6108.

PMID- 17617640
VI  - 35
DP  - 2007
TI  - Nucleotide flipping by restriction enzymes analyzed by 2-aminopurine steady-state fluorescence.
PG  - 4792-4799
AB  - Many DNA modification and repair enzymes require access to DNA bases and therefore flip
      nucleotides. Restriction endonucleases (REases) hydrolyze the phosphodiester backbone within
      or in the vicinity of the target recognition site and do not require base extrusion for the
      sequence readout and catalysis. Therefore, the observation of extrahelical nucleotides in a
      co-crystal of REase Ecl18kI with the cognate sequence, CCNGG, was unexpected. It turned out
      that Ecl18kI reads directly only the CCGG sequence and skips the unspecified N nucleotides,
      flipping them out from the helix. Sequence and structure conservation predict nucleotide
      flipping also for the complexes of PspGI and EcoRII with their target DNAs (/CCWGG), but data
      in solution are limited and indirect. Here, we demonstrate that Ecl18kI, the C-terminal domain
      of EcoRII (EcoRII-C) and PspGI enhance the fluorescence of 2-aminopurines (2-AP) placed at the
      centers of their recognition sequences. The fluorescence increase is largest for PspGI,
      intermediate for EcoRII-C and smallest for Ecl18kI, probably reflecting the differences in the
      hydrophobicity of the binding pockets within the protein. Omitting divalent metal cations and
      mutation of the binding pocket tryptophan to alanine strongly increase the 2-AP signal in the
      Ecl18kI-DNA complex. Together, our data provide the first direct evidence that Ecl18kI,
      EcoRII-C and PspGI flip nucleotides in solution.
AU  - Tamulaitis G
AU  - Zaremba M
AU  - Szczepanowski RH
AU  - Bochtler M
AU  - Siksnys V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2007 35: 4792-4799.

PMID- 9321674
VI  - 25
DP  - 1997
TI  - Determination of methylation specificity of sequence-specific DNA methyltransferases using matrix assisted laser desorption/ionization time-of-flight mass spectrometry.
PG  - 4162-4164
AB  - We describe here a sensitive and straightforward method for characterizing the methylation
      specificity of type II DNA methyltransferases (Mtases) using matrix-assisted laser
      desorption/ionization time-of-flight mass spectrometry.  DNA substrate, prepared by ligation
      of a commercially available oligonucleotide, was modified by the subject MTase and was
      derivatized to a mixture of single-stranded oligonucleotides through endonuclease treatment,
      heat-denaturation and limited digestion by 3'-terminus-specific phosphodiesterase I.
      MALDI-TOF mass spectrometry was used to determine the mass differences between the digestion
      products, and the methylated nucleotide was explicitly identified by the mass increase in 14
      Da due to the base modification.  The method was applicable to the three representative MTases
      M.EcoRI, M.BamHI and M.HaeIII.
AU  - Tamura T
AU  - Araki Y
AU  - Yamaoka S
AU  - Inagaki K
AU  - Tanaka H
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1997 25: 4162-4164.

PMID- 11942678
VI  - 16
DP  - 2002
TI  - An in vitro Screening Method for DNA Cytosine-C5-Methylase Inhibitor.
PG  - 25-27
AB  - A specific inhibitor of DNA cytosine C-5-methylases would be useful for studying genomic
      imprinting, X-chromosome inactivation, carcinogenesis,
      and regulation of tissue-specific gene expression, for these
      physiological phenomena appears to be regulated through DNA methylation
      in promoter sequences. This paper reports a novel convenient in vitro
      assay method for screening DNA cytosine C-5-methylase inhibitor. Our
      method uses a commercially available HaeIII methylase (cytosine C-5
      methylase), its corresponding HaeIII endonuclease, and lambda DNA as
      their substrate.
AU  - Tamura T
AU  - Kataoka A
AU  - Shu LY
AU  - Ashida A
AU  - Tanaka H
AU  - Inagaki K
PT  - Journal Article
TA  - Nat. Prod. Lett.
JT  - Nat. Prod. Lett.
SO  - Nat. Prod. Lett. 2002 16: 25-27.

PMID- 28018352
VI  - 7
DP  - 2016
TI  - The Capricious Nature of Bacterial Pathogens: Phasevarions and Vaccine Development.
PG  - 586
AB  - Infectious diseases are a leading cause of morbidity and mortality worldwide, and vaccines are
      one of the most successful and cost-effective tools for disease prevention. One of the key
      considerations for rational vaccine development is the selection of appropriate antigens.
      Antigens must induce a protective immune response, and this response should be directed to
      stably expressed antigens so the target microbe can always be recognized by the immune system.
      Antigens with variable expression, due to environmental signals or phase variation (i.e., high
      frequency, random switching of expression), are not ideal vaccine candidates because variable
      expression could lead to immune evasion. Phase variation is often mediated by the presence of
      highly mutagenic simple tandem DNA repeats, and genes containing such sequences can be easily
      identified, and their use as vaccine antigens reconsidered. Recent research has identified
      phase variably expressed DNA methyltransferases that act as global epigenetic regulators.
      These phase-variable regulons, known as phasevarions, are associated with altered virulence
      phenotypes and/or expression of vaccine candidates. As such, genes encoding candidate vaccine
      antigens that have no obvious mechanism of phase variation may be subject to indirect,
      epigenetic control as part of a phasevarion. Bioinformatic and experimental studies are
      required to elucidate the distribution and mechanism of action of these DNA
      methyltransferases, and most importantly, whether they mediate epigenetic regulation of
      potential and current vaccine candidates. This process is essential to define the stably
      expressed antigen target profile of bacterial pathogens and thereby facilitate efficient,
      rational selection of vaccine antigens.
AU  - Tan A
AU  - Atack JM
AU  - Jennings MP
AU  - Seib KL
PT  - Journal Article
TA  - Front. Immunol.
JT  - Front. Immunol.
SO  - Front. Immunol. 2016 7: 586.

PMID- 28546484
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Moraxella catarrhalis Strain CCRI-195ME, Isolated from the Middle Ear.
PG  - e00384-17
AB  - Moraxella catarrhalis is an important bacterial pathogen that causes otitis media and
      exacerbations of chronic obstructive pulmonary disease. Here, we report the
      complete genome sequence of M. catarrhalis strain CCRI-195ME, which contains the
      phase-variable epigenetic regulator ModM3.
AU  - Tan A
AU  - Blakeway LV
AU  - Bakaletz LO
AU  - Boitano M
AU  - Clark TA
AU  - Korlach J
AU  - Jennings MP
AU  - Peak IR
AU  - Seib KL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00384-17.

PMID- 26867950
VI  - 6
DP  - 2016
TI  - Distribution of the type III DNA methyltransferases modA, modB and modD among Neisseria meningitidis genotypes: implications for gene regulation and virulence.
PG  - 21015
AB  - Neisseria meningitidis is a human-specific bacterium that varies in invasive potential. All
      meningococci are carried in the nasopharynx, and most genotypes
      are very infrequently associated with invasive meningococcal disease; however,
      those belonging to the 'hyperinvasive lineages' are more frequently associated
      with sepsis or meningitis. Genome content is highly conserved between carriage
      and disease isolates, and differential gene expression has been proposed as a
      major determinant of the hyperinvasive phenotype. Three phase variable DNA
      methyltransferases (ModA, ModB and ModD), which mediate epigenetic regulation of
      distinct phase variable regulons (phasevarions), have been identified in N.
      meningitidis. Each mod gene has distinct alleles, defined by their Mod DNA
      recognition domain, and these target and methylate different DNA sequences,
      thereby regulating distinct gene sets. Here 211 meningococcal carriage and >1,400
      disease isolates were surveyed for the distribution of meningococcal mod alleles.
      While modA11-12 and modB1-2 were found in most isolates, rarer alleles (e.g.,
      modA15, modB4, modD1-6) were specific to particular genotypes as defined by
      clonal complex. This suggests that phase variable Mod proteins may be associated
      with distinct phenotypes and hence invasive potential of N. meningitidis strains.
AU  - Tan A
AU  - Hill DM
AU  - Harrison OB
AU  - Srikhanta YN
AU  - Jennings MP
AU  - Maiden MC
AU  - Seib KL
PT  - Journal Article
TA  - Sci. Rep.
JT  - Sci. Rep.
SO  - Sci. Rep. 2016 6: 21015.

PMID- 25212628
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Uncultivated Firmicutes (Peptococcaceae SCADC) Single Cells Sorted from Methanogenic Alkane-Degrading Cultures.
PG  - e00909-14
AB  - The draft genome of an uncultivated bacterium affiliated with the Peptococcaceae  was
      reconstructed by co-assembling Illumina MiSeq sequences from three single
      cells sorted by microfluidics from two methanogenic alkane-degrading cultures.
      Peptococcaceae SCADC (short-chain alkane-degrading culture) may be genetically
      capable of anaerobic alkane activation by fumarate addition in the absence of
      sulfate.
AU  - Tan B
AU  - Charchuk R
AU  - Li C
AU  - Nesbo C
AU  - Abu LN
AU  - Foght J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00909-14.

PMID- 25342693
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Three Smithella spp. Obtained from a Methanogenic Alkane-Degrading Culture and Oil Field Produced Water.
PG  - e01085-14
AB  - Two draft genomes affiliated with Smithella spp. were obtained from a methanogenic
      alkane-degrading enrichment culture by single-cell sorting and
      metagenome contig binning, and a third was obtained by single-cell sorting of oil
      field produced water. Two genomes contained putative assABC genes encoding
      alkylsuccinate synthase, indicating genetic potential for fumarate activation of
      alkanes.
AU  - Tan B
AU  - de Araujo ESR
AU  - Rozycki T
AU  - Nesbo C
AU  - Foght J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01085-14.

PMID- 25323712
VI  - 2
DP  - 2014
TI  - Draft genome sequences of campylobacterales (epsilonproteobacteria) obtained from methanogenic oil sands tailings pond metagenomes.
PG  - e01034-14
AB  - Draft genome sequences of two Campylobacterales (Sulfurospirillum sp. strain SCADC and
      Sulfuricurvum sp. strain MLSB [Mildred Lake Settling Basin]) were
      obtained by taxonomic binning of metagenomes originating from an oil sands
      tailings pond. Both genomes contain soxABXYZ genes involved in sulfur oxidation,
      highlighting their potential roles in sulfur cycling in oil sands tailings ponds.
AU  - Tan B
AU  - Foght J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01034-14.

PMID- 27594977
VI  - 11
DP  - 2016
TI  - Insights from the draft genome of the subsection V (Stigonematales) cyanobacterium Hapalosiphon sp. Strain MRB220 associated with 2-MIB production.
PG  - 58
AB  - A non-axenic unialgal culture containing a Subsection V (Stigonematales) cyanobacterium,
      Hapalosiphon strain MRB 220, was obtained from a benthic
      freshwater algal mat through multiple transfers following growth in sterile
      media. Physiological characterization demonstrated the culture was capable of
      nitrogen-fixation and production of the off flavor compound 2-methylisoborneol
      (2-MIB). Total DNA isolated from this culture was sequenced using Illumina HiSeq
      and de novo assembled into contigs. The genome of MRB 220 was separated from
      co-occurring heterotrophic bacteria using sequence homology and compositional
      approaches, and its purity was confirmed based on best BLAST hit classification
      and principle component analysis of the tetranucleotide frequencies of fragmented
      contigs. The genome of ~7.4 Mbp contains 6,345 protein coding genes with 4,320 of
      these having functional prediction including predicted pathways for biosynthesis
      of the secondary metabolite welwitindolinone. Analyses of 16S rRNA gene and whole
      genome sequence average nucleotide identity indicated close relatedness of MRB
      220 to the genera Hapalosiphon and Fischerella within the order Stigonematales.
      Microscopic examination showed that MRB 220 formed heterocystous branched
      filaments, thereby supporting identification of strain MRB 220 as a morphospecies
      of Hapalosiphon. Availability of the draft genome of Hapalosiphon strain MRB 220
      enables future work to elucidate the pathway and dynamics for biosynthesis of
      2-MIB and other secondary metabolites and understand the ecology and physiology
      of Stigonematales cyanobacteria in tropical freshwaters.
AU  - Tan BF
AU  - Te SH
AU  - Boo CY
AU  - Gin KY
AU  - Thompson JR
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 58.

PMID- 27795269
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a Tropical Freshwater Cyanobacterium, Limnothrix sp. Strain P13C2.
PG  - e01117-16
AB  - A nonaxenic unialgal culture of Limnothrix sp. strain P13C2 was obtained through  multiple
      subculturing of an inoculum obtained from a tropical freshwater lake.
      Here, we report the genome of P13C2 of 4.6 Mbp, extracted from the metagenome of
      this coculture.
AU  - Tan BF
AU  - Te SH
AU  - Gin KY
AU  - Thompson JR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01117-16.

PMID- 21742868
VI  - 193
DP  - 2011
TI  - Genome Sequence of Porcine Extraintestinal Pathogenic Escherichia coli strain.
PG  - 5038
AB  - Extraintestinal Pathogenic Escherichia coli is an important pathogen which can infect human
      and animals and causing many diseases outside the
      intestinal. Here, we report the first draft genome sequence of a porcine
      ExPEC strain, PCN033, isolated from the pig with meningitis.
AU  - Tan C
AU  - Xu Z
AU  - Zheng H
AU  - Liu W
AU  - Tang X
AU  - Shou J
AU  - Wu B
AU  - Wang S
AU  - Zhao GP
AU  - Chen H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5038.

PMID- 25301655
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Thermoanaerobacterium saccharolyticum Strain NTOU1, a Thermophilic Bacterium Isolated from Marine Shallow Hydrothermal Vents.
PG  - e01019-14
AB  - Thermoanaerobacterium saccharolyticum strain NTOU1 has the ability to utilize several kinds of
      sugars in lignocellulosic biomass to produce ethanol more
      efficiently than other bacteria. Here, we report the draft genome sequence and
      annotation of this strain, which may provide insights into the possible genes and
      metabolic pathways related to ethanol production.
AU  - Tan E
AU  - Chen Y
AU  - Kuan J
AU  - Lin C
AU  - Jagoda SS
AU  - Lin F
AU  - Tzou W
AU  - Kinoshita S
AU  - Watabe S
AU  - Asakawa S
AU  - Liu S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01019-14.

PMID- 25540339
VI  - 2
DP  - 2014
TI  - Genome Sequence of a Pandrug-Resistant Pseudomonas aeruginosa Strain, YN-1.
PG  - e01280-14
AB  - A highly rampant multidrug-resistant strain of Pseudomonas aeruginosa appeared in a hospital
      in Yunnan Province, China. Here, we report the genome sequence of the
      pandrug-resistant (PDR) P. aeruginosa strain recovered from a patient in 2013.
AU  - Tan HL
AU  - Wang Y
AU  - Cheng XQ
AU  - Huang YM
AU  - Liu W
AU  - Zhang LJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01280-14.

PMID- 25573939
VI  - 3
DP  - 2015
TI  - Genome Sequence of an Extensively Drug-Resistant Strain of Klebsiella pneumoniae, Strain YN-1, with Carbapenem Resistance.
PG  - e01279-14
AB  - The emergence and spread of multidrug-resistant (MDR) Klebsiella pneumoniae has been regarded
      as one of the major challenges among health care-associated
      infections worldwide. Here, we report the draft genome sequence of an extensively
      drug-resistant (XDR) K. pneumoniae strain isolated in 2013 from Yunnan Province,
      China.
AU  - Tan HL
AU  - Wang Y
AU  - Cheng XQ
AU  - Huang YM
AU  - Liu W
AU  - Zhang LJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01279-14.

PMID- 24072861
VI  - 1
DP  - 2013
TI  - First Whole-Genome Sequence of Mycobacterium iranicum, a Newly Reported Mycobacterial Species.
PG  - e00732-13
AB  - Mycobacterium iranicum is a new species of nontuberculous mycobacterium reported  in 2013.
      Here, we describe the first whole-genome sequence of this species, that
      of M. iranicum strain UM_TJL, isolated from a patient in Malaysia.
AU  - Tan JL
AU  - Ng HF
AU  - Wee WY
AU  - Ang MY
AU  - Wong GJ
AU  - Ngeow YF
AU  - Choo SW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00732-13.

PMID- 25075225
VI  - 6
DP  - 2014
TI  - Gene clusters of Hafnia alvei strain FB1 important in survival and pathogenesis: a draft genome perspective.
PG  - 29
AB  - BACKGROUND: Hafnia alvei is an opportunistic pathogen involved in various types of nosocomical
      infections. The species has been found to inhabit food and mammalian guts. However, its status
      as an enteropathogen, and whether the food-inhabiting strains could be a source of
      gastrointestinal infection remains obscure. In this report we present a draft genome of H.
      alvei strain FB1 isolated from fish paste meatball, a food popular among Malaysian and Chinese
      populations.
      The data was generated on the Illumina MiSeq platform. RESULTS: A comparative study was
      carried out on FB1 against two other previously sequenced H. alvei genomes. Several gene
      clusters putatively involved in survival and pathogenesis of H. alvei FB1 in food and gut
      environment were characterised in this study.
      These include the widespread colonisation island (WCI), the tad locus that is known to play an
      essential role in biofilm formation, a eut operon that might contribute to advantage in
      nutrient acquisition in gut environment, and genes responsible for siderophore production This
      features enable the bacteria to successful colonise in the host gut environment. CONCLUSION:
      With the whole genome data of H. alvei FB1 presented in this study, we hope to provide an
      insight into future studies on this candidate of enteropathogen by looking into the possible
      mechanisms employed to survive stresses and gain advantage in competitions, which eventually
      leads to successful colonisation and pathogenesis.
      This is to serve as the basis for more effective clinical diagnosis and treatment.
AU  - Tan JY
AU  - Yin WF
AU  - Chan KG
PT  - Journal Article
TA  - Gut Pathog.
JT  - Gut Pathog.
SO  - Gut Pathog. 2014 6: 29.

PMID- 25657288
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of a Quorum-Sensing Bacterium, Dickeya sp. Strain 2B12, Isolated from a Freshwater Lake.
PG  - e01542-14
AB  - Dickeya sp. strain 2B12 was isolated from a freshwater lake in Malaysia. Here, we report the
      draft genome sequence of Dickeya sp. 2B12 sequenced by the Illumina
      MiSeq platform. With the genome sequence available, this genome sequence will be
      useful for the study of quorum-sensing activity in this isolate.
AU  - Tan KH
AU  - Sheng KY
AU  - Chang CY
AU  - Yin WF
AU  - Chan KG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01542-14.

PMID- 2271591
VI  - 29
DP  - 1990
TI  - Interaction of oligonucleotides containing 6-O-methylguanine with human DNA (cytosine-5-)-methyltransferase.
PG  - 9234-9240
AB  - Thirty-base-pair synthetic oligonucleotide duplexes containing a single meG.C
      (meG=6-O-methylguanine) or A.C base pair at the 16th position (i.e.,
      5'-CCCGTTTAAATATACXTATACCCGGGTACC-3', where X=A or meG) were used to study de
      novo methylation by the purified human DNA (cytosine-5)-methyltransferase
      isolated from CEM cells.  Both duplexes containing meG.C and A.C base pairs
      show enhanced methyl group acceptor properties.  Subsequent introduction of
      hemimethylated sites at the 15th position of the top strand (the C residue next
      to the abnormal base pair) and the 7th, 15th (which represents the C residue in
      the 6meG.C and A.C base pairs), and 27th positions of the bottom strand were
      used to study the maintenance methylation of the hemimethylated duplexes by the
      methylase.  This revealed striking differences in the rate, amount, and sites
      of methylation, which are dependent on the position of the hemimethylated site
      in the duplex.  The possible mechanism of action of the methylase is discussed.
      The data show that 6-O-methylguanine residues in DNA can have other genetic
      effects apart from their miscoding behavior and that meG.C and A.C base pairs
      exert different effects in terms of methylation.
AU  - Tan N-W
AU  - Li FFL
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1990 29: 9234-9240.

PMID- 27231363
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Bacillus subtilis subsp. natto Strain CGMCC 2108, a High Producer of Poly-gamma-Glutamic Acid.
PG  - e00426-16
AB  - Here, we report the 4.1-Mb draft genome sequence of Bacillus subtilis subsp. natto strain
      CGMCC 2108, a high producer of poly-gamma-glutamic acid (gamma-PGA).
      This sequence will provide further help for the biosynthesis of gamma-PGA and
      will greatly facilitate research efforts in metabolic engineering of B. subtilis
      subsp. natto strain CGMCC 2108.
AU  - Tan S
AU  - Meng Y
AU  - Su A
AU  - Zhang C
AU  - Ren Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00426-16.

PMID- 25593254
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Listeria monocytogenes NTSN, a Serovar 4b and Animal  Source Strain.
PG  - e01403-14
AB  - Listeria monocytogenes is an important foodborne pathogen that causes infections  in humans
      and animals and has a high mortality rate. The complete genome sequence
      of L. monocytogenes strain NTSN, a highly virulent and serovar 4b strain isolated
      from the brains of sheep in Jiangsu Province, China, is presented here.
AU  - Tan W
AU  - Wang G
AU  - Pan Z
AU  - Yin Y
AU  - Jiao X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01403-14.

PMID- 15165820
VI  - 323
DP  - 2004
TI  - Comparative genomic analyses of frog virus 3, type species of the genus Ranavirus (family Iridoviridae).
PG  - 70-84
AB  - Frog virus 3 (FV3) is the type species member of the genus Ranavirus (family Iridoviridae). To
      better understand the molecular mechanisms involved in the replication of FV3, including
      transcription of its highly methylated DNA genome, we have determined the complete nucleotide
      sequence of the FV3 genome. The FV3 genome is 105903 bp long excluding the terminal
      redundancy. The G + C content of FV3 genome is 55% and it encodes 98 nonoverlapping potential
      open reading frames (ORFs) containing 50-1293 amino acids. Eighty-four ORFs have significant
      homology to known proteins of other iridoviruses, whereas twelve of these unique FV3 proteins
      do not share homology to any known protein. A microsatellite containing a stretch of 34
      tandemly repeated CA dinucleotide in a noncoding region was detected. To date, no such
      sequence has been reported in any animal virus.
AU  - Tan WGH
AU  - Barkman TJ
AU  - Gregory CV
AU  - Essani K
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 2004 323: 70-84.

PMID- 25635007
VI  - 3
DP  - 2015
TI  - Understanding the Quorum-Sensing Bacterium Pantoea stewartii Strain M009 with Whole-Genome Sequencing Analysis.
PG  - e01509-14
AB  - Pantoea stewartii is known to be the causative agent of Stewart's wilt, which usually affects
      sweet corn (Zea mays) with the corn flea beetle as the
      transmission vector. In this work, we present the whole-genome sequence of
      Pantoea stewartii strain M009, isolated from a Malaysian tropical rainforest
      waterfall.
AU  - Tan WS
AU  - Chang CY
AU  - Yin WF
AU  - Chan KG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01509-14.

PMID- 25555739
VI  - 3
DP  - 2015
TI  - Insights into the Quorum-Sensing Activity in Aeromonas hydrophila Strain M013 as  Revealed by Whole-Genome Sequencing.
PG  - e01372-14
AB  - Aeromonas hydrophila species can be found in warm climates and can survive in different
      environments. They possess the ability to communicate within their
      populations, which is known as quorum sensing. In this work, we present the draft
      genome sequence of A. hydrophila M013, a bacterium isolated from a Malaysian
      tropical rainforest waterfall.
AU  - Tan WS
AU  - Yin WF
AU  - Chan KG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01372-14.

PMID- 25700404
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequencing Analysis of Quorum-Sensing Aeromonas hydrophila Strain M023 from Freshwater.
PG  - e01548-14
AB  - Aeromonas hydrophila is a well-known waterborne pathogen that recently was found to infect
      humans. Here, we report the draft genome of a freshwater isolate from a Malaysian waterfall,
      A. hydrophila strain M023, which portrays N-acylhomoserine lactone-dependent quorum sensing.
AU  - Tan WS
AU  - Yin WF
AU  - Chang CY
AU  - Chan KG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01548-14.

PMID- 29748407
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of 'Candidatus Phycosocius bacilliformis,' an Alphaproteobacterial Ectosymbiont of the Hydrocarbon-Producing Green Alga  Botryococcus braunii.
PG  - e00396-18
AB  - 'Candidatus Phycosocius bacilliformis' is an alphaproteobacterial ectosymbiont of the
      hydrocarbon-producing green alga Botryococcus braunii We sequenced the whole
      genome of 'Ca. P. bacilliformis' BOTRYCO-2, isolated from a two-membered culture
      with B. braunii The genome contains approximately 3.3 Mb, with an average G+C
      content of 56.91% and 3,125 predicted protein-coding genes.
AU  - Tanabe Y
AU  - Yamaguchi H
AU  - Watanabe MM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00396-18.

PMID- 27856598
VI  - 4
DP  - 2016
TI  - Genome Sequence of Formosa haliotis Strain MA1, a Brown Alga-Degrading Bacterium  Isolated from the Gut of Abalone Haliotis gigantea.
PG  - e01312-16
AB  - Formosa haliotis is a brown alga-degrading bacterium isolated from the gut of abalone Haliotis
      gigantea Here, we report the draft genome sequence of this
      bacterium and pointed out possible important features related to alginate
      degradation.
AU  - Tanaka R
AU  - Mizutani Y
AU  - Shibata T
AU  - Miyake H
AU  - Iehata S
AU  - Mori T
AU  - Kuroda K
AU  - Ueda M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01312-16.

PMID- 117281
VI  - 175
DP  - 1979
TI  - Restriction of plasmid-mediated transformation in Bacillus subtilis 168.
PG  - 235-237
AB  - When plasmids carrying leucine genes of Bacillus subtilis 168 were isolated
      from a restriction and modification deficient (r-m-) strain and used for
      transformation of a restricting strain B. subtilis 168 leu recE4, the number of
      transformants was greatly reduced.  Transformation of a rec+ strain
      (transformation by integration of the donor DNA into the chromosome) with the
      plasmids was not affected irrespective of whether the recipient carried the r+
      or r- phenotype.  These results show that the plasmid-mediated transformation
      is subject to the host controlled restriction and suggest that r-m- strains
      should be used for construction of recombinant DNA molecules in B. subtilis
      168.
AU  - Tanaka T
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1979 175: 235-237.

PMID- Not carried by PubMed...
VI  - 0
DP  - 1987
TI  - Advances in cyanobacterial molecular genetics.
PG  - 251-302
AB  - Until recently, the development of cyanobacteial genetics was limited by our
      inability to transfer genetic material, both within a given species and between
      different cyanobacterial species.  About 300 cyanobacterial strains have been
      isolated as axenic cultures but less than 10, all unicellular species, have
      been shown to be transformable by DNA.  Moreover, while specific
      cyanobacteriophages have been described, gene transduction has not yet been
      demonstrated.  Molecular genetics offers new possibilities for studying various
      properties of cyanobacteria, such as oxygenic photosynthesis, aerobic and
      anaerobic nitrogen fixation, light-regulated gene expression and cell
      differentiation, properties for which biochemical and physiological data are
      already available.  An increasing number of laboratories are now studying this
      widespread and very large group of microorganisms using such genetic
      approaches.  Recent reports that conjugation can occur in Anabaena/Nostoc
      strains pave the way for the transfer of genetic material among filamentous
      cyanobacteria and strengthen the work already initiated in order to understand,
      at the molecular level, the important processes mentioned above.  We will
      review current knowledge on cyanobacterial plasmids and restriction enzymes,
      such data being of special interest for both molecular genetics and the
      development of DNA transfer systems, and we will describe which cyanobacterial
      genes have been cloned and characterized.  Finally, we will present some of the
      features which have emerged from both sequence data and gene expression
      experiments in homologous and/or heterologous hosts, as well as the
      methodological approaches used.
AU  - Tandeau de Marsac N
AU  - Houmard J
PT  - Journal Article
TA  - Cyanobacteria
JT  - Cyanobacteria
SO  - Cyanobacteria 1987 0: 251-302.

PMID- 29439049
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Endozoicomonas acroporae Strain Acr-14(T), Isolated from Acropora Coral.
PG  - e01576-17
AB  - A lacuna exists in our understanding of the genetic makeup of Endozoicomonas bacteria, due to
      scarcity of genome sequences. We report here the first draft
      genome sequence of Endozoicomonas acroporae Acr-14, a type strain isolated from
      the coral Acropora This sequence will foster an understanding of the genetic
      makeup and role of hosts in shaping gene repertoires.
AU  - Tandon K
AU  - Chiang PW
AU  - Chen WM
AU  - Tang SL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01576-17.

PMID- 16580669
VI  - 580
DP  - 2006
TI  - Molecular nature of methicillin-resistant Staphylococcus aureus derived from explosive nosocomial outbreaks of the 1980s in Japan.
PG  - 2323-2334
AB  - Community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA)
      with Panton-Valentine leukocidin (PVL) genes is increasing worldwide.
      Nosocomial outbreak-derived (hospital-acquired) MRSA (HA-MRSA) in Japan in
      the 1980s was also largely PVL(+). PVL(+) HA-MRSA and CA-MRSA shared the
      same multi-locus sequence type (ST30) and methicillin resistance cassette
      (SCCmecIV), but were divergent in oxacillin resistance, spa typing, PFGE
      analysis or clfA gene analysis. PVL(+) HA-MRSA, which probably originated
      in PVL(+)S. aureus ST30, was highly adhesive (carrying cna and bbp genes),
      highly-toxic (carrying luk(PV) and sea genes) and highly drug-resistant.
      PVL(+) HA-MRSA was once replaced by other PVL(-) HA-MRSA (e.g., ST5), and
      is re-emerging as CA-MRSA.
AU  - Taneike I
AU  - Otsuka T
AU  - Dohmae S
AU  - Saito K
AU  - Ozaki K
AU  - Takano M
AU  - Higuchi W
AU  - Takano T
AU  - Yamamoto T
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 2006 580: 2323-2334.

PMID- 23627759
VI  - 14
DP  - 2013
TI  - ContigScape: a Cytoscape plugin facilitating microbial genome gap closing.
PG  - 289
AB  - BACKGROUND: With the emergence of next-generation sequencing, the availability of
      prokaryotic genome sequences is expanding rapidly. A total of 5,276 genomes have
      been released since 2008, yet only 1,692 genomes were complete. The final phase
      of microbial genome sequencing, particularly gap closing, is frequently the
      rate-limiting step either because of complex genomic structures that cause
      sequence bias even with high genomic coverage, or the presence of repeat
      sequences that may cause gaps in assembly. RESULTS: We have developed a Cytoscape
      plugin to facilitate gap closing for high-throughput sequencing data from
      microbial genomes. This plugin is capable of interactively displaying the
      relationships among genomic contigs derived from various sequencing formats. The
      sequence contigs of plasmids and special repeats (IS elements, ribosomal RNAs,
      terminal repeats, etc.) can be displayed as well. CONCLUSIONS: Displaying
      relationships between contigs using graphs in Cytoscape rather than tables
      provides a more straightforward visual representation. This will facilitate a
      faster and more precise determination of the linkages among contigs and greatly
      improve the efficiency of gap closing.
AU  - Tang B
AU  - Wang Q
AU  - Yang M
AU  - Xie F
AU  - Zhu Y
AU  - Zhuo Y
AU  - Wang S
AU  - Gao H
AU  - Ding X
AU  - Zhang L
AU  - Zhao G
AU  - Zheng H
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2013 14: 289.

PMID- 26514767
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Streptothricin-Producing Strain Streptomyces sp. fd2-tb.
PG  - e01277-15
AB  - Streptomyces sp. fd2-tb can produce streptothricin class antibiotics with broad antimicrobial
      spectra. To better understand the mechanism of streptothricin
      biosynthesis and to assess the capacity of this strain in secondary metabolism,
      we report the draft genome sequence of Streptomyces sp. strain fd2-tb.
AU  - Tang B
AU  - Yu Y
AU  - Cen X
AU  - Zhu Y
AU  - Dai R
AU  - Wang X
AU  - Zhao G
AU  - Ding X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01277-15.

PMID- 23012281
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Amycolatopsis mediterranei S699 Based on De Novo Assembly via a Combinatorial Sequencing Strategy.
PG  - 5699-5700
AB  - The genome of Amycolatopsis mediterranei S699 was resequenced and assembled de novo. By
      comparing the sequences of S699 previously released and that of A.
      mediterranei U32, about 10 kb of major indels was found to differ between the two
      S699 genomes, and the differences are likely attributable to their different
      assembly strategies.
AU  - Tang B
AU  - Zhao W
AU  - Zheng H
AU  - Zhuo Y
AU  - Zhang L
AU  - Zhao GP
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5699-5700.

PMID- 29853496
VI  - 6
DP  - 2018
TI  - Complete Genomic Sequence of Pseudoalteromonas sp. Strain SAO4-4, a Protease-Producing Bacterium Isolated from Seawater of the Atlantic Ocean.
PG  - e00284-18
AB  - The complete genome of Pseudoalteromonas sp. strain SAO4-4, a protease-producing  bacterium
      from seawater, is composed of two circular chromosomes and one plasmid.
      This genome sequence will provide a better understanding of the ecological roles
      of protease-producing bacteria in the degradation of organic matter in marine
      aquatic environments.
AU  - Tang BL
AU  - Rong JC
AU  - Dang YR
AU  - Xie BB
AU  - Chen XL
AU  - Zhang XY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00284-18.

PMID- 10810160
VI  - 13
DP  - 2000
TI  - Mutational analyses of restriction endonuclease-HindIII mutant E86K with higher activity and altered specificity.
PG  - 283-289
AB  - We have performed mutational analyses of restriction endonuclease HindIII in order to identify
      the amino acid residues responsible for enzyme activity. Four of the seven HindIII mutants,
      which had His-tag sequences at the N-termini, were expressed in Escherichia coli, and purified
      to homogeneity. The His-tag sequence did not affect enzyme activity, whereas it hindered
      binding of the DNA probe in gel retardation assays. A mutant E86K in which Lys was substituted
      for Glu at residue 86 exhibited high endonuclease activity. Gel retardation assays showed high
      affinity of this mutant to the DNA probe. Surprisingly, in the presence of a transition metal,
      Mo(2+) or Mn(2+), the E86K mutant cleaved substrate DNA at a site other than HindIII.
      Substitution of Glu for Val at residue 106 (V106E), and Asn for Lys at residue 125 (K125N)
      resulted in a decrease in both endonucleolytic and DNA binding activities of the enzyme.
      Furthermore, substitution of Leu for Asp at residue 108 (D108L) abolished both HindIII
      endonuclease and DNA binding activities. CD spectra of the wild type and the two mutants, E86K
      and D108L, were similar to each other, suggesting that there was little change in conformation
      as a result of the mutations. These results account for the notion that Asp108 could be
      directly involved in HindIII catalytic function, and that the substitution at residue 86 may
      bring about new interactions between DNA and cations.
AU  - Tang D
AU  - Ando S
AU  - Takasaki Y
AU  - Tadano J
PT  - Journal Article
TA  - Protein Eng.
JT  - Protein Eng.
SO  - Protein Eng. 2000 13: 283-289.

PMID- 28839015
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Pacificimonas aurantium Type Strain JLT2012, Isolated from the Seawater of the Pacific Ocean.
PG  - e00755-17
AB  - Type strain JLT2012 was isolated from the southeastern Pacific. Here, we report the draft
      genome sequence and the initial findings from a preliminary analysis of
      strain JLT2012, which represents a novel species and should be classified in the
      existing genus Pacificimonas.
AU  - Tang G
AU  - Cui R
AU  - Tian Y
AU  - Lin X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00755-17.

PMID- 22072645
VI  - 193
DP  - 2011
TI  - Genome Sequence of Pseudomonas putida Strain B6-2, a Superdegrader of Polycyclic Aromatic Hydrocarbons and Dioxin-Like Compounds.
PG  - 6789-6790
AB  - Pseudomonas putida strain B6-2 can efficiently degrade environmental pollutants/toxicants,
      such as polycyclic aromatic hydrocarbons and
      dioxin-like compounds, and has unique tolerance to organic solvents. Here,
      we present a 6.24-Mb draft genome sequence of B6-2, which could provide
      further insights into the biodegradative mechanisms of a diverse range of
      chemical compounds.
AU  - Tang H
AU  - Yu H
AU  - Li Q
AU  - Wang X
AU  - Gai Z
AU  - Yin G
AU  - Su F
AU  - Tao F
AU  - Ma C
AU  - Xu P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6789-6790.

PMID- 22689240
VI  - 194
DP  - 2012
TI  - Genome Sequence of a Novel Nicotine-Degrading Strain, Pseudomonas geniculata N1.
PG  - 3553-3554
AB  - A newly isolated bacterium, Pseudomonas geniculata N1, can efficiently degrade nicotine. Here
      we present a 4.51-Mb assembly of its genome, which is the first
      sequence of the P. geniculata group. The sequence contains the genes related to
      nicotine catabolism and may provide insights into its molecular mechanism for
      N-heterocyclic degradation.
AU  - Tang H
AU  - Yu H
AU  - Tai C
AU  - Huang K
AU  - Liu Y
AU  - Wang L
AU  - Yao Y
AU  - Wu G
AU  - Xu P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3553-3554.

PMID- 25687447
VI  - 99
DP  - 2015
TI  - Genome sequence and genome mining of a marine-derived antifungal bacterium Streptomyces sp. M10.
PG  - 2763-2772
AB  - A marine-derived actinobacteria Streptomyces sp. M10 was identified as a prolific
      antifungal compounds producer and shared a 99.02 % 16S ribosomal RNA (rRNA)
      sequence similarity with that of Streptomyces marokkonensis Ap1(T), which can
      produce polyene macrolides. To further evaluate its biosynthetic potential, the
      7,207,169 bp Streptomyces sp. M10 linear chromosome was sequenced and mined for
      identifiable secondary metabolite-associated gene clusters. A total of 20
      secondary metabolite-associated gene clusters were deduced, including three
      polyketide synthases (PKSs), four non-ribosomal peptide synthetases (NRPSs), four
      hybrid NRPS-PKSs, three NRPS-independent siderophores, and two lantibiotic and
      four terpene biosynthetic gene clusters. One of the type I PKS gene cluster,
      pks1, shared a 85 % nucleotide similarity with candicidin/FR008 gene cluster,
      indicating the capacity of this organism to produce polyene macrolides. This
      assumption was verified by a scale-up culturing of Streptomyces sp. M10 on A1
      agar plates, which lead to the isolation of two polyene families PF1 and PF2,
      with characteristic UV adsorption at 269, 278, and 290 nm (PF1) and 363, 386, and
      408 nm (PF2), respectively. Compound 9-04 was further purified from PF1, and its
      chemical structure was partially elucidated to be a typical polyene macrolide by
      NMR and UV spectrum. This study affirmatively identified Streptomyces sp. M10 as
      a source of polyene metabolites and highlighted genome mining of interested
      organism as a powerful tool for natural product discovery.
AU  - Tang J
AU  - Liu X
AU  - Peng J
AU  - Tang Y
AU  - Zhang Y
PT  - Journal Article
TA  - Appl. Microbiol. Biotechnol.
JT  - Appl. Microbiol. Biotechnol.
SO  - Appl. Microbiol. Biotechnol. 2015 99: 2763-2772.

PMID- 24356831
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Exiguobacterium sp. Strain MH3, Isolated from Rhizosphere of Lemna minor.
PG  - e01059-13
AB  - We report the complete genome sequence of Exiguobacterium sp. strain MH3, isolated from the
      rhizosphere of duckweed. The genome assembly is 3.16 Mb, with a
      G+C content of 47.24%, and it may provide useful information about plant-microbe
      interactions and the genetic basis for the tolerance of the strain to various
      environmental stresses.
AU  - Tang J
AU  - Zhang Y
AU  - Meng H
AU  - Xue Z
AU  - Ma J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01059-13.

PMID- 8155898
VI  - 8
DP  - 1994
TI  - Matrix-assisted laser desorption/ionization of restriction enzyme-digested DNA.
PG  - 183-186
AB  - Matrix-assisted laser desorption/ionization, by a time-of-flight mass spectrometer, has been
      successfully used for detection of restriction enzyme-digested DNA. However, the
      oligonucleotide segments detected correspond to the molecular weights of single strands.
AU  - Tang K
AU  - Allman SL
AU  - Chen CH
AU  - Chang LY
AU  - Schell M
PT  - Journal Article
TA  - Rapid Commun. Mass. Spectrom.
JT  - Rapid Commun. Mass. Spectrom.
SO  - Rapid Commun. Mass. Spectrom. 1994 8: 183-186.

PMID- 23144420
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Oceaniovalibus guishaninsula JLT2003T.
PG  - 6683
AB  - Oceaniovalibus guishaninsula, as a representative of a new genus within the family
      Rhodobacteraceae, was isolated from surface seawater that was sulfidic.
      Here, we present the draft genome sequence of the type strain, JLT2003(T).
AU  - Tang K
AU  - Liu K
AU  - Jiao N
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6683.

PMID- 23661488
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Strain JLT2015T, Belonging to the Family Sphingomonadaceae of the Alphaproteobacteria.
PG  - e00226-13
AB  - Strain JLT2015(T) was isolated from the southeastern Pacific, as a representative of a new
      genus of the family Sphingomonadaceae of the Alphaproteobacteria. Here,
      we present the draft genome sequence of strain JLT2015(T), which provides insight
      into the oligotrophic strategy of this organism.
AU  - Tang K
AU  - Liu K
AU  - Li S
AU  - Jiao N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00226-13.

PMID- 12819212
VI  - 278
DP  - 2003
TI  - The eukaryotic DNMT2 genes encode a new class of cytosine-5 DNA methyltransferases.
PG  - 33613-33616
AB  - DNMT2 is a subgroup of the eukaryotic cytosine-5 DNA methyltransferase gene family. Unlike the
      other family members, proteins encoded by DNMT2
      genes were not known before to possess DNA methyltransferase activities.
      Most recently, we have shown that the genome of Drosophila S2 cells stably
      expressing an exogenous Drosophila dDNMT2 cDNA became anomalously
      methylated at the 5'-positions of cytosines (Reddy, M. N., Tang, L. Y.,
      Lee, T. L., and Shen, C.-K. J. (2003) Oncogene, in press). We present
      evidence here that the genomes of transgenic flies overexpressing the
      dDnmt2 protein also became hypermethylated at specific regions.
      Furthermore, transient transfection studies in combination with sodium
      bisulfite sequencing demonstrated that dDnmt2 as well as its mouse
      ortholog, mDnmt2, are capable of methylating a cotransfected plasmid DNA.
      These data provide solid evidence that the fly and mouse DNMT2 gene
      products are genuine cytosine-5 DNA methyltransferases.
AU  - Tang LY
AU  - Reddy MN
AU  - Rasheva V
AU  - Lee TL
AU  - Lin MJ
AU  - Hung MS
AU  - Shen CK
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2003 278: 33613-33616.

PMID- 24356833
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Bacteroidales Strain CF from a Chloroform-Dechlorinating Enrichment Culture.
PG  - e01066-13
AB  - Bacteroidales strain CF is the most abundant nondechlorinating organism in a
      Dehalobacter-containing enrichment culture that consistently reductively
      dechlorinates >50 mg/liter chloroform or 1,1,1-trichloroethane (methyl
      chloroform). We assembled and closed the complete genome sequence of this
      organism from the metagenomic sequencing data for enrichment cultures. This
      organism is predicted to ferment l-lactate and ethanol.
AU  - Tang S
AU  - Edwards EA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01066-13.

PMID- 11967086
VI  - 44
DP  - 2002
TI  - HF2: a double-stranded DNA tailed haloarchaeal virus with a mosaic genome.
PG  - 283-296
AB  - HF2 is a haloarchaeal virus infecting two Halorubrum species (Family Halobacteriaceae). It is
      lytic, has a head-and-tail morphology and belongs
      to the Myoviridae (contractile tails). The linear double-stranded DNA
      genome was sequenced and found to be 77 670 bp in length, with a mol% G+C
      of 55.8. A total of 121 likely open reading frames (ORFs) were identified,
      of which 37 overlapped at start and stop codons. The predicted proteins
      were usually acidic (average pI of 4.8), and less than about 12% of them
      had homologues in the sequence databases. Four complete tRNA-like
      sequences (tRNA-Arg, -Asx, -Pro and -Tyr) and an incomplete tRNA-Thr were
      detected. A transcription map showed that most of the genome was
      transcribed and that the synthesis of transcripts occurred in a highly
      organized and reproducible pattern over a 5 h infection cycle. Transcripts
      often spanned multiple ORFs, suggesting that viral genes were organized
      into operons. The predicted ORF and observed transcript directions matched
      well and showed that transcription is mainly directed inwards from the
      genome termini, meeting at about 45-48 kb, and this was also a turning
      point in a cumulative GC-skew plot. The low point in cumulative GC-skew,
      near the left end, was a region rich in short repeats and lacking ORFs,
      which is likely to be an origin of replication. The HF2 genome is a mosaic
      of components from widely different sources, demonstrating clearly that
      viruses of haloarchaea, like their bacteriophage counterparts, are vectors
      for the exchange and transmission of genetic material between wide
      taxonomic distances, even across domains.
AU  - Tang SL
AU  - Nuttall S
AU  - Ngui K
AU  - Fisher C
AU  - Lopez P
AU  - Dyall-Smith M
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2002 44: 283-296.

PMID- 25953182
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of a Phthalate Ester-Degrading Bacterium, Rhizobium sp. LMB-1, Isolated from Cultured Soil.
PG  - e00392-15
AB  - Rhizobium sp. LMB-1, newly isolated from greenhouse soil, can effectively degrade phthalate.
      Here, we present a 5.2-Mb assembly of this Rhizobium sp. genome for
      the first time. It may provide abundant molecular information for the
      transformation of phthalates.
AU  - Tang WJ
AU  - Zhou Y
AU  - Ye BC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00392-15.

PMID- 25858842
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Methylobacterium aquaticum Strain 22A, Isolated from  Racomitrium japonicum Moss.
PG  - e00266-15
AB  - Methylobacterium species colonize plant surfaces and utilize methanol emitted from plants.
      Methylobacterium aquaticum strain 22A was isolated from a hydroponic
      culture of a moss, Racomitrium japonicum, and is a potent plant growth promoter.
      The complete genome sequencing of the strain confirmed the presence of genes
      related to plant growth promotion and methylotrophy.
AU  - Tani A
AU  - Ogura Y
AU  - Hayashi T
AU  - Kimbara K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00266-15.

PMID- 
VI  - 87
DP  - 2018
TI  - Diffusely adherent Escherichia coli strains isolated from healthy carriers suppress cytokine secretions of epithelial cells stimulated by inflammatory substances.
PG  - 0
AB  - Diarrheagenicity of diffusely adherent Escherichia coli (DAEC) remains controversial.
      Previously, we found that motile DAEC strains isolated from diarrheal patients induced high
      levels of interleukin 8 (IL-8) secretion via Toll-like receptor 5 (TLR5). However, DAEC
      strains from healthy carriers hardly induced IL-8 secretion, irrespective of their possessing
      flagella.  In this study, we demonstrated that SK1144, a DAEC strain from a healthy carrier,
      suppressed IL-8 and IL-6 secretion from human epithelial cell lines. Suppression of IL-8 in
      human embryonic kidney (HEK293) cells that were transformed to express TLR5 was observed not
      only upon inflammatory stimulation by flagellin but also in response to tumor necrosis
      factor-alpha (TNF- and #945;) and phorbol myristate acetate(PMA), despite the fact that the
      TNF- and #945;- and PMA-induced inflammatory pathways reportedly are not TLR5-mediated. SK1144
      neither decreased IL-8 transcript accumulation nor increased intracellular retention of IL-8.
      No suppression was observed when the bacteria were cultured in Transwell cups above the
      epithelial cells; however, a non-adherent bacterial mutant (lacking the afimbrial adhesin
      gene) still inhibited IL-8 secretion. Direct contact between the bacteria and epithelial cells
      was necessary, but diffuse adhesion was dispensable for the inhibitory effects.  Infection in
      the presence of chloramphenicol did not suppress cytokine release by the epithelial cells,
      suggesting that suppression depended on effectors synthesized de novo.  Inflammatory
      suppression was attenuated with infection by a bacterial mutant deleted for hcp (encoding
      a component of a type-VI secretion system). In conclusion, DAEC strains from healthy carriers
      impede epithelial cell cytokine secretion, possibly by interfering with translation via the
      type-VI secretion system.
AU  - Tanimoto Y
AU  - Tamai S
AU  - Matsuzaki T
AU  - Takeuchi N
AU  - Noju T
AU  - Yanagida S
AU  - Kage-Nakadai E
AU  - Yamaguchi Y
AU  - Kodama T
AU  - Nakamura S
AU  - Motooka D
AU  - Iida T
AU  - Nishikawa Y
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2018 87: 0.

PMID- 25169865
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Lactobacillus oryzae Strain SG293T.
PG  - e00861-14
AB  - We report the 1.86-Mb draft genome and annotation of Lactobacillus oryzae SG293(T) isolated
      from fermented rice grains. This genome information may provide
      further insights into the mechanisms underlying the fermentation of rice grains.
AU  - Tanizawa Y
AU  - Fujisawa T
AU  - Mochizuki T
AU  - Kaminuma E
AU  - Nakamura Y
AU  - Tohno M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00861-14.

PMID- 25013139
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Weissella oryzae SG25T, Isolated from Fermented Rice Grains.
PG  - e00667-14
AB  - Weissella oryzae was originally isolated from fermented rice grains. Here we report the draft
      genome sequence of the type strain of W. oryzae. This first
      report on the genomic sequence of this species may help identify the mechanisms
      underlying bacterial adaptation to the ecological niche of fermented rice grains.
AU  - Tanizawa Y
AU  - Fujisawa T
AU  - Mochizuki T
AU  - Kaminuma E
AU  - Suzuki Y
AU  - Nakamura Y
AU  - Tohno M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00667-14.

PMID- 28619803
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of the Photoautotrophic and Bacteriochlorophyll e-Synthesizing Green Sulfur Bacterium Chlorobaculum limnaeum DSM 1677T.
PG  - e00529-17
AB  - Chlorobaculum limnaeum DSM 1677T is a mesophilic, brown-colored, chlorophototrophic green
      sulfur bacterium that produces bacteriochlorophyll e and
      the carotenoid isorenieratene as major pigments. This bacterium serves as a model
      organism in molecular research on photosynthesis, sulfur metabolism, and
      bacteriochlorophyll biosynthesis. We report here the complete genome sequence.
AU  - Tank M
AU  - Liu Z
AU  - Frigaard NU
AU  - Tomsho LP
AU  - Schuster SC
AU  - Bryant DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00529-17.

PMID- 1086198
VI  - 231
DP  - 1976
TI  - New endonuclease Hind GLU in Haemophilus influenzae Rd123.
PG  - 226-228
AB  - None
AU  - Tanyashin VI
AU  - Li LI
AU  - Muijnieks IO
AU  - Baev AA
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1976 231: 226-228.

PMID- 12942776
VI  - 39
DP  - 2003
TI  - Transduction of plasmid antibiotic resistance determinants with pseudoT-even bacteriophages.
PG  - 914-926
AB  - Transduction of antibiotic resistance determinants of the plasmid pBR322 with pseudoT-even
      bacteriophages RB42, RB43, and RB49 was
      studied. It is established that antibiotic resistance determinants of
      plasmid pBR322 from Escherichia coli recA(+) and recA(-) donor strains
      do not differ significantly in respect to the efficiency of
      transduction. Amber mutants RB43-21, RB43-33, and a double amber mutant
      RB43am21am33 were obtained. These mutants facilitated transduction
      experiments in some cases. Transduction of antibiotic resistance
      markers of the vector plasmid pBR325 and recombinant plasmid pVT123,
      containing a DNA fragment with hoc-segE-uvsW genes of phage T4, was
      studied. The frequency of appearance of transductants resistant to
      pseudoT-even bacteriophages used in transduction was determined, and
      the sensitivity of resistant transductants to 32 RB bacteriophages and
      also to phages lambda, T2, T4, T5, T6, T7, and BF23 was estimated. The
      efficiency of plating pseudoT-even bacteriophages RB42 and RB43 on
      strain E. coli 802 himA hip carrying mutations in genes that encode
      subunits of the Integration Host Factor (IHF) was shown to be higher
      than on isogenic strain E. coli 802. The growth of pseudoT-even
      bacteriophages limited in vivo by modification - restriction systems of
      chromosomal (EcoKI, EcoBI), phage ( EcoP1I), and plasmid (EcoRI,
      EcoR124I, and EcoR124II) localization was analyzed. It was shown that
      these phages were only slightly restricted by the type I modification -
      restriction systems EcoBI, EcoR124I, and EcoR124II. Phage RB42 was
      restricted by systems EcoKI, EcoP1I, and EcoRI; phage RB43, by
      systems EcoKI and EcoRI; and phage RB49, by the Eco RI modification -
      restriction system.
AU  - Tanyashin VI
AU  - Zimin AA
AU  - Shlyapnikov MG
AU  - Boronin AM
PT  - Journal Article
TA  - Genetika
JT  - Genetika
SO  - Genetika 2003 39: 914-926.

PMID- 23045497
VI  - 194
DP  - 2012
TI  - Genome Sequence of Pseudomonas putida S12, a Potential Platform Strain for Industrial Production of Valuable Chemicals.
PG  - 5985-5986
AB  - Pseudomonas putida strain S12, a well-studied solvent-tolerant bacterium, is considered a
      platform strain for the production of many chemicals. Here, we
      present a 6.28-Mb assembly of its genome sequence. We have annotated 32 coding
      sequences (CDSs) encoding efflux systems of organic compounds and 195 CDSs
      responsible for the metabolism of aromatic compounds.
AU  - Tao F
AU  - Shen Y
AU  - Fan Z
AU  - Tang H
AU  - Xu P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5985-5986.

PMID- 22843590
VI  - 194
DP  - 2012
TI  - Genome Sequence of Klebsiella pneumoniae LZ, a Potential Platform Strain for 1,3-Propanediol Production.
PG  - 4457-4458
AB  - Klebsiella pneumoniae LZ is a bacterium isolated from soil which can produce 1,3-propanediol
      from glycerol. Here we present a 5,431,750-bp assembly of its
      genome sequence. We annotated 9 coding sequences (CDSs) responsible for glycerol
      fermentation to 1,3-propanediol, 19 CDSs encoding glycerol utilization, and 134
      CDSs related to its virulence and defense.
AU  - Tao F
AU  - Tai C
AU  - Liu Z
AU  - Wang A
AU  - Wang Y
AU  - Li L
AU  - Gao C
AU  - Ma C
AU  - Xu P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4457-4458.

PMID- 22123764
VI  - 193
DP  - 2011
TI  - Genome Sequence of Pseudomonas putida Idaho, a Unique Organic-Solvent-Tolerant Bacterium.
PG  - 7011-7012
AB  - Pseudomonas putida Idaho is an organic-solvent-tolerant strain which can degrade and adapt to
      high concentrations of organic solvents. Here, we
      announce its first draft genome sequence (6,363,067 bp). We annotated 192
      coding sequences (CDSs) responsible for aromatic compound metabolism, 40
      CDSs encoding phospholipid synthesis, and 212 CDSs related to stress
      response.
AU  - Tao F
AU  - Tang H
AU  - Gai Z
AU  - Su F
AU  - Wang X
AU  - He X
AU  - Xu P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 7011-7012.

PMID- 22887662
VI  - 194
DP  - 2012
TI  - Genome Sequence of Xanthomonas campestris JX, an Industrially Productive Strain for Xanthan Gum.
PG  - 4755-4756
AB  - Xanthomonas campestris JX, a soil bacterium, is an industrially productive strain for xanthan
      gum. Here we present a 5.0-Mb assembly of its genome sequence. We
      have annotated 12 coding sequences (CDSs) responsible for xanthan gum
      biosynthesis, 346 CDSs encoding carbohydrate metabolism, and 69 CDSs related to
      virulence, defense, and plant disease.
AU  - Tao F
AU  - Wang X
AU  - Ma C
AU  - Yang C
AU  - Tang H
AU  - Gai Z
AU  - Xu P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4755-4756.

PMID- 22038975
VI  - 193
DP  - 2011
TI  - Genome Sequence of Rhodococcus erythropolis XP, a Biodesulfurizing Bacterium with Industrial Potential.
PG  - 6422-6423
AB  - Rhodococcus erythropolis strains have shown excellent characteristics in petroleum oil
      biodesulfurization. Here we present the first announcement
      of the draft genome sequence of an efficient biodesulfurizing bacterium
      named R. erythropolis XP (7,229,582 bp). The biodesulfurizing genes dszABC
      are located on a plasmid, while the flavin reductase gene dszD is located
      on the chromosome.
AU  - Tao F
AU  - Zhao P
AU  - Li Q
AU  - Su F
AU  - Yu B
AU  - Ma C
AU  - Tang H
AU  - Tai C
AU  - Wu G
AU  - Xu P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6422-6423.

PMID- Not carried by PubMed...
VI  - 53
DP  - 1992
TI  - Characterization of the cloned PvuII type II restriction-modification system in Escherichia coli.
PG  - 115B
AB  - The PvuII type II restriction-modification system (RMS2) cloned from Proteus vulgaris has been
      sequenced in full and characterized in Escherichia coli. The sequence of pvuIIM showed that
      this N4-methylcytosine (N4mC) generating DNA methyltransferase (MTase) is similar to
      N6-methyladenine (N6mA) DNA MTases. Newly available data on other N4mC MTases support this
      observation. Together with the known DNA structural data, this strongly suggests that these
      two groups of DNA amino MTases are functionally and possibly evolutionarily related. It was
      also found that M.PvuII contains an internal homology so far unique among type II DNA MTases.
      Each homologous part includes its own DPPY and F/GXGXG motifs, which are sequences common to
      all DNA amino MTases. Hypotheses for this homology were proposed. R.PvuII was shown to be a
      homodimer. A segment of R.PvuII was found to be similar to R.BamHI at the amino acid sequence
      level. The importance of this similarity is not known, but such similarities are very rare
      among the sequenced endonuclease genes. A third open reading frame (ORF), 84 codons in length
      with potential transcription and translation elements, was found to be associated with this
      RMS2. Sequence comparison has revealed strong homology between this ORF and that of bacterial
      and bacterial phage repressors. Genetic assays on this ORF showed that mutations introduced
      into this ORF resulted in the reduction of R.PvuII production up to a 10/5-fold in vivo. This
      effect could be complemented by providing the third ORF in trans. The third ORF was named
      pvuIIC (for controller). Further experiments showed that a product of the expected size was
      indeed made by pvuIIC both in vivo and in vitro. The pvuIIC product, C.PvuII, was shown to
      bind to DNA, either alone or with other proteins. The binding site responsible for pvuIIR
      regulation was narrowed down to a 70 bp fragment upstream of pvuIIR by deletion analysis. The
      binding specificity has not yet been defined in vitro. A regulatory mechanism incorporating
      these findings was hypothesized and further experiments to test the hypotheses discussed.
AU  - Tao T
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1992 53: 115B.

PMID- Not carried by PubMed...
VI  - 91
DP  - 1991
TI  - Sequence and subunit structure of restriction endonuclease PvuII.
PG  - 175
AB  - We have determined the DNA base sequence of the pvuIIR gene and the subunit
      structure of its protein product.  The pvuIIR gene codes for a type II
      restriction endonuclease, PvuII, which cleaves the sequence 5'-CAGCTG-3'
      between the central two bases.  The pvuIIR open reading frame predicts a 157
      amino acid, 18.4 kDa polypeptide.  The predicted size and amino acid sequence
      are consistent with previous analyses of in vitro translation products and of
      the N-terminal sequence of the purified protein.  The elution profile of active
      PvuII endonuclease from a calibrated gel filtration column suggests a molecular
      mass of about 40.5 kDa, with a Stokes radius of about 1.8nm, implying that the
      enzyme is a homodimer.  The pvuIIR gene shows no obvious relationship to that
      of pvuIIM, which codes for the PvuII methylase, but a region of similarity has
      been found among the amino acid sequences of pvuIIR and those of four other
      restriction endonucleases.  Combining the pvuIIR and pvuIIM sequence data, to
      yield the full sequence of the divergently-transcribed restriction-modification
      system, revealed an additional open reading frame between these two genes.  In
      a separate study, this third open reading frame has been shown to regulate the
      expression of pvuIIR.
AU  - Tao T
AU  - Blumenthal RM
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1991 91: 175.

PMID- 1577705
VI  - 174
DP  - 1992
TI  - Sequence and characterization of pvuIIR, the PvuII endonuclease gene, and of pvuIIC, its regulatory gene.
PG  - 3395-3398
AB  - An open reading frame partially overlaps pvuIIR, and genetic evidence implies that this open
      reading frame, named pvuIIC, specifies a positive regulator of pvuIIR (T. Tao, J.C. Bourne,
      and R.M. Blumenthal, J. Bacteriol. 173:1367-1375, 1991). Inducible constructs of pvuIIC
      produced a protein of the expected size. The site of C.PvuII action appears to lie within
      pvuIIC itself; thus, pvuIIC may be a self-contained regulatory cassette.
AU  - Tao T
AU  - Blumenthal RM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1992 174: 3395-3398.

PMID- 1995588
VI  - 173
DP  - 1991
TI  - A family of regulatory genes associated with Type II restriction-modification systems.
PG  - 1367-1375
AB  - Restriction-modification systems must be regulated to avoid autorestriction and
      death of the host cell.  An open reading frame (ORF) in the PvuII
      restriction-modification system appears to code for a regulatory protein from a
      previously unrecognized family.  First, interruptions of this ORF result in a
      nonrestricting phenotype.  Second, this ORF can restore restriction competence
      to such interrupted mutants in trans.  Third, the predicted amino acid sequence
      of this ORF resembles those of known DNA-binding proteins and includes a
      probable helix-turn-helix motif.  A survey of unattributed ORFs in 15 other
      type II restriction-modification systems revealed three that closely resemble
      the PvuII ORF.  All four members of this putative regulatory gene family have a
      common position relative to the endonuclease genes, suggesting a common
      regulatory mechanism.
AU  - Tao T
AU  - Bourne JC
AU  - Blumenthal RM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1991 173: 1367-1375.

PMID- 2662138
VI  - 17
DP  - 1989
TI  - Sequence, internal homology and high-level expression of the gene for a DNA-(cytosine N4)-methyltransferase, M.Pvu II.
PG  - 4161-4175
AB  - The base sequence of the pvuIIM gene has been determined.  This gene codes for
      a DNA-(cytosine N4)-methyltransferase, M.Pvu II.  The base sequence contains a
      single large open reading frame that predicts a 38.3kDa polypeptide, consistent
      with experimental data.  The pvuIIM gene contains some sequences common to DNA
      methyltransferases in general, but includes none of the sequences specifically
      conserved among DNA-(cytosine 5)-methyltransferases.  The pvuIIM sequence also
      reveals an internal homology at the amino acid level, each half of which spans
      over 100 amino acids and is itself homologous to the sequences of some
      DNA-(adenine N6)-methyltransferases.  A derivative of the pvuIIM plasmid was
      constructed to allow high-level production of M.Pvu II.  Specifically, the
      composite Ptac promoter was inserted 5' to pvuIIM, intervening DNA was deleted,
      and the resulting construct was used to transform an mcrB lacIq strain of
      Escherichia coli.  When this transformant was induced with
      isopropyl-B-D-galactopyranoside (IPTG), growth rapidly ceased and M.Pvu II
      accumulated to the point of comprising over 10% of the total soluble protein.
AU  - Tao T
AU  - Walter J
AU  - Brennan KJ
AU  - Cotterman MM
AU  - Blumenthal RM
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 4161-4175.

PMID- 26659683
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Lactobacillus plantarum WLPL04, Isolated from Human Breast Milk.
PG  - e01443-15
AB  - Lactobacillus plantarum WLPL04, a novel strain, was isolated from a breast milk sample from a
      healthy woman and demonstrated several probiotic functions. Here,
      we present the draft genome sequence of this strain, which contains 3,192,587 bp,
      a G+C content of 44.52%, 3,158 protein-coding genes, and 53 tRNA genes.
AU  - Tao X
AU  - Jiang M
AU  - Zhang F
AU  - Xu F
AU  - Wei H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01443-15.

PMID- 23087115
VI  - 86
DP  - 2012
TI  - Complete Genome Sequence of Temperate Bacteriophage AcaML1 from the Extreme Acidophile Acidithiobacillus caldus ATCC 51756.
PG  - 12452-12453
AB  - Development of reproducible genetic tools in the industrially important
      acidithiobacilli is urgently required. Inducible temperate phages which may be
      modified in vitro, propagated in suitable hosts, and used to transduce relevant
      genetic information to other strains and/or species are potentially valuable
      tools in this field of research. In order to address these current limitations,
      the genome sequence of an inducible temperate Myoviridae-like bacteriophage from
      the Acidithiobacillus caldus type strain was annotated and analyzed
      bioinformatically. Here, we announce the genome sequence of AcaML1 and report
      major findings from its annotation.
AU  - Tapia P
AU  - Flores FM
AU  - Covarrubias PC
AU  - Acuna LG
AU  - Holmes DS
AU  - Quatrini R
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 2012 86: 12452-12453.

PMID- 23950129
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Lactobacillus rhamnosus CRL1505, an Immunobiotic Strain  Used in Social Food Programs in Argentina.
PG  - e00627-13
AB  - We report the draft genome sequence of the probiotic Lactobacillus rhamnosus strain CRL1505.
      This new probiotic strain has been included into official Nutritional Programs in Argentina.
      The draft genome sequence is composed of 3,417,633 bp with 3,327 coding sequences.
AU  - Taranto MP
AU  - Villena J
AU  - Salva S
AU  - Alvarez S
AU  - Savoy-de-Giori G
AU  - Font-de-Valdez G
AU  - Hebert EM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00627-13.

PMID- 18194583
VI  - 9
DP  - 2008
TI  - Substrate specificity of new methyl-directed DNA endonuclease GlaI.
PG  - 7
AB  - Recently, we have discovered site-specific endonucleases, which recognize and cleave only DNA
      sequences with 5-methylcytosine. Two specificities of such endonucleases have been described.
      Enzymes BisI, BlsI, and GluI are isoschizomers and hydrolyze the DNA sequence
      5'-GCNGC-3'/3'-CGNCG-5', which is methylated in different ways. The enzyme GlaI cleaves
      the DNA sequence 5'-GCGC-3'/3'-CGCG-5' if there are two, three or four 5-methylcytosines.
      The goal of the present work is to study in detail the composition of recognition sequence and
      effect of the methylated cytosines on the efficiency of DNA cleavage by the methyl-directed
      DNA endonuclease GlaI. In a recent work we have studied the dependence of GlaI activity on the
      quantity and location of 5-methylcytosines in the enzyme recognition sequence
      5'-GCGC-3'/3'-CGCG-5'. A significant DNA cleavage has been observed for oligonucleotide
      duplexes, which include either three or four 5-methylcytosines. In this work we have studied
      dependence of the GlaI activity on quantity and location of methylated cytosines, as well as
      on composition of the recognition sequence.The list of good substrates for GlaI includes a
      fully methylated site 5'-CGCG-3'/3'-GCGC-5', sites with three cytosines of a general
      structure 5'-PuMGM-3'/3'-PyGMG-5', and one recognition sequence with two methylated
      cytosines 5'-AMGT-3'/3'-TGMA-5', where M is 5-methylcytosine. GlaI intermediate substrates
      include sites with three methylated cytosines of a general structure
      5'-GMPuM-3'/3'-MGPyG-5', as well as a site with two methylcytosines
      5'-GMGT-3'/3'-CGMA-5'. The site 5'-GMGC-3'/3'-CGMG-5' may be considered a low activity
      substrate.
AU  - Tarasova GV
AU  - Nayakshina TN
AU  - Degtyarev SK
PT  - Journal Article
TA  - BMC Mol. Biol.
JT  - BMC Mol. Biol.
SO  - BMC Mol. Biol. 2008 9: 7.

PMID- 
VI  - 0
DP  - 2011
TI  - Cloning and analysis of biochemical and catalytic properties of DNA methyltransferase M1.BspACI.
PG  - 38-40
AB  - Genes coding for the DNA methyltransferases of restriction-modification system BspACI from
      Bacillus psychrodurans AC have been cloned in E. coli cells. The analysis of amino acid
      sequences of the proteins showed that both these genes belong to C5 DNA methyltransferases.
      Gene bspACIMI has been subcloned in pJW2 vector. High-purity recombinant enzyme has been
      obtained with chromatography on different carriers. It has been shown that M1.BspACI modifies
      the first cytosine residue in the sequence 5'-CCGC-3'. Kinetic parameters have been
      determined. The catalytic constant appears to be 0,095 +/- 0,002 min(-1), K-m, (Delta HK phi
      ara lambda) - 0,053 +/- 0,007 (MKM), K-m (SAM) - 5,1 +/- 0,3 (MKM).
AU  - Tarasova MV
AU  - Kuznetsov VV
AU  - Netesova NA
AU  - Gonchar DA
AU  - Degtyarev SC
PT  - Journal Article
TA  - Vestn. Mosk. Univ.
JT  - Vestn. Mosk. Univ.
SO  - Vestn. Mosk. Univ. 2011 0: 38-40.

PMID- 21314619
VI  - 75
DP  - 2010
TI  - Recombinant DNA-Methyltransferase M1.BspACI from Bacillus psychrodurans AC: Purification and Properties.
PG  - 1484-1490
AB  - A restriction-modification system from Bacillus psychrodurans AC ( recognition sequence
      5'-CCGC-3') comprises two DNA methyltransferases:
      M1.BspACI and M2.BspACI. The bspACIM1 gene was cloned in the pJW2
      vector and expressed in Escherichia coli cells. High-purity M1.BspACI
      preparation has been obtained by chromatography on different carriers.
      M1.BspACI has a temperature optimum of 30 C and demonstrates maximum
      activity at pH 8.0. M1.BspACI modifies the first cytosine in the
      recognition sequence 5'-CCGC-3'. The kinetic parameters of M1.BspACI
      DNA methylation are as follows: K-m for phage lambda DNA is 0.053 mu M
      and K-m for S-adenosyl-L-methionine is 5.1 mu M. The catalytic constant
      (k(cat)) is 0.095 min(-1).
AU  - Tarasova MV
AU  - Kuznetsov VV
AU  - Netesova NA
AU  - Gonchar DA
AU  - Degtyarev SK
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2010 75: 1484-1490.

PMID- 24578269
VI  - 2
DP  - 2014
TI  - Functional Analysis Using Whole-Genome Sequencing of a Drug-Sensitive Mycobacterium tuberculosis Strain from Peru.
PG  - e00087-14
AB  - We report the whole-genome sequence of a Latin American-Mediterranean (LAM) lineage
      drug-sensitive Mycobacterium tuberculosis strain from Peru, INS-SEN. The
      functional analysis revealed more mutations in secondary metabolite biosynthesis,
      transport, and catabolism (clusters of orthologous groups [COG] category Q) than
      for other LAM-sensitive strains. This study contributes to the understanding of
      the genomic diversity of drug-sensitive M. tuberculosis.
AU  - Tarazona D
AU  - Borda V
AU  - Galarza M
AU  - Agapito JC
AU  - Guio H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00087-14.

PMID- 23409255
VI  - 1
DP  - 2013
TI  - Whole Genome Sequencing and Comparative Analysis of Bartonella bacilliformis Strain INS, the Causative Agent of Carrion's Disease.
PG  - e00053-12
AB  - Bartonella bacilliformis is the etiological agent of human bartonellosis, which is highly
      endemic to Peru. Here, we report the first genome that was sequenced
      and analyzed from an isolate of B. bacilliformis strain INS, which originally was
      isolated from the blood of an infected patient with an acute phase of Carrion's
      disease from Jaen-Cajamarca, Peru.
AU  - Tarazona D
AU  - Padilla C
AU  - Caceres O
AU  - Montenegro JD
AU  - Bailon H
AU  - Ventura G
AU  - Mendoza G
AU  - Anaya E
AU  - Guio H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00053-12.

PMID- 9016595
VI  - 25
DP  - 1997
TI  - Solid phase synthesis and restriction endonuclease cleavage of oligodeoxynucleotides containing 5-(hydroxymethyl)-cytosine.
PG  - 553-558
AB  - Emerging data suggest an important role for cytosine methylation in tumorigenesis.
      Simultaneously, recent studies indicate a significant contribution of endogenous oxidative DNA
      damage to the development of human disease.  Oxidation of the 5-methyl group of
      5-methylcytosine (5mC) residues in DNA results in the formation of 5-(hydroxymethyl)cytosine
      (hmC).  The biological consequences of hmC residues in vertebrate DNA are as yet unknown;
      however, conversion of the hydrophobic methyl group to the hydrophilic hydroxymethyl group may
      substantially alter the interaction of sequence-specific binding proteins with DNA.  Central
      to both biophysical and biochemical studies on the potential consequences of specific DNA
      damage products such as hmC are efficient methods for the synthesis of oligodeoxynucleotides
      containing such modified bases at selected positions.  In this paper, we describe a method for
      the placement of hmC residues in oligodeoxynucleotides using established phosphoramidite
      chemistry.  In addition, we have examined the influence of specific hmC residues on enzymatic
      cleavage of oligodeoxynucleotides by the methylation-sensitive restriction endonucleases MspI
      and HpaII.
AU  - Tardy-Planechaud S
AU  - Fujimoto J
AU  - Lin SS
AU  - Sowers LC
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1997 25: 553-558.

PMID- 26067954
VI  - 3
DP  - 2015
TI  - Genome Sequence of Lactobacillus rhamnosus Strain CNCM I-3698.
PG  - e00582-15
AB  - Lactobacillus rhamnosus CNCM I-3698 is a commercially available probiotic that is used in
      animal feed as an additive. Here, we announce the draft genome sequence
      for this strain, consisting of 71 contigs corresponding to 2,966,480 bp and a G+C
      content of 46.69%.
AU  - Tareb R
AU  - Bernardeau M
AU  - Vernoux JP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00582-15.

PMID- 26383668
VI  - 3
DP  - 2015
TI  - Genome Sequence of Rough and Smooth Variants of Pleomorphic Strain Lactobacillus  farciminis CNCM-I-3699.
PG  - e01059-15
AB  - The probiotic Lactobacillus farciminis CNCM-I-3699 is a pleomorphic strain exhibiting smooth
      and rough variants. We report their complete genomes consisting of a chromosome of 2, 4 Mb and
      a plasmid of 6,417 bp. The smooth variant differs  by the presence of an additional plasmid of
      35,418 bp.
AU  - Tareb R
AU  - Bernardeau M
AU  - Vernoux JP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01059-15.

PMID- 25838498
VI  - 3
DP  - 2015
TI  - Genome Sequence of the Mycorrhiza Helper Bacterium Streptomyces sp. Strain AcH 505.
PG  - e01386-14
AB  - A draft genome sequence of Streptomyces sp. strain AcH 505 is presented here. The genome
      encodes 22 secondary metabolite gene clusters and a large arsenal of
      secreted proteins, and their comparative and functional analyses will help to
      advance our knowledge of symbiotic interactions and fungal and plant biomass
      degradation.
AU  - Tarkka MT
AU  - Feldhahn L
AU  - Buscot F
AU  - Wubet T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01386-14.

PMID- 25838499
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Streptomyces sp. Strain 150FB, a Mushroom Mycoparasite Antagonist.
PG  - e01441-14
AB  - Streptomyces sp. strain 150FB, isolated from the cap surface of a bolete mushroom, inhibits
      the growth of the mycoparasitic Sepedonium species. Functional
      annotation of the strain 150FB draft genome identified 22 putative secondary
      metabolite biosynthetic gene clusters and genes encoding secreted proteins, which
      may contribute to the inhibition of the mycoparasite.
AU  - Tarkka MT
AU  - Feldhahn L
AU  - Kruger D
AU  - Arnold N
AU  - Buscot F
AU  - Wubet T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01441-14.

PMID- 
VI  - 49
DP  - 2014
TI  - Cloning, purification and characterization of translationally fused protein DNA methyltransferase MoHhaI-EGFP.
PG  - 2170-2173
AB  - Design of the transcriptionally-fused protein MoHhaI-EGFP, composed of bacterial
      DNA-methyltransferase MoHhaI and enhanced green fluorescent protein (GFP) is described. The
      mentioned MoHhaI-EGFP was expressed in Escherichia coli ER1821 and purified by affinity
      chromatography on Ni-NTA agarose. According to expectations MoHhaI-EGFP fused protein retained
      significant features of corresponding original proteins: the ability to transfer methyl group
      to the C5 carbon atom of internal cytosine in CGCG site and absorption-emission spectral
      characteristics. The created transcriptionally-fused protein MoHhaI-EGFP could be used in
      various experiments in molecular biology.
AU  - Tarlachkov SV
AU  - Dyachenko OV
AU  - Cherevatenko AM
AU  - Rudenko NV
AU  - Shevchuk TV
PT  - Journal Article
TA  - Process. Biochem.
JT  - Process. Biochem.
SO  - Process. Biochem. 2014 49: 2170-2173.

PMID- 7698663
VI  - 155
DP  - 1995
TI  - Cloning and expression of the NaeI restriction endonuclease-encoding gene and sequence analysis of the NaeI restriction-modification system.
PG  - 19-25
AB  - NaeI, a type-II restriction-modification (R-M) system from the bacterium Nocardia
      aerocolonigenes, recognizes the sequence 5'-GCCGGC. The NaeI DNA methyltransferase
      (MTase)-encoding gene, naeIM, had been cloned previously in Escherichia coli. However, none of
      these clones expressed detectable levels of the restriction endonuclease (ENase). The absence
      of the intact ENase-encoding gene (naeIR) within the isolated MTase clones was confirmed by
      recloning the MTase clones into Streptomyces lividans. The complete NaeI system was finally
      cloned using E. coli AP1-200 and less stringent MTase-selection conditions. The naeIR gene was
      expressed first by cloning into S. lividans, and later by cloning under control of a regulated
      promoter in an E. coli strain preprotected by the heterologous MspI MTase (M.MspI). The DNA
      sequence of the NaeI R-M system has been determined, analyzed and compared to previously
      sequenced R-M systems.
AU  - Taron CH
AU  - Van Cott EM
AU  - Wilson GG
AU  - Moran LS
AU  - Slatko BE
AU  - Hornstra LJ
AU  - Benner JS
AU  - Kucera RB
AU  - Guthrie EP
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 155: 19-25.

PMID- 8095080
VI  - 17C
DP  - 1993
TI  - Cloning, sequencing and overexpressing the NaeI restriction endonuclease gene from Nocardia aerocolonigenes.
PG  - 175
AB  - NaeI is a type II restriction-modification system from Nocardia aerocolonigenes. The
      endonuclease recognizes the palindromic hexanucleotide sequence 5'GCC^GGC 3' and cleaves to
      produce a blunt end. The NaeI methylase gene (naeIM) was cloned previously by Van Cott and
      Wilson (Gene 74: 55-59, 1988). This clone exhibited methylase activity but no levels of
      endonuclease activity were detected, suggesting the endonuclease gene (naeIR) was either not
      present intact on the clone, or was present but not expressed. Subcloning the methylase clone
      into Streptomyces lividans, an organism more closely related to Nocardia, confirmed the
      absence of naeIR. To clone naeIR, a SacI genomic DNA library was made using the original
      methylase clone in pBR322 as a cloning vector. This library was selected for naeIM by
      digestion with NaeI, transformed into E. coli AP1-200 and positive clones appeared as blue
      clonies on LB agar plates containing X-gal. Nucleotide sequencing of naeIM and naeIR yielded
      two large open reading frames (ORFs). The naeIR ORF was identified by correlation of its
      translated peptide sequence to the amino terminal peptide sequence of the NaeI endonuclease.
      The endonuclease gene was amplified by PCR and cloned behind the strong promoter Ptac. This
      clone was transformed into E. coli K802 containing the MspI methylase gene. The MspI
      recognition sequence is 5'CCGG 3' (the internal tetramer of the NaeI recognition site) with
      MspI modification fully protecting against NaeI digestion. This construct yielded
      approximately 750 fold overexpression of NaeI.
AU  - Taron CH
AU  - Van Cott EM
AU  - Wilson GG
AU  - Moran LS
AU  - Slatko BE
AU  - Hornstra LJ
AU  - Benner JS
AU  - Kucera RB
AU  - Guthrie EP
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1993 17C: 175.

PMID- 26021930
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Listeria monocytogenes N2306, a Strain Associated with the 2013-2014 Listeriosis Outbreak in Switzerland.
PG  - e00553-15
AB  - We present the complete genome sequence of Listeria monocytogenes N2306, a serotype 4b
      clinical strain isolated during the 2013-2014 nationwide listeriosis
      outbreak in Switzerland.
AU  - Tasara T
AU  - Ebner R
AU  - Klumpp J
AU  - Stephan R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00553-15.

PMID- 28232433
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Five Shiga Toxin-Producing Escherichia coli Isolates Harboring the New and Recently Described Subtilase Cytotoxin Allelic Variant  subAB2-3.
PG  - e01582-16
AB  - We present here the draft genome sequences of five Shiga toxin-producing Escherichia coli
      (STEC) strains which tested positive in a primary subAB
      screening. Assembly and annotation of the draft genomes revealed that all strains
      harbored the recently described allelic variant subAB2-3 Based on the sequence
      data, primers were designed to identify and differentiate this variant.
AU  - Tasara T
AU  - Fierz L
AU  - Klumpp J
AU  - Schmidt H
AU  - Stephan R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01582-16.

PMID- 26966206
VI  - 4
DP  - 2016
TI  - Genome Sequences of Listeria monocytogenes Strains Responsible for Cheese- and Cooked Ham Product-Associated Swiss Listeriosis Outbreaks in 2005 and 2011.
PG  - e00106-16
AB  - The complete genome sequences of three Listeria monocytogenes serotype 1/2a strains, Lm 3136,
      Lm 3163, and Lm N1546, which were responsible for listeriosis
      outbreaks in 2005 and 2011 in Switzerland, are presented here.
AU  - Tasara T
AU  - Klumpp J
AU  - Bille J
AU  - Stephan R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00106-16.

PMID- 28798191
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Anoxybacillus flavithermus Strain 52-1A Isolated from a Heat-Processed Powdered Milk Concentrate.
PG  - e00800-17
AB  - The thermophilic spore-forming bacterium Anoxybacillus flavithermus is responsible for
      powdered milk product spoilage, and its presence in dairy
      processing environments is a concern. Here, the complete genome sequence of the
      A. flavithermus strain 52-1A isolated from a heat-processed powdered milk product
      concentrate in Switzerland is presented.
AU  - Tasara T
AU  - Morach M
AU  - Klumpp J
AU  - Stephan R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00800-17.

PMID- 25477407
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Listeria monocytogenes Lm60, a Strain with an Enhanced Cold Adaptation Capacity.
PG  - e01248-14
AB  - The complete genome sequence of Listeria monocytogenes Lm60, a fast cold-adapting serotype
      1/2a human isolate, is presented.
AU  - Tasara T
AU  - Weinmaier T
AU  - Klumpp J
AU  - Rattei T
AU  - Stephan R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01248-14.

PMID- 27313837
VI  - 11
DP  - 2016
TI  - High-quality draft genome sequence of Flavobacterium suncheonense GH29-5(T) (DSM  17707(T)) isolated from greenhouse soil in South Korea, and emended description of Flavobacterium suncheonense GH29-5(T).
PG  - 42
AB  - Flavobacterium suncheonense is a member of the family Flavobacteriaceae in the phylum
      Bacteroidetes. Strain GH29-5(T) (DSM 17707(T)) was isolated from
      greenhouse soil in Suncheon, South Korea. F. suncheonense GH29-5(T) is part of
      the G enomic E ncyclopedia of B acteria and A rchaea project. The 2,880,663 bp
      long draft genome consists of 54 scaffolds with 2739 protein-coding genes and 82
      RNA genes. The genome of strain GH29-5(T) has 117 genes encoding peptidases but a
      small number of genes encoding carbohydrate active enzymes (51 CAZymes). Metallo
      and serine peptidases were found most frequently. Among CAZymes, eight glycoside
      hydrolase families, nine glycosyl transferase families, two carbohydrate binding
      module families and four carbohydrate esterase families were identified.
      Suprisingly, polysaccharides utilization loci (PULs) were not found in strain
      GH29-5(T). Based on the coherent physiological and genomic characteristics we
      suggest that F. suncheonense GH29-5(T) feeds rather on proteins than saccharides
      and lipids.
AU  - Tashkandy N et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 42.

PMID- 20841432
VI  - 20
DP  - 2010
TI  - Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes.
PG  - 1605-1612
AB  - The human gut microbiome is a complex ecosystem composed mainly of
      uncultured bacteria. It plays an essential role in the catabolism of
      dietary fibers, the part of plant material in our diet that is not
      metabolized in the upper digestive tract, because the human genome does
      not encode adequate carbohydrate active enzymes (CAZymes). We describe a
      multi-step functionally based approach to guide the in-depth
      pyrosequencing of specific regions of the human gut metagenome encoding
      the CAZymes involved in dietary fiber breakdown. High-throughput
      functional screens were first applied to a library covering 5.4 x 10(9) bp
      of metagenomic DNA, allowing the isolation of 310 clones showing
      beta-glucanase, hemicellulase, galactanase, amylase, or pectinase
      activities. Based on the results of refined secondary screens, sequencing
      efforts were reduced to 0.84 Mb of nonredundant metagenomic DNA,
      corresponding to 26 clones that were particularly efficient for the
      degradation of raw plant polysaccharides. Seventy-three CAZymes from 35
      different families were discovered. This corresponds to a fivefold
      target-gene enrichment compared to random sequencing of the human gut
      metagenome. Thirty-three of these CAZy encoding genes are highly
      homologous to prevalent genes found in the gut microbiome of at least 20
      individuals for whose metagenomic data are available. Moreover, 18
      multigenic clusters encoding complementary enzyme activities for plant
      cell wall degradation were also identified. Gene taxonomic assignment is
      consistent with horizontal gene transfer events in dominant gut species
      and provides new insights into the human gut functional trophic chain.
AU  - Tasse L
AU  - Bercovici J
AU  - Pizzut-Serin S
AU  - Robe P
AU  - Tap J
AU  - Klopp C
AU  - Cantarel BL
AU  - Coutinho PM
AU  - Henrissat B
AU  - Leclerc M
AU  - Dore J
AU  - Monsan P
AU  - Remaud-Simeon M
AU  - Potocki-Veronese G
PT  - Journal Article
TA  - Genome Res.
JT  - Genome Res.
SO  - Genome Res. 2010 20: 1605-1612.

PMID- 2854803
VI  - 74
DP  - 1988
TI  - The ability of the restriction endonuclease EcoRI to digest hemi-methylated versus fully cytosine-methylated DNA of the herpes tk promoter region.
PG  - 147-149
AB  - None
AU  - Tasseron-de Jong JG
AU  - Aker J
AU  - Giphart-Gassler M
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 147-149.

PMID- 23105072
VI  - 194
DP  - 2012
TI  - Whole-Genome Sequence of the Hypervirulent Clinical Strain Mycobacterium intracellulare M.i.198.
PG  - 6336
AB  - We report herein the draft genome sequence of Mycobacterium intracellulare clinical strain
      M.i.198, which consistently exhibits hypervirulence in human
      patients, human macrophages in vitro, and immunocompetent mice.
AU  - Tateishi Y
AU  - Kitada S
AU  - Miki K
AU  - Maekura R
AU  - Ogura Y
AU  - Ozeki Y
AU  - Nishiuchi Y
AU  - Niki M
AU  - Hayashi T
AU  - Hirata K
AU  - Kobayashi K
AU  - Matsumoto S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6336.

PMID- 23929492
VI  - 1
DP  - 2013
TI  - Whole-Genome Sequence of the Potentially Hypertransmissible Multidrug-Resistant Mycobacterium tuberculosis Beijing Strain OM-V02_005.
PG  - e00608-13
AB  - We report the draft genome sequence of Mycobacterium tuberculosis Beijing strain  OM-V02_005,
      which exhibits possible hypertransmissible characteristics among the
      population of patients with multidrug-resistant tuberculosis in Osaka Prefecture,
      the largest urban area in western Japan.
AU  - Tateishi Y
AU  - Tamaru A
AU  - Ogura Y
AU  - Niki M
AU  - Wada T
AU  - Yamamoto T
AU  - Hirata K
AU  - Hayashi T
AU  - Matsumoto S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00608-13.

PMID- 23516195
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences of Bordetella holmesii Strains from Blood (F627) and Nasopharynx (H558).
PG  - e0005613
AB  - Bordetella holmesii, a human pathogen, can confound the diagnosis of respiratory  illness
      caused by Bordetella pertussis. We present the draft genome sequences of
      two B. holmesii isolates, one from blood, F627, and one from the nasopharynx,
      H558. Interestingly, important virulence genes that are present in B. pertussis
      are not found in B. holmesii.
AU  - Tatti KM
AU  - Loparev VN
AU  - Ranganathanganakammal S
AU  - Changayil S
AU  - Frace M
AU  - Weil MR
AU  - Sammons S
AU  - Maccannell D
AU  - Mayer LW
AU  - Tondella ML
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0005613.

PMID- Not carried by PubMed...
VI  - 93
DP  - 1993
TI  - Isolation, identification, and cloning of a non-palindromic type II DNA restriction endonuclease, PhaI, from Pasteurella haemolytica.
PG  - 199
AB  - Pasteurella haemolytica is an important cause of bovine pneumonic pasteurellosis. PhaI, an
      isoschizomer of SfaNI, was isolated from P. haemolytica, strain #NADC-60, a plasmidless
      isolate of serotype 1. PhaI recognizes the 5 base non-palindromic sequence 5'-GATGC-3'.
      Analysis of the restriction products on sequencing gels showed that cleavage occurs 5 bases to
      the right of the noted recognition site and 9 bases to the right on the opposite strand. A
      clone encoding the PhaI restriction endonuclease and PhaI methyltransferase was isolated from
      a P. haemolytica cosmid library and functional expression of both genes was obtained in
      Escherichia coli. Preliminary results indicate that PhaI restriction activity is a barrier to
      the introduction or establishment of exogenous DNA into this bacterium.
AU  - Tatum FM
AU  - Briggs RE
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1993 93: 199.

PMID- 15968079
VI  - 187
DP  - 2005
TI  - Complete genome sequence and analysis of the multiresistant nosocomial pathogen Corynebacterium jeikeium K411, a lipid-requiring bacterium of the human skin flora.
PG  - 4671-4682
AB  - Corynebacterium jeikeium is a "lipophilic" and multidrug-resistant bacterial species of the
      human skin flora that has been recognized with increasing frequency as a serious nosocomial
      pathogen. Here we report the genome sequence of the clinical isolate C. jeikeium K411, which
      was initially recovered from the axilla of a bone marrow transplant patient. The genome of C.
      jeikeium K411 consists of a circular chromosome of 2,462,499 bp and the 14,323-bp
      bacteriocin-producing plasmid pKW4. The chromosome of C. jeikeium K411 contains 2,104
      predicted coding sequences, 52% of which were considered to be orthologous with genes in the
      Corynebacterium glutamicum, Corynebacterium efficiens, and Corynebacterium diphtheriae
      genomes. These genes apparently represent the chromosomal backbone that is conserved between
      the four corynebacteria. Among the genes that lack an ortholog in the known corynebacterial
      genomes, many are located close to transposable elements or revealed an atypical G+C content,
      indicating that horizontal gene transfer played an important role in the acquisition of genes
      involved in iron and manganese homeostasis, in multidrug resistance, in bacterium-host
      interaction, and in virulence. Metabolic analyses of the genome sequence indicated that the
      "lipophilic" phenotype of C. jeikeium most likely originates from the absence of fatty acid
      synthase and thus represents a fatty acid auxotrophy. Accordingly, both the complete gene
      repertoire and the deduced lifestyle of C. jeikeium K411 largely reflect the strict dependence
      of growth on the presence of exogenous fatty acids. The predicted virulence factors of C.
      jeikeium K411 are apparently involved in ensuring the availability of exogenous fatty acids by
      damaging the host tissue.
AU  - Tauch A
AU  - Kaiser O
AU  - Hain T
AU  - Goesmann A
AU  - Weisshaar B
AU  - Albersmeier A
AU  - Bekel T
AU  - Bischoff N
AU  - Brune I
AU  - Chakraborty T
AU  - Kalinowski J
AU  - Meyer F
AU  - Rupp O
AU  - Schneiker S
AU  - Viehoever P
AU  - Puhler A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2005 187: 4671-4682.

PMID- 12232668
VI  - 45
DP  - 2002
TI  - Efficient electrotransformation of Corynebacterium diphtheriae with a mini-replicon derived from the Corynebacterium glutamicum plasmid pGA1.
PG  - 362-367
AB  - Efficient transformation of the human pathogen Corynebacterium
      diphtheriae was achieved with novel cloning vectors consisting of a mini-replicon from the
      cryptic C. glutamicum plasmid pGA1 as well as of the aph(3')-IIa or tetA(Z) antibiotic
      resistance genes. Plasmid-containing transformants of C. diphtheriae were recovered at
      frequencies ranging from 1.3 x 10^5 to 4.8 x 10^6 colony forming units (cfu)/microgram of
      plasmid DNA. Vector DNA was directly transferred from Escherichia coli into C. diphtheriae
      with frequencies up to 5.6 x 10^5 cfu/microgram of plasmid DNA. On the basis of the pGA1
      mini-replicon, an expression vector system was established for C. diphtheriae by means of the
      P-tac promoter and the green fluorescent reporter protein. In addition, other commonly used
      vector systems from C. glutamicum, including the pBL1 and pHM1519 replicons, and the sacB
      conditionally lethal selection market from Bacillus subtilis, were shown to be functional in
      C. diphtheriae. Thus, the ability to apply the standard methods of C. glutamicum recombinant
      DNA technology will greatly facilitate the functional analysis of the recently completed C.
      diphtheriae genome sequence.
AU  - Tauch A
AU  - Kirchner O
AU  - Loffler B
AU  - Gotker S
AU  - Puhler A
AU  - Kalinowski J
PT  - Journal Article
TA  - Curr. Microbiol.
JT  - Curr. Microbiol.
SO  - Curr. Microbiol. 2002 45: 362-367.

PMID- 7988915
VI  - 123
DP  - 1994
TI  - Corynebacterium glutamicum DNA is subjected to methylation-restriction in Escherichia coli.
PG  - 343-347
AB  - Efficient electroporation of Escherichia coli with plasmid DNA isolated from Corynebacterium
      glutamicum depends on the use of Mcr-deficient E. coli strains. The transformation frequency
      increased nearly 800-fold when the Mcr-deficient E. coli DH5a MCR was used instead of E. coli
      DH5a. We used E. coli strains with different mutations in the methyl-specific restriction
      systems to show that McrBC-deficiency is sufficient to generate this effect. The results imply
      that C. glutamicum DNA contains methylcytosine in specific sequences recognized by the E. coli
      McrBC system.
AU  - Tauch A
AU  - Kirchner O
AU  - Wehmeier L
AU  - Kalinowski J
AU  - Puhler A
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1994 123: 343-347.

PMID- 10732668
VI  - 263
DP  - 2000
TI  - The 51,409-bp R-plasmid pTP10 from the multiresistant clinical isolate Corynebacterium striatum M82B is composed of DNA segments initially identified in soil bacteria and in plant, animal, and human pathogens.
PG  - 1-11
AB  - The 51,409-bp DNA sequence of the multiresistance plasmid pTP10 from the
      gram-positive opportunistic human pathogen Corynebacterium striatum M82B
      has been determined. Fully automated genome interpretation led to the
      identification of 47 ORFs. Analysis of the genetic organization of pTP10
      suggests that the plasmid is composed of eight DNA segments, the
      boundaries of which are represented by transposons and insertion
      sequences. The DNA segments of pTP10 are highly similar to (1) a
      plasmid-encoded erythromycin resistance region from the human pathogen
      Corynebacterium diphtheriae; (2) a chromosomal DNA region from
      Mycobacterium tuberculosis; (3) a plasmid-encoded chloramphenicol
      resistance region from the soil bacterium Corynebacterium glutamicum; (4)
      transposable elements from phytopathogenic gram-negative Pseudomonas,
      Xanthomonas and Erwinia species; and (5) a plasmid-encoded aminoglycoside
      resistance region from the gram-negative fish pathogen Pasteurella
      piscicida. The complete DNA sequence of pTP10 provides genetic information
      regarding the mechanisms of resistance to 16 antimicrobial agents that
      belong to six structural classes. In addition, the mosaic structure of
      pTP10 represents the evolutionary consolidation into a single plasmid
      molecule of antimicrobial resistances from microorganisms found in
      different habitats by means of mobile elements, resulting in the
      generation of a multiresistant bacterium that can infect humans.
AU  - Tauch A
AU  - Krieft S
AU  - Kalinowski J
AU  - Puhler A
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 2000 263: 1-11.

PMID- 18367281
VI  - 136
DP  - 2008
TI  - The lifestyle of Corynebacterium urealyticum derived from its complete genome sequence established by pyrosequencing.
PG  - 11-21
AB  - Corynebacterium urealyticum is a lipid-requiring, urealytic bacterium of the human skin flora
      that has been recognized as causative agent of
      urinary tract infections. We report the analysis of the complete genome
      sequence of C. urealyticum DSM7109, which was initially recovered from a
      patient with alkaline-encrusted cystitis. The genome sequence was
      determined by a combination of pyrosequencing and Sanger technology. The
      chromosome of C. urealyticum DSM7109 has a size of 2,369,219bp and
      contains 2024 predicted coding sequences, of which 78% were considered as
      orthologous with genes in the Corynebacterium jeikeium K411 genome.
      Metabolic analysis of the lipid-requiring phenotype revealed the absence
      of a fatty acid synthase gene and the presence of a beta-oxidation pathway
      along with a large repertoire of auxillary genes for the degradation of
      exogenous fatty acids. A urease locus with the gene order ureABCEFGD may
      play a pivotal role in virulence of C. urealyticum by the alkalinization
      of human urine and the formation of struvite stones. Multidrug resistance
      of C. urealyticum DSM7109 is mediated by transposable elements, conferring
      resistances to macrolides, lincosamides, ketolides, aminoglycosides,
      chloramphenicol, and tetracycline. The complete genome sequence of C.
      urealyticum revealed a detailed picture of the lifestyle of this
      opportunistic human pathogen.
AU  - Tauch A
AU  - Trost E
AU  - Tilker A
AU  - Ludewig U
AU  - Schneiker S
AU  - Goesmann A
AU  - Arnold W
AU  - Bekel T
AU  - Brinkrolf K
AU  - Brune I
AU  - Gotker S
AU  - Kalinowski J
AU  - Kamp PB
AU  - Lobo FP
AU  - Viehoever P
AU  - Weisshaar B
AU  - Soriano F
AU  - Droge M
AU  - Puhler A
PT  - Journal Article
TA  - J. Biotechnol.
JT  - J. Biotechnol.
SO  - J. Biotechnol. 2008 136: 11-21.

PMID- 2161521
VI  - 18
DP  - 1990
TI  - SgrAI, a novel class-II restriction endonuclease from Streptomyces griseus recognizing the octanucleotide sequence 5'-CR/CCGGYG-3' .
PG  - 3087
AB  - 
AU  - Tautz N
AU  - Kaluza K
AU  - Frey B
AU  - Jarsch M
AU  - Schmitz GG
AU  - Kessler C
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 3087.

PMID- 25146148
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence and Annotation of a Campylobacter jejuni Strain, MTVDSCj20, Isolated from a Naturally Colonized Farm-Raised Chicken.
PG  - e00852-14
AB  - Campylobacter jejuni is a major cause of human food-borne illness, with contaminated poultry
      products serving as a main source of human infection. C.
      jejuni strain MTVDSCj20 was isolated from the cecal contents of a farm-raised
      chicken that was naturally colonized with Campylobacter. We present here the
      complete annotated genome sequence of MTVDSCj20.
AU  - Taveirne ME
AU  - Dunham DT
AU  - Miller WG
AU  - Parker CT
AU  - Huynh S
AU  - DiRita VJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00852-14.

PMID- 28126931
VI  - 5
DP  - 2017
TI  - Complete Annotated Genome Sequences of Three Campylobacter jejuni Strains Isolated from Naturally Colonized Farm-Raised Chickens.
PG  - e01407-16
AB  - Campylobacter jejuni is a leading cause of bacterially derived foodborne illness. Human
      illness is commonly associated with the handling and consumption of
      contaminated poultry products. Three C. jejuni strains were isolated from cecal
      contents of three different naturally colonized farm-raised chickens. The
      complete genomes of these three isolates are presented here.
AU  - Taveirne ME
AU  - Dunham DT
AU  - Perault A
AU  - Beauchamp JM
AU  - Huynh S
AU  - Parker CT
AU  - DiRita VJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01407-16.

PMID- 9661199
VI  - 16
DP  - 1998
TI  - Man-made cell-like compartments for molecular evolution.
PG  - 652-656
AB  - Cellular compartmentalization is vital for the evolution of all living organisms.  Cells keep
      together the genes, the RNAs and proteins that they encode, and the products of their
      activities, thus linking genotype to phenotype.  We have reproduced this linkage in the test
      tube by transcribing and translating single genes in the aqueous compartments of water-in-oil
      emulsions.  These compartments, with volumes close to those of bacteria, can be recruited to
      select genes encoding catalysts.  A protein or RNA with a desired catalytic activity converts
      a substrate attached to the gene that encodes it to product.  In other compartments,
      substrates attached to genes that do not encode catalysts remain unmodified.  Subsequently,
      genes encoding catalysts are selectively enriched by virtue of their linkage to the product.
      We demonstrate the linkage of genotype to phenotype in man-made compartments using a model
      system.  A selection for target-specific DNA methylation was based on the resistance of the
      product (methylated DNA) to restriction digestion.  Genes encoding HaeIII methyltransferase
      were selected from a 10^7-fold excess of genes encoding another enzyme.
AU  - Tawfik DS
AU  - Griffiths AD
PT  - Journal Article
TA  - Nat. Biotechnol.
JT  - Nat. Biotechnol.
SO  - Nat. Biotechnol. 1998 16: 652-656.

PMID- 23409253
VI  - 1
DP  - 2013
TI  - Genome Sequence of Campylobacter showae UNSWCD, Isolated from a Patient with Crohn's Disease.
PG  - e00193-12
AB  - Campylobacter showae UNSWCD was isolated from a patient with Crohn's disease. Here we present
      a 2.1 Mb draft assembly of its genome.
AU  - Tay AP
AU  - Kaakoush NO
AU  - Deshpande NP
AU  - Chen Z
AU  - Mitchell H
AU  - Wilkins MR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00193-12.

PMID- 24435866
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Model Naphthalene-Utilizing Organism Pseudomonas putida OUS82.
PG  - e01161-13
AB  - Pseudomonas putida OUS82 was isolated from petrol- and oil-contaminated soil in 1992, and ever
      since, it has been used as a model organism to study the microbial
      assimilation of naphthalene and phenanthrene. Here, we report the 6.7-Mb draft
      genome sequence of P. putida OUS82 and analyze its featured pathways for
      biodegradation.
AU  - Tay M
AU  - Roizman D
AU  - Cohen Y
AU  - Tolker-Nielsen T
AU  - Givskov M
AU  - Yang L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01161-13.

PMID- Not carried by PubMed...
VI  - 94
DP  - 1994
TI  - Purification and characterization of a restriction endonuclease (CpfI) from Clostridium perfringens 10543A.
PG  - 224
AB  - Nucleases may play an important role in plasmid recovery and uptake in Clostridium
      perfringens. A type II restriction endonuclease designated CpfI was isolated from C.
      perfringens 10543A. CpfI was purified to homogeneity using a combination of heparin-based
      affinity chromatography, DEAE-anion exchange chromatography, and gel permeation
      chromatography. The molecular weight of the purified enzyme was determined by gel filtration
      and sodium dodecyl sulfate polyacrylamide gel electrophoresis to be 40 and 44 kdal,
      respectively. The isoelectric point of the endonuclease is approximately 3.7, and the activity
      of the enzyme is inhibited above 45oC. Digestion of methylated and non-methylated pBR322 and
      phage DNA substrates suggested CpfI is an isoschizomer of MboI (Sau3A) with a unique
      sensitivity to methylation. Enzymes with this particular specificity may prove to be widely
      distributed in the genus Clostridium.
AU  - Tay NK
AU  - Blaschek HP
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1994 94: 224.

PMID- 8484730
VI  - 291
DP  - 1993
TI  - Determination of the order of substrate addition to MspI DNA methyltransferase using a novel mechanism-based inhibitor.
PG  - 493-504
AB  - The cloning and overexpression of the MspI DNA methyltransferase as a functional fusion with
      glutathione S-transferase is described. The fusion enzyme reatains full biological activity
      and has been used to investigate the interaction of substrates and inhibitors with MspI DNA
      methyltransferase. The fusion enzyme has been purifed to homogeneity in a single step on
      GSH-agarose and is free from contaminating exonuclease activity. The enzyme can be
      photolabelled with S-adenosyl-L-methionine and the level of incorporation of label is enhanced
      by the presence of a non-specific DNA duplex. In the presence of a cognate
      oligo-deoxynucleotide, no photolabelling was observed since methyl transfer occurs instead.
      The inclusion of a mechanism-based inhibitor of C-5 deoxycytidine DNA methylation (an
      oligodeoxynucleotide containing the base 2-pyrimidinone-1-beta-d-2'-deoxyribofuranoside in
      the position of the deoxycytidine to which methyl addition occurs), which is thought to form a
      covalent interaction with the reactive cysteine of such enzymes, led to an enhancement of
      S-adenosyl-L-methionine photolabelling which suggests that, in contrast with results obtained
      with EcoRII DNA methyltransferase [Som and Friedman (1991) J. Biol. Chem. 266, 2937-2945],
      methylcysteine is not the photolabelled product. The implications of the results obtained with
      this mechanism-based inhibitor are discussed with respect to other C-5-specific DNA
      methyltransferases. Gel-retardation assays in the presence of cognate oligodeoxynucleotides
      that contain the reactive pyrimidinone base in place of the deoxycytidine target base are
      described. These demonstrate that most probably a stable covalent bond is formed between the
      methyltransferase and this oligodeoxynucleotide. However, the alternative of extremely tight
      non-covalent binding cannot be rigorously excluded. Furthermore, the results from these
      experiments indicate that the reaction mechanism proceeds in a manner similar to that of HhaI
      DNA methyltransferase with sequence-specific DNA binding being followed by addition of
      S-adenosyl-L-methionine and concomitant isomerization of the ternary complex leading to methyl
      transfer. S-Adenosyl-L-homocysteine appears to inhibit the reaction pathway was as a result of
      either competition with the methyl donor and potentiation of a high affinity interaction
      between the enzyme and DNA in an abortive ternary complex or through an allosteric
      interaction.
AU  - Taylor C
AU  - Ford K
AU  - Connolly BA
AU  - Hornby DP
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 1993 291: 493-504.

PMID- 1400229
VI  - 174
DP  - 1992
TI  - Construction of a Helicobacter pylori genome map and demonstration of diversity at the genome level.
PG  - 6800-6806
AB  - Genomic DNA from 30 strains of Helicobacter pylori was subjected to pulsed-field gel
      electrophoresis after digestion with NotI and NruI.  The genome sizes of the strains ranged
      from 1.6 to 1.73 Mb, with an average size of 1.67 Mb. By using NotI and NruI, a circular map
      of H. pylori UA802 (1.7 Mb) which contained three copies of 16S and 23S rRNA genes was
      constructed.  An unusual feature of the H. pylori genome was the separate location of at least
      two copies of 16S and 23S rRNA genes.  Almost all strains had diferent PFGE patterns after
      NotI and NruI digestion, suggesting that the H. pylori genome possesses a considerable degree
      of genetic variability.  However, three strains from different sites (the fundus, antrum, and
      body of the stomach) within the same patient gave identical PFGE patterns.  The genomic
      pattern of individual isolates remained constant during multiple subcultures in vitro.  The
      reason for the genetic diversity observed among H. pylori strains remains to be explained.
AU  - Taylor DE
AU  - Eaton M
AU  - Chang N
AU  - Salama SM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1992 174: 6800-6806.

PMID- 21890897
VI  - 39
DP  - 2011
TI  - Activity, specificity and structure of I-Bth0305I: a representative of a new homing endonuclease family.
PG  - 9705-9719
AB  - Novel family of putative homing endonuclease genes was recently discovered during analyses of
      metagenomic and genomic sequence data. One such protein is encoded within a group I intron
      that resides in the recA gene of the Bacillus thuringiensis 03058-36 bacteriophage. Named
      I-Bth0305I, the endonuclease cleaves a DNA target in the uninterrupted recA gene at a position
      immediately adjacent to the intron insertion site. The enzyme displays a multidomain,
      homodimeric architecture and footprints a DNA region of  approximately 60 bp. Its highest
      specificity corresponds to a 14-bp pseudopalindromic sequence that is directly centered across
      the DNA cleavage site. Unlike many homing endonucleases, the specificity profile of the enzyme
      is evenly distributed across much of its target site, such that few single base pair
      substitutions cause a significant decrease in cleavage activity. A crystal structure of its
      C-terminal domain confirms a nuclease fold that is homologous to very short patch repair (Vsr)
      endonucleases. The domain architecture and DNA recognition profile displayed by I-Bth0305I,
      which is the prototype of a homing lineage that we term the 'EDxHD' family, are distinct
      from previously characterized homing endonucleases.
AU  - Taylor GK
AU  - Heiter DF
AU  - Pietrokovski S
AU  - Stoddard BL
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2011 39: 9705-9719.

PMID- 22570419
VI  - 40
DP  - 2012
TI  - LAHEDES: the LAGLIDADG homing endonuclease database and engineering server.
PG  - W110-W116
AB  - LAGLIDADG homing endonucleases (LHEs) are DNA cleaving enzymes, also termed 'meganucleases'
      that are employed as gene-targeting reagents. This use of LHEs requires that their DNA
      specificity be altered to match sequences in genomic targets. The choice of the most
      appropriate LHE to target a particular gene is facilitated by the growing number of such
      enzymes with well-characterized activities and structures. 'LAHEDES' (The LAGLIDADG Homing
      Endonuclease Database and Engineering Server) provides both an online archive of LHEs with
      validated DNA cleavage specificities and DNA-binding interactions, as well as a tool for the
      identification of DNA sequences that might be targeted by various LHEs. Searches can be
      performed using four separate scoring algorithms and user-defined choices of LHE scaffolds.
      The webserver subsequently provides information regarding clusters of amino acids that should
      be interrogated during engineering and selection experiments. The webserver is fully open
      access and can be found at http://homingendonuclease.net.
AU  - Taylor GK
AU  - Petrucci LH
AU  - Lambert AR
AU  - Baxter SK
AU  - Jarjour J
AU  - Stoddard BL
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: W110-W116.

PMID- 22406833
VI  - 40
DP  - 2012
TI  - Structural, functional and evolutionary relationships between homing endonucleases and proteins from their host organisms.
PG  - 5189-5200
AB  - Homing endonucleases (HEs) are highly specific DNA-cleaving enzymes that are encoded by
      invasive DNA elements (usually mobile introns or inteins) within the genomes of phage,
      bacteria, archea, protista and eukaryotic organelles. Six unique structural HE families, that
      collectively span four distinct nuclease catalytic motifs, have been characterized to date.
      Members of each family display structural homology and functional relationships to a wide
      variety of proteins from various organisms. The biological functions of those proteins are
      highly disparate and include non-specific DNA-degradation enzymes, restriction endonucleases,
      DNA-repair enzymes, resolvases, intron splicing factors and transcription factors. These
      relationships suggest that modern day HEs share common ancestors with proteins involved in
      genome fidelity, maintenance and gene expression. This review summarizes the results of
      structural studies of HEs and corresponding proteins from host organisms that have illustrated
      the manner in which these factors are related.
AU  - Taylor GK
AU  - Stoddard BL
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: 5189-5200.

PMID- 1741244
VI  - 20
DP  - 1992
TI  - Purification and biochemical characterisation of the EcoR124 type I modification methylase.
PG  - 179-186
AB  - Large scale purification of the type I modification methylase EcoR124 has been
      achieved from an overexpressing strain by a two step procedure using
      ion-exchange and heparin chromatography.  Pure methylase is obtained at a yield
      of 30mg per gm of cell paste.  Measurements of the molecular weight and subunit
      stoichiometry show that the enzyme is a trimeric complex of 162 kDa consisting
      of two subunits of HsdM (58 kDa) and one subunit of HsdS (46 kDa).  The
      purified enzyme can methylate a DNA fragment bearing its cognate recognition
      sequence.  Binding of the methylase to synthetic DNA fragments containing
      either the EcoR124 recognition sequence GAAN6RT-CG, or the recognition sequence
      GAAN7RTCG of the related enzyme EcoR124/3, was followed by fluorescence
      competition assays and by gel retardation analysis.  The results show that the
      methylase binds to its correct sequence with an affinity of the order 10/8 M-1
      forming a 1:1 complex with the DNA.  The affinity for the incorrect sequence,
      differing by an additional base pair in the non-specific spacer, is almost two
      orders of magnitude lower.
AU  - Taylor I
AU  - Patel J
AU  - Firman K
AU  - Kneale G
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 179-186.

PMID- 8177741
VI  - 21
DP  - 1993
TI  - Substrate recognition and selectivity in the type IC DNA modification methylase M.EcoR124I.
PG  - 4929-4935
AB  - The type I DNA modification methylase M.EcoR124I binds sequence specifically to DNA and
      protects a 25bp fragment containing its cognate recognition sequence from digestion by
      exonuclease III. Using modified synthetic oligonucleotide duplexes we have investigated the
      catalytic properties of the methylase, and have established that a specific adenine on each
      strand of DNA is the site of methylation. We show that the rate of methylation of each adenine
      is increased at least 100 fold by prior methylation at the other site. However this is
      accompanied by a significant decrease in the affinity of the methylase for these substrates
      according to competitive gel retardation assays. In contrast, methylation of an adenine in the
      recognitiom site which is not a target for the enzyme results in only a small decrease in both
      DNA binding affinity and rate of methylation by the enzyme.
AU  - Taylor I
AU  - Watts D
AU  - Kneale G
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 4929-4935.

PMID- Not carried by PubMed...
VI  - 53
DP  - 1993
TI  - Biochemical characterisation of the EcoR124 type I DNA modification methylase.
PG  - 3942
AB  - The hsdS and hsdM genes constituting the EcoR124I type I DNA modification methylase have been
      expressed independently in Escherichia coli (E. coli) using the high level expression vectors
      pUM120 and pJS491. Analysis of cell extracts demonstrated that the HsdM potein is found in the
      E. coli soluble fraction whilst the HsdS protein is found only in the E. coli insoluble pellet
      fraction. Protocols have been developed for the purification of both the HsdM and HsdS
      proteins and a preliminary biochemical analysis undertaken involving an investigation of the
      denaturation of both proteins by fluorescence spectroscopy. A more extensive analysis of the
      HsdM protein has allowed estimations of its solution molecular mass and secondary structure to
      be made. The hsdS and hsdM genes have also been co-expressed using the high level expression
      vector pJS4M. The analysis of cell extracts in this case revealed that both polypeptides are
      present in the E. coli soluble fraction. A protocol has been developed in which both
      polypeptides co-purify as a complex which is capable of methylating the EcoR124I recognition
      sequence. The enzyme complex has been shown to exist predominantly in solution as a trimer
      consisting of two copies of the HsdM polypeptide and a single copy of the HsdS polypeptide.
      Further experiments with the purified enzyme show that it can bind its recognition sequence
      with a dissociation constant of around 5x10-9 and that it can also bind the recognition
      sequence of the related type I DNA methylase EcoR124/3I with a lower affinity. A protein
      nucleic acid complex consisting of methylase and a 30 base pair synthetic oligonucleotide
      duplex has been investigated using 1H NMR spectroscopy and footprinting experiments. The
      results suggest that contacts are made between bases within the recognition sequence and the
      protein and also that the normal geometry of the nucleic acid may be distorted.
AU  - Taylor IA
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1993 53: 3942.

PMID- 7988573
VI  - 13
DP  - 1994
TI  - DNA binding induces a major structural transition in a type I methyltransferase.
PG  - 5772-5778
AB  - The type IC DNA methyltransferase M.EcoR124I is a complex multisubunit enzyme that recognizes
      the nonpalindromic DNA sequence GAAN6RTCG. Small angle X-ray scattering has been used to
      investigate the solution structure of the methyltransferase and of complexes of the enzyme
      with unmethylated and hemimethylated 30 bp DNA duplexes containing the specific recognition
      sequence. A major change in the quaternary structure of the enzyme is observed following DNA
      binding, based on a decrease in the radius of gyration from 56 to 40 A and a reduction in the
      maximum dimension of the enzyme from 180 to 112 A. The structural transition observed is
      independent of the methylation state of the DNA. CD shows that there is no change in the
      secondary structure of the protein subunits when DNA is bound. In contrast, there is a large
      increase in the CD signal arising from the DNA, suggesting considerable structural distortion
      which may allow access to the bases targeted for methylation. We propose that DNA binding
      induces a large rotation of the two HsdM subunits towards the DNA, mediated by hinge bending
      domains in the specificity subunit HsdS.
AU  - Taylor IA
AU  - Davis KG
AU  - Watts D
AU  - Kneale GG
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1994 13: 5772-5778.

PMID- 19378188
VI  - 543
DP  - 2009
TI  - A competition assay for DNA binding using the fluorescent probe ANS.
PG  - 577-587
AB  - Fluorescence spectroscopy is a technique frequently employed to stud), protein-nucleic acid
      interactions. Often, the intrinsic fluorescence
      emission spectrum of tryptophan residues in a nucleic-acid-binding
      protein is strongly perturbed upon interaction with a target DNA or
      RNA. These spectral changes can then be exploited in order to construct
      binding isotherms and the extract equilibrium association constant
      together with the stoichiometry of an interaction. However, when a
      protein contains many tryptophan residues that are not located in the
      proximity of the nucleic-acid-binding site, changes in the fluorescence
      emission spectrum may not be apparent or the magnitude too small to be
      useful. Here, we make use of an extrinsic fluorescence probe, the
      environmentally sensitive fluorophore 1-anilinonaphthalene-8-sulphonic
      acid (1,8-ANS). Displacement by DNA of 1,8-ANS Molecules from the
      nucleic-acid-binding site of the Type I modification methylase EcoR124I
      results in red shifting and an intensity decrease of the 1,8-ANS
      fluorescence emission spectrum. These spectral changes have been used
      to investigate the interaction of EcoR124I with DNA target recognition
      sequences.
AU  - Taylor IA
AU  - Kneale GG
PT  - Journal Article
TA  - Methods Mol. Biol.
JT  - Methods Mol. Biol.
SO  - Methods Mol. Biol. 2009 543: 577-587.

PMID- 8613993
VI  - 258
DP  - 1996
TI  - Surface labelling of the type I methyltransferase M.EcoR124I reveals lysine residues critical for DNA binding.
PG  - 62-73
AB  - The type IC methyltransferase M.EcoR124I consists of a specificity subunit
      (HsdS) and two methylation subunits (HsdM).  Using chemical modification, we have investigated
      the accessibility of lysine residues in the free enzyme and in the complex with its DNA
      recognition
      sequence.  A total of 41 of the 109 lysine residues in the enzyme are susceptible to
      modification, of
      which 19 are located in the HsdS subunit and 11 in each of the two HsdM subunits.  DNA binding
      results in extensive protection of lysine residues in the HsdS subunit, while those in the
      HsdM
      subunit are only protected weakly.  The DNA binding activity of the methylase is abolished
      when a
      small fraction of the accessible lysine residues are modified.  Peptide mapping and N-terminal
      sequencing has been used to locate the rapidly modified lysine residues in HsdS that are
      critical for
      DNA binding.  Highly modified residues (K297, K261 and K327) are found in the C-terminal
      variable domain that is responsible for DNA recognition, but others (K196, K203 and K210) are
      found in the conserved regions that had not previously been implicated in DNA binding.
AU  - Taylor IA
AU  - Webb M
AU  - Kneale GG
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1996 258: 62-73.

PMID- 18951375
VI  - 76
DP  - 2009
TI  - Cloning and Expression of Sheep DNA Methyltransferase 1 and Its Development-Specific Isoform.
PG  - 501-513
AB  - Unlike the mouse embryo, where loss of DNA methylation in the embryonic nucleus leaves
      cleavage stage embryos globally hypomethylated, sheep
      preimplantation embryos retain high levels of methylation until the
      blastocyst stage. We have cloned and sequenced sheep Dnmt1 and found it
      to be highly conserved with both the human and mouse homologues.
      Furthermore, we observed that the transcript normally expressed in
      adult somatic tissues is highly abundant in sheep oocytes. Throughout
      sheep preimplantation development the protein is retained in the
      cytoplasm whereas Dnmt1 transcript production declines after the
      embryonic genome activation at the 8-16 cell stage. Attempts to clone
      oocyte-specific 5' regions of Dnmt1, known to be present in the mouse
      and human gene, were unsuccessful. However, a novel ovine Dnmt1 exon,
      theoretically encoding 13 amino acids, was found to be expressed in
      sheep oocytes, preimplantation embryos and early fetal lineages, but
      not in the adult tissue. RNAi-mediated knockdown of this novel
      transcript resulted in embryonic developmental arrest at the late
      morula stage, suggesting an essential role for this isoform in sheep
      blastocyst formation.
AU  - Taylor J
AU  - Moore H
AU  - Beaujean N
AU  - Gardner J
AU  - Wilmut I
AU  - Meehan R
AU  - Young L
PT  - Journal Article
TA  - Mol. Reprod. Dev.
JT  - Mol. Reprod. Dev.
SO  - Mol. Reprod. Dev. 2009 76: 501-513.

PMID- 
VI  - 0
DP  - 2000
TI  - The gel shift assay for the analysis of DNA-protein interactions.
PG  - 745-756
AB  - The gel shift assay is one of the most powerful methods for the analysis of DNA-protein
      interactions.  The assay itself is simple.  DNA and protein are mixed together, the solution
      subjected to electrophoresis through polyacrylamide, and the gel is then analyzed for DNA,
      usually by autoradiography of radiolabeled DNA.  Binding of the protein to the DNA can result
      in a complex that has a different electrophoretic mobility from the free DNA.  In general, the
      mobility of the complex is retarded relative to the unbound DNA and thus the assay is often
      called gel retardation.  However, with circular DNA substrates (typically, minicircles of
      200-400 bp), the DNA-protein complex can migrate faster than the free DNA.  The separation of
      the complex from the free DNA, and therefore the detection of the complex, is dependent on a
      variety of factors.  These must be determined experimentally for each system.  However, the
      ease with which the assay can be performed means that the optimal conditions can be discovered
      quickly.  Factors that influence the electrophoretic mobility of DNA-protein complexes include
      the molecular weight of the protein and the DNA, the ionic strength and the pH of the
      electrophoresis buffer, the concentration of the gel matrix, and the temperature. Particularly
      useful accounts of how modifications to the assay can affect the mobility of DNA-protein
      complexes have been published.
AU  - Taylor JD
AU  - Ackroyd AJ
AU  - Halford SE
PT  - Journal Article
TA  - The Nucleic Acid Protocols Handbook
JT  - The Nucleic Acid Protocols Handbook
SO  - The Nucleic Acid Protocols Handbook 2000 0: 745-756.

PMID- 8004201
VI  - 30
DP  - 1994
TI  - The gel shift assay for the analysis of DNA-protein interactions.
PG  - 263-279
AB  - The gel shift assay is one of the most powerful methods for the analysis of DNA-protein
      interactions.  The assay itself is simple.  DNA and protein are mixed together, the solution
      subjected to electrophoresis through polyacrylamide, and the gel is then analyzed for DNA,
      usually by autoradiography of radiolabeled DNA.  Binding of the protein to the DNA can result
      in a complex that has a different electrophoretic mobility from the free DNA.  In general, the
      mobility of the complex is retarded relative to the unbound DNA and thus the assay is often
      called gel retardation.  However, with circular DNA substrates (typically, minicircles of
      200-400 bp), the DNA-protein complex can migrate faster than the free DNA.  The separation of
      the complex from the free DNA, and therefore the detection of the complex, is dependent on a
      variety of factors.  These must be determined experimentally for each system.  However, the
      ease with which the assay can be performed means that the optimal conditions can be discovered
      quickly.  Factors that influence the electrophoretic mobility of DNA-protein complexes include
      the molecular weight of the protein and the DNA, the ionic strength and the pH of the
      electrophoresis buffer, the concentration of the gel matrix, and the temperature.
      Particularly useful accounts of how modifications to the assay can affect the mobility of
      DNA-protein complexes have been published.
AU  - Taylor JD
AU  - Ackroyd AJ
AU  - Halford SE
PT  - Journal Article
TA  - Methods Mol. Biol.
JT  - Methods Mol. Biol.
SO  - Methods Mol. Biol. 1994 30: 263-279.

PMID- 1909572
VI  - 30
DP  - 1991
TI  - EcoRV restriction endonuclease binds all DNA sequences with equal affinity.
PG  - 8743-8753
AB  - In the presence of MgCl2, the EcoRV restriction endonuclease cleaves its
      recognition sequence on DNA at least a million times more readily than any
      other sequence.  In this study, the binding of the EcoRV restriction enzyme to
      DNA was examined in the absence of Mg2+.  With each DNA fragment tested,
      several DNA-protein complexes were detected by electrophoresis through
      polyacrylamide.  No differences were observed between isogenic DNA molecules
      that either contained or lacked the EcoRV recognition site.  The number of
      complexes with each fragment varied with the length of the DNA.  Three
      complexes were formed with a DNA molecule of 55 base pairs, corresponding to
      the DNA bound to 1,2,3 molecules of the protein, while >15 complexes were
      formed with a DNA of 381 base pairs.  A new method was developed to analyze the
      binding of a protein to multiple sites on DNA.  The method showed that the
      EcoRV enzyme binds to all DNA sequences, including the EcoRV recognition site,
      with the same equilibrium constant, though two molecules of the protein bind
      preferentially to adjacent sites on the DNA in a cooperative fashion.  All of
      the complexes with a substrate that contained the EcoRV site dissociated upon
      addition of competitor DNA, but when the competitor was mixed with MgCl2, a
      fraction of the substrate was cleaved at the EcoRV site.  The fraction cleaved
      was due mainly to the translocation of the enzyme from nonspecific sites on the
      DNA to the specific site.
AU  - Taylor JD
AU  - Badcoe IG
AU  - Clarke AR
AU  - Halford SE
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1991 30: 8743-8753.

PMID- 2176880
VI  - 29
DP  - 1990
TI  - Fidelity of DNA recognition by the EcoRV restriction/modification system in vivo.
PG  - 10727-10733
AB  - The EcoRV restriction/modification system consists of two enzymes that recognize the DNA
      sequence GATATC. The EcoRV restriction endonuclease cleaves DNA at this site, but the DNA of
      Escherichia coli carrying the EcoRV system is protected from this reaction by the EcoRV
      methyltransferase. However, in vitro, the EcoRV nuclease also cleaves DNA at most sites that
      differ from the recognition sequence by one base pair. Though the reaction of the nuclease at
      these sites is much slower than that at the cognate site, it still appears to be fast enough
      to cleave the chromosome of the cell into many fragments. The possibility that the EcoRV
      methyltransferase also protects the noncognate sites on the chromosome was examined. The
      modification enzyme methylated alternate sites in vivo, but these were not the same as the
      alternate sites for the nuclease. The excess methylation was found at GATC sequences, which
      are also the targets for the dam methyltransferase of E. coli, a protein that is homologous to
      the EcoRV methyltransferase. Methylation at these sites gave virtually no protection against
      the EcoRV nuclease: even when the EcoRV methyltransferase had been overproduced, the cellular
      DNA remained sensitive to the EcoRV nuclease at its noncognate sites. The viability of E. coli
      carrying the EcoRV restriction/modification R/M system was found instead to depend on the
      activity of DNA ligase. Ligase appears to proofread the EcoRV R/M system in vivo: DNA, cut
      initially in one strand at a noncognate site for the nuclease, is presumably repaired by
      ligase before the scission of the second strand.
AU  - Taylor JD
AU  - Goodall AJ
AU  - Vermote CL
AU  - Halford SE
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1990 29: 10727-10733.

PMID- 2675966
VI  - 28
DP  - 1989
TI  - Discrimination between DNA sequences by the EcoRV restriction endonuclease.
PG  - 6198-6207
AB  - The EcoRV restriction endonuclease cleaves not only its recognition sequence on
      DNA, GATATC, but also, at vastly reduced rates, a number of alternative DNA
      sequences.  The plasmid pAT153 contains 12 alternative sites, each of which
      differs from the recognition sequence by one base pair.  The EcoRV nuclease
      showed a marked preference for one particular site from among these
      alternatives.  This noncognate site was located at the sequence GTTATC, and the
      mechanism of action of EcoRV at this site was analyzed.  The mechanism differed
      from that at the cognate site in three respects.  First, the affinity of the
      enzyme for the noncognate site was lower than that for the cognate site, but,
      by itself, this cannot account for the specificity of EcoRV as measured from
      the values of Kcat/Km.  Second, the enzyme had a lower affinity for Mg2+ when
      it was bound to the noncognate site than when it was bound to its cognate site:
      this appears to be a key factor in limiting the rates of DNA cleavage at
      alternative sites.  Third, the reaction pathway at the noncognate site differed
      from that at the cognate site.  At the former, the EcoRV enzyme cleaved first
      one strand of the DNA and then the other while at the latter, both strands were
      cut in one concerted reaction.  The difference in reaction pathway allows DNA
      ligase to proofread the activity of EcoRV by selective repair of single-strand
      breaks at noncognate sites, as opposed to double-strand breaks at the cognate
      site.  The addition of DNA ligase to reactions with EcoRV made no difference to
      product formation at the cognate site, but products from reactions at
      noncognate sites were no longer detected.
AU  - Taylor JD
AU  - Halford SE
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1989 28: 6198-6207.

PMID- 1731888
VI  - 31
DP  - 1992
TI  - The activity of the EcoRV restriction endonuclease is influenced by flanking DNA sequences both inside and outside the DNA-protein complex.
PG  - 90-97
AB  - The EcoRV restriction endonuclease cleaves DNA not only at its recognition
      sequence but also at most other sequences that differ from the recognition site
      by one base pair.  Compared to the reaction at the recognition site, the
      reactions at noncognate sites are slow but 1 out of the 12 noncognate sites on
      the plasmid pAT153 is cleaved more than 50 times faster than any other.  The
      increase in the reaction rate at the preferred noncognate site, relative to
      other sites, was caused by the DNA sequences in the 4 base pairs from either
      side of the site.  For enhanced activity by EcoRV, particular bases were needed
      immediately adjacent to the site, inside the DNA-protein complex.  At these
      loci, the protein interacts with the phosphate groups in the DNA and the
      flanking sequence may control the activity of the enzyme by determining the
      conformation of the DNA, thus aligning the phosphate contacts.  But the
      preferential cleavage also depended on sequences further away from the site, at
      loci outside the complex.  At external positions, beyond the reach of the
      protein, the EcoRV enzyme required flanking sequences that give rise to
      flexibility in DNA conformation.  These may facilitate the distortion of the
      DNA required for catalysis by EcoRV.
AU  - Taylor JD
AU  - Halford SE
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1992 31: 90-97.

PMID- 20302878
VI  - 398
DP  - 2010
TI  - Structural and functional analysis of the engineered type I DNA methyltransferase EcoR124I(NT).
PG  - 391-399
AB  - The Type I R-M system EcoR124I is encoded by three genes. HsdM is responsible for modification
      (DNA methylation), HsdS for DNA sequence
      specificity and HsdR for restriction endonuclease activity. The trimeric
      methyltransferase (M(2)S) recognises the asymmetric sequence
      (GAAN(6)RTCG). An engineered R-M system, denoted EcoR124I(NT), has two
      copies of the N-terminal domain of the HsdS subunit of EcoR124I, instead
      of a single S subunit with two domains, and recognises the symmetrical
      sequence GAAN(7)TTC. We investigate the methyltransferase activity of
      EcoR124I(NT), characterise the enzyme and its subunits by analytical
      ultracentrifugation and obtain low-resolution structural models from
      small-angle neutron scattering experiments using contrast variation and
      selective deuteration of subunits.
AU  - Taylor JE
AU  - Callow P
AU  - Swiderska A
AU  - Kneale GG
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2010 398: 391-399.

PMID- 22493743
VI  - 7
DP  - 2012
TI  - Structural and Functional Analysis of the Symmetrical Type I Restriction Endonuclease R.EcoR124I(NT).
PG  - e35263
AB  - Type I restriction-modification (RM) systems are comprised of two multi-subunit enzymes, the
      methyltransferase (similar to 160 kDa),
      responsible for methylation of DNA, and the restriction endonuclease
      (similar to 400 kDa), responsible for DNA cleavage. Both enzymes share
      a number of subunits. An engineered RM system, EcoR124I(NT), based on
      the N-terminal domain of the specificity subunit of EcoR124I was
      constructed that recognises the symmetrical sequence GAAN(7)TTC and is
      active as a methyltransferase. Here, we investigate the restriction
      endonuclease activity of R.EcoR124I(NT) in vitro and the subunit
      assembly of the multi-subunit enzyme. Finally, using small-angle
      neutron scattering and selective deuteration, we present a
      low-resolution structural model of the endonuclease and locate the
      motor subunits within the multi-subunit enzyme. We show that the
      covalent linkage between the two target recognition domains of the
      specificity subunit is not required for subunit assembly or enzyme
      activity, and discuss the implications for the evolution of Type I
      enzymes.
AU  - Taylor JE
AU  - Swiderska A
AU  - Artero J-B
AU  - Callow P
AU  - Kneale G
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2012 7: e35263.

PMID- 23201446
VI  - 87
DP  - 2013
TI  - A rapid purification procedure for the HsdM protein of EcoR124I and biophysical characterization of the purified protein.
PG  - 136-140
AB  - Type I restriction-modification (R-M) systems are comprised of two multi-subunit enzymes with
      complementary functions: the
      methyltransferase (similar to 160 kDa), responsible for methylation of
      DNA, and the restriction endonuclease (similar to 400 kDa), responsible
      for DNA cleavage. Both enzymes share a number of subunits, including
      HsdM. Characterisation of either enzyme first requires the expression
      and purification of its constituent subunits, before reconstitution of
      the multisubunit complex. Previously, purification of the HsdM protein
      had proved problematic, due to the length of time required for the
      purification and its susceptibility to degradation. A new protocol was
      therefore developed to decrease the length of time required to purify
      the HsdM protein and thus prevent degradation. Finally, we show that
      the HsdM subunit exhibits a concentration dependent monomer-dimer
      equilibrium.
AU  - Taylor JE
AU  - Swiderska A
AU  - Kneale GG
PT  - Journal Article
TA  - Protein Expr. Purif.
JT  - Protein Expr. Purif.
SO  - Protein Expr. Purif. 2013 87: 136-140.

PMID- 10815954
VI  - 72
DP  - 2000
TI  - Probing specific sequences on single DNA molecules with bioconjugated fluorescent nanoparticles.
PG  - 1979-1986
AB  - Nanometer-sized fluorescent particles (latex nanobeads) have been covalently linked to DNA
      binding proteins to probe specific sequences on stretched single DNA molecules.  In comparison
      with single organic fluorophores, these nanoparticle probes are brighter, are more stable
      against photobleaching, and do not suffer from intermittent on/off light emission (blinking).
      Specifically, we demonstrate that the site-specific restriction enzyme EcoRI can be conjugated
      to 20 nm fluorescent nanoparticles and that the resulting nanoconjugates display DNA binding
      and cleavage activities of the native enzyme.  In the absence of cofactor magnesium ions, the
      EcoRI conjugates bind to specific sequences on double-stranded DNA but do not initiate
      enzymatic cutting.  For single DNA molecules that are stretched and immobilized on a solid
      surface, nanoparticles bound at specific sites can be directly visualized by multicolor
      fluorescence microscopy.  Direct observation os site-specific probes on single DNA molecules
      opens new possibilities in optical gene mapping and in fundamental study of DNA-protein
      interactions.
AU  - Taylor JR
AU  - Fang MM
AU  - Nie S
PT  - Journal Article
TA  - Anal. Chem.
JT  - Anal. Chem.
SO  - Anal. Chem. 2000 72: 1979-1986.

PMID- 3001649
VI  - 13
DP  - 1985
TI  - The use of phosphorothioate-modified DNA in restriction enzyme reactions to prepare nicked DNA.
PG  - 8749-8763
AB  - The RF IV form of M13 DNA was synthesized enzymatically in vitro, using the
      viral (+)strand as template, to contain phosphorothioate-modified
      internucleotidic linkages of the Rp configuration on the 5' side of every base
      of a particular type in the newly-synthesized (-)strand.  Twenty nine
      restriction enzymes were then tested for their reactions with the appropriate
      modified DNA types having a phosphorothioate linkage placed exactly at the
      cleavage site(s) of these enzymes in the (-)strand.  Eleven of the seventeen
      restriction enzymes tested that had recognition sequences of five bases or more
      could be used to convert the phosphorothioate DNA entirely into the nicked
      form, either by simply allowing the reaction to go to completion with excess
      enzyme (AvaI, AvaII, BanII, HindII, NciI, PstI or PvuI) or by stopping the
      reaction at the appropriate time before the nicked DNA is linearized (BamHI,
      BglI, EcoRI or HindIII).  Only modification of the exact cleavage site in the
      (-)strand could block linearization by the first class of enzymes.  The results
      presented imply that the restriction enzyme-directed nicking of
      phosphorothioate M13 DNA occurs exclusively in the (+)strand.
AU  - Taylor JW
AU  - Schmidt W
AU  - Cosstick R
AU  - Okruszek A
AU  - Eckstein F
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1985 13: 8749-8763.

PMID- 15941999
VI  - 151
DP  - 2005
TI  - Oral immunization with a dam mutant of Yersinia pseudotuberculosis protects against plague.
PG  - 1919-1926
AB  - Inactivation of the gene encoding DNA adenine methylase (dam) has been shown to attenuate some
      pathogens such as Salmonella enterica serovar
      Typhimurium and is a lethal mutation in others such as Yersinia
      pseudotuberculosis strain YPIII. In this study the dam methylase gene
      in Yersinia pseudotuberculosis strain IP32953 was inactivated. Unlike
      the wild-type, DNA isolated from the mutant could be digested with
      Mbol, which is consistent with an altered pattern of DNA methylation.
      The mutant was sensitive to bile salts but not to 2-aminopurine. The
      effect of dam inactivation on gene expression was examined using a DNA
      microarray. In BALB/c mice inoculated orally or intravenously with the
      dam mutant, the median lethal dose (MLD) was at least 10(6)-fold higher
      than the MLD of the wild-type. BALB/c mice inoculated with the mutant
      were protected against a subcutaneous challenge with 100 MLDs of
      Yersinia pestis strain GB and an intravenous challenge with 300 MLDs of
      Y. pseudotuberculosis IP32953.
AU  - Taylor VL
AU  - Titball RW
AU  - Oyston PCF
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2005 151: 1919-1926.

PMID- 27795242
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Two Novel Pseudomonas Strains Exhibiting Differential Hypersensitivity Reactions on Tobacco and Corn Seedlings.
PG  - e01057-16
AB  - Two novel Pseudomonas strains (S1E40 and S3E12) isolated from corn roots are antagonistic to
      Rhizoctonia solani and exhibit differential hypersensitivity
      reactions on tobacco and corn seedlings. We report here the draft genome
      sequences of strains S1E40 and S3E12, consisting of 6.98 and 7.06 Mb with 6,150
      and 6,129 predicted protein-coding sequences, respectively.
AU  - Tchagang CF
AU  - Xu R
AU  - Mehrtash S
AU  - Rahimi S
AU  - Sidibe A
AU  - Li X
AU  - Bromfield ES
AU  - Tambong JT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01057-16.

PMID- 18295883
VI  - 59
DP  - 2008
TI  - Actinomycete integrative and conjugative pMEA-like elements of Amycolatopsis and Saccharopolyspora decoded.
PG  - 202-216
AB  - Actinomycete integrative and conjugative elements (AICEs) are present in
      diverse genera of the actinomycetes, the most important bacterial
      producers of bioactive secondary metabolites. Comparison of pMEA100 of
      Amycolatopsis mediterranei, pMEA300 of Amycolatopsis methanolica and
      pSE211 of Saccharopolyspora erythraea, and other AICEs, revealed a highly
      conserved structural organisation, consisting of four functional modules
      (replication, excision/integration, regulation, and conjugative transfer).
      Features conserved in all elements, or specific for a single element, are
      discussed and analysed. This study also revealed two novel putative AICEs
      (named pSE222 and pSE102) in the Sac. erythraea genome, related to the
      previously described pSE211 and pSE101 elements. Interestingly, pSE102
      encodes a putative aminoglycoside phosphotransferase which may confer
      antibiotic resistance to the host. Furthermore, two of the six pSAM2-like
      insertions in the Streptomyces coelicolor genome described by Bentley et
      al. [Bentley, S.D., Chater, K.F., Cerdeno-Tarraga, A.M., et al., 2002.
      Complete genome sequence of the model actinomycete Streptomyces coelicolor
      A3(2). Nature 417, 141-147] could be functional AICEs. Homologues of
      various AICE proteins were found in other actinomycetes, in Frankia
      species and in the obligate marine genus Salinispora and may be part of
      novel AICEs as well. The data presented provide a better understanding of
      the origin and evolution of these elements, and their functional
      properties. Several AICEs are able to mobilise chromosomal markers,
      suggesting that they play an important role in horizontal gene transfer
      and spread of antibiotic resistance, but also in evolution of genome
      plasticity.
AU  - te Poele EM
AU  - Samborskyy M
AU  - Oliynyk M
AU  - Leadlay PF
AU  - Bolhuis H
AU  - Dijkhuizen L
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 2008 59: 202-216.

PMID- 28593028
VI  - 12
DP  - 2017
TI  - Genomics insights into production of 2-methylisoborneol and a putative cyanobactin by Planktothricoides sp. SR001.
PG  - 35
AB  - Planktothricoides is a free-living filamentous cyanobacterium belonging to the order
      Oscillatoriales and the family Phormidiaceae, capable of forming bloom in
      fresh and brackish waters. A unicyanobacterial non-axenic culture dominated by
      Planktothricoides sp. SR001 was obtained from a freshwater reservoir in
      Singapore. The draft genome presented here is the first tropical freshwater
      Planktothricoides sp. ever sequenced. The genome of 7.0Mbp contains 5,776 genes
      predicted using the JGI IMG pipeline. The whole genome sequence allows
      identification of genes encoding for nitrogen-fixation, accessory photosynthetic
      pigments and biosynthesis of an off-flavor compound, 2-methylisoborneol, which
      has been experimentally verified here based on metabolite detection. In addition,
      strain SR001 genome contains an operon putatively involved in the production of a
      linear tripeptide cyanobactin related to viridisamide A and aeruginosamide, with
      the later known to possess anti-microbial or cytotoxic effect.
AU  - Te SH
AU  - Tan BF
AU  - Boo CY
AU  - Thompson JR
AU  - Gin KY
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 35.

PMID- 27738032
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Two Benthic Cyanobacteria, Oscillatoriales USR 001 and  Nostoc sp. MBR 210, Isolated from Tropical Freshwater Lakes.
PG  - e01115-16
AB  - Genomes of two filamentous benthic cyanobacteria were obtained from cocultures obtained from
      two freshwater lakes. The cultures were obtained by first growing
      cyanobacterial trichome on solid medium, followed by subculturing in freshwater
      media. Subsequent shotgun sequencing, de novo assembly, and genomic binning
      yielded almost complete genomes of Oscillatoriales USR 001 and Nostoc sp. MBR
      210.
AU  - Te SH
AU  - Tan BF
AU  - Thompson JR
AU  - Gin KY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01115-16.

PMID- 
VI  - 101
DP  - 2001
TI  - Variations in the surface proteins and in the restriction and modification systems of Mycoplasma pulmonis in the respiratory tract of  infected rats.
PG  - 386
AB  - Restriction and modification (R-M) systems are thought to afford bacteria protection from
      invading foreign DNA. We hypothesize that the
      phase-variable R-M systems found within the hsd loci, as well as the
      variable surface antigens, of Mycoplasma pulmonis may additionally have
      a critical role in survival within the rat respiratory tract.
      Populations of M. pulmonis strain X1048 were isolated from
      experimentally infected Fischer F344 rats and assayed by a combination
      of Western blot, PCR and phage plaquing experiments to determine the
      predominant variable surface antigen (Vsa) and Hsd proteins. Isolates
      from the nose were found to produce VsaA and possessed no R-M activity,
      while 38% of isolates from the throat at 14 days postinfection produced
      a protein other than VsaA with 31% having active R-M systems. To assess
      the stability of various isolates from the rat throat, selected
      isolates were passaged 30 times in vitro and were found to revert to a
      phenotype of VsaA with inactive R-M systems. Therefore, the data
      suggest that different selection pressures within tissues influence the
      cell population in regards to surface antigen variation and R-M
      production, and subsequently may affect survival of the mycoplasma
      within an animal.
AU  - Teachman AM
AU  - Gumulak-Smith JJ
AU  - Tu AT
AU  - Simecka JW
AU  - Lindsey JR
AU  - Dybvig K
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 2001 101: 386.

PMID- 29780850
VI  - 5
DP  - 2018
TI  - Canada-Wide Epidemic of emm74 Group A Streptococcus Invasive Disease.
PG  - ofy085
AB  - Background: The number of invasive group A Streptococcus (iGAS) infections due to
      hitherto extremely rare type emm74 strains has increased in several Canadian
      provinces since late 2015. We hypothesized that the cases recorded in the
      different provinces are linked and caused by strains of an emm74 clone that
      recently emerged and expanded explosively. Methods: We analyzed both active and
      passive surveillance data for iGAS infections and used whole-genome sequencing to
      investigate the phylogenetic relationships of the emm74 strains responsible for
      these invasive infections country-wide. Results: Genome analysis showed that
      highly clonal emm74 strains, genetically different from emm74 organisms
      previously circulating in Canada, were responsible for a country-wide epidemic of
      >160 invasive disease cases. The emerging clone belonged to multilocus sequence
      typing ST120. The analysis also revealed dissemination patterns of emm74
      subclonal lineages across Canadian provinces. Clinical data analysis indicated
      that the emm74 epidemic disproportionally affected middle-aged or older male
      individuals. Homelessness, alcohol abuse, and intravenous drug usage were
      significantly associated with invasive emm74 infections. Conclusions: In a period
      of 20 months, an emm74 GAS clone emerged and rapidly spread across several
      Canadian provinces located more than 4500 km apart, causing invasive infections
      primarily among disadvantaged persons.
AU  - Teatero S
AU  - McGeer A
AU  - Tyrrell GJ
AU  - Hoang L
AU  - Smadi H
AU  - Domingo MC
AU  - Levett PN
AU  - Finkelstein M
AU  - Dewar K
AU  - Plevneshi A
AU  - Athey TB
AU  - Gubbay JB
AU  - Mulvey MR
AU  - Martin I
AU  - Demczuk W
AU  - Fittipaldi N
PT  - Journal Article
TA  - Open Forum Infect. Dis.
JT  - Open Forum Infect. Dis.
SO  - Open Forum Infect. Dis. 2018 5: ofy085.

PMID- 1665360
VI  - 112
DP  - 1991
TI  - New systems of host specificity of DNA Pae610 and Pae603.
PG  - 91-94
AB  - In order to find new systems of host specificity, wide screening among different strains of P.
      aeruginosa was carried out.  By means of cross-titration of phages BT and FP-series two new
      systems of modification-restriction were identified: Pae610 and Pae603.  They differ from the
      known system of host specificity PaeR7.
AU  - Tediashivili MI
AU  - Goryan TV
AU  - Koberidse TD
AU  - Chanishvili TG
AU  - Nikolskaya II
PT  - Journal Article
TA  - Biull. Eksp. Biol. Med.
JT  - Biull. Eksp. Biol. Med.
SO  - Biull. Eksp. Biol. Med. 1991 112: 91-94.

PMID- Not included in PubMed...
VI  - 112
DP  - 1991
TI  - New host DNA specificity systems Pae 610 and Pae 603.
PG  - 91-94
AB  - To find new systems of host specificity (SHS), wide screening among different
      strains of Pseudomonas aeruginosa was carried out.  By means of cross-titration
      of phages BT and FP-series two new systems of restriction-modification were
      identified:  Pae610 and Pae603.  They differ from the known system of host
      specificity PaeR7.
AU  - Tediashvili MI
AU  - Goryan TV
AU  - Koberidze TD
AU  - Chanishvili TG
AU  - Nikolskaya II
PT  - Journal Article
TA  - Bull. Exp. Biol. Med.
JT  - Bull. Exp. Biol. Med.
SO  - Bull. Exp. Biol. Med. 1991 112: 91-94.

PMID- 7000200
VI  - 90
DP  - 1980
TI  - Identification of host specific system in Shigella.
PG  - 324-325
AB  - The presence of a DNA host specific system in Shigella sonnei 47843 bacteria has been
      demonstrated.  Phage DDIII grown on the cells of Shigella stutzeri 2, in Shigella sonnei 47843
      cells is restricted by a factor of 10^5.  Phage T3 of EcoB phenotype as well as DDIII phage is
      restricted in these cells.  This circumstance means that the restriction-modification system
      of Shigella sonnei 47843 differs in specificity from the well known system E. coli.  The
      results obtained are the second case of host specific system identification in Shigella.  The
      biological properties of the strain (form of the colonies, colicinogenic activity, antibiotic
      resistance, ability to ferment sugars, etc.) have been studied.
AU  - Tediashvili MI
AU  - Uporova TM
AU  - Nikolskaya II
AU  - Debov SS
PT  - Journal Article
TA  - Biull. Eksp. Biol. Med.
JT  - Biull. Eksp. Biol. Med.
SO  - Biull. Eksp. Biol. Med. 1980 90: 324-325.

PMID- 28360174
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of Isolates of Enterococcus faecium Sequence Type 117,  a Globally Disseminated Multidrug-Resistant Clone.
PG  - e01553-16
AB  - The emergence of nosocomial infections by multidrug-resistant sequence type 117 (ST117)
      Enterococcus faecium has been reported in several European countries.
      ST117 has been detected in Spanish hospitals as one of the main causes of
      bloodstream infections. We analyzed genome variations of ST117 strains isolated
      in Madrid and describe the first ST117 closed genome sequences.
AU  - Tedim AP
AU  - Lanza VF
AU  - Manrique M
AU  - Pareja E
AU  - Ruiz-Garbajosa P
AU  - Canton R
AU  - Baquero F
AU  - Coque TM
AU  - Tobes R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01553-16.

PMID- 12117937
VI  - 70
DP  - 2002
TI  - One of Two Copies of the Gene for the Activatable Shiga Toxin Type 2d in Escherichia coli O91:H21 Strain B2F1 Is Associated with an Inducible Bacteriophage.
PG  - 4282-4291
AB  - Shiga toxin (Stx) types 1 and 2 are encoded within intact or defective temperate
      bacteriophages in Stx-producing Escherichia coli (STEC), and expression of these toxins is
      linked to bacteriophage induction. Among Stx2 variants, only stx(2e) from one human STEC
      isolate has been reported to be carried within a toxin-converting phage. In this study, we
      examined the O91:H21 STEC isolate B2F1, which carries two functional alleles for the potent
      activatable Stx2 variant toxin, Stx2d, for the presence of Stx2d-converting bacteriophages. We
      first constructed mutants of B2F1 that produced one or the other Stx2d toxin and found that
      the mutant that produced only Stx2d1 made less toxin than the Stx2d2-producing mutant.
      Consistent with that result, the Stx2d1-producing mutant was attenuated in a
      streptomycin-treated mouse model of STEC infection. When the mutants were treated with
      mitomycin C to promote bacteriophage induction, Vero cell cytotoxicity was elevated only in
      extracts of the Stx2d1-producing mutant. Additionally, when mice were treated with
      ciprofloxacin, an antibiotic that induces the O157:H7 Stx2-converting phage, the animals were
      more susceptible to the Stx2d1-producing mutant. Moreover, an stx(2d1)-containing lysogen was
      isolated from plaques on strain DH5alpha that had been exposed to lysates of the mutant that
      produced Stx2d1 only, and supernatants from that lysogen transformed with a plasmid encoding
      RecA were cytotoxic when the lysogen was induced with mitomycin C. Finally,
      electron-microscopic examination of extracts from the Stx2d1-producing mutant showed hexagonal
      particles that resemble the prototypic Stx2-converting phage 933W. Together these observations
      provide strong evidence that expression of Stx2d1 is bacteriophage associated. We conclude
      that despite the sequence similarity of the stx(2d1)- and stx(2d2)-flanking regions in B2F1,
      Stx2d1 expression is repressed within the context of its toxin-converting phage while Stx2d2
      expression is independent of phage induction.
AU  - Teel LD
AU  - Melton-Celsa AR
AU  - Schmitt CK
AU  - O'Brien AD
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2002 70: 4282-4291.

PMID- 14513380
VI  - 218
DP  - 2004
TI  - Characterization of two rice DNA methyltransferase genes and RNAi-mediated reactivation of a silenced transgene in rice callus.
PG  - 337-349
AB  - Two genomic clones (OsMET1-1, AF462029 and OsMET1-2, TPA BK001405), each encoding a
      cytosine-5 DNA methyltransferase (MTase), were isolated
      from rice (Oryza sativa L.) BAC libraries. OsMET1-1 has an open reading
      frame of 4,566 nucleotides with 12 exons and 11 introns while OsMET1-2
      has an open reading frame of 4,491 nucleotides with 11 exons and 10
      introns. Although OsMET1-1 and OsMET1-2 have high sequence similarity
      overall, they share only 24% identity in exon 1, and intron 3 of
      OsMET1-1 is absent from OsMET1-2. As for other eukaryotic DNA MTases of
      the Dnmt1/MET l class, the derived amino acid sequences of OsMET1-1 and
      OsMET1-2 suggest that they are comprised of two-thirds regulatory
      domain and one-third catalytic domain. Most functional domains
      identified for other MTases were present in the rice MET1 sequences.
      Amino acid sequence comparison indicated high similarity (56-75%
      identity) of rice MET1 proteins to other plant MET1 sequences but
      limited similarity (approx. 24% identity) to animal Dnmt1 proteins.
      Genomic blot and database analysis indicated the presence of a single
      copy of OsMET1-1 (on chromosome 3) and single copy of OsMET1-2 (on
      chromosome 7). Ribonuclease protection assays revealed expression of
      both OsMET1-1 and OsMET1-2 in highly dividing cells, but the
      steady-state level of OsMET1-2 was 7- to 12-fold higher than that for
      OsMET1-1 in callus, root and inflorescence. The functional involvement
      of the rice DNA MTases in gene silencing was investigated using an RNAi
      strategy. Inverted repeat constructs of either the N- or C-terminal
      regions of OsMET1-1 were supertransformed into calli derived from a
      rice line bearing a silenced 35S-uidA-nos transgene. Restoration of
      uidA expression in the bombarded calli was consistent with the
      inactivation of maintenance methylation and with previous evidence for
      the involvement of methylation in silencing of this line.
AU  - Teerawanichpan P
AU  - Chandrasekharan MB
AU  - Jiang YM
AU  - Narangajavana J
AU  - Hall TC
PT  - Journal Article
TA  - Planta
JT  - Planta
SO  - Planta 2004 218: 337-349.

PMID- 
VI  - 0
DP  - 2001
TI  - DNA methyltransferase and developmental processes in rice.
PG  - 155-156
AB  - Expression of antisense constructs of Arabidopsis methyltransferase (METI) results in
      decreased methylation and multiple morphological abnormalities. To explore the involvement of
      DNA methylation in monocot plant development and gene silencing, the endogenous Dnmt1 of rice
      (GenBank AF155874) was debilitated by either antisense RNA or dsRNA. N- and C- terminal
      regions (N-Dnmt1 and C-Dnmt1) of rice Dnmt1 in pRM1 were separately cloned into a binary
      vector (pPT2) in order to investigate the importance of each domain in developmental
      processes. Each gene construct had a maize ubiquitin promoter, a nos terminator and included
      either gfp or uidA as a reporter. Agrobacterium-mediated transformation was used to introduce
      either antisense (as-N-Dnmt1 and as-C-Dnmt1) or inverted repeat (ir-N-Dnmt1 or ir-C-Dnmt1)
      constructs of Dnmt1 into rice in order to silence expression of endogenous Dnmt1. Compared
      with wt plants, transgenic plants PT41-1, PT41-2 and PT41-3 (carrying as-N-Dnmt1) showed
      decreased fertility (80-100%), smaller leaves and reduced height (33%). Plants PT41-1 and -2
      had 7-10 tillers while PT41-3 had multiple (20) tillers. Various defects in flower morphology
      were noted, including stunted flowers with curled lemma and palea; stamen with short
      filaments, and anthers with little pollen. Plants containing the dsRNA (ir) constructs are in
      regeneration. Detailed molecular analyses of the methylation-deficient transformants are
      underway and the relationship between the severity of phenotypic defects and DNA methylation
      levels will be determined. The ability of the constructs to release silencing in other rice
      lines is being evaluated using both in vitro and in vivo approaches.
AU  - Teerawanichpan P
AU  - Jiang Y
AU  - Dong J
AU  - Hall TC
AU  - Narangajavana J
PT  - Journal Article
TA  - Plant Biol.
JT  - Plant Biol.
SO  - Plant Biol. 2001 0: 155-156.

PMID- 19401269
VI  - 47
DP  - 2009
TI  - Purification and characterization of rice DNA methyltransferase.
PG  - 671-680
AB  - Epigenetic modification is essential for normal development and plays important roles in gene
      regulation in higher plants. Multiple factors
      interact to regulate the establishment and maintenance of DNA
      methylation in plant genome. We had previously cloned and characterized
      DNA methyltransferase (DNA MTase) gene homologues (OsMET1) from rice.
      In this present study, determination of DNA MTase activity in different
      cellular compartments showed that DNA MTase was enriched in nuclei and
      the activity was remarkably increased during imbibing dry seeds. We had
      optimized the purification technique for DNA MTase enzyme from shoots
      of 10-day-old rice seedlings using the three successive chromatographic
      columns. The Econo-Pac Q the Hitrap-Heparin and the Superdex-200
      columns yielded a protein fraction of a specific activity of 29, 298
      and 800 purification folds, compared to the original nuclear extract,
      respectively. The purified protein preferred hemi-methylated DNA
      substrate, suggesting the maintenance activity of methylation. The
      native rice DNA MTase was approximately 160-170 kDa and exhibited a
      broad pH optimum in the range of 7.6 and 8.0. The enzyme kinetics and
      inhibitory effects by methyl donor analogs, base analogs, cations, and
      cationic amines on rice DNA MTase were examined. Global cytosine
      methylation status of rice genome during development and in various
      tissue culture systems were monitored and the results suggested that
      the cytosine methylation level is not directly correlated with the DNA
      MTase activity. The purification and characterization of rice DNA MTase
      enzyme are expected to enhance our understanding of this enzyme
      function and their possible contributions in Gramineae plant
      development.
AU  - Teerawanichpan P
AU  - Krittanai P
AU  - Chauvatcharin N
AU  - Narangajavana J
PT  - Journal Article
TA  - Plant Physiol. Biochem.
JT  - Plant Physiol. Biochem.
SO  - Plant Physiol. Biochem. 2009 47: 671-680.

PMID- 29295750
VI  - 41
DP  - 2018
TI  - Ereboglobus luteus gen. nov. sp. nov. from cockroach guts, and new insights into the oxygen relationship of the genera Opitutus and Didymococcus (Verrucomicrobia: Opitutaceae).
PG  - 101-112
AB  - We isolated a novel member of the phylum Verrucomicrobia from the hindgut of the
      cockroach Shelfordella lateralis. Strain Ho45 is a yellow-pigmented, motile
      coccus that represents a new genus-level lineage with less than 93% sequence
      similarity to the 16S rRNA genes of other species in the family Opitutaceae.
      Ultrastructural analysis revealed a Gram-negative cell envelope with an outer
      membrane and a periplasmic space. In its ability to ferment sugars to propionate
      and acetate as major products, strain Ho45 resembles its closest relative,
      Opitutus terrae. However, the strains differed in their relationship to oxygen.
      Although strain Ho45 grew and consumed oxygen at sub-atmospheric concentrations
      (1-4%), both growth rate and cell yield decreased strongly with increasing oxygen
      concentration in the headspace. By contrast, O. terrae, previously described as
      an obligate anaerobe, proved to be facultatively aerobic, with highest growth
      rates and cell yields at 2% and 16% oxygen, respectively. Also the closely
      related Didymococcus (Diplosphaera) colitermitum, previously described as an
      obligately aerobic microaerophile, showed a fermentative metabolism under anoxic
      conditions, forming the same products from glucose as strain Ho45 and O. terrae.
      Based on phenotypic and phylogenetic evidence, we propose strain Ho45 as the type
      strain of a novel genus, Ereboglobus luteus gen. nov. sp. nov., and provide an
      emended description of the family Opitutaceae and the genera Opitutus and
      Didymococcus.
AU  - Tegtmeier D
AU  - Belitz A
AU  - Radek R
AU  - Heimerl T
AU  - Brune A
PT  - Journal Article
TA  - Syst. Appl. Microbiol.
JT  - Syst. Appl. Microbiol.
SO  - Syst. Appl. Microbiol. 2018 41: 101-112.

PMID- 27151799
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Three Multiantibiotic-Resistant Campylobacter jejuni Strains (2865, 2868, and 2871) Isolated from Poultry at Retail Outlets in  Malaysia.
PG  - e00331-16
AB  - Campylobacter jejuni is a frequent cause of human bacterial gastrointestinal foodborne disease
      worldwide. Antibiotic resistance in this species is of public
      health concern. The draft genome sequences of three multiantibiotic-resistant C.
      jejuni strains (2865, 2868, and 2871) isolated from poultry at retail outlets in
      Malaysia are presented here.
AU  - Teh AH
AU  - Lee SM
AU  - Dykes GA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00331-16.

PMID- 26457128
VI  - 10
DP  - 2015
TI  - Complete genome sequence of the thermophilic Thermus sp. CCB_US3_UF1 from a hot spring in Malaysia.
PG  - 76
AB  - Thermus sp. strain CCB_US3_UF1 is a thermophilic bacterium of the genus Thermus,  a member of
      the family Thermaceae. Members of the genus Thermus have been widely
      used as a biological model for structural biology studies and to understand the
      mechanism of microbial adaptation under thermal environments. Here, we present
      the complete genome sequence of Thermus sp. CCB_US3_UF1 isolated from a hot
      spring in Malaysia, which is the fifth member of the genus Thermus with a
      completely sequenced and publicly available genome (Genbank date of release:
      December 2, 2011). Thermus sp. CCB_US3_UF1 has the third largest genome within
      the genus. The complete genome comprises of a chromosome of 2.26 Mb and a plasmid
      of 19.7 kb. The genome contains 2279 protein-coding and 54 RNA genes. In
      addition, its genome revealed potential pathways for the synthesis of secondary
      metabolites (isoprenoid) and pigments (carotenoid).
AU  - Teh BS
AU  - Lau NS
AU  - Ng FL
AU  - Abdul RAY
AU  - Wan X
AU  - Saito JA
AU  - Hou S
AU  - Teh AH
AU  - Najimudin N
AU  - Alam M
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 76.

PMID- 25908146
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Fish Pathogen Aeromonas hydrophila AL06-06.
PG  - e00368-15
AB  - Aeromonas hydrophila occurs in freshwater environments and infects fish and mammals. Here, we
      report the complete genome sequence of Aeromonas hydrophila
      AL06-06, which was isolated from diseased goldfish and is being used for
      comparative genomic studies with A. hydrophila strains that cause bacterial
      septicemia in channel catfish aquaculture.
AU  - Tekedar HC
AU  - Karsi A
AU  - Akgul A
AU  - Kalindamar S
AU  - Waldbieser GC
AU  - Sonstegard T
AU  - Schroeder SG
AU  - Lawrence ML
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00368-15.

PMID- 22535941
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Fish Pathogen Flavobacterium columnare ATCC 49512.
PG  - 2763-2764
AB  - Flavobacterium columnare is a Gram-negative, rod-shaped, motile, and highly prevalent fish
      pathogen causing columnaris disease in freshwater fish worldwide.
      Here, we present the complete genome sequence of F. columnare strain ATCC 49512.
AU  - Tekedar HC
AU  - Karsi A
AU  - Gillaspy AF
AU  - Dyer DW
AU  - Benton NR
AU  - Zaitshik J
AU  - Vamenta S
AU  - Banes MM
AU  - Gulsoy N
AU  - Aboko-Cole M
AU  - Waldbieser GC
AU  - Lawrence ML
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2763-2764.

PMID- 28104665
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Three Aeromonas hydrophila Isolates from Catfish and Tilapia.
PG  - e01509-16
AB  - Aeromonas hydrophila is a Gram-negative bacterium that is particularly adapted to freshwater
      environments and can cause severe infections in fish and humans. Here,
      we report the draft genomes of three A. hydrophila catfish and tilapia isolates.
AU  - Tekedar HC
AU  - Kumru S
AU  - Kalindamar S
AU  - Karsi A
AU  - Waldbieser GC
AU  - Sonstegard T
AU  - Schroeder SG
AU  - Liles MR
AU  - Griffin MJ
AU  - Lawrence ML
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01509-16.

PMID- 27231367
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Aeromonas hydrophila TN97-08.
PG  - e00436-16
AB  - Aeromonas hydrophila is an opportunistic pathogen residing in freshwater environments that
      causes infection in fish and mammals. Here, we report the draft
      genome sequence of A. hydrophila strain TN97-08 isolated from a diseased bluegill
      (Lepomis macrochirus) in 1997.
AU  - Tekedar HC
AU  - Kumru S
AU  - Karsi A
AU  - Waldbieser GC
AU  - Sonstegard T
AU  - Schroeder SG
AU  - Liles MR
AU  - Griffin MJ
AU  - Lawrence ML
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00436-16.

PMID- 27540076
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Four Virulent Aeromonas hydrophila Strains from Catfish Aquaculture.
PG  - e00860-16
AB  - Since 2009, a clonal group of virulent Aeromonas hydrophila strains has been causing severe
      disease in the catfish aquaculture industry in the southeastern
      United States. Here, we report draft genomes of four A. hydrophila isolates from
      catfish aquaculture that represent this clonal group.
AU  - Tekedar HC
AU  - Kumru S
AU  - Karsi A
AU  - Waldbieser GC
AU  - Sonstegard T
AU  - Schroeder SG
AU  - Liles MR
AU  - Griffin MJ
AU  - Lawrence ML
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00860-16.

PMID- 21677855
VI  - 4
DP  - 2011
TI  - Permanent draft genome sequence of Vibrio tubiashii strain NCIMB 1337 (ATCC19106).
PG  - 183-190
AB  - Vibrio tubiashii NCIMB 1337 is a major and increasingly prevalent pathogen of bivalve
      mollusks, and shares a close phylogenetic relationship with both V.
      orientalis and V. coralliilyticus. It is a Gram-negative, curved rod-shaped
      bacterium, originally isolated from a moribund juvenile oyster, and is both
      oxidase and catalase positive. It is capable of growth under both aerobic and
      anaerobic conditions. Here we describe the features of this organism, together
      with the draft genome and annotation. The genome is 5,353,266 bp long, consisting
      of two chromosomes, and contains 4,864 protein-coding and 86 RNA genes.
AU  - Temperton B
AU  - Thomas S
AU  - Tait K
AU  - Parry H
AU  - Emery M
AU  - Allen M
AU  - Quinn J
AU  - Macgrath J
AU  - Gilbert J
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 4: 183-190.

PMID- 26383666
VI  - 3
DP  - 2015
TI  - Complete DNA Sequence of Pseudomonas syringae pv. actinidiae, the Causal Agent of Kiwifruit Canker Disease.
PG  - e01054-15
AB  - Pseudomonas syringae pv. actinidiae is the causal agent of bacterial canker of kiwifruit, a
      disease that has rapidly spread worldwide. We have fully sequenced and assembled the
      chromosomal and plasmid DNA from P. syringae pv. actinidiae ICMP 18884 using the PacBio RS II
      platform.
AU  - Templeton MD
AU  - Warren BA
AU  - Andersen MT
AU  - Rikkerink EH
AU  - Fineran PC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01054-15.

PMID- 28302770
VI  - 5
DP  - 2017
TI  - Genome Sequence of Hypervirulent Aeromonas hydrophila Strain HZAUAH.
PG  - e00012-17
AB  - Aeromonas hydrophila, a zoonotic bacterium found in an expansive range of aquatic ecosystems,
      has been reported to cause severe diseases in fish, amphibians,
      reptiles, and mammals, including humans. Herein, we report the draft genome of
      the hypervirulent A. hydrophila strain HZAUAH isolated from a crucian in China.
AU  - Teng L
AU  - Deng L
AU  - Dong X
AU  - Wei S
AU  - Li J
AU  - Li N
AU  - Zhou Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00012-17.

PMID- 28104658
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Hypervirulent and Vaccine Candidate Streptococcus suis Strain SC19.
PG  - e01484-16
AB  - Streptococcus suis, a zoonotic bacterium found primarily in pigs, has been recognized recently
      as an emerging pathogen of humans. Herein, we describe the
      genome of Streptococcus suis strain SC19, a hypervirulent and vaccine candidate
      strain isolated from a pig amid the 2005 outbreak in China.
AU  - Teng L
AU  - Dong X
AU  - Zhou Y
AU  - Li Z
AU  - Deng L
AU  - Chen H
AU  - Wang X
AU  - Li J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01484-16.

PMID- 27056233
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of an Escherichia coli O157:H7 Strain Isolated from a Super-Shedder Steer.
PG  - e00258-16
AB  - We report here the complete genome sequence ofEscherichia coliO157:H7 strain JEONG-1266
      isolated from a super- shedder steer in northwest Florida. Cattle are
      considered a primary reservoir ofE. coliO157:H7, and those cattle that excrete
      this pathogen in their feces at levels >/=10(4) CFU/g are known as
      super-shedders.
AU  - Teng L
AU  - Ginn A
AU  - Jeon S
AU  - Kang M
AU  - Jeong KC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00258-16.

PMID- 15329383
VI  - 32
DP  - 2004
TI  - Genomic representations using concatenates of Type IIB restriction endonuclease digestion fragments.
PG  - e121
AB  - We have developed a method for genomic representation using Type IIB restriction
      endonucleases. Representation by concatenation of restriction
      digests, or RECORD, is an approach to sample the fragments generated by
      cleavage with these enzymes. Here, we show that the RECORD libraries may
      be used for digital karyotyping and for pathogen identification by
      computational subtraction.
AU  - Tengs T
AU  - LaFramboise T
AU  - Den RB
AU  - Hayes DN
AU  - Zhang J
AU  - DebRoy S
AU  - Gentleman RC
AU  - O'Neill K
AU  - Birren B
AU  - Meyerson M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2004 32: e121.

PMID- 6251853
VI  - 95
DP  - 1980
TI  - Presence of methyl adenine in the DNA of some strains of Neisseria Gonorrhoeae.
PG  - 1796-1800
AB  - Sixteen strains of Neisseria gonorrhoeae were examined for the presence of
      methyl adenine using the site-specific restriction endonucleases MboI and DpnI.
      The DNA of four strains, all of which require arginine, hypoxanthine and
      uracil for growth, contained methyl adenine.  Plasmid DNA from a
      non-methylating strain transformed into methylating strains contained methyl
      adenine when re-isolated.
AU  - Tenover FC
AU  - Clark VL
AU  - Young FE
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1980 95: 1796-1800.

PMID- 24012265
VI  - 382
DP  - 2013
TI  - First case of E anophelis outbreak in an intensive-care unit.
PG  - 855-856
AB  - The hospital infection-control team at the National University Hospital of Singapore
      identified three patients in the cardiothoracic intensive-care unit and two patients from the
      surgical ICU that were colonized with Elizabethkingia during a 3 week period in 2012.  The
      Elizabethkingia strains were identified as Elizabethkingia meningoseptica on the basis of
      matrix-assisted laser desorption-ionization time-of-flight mass spectrometry analysis.  The
      five patients, who were ventilated via tracheostomy and had central venous catheters in situ,
      received multiple courses of brad-spectrum antibiotics.  Before isolation of Elizabethkingia,
      three of the patients had underlying solid-organ malignancy, one patient had multiple
      abdominal surgeries, two patients underwent thoracic surgery, and one patient was on
      extracorporeal membrane oxygenation.  After isolation of the Elizabethkingia strain, all
      patients were treated with intravenous piperacillin and taxobactam, cotrimoxazole, or
      levofloxacin, either alone or in combination.  Three of the five patients died during their
      intensive-care admission, with sepsis contributing to the death of two patients.  Isolates of
      Elizabethkingia (designated as NUHP1, NUHP2, and NUHP3) were obtained from the three patients
      who had been warded at the cardiothoracic ICU.  NUHP1 and NUHP3 isolates were recovered from
      the sputum, whereas NUHP2 was isolated froma blood specimen.  Unfortunately, isolates from
      patients who had been warded in the surgical ICU were no longer available for further
      analysis.
AU  - Teo J
AU  - Tan SY
AU  - Tay M
AU  - Ding Y
AU  - Kjelleberg S
AU  - Givskov M
AU  - Lin RT
AU  - Yang L
PT  - Journal Article
TA  - Lancet
JT  - Lancet
SO  - Lancet 2013 382: 855-856.

PMID- 25278532
VI  - 2
DP  - 2014
TI  - First Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Typhimurium Strain ATCC 13311 (NCTC 74), a Reference Strain of Multidrug  Resistance, as Achieved by Use of PacBio Single-Molecule Real-Time Technology.
PG  - e00986-14
AB  - We report the first complete genomic sequence of Salmonella enterica subsp. enterica serovar
      Typhimurium strain ATCC 13311, the leading food-borne pathogen
      and a reference strain used in drug resistance studies. De novo assembly with
      PacBio sequencing completed its chromosome and one plasmid. They will accelerate
      the investigation into multidrug resistance in Salmonella Typhimurium.
AU  - Terabayashi Y
AU  - Juan A
AU  - Tamotsu H
AU  - Ashimine N
AU  - Nakano K
AU  - Shimoji M
AU  - Shiroma A
AU  - Teruya K
AU  - Satou K
AU  - Hirano T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00986-14.

PMID- 27365358
VI  - 4
DP  - 2016
TI  - Genome Sequence of the Psychrophilic Bacterium Tenacibaculum ovolyticum Strain da5A-8 Isolated from Deep Seawater.
PG  - e00644-16
AB  - Some bacterial species of the genus Tenacibaculum, including Tenacibaculum ovolyticum, have
      been known as fish pathogens in the sea. So far, the only published genome sequence for this
      genus is for Tenacibaculum dicentrarchi, which could also be a fish pathogen. Strain da5A-8,
      showing 100% identity to the 16S rRNA gene sequence of T. ovolyticum DSM 18103(T), was
      isolated from seawater at a depth of 344 m in Kochi, Japan, and grew optimally at 10 to 20
      degrees C. The genome sequence of strain da5A-8 revealed the possible virulence genes commonly
      observed in the genus Tenacibaculum.
AU  - Teramoto M
AU  - Zhai Z
AU  - Komatsu A
AU  - Shibayama K
AU  - Suzuki M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00644-16.

PMID- 28663298
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Lactobacillus curvatus FLEC03, a Meat-Borne Isolate from Beef Carpaccio Packaged in a Modified Atmosphere.
PG  - e00584-17
AB  - In this study, we present the draft genome sequence for Lactobacillus curvatus FLEC03. This
      strain was isolated from beef carpaccio packaged in a modified
      atmosphere. The draft genome will contribute to understanding the role of L.
      curvatus strains in food products (fermentation, biopreservation, or spoilage)
      through comparative genomics with other strains.
AU  - Teran LC
AU  - Coeuret G
AU  - Raya R
AU  - Champomier-Verges MC
AU  - Chaillou S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00584-17.

PMID- 25291769
VI  - 2
DP  - 2014
TI  - Genome Sequence and Annotation of Acremonium chrysogenum, Producer of the beta-Lactam Antibiotic Cephalosporin C.
PG  - e00948-14
AB  - The filamentous fungus Acremonium chrysogenum is the industrial producer of the beta-lactam
      antibiotic cephalosporin C. Here, we present the genome sequence of
      strain ATCC 11550, which contains genes for 8,901 proteins, 127 tRNAs, and 22
      rRNAs. Genome annotation led to the prediction of 42 gene clusters for secondary
      metabolites.
AU  - Terfehr D
AU  - Dahlmann TA
AU  - Specht T
AU  - Zadra I
AU  - Kurnsteiner H
AU  - Kuck U
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00948-14.

PMID- 24976897
VI  - 9
DP  - 2013
TI  - Genome sequence of Ensifer medicae strain WSM1369; an effective microsymbiont of  the annual legume Medicago sphaerocarpos.
PG  - 420-430
AB  - Ensifer medicae WSM1369 is an aerobic, motile, Gram-negative, non-spore-forming rod that can
      exist as a soil saprophyte or as a legume microsymbiont of Medicago.
      WSM1369 was isolated in 1993 from a nodule recovered from the roots of Medicago
      sphaerocarpos growing at San Pietro di Rudas, near Aggius in Sardinia (Italy).
      WSM1369 is an effective microsymbiont of the annual forage legumes M. polymorpha
      and M. sphaerocarpos. Here we describe the features of E. medicae WSM1369,
      together with genome sequence information and its annotation. The 6,402,557 bp
      standard draft genome is arranged into 307 scaffolds of 307 contigs containing
      6,656 protein-coding genes and 79 RNA-only encoding genes. This rhizobial genome
      is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 Genomic
      Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.
AU  - Terpolilli J
AU  - Garau G
AU  - Hill Y
AU  - Tian R
AU  - Howieson J
AU  - Brau L
AU  - Goodwin L
AU  - Han J
AU  - Liolios K
AU  - Huntemann M
AU  - Pati A
AU  - Woyke T
AU  - Mavromatis K
AU  - Markowitz V
AU  - Ivanova N
AU  - Kyrpides N
AU  - Reeve W
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 9: 420-430.

PMID- 24976888
VI  - 9
DP  - 2013
TI  - Genome sequence of Ensifer meliloti strain WSM1022; a highly effective microsymbiont of the model legume Medicago truncatula A17.
PG  - 315-324
AB  - Ensifer meliloti WSM1022 is an aerobic, motile, Gram-negative, non-spore-forming  rod that can
      exist as a soil saprophyte or as a legume microsymbiont of Medicago.
      WSM1022 was isolated in 1987 from a nodule recovered from the roots of the annual
      Medicago orbicularis growing on the Cyclades Island of Naxos in Greece. WSM1022
      is highly effective at fixing nitrogen with M. truncatula and other annual
      species such as M. tornata and M. littoralis and is also highly effective with
      the perennial M. sativa (alfalfa or lucerne). In common with other characterized
      E. meliloti strains, WSM1022 will nodulate but fixes poorly with M. polymorpha
      and M. sphaerocarpos and does not nodulate M. murex. Here we describe the
      features of E. meliloti WSM1022, together with genome sequence information and
      its annotation. The 6,649,661 bp high-quality-draft genome is arranged into 121
      scaffolds of 125 contigs containing 6,323 protein-coding genes and 75 RNA-only
      encoding genes, and is one of 100 rhizobial genomes sequenced as part of the DOE
      Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root
      Nodule Bacteria (GEBA-RNB) project.
AU  - Terpolilli J
AU  - Hill Y
AU  - Tian R
AU  - Howieson J
AU  - Brau L
AU  - Goodwin L
AU  - Han J
AU  - Liolios K
AU  - Huntemann M
AU  - Pati A
AU  - Woyke T
AU  - Mavromatis K
AU  - Markowitz V
AU  - Ivanova N
AU  - Kyrpides N
AU  - Reeve W
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 9: 315-324.

PMID- 25197438
VI  - 9
DP  - 2014
TI  - Genome sequence of Rhizobium leguminosarum bv trifolii strain WSM1689, the microsymbiont of the one flowered clover Trifolium uniflorum.
PG  - 527-539
AB  - Rhizobium leguminosarum bv. trifolii is a soil-inhabiting bacterium that has the  capacity to
      be an effective N2-fixing microsymbiont of Trifolium (clover)
      species. R. leguminosarum bv. trifolii strain WSM1689 is an aerobic, motile,
      Gram-negative, non-spore-forming rod that was isolated from a root nodule of
      Trifolium uniflorum collected on the edge of a valley 6 km from Eggares on the
      Greek Island of Naxos. Although WSM1689 is capable of highly effective
      N2-fixation with T. uniflorum, it is either unable to nodulate or unable to fix
      N2 with a wide range of both perennial and annual clovers originating from
      Europe, North America and Africa. WSM1689 therefore possesses a very narrow host
      range for effective N2 fixation and can thus play a valuable role in determining
      the geographic and phenological barriers to symbiotic performance in the genus
      Trifolium. Here we describe the features of R. leguminosarum bv. trifolii strain
      WSM1689, together with the complete genome sequence and its annotation. The
      6,903,379 bp genome contains 6,709 protein-coding genes and 89 RNA-only encoding
      genes. This multipartite genome contains six distinct replicons; a chromosome of
      size 4,854,518 bp and five plasmids of size 667,306, 518,052, 341,391, 262,704
      and 259,408 bp. This rhizobial genome is one of 20 sequenced as part of a DOE
      Joint Genome Institute 2010 Community Sequencing Program.
AU  - Terpolilli J
AU  - Rui T
AU  - Yates R
AU  - Howieson J
AU  - Poole P
AU  - Munk C
AU  - Tapia R
AU  - Han C
AU  - Markowitz V
AU  - Tatiparthi R
AU  - Mavrommatis K
AU  - Ivanova N
AU  - Pati A
AU  - Goodwin L
AU  - Woyke T
AU  - Kyrpides N
AU  - Reeve W
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 527-539.

PMID- 2997157
VI  - 260
DP  - 1985
TI  - Facilitated diffusion during catalysis by EcoRI endonuclease:  nonspecific interactions in EcoRI catalysis.
PG  - 13130-13137
AB  - The potential for processive EcoRI endonuclease hydrolysis has been examined on
      several DNA substrates containing two EcoRI sites which were embedded in
      identical sequence environments.  With a 388-base pair circular DNA, in which
      the two recognition sites are separated by 51 base pairs (shorter distance) or
      337 base pairs (longer distance), 77 and 34% of all events involved processive
      hydrolysis at ionic strengths of 0.059 and 0.13, respectively.  However, the
      frequency of processive action on linear substrates, in which the two sites
      were separated by 51 base pairs, was only 42 and 17% at these ionic strengths,
      values half those observed with the circular DNA.  Processive action not
      detectable on circular or linear substrates at an ionic strength of 0.23.
      These findings indicate that DNA search by the endonuclease occurs by
      facilitated diffusion, a mechanism in which the protein locates and leaves it
      recognition sequence by interacting with nonspecific DNA sites.  We suggest
      that processivity on linear substrates is limited to values half that for small
      circles due to partitioning of the enzyme between the two products generated by
      cleavage of a linear molecule.  Given such topological effects, measured
      processivity values imply that the endonuclease can diffuse within a DNA domain
      to locate and recognize an EcoRI site 50 to 300 base pairs distant from an
      initial binding site, with minimum search efficiencies being 80 and 30% at
      ionic strengths of 0.059 and 0.13, respectively.  The high efficiency of
      processive action indicates that a positionally correlated mode of search plays
      a major role in facilitated diffusion in this system under such conditions.
      Also consistent with this view was the identication of a striking position
      effect when two closely spaced EcoRI sites were asymmetrically positioned near
      the end of a linear DNA.  The endonuclease displays a substantial preference
      for the more centrally located recognition sequence.  This preference does not
      reflect differential sensitivity of the two sites to cleavage per se, but can
      be simply explained by preferential entry of the enzyme via the larger
      nonspecific target available to the more centrally positioned recognition
      sequence.  These conclusions differ from those of a previous qualitative
      analysis of endonuclease processivity over short distances.
AU  - Terry BJ
AU  - Jack WE
AU  - Modrich P
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1985 260: 13130-13137.

PMID- 3333364
VI  - 5
DP  - 1987
TI  - Mechanism of specific site location and DNA cleavage by EcoRI endonuclease.
PG  - 103-118
AB  - The EcoRI restriction and modification system has become one of the most
      convenient systems in which to study protein-DNA interactions.  Both EcoRI
      endonuclease and methylase recognize a two-fold symmetrical DNA sequence.  The
      endonuclease cleaves at sites indicated by arrows while the central adenines
      are methylated on the 6-amino group by the methylase (*), with the latter
      modification rendering the EcoRI sequence resistant to cleavage by the
      endonuclease.  Like all sequence specific proteins, EcoRI endonuclease displays
      finite affinity for nonspecific DNA sequences.  In this context, the problem of
      specific recognition can be divided into two questions:  (i) what is the
      mechanistic basis for discrimination of specific and nonspecific sites in
      thermodynamic and molecular terms?  (ii) what role do nonspecific interactions
      play in the kinetic path(s) utilized for specific site location?  In this paper
      we will summarize work on the thermodynamics of specific and nonspecific
      interactions and will discuss evidence indicating that nonspecific interactions
      are involved in the pathways by which EcoRI endonuclease locates an EcoRI
      sequence and leaves a cleaved site.  For discussion of molecular details of
      endonuclease DNA interactions, see chapter by Rosenberg, et al., this volume.
AU  - Terry BJ
AU  - Jack WE
AU  - Modrich P
PT  - Journal Article
TA  - Gene Amplif. Anal.
JT  - Gene Amplif. Anal.
SO  - Gene Amplif. Anal. 1987 5: 103-118.

PMID- 6309785
VI  - 258
DP  - 1983
TI  - Thermodynamic parameters governing interaction of EcoRI endonuclease with specific and nonspecific DNA sequences.
PG  - 9820-9825
AB  - Equilibrium binding of EcoRI endonuclease to DNA has been analyzed by
      nitrocellulose filter and preferential DNA cleavage methods.  Association
      constants for pBR322 and a 34-base pair molecule containing the EcoRI site of
      this plasmid in a central position were determined to be 1.9 x 10(11) M-1 and
      1.0 x 10(11) M-1 at 37C, respectively, with the stoichiometry of binding being
      0.8-+ 0.1 mol of endonuclease dimer per mol of DNA.  In contrast, the affinity
      of the enzyme for a pBR322 derivative from which the EcoRI site has been
      deleted is 3.2 x 10(9) M-1 as judged by competitive binding experiments.  If it
      is assumed that each base pair can define the beginning of a nonspecific
      binding site, this value corresponds to an affinity for nonspecific sites of
      7.4 x 10(5) M-1.  Furthermore, the affinity of the endonuclease for the
      EcoRI-methylated sequence is at least three orders of magnitude less than that
      for the unmodified recognition site.  The dependence on temperature and ionic
      strength of the equilibrium constant governing specific interactions has also
      been examined.  The temperature dependence of the reaction indicates that
      entropy increase accounts for 70% of the free energy of specific binding at
      37C.  Affinity of the endonuclease for the EcoRI site is highly dependent on
      NaCl concentration.  Analysis of this dependence according to the theory of
      Record and colleagues (Record, T.M., Jr., Lohman, T.M., and deHaseth, P. (1976)
      J. Mol. Biol. 107, 145-158) has implicated 8 ion pairs in the stability of
      specific complexes, a value identical with the number of phosphate contacts
      determined by ethylation interference analysis (Lu, A.L., Jack, W.E., and
      Modrich, P. (1981) J. Biol. Chem. 256, 13200-13206).  Extrapolation to 1 M NaCl
      suggests that nonelectrostatic interactions account for 40% of the free energy
      change associated with specific complex formation.
AU  - Terry BJ
AU  - Jack WE
AU  - Rubin RA
AU  - Modrich P
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1983 258: 9820-9825.

PMID- 3116167
VI  - 198
DP  - 1987
TI  - Recombinant derivatives of Bacillus subtilis phage Z containing the DNA methyltransferase genes of related methylation-proficient phages.
PG  - 945-952
AB  - The DNA methyltransferase (Mtase) genes of temperate Bacillus subtilis phages
      SPR, Phi3T, SPbeta and alpha11 can be transferred by transfection and
      recombination to the genome of the related nonmodifying phage Z.  Integration
      of the Mtase genes occurs in phage Z DNA at a unique location which is
      homologous with the flanking regions of the Mtase genes of the related phages.
      In lysogenic cells carrying recombinant phages, expression of the Mtase genes
      if repressed, irrespective of whether the Mtase genes were derived from phage
      donors which were homo- or heteroimmune to phage Z.
AU  - Terschuren P-A
AU  - Noyer-Weidner M
AU  - Trautner TA
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1987 198: 945-952.

PMID- 28729261
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequence of Photobacterium damselae subsp. piscicida Strain 91-197,  Isolated from Hybrid Striped Bass (Morone sp.) in the United States.
PG  - e00600-17
AB  - Photobacterium damselae subsp. piscicida is a causative bacterium of fish pasteurellosis,
      which has caused serious economic damage to aquaculture farms
      worldwide. Here, the whole-genome sequence of P. damselae subsp. piscicida
      91-197, isolated in the United States, suggests that this genome consists of two
      chromosomes and two plasmids.
AU  - Teru Y
AU  - Hikima JI
AU  - Kono T
AU  - Sakai M
AU  - Takano T
AU  - Hawke JP
AU  - Takeyama H
AU  - Aoki T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00600-17.

PMID- 21504983
VI  - 39
DP  - 2011
TI  - Evidence for an evolutionary antagonism between Mrr and Type III modification systems.
PG  - 5991-6001
AB  - The Mrr protein of Escherichia coli is a laterally acquired Type IV restriction endonuclease
      with specificity for methylated DNA. While Mrr nuclease activity can be elicited by
      high-pressure stress in E. coli MG1655, its (over)expression per se does not confer any
      obvious toxicity. In this study, however, we discovered that Mrr of E. coli MG1655 causes
      distinct genotoxicity when expressed in Salmonella typhimurium LT2. Genetic screening enabled
      us to contribute this toxicity entirely to the presence of the endogenous Type III restriction
      modification system (StyLTI) of S. typhimurium LT2. The StyLTI system consists of the Mod DNA
      methyltransferase and the Res restriction endonuclease, and we revealed that expression of the
      LT2 mod gene was sufficient to trigger Mrr activity in E. coli MG1655. Moreover, we could
      demonstrate that horizontal acquisition of the MG1655 mrr locus can drive the loss of
      endogenous Mod functionality present in S. typhimurium LT2 and E. coli ED1a, and observed a
      strong anti-correlation between close homologues of MG1655 mrr and LT2 mod in the genome
      database. This apparent evolutionary antagonism is further discussed in the light of a
      possible role for Mrr as defense mechanism against the establishment of epigenetic regulation
      by foreign DNA methyltransferases.
AU  - Tesfazgi-Mebrhatu M
AU  - Wywial E
AU  - Ghosh A
AU  - Michiels CW
AU  - Lindner AB
AU  - Taddei F
AU  - Bujnicki JM
AU  - Van Melderen L
AU  - Aertsen A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2011 39: 5991-6001.

PMID- 10710307
VI  - 287
DP  - 2000
TI  - Complete genome sequence of Neisseria meningitidis serogroup B strain MC58.
PG  - 1809-1815
AB  - The 2,272,351-base pair genome of Neisseria meningitidis strain MC58 (serogroup B), a
      causative agent of meningitis and septicemia, contains 2158 predicted coding regions, 1158
      (53.7%) of which were assigned a biological role. Three major islands of horizontal DNA
      transfer were identified; two of these contain genes encoding proteins involved in
      pathogenicity, and the third island contains coding sequences only for hypothetical proteins.
      Insights into the commensal and virulence behavior of N. meningitidis can be gleaned from the
      genome, in which sequences for structural proteins of the pilus are clustered and several
      coding regions unique to serogroup B capsular polysaccharide synthesis can be identified.
      Finally, N. meningitidis contains more genes that undergo phase variation than any pathogen
      studied to date, a mechanism that controls their expression and contributes to the evasion of
      the host immune system.
AU  - Tettelin H et al
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2000 287: 1809-1815.

PMID- 16172379
VI  - 102
DP  - 2005
TI  - Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial "pan-genome".
PG  - 13950
AB  - The development of efficient and inexpensive genome sequencing methods has revolutionized the
      study of human bacterial pathogens and improved vaccine design. Unfortunately, the sequence of
      a single genome does not reflect how genetic variability drives pathogenesis within a
      bacterial species and also limits genome-wide screens for vaccine candidates or for
      antimicrobial targets. We have generated the genomic sequence of six strains representing the
      five major disease-causing serotypes of Streptococcus agalactiae, the main cause of neonatal
      infection in humans. Analysis of these genomes and those available in databases showed that
      the S. agalactiae species can be described by a pan-genome consisting of a core genome shared
      by all isolates, accounting for approximately 80% of any single genome, plus a dispensable
      genome consisting of partially shared and strain-specific genes. Mathematical extrapolation of
      the data suggests that the gene reservoir available for inclusion in the S. agalactiae
      pan-genome is vast and that unique genes will continue to be identified even after sequencing
      hundreds of genomes.
AU  - Tettelin H et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2005 102: 13950.

PMID- 11463916
VI  - 293
DP  - 2001
TI  - Complete genome sequence of a virulent isolate of Streptococcus pneumoniae.
PG  - 498-506
AB  - The 2,160,837-base pair genome sequence of an isolate of Streptococcus pneumoniae, a
      Gram-positive pathogen that causes pneumonia, bacteremia, meningitis, and otitis media,
      contains 2236 predicted coding regions; of these, 1440 (64%) were assigned a biological role.
      Approximately 5% of the genome is composed of insertion sequences that may contribute to
      genome rearrangements through uptake of foreign DNA. Extracellular enzyme systems for the
      metabolism of polysaccharides and hexosamines provide a substantial source of carbon and
      nitrogen for S. pneumoniae and also damage host tissues and facilitate colonization. A motif
      identified within the signal peptide of proteins is potentially involved in targeting these
      proteins to the cell surface of low-guanine/cytosine (GC) Gram-positive species. Several
      surface-exposed proteins that may serve as potential vaccine candidates were identified.
      Comparative genome hybridization with DNA arrays revealed strain differences in S. pneumoniae
      that could contribute to differences in virulence and antigenicity.
AU  - Tettelin H et al
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2001 293: 498-506.

PMID- 28963213
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequences of Bacteremia Isolates of Bordetella holmesii.
PG  - e01023-17
AB  - Bordetella holmesii causes respiratory and invasive diseases in humans, but its pathogenesis
      remains poorly understood. We report here the genome sequences of
      seven bacteremia isolates of B. holmesii, including the type strain. Comparative
      analysis of these sequences may aid studies of B. holmesii biology and assist in
      the development of species-specific diagnostic strategies.
AU  - Tettelin H
AU  - Hooven TA
AU  - Zhao X
AU  - Su Q
AU  - Sadzewicz L
AU  - Tallon LJ
AU  - Fraser CM
AU  - Ratner AJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01023-17.

PMID- 22965080
VI  - 194
DP  - 2012
TI  - Genomic Insights into the Emerging Human Pathogen Mycobacterium massiliense.
PG  - 5450
AB  - Mycobacterium massiliense (Mycobacterium abscessus group) is an emerging pathogen causing
      pulmonary disease and skin and soft tissue infections. We report the
      genome sequence of the type strain CCUG 48898.
AU  - Tettelin H
AU  - Sampaio EP
AU  - Daugherty SC
AU  - Hine E
AU  - Riley DR
AU  - Sadzewicz L
AU  - Sengamalay N
AU  - Shefchek K
AU  - Su Q
AU  - Tallon LJ
AU  - Conville P
AU  - Olivier KN
AU  - Holland SM
AU  - Fraser CM
AU  - Zelazny AM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5450.

PMID- 26472843
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Acinetobacter sp. Strain VT-511 Isolated from the Stomach of a Patient with Gastric Cancer.
PG  - e01202-15
AB  - We report the draft genome sequence of Acinetobacter sp. strain VT-511, which was obtained
      from the stomach of a patient with gastric cancer. The genome of Acinetobacter sp. VT-511 is
      composed of approximately 3,416,321 bp and includes 3,214 predicted protein-coding genes.
AU  - Tetz G
AU  - Tetz V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01202-15.

PMID- 28007864
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Kluyvera intestini Strain GT-16 Isolated from the Stomach of a Patient with Gastric Cancer.
PG  - e01432-16
AB  - Here, we report the complete genome sequence of the novel, non-spore-forming Kluyvera
      intestini strain GT-16, isolated from the stomach of a patient with gastric cancer. The genome
      is 5,868,299 bp in length with a G+C content of 53.0%. It possesses 5,350 predicted
      protein-coding genes encoding virulence factors and  antibiotic resistance proteins.
AU  - Tetz G
AU  - Tetz V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01432-16.

PMID- 29371362
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Tetzosporium hominis VT-49 gen. nov., sp. nov., Isolated from the Dental Decay Plaque of a Patient with Periodontitis.
PG  - e01541-17
AB  - Here, we report the draft genome sequence of Tetzosporium hominis VT-49 gen. nov., sp. nov.,
      isolated from the dental plaque of a patient with severe
      periodontal disease. The draft genome sequence was 2,780,751 bp in length with a
      43.3% G+C content. We detected 3,001 genes, which are predicted to encode
      proteins that regulate both virulence and antibiotic resistance.
AU  - Tetz G
AU  - Tetz V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01541-17.

PMID- 26139715
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Bacilli bacterium Strain VT-13-104 Isolated from the  Intestine of a Patient with Duodenal Cancer.
PG  - e00705-15
AB  - We report the complete genome sequence of Bacilli bacterium strain VT-13-104 isolated from the
      intestine of a patient with duodenal cancer. The genome is
      composed of 3,573,421 bp, with a G+C content of 35.7%. It possesses 3,254
      predicted protein-coding genes encoding multidrug resistance transporters,
      resistance to antibiotics, and virulence factors.
AU  - Tetz G
AU  - Tetz V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00705-15.

PMID- 29326226
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Chryseobacterium mucoviscidosis sp. nov. Strain VT16-26, Isolated from the Bronchoalveolar Lavage Fluid of a Patient with Cystic Fibrosis.
PG  - e01473-17
AB  - We report here the draft genome sequence of Chryseobacterium mucoviscidosis VT16-26, a novel
      bacterium isolated from the lungs of a patient with cystic
      fibrosis. The genome was composed of 4,403,956 bp and had 36.2% G+C content. We
      detected 4,048 genes with predicted protein-coding functions, including those
      associated with antibiotic resistance and virulence.
AU  - Tetz G
AU  - Tetz V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01473-17.

PMID- 27491975
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of a Novel Bacillus sp. VT 712 Strain Isolated from the  Duodenum of a Patient with Intestinal Cancer.
PG  - e00786-16
AB  - We report here the complete genome sequence of the spore-forming Bacillus sp. strain VT 712
      isolated from the duodenum of a patient with intestinal cancer. The
      genome is 3,921,583 bp, with 37.9% G+C content. It contains 3,768 predicted
      protein-coding genes for multidrug resistance transporters, virulence factors,
      and daunorubicin resistance.
AU  - Tetz G
AU  - Tetz V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00786-16.

PMID- 26272571
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Paenibacillus sp. Strain VT 400, Isolated from the Saliva of a Child with Acute Lymphoblastic Leukemia.
PG  - e00894-15
AB  - We report here the complete genome sequence of spore-forming Paenibacillus sp. strain VT 400,
      isolated from the saliva of a child with acute lymphoblastic
      leukemia. The genome consists of 6,986,122 bp, with a G+C content of 45.8%. It
      possesses 5,777 predicted protein-coding genes encoding multidrug resistance
      transporters, virulence factors, and resistance to chemotherapeutic drugs.
AU  - Tetz G
AU  - Tetz V
AU  - Vecherkovskaya M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00894-15.

PMID- 29074664
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Kluyvera intestini sp. nov., Isolated from the Stomach of a Patient with Gastric Cancer.
PG  - e01184-17
AB  - We report here an update to the draft genome sequence of Kluyvera intestini sp. nov. strain
      GT-16, generated using MinION long-read sequencing technology. The
      complete genome sequence of the human-derived strain GT-16 measured 5,768,848 bp.
      An improved high-quality complete genome sequence provides insights into the
      mobility potential of resistance genes in this species.
AU  - Tetz G
AU  - Vecherkovskaya M
AU  - Zappile P
AU  - Dolgalev I
AU  - Tsirigos A
AU  - Heguy A
AU  - Tetz V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01184-17.

PMID- 28572333
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of a Strain of Bacillus intestinalis sp. nov., a New Member of Sporobiota Isolated from the Small Intestine of a Single Patient with Intestinal Cancer.
PG  - e00489-17
AB  - We report here the draft genome sequence of Bacillus intestinalis strain 1731, a  novel
      spore-forming bacterium isolated from the small intestine of a patient with
      intestinal cancer. The genome comprised 4,047,276 bp, with 43.9% G+C content.
      There were 3,913 predicted protein-coding genes, including those associated with
      antibiotic resistance and virulence.
AU  - Tetz V
AU  - Tetz G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00489-17.

PMID- 28254994
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Bacillus obstructivus VT-16-70 Isolated from the Bronchoalveolar Lavage Fluid of a Patient with Chronic Obstructive Pulmonary  Disease.
PG  - e01754-16
AB  - We report here the draft genome sequence of Bacillus obstructivus VT-16-70, a novel
      spore-forming bacterium isolated from the lungs of a patient with chronic
      obstructive pulmonary disease. The genome comprised 5,220,753 bp, with 35.2% G+C
      content. There were 4,972 predicted protein-coding genes, including those
      associated with antibiotic resistance and virulence.
AU  - Tetz V
AU  - Tetz G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01754-16.

PMID- 28450527
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Uropathogenic Herbaspirillumfrisingense Strain ureolyticus VT-16-41.
PG  - e00279-17
AB  - Herbaspirillum frisingense strain ureolyticus VT-16-41 is a clinical cystitis isolate. Here,
      we report the draft genome sequence of the uropathogenic H.
      frisingense strain ureolyticus VT-16-41, which contains various antibiotic
      resistance genes and virulence factors that enable it to colonize and persist in
      the urinary tract.
AU  - Tetz V
AU  - Tetz G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00279-17.

PMID- 28450522
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Bacillus respiratorii VT-16-64, Isolated from the Bronchiolar Alveolar Lavage Fluid of a Patient with Chronic Obstructive Pulmonary  Disease.
PG  - e00264-17
AB  - We report here the draft genome sequence of Bacillus respiratorii VT-16-64, a novel
      spore-forming bacterium isolated from the bronchiolar alveolar lavage fluid
      of a patient with chronic obstructive pulmonary disease. The genome was comprised
      4,831,386 bp with 4,399 predicted protein-coding genes, including those
      associated with antibiotic resistance and virulence.
AU  - Tetz V
AU  - Tetz G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00264-17.

PMID- 29700135
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Multidrug-Resistant Escherichia coli NIVEDI-P44, Isolated from a Chicken Fecal Sample in Northeast India.
PG  - e00205-18
AB  - We report here the draft genome sequence of a multidrug-resistant Escherichia coli strain
      (NIVEDI-P44) isolated from a chicken fecal sample. The estimated
      genome size is 4.76 Mb, with a G+C content of 50.65%. The genome harbors multiple
      antibiotic resistance genes, blaDHA-1, mph(A), strA, strB, dfrA14, sul-2, tet(A),
      and qnrS1.
AU  - Tewari R
AU  - Das Mitra S
AU  - Das S
AU  - Jadhao S
AU  - Mishra G
AU  - Ganaie F
AU  - Shome R
AU  - Rahman H
AU  - Shome BR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00205-18.

PMID- 28839016
VI  - 5
DP  - 2017
TI  - Genome Sequences of Escherichia coli Strains That Cause Persistent and Transient  Mastitis.
PG  - e00775-17
AB  - We report here the genome sequences of two strains of Escherichia coli (ECA-B and ECC-M) that
      cause bovine mastitis. These strains are known to be associated with
      persistent and transient mastitis; strain ECA-B causes a transient infection, and
      ECC-M leads to a persistent infection.
AU  - Thacker TC
AU  - Lippolis JD
AU  - Brunelle BW
AU  - Casey TA
AU  - Reinhardt TA
AU  - Sacco RE
AU  - Holman DB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00775-17.

PMID- 2587237
VI  - 17
DP  - 1989
TI  - Isolation and identification of restriction endonuclease BseAI.
PG  - 8881
AB  - None
AU  - Thanos D
AU  - Scarpelis G
AU  - Papamatheakis J
AU  - Bouriotis V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 8881.

PMID- 26966221
VI  - 4
DP  - 2016
TI  - Genome Sequences of Two Pseudomonas syringae pv. tomato Race 1 Strains, Isolated  from Tomato Fields in California.
PG  - e01671-15
AB  - Pseudomonas syringae pv. tomato race 1 strains have evolved to overcome genetic resistance in
      tomato. Here, we present the draft genome sequences of two race 1
      P. syringae pv. tomato strains, A9 and 407, isolated from diseased tomato plants
      in California.
AU  - Thapa SP
AU  - Coaker G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01671-15.

PMID- 28495774
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequence of Endophytic Plant Growth-Promoting Escherichia coli USML2.
PG  - e00305-17
AB  - Escherichia coli strain USML2 was originally isolated from the inner leaf tissues of
      surface-sterilized phytopathogenic-free oil palm (Elaeis guineensis Jacq.). We
      present here the whole-genome sequence of this plant-endophytic strain. The
      genome consists of a single circular chromosome of 4,502,758 bp, 4,315 predicted
      coding sequences, and a G+C content of 50.8%.
AU  - Tharek M
AU  - Sim KS
AU  - Khairuddin D
AU  - Ghazali AH
AU  - Najimudin N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00305-17.

PMID- 28546474
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Rhodococcus sp. Strain 66b.
PG  - e00229-17
AB  - We report here the draft genome sequence and annotation of Rhodococcus sp. strain 66b isolated
      from the soil of southwest Western Australia. This strain exhibits a
      range of bioactivities, including plant growth promotion, biosurfactant
      production, and wax degradation. Whole-genome sequencing was conducted to uncover
      the underlying mechanisms.
AU  - Thatcher LF
AU  - Myers CA
AU  - O'Sullivan CA
AU  - Roper MM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00229-17.

PMID- 29724840
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Streptomyces sp. Strains MH60 and 111WW2.
PG  - e00356-18
AB  - We report here the draft genome sequences, annotations, and predictions of secondary
      metabolite gene clusters of two endophytic Streptomyces species
      isolated from wheat plants growing in the Western Australian wheat belt. These
      strains, Streptomyces sp. strains MH60 and 111WW2, possess antifungal and/or
      plant growth-promoting activities.
AU  - Thatcher LF
AU  - Myers CA
AU  - O'Sullivan CA
AU  - Roper MM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00356-18.

PMID- 11130711
VI  - 408
DP  - 2000
TI  - Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.
PG  - 796-815
AB  - The flowering plant Arabidopsis thaliana is an important model system for identifying genes
      and determining their functions.  Here we report the analysis of the genomic sequence of
      Arabidopsis.  The sequenced regions cover 115.4 megabases of the 125-megabase genome and
      extend into centromeric regions.  The evolution of Arabidopsis involved a whole-genome
      duplication, followed by subsequent gene loss and extensive local gene duplications, giving
      rise to a dynamic genome enriched by lateral gene transfer from a cyanobacterial-like ancestor
      of the plastid.  The genome contains 25,498 genes encoding proteins from 11,000 families,
      similar to the functional diversity of Drosophila and Caenorhabditis elegans-the other
      sequenced multicellular eukaryotes.  Arabidopsis has many families of new proteins but also
      lacks several common protein families, indicating that the sets of common proteins have
      undergone differential expansion and contraction in the three multicellular eukaryotes.  This
      is the first complete genome sequence of a plant and provides the foundations for more
      comprehensive comparison of conserved processes in all eukaryotes, identifying a wide range of
      plant-specific gene functions and establishing rapid systematic ways to identify genes for
      crop improvement.
AU  - The AGI
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2000 408: 796-815.

PMID- 23846275
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of a Highly Flagellated, Fast-Swimming Archaeon, Methanocaldococcus villosus Strain KIN24-T80 (DSM 22612).
PG  - e00481-13
AB  - We report the draft genome sequence of a hyperthermophilic Methanocaldococcus villosus strain,
      KIN24-T80. The gene associated with its heavy flagellum
      formation was annotated in the 1.2-Mb draft genome sequence, and this strain may
      be a good model system to study the extensive functional role of flagella and
      their fast motor activity.
AU  - Thennarasu S
AU  - Polireddy D
AU  - Antony A
AU  - Yada MR
AU  - Algarawi S
AU  - Sivakumar N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00481-13.

PMID- 6295887
VI  - 19
DP  - 1982
TI  - Cloning of Pseudomonas plasmid pMG7 and its restriction-modification system in Escherichia coli.
PG  - 355-359
AB  - Plasmid pMG7 of Pseudomonas aeruginosa codes for a type II DNA
      restriction-modification (r-m) system, PaeR7.  This plasmid has not been
      observed to transfer to Escherichia coli either by conjugation or by
      transformation.  We have cloned BglII linears (42 kb) and the BamHI large
      fragment (37 kb) of pMG7 into cosmid pHC79 (6.4 kb) and introduced the
      recombinant molecules into E. coli by in vitro packaging.  Several clones were
      obtained which demonstrated in vivo restriction of phage u80.  One of these
      clones, GT138, was further tested and showed in vivo modification of Phi80.
      Extracts from two clones, GT138 and GT125, yielded a restriction endonuclease
      activity which produced fragments of u80 DNA identical to those produced by
      PaeR7.  Cosmid cloning should be useful for obtaining substantial yields of
      large fragments of plasmids that are difficult to purify in their native
      strains.
AU  - Theriault G
AU  - Roy PH
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1982 19: 355-359.

PMID- 3001639
VI  - 13
DP  - 1985
TI  - Nucleotide sequence of the PaeR7 restriction/modification system and partial characterization of its protein products.
PG  - 8441-8461
AB  - Bal31 deletion experiments on clones of the PaeR7 restriction-modification
      system from Pseudomonas aeruginosa demonstrate that it is arranged as an
      operon, with the methylase gene preceding the endonuclease gene.  The DNA
      sequence of this operon agrees with in vitro transcription-translation assays
      which predict proteins of 532 amino acids, Mr = 59,260 daltons, and 246 amino
      acids, Mr = 27,280 daltons, coincident with the methylase and endonuclease
      genes, respectively.  These predicted values coincide with the measured
      molecular weights of the purified, denatured PaeR7 endonuclease and methylase
      proteins.  The first twenty amino acids from the amino-terminus of the purified
      endonuclease exactly match those predicted from the DNA sequence.  Finally,
      potential regulatory mechanisms for the expression of phage restriction are
      described based on the properties of several PaeR7 subclones.
AU  - Theriault G
AU  - Roy PH
AU  - Howard KA
AU  - Benner JS
AU  - Brooks JS
AU  - Waters AF
AU  - Gingeras TR
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1985 13: 8441-8461.

PMID- 26929322
VI  - 113
DP  - 2016
TI  - Novel genomic island modifies DNA with 7-deazaguanine derivatives.
PG  - E1452-E1459
AB  - The discovery of approximately 20-kb gene clusters containing a family of paralogs of tRNA
      guanosine transglycosylase genes, called tgtA5, alongside
      7-cyano-7-deazaguanine (preQ0) synthesis and DNA metabolism genes, led to the
      hypothesis that 7-deazaguanine derivatives are inserted in DNA. This was
      established by detecting 2'-deoxy-preQ0 and 2'-deoxy-7-amido-7-deazaguanosine in
      enzymatic hydrolysates of DNA extracted from the pathogenic, Gram-negative
      bacteria Salmonella enterica serovar Montevideo. These modifications were absent
      in the closely related S. enterica serovar Typhimurium LT2 and from a mutant of
      S. Montevideo, each lacking the gene cluster. This led us to rename the genes of
      the S. Montevideo cluster as dpdA-K for 7-deazapurine in DNA. Similar gene
      clusters were analyzed in approximately 150 phylogenetically diverse bacteria,
      and the modifications were detected in DNA from other organisms containing these
      clusters, including Kineococcus radiotolerans, Comamonas testosteroni, and
      Sphingopyxis alaskensis. Comparative genomic analysis shows that, in
      Enterobacteriaceae, the cluster is a genomic island integrated at the leuX locus,
      and the phylogenetic analysis of the TgtA5 family is consistent with widespread
      horizontal gene transfer. Comparison of transformation efficiencies of modified
      or unmodified plasmids into isogenic S. Montevideo strains containing or lacking
      the cluster strongly suggests a restriction-modification role for the cluster in
      Enterobacteriaceae. Another preQ0 derivative,
      2'-deoxy-7-formamidino-7-deazaguanosine, was found in the Escherichia coli
      bacteriophage 9g, as predicted from the presence of homologs of genes involved in
      the synthesis of the archaeosine tRNA modification. These results illustrate a
      deep and unexpected evolutionary connection between DNA and tRNA metabolism.
AU  - Thiaville JJ
AU  - Kellner SM
AU  - Yuan Y
AU  - Hutinet G
AU  - Thiaville PC
AU  - Jumpathong W
AU  - Mohapatra S
AU  - Brochier-Armanet C
AU  - Letarov AV
AU  - Hillebrand R
AU  - Malik CK
AU  - Rizzo CJ
AU  - Dedon PC
AU  - de Crecy-Lagard V
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2016 113: E1452-E1459.

PMID- 27257195
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Streptomyces ambofaciens DSM 40697, a Paradigm for Genome Plasticity Studies.
PG  - e00470-16
AB  - The sequence of Streptomyces ambofaciens DSM 40697 was completely determined. The genome
      consists of an 8.1-Mbp linear chromosome with terminal inverted repeats of
      210 kb. Genomic islands were identified, one of which corresponds to a new
      putative integrative and conjugative element (ICE) called pSAM3.
AU  - Thibessard A
AU  - Leblond P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00470-16.

PMID- 25197444
VI  - 9
DP  - 2014
TI  - Complete genome sequence of Anabaena variabilis ATCC 29413.
PG  - 562-573
AB  - Anabaena variabilis ATCC 29413 is a filamentous, heterocyst-forming cyanobacterium that has
      served as a model organism, with an extensive literature
      extending over 40 years. The strain has three distinct nitrogenases that function
      under different environmental conditions and is capable of photoautotrophic
      growth in the light and true heterotrophic growth in the dark using fructose as
      both carbon and energy source. While this strain was first isolated in 1964 in
      Mississippi and named Anabaena flos-aquae MSU A-37, it clusters phylogenetically
      with cyanobacteria of the genus Nostoc. The strain is a moderate thermophile,
      growing well at approximately 40( degrees ) C. Here we provide some additional
      characteristics of the strain, and an analysis of the complete genome sequence.
AU  - Thiel T
AU  - Pratte BS
AU  - Zhong J
AU  - Goodwin L
AU  - Copeland A
AU  - Lucas S
AU  - Han C
AU  - Pitluck S
AU  - Land ML
AU  - Kyrpides NC
AU  - Woyke T
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 562-573.

PMID- 28619807
VI  - 5
DP  - 2017
TI  - Genome Sequence of Prosthecochloris sp. Strain HL-130-GSB from the Phylum Chlorobi.
PG  - e00538-17
AB  - The genome of the green sulfur bacterium Prosthecochloris sp. strain HL-130-GSB,  isolated
      from a cyanobacterial mat obtained from Hot Lake, a saline meromictic
      lake in Washington, USA, comprises 2,437,774 bp in a single contig. The genome is
      predicted to encode 2,565 proteins and contain 47 tRNA genes and 2 rRNA operons.
AU  - Thiel V
AU  - Drautz-Moses DI
AU  - Purbojati RW
AU  - Schuster SC
AU  - Lindemann S
AU  - Bryant DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00538-17.

PMID- 25169864
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Moderately Thermophilic Bacterium Schleiferia thermophila Strain Yellowstone (Bacteroidetes).
PG  - e00860-14
AB  - The draft genome sequence of the moderately thermophilic bacterium Schleiferia thermophila
      strain Yellowstone (Bacteroidetes), isolated from Octopus Spring
      (Yellowstone National Park, WY, USA) was sequenced and comprises 2,617,694 bp in
      35 contigs. The draft genome is predicted to encode 2,457 protein coding genes
      and 37 tRNA encoding genes and two rRNA operons.
AU  - Thiel V
AU  - Hamilton TL
AU  - Tomsho LP
AU  - Burhans R
AU  - Gay SE
AU  - Ramaley RF
AU  - Schuster SC
AU  - Steinke L
AU  - Bryant DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00860-14.

PMID- 25189583
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of a Sulfide-Oxidizing, Autotrophic Filamentous Anoxygenic  Phototrophic Bacterium, Chloroflexus sp. Strain MS-G (Chloroflexi).
PG  - e00872-14
AB  - The draft genome sequence of the thermophilic filamentous anoxygenic phototrophic bacterium
      Chloroflexus sp. strain MS-G (Chloroflexi), isolated from Mushroom
      Spring (Yellowstone National Park, WY, USA) was sequenced and comprises 4,784,183
      bp in 251 contigs. The draft genome is predicted to encode 4,059 protein coding
      genes, 49 tRNA encoding genes, and 3 rRNA operons.
AU  - Thiel V
AU  - Hamilton TL
AU  - Tomsho LP
AU  - Burhans R
AU  - Gay SE
AU  - Schuster SC
AU  - Ward DM
AU  - Bryant DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00872-14.

PMID- 28663291
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Anoxybacillusayderensis Strain MT-Cab (Firmicutes).
PG  - e00547-17
AB  - The draft genome of the Gram-positive spore-forming Anoxybacillus ayderensis strain MT-Cab
      (Firmicutes), isolated from an enrichment culture of
      Chloracidobacterium thermophilum, was sequenced and comprises 2,577,015 bp in 92
      contigs. The draft genome is predicted to consist of 2,699 protein-coding genes,
      73 tRNA-coding genes, and an estimated 8 rRNA operons.
AU  - Thiel V
AU  - Tank M
AU  - Tomsho LP
AU  - Burhans R
AU  - Gay SE
AU  - Hamilton TL
AU  - Schuster SC
AU  - Bryant DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00547-17.

PMID- 25814606
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Deinococcus-Thermus Bacterium Meiothermus ruber Strain A.
PG  - e00202-15
AB  - The draft genome sequence of the Deinococcus-Thermus group bacterium Meiothermus  ruber strain
      A, isolated from a cyanobacterial enrichment culture obtained from
      Octopus Spring (Yellowstone National Park, WY), comprises 2,968,099 bp in 170
      contigs. It is predicted to contain 2,895 protein-coding genes, 44 tRNA-coding
      genes, and 2 rRNA operons.
AU  - Thiel V
AU  - Tomsho LP
AU  - Burhans R
AU  - Gay SE
AU  - Schuster SC
AU  - Ward DM
AU  - Bryant DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00202-15.

PMID- 
VI  - 
DP  - 1988
TI  - Oligodeoxynucleotides with basepair mismatches as a substrate for EcoRI and EcoRV.
PG  - 1-84
AB  - 
AU  - Thielking V
PT  - Journal Article
TA  - Ph.D. Thesis, Medizinische Hochscule Hannover, W. Germany
JT  - Ph.D. Thesis, Medizinische Hochscule Hannover, W. Germany
SO  - Ph.D. Thesis, Medizinische Hochscule Hannover, W. Germany 1988 : 1-84.

PMID- 2372551
VI  - 29
DP  - 1990
TI  - Accuracy of the EcoRI restriction endonuclease:  Binding and cleavage studies with oligodeoxynucleotide substrates containing degenerate recognition sequences.
PG  - 4682-4691
AB  - We have synthesized a series of 18 non palindromic oligodeoxynucleotides that
      carry all possible base changes within the recognition sequence of EcoRI.
      These single strands can be combined with their complementary single strands to
      obtain all possible EcoRI sequences (left), or they can be combined with a
      single strand containing the canonical sequence to obtain double strands with
      all possible mismatches within the recognition sequence (right):
      GCGCAAATTCCGCG               GCGCAAATTCCGCG
      CGCGTTTAAGGCGC               CGCGCTTAAGGCGC
      The rate of phosphodiester bond cleavage of these oligodeoxynucleotides by
      EcoRI was determined in single-turnover experiments under normal buffer
      conditions in order to find out to what extent the canonical recognition site
      can be distorted and yet serve as a substrate for EcoRI.  Our results show that
      oligodeoxynucleotides containing mismatch base pairs are in general more
      readily attacked by EcoRI than oligodeoxynucleotides containing EcoRI sites and
      that the rates of cleavage of the two complementary strands of degenerate
      oligodeoxynucleotides are quite different.  We have also determined the
      affinities of these oligodeoxynucleotides to EcoRI.  They are higher for
      oligodeoxynucleotides carrying a mismatch within the EcoRI recognition site
      than for oligodeoxynucleotides containing an EcoRI site but otherwise do not
      correlate with the rate with which these oligodeoxynucleotides are cleaved by
      EcoRI.  Our results allow details to be given for the probability of EcoRI
      making mistakes in cleaving DNA not only in its recognition sequence but also
      in sequences closely related to it.  Due to the fact that the rates of cleavage
      in the two strands of a degenerate sequence generally are widely different,
      these mistakes are most likely not occurring in vivo since nicked intermediates
      can be repaired by DNA ligase.
AU  - Thielking V
AU  - Alves J
AU  - Fliess A
AU  - Maass G
AU  - Pingoud A
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1990 29: 4682-4691.

PMID- 9191027
VI  - 378
DP  - 1997
TI  - Dam methyltransferase from Escherichia coli: Kinetic studies using modified DNA oligomers: nonmethylated substrates.
PG  - 407-415
AB  - Steady-state kinetics of the N6-adenine Dam methyltransferase have been measured using as
      substrates non-self-complementary tetradecanucleotide duplexes that contain the GATC target
      sequence.  Modifications in the GATC target sequence of one or both of the strands included
      substitution of guanine by hypoxanthine, thymine by uracil or 5-ethyl-uracil and adenine by
      diamino-purine (2-amino-adenine).  Thermodynamic parameters for the 14-mer duplexes were also
      determined.  DNA methylation of duplexes containing single dI for dG substitution of the Dam
      recognition site was little perturbed compared with the canonical substrate.  Replacement of
      dG residues by dI in both strands resulted in a decrease of the specificity constant.
      Substitution in both strands appears to be cumulative.  Substitution of the methyl-accepting
      adenine residues by 2-amino-adenine resulted in surprisingly little perturbation.  Dam
      methyltransferase is rather tolerant to different substitutions.  The results show much less
      spread than those for the analogous hemimethylated substrates studied previously.  The absence
      of the methylation marker appears to be deleterious to the specificity of the transition state
      of the active complex, while the binding of the DNA substrate to the enzyme appears to be
      mostly determined by the thermodynamic stability of the DNA duplex.
AU  - Thielking V
AU  - Du Bois S
AU  - Eritja R
AU  - Guschlbauer W
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1997 378: 407-415.

PMID- 1567826
VI  - 31
DP  - 1992
TI  - Mg2+ confers DNA binding specificity to the EcoRV restriction endonuclease.
PG  - 3727-3732
AB  - The EcoRV mutant D90A which carries an amino acid substitution in its active center does not
      cleave DNA. Therefore, it is possible to perform DNA binding experiments with the EcoRV-D90A
      mutant both in the absence and in the presence of Mg2+. Like wild-type EcoRV [Taylor et al.
      (1991) Biochemistry 30, 8743-8753], it does not show a pronounced specificity for binding to
      its recognition site in the absence of Mg2+ as judged by the appearance of multiple shifted
      bands in an electrophoresis mobility shift assay with a 377-bp DNA fragment carrying a single
      EcoRV recognition sequence. In the presence of Mg2+, however, only one band corresponding to a
      1:1 complex appears even with a high excess of protein over DNA. This complex most likely is
      the specific one because its formation is suppressed much more effectively by a 13-bp
      oligodeoxynucleotide with an EcoRV site than by a corresponding oligodeoxynucleotide without
      an EcoRV site. The preferential interaction of the EcoRV-D90A mutant with specific DNA in the
      presence of Mg2+ was also demonstrated directly: a 20-bp oligodeoxynucleotide with an EcoRV
      site is bound with Kass=4x10/8 M-1, while a corresponding oligodeoxynucleotide without an
      EcoRV site is bound with Kass<or=1x10/5 M-1. From these data it appears that Mg2+ confers DNA
      binding specificity to this mutant by lowering the affinity to nonspecific sites and raising
      the affinity to specific sites as compared to binding in the absence of Mg2+. It is concluded
      that this is also true for wild-type EcoRV.
AU  - Thielking V
AU  - Selent U
AU  - Kohler E
AU  - Landgraf Z
AU  - Wolfes H
AU  - Alves J
AU  - Pingoud A
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1992 31: 3727-3732.

PMID- 1647200
VI  - 30
DP  - 1991
TI  - Site-directed mutagenesis studies with EcoRV restriction endonuclease to identify regions involved in recognition and catalysis.
PG  - 6416-6422
AB  - Guided by the X-ray structure analysis of a crystalline EcoRV-d(GGGATATCCC)
      complex (Winkler, in preparation), we have begun to identify functionally
      important amino acid residues of EcoRV.  We show here that Asn70, Asp74,
      Ser183, Asn185, Thr186, and Asn188 are most likely involved in the binding
      and/or cleavage of the DNA, because their conservative substitution leads to
      mutants of no or strongly reduced activity.  In addition, C-terminal amino acid
      residues of EcoRV seem to be important for its activity, since their deletion
      inactivates the enzyme.  Following the identification of three functionally
      important regions, we have inspected the sequences of other restriction and
      modification enzymes for homologous regions.  It was found that two restriction
      enzymes that recognize similar sequences as EcoRV (DpnII and HincII), as well
      as two modification enzymes (M.DpnII and, in a less apparent form, M.EcoRV),
      have the sequence motif -SerGlyXXXAsnIleXSer- in common, which in EcoRV
      contains the essential Ser183 and Asn188 residues.  Furthermore, the C-terminal
      region, shown to be essential for EcoRV, is highly homologous to a similar
      region in the restriction endonuclease SmaI.  On the basis of these findings we
      propose that these restriction enzymes and to a certain extent also some of
      their corresponding modification enzymes interact with DNA in a similar manner.
AU  - Thielking V
AU  - Selent U
AU  - Kohler E
AU  - Wolfes H
AU  - Pieper U
AU  - Geiger R
AU  - Urbanke C
AU  - Winkler FK
AU  - Pingoud A
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1991 30: 6416-6422.

PMID- 16237009
VI  - 187
DP  - 2005
TI  - Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete   genome sequence.
PG  - 7254-7266
AB  - The gram-negative plant-pathogenic bacterium Xanthomonas campestris pv. vesicatoria is the
      causative agent of bacterial spot disease in pepper and
      tomato plants, which leads to economically important yield losses. This
      pathosystem has become a well-established model for studying bacterial
      infection strategies. Here, we present the whole-genome sequence of the
      pepper-pathogenic Xanthomonas campestris pv. vesicatoria strain 85-10,
      which comprises a 5.17-Mb circular chromosome and four plasmids. The
      genome has a high G+C content (64.75%) and signatures of extensive genome
      plasticity. Whole-genome comparisons revealed a gene order similar to both
      Xanthomonas axonopodis pv. citri and Xanthomonas campestris pv. campestris
      and a structure completely different from Xanthomonas oryzae pv. oryzae. A
      total of 548 coding sequences (12.2%) are unique to X. campestris pv.
      vesicatoria. In addition to a type III secretion system, which is
      essential for pathogenicity, the genome of strain 85-10 encodes all other
      types of protein secretion systems described so far in gram-negative
      bacteria. Remarkably, one of the putative type IV secretion systems
      encoded on the largest plasmid is similar to the Icm/Dot systems of the
      human pathogens Legionella pneumophila and Coxiella burnetii. Comparisons
      with other completely sequenced plant pathogens predicted six novel type
      III effector proteins and several other virulence factors, including
      adhesins, cell wall-degrading enzymes, and extracellular polysaccharides.
AU  - Thieme F et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2005 187: 7254-7266.

PMID- 2011508
VI  - 19
DP  - 1991
TI  - Cleavage of yeast and bacteriophage T7 genomes at a single site using the rare cutter endonuclease I-SceI.
PG  - 189-190
AB  - It is obvious that the availability of rare cutter restriction endonucleases would facilitate
      large scale genome mapping, cloning and sequencing projects.  Restriction endonucleases of
      bacterial origin have recognition sites of 8 bp long, at most, and even when used in
      combination with methylases they can produce cleavage specificities of up to 12 bp only.
      Artificial endonucleases have been made by chemical modifications of either DNA binding
      proteins or synthetic oligodeoxynucleotides.  Although this last strategy can, in principle,
      be generalized to many sequences, cleavage occurs at low efficiency.  Cleavage of yeast and E.
      coli genomic DNAs at a single predetermined site using a frequent cutter bacterial
      endonuclease has recently been achieved by the Achille's heel method, an elegant three step
      procedure combining the action of the lac repressor on artificially inserted sites with that
      of a methylase.  We present here the first evidence for cleavage of total yeast genomic DNA at
      a single predetermined site in a one step procedure using a new endonuclease, I-SceI, encoded
      by a mobile group I intron of yeast mitochondria.  We further show that, although I-SceI is
      extremely specific, cleavable sites can also be found in natural DNA.
AU  - Thierry A
AU  - Perrin A
AU  - Boyer J
AU  - Fairhead C
AU  - Dujon B
AU  - Frey B
AU  - Schmitz G
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 189-190.

PMID- 24874678
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Raoultella ornithinolytica TNT, a Trinitrotoluene-Denitrating and Plant Growth-Promoting Strain Isolated from  Explosive-Contaminated Soil.
PG  - e00491-14
AB  - We report the draft genome of Raoultella ornithinolytica TNT, a Gram-negative bacterium of the
      Enterobacteriaceae isolated from military soil in Belgium.
      Strain TNT uses nitrite released from trinitrotoluene (TNT) for growth and is a
      potent plant growth promoter. An analysis of its 5.6-Mb draft genome will bring
      insights into TNT degradation-reinforcing bioremediation applications.
AU  - Thijs S
AU  - Van Hamme J
AU  - Gkorezis P
AU  - Rineau F
AU  - Weyens N
AU  - Vangronsveld J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00491-14.

PMID- 12239210
VI  - 277
DP  - 2002
TI  - The two-step cleavage activity of PI-TfuI intein endonuclease demonstrated by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.
PG  - 45442-45450
AB  - PI-TfuI, an intein spliced from the DNA polymerase of Thermococcus fumicolans, is a highly
      specific endonuclease, whose cleavage efficiency and specificity depend on both the substrate
      topology and the divalent cation used as cofactor. An open-circular intermediate was observed
      during the cleavage of supercoiled DNA by PI-TfuI, suggesting a two-step cleavage of the DNA.
      We characterised this nicked intermediate and, through the development of a method of analysis
      of the cleavage reaction based on MALDI-tof mass spectrometry, we demonstrated that the
      cleavage of DNA by PI-TfuI indeed results from two cleavage events. One step results in the
      cleavage of the bottom strand, that is independent of the DNA conformation or choice of the
      metal ion cofactor. A second step, which is slower, leads to the cleavage of the top strand
      and governs the specific requirements of PI-TfuI concerning the essential cofactor and the DNA
      topology. These two steps were shown to be independent in optimal conditions of cleavage.
      These data give support to the existence of two distinct and independent active sites in the
      endonuclease domain of the archaeal intein.
AU  - Thion L
AU  - Laurine E
AU  - Erard M
AU  - Burlet-Schiltz O
AU  - Monsarrat B
AU  - Masson JM
AU  - Saves I
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2002 277: 45442-45450.

PMID- 22717884
VI  - 6
DP  - 2012
TI  - Phaeobacter gallaeciensis genomes from globally opposite locations reveal high similarity of adaptation to surface life.
PG  - 2229-2244
AB  - Phaeobacter gallaeciensis, a member of the abundant marine Roseobacter clade, is
      known to be an effective colonizer of biotic and abiotic marine surfaces.
      Production of the antibiotic tropodithietic acid (TDA) makes P. gallaeciensis a
      strong antagonist of many bacteria, including fish and mollusc pathogens. In
      addition to TDA, several other secondary metabolites are produced, allowing the
      mutualistic bacterium to also act as an opportunistic pathogen. Here we provide
      the manually annotated genome sequences of the P. gallaeciensis strains DSM 17395
      and 2.10, isolated at the Atlantic coast of north western Spain and near Sydney,
      Australia, respectively. Despite their isolation sites from the two different
      hemispheres, the genome comparison demonstrated a surprisingly high level of
      synteny (only 3% nucleotide dissimilarity and 88% and 93% shared genes). Minor
      differences in the genomes result from horizontal gene transfer and phage
      infection. Comparison of the P. gallaeciensis genomes with those of other
      roseobacters revealed unique genomic traits, including the production of
      iron-scavenging siderophores. Experiments supported the predicted capacity of
      both strains to grow on various algal osmolytes. Transposon mutagenesis was used
      to expand the current knowledge on the TDA biosynthesis pathway in strain DSM
      17395. This first comparative genomic analysis of finished genomes of two closely
      related strains belonging to one species of the Roseobacter clade revealed
      features that provide competitive advantages and facilitate surface attachment
      and interaction with eukaryotic hosts.The ISME Journal advance online
      publication, 21 June 2012; doi:10.1038/ismej.2012.62.
AU  - Thole S
AU  - Kalhoefer D
AU  - Voget S
AU  - Berger M
AU  - Engelhardt T
AU  - Liesegang H
AU  - Wollherr A
AU  - Kjelleberg S
AU  - Daniel R
AU  - Simon M
AU  - Thomas T
AU  - Brinkhoff T
PT  - Journal Article
TA  - ISME J.
JT  - ISME J.
SO  - ISME J. 2012 6: 2229-2244.

PMID- 12618468
VI  - 185
DP  - 2003
TI  - Plasmid R16 ArdA protein preferentially targets restriction activity of the type I restriction-modification system EcoKI.
PG  - 2022-2025
AB  - The ArdA antirestriction protein of the IncB plasmid R16 selectively inhibited the restriction
      activity of EcoKI, leaving significant levels of
      modification activity under conditions in which restriction was almost
      completely prevented. The results are consistent with the hypothesis that
      ArdA functions in bacterial conjugation to allow an unmodified plasmid to
      evade restriction in the recipient bacterium and yet acquire cognate
      modification.
AU  - Thomas AT
AU  - Brammar WJ
AU  - Wilkins BM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2003 185: 2022-2025.

PMID- 16464821
VI  - 34
DP  - 2006
TI  - Dimerization of the bacterial RsrI N6-adenine DNA methyltransferase.
PG  - 806-815
AB  - Dimeric restriction endonucleases and monomeric modification methyltransferases were long
      accepted as the structural paradigm for Type
      II restriction systems. Recent studies, however, have revealed an
      increasing number of apparently dimeric DNA methyltransferases. Our
      initial characterization of RsrI methyltransferase (M.RsrI) was consistent
      with the enzyme functioning as a monomer, but, subsequently, the enzyme
      crystallized as a dimer with 1500 A2 of buried surface area. This result
      led us to re-examine the biochemical properties of M.RsrI. Gel-shift
      studies of M.RsrI binding to DNA suggested that binding cooperativity
      targets hemimethylated DNA preferentially over unmethylated DNA.
      Size-exclusion chromatography indicated that the M.RsrI-DNA complex had a
      size and stoichiometry consistent with a dimeric enzyme binding to the
      DNA. Kinetic measurements revealed a quadratic relationship between enzyme
      velocity and concentration. Site-directed mutagenesis at the dimer
      interface affected the kinetics and DNA-binding of the enzyme, providing
      support for a model proposing an active enzyme dimer. We also identified a
      conserved motif in the dimer interfaces of the beta-class
      methyltransferases M.RsrI, M.MboIIA and M2.DpnII. Taken together, these
      data suggest that M.RsrI may be part of a sub-class of MTases that
      function as dimers.
AU  - Thomas CB
AU  - Gumport RI
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2006 34: 806-815.

PMID- 
VI  - 16
DP  - 2002
TI  - A tale of three tails, a mutant, and a dimer: Structural studies of RsrI methyltransferase.
PG  - A923-A924
AB  - DNA methyltransferases are a ubiquitous class of enzymes first observed as component enzymes
      of restriction-modification systems and implicated in many biological phenomena.  Recent
      reports have shown them to be involved in genetic diseases such as fragile X-syndrome,
      X-chromosome inactivation, gene regulation, cancer, and immunity.  RsrI DNA methyltransferase
      methylates the exocyclic amino group of the central adenine of the double-stranded DNA
      sequence GAATTC.  Using X-ray crystallography, we report co-crystal structures of the enzyme
      with the methyl donor S-adenosylmethionine, the product S-adenosylhomocysteine, and the
      inhibitor sinefungin.  The co-crystal structures reveal two ligand sites of varying affinity
      and possibly by lipid raft-mediated clustering on the plasma membrane.
AU  - Thomas CB
AU  - Scavetta R
AU  - Churchill MEA
AU  - Gumport RI
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 2002 16: A923-A924.

PMID- 12732637
VI  - 278
DP  - 2003
TI  - Structures of liganded and unliganded RsrI N6-adenine DNA methyltransferase: a distinct orientation for active cofactor binding.
PG  - 26094-26101
AB  - The structures of RsrI DNA methyltransferase (M.RsrI) bound to the substrate
      S-adenosyl-l-methionine (AdoMet), the product
      S-adenosyl-l-homocysteine (AdoHcy), the inhibitor sinefungin, as well as a
      mutant apo-enzyme have been determined by x-ray crystallography. Two
      distinct binding configurations were observed for the three ligands. The
      substrate AdoMet adopts a bent shape that directs the activated methyl
      group toward the active site near the catalytic DPPY motif. The product
      AdoHcy and the competitive inhibitor sinefungin bind with a straight
      conformation in which the amino acid moiety occupies a position near the
      activated methyl group in the AdoMet complex. Analysis of ligand binding
      in comparison with other DNA methyltransferases reveals a small, common
      subset of available conformations for the ligand. The structures of M.RsrI
      with the non-substrate ligands contained a bound chloride ion in the
      AdoMet carboxylate-binding pocket, explaining its inhibition by chloride
      salts. The L72P mutant of M.RsrI is the first DNA methyltransferase
      structure without bound ligand. With respect to the wild-type protein, it
      had a larger ligand-binding pocket and displayed movement of a loop
      (223-227) that is responsible for binding the ligand, which may account
      for the weaker affinity of the L72P mutant for AdoMet. These studies show
      the subtle changes in the tight specific interactions of substrate,
      product, and an inhibitor with M.RsrI and help explain how each displays
      its unique effect on the activity of the enzyme.
AU  - Thomas CB
AU  - Scavetta RD
AU  - Gumport RI
AU  - Churchill MEA
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2003 278: 26094-26101.

PMID- 24516617
VI  - 9
DP  - 2014
TI  - Comparative Variation within the Genome of Campylobacter jejuni NCTC 11168 in Human and Murine Hosts.
PG  - E88229
AB  - Campylobacteriosis incited by C. jejuni is a significant enteric disease of human
      beings. A person working with two reference strains of C. jejuni National
      Collection of Type Cultures (NCTC) 11168 developed symptoms of severe enteritis
      including bloody diarrhea. The worker was determined to be infected by C. jejuni.
      In excess of 50 isolates were recovered from the worker's stool. All of the
      recovered isolates and the two reference strains were indistinguishable from each
      other based on comparative genomic fingerprint subtyping. Whole genome sequence
      analysis indicated that the worker was infected with a C. jejuni NCTC 11168
      obtained from the American Type Culture Collection; this strain (NCTC 11168-GSv)
      is the genome sequence reference. After passage through the human host, major
      genetic changes including indel mutations within twelve contingency loci
      conferring phase variations were detected in the genome of C. jejuni. Specific
      and robust single nucleotide polymorphism (SNP) changes in the human host were
      also observed in two loci (Cj0144c, Cj1564). In mice inoculated with an isolate
      of C. jejuni NCTC 11168-GSv from the infected person, the isolate underwent
      further genetic variation. At nine loci, mutations specific to inoculated mice
      including five SNP changes were observed. The two predominant SNPs observed in
      the human host reverted in mice. Genetic variations occurring in the genome of C.
      jejuni in mice corresponded to increased densities of C. jejuni cells associated
      with cecal mucosa. In conclusion, C. jejuni NCTC 11168-GSv was found to be highly
      virulent in a human being inciting severe enteritis. Host-specific mutations in
      the person with enteritis occurred/were selected for in the genome of C. jejuni,
      and many were not maintained in mice. Information obtained in the current study
      provides new information on host-specific genetic adaptation by C. jejuni.
AU  - Thomas DK
AU  - Lone AG
AU  - Selinger LB
AU  - Taboada EN
AU  - Uwiera RR
AU  - Abbott DW
AU  - Inglis GD
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2014 9: E88229.

PMID- 2719943
VI  - 28
DP  - 1989
TI  - Environmentally induced conformational changes in B-type DNA:  Comparison of the conformation of the oligonucleotide d(TCGCGAATTCGCG) in solution and in its crystalline complex with the restriction nuclease EcoRI.
PG  - 2001-2009
AB  - Raman spectroscopic analysis of the secondary structure of the crystalline
      restriction endonuclease EcoRI, the oligonucleotide d(TCGCGAATTCGCG) in
      solution, and the corresponding crystalline EcoRI-oligonucleotide complex
      reveals structural differences between the complexed and uncomplexed protein
      and oligonucleotide components that appear to be linked to complex formation.
      Structural differences that are spectroscopically identified include (1) an
      increase in the population of furanose rings adopting the C3'-endo conformation
      and (2) spectroscopically observed changes in base stacking which are probably
      associated with the crystallographically observed distortion of the phosphate
      backbone about positions C(3)-G(4) and C(9)-G(10) and unwinding between the
      symmetry-related segments GAA-TTC which make up the central recognition core
      (McClarin et al., 1986).  Changes in base stacking due to distortions and
      unwinding along the oligonucleotide result in differences in the base
      vibrational region between spectra of the complex and the oligonucleotide in
      solution.  The spectroscopic analysis indicates that the C2'-endo population is
      similar for the oligonucleotide in solution and in the complex.  The additional
      C3'-endo population in the complex appears to arise from the conversion of
      rings adopting alternative conformations such as C1'-exo and O1'-endo.
      Analysis of the vibrational bands derived from guanine indicates that the
      population of guanine residues associated with furanose rings in a C2'-endo
      conformation is similar for the oligonucleotide in solution and in the
      crystalline complex.  This implies that the increase in C3'-endo population is
      not associated with guanine residues.  Large conformational distortions such as
      those observed in the crystal are not observed for the oligonucleotide in
      solution.  Furthermore, Raman evidence is presented that these distortions are
      not observed in either the crystal or the solution of the oligomer
      d(CGCGAATTCGCG).  These data suggest that static distortions such as those
      observed in the crystal are not employed for initial sequence recognition.
      They appear either as a secondary response to interaction with the protein or
      as transient fluctuations which exist at a very low level in solution.
AU  - Thomas GA
AU  - Kubasek WL
AU  - Peticolas WL
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1989 28: 2001-2009.

PMID- 22535928
VI  - 194
DP  - 2012
TI  - Draft Genome Sequences of Staphylococcus aureus Sequence Type 34 (ST34) and ST42  Hybrids.
PG  - 2740-2741
AB  - Staphylococcus aureus is a major cause of antimicrobial-resistant infections of humans.
      Hybrids of S. aureus, which originate from large-scale chromosomal
      recombinations between parents of distinct genetic backgrounds, are of interest
      from clinical and evolutionary perspectives. We present draft genome sequences of
      two S. aureus hybrids of sequence type 34 (ST34) and ST42.
AU  - Thomas JC
AU  - Godfrey PA
AU  - Feldgarden M
AU  - Robinson DA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2740-2741.

PMID- 21551297
VI  - 193
DP  - 2011
TI  - Streptococcus pneumoniae serotype 6C: An Intra- and Interclonal Complex Comparison.
PG  - 3409-3410
AB  - We report the annotated draft genome sequences of four serotype 6C Streptococcus pneumoniae
      isolates of differing genetic backgrounds.
      Serotype 6C isolates are increasing in prevalence and becoming
      progressively more resistant to antibiotics. As a result these strains are
      likely to become more important in the near future.
AU  - Thomas JC
AU  - Kong Y
AU  - Sabharwal V
AU  - Pelton SI
AU  - Pettigrew MM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3409-3410.

PMID- 28280028
VI  - 5
DP  - 2017
TI  - Genome Sequences of Two Spore-Forming Bacteria Isolated from the Shore of Mono Lake, California.
PG  - e01742-16
AB  - Here, we report the draft genome sequences of two Bacillus spore-forming Gram-positive
      bacteria, isolated from soil on the shore of Mono Lake.
AU  - Thomas JM
AU  - Ghebrendrias N
AU  - Rawat M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01742-16.

PMID- 1102702
VI  - 91
DP  - 1975
TI  - Studies on the cleavage of bacteriophage lambda DNA with EcoRI restriction endonuclease.
PG  - 315-328
AB  - The five EcoRI restriction sites in bacteriophage lambda DNA have been mapped
      at 0.445, 0.543, 0.656, 0.810, and 0.931 fractional lengths from the left end
      of the DNA molecule.  These positions were determined electron-microscopically
      by single-site cleavage of hydrogen-bonded circular lambda DNA molecules and by
      cleavage of various DNA heteroduplexes between lambda DNA and DNA from well
      defined lambdamutants.  The DNA lengths of the EcoRI fragments are in agreement
      with their electrophoretic mobility on agarose gels but are not in agreement
      with their mobilities on polyacrylamide gels.  These positions are different
      from those previously published by Allet et al. (1973).  Partial cleavage of
      pure lambda DNA by addition of small amounts of EcoRI endonuclease does not
      lead to random cleavage between molecules.  Also, the first site cleaved is not
      randomly distributed among the five sites within a molecule.  The site nearest
      the right end is cleaved first about ten times more frequently than either of
      the two center sites.
AU  - Thomas M
AU  - Davis RW
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1975 91: 315-328.

PMID- 29773629
VI  - 6
DP  - 2018
TI  - First complete genome sequence of Yersinia massiliensis.
PG  - e00416-18
AB  - Chemotherapeutic options are very limited against Mycobacterium abscessus infections.
      Bedaquiline, a new anti-tuberculosis drug, is effective for the treatment of
      multidrug-resistant TB. However, little data is available on bedaquiline in treating M.
      abscessus infections. In this study, we reported the in vitro susceptibility profile of M.
      abscessus clinical isolates to bedaquiline and investigated the potential molecular mechanisms
      of decreased susceptibility. A total of 197 M. abscessus clinical isolates were collected from
      sputum and bronchoalveolar fluid of patients with lung infections. Standard broth
      microdilution test revealed that bedaquiline exhibited high in vitro killing activity against
      M. abscessus isolates, with MIC50 of 0.062 and MIC90 of 0.125 mg/L. Whole genome sequencing
      data showed that no nonsynonymous mutation occurred in atpE, the gene encoding the bedaquiline
      targeted protein. However, of 6 strains with decreased susceptibility of bedaquiline
      (MIC=0.5-1 mg/L), 3 strains had nonsynonymous mutations in mab_4384, the gene encoding the
      repressor of efflux pump MmpS5/MmpL5. qRT-PCR analysis showed that the expression of
      MmpS5/MmpL5 in the group with decreased susceptibility to bedaquiline were significantly
      higher than those with medium MIC (MIC=0.125-0.5 mg/L) or low MIC group (MIC 0.062 mg/L). Two
      isolates with increased MIC didnt show overexpression 48 of MmpS5/MmpL5, which couldnt be
      explained by known molecular mechanisms. This is the first report showing the association of
      MmpS5/MmpL5 with decreased bedaquiline susceptibility in M. abscessus clinical isolates, and
      suggesting the presence of other yet-to-be identified mechanisms for decreased bedaquiline
      susceptibility in M. abscessus.
AU  - Thomas MC
AU  - Arling V
AU  - Goji N
AU  - Janzen TW
AU  - Duceppe M-O
AU  - Mathews A
AU  - Carrillo C
AU  - Amoako K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00416-18.

PMID- 10446231
VI  - 27
DP  - 1999
TI  - Structural analysis of a mutational hot-spot in the EcoRV restriction endonuclease: a catalytic role for a main chain carbonyl group.
PG  - 3438-3445
AB  - Following random mutagenesis of the Eco RV endonuclease, a high
      proportion of the null mutants carry substitutions at Gln69. Such
      mutants display reduced rates for the DNA cleavage step in the reaction
      pathway, yet the crystal structures of wild-type Eco RV fail to explain
      why Gln69 is crucial for activity. In this study, crystal structures
      were determined for two mutants of Eco RV, with Leu or Glu at residue
      69, bound to specific DNA. The structures of the mutants are similar to
      the native protein and no function can be ascribed to the side chain of
      the amino acid at this locus. Instead, the structures of the mutant
      proteins suggest that the catalytic defect is due to the positioning of
      the main chain carbonyl group. In the enzyme-substrate complex for Eco
      RV, the main chain carbonyl of Gln69 makes no interactions with
      catalytic functions but, in the enzyme-product complex, it coordinates
      a metal ion bound to the newly liberated 5'-phosphate. This re-
      positioning may be hindered in the mutant proteins. Molecular dynamics
      calculations indicate that the metal on the phosphoryl oxygen interacts
      with the carbonyl group upon forming the pentavalent intermediate
      during phosphodiester hydrolysis. A main chain carbonyl may thus play a
      role in catalysis by Eco RV.
AU  - Thomas MP
AU  - Brady RL
AU  - Halford SE
AU  - Sessions RB
AU  - Baldwin GS
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1999 27: 3438-3445.

PMID- 28720440
VI  - 54
DP  - 2017
TI  - First report of two complete Clostridium chauvoei genome sequences and detailed in silico genome analysis.
PG  - 287-298
AB  - Clostridium (C.) chauvoei is a Gram-positive, spore forming, anaerobic bacterium. It causes
      black leg in ruminants, a typically fatal histotoxic myonecrosis. High
      quality circular genome sequences were generated for the C. chauvoei type strain
      DSM 7528T (ATCC 10092T) and a field strain 12S0467 isolated in Germany. The
      origin of replication (oriC) was comparable to that of Bacillus subtilis in
      structure with two regions containing DnaA boxes. Similar prophages were
      identified in the genomes of both C. chauvoei strains which also harbored
      hemolysin and bacterial spore formation genes. A CRISPR type I-B system with
      limited variations in the repeat number was identified. Sporulation and
      germination process related genes were homologous to that of the Clostridia
      cluster I group but novel variations for regulatory genes were identified
      indicative for strain specific control of regulatory events. Phylogenomics showed
      a higher relatedness to C. septicum than to other so far sequenced genomes of
      species belonging to the genus Clostridium. Comparative genome analysis of three
      C. chauvoei circular genome sequences revealed the presence of few inversions and
      translocations in locally collinear blocks (LCBs). The species genome also shows
      a large number of genes involved in proteolysis, genes for glycosyl hydrolases
      and metal iron transportation genes which are presumably involved in virulence
      and survival in the host. Three conserved flagellar genes (fliC) were identified
      in each of the circular genomes. In conclusion this is the first comparative
      analysis of circular genomes for the species C. chauvoei, enabling insights into
      genome composition and virulence factor variation.
AU  - Thomas P
AU  - Semmler T
AU  - Eichhorn I
AU  - Lubke-Becker A
AU  - Werckenthin C
AU  - Abdel-Glil MY
AU  - Wieler LH
AU  - Neubauer H
AU  - Seyboldt C
PT  - Journal Article
TA  - Infect. Genet. Evol.
JT  - Infect. Genet. Evol.
SO  - Infect. Genet. Evol. 2017 54: 287-298.

PMID- Not included in PubMed...
VI  - 52
DP  - 1988
TI  - MvnI: a restriction enzyme in the archaebacterium Methanococcus vannielii.
PG  - 229-234
AB  - The methanogenic archaebacerium Methanococcus vannielii contains a type II
      restriction endonuclease.  The enzyme was purified by a simple three-step
      procedure resulting in enzyme preparations free of contaminating unspecific
      nucleases.  The restriction enzyme recognizes and cleaves the sequence
      5'-CG^CG-3' (FnuDII and ThaI isoschizomer) and generates DNA fragments with
      blunt ends.  Due to its purity and activity at moderate temperatures, MvnI
      might be a useful alternative to FnuDII and ThaI active at 60C.
AU  - Thomm M
AU  - Frey G
AU  - Bolton BJ
AU  - Laue F
AU  - Kessler C
AU  - Stetter KO
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1988 52: 229-234.

PMID- 1721704
VI  - 19
DP  - 1991
TI  - In vitro self-splicing reactions of the chloroplast group I intron Cr.LSU from Chlamydomonas reinhardtii and in vivo manipulation via gene-replacement.
PG  - 6611-6618
AB  - The group I intron from the chloroplast rRNA large subunit of Chlamydomonas reinhardtii
      (Cr.LSU) undergoes autocatalytic splicing in vitro. Cr.LSU displays a range of reactions
      typical of other group I introns. Under optimal conditions, the 5' cleavage step proceeds
      rapidly, but the exon-ligation step is relatively slow, and no pH dependent hydrolysis of the
      3' splicing site occurs. A requirement for high temperature and high [Mg2+] suggests
      involvement of additional splicing factors in vivo. The positions of three cyclization sites
      of the free intron have been mapped; two of these sites represent reactions analogous to
      5'-splice site cleavage, whereas the third is an example of G-exchange. Cr.LSU contains an
      open reading frame (ORF) potentially encoding a 163 amino acid polypeptide. ORF function has
      been investigated by using chloroplast gene replacement via particle bombardment. We have
      shown that the ORF can be deleted from Cr.LSU without affecting splicing in vivo and it thus
      does not encode an essential splicing factor.
AU  - Thompson AJ
AU  - Herrin DL
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 6611-6618.

PMID- 1398106
VI  - 119
DP  - 1992
TI  - Cleavage and recognition pattern of a double-strand-specific endonuclease (I-CreI) endcoded by the chloroplast 23S rRNA intron of Chlamydomonas reinhardtii.
PG  - 247-251
AB  - Several group-I introns have been shown to specifically invade intron-minus alleles of the
      genes that contain them. This type of intron mobility is referred to as "intron homing" and
      depends on restriction endonucleases (ENases) encoded by the mobile introns. The ENase cleaves
      the intron-minus allele near the site of intron insertion, thereby initiating gene conversion.
      The 23S (LSU) rRNA-encoding gene (LSU) of the chloroplast genome of Chlamydomonas reinhardtii
      contains a self-splicing group-I intron (CrLSU) that has a free-standing open reading frame
      (ORF) of 163 codons. Translation of CrLSU intron RNA in cell-free systems produces a
      polypeptide of approximately 18 kDa, the size expected for correct translation of the ORF. The
      in vitro-synthesized 18-kDa protein cleaves plasmid DNA that contains a portion of LSU where
      the intron normally resides, but lacking the intron itself. Cleavage by the intron-encoded
      enzyme (I-CreI) occurs 5 bp and 1 bp 3' to the intron insertion site (in the 3'-exon) in the
      top (/) and bottom (,) strands, respectively, resulting in 4-nt single-stranded overhangs with
      3'-OH termini. We also show that the recognition sequence of I-CreI spans the cleavage site
      and is 24 bp in length (5'-CAAAACGTC,GTGA/GACAGTTTGGT).
AU  - Thompson AJ
AU  - Yuan X
AU  - Kudlicki W
AU  - Herrin DL
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1992 119: 247-251.

PMID- 21952545
VI  - 193
DP  - 2011
TI  - Genome Sequence of the Human Pathogen Vibrio cholerae Amazonia.
PG  - 5877-5878
AB  - Vibrio cholerae O1 Amazonia is a pathogen that was isolated from cholera-like diarrhea cases
      in at least two countries, Brazil and Ghana.
      Based on multilocus sequence analysis, this lineage belongs to a distinct
      profile compared to strains from El Tor and classical biotypes. The
      genomic analysis revealed that it contains Vibrio pathogenicity island 2
      and a set of genes related to pathogenesis and fitness, such as the type
      VI secretion system, present in choleragenic V. cholerae strains.
AU  - Thompson CC
AU  - Marin MA
AU  - Dias GM
AU  - Dutilh BE
AU  - Edwards RA
AU  - Iida T
AU  - Thompson FL
AU  - Vicente AC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5877-5878.

PMID- 4614064
VI  - 133
DP  - 1974
TI  - Plasmid identification using specific endonucleases.
PG  - 141-149
AB  - Digestion with specific endonucleases followed by agarose gel electrophoresis
      yields characteristic fragment patterns from different plasmid DNAs.  Since
      even the very closely related R factors F100-1 and R6, for example, can be
      distinguished this method provides a powerful test of the identity of two
      plasmid DNAs.
AU  - Thompson R
AU  - Hughes SG
AU  - Broda P
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1974 133: 141-149.

PMID- 14506783
VI  - 293
DP  - 2003
TI  - Mutation of a predicted Campylobacter jejuni DNA methylase affects the expression of multiple genes.
PG  - 21-22
AB  - In the course of studies examining temperature regulated genes of Campylobacter jejuni 81-176,
      we identified an ortholog of NCTC11168 CJ1461 as a gene that is more highly expressed at 37oC
      than at 42oC.  CJ1461 encodes a predicted DNA methylase that is not associated with a cognate
      restriction endonuclease, implying that its cellular role is not to protect DNA from
      restriction endonucleases.  Since DNA methylases may have gene regulatory functions separate
      from their housekeeping roles in protecting DNA from restriction enzymes or in DNA repair, we
      inactivated the CJ1461 ortholog in strain 81-176, suggesting a regulatory role for CJ1461.
      Some of these proteins were shown to be temperature regulated by other methods, suggesting
      that a component of the putative CJ1461 regulon was mediated by growth temperature.
      Importantly, one of the proteins that was over expressed in the CJ1461 mutant was CJ0355.
      CJ0355 itself is the predicted response regulator of a two component regulatory system,
      although CJ0355 is an "orphan" response regulator that lacks an associated histidine kinase
      sensor protein.  These studies suggest that temperature regulation of multiple genes in C.
      jejuni 81-176 may be complex and can be mediated in part by DNA methylation and by an orphan
      response regulator.
AU  - Thompson SA
AU  - Hall JE
AU  - Baltzegar AD
AU  - Yates BD
AU  - Maani EV
AU  - Pajaniappan M
AU  - Falkow S
AU  - Gaynor EC
AU  - Mishra AK
AU  - Burns CM
PT  - Journal Article
TA  - Int. J. Med. Microbiol.
JT  - Int. J. Med. Microbiol.
SO  - Int. J. Med. Microbiol. 2003 293: 21-22.

PMID- 6187366
VI  - 739
DP  - 1983
TI  - Expression of ultraviolet-induced restriction alleviation in Escherichia coli K-12.
PG  - 42-47
AB  - Ultraviolet-induced restriction alleviation is an SOS function which partially relieves the
      K-12-specific DNA restriction in Escherichia coli.  Restriction alleviation is determined by
      observing elevated survival of unmodified phage lambda in cells irradiated with ultraviolet
      prior to infection.  We demonstrate that restriction of lambda is also relieved when log-phase
      cells are irradiated as late as 50 min after adsorption of lambda.  At this time more than 60%
      of the lambda DNA is already released as acid-soluble material from the cells.  Experiments
      involving reextraction of lambda DNA from infected cells and a mild detergent treatment
      removing adsorbed phages from the cellular surface showed that only a small specific fraction
      of all lambda infections is destined to escape restriction due to restriction alleviation.
      This fraction (10-20%) has a retarded mode of DNA injection (60 min or longer) after
      adsorption which allows the expression of the restriction alleviation function before the
      phage DNA is exposed to restriction endonucleases.  This behavior of a fraction of lambda
      phages explains why the SOS function restriction alleviation could initially be discovered.
      We show that the retarded mode of DNA injection is not required for another SOS function
      acting on lambda DNA, the increased repair of ultraviolet-irradiated DNA (Weigle
      reactivation).
AU  - Thoms B
AU  - Wackernagel W
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1983 739: 42-47.

PMID- 6213835
VI  - 186
DP  - 1982
TI  - UV-induced allevation of lambda restriction in Escherichia coli K-12:  Kinetics of induction and specificity of this SOS function.
PG  - 111-117
AB  - In UV-irradiated cells of Escherichia coli K-12 a partial release of the
      restriction of non-modified phage lambda is observed when the cells are recA+
      lexA+.  We show here that the induction of this restriction allevation (RA)
      also depends on the recBC enzyme and that the expression of RA requires protein
      synthesis.  Maximum expression was reached within 60 to 90 min after
      irradiation.  Experiments are presented which show that upon UV-irradiation a
      signal is created which triggers the development of RA when protein synthesis
      is allowed.  This signal decayed with a half-life of only a few minutes in
      cells treated with chloramphenicol.  The decay kinetics were similar in uvr+
      and uvrA mutants.  RA appeared to be specific for EcoKI insofar as no
      allevation of lambda restriction by EcoRI, EcoRII and EcoPI occurred.  During
      maximum expression of RA no gross reduction of the activities of the recBC
      enzyme (exonuclease V) and the restriction endonuclease EcoKI was observed and
      no new DNA modifying activity appeared in the cells.  Since, in fully expressed
      cells, up to 75% of the infecting lambda DNA was converted to acid-soluble
      material within 20 min after infection we suggest that only a small specific
      fraction of lambda infections may undergo RA.
AU  - Thoms B
AU  - Wackernagel W
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1982 186: 111-117.

PMID- 17173484
VI  - 2
DP  - 2006
TI  - The Complete Genome Sequence and Comparative Genome Analysis of the High Pathogenicity Yersinia enterocolitica Strain 8081.
PG  - E206
AB  - The human enteropathogen, Yersinia enterocolitica, is a significant link
      in the range of Yersinia pathologies extending from mild gastroenteritis
      to bubonic plague. Comparison at the genomic level is a key step in our
      understanding of the genetic basis for this pathogenicity spectrum. Here
      we report the genome of Y. enterocolitica strain 8081 (serotype 0:8;
      biotype 1B) and extensive microarray data relating to the genetic
      diversity of the Y. enterocolitica species. Our analysis reveals that the
      genome of Y. enterocolitica strain 8081 is a patchwork of horizontally
      acquired genetic loci, including a plasticity zone of 199 kb containing an
      extraordinarily high density of virulence genes. Microarray analysis has
      provided insights into species-specific Y. enterocolitica gene functions
      and the intraspecies differences between the high, low, and nonpathogenic
      Y. enterocolitica biotypes. Through comparative genome sequence analysis
      we provide new information on the evolution of the Yersinia. We identify
      numerous loci that represent ancestral clusters of genes potentially
      important in enteric survival and pathogenesis, which have been lost or
      are in the process of being lost, in the other sequenced Yersinia
      lineages. Our analysis also highlights large metabolic operons in Y.
      enterocolitica that are absent in the related enteropathogen, Yersinia
      pseudotuberculosis, indicating major differences in niche and nutrients
      used within the mammalian gut. These include clusters directing, the
      production of hydrogenases, tetrathionate respiration, cobalamin
      synthesis, and propanediol utilisation. Along with ancestral gene
      clusters, the genome of Y. enterocolitica has revealed species-specific
      and enteropathogen-specific loci. This has provided important insights
      into the pathology of this bacterium and, more broadly, into the evolution
      of the genus. Moreover, wider investigations looking at the patterns of
      gene loss and gain in the Yersinia have highlighted common themes in the
      genome evolution of other human enteropathogens.
AU  - Thomson NR et al
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2006 2: E206.

PMID- 18583645
VI  - 18
DP  - 2008
TI  - Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways.
PG  - 1624-1637
AB  - We have determined the complete genome sequences of a host-promiscuous Salmonella enterica
      serovar Enteritidis PT4 isolate P125109 and a chicken-restricted Salmonella enterica serovar
      Gallinarum isolate 287/91. Genome comparisons between these and other Salmonella isolates
      indicate that S. Gallinarum 287/91 is a recently evolved descendent of S. Enteritidis.
      Significantly, the genome of S. Gallinarum has undergone extensive degradation through
      deletion and pseudogene formation. Comparison of the pseudogenes in S. Gallinarum with those
      identified previously in other host-adapted bacteria reveals the loss of many common
      functional traits and provides insights into possible mechanisms of host and tissue
      adaptation. We propose that experimental analysis in chickens and mice of S.
      Enteritidis-harboring mutations in functional homologs of the pseudogenes present in S.
      Gallinarum could provide an experimentally tractable route toward unraveling the genetic basis
      of host adaptation in S. enterica.
AU  - Thomson NR et al
PT  - Journal Article
TA  - Genome Res.
JT  - Genome Res.
SO  - Genome Res. 2008 18: 1624-1637.

PMID- 27789632
VI  - 4
DP  - 2016
TI  - Complete Genome Sequences of Two Marine Vibrio cholerae Strains Isolated from the South Coast of Sweden.
PG  - e01118-16
AB  - Vibrio cholerae serogroups O1 and O139 are commonly associated with diarrhea, while
      non-O1-O139 strains may cause wound infections. Here, we present the genome
      sequences of two V. cholerae strains isolated from blue mussels (Mytilus edulis)
      collected in coastal waters of southern Sweden.
AU  - Thorell K
AU  - Collin B
AU  - Hernroth B
AU  - Sjoling A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01118-16.

PMID- 8621526
VI  - 271
DP  - 1996
TI  - Influence of the phosphate backbone on the restriction and hydrolysis of DNA by the EcoRV restriction endonuclease.
PG  - 8855-8862
AB  - A set of phosphorothioate-containing oligonucleotides based on pGACGATATCGTC, a
      self-complementary dodecamer that contains the EcoRV recognition sequence (GATATC), has been
      prepared.  The phosphorothioate group has been individually introduced at the central nine
      phosphate positions and the two diastereomers produced at each site separated and purified.
      The Km and Vmax values found for each of these modified DNA molecules with the EcoRV
      restriction endonuclease have been determined and compared with those seen for the unmodified
      all-phosphate-containing dodecamer.  This has enabled an evaluation of the roles that both of
      the non-esterified oxygen atoms in the individual phosphates play in DNA binding and
      hydrolysis by the endonuclease.  The results have also been compared with crystal structures
      of the EcoRV endonuclease, complexed with an oligodeoxynucleotide, to allow further definition
      of phosphate group function during substrate binding and turnover.
AU  - Thorogood H
AU  - Grasby JA
AU  - Connolly BA
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1996 271: 8855-8862.

PMID- 8679635
VI  - 35
DP  - 1996
TI  - Resonance raman spectroscopy of 4-thiothymidine and oligodeoxynucleotides containing this base both free in solution and bound to the restriction endonuclease EcoRV.
PG  - 8723-8733
AB  - The resonance Raman spectra of 4-thiothymidine [4ST] have been recorded (a) in
      the free deoxynucleoside form, (b) when incorporated into the single stranded
      oligodeoxynucleotide d(AG[4ST]-TC), and (c) within the double-stranded self-complementary
      dodecamer d(GACGA[4sT]ATCGTC).  Vibrational mode assignments of almost all the major
      Raman bands observed in each spectra have been made, mainly by comparison with the published
      assignments of related nucleosides and nucleotides.  Differences between the spectra were
      observed, particularly when [4sT] and d(AG[4ST]TC) were compared to
      d(GACGA[4ST]ATCGTC).  This is explained in terms of the variations in structure between
      single- and double-stranded DNA.  Good quality spectra were obtained at
      nucleotide/oligonucleotide concentrations of between 100 and 500 uM and this coupled with an
      apparatus that uses small volumes (100 uL) allowed measurement of the spectrum of
      d(GACGA[4ST]ATCGTC) bound to the EcoRV endonuclease.  This well characterized nuclease,
      for which crystal structures are available, recognizes d(GATAT) sequences.  When this is
      replaced
      with d(GA[4ST]ATC), a poor substrate results, but turnover can be prevented during data
      accumulation by omission of the essential cation Mg2+.  Large shifts in several of the Raman
      bands were observed, and these have been related to the environment of the [4ST] base in the
      protein-bound oligonucleotide as deduced from the crystal structure.  The wavenumber for the
      C=S stretch vibration in free d(GACGA[4ST]ATCGTC) has been used to calculate the strength of
      the Watson-Crick hydrogen bond between the sulphur atom in [4ST] and the 6-NH2 group on its
      partner dA.  On binding to the enzyme, the shift in the wavenumber of the C=S stretch
      indicates
      this Watson-Crick hydrogen bond is weakened, in good agreement with X-ray structures.  The
      advantage of using [4ST] as a resonance Raman probe is that it absorbs at 340 nM, a wavelength
      where other nucleic acid and protein absorbance is minimal.  Thus the spectra obtained are
      very
      simple and consist of signals that arise predominantly from the thiobase alone, and this
      facilitates
      data interpretation.
AU  - Thorogood H
AU  - Waters TR
AU  - Parker AW
AU  - Wharton C
AU  - Connolly BA
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1996 35: 8723-8733.

PMID- 
VI  - 
DP  - 1995
TI  - The DNA specificity of type I restriction and modification enzymes.
PG  - 1-176
AB  - The type I restriction and modification enzymes were the first R-M systems characterized and
      provide a valuable system for studying protein-protein and protein-DNA interactions.  These
      complex, multi-subunit enzymes are encoded for by three genes hsdR, M and S, although only one
      of these, hsdS, is responsible for determining the specific DNA target sequence that the
      enzyme recognizes.  Differences in the type I enzymes characterized have lead to their
      subdivision into separate families.  The type I enzymes recognize a bipartite DNA target,
      which has two, short, defined elements separated by a non-specific spacer.  For example, the
      DNA target of EcoKI is 5'AACNNNNNNGTGC3'.  A series of observations and experiments have
      lead to a limited understanding of how the HsdS subunit recognizes its DNA target.  Within
      each family of type I enzymes HsdS subunits share regions of very similar amino acid sequence,
      separating two larger regions of variable sequence.  Each variable region forms a domain that
      specifies one half of the bipartite DNA target, and has been termed a Target Recognition
      Domains (or TRD).  No structural information is available for the TRDs although recent crystal
      structures of type II enzymes may give clues relevant to DNA interactions of type I enzymes.
      A deletion analysis of the hsdS gene of EcoKI was initiated to provide information on the
      roles of the conserved and variable regions.  The aim was to correlate phenotype with an
      analysis of protein products, but attempts to overexpress the hsdS gene of EcoKI in a soluble
      form were unsuccessful, and the HsdS subunit could not be purified.  Another approach to
      studying the interaction of TRDs with their DNA targets is to compare the amino acid sequences
      of those TRDs that specify the same DNA target.  Areas of sequence which are similar within
      these TRDs may reflect a similarity of DNA recognition function.  From amongst the limited
      number of TRDs available, there are several sequence alignments of TRDs which specify the same
      DNA target.  A method based upon the Polymerase Chain Reaction was developed to amplify new
      variable regions, which encode TRDs, from wild-type bacteria.  In a DNA hybridization screen
      of members of the ECOR collection of wild-type Escherichia coli, Barcus et al. (1995) found
      that almost half contained hsd genes.  The conserved regions of the hsd genes were used to
      design primers that would amplify 5' variable regions of members of a given type I family.
      Nine IA family and four IB family 5' variable regions were amplified and their DNA sequences
      determined.  The information derived from these sequences illustrates both the evolutionary
      diversity of the hsdS genes, and the flexible nature of the TRDs as independent target
      recognizing domains.  The sequence of the N-terminal TRD from ECOR17 shares 28% identity with
      those of EcoKI and StySPI.  A method dependent on the construction of hybrid hsdS genes, was
      devised to find the DNA targets of these new TRD sequences.  Hybrid type I hsdS genes have
      been shown to be functional for members of the IA and IC families.  Deletion derivatives of
      the IA and IB family hsdS genes lacking the coding sequence for the amino-TRD were used to
      insert coding sequences for alternative TRDs.  The four hybrid genes isolated all encoded
      functional HsdS polypeptides conferring novel specificities.  The DNA targets of two hybrid
      systems were determined, including that from ECOR17.  The sequence recognized was 5' ATR, and
      not that expected (5' AAC) from its similarity to EcoKI.
AU  - Thorpe PH
PT  - Journal Article
TA  - Ph.D. Thesis
JT  - Ph.D. Thesis
SO  - Ph.D. Thesis 1995 : 1-176.

PMID- 9108149
VI  - 25
DP  - 1997
TI  - The specificity of StySKI, a type I restriction enzyme, implies a structure with rotational symmetry.
PG  - 1694-1700
AB  - The type I restriction and modification (R-M) enzyme from Salmonella enterica serovar kaduna
      (StySKI) recognizes the DNA sequence 5'-CGAT(N)7GTTA, an unusual target for a type I R-M
      system in that it comprises two tetranucleotide components.  The amino target recognition
      domain (TRD) of StySKI recognizes 5'-CGAT and shows 35% amino acid identity with the carboxy
      TRD of EcoR124I which recognizes the complementary, but degenerate, sequence 5'-RTCG.
      Current models predict that the amino and carboxy TRDs of the specificity subunit are in
      inverted orientations within a structure with 2-fold rotational symmetry.  The complementary
      target sequences recognized by the amino TRD of StySKI and the carboxy TRD of EcoR124I are
      consistent with the predicted inverted positions of the TRDs.  Amino TRDs of similar amino
      acid sequence have been shown to recognize the same nucleotide sequence.  The similarity
      reported here, the first example of one between amino and carboxy TRDs, while consistent with
      a conserved mechanism of target recognition, offers additional flexibility in the evolution of
      sequence specificity by increasing the potential diversity of DNA targets for a given number
      of TRDs.  StySKI identifies the first member of the IB family in Salmonella species.
AU  - Thorpe PH
AU  - Ternent D
AU  - Murray NE
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1997 25: 1694-1700.

PMID- 9753548
VI  - 282
DP  - 1998
TI  - Complete sequence of the IncPbeta plasmid R751: implications for evolution and organisation of the IncP backbone.
PG  - 969-990
AB  - The broad host range IncP plasmids are of particular interest because of
      their ability to promote gene spread between diverse bacterial species. To
      facilitate study of these plasmids we have compiled the complete sequence
      of the IncPbeta plasmid R751. Comparison with the sequence of the
      IncPalpha plasmids confirms the conservation of the IncP backbone of
      replication, conjugative transfer and stable inheritance functions between
      the two branches of this family. As in the IncPalpha genome the DNA of
      this backbone appears to have been enriched for the GCCG/CGGC motifs
      characteristic of the genome of organisms with a high G+C content, such as
      P. aeruginosa, suggesting that IncPbeta plasmids have been subjected
      during their evolution to similar mutational and selective forces as
      IncPalpha plasmids and may have evolved in pseudomonad hosts. The IncP
      genome is consistently interrupted by insertion of phenotypic markers
      and/or transposable elements between oriV and trfA and between the tra and
      trb operons. The R751 genome reveals a family of repeated sequences in
      these regions which may form the basis of a hot spot for insertion of
      foreign DNA. Sequence analysis of the cryptic transposon Tn4321 revealed
      that it is not a member of the Tn21 family as we had proposed previously
      from an inspection of its ends. Rather it is a composite transposon
      defined by inverted repeats of a 1347 bp IS element belonging to a
      recently discovered family which is distributed throughout the
      prokaryotes. The central unique region of Tn4321 encodes two predicted
      proteins, one of which is a regulatory protein while the other is
      presumably responsible for an as yet unidentified phenotype. The most
      striking feature of the IncPalpha plasmids, the global regulation of
      replication and transfer by the KorA and KorB proteins encoded in the
      central control operon, is conserved between the two plasmids although
      there appear to be significant differences in the specificity of
      repressor-operator interactions. The importance of these global regulatory
      circuits is emphasised by the observation that the operator sequences for
      KorB are highly conserved even in contexts where the surrounding region,
      either a protein coding or intergenic sequence, has diverged considerably.
      There appears to be no equivalent of the parABCDE region which in the
      IncPalpha plasmids provides multimer resolution, lethality to plasmid-free
      segregants and active partitioning functions. However, we found that the
      continuous sector from co-ordinate 0 to 9100 bp, encoding the co-regulated
      klc and kle operons as well as the central control region, could confer a
      high degree of segregational stability on a low copy number test vector.
      Thus R751 appears to exhibit very clearly what was first revealed by study
      of the IncPalpha plasmids, namely a fully functional co-ordinately
      regulated set of replication, transfer and stable inheritance functions.
AU  - Thorsted PB
AU  - Macartney DP
AU  - Akhtar P
AU  - Haines AS
AU  - Ali N
AU  - Davidson P
AU  - Stafford T
AU  - Pocklington MJ
AU  - Pansegrau W
AU  - Wilkins BM
AU  - Lanka E
AU  - Thomas CM
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1998 282: 969-990.

PMID- 21075932
VI  - 193
DP  - 2010
TI  - Genome sequence of the marine Janibacter sp. strain HTCC2649.
PG  - 584-585
AB  - Janibacter sp. strain HTCC2649 is a novel marine member of the Actinobacteria, family
      Intrasporangiaceae, closely related to Janibacter melonis CM2104(T) and Knoellia sinensis HKI
      0119(T). The organism was isolated from a sample collected at Hydrostation S south of Bermuda
      using high throughput culturing techniques. Here we present the genome sequence of Janibacter
      sp. strain HTCC2649.
AU  - Thrash JC
AU  - Cho JC
AU  - Bertagnolli AD
AU  - Ferriera S
AU  - Johnson J
AU  - Vergin KL
AU  - Giovannoni SJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 193: 584-585.

PMID- 20472793
VI  - 192
DP  - 2010
TI  - Genome sequences of strains HTCC2148 and HTCC2080, belonging to the OM60/NOR5 clade of the Gammaproteobacteria.
PG  - 3842-3843
AB  - Organisms in the OM60/NOR5 clade of the Gammaproteobacteria are ubiquitous in the
      world's oceans and can make up as much as 11% of bacterial cells in certain
      areas. Isolated from coastal Oregon water, Gammaproteobacteria HTCC2148 and
      HTCC2080 are two members of this important clade. Here we present the genome
      sequences of the OM60 Gammaproteobacteria HTCC2148 and HTCC2080.
AU  - Thrash JC
AU  - Cho JC
AU  - Ferriera S
AU  - Johnson J
AU  - Vergin KL
AU  - Giovannoni SJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 3842-3843.

PMID- 20729358
VI  - 192
DP  - 2010
TI  - Genome sequences of Pelagibaca bermudensis HTCC2601T and Maritimibacter alkaliphilus HTCC2654T, the type strains of two marine roseobacter genera.
PG  - 5552-5553
AB  - Pelagibaca bermudensis HTCC2601(T) and Maritimibacter alkaliphilus HTCC2654(T) represent two
      marine genera in the globally significant
      Roseobacter clade of the Alphaproteobacteria. Here, we present the genome
      sequences of these organisms, isolated from the Sargasso Sea using
      dilution-to-extinction culturing, which offer insight into the genetic
      basis for the metabolic and ecological diversity of this important group.
AU  - Thrash JC
AU  - Cho JC
AU  - Ferriera S
AU  - Johnson J
AU  - Vergin KL
AU  - Giovannoni SJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 5552-5553.

PMID- 20418400
VI  - 192
DP  - 2010
TI  - Genome Sequences of Oceanicola granulosus HTCC2516T and Oceanicola batsensis HTCC2597T.
PG  - 3549-3550
AB  - Genome sequences from the prolific Roseobacter clade in the Alphaproteobacteria are beginning
      to reveal the genetic basis for the
      diverse lifestyles of these organisms. Here we present the genome
      sequences of Oceanicola granulosus HTCC2516(T) and Oceanicola batsensis
      HTCC2597(T), two marine Roseobacter species isolated from the Sargasso Sea
      using dilution-to-extinction culturing, whose genomes encode for
      significant differences in metabolic potential.
AU  - Thrash JC
AU  - Cho JC
AU  - Vergin KL
AU  - Giovannoni SJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 3549-3550.

PMID- 20363947
VI  - 192
DP  - 2010
TI  - Genome sequence of Lentisphaera araneosa HTCC2155T, the type species of the order Lentisphaerales in the phylum Lentisphaerae.
PG  - 2938-2939
AB  - Information on the genome content of deeply branching phyla with very few cultured members is
      invaluable for expanding understanding of microbial evolution. Lentisphaera araneosa
      HTCC2155(T) was isolated from the Oregon coast using dilution-to-extinction culturing. It is a
      marine heterotroph found in surface and mesopelagic waters in both the Pacific and Atlantic
      oceans and has the unusual property of producing a net-like matrix of secreted
      exopolysaccharide. Here we present the genome sequence of L.
      araneosa HTCC2155(T), importantly, one of only two sequenced members of
      the phylum Lentisphaerae.
AU  - Thrash JC
AU  - Cho JC
AU  - Vergin KL
AU  - Morris RM
AU  - Giovannoni SJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 2938-2939.

PMID- 22426128
VI  - 419
DP  - 2012
TI  - Improved Modeling of Side-Chain-Base Interactions and Plasticity in Protein-DNA Interface Design.
PG  - 255-274
AB  - Combinatorial sequence optimization for protein design requires libraries of discrete
      side-chain conformations. The discreteness of
      these libraries is problematic, particularly for long, polar side
      chains, since favorable interactions can be missed. Previously, an
      approach to loop remodeling where protein backbone movement is directed
      by side-chain rotamers predicted to form interactions previously
      observed in native complexes (termed 'motifs') was described. Here, we
      show how such motif libraries can be incorporated into combinatorial
      sequence optimization protocols and improve native complex
      recapitulation. Guided by the motif rotamer searches, we made
      improvements to the underlying energy function, increasing
      recapitulation of native interactions. To further test the methods, we
      carried out a comprehensive experimental scan of amino acid preferences
      in the I-AniI protein-DNA interface and found that many positions
      tolerated multiple amino acids. This sequence plasticity is not
      observed in the computational results because of the fixed-backbone
      approximation of the model. We improved modeling of this diversity by
      introducing DNA flexibility and reducing the convergence of the
      simulated annealing algorithm that drives the design process. In
      addition to serving as a benchmark, this extensive experimental data
      set provides insight into the types of interactions essential to
      maintain the function of this potential gene therapy reagent.
AU  - Thyme SB
AU  - Baker D
AU  - Bradley P
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2012 419: 255-274.

PMID- 24270794
VI  - 42
DP  - 2014
TI  - Reprogramming homing endonuclease specificity through computational design and directed evolution.
PG  - 2564-2576
AB  - Homing endonucleases (HEs) can be used to induce targeted genome modification to reduce the
      fitness of pathogen vectors such as the malaria-transmitting Anopheles gambiae and to correct
      deleterious mutations in genetic diseases. We describe the creation of an extensive set of HE
      variants with novel DNA cleavage specificities using an integrated experimental and
      computational approach. Using computational modeling and an improved selection strategy, which
      optimizes specificity in addition to activity, we engineered an endonuclease to cleave in a
      gene associated with Anopheles sterility and another to cleave near a mutation that causes
      pyruvate kinase deficiency. In the course of this work we observed unanticipated
      context-dependence between bases which will need to be mechanistically understood for
      reprogramming of specificity to succeed more generally.
AU  - Thyme SB
AU  - Boissel SJS
AU  - Quadri S
AU  - Arshiya N
AU  - Tony B
AU  - Dean A
AU  - Park RU
AU  - Kusak L
AU  - Ashworth J
AU  - Baker D
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2014 42: 2564-2576.

PMID- 19865174
VI  - 461
DP  - 2009
TI  - Exploitation of binding energy for catalysis and design.
PG  - 1300-1304
AB  - Enzymes use substrate-binding energy both to promote ground-state association and to stabilize
      the reaction transition state
      selectively1. The monomeric homing endonuclease I-AniI cleaves with
      high sequence specificity in the centre of a 20-base-pair ( bp) DNA
      target site, with the amino (N)-terminal domain of the enzyme making
      extensive binding interactions with the left (-) side of the target
      site and the similarly structured carboxy (C)-terminal domain
      interacting with the right (+) side(2). Here we show that, despite the
      approximate twofold symmetry of the enzyme-DNA complex, there is almost
      complete segregation of interactions responsible for substrate binding
      to the (-) side of the interface and interactions responsible for
      transition-state stabilization to the (+) side. Although single
      base-pair substitutions throughout the entire DNA target site reduce
      catalytic efficiency, mutations in the (-) DNA half-site almost
      exclusively increase the dissociation constant (K-D) and the Michaelis
      constant under single-turnover conditions (K-M*), and those in the (+)
      half-site primarily decrease the turnover number (k(cat)*). The
      reduction of activity produced by mutations on the (-) side, but not
      mutations on the (+) side, can be suppressed by tethering the substrate
      to the endonuclease displayed on the surface of yeast. This dramatic
      asymmetry in the use of enzyme-substrate binding energy for catalysis
      has direct relevance to the redesign of endonucleases to cleave genomic
      target sites for gene therapy and other applications. Computationally
      redesigned enzymes that achieve new specificities on the (-) side do so
      by modulating K-M*, whereas redesigns with altered specificities on the
      (+) side modulate k(cat)*. Our results illustrate how classical
      enzymology and modern protein design can each inform the other.
AU  - Thyme SB
AU  - Jarjour J
AU  - Takeuchi R
AU  - Havranek JJ
AU  - Ashworth J
AU  - Scharenberg AM
AU  - Stoddard BL
AU  - Baker D
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2009 461: 1300-1304.

PMID- 25389263
VI  - 42
DP  - 2014
TI  - Massively parallel determination and modeling of endonuclease substrate specificity.
PG  - 13839-13852
AB  - We describe the identification and characterization of novel homing endonucleases using genome
      database mining to identify putative target sites, followed by high throughput activity
      screening in a bacterial selection system. We characterized the substrate specificity and
      kinetics of these endonucleases by monitoring DNA cleavage events with deep sequencing. The
      endonuclease specificities revealed by these experiments can be partially recapitulated using
      3D structure-based computational models. Analysis of these models together with genome
      sequence data provide insights into how alternative endonuclease specificities were generated
      during natural evolution.
AU  - Thyme SB
AU  - Song Y
AU  - Brunette TJ
AU  - Szeto MD
AU  - Kusak L
AU  - Bradley P
AU  - Baker D
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2014 42: 13839-13852.

PMID- 23209251
VI  - 194
DP  - 2012
TI  - Genome Sequence of Mycobacterium hassiacum DSM 44199, a Rare Source of Heat-Stable Mycobacterial Proteins.
PG  - 7010-7011
AB  - Mycobacterium hassiacum is a rapidly growing mycobacterium isolated from human urine and so
      far the most thermophilic among mycobacterial species. Its
      thermotolerance and phylogenetic relationship to M. tuberculosis render its
      proteins attractive tools for crystallization and structure-guided drug design.
      We report the draft genome sequence of M. hassiacum DSM 44199.
AU  - Tiago I
AU  - Maranha A
AU  - Mendes V
AU  - Alarico S
AU  - Moynihan PJ
AU  - Clarke AJ
AU  - Macedo-Ribeiro S
AU  - Pereira PJ
AU  - Empadinhas N
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 7010-7011.

PMID- 27284146
VI  - 4
DP  - 2016
TI  - Genome Sequence of Hafnia alvei bta3_1, a Bacterium with Antimicrobial Properties Isolated from Honey Bee Gut.
PG  - e00439-16
AB  - Hafnia alvei bta3_1, a strain with antibacterial properties, was isolated from honey bee gut
      and cultured under aerobic and anaerobic conditions. To explore the
      potential genetic bases of its antibacterial and possible pathogenic properties,
      the complete genome of this organism was sequenced and analyzed.
AU  - Tian B
AU  - Moran NA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00439-16.

PMID- 22586130
VI  - 109
DP  - 2012
TI  - Comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations.
PG  - 8629-8634
AB  - The rhizobium-legume symbiosis has been widely studied as the model of
      mutualistic evolution and the essential component of sustainable agriculture.
      Extensive genetic and recent genomic studies have led to the hypothesis that many
      distinct strategies, regardless of rhizobial phylogeny, contributed to the varied
      rhizobium-legume symbiosis. We sequenced 26 genomes of Sinorhizobium and
      Bradyrhizobium nodulating soybean to test this hypothesis. The Bradyrhizobium
      core genome is disproportionally enriched in lipid and secondary metabolism,
      whereas several gene clusters known to be involved in osmoprotection and
      adaptation to alkaline pH are specific to the Sinorhizobium core genome. These
      features are consistent with biogeographic patterns of these bacteria.
      Surprisingly, no genes are specifically shared by these soybean microsymbionts
      compared with other legume microsymbionts. On the other hand, phyletic patterns
      of 561 known symbiosis genes of rhizobia reflected the species phylogeny of these
      soybean microsymbionts and other rhizobia. Similar analyses with 887 known
      functional genes or the whole pan genome of rhizobia revealed that only the
      phyletic distribution of functional genes was consistent with the species tree of
      rhizobia. Further evolutionary genetics revealed that recombination dominated the
      evolution of core genome. Taken together, our results suggested that faithfully
      vertical genes were rare compared with those with history of recombination
      including lateral gene transfer, although rhizobial adaptations to symbiotic
      interactions and other environmental conditions extensively recruited
      lineage-specific shell genes under direct or indirect control through the
      speciation process.
AU  - Tian CF
AU  - Zhou YJ
AU  - Zhang YM
AU  - Li QQ
AU  - Zhang YZ
AU  - Li DF
AU  - Wang S
AU  - Wang J
AU  - Gilbert LB
AU  - Li YR
AU  - Chen WX
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2012 109: 8629-8634.

PMID- 1708831
VI  - 218
DP  - 1991
TI  - Incipient mitochondrial evolution in yeasts.  II.  The complete sequence of the gene coding for cytochrome b in S. douglasii reveals the presence of both new and conserved introns and discloses major differences in the fixation of mutations in evolution.
PG  - 747-760
AB  - We have determined the complete sequence of the mitochondrial gene coding for cytochrome b in
      Saccharomyces douglasii.  The gene is 6310 base-pairs long and is interrupted by four introns.
      The first one (1311 base-pairs) belongs to the group ID of secondary structure, contains a
      fragment open reading frame with a characteristic GIY . . . YIG motif, is absent from
      Saccharomyces cerevisiae and is inserted in the same site in which introns 1 and 2 are
      inserted in Neurospora crassa and Podospora anserina, respectively.  The next three S.
      douglasii introns are homologous to the first three introns of S. cerevisiae, are inserted at
      the same positions and display various degrees of similarity ranging from an almost complete
      identity (intron 2 and 4) to a moderate one (intron 3).  We have compared secondary structures
      of intron RNAs, and nucleotide and amino acid sequences of cytochrome b exons and intron open
      reading grames in the two Saccharomyces species.  The rules that govern fixation of mutations
      in exon and intron open reading frames are different:  the relative proportion of mutations
      occurring in synonymous codons is low in some introns and high in exons.  The overall
      frequency of mutations in cytochrome b exons is much smaller than in nuclear genes of yeasts,
      contrary to what has been found in vertebrates, where mitochrondrial mutations are more
      frequent.  The divergence of the cytochrome b gene is modular: various parts of the gene have
      changed with a different mode and tempo of evolution.
AU  - Tian G-L
AU  - Michel F
AU  - Macadre C
AU  - Slonimski PP
AU  - Lazowska J
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1991 218: 747-760.

PMID- 24723713
VI  - 2
DP  - 2014
TI  - Genome Sequence of the Aerobic Arsenate-Reducing Bacterium Pantoea sp. Strain IMH.
PG  - e00267-14
AB  - We here report the draft assembly for the genome of Pantoea sp. strain IMH, isolated from
      arsenic-contaminated soil in Inner Mongolia, China, with the ability to aerobically reduce
      arsenate to arsenite. The genome sequence will allow for the characterization of the molecular
      mechanisms of arsenate reduction.
AU  - Tian H
AU  - Jing C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00267-14.

PMID- 25278536
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Organophosphorus-Degrading Bacterium Pseudomonas sp. Strain 1-7, Isolated from Organophosphorus-Polluted Sludge.
PG  - e00993-14
AB  - Pseudomonas sp. strain 1-7, isolated from organophosphorus-polluted sludge, is able to degrade
      many organophosphorus compounds. Here, we report the draft genome
      sequence of Pseudomonas sp. strain 1-7.
AU  - Tian J
AU  - Xu L
AU  - Zhang S
AU  - Sun W
AU  - Chu X
AU  - Wu N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00993-14.

PMID- 26380037
VI  - 10
DP  - 2015
TI  - High-quality permanent draft genome sequence of Bradyrhizobium sp. Ai1a-2; a microsymbiont of Andira inermis discovered in Costa Rica.
PG  - 33
AB  - Bradyrhizobium sp. Ai1a-2 is is an aerobic, motile, Gram-negative, non-spore-forming rod that
      was isolated from an effective nitrogen fixing root nodule of Andira inermis collected from
      Tres Piedras in Costa Rica. In this report we describe, for the first time, the genome
      sequence information and annotation of this legume microsymbiont. The 9,029,266 bp genome has
      a GC content of 62.56% with 247 contigs arranged into 246 scaffolds. The assembled genome
      contains 8,482 protein-coding genes and 102 RNA-only encoding genes. This rhizobial genome was
      sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and
      Archaea-Root Nodule Bacteria (GEBA-RNB) project proposal.
AU  - Tian R
AU  - Parker M
AU  - Seshadri R
AU  - Reddy T
AU  - Markowitz V
AU  - Ivanova N
AU  - Pati A
AU  - Woyke T
AU  - Baeshen M
AU  - Baeshen N
AU  - Kyrpides N
AU  - Reeve W
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 33.

PMID- 26203338
VI  - 10
DP  - 2015
TI  - High-quality permanent draft genome sequence of Bradyrhizobium sp. Tv2a.2, a microsymbiont of Tachigali versicolor discovered in Barro Colorado Island of  Panama.
PG  - 27
AB  - Bradyrhizobiumsp. Tv2a.2 is an aerobic, motile, Gram-negative, non-spore-forming  rod that was
      isolated from an effective nitrogen-fixing root nodule of Tachigali
      versicolor collected in Barro Colorado Island of Panama. Here we describe the
      features of Bradyrhizobiumsp. Tv2a.2, together with high-quality permanent draft
      genome sequence information and annotation. The 8,496,279 bp high-quality draft
      genome is arranged in 87 scaffolds of 87 contigs, contains 8,109 protein-coding
      genes and 72 RNA-only encoding genes. This rhizobial genome was sequenced as part
      of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and
      Archaea-Root Nodule Bacteria (GEBA-RNB) project.
AU  - Tian R
AU  - Parker M
AU  - Seshadri R
AU  - Reddy T
AU  - Markowitz V
AU  - Ivanova N
AU  - Pati A
AU  - Woyke T
AU  - Baeshen MN
AU  - Baeshen NA
AU  - Kyrpides N
AU  - Reeve W
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 27.

PMID- 26203336
VI  - 10
DP  - 2015
TI  - High-quality permanent draft genome sequence of Bradyrhizobium sp. Th.b2, a microsymbiont of Amphicarpaea bracteata collected in Johnson City, New York.
PG  - 24
AB  - Bradyrhizobium sp. Th.b2 is an aerobic, motile, Gram-negative, non-spore-forming  rod that was
      isolated from an effective nitrogen-fixing root nodule of
      Amphicarpaea bracteata collected in Johnson City, New York. Here we describe the
      features of Bradyrhizobium sp. Th.b2, together with high-quality permanent draft
      genome sequence information and annotation. The 10,118,060 high-quality draft
      genome is arranged in 266 scaffolds of 274 contigs, contains 9,809 protein-coding
      genes and 108 RNA-only encoding genes. This rhizobial genome was sequenced as
      part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and
      Archaea-Root Nodule Bacteria (GEBA-RNB) project.
AU  - Tian R
AU  - Parker M
AU  - Seshadri R
AU  - Reddy T
AU  - Markowitz V
AU  - Ivanova N
AU  - Pati A
AU  - Woyke T
AU  - Baeshen MN
AU  - Baeshen NA
AU  - Kyrpides N
AU  - Reeve W
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 24.

PMID- 28774986
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of the Multiresistant Escherichia coli C20 Strain, Isolated from Domestic Chicken Gut Microbiota.
PG  - e00751-17
AB  - Escherichia coli C20, isolated from domestic chicken gut microbiota, demonstrated multidrug
      resistance to the tested antibiotics. Here, we present the draft
      genomic sequences of E. coli C20, along with that of its plasmid. The final
      assembly yielded a chromosome of 4,640,940 bp and plasmid of 277,380 bp, with
      average coverages of 146.95-fold and 35.63-fold, respectively.
AU  - Tian RC
AU  - Huang W
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00751-17.

PMID- 26893438
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Acinetobacter johnsonii MB44, Exhibiting Nematicidal Activity against Caenorhabditis elegans.
PG  - e01772-15
AB  - Acinetobacter johnsonii MB44 was isolated from a frost-plant-tissue sample, which showed
      noteworthy nematicidal activity against the model organism Caenorhabditis
      elegans. Here, we report the 3.4 Mb draft genome of A. johnsonii MB44, which will
      help in understanding the molecular mechanism of its ability to infect nematodes.
AU  - Tian S
AU  - Ali M
AU  - Xie L
AU  - Li L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01772-15.

PMID- 12114964
VI  - 31
DP  - 1999
TI  - Effect of high hydrostatic pressure on activity of restriction endonucleases.
PG  - 523-526
AB  - The effect of high hydrostatic pressure on the activities of type II restriction enzymes
      HindIII and XbaI in digesting plasmid pSPORT1 was studied.  The endonuclease activity of
      HindIII and XbaI at 37 C were gradually inhibited by increasing pressure and completely
      inhibited at 200 and 180 MPa, respectively.  No obvious irreversible effect was observed for
      HindIII after suffering high pressure, while a considerable irreversible inactivation was
      observed for XbaI.  The standard molar volume changes for HindIII and XbaI estimated from the
      inhibition of endonuclease activity at different pressures were 213 and 103 ml/mol,
      respectively.  It was also concluded that pressurization did not change the substrate sequence
      specificity of both HindIII and XbaI.
AU  - Tian S-M
AU  - Gong Z-Z
AU  - Xie W-J
AU  - Zheng L
AU  - Ruan K-C
PT  - Journal Article
TA  - Acta Biochim. Biophys. Sin.
JT  - Acta Biochim. Biophys. Sin.
SO  - Acta Biochim. Biophys. Sin. 1999 31: 523-526.

PMID- 29449396
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of a Pathogenic Vibrio vulnificus Strain Isolated in Brazil.
PG  - e01274-17
AB  - We describe the draft genome sequence of the clinical Vibrio vulnificus strain 03_7315,
      isolated in 2016 from the blood of a diabetic patient who died of
      septicemia after ingestion of seafood. The draft genome, with 4,755,588 bp
      covering two chromosomes, presented 4,434 genes, 4,213 coding sequences, and 117
      pseudogenes.
AU  - Tiba-Casas MR
AU  - Lemes-Marques EG
AU  - Almeida EA
AU  - Soares FB
AU  - Camargo CH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01274-17.

PMID- 21304699
VI  - 2
DP  - 2010
TI  - Complete genome sequence of Nakamurella multipartita type strain (Y-104).
PG  - 168-175
AB  - Nakamurella multipartita (Yoshimi et al. 1996) Tao et al. 2004 is the type species of the
      monospecific genus Nakamurella in the actinobacterial suborder
      Frankineae. The nonmotile, coccus-shaped strain was isolated from activated
      sludge acclimated with sugar-containing synthetic wastewater, and is capable of
      accumulating large amounts of polysaccharides in its cells. Here we describe the
      features of the organism, together with the complete genome sequence and
      annotation. This is the first complete genome sequence of a member of the family
      Nakamurellaceae. The 6,060,298 bp long single replicon genome with its 5415
      protein-coding and 56 RNA genes is part of the Genomic Encyclopedia of Bacteria
      and Archaea project.
AU  - Tice H et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 2: 168-175.

PMID- 8883359
VI  - 12
DP  - 1996
TI  - Identification of the gene encoding the DNA (cytosine-5) methyltransferase of lymphocystis disease virus.
PG  - 219-229
AB  - The gene encoding the DNA (cytosine-5) methyltransferase (m5C-MTase) of lymphocystis disease
      virus (flounder isolate, LCDV-1) has been identified by polymerase chain reaction (PCR) using
      oligonucleotide primers synthesized corresponding to different regions of the m5C-MTase gene
      of frog virus 3 (FV3).  A DNA fragment of 487 bp was amplified using oligonucleotide primers
      L3 and R4 which correspond to the nucleotide positions 87 to 109 and 530 to 550 of the
      m5C-MTase gene of FV3, respectively.  The DNA nucleotide sequence of the PCR product was
      determined by direct cycle sequencing.  The alignment of the deduced amino acid sequence
      derived from the PCR product and the m5C-MTase protein of FV3 revealed a homology of 55.4%
      identity and 29.1% similarity.  The amino acid sequence which was found to be significantly
      homologous to the amino acid sequence deduced from the nucleotide sequence of the PCR product
      was located at the amino acid position 37 to 175 of the m5C-MTase of FV3 indicating the
      specificity of the amplified PCR product.  The DNA nucleotide sequence of the LCDV-1 genome
      corresponding to the 5' and 3' termini of the m5C-MTase gene was determined by primer
      walking.  The locus of the m5C-MTase gene of LCDV-1 was identified within the EcoRI DNA
      fragment G of LCDV-1 (7.9 kbp; 0.947 to 0.034 map units).  The m5C-MTase gene of LCDV-1
      comprises 684 nucleotides coding for a putative protein of 228 amino acid residues.  A high
      degree of amino acid sequence homology (53.3% identity and 25.8% similarity) was detected
      between the m5C-MTases of LCDV01 and FV3.
AU  - Tidona CA
AU  - Schnitzler P
AU  - Kehm R
AU  - Darai G
PT  - Journal Article
TA  - Virus Genes
JT  - Virus Genes
SO  - Virus Genes 1996 12: 219-229.

PMID- 24459261
VI  - 2
DP  - 2014
TI  - Genome Sequence of the Small-Colony Variant Pseudomonas aeruginosa MH27, Isolated from a Chronic Urethral Catheter Infection.
PG  - e01174-13
AB  - Pseudomonas aeruginosa is a notable nosocomial pathogen causing severe chronic infections.
      Here we present the draft genome sequence of P. aeruginosa MH27,
      isolated from a patient with a chronic hospital-acquired catheter-associated
      urinary tract infection. The 7.1-Mb genome sequence organized in 24 scaffolds
      contributes to the understanding of biofilm formation and antibiotic resistance.
AU  - Tielen P
AU  - Wibberg D
AU  - Blom J
AU  - Rosin N
AU  - Meyer AK
AU  - Bunk B
AU  - Schobert M
AU  - Tupker R
AU  - Schatschneider S
AU  - Ruckert C
AU  - Albersmeier A
AU  - Goesmann A
AU  - Vorholter FJ
AU  - Jahn D
AU  - Puhler A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01174-13.

PMID- 33871
VI  - 4
DP  - 1978
TI  - EcoRI* activity:  Enzyme modification or activation of accompanying endonuclease?
PG  - 195-212
AB  - A study has been made of the factors and mechanism leading to appearance of the
      so-called EcoRI* activity described by Polisky et al. (1975) in the restrictase
      EcoRI preparations.  The preparations of purified restrictase EcoRI,
      precipitated at 0.9 ammonium sulphate saturation, as well as that obtained
      using standard techniques have been found to contain an admixture of an
      endonuclease which at neutral pH and high ionic strength multiply cleaves those
      DNAs which normally have only one recognition site for EcoRI.  Under the
      standard conditions for EcoRI digestion this activity is found only when large
      amounts of freshly isolated enzyme are added to the incubation mixture and it
      is sharply enhanced by replacement of Mg2+ with Mn2+.  The number and size of
      DNa fragments produced under such conditions practically do not differ from
      those found under the so-called EcoRI* conditions, that is for alkaline pH
      values and low ionic strength.  The optimum incubation mixture for the EcoRI*
      activity has been found to be 10 mM Tris-HCl buffer (pH 8.8) + 2 mM Mn2+.
      Similar activity is induced also by addition to EcoRI solution of 40-50%
      glycerol or a number of organic solvents (dimethylacetamide (DMA),
      dimethylformamide (DMF), dimethylsulphoxide (DMSO), sulphalane (SP)) in
      concentrations from 1 to 6%.  The EcoRI* activity induced by 50% glycerol or at
      alkaline pH values and low ionic strength is suppressed or sharply inhibited by
      2-3 mM parachloromercuribenzoate (PCMB), while EcoRI is not sensitive to this
      agent.  The DNA fragments cleaved by EcoRI* have cohesive termini and can be
      easily ligated.  It is suggested that the EcoRI* activity can be due not only
      (or largely not) to modification of the "recognizing capacity" of the EcoRI
      restrictase but to activation of a latent specific endonuclease which is
      present in the restrictase preparation as an impurity.
AU  - Tikchonenko TI
AU  - Karamov EV
AU  - Zavizion BA
AU  - Naroditsky BS
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1978 4: 195-212.

PMID- 3102953
VI  - 11
DP  - 1986
TI  - DNA-methyltransferases from different Bacillus subtilis and Bacillus natto strains.
PG  - 40-44
AB  - DNA-methyltransferase activity has been detected in some Bacillus subtilis and Bacillus natto
      strains.  Two strains of Bacillus subtilis exhibited DNA-cytosine methyltransferase activity,
      and the strains of Bacillus natto exhibited DNA-adenine methyltransferase activity.  A
      possible effect of DNA-methyltransferase specificity on transformation efficiency is
      discussed.
AU  - Tikhonova TN
AU  - Malyuta SS
AU  - Nesterenko VF
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1986 11: 40-44.

PMID- 8415603
VI  - 90
DP  - 1993
TI  - DNA methylation: A phoenix rises.
PG  - 8761-8762
AB  - A report in this issue of the Proceedings by Baylin and his colleagues describes a potential
      new way in which DNA methylation affects the physiology of the mammalian cell. The authors
      begin from the observation that transformed cells often display higher overall levels of DNA
      methylation, as well as increased levels of the hemimethylase, DNA methyltransferase. The
      preferred substrate for this enzyme is double-stranded DNA which is hemimethylated on the
      cytosine residue of the dinucleotide CpG. When the investigators introduced extra copies of
      the enzyme into nontumorigenic NIH 3T3 mouse fibroblasts by gene transfer, the cells acquired
      tumorigenic properties, such as loss of contact inhibition, growth in soft agar, and the
      ability to form tumors in nude mice.
AU  - Tilghman SM
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1993 90: 8761-8762.

PMID- 15273276
VI  - 32
DP  - 2004
TI  - Changing the recognition specificity of a DNA-methyltransferase by in vitro evolution.
PG  - 3898-3903
AB  - The gene coding for the SinI DNA-methyltransferase, a modification enzyme able to recognize
      and methylate the internal cytosine of the GGWCC sequence, was subjected to in vitro
      mutagenesis, DNA-shuffling and a strong selection for relaxed GGNCC recognition specificity.
      As a result of this in vitro evolution experiment, a mutant gene with the required phenotype
      was selected. The mutant SinI methyltransferase carried five amino acid substitutions. None of
      these was found in the 'variable region' that were thought to be responsible for sequence
      specificity. Three were located near the N-terminal end, preceding the first conserved
      structural motif of the enzyme; two were found between conserved motifs VI and VII. A clone
      engineered to carry out only the latter two replacements (L214S and Y229H) displays relaxed
      recognition specificity similar to that of the parental mutant, whereas the clone carrying
      only the N-terminal replacements showed a much weaker change in recognition specificity. The
      enzyme with two internal mutations was purified and characterized. Its catalytic activity
      (kcat/Km) was  5-fold lower towards GGWCC and 20-fold higher towards GGSCC than that of the
      wild-type enzyme.
AU  - Timar E
AU  - Groma G
AU  - Kiss A
AU  - Venetianer P
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2004 32: 3898-3903.

PMID- 18849437
VI  - 190
DP  - 2008
TI  - In vivo DNA protection by relaxed-specificity SinI DNA methyltransferase variants.
PG  - 8003-8008
AB  - The SinI DNA methyltransferase, a component of the SinI restriction-modification system,
      recognizes the sequence GG(A/T)CC and
      methylates the inner cytosine to produce 5-methylcytosine. Previously
      isolated relaxed-specificity mutants of the enzyme also methylate, at a
      lower rate, GG(G/C)CC sites. In this work we tested the capacity of the
      mutant enzymes to function in vivo as the counterpart of a restriction
      endonuclease, which can cleave either site. The viability of Escherichia
      coli cells carrying recombinant plasmids with the mutant methyltransferase
      genes and expressing the GGNCC-specific Sau96I restriction endonuclease
      from a compatible plasmid was investigated. The sau96IR gene on the latter
      plasmid was transcribed from the araBAD promoter, allowing tightly
      controlled expression of the endonuclease. In the presence of low
      concentrations of the inducer arabinose, cells synthesizing the N172S or
      the V173L mutant enzyme displayed increased plating efficiency relative to
      cells producing the wild-type methyltransferase, indicating enhanced
      protection of the cell DNA against the Sau96I endonuclease. Nevertheless,
      this protection was not sufficient to support long-term survival in the
      presence of the inducer, which is consistent with incomplete methylation
      of GG(G/C)CC sites in plasmid DNA purified from the N172S and V173L
      mutants. Elevated DNA ligase activity was shown to further increase
      viability of cells producing the V173L variant and Sau96I endonuclease.
AU  - Timar E
AU  - Venetianer P
AU  - Kiss A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2008 190: 8003-8008.

PMID- 7607512
VI  - 157
DP  - 1995
TI  - Sequence motifs characteristic for DNA [cytosine-N4] and DNA [adenine-N6] methyltransferases.  Classification of all DNA methyltransferases.
PG  - 3-11
AB  - Two additional conserved motifs (CM), CMIs and CMIII, have been found in addition to
      well-known CMI and CMII within the primary amino acid sequences of almost all m6A- and
      m4C-methyltransferases (MTases).  The boundaries of all four CM were defined and their
      consensus sequences characteristic both for different classes, as well as for all N-MTases,
      were derived.  Some regular deviations at fixed positions of the consensus sequences CMIs, CMI
      and CMiI, typical for separate classes of N-MTases, were presumed to correlate.  A possible
      structural basis for the supposed interregional correlations is discussed and experiments for
      verification of the assumed interactions between CM are suggested.  A classification scheme
      for all N-MTases is provided.
AU  - Timinskas A
AU  - Butkus V
AU  - Janulaitis A
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 3-11.

PMID- 6257655
VI  - 145
DP  - 1981
TI  - Characterization of a site-specific restriction endonuclease from Streptomyces aureofaciens.
PG  - 873-877
AB  - A new type II sequence-specific restriction endonuclease, SauI, was isolated
      from Streptomyces aureofaciens IKA18/4.  The purified enzyme was free of
      contaminating exonuclease and phosphatase activities.  SauI cleaved lambda DNA
      at two sites, but did not cleave pBR322, simian virus 40, or PhiX174 DNA.  SauI
      recognized the septanucleotide sequence 5'-CC^TNAGG-3' and cleaved at the
      position indicated by the arrow, producing a trinucleotide 5'-terminal
      extension.
AU  - Timko J
AU  - Horwitz AH
AU  - Zelinka J
AU  - Wilcox G
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1981 145: 873-877.

PMID- 97188
VI  - 23
DP  - 1978
TI  - Specific endonucleases in Streptomyces aureofaciens.
PG  - 243-245
AB  - Two strains of Streptomyces aureofaciens were found to contain restriction
      endodeoxynucleases; S. aureofaciens TKA 18/4 contains SauI which splits lambda
      DNA into three fragments, S. aureofaciens IKA 22201 contains SauI which splits
      lambda DNA into more than 15 fragments.
AU  - Timko J
AU  - Matuskova M
AU  - Zelinkova E
AU  - Zelinka J
PT  - Journal Article
TA  - Folia Microbiol. (Praha)
JT  - Folia Microbiol. (Praha)
SO  - Folia Microbiol. (Praha) 1978 23: 243-245.

PMID- Not included in PubMed...
VI  - 43
DP  - 1988
TI  - Restriction endonuclease SauI from Streptomyces aureofaciens - some physical and chemical properties.
PG  - 681-689
AB  - Some physical and chemical properties of restriction endonuclease SauI, which
      was isolated from Streptomyces aureofaciens IKA 18/4, were studied.  The
      effects of divalent ions, monovalent ions, pH and temperature on enzyme
      activity were determined.  For cleavage of substrate DNA by endonuclease SauI
      the optimal reaction mixture was determined as: 10 mM Tris-HCl, pH 7.5, 10 mM
      MgCl2, 75 mM NaCl at 37C.
AU  - Timko J
AU  - Sisova M
AU  - Ugorcakova J
AU  - Zelinka J
PT  - Journal Article
TA  - Biologia (Bratisl)
JT  - Biologia (Bratisl)
SO  - Biologia (Bratisl) 1988 43: 681-689.

PMID- 
VI  - 6
DP  - 1987
TI  - Site-specific restriction endonuclease SauBMKI from Streptomyces aureofaciens.
PG  - 107-118
AB  - Type II restriction endonucleases have been isolated from many bacteria
      including Streptomycetes and their specificities have been characterized
      (Roberts, 1985).  From Streptomyces aureofaciens restriction endonucleases SauI
      (Timko et al., 1981) and Sau3239I (Gasperik et al., 1983; Simbochova et al.,
      1986) have been isolated and characterized.  In this paper we describe a new
      restriction endonuclease, SauBMKI from Streptomyces aureofaciens, strain BM-K,
      producing about 2500 micrograms of CTC per ml.
AU  - Timko J
AU  - Turna J
AU  - Zelinka J
PT  - Journal Article
TA  - Metabolism and Enzymology of Nucleic Acids
JT  - Metabolism and Enzymology of Nucleic Acids
SO  - Metabolism and Enzymology of Nucleic Acids 1987 6: 107-118.

PMID- 
VI  - 4
DP  - 1982
TI  - Properties of the restriction endonuclease Saul.
PG  - 319-324
AB  - None
AU  - Timko J
AU  - Zelinka J
AU  - Wilcox G
PT  - Journal Article
TA  - Metabolism and Enzymology of Nucleic Acids
JT  - Metabolism and Enzymology of Nucleic Acids
SO  - Metabolism and Enzymology of Nucleic Acids 1982 4: 319-324.

PMID- 23045502
VI  - 194
DP  - 2012
TI  - Draft Genome Sequences of 21 Salmonella enterica Serovar Enteritidis Strains.
PG  - 5994-5995
AB  - Salmonella enterica subsp. enterica serovar Enteritidis is a common food-borne pathogen, often
      associated with shell eggs and poultry. Here, we report draft
      genomes of 21 S. Enteritidis strains associated with or related to the U.S.-wide
      2010 shell egg recall. Eleven of these genomes were from environmental isolates
      associated with the egg outbreak, and 10 were reference isolates from previous
      years, unrelated to the outbreak. The whole-genome sequence data for these 21
      human pathogen strains are being released in conjunction with the newly formed
      100K Genome Project.
AU  - Timme RE
AU  - Allard MW
AU  - Luo Y
AU  - Strain E
AU  - Pettengill J
AU  - Wang C
AU  - Li C
AU  - Keys CE
AU  - Zheng J
AU  - Stones R
AU  - Wilson MR
AU  - Musser SM
AU  - Brown EW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5994-5995.

PMID- 24158624
VI  - 5
DP  - 2013
TI  - Phylogenetic diversity of the enteric pathogen Salmonella enterica subsp. enterica inferred from genome-wide reference-free SNP characters.
PG  - 2109-2123
AB  - The enteric pathogen Salmonella enterica is one of the leading causes of
      foodborne illness in the world. The species is extremely diverse, containing more
      than 2,500 named serovars that are designated for their unique antigen characters
      and pathogenicity profiles-some are known to be virulent pathogens, while others
      are not. Questions regarding the evolution of pathogenicity, significance of
      antigen characters, diversity of clustered regularly interspaced short
      palindromic repeat (CRISPR) loci, among others, will remain elusive until a
      strong evolutionary framework is established. We present the first large-scale S.
      enterica subsp. enterica phylogeny inferred from a new reference-free k-mer
      approach of gathering single nucleotide polymorphisms (SNPs) from whole genomes.
      The phylogeny of 156 isolates representing 78 serovars (102 were newly sequenced)
      reveals two major lineages, each with many strongly supported sublineages. One of
      these lineages is the S. Typhi group; well nested within the phylogeny.
      Lineage-through-time analyses suggest there have been two instances of
      accelerated rates of diversification within the subspecies. We also found that
      antigen characters and CRISPR loci reveal different evolutionary patterns than
      that of the phylogeny, suggesting that a horizontal gene transfer or possibly a
      shared environmental acquisition might have influenced the present character
      distribution. Our study also shows the ability to extract reference-free SNPs
      from a large set of genomes and then to use these SNPs for phylogenetic
      reconstruction. This automated, annotation-free approach is an important step
      forward for bacterial disease tracking and in efficiently elucidating the
      evolutionary history of highly clonal organisms.
AU  - Timme RE
AU  - Pettengill JB
AU  - Allard MW
AU  - Strain E
AU  - Barrangou R
AU  - Wehnes C
AU  - Van Kessel JS
AU  - Karns JS
AU  - Musser SM
AU  - Brown EW
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2013 5: 2109-2123.

PMID- 20353581
VI  - 11
DP  - 2010
TI  - Evidence for a lineage of virulent bacteriophages that target Campylobacter.
PG  - 214
AB  - Background: Our understanding of the dynamics of genome stability versus gene flux within
      bacteriophage lineages is limited. Recently,
      there has been a renewed interest in the use of bacteriophages as
      'therapeutic' agents; a prerequisite for their use in such therapies is
      a thorough understanding of their genetic complement, genome stability
      and their ecology to avoid the dissemination or mobilisation of phage
      or bacterial virulence and toxin genes. Campylobacter, a food-borne
      pathogen, is one of the organisms for which the use of bacteriophage is
      being considered to reduce human exposure to this organism.
      Results: Sequencing and genome analysis was performed for two
      Campylobacter bacteriophages. The genomes were extremely similar at the
      nucleotide level (>= 96%) with most differences accounted for by novel
      insertion sequences, DNA methylases and an approximately 10 kb
      contiguous region of metabolic genes that were dissimilar at the
      sequence level but similar in gene function between the two phages.
      Both bacteriophages contained a large number of radical
      S-adenosylmethionine (SAM) genes, presumably involved in boosting host
      metabolism during infection, as well as evidence that many genes had
      been acquired from a wide range of bacterial species. Further
      bacteriophages, from the UK Campylobacter typing set, were screened for
      the presence of bacteriophage structural genes, DNA methylases, mobile
      genetic elements and regulatory genes identified from the genome
      sequences. The results indicate that many of these bacteriophages are
      related, with 10 out of 15 showing some relationship to the sequenced
      genomes.
      Conclusions: Two large virulent Campylobacter bacteriophages were
      found to show very high levels of sequence conservation despite
      separation in time and place of isolation. The bacteriophages show
      adaptations to their host and possess genes that may enhance
      Campylobacter metabolism, potentially advantaging both the
      bacteriophage and its host. Genetic conservation has been shown to
      extend to other Campylobacter bacteriophages, forming a highly
      conserved lineage of bacteriophages that predate upon campylobacters
      and indicating that highly adapted bacteriophage genomes can be stable
      over prolonged periods of time.
AU  - Timms AR
AU  - Cambray-Young J
AU  - Scott AE
AU  - Petty NK
AU  - Connerton PL
AU  - Clarke L
AU  - Seeger K
AU  - Quail M
AU  - Cummings N
AU  - Maskell DJ
AU  - Thomson NR
AU  - Connerton IF
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2010 11: 214.

PMID- 21304667
VI  - 1
DP  - 2009
TI  - Complete genome sequence of Halomicrobium mukohataei type strain (arg-2).
PG  - 270-277
AB  - Halomicrobium mukohataei (Ihara et al. 1997) Oren et al. 2002 is the type species of the genus
      Halomicrobium. It is of phylogenetic interest because of its
      isolated location within the large euryarchaeal family Halobacteriaceae. H.
      mukohataei is an extreme halophile that grows essentially aerobically, but can
      also grow anaerobically under a change of morphology and with nitrate as electron
      acceptor. The strain, whose genome is described in this report, is a free-living,
      motile, Gram-negative euryarchaeon, originally isolated from Salinas Grandes in
      Jujuy, Andes highlands, Argentina. Its genome contains three genes for the 16S
      rRNA that differ from each other by up to 9%. Here we describe the features of
      this organism, together with the complete genome sequence and annotation. This is
      the first completed genome sequence from the poorly populated genus
      Halomicrobium, and the 3,332,349 bp long genome (chromosome and one plasmid) with
      its 3416 protein-coding and 56 RNA genes is part of the Genomic Encyclopedia of
      Bacteria and Archaea project.
AU  - Tindall BJ et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2009 1: 270-277.

PMID- 21304689
VI  - 3
DP  - 2010
TI  - Complete genome sequence of Meiothermus ruber type strain (21T).
PG  - 26-36
AB  - Meiothermus ruber (Loginova et al. 1984) Nobre et al. 1996 is the type species of the genus
      Meiothermus. This thermophilic genus is of special interest, as its members share relatively
      low degrees of 16S rRNA gene sequence similarity and constitute a separate evolutionary
      lineage from members of the genus Thermus, from which they can generally be distinguished by
      their slightly lower temperature optima. The temperature related split is in accordance with
      the chemotaxonomic feature of the polar lipids. M. ruber is a representative of the
      low-temperature group. This is the first completed genome sequence of the genus Meiothermus
      and only the third genome sequence to be published from a member of the family Thermaceae. The
      3,097,457 bp long genome with its 3,052 protein-coding and 53 RNA genes is a part of the
      Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Tindall BJ et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 3: 26-36.

PMID- 25414509
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Corynebacterium ureicelerivorans DSM 45051, a Lipophilic and Urea-Splitting Isolate from the Blood Culture of a Septicemia  Patient.
PG  - e01211-14
AB  - Corynebacterium ureicelerivorans is an opportunistic pathogen with a lipophilic lifestyle and
      an exceptionally high urease activity. The genome sequence of the
      type strain revealed that lipophilism is caused by the lack of a fatty acid
      synthase gene. The ureABCEFGD genes are similar to the urease gene region of
      Corynebacterium glucuronolyticum.
AU  - Tippelt A
AU  - Albersmeier A
AU  - Brinkrolf K
AU  - Ruckert C
AU  - Fernandez-Natal I
AU  - Soriano F
AU  - Tauch A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01211-14.

PMID- 25146145
VI  - 2
DP  - 2014
TI  - Mycolic Acid Biosynthesis Genes in the Genome Sequence of Corynebacterium atypicum DSM 44849.
PG  - e00845-14
AB  - The complete chromosomal sequence of the type strain Corynebacterium atypicum DSM 44849
      comprises 2,311,380 bp. A functional annotation revealed the presence of
      genes involved in the synthesis and export of mycolic acids and in trehalose
      corynomycolate biosynthesis, supporting the view that the cell envelope of C.
      atypicum contains mycolic acids.
AU  - Tippelt A
AU  - Mollmann S
AU  - Albersmeier A
AU  - Jaenicke S
AU  - Ruckert C
AU  - Tauch A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00845-14.

PMID- 23799069
VI  - 8
DP  - 2013
TI  - Candidate genes that may be responsible for the unusual resistances exhibited by Bacillus pumilus SAFR-032 spores.
PG  - e66012
AB  - The spores of several Bacillus species, including Bacillus pumilus SAFR-032 and
      B. safensis FO-36b, which were isolated from the spacecraft assembly facility at
      NASA's Jet Propulsion Laboratory, are unusually resistant to UV radiation and
      hydrogen peroxide. In order to identify candidate genes that might be associated
      with these resistances, the whole genome of B. pumilus SAFR-032, and the draft
      genome of B. safensis FO-36b were compared in detail with the very closely
      related type strain B. pumilus ATCC7061(T). 170 genes are considered
      characteristic of SAFR-032, because they are absent from both FO-36b and
      ATCC7061(T). Forty of these SAFR-032 characteristic genes are entirely unique
      open reading frames. In addition, four genes are unique to the genomes of the
      resistant SAFR-032 and FO-36b. Fifty three genes involved in spore coat
      formation, regulation and germination, DNA repair, and peroxide resistance, are
      missing from all three genomes. The vast majority of these are cleanly deleted
      from their usual genomic context without any obvious replacement. Several DNA
      repair and peroxide resistance genes earlier reported to be unique to SAFR-032
      are in fact shared with ATCC7061(T) and no longer considered to be promising
      candidates for association with the elevated resistances. Instead, several
      SAFR-032 characteristic genes were identified, which along with one or more of
      the unique SAFR-032 genes may be responsible for the elevated resistances. These
      new candidates include five genes associated with DNA repair, namely, BPUM_0608 a
      helicase, BPUM_0652 an ATP binding protein, BPUM_0653 an endonuclease, BPUM_0656
      a DNA cytosine-5- methyltransferase, and BPUM_3674 a DNA helicase. Three of these
      candidate genes are in immediate proximity of two conserved hypothetical
      proteins, BPUM_0654 and BPUM_0655 that are also absent from both FO-36b and
      ATCC7061(T). This cluster of five genes is considered to be an especially
      promising target for future experimental work.
AU  - Tirumalai MR
AU  - Rastogi R
AU  - Zamani N
AU  - O'Bryant-Williams E
AU  - Allen S
AU  - Diouf F
AU  - Kwende S
AU  - Weinstock GM
AU  - Venkateswaran KJ
AU  - Fox GE
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2013 8: e66012.

PMID- 26251504
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Frankia sp. Strain DC12, an Atypical, Noninfective, Ineffective Isolate from Datisca cannabina.
PG  - e00889-15
AB  - Frankia sp. strain DC12, isolated from root nodules of Datisca cannabina, is a member of the
      fourth lineage of Frankia, which is unable to reinfect actinorhizal
      plants. Here, we report its 6.88-Mbp high-quality draft genome sequence, with a
      G+C content of 71.92% and 5,858 candidate protein-coding genes.
AU  - Tisa LS et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00889-15.

PMID- 
VI  - 21
DP  - 2005
TI  - Methyltransferases of plants.
PG  - 463-472
AB  - In the review the current data on the plant cytosine-C5-DNA-methyltransferases
      (methyltransferase) are summarized.  Three different classes of these enzymes - Snmt1/MET1,
      Dnmt3 and CMT are described. The proposed function, dealing with maintenance and de novo
      methylation of cytosine residues in symmetric and asymmetric motifs of DNA, is under
      discussion.
AU  - Tishchenko EN
AU  - Dubrovnaya OV
PT  - Journal Article
TA  - Biopol. Kletka
JT  - Biopol. Kletka
SO  - Biopol. Kletka 2005 21: 463-472.

PMID- 3015153
VI  - 12
DP  - 1986
TI  - Specific features of the restriction endonuclease BamHI interaction with oligodeoxynucleotides.
PG  - 640-646
AB  - Interaction of the restriction endonuclease BamHI with a series of synthetic
      oligodeoxynucleotides containing the restriction site has been studied.  The
      enzyme is shown to specifically cut the BamHI site in hexanucleotide (I) and in
      non-selfcomplementary deca- and octanucleotides (II)-(IV).  The data obtained
      led to the conclusion that BamHI reacts with duplex structures, while playing
      an important role in their stabilization.  In 14-mer (V) BamHI cuts a
      non-standard half-site GAA to yield the 5'-terminal tri- (rather than hepta-)
      nucleotide.  Hypothetical mechanisms of the process are discussed basing on
      conception of the role of higher DNA structures in the interaction with
      restriction endonucleases.
AU  - Titeeva GR
AU  - Vinogradov SV
AU  - Berlin YA
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1986 12: 640-646.

PMID- 3026408
VI  - 12
DP  - 1986
TI  - Complexes of the phage single-stranded DNA with synthetic oligodeoxynucleotides and their interaction with DNA polymerase and restriction endonucleases.
PG  - 1484-1491
AB  - Hybridization of synthetic oligodeoxynucleotides with single-stranded phage
      M13mp2 DNA has been studied in terms of temperature, ionic strength,
      oligonucleotide molar excess and chain length, and DNA secondary structure.
      Combination of two decadeoxynucleotides corresponding to a nicked eicosamer
      (composite primer) was found to be efficient in the template-directed DNA
      polymerase-catalyzed chain elongation, where both decamers separately failed.
      Circular SS DNA was specifically linearized by BamHI cleavage of a SS DNA -
      tetradecadeoxynucleotide duplex.
AU  - Titeeva GR
AU  - Vinogradov SV
AU  - Berlin YA
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1986 12: 1484-1491.

PMID- 11600708
VI  - 29
DP  - 2001
TI  - Families of restriction enzymes: an analysis prompted by molecular and genetic data for type ID restriction and modification systems.
PG  - 4195-4205
AB  - Current genetic and molecular evidence places all the known type I restriction and
      modification systems of Escherichia coli and Salmonella enterica into one of four discrete
      families: type IA, IB, IC or ID. StySBLI is the founder member of the ID family. Similarities
      of coding sequences have identified restriction systems in E.coli and Klebsiella pneumoniae as
      probable members of the type ID family. We present complementation tests that confirm the
      allocation of EcoR9I and KpnAI to the ID family. An alignment of the amino acid sequences of
      the HsdS subunits of StySBLI and EcoR9I identify two variable regions, each predicted to be a
      target recognition domain (TRD). Consistent with two TRDs, StySBLI was shown to recognise a
      bipartite target sequence, but one in which the adenine residues that are the substrates for
      methylation are separated by only 6 bp. Implications of family relationships are discussed and
      evidence is presented that extends the family affiliations identified in enteric bacteria to a
      wide range of other genera.
AU  - Titheradge AJ
AU  - King J
AU  - Ryu J
AU  - Murray NE
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2001 29: 4195-4205.

PMID- 8939428
VI  - 22
DP  - 1996
TI  - A third family of allelic hsd genes in Salmonella enterica: sequence comparisons with related proteins identify conserved regions implicated in restriction of DNA.
PG  - 437-447
AB  - Salmonella enterica serovar blegdam has a restriction and modification system encoded by genes
      linked to serB.  We have cloned these genes, putative alleles of the hsd locus of Escherichia
      coli K-12, and confirmed by the sequence similarities of flanking DNA that the hsd genes of S.
      enterica serovar blegdam have the same chromosomal location as those of E. coli K-12 and
      Salmonella enterica serovar typhimurium LT2.  There is, however, no obvious similarity in
      their nucleotide sequences, and while the gene order in S. enterica serovar blegdam is serB
      hsdM, S and R, that in E. coli K-12 and S. enterica serovar typhimurium LT2 is serB hsdR, M
      and S.  The hsd genes of S. enterica serovar blegdam identify a third family of serB-linked
      hsd genes (type ID).  The polypeptide sequence predicted from the three hsd genes show some
      similarities (18-50% identity) with the polypeptides of known and putative type I restriction
      and modification systems; the highest levels of identity are with sequences of Haemophilus
      influenzae Rd.  The HsdM polypeptide has the motifs characteristic of adenine
      methyltransferases.  Comparisons of the HsdR sequence with those for three other families of
      type I systems and three putative HsdR polypeptides identify two highly conserved regions in
      addition to the seven proposed DEAD-box motifs.
AU  - Titheradge AJB
AU  - Ternent D
AU  - Murray NE
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1996 22: 437-447.

PMID- 24482521
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Urease-Producing Sporosarcina pasteurii with Potential Application in Biocement Production.
PG  - e01256-13
AB  - We describe here the draft genome sequence of Sporosarcina pasteurii, a urease-producing
      bacterium with potential applications in biocement production.
AU  - Tiwari PK
AU  - Joshi K
AU  - Rehman R
AU  - Bhardwaj V
AU  - Shamsudheen KV
AU  - Sivasubbu S
AU  - Scaria V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01256-13.

PMID- 26629308
VI  - 10
DP  - 2015
TI  - Genome sequence of Bradyrhizobium sp. WSM1253; a microsymbiont of Ornithopus compressus from the Greek Island of Sifnos.
PG  - 113
AB  - Bradyrhizobium sp. WSM1253 is a novel N2-fixing bacterium isolated from a root nodule of the
      herbaceous annual legume Ornithopus compressus that was growing on
      the Greek Island of Sifnos. WSM1253 emerged as a strain of interest in an
      Australian program that was selecting inoculant quality bradyrhizobial strains
      for inoculation of Mediterranean species of lupins (Lupinus angustifolius, L.
      princei, L. atlanticus, L. pilosus). In this report we describe, for the first
      time, the genome sequence information and annotation of this legume
      microsymbiont. The 8,719,808 bp genome has a G + C content of 63.09 % with 71
      contigs arranged into two scaffolds. The assembled genome contains 8,432
      protein-coding genes, 66 RNA genes and a single rRNA operon. This
      improved-high-quality draft rhizobial genome is one of 20 sequenced through a DOE
      Joint Genome Institute 2010 Community Sequencing Project.
AU  - Tiwari R
AU  - Howieson J
AU  - Yates R
AU  - Tian R
AU  - Held B
AU  - Tapia R
AU  - Han C
AU  - Seshadri R
AU  - Reddy TB
AU  - Huntemann M
AU  - Pati A
AU  - Woyke T
AU  - Markowitz V
AU  - Ivanova N
AU  - Kyrpides N
AU  - Reeve W
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 113.

PMID- 27516502
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequence of Corynebacterium auriscanis Strain CIP 106629 Isolated from a Dog with Bilateral Otitis from the United Kingdom.
PG  - e00683-16
AB  - In this work, we describe a set of features of Corynebacterium auriscanis CIP 106629 and
      details of the draft genome sequence and annotation. The genome
      comprises a 2.5-Mbp-long single circular genome with 1,797 protein-coding genes,
      5 rRNA, 50 tRNA, and 403 pseudogenes, with a G+C content of 58.50%.
AU  - Tiwari S et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00683-16.

PMID- 25212181
VI  - 6
DP  - 2014
TI  - C. pseudotuberculosis Phop confers virulence and may be targeted by natural compounds.
PG  - 1088-1099
AB  - The bacterial two-component system (TCS) regulates genes that are crucial for
      virulence in several pathogens. One of such TCS, the PhoPR system, consisting of
      a transmembrane sensory histidine kinase protein (PhoR) and an intracellular
      response regulator protein (PhoP), has been reported to have a major role in
      mycobacterial pathogenesis. We knocked out the phoP in C. pseudotuberculosis, the
      causal organism of caseous lymphadenitis (CLA), and using a combination of in
      vitro and in vivo mouse system, we showed for the first time, that the PhoP of C.
      pseudotuberculosis plays an important role in the virulence and pathogenicity of
      this bacterium. Furthermore, we modeled the PhoP of C. pseudotuberculosis and our
      docking results showed that several natural compounds including Rhein, an
      anthraquinone from Rheum undulatum, and some drug-like molecules may target PhoP
      to inhibit the TCS of C. pseudotuberculosis, and therefore may facilitate a
      remarkable attenuation of bacterial pathogenicity being the CLA. Experiments are
      currently underway to validate these in silico docking results.
AU  - Tiwari S
AU  - da Costa MP
AU  - Almeida S
AU  - Hassan SS
AU  - Jamal SB
AU  - Oliveira A
AU  - Folador EL
AU  - Rocha F
AU  - de Abreu VA
AU  - Dorella F
AU  - Hirata R
AU  - de Oliveira DM
AU  - da Silva-Teixeira MF
AU  - Silva A
AU  - Barh D
AU  - Azevedo V
PT  - Journal Article
TA  - Integr Biol (Camb)
JT  - Integr Biol (Camb)
SO  - Integr Biol (Camb) 2014 6: 1088-1099.

PMID- Not carried by PubMed...
VI  - 10
DP  - 1988
TI  - Functioning of EcoRI, BamHI and HindIII restriction enzymes as affected by (2',5') oligoadenylates.
PG  - 78-81
AB  - Peculiarities of the functioning of restriction enzymes EcoRI, BamHI and
      HindIII in the presence of core trimers of (2'-5') oligoadenylic acid, viz.,
      (2'-5') A3 and (2'-5')3'dA3, have been studied.  Depending on the enzyme, the
      structure of the (2'-5') trimer, its concentration and method of its use
      (preincubation of the enzyme and the trimer or successive mixing of the
      reaction components), an inhibition of the restriction reaction, or
      site-specific restriction of lambda DNA or non-specific hydrolysis of lambda
      DNA are observed.  In the latter case, the restriction enzymes function as
      nonspecific DNases.
AU  - Tkachuk JY
AU  - Tkachuk LV
AU  - Kvasnyuk EI
AU  - Zaitseva GV
AU  - Kalinichenko EM
AU  - Mikhailopulo IO
AU  - Matsuka GK
PT  - Journal Article
TA  - Dokl. Akad. Nauk UKR SSR Ser. B Geol. Khim. Biol. Nauk
JT  - Dokl. Akad. Nauk UKR SSR Ser. B Geol. Khim. Biol. Nauk
SO  - Dokl. Akad. Nauk UKR SSR Ser. B Geol. Khim. Biol. Nauk 1988 10: 78-81.

PMID- Not carried by PubMed...
VI  - 5
DP  - 1989
TI  - Changes in functional properties of restriction enzymes under the influence of (2'-5') oligoadenylates in vitro.
PG  - 69-73
AB  - It is found that core trimers of (2'-5') oligoadenylic acid. viz., (A2'p)2A and
      (3'dA2'p)2/3'dA, exert an influence on functional properties of restriction
      enzymes EcoRI, BamHI, and HindIII.  The presence of (2'-5') trimers in the
      reaction mixture containing DNA and the restriction enzyme results in (i) an
      inhibition of the restriction reaction, (ii) site-specific restriction of DNA
      lambda, or (iii) nonspecific hydrolysis of DNA lambda.  In the last case
      restriction enzymes function as nonspecific DNAses.
AU  - Tkachuk ZY
AU  - Tkachuk LV
AU  - Kvasyuk EI
AU  - Zaitseva GV
AU  - Kalinichenko EN
AU  - Mikhailopulo IA
AU  - Matsuka GK
PT  - Journal Article
TA  - Biopol. Kletka
JT  - Biopol. Kletka
SO  - Biopol. Kletka 1989 5: 69-73.

PMID- 16433904
VI  - 6
DP  - 2006
TI  - Molecular phylogenetics and comparative modeling of HEN1, a methyltransferase involved in plant microRNA biogenesis.
PG  - 6
AB  - BACKGROUND: Recently, HEN1 protein from Arabidopsis thaliana was discovered as an essential
      enzyme in plant microRNA (miRNA) biogenesis. HEN1 transfers a methyl group from
      S-adenosylmethionine to the 2'-OH or 3'-OH group of the last nucleotide of miRNA/miRNA*
      duplexes produced by the nuclease Dicer. Previously it was found that HEN1 possesses a
      Rossmann-fold methyltransferase (RFM) domain and a long N-terminal extension including a
      putative double-stranded RNA-binding motif (DSRM). However, little is known about the details
      of the structure and the mechanism of action of this enzyme, and about its phylogenetic
      origin. RESULTS: Extensive database searches were carried out to identify orthologs and close
      paralogs of HEN1. Based on the multiple sequence alignment a phylogenetic tree of the HEN1
      family was constructed. The fold-recognition approach was used to identify related
      methyltransferases with experimentally solved structures and to guide the homology modeling of
      the HEN1 catalytic domain. Additionally, we identified a La-like predicted RNA binding domain
      located C-terminally to the DSRM domain and a domain with a peptide prolyl cis/trans isomerase
      (PPIase) fold, but without the conserved PPIase active site, located N-terminally to the
      catalytic domain. CONCLUSION: The bioinformatics analysis revealed that the catalytic domain
      of HEN1 is not closely related to any known RNA:2'-OH methyltransferases (e.g. to the
      RrmJ/fibrillarin superfamily), but rather to small-molecule methyltransferases. The structural
      model was used as a platform to identify the putative active site and substrate-binding
      residues of HEN and to propose its mechanism of action.
AU  - Tkaczuk KL
AU  - Obarska A
AU  - Bujnicki JM
PT  - Journal Article
TA  - BMC Evol. Biol.
JT  - BMC Evol. Biol.
SO  - BMC Evol. Biol. 2006 6: 6.

PMID- 27056232
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Low-Passage Clinical Isolate Porphyromonas gingivalis MP4-504.
PG  - e00256-16
AB  - We present the draft genome ofPorphyromonas gingivalisMP4-504, a low-passage clinical isolate
      obtained from a periodontitis patient. The genome is composed of
      92 contigs for a length of 2,373,453 bp and a G+C of 48.3%. ThetraA-Qconjugative
      transfer locus is genetically distinct from W83 but highly similar to ATCC 33277.
AU  - To TT
AU  - Liu Q
AU  - Watling M
AU  - Bumgarner RE
AU  - Darveau RP
AU  - McLean JS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00256-16.

PMID- 23469341
VI  - 1
DP  - 2013
TI  - Genome Sequence of Klebsiella pneumoniae KpQ3, a DHA-1 beta-Lactamase-Producing Nosocomial Isolate.
PG  - e00167-12
AB  - KpQ3 is a multidrug-resistant isolate obtained from a blood culture of a patient  in a burn
      unit in the Hospital Universitario La Paz (Madrid, Spain) in 2008. The
      genome contains multiple antibiotic resistance genes, including a
      plasmid-mediated DHA-1 cephalosporinase gene.
AU  - Tobes R
AU  - Codoner FM
AU  - Lopez-Camacho E
AU  - Salanueva IJ
AU  - Manrique M
AU  - Brozynska M
AU  - Gomez-Gil R
AU  - Martinez-Blanch JF
AU  - Alvarez-Tejado M
AU  - Pareja E
AU  - Mingorance J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00167-12.

PMID- 23704175
VI  - 1
DP  - 2013
TI  - Noncontiguous Finished Genome Sequence of Staphylococcus aureus KLT6, a Staphylococcal Enterotoxin B-Positive Strain Involved in a Food Poisoning  Outbreak in Switzerland.
PG  - e00214-13
AB  - We present the first complete genome sequence of a Staphylococcus aureus strain assigned to
      clonal complex 12. The strain was isolated in a food poisoning
      outbreak due to contaminated potato salad in Switzerland in 2009, and it produces
      staphylococcal enterotoxin B.
AU  - Tobes R
AU  - Manrique M
AU  - Brozynska M
AU  - Stephan R
AU  - Pareja E
AU  - Johler S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00214-13.

PMID- 23204453
VI  - 195
DP  - 2012
TI  - Complete Genome Sequence of the Frog Pathogen Mycobacterium ulcerans ecovar Liflandii.
PG  - 556-564
AB  - In 2004, a previously undiscovered mycobacterium resembling Mycobacterium ulcerans (the agent
      of Buruli ulcer) was reported in an outbreak of a lethal mycobacteriosis in a laboratory
      colony of the African clawed-frog Xenopus tropicalis. This mycobacterium makes mycolactone and
      is one of several strains of M. ulcerans-like mycolactone-producing mycobacteria recovered
      from ectotherms around the world. Here we describe the complete 6,399,543 bp genome of this
      frog pathogen (previously unofficially named Mycobacterium 'liflandii') and we show that it
      has undergone an intermediate degree of reductive evolution, between M. ulcerans Agy99 and the
      fish pathogen Mycobacterium marinum M. Like M. ulcerans Agy99, it has the pMUM mycolactone
      plasmid, over 200 chromosomal copies of the insertion sequence IS2404 and a high proportion of
      pseudogenes. However, M. 'liflandii' has a larger genome that is closer in length, sequence
      and architecture to M. marinum M than to M. ulcerans Agy99, suggesting that M. ulcerans Agy99
      has undergone accelerated evolution. Scrutiny of genes specifically lost suggests M.
      'liflandii' is a tryptophan, tyrosine and phenylalanine auxotroph. A once extensive M.
      marinum-like secondary metabolome has also been diminished through reductive evolution. Our
      analysis shows that M. 'liflandii', like M. ulcerans Agy99, has the characteristics of a
      niche-adapted mycobacterium but with several distinctive features in important metabolic
      pathways that suggests it is responding to different environmental pressures, supporting
      earlier proposals that it could be considered an M. ulcerans ecotype, hence the name M.
      ulcerans ecovar Liflandii.
AU  - Tobias NJ
AU  - Doig KD
AU  - Medema MH
AU  - Chen H
AU  - Haring V
AU  - Moore R
AU  - Seemann T
AU  - Stinear TP
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 195: 556-564.

PMID- 25838481
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Ochrobactrum anthropi Strain ML7 Isolated from Soil Samples in Vinhphuc Province, Vietnam.
PG  - e00218-15
AB  - Ochrobactrum species are widespread in the environment and can colonize a wide variety of
      habitats. Here, we describe the sequencing of a new environmental
      isolate of Ochrobactrum anthropi isolated from northern Vietnam.
AU  - Tobias NJ
AU  - Mishra B
AU  - Gupta DK
AU  - Ke LP
AU  - Thines M
AU  - Bode HB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00218-15.

PMID- 15979932
VI  - 8
DP  - 2005
TI  - The biology of restriction and anti-restriction.
PG  - 466-472
AB  - The phenomena of prokaryotic restriction and modification, as well as anti-restriction, were
      first discovered five decades ago but have
      yielded only gradually to rigorous analysis. Work presented at the
      5(th) New England Biolabs Meeting on Restriction-Modification
      (available on REBASE, http://www.rebase.com) and several recently
      published genetic, biochemical and biophysical analyses indicate that
      these fields continue to contribute significantly to basic science.
      Recently, there have been several studies that have shed light on the
      still developing field of restriction-modification and on the newly
      re-emerging field of anti-restriction.
AU  - Tock MR
AU  - Dryden DTF
PT  - Journal Article
TA  - Curr. Opin. Microbiol.
JT  - Curr. Opin. Microbiol.
SO  - Curr. Opin. Microbiol. 2005 8: 466-472.

PMID- 25858847
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Bifidobacterium dentium Strain JCM 1195T, Isolated from Human Dental Caries.
PG  - e00284-15
AB  - Bifidobacterium dentium strain JCM 1195(T) was isolated from human dental caries. Here, we
      report the complete genome sequence of this organism.
AU  - Toh H
AU  - Hayashi J
AU  - Oshima K
AU  - Nakano A
AU  - Takayama Y
AU  - Takanashi K
AU  - Morita H
AU  - Hattori M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00284-15.

PMID- 28232445
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Bifidobacterium lemurum DSM 28807T Isolated from the Gastrointestinal Tracts of Ring-Tailed Lemurs (Lemur catta).
PG  - e01656-16
AB  - Bifidobacterium lemurum DSM 28807T was isolated from the gastrointestinal tracts  of
      ring-tailed lemurs (Lemur catta). Here, we report the first draft genome
      sequence of this organism.
AU  - Toh H
AU  - Matsubara T
AU  - Tomida S
AU  - Mimura I
AU  - Arakawa K
AU  - Kikusui T
AU  - Morita H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01656-16.

PMID- 26847890
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Coccoid Lactobacillus equigenerosi NRIC 0697T Isolated from the Gastrointestinal Tracts of Healthy Thoroughbreds.
PG  - e01679-15
AB  - Lactobacillus equigenerosi NRIC 0697(T) was isolated from the gastrointestinal tracts of
      healthy thoroughbreds. This strain produced unique spherical or oval
      cells, which is rare in the genus Lactobacillus. Here, we report the draft genome
      sequence of this strain.
AU  - Toh H
AU  - Nakano A
AU  - Nguyen CT
AU  - Mimura I
AU  - Arakawa K
AU  - Tashiro K
AU  - Kikusui T
AU  - Morita H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01679-15.

PMID- 24116025
VI  - 8
DP  - 2013
TI  - Genomic adaptation of the Lactobacillus casei group.
PG  - e75073
AB  - Lactobacillus casei, L. paracasei, and L. rhamnosus form a closely related taxonomic group
      (Lactobacillus casei group) within the facultatively heterofermentative lactobacilli. Here, we
      report the complete genome sequences of L. paracasei JCM 8130 and L. casei ATCC 393, and the
      draft genome sequence of L. paracasei COM0101, all of which were isolated
      from daily products. Furthermore, we re-annotated the genome of L. rhamnosus ATCC 53103 (also
      known as L. rhamnosus GG), which we have previously reported. We confirmed that ATCC 393 is
      distinct from other strains previously described as L. paracasei. The core genome of 10
      completely sequenced strains of the L. casei group comprised 1,682 protein-coding genes.
      Although extensive genome-wide synteny was found among the L. casei group, the genomes of ATCC
      53103, JCM 8130, and ATCC 393 contained genomic islands compared with L. paracasei ATCC 334.
      Several genomic islands, including carbohydrate utilization gene clusters, were found at the
      same loci in the chromosomes of the L. casei group. The spaCBA pilus gene cluster, which was
      first identified in GG, was also found in other strains of the L. casei group, but several L.
      paracasei strains including COM0101 contained truncated spaC gene. ATCC 53103 encoded a higher
      number of proteins involved in carbohydrate utilization compared with intestinal
      lactobacilli, and extracellular adhesion proteins, several of which are absent in other
      strains of the L. casei group. In addition to previously fully sequenced L. rhamnosus and L.
      paracasei strains, the complete genome sequences of L. casei will provide valuable insights
      into the evolution of the L. casei group.
AU  - Toh H
AU  - Oshima K
AU  - Nakano A
AU  - Takahata M
AU  - Murakami M
AU  - Takaki T
AU  - Nishiyama H
AU  - Igimi S
AU  - Hattori M
AU  - Morita H
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2013 8: e75073.

PMID- 25858848
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Bifidobacterium scardovii Strain JCM 12489T, Isolated from Human Blood.
PG  - e00285-15
AB  - Bifidobacterium scardovii strain JCM 12489(T) was isolated from human blood and has the
      largest bifidobacterial genome reported to date. Here, we report the
      complete genome sequence of this organism. This paper is the first report
      demonstrating the fully sequenced and completely annotated genome of a B.
      scardovii strain.
AU  - Toh H
AU  - Oshima K
AU  - Nakano A
AU  - Yamashita N
AU  - Iioka E
AU  - Kurokawa R
AU  - Morita H
AU  - Hattori M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00285-15.

PMID- 24051320
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of the Equol-Producing Bacterium Adlercreutzia equolifaciens DSM 19450T.
PG  - e00742-13
AB  - Adlercreutzia equolifaciens DSM 19450(T) was isolated from human feces and is able to
      metabolize daidzeins (soybean isoflavonoids) to equol. Here, we report
      the finished and annotated genome sequence of this organism.
AU  - Toh H
AU  - Oshima K
AU  - Suzuki T
AU  - Hattori M
AU  - Morita H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00742-13.

PMID- 20008064
VI  - 192
DP  - 2009
TI  - Complete genome sequence of the wild-type commensal Escherichia coli strain SE15 belonging to phylogenetic group B2.
PG  - 1165-1166
AB  - Escherichia coli SE15 (O150:H5) is a human commensal bacterium recently isolated from feces of
      a healthy adult and classified into E. coli
      phylogenetic group B2 that includes the majority of extraintestinal
      pathogenic E. coli (ExPEC). Here, we report the finished and annotated
      genome sequence of this organism.
AU  - Toh H
AU  - Oshima K
AU  - Toyoda A
AU  - Ogura Y
AU  - Ooka T
AU  - Sasamoto H
AU  - Park SH
AU  - Iyoda S
AU  - Kurokawa K
AU  - Morita H
AU  - Itoh K
AU  - Taylor TD
AU  - Hayashi T
AU  - Hattori M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2009 192: 1165-1166.

PMID- 22038970
VI  - 193
DP  - 2011
TI  - Complete Genome Sequences of Arcobacter butzleri ED-1 and Arcobacter sp. Strain L, Both Isolated from a Microbial Fuel Cell.
PG  - 6411-6412
AB  - Arcobacter butzleri strain ED-1 is an exoelectrogenic epsilonproteobacterium isolated from the
      anode biofilm of a microbial fuel
      cell. Arcobacter sp. strain L dominates the liquid phase of the same fuel
      cell. Here we report the finished and annotated genome sequences of these
      organisms.
AU  - Toh H
AU  - Sharma VK
AU  - Oshima K
AU  - Kondo S
AU  - Hattori M
AU  - Ward FB
AU  - Free A
AU  - Taylor TD
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6411-6412.

PMID- 16365377
VI  - 16
DP  - 2006
TI  - Massive genome erosion and functional adaptations provide insights into the symbiotic lifestyle of Sodalis glossinidius in the tsetse host.
PG  - 149-156
AB  - Sodalis glossinidius is a maternally transmitted endosymbiont of tsetse flies (Glossina spp.),
      an insect of medical and veterinary significance. Analysis of the complete sequence of
      Sodalis' chromosome (4,171,146 bp, encoding 2,432 protein coding sequences) indicates a
      reduced coding capacity of 51%. Furthermore, the chromosome contains 972 pseudogenes, an
      inordinately high number compared with that of other bacterial species. A high proportion of
      these pseudogenes are homologs of known proteins that function either in defense or in the
      transport and metabolism of carbohydrates and inorganic ions, suggesting Sodalis'
      degenerative adaptations to the immunity and restricted nutritional status of the host.
      Sodalis possesses three chromosomal symbiosis regions (SSR): SSR-1, SSR-2, and SSR-3, with
      gene inventories similar to the Type-III secretion system (TTSS) ysa from Yersinia
      enterolitica and SPI-1 and SPI-2 from Salmonella, respectively. While core components of the
      needle structure have been conserved, some of the effectors and regulators typically
      associated with these systems in pathogenic microbes are modified or eliminated in Sodalis.
      Analysis of SSR-specific invA transcript abundance in Sodalis during host development
      indicates that the individual symbiosis regions may exhibit different temporal expression
      profiles. In addition, the Sodalis chromosome encodes a complete flagella structure, key
      components of which are expressed in immature host developmental stages. These features may be
      important for the transmission and establishment of symbiont infections in the intra-uterine
      progeny. The data suggest that Sodalis represents an evolutionary intermediate transitioning
      from a free-living to a mutualistic lifestyle.
AU  - Toh H
AU  - Weiss BL
AU  - Perkin SA
AU  - Yamashita A
AU  - Oshima K
AU  - Hattori M
AU  - Aksoy S
PT  - Journal Article
TA  - Genome Res.
JT  - Genome Res.
SO  - Genome Res. 2006 16: 149-156.

PMID- 26659692
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Bifidobacterium aesculapii DSM 26737T, Isolated from Feces of Baby Common Marmoset.
PG  - e01463-15
AB  - Bifidobacterium aesculapii DSM 26737(T) was isolated from feces of baby common marmoset. Here,
      we report the draft genome sequence of this organism. This paper
      is the first published report of the genomic sequence of B. aesculapii.
AU  - Toh H
AU  - Yamazaki Y
AU  - Tashiro K
AU  - Kawarai S
AU  - Oshima K
AU  - Nakano A
AU  - Kim CN
AU  - Mimura I
AU  - Arakawa K
AU  - Iriki A
AU  - Kikusui T
AU  - Morita H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01463-15.

PMID- 29659811
VI  - 10
DP  - 2018
TI  - Complete genome sequence of Streptococcus ruminantium sp. nov. GUT-187T (=DSM 104980 T =JCM 31869 T), the type strain of S. ruminantium, and comparison with genome sequences of S. suis strains.
PG  - 1180-1184
AB  - Streptococcus ruminantium sp. nov. of type strain GUT-187T, previously classified as
      Streptococcus suis serotype 33, is a
      recently described novel streptococcal species. This study was designed to determine the
      complete genome sequence of
      S. ruminantium GUT-187T using a combination ofOxford Nanopore and the Illumina platform, and
      to compare this sequence
      with the genomes of 27 S. suis representative strains. The genome of GUT-187T was 2,090,539 bp
      in size, with a GC content
      of 40.01%. This genome contained 1,961 predicted protein coding DNA sequences (CDSs); of
      these, 1,685 (85.9%) showed
      similarity with S. suis CDSs. Of the remaining 276 CDSs, 81 (29.3%) showed some degree of
      similarity with CDSs of other
      streptococcal species. The genome of GUT-187T contained no intact prophage. The numbers of
      prophages and CRISPR
      spacers, as well as the presence or absence of genes encoding CRISPR-associated proteins,
      differed in S. ruminantium and
      S. suis. Aphylogenetic analysis indicates thatGUT-187Tmay be outgroup to the S. suis strains
      in our sample, thereby justifying
      its classification as distinct species. Gene mapping indicated 10.2 times of massive genome
      rearrangements in average
      occurred between S. ruminantium and S. suis. There was no significant statistical difference
      in clusters of orthologous group
      distribution between S. ruminantium and S. suis.
AU  - Tohya M
AU  - Sekizaki T
AU  - Miyoshi-Akiyama T
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2018 10: 1180-1184.

PMID- 24831139
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Streptococcus pyogenes Strains Associated with Throat and Skin Infections in Lebanon.
PG  - e00358-14
AB  - We present the draft genome sequences of nine clinical Streptococcus pyogenes isolates
      recovered from patients suffering from sore throat and skin infections.
      An average of 2,454,334 paired-end reads per sample were generated, which
      assembled into 21 to 198 contigs, with a G+C content of 38.4 to 38.5%.
AU  - Tokajian S
AU  - Eisen JA
AU  - Jospin G
AU  - Coil DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00358-14.

PMID- 24558252
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Extended-Spectrum beta-Lactamase-Producing Escherchia coli Strains Isolated from Patients in Lebanon.
PG  - e00123-14
AB  - We present the draft genome sequences of nine extended-spectrum beta-lactamase
      (ESBL)-producing Escherichia coli strains isolated from stool samples collected
      from patients admitted for gastrointestinal and urological procedures/surgeries.
      An average of 3,889,300 paired-end reads per sample were generated, which
      assembled in 77 to 157 contigs.
AU  - Tokajian S
AU  - Eisen JA
AU  - Jospin G
AU  - Farra A
AU  - Coil DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00123-14.

PMID- 24558251
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Extended-Spectrum beta-Lactamase-Producing Klebsiella pneumoniae Isolated from a Patient in Lebanon.
PG  - e00121-14
AB  - We present the draft genome sequence of extended-spectrum beta-lactamase (ESBL)-producing
      Klebsiella pneumoniae isolated from a stool sample collected
      from a patient admitted for a gastrointestinal procedure. The draft genome
      sequence consists of 86 contigs, including a combined 5,632,663 bases with 57%
      G+C content.
AU  - Tokajian S
AU  - Eisen JA
AU  - Jospin G
AU  - Farra A
AU  - Coil DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00121-14.

PMID- 26823599
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Acinetobacter baumannii Strains Harboring the blaNDM-1  Gene Isolated in Lebanon from Civilians Wounded during the Syrian Civil War.
PG  - e01678-15
AB  - We present here the draft genome sequences of multidrug-resistant blaNDM-1-positive
      Acinetobacter baumannii strains ACMH-6200 and ACMH-6201,
      isolated in north Lebanon from civilians wounded during the Syrian civil war. The
      draft genomes were contained in 217 contigs for ACMH-6200 and 83 contigs for
      ACMH-6201, including a combined 3,997,237 bases for ACMH-6200 and 3,983,110 bases
      for ACMH-6201, with 39% and 38.9% G+C content, respectively.
AU  - Tokajian S
AU  - Eisen JA
AU  - Jospin G
AU  - Hamze M
AU  - Rafei R
AU  - Salloum T
AU  - Ibrahim J
AU  - Coil DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01678-15.

PMID- 26823584
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Klebsiella pneumoniae KGM-IMP216 Harboring blaCTX-M-15,  blaDHA-1, blaTEM-1B, blaNDM-1, blaSHV-28, and blaOXA-1, Isolated from a Patient  in Lebanon.
PG  - e01632-15
AB  - We present the draft genome of highly drug-resistant Klebsiella pneumoniae KGM-IMP216,
      isolated from a urine sample collected from a patient in Lebanon. The
      draft genome sequence consisted of 77 contigs, including a combined 5,731,500
      bases with 57% G+C content.
AU  - Tokajian S
AU  - Eisen JA
AU  - Jospin G
AU  - Matar G
AU  - Araj GF
AU  - Coil DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01632-15.

PMID- 28522715
VI  - 5
DP  - 2017
TI  - Complete Draft Genome Sequence of the Actinobacterium Nocardiopsis sinuspersici UTMC102 (DSM 45277T), Which Produces Serine Protease.
PG  - e00362-17
AB  - The genome sequence of alkalohalophilic actinobacterium Nocardiopsis sinuspersici UTMC102 is
      provided. N. sinuspersici UTMC102 produces a highly active serine
      alkaline protease, and contains at least 11 gene clusters encoding the
      biosynthesis of secondary metabolites. The N. sinuspersici UTMC102 genome was
      assembled into a single chromosomal scaffold.
AU  - Tokovenko B
AU  - Ruckert C
AU  - Kalinowski J
AU  - Mohammadipanah F
AU  - Wink J
AU  - Rosenkranzer B
AU  - Myronovskyi M
AU  - Luzhetskyy A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00362-17.

PMID- 
VI  - 18
DP  - 2002
TI  - Expression of a thermostable restriction endonuclease in recombinant Escherichia coli cells and optimization of fermentation conditions.
PG  - 23-27
AB  - TaqI restriction endonuclease gene of the thermophilic eubacterium Thermus aquaticus YT-1
      (ATCC 25104) was successfully cloned and expressed in recombinant Escherichia coli cells under
      the control of the lac promoter/operator system.  Higher TaqI endonuclease specific activities
      and biomass yields were obtained from E. coli ER2508(pUCTaq) cells when they were induced at
      the late-exponential phase of their growth.  TaqI endonuclease expression was found to be
      host-strain-dependent such that, among the three different strains examined, E. coli
      XL1(pUCTaq) produced the highest specific TaqI endonuclease activities for longer induction
      periods.  Decreasing the inducer concentration from 1 to 0.1 mM not only improved the specific
      enzyme activity yields but also is more economical, considering the high cost of
      isopropyl-beta-D-thiogalactopyranoside (PTG).  The optimum culture temperature was found to be
      37 C.  TaqI endonuclease specific activity recovered from E. coli XL1(pUCTaq) cells was 935
      U/mg under optimum conditions.
AU  - Toksoy E
AU  - Onsan ZI
AU  - Kirdar B
PT  - Journal Article
TA  - World J. Microbiol. Biotechnol.
JT  - World J. Microbiol. Biotechnol.
SO  - World J. Microbiol. Biotechnol. 2002 18: 23-27.

PMID- 
VI  - 37
DP  - 2001
TI  - Effect of the co-expression of methyltransferase activity on extracellular production of TaqI restriction endonuclease in recombinant E. coli cells.
PG  - 527-534
AB  - TaqI methylase gene was cloned and expressed constitutively under the control of the
      tetracycline resistance gene promoter.  The effect of TaqI methylase protection on the growth
      kinetics, plasmid stability and production of MBP - TaqI fusion protein by recombinant E. coli
      cells was investigated both in shake flasks and under controlled bioreactor conditions.  Shake
      flask experiments indicated that the use of nutritionally richer medium formulations may
      improve the growth characteristics, plasmid stability and also the total and extracellular
      TaqI endonuclease recovery yields by the methylase protected cells.  Under controlled
      bioreactor conditions, co-expression of the methylase gene led to higher plasmid stabilities
      and improved the excretion levels considerably.
AU  - Toksoy E
AU  - Onsan ZI
AU  - Kirdar B
PT  - Journal Article
TA  - Process. Biochem.
JT  - Process. Biochem.
SO  - Process. Biochem. 2001 37: 527-534.

PMID- 12111152
VI  - 59
DP  - 2002
TI  - High-level production of TaqI restriction endonuclease by three different expression systems in Escherichia coli cells using the T7 phage promoter.
PG  - 239-245
AB  - Three different expression systems were constructed for the high-level production of TaqI
      restriction endonuclease in recombinant Escherichia coli cells. In system [R], the TaqI
      endonuclease gene was cloned and expressed under the control of the strong T7 RNA polymerase
      promoter. To protect cellular DNA, methylase protection was provided by constitutive
      co-expression of TaqI methylase activity either by cloning the TaqI methylase gene on a second
      plasmid (system [R,M]) or by constructing a recombinant plasmid harboring both the
      endonuclease and methylase genes (system [R+M]). In batch shake flasks containing complex
      media, co-expression of the methylase gene in systems [R,M] and [R+M] resulted in a 2- and
      3-fold increase in volumetric productivity over system [R], yielding activities of 250x10^6 U
      l^-1 and 350x10^6 U l^-1, which were 28 and 39 times higher than the data in the
      literature, respectively. Under controlled bioreactor conditions in chemically defined medium,
      co-expression of methylase activity greatly improved the yield and specific TaqI endonuclease
      productivity of the recombinant cells, and reduced acetic acid excretion levels. System [R,M]
      is preferable for high expression levels at longer operation periods, while system [R+M] is
      well-suited for high expression levels in short-term bioreactor operation.
AU  - Toksoy E
AU  - Onsan ZI
AU  - Kirdar B
PT  - Journal Article
TA  - Appl. Microbiol. Biotechnol.
JT  - Appl. Microbiol. Biotechnol.
SO  - Appl. Microbiol. Biotechnol. 2002 59: 239-245.

PMID- 25858827
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Salmonella enterica Serovar Typhimurium Myophage Mushroom.
PG  - e00154-15
AB  - Salmonella enterica serovar Typhimurium (S. Typhimurium) is a leading cause of foodborne
      illness worldwide. Over the past two decades, strains resistant to
      antibiotics have begun to emerge, highlighting the need for alternative treatment
      strategies such as bacteriophage therapy. Here, we present the complete genome of
      Mushroom, an S. Typhimurium myophage.
AU  - Tolen TN
AU  - Xie Y
AU  - Hernandez AC
AU  - Kuty EGF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00154-15.

PMID- 29471489
VI  - 46
DP  - 2018
TI  - The H-subunit of the restriction endonuclease CglI contains a prototype DEAD-Z1 helicase-like motor.
PG  - 2560-2572
AB  - CglI is a restriction endonuclease from Corynebacterium glutamicum that forms a complex
      between: two R-subunits that have site specific-recognition and nuclease domains; and two
      H-subunits, with Superfamily 2 helicase-like DEAD domains, and uncharacterized Z1 and
      C-terminal domains. ATP hydrolysis by the H-subunits catalyses dsDNA translocation that is
      necessary for long-range movement along DNA that activates nuclease activity. Here, we provide
      biochemical and molecular modelling evidence that shows that Z1 has a fold distantly-related
      to RecA, and that the DEAD-Z1 domains together form an ATP binding interface and are the
      prototype of a previously undescribed monomeric helicase-like motor. The DEAD-Z1 motor has
      unusual Walker A and Motif VI sequences those nonetheless have their expected functions.
      Additionally, it contains DEAD-Z1-specific features: an H/H motif and a loop (aa 163-aa 172),
      that both play a role in the coupling of ATP hydrolysis to DNA cleavage. We also solved the
      crystal structure of the C-terminal domain which has a unique fold, and demonstrate that the
      Z1-C domains are the principal DNA binding interface of the H-subunit. Finally, we use small
      angle X-ray scattering to provide a model for how the H-subunit domains are arranged in a
      dimeric complex.
AU  - Toliusis P
AU  - Tamulaitiene G
AU  - Grigaitis R
AU  - Tuminauskaite D
AU  - Silanskas A
AU  - Manakova E
AU  - Venclovas C
AU  - Szczelkun MD
AU  - Siksnys V
AU  - Zaremba M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2018 46: 2560-2572.

PMID- 28854738
VI  - 45
DP  - 2017
TI  - CgII cleaves DNA using a mechanism distinct from other ATP-dependent restriction  endonucleases.
PG  - 8435-8447
AB  - The restriction endonuclease CglI from Corynebacterium glutamicum recognizes an asymmetric
      5'-GCCGC-3' site and cleaves the DNA 7 and 6/7 nucleotides downstream
      on the top and bottom DNA strands, respectively, in an NTP-hydrolysis dependent
      reaction. CglI is composed of two different proteins: an endonuclease (R.CglI)
      and a DEAD-family helicase-like ATPase (H.CglI). These subunits form a
      heterotetrameric complex with R2H2 stoichiometry. However, the R2H2.CglI complex
      has only one nuclease active site sufficient to cut one DNA strand suggesting
      that two complexes are required to introduce a double strand break. Here, we
      report studies to evaluate the DNA cleavage mechanism of CglI. Using one- and
      two-site circular DNA substrates we show that CglI does not require two sites on
      the same DNA for optimal catalytic activity. However, one-site linear DNA is a
      poor substrate, supporting a mechanism where CglI complexes must communicate
      along the one-dimensional DNA contour before cleavage is activated. Based on
      experimental data, we propose that adenosine triphosphate (ATP) hydrolysis by
      CglI produces translocation on DNA preferentially in a downstream direction from
      the target, although upstream translocation is also possible. Our results are
      consistent with a mechanism of CglI action that is distinct from that of other
      ATP-dependent restriction-modification enzymes.
AU  - Toliusis P
AU  - Zaremba M
AU  - Silanskas A
AU  - Szczelkun MD
AU  - Siksnys V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2017 45: 8435-8447.

PMID- 9588173
VI  - 245
DP  - 1998
TI  - Analysis in Escherichia coli of the effects of in vivo CpG methylation catalyzed by the cloned murine maintenance methyltransferase.
PG  - 670-678
AB  - Due in part to the complexity of mammalian systems, some of the proposed biological influences
      of mammalian DNA methylation have not been fully established.  Escherichia coli cells, which
      normally contain negligible CpG methylation, exhibited progressive slowing of replication and
      lengthened generation times when expressing the murine DNA maintenance methyltransferase.
      Genomic analysis indicated significant amounts of CpG methylation in expressing cells which
      was absent from control cells.  Expressing cells exposed to the cytosine demethylating agent,
      5-azacytidine, rapidly reverted to propagation levels of controls.  Substitution of cysteine
      with alanine in the carboxyl-terminal region proline-cysteine dipeptide of the
      methyltransferase completely inactivated methylating activity and cells expressing the
      inactive enzyme replicated as well as controls.  These findings strongly implicate a role of
      epigenetic de novo CpG methylation in modulating cellular propagation, demonstrate that the
      maintenance methyltransferase can de novo methylate in vivo, and show that the
      methyltransferase requires an active site cysteine for activity.
AU  - Tollefsbol TO
AU  - Hutchinson CA III
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1998 245: 670-678.

PMID- 9217255
VI  - 269
DP  - 1997
TI  - Control of methylation spreading in synthetic DNA sequences by the murine DNA methyltransferase.
PG  - 494-504
AB  - Methylation spreading, which involves a propensity for the mammalian
      DNA-(cytosine-5)-methyltransferase to de novo methylate cytosine-guanine dinucleotides (CpGs)
      near pre-existing 5-methylcytosine bases, has been implicated in the control of numerous
      biological processes.  We have assessed methylation spreading by the murine DNA
      methyltransferase in vitro using synthetic copolymers and oligonucleotides which differ only
      in their methylation state.  Double-stranded oligonucleotides were found to undergo higher
      levels of de novo methylation overall than other identical single-stranded oligonucleotides.
      This difference reflects the greater number of de novo methylatable cytosine bases in
      double-stranded than single-stranded sequences.  All tested oligonucleotides containing
      pre-existing 5-methyl-cytosine(s) were de novo methylated at several fold the rates of
      non-methylated controls.  No mammalian proteins besides the DNA methyltransferase were
      required for this observed enhancement of de novo methylation.  Studies using oligonucleotides
      differing in patterns of pre-methylation showed that methylation spreading can be initiated by
      hemimethylated or duplex methylated CpGs indicating that recognition of 5-methylcytosine by
      the enzyme is sufficient to stimulate methylation spreading. Double and single-stranded
      oligonucleotides with several bases between CpGs underwent considerably more de novo
      methylation per CpG than sequences containing sequential uninterrupted methylatable sites.
      Spacing preferences by the DNA methyltransferase were also observed in hemimethylated
      oligonucleotides, suggesting that this is a general property of the enzyme.  Although
      methylation spreading outside of CpG dinucleotides was relatively rare, single-stranded DNA
      incurred higher levels of de novo methylation at sites other than CpG as compared to
      double-stranded DNA.  This indicates less specificity of methylation spreading in
      single-stranded sequences.  Finally, enhanced de novo methylation in the presence of fully
      methylated CpG sites in double-stranded oligonucleotides was not as high as the rates of
      methylation of hemimethylated CpGs in otherwise identical oligonucleotides.  These studies
      provide further elucidation of the mechanisms and regulation of the methylation spreading
      process and its potential role in the biological processes it influences.
AU  - Tollefsbol TO
AU  - Hutchison CA III
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1997 269: 494-504.

PMID- 7629184
VI  - 270
DP  - 1995
TI  - Mammalian DNA (cytosine-5-)-methyltransferase expressed in Escherichia coli, purified and characterized.
PG  - 18543-18550
AB  - Besides modulating specific DNA-protein interactions, methylated cytosine, frequently referred
      to as the fifth base of the genome, also influences DNA structure, recombination,
      transposition, repair, transcription, imprinting, and mutagenesis.  DNA
      (cytosine-5-)-methyltransferase catalyzes cytosine methylation in eukaryotes.  We have cloned
      and expressed this enzyme in Escherichia coli, purified it to apparent homogeneity,
      characterized its properties, and we have shown that it hemimethylates DNA.  The cDNA for
      murine maintenance methyltransferase was reconstructed and cloned for direct expression in
      native form.  Immunoblotting revealed a unique protein (Mr=190,000) not present in control
      cells.  The mostly soluble overexpressed protein was purified by DEAE, Sephadex, and DNA
      cellulose chromatography.  Peak methylating activity correlated with methyltransferase
      immunoblots.  The purified enzyme preferentially transferred radioactive methyl moieties to
      hemimethylated DNA in assays and on autoradiograms.  All of the examined properties of the
      purified recombinant DNA methyltransferase are consistent with the enzyme purified from
      mammalian cells.  Further characterization revealed enhanced in vitro methylation of
      premethylated oligodeoxynucleotides.  The cloning of hemimethyltransferase in E. coli should
      allow facilitated structure-function mutational analysis of this enzyme, studies of its
      biological effects in prokayotes, and potential large scale methyltransferase production for
      crystallography, and it may have broad applications in maintaining the native methylated state
      of cloned DNA.
AU  - Tollefsbol TO
AU  - Hutchison CA III
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1995 270: 18543-18550.

PMID- 6278401
VI  - 10
DP  - 1982
TI  - RSITE: a computer program to predict the recognition sequence of a restriction enzyme.
PG  - 1-17
AB  - A computer program (RSITE) was developed which predicts the recognition
      sequence of a restriction endonuclease.  The sizes of fragments experimentally
      determined on cleavage of a DNA of known sequence were input.  Possible
      recognition sequences producing fragments of sizes matching those determined
      empirically were printed out.  The program faithfully predicted the specificity
      of restriction enzymes of known recognition sequence and also determined the
      recognition sequence of a new restriction enzyme from Haemophilus influenzae GU
      (HinGUII).
AU  - Tolstoshev CM
AU  - Blakesley RW
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1982 10: 1-17.

PMID- 3575111
VI  - 15
DP  - 1987
TI  - Nucleotide sequence and primary structures of gene products coded for by the T4 genome between map positions 48.266 kb and 39.166 kb.
PG  - 3632-3633
AB  - This sequence comprises 19 open reading frames (orfs) including T4 genes 49 and nrdC which
      were identified. The nomenclature of the orfs within this sequence is in agreement with the T4
      genomic map.
AU  - Tomaschewski J
AU  - Ruger W
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1987 15: 3632-3633.

PMID- 82935
VI  - 5
DP  - 1978
TI  - Recognition sequence of restriction endonuclease KpnI from Klebsiella pneumoniae.
PG  - 4055-4064
AB  - We have determined the recognition sequence of the restriction endonuclease
      KpnI, previously isolated from Klebsiella pneumoniae.  The enzyme cleaves the
      twofold rotationally symmetric sequence 5'-G-G-T-A-C-^C-3' 3'-C-^C-A-T-G-G-5'
      at the positions indicated by the arrows, producing 3' protruding cohesive
      ends, four nucleotides in length.  The specific cleavage site was unambiguously
      deduced using both 3' and 5' end analysis of KpnI generated restriction
      fragments of simian-virus 40 (SV40) DNA (1 site), adenovirus-2 (Ad-2) DNA (8
      sites), and a plasmid (pCRI) DNA (2 sites).
AU  - Tomassini J
AU  - Roychoudhury R
AU  - Wu R
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1978 5: 4055-4064.

PMID- 9252185
VI  - 388
DP  - 1997
TI  - The complete genome sequence of the gastric pathogen Helicobacter pylori.
PG  - 539-547
AB  - Helicobacter pylori, strain 26695, has a circular genome of 1,667,867 base pairs and 1,590
      predicted coding sequences.  Sequence analysis indicates that H. pylori has well-developed
      systems for motility, for scavenging iron, and for DNA restriction and modification.  Many
      putative adhesins, lipoproteins and other outer membrane proteins were identified,
      underscoring the potential complexity of host-pathogen interaction.  Based on the large number
      of sequence-related genes encoding outer membrane proteins and the presence of homopolymeric
      racts and dinucleotide repeats in coding sequences, H. pylori, like several other mucosal
      pathogens, probably uses recombination and slipped-strand mispairing within repeats as
      mechanisms for antigenic variation and adaptive evolution.  Consistent with its restricted
      niche, H. pylori has a few regulatory networks, and a limited metabolic repertoire and
      biosynthetic capacity.  Its survival in acid conditions depends, in part, on its ability to
      establish a positive inside-membrane potential in low pH.
AU  - Tomb J-F et al
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1997 388: 539-547.

PMID- 26941144
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Streptomyces scabiei S58, Streptomyces turgidiscabies T45, and Streptomyces acidiscabies a10, the Pathogens of Potato Common Scab,  Isolated in Japan.
PG  - e00062-16
AB  - The draft genome sequences of the three pathogens of potato common scab, Streptomyces scabiei
      S58, Streptomyces turgidiscabies T45, and Streptomyces
      acidiscabies a10, isolated in Japan, are presented here. The genome size of each
      strain is >10 Mb, and the three pathogenic strains share genes located in a
      pathogenicity island previously described in other pathogenic Streptomyces
      species.
AU  - Tomihama T
AU  - Nishi Y
AU  - Sakai M
AU  - Ikenaga M
AU  - Okubo T
AU  - Ikeda S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00062-16.

PMID- 
VI  - 274
DP  - 2007
TI  - Cleavage of mammalian chromosomal DNA by restriction enzymes in silico.
PG  - 73
AB  - A theoretical method to simulate the digestion patterns of mammalian chromosomal DNA cleavage
      by restriction endonucleases was proposed. New software for long mammalian DNAs analysis using
      routine personal computers was developed. This computational technique includes short DNA
      sequences searching, DNA cleavage simulation, data treatment and verification. Recently
      published primary structures of mammalian genomes (Rattus norvegicus, Mus musculus and Homo
      sapiens) were presented like databases and the analysis of short nucleotide sequences
      distribution in the corresponding genomes was performed. Computational DNA cleavage of genomes
      within the nucleotides sequences 5'-GGCC-3', 5'GATC-3', 5'-CC(A/T)GG-3' and
      5'-CCGG-3', which are the recognition sites of well known restriction endonucleases, was
      carried out and the diagrams of chromosomal DNA fragments distribution were obtained.
      Experiments on the chromosomal DNA digestion by corresponding restriction endonucleases were
      undertaken. The comparison of computational diagrams and results of chromosomal DNA cleavage
      was done and a high accordance of theoretical and experimental data was shown.
AU  - Tomilov VN
AU  - Chernukhin VA
AU  - Abdurashitov MA
AU  - Gonchar DA
AU  - Degtyarev SK
PT  - Journal Article
TA  - FEBS J.
JT  - FEBS J.
SO  - FEBS J. 2007 274: 73.

PMID- 
VI  - 2
DP  - 2006
TI  - Dependence of site-specific endonuclease GlaI activity on quantity and location of methylcytosines in the recognition sequence 5'-GCGC-3'.
PG  - 30-39
AB  - The activity dependence of site-specific endonuclease GlaI that recognizes and hydrolyzes only
      methylated DNA sequence 5'-GCGC-3' on the quantity and location of 5-methylcytosines in
      enzyme's recognition sequence has been studied. A significant DNA cleavage has been observed
      for oligonucleotides duplexes containing four and three 5-methylcytosines or two internal
      modified bases. The cleavage efficiency is maximal for DNA duplex with four 5-methylcytosine
      and decreases when a number of methylated bases are lower. GlaI hydrolyzes recognition
      sequences with 5-methylcytosines but not with N4-methylcytosines.
AU  - Tomilova JE
AU  - Chernukhin VA
AU  - Degtyarev SK
PT  - Journal Article
TA  - Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol.
JT  - Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol.
SO  - Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol. 2006 2: 30-39.

PMID- 
VI  - 44
DP  - 2010
TI  - Recombinant DNA-methyltransferase M1.Bst19I from Bacillus stearothermophilus 19: Purification, properties, and amino acid sequence analysis.
PG  - 606-615
AB  - The M1.Bst19I DNA-methyltransferase gene from restriction-modification system Bst19I
      (recognition sequence 5'-GCATC-3') in Bacillus
      stearothermophilus 19 has been cloned in the expressing vector pJW that
      carries a tandem of thermo inducible promoters P (R) /P (L) from phage
      lambda. Highly purified enzyme has been isolated by chromatography on
      various resins from Escherichia coli cells where it is accumulated in a
      soluble form. The study of M1.Bst19I properties has revealed that the
      enzyme has a temperature optimum at 50A degrees C and demonstrates
      maximal activity at pH 8.0. M1.Bst19I modifies adenine in sequence
      5'-GCATC-3'. Kinetic parameters of M1.Bst19I DNA methylation reaction
      have been determined as follows: Km for lambda DNA is 0.68 +/- 0.07 mu
      M, Km for S-adenosyl-L-methionine is 2.02 +/- 0.31 mu M. Catalytical
      constant (k (cat)) is 1.8 +/- 0.05 min(-1). Comparative analysis of
      Target Recognition Domain amino acid sequences for M1.Bst19I and other
      alpha-N6-DNA-methyltransferases has allowed us to suggest the presence
      of two types of the enzymes containing ATG or ATC triplets in the
      recognition sequence.
AU  - Tomilova JE
AU  - Kuznetsov VV
AU  - Abdurashitov MA
AU  - Netesova NA
AU  - Degtyarev SK
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2010 44: 606-615.

PMID- 
VI  - 38
DP  - 2004
TI  - Cloning of the genes for DNA methyltransferases of the SfaNI and Bst19I restriction-modification systems and primary structure analysis of  protein products.
PG  - 850-856
AB  - The Streptococcus faecalis ND547 and Bacillus stearothermophilus 19 genes that code for DNA
      methyltransferases (MTases, M.) of
      restriction-modification (RM) systems with the same recognition
      sequence, 5'-GCATC-3' were cloned and sequenced. The Bst19I RM system
      includes two MTases, M1.Bst19I and M2.Bst19I. The SfaNI RM system has
      only one MTase, M.SfaNI, whose N and C domains are homologous to
      M2.Bst19I and M1.Bst19I, respectively. Both M1.Bst19I and M2.Bst19I and
      the two domains of M.SfaNI contain conserved elements, which are
      arranged in the order characteristic of class alpha N6-adenine MTases.
      The enzymes of the SfaNI and Bst19I RM systems proved to be highly
      homologous to their FokI and BstF5I counterparts, which was explained
      by the presence of the common tetranucleotide 5'-GATG-3' in their
      recognition sites. Based on sequence homology, the spatial arrangement
      of highly conserved amino acid residues was determined using the known
      three-dimensional model of M.DpnIIA, which belongs to the same MTase
      class.
AU  - Tomilova YE
AU  - Abdurashitov MA
AU  - Golikova LN
AU  - Netesova NA
AU  - Degtyarev SK
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2004 38: 850-856.

PMID- 
VI  - 6
DP  - 2002
TI  - Restriction endonuclease Bst19I from Bacillus stearothermophilus recognizing the 5'-GCATC-3' DNA sequence.
PG  - 17-20
AB  - A Bacillus stearothermophilus 19 strain, a producer of a new Bst19I restriction endonuclease
      has been isolated. The indicated enzyme was
      isolated and its characteristics including the substrate specificity
      and site of DNA restriction were studied. The Bst19I restriction
      endonuclease was identified as a heteroschizomer of SfaNI restrictase
      who recognizes the 5'-GCATC-3' DNA sequence and cleaves DNA at the
      distance of 4 and 6 nucleotides from the site of recognition in upper
      and lower chains, respectively.
AU  - Tomilova YE
AU  - Dedkov VS
AU  - Shinkarenko NM
AU  - Popichenko DV
AU  - Degtyarev SK
PT  - Journal Article
TA  - Biotekhnologiya
JT  - Biotekhnologiya
SO  - Biotekhnologiya 2002 6: 17-20.

PMID- 11483585
VI  - 11
DP  - 2001
TI  - A marker-dense, sequence-ready map of the Bradyrhizobium japonicum genome.
PG  - 1434-1440
AB  - Bacterial artificial chromosome (BAC) clones are effective mapping and
      sequencing reagents for use with a wide variety of small and large
      genomes. This report describes the development of a physical framework for
      the genome of Bradyrhizobium japonicum, the nitrogen-fixing symbiont of
      soybean. A BAC library for B. japonicum was constructed that provides a
      77-fold genome coverage based on an estimated genome size of 8.7 Mb. The
      library contains 4608 clones with an average insert size of 146 kb. To
      generate a physical map, the entire library was fingerprinted with
      HindIII, and the fingerprinted clones were assembled into contigs using
      the software (; Sanger Centre, UK). The analysis placed 3410 clones in six
      large contigs. The ends of 1152 BAC inserts were sequenced to generate a
      sequence-tagged connector (STC) framework. To join and orient the contigs,
      high-density BAC colony filters were probed with 41 known gene probes and
      17 end sequences from contig boundaries. STC sequences were searched
      against the public databases using and algorithms. Query results allowed
      the identification of 113 high probability matches with putative
      functional identities that were placed on the physical map. Combined with
      the hybridization data, a high-resolution physical map with 194 positioned
      markers represented in two large contigs was developed, providing a marker
      every 45 kb. Of these markers, 177 are known or putative B. japonicum
      genes. Additionally, 1338 significant results (E < 10(-4)) were manually
      sorted by function to produce a functionally categorized database of
      relevant B. japonicum STC sequences that can also be traced to specific
      locations in the physical map.
AU  - Tomkins JP
AU  - Wood TC
AU  - Stacey MG
AU  - Loh JT
AU  - Judd A
AU  - Goicoechea JL
AU  - Stacey G
AU  - Sadowsky MJ
AU  - Wing RA
PT  - Journal Article
TA  - Genome Res.
JT  - Genome Res.
SO  - Genome Res. 2001 11: 1434-1440.

PMID- 11790305
VI  - 12
DP  - 2002
TI  - Genome-Wide Profiling of DNA Methylation Reveals Transposon Targets of CHROMOMETHYLASE3.
PG  - 65-68
AB  - DNA methylation has been implicated in a variety of epigenetic processes, and abnormal
      methylation patterns have been seen in tumors. Analysis of methylation patterns has
      traditionally been conducted either by using Southern analysis after cleavage with
      methyl-sensitive restriction endonucleases or by bisulfite sequencing. However, neither method
      is practical for analyzing more than a few genes. Here, we describe a simple technique for
      genome-wide mapping of DNA methylation patterns. Fragmentation by a methyl-sensitive
      restriction endonuclease is followed by size fractionation and hybridization to microarrays.
      We demonstrate the utility of this method by characterizing methylation patterns in
      Arabidopsis methylation mutants. This analysis reveals that CHROMOMETHYLASE3 (CMT3), which was
      previously shown to maintain CpXpG methylation, preferentially methylates transposons, even
      when they are present as single copies within the genome. Methylation profiling has potential
      applications in disease research and diagnostic screening.
AU  - Tompa R
AU  - McCallum CM
AU  - Delrow J
AU  - Henikoff JG
AU  - van Steensel B
AU  - Henikoff S
PT  - Journal Article
TA  - Curr. Biol.
JT  - Curr. Biol.
SO  - Curr. Biol. 2002 12: 65-68.

PMID- 23105080
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Lactobacillus helveticus R0052, a Commercial Probiotic Strain.
PG  - 6349
AB  - Lactobacillus helveticus R0052 is a commercially available strain that is widely  used in
      probiotic preparations. The genome sequence consisted of 2,129,425 bases.
      Comparative analysis showed that it was unique among L. helveticus strains in
      that it contained genes encoding mucus-binding proteins similar to those found in
      Lactobacillus acidophilus.
AU  - Tompkins TA
AU  - Barreau G
AU  - Broadbent JR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6349.

PMID- 22275100
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Probiotic Strain Lactobacillus rhamnosus R0011.
PG  - 902
AB  - Lactobacillus rhamnosus R0011 is a commercially available probiotic that is widely used in
      human dietary supplements and pharmaceutical products.
      We prepared a draft genome sequence consisting of 10 contigs totaling
      2,900,620 bases and a G+C content of 46.7% for this strain.
AU  - Tompkins TA
AU  - Barreau G
AU  - de Carvalho VG
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 902.

PMID- 23788543
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of an Oral Commensal, Streptococcus oligofermentans Strain AS 1.3089.
PG  - e00353-13
AB  - Streptococcus oligofermentans, an oral commensal, inhibits the growth of the dental caries
      pathogen Streptococcus mutans by producing large amounts of
      hydrogen peroxide. Therefore, it can be a potential probiotic for oral health.
      Here we report the complete genome sequence of S. oligofermentans strain AS
      1.3089.
AU  - Tong H
AU  - Shang N
AU  - Liu L
AU  - Wang X
AU  - Cai J
AU  - Dong X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00353-13.

PMID- 29531068
VI  - 115
DP  - 2018
TI  - Occurrence, evolution, and functions of DNA phosphorothioate epigenetics in bacteria.
PG  - E2988-E2996
AB  - The chemical diversity of physiological DNA modifications has expanded with the identification
      of phosphorothioate (PT) modification in which the nonbridging
      oxygen in the sugar-phosphate backbone of DNA is replaced by sulfur. Together
      with DndFGH as cognate restriction enzymes, DNA PT modification, which is
      catalyzed by the DndABCDE proteins, functions as a bacterial
      restriction-modification (R-M) system that protects cells against invading
      foreign DNA. However, the occurrence of dnd systems across a large number of
      bacterial genomes and their functions other than R-M are poorly understood. Here,
      a genomic survey revealed the prevalence of bacterial dnd systems: 1,349
      bacterial dnd systems were observed to occur sporadically across diverse
      phylogenetic groups, and nearly half of these occur in the form of a solitary
      dndBCDE gene cluster that lacks the dndFGH restriction counterparts. A
      phylogenetic analysis of 734 complete PT R-M pairs revealed the coevolution of M
      and R components, despite the observation that several PT R-M pairs appeared to
      be assembled from M and R parts acquired from distantly related organisms.
      Concurrent epigenomic analysis, transcriptome analysis, and metabolome
      characterization showed that a solitary PT modification contributed to the
      overall cellular redox state, the loss of which perturbed the cellular redox
      balance and induced Pseudomonas fluorescens to reconfigure its metabolism to fend
      off oxidative stress. An in vitro transcriptional assay revealed altered
      transcriptional efficiency in the presence of PT DNA modification, implicating
      its function in epigenetic regulation. These data suggest the versatility of PT
      in addition to its involvement in R-M protection.
AU  - Tong T
AU  - Chen S
AU  - Wang L
AU  - Tang Y
AU  - Ryu JY
AU  - Jiang S
AU  - Wu X
AU  - Chen C
AU  - Luo J
AU  - Deng Z
AU  - Li Z
AU  - Lee SY
AU  - Chen S
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2018 115: E2988-E2996.

PMID- 23908297
VI  - 1
DP  - 2013
TI  - Genome Sequence of Paenibacillus polymyxa ATCC 12321, a Promising Strain for Optically Active (R,R)-2,3-Butanediol Production.
PG  - e00572-13
AB  - Paenibacillus polymyxa is a potential strain for (R,R)-2,3-butanediol production. Here, we
      report an annotated draft genome sequence of P. polymyxa strain ATCC
      12321, which contains 4,429 protein-coding genes and 49 structural RNAs. This
      genome sequence provides a genetic basis for a better understanding of the
      mechanism for the accumulation of highly optically active (R,R)-2,3-butanediol.
AU  - Tong YJ
AU  - Ji XJ
AU  - Liu LG
AU  - Shen MQ
AU  - Huang H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00572-13.

PMID- 26205860
VI  - 3
DP  - 2015
TI  - Genome Sequence of Klebsiella pneumoniae CICC10011, a Promising Strain for High 2,3-Butanediol Production.
PG  - e00802-15
AB  - Klebsiella pneumoniae CICC10011, a promising 2,3-butanediol producer, has received much
      attention because of its high productivity. Here, the first draft
      genome sequence of this efficient strain may provide the genetic basis for
      further insights into the metabolic and regulatory mechanisms underlying the
      production of 2,3-butanediol at a high titer.
AU  - Tong YJ
AU  - Ji XJ
AU  - Liu LG
AU  - Shen MQ
AU  - Huang H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00802-15.

PMID- 25977440
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Anaeromyxobacter sp. Strain PSR-1, an Arsenate-Respiring Bacterium Isolated from Arsenic-Contaminated Soil.
PG  - e00472-15
AB  - Here, we report a draft genome sequence of Anaeromyxobacter sp. strain PSR-1, an
      arsenate-respiring bacterium isolated from arsenic-contaminated soil. It
      contained three distinct arsenic resistance gene clusters (ars operons), while no
      respiratory arsenate reductase gene (arr) was identified.
AU  - Tonomura M
AU  - Ehara A
AU  - Suzuki H
AU  - Amachi S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00472-15.

PMID- 29930066
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Paraburkholderia sp. Strain C35, Isolated from a Malaysian Tropical Peat Swamp Forest.
PG  - e00561-18
AB  - We report the draft genome sequence of a bacterial isolate, Paraburkholderia sp.  strain C35,
      which was isolated from a Malaysian tropical peat swamp forest. The
      putative genes for the biogeochemical processes were annotated and are publicly
      available in the online databases.
AU  - Too CC
AU  - Ong KS
AU  - Ankenbrand MJ
AU  - Lee SM
AU  - Yule CM
AU  - Keller A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00561-18.

PMID- 29930065
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Klebsiella sp. Strain C31 Isolated from a Malaysian Tropical Peat Swamp Forest.
PG  - e00560-18
AB  - We report here the draft genome of Klebsiella sp. strain C31, a bacterial isolate from the
      North Selangor peat swamp forest in Malaysia. The putative genes for the
      biogeochemical processes of the genome were annotated and investigated.
AU  - Too CC
AU  - Ong KS
AU  - Ankenbrand MJ
AU  - Lee SM
AU  - Yule CM
AU  - Keller A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00560-18.

PMID- 29930031
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Dyella sp. Strain C11, Isolated from a Malaysian Tropical Peat Swamp Forest.
PG  - e00459-18
AB  - We report here the draft genome sequences of a bacterial isolate, Dyella sp. strain C11, which
      was isolated from a Malaysian tropical peat swamp forest. The
      putative genes for the biogeochemical processes were annotated, and the genome
      was deposited in an online database.
AU  - Too CC
AU  - Ong KS
AU  - Lee SM
AU  - Yule CM
AU  - Keller A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00459-18.

PMID- 19955230
VI  - 38
DP  - 2010
TI  - Engineering Nt.BtsCI and Nb.BtsCI nicking enzymes and applications in generating long overhangs.
PG  - 1294-1303
AB  - Type IIS restriction endonuclease BtsCI (GGATG 2/0) is a neoschizomer of FokI (GGATG 9/13) and
      cleaves closer to the recognition sequence. Although
      M.BtsCI shows 62% amino acid sequence identity to M.FokI, BtsCI and FokI
      restriction endonucleases do not share significant amino acid sequence
      similarity. BtsCI belongs to a group of Type IIS restriction
      endonucleases, BsmI, Mva1269I and BsrI, that carry two different catalytic
      sites in a single polypeptide. By inactivating one of the catalytic sites
      through mutagenesis, we have generated nicking variants of BtsCI that
      specifically nick the bottom-strand or the top-strand of the target site.
      By treating target DNA sequentially with the appropriate combinations of
      FokI and BtsCI nicking variants, we are able to generate long overhangs
      suitable for fluorescent labeling through end-filling or other techniques
      based on annealing of complementary DNA sequences.
AU  - Too PH
AU  - Zhu Z
AU  - Chan SH
AU  - Xu SY
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2010 38: 1294-1303.

PMID- 6264133
VI  - 38
DP  - 1981
TI  - Restriction alleviation by bacteriophages lambda and lambda reverse.
PG  - 621-631
AB  - Deletion analysis indicated that the phage lambda restriction alleviation
      gene(s) ral resides between the cIII and N genes.  The Ral+ phenotype was expressed only
      when lambda-ral+ carried a modification such that it was resistant to restriction by the host
      specificity system.  Under these conditions, Ral function protected superinfecting
      unmodified phages from restriction by EcoK or EcoB but not from restriction by EcoP1.
      Ral-protected phage DNA was not concomitantly K and B modified, but rather received
      only the modification specified by the system of the restricting host.  Possible mechanisms
      for Ral action are discussed.  Of the other lambdoid phages tested, the hybrid phage
      lambda-rev had Ral activity, whereas omega-80vir and one lambda-P22 hybrid did not.
      The restriction alleviation activity of lambda-rev called Lar, may be the same as the activity
      expressed in sbcA- strains of Escherichia coli, but it was functionally separable from
      exonuclease VIII activity (the product of the recE gene), which is also expressed in sbcA-
      strains.
AU  - Toothman P
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1981 38: 621-631.

PMID- 8392701
VI  - 21
DP  - 1993
TI  - Changing endonuclease EcoRII Tyr308 to Phe abolishes cleavage but not recognition: possible homology with the Int-family of recombinases.
PG  - 2599-2603
AB  - Endonuclease EcoRII is one of a group of type II restriction enzymes, including NaeI, NarI,
      BspMI, HpaII, and SacII, that require binding of an enhancer sequence to cleave DNA.
      Comparison of the EcoRII amino-acid sequence with the amino-acid consensus motifs that
      differentiate between recombinase families uncovered similarity between a 29 amino-acid
      sequence in the carboxyl end of EcoRII and the motif defining the integrase family of
      recombinases. This similarity implied that EcoRII tyrosine 308 should be involved in
      catalyzing hydrolysis of the scissile bond. Site-directed mutagenesis was used to mutate
      Tyr308 to Phe. The phenylalanine-substituted enzyme could not cleave T5 DNA under conditions
      in which wild-type enzyme completely cleaved this DNA. The Tyr308 to Phe mutation abolished
      cleavage activity but not specific binding to DNA. No evidence was found for the existence
      during the cleavage reaction of a covalent linkage between Tyr308 and DNA.
AU  - Topal MD
AU  - Conrad M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 2599-2603.

PMID- 1847081
VI  - 30
DP  - 1991
TI  - NaeI endonuclease binding to pBR322 DNA induces looping.
PG  - 2006-2010
AB  - Previous work has demonstrated the existence of both resistant and cleavable
      NaeI sites.  Cleavable sites introduced on exogenous DNA can act in trans to
      increase the catalysis of NaeI endonuclease cleavage at resistant sites without
      affecting the apparent binding affinity of the enzyme for the resistant site
      [Conrad, M. & Topal, M.D. (1988) Proc. Natl. Acad. Sci. 86, 9707-9711].  This
      activation suggests allosteric regulation of NaeI cleavage by distant cis- and
      trans-acting sites in DNAs containing both resistant and cleavable sites.
      Plasmid pBR322 contains four NaeI sites, at least one of which is resistant to
      cleavage.  Electron microscopy is used here to demonstrate that NaeI
      endonuclease simultaneously binds to multiple recognition sites in pBR322 DNA
      to form loops with NaeI protein bound at the loop's base.  The maximum number
      of loops formed with a common base suggests four binding sites per enzyme
      molecule.  Looping was inhibited by addition of enzyme-saturating amounts of
      double-strand oligonucleotide without the NaeI site had no effect.  The number
      of loops seen was not above background when double-stranded M13 DNA, which
      contains only a single NaeI recognition site, was used as substrate.
AU  - Topal MD
AU  - Thresher RJ
AU  - Conrad M
AU  - Griffith J
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1991 30: 2006-2010.

PMID- 29567748
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Loktanella vestfoldensis Strain SMR4r, a Novel Strain Isolated from a Culture of the Chain-Forming Diatom Skeletonema marinoi.
PG  - e01558-17
AB  - We report here the genome sequence of Loktanella vestfoldensis strain SMR4r, isolated from the
      marine diatom Skeletonema marinoi strain RO5AC. Its
      3,987,360-bp genome consists of a circular chromosome and two circular plasmids,
      one of which appears to be shared with an S. marinoi-associated Roseovarius
      species.
AU  - Topel M
AU  - Pinder MIM
AU  - Johansson ON
AU  - Kourtchenko O
AU  - Godhe A
AU  - Clarke AK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01558-17.

PMID- 28572309
VI  - 5
DP  - 2017
TI  - Genome Sequence of Roseovarius mucosus Strain SMR3, Isolated from a Culture of the Diatom Skeletonema marinoi.
PG  - e00394-17
AB  - We present the genome of Roseovarius mucosus strain SMR3, a marine bacterium isolated from the
      diatom Skeletonema marinoi strain RO5AC sampled from top layer
      sediments at 14 m depth. Its 4,381,426 bp genome consists of a circular
      chromosome and two circular plasmids and contains 4,178 coding sequences (CDSs).
AU  - Topel M
AU  - Pinder MIM
AU  - Johansson ON
AU  - Kourtchenko O
AU  - Godhe A
AU  - Clarke AK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00394-17.

PMID- 
VI  - 17
DP  - 1998
TI  - Synthesis of a new photo-cross-linking nucleoside analogue containing an Aryl(trifluoromethyl)Diazirine group: Application for EcoRII and MvaI restriction-modification enzymes.
PG  - 1163-1175
AB  - A new photo-cross-linking dU analog,
      5-[4-(3-(trifluoromethyl)-3H-diazirin-3-yl)phenyl]-2'deoxyuridine, was synthesized and
      incorporated into the recognition site of EcoRII and MvaI restriction-modification enzymes.
      The resulting base-modified 14-mer substrate was tested for cross-linking to these enzymes.
      Cross-linking is effected by irradiation of the enzyme-substrate complexes as 366 nm.
AU  - Topin AN
AU  - Gritsenko OM
AU  - Brevnov MG
AU  - Gromova ES
AU  - Korshunova GA
PT  - Journal Article
TA  - Nucleosides and Nucleotides
JT  - Nucleosides and Nucleotides
SO  - Nucleosides and Nucleotides 1998 17: 1163-1175.

PMID- 26430026
VI  - 3
DP  - 2015
TI  - Genome Sequences of 64 Non-O157:H7 Shiga Toxin-Producing Escherichia coli Strains.
PG  - e01067-15
AB  - Shiga toxin-producing Escherichia coli (STEC) strains are human pathogens. Although >400
      non-O157 serotypes have been involved in human disease, whole-genome sequencing information is
      missing for many serotypes. We sequenced 64 STEC strains comprising 38 serotypes, isolated
      from clinical sources, animals, and environmental samples, to improve the phylogenetic
      understanding of these important foodborne pathogens.
AU  - Toro M
AU  - Cao G
AU  - Rump L
AU  - Nagaraja TG
AU  - Meng J
AU  - Gonzalez-Escalona N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01067-15.

PMID- 25792040
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of 33 Salmonella enterica Clinical and Wildlife Isolates from Chile.
PG  - e00054-15
AB  - Salmonella enterica causes health problem worldwide. The relationships among strains that are
      from the same serotype but different hosts, countries, and
      continents remain elusive. Few genome sequences are available from S. enterica
      isolates from South America. Therefore, we sequenced the genomes of 33 strains
      from diverse sources isolated in Chile and determined that they were of different
      serotypes. These genomes will improve phylogenetic analysis of Salmonella strains
      from Chile and the rest of South America.
AU  - Toro M
AU  - Retamal P
AU  - Allard M
AU  - Brown EW
AU  - Evans P
AU  - Gonzalez-Escalona N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00054-15.

PMID- 25301650
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of the RmInt1 Group II Intronless Sinorhizobium meliloti Strain RMO17.
PG  - e01001-14
AB  - We report the complete genome sequence of the RmInt1 group II intronless Sinorhizobium
      meliloti strain RMO17 isolated from Medicago orbicularis nodules
      from Spanish soil. The genome consists of 6.73 Mb distributed between a single
      chromosome and two megaplasmids (the chromid pSymB and pSymA).
AU  - Toro N
AU  - Martinez-Abarca F
AU  - Nisa-Martinez R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01001-14.

PMID- 29545307
VI  - 6
DP  - 2018
TI  - Complete Genome Sequences of the Probiotic Lactic Acid Bacteria Lactobacillus helveticus D75 and D76.
PG  - e01552-17
AB  - Lactobacillus helveticus D75 and D76 were isolated from the intestinal tract of a healthy
      child. Both strains possess symbiotic, probiotic, and antagonistic
      activities. We have sequenced and annotated the whole genomes of L. helveticus
      D75 and D76 and have conducted a preliminary genome comparative analysis.
AU  - Toropov VA
AU  - Vakhitov TY
AU  - Shalaeva ON
AU  - Roshchina EK
AU  - Sitkin SI
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01552-17.

PMID- 2842671
VI  - 0
DP  - 1988
TI  - Influence of recB and recA mutations on bacteriophage restriction by different restriction modification plasmid systems of E. coli.
PG  - 36-41
AB  - The effect of recB and recA mutations on lambda vir and P1 vir restriction by
      different restriction-modification plasmid systems of E. coli was studied.  It
      was shown that the effect of RI plasmid coded restriction-modification in E.
      coli K12 and E. coli B strains and pJA4620 plasmid coded restriction in E. coli
      K12 is observed only in RecB+ strain.  Phenomenon of restriction-modification
      determined by R124, R245 plasmids does not depend of recB mutation.  Effect of
      recA mutation has not been found in cultures harbouring R1, R245, R124 pJA4620
      plasmids.
AU  - Torosian MV
AU  - Shishkova OV
AU  - Rabinkova EV
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1988 0: 36-41.

PMID- 2963212
VI  - 10
DP  - 1987
TI  - Phenomenon of restriction alleviation in Escherichia coli strains.
PG  - 37-40
AB  - The alleviation of foreign DNA restriction after treatment of cells by UV and gamma-rays or
      ocr+-gene product of T3, T7 phages has been studied.  Both UV and gamma-radiation were shown
      to induce restriction alleviation of unmodified phage.  The results of restriction alleviation
      caused by T3 and T7 ocr+-gene products have been evaluated by F-lac+ transfer efficiencies in
      heterologic crosses and plating of unmodified phage lambda.  The phenomenon of restriction
      alleviation was established to depend on the strain used and to be expressed mostly in AB157
      and its derivatives.
AU  - Torosyan MV
AU  - Rainkova EV
AU  - Shishkova LA
AU  - Naumova LA
AU  - Fradkin GE
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1987 10: 37-40.

PMID- 8878670
VI  - 144
DP  - 1996
TI  - DNA adenine methylase mutants of Salmonella typhimurium and a novel Dam-regulated locus.
PG  - 15-26
AB  - Mutants of Salmonella typhimurium lacking DNA adenine methylase were isolated; they include
      insertion and deletion alleles.  The dam locus maps at 75 min between cysG and aroB, similar
      to the Escherichia coli dam gene.  Dam- mutants of S. typhimurium resemble those of E. coli in
      the following phenotypes: (1) increased spontaneous mutations, (2) moderate SOS induction, (3)
      enhancement of duplication segregation, (4) inviability of dam recA and dam recB mutants, and
      (5) suppression of the inviability of the dam recA and dam recB combinations by mutations that
      eliminate mismatch repair.  However, differences between S. typhimurium and E. coli dam
      mutants are also found: (1) S. typhimurium dam mutants do not show increased UV sensitivity,
      suggesting that methyl-directed mismatch repair does not participate in the repair of
      UV-induced DNA damage in Salmonella.  (2) S. typhimurium dam recJ mutants are viable,
      suggesting that the Salmonella RecJ function does not participate in the repair of DNA strand
      breaks formed in the absence of Dam methylation.  We also describe a genetic screen for
      detecting novel genes regulated by Dam methylation and a locus repressed by Dam methylation in
      the S. typhimurium virulence (or "cryptic") plasmid.
AU  - Torreblanca J
AU  - Casadesus J
PT  - Journal Article
TA  - Genetics
JT  - Genetics
SO  - Genetics 1996 144: 15-26.

PMID- 9872946
VI  - 151
DP  - 1999
TI  - Synthesis of FinP RNA by plasmids F and pSLT is regulated by DNA adenine methylation.
PG  - 31-45
AB  - DNA adenine methylase mutants of Salmonella typhimurium contain reduced amounts of FinP, an
      antisense RNA encoded by the virulence plasmid pSLT.  Lowered FinP levels are detected in both
      Dam- FinO+ and Dam- FinO- backgrounds, suggesting that Dam methylation regulates FinP
      production rather than FinP half-life.  Reduced amounts of F-encoded FinP RNA are likewise
      found in Dam- mutants of Escherichia coli.  A consequence of FinP RNA scarcity in the absence
      of DNA adenine methylation is that Dam- mutants of both S. typhimurium and E. coli show
      elevated levels of F plasmid transfer.  Inhibition of F fertility by the S. typhimurium
      virulence plasmid is also impaired in a Dam- background.
AU  - Torreblanca J
AU  - Marques S
AU  - Casadesus J
PT  - Journal Article
TA  - Genetics
JT  - Genetics
SO  - Genetics 1999 151: 31-45.

PMID- 27563038
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Lactobacillus reuteri Strain CRL 1098, an Interesting Candidate for Functional Food Development.
PG  - e00806-16
AB  - We report here the draft genome sequence of Lactobacillus reuteri strain CRL 1098. This strain
      represents an interesting candidate for functional food
      development because of its proven probiotic properties. The draft genome sequence
      is composed of 1,969,471 bp assembled into 45 contigs and an average G+C content
      of 38.8%.
AU  - Torres AC
AU  - Suarez NE
AU  - Font G
AU  - Saavedra L
AU  - Taranto MP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00806-16.

PMID- 11233163
VI  - 2
DP  - 2000
TI  - A gene containment strategy based on a restriction-modification system.
PG  - 555-563
AB  - Engineering barriers to the spread of specific genes are of great interest both to increase
      the predictability of recombinant microorganisms used for environmental applications and to
      study the role of gene transfer in the adaptation of microbial communities to changing
      environments. We report here a new gene containment circuit based on a toxin-antidote pair
      that targets the cell DNA, i.e. the type II EcoRI restriction-modification system. The set-up
      involved linkage of the ecoRIR lethal gene encoding the EcoRI endonuclease (toxin) to the
      contained character in a plasmid and chromosomal insertion of the ecoRIM gene encoding the
      cognate EcoRI methylase (antidote) that protects the target DNA from restriction. Transfer of
      the contained character to a recipient cell lacking the antidote caused EcoRI-mediated
      chromosomal breaks, leading to cell death, thereby preventing gene spread. Using
      transformation and conjugation as mechanisms of DNA transfer and different environmentally
      relevant bacteria as recipients, we have shown that the potentially universal EcoRI-based
      containment system decreases gene transfer frequencies by more than four orders of magnitude.
      Analyses of the survivors escaping killing revealed a number of possible inactivation
      mechanisms.
AU  - Torres B
AU  - Jaenecke S
AU  - Timmis KN
AU  - Garcia JL
AU  - Diaz E
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2000 2: 555-563.

PMID- 14663091
VI  - 149
DP  - 2003
TI  - A dual lethal system to enhance containment of recombinant micro-organisms.
PG  - 3595-3601
AB  - Active containment systems based on the controlled expression of a lethal gene are designed to
      increase containment of recombinant micro-organisms
      used for environmental applications. A major drawback in containment is
      the existence of mutations that generate surviving cells that cease to
      respond to the toxic effect of the lethal function. In this work the
      authors have developed for the first time a strategy to reduce the problem
      of mutations and increase the efficiency of containment based on the
      combination of two lethal functions acting on different cellular targets
      of major concern in containment, DNA and RNA, and whose expression is
      under control of different regulatory signals. To engineer the dual gene
      containment circuit, two toxin-antitoxin pairs, i.e. the colicin
      E3-immunity E3 and the EcoRI restriction-modification systems, were
      combined. The genes encoding the immunity E3 and the EcoRI
      methyltransferase proteins (antitoxins) were stably inserted into the
      chromosome of the host cell, whereas the broad-host-range lethal genes
      encoding the colicin E3 RNase and the EcoRI restriction endonuclease
      (toxins) were flanking the contained trait in a plasmid. This dual lethal
      cassette decreased gene transfer frequencies, through killing of the
      recipient cells, by eight orders of magnitude, which provides experimental
      evidence that the anticipated containment level due to the combination of
      single containment systems is generally achieved. Survivors that escaped
      killing were analysed and the mutational events involved were
      characterized.
AU  - Torres B
AU  - Jaenecke S
AU  - Timmis KN
AU  - Garcia JL
AU  - Diaz E
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2003 149: 3595-3601.

PMID- 25700406
VI  - 3
DP  - 2015
TI  - Genome Sequence of Bradyrhizobium japonicum E109, One of the Most Agronomically Used Nitrogen-Fixing Rhizobacteria in Argentina.
PG  - e01566-14
AB  - We present here the complete genome sequence of Bradyrhizobium japonicum strain E109, one of
      the most used rhizobacteria for soybean inoculation in Argentina since the 1970s. The genome
      consists of a 9.22-Mbp single chromosome and contains several genes related to nitrogen
      fixation, phytohormone biosynthesis, and a rhizospheric lifestyle.
AU  - Torres D
AU  - Revale S
AU  - Obando M
AU  - Maroniche G
AU  - Paris G
AU  - Perticari A
AU  - Vazquez M
AU  - Wisniewski-Dye F
AU  - Martinez-Abarca F
AU  - Cassan F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01566-14.

PMID- 23209231
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of the Bean-Nodulating Sinorhizobium fredii Strain GR64.
PG  - 6978
AB  - Sinorhizobium fredii GR64 is a peculiar strain that is able to effectively nodulate bean but
      not soybean, the common host of S. fredii. Here we present the
      draft genome of S. fredii GR64. This information will contribute to a better
      understanding of the symbiotic rhizobium-plant interaction and of rhizobial
      evolution.
AU  - Torres TG
AU  - Lozano L
AU  - Gonzalez V
AU  - Bustos P
AU  - Romero D
AU  - Brom S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6978.

PMID- 28126941
VI  - 5
DP  - 2017
TI  - Genome Sequence of the Symbiotic Type Strain Rhizobium tibeticum CCBAU85039T.
PG  - e01513-16
AB  - Rhizobium tibeticum was originally isolated from root nodules of Trigonella archiducis-nicolai
      grown in Tibet, China. This species is also able to nodulate Medicago sativa and Phaseolus
      vulgaris The whole-genome sequence of the type strain, R. tibeticum CCBAU85039T, is reported
      in this study.
AU  - Torres-Tejerizo G
AU  - Wibberg D
AU  - Winkler A
AU  - Ormeno-Orrillo E
AU  - Martinez-Romero E
AU  - Niehaus K
AU  - Puhler A
AU  - Kalinowski J
AU  - Lagares A
AU  - Schluter A
AU  - Pistorio M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01513-16.

PMID- 26664700
VI  - 10
DP  - 2015
TI  - Complete genome sequence of and proposal of Thermofilum uzonense sp. nov. a novel hyperthermophilic crenarchaeon and emended description of the genus Thermofilum.
PG  - 122
AB  - A strain of a hyperthermophilic filamentous archaeon was isolated from a sample of Kamchatka
      hot spring sediment. Isolate 1807-2 grew optimally at 85 degrees C,
      pH 6.0-6.5, the parameters being close to those at the sampling site. 16S rRNA
      gene sequence analysis placed the novel isolate in the crenarchaeal genus
      Thermofilum; Thermofilum pendens was its closest valid relative (95.7 % of
      sequence identity). Strain 1807-2 grew organothrophically using polysaccharides
      (starch and glucomannan), yeast extract or peptone as substrates. The addition of
      other crenarchaea culture broth filtrates was obligatory required for growth and
      could not be replaced by the addition of these organisms' cell wall fractions, as
      it was described for T. pendens. The genome of strain 1807-2 was sequenced using
      Illumina and PGM technologies. The average nucleotide identities between genome
      of strain 1807-2 and T. pendens strain HRK 5(T) and 'T. adornatus' strain 1910b
      were 85 and 82 %, respectively. On the basis of 16S rRNA gene sequence phylogeny,
      ANI calculations and phenotypic differences we propose a novel species
      Thermofilum uzonense with the type strain 1807-2(T) (= DSM 28062(T) = JCM
      19810(T)). Project information and genome sequence was deposited in Genbank under
      IDs PRJNA262459 and CP009961, respectively.
AU  - Toshchakov SV
AU  - Korzhenkov AA
AU  - Samarov NI
AU  - Mazunin IO
AU  - Mozhey OI
AU  - Shmyr IS
AU  - Derbikova KS
AU  - Taranov EA
AU  - Dominova IN
AU  - Bonch-Osmolovskaya EA
AU  - Patrushev MV
AU  - Podosokorskaya OA
AU  - Kublanov IV
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 122.

PMID- 23846276
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Lignocellulose Decomposer Thermobifida fusca Strain  TM51.
PG  - e00482-13
AB  - Here, we present the complete genome sequence of Thermobifida fusca strain TM51,  which was
      isolated from the hot upper layer of a compost pile in Hungary. T.
      fusca TM51 is a thermotolerant, aerobic actinomycete with outstanding
      lignocellulose-decomposing activity.
AU  - Toth A
AU  - Barna T
AU  - Nagy I
AU  - Horvath B
AU  - Nagy I
AU  - Tancsics A
AU  - Kriszt B
AU  - Baka E
AU  - Fekete C
AU  - Kukolya J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00482-13.

PMID- 24618593
VI  - 9
DP  - 2014
TI  - Restriction enzyme body doubles and PCR cloning: on the general use of type IIs restriction enzymes for cloning.
PG  - e90896
AB  - The procedure described here allows the cloning of PCR fragments containing a recognition site
      of the restriction endonuclease (Type IIP) used for cloning in
      the sequence of the insert. A Type IIS endonuclease - a Body Double of the Type
      IIP enzyme - is used to generate the same protruding palindrome. Thus, the insert
      can be cloned to the Type IIP site of the vector without digesting the PCR
      product with the same Type IIP enzyme. We achieve this by incorporating the
      recognition site of a Type IIS restriction enzyme that cleaves the DNA outside of
      its recognition site in the PCR primer in such a way that the cutting positions
      straddle the desired overhang sequence. Digestion of the PCR product by the Body
      Double generates the required overhang. Hitherto the use of Type IIS restriction
      enzymes in cloning reactions has only been used for special applications, the
      approach presented here makes Type IIS enzymes as useful as Type IIP enzymes for
      general cloning purposes. To assist in finding Body Double enzymes, we summarised
      the available Type IIS enzymes which are potentially useful for Body Double
      cloning and created an online program
      (http://group.szbk.u-szeged.hu/welkergr/body_double/index.html) for the selection
      of suitable Body Double enzymes and the design of the appropriate primers.
AU  - Toth E
AU  - Huszar K
AU  - Bencsura P
AU  - Kulcsar PI
AU  - Vodicska B
AU  - Nyeste A
AU  - Welker Z
AU  - Toth S
AU  - Welker E
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2014 9: e90896.

PMID- 26538601
VI  - 43
DP  - 2015
TI  - Re-evaluating the kinetics of ATP hydrolysis during initiation of DNA sliding by  Type III restriction enzymes.
PG  - 10870-10881
AB  - DNA cleavage by the Type III restriction enzymes requires long-range protein communication
      between recognition sites facilitated by thermally-driven 1D
      diffusion. This 'DNA sliding' is initiated by hydrolysis of multiple ATPs
      catalysed by a helicase-like domain. Two distinct ATPase phases were observed
      using short oligoduplex substrates; the rapid consumption of approximately 10
      ATPs coupled to a protein conformation switch followed by a slower phase, the
      duration of which was dictated by the rate of dissociation from the recognition
      site. Here, we show that the second ATPase phase is both variable and only
      observable when DNA ends are proximal to the recognition site. On DNA with sites
      more distant from the ends, a single ATPase phase coupled to the conformation
      switch was observed and subsequent site dissociation required little or no
      further ATP hydrolysis. The overall DNA dissociation kinetics (encompassing site
      release, DNA sliding and escape via a DNA end) were not influenced by the second
      phase. Although the data simplifies the ATP hydrolysis scheme for Type III
      restriction enzymes, questions remain as to why multiple ATPs are hydrolysed to
      prepare for DNA sliding.
AU  - Toth J
AU  - Bollins J
AU  - Szczelkun MD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2015 43: 10870-10881.

PMID- 22523084
VI  - 40
DP  - 2012
TI  - Dissociation from DNA of Type III Restriction-Modification enzymes during helicase-dependent motion and following endonuclease activity.
PG  - 6752-6764
AB  - DNA cleavage by the Type III Restriction-Modification (RM) enzymes requires the binding of a
      pair of RM enzymes at two distant, inversely orientated recognition
      sequences followed by helicase-catalysed ATP hydrolysis and long-range
      communication. Here we addressed the dissociation from DNA of these enzymes at
      two stages: during long-range communication and following DNA cleavage. First, we
      demonstrated that a communicating species can be trapped in a DNA domain without
      a recognition site, with a non-specific DNA association lifetime of approximately
      200 s. If free DNA ends were present the lifetime became too short to measure,
      confirming that ends accelerate dissociation. Secondly, we observed that Type III
      RM enzymes can dissociate upon DNA cleavage and go on to cleave further DNA
      molecules (they can 'turnover', albeit inefficiently). The relationship between
      the observed cleavage rate and enzyme concentration indicated independent binding
      of each site and a requirement for simultaneous interaction of at least two
      enzymes per DNA to achieve cleavage. In light of various mechanisms for
      helicase-driven motion on DNA, we suggest these results are most consistent with
      a thermally driven random 1D search model (i.e. 'DNA sliding').
AU  - Toth J
AU  - van Aelst K
AU  - Salmons H
AU  - Szczelkun MD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: 6752-6764.

PMID- 
VI  - 62
DP  - 2007
TI  - Production of SacI and SacII isoschizomers by soil streptomycetes.
PG  - 381-385
AB  - Five fresh soil Streptomyces spp. strains were isolated, phylogenetically characterized on the
      basis of 16S rDNA sequences and
      analyzed for the presence of restriction modification systems. Three
      type II site-specific endonucleases were detected and partially
      purified. Two isolated enzymes were isoschizomers of SacI restriction
      endonuclease recognizing 5'-GAGCTC-3' sequence; the third one
      recognised 5'-CCGCGG-3' sequence and it was an isoschizomer of SacII.
      SacII like modification was observed in other two isolates having no
      detectable restriction activity. The lack of correlation between
      restriction and modification phenotypes and phylogenetic classification
      of the isolates indicates efficient gene transfer mechanism in the
      Streptomyces genus.
AU  - Tothova T
AU  - Godany A
AU  - Javorsky P
AU  - Pristas P
PT  - Journal Article
TA  - Biologia (Bratisl)
JT  - Biologia (Bratisl)
SO  - Biologia (Bratisl) 2007 62: 381-385.

PMID- 22053197
VI  - 6
DP  - 2011
TI  - Insights into a multidrug resistant Escherichia coli pathogen of the globally disseminated ST131 lineage: genome analysis and virulence mechanisms.
PG  - E26578
AB  - Escherichia coli strains causing urinary tract infection (UTI) are increasingly
      recognized as belonging to specific clones. E. coli clone O25b:H4-ST131 has
      recently emerged globally as a leading multi-drug resistant pathogen causing
      urinary tract and bloodstream infections in hospitals and the community. While
      most molecular studies to date examine the mechanisms conferring multi-drug
      resistance in E. coli ST131, relatively little is known about their virulence
      potential. Here we examined E. coli ST131 clinical isolates from two
      geographically diverse collections, one representing the major pathogenic
      lineages causing UTI across the United Kingdom and a second representing UTI
      isolates from patients presenting at two large hospitals in Australia. We
      determined a draft genome sequence for one representative isolate, E. coli EC958,
      which produced CTX-M-15 extended-spectrum beta-lactamase, CMY-23 type AmpC
      cephalosporinase and was resistant to ciprofloxacin. Comparative genome analysis
      indicated that EC958 encodes virulence genes commonly associated with
      uropathogenic E. coli (UPEC). The genome sequence of EC958 revealed a transposon
      insertion in the fimB gene encoding the activator of type 1 fimbriae, an
      important UPEC bladder colonization factor. We identified the same fimB
      transposon insertion in 59% of the ST131 UK isolates, as well as 71% of ST131
      isolates from Australia, suggesting this mutation is common among E. coli ST131
      strains. Insertional inactivation of fimB resulted in a phenotype resembling a
      slower off-to-on switching for type 1 fimbriae. Type 1 fimbriae expression could
      still be induced in fimB-null isolates; this correlated strongly with adherence
      to and invasion of human bladder cells and bladder colonisation in a mouse UTI
      model. We conclude that E. coli ST131 is a geographically widespread, antibiotic
      resistant clone that has the capacity to produce numerous virulence factors
      associated with UTI.
AU  - Totsika M
AU  - Beatson SA
AU  - Sarkar S
AU  - Phan MD
AU  - Petty NK
AU  - Bachmann N
AU  - Szubert M
AU  - Sidjabat HE
AU  - Paterson DL
AU  - Upton M
AU  - Schembri MA
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2011 6: E26578.

PMID- 19165319
VI  - 5
DP  - 2009
TI  - Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths.
PG  - e1000344
AB  - The Escherichia coli species represents one of the best-studied model organisms,  but also
      encompasses a variety of commensal and pathogenic strains that diversify
      by high rates of genetic change. We uniformly (re-) annotated the genomes of 20
      commensal and pathogenic E. coli strains and one strain of E. fergusonii (the
      closest E. coli related species), including seven that we sequenced to
      completion. Within the approximately 18,000 families of orthologous genes, we
      found approximately 2,000 common to all strains. Although recombination rates are
      much higher than mutation rates, we show, both theoretically and using
      phylogenetic inference, that this does not obscure the phylogenetic signal, which
      places the B2 phylogenetic group and one group D strain at the basal position.
      Based on this phylogeny, we inferred past evolutionary events of gain and loss of
      genes, identifying functional classes under opposite selection pressures. We
      found an important adaptive role for metabolism diversification within group B2
      and Shigella strains, but identified few or no extraintestinal virulence-specific
      genes, which could render difficult the development of a vaccine against
      extraintestinal infections. Genome flux in E. coli is confined to a small number
      of conserved positions in the chromosome, which most often are not associated
      with integrases or tRNA genes. Core genes flanking some of these regions show
      higher rates of recombination, suggesting that a gene, once acquired by a strain,
      spreads within the species by homologous recombination at the flanking genes.
      Finally, the genome's long-scale structure of recombination indicates lower
      recombination rates, but not higher mutation rates, at the terminus of
      replication. The ensuing effect of background selection and biased gene
      conversion may thus explain why this region is A+T-rich and shows high sequence
      divergence but low sequence polymorphism. Overall, despite a very high gene flow,
      genes co-exist in an organised genome.
AU  - Touchon M et al
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2009 5: e1000344.

PMID- 21926215
VI  - 77
DP  - 2011
TI  - Complete genome sequence of the fish pathogen Flavobacterium branchiophilum.
PG  - 7656-7662
AB  - Members of the genus Flavobacterium occur in a variety of ecological niches and represent an
      interesting diversity of lifestyles. Flavobacterium branchiophilum is the main causative agent
      of bacterial gill disease, a severe condition affecting various cultured freshwater fish
      species worldwide, in particular salmonids in Canada and Japan. We report here the complete
      genome sequence of strain FL-15 isolated from a diseased sheatfish (Silurus glanis) in
      Hungary. The analysis of the F. branchiophilum genome revealed putative mechanisms of
      pathogenicity strikingly different from those of the other, closely related fish pathogen
      Flavobacterium psychrophilum, including the first cholera-like toxin in a non-Proteobacteria
      and a wealth of adhesins. The comparison with available genomes of other Flavobacterium
      species revealed a small genome size, large differences in chromosome organization, and fewer
      rRNA and tRNA genes, in line with its more fastidious growth. In addition, horizontal gene
      transfer shaped the evolution of F. branchiophilum, as evidenced by its virulence factors,
      genomic islands, and CRISPR (clustered regularly interspaced short palindromic repeats)
      systems. Further functional analysis should help in the understanding of host-pathogen
      interactions and in the development of rational diagnostic tools and control strategies in
      fish farms.
AU  - Touchon M
AU  - Barbier P
AU  - Bernardet JF
AU  - Loux V
AU  - Vacherie B
AU  - Barbe V
AU  - Rocha E
AU  - Duchaud E
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2011 77: 7656-7662.

PMID- 26450736
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Bacteroidales Strain 6E, Isolated from a Rice Paddy Field in Japan.
PG  - e01167-15
AB  - We generated a high-quality draft genome sequence of Bacteroidales strain 6E, a strict
      anaerobe newly isolated from Japanese rice paddy field soil. The genome consists of 61
      contigs, with a total size of 4,436,542 bp and mean G+C content of 45.4%. Annotation predicted
      3,620 protein-coding and 54 RNA genes.
AU  - Tourlousse DM
AU  - Honda T
AU  - Matsuura N
AU  - Ohashi A
AU  - Tonouchi A
AU  - Sekiguchi Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01167-15.

PMID- 26450737
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Bacteroidales Strain TBC1, a Novel Isolate from a Methanogenic Wastewater Treatment System.
PG  - e01168-15
AB  - We report here the draft genome sequence of Bacteroidales strain TBC1, isolated from a
      methanogenic wastewater treatment system. The draft genome has a size of 4,514,407 bp and a
      G+C content of 46.7%. The predicted genomic content provides the basis for characterizing the
      metabolism and ecological strategies of strain TBC1.
AU  - Tourlousse DM
AU  - Matsuura N
AU  - Sun L
AU  - Toyonaga M
AU  - Kuroda K
AU  - Ohashi A
AU  - Cruz R
AU  - Yamaguchi T
AU  - Sekiguchi Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01168-15.

PMID- 29360838
VI  - 13
DP  - 2018
TI  - Characterization of plasmids harboring blaCTX-M and blaCMY genes in E. coli from  French broilers.
PG  - e0188768
AB  - Resistance to extended-spectrum cephalosporins (ESC) is a global health issue. The aim of this
      study was to analyze and compare plasmids coding for resistance
      to ESC isolated from 16 avian commensal and 17 avian pathogenic Escherichia coli
      (APEC) strains obtained respectively at slaughterhouse or from diseased broilers
      in 2010-2012. Plasmid DNA was used to transform E. coli DH5alpha, and the
      resistances of the transformants were determined. The sequences of the
      ESC-resistance plasmids prepared from transformants were obtained by Illumina (33
      plasmids) or PacBio (1 plasmid). Results showed that 29 of these plasmids
      contained the blaCTX-M-1 gene and belonged to the IncI1/ST3 type, with 27 and 20
      of them carrying the sul2 or tet(A) genes respectively. Despite their diverse
      origins, several plasmids showed very high percentages of identity. None of the
      blaCTX-M-1-containing plasmid contained APEC virulence genes, although some of
      them were detected in the parental strains. Three plasmids had the blaCMY-2 gene,
      but no other resistance gene. They belonged to IncB/O/K/Z-like or IncFIA/FIB
      replicon types. The blaCMY-2 IncFIA/FIB plasmid was obtained from a strain
      isolated from a diseased broiler and also containing a blaCTX-M-1 IncI1/ST3
      plasmid. Importantly APEC virulence genes (sitA-D, iucA-D, iutA, hlyF, ompT,
      etsA-C, iss, iroB-E, iroN, cvaA-C and cvi) were detected on the blaCMY-2 plasmid.
      In conclusion, our results show the dominance and high similarity of blaCTX-M-1
      IncI1/ST3 plasmids, and the worrying presence of APEC virulence genes on a
      blaCMY-2 plasmid.
AU  - Touzain F
AU  - Le Devendec L
AU  - de Boisseson C
AU  - Baron S
AU  - Jouy E
AU  - Perrin-Guyomard A
AU  - Blanchard Y
AU  - Kempf I
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2018 13: e0188768.

PMID- 11910812
VI  - 71
DP  - 2002
TI  - A study of Erwinia carotovora phage resistance with the use of temperate bacteriophage ZF40.
PG  - 82-88
AB  - The causes of the unique phage resistance of the pectinolytic phytopathogenic strains of
      Erwinia carotovora were studied with the use of temperate bacteriophage ZF40. It was shown
      that, in these bacteria, the bacteriophage-cell interaction can be substantially blocked at
      the adsorption level. An adequate indicator for studying the temperate bacteriophages of
      Erwinias was developed on the basis of mutants resistant to macromolecular bacteriocins.
      Various restriction-modification systems, which influence cell resistance to bacteriophages,
      were revealed for the first time in E. carotovora. The phage resistance was shown to be
      determined by the wide occurrence of homoimmune temperate viruses in pectinolytic Erwinias.
AU  - Tovkach FI
PT  - Journal Article
TA  - Mikrobiologiia
JT  - Mikrobiologiia
SO  - Mikrobiologiia 2002 71: 82-88.

PMID- 17243364
VI  - 68
DP  - 2006
TI  - Phage system for studying the restriction-modification system of Erwinia carotovora.
PG  - 27-35
AB  - A model for revealing and type identifying the systems of restriction-modification of
      phytopathogenic bacterium Ewinia carotovora with the help of two virulent polyvalent phages-FE
      44 and T7 is proposed in the work.  The joint use of the phages permits to identify both the
      limitations of phages development on the part of RM-systems of three major types, and on the
      part of the competing episomes.  The proposed system also allows to reveal other kinds of
      limitations, in particular those connected with the adsorption of the phage particles.
AU  - Tovkach FI
AU  - Chervatyuk NV
PT  - Journal Article
TA  - Mikrobiol. Zh.
JT  - Mikrobiol. Zh.
SO  - Mikrobiol. Zh. 2006 68: 27-35.

PMID- 27340068
VI  - 4
DP  - 2016
TI  - High-Quality Draft Genome Sequence of Bacillus subtilis Strain WAUSV36.
PG  - e00586-16
AB  - Bacillus subtilis strain WAUSV36 inhibits the growth of and decreases disease symptoms caused
      by the potato pathogen Phytophthora infestans We determined the
      sequence of the 4.7-Mbp genome of this strain. WAUSV36 shared very high
      nucleotide sequence identity with previously sequenced strains of B. subtilis.
AU  - Town J
AU  - Audy P
AU  - Boyetchko SM
AU  - Dumonceaux TJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00586-16.

PMID- 27340067
VI  - 4
DP  - 2016
TI  - High-Quality Draft Genome Sequence of Arthrobacter sp. OY3WO11, a Strain That Inhibits the Growth of Phytophthora infestans.
PG  - e00585-16
AB  - Arthrobacter sp. strain OY3WO11 inhibits the growth of the potato pathogen Phytophthora
      infestans in in vivo growth challenge assays. We determined the
      draft genome sequence of this strain, assembling it into 3 scaffolds of 4.2 Mbp
      total length. OY3WO11 may represent a novel species of Arthrobacter.
AU  - Town J
AU  - Audy P
AU  - Boyetchko SM
AU  - Dumonceaux TJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00585-16.

PMID- 27340064
VI  - 4
DP  - 2016
TI  - High-Quality Draft Genome Sequence of Biocontrol Strain Pantoea sp. OXWO6B1.
PG  - e00582-16
AB  - Pantoea sp. strain OXWO6B1 inhibits the growth of the potato pathogen Phytophthora infestans
      We determined the 5.2-Mbp genome sequence of this strain,
      which featured at least 3 confirmed plasmids of up to 250 kbp. The genome
      sequence of OXWO6B1 is different from that of all previously sequenced strains of
      Pantoea.
AU  - Town J
AU  - Audy P
AU  - Boyetchko SM
AU  - Dumonceaux TJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00582-16.

PMID- 27340063
VI  - 4
DP  - 2016
TI  - Genome Sequence of Pseudomonas chlororaphis Strain 189.
PG  - e00581-16
AB  - Pseudomonas chlororaphis strain 189 is a potent inhibitor of the growth of the potato pathogen
      Phytophthora infestans We determined the complete, finished
      sequence of the 6.8-Mbp genome of this strain, consisting of a single contiguous
      molecule. Strain 189 is closely related to previously sequenced strains of P.
      chlororaphis.
AU  - Town J
AU  - Audy P
AU  - Boyetchko SM
AU  - Dumonceaux TJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00581-16.

PMID- 27231365
VI  - 4
DP  - 2016
TI  - Improved High-Quality Draft Genome Sequence of Pseudomonas fluorescens KENGFT3.
PG  - e00428-16
AB  - Pseudomonas sp. strain KENGFT3 inhibits the growth of Phytophthora infestans and  is a
      potentially useful biopesticide for plant diseases, including potato late
      blight. We sequenced the 6.2-Mbp genome of this strain and assembled it into a
      single scaffold with 9 contigs. KENGFT3 is related to previously sequenced
      strains of P. fluorescens.
AU  - Town J
AU  - Cui N
AU  - Audy P
AU  - Boyetchko S
AU  - Dumonceaux TJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00428-16.

PMID- 27313290
VI  - 4
DP  - 2016
TI  - High-Quality Draft Genome Sequences of Pantoea agglomerans Isolates Exhibiting Antagonistic Interactions with Wheat Seed-Associated Fungi.
PG  - e00511-16
AB  - Pantoea agglomerans isolates 3 and 4 were retrieved from the bacterial community  associated
      with wheat seeds. These isolates differ in their pattern of growth
      antagonism toward Alternaria species. A comparison of the genome sequences of
      these two isolates revealed a high sequence identity with previously sequenced
      strains of P. agglomerans.
AU  - Town J
AU  - Dumonceaux TJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00511-16.

PMID- 26481626
VI  - 100
DP  - 2016
TI  - Laboratory-scale bioaugmentation relieves acetate accumulation and stimulates methane production in stalled anaerobic digesters.
PG  - 1009-1017
AB  - An imbalance between acidogenic and methanogenic organisms during anaerobic digestion can
      result in increased accumulation of volatile fatty acids, decreased reactor pH, and inhibition
      of methane-producing Archaea.  Most commonly the result of organic input overload or poor
      inoculum selection, these microbiological and biochemical changes severely hamper reactor
      performance, and there are a few tools available to facilitate reactor recovery.  A small,
      stable consortium capable of catabolizing acetate and producing methane was propagated I vitro
      and evaluated as a potential bioaugmentation tool for stimulating methanogenesis in acidified
      reactors.  Replicate laboratory-scale batch digesters were seeded with a combination of
      bioethanol stillage waste and a dairy manure inoculum previously observed to result in high
      volatile fatty acid accumulation and reactor failure.  Experimental reactors were then amended
      with the acetoclastic consortium, and control reactors were amended with sterile culture
      media.  Within 7 days, bioaugmented reactors had significantly reduced acetate accumulation
      and the proportion of methane in the biogas increased from 0.2+/-0 to 74.4+/-9.9% while
      control reactors showed no significant reduction in acetate accumulation or increase in
      methane production.  Organisms from the consortium were enumerated using specific quantitative
      PCR assays to evaluate their growth I the experimental reactors.  While the abundance of
      hydrogenotrophic microorganisms remained stale during the recovery period, an acetoclastic
      methanogen phylogenetically similar to Methanosarcina sp. increased more than 100-fold and is
      hypothesized to be the primary contributor to reactor recovery.  Genomic sequencing of this
      organism revealed genes related to the production of methane from acetate, hydrogen, and
      methanol.
AU  - Town JR
AU  - Dumonceaux TJ
PT  - Journal Article
TA  - Appl. Microbiol. Biotechnol.
JT  - Appl. Microbiol. Biotechnol.
SO  - Appl. Microbiol. Biotechnol. 2016 100: 1009-1017.

PMID- 27795273
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Bacillus luciferensis Isolated from Soil.
PG  - e01140-16
AB  - Bacillus luciferensis is a Gram-positive, facultatively anaerobic, motile rod. Here, we report
      the first draft genome sequence, to our knowledge, of a B.
      luciferensis strain (CH01), which will provide useful information for Bacillus
      and soil bacteria research.
AU  - Townsley L
AU  - Caro L
AU  - Kelkar H
AU  - Shank EA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01140-16.

PMID- 17437717
VI  - 15
DP  - 2007
TI  - BstYI Bound to Noncognate DNA Reveals a "Hemispecific" Complex: Implications for DNA Scanning.
PG  - 449-459
AB  - DNA recognition by proteins is essential for specific expression of genes in a living
      organism. En route to a target DNA site, a protein will often
      sample noncognate DNA sites through nonspecific protein-DNA interactions,
      resulting in a variety of conformationally different binding states. We
      present here the crystal structure of endonuclease BstYI bound to a
      noncognate DNA. Surprisingly, the structure reveals the enzyme in a
      "hemispecific" binding state on the pathway between nonspecific and
      specific recognition. A single base pair change in the DNA abolishes
      binding of only one monomer, with the second monomer bound specifically.
      We show that the enzyme binds essentially as a rigid body, and that one
      end of the DNA is accommodated loosely in the binding cleft while the
      other end is held tightly. Another intriguing feature of the structure is
      Ser172, which has a dual role in establishing nonspecific and specific
      contacts. Taken together, the structure provides a snapshot of an enzyme
      in a "paused" intermediate state that may be part of a more general
      mechanism of scanning DNA.
AU  - Townson SA
AU  - Samuelson JC
AU  - Bao Y
AU  - Xu SY
AU  - Aggarwal AK
PT  - Journal Article
TA  - Structure
JT  - Structure
SO  - Structure 2007 15: 449-459.

PMID- 15099740
VI  - 338
DP  - 2004
TI  - Crystal structure of BstYI at 1.85 .ANG. resolution: A thermophilic restriction endonuclease with overlapping specificities to BamHI and  BglII.
PG  - 725-733
AB  - We report here the structure of BstYI, an "intermediate" type II restriction endonuclease with
      overlapping sequence specificities to BamHI and BglII. BstYI, a thermophilic endonuclease,
      recognizes and cleaves the degenerate hexanucleotide sequence 5'-RGATCY-3' (where R=A or G
      and Y=C or T), cleaving DNA after the 5'-R on each strand to produce four-base (5')
      staggered ends. The crystal structure of free BstYI was solved at 1.85A resolution by
      multi-wavelength anomalous dispersion (MAD) phasing. Comparison with BamHI and BglII reveals a
      strong structural consensus between all three enzymes mapping to the alpha/beta core domain
      and residues involved in catalysis. Unexpectedly, BstYI also contains an additional "arm"
      substructure outside of the core protein, which enables the enzyme to adopt a more compact,
      intertwined dimer structure compared with BamHI and BglII. This arm substructure may underlie
      the thermostability of BstYI. We identify putative DNA recognition residues and speculate as
      to how this enzyme achieves a "relaxed" DNA specificity.
AU  - Townson SA
AU  - Samuelson JC
AU  - Vanamee ES
AU  - Edwards TA
AU  - Escalante CR
AU  - Xu S-Y
AU  - Aggarwal AK
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2004 338: 725-733.

PMID- 15893669
VI  - 13
DP  - 2005
TI  - Implications for switching restriction enzyme specificities from the structure of BstYI bound to a BglII DNA sequence.
PG  - 791-801
AB  - The type II restriction endonuclease BstYI recognizes the degenerate sequence 5'-RGATCY-3'
      (where R = A/G and Y = C/T), which overlaps with both BamHI (GGATCC) and BglII (AGATCT), and
      thus raises the question of whether BstYI DNA recognition will be more BamHI-like or
      BglII-like.  We present here the structure of BstYI bound to a cognate DNA sequence (AGATCT).
      We find the complex to be more BglII-like with similarities mapping to DNA conformation,
      domain organization, and residues involved in catalysis.  However, BstYI is unique in
      containing an extended arm subdomain, and the mechanism of DNA capture has both BglII-like and
      BamHI-like elements.  Further, DNA recognition is more minimal than BglII and BamHI, where
      only two residues mediate recognition of the entire core sequence.  Taken together, the
      structure reveals a mechanism of degenerate DNA recognition and offers insights into the
      possibilities and limitations in altering specificities of closely related restriction
      enzymes.
AU  - Townson SA
AU  - Samuelson JC
AU  - Xu S-Y
AU  - Aggarwal AK
PT  - Journal Article
TA  - Structure
JT  - Structure
SO  - Structure 2005 13: 791-801.

PMID- 26272561
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Bacillus ginsengihumi Strain M2.11 with Phytase Activity.
PG  - e00851-15
AB  - This paper announces the genome sequence of Bacillus ginsengihumi strain M2.11, which has been
      characterized as a strain which produces the enzyme with the
      ability to degrade phytase. The genome of the strain M2.11 is 3.7 Mb and harbors
      3,082 coding sequences.
AU  - Toymentseva AA
AU  - Suleimanova AD
AU  - Boulygina EA
AU  - Kazakov SV
AU  - Baranova DS
AU  - Akhmetova AI
AU  - Mardanova AM
AU  - Sharipova MR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00851-15.

PMID- 28546488
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Salt Water Bacterium Oceanospirillum linum ATCC 11336T.
PG  - e00395-17
AB  - Oceanospirillum linum ATCC 11336T is an aerobic, bipolar-tufted gammaproteobacterium first
      isolated in the Long Island Sound in the 1950s. This
      announcement offers a genome sequence for O. linum ATCC 11336T, which has a
      predicted genome size of 3,782,189 bp (49.13% G+C content) containing 3,540 genes
      and 3,361 coding sequences.
AU  - Trachtenberg AM
AU  - Carney JG
AU  - Linnane JD
AU  - Rheaume BA
AU  - Pitts NL
AU  - Mykles DL
AU  - MacLea KS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00395-17.

PMID- 29930075
VI  - 6
DP  - 2018
TI  - Genome Sequences for Three Strains of Kocuria rosea, Including the Type Strain.
PG  - e00594-18
AB  - Genomes from three strains of Kocuria rosea were sequenced. K. rosea ATCC 186, the type
      strain, was 3,958,612 bp in length with a total G+C content of 72.70%.
      When assembled, K. rosea ATCC 516 was 3,862,128 bp with a 72.82% G+C content. K.
      rosea ATCC 49321 was 4,018,783 bp in size with a 72.49% G+C content.
AU  - Trachtenberg AM
AU  - Goen AE
AU  - MacLea KS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00594-18.

PMID- 25395633
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of an Extensively Drug-Resistant Acinetobacter baumannii Indigo-Pigmented Strain.
PG  - e01146-14
AB  - Last year in 2013, we reported an outbreak due to indigo-pigmented Acinetobacter  baumannii
      strains in a hospital from Buenos Aires, Argentina. Here, we present
      the draft genome sequence of one of the strains (A. baumannii A33405) involved in
      the outbreak. This isolate was categorized as extensively drug-resistant (XDR)
      and harbors different genetic elements associated with horizontal genetic
      transfer and multiple antibiotic resistances.
AU  - Traglia G
AU  - Vilacoba E
AU  - Almuzara M
AU  - Diana L
AU  - Iriarte A
AU  - Centron D
AU  - Ramirez MS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01146-14.

PMID- 25744988
VI  - 3
DP  - 2015
TI  - Draft genome sequence of a taxonomically unique acinetobacter clinical strain with proteolytic and hemolytic activities.
PG  - e00030-15
AB  - Acinetobacter sp. strain A47, which has been recovered from several soft tissue samples from a
      patient undergoing reconstructive surgery due to a traumatic
      amputation, was categorized as a taxonomically unique bacterial strain. The
      molecular analysis based on three housekeeping protein-coding genes (16S rRNA,
      rpoB, and gyrB) showed that strain A47 does not belong to any of the hitherto
      known taxa and may represent a previously undescribed Acinetobacter species.
AU  - Traglia GM
AU  - Almuzara M
AU  - Barberis C
AU  - Montana S
AU  - Schramm ST
AU  - Enriquez B
AU  - Mussi MA
AU  - Vay C
AU  - Iriarte A
AU  - Ramirez MS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00030-15.

PMID- 25838490
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Empedobacter (Formerly Wautersiella) falsenii comb. nov. Wf282, a Strain Isolated from a Cervical Neck Abscess.
PG  - e00235-15
AB  - Empedobacter (formerly Wautersiella) falsenii comb. nov. strain Wf282 was isolated from a
      cervical neck abscess sample from an 18-year-old female patient.
      The isolate was resistant to many antibiotics, including meropenem and colistin.
      The total DNA from the multidrug-resistant E. falsenii comb. nov. Wf282 clinical
      isolate was sequenced.
AU  - Traglia GM
AU  - Dixon C
AU  - Chiem K
AU  - Almuzara M
AU  - Barberis C
AU  - Montana S
AU  - Merino C
AU  - Mussi MA
AU  - Tolmasky ME
AU  - Iriarte A
AU  - Vay C
AU  - Ramirez MS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00235-15.

PMID- Not carried by PubMed...
VI  - 7
DP  - 1995
TI  - Characterization of DNA restriction-modification systems in Spirulina platensis strain pacifica.
PG  - 561-564
AB  - Four unique restriction enzymes were identified in the soluble protein fraction of Spirulina
      platensis strain pacifica, a commercially important strain of marine cyanobacterium that is
      used as a supplement in human diets.  These are SpaI, SpaII, SpaII and SpaIV, which are
      isoschizomers of Tth111I, PvuI, PvuII and HindIII, respectively.  The recognition sites of
      each of these four enzymes were identified by restriction digests of different plasmid DNAs of
      known sequence and determining the cleavage sites by sequencing.  SpaI is the most predominant
      restriction enzyme present in S. platensis strain pacifica.  It shows high activity at 37oC
      compared to 65oC for its isoschizomer Tth111I.
AU  - Tragut V
AU  - Xiao J
AU  - Bylina EJ
AU  - Borthakur D
PT  - Journal Article
TA  - J. Appl. Phycol.
JT  - J. Appl. Phycol.
SO  - J. Appl. Phycol. 1995 7: 561-564.

PMID- 
VI  - 61
DP  - 2001
TI  - X-ray crystal structure of N-6 adenine deoxyribose nucleic acid methyltransferase from Streptococcus pneumoniae.
PG  - 4801-B-4802-B
AB  - X-ray diffraction by using resonant anomalous scattering has become a popular tool for solving
      crystal structures in the last ten years with the expanded availability of tunable synchrotron
      radiation for protein crystallography.  Mercury atoms were used for phasing.  The crystal
      structure of N-6 deoxyribose nucleic acid methyltransferase from Streptococcus pneumoniae
      (DpnM) was solved by using the Multiple Anomalous Diffraction technique.  The crystal
      structure reveals the formation of mercaptide between the mercury ion and the thiol group on
      the cysteine amino acid inn a hydrophobic environment.  The crystal structure contains the
      bound ligand, S-adenosyl-L-methionine on the surface of the concave opening.  The direction of
      the beta-strands on the beta sheets are identical to other solved methyltransferases.  The
      highly conserved motifs, DPPY and the FxGxG, are found to be important in ligand binding and
      possibly in methyl group transfer.  The structure has a concave cleft with an opening on the
      order of 30 Angstroms that can accommodate a DNA duplex.  By molecular modeling coupled to
      sequence alignment, two other highly conserved residues Arg21 and Gly19 are found to be
      important in catalysis.
AU  - Tran PH
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 2001 61: 4801-B-4802-B.

PMID- 9862809
VI  - 6
DP  - 1998
TI  - Crystal structure of the DpnM DNA adenine methyltransferase from the DpnII restriction system of Streptococcus pneumoniae bound to S-adenosylmethionine.
PG  - 1563-1575
AB  - Methyltransferases catalyze the transfer of methyl groups from S-adenosylmethionine to a
      variety of small molecular and macromolecular substrates.  These enzymes contain a
      characteristic alpha/beta structural fold.  Four groups of DNA Mtases have been defined and
      representative structures have been determined for three groups.  DpnM is a DNA Mtase that
      acts on adenine N6 in the sequence GATC; the enzyme represents group alpha DNA Mtases, for
      which no structures are known.
AU  - Tran PH
AU  - Korszun ZR
AU  - Cerritelli S
AU  - Springhorn SS
AU  - Lacks SA
PT  - Journal Article
TA  - Structure
JT  - Structure
SO  - Structure 1998 6: 1563-1575.

PMID- 26586879
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequence and Classification of 11 Endophytic Bacteria from Poison Ivy (Toxicodendron radicans).
PG  - e01319-15
AB  - Here, we report the whole-genome sequences and annotation of 11 endophytic bacteria from
      poison ivy (Toxicodendron radicans) vine tissue. Five bacteria
      belong to the genus Pseudomonas, and six single members from other genera were
      found present in interior vine tissue of poison ivy.
AU  - Tran PN
AU  - Tan NE
AU  - Lee YP
AU  - Gan HM
AU  - Polter SJ
AU  - Dailey LK
AU  - Hudson AO
AU  - Savka MA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01319-15.

PMID- 29930072
VI  - 6
DP  - 2018
TI  - Complete Genome Sequences of Three Bacillus amyloliquefaciens Strains That Inhibit the Growth of Listeria monocytogenes In Vitro.
PG  - e00579-18
AB  - Here, we report the complete genome sequences of three Bacillus amyloliquefaciens strains
      isolated from alfalfa, almond drupes, and grapes that inhibited the
      growth of Listeria monocytogenes strain 2011L-2857 in vitro We also report
      multiple gene clusters encoding secondary metabolites that may be responsible for
      the growth inhibition of L. monocytogenes.
AU  - Tran TD
AU  - Huynh S
AU  - Parker CT
AU  - Hnasko R
AU  - Gorski L
AU  - McGarvey JA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00579-18.

PMID- 3087819
VI  - 42
DP  - 1986
TI  - DNA methyltransferase genes of Bacillus subtilis phages: comparison of their nucleotide sequences.
PG  - 89-96
AB  - The Phi3T DNA methyltransferase (Mtase) and most of the SPbeta Mtase genes have
      been sequenced.  With the exception of their promoters, no difference was found
      between the Phi3T and SPbeta Mtase genes which code for an enzyme with a Mr, of
      50507, consisting of 443 amino acids (aa).  Comparison of the deduced aa
      sequence of the Phi3T/SPbeta type Mtase (target specificity: GGCC and GCNGC)
      with that of the previously established sequence of the SPR Mtase (Buhk et al.,
      1984) which has the target specificity GGCC and CCGG, reveals strong
      similarities between these two types of enzymes.  There is, however, one
      striking difference: both the Phi3T/SPbeta and the SPR enzymes contain at
      different positions inserts of 33 aa, which have no homology to each other.  We
      suggest that the methylation specificity unique to each of the two types of
      Mtases (GCNGC in Phi3T/SPbeta ; CCGG in SPR) depends on these inserts, while
      the GGCC-specific modification potential common to all Mtases is determined by
      structures conserved in both types of enzymes.  A DNA fragment of non-modifying
      phage Z, which shows homology to both flanks of the SPR Mtase gene, was also
      sequenced.  This segment can be described as a derivative of SPR DNA, in which
      the Mtase gene and sequences at its 5' end have been deleted, with the deletion
      extending between two direct repeats of 25 bp.
AU  - Tran-Betcke A
AU  - Behrens B
AU  - Noyer-Weidner M
AU  - Trautner TA
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1986 42: 89-96.

PMID- 18359806
VI  - 190
DP  - 2008
TI  - Comparative genome analysis of "Candidatus Phytoplasma australiense" (subgroup tuf-Australia I; rp-A) and "Ca. Phytoplasma asteris" Strains  OY-M and AY-WB.
PG  - 3979-3991
AB  - The chromosome sequence of "Candidatus Phytoplasma australiense" (subgroup tuf-Australia I;
      rp-A), associated with dieback in papaya, Australian
      grapevine yellows in grapevine, and several other important plant
      diseases, was determined. The circular chromosome is represented by
      879,324 nucleotides, a GC content of 27%, and 839 protein-coding genes.
      Five hundred two of these protein-coding genes were functionally assigned,
      while 337 genes were hypothetical proteins with unknown function.
      Potential mobile units (PMUs) containing clusters of DNA repeats comprised
      12.1% of the genome. These PMUs encoded genes involved in DNA replication,
      repair, and recombination; nucleotide transport and metabolism;
      translation; and ribosomal structure. Elements with similarities to phage
      integrases found in these mobile units were difficult to classify, as they
      were similar to both insertion sequences and bacteriophages. Comparative
      analysis of "Ca. Phytoplasma australiense" with "Ca. Phytoplasma asteris"
      strains OY-M and AY-WB showed that the gene order was more conserved
      between the closely related "Ca. Phytoplasma asteris" strains than to "Ca.
      Phytoplasma australiense." Differences observed between "Ca. Phytoplasma
      australiense" and "Ca. Phytoplasma asteris" strains included the
      chromosome size (18,693 bp larger than OY-M), a larger number of genes
      with assigned function, and hypothetical proteins with unknown function.
AU  - Tran-Nguyen LT
AU  - Kube M
AU  - Schneider B
AU  - Reinhardt R
AU  - Gibb KS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2008 190: 3979-3991.

PMID- 1598212
VI  - 20
DP  - 1992
TI  - DNA methyltransferase is developmentally expressed in replicating and non-replicating male germ cells.
PG  - 2541-2545
AB  - Genomic methylation patterns are established during maturation of primordial germ cells and
      during gametogenesis. While methylation is linked to DNA replication in somatic cells, active
      de novo methylation and demethylation occur in post-replicative spermatocytes during meiotic
      prophase. We have examined differentiating male germ cells for alternative forms of DNA
      (cytosine-5)-methyltransfease (DNA MTase) and have found a 6.2 kb DNA MTase mRNA that is
      present in appreciable quantitites only in testis; in post-replicative pachytene spermatocytes
      it is the predominant form of DNA MTase mRNA. The 5.2 kb DNA MTase mRNA, characteristic of all
      somatic cells, was detected in isolated type A and B spermatogonia and haploid round
      spermatids. Immunoblot analysis detected a protein in spermatogenic cells with a relative mass
      of 180,000-200,000, which is close to the known size of the somatic form of mammalian DNA
      MTase. The demonstration of the differential developmental expression of DNA MTase in male
      germ cells argues for a role for testicular DNA methylation events, not only during
      replication in premeiotic cells, but also during meiotic prophase and postmeiotic development.
AU  - Trasler JM
AU  - Alcivar AA
AU  - Hake LE
AU  - Bestor T
AU  - Hecht NB
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 2541-2545.

PMID- 8896980
VI  - 206
DP  - 1996
TI  - DNA methyltransferase in normal and Dnmtn/Dnmtn mouse embryos.
PG  - 239-247
AB  - The mouse genome experiences a large decrease in net 5-methylcytosine
      between fertilization and implantation; de novo methylation brings 5-methylcytosine to
      adult somatic cell levels between implantation and gastrulation.  Very little is known of the
      regulation of demethylation or de novo methylation.  Levels of the one known form of
      DNA methyltransferase are very high in early embryos, but the enzyme is localized to the
      cytoplasm during most of preimplantation development.  We show here that DNA
      methyltransferase is found exclusively in nuclei of the conceptus after implantation, and
      that nuclei of proximal decidual cells are free of detectable DNA methyltransferase.  High
      levels of DNA methyltransferase were seen in all tissues, including the developing nervous
      system, of 9.5- to 12.5-day embryos.  The large maternal stores of DNA methyltransferase
      become limiting prior to embryonic day 9.5, as shown by barely detectable immunostaining
      in 9.5-day embryos homozygous for a loss-of-function mutation (Dnmtn) in the DNA
      methyltransferase gene.  These mutant embryos failed to develop past the 25-somite stage
      and showed evidence of developmental delay and some developmental asynchrony.
      Normal embryonic and extraembryonic tissues contained similar levels of DNA
      methyltransferase, even though severely reduced methylation levels and a loss of
      imprinting have previously been observed in extraembryonic tissues.  These findings
      suggest that methylation patterns are not a simple function of the concentration of DNA
      methyltransferase, and that unidentified factors must be involved in the regulation of de
      novo methylation during early development of the mouse.
AU  - Trasler JM
AU  - Trasler DG
AU  - Beston TH
AU  - Li E
AU  - Ghibu F
PT  - Journal Article
TA  - Dev. Dyn.
JT  - Dev. Dyn.
SO  - Dev. Dyn. 1996 206: 239-247.

PMID- 23069868
VI  - 19
DP  - 2012
TI  - Microevolution in cyanobacteria: re-sequencing a motile substrain of Synechocystis sp. PCC 6803.
PG  - 435-448
AB  - Synechocystis sp. PCC 6803 is a widely used model cyanobacterium for studying
      photosynthesis, phototaxis, the production of biofuels and many other aspects.
      Here we present a re-sequencing study of the genome and seven plasmids of one of
      the most widely used Synechocystis sp. PCC 6803 substrains, the glucose tolerant
      and motile Moscow or 'PCC-M' strain, revealing considerable evidence for recent
      microevolution. Seven single nucleotide polymorphisms (SNPs) specifically shared
      between 'PCC-M' and the 'PCC-N and PCC-P' substrains indicate that 'PCC-M'
      belongs to the 'PCC' group of motile strains. The identified indels and SNPs in
      'PCC-M' are likely to affect glucose tolerance, motility, phage resistance,
      certain stress responses as well as functions in the primary metabolism,
      potentially relevant for the synthesis of alkanes. Three SNPs in intergenic
      regions could affect the promoter activities of two protein-coding genes and one
      cis-antisense RNA. Two deletions in 'PCC-M' affect parts of clustered regularly
      interspaced short palindrome repeats-associated spacer-repeat regions on plasmid
      pSYSA, in one case by an unusual recombination between spacer sequences.
AU  - Trautmann D
AU  - Voss B
AU  - Wilde A
AU  - Al-Babili S
AU  - Hess WR
PT  - Journal Article
TA  - DNA Res.
JT  - DNA Res.
SO  - DNA Res. 2012 19: 435-448.

PMID- 3150362
VI  - 74
DP  - 1988
TI  - Organization of target-recognizing domains in the multispecific DNA (cytosine-5) methyltransferases of Bacillus subtilis phages SPR and Phi-3T.
PG  - 267
AB  - Meeting Abstract
AU  - Trautner TA
AU  - Balganesh T
AU  - Wilke K
AU  - Noyer-Weidner M
AU  - Rauhut E
AU  - Lauster R
AU  - Behrens B
AU  - Pawlek B
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 267.

PMID- 3041380
VI  - 16
DP  - 1988
TI  - Chimeric multispecific DNA methyltransferases with novel combinations of target recognition.
PG  - 6649-6658
AB  - DNA target recognizing domains of different multispecific
      DNA-cytosine-methyltransferases can be rearranged through engineering of the
      corresponding genes to generate enzymes with novel combinations of target
      recognition.
AU  - Trautner TA
AU  - Balganesh TS
AU  - Pawlek B
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1988 16: 6649-6658.

PMID- 
VI  - 0
DP  - 1993
TI  - Restriction/modification and methylation systems in Bacillus subtilis, related species, and their phages.
PG  - 539-552
AB  - Several restriction/modification (R/M) systems have been identified in Bacillus subtilis and
      related bacteria and will be described here. Accepting the view that R/M systems have evolved
      to defend bacteria effectively against attack by bacterial viruses, we shall discuss the
      question of what mechanisms bacteriophages have developed to overcome barriers provided by
      host R/M systems. To what extent do R/M systems affect other inter- and intra-specific
      transport of DNA? In this connection, we shall discuss the usefulness of restriction systems,
      with their high substrate specificities for double-stranded DNA, in understanding the
      processing of free or packaged DNA during uptake into B. subtilis cells or subcellular
      structures. Recent progress in the characterization of genes encoding restriction
      endonucleases (ENases) and modification methyltransferases (MTases) from a wide range of
      organisms has made such systems per se interesting paradigms for the study of the evolution of
      highly specific DNA-binding proteins. In particular, our interest is focused here on the
      phylogenetic relationship among the various ENases and MTases of Bacillus and other bacterial
      species. Furthermore, the requirement of coexistence of an ENase with an MTase represents an
      interesting case of obligatory coevolution of two genes. The study of multispecific MTases,
      discovered so far only in some temperate B. subtilis and Bacillus amyloliquefaciens phages,
      has made significant contribution to our present understanding of the nature, function, and
      evolution of R/M systems and particularly of their MTases. The interesting biochemical aspects
      of the action of ENases and MTases will not be covered here. Such discussions are included in
      a recent review.
AU  - Trautner TA
AU  - Noyer-Weidner M
PT  - Journal Article
TA  - Bacillus subtilis and other gram-positive bacteria: Biochemistry, Physiology, and Molecular Genetics
JT  - Bacillus subtilis and other gram-positive bacteria: Biochemistry, Physiology, and Molecular Genetics
SO  - Bacillus subtilis and other gram-positive bacteria: Biochemistry, Physiology, and Molecular Genetics 1993 0: 539-552.

PMID- 8635476
VI  - 15
DP  - 1996
TI  - Exact size and organization of DNA target-recognizing domains of multispecific DNA-(cytosine-C5)-methyltransferases.
PG  - 1434-1442
AB  - A large portion of the sequences of type II DNA-(cytosine-C5)-methyltransferases (C5-MTases)
      represent highly conserved blocks of amino acids.  General steps in the methylation reaction
      performed by C5-MTases have been found to be mediated by some of these domains.  C5-MTases
      carry, in addition at the same relative location, a region variable in size and amino acid
      composition, part of which is associated with the capacity of each C5-MTase to recognize its
      characteristic target.  Individual target-recognizing domains (TRDs) for the targets CCGG (M),
      CC(A/T)GG (E), GGCC (H), GCNGC (F) and G(G/A/T)GC(C/A/T)C (B) could be identified in the
      C-terminal part of the variable region of multispecific C5-MTases.  With experiments reported
      here, we have established the organization of the variable regions of the multispecific MTases
      M.SPRI, M.Phi3TI, M.H2I and M.Rho11sI at the resolution of individual amino acids.  These
      regions comprise 204, 175, 268 and 268 amino acids, respectively.  All variable regions are
      bipartite.  They contain at their N-terminal side a very similar sequence of 71 amino acids.
      The integrity of this sequence must be assured to provide enzyme activity.  Bracketed by 6-10
      linker amino acids, they have, depending on the enzyme studied, towards their C-terminal end
      ensembles of individual TRDs of 38 (M), 39 (E), 40 (H), 44 (F) and 54 (B) amino acids.  TRDs
      of different enzymes with equal specificity have the same size.  TRDs do not overlap but are
      either separated by linker amino acids or abut each other.
AU  - Trautner TA
AU  - Pawlek B
AU  - Behrens B
AU  - Willert J
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1996 15: 1434-1442.

PMID- 4215951
VI  - 131
DP  - 1974
TI  - Restriction and Modification in B. subtilis.
PG  - 181-191
AB  - Restriction and modification observed in Bacillus subtilis strain "R" affects
      infection and transfection with phages SPP1, Phi105 and SPO2, but not with SP8,
      Phi29, SP82, Sp50, H1 or PBS1.  It affects also PBS1 mediated transduction, but
      not transformation with bacterial DNA.  The marker(s) determining
      restriction/modification map between the origin of replication of the B.
      subtilis chromosome and purA16.
AU  - Trautner TA
AU  - Pawlek B
AU  - Bron S
AU  - Anagnostopoulos C
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1974 131: 181-191.

PMID- 6258025
VI  - 180
DP  - 1980
TI  - Restriction and modification in Bacillus subtilis: Identification of a gene in the temperate phage SPbeta coding for a BsuR specific modification methyltransferase.
PG  - 361-367
AB  - A gene coding for a modifying DNA-methyltransferase which methylates the
      central C in the BsuR recognition sequence 5'GGCC was identified in the genome
      of the temperate Bacillus subtilis phage SPbeta.  This gene is expressed only
      after induction of the prophage by either mitomycin C or UV.  The presence of
      active methyltransferase in induced cells leads to modification of BsuR
      recognition sites in SPbeta DNA as well as in heterologous DNA.
AU  - Trautner TA
AU  - Pawlek B
AU  - Gunthert U
AU  - Canosi U
AU  - Jentsch S
AU  - Freund M
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1980 180: 361-367.

PMID- 26543119
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of the Human Gut Symbiont Roseburia hominis.
PG  - e01286-15
AB  - We report here the complete genome sequence of the human gut symbiont Roseburia hominis
      A2-183(T) (= DSM 16839(T) = NCIMB 14029(T)), isolated from human feces.
      The genome is represented by a 3,592,125-bp chromosome with 3,405 coding
      sequences. A number of potential functions contributing to host-microbe
      interaction are identified.
AU  - Travis AJ
AU  - Kelly D
AU  - Flint HJ
AU  - Aminov RI
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01286-15.

PMID- Not carried by PubMed...
VI  - 148
DP  - 1995
TI  - DNA flips out!  Enzymes repair and modify DNA in a surprising way.
PG  - 188-189
AB  - According to recent research, enzymes have another way of tackling DNA.  Some apparently pry
      apart a base pair, then rotate one of the freed nucleotides, bringing its base out of the
      confines of the double helix and into the enzyme's active site, a pocket within the
      protein's structure.  The enzyme can then remove this pocketed base from its nucleotide or
      modify the base and sling it back into its proper position.
AU  - Travis J
PT  - Journal Article
TA  - Sci. News
JT  - Sci. News
SO  - Sci. News 1995 148: 188-189.

PMID- 23105067
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of the Sulfobacillus thermosulfidooxidans Cutipay Strain, an Indigenous Bacterium Isolated from a Naturally Extreme Mining Environment in  Northern Chile.
PG  - 6327-6328
AB  - Sulfobacillus thermosulfidooxidans strain Cutipay is a mixotrophic, acidophilic,  moderately
      thermophilic bacterium isolated from mining environments of the north
      of Chile, making it an interesting subject for studying the bioleaching of
      copper. We introduce the draft genome sequence and annotation of this strain,
      which provide insights into its mechanisms for heavy metal resistance.
AU  - Travisany D
AU  - Di Genova A
AU  - Sepulveda A
AU  - Bobadilla-Fazzini RA
AU  - Parada P
AU  - Maass A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6327-6328.

PMID- 25377701
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of the Quality Control Strain Staphylococcus aureus subsp. aureus ATCC 25923.
PG  - e01110-14
AB  - Staphylococcus aureus subsp. aureus ATCC 25923 is commonly used as a control strain for
      susceptibility testing to antibiotics and as a quality control strain
      for commercial products. We present the completed genome sequence for the strain,
      consisting of the chromosome and a 27.5-kb plasmid.
AU  - Treangen TJ
AU  - Maybank RA
AU  - Enke S
AU  - Friss MB
AU  - Diviak LF
AU  - Karaolis DK
AU  - Koren S
AU  - Ondov B
AU  - Phillippy AM
AU  - Bergman NH
AU  - Rosovitz MJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01110-14.

PMID- 25103754
VI  - 2
DP  - 2014
TI  - Genome Sequences of 228 Shiga Toxin-Producing Escherichia coli Isolates and 12 Isolates Representing Other Diarrheagenic E. coli Pathotypes.
PG  - e00718-14
AB  - Shiga toxin-producing Escherichia coli (STEC) are a common cause for food-borne diarrheal
      illness outbreaks and sporadic cases. Here, we report the availability
      of the draft genome sequences of 228 STEC strains representing 32 serotypes with
      known pulsed-field gel electrophoresis (PFGE) types and epidemiological
      relationships, as well as 12 strains representing other diarrheagenic E. coli
      pathotypes.
AU  - Trees E
AU  - Strockbine N
AU  - Changayil S
AU  - Ranganathan S
AU  - Zhao K
AU  - Weil R
AU  - MacCannell D
AU  - Sabol A
AU  - Schmidtke A
AU  - Martin H
AU  - Stripling D
AU  - Ribot EM
AU  - Gerner-Smidt P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00718-14.

PMID- 15186344
VI  - 6
DP  - 2004
TI  - Genetic organization of the catabolic plasmid pJP4 from Ralstonia eutropha JMP134 (pJP4) reveals mechanisms of adaptation to chloroaromatic   pollutants and evolution of specialized chloroaromatic degradation   pathways.
PG  - 655-668
AB  - Ralstonia eutropha JMP134 (pJP4) is a useful model for the study of bacterial degradation of
      substituted aromatic pollutants. Several key
      degrading capabilities, encoded by tfd genes, are located in the 88 kb,
      self-transmissible, IncP-1 beta plasmid pJP4. The complete sequence of the
      87,688 nucleotides of pJP4, encoding 83 open reading frames (ORFs), is
      reported. Most of the coding sequence corresponds to a well-conserved
      IncP-1 beta backbone and the previously reported tfd genes. In addition,
      we found hypothetical proteins putatively involved in the transport of
      aromatic compounds and short-chain fatty acid oxidation. ORFs related to
      mobile elements, including the Tn501-encoded mercury resistance
      determinants, an IS1071-based composite transposon and a cryptic class II
      transposon, are also present in pJP4. These mobile elements are
      inefficient in transposition and are located in two regions of pJP4 that
      are rich in remnants of lateral gene transfer events. pJP4 plasmid was
      able to capture chromosomal genes and form hybrid plasmids with the IncP-1
      alpha plasmid RP4. These observations are integrated into a model for the
      evolution of pJP4, which reveals mechanisms of bacterial adaptation to
      degrade pollutants.
AU  - Trefault N
AU  - De la Iglesia R
AU  - Molina AM
AU  - Manzano M
AU  - Ledger T
AU  - Perez-Pantoja D
AU  - Sanchez MA
AU  - Stuardo M
AU  - Gonzalez B
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2004 6: 655-668.

PMID- Not included in PubMed...
VI  - 40
DP  - 1994
TI  - Ambient-temperature-stable restriction endonucleases for use in forensic DNA applications.
PG  - 1092
AB  - We have stabilized restriction endonucleases including HaeIII, HinfI, and PstI, which are
      commonly used in forensic and paternity DNA profiling. Using a patented process (US patents
      5098893 and 5250429) the enzyme and reaction buffer are stabilized as a glassy matrix of
      carbohydrate polymers. These glassified reaction systems show excellent stability at ambient
      temperatures for prolonged periods of time. The glass transition temperature (Tg) is a
      physical property of the material and can be determined using a Differential Scanning
      Calorimeter. At temperatures equal to or lower than the Tg the material remains a glass.
      Stability studies show the recovery of enzyme activity immediately after processing is 75-100%
      of activity prior to processing, and there is no further loss of activity over extended
      periods of time provided the enzyme is stored at temperatures below the Tg. We have dried the
      enzymes HinfI, HaeIII, and PstI by this process. The Gg's (oC) were 41.0, 45.2, and 47.4
      respectively. After processing, the enzymes were stored at 25, 37, and 55oC for extended
      periods of time. After 34 weeks HinfI retains 100% of initial activity at 25 and 37oC and 70%
      of initial activity at 55oC. After 30 weeks HaeIII retains 100% initial activity at all three
      storage temperatures. PstI after 36 weeks of storage retains 100% initial activity at all
      three storage temperatures. PstI after 36 weeks of storage retains 100% of initial activity at
      25 and 37oC and 75% of initial activity at 55oC. These pre-mixed single dose reactions also
      offer convenience and reproducibility by reducing pipeting steps and possible cross
      contamination. Since the enzymes are stable at ambient temperatures they offer the added
      convenience of room temperature shipping and storage. The enzymes are readily rehydrated by
      simply adding water and the DNA to be analyzed. The stabilizer used in this process eliminates
      the need for glycerol in the enzyme preparation. The absence of glycerol reduces star activity
      that is sometimes observed when digests are carried out in the presence of high glycerol
      concentrations due to a high ratio of enzyme units to DNA. The stabilized enzymes have been
      used in side by side studies with standard RFLP protocols. A PstI paternity analysis was done
      using Lifecodes procedures with standard PstI and our stabilized PstI. The analysis done with
      standard PstI resulted in an extra band due to partial digestions. The extra band was not
      present in the analysis done with stabilized PstI. The stabilized restriction enzymes offer
      quick, reliable and reproducible results for standard forensic and paternity profiling
      protocols.
AU  - Treml S
AU  - Draveling C
AU  - Huang C
AU  - Heaster J
AU  - Walker D
AU  - DiFrancesco R
AU  - Jolly J
PT  - Journal Article
TA  - Clin. Chem.
JT  - Clin. Chem.
SO  - Clin. Chem. 1994 40: 1092.

PMID- 29242223
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequences of Three Streptococcus macedonicus Strains Isolated from Italian Cheeses in the Veneto Region.
PG  - e01358-17
AB  - We report here the genome sequences of three Streptococcus macedonicus strains isolated from
      different cheeses in the Veneto region of Italy. The presented data
      aim at increasing the scarce genomic information available for this species,
      which is frequently encountered in fermented foods and appears to be a promising
      technological microorganism.
AU  - Treu L
AU  - de Diego-Diaz B
AU  - Papadimitriou K
AU  - Tsakalidou E
AU  - Giacomini A
AU  - Corich V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01358-17.

PMID- 24526643
VI  - 2
DP  - 2014
TI  - Genome Sequences of Streptococcus thermophilus Strains MTH17CL396 and M17PTZA496  from Fontina, an Italian PDO Cheese.
PG  - e00067-14
AB  - Here is presented the whole-genome sequences of Streptococcus thermophilus strains MTH17CL396
      and M17PTZA496, isolated from fontina protected designation of
      origin (PDO) cheese in the Valle d'Aosta Region (Italy). S. thermophilus is a
      lactic acid bacterium widely present in dairy products, and these are the first
      publicly available genome sequences of S. thermophilus strains isolated from
      cheese.
AU  - Treu L
AU  - Vendramin V
AU  - Bovo B
AU  - Campanaro S
AU  - Corich V
AU  - Giacomini A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00067-14.

PMID- 24435859
VI  - 2
DP  - 2014
TI  - Whole-Genome Sequences of Streptococcus thermophilus Strains TH1435 and TH1436, Isolated from Raw Goat Milk.
PG  - e01129-13
AB  - We report the genome sequences of two Streptococcus thermophilus strains, TH1435  and TH1436,
      isolated from raw goat milk devoted to the production of artisanal
      cheese in the Friuli-Venezia Giulia region in Italy. The genome sequences of
      these two quickly acidifying strains are the first available genome sequences of
      S. thermophilus strains isolated in Italy.
AU  - Treu L
AU  - Vendramin V
AU  - Bovo B
AU  - Campanaro S
AU  - Corich V
AU  - Giacomini A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01129-13.

PMID- 24625867
VI  - 2
DP  - 2014
TI  - Genome Sequences of Four Italian Streptococcus thermophilus Strains of Dairy Origin.
PG  - e00126-14
AB  - This report describes the genome sequences of four Streptococcus thermophilus strains, namely,
      TH982, TH985, TH1477, and 1F8CT, isolated from different dairy
      environments from the Campania and the Veneto regions in Italy. These data are
      aimed at increasing the genomic information available on this species, which is
      of paramount importance for the dairy industry.
AU  - Treu L
AU  - Vendramin V
AU  - Bovo B
AU  - Campanaro S
AU  - Corich V
AU  - Giacomini A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00126-14.

PMID- 24558238
VI  - 2
DP  - 2014
TI  - Genome Sequence of Lactobacillus fabifermentans Strain T30PCM01, Isolated from Fermenting Grape Marc.
PG  - e00060-14
AB  - Here, we report the draft genome assembly of Lactobacillus fabifermentans strain  T30PCM01
      isolated from grape marc. Its genome is the largest (3.58 Mbp) among
      Lactobacillus species and reveals an enormous potential for carbohydrate
      utilization and transcriptional regulation.
AU  - Treu L
AU  - Vendramin V
AU  - Bovo B
AU  - Giacomini A
AU  - Corich V
AU  - Campanaro S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00060-14.

PMID- 28983009
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of the Fruiting Myxobacterium Myxococcus macrosporus Strain DSM 14697, Generated by PacBio Sequencing.
PG  - e01127-17
AB  - Members of the Myxococcales order initiate a developmental program in response to starvation
      that culminates in formation of spore-filled fruiting bodies. To
      investigate the genetic basis for fruiting body formation, we present the
      complete 8.9-Mb genome sequence of Myxococcus macrosporus strain DSM 14697,
      generated using the PacBio sequencing platform.
AU  - Treuner-Lange A
AU  - Bruckskotten M
AU  - Rupp O
AU  - Goesmann A
AU  - Sogaard-Andersen L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01127-17.

PMID- 29074673
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Fruiting Myxobacterium Nannocystis exedens DSM 71.
PG  - e01227-17
AB  - In response to starvation, members of the order Myxococcales form morphologically very
      different fruiting bodies. To determine whether fruiting myxobacteria share
      a common genetic program that leads to fruiting body formation, we sequenced and
      assembled the genome of Nannocystis exedens DSM 71 as two contigs with a total GC
      content of 72%.
AU  - Treuner-Lange A
AU  - Bruckskotten M
AU  - Rupp O
AU  - Goesmann A
AU  - Sogaard-Andersen L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01227-17.

PMID- 29122879
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of the Fruiting Myxobacterium Melittangium boletus DSM 14713.
PG  - e01262-17
AB  - The formation of spore-filled fruiting bodies in response to starvation represents a hallmark
      of many members of the order Myxococcales Here, we present
      the complete 9.9-Mb genome of the fruiting type strain Melittangium boletus DSM
      14713, the first member of this genus to have its genome sequenced.
AU  - Treuner-Lange A
AU  - Bruckskotten M
AU  - Rupp O
AU  - Goesmann A
AU  - Sogaard-Andersen L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01262-17.

PMID- 29074667
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequence of the Fruiting Myxobacterium Cystobacter fuscus DSM 52655.
PG  - e01196-17
AB  - Among myxobacteria, the genus Cystobacter is known not only for fruiting body formation but
      also for formation of secondary metabolites, such as cystobactamids
      and cystothiazols. Here, we present the complete genome sequence of the
      Cystobacter fuscus strain DSM 52655, which comprises 12,349,744 bp and 9,836
      putative protein-coding sequences.
AU  - Treuner-Lange A
AU  - Bruckskotten M
AU  - Rupp O
AU  - Goesmann A
AU  - Sogaard-Andersen L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01196-17.

PMID- 25059871
VI  - 2
DP  - 2014
TI  - Improved Draft Genome Sequence of Probiotic Strain Lactobacillus gasseri K7.
PG  - e00725-14
AB  - Lactobacillus gasseri K7 is an isolate from infant feces and has in vitro and in  vivo
      established probiotic properties. Here, we report the improved version of
      the draft genome sequence, which comprises 8 scaffolds (13 contigs), a total
      length of 1.99 Mb, and 1,841 predicted protein-coding sequences.
AU  - Treven P
AU  - Trmcic A
AU  - Bogovic MB
AU  - Rogelj I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00725-14.

PMID- 
VI  - 96
DP  - 1998
TI  - Molecular evolution in bacteria: genome size, cell size, restriction-modification and recognition.
PG  - 25-33
AB  - The ability of bacteria to alter their genome sizes and the order of their genes, yet maintain
      a relatively constant genome, provides a mechanism for diversity and evolution in bacteria.
      Moreover, bacteria may have evolved by increasing their genome sizes and rearranging gene
      orders with the assistance of restriction endonucleases cleaving foreign DNA and providing a
      diverse pool of DNA sequences for genetic recombination.  This review examines some of these
      evolutionary aspects of bacteria including molecular recognition of biomolecules.
AU  - Trevors JT
PT  - Journal Article
TA  - Bull. Inst. Pasteur
JT  - Bull. Inst. Pasteur
SO  - Bull. Inst. Pasteur 1998 96: 25-33.

PMID- Not carried by PubMed...
VI  - 14
DP  - 1998
TI  - Review: Bacterial population genetics.
PG  - 1-5
AB  - Bacterial population genetics is the study of natural bacterial genetic diversity arising from
      evolutionary processes.  The roles of molecular mistakes, restriction-modification, plasmids
      and gene transfer in bacteria are also important components of population genetics.  These
      aspects are of considerable scientific importance from a fundamental perspective, because of
      the short generation times of bacteria, their microscopic cell size, the large population
      sizes bacteria can achieve and their different mechanisms of gene transfer.
AU  - Trevors JT
PT  - Journal Article
TA  - World J. Microbiol. Biotechnol.
JT  - World J. Microbiol. Biotechnol.
SO  - World J. Microbiol. Biotechnol. 1998 14: 1-5.

PMID- 7574546
VI  - 67
DP  - 1995
TI  - Molecular evolution in bacteria.
PG  - 315-324
AB  - Recent advances in microbiology and molecular biology have a unifying influence on our
      understanding of genetic diversity/similarity and evolutionary relationships in
      microorganisms.  This article attempts to unify information from diverse areas such as
      microbiology, molecular biology, microbial physiology, clay crystal genes, metals-microbe-clay
      interactions and bacterial DNA restriction-modification systems (R-M) as they may apply to
      molecular evolution of bacteria.  The possibility is discussed that the first informational
      molecules may have been catalytic RNA (micro-assembler) not DNA (now the master copy) and
      these first micro-assemblers may have been precursors of ribosomes.
AU  - Trevors JT
PT  - Journal Article
TA  - Antonie Van Leeuwenhoek
JT  - Antonie Van Leeuwenhoek
SO  - Antonie Van Leeuwenhoek 1995 67: 315-324.

PMID- 22493195
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Polyhydroxybutyrate Producer Pseudomonas extremaustralis,  a Highly Stress-Resistant Antarctic Bacterium.
PG  - 2381-2382
AB  - Pseudomonas extremaustralis 14-3b presents genes involved in the synthesis of different
      polyhydroxyalkanoates, in tolerance and degradation of pollutants, and
      in microaerobic metabolism. Several genomic islands were detected. Genetic
      machinery could contribute to the adaptability to stressful conditions. This is
      the first genome sequence reported from a Pseudomonas isolated from cold
      environments.
AU  - Tribelli PM
AU  - Raiger ILJ
AU  - Catone MV
AU  - Di Martino C
AU  - Revale S
AU  - Mendez BS
AU  - Lopez NI
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2381-2382.

PMID- 8319881
VI  - 109
DP  - 1993
TI  - Enhanced conjugative transfer of plasmid DNA from Escherichia coli to Staphylococcus aureus and Listeria monocytogenes.
PG  - 19-23
AB  - Transfer of mobilizable shuttle cloning vectors by conjugation from Escherichia coli to
      Staphylococcus aureus occurred at a very low frequency (10-9 transconjugants per donor
      colony-forming unit after the mating period). It was observed that subinhibitory
      concentrations of penicillins (oxacillin or penicillin G) in the mating medium resulted in
      increased transfer frequency by conjugation of the shuttle vector pAT18 from E. coli SM10 to
      S. aureus 80CR5 Str (54-fold) and to Listeria monocytogenes LO17RF (45-fold). These results
      were interpreted as indicating that the cell wall of Gram-positive bacteria constitutes an
      important barrier for conjugative transfer of genetic information delivered from E. coli. It
      was also demonstrated that the presence of a restriction system(s) in S. aureus recipients
      represented a major barrier to introduction of foreign DNA.
AU  - Trieu-Cuot P
AU  - Derlot E
AU  - Courvalin P
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1993 109: 19-23.

PMID- 23209236
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Agrobacterium albertimagni Strain AOL15.
PG  - 6986-6987
AB  - Agrobacterium albertimagni strain AOL15 is an alphaproteobacterium isolated from
      arsenite-oxidizing biofilms whose draft genome contains 5.1 Mb in 55 contigs with
      61.2% GC content and includes a 21-gene arsenic gene island. This is the first
      available genome for this species and the second Agrobacterium arsenic gene
      island.
AU  - Trimble WL
AU  - Phung LT
AU  - Meyer F
AU  - Gilbert JA
AU  - Silver S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6986-6987.

PMID- 23105084
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Achromobacter piechaudii Strain HLE.
PG  - 6355
AB  - Achromobacter piechaudii strain HLE is a betaproteobacterium (previously known as Alcaligenes
      faecalis) that was an early isolate with arsenite oxidase activity.
      This draft genome of 6.89 Mb is the second available genome for this species in
      the opportunistic pathogen Alcaligenaceae family.
AU  - Trimble WL
AU  - Phung LT
AU  - Meyer F
AU  - Silver S
AU  - Gilbert JA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6355.

PMID- 29348331
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Two Vibrio parahaemolyticus Strains Associated with Gastroenteritis after Raw Seafood Ingestion in Colorado.
PG  - e01387-17
AB  - Vibrio parahaemolyticus is a Gram-negative pathogen associated with gastrointestinal and wound
      infections after exposure to raw seafood or
      contaminated waters. We report here the whole-genome sequences of two stool
      isolates (CDC-AM50933 and CDC-AM43539) from patients in Colorado presenting with
      gastroenteritis after ingesting raw seafood.
AU  - Trinh SA
AU  - Leyn SA
AU  - Rodionov ID
AU  - Godzik A
AU  - Satchell KJF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01387-17.

PMID- 27610214
VI  - 11
DP  - 2016
TI  - Draft genome sequence of Lampropedia cohaerens strain CT6(T) isolated from arsenic rich microbial mats of a Himalayan hot water spring.
PG  - 64
AB  - Lampropedia cohaerens strain CT6(T), a non-motile, aerobic and coccoid strain was isolated
      from arsenic rich microbial mats (temperature ~45 degrees C) of a hot
      water spring located atop the Himalayan ranges at Manikaran, India. The present
      study reports the first genome sequence of type strain CT6(T) of genus
      Lampropedia cohaerens. Sequencing data was generated using the Illumina HiSeq
      2000 platform and assembled with ABySS v 1.3.5. The 3,158,922 bp genome was
      assembled into 41 contigs with a mean GC content of 63.5 % and 2823 coding
      sequences. Strain CT6(T) was found to harbour genes involved in both the
      Entner-Duodoroff pathway and non-phosphorylated ED pathway. Strain CT6(T) also
      contained genes responsible for imparting resistance to arsenic, copper, cobalt,
      zinc, cadmium and magnesium, providing survival advantages at a thermal location.
      Additionally, the presence of genes associated with biofilm formation,
      pyrroloquinoline-quinone production, isoquinoline degradation and mineral
      phosphate solubilisation in the genome demonstrate the diverse genetic potential
      for survival at stressed niches.
AU  - Tripathi C
AU  - Mahato NK
AU  - Rani P
AU  - Singh Y
AU  - Kamra K
AU  - Lal R
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 64.

PMID- 27284139
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Carbaryl-Degrading Soil Isolate Pseudomonas sp. Strain C5pp.
PG  - e00526-16
AB  - We report the draft genome sequence of carbaryl-degrading Pseudomonas sp. strain  C5pp. Genes
      encoding salicylate and gentisate metabolism, large amounts of
      oxygenase, nitrogen metabolism, and heavy metal tolerance were identified. The
      sequence will provide further insight into the biochemical and evolutionary
      aspects of carbaryl degradation.
AU  - Trivedi VD
AU  - Jangir PK
AU  - Sharma R
AU  - Phale PS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00526-16.

PMID- 27811106
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Methylophaga muralis Bur 1, a Haloalkaliphilic (Non-Methane-Utilizing) Methylotroph Isolated from a Soda Lake.
PG  - e01227-16
AB  - The draft genome sequence of Methylophaga muralis strain Bur 1 (VKM B-3046T), a
      non-methane-utilizing methylotroph isolated from a soda lake, is reported here.
      Strain Bur 1 possesses genes for methanol and methylamine (methylamine
      dehydrogenase and N-methylglutamate pathway) oxidation. Genes for the
      biosynthesis of ectoine were also found.
AU  - Trotsenko YA
AU  - Shmareva MN
AU  - Doronina NV
AU  - Tarlachkov SV
AU  - Mustakhimov II
AU  - Vasilenko OV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01227-16.

PMID- 16325353
VI  - 366
DP  - 2006
TI  - Genome analysis of the obligately lytic bacteriophage 4268 of Lactococcus lactic provides insight into its adaptable nature.
PG  - 189-199
AB  - Analysis of the complete nucleotide sequence of the lactococcal phage 4268, which is lytic for
      the cheese starter Lactococcus lactis DPC4268, is presented. Phage 4268 has a linear genome of
      36,596 bp, which is modularly organised and encompasses 49 open reading frames. Putative
      functions were assigned to approximately 45% of the predicted products of these open reading
      frames based on sequence similarity with known proteins, N-terminal sequence analysis and
      identification of conserved domains. Significantly, a segment of the genome has homology to
      the recently sequenced lysogenic module in lactococcal phage phi 31 that contains a lytic
      switch but no phage integrase or attachment site. This suggests that it is derived from a
      prophage. A phage 4268-encoded and a host-encoded methylase were found to be highly similar,
      having only two nucleotide mismatches, suggesting that the phage acquired the methylase gene
      to protect it from a host endonuclease. Comparative genomic analysis revealed significant
      homology between phage 4268 and the lactococcal phage BK5-T. The comparative analysis also
      supported the classification of phage 4268 and other BK5-T-related phage as separate from the
      proposed P335 species of lactococcal phage.
AU  - Trotter M
AU  - McAuliffe O
AU  - Callanan M
AU  - Edwards R
AU  - Fitzgerald GF
AU  - Coffey A
AU  - Ross RP
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 2006 366: 189-199.

PMID- 12067382
VI  - 93
DP  - 2002
TI  - Lactococcus lactis DPC5598, a plasmid-free derivative of a commercial starter, provides a valuable alternative host for culture improvement studies.
PG  - 134-143
AB  - Aims: To generate a plasmid-free derivative of an extensively used industrial starter strain
      Lactococcus lactis DPC4268, which could be used as a backbone strain for starter improvement
      programmes. Methods and Results: DPC4268, containing four large plasmids, was subjected to
      high temperature plasmid curing resulting in derivatives, each with a different plasmid
      complement of one, two or three different plasmids in addition to a plasmid-free derivative.
      Industrially relevant phenotypes were assigned to each plasmid on the basis of detailed
      phenotypic and genetic analyses and these were (a) proteinase activity (Prt, 60 kb) (b)
      lactose fermentation (Lac, 55 kb) (c) bacteriophage adsorption inhibition (Ads, 44 kb) and (d)
      type I restriction/modification (R/M, 40 kb). The plasmid-free variant of DPC4268 was shown to
      be transformable at frequencies comparable to the common laboratory strain L. lactis MG1614.
      Furthermore its genome was demonstrated to be significantly different from the laboratory
      strains L. lactis MG1614 and the recently sequenced L. lactis IL1403 genomes by pulsed-field
      gel electrophoresis. Conclusions: This study produced an easily transformable plasmid-free
      derivative which was genomically different from both MG1614 and IL1403. In addition, important
      plasmid-borne industrial traits, including two phage-resistance mechanisms, were identified in
      DPC4268. Significance and Impact of the Study: L. DPC4268 is a vitally important commercial
      strain used in the manufacture of Cheddar cheese. The generation of a plasmid-free derivative
      may provide an important backbone strain as a basis for future strain improvement purposes.
AU  - Trotter M
AU  - Ross RP
AU  - Fitzgerald GF
AU  - Coffey A
PT  - Journal Article
TA  - J. Appl. Microbiol.
JT  - J. Appl. Microbiol.
SO  - J. Appl. Microbiol. 2002 93: 134-143.

PMID- 26918656
VI  - 18
DP  - 2016
TI  - Adaptive processes of Staphylococcus aureus isolates during the progression from acute to chronic bone and joint infections in patients.
PG  - 1405-1414
AB  - Staphylococcus aureus bone and joint infection (BJI) is associated with significant rates of
      chronicity and relapse. In this study, we investigated how S. aureus is able to adapt to the
      human environment by comparing isolates from single patients with persisting or relapsing BJIs
      that were recovered during the initial and recurrent BJI episodes. In vitro and in vivo assays
      and whole-genome sequencing analyses revealed that the recurrent isolates induced a reduced
      inflammatory response, formed more biofilm, persisted longer in the intracellular compartments
      of host bone cells, were less cytotoxic and induced less mortality in a mouse infection model
      compared to the initial isolates despite the lack of significant changes at the genomic level.
      These findings suggest that S. aureus BJI chronicization is associated with an in vivo
      bacterial phenotypical adaptation that leads to decreased virulence and host immune escape,
      which is linked to increased intraosteoblastic persistence and biofilm formation. This article
      is protected by copyright. All rights reserved.
AU  - Trouillet-Assant S et al
PT  - Journal Article
TA  - Cell. Microbiol.
JT  - Cell. Microbiol.
SO  - Cell. Microbiol. 2016 18: 1405-1414.

PMID- 19796624
VI  - 5
DP  - 2009
TI  - DNA Methyltransferase 1 Is Essential for and Uniquely Regulates Hematopoietic Stem and Progenitor Cells.
PG  - 442-449
AB  - DNA methylation is essential for development and in diverse biological processes. The DNA
      methyltransferase Dnmt1 maintains parental cell
      methylation patterns on daughter DNA strands in mitotic cells; however,
      the precise role of Dnmt1 in regulation of quiescent adult stem cells
      is not known. To examine the role of Dnmt1 in adult hematopoietic stem
      cells (HSCs), we conditionally disrupted Dnmt1 in the hematopoietic
      system. Defects were observed in Dnmt1 deficient HSC self-renewal,
      niche retention, and in the ability of Dnmt1-deficient HSCs to give
      rise to multilineage hematopoiesis. Loss of Dnmt1 also had specific
      impact on myeloid progenitor cells, causing enhanced cell cycling and
      inappropriate expression of mature lineage genes. Dnmt1 regulates
      distinct patterns of methylation and expression of discrete gene
      families in long-term HSCs and multipotent and lineage-restricted
      progenitors, suggesting that Dnmt1 differentially controls these
      populations. These findings establish a unique and critical role for
      Dnmt1 in the primitive hematopoietic compartment.
AU  - Trowbridge JJ
AU  - Snow JW
AU  - Kim J
AU  - Orkin SH
PT  - Journal Article
TA  - Cell Stem Cell
JT  - Cell Stem Cell
SO  - Cell Stem Cell 2009 5: 442-449.

PMID- 27738027
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of NC983, a Live Attenuated Strain of Salmonella enterica Serovar Typhimurium.
PG  - e01074-16
AB  - Foodborne infections caused by Salmonella enterica serovars are a significant problem
      worldwide. Presented here is the genome sequence of the nontyphoidal S.
      enterica serovar Typhimurium mutant strain NC983, a potential vaccine candidate.
AU  - Troxell B
AU  - Fink RC
AU  - Dickey AN
AU  - Scholl EH
AU  - Hassan HM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01074-16.

PMID- 27881550
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Magnetovibrio blakemorei Strain MV-1, a Marine Vibrioid  Magnetotactic Bacterium.
PG  - e01330-16
AB  - We report here the genome sequence of Magnetovibrio blakemorei MV-1, a marine vibrioid
      magnetotactic bacterium with a single polar flagellum. The current
      assembly consists of 91 contigs with a combined size of 3,638,804 bp (54.3% G+C
      content). This genome allows for further investigations of the molecular
      biomineralization mechanisms of magnetosome formation.
AU  - Trubitsyn D
AU  - Abreu F
AU  - Ward FB
AU  - Taylor T
AU  - Hattori M
AU  - Kondo S
AU  - Trivedi U
AU  - Staniland S
AU  - Lins U
AU  - Bazylinski DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01330-16.

PMID- 25081260
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Obligately Alkaliphilic Sulfate-Reducing Bacterium Desulfonatronum thiodismutans Strain MLF1.
PG  - e00741-14
AB  - Desulfonatronum thiodismutans strain MLF1, an alkaliphilic bacterium capable of sulfate
      reduction, was isolated from Mono Lake, California. Here we report the
      3.92-Mb draft genome sequence comprising 34 contigs and some results of its
      automated annotation. These data will improve our knowledge of mechanisms by
      which bacteria withstand extreme environments.
AU  - Trubitsyn D
AU  - Geurink C
AU  - Pikuta E
AU  - Lefevre CT
AU  - McShan WM
AU  - Gillaspy AF
AU  - Bazylinski DA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00741-14.

PMID- Not carried by PubMed...
VI  - 7
DP  - 1990
TI  - Purification of SmaI restriction enzyme.
PG  - 326-332
AB  - SmaI restriction endonuclease produced by Serratia marcescens, has been
      purified in our laboratory using PEG-6000 precipitation and ion exchange
      chromatography in Phosphocellulose (P-11 Whatman).  We have obtained by this
      way a final enzymatic preparation with a specific activity of 2972 U/mg of
      total protein and 35% of global recovery of the process, that may be used in
      cloning and other recombinant DNA techniques.
AU  - Trujillo LE
AU  - Brito JE
AU  - Reyes G
AU  - Garcia O
PT  - Journal Article
TA  - Biotecnol. Apl.
JT  - Biotecnol. Apl.
SO  - Biotecnol. Apl. 1990 7: 326-332.

PMID- 8783903
VI  - 38
DP  - 1996
TI  - Correspondence between radioactive and functional methods in the quality control of DNA restriction and modifying enzymes.
PG  - 31-37
AB  - We evaluated the use of two radiolabeled lambda DNA/HpaII substrates to detect 5'-3' single
      and double stranded DNA dependent exonuclease and phosphatase activities found as contaminants
      in restriction and modifying enzyme preparations.  Looking for the meaning of the radioactive
      assays results in a real cloning experience, we performed a cloning simulation assay using the
      same conditions established for the radioactive assay (enzyme units and pmols of DNA ends).
      As a result, we found that for degradation percentages of the radioactive DNA substrate per
      enzyme unit below 0.5, the false positives in the cloning simulation assay were less than 5%.
      This conditions could ensure a good performance of the enzyme preparations for cloning
      experiments.  Finally, we described the use of the radiolabeled [gamma 32P] ATP lambda HpaII
      DNA substrate to detect 5'-3' single stranded DNA dependent exonuclease and phosphatase
      contaminating activities in some critical steps of the purification process of the restriction
      enzyme KpnI.
AU  - Trujillo LE
AU  - Pupo E
AU  - Miranda F
AU  - Perez E
AU  - Gonzalez E
PT  - Journal Article
TA  - Rev. Latinoam. Microbiol.
JT  - Rev. Latinoam. Microbiol.
SO  - Rev. Latinoam. Microbiol. 1996 38: 31-37.

PMID- Not carried by PubMed...
VI  - 7
DP  - 1990
TI  - Purification of NciI restriction endonuclease.
PG  - 320-325
AB  - NciI restriction endonuclease isolated from Neisseria cinerea, has been
      purified in our laboratory using affinity and ion exchange chromatography.  We
      have obtained an enzymatic preparation with a specific activity of 20,000 U/mg
      of proteins and 67.2% of global recovery of the process, that may be used in
      different genetic engineering techniques.
AU  - Trujillo LE
AU  - Reyes G
AU  - Bayolo E
AU  - Vazquez MM
AU  - Garcia O
PT  - Journal Article
TA  - Biotecnol. Apl.
JT  - Biotecnol. Apl.
SO  - Biotecnol. Apl. 1990 7: 320-325.

PMID- 28827753
VI  - 7
DP  - 2017
TI  - Restriction and modification of deoxyarchaeosine (dG+)-containing phage 9 g DNA.
PG  - 8348
AB  - E. coli phage 9 g contains the modified base deoxyarchaeosine (dG+) in its genome. The phage
      encodes its own primase, DNA ligase, DNA polymerase, and
      enzymes necessary to synthesize and incorporate dG+. Here we report phage 9 g DNA
      sensitivity to >200 Type II restriction endonucleases (REases). Among the REases
      tested approximately 29% generated complete or partial digestions, while the
      remaining 71% displayed resistance to restriction. Phage 9 g restriction
      fragments can be degraded by DNA exonucleases or ligated by T3 and T4 DNA
      ligases. In addition, we examined a number of cytosine and adenine
      methyltransferases to generate double base modifications. M.AluI, M.CviPI,
      M.HhaI, and M.EcoGII were able to introduce 5mC or N6mA into 9 g DNA as confirmed
      by partial resistance to restriction and by liquid chromatography-mass
      spectrometry. A number of wild-type E. coli bacteria restricted phage 9 g,
      indicating natural restriction barriers exist in some strains. A BlastP search of
      GenBank sequences revealed five glutamine amidotransferase-QueC homologs in
      Enterobacteria and Pseudomonas phage, and distant homologs in other phage and
      bacterial genomes, suggesting that dG+ is not a rare modification. We also mapped
      phage 9 g DNA packaging (pac) site containing two 21-bp direct repeats and a
      major terminase cleavage site in the phage genome.
AU  - Tsai R
AU  - Correa IR
AU  - Xu MY
AU  - Xu SY
PT  - Journal Article
TA  - Sci. Rep.
JT  - Sci. Rep.
SO  - Sci. Rep. 2017 7: 8348.

PMID- 2697751
VI  - 135
DP  - 1989
TI  - Transformation in restriction-deficient Salmonella typhimurium LT2.
PG  - 2561-2567
AB  - Stable restriction-deficient, modification-proficient galE (JR501) and F'galE+
      (JR502) strains of Salmonella typhimurium were constructed and the effects of
      restriction on transformation by plasmid pBR322 were tested.  Several factors
      which affect transformation efficiency were systematically examined to
      determine optimum transformation conditions and a simplified method is
      presented.
AU  - Tsai SP
AU  - Hartin RJ
AU  - Ryu J-I
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1989 135: 2561-2567.

PMID- 26861018
VI  - 7
DP  - 2016
TI  - Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing.
PG  - e01948-15
AB  - Deep metagenomic shotgun sequencing has emerged as a powerful tool to interrogate composition
      and function of complex microbial communities. Computational approaches to assemble genome
      fragments have been demonstrated to be an effective tool for de novo reconstruction of genomes
      from these communities. However, the resultant "genomes" are typically fragmented and
      incomplete due to the limited ability of short-read sequence data to assemble complex or
      low-coverage regions.
      Here, we use single-molecule, real-time (SMRT) sequencing to reconstruct a high-quality,
      closed genome of a previously uncharacterized Corynebacterium simulans and its companion
      bacteriophage from a skin metagenomic sample.
      Considerable improvement in assembly quality occurs in hybrid approaches incorporating
      short-read data, with even relatively small amounts of long-read data being sufficient to
      improve metagenome reconstruction. Using short-read data to evaluate strain variation of this
      C. simulans in its skin community at single-nucleotide resolution, we observed a dominant C.
      simulans strain with moderate allelic heterozygosity throughout the population. We demonstrate
      the utility of SMRT sequencing and hybrid approaches in metagenome quantitation,
      reconstruction, and annotation. IMPORTANCE: The species comprising a microbial community are
      often difficult to deconvolute due to technical limitations inherent to most short-read
      sequencing technologies. Here, we leverage new advances in sequencing technology,
      single-molecule sequencing, to significantly improve reconstruction of a complex human skin
      microbial community. With this long-read technology, we were able to reconstruct and annotate
      a closed, high-quality genome of a previously uncharacterized skin species. We demonstrate
      that hybrid approaches with short-read technology are sufficiently powerful to reconstruct
      even single-nucleotide polymorphism level variation of species in this a community.
AU  - Tsai YC
AU  - Conlan S
AU  - Deming C
AU  - Segre JA
AU  - Kong HH
AU  - Korlach J
AU  - Oh J
PT  - Journal Article
TA  - MBio
JT  - MBio
SO  - MBio 2016 7: e01948-15.

PMID- 28912320
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Spiroplasma corruscae EC-1T (DSM 19793), a Bacterium  Isolated from a Lampyrid Beetle (Ellychnia corrusca).
PG  - e00964-17
AB  - Spiroplasma corruscae EC-1T (DSM 19793) was isolated from the gut of a lampryid beetle
      (Ellychnia corrusca) collected in Beltsville, MD, USA, in 1983. Here, we
      report the complete genome sequence of this bacterium to facilitate the
      investigation of its biology and the comparative genomics among Spiroplasma
      species.
AU  - Tsai YM
AU  - Lo WS
AU  - Kuo CH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00964-17.

PMID- 29724836
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Spiroplasma monobiae MQ-1(T) (ATCC 33825), a Bacterium Isolated from the Vespid Wasp (Monobia quadridens).
PG  - e00347-18
AB  - Spiroplasma monobiae MQ-1(T) (ATCC 33825) was isolated from the hemolymph of an adult vespid
      wasp (Monobia quadridens) collected in Maryland. Here, we report the
      complete genome sequence of this bacterium to facilitate the investigation of its
      biology and the comparative genomics among Spiroplasma species.
AU  - Tsai YM
AU  - Lo WS
AU  - Wu PS
AU  - Cho ST
AU  - Kuo CH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00347-18.

PMID- 29674553
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Spiroplasma floricola 23-6(T) (ATCC 29989), a Bacterium Isolated from a Tulip Tree (Liriodendron tulipifera L.).
PG  - e00302-18
AB  - Spiroplasma floricola 23-6(T) (ATCC 29989) was isolated from the flower surface of a tulip
      tree (Liriodendron tulipifera L.). Here, we report the complete genome
      sequence of this bacterium to facilitate the investigation of its biology and the
      comparative genomics among Spiroplasma species.
AU  - Tsai YM
AU  - Wu PS
AU  - Lo WS
AU  - Kuo CH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00302-18.

PMID- 27542933
VI  - 82
DP  - 2016
TI  - Borneol dehydrogenase from Pseudomonas sp. TCU-HL1 catalyzes the oxidation of (+)-borneol and its isomers to camphor.
PG  - 6378-6385
AB  - Most plant-produced monoterpenes can be degraded by soil microorganisms. Borneol is a plant
      terpene which is widely used in traditional Chinese medicine. Neither microbial borneol
      dehydrogenase (BDH) nor a microbial borneol degradation pathway has been reported previously.
      One borneol-degrading strain, Pseudomonas sp. TCU-HL1, was isolated by our group. Its genome
      was sequenced and annotated. The genome of TCU-HL1 consists of a 6.2-Mbp circular chromosome
      and one circular plasmid, pTHL1 (12.6 kbp). Our results suggest that borneol is first
      converted into camphor by BDH in TCU-HL1, and further decomposed through a camphor degradation
      pathway. The recombinant BDH was produced in the form of inclusion bodies. The apparent Km
      values of refolded recombinant BDH for (+)-borneol and (-)-borneol are 0.20 +/- 0.01 and 0.16
      +/- 0.01 mM, and the kcat values for (+)-borneol and (-)-borneol are 0.75 +/- 0.01, and 0.53
      +/- 0.01 sec-1, respectively. Two plant BDH genes have been previously reported. The kcat and
      kcat/Km values of lavender's BDH are about 1800-fold and 500-fold lower than those of
      TCU-HL1. IMPORTANCE: The degradation of borneol in a soil microorganism through a camphor
      degradation pathway was first shown in this study. This is also the first microbial borneol
      dehydrogenase reported. The kcat and kcat/Km values of lavender's BDH are about 1800-fold and
      500-fold lower than those of TCU-HL1. This indigenous isolated borneol and camphor-degrading
      strain TCU-HL1 reminds us of the time one hundred years ago when Taiwan was the major producer
      of natural camphor in the world.
AU  - Tsang HL
AU  - Huang JL
AU  - Lin YH
AU  - Huang KF
AU  - Lu PL
AU  - Lin GH
AU  - Khine AA
AU  - Hu A
AU  - Chen HP
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2016 82: 6378-6385.

PMID- 2021649
VI  - 30
DP  - 1991
TI  - Optically detected magnetic resonance study of the interaction of an Arsenic(III) derivative of cacodylic acid with EcoRI methyl transferase.
PG  - 4565-4572
AB  - The interaction of the enzyme Escherichia coli RI methyl transferase
      (methylase) with an arsenic(III) derivative of cacodylic acid has been
      investigated by optical detection of triplet-state magnetic resonance (ODMR)
      spectroscopy in zero applied magnet field.  The reactive derivative (CH3)2AsSR
      is formed by the reduction of cacodylate by a thiol.  The As(III) derivative
      binds to the enzyme by mercaptide exchange with a cysteine (Cys) residue
      located close to a tryptophan (Trp) site.  The arsenical binding selectively
      induces an external heavy-atom effect, perturbing the nearby Trp residue in the
      enzyme.  Zero-field splittings (ZFS) and total decay rate constants of the
      individual triplet-state sublevels of the Trp residue in the presence and
      absence of perturbation by As(III) have been determined.  The perturbed Trp
      shows a large reduction in the overall decay lifetime compared with unperturbed
      Trp residue, exhibiting a high selectivity for the Tx sublevel.  This
      selectivity suggests that the As atom lies in the xz plane of the principal
      magnetic axis system of Trp, but not directly along the z (out-of-plane) axis.
      The accessibility of this enzyme binding site to the arsenical is decreased
      upon forming a ternary complex of methylase with sinefungin and a DNA oligomer,
      d[GCGAA(BrU)(BrU)CGC], containing two 5-bromouracil (BrU) bases in place of
      thymine within the hexadeoxynucleotide recognition sequence.  This result
      indicates that the arsenical binding site in methylase which produces the Trp
      heavy-atom effect is protected from this ligand by ternary complex formation or
      the enzyme undergoes a conformation change, removing the Cys from the Trp site.
      This protection is also observed in fluorescence quenching experiments.  The
      As(III) reagent, upon binding to methylase, quenches the Trp fluorescence by
      46%.  When the ternary complex is formed, the quenching of Trp fluorescence is
      only 17%.  A binding constant for the arsenical to the high-affinity enzyme
      site was obtained which is at least 27 times that of binding to a free
      sulfhydryl residue.  The addition of a 1:1 molar ratio of the arsenical to
      methylase did not affect the activity of the enzyme, but incubation with excess
      arsenical quenches the activity, suggesting that the high-affinity Cys residue
      is not involved in the DNA methylation process.  In the ternary complex
      methylase-sinefungin-DNA, no heavy-atom perturbation of the two Trp residues in
      the enzyme by BrU was observed, demonstrating that Trp residues are not
      involved in close-range interactions with the two heavy-atom-derivatized
      nucleic acid bases.  A similar result was observed previously with the
      analogous E. coli RI endonuclease-decanucleotide complex [John, N.-I.,
      Casas-Finet, J.R., Maki, A.H., & Modrich, P. (1988) Biochim. Biophys. Acta 949,
      189-194].
AU  - Tsao DHH
AU  - Maki AH
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1991 30: 4565-4572.

PMID- 25395632
VI  - 2
DP  - 2014
TI  - Exploring the Genome of Cheese Starter Lactic Acid Bacterium Lactococcus lactis subsp. lactis CECT 4433.
PG  - e01142-14
AB  - Here, we present the draft genome sequences of Lactococcus lactis subsp. lactis CECT 4433, a
      cheese fermentation starter strain. The genome provides further
      insight into the genomic plasticity, biocomplexity (including gene strain
      specifics), and evolution of these genera.
AU  - Tschoeke DA
AU  - Moreira AP
AU  - Chimetto TLA
AU  - de Mesquita MM
AU  - Gregoracci GB
AU  - Gomez-Gil B
AU  - Valle R
AU  - Thompson CC
AU  - Thompson FL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01142-14.

PMID- 20047907
VI  - 192
DP  - 2010
TI  - Complete Genome Sequence of Staphylococcus lugdunensis strain HKU09-01.
PG  - 1471-1472
AB  - Staphylococcus lugdunensis is a member of the coagulase-negative staphylococci and commonly
      found as part of the human skin flora. It is a significant cause of catheter-related
      bacteremia, and also causes serious infections like native valve endocarditis in previously
      healthy individuals. We report the complete genome sequence of this medically important
      bacterium.
AU  - Tse H
AU  - Tsoi HW
AU  - Leung SP
AU  - Lau SK
AU  - Woo PC
AU  - Yuen KY
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 1471-1472.

PMID- 21278300
VI  - 193
DP  - 2011
TI  - Complete genome sequence of the veterinary pathogen Staphylococcus pseudintermedius strain HKU10-03 isolated from a case of canine pyoderma.
PG  - 1783-1784
AB  - Staphylococcus pseudintermedius is a member of the coagulase-positive staphylococci, and is
      the commonest cause of canine pyoderma. We report the first genome sequence of S.
      pseudintermedius, which showed the presence of numerous virulence factors akin to the related
      human pathogen Staphylococcus aureus.
AU  - Tse H
AU  - Tsoi HW
AU  - Leung SP
AU  - Urquhart IJ
AU  - Lau SK
AU  - Woo PC
AU  - Yuen KY
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 1783-1784.

PMID- 17846142
VI  - 51
DP  - 2007
TI  - Tn6001, a Transposon-Like Element Containing the blaVIM-3-Harboring Integron In450.
PG  - 4187-4190
AB  - We describe the structure of a transposon-like element named Tn6001, which
      contains a bla(VIM-3)-harboring integron In450, which was derived from a
      multidrug-resistant Pseudomonas aeruginosa clinical isolate in Taiwan. The
      transposon backbone structure is most closely related to those of Tn1404*
      and Tn1403. Tn6001 was inserted into the chromosome of the clinical
      isolate.
AU  - Tseng SP
AU  - Hsueh PR
AU  - Tsai JC
AU  - Teng LJ
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2007 51: 4187-4190.

PMID- 15716310
VI  - 33
DP  - 2005
TI  - A new computational method for the detection of horizontal gene transfer events.
PG  - 922-933
AB  - In recent years, the increase in the amounts of available genomic data has made it easier to
      appreciate the extent by which organisms increase
      their genetic diversity through horizontally transferred genetic
      material. Such transfers have the potential to give rise to extremely
      dynamic genomes where a significant proportion of their coding DNA has
      been contributed by external sources. Because of the impact of these
      horizontal transfers on the ecological and pathogenic character of the
      recipient organisms, methods are continuously sought that are able to
      computationally determine which of the genes of a given genome are
      products of transfer events. In this paper, we introduce and discuss a
      novel computational method for identifying horizontal transfers that
      relies on a gene's nucleotide composition and obviates the need for
      knowledge of codon boundaries. In addition to being applicable to
      individual genes, the method can be easily extended to the case of
      clusters of horizontally transferred genes. With the help of an
      extensive and carefully designed set of experiments on 123 archaeal and
      bacterial genomes, we demonstrate that the new method exhibits
      significant improvement in sensitivity when compared to previously
      published approaches. In fact, it achieves an average relative
      improvement across genomes of between 11 and 41% compared to the Codon
      Adaptation Index method in distinguishing native from foreign genes.
      Our method's horizontal gene transfer predictions for 123 microbial
      genomes are available online at http://cbcsrv.watson.ibm.com/HGT/.
AU  - Tsirigos A
AU  - Rigoutsos I
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2005 33: 922-933.

PMID- 23118449
VI  - 86
DP  - 2012
TI  - Complete Genome Sequence of the Novel Escherichia coli Phage phAPEC8.
PG  - 13117-13118
AB  - Bacteriophage phAPEC8 is an Escherichia coli-infecting myovirus, isolated on an
      avian pathogenic Escherichia coli (APEC) strain. APEC strains cause
      colibacillosis in poultry, resulting in high mortality levels and important
      economic losses. Genomic analysis of the 147,737-bp double-stranded DNA phAPEC8
      genome revealed that 53% of the 269 encoded proteins are unique to this phage.
      Its closest relatives include the Salmonella phage PVP-SE1 and the coliphage rv5,
      with 19% and 18% similar proteins, respectively. As such, phAPEC8 represents a
      novel, phylogenetically distinct clade within the Myoviridae, with molecular
      properties suitable for phage therapy applications.
AU  - Tsonos J
AU  - Adriaenssens EM
AU  - Klumpp J
AU  - Hernalsteens JP
AU  - Lavigne R
AU  - De Greve H
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 2012 86: 13117-13118.

PMID- 29167254
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Arsenic-Resistant Bacterium Brevundimonas denitrificans TAR-002T.
PG  - e01326-17
AB  - We report the 3.2-Mb draft genome sequence of Brevundimonas denitrificans strain  TAR-002T,
      isolated from deep-sea floor sediment. The draft genome sequence of
      strain TAR-002T consists of 3,231,216 bp in 44 contigs, with a G+C content of
      68.47%, 3,866 potential coding sequences (CDSs), 3 rRNAs, and 45 tRNAs.
AU  - Tsubouchi T
AU  - Kaneko Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01326-17.

PMID- 26021921
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Aneurinibacillus tyrosinisolvens LL-002T, Which Possesses Some Pseudouridine Synthases.
PG  - e00529-15
AB  - We report the 5.7-Mb draft genome sequence of Aneurinibacillus tyrosinisolvens strain
      LL-002(T), isolated from organic- and methane-rich sea sediments. The
      draft genome sequence of strain LL-002(T) consists of 5,693,818 bp in 136
      contigs, with a G+C content of 44.5%, 5,946 potential coding sequences (CDS), 2
      rRNAs, and 39 tRNAs.
AU  - Tsubouchi T
AU  - Nishi S
AU  - Maruyama T
AU  - Hatada Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00529-15.

PMID- 24136847
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Dimorphic Prosthecate Bacterium Brevundimonas abyssalis TAR-001T.
PG  - e00826-13
AB  - We report the 3.0-Mb draft genome sequence of Brevundimonas abyssalis strain TAR-001(T),
      isolated from deep-sea floor sediment. The draft genome sequence of
      strain TAR-001(T) consists of 2,979,700 bp in 128 contigs, with a G+C content of
      68.2%, 2,946 potential coding sequences (CDS), 3 rRNAs, and 41 tRNAs.
AU  - Tsubouchi T
AU  - Nishi S
AU  - Usui K
AU  - Shimane Y
AU  - Takaki Y
AU  - Maruyama T
AU  - Hatada Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00826-13.

PMID- 26472838
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Lactobacillus gorillae Strain KZ01T, Isolated from a Western Lowland Gorilla.
PG  - e01196-15
AB  - Here, we report the draft genome sequence of Lactobacillus gorillae strain KZ01(T) isolated
      from a western lowland gorilla (Gorilla gorilla gorilla). This genome sequence will be helpful
      for the comparative genomics between human and nonhuman primate-associated Lactobacillus.
AU  - Tsuchida S
AU  - Nezuo M
AU  - Tsukahara M
AU  - Ogura Y
AU  - Hayashi T
AU  - Ushida K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01196-15.

PMID- 14576333
VI  - 31
DP  - 2003
TI  - One step assembly of multiple DNA fragments with a designed order and orientation in Bacillus subtilis plasmid.
PG  - e133
AB  - A universal method to reconstitute sets of genes was developed. Owing to the intrinsic nature
      of the plasmid establishment mechanism in Bacillus
      subtilis, the assembly of five antibiotic resistance genes with a defined
      order and orientation was achieved. These five fragments and the plasmid
      have three-base protruding sequences at both ends. The protruding
      sequences are designed so that each fragment is ligated once in a row
      according to the pairing. Ligation by T4 DNA ligase in the presence of 150
      mM NaCl and 10% polyethylene glycol at 37 degrees C yielded high molecular
      tandem repeat linear form DNA. This multimeric form of DNA was
      preferentially used for plasmid establishment in B.subtilis. The method,
      referred to as Ordered Gene Assembly in B.subtilis (OGAB), allows for the
      design of multiple fragments with very high efficiency and great fidelity.
AU  - Tsuge K
AU  - Matsui K
AU  - Itaya M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2003 31: e133.

PMID- 29097456
VI  - 5
DP  - 2017
TI  - Genome Sequences of the Mycobacterium tuberculosis H37Rv-ptkA Deletion Mutant and Its Parental Strain.
PG  - e01156-17
AB  - Mycobacterium tuberculosis, the etiological agent of tuberculosis, is one of the  most
      devastating infectious agents in the world. Here, we report the draft genome
      sequences of the M. tuberculosis protein tyrosine kinase (ptkA) deletion mutant
      and its parental strain H37Rv, which are used in genetic studies and for drug
      discovery.
AU  - Tsui CKM
AU  - Wong D
AU  - Narula G
AU  - Gardy JL
AU  - Hsiao WWH
AU  - Av-Gay Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01156-17.

PMID- 2836816
VI  - 16
DP  - 1988
TI  - RspX I:  a new restriction endonuclease with a recognition sequence of 5'T^CATGA3'.
PG  - 4178
AB  - A new TypeII restriction endonuclease, RspXI, was purified from a Rhodococcus
      species isolated in our laboratory.  The Rhodococcus species grows well at 30C
      in the following medium:  0.8% glucose, 0.8% yeast extract and 2% malt extract
      at pH 7.2.  The yield of cell is 5 g/l.  RspXI recognizes the sequence
      5'TCATGA3' and cleaves between T and C giving a four base 5' overhang.  An
      enzyme BspH1 reported recently has the same cutting site.  (1) the enzyme was
      purified by the following chromatographic steps:   1) phosphocellulose 2)
      biorex-70 3) S-200.  It was judged to be essentially free of contaminating
      nuclease activity.  After 10 fold overdigestion on lambda DNA greater than 95%
      of the DNA fragments can be ligated and greater than 95% of the ligated DNA can
      be recut by RspXI.  At 37C, the optimal conditions for RspXI activity are:  10
      mM Tris, pH 7.5, 50 mM NaCl, 50 mM KCl and 10 mM MgCl2.  KCl is essential for
      optimal activity.  The number of fragments generated by digestion with RspXI on
      the following DNAs are:  lambda, 9; pBR322, 4; phiX174, 3; Adeno 2, 4 and
      M13mp18, 1 (Fig. 1).  A computer search with Microgenie(TM) (Beckman Inst.
      Inc.) suggested a recognition sequence of 5'TCATGA3'.  The cleavage site was
      determined as follows:  pBR322 DNA was digested with RspXI.  DNA fragments were
      then end-filled with DNA polymerase (Klenow fragment).  The resulting blunt-end
      fragments were ligated into SmaI site of pUC18.  The recombinant plasmids were
      transformed into E. Coli K803.  Ampicillin resistant and Lac- clones were
      identified and plasmid DNAs were prepared from these clones.  The sequence of
      the DNA fragment cloned into SmaI was determined by dideoxy Chain-termination
      method (2).  The sequence over the cloning site is CATGAGCCC on one gel (not
      shown) and is CATGAGCGT on the other gel.  This confirms that the cutting site
      is between bases T and C.
AU  - Tsui W-C
AU  - Elgar G
AU  - Merrill C
AU  - Maunders M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1988 16: 4178.

PMID- 28360164
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Caenibacillus caldisaponilyticus B157T, a Thermophilic and Phospholipase-Producing Bacterium Isolated from Acidulocompost.
PG  - e00089-17
AB  - Caenibacillus caldisaponilyticus B157T (= NBRC 111400T = DSM 101100T), in the family
      Sporolactobacillaceae, was isolated from acidulocompost as a thermophilic
      and phospholipid-degrading bacterium. Here, we report the 3.36-Mb draft genome
      sequence, with a G+C content of 51.8%, to provide the genetic information coding
      for phospholipases.
AU  - Tsujimoto Y
AU  - Saito R
AU  - Sahara T
AU  - Kimura N
AU  - Tsuruoka N
AU  - Shigeri Y
AU  - Watanabe K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00089-17.

PMID- 24316126
VI  - 535
DP  - 2014
TI  - Genome-guided analysis of transformation efficiency and carbon dioxide assimilation by Moorella thermoacetica Y72.
PG  - 150-155
AB  - We determined a draft genome sequence for Moorella thermoacetica strain Y72, a
      syngas-assimilating bacterium with high transformation efficiency. This strain was confirmed
      to be M. thermoacetica because its overall genome sequence characteristics were similar to
      those of M. thermoacetica strain ATCC39073. Y72 was confirmed to carry all the genes encoding
      the enzymes in the reductive acetyl-CoA pathway, with very high similarities to those of
      ATCC39073. In addition, it was confirmed to assimilate carbon dioxide using this pathway.
      However, although both Y72 and ATCC39073 carried common genes encoding several enzymes related
      to the reductive tricarboxylic acid (TCA) cycle, their gene sets were different. Our results
      suggested that the reason for higher transformation efficiency in Y72 than that in ATC09073, a
      reference strain of M. thermoacetica, may be that Y72 possesses only 2 sets of genes
      considered to be involved in a restriction-modification system, which was half of those found
      in ATCC39073.
AU  - Tsukahara K
AU  - Kita A
AU  - Nakashimada Y
AU  - Hoshino T
AU  - Murakami K
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 2014 535: 150-155.

PMID- 8240378
VI  - 196
DP  - 1993
TI  - Inhibition of restriction endonuclease cleavage site via triple helix formation by homopyrimidine phosphorothioate oligonucleotides.
PG  - 990-996
AB  - The ability of pyrimidine rich oligonucleotide phosphorothioate to form stable triple helical
      structures with the sequence containing the recognition site for the class IIS restriction
      enzyme Ksp632I was examined. First, we synthesized double strand oligonucleotides
      corresponding to the SV40 sites and studied their interaction with homopyrimidine
      oligodeoxyribonucleotides including replacement of the other chain either with PS group
      (SO-ODNs) in the second nucleotide position (from 5'-terminus) and end capped with the PS
      group at both 3'- and 5'-ends (S2O-ODNs). The resulting perfect DNA triplexes were detected
      by gel-mobility shift. The phosphorothioate oligonucleotide analogues (SO-ODNs) and (S2O-ODNs)
      were shown to inhibit enzymatic cleavage under conditions that allow for triple helix
      formation. Inhibition is sequence-specific and occurs in the micromolar concentration range.
      Of particular interest is the Sp-phosphorothioate analogue (Sp-SO-ODNs) which inhibited the
      endonuclease more than the other phosphorothioate oligonucleotide analogues (Rp-SO-ODNs or
      S2O-ODNs).
AU  - Tsukahara S
AU  - Kim S-G
AU  - Takaku H
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1993 196: 990-996.

PMID- Not carried by PubMed...
VI  - 13
DP  - 1994
TI  - Inhibition of restriction enzyme Ksp632I via triple helix formation by phosphorothioate oligonucleotides.
PG  - 1617-1626
AB  - The ability of pyrimidine-rich oligonucleotide phosphorothioate to form stable triple helical
      structures with the sequence containing the recognition site for the class II-S restriction
      enzyme Ksp632I was examined. First, we prepared double strand oligonucleotides corresponding
      to the major groove of SV40 DNA at 17 base pair homopurine-homopyrimidine sequences, and
      studied their interaction with homopyrimidine oligodeoxyribonucleotides including replacement
      of the PS group in the second nucleotide position from the 5'-terminus (SO-ODNs) and of the
      PS group at both the 3'- and 5'ends (S2O-ODNs). The resulting perfect DNA triplexes were
      detected by the gel-mobility shift. The phosphorothioate oligonucleotide analogues (SO-ODNs)
      and (S2O-ODNs) were shown to inhibit enzymatic cleavage under conditions that allow for triple
      helix formation. Inhibition is sequence-specific and occurs in the micromolar concentration
      range. Of particular interest is the Sp-phosphorothioate analogue (Sp-SO-ODNs) which inhibited
      endonuclease more than the other phosphorothioate oligonucleotide analogues (Rp-SO-ODNs or
      S2O-ODNs).
AU  - Tsukahara S
AU  - Yamakawa H
AU  - Takai K
AU  - Takaku H
PT  - Journal Article
TA  - Nucleosides and Nucleotides
JT  - Nucleosides and Nucleotides
SO  - Nucleosides and Nucleotides 1994 13: 1617-1626.

PMID- 26337894
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of the Bacteriochlorophyll b-Producing Photosynthetic Bacterium Blastochloris viridis.
PG  - e01006-15
AB  - We report the complete genome sequence of the purple photosynthetic bacterium Blastochloris
      viridis belonging to alpha-Proteobacteria. This is the first completed genome sequence of a
      phototroph producing bacteriochlorophyll b. The genome information will be useful for further
      analysis of the photosynthetic energy conversion system and bacteriochlorophyll pigment
      biosynthesis.
AU  - Tsukatani Y
AU  - Hirose Y
AU  - Harada J
AU  - Misawa N
AU  - Mori K
AU  - Inoue K
AU  - Tamiaki H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01006-15.

PMID- 16824199
VI  - 11
DP  - 2006
TI  - Maintenance of self-renewal ability of mouse embryonic stem cells in the absence of DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b.
PG  - 805-814
AB  - DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b cooperatively regulate cytosine methylation in
      CpG dinucleotides in mammalian genomes,
      providing an epigenetic basis for gene silencing and maintenance of
      genome integrity. Proper CpG methylation is required for the normal
      growth of various somatic cell types, indicating its essential role in
      the basic cellular function of mammalian cells. Previous studies using
      Dnmt1(-/-) or Dnmt3a(-/-)Dnmt3b(-/-) ES cells, however, have shown that
      undifferentiated embryonic stem (ES) cells can tolerate hypomethylation
      for their proliferation. In an attempt to investigate the effects of
      the complete loss of CpG DNA methyltransferase function, we established
      mouse ES cells lacking all three of these enzymes by gene targeting.
      Despite the absence of CpG methylation, as demonstrated by genome-wide
      methylation analysis, these triple knockout (TKO) ES cells grew
      robustly and maintained their undifferentiated characteristics. TKO ES
      cells retained pericentromeric heterochromatin domains marked with
      methylation at Lys9 of histone H3 and heterochromatin protein-1, and
      maintained their normal chromosome numbers. Our results indicate that
      ES cells can maintain stem cell properties and chromosomal stability in
      the absence of CpG methylation and CpG DNA methyltransferases.
AU  - Tsumura A
AU  - Hayakawa T
AU  - Kumaki Y
AU  - Takebayashi S
AU  - Sakaue M
AU  - Matsuoka C
AU  - Shimotohno K
AU  - Ishikawa F
AU  - Li E
AU  - Ueda HR
AU  - Nakayama J
AU  - Okano M
PT  - Journal Article
TA  - Genes Cells
JT  - Genes Cells
SO  - Genes Cells 2006 11: 805-814.

PMID- 16601000
VI  - 23
DP  - 2006
TI  - Evolution of paralogous genes: Reconstruction of genome rearrangements through comparison of multiple genomes within Staphylococcus aureus.
PG  - 1269-1285
AB  - Analysis of evolution of paralogous genes in a genome is central to our understanding of
      genome evolution. Comparison of closely related
      bacterial genomes, which has provided clues as to how genome sequences
      evolve under natural conditions, would help in such an analysis. With
      species Staphylococcus aureus, whole-genome sequences have been decoded
      for seven strains. We compared their DNA sequences to detect large
      genome polymorphisms and to deduce mechanisms of genome rearrangements
      that have formed each of them. We first compared strains N315 and Mu50,
      which make one of the most closely related strain pairs, at the
      single-nucleotide resolution to catalogue all the middle-sized (more
      than 10 bp) to large genome polymorphisms such as indels and
      substitutions. These polymorphisms include two paralogous gene sets,
      one in a tandem paralogue gene cluster for toxins in a genomic island
      and the other in a ribosomal RNA operon. We also focused on two other
      tandem paralogue gene clusters and type I restriction-modification (RM)
      genes on the genomic islands. Then we reconstructed rearrangement
      events responsible for these polymorphisms, in the paralogous genes and
      the others, with reference to the other five genomes. For the tandem
      paralogue gene clusters, we were able to infer sequences for homologous
      recombination generating the change in the repeat number. These
      sequences were conserved among the repeated paralogous units likely
      because of their functional importance. The sequence specificity (S)
      subunit of type I RM systems showed recombination, likely at the
      homology of a conserved region, between the two variable regions for
      sequence specificity. We also noticed novel alleles in the ribosomal
      RNA operons and suggested a role for illegitimate recombination in
      their formation. These results revealed importance of recombination
      involving long conserved sequence in the evolution of paralogous genes
      in the genome.
AU  - Tsuru T
AU  - Kawai M
AU  - Mizutani-Ui Y
AU  - Uchiyama I
AU  - Kobayashi I
PT  - Journal Article
TA  - Mol. Biol. Evol.
JT  - Mol. Biol. Evol.
SO  - Mol. Biol. Evol. 2006 23: 1269-1285.

PMID- 25523773
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Bradyrhizobium japonicum Is-34, Which Is Incompatible with Rj4 Genotype Soybeans.
PG  - e01316-14
AB  - We report here the draft genome sequence of Bradyrhizobium japonicum Is-34, which is
      incompatible with Rj4 genotype soybeans. A candidate gene involved in this
      incompatibility was found to be present in this genome.
AU  - Tsurumaru H
AU  - Kanesaki Y
AU  - Hashimoto S
AU  - Okizaki K
AU  - Yoshikawa H
AU  - Yamakawa T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01316-14.

PMID- 10612397
VI  - 99
DP  - 1999
TI  - Recognition of a TG mismatch: The crystal structure of very short patch repair endonuclease in complex with a DNA duplex.
PG  - 615-623
AB  - The crystal structure of very short patch repair (Vsr) endonuclease, in complex with Mg2+ and
      with duplex DNA containing a TG mismatch, has been determined at 2.3 A resolution. In E. coli,
      the enzyme recognizes a TG mismatched base pair, generated after spontaneous deamination of
      methylated cytosines, and cleaves the phosphate backbone on the 5' side of the thymine.
      Extensive interactions between the DNA and the protein characterize a novel recognition
      mechanism, where three aromatic residues intercalate from the major groove into the DNA to
      strikingly deform the base pair stacking. With the presence of a cleaved DNA intermediate in
      the active center, the structure of the Vsr/DNA complex provides detailed insights into the
      catalytic mechanism for endonuclease activity.
AU  - Tsutakawa SE
AU  - Jingami H
AU  - Morikawa K
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1999 99: 615-623.

PMID- 12760037
VI  - 65
DP  - 2000
TI  - New recognition mode for a TG mismatch: The atomic structure of a very short patch repair endonuclease-DNA complex.
PG  - 233-239
AB  - The crystal structure determination of the T4 endo-V pyrimidine photodimer DNA glycosylase
      provided the first direct view of DNA lesion recognition by a repair enzyme.  Similar damaged
      DNA recognition modes, involving nucleotide flipping, were observed in various base excision
      repair enzymes.  The implications of nucleotide flipping raised the new question of how DNA
      endonucleases other than base excision repair enzymes recognize mismatched base pairs.  The
      Escherichia coli very short patch repair endonuclease is a good target to address this
      question in terms of three-dimensional structures.  The Vsr endonuclease is involved in the
      initial reaction for the repair of mismatched TG base pairs generated through spontaneous
      deamination of methylated cytosine.  This enzyme recognizes a TG mismatch within the duplex
      5'CT(A/T)GG, where the second T forms the mismatch and all of the other bases are in standard
      Watson-Crick base pairing.  It catalyzes the cleavage at the 5' side of the thymine, leaving
      a 5' phosphate and a 3' hydroxyl at the termini.  The crystal structure of a truncated form
      of this endonuclease was determined at 1.8 angstroms resolution.  The protein was found to
      contain one structural zinc-binding module.  Unexpectedly, its overall topology resembles
      members of the type II restriction endonuclease family, although the catalytic center with
      critical histidines is distinct from those of restriction enzymes.  More recently, the crystal
      structure of Vsr endonuclease in complex with DNA has been determined at 2.3 angstroms
      resolution.  This endonuclease has been found to employ a novel mismatch base-pair recognition
      scheme that does not involve base flipping-out.  Extensive interactions between the DNA and
      the protein characterize the recognition mechanism, where three aromatic residues intercalate
      from the major groove into the DNA to strikingly deform the base-pair stacking.  An
      amino-terminal alpha-helix is accommodated into the expanded minor groove so that the amino
      acid side chains make additional contacts with the DNA duplexes.  With the presence of a
      cleaved DNA intermediate in the active center, the structure of the Vsr/DNA complex provides
      detailed insights into the catalytic mechanism for endonuclease activity.
AU  - Tsutakawa SE
AU  - Morikawa K
PT  - Journal Article
TA  - Cold Spring Harb. Symp. Quant. Biol.
JT  - Cold Spring Harb. Symp. Quant. Biol.
SO  - Cold Spring Harb. Symp. Quant. Biol. 2000 65: 233-239.

PMID- 11557809
VI  - 29
DP  - 2001
TI  - The structural basis of damaged DNA recognition and endonucleolytic cleavage for very short patch repair endonuclease.
PG  - 3775-3783
AB  - Endonucleases in DNA repair must be able to recognize damaged DNA as well as cleave the
      phosphodiester backbone. These functional prerequisites are manifested in very short patch
      repair (Vsr) endonuclease through a common endonuclease topology that has been tailored for
      recognition of TG mismatches. Structural and biochemical comparison with type II restriction
      enzymes illustrates how Vsr resembles these endonucleases in overall topology but also how Vsr
      diverges in terms of the detailed catalytic mechanism. A histidine and two metal-water
      clusters catalyze the phosphodiester cleavage. The mode of DNA damage recognition is also
      unique to Vsr. All other structurally characterized DNA damage-binding enzymes employ a
      nucleotide flipping mechanism for substrate recognition and for catalysis. Vsr, on the other
      hand, recognizes the TG mismatch as a wobble base pair and penetrates the DNA with three
      aromatic residues on one side of the mismatch. Thus, Vsr endonuclease provides important
      counterpoints in our understanding of endonucleolytic mechanisms and of damaged DNA
      recognition.
AU  - Tsutakawa SE
AU  - Morikawa K
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2001 29: 3775-3783.

PMID- 10360178
VI  - 3
DP  - 1999
TI  - Crystallographic and functional studies of very short patch repair endonuclease.
PG  - 621-628
AB  - Vsr endonuclease plays a crucial role in the repair of TG mismatched base pairs, which are
      generated by the spontaneous degradation of methylated cytidines; Vsr recognizes the
      mismatched base pair and cleaves the phosphate backbone 5' to the thymidine. We have
      determined the crystal structure of a truncated form of this endonuclease at 1.8 A resolution.
      The protein contains one structural zinc-binding module. Unexpectedly, its overall topology
      resembles members of the type II restriction endonuclease family. Subsequent mutational and
      biochemical analyses showed that certain elements in the catalytic site are also conserved.
      However, the identification of a critical histidine and evidence of an active site
      metal-binding coordination that is novel to endonucleases indicate a distinct catalytic
      mechanism.
AU  - Tsutakawa SE
AU  - Muto T
AU  - Kawate T
AU  - Jingami H
AU  - Kunishima N
AU  - Ariyoshi M
AU  - Kohda D
AU  - Nakagawa M
AU  - Morikawa K
PT  - Journal Article
TA  - Mol. Cell
JT  - Mol. Cell
SO  - Mol. Cell 1999 3: 621-628.

PMID- 2823510
VI  - 7
DP  - 1987
TI  - Development of rational schemes of the purification of restriction endonucleases.
PG  - 77-81
AB  - The work deals with the search for rational schemes of the purification of
      endonucleases, suitable for the isolation of different enzymes.  The scheme
      using the combination of Blue Sepharose and phosphocellulose has proved to be
      most universal.  The expediency of starting the purification of Haemophilus
      enzymes on Biogel A-0.5 m has been established.
AU  - Tsvetkova NV
PT  - Journal Article
TA  - Zh. Mikrobiol. Epidemiol. Immunobiol.
JT  - Zh. Mikrobiol. Epidemiol. Immunobiol.
SO  - Zh. Mikrobiol. Epidemiol. Immunobiol. 1987 7: 77-81.

PMID- 3037358
VI  - 0
DP  - 1987
TI  - Purification and determination of the substrate specificity of restriction endonuclease BcmI.
PG  - 19-22
AB  - The vigorous development of recombinant DNA and biotechnology is leading to
      growing requirements for varied restriction enzymes; therefore the search for
      new specific endonucleases remains urgent.  The restriction endonuclease BcmI
      has been isolated from a Bacillus strain.  It was purified by chromatography on
      blue Sepharose, phosphocellulose P-II, and heparin-Sepharose.  The new domestic
      adsorbent, orange Sepharose, can also be used for the purification of the
      restriction endonuclease.  The nucleotide sequence recognized by BcmI was
      determined by a comparison of the nature of the digestion of DNA by known
      enzymes and by the investigated enzyme.  The site of cleavage of the substrate
      was determined by direct methods on pBR322 DNA.  The aggregate of data obtained
      permits us to assert that the restriction endonuclease BcmI is a true
      isoschizomer of the restriction endonuclease ClaI.
AU  - Tsvetkova NV
AU  - Mileikovskaya MM
AU  - Gruber IM
AU  - Polyachenko VM
AU  - Butkus VV
AU  - Janulaitis A
AU  - Sudzhyuvene OF
AU  - Tarasov AP
PT  - Journal Article
TA  - Mol. Gen. Mikrobiol. Virusol.
JT  - Mol. Gen. Mikrobiol. Virusol.
SO  - Mol. Gen. Mikrobiol. Virusol. 1987 0: 19-22.

PMID- 
VI  - 0
DP  - 2011
TI  - Site-specific endonuclease activity of filamentous cyanobacterium Plectonema boryanum.
PG  - 146-149
AB  - The site-specific endonuclease PboI was isolated from the filamentous cyanobacterium
      Plectonema boryanum.  The purification included successive column chromatographies on
      DEAE-Toyopearl, phosphocellulose, and blue sepharose.  Purified enzyme recognizes and cleaves
      GGATCC-palindrome sequence is analogously to BamHI.  The enzyne belongs to type II restriction
      endonucleases.  The enzyme activity is optimal at a temperature 45oC, pH 7.5, and ionic
      stength 100mM.
AU  - Tsymbal NV
AU  - Samoilenko VA
AU  - Tovkach FI
PT  - Journal Article
TA  - Dopov. Nats. Akad. Nauk Ukr.
JT  - Dopov. Nats. Akad. Nauk Ukr.
SO  - Dopov. Nats. Akad. Nauk Ukr. 2011 0: 146-149.

PMID- 962085
VI  - 74
DP  - 1976
TI  - A reliable mapping method for sequence determination of oligodeoxyribonucleotides by mobility shift analysis.
PG  - 73-93
AB  - The method for sequence analysis of large oligodeoxyribonucleotides based on
      the characteristic mobility shifts of their sequential partial degradation
      products on two-dimensional homochromatography has been perfected using a large
      number of synthetic oligodeoxyribonucleotides of defined sequences as
      standards.  Flat bed electrophoresis with careful temperature control gave
      entirely reproducible mobilities in the first dimension.  Using this
      information, an accurate formula has been derived for calculating the relative
      electrophoretic mobilities of oligodeoxyribonucleotides of any composition.
      This formula is used to calculate the mobility shifts between two consecutive
      oligodeoxyribonucleotides in a series of partial products of an unknown
      oligomer distributed in the two-dimensional homochromatogram which differ by
      one nucleotide in length.  This is compared with the observed mobility shift
      value to identify the added nucleotide.  This provides a direct and rapid
      method for obtaining the unambiguous sequence of an entire
      oligodeoyribonucleotide up to 15 nucleotides in length.
AU  - Tu C-PD
AU  - Jay E
AU  - Bahl CP
AU  - Wu R
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 1976 74: 73-93.

PMID- 985479
VI  - 72
DP  - 1976
TI  - Nucleotide recognition sequence at the cleavage site of Haemophilus aegyptius II (HaeII) restriction endonuclease.
PG  - 355-362
AB  - We have determined the nucleotide sequence recognized by the restriction
      endonuclease HaeII from Haemophilus aegyptius which cleaves the simian virus 40
      (SV40) DNA at a single specific site.  By using terminal radioactive labeling
      of the cleavage site at both the 5' and 3'-ends we have deduced the recognition
      sequence, 3'...A-G-C-G-C^pT...3' 3'..Tp^C-G-C-G--A...5' with elements of a
      two-fold rotational symmetry.  The endonuclease produces staggered ends with
      protruding 3'-terminated single-strands, four nucleotides in length.  In
      plasmid RSF 2124 DNA, which contains multiple HaeII cleavage sites, it was
      observed that the 5th nucleotide from the 3' terminus is either a pdA or a pdG,
      indicating alternating recognition sequences.
AU  - Tu C-PD
AU  - Roychoudhury R
AU  - Wu R
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1976 72: 355-362.

PMID- 7607532
VI  - 157
DP  - 1995
TI  - MmeI, a class-IIS restriction endonuclease: purification and characterization.
PG  - 87-92
AB  - Two restriction endonucleases, MmeI and MmeII, from Methylophilus methylotrophus were purified
      to homogeneity.  Both enzymes belong to the class-II restriction endonucleases (ENases) but
      exhibit very different enzymatic and physical properties.  MmeII is a typical member of
      class-II ENases.  It is a polymeric protein composed of 50-kDa subunits.  In contrast to
      MmeII, MmeI is a monomeric protein of 101 kDa, cleaving a DNA molecule 20/18 nucleotides away
      from the asymmetric recognition sequence (5'-TCCRAC-3'); therefore, it is classified as a
      member of subclass-IIS.  MmeI has a pI of 7.85 and is active in the pH range 6.5 to 10 with
      the optimum at 7 to 8.  Increasing salt concentration creates an inhibitory effect on MmeI: 40
      mM KCl decreases activity by 50%, 100 mM completely inhibits DNA cleavage.  Tris.HCl (pH
      7.5)  at a concentration exceeding 20 mM inhibits MmeI activity.  Mg2+ stimulates MmeI in the
      range  of 0.2 to 35 mM, with the optimum between 0.5 and 10 mM.
AU  - Tucholski J
AU  - Skowron PM
AU  - Podhajska AJ
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 87-92.

PMID- 9858752
VI  - 223
DP  - 1998
TI  - Two intertwined methylation activities of the MmeI restriction-modification class-IIS system from Methylophilus methylotrophus.
PG  - 293-302
AB  - The class-IIS restriction endonuclease, R.MmeI, was isolated from Methylophilus
      methylotrophus.  It was originally described as a monomeric enzyme, with the native Mr
      105,000+/-7,000, which did not cleave DNA efficiently.  However, it was discovered that R.MmeI
      endonucleolytic activity is enhanced by S-adenosyl-L-methionine and sinefungin, an analogue of
      AdoMet.  Surprisingly, the purified R.MmeI endonuclease was found to have a second enzymatic
      activity, namely methylation of the adenine residue to N6-methyladenine in the top strand of
      the MmeI-recognition sequence, 5'-TCCR*AC-3' (*A = meA).  The R.MmeI methylating activity
      requires AdoMet and is increased in the presence of several divalent cations, 20-fold by Mg2+
      or Ca2+, and less by Mn2+, Zn2+ and Co2+; however, methylation is inhibited entirely by
      sinefungin, at concentrations above 9 microM.  The latter observation shows that the enhancing
      effect of AdoMet or sinefungin on the DNA cleavage was not related to the process of DNA
      methylation.  Furthermore, a second component of the MmeI restriction-modification system, an
      M.MmeI methyltransferase, was isolated and purified.  The M.MmeI protein was found to have an
      Mr of 48,000 +/- 2,000 (under denaturing conditions) and to methylate both adenine residues
      (*A) in the MmeI-recognition sequence 5'-TCCR*AC-3'/3'-*AGGYTG-5'.  Methylation of the top
      strand does not inhibit the DNA cleavage by R.MmeI, whereas methylation of both DNA strands
      blocks the cleavage process.
AU  - Tucholski J
AU  - Zmijewski JW
AU  - Podhajska AJ
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1998 223: 293-302.

PMID- 
VI  - 
DP  - 1997
TI  - A genetic investigation of the establishment of genomic imprinting.
PG  - 1-80
AB  - Much evidence indicates that in vertebrates the methylation of DNA at cytosine residues
      correlates with gene inactivity.  A single methyltransferase activity, DNA
      (cytosine-5)-methyltransferase, has been purified from mammalian cells and its gene (Dnmt)
      cloned.  The crucial importance of DNA methylation in development was demonstrated by the
      targeted mutation of Dnmt in murine embryonic stem cells.  Embryos with homozygous disruptions
      of Dnmt die in mid-gestation.  In contrast, homozygous mutant ES cells proliferate normally
      with their DNA highly demethylated, though they die upon differentiation.  The research
      presented in this thesis focused on expressing the Dnmt cDNA in the backgroud of Dnmt mutant
      ES cells.  Initial attempts using a cDNA and a corresponding promoter region were unsuccessful
      in effecting adequate levels of functional Mtase expression.  A complete cDNA sequence was
      obtained through the cloning of two new 5'-proximal exons, which extend the open reading
      frame up to 171 codons upstream of the previously defined start site.  This showed the
      previously-reported promoter sequence to lie in the second intron of the gene, with no
      evidence that it functions in ES cells.  It was found that the extra coding sequence was
      necessary for functional expression of the gene in ES cells.  Expression of the wild type Dnmt
      cDNA in mutant ES cells caused an increase in methylation of bulk DNA to normal levels, but
      did not restore the methylation of imprinted genes, whose expression is monoallelic and
      dependent upon their parental derivation.  The expression of these genes was deregulated
      because of this hypomethylation, as shown previously in Dnmt mutant embryos.  Full restoration
      of monoallelic methylation and expression was imposed on imprinted genes upon germline
      transmission.  These results are consistent with the presence of distanct de novo DNA
      methyltransferase activities during oogenesis and spermatogenesis which specifically recognize
      imprinted genes but which are absent in the post-implantation embryo and in ES cells.  Because
      the "rescued" ES cells display biallelic hypomethylation and expression of imprinted genes,
      their developmental capacities may be impaired, as is seen with cells derived from
      parthenogenetic or androgenetic embryos, which also display biallelic expression of imprinted
      genes.  Alternatively, the rescued ES cells may have normal developmental capacities, as
      predicted by a model which explains genomic imprinting as a nonessential,
      evolutionarily-recent addition to the basic mammalian developmental program.  Rescued cells
      differentiated normally in vitro, formed teratomas with a wide variety of differentiated cell
      types, and contributed substantially to coat color in adult chimeras.  Further analysis of
      tissue-specific distribution of rescued ES cells in chimeras will allow a full assessment of
      the developmental potential of a mouse lacking an imprinted genome.
AU  - Tucker KL
PT  - Journal Article
TA  - Ph.D. Thesis, MIT, USA
JT  - Ph.D. Thesis, MIT, USA
SO  - Ph.D. Thesis, MIT, USA 1997 : 1-80.

PMID- 8608936
VI  - 10
DP  - 1996
TI  - Germ-line passage is required for establishment of methylation and expression patterns of imprinted but not of nonimprinted genes.
PG  - 1008-1020
AB  - Embryonic stem cells homozygous for a disruption of the DNA (cytosine-5)-methyltransferase
      gene (Dnmt) proliferate normally with their DNA highly demethylated but die upon
      differentiation.  Expression of the wild-type Dnmt cDNA in mutant male ES cells caused an
      increase in methylation of bulk DNA and of the Xist and Igf2 genes to normal levels, but did
      not restore the methylation of the imprinted genes H19 and Igf2r.  These cells differentiated
      normally in vitro and contributed substantially to adult chimeras.  While the Xist gene was
      not expressed in the remethylated male ES cells, no restoration of the normal expression
      profile was seen for H19, Igf2r, or Igf2.  This indicates that ES cells can faithfully
      reestablish normal methylation and expression patterns of nonimprinted genes but lack the
      ability to restore those of imprinted genes.  Full restoration of monoallelic methylation and
      expression was imposed on H19, Igf2, and Igf2r upon germ-line transmission.  These results are
      consistent with the presence of distinct de novo DNA methyltransferase activities during
      oogenesis and spermatogenesis, which specifically recognize imprinted genes but are absent in
      the postimplantation embryo and in ES cells.
AU  - Tucker KL
AU  - Beard C
AU  - Dausman J
AU  - Jackson-Grusby L
AU  - Laird PW
AU  - Lei H
AU  - Li E
AU  - Jaenisch R
PT  - Journal Article
TA  - Genes Dev.
JT  - Genes Dev.
SO  - Genes Dev. 1996 10: 1008-1020.

PMID- 8917520
VI  - 93
DP  - 1996
TI  - Complementation of methylation deficiency in embryonic stem cells by a DNA methyltransferase minigene.
PG  - 12920-12925
AB  - Previous attempts to express functional DNA cytosine methyltransferase (EC 2.1.1.37) in cells
      transfected with the available Dnmt cDNAs have met with little or no success.  We show that
      the published Dnmt sequence encodes an amino terminal-truncated protein that is tolerated only
      at very low levels when stably expressed in embryonic stem cells.  Normal expression levels
      were, however, obtained with constructs containing a continuation of an ORF with a coding
      capacity of up to 171 amino acids upstream of the previously defined start site.  The protein
      encoded by these constructs comigrated in SDS/PAGE with the endogenous enzyme and restored
      methylation activity in transfected cells.  This was shown by functional rescue of Dnmt mutant
      embryonic stem cells that contain highly demethylated genomic DNA and fail to differentiate
      normally.  When transfected with the minigene construct, the genomic DNA became remethylated
      and the cells regained the capacity to form teratomas that displayed a wide variety of
      differentiated cell types.  Our results define an amino-terminal domain of the mammalian Mtase
      that is crucial for stable expression and function in vivo.
AU  - Tucker KL
AU  - Talbot D
AU  - Lee MA
AU  - Leonhardt H
AU  - Jaenisch R
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1996 93: 12920-12925.

PMID- 26578674
VI  - 6
DP  - 2015
TI  - The Complete Genome Sequence of the Emerging Pathogen Mycobacterium haemophilum Explains Its Unique Culture Requirements.
PG  - e01313-15
AB  - Mycobacterium haemophilum is an emerging pathogen associated with a variety of clinical
      syndromes, most commonly skin infections in immunocompromised
      individuals. M. haemophilum exhibits a unique requirement for iron
      supplementation to support its growth in culture, but the basis for this property
      and how it may shape pathogenesis is unclear. Using a combination of Illumina,
      PacBio, and Sanger sequencing, the complete genome sequence of M. haemophilum was
      determined. Guided by this sequence, experiments were performed to define the
      basis for the unique growth requirements of M. haemophilum. We found that M.
      haemophilum, unlike many other mycobacteria, is unable to synthesize iron-binding
      siderophores known as mycobactins or to utilize ferri-mycobactins to support
      growth. These differences correlate with the absence of genes associated with
      mycobactin synthesis, secretion, and uptake. In agreement with the ability of
      heme to promote growth, we identified genes encoding heme uptake machinery.
      Consistent with its propensity to infect the skin, we show at the whole-genome
      level the genetic closeness of M. haemophilum with Mycobacterium leprae, an
      organism which cannot be cultivated in vitro, and we identify genes uniquely
      shared by these organisms. Finally, we identify means to express foreign genes in
      M. haemophilum. These data explain the unique culture requirements for this
      important pathogen, provide a foundation upon which the genome sequence can be
      exploited to improve diagnostics and therapeutics, and suggest use of M.
      haemophilum as a tool to elucidate functions of genes shared with M. leprae.
      IMPORTANCE: Mycobacterium haemophilum is an emerging pathogen with an unknown
      natural reservoir that exhibits unique requirements for iron supplementation to
      grow in vitro. Understanding the basis for this iron requirement is important
      because it is fundamental to isolation of the organism from clinical samples and
      environmental sources. Defining the molecular basis for M. haemophilium's growth
      requirements will also shed new light on mycobacterial strategies to acquire iron
      and can be exploited to define how differences in such strategies influence
      pathogenesis. Here, through a combination of sequencing and experimental
      approaches, we explain the basis for the iron requirement. We further demonstrate
      the genetic closeness of M. haemophilum and Mycobacterium leprae, the causative
      agent of leprosy which cannot be cultured in vitro, and we demonstrate methods to
      genetically manipulate M. haemophilum. These findings pave the way for the use of
      M. haemophilum as a model to elucidate functions of genes shared with M. leprae.
AU  - Tufariello JM
AU  - Kerantzas CA
AU  - Vilcheze C
AU  - Calder RB
AU  - Nordberg EK
AU  - Fischer JA
AU  - Hartman TE
AU  - Yang E
AU  - Driscoll T
AU  - Cole LE
AU  - Sebra R
AU  - Maqbool SB
AU  - Wattam AR
AU  - Jacobs WR Jr
PT  - Journal Article
TA  - MBio
JT  - MBio
SO  - MBio 2015 6: e01313-15.

PMID- 2838132
VI  - 4
DP  - 1988
TI  - Restriction map construction using a 'complete sentences compatibility' algorithm.
PG  - 103-110
AB  - We have developed a new algorithm 'Complete sentences compatibility' (CSC)
      which uses single and double digestion fragments to rapidly determine
      restriction maps of circular DNA.  From possible combinations of fragments of
      each simple digestion, which we call "sentences of decomposition", we construct
      a restriction map which combines the sentences while taking into account
      compatibility rules.  The algorithm can also deal with experimental errors of
      fragment weight and can suggest solutions that account for non-readable bands
      (fragments of zero length or multiple bands) on the gel.  Because experiments
      using pairs of restrictive enzymes often result in multiple solutions, a
      complementary algorithm tries to reduce the number of proposed solutions by
      establishing consensus maps.  The restriction map construction algorithm was
      tested on real cases, some containing more than fifteen fragments.  Execution
      times range from 1-10 s on an IBM PC compatible microcomputer.
AU  - Tuffery P
AU  - Dessen P
AU  - Mugnier C
AU  - Hazout S
PT  - Journal Article
TA  - Comput. Appl. Biosci.
JT  - Comput. Appl. Biosci.
SO  - Comput. Appl. Biosci. 1988 4: 103-110.

PMID- 17048701
VI  - 57
DP  - 2006
TI  - Identification of adsorption inhibition, restriction/modification and abortive infection type phage resistance systems in Lactococcus lactis strains.
PG  - 377-385
AB  - 98 Lactococcus lactis strains were isolated from traditional fermented milk products in Turkey
      tested against 60 lactococcal lytic phages to
      determine their resistance levels. While 82 L. lactis strains were
      sensitive against lactic phages at different levels, 16 L. lactis
      strains showed resistance to all phages tested. Types of phage
      resistance among 16 L. lactis strains were identified as phage
      adsorption inhibition in eight strains, restriction/modification in six
      strains and abortive infection (heat sensitive phage resistance) in two
      strains, using three broad-spectrum phages Phi p11 98-32, Phi pld 67-42
      and Phi pld 67-44.
AU  - Tukel C
AU  - Sanlibaba P
AU  - Ozden B
AU  - Akcelik M
PT  - Journal Article
TA  - Acta Biol. Hung.
JT  - Acta Biol. Hung.
SO  - Acta Biol. Hung. 2006 57: 377-385.

PMID- 28596393
VI  - 5
DP  - 2017
TI  - Genome Sequence of Geothermobacter sp. Strain EPR-M, a Deep-Sea Hydrothermal Vent Iron Reducer.
PG  - e00424-17
AB  - Geothermobacter sp. strain EPR-M was isolated from a hydrothermal vent on the East Pacific
      Rise and has been shown to participate in the reduction of Fe(III)
      oxides. Here, we report its 3.73-Mb draft genome sequence.
AU  - Tully B
AU  - Savalia P
AU  - Abuyen K
AU  - Baughan C
AU  - Romero E
AU  - Ronkowski C
AU  - Torres B
AU  - Tremblay J
AU  - Trujillo A
AU  - Tyler M
AU  - Perez-Rodriguez I
AU  - Amend J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00424-17.

PMID- Not included in PubMed...
VI  - 121
DP  - 1994
TI  - Transformation of Methanococcus maripaludis and identification of a PstI-like restriction system.
PG  - 309-314
AB  - An optimized polyethylene glycol (PEG) method of transformation was developed for
      Methanococcus maripaludis using the pKAS102 integration vector. The frequency of
      transformation with 0.8 ug of plasmid and 3x10/9 cells was 4.8x10-5 transformants cfu-1, or
      1.8x10/5 transformants per ug, which was four orders of magnitude greater than with the
      natural transformation method. A PstI restriction activity in M. maripaludis was also
      identified. Methylation of the plasmid with PstI methylase increased the methanococcal
      transformation frequency at least four-fold. Also, chromosomal DNA from M. maripaludis was
      resistant to digestion by the PstI endonuclease.
AU  - Tumbula DL
AU  - Makula RA
AU  - Whitman WB
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1994 121: 309-314.

PMID- 29622606
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Marinobacter Strains Recovered from Utica Shale-Produced Fluids.
PG  - e00155-18
AB  - The genomes of three Marinobacter strains, isolated from saline fluids produced from a
      Utica-Point Pleasant shale well, have been sequenced. These genomes
      provide novel information on the degradation of petroleum distillates and
      virulence mechanisms under microaerophilic conditions in fractured shale.
AU  - Tummings S
AU  - Panescu J
AU  - Daly RA
AU  - Wrighton KC
AU  - Mouser PJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00155-18.

PMID- 16328134
VI  - 151
DP  - 2006
TI  - The genome of the virulent phage Lc-Nu of probiotic Lactobacillus rhamnosus, and comparative genomics with Lactobacillus casei phages.
PG  - 947-965
AB  - The complete 36,466-bp genome sequence of the virulent phage Lc-Nu of probiotic Lactobacillus
      rhamnosus was determined. The linear dsDNA with
      a GC-content of 44.2% contained 3' single-stranded cohesive ends of 12
      nucleotides. A total of 51 putative open reading frames (orfs) were
      predicted. Lc-Nu showed to be evolutionary closely related to the
      temperate Lactobacillus casei phages phi AT3 and A2. High DNA homology
      with phi AT3 was shared over the late transcribed genes, and the
      highest homology with A2 was within the genetic switch region. The
      truncated cI-like repressor was the only lysogeny related gene left,
      which strongly suggested Lc-Nu to be recently evolved from a temperate
      origin. Three putative methylases and endonucleases were detected from
      the region of early-transcribed genes. The putative origin of
      replication within the putative gene orf34 homologous to replisome
      organizers resembled to that of lambdoid phages. The present study
      suggested Lc-Nu to be a new candidate for the proposed Sfi21-like
      species.
AU  - Tuohimaa A
AU  - Riipinen KA
AU  - Brandt K
AU  - Alatossava T
PT  - Journal Article
TA  - Arch. Virol.
JT  - Arch. Virol.
SO  - Arch. Virol. 2006 151: 947-965.

PMID- 29472328
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of a Propanotroph, Rhodococcus sp. Strain ENV425, Capable of Degrading Methyl tert-Butyl Ether and N-Nitrosodimethylamine.
PG  - e00051-18
AB  - In this study, the draft genome of Rhodococcus sp. strain ENV425 was determined.  The
      propane-grown strain ENV425 cometabolically degrades environmental
      contaminants such as methyl tert-butyl ether and N-nitrosodimethylamine. The
      sequence revealed the presence of multiple hydrocarbon metabolic genes that could
      play pivotal roles in the biodegradation of pollutants.
AU  - Tupa PR
AU  - Masuda H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00051-18.

PMID- 27979954
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the Probiotic Bifidobacterium longum subsp. longum Strain MC-42.
PG  - e01411-16
AB  - Here, we report the draft genome sequence of Bifidobacterium longum subsp. longum strain MC-42
      isolated from the feces of a healthy infant, and which was used in
      the commercially available probiotic product Biovestin.
AU  - Tupikin AE
AU  - Kalmykova AI
AU  - Kabilov MR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01411-16.

PMID- 7767994
VI  - 16
DP  - 1995
TI  - DNA adduct 8-hydroxyl-2'-deoxyguanosine (8-hydroxyguanine) affects function of human DNA methyltransferase.
PG  - 1253-1255
AB  - 8-Hydroxyl-2'-deoxyguanosine (also referred to as 8-hydroxyguanine [8-OH-dG] or
      7,8-dihydro-8-oxoguanine), a common DNA adduct resulting from injury to DNA via reactive
      oxygen species, affects the in vitro methylation of nearby cytosine moieties by the human DNA
      methyltransferase. The exact position of 8-OH-deoxyguanosine relative to a CpG dinucleotide
      appears important to this effect. Our data indicate that 8-OH-deoxyguanosine diminishes the
      ability of the methyltransferase to methylate a target cytosine when the 8-OH-deoxyguanosine
      is one or two nucleotides 3' from the cytosine, on the same strand. On the other hand
      8-OH-deoxyguanosine does not diminish the ability of the enzyme to respond to a methyl
      director (5-methylcytosine) when the 8-OH-deoxyguanosine is on the same strand but one or two
      nucleotides 3' from the methyl director. Differences in methylation rates as great as 13-fold
      have been detected using various 8-OH-deoxyguanosine-containing oligonucleotides as substrates
      in methylation assays. Our findings suggest that oxidative damage of parental strand guanines
      would permit normal copying of methylation patterns through maintenance methylation, while
      oxidative damage of guanines in the nascent strand DNA would inhibit such methylation.
AU  - Turk PW
AU  - Laayoun A
AU  - Smith SS
AU  - Weitzman SA
PT  - Journal Article
TA  - Carcinogenesis
JT  - Carcinogenesis
SO  - Carcinogenesis 1995 16: 1253-1255.

PMID- 7581820
VI  - 23
DP  - 1995
TI  - Free radical DNA adduct 8-OH-deoxyguanosine affects activity of HpaII and MspI restriction endonuclease.
PG  - 255-258
AB  - 8-OH-deoxyguanosine can diminish the ability of the restriction endonucleases HpaII and MspI
      to cleave DNA.  The exact position of the adduct within the recognition site appears to
      determine the extent of the effect.
AU  - Turk PW
AU  - Weitzman SA
PT  - Journal Article
TA  - Free Radic. Res.
JT  - Free Radic. Res.
SO  - Free Radic. Res. 1995 23: 255-258.

PMID- 1849178
VI  - 218
DP  - 1991
TI  - Six group I introns and three internal transcribed spacers in the chloroplast large subunit ribosomal RNA gene of the green alga Chlamydomonas eugametos.
PG  - 293-311
AB  - The chloroplast large subunit rRNA gene of Chlamydomonas eugametos and its 5' flanking region
      encoding tRNA-Ile (GAU) and tRNA-Ala (UGC) have been sequenced. The DNA sequence data along
      with the results of a detailed RNA analysis disclosed two unusual features of this green algal
      large subunit rRNA gene: (1) the presence of six group I introns (CeLSU.1-CeLSU.6) whose
      insertion positions have not been described previously, and (2) the presence of three short
      internal transcribed spacers that are post-transcriptionally excised to yield four rRNA
      species of 380, 52, 810 and 1720 nucleotides, positioned in this order (5' to 3') in the
      primary transcript. Together, these RNA species can assume a secondary structure that is
      almost identical to that proposed for the 23S rRNA of Escherichia coli. All three internal
      transcribed spacers map to variable regions of primary sequence and/or potential secondary
      structure, whereas all six introns lie within highly conserved regions. The first three
      introns are inserted within the sequence encoding the 810 nucleotide rRNA species and map
      within domain II of the large subunit rRNA structure; the remaining introns, found in the
      sequence encoding the 1720 nucleotide rRNA species, lie within either domain IV or V, as is
      the case for all other large subunit rDNA introns that have been documented to date. CeLSU.5
      and CeLSU.6 each contain a long open reading frame (ORF) of more than 200 codons. While the
      CeLSU.6 ORF is not related to any known ORFs, the CeLSU.5 ORF belongs to a fmaily of ORFs that
      have been identified in Podospora and Neuospora mitochondrial group I introns. The finding
      that a polymorphic marker showing unidirectional gene conversion during crosses between C.
      eugametos and Chlamydomonas moewusii is located within the CeLSU.5 ORF makes it likely that
      this intron is a mobile element and that its ORF encodes a site-specific endonuclease
      promoting the transfer of the intron DNA sequence.
AU  - Turmel M
AU  - Boulanger J
AU  - Schnare MN
AU  - Gray MW
AU  - Lemieux C
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1991 218: 293-311.

PMID- 7659010
VI  - 12
DP  - 1995
TI  - Evolutionary transfer of ORF-containing group I introns between different subcellular compartments (chloroplast and mitochondrion).
PG  - 533-545
AB  - We describe here a case of homologous introns containing homologous open reading frames (ORFs)
      that are inserted at the same site in the large subunit (LSU) rRNA gene of different
      organelles in distantly related organisms.  We show that the chloroplast LSU rRNA gene of the
      green alga Chlamydomonas pallidostigmatica contains a group I intron (CpLSU.2) encoding a
      site-specific endonuclease (I-CpaI).  This intron is inserted at the identical site
      (corresponding to positions 1931-1932 of the Escherichia coli 23S rRNA sequence) as a group I
      intron (AcLSU.m1) in the mitochondrial LSU rRNA gene of the amoeboid protozoon Acanthamoeba
      castellanii.  The CpLSU.2 intron displays a rmarkable degree of nucleotide similarity in both
      primary sequence and secondary structure to the AcLSU.m1 intron; moreover, the Acanthamoeba
      intron contains an ORF in the same location within its secondary structure as the CpLSU.2 ORF
      and shares with it a strikingly high level of amino acid similarity (65%; 42% identity).  A
      comprehensive survey of intron distribution at site 1931 of the chloroplast LSU rRNA gene
      reveals a rather restricted occurrence within the polyphyletic genus Chlamydomonas, with no
      evidence of this intron among a number of non-Chlamydomonad green algae surveyed, nor in land
      plants.  A parallel survey of homologues of a previously described and similar intron/ORF pair
      (C. reinhardtii chloroplast CrLSU/A. castellanii mitochondrial AcLSU.m3) also shows a
      restricted occurrence of this intron (site 2593) among chloroplasts, although the intron
      distribution is somewhat broader than that observed at site 1931, with site-2593 introns
      appearing in several green algal branches outside of the Chlamydomonas lineage.  The available
      data, while not definitive, are most consistent with a relatively recent horizontal transfer
      of both site-1931 and site-2593 introns (and their contained ORFs) between the chloroplast of
      a Chlamydomonas-type organism and the mitochondrial of an Acanthamoeba-like organism, probably
      in the direction chlorplast to mitochondrion.  The data also suggest that both introns could
      have been acquired in a single event.
AU  - Turmel M
AU  - Cote V
AU  - Otis C
AU  - Mercier J-P
AU  - Gray MW
AU  - Lonergan KM
AU  - Lemieux C
PT  - Journal Article
TA  - Mol. Biol. Evol.
JT  - Mol. Biol. Evol.
SO  - Mol. Biol. Evol. 1995 12: 533-545.

PMID- 8393936
VI  - 232
DP  - 1993
TI  - Analysis of the chloroplast large subunit ribosomal RNA gene from 17 Chlamydomonas taxa.
PG  - 446-467
AB  - Previous reports on the chloroplast large subunit rRNA genes of the two distantly related
      green algae Chlamydomonas eugametos and Chlamydomonas reinhardtii indicate differences in the
      distribution of group I introns and suggest a different arrangement of internal transcribed
      spacers. To provide insights into the origin of these two types of intervening sequences, we
      have undertaken the sequencing of the chlorplast rrnL genes of 15 additional Chlamydomonas
      taxa and have characterized the mature large subunit rRNA species they encode in addition to
      those specified by the C. reinhardtii rrnL. These analyses disclosed the presence of three
      internal transcribed spaces sharing the same positions in all of the 17 taxa as well as the
      presence of a total of 39 group I introns representing 12 insertion sites. Of these insertion
      sites, only one has been identified in non-Chlamydomonas taxa. The distribution of
      Chlamydomonas introns is highly variable and, in many respects, is not consistent with the
      phylogeny deduced from chloroplast rRNA sequence comparisons. This phylogeny features two main
      lineages of Chlamydomonas taxa forming sister groups. Because earlier branching organisms in
      the green algal/land plant lineage display no chloroplast rRNA introns, it appears that all of
      the intron insertion positions in Chlamydomonas are of recent origins, with some of the
      positions having arisen subsequent to the divergence of the two main Chlamydomonas lineages.
      Remarkably, the rRNA regions corresponding to most of the group I intron insertion positions
      in rRNA genes have been assigned functional roles suggesting that they lie in exposed regions
      of the ribosome. On the basis of this striking correlation between exposed rRNA regions and
      intron insertion sites, we speculate that the reversal of the self-splicing reaction has
      played a major role in the creation of the multiple intron insertion positions found in rRNA
      genes as well as in the proliferation of group I introns elsewhere in the Chlamydomonas
      chloroplast genome.
AU  - Turmel M
AU  - Gutell RR
AU  - Mercier J-P
AU  - Otis C
AU  - Lemieux C
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1993 232: 446-467.

PMID- 7630730
VI  - 23
DP  - 1995
TI  - The site-specific DNA endonuclease encoded by a group I intron in the Chlamydomonas pallidostigmatica chloroplast small subunit rRNA gene introduces a single-strand break at low concentrations of Mg2+.
PG  - 2519-2525
AB  - Two group I introns (CpSSU.1 and CpSSU.2) that each potentially encode a protein with two
      copies of the LAGLI-DADG motif were identified in the Chlamydomonas pallidostigmatica
      chloroplast small subunit rRNA gene. They both belong to subgroup IA3 and represent novel
      insertion positions in this gene (sites 508 and 793 in the Escherichia coli 16S rRNA). The
      proteins encoded by the two introns were synthesized in vitro and tested for their ability to
      cleave the homing site of their respective introns. Only the CpSSU.1-encoded protein (I-CpaII)
      was found to display specific DNA endonuclease activity. At 0.1 mM MgCl2, I-CpaII nicks only
      the bottom (transcribed) DNA strand, but at concentrations ranging from 0.5 to 5.0 mM, it
      cleaves both DNA strands (leaving a 4 nucleotide single-stranded extension with 3'-OH
      overhangs) while preferentially nicking the bottom strand. The rate of cleavage of the top
      strand increases with increasing concentration of MgCl2. The preliminary data derived from
      these endonuclease assays suggest that the mode of DNA cleavage by I-CpaII is directed by the
      availability of Mg2+ and the affinity of different binding sites for this cation.
AU  - Turmel M
AU  - Mercier J-P
AU  - Cote V
AU  - Otis C
AU  - Lemieux C
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1995 23: 2519-2525.

PMID- 9185572
VI  - 25
DP  - 1997
TI  - Evolutionarily conserved and functionally important residues in the I-CeuI homing endonuclease.
PG  - 2610-2619
AB  - Two approaches were used to discern critical amino acid residues for the function of the
      I-CeuI homing endonuclease: sequence comparison of subfamilies of homologous proteins and
      genetic selection.  The first approach revealed residues potentially involved in catalysis and
      DNA recognition.  Because I-CeuI is lethal in Escherichia coli, enzyme variants not perturbing
      cell viability were readily selected from an expression library.  A collection of 49 variants
      with single amino acid substitutions at 37 positions was assembled.  Most of these positions
      are clustered within or around the LAGLI-DADG dodecapeptide and the TQH sequence, two motifs
      found in all protein subfamilies examined.  The Km and kcat values of the wild-type and nine
      variant enzymes synthesized in vitro were determined.  Three variants, including one showing a
      substituion of the glutamine residue in the TQH motif, revealed no detectable endonuclease
      activity; five others showed reduced activity compared to the wild-type enzyme; whereas the
      remaining variant cleaved the top strand about three times more efficiently than the
      wild-type.  Our results not only confirm recent reports indicating that amino acids in the
      LAGLI-DADG dodecapeptide are functionally critical, but they also suggest that some residues
      outside this motif directly participate in catalysis.
AU  - Turmel M
AU  - Otis C
AU  - Cote V
AU  - Lemieux C
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1997 25: 2610-2619.

PMID- Not included in PubMed...
VI  - 45
DP  - 1990
TI  - Purification of restriction endonuclease SauBMKI.
PG  - 281-288
AB  - The type II restriction endonuclease designated SauBMKI was isolated from Streptomyces
      aureofaciens, strain BMK.  The enzyme was purified by chromatography using DEAE-cellulose,
      ssDNA cellulose and phosphocellulose to the grade when no unspecific endo- and exonucleases
      were detectable.  The optimal reaction conditions were established: glycine 20 mmol/l (pH
      8.7), NaCl 20 mmol/l, MgCl2 20 mmol/l, 2-ME 7 mmol/l and BSA 100 micrograms/ml.
AU  - Turna J
AU  - Mikulasova D
AU  - Timko J
AU  - Zelinka J
PT  - Journal Article
TA  - Biologia (Bratisl)
JT  - Biologia (Bratisl)
SO  - Biologia (Bratisl) 1990 45: 281-288.

PMID- 11124025
VI  - 304
DP  - 2000
TI  - Interaction of the E-coli DNA G : T-mismatch endonuclease (vsr protein) with oligonucleotides containing its target sequence.
PG  - 765-778
AB  - The Escherichia coli vsr endonuclease recognises G:T base-pair mismatches in double-stranded
      DNA and initiates a repair pathway by
      hydrolysing the phosphate group 5' to the incorrectly paired T. The
      enzyme shows a preference for G:T mismatches within a particular
      sequence context, derived from the recognition site of the E. coli dcm
      DNA-methyltransferase (CC[A/T]GG). Thus, the preferred substrate for
      the vsr protein is (CT[A/T]GG), where the underlined T is opposed by a
      dG base. This paper provides quantitative data for the interaction of
      the vsr protein with a number of oligonucleotides containing G:T
      mismatches. Evaluation of specificity constant (k(st)/K-D; k(st) = rate
      constant for single turnover, K-D = equilibrium dissociation constant)
      confirms vsr's preference for a G:T mismatch within a hemi-methylated
      dcm sequence, i.e. the best substrate is a duplex (both strands written
      in the 5'-3' orientation) composed of CT[A/T]CG and C-5Me[T/A]GG.
      Conversion of the mispaired T (underlined) to dU or the d(5Me)C to dC
      gave poorer substrates. No interaction was observed with
      oligonucleotides that lacked a G:T mismatch or did not possess a dcm
      sequence. An analysis of the fraction of active protein, by
      "reverse-titration" (i.e. adding increasing amounts of DNA to a fixed
      amount of protein followed by gel-mobility shift analysis) showed that
      less than 1% of the vsr endonuclease was able to bind to the substrate.
      This was confirmed using "competitive titrations" (where competitor
      oligonucleotides are used to displace a P-32-labelled nucleic acid from
      the vsr protein) and burst kinetic analysis. This result is discussed
      in the light of previous in vitro and in vivo data which indicate that
      the MutL protein may be needed for full vsr activity.
AU  - Turner DP
AU  - Connolly BA
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2000 304: 765-778.

PMID- 22075923
VI  - 39
DP  - 2012
TI  - Optical mapping and sequencing of the Escherichia coli KO11 genome reveal extensive chromosomal rearrangements, and multiple tandem copies of the Zymomonas mobilis pdc and adhB genes.
PG  - 629-639
AB  - Escherichia coli KO11 (ATCC 55124) was engineered in 1990 to produce ethanol by
      chromosomal insertion of the Zymomonas mobilis pdc and adhB genes into E. coli W
      (ATCC 9637). KO11FL, our current laboratory version of KO11, and its parent E.
      coli W were sequenced, and contigs assembled into genomic sequences using optical
      NcoI restriction maps as templates. E. coli W contained plasmids pRK1 (102.5 kb)
      and pRK2 (5.4 kb), but KO11FL only contained pRK2. KO11FL optical maps made with
      AflII and with BamHI showed a tandem repeat region, consisting of at least 20
      copies of a 10-kb unit. The repeat region was located at the insertion site for
      the pdc, adhB, and chloramphenicol-resistance genes. Sequence coverage of these
      genes was about 25-fold higher than average, consistent with amplification of the
      foreign genes that were inserted as circularized DNA. Selection for higher levels
      of chloramphenicol resistance originally produced strains with higher pdc and
      adhB expression, and hence improved fermentation performance, by increasing the
      gene copy number. Sequence data for an earlier version of KO11, ATCC 55124,
      indicated that multiple copies of pdc adhB were present. Comparison of the W and
      KO11FL genomes showed large inversions and deletions in KO11FL, mostly enabled by
      IS10, which is absent from W but present at 30 sites in KO11FL. The early KO11
      strain ATCC 55124 had no rearrangements, contained only one IS10, and lacked most
      accumulated single nucleotide polymorphisms (SNPs) present in KO11FL. Despite
      rearrangements and SNPs in KO11FL, fermentation performance was equal to that of
      ATCC 55124.
AU  - Turner PC
AU  - Yomano LP
AU  - Jarboe LR
AU  - York SW
AU  - Baggett CL
AU  - Moritz BE
AU  - Zentz EB
AU  - Shanmugam KT
AU  - Ingram LO
PT  - Journal Article
TA  - J. Ind. Microbiol. Biotechnol.
JT  - J. Ind. Microbiol. Biotechnol.
SO  - J. Ind. Microbiol. Biotechnol. 2012 39: 629-639.

PMID- 20974960
VI  - 107
DP  - 2010
TI  - Genome analysis of Bifidobacterium bifidum PRL2010 reveals metabolic pathways for host-derived glycan foraging.
PG  - 19514-19519
AB  - The human intestine is densely populated by a microbial consortium whose
      metabolic activities are influenced by, among others, bifidobacteria.
      However, the genetic basis of adaptation of bifidobacteria to the human
      gut is poorly understood. Analysis of the 2,214,650-bp genome of
      Bifidobacterium bifidum PRL2010, a strain isolated from infant stool,
      revealed a nutrient-acquisition strategy that targets host-derived
      glycans, such as those present in mucin. Proteome and transcriptome
      profiling revealed a set of chromosomal loci responsible for mucin
      metabolism that appear to be under common transcriptional control and with
      predicted functions that allow degradation of various O-linked glycans in
      mucin. Conservation of the latter gene clusters in various B. bifidum
      strains supports the notion that host-derived glycan catabolism is an
      important colonization factor for B. bifidum with concomitant impact on
      intestinal microbiota ecology.
AU  - Turroni F et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2010 107: 19514-19519.

PMID- 26067979
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Antimicrobial-Producing Clostridium sp. JC272, Isolated  from Marine Sediment.
PG  - e00650-15
AB  - We announce the draft genome sequence of Clostridium sp. JC272, isolated from a sediment
      sample collected from marine habitats of Gujarat, India. Clostridium sp.
      JC272 is an obligate anaerobe and has the ability to produce antimicrobial
      compounds. The genome sequence indicates the strain's capability of producing
      small peptides (microcins), which are potential novel antibiotics.
AU  - Tushar L
AU  - Sasi JTS
AU  - Sasikala C
AU  - Ramana CV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00650-15.

PMID- 25614577
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Spirochaeta sp. Strain JC202, an Endosymbiont of the Termite (Isoptera) Gut.
PG  - e01481-14
AB  - We announce here the draft genome sequence of Spirochaeta sp. strain JC202 isolated from gut
      of a termite (Isoptera). The genome suggests that Spirochaeta
      sp. JC202 has the capability for natural conjugation with the help of fimbriae
      and pili. Experimental evidence and the genome sequence suggest that strain JC202
      is capable of producing colicin V and a bacteriocin group of peptides in a
      specific interaction.
AU  - Tushar L
AU  - Sravanthi T
AU  - Sasikala C
AU  - Ramana CV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01481-14.

PMID- 9173252
VI  - 31
DP  - 1997
TI  - Study of the equilibrium interation of T4 phage Dam-DNA-(N-adenine)-methyltransferase with substrates and ligands by fluorescence quenching method.
PG  - 86-90
AB  - 
AU  - Tuzikov FV
AU  - Tuzikova NA
AU  - Naumochkin AN
AU  - Zinovev VV
AU  - Malygin EG
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1997 31: 86-90.

PMID- Not included in PubMed...
VI  - 31
DP  - 1997
TI  - Fluorescence quenching study of equilibrium binding of phage T4 dam DNA-[N6-adenine]-methyltransferase with substrates and ligands.
PG  - 73-76
AB  - Selective fluorescence quenching by iodide ions was used to evaluate the surface accessibility
      of tryptophan residues in T4 Dam DNA methyltransferase (T4 MTase).  Two of the three MTase
      tryptophans proved fully accessible for iodide ions, suggesting that they are located near the
      surface of the molecule.  Quenching of intrinsic fluorescence of T4 MTase tryptophans was used
      to determine the parameters of enzyme binding with substrates (20-bp oligonucleotide duplex
      with a GATC site, and S-adenosyl-L-methionine (SAM)) and substrate analogs (duplex without a
      GATC site and S-adenosyl-L-homocysteine (SAH)).  Enzyme binding with small ligands (SAM and
      SAH) conforms with the modified Sterm-Volmer equation applicable to 1:1 complexes.  The
      dissociation constants for SAM and SAH were 0.24 and 2.3 microM, respectively.  In both cases,
      about one third of the total Mtase fluorescence could be quenched by these ligands.
      Saturating binding of oligonucleotide duplexes resulted in 12% (oligonucleotide with GATC) or
      19% (without GATC) quenching.  In both cases, experimental quenching curves did not fit the
      modified Sterm-Volmer equation, suggesting that the mechanism of oligonucleotide binding is
      more complex than that for small ligands.
AU  - Tuzikov FV
AU  - Tuzikova NA
AU  - Naumochkin AN
AU  - Zinovev VV
AU  - Malygin EG
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1997 31: 73-76.

PMID- 2661181
VI  - 304
DP  - 1989
TI  - Interaction between Ecodam methylase and double-stranded oligodeoxyribonucleotides.
PG  - 231-234
AB  - None
AU  - Tuzikov FV
AU  - Zinovev VV
AU  - Vavilin VI
AU  - Malygin EG
AU  - Buryanov YI
AU  - Baev AA
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1989 304: 231-234.

PMID- 10581020
VI  - 23
DP  - 1999
TI  - Vestiges of a DNA methylation system in Drosophila melanogaster?
PG  - 389-390
AB  - The insect Drosophila melanogaster belongs to an atypical group of animals with no detectable
      genomic 5-methylcytosine.  We found, unexpectedly, that the Drosophila genome potentially
      encodes two proteins that resemble a cytosine DNA methyltransferase and a mammalian
      methyl-CpG-binding -domain protein, respectively.  The hypothetical DNA methyltransferase,
      dDNMT, is closely related to the pmt1/DNMT2 family identified in fission yeast and mouse.
AU  - Tweedie S
AU  - Ng H-H
AU  - Barlow AL
AU  - Turner BM
AU  - Hendrich B
AU  - Bird A
PT  - Journal Article
TA  - Nat. Genet.
JT  - Nat. Genet.
SO  - Nat. Genet. 1999 23: 389-390.

PMID- Not included in PubMed...
VI  - 136
DP  - 1993
TI  - Sequence of the gene encoding a second ScrFI m5C methyltransferase of Lactococcus lactis.
PG  - 205-209
AB  - The nucleotide (nt) sequence of a second methyltransferase (MTase) encoding gene associated
      with the ScrFI restriction/modification (R/M) system (5'CCNGG3') of Lactococcus lactis ssp.
      cremoris UC503 has been determined. The coding region was 1080 nt in length and capable of
      specifying a 41,847-Da protein of 360 amino acids (aa). The deduced aa sequence displayed
      motifs characteristic of all prokaryotic 5-methylcytosine (m5C) MTases. Significant similarity
      was observed with other m5C MTases, apart from the variable region which has been deemed
      responsible for target sequence specificity. A larger than normal spacing between motif II and
      motif III, comparable in length and bearing homology to a similar region in the SssI MTase,
      was observed. A second open reading frame (ORF) of unknown function, which has the capacity to
      encode a protein of 155 aa, was observed three nt upstream from the m5C MTase ORF.
AU  - Twomey DP
AU  - Davis R
AU  - Daly C
AU  - Fitzgerald GF
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1993 136: 205-209.

PMID- Not carried by PubMed...
VI  - 32
DP  - 1993
TI  - Molecular characterisation of the ScrFI restriction-modification system.
PG  - 217
AB  - The elucidation of the genetic determinants of bacteriophage resistance assists rational
      approaches to designing and improving cheese-starter cultures. Lactococcus lactis subsp.
      cremoris UC503 exhibits restriction-modification (R/M) activity, through the restriction
      endonuclease, ScrFI, and the products of two methylase genes. Both of these methylases
      independently confer resistance to ScrFI digestion in E. coli ED8739. These genes, designated
      mscrFIA and mscrFIB, have been cloned from the chromosome of strain UC503 and their nucleotide
      sequences determined. Both of the predicted amino acid sequences display 10 motifs with an
      alignment and architecture characteristic of all procaryotic 5-methylcytosine methylases. The
      so-called variable regions, located between motif VIII and motif IX, are responsible for the
      target sequence specificity of these enzymes. However, the respective variable regions of
      M.ScrFIA and M.ScrFIB display no significant similarity to each other, suggesting that the
      enzymes have different recognition specificities. The variable region of M.ScrFIA displayed
      substantial similarity to equivalent regions in M.EcoRII and dcm, both of which recognise 5'
      CC(A/T)GG 3', a subset of the ScrFI endonuclease recognition site. In M.ScrFIA, a larger than
      normal spacing between motifs II and III, comparable in length and bearing marginal homology
      to a similar region in the SssI methylase, was observed. Recent evidence suggests that the
      ScrFI restriction endonuclease gene resides in the 1 kb intervening region between mscrFIA and
      mscrFIB. Furthermore, it is proposed that a gene (orfX) located three nucleotides upstream of
      mscrFIB encodes a repair endonuclease which compensates for the inherent ability of
      5-methylcytosine to deaminate spontaneously to thymine.
AU  - Twomey DP
AU  - Davis R
AU  - Daly C
AU  - Fitzgerald GF
PT  - Journal Article
TA  - Irish J. Agr. Food Res.
JT  - Irish J. Agr. Food Res.
SO  - Irish J. Agr. Food Res. 1993 32: 217.

PMID- 10831451
VI  - 66
DP  - 2000
TI  - Characterization of AbiR, a novel multicomponent abortive infection mechanism encoded by plasmid pKR223 of Lactococcus lactis subsp. lactis KR2.
PG  - 2647-2651
AB  - The native lactococcal plasmid pKR223 encodes two distinct phage resistance mechanisms, a
      restriction and modification (R/M) system designated LlaKR2I and an abortive infection
      mechanism (Abi) which affects prolate-headed-phage proliferation. The nucleotide sequence of a
      16,174-bp segment of pKR223 encompassing both the R/M and Abi determinants has been
      determined, and sequence analysis has validated the novelty of the Abi system, which has now
      been designated AbiR. Analysis of deletion and insertion clones demonstrated that AbiR was
      encoded by two genetic loci, separated by the LlaKR2I R/M genes. Mechanistic studies on the
      AbiR phenotype indicated that it was heat sensitive and that it impeded phage DNA replication.
      These data indicated that AbiR is a novel multicomponent, heat-sensitive, "early"-functioning
      Abi system and is the first lactococcal Abi system described which is encoded by two separated
      genetic loci.
AU  - Twomey DP
AU  - De Urraza PJ
AU  - McKay LL
AU  - O'Sullivan DJ
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2000 66: 2647-2651.

PMID- 9245816
VI  - 143
DP  - 1997
TI  - Molecular characterization of the restriction endonuclease gene (scrFIR) associated with the ScrFI restriction/modification system from Lactococcus lactis subsp. cremoris UC503.
PG  - 2277-2286
AB  - The nucleotide sequence of the chromosomally encoded type II ScrFI restriction/modification
      system from Lactococcus lactis subsp. cremoris UC503 was completed.  The ScrFI restriction
      endonuclease has previously been shown to specifically recognize 5' CCNGG 3' sites, cleaving
      after the second cytosine and the degenerate central base.  The Enase gene was located
      between, and co-directionally transcribed with, two formerly characterized 5-methylcytosine
      methyltransferase genes, which encode proteins that independently confer protection against
      ScrFI digestion.  scrFIR codes for a protein of 272 amino acids with a predicted molecular
      mass of 31470 Da, which agrees favorably with a previously estimated molecular mass of 34 kDa
      for this enzyme.  The deduced sequence of this protein did not show any significant homology
      with known protein sequences, including the isoschizomeric SsoII Enase from Shigella sonnei.
      The Enase gene was cloned and expressed in Escherichia coli and lactococcus; however, no in
      vivo restriction of phage was observed, suggesting that expression of the Enase gene may be
      repressed, or that the appropriate expression signals may be absent in the cloned constructs.
      The ability of ScrFi to cleave non-canonically modified 5'CCNGG3' sequences suggested that
      some ScrFI sites may require complex modifications to fully impair digestion by this enzyme.
AU  - Twomey DP
AU  - Gabillet N
AU  - Daly C
AU  - Fitzgerald GF
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 1997 143: 2277-2286.

PMID- 9811640
VI  - 180
DP  - 1998
TI  - Molecular characterization of the Lactococcus lactis LlaKR2I restriction-modification system and effect of an IS982 element positioned between the restriction and modification genes.
PG  - 5844-5854
AB  - The nucleotide sequence of the plasmid-encoded LlaKR2I restriction-modification system of
      Lactococcus lactis subsp. lactis biovar diacetylactis KR2 was determined.  This R-M system
      comprises divergently transcribed endonuclease (llaKR2IR) and methyltransferase llaKR2IM)
      genes; located in the intergenic region is a copy of the insertion element IS982, whose
      putative transposase gene is codirectionally transcribed with llaKR2IM.  The deduced sequence
      of the LlaKR2I endonuclease shared homology with the type II endonuclease Sau3AI and with the
      MutH mismatch repair protein, both of which recognize and cleave the sequence 5'GATC3'.  In
      addition, M.LlaKR2I displayed homology with the 5-methycytosine methyltransferase family of
      proteins, exhibiting greatest identity with M.Sau3AI.  Both of these proteins shared notable
      homology throughout their putative target recognition domains.  Furthermore, subclones of the
      native parental lactococcal plasmid pKR223, which encode M.LlaKR2I, all remained undigested
      after treatment with Sau3AI despite the presence of multiple 5'GATC3' sites.  The
      combination of these data suggested that the specificity of the LlaKR2I R-M system was likely
      to be 5'GATC3', with the cytosine residue being modified to 5-methylcytosine.  The IS982
      element located within the LlaKR2I R-M system contained at its extremities two 16-bp perfect
      inverted repeats flanked by two 7-bp direct repeats.  A perfect extended promoter consensus,
      which represented the likely original promoter of the llaKR21I gene, was shown to overlap the
      direct repeat sequence on the other side of IS982.  Specific deletion of IS982 and one of
      these direct repeats via a PCR strategy indicated that the LlaKR2I R-M determinants do not
      rely on elements within IS982 for expression and that the efficiency of bacteriophage
      restriction was not impaired.
AU  - Twomey DP
AU  - McKay LL
AU  - O'Sullivan DJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1998 180: 5844-5854.

PMID- Not carried by PubMed...
VI  - 97
DP  - 1997
TI  - Molecular characterization of the LlaKR2I restriction and modification system from Lactococcus lactis ssp. lactis KR2.
PG  - 426
AB  - Lactococcus lactis ssp. lactis KR2 contains at least two plasmid-encoded restriction and
      modification (R/M) systems and the genetic determinants of one of these systems, designated
      LlaKR2I, have been localized on the 36 kb plasmid, pKR223, and sequenced.  The LlaKR2I R/M
      genes were found to be divergently transcribed with respect to each other, with a complete
      copy of the IS-like element, IS982, located in the intergenic region.  The deduced protein
      sequence of the modification component displayed greatest identity with M.Sau3AI throughout
      the entire length of the protein.  Both methylases contained motifs characteristic of
      5-methylcytosine methylases and shared extensive homology throughout their predicted target
      recognition domains, regions responsible for the sequence specificity of these proteins.  In
      pKR223, and various derivatives, M.LlaKR2I prevented Sau3AI from digesting at 5' GATC 3'
      sites.  Furthermore, since the deduced protein sequence of the LlaKR2I endonuclease shared
      significant homology with Sau3AI, the specificity of the LlaKR2I R/M system is believed to be
      5' GATC 3', with the cytosine residue the target base for methylation.  The small
      isometric-headed phage, osk11, was only modestly restricted on lactococcal cells harboring the
      LlaKR2I R/M system and despite the presence of 5' GATC 3' sites in the genome of the
      prolate-headed phage oc2, no detectable restriction occurred.  The poor in vivo restriction
      may have resulted from either decreased expression of the endonuclease and/or enhanced
      expression of the methylase and may be due, in part, to the presence of IS982 located between
      the endonuclease and methylase genes, whose putative transposase gene is co-directionally
      transcribed with the methylase gene.
AU  - Twomey DP
AU  - McKay LL
AU  - O'Sullivan DJ
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1997 97: 426.

PMID- 9157244
VI  - 23
DP  - 1997
TI  - The type IC hsd loci of the enterobacteria are flanked by DNA with high homology to the phage P1 genome: implications for the evolution and spread of DNA restriction systems.
PG  - 729-736
AB  - EcoR124I, EcoDXXI and EcoprrI are the known members of the type IC family of DNA restriction
      and modification systems.  The first three are carried on large conjugative plasmids, while
      EcoprrI is chromosomally encoded.  The enzymes are coded by three genes, hsdR, hsdM and hsdS.
      Analysis of the DNA sequences upstream and downstream of the type IC hsd loci shows that all
      are highly homologous to each other and also to sequences present in the bacteriophage P1
      genome.  The upstream sequences include functional phd and doc genes, which encode an
      addiction system that stabilizes the P1 prophage state, and extend to and beyond pac, the site
      at which phage DNA packaging begins.  Downstream of the hsd loci, P1 DNA sequences begin at
      exactly the same place for all of the systems.  For EcoDXXI and EcoprrI the P1 homology
      extends for thousands of base pairs while for EcoR124I an IS1 insertion and an associated
      deletion have removed most of the P1-homologous sequences.  The significance of these results
      for the evolution of DNA restriction and modification systems is discussed.
AU  - Tyndall C
AU  - Lehnherr H
AU  - Sandmeier U
AU  - Kulik E
AU  - Bickle TA
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1997 23: 729-736.

PMID- 8145241
VI  - 237
DP  - 1994
TI  - The Escherichia coli prr region encodes a functional type IC DNA restriction system closely integrated with an anticodon nuclease gene.
PG  - 266-274
AB  - The prr locus was originally described as coding a ribonuclease that is activated after phage
      T4 infection to cut within the anticodon of a specific tRNA, inactivating protein synthesis
      and thus blocking phage development. Wild-type T4 phage has two genes coding the enzymes
      polynucleotide kinase and RNA ligase, whose only function seems to be to repair the damage
      done by the anticodon nuclease. As the only apparent function of the prr ribonuclease is to
      combat phage infection, it can be considered as an RNA-based restriction enzyme. In
      non-infected cells, the prr enzyme is kept inactive in a complex with three other proteins
      which were predicted on the basis of DNA homologies to be the subunits of a type IC DNA
      restriction and modifiction system. Unlike other type IC systems so far characterized, prr is
      chromosomally rather than plasmid coded. However, sequences upstream from prr also have
      homology with sequences from the plasmid R124 and the prophage P1. We have now investigated
      the prr system and shown that it is indeed a bona fide type IC system which we call EcoprrI,
      and which is active both in vivo and in vitro. The system is fully functional even in the
      absence of the anticodon nuclease and seems to be a typical type I enzyme. EcoprrI recognizes
      the sequence CCA(N7)RTGC. One peculiarity is that, with low efficiency, EcoprrI will recognize
      and methylate variants of its recognition sequence such as CCT(N7)ATGC, which is methylated in
      one strand of the DNA only.
AU  - Tyndall C
AU  - Meister J
AU  - Bickle TA
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1994 237: 266-274.

PMID- 14961025
VI  - 428
DP  - 2004
TI  - Community structure and metabolism through reconstruction of microbial genomes from the environment.
PG  - 37-43
AB  - Microbial communities are vital in the functioning of all ecosystems; however, most
      microorganisms are uncultivated, and their roles in natural
      systems are unclear. Here, using random shotgun sequencing of DNA from a
      natural acidophilic biofilm, we report reconstruction of near-complete
      genomes of Leptospirillum group II and Ferroplasma type II, and partial
      recovery of three other genomes. This was possible because the biofilm was
      dominated by a small number of species populations and the frequency of
      genomic rearrangements and gene insertions or deletions was relatively
      low. Because each sequence read came from a different individual, we could
      determine that single-nucleotide polymorphisms are the predominant form of
      heterogeneity at the strain level. The Leptospirillum group II genome had
      remarkably few nucleotide polymorphisms, despite the existence of
      low-abundance variants. The Ferroplasma type II genome seems to be a
      composite from three ancestral strains that have undergone homologous
      recombination to form a large population of mosaic genomes. Analysis of
      the gene complement for each organism revealed the pathways for carbon and
      nitrogen fixation and energy generation, and provided insights into
      survival strategies in an extreme environment.
AU  - Tyson GW
AU  - Chapman J
AU  - Hugenholtz P
AU  - Allen EE
AU  - Ram RJ
AU  - Richardson PM
AU  - Solovyev VV
AU  - Rubin EM
AU  - Rokhsar DS
AU  - Banfield JF
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2004 428: 37-43.

PMID- 26988041
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Enterococcus faecium Commensal Isolate E1002.
PG  - e00113-16
AB  - The emergence of vancomycin-resistant enterococci (VRE) has been associated with  an increase
      in multidrug-resistant nosocomial infections. Here, we report the
      2.614-Mb genome sequence of the Enterococcus faecium commensal isolate E1002,
      which will be instrumental in further understanding the determinants of the
      commensal and pathogenic lifestyle of E. faecium.
AU  - Tytgat HL
AU  - Douillard FP
AU  - Laine PK
AU  - Paulin L
AU  - Willems RJ
AU  - de Vos WM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00113-16.

PMID- 2602152
VI  - 17
DP  - 1989
TI  - High resolution footprinting of EcoRI and distamycin with Rh(phi)2(bpy)3+, a new photofootprinting reagent.
PG  - 10259-10279
AB  - The complex bis(phenanthrenequinone diimine)(bipyridyl)rhodium(III),
      Rh(phi)2(bpy)3+, cleaves DNA efficiently in a sequence-neutral fashion upon
      photoactivation so as to provide a novel, high resolution, chemical
      photofootprinting reagent.  Photofootprinting of two crystallographically
      characterized DNA-binding agents, distamycin, a small natural product which
      binds to DNA in the minor groove, and the endonuclease EcoRI, which binds in
      the major groove, gave respectively a 5-7 base pair footprint for the drug at
      its A6 binding site and a 10-12 base pair footprint for the enzyme centered at
      its recognition site (5'-GAATTC-3').  Both footprints agree closely with the
      crystallographic results.  The photocleavage reaction can be performed using
      either a high intensity lamp or, conveniently, a simple transilluminator box,
      and the photoreaction is not inhibited by moderate concentrations of reagents
      which are sometimes required for examining interactions of molecules with DNA.
      When compared with other popular footprinting agents, the rhodium complex shows
      a number of distinct advantages:  sequence-neutrality, high resolution, ability
      to footrpint major as well as minor groove-binding ligands, applicability in
      the presence of additives such as Mg2+ or glycerol, ease of handling, and a
      sharply footprinted pattern.  Light activated footprinting reactions
      furthermore offer the possibility of examining DNA-binding interactions with
      time resolution and within the cell.
AU  - Uchida K
AU  - Pyle AM
AU  - Morii T
AU  - Barton JK
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 10259-10279.

PMID- 27634994
VI  - 4
DP  - 2016
TI  - Complete Genome Sequences of 12 Species of Stable Defined Moderately Diverse Mouse Microbiota 2.
PG  - e00951-16
AB  - We report here the complete genome sequences of 12 bacterial species of stable defined
      moderately diverse mouse microbiota 2 (sDMDMm2) used to colonize
      germ-free mice with defined microbes. Whole-genome sequencing of these species
      was performed using the PacBio sequencing platform yielding circularized genome
      sequences of all 12 species.
AU  - Uchimura Y
AU  - Wyss M
AU  - Brugiroux S
AU  - Limenitakis JP
AU  - Stecher B
AU  - McCoy KD
AU  - Macpherson AJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00951-16.

PMID- 26568785
VI  - 10
DP  - 2015
TI  - Complete genome sequencing of Dehalococcoides sp. strain UCH007 using a differential reads picking method.
PG  - 102
AB  - A novel Dehalococcoides sp. strain UCH007 was isolated from the groundwater polluted with
      chlorinated ethenes in Japan. This strain is capable of
      dechlorinating trichloroethene, cis-1,2-dichloroethene and vinyl chloride to
      ethene. Dehalococcoides bacteria are hardly cultivable, so genome sequencing has
      presented a challenge. In this study, we developed a differential reads picking
      method for mixed genomic DNA obtained from a co-culture, and applied it to the
      sequencing of strain UCH007. The genome of strain UCH007 consists of a
      1,473,548-bp chromosome that encodes 1509 coding sequences including 29 putative
      reductive dehalogenase genes. Strain UCH007 is the first strain in the Victoria
      subgroup found to possess the pceA, tceA and vcrA genes.
AU  - Uchino Y
AU  - Miura T
AU  - Hosoyama A
AU  - Ohji S
AU  - Yamazoe A
AU  - Ito M
AU  - Takahata Y
AU  - Suzuki K
AU  - Fujita N
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 102.

PMID- 29700148
VI  - 6
DP  - 2018
TI  - Reevaluation of the Complete Genome Sequence of Magnetospirillum gryphiswaldense  MSR-1 with Single-Molecule Real-Time Sequencing Data.
PG  - e00309-18
AB  - Magnetospirillum gryphiswaldense is a key organism for understanding magnetosome  formation
      and magnetotaxis. As earlier studies suggested a high genomic
      plasticity, we (re)sequenced the type strain MSR-1 and the laboratory strain
      R3/S1. Both sequences differ by only 11 point mutations, but organization of the
      magnetosome island deviates from that of previous genome sequences.
AU  - Uebe R
AU  - Schuler D
AU  - Jogler C
AU  - Wiegand S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00309-18.

PMID- 15383646
VI  - 32
DP  - 2004
TI  - Genome sequence of Symbiobacterium thermophilum, an uncultivable bacterium that depends on microbial commensalisms.
PG  - 4937-4944
AB  - Symbiobacterium thermophilum is an uncultivable bacterium isolated from compost that depends
      on microbial commensalism. The 16S ribosomal DNA-based phylogeny suggests that this bacterium
      belongs to an unknown taxon in the Gram-positive bacterial cluster. Here, we describe the 3.57
      Mb genome sequence of S.thermophilum. The genome consists of 3338 protein-coding sequences,
      out of which 2082 have functional assignments. Despite the high G + C content (68.7%), the
      genome is closest to that of Firmicutes, a phylum consisting of low G + C Gram-positive
      bacteria. This provides evidence for the presence of an undefined category in the
      Gram-positive bacterial group. The presence of both spo and related genes and microscopic
      observation indicate that S.thermophilum is the first high G + C organism that forms
      endospores. The S.thermophilum genome is also characterized by the widespread insertion of
      class C group II introns, which are oriented in the same direction as chromosomal replication.
      The genome has many membrane transporters, a number of which are involved in the uptake of
      peptides and amino acids. The genes involved in primary metabolism are largely identified,
      except those that code several biosynthetic enzymes and carbonic anhydrase. The organism also
      has a variety of respiratory systems including Nap nitrate reductase, which has been found
      only in Gram-negative bacteria. Overall, these features suggest that S.thermophilum is
      adaptable to and thus lives in various environments, such that its growth requirement could be
      a substance or a physiological condition that is generally available in the natural
      environment rather than a highly specific substance that is present only in a limited niche.
      The genomic information from S.thermophilum offers new insights into microbial diversity and
      evolutionary sciences, and provides a framework for characterizing the molecular basis
      underlying microbial commensalism.
AU  - Ueda K
AU  - Yamashita A
AU  - Ishikawa J
AU  - Shimada M
AU  - Watsuji T-o
AU  - Morimura K
AU  - Ikeda H
AU  - Hattori M
AU  - Beppu T
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2004 32: 4937-4944.

PMID- 8710495
VI  - 24
DP  - 1996
TI  - Cloning and expression of the BalI restriction-modification system.
PG  - 2268-2270
AB  - BalI, a type II restriction-modification (R-M) system from the bacterium,
      Brevibacterium albidum, recognizes the DNA sequence 5'-TGGCCA-3'.  We cloned the genes
      encoding the BalI restriction endonuclease and methyltransferase and expressed them in
      Escherichia coli.  The two genes were aligned tail-to-tail and their termination codons
      overlapped.
      BalI restriction endonuclease and methyltransferase comprise 260 and 280 amino acids,
      respectively, and have molecular weights of 29,043 and 31,999 Da.  The amino acid sequence of
      BalI methyltransferase is similar to that of other m6A Mtases, although it has been
      categorized as
      an m5C methyltransferase.  A high expression system for the BalI restriction endonuclease was
      constructed in E.coli for the production of large quantities of enzyme.
AU  - Ueno H
AU  - Kato I
AU  - Ishino Y
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1996 24: 2268-2270.

PMID- Not included in PubMed...
VI  - 61
DP  - 1997
TI  - Production of new restriction endonuclease VpaK11BI recognizing sequence 5'-GGWCC-3' in a Haemolysin-less mutant of Vibrio parahaemolyticus.
PG  - 2129-2130
AB  - High restriction endonuclease activity was found in a haemolysinless mutant of the Vibrio
      parahaemolyticus 1743-1 strain.  The endonuclease, named VpaK11BI, recognized the palindromic
      pentanucleotide sequence of 5'-GGWCC-3' and cleaved double-stranded DNA after the first G,
      which is exactly the same as the specificity of AvaII.  The haemolysin-less mutant of V.
      parahaemolyticus is now available for producing the valuable restriction endonuclease on a
      commercial scale.
AU  - Ueno H
AU  - Kita A
AU  - Miyahara M
AU  - Ishiwata N
AU  - Mise K
AU  - Kato I
AU  - Ishino Y
PT  - Journal Article
TA  - Biosci. Biotechnol. Biochem.
JT  - Biosci. Biotechnol. Biochem.
SO  - Biosci. Biotechnol. Biochem. 1997 61: 2129-2130.

PMID- 8506128
VI  - 21
DP  - 1993
TI  - Gene structure and expression of the MboI restriction-modification system.
PG  - 2309-2313
AB  - The genes from Moraxella bovis encoding the MboI restriction-modification system were cloned
      and expressed in Escherichia coli. Three open reading frames were found in the sequence
      containing the genes. These genes, which we named mboA, mboB, and mboC, had the same
      orientation in the genome. Genes mboA and mboC encoded MboI methyltransferases (named M.MboA
      and M.MboC) with 294 and 273 amino acid residues, respectively. The mboB gene coded for MboI
      restriction endonuclease (R.MboI) with 280 amino acid residues. Recombinant E. coli-MBOI,
      which contained the whole MboI system, overproduced R.MboI. R.MboI activity from E.coli-MBOI
      was 480-fold that of M.bovis. The amino acid sequences deduced from these genes were compared
      with those of other restriction-modification systems. The protein sequences of the MboI system
      had 38-49% homology with those of the DpnII system.
AU  - Ueno T
AU  - Ito H
AU  - Kimizuka F
AU  - Kotani H
AU  - Nakajima K
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 2309-2313.

PMID- 8367311
VI  - 21
DP  - 1993
TI  - Cloning and expression of the NspV restriction modification genes of Nostoc sp. strain PCC7524.
PG  - 3899
AB  - The NspV restriction-modification system of the filamentous cyanobacterium Nostoc sp. strain
      PCC7524 consists of NspV restriction endonuclease (R.NspV) and NspV modification enzyme
      (M.NspV). R.NspV recognizes and cleaves double-stranded DNA at the sequence 5'-TTCGAA-3',
      and M.NspV recognizes and protects this sequence by methylation against R.NspV. We cloned the
      genes in Escherichia coli and analyzed their structure.
AU  - Ueno T
AU  - Ito H
AU  - Kotani H
AU  - Kimizuka F
AU  - Nakajima K
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 3899.

PMID- Not carried by PubMed...
VI  - 14
DP  - 1996
TI  - Nsp7524V restriction-modification genes.
PG  - 465
AB  - To provide Nsp7524V restriction-modification genes and a method for producing Nsp7524V
      restriction enzyme and Nsp7524V modification enzyme by using a novel microorganism having,
      introduced thereinto, plasmids containing said genes, Nsp7524V restriction-modification genes.
      A method for producing Nsp7524V restriction enzyme and/or Nsp7524V modification enzyme which
      comprises incubating a microorganism carrying a plasmid having, integrated thereinto, Nsp7524V
      restriction-modification genes, and recovering the Nsp7524V restriction enzyme and/or Nsp7524V
      modification enzyme thus produced from the culture.  It becomes possible to efficiently
      produce Nsp7524V restriction enzyme and/or Nsp7524V modification enzyme which are useful in
      the field of genetic engineering.
AU  - Ueno T
AU  - Ito I
AU  - Kotani H
AU  - Nakajima K
PT  - Journal Article
TA  - Biotech. Advances
JT  - Biotech. Advances
SO  - Biotech. Advances 1996 14: 465.

PMID- 14165325
VI  - 22
DP  - 1964
TI  - On the mechanism of host-induced modification:  Multiplicity activation and thermolabile factor responsible for phage growth restriction.
PG  - 202-213
AB  - Salmonella phage sigma15 grown undergoes host-induced modification (HIM).
      Phage sigma15[A] (phage sigma15 grown on Salmonella anatum, called strain A)
      plates with low EOP on Salmonella butantan (=I-1) and vice versa.  The
      restricting properties of the host cells on phage growth can be overcome by
      multiple infection (multiplicity activation) with restricted normal phage or
      with its temperature-sensitive mutant, but not with ultraviolet
      (UV)-inactivated phage.  The phage-growth restricting factor is inactivated by
      a short exposure of cells to slight heat, and its synthesis is inhibited by
      chloramphenicol, but not by mitomycin C.  Experiments with P32-labeled phages
      shown that the DNA of the restricted phage is degraded rapidly after injection
      of the nonpermissive host, and that the degradation of injected DNA is
      prevented by heating the host cells prior to infection or by UV irradiation of
      the restricted phage.
AU  - Uetake H
AU  - Toyama S
AU  - Hagiwara S
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1964 22: 202-213.

PMID- 24336364
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of 'Candidatus Halobonum tyrrellensis' Strain G22, Isolated from the Hypersaline Waters of Lake Tyrrell, Australia.
PG  - e01001-13
AB  - We report the draft 3.675-Mbp genome sequence of 'Candidatus Halobonum tyrrellensis' strain
      G22, a novel halophilic archaeon isolated from the surface
      hypersaline waters of Lake Tyrrell, Australia. The availability of the first
      genome from the 'Candidatus Halobonum' genus provides a new genomic resource for
      the comparative genomic analysis of halophilic Archaea.
AU  - Ugalde JA
AU  - Narasingarao P
AU  - Kuo S
AU  - Podell S
AU  - Allen EE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01001-13.

PMID- 22375071
VI  - 3
DP  - 2012
TI  - Identification of a highly transmissible animal-independent Staphylococcus aureus ST398 clone with distinct genomic and cell adhesion properties.
PG  - e00027-12
AB  - A methicillin-resistant Staphylococcus aureus (MRSA) clone known as ST398 has
      emerged as a major cause of acute infections in individuals who have close
      contact with livestock. More recently, the emergence of an animal-independent
      ST398 methicillin-sensitive S. aureus (MSSA) clone has been documented in several
      countries. However, the limited surveillance of MSSA has precluded an accurate
      assessment of the global spread of ST398 and its clinical relevance. Here we
      provide evidence that ST398 is a frequent source of MSSA infections in northern
      Manhattan and is readily transmitted between individuals in households. This
      contrasts with the limited transmissibility of livestock-associated ST398
      (LA-ST398) MRSA strains between humans. Our whole-genome sequence analysis
      revealed that the chromosome of the human-associated ST398 MSSA clone is smaller
      than that of the LA-ST398 MRSA reference strain S0385, due mainly to fewer mobile
      genetic elements (MGEs). In contrast, human ST398 MSSA isolates harbored the
      prophage varphi3 and the human-specific immune evasion cluster (IEC) genes chp
      and scn. While most of the core genome was conserved between the human ST398 MSSA
      clone and S0385, these strains differed substantially in their repertoire and
      composition of intact adhesion genes. These genetic changes were associated with
      significantly enhanced adhesion of human ST398 MSSA isolates to human skin
      keratinocytes and keratin. We propose that the human ST398 MSSA clone can spread
      independent of animal contact using an optimized repertoire of MGEs and adhesion
      molecules adapted to transmission among humans. IMPORTANCE: Staphylococcus aureus
      strains have generally been considered to be species specific. However,
      cross-species transfers of S. aureus clones, such as ST398 methicillin-resistant
      S. aureus (MRSA), from swine to humans have been reported. Recently, we observed
      the emergence of ST398 methicillin-susceptible S. aureus (MSSA) as a colonizing
      strain of humans in northern Manhattan. Here we report that ST398 is a frequent
      cause of MSSA infections in this urban setting. The ST398 MSSA clone was readily
      transmitted within households, independent of animal contact. We discovered that
      human ST398 MSSA genomes were smaller than that of the LA-ST398 strain S0385 due
      to fewer mobile genetic elements. Human and LA-ST398 strains also differed in
      their composition of adhesion genes and their ability to bind to human skin
      keratinocytes, providing a potential mechanism of S. aureus host adaptation. Our
      findings illustrate the importance of implementing molecular surveillance of MSSA
      given the evidence for the rapid and clinically undetected spread of ST398 MSSA.
AU  - Uhlemann AC
AU  - Porcella SF
AU  - Trivedi S
AU  - Sullivan SB
AU  - Hafer C
AU  - Kennedy AD
AU  - Barbian KD
AU  - McCarthy AJ
AU  - Street C
AU  - Hirschberg DL
AU  - Lipkin WI
AU  - Lindsay JA
AU  - DeLeo FR
AU  - Lowy FD
PT  - Journal Article
TA  - MBio
JT  - MBio
SO  - MBio 2012 3: e00027-12.

PMID- 27417834
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequence of Escherichia coli Serotype O157:H7 Strain EDL932 (ATCC 43894).
PG  - e00647-16
AB  - The genome sequence of Escherichia coli serotype O157:H7 EDL933, a ground beef isolate from a
      1983 hemorrhagic colitis outbreak, is a standard reference for
      comparative genomic studies of Shiga toxin-producing E. coli strains. Here, we
      report the genome sequence of a patient stool isolate from that outbreak, strain
      EDL932.
AU  - Uhlich GA
AU  - Paoli GC
AU  - Chen CY
AU  - Cottrell BJ
AU  - Zhang X
AU  - Yan X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00647-16.

PMID- 28082498
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequence of Escherichia coli Serotype O157:H7 Strain PA20.
PG  - e01460-16
AB  - Escherichia coli serotype O157:H7 strain PA20 is a Pennsylvania Department of Health clinical
      isolate. It has been used to study biofilm formation in O157:H7
      clinical isolates, where the high incidence of prophage insertions in the mlrA
      transcription factor disrupts traditional csgD biofilm regulation. Here, we
      report the complete PA20 genome sequence.
AU  - Uhlich GA
AU  - Paoli GC
AU  - Zhang X
AU  - Dudley EG
AU  - Figler HM
AU  - Cottrell BJ
AU  - Andreozzi E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01460-16.

PMID- 29097463
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequence of Escherichia coli Serotype O157:H7 Strain B6914-ARS.
PG  - e01191-17
AB  - Escherichia coli serotype O157:H7 strain B6914-MS1 is an isolate from the Centers for Disease
      Control and Prevention that is missing both Shiga toxin genes and has
      been used extensively in applied research studies. Here we report the genome
      sequence of strain B6914-ARS, a B6914-MS1 clone that has unique biofilm
      properties.
AU  - Uhlich GA
AU  - Reichenberger ER
AU  - Cottrell BJ
AU  - Fratamico P
AU  - Andreozzi E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01191-17.

PMID- 27284147
VI  - 4
DP  - 2016
TI  - Genome Sequence of the Autotrophic Acetogen Clostridium magnum DSM 2767.
PG  - e00464-16
AB  - Here we report the draft genome sequence (6.6 Mbp) of the type strain Clostridium magnum, an
      acetogen with two operons coding for two separate Rnf complexes. C.
      magnum grows on a broad range of organic substrates and converts CO2 and H2 to
      acetate using the Wood-Ljungdahl pathway.
AU  - Uhlig R
AU  - Poehlein A
AU  - Fischer RJ
AU  - Daniel R
AU  - Bahl H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00464-16.

PMID- 22753027
VI  - 40
DP  - 2012
TI  - Screening for catalytically active Type II restriction endonucleases using segregation-induced methylation deficiency.
PG  - e149
AB  - Type II restriction endonucleases (REases) are one of the basic tools of recombinant DNA
      technology. They also serve as models for elucidation of
      mechanisms for both site-specific DNA recognition and cleavage by proteins.
      However, isolation of catalytically active mutants from their libraries is
      challenging due to the toxicity of REases in the absence of protecting
      methylation, and techniques explored so far had limited success. Here, we present
      an improved SOS induction-based approach for in vivo screening of active REases,
      which we used to isolate a set of active variants of the catalytic mutant,
      Cfr10I(E204Q). Detailed characterization of plasmids from 64 colonies screened
      from the library of approximately 200 000 transformants revealed 29 variants of
      cfr10IR gene at the level of nucleotide sequence and 15 variants at the level of
      amino acid sequence, all of which were able to induce SOS response. Specific
      activity measurements of affinity-purified mutants revealed >200-fold variance
      among them, ranging from 100% (wild-type isolates) to 0.5% (S188C mutant),
      suggesting that the technique is equally suited for screening of mutants
      possessing high or low activity and confirming that it may be applied for
      identification of residues playing a role in catalysis.
AU  - Ukanis M
AU  - Sapranauskas R
AU  - Lubys A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: e149.

PMID- 21288879
VI  - 39
DP  - 2011
TI  - Comprehensive computational design of mCreI homing endonuclease cleavage specificity for genome engineering.
PG  - 4330-4339
AB  - Homing endonucleases (HEs) cleave long ( approximately 20 bp) DNA target sites with high site
      specificity to catalyze the lateral transfer of
      parasitic DNA elements. In order to determine whether comprehensive
      computational design could be used as a general strategy to engineer new
      HE target site specificities, we used RosettaDesign (RD) to generate 3200
      different variants of the mCreI LAGLIDADG HE towards 16 different base
      pair positions in the 22 bp mCreI target site. Experimental verification
      of a range of these designs demonstrated that over 2/3 (24 of 35 designs,
      69%) had the intended new site specificity, and that 14 of the 15
      attempted specificity shifts (93%) were achieved. These results
      demonstrate the feasibility of using structure-based computational design
      to engineer HE variants with novel target site specificities to facilitate
      genome engineering.
AU  - Ulge UY
AU  - Baker DA
AU  - Monnat RJ Jr
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2011 39: 4330-4339.

PMID- 26380040
VI  - 10
DP  - 2015
TI  - Permanent draft genome sequence of Acidiphilium sp. JA12-A1.
PG  - 56
AB  - The tenacious association between strains of the heterotrophic alphaproteobacterial genus
      Acidiphilium and chemolithotrophic iron oxidizing bacteria has long been known. In this
      context the genome of the heterotroph Acidiphilium sp. JA12-A1, an isolate from an iron
      oxidizing mixed culture derived from a pilot plant for bioremediation of acid mine drainage,
      was determined with  the aim to reveal metabolic properties that are fundamental for the
      syntrophic interaction between Acidiphilium sp. JA12-A1 and the co-occurring
      chemolithoautotrophic iron oxidizer. The genome sequence consists of 4.18 Mbp on  297 contigs
      and harbors 4015 protein-coding genes and 50 RNA genes. Additionally, the molecular and
      functional organization of the Acidiphilium sp. JA12-A1 draft genome was compared to those of
      the close relatives Acidiphilium cryptum JF-5, Acidiphilium multivorum AIU301 and Acidiphilium
      sp. PM DSM 24941. The comparative genome analysis underlines the close relationship between
      these strains and the highly similar metabolic potential supports the idea that other
      Acidiphilium strains play a similar role in various acid mine drainage communities.
      Nevertheless, in contrast to other closely related strains Acidiphilium sp. JA12-A1 may be
      able to take up phosphonates as an additional source of phosphor.
AU  - Ullrich SR
AU  - Poehlein A
AU  - Voget S
AU  - Hoppert M
AU  - Daniel R
AU  - Leimbach A
AU  - Tischler JS
AU  - Schlomann M
AU  - Muhling M
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 56.

PMID- 25059870
VI  - 2
DP  - 2014
TI  - Draft Whole Genome Sequence of Bacillus pumilus Strain 3-19, a Chemical Mutant Overproducing Extracellular Ribonuclease.
PG  - e00724-14
AB  - Here, we present a draft genome sequence of Bacillus pumilus strain 3-19. It was  derived from
      soil-isolated B. pumilus 7P using chemical mutagenesis and is
      characterized by elevated production of extracellular ribonuclease which is known
      to possess different biological activities with potential of applications in
      experimental research, medicine, and biotechnology.
AU  - Ulyanova V
AU  - Shah MR
AU  - Dudkina E
AU  - Vershinina V
AU  - Ilinskaya O
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00724-14.

PMID- Not carried by PubMed...
VI  - 27
DP  - 1994
TI  - Alteration of specificity of restriction endonuclease EcoRI in organic solvent.
PG  - 401-407
AB  - In molecular biology, type-II restriction endonucleases, which specifically cleave DNA at a
      limited number of sites, have been exploited as a means of characterizing DNA fragments, DNA
      mapping and of modifying DNA for genetic engineering. Recently, many type-II restriction
      endonucleases have been found to decrease their substrate specificity under modified
      conditions such as extreme pH, low ionic strength, high enzyme concentration, substitution of
      metallic cofactors, or addition of organic solvents. This study used restriction endonuclease
      EcoRI which is used most frequently in genetic engineering. We investigated their specificity
      change in buffer conditions including various organic solvents. The specificity of cleavage of
      EcoRI is altered in the presence of hydrophobic reagents, such as ethanol, ethyleneglycol and
      DMSO. The enzyme recognition site was not changed randomly but by preferential order by
      increasing the concentration of organic solvent. When EcoRI reacted with substrate pGEM3
      vector which has one canonical recognition site (GAATTC), EcoRI cleaved the noncanonical
      TAATTC and GAGTTC subsequently in more than 10% DMSO solution. These changes of specificities
      depended on the hydrophobicity of organic solvent (LogP: partition coefficient). As a result,
      the recognition sequence site was changed in the presence of organic solvents whose LogP are
      -2.0 to 0. The specificities were not easily changed in enzyme inactivating organic solvent
      such as acetone, 2-methyl-2-propanol, 2-methyl-1-propanol. These results show that restriction
      enzyme could be used to cleave at unusual site by changing the reaction conditions.
AU  - Um J
AU  - Park C
AU  - Lee K
PT  - Journal Article
TA  - Korean Biochem. J.
JT  - Korean Biochem. J.
SO  - Korean Biochem. J. 1994 27: 401-407.

PMID- 27651857
VI  - 11
DP  - 2016
TI  - The complete genome sequences of sulfur-oxidizing Gammaproteobacteria Sulfurifustis variabilis skN76(T) and Sulfuricaulis limicola HA5(T).
PG  - 71
AB  - Sulfurifustis variabilis and Sulfuricaulis limicola are autotrophic sulfur-oxidizing bacteria
      belonging to the family Acidiferrobacteraceae in the
      order Acidiferrobacterales. The type strains of these species, strain skN76(T)
      and strain HA5(T), were isolated from lakes in Japan. Here we describe the
      complete genome sequences of Sulfurifustis variabilis skN76(T) and Sulfuricaulis
      limicola HA5(T). The genome of Sulfurifustis variabilis skN76(T) consists of one
      circular chromosome with size of 4.0 Mbp including 3864 protein-coding sequences.
      The genome of Sulfuricaulis limicola HA5(T) is 2.9 Mbp chromosome with 2763
      protein-coding sequences. In both genomes, 46 transfer RNA-coding genes and one
      ribosomal RNA operon were identified. In the genomes, redundancies of the genes
      involved in sulfur oxidation and inorganic carbon fixation pathways were
      observed. This is the first report to show the complete genome sequences of
      bacteria belonging to the order Acidiferrobacterales in the class
      Gammaproteobacteria.
AU  - Umezawa K
AU  - Watanabe T
AU  - Miura A
AU  - Kojima H
AU  - Fukui M
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 71.

PMID- 27486455
VI  - 7
DP  - 2016
TI  - Exploring the Diversity and Antimicrobial Potential of Marine Actinobacteria from the Comau Fjord in Northern Patagonia, Chile.
PG  - 1135
AB  - Bioprospecting natural products in marine bacteria from fjord environments are
      attractive due to their unique geographical features. Although, Actinobacteria
      are well known for producing a myriad of bioactive compounds, investigations
      regarding fjord-derived marine Actinobacteria are scarce. In this study, the
      diversity and biotechnological potential of Actinobacteria isolated from marine
      sediments within the Comau fjord, in Northern Chilean Patagonia, were assessed by
      culture-based approaches. The 16S rRNA gene sequences revealed that members
      phylogenetically related to the Micrococcaceae, Dermabacteraceae,
      Brevibacteriaceae, Corynebacteriaceae, Microbacteriaceae, Dietziaceae,
      Nocardiaceae, and Streptomycetaceae families were present at the Comau fjord. A
      high diversity of cultivable Actinobacteria (10 genera) was retrieved by using
      only five different isolation media. Four isolates belonging to Arthrobacter,
      Brevibacterium, Corynebacterium and Kocuria genera showed 16S rRNA gene identity
      <98.7% suggesting that they are novel species. Physiological features such as
      salt tolerance, artificial sea water requirement, growth temperature,
      pigmentation and antimicrobial activity were evaluated. Arthrobacter,
      Brachybacterium, Curtobacterium, Rhodococcus, and Streptomyces isolates showed
      strong inhibition against both Gram-negative Pseudomonas aeruginosa, Escherichia
      coli and Salmonella enterica and Gram-positive Staphylococcus aureus, Listeria
      monocytogenes. Antimicrobial activities in Brachybacterium, Curtobacterium, and
      Rhodococcus have been scarcely reported, suggesting that non-mycelial strains are
      a suitable source of bioactive compounds. In addition, all strains bear at least
      one of the biosynthetic genes coding for NRPS (91%), PKS I (18%), and PKS II
      (73%). Our results indicate that the Comau fjord is a promising source of novel
      Actinobacteria with biotechnological potential for producing biologically active
      compounds.
AU  - Undabarrena A
AU  - Beltrametti F
AU  - Claverias FP
AU  - Gonzalez M
AU  - Moore ER
AU  - Seeger M
AU  - Camara B
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2016 7: 1135.

PMID- 28183776
VI  - 5
DP  - 2017
TI  - Genome Sequence of Streptomyces sp. H-KF8, a Marine Actinobacterium Isolated from a Northern Chilean Patagonian Fjord.
PG  - e01645-16
AB  - Streptomyces sp. H-KF8 is a fjord-derived marine actinobacterium capable of producing
      antimicrobial activity. Streptomyces sp. H-KF8 was isolated from
      sediments of the Comau fjord, located in the northern Chilean Patagonia. Here, we
      report the 7.7-Mb genome assembly, which represents the first genome of a Chilean
      marine actinobacterium.
AU  - Undabarrena A
AU  - Ugalde JA
AU  - Castro-Nallar E
AU  - Seeger M
AU  - Camara B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01645-16.

PMID- 3956763
VI  - 45
DP  - 1986
TI  - Site-specific mutagenesis of the EcoRI restriction endonuclease: substitution of cysteine-217 with glycine affects in vivo but not in vitro enzyme function.
PG  - 1875
AB  - Using oligonucleotide-directed mutagenesis, we have introduced a T - G
      transversion mutation in the cloned EcoRI restriction endonuclease gene,
      thereby substituting a glycine for the single cysteine-217.  Mutant clones were
      identified by differential colony hybridization using the mutagenesis
      oligonucleotide.  The structure of the mutant was confirmed by DNA sequence
      analysis.  Cells producing the mutant endonuclease showed a four-log increase
      in sensitivity to infection by bacteriophage lambda.  The mutant enzyme was
      partially purified and characterized.  It did not show any changes in
      recognition site-specificity or in kinetic behavior compared with that of the
      wild-type enzyme either in standard assay buffer or under altered solvent
      conditions that promoted its ability to cleave subcanonical sequences.  The
      mutant and wild-type enzymes behaved identically during analytical gel
      chromatography.  Reaction of the wild-type endonuclease with the sulfhydryl
      inhibitor parahydroxymercuribenzoate resulted in a complete loss of enzyme
      activity compared with less than tenfold inhibition for the mutant enzyme.We
      conclude that cysteine-217 may play an important role in the in vivo function
      of the EcoRI endonuclease but not in its in vitro enzymatic activity.
AU  - Underhill PA
AU  - Johnson PH
PT  - Journal Article
TA  - Fed. Proc.
JT  - Fed. Proc.
SO  - Fed. Proc. 1986 45: 1875.

PMID- 25540335
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Novel Black-Pigmented Planococcus sp. Strain CAU13.
PG  - e01160-14
AB  - Presented here is the whole-genome sequence of a previously uncharacterized species of the
      genus Planococcus. A 16S sequence analysis shows that this
      bacterium exhibits 98% sequence identity to the closest relative of Planococcus
      kocurii. Whereas most species of Planococcus produce yellow to orange pigments,
      the species described here produces black pigmentation.
AU  - Unverferth CA
AU  - Santisteban IC
AU  - Setterdahl AT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01160-14.

PMID- 12355465
VI  - 80
DP  - 2002
TI  - Modeling of the controlled expression of a harmful protein by a three-plasmid harboring system.
PG  - 544-551
AB  - A genetically structured mathematical model was developed and used to evaluate the influence
      of molecular parameters involved in the expression
      of a harmful recombinant protein (SPA::EcoRI). The system consists of the
      controlled expression of the endonuclease EcoRI cloned in the plasmid
      pMTC48. The control is exerted by the lambda Cl repressor expressed from
      the plasmid pRK248clts. The deleterious effect of the activity of the
      enzyme EcoRl on the host DNA is prevented by the action of the EcoRl
      methylase that is expressed constitutively from a third plasmid, pEcoR4.
      The model includes molecular mechanisms involved in the regulation of the
      expression of these genes and is used to determine cultural conditions
      that maximize the production of the recombinant protein.
AU  - Unzaga TV
AU  - Diaz-Ricci JC
AU  - Rhee JI
AU  - Hernandez MR
AU  - Schugerl K
PT  - Journal Article
TA  - Biotechnol. Bioeng.
JT  - Biotechnol. Bioeng.
SO  - Biotechnol. Bioeng. 2002 80: 544-551.

PMID- 405561
VI  - 152
DP  - 1977
TI  - Restriction and modification in Bacillus species.
PG  - 65-69
AB  - Host specific restriction was detected in 13 Bacillus strains, when 63 strains of Bacillus
      subtilis and 15 other Bacillus strains were tested with phage phi 105C. These 13 strains were
      classified into 8 groups (M,H,C,N,E,F,G,P) by the type of restriction. M-type strains (B.
      subtilis Marburg 168, its derivatives, and two other strains) showed relatively weak
      restriction, restricting phi 105C from other groups of Bacillus by ratios of 10(-1) to 10(-3).
      Strains of groups H,C,N,E,F,G, and P restricted phi 105C from other groups by ratios of 10(-2)
      to 10(-8). It was confirmed with some of the strains that type-specific modification was
      endowed only by the last host. Furthermore, we isolated one restriction deficient mutant of B.
      subtilis Marburg 168-YS11, which had also lost its modification phenotype.
AU  - Uozumi T
AU  - Hoshino T
AU  - Miwa K
AU  - Horinouchi S
AU  - Beppu T
AU  - Arima K
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1977 152: 65-69.

PMID- 27103711
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Bacillus clausii UBBC07, a Spore-Forming Probiotic Strain.
PG  - e00235-16
AB  - ITALIC! Bacillus clausiiUBBC07 is a safe endospore-forming strain, characterized  for defined
      therapeutic effects. The finished draft whole-genome sequence is
      presented here to scan its genetic constitution for its expanded use as a
      probiotic in various health sectors.
AU  - Upadrasta A
AU  - Pitta S
AU  - Madempudi RS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00235-16.

PMID- 27103709
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the Spore-Forming Probiotic Strain Bacillus coagulans Unique IS-2.
PG  - e00225-16
AB  - ITALIC! Bacillus coagulansUnique IS-2 is a potential spore-forming probiotic that is
      commercially available on the market. The draft genome sequence presented here
      provides deep insight into the beneficial features of this strain for its safe
      use as a probiotic for various human and animal health applications.
AU  - Upadrasta A
AU  - Pitta S
AU  - Madempudi RS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00225-16.

PMID- 2988201
VI  - 31
DP  - 1985
TI  - Restricting endonucleases from Shigella sonnei 47.
PG  - 131-136
AB  - Two restrictases SsoI and SsoII, belonging to the enzymes of restriction of the class II, were
      isolated from a strain of dysenteric bacteria.  The structure of the site sensitive to SsoI
      and SsoII was studied after fragmentation of testor DNA as well as by means of direct
      determination of nucleotide sequency.  SsoI was shown to be an isoschizomer of the EcoRI
      restrictase from E. coli. Restrictase SsoII proved to a new enzyme, which hydrolyzed the
      sequence 5'...CCNGG..3' and was distinct from the known restrictases as shown by studies of
      the type of DNA hydrolyzed.  A three-step procedure is developed for isolation of SsoII
      restrictase involving the consecutive chromatography on blue sepharose, phosphocellulose P11
      and phenyl-sepharose.  Restrictases SsoI and EcoRI were isolated by means of
      isoelectrofocusing using ampholines.
AU  - Uporova TM
AU  - Kartasheva IM
AU  - Skripkin EA
AU  - Lopareva EN
AU  - Nikolskaya II
AU  - Debov SS
PT  - Journal Article
TA  - Vopr. Med. Khim.
JT  - Vopr. Med. Khim.
SO  - Vopr. Med. Khim. 1985 31: 131-136.

PMID- 6264705
VI  - 2
DP  - 1981
TI  - Purification and identification of Eco CK restrictional endonuclease.
PG  - 21-26
AB  - A fundamentally new scheme for purifying the restrictional endonuclease from E.
      coli CK cells has been developed, involving 3 consecutive stages:  gel
      filtration (on biogel A-0.5 m), chromatography on single-stranded
      DNA-cellulose, and fractionation on heparin-sepharose.  The proposed variant of
      REco CK purification results in an enzyme preparation completely free from
      nonspecific endonucleases and exonucleases which can be used in genetic
      engineering and physical mapping work.  The fragmentation pattern of phage
      lambda DNA has been defined more precisely:  as a result of complete
      hydrolysis, 4 fragments with molecular masses of 13.25, 12.0, 5.15, and 0.7
      megadaltons are formed.  It is shown that in as far as the fragmentation
      pattern of the test phage lambda DNA is concerned, the REco CK enzyme has no
      analogues among the enzymes described so far in the literature.
AU  - Uporova TM
AU  - Nikolskaya II
AU  - Rubtsova EN
AU  - Debov SS
PT  - Journal Article
TA  - Vestn. Akad. Med. Nauk SSSR
JT  - Vestn. Akad. Med. Nauk SSSR
SO  - Vestn. Akad. Med. Nauk SSSR 1981 2: 21-26.

PMID- 25336720
VI  - 65
DP  - 2015
TI  - Nitrosospira lacus sp. nov., a psychrotolerant, ammonia-oxidizing bacterium from sandy lake sediment.
PG  - 242-250
AB  - A Gram-negative, spiral-shaped, chemolithotrophic, ammonia-oxidizing bacterium,
      designated APG3(T), was isolated into pure culture from sandy lake sediment
      collected from Green Lake, Seattle, WA, USA. Phylogenetic analyses based on the
      16S rRNA gene sequence showed that strain APG3(T) belongs to cluster 0 of the
      genus Nitrosospira, which is presently not represented by described species, with
      Nitrosospira multiformis (cluster 3) as the closest species with a validly
      published name (identity of 98.6 % to the type strain). Strain APG3(T) grew at 4
      degrees C but could not grow at 35 degrees C, indicating that this bacterium is
      psychrotolerant. Remarkably, the strain was able to grow over a wide range of pH
      (pH 5-9), which was greater than the pH range of any studied ammonia-oxidizing
      bacteria in pure culture. The DNA G+C content of the APG3(T) genome is 53.5 %,
      which is similar to that of Nitrosospira multiformis ATCC 25196(T) (53.9 %) but
      higher than that of Nitrosomonas europaea ATCC 19718 (50.7 %) and Nitrosomonas
      eutropha C71 (48.5 %). The average nucleotide identity (ANI) calculated for the
      genomes of strain APG3(T) and Nitrosospira multiformis ATCC 25196(T) was 75.45 %,
      significantly lower than the value of 95 % ANI that corresponds to the 70 %
      species-level cut-off based on DNA-DNA hybridization. Overall polyphasic taxonomy
      study indicated that strain APG3(T) represents a novel species in the genus
      Nitrosospira, for which the name Nitrosospira lacus sp. nov. is proposed (type
      strain APG3(T) = NCIMB 14869(T) = LMG 27536(T) = ATCC BAA-2542(T)).
AU  - Urakawa H
AU  - Garcia JC
AU  - Nielsen JL
AU  - Le VQ
AU  - Kozlowski JA
AU  - Stein LY
AU  - Lim CK
AU  - Pommerening-Roser A
AU  - Martens-Habbena W
AU  - Stahl DA
AU  - Klotz MG
PT  - Journal Article
TA  - Int. J. Syst. Evol. Microbiol.
JT  - Int. J. Syst. Evol. Microbiol.
SO  - Int. J. Syst. Evol. Microbiol. 2015 65: 242-250.

PMID- 25527835
VI  - 7
DP  - 2014
TI  - Contrasting inter- and intraspecies recombination patterns in the 'Harveyi clade' Vibrio collected over large spatial and temporal scales.
PG  - 71-80
AB  - Recombination plays an important role in the divergence of bacteria, but the frequency of
      interspecies and intraspecies recombination events remains poorly understood. We investigated
      recombination events that occurred within core genomes of 35 Vibrio strains (family
      Vibrionaceae, Gammaproteobacteria), from six closely related species in the so-called "Harveyi
      clade." The strains were selected from a collection of strains isolated in the last 90 years,
      from various environments worldwide. We found a close relationship between the number of
      interspecies recombination events within core genomes of the 35 strains and the overall
      genomic identity, as inferred from calculations of the average nucleotide identity. The
      relationship between the overall nucleotide identity and the number of detected interspecies
      recombination events was comparable when analyzing strains isolated over 80 years apart, from
      different hemispheres, or from different ecologies, as well as in strains isolated from the
      same geographic location within a short time frame. We further applied the same method of
      detecting recombination events to analyze 11 strains of Vibrio campbellii, and identified
      disproportionally high number of intraspecies recombination events within the core genomes of
      some, but not all, strains. The high number of recombination events was detected between V.
      campbellii strains that have significant temporal (over 18 years) and geographical (over
      10,000 km) differences in their origins of isolation. Results of this study reveal a
      remarkable stability of Harveyi clade species, and give clues about the origins and
      persistence of species in the clade.
AU  - Urbanczyk H
AU  - Ogura Y
AU  - Hayashi T
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2014 7: 71-80.

PMID- 21478348
VI  - 193
DP  - 2011
TI  - Genome Sequence of Photobacterium mandapamensis svers. 1.1., Bioluminescent Symbiont of the Cardinalfish Siphamia versicolor.
PG  - 3144-3145
AB  - Photobacterium mandapamensis is one of three luminous Photobacterium species able to form
      species-specific bioluminescent symbioses with marine
      fishes. Here, we present the draft genome sequence of P. mandapamensis
      svers.1.1, bioluminescent symbiont of the cardinalfish, Siphamia
      versicolor, the first genome of a symbiotic, luminous Photobacterium
      species to be sequenced. Analysis of the sequence provides insight into
      differences between P. mandapamensis and other luminous and symbiotic
      bacteria in genes involved in quorum sensing regulation of light
      production and establishment of symbiosis.
AU  - Urbanczyk H
AU  - Ogura Y
AU  - Hendry TA
AU  - Gould AL
AU  - Kiwaki N
AU  - Atkinson JT
AU  - Hayashi T
AU  - Dunlap PV
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3144-3145.

PMID- 24812211
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Novel Thermoacidophilic Archaeon Acidianus copahuensis Strain ALE1, Isolated from the Copahue Volcanic Area in Neuquen,  Argentina.
PG  - e00259-14
AB  - Acidianus copahuensis is a recently characterized thermoacidophilic archaeon isolated from the
      Copahue volcanic area in Argentina. Here, we present its draft
      genome sequence, in which we found genes involved in key metabolic pathways for
      developing under Copahue's extreme environmental conditions, such as sulfur and
      iron oxidation, carbon fixation, and metal tolerance.
AU  - Urbieta MS
AU  - Rascovan N
AU  - Castro C
AU  - Revale S
AU  - Giaveno MA
AU  - Vazquez M
AU  - Donati ER
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00259-14.

PMID- 6336735
VI  - 153
DP  - 1983
TI  - Sequence and substrate specificity of isolated DNA methylases from Escherichia coli C.
PG  - 274-280
AB  - Two DNA methylase activities of Escherichia coli C, the mec (designates DNA-cytosine-methylase
      gene, which is also designated dcm) and dam gene products, were physically separated by
      DEAE-cellulose column chromatography. The sequence and substrate specificity of the two
      enzymes were studied in vitro. The experiments revealed that both enzymes show their expected
      sequence specificity under in vitro conditions, methylating symmetrically on both DNA strands.
      The mec enzyme methylates exclusively the internal cytosine residue of CC(A/T)GG sequences,
      and the dam enzyme methylates adenine residues at GATC sites. Substrate specificity
      experiments revealed that both enzyes methylate in vitro unmethylated duplex DNA as
      efficiently as hemimethylated DNA. The results of these experiments suggest that the
      methylation at a specific site takes place by two independent events. A methyl group in a site
      on one strand of the DNA does not facilitate the methylation of the same site on the opposite
      strand. With the dam methylase it was found that enzyme is incapable of methylating GATC sites
      located at the ends of DNA molecules.
AU  - Urieli-Shoval S
AU  - Gruenbaum Y
AU  - Razin A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1983 153: 274-280.

PMID- 12079349
VI  - 319
DP  - 2002
TI  - The Escherichia coli Dam DNA methyltransferase modifies DNA in a highly processive reaction.
PG  - 1085-1096
AB  - The Escherichia coli dam adenine-N6 methyltransferase modifies DNA at G A TC sequences. It is
      involved in post-replicative mismatch repair, control of DNA replication and gene regulation.
      We show that E. coli dam acts as a functional monomer and methylates only one strand of the
      DNA in each binding event. The preferred way of ternary complex assembly is that the enzyme
      first binds to DNA and then to S-adenosylmethionine. The enzyme methylates an oligonucleotide
      containing two dam sites and an 879 bp PCR product with four sites in a fully processive
      reaction. On -DNA comprising 48,502 bp and 116 dam sites, E. coli dam scans 3000 dam sites per
      binding event in a random walk, that on average leads to a processive methylation of 55 sites.
      Processive methylation of DNA considerably accelerates DNA methylation. The highly processive
      mechanism of E. coli dam could explain why small amounts of E. coli dam are able to maintain
      the methylation state of dam sites during DNA replication. Furthermore, our data support the
      general rule that solitary DNA methyltransferase modify DNA processively whereas
      methyltransferases belonging to a restriction-modification system show a distributive
      mechanism, because processive methylation of DNA would interfere with the biological function
      of restriction-modification systems.
AU  - Urig S
AU  - Gowher H
AU  - Hermann A
AU  - Beck C
AU  - Fatemi M
AU  - Humeny A
AU  - Jeltsch A
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2002 319: 1085-1096.

PMID- 7592538
VI  - 117
DP  - 1995
TI  - Protective effect of disaccharides on restriction endonucleases during drying under vacuum.
PG  - 774-779
AB  - Desiccation by vacuum-drying inactivates the restriction endonuclease HindIII completely.
      However, when dried in the presence of a disaccharide such as trehalose, maltose, or sucrose,
      the endonuclease retains its phage DNA-cleaving activity and produces the same digestive
      fragments as does the intact enzyme. Thus, the disaccharides are effective in protecting the
      restriction enzyme in terms of both recognition and accurate cleavage of the substrate. Among
      the disaccharides, trehalose protects the enzyme most effectively; and it also stabilizes the
      enzyme during dilution in aqueous solution. The restriction enzyme dried with trehalose
      maintains its activity without detectable loss for at least 4 days at 37oC, but it shows
      reduced activity after 30-day storage at either 4oC or room temperature. Trehalose also
      protects other restriction endonucleases, EcoRI and BamHI, from inactivation during
      vacuum-drying, whereas drying them alone leads to severe loss of their activity. The
      restriction endonucleases dried with trehalose retain their activities for at least 20 days at
      4oC and for 7 days at room temperature.
AU  - Uritani M
AU  - Takai M
AU  - Yoshinaga K
PT  - Journal Article
TA  - J. Biochem. (Tokyo)
JT  - J. Biochem. (Tokyo)
SO  - J. Biochem. (Tokyo) 1995 117: 774-779.

PMID- 29674537
VI  - 6
DP  - 2018
TI  - Near-Complete Genome Sequence of Pseudomonas palleroniana MAB3, a Beneficial 1-Aminocyclopropane-1-Carboxylate Deaminase-Producing Bacterium Able To Promote  the Growth of Mushrooms and Plants.
PG  - e00242-18
AB  - The near-complete genome sequence of Pseudomonas palleroniana MAB3, a
      1-aminocyclopropane-1-carboxylate deaminase-producing bacterium isolated from an
      environmental soil Amanita mushroom, is presented here. The genome of P.
      palleroniana MAB3 contains a single circular chromosome of 6.29 Mb and an average
      GC content of 60.5%.
AU  - Uron P
AU  - Giachini AJ
AU  - Glick BR
AU  - Rossi MJ
AU  - Nascimento FX
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00242-18.

PMID- 26205858
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Burkholderia sp. Strain PML1(12), an Ectomycorrhizosphere-Inhabiting Bacterium with Effective Mineral-Weathering  Ability.
PG  - e00798-15
AB  - We report the draft genome sequence of Burkholderia sp. PML1(12), a soil bacterium isolated
      from the Oak-Scleroderma citrinum ectomycorrhizosphere in the
      experimental forest site of Breuil-Chenue (France).
AU  - Uroz S
AU  - Oger P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00798-15.

PMID- 
VI  - 69
DP  - 2014
TI  - Structure and function of bacterial communities in ageing soils: insights from the Mendocino ecological staircase.
PG  - 265-274
AB  - 
AU  - Uroz S
AU  - Tech JJ
AU  - Sawaya NA
AU  - Frey-Klett P
AU  - Leveau JHJ
PT  - Journal Article
TA  - Soil Biol. Biochem.
JT  - Soil Biol. Biochem.
SO  - Soil Biol. Biochem. 2014 69: 265-274.

PMID- 27795256
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus LBB.B5.
PG  - e01090-16
AB  - Lactobacillus delbrueckii subsp. bulgaricus LBB.B5 originates from homemade Bulgarian yogurt
      and was selected for its ability to form a strong association
      with Streptococcus thermophilus The genome sequence will facilitate elucidating
      the genetic background behind the contribution of LBB.B5 to the taste and aroma
      of yogurt and its exceptional protocooperation with S. thermophilus.
AU  - Urshev Z
AU  - Hajo K
AU  - Lenoci L
AU  - Bron PA
AU  - Dijkstra A
AU  - Alkema W
AU  - Wels M
AU  - Siezen RJ
AU  - Minkova S
AU  - van Hijum SA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01090-16.

PMID- 22563013
VI  - 67
DP  - 2012
TI  - Two novel arginine catabolic mobile elements and staphylococcal chromosome cassette mec composite islands in community-acquired methicillin-resistant Staphylococcus aureus genotypes ST5-MRSA-V and ST5-MRSA-II.
PG  - 1828-1834
AB  - Objectives: The arginine catabolic mobile element (ACME) is a novel staphylococcal genetic
      island. ACME is located downstream of the staphylococcal cassette chromosome mec (SCCmec),
      forming the ACME-SCCmec composite island. Recently, ACME II (located upstream of SCCmec IV)
      was described from a methicillin-resistant Staphylococcus aureus (MRSA) strain M1 in Denmark
      (ST8-MRSA-IVa) and 15 MRSA isolates in Ireland (ST22- MRSA-IVh). We report the novel genetic
      characteristics of the ACME-SCCmec composite islands found in Japanese community-acquired MRSA
      (CA-MRSA) isolates.  Methods: ACME-SCCmec composite islands from two ACME-arcA-positive
      CA-MRSA isolates with the genotypes ST5-MRSA-V (SR141) and ST5-MRSA-II (SR388) were
      characterized using long-range PCR and nucleotide sequencing. Results: Both isolates harboured
      a 12 kb DNA region primarily identified in ACME II in Staphylococcus epidermidis ATCC 12228
      upstream of each SCCmec. The arcA and its flanking regions in SR141 and SR388 showed high
      sequence identity (99.8% at the highest) to those in MRSA M1 and M08/0126 (the representative
      of 15 Irish ST22-MRSA-IVh isolates), suggesting that the ACMEs of these four isolates
      originated from the same ancestral gene. The ACME II-like element in SR141 included an
      insertion sequence IS1182 at a position close to SCCmec, resulting in a new variant. SR388
      contained approximately 11.5 kb of the J1 region of type I SCCmec (J1 SCCmecI) between orfX
      and ACME (orfX-J1 SCCmecI-ACME II), unlike the homologous region in M08/0126 (orfX-ACME II-J1
      SCCmecI).  Conclusions: This is the first report of the ACME II-like element inserted upstream
      of SCCmec in CA-MRSA with the genotypes ST5-MRSA-V and ST5-MRSA-II.
AU  - Urushibara N
AU  - Kawaguchiya M
AU  - Kobayashi N
PT  - Journal Article
TA  - J. Antimicrob. Chemother.
JT  - J. Antimicrob. Chemother.
SO  - J. Antimicrob. Chemother. 2012 67: 1828-1834.

PMID- 27151793
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of 37 Salmonella enterica Strains Isolated from Poultry Sources in Nigeria.
PG  - e00315-16
AB  - Here, we report the availability of draft genomes of several Salmonella serotypes, isolated
      from poultry sources from Nigeria. These genomes will help to
      further understand the biological diversity of S. enterica and will serve as
      references in microbial trace-back studies to improve food safety.
AU  - Useh NM
AU  - Ngbede EO
AU  - Akange N
AU  - Thomas M
AU  - Foley A
AU  - Keena MC
AU  - Nelson E
AU  - Christopher-Hennings J
AU  - Tomita M
AU  - Suzuki H
AU  - Scaria J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00315-16.

PMID- 11852561
VI  - 38
DP  - 2002
TI  - Restriction endonuclease Sst12I from a strain of Streptomyces - Recognizing the nucleotide sequence 5 '-CTGCAG-3 '.
PG  - 25-28
AB  - A new restriction endonuclease Sst12I belonging to type II and recognizing the sequence
      5'-CTGCAG-3' was isolated from the bacterial
      strain Streptomyces sp. St-12. The enzyme hydrolyzes DNA between
      adenine and guanine residues thus, it is a true isoschizomer of
      restrictase PstI. In contrast to PstI, the restriction endonuclease
      Sst12I hydrolyses DNA both at 37 and 55 C and remains active
      after long-term storage.
AU  - Ushakova TA
AU  - Puchkova LI
AU  - Gutorov VV
AU  - Kuvshinov VN
AU  - Repin VE
PT  - Journal Article
TA  - Prikl. Biokhim. Mikrobiol.
JT  - Prikl. Biokhim. Mikrobiol.
SO  - Prikl. Biokhim. Mikrobiol. 2002 38: 25-28.

PMID- 
VI  - 44
DP  - 2008
TI  - Restriction endonuclease Asi256I recognizes and cuts the nucleotide sequence 5'-GATC-3'.
PG  - 28-31
AB  - A strain producing a restriction endonuclease was isolated from soil samples and identified as
      the Arthrobacter sp. strain Ck256. The enzyme
      produced by this strain was termed Asi256I. The isolation procedure for
      this enzyme was described, and the optimal conditions for its function
      were determined. It was shown that the restriction endonuclease Asi256I
      is a true isoschizomer of MboI, it has a temperature optimum of 6
      degrees C, and can be used in molecular-biological and
      genetic-engineering studies performed at low temperatures.
AU  - Ushakova TA
AU  - Puchkova LI
AU  - Gutorov VV
AU  - Totmenina OD
AU  - Repin VE
PT  - Journal Article
TA  - Prikl. Biokhim. Mikrobiol.
JT  - Prikl. Biokhim. Mikrobiol.
SO  - Prikl. Biokhim. Mikrobiol. 2008 44: 28-31.

PMID- 
VI  - 0
DP  - 2004
TI  - Restriction endonuclease SpmI recognizing the 5'-AT/CGAT-3' nucleotide sequence.
PG  - 38-42
AB  - A strain producer of a restriction endonuclease (restrictase), that was identified as a
      species of Sphingobacterium mizutae has been isolated from snow water, and its restrictase was
      named SpmI.  The method of the enzymne isolation was described, and optimal conditions of its
      action were determined.  It was shown that SpmI restrictase is a true isoschizomer of ClaI
      restrictase.  The temperature optimum of SpmI restrictase is 6oC, and it can be used in
      molecular biology and genetic engineering researches that need carrying out at low
      temperatures.
AU  - Ushakova TA
AU  - Puchkova LI
AU  - Radionenko YV
AU  - Gutorov VV
AU  - Kuvshinov VN
AU  - Repin VE
PT  - Journal Article
TA  - Biotekhnologiya
JT  - Biotekhnologiya
SO  - Biotekhnologiya 2004 0: 38-42.

PMID- 
VI  - 0
DP  - 2003
TI  - Restriction endonuclease Bst221 from Bacillus stearothermophilus 22 strain recognizing the 5'-CCNNNNN^NNGG-3' nucleotide sequence.
PG  - 11-15
AB  - A strain producing the restriction endonuclease (restrictase) which was identified as a
      species of Bacillus stearothermophilus 22 has been isolated by the authors, and its
      restrictase was called Bst221.  The method of the enzyme isolation was described, and optimal
      conditions of its action were determined.  It was shown that Bst221 restrictase is a true
      isoschizomer of BsiYI restrictase.  Bst221 restrictase is active in a broad temperature range
      and shows promise for molecular biology research.
AU  - Ushakova TA
AU  - Puchkova LI
AU  - Radionenko YV
AU  - Kuvshinov VN
AU  - Repin VE
PT  - Journal Article
TA  - Biotekhnologiya
JT  - Biotekhnologiya
SO  - Biotekhnologiya 2003 0: 11-15.

PMID- 6268142
VI  - 20
DP  - 1981
TI  - Inhibition of the BamHI cleavage and unwinding of pBR322 deoxyribonucleic acid by the antitumor drug cis-dichlorodiammineplatinum(II).
PG  - 3744-3748
AB  - The antitumor drug cis-dichlorodiammineplatinum(II) (cis-DDP) binds to pBR322 DNA and inhibits
      the cleavage of this circular DNA into a linear form by the restriction endonuclease BamHI.
      The binding of platinum to DNA was monitored by agarose gel electrophoresis, and the amount of
      platinum bound per nucleotide (rb) was measured by carbon rod atomic absorption spectroscopy.
      Electrophoretic mobility changes reflect a shortening and unwinding of the DNA duplex upon
      platinum binding as observed previously for the reaction of cis- and trans-DDP with pSM2 DNA
      [Cohen, G.L., Bauer, W.R., Barton, J.K., & Lippard, S.J. (1979) Science (Washington, DC) 203,
      1014-1016].  The inhibition of BamHI nuclease activity occurs at very low binding levels and
      is complete at rb = 0.045.  This value corresponds to the binding of one platinum atom within
      +/- 3 base pairs of the recognition sequence of the enzyme shown below.  Treatment of the DNA
      with 0.2 M sodium cyanide after BamHI cutting removes the platinum but does not alter the
      point at which cis-DDP inhibits the formation of the linear form III DNA.  This result is in
      contrast with a previous report claiming that BamHI could cut across a cis-DDP-induced GpG
      cross-link in DNA which could be subsequently revealed by cyanide reversal of platinum
      binding.  When the platinum is removed by cyanide treatment, the drug-induced mobility changes
      are reversed and there is a pronounced sharpening of the bands in the gel. Quantitative study
      of the cyanide reversal shows the presence of a small amount of unremovable platinum tightly
      bound to the DNA at high ratios (~0.1) of bound platinum per nucleotide -G^GATCC- -CCTAG^G-.
AU  - Ushay HM
AU  - Tullius TD
AU  - Lippard SJ
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1981 20: 3744-3748.

PMID- 26847899
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Sarcina ventriculi Strains Isolated from Wild Japanese  Macaques in Yakushima Island.
PG  - e01694-15
AB  - We report the draft genome sequences of Sarcina ventriculi strains 14 and 17, both isolated
      from feces of wild Yakushima macaques (Macaca fuscata yakui). These
      genomic sequences will be helpful for the phylogenetic consideration of the
      family Clostridiaceae and understanding of the contribution of intestinal
      microbiota to the survival of Yakushima macaques.
AU  - Ushida K
AU  - Tsuchida S
AU  - Ogura Y
AU  - Hayashi T
AU  - Sawada A
AU  - Hanya G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01694-15.

PMID- 24092784
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Vibrio coralliilyticus Strain OCN008, Isolated from Kane'ohe Bay, Hawai'i.
PG  - e00786-13
AB  - Vibrio coralliilyticus is a Gram-negative bacterium found in seawater and is associated with
      diseased marine organisms. Strains of V. coralliilyticus have
      been shown to infect coral from multiple genera. We report the draft genome
      sequence of V. coralliilyticus strain OCN008, the third V. coralliilyticus genome
      to be sequenced.
AU  - Ushijima B
AU  - Videau P
AU  - Aeby GS
AU  - Callahan SM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00786-13.

PMID- 25523774
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Vibrio coralliilyticus Strain OCN014, Isolated from a Diseased Coral at Palmyra Atoll.
PG  - e01318-14
AB  - Vibrio coralliilyticus is a marine gammaproteobacterium that has been implicated  as an
      etiological agent of disease for multiple coral genera on reefs worldwide.
      We report the complete genome of V. coralliilyticus strain OCN014, isolated from
      a diseased Acropora cytherea colony off the western reef terrace of Palmyra
      Atoll.
AU  - Ushijima B
AU  - Videau P
AU  - Poscablo D
AU  - Vine V
AU  - Salcedo M
AU  - Aeby G
AU  - Callahan SM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01318-14.

PMID- 
VI  - 52
DP  - 2000
TI  - Inhibition of restriction endonuclease cleavage by triplex formation with oligo-2'-O-methyl-ribonucleotides containing 8-oxo-2'-O-methyladenosine in place of cytidine.
PG  - 389-398
AB  - The ability of homopyrimidine oligoribonucleotides and oligo-2'-O-methyl-ribonucleotides
      containing 8-oxo-adenosine and 8-oxo-2'-O-methyl-adenosine to form stable, triple-helical
      structures with sequences containing the recognition site for the class II-S restriction
      enzyme, Ksp632I, was studied as a function of pH.  The AOH- and AmOH-substituted
      oligoribonucleotides and oligo-2'-O-methyl-ribonucleotides were shown to bind within the
      physiological pH range in a pH-independent fashion, without a compromise in specificity.  The
      substitutions of three cytidine residues with AOH showed higher endonuclease inhibition than
      the substitution of either one or two cytidine residues with AOH.  In particular, the
      oligo-2'-O-methyl-ribonucleotide with only one cytidine substituted with AmOH showed higher
      endonuclease inhibition.  Increased resistance to nucleases is observed with the introduction
      of 2-O-methylnucleosides.  This stabilization should help us to design much more efficient
      third strand homopyrimidine oligomer and antisense nucleic acid, which can be used as tools in
      cellular biology and anti-viral therapy.
AU  - Ushijima K
AU  - Ishibashi T
AU  - Tsukahara S
AU  - Takai K
AU  - Takaku H
PT  - Journal Article
TA  - Heterocycles
JT  - Heterocycles
SO  - Heterocycles 2000 52: 389-398.

PMID- 10350475
VI  - 38
DP  - 1999
TI  - Inhibition of restriction endonuclease cleavage by triple helix formation with RNA and 2'-O-methyl RNA oligonucleotides containing 8-oxo-adenosine in place of cytidine.
PG  - 6570-6575
AB  - The ability of homopyrimidine oligoribonucleotides (RNA) and
      oligo-2'-O-methyl-ribonucleotides (2'-O-methyl RNA) containing 8-oxo-adenosine (AOH) and
      8-oxo-2'-O-methyl (AmOH) adenosine to form stable, triple-helical structures with sequences
      containing the recognition site for the class II-S restriction enzyme, Ksp632-I, was studied
      as a function of pH. The AOH- and AmOH-substituted RNA and 2'-O-methyl RNA oligonucleotides
      were shown to bind within the physiological pH range in a pH-independent fashion, without a
      compromise in specificity. The substitutions of three cytidine residues with AOH showed higher
      endonuclease inhibition than the substitution of either one or two cytidine residues with AOH.
      In particular, the 2'-O-methyl RNA oligonucleotide with only one cytidine substituted with
      AmOH showed higher endonuclease inhibition than the homopyrimidine RNA and 2'-O-methyl RNA
      oligonucleotides and the RNA oligonucleotides containing either one or two AOH moieties.
      Furthermore, the AmOH-substituted 2'-O-methyl RNA oligonucleotides were stable (53%) after an
      incubation in 10% fetal bovine serum for 8 h, whereas the RNA oligonucleotides were completely
      degraded. Increased resistance to nucleases is observed with the introduction of
      2'-O-methylnucleosides. This stabilization should help us to design much more efficient third
      strand homopyrimidine oligomer and antisense nucleic acid-based antiviral therapies, which
      could be used as tools in cellular biology.
AU  - Ushijima K
AU  - Ishibashi T
AU  - Yamakawa H
AU  - Tsukahara S
AU  - Takai K
AU  - Maruyama T
AU  - Takaku H
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1999 38: 6570-6575.

PMID- 27365356
VI  - 4
DP  - 2016
TI  - First Draft Genome Sequence of a Mycobacterium gordonae Clinical Isolate.
PG  - e00638-16
AB  - Here, we report the first draft genome sequence of the clinically relevant species
      Mycobacterium gordonae The clinical isolate Mycobacterium gordonae 14-8773 was obtained from
      the sputum of a patient with mycobacteriosis.
AU  - Ustinova V
AU  - Smirnova T
AU  - Blagodatskikh K
AU  - Varlamov D
AU  - Sochivko D
AU  - Larionova E
AU  - Andreevskaya S
AU  - Andrievskaya I
AU  - Chernousova L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00638-16.

PMID- 29599152
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of a Mycobacterium heckeshornense Clinical Isolate.
PG  - e00178-18
AB  - We report here the draft genome sequence of Mycobacterium heckeshornense, isolated from the
      sputum of a patient admitted to a tuberculosis hospital with
      suspected pulmonary tuberculosis.
AU  - Ustinova V
AU  - Smirnova T
AU  - Varlamov D
AU  - Monakhova Y
AU  - Larionova E
AU  - Andreevskaya S
AU  - Andrievskaya I
AU  - Chernousova L
AU  - Ergeshov A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00178-18.

PMID- 24963913
VI  - 9
DP  - 2014
TI  - Beyond the Chromosome: The Prevalence of Unique Extra-Chromosomal Bacteriophages with Integrated Virulence Genes in Pathogenic Staphylococcus aureus.
PG  - E100502
AB  - In Staphylococcus aureus, the disease impact of chromosomally integrated
      prophages on virulence is well described. However, the existence of
      extra-chromosomal prophages, both plasmidial and episomal, remains obscure.
      Despite the recent explosion in bacterial and bacteriophage genomic sequencing,
      studies have failed to specifically focus on extra-chromosomal elements. We
      selectively enriched and sequenced extra-chromosomal DNA from S. aureus isolates
      using Roche-454 technology and uncovered evidence for the widespread distribution
      of multiple extra-chromosomal prophages (ExPPhis) throughout both
      antibiotic-sensitive and -resistant strains. We completely sequenced one such
      element comprised of a 43.8 kbp, circular ExPPhi (designated capital EF,
      CyrillicBU01) from a vancomycin-intermediate S. aureus (VISA) strain. Assembly
      and annotation of capital EF, CyrillicBU01 revealed a number of putative
      virulence determinants encoded within a bacteriophage immune evasion cluster
      (IEC). Our identification of several potential ExPPhis and mobile genetic
      elements (MGEs) also revealed numerous putative virulence factors and antibiotic
      resistance genes. We describe here a previously unidentified level of genetic
      diversity of stealth extra-chromosomal elements in S. aureus, including phages
      with a larger presence outside the chromosome that likely play a prominent role
      in pathogenesis and strain diversity driven by horizontal gene transfer (HGT).
AU  - Utter B
AU  - Deutsch DR
AU  - Schuch R
AU  - Winer BY
AU  - Verratti K
AU  - Bishop-Lilly K
AU  - Sozhamannan S
AU  - Fischetti VA
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2014 9: E100502.

PMID- 27688341
VI  - 4
DP  - 2016
TI  - Application of Long Sequence Reads To Improve Genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7.
PG  - e01043-16
AB  - We and others have shown the utility of long sequence reads to improve genome assembly
      quality. In this study, we generated PacBio DNA sequence data to improve
      the assemblies of draft genomes for Clostridium thermocellum AD2, Clostridium
      thermocellum LQRI, and Pelosinus fermentans R7.
AU  - Utturkar SM et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01043-16.

PMID- 23792749
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence for Caulobacter sp. Strain OR37, a Bacterium Tolerant to Heavy Metals.
PG  - e00322-13
AB  - Caulobacter sp. strain OR37 belongs to the class Alphaproteobacteria and was isolated from
      subsurface sediments in Oak Ridge, TN. Strain OR37 is noteworthy
      due to its tolerance to high concentrations of heavy metals, such as uranium,
      nickel, cobalt, and cadmium, and we present its draft genome sequence here.
AU  - Utturkar SM
AU  - Bollmann A
AU  - Brzoska RM
AU  - Klingeman DM
AU  - Epstein SE
AU  - Palumbo AV
AU  - Brown SD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00322-13.

PMID- 23792748
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence for Ralstonia sp. Strain OR214, a Bacterium with Potential  for Bioremediation.
PG  - e00321-13
AB  - Ralstonia sp. strain OR214 belongs to the class Betaproteobacteria and was isolated from
      subsurface sediments in Oak Ridge, TN. A member of this genus has
      been described as a potential bioremediation agent. Strain OR214 is tolerant to
      various heavy metals, such as uranium, nickel, cobalt, and cadmium. We present
      its draft genome sequence here.
AU  - Utturkar SM
AU  - Bollmann A
AU  - Brzoska RM
AU  - Klingeman DM
AU  - Epstein SE
AU  - Palumbo AV
AU  - Brown SD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00321-13.

PMID- 26950321
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Pyrodictium occultum PL19T, a Marine Hyperthermophilic Species of Archaea That Grows Optimally at 105 degrees C.
PG  - e00016-16
AB  - We report here the draft genome sequence of Pyrodictium occultum PL19(T), a marine
      hyperthermophilic archaeon. The genome provides insights into molecular
      and cellular adaptation mechanisms to life in extreme environments and the
      evolution of early organisms on Earth.
AU  - Utturkar SM
AU  - Huber H
AU  - Leptihn S
AU  - Loh B
AU  - Brown SD
AU  - Stetter KO
AU  - Podar M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00016-16.

PMID- 21791727
VI  - 8
DP  - 2011
TI  - The elastic network model reveals a consistent picture on intrinsic functional dynamics of type II restriction endonucleases.
PG  - 056001
AB  - The vibrational dynamics of various type II restriction endonucleases, in complex with
      cognate/non-cognate DNA and in the apo form, are
      investigated with the elastic network model in order to reveal common
      functional mechanisms in this enzyme family. Scissor-like and tong-like
      motions observed in the slowest modes of all enzymes and their
      complexes point to common DNA recognition and cleavage mechanisms.
      Normal mode analysis further points out that the scissor-like motion
      has an important role in differentiating between cognate and
      non-cognate sequences at the recognition site, thus implying its
      catalytic relevance. Flexible regions observed around the DNA-binding
      site of the enzyme usually concentrate on the highly conserved
      beta-strands, especially after DNA binding. These beta-strands may have
      a structurally stabilizing role in functional dynamics for target site
      recognition and cleavage. In addition, hot spot residues based on
      high-frequency modes reveal possible communication pathways between the
      two distant cleavage sites in the enzyme family. Some of these hot
      spots also exist on the shortest path between the catalytic sites and
      are highly conserved.
AU  - Uyar A
AU  - Kurkcuoglu O
AU  - Nilsson L
AU  - Doruker P
PT  - Journal Article
TA  - Phys. Biol.
JT  - Phys. Biol.
SO  - Phys. Biol. 2011 8: 056001.

PMID- 18931437
VI  - 64
DP  - 2008
TI  - Crystallization and preliminary X-ray diffraction analysis of the HsdR subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016.
PG  - 926-928
AB  - Type I restriction enzymes are multimeric proteins that consist of three subunits. The HsdS
      and HsdM subunits form a complex protein that
      shows methyltransferase activity, while the HsdR subunit functions as
      an endonuclease as well as as a translocase. Of these three subunits,
      no structural information on the HsdR subunit is yet available. The
      putative HsdR gene from Vibrio vulnificus YJ016 (HsdR Vv) was cloned
      and expressed and the expressed protein HsdR Vv was purified. HsdR Vv
      was crystallized from 8%(w/v) polyethylene glycol 3350, 0.15 M ammonium
      chloride, 0.1 M HEPES pH 7.5 and 2 mM beta-mercaptoethanol. Diffraction
      data were collected to 2.60 angstrom resolution using synchrotron
      radiation. The crystal belongs to the orthorhombic space group
      P2(1)2(1)2(1), with unit-cell parameters a = 71.01, b = 89.04, c =
      113.66 angstrom. With one HsdR Vv molecule in the asymmetric unit, the
      Matthews coefficient was 2.14 angstrom(3) Da(-1) and the solvent
      content was 42%.
AU  - Uyen NT
AU  - Nishi K
AU  - Park SY
AU  - Choi JW
AU  - Lee HJ
AU  - Kim JS
PT  - Journal Article
TA  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
JT  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
SO  - Acta Crystallogr. F Struct. Biol. Cryst. Commun. 2008 64: 926-928.

PMID- 19625490
VI  - 37
DP  - 2009
TI  - The fragment structure of a putative HsdR subunit of a type I restriction enzyme from Vibrio vulnificus YJ016: implications for DNA restriction and  translocation activity.
PG  - 6960-6969
AB  - Among four types of bacterial restriction enzymes that cleave a foreign DNA depending on its
      methylation status, type I enzymes composed of three subunits are interesting because of their
      unique DNA cleavage and translocation mechanisms performed by the restriction subunit (HsdR).
      The elucidated N-terminal fragment structure of a putative HsdR subunit from Vibrio vulnificus
      YJ016 reveals three globular domains. The nucleolytic core within an N-terminal nuclease
      domain (NTD) is composed of one basic and three acidic residues, which include a metal-binding
      site. An ATP hydrolase (ATPase) site at the interface of two RecA-like domains (RDs) is
      located close to the probable DNA-binding site for translocation, which is far from the NTD
      nucleolytic core. Comparison of relative domain arrangements with other functionally related
      ATP and/or DNA complex structures suggests a possible translocation and restriction mechanism
      of the HsdR subunit. Furthermore, careful analysis of its sequence and structure implies that
      a linker helix connecting two RDs and an extended region within the nuclease domain may play a
      central role in switching the DNA translocation into the restriction activity.
AU  - Uyen NT
AU  - Park SY
AU  - Choi JW
AU  - Lee HJ
AU  - Nishi K
AU  - Kim JS
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: 6960-6969.

PMID- 24994800
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Beneficial Rice Rhizosphere Isolate Pseudomonas aeruginosa PUPa3.
PG  - e00654-14
AB  - Pseudomonas aeruginosa PUPa3 is a rhizosphere-colonizing and plant growth-promoting strain
      isolated from the rhizosphere of rice. This strain has, however, been shown to be pathogenic
      in two nonmammalian infection models. Here we report the draft genome sequence of P.
      aeruginosa PUPa3.
AU  - Uzelac G
AU  - Bertani I
AU  - Kojic M
AU  - Paszkiewicz KH
AU  - Studholme DJ
AU  - Passos-da-Silva D
AU  - Venturi V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00654-14.

PMID- 28408666
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Chryseobacterium sp. JV274 Isolated from Maize Rhizosphere.
PG  - e00122-17
AB  - We report the draft genome sequence of Chryseobacterium sp. JV274. This strain was isolated
      from the rhizosphere of maize during a greenhouse experiment. JV274
      harbors genes involved in flexirubin production (darA and darB genes), bacterial
      competition (type VI secretion system), and gliding (bacterial motility; type IX
      secretion system).
AU  - Vacheron J
AU  - Dubost A
AU  - Chapulliot D
AU  - Prigent-Combaret C
AU  - Muller D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00122-17.

PMID- 10022842
VI  - 18
DP  - 1999
TI  - In vivo expression of the nucleolar group I intron-encoded I-DirI homing endonuclease involves the removal of a spliceosomal intron.
PG  - 1003-1013
AB  - The Didymium iridis DiSSU1 intron is located in the nuclear SSU rDNA and has an unusual
      twin-ribozyme organization.  One of the ribozymes (DiGIR2) catalyses intron excision and exon
      ligation.  The other ribozyme (DiGIR1), which along with the endonuclease-encoding I-DirI open
      reading frame is inserted in DiGIR2, carries out hydrolysis at internal processing sites (IPS1
      and IPS2) located at its 3' end.  Examination of the in vivo expression of DiSSU1 shows that
      after excision, DiSSU1 is matured further into the I-DirI mRNA by internal DiGIR1-catalysed
      cleavage upstream of the ORF 5' end, as well as truncation and polyadenylation downstream of
      the ORF 3' end.  A spliceosomal intron, the first to be reported within a group I intron and
      the rDNA, is removed before the I-DirI mRNA associates with the polysomes.  Taken together,
      our results imply that DiSSU1 uses a unique combination of intron-supplied ribozyme activity
      and adaptation to the general RNA polymerase II pathway of mRNA expression to allow a protein
      to be produced from the RNA polymerase I-transcribed rDNA.
AU  - Vader A
AU  - Nielsen H
AU  - Johansen S
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1999 18: 1003-1013.

PMID- 26494667
VI  - 3
DP  - 2015
TI  - First Draft Genome Sequence of Salmonella enterica Serovar Gallinarum Strain VTCCBAA614, Isolated from Chicken in India.
PG  - e01221-15
AB  - Salmonella enterica subsp. enterica serovar Gallinarum biovar Gallinarum causes fowl typhoid
      (FT), which results in huge economic losses to poultry farmers in India. We report the draft
      genome sequence of Salmonella biovar Gallinarum strain VTCCBAA614, isolated from a chicken in
      an FT affected broiler flock.
AU  - Vaid RK
AU  - Jindal N
AU  - Anand T
AU  - Bera BC
AU  - Riyesh T
AU  - Virmani N
AU  - Barua S
AU  - Gupta R
AU  - Mahajan NK
AU  - Joshi CG
AU  - Singh RK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01221-15.

PMID- 25081265
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Pasteurella multocida subsp. multocida B:2 Strain VTCCBAA264 Isolated from Bubalus bubalis in North India.
PG  - e00755-14
AB  - The Pasteurella multocida subsp. multocida B:2 serotype causes hemorrhagic septicemia in
      bubalines with high morbidity and mortality in the Indian
      subcontinent. We report the draft genome sequence of Pasteurella multocida strain
      VTCCBAA264 isolated from the small-intestine of a buffalo calf that died of high
      fever.
AU  - Vaid RK
AU  - Shanmugasundaram K
AU  - Boora A
AU  - Bera BC
AU  - Shukla BN
AU  - Anand T
AU  - Singha H
AU  - Riyesh T
AU  - Virmani N
AU  - Barua S
AU  - Ahir VB
AU  - Koringa PG
AU  - Sajnani MR
AU  - Bhat VD
AU  - Rana N
AU  - Singh KP
AU  - Malik P
AU  - Singh RK
AU  - Joshi CG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00755-14.

PMID- 8265344
VI  - 21
DP  - 1993
TI  - Enzymic removal of 5-methylcytosine from DNA by a hyman DNA-glycosylase.
PG  - 5323-5327
AB  - DNA 5-methylcytosine is a major factor in the silencing of mammalian genes; it is involved in
      gene expression, differentiation, embryogenesis and neoplastic transformation. A decrease in
      DNA 5-methylcytosine content is associated with activation of specific genes. There is much
      evidence indicating this to be an enzymic process, with replacement of 5-methylcytosine by
      cytosine. We demonstrate here enzymic release of 5-methylcytosines from DNA by a human
      5-methylcytosine-DNA glycosylase activity, which affords a possible mechanism for such
      replacement. This activity generates promutagenic apyrimidinic sites, which can be related to
      the high frequency of mutations found at DNA 5-methylcytosine loci. The recovery of most
      released pyrimidines as thymines indicates subsequent deamination of free 5-methylcytosines by
      a 5-methylcytosine deaminase activity. This prevents possible recycling of 5-methylcytosine
      into replicative DNA synthesis via a possible 5-methyl-dCTP intermediate synthesized through
      the pyrimidine salvage pathway. Taken together, these findings indicate mechanisms for removal
      of 5-methylcytosines from DNA, hypermutability of DNA 5-methylcytosine sites, and exclusion of
      5-methylcytosines from DNA during replication.
AU  - Vairapandi M
AU  - Duker NJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 5323-5327.

PMID- 20333224
VI  - 2
DP  - 2010
TI  - Comparative metagenomics and population dynamics of the gut microbiota in mother and infant.
PG  - 53-66
AB  - Colonization of the gastrointestinal tract (GIT) of human infants with a suitable microbial
      community is essential for numerous aspects of health, but the progression of events by which
      this microbiota becomes established is poorly understood. Here, we investigate two previously
      unexplored areas of microbiota development in infants: the deployment of functional
      capabilities at the community level and the population genetics of its most abundant genera.
      To assess the progression of the infant microbiota toward an adult-like state and to evaluate
      the contribution of maternal GIT bacteria to the infant gut, we compare the infant's
      microbiota with that of the mother at 1 and 11 months after delivery. These comparisons reveal
      that the infant's microbiota rapidly acquires and maintains the range of gene functions
      present in the mother, without replicating the phylogenetic composition of her microbiota.
      Microdiversity analyses for Bacteroides and Bifidobacterium, two of the main microbiota
      constituents, reveal that by 11 months, the phylotypes detected in the infant are distinct
      from those in the mother, although the maternal Bacteroides phylotypes were transiently
      present at 1 month of age. The configuration of genetic variants within these genera reveals
      populations far from equilibrium and likely to be undergoing rapid growth, consistent with
      recent population turnovers. Such compositional turnovers and the associated loss of maternal
      phylotypes should limit the potential for long-term coadaptation between specific bacterial
      and host genotypes.
AU  - Vaishampayan PA
AU  - Kuehl JV
AU  - Froula JL
AU  - Morgan JL
AU  - Ochman H
AU  - Francino MP
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2010 2: 53-66.

PMID- 11072067
VI  - 1494
DP  - 2000
TI  - The LipB protein is a negative regulator of dam gene expression in Escherichia coli.
PG  - 43-53
AB  - Transcription initiation of the major promoter (P2) of the Escherichia coli dam gene increases
      with growth rate.  The presence of three partially palindromic motifs, (TTCAGT(N(20))TGAG),
      designated G (growth)-boxes, within the -52 to +31 region of the promoter, may be related to
      growth rate control. Deletion of two of these repeats, downstream of the transcription
      initiation point, result in constitutive high activity of the promoter. The unlinked
      cde-4::miniTn10 insertion also results in several fold higher activity of the dam P2 promoter,
      suggesting that this mutation resulted in the loss of a putative dam P2 repressor. The cde-4
      mutation was mapped to the lipB (lipoic acid) gene, which we show encodes a 24 kDa protein
      initiating at a TTG codon. LipB is a highly conserved protein in animal and plant species,
      other bacteria, Archaea, and yeast. Plasmids expressing the native or hexahistidine-tagged
      LipB complement the phenotype of the cde-4 mutant strain. The level of LipB in vivo was higher
      in exponentially growing cells than those in the stationary phase. Three G-box motifs were
      also found in the lipB region. Models for the regulation of expression of the two genes are
      discussed.
AU  - Vaisvila R
AU  - Rasmussen LJ
AU  - Lobner-Olesen A
AU  - von Freiesleben U
AU  - Marinus MG
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 2000 1494: 43-53.

PMID- 7607525
VI  - 157
DP  - 1995
TI  - Cloning of the ppu21IM gene using a in vivo selection method.
PG  - 55-57
AB  - A genetic system enabling the in vivo selection of genes encoding the DNA-modifying enzymes
      was developed.  A gene library is transformed into a strain harboring the
      restriction-modification (R-M) system which a recognition sequence is a subset of the target
      sequence of the DNA methyltransferase (MTase) to be cloned.  If the residing MTase is
      temperature sensitive, the inability of transformants to grow at 42oC provides a simple and
      convenient procedure for the isolation of new MTase-encoding genes.  The feasibility of this
      procedure has been demonstrated by the isolation of the ppu21IM gene from a Pseudomonas putida
      RFL21 gene library.
AU  - Vaisvila R
AU  - Sliesaraviciute Z
AU  - Kulakauskas S
AU  - Janulaitis A
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 55-57.

PMID- 7607531
VI  - 157
DP  - 1995
TI  - Identification of a gene encoding a DNA invertase-like enzyme adjacent to the PaeR7I restriction-modification system.
PG  - 81-84
AB  - A gene encoding a DNA invertase-like enzyme was identified adjacent to the PaeR7I
      restriction-modification system (R-M), and was named paeR7IN (N for iNvertase).  Sequence
      analysis revealed that this gene has the same polarity as the PaeR7IRM operon, and would
      encode a polypeptide of 21,506 Da.  An amino-acid sequence similarity of 45-49% was found
      between the deduced protein product and various DNA invertases.
AU  - Vaisvila R
AU  - Vilkaitis G
AU  - Janulaitis A
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 81-84.

PMID- Not carried by PubMed...
VI  - 1
DP  - 1991
TI  - Advanced method for obtaining highly purified restriction enzyme preparations.
PG  - 35-41
AB  - Using Eco130I restrictase isolated from cells of Escherichia coli RFL 130, a
      possibility was investigated for selecting a scheme for restriction enzyme
      purification under static conditions by analyzing the binding of protein to
      various absorbents and evaluating the functional purity of the samples of
      enzyme preparations.  The nature of restrictase and adsorbent interaction under
      static conditions made it possible to define the restrictase's sorption
      behavior in column chromatography and to select chromatography conditions.
      Evaluation of concomitant nonspecific nucleases allowed to specify the
      adsorbents that could be most effective from the point of view of functional
      purification.  A highly effective scheme for Eco130I restrictase purification
      has been developed.  Fractionation of cell-free extracts of E. coli RFL 130 on
      heparin-sepharose, DEAE-cellulose and phosphocellulose yielded an enzyme
      preparation of high functional purity.
AU  - Vaitkevicius D
AU  - Naureckiene S
AU  - Janulaitis A
PT  - Journal Article
TA  - Biotekhnologiya
JT  - Biotekhnologiya
SO  - Biotekhnologiya 1991 1: 35-41.

PMID- 26868385
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Enterohemorrhagic Escherichia coli Encoding Extended-Spectrum Beta-Lactamases.
PG  - e01633-15
AB  - Extended-spectrum beta-lactamases (ESBLs) have rarely been observed among Shiga toxigenic
      Escherichia coli (STEC), and, to our best knowledge, only three
      ESBL-positive isolates of the enterohemorrhagic E. coli (EHEC) subpathotype have
      been reported. Here, we present the first draft genome sequences of two
      ESBL-positive EHEC isolates belonging to serotypes O111:H8 and O151:H16.
AU  - Valat C
AU  - Goldstone RJ
AU  - Hirchaud E
AU  - Haenni M
AU  - Smith DG
AU  - Madec JY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01633-15.

PMID- 28982999
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Type Strain Aeromonas salmonicida subsp. salmonicida ATCC 33658.
PG  - e01064-17
AB  - Here, we report the draft genome sequence of the type strain Aeromonas salmonicida subsp.
      salmonicida ATCC 33658 isolated from Salmo salar The size of
      the genome is 4,728,143 bp with a G+C content of 58.5%. The A. salmonicida subsp.
      salmonicida ATCC 33658 genome lacks essential virulence genes that were likely
      lost during genomic rearrangements.
AU  - Valderrama K
AU  - Soto-Davila M
AU  - Santander J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01064-17.

PMID- 22123759
VI  - 193
DP  - 2011
TI  - Draft Genome Sequence of the Extremely Acidophilic Biomining Bacterium Acidithiobacillus thiooxidans ATCC 19377 Provides Insights into the  Evolution of the Acidithiobacillus Genus.
PG  - 7003-7004
AB  - Acidithiobacillus thiooxidans is a mesophilic, extremely acidophilic, chemolithoautotrophic
      gammaproteobacterium that derives energy from the
      oxidation of sulfur and inorganic sulfur compounds. Here we present the
      draft genome sequence of A. thiooxidans ATCC 19377, which has allowed the
      identification of genes for survival and colonization of extremely acidic
      environments.
AU  - Valdes J
AU  - Ossandon F
AU  - Quatrini R
AU  - Dopson M
AU  - Holmes DS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 7003-7004.

PMID- 19617360
VI  - 191
DP  - 2009
TI  - Draft genome sequence of the extremely acidophilic bacterium Acidithiobacillus caldus ATCC 51756 reveals metabolic versatility in the genus Acidithiobacillus.
PG  - 5877-5878
AB  - Acidithiobacillus caldus is an extremely acidophilic, moderately thermophilic,
      chemolithoautotrophic gammaproteobacterium that derives energy from the oxidation
      of sulfur and reduced inorganic sulfur compounds. Here we present the draft
      genome sequence of Acidithiobacillus caldus ATCC 51756 (the type strain of the
      species), which has permitted the prediction of genes for survival in extremely
      acidic environments, including genes for sulfur oxidation and nutrient
      assimilation.
AU  - Valdes J
AU  - Quatrini R
AU  - Hallberg K
AU  - Dopson M
AU  - Valenzuela PD
AU  - Holmes DS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2009 191: 5877-5878.

PMID- 25414492
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Nitrincola sp. Strain A-D6, an Arsenic-Resistant Gammaproteobacterium Isolated from a Salt Flat.
PG  - e01144-14
AB  - We report Nitrincola sp. strain A-D6, which was characterized as an arsenic-resistant
      bacterium isolated from the Ascotan Salt Flat in northern
      Chile. The size of the genome is 3,795,776 bp, with a G+C content of 49.96%.
      Genes for the arsenic-resistant Ars system and arsenic oxidation have been
      encoded.
AU  - Valdes N
AU  - Rivera-Araya J
AU  - Bijman J
AU  - Escudero L
AU  - Demergasso C
AU  - Fernandez S
AU  - Ferrer A
AU  - Chavez R
AU  - Levican G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01144-14.

PMID- 26605004
VI  - 10
DP  - 2015
TI  - Draft genome sequence of strain MTR reveals its mechanism of capnophilic behavior.
PG  - 110
AB  - Janthinobacterium lividum is a Gram-negative bacterium able to produce violacein, a pigment
      with antimicrobial and antitumor properties. Janthinobacterium lividum
      colonizes the skin of some amphibians and confers protection against fungal
      pathogens. The mechanisms underlying this association are not well understood. In
      order to identify the advantages for the bacterium to colonize amphibian skin we
      sequenced Janthinobacterium lividum strain MTR, a strain isolated from Cajon del
      Maipo, Chile. The strain has capnophilic behavior, with growth favored by high
      concentrations (5 %) of carbon dioxide. Its genome is 6,535,606 bp in size, with
      5,362 coding sequences and a G + C content of 62.37 %. The presence of genes
      encoding for products that participate in the carbon fixation pathways (dark CAM
      pathways), and the entire set of genes encoding for the enzymes of the glyoxylate
      cycle may explain the capnophilic behavior and allow us to propose that the CO2
      secreted by the skin of amphibians is the signal molecule that guides
      colonization by Janthinobacterium lividum.
AU  - Valdes N
AU  - Soto P
AU  - Cottet L
AU  - Alarcon P
AU  - Gonzalez A
AU  - Castillo A
AU  - Corsini G
AU  - Tello M
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 110.

PMID- 29146850
VI  - 5
DP  - 2017
TI  - First Insight into the Genome Sequences of Two Linezolid-Resistant Nocardia farcinica Strains Isolated from Patients with Cystic Fibrosis.
PG  - e01212-17
AB  - The draft genome sequences of two Nocardia farcinica strains isolated from two patients with
      cystic fibrosis (CF), resistant to trimethoprim/sulfamethoxazole
      and linezolid, are reported here. The estimated genome sizes were 5.8 Mb with a
      70.63% G+C content. Transposases from Tn916 were detected, but not 23S rRNA
      mutation (G2576T) related to linezolid resistance.
AU  - Valdezate S
AU  - Monzon S
AU  - Garrido N
AU  - Zaballos A
AU  - Medina-Pascual MJ
AU  - Azcona-Gutierrez JM
AU  - Vilar B
AU  - Cuesta I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01212-17.

PMID- 14506783
VI  - 293
DP  - 2003
TI  - Helicobacter pylori genomic DNA methylation status: strain typing.
PG  - 109
AB  - The complete genome sequence of two different strains of H. pylori, revealed extreme genetic
      diversity.  It also showed that both strains have an unusually high number of restriction and
      modification systems (RM).  Based on the knowledge that in RM systems the restriction
      endonuclease (ENase) impose high pressure on the expression of the companion methyltransferase
      (MTase) it was hypothesised that genomic DNA methylation status could be used to develop a new
      typing method of H. pylori.  To test this hypothesis 51 strains of H. pylori were studied, 28
      of which were epidemiologically related.  Genomic DNA was isolated and digested with 33
      different ENases.  After reisolation of DNA from seven strains we replicated 3.5% of the ENase
      digests (59/1683) with 100% concordance.  The results were grouped as a data matrix, where "0"
      means presence of unmethylated DNA and "1" presence of methylated DNA.  Dendrograms were
      constructed with UPGMA method and Jaccard coefficient. After statistical cluster analysis
      (NTSYSpc) and correspondence factorial analysis (PSS 11.0) ENases were gradually eliminated
      until a final group of 16 ENases were selected as a tool to type H. pylori: Acil, BssHII,
      BstUI, DdeI, DraI, FauI, HaeIII, Hpy181I, Hpy99I, HpyCH4III, HpyCH4IV, HpyCH4V, MspI, Sau96I,
      ScrFI and TaqI.  The method has high discriminatory power (Simpson index of diversity=0,99,
      strain group frequency nj/N=0.039), has adequate cophenetic correlation coefficient, r=0.782
      and high typability.  That is adequate for typing H. pylori. A high number of MTases were
      expressed in all strains (between 14 and 22) and 9 of which were common (M.ApaI, M.BseRI,
      M.DpnI, M.EagI, M.HhaI, M.HinT1I, M.NaeI, M.NgoMIV and M.NIaIII).
AU  - Vale A
AU  - Vitor J
PT  - Journal Article
TA  - Int. J. Med. Microbiol.
JT  - Int. J. Med. Microbiol.
SO  - Int. J. Med. Microbiol. 2003 293: 109.

PMID- 18086685
VI  - 24
DP  - 2008
TI  - A new algorithm for cluster analysis of genomic methylation: the Helicobacter pylori case.
PG  - 383-388
AB  - Motivation: The genomic methylation analysis is useful to type bacteria that have a high
      number of expressed type II methyltransferases.
      Methyltransferases are usually committed to Restriction and
      Modification (R-M) systems, in which the restriction endonuclease
      imposes high pressure on the expression of the cognate
      methyltransferase that hinder R-M system loss. Conventional cluster
      methods do not reflect this tendency. An algorithm was developed for
      dendrogram construction reflecting the propensity for conservation of
      R-M Type II systems.
      Results: The new algorithm was applied to 52 Helicobacter pylori
      strains from different geographical regions and compared with
      conventional clustering methods. The algorithm works by first grouping
      strains that share a common minimum set of R-M systems and gradually
      adds strains according to the number of the R-M systems acquired.
      Dendrograms revealed a cluster of African strains, which suggest that
      R-M systems are present in H.pylori genome since its human host
      migrates from Africa.
AU  - Vale FF
AU  - Encarnacao P
AU  - Vitor JMB
PT  - Journal Article
TA  - Bioinformatics
JT  - Bioinformatics
SO  - Bioinformatics 2008 24: 383-388.

PMID- 19737407
VI  - 9
DP  - 2009
TI  - Geographic distribution of methyltransferases of Helicobacter pylori: evidence of human host population isolation and migration.
PG  - 193
AB  - ABSTRACT: BACKGROUND: Helicobacter pylori colonizes the human stomach and is associated with
      gastritis, peptic ulcer, and gastric cancer. This
      ubiquitous association between H. pylori and humans is thought to be
      present since the origin of modern humans. The H. pylori genome encodes
      for an exceptional number of restriction and modifications (R-M) systems.
      To evaluate if R-M systems are an adequate tool to determine the
      geographic distribution of H. pylori strains, we typed 221 strains from
      Africa, America, Asia, and Europe, and evaluated the expression of 29
      methyltransferases. RESULTS: Independence tests and logistic regression
      models revealed that 10 R-M systems correlate with geographical
      localization. The distribution pattern of these methyltransferases may
      have been originated by co-divergence of regional H. pylori after its
      human host migrated out of Africa. The expression of specific
      methyltransferases in the H. pylori population may also reflect the
      genetic and cultural background of its human host. Methyltransferases
      common to all strains, M.HhaI and M.NaeI, are likely conserved in H.
      pylori, and may have been present in the bacteria genome since the human
      diaspora out of Africa. CONCLUSIONS: This study indicates that
      methyltransferases are useful geomarkers, which allow discrimination of
      bacterial populations, and that can be added to our tools to investigate
      human migrations.
AU  - Vale FF
AU  - Megraud F
AU  - Vitor JM
PT  - Journal Article
TA  - BMC Microbiol.
JT  - BMC Microbiol.
SO  - BMC Microbiol. 2009 9: 193.

PMID- 17483255
VI  - 73
DP  - 2007
TI  - Genomic Methylation: a Tool for Typing Helicobacter pylori Isolates.
PG  - 4243-4249
AB  - The genome sequences of three Helicobacter pylori strains revealed an abundant number of
      putative restriction and modification (R-M) systems
      within a small genome (1.60 to 1.67 Mb). Each R-M system includes an
      endonuclease that cleaves a specific DNA sequence and a DNA
      methyltransferase that methylates either adenosine or cytosine within the
      same DNA sequence. These are believed to be a defense mechanism,
      protecting bacteria from foreign DNA. They have been classified as selfish
      genetic elements; in some instances it has been shown that they are not
      easily lost from their host cell. Possibly because of this phenomenon, the
      H. pylori genome is very rich in R-M systems, with considerable variation
      in potential recognition sequences. For this reason the protective aspect
      of the methyltransferase gene has been proposed as a tool for typing H.
      pylori isolates. We studied the expression of H. pylori methyltransferases
      by digesting the genomic DNAs of 50 strains with 31 restriction
      endonucleases. We conclude that methyltransferase diversity is
      sufficiently high to enable the use of the genomic methylation status as a
      typing tool. The stability of methyltransferase expression was assessed by
      comparing the methylation status of genomic DNAs from strains that were
      isolated either from the same patient at different times or from different
      stomach locations (antrum and corpus). We found a group of five
      methyltransferases common to all tested strains. These five may be
      characteristic of the genetic pool analyzed, and their biological role may
      be important in the host/bacterium interaction.
AU  - Vale FF
AU  - Vitor JM
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2007 73: 4243-4249.

PMID- 
VI  - 1
DP  - 2008
TI  - Genomic methylation status for discrimination among Helicobacter species: A bioinformatics approach.
PG  - 258-266
AB  - The genus Helicobacter comprises several species of both gastric and enterohepatic intestinal
      bacteria. H. pylori, the type species of the genus, is associated with gastritis, peptic ulcer
      and gastric cancer in humans. H. pylori genome has a high number of restriction and
      modification (R-M) systems and their diversity is useful for strain typing. To analyse if such
      a high number of expressed methyltransferases is a characteristic of the genus Helicobacter,
      the genomic methylation of five non-pylori Helicobacter spp. (H. canadensis, H. canis, H.
      felis, H.mustelae and H. pullorum) was determined. The results revealed that the number of R-M
      systems among nonpylori Helicobacter spp. is smaller than those observed among a group of 221
      H. pylori strains (p<0,001), but is greater than those observed for the mean of all bacteria
      sequenced genomes (p=0,005). 16S ribosomal RNA analysis of H. pylori sequenced strains and
      five non-pylori Helicobacter spp. clearly isolate H. pylori species.  Surprisingly, the
      analysis of the genomic methylation status by MCRM algorithm performs similarly. This suggests
      that R-M systems do not appear to be spread in a miscellaneous manner, once even that these
      genes may be subjected to acquisition and loss; their expression still allows discriminating
      among Helicobacter spp.
AU  - Vale FF
AU  - Vitor JMB
PT  - Journal Article
TA  - J. Proteomics Bioinformatics
JT  - J. Proteomics Bioinformatics
SO  - J. Proteomics Bioinformatics 2008 1: 258-266.

PMID- 24558245
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Salmonella enterica Serovar Typhi Strain STH2370.
PG  - e00104-14
AB  - We report the draft genome sequence of Salmonella enterica serovar Typhi strain STH2370,
      isolated from a typhoid fever patient in Santiago, Chile. This clinical
      isolate has been used as the reference wild-type strain in numerous studies
      conducted in our laboratories during the last 15 years.
AU  - Valenzuela C
AU  - Ugalde JA
AU  - Mora GC
AU  - Alvarez S
AU  - Contreras I
AU  - Santiviago CA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00104-14.

PMID- 26494678
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Komagataeibacter europaeus CECT 8546, a Cellulose-Producing Strain of Vinegar Elaborated by the Traditional Method.
PG  - e01231-15
AB  - The present article reports the draft genome sequence of the strain Komagataeibacter europaeus
      CECT 8546, an acetic acid bacterium characterized by its ability to overproduce cellulose.
      This species is highly resistant to acetic  acid and commonly found during vinegar
      elaboration.
AU  - Valera MJ
AU  - Poehlein A
AU  - Torija MJ
AU  - Haack FS
AU  - Daniel R
AU  - Streit WR
AU  - Mateo E
AU  - Mas A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01231-15.

PMID- 27609919
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Tepidimonas taiwanensis Strain VT154-175.
PG  - e00942-16
AB  - The slightly thermophilic bacterium Tepidimonas taiwanensis strain VT154-175 has  been
      isolated from a hot spring in the area of Viterbo, Italy. The whole draft
      genome of 2.9 Mb obtained by paired-end next-generation sequencing and divided
      into 60 scaffolds is presented.
AU  - Valeriani F
AU  - Biagini T
AU  - Giampaoli S
AU  - Crognale S
AU  - Santoni D
AU  - Romano SV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00942-16.

PMID- Not carried by PubMed...
VI  - 53
DP  - 1992
TI  - Characterization of restriction-modification systems in Klebsiella pneumoniae.
PG  - 2701B
AB  - Two restriction-modification (R-M) systems, KpnAI and KpnBI, found in Klebsiella pneumoniae
      strains M5a1 and GM236, respectively, have been studied and confirmed to be different from
      other R-M systems reported in K. pneumoniae. Mutant studies suggest that the KpnAI and KpnBI
      systems may belong to either a type I or type III system, since approximately equal numbers of
      r-m+ and r-m- mutants were obtained. However, a DNA hybridization study using representative
      type I and type III probes from E. coli and S. typhimurium failed to show homologies to either
      KpnAI or KpnBI. The restriction endonuclease KpnBI was found to be temperature-sensitive with
      maximum restriction activity at 30oC and no restriction activity at 42oC. Further, the
      activity of endonuclease KpnBI was found to be reduced to almost zero level by growing the
      bacteria in the presence of 10% glycerol. Although the mechanism is not known, this is the
      first time such a phenomenon has been observed in any of the reported R-M systems. These
      studies also compared the efficiency of transformation in K. pneumoniae of three plasmid
      transformation methods; CaCl2 heat-shock; freezing and thawing in the presence of CaCl2; and
      electroporation. Electroporation was shown to be the most efficient method. Transformation
      efficiency in both the r+KpnAI and r+KpnBI strains was 20- to 100-fold less than the
      transformation efficiency of the r- strains, depending on plasmid size. Four different
      approaches have been used to clone the hsd genes of the KpnBI system. Two clones were
      obtained; these were named pKpnB1 and pKpnB2. The pKpnB1 and pKpnB2 clones were found to
      complement the restriction activity of an r- KpnBIm+KpnBI K. pneumoniae mutant and were also
      found to complement both the restriction and modification activities of an r-KpnBIm-KpnBI K.
      pneumoniae mutant. A quick subcloning method which involves making subclones from a plasmid
      clone in a single step was also developed. A preliminary analysis, based on complementation
      studies, of the gene structure suggested that the KpnBI system may consist of three structural
      genes, a characteristic of the type I R-M system.
AU  - Valinluck B
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1992 53: 2701B.

PMID- 8566812
VI  - 167
DP  - 1995
TI  - A new restriction-modification system, KpnBI, recognized in Klebsiella pneumoniae.
PG  - 59-62
AB  - A unique DNA restriction-modification (R-M) system has been identified in the GM236 strain of
      Klebsiella pneumoniae using the newly isolated phage, SBS.  The system was designated KpnBI.
      The gene (hsdRKpnBI) complementing the restriction activity of the KpnBI system was cloned in
      pBR322.  The nucleotide sequence of the cloned DNA revealed one open reading frame (ORF) of
      3035 bp.  Analysis of the deduced amino-acid sequence shows seven helicase motifs which are
      common to the restriction (R) subunit of both type-I and type-III R-M systems.  Computer
      analysis (Dendrogram) of the R polypeptide of KpnBI suggests a closer relationship to
      EcoR124/3I, a member of type-IC family, than to other representative type-I and type-III
      systems.
AU  - Valinluck B
AU  - Lee NS
AU  - Ryu J
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 167: 59-62.

PMID- Not carried by PubMed...
VI  - 89
DP  - 1989
TI  - Two new restriction-modification systems, KpnA and KpnB, in Klebsiella pneumoniae.
PG  - 180
AB  - Strains of K. pneumoniae, M5a1 and GM236, each possess a unique restriction-modification (R-M)
      system. These two systems differ from KpnI, a type II system reported previously in K.
      pneumoniae, since the KpnI endonuclease degrades chromosomal DNA from both M5a1 and GM236. No
      plasmids or type II restriction endonuclease activity have so far been identified from these
      two strains. Mutant analysis suggests that these two Klebsiella R-M systems may be classified
      as type I since almost equal numbers of r- m+ and r- m- mutants were obtained from a single
      mutagenic treatment. DNA hybridization revealed a weak but significant homology between an
      hsdSB probe derived from S. typhimurium and GM236 chromosome. No homology was observed between
      an hsdA probe derived from E. coli 15T and chromosomal DNA from either of the two Klebsiella
      strains. A 7.2 kb EcoRI fragment of GM236 identified by its hybridization to the S.
      typhimurium hsdSB probe was cloned in pBluescript (Stratagene). Only one PvuII fragment (1.7
      kb) derived from it showed hybridization to hsdM region of hsdSB and hsdK (from E. coli K12)
      clones. From the above observations, we concluded that M5a1 and GM236 have new R-M systems
      which we designated provisionally KpnA and KpnB, respectively.
AU  - Valinluck B
AU  - Reyno M
AU  - Ryu J
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1989 89: 180.

PMID- 17283125
VI  - 67
DP  - 2007
TI  - Endogenous cytosine damage products alter the site selectivity of human DNA maintenance methyltransferase DNMT1.
PG  - 946-950
AB  - Alterations in cytosine methylation patterns are usually observed in human tumors. The
      consequences of altered cytosine methylation patterns
      include both inappropriate activation of transforming genes and
      silencing of tumor suppressor genes. Despite the biological effect of
      methylation changes, little is known about how such changes are caused.
      The heritability of cytosine methylation patterns from parent to
      progeny cells is attributed to the fidelity of the
      methylation-sensitive human maintenance methyltransferase DNMT1, which
      methylates with high specificity the unmethylated strand of a
      hemimethylated CpG sequence following DNA replication. We have been
      studying DNA damage that might alter the specificity of DNMTl, either
      inhibiting the methylation of hemimethylated sites or triggering the
      inappropriate methylation of previously unmethylated sites. Here, we
      show that known forms of endogenous DNA damage can cause either
      hypermethylation or hypomethylation. Inflammation-induced 5-halogenated
      cytosine damage products, including 5-chlorocytosine, mimic
      5-methylcytosine and induce inappropriate DNMTl methylation within a
      CpG sequence. In contrast, oxidation damage of the methyl group of
      5-methylcytosine, with the formation of 5-hydroxymethylcytosine,
      prevents DNMTI methylation of the target cytosine. We propose that
      reduced DNMTI selectivity resulting from DNA damage could cause
      heritable changes in cytosine methylation patterns, resulting in human
      tumor formation. These data may provide a mechanistic link for the
      associations documented between inflammation and cancer.
AU  - Valinluck V
AU  - Sowers LC
PT  - Journal Article
TA  - Cancer Res.
JT  - Cancer Res.
SO  - Cancer Res. 2007 67: 946-950.

PMID- 16608167
VI  - 19
DP  - 2006
TI  - Impact of cytosine 5-halogens on the interaction of DNA with restriction endonucleases and methyltransferase.
PG  - 556-562
AB  - Growing evidence from both prokaryotes and eukaryotes indicates that pyrimidine 5-methyl
      groups can have profound biological consequences
      that are mediated by the affinity of DNA-protein interactions. The
      presence of the 5-methyl group could potentially create a steric block
      preventing the binding of some proteins whereas the affinity of many
      other proteins is substantially increased by pyrimidine methylation. In
      this paper, we have constructed a series of oligonucleotides containing
      cytosine and a series of 5-substituted cytosine analogues including all
      halogens. This set of oligonucleotides has been used to probe the
      relationship between the size of the substituent and its capacity to
      modulate cleavage by the methylation-sensitive restriction
      endonucleases MspI and HpaII. Additionally, we have examined the impact
      of the halogen substitution on the corresponding bacterial
      methyltransferase (M.HpaII). We observed that MspI cleavage is only
      subtly affected by substituted cytosine analogues at the inner position
      of the CCGG recognition site. In contrast, HpaII cleaves
      cytosine-containing oligonucleotides completely whereas
      5-fluorocytosine-containing oligonucleotides are cleaved at a reduced
      rate. The presence of the larger halogens Cl, Br, or I as well as a
      methyl group completely prevents cleavage by HpaII. These data suggest
      that the steric wall is encountered by HpaII slightly beyond the
      fluorine substituent, at about 2.65 angstrom from the pyrimidine
      C5-position. It is known that 5-fluorocytosine in an oligonucleotide
      can form a covalent irreversible suicide complex with either
      prokaryotic or eukaryotic methyltransferases. Kinetic data reported
      here suggest that the 5-fluorocytosine-containing oligonucleotide can
      also inhibit M.HpaII by formation of a reversible, noncovalent complex.
      Our results indicate that although a 5-Cl substituent has electronic
      properties similar to 5-F, 5-chlorocytosine duplexes neither form a
      complex with M.HpaII nor inhibit enzymatic methylation. Emerging data
      suggest that halogenation of cytosine can occur in DNA in vivo from
      inflammation-mediated reactive molecules. The results reported here
      suggest that the inadvertent halogenation of cytosine residues in DNA
      could alter the affinity of sequence-specific DNA-binding proteins.
AU  - Valinluck V
AU  - Wu W
AU  - Liu PF
AU  - Neidigh JW
AU  - Sowers LC
PT  - Journal Article
TA  - Chem. Res. Toxicol.
JT  - Chem. Res. Toxicol.
SO  - Chem. Res. Toxicol. 2006 19: 556-562.

PMID- 18350144
VI  - 3
DP  - 2008
TI  - Comparative analysis of Acinetobacters: three genomes for three lifestyles.
PG  - e1805
AB  - Acinetobacter baumannii is the source of numerous nosocomial infections in humans and
      therefore deserves close attention as multidrug or even pandrug
      resistant strains are increasingly being identified worldwide. Here we
      report the comparison of two newly sequenced genomes of A. baumannii. The
      human isolate A. baumannii AYE is multidrug resistant whereas strain SDF,
      which was isolated from body lice, is antibiotic susceptible. As reference
      for comparison in this analysis, the genome of the soil-living bacterium
      A. baylyi strain ADP1 was used. The most interesting dissimilarities we
      observed were that i) whereas strain AYE and A. baylyi genomes harbored
      very few Insertion Sequence elements which could promote expression of
      downstream genes, strain SDF sequence contains several hundred of them
      that have played a crucial role in its genome reduction (gene disruptions
      and simple DNA loss); ii) strain SDF has low catabolic capacities compared
      to strain AYE. Interestingly, the latter has even higher catabolic
      capacities than A. baylyi which has already been reported as a very
      nutritionally versatile organism. This metabolic performance could explain
      the persistence of A. baumannii nosocomial strains in environments where
      nutrients are scarce; iii) several processes known to play a key role
      during host infection (biofilm formation, iron uptake, quorum sensing,
      virulence factors) were either different or absent, the best example of
      which is iron uptake. Indeed, strain AYE and A. baylyi use
      siderophore-based systems to scavenge iron from the environment whereas
      strain SDF uses an alternate system similar to the Haem Acquisition System
      (HAS). Taken together, all these observations suggest that the genome
      contents of the 3 Acinetobacters compared are partly shaped by life in
      distinct ecological niches: human (and more largely hospital environment),
      louse, soil.
AU  - Vallenet D et al
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2008 3: e1805.

PMID- 10869190
VI  - 39
DP  - 2000
TI  - Thermodynamic, spectroscopic, and equilibrium binding studies of DNA sequence context effects in four 40 base pair deoxyoligonucleotides.
PG  - 7835-7846
AB  - Effects of different end sequences on melting, circular dichroism spectra (CD), and enzyme
      binding properties were investigated for four 40 base pair, non-self-complementary duplex DNA
      oligomers. The center sequences of these oligoduplexes have either of two 22 base pair modules
      flanked on both sides by sequences differing in AT content. Temperature-induced melting
      transitions monitored by differential scanning calorimetry (DSC) and ultraviolet absorbance
      were measured for the six duplexes in buffered 115 mM Na(+) solutions. Values of the melting
      transition enthalpy, DeltaH(cal), and entropy, DeltaS(cal), were obtained directly from DSC
      experiments. Melting transition parameters, DeltaH(vH) and DeltaS(vH), were also estimated
      from a van't Hoff analysis of optical melting curves collected as a function of DNA
      concentration, assuming that the melting transition is two-state. Melting free energies (20
      degrees C) evaluated from DSC melting experiments on the four duplex DNAs ranged from -52.2 to
      -77.5 kcal/mol. Free energies based on the van't Hoff analysis were -37.9 to -58.8 kcal/mol.
      Although the values are different, trends in the melting free energies of the four duplex DNAs
      as a function of sequence were identical in both DSC and optical analyses. Subject to several
      assumptions, values for the initiation free energy were estimated for each duplex, defined as
      DeltaG(int) = DeltaG(cal) - DeltaG(pred), where DeltaG(cal) is the experimental free energy at
      20 degrees C determined from the experimentally measured values of the transition enthalpy,
      DeltaH(cal), and entropy, DeltaS(cal). The predicted free energy of the sequence,
      DeltaG(pred)(20 degrees C), is obtained using published nearest-neighbor sequence stability
      values. For three of the four duplexes, values of DeltaG(int) are essentially nil. In
      contrast, the duplex with 81.8% GC has a considerably higher estimate of DeltaG(int) = 7.1
      kcal/mol. The CD spectra for the six duplexes collected over the wavelength range from 200 to
      320 nm are also sequence-dependent. Factor analysis of the CD spectra by singular value
      decomposition revealed that the experimental CD spectra could be reconstructed from linear
      combinations of two minor and one major subspectra. Changes in the coefficients of the major
      subspectrum for different sequences reflect incremental sequence-dependent variations of the
      CD spectra. Equilibrium binding by BamHI restriction endonuclease to the 40 base pair DNAs
      whose central eight base pairs contain the recognition sequence for BamHI restriction enzyme
      bounded by A.T base pairs, 5'-A-GGATCC-A-3' was investigated. Binding assays were performed
      by titering BamHI against a constant concentration of each of the duplex DNA substrates, in
      the absence of Mg(2+), followed by analysis by gel retardation. Under the conditions employed,
      the enzyme binds but does not cleave the DNAs. Results of the assays revealed two binding
      modes with retarded gel mobilities. Binding isotherms for the fraction of bound DNA species
      versus enzyme concentration for each binding mode were constructed and analyzed with a simple
      two-step equilibrium binding model. This analysis provided semiquantitative estimates on the
      equilibrium binding constants for BamHI to the four DNAs. Values obtained for the binding
      constants varied only 7-fold and ranged from 6 x 10^-8 to 42 x 10^-8 M, with binding
      free energies from -8.6 to -9.7 (+/- 0.2) kcal/mol depending on the sequence that flanks the
      enzyme binding site. Unlike what was found earlier in binding studies of the 22 base pair
      duplexes that constitute the core modules of the present 40-mers [Riccelli, P. V., Vallone, P.
      M., Kashin, I., Faldasz, B. D., Lane, M. J., and Benight, A. S. (1999) Biochemistry 38,
      11197-11208], no obvious relationship between binding and stability was found for these longer
      DNAs. Apparently, effects of flanking sequence stability on restriction enzyme binding may
      only be measurable in very short duplex deoxyoligonucleotides.
AU  - Vallone PM
AU  - Benight AS
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2000 39: 7835-7846.

PMID- 24874685
VI  - 2
DP  - 2014
TI  - Comparative Genomic Analysis of Two Multidrug-Resistant Clinical Isolates of ST395 Epidemic Strain of Pseudomonas aeruginosa Obtained 12 Years Apart.
PG  - e00515-14
AB  - Pseudomonas aeruginosa can cause large and prolonged outbreaks in hospitals. We have sequenced
      and annotated the genomes of two multidrug-resistant P. aeruginosa
      isolates from the same strain obtained 12 years apart from different patients.
      Genomic analysis provided insight on the genes acquired and lost by P. aeruginosa
      during its spread.
AU  - Valot B
AU  - Rohmer L
AU  - Jacobs MA
AU  - Miller SI
AU  - Bertrand X
AU  - Hocquet D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00515-14.

PMID- 27563043
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Two Bacillus anthracis Strains from Etosha National Park, Namibia.
PG  - e00861-16
AB  - Bacillus anthracis strains K1 and K2 were isolated from two plains zebra anthrax  carcasses in
      Etosha National Park, Namibia. These are draft genomes obtained by
      Illumina MiSeq sequencing of isolates collected from culture of blood-soaked soil
      from each carcass.
AU  - Valseth K
AU  - Nesbo CL
AU  - Easterday WR
AU  - Turner WC
AU  - Olsen JS
AU  - Stenseth NC
AU  - Haverkamp TH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00861-16.

PMID- 22740697
VI  - 287
DP  - 2012
TI  - 5 '-Cytosine-Phosphoguanine (CpG) Methylation Impacts the Activity of Natural and Engineered Meganucleases.
PG  - 30139-30150
AB  - In this study, we asked whether CpG methylation could influence the DNA binding affinity and
      activity of meganucleases used for genome
      engineering applications. A combination of biochemical and structural
      approaches enabled us to demonstrate that CpG methylation decreases
      I-CreI DNA binding affinity and inhibits its endonuclease activity in
      vitro. This inhibition depends on the position of the methylated
      cytosine within the DNA target and was almost total when it is located
      inside the central tetrabase. Crystal structures of I-CreI bound to
      methylated cognate target DNA suggested a molecular basis for such
      inhibition, although the precise mechanism still has to be specified.
      Finally, we demonstrated that the efficacy of engineered meganucleases
      can be diminished by CpG methylation of the targeted endogenous site,
      and we proposed a rational design of the meganuclease DNA binding
      domain to alleviate such an effect. We conclude that although activity
      and sequence specificity of engineered meganucleases are crucial
      parameters, target DNA epigenetic modifications need to be considered
      for successful gene editions.
AU  - Valton J
AU  - Daboussi F
AU  - Leduc S
AU  - Molina R
AU  - Redondo P
AU  - Macmaster R
AU  - Montoya G
AU  - Duchateau P
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2012 287: 30139-30150.

PMID- 10518532
VI  - 96
DP  - 1999
TI  - A structural snapshot of base-pair opening in DNA.
PG  - 11809-11814
AB  - The response of double-helical DNA to torsional stress may be a driving force for many
      processes acting on DNA. The 1.55-A crystal structure of a duplex DNA oligonucleotide
      d(CCAGGCCTGG)(2) with an engineered crosslink in the minor groove between the central guanine
      bases depicts how the duplex can accommodate such torsional stress. We have captured in the
      same crystal two rather different conformational states. One duplex contains a strained
      crosslink that is stabilized by calcium ion binding in the major groove, directly opposite the
      crosslink. For the other duplex, the strain in the crosslink is relieved through partial
      rupture of a base pair and partial extrusion of a cytosine accompanied by helix bending. The
      sequence used is the target sequence for the HaeIII methylase, and this partially flipped
      cytosine is the same nucleotide targeted for extrusion by the enzyme. Molecular dynamics
      simulations of these structures show an increased mobility for the partially flipped-out
      cytosine.
AU  - van Aalten DMF
AU  - Erlanson DA
AU  - Verdine GL
AU  - Joshua-Tor L
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1999 96: 11809-11814.

PMID- 26507855
VI  - 43
DP  - 2015
TI  - Mapping DNA cleavage by the Type ISP restriction-modification enzymes following long-range communication between DNA sites in different orientations.
PG  - 10430-10443
AB  - The prokaryotic Type ISP restriction-modification enzymes are single-chain proteins comprising
      an Mrr-family nuclease, a superfamily 2 helicase-like ATPase,
      a coupler domain, a methyltransferase, and a DNA-recognition domain. Upon
      recognising an unmodified DNA target site, the helicase-like domain hydrolyzes
      ATP to cause site release (remodeling activity) and to then drive downstream
      translocation consuming 1-2 ATP per base pair (motor activity). On an invading
      foreign DNA, double-strand breaks are introduced at random wherever two
      translocating enzymes form a so-called collision complex following long-range
      communication between a pair of target sites in inverted (head-to-head) repeat.
      Paradoxically, structural models for collision suggest that the nuclease domains
      are too far apart (>30 bp) to dimerise and produce a double-strand DNA break
      using just two strand-cleavage events. Here, we examined the organisation of
      different collision complexes and how these lead to nuclease activation. We
      mapped DNA cleavage when a translocating enzyme collides with a static enzyme
      bound to its site. By following communication between sites in both head-to-head
      and head-to-tail orientations, we could show that motor activity leads to
      activation of the nuclease domains via distant interactions of the helicase or
      MTase-TRD. Direct nuclease dimerization is not required. To help explain the
      observed cleavage patterns, we also used exonuclease footprinting to demonstrate
      that individual Type ISP domains can swing off the DNA. This study lends further
      support to a model where DNA breaks are generated by multiple random nicks due to
      mobility of a collision complex with an overall DNA-binding footprint of
      approximately 30 bp.
AU  - van Aelst K
AU  - Saikrishnan K
AU  - Szczelkun MD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2015 43: 10430-10443.

PMID- 23221632
VI  - 41
DP  - 2013
TI  - DNA cleavage by Type ISP Restriction-Modification enzymes is initially targeted to the 3'-5' strand.
PG  - 1081-1090
AB  - The mechanism by which a double-stranded DNA break is produced following collision of two
      translocating Type I Restriction-Modification enzymes is not
      fully understood. Here, we demonstrate that the related Type ISP
      Restriction-Modification enzymes LlaGI and LlaBIII can cooperate to cleave DNA
      following convergent translocation and collision. When one of these enzymes is a
      mutant protein that lacks endonuclease activity, DNA cleavage of the 3'-5' strand
      relative to the wild-type enzyme still occurs, with the same kinetics and at the
      same collision loci as for a reaction between two wild-type enzymes. The DNA
      nicking activity of the wild-type enzyme is still activated by a protein variant
      entirely lacking the Mrr nuclease domain and by a helicase mutant that cannot
      translocate. However, the helicase mutant cannot cleave the DNA despite the
      presence of an intact nuclease domain. Cleavage by the wild-type enzyme is not
      activated by unrelated protein roadblocks. We suggest that the nuclease activity
      of the Type ISP enzymes is activated following collision with another Type ISP
      enzyme and requires adenosine triphosphate binding/hydrolysis but, surprisingly,
      does not require interaction between the nuclease domains. Following the initial
      rapid endonuclease activity, additional DNA cleavage events then occur more
      slowly, leading to further processing of the initial double-stranded DNA break.
AU  - van Aelst K
AU  - Sisakova E
AU  - Szczelkun MD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2013 41: 1081-1090.

PMID- 20435912
VI  - 107
DP  - 2010
TI  - Type III restriction enzymes cleave DNA by long-range interaction between sites in both head-to-head and tail-to-tail inverted repeat.
PG  - 9123-9128
AB  - Cleavage of viral DNA by the bacterial Type III Restriction-Modification enzymes requires the
      ATP-dependent long-range communication between a
      distant pair of DNA recognition sequences. The classical view is that Type
      III endonuclease activity is only activated by a pair of asymmetric sites
      in a specific head-to-head inverted repeat. Based on this assumption and
      due to the presence of helicase domains in Type III enzymes, various
      motor-driven DNA translocation models for communication have been
      suggested. Using both single-molecule and ensemble assays we demonstrate
      that Type III enzymes can also cleave DNA with sites in tail-to-tail
      repeat with high efficiency. The ability to distinguish both inverted
      repeat substrates from direct repeat substrates in a manner independent of
      DNA topology or accessory proteins can only be reconciled with an
      alternative sliding mode of communication.
AU  - van Aelst K
AU  - Toth J
AU  - Ramanathan SP
AU  - Schwarz FW
AU  - Seidel R
AU  - Szczelkun MD
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2010 107: 9123-9128.

PMID- 19002726
VI  - 28
DP  - 2009
TI  - Can Campylobacter coli induce Guillain-Barre syndrome?
PG  - 557-560
AB  - Campylobacter jejuni enteritis is the most frequently identified infection preceding the
      Guillain-Barre syndrome (GBS) and neural damage is thought to be induced through molecular
      mimicry between C. jejuni lipo-oligosaccharide (LOS) and human gangliosides [1]. It has been
      questioned whether or not other Campylobacter species, including C. curvus, C. upsaliensis and
      C. coli, could be similarly involved [2-4]. This is relevant because it would imply that
      bacterial factors considered important in the aetiology of GBS crossed species barriers. Two
      prior reports have appeared where C. coli was putatively associated with a case of GBS.
AU  - van Belkum A
AU  - Jacobs B
AU  - van Beek E
AU  - Louwen R
AU  - van Rijs W
AU  - Debruyne L
AU  - Gilbert M
AU  - Li J
AU  - Jansz A
AU  - Megraud F
AU  - Endtz H
PT  - Journal Article
TA  - Eur. J. Clin. Microbiol. Infect. Dis.
JT  - Eur. J. Clin. Microbiol. Infect. Dis.
SO  - Eur. J. Clin. Microbiol. Infect. Dis. 2009 28: 557-560.

PMID- 25908148
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Paenibacillus polymyxa NRRL B-30509 and Paenibacillus terrae NRRL B-30644, Strains from a Poultry Environment That Produce Tridecaptin   A and Paenicidins.
PG  - e00372-15
AB  - Paenibacillus polymyxa NRRL B-30509 and Paenibacillus terrae NRRL B-30644 produce tridecaptin
      A that is inhibitory to Campylobacter jejuni, as well as lantibiotics
      in the paenicidin family. Here, we report the draft genome sequences of P.
      polymyxa NRRL B-30509 and P. terrae NRRL B-30644 that contain gene clusters for
      various nonribosomal lipopeptides.
AU  - van Belkum MJ
AU  - Lohans CT
AU  - Vederas JC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00372-15.

PMID- 19467223
VI  - 78
DP  - 2009
TI  - DNA (Cytosine-C5) methyltransferase inhibition by oligodeoxyribonucleotides containing 2-(1H)-pyrimidinone (zebularine aglycon) at the enzymatic target site.
PG  - 633-641
AB  - Aberrant cytosine methylation in promoter regions leads to gene silencing associated with
      cancer progression. A number of DNA
      methyltransferase inhibitors are known to reactivate silenced genes:
      including 5-azacytidine and 2-(1H)-pyrimidinone riboside (zebularine).
      Zebularine is a more stable, less cytotoxic inhibitor compared to
      5-azacytidine. To determine the mechanistic basis for this difference,
      we carried out a detailed comparisons of the interaction between
      purified DNA methyltransferases and oligodeoxyribonucleotides (ODNs)
      containing either 5-azacytosine or 2-(1H)-pyrimidinone in place of the
      cytosine targeted for methylation. When incorporated into small ODNs,
      the rate of C5 DNA methyltransferase inhibition by both nucleosides is
      essentially identical. However, the stability and reversibility of the
      enzyme complex in the absence and presence of cofactor differs.
      5-Azacytosine ODNs form complexes with C5 DNA methyltransferases that
      are irreversible when the 5-azacytosine ring is intact. ODNs containing
      2-(1H)-pyrimidinone at the enzymatic target site are competitive
      inhibitors of both prokaryotic and mammalian DNA C5 methyltransferases.
      We determined that the ternary complexes between the enzymes,
      2-(1H)-pyrimidinone inhibitor, and the cofactor S-adenosyl methionine
      are maintained through the formation of a reversible covalent
      interaction. The differing stability and reversibility of the covalent
      bonds may partially account for the observed differences in
      cytotoxicity between zebularine and 5-azacytidine inhibitors.
AU  - van Bemmel DM
AU  - Brank AS
AU  - Eritja R
AU  - Marquez VE
AU  - Christman JK
PT  - Journal Article
TA  - Biochem. Pharmacol.
JT  - Biochem. Pharmacol.
SO  - Biochem. Pharmacol. 2009 78: 633-641.

PMID- 
VI  - 44
DP  - 2003
TI  - Characterization of the cytidine analog zebularine as an inhibitor of mammalian DNA (cytosine C5)-methyltransferase.
PG  - 430
AB  - Aberrant methylation of the promoter regions of genes has been shown to result in gene
      silencing associated with cancer progression.  Reactivation of silenced genes in cultured
      cells by methylation inhibitors can be induced by 5-azacytidine (5-AzaC) and
      5-aza-2-deoxycytidine (5-AzadC), which inhibit DNA methyltransferases when incorporated into
      DNA.  Since both 5-AzaC and 5-AzadC are chemically unstable and toxic, these results have
      stimulated the search for alternate inhibitors of the mammalian methyltransferase DNMT1.  We
      analyzed the inhibitory capacity of the cytidine analog zebularine (2-H pyrimidione).
      Zebularine is stable under both acidic and neutral conditions, and is minimally cytotoxic,
      making it a promising therapeutic agent.  We show that, when incorporated in place of the
      cytosine target in double stranded or looped oligodeoxyribonucleotides containing recognition
      sites for the bacterial methyltransferase (M.HhaI) and DNMT1 respectively, zebularine is
      equivalent to
      5-AzaC as an inhibitor of DNA methylation.  Despite the effective inhibition of DNMT1 in vitro
      by ODNs containing zebularine, no decrease in DNA methylation was observed in LNCaP cells
      treated with zebularine.  GSTP1 transcription was detected by RT-PCR after 5-AzadC treatment
      but not after zebularine treatment.  Analysis of the heavily methylated promoter region of the
      GSTP1 gene by bisulfite sequencing of DNA showed that DNA methylation was inhibited by 5-AzadC
      but not zebularine.  Interestingly, LNCaP cells grown in the presence of zebularine did
      display a marked change in morphology.  These results suggest that zebularine may not be
      efficiently incorporated into DNA in vivo, but may be able to alter cellular phenotype by
      interfering with other processes including RNA methylation.
AU  - Van Bemmel DM
AU  - Marquez VE
AU  - Christman JK
PT  - Journal Article
TA  - Proc. Amer. Assoc. Cancer Res.
JT  - Proc. Amer. Assoc. Cancer Res.
SO  - Proc. Amer. Assoc. Cancer Res. 2003 44: 430.

PMID- 9753779
VI  - 15
DP  - 1998
TI  - Developmental abnormalities associated with deoxyadenosine methylation in transgenic tobacco.
PG  - 543-551
AB  - As in other higher eukaryotes, DNA methylation in plants is predominantly found at
      deoxycytosine residues, while deoxyadenosine residues are not methylated at significant
      levels. 6mdA methylation has been successfully introduced into yeast and Drosophila via
      expression of a heterologous methyltransferase, but similar attempts in tobacco had, up until
      now, proved unsuccessful despite the correct expression of a methyltransferase construct. It
      was unclear whether this result reflected the failure of heterologous methyltransferases to
      enter the nucleus, or whether 6mdA methylation, which has been shown to interfere with
      promoter activity, was toxic for plants. Here we show that 6mdA methylation can be
      successfully introduced into transgenic tobacco plants via expression of the bacterial dam
      enzyme. The efficiency of 6mdA methylation was directly proportional to expression levels of
      the dam construct, and methylation of all GATC sites was observed in a highly expressing line.
      Increasing expression levels of the enzyme in different plants correlated with increasingly
      abnormal phenotypes affecting leaf pigmentation, apical dominance, and leaf and floral
      structure. Whilst introduction of dam-specific methylation does not cause any developmental
      abnormalities in yeast or Drosophila, our data suggest that methylation of deoxyadenine
      residues in plants interferes with the expression of genes involved in leaf and floral
      development.
AU  - van Blokland R
AU  - Ross S
AU  - Corrado G
AU  - Scollan C
AU  - Meyer P
PT  - Journal Article
TA  - Plant J.
JT  - Plant J.
SO  - Plant J. 1998 15: 543-551.

PMID- 4278944
VI  - 236
DP  - 1974
TI  - Restriction and modification of phages in Staphylococcal phage typing.
PG  - 376-388
AB  - Staphylococcus aureus is a remarkably versatile species, which has been very successful in
      establishing itself as a commensal in various niches on the human and animal body.  No two
      staphylococci are really alike, even if they have the same phage pattern or drug sensitivity.
AU  - van Boven CPA
PT  - Journal Article
TA  - Ann. NY Acad. Sci.
JT  - Ann. NY Acad. Sci.
SO  - Ann. NY Acad. Sci. 1974 236: 376-388.

PMID- 356952
VI  - 46
DP  - 1987
TI  - Effect of flanking sequence length on EcoRI endonuclease reaction.
PG  - 2041
AB  - Michaelis-Menten parameters were determined for the cleavages by EcoRI
      endonuclease of both scission points in a duplex composed of the pentadecamer
      d(pATCGAATTCCGGCCA) and its complement.  The Km for this substrate is 38.6 +/-
      2 nM, a value between those determined for plasmid DNA and an octameric
      oligodeoxyribonucleotide.  Since the two scission points are flanked by
      different lengths of sequence, comparison of turnover numbers for the two
      cleavages may reflect interactions of the enzyme with nucleotides outside its
      recognition sequence.  Preliminary results indicate that the scissile bond in
      the above indicated oligomer is cleaved twice as fast as the hydrolyzed bond in
      its complement.  The more rapidly cleaved bond is four residues from the 5'
      terminus, whereas the more slowly hydrolyzed bond is seven base pairs from the
      end of the duplex.
AU  - Van Cleve M
AU  - Gumport RI
PT  - Journal Article
TA  - Fed. Proc.
JT  - Fed. Proc.
SO  - Fed. Proc. 1987 46: 2041.

PMID- 3192615
VI  - 107
DP  - 1988
TI  - Effect of flanking sequence length on EcoRI endonuclease reaction.
PG  - 403a
AB  - Michaelis-Menten parameters were determined for the cleavages by EcoRI
      endonuclease at both scission points in a series of oligomeric DNA duplexes.
      Each member of the series contains the EcoRI recognition sequence (GAATTC)
      located with six base pairs flanking the 3' end and from zero to three base
      pairs flanking the 5' end, e.g., ATCGAATTCCGGCCA.  Thus, cleavage at both
      strands produces two different sized and 32P-labeled products, in the above
      case a tetramer and heptamer.  Kinetic parameters were determined for both
      strands independently.  In each duplex tested, the cleavage rates are different
      for the two oligomers, with the rate for each strand varying inversely as the
      length of its 5' flanking sequence from Kcat=11.5 min-1 with three base pairs,
      to 14.0 min-1 with two, to 20.0 min-1 with one.  Km's also vary with length,
      and are different for the two strands at each duplex.
AU  - Van Cleve M
AU  - Gumport RI
PT  - Journal Article
TA  - J. Cell Biol.
JT  - J. Cell Biol.
SO  - J. Cell Biol. 1988 107: 403a.

PMID- 1731891
VI  - 31
DP  - 1992
TI  - Influence of enzyme-substrate contacts located outside the EcoRI recognition site on cleavage of duplex oligodeoxyribonucleotide substrates by EcoRI endonuclease.
PG  - 334-339
AB  - A complete understanding of the sequence-specific interaction between the EcoRI
      restriction endonuclease and its DNA substrate requires identification of all
      contacts between the enzyme and substrate, and evaluation of their
      significance.  We have searched for possible contacts adjacent to the
      recognition site, GAATTC, by using a series of substrates with differing
      lengths of flanking sequence.  Each substrate is a duplex of
      non-self-complementary oligodeoxyribonucleotides in which the recognition site
      is flanked by six base pairs on one side and from zero to three base pairs on
      the other.  Steady-state kinetic values were determined for the cleavage of
      each strand of these duplexes.  A series of substrates in which the length of
      flanking sequences was varied on both sides of the hexamer was also examined.
      The enzyme cleaved both strands of each of the substrates.  Decreasing the
      flanking sequence to fewer than three base pairs on one side of the recognition
      site induced an asymmetry in the rates of cleavage of the two strands.  The
      scissile bond nearest the shortening sequence was hydrolyzed with increasing
      rapidity as base pairs were successively removed.  Taken together, the Km and
      kcat values obtained may be interpreted to indicate the relative importance of
      several likely enzyme-substrate contacts located outside the canonical
      hexameric recognition site.
AU  - Van Cleve MD
AU  - Gumport RI
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1992 31: 334-339.

PMID- 3074019
VI  - 74
DP  - 1988
TI  - Cloning the FnuDI, NaeI, NcoI and XbaI restriction-modification systems.
PG  - 55-59
AB  - Methyltransferase genes from the FnuDI, NaeI, NcoI, and XbaI
      restriction-modification systems have been isolated in Escherichia coli by
      shot-gun cloning bacterial DNA fragments into plasmid vectors and selecting for
      protectively modified molecules that resist digestion by the corresponding
      endonuclease.
AU  - Van Cott EM
AU  - Wilson GG
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 55-59.

PMID- 16754859
VI  - 103
DP  - 2006
TI  - The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution.
PG  - 9274-9279
AB  - Lactobacillus delbrueckii ssp. bulgaricus (L. bulgaricus) is a representative of the group of
      lactic acid-producing bacteria, mainly known for its worldwide application in yogurt
      production. The genome sequence of this bacterium has been determined and shows the signs of
      ongoing specialization, with a substantial number of pseudogenes and incomplete metabolic
      pathways and relatively few regulatory functions. Several unique features of the L. bulgaricus
      genome support the hypothesis that the genome is in a phase of rapid evolution. (i)
      Exceptionally high numbers of rRNA and tRNA genes with regard to genome size may indicate that
      the L. bulgaricus genome has known a recent phase of important size reduction, in agreement
      with the observed high frequency of gene inactivation and elimination; (ii) a much higher GC
      content at codon position 3 than expected on the basis of the overall GC content suggests that
      the composition of the genome is evolving toward a higher GC content; and (iii) the presence
      of a 47.5-kbp inverted repeat in the replication termination region, an extremely rare feature
      in bacterial genomes, may be interpreted as a transient stage in genome evolution. The results
      indicate the adaptation of L. bulgaricus from a plant-associated habitat to the stable protein
      and lactose-rich milk environment through the loss of superfluous functions and
      protocooperation with Streptococcus thermophilus.
AU  - van de Guchte M et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2006 103: 9274-9279.

PMID- 24336366
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Enterococcus sp. Strain HSIEG1, Isolated from the Human  Small Intestine.
PG  - e01013-13
AB  - Enterococcus sp. strain HSIEG1 was isolated from the human small intestine. Its draft genome
      predicts a broad carbohydrate fermentation capability, which matches
      well with the observed physiological characteristics of this strain. This
      metabolic flexibility is expected to be of importance for survival and growth in
      the small intestinal habitat.
AU  - van den Bogert B
AU  - Boekhorst J
AU  - Smid EJ
AU  - Zoetendal EG
AU  - Kleerebezem M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01013-13.

PMID- 24309734
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Veillonella parvula HSIVP1, Isolated from the Human Small Intestine.
PG  - e00977-13
AB  - Veillonella species are frequently encountered commensals in the human small intestine. Here,
      we report the draft genome sequence of the first cultured
      representative from this ecosystem, Veillonella parvula strain HSIVP1. The genome
      is predicted to encode all the necessary enzymes required for the pathway
      involved in the conversion of lactate to propanoate.
AU  - van den Bogert B
AU  - Boekhorst J
AU  - Smid EJ
AU  - Zoetendal EG
AU  - Kleerebezem M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00977-13.

PMID- 15475578
VI  - 88
DP  - 2005
TI  - DNA-tension dependence of restriction enzyme cleavage reveals details of the reaction pathway.
PG  - 184A
AB  - Restriction endonucleases cleave recognition sequences on double-stranded DNA with
      extraordinary specificity.  This capability arises from conformation changes in enzyme and/or
      DNA upon binding to such a recognition site.  Here we present measurements of energy and rate
      changes in the raction pathway as a function of tension on the DNA.  The experiments were
      performed using single DNA molecules held between beads kept in laser tweezers while recording
      the cleavage times after introduction of the restriction enzymes.  The data shows that EcoRV
      cleavage rates drop with increasing tension, while BamHI activity does not decrease.  From the
      force-rate curves of EcoRV, we are able to obtain values for the DNA bending angle (51o),
      induced-fit rate (~100 s-1) and dsDNA hydrolysis (0.28 s-1).  BamHI, however, does not show
      any sign of DNA bending.  For both enzymes a reduced association rate of ~5.106 M-1 s-1 is
      found, presumably due to absence of intradomain dissociation-reassociation (jumping) between
      non-specific sites on stretched DNA.  These measurements thus illustrate the relative
      importance of jumping in the searching process.  Moreover, the tension dependence of the
      induced-fit reaction reveals some of the underlying energetics of binding a specific site.
      Finally, single-molecule detection of DNA cleavage allows for direct measurements of many of
      the reaction steps and is generally applicable to other type II restriction enzymes.
AU  - van den Broek B
AU  - Noom MC
AU  - Wuike GJL
PT  - Journal Article
TA  - Biophys. J.
JT  - Biophys. J.
SO  - Biophys. J. 2005 88: 184A.

PMID- 15886396
VI  - 33
DP  - 2005
TI  - DNA-tension dependence of restriction enzyme activity reveals mechanochemical properties of the reaction pathway.
PG  - 2676-2684
AB  - Type II restriction endonucleases protect bacteria against phage infections by cleaving
      recognition sites on foreign double-stranded DNA (dsDNA) with extraordinary specificity. This
      capability arises primarily from large conformational changes in enzyme and/or DNA upon target
      sequence recognition. In order to elucidate the connection between the mechanics and the
      chemistry of DNA recognition and cleavage, we used a single-molecule approach to measure rate
      changes in the reaction pathway of EcoRV and BamHI as a function of DNA tension. We show that
      the induced-fit rate of EcoRV is strongly reduced by such tension. In contrast, BamHI is found
      to be insensitive, providing evidence that both substrate binding and hydrolysis are not
      influenced by this force. Based on these results, we propose a mechanochemical model of
      induced-fit reactions on DNA, allowing determination of induced-fit rates and DNA bend angles.
      Finally, for both enzymes a strongly decreased association rate is obtained on stretched DNA,
      presumably due to the absence of intradomain dissociation/re-association between non-specific
      sites (jumping). The obtained results should apply to many other DNA-associated proteins.
AU  - van den Broek B
AU  - Noom MC
AU  - Wuite GJL
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2005 33: 2676-2684.

PMID- 
VI  - 84
DP  - 2003
TI  - The effect of DNA tension on restriction-enzyme cutting rates studied with optical tweezers.
PG  - 141a
AB  - Restriction enzymes recognize base pair sequences on DNA with high specificity.  These sites
      trigger a conformational change in the enzyme and/or DNA, permitting the cleavage of both
      strands.  Here we report single-molecule measurements of the effect of DNA tension on the
      cleavage rate of restriction enzymes BamHI, EcoRV,
AU  - van den Broek B
AU  - Schmidt CF
AU  - Wuite GJL
PT  - Journal Article
TA  - Biophys. J.
JT  - Biophys. J.
SO  - Biophys. J. 2003 84: 141a.

PMID- 16407332
VI  - 34
DP  - 2006
TI  - Real-time observation of DNA looping dynamics of Type IIE restriction enzymes NaeI and NarI.
PG  - 167-174
AB  - Many restriction enzymes require binding of two copies of a recognition sequence for DNA
      cleavage, thereby introducing a loop in the DNA. We investigated looping dynamics of Type IIE
      restriction enzymes NaeI and NarI by tracking the Brownian motion of single tethered DNA
      molecules. DNA containing two endonuclease recognition sites spaced a few 100 bp apart connect
      small polystyrene beads to a glass surface. The position of a bead is tracked through video
      microscopy. Protein-mediated looping and unlooping is then observed as a sudden specific
      change in Brownian motion of the bead. With this method we are able to directly follow DNA
      looping kinetics of single protein-DNA complexes to obtain loop stability and loop formation
      times. We show that, in the absence of divalent cations, NaeI induces DNA loops of specific
      size. In contrast, under these conditions NarI mainly creates non-specific loops, resulting in
      effective DNA compaction for higher enzyme concentrations. Addition of Ca2+ increases the
      NaeI-DNA loop lifetime by two orders of magnitude and stimulates specific binding by NarI.
      Finally, for both enzymes we observe exponentially distributed loop formation times,
      indicating that looping is dominated by (re)binding the second recognition site.
AU  - van den Broek B
AU  - Vanzi F
AU  - Normanno D
AU  - Pavone FS
AU  - Wuite GJL
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2006 34: 167-174.

PMID- 
VI  - 82
DP  - 2002
TI  - Single molecule study of DNA tension on restriction enzyme cleavage activity.
PG  - 51a
AB  - Restriction enzymes recognizes dsDNA at highly specific base pair sequences.  These sites
      trigger a large conformational change in the enzyme, permitting the cleavage of DNA.  During
      this conformational change the DNA is often bent, although some enzymes do not deform the DNA
      at all.  While the biochemistry and structure of many restriction enzymes are well studied,
      these studies only superficially address the dynamics of enzyme-DNA interactions.  Here we
      report single molecule measurements of the effect of DNA tension on the cleavage activity of
      restriction enzymes in order to elucidate some of the enzyme dynamics.  DNA is held under
      various tensions between two beads in optical tweezers while the time it takes for the enzymes
      to cut is recorded; this allows us to obtain force vs. rate curves.  We present our first
      results for the restriction enzyme NaeI, which kinks the DNA by 45 degrees before cutting it.
      We expect to see several trends: DNA tension reduces the binding energy of the sugar backbone,
      suggesting an increase in cutting rate.  At the same time, this tension opposes the DNA
      bending by the enzyme.  Moreover, pulling on the DNA slightly deforms the base stacking,
      degrading the recognition efficiency.  These effects should slow down the cutting.
AU  - van den Broek B
AU  - Wuite GJL
PT  - Journal Article
TA  - Biophys. J.
JT  - Biophys. J.
SO  - Biophys. J. 2002 82: 51a.

PMID- Not included in PubMed...
VI  - 16
DP  - 1983
TI  - Sequence-specific nucleases from the cyanobacterium Fremyella diplosiphon, and a peculiar resistance of its chromosomal DNA towards cleavage by other restriction enzymes.
PG  - 7-12
AB  - The filamentous cyanobacterium Fremyella diplosiphon PCC7601 is facultatively
      heterotrophic.  Cells can grow in the dark at the expense of certain organic
      substrates like sugars as an exogenous energy source, the utilization of which
      probably depends on the presence in the cell of the appropriate permeases.  As
      a first step in cloning the F. diplosiphon genetic information for these
      permeases into the transformable strain R-2 of the unicellular, strictly
      photoautotrophic cyanobacterium Anacystis nidulans, chromosomal DNA of F.
      diplosiphon was digested with several bacterial sequence-specific
      endodeoxyribonucleases.  As the DNA appeared to be resistant to an unexpectedly
      large number of them, a restriction enzyme analysis with 31 different
      endonucleases was made to elucidate the underlying modification pattern.  In
      addition, F. diplosiphon cells were anlysed for the presence of restriction
      endonucleases, and two were found:  FdiI and FdiII, which cleave the nucleotide
      sequences 5'-G^G(A/T)CC and 5'-TGC^GCA, respectively.  EndoR.FdiI is an
      isoschizomer of AvaII and endoR.FdiII is an isoschizomer of AosI.
AU  - van den Hondel CAMJJ
AU  - van Leen RW
AU  - van Arkel GA
AU  - Duyvesteyn M
AU  - de Waard A
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1983 16: 7-12.

PMID- 9599025
VI  - 426
DP  - 1998
TI  - Cloning and analysis of a novel human putative DNA methyltransferase.
PG  - 283-289
AB  - DNA methylation is intricately involved in a variety of cellular processes, such as
      differentiation, cell cycle progression, X-chromosome inactivation and genomic imprinting.
      However, little is known about how specific DNA methylation patterns are established and
      maintained.  Previously one mammalian DNA methyltransferase has been described, but there has
      been considerable speculation about the presence of a second activity capable of methylation.
      Here we report the identification and characterization of a novel human putative DNA
      methyltransferase.  Using a bioinformatics screen we have identified several expressed
      sequence tags which show high sequence similarity to the Schizosaccharomyces pombe gene pmt1+.
      The cDNA for PuMet was cloned and the predicted amino acid sequence deduced.  The gene is
      ubiquitously expressed, albeit at low levels.  Like several other DNA methyltransferases, the
      bacterially overexpressed protein is not active in methylation assays.
AU  - Van den Wyngaert I
AU  - Sprengel J
AU  - Kass SU
AU  - Luyten WHML
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1998 426: 283-289.

PMID- 24092776
VI  - 1
DP  - 2013
TI  - Whole-Genome Sequences of 94 Environmental Isolates of Bacillus cereus Sensu Lato.
PG  - e00380-13
AB  - Bacillus cereus sensu lato is a species complex that includes the anthrax pathogen Bacillus
      anthracis and other bacterial species of medical, industrial,
      and ecological importance. Their phenotypes of interest are typically linked to
      large plasmids that are closely related to the anthrax plasmids pXO1 and pXO2.
      Here, we present the draft genome sequences of 94 isolates of B. cereus sensu
      lato, which were chosen for their plasmid content and environmental origins.
AU  - Van der Auwera GA
AU  - Feldgarden M
AU  - Kolter R
AU  - Mahillon J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00380-13.

PMID- 24503995
VI  - 2
DP  - 2014
TI  - First Closed Genome Sequence of Campylobacter fetus subsp. venerealis bv. intermedius.
PG  - e01246-13
AB  - Campylobacter fetus subsp. venerealis bv. intermedius is a variant of C. fetus subsp.
      venerealis, the causative agent of bovine genital campylobacteriosis, a
      venereal disease associated with abortion and infertility in cattle. We report
      the first closed whole-genome sequence of this biovar.
AU  - van der Graaf-van BL
AU  - Miller WG
AU  - Yee E
AU  - Bono JL
AU  - Rijnsburger M
AU  - Campero C
AU  - Wagenaar JA
AU  - Duim B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01246-13.

PMID- 20593890
VI  - 21
DP  - 2010
TI  - Targeted DNA Methylation by a DNA Methyltransferase Coupled to a Triple Helix Forming Oligonucleotide To Down-Regulate the Epithelial Cell Adhesion Molecule.
PG  - 1239-1245
AB  - The epithelial cell adhesion molecule (EpCAM) is a membrane glycoprotein that has been
      identified as a marker of cancer-initiating
      cells. EpCAM is highly expressed on most carcinomas, and transient
      silencing of EpCAM expression leads to reduced oncogenic potential. To
      silence (he EpCAM gene in a persistent manner via targeted DNA
      methylation, a low activity mutant (C141S) of the CpG-specific DNA
      methyltransferase M.Sssl was coupled to a triple-helix-forming
      oligonucleotide (TFO-C141S) specifically designed for the EpCAM gene.
      Reporter plasmids encoding the green fluorescent protein under control
      of different EpCAM promoter fragments were treated with the TFO-C141S
      conjugate to determine the specificity of targeted DNA methylation in
      the context of a functional EpCAM promoter. Treatment of the plasmids
      with TFO-C141S resulted in efficient and specific methylation of the
      targeted CpG located directly downstream of the triple helix forming
      site (TFS). No background DNA methylation was observed neither in a 700
      bp region of the EpCAM promoter nor in a 400 bp region of the reporter
      gene downstream of the TFS. Methylation of the target CpG did not have
      a detectable effect on promoter activity. This study shows that the
      combination of a specific TFO and a reduced activity methyltransferase
      variant can be used to target DNA methylation to predetermined sites
      with high specificity, allowing determination of crucial CpGs for
      promoter activity.
AU  - van der Gun BTF
AU  - Maluszynska-Hoffman M
AU  - Kiss A
AU  - Arendzen AJ
AU  - Ruiters MHJ
AU  - McLaughlin PMJ
AU  - Weinhold E
AU  - Rots MG
PT  - Journal Article
TA  - Bioconjugate Chem.
JT  - Bioconjugate Chem.
SO  - Bioconjugate Chem. 2010 21: 1239-1245.

PMID- 23990588
VI  - 1
DP  - 2013
TI  - Whole-Genome Sequence of the Ancestral Animal-Borne ST398 Staphylococcus aureus Strain S123.
PG  - e00692-13
AB  - Sequence type 398 (ST398) Staphylococcus aureus was originally reported in livestock. We
      announce the complete genome sequence of an ST398
      methicillin-susceptible S. aureus strain of animal origin, S123. The genome
      sequence reveals a wild-type genome that probably corresponds to an ancestral
      clone.
AU  - van der Mee-Marquet N
AU  - Hernandez D
AU  - Bertrand X
AU  - Quentin R
AU  - Corvaglia AR
AU  - Francois P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00692-13.

PMID- 6247075
VI  - 19
DP  - 1980
TI  - DNA methylation in the human cdb-globin locus in Erythroid and Nonerythroid tissues.
PG  - 947-958
AB  - We have analyzed DNA modification in the human cdb-globin gene region at 17
      cleavage sites of restriction endonucleases which are unable to cleave DNA if
      5-methylcytosine is present at certain positions in their respective cleavage
      sites.  Using this criterion, all sites tested in the globin gene region are
      fully modified in the germ line (sperm) DNA.  In somatic tissues, however,
      methyl groups are absent at specific sites in the globin gene region.  In
      tissues not expressing the genes, these losses range from one of these cleavage
      sites in lymphocyte DNA to essentially all of these sites in the entire region
      in placental DNA.  In the DNA of tissues expressing the globin genes, the
      region surrounding and including the genes expressed shows a low level of
      modification, whereas the neighboring DNA regions have a high level of
      modification.  The data suggest that a low level of DNA methylation may be a
      necessary, but not a sufficient, condition for gene expression in higher
      eucaryotes.
AU  - van der Ploeg LHT
AU  - Flavell RA
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1980 19: 947-958.

PMID- 11250198
VI  - 9
DP  - 2001
TI  - Restriction enzyme BsoBI-DNA complex: A tunnel for recognition of degenerate DNA sequences and potential histidine catalysis.
PG  - 133-144
AB  - Background: Restriction endonucleases form a diverse family of proteins with substantial
      variation in sequence, structure, and interaction with recognition site DNA. BsoBI is a
      thermophilic restriction endonuclease that exhibits both base-specific and degenerate
      recognition within the sequence CPyCGPuG.  Results: The structure of BsoBI complexed to
      cognate DNA has been determined to 1.7 Angstrom resolution, revealing several unprecedented
      features. Each BsoBI monomer is formed by inserting a helical domain into an expanded
      EcoRI-type catalytic domain. DNA is completely encircled by a BsoBI dimer. Recognition
      sequence DNA lies within a 20 Angstrom long tunnel of protein that excludes bulk solvent.
      Interactions with the specific bases are made in both grooves through direct and
      water-mediated hydrogen bonding. Interaction with the degenerate position is mediated by a
      purine-specific hydrogen bond to N7, ensuring specificity, and water-mediated H bonding to the
      purine N6/O6 and pyrimidine N4/O4, allowing degeneracy. In addition to the conserved active
      site residues of the DXn(E/D)ZK restriction enzyme motif, His253 is positioned to act as a
      general base.  Conclusions: A catalytic mechanism employing His253 and two metal ions is
      proposed. If confirmed, this would be the first example of histidine-mediated catalysis in a
      restriction endonuclease. The structure also provides two novel examples of the role of water
      in protein-DNA interaction. Degenerate recognition may be mediated by employing water as a
      hydrogen bond donor or acceptor. The structure of DNA in the tunnel may also be influenced by
      the absence of bulk solvent.
AU  - van der Woerd MJ
AU  - Pelletier JJ
AU  - Xu S-Y
AU  - Friedman AM
PT  - Journal Article
TA  - Structure
JT  - Structure
SO  - Structure 2001 9: 133-144.

PMID- 9811649
VI  - 180
DP  - 1998
TI  - Formation of DNA methylation patterns: Nonmethylated GATC sequences in gut and pap operons.
PG  - 5913-5920
AB  - Most of the adenine residues in GATC sequences in the Escherichia coli chromosome are
      methylated by the enzyme deoxyadenosine methyltransferase.  However, at least 20 GATC
      sequences remain nonmethylated throughout the cell cycle.  Here we examined how the DNA
      methylation patterns of GATC sequences within the regulatory regions of the
      pyelonephritis-associated pilus operon and the glucitol utilization operon were formed.  The
      results obtained with an in vitro methylation protection assay showed that the addition of the
      leucine-responsive regulatory protein to pap DNA was sufficient to protect the two GATC
      sequences in the pap regulatory region, GATC-I and GATC-II, from methylation by Dam.  This
      finding was consistent with previously published data showing that Lrp was essential for
      methylation protection of these DNA sites in vivo.  Methylation protection also occurred at a
      GATC site (GATC-44.5) centered 44.5 bp upstream of the transcription start site of the gutABD
      operon.  Two proteins, GutR and the catabolite gene activator protein, bound to DNA sites
      overlapping the GATC-44.5-containing region of the gutABD operon.  GutR, an operon-specific
      repressor, was essential for methylation protection in vivo, and binding of GutR protected
      GATC-44.5 from methylation in vitro.  In contrast, binding of CAP at a site overlapping
      GATC-44.5 did not protect this site from methylation.  Mutational anlayses indicated that
      gutABD gene regulation was not controlled by methylation of GATC-44.5, in contrast to
      regulation of Pap pilus expression, which is directly controlled by methylation of the pap
      GATC-I and GATC-II sites.
AU  - van der Woude M
AU  - Hale WB
AU  - Low DA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1998 180: 5913-5920.

PMID- 
VI  - 3
DP  - 2008
TI  - Some types of bacterial phase variation are epigenetic.
PG  - 21-26
AB  - Individual bacterial cells can vary phenotypically, even within a clonal population.  Phase
      variation provides a means for regulating specific genes between an expressed, or "on" state,
      and a nonexpressed, or "off" state; these two expression states are heritable and reversible.
      The mechanisms that lead to phase variation are either genetic or epigenetic; if epigenetic,
      they entail no changes in DNA sequence.  More generally, phase variation apparently provides a
      means for generating diversity and thereby increasing the changes of survival amid changing
      environmental conditions.  Understanding phase variation may allow us to manipulate bacterial
      populations to provide health benefits, including better diagnostic tests and vaccines.
AU  - van der Woude MW
PT  - Journal Article
TA  - Microbe
JT  - Microbe
SO  - Microbe 2008 3: 21-26.

PMID- 15258095
VI  - 17
DP  - 2004
TI  - Phase and antigenic variation in bacteria.
PG  - 581-611
AB  - Phase and antigenic variation result in a heterogenic phenotype of a clonal bacterial
      population, in which individual cells either express the phase-variable protein(s) or not, or
      express one of multiple antigenic forms of the protein, respectively. This form of regulation
      has been identified mainly, but by no means exclusively, for a wide variety of surface
      structures in animal pathogens and is implicated as a virulence strategy. This review provides
      an overview of the many bacterial proteins and structures that are under the control of phase
      or antigenic variation. The context is mainly within the role of the proteins and variation
      for pathogenesis, which reflects the main body of literature. The occurrence of phase
      variation in expression of genes not readily recognizable as virulence factors is highlighted
      as well, to illustrate that our current knowledge is incomplete. From recent genome sequence
      analysis, it has become clear that phase variation may be more widespread than is currently
      recognized, and a brief discussion is included to show how genome sequence analysis can
      provide novel information, as well as its limitations. The current state of knowledge of the
      molecular mechanisms leading to phase variation and antigenic variation are reviewed, and the
      way in which these mechanisms form part of the general regulatory network of the cell is
      addressed. Arguments both for and against a role of phase and antigenic variation in immune
      evasion are presented and put into new perspective by distinguishing between a role in
      bacterial persistence in a host and a role in facilitating evasion of cross-immunity. Finally,
      examples are presented to illustrate that phase-variable gene expression should be taken into
      account in the development of diagnostic assays and in the interpretation of experimental
      results and epidemiological studies.
AU  - van der Woude MW
AU  - Baumler AJ
PT  - Journal Article
TA  - Clin. Microbiol. Rev.
JT  - Clin. Microbiol. Rev.
SO  - Clin. Microbiol. Rev. 2004 17: 581-611.

PMID- 1357527
VI  - 6
DP  - 1992
TI  - Evidence for global regulatory control of pilus expression in Escherichia coli by Lrp and DNA methylation: model building based on analysis of pap.
PG  - 2429-2435
AB  - Pyelonephritis-associated pilus (Pap) expression is regulated by a phase variation control
      mechanism involving PapB, Papl, catabolite activator protein (CAP), leucine-responsive
      regulatory protein (Lrp) and deoxyadenosine methylase (Dam). Lrp and Papl bind to a specific
      non-methylated pap regulatory DNA region containing the sequence 'GATC' and facilitate the
      formation of an active transcriptional complex.  Evidence indicates that binding of Lrp and
      Papl to this region inhibits methylation of the GATC site by Dam.  However, if this GATC site
      is first methylated by Dam, binding of Lrp and Papl is inhibited. These events lead to the
      formation of two different pap methylation states characteristic of active (ON) and inactive
      (OFF) pap transcription states. The fae (K88), daa (F1845) and sfa (S) pilus operons share
      conserved 'GATC-box' domains with pap and may be subject to a similar regulatory control
      mechanism involving Lrp and DNA methylation.
AU  - van der Woude MW
AU  - Braaten BA
AU  - Low DA
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1992 6: 2429-2435.

PMID- 
VI  - 6
DP  - 1987
TI  - Nucleotide sequence of a DNA fragment encoding a Vibrio cholerae haemagglutinin.
PG  - 85-91
AB  - 
AU  - Van Dongen WMAM
AU  - Van Vlerken MMA
AU  - De Graaf FK
PT  - Journal Article
TA  - Genetics (Life Sci. Adv.)
JT  - Genetics (Life Sci. Adv.)
SO  - Genetics (Life Sci. Adv.) 1987 6: 85-91.

PMID- 
VI  - 0
DP  - 2008
TI  - DNA methyltransferases and methyl-CPG binding proteins as multifunctional regulators of chromatin structure and development in mammalian cells.
PG  - 23-61
AB  - The epigenetic modification of DNA with 5-methylcytosine is an important regulatory event
      involved in chromatin structure, genomic imprinting, inactivation of the X chromosome,
      transcription, and retrotransposon silencing. This modification is catalysed and maintained by
      the DNA methyltransferases and is interpreted by the methyl-CpG binding proteins. DNA
      methyltransferases are not limited to catalysing DNA methylation, but also take part in the
      regulation of gene expression through interactions with other proteins that repress
      transcription and modify chromatin structure. The use of mouse models, as well as human
      diseases resulting from deficiencies in the rnethylation machinery, have been integral parts
      of understanding the role of these proteins in development and cellular homeostasis. More and
      more studies are reporting additional roles within the cell beyond their DNA methyltransferase
      and methyl-CpG binding properties. There is at this point, though, only limited understanding
      of how these enzymes and proteins are targeted to specific genomic regions. The
      methyltransferases that will be discussed in this review include DNMT1, DNMT2, and the DNMT3
      family of enzymes as well as the methyl-CpG binding proteins MeCP2, MBD1, MBD2, MBD3, and
      MBD4. The function of these enzymes, as well as their interactions with other cellular
      proteins and each other, will be discussed along with the diseases attributed to aberrations
      in the DNA methylation machinery.
AU  - Van Emburgh BO
AU  - Robertson KD
PT  - Journal Article
TA  - EPIGENETICS
JT  - EPIGENETICS
SO  - EPIGENETICS 2008 0: 23-61.

PMID- 21378119
VI  - 39
DP  - 2011
TI  - Modulation of Dnmt3b function in vitro by interactions with Dnmt3L, Dnmt3a and Dnmt3b splice variants.
PG  - 4984-5002
AB  - DNA methylation, an essential regulator of transcription and chromatin structure, is
      established and maintained by the coordinated action of
      three DNA methyltransferases: DNMT1, DNMT3A and DNMT3B, and the inactive
      accessory factor DNMT3L. Disruptions in DNMT3B function are linked to
      carcinogenesis and genetic disease. DNMT3B is also highly alternatively
      spliced in a tissue- and disease-specific manner. The impact of
      intra-DNMT3 interactions and alternative splicing on the function of DNMT3
      family members remains unclear. In the present work, we focused on DNMT3B.
      Using a panel of in vitro assays, we examined the consequences of DNMT3B
      splicing and mutations on its ability to bind DNA, interact with itself
      and other DNMT3's, and methylate DNA. Our results show that, while the
      C-terminal catalytic domain is critical for most DNMT3B functions, parts
      of the N-terminal region, including the PWWP domain, are also important.
      Alternative splicing and domain deletions also influence DNMT3B's cellular
      localization. Furthermore, our data reveal the existence of extensive
      DNMT3B self-interactions that differentially impact on its activity.
      Finally, we show that catalytically inactive isoforms of DNMT3B are
      capable of modulating the activity of DNMT3A-DNMT3L complexes. Our studies
      therefore suggest that seemingly 'inactive' DNMT3B isoforms may influence
      genomic methylation patterns in vivo.
AU  - Van Emburgh BO
AU  - Robertson KD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2011 39: 4984-5002.

PMID- Not included in PubMed...
VI  - 27
DP  - 1991
TI  - DNA methyltransferases and DNA site-specific endonucleases encoded by Chlorella viruses.
PG  - 74
AB  - Thirty seven large, polyhedral, dsDNA-containing (>300 kb in size),
      plaque-forming viruses which infect a unicellular, eukaryotic, green alga,
      Chlorella strain NC64A have been partially characterized.  Each of the viral
      DNAs contains 5mC; the concentration of 5mC as a percentage of cytosine, ranges
      from 0.1 to 47%.  In addition, 25 of the 37 viral DNAs also contain 6mA; the
      concentration of 6mA, as a percentage of adenine, ranges from 1.45% to 37%.
      The finding that methylation is sequence specific led to the discovery that at
      least some of the viruses code for DNA methyltransferases and DNA site-specific
      (restriction) endonucleases.  Some of the site-specific endonucleases recognize
      and cleave the same base sequences as bacterial enzymes whereas, others have
      unique specificities and cleavage sites.  Two additional site-specific
      endonucleases are unusual because they cleave one strand of DNA at specific
      sequences.  The presence of DNA methylating and site-specific endonucleases in
      the virus infected cells leads to two questions. (i) What is the evolutionary
      origin of these enzymes? (ii) What is the function of these enzymes.
      Experiments designed to address these questions will be presented.
AU  - Van Etten JL
PT  - Journal Article
TA  - J. Phycol.
JT  - J. Phycol.
SO  - J. Phycol. 1991 27: 74.

PMID- 10547698
VI  - 53
DP  - 1999
TI  - Giant viruses infecting algae.
PG  - 447-494
AB  - Paramecium bursaria chlorella virus (PBCV-1) is the prototype of a family of large,
      icosahedral, plaque-forming, double-stranded-DNA-containing viruses that replicate in certain
      unicellular, eukaryotic chlorella-like green algae. DNA sequence analysis of its 330, 742-bp
      genome leads to the prediction that this phycodnavirus has 376 protein-encoding genes and 10
      transfer RNA genes. The predicted gene products of approximately 40% of these genes resemble
      proteins of known function. The chlorella viruses have other features that distinguish them
      from most viruses, in addition to their large genome size. These features include the
      following: (a) The viruses encode multiple DNA methyltransferases and DNA site-specific
      endonucleases; (b) PBCV-1 encodes at least part, if not the entire machinery to glycosylate
      its proteins; (c) PBCV-1 has at least two types of introns--a self-splicing intron in a
      transcription factor-like gene and a splicesomal processed type of intron in its DNA
      polymerase gene. Unlike the chlorella viruses, large double-stranded-DNA-containing viruses
      that infect marine, filamentous brown algae have a circular genome and a lysogenic phase in
      their life cycle.
AU  - Van Etten JL
AU  - Meints RH
PT  - Journal Article
TA  - Annu. Rev. Microbiol.
JT  - Annu. Rev. Microbiol.
SO  - Annu. Rev. Microbiol. 1999 53: 447-494.

PMID- 4011432
VI  - 13
DP  - 1985
TI  - DNA methylation of viruses infecting a eukaryotic Chlorella-like green alga.
PG  - 3471-3478
AB  - The genomic DNAs of the eukaryotic Chlorella-like green alga, strain NC64A, and
      eleven of its viruses all contain significant levels of 5-methyldeoxycytidine.
      In addition, the host DNA as well as six of the viral DNAs also contain
      N6-methyldeoxyadenosine.  At least some of the methylated bases in the host
      reside in different base sequences than the methylated bases in the viruses as
      shown by differential susceptibility to restriction endonuclease enzymes.  This
      suggests that the viruses encode for DNA methyltransferases with sequence
      specificities different from that of the host enzyme.
AU  - Van Etten JL
AU  - Schuster AM
AU  - Girton L
AU  - Burbank DE
AU  - Swinton D
AU  - Hattman S
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1985 13: 3471-3478.

PMID- 2467142
VI  - 13D
DP  - 1989
TI  - Viruses infecting a eukaryotic green alga are a new source of DNA methyltransferases and DNA site-specific endonucleases.
PG  - 199
AB  - We have isolated and partially characterized several large, complex, dsDNA
      containing (ca. 330kbp), plaque forming viruses (NC64A viruses) which infect
      the unicellular, eukaryotic, Chlorella-like green alga strain NC64A.  These
      viruses can be distinguished on the basis of plaque size, reaction with
      antibody, and the nature and abundance of methylated bases in their genomic
      DNAs.  The concentration of methylated bases varies from viruses containing no
      6-methyladenine (6mA) and 0.1% 5-methylcytosine (5mC) to one virus with 37% 6mA
      and 45% 5mC.  Even though the host nuclear DNA contains 21% 5mC and 0.6% 6mA,
      at least some of the methylated bases in the viruses reside in different DNA
      sequences than those in the host.  This result led to the finding that virus
      infection of the host results in the synthesis of DNA methyltransferases and
      DNA site-specific (restriction) endonucleases.  Five different site-specific
      endonucleases have been identified so far.  For example, virus NC-1A infected
      Chlorella NC64A cells contain an endonuclease, named CviBI, which recognizes
      the sequence GANTC and cleaves between G and A; CviBI does not cleave GmANTC
      sequences.  NC-1A infected Chlorella cells contain the cognate
      methyltransferase, M.CviBI, which specifically methylates adenine in GANTC
      sequences and at least two other distinct methyltransferases; M.CviBII and
      M.CviBIII methylate adenine in GATC and TCGA sequences, respectively.  The
      M.CviBIII gene was cloned, sequenced and a single open reading frame of 1131 bp
      identified.  A comparison of the predicted amino acid sequence of M.CviBIII
      with M.TaqI, a bacterial isoschizomer, revealed 39% identity.  A second family
      of viruses that infect another strain of Chlorella (Pbi) have recently been
      isolated.  Like the NC64A viruses, the Pbi viruses contain large dsDNAs genomes
      with various levels of methylated bases.  Infection of Chlorella Pbi with the
      Pbi viruses also results in the synthesis of DNA methyltransferases and DNA
      site-specific endonucleases.  Thus these Chlorella viruses are a new source of
      both adenine and cytosine methyltransferases and DNA site-specific
      endonucleases.
AU  - Van Etten JL
AU  - Xia Y
AU  - Burbank DE
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1989 13D: 199.

PMID- 2854800
VI  - 74
DP  - 1988
TI  - Chlorella viruses code for restriction and modification enzymes.
PG  - 113-115
AB  - Meeting Abstract
AU  - Van Etten JL
AU  - Xia Y
AU  - Burbank DE
AU  - Narva KE
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 113-115.

PMID- 6248426
VI  - 9
DP  - 1980
TI  - Recognition sequence for the restriction endonuclease BglI from Bacillus globigii.
PG  - 195-203
AB  - Restriction endonuclease BglI recognizes the DNA sequence ...CCCNNNN^NGGC...3'
      ...CGGN^NNNNCCG...5' and cleaves each strand at the site indicated, thus
      generating 3' protruding ends.  The recognition sequence was deduced by
      correlating mapping data with nucleotide sequence information and the position
      of cleavage was unambiguously determined by 32P labeling of 5' termini produced
      by BglI digestion.
AU  - Van Heuverswyn H
AU  - Fiers W
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1980 9: 195-203.

PMID- 14993311
VI  - 150
DP  - 2004
TI  - Biochemical and molecular characterization of a levansucrase from Lactobacillus reuteri.
PG  - 621-630
AB  - Lactobacillus reuteri strain 121 employs a fructosyltransferase (FTF) to synthesize a fructose
      polymer [a fructan of the levan type, with
      beta(2-->6) linkages] from sucrose or raffinose. Purification of this FTF
      (a levansucrase), and identification of peptide amino acid sequences,
      allowed isolation of the first Lactobacillus levansucrase gene (lev),
      encoding a protein (Lev) consisting of 804 amino acids. Lev showed highest
      similarity with an inulosucrase of L. reuteri 121 [Inu; producing an
      inulin polymer with beta(2-->1)-linked fructosyl units] and with FTFs from
      streptococci. Expression of lev in Escherichia coli resulted in an active
      FTF (Lev Delta 773His) that produced the same levan polymer [with only 2-3
      % beta(2-->1-->6) branching points] as L. reuteri 121 cells grown on
      raffinose. The low degree of branching of the L. reuteri levan is very
      different from bacterial levans known up to now, such as that of
      Streptococcus salivarius, having up to 30 % branches. Although Lev is
      unusual in showing a higher hydrolysis than transferase activity,
      significant amounts of levan polymer are produced both in vivo and in
      vitro. Lev is strongly dependent on Ca(2+) ions for activity. Unique
      properties of L. reuteri Lev together with Inu are: (i) the presence of a
      C-terminal cell-wall-anchoring motif causing similar expression problems
      in Escherichia coli, (ii) a relatively high optimum temperature for
      activity for FTF enzymes, and (iii) at 50 degrees C, kinetics that are
      best described by the Hill equation.
AU  - van Hijum SA
AU  - Szalowska E
AU  - van der Maarel MJ
AU  - Dijkhuizen L
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2004 150: 621-630.

PMID- 28183766
VI  - 5
DP  - 2017
TI  - De Novo Whole-Genome Sequence of Xylella fastidiosa subsp. multiplex Strain BB01  Isolated from a Blueberry in Georgia, USA.
PG  - e01598-16
AB  - This study reports a de novo-assembled draft genome sequence of Xylella fastidiosa subsp.
      multiplex strain BB01 causing blueberry bacterial leaf scorch
      in Georgia, USA. The BB01 genome is 2,517,579 bp, with a G+C content of 51.8%,
      2,943 open reading frames (ORFs), and 48 RNA genes.
AU  - Van Horn C
AU  - Chang CJ
AU  - Chen J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01598-16.

PMID- 24503985
VI  - 2
DP  - 2014
TI  - Genome Sequence of Serratia plymuthica RVH1, Isolated from a Raw Vegetable-Processing Line.
PG  - e00021-14
AB  - We announce the genome sequence of Serratia plymuthica strain RVH1, a psychroloterant strain
      that was isolated from a raw vegetable-processing line and
      that regulates the production of primary metabolites (acetoin and butanediol),
      antibiotics, and extracellular enzymes through quorum sensing.
AU  - Van Houdt R
AU  - Van der Lelie D
AU  - Izquierdo JA
AU  - Aertsen A
AU  - Masschelein J
AU  - Lavigne R
AU  - Michiels CW
AU  - Taghavi S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00021-14.

PMID- 28711585
VI  - 17
DP  - 2017
TI  - Global outbreak of severe Mycobacterium chimaera disease after cardiac surgery: a molecular epidemiological study.
PG  - 1033-1041
AB  - Since 2013, over 100 severe cases of Mycobacterium chimaera infections, often fatal, have been
      notified in four European countries (Switzerland, Germany, the Netherlands, and the UK), the
      USA, and Australia, all among patients who had undergone cardiothoracic surgery.17 Initial
      epidemiological investigations suggested a link to the use of specific heatercooler units
      (HCUs) that are used to control temperature within the extracorporeal circulation during
      cardiac surgery.17 The possibility of a global outbreak caused by HCUs sparked investigations
      by the European Centre for Disease Prevention and Control (ECDC) and the US Centers for
      Disease Control and Prevention (CDC).
AU  - van Ingen J et al
PT  - Journal Article
TA  - Lancet Infect Dis
JT  - Lancet Infect Dis
SO  - Lancet Infect Dis 2017 17: 1033-1041.

PMID- 9765557
VI  - 180
DP  - 1998
TI  - Characterization of multiple regions involved in replication and mobilization of plasmid pNZ4000 coding for exopolysaccharide production in   Lactococcus lactis.
PG  - 5285-5290
AB  - We characterized the regions involved in replication and mobilization of the 40-kb plasmid
      pNZ4000, encoding exopolysaccharide (EPS) production in
      Lactococcus lactis NIZO B40. The plasmid contains four highly conserved
      replication regions with homologous rep genes (repB1, repB2, repB3, and
      repB4) that belong to the lactococcal theta replicon family. Subcloning of
      each replicon individually showed that all are functional and compatible
      in L. lactis. Plasmid pNZ4000 and genetically labeled derivatives could be
      transferred to different L. lactis strains by conjugation, and pNZ4000 was
      shown to be a mobilization plasmid. Two regions involved in mobilization
      were identified near two of the replicons; both included an oriT sequence
      rich in inverted repeats. Conjugative mobilization of the nonmobilizable
      plasmid pNZ124 was promoted by either one of these oriT sequences,
      demonstrating their functionality. One oriT sequence was followed by a
      mobA gene, coding for a trans-acting protein, which increased the
      frequency of conjugative transfer 100-fold. The predicted MobA protein and
      the oriT sequences show protein and nucleotide similarity, respectively,
      with the relaxase and with the inverted repeat and nic site of the oriT
      from the Escherichia coli plasmid R64. The presence on pNZ4000 of four
      functional replicons, two oriT sequences, and several insertion
      sequence-like elements strongly suggests that this EPS plasmid is a
      naturally occurring cointegrate.
AU  - van Kranenburg R
AU  - de Vos WM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1998 180: 5285-5290.

PMID- 10686131
VI  - 43
DP  - 2000
TI  - Nucleotide sequence analysis of the lactococcal EPS plasmid pNZ4000.
PG  - 130-136
AB  - The complete 42180-bp nucleotide sequence of the mobilization plasmid
      pNZ4000, coding for exopolysaccharide (EPS) production in Lactococcus
      lactis, was determined. This plasmid contains a region involved in EPS
      biosynthesis, four functional replicons, a region containing mobilization
      genes, and three origin of transfer (oriT) sequences. Sequences identical
      to these oriT sequences were also found on two other lactococcal plasmids
      and a plasmid from Lactobacillus helveticus. Several complete and partial
      IS elements were identified on pNZ4000, including iso-ISS1, iso-IS946, and
      iso-IS982 sequences. Furthermore, pNZ4000 contains a gene cluster that may
      encode a cobalt transport system and a gene that encodes a CorA homologue
      which may function as a magnesium transporter.
AU  - van Kranenburg R
AU  - Kleerebezem M
AU  - de Vos WM
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 2000 43: 130-136.

PMID- 25428975
VI  - 2
DP  - 2014
TI  - Genome Sequence of a Multidrug-Resistant Strain of Klebsiella pneumoniae, BAMC 07-18, Isolated from a Combat Injury Wound.
PG  - e01230-14
AB  - Klebsiella pneumoniae is an important infectious agent of surgical sites and combat wounds.
      Antibiotic resistance and tolerance are common impediments to the
      healing of chronic infections. Here, we report the genome sequence of a highly
      multidrug-resistant strain of K. pneumoniae, BAMC 07-18, isolated from a combat
      wound of a soldier.
AU  - Van Laar TA
AU  - Chen T
AU  - Childers BM
AU  - Chen P
AU  - Abercrombie JJ
AU  - Leung KP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01230-14.

PMID- 
VI  - 82
DP  - 2002
TI  - Genetics and molecular biology of propionibacteria.
PG  - 45-57
AB  - Research in the genetics and molecular biology of propionibacteria is currently making much
      progress. In order to develop efficient DNA
      transfer systems for the genus Propionibacterium, dairy and
      environmental propionibacteria were screened for the presence of
      suitable plasmids as a first step. Following nucleotide sequence
      analysis, potential replication functions were identified on several
      Propionibacterium plasmids such as pLME 106/pRGO1, p545 and pLME108.
      Furthermore, ppnA, the gene encoding the propionicin SM1, was detected
      on pLME106. Three of these plasmids which had been fused with
      antibiotic resistance selection markers (ermE, cml, hygB) originating
      from bacteria with high G+C DNA content were recently successfully used
      as Escherichia coli - Propionibacterium shuttle vectors. DNA
      restriction/modification systems observed in propionibacteria have to
      be taken into account since successful DNA transformation at high rates
      (up to 10^8 Propionibacterium transformants/microgram of DNA) succeeds only
      with plasmid DNA originating from propionibacteria with the same
      restriction/modification system(s) as the strain to be transformed, and
      not from E. coli hosts. The basis for an integrating vector has been
      set up after identification of a potential attP site and an adjacent
      integrase gene from a Propionibacterium phage/prophage system. Finally,
      approximately 30 gene sequences with attributed coding functions from
      propionibacteria are available on databases.
AU  - van Luijk N
AU  - Stierli MP
AU  - Schwenninger SM
AU  - Herve C
AU  - Dasen G
AU  - Jore JPM
AU  - Pouwels PH
AU  - van der Werf MJ
AU  - Teuber M
AU  - Meile L
PT  - Journal Article
TA  - Lait
JT  - Lait
SO  - Lait 2002 82: 45-57.

PMID- 28705980
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of Lactococcus lactis subsp. lactis bv. diacetylactis FM03 and Leuconostoc mesenteroides FM06 Isolated from Cheese.
PG  - e00633-17
AB  - Here, the genome sequences of Lactococcus lactis subsp. lactis bv. diacetylactis  FM03 and
      Leuconostoc mesenteroides FM06, both isolated from cheese, are
      presented. FM03 and FM06 contain 7 and 3 plasmids, respectively, that carry genes
      encoding functions important for growth and survival in dairy fermentations.
AU  - van Mastrigt O
AU  - Abee T
AU  - Smid EJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00633-17.

PMID- 15598825
VI  - 32
DP  - 2004
TI  - Initiation of translocation by Type I restriction-modification enzymes is associated with a short DNA extrusion.
PG  - 6540-6547
AB  - Recognition of 'foreign' DNA by Type I restriction-modification (R-M) enzymes elicits an
      ATP-dependent switch from methylase to endonuclease activity, which involves DNA translocation
      by the restriction subunit HsdR. Type I R-M enzymes are composed of three (Hsd) subunits with
      a stoichiometry of HsdR2:HsdM2:HsdS1 (R2-complex). However, the EcoR124I R-M enzyme can also
      exist as a cleavage deficient, sub-assembly of HsdR1:HsdM2:HsdS1 (R1-complex). ATPS was used
      to trap initial translocation complexes, which were visualized by Atomic Force Microscopy
      (AFM). In the R1-complex, a small bulge, associated with a shortening in the contour-length of
      the DNA of 8 nm, was observed. This bulge was found to be sensitive to single-strand DNA
      nucleases, indicative of non-duplexed DNA. R2-complexes appeared larger in the AFM images and
      the DNA contour length showed a shortening of approximately 11 nm, suggesting that two bulges
      were formed. Disclosure of the structure of the first stage after the
      recognition-translocation switch of Type I restriction enzymes forms an important first step
      in resolving a detailed mechanistic picture of DNA translocation by SF-II DNA translocation
      motors.
AU  - van Noort J
AU  - van der Heijden T
AU  - Dutta FC
AU  - Firman K
AU  - Dekker C
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2004 32: 6540-6547.

PMID- 
VI  - 84
DP  - 2003
TI  - Single molecule characterization of DNA translocation by the type I restriction enzyme EcoR124I.
PG  - 304a
AB  - In bacteria, viral DNA is degraded by dedicated type I restriction enzymes.  When DNA is not
      methylated, it is recognized as foreign and the enzyme starts DNA translocation consuming ATP,
      to form a loop.  Cleavage will occur when translocation is blocked.  In this study the motor
      properties of EcoR124I are investigated with Atomic Force Microscopy and Magnetic Tweezers.
      Energetic barriers due to DNA bending and torsion, can be expected when EcoR124I moves over
      DNA.  In the initial DNA EcoR124I complex AFM images show DNA tightly wrapped around the
      enzyme.  In circular DNA no supercoiling is observed in front and behind the complex after
      translocation.  Magnetic tweezers data however, show that the translocation does impose a
      twist on the DNA.  Time traces of the length of single DNA molecules being processed by
      EcoR124I show a non-constant translocation velocity, and repeated hick-ups.  A discrepancy is
      observed between the translocation distance and the expected imposed twist.  The observed
      behavior is consistent with frequent slipping events, both in translation and in rotation.
AU  - van Noort J
AU  - van der Heijden T
AU  - van der Scheer C
AU  - Firman K
AU  - Dekker C
PT  - Journal Article
TA  - Biophys. J.
JT  - Biophys. J.
SO  - Biophys. J. 2003 84: 304a.

PMID- 1101223
VI  - 2
DP  - 1975
TI  - Specificity of a deoxyribonucleic acid transmethylase induced by bacteriophage T2.  I. Nucleotide sequences isolated from Micrococcus luteus DNA methylated in vitro.
PG  - 1391-1400
AB  - Deoxyribonucleic acid from Micrococcus luteus was methylated in vitro in the presence of
      S-adenosyl-(14C methyl)methionine with a DNA methyltransferase purified from extracts of E.
      coli infected with bacteriophage T2. The labelled DNA was degraded by enzymatic and specific
      chemical methods and the resulting short oligonucleotides were separated and characterized.
      The analytical data permit the conclusion that the DNA transmethylase reacts specifically with
      N-G-A-T-C-N sequences in which it converts adenine to a 6-methyl-aminopurine residue.
AU  - van Ormondt H
AU  - Gorter J
AU  - Havelaar KJ
AU  - de Waard A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1975 2: 1391-1400.

PMID- 4580897
VI  - 33
DP  - 1973
TI  - Methylated oligonucleotides derived from bacteriophage fd RF-DNA modified in vitro by E. coli B modification methylase.
PG  - 177-180
AB  - E. coli B modification methylase converts four adenine residues (presumably two
      per strand) to N(6)-methylaminopurine in wild-type unmodified fd RF-DNA.  When
      RF-DNA of the one-site mutant fd sB01 sB2 (strain 101) is the substrate, the
      DNA receives two methyl groups while fd sB01 sB02 RF-DNA has lost is
      susceptibility to the methylase by mutation.  This methylation is concomitant
      with an increase in infectivity on E. coli B spheroplasts.  These results
      probably mean that wild-type RF-DNA has two recognizable and specific
      nucleotide sequences ("sites"), fd sB01 sB2 one, and fd sB01 sB02 none, which
      by becoming methylated confer resistance to the E. coli B restriction enzyme.
      The present study was undertaken to elucidate the structure of those sites
      which bear "E. coli B specificity".  To this end, unmodified RF-DNA of
      wild-type fd was methylated in vitro in the presence of purified modification
      methylase from E. coli B and methyl tritiated S-adenosylmethionine.  The
      [3H-methyl]RF-DNA was degraded to small fragments, and the tritiated
      oligonucleotides characterized as to their sequence. Although a definitive
      sequence was not obtained by this approach, an analysis of the sequenced
      oligonucleotides showed the 3'- and 5'-nearest neighbors of the methylated
      adenine residues to be A or C, G or C, respectively.  This finding demonstrates
      that the sequence surrounding the modified base does not contain a twofold
      rotational symmetry.
AU  - van Ormondt H
AU  - Lautenberger JA
AU  - Linn S
AU  - de Waard A
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1973 33: 177-180.

PMID- 21398537
VI  - 193
DP  - 2011
TI  - Genome sequence of Victivallis vadensis ATCC BAA-548, an anaerobic bacterium from the phylum Lentisphaerae, isolated from the human  gastro-intestinal tract.
PG  - 2373-2374
AB  - Victivallis vadensis ATCC BAA-548 represents the first cultured representative from the novel
      phylum Lentisphaerae, a deep-branching bacterial lineage. Few cultured bacteria from this
      phylum are known, and V. vadensis therefore represents an important organism for evolutionary
      studies. V. vadensis is a strictly anaerobic sugar-fermenting isolate from the human
      gastro-intestinal tract.
AU  - van Passel MW et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 2373-2374.

PMID- 21398538
VI  - 193
DP  - 2011
TI  - Genome sequence of the Verrucomicrobium Opitutus terrae PB90-1, an abundant inhabitant of rice paddy soil ecosystems.
PG  - 2367-2368
AB  - Bacteria of the deeply branching phylum Verrucomicrobia are rarely cultured, yet commonly
      detected in metagenomic libraries from aquatic, terrestrial and intestinal environments. We
      have sequenced the genome of Opitutus terrae PB90-1, a fermentative anaerobe within this
      phylum, isolated from rice paddy soil and capable of propionate production from plant-derived
      polysaccharides.
AU  - van Passel MW et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 2367-2368.

PMID- 4614084
VI  - 135
DP  - 1974
TI  - DNA restriction and modification systems in Salmonella:  II. Genetic complementation between the K and B systems of Escherichia coli and the Salmonella typhimurium system SB, with the same chromosomal location.
PG  - 51-60
AB  - E. coli x S. typhimurium partially diploid hybrids were constructed to
      investigate the possibility of genetic complementation between the SA and the
      SB restriction and modification systems of S. typhimurium and the K and B
      systems of E. coli.  An hsdR-K mutation was complemented in a stable hybrid in
      which the hsd+SA-hsd+SB-serB+ portion of the S. typhimurium chromosome was
      integrated at a non-homologous locus.  By isolating hsd- mutants in that
      hybrid, it was shown that complementation occurred between K and SB, but not
      between K and SA.  Similarly, in a set of F-prime merodiploids bearing the SA,
      SB and B systems, complementation was observed between B and SB, but not
      between B and SA.
AU  - Van Pel A
AU  - Colson C
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1974 135: 51-60.

PMID- 
VI  - 0
DP  - 2005
TI  - Homing endonuclease I-TevI: An atypical zinc finger with a novel function.
PG  - 35-38
AB  - I-TevI is a site-specific, sequence-tolerant homing endonuclease encoded by the td intron of
      bacteriophage T4.  The enzyme consists of an N-terminal catalytic domain and a C-terminal
      DNA-binding domain that are connected by a long, flexible linker.  The crystal structure of
      the DNA-binding domain of I-TevI, residues 130 to 245, complexed with the 20-bp primary
      binding region of its DNA target, reveals the presence of a zinc finger, comprising residues
      151 to 167, that makes backbone contacts with the DNA from the minor groove.  Biochemical data
      have shown that the zinc finger does not contribute to the DNA-binding affinity or to the
      specificity of the enzyme, but rather that it has a novel function and acts as a distance
      determinant that controls the relative positions of the catalytic and DNA-binding domains.
AU  - Van Roey P
AU  - Belfort M
AU  - Derbyshire V
PT  - Journal Article
TA  - Zinc Finger Proteins: from Atomic Contact to Cellular Function; Molecular Biology Intelligence Unit
JT  - Zinc Finger Proteins: from Atomic Contact to Cellular Function; Molecular Biology Intelligence Unit
SO  - Zinc Finger Proteins: from Atomic Contact to Cellular Function; Molecular Biology Intelligence Unit 2005 0: 35-38.

PMID- 
VI  - 16
DP  - 2005
TI  - GIY-YIG homing endonucleases - beads on a string.
PG  - 67-83
AB  - Homing endonucleases are intron- and intein-encoded proteins that initiate the mobility of
      their particular host elements.  They recognize an intron- or intein-less version of their
      host gene and introduce a double-strand break in the DNA.  This break is then repaired by
      copying the intron- or intein-plus allele, using the hosts cellular machinery.  This results
      in a gene-conversion event whereby both alleles become intron- or intein-plus.  Homing
      endonucleases can be classified into four distinct families, based on the presence of
      conserved sequence elements: the LAGLIDADG, GIY-YIG, His-Cys box, and HNH families.  However,
      the His-Cys box and HNH families have been hypothesized to constitute a single bba-Me family,
      and recent structural data support this classification.
AU  - Van Roey P
AU  - Derbyshire V
PT  - Journal Article
TA  - Nucleic Acids Mol. Biol.
JT  - Nucleic Acids Mol. Biol.
SO  - Nucleic Acids Mol. Biol. 2005 16: 67-83.

PMID- 12379841
VI  - 9
DP  - 2002
TI  - Catalytic domain structure and hypothesis for function of GIY-YIG intron endonuclease I-TevI.
PG  - 806-811
AB  - I-TevI, a member of the GIY-YIG family of homing endonucleases, consists of an N-terminal
      catalytic domain and a C-terminal DNA-binding domain joined by a flexible linker. The GIY-YIG
      motif is in the N-terminal domain of I-TevI, which corresponds to a phylogenetically
      widespread catalytic cartridge that is often associated with mobile genetic elements. The
      crystal structure of the catalytic domain of I-TevI, the first of any GIY-YIG endonuclease,
      reveals a novel alpha/beta-fold with a central three-stranded antiparallel beta-sheet flanked
      by three helices. The most conserved and putative catalytic residues are located on a shallow,
      concave surface and include a metal coordination site. Similarities in the three-dimensional
      arrangement of the catalytically important residues and the cation-binding site with those of
      the His-Cys box endonuclease I-PpoI suggest the possibility of mechanistic relationships among
      these different families of homing endonucleases despite completely different folds.
AU  - Van Roey P
AU  - Meehan L
AU  - Kowalski JC
AU  - Belfort M
AU  - Derbyshire V
PT  - Journal Article
TA  - Nat. Struct. Biol.
JT  - Nat. Struct. Biol.
SO  - Nat. Struct. Biol. 2002 9: 806-811.

PMID- 11447104
VI  - 20
DP  - 2001
TI  - Intertwined structure of the DNA-binding domain of intron endonuclease I-TevI with its substrate.
PG  - 3631-3637
AB  - I-TevI is a site-specific, sequence-tolerant intron endonuclease. The crystal structure of the
      DNA-binding domain of I-TevI complexed with the 20 bp primary binding region of its DNA target
      reveals an unusually extended structure composed of three subdomains: a Zn finger, an
      elongated segment containing a minor groove-binding alpha-helix, and a helix-turn-helix. The
      protein wraps around the DNA, mostly following the minor groove, contacting the phosphate
      backbone along the full length of the duplex. Surprisingly, while the minor groove-binding
      helix and the helix-turn- helix subdomain make hydrophobic contacts, the few base-specific
      hydrogen bonds occur in segments that lack secondary structure and flank the intron insertion
      site. The multiple base-specific interactions over a long segment of the substrate are
      consistent with the observed high site specificity in spite of sequence tolerance, while the
      modular composition of the domain is pertinent to the evolution of homing endonucleases.
AU  - Van Roey P
AU  - Waddling CA
AU  - Fox KM
AU  - Belfort M
AU  - Derbyshire V
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 2001 20: 3631-3637.

PMID- 20398277
VI  - 11
DP  - 2010
TI  - Pyrosequencing-based comparative genome analysis of the nosocomial pathogen Enterococcus faecium and identification of a large transferable pathogenicity island.
PG  - 239
AB  - BACKGROUND: The Gram-positive bacterium Enterococcus faecium is an
      important cause of nosocomial infections in immunocompromized patients.
      RESULTS: We present a pyrosequencing-based comparative genome analysis of
      seven E. faecium strains that were isolated from various sources. In the
      genomes of clinical isolates several antibiotic resistance genes were
      identified, including the vanA transposon that confers resistance to
      vancomycin in two strains. A functional comparison between E. faecium and
      the related opportunistic pathogen E. faecalis based on differences in the
      presence of protein families, revealed divergence in plant carbohydrate
      metabolic pathways and oxidative stress defense mechanisms. The E. faecium
      pan-genome was estimated to be essentially unlimited in size, indicating
      that E. faecium can efficiently acquire and incorporate exogenous DNA in
      its gene pool. One of the most prominent sources of genomic diversity
      consists of bacteriophages that have integrated in the genome. The
      CRISPR-Cas system, which contributes to immunity against bacteriophage
      infection in prokaryotes, is not present in the sequenced strains. Three
      sequenced isolates carry the esp gene, which is involved in urinary tract
      infections and biofilm formation. The esp gene is located on a large
      pathogenicity island (PAI), which is between 64 and 104 kb in size.
      Conjugation experiments showed that the entire esp PAI can be transferred
      horizontally and inserts in a site-specific manner. CONCLUSIONS: Genes
      involved in environmental persistence, colonization and virulence can
      easily be aquired by E. faecium. This will make the development of
      successful treatment strategies targeted against this organism a challenge
      for years to come.
AU  - van Schaik W
AU  - Top J
AU  - Riley DR
AU  - Boekhorst J
AU  - Vrijenhoek JE
AU  - Schapendonk CM
AU  - Hendrickx AP
AU  - Nijman IJ
AU  - Bonten MJ
AU  - Tettelin H
AU  - Willems RJ
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2010 11: 239.

PMID- 12533478
VI  - 185
DP  - 2003
TI  - Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa.
PG  - 1018-1026
AB  - Xylella fastidiosa is a xylem-dwelling, insect-transmitted, gamma-proteobacterium that causes
      diseases in many plants, including
      grapevine, citrus, periwinkle, almond, oleander, and coffee. X. fastidiosa
      has an unusually broad host range, has an extensive geographical
      distribution throughout the American continent, and induces diverse
      disease phenotypes. Previous molecular analyses indicated three distinct
      groups of X. fastidiosa isolates that were expected to be genetically
      divergent. Here we report the genome sequence of X. fastidiosa (Temecula
      strain), isolated from a naturally infected grapevine with Pierce's
      disease (PD) in a wine-grape-growing region of California. Comparative
      analyses with a previously sequenced X. fastidiosa strain responsible for
      citrus variegated chlorosis (CVC) revealed that 98% of the PD X.
      fastidiosa Temecula genes are shared with the CVC X. fastidiosa strain
      9a5c genes. Furthermore, the average amino acid identity of the open
      reading frames in the strains is 95.7%. Genomic differences are limited to
      phage-associated chromosomal rearrangements and deletions that also
      account for the strain-specific genes present in each genome. Genomic
      islands, one in each genome, were identified, and their presence in other
      X. fastidiosa strains was analyzed. We conclude that these two organisms
      have identical metabolic functions and are likely to use a common set of
      genes in plant colonization and pathogenesis, permitting convergence of
      functional genomic strategies.
AU  - Van Sluys MA et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2003 185: 1018-1026.

PMID- 8550446
VI  - 178
DP  - 1996
TI  - Host-mediated modification of PvuII restriction in Mycobacterium tuberculosis.
PG  - 78-84
AB  - Restriction endonuclease PvuII plays a central role in restriction fragment length
      polymorphism analysis of Mycobacterium tuberculosis complex isolates with IS6110 as a genetic
      marker.  We have investigated the basis for an apparent dichotomy in PvuII restriction
      fragment patterns observed among strains of the M. tuberculosis complex.  The chromosomal
      regions of two modified PvuII restriction sites, located upstream of the katG gene and
      downstream of an IS108I insertion sequence, were studied in more detail.  An identical 10-bp
      DNA sequence (CAGCTGGAGC) containing a PvuII site was found in both regions, and site-directed
      mutagenesis analysis revealed that this sequence was a target for modification.
      Strain-specific modification of PvuII sites was identified in DNA from over 80% of the nearly
      800 isolates examined.  Furthermore, the proportion of modifying and nonmodifying strains
      differs significantly from country to country.
AU  - van Soolingen D
AU  - de Haas PEW
AU  - Blumenthal RM
AU  - Kremer K
AU  - Sluijter M
AU  - Pijnenburg JEM
AU  - Schouls LM
AU  - Thole JER
AU  - Desens-Kroon MWG
AU  - van Embden JDA
AU  - Hermans PWM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1996 178: 78-84.

PMID- 12951776
VI  - 35
DP  - 2003
TI  - Epigenomic profiling using microarrays.
PG  - 346-357
AB  - Genes occupy only a minor fraction of genomes such as ours; however, histone and nonhistone
      chromosomal proteins and methylated DNA bases are
      distributed over both genic and nongenic regions. These widespread
      "epigenomic" features can be mapped and characterized by alternative
      applications of the same microarray technologies that have been used for
      conventional transcriptional profiling. Here we describe diverse
      microarray-based strategies for profiling patterns of DNA methylation, DNA
      replication, DNA binding, and chromatin-associated proteins and histone
      modifications. The rapid progress that is being made in developing and
      applying epigenomic profiling methods and the increasing availability of
      microarrays mean that epigenomic profiling is likely to become a standard
      research tool for understanding chromatin structure and gene expression
      during development.
AU  - van Steensel B
AU  - Henikoff S
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 2003 35: 346-357.

PMID- 10748524
VI  - 18
DP  - 2000
TI  - Identification of in vivo DNA targets of chromatin proteins using tethered Dam methyltransferase.
PG  - 424-428
AB  - We have developed a novel technique, named DamID, for the identification of DNA loci that
      interact in vivo with specific nuclear proteins in eukaryotes. By tethering Escherichia coli
      DNA adenine methyltransferase (Dam) to a chromatin protein, Dam can be targeted in vivo to
      native binding sites of this protein, resulting in local DNA methylation. Sites of methylation
      can subsequently be mapped using methylation-specific restriction enzymes or antibodies. We
      demonstrate the successful application of DamID both in Drosophila cell cultures and in whole
      flies. When Dam is tethered to the DNA-binding domain of GAL4, targeted methylation is limited
      to a region of a few kilobases surrounding a GAL4 binding sequence. Using DamID, we identified
      a number of expected and unexpected target loci for Drosophila heterochromatin protein 1.
      DamID has potential for genome-wide mapping of in vivo targets of chromatin proteins in
      various eukaryotes.
AU  - van Steensel B
AU  - Henikoff S
PT  - Journal Article
TA  - Nat. Biotechnol.
JT  - Nat. Biotechnol.
SO  - Nat. Biotechnol. 2000 18: 424-428.

PMID- 18515486
VI  - 74
DP  - 2008
TI  - Presence of a family of plasmids (29 to 65 kilobases) with a 26-kilobase common region in different strains of the sulfur-oxidizing bacterium Acidithiobacillus caldus.
PG  - 4300-4308
AB  - Three large cryptic plasmids from different isolates of Acidithiobacillus caldus were rescued
      by using an in vitro
      transposition system that delivers a kanamycin-selectable marker and an
      Escherichia coli plasmid origin of replication. The largest of the
      plasmids, the 65-kb plasmid pTcM1, was isolated from a South African A.
      caldus strain, MNG. This plasmid was sequenced and compared to that of
      pTcF1 (39 kb, from strain "f," South Africa) and pC-SH12 (29 kb, from
      strain C-SH12, Australia). With the exception of a 2.7-kb insertion
      sequence, pC-SH12 appears to represent the DNA common to all three
      plasmids and includes a number of accessory genes plus the plasmid
      "backbone" containing the replication region. The two larger plasmids
      carry, in addition, a number of insertion sequences of the ISL3 family
      and a composite transposon related to the Tn21 subfamily containing a
      highly mosaic region within the borders of the inverted repeats. Genes
      coding for arsenic resistance, plasmid mobilization, plasmid stability,
      and a putative restriction-modification system occur within these
      mosaic regions.
AU  - van Zyl LJ
AU  - Deane SM
AU  - Louw LA
AU  - Rawlings DE
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2008 74: 4300-4308.

PMID- 27056214
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Three Bacillus Species from South African Marine Sponges.
PG  - e00143-16
AB  - The rise in antibiotic-resistant bacteria has spurred efforts to identify novel compounds with
      antimicrobial activity. This brief report describes the genome
      sequence of threeBacillusspecies isolates from South African marine sponges,
      which produce compounds with antimicrobial activity. A search for secondary
      metabolite clusters revealed several secondary metabolite pathways in these
      genomes, which may hold promise as novel antibiotics.
AU  - van Zyl LJ
AU  - Matobole R
AU  - Augustin NBF
AU  - Klein T
AU  - Kirby B
AU  - Trindade M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00143-16.

PMID- 
VI  - 3
DP  - 2004
TI  - Metal-dependent type II restriction endonucleases.
PG  - 742-756
AB  - Restriction endonucleases are phosphodiesterases that bind double-stranded DNA with high
      specificity and cleave the DNA to yield 5'-phosphate and 3'-hydroxyl groups as products.
      Restriction endonucleases with their corresponding methyltransferases form the
      restriction-modification systems of bacteria.  R-M systems are ubiquitous in bacteria; only a
      few are known not to contain any R-M gene.  The recently sequenced Helicobacter pylori strain
      26695, for instance, reveals more than a dozen R-M systems, though less than 30% are
      functional.
AU  - Vanamee ES
AU  - Aggarwal AK
PT  - Journal Article
TA  - Handbook of Metalloproteins
JT  - Handbook of Metalloproteins
SO  - Handbook of Metalloproteins 2004 3: 742-756.

PMID- 17524420
VI  - 370
DP  - 2007
TI  - An EM View of the FokI Synaptic Complex by Single Particle Analysis.
PG  - 207-212
AB  - FokI is a type IIS restriction endonuclease that recognizes the 5'-GGATG-3' sequence and
      cleaves non-specifically at 9 and 13 base-pairs away on the top and bottom strands,
      respectively, to produce a 5' overhang. FokI is a bipartite endonuclease with separate
      recognition and cleavage domains. Because of its bipartite nature, FokI has received
      considerable interest in generating chimeric nucleases for use in biotechnology, and recently
      as possible therapeutic agents in gene therapy by initiating homologous gene recombination and
      repair. Here we show, using single-particle electron microscopic studies, that the FokI active
      complex prefers a single conformation in which the subunits are arranged in a doughnut shape
      complex with protein-protein and possibly protein-DNA interactions stabilizing the cleavage
      complex. Our electron microscopy (EM) model provides new insights into the activation
      mechanism of FokI and how non-specific cleavage is avoided.
AU  - Vanamee ES
AU  - Berriman J
AU  - Aggarwal AK
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2007 370: 207-212.

PMID- 14623197
VI  - 334
DP  - 2003
TI  - Glucocorticoid receptor-like Zn(Cys)(4) motifs in BslI restriction endonuclease.
PG  - 595-603
AB  - BslI restriction endonuclease cleaves the symmetric sequence CCN(7)GG (where N=A, C, G or T).
      The enzyme is composed of two subunits, alpha and
      beta, that form a heterotetramer (alpha(2)beta(2)) in solution. The alpha
      subunit is believed to be responsible for DNA recognition, while the beta
      subunit is thought to mediate cleavage. Here, for the first time, we
      provide experimental evidence that BslI binds Zn(II). Specifically, using
      X-ray absorption spectroscopic analysis we show that the alpha subunit of
      BslI contains two Zn(Cys)(4)-type zinc motifs similar to those in the
      DNA-binding domain of the glucocorticoid receptor. This conclusion is
      supported by genetic analysis of the zinc-binding motifs, whereby amino
      acid substitutions in the zinc finger motifs are demonstrated to abolish
      or impair cleavage activity. An additional putative zinc-binding motif was
      identified in the beta subunit, consistent with the X-ray absorption data.
      These data were corroborated by proton induced X-ray emission measurements
      showing that full BslI contains at least three fully occupied Zn sites per
      alpha/beta heterodimer. On the basis of these data, we propose a role for
      the BslI Zn motifs in protein-DNA as well as protein-protein interactions.
AU  - Vanamee ES
AU  - Hsieh PC
AU  - Zhu ZY
AU  - Yates D
AU  - Garman E
AU  - Xu SY
AU  - Aggarwal AK
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2003 334: 595-603.

PMID- 11491302
VI  - 309
DP  - 2001
TI  - FokI requires two specific DNA sites for cleavage.
PG  - 69-78
AB  - FokI is a bipartite restriction endonuclease that recognizes a non-palindromic DNA sequence,
      and then makes double-stranded cuts
      outside of that sequence to leave a 5' overhang. Earlier kinetic and
      crystallographic studies suggested that FokI might function as a dimer.
      Here, we show, using dynamic light-scattering, gel-filtration and
      analytical ultracentrifugation, that FokI dimerizes only in the
      presence of divalent metal ions. Furthermore, analysis of the DNA-bound
      complex reveals that two copies of the recognition sequence are
      incorporated into the dimeric complex and that formation of this
      complex is essential for full activation of cleavage. These results
      have broad implications for the mechanism by which monomeric type II
      endonucleases achieve high fidelity.
AU  - Vanamee ES
AU  - Santagata S
AU  - Aggarwal AK
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2001 309: 69-78.

PMID- 20833632
VI  - 39
DP  - 2011
TI  - Asymmetric DNA recognition by the OkrAI endonuclease, an isoschizomer of BamHI.
PG  - 712-719
AB  - Restriction enzymes share little or no sequence homology with the exception of isoschizomers,
      or enzymes that recognize and cleave the same DNA sequence. We present here the structure of a
      BamHI isoschizomer, OkrAI, bound to the same DNA sequence (TATGGATCCATA) as that
      cocrystallized with BamHI. We show that OkrAI is a more minimal version of BamHI, lacking not
      only the N- and C-terminal helices but also an internal 3(10) helix and containing ?-strands
      that are shorter than those in BamHI. Despite these structural differences, OkrAI recognizes
      the DNA in a remarkably similar manner to BamHI, including asymmetric contacts via C-terminal
      'arms' that appear to 'compete' for the minor groove. However, the arms are shorter than
      in BamHI. We observe similar DNA-binding affinities between OkrAI and BamHI but OkrAI has
      higher star activity (at 37=B0C) compared to BamHI. Together, the OkrAI and BamHI structures
      offer a rare opportunity to compare two restriction enzymes that work on exactly the same DNA
      substrate.
AU  - Vanamee ES
AU  - Viadiu H
AU  - Chan SH
AU  - Ummat A
AU  - Hartline AM
AU  - Xu SY
AU  - Aggarwal AK
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2011 39: 712-719.

PMID- 16308566
VI  - 24
DP  - 2005
TI  - A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA.
PG  - 4198-4208
AB  - Many reactions in cells proceed via the sequestration of two DNA molecules in a synaptic
      complex. SfiI is a member of a growing family of restriction enzymes that can bind and cleave
      two DNA sites simultaneously. We present here the structures of tetrameric SfiI in complex
      with cognate DNA. The structures reveal two different binding states of SfiI: one with both
      DNA-binding sites fully occupied and the other with fully and partially occupied sites. These
      two states provide details on how SfiI recognizes and cleaves its target DNA sites, and gives
      insight into sequential binding events. The SfiI recognition sequence (GGCCNNNN[downward
      arrow]NGGCC) is a subset of the recognition sequence of BglI (GCCNNNN[downward arrow]NGGC),
      and both enzymes cleave their target DNAs to leave 3-base 3' overhangs. We show that even
      though SfiI is a tetramer and BglI is a dimer, and there is little sequence similarity between
      the two enzymes, their modes of DNA recognition are unusually similar.
AU  - Vanamee ES
AU  - Viadiu H
AU  - Kucera R
AU  - Dorner L
AU  - Picone S
AU  - Schildkraut I
AU  - Aggarwal AK
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 2005 24: 4198-4208.

PMID- 7764381
VI  - 17
DP  - 1993
TI  - SbvI restriction endonuclease from Streptococcus bovis.
PG  - 297-299
AB  - Restriction endonuclease SbvI, an isoschizomer of HaeIII, has been isolated from the rumen
      amylolytic bacterium Streptococcus bovis II/1. SbvI was purified from a cell extract by
      phosphocellulose chromatography and heparin-Sepharose chromatography. The recognition sequence
      of SbvI was identified by digestion of pBR322, pUC9 and lambda DNA and comparing the cleavage
      patterns obtained with computer-derived data. SbvI recognizes the 4-bp palindrome,
      5'-GGCC-3' and cleaves DNA after the second G in the sequence, producing blunt ends.
AU  - Vanat I
AU  - Pristas P
AU  - Kutejova E
AU  - Judova J
AU  - Godany A
AU  - Jovorsky P
PT  - Journal Article
TA  - Lett. Appl. Microbiol.
JT  - Lett. Appl. Microbiol.
SO  - Lett. Appl. Microbiol. 1993 17: 297-299.

PMID- 8262361
VI  - 113
DP  - 1993
TI  - SruI restriction endonuclease from Selenomonas ruminantium.
PG  - 129-132
AB  - SruI, specific restriction endonuclease, has been characterized from Selenomonas ruminantium
      isolated from the rumen of fallow deer. Results from the study demonstrate that S. ruminantium
      18D possesses a type II restriction endonuclease, which recognizes the sequence 5'TTTAAA 3'.
      The recognition sequence of SruI was identified using digestions on pBR322, pBR328, pUC18,
      M13mp18RF, pACYC184 and lambda DNA. The cleavage patterns obtained were compared with
      computer-derived data. SruI recognizes the palindromic hexanucleotide sequence and cleaves DNA
      after the third T in the sequence, producing blunt ends. The purification and characterization
      of restriction endonuclease SruI presented here is the first described for Selenomonas
      ruminantium spp. and demonstrates that this microorganism possesses a DNA-cleaving enzyme with
      the same specificity as DraI or AhaIII.
AU  - Vanat I
AU  - Pristas P
AU  - Rybosoval E
AU  - Godany A
AU  - Javorsky P
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1993 113: 129-132.

PMID- 25676765
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Two Xanthomonas vesicatoria Strains from the Balkan Peninsula.
PG  - e01558-14
AB  - Xanthomonas vesicatoria causes bacterial spot disease of pepper and tomato plants. We report
      here the first genome sequences of X. vesicatoria strains that
      have been isolated from pepper plants. These data will be used for comparative
      genomics and will allow the development of new detection and typing tools for
      epidemiological surveillance.
AU  - Vancheva T
AU  - Bogatzevska N
AU  - Moncheva P
AU  - Lefeuvre P
AU  - Koebnik R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01558-14.

PMID- 25657284
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Two Xanthomonas euvesicatoria Strains from the Balkan Peninsula.
PG  - e01528-14
AB  - We report the draft genome sequences of two Xanthomonas euvesicatoria strains from the Balkan
      Peninsula, which were isolated from symptomatic pepper plants.
      The availability of these genome sequences will facilitate the development of
      modern genotyping assays for X. euvesicatoria strains and to define targets for
      resistance breeding.
AU  - Vancheva T
AU  - Lefeuvre P
AU  - Bogatzevska N
AU  - Moncheva P
AU  - Koebnik R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01528-14.

PMID- 24874691
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Methicillin-Resistant Staphylococcus epidermidis Strain  ET-024, Isolated from an Endotracheal Tube Biofilm of a Mechanically Ventilated  Patient.
PG  - e00527-14
AB  - Staphylococcus epidermidis strain ET-024 was isolated from a biofilm on an endotracheal tube
      of a mechanically ventilated patient. This strain is resistant
      to methicillin, and the draft genome sequence shares some characteristics with
      other nosocomial S. epidermidis strains (such as S. epidermidis RP62A).
AU  - Vandecandelaere I
AU  - Van Nieuwerburgh F
AU  - Deforce D
AU  - Nelis HJ
AU  - Coenye T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00527-14.

PMID- 12762852
VI  - 3
DP  - 2003
TI  - Analysis of bacterial RM-systems through genome-scale analysis and related taxonomy issues.
PG  - 127-143
AB  - Recognition sites for type II restriction and modification enzymes in genomes of several
      bacteria are recognized as semi-palindromic motifs and
      are avoided at a significant degree. The key idea of contrast word
      analysis with respect to RMS recognition sites, is that under-represented
      words are likely to be selected against. Starting from over- or
      underrepresented words corresponding to RMS recognition sites in specific
      clades, the specificity of unknown R-M systems can be highlighted. Among
      the known restriction enzymes, that are described in the REBASE database
      of restriction and modification systems, many of their recognition sites
      are still uncharacterized. Eventually, this motivates studies aimed at
      assessing horizontal transferring events of RMS in micro-organisms through
      the analysis of word usage biases in well-determined genomic regions. A
      probabilistic model is built on a first-order Markovian chain. Statistics
      on the k-neighborhood of a word is carried out to assess the biological
      significance of a genomic motif. Efficient word counting procedures have
      been implemented and statistics are used for the assessment of the
      significance of individual words in large sequences. On the basis of the
      set of most avoided words, and in accordance to the IUPAC coding
      standards, suggestions are made regarding potential recognition sequences.
      In certain cases, a comparison of avoided palindromic words in
      taxonomically related bacteria shows a pattern of relatedness of their R-M
      systems. For strengthening this analysis, the primary protein structure of
      all type II R-M systems known in REBASE have been blasted against the
      nr-GENBANK database. The combination of these analyses has revealed some
      interesting examples of possible horizontal transfer events of R-M
      systems.
AU  - Vandenbogaert M
AU  - Makeev V
PT  - Journal Article
TA  - In Silico Biology
JT  - In Silico Biology
SO  - In Silico Biology 2003 3: 127-143.

PMID- 23302893
VI  - 87
DP  - 2013
TI  - Romulus and Remus, Two Phage Isolates Representing a Distinct Clade within the Twortlikevirus Genus, Display Suitable Properties for Phage Therapy Applications.
PG  - 3237-3247
AB  - The renewed interest in controlling Staphylococcus aureus infections using their
      natural enemies, bacteriophages, has led to the isolation of a limited number of
      virulent phages so far. These phages are all members of the Twortlikevirus,
      displaying little variance. We present two novel closely related (95.9% DNA
      homology) lytic myoviruses, Romulus and Remus, with double-stranded DNA (dsDNA)
      genomes of 131,333 bp and 134,643 bp, respectively. Despite their relatedness to
      Staphylococcus phages K, G1, ISP, and Twort and Listeria phages A511 and P100,
      Romulus and Remus can be proposed as isolates of a new species within the
      Twortlikevirus genus. A distinguishing feature for these phage genomes is the
      unique distribution of group I introns compared to that in other staphylococcal
      myoviruses. In addition, a hedgehog/intein domain was found within their DNA
      polymerase genes, and an insertion sequence-encoded transposase exhibits splicing
      behavior and produces a functional portal protein. From a phage therapy
      application perspective, Romulus and Remus infected approximately 70% of the
      tested S. aureus isolates and displayed promising lytic activity against these
      isolates. Furthermore, both phages showed a rapid initial adsorption and
      demonstrated biofilm-degrading capacity in a proof-of-concept experiment.
AU  - Vandersteegen K
AU  - Kropinski AM
AU  - Nash JH
AU  - Noben JP
AU  - Hermans K
AU  - Lavigne R
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 2013 87: 3237-3247.

PMID- 22528312
VI  - 57
DP  - 2012
TI  - Antibiotic resistance and restriction endonucleases in fecal enterococci of chamois (Rupicapra rupicapra Linnaeus, 1758).
PG  - 355-358
AB  - Two hundred eighty-four isolates of enterococci from feces of wild living chamois from alpine
      environments were tested for sensitivity to
      three antibiotics. Low frequency of resistance was observed in studied
      enterococcal populations (about 5 % for tetracycline and erythromycin
      and 0 % for ampicillin). In six animals, the population of enterococci
      lacked any detectable resistance. Our data indicated that enterococcal
      population in feces of the majority of studied animals did not
      encounter mobile genetic elements encoding antibiotic resistance
      probably due to spatial separation and/or due to low exposure to the
      antibiotics. Based on resistance profiles observed, three populations
      were analyzed for the presence of restriction endonucleases. The
      restriction enzymes from two isolates-31K and 1K-were further purified
      and characterized. Restriction endonuclease Efa1KI recognizes CCWGG
      sequence and is an isoschizomer of BstNI. Endonuclease Efc31KI, a BsmAI
      isoschizomer, recognizes the sequence GTCTC and it is a first
      restriction endonuclease identified in Enterococcus faecium. Our data
      indicate that restriction-modification (R-M) systems do not represent
      an efficient barrier for antibiotic resistance spreading; enterococcal
      populations colonized by antibiotics resistance genes were also
      colonized by the R-M systems.
AU  - Vandzurova A
AU  - Hraskova I
AU  - Judova J
AU  - Javorsky P
AU  - Pristas P
PT  - Journal Article
TA  - Folia Microbiol. (Praha)
JT  - Folia Microbiol. (Praha)
SO  - Folia Microbiol. (Praha) 2012 57: 355-358.

PMID- 
VI  - 
DP  - 1991
TI  - Cloning and characterization of the BamHI restriction-modification methylase gene from Bacillus amyloliquefaciens.
PG  - 1-195
AB  - The gene encoding the restriction-modification methylase (M.BamHI) from Bacillus
      amyloliquefaciens has been successfully cloned into Escherichia coli. The clone encodes a 423
      amino acids methyltransferase with identical sequence specificity as the BamHI endonuclease.
      Plasmid pBamM9.0 containing this methylase gene was isolated from a Bacillus amyloliquefaciens
      genomic library in the pSP64 cloning vector. A subclone, pBamH2.0, contains a 1.86 kb
      HindIII/XmnI fragment of pBamM9.0 ligated into plasmid pSP64. Plasmid and genomic DNA isolated
      from Epicurean Coli SURE cells harboring plasmid pBamM2.0 was resistant to cleavage by BamHI
      endonuclease. During the course of cloning the cellular methylase gene, a provirally encoded
      methylase (M.BamH2) with identical sequence specificity as the cellular methylase was also
      cloned. Restriction mapping and Southern analysis confirmed the identity of two separate
      methylase genes. The sequence predicted from the cellular methylase DNA clone show two
      distinct regions of sequence similarity with N6-methyladenine and N4-methycytosine
      methyltransferases. These two regions were very highly conserved in the cellular and proviral
      methylases at both the protein and DNA level. Amino terminal sequencing of the cellular
      methylase protein produced in E. coli indicated that translation begins at a rare UUG
      initiation site. Southern analysis using the cloned methylase gene as a probe identified
      similar genes in Bacillus amyloliquefaciens strains F and H, but not in any other BamHI
      isoschizomeric bearing strains. The DNA sequence contains a 1269 base pair open reading frame
      (ORF) which encodes a 49.1 kDa protein. A cell free DNA directed transcription translation
      assay using a subclone pBSBamM2.0 as a template produced a single protein with an apparent
      molecular weight of 49,000, which is in agreement with the molecular weight predicted from the
      cloned sequence and of the purified protein. The methylase protein was purified to apparent
      homogeneity by a three step chromatographic procedure utilizing phosphocellulose,
      phenyl-sepharose, and sephadex G-150 column matrices. Fourty-four grams of E. coli harboring
      pBamM2.0 yielded 1.75 mg methylase protein, an approximate 100 fold increase in protein
      production as compared to Bacillus amyloliquefaciens (Nardone et al. 1983).
AU  - Vanek PG
PT  - Journal Article
TA  - Ph.D. Thesis, Georgetown University, USA
JT  - Ph.D. Thesis, Georgetown University, USA
SO  - Ph.D. Thesis, Georgetown University, USA 1991 : 1-195.

PMID- 2323503
VI  - 4
DP  - 1990
TI  - Comparison of cellular and viral methyltransferase genes from Bacillus amyloliquefaciens.
PG  - A2295
AB  - The restriction modification system of B. amyloliquefaciens consists of a
      restriction endonuclease, BamHI, and a cognate methyltransferase, each of which
      recognize the hexanucleotide palindrome GGATCC.  In addition to the 56 kd
      cellular methyltransferase, B. amyloliquefaciens contains a 30 kd prophage
      encoded methylase which exhibits identical sequences specificity.  Recombinant
      clones of both methyltransferases have been characterized in our laboratory.
      The two clones, pBamM2.5 (prophage methylase), and pBamM2.0 (cellular
      methylase) have been shown to produce methyltransferases capable of protecting
      host genomic DNA from BamHI endonuclease.  Further, a lysate from cells
      harboring clone pBamM2.0 has been shown to be capable of protecting lamda DNA
      from BamHI cleavage in an in vitro assay.  For sequence comparison restriction
      fragments from both pBamM2.5 and pBamM2.0 have been subcloned into M13 and
      sequenced by dideoxy sequence analysis.  The clones have also been tested as
      probes for the identification of methyltransferase genes in each of the
      following BamHI isoschizomer containing strains; B. amyloliquefaciens strain F,
      B. amyloliquefaciens strain N, A. liquefaciens NCIB 9417, B.
      stearothermophilus, G. industricus IFO3260, and G. oxydans sub. melonogenes.
      Southern blot analysis using pBamM2.5 as a probe has identified prophage
      methyltransferase genes in each of the isoschizomer bearing bacterial strains
      identified above.  The characterization of the two clones should facilitate
      further studies of the restriction modification system of B. amyloliquefaciens.
AU  - Vanek PG
AU  - Connaughton JF
AU  - Kaloss WD
AU  - Chirikijian G
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1990 4: A2295.

PMID- 2235511
VI  - 18
DP  - 1990
TI  - The complete sequence of the Bacillus amyloliquefaciens strain H, cellular BamHI methylase gene.
PG  - 6145
AB  - None
AU  - Vanek PG
AU  - Connaughton JF
AU  - Kaloss WD
AU  - Chirikjian JG
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 6145.

PMID- 21217005
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of the Hyperthermophilic, Piezophilic, Heterotrophic, and Carboxydotrophic Archaeon Thermococcus barophilus MP.
PG  - 1481-1482
AB  - Thermococcus barophilus is a hyperthermophilic, anaerobic, mixed heterotrophic, and
      carboxydotrophic euryarchaeon isolated from the deep
      sea hydrothermal vent Snakepit site on the mid-Atlantic ridge at a depth
      of 3,550 m. T. barophilus is the first true piezophilic, hyperthermophilic
      archaeon isolated, having an optimal growth at 40 MPa. Here we report the
      complete genome sequence of strain MP, the type strain of T. barophilus.
      The genome data reveal a close proximity with Thermococcus sibiricus,
      another Thermococcus isolated from the deep biosphere and a possible
      connection to life in the depths.
AU  - Vannier P
AU  - Marteinsson VT
AU  - Fridjonsson OH
AU  - Oger P
AU  - Jebbar M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 1481-1482.

PMID- 26404588
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Six Nontypeable Haemophilus influenzae Strains That Establish Bacteremia in the Infant Rat Model of Invasive Disease.
PG  - e00899-15
AB  - Haemophilus influenzae is an important cause of invasive disease. The infant rat  is the
      accepted model of invasive H. influenzae disease. Here, we report the genome sequences of six
      nontypeable H. influenzae strains that establish bacteremia in the infant rat.
AU  - VanWagoner TM
AU  - Morton DJ
AU  - Seale TW
AU  - Mussa HJ
AU  - Cole BK
AU  - Whitby PW
AU  - Stull TL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00899-15.

PMID- 15948703
VI  - 70
DP  - 2005
TI  - Enzymatic DNA methylation is an epigenetic control for genetic functions of the cell.
PG  - 598-611
AB  - In eukaryotic cells nuclear DNA is subjected to enzymatic methylation resulting in formation
      of 5-methylcytosine residues mainly in CG and
      CNG sequences. In plants and animals, this DNA methylation is species-,
      tissue-, and organelle-specific. It changes (diminishes) with age and
      is regulated by hormones. On the other hand, genome methylation can
      control hormonal signal. There are replicative and postreplicative DNA
      methylations. They are served by multiple DNA-methyl-transferases with
      different site specificity. Replication is accompanied by appearance of
      hemimethylated sites in DNA; pronounced asymmetry of DNA chain
      methylation disappears at the end of the cell cycled a model of
      regulation of replication by DNA methylation is suggested. DNA
      methylation controls all genetic processes in the cell (replication,
      transcription, DNA repair, recombination, gene transposition) and it is
      a mechanism of cell differentiation, gene discrimination, and
      silencing. Prohibition of DNA methylation stops development
      (embryogenesis), switches on apoptosis, and is usually lethal.
      Distortions in DNA methylations result in cancerous cell
      transformation, and the DNA methylation pattern is one of the safe
      cancer diagnostics at early stages of carcinogenesis. The malignant
      cell has a different DNA methylation pattern and a set of
      DNA-methyltransferase activities expressed as compared with normal
      cells. Inhibition of DNA methylation in plants is accompanied by
      induction of genes of seed storage proteins and flowering. In
      eukaryotes one and the same gene can be methylated both on cytosine and
      adenine residues; thus, there are, at least, two different and probably
      interdependent systems of DNA methylation in the cell. First higher
      eukaryotic adenine DNA-methyltransferase was isolated from plants; this
      enzyme methylates DNA with formation of N-6-methyladenine residues in
      the sequence TGATCA -> TGm(6)ATCA. Plants have AdoMet-dependent
      endonucleases sensitive to DNA methylation status, therefore, like
      microorganisms, plants seem to have a restriction-modification (R-S)
      system. Revelation of an essential role of DNA methylation in the
      regulation of genetic processes has laid a foundation for and
      materialized epigenetics and epigenomics.
AU  - Vanyushin BF
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2005 70: 598-611.

PMID- 16570846
VI  - 301
DP  - 2006
TI  - DNA methylation in plants.
PG  - 67-122
AB  - DNA in plants is highly methylated, containing 5-methylcytosine (m(5)C) and N-6-methyladenine
      (m(6)A); m(5)C is located mainly in symmetrical CG and CNG sequences but it may occur also in
      other non-symmetrical contexts. m(6)A but not m(5)C was found in plant mitochondrial DNA. DNA
      methylation in plants is species-, tissue-, organelle- and age-specific. It is controlled by
      phytohormones and changes on seed germination, flowering and under the influence of various
      pathogens (viral, bacterial, fungal). DNA methylation controls plant growth and development,
      with particular involvement in regulation of gene expression and DNA replication. DNA
      replication is accompanied by the appearance of under-methylated, newly formed DNA strands
      including Okazaki fragments; asymmetry of strand DNA methylation disappears until the end of
      the cell cycle. A model for regulation of DNA replication by methylation is suggested.
      Cytosine DNA methylation in plants is more rich and diverse compared with animals. It is
      carried out by the families of specific enzymes that belong to at least three classes of DNA
      methyltransferases. Open reading frames (ORF) for adenine DNA methyltransferases are found in
      plant and animal genomes, and a first eukaryotic (plant) adenine DNA methyltransferase
      (wadmtase) is described; the enzyme seems to be involved in regulation of the mitochondria
      replication. Like in animals, DNA methylation in plants is closely associated with histone
      modifications and it affects binding of specific proteins to DNA and formation of respective
      transcription complexes in chromatin. The same gene (DRM2) in Arabidopsis thaliana is
      methylated both at cytosine and adenine residues; thus, at least two different, and probably
      interdependent, systems of DNA modification are present in plants. Plants seem to have a
      restriction-modification (R-M) system. RNA-directed DNA methylation has been observed in
      plants; it involves de novo methylation of almost all cytosine residues in a region of
      siRNA-DNA sequence identity; therefore, it is mainly associated with CNG and non-symmetrical
      methylations (rare in animals) in coding and promoter regions of silenced genes. Cytoplasmic
      viral RNA can affect methylation of homologous nuclear sequences and it may be one of the
      feedback mechanisms between the cytoplasm and the nucleus to control gene expression.
AU  - Vanyushin BF
PT  - Journal Article
TA  - Curr. Top. Microbiol. Immunol.
JT  - Curr. Top. Microbiol. Immunol.
SO  - Curr. Top. Microbiol. Immunol. 2006 301: 67-122.

PMID- 18205613
VI  - 72
DP  - 2007
TI  - A view of an elemental naturalist at the DNA world (base composition, sequences, methylation).
PG  - 1289-1298
AB  - The pioneering data on base composition and pyrimidine sequences in DNA of pro- and eukaryotes
      are considered , and their significance for the origin of genosystematics is discussed. The
      modern views on specificity and functional role of enzymatic DNA methylation in eukaryotes are
      described. DNA methylation controls all genetic functions and is a mechanism of cellular
      differentiation and gene silencing. A model of regulation of DNA replication by methylation is
      suggested . Adenine DNA methylation in higher eukaryotes ( higher plants) was first observed,
      and it was established that one and the same gene can be methylated at both cytosine and
      adenine moieties. Thus, there are at least two different and seemingly interdependent DNA
      methylation systems present in eukaryotic cells. The first eukaryotic adenine DNA-methyl-
      transferase is isolated from wheat seedlings and described: the enzyme methylates DNA with
      formation of N-6-methylade- nine in the sequence TGATCA -> TGm(6)ATCA. It is found that higher
      plants have endonucleases that are dependent on S- adenosyl-L-methionine (SAM) and sensitive
      to DNA methylation status. Therefore, as in bacteria, plants seem to have a
      restriction-modification (R-M) system. A system of conjugated up- and down-regulation of
      SAM-dependent endonucleases by SAM modulations is found in plants. Revelation of an essential
      role of DNA methylation in regulation of genetic processes is a fundament of materialization
      of epigenetics and epigenomics.
AU  - Vanyushin BF
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2007 72: 1289-1298.

PMID- 2690961
VI  - 54
DP  - 1989
TI  - Cytokinins do not markedly affect the methylation of DNA adenine residues in cell cultures of Escherichia coli B.
PG  - 1666-1672
AB  - 6-Benzylaminopurine (1mg/ml) does not influence the growth of E. coli B cell cultures or the
      number of [8-14C] labeled N6-methyladenine residues in the total DNA [(100 m6A/(A + m6A)=
      1.7].  The growth of bacterial cells in the presence of adenine or cytokinins (6-BAP, kinetin,
      zeatin) (1 mg/ml) was unaccompanied by significant changes in the intracellular content of
      plasmid pBR322.  The mode of restriction by endonuclease CfuI hydrolyzing the Gm6ATC site of
      plasmid pBR322 from E. coli B cells grown in the presence of adenine or one of the
      above-mentioned cytokinins is identical.  These plasmids also have identical restriction
      products with MboI or Sau3AI.  Thus, the cytokinins under study do not markedly affect the
      methylation of adenine residues in total DNA of E. coli B cell cultures and the GATC sequence
      in plasmids pBR322 isolated from these cells.
AU  - Vanyushin BF
AU  - Aleksandrushkina NI
AU  - Agarkova OA
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1989 54: 1666-1672.

PMID- 4936951
VI  - 230
DP  - 1971
TI  - Distribution of N6-methyladenine in DNA of T2 phage and its host Escherichia coli B.
PG  - 25-27
AB  - N6-methyladenine (6-MeAde) and 5-methylcytosine occur as minor bases in
      bacterial and phage DNA and seem to result from the selective methylation of
      adenine and cytosine residues by specific DNA methylases.  Methylation is the
      final stage in DNA synthesis and is essential for the phenomenon of host
      modification of phages; it is one of the mechanisms controlling DNA replication
      in the cell.  A study of the distribution of minor bases in DNA is important
      not only for the elucidation of the specificity and mechanism of action of DNA
      methylases but also for an understanding of the purpose of this methylation.
      Until recently there has been a lack of adequate methods for an analysis of the
      distribution of purines, including 6-MeAde, in DNA.  We have developed a method
      for the specific chemical degradation of DNA into purine sequences, based on
      the hydrolysis of apyrimidinic DNA by aniline, which facilities a study of the
      content and position of 6-MeAde residues in unmodified purine sequences.  By
      means of this method we have hydrolysed E. coli B and T2 phage DNA to yield
      purine sequences and have determined the frequency of different purine
      isostichs (fragments with equal numbers of nucleotide residues) and the amounts
      of 6-MeAde in each.  We have checked that 6-MeAde, and also the isolated purine
      sequences, do not undergo marked degradation either in the course of DNA
      hydrazinolysis or in the subsequent hydrolysis of the apyrimidinic acid by
      aniline.  DNA was isolated from T2 phage and E. coli B cells collected at the
      end of the logarithmic phage of growth, according to the procedure of Marmur,
      with additional phenol deproteinziation.
AU  - Vanyushin BF
AU  - Buryanov YI
AU  - Belozersky AN
PT  - Journal Article
TA  - Nature New Biol.
JT  - Nature New Biol.
SO  - Nature New Biol. 1971 230: 25-27.

PMID- 4618127
VI  - 39
DP  - 1974
TI  - Location of 5-methylcytosine in Escherichia coli and phage DD7 DNA.
PG  - 1293-1301
AB  - After the cultivation of E. coli C Met cells, infected and uninfected by phage
      DD7, with (H3-methyl)-Met, the bacterial and phage DNA were isolated and the
      distribution and location of 5-methylcytosine (MC) were studied in different
      pyrimidine sequences.  Methylcytosine was not found in the monopyrimidine
      fragments of phage DD7 and E. coli C MC DNA and was present mainly in the di-
      and tripyrimidine sequences (about 75% of all the MC).  A small amount of MC
      was found in long pyrimidine units (4-7 long).  The DNAs of different strains
      of E. coli (C and K12) did not differ in frequency of occurrence of MC in
      different isopliths and were very similar to the DNA of phage DD7.  The
      specificity of the methylation of cytosine residues in phage DD7 DNA and its
      host E. coli C was the same.  In phage DD7 and E. coli C-MC DNA MC is located
      in the following sequences: ...Pu-C-MC-Pu...; ...Pu-C-MC-C-Pu...;
      Pu-C-MC-T-Pu...
AU  - Vanyushin BF
AU  - Danilevich VN
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1974 39: 1293-1301.

PMID- 1180970
VI  - 407
DP  - 1975
TI  - On the nature of the cytosine-methylated sequence in DNA of Bacillus brevis var. G.-B.
PG  - 61-72
AB  - On growing the cells of Bacillus brevis S methionine-auxotroph mutant in the
      presence of [Me-3 H] methionine, practically all the radioactivity incorporated
      into DNA is found to exist in 5-methylcytosine and N6-methyladenine.  The
      analysis of pyrimidine isopliths isolated from DNA shows that radioactivity
      only exists in mono- and dinucleotides and the content of 5-methylcytosine in
      R-m5 C-R and R-m5 C-T-R oligonucleotides is equal.  The analysis of
      dinucleotides isolated from DNA by means of pancreatic DNAase hydrolysis allows
      the nature of purine residues neighbouring 5-methylcytosine to be identified
      and shows that 5-methylcytosine localizes in G-m5 C-A and G-m5 C-T-R fragments.
      B. brevis S DNA methylase modifying cytosine residues recognizes the GC(A/T)GC
      degenerate nucleotide sequence which is a part of the following complementary
      structure with a two-fold rotational axis of symmetry: (5')
      ...N'-G-C*-T-G-C-N... (3') (3') ...N -C-G-A-C*-G-N'... (5') (Methylated
      cytosine residues are asterisked).  Cytosine-modifying DNA methylase activity
      is isolated from B. brevis cells; it is capable of methylating in vitro
      homologous and heterologous DNA.  Hence DNA in bacterial cells can be
      undermethylated.  This enzyme methylates cytosine residues in native and
      denatured DNA in the same nucleotide sequences.  Specificity of methylation of
      cytosine residues in vitro and in vivo does not depend on the nature of
      substrate DNA.  DNA methylases of different variants of B. brevis (R, S, P+,
      P-) methylate cytosine residues in the same nucleotide sequences.  It means
      that specificity or methylation of DNA cytosine residues in the cells of
      different variants of B. brevis is the same.
AU  - Vanyushin BF
AU  - Dobritsa AP
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1975 407: 61-72.

PMID- 1219384
VI  - 9
DP  - 1975
TI  - Specificity of the methylation of the cytosine residues in the DNA of Bacillus brevis var. G-B.
PG  - 283-295
AB  - After the growth of a methionine-auxotrophic mutant of Bacillus brevis S in the
      prsence of [methyl-3H]-methionine, practically all the label incorporated into
      DNA was detected in 5-methylcytosine and N6-methyladenine.  In an analysis of
      the pyrimidine isopliths isolated from DNA, it was shown that all the
      radioactivity of MC is uniformly contained in the oligonucleotides Pur-MC-Pur
      and Pur-MC-T-Pur.  An analysis of the dinucleotides isolated from the DNA by
      pancreatic DNAase made it possible to establish that MC is localized in the
      fragments G-MC-A and G-MC-T-Pur.  DNA methylase of B. brevis S, which modifies
      cytosine residues, recognizes the degenerate nucleotide sequence GC(T/A)GC,
      which is included in the complementary structure with second-order rotational
      symmetry:   (5') ...N'-G-MC-T-G-C-N...(3') (3') ....N-C-G-A-MC-G-N'...(5') an
      extract possessing cytosine-modifying methylase activity and capable of
      methylating homologous and heterologous DNA's in vitro was isolated from cells
      of B. brevis.  This means that in the cells of the bacterium, DNA may be
      partially undermethylated.  This enzyme methylates cytosine residues in native
      and denatured DNA's in the same nucleotide sequence.  In comparison with the
      native DNA, in the denatured DNA the level of methylation of the adenine
      residues, but not of the cytosine residues, is decreased.  The specificity of
      the methylation of the cytosine residues in vitro and in vivo is the same and
      does not depend on the nature of the substrate DNA's (calf thymus, Pseudomonas
      aeruginosa, etc.).  DNA methylases from different variants of B. brevis
      (R,S,P+,P-) methylate the cytosine residues in the same nucleotide sequences.
      Consequently, the specificity of the methylation of the cytosine residues in
      the cells of different variants of B. brevis is the same.
AU  - Vanyushin BF
AU  - Dobritsa AP
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1975 9: 283-295.

PMID- 8799463
VI  - 39
DP  - 1996
TI  - Drosophila melanogaster genomic DNA sequence homologous to mammalian cytosine DNA-methyltransferase gene.
PG  - 353-358
AB  - Using the Southern blotting procedure we have shown that Drosophila genomic
      DNA hybridizes with 4423-bp C-terminal fragment of murine cytosine DNA-methyltransferase
      gene.  Thus, the Drosophila genome has a sequence homologous to the mammalian cytosine DNA-
      methyltransferase gene.  We assume that DNA methylation most likely responsible for strong CpG
      suppression in the Drosophila genome mainly was catalyzed by a cytosine DNA-methyltransferase
      that has since been lost.
AU  - Vanyushin BF
AU  - Poirier LA
PT  - Journal Article
TA  - Biochem. Mol. Biol. Int.
JT  - Biochem. Mol. Biol. Int.
SO  - Biochem. Mol. Biol. Int. 1996 39: 353-358.

PMID- 24115545
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Bacillus thuringiensis var. thuringiensis Strain T01-328, a Brazilian Isolate That Produces a Soluble Pesticide Protein, Cry1Ia.
PG  - e00817-13
AB  - Bacillus thuringiensis var. thuringiensis strain T01-328, isolated from Cubatao county (Sao
      Paulo State, Brazil), produces a soluble pesticide protein, Cry1Ia,
      during vegetative growth. Here, we report the 7.089-Mbp draft genome sequence,
      composed of a 5.5-Mb chromosome and 14 plasmids, which is the largest B.
      thuringiensis genome sequenced to date.
AU  - Varani AM
AU  - Lemos MV
AU  - Fernandes CC
AU  - Lemos EG
AU  - Alves EC
AU  - Desiderio JA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00817-13.

PMID- 14582198
VI  - 2
DP  - 1982
TI  - In vitro methylation of the BsuRI (5'-GGCC-3') sites in the E2a region of adenovirus type 2 DNA does not affect expression in Xenopus laevis oocytes.
PG  - 1574-1580
AB  - The early region 2a (E2a) of adenovirus type 2 (Ad2) DNA codes for a 72,000-dalton DNA-binding
      protein and is expressed in the Ad2-transformed hamster cell line HE1 but not in cell lines
      HE2 and HE3 (H. Esche, J. Virol. 41:1076-1082, 1982; K. Johansson et al., J. Virol.
      27:628-639, 1978). An inverse correlation between DNA methylation at the 5'-CCGG-3' sites of
      the E2a region and of gene expression in these cell lines has been observed (L. Vardimon et
      al., Nucleic Acids Res. 8:2461-2473, 1980). When the cloned E2a region of Ad2 DNA is
      methylated in vitro at the 5'-CCGG-3' sites, the gene is not transcribed after being
      injected into the nuclei of Xenopus laevis oocytes, whereas unmethylated DNA is expressed (L.
      Vardimon et al., Eur. J. Cell Biol. 25:13-15, 1981; L. Vardimon et al., Proc. Natl. Acad. Sci.
      U.S.A. 79:1073-1077, 1982). These data demonstrate that DNA methylation is directly involved
      in the shut-off of transcription. In the present communication we investigated in detail the
      control region of the gene for the DNA-binding protein in Ad2-transformed cell lines and
      showed that the first late control region (map coordinate 72 on the viral DNA) of the E2a
      region is present in its entirety in cell lines HE1, HE2, and HE3. The HaeIII sites
      (5'-GGCC-3') in the E2a region in all three cell lines were not methylated. When the DNA
      methyltransferase BsuRI was used, all 5'-GGCC-3' sites in the cloned E2a region of Ad2 DNA
      were methylated in vitro. It was shown that methylation of these sites did not inhibit the
      expression of this viral gene in X. laevis oocytes. Thus, for methylation to affect gene
      expression in the E2a region it has to occur at specific sites (e.g., 5'-CCGG-3') which may
      be different for other genes.
AU  - Vardimon L
AU  - Gunthert U
AU  - Doerfler W
PT  - Journal Article
TA  - Mol. Cell. Biol.
JT  - Mol. Cell. Biol.
SO  - Mol. Cell. Biol. 1982 2: 1574-1580.

PMID- 6328508
VI  - 81
DP  - 1984
TI  - In Z-DNA the sequence G-C-G-C is neither methylated by HhaI methyltransferase nor cleaved by HhaI restriction endonuclease.
PG  - 3268-3272
AB  - Plasmids carrying 24- or 32-base-pair inserts of alternating (dG-dC) residues
      were used to analyze the level of methylation of the G-C-G-C sites by HhaI DNA
      methyltransferase and their cleavage by HhaI endonuclease in the B-DNA or Z-DNA
      conformation.  In supercoiled plasmids in which the inserts formed Z-DNA, the
      extent of methylation at the insert G-C-G-C sites was dramatically lower than
      the level of methylation at the G-C-G-C sites located outside the insert in the
      same plasmid.  Similarly, cleavage by HhaI endonuclease was sharply lowered
      when the insert was in the Z-DNA form.  In the relaxed plasmid, all its G-C-G-C
      sites were methylated to the same extent and the unmethylated sites were
      readily cleaved.  After treatment with the methylase, the supercoiled plasmid
      was linearized and then digested with Hha restriction endonuclease.  This
      exposed unmethylated G-C-G-C sites from the insert that had been protected
      against cleavage in the Z conformation.  A chemical reaction was used to study
      the distribution of the unmethylated cytosine residues.  No accumulation of
      unmethylated cytosine residues was found anywhere along the entire 32-base-pair
      insert, which is consistent with a cooperative B-Z transition.
AU  - Vardimon L
AU  - Rich A
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1984 81: 3268-3272.

PMID- 23105085
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence Determination for Cystic Fibrosis and Chronic Granulomatous Disease Burkholderia multivorans Isolates.
PG  - 6356-6357
AB  - Burkholderia multivorans is a Gram-negative bacterium and a member of the Burkholderia cepacia
      complex, which is frequently associated with respiratory
      infections in people with cystic fibrosis (CF) and chronic granulomatous disease
      (CGD). We are reporting the genome sequences of 4 B. multivorans strains, 2 from
      CF patients and 2 from CGD patients.
AU  - Varga JJ
AU  - Losada L
AU  - Zelazny AM
AU  - Brinkac L
AU  - Harkins D
AU  - Radune D
AU  - Hostetler J
AU  - Sampaio EP
AU  - Ronning CM
AU  - Nierman WC
AU  - Greenberg DE
AU  - Holland SM
AU  - Goldberg JB
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6356-6357.

PMID- 24136849
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences of Burkholderia cenocepacia ET12 Lineage Strains K56-2 and BC7.
PG  - e00841-13
AB  - The Burkholderia cepacia complex (BCC) is a group of closely related bacteria that are
      responsible for respiratory infections in immunocompromised humans, most
      notably those with cystic fibrosis (CF). We report the genome sequences for
      Burkholderia cenocepacia ET12 lineage CF isolates K56-2 and BC7.
AU  - Varga JJ
AU  - Losada L
AU  - Zelazny AM
AU  - Kim M
AU  - McCorrison J
AU  - Brinkac L
AU  - Sampaio EP
AU  - Greenberg DE
AU  - Singh I
AU  - Heiner C
AU  - Ashby M
AU  - Nierman WC
AU  - Holland SM
AU  - Goldberg JB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00841-13.

PMID- 27198013
VI  - 4
DP  - 2016
TI  - First Genome Sequence of Leptospira interrogans Serovar Pomona, Isolated from a Bovine Abortion.
PG  - e00345-16
AB  - Leptospirosis is a widespread zoonosis and a re-emergent disease of global distribution with
      major relevance in veterinary production. Here, we report the
      whole-genome sequence of Leptospira interrogans serovar Pomona strain AKRFB,
      isolated from a bovine abortion during a leptospirosis outbreak in Argentina.
AU  - Varni V
AU  - Koval A
AU  - Nagel A
AU  - Ruybal P
AU  - Caimi K
AU  - Amadio AF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00345-16.

PMID- 
VI  - 25
DP  - 1999
TI  - Immobilization of the restriction endonuclease EcoRI.  Usefulness of a polyclonal antibody support.
PG  - 172-176
AB  - The restriction enzyme EcoRI has been immobilized by using an immunoaffinity-based procedure
      on Sepharose 4B.  The antibody support, prepared by coupling the gamma-globulin fraction of
      serum of immunized rabbits to CNBr-activated Sepharose-4B, was highly effective in binding
      EcoRI from solution although only about half of the bound activity appeared to be expressed by
      the immobilized preparations.  Restriction activity of EcoRI immobilized on the antibody
      support was indistinguishable from that of soluble enzyme on the linear phage-DNA and
      supercoiled plasmids pBR322 and pBHLUC P.  Binding to the antibody support markedly enhanced
      the resistance of EcoRI to heat inactivation, and the preparation, unlike the native enzyme,
      retained significant activity after exposure to a temperature of 65 C.  It was also possible
      to immobilize EcoRI directly from the cell lysates of Escherichia coli pMB4, an EcoRI
      overproducing strain.  The immobilized preparation did not possess nonspecific nuclease
      activity that was prominent in the lysates, suggesting specificity in the binding of EcoRI to
      the antibody support.
AU  - Varshney H
AU  - Iqbal J
AU  - Seleemuddin M
PT  - Journal Article
TA  - Enzyme Microb. Technol.
JT  - Enzyme Microb. Technol.
SO  - Enzyme Microb. Technol. 1999 25: 172-176.

PMID- 
VI  - 37
DP  - 2001
TI  - Immobilization of SpA::EcoRI on IgG support improves the thermal stability of restriction activity.
PG  - 275-278
AB  - A plasmid-harbouring E. coli JM109 (3P) strain was cultivated for the overproduction of the
      genetically engineered fusion protein SpA::EcoRI. The fusion protein could be affinity bound
      selectively and directly from the 25-50% ammonium sulphate fraction of the lysate of E. coli
      JM109 on to IgG-Sepharose.  The preparation obtained thus exhibited high restriction activity
      on lambda DNA and linearized the plasmids pBR322 and pUC19.  As compared to the native EcoRI
      the activity of the immobilized preparation was more resistant to thermal inactivation.
AU  - Varshney H
AU  - Saleemuddin M
AU  - Rhee JI
AU  - Schugerl K
PT  - Journal Article
TA  - Process. Biochem.
JT  - Process. Biochem.
SO  - Process. Biochem. 2001 37: 275-278.

PMID- 23354103
VI  - 31
DP  - 2013
TI  - Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement.
PG  - 240-246
AB  - Chickpea (Cicer arietinum) is the second most widely grown legume crop after soybean,
      accounting for a substantial proportion of human dietary nitrogen intake
      and playing a crucial role in food security in developing countries. We report
      the approximately 738-Mb draft whole genome shotgun sequence of CDC Frontier, a
      kabuli chickpea variety, which contains an estimated 28,269 genes. Resequencing
      and analysis of 90 cultivated and wild genotypes from ten countries identifies
      targets of both breeding-associated genetic sweeps and breeding-associated
      balancing selection. Candidate genes for disease resistance and agronomic traits
      are highlighted, including traits that distinguish the two main market classes of
      cultivated chickpea--desi and kabuli. These data comprise a resource for chickpea
      improvement through molecular breeding and provide insights into both genome
      diversity and domestication.
AU  - Varshney RK et al
PT  - Journal Article
TA  - Nat. Biotechnol.
JT  - Nat. Biotechnol.
SO  - Nat. Biotechnol. 2013 31: 240-246.

PMID- 24285649
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Pseudomonas sp. Strain CMAA 1215, a Plant Growth-Promoting Bacterium Isolated from a Brazilian Mangrove.
PG  - e00995-13
AB  - The aim of this study was to sequence the genome of the plant growth-promoting Pseudomonas sp.
      strain CMAA 1215, an osmotolerant bacterium isolated from
      mangrove soil.
AU  - Vasconcellos RL
AU  - Mendes R
AU  - Taketani RG
AU  - Zucchi TD
AU  - Melo IS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00995-13.

PMID- 16077101
VI  - 187
DP  - 2005
TI  - Swine and Poultry Pathogens: the Complete Genome Sequences of Two Strains of Mycoplasma hyopneumoniae and a Strain of Mycoplasma synoviae.
PG  - 5568-5577
AB  - This work reports the results of analyses of three complete mycoplasma genomes, a pathogenic
      (7448) and a nonpathogenic (J) strain of the swine
      pathogen Mycoplasma hyopneumoniae and a strain of the avian pathogen
      Mycoplasma synoviae; the genome sizes of the three strains were 920,079
      bp, 897,405 bp, and 799,476 bp, respectively. These genomes were compared
      with other sequenced mycoplasma genomes reported in the literature to
      examine several aspects of mycoplasma evolution. Strain-specific regions,
      including integrative and conjugal elements, and genome rearrangements and
      alterations in adhesin sequences were observed in the M. hyopneumoniae
      strains, and all of these were potentially related to pathogenicity.
      Genomic comparisons revealed that reduction in genome size implied loss of
      redundant metabolic pathways, with maintenance of alternative routes in
      different species. Horizontal gene transfer was consistently observed
      between M. synoviae and Mycoplasma gallisepticum. Our analyses indicated a
      likely transfer event of hemagglutinin-coding DNA sequences from M.
      gallisepticum to M. synoviae.
AU  - Vasconcelos AT et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2005 187: 5568-5577.

PMID- 27789642
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Methyloligella halotolerans capital ES, Cyrillic2T, a New Halotolerant Methylotroph, Accumulating Poly-3-Hydroxybutyrate and Ectoine.
PG  - e01189-16
AB  - Methyloligella halotolerans capital ES, Cyrillic2T is a moderate halophilic obligate
      methylotroph, accumulating ultra-high-molecular-weight
      poly-3-hydroxybutyrate (up to 8 to 10 MDa) from methanol. Here we report a draft
      genome and annotation of Methyloligella halotolerans C2T (VKM B-2706T = CCUG
      61687T = DSM 25045T).
AU  - Vasilenko OV
AU  - Doronina NV
AU  - Shmareva MN
AU  - Tarlachkov SV
AU  - Trotsenko YA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01189-16.

PMID- 27313291
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of 'Rathayibacter tanaceti' Strain VKM Ac-2596 Isolated from Tanacetum vulgare Infested by a Foliar Nematode.
PG  - e00512-16
AB  - The draft genome of 'Rathayibacter tanaceti' VKM Ac-2596 is 3.17 Mb in size with  an average
      G+C content of 70.7% and comprises at least two nonidentical copies of
      ribosomal small subunit (SSU-rRNA) genes. The semiconductor sequencing platform
      Ion Torrent was used.
AU  - Vasilenko OV
AU  - Starodumova IP
AU  - Tarlachkov SV
AU  - Dorofeeva LV
AU  - Avtukh AN
AU  - Evtushenko LI
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00512-16.

PMID- 9156557
VI  - 61
DP  - 1996
TI  - A site-specific endonuclease BspR7I from Thermophilic strain.
PG  - 2147-2157
AB  - A site-specific endonuclease BspR7I preparation has been isolated and purified to homogeneity
      from the thermophilic strain Bacillus sp. R7.  DNA cleavage proceeds according to the scheme
      5'-CC/TNAGC-3' 3'-GGANT/CC-5' and thus the enzyme belongs to the second class of
      restriction endonucleases and is an isoschizomer of Bsu36I.  The isolated protein has a
      molecular mass of 37 kD and is present in solution in the form of a monomer.  BspR7I is active
      over a wide range of temperatures, from 37 to 48oC.  The enzyme is relatively stable.
AU  - Vasiljeva LY
AU  - Zheleznaya LA
AU  - Matvienko NI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1996 61: 2147-2157.

PMID- 10851033
VI  - 65
DP  - 2000
TI  - Cloning and expression of a new site-specific methyltransferase M.SscL1I from Staphylococcus sp. L1.
PG  - 565-570
AB  - The gene of the new site-specific methyltransferase M.SscL1I belonging to the same
      modification-restriction system as the previously described site-specific endonuclease
      SscL1I has been cloned from the natural strain Staphylococcus sp. L1. A plasmid to express the
      methylase gene under control of the T7 phage-specific promoter has been constructed.
      Conditions were found to express the recombinant methylase M.SscL1I and to purify it to near
      homogeneity. It is shown that the methylase modifies the adenine base in the recognition site
      5'-GANTC-3'.
AU  - Vasiljeva LY
AU  - Zheleznaya LA
AU  - Matvienko NI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 2000 65: 565-570.

PMID- 9526117
VI  - 63
DP  - 1998
TI  - Site-specific endonuclease SscL1I from strain Staphylococcus species L1.
PG  - 212-218
AB  - A site-specific endonuclease SscL1I preparation has been isolated and purified to near
      homogeneity from the strain Staphylococcus sp. L1 without admixtures of other nuclease
      activity.  DNA cleavage proceeds according to the scheme: 5'-G/ANTC-3' 3'-CTNA/G-5, and
      thus the isolated enzyme is an isoschizomer of restriction endonuclease HinfI and belongs to
      the second class of restriction endonucleases.  SscL1I works over a broad range of temperature
      and pH.  The enzyme is characterized by high stability during storage.
AU  - Vasiljeva LY
AU  - Zheleznaya LA
AU  - Matvienko NI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1998 63: 212-218.

PMID- 26634752
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Agreia bicolorata Strain AC-1804, a Producer of Large Amounts of Carotenoid Pigments, Isolated from Narrow Reed Grass Infected by the  Phytoparasitic Nematode.
PG  - e01383-15
AB  - Here, we report the draft genome sequence of Agreia bicolorata strain AC-1804, isolated from
      narrow reed grass galls induced by a plant-parasitic nematode which
      is able to produce large amounts of carotenoid pigments. The draft genome
      sequence of 3,919,485 bp provides a resource for carotenoid pathway research.
AU  - Vasilyev I
AU  - Siniagina M
AU  - Malanin S
AU  - Boulygina E
AU  - Grygoryeva T
AU  - Yarullina D
AU  - Ilinskaya O
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01383-15.

PMID- 2992515
VI  - 10
DP  - 1985
TI  - Isolation and partial characterization of BstVI, a thermostable isoschizomer of XhoI.
PG  - 655-662
AB  - A type II restriction endonuclease, which has been named BstVI, was isolated and partially
      purified from a spore-forming, gram-positive thermophilic bacilli.  On the basis of its
      digestion patterns on varous DNA's, it was concluded that this enzyme is an isoschizomer of
      XhoI, isolated originally from Xanthomonas holcicola.  Besides being highly thermostable, the
      enzyme is produced in very large amounts by this bacterial strain.  A single purification step
      renders it free of unspecific nucleases and suitable for performing restriction analysis and
      cloning experiments.
AU  - Vasquez C
PT  - Journal Article
TA  - Biochem. Int.
JT  - Biochem. Int.
SO  - Biochem. Int. 1985 10: 655-662.

PMID- 3153122
VI  - 21
DP  - 1988
TI  - Structural and biochemical characterization of the modification-restriction system of Bacillus stearothermophilus V.
PG  - r338
AB  - None
AU  - Vasquez C
PT  - Journal Article
TA  - Arch. Biol. Med. Exp. (Santiago)
JT  - Arch. Biol. Med. Exp. (Santiago)
SO  - Arch. Biol. Med. Exp. (Santiago) 1988 21: r338.

PMID- 3838039
VI  - 18
DP  - 1985
TI  - Aislamiento Y caracterizacion de endonucleasas termoestables:  BstVI, un isosquizomero de XhoI (isolation and characterization of thermostable endonucleases:  BstVI, an isoschizomer of XhoI).
PG  - r371
AB  - Recientemente hemos purificado una endonucleasa de restriccion tipo II, la cual
      fue aislade de un bacilo termofilico gram positivo.  De acuerdo a pruebas
      microbiologicas estandares, la bacteria resulto ser del tipo Bacillus
      stearothersophilus y la enzima fue denominada BstVI.  Sobre la base de los
      patrones de digestion de los diversos DNAs utilizados como sustrato, hemos
      concluido que BstVI es un isosquizomero de XhoI, aislada originalmente de
      Xanthomonas holcicola.  Ademas de ser muy termoestable (tempertura optima de
      75C), BstVI es producida en gran cantidad por esta cepa bacteriana.
      Practicamente un solo paso de purificacion hace possible la eliminacion de
      nucleasas inespecificas y port lo tanto, su uso con fines de analisis de
      restriccion y de clonamiento molecular.  Se han determinado algunas de las
      condiciones optimas para la activated enzimatica, ademas de probar la
      estabilidad de la enzima frente a una serie de agentes desnaturantes de
      proteinas.
AU  - Vasquez C
AU  - Adasme A
AU  - Gonzalez E
PT  - Journal Article
TA  - Arch. Biol. Med. Exp. (Santiago)
JT  - Arch. Biol. Med. Exp. (Santiago)
SO  - Arch. Biol. Med. Exp. (Santiago) 1985 18: r371.

PMID- 1864512
VI  - 102
DP  - 1991
TI  - Cloning the BstVI restriction-modification system in Escherichia coli.
PG  - 83-85
AB  - A standard DNA modification methyltransferase (MTase) selection protocol was
      followed to clone the BstVI restriction and modification system from Bacillus
      stearothermophilus in Escherichia coli.  Both genes were contained in a 4.4-kb
      EcoRI fragment from B. stearothermophilus V chromosomal DNA.  The heterologous
      expression of these genes did not depend on their orientation in the vector,
      suggesting that the genes are expressed in E. coli under the control of
      promoters located on the cloned fragment.  Subcloning experiments demonstrated
      that the bstVIR gene was expressed in the absence of its cognate MTase.
AU  - Vasquez C
AU  - Saavedra C
AU  - Gonzalez E
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1991 102: 83-85.

PMID- Not included in PubMed...
VI  - 15
DP  - 1982
TI  - The genus Thermus: restriction endonucleases and modification methylases.
PG  - 417-421
AB  - This work reviews the present knowledge of the site-specific endonucleases and
      methylases involved in the restriction-modification systems in bacteria
      belonging to the genus Thermus.  In addition, we describe part of our work
      concerning the purification and properties of these enzymes from Thermus
      thermophilus HB8 and Thermus flavus AT-62.
AU  - Vasquez C
AU  - Vicuna R
PT  - Journal Article
TA  - Arch. Biol. Med. Exp. (Santiago)
JT  - Arch. Biol. Med. Exp. (Santiago)
SO  - Arch. Biol. Med. Exp. (Santiago) 1982 15: 417-421.

PMID- 10594225
VI  - 40
DP  - 2000
TI  - Nucleotide sequence of the gene encoding the BstLVI DNA methyltransferase: comparison with other amino-DNA methyltransferases.
PG  - 114-118
AB  - The nucleotide sequence of a 2837-base pairs (bp) EcoRI-PvuI fragment of Bacillus
      stearothermophilus LV chromosomal DNA encoding the bstLVIM gene was determined. It revealed a
      large open reading frame (ORF) of 1737 bp specifying a methylase of 579 amino acid (aa)
      residues and Mr 66,831. This was in agreement with the size estimated for the M. BstLVI (
      approximately 67 kDa) purified from Escherichia coli cells harboring a recombinant plasmid
      containing the bstLVIM gene and with results of transcription-translation experiments
      performed in vitro. Upstream the bstLVIM gene and in the opposite transcriptional orientation,
      there is an 81-aa ORF that showed great homology with the regulatory C proteins identified in
      other type II restriction and modification (R-M) systems. This 81-aa ORF precedes a truncated
      ORF of 86 aa which in turn may represent the structural gene for the BstLVI restriction
      endonuclease.
AU  - Vasquez CC
AU  - Saavedra CP
AU  - Pichuantes SE
PT  - Journal Article
TA  - Curr. Microbiol.
JT  - Curr. Microbiol.
SO  - Curr. Microbiol. 2000 40: 114-118.

PMID- 22509013
VI  - 109
DP  - 2012
TI  - Promiscuous restriction is a cellular defense strategy that confers fitness advantage to bacteria.
PG  - E1287-1293
AB  - Most bacterial genomes harbor restriction-modification systems, encoding a REase  and its
      cognate MTase. On attack by a foreign DNA, the REase recognizes it as
      nonself and subjects it to restriction. Should REases be highly specific for
      targeting the invading foreign DNA? It is often considered to be the case.
      However, when bacteria harboring a promiscuous or high-fidelity variant of the
      REase were challenged with bacteriophages, fitness was maximal under conditions
      of catalytic promiscuity. We also delineate possible mechanisms by which the
      REase recognizes the chromosome as self at the noncanonical sites, thereby
      preventing lethal dsDNA breaks. This study provides a fundamental understanding
      of how bacteria exploit an existing defense system to gain fitness advantage
      during a host-parasite coevolutionary 'arms race.'
AU  - Vasu K
AU  - Nagamalleswari E
AU  - Nagaraja V
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2012 109: E1287-1293.

PMID- 23963701
VI  - 41
DP  - 2013
TI  - Increasing cleavage specificity and activity of restriction endonuclease KpnI.
PG  - 9812-9824
AB  - Restriction enzyme KpnI is a HNH superfamily endonuclease requiring divalent metal ions for
      DNA cleavage but not for binding. The active site of KpnI can accommodate metal ions of
      different atomic radii for DNA cleavage. Although Mg2+ ion higher than 500 muM mediates
      promiscuous activity, Ca2+ suppresses the promiscuity and induces high cleavage fidelity.
      Here, we report that a conservative mutation of the metal-coordinating residue D148 to Glu
      results in the elimination of the Ca2+-mediated cleavage but imparting high cleavage fidelity
      with Mg2+. High cleavage fidelity of the mutant D148E is achieved through better
      discrimination of the target site at the binding and cleavage steps. Biochemical experiments
      and molecular dynamics simulations suggest that the mutation inhibits Ca2+-mediated cleavage
      activity by altering the geometry of the Ca2+-bound HNH active site. Although the D148E mutant
      reduces the specific activity of the enzyme, we identified a suppressor mutation that
      increases the turnover rate to restore the specific activity of the high fidelity mutant to
      the wild-type level. Our results show that active site plasticity in coordinating different
      metal ions is related to KpnI promiscuous activity, and tinkering the metal ion coordination
      is a plausible way to reduce promiscuous activity of metalloenzymes.
AU  - Vasu K
AU  - Nagamalleswari E
AU  - Zahran M
AU  - Imhof P
AU  - Xu SY
AU  - Zhu Z
AU  - Chan SH
AU  - Nagaraja V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2013 41: 9812-9824.

PMID- 23471617
VI  - 77
DP  - 2013
TI  - Diverse Functions of Restriction-Modification Systems in Addition to Cellular Defense.
PG  - 53-72
AB  - Restriction-modification (R-M) systems are ubiquitous and are often considered primitive
      immune systems in bacteria. Their diversity and prevalence across the prokaryotic kingdom are
      an indication of their success as a defense mechanism against invading genomes. However, their
      cellular defense function does not adequately explain the basis for their immaculate
      specificity in sequence recognition and nonuniform distribution, ranging from none to too
      many, in diverse species. The present review deals with new developments which provide
      insights into the roles of these enzymes in other aspects of cellular function. In this
      review, emphasis is placed on novel hypotheses and various findings that have not yet been
      dealt with in a critical review. Emerging studies indicate their role in various cellular
      processes other than host defense, virulence, and even controlling the rate of evolution of
      the organism. We also discuss how R-M systems could have successfully evolved and be involved
      in additional cellular portfolios, thereby increasing the relative fitness of their hosts in
      the population.
AU  - Vasu K
AU  - Nagaraja V
PT  - Journal Article
TA  - Microbiol. Mol. Biol. Rev.
JT  - Microbiol. Mol. Biol. Rev.
SO  - Microbiol. Mol. Biol. Rev. 2013 77: 53-72.

PMID- 18329982
VI  - 1784
DP  - 2008
TI  - Structural integrity of the Beta Beta Alpha-Metal finger motif is required for DNA binding and stable protein-DNA complex formation in R.KpnI.
PG  - 269-275
AB  - Restriction endonuclease (REase) R.KpnI from Klebsiella pneumoniae is a homodimeric enzyme,
      which recognizes palindromic sequence GGTAC|C and
      cleaves generating 4 base 3' end overhangs. R.KpnI belongs to the HNH
      superfamily of nucleases, which are characterized by the presence of the
      beta beta alpha-Me finger motif. Structurally, this motif consists of a
      twisted beta-hairpin followed by an alpha-helix, and serves as a scaffold
      for side chains of residues involved in co-ordination of a divalent metal
      ion that is required for catalysis. Homology modeling studies of R.KpnI
      suggested a crossover structure for the alpha-helix, which could possibly
      form dimeric interface and/or structural scaffold for the active site. We
      have evaluated the role of the residues present in this alpha-helix in
      intersubunit interactions and/or stabilization of the active site. We show
      here that mutations of residues in the alpha-helix lead to a loss of the
      enzyme activity, but not dimerization ability. Intrinsic fluorescence and
      circular dichroism studies revealed that the loss of function phenotype
      was due to the structural perturbation of the beta beta alpha-Me finger
      motif. The results of mutational analysis suggest that the alpha-helix of
      the beta beta alpha-Me finger of R.KpnI plays an important role for the
      stability of the protein-DNA complex.
AU  - Vasu K
AU  - Saravanan M
AU  - Bujnicki JM
AU  - Nagaraja V
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 2008 1784: 269-275.

PMID- 20734974
VI  - 49
DP  - 2010
TI  - Generation of a Manganese Specific Restriction Endonuclease with Nicking Activity.
PG  - 8425-8433
AB  - A typical feature of type II restriction endonucleases (REases) is their obligate sequence
      specificity and requirement for Mg2+ during
      catalysis. R.KpnI is an exception. Unlike most other type II REases,
      the active site of this enzyme can accommodate Mg2+, Mn2+, Ca2+, or
      Zn2+ and cleave DNA. The enzyme belongs to the HNH superfamily of
      nucleases and is characterized by the presence of a beta beta alpha-Me
      finger motif. Residues D148, H149, and Q175 together form the HNH
      active site and are essential for Mg2+ binding and catalysis. The
      unique ability of the enzyme to cleave DNA in the presence of different
      metal ions is exploited to generate mutants that are specific to one
      particular metal ion. We describe the generation of a Mn2+-dependent
      sequence specific endonuclease, defective in DNA cleavage with Mg2+ and
      other divalent metal ions. In the engineered mutant, only Mn2+ is
      selectively bound at the active site, imparting Mn2+-mediated cleavage.
      The mutant is impaired in concerted double-stranded DNA cleavage,
      leading to accumulation of nicked intermediates. The nicking activity
      of the mutant enzyme is further enhanced by altered reaction
      conditions. The active site fluidity of R Eases allowing flexible
      accommodation of catalytic cofactors thus forms a basis for engineering
      selective metal ion-dependent REase additionally possessing nicking
      activity.
AU  - Vasu K
AU  - Saravanan M
AU  - Rajendra BVRN
AU  - Nagaraja V
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2010 49: 8425-8433.

PMID- 2827015
VI  - 197
DP  - 1988
TI  - Evidence for a receptor-mediated endocytosis of AluI in chinese hamster ovary cells.
PG  - 109-116
AB  - Pretreatment of Chinese hamster ovary cells with proteases or with NaN3 leads to less
      chromosomal aberrations when the cells are posttreated with AluI compared to the treatment of
      cells with AluI alone.  The same result is obtained when the cells are treated with AluI at
      0oC instead of 37oC.  The cells recover from the protease treatment when they are kept in
      medium before treatment with AluI.  These results are interpreted to mean that AluI is bound
      by surface receptors and that the AluI-receptor complexes are internalized by an
      energy-dependent endocytotic process.
AU  - Vasudev V
AU  - Obe G
PT  - Journal Article
TA  - Mutat. Res.
JT  - Mutat. Res.
SO  - Mutat. Res. 1988 197: 109-116.

PMID- 27635000
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Shewanella sp. Strain UCD-FRSP16_17 and Nine Vibrio Strains Isolated from Abalone Feces.
PG  - e00977-16
AB  - We present here the draft genome sequences for nine strains of Vibrio (V. cyclitrophicus, V.
      splendidus, V. tasmaniensis, and three unidentified) and one
      Shewanella strain. Strains were isolated from red (Haliotis rufescens) and white
      (Haliotis sorenseni) abalone, with and without exposure to 'Candidatus
      Xenohaliotis californiensis,' the causative agent of abalone withering syndrome.
AU  - Vater A et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00977-16.

PMID- 26494685
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Streptomyces fradiae olg1-1, a Strain Resistant to Nitrone-Oligomycin.
PG  - e01252-15
AB  - We report a draft genome sequence of Streptomyces fradiae olg1-1, a mutant strain derived from
      the model object S. fradiae ATCC 19609, which is resistant to nitrone-oligomycin and has a
      mutation in the DNA-binding domain of a transcriptional regulator PadR.
AU  - Vatlin AA
AU  - Bekker OB
AU  - Lysenkova LN
AU  - Danilenko VN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01252-15.

PMID- 7490770
VI  - 41
DP  - 1995
TI  - Fungal origin by horizontal transfer of a plant mitochondrial group I intron in the chimeric CoxI gene of Peperomia.
PG  - 563-572
AB  - We present phylogenetic evidence that a group I intron in an angiosperm mitochondrial gene
      arose recently by horizontal transfer from a fungal donor species.  A 1,716-bp fragment of the
      mitochondrial coxI gene from the angiosperm Peperomia polybotrya was amplified via the
      polymerase chain reaction and sequenced.  Comparison to other coxI genes revealed a 966-bp
      group I intron, which, based on homology with the related yeast coxI intron aI4, potentially
      encodes a 279-amino-acid site-specific DNA endonuclease.  This intron, which is believed to
      function as a ribozyme during its own splicing, is not present in any of 19 coxI genes
      examined from other diverse vascular plant species.  Phylogenetic analysis of intron origin
      was carried out using three different tree-generating algorithms, and on a variety of
      nucleotide and amino acid data sets from the intron and its flanking exon sequences.  These
      analyses show that the Peperomia coxI gene intron and exon sequences are of fundamentally
      different evolutionary origin. The Peperomia intron is more closely related to several fungal
      mitochondrial introns, two of which are located at identical positions in coxI, than to
      identically located coxI introns from the land plant Marchantia and the green alga Prototheca.
      Conversely, the exon sequence of this gene is, as expected, most closely related to other
      angiosperm coxI genes.  These results, together with evidence suggestive of co-conversion of
      exonic markers immediately flanking the intron insertion site, lead us to conclude that the
      Peperomia coxI intron probably arose by horizontal transfer from a fungal donor, using the
      double-strand-break repair pathway.  The donor species may have been one of the symbiotic
      mycorrhizal fungi that live in close obligate association with most plants.
AU  - Vaughn JC
AU  - Mason MT
AU  - Sper-Whitis GL
AU  - Kuhlman P
AU  - Palmer JD
PT  - Journal Article
TA  - J. Mol. Evol.
JT  - J. Mol. Evol.
SO  - J. Mol. Evol. 1995 41: 563-572.

PMID- 27834709
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Two Ralstonia pickettii Strains with Different Aminoglycoside Resistance Phenotypes.
PG  - e01257-16
AB  - The genomes of two Ralstonia pickettii strains (H2Cu2 and H2Cu5), isolated from hospital
      effluent in a selective medium containing CuSO4, were sequenced. They
      presented MICs of >256 and 6 microg/ml for the aminoglycoside gentamicin,
      respectively. The 5.2-Mb draft genomes have 40 contigs for strain H2Cu2 and 113
      for H2Cu5.
AU  - Vaz-Moreira I
AU  - Tamames J
AU  - Martinez JL
AU  - Manaia CM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01257-16.

PMID- Not carried by PubMed...
VI  - 13
DP  - 1996
TI  - Purification of the restriction endonuclease SacI, free of SacII and SacIII contaminants.
PG  - 21-24
AB  - The restriction endonuclease SacI was isolated from Streptomyces achromogenes and was purified
      to homogeneity, until no contaminant nuclease activities were detected.  On the basis of ion
      exchange chromatography (Q-Sepharose and phosphocellulose P-11), SacI can be obtained with a
      high level of purity and used in molecular cloning.  The practical utility of SacI enzyme is
      given by a high stability, high yield, easy handling of producing cells, and the ability to
      recognize new sequences, such as GAGCTC.  The molecular weight (MW) of this enzyme was
      estimated by High Performance Liquid Chromatography and SDS polyacrylamide gel
      electrophoresis, being of about 50 kDa approximately.  According to the results obtained from
      the accelerated stability study, the enzyme preparation is stable for at least 20 months.
AU  - Vazquez R
AU  - Brito J
AU  - Guerra M
PT  - Journal Article
TA  - Biotecnol. Apl.
JT  - Biotecnol. Apl.
SO  - Biotecnol. Apl. 1996 13: 21-24.

PMID- Not carried by PubMed...
VI  - 13
DP  - 1996
TI  - Purification of NcoI restriction endonuclease free of exonucleases and contaminant endonucleases.
PG  - 289-290
AB  - 
AU  - Vazquez R
AU  - Martinez D
AU  - Reyes G
AU  - Marquez G
AU  - Ryes N
AU  - Diaz Y
AU  - Luis M
AU  - Gonzalez B
AU  - Gonzalez N
PT  - Journal Article
TA  - Biotecnol. Apl.
JT  - Biotecnol. Apl.
SO  - Biotecnol. Apl. 1996 13: 289-290.

PMID- 25614572
VI  - 3
DP  - 2015
TI  - Complete and Assembled Genome Sequence of Bifidobacterium kashiwanohense PV20-2,  Isolated from the Feces of an Anemic Kenyan Infant.
PG  - e01467-14
AB  - The complete genome sequence of Bifidobacterium kashiwanohense strain PV20-2, an  infant feces
      isolate, was determined using single-molecule real-time sequencing
      (SMRT). Hierarchical genome assembly resulted in a completely assembled genome of
      2,370,978 bp. The B. kashiwanohense PV20-2 genome is the first completely
      sequenced and assembled genome of the species.
AU  - Vazquez-Gutierrez P
AU  - Lacroix C
AU  - Chassard C
AU  - Klumpp J
AU  - Jans C
AU  - Stevens MJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01467-14.

PMID- 25614573
VI  - 3
DP  - 2015
TI  - Bifidobacterium pseudolongum Strain PV8-2, Isolated from a Stool Sample of an Anemic Kenyan Infant.
PG  - e01469-14
AB  - The complete genome sequence of Bifidobacterium pseudolongum PV8-2, isolated from feces of an
      anemic Kenyan infant, was determined using single-molecule real-time
      (SMRT) technology. The genome consists of a 2-Mbp chromosome and a 4-kb plasmid.
AU  - Vazquez-Gutierrez P
AU  - Lacroix C
AU  - Chassard C
AU  - Klumpp J
AU  - Stevens MJ
AU  - Jans C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01469-14.

PMID- 28450524
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Streptomyces scabrisporus NF3, an Endophyte Isolated from Amphipterygium adstringens.
PG  - e00267-17
AB  - We report the draft genome sequence of Streptomyces scabrisporus NF3, an endophyte isolated
      from Amphipterygium adstringens in Chiapas, Mexico. This
      strain produces a new modified linaridin peptide. The genome harbors at least 50
      gene clusters for synthases of polyketide and nonribosomal peptides, suggesting a
      prospective production of various secondary metabolites.
AU  - Vazquez-Hernandez M
AU  - Ceapa CD
AU  - Rodriguez-Luna SD
AU  - Rodriguez-Sanoja R
AU  - Sanchez S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00267-17.

PMID- 25013137
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of the Streptococcus sp. Strain VT 162, Isolated from the Saliva of Pediatric Oncohematology Patients.
PG  - e00647-14
AB  - Streptococcus sp. strain VT 162 was isolated from the saliva of pediatric oncohematology
      patients. Its full genome is 2,045,418 bp. The availability of
      this genome will provide insights into the composition of microbial flora among
      pediatric oncohematology patients and the host interaction and pathogenicity of
      this species.
AU  - Vecherkovskaya MF
AU  - Tetz GV
AU  - Tetz VV
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00647-14.

PMID- 11790742
VI  - 184
DP  - 2002
TI  - Isolation and characterization of BTF-37: Chromosomal DNA captured from Bacteroides fragilis that confers self-transferability and expresses a pilus-like structure in Bacteroides spp. and Escherichia coli.
PG  - 728-738
AB  - We report the isolation and preliminary characterization of BTF-37, a new 52-kb transfer
      factor isolated from Bacteroides fragilis clinical isolate LV23. BTF-37 was obtained by the
      capture of new DNA in the nonmobilizable Bacteroides-Escherichia coli shuttle vector
      pGAT400DeltaBglII using a functional assay. BTF-37 is self-transferable within and from
      Bacteroides and also self-transfers in E. coli. Partial DNA sequencing, colony hybridization,
      and PCR revealed the presence of Tet element-specific sequences in BTF-37. In addition,
      Tn5520, a small mobilizable transposon that we described previously (G. Vedantam, T. J.
      Novicki, and D. W. Hecht, J. Bacteriol. 181:2564-2571, 1999), was also coisolated within
      BTF-37. Scanning and transmission electron microscopy of Tet element-containing Bacteroides
      spp. and BTF-37-harboring Bacteroides and E. coli strains revealed the presence of pilus-like
      cell surface structures. These structures were visualized in Bacteroides spp. only when BTF-37
      and Tet element strains were induced with subinhibitory concentrations of tetracycline and
      resembled those encoded by E. coli broad-host-range plasmids. We conclude that we have
      captured a new, self-transferable transfer factor from B. fragilis LV23 and that this new
      factor encodes a tetracycline-inducible Bacteroides sp. conjugation apparatus.
AU  - Vedantam G
AU  - Hecht DW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2002 184: 728-738.

PMID- 15489427
VI  - 186
DP  - 2004
TI  - The Completely Sequenced Plasmid pEST4011 Contains a Novel IncP1 Backbone and a Catabolic Transposon Harboring tfd Genes for 2,4-Dichlorophenoxyacetic Acid Degradation.
PG  - 7161-7174
AB  - The herbicide 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacterium
      Achromobacter xylosoxidans subsp. denitrificans strain EST4002 contains
      plasmid pEST4011. This plasmid ensures its host a stable 2,4-D(+)
      phenotype. We determined the complete 76,958-bp nucleotide sequence of
      pEST4011. This plasmid is a deletion and duplication derivative of pD2M4,
      the 95-kb highly unstable laboratory ancestor of pEST4011, and was
      self-generated during different laboratory manipulations performed to
      increase the stability of the 2,4-D(+) phenotype of the original strain,
      strain D2M4(pD2M4). The 47,935-bp catabolic region of pEST4011 forms a
      transposon-like structure with identical copies of the hybrid insertion
      element IS1071::IS1471 at the two ends. The catabolic regions of pEST4011
      and pJP4, the best-studied 2,4-D-degradative plasmid, both contain
      homologous, tfd-like genes for complete 2,4-D degradation, but they have
      little sequence similarity other than that. The backbone genes of pEST4011
      are most similar to the corresponding genes of broad-host-range
      self-transmissible IncP1 plasmids. The backbones of the other three IncP1
      catabolic plasmids that have been sequenced (the 2,4-D-degradative plasmid
      pJP4, the haloacetate-catabolic plasmid pUO1, and the atrazine-catabolic
      plasmid pADP-1) are nearly identical to the backbone of R751, the
      archetype plasmid of the IncP1 beta subgroup. We show that despite the
      overall similarity in plasmid organization, the pEST4011 backbone is
      sufficiently different (51 to 86% amino acid sequence identity between
      individual backbone genes) from the backbones of members of the three
      IncP1 subgroups (the alpha, beta, and gamma subgroups) that it belongs to
      a new IncP1subgroup, the delta subgroup. This conclusion was also
      supported by a phylogenetic analysis of the trfA2, korA, and traG gene
      products of different IncP1 plasmids.
AU  - Vedler E
AU  - Vahter M
AU  - Heinaru A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2004 186: 7161-7174.

PMID- 27516521
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Colistin-Resistant Acinetobacter baumannii Strain VB22595 Isolated from a Central Line-Associated Bloodstream Infection.
PG  - e00835-16
AB  - Acinetobacter baumannii is an important emerging pathogen that causes health care-associated
      infections. In this study, we determined the genome of a
      multidrug-resistant clinical strain, VB22595, isolated from a hospital in
      Southern India. The draft genome indicates that strain VB22595 encodes a genome
      of ~3.92 Mb in size and does not contain plasmid derived MCR-1 for colistin
      resistance.
AU  - Veeraraghavan B
AU  - Anandan S
AU  - Ragupathi NK
AU  - Vijayakumar S
AU  - Sethuvel DP
AU  - Biswas I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00835-16.

PMID- 27881543
VI  - 4
DP  - 2016
TI  - First Report on the Draft Genome Sequences of Corynebacterium diphtheriae Isolates from India.
PG  - e01316-16
AB  - We report here the draft genome sequences of five Corynebacterium diphtheriae isolates of
      Indian origin. The C. diphtheriae isolates TH1141, TH510, TH1526,
      TH1337, and TH2031 belong to sequence type ST-50, ST-295, ST-377, ST-405, and
      ST-405, with an average genome size of 2.5 Mbp.
AU  - Veeraraghavan B
AU  - Anandan S
AU  - Rajamani SSK
AU  - Gopi R
AU  - Devanga RNK
AU  - Ramesh S
AU  - Verghese VP
AU  - Korulla S
AU  - Mathai S
AU  - Sangal L
AU  - Joshi S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01316-16.

PMID- 27811110
VI  - 4
DP  - 2016
TI  - Whole-Genome Shotgun Sequencing of the First Observation of Neisseria meningitidis Sequence Type 6928 in India.
PG  - e01232-16
AB  - Neisseria meningitidis is one of the leading global causes of bacterial meningitis. Here, we
      discuss the draft genome sequences of two N. meningitidis
      strains, isolated from bloodstream infections in two pediatric patients at a
      tertiary care hospital in South India. The sequence data indicate that strains
      VB13856 and VB15548 encode genomes of ~2.09 Mb in size with no plasmids.
AU  - Veeraraghavan B
AU  - Neeravi AR
AU  - Devanga RNK
AU  - Inbanathan FY
AU  - Pragasam AK
AU  - Verghese VP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01232-16.

PMID- 27881539
VI  - 4
DP  - 2016
TI  - Coexistence of Fosfomycin and Colistin Resistance in Klebsiella pneumoniae: Whole-Genome Shotgun Sequencing.
PG  - e01303-16
AB  - Resistance to colistin is a major threat that limits therapeutic choices for treating
      carbapenem-resistant Klebsiella pneumoniae infections. Herein, we report
      the draft genome sequences of two colistin-resistant K. pneumoniae isolates
      (BA41763 and B6753). The sequence data indicate that BA41763 and B6753 contain
      genomes of ~5.9 and 5.7 Mb in size with several plasmids.
AU  - Veeraraghavan B
AU  - Perumalla SK
AU  - Devanga RNK
AU  - Pragasam AK
AU  - Muthuirulandi SDP
AU  - Inian S
AU  - Inbanathan FY
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01303-16.

PMID- 19304835
VI  - 75
DP  - 2009
TI  - Inactivation of the SauI Type I Restriction-Modification System Is Not Sufficient To Generate Staphylococcus aureus Strains Capable of Efficiently Accepting Foreign DNA.
PG  - 3034-3038
AB  - Genetic manipulation of Staphylococcus aureus is limited by the availability of only a single
      strain, RN4220, that is capable of easily
      accepting foreign DNA. Inactivation of the hsdR gene of the SauI type I
      restriction-modification system was shown previously to be responsible
      for the high transformation efficiency of RN4220 (D. E. Waldron and J.
      A. Lindsay, J Bacteriol. 188:5578-5585, 2006). However, deletion of
      this gene in three different S. aureus strains was not sufficient to
      make them readily transformable, which would be remarkably useful for
      genetic studies of this pathogenic organism. These results indicate
      that another unknown factor(s) is required for the transformable
      phenotype in S. aureus.
AU  - Veiga H
AU  - Pinho MG
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2009 75: 3034-3038.

PMID- 15383718
VI  - 7
DP  - 2004
TI  - The complete genome sequence of Bacillus licheniformis DSM13, an organism with great industrial potential.
PG  - 204-211
AB  - The genome of Bacillus licheniformis DSM13 consists of a single chromosome that has a size of
      4,222,748 base pairs. The average G+C ratio is 46.2%. 4,286 open
      reading frames, 72 tRNA genes, 7 rRNA operons and 20 transposase genes were
      identified. The genome shows a marked co-linearity with Bacillus subtilis but
      contains defined inserted regions that can be identified at the sequence as well
      as at the functional level. B. licheniformis DSM13 has a well-conserved secretory
      system, no polyketide biosynthesis, but is able to form the lipopeptide
      lichenysin. From the further analysis of the genome sequence, we identified
      conserved regulatory DNA motives, the occurrence of the glyoxylate bypass and the
      presence of anaerobic ribonucleotide reductase explaining that B. licheniformis
      is able to grow on acetate and 2,3-butanediol as well as anaerobically on
      glucose. Many new genes of potential interest for biotechnological applications
      were found in B. licheniformis; candidates include proteases, pectate lyases,
      lipases and various polysaccharide degrading enzymes.
AU  - Veith B
AU  - Herzberg C
AU  - Steckel S
AU  - Feesche J
AU  - Maurer KH
AU  - Ehrenreich P
AU  - Baumer S
AU  - Henne A
AU  - Liesegang H
AU  - Merkl R
AU  - Ehrenreich A
AU  - Gottschalk G
PT  - Journal Article
TA  - J. Mol. Microbiol. Biotechnol.
JT  - J. Mol. Microbiol. Biotechnol.
SO  - J. Mol. Microbiol. Biotechnol. 2004 7: 204-211.

PMID- 2162526
VI  - 18
DP  - 1990
TI  - SfuI, a novel AsuII isoschizomer from Streptomyces fulvissimus recognizing 5'-TT/CGAA-3'.
PG  - 3424
AB  - None
AU  - Veitinger S
AU  - Schmitz GG
AU  - Kaluza K
AU  - Jarsch M
AU  - Braun V
AU  - Kessler C
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 3424.

PMID- 30533913
VI  - 7
DP  - 2018
TI  - Complete Genome Sequence of the Marine Carbazole-Degrading Bacterium Erythrobacter sp. Strain KY5.
PG  - e00935-18
AB  - We determined the complete genome sequence of Erythrobacter sp. strain KY5, a bacterium
      isolated from Tokyo Bay and capable of degrading carbazole. The genome
      consists of a 3.3-Mb circular chromosome that carries the gene clusters involved
      in carbazole degradation and biosynthesis of the photosynthetic apparatus of
      aerobic anoxygenic phototrophic bacteria.
AU  - Vejarano F
AU  - Suzuki-Minakuchi C
AU  - Ohtsubo Y
AU  - Tsuda M
AU  - Okada K
AU  - Nojiri H
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e00935-18.

PMID- 25573944
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Actinoplanes utahensis NRRL 12052, a Microorganism Involved in Industrial Production of Pharmaceutical Intermediates.
PG  - e01411-14
AB  - Here, we describe the draft genome sequence of Actinoplanes utahensis NRRL 12052, a
      filamentous bacterium that encodes an aculeacin A acylase and a putative
      N-acyl-homoserine lactone acylase of biotechnological interest. Moreover, several
      nonribosomal peptide synthase (NRPS) and polyketide synthase (PKS) clusters and
      antibiotic resistance genes have been identified.
AU  - Velasco-Bucheli R
AU  - Del Cerro C
AU  - Hormigo D
AU  - Acebal C
AU  - Arroyo M
AU  - Garcia JL
AU  - de la Mata I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01411-14.

PMID- 27777652
VI  - 11
DP  - 2016
TI  - Draft genome of Prochlorothrix hollandica CCAP 1490/1T (CALU1027), the chlorophyll a/b-containing filamentous cyanobacterium.
PG  - 82
AB  - Prochlorothrix hollandica is filamentous non-heterocystous cyanobacterium which possesses the
      chlorophyll a/b light-harvesting complexes. Despite the growing
      interest in unusual green-pigmented cyanobacteria (prochlorophytes) to date only
      a few sequenced genome from prochlorophytes genera have been reported. This study
      sequenced the genome of Prochlorothrix hollandica CCAP 1490/1T (CALU1027). The
      produced draft genome assembly (5.5 Mb) contains 3737 protein-coding genes and
      114 RNA genes.
AU  - Velichko N
AU  - Rayko M
AU  - Chernyaeva E
AU  - Lapidus A
AU  - Pinevich A
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 82.

PMID- 
VI  - 24
DP  - 1999
TI  - How environmental factors regulate mutagenesis and gene transfer in microorganisms.
PG  - 529-559
AB  - This review is focused on the physiological and evolutionary strategies of the processes
      occurring during the entry of microbial cells into
      stationary phase and the subsequent period of stasis. The molecular
      mechanisms adapting microorganisms from exponential growth to a static
      state involve activation and complex regulation of the stationary
      factor Sigma-S, which directs RNA polymerase to the specific promoters.
      As a result the static cells acquire general resistance (simultaneous
      tolerances) to different environmental stresses. In parallel with the
      physiological adaptation to stasis, diverse genetical processes are
      aimed towards resuming the growth of the static cells. Different types
      of mutagenesis occur: (i) in cells entering stasis and (ii) in static
      cells (adaptive mutagenesis). Cessation of growth induces the transient
      hypermutator state resulting in the accumulation of random mutations in
      the subpopulation of the static cells. If by chance, one or a few of
      such mutations lead to resumption of division, the growing cell will
      return to a normal mechanism of spontaneous mutagenesis. Another
      mechanism for generating genetical variability in stressed cells
      involves transposons and conjugative plasmids. Stresses can stimulate
      the excision of some transposons, which, in turn, can generate
      chromosomal mutations and activate intracellular mechanisms of
      mutagenesis. Under stress some conjugative plasmids activate genes
      encoding antirestriction proteins that repress restriction-modification
      systems of the recipient cells. Moreover, under stress special cellular
      mechanisms decrease (alleviate) the activity of
      restriction-modification systems which, in turn, enhance the
      probability of gene transfer into the stressed cells. Under stress, the
      efficiency of inter-species genetical barriers also decreases. This,
      stimulates inter-species gene transfer and may lead to a burst of
      incipient speciation in the population of non-growing cells. After
      resumption of growth the genetical barriers leading to isolation will
      be restored. In general, the cessation of growth "switches on", and
      resumption of growth "switches off", a set of special processes that
      are responsible for generating bursts of genetical variability in
      populations of microorganisms.
AU  - Velkov VV
PT  - Journal Article
TA  - J. Biosci.
JT  - J. Biosci.
SO  - J. Biosci. 1999 24: 529-559.

PMID- 24265496
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of a Multidrug-Resistant Clinical Isolate of Mycobacterium  tuberculosis Belonging to a Novel Spoligotype.
PG  - e00965-13
AB  - We describe the genome sequencing and analysis of a multidrug-resistant (MDR) clinical isolate
      of Mycobacterium tuberculosis, strain OSDD105 from India,
      belonging to a novel spoligotype.
AU  - Vellarikkal SK
AU  - Singh AV
AU  - Singh PK
AU  - Garg P
AU  - Katoch VM
AU  - Katoch K
AU  - Chauhan DS
AU  - Sivasubbu S
AU  - Scaria V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00965-13.

PMID- 24265488
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Multidrug-Resistant Mycobacterium tuberculosis Clinical  Isolate OSDD515, Belonging to the Uganda I Genotype.
PG  - e00750-13
AB  - We describe the genome sequencing and analysis of a clinical isolate of the
      multidrug-resistant Mycobacterium tuberculosis Uganda I genotype (OSDD515) from
      India.
AU  - Vellarikkal SK
AU  - Singh AV
AU  - Singh PK
AU  - Garg P
AU  - Katoch VM
AU  - Katoch K
AU  - Chauhan DS
AU  - Sivasubbu S
AU  - Scaria V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00750-13.

PMID- 25377704
VI  - 2
DP  - 2014
TI  - Genome Sequence of the Lactic Acid Bacterium Lactococcus lactis subsp. lactis TOMSC161, Isolated from a Nonscalded Curd Pressed Cheese.
PG  - e01121-14
AB  - Lactococcus lactis is a lactic acid bacterium used in the production of many fermented foods,
      such as dairy products. Here, we report the genome sequence of
      L. lactis subsp. lactis TOMSC161, isolated from nonscalded curd pressed cheese.
      This genome sequence provides information in relation to dairy environment
      adaptation.
AU  - Velly H
AU  - Renault P
AU  - Abraham AL
AU  - Loux V
AU  - Delacroix-Buchet A
AU  - Fonseca F
AU  - Bouix M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01121-14.

PMID- 24652976
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Staphylococcus aureus AMRF1 (ST22) and AMRF2 (ST672), Ocular Methicillin-Resistant Isolates.
PG  - e00168-14
AB  - Sequence type 22 (ST22) and ST672 are the two major emerging clones of community-acquired
      methicillin-resistant Staphylococcus aureus in India. ST672
      strains were found to cause severe ocular infections. We report the draft genome
      sequences of two emerging strains of methicillin-resistant S. aureus, AMRF1
      (ST22) and AMRF2 (ST672), isolated from patients with ocular infections.
AU  - Velusamy N
AU  - Prakash L
AU  - Sivakumar N
AU  - Antony A
AU  - Prajna L
AU  - Mohankumar V
AU  - Devarajan B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00168-14.

PMID- 7552704
VI  - 2
DP  - 1995
TI  - Different enzymes with similar structures involved in Mg2+-mediated polynucleotidyl transfer.
PG  - 838-841
AB  - Comparison of x-ray structures of restriction endonucleases and polynucleotidyl transferase
      superfamily enzymes reveals a structural resemblance.  Transfer of polynucleotidyl residues
      plays a fundamental role in such critical cellular events as genetic recombination,
      transposition and viral DNA integration.  A number of different enzymes is directly implicated
      in this process.  Recently X-ray structures of RuvC protein, a Holliday junction resolvase
      from Escherichia coli and HIV-1 integrase, involved in viral DNA integration, have been
      solved.  Surprisingly, RuvC, HIV-integrase and ribonuclease H (RNase H) appear to have similar
      three-dimensional structures, despite the lack of protein sequence similarities.  On the
      basis of fold resemblance it was proposed that all these enzymes belong to the new superfamily
      of polynucleotidyl transferases (PNT).
AU  - Venclovas C
AU  - Siksnys V
PT  - Journal Article
TA  - Nat. Struct. Biol.
JT  - Nat. Struct. Biol.
SO  - Nat. Struct. Biol. 1995 2: 838-841.

PMID- 7892176
VI  - 20
DP  - 1994
TI  - Five-stranded beta-sheet sandwiched with two a-helices: a structural link between restriction endonucleases EcoRI and EcoRV.
PG  - 279-282
AB  - Examination of crystal structures of restriction endonucleases EcoRI and EcoRV complexes with
      their cognate DNA revealed a common structural element, which forms the core of both proteins.
      This element consists of a five-stranded beta-sheet and two alpha-helices packed against it
      and could be described as alpha-beta sandwich in which helices and beta-strands lie in two
      stacked layers. While the spatial structure of this alpha-beta sandwich is conserved in both
      enzymes, there are no detectable similarities between amino acid sequences except of a few
      residues involved in active site formation. Probably, other restriction endonucleases which
      have similar organization of the active site might possess similar structural element
      regardless of DNA sequence recognized and recognition elements in the enzyme used.
AU  - Venclovas C
AU  - Timinskas A
AU  - Siksnys V
PT  - Journal Article
TA  - Proteins
JT  - Proteins
SO  - Proteins 1994 20: 279-282.

PMID- 1885606
VI  - 266
DP  - 1991
TI  - A DNA conformational alteration induced by a neighboring oligopurine tract on GAATTA enables nicking by EcoRI.
PG  - 16786-16790
AB  - The pseudo EcoRI site GAATTA in the U3 region of the long terminal repeat of
      human immunodeficiency virus, which is flanked by a 26-base pair oligopurine
      tract, is readily nicked by either EcoRI or RsrI.  The strand-specific nick
      occurs predominantly between the G and A residues and is independent of
      negative supercoiling.  Other GAATTA sites surrounded by random
      (non-oligopurine) sequences are not nicked by these restriction endonucleases.
      However, other types and lengths of oligopurine tracts are effective in
      inducing the nicking in neighboring GAATTA sites.  Hence, we propose that the
      flanking oligopurine tracts induce an altered DNA conformation on the GAATTA
      target site which may be similar to the transition state induced by EcoRI when
      binding to its canonical recognition site.  Gel retardation analyses on
      restriction fragments containing the oligopurine-GAATTA-oligopurine sequences
      suggest the presence of helical axis distortions which are consistent with this
      interpretation.
AU  - Venditti S
AU  - Wells RD
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1991 266: 16786-16790.

PMID- 25103758
VI  - 2
DP  - 2014
TI  - Whole-Genome Sequence of Streptococcus macedonicus Strain 33MO, Isolated from the Curd of Morlacco Cheese in the Veneto Region (Italy).
PG  - e00746-14
AB  - A genetic characterization of Streptococcus macedonicus is important to better understand the
      characteristics of this lactic acid bacterium, frequently detected
      in fermented food bacteria communities. This report presents the draft genome
      sequence description of strain 33MO, the first publicly available genome sequence
      of an Italian S. macedonicus isolate.
AU  - Vendramin V
AU  - Treu L
AU  - Bovo B
AU  - Campanaro S
AU  - Corich V
AU  - Giacomini A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00746-14.

PMID- 6269892
VI  - 130
DP  - 1981
TI  - Conditions affecting DNA cleavage by TthI at a TthI endonuclease-dam methylase overlapping sequence.
PG  - 272-274
AB  - The Escherichia coli dam gene codes for a site-specific DNA methylase which methylates adenine
      in the sequence GATC at the N6 position of the purine ring. The effect of this modification on
      the action of several restriction enzymes whose recognition sites are equal or include the
      methylated sequence depends on the endonuclease itself. For example, the enzymes MboI, BclI
      and DpnII do not cleave a sequence containing GAme^TC, while DpnI requires the presence of
      6MeAde in GATC sites in order to cleave the DNA. On the other hand, isoschizomers Sau3AI,
      FnuEI and PfaI actively hydrolyze sequences that have undergone adenine methylation; Sau3AI,
      however, is inhibited by the methylation of cytosine of the indicated sequence.
AU  - Venegas A
AU  - Motles M
AU  - Vasquez C
AU  - Vicuna R
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1981 130: 272-274.

PMID- 6243575
VI  - 109
DP  - 1980
TI  - A rapid procedure for purifying a restriction endonuclease from Thermus thermophilus (TthI).
PG  - 156-158
AB  - Restriction enzymes have proved to be a powerful tool for mapping genomes and
      developing molecular cloning and DNA sequencing techniques.  A few restriction
      enzymes have been isolated from thermophilic bacteria, showing a high
      thermostability and resistance to protein denaturing agents.  These properties
      could be useful to study DNA structure at higher temperatures.  Looking for a
      stable enzyme with a new recognition sequence, we have isolated TthI, an enzyme
      from the extreme thermophile Thermus thermophilus HB8. This thermostable enzyme
      turned out to be an isoschizomer of TaqI, which recognizes the sequence
      5'-TCGA-3'.  Thermus thermophilus is a very convenient source for purifying
      this enzyme since this bacterium does not produce the pigmented 'slime'
      described in Thermus aquaticus, which interferes with the Purification of TawI
      and other enzymes.  Furthermore, TthI was readily released by osmotic shock,
      which allowed us to develop a simplified, rapid two-step procedure to obtain an
      enzyme preparation free of contaminating nucleases.  We report here the
      purifiction method and some of the properties of TthI.
AU  - Venegas A
AU  - Vicuna R
AU  - Alonso A
AU  - Valdes F
AU  - Yudelevich A
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1980 109: 156-158.

PMID- 6246331
VI  - 65
DP  - 1980
TI  - Purification and properties of the Bsp endonuclease.
PG  - 109-112
AB  - None
AU  - Venetianer P
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1980 65: 109-112.

PMID- 6765640
VI  - 1
DP  - 1981
TI  - The restriction-modification enzymes of Bacillus sphaericus R.
PG  - 209-215
AB  - *

        I. Biochemical characterization of the BspI restriction endonuclease

       II. Biochemical characterization of the BspI modification methylase

      III. The genes of the Bsp restriction-modification system

       IV. Conclusion

      

AU  - Venetianer P
AU  - Kiss A
PT  - Journal Article
TA  - Gene Amplif. Anal.
JT  - Gene Amplif. Anal.
SO  - Gene Amplif. Anal. 1981 1: 209-215.

PMID- 2835751
VI  - 16
DP  - 1988
TI  - BcefI, a new type IIS restriction endonuclease.
PG  - 3053-3060
AB  - A new Type IIS restriction endonuclease was identified, partially purified and characterized
      from a Bacillus cereus subsp. fluorescens strain.  The enzyme recognized the nonpalindromic
      sequence ACGGC and cleaves at a distance from it.  The cleavage appears to occur with a +/-1
      basepair uncertainity.  Thus the cleavage and recognition site is as shown below:
      ACGGC(N) 11-13
      TGCCG(N) 12-14.
AU  - Venetianer P
AU  - Orosz A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1988 16: 3053-3060.

PMID- 3248715
VI  - 74
DP  - 1988
TI  - Isolation and characterization of two new restriction endonucleases (BepI and BcefI) .
PG  - 99
AB  - Meeting Abstract
AU  - Venetianer P
AU  - Orosz A
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 99.

PMID- 2829121
VI  - 16
DP  - 1988
TI  - BepI restriction endonuclease, a new isoschizomer of FnuDII.
PG  - 350
AB  - A new TypeII restriction endonuclease was isolated and characterized from a bacterial strain
      identified as Brevibacterium epidermidis by Dr. M. Konkoly-Thege (Budapest).  The strain grows
      well in yeast-tryptone broth aerobically with a doubling time of 50 min at 25-30 C.  The
      enzyme was purified by a conventional procedure, employing Bio-Gel A-0.5 m, DEAE-cellulose and
      phosphocellulose chromatography.  The enzyme at this stage of purification was applicable for
      all practical purposes, it was virtually free from contaminating nucleases.  The yield of the
      enzyme was approximately 3-400 units/g wet weight of cell.  The optimal conditions for the
      activity of the enzyme are as follows:  temperature 25-30 C., Mg2+ ions 10 mM, pH 7.4, no
      salts.  The cleavage pattern of the enzyme tested with known DNA molecules (lambda phage,
      pBR322) was identical with the pattern obtained with FnuDII.  This identity was confirmed by
      parallel digestions with the new enzyme and commercial FnuDII, and double digestions with both
      enzymes, that resulted in unaltered digestion patterns. The cleavage site was established by
      running a Maxam-Gilbert sequence gel from a DNA fragment of known sequence, which contained a
      FnuDII site.  The same end-labelled DNA fragment was then digested with the new enzyme, and it
      was electrophoresed alongside the sequence ladder.  This experiment unambiguously proved that
      the cleavage occured in the middle of the palindromic CGCG sequence, generating flush ends.
      Thus the enzyme does not represent a new specificity, it is an isoschizomer of the well known
      FnuDII enzyme. Nevertheless it offers some practical advantages.  The Fusobacterium nucleatum
      strain, from which FnuDII is isolated, is an obligately anaerobic pathogenic microorganism,
      therefore FnuDII is fairly expensive.  The only other commercially available isoschisomer,
      ThaI is purified from an extremely thermophilic and acidophilic organism, the other described
      isoschisomers (3,4) have not been characterized.  It is hoped that the BepI enzyme will be a
      better substitute for these isoschisomers.
AU  - Venetianer P
AU  - Orosz A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1988 16: 350.

PMID- 11292750
VI  - 69
DP  - 2001
TI  - Complete DNA sequence and analysis of the large virulence plasmid of Shigella flexneri.
PG  - 3271-3285
AB  - The complete sequence analysis of the 210-kb Shigella flexneri 5a
      virulence plasmid was determined. Shigella spp. cause dysentery and
      diarrhea by invasion and spread through the colonic mucosa. Most of the
      known Shigella virulence determinants are encoded on a large plasmid that
      is unique to virulent strains of Shigella and enteroinvasive Escherichia
      coli; these known genes account for approximately 30 to 35% of the
      virulence plasmid. In the complete sequence of the virulence plasmid, 286
      open reading frames (ORFs) were identified. An astonishing 153 (53%) of
      these were related to known and putative insertion sequence (IS) elements;
      no known bacterial plasmid has previously been described with such a high
      proportion of IS elements. Four new IS elements were identified. Fifty
      putative proteins show no significant homology to proteins of known
      function; of these, 18 have a G+C content of less than 40%, typical of
      known virulence genes on the plasmid. These 18 constitute potentially
      unknown virulence genes. Two alleles of shet2 and five alleles of ipaH
      were also identified on the plasmid. Thus, the plasmid sequence suggests a
      remarkable history of IS-mediated acquisition of DNA across bacterial
      species. The complete sequence will permit targeted characterization of
      potential new Shigella virulence determinants.
AU  - Venkatesan MM
AU  - Goldberg MB
AU  - Rose DJ
AU  - Grotbeck EJ
AU  - Burland V
AU  - Blattner FR
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2001 69: 3271-3285.

PMID- 28798168
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences from a Novel Clade of Bacillus cereus Sensu Lato Strains,  Isolated from the International Space Station.
PG  - e00680-17
AB  - The draft genome sequences of six Bacillus strains, isolated from the International Space
      Station and belonging to the Bacillus anthracis-B. cereus-B.
      thuringiensis group, are presented here. These strains were isolated from the
      Japanese Experiment Module (one strain), U.S. Harmony Node 2 (three strains), and
      Russian Segment Zvezda Module (two strains).
AU  - Venkateswaran K et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00680-17.

PMID- 23833140
VI  - 1
DP  - 2013
TI  - Genome sequences for three denitrifying bacterial strains isolated from a uranium- and nitrate-contaminated subsurface environment.
PG  - e00449-13
AB  - Genome sequences for three strains of denitrifying bacteria (Alphaproteobacteria-Afipia sp.
      strain 1NLS2 and Hyphomicrobium denitrificans
      strain 1NES1; Firmicutes-Bacillus sp. strain 1NLA3E) isolated from the nitrate-
      and uranium-contaminated subsurface of the Oak Ridge Integrated Field Research
      Challenge (ORIFRC) site, Oak Ridge Reservation, TN, are reported.
AU  - Venkatramanan R
AU  - Prakash O
AU  - Woyke T
AU  - Chain P
AU  - Goodwin LA
AU  - Watson D
AU  - Brooks S
AU  - Kostka JE
AU  - Green SJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00449-13.

PMID- 15001713
VI  - 304
DP  - 2004
TI  - Environmental Genome Shotgun Sequencing of the Sargasso Sea.
PG  - 66-74
AB  - We have applied "whole-genome shotgun sequencing" to microbial populations
      collected en masse on tangential flow and impact filters from seawater
      samples collected from the Sargasso Sea near Bermuda. A total of 1.045
      billion base pairs of nonredundant sequence was generated, annotated, and
      analyzed to elucidate the gene content, diversity, and relative abundance
      of the organisms within these environmental samples. These data are
      estimated to derive from at least 1800 genomic species based on sequence
      relatedness, including 148 previously unknown bacterial phylotypes. We
      have identified over 1.2 million previously unknown genes represented in
      these samples, including more than 782 new rhodopsin-like photoreceptors.
      Variation in species present and stoichiometry suggests substantial
      oceanic microbial diversity.
AU  - Venter JC et al
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2004 304: 66-74.

PMID- 20041198
VI  - 5
DP  - 2009
TI  - The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity.
PG  - e1000785
AB  - Bifidobacteria, one of the relatively dominant components of the human intestinal microbiota,
      are considered one of the key groups of beneficial
      intestinal bacteria (probiotic bacteria). However, in addition to
      health-promoting taxa, the genus Bifidobacterium also includes
      Bifidobacterium dentium, an opportunistic cariogenic pathogen. The genetic
      basis for the ability of B. dentium to survive in the oral cavity and
      contribute to caries development is not understood. The genome of B.
      dentium Bd1, a strain isolated from dental caries, was sequenced to
      completion to uncover a single circular 2,636,368 base pair chromosome
      with 2,143 predicted open reading frames. Annotation of the genome
      sequence revealed multiple ways in which B. dentium has adapted to the
      oral environment through specialized nutrient acquisition, defences
      against antimicrobials, and gene products that increase fitness and
      competitiveness within the oral niche. B. dentium Bd1 was shown to
      metabolize a wide variety of carbohydrates, consistent with genome-based
      predictions, while colonization and persistence factors implicated in
      tissue adhesion, acid tolerance, and the metabolism of human
      saliva-derived compounds were also identified. Global transcriptome
      analysis demonstrated that many of the genes encoding these predicted
      traits are highly expressed under relevant physiological conditions. This
      is the first report to identify, through various genomic approaches,
      specific genetic adaptations of a Bifidobacterium taxon, Bifidobacterium
      dentium Bd1, to a lifestyle as a cariogenic microorganism in the oral
      cavity. In silico analysis and comparative genomic hybridization
      experiments clearly reveal a high level of genome conservation among
      various B. dentium strains. The data indicate that the genome of this
      opportunistic cariogen has evolved through a very limited number of
      horizontal gene acquisition events, highlighting the narrow boundaries
      that separate commensals from opportunistic pathogens.
AU  - Ventura M et al
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2009 5: e1000785.

PMID- 19917674
VI  - 24
DP  - 2010
TI  - Multiple antibiotic resistance gene recruitment onto the enterohemorrhagic Escherichia coli virulence plasmid.
PG  - 1160-1166
AB  - Enterohemorrhagic Escherichia coli (EHEC) strains are zoonotic pathogens
      responsible for a range of severe human disease. The repertoire of
      virulence determinants promoting EHEC disease is encoded on both the main
      chromosome and virulence plasmid. We examined a multiply
      antibiotic-resistant O26 EHEC strain for carriage of resistance genes on
      the virulence plasmid. The EHEC virulence plasmid containing a complex
      antibiotic-resistance gene locus, designated as pO26-CRL, was purified
      from EHEC O26:H(-) (patient with hemorrhagic colitis) and subjected to
      shotgun-sequencing and bioinformatic analysis. Determination of the
      111,481-bp sequence of pO26-CRL revealed genes encoding a functional
      enterohemolysin operon (ehxCABD), STEC-specific extracellular serine
      protease (espP), putative EHEC adhesin (toxB), catalase/peroxidase (katP),
      and myristoyl transferase (msbB) involved in lipid A synthesis. A
      22,609-bp Tn21 derivative is inserted within the conjugal transfer gene
      traC and encodes resistance to trimethoprim, streptomycin, sulfathiozole,
      kanamycin, neomycin, beta-lactams, and mercuric chloride. Plasmid pO26-CRL
      is nonconjugative but is mobilizable. This is the first report of an EHEC
      virulence plasmid containing a complex antibiotic resistance locus, and
      raises the concern that antibiotic use will coselect for virulence
      determinants, leading to increased disease potential in both commensal and
      pathogenic E. coli populations.-Venturini, C., Beatson, S. A., Djordjevic,
      S. P., Walker, M. J. Multiple antibiotic resistance gene recruitment onto
      the enterohemorrhagic Escherichia coli virulence plasmid.
AU  - Venturini C
AU  - Beatson SA
AU  - Djordjevic SP
AU  - Walker MJ
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 2010 24: 1160-1166.

PMID- 24223859
VI  - 8
DP  - 2013
TI  - Sequences of Two Related Multiple Antibiotic Resistance Virulence Plasmids Sharing a Unique IS26-Related Molecular Signature Isolated from Different Escherichia coli Pathotypes from Different Hosts.
PG  - E78862
AB  - Enterohemorrhagic Escherichia coli (EHEC) and atypical enteropathogenic E. coli
      (aEPEC) are important zoonotic pathogens that increasingly are becoming resistant
      to multiple antibiotics. Here we describe two plasmids, pO26-CRL125 (125 kb) from
      a human O26:H- EHEC, and pO111-CRL115 (115kb) from a bovine O111 aEPEC, that
      impart resistance to ampicillin, kanamycin, neomycin, streptomycin,
      sulfathiazole, trimethoprim and tetracycline and both contain atypical class 1
      integrons with an identical IS26-mediated deletion in their 3 -conserved segment.
      Complete sequence analysis showed that pO26-CRL125 and pO111-CRL115 are
      essentially identical except for a 9.7 kb fragment, present in the backbone of
      pO26-CRL125 but absent in pO111-CRL115, and several indels. The 9.7 kb fragment
      encodes IncI-associated genes involved in plasmid stability during conjugation, a
      putative transposase gene and three imperfect repeats. Contiguous sequence
      identical to regions within these pO26-CRL125 imperfect repeats was identified in
      pO111-CRL115 precisely where the 9.7 kb fragment is missing, suggesting it may be
      mobile. Sequences shared between the plasmids include a complete IncZ replicon, a
      unique toxin/antitoxin system, IncI stability and maintenance genes, a novel
      putative serine protease autotransporter, and an IncI1 transfer system including
      a unique shufflon. Both plasmids carry a derivate Tn21 transposon with an
      atypical class 1 integron comprising a dfrA5 gene cassette encoding resistance to
      trimethoprim, and 24 bp of the 3 -conserved segment followed by Tn6026, which
      encodes resistance to ampicillin, kanymycin, neomycin, streptomycin and
      sulfathiazole. The Tn21-derivative transposon is linked to a truncated Tn1721,
      encoding resistance to tetracycline, via a region containing the IncP-1alpha
      oriV. Absence of the 5 bp direct repeats flanking Tn3-family transposons,
      indicates that homologous recombination events played a key role in the formation
      of this complex antibiotic resistance gene locus. Comparative sequence analysis
      of these closely related plasmids reveals aspects of plasmid evolution in
      pathogenic E. coli from different hosts.
AU  - Venturini C
AU  - Hassan KA
AU  - Roy-Chowdhury P
AU  - Paulsen IT
AU  - Walker MJ
AU  - Djordjevic SP
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2013 8: E78862.

PMID- 2346515
VI  - 16
DP  - 1990
TI  - UV- and CD-spectra of restriction endonuclease EcoRII and DNA-methylase EcoRII.
PG  - 47-51
AB  - UV- and CD-spectra of homogeneous enzymes have been measured.  Extinction
      coefficients estimated from the UV-spectra are 0.97 for restriction
      endonuclease EcoRII at 279.5 nm and 1.17 for DNA-methylase EcoRII at 279 nm.
      As it follows from the CD spectra, both enzymes have a well developed tertiary
      structure and a highly ordered secondary structure, which consists of 22%
      alpha-helices, 64% beta-structure and 9% bends for R.EcoRII and of 44%
      alpha-helices, 48% beta-structure and 4% bends for M.EcoRII.  Restriction
      endonuclease denatures at 50C, while DNA -methylase denatures at 45C, with
      partial reversibility upon cooling.
AU  - Venyaminov SY
AU  - Kosykh VG
AU  - Kholodkov OA
AU  - Buryanov YI
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1990 16: 47-51.

PMID- 24675856
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Actinomadura madurae LIID-AJ290, Isolated from a Human Mycetoma Case.
PG  - e00201-14
AB  - Here we present the draft genome sequence of a member of the Thermomonosporaceae, Actinomadura
      madurae LIID-AJ290, isolated from a human case of mycetoma. The
      assembly contains 10,308,866 bp. This is to our knowledge the first reported
      genome of a human-pathogenic Actinomadura species.
AU  - Vera-Cabrera L
AU  - Ortiz-Lopez R
AU  - Elizondo-Gonzalez R
AU  - Campos-Rivera MP
AU  - Gallardo-Rocha A
AU  - Molina-Torres CA
AU  - Ocampo-Candiani J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00201-14.

PMID- 22535940
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Nocardia brasiliensis HUJEG-1.
PG  - 2761-2762
AB  - In Mexico, actinomycetoma is mainly caused by Nocardia brasiliensis, which is a soil
      inhabitant actinobacterium. Here, we report for the first time the draft
      genome of a strain isolated from a human case that has largely been found in in
      vitro and experimental models of actinomycetoma, N. brasiliensis HUJEG-1.
AU  - Vera-Cabrera L
AU  - Ortiz-Lopez R
AU  - Elizondo-Gonzalez R
AU  - Perez-Maya AA
AU  - Ocampo-Candiani J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2761-2762.

PMID- 29748398
VI  - 6
DP  - 2018
TI  - Complete and Annotated Genome Sequence of the Sourdough Lactic Acid Bacterium Lactobacillus fermentum IMDO 130101.
PG  - e00256-18
AB  - Lactobacillus fermentum is a species of lactic acid bacteria that is frequently found in
      sourdough, a fermented flour-water mixture used in the production of
      bread and other baked goods. Here, we present the complete genome sequence of L.
      fermentum IMDO 130101, a candidate sourdough starter culture strain isolated from
      a backslopped rye sourdough.
AU  - Verce M
AU  - De Vuyst L
AU  - Weckx S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00256-18.

PMID- 19596889
VI  - 53
DP  - 2009
TI  - Genetic context of plasmid-carried blaCMY-2-like genes in Enterobacteriaceae.
PG  - 4002-4006
AB  - Analysis of 15 European clinical Enterobacteriaceae isolates showed that
      differences in the genetic context of blaCMY-2-like genes reflected the
      replicon type, usually IncA/C or IncI1. These blaCMY-2 loci may originate
      from the same ISEcp1-mediated mobilization from the Citrobacter freundii
      chromosome as structures described in earlier studies.
AU  - Verdet C
AU  - Gautier V
AU  - Chachaty E
AU  - Ronco E
AU  - Hidri N
AU  - Decre D
AU  - Arlet G
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2009 53: 4002-4006.

PMID- 8293456
VI  - 76
DP  - 1994
TI  - The flip side of DNA methylation.
PG  - 197-200
AB  - DNA methylation has come of age. For more than 40 years, it has been known that eukaryotes tag
      their DNA by the covalent addition of a methyl group to cytosine residues; however, until very
      recently, the functional significance of this modification has remained on a precariously
      speculative footing. A series of discoveries over the last few years has thrust DNA
      methylation firmly into the mainstream of biology and medicine, thereby invigorating the field
      with a firmly established sense of mission. Fragile X syndrome, the leading cause of inherited
      mental retardation, has been traced to expansion and abnormal methylation of a triplet repeat,
      through which transcription of the FMR-1 gene becomes silenced (Trottier et al., 1993).
      Aberrant promoter methylation of tumor suppressor genes has now emerged as an epigenetic
      inactivation pathway contributing to tumorigenesis; evidence increasingly supports the notion
      that ectopic methylation may play a broad role in gene inactivation and mutation in mammals
      (reviewed by Bestor and Coxon, 1993). Much excitement has revolved around the role of DNA
      methylation in genomic imprinting, a phenomenon in which parental alleles of the same gene are
      expressed at unequal dosages (Barlow, 193). Abnormal expression of imprinted loci is now
      implicated in several human disorders (Ogawa et al., 1993; Rainier et al., 1993; Davies,
      1992), and more instances seem likely to be discovered. The entire field of DNA methylation,
      with its foundations resting largely on the strength of correlative data, took both a
      collective breath of relief and a bold step forward with the direct demonstration of Li et al.
      (1992) that the DNA MTase gene is essential for development in mice. A molecular mechanism for
      spatiotemporal coupling of DNA replication and methylation has been suggested by the finding
      that DNA MTase interacts directly with the replication apparatus (Leonhardt et al., 1992).
AU  - Verdine G
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1994 76: 197-200.

PMID- 9195879
VI  - 4
DP  - 1997
TI  - How do DNA repair proteins locate damaged bases in the genome?
PG  - 329-334
AB  - The genome is susceptible to the attack of reactive species that chemically modify the bases
      of DNA.  If genetic information is to be transmitted faithfully to successive generations, it
      is essential that the genome be repaired.  All organisms express proteins specifically
      dedicated to this task.  But how do these proteins find the aberrant bases amongst the
      enormous number of normal ones?
AU  - Verdine GL
AU  - Bruner SD
PT  - Journal Article
TA  - Chem. Biol.
JT  - Chem. Biol.
SO  - Chem. Biol. 1997 4: 329-334.

PMID- 1081295
VI  - 68
DP  - 1975
TI  - Arthrobacter luteus Restriction endonuclease Cleavage Map of PhiX174 RF DNA.
PG  - 221-233
AB  - Cleavage of PhiX174 RF DNA with the restriction endonuclease from Arthrobacter
      luteus (AluI) produces 23 fragments of approximately 24-1100 base pairs in
      length.  The order of most of these fragments has been established by digestion
      of Haemophilus influenzae Rd (HindII) and Haemophilus aegyptius (HaeIII)
      endonuclease fragments of PhiX RF with AluI and by reciprocal digestions of
      AluI fragments with HindII and HaeIII.  In this way the Arthrobacter luteus map
      could be aligned with the HindII and HaeIII cleavage maps of PhiX174 RF DNA of
      A.S. Lee and R.L. Sinsheimer (1974) Proc. Natl. Acad. Sci. USA 71: 2882-2886).
AU  - Vereijken JM
AU  - van Mansfeld ADM
AU  - Baas PD
AU  - Jansz HS
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1975 68: 221-233.

PMID- 28751408
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Saccharibacter sp. Strains 3.A.1 and M18 Isolated from  Honey and a Honey Bee (Apis mellifera) Stomach.
PG  - e00744-17
AB  - The annotated draft genome sequences of two recent Saccharibacter sp. strains isolated from
      honey and a honey bee stomach in 2014 are reported here. Currently,
      two Saccharibacter whole-genome sequences are available in databases; thus, the
      sequences of our new isolates will contribute to a better understanding of
      Saccharibacter genomes.
AU  - Veress A
AU  - Wilk T
AU  - Kiss J
AU  - Olasz F
AU  - Papp PP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00744-17.

PMID- 29192084
VI  - 5
DP  - 2017
TI  - Two Draft Genome Sequences of Sphingobacterium sp. Strains Isolated from Honey.
PG  - e01364-17
AB  - Here, we report two annotated draft genome sequences of Sphingobacterium sp. strains isolated
      from honey. The genomes of strains 1.A.4 and 1.A.5 show a
      limited similarity to each other and to genomes of other Sphingobacterium
      species, indicating that these isolates may represent new species.
AU  - Veress A
AU  - Wilk T
AU  - Kiss J
AU  - Papp PP
AU  - Olasz F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01364-17.

PMID- 
VI  - 0
DP  - 1971
TI  - Restriction and modification of phages in Staphylococcus epidermidis.
PG  - 213-220
AB  - The present results demonstrate the occurrence of host-controlled modification
      of phage DNA in coagulase-negative staphylococci.  Three modification and
      restriction systems, which seem to determine the observed phage typing patterns
      to a large extent, could be detected.  In these staphylococci, restrictive
      cells appear to break down modified DNA.
AU  - Verhoef J
AU  - van Boven CPA
AU  - Holtrigter B
PT  - Journal Article
TA  - Informative molecules in biological systems.
JT  - Informative molecules in biological systems.
SO  - Informative molecules in biological systems. 1971 0: 213-220.

PMID- 4253668
VI  - 37
DP  - 1971
TI  - Restriction and modification of phages in coagulase-negative staphylococci.
PG  - 256-267
AB  - Phage typing of coagulase-negative staphylococci showed that certain
      combination of phage reactions (phage patterns a-g) occurred frequently.  Six
      of these could be arranged in three groups (M1, M2, M3) leaving the strains
      with pattern g which are sensitive to all phages.  The differences in
      susceptibility in patterns a to g were not due to resistance (as all strains
      adsorbed all phages) and could not be explained by immunity.  A correlation was
      observed between host range of the phage and the pattern of the propagating
      strain.
AU  - Verhoef J
AU  - van Boven CPA
AU  - Holtrigter B
PT  - Journal Article
TA  - Antonie Van Leeuwenhoek
JT  - Antonie Van Leeuwenhoek
SO  - Antonie Van Leeuwenhoek 1971 37: 256-267.

PMID- 4261790
VI  - 71
DP  - 1972
TI  - Host-controlled modification and restriction of phages in coagulase-negative Staphylococci.
PG  - 231-239
AB  - Three host-controlled modification and restriction systems occurring among
      coagulase-negative staphlococci belonging to the Staphylococcus subgroup II are
      described.  The phage patterns, observed by typing the staphylococci with a
      provisional typing set of eighteen phages, are mainly determined by these host
      specificity systems.  A strain, which was not restrictive to the phages did not
      become restrictive after lysogenization with any of the eighteen phages.
      Infection of a restricting host with 3H-labelled phages was followed by a rapid
      breakdown of phage DNA, as demonstrated by the appearance of radioactive label
      in the cold-acid-soluble DNA fraction of extracted adsorption mixtures.
AU  - Verhoef J
AU  - van Boven CPA
AU  - Holtrigter B
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1972 71: 231-239.

PMID- 21914879
VI  - 193
DP  - 2011
TI  - Whole Genome Sequence of the Rifamycin B-Producing Strain Amycolatopsis mediterranei S699.
PG  - 5562-5563
AB  - Amycolatopsis mediterranei S699 is an actinomycete that produces an important antibiotic,
      rifamycin B. Semisynthetic derivatives of rifamycin
      B are used for the treatment of tuberculosis, leprosy, and AIDS-related
      mycobacterial infections. Here, we report the complete genome sequence
      (10.2 Mb) of A. mediterranei S699, with 9,575 predicted coding sequences.
AU  - Verma M
AU  - Kaur J
AU  - Kumar M
AU  - Kumari K
AU  - Saxena A
AU  - Anand S
AU  - Nigam A
AU  - Ravi V
AU  - Raghuvanshi S
AU  - Khurana P
AU  - Tyagi AK
AU  - Khurana JP
AU  - Lal R
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5562-5563.

PMID- 2820844
VI  - 54
DP  - 1987
TI  - The use of a selectable FokI cassette in DNA replacement mutagenesis of the R388 dihydrofolate reductase gene.
PG  - 229-238
AB  - FokI, a class-IIS restriction endonuclease, cleaves double-stranded DNA to
      produce a protruding 5' end consisting of four nucleotides, 10-13 residues 3'
      from the nonpalindromic recognition sequence, GGATG.  Cassettes which utilize
      this separation of cleavage and recognition site have been constructed for the
      purpose of linker mutagenesis and DNA replacement experiments.  The cassettes
      are flanked by FokI recognition sequences oriented such that the FokI cleavage
      sites are several nucleotides beyond the cassette/vector fusion sites.  FokI
      excises the cassette and several base pairs of the neighboring vector sequence.
      The ends produced in the vector by FokI cleavage are generally
      noncomplementary and suitable for the insertion of a segment of synthesized
      double-stranded replacement DNA.  A cassette which contains a tyrosine tRNA
      suppressor gene (supF) is selectable by the suppression of amber mutations in
      the recipient host.  A vector containing a pBR322-derived origin of
      replication, the Escherichia coli xanthine-guanine phosphoribosyl tranasferase
      gene as a selectable marker, and no FokI sites has been constructed for use
      with the FokI cassettes.  An experiment which utilized the FokI/supF cassette
      to modify the N-terminal coding region of the R388 dihydrofolate reductase gene
      is described.
AU  - Vermersch PS
AU  - Bennett GN
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1987 54: 229-238.

PMID- 1627551
VI  - 31
DP  - 1992
TI  - EcoRV restriction endonuclease:  communication between catalytic metal ions and DNA recognition.
PG  - 6082-6089
AB  - In the absence of magnesium ions, the EcoRV restriction endonuclease binds all DNA sequences
      with equal affinity but cannot cleave DNA. In the presence of Mg2+, the EcoRV endonuclease
      cleaves a DNA at one particular sequence, GATATC, at least a million times more readily than
      any other sequence. To elucidate the role of the metal ion, the reactions of the EcoRV
      restriction enzyme were studied in the presence of MnCl2 instead of MgCl2. The reaction at the
      EcoRV recognition site was slower with Mn2+. This was caused partly by reduced rates for
      phosphodiester hydrolysis but also by the translocation of the enzyme along the DNA after
      cleaving it in one strand. In contrast, alternative sites that differ from the recognition
      site by one base pair were cleaved faster in the presence of Mn2+ relative to Mg2+. When
      located at an alternative site on the DNA, the EcoRV enzyme bound Mn2+ ions readily but had a
      very low affinity for Mg2+. The EcoRV nuclease is thus restrained from cleaving DNA at
      alternate sites in the presence of Mg2+, but the restraint fails to operate with Mn2+. A
      discrimination factor, which measures the ratio of the activity of the EcoRV nuclease at its
      recognition site over that at an alternative site, had values of 3 x 10/5 in MgCl2 and 6 in
      MnCl2.
AU  - Vermote CLM
AU  - Halford SE
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1992 31: 6082-6089.

PMID- 1627552
VI  - 31
DP  - 1992
TI  - EcoRV restriction endonuclease:  communication between DNA recognition and catalysis.
PG  - 6089-6097
AB  - A genetic system was constructed for the mutagenesis of the EcoRV restriction endonuclease and
      for the overproduction of mutant proteins. The system was used to make two mutants of EcoRV,
      with Ala in place of either Asn185 or Asn188. In the crystal structure of the EcoRV-DNA
      complex, both Asn185 and Asn188 contact the DNA within the EcoRV recognition sequence. But
      neither mutation affected the ability of the protein to bind to DNA. In the absence of metal
      ion cofactors, the mutants bound DNA with almost the same affinity as that of the wild-type
      enzyme. In the presence of Mg2+, both mutants retained the ability to cleave DNA specifically
      at the EcoRV recognition sequence, but their activities were severely depressed relative to
      that of the wild-type. In contrast, with Mn2+ as the cofactor, the mutant enzymes cleaved the
      EcoRV recognition site with activities that were close to that of the wild-type. When bound to
      DNA at the EcoRV recognition site, the mutant proteins bound Mn2+ ions readily, but they had
      much lower affinities for Mg2+ ions than the wild-type enzyme. This was the reason for their
      low activities with Mg2+ as the cofactor. The arrangement of the DNA recognition functions, at
      one location in the EcoRV restriction enzyme, are therefore responsible for organizing the
      catalytic functions at a separate location in the protein.
AU  - Vermote CLM
AU  - Vipond IB
AU  - Halford SE
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1992 31: 6089-6097.

PMID- 8210675
VI  - 144
DP  - 1993
TI  - Presence of mrr- and mcr-like restriction systems in coryneform bacteria.
PG  - 181-185
AB  - Efficient transformation of Brevibacterium flavum MJ233C and Corynebacterium glutamicum ATCC
      31831 (up to 5.0 x 107 transformants/ug DNA) depends on the source of plasmid DNA. The
      transformation efficiencies of B. flavum MJ233C and C. glutamicum ATCC 31831 increased nearly
      103-fold when plasmid DNA was isolated from the recipient strain itself or from a damdcm
      Escherichia coli mutant, as compared with DNA passed through a modification-proficient E. coli
      strain. These results suggest the presence of a methyl-specific restriction system in certain
      strains of coryneform bacteria. In addition, electroporation conditions were optimized.
AU  - Vertes AA
AU  - Inui M
AU  - Kobayashi M
AU  - Kurusu Y
AU  - Yukawa H
PT  - Journal Article
TA  - Res. Microbiol.
JT  - Res. Microbiol.
SO  - Res. Microbiol. 1993 144: 181-185.

PMID- 
VI  - 0
DP  - 1999
TI  - Eukaryotic DNA methyltransferases.
PG  - 341-372
AB  - The post-replicative modification of cytosine is an important part of many
      restriction-modification systems that defend prokaryotic organisms from invading parasitic
      sequences.  DNA cytosine methylation may also play a role in genome defense in eukaryotes, but
      has also evolved into a key determinant of epigenetic regulation (for an excellent
      comprehensive volume on the topic of epigenetics, the reader is referred to ref 136) and is
      involved in such diverse biological functions as gene repression, X-chromosome inactivation,
      genome imprinting, and replication timing.  DNA methylation is essential for the normal
      development of plant and animal species.  Moreover, somatic alterations in genome methylation
      patterns contribute to the genesis of human cancers.  Therefore, just as preservation of the
      primary genetic code is important, proper establishment and maintenance of DNA methylation
      patterns is also critical to the well-being of the organism.  Until very recently, a single
      species of DNA MTase was thought to be responsible for all cytosine methylation in eukaryotes.
      Over the last two years, the identification of several new eukaryotic DNA MTases suggests that
      the establishment of methylation patterns in early development and their maintenance in the
      adult organism requires the activity of several enzymes with distinct cellular or
      developmental roles.  This chapter will start with an overview of genome methylation patterns
      in higher organisms and the current understanding of how these patterns are established and
      maintained, before moving into a discussion of what is known about the structure and function
      of the eukaryotic DNA MTases.  I will also discuss some of the evidence suggesting that DNA
      MTases affect genome function not only through the passive maintenance of methylation patterns
      but also by actively participating in the organization of chromatin and in the genesis of
      human disease.
AU  - Vertino PM
PT  - Journal Article
TA  - S-Adenosylmethionine-dependent Methyltransferases: Structures and Functions.
JT  - S-Adenosylmethionine-dependent Methyltransferases: Structures and Functions.
SO  - S-Adenosylmethionine-dependent Methyltransferases: Structures and Functions. 1999 0: 341-372.

PMID- 
VI  - 39
DP  - 1998
TI  - Identification of DNA (cytosine-5)-methyltransferase as a component of a multiprotein DNA replication complex isolated from human cells.
PG  - 92
AB  - The aberrant methylation of normally unmethylated CpG island-containing gene promoters is a
      somatic genetic alteration that has been implicated in the inactivation tumor suppressor and
      other genes in human cancers.  The mechanisms underlying aberrant methylation are not well
      understood, but recent studies showing that increased levels of the enzyme that normally
      catalyzes DNA methylation in mammalian cells, DNA (cytosine-5)-methyltransferase (DNA MTase),
      can promote aberrant CpG island methylation suggest that DNA MTase itself could play a role.
      Little is known about the normal regulation of DNA MTase nor the precise molecular
      determinants of its activity in vivo.  In this study, we show that DNA MTase is a component of
      the DNA 'synthesome', a multiprotein complex isolated from whole cells that fully supports
      origin-dependent DNA synthesis in a cell-free system.  DNA synthesome was purified from two
      human cell lines through a series of cell fractionation and chromatography steps.  DNA MTase
      protein and activity co-purified with DNA replication activity and were found only in the
      replication-competent fractions.  DNA MTase in the replication complex displayed substrate
      specificity similar to DNA MTase activity from whole cells.  Specific activity determinations
      suggested that most of the cellular DNA MTase exists in a larger complex with the replication
      machinery.  Other proteins that have been identified in the synthesome include DNA polymerases
      a, b, and e, RP-A, RF-C, DNA primase, PCNA, and topoisomerases I and II.  The definition of
      the molecular interactions between DNA MTase and other proteins in replication complex in
      normal and neoplastic cells will provide further insight into the regulation of cellular DNA
      methylation and the role of DNA/MTase in the establishment of altered DNA methylation patterns
      during carcinogenesis.
AU  - Vertino PM
AU  - Coll JM
AU  - Applegren N
AU  - Malkas LH
PT  - Journal Article
TA  - Proc. Amer. Assoc. Cancer Res.
JT  - Proc. Amer. Assoc. Cancer Res.
SO  - Proc. Amer. Assoc. Cancer Res. 1998 39: 92.

PMID- 8754856
VI  - 16
DP  - 1996
TI  - De Novo methylation of CpG island sequences in human fibroblasts overexpressing DNA (cytosine-5-)-methyltransferase.
PG  - 4555-4565
AB  - Recent studies showing a correlation between the levels of DNA (cytosine-5-)-methyltransferase
      (DNA Mtase) enzyme activity and tumorigenicity have implicated this enzyme in the carcinogenic
      process.  Moreover, hypermethylation of CpG island-containing promoters is associated with the
      inactivation of genes important to tumor initiation and progression.  One proposed role for
      DNA Mtase in tumorigenesis is therefore a direct role in the de novo methylation of these
      otherwise unmethylated CpG islands.  In this study, we sought to determine whether increased
      levels of DNA Mtase could directly affect CpG island methylation.  A full-length cDNA for
      human DNA Mtase driven by the cytomegalovirus promoter was constitutively expressed in human
      fibroblasts.  Individual clones derived from cells transfected with DNA Mtase (HMT) expressed
      1- to 50-fold the level of DNA Mtase protein and enzyme activity of the parental cell line or
      clones transfected with the control vector alone (neo).  To determine the effects of DNA Mtase
      overexpression on CpG island methylation, we examined 12 endogenous CpG island loci in the HMT
      clones.  HMT clones expressing greater-than or equal-to 9-fold the parental levels of DNA
      Mtase activity was significantly hypermethylated relative to at least 11 Neo clones at five
      CpG island loci.  In the HMT clones, methylation reached nearly 100% at susceptible CpG island
      loci with time in culture.  In contrast, there was little change in the methylation status in
      the Neo clones over the same time frame.  Taken together, the data indicate that
      overexpression of DNA Mtase can drive the de novo methylation of susceptible CpG island loci,
      thus providing support for the idea that DNA Mtase can contribute to tumor progression through
      CpG island methylation-mediated gene inactivation.
AU  - Vertino PM
AU  - Yen R-WC
AU  - Gao J
AU  - Baylin SB
PT  - Journal Article
TA  - Mol. Cell. Biol.
JT  - Mol. Cell. Biol.
SO  - Mol. Cell. Biol. 1996 16: 4555-4565.

PMID- 30533886
VI  - 7
DP  - 2018
TI  - Complete Genome Sequence of Vitreoscilla sp. Strain C1, Source of the First Bacterial Hemoglobin.
PG  - e00922-18
AB  - Vitreoscilla sp. strain C1 is of historical importance as the source of the first prokaryotic
      hemoglobin identified. Vitreoscilla spp. rely on their hemoglobin and
      cytochrome oxidase to grow in microaerobic environments despite their aerobic
      nature. To help characterize this historically relevant strain, we sequenced the
      complete Vitreoscilla sp. strain C1 genome.
AU  - Veseli IA
AU  - Mascarenhas DSAC
AU  - Juarez O
AU  - Stark BC
AU  - Pombert JF
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e00922-18.

PMID- 28642379
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Staphylococcus lutrae ATCC 700373, a Potential Pathogen Isolated from Deceased Otters.
PG  - e00572-17
AB  - Despite their relevance to human health, not all staphylococcal species have been
      characterized. As such, the potential zoonotic threats posed by uninvestigated
      species and their contribution to the staphylococcal pangenome are unclear. Here,
      we report the complete genome sequence of Staphylococcus lutrae ATCC 700373, a
      coagulase-positive species isolated from deceased otters.
AU  - Veseli IA
AU  - Tang C
AU  - Pombert JF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00572-17.

PMID- 8692685
VI  - 24
DP  - 1996
TI  - A new class of genome rare cutters.
PG  - 2483-2487
AB  - Although significant efforts have been directed at developing efficient techniques
      for rare and super rare genome cutting, only limited success has been achieved.  Here we
      propose
      a new approach to solve this problem.  We demonstrate that peptide nucleic acid 'clamps'
      (bis-
      PNAs) bind strongly and sequence specifically to short homopyrimidine sites on lambda and
      yeast
      genomic DNAs.  Such binding efficiently shields methylation/restriction sites which overlap
      with
      the bis-PNA binding sites from enzymatic methylation.  After removing the bis-PNA, the genomic
      DNAs are quantitatively cleaved by restriction enzymes into a limited number of pieces of
      lengths
      from several hundred kbp to several Mbp.  By combining various bis-PNAs with different
      methylation/restriction enzyme pairs, a huge new class of genome rare cutters can be created.
      These cutters cover the range of recognition specificities where very few, if any, cutters are
      now
      available.
AU  - Veselkov AG
AU  - Demidov VV
AU  - Nielsen PE
AU  - Frank-Kamenetskii MD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1996 24: 2483-2487.

PMID- 2253885
VI  - 95
DP  - 1990
TI  - RleAI: a novel class-IIS restriction endonuclease from Rhizobium leguminosarum recognizing 5'-CCCACA(N)12-3' and 3'-GGGTGT(N)9-5'.
PG  - 129-131
AB  - The novel class-IIS restriction endonuclease, RleAI, has the
      5'-CCCACA(N)12-3'
      3'-GGGTGT(N)9-5' specificity.
AU  - Vesely Z
AU  - Muller A
AU  - Schmitz GG
AU  - Kaluza K
AU  - Jarsch M
AU  - Kessler C
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1990 95: 129-131.

PMID- 2162525
VI  - 18
DP  - 1990
TI  - BbrPI, a novel PmaCI isoschizomer from Bacillus brevis recognizing 5'-CAC/GTG-3'.
PG  - 3423
AB  - None
AU  - Vesely Z
AU  - Schmitz GG
AU  - Jarsch M
AU  - Kessler C
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 3423.

PMID- 29122878
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Bacillus altitudinis Type Strain SGAir0031 Isolated from Tropical Air Collected in Singapore.
PG  - e01260-17
AB  - Bacillus altitudinis strain SGAir0031 (Firmicutes) was isolated from tropical air samples
      collected in Singapore. Its genome was assembled using short reads and
      single-molecule real-time sequencing, comprising one chromosome with 3.81 Mb and
      one plasmid with 32 kb. The genome consists of 3,820 protein-coding genes, 81
      tRNAs, and 24 rRNAs.
AU  - Vettath VK et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01260-17.

PMID- 29724855
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Acinetobacter indicus Type Strain SGAir0564 Isolated  from Tropical Air Collected in Singapore.
PG  - e00230-18
AB  - Acinetobacter indicus (Gammaproteobacteria) is a strict aerobic nonmotile bacterium. The
      strain SGAir0564 was isolated from air samples collected in
      Singapore. The complete genome is 3.1 Mb and was assembled using a combination of
      short and long reads. The genome contains 2,808 protein-coding genes, 80 tRNAs,
      and 21 rRNA subunits.
AU  - Vettath VK et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00230-18.

PMID- 24356847
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Strain X47-2AL, a Feline Helicobacter pylori Isolate.
PG  - e01095-13
AB  - Helicobacter pylori is a human-specific pathogen that exclusively inhabits the human gastric
      mucosa. However, occasionally, humans transmit H. pylori to
      susceptible animal hosts bred in colonies. Here, we report the genome sequence of
      strain X47-2AL, isolated from a domestic cat and used in anti-H. pylori
      immunization studies.
AU  - Veyrier FJ
AU  - Ecobichon C
AU  - Boneca IG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01095-13.

PMID- 24092789
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of a Neisseria meningitidis Serogroup C Isolate of Sequence Type 11 Linked to an Outbreak among Men Who Have Sex with Men.
PG  - e00795-13
AB  - Meningococcal disease occurs as sporadic cases in developed countries, with the occasional
      emergence of new clones of Neisseria meningitidis. Here, we report the
      genome sequence of N. meningitidis strain LNP27256, an isolate of sequence type
      11 linked to a recent outbreak among men who have sex with men in Europe.
AU  - Veyrier FJ
AU  - Hong E
AU  - Deghmane AE
AU  - Taha MK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00795-13.

PMID- 10882125
VI  - 5
DP  - 2000
TI  - Structure of BamHI bound to nonspecific DNA: A model for DNA sliding.
PG  - 889-895
AB  - The central problem faced by DNA binding proteins is how to select the correct DNA sequence
      from the sea of nonspecific sequences in a cell.  The problem is particularly acute for
      bacterial restriction enzymes because cleavage at an incorrect DNA site could be lethal.  To
      understand the basis of this selectivity, we report here the crystal structure of endonuclease
      BamHI bound to noncognate DNA.  We show that, despite only a single base pair change in the
      recognition sequence, the enzyme adopts an open configuration that is on the pathway between
      free and specifically bound forms of the enzyme.  Surprisingly, the DNA drops out of the
      binding cleft with a total loss of base-specific and backbone contacts.  Taken together, the
      structure provides a remarkable snapshot of an enzyme poised for linear diffusion (rather than
      cleavage) along the DNA.
AU  - Viadiu H
AU  - Aggarwal AK
PT  - Journal Article
TA  - Mol. Cell
JT  - Mol. Cell
SO  - Mol. Cell 2000 5: 889-895.

PMID- 9783752
VI  - 5
DP  - 1998
TI  - The role of metals in catalysis by the restriction endonuclease BamHI.
PG  - 910-916
AB  - Type II restriction enzymes are characterized by their remarkable specificity and simplicity.
      They require only divalent metals (such as Mg2+ or Mn2+) as cofactors to catalyze the
      hydrolysis of DNA. However, most of the structural work on endonucleases has been performed in
      the absence of metals, leaving unanswered questions about their mechanisms of DNA cleavage.
      Here we report structures of the endonuclease BamHI-DNA complex, determined in the presence of
      Mn2+ and Ca2+, that describe the enzyme at different stages of catalysis. Overall, the results
      support a two-metal mechanism of DNA cleavage for BamHI which is distinct from that of EcoRV.
AU  - Viadiu H
AU  - Aggarwal AK
PT  - Journal Article
TA  - Nat. Struct. Biol.
JT  - Nat. Struct. Biol.
SO  - Nat. Struct. Biol. 1998 5: 910-916.

PMID- 10806094
VI  - 130
DP  - 2000
TI  - Crystallization of Restriction Endonuclease BamHI with Nonspecific DNA.
PG  - 81-85
AB  - Restriction endonucleases show extraordinary specificity in distinguishing specific from
      nonspecific DNA sequences. A single basepair change within the recognition sequence results in
      over a million-fold loss in activity. To understand the basis of this sequence discrimination,
      it is just as important to study the nonspecific complex as the specific complex. We describe
      here the crystallization of restriction endonuclease BamHI with several nonspecific
      oligonucleotides. The 11-mer, 5'-ATGAATCCATA-3', yielded cocrystals with BamHI, in the
      presence of low salt, that diffracted to 1.9 A with synchrotron radiation. The cocrystals
      belong to the space group P2(1)2(1)2(1) with unit cell dimensions of a = 114.8 A, b = 91.1 A,
      c = 66.4 A, alpha = 90 degrees, beta = 90 degrees, gamma = 90 degrees. This success in the
      cocrystallization of BamHI with a nonspecific DNA provides insights for future attempts at
      crystallization of other nonspecific DNA-protein complexes. Copyright 2000 Academic Press.
AU  - Viadiu H
AU  - Kucera R
AU  - Schildkraut I
AU  - Aggarwal AK
PT  - Journal Article
TA  - J. Struct. Biol.
JT  - J. Struct. Biol.
SO  - J. Struct. Biol. 2000 130: 81-85.

PMID- 12876363
VI  - 59
DP  - 2003
TI  - Crystallization of restriction endonuclease SfiI in complex with DNA.
PG  - 1493-1495
AB  - The SfiI endonuclease from Streptomyces fimbriatus (EC 3.1.21.4) is a tetrameric enzyme that
      binds simultaneously to two recognition sites and
      cleaves both sites concertedly. It serves as a good model system for
      studying both specificity and cooperative DNA binding. Crystals of the
      enzyme were obtained by the hanging-drop vapor-diffusion method in complex
      with a 21-mer oligonucleotide. The crystals are trigonal, with unit-cell
      parameters a = b = 85.7, c = 202.6 A, and diffract to 2.6 A resolution on
      a rotating-anode X-ray generator. Preliminary X-ray analysis reveals the
      space group to be either P3(1)21 or P3(2)21. Interestingly, the crystals
      change to space group P6(1)22, with unit-cell parameters a = b = 85.5, c =
      419.6 A, when the selenomethionyl (SeMet) derivative of the enzyme is
      co-crystallized with the same DNA. Phase information is currently being
      derived from this SeMet SfiI-DNA complex.
AU  - Viadiu H
AU  - Vanamee ES
AU  - Jacobson EM
AU  - Schildkraut I
AU  - Aggarwal AK
PT  - Journal Article
TA  - Acta Crystallogr. D Biol. Crystallogr.
JT  - Acta Crystallogr. D Biol. Crystallogr.
SO  - Acta Crystallogr. D Biol. Crystallogr. 2003 59: 1493-1495.

PMID- 
VI  - 60
DP  - 2000
TI  - Structural study of specificity and catalysis by restriction endonuclease BamHI.
PG  - 5978
AB  - The restriction endonuclease BamHI is a phosphoryl-transferase that recognizes the DNA
      sequence 5'-GGATCC-3' and cleaves the phosphodiester bond between the first and the second
      bases.  In this work we used X-ray crystallography to analyze the different steps in the
      mechanism of DNA recognition and catalysis by BamHI.  BamHI, a polypeptide of 213 amino acids,
      forms a dimer in solution and starts its catalytic mechanism binding DNA non-specifically.
      Initially, the crystal structure of BamHI bound to a non-specific DNA (5'-GAATCC-3') at 2.0
      A is presented.  The analysis of the non-specific DNA-BamHI structure shows striking
      differences with the previously reported specific complex.  In the non-specific complex, BamHI
      has very few contacts to the DNA which shows exceptionally high B-factors and its position in
      the DNA cavity drops 7A with respect to the specific complex.  Although the protein
      conformation is symmetrical and it closely resembles the one in the absence of DNA, the
      quaternary arrangement results in a DNA cavity with an intermediate width between the ones
      observed for the five protein and the specific complex.  In summary, the non-specific
      DNA-BamHI complex explains the electrostatic character of the non-specific DNA-protein binding
      and suggest that BamHI is trapped in a conformation suitable for sliding along the DNA.  Once
      BamHI has found the specific site, it cleaves both DNA strands in a sequential manner.  In
      this work, the crystal structures of BamHI before and after the reaction are presented, at 2.0
      A and 1.8 A respectively.  These data shows evidence to support a two-metal mechanism for
      BamHI catalysis.  The metals are coordinated by three acidic residues and they stabilize the
      transition state.  The residue Glu113 was identified as a general base.  A water molecule
      attacking the phosphate group, and a water donating a proton to the leaving group were also
      located.  Furthermore, the comparison of BamHI, BamHI Glu113Lys mutant, and other restriction
      endonucleases suggest a catalytic mechanism for those enzymes that contain three acidic
      residues and a lysine in the active site.  Overall the work presented here represents the most
      comprehensive study of different stages in the catalytic cycle of a restriction endonuclease.
AU  - Viadiu-Ilarraza H
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 2000 60: 5978.

PMID- 28254974
VI  - 5
DP  - 2017
TI  - Genome Sequences of Two Brucella suis Strains Isolated from the Same Patient, 8 Years Apart.
PG  - e01687-16
AB  - Brucella suis is a Gram-negative, facultative intracellular pathogen that has pigs as its
      preferred host, but it can also infect humans. Here, we report the
      draft genome sequences of two B. suis strains that were isolated from the same
      patient, 8 years apart.
AU  - Viana MV
AU  - Wattam AR
AU  - Govil BD
AU  - Boisvert S
AU  - Brettin TS
AU  - Frace M
AU  - Xia F
AU  - Azevedo V
AU  - Tiller R
AU  - Hoffmaster AR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01687-16.

PMID- 28232424
VI  - 5
DP  - 2017
TI  - Genome Sequences of Three Brucella canis Strains Isolated from Humans and a Dog.
PG  - e01688-16
AB  - Brucella canis is a facultative intracellular pathogen that preferentially infects members of
      the Canidae family. Here, we report the genome sequencing of
      two Brucella canis strains isolated from humans and one isolated from a dog host.
AU  - Viana MV
AU  - Wattam AR
AU  - Govil BD
AU  - Boisvert S
AU  - Brettin TS
AU  - Frace M
AU  - Xia F
AU  - Azevedo V
AU  - Tiller R
AU  - Hoffmaster AR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01688-16.

PMID- 25883282
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequences of Five Burkholderia pseudomallei Isolates from Australian Cystic Fibrosis Patients.
PG  - e00254-15
AB  - We report here five improved high-quality draft genomes of Burkholderia pseudomallei isolated
      from Australian cystic fibrosis (CF) patients. This
      pathogen is rarely seen in CF patients. These genomes will be used to better
      understand chronic carriage of B. pseudomallei in the CF lung and the within-host
      evolution of longitudinal isolates from these patients.
AU  - Viberg LT
AU  - Price EP
AU  - Kidd TJ
AU  - Bell SC
AU  - Currie BJ
AU  - Sarovich DS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00254-15.

PMID- 30533925
VI  - 7
DP  - 2018
TI  - Draft Genome Sequence of the Cadmium-Resistant Strain JJU2, Belonging to the Family Hapalosiphonaceae of the Cyanobacteria.
PG  - e00876-18
AB  - Here, we report the genome of strain JJU2, a cyanobacterium of the family Hapalosiphonaceae
      known to be resistant to high cadmium levels, assembled from a
      nonaxenic, unialgal culture from Marinduque, Philippines. The draft genome is 7.1
      Mb long with a GC content of 40.05% and contains 5,625 protein-coding genes.
AU  - Victoria AJ
AU  - Cao E
AU  - Salmaso N
AU  - Segata N
AU  - Donati C
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e00876-18.

PMID- 19211756
VI  - 83
DP  - 2009
TI  - Metagenomic analyses of viruses in stool samples from children with acute flaccid paralysis.
PG  - 4642-4651
AB  - We analyzed viral nucleic acids in stool samples collected from 35 South
      Asian children with nonpolio acute flaccid paralysis (AFP).
      Sequence-independent reverse transcription and PCR amplification of
      capsid-protected, nuclease-resistant viral nucleic acids were followed by
      DNA sequencing and sequence similarity searches. Limited Sanger sequencing
      (35 to 240 subclones per sample) identified an average of 1.4 distinct
      eukaryotic viruses per sample, while pyrosequencing yielded 2.6 viruses
      per sample. In addition to bacteriophage and plant viruses, we detected
      known enteric viruses, including rotavirus, adenovirus, picobirnavirus,
      and human enterovirus species A (HEV-A) to HEV-C, as well as numerous
      other members of the Picornaviridae family, including parechovirus, Aichi
      virus, rhinovirus, and human cardiovirus. The viruses with the most
      divergent sequences relative to those of previously reported viruses
      included members of a novel Picornaviridae genus and four new viral
      species (members of the Dicistroviridae, Nodaviridae, and Circoviridae
      families and the Bocavirus genus). Samples from six healthy contacts of
      AFP patients were similarly analyzed and also contained numerous viruses,
      particularly HEV-C, including a potentially novel Enterovirus genotype.
      Determining the prevalences and pathogenicities of the novel genotypes,
      species, genera, and potential new viral families identified in this study
      in different demographic groups will require further studies with
      different demographic and patient groups, now facilitated by knowledge of
      these viral genomes.
AU  - Victoria JG
AU  - Kapoor A
AU  - Li L
AU  - Blinkova O
AU  - Slikas B
AU  - Wang C
AU  - Naeem A
AU  - Zaidi S
AU  - Delwart E
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 2009 83: 4642-4651.

PMID- 28385848
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Rhizobacterium Pseudomonas chlororaphis PCL1601, Displaying Biocontrol against Soilborne Phytopathogens.
PG  - e00130-17
AB  - In this study, we present the draft genome sequence of the bacterial strain Pseudomonas
      chlororaphis PCL1601. This bacterium was isolated from the
      rhizosphere of healthy avocado trees and displayed antagonistic and biological
      control activities against different soilborne phytopathogenic fungi and
      oomycetes.
AU  - Vida C
AU  - de Vicente A
AU  - Cazorla FM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00130-17.

PMID- 23580706
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of VIM-2-Producing Multidrug-Resistant Pseudomonas aeruginosa ST175, an Epidemic High-Risk Clone.
PG  - e00112-13
AB  - The VIM-2-producing multidrug-resistant high-risk clone Pseudomonas aeruginosa sequence type
      (ST) 175 was isolated in the setting of a large outbreak in
      Hospital Universitario 12 de Octubre (Spain) from 2007 to 2010. This strain was
      resistant to all beta-lactams, fluoroquinolones, and aminoglycosides, with the
      exception of amikacin, and has become an endemic clone in our institution.
AU  - Viedma E
AU  - Juan C
AU  - Otero JR
AU  - Oliver A
AU  - Chaves F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00112-13.

PMID- 25359914
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Colistin-Only-Susceptible Pseudomonas aeruginosa Strain  ST235, a Hypervirulent High-Risk Clone in Spain.
PG  - e01097-14
AB  - We report the genome of colistin-only-susceptible Pseudomonas aeruginosa strain ST235
      (PA_ST235). This isolate was obtained in the setting of an outbreak in a
      tertiary hospital in Spain. This clone was apparently associated with a
      significantly higher mortality rate. The ST235 clone also appears to be
      associated with greater virulence.
AU  - Viedma E
AU  - Villa J
AU  - Juan C
AU  - Oliver A
AU  - Chaves F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01097-14.

PMID- 2408684
VI  - 50
DP  - 1985
TI  - Effect of 5-azacytidine on E. coli cells with different DNA methylases.
PG  - 749-754
AB  - A correlation was found between the bacteriocide effect of 5-aza-C and the amount of cytosine
      DNA-methylases in E. coli cells.  5-Aza-C-DNA on cytosine DNA-methylases was due to the
      formation of stable inactive complexes between the enzyme and the non-methylating cytosine
      analog in the recognition sites.  Cytosine DNA-methylase EcoRII formed a relatively firm bond
      with 5-aza-C-DNA, which could be disrupted by 1 M KCl; this disruption restores the
      DNA-methylase activity and the inhibiting capacity of 5-aza-C-DNA.  Thus, the binding of
      cytosine DNA-methylase to 5-aza-C in DNA is noncovalent; the inhibition of the enzyme by
      5-aza-C-DNA is reversible.
AU  - Vienozinskis MT
AU  - Nesterenko VF
AU  - Kanopkaite SI
AU  - Buryanov YI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1985 50: 749-754.

PMID- 26294640
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Acinetobacter baumannii Strain B8300, Which Displays  High Twitching Motility.
PG  - e00956-15
AB  - Acinetobacter baumannii has emerged as an important nosocomial pathogen causing health
      care-associated infections. In this study, we determined the genome of a
      twitching-positive clinical strain, B8300, isolated from a hospital in southern
      India. De novo assembly of PacBio long-read sequencing data generated the B8300
      genome that consists of a chromosome of 3.82 Mbp and a plasmid of 25.15 kbp.
AU  - Vijaykumar S
AU  - Balaji V
AU  - Biswas I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00956-15.

PMID- 26294630
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Acinetobacter baumannii Strain B8342, a Motility-Positive Clinical Isolate.
PG  - e00925-15
AB  - Acinetobacter baumannii is an emerging Gram-negative pathogen responsible for health
      care-associated infections. In this study, we determined the genome of a
      motility-positive clinical strain, B8342, isolated from a hospital in southern
      India. The B8342 genome, which is 3.94 Mbp, was generated by de novo assembly of
      PacBio long-read sequencing data.
AU  - Vijaykumar S
AU  - Balaji V
AU  - Biswas I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00925-15.

PMID- Not carried by PubMed...
VI  - 57
DP  - 1997
TI  - Regulation of the gene expression of the PvuII restriction-modification system.
PG  - 7379B-7380B
AB  - The pvuIIC gene of the PvuII restriction-modification system of Proteus vulgaris encodes the
      9.4 kDa C.PvuII protein.  This protein has a helix-turn-helix motif and is a DNA binding
      protein.  The C.PvuII protein binds to the C-box sequence located within the pvuIIM gene;
      C.PvuII binding to its target sequence would interfere with transcription of pvuIIM.
      Therefore, C.PvuII may play the role of a repressor of methyltransferase expression.  Previous
      studies have shown that the overexpression of the methyltransferase is lethal to the cell; as
      such, the C.PvuII protein may be involved in preventing the overexpression of the
      methyltransferase, thereby preventing the deleterious effects of hypermethylation.  This work
      shows that the overexpression of C.PvuII is lethal to cells also containing the intact PvuII
      restriction-modification system, perhaps due to the repression of pvuIIM, paving the way for
      autorestriction.  The C.PvuII protein does not appear to regulate the transcription of either
      the pvuIIC or pvuIIR genes, as seen in primer extension analyses.  In addition, the pvuIIC and
      pvuIIR genes are transcribed as a polycistronic message, since the pvuIIR gene itself does not
      appear to have a strong promoter; the polycistronic message originates from the relatively
      stronger pvuIIC promoter.  The 'C-proteins', of which C.PvuII is a member, are encoded by
      genes of several restriction-modification systems, and appear to enhance endonuclease
      expression, while downregulating that of the methyltransferase.  This work suggests that
      C.PvuII, like its counterparts of other restriction-modification systems, diminishes
      methyltransferase expression.
AU  - Vijesurier RM
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1997 57: 7379B-7380B.

PMID- 10629196
VI  - 182
DP  - 2000
TI  - Role and mechanism of action of C.PvuII, a regulatory protein conserved among restriction-modification systems.
PG  - 477-487
AB  - The PvuII restriction-modification system is a type II system, which means that its
      restriction endonuclease and modification methyltransferase are independently active proteins.
      The PvuII system is carried on a plasmid, and its movement into a new host cell is expected to
      be followed initially by expression of the methyltransferase gene alone so that the new
      host's DNA is protected before endonuclease activity appears.  Previous studies have
      identified a regulatory gene (pvuIIC) between the divergently oriented genes for the
      restriction endonuclease (pvuIIR) and modification methyltransferase (pvuIIM), with pvuIIC in
      the same orientation as and partially overlapping pvuIIR.  This product of pvuIIC, C.PvuII,
      was found to act in trans and to be required for expression of pvuIIR.  In this study we
      demonstrate that premature expression of pvuIIC prevents establishment of the PvuII genes,
      consistent with the model that requiring C.PvuII for pvuIIR expression provides a timing delay
      essential for protection of the new host's DNA.  We find that the opposing pvuIIC and pvuIIM
      transcripts overlap by over 60 nucleotides at their 5' ends, raising the possibility that
      their hybridization might play a regulatory role.  We furthermore characterize the action of
      C.PvuII, demonstrating that it is a sequence-specific DNA-binding protein that binds to the
      pvuIIC promoter and stimulates transcription of both pvuIIC and pvuIIR into a polycistronic
      mRNA.  The apparent location of C.PvuII binding, overlapping the -10 promoter hexamer and the
      pvuIICR transcriptional starting points, is highly unusual for transcriptional activators.
AU  - Vijesurier RM
AU  - Carlock L
AU  - Blumenthal RM
AU  - Dunbar JC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2000 182: 477-487.

PMID- 22689233
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of the Nitrophenol-Degrading Actinomycete Rhodococcus imtechensis RKJ300.
PG  - 3543
AB  - We report the 8.231-Mb genome sequence of Rhodococcus imtechensis RKJ300, isolated from
      pesticide-contaminated soil in Punjab, India. The genome sequence
      of the strain RKJ300 will be helpful in exploring the molecular pathways involved
      in the degradation of nitrophenols.
AU  - Vikram S
AU  - Kumar S
AU  - Subramanian S
AU  - Raghava GP
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3543.

PMID- 23516196
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the 2-Chloro-4-Nitrophenol-Degrading Bacterium Arthrobacter sp. Strain SJCon.
PG  - e0005813
AB  - We report the 4.39-Mb draft genome sequence of the 2-chloro-4-nitrophenol-degrading bacterium
      Arthrobacter sp. strain SJCon,
      isolated from a pesticide-contaminated site. The draft genome sequence of strain
      SJCon will be helpful in studying the genetic pathways involved in the
      degradation of several aromatic compounds.
AU  - Vikram S
AU  - Kumar S
AU  - Vaidya B
AU  - Pinnaka AK
AU  - Raghava GP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0005813.

PMID- 25428965
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of an International Clonal Lineage 1 Acinetobacter baumannii Strain from Argentina.
PG  - e01190-14
AB  - In the last few years Acinetobacter baumannii has emerged worldwide as an important nosocomial
      pathogen in medical institutions. Here, we present the draft
      genome sequence of the international clonal lineage 1 (ICL1) A. baumannii strain
      A144 that was isolated in a hospital in Buenos Aires City in the year 1997. The
      strain is susceptible to carbapenems and resistant to trimethoprim and
      gentamicin.
AU  - Vilacoba E
AU  - Deraspe M
AU  - Traglia GM
AU  - Roy PH
AU  - Ramirez MS
AU  - Centron D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01190-14.

PMID- 9763678
VI  - 82
DP  - 1998
TI  - Assignment  of candidate DNA methyltransferase gene (DNMT2) to human chromosome band 10p15.1 by in situ hybridization.
PG  - 120
AB  - Methylation of deoxycytidine in mammalian DNA is thought to be involved in many biological
      phenomena.  Only one DNA methyltransferase was known in human.  The gene (DNMT1) was localized
      to 19p13.2.  Recently a putative new DNA methyltransferase (DNMT2) has been cloned and
      characterized.  Using a panel of radiation hybrids, this gene has been mapped to 10p14-p12.
AU  - Vilain A
AU  - Apiou F
AU  - Dutrillaux B
AU  - Malfoy B
PT  - Journal Article
TA  - Cytogenet. Cell Genet.
JT  - Cytogenet. Cell Genet.
SO  - Cytogenet. Cell Genet. 1998 82: 120.

PMID- 28082497
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Streptococcus iniae UEL-Si1, Isolated in Diseased Nile Tilapia (Oreochromis niloticus) from Northern Parana, Southern Brazil.
PG  - e01458-16
AB  - The Streptococcus iniae UEL-Si1 strain was isolated from diseased Nile tilapia within the
      Paranapanema River Basin, Northern Parana, Brazil. This is an emerging
      infectious disease agent of fish from Brazil, and sequencing of the complete
      genome is fundamental to understanding aspects relative to pathogenesis,
      infection, epidemiology, and immunity.
AU  - Vilas-Boas LA
AU  - Headley SA
AU  - Goncalves KB
AU  - Scarpassa JA
AU  - Pretto-Giordano LG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01458-16.

PMID- 29748401
VI  - 6
DP  - 2018
TI  - Genome Sequence of Bacillus cereus Strain TG1-6, a Plant-Beneficial Rhizobacterium That Is Highly Salt Tolerant.
PG  - e00351-18
AB  - The complete genome sequence of Bacillus cereus strain TG1-6, which is a highly salt-tolerant
      rhizobacterium that enhances plant tolerance to drought stress, is
      reported here. The sequencing process was performed based on a combination of
      pyrosequencing and single-molecule sequencing. The complete genome is estimated
      to be approximately 5.42 Mb, containing a total of 5,610 predicted protein-coding
      DNA sequences (CDSs).
AU  - Vilchez JI
AU  - Tang Q
AU  - Kaushal R
AU  - Chen S
AU  - Liu R
AU  - Zhang H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00351-18.

PMID- 29930045
VI  - 6
DP  - 2018
TI  - Genome Sequence of Bacillus megaterium Strain YC4-R4, a Plant Growth-Promoting Rhizobacterium Isolated from a High-Salinity Environment.
PG  - e00527-18
AB  - Here, we report the complete genome sequence for Bacillus megaterium strain YC4-R4, a highly
      salt-tolerant rhizobacterium that promotes growth in plants. The
      sequencing process was performed by combining pyrosequencing and single-molecule
      sequencing techniques. The complete genome is estimated to be approximately 5.44
      Mb, containing a total of 5,673 predicted protein-coding DNA sequences (CDSs).
AU  - Vilchez JI
AU  - Tang Q
AU  - Kaushal R
AU  - Wang W
AU  - Lv S
AU  - He D
AU  - Chu Z
AU  - Zhang H
AU  - Liu R
AU  - Zhang H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00527-18.

PMID- 11102456
VI  - 275
DP  - 2000
TI  - Functional roles of the conserved threonine 250 in the target recognition domain of HhaI DNA methyltransferase.
PG  - 38722-38730
AB  - DNA cytosine-5-methyltransferase HhaI recognizes the GCGC sequence and flips the inner
      cytosine out of the DNA helix and into the catalytic site for methylation. The 5'-phosphate
      of the flipped out cytosine is in contact with the conserved Thr-250 from the target
      recognition domain. We have produced 12 mutants of Thr-250 and examined their methylation
      potential in vivo. Six active mutants were subjected to detailed biochemical and structural
      studies. Mutants with similar or smaller side chains (Ser, Cys, and Gly) are very similar to
      wild-type enzyme in terms of steady-state kinetic parameters k(cat), K(m)(DNA), K(m)(AdoMet).
      In contrast, the mutants with bulkier side chains (Asn, Asp, and His) show increased K(m)
      values for both substrates. Fluorescence titrations and stopped-flow kinetic analysis of
      interactions with duplex oligonucleotides containing 2-aminopurine at the target base position
      indicate that the T250G mutation leads to a more polar but less solvent-accessible position of
      the flipped out target base. The x-ray structure of the ternary M.HhaI(T250G).DNA. AdoHcy
      complex shows that the target cytosine is locked in the catalytic center of enzyme. The space
      created by the mutation is filled by water molecules and the adjacent DNA backbone atoms
      dislocate slightly toward the missing side chain. In aggregate, our results suggest that the
      side chain of Thr-250 is involved in constraining the conformation the DNA backbone and the
      target base during its rotation into the catalytic site of enzyme.
AU  - Vilkaitis G
AU  - Dong A
AU  - Weinhold E
AU  - Cheng X
AU  - Klimasauskas S
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2000 275: 38722-38730.

PMID- 10361019
VI  - 271
DP  - 1999
TI  - Bisulfite sequencing protocol displays both 5-methylcytosine and N4-methylcytosine.
PG  - 116-119
AB  - DNA premethylated in vitro or in vivo with a DNA cytosine-N4 methyltransferase, M.MvaI, was
      analyzed using a bisulfite DNA sequencing technique. We find that, under reaction conditions
      reliably displaying 5-methylcytosine on the sequencing ladder, N4-methylcytosine residues are
      displayed with efficiencies from 33 to 100%, depending on a sequence context. This finding
      offers a convenient tool for determining sequence specificity of cytosine-N4
      methyltransferases and demonstrates that the two types of biological cytosine methylation are
      not reliably distinguished by this technique.
AU  - Vilkaitis G
AU  - Klimasauskas S
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 1999 271: 116-119.

PMID- 11917015
VI  - 30
DP  - 2002
TI  - Circular permutation of DNA cytosine-N4 methyltransferases: in vivo coexistence in the BcnI system and in vitro probing by hybrid formation.
PG  - 1547-1557
AB  - Sequence analysis of the BcnI restriction-modification system from Bacillus centrosporus
      revealed four open reading frames (bcnIC, bcnIR, bcnIB and bcnIA) that are arranged as two
      converging collinear pairs. One pair encodes a putative small regulatory protein, C.BcnI, and
      the restriction endonuclease R.BcnI. The other two gene products are the DNA cytosine-N4
      methyltransferases M.BcnIA and M.BcnIB, which differ by circular permutation of conserved
      sequence motifs. The BcnI methyltransferases are isospecific on double-stranded DNA
      [methylation specificity CC(C/G)GG], but M.BcnIA can also methylate the target sites in
      single-stranded DNA. Functional analysis shows that bcnIA is dispensable (bcnIB is capable of
      protecting the DNA against the in vivo activity of bcnIR); in contrast, no stable clones were
      obtained if bcnIB alone was deleted from the system. By analogy with the DpnII system, the
      second methylase M.BcnIA may play a role in the transformation proficiency of its
      gram-positive host. The interchangeability of homologous elements in the beta class of
      cytosine-N4 methylases was probed by hybrid formation between M.BcnIB and its closest homolog
      M.Cfr9I (CCCGGG) employing a novel semi-random strategy combined with selection for catalytic
      activity. The fusion points in the active hybrids mapped in a narrow region located between
      sequence motifs X and I. Our data illustrate that recombination of two related sequences by
      circular permutation may serve as an evolutionary mechanism for creating new specificities of
      amino MTases.
AU  - Vilkaitis G
AU  - Lubys A
AU  - Merkiene E
AU  - Timinskas A
AU  - Janulaitis A
AU  - Klimasauskas S
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2002 30: 1547-1557.

PMID- 11283006
VI  - 276
DP  - 2001
TI  - The mechanism of DNA cytosine-5 methylation. Kinetic and mutational dissection of HhaI methyltransferase.
PG  - 20924-20934
AB  - Kinetic and binding studies involving a model DNA cytosine-5-methyltransferase, M.HhaI, and a
      37-mer DNA duplex containing a single hemimethylated target site were applied to characterize
      intermediates on the reaction pathway. Stopped-flow fluorescence studies reveal that cofactor
      S-adenosyl-l-methionine (AdoMet) and product S-adenosyl-l-homocysteine (AdoHcy) form similar
      rapidly reversible binary complexes with the enzyme in solution. The M.HhaI.AdoMet complex
      (k(off) = 22 s^-1, KD = 6 microM) is partially converted into products during
      isotope-partitioning experiments, suggesting that it is catalytically competent. Chemical
      formation of the product M.HhaI.(Me)DNA.AdoHcy (k(chem) = 0.26 s^-1) is followed by a slower
      decay step (k(off) = 0.045 s^-1), which is the rate-limiting step in the catalytic cycle
      (k(cat) = 0.04 s^-1). Analysis of reaction products shows that the hemimethylated substrate
      undergoes complete (>95%) conversion into fully methylated product during the initial burst
      phase, indicating that M.HhaI exerts high binding selectivity toward the target strand. The
      T250N, T250D, and T250H mutations, which introduce moderate perturbation in the catalytic
      site, lead to substantially increased KD(DNA(ternary)), k(off)(DNA(ternary)),
      KM(AdoMet(ternary)) values but small changes in KD(DNA(binary)), KD(AdoMet(binary)),
      k(chem), and k(cat). When the target cytosine is replaced with 5-fluorocytosine, the chemistry
      step leading to an irreversible covalent M.HhaI.DNA complex is inhibited 400-fold
      (k(chem)(5FC) = 0.7 x 10^-3 s^-1), and the Thr-250 mutations confer further dramatic
      decrease of the rate of the covalent methylation k(chem). We suggest that activation of the
      pyrimidine ring via covalent addition at C-6 is a major contributor to the rate of the
      chemistry step (k(chem)) in the case of cytosine but not 5-fluorocytosine. In contrast to
      previous reports, our results imply a random substrate binding order mechanism for M.HhaI.
AU  - Vilkaitis G
AU  - Merkiene E
AU  - Serva S
AU  - Weinhold E
AU  - Klimasauskas S
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2001 276: 20924-20934.

PMID- 15509558
VI  - 280
DP  - 2005
TI  - Processive methylation of hemimethylated CpG sites by mouse Dnmt1 DNA methyltransferase.
PG  - 64-72
AB  - DNA methyltransferase Dnmt1 ensures clonal transmission of lineage-specific DNA methylation
      patterns in a mammalian genome during
      replication. Dnmt1 is targeted to replication foci, interacts with
      PCNA, and favors methylating the hemimethylated form of CpG sites. To
      understand the underlying mechanism of its maintenance function, we
      purified recombinant forms of full-length Dnmt1, a truncated form of
      Dnmt1-(291-1620)lacking the binding sites for PCNA and DNA and examined
      their processivity using a series of long unmethylated and
      hemimethylated DNA substrates. Direct analysis of methylation patterns
      using bisulfite-sequencing and hairpin-PCR techniques demonstrated that
      full-length Dnmt1 methylates hemimethylated DNA with high processivity
      and a fidelity of over 95%, but unmethylated DNA with much less
      processivity. The truncated form of Dnmt1 showed identical properties
      to full-length Dnmt1 indicating that the N-terminal 290-amino acid
      residue region of Dnmt1 is not required for preferential activity
      toward hemimethylated sites or for processivity of the enzyme.
      Remarkably, our analyses also revealed that Dnmt1 methylates
      hemimethylated CpG sites on one strand of double-stranded DNA during a
      single processive run. Our findings suggest that these inherent
      enzymatic properties of Dnmt1 play an essential role in the faithful
      and efficient maintenance of methylation patterns in the mammalian
      genome.
AU  - Vilkaitis G
AU  - Suetake I
AU  - Klimasauskas S
AU  - Tajima S
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2005 280: 64-72.

PMID- 23118463
VI  - 86
DP  - 2012
TI  - Complete Genome Sequence of Vibrio parahaemolyticus Bacteriophage vB_VpaM_MAR.
PG  - 13138-13139
AB  - Vibrio parahaemolyticus is a major pathogen that is mainly associated with seafood and is a
      global food safety issue. Our objective was to isolate and completely sequence a specific
      phage against this bacterium. Phage vB_VpaM_MAR is able to lyse 76% of the V. parahaemolyticus
      strains tested. MAR belongs to the Myoviridae family and has a genome comprised of
      double-stranded DNA with a size of 41,351 bp, a G+C content of 51.3%, and 62 open reading
      frames (ORFs). Bioinformatic analysis showed that phage MAR is closely related to Vibrio
      phages VHML, VP58.5, and VP882 and Halomonas aquamarina phage PhiHAP-1.
AU  - Villa AA
AU  - Kropinski AM
AU  - Abbasifar R
AU  - Griffiths MW
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 2012 86: 13138-13139.

PMID- 25081259
VI  - 2
DP  - 2014
TI  - Draft Whole-Genome Sequence of OXA-48-Producing Multidrug-Resistant Klebsiella pneumoniae KP_ST11_OXA-48.
PG  - e00737-14
AB  - We present the draft genome sequence of a blood culture isolate of OXA-48-producing Klebsiella
      pneumoniae (sequence type 11 [ST11]) obtained in the
      course of a hospital outbreak in Spain. Sequence analysis showed 121 genes
      related to antibiotic and antiseptic resistance, including blaOXA-48, which was
      located in an IncL/M plasmid.
AU  - Villa J
AU  - Viedma E
AU  - Branas P
AU  - Mingorance J
AU  - Chaves F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00737-14.

PMID- 24009122
VI  - 1
DP  - 2013
TI  - Draft Whole-Genome Sequence of VIM-1-Producing Multidrug-Resistant Enterobacter cloacae EC_38VIM1.
PG  - e00694-13
AB  - The VIM-1-producing multidrug-resistant strain Enterobacter cloacae was isolated  from blood
      culture. The strain showed multiple resistances to clinically used
      antibiotics, including all beta-lactams, fluoroquinolones, aminoglycosides, and
      sulfonamides. Sequence analysis showed the presence of 14 genes associated with
      resistance to antibiotics, including the metallo-beta-lactamase VIM-1 gene, which
      was located in a class 1 integron.
AU  - Villa J
AU  - Viedma E
AU  - Otero JR
AU  - Chaves F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00694-13.

PMID- 27056222
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of KPC-3- and CTX-M-15-Producing Klebsiella pneumoniae Sequence Type 307.
PG  - e00213-16
AB  - Klebsiella pneumoniaesequence type (ST) 307,
      carryingblaKPC-3,blaCTX-M-15,blaOXA-1,aac(6')-Ib-cr, andqnrB1 genes, is replacing
      the predominant hyperepidemic ST258 clone in Italy. Whole-genome and complete
      plasmid sequencing of one ST307 strain was performed and new features were
      identified.
AU  - Villa L
AU  - Feudi C
AU  - Fortini D
AU  - Iacono M
AU  - Bonura C
AU  - Endimiani A
AU  - Mammina C
AU  - Carattoli A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00213-16.

PMID- 28336590
VI  - 5
DP  - 2017
TI  - First Insights into the Genome Sequence of the Strictly Anaerobic Homoacetogenic  Sporomusa sphaeroides Strain E (DSM 2875).
PG  - e00037-17
AB  - Here, we report the draft genome sequence of Sporomusa sphaeroides strain E (DSM  2875), a
      strict anaerobic homoacetogenic bacterium. It is able to grow
      autotrophically on different one-carbon compounds. The strain possesses several
      genes of the Wood-Ljungdahl pathway. The genome consists of a single chromosome
      (4.98 Mb).
AU  - Villamizar GA
AU  - Daniel R
AU  - Poehlein A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00037-17.

PMID- 24744340
VI  - 2
DP  - 2014
TI  - Genome Sequence of Bacillus pumilus MTCC B6033.
PG  - e00327-14
AB  - Bacillus pumilus is a Gram-positive, rod-shaped, aerobic bacterium isolated from
      the soil. B. pumilus strain B6033 was originally selected as a biocatalyst for
      the stereospecific oxidation of beta-lactams. Here, we present a 3.8-Mb assembly
      of its genome, which is the second fully assembled genome of a B. pumilus strain.
AU  - Villanueva J
AU  - Switala J
AU  - Ivancich A
AU  - Loewen PC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00327-14.

PMID- 29097460
VI  - 5
DP  - 2017
TI  - Twelve Complete Reference Genomes of Clinical Isolates in the Capnocytophaga Genus.
PG  - e01186-17
AB  - We report here 1 near-complete genome sequence and 12 complete genome sequences for clinical
      Capnocytophaga isolates. Total read coverages ranged from 211x to
      737x, and genome sizes ranged from 2.41 Mb to 3.10 Mb. These genomes will enable
      a more comprehensive taxonomic evaluation of the Capnocytophaga genus.
AU  - Villarma A
AU  - Gulvik CA
AU  - Rowe LA
AU  - Sheth M
AU  - Juieng P
AU  - Nicholson AC
AU  - Loparev VN
AU  - McQuiston JR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01186-17.

PMID- 28254966
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Immunobiotic Strain Lactobacillus jensenii TL2937.
PG  - e00005-17
AB  - The genome of the immunomodulatory strain Lactobacillus jensenii TL2937 is described here. The
      draft genome has a total length of 1,678,416 bp, a G+C
      content of 34.3%, and 1,470 predicted protein-coding sequences. The genome
      information will be useful for gaining insight into the immunomodulatory
      properties of the TL2937 strain in the porcine host.
AU  - Villena J
AU  - Masumizu Y
AU  - Iida H
AU  - Ikeda-Ohtsubo W
AU  - Albarracin L
AU  - Makino S
AU  - Ohkawara S
AU  - Kimura K
AU  - Saavedra L
AU  - Hebert EM
AU  - Kitazawa H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00005-17.

PMID- 27881548
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Lactobacillus plantarum TL2766, a Strain with the Ability To Ferment Wakame.
PG  - e01328-16
AB  - The genome sequence of Lactobacillus plantarum TL2766, a strain with the ability  to ferment
      wakame (Undaria pinnatifida), is described here. The reads were
      assembled into contigs, with a total size of 3,310,195 bp. The genome information
      will be useful for further specific genetic studies of this strain and for its
      biotechnological applications.
AU  - Villena J
AU  - Saavedra L
AU  - Hebert EM
AU  - Masumizu Y
AU  - Sato N
AU  - Humayun KAK
AU  - Albarracin L
AU  - Ikeda-Ohtsubo W
AU  - Makino S
AU  - Kimura K
AU  - Ohkawara S
AU  - Kitazawa H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01328-16.

PMID- 28280008
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Lactobacillus plantarum MPL16, a Wakame-Utilizing Immunobiotic Strain Isolated from Swine Feces.
PG  - e00006-17
AB  - The genome of the immunomodulatory Lactobacillus plantarum MPL16, a strain able to ferment
      wakame (Undaria pinnatifida), is described here. The reads were
      assembled into contigs with a total size 3,278,495 bp. The genome information
      will be useful for further specific genetic studies of this strain that evaluate
      its immunomodulatory and biotechnological properties.
AU  - Villena J
AU  - Saavedra L
AU  - Hebert EM
AU  - Suda Y
AU  - Masumizu Y
AU  - Albarracin L
AU  - Clua P
AU  - Ikeda-Ohtsubo W
AU  - Kitazawa H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00006-17.

PMID- 22815445
VI  - 194
DP  - 2012
TI  - Complete Genome Sequences of Methylophaga sp. Strain JAM1 and Methylophaga sp. Strain JAM7.
PG  - 4126-4127
AB  - Methylophaga sp. strains JAM1 and JAM7 have been isolated from a denitrification  system.
      Strain JAM1 was the first Methylophaga strain reported to be able to grow
      under denitrifying conditions. Here, we report the complete genome sequences of
      the two strains, which allowed prediction of gene clusters involved in
      denitrification in strain JAM1.
AU  - Villeneuve C
AU  - Martineau C
AU  - Mauffrey F
AU  - Villemur R
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4126-4127.

PMID- 19349056
VI  - 388
DP  - 2009
TI  - P087, a lactococcal phage with a morphogenesis module similar to an Enterococcus faecalis prophage.
PG  - 49-56
AB  - The virulent lactococcal phage P087 was isolated from a dairy environment
      in 1978. This phage was then recognized as the reference member for one of
      the ten phage groups currently known to infect Lactococcus lactis strains.
      The double-stranded DNA genome of this Siphoviridae phage is composed of
      60,074 bp and is circularly permuted. Five tRNA and 88 orfs were found
      within an uncommon genome architecture. Eleven structural proteins were
      also identified through SDS-PAGE and LC-MS/MS analyses. Of note, 11
      translated orfs from the structural module of phage P087 have identities
      to gene products found in a prophage located in the genome of Enterococcus
      faecalis V583. The alignment of both genomic sequences suggests that DNA
      exchanges could occur between these two phages which are infecting low G+C
      bacteria found in similar ecological niches.
AU  - Villion M
AU  - Chopin MC
AU  - Deveau H
AU  - Ehrlich SD
AU  - Moineau S
AU  - Chopin A
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 2009 388: 49-56.

PMID- 24994805
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Cupriavidus sp. Strain SK-3, a 4-Chlorobiphenyl- and 4-Clorobenzoic Acid-Degrading Bacterium.
PG  - e00664-14
AB  - We report the draft genome sequence of Cupriavidus sp. strain SK-3, which can use
      4-chlorobiphenyl and 4-clorobenzoic acid as the sole carbon source for growth.
      The draft genome sequence allowed the study of the polychlorinated biphenyl
      degradation mechanism and the recharacterization of the strain SK-3 as a
      Cupriavidus species.
AU  - Vilo C
AU  - Benedik MJ
AU  - Ilori M
AU  - Dong Q
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00664-14.

PMID- 24855306
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Cupriavidus sp. Strain SK-4, a di-ortho-Substituted Biphenyl-Utilizing Bacterium Isolated from Polychlorinated Biphenyl-Contaminated   Sludge.
PG  - e00474-14
AB  - Cupriavidus sp. strain SK-4 is a bacterium capable of growing aerobically on
      monochlorobiphenyls and dichlorobiphenyls as the sole carbon sources for growth.
      Here, we report its draft genome sequence with the aim of facilitating an
      understanding of polychlorinated biphenyl biodegradation mechanisms.
AU  - Vilo C
AU  - Benedik MJ
AU  - Ilori M
AU  - Dong Q
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00474-14.

PMID- 26294639
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of a Bacillus Bacterium from the Atacama Desert Wetlands Metagenome.
PG  - e00955-15
AB  - We report here the draft genome sequence of a Bacillus bacterium isolated from the microflora
      of Nostoc colonies grown at the Andean wetlands in northern Chile.
      We consider this genome sequence to be a molecular tool for exploring microbial
      relationships and adaptation strategies to the prevailing extreme conditions at
      the Atacama Desert.
AU  - Vilo C
AU  - Galetovic A
AU  - Araya JE
AU  - Gomez-Silva B
AU  - Dong Q
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00955-15.

PMID- 7862175
VI  - 316
DP  - 1995
TI  - Restriction, methylation and ligation of 5-hydroxymethyluracil-containing DNA.
PG  - 123-131
AB  - Oxidation of DNA and its components can cause genetic mutations and chromosomal instability.
      These changes have generally been implicated in aging. Oxidation of the methyl group of
      thymidine residues in DNA is known to result in the formation of
      5-hydroxymethyl-2'-deoxyuridine (5HmdUrd). We have utilized Bacillus subtilis phage SPO1 DNA
      as a model of oxidatively damaged DNA. In this phage, all thymine (Thy) residues are replaced
      by 5-hydroxymethyluracil (5HmUra), but the species is naturally devoid of other
      oxidatively-induced DNA lesions. Particular attention was paid to the behavior of
      5HmUra-containing DNA as a target for several enzymes employing DNA as substrate; restriction
      endonucleases, dam DNA methylase and T4 DNA ligase. We noticed that susceptibility of SPO1 DNA
      varied when different restriction endonucleases having 5HmUra in the restriction sites were
      tested. Endonucleolytic cleavage brought about by Sau3AI proceeded as effectively with SPO1
      DNA as with conventional DNA (lambda phage). The same was true when the ligation of Sau3AI
      sites was performed with T7 DNA ligase. In contrast, both endonucleolytic cleavage and
      ligation were slower in SPO1 DNA, compared with lambda phage, when TaqI and T4 DNA ligase were
      used for restriction and ligation, respectively. We also noticed that SPO1 phage does not
      naturally contain N6-methyladenine (N6MeAde) opposite 5HmUra, i.e., no hydrolysis of SPO1 DNA
      was observed when assessed with methylation-dependent restriction endonuclease DpnI. Our
      results show that the presence of 5HmUra in the respective site of DNA does not, per se,
      prevent the activity of restriction endonucleases, ligases or DNA methylases. These data
      support the view that oxidation of Thy to 5HmUra in target DNA does not necessarily result in
      substantial deterioration in the functions of DNA processing enzymes.
AU  - Vilpo JA
AU  - Vilpo LM
PT  - Journal Article
TA  - Mutat. Res.
JT  - Mutat. Res.
SO  - Mutat. Res. 1995 316: 123-131.

PMID- 29983988
VI  - 25
DP  - 2018
TI  - Completion of genome of Aeromonas salmonicida subsp. salmonicida 01-B526 reveals how sequencing technologies can influence sequence quality and result interpretations.
PG  - 24-26
AB  - Aeromonas salmonicida subsp. salmonicida is a pathogen that primarily infects
      salmonids. A strain of this bacterium, 01-B526, has been used in several studies
      as a reference. The genomic sequence of this strain is available, but comes from
      pyrosequencing and is the second most fragmented assembly for this bacterium. We
      generated its closed genome sequence and found a pitfall in result
      interpretations associated with low-quality genomic sequences.
AU  - Vincent AT
AU  - Charette SJ
PT  - Journal Article
TA  - New Microbes New Infect.
JT  - New Microbes New Infect.
SO  - New Microbes New Infect. 2018 25: 24-26.

PMID- 28934400
VI  - 93
DP  - 
TI  - Genomic characterisation of environmental Pseudomonas aeruginosa isolated from dental unit waterlines revealed the insertion sequence ISPa11 as a chaotropic element.
PG  - fix106
AB  - The bacterium Pseudomonas aeruginosa is well known to have a remarkable adaptive capacity
      allowing it to colonise many environments. A recent study on environmental isolates from
      dental unit waterlines (DUWLs) hinted at a genetic clustering into two groups. Isolates from
      one of these groups, named cluster III, were shown to have unusual phenotypes for
      environmental isolates, such as an increased biofilm production. To have a better ecological
      view, more specifically on isolates from cluster III, the complete genomes of 39 isolates
      including 16 from DUWLs were sequenced. In addition to an investigation of antibiotic
      resistance and secretion system gene content, a molecular phylogeny allowed confirmation of
      the split of the 16 environmental isolates in two groups and also sheds light on a correlation
      between the phylogenetic positions and the serotypes of the isolates. Isolates from cluster
      III harboured insertion sequences ISPa11 inserted into the O-specific antigen biosynthesis
      clusters and the gene lasR, encoding for a master regulator of the quorum sensing.
      Investigation of key regulators revealed another truncated gene, gacS. Alteration in lasR and
      gacS genes was consistent with phenotypic assays confirming their inactivation. These results
      bring new perspectives regarding the ecological adaptive potential of P. aeruginosa.
AU  - Vincent AT
AU  - Freschi L
AU  - Jeukens J
AU  - Kukavica-Ibrulj I
AU  - Emond-Rheault JG
AU  - Leduc A
AU  - Boyle B
AU  - Jean-Pierre F
AU  - Groleau MC
AU  - Deziel E
AU  - Barbeau J
AU  - Charette SJ
AU  - Levesque RC
PT  - Journal Article
TA  - FEMS Microbiol. Ecol.
JT  - FEMS Microbiol. Ecol.
SO  - FEMS Microbiol. Ecol.  93: fix106.

PMID- 29126137
VI  - 364
DP  - 2017
TI  - Study of mesophilic Aeromonas salmonicida A527 strain sheds light on the species lifestyles and taxonomic dilemma.
PG  - fnx239
AB  - The Gram-negative bacterium Aeromonas salmonicida contains five subspecies:
      salmonicida, smithia, achromogenes, masoucida and pectinolytica. Pectinolytica is
      a mesophilic subspecies with the ability to thrive at a wide range of
      temperatures, including 37 degrees C, while the four other subspecies are
      psychrophilic, restricted to lower temperatures. The psychrophilic subspecies are
      known to infect a wide range of fishes. However, there is no evidence of
      pathogenicity for the mesophilic subspecies pectinolytica. Study of the
      differences between the mesophilic and psychrophilic subspecies is hampered by
      the lack of completely sequenced and closed genomes from the mesophilic
      subspecies. A previous study reported that insertion sequences, which can induce
      genomic rearrangements at temperatures around 25 degrees C, could be one of the
      determinants explaining the differences in lifestyle (mesophilic or
      psychrophilic) between the subspecies. In this study, the genome of mesophilic
      strain A527 of A. salmonicida was sequenced, closed and analyzed to investigate
      the mesophilic-psychrophilic discrepancy. This reference genome supports the
      hypothesis that insertion sequences are major determinants of the lifestyle
      differences between the A. salmonicida subspecies. Moreover, the phylogenetic
      analysis performed to position strain A527 within the taxonomy raises an issue
      regarding the intraspecies structure of A. salmonicida.
AU  - Vincent AT
AU  - Rouleau FD
AU  - Moineau S
AU  - Charette SJ
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2017 364: fnx239.

PMID- 25267667
VI  - 58
DP  - 2014
TI  - Detection of Variants of the pRAS3, pAB5S9, and pSN254 Plasmids in Aeromonas salmonicida subsp. salmonicida: Multidrug Resistance, Interspecies Exchanges, and Plasmid Reshaping.
PG  - 7367-7374
AB  - The ubiquitous water-borne Gram-negative bacterium Aeromonas salmonicida subsp.
      salmonicida is the causative agent of furunculosis, a worldwide disease in fish
      farms. Plasmids carrying antibiotic resistance genes have already been described
      for this bacterium. The aim of the present study was to identify and characterize
      additional multidrug resistance plasmids in A. salmonicida subsp. salmonicida. We
      sequenced the plasmids present in two multiple antibiotic-resistant isolates
      using high-throughput technologies. We also investigated 19 other isolates with
      various multidrug resistance profiles by genotyping PCR and assessed their
      resistance to tetracycline. We identified variants of the pAB5S9 and pSN254
      plasmids that carry several antibiotic resistance genes and that have been
      previously reported in bacteria other than A. salmonicida subsp. salmonicida,
      which suggests a high level of interspecies exchange. Genotyping analyses and the
      antibiotic resistance profiles of the 19 other isolates support the idea that
      multiple versions of pAB5S9 and pSN254 exist in A. salmonicida subsp.
      salmonicida. We also identified variants of the pRAS3 plasmid. The present study
      revealed that A. salmonicida subsp. salmonicida harbors a wide variety of
      plasmids, which suggests that this ubiquitous bacterium may contribute to the
      spread of antibiotic resistance genes in the environment.
AU  - Vincent AT
AU  - Trudel MV
AU  - Paquet VE
AU  - Boyle B
AU  - Tanaka KH
AU  - Dallaire-Dufresne S
AU  - Daher RK
AU  - Frenette M
AU  - Derome N
AU  - Charette SJ
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2014 58: 7367-7374.

PMID- 12824395
VI  - 31
DP  - 2003
TI  - NEBcutter: a program to cleave DNA with restriction enzymes.
PG  - 3688-3691
AB  - NEBcutter, version 1.0, is a program available via a web server
      (http://tools.neb.com/NEBcutter) that will accept an input DNA sequence
      and produce a comprehensive report of the restriction enzymes that will
      cleave the sequence. It produces a variety of outputs including
      restriction enzyme maps, theoretical digests and links into the
      restriction enzyme database, REBASE (http://www.neb.com/rebase).
      Importantly, its table of recognition sites is updated daily from REBASE
      and it marks all sites that are potentially affected by DNA methylation
      (Dam, Dcm, etc.). Many options exist to choose the enzymes used for
      digestion, including all known specificities, subsets of those that are
      commercially available or sets of enzymes that produce compatible termini.
AU  - Vincze T
AU  - Posfai J
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2003 31: 3688-3691.

PMID- 1551854
VI  - 174
DP  - 1992
TI  - Chromosome partitioning in Escherichia coli in the absence of Dam-directed methylation.
PG  - 2388-2390
AB  - Escherichia coli dam mutants, lacking the GATC DNA methylase, do not produce anucleate cells
      at high frequencies, suggesting that hemimethylation of the chromosome origin of replication,
      oriC, is not essential for correct chromosome partitioning.
AU  - Vinella D
AU  - Jaffe A
AU  - D'Ari R
AU  - Kohiyama M
AU  - Hughes P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1992 174: 2388-2390.

PMID- 2827691
VI  - 13
DP  - 1987
TI  - Interaction of EcoRII restriction and modification enzymes with synthetic DNA fragments.  IX:  Cleavage of substrates with point modifications in the recognition site and flanking sequences.
PG  - 1194-1204
AB  - Ability of the EcoRII restriction endonuclease to cleave 14-base-pair DNA
      duplexes with nucleotide substitutions in the recognition site CC(A/T)GG and in
      the adjacent base pair has been studied.  Modifications leading to a local
      change in the substrate conformation (rU residue in and outside the recognition
      site, A.A- or A.C-pairs in the flanking sequences) reduce the rate of
      hydrolysis, the effect being maximal when the modified base pair is outside the
      recognition site.  No digestion occurs when the internal dC-residue of the
      recognition site is 5-methylated in one or both strands.  Replacement of dT
      residue in the EcoRII recognition site by dF5U residue results in a dramatic
      inhibition of hydrolysis.  Km and Kcat for the cleavage of 14-base-pair DNA
      duplex have been determined.  The cleavage rate of the dT-containing strand of
      the recognition site is 1.5 fold higher comparing with the dA-containing
      strand.  The cleavage of both strands of the substrate by EcoRII endonuclease
      is confirmed to proceed in one enzyme-substrate complex.
AU  - Vinogradova MN
AU  - Gromova ES
AU  - Gryaznova OI
AU  - Isagulyants MD
AU  - Kuznetsova SA
AU  - Kosych VG
AU  - Shabarova ZA
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1987 13: 1194-1204.

PMID- 2402242
VI  - 24
DP  - 1990
TI  - Interaction of EcoRII restriction and modification enzymes with synthetic DNA fragments.  XI. Determination of the EcoRII binding site.
PG  - 847-850
AB  - EcoRII restriction endonuclease binding site has been determined on the basis
      of comparison of the binding parameters of the enzyme with synthetic
      DNA-duplexes of concatemer type containing a different number of EcoRII
      recognition sites.  It has been shown that it consists of 21 +/- 1 base pairs.
AU  - Vinogradova MN
AU  - Gromova ES
AU  - Kosykh VG
AU  - Buryanov YI
AU  - Shabarova ZA
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1990 24: 847-850.

PMID- 3022126
VI  - 20
DP  - 1986
TI  - Interaction of restriction and modification enzymes EcoRII with synthetic fragments of DNA.
PG  - 1329-1336
AB  - It was shown by the method of binding on nitrocellulose filters that the
      restriction endonuclease EcoRII in the absence of Mg2+ ions is specifically
      bonded to synthetic DNA duplexes of the concatamer type of different lengths,
      containing natural recognition sites for the enzyme CAA/TGG, as well as with
      substrates possessing a noncomplementary AA or TT pair in the recognition site
      of cleavage by the enzyme.  The degree of binding of substrates containing a
      central AT, TT, or AA pair in the recognition site decreases in the series AT >
      TT >> AA.  Replacement of the phosphodiester bond in the recognition site by a
      pyrophosphate or phosphoamide bond has little effect on the stability of the
      complexes.  The affinity of the enzyme for nonspecific DNA sequences is two
      orders of magnitude lower than for the specific recognition sites of EcoRII.
      The equilibrium constant of association for a substrate with one recognition
      site is 3.9 x 10(8) M-1.  The introduction of Mg2+ ions into the incubation
      mixture leads to destabilization of the complex of EcoRII endonuclease with the
      DNA duplex containing pyrophosphate bonds.  The rate constants of dissociation
      and the half-lives of the cocomplexes of the endonuclease EcoRII with synthetic
      substrates were determined.
AU  - Vinogradova MN
AU  - Gromova ES
AU  - Purmal AA
AU  - Kosykh VG
AU  - Shabarova ZA
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1986 20: 1329-1336.

PMID- 3040367
VI  - 295
DP  - 1987
TI  - Restriction endonuclease SsoII:  interaction with modified substrates.
PG  - 732-736
AB  - None
AU  - Vinogradova MN
AU  - Gromova ES
AU  - Uporova TM
AU  - Nikolskaya II
AU  - Shabarova ZA
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1987 295: 732-736.

PMID- 26659678
VI  - 3
DP  - 2015
TI  - Complete Genome Sequencing of Stenotrophomonas acidaminiphila ZAC14D2_NAIMI4_2, a Multidrug-Resistant Strain Isolated from Sediments of a Polluted River in Mexico,  Uncovers New Antibiotic Resistance Genes and a Novel Class-II Lasso Peptide  Biosynthesis.
PG  - e01433-15
AB  - Here, we report the first complete genome sequence of a Stenotrophomonas acidaminiphila
      strain, generated with PacBio RS II single-molecule real-time
      technology, consisting of a single circular chromosome of 4.13 Mb. We annotated
      mobile genetic elements and natural product biosynthesis clusters, including a
      novel class-II lasso peptide with a 7-residue macrolactam ring.
AU  - Vinuesa P
AU  - Ochoa-Sanchez LE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01433-15.

PMID- 29765358
VI  - 9
DP  - 2018
TI  - GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan-Genome Phylogenies, Used for a Critical Geno-Taxonomic Revision of the Genus Stenotrophomonas.
PG  - 771
AB  - The massive accumulation of genome-sequences in public databases promoted the proliferation of
      genome-level phylogenetic analyses in many areas of biological research. However, due to
      diverse evolutionary and genetic processes, many loci have undesirable properties for
      phylogenetic reconstruction. These, if undetected, can result in erroneous or biased
      estimates, particularly when estimating species trees from concatenated datasets. To deal with
      these problems, we developed GET_PHYLOMARKERS, a pipeline designed to identify high-quality
      markers to estimate robust genome phylogenies from the orthologous clusters, or the pan-genome
      matrix (PGM), computed by GET_HOMOLOGUES. In the first context, a set of sequential filters
      are applied to exclude recombinant alignments and those producing anomalous or poorly resolved
      trees. Multiple sequence alignments and maximum likelihood (ML) phylogenies are computed in
      parallel on multi-core computers. A ML species tree is estimated from the concatenated set of
      top-ranking alignments at the DNA or protein levels, using either FastTree or IQ-TREE (IQT).
      The latter is used by default due to its superior performance revealed in an extensive
      benchmark analysis. In addition, parsimony and ML phylogenies can be estimated from the PGM.
      We demonstrate the practical utility of the software by analyzing 170 Stenotrophomonas genome
      sequences available in RefSeq and 10 new complete genomes of Mexican environmental S.
      maltophilia complex (Smc) isolates reported herein. A combination of core-genome and PGM
      analyses was used to revise the molecular systematics of the genus. An unsupervised learning
      approach that uses a goodness of clustering statistic identified 20 groups within the Smc at a
      core-genome average nucleotide identity (cgANIb) of 95.9% that are perfectly consistent with
      strongly supported clades on the core- and pan-genome trees. In addition, we identified 16
      misclassified RefSeq genome sequences, 14 of them labeled as S. maltophilia, demonstrating the
      broad utility of the software for phylogenomics and geno-taxonomic studies. The code, a
      detailed manual and tutorials are freely available for Linux/UNIX servers under the GNU GPLv3
      license at https://github.com/vinuesa/get_phylomarkers. A docker image bundling
      GET_PHYLOMARKERS with GET_HOMOLOGUES is available at https://hub.
      docker.com/r/csicunam/get_homologues/, which can be easily run on any platform.
AU  - Vinuesa P
AU  - Ochoa-Sanchez LE
AU  - Contreras-Moreira B
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2018 9: 771.

PMID- 27103717
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Salmonella enterica Serovar Typhimurium Strain SO3 (Sequence Type 302) Isolated from a Baby with Meningitis in Mexico.
PG  - e00285-16
AB  - The complete genome of ITALIC! Salmonella entericaserovar Typhimurium strain SO3  (sequence
      type 302), isolated from a fatal meningitis infection in Mexico, was
      determined using PacBio technology. The chromosome hosts six complete prophages
      and is predicted to harbor 51 genomic islands, including 13 pathogenicity islands
      (SPIs). It carries the ITALIC! Salmonellavirulence plasmid (pSTV).
AU  - Vinuesa P
AU  - Puente JL
AU  - Calva E
AU  - Zaidi MB
AU  - Silva C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00285-16.

PMID- 8412677
VI  - 9
DP  - 1993
TI  - Structure-function correlation for the EcoRV restriction enzyme: from non-specific binding to specific DNA cleavage.
PG  - 225-231
AB  - The EcoRV restriction endonuclease cleaves DNA at its recognition sequence at least a million
      times faster than at any other DNA sequence. The only cofactor it requires for activity is
      Mg2+; but in binding to DNA in the absence of Mg2+, the EcoRV enzyme shows no specificity for
      its recognition site. Instead, the reason why EcoRV cuts one DNA sequence faster than any
      other is that the rate of cleavage is controlled by the binding of Mg2+ to EcoRV-DNA
      complexes; the complex at the recognition site has a high affinity for Mg2+, while the
      complexes at other DNA sequences have low affinities for Mg2+. The structures of the EcoRV
      endonuclease, and of its complexes with either specific or non-specific DNA, have been solved
      by X-ray crystallography. In the specific complex, the protein interacts with the bases in the
      recognition sequence and the DNA takes up a highly distorted structure. In the non-specific
      complex with an unrelated DNA sequence, there are virtually no interactions with the bases and
      the DNA retains a B-like structure. Since the free energy changes for the formation of
      specific and non-specific complexes are the same, the energy from the specific interactions
      balances that required for the distortion of the DNA. The distortion inserts the phosphate at
      the scissile bond into the active site of the enzyme, where it forms part of the binding site
      for Mg2+. Without this distortion, the EcoRV-DNA complex would be unable to bind Mg2+ and thus
      unable to cleave DNA. The specificity of the EcoRV restriction enzyme is therefore governed,
      not by DNA binding as such, but by its ability to organize the structure of the DNA to which
      it is bound.
AU  - Vipond B
AU  - Halford SE
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1993 9: 225-231.

PMID- 7819265
VI  - 34
DP  - 1995
TI  - Divalent metal ions at the active sites of the EcoRV and EcoRI restriction endonucleases.
PG  - 697-704
AB  - Restriction enzymes cannot cleave DNA without a metal ion cofactor. The specificities of the
      EcoRV and EcoRI endonucleases for metals were studied by measuring DNA cleavage rates with
      several metal ions and with combinations of metal ions. Both EcoRV and EcoRI had optimal
      activities with Mg2+, were less active with several other ions including Mn2+, and had
      virtually no activity with Ca2+. But the activities of EcoRV and EcoRI with either Mg2+ or
      Mn2+ were perturbed by Ca2+. For EcoRI, both Mg2+- and Mn2+-dependent activities, at both
      cognate and noncognate sites, were all inhibited by Ca2+. The activity of EcoRV at its
      recognition site with Mg2+ was also inhibited by Ca2+. But the Mn2+-dependent reaction at the
      EcoRV recognition site was stimulated by Ca2+. EcoRV activities at noncognate sites with
      either Mg2+ or Mn2+ displayed a biphasic response to Ca2+: stimulation at low concentrations
      of Ca2+ and inhibition at higher concentrations. These observations, together with the known
      structures of the proteins, indicate that EcoRI needs only one metal ion per active site and
      is inactive when Mg2+ is displaced by Ca2+, while EcoRV needs two and that the displacement of
      one by Ca2+ can enhance activity. We propose a mechanism for phosphodiester hydrolysis by
      EcoRV that involves two metal ions.
AU  - Vipond IB
AU  - Baldwin GS
AU  - Halford SE
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1995 34: 697-704.

PMID- 8680932
VI  - 4
DP  - 1995
TI  - A general assay for restriction endonucleases and other DNA-modifying enzymes with plasmid substrates.
PG  - 259-268
AB  - A procedure for measuring the activities of enzymes that alter the covalent structure of DNA
      is described.  The assay utilizes covalently closed circles of DNA as the substrate and yields
      quantitative data on the fraction of this DNA converted to both open-circle and linear forms.
AU  - Vipond IB
AU  - Baldwin GS
AU  - Oram M
AU  - Erskine SG
AU  - Wentzell LM
AU  - Szczelkun MD
AU  - Nobbs TJ
AU  - Halford SE
PT  - Journal Article
TA  - Mol. Biotechnol.
JT  - Mol. Biotechnol.
SO  - Mol. Biotechnol. 1995 4: 259-268.

PMID- 8639649
VI  - 35
DP  - 1996
TI  - Random mutagenesis targeted to the active site of the EcoRV restriction endonuclease.
PG  - 1701-1711
AB  - Two segments of the gene for the EcoRV restriction endonuclease, each encoding 10 amino acids
      at the active site, were subjected to random mutagenesis with degenerate oligonucleotides.
      Mutations that abolished the activity of the EcoRV endonuclease were selected by viability in
      a strain of Escherichia coli that lacks the EcoRV methyltransferase, under conditions where
      the gene for the wild-type endonuclease is lethal to the cell.  Sixty-five mutants were
      isolated and analyzed by DNA sequencing to identify the mutations.  The collection of null
      mutants contained 49 with single amino acid substitutions, 15 with double substitutions, and
      one with a triple substitution.  The single substitutions were located at many different
      positions within the two 10-amino acid segments, though several hot-spots gave rise to null
      mutants at high frequencies.  Some hot-spots were readily explained by reference to the
      crystal structure of EcoRV since they were at the amino acids immediately adjacent to the
      scissile phosphodiester bond: for example, Asp90 and Lys92.  These residues may be directly
      involved in the catalytic mechanism.  Other hot-spots, such as Gln69, Tyr72, and Ala88, were
      at unexpected positions that appear to have no direct role in DNA binding or catalysis.  At
      some of the unexpected hot-spots, the side chain of the amino acid lies distant from the DNA,
      yet the enzyme was still inactivated by conservative substitutions at these positions.  The
      sensitivity of the EcoRV endonuclease to conservative substitutions may be due to its
      requirement to take up one particular conformation at the DNA--protein interface out of a
      large number of alternative conformations.
AU  - Vipond IB
AU  - Halford SE
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1996 35: 1701-1711.

PMID- 7827059
VI  - 34
DP  - 1995
TI  - Specific DNA recognition by EcoRV restriction endonuclease induced by Calcium ions.
PG  - 1113-1119
AB  - In the presence of Mg2+, the EcoRV restriction endonuclease cleaves DNA specifically at its
      recognition sequence, but in the absence of divalent metal ions, it binds DNA without any
      specificity: gel-shift experiments had revealed multiple EcoRV-DNA complexes, due to the
      binding of one, two, three, or more molecules of protein per molecule of DNA, with the same
      equilibrium constant for each association. In this study, the binding of EcoRV to DNA was
      measured by gel shift in the presence of Ca2+, an ion that perturbs the Mg2+-dependent
      activity of EcoRV but that fails to support DNA cleavage. With Ca2+, and at a lower
      concentration of EcoRV protein than that required for binding in the absence of divalent metal
      ions, a single complex was observed with DNA containing the EcoRV recognition site. This
      complex was not formed with DNA that had been methylated at the EcoRV site nor with an
      isogenic DNA lacking the EcoRV recognition site. The single complex thus is due to the
      specific binding of EcoRV to its recognition site on the DNA. From gel shifts with a permuted
      set of DNA fragments, the degree of DNA bending by EcoRV at this recognition site was
      estimated to be 53 degrees +/- 4 degrees. This angle is similar to that seen in the crystal
      structure of the cognate DNA-protein complex. Calcium ions thus appear to mimic the role of
      Mg2+ in generating a specific protein-metal-DNA complex, but in contrast to Mg2+, Ca2+ gives a
      stable ternary complex in which the DNA-bound nuclease cannot cleave the DNA.
AU  - Vipond IB
AU  - Halford SE
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1995 34: 1113-1119.

PMID- 8639650
VI  - 35
DP  - 1996
TI  - An isoleucine to leucine mutation that switches the cofactor requirement of the EcoRV restriction endonuclease from magnesium to manganese.
PG  - 1712-1721
AB  - The EcoRV restriction endonuclease cleaves DNA at its recognition sequence more readily with
      Mg2+ as the cofactor than with Mn2+ but, at noncognate sequences that differ from the EcoRV
      site by one base pair, Mn2+ gives higher rates than Mg2+.  A mutant of EcoRV, in which an
      isoleucine near the active site was replaced by leucine, showed the opposite behavior.  It had
      low activity with Mg2+, but, in the presence of Mn2+ ions, it cleaved the recognition site
      faster than wild-type EcoRV with either Mn2+ or Mg2+.  The mutant was also more specific for
      the recognition sequence than the native enzyme: the noncognate DNA cleavages by wild-type
      EcoRV and Mn2+ were not detected with the mutant.  Further mutagenesis showed that the protein
      required the same acidic residues at its active site as wild-type EcoRV.  The Ile-Leu mutation
      seems to perturb the configuration of the metal-binding ligands at the active site so that the
      protein has virtually no affinity for Mg2+ yet it can still bind Mn2+ ions, though the latter
      only occurs when the protein is at the recognition site.  This contrasts to wild-type EcoRV,
      where Mn2+ ions bind readily to complexes with either cognate and noncognate DNA and only Mg2+
      shows the discrimination between the complexes.  The structural perturbation is a specific
      consequence of leucine in place of isoleucine, since mutants with valine or alanine were
      similar to wild-type EcoRV.
AU  - Vipond IB
AU  - Moon B-J
AU  - Halford SE
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1996 35: 1712-1721.

PMID- 7821560
VI  - 22
DP  - 1994
TI  - An Ile-to-Leu mutant of the EcoRV restriction endonuclease that requires Mn2+ as catalytic cofactor.
PG  - 301S
AB  - The EcoRV restriction endonuclease recognizes and cleaves the sequence GAT^ATC with extreme
      precision. The accuracy is such that alternate sites one bp different are cleaved at least a
      million times slower. However, contrary to many DNA binding proteins, the basis of this
      specificity is not due to preferred binding by EcoRV to its recognition sequence. In fact, the
      EcoRV nuclease binds all DNA sequences with equal affinity. Instead, it is due to the affinity
      of the enzyme-DNA complex for the divalent metal ion which serves as the catalytic cofactor.
      Thus, EcoRV bound to GATATC has a high affinity for Mg2+, while the enzyme bound to any other
      sequence has a low affinity for the metal ion.
AU  - Vipond IB
AU  - Moon BJ
AU  - Halford SE
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 1994 22: 301S.

PMID- 11178268
VI  - 1
DP  - 2000
TI  - Genetic snapshots of the Rhizobium species NGR234 genome.
PG  - RESEARCH0014
AB  - BACKGROUND: In nitrate-poor soils, many leguminous plants form
      nitrogen-fixing symbioses with members of the bacterial family
      Rhizobiaceae. We selected Rhizobium sp. NGR234 for its exceptionally broad
      host range, which includes more than I 12 genera of legumes. Unlike the
      genome of Bradyrhizobium japonicum, which is composed of a single 8.7 Mb
      chromosome, that of NGR234 is partitioned into three replicons: a
      chromosome of about 3.5 Mb, a megaplasmid of more than 2 Mb (pNGR234b) and
      pNGR234a, a 536,165 bp plasmid that carries most of the genes required for
      symbioses with legumes. Symbiotic loci represent only a small portion of
      all the genes coded by rhizobial genomes, however. To rapidly characterize
      the two largest replicons of NGR234, the genome of strain ANU265 (a
      derivative strain cured of pNGR234a) was analyzed by shotgun sequencing.
      RESULTS: Homology searches of public databases with 2,275 random sequences
      of strain ANU265 resulted in the identification of 1,130 putative
      protein-coding sequences, of which 922 (41%) could be classified into
      functional groups. In contrast to the 18% of insertion-like sequences
      (ISs) found on the symbiotic plasmid pNGR234a, only 2.2% of the shotgun
      sequences represent known ISs, suggesting that pNGR234a is enriched in
      such elements. Hybridization data also indicate that the density of known
      transposable elements is higher in pNGR234b (the megaplasmid) than on the
      chromosome. Rhizobium-specific intergenic mosaic elements (RIMEs) were
      found in 35 shotgun sequences, 6 of which carry RIME2 repeats previously
      thought to be present only in Rhizobium meliloti. As non-overlapping
      shotgun sequences together represent approximately 10% of ANU265 genome,
      the chromosome and megaplasmid may carry a total of over 200 RIMEs.
      CONCLUSIONS: 'Skimming' the genome of Rhizobium sp. NGR234 sheds new light
      on the fine structure and evolution of its replicons, as well as on the
      integration of symbiotic functions in the genome of a soil bacterium.
      Although most putative coding sequences could be distributed into
      functional classes similar to those in Bacillus subtilis, functions
      related to transposable elements were more abundant in NGR234. In contrast
      to ISs that accumulated in pNGR234a and pNGR234b, the hundreds of RIME
      elements seem mostly attributes of the chromosome.
AU  - Viprey V
AU  - Rosenthal A
AU  - Broughton WJ
AU  - Perret X
PT  - Journal Article
TA  - Genome Biology
JT  - Genome Biology
SO  - Genome Biology 2000 1: RESEARCH0014.

PMID- 24092792
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Mycobacterium tuberculosis Strain 43-16836, Belonging to the Indo-Oceanic Lineage, Isolated From Tuberculous Meningitis in  Thailand.
PG  - e00801-13
AB  - We present the draft genome sequence of Mycobacterium tuberculosis strain 43-16836, belonging
      to the Indo-Oceanic lineage, isolated from a tuberculous
      meningitis patient in Thailand. The genome is 4,381,942 bp long with 4,316
      protein-coding genes and contains new single nucleotide polymorphisms (SNPs),
      including SNPs of genes that may encode cell wall components and possibly
      influence virulence.
AU  - Viratyosin W
AU  - Kulawonganunchai S
AU  - Smittipat N
AU  - Juthayothin T
AU  - Penpassakarn P
AU  - Pasomsub E
AU  - Chantratita W
AU  - Chaiprasert A
AU  - Palittapongarnpim P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00801-13.

PMID- 25323723
VI  - 2
DP  - 2014
TI  - Draft genome sequences of 10 strains of the genus exiguobacterium.
PG  - e01058-14
AB  - High-quality draft genome sequences were determined for 10 Exiguobacterium strains in order to
      provide insight into their evolutionary strategies for
      speciation and environmental adaptation. The selected genomes include
      psychrotrophic and thermophilic species from a range of habitats, which will
      allow for a comparison of metabolic pathways and stress response genes.
AU  - Vishnivetskaya TA et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01058-14.

PMID- 27056212
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of 18 Strains of Pseudomonas Isolated from Kiwifruit Plants in New Zealand and Overseas.
PG  - e00061-16
AB  - In this paper, we present the draft sequences of 18 genetically diversePseudomonasstrains
      isolated from kiwifruit plants in New Zealand and
      overseas, including a number that are currently not fully characterized. These
      sequences will aid in the diagnosis ofPseudomonason kiwifruit for future pest
      management and border security decision-making.
AU  - Visnovsky SB
AU  - Fiers M
AU  - Lu A
AU  - Panda P
AU  - Taylor R
AU  - Pitman AR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00061-16.

PMID- 29348350
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of 14 Strains of Pseudomonas Isolated from Prunus sp. Plants.
PG  - e01481-17
AB  - We present here the draft genome sequences of 14 Pseudomonas strains isolated from Prunus sp.
      plants in New Zealand and overseas. These new genomic data will
      be used to improve the detection of Pseudomonas strains found in imported plant
      material at the New Zealand border, improving the time involved in the process of
      biosecurity decision-making.
AU  - Visnovsky SB
AU  - Lu A
AU  - Panda P
AU  - Taylor R
AU  - Pitman AR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01481-17.

PMID- 28385839
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Pectobacterium carotovorum subsp. actinidiae ICMP 19971 and ICMP 19972, Two Strains Isolated from Actinidia chinensis with Symptoms of  Summer Canker in South Korea.
PG  - e00104-17
AB  - Pectobacterium carotovorum subsp. actinidiae is the causal agent of summer canker in kiwifruit
      plants in South Korea. We report here the draft genome sequences of
      two P. carotovorum subsp. actinidiae strains, ICMP 19971 and ICMP 19972, which
      were originally isolated from Actinidia chinensis with symptoms of summer canker.
      These genome sequences will aid in the identification of genetic traits
      associated with their unusual capacity to cause canker and help understanding of
      the threat these exotic enterobacteria pose to the New Zealand kiwifruit
      industry.
AU  - Visnovsky SB
AU  - Panda P
AU  - Taylor R
AU  - Pitman AR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00104-17.

PMID- 2837743
VI  - 16
DP  - 1988
TI  - Altered activity of restriction endonuclease MnlI cleavage of mouse satellite DNA.
PG  - 4731
AB  - MnlI is reported to recognise the sequence CCTCN7, cleaving after the N7
      position to produce a blunt ended fragment.  However, we have observed that
      following MnlI cleavage of mouse satellite DNA, the monomeric units that were
      subsequently cloned uniformly lacked the N7 base.  Mouse satellite DNA is
      composed of tandemly repeated 234bp monomeric units, most of which contain an
      MnlI site.  As shown in Fig. 1, direct cloning and sequencing of the MnlI
      monomeric units revealed that the N7 base was consistently absent from the end
      of the clone with the MnlI site (Fig. 1C, D and G).  These results suggest that
      cleavage of mouse satellite DNA by MnlI occurs after the N6, in addition to
      after the N7 position.  It is not clear, however, if MnlI removes the N7 base
      from both strands simultaneously, or, cleaves to leave a single-base 5' or 3'
      extension that is subsequently lost during the cloning procedure.  This unusual
      activity of MnlI may be related to the high AT content or methylated nature of
      the mouse satellite DNA.
AU  - Vissel B
AU  - Choo KH
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1988 16: 4731.

PMID- 25197452
VI  - 9
DP  - 2014
TI  - Genome analyses of the carboxydotrophic sulfate-reducers Desulfotomaculum nigrificans and Desulfotomaculum carboxydivorans and reclassification of  Desulfotomaculum caboxydivorans as a later synonym of Desulfotomaculum  nigrificans.
PG  - 655-675
AB  - Desulfotomaculum nigrificans and D. carboxydivorans are moderately thermophilic members of the
      polyphyletic spore-forming genus Desulfotomaculum in the family
      Peptococcaceae. They are phylogenetically very closely related and belong to
      'subgroup a' of the Desulfotomaculum cluster 1. D. nigrificans and D.
      carboxydivorans have a similar growth substrate spectrum; they can grow with
      glucose and fructose as electron donors in the presence of sulfate. Additionally,
      both species are able to ferment fructose, although fermentation of glucose is
      only reported for D. carboxydivorans. D. nigrificans is able to grow with 20%
      carbon monoxide (CO) coupled to sulfate reduction, while D. carboxydivorans can
      grow at 100% CO with and without sulfate. Hydrogen is produced during growth with
      CO by D. carboxydivorans. Here we present a summary of the features of D.
      nigrificans and D. carboxydivorans together with the description of the complete
      genome sequencing and annotation of both strains. Moreover, we compared the
      genomes of both strains to reveal their differences. This comparison led us to
      propose a reclassification of D. carboxydivorans as a later heterotypic synonym
      of D. nigrificans.
AU  - Visser M et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 655-675.

PMID- 23961313
VI  - 8
DP  - 2013
TI  - Genome analysis of Desulfotomaculum kuznetsovii strain 17(T) reveals a physiological similarity with Pelotomaculum thermopropionicum strain SI(T).
PG  - 69-87
AB  - Desulfotomaculum kuznetsovii is a moderately thermophilic member of the polyphyletic
      spore-forming genus Desulfotomaculum in the family Peptococcaceae.
      This species is of interest because it originates from deep subsurface thermal
      mineral water at a depth of about 3,000 m. D. kuznetsovii is a rather versatile
      bacterium as it can grow with a large variety of organic substrates, including
      short-chain and long-chain fatty acids, which are degraded completely to carbon
      dioxide coupled to the reduction of sulfate. It can grow methylotrophically with
      methanol and sulfate and autotrophically with H2 + CO2 and sulfate. For growth it
      does not require any vitamins. Here, we describe the features of D. kuznetsovii
      together with the genome sequence and annotation. The chromosome has 3,601,386 bp
      organized in one contig. A total of 3,567 candidate protein-encoding genes and 58
      RNA genes were identified. Genes of the acetyl-CoA pathway, possibly involved in
      heterotrophic growth with acetate and methanol, and in CO2 fixation during
      autotrophic growth are present. Genomic comparison revealed that D. kuznetsovii
      shows a high similarity with Pelotomaculum thermopropionicum. Genes involved in
      propionate metabolism of these two strains show a strong similarity. However,
      main differences are found in genes involved in the electron acceptor metabolism.
AU  - Visser M et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 69-87.

PMID- 9776753
VI  - 26
DP  - 1998
TI  - AbeI, a restriction endonuclease from Azotobacter beijerinckii, which recognizes the asymmetric heptanucleotide sequence 5'-CCTCAGC-3'(-5/-2).
PG  - 4917-4918
AB  - A new restriction endonuclease AbeI has been isolated from Azotobacter beijerinckii.  This
      enzyme recognizes the asymmetric heptanucleotide sequence 5'-CCTCAGC-3' and cleaves within
      it symmetrically at positions -5/-2 in the opposing strands, producing three base protruding
      5'-ends.
AU  - Vitkute J
AU  - Maneliene Z
AU  - Janulaitis A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1998 26: 4917-4918.

PMID- 11731131
VI  - 204
DP  - 2001
TI  - Two new thermostable type II restriction endonucleases from Thermus aquaticus: TatI and TauI, which recognize the novel nucleotide sequences 5'-W^GTACW-3' and 5'-GCSG^C-3' respectively.
PG  - 253-257
AB  - One hundred and forty isolates of thermophilic bacteria from the genus Thermus were screened
      for the presence of restriction endonuclease activity. Thermostable isoschizomers of
      restriction endonucleases, such as AceIII, BbvI, BglI, BsePI, FnuDII, HgiAI, MaeII, MboI,
      MseI, PvuII, StuI, TaqI, Tsp4CI, TspEI, XhoI and XmaIII, were isolated. Two restriction
      enzymes, TatI and TauI, recognizing novel degenerate sequences 5'-W^GTACW-3' and
      5'-GCSG^C-3' respectively were partially purified and the recognition and cleavage sites
      were determined.
AU  - Vitkute J
AU  - Maneliene Z
AU  - Janulaitis A
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2001 204: 253-257.

PMID- 9358150
VI  - 25
DP  - 1997
TI  - BplI, a new BcgI-like restriction endonuclease, which recognizes a symmetric sequence.
PG  - 4444-4446
AB  - BcgI and BcgI-like restriction endonucleases cleave double stranded DNA specifically on both
      sides of their asymmetric recognition sequences which are interrupted by several ambiguous
      base pairs.  Their heterosubunit structure, bifunctionality and stimulation by AdoMet make
      them different from other classified restriction enzymes.  Here we report on a new BcgI-like
      enzyme, which in contrast to all other BcgI-like enzymes, recognizes a symmetric interrupted
      sequence, and which, like BcgI, cleaves double stranded DNA upstream and downstream of its
      recognition sequence (8/13)GAGN5CTC(13/8).  Like BcgI, BplI is a bifunctional enzyme revealing
      both DNA cleavage and methyltransferase activities.  There are two polypeptides in the
      homogeneous preparation of BplI with molecular masses of ~74 and 37 kDa.  The sizes of the
      BplI subunits are close to those of BcgI, but the proportion 1:1 in the final preparation is
      different from that of 2:1 in BcgI.  Low activity observed with Mg2+ increases >100-fold in
      the presence of AdoMet.  Even with AdoMet though, specific cleavage is incomplete.
      S-adenosyl-homocysteine (AdoHcy) or sinefungin can replace AdoMet in the cleavage reaction.
      AdoHcy activated BplI yields complete cleavage of DNA.
AU  - Vitkute J
AU  - Maneliene Z
AU  - Petrusyte M
AU  - Janulaitis A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1997 25: 4444-4446.

PMID- 9649617
VI  - 26
DP  - 1998
TI  - BfiI, a restriction endonuclease from Bacillus firmus S8120, which recognizes the novel non-palindromic sequence 5'-ACTGGG(N)5/4-3'.
PG  - 3348-3349
AB  - A new type IIS restriction endonuclease BfiI has been partially purified from Bacillus firmus
      S8120.  BfiI recognizes the non-palindromic hexanucleotide sequence 5'-ACTGGG(N)5/4-3' and
      makes a staggered cut at the fifth base pair downstream of the recognition sequence on the
      upper strand, producing a single base 3' protruding end.
AU  - Vitkute J
AU  - Maneliene Z
AU  - Petrusyte M
AU  - Janulaitis A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1998 26: 3348-3349.

PMID- 11133936
VI  - 183
DP  - 2001
TI  - Specificities of eleven different DNA methyltransferases of Helicobacter pylori strain 26695.
PG  - 443-450
AB  - Methyltransferases (MTases) of prokaryotes affect general cellular processes such as mismatch
      repair, regulation of transcription, replication, and transposition, and in some cases may be
      essential for viability. As components of restriction-modification systems, they contribute to
      bacterial genetic diversity. The genome of Helicobacter pylori strain 26695 contains 25 open
      reading frames encoding putative DNA MTases. To assess which MTase genes are active, strain
      26695 genomic DNA was tested for cleavage by
      147 restriction endonucleases; 24 were found that did not cleave this DNA. The specificities
      of 11 expressed MTases and the genes encoding them were identified from this restriction data,
      combined with the known sensitivities of restriction endonucleases to specific DNA
      modification, homology searches, gene cloning and genomic mapping of the methylated bases m4C,
      m5C, and m6A.
AU  - Vitkute J
AU  - Stankevicius K
AU  - Tamulaitiene G
AU  - Maneliene Z
AU  - Timinskas A
AU  - Berg DE
AU  - Janulaitis A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2001 183: 443-450.

PMID- 11697346
VI  - 291S
DP  - 2001
TI  - Potential of H. pylori to produce R-M enzymes and their possible biological role.
PG  - 95
AB  - The unprecedented abundance of putative restriction-modification (R-M) genes found in H.
      pylori genomes raises question on their role in life cycle of bacteria.  As a prerequisite to
      such studies we screened 156 independent isolates for restriction endonucleases to assess
      expression and specificity variability of H. pylori enzymes.  386 REs has been characterized
      with 26 different specificities.  Every screened strain contained REs and their set was
      specific for the majority of them.  In addition a set of seven selected strains was
      investigated for DNA methylases, including J99 and 26695 strains.  We found 87 MTases with 22
      different specificities.  Given that cognate MTase accompanies every RE, altogether 32 MTases
      of different specificity has been identified.  Modeling indicates that this variability is
      near the limit of potential specificity variability for R-M enzymes in H. pylori.  The
      conclusion reinforces previous observations in Enterobacteriaceae on the phenomenon of
      taxonomic specificity of R-M systems.  The character of taxonospecificity represents the first
      nonexperimental evidence supporting hypothesis on "selfishness" of R-M genes.  The main role
      of H. pylori R-M systems is likely to modulate involvement of H. pylori and non-H. pylori DNA
      in genetic exchange of the bacteria.  Arguments are provided to support this hypothesis.
      Other possible functions of R-M systems are also discussed.
AU  - Vitkute J
AU  - Tamulaitiene G
AU  - Chalkauskas H
AU  - Janulaitis A
PT  - Journal Article
TA  - Int. J. Med. Microbiol.
JT  - Int. J. Med. Microbiol.
SO  - Int. J. Med. Microbiol. 2001 291S: 95.

PMID- 
VI  - 
DP  - 1999
TI  - Restriction and modification systems in Campylobacter jejuni and Campylobacter coli.
PG  - 1-220
AB  - The restriction endonucleases are one of the most widely used
      tools in molecular biology and acronyms like EcoRI or BamHI are used
      daily in any laboratory all over the world.  Although ubiquitous among
      the prokaryotes there are only a few scientific groups studying these
      systems.  The RE are a part of the restriction and modification systems
      and it is believed that they are a defense mechanism of the host
      bacteria against bacteriophages, although not all scientists agree with
      this theory.  It is also believed that RM systems can act as intra and
      inter-specific barriers to the exchange of genetic information and may
      be involved in genetic recombination since they produce DNA fragments
      that can be integrated in the host genome or in an extrachromosomal
      element.
AU  - Vitor JMB
PT  - Journal Article
TA  - Ph.D. Thesis, University of Lisbon
JT  - Ph.D. Thesis, University of Lisbon
SO  - Ph.D. Thesis, University of Lisbon 1999 : 1-220.

PMID- 
VI  - 16
DP  - 2011
TI  - Helicobacter pylori type IIG restriction and modification loci.
PG  - 98
AB  - Helicobacter pylori complete sequenced genomes have a large number of putative restriction and
      modification systems between 26 and 34.  The major consequence of RMS is keeping the bacterial
      genomes free from alien DNA, acting as a speciation barrier.  RMS are classified into four
      major types and several subtypes.  The H. pylori genomes annotated in REBASE were analyzed and
      it was found that RMS are not randomly distributed over the genome.  Using H. pylori 26695 as
      model, four type IIG RMS loci were found: 1st - glpC.horF; 2nd - nadC-HINFIM; 3rd - tmk-polA;
      4th - res-nusA.  Primers were designed for the four loci and tested in 17 different H. pylori
      strains, isolated from asymptomatic patients.  PCR products were obtained in all loci but
      differences were observed among them.  All the PCR products were digested with HindIII to
      evaluate the variability of the amplified genes.  Locus 1 and 4 are empty in a large
      percentage of strains, 64.7 and 52.9 respectively.  Locus 2 has a high percentage of strains
      with unspecific PCR products, 58.8%.  Different HindIII profiles were observed: 2 in locus 1,
      5 in locus 2 and 4, and 6 in locus 3.  This might correspond to 18 different type IIG RMS in
      17 strains, thus being one more example of H. pylori genetic diversity although their species
      genomic organization might be conservative.
AU  - Vitor JMB
AU  - Alves P
AU  - Marques M
AU  - Vital J
PT  - Journal Article
TA  - Helicobacter
JT  - Helicobacter
SO  - Helicobacter 2011 16: 98.

PMID- Not carried by PubMed...
VI  - 4
DP  - 1991
TI  - Restriction enzymes in Campylobacter strains.
PG  - S50
AB  - Restriction enzymes (RE) are very important tools in Genetic Engineering.  They
      are a part of the Restriction Modification (RM) systems, that are ubiquitous in
      prokaryotes.  We have searched for RE activity in 100 enteropathogenic
      Campylobacter strains (52 C. jejuni and 58 C. coli strains) from human and
      animal origin.  The strains were isolated, subcultured and identified by
      routine methods.  DNAse activity was searched for as described by Lior and the
      RE screening by Whitehead and Brown's method, with modifications concerning the
      time of lysis by lysozyme, the time and temperature of the detergent step and
      the saline concentration of the digestion buffer.  The DNA used was from
      bacteriophage lambda methyl free.
AU  - Vitor JMB
AU  - Costa L
AU  - Pires I
AU  - Cabrita J
AU  - Correia RV
PT  - Journal Article
TA  - Microb. Ecol. Health Dis.
JT  - Microb. Ecol. Health Dis.
SO  - Microb. Ecol. Health Dis. 1991 4: S50.

PMID- 7607469
VI  - 157
DP  - 1995
TI  - Two novel restriction endonucleases from Campylobacter jejuni.
PG  - 109-110
AB  - We have discovered two unusual restriction endonucleases (ENases) in two Campylobacter jejuni
      strains that recognize asymmetrical, interrupted sequences and cleave the DNA both before and
      after their recognition sites.  Both enzymes require AdoMet as a cofactor for their ENase
      activity.
AU  - Vitor JMB
AU  - Morgan RD
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 109-110.

PMID- 7914389
VI  - 56
DP  - 1993
TI  - Restriction enzymes from Campylobacter coli strains.
PG  - 41
AB  - The type II restriction enzymes (RE) are ubiquitous among Prokaryotes. These enzymes belong to
      restriction-modification systems, which include a methyltransferase. One function is thought
      to protect the genomic information from other genetic pools. Also it is believed that when a
      strain exhibits restriction activity there will be a methyltransferase. Eight Campylobacter
      coli strains known to have RE activity from previous screening, isolated from human, pig and
      chicken, were plated on BHI agar and incubated for 20h at 42C, in an anaerobic jar (5% O2, 10%
      CO2). 1g of cells were lysed by sonication and centrifuged 25 min at 40,000g. The assay for RE
      was made in NEB buffer no2, 1h at 37C with lambda and T7 DNAs. If necessary, the extract was
      purified by affinity chromatography, with Heparin-Sepharose CL-6B. We have identified nine RE:
      CcoP95I (GCGC) isoschizomer of HhaI; CcoP215I and CcoP216I (GCNGC) isoschizomers of Fnu4HI;
      CcoP31I, CcoP84I and CcoP219I (GATC) isoschizomers of MboI; CcoP73I and CcoP76I (GTAC)
      isoschizomers of RsaI. Although we have studied a small number of isolates, the results
      suggest that the REs detected in Campylobacter coli recognize mainly GC-rich sequences. This
      finding may explain the prevalence in those strains of AT-rich plasmid DNA as well as the low
      chromosomal GC content (32-34%) of them.
AU  - Vitor JMB
AU  - Polisson C
AU  - Cabrita J
AU  - Silva RVC
PT  - Journal Article
TA  - Acta Gastroenterol. Belg.
JT  - Acta Gastroenterol. Belg.
SO  - Acta Gastroenterol. Belg. 1993 56: 41.

PMID- 23480599
VI  - 114
DP  - 2013
TI  - Proteome variability among Helicobacter pylori isolates clustered according to genomic methylation.
PG  - 1817-1832
AB  - Aims To understand whether the variability found in the proteome of Helicobacter pylori
      relates to the genomic methylation, virulence and
      associated gastric disease. Methods and Results We applied the
      Minimum-Common-Restriction-Modification (MCRM) algorithm to genomic
      methylation data of 30 Portuguese H.pylori strains, obtained by genome
      sensitivity to Type II restriction enzymes' digestion. All the
      generated dendrograms presented three clusters with no association with
      gastric disease. Comparative analysis of two-dimensional gel
      electrophoresis (2DE) maps obtained for total protein extracts of 10 of
      these strains, representative of the three main clusters, revealed that
      among 70 matched protein spots (in a universe of 300), 16 were
      differently abundant (P<0 center dot 05) among clusters. Of these, 13
      proteins appear to be related to the cagA genotype or gastric disease.
      The abundance of three protein species, DnaK, GlnA and HylB, appeared
      to be dictated by the methylation status of their gene promoter.
      Conclusions Variations in the proteome profile of strains with common
      geographic origin appear to be related to differences in cagA genotype
      or gastric disease, rather than to clusters organized according to
      strain genomic methylation. Significance and Impact of the Study The
      simultaneous study of the genomic methylation and proteome is important
      to correlate epigenetic modifications with gene expression and pathogen
      virulence.
AU  - Vitoriano I
AU  - Vitor JMB
AU  - Oleastro M
AU  - Roxo-Rosa M
AU  - Vale FF
PT  - Journal Article
TA  - J. Appl. Microbiol.
JT  - J. Appl. Microbiol.
SO  - J. Appl. Microbiol. 2013 114: 1817-1832.

PMID- 26294632
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Phenol-Degrading Bacterium Pseudomonas putida H.
PG  - e00936-15
AB  - In this study, we report the draft genome of Pseudomonas putida H, a well-known bacterium
      capable of degrading various aromatic compounds. Its genome size is
      6,065 Mbp with a GC content of 61.6%. This work will aid future studies on this
      versatile bacterium.
AU  - Vizoso P
AU  - Pacheco N
AU  - Bastias-Molina M
AU  - Meneses C
AU  - Poblete-Castro I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00936-15.

PMID- 29242218
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Immunobiotic Lactobacillus rhamnosus Strain IBL027, a Potential Adjuvant for Mucosal Vaccine Development.
PG  - e01268-17
AB  - The genome sequence of the immunomodulatory strain Lactobacillus rhamnosus strain IBL027 is
      described here. The reads were assembled into contigs with a total size
      2,898,501 bp. The genome information will be useful for further specific genetic
      studies of this strain to evaluate its immunomodulatory and biotechnological
      properties as a vaccine adjuvant.
AU  - Vizoso-Pinto MG
AU  - Saavedra L
AU  - Hebert EM
AU  - Raya TF
AU  - Albarracin L
AU  - Alvarez S
AU  - Kitazawa H
AU  - Villena J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01268-17.

PMID- 29853503
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Muricauda sp. Strain K001 Isolated from a Marine Cyanobacterial Culture.
PG  - e00451-18
AB  - We report the whole-genome sequence of Muricauda sp. strain K001 isolated from a  marine
      cyanobacterial culture. This genome sequence will improve our
      understanding of the influence of heterotrophic bacteria on the physiology of
      cyanobacteria and may contribute to the development of new natural products.
AU  - Vizzotto CS
AU  - Lopes FAC
AU  - Green SJ
AU  - Steindorff AS
AU  - Walter JM
AU  - Thompson FL
AU  - Kruger RH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00451-18.

PMID- 7607508
VI  - 157
DP  - 1995
TI  - In vitro DNA methylation by wheat nuclear cytosine DNA methyltransferase: effect of phytohormones.
PG  - 279-281
AB  - Cytosine DNA methyltransferases (MTases) were isolated from nuclei of wheat seedlings and
      germinating embryos.  The MTases isolated from both sources were able to perform de novo and
      maintenance DNA methylations.  The most purified MTase fraction showed the presence of one
      main 67-kDa protein (embryos) and of an 85-kDa protein (in seedlings) in SDS-PAGE.  Some plant
      growth regulators (gibberellic acid A3, 6-benzylaminopurine and fusicoccin) elevate by 30-65%
      the extent of in vitro DNA methylation by nuclear extracts with a maximal effect at 10 microM
      phytohormone concentration.  The same phytohormones do not increase the extent of in vitro
      DNA methylation by purified wheat MTase; rather they inhibit it at concentrations of 10/-4 to
      10/-5 M.  Thus, DNA methylation in the plant nucleus is controlled by phytohormones.  The
      phytohormone effect may be mediated by other proteins in nuclear extracts.
AU  - Vlasova TI
AU  - Demidenko ZN
AU  - Kirnos M
AU  - Vanyushin BF
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 279-281.

PMID- Not included in PubMed...
VI  - 61
DP  - 1996
TI  - Cytosine DNA-methyltransferase from wheat seedlings.
PG  - 774-780
AB  - A cytosine DNA methyltransferase has been isolated from wheat seedling nuclei and purified by
      chromatography on DEAE-cellulose, heparin-Sepharose, and Mono-Q FPLC.  The specific activity
      of the enzyme was 236 units/mg protein; its molecular mass by SDS-PAGE was 85-kD.  The enzyme
      catalyzes in vitro DNA methylation for a relatively long period, but it is very unstable in
      solution in the absence of substrates.  The apparent Km value for S-adenosylmethionine is 6
      microM.  The enzyme is active over a wide pH range (5.5-8.5); it is inhibited by NaCl and by
      the reaction product S-adenosylhomocysteine with [I]50 values of 0.2M and 12uM, respectively.
      The enzyme catalyzes both de novo and maintenance DNA methylation and displays a high rate of
      de novo methylation.  The wheat seedling enzyme is similar to known plant cytosine DNA
      methyltransferases.
AU  - Vlasova TI
AU  - Kirnos MD
AU  - Vanyushin BF
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1996 61: 774-780.

PMID- 9635138
VI  - 45
DP  - 1998
TI  - DNA methylation by wheat cytosine DNA methyltransferase: modulation by protease inhibitor E-64.
PG  - 145-153
AB  - Cytosine DNA methyltransferase isolated from wheat seedlings and purified in the presence of
      metalloprotease and serine protease inhibitors has molecular mass and specific activity equal
      to about 85 kDa and 250 units/mg protein, respectively.  Apparent Km for AdoMet and [I]50 for
      AdoHcy values are about 6 microM and 12 microM, respectively.  The enzyme is active in a wide
      pH range (pH 5.5 - 8.5) and is inhibited by NaCl.  The enzyme rapidly loses its
      methyltransferase activity in the absence of substrates.  Using the cysteine protease
      inhibitor E-64 it has been shown that rapid enzyme inactivation is caused by disappearance of
      essential enzyme SH-groups but is not due to proteolytic enzyme cleavage.
AU  - Vlasova TI
AU  - Vanyushin BF
PT  - Journal Article
TA  - Biochem. Mol. Biol. Int.
JT  - Biochem. Mol. Biol. Int.
SO  - Biochem. Mol. Biol. Int. 1998 45: 145-153.

PMID- 2016384
VI  - 538
DP  - 1991
TI  - Affinity partitioning of restriction endonucleases:  Application to the purification of EcoRI and EcoRV.
PG  - 311-321
AB  - Partitioning of restriction endonucleases between two liquid aqueous phases can
      be strongly influenced by group-specific ligands included in the two-phase
      system.  Three restriction endonucleases, namely EcoRI, EcoRV and BamHI, were
      partitioned within an aqueous dextran-polyethylene glycol (PEG) system.  The
      enzymes could be extracted into the upper PEG phase by using either triazine
      dyes or herring DNA as affinity ligands.  The influence of the endogenous
      bacterial nucleic acids, concentration of polymer-bound dye and concentration
      of sodium chloride on the system were examined.  A partial purification of
      EcoRI (up to 52-fold) and EcoRV (up to 37-fold) was achieved using a
      combination of affinity partitioning and ion-exchange chromatography, providing
      an extremely fast and economical method for the isolation of restriction
      endonucleases free from contaminating nuclease activities.
AU  - Vlatakis G
AU  - Bouriotis V
PT  - Journal Article
TA  - J. Chromatogr.
JT  - J. Chromatogr.
SO  - J. Chromatogr. 1991 538: 311-321.

PMID- 1750690
VI  - 195
DP  - 1991
TI  - Sequence-specific DNA affinity chromatography:  Application to the purification of EcoRI and SphI.
PG  - 352-357
AB  - Several rapid and effective methods have been described to obtain restriction
      endonucleases suitable for commercial exploitation.  However, lengthy and
      laborious protocols have been necessary to obtain homogeneous enzymes.  We now
      report the use of sequence-specific DNA affinity chromatography to purify
      restriction endonucleases to near homogeneity.  Restriction endonucleases EcoRI
      and SphI from the microorganisms Escherichia coli RY 13 and Streptomyces
      phaeochromogenes, respectively, were purified to near homogeneity employing a
      two-step procedure which involves DNA-cellulose chromatography and
      oligonucleotide-ligand affinity chromatography.
AU  - Vlatakis G
AU  - Bouriotis V
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 1991 195: 352-357.

PMID- 2587238
VI  - 17
DP  - 1989
TI  - Isolation and identification of restriction endonuclease BshFI.
PG  - 8882
AB  - None
AU  - Vlatakis G
AU  - Clark D
AU  - Bouriotis V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 8882.

PMID- 2840853
VI  - 15
DP  - 1987
TI  - Dye-ligand chromatography for the resolution and purification of restriction endonucleases.
PG  - 201-212
AB  - The resolution of restriction endonucleases from the same microorganism is
      conventionally achieved by length fractionation protocols.  We now report
      effective single-step procedures that exploit dye-ligand chromatography for the
      resolution and purification of restriction enzymes.  After suitable initial
      screening, we demonstrated that resolution of two restriction activities can be
      achieved in one chromatographic step, and further purification can subsequently
      be effected using selected dye-adsorbents.  Accordingly, we resolved in one
      step, HpaI from HpaII, HindII from HindIII, and SacI from SacII.  Furthermore,
      a three-step chromatographic procedure has been developed to purify EcoRV
      suitable for commercial exploitation, as judged by the overdigestion and
      cut-ligate-recut quality control tests.
AU  - Vlatakis G
AU  - Skarpelis G
AU  - Stratidaki I
AU  - Bouriotis V
PT  - Journal Article
TA  - Appl. Biochem. Biotechnol.
JT  - Appl. Biochem. Biotechnol.
SO  - Appl. Biochem. Biotechnol. 1987 15: 201-212.

PMID- 24744330
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Bacillus pumilus Fairview, an Isolate Recovered from a Microbial Methanogenic Enrichment of Coal Seam Gas Formation Water from Queensland, Australia.
PG  - e00279-14
AB  - Despite its global abundance, Bacillus pumilus is poorly studied. The Fairview strain was
      obtained from a methanogenic anaerobic coal digester. The draft genome sequence was 3.8 Mbp
      long and contained 3,890 protein-coding genes. Like the SAFR-032 strain, it includes B.
      pumilus-specific proteins that likely confer enhanced resistance to environmental stresses.
AU  - Vockler CJ
AU  - Greenfield P
AU  - Tran-Dinh N
AU  - Midgley DJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00279-14.

PMID- 8830712
VI  - 178
DP  - 1996
TI  - Gene transfer in Mycoplasma arthritidis: Transformation, conjugal transfer of Tn916, and evidence for a restriction system recognizing AGCT.
PG  - 6078-6081
AB  - Mycoplasma arthritidis is a rat pathogen causing a severe polyarthritis.  The study of its
      pathogenic mechanisms has been hampered by the lack of genetic systems for use with M.
      arthritidis.  Described here are procedures for genetic transformation of M. arthritidis and
      conjugal transfer of Tn916 from an enterococcal donor to M. arthritidis.  The location of
      Tn916 insertion sites in the mycoplasmal chromosome was random, suggesting that Tn916 may be
      useful as an insertional mutagen in this organism.  Additionally, a restriction and
      modification system was identified which presented a strong barrier to gene transfer.  For
      transformation, the restriction system was circumvented by using DNA that was modified in
      vitro with the appropriate site-specific methylase (AluI).
AU  - Voelker LL
AU  - Dybvig K
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1996 178: 6078-6081.

PMID- 10375626
VI  - 233
DP  - 1999
TI  - Sequence analysis of the Mycoplasma arthritidis bacteriophage MAV1 genome identifies the putative virulence factor.
PG  - 101-107
AB  - The bacteriophage MAV1 is required for the development of arthritis in rats after infection
      with its host Mycoplasma arthritidis.  To identify the phage-encoded virulence factor for this
      arthritis, the complete nucleotide sequence of MAV1 was determined. The linear double-stranded
      genome of MAV1 is 15644bp and contains 15 ORFs. Putative protein products from these ORFs were
      identified by comparison of the deduced amino acid sequences to known proteins and comprise
      DNA replication, restriction-modification, structural, regulatory, and integration/excision
      proteins. Eight putative promoters were identified; four of these would produce polycistronic
      transcripts. Translation of each ORF appears to be initiated independently, with each having
      its own RBS. A single ORF, vir, was identified on the minus strand of the phage genome. The
      putative protein product of vir contains a classic prokaryotic lipoprotein signal sequence and
      is a strong candidate for the MAV1-encoded virulence determinant.
AU  - Voelker LL
AU  - Dybvig K
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1999 233: 101-107.

PMID- 9279140
VI  - 11
DP  - 1997
TI  - DNA structure and restriction/modification visualized with kinemages.
PG  - A843
AB  - Teaching nucleic acid structure in more than a cursory way can be difficult.  What is it that
      is different about the structures of the A and B conformations of DNA?  How do we identify the
      Major and Minor grooves?  How do proteins interact with DNA in a specific manner?  How do
      proteins cleave and modify DNA?  Students carry out restriction digestion of DNA and make
      restriction maps in introductory biology courses.  But do they actually know what is
      happening?  We have tried to remedy this problem by instituting the use of Kinemage
      visualizations.  These accompany a set of laboratory experiments derived largely from Micklos,
      D.A. and Freyer, G.A., DNA Science, a first course in recombinant DNA Technology, Cold Spring
      Harbor Laboratory Press, 1990, on plasmid isolation, restriction mapping, and the effect of
      methylation on restriction.  The kinemages we have made show the different conformations of
      DNA and the complementary base pairs but, in addition, identify the functional groups of the
      bases that line the major and minor grooves and how the different types of sugar puckers
      associated with the different conformations.  We have also made kinemages showing the specific
      interactions of EcoRI and EcoRV restriction endonucleases with DNA as well as the interactions
      of HhaI methylase with DNA.  In this last kinemage we show the mechanism of methylation as
      well as the dramatic conformational change in the DNA induced by the enzyme and the
      protein-DNA interactions involved.  We will demonstrate these kinemages at the poster session.
AU  - Voet JG
AU  - Voet D
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1997 11: A843.

PMID- 7195861
VI  - 17
DP  - 1981
TI  - Restriction and modification of Actinophage omega-C31.
PG  - 1132-1135
AB  - Actinophage omega-C31 was shown to be insensitive to a number of restriction and modification
      systems.  Phage sensitivity to RM systems of those strains to which phage cannot adsorb, may
      be tested using protoplast transfection.  For instance, the absence of omega-C13 transfection
      in Streptomyces griseus Kr15 protoplasts, as compared to efficient transfection in protoplasts
      of R- M+ mutant of this strain seems to imply the sensitivity of omega-C31 to the RM system of
      S. griseus Kr15.  Restriction of mutant omega-C31 phage modified by S. albus G RM system has
      been detected in S. coelicolor A3(2).  This effect being dependent on a previous host may
      indicate that the mutant phage was rendered sensitive to an RM system of S. coelicolor A3(2).
AU  - Voeykova TA
AU  - Lomovskaya ND
PT  - Journal Article
TA  - Genetika
JT  - Genetika
SO  - Genetika 1981 17: 1132-1135.

PMID- 115749
VI  - 15
DP  - 1979
TI  - Identification of restriction and modification systems in Streptomyces strains.
PG  - 1746-1754
AB  - Host range of actinophage phi C31, VP5 and Pg81 in respect to 109 strains of Streptomyces
      genus and hybrid strain Rcg2 from the cross S. coelicolor
      A3(2)XS. griseus Kr was studied. The existence of RM-systems in strains S.
      griseus Kr15, S. griseus Kr20, Rcg2, S. griseofovillus 43 was shown using
      phage Pg81. Mutants of Pg81 were observed which to some extent lost
      snesitivity to RM-system in the strain Rcg2. The presence of RM-system in
      S. lividans 67 was demonstrated by the phage VP5.
AU  - Voeykova TA
AU  - Slavinskaya EV
AU  - Orechov AV
AU  - Lomovskaya ND
PT  - Journal Article
TA  - Genetika
JT  - Genetika
SO  - Genetika 1979 15: 1746-1754.

PMID- 22720005
VI  - 7
DP  - 2012
TI  - Short term evolution of a highly transmissible methicillin-resistant Staphylococcus aureus clone (ST228) in a tertiary care hospital.
PG  - E38969
AB  - Staphylococcus aureus is recognized as one of the major human pathogens and is by
      far one of the most common nosocomial organisms. The genetic basis for the
      emergence of highly epidemic strains remains mysterious. Studying the
      microevolution of the different clones of S. aureus is essential for identifying
      the forces driving pathogen emergence and spread. The aim of the present study
      was to determine the genetic changes characterizing a lineage belonging to the
      South German clone (ST228) that spread over ten years in a tertiary care hospital
      in Switzerland. For this reason, we compared the whole genome of eight isolates
      recovered between 2001 and 2008 at the Lausanne hospital. The genetic comparison
      of these isolates revealed that their genomes are extremely closely related. Yet,
      a few more important genetic changes, such as the replacement of a plasmid, the
      loss of large fragments of DNA, or the insertion of transposases, were observed.
      These transfers of mobile genetic elements shaped the evolution of the ST228
      lineage that spread within the Lausanne hospital. Nevertheless, although the
      strains analyzed differed in their dynamics, we have not been able to link a
      particular genetic element with spreading success. Finally, the present study
      showed that new sequencing technologies improve considerably the quality and
      quantity of information obtained for a single strain; but this information is
      still difficult to interpret and important investments are required for the
      technology to become accessible for routine investigations.
AU  - Vogel V
AU  - Falquet L
AU  - Calderon-Copete SP
AU  - Basset P
AU  - Blanc DS
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2012 7: E38969.

PMID- Not included in PubMed...
VI  - 211
DP  - 1988
TI  - Isolation of a halobacterial phage with a fully cytosine-methylated genome.
PG  - 407-414
AB  - A new bacteriophage from Halobacterium halobium has been isolated and partially characterized.
      It is not homologous to the phage PhiH (Schnabel et al. 1982) which infects the same
      bacterium, though it appeared spontaneously in a culture of PhiH adapted to H. halobium
      NRL/JW. The size and morphology of PhiN are comparable to that of other known halophages. The
      genome of PhiN consists of linear double-stranded DNA, 56 kb in size, whose dCMP is totally
      replaced by 5-methyl-dCMP. This is the second case of a fully cytosine-methylated genome, the
      bacteriophage XP12 from Xanthomonas oryzae being so far the only one reported. Like PhiH, the
      PhiN genome seems to have terminal redundancy and circular permutation. PhiN is the first
      halobacterial phage which survives prolonged exposure to low ionic strength environments.
      After 48 h incubation in distilled water a loss in infectivity of less than 50% is observed.
AU  - Vogelsang-Wenke H
AU  - Oesterhelt D
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1988 211: 407-414.

PMID- Not included in PubMed...
VI  - 46
DP  - 1987
TI  - Genetic and biological evidence for 5 different plasmid-encoded restriction and modification systems in Streptococcus cremoris strains.
PG  - 44
AB  - From plasmid curing data it was indicated that restriction- and modification systems
      (R/M-systems) were plasmid-encoded in Streptococcus cremoris KH, V32.2, T29W5 and Tk5-56 (2
      R/M-systems on different plasmids). 4 of the suspected R/M encoding plasmids were purified and
      cotransformed together with pVS2 into Streptococcus lactis MG1614. Transformants containing
      the individual suspected R/M encoding plasmids together with pVS2, showed restriction against
      Phijj50 grown on S. lactis MG1614 containing pVS2, giving genetic evidence that the suspected
      plasmids actually coded for R/M systems. The strength in the new host were in two cases lower
      than that in the original host. Whether this is due to the host or the different phage is not
      known. When Phijj50 were grown on transformants containing the different R/M encoding plasmids
      it was in all cases restricted by the other R/M containing transformants, indicating 4
      biological different R/M-systems were acting. The size of the 4 plasmids were in the range of
      13-18 Kb. Additionally S. cremoris Tk5-56 contained a second plasmid encoded R/M-system. From
      curing data and from transformation with total plasmid DNA from S. cremoris Tk5-56 into S.
      lactis MG1614 it could be concluded that the second R/M-system is encoded either on
      approximately 18 Kb or approximately 45 Kb plasmids. From biological data it can be concluded
      that this system differs from the above 4 R/M systems mentioned.
AU  - Vogensen FK
AU  - Pedersen BM
AU  - Nielsen EW
AU  - Josephsen J
PT  - Journal Article
TA  - FEMS Microbiol. Rev.
JT  - FEMS Microbiol. Rev.
SO  - FEMS Microbiol. Rev. 1987 46: 44.

PMID- 26358607
VI  - 3
DP  - 2015
TI  - Closed Genome Sequence of Octadecabacter temperatus SB1, the First Mesophilic Species of the Genus Octadecabacter.
PG  - e01051-15
AB  - The Gram-negative alphaproteobacterium Octadecabacter temperatus SB1 (DSM 26878)  belongs to
      the marine Roseobacter clade. The genome of this strain is the smallest closed genome of the
      Roseobacter clade. O. temperatus SB1 is the first described nonpolar mesophilic isolate of the
      genus Octadecabacter and the type strain of the species.
AU  - Voget S
AU  - Billerbeck S
AU  - Simon M
AU  - Daniel R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01051-15.

PMID- 26404611
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Roseovarius tolerans EL-164, a Producer of N-Acylated Alanine Methyl Esters and N-Acylhomoserine Lactones.
PG  - e01096-15
AB  - Roseovarius tolerans EL-164 is a member of the Roseobacter clade, a group of marine bacteria
      within the Alphaproteobacteria. It produces different N-acylhomoserine lactone (AHL)
      autoinducers as well as five AHL-related but functionally different compounds, the N-acylated
      alanine methyl esters. The size  of the draft genome is 3,749,755 bp.
AU  - Voget S
AU  - Bruns H
AU  - Wagner-Dobler I
AU  - Schulz S
AU  - Daniel R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01096-15.

PMID- 25908144
VI  - 3
DP  - 2015
TI  - Genome Sequence of Jannaschia aquimarina GSW-M26, a Member of the Roseobacter Clade.
PG  - e00353-15
AB  - The Gram-negative alphaproteobacterium Jannaschia aquimarina GSW-M26 (DSM 28248)  is a member
      of the Roseobacter clade. The size of the draft genome is 4.1 Mb.
      Genome analysis revealed the presence of genes encoding a complete gene transfer
      agent and aerobic anoxygenic photosynthesis. The latter indicated a
      photoheterotrophic lifestyle.
AU  - Voget S
AU  - Diaz VSM
AU  - von Hoyningen-Huene AJ
AU  - Nattramilarasu PK
AU  - Vollheyde K
AU  - Xiao S
AU  - Daniel R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00353-15.

PMID- 21551290
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Carnobacterium sp. 17-4.
PG  - 3403-3404
AB  - Members of the Carnobacteria have been extensively studied as probiotic cultures in
      aquacultures and protective cultures in seafood, diary and
      meat. We report on the finished genome sequence of Carnobacterium sp.
      17-4, which has been isolated from permanently cold seawater. The genetic
      information reveals a new circular bacteriocin biosynthesis cluster.
AU  - Voget S
AU  - Klippel B
AU  - Daniel R
AU  - Antranikian G
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3403-3404.

PMID- 25083934
VI  - 9
DP  - 2015
TI  - Adaptation of an abundant Roseobacter RCA organism to pelagic systems revealed by genomic and transcriptomic analyses.
PG  - 371-384
AB  - The RCA (Roseobacter clade affiliated) cluster, with an internal 16S rRNA gene
      sequence similarity of >98%, is the largest cluster of the marine Roseobacter
      clade and most abundant in temperate to (sub)polar oceans, constituting up to 35%
      of total bacterioplankton. The genome analysis of the first described species of
      the RCA cluster, Planktomarina temperata RCA23, revealed that this phylogenetic
      lineage is deeply branching within the Roseobacter clade. It shares not >65.7% of
      homologous genes with any other organism of this clade. The genome is the
      smallest of all closed genomes of the Roseobacter clade, exhibits various
      features of genome streamlining and encompasses genes for aerobic anoxygenic
      photosynthesis (AAP) and CO oxidation. In order to assess the biogeochemical
      significance of the RCA cluster we investigated a phytoplankton spring bloom in
      the North Sea. This cluster constituted 5.1% of the total, but 10-31% (mean
      18.5%) of the active bacterioplankton. A metatranscriptomic analysis showed that
      the genome of P. temperata RCA23 was transcribed to 94% in the bloom with some
      variations during day and night. The genome of P. temperata RCA23 was also
      retrieved to 84% from metagenomic data sets from a Norwegian fjord and to 82%
      from stations of the Global Ocean Sampling expedition in the northwestern
      Atlantic. In this region, up to 6.5% of the total reads mapped on the genome of
      P. temperata RCA23. This abundant taxon appears to be a major player in ocean
      biogeochemistry.The ISME Journal advance online publication, 1 August 2014;
      doi:10.1038/ismej.2014.134.
AU  - Voget S
AU  - Wemheuer B
AU  - Brinkhoff T
AU  - Vollmers J
AU  - Dietrich S
AU  - Giebel HA
AU  - Beardsley C
AU  - Sardemann C
AU  - Bakenhus I
AU  - Billerbeck S
AU  - Daniel R
AU  - Simon M
PT  - Journal Article
TA  - ISME J.
JT  - ISME J.
SO  - ISME J. 2015 9: 371-384.

PMID- 2159342
VI  - 29
DP  - 1990
TI  - O6 methylguanine in place of guanine causes asymmetric single-strand cleavage of DNA by some restriction enzymes.
PG  - 1632-1637
AB  - The interactions of restriction enzymes with their cognate DNA recognition sequences present a
      model for protein-DNA interactions. We have investigated the effect of O6-methylguanine on
      restriction enzyme cleavage of DNA; O6-methylguanine is a carcinogenic lesion and a structural
      analogue of the biological restriction inhibitor N6-methyladenine. O6-methylguanine was
      synthesized into oligonucleotides at unique positions. The oligonucleotides were purified and
      analyzed by high-pressure liquid chromatography to assure that, within the limits of our
      detection, O6-methylguanine was the only modified base present. These oligonucleotides were
      annealed with their complement so that cytosine, and in one case thymine, opposed
      O6-methylguanine. DNA cleavage by restriction enzymes that recognize a unique DNA sequence,
      HpaII, HhaI, HinPI, NaeI, NarI, PvuII, and XhoI, was inhibited by a single O6-methylguanine in
      place of guanine (adenine for PvuII) within the appropriate recognition sequences. However,
      only the modified strand was nicked by HpaII, NaeI, and XhoI with O6-methylguanine at certain
      positions, indicating asymmetric strand cleavage. For all the restriction enzymes studied but
      AhaII, BanI, and NarI, lack of double- or single-strand cleavage correlated with inability of
      the O6-methylguanine-containing recognition sequence to measurably bind enzyme. None of the
      restriction enzymes studied were inhibited by O6-methylguanine outside their cognate
      recognition sequences.
AU  - Voigt JM
AU  - Topal MD
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1990 29: 1632-1637.

PMID- 25999572
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Chromobacterium vaccinii, a Potential Biocontrol Agent against Mosquito (Aedes aegypti) Larvae.
PG  - e00477-15
AB  - Chromobacterium vaccinii has been isolated only from cranberry bogs in Massachusetts. While it
      is unknown what role these bacteria play in their natural
      environments, they hold potential as biological control agents against the larvae
      of insect pests. Potential virulence genes were identified, including the
      violacein synthesis pathway, siderophores, and chitinases.
AU  - Voing K
AU  - Harrison A
AU  - Soby SD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00477-15.

PMID- 28336605
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Chromobacterium subtsugae MWU12-2387 Isolated from a Wild Cranberry Bog in Truro, Massachusetts.
PG  - e01633-16
AB  - Chromobacterium subtsugae MWU12-2387 was isolated from the rhizosphere of cranberry plants.
      While it is unknown what environmental role these bacteria play
      in bog soils, they hold potential as biological control agents against nematodes
      and insect pests. Potential virulence genes were identified, including the
      violacein synthesis pathway, siderophores, and several chitinases.
AU  - Voing K
AU  - Harrison A
AU  - Soby SD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01633-16.

PMID- 26358592
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Three Chromobacterium subtsugae Isolates from Wild and  Cultivated Cranberry Bogs in Southeastern Massachusetts.
PG  - e00998-15
AB  - Chromobacterium subtsugae was isolated from cranberry bogs in Massachusetts. While it is
      unknown what environmental role these bacteria play in bog soils, they hold potential as
      biological control agents against the larvae of insect pests. Potential virulence genes were
      identified, including the violacein synthesis pathway, siderophores, and several chitinases.
AU  - Voing K
AU  - Harrison A
AU  - Soby SD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00998-15.

PMID- 21742883
VI  - 193
DP  - 2011
TI  - Complete genome sequences of the chemolithoautotrophic Oligotropha carboxidovorans strains OM4 and OM5.
PG  - 5043
AB  - We report on genome sequencing of Oligotropha carboxidovorans strain OM4 and resequencing of
      strain OM5. The genomes of both are composed of one
      chromosome and two plasmids. The presence of two plasmids in the OM5
      genome is inconsistent with the previously published sequence in which
      only one plasmid was described (D. Paul, S. Bridges, S. Burgess, Y.
      Dandass, and M. Lawrence. BMC Genomics 11:511, 2010).
AU  - Volland S
AU  - Rachinger M
AU  - Strittmatter A
AU  - Daniel R
AU  - Gottschalk G
AU  - Meyer O
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5043.

PMID- 17426121
VI  - 35
DP  - 2007
TI  - Flow cytometric analysis of DNA binding and cleavage by cell surface-displayed homing endonucleases.
PG  - 2748-2758
AB  - LAGLIDADG homing endonucleases (LHEs) cleave 18-24 bp DNA sequences and are promising enzymes
      for applications requiring sequence-specific DNA cleavage amongst genome-sized DNA
      backgrounds. Here, we report a method for cell surface display of LHEs, which facilitates
      analysis of their DNA binding and cleavage properties by flow cytometry. Cells expressing
      surface LHEs can be stained with fluorescently conjugated double-stranded oligonucleotides
      (dsOligos) containing their respective target sequences. The signal is absolutely sequence
      specific and undetectable with dsOligos carrying single base-pair substitutions. LHE-dsOligo
      interactions facilitate rapid enrichment and viable recovery of rare LHE expressing cells by
      both fluorescence-activated cell sorting (FACS) and magnetic cell sorting (MACS).
      Additionally, dsOligos conjugated with unique fluorophores at opposite termini can be tethered
      to the cell surface and used to detect DNA cleavage. Recapitulation of DNA binding and
      cleavage by surface-displayed LHEs provides a high-throughput approach to library screening
      that should facilitate rapid identification and analysis of enzymes with novel sequence
      specificities.
AU  - Volna P
AU  - Jarjour J
AU  - Baxter S
AU  - Roffler SR
AU  - Monnat RJ Jr
AU  - Stoddard BL
AU  - Scharenberg AM
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2007 35: 2748-2758.

PMID- 29051261
VI  - 5
DP  - 2017
TI  - Genome Sequences of Two NDM-1 Metallo-beta-Lactamase-Producing Multidrug-Resistant Strains of Klebsiella pneumoniae with a High Degree of  Similarity, One of Which Contains Prophage.
PG  - e01173-17
AB  - We report genome sequences of two NDM-1 metallo-beta-lactamase-producing multidrug-resistant
      Klebsiella pneumoniae isolates of sequence type 147 (ST147)
      from one hospital. The genomes are highly similar and differ in prophage located
      in the chromosome of K. pneumoniae KPB-1470/16 and in the additional
      plasmid-carrying blaOXA-48 gene in K. pneumoniae KPB-417/16.
AU  - Volozhantsev NV
AU  - Kislichkina AA
AU  - Lev AI
AU  - Mukhina TN
AU  - Bogun AA
AU  - Ershova ON
AU  - Alexandrova IA
AU  - Fursova NK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01173-17.

PMID- 21304717
VI  - 2
DP  - 2010
TI  - Complete genome sequence of Archaeoglobus profundus type strain (AV18).
PG  - 327-346
AB  - Archaeoglobus profundus (Burggraf et al. 1990) is a hyperthermophilic archaeon in the
      euryarchaeal class Archaeoglobi, which is currently represented by the single
      family Archaeoglobaceae, containing six validly named species and two strains
      ascribed to the genus 'Geoglobus' which is taxonomically challenged as the
      corresponding type species has no validly published name. All members were
      isolated from marine hydrothermal habitats and are obligate anaerobes. Here we
      describe the features of the organism, together with the complete genome sequence
      and annotation. This is the second completed genome sequence of a member of the
      class Archaeoglobi. The 1,563,423 bp genome with its 1,858 protein-coding and 52
      RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - von Jan M et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 2: 327-346.

PMID- 8316832
VI  - 260
DP  - 1993
TI  - Arabidopis thaliana DNA methylation mutants.
PG  - 1926-1928
AB  - Three DNA hypomethylation mutants of the flowering plant Arabidopsis thaliana were isolated by
      screening mutagenized populations for plants containing centromeric repetitive DNA arrays
      susceptible to digestion by restriction endonuclease that was sensitive to methylated
      cytosines. The mutations are recessive, and at least two are alleles of a single locus,
      designated DDM1 (for decrease in DNA methylation). Amounts of 5-methylcytosine were reduced
      over 70 percent in ddm1 mutants. Despite this reduction in DNA methylation levels, ddm1
      mutants developed normally and exhibited no striking morphological phenotypes. However, the
      ddm1 mutations are associated with a segregation distortion phenotype. The ddm1 mutations were
      used to demonstrate that de novo DNA methylation in vivo is slow.
AU  - Vongs A
AU  - Kakutani T
AU  - Martienssen RA
AU  - Richards EJ
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1993 260: 1926-1928.

PMID- 25743074
VI  - 362
DP  - 2015
TI  - The genome of Shigella dysenteriae strain Sd1617 comparison to representative strains in evaluating pathogenesis.
PG  - fnv011
AB  - We sequenced and analyzed Shigella dysenteriae strain Sd1617 serotype 1 that is widely used as
      model strain for vaccine design, trials and research. A combination of next-generation
      sequencing platforms and assembly yielded two contigs representing a chromosome size of 4.34
      Mb and the large virulence plasmid of 177 kb. This genome sequence is compared with other
      Shigella genomes in order to understand gene complexity and pathogenic factors.
AU  - Vongsawan AA
AU  - Kapatral V
AU  - Vaisvil B
AU  - Burd H
AU  - Serichantalergs O
AU  - Venkatesan MM
AU  - Mason CJ
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2015 362: fnv011.

PMID- 
VI  - 0
DP  - 1999
TI  - Cloning of a mammalian transcriptional activator that binds unmethylated CpG motifs and shares a CXXC domain with DNA methyltransferase, human trithorax, and methyl-CpG binding domain protein 1.
PG  - 469a
AB  - Cytosine methylation of DNA at CpG motifs provides an important mechanism for controlling gene
      expression.  Hypermethylation or hypomethylation of tumor suppressor genes and oncogenes,
      respectively, has been associated with the progression of cancer.  Ligand screening was
      utilized to isolate a human cDNA that encodes a novel CpG binding protein (hCGBP) that is
      highly expressed in hematopoietic cell lines.  This factor contains three cysteine rich
      domains, two of which exhibit homology to the plant homeodomain finger motif.  A third
      cysteine rich domain conforms to the CXXC motif identified in DNA methyltransferase, human
      thithorax, and methyl-CpG binding domain protein 1.  Interestingly, database searching
      revealed that the hCGBP gene is located within 1 kilobase of the gene encoding methyl-CpG
      binding domain protein 1, a factor that binds to methylated CpG motifs and functions as a
      transcriptional repressor.  A fragment of hCGBP that contains the CXXC domain binds to an
      oligonucleotide probe containing a single CpG site, and this complex is disrupted by distinct
      oligonucleotide competitors that also contain CpG motif(s).  However, hCGBP fails to bind
      oligonucleotides in which the CpG motif is either mutated or methylated.  Native hCGBP is
      detected as an 88 kDa protein by Western analysis and is ubiquitously expressed.  The
      DNA-binding activity of native hCGBP is apparent in electrophoretic mobility shift assays, and
      hCGBP trans-activates promoters that contain CpG motifs, but not promoters in which the CpG is
      ablated.  These data indicate that hCGBP is a transcriptional activator that recognizes
      unmethylated CpG dinucleotides, suggesting a role in modulating the expression of genes
      located within CpG islands.
AU  - Voo K
AU  - Carlone D
AU  - Jacobsen B
AU  - Flodin A
AU  - Skalnik D
PT  - Journal Article
TA  - Blood
JT  - Blood
SO  - Blood 1999 0: 469a.

PMID- 9076739
VI  - 23
DP  - 1997
TI  - A selenium-dependent and a selenium-independent formylmethanofuran dehydrogenase and their transcriptional regulation in the hyperthermophilic Methanopyrus kandleri.
PG  - 1033-1042
AB  - The genome of Methanopyrus kandleri was found to harbour a gene, fwuB, predicted to encode the
      catalytic subunit of a tungsten formylmethanofuran dehydrogenase with an active site
      selenocysteine, and a second gene, fwcB, encoding a tungsten formylmethanofuran dehydrogenase
      with an active site cysteine. Northern blot and primer-extension analysis revealed that both
      genes were differentially transcribed. During growth of the methanogen on medium supplemented
      with selenium only fwuB was transcribed, whereas transcription of both fwuB and fwcB was
      observed on selenium-deprived medium. Growth of M. kandleri was stimulated by tungstate and
      selenite but not by molybdate. The findings indicate that the hyperthermophilic archaeon
      contains two tungsten isoenzymes of formylmethanofuran dehydrogenase, one of which is a novel
      selenium enzyme. They also indicate that the hyperthermophilic methanogen probably does not
      contain a molybdenum formylmethanofuran dehydrogenase which appears to be present only in
      thermophilic and mesophilic methanogens.
AU  - Vorholt JA
AU  - Vaupel M
AU  - Thauer RK
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1997 23: 1033-1042.

PMID- 25523779
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Pseudomonas aeruginosa Strain WS394, a Multidrug-Resistant and Highly Cytotoxic Wound Isolate from Chronic Ulcus Cruris.
PG  - e01325-14
AB  - Pseudomonas aeruginosa is a frequent human pathogen that increasingly causes chronic
      infections of nonhealing wounds. Here we present the 6.8 Mb draft genome
      of strain WS394, a multidrug-resistant chronic ulcer isolate that exhibited
      outstanding high cell cytotoxicity despite defective secretion of exotoxin U,
      suggesting a habitat-dependent adaptation process.
AU  - Vorholter FJ
AU  - Arnold M
AU  - Wibberg D
AU  - Blom J
AU  - Winkler A
AU  - Viehoever P
AU  - Albersmeier A
AU  - Goesmann A
AU  - Zange S
AU  - Heesemann J
AU  - Puhler A
AU  - Hogardt M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01325-14.

PMID- 18304669
VI  - 134
DP  - 2008
TI  - The genome of Xanthomonas campestris pv. campestris B100 and its use for the reconstruction of metabolic pathways involved in xanthan biosynthesis.
PG  - 33-45
AB  - The complete genome sequence of the Xanthomonas campestris pv. campestris strain B100 was
      established. It consisted of a chromosome of 5,079,003bp,
      with 4471 protein-coding genes and 62 RNA genes. Comparative genomics
      showed that the genes required for the synthesis of xanthan and xanthan
      precursors were highly conserved among three sequenced X. campestris pv.
      campestris genomes, but differed noticeably when compared to the remaining
      four Xanthomonas genomes available. For the xanthan biosynthesis genes
      gumB and gumK earlier translational starts were proposed, while gumI and
      gumL turned out to be unique with no homologues beyond the Xanthomonas
      genomes sequenced. From the genomic data the biosynthesis pathways for the
      production of the exopolysaccharide xanthan could be elucidated. The first
      step of this process is the uptake of sugars serving as carbon and energy
      sources wherefore genes for 15 carbohydrate import systems could be
      identified. Metabolic pathways playing a role for xanthan biosynthesis
      could be deduced from the annotated genome. These reconstructed pathways
      concerned the storage and metabolization of the imported sugars. The
      recognized sugar utilization pathways included the Entner-Doudoroff and
      the pentose phosphate pathway as well as the Embden-Meyerhof pathway
      (glycolysis). The reconstruction indicated that the nucleotide sugar
      precursors for xanthan can be converted from intermediates of the pentose
      phosphate pathway, some of which are also intermediates of glycolysis or
      the Entner-Doudoroff pathway. Xanthan biosynthesis requires in particular
      the nucleotide sugars UDP-glucose, UDP-glucuronate, and GDP-mannose, from
      which xanthan repeat units are built under the control of the gum genes.
      The updated genome annotation data allowed reconsidering and refining the
      mechanistic model for xanthan biosynthesis.
AU  - Vorholter FJ
AU  - Schneiker S
AU  - Goesmann A
AU  - Krause L
AU  - Bekel T
AU  - Kaiser O
AU  - Linke B
AU  - Patschkowski T
AU  - Ruckert C
AU  - Schmid J
AU  - Sidhu VK
AU  - Sieber V
AU  - Tauch A
AU  - Watt SA
AU  - Weisshaar B
AU  - Becker A
AU  - Niehaus K
AU  - Puhler A
PT  - Journal Article
TA  - J. Biotechnol.
JT  - J. Biotechnol.
SO  - J. Biotechnol. 2008 134: 33-45.

PMID- 25767242
VI  - 3
DP  - 2015
TI  - Genome Sequence of the Urethral Catheter Isolate Pseudomonas aeruginosa MH19.
PG  - e00115-15
AB  - Pseudomonas aeruginosa is a frequent agent of complicated catheter-associated urinary tract
      infections (CAUTIs). Here, we present the improved 7.1-Mb draft
      genome sequence of P. aeruginosa MH19, which was isolated from a patient with an
      acute hospital-acquired CAUTI. It includes unique genes not represented in other
      P. aeruginosa genomes.
AU  - Vorholter FJ
AU  - Tielen P
AU  - Wibberg D
AU  - Narten M
AU  - Schobert M
AU  - Tupker R
AU  - Blom J
AU  - Schatschneider S
AU  - Winkler A
AU  - Albersmeier A
AU  - Goesmann A
AU  - Puhler A
AU  - Jahn D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00115-15.

PMID- 12408024
VI  - 28
DP  - 2002
TI  - An analysis of methyltransferase SsoII-DNA contacts in the enzyme-substrate complex.
PG  - 402-410
AB  - The functional groups of the DNA methylation site that are involved in the DNA interaction
      with methyltransferase SsoII at the recognition stage were identified. The contacts in the
      enzyme-substrate complex were analyzed in the presence of S-adenosyl-L-homocysteine using the
      interference footprinting assay with formic acid, hydrazine, dimethyl sulfate, or
      N-ethyl-N-nitrosourea as a modifying reagent. It was shown that the replacement of the central
      A.T by the G.C pair in the methylation site did not affect the enzyme-DNA interaction, whereas
      the use of a substrate with one chain methylated (monomethylated substrate) instead of the
      unmethylated substrate dramatically changes the DNA contacts. The binding constants of
      unmethylated and monomethylated substrates with methyltransferase Ssoll in the presence of
      S-adenosyl-L-homocysteine were calculated.
AU  - Vorobeva OV
AU  - Karyagina AS
AU  - Volkov EM
AU  - Viryasov MB
AU  - Oretskaya TS
AU  - Kubareva EA
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 2002 28: 402-410.

PMID- 14593929
VI  - 37
DP  - 2003
TI  - Crosslinking of Cys142 of Methyltransferase SsoII with DNA Duplexes Containing a Single Internucleotide Phosphoryldisulfide Link.
PG  - 906-915
AB  - DNA duplexes containing a single phosphoryldisulfide link in place of the natural
      internucleotide phosphodiester bond were employed in affinity
      modification of Cys142 in cytosine-C5 DNA methyltransferase SsoII
      (M.SsoII). The possibility of duplex-M.SsoII conjugation as a result of
      disulfide exchange was demonstrated. The crosslinking efficiency proved to
      depend on the DNA primary structure, modification position, and the
      presence of S-adenosyl-L-homocysteine, a nonreactive analog of the
      methylation cofactor. The SH group of M.SsoII Cys142 was assumed to be
      close to the DNA sugar-phosphate backbone in the DNA-enzyme complex.
AU  - Vorobeva OV
AU  - Romanenkov AS
AU  - Metelev VG
AU  - Karyagina AS
AU  - Lavrova NV
AU  - Oretskaya TS
AU  - Kubareva EA
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2003 37: 906-915.

PMID- 11186007
VI  - 34
DP  - 2000
TI  - Analysis of DNA-protein contacts in a complex between methyltransferase SsoII and a promoter region of the SsoII restriction-modification genes.
PG  - 1074-1080
AB  - .
AU  - Vorobeva OV
AU  - Vasilev SA
AU  - Karyagina AS
AU  - Oretskaya TS
AU  - Kubareva EA
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2000 34: 1074-1080.

PMID- 22374954
VI  - 194
DP  - 2012
TI  - Complete Genome Sequences of Three Propionibacterium acnes Isolates from the Type IA2 Cluster.
PG  - 1621-1622
AB  - Propionibacterium acnes is an anaerobic Gram-positive bacterium that has been linked to a wide
      range of opportunistic human infections and conditions, most
      notably acne vulgaris (I. Kurokawa et al., Exp. Dermatol. 18:821-832, 2009). We
      now present the whole-genome sequences of three P. acnes strains from the type
      IA(2) cluster which were recovered from ophthalmic infections (A. McDowell et
      al., Microbiology 157:1990-2003, 2011).
AU  - Voros A
AU  - Horvath B
AU  - Hunyadkurti J
AU  - McDowell A
AU  - Barnard E
AU  - Patrick S
AU  - Nagy I
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1621-1622.

PMID- 26259566
VI  - 98
DP  - 2015
TI  - A transferable plasticity region in Campylobacter coli allows isolates of an otherwise non-glycolytic food-borne pathogen to catabolize glucose.
PG  - 809830
AB  - Thermophilic Campylobacter species colonize the intestine of agricultural and
      domestic animals commensally, but cause severe gastroenteritis in humans. In
      contrast to other enteropathogenic bacteria, Campylobacter have been considered
      to be non-glycolytic, a metabolic property originally used for their taxonomic
      classification. Contrary to this dogma, we demonstrate that several Campylobacter
      coli strains are able to utilize glucose as a growth substrate. Isotopologue
      profiling experiments with 13 C-labeled glucose suggested that these strains
      catabolize glucose via the pentose phosphate and Entner-Doudoroff (ED) pathways
      and use glucose efficiently for de novo synthesis of amino acids and cell surface
      carbohydrates. Whole genome sequencing of glycolytic C. coli isolates identified
      a genomic island located within a ribosomal RNA gene cluster that encodes for all
      ED pathway enzymes and a glucose permease. We could show in vitro that a
      non-glycolytic C. coli strain could acquire glycolytic activity through natural
      transformation with chromosomal DNA of C. coli and C. jejuni subsp. doylei
      strains possessing the ED pathway encoding plasticity region. These results
      reveal for the first time the ability of a Campylobacter species to catabolize
      glucose and provide new insights into how genetic macrodiversity through intra-
      and interspecies gene transfer expand the metabolic capacity of this food-borne
      pathogen.
AU  - Vorwerk H
AU  - Huber C
AU  - Mohr J
AU  - Bunk B
AU  - Bhuju S
AU  - Wensel O
AU  - Sproer C
AU  - Fruth A
AU  - Flieger A
AU  - Schmidt-Hohagen K
AU  - Schomburg D
AU  - Eisenreich W
AU  - Hofreuter D
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2015 98: 809830.

PMID- 6281279
VI  - 257
DP  - 1982
TI  - Effect of deoxynucleoside phosphorothioates incorporated in DNA on cleavage by restriction enzymes.
PG  - 6595-6599
AB  - DNA synthesized in vitro using deoxynucleoside phosphorothioates as substrates is quite
      similar to normal DNA in its biochemical properties. In order to investigate the effect of
      phosphorothioate groups in DNA on the cleavage pattern of restriction endonucleases
      phosphorothioate double-stranded, circular, replicative form of fd DNA was synthesized in
      vitro with Escherichia coli DNA polymerase I using native single-stranded DNA as template and
      mixtures of three normal nucleotides and one nucleoside phosphorothioate analogue as
      substrates. The double-stranded products were hybrids with respect to their phosphorothioate
      content. Restriction analysis of normal and phosphorothioate DNA with the restriction
      endonucleases HaeIII, BamHI, HpaII, HindII, Alu I, and TaqI showed that the enzymes were
      inhibited to different degrees depending on which of the nucleotides was replaced by the
      phosphorothioate. Most significant, inhibition was seen throughout with those DNAs which
      contained a phosphorothioate exactly at the cleavage site. Phosphorothioate substitutions at
      other positions, but still within the recognition sequences, were, except for AluI, not or
      weakly inhibitory. Phosphorothioate nucleotides not present in the recognition sequences did
      not affect at all the fragment patterns. The results show that recognition sequences of
      restriction endonucleases can be selectively protected against cleavage by base-specific
      introduction of phosphorothioate groups into DNA.
AU  - Vosberg H-P
AU  - Eckstein F
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1982 257: 6595-6599.

PMID- 23555932
VI  - 8
DP  - 2013
TI  - Insights into the physiology and ecology of the brackish-water-adapted Cyanobacterium Nodularia spumigena CCY9414 based on a genome-transcriptome analysis.
PG  - E60224
AB  - Nodularia spumigena is a filamentous diazotrophic cyanobacterium that dominates
      the annual late summer cyanobacterial blooms in the Baltic Sea. But N. spumigena
      also is common in brackish water bodies worldwide, suggesting special adaptation
      allowing it to thrive at moderate salinities. A draft genome analysis of N.
      spumigena sp. CCY9414 yielded a single scaffold of 5,462,271 nucleotides in
      length on which genes for 5,294 proteins were annotated. A subsequent
      strand-specific transcriptome analysis identified more than 6,000 putative
      transcriptional start sites (TSS). Orphan TSSs located in intergenic regions led
      us to predict 764 non-coding RNAs, among them 70 copies of a possible
      retrotransposon and several potential RNA regulators, some of which are also
      present in other N2-fixing cyanobacteria. Approximately 4% of the total coding
      capacity is devoted to the production of secondary metabolites, among them the
      potent hepatotoxin nodularin, the linear spumigin and the cyclic nodulapeptin.
      The transcriptional complexity associated with genes involved in nitrogen
      fixation and heterocyst differentiation is considerably smaller compared to other
      Nostocales. In contrast, sophisticated systems exist for the uptake and
      assimilation of iron and phosphorus compounds, for the synthesis of compatible
      solutes, and for the formation of gas vesicles, required for the active control
      of buoyancy. Hence, the annotation and interpretation of this sequence provides a
      vast array of clues into the genomic underpinnings of the physiology of this
      cyanobacterium and indicates in particular a competitive edge of N. spumigena in
      nutrient-limited brackish water ecosystems.
AU  - Voss B
AU  - Bolhuis H
AU  - Fewer DP
AU  - Kopf M
AU  - Moke F
AU  - Haas F
AU  - El-Shehawy R
AU  - Hayes P
AU  - Bergman B
AU  - Sivonen K
AU  - Dittmann E
AU  - Scanlan DJ
AU  - Hagemann M
AU  - Stal LJ
AU  - Hess WR
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2013 8: E60224.

PMID- 4586117
VI  - 246
DP  - 1973
TI  - Restriction endonuclease B and f1 heteroduplex DNA.
PG  - 13-16
AB  - In many strains of Escherichia coli, strain-specific restriction system
      recognises phage and bacterial DNA synthesis in a different strain and
      initiates its degradation.  The recognition and initial hydrolysis can
      apparently occur at the same or different sites on the DNA molecule (resistance
      transfer factor R1, (refs 1-3) and E. coli B4 restriction, respectively) and
      are mediated by a strain-specific endonuclease.  Protection is afforded by
      modification (glucosylation and methylation) and mutation of the DNA,
      presumably at the recognition site(s).  A DNA duplex, only one of whose strands
      is modified (by methylation) is resistant to restriction endonuclease K.
      Similar conclusions about the sensitivity of hybrid molecules containing one
      modified DNA strand were made from in vivo observations with T2 and lambda
      phage with regard to restriction in E. coli B and P1 lysogens, respectively.
AU  - Vovis GF
AU  - Horiuchi K
AU  - Hartman N
AU  - Zinder ND
PT  - Journal Article
TA  - Nature New Biol.
JT  - Nature New Biol.
SO  - Nature New Biol. 1973 246: 13-16.

PMID- 1159896
VI  - 16
DP  - 1975
TI  - Endonuclease R.EcoRII restriction of bacteriophage f1 DNA in vitro:  Ordering of genes V and VII, location of an RNA promotor for Gene VIII.
PG  - 674-684
AB  - Replicative form DNA of bacteriophage f1 was found to be sensitive in vitro to
      restriction by endonuclease R.EcoRII if the DNA was isolated from an
      Escherichia coli strain deficient in cytosine methylase activity.  A similar
      observation was previously made with DNA from the closely related bacteriophage
      fd (S. Schlagman, S. Hattman, M.S. May and L. Berger, submitted for
      publication).  The two DNA fragments produced by the endo R.EcoRII digestion of
      f1 DNA were localized on the f1 cleavage map and their genetic content was
      determined.  The polypeptides synthesized in a "coupled"
      transcription-translation system under the direction of each RII fragment were
      examined.  The results of such experiments allow the ordering of genes V and
      VII and indicate the location of a RNA promoter for gene VIII.
AU  - Vovis GF
AU  - Horiuchi K
AU  - Zinder ND
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1975 16: 674-684.

PMID- 4610561
VI  - 71
DP  - 1974
TI  - Kinetics of methylation of DNA by a restriction endonuclease from Escherichia coli B.
PG  - 3810-3813
AB  - The restriction endonuclease from E. coli B is both an endonuclease and a DNA
      methylase.  Both activities either require or are stimulated by Mg++, adenosine
      triphosphate, and S-adenosyl-L-methionine.  The particular activity which the
      enzyme exhibits depends upon the nature of the SB sites, the genetic sites that
      identify substrate DNA.  Enzymatic treatment of DNA that has an unmodified,
      wild-type SB site results in either rapid restriction of the DNA or very slow
      methylation of the SB site.  On the other hand, a hybrid SB site (modified),
      which protects the DNA molecule from restriction, results in rapid methylation
      of that SB site.
AU  - Vovis GF
AU  - Horiuchi K
AU  - Zinder ND
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1974 71: 3810-3813.

PMID- 592372
VI  - 115
DP  - 1977
TI  - Complementary action of restriction enzymes Endo R.DpnI and Endo R.DpnII on bacteriophage f1 DNA.
PG  - 525-538
AB  - Bacteriophage f1 duplex DNA was isolated from Escherichia coli strains containing different
      DNA methylases and assayed for its sensitivity to endonucleolytic cleavage by the enzymes endo
      R.DpnI and endo R.DpnII. the former enzyme is specific for methylated DNA, the latter for
      unmethylated DNA (Lacks & Greenberg, 1975). The E. coli dam methylase was found to be
      responsible for making f1 resistant to endo R.DpnII and sensitive to endo R.DpnI. Endo R.DpnI
      cleaved f1 DNA from dam+ cells at four sites. Additional methylation by enzymes other than the
      dam methylase gave no further cleavage. Endo R.DpnII cleaved f1 DNA from dam- cells also at
      four sites to give restriction fragments identical to those obtained with endo R.DpnI
      cleavage. Thus, the two enzymes are complementary in that they recognize and cleave within the
      same DNA sequence, one if the DNA is methylated, the other if it is unmethylated. DNA duplexes
      containing one methylated strand (dam+) and one unmethylated strand (dam-) were prepared in
      vitro. These methylated hybrids were refractory to endonucleolytic cleavage by both endo
      R.DpnI and endo R.DpnII. Neither enzyme, therefore, appears to make even a single strand break
      at a methylated/unmethylated hybrid site.
AU  - Vovis GF
AU  - Lacks S
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1977 115: 525-538.

PMID- 1097718
VI  - 95
DP  - 1975
TI  - Methylation of f1 DNA by a restriction endonuclease from Escherichia coli B.
PG  - 557-568
AB  - Bacteriophage f1 duplex DNA containing hybrid SB sites, the genetic sites which
      confer upon DNA sensitivity to Escherichia coli B-specific restriction and
      modification, were prepared in vitro.  The hybrid SB sites (modified and
      mutant) were tested for their ability to be methylated in vitro by endonuclease
      R.EcoB, the enzyme responsible for both B-specific restriction and modification
      in vivo.  DNA containing hybrid (modified) SB sites can be methylated.  One
      methyl group is added to the DNA per hybrid (modified) SB site.  On the other
      hand, DNA containing hybrid (mutant) SB sites is refractory to modification.
      The nature and the function of the SB site as well as the implications of these
      observations for f1 recombination are discussed.
AU  - Vovis GF
AU  - Zinder ND
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1975 95: 557-568.

PMID- 24452797
VI  - 42
DP  - 2014
TI  - Super-resolution optical DNA Mapping via DNA methyltransferase-directed click chemistry.
PG  - e50
AB  - We demonstrate an approach to optical DNA mapping, which enables near single-molecule
      characterization of whole bacteriophage genomes. Our approach
      uses a DNA methyltransferase enzyme to target labelling to specific sites and
      copper-catalysed azide-alkyne cycloaddition to couple a fluorophore to the DNA.
      We achieve a labelling efficiency of approximately 70% with an average labelling
      density approaching one site every 500 bp. Such labelling density bridges the gap
      between the output of a typical DNA sequencing experiment and the long-range
      information derived from traditional optical DNA mapping. We lay the foundations
      for a wider-scale adoption of DNA mapping by screening 11 methyltransferases for
      their ability to direct sequence-specific DNA transalkylation; the first step of
      the DNA labelling process and by optimizing reaction conditions for fluorophore
      coupling via a click reaction. Three of 11 enzymes transalkylate DNA with the
      cofactor we tested (a readily prepared s-adenosyl-l-methionine analogue).
AU  - Vranken C
AU  - Deen J
AU  - Dirix L
AU  - Stakenborg T
AU  - Dehaen W
AU  - Leen V
AU  - Hofkens J
AU  - Neely RK
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2014 42: e50.

PMID- 19440302
VI  - 4
DP  - 2009
TI  - Methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources.
PG  - E5584
AB  - BACKGROUND: Methylotrophy describes the ability of organisms to grow on
      reduced organic compounds without carbon-carbon bonds. The genomes of two
      pink-pigmented facultative methylotrophic bacteria of the
      Alpha-proteobacterial genus Methylobacterium, the reference species
      Methylobacterium extorquens strain AM1 and the dichloromethane-degrading
      strain DM4, were compared. METHODOLOGY/PRINCIPAL FINDINGS: The 6.88 Mb
      genome of strain AM1 comprises a 5.51 Mb chromosome, a 1.26 Mb megaplasmid
      and three plasmids, while the 6.12 Mb genome of strain DM4 features a 5.94
      Mb chromosome and two plasmids. The chromosomes are highly syntenic and
      share a large majority of genes, while plasmids are mostly
      strain-specific, with the exception of a 130 kb region of the strain AM1
      megaplasmid which is syntenic to a chromosomal region of strain DM4. Both
      genomes contain large sets of insertion elements, many of them
      strain-specific, suggesting an important potential for genomic plasticity.
      Most of the genomic determinants associated with methylotrophy are nearly
      identical, with two exceptions that illustrate the metabolic and genomic
      versatility of Methylobacterium. A 126 kb dichloromethane utilization
      (dcm) gene cluster is essential for the ability of strain DM4 to use DCM
      as the sole carbon and energy source for growth and is unique to strain
      DM4. The methylamine utilization (mau) gene cluster is only found in
      strain AM1, indicating that strain DM4 employs an alternative system for
      growth with methylamine. The dcm and mau clusters represent two of the
      chromosomal genomic islands (AM1: 28; DM4: 17) that were defined. The mau
      cluster is flanked by mobile elements, but the dcm cluster disrupts a gene
      annotated as chelatase and for which we propose the name "island
      integration determinant" (iid). CONCLUSION/SIGNIFICANCE: These two genome
      sequences provide a platform for intra- and interspecies genomic
      comparisons in the genus Methylobacterium, and for investigations of the
      adaptive mechanisms which allow bacterial lineages to acquire
      methylotrophic lifestyles.
AU  - Vuilleumier S et al
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2009 4: E5584.

PMID- 22207753
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Haloalkaliphilic Methanotrophic Bacterium Methylomicrobium alcaliphilum 20Z.
PG  - 551-552
AB  - Methylomicrobium strains are widespread in saline environments. Here, we report the complete
      genome sequence of Methylomicrobium alcaliphilum 20Z,
      a haloalkaliphilic methanotrophic bacterium, which will provide the basis
      for detailed characterization of the core pathways of both single-carbon
      metabolism and responses to osmotic and high-pH stresses. Final assembly
      of the genome sequence revealed that this bacterium contains a 128-kb
      plasmid, making M. alcaliphilum 20Z the first methanotrophic bacterium of
      known genome sequence for which a plasmid has been reported.
AU  - Vuilleumier S et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 551-552.

PMID- 21868803
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of the Chloromethane-Degrading Hyphomicrobium sp. Strain MC1.
PG  - 5035-5036
AB  - Hyphomicrobium sp. strain MC1 is an aerobic methylotroph originally isolated from industrial
      sewage. This prosthecate bacterium was the first
      strain reported to grow with chloromethane as the sole carbon and energy
      source. Its genome, consisting of a single 4.76-Mb chromosome, is the
      first for a chloromethane-degrading bacterium to be formally reported.
AU  - Vuilleumier S
AU  - Nadalig T
AU  - Ul-Haque MF
AU  - Magdelenat G
AU  - Lajus A
AU  - Roselli S
AU  - Muller EE
AU  - Gruffaz C
AU  - Barbe V
AU  - Medigue C
AU  - Bringel F
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5035-5036.

PMID- 1550825
VI  - 31
DP  - 1992
TI  - Sequence- and strand-specific cleavage in oligodeoxyribonucleotides and DNA containing 3'-thiothymidine.
PG  - 3012-3018
AB  - Oligonucleotides containing a 3'-thiothymidine residue (T3's) at the cleavage site for the
      EcoRV restriction endonuclease (between the central T and A residues of the sequence GATATC)
      have been prepared on an automated DNA synthesizer using 5'-O-monomethoxytritylthymidine
      3'-S-(2-cyanoethyl N,N-di-isopropylphosphorothioamidite).  The self-complementary sequence
      GACGAT3'sATCGTC was completely resistant to cleavage by EcoRV, while the heteroduplex
      composed of 5'-TCTGAT3'sATCCTC and 5'-GAGGATATCAGA (duplex 4) was cleaved only in the
      unmodified strand (5'-GAGGATATCAGA).  In contrast, strands containing a
      3'-S-phosphorothiolate linkage could be chemically cleaved specifically at this site with
      Ag+.  A T3's residue has also been incorporated in the (-) strand of double-stranded closed
      circular (RF IV) M13mp18 DNA at the cleavage site of a unique EcoRV recognition sequence by
      using 5'-pCGAGCTCGAT3'sATCGTAAT as a primer for polymerization on the template (+) strand of
      M13mp18 DNA.  On treatment of this substrate with EcoRV, only one strand was cleaved to
      produce the RFII or nicked DNA.  Taken in conjunction with the cleavage studies on the
      oligonucleotides, this result demonstrates that the 3'-S-phosphorothiolate linkage is
      resistant to scission by EcoRV.  Additionally, the phosphorothiolate-containing strand of the
      M13mp18 DNA could be cleaved specifically at the point of modification using iodine in aqueous
      pyridine.  The combination of enzymatic and chemical techniques provides, for the first time,
      a demonstrated method for the sequence-specific cleavage of either the (+) or (-) strand.
AU  - Vyle JS
AU  - Connolly BA
AU  - Kemp D
AU  - Cosstick R
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1992 31: 3012-3018.

PMID- 704354
VI  - 5
DP  - 1978
TI  - MspI, an isochizomer of HpaII which cleaves both unmethylated and methylated HpaII sites.
PG  - 3231-3236
AB  - The cleavage of DNA by restriction endonucleases HpaII and HapII is prevented
      by the presence of a 5-methyl group at the internal C residue of its
      recognition sequence CCGG.  MspI, an isoschizomer of HpaII available from New
      England Biolabs, cleaves DNA irrespective of the presence of a methyl group at
      this position.  This enzyme cleaves DNA from Haemophilus parainfluenzae and
      Haemophilus aphrophilus readily while HpaII and HapII cannot degrade these
      DNAs.  Practically all HpaII sites in mammalian sperm DNA are also protected by
      methylation at the internal C position since HpaII and HapII barely cleave this
      DNA (average molecular weight 40 kb).  MspI, however, cleaves the DNA to an
      average size of about 5 kb.
AU  - Waalwijk C
AU  - Flavell RA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1978 5: 3231-3236.

PMID- 17875999
VI  - 51
DP  - 2007
TI  - Novel plasmid-mediated 16S rRNA m1A1408 methyltransferase, NpmA, found in a clinically isolated Escherichia coli strain resistant to structurally diverse  aminoglycosides.
PG  - 4401-4409
AB  - We have isolated a multiple-aminoglycoside-resistant Escherichia coli strain, strain ARS3, and
      have been the first to identify a novel plasmid-mediated 16S
      rRNA methyltransferase, NpmA. This new enzyme shared a relatively low level of
      identity (30%) to the chromosomally encoded 16S rRNA methyltransferase (KamA) of
      Streptomyces tenjimariensis, an actinomycete aminoglycoside producer. The
      introduction of a recombinant plasmid carrying npmA could confer on E. coli
      consistent resistance to both 4,6-disubstituted 2-deoxystreptamines, such as
      amikacin and gentamicin, and 4,5-disubstituted 2-deoxystreptamines, including
      neomycin and ribostamycin. The histidine-tagged NpmA elucidated methyltransferase
      activity against 30S ribosomal subunits but not against 50S subunits and the
      naked 16S rRNA molecule in vitro. We further confirmed that NpmA is an adenine
      N-1 methyltransferase specific for the A1408 position at the A site of 16S rRNA.
      Drug footprinting data indicated that binding of aminoglycosides to the target
      site was apparently interrupted by methylation at the A1408 position. These
      observations demonstrate that NpmA is a novel plasmid-mediated 16S rRNA
      methyltransferase that provides a panaminoglycoside-resistant nature through
      interference with the binding of aminoglycosides toward the A site of 16S rRNA
      through N-1 methylation at position A1408.
AU  - Wachino J
AU  - Shibayama K
AU  - Kurokawa H
AU  - Kimura K
AU  - Yamane K
AU  - Suzuki S
AU  - Shibata N
AU  - Ike Y
AU  - Arakawa Y
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2007 51: 4401-4409.

PMID- 9129674
VI  - 375
DP  - 1997
TI  - DNA methylation and the association between genetic and epigenetic changes: relation to carcinogenesis.
PG  - 1-8
AB  - This paper examines the relationship between DNA mutagenic lesions, DNA methylation and the
      involvement of these changes in the process of carcinogenesis.  Many types of DNA damage
      (oxidative lesions, alkylation of bases, abasic sites, photodimers, etc.) interfere with the
      ability of mammalian cell  DNA to be methylated at CpG dinucleotides by DNA-methyltransferases
      (DNA-MTases).  This can result in altered patterns in the distribution of 5-methylcytosine
      (5MeC) residues at CpG sites.  Methylation of DNA is an epigenetic change that by definition
      is heritable, can result in changes in chromatin structure, and is often accompanied by
      modified patterns of gene expression.  The presence of 5MeC in DNA, as well as oxidative
      stress induced by the free radical nitric oxide, can interfere with the repair of alkylation
      damage, thereby increasing the level fo potentially mutagenic lesions. CpG sites in DNA
      represent mutational hotspots, with both the presence of 5MeC in DNA and the catalytic
      activity of DNA-MTases being intrinsically mutagenic.  The process of carcinogenesis has
      frequently been associated with an increased expression of DNA-MTase activity, accompanied by
      either hypermethylation or hypomethylation of target cell (progenitor tumor cell) DNA.  In
      addition, there is evidence that overexpression of DNA-MTase activity could result in
      increased cytosine methylation at non-CpG sites.  A variety of chemicals can alter the extent
      of DNA methylation in mammalian cells.  These include inhibitors of topisomerase II, as well
      as inhibitors of DNA synthesis, microtubule formation, histone deacetylation,
      transmethylation, etc.  Genetic and epigenetic changes in DNA have a profound influence on one
      another and could play a major role in the process of carcinogenesis, by modulating both the
      extent and the pattern of gene expression.
AU  - Wachsman JT
PT  - Journal Article
TA  - Mutat. Res.
JT  - Mutat. Res.
SO  - Mutat. Res. 1997 375: 1-8.

PMID- 28619797
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of a Mycobacterium tuberculosis Strain Belonging to the  East African-Indian Family in the Indo-Oceanic Lineage, Isolated in Hanoi,  Vietnam.
PG  - e00509-17
AB  - The East African-Indian (EAI) family of Mycobacterium tuberculosis is an endemic  group mainly
      observed in Southeast Asia. Here, we report the complete genome
      sequence of an M. tuberculosis strain isolated as a member of the EAI family in
      Hanoi, Vietnam, a country with a high incidence of tuberculosis.
AU  - Wada T
AU  - Hijikata M
AU  - Maeda S
AU  - Hang NTL
AU  - Thuong PH
AU  - Hoang NP
AU  - Hung NV
AU  - Keicho N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00509-17.

PMID- 28684565
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of Three Representative Mycobacterium tuberculosis Beijing Family Strains Belonging to Distinct Genotype Clusters in Hanoi, Vietnam, during 2007 to 2009.
PG  - e00510-17
AB  - We present here three complete genome sequences of Mycobacterium tuberculosis Beijing family
      strains isolated in Hanoi, Vietnam. These three strains were
      selected from major genotypic clusters (15-MIRU-VNTR) identified in a previous
      population-based study. We emphasize their importance and potential as reference
      strains in this Asian region.
AU  - Wada T
AU  - Hijikata M
AU  - Maeda S
AU  - Hang NTL
AU  - Thuong PH
AU  - Hoang NP
AU  - Hung NV
AU  - Keicho N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00510-17.

PMID- 
VI  - 22
DP  - 2005
TI  - Physiological functions of plant DNA methyltransferases.
PG  - 71-80
AB  - Epigenetic regulation is defined as mechanisms that control gene expression without altering
      base sequences.  Cytosine methylation, chromatin remodeling, and modifications at the
      N-termini of core histones are key factors in this regard.  Epigenetic modifications are found
      throughout the eukaryotes, suggesting that they developed at an early stage in biological
      evolution, although actual molecular mechanisms show considerable variation among species.  In
      particular, plants are unique in establishment and maintenance of epigenetic states, as
      examplified by species-specific enzymes that catalyze DNA methylation.  Since the function and
      diversity of DNA methyltransferases in individual species are not fully understood, I here
      summarize recent findings in plant epigenetics, focusing on DNA methyltransferases classified
      into three major groups.  Their possible biological functions are also discussed with
      reference to histone modification and chromatin remodeling.
AU  - Wada Y
PT  - Journal Article
TA  - Plant Biotechnol.
JT  - Plant Biotechnol.
SO  - Plant Biotechnol. 2005 22: 71-80.

PMID- 9487689
VI  - 33
DP  - 1998
TI  - Separate analysis of complementary strands of restriction enzyme-digested DNA.  An application of restriction fragment mass mapping by matrix-assisted laser desorption/ionization mass spectrometry.
PG  - 187-192
AB  - Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry   MALDI/TOF-MS)
      of a restriction endonuclease digest determines the molecular mass of PCR-amplified DNA more
      easily than measurement of undigested DNA. With this method, a 664 bp region from the FAS gene
      could be analyzed and a two-nucleotide deletion in the L1CAM gene was detected in a
      restriction fragment of 105 nucleotides. Furthermore, the analysis of smaller fragments
      allowed separate detection of single-stranded oligonucleotides comprising individual digested
      fragments. This mixture analysis of restriction enzyme digests improves the resolution,
      sensitivity and accuracy of MALDI/TOF-MS of DNA and is thus expected to facilitate its
      application to genetic diagnosis.
AU  - Wada Y
PT  - Journal Article
TA  - J. Mass Spectrom.
JT  - J. Mass Spectrom.
SO  - J. Mass Spectrom. 1998 33: 187-192.

PMID- 12917429
VI  - 278
DP  - 2003
TI  - Preferential de novo methylation of cytosine residues in non-CpG sequences by a domains rearranged DNA methyltransferase from tobacco plants.
PG  - 42386-42393
AB  - In plant DNA, cytosines in symmetric CpG and CpNpG (N is A, T, or C) are thought to be
      methylated by DNA methyltransferases, MET1 and CMT3,
      respectively. Cytosines in asymmetric CpNpN are also methylated, and
      genetic analysis has suggested the responsible enzyme to be domains
      rearranged methyltransferase (DRM). We cloned a tobacco cDNA, encoding a
      novel protein consisting of 608 amino acids, that resembled DRMs found in
      maize and Arabidopsis and designated this as NtDRM1. The protein could be
      shown to be localized exclusively in the nucleus and exhibit methylation
      activity toward unmethylated synthetic as well as native DNA samples upon
      expression in Sf9 insect cells. It also methylated hemimethylated DNA, but
      the activity was lower than that for unmethylated substrates. Methylation
      mapping of a 962-bp DNA, treated with NtDRM1 in vitro, directly
      demonstrated methylation of approximately 70% of the cytosines in
      methylatable CpNpN and CpNpG sequences but only 10% in CpG. Further
      analyses indicated that the enzyme apparently non-selectively methylates
      any cytosines except in CpG, regardless of the adjacent nucleotide at both
      5' and 3' ends. Transcripts of NtDRM1 ubiquitously accumulated in all
      tissues and during the cell cycle in tobacco cultured BY2 cells. These
      results indicate that NtDRM1 is a de novo cytosine methyltransferase,
      which actively excludes CpG substrate.
AU  - Wada Y
AU  - Ohya H
AU  - Yamaguchi Y
AU  - Koizumi N
AU  - Sano H
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2003 278: 42386-42393.

PMID- 28818901
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Lactobacillus fermentum BFE 6620, a Potential Starter Culture for African Vegetable Foods, Isolated from Fermented Cassava.
PG  - e00801-17
AB  - We report the draft genome sequence of Lactobacillus fermentum BFE 6620 from fermented cassava
      used as a potential starter culture for African vegetable
      fermentation. Sequence analysis showed the assembled genome size to be 1,982,893
      bp, encoding a predicted total of 2,003 protein-coding genes, 14 rRNAs, 54 tRNAs,
      and 3 noncoding RNAs (ncRNAs).
AU  - Wafula EN
AU  - Brinks E
AU  - Becker B
AU  - Huch M
AU  - Trierweiler B
AU  - Mathara JM
AU  - Oguntoyinbo FA
AU  - Cho GS
AU  - Franz CMAP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00801-17.

PMID- 17156795
VI  - 366
DP  - 2007
TI  - Structural domains in the type III restriction endonuclease EcoP15I: Characterization by limited proteolysis, mass spectrometry and insertional mutagenesis.
PG  - 93-102
AB  - The Type III restriction endonuclease EcoP15I forms a hetero-oligomeric enzyme complex that
      consists of two modification (Mod) subunits and two
      restriction (Res) subunits. Structural data on Type III restriction
      enzymes in general are lacking because of their remarkable size of more
      than 400 kDa and the laborious and low-yield protein purification
      procedures. We took advantage of the EcoP15I-overexpressing vector pQEP15
      and affinity chromatography to generate a quantity of EcoP15I high enough
      for comprehensive proteolytic digestion studies and analyses of the
      proteolytic fragments by mass spectrometry. We show here that in the
      presence of specific DNA the entire Mod subunit is protected from trypsin
      digestion, whereas in the absence of DNA stable protein domains of the Mod
      subunit were not detected. In contrast, the Res subunit is comprised of
      two trypsin-resistant domains of approximately 77-79 kDa and 27-29 kDa,
      respectively. The cofactor ATP and the presence of DNA, either specific or
      unspecific, are important stabilizers of the Res subunit. The large
      N-terminal domain of Res contains numerous functional motifs that are
      predicted to be involved in ATP-binding and hydrolysis and/or DNA
      translocation. The C-terminal small domain harbours the catalytic center.
      Based on our data, we conclude that both structural Res domains are
      connected by a flexible linker region that spans 23 amino acid residues.
      To confirm this conclusion, we have investigated several EcoP15I enzyme
      mutants obtained by insertion mutagenesis in and around the predicted
      linker region within the Res subunit. All mutants tolerated the genetic
      manipulation and did not display loss of function or alteration of the DNA
      cleavage position.
AU  - Wagenfuhr K
AU  - Pieper S
AU  - Mackeldanz P
AU  - Linscheid M
AU  - Kruger DH
AU  - Reuter M
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2007 366: 93-102.

PMID- 2161522
VI  - 18
DP  - 1990
TI  - BmyI, a novel SduI isoschizomer from Bacillus mycoides recognizing 5'-GDGCH/C-3'.
PG  - 3088
AB  - None
AU  - Wagner E
AU  - Schmitz GG
AU  - Kaluza K
AU  - Jarsch M
AU  - Gotz F
AU  - Kessler C
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 3088.

PMID- 
VI  - 
DP  - 1998
TI  - Structural study of the type IIs restriction endonuclease FokI.
PG  - 1-108
AB  - This work presents the first three-dimensional structures of a type IIs restriction
      endonuclease.  The type IIs restriction endonucleases are an unusual class of enzymes that
      recognize a specific DNA sequence and cleave DNA non-specifically a short distance away from
      that sequence.  FokI, from Flavobacterium okeanokoites, is a type IIs restriction endonuclease
      that binds the cognate sequence 5'-GGATG-3' and cleaves DNA phosphodiester groups 9 base
      pairs away on this strand and 13 base pairs away on the complementary strand.  Because of its
      unusual bipartite nature, FokI has been used to create artificial enzymes with new DNA-binding
      specificities.  The three-dimensional structures of the complete FokI enzyme in complex with
      DNA and without DNA have been determined by X-ray crystallography at 2.8A and 2.3A resolution,
      respectively.  As anticipated, the enzyme contains amino- and carboxy-terminal domains
      corresponding to the DNA-recognition and cleavage functions.  The recognition domain is made
      of three smaller subdomains that are evolutionarily related to the helix-turn-helix containing
      DNA-binding domain of the catabolite gene activator protein CAP.  However, the CAP core has
      been extensively embellished in the first two subdomains while in the third subdomain it has
      been co-opted for protein-protein interactions.  Surprisingly, the cleavage domain resembles a
      monomer of the type II restriction endonuclease BamHI and contains only a single catalytic
      center.  Unexpectedly, the cleavage domain is sequestered in a "piggyback" fashion by the
      recognition domain until its DNA cleavage activity is required.  The structure of FokI in the
      absence of DNA reveals a dimer.  In corroboration with binding data, a model is proposed in
      which DNA cleavage requires the dimerization of two FokI molecules, each recognizing an
      independent FokI cognate sequence.  Taken together, the structures have implications for the
      evolution of helix-turn-helix domains, suggest a novel mechanism of nuclease activation, and
      provide a framework for the design of chimeric enzymes with altered specificities.
AU  - Wah DA
PT  - Journal Article
TA  - Ph.D. Thesis, Columbia University
JT  - Ph.D. Thesis, Columbia University
SO  - Ph.D. Thesis, Columbia University 1998 : 1-108.

PMID- 
VI  - 58
DP  - 1998
TI  - Structural study of the type IIs restriction endonuclease FokI.
PG  - 6439B
AB  - This work represents the first three-dimensional structures of a type IIs restriction
      endonuclease.  The type IIs restriction endonucleases are an unusual class of enzymes that
      recognize a specific DNA sequence and cleave DNA non-specifically a short distance away from
      that sequence.  FokI, from Flavobacterium okeanokoites, is a type IIs restriction endonuclease
      that binds the cognate sequence 5'-GGATG-3' and cleaves DNA phosphodiester groups 9 base
      pairs away on this strand and 13 base pairs away on the complementary strand.  Because of its
      unusual bipartite nature, FokI has been used to create artificial enzymes with new DNA-binding
      specificities.  The three-dimensional structures of the complete FokI enzyme in complex with
      DNA and without DNA have been determined by X-ray crystallography at 2.8 and 2.3 angstroms
      resolution, respectively.  As anticipated, the enzyme contains amino- and carboxy-terminal
      domains corresponding to the DNA-recognition and cleavage functions.  The recognition domain
      is made of three smaller subdomains that are evolutionarily related to the helix-turn-helix
      containing DNA-binding domain of the catabolite gene activator protein CAP.  However, the CAP
      core has been extensively embellished in the first two subdomains while in the third subdomain
      it has been co-opted for protein-protein interactions.  Surprisingly, the cleavage domain
      resembles a monomer of the type II restriction endonuclease BamHI and contains only a single
      catalytic center.  Unexpectedly, the cleavage domain is sequestered in a "piggyback" fashion
      by the recognition domain until its DNA cleavage activity is required.  The structure of FokI
      in the absence of DNA reveals a dimer.  In corroboration with binding data, a model is
      proposed in which DNA cleavage requires the dimerization of two FokI molecules, each
      recognizing an independent FokI cognate sequence.  Taken together, the structures have
      implications for the evolution of helix-turn-helix domains, suggest a novel mechanism of
      nuclease activation, and provide a framework for the design of chimeric enzymes with altered
      specificities.
AU  - Wah DA
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1998 58: 6439B.

PMID- 9724743
VI  - 95
DP  - 1998
TI  - Structure of FokI has implications for DNA cleavage.
PG  - 10564-10569
AB  - FokI is a member of an unusual class of restriction enzymes that recognize a specific DNA
      sequence and cleave nonspecifically a short distance away from that sequence.  FokI consists
      of an N-terminal DNA recognition domain and a C-terminal cleavage domain.  The bipartite
      nature of FokI has led to the development of artificial enzymes with novel specificities.  We
      have solved the structure of FokI to 2.3 A resolution.  The structure reveals a dimer, in
      which the dimerization interface is mediated by the cleavage domain.  Each monomer has an
      overall conformation similar to that found in the FokI-DNA complex, with the cleavage domain
      packing alongside the DNA recognition domain.  In corroboration with the cleavage data
      presented in the accompanying paper in this issue of Proceedings, we propose a model for FokI
      DNA cleavage that requires the dimerization of FokI on DNA to cleave both DNA strands.
AU  - Wah DA
AU  - Bitinaite J
AU  - Schildkraut I
AU  - Aggarwal AK
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1998 95: 10564-10569.

PMID- 9214510
VI  - 388
DP  - 1997
TI  - Structure of the multimodular endonuclease FokI bound to DNA.
PG  - 97-100
AB  - FokI is a member of an unusual class of bipartite restriction enzymes that recognize a
      specific DNA sequence and cleave DNA nonspecifically a short distance away from that sequence.
      Because of its unusual bipartite nature, FokI has been used to create artificial enzymes with
      new specificities.  We have determined the crystal structure at 2.8A resolution of the
      complete FokI enzyme bound to DNA.  As anticipated, the enzyme contains amino- and
      carboxy-terminal domains corresponding to the DNA-recognition and cleavage functions,
      respectively.  The recognition domain is made of three smaller subdomains (D1, D2 and D3)
      which are evolutionarily related to the helix-turn-helix-containing DNA-binding domain of the
      catabolite gene activator protein CAP.  The CAP core has been extensively embellished in the
      first two subdomains, whereas in the third subdomain it has been co-opted for protein-protein
      interactions.  Surprisingly, the cleavage domain contains only a single catalytic center,
      raising the question of how monomeric FokI manages to cleave both DNA strands.  Unexpectedly,
      the cleavage domain is sequestered in a 'piggyback' fashion by the recognition domain.  The
      structure suggests a new mechanism for nuclease activation and provides a framework for the
      design of chimeric enzymes with altered specificities.
AU  - Wah DA
AU  - Hirsch JA
AU  - Dorner LF
AU  - Schildkraut I
AU  - Aggarwal AK
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1997 388: 97-100.

PMID- 25278518
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Brucella suis Biovar 4 Strain NCTC 10385, Brucella ceti Strain NCTC 12891T, Brucella inopinata Strain CAMP 6436T, and Brucella neotomae  Strain ATCC 23459T.
PG  - e00783-14
AB  - With the aim of developing quantitative PCR methods for the detection and differentiation of
      Brucella species, the genomes of Brucella ceti, Brucella
      inopinata, Brucella netotomae, and Brucella suis biovar 4 were sequenced and
      analyzed.
AU  - Wahab T
AU  - Ferrari S
AU  - Lindberg M
AU  - Backman S
AU  - Kaden R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00783-14.

PMID- 11456633
VI  - 123
DP  - 2001
TI  - Mechanism-based inhibition of an essential bacterial adenine DNA methyltransferase: Rationally designed antibiotics.
PG  - 976-977
AB  - The emergence of bacteria resistant to available antibiotics has caused great concern in the
      medical community and has created a need for the discovery of novel antibiotic agents.  In the
      past, new antibiotics have been discovered by the random screening of natural products and the
      subsequent identification of the target protein.  In addition to this drug discovery method,
      the recent advances in genome sequencing have made it possible to envision a complementary
      drug discovery method in which a bacterial enzyme target is first identified and new
      antibiotic compounds are discovered from the targeted inhibition of this enzyme.  Successful
      antibiotics would be inhibitors of an essential bacterial enzyme that is unique to bacteria
      and has no mammalian homologue.  Here we report on the progress toward the development of
      small-molecule selective inhibitors of an essential bacterial N-6 adenine DNA
      methyltransferase, using a mechanism-based multisubstrate adduct approach and demonstrate the
      inhibition using CcrM (cell cycle regulated DNA MTase) from the pathogenic Brucella abortus.
AU  - Wahnon DC
AU  - Shier VK
AU  - Benkovic SJ
PT  - Journal Article
TA  - J. Am. Chem. Soc.
JT  - J. Am. Chem. Soc.
SO  - J. Am. Chem. Soc. 2001 123: 976-977.

PMID- 25858833
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of NDM-5-Producing Escherichia coli Sequence Type 648 and Genetic Context of blaNDM-5 in Australia.
PG  - e00194-15
AB  - We report here the draft genome sequence of uropathogenic Escherichia coli sequence type 648
      (ST648) possessing blaNDM-5 from a 55-year-old female in
      Australia with a history of travel to India. The plasmid-mediated blaNDM-5 was in
      a genetic context nearly identical to that of the GenBank entry of an IncX3
      blaNDM-5 plasmid previously reported from India (Klebsiella pneumoniae MGR-K194).
AU  - Wailan AM
AU  - Paterson DL
AU  - Caffery M
AU  - Sowden D
AU  - Sidjabat HE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00194-15.

PMID- 1650347
VI  - 173
DP  - 1991
TI  - Characterization and expression of the Escherichia coli Mrr restriction system.
PG  - 5207-5219
AB  - The mrr gene of Escherichia coli K-12 is involved in the acceptance of foreign DNA which is
      modified.  The introduction of plasmids carrying the HincII, HpaI, and TaqI R and M genes is
      severely restricted in E. coli strains that are Mrr+. A 2-kb EcoRI fragment from the plasmid
      pBg3 (B. Sain and N.E. Murray, Mol. Gen. Genet. 180:35-46, 1980) was cloned.  The resulting
      plasmid restores Mrr function to mrr strains of E. coli.  The boundaries of the mrr gene were
      determined from an analysis of subclones, and plasmids with a functional mrr gene produce a
      polypeptide of 33.5 kDa.  The nucleotide sequence of the entire fragment was determined; in
      addition to mrr, it includes two open reading frames, one of which encodes part of the hsdR.
      By using Southern blot analysis, E. coli RR1 and HB101 were found to lack the region
      containing mrr. The acceptance of various cloned methylases in E. coli containing the cloned
      mrr gene was tested.  Plasmid constructs containing the AccI, CviRI, HincII, HinfI (HhaII),
      HpaI, NlaIII, PstI, and TaqI N6-adenine methylases and SssI and HhaI C5-cytosine methylases
      were found to be restricted.  Plasmid constructs containing 16 other adenine methylases and 12
      cytosine methylases were not restricted.  No simple consensus sequence causing restriction has
      been determined.  The Mrr protein has been overproduced, an antibody has been prepared, and
      the expression of mrr under various conditions has been examined. The use of mrr strains of E.
      coli is suggested for the cloning of N6-adenine and C5-cytosine methyl-containing DNA.
AU  - Waite-Rees PA
AU  - Keating CJ
AU  - Moran LS
AU  - Slatko BE
AU  - Hornstra LJ
AU  - Benner JS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1991 173: 5207-5219.

PMID- 23933356
VI  - 70
DP  - 2013
TI  - Entire sequence of the colonization factor coli surface antigen 6-encoding plasmid pCss165 from an enterotoxigenic Escherichia coli clinical isolate.
PG  - 343-352
AB  - Coli surface antigen 6 (CS6) is one of the most prevalent colonization factors among
      enterotoxigenic Escherichia coli (ETEC) isolated in developing countries. Although it is known
      that CS6 is encoded by a plasmid, there are no reports on the sequence analysis of the
      CS6-encoding plasmid or genes exhibiting similar behavior to CS6. Here, we report the
      isolation of the CS6-encoding plasmid, pCss165Kan, from 4266 DcssB::kanamycin (Km) and its
      complete nucleotide sequence. This plasmid consisted of 165,311 bp and 222 predicted coding
      sequences. Remarkably, there were many insertion sequence (IS) elements, which comprised 24.4%
      of the entire sequence. Virulence-associated genes such as heat-stable enterotoxin, homologues
      of ATP-binding cassette transporter in enteroaggregative E. coli (EAEC), and ETEC
      autotransporter A were also present, although the ETEC autotransporter A gene was disrupted by
      the integration of IS629. We found that 2 transcriptional regulators belonging to the AraC
      family were not involved in CS6 expression. Interestingly, pCss165 had conjugative transfer
      genes, as well as 3 toxin-antitoxin
      systems that potentially exclude other plasmid-free host bacteria. These genes might be
      involved in the prevalence of CS6 among ETEC isolates
AU  - Wajima T
AU  - Sabui S
AU  - Kano S
AU  - Ramamurthy T
AU  - Chatterjee NS
AU  - Hamabata T
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 2013 70: 343-352.

PMID- 10518942
VI  - 291
DP  - 1999
TI  - The solution structure of the domain from MeCP2 that binds to methylated DNA.
PG  - 1055-1065
AB  - MeCP2 is an abundant mammalian protein that binds methylated CpG (mCpG) sequences within
      double-stranded DNA, represses transcription by recruiting histone deacetylases, and is
      essential for embryonic development. It is one of a family of proteins which mediate the
      biological consequences of DNA methylation. These proteins each possess a sequence motif of
      about 70 residues which, in MeCP2, form a domain necessary and sufficient for binding to mCpG.
      The solution structure of the mCpG-binding domain (MBD) from MeCP2 has been solved and the
      DNA-binding surface of the domain mapped using NMR spectroscopy. Residues 95-162 of MeCP2
      adopt a novel fold forming a wedge-shaped structure. An N-terminal four-stranded antiparallel
      beta-sheet forms one face of the wedge, while the other face is formed mainly by a C-terminal
      helical region. The thin end of the wedge is extended by a long loop between beta-strands B
      and C containing many basic residues. The B-C loop together with residues in strands B, C and
      D, and at the N terminus of the alpha-helix, appears to form an interface with methylated DNA.
      Unstructured residues at the NH2 terminus of the domain are also involved in formation of the
      complex. The presence of numerous arginine and lysine side-chains on the DNA-binding surface
      of MBD is consistent with the requirement for the mCpG site to be flanked by non-specific
      sequences of base-pairs. The absence of symmetry in the domain implies that recognition does
      not exploit the symmetry of the binding site. A conserved hydrophobic pocket containing the
      side-chains of Tyr123 and Ile125 on the positively charged beta-sheet face is a candidate for
      the region of contact with the methyl-groups of the modified cytosine residues.
AU  - Wakefield RID
AU  - Smith BO
AU  - Nan X
AU  - Free A
AU  - Soteriou A
AU  - Uhrin D
AU  - Bird AP
AU  - Barlow PN
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1999 291: 1055-1065.

PMID- 29682167
VI  - 13
DP  - 2018
TI  - Draft genome sequence of Bosea sp. WAO an arsenite and sulfide oxidizer isolated  from a pyrite rock outcrop in New Jersey.
PG  - 6
AB  - This genome report describes the draft genome and physiological characteristics of Bosea sp.
      WAO (=DSM 102914), a novel strain of the genus Bosea in the family
      Bradyrhizobiaceae. Bosea sp. WAO was isolated from pulverized pyritic shale
      containing elevated levels of arsenic. This aerobic, gram negative microorganism
      is capable of facultative chemolithoautotrophic growth under aerobic conditions
      by oxidizing the electron donors arsenite, elemental sulfur, thiosulfate,
      polysulfide, and amorphous sulfur. The draft genome is of a single circular
      chromosome 6,125,776 bp long consisting of 21 scaffolds with a G + C content of
      66.84%. A total 5727 genes were predicted of which 5665 or 98.92% are
      protein-coding genes and 62 RNA genes. We identified the genes aioA and aioB,
      which encode the large and small subunits of the arsenic oxidase respectively. We
      also identified the genes for the complete sulfur oxidation pathway sox which is
      used to oxidize thiosulfate to sulfate.
AU  - Walczak AB
AU  - Yee N
AU  - Young LY
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2018 13: 6.

PMID- Not included in PubMed...
VI  - 40
DP  - 1981
TI  - The DNA Sequence and Organization of the PstI Restriction-Modification Genes.
PG  - 1647
AB  - We have determined the sequence of a 4000 base pair DNA fragment from P. stuartii 164 that
      contains the genes for the PstI restriction-modification system.  The cloning and expression
      of these genes in E. coli and their re-introduction into P. stuartii 164 was reported earlier
      (Fed. proc. 39 (6) 1413, (198); Proc. Natl. Acad. Sci., in press).  Within the sequence, two
      large open reading frames were identified; one corresponding to the restriction enzyme, the
      other to the modification methylase as determined by site directed mutagenesis and subcloning
      experiments.  The genes are encoded on opposite DNA strands, unlike the two other
      restriction-modification systems that have been studied, HhaII and EcoRI, in which the two
      genes are colinear on the same strand (Fed. Proc. 39 (6) 946, (1980); Fed. Proc. 39 (6) 1415,
      91980)).  This rules out the possibility, at least in this system, that the two genes are
      expressed on a polycistronic transcript.  The locations of the putative promoters for the two
      genes corresponds well with the sites of initiation of transcription mapped in vitro.  The
      4000 base pair fragment is now being used to study the control of expression of these two
      genes.
AU  - Walder R
AU  - Walder J
AU  - Donelson J
PT  - Journal Article
TA  - Fed. Proc.
JT  - Fed. Proc.
SO  - Fed. Proc. 1981 40: 1647.

PMID- 
VI  - 
DP  - 1984
TI  - The cloning and sequence organization of the PstI restriction-modification system.
PG  - 1-228
AB  - The genes for the type II restriction and modification enzymes of the bacterium Providencia
      stuartii 164, were cloned and expressed in the Escherichia coli strain HB101.  The two genes
      are closely linked and are located within a 4.0 kilobase DNA region.  The complete nucleotide
      sequence of the 4.0 kilobase fragment was determined.  Two large open reading frames were
      identified within the sequence and were ascribed to the restriction endonuclease (PstI) and
      the modification (methylase) enzyme by the analysis of a series of deletion and insertion
      mutants.  The two genes are encoded on opposite DNA strands, and hence must be transcribed
      from separate promoters rather than as a polycistronic message.  The sequence of the first ten
      amino acids of the restriction endonuclease was determined by sequential Edman degradation of
      the purified protein, permitting the alignment of the polypeptide with the DNA sequence.  The
      amino terminus of the modification enzyme was established by sequential Edman degradation of
      the protein synthesized in bacterial minicells with different radiolabeled amino acids.  The
      initiation codons of the two genes are separated by 130 base pairs.  The deduced amino acid
      sequences indicate that the restriction endonuclease contains 326 amino acids with a
      calculated molecular weight of 37,370; the modification enzyme is composed of 507 amino acids
      with a calculated molecular weight of 56,830.  There is no significant homology between the
      two proteins at the level of the primary structure.  Antibody raised against the purified
      restriction endonuclease did not immunoprecipitate the modification enzyme.  The transcription
      initiation sites were mapped using mung bean nuclease.  Both of the transcripts begin with
      adenosine.  The initiation sites are separated by only 70 base pairs.  This close proximity
      requires that the promoter sites for the two divergent genes overlap.  Dnase I protection
      experiments show a higher affinity of E. coli RNA polymerase for the methylase promoter than
      for the restriction enzyme promoter.  The expression of the PstI restriction and modification
      genes was also examined in bacteriophage lambda and in yeast.
AU  - Walder RY
PT  - Journal Article
TA  - Ph.D. Thesis
JT  - Ph.D. Thesis
SO  - Ph.D. Thesis 1984 : 1-228.

PMID- 6765641
VI  - 1
DP  - 1981
TI  - Cloning of the PstI restriction-modification system.
PG  - 217-226
AB  - I. Introduction II. Selection and characterization of clones carrying the PstI
      restriction-modification system III. Transformation of P. stuartii 164:
      Construction of a stable overproducing strain IV. Gene products of the PstI
      restriction-modification system V. In vitro transcription of the PstI system
      VI. Discussion
AU  - Walder RY
AU  - Hartley JL
AU  - Donelson JE
AU  - Walder JA
PT  - Journal Article
TA  - Gene Amplif. Anal.
JT  - Gene Amplif. Anal.
SO  - Gene Amplif. Anal. 1981 1: 217-226.

PMID- 6262807
VI  - 78
DP  - 1981
TI  - Cloning and expression of the PstI restriction-modification system in Escherichia coli.
PG  - 1503-1507
AB  - Here we report the cloning and preliminary characterization of the PstI
      restriction-modification system of Providencia stuartii 164.  Transformants of
      Escherichia coli carrying the PstI gene system inserted into the cloning vector
      pBR322 were selected on the basis of acquired resistance to bacteriophage
      lambda infection.  PstI endonuclease was detected in osmotic shock fluid from
      each of the resistant clones.  Plasmid and chromosomal DNA from these clones
      could not be digested by PstI, indicating that the gene for the corresponding
      modification enzyme had also been cloned and was being expressed.  The smallest
      recombinant plasmid encoding both activities, pPst201, contains an insert of
      approximately 4000 base pairs.  In vitro transcription studies indicate that
      this DNA fragment also contains the endogenous promoter(s) of the system.  When
      pPst201 was introduced into a minicell-producing strain of E. coli, two new
      proteins, 32,000 and 35,000 daltons, were synthesized.  We have assigned these
      to the PstI modification (methylase) and restriction enzymes, respectively.
      The active form of the restriction enzyme is a dimer, as determined by gel
      filtration.  Constructed transformants of P. stuartii 164 that carry the PstI
      system inserted into pBR322 produce approximately 10 times more PstI
      endonuclease activity than does the native strain.
AU  - Walder RY
AU  - Hartley JL
AU  - Donelson JE
AU  - Walder JA
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1981 78: 1503-1507.

PMID- 6185476
VI  - 258
DP  - 1983
TI  - Cloning of the MspI modification enzyme.
PG  - 1235-1241
AB  - The gene for the MspI modification enzyme from Moraxella was cloned in
      Escherichia coli using the plasmid vector pBR322.  Selection of transformants
      carrying the gene was based on the resistance of the modified plasmid encoding
      the enzyme to cleavage by MspI.  Both chromosomal and plasmid DNA were modified
      in the selected clones.  None of the clones obtained produced the cognate
      restriction enzyme which suggests that in this system the genes for the
      restriction enzyme and methylase are not closely linked.  Crude cell extracts
      prepared from the recombinant strains, but not the host (E. coli HB101),
      contain an S-adenosylmethionine-dependent methyltransferase specific for the
      MspI recognition site, CCGG.  Production of the enzyme is 3-4-fold greater in
      the transformants than in the original Moraxella strain.  5-Methylcytosine was
      identified as the product of the reaction chromatographically.  The outer
      cytosine of the recognition sequence, *CCGG, was shown to be the site of
      methylation by DNA-sequencing methods.  This modification blocks cleavage by
      both MspI and its isoschizomer HpaII.  HpaII, but not MspI, is able to cleave
      the unmethylated strand of a hemimethylated substrate.  The relevance of these
      results to the use of MspI and HpaII to analyze patterns of methylation in
      genomic DNA is discussed.
AU  - Walder RY
AU  - Langtimm CJ
AU  - Catterjee R
AU  - Walder JA
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1983 258: 1235-1241.

PMID- 7056404
VI  - 41
DP  - 1982
TI  - Cloning of the MspI modification enzyme:  the site of modification and its effects on cleavage by MspI and HpaII.
PG  - 1199
AB  - The gene for the MspI modification enzyme from Moraxella was cloned in E. coli
      using the plasmid vector pBR322.  Selection of transformants carrying the gene
      was based on the resistance of the modified plasmid encoding the enzyme to
      cleavage by MspI.  Both chromosomal and plasmid DNA were modified in these
      clones.  None of the clones obtained produced the cognate restriction enzyme
      indicating either that the genes for the restriction enzyme and methylase are
      not closely linked or that simply the restriction enzyme is not expressed in E.
      coli.  Crude extracts prepared from these clones, but not the host (E. coli
      HB101), contain a methyl transferase specific for the MspI recognition
      sequence, CCGG, which uses SAM as the methyl donor.  The level of this activity
      is approximately 3 fold greater in the transformants than in the original
      Moraxella strain.  5-methylcytidine was identified as the product of the
      reaction by thin layer chromatography.  DNA sequencing showed that only the
      external cytidine residue within the recognition sequence is methylated.  This
      modification blocks cleavage by both MspI and its isoschizomer HpaII.  A
      hemimethylated substance constructed in vitro was cleaved, although at a much
      reduced rate, on the unmethylated strand by HpaII but not MspI.  The relevance
      of these results to the use of MspI and HpaII to analyze patterns of
      methylation in genomic DNA will be discussed.
AU  - Walder RY
AU  - Langtimm CJ
AU  - Chatterjee R
AU  - Walder JA
PT  - Journal Article
TA  - Fed. Proc.
JT  - Fed. Proc.
SO  - Fed. Proc. 1982 41: 1199.

PMID- 3333366
VI  - 5
DP  - 1987
TI  - The organization and control of expression of the PstI restriction modification system.
PG  - 209-226
AB  - In Volume I of this series, we first reported the cloning and expression of the
      PstI restriction-modification system in Escherichia coli.  The PstI restriction
      enzyme and methylasae genes were isolated from a genomic library of Providencia
      stuartii 164 DNA in E. coli HB101 on the basis of acquired resistance of the
      host to infection by bacteriophage lambda.  Subcloning experiments localized
      the two genes to a 4.0 kilobase HindIII fragment, the complete sequence of
      which has been determined.  In this report we review the organization and
      studies of the expression of the PstI genes, and report the cloning of the PstI
      restriction enzyme and methylase genes in yeast.
AU  - Walder RY
AU  - Walder JA
PT  - Journal Article
TA  - Gene Amplif. Anal.
JT  - Gene Amplif. Anal.
SO  - Gene Amplif. Anal. 1987 5: 209-226.

PMID- 6330092
VI  - 259
DP  - 1984
TI  - The Organization and Complete Nucleotide Sequence of the PstI Restriction-Modification System.
PG  - 8015-8026
AB  - We have determined the nucleotide sequence of a 4.0-kilobase DNA fragment
      containing the genes of the PstI restriction-modification system.  Two large
      open reading frames were identified within the sequence and were ascribed to
      the restriction enzyme and methylase by the analysis of a series of deletion
      mutants.  The two genes are encoded on opposite DNA strands, and hence must be
      transcribed from separate promoters rather than as a polycistronic message.
      The sequence of the first 10 amino acids of the restriction endonuclease was
      determined by sequential Edman degradation of the purified protein, permitting
      the alignment of the polypeoptide with the DNA sequence.  The NH2 terminus of
      the modification enzme was established by sequential Edman degradation of the
      protein synthesized in bacterial minicells with different radiolabeled amino
      acids.  The initiation codons of the two genes are separated by 130 base pairs.
      The deduced amino acid sequences indicate that the restriction endonuclease
      contains 326 amino acids with a calculated Mr = 37,370; the modification enzyme
      is composed of 507 amino acids with a calculated Mr = 56,830.  There is no
      significant homology between the two proteins at the level of the primary
      structure.  Antibody raised against the purified restriction endonuclease did
      not immunoprecipitate the modification enzyme.  The transcription initiation
      sites were mapped using mung bean nuclease.  Both of the transcripts begin with
      adenosine.  The initiation sites are separated by only 70 base pairs.  This
      close proximity suggests that the promoters for the two divergent genes
      overlap.  DNase I protection experiments show that Escherichia coli RNA
      polymerase has a higher affinity for the methylase promoter than for the
      restriction enzyme promoter.
AU  - Walder RY
AU  - Walder JA
AU  - Donelson JE
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1984 259: 8015-8026.

PMID- 28209820
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Suttonellaornithocola Bacterium.
PG  - e01592-16
AB  - We report here the draft genome sequence of the Suttonella ornithocola bacterium. To date,
      this bacterium, found in birds, passed only phylogenetic and phenotypic
      analyses. To our knowledge, this is the first publication of the Suttonella
      ornithocola genome sequence. The genetic profile provides a basis for further
      analysis of its infection pathways.
AU  - Waldman B-AH
AU  - Yerushalmi R
AU  - Wachtel C
AU  - Barbiro-Michaely E
AU  - Sompolinsky D
AU  - Gerber D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01592-16.

PMID- 28183765
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of a New Bacterium Named Rappaport israeli, gen. nov., sp.  nov., Isolated from a Blood Culture.
PG  - e01595-16
AB  - Here, we report the draft genome sequence of a Gram-negative microbe found in a blood culture
      (B08008) from a patient. The organism was proposed to be from a new unknown genus and species.
      This publication will increase worldwide microbial knowledge and may improve microbial
      identification and antibiotic treatment for patients.
AU  - Waldman-Ben-Asher H
AU  - Yerushalmi R
AU  - Wachtel C
AU  - Barbiro-Michaely E
AU  - Sompolinsky D
AU  - Gerber D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01595-16.

PMID- 16855248
VI  - 188
DP  - 2006
TI  - Sau1: a novel lineage-specific type I restriction-modification system that blocks horizontal gene transfer into Staphylococcus aureus and between S.  aureus isolates of different lineages.
PG  - 5578-5585
AB  - The Sau1 type I restriction-modification system is found on the chromosome of all nine
      sequenced strains of Staphylococcus aureus and includes a single hsdR (restriction) gene and
      two copies of hsdM (modification) and sdS (sequence specificity) genes. The strain S. aureus
      RN4220 is a vital intermediate for laboratory S. aureus manipulation, as it can accept plasmid
      DNA from Escherichia coli. We show that it carries a mutation in the sau1hsdR gene and that
      complementation restored a nontransformable phenotype. Sau1 was also responsible for reduced
      conjugative transfer from enterococci, a model of vancomycin resistance transfer. This may
      explain why only four vancomycin-resistant S. aureus strains have been identified despite
      substantial selective pressure in the clinical setting. Using a multistrain S. aureus
      microarray, we show that the two copies of sequence specificity genes (sau1hsdS1 and
      sau1hsdS2) vary substantially between isolates and that the variation corresponds to the 10
      dominant S. aureus lineages. Thus, RN4220 complemented with sau1hsdR was resistant to
      bacteriophage lysis but only if the phage was grown on S. aureus of a different lineage.
      Similarly, it could be transduced with DNA from its own lineage but not with the phage grown
      on different S. aureus lineages.  Therefore, we propose that Sau1 is the major mechanism for
      blocking transfer of resistance genes and other mobile genetic elements into S. aureus
      isolates from other species, as well as for controlling the spread of resistance genes between
      isolates of different S. aureus lineages.  Blocking Sau1 should also allow genetic
      manipulation of clinical strains of S. aureus.
AU  - Waldron DE
AU  - Lindsay JA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2006 188: 5578-5585.

PMID- 11972787
VI  - 44
DP  - 2002
TI  - Competitive interaction of the OxyR DNA-binding protein and the Dam methylase at the antigen 43 gene regulatory region in Escherichia coli.
PG  - 509-520
AB  - The antigen 43 surface protein of Escherichia coli is expressed in a phase-variable manner by
      a mechanism involving alternative activation
      and repression of transcription of the agn43 gene. The repressor is the
      OxyR DNA-binding protein, and its binding site was found to be located
      downstream of the agn43 transcription start site in a region of DNA
      that encompasses three 5' -GATC-3' sequences that are subject to
      Dam-mediated DNA methylation. It has been suggested previously that the
      phase-variable expression of antigen 43 results from a competition
      between Dam methylase and the OxyR repressor for these sites. The 5'
      -GATC-3' sequences were inactivated for methylation by site-directed
      mutagenesis, and all possible combinations of inactive and active sites
      were assessed for effects on phase-variable expression of the agn43
      gene. Inactivation of any 5' -GATC-3' site individually had no effect;
      at least two sites had to be inactivated to disrupt the normal pattern
      of expression. Studies of OxyR interaction with agn43 DNA showed that
      methylation of any two 5' -GATC-3' sites was necessary and sufficient
      to block binding of the repressor. It was also found that the adenines
      of the second and third 5' -GATC-3' sites are required for OxyR
      binding, demonstrating that the sites for Dam methylation and for
      repressor binding are intimately associated. This is consistent with a
      competition model in which Dam and OxyR share a preference for specific
      DNA sequences in the regulatory region of the agn43 gene.
AU  - Waldron DE
AU  - Owen P
AU  - Dorman CJ
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2002 44: 509-520.

PMID- 
VI  - 2
DP  - 2006
TI  - 50 years of studies of restriction - modification systems (Systemy restrykcyjno-modyfikacyjne - 50 lat badan).
PG  - 65-88
AB  - The basic function of restriction endonucleases and methyltransferases is protection of the
      host genome against foreign DNA. Their
      recombination and transposition related functions are still being
      discussed. Some authors postulate that R-M genes may act as selfish
      genetic elements. Restriction endonucleases are indispensable tools in
      molecular biology. As these enzymes recognize DNA sequence very
      specifically, they serve as a model for protein-DNA interaction.
      Restriction-modification genes have also played the same role as a
      model for evolutionary studies as well as protein structure - function
      relations. So far, there have been more than 3500 bacterial strains
      studied which possessed R-M genes of more than 280 different
      specificities towards recognition sequence and cleavage sites. They
      became a very good commercial product for many biotechnological
      companies. At present, in a genome sequencing era, R-M genes seem to be
      much more common than it was thought before.
AU  - Waleron K
AU  - Nakonieczna J
AU  - Waleron M
AU  - Podhajska AJ
PT  - Journal Article
TA  - Biotechnologia (Poznan)
JT  - Biotechnologia (Poznan)
SO  - Biotechnologia (Poznan) 2006 2: 65-88.

PMID- 16430511
VI  - 100
DP  - 2006
TI  - Identification of a DNA restriction-modification system in Pectobacterium carotovorum strains isolated from Poland.
PG  - 343-351
AB  - Aims: Polish isolates of pectinolytic bacteria from the species Pectobacterium carotovorum
      were screened for the presence of a DNA
      restriction-modification (R-M) system.
      Methods and Results: Eighty-nine strains of P. carotovorum were
      isolated from infected potato plants. Sixty-six strains belonged to P.
      carotovorum ssp. atrosepticum and 23 to P. carotovorum ssp.
      carotovorum. The presence of restriction enzyme Pca17AI, which is an
      isoschizomer of EcoRII endonuclease, was observed in all isolates of P.
      c. atrosepticum but not in P. c. carotovorum. The biochemical
      properties, PCR amplification, and sequences of the Pca17AI restriction
      endonuclease and methyltransferase genes were compared with the
      prototype EcoRII R-M system genes. Only when DNA isolated from cells of
      P. c. atrosepticum was used as a template, amplification of a 680 bp
      homologous to the gene coding EcoRII endonuclease.
      Conclusions: Endonuclease Pca17AI, having a relatively low
      temperature optimum, was identified. PCR amplification revealed that
      the nucleotide sequence of genes for EcoRII and Pca17AI R-M are
      different. Dcm methylation was observed in all strains of
      Pectobacterium and other Erwinia species tested. The sequence of a DNA
      fragment coding Dcm methylase in P. carotovorum was different from that
      of Escherichia coli.
      Significance and Impact of the Study: Pca17AI is the first
      psychrophilic isoschizomer of EcoRII endonuclease. The presence of
      specific Dcm methylation in chromosomal DNA isolated from P.
      carotovorum is described for the first time. A 680 bp PCR product,
      unique for P. c. atrosepticum strains, could serve as a molecular
      marker for detection of these bacteria in environmental samples.
AU  - Waleron K
AU  - Waleron M
AU  - Osipiuk J
AU  - Podhajska AJ
AU  - Lojkowska E
PT  - Journal Article
TA  - J. Appl. Microbiol.
JT  - J. Appl. Microbiol.
SO  - J. Appl. Microbiol. 2006 100: 343-351.

PMID- 23409256
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Mycoplasma cynos Strain C142.
PG  - e00196-12
AB  - Here we report the de novo genome sequencing of Mycoplasma cynos strain C142, isolated from a
      dog with canine infectious respiratory disease (CIRD) in the
      United States.
AU  - Walker CA
AU  - Mannering SA
AU  - Shields S
AU  - Blake DP
AU  - Brownlie J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00196-12.

PMID- 20421470
VI  - 107
DP  - 2010
TI  - Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea.
PG  - 8818-8823
AB  - Ammonia-oxidizing archaea are ubiquitous in marine and terrestrial environments and now
      thought to be significant contributors to carbon and
      nitrogen cycling. The isolation of Candidatus 'Nitrosopumilus maritimus'
      strain SCM1 provided the opportunity for linking its chemolithotrophic
      physiology with a genomic inventory of the globally distributed archaea.
      Here we report the 1,645,259-bp closed genome of strain SCM1, revealing
      highly copper-dependent systems for ammonia oxidation and electron
      transport that are distinctly different from known ammonia-oxidizing
      bacteria. Consistent with in situ isotopic studies of marine archaea, the
      genome sequence indicates N. maritimus grows autotrophically using a
      variant of the 3-hydroxypropionate/4-hydroxybutryrate pathway for carbon
      assimilation, while maintaining limited capacity for assimilation of
      organic carbon. This unique instance of archaeal biosynthesis of the
      osmoprotectant ectoine and an unprecedented enrichment of multicopper
      oxidases, thioredoxin-like proteins, and transcriptional regulators points
      to an organism responsive to environmental cues and adapted to handling
      reactive copper and nitrogen species that likely derive from its
      distinctive biochemistry. The conservation of N. maritimus gene content
      and organization within marine metagenomes indicates that the unique
      physiology of these specialized oligophiles may play a significant role in
      the biogeochemical cycles of carbon and nitrogen.
AU  - Walker CB et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2010 107: 8818-8823.

PMID- 1309614
VI  - 89
DP  - 1992
TI  - Isothermal in vitro amplification of DNA by a restriction enzyme/DNA polymerase system.
PG  - 392-396
AB  - An isothermal in vitro DNA amplification method was developed based upon the
      following sequence of reaction events.  Restriction enzyme cleavage and
      subsequent heat denaturation of a DNA sample generates two single-stranded
      target DNA fragments (T1 and T2). Present in excess are two DNA amplification
      primers (P1 and P2).  The 3' end of P1 binds to the 3' end of T1, forming a
      duplex with 5' overhangs.  Likewise, P2 binds to T2.  The 5' overhangs of P1
      and P2 contain a recognition sequence (5'-GTTGAC-3') for the restriction enzyme
      HincII.  An exonuclease-deficient form of the large fragment of Escherichia
      coli DNA polymerase I (exo- Klenow polymerase) [Derbyshire, V., Freemont, P.S.,
      Sanderson, M.R., Beese, L., Friedman, J.M., Joyce, C.M. & Steitz, T.A. (1988)]
      Science 240, 199-201] extends the 3' ends of the duplexes using dGTP, dCTP,
      TTP, and deoxyadenosine 5'-[alpha-thio] triphosphate, which produces
      hemiphosphorothioate recognition sites on P1T1 and P2T2.  HincII nicks the
      unprotected primer strands of the hemiphosphorothioate recognition sites,
      leaving intact the modified complementary strands.  The exo- Klenow polymerase
      extends the 3' end at the nick on P1T1 and displaces the downstream strand that
      is functionally equivalent to T2.  Likewise, extension at the nick on P2T2
      results in displacement of a downstream strand functionally equivalent to T1.
      Nicking and polymerization/displacement steps cycle continuously on P1T1 and
      P2T2 because extension at a nick regenerates a nickable HincII recognition
      site.  Target amplification is exponential because strands displaced from P1T1
      serve as targets for P2 and strands displaced from P2T2 serve as targets for
      P1.  A 10/6-fold amplification of a genomic sequence from Mycobacterium
      tuberculosis or Mycobacterium bovis was achieved in 4 h at 37C.
AU  - Walker GT
AU  - Little MC
AU  - Nadeau JG
AU  - Shank DD
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1992 89: 392-396.

PMID- 3005970
VI  - 14
DP  - 1986
TI  - Identification and characterisation of PmaCI an endonuclease of novel specificity from Pseudomonas maltophila.
PG  - 1293-1301
AB  - We report the use of MonoQ FPLC (Fast Protein Liquid Chromatography) for the
      rapid purification of a novel Type II restriction endonuclease PmaCI, from
      Pseudomonas maltophila, which recognises the sequence 5'-CAC^GTG-3'.  The
      resulting enzyme is free of other nucleases to a level suitable for its
      characterisation by multiple-substrate digestion and DNA sequencing techniques.
      This method appears to be widely applicable and we have used it for the
      isolation of restriction endonucleases of comparable purity from a range of
      other organisms.  Also described is a rapid method for screening a library of
      small inserted regions in recombinant M13 molecules for the presence and
      subsequent screening of restriction sites of interest.
AU  - Walker JNB
AU  - Dean PDG
AU  - Saunders JR
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1986 14: 1293-1301.

PMID- 25197440
VI  - 9
DP  - 2014
TI  - Genome sequence of the acid-tolerant Burkholderia sp. strain WSM2230 from Karijini National Park, Australia.
PG  - 551-561
AB  - Burkholderia sp. strain WSM2230 is an aerobic, motile, Gram-negative, non-spore-forming
      acid-tolerant rod isolated from acidic soil collected in 2001
      from Karijini National Park, Western Australia, using Kennedia coccinea (Coral
      Vine) as a host. WSM2230 was initially effective in nitrogen-fixation with K.
      coccinea, but subsequently lost symbiotic competence. Here we describe the
      features of Burkholderia sp. strain WSM2230, together with genome sequence
      information and its annotation. The 6,309,801 bp high-quality-draft genome is
      arranged into 33 scaffolds of 33 contigs containing 5,590 protein-coding genes
      and 63 RNA-only encoding genes. The genome sequence of WSM2230 failed to identify
      nodulation genes and provides an explanation for the observed failure of the
      laboratory grown strain to nodulate. The genome of this strain is one of 100
      sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for
      Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.
AU  - Walker R
AU  - Watkin E
AU  - Tian R
AU  - Brau L
AU  - O'Hara G
AU  - Goodwin L
AU  - Han J
AU  - Lobos E
AU  - Huntemann M
AU  - Pati A
AU  - Woyke T
AU  - Mavromatis K
AU  - Markowitz V
AU  - Ivanova N
AU  - Kyrpides N
AU  - Reeve W
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 551-561.

PMID- 25197442
VI  - 9
DP  - 2014
TI  - Genome sequence of the acid-tolerant Burkholderia sp. strain WSM2232 from Karijini National Park, Australia.
PG  - 1168-1180
AB  - Burkholderia sp. strain WSM2232 is an aerobic, motile, Gram-negative, non-spore-forming
      acid-tolerant rod that was trapped in 2001 from acidic soil
      collected from Karijini National Park (Australia) using Gastrolobium capitatum as
      a host. WSM2232 was effective in nitrogen fixation with G. capitatum but
      subsequently lost symbiotic competence during long-term storage. Here we describe
      the features of Burkholderia sp. strain WSM2232, together with genome sequence
      information and its annotation. The 7,208,311 bp standard-draft genome is
      arranged into 72 scaffolds of 72 contigs containing 6,322 protein-coding genes
      and 61 RNA-only encoding genes. The loss of symbiotic capability can now be
      attributed to the loss of nodulation and nitrogen fixation genes from the genome.
      This rhizobial genome is one of 100 sequenced as part of the DOE Joint Genome
      Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria
      (GEBA-RNB) project.
AU  - Walker R
AU  - Watkin E
AU  - Tian R
AU  - Brau L
AU  - O'Hara G
AU  - Goodwin L
AU  - Han J
AU  - Reddy T
AU  - Huntemann M
AU  - Pati A
AU  - Woyke T
AU  - Mavromatis K
AU  - Markowitz V
AU  - Ivanova N
AU  - Kyrpides N
AU  - Reeve W
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 1168-1180.

PMID- 
VI  - 3
DP  - 2003
TI  - The Genetics of Phage Resistance in Lactococcus lactis.
PG  - 291-315
AB  - 
AU  - Walker SA
AU  - Klaenhammer TR
PT  - Journal Article
TA  - Genetics of Phage Resistance
JT  - Genetics of Phage Resistance
SO  - Genetics of Phage Resistance 2003 3: 291-315.

PMID- 11804597
VI  - 9
DP  - 2002
TI  - Structure of Ocr from bacteriophage T7, a protein that mimics B-form DNA.
PG  - 187-194
AB  - We have solved, by X-ray crystallography to a resolution of 1.8 A, the structure of a protein
      capable of mimicking approximately 20 base pairs of
      B-form DNA. This ocr protein, encoded by gene 0.3 of bacteriophage T7,
      mimics the size and shape of a bent DNA molecule and the arrangement of
      negative charges along the phosphate backbone of B-form DNA. We also
      demonstrate that ocr is an efficient inhibitor in vivo of all known
      families of the complex type I DNA restriction enzymes. Using atomic force
      microscopy, we have also observed that type I enzymes induce a bend in DNA
      of similar magnitude to the bend in the ocr molecule. This first structure
      of an antirestriction protein demonstrates the construction of structural
      mimetics of long segments of B-form DNA.
AU  - Walkinshaw MD
AU  - Taylor P
AU  - Sturrock SS
AU  - Atanasiu C
AU  - Berge T
AU  - Henderson RM
AU  - Edwardson JM
AU  - Dryden DT
PT  - Journal Article
TA  - Mol. Cell
JT  - Mol. Cell
SO  - Mol. Cell 2002 9: 187-194.

PMID- 23846281
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Frankia sp. Strain BCU110501, a Nitrogen-Fixing Actinobacterium Isolated from Nodules of Discaria trinevis.
PG  - e00503-13
AB  - Frankia forms a nitrogen-fixing symbiosis with actinorhizal plants. We report a draft genome
      sequence for Frankia sp. strain BCU110501, a nitrogen-fixing
      actinobacterium isolated from nodules of Discaria trinevis grown in the Patagonia
      region of Argentina.
AU  - Wall LG et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00503-13.

PMID- 17449683
VI  - 73
DP  - 2007
TI  - The Early Response to Acid Shock in Lactobacillus reuteri Involves the ClpL Chaperone and a Putative Cell Wall-Altering Esterase.
PG  - 3924-3935
AB  - To be able to function as a probiotic, bacteria have to survive the
      passage through the gastrointestinal tract. We have examined survival and
      gene expression of Lactobacillus reuteri ATCC 55730 after a sudden shift
      in environmental acidity to a pH close to the conditions in the human
      stomach. More than 80% of the L. reuteri cells survived at pH 2.7 for 1 h.
      A genomewide expression analysis experiment using microarrays displayed 72
      differentially expressed genes at this pH. The early response to severe
      acid shock in L. reuteri differed from long-term acid adaptation to milder
      acid stress studied in other lactic acid bacteria. The genes induced
      included the following: clpL, genes putatively involved in alterations of
      the cell membrane and the cell wall; genes encoding transcriptional
      regulators; phage genes; and genes of unknown function. Two genes, clpL,
      encoding an ATPase with chaperone activity, and lr1516, encoding a
      putative esterase, were selected for mutation analyses. The mutants were
      significantly more sensitive to acid than the wild type was. Thus, these
      genes could contribute to the survival of L. reuteri in the
      gastrointestinal tract.
AU  - Wall T
AU  - Bath K
AU  - Britton RA
AU  - Jonsson H
AU  - Versalovic J
AU  - Roos S
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2007 73: 3924-3935.

PMID- 8495192
VI  - 2
DP  - 1993
TI  - The curious case of protein splicing: mechanistic insights suggested by protein semisynthesis.
PG  - 697-705
AB  - The gradual accumulation of examples of protein splicing, in which a
      nested intervening sequence is spliced out of the interior of a polyprotein precursor,
      suggests that this curious phenomenon might prove to have universal phylogenetic
      distribution and biological significance.  The known examples are reviewed, with the aim
      of establishing underlying patterns, and a generalized mechanism of autocatalytic protein
      splicing is proposed.  The testable consequences of such a proposal and the possible
      evolutionary origins of the phenomenon are discussed.
AU  - Wallace CJA
PT  - Journal Article
TA  - Protein Sci.
JT  - Protein Sci.
SO  - Protein Sci. 1993 2: 697-705.

PMID- 21362000
VI  - 52
DP  - 2011
TI  - Improved genetic transformation methods for the model alkaliphile Bacillus halodurans C-125.
PG  - 430-432
AB  - Aims: Bacillus halodurans C-125 is a Gram-positive bacterium that was the
      first alkaliphilic species to have its genome completely sequenced.
      Despite its many years as a model for alkaliphily and source of
      industrially important enzymes, genetic manipulation of B. halodurans
      C-125 remains difficult, and therefore, we sought to develop a robust
      method to allow routine transformation of this organism.
      Methods and Results:
      A plasmid artificial modification system (PAM system, <link
      rid='b7'>Yasui et al. 2008) for B. halodurans C-125 was created that
      increases transformation efficiency by 10- to 1000-fold. Also,
      recovering transformed protoplasts on succinate nutrient agar (SNA)
      yields faster, more robust colony recovery than on the traditional
      recovery medium. Combining these two techniques often allows recovery
      of transformants in as little as 48 h.
      Conclusions:
      Use of the B. halodurans C-125 PAM system and SNA greatly improves
      the efficiency and speed of protoplast transformation of B. halodurans
      C-125.
      Significance and Impact of the Study:
      These techniques allow routine genetic manipulation of B.
      halodurans C-125, a model alkaliphilic bacterium with important
      industrial properties.
AU  - Wallace JG
AU  - Breaker RR
PT  - Journal Article
TA  - Lett. Appl. Microbiol.
JT  - Lett. Appl. Microbiol.
SO  - Lett. Appl. Microbiol. 2011 52: 430-432.

PMID- 9887097
VI  - 13
DP  - 1999
TI  - Cytosine methylation and mammalian development.
PG  - 26-34
AB  - Programmed methylation and demethylation of regulatory sequences has been proposed to play a
      central role in vertebrate development.  We report here that the methylation status of the 5'
      regions of a panel of tissue-specific genes could not be correlated with expression in tissues
      of fetal and newborn mice.  Genes reported to be regulated by reversible methylation were not
      expressed ectopically or precociously in Dnmt1-deficient mouse embryos under conditions where
      demethylation caused biallelic expression of imprinted genes and activated transcription of
      endogenous retroviruses of the IAP class.  These and other data suggest that the numerous
      published expression-methylation correlations may have described not a cause but a consequence
      of transcriptional activation.  A model is proposed under which cytosine methylation
      represents a biochemical specialization of large genomes that participates in specialized
      biological functions such as allele-specific gene expression and the heritable transcriptional
      silencing of parasitic sequence elements, whereas cellular differentiation is controlled by
      conserved regulatory networks that do not depend on covalent modification of the genome.
AU  - Walsh CP
AU  - Bestor TH
PT  - Journal Article
TA  - Genes Dev.
JT  - Genes Dev.
SO  - Genes Dev. 1999 13: 26-34.

PMID- 16570853
VI  - 301
DP  - 2006
TI  - Cytosine methylation and DNA repair.
PG  - 283-315
AB  - Cytosine methylation is a common form of post-replicative DNA modification seen in both
      bacteria and eukaryotes. Modified cytosines have long been known to act as hotspots for
      mutations due to the high rate of spontaneous deamination of this base to thymine, resulting
      in a G/T mismatch. This will be fixed as a C -> T transition after replication if not repaired
      by the base excision repair (BER) pathway or specific repair enzymes dedicated to this
      purpose. This hypermutability has led to depletion of the target dinucleotide CpG outside of
      special CpG islands in mammals, which are normally unmethylated. We review the importance of C
      -> T transitions at non-island CpGs in human disease: When these occur in the germline, they
      are a common cause of inherited diseases such as epidermolysis bullosa and
      mucopolysaccharidosis, while in the soma they are frequently found in the genes for tumor
      suppressors such as p53 and the retinoblastoma protein, causing cancer. We also examine the
      specific repair enzymes involved, namely the endonuclease Vsr in Escherichia coli and two
      members of the uracil DNA glycosylase (UDG) superfamily in mammals, TDG and MBD4. Repair
      brings its own problems, since it will require remethylation of the replacement cytosine,
      presumably coupling repair to methylation by either the maintenance methylase Dnmt1 or a de
      novo enzyme such as Dnmt3a. Uncoupling of methylation from repair may be one way to remove
      methylation from DNA. We also look at the possible role of specific cytosine deaminases such
      as Aid and Apobec in accelerating deamination of methylcytosine and consequent DNA
      demethylation.
AU  - Walsh CP
AU  - Xu GL
PT  - Journal Article
TA  - Curr. Top. Microbiol. Immunol.
JT  - Curr. Top. Microbiol. Immunol.
SO  - Curr. Top. Microbiol. Immunol. 2006 301: 283-315.

PMID- 19900896
VI  - 326
DP  - 2009
TI  - Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones.
PG  - 578-582
AB  - Oxygen minimum zones, also known as oceanic "dead zones," are widespread
      oceanographic features currently expanding because of global warming. Although
      inhospitable to metazoan life, they support a cryptic microbiota whose metabolic
      activities affect nutrient and trace gas cycling within the global ocean. Here,
      we report metagenomic analyses of a ubiquitous and abundant but uncultivated
      oxygen minimum zone microbe (SUP05) related to chemoautotrophic gill symbionts of
      deep-sea clams and mussels. The SUP05 metagenome harbors a versatile repertoire
      of genes mediating autotrophic carbon assimilation, sulfur oxidation, and nitrate
      respiration responsive to a wide range of water-column redox states. Our analysis
      provides a genomic foundation for understanding the ecological and biogeochemical
      role of pelagic SUP05 in oxygen-deficient oceanic waters and its potential
      sensitivity to environmental changes.
AU  - Walsh DA
AU  - Zaikova E
AU  - Howes CG
AU  - Song YC
AU  - Wright JJ
AU  - Tringe SG
AU  - Tortell PD
AU  - Hallam SJ
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2009 326: 578-582.

PMID- 19900896
VI  - 326
DP  - 2009
TI  - Metagenome of a versatile chemolithoautotroph from expanding oxygen minimum zones.
PG  - 578-582
AB  - Oxygen minimum zones, also known as oceanic "dead zones", are widesprad oceanographic features
      currently expanding because of global warming.  Although inhospitable to metazoan life, they
      support a cryptic microbiota whose metabolic activities affect nutrient and trace gas cycling
      within the global ocean.  Here, we report metagenomic analyses of a ubiquitous and abundant
      but uncultivated oxygen minimum zone microbe (SUPO5) related to chemoautotrophic gill
      symbionts of deep-sea clams and mussels.  The SUP05 metagenome harbors a versatile repertoire
      of genes mediating autotrophic carbon assimilation, sulfur oxidation, and nitrate respiration
      responsive to a wide range of water-column redox states. Our analysis provides a genomic
      foundation for understanding the ecological and biogeochemical role of pelagic SUP05 in
      oxygen-deficient oceanic waters and its potential sensitivity to environmental changes.
AU  - Walsh DA
AU  - Zaikova E
AU  - Howes CL
AU  - Song YC
AU  - Wright J
AU  - Tringe SG
AU  - Tortell PD
AU  - Hallam SJ
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2009 326: 578-582.

PMID- 25977439
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Six Different Staphylococcus epidermidis Clones, Isolated Individually from Preterm Neonates Presenting with Sepsis at Edinburgh's  Royal Infirmary.
PG  - e00471-15
AB  - Herein, we report the draft genome sequences of six individual Staphylococcus epidermidis
      clones, cultivated from blood taken from different preterm neonatal
      sepsis patients at the Royal Infirmary, Edinburgh, Scotland, United Kingdom.
AU  - Walsh P
AU  - Bekaert M
AU  - Carroll J
AU  - Manning T
AU  - Kelly B
AU  - O'Driscoll A
AU  - Lu X
AU  - Smith C
AU  - Dickinson P
AU  - Templeton K
AU  - Ghazal P
AU  - Sleator RD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00471-15.

PMID- Not carried by PubMed...
VI  - 0
DP  - 1978
TI  - Purification and characterization of a site specific endonuclease from Streptomyces hygroscopicus.
PG  - 648
AB  - The isolation procedure of a new site specific endonuclease from Streptomyces
      hygroscopicus J 0477 is described.  Using the Lysozyme treatment, we have
      partially purified this enzyme (ShyI) by chromatography on Bio-Gel A0.5m, DEAE
      Cellulose and Sepharose 4B coupled with 1,5-Diaminopentan ShyI require Mg2+ as
      cofactor.  Salt concentrations higher than 0.2M NaCl inhibit the enzyme.  The
      enzyme cleaves wild type lambda-DNA at two sites.
AU  - Walter F
AU  - Hartmann M
AU  - Roth M
PT  - Journal Article
TA  - Abstracts of 12th FEBS Symposium, Dresden.
JT  - Abstracts of 12th FEBS Symposium, Dresden.
SO  - Abstracts of 12th FEBS Symposium, Dresden. 1978 0: 648.

PMID- 2108858
VI  - 9
DP  - 1990
TI  - The amino acid sequence of the CCGG recognizing DNA methyltransferase M.BsuFI: implications for the analysis of sequence recognition by cytosine DNA methyltransferases.
PG  - 1007-1013
AB  - The Bacillus subtilis FI DNA methyltransferase (M.BsuFI) modifies the outer
      cytosine of the DNA sequence CCGG, causing resistance against R.BsuFI and
      R.MspI restriction.  The M.BsuFI gene was cloned and expressed in B.subtilis
      and Escherichia coli.  As derived from the nucleotide sequence, the M.BsuFI
      protein has 409 amino acids, corresponding to a molecular mass of 46918
      daltons.  Including these data we have compared the nucleotide and amino acid
      sequences of different CCGG recognizing enzymes.  These analyses showed that
      M.BsuFI is highly related to two other CCGG specific methyltransferases, M.MspI
      and M.HpaII, which were isolated from Gram-negative bacteria.  Between M.BsuFI
      and M.MspI the sequence similarity is particularly significant in a region,
      which has been postulated to contain the target recognition domains (TRDs) of
      cytosine-specific DNA methyltransferases.  Apparently M.BsuFI and M.MspI,
      derived from phylogenetic distant organisms, use highly conserved structural
      elements for the recognition of the CCGG target sequence.  In contrast the very
      same region of M.HpaII is quite different from those of M.BsuFI and M.MspI.  We
      attribute this difference to the different targeting of methylation within the
      sequence CCGG, where M.HpaII methylates the inner, M.BsuFI/M.MspI the outer
      cytosine.  Also the CCGG recognizing TRD of the multispecific B. subtilis phage
      SPR Mtase is distinct from that of the host enzyme, possibly indicating
      different requirements for TRDs operative in mono- and multispecific enzymes.
AU  - Walter J
AU  - Noyer-Weidner M
AU  - Trautner TA
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1990 9: 1007-1013.

PMID- 1425579
VI  - 11
DP  - 1992
TI  - High plasticity of multispecific DNA methyltransferases in the region carrying DNA target recognizing enzyme modules.
PG  - 4445-4450
AB  - Multispecific cytosine C5 DNA methyltransferases (MTases) methylate more than one specific DNA
      target. This is due to the presence of several target recognizing domains (TRDs) in these
      enzymes. Such TRDs form part of a variable center in the MTase primary sequence, which
      separates conserved enzyme core sequences responsible for general steps in the methylation
      reaction. By deleting, rearranging and exchanging several TRDs of multispecific MTases, we
      demonstrate their modular character; they mediate target recognition independent of a
      particular TRD or core sequence context. We show also that multipsecific MTases can
      accommodate inert material of non-MTase origin within their variable region without losing
      their activity. The remarkable plasticity with respect to the material that can be integrated
      into this region suggests that the enzyme core sequences preceding or following it form
      separable functional domains. In spite of the documented flexibitity multispecific MTass could
      not be endowed with novel specificities by integration of putative TRDs of monospecific
      MTases, pointing to differences between multi-and monospecific MTases in the way their core
      and TRD sequences interact.
AU  - Walter J
AU  - Trautner TA
AU  - Noyer-Weidner M
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1992 11: 4445-4450.

PMID- 29798926
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Enterococcus mundtii Strains Isolated from Beef Slaughterhouses in Kenya.
PG  - e00446-18
AB  - We present here draft genome sequences of Enterococcus mundtii strains K7-EM, P2-EM, C11-EM,
      and H18-EM, which were isolated from slaughterhouse equipment,
      carcasses, and personnel of small- and medium-sized beef slaughterhouses in
      Kenya.
AU  - Wambui J
AU  - Stevens M
AU  - Njage PMK
AU  - Wuthrich D
AU  - Egli A
AU  - Stephan R
AU  - Tasara T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00446-18.

PMID- 29192079
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Acetobacter pomorum Oregon-R-modENCODE Strain BDGP5,  an Acetic Acid Bacterium Found in the Drosophila melanogaster Gut.
PG  - e01333-17
AB  - Acetobacter pomorum Oregon-R-modENCODE strain BDGP5 was isolated from Drosophila  melanogaster
      for functional host-microbe interaction studies. The complete genome
      is composed of a single chromosomal circle of 2,848,089 bp, with a G+C content of
      53% and three plasmids of 131,455 bp, 19,216 bp, and 9,160 bp.
AU  - Wan KH
AU  - Yu C
AU  - Park S
AU  - Hammonds AS
AU  - Booth BW
AU  - Celniker SE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01333-17.

PMID- 28983001
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Bacillus kochii Oregon-R-modENCODE Strain BDGP4, Isolated from Drosophila melanogaster Gut.
PG  - e01074-17
AB  - Bacillus kochii Oregon-R-modENCODE strain BDGP4 was isolated from the gut of Drosophila
      melanogaster for functional host microbial interaction studies. The
      complete genome comprised a single chromosomal circle of 4,557,232 bp with a G+C
      content of 37% and a single plasmid of 137,143 bp.
AU  - Wan KH
AU  - Yu C
AU  - Park S
AU  - Hammonds AS
AU  - Booth BW
AU  - Celniker SE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01074-17.

PMID- 28982997
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Enterococcus durans Oregon-R-modENCODE Strain BDGP3,  a Lactic Acid Bacterium Found in the Drosophila melanogaster Gut.
PG  - e01041-17
AB  - Enterococcus durans Oregon-R-modENCODE strain BDGP3 was isolated from the Drosophila
      melanogaster gut for functional host-microbe interaction studies. The
      complete genome is composed of a single circular genome of 2,983,334 bp, with a
      G+C content of 38%, and a single plasmid of 5,594 bp.
AU  - Wan KH
AU  - Yu C
AU  - Park S
AU  - Hammonds AS
AU  - Booth BW
AU  - Celniker SE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01041-17.

PMID- 29025953
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Lactobacillus plantarum Oregon-R-modENCODE Strain BDGP2 Isolated from Drosophila melanogaster Gut.
PG  - e01155-17
AB  - Lactobacillus plantarum Oregon-R-modENCODE strain BDGP2 was isolated from the gut of
      Drosophila melanogaster for functional host microbial interaction studies. The
      complete genome comprised a single circular genome of 3,407,160 bp, with a G+C
      content of 44%, and four plasmids.
AU  - Wan KH
AU  - Yu C
AU  - Park S
AU  - Hammonds AS
AU  - Booth BW
AU  - Celniker SE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01155-17.

PMID- 29146844
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Acetobacter tropicalis Oregon-R-modENCODE Strain BDGP1, an Acetic Acid Bacterium Found in the Drosophila melanogaster Gut.
PG  - e01020-17
AB  - Acetobacter tropicalis Oregon-R-modENCODE strain BDGP1 was isolated from Drosophila
      melanogaster for functional host-microbe interaction studies. The
      complete genome comprises a single chromosomal circle of 3,988,649 bp with a G+C
      content of 56% and a conjugative plasmid of 151,013 bp.
AU  - Wan KH
AU  - Yu C
AU  - Park S
AU  - Hammonds AS
AU  - Booth BW
AU  - Celniker SE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01020-17.

PMID- 29117225
VI  - 12
DP  - 2017
TI  - Genomic comparison between Staphylococcus aureus GN strains clinically isolated from a familial infection case: IS1272 transposition through a novel inverted repeat-replacing mechanism.
PG  - E0187288
AB  - A bacterial insertion sequence (IS) is a mobile DNA sequence carrying only the
      transposase gene (tnp) that acts as a mutator to disrupt genes, alter gene
      expressions, and cause genomic rearrangements. "Canonical" ISs have historically
      been characterized by their terminal inverted repeats (IRs), which may form a
      stem-loop structure, and duplications of a short (non-IR) target sequence at both
      ends, called target site duplications (TSDs). The IS distributions and virulence
      potentials of Staphylococcus aureus genomes in familial infection cases are
      unclear. Here, we determined the complete circular genome sequences of familial
      strains from a Panton-Valentine leukocidin (PVL)-positive ST50/agr4 S. aureus
      (GN) infection of a 4-year old boy with skin abscesses. The genomes of the
      patient strain (GN1) and parent strain (GN3) were rich for "canonical" IS1272
      with terminal IRs, both having 13 commonly-existing copies (ce-IS1272). Moreover,
      GN1 had a newly-inserted IS1272 (ni-IS1272) on the PVL-converting prophage, while
      GN3 had two copies of ni-IS1272 within the DNA helicase gene and near rot. The
      GN3 genome also had a small deletion. The targets of ni-IS1272 transposition were
      IR structures, in contrast with previous "canonical" ISs. There were no TSDs.
      Based on a database search, the targets for ce-IS1272 were IRs or "non-IRs".
      IS1272 included a larger structure with tandem duplications of the left (IRL)
      side sequence; tnp included minor cases of a long fusion form and truncated form.
      One ce-IS1272 was associated with the segments responsible for immune evasion and
      drug resistance. Regarding virulence, GN1 expressed cytolytic peptides
      (phenol-soluble modulin alpha and delta-hemolysin) and PVL more strongly than
      some other familial strains. These results suggest that IS1272 transposes through
      an IR-replacing mechanism, with an irreversible process unlike that of
      "canonical" transpositions, resulting in genomic variations, and that, among the
      familial strains, the patient strain has strong virulence potential based on
      community-associated virulence factors.
AU  - Wan TW
AU  - Higuchi W
AU  - Khokhlova OE
AU  - Hung WC
AU  - Iwao Y
AU  - Wakayama M
AU  - Inomata N
AU  - Takano T
AU  - Lin YT
AU  - Peryanova OV
AU  - Kojima KK
AU  - Salmina AB
AU  - Teng LJ
AU  - Yamamoto T
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2017 12: E0187288.

PMID- 27741255
VI  - 11
DP  - 2016
TI  - Complete Circular Genome Sequence of Successful ST8/SCCmecIV Community-Associated Methicillin-Resistant Staphylococcus aureus (OC8) in Russia: One-Megabase Genomic Inversion, IS256's Spread, and Evolution of Russia ST8-IV.
PG  - E0164168
AB  - ST8/SCCmecIV community-associated methicillin-resistant Staphylococcus aureus
      (CA-MRSA) has been a common threat, with large USA300 epidemics in the United
      States. The global geographical structure of ST8/SCCmecIV has not yet been fully
      elucidated. We herein determined the complete circular genome sequence of
      ST8/SCCmecIVc strain OC8 from Siberian Russia. We found that 36.0% of the genome
      was inverted relative to USA300. Two IS256, oppositely oriented, at
      IS256-enriched hot spots were implicated with the one-megabase genomic inversion
      (MbIN) and vSabeta split. The behavior of IS256 was flexible: its insertion site
      (att) sequences on the genome and junction sequences of extrachromosomal circular
      DNA were all divergent, albeit with fixed sizes. A similar multi-IS256 system was
      detected, even in prevalent ST239 healthcare-associated MRSA in Russia,
      suggesting IS256's strong transmission potential and advantage in evolution.
      Regarding epidemiology, all ST8/SCCmecIVc strains from European, Siberian, and
      Far Eastern Russia, examined had MbIN, and geographical expansion accompanied
      divergent spa types and resistance to fluoroquinolones, chloramphenicol, and
      often rifampicin. Russia ST8/SCCmecIVc has been associated with life-threatening
      infections such as pneumonia and sepsis in both community and hospital settings.
      Regarding virulence, the OC8 genome carried a series of toxin and immune evasion
      genes, a truncated giant surface protein gene, and IS256 insertion adjacent to a
      pan-regulatory gene. These results suggest that unique single
      ST8/spa1(t008)/SCCmecIVc CA-MRSA (clade, Russia ST8-IVc) emerged in Russia, and
      this was followed by large geographical expansion, with MbIN as an
      epidemiological marker, and fluoroquinolone resistance, multiple virulence
      factors, and possibly a multi-IS256 system as selective advantages.
AU  - Wan TW
AU  - Khokhlova OE
AU  - Iwao Y
AU  - Higuchi W
AU  - Hung WC
AU  - Reva IV
AU  - Singur OA
AU  - Gostev VV
AU  - Sidorenko SV
AU  - Peryanova OV
AU  - Salmina AB
AU  - Reva GV
AU  - Teng LJ
AU  - Yamamoto T
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2016 11: E0164168.

PMID- 27795280
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Terasakiispira papahanaumokuakeensis PH27AT, a Spiral Bacterium from the Northwestern Hawaiian Islands.
PG  - e01166-16
AB  - The genus Terasakiispira hosts only Terasakiispira papahanaumokuakeensis PH27AT,  cultivated
      from an anchialine pond on Pearl and Hermes Atoll, Northwestern
      Hawaiian Islands. The strain's genome sequence may provide insights into the
      evolution of free-living Oceanospirillaceae.
AU  - Wan X
AU  - Dasilveira L
AU  - Hou S
AU  - Saito JA
AU  - Donachie SP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01166-16.

PMID- 27932650
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a Novel Marinobacter sp. Strain from Honolulu Harbor, Hawai'i.
PG  - e01354-16
AB  - Marinobacter sp. strain X15-166BT was cultivated from sediment in Honolulu Harbor, Hawai'i.
      The X15-166BT draft genome of 3,490,661 bp encodes 3,115
      protein-coding open reading frames. We anticipate that the genome will provide
      insights into the strain's lifestyle and the evolution of Marinobacter.
AU  - Wan X
AU  - Hou S
AU  - Burns SL
AU  - Saito JA
AU  - Donachie SP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01354-16.

PMID- 27979942
VI  - 4
DP  - 2016
TI  - Genome Sequence of Rheinheimera salexigens sp. nov. Isolated from a Fishing Hook  off O'ahu, Hawai'i.
PG  - e01390-16
AB  - Rheinheimera salexigens KH87T is an obligately halophilic gammaproteobacterium. The strain's
      draft genome sequence, generated by the Roche 454 GS FLX+ platform,
      comprises two scaffolds of ~3.4 Mbp and ~3 kbp, with 3,030 protein-coding
      sequences and 58 tRNA coding regions. The G+C content is 42 mol%.
AU  - Wan X
AU  - Hou S
AU  - Hayashi K
AU  - Anderson J
AU  - Donachie SP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01390-16.

PMID- 25977417
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Pantoea anthophila Strain 11-2 from Hypersaline Lake Laysan, Hawaii.
PG  - e00321-15
AB  - Most Pantoea spp. have been isolated from plant sources or clinical samples. However, we
      cultivated Pantoea anthophila 11-2 from hypersaline water from the
      lake on Laysan, Northwestern Hawaiian Islands. Draft genome sequencing of 11-2
      provides a molecular basis for studies in evolution and pathogenicity in Pantoea
      spp.
AU  - Wan X
AU  - Hou S
AU  - Phan N
AU  - Malone MJS
AU  - Donachie SP
AU  - Alam M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00321-15.

PMID- 26494668
VI  - 3
DP  - 2015
TI  - Genome Sequence of Flavobacterium akiainvivens IK-1T, Isolated from Decaying Wikstroemia oahuensis, an Endemic Hawaiian Shrub.
PG  - e01222-15
AB  - Flavobacterium spp. have been cultivated from diverse aquatic and terrestrial habitats. F.
      akiainvivens IK-1(T) was cultivated from decaying wood of Wikstroemia oahuensis, an endemic
      Hawaiian shrub. The strain's genome sequence may provide insights into niche adaptation and
      evolution of the genus in a mid-ocean archipelago.
AU  - Wan X
AU  - Hou S
AU  - Saito JA
AU  - Kaneshiro KY
AU  - Donachie SP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01222-15.

PMID- 27811116
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Piscirickettsia litoralis, Isolated from Seawater.
PG  - e01252-16
AB  - One species of Piscirickettsia, a pathogen of salmonid fish, has been described.  The genome
      sequence of a putative second and free-living species may provide
      insights into the evolution of pathogenicity in the genus.
AU  - Wan X
AU  - Lee AJ
AU  - Hou S
AU  - Ushijima B
AU  - Nguyen YP
AU  - Thawley JA
AU  - Donachie SP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01252-16.

PMID- 27811107
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a Novel Luteimonas sp. Strain from Coral Mucus, Hawai'i.
PG  - e01228-16
AB  - Luteimonas sp. strain JM171 was cultivated from mucus collected around the coral  Porites
      lobata The JM171 draft genome of 2,992,353 bp contains 2,672
      protein-coding open reading frames, 45 tRNA coding regions, and encodes a
      putative globin-coupled diguanylate cyclase, JmGReg.
AU  - Wan X
AU  - Miller JM
AU  - Rowley SJ
AU  - Hou S
AU  - Donachie SP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01228-16.

PMID- 25395630
VI  - 2
DP  - 2014
TI  - Complete Genome Sequences of Beijing and Manila Family Strains of Mycobacterium tuberculosis.
PG  - e01135-14
AB  - The majority of isolates from tuberculosis patients in Hawaii arrive through the  immigration
      of infected individuals from the western Pacific. We report here on
      the annotated complete genomes of two strains of Mycobacterium tuberculosis from
      the two main lineages/families in Hawaii, Beijing and Manila.
AU  - Wan X
AU  - Qian L
AU  - Hou S
AU  - Drees KP
AU  - Foster JT
AU  - Douglas JT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01135-14.

PMID- 26337895
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of a Clinical Isolate of Serratia marcescens, Strain AH0650_Sm1.
PG  - e01007-15
AB  - Serratia marcescens strain AH0650_Sm1 is a clinical multidrug-resistant isolate from
      Australia. Here, we report its annotated draft genome comprising 20 contigs. We identified
      chromosomal antimicrobial resistance genes including a tet(41) variant, an aac(6')-Ic
      variant, ampC, a metallo-beta-lactamase, and several putative multidrug efflux pumps, as well
      as a novel prophage.
AU  - Wan Y
AU  - Gorrie CL
AU  - Jenney A
AU  - Mirceta M
AU  - Holt KE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01007-15.

PMID- 20625514
VI  - 5
DP  - 2010
TI  - The Complete Genome Sequence of the Pathogenic Intestinal Spirochete Brachyspira pilosicoli and Comparison with Other Brachyspira Genomes.
PG  - E11455
AB  - BACKGROUND: The anaerobic spirochete Brachyspira pilosicoli colonizes the
      large intestine of various species of birds and mammals, including humans.
      It causes "intestinal spirochetosis", a condition characterized by mild
      colitis, diarrhea and reduced growth. This study aimed to sequence and
      analyse the bacterial genome to investigate the genetic basis of its
      specialized ecology and virulence. METHODOLOGY/PRINCIPAL FINDINGS: The
      genome of B. pilosicoli 95/1000 was sequenced, assembled and compared with
      that of the pathogenic Brachyspira hyodysenteriae and a near-complete
      sequence of Brachyspira murdochii. The B. pilosicoli genome was circular,
      composed of 2,586,443 bp with a 27.9 mol% G+C content, and encoded 2,338
      genes. The three Brachyspira species shared 1,087 genes and showed
      evidence of extensive genome rearrangements. Despite minor differences in
      predicted protein functional groups, the species had many similar features
      including core metabolic pathways. Genes distinguishing B. pilosicoli from
      B. hyodysenteriae included those for a previously undescribed
      bacteriophage that may be useful for genetic manipulation, for a glycine
      reductase complex allowing use of glycine whilst protecting from oxidative
      stress, and for aconitase and related enzymes in the incomplete TCA cycle,
      allowing glutamate synthesis and function of the cycle during oxidative
      stress. B. pilosicoli had substantially fewer methyl-accepting chemotaxis
      genes than B. hyodysenteriae and hence these species are likely to have
      different chemotactic responses that may help to explain their different
      host range and colonization sites. B. pilosicoli lacked the gene for a new
      putative hemolysin identified in B. hyodysenteriae WA1. Both B. pilosicoli
      and B. murdochii lacked the rfbBADC gene cluster found on the B.
      hyodysenteriae plasmid, and hence were predicted to have different
      lipooligosaccharide structures. Overall, B. pilosicoli 95/1000 had a
      variety of genes potentially contributing to virulence.
      CONCLUSIONS/SIGNIFICANCE: The availability of the complete genome sequence
      of B. pilosicoli 95/1000 will facilitate functional genomics studies aimed
      at elucidating host-pathogen interactions and virulence.
AU  - Wanchanthuek P
AU  - Bellgard MI
AU  - La T
AU  - Ryan K
AU  - Moolhuijzen P
AU  - Chapman B
AU  - Black M
AU  - Schibeci D
AU  - Hunter A
AU  - Barrero R
AU  - Phillips ND
AU  - Hampson DJ
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2010 5: E11455.

PMID- 29798918
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of the Plant Growth-Promoting Sphingobium sp. Strain AEW4,  Isolated from the Rhizosphere of the Beachgrass Ammophila breviligulata.
PG  - e00410-18
AB  - Sphingobium sp. strain AEW4 is a novel isolate from rhizosphere soil attached to  the root of
      the American beachgrass Ammophila breviligulata The genomic sequence
      consisted of 4,678,518 bp and 4,428 protein-coding sequences. Here we report the
      draft genome sequence of this strain and some initial insights on its plant
      growth-promoting capabilities.
AU  - Wanees AE
AU  - Zaslow SJ
AU  - Potter SJ
AU  - Hsieh BP
AU  - Boss BL
AU  - Izquierdo JA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00410-18.

PMID- 23516227
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Bacillus thuringiensis Strain DAR 81934, Which Exhibits  Molluscicidal Activity.
PG  - e0017512
AB  - Bacillus thuringiensis has been widely used as a biopesticide for a long time. Its
      molluscicidal activity, however, is rarely realized. Here, we report the
      genome sequence of B. thuringiensis strain DAR 81934, a strain with molluscicidal
      activity against the pest snail Cernuella virgata.
AU  - Wang A
AU  - Pattemore J
AU  - Ash G
AU  - Williams A
AU  - Hane J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0017512.

PMID- 22933761
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Streptococcus agalactiae ZQ0910, a Pathogen Causing Meningoencephalitis in the GIFT Strain of Nile Tilapia (Oreochromis niloticus).
PG  - 5132-5133
AB  - Streptococcus agalactiae (group B streptococcus [GBS]) is a pathogen that causes
      meningoencephalitis in Nile tilapia (Oreochromis niloticus). Here, we reported
      the complete genome sequence of S. agalactiae strain ZQ0910, which was isolated
      from the GIFT strain of Nile tilapia in Guangdong, China.
AU  - Wang B
AU  - Jian J
AU  - Lu Y
AU  - Cai S
AU  - Huang Y
AU  - Tang J
AU  - Wu Z
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5132-5133.

PMID- 28619794
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Biocontroller Bacillus velezensis Strain JTYP2, Isolated from Leaves of Echeveria laui.
PG  - e00505-17
AB  - Bacillus velezensis JTYP2 was isolated from the leaves of Echeveria laui in Qingzhou, China,
      and may control some of the fungal pathogens of the plant. Here,
      we present the complete genome sequence of B. velezensis JTYP2. Several gene
      clusters related to its biosynthesis of antimicrobial compounds were predicted.
AU  - Wang B
AU  - Liu H
AU  - Ma H
AU  - Wang C
AU  - Liu K
AU  - Li Y
AU  - Hou Q
AU  - Ge R
AU  - Zhang T
AU  - Liu F
AU  - Ma J
AU  - Wang Y
AU  - Wang H
AU  - Xu B
AU  - Yao G
AU  - Xu W
AU  - Fan L
AU  - Ding Y
AU  - Du B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00505-17.

PMID- 24747891
VI  - 80
DP  - 2014
TI  - A Novel Angular Dioxygenase Gene Cluster, Encoding 3-Phenoxybenzoate 1', 2' -Dioxygenase in Sphingobium wenxiniae JZ-1.
PG  - 3811-3818
AB  - Sphingobium wenxiniae JZ-1 utilizes a wide range of pyrethroids and their
      metabolic product 3-phenoxybenzoate as source of carbon and energy. A mutant
      MJZ-1 defective in the degradation of 3-phenoxybenzoate was obtained by
      successive streaking on LB agar. Comparison of the draft genomes of strain JZ-1
      and MJZ-1 revealed that a 29,371 bp DNA fragment containing a putative angular
      dioxygenase gene cluster pbaA1A2B is missing in strain MJZ-1. PbaA1, PbaA2 and
      PbaB share 65%, 52% and 10% identities with the corresponding alpha, beta
      subunits and the ferredoxin component of dioxin dioxygenase from Sphingomonas
      wittichii RW1, respectively. Complementation of pbaA1A2B in strain MJZ-1 resulted
      in the active 3-phenoxybenzoate 1' , 2' -dioxygenase, but the enzyme activity in
      Escherichia coli cells was achieved only through the co-expression of pbaA1A2B
      and a GR (glutathione reductase)-type reductase gene pbaC, indicating that the
      3-phenoxybenzoate 1' , 2' -dioxygenase belongs to Type IV Rieske non-heme iron
      aromatic ring-hydroxylating oxygenase system consisting of an hetero-oligomeric
      oxygenase, a [2Fe-2S]-type ferredoxin and a GR-type reductase. pbaC gene is not
      located in the immediate vicinity of pbaA1A2B. 3-Phenoxybenzoate 1' , 2'
      -dioxygenase catalyzes the hydroxylation in the 1' , 2' -positions of the phenol
      moiety of 3-phenoxybenzoate, yielding 3-hydroxybenzoate and catechol. The
      transcription of pbaA1A2B and pbaC were both induced by 3-phenoxybenzoate, but
      the transcription level of pbaC was far low than that of pbaA1A2B, implying the
      possibility that PbaC may be not the only reductase that can physiologically
      transfer electrons to PbaA1A2B in strain JZ-1. Some GR-type reductases from other
      sphingomonad strains could also transfer electrons to PbaA1A2B, suggesting that
      PbaA1A2B has low specificity for reductase.
AU  - Wang C
AU  - Chen Q
AU  - Wang R
AU  - Shi C
AU  - Yan X
AU  - He J
AU  - Hong Q
AU  - Li S
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2014 80: 3811-3818.

PMID- 26868409
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Bacillus methylotrophicus FKM10, a Plant Growth-Promoting Rhizobacterium Isolated from Apple Rhizosphere.
PG  - e01739-15
AB  - Bacillus methylotrophicus FKM10 is a strain of plant growth-promoting rhizobacterium with
      antimicrobial activity, which was isolated from apple
      rhizosphere. Here, we present the genome sequence of B. methylotrophicus FKM10.
      Two scaffolds were finally assembled, and several functional genes related to its
      antimicrobial activity were discovered.
AU  - Wang C
AU  - Hu X
AU  - Liu K
AU  - Hou Q
AU  - Yang Q
AU  - Ding Y
AU  - Du B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01739-15.

PMID- 25700400
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Campylobacter fetus subsp. testudinum Strain Pet-3, Isolated from a Lizard (Hydrosaurus pustulatus).
PG  - e01420-14
AB  - The whole-genome sequence for Campylobacter fetus subsp. testudinum, a pathogen isolated from
      humans and turtles, has been reported recently. We present another  completed genome sequence
      of the C. fetus subsp. testudinum strain pet-3, which was isolated from a lizard in Taiwan,
      for further genomic comparison study.
AU  - Wang CM
AU  - Wu ZY
AU  - Shia WY
AU  - Jhou YJ
AU  - Tung KC
AU  - Shyu CL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01420-14.

PMID- 26203341
VI  - 10
DP  - 2015
TI  - Complete genome sequence of Salmonella enterica subspecies arizonae str. RKS2983.
PG  - 30
AB  - Salmonella arizonae (also called Salmonella subgroup IIIa) is a Gram-negative,
      non-spore-forming, motile, rod-shaped, facultatively anaerobic bacterium. S.
      arizonae strain RKS2983 was isolated from a human in California, USA. S. arizonae
      lies somewhere between Salmonella subgroups I (human pathogens) and V (also
      called S. bongori; usually non-pathogenic to humans) and so is an ideal model
      organism for studies of bacterial evolution from non-human pathogen to human
      pathogens. We hence sequenced the genome of RKS2983 for clues of genomic events
      that might have led to the divergence and speciation of Salmonella into distinct
      lineages with diverse host ranges and pathogenic features. The 4,574,836 bp
      complete genome contains 4,203 protein-coding genes, 82 tRNA genes and 7 rRNA
      operons. This genome contains several characteristics not reported to date in
      Salmonella subgroup I or V and may provide information about the genetic
      divergence of Salmonella pathogens.
AU  - Wang CX
AU  - Zhu SL
AU  - Wang XY
AU  - Feng Y
AU  - Li B
AU  - Li YG
AU  - Johnston RN
AU  - Liu GR
AU  - Zhou J
AU  - Liu SL
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 30.

PMID- 28428312
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of a Chromium-Reducing Strain, Pseudomonas fluorescens S613, Isolated from a Chromium-Contaminated Aquifer in Los Alamos, New Mexico.
PG  - e00241-17
AB  - In this report, a chromium-reducing bacterium, Pseudomonas fluorescens strain S613, was
      isolated from a Cr(VI)-contaminated aquifer at Los Alamos, NM, and
      sequenced. The size of the draft genome sequence is approximately 6.7 Mb.
AU  - Wang D
AU  - Boukhalfa H
AU  - Ware DS
AU  - Daligault HE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00241-17.

PMID- 26659672
VI  - 3
DP  - 2015
TI  - Genome Sequence of a Chromium-Reducing Strain, Bacillus cereus S612.
PG  - e01392-15
AB  - We report here the genome sequence of an effective chromium-reducing bacterium, Bacillus
      cereus strain S612. The size of the draft genome sequence is
      approximately 5.4 Mb, with a G+C content of 35%, and it is predicted to contain
      5,450 protein-coding genes.
AU  - Wang D
AU  - Boukhalfa H
AU  - Ware DS
AU  - Reimus PW
AU  - Daligault HE
AU  - Gleasner CD
AU  - Johnson SL
AU  - Li PE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01392-15.

PMID- 25502660
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Enterobacter cloacae Strain S611.
PG  - e00710-14
AB  - We report draft genomes of Enterobacter cloacae strain S611, an endophytic bacterium isolated
      from surface-sterilized germinating wheat seeds. We present
      the assembly and annotation of its genome, which may provide insights into the
      metabolic pathways involved in adaptation.
AU  - Wang D
AU  - Han CS
AU  - Dichosa AE
AU  - Gleasner CD
AU  - Johnson SL
AU  - Daligault HE
AU  - Davenport KW
AU  - Li PE
AU  - Pierson EA
AU  - Pierson LSIII
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00710-14.

PMID- 24371199
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Pseudomonas putida Strain S610, a Seed-Borne Bacterium of Wheat.
PG  - e01048-13
AB  - We report the genome sequence of a seed-borne bacterium, Pseudomonas putida strain S610. The
      size of the draft genome sequence is approximately 4.6 Mb, which
      is the smallest among all P. putida strains sequenced to date.
AU  - Wang D
AU  - Han CS
AU  - Dichosa AE
AU  - Gleasner CD
AU  - Johnson SL
AU  - Daligault HE
AU  - Davenport KW
AU  - Li PE
AU  - Pierson EA
AU  - Pierson LSIII
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01048-13.

PMID- 25908149
VI  - 3
DP  - 2015
TI  - Genome Sequence of Mucoid Pseudomonas aeruginosa Strain FRD1.
PG  - e00376-15
AB  - Pseudomonas aeruginosa is an important opportunistic pathogen. Strain FRD1 is a mucoid isolate
      from the sputum of a cystic fibrosis patient. It has been widely
      studied and has many different phenotypes compared to nonmucoid strains. Here, we
      present the draft genome sequence of P. aeruginosa strain FRD1 to gain insight
      into mucoid isolates.
AU  - Wang D
AU  - Hildebrand F
AU  - Ye L
AU  - Wei Q
AU  - Ma LZ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00376-15.

PMID- 27731370
VI  - 6
DP  - 2016
TI  - Tetrameric structure of the restriction DNA glycosylase R.PabI in complex with nonspecific double-stranded DNA.
PG  - 35197
AB  - R.PabI is a type II restriction enzyme that recognizes the 5'-GTAC-3' sequence and belongs
      to the HALFPIPE superfamily. Although most restriction enzymes cleave
      phosphodiester bonds at specific sites by hydrolysis, R.PabI flips the guanine
      and adenine bases of the recognition sequence out of the DNA helix and hydrolyzes
      the N-glycosidic bond of the flipped adenine in a similar manner to DNA
      glycosylases. In this study, we determined the structure of R.PabI in complex
      with double-stranded DNA without the R.PabI recognition sequence by X-ray
      crystallography. The 1.9 A resolution structure of the complex showed that R.PabI
      forms a tetrameric structure to sandwich the double-stranded DNA and the
      tetrameric structure is stabilized by four salt bridges. DNA binding and DNA
      glycosylase assays of the R.PabI mutants showed that the residues that form the
      salt bridges (R70 and D71) are essential for R.PabI to find the recognition
      sequence from the sea of nonspecific sequences. R.PabI is predicted to utilize
      the tetrameric structure to bind nonspecific double-stranded DNA weakly and slide
      along it to find the recognition sequence.
AU  - Wang D
AU  - Miyazono KI
AU  - Tanokura M
PT  - Journal Article
TA  - Sci. Rep.
JT  - Sci. Rep.
SO  - Sci. Rep. 2016 6: 35197.

PMID- 26221419
VI  - 10
DP  - 2015
TI  - Draft genomic sequence of a selenite-reducing bacterium, Paenirhodobacter enshiensis DW2-9(T).
PG  - 38
AB  - Paenirhodobacter enshiensis is a non-photosynthetic species that belongs to family
      Rhodobacteraceae. Here we report the draft genome sequence of
      Paenirhodobacter enshiensis DW2-9(T) and comparison results to the available
      related genomes. The strain has a 3.4 Mbp genome sequence with G + C content of
      66.82 % and 2781 protein-coding genes. It lacks photosynthetic gene clusters and
      putative proteins necessary in Embden-Meyerhof-Parnas (EMP) pathway, but contains
      proteins in Entner-Doudoroff (ED) pathway instead. It shares 699 common genes
      with nine related Rhodobacteraceae genomes, and possesses 315 specific genes.
AU  - Wang D
AU  - Zhu F
AU  - Zhu X
AU  - Zheng S
AU  - Wang R
AU  - Wang G
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 38.

PMID- 
VI  - 230
DP  - 2005
TI  - Base-displaced intercalated structure of the food mutagen 2-amino-3methylimidazo[4,5-f]quinoline (IQ) in the recognition sequence  of the NarI restriction enzyme, a hotspot for-2 bp deletions.
PG  - U1858-U1859
AB  - 2-Amino-3-methylimidazo[4,5-f]quinoline (IQ) is a prominent member of heterocyclic mutagens
      and carcinogens found during the cooking of meats. The C-G1-G2-C-G3-C-C recognition sequence
      of the NarI restriction enzyme represents a hot spot for -2 frameshift mutations at G3. We
      prepared and purified the oligodeoxynucleotide duplex containing the [IQ]dG adduct positioned
      in the C-[IQ]G3-C NarI context, which was named NarIIQ3. NMR data revealed a base-displaced
      intercalated conformation. Watson-Crick base pairing was perturbed at the adduct site. The
      largest chemical shift perturbations were observed for the base aromatic protons in the
      complementary strand, opposite to the adduct. Chemical shift perturbations were also observed
      for the 31P resonances corresponding to the linkages between C6 and [IQ]G7, [IQ]G7 and C8, G17
      and C18, and C18 and G19, the phosphodiesters around the adduct. There were twenty-one NOEs
      observed between the IQ moiety and DNA protons. The [IQ]G3 aromatic protons had strong NOEs
      with the sugar protons of the opposite C18, G17 and G19 in the complementary strand, and the
      methyl protons of [IQ]G3 showed NOEs to C8 H6, G19 H8, G17 NH1 and G19 NH1. Deoxyribose
      pseudorotational angles (P) were estimated by examining the 3JHH of sugar protons. J1'-2'
      and J1'-2' were measured from ECOSY spectra, while the intensities of H2'-H3' and
      H3'-H4' crosspeaks were determined from DQF-COSY spectra. Molecular dynamics calculations on
      NarIIQ3, restrained by 1H NOEs and J couplings, yielded ensembles of intercalated structures
      in which the modified guanine was in a syn alignment and displaced. NOE intensities calculated
      using complete relaxation matrix theory were in agreement with experimental NOE intensities.
      Structural differences between NarIIQ3 and NarIAF3 could provide insight into the greater
      biological activity of IQ than that of AF. Funded by grant CA-55678.
AU  - Wang F
AU  - Elmquist CE
AU  - Rizzo CJ
AU  - Stone MP
PT  - Journal Article
TA  - ACS Abstracts
JT  - ACS Abstracts
SO  - ACS Abstracts 2005 230: U1858-U1859.

PMID- 29674533
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of the Poly-gamma-Glutamate-Synthesizing Bacterium Bacillus subtilis Bs-115.
PG  - e00197-18
AB  - Bacillus subtilis Bs-115 was isolated from the soil of a corn field in Yutai County, Jinan
      City, Shandong Province, People's Republic of China, and is
      characterized by the efficient synthesis of poly-gamma-glutamate (gamma-PGA),
      with corn saccharification liquid as the sole energy and carbon source during the
      process of gamma-PGA formation. Here, we report the complete genome sequence of
      Bacillus subtilis Bs-115 and the genes associated with poly-gamma-glutamate
      synthesis.
AU  - Wang F
AU  - Gong L
AU  - Zhou L
AU  - Liang J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00197-18.

PMID- 18398463
VI  - 3
DP  - 2008
TI  - Environmental adaptation: genomic analysis of the piezotolerant and psychrotolerant deep-sea iron reducing bacterium Shewanella piezotolerans WP3.
PG  - E1937
AB  - Shewanella species are widespread in various environments. Here, the
      genome sequence of Shewanella piezotolerans WP3, a piezotolerant and
      psychrotolerant iron reducing bacterium from deep-sea sediment was
      determined with related functional analysis to study its environmental
      adaptation mechanisms. The genome of WP3 consists of 5,396,476 base pairs
      (bp) with 4,944 open reading frames (ORFs). It possesses numerous genes or
      gene clusters which help it to cope with extreme living conditions such as
      genes for two sets of flagellum systems, structural RNA modification,
      eicosapentaenoic acid (EPA) biosynthesis and osmolyte transport and
      synthesis. And WP3 contains 55 open reading frames encoding putative
      c-type cytochromes which are substantial to its wide environmental
      adaptation ability. The mtr-omc gene cluster involved in the insoluble
      metal reduction in the Shewanella genus was identified and compared. The
      two sets of flagellum systems were found to be differentially regulated
      under low temperature and high pressure; the lateral flagellum system was
      found essential for its motility and living at low temperature.
AU  - Wang F
AU  - Wang J
AU  - Jian H
AU  - Zhang B
AU  - Li S
AU  - Wang F
AU  - Zeng X
AU  - Gao L
AU  - Bartlett DH
AU  - Yu J
AU  - Hu S
AU  - Xiao X
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2008 3: E1937.

PMID- 28153886
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Deep-Sea Alteromonas sp. Strain V450 Isolated from the Marine Sponge Leiodermatium sp.
PG  - e01508-16
AB  - The proteobacterium Alteromonas sp. strain V450 was isolated from the Atlantic deep-sea sponge
      Leiodermatium sp. Here, we report the draft genome sequence of
      this strain, with a genome size of approx. 4.39 Mb and a G+C content of 44.01%.
      The results will aid deep-sea microbial ecology, evolution, and sponge-microbe
      association studies.
AU  - Wang G
AU  - Barrett NH
AU  - McCarthy PJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01508-16.

PMID- 24077701
VI  - 79
DP  - 2013
TI  - High-Efficiency Thermal Asymmetric Interlaced PCR (hiTAIL-PCR) for Determination of a Highly Degenerated Prophage WO Genome in a Wolbachia Strain Infecting a Fig Wasp Species.
PG  - 7476-7481
AB  - 
AU  - Wang GH
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2013 79: 7476-7481.

PMID- 23473252
VI  - 768
DP  - 2013
TI  - Electrochemical strategy for sensing DNA methylation and DNA methyltransferase activity.
PG  - 76-81
AB  - The present work demonstrates a novel signal-off electrochemical method for the determination
      of DNA methylation and the assay of
      methyltransferase activity using the electroactive complex
      [Ru(NH3)(6)](3+) (RuHex) as a signal transducer. The assay exploits the
      electrostatic interactions between RuHex and DNA strands. Thiolated
      single strand DNA1 was firstly self-assembled on a gold electrode via
      Au-S bonding, followed by hybridization with single strand DNA2 to form
      double strand DNA containing specific recognition sequence of DNA
      adenine methylation MTase and methylation-responsive restriction
      endonuclease Dpn I. The double strand DNA may adsorb lots of
      electrochemical species (Ru(NH3)(6)](3+)) via the electrostatic
      interaction, thus resulting in a high electrochemical signal. In the
      presence of DNA adenine methylation methyltransferase and
      S-adenosyl-L-methionine, the formed double strand DNA was methylated by
      DNA adenine methylation methyltransferase, then the double strand DNA
      can be cleaved by methylation-responsive restriction endonuclease Dpn
      I, leading to the dissociation of a large amount of signaling probes
      from the electrode. As a result, the adsorption amount of RuHex
      reduced, resulting in a decrease in electrochemical signal. Thus, a
      sensitive electrochemical method for detection of DNA methylation is
      proposed. The proposed method yielded a linear response to
      concentration of Dam MTase ranging from 0.25 to IOU mL(-1) with a
      detection limit of 0.18 U mL(-1) (S/N = 3), which might promise this
      method as a good candidate for monitoring DNA methylation in the
      future.
AU  - Wang GL
AU  - Zhou LY
AU  - Luo HQ
AU  - Li NB
PT  - Journal Article
TA  - Anal. Chim. Acta
JT  - Anal. Chim. Acta
SO  - Anal. Chim. Acta 2013 768: 76-81.

PMID- 26139723
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Give, Isolated from an Imported Chili Powder Product.
PG  - e00726-15
AB  - We report the genome sequence of Salmonella enterica subsp. enterica serovar Give
      (CFSAN012622), isolated from imported chili powder in 2014. This genome contains
      genes previously reported to be specific only to S. enterica serovar Enteritidis.
      This strain shows a unique pulsed-field gel electrophoresis (PFGE) pattern
      clustering with serovar Enteritidis (JEG X01.0005).
AU  - Wang H
AU  - Chen Y
AU  - Ayers S
AU  - Melka D
AU  - Laasri A
AU  - Payne JS
AU  - Zheng J
AU  - Son I
AU  - Timme R
AU  - Kastanis G
AU  - Hammack TS
AU  - Strain E
AU  - Allard MW
AU  - Evans PS
AU  - Brown EW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00726-15.

PMID- 21813453
VI  - 39
DP  - 2011
TI  - Comparative characterization of the PvuRts1I family of restriction enzymes and their application in mapping genomic 5-hydroxymethylcytosine.
PG  - 9294-9305
AB  - PvuRts1I is a modification-dependent restriction endonuclease that recognizes
      5-hydroxymethylcytosine (5hmC) as well as
      5-glucosylhydroxymethylcytosine (5ghmC) in double-stranded DNA. Using
      PvuRts1I as the founding member, we define a family of homologous proteins
      with similar DNA modification-dependent recognition properties. At the
      sequence level, these proteins share a few uniquely conserved features. We
      show that these enzymes introduce a double-stranded cleavage at the
      3'-side away from the recognized modified cytosine. The distances between
      the cleavage sites and the modified cytosine are fixed within a narrow
      range, with the majority being 11-13 nt away in the top strand and 9-10 nt
      away in the bottom strand. The recognition sites of these enzymes
      generally require two cytosines on opposite strand around the cleavage
      sites, i.e. 5'-CN(11-13) downward arrowN(9-10)G-3'/3'-GN(9-10) downward
      arrowN(11-13)C-5', with at least one cytosine being modified for efficient
      cleavage. As one potential application for these enzymes is to provide
      useful tools for selectively mapping 5hmC sites, we have compared the
      relative selectivity of a few PvuRts1I family members towards different
      forms of modified cytosines. Our results show that the inherently
      different relative selectivity towards modified cytosines can have
      practical implications for their application. By using AbaSDFI, a PvuRts1I
      homolog with the highest relative selectivity towards 5ghmC, to analyze
      rat brain DNA, we show it is feasible to map genomic 5hmC sites close to
      base resolution. Our study offers unique tools for determining more
      accurate hydroxymethylomes in mammalian cells.
AU  - Wang H
AU  - Guan S
AU  - Quimby A
AU  - Cohen-Karni D
AU  - Pradhan S
AU  - Wilson G
AU  - Roberts RJ
AU  - Zhu Z
AU  - Zheng Y
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2011 39: 9294-9305.

PMID- 22275098
VI  - 194
DP  - 2012
TI  - Genome Sequence of Deep-Sea Manganese-Oxidizing Bacterium Marinobacter manganoxydans MnI7-9.
PG  - 899-900
AB  - Here we report the draft genome of Marinobacter manganoxydans MnI7-9, isolated from a deep-sea
      hydrothermal vent in the Indian Ocean and capable
      of oxidizing manganese even when there is a very high concentration of
      Mn(2+). The strain also displayed high resistance and adsorption ability
      toward many metal(loid)s.
AU  - Wang H
AU  - Li H
AU  - Shao Z
AU  - Liao S
AU  - Johnstone L
AU  - Rensing C
AU  - Wang G
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 899-900.

PMID- 25908130
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Ruminoclostridium sp. Ne3, Clostridia from an Enrichment Culture Obtained from Australian Subterranean Termite, Nasutitermes exitiosus.
PG  - e00305-15
AB  - The draft genome sequence of Ruminoclostridium sp. Ne3 was reconstructed from the metagenome
      of a hydrogenogenic microbial consortium growing on xylan. The
      organism is likely the primary hemicellulose degrader within the consortium.
AU  - Wang H
AU  - Lin H
AU  - Tran-Dinh N
AU  - Li D
AU  - Greenfield P
AU  - Midgley DJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00305-15.

PMID- 25908129
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Clostridium sp. Ne2, Clostridia from an Enrichment Culture Obtained from Australian Subterranean Termite, Nasutitermes exitiosus.
PG  - e00304-15
AB  - The draft genome sequence of Clostridium sp. Ne2 was reconstructed from a metagenome of a
      hydrogenogenic microbial consortium. The organism is most closely
      related to Clostridium magnum and is a strict anaerobe that is predicted to
      ferment a range of simple sugars.
AU  - Wang H
AU  - Lin H
AU  - Tran-Dinh N
AU  - Li D
AU  - Greenfield P
AU  - Midgley DJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00304-15.

PMID- 25908128
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Clostridium beijerinckii Ne1, Clostridia from an Enrichment Culture Obtained from Australian Subterranean Termite, Nasutitermes  exitiosus.
PG  - e00303-15
AB  - The draft genome of Clostridium beijerinckii strain Ne1 was reconstructed from the metagenomic
      sequence of a mixed-microbial consortium that produced
      commercially significant quantities of hydrogen from xylan as a sole feedstock.
      The organism possesses relatively limited hemicellulolytic capacity and likely
      requires the action of other organisms to completely degrade xylan.
AU  - Wang H
AU  - Lin H
AU  - Tran-Dinh N
AU  - Li D
AU  - Greenfield P
AU  - Midgley DJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00303-15.

PMID- 23148582
VI  - 13
DP  - 2012
TI  - Genome-derived insights into the biology of the hepatotoxic bloom-forming cyanobacterium Anabaena sp. strain 90.
PG  - 613
AB  - ABSTRACT: BACKGROUND: Cyanobacteria can form massive toxic blooms in fresh and
      brackish bodies of water and are frequently responsible for the poisoning of
      animals and pose a health risk for humans. Anabaena is a genus of filamentous
      diazotrophic cyanobacteria commonly implicated as a toxin producer in blooms in
      aquatic ecosystems throughout the world. The biology of bloom-forming
      cyanobacteria is poorly understood at the genome level. RESULTS: Here, we report
      the complete sequence and comprehensive annotation of the bloom-forming Anabaena
      sp. strain 90 genome. It comprises two circular chromosomes and three plasmids
      with a total size of 5.3 Mb, encoding a total of 4,738 genes. The genome is
      replete with mobile genetic elements. Detailed manual annotation demonstrated
      that almost 5% of the gene repertoire consists of pseudogenes. A further 5% of
      the genome is dedicated to the synthesis of small peptides that are the products
      of both ribosomal and nonribosomal biosynthetic pathways. Inactivation of the
      hassallidin (an antifungal cyclic peptide) biosynthetic gene cluster through a
      deletion event and a natural mutation of the buoyancy-permitting gvpG gas vesicle
      gene were documented. The genome contains a large number of genes encoding
      restriction-modification systems. Two novel excision elements were found in the
      nifH gene that is required for nitrogen fixation. CONCLUSIONS: Genome analysis
      demonstrated that this strain invests heavily in the production of bioactive
      compounds and restriction-modification systems. This well-annotated genome
      provides a platform for future studies on the ecology and biology of these
      important bloom-forming cyanobacteria.
AU  - Wang H
AU  - Sivonen K
AU  - Rouhiainen L
AU  - Fewer DP
AU  - Lyra C
AU  - Rantala-Ylinen A
AU  - Vestola J
AU  - Jokela J
AU  - Rantasarkka K
AU  - Li Z
AU  - Liu B
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2012 13: 613.

PMID- 24371202
VI  - 1
DP  - 2013
TI  - Genome Sequence of Sporolactobacillus laevolacticus DSM442, an Efficient Polymer-Grade D-Lactate Producer from Agricultural Waste Cottonseed as a Nitrogen  Source.
PG  - e01100-13
AB  - Sporolactobacillus laevolacticus DSM442 is an efficient polymer-grade d-lactic acid producer
      from low-cost agricultural waste cottonseed powder as the sole
      nitrogen source. Here we present a 3.59-Mb assembly of its genome sequence, which
      might provide useful information to further improve the strain for higher
      production titers.
AU  - Wang H
AU  - Wang L
AU  - Ju J
AU  - Yu B
AU  - Ma Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01100-13.

PMID- 27445384
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Salmonella enterica subsp. enterica Serovars Typhimurium and Nottingham Isolated from Food Products.
PG  - e00699-16
AB  - A quantitative real-time PCR (qPCR) designed to detect Salmonella enterica subsp. enterica
      serovar Enteritidis, targeting the sdf gene, generated positive results
      for S. enterica subsp. enterica serovar Typhimurium (CFSAN033950) and S. enterica
      subsp. enterica serovar Nottingham (CFSAN006803) isolated from food samples. Both
      strains show pulsed-field gel electrophoresis (PFGE) patterns distinct from those
      of S Enteritidis. Here, we report the genome sequences of these two strains.
AU  - Wang H
AU  - Zheng J
AU  - Ayers S
AU  - Melka DC
AU  - Curry PE
AU  - Payne JS
AU  - Laasri A
AU  - Wang C
AU  - Hammack TS
AU  - Brown EW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00699-16.

PMID- 18062262
VI  - 47
DP  - 2007
TI  - Cloning and analysis of the Vibrio harveyi dam gene.
PG  - 855-859
AB  - The DNA adenine methylase (dam) gene was cloned by degenerate PCR from Vibrio harveyi strain
      T4. The gene was 840bp in length and encoded a
      putative protein of 279 amino acids that shared relatively high
      homology with the Dam of other Vibrias, especially with that of V.
      parahaemolyticus (96% in identity). The V. harveyi dam gene was
      subcloned into plasmid pBR322 and the resulting plasmid pBD was
      introduced into the E. coli strain ER2925 in which the dam gene had
      been knocked out. Dpn I, Dpn II, and Sau3A I restriction enzyme
      analysis of the genomic DNA of ER2925 transformed with p13D indicated
      that the cloned V. harveyi dam gene could functionally complement the
      E. coli dam mutant and methylate E. coli chromosome at the GATC sites.
      The 3251 bp upstream region of V. harveyi dam was obtained by genome
      walking and analyzed at the sequence level. It was found that this 3251
      bp region contained two complete open reading frames (ORF) : one was of
      1101 bp in length and the other was of 1503 bp in length. The predicted
      amino acid sequence of ORF1101 shared 91% identity with the
      3-dehydroquinate synthase of V. parahaemolyticus. The amino acid
      sequence of ORF1503 shared 80% identity with V. parahaemolylicus DamX.
      A truncated ORF was found at the upstream of ORF1101, encoding 169
      amino acids that shared 94% identity with the shikimate kinase of V.
      parahaemolyticus. These three genes, together with dam, were arranged
      in the order of shikimate kinase-3-dehydroquinate synthase-damX-dam.
      The region immediate upstream of the V. harveyi dam structural gene was
      cloned in three fragments of different length: 78bp, 112 bp and 477bp
      (named P78, P112, and P477, respectively) and tested for promoter
      activity. The results showed that, while all the three fragments had
      detectable promoter activities, the activity of P78 appeared to be
      higher than that of P-112 and P-477.
AU  - Wang H-L
AU  - Wang H-R
AU  - Zhang W-W
AU  - Sun L
PT  - Journal Article
TA  - Wei Sheng Wu Xue Bao
JT  - Wei Sheng Wu Xue Bao
SO  - Wei Sheng Wu Xue Bao 2007 47: 855-859.

PMID- 25908123
VI  - 3
DP  - 2015
TI  - Genome Sequences of Three Helicobacter pylori Strains from Patients with Gastric  Mucosa-Associated Lymphoid Tissue Lymphoma.
PG  - e00229-15
AB  - Most of the published complete genome sequences of Helicobacter pylori strains are limited to
      clinical isolates associated with gastritis, peptic ulcers, or
      gastric cancer. The genome sequences of three H. pylori strains isolated from
      patients with gastric mucosa-associated lymphoid tissue (MALT) lymphoma are
      presented here to facilitate studies of H. pylori-associated MALT
      lymphomagenesis.
AU  - Wang HC
AU  - Cheng FC
AU  - Wu MS
AU  - Shu HY
AU  - Sun HS
AU  - Wang YC
AU  - Su IJ
AU  - Wu CJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00229-15.

PMID- 24926060
VI  - 2
DP  - 2014
TI  - Genome Sequence of Aeromonas taiwanensis LMG 24683T, a Clinical Wound Isolate from Taiwan.
PG  - e00579-14
AB  - Aeromonas taiwanensis was first described in 2010 on the basis of one clinical wound isolate
      (strain LMG 24683(T) = A2-50(T) = CECT 7403(T)) from Taiwan. We
      present here the genome sequence of A. taiwanensis LMG 24683(T), which carries
      several genes encoding virulence determinants and Ambler class C and D
      beta-lactamases.
AU  - Wang HC
AU  - Ko WC
AU  - Shu HY
AU  - Chen PL
AU  - Wang YC
AU  - Wu CJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00579-14.

PMID- 22822424
VI  - 3
DP  - 2012
TI  - Transducing methyltransferase activity into electrical signals in a carbon nanotube-DNA device.
PG  - 62-65
AB  - This study creates a device where the DNA is electronically integrated to serve as both the
      biological target and electrical transducer in a CNT-DNA-CNT device. We detect DNA binding and
      methylation by the methyltransferase M.SssI at the single molecule level. We demonstrate
      sequence-specific, reversible binding of M.SssI and protein-catalyzed methylation that alters
      the protein-binding affinity of the device. This device, which relies on the exquisite
      electrical sensitivity of DNA, represents a unique route for the specific, single molecule
      detection of enzymatic activity.
AU  - Wang HF
AU  - Muren NB
AU  - Ordinario D
AU  - Gorodetsky AA
AU  - Barton JK
AU  - Nuckolls C
PT  - Journal Article
TA  - Chem. Sci.
JT  - Chem. Sci.
SO  - Chem. Sci. 2012 3: 62-65.

PMID- 19236003
VI  - 48
DP  - 2009
TI  - 6-Thioguanine Perturbs Cytosine Methylation at the CpG Dinucleotide Site by DNA Methyltransferases in Vitro and Acts as a DNA Demethylating Agent in Vivo.
PG  - 2290-2299
AB  - Thiopurines are among the most successful chemotherapeutic agents for treating a number of
      human diseases including acute lymphoblastic
      leukemia. The mechanisms through which the thiopurines elicit their
      cytotoxic effects remain unclear. We postulate that the incorporation
      of 6-thioguanine into the CpG site may perturb the
      methyltransferase-mediated cytosine methylation at this site, thereby
      interfering with the epigenetic pathways of gene regulation. To gain
      biochemical evidence for this hypothesis, we assessed, by using a
      restriction enzyme digestion coupled with LC-MS/MS method, the impact
      of 6-thioguanine on cytosine methylation mediated by two DNA
      methyltransferases, human DNMT1 and bacterial HpaII. Our results
      revealed that the incorporation of 6-thioguanine into the CpG site
      could affect the methylation of the cytosine residue by both
      methyltransferases and the effect on cytosine methylation is dependent
      on the position of 6-thioguanine with respect to the cytosine to be
      methylated. The presence of 6-thioguanine at the methylated CpG site
      enhanced the DNMT1-mediated methylation of the opposing cytosine in the
      complementary strand, whereas the presence of 6-thioguanine at the
      unmethylated CpG site abolished almost completely the methylation of
      its 5' adjacent cytosine by both DNMT1 and HpaII. We further
      demonstrated that the treatment of Jurkat T cells, which were derived
      from acute lymphoblastic leukemia, with 6-thioguanine could result in
      an appreciable drop in the level of global cytosine methylation. These
      results showed that 6-thioguanine, after being incorporated into DNA,
      may perturb the epigenetic pathway of gene regulation.
AU  - Wang HX
AU  - Wang YS
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2009 48: 2290-2299.

PMID- 16751568
VI  - 72
DP  - 2006
TI  - Identification of a DNA methyltransferase gene carried on a pathogenicity island-like element (VPAI) in Vibrio parahaemolyticus and  its prevalence among clinical and environmental isolates.
PG  - 4455-4460
AB  - In this study we identified a putative virulence-associated DNA methyltransferase (MTase) gene
      carried on a novel 22.79-kb
      pathogenicity island-like element (VPAI) in V. parahaemolyticus. The V.
      parahaemolyticus MTase gene was shown by PCR to be prevalent (> 98%) in
      pandemic thermostable direct hemolysin gene-positive isolates, which
      suggests that VPAI may confer unique virulence traits to pandemic
      strains of V. parahaemolyticus.
AU  - Wang HZ
AU  - Wong MML
AU  - O'Toole D
AU  - Mak MMH
AU  - Wu RSS
AU  - Kong RYC
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2006 72: 4455-4460.

PMID- 29472327
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Methylocella silvestris TVC, a Facultative Methanotroph  Isolated from Permafrost.
PG  - e00040-18
AB  - Permafrost environments play a crucial role in global carbon and methane cycling. We report
      here the draft genome sequence of Methylocella silvestris TVC, a new
      facultative methanotroph strain, isolated from the Siksik Creek catchment in the
      continuous permafrost zone of Inuvik (Northwest Territories, Canada).
AU  - Wang J
AU  - Geng K
AU  - Farhan UlHM
AU  - Crombie A
AU  - Street LE
AU  - Wookey PA
AU  - Ma K
AU  - Murrell JC
AU  - Pratscher J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00040-18.

PMID- 19098913
VI  - 41
DP  - 2009
TI  - The lysine demethylase LSD1 (KDM1) is required for maintenance of global DNA methylation.
PG  - 125-129
AB  - Histone methylation and DNA methylation cooperatively regulate chromatin structure and gene
      activity. How these two systems coordinate with each
      other remains unclear. Here we study the biological function of
      lysine-specific demethylase 1 (LSD1, also known as KDM1 and AOF2), which
      has been shown to demethylate histone H3 on lysine 4 (H3K4) and lysine 9
      (H3K9). We show that LSD1 is required for gastrulation during mouse
      embryogenesis. Notably, targeted deletion of the gene encoding LSD1
      (namely, Aof2) in embryonic stem (ES) cells induces progressive loss of
      DNA methylation. This loss correlates with a decrease in DNA
      methyltransferase 1 (Dnmt1) protein, as a result of reduced Dnmt1
      stability. Dnmt1 protein is methylated in vivo, and its methylation is
      enhanced in the absence of LSD1. Furthermore, Dnmt1 can be methylated by
      Set7/9 (also known as KMT7) and demethylated by LSD1 in vitro. Our
      findings suggest that LSD1 demethylates and stabilizes Dnmt1, thus
      providing a previously unknown mechanistic link between the histone and
      DNA methylation systems.
AU  - Wang J
AU  - Hevi S
AU  - Kurash JK
AU  - Lei H
AU  - Gay F
AU  - Bajko J
AU  - Su H
AU  - Sun W
AU  - Chang H
AU  - Xu G
AU  - Gaudet F
AU  - Li E
AU  - Chen T
PT  - Journal Article
TA  - Nat. Genet.
JT  - Nat. Genet.
SO  - Nat. Genet. 2009 41: 125-129.

PMID- 21378184
VI  - 193
DP  - 2011
TI  - Natural Transformation of Myxococcus xanthus.
PG  - 2122-2132
AB  - Myxococcus xanthus belongs to the delta class of the proteobacteria and is notable for its
      complex life-style with social behaviors and
      relatively large genome. Although previous observations have suggested
      the existence of horizontal gene transfer in M. xanthus, its ability to
      take up exogenous DNA via natural transformation has not been
      experimentally demonstrated. In this study, we achieved natural
      transformation in M. xanthus using the autonomously replicating
      myxobacterial plasmid pZJY41 as donor DNA. M. xanthus exopolysaccharide
      (EPS) was shown to be an extracellular barrier for transformation.
      Cells deficient in EPS production, e. g., mutant strains carrying Delta
      difA or Delta epsA, became naturally transformable. Among the inner
      barriers to transformation were restriction-modification systems in M.
      xanthus, which could be partially overcome by methylating DNA in vitro
      using cell extracts of M. xanthus prior to transformation. In addition,
      the incubation time of DNA with cells and the presence of divalent
      magnesium ion affected transformation frequency of M. xanthus.
      Furthermore, we also observed a potential involvement of the type IV
      pilus system in the DNA uptake machinery of M. xanthus. The natural
      transformation was totally eliminated in the Delta pilQ/epsA and Delta
      tgl/epsA mutants, and null mutation of pilB or pilC in an Delta epsA
      background diminished the transformation rate. Our study, to the best
      of our knowledge, provides the first example of a naturally
      transformable species among deltaproteobacteria.
AU  - Wang J
AU  - Hu W
AU  - Lux R
AU  - He X
AU  - Li Y
AU  - Shi W
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 2122-2132.

PMID- 27795232
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Escherichia coli 26R 793, a Plasmid-Free Recipient Strain Commonly Used in Conjugation Assays.
PG  - e00707-16
AB  - Here, we report the draft genome sequence of the lactose-negative, rifampin-resistant,
      Escherichia coli strain 26R 793. This isolate has been widely
      used in conjugation experiments as a general recipient strain.
AU  - Wang J
AU  - Hurley D
AU  - McGrath K
AU  - Bai L
AU  - Hachler H
AU  - Stephan R
AU  - Fanning S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00707-16.

PMID- 15661140
VI  - 332
DP  - 2005
TI  - Complete genome sequence of bacteriophage T5.
PG  - 45-65
AB  - The 121,752-bp genome sequence of bacteriophage T5 was determined; the
      linear, double-stranded DNA is nicked in one of the strands and has large
      direct terminal repeats of 10,139 bp (8.3%) at both ends. The genome
      structure is consistently arranged according to its lytic life cycle. Of
      the 168 potential open reading frames (ORFs), 61 were annotated; these
      annotated ORFs are mainly enzymes involved in phage DNA replication,
      repair, and nucleotide metabolism. At least five endonucleases that
      believed to help inducing nicks in T5 genomic DNA, and a DNA ligase gene
      was found to be split into two separate ORFs. Analysis of T5 early
      promoters suggests a probable motif AAA{3, 4 T}nTTGCTT{17, 18
      n}TATAATA{12, 13 W}{10 R} for strong promoters that may strengthen the
      step modification of host RNA polymerase, and thus control transcription
      of phage DNA. The distinct protein domain profile and a mosaic genome
      structure suggest an origin from the common genetic pool.
AU  - Wang J
AU  - Jiang Y
AU  - Vincent M
AU  - Sun Y
AU  - Yu H
AU  - Wang J
AU  - Bao Q
AU  - Kong H
AU  - Hu S
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 2005 332: 45-65.

PMID- 9380496
VI  - 25
DP  - 1997
TI  - Purification, biochemical characterization and protein-DNA interactions of the I-CreI endonuclease produced in Escherichia coli.
PG  - 3767-3776
AB  - I-CreI is a member of the LAGLI-DADG family of homing nucleases; however, unlike most members
      of this family it contains only a single copy of this signature motif.  I-CreI was
      over-expressed in Escherichia coli, and a simple purification protocol developed that gave
      reasonably pure protein in high yield.  Size-exclusion chromatography and chemical
      cross-linking indicated that the protein is a dimer in solution.  DNA cleavage by I-CreI was
      absolutely dependent on Mg2+ (or Mn2+), and was inhibited by monovalent cations.  I-CreI
      displayed a surprisingly high temperature optimum (>50oC), with full activity occurring even
      at 70oC.  Interestingly, SDS was needed for efficient release of the cleavage products from
      the protein, indicating formation of very stable DNA-protein complexes.  In contrast to these
      robust characteristics, purified I-CreI was unstable; however, it could be stabilized by the
      addition of either target or non-target DNA.  Mobility shift assays revealed that I-CreI binds
      to DNA in the absence of Mg2+.  Hydroxyl radical footprinting showed that I-CreI strongly
      protected the backbone of a continuous stretch of at least 12 nt on each strand that were
      shifted, relative to each other, by 2 bp in the 3' direction.  Methylation protection and
      interference analyses were also performed, and together with the hydroxyl radical
      footprinting, indicate that I-CreI binds in both the major and minor grooves of its target
      DNA.
AU  - Wang J
AU  - Kim H-H
AU  - Yuan X
AU  - Herrin DL
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1997 25: 3767-3776.

PMID- 24435862
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of 11 Staphylococcus epidermidis Strains Isolated from Wild Mouse Species.
PG  - e01148-13
AB  - We report here the draft genome sequences of 11 strains of Staphylococcus epidermidis, a
      common bacterium inhabiting the skin of humans and other animals.
      These isolates, obtained from five mouse species, provide valuable information on
      the native Staphylococcus spp. of this important model organism and form a basis
      for studying host-bacterial interactions in their natural environment.
AU  - Wang J
AU  - Kuenzel S
AU  - Baines JF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01148-13.

PMID- 29103683
VI  - 210
DP  - 2017
TI  - Complete genetic analysis of a Salmonella enterica serovar Indiana isolate accompanying four plasmids carrying mcr-1, ESBL and other resistance genes in China.
PG  - 142-146
AB  - One mcr-1-carrying Salmonella enterica serovar Indiana strain D90, was identi and #64257;ed
      from 1320 Salmonella enterica isolates from poultry slaughterhouse in 2012 in China. The
      objective of this study was to verify the transferability of the mcr-1 gene and also
      completely characterize the sequence of the strain at the whole-genome level. Broth matting
      assays were carried out to detect the transferability and whole-genome sequencing (WGS) of S.
      enterica serovar Indiana D90 was performed using the PacBio RS II system. Open reading frames
      were assigned using Rapid Annotation using Subsystem Technology (RAST) and analysed by BLASTn
      and BLASTp. Salmonella Pathogenisity Islands (SPIs) were annotated by SPIFinder platform. The
      complete genome sequence of S. enterica serovar Indiana D90 contained a circular 4,779,514-bp
      chromosome and four plasmids. Genome analysis and sequencing revealed that 24 multi-drug
      resistance (MDR) genes were located on plasmids. The largest plasmid pD90-1, was found to be
      of an IncHI2/HI2A/Q1/N type that encoded a blaCTX-M-65 gene along with 20 additional
      antimicrobial resistance genes. A 60.5-kbp IncI2 plasmid pD90-2 contained a nikA-nikB-mcr-1
      genetic structure, that can be successfully transferred to E. coli and S. enterica serovar
      Typhimurium at low transfer rates. Interestingly, comparative sequence analysis revealed the
      plasmids pD90-1 and pD90-2 showed considerable nucleotide similarity to pHNSHP45-2 and
      pHNSHP45, respectively. Moreover, the genome and the plasmid pD90-2 also showed high
      similarity to one carbapenem resistant S. enterica serovar Indiana strain, C629 and its
      plasmid pC629, respectively. This is the  and #64257;rst report of the complete nucleotide
      sequence of one mcr-1-carrying MDR S. enterica serovar Indiana strain.
AU  - Wang J
AU  - Li X
AU  - Li J
AU  - Hurley D
AU  - Bai X
AU  - Yu Z
AU  - Cao Y
AU  - Wall E
AU  - Fanning S
AU  - Bai L
PT  - Journal Article
TA  - Vet. Microbiol.
JT  - Vet. Microbiol.
SO  - Vet. Microbiol. 2017 210: 142-146.

PMID- 24558241
VI  - 2
DP  - 2014
TI  - Genome Sequence of Staphylococcus aureus Strain LCT-SA67, a Space Flight Strain with Altered Carbon Source Utilization Properties.
PG  - e00095-14
AB  - An increasing number of studies have confirmed that space flight environments can have a
      significant effect on a variety of microbial properties. To explore the
      effect of these environments on Staphylococcus aureus, we present the draft
      genome sequence of an S. aureus strain, named LCT-SA67, which was isolated after
      space flight.
AU  - Wang J
AU  - Li Y
AU  - Guo J
AU  - Zhang X
AU  - Guo Y
AU  - Chang D
AU  - Li T
AU  - Xu G
AU  - Dai W
AU  - Liu C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00095-14.

PMID- 22815443
VI  - 194
DP  - 2012
TI  - Whole-Genome Sequence of Staphylococcus aureus Strain LCT-SA112.
PG  - 4124
AB  - Staphylococcus aureus is a facultative anaerobic Gram-positive coccal bacterium.  S. aureus is
      the most common species of Staphylococcus to cause staphylococcal
      infections, which are very common in clinical medicine. Here we report the genome
      sequence of S. aureus strain LCT-SA112, which was isolated from S. aureus subsp.
      aureus CGMCC 1.230.
AU  - Wang J
AU  - Liu Y
AU  - Wan D
AU  - Fang X
AU  - Li T
AU  - Guo Y
AU  - Chang D
AU  - Su L
AU  - Wang Y
AU  - Zhao J
AU  - Liu C
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4124.

PMID- 25716827
VI  - 7
DP  - 2015
TI  - Insights on the emergence of Mycobacterium tuberculosis from the analysis of Mycobacterium kansasii.
PG  - 856-870
AB  - By phylogenetic analysis, Mycobacterium kansasii is closely related to Mycobacterium
      tuberculosis. Yet, although both organisms cause pulmonary disease,
      M. tuberculosis is a global health menace, whereas M. kansasii is an
      opportunistic pathogen. To illuminate the differences between these organisms, we
      have sequenced the genome of M. kansasii ATCC 12478 and its plasmid (pMK12478)
      and conducted side-by-side in vitro and in vivo investigations of these two
      organisms. The M. kansasii genome is 6,432,277 bp, more than 2 Mb longer than
      that of M. tuberculosis H37Rv, and the plasmid contains 144,951 bp. Pairwise
      comparisons reveal conserved and discordant genes and genomic regions. A notable
      example of genomic conservation is the virulence locus ESX-1, which is intact and
      functional in the low-virulence M. kansasii, potentially mediating phagosomal
      disruption. Differences between these organisms include a decreased predicted
      metabolic capacity, an increased proportion of toxin-antitoxin genes, and the
      acquisition of M. tuberculosis-specific genes in the pathogen since their common
      ancestor. Consistent with their distinct epidemiologic profiles, following
      infection of C57BL/6 mice, M. kansasii counts increased by less than 10-fold over
      6 weeks, whereas M. tuberculosis counts increased by over 10,000-fold in just 3
      weeks. Together, these data suggest that M. kansasii can serve as an image of the
      environmental ancestor of M. tuberculosis before its emergence as a professional
      pathogen, and can be used as a model organism to study the switch from an
      environmental opportunistic pathogen to a professional host-restricted pathogen.
AU  - Wang J
AU  - McIntosh F
AU  - Radomski N
AU  - Dewar K
AU  - Simeone R
AU  - Enninga J
AU  - Brosch R
AU  - Rocha EP
AU  - Veyrier FJ
AU  - Behr MA
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2015 7: 856-870.

PMID- 26089406
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Escherichia coli O145:NM Bacteriophage vB_EcoM_AYO145A, a New Member of O1-Like Phages.
PG  - e00539-15
AB  - Previously, bacteriophage vB_EcoM_AYO145A, which lyses Shiga toxin-producing Escherichia coli
      O145:NM, was classified as an O1-like virus of the Myoviridae
      family. Here, we report the complete genome sequence of this phage and a
      comparative genomic analysis with other known O1-like phages.
AU  - Wang J
AU  - Niu YD
AU  - Chen J
AU  - McAllister TA
AU  - Stanford K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00539-15.

PMID- 30231900
VI  - 19
DP  - 2018
TI  - Comparative genome analysis of jujube witches'-broom Phytoplasma, an obligate pathogen that causes jujube witches'-broom disease.
PG  - 689
AB  - BACKGROUND: JWB phytoplasma is a kind of insect-transmitted and uncultivable
      bacterial plant pathogen causeing a destructive Jujube disease. To date, no
      genome information about JWB phytoplasma has been published, which hindered its
      characterization at genomic level. To understand its pathogenicity and ecology,
      the genome of a JWB phytoplasma isolate jwb-nky was sequenced and compared with
      other phytoplasmas enabled us to explore the mechanisms of genomic rearrangement.
      RESULTS: The complete genome sequence of JWB phytoplasma (jwb-nky) was
      determined, which consisting of one circular chromosome of 750,803 bp with a GC
      content of 23.3%. 694 protein-encoding genes, 2 operons for rRNA genes and 31
      tRNA genes as well as 4 potential mobile units (PMUs) containing clusters of DNA
      repeats were identified. Based on PHIbaes analysis, a large number of genes were
      genome-specific and approximately 13% of JWB phytoplasma genes were predicted to
      be associated with virulence. Although transporters for maltose,
      dipeptides/oligopeptides, spermidine/putrescine, cobalt, Mn/Zn and methionine
      were identified, KEGG pathway analysis revealed the reduced metabolic
      capabilities of JWB phytoplasma. Comparative genome analyses between JWB
      phytoplasma and other phytoplasmas shows the occurrence of large-scale gene
      rearrangements. The low synteny with other phytoplasmas indicated that the
      expansion of multiple gene families/duplication probably occurred separately
      after differentiation. CONCLUSIONS: In this study, the complete genome sequence
      of a JWB phytoplasma isolate jwb-nky that causing JWB disease was reported for
      the first time and a number of species-specific genes were identified in the
      genome. The study enhanced our understandings about genomic basis and the
      pathogenicity mechanism of this pathogen, which will aid in the development of
      improved strategies for efficient management of JWB diseases.
AU  - Wang J
AU  - Song L
AU  - Jiao Q
AU  - Yang S
AU  - Gao R
AU  - Lu X
AU  - Zhou G
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2018 19: 689.

PMID- 24920651
VI  - 69
DP  - 2014
TI  - Nucleotide sequences of 16 transmissible plasmids identified in nine multidrug-resistant Escherichia coli isolates expressing an ESBL phenotype isolated from food-producing animals and healthy humans.
PG  - 2658-2668
AB  - OBJECTIVES: Nine extended-spectrum beta-lactamase (ESBL)-producing Escherichia
      coli isolated from healthy humans and food-producing animals were found to
      transfer their cefotaxime resistance marker at high frequency in laboratory
      conjugation experiments. The objective of this study was to completely
      characterize 16 transmissible plasmids that were detected in these bacterial
      isolates. METHODS: The nucleotide sequences of all 16 plasmids were determined
      from transconjugants using next-generation sequencing technology. Open reading
      frames were assigned using Rapid Annotation using Subsystem Technology and
      analysed by BLASTn and BLASTp. The standard method was used for plasmid
      multilocus sequence typing (pMLST) analysis. Plasmid structures were subsequently
      confirmed by PCR amplification of selected regions. RESULTS: The complete
      circularized nucleotide sequence of 14 plasmids was determined, along with that
      of a further two plasmids that could not be confirmed as closed. These ranged in
      size from 1.8 to 166.6 kb. Incompatibility groups and pMLSTs identified included
      IncI1/ST3, IncI1/ST36, IncN/ST1, IncF and IncB/O, and those of the same Inc types
      presented a similar backbone structure despite being isolated from different
      sources. Eight plasmids contained bla(CTX-M-1) genes that were associated with
      either ISEcp1 or IS26 insertion sequence elements. Six plasmids isolated from
      humans and chickens were identical or closely related to the IncI1 reference
      plasmid, R64. CONCLUSIONS: These data, based on comparative sequence analysis,
      highlight the successful spread of blaESBL-harbouring plasmids of different Inc
      types among isolates of human and food-producing animal origin and provide
      further evidence for potential dissemination routes.
AU  - Wang J
AU  - Stephan R
AU  - Power K
AU  - Yan Q
AU  - Hachler H
AU  - Fanning S
PT  - Journal Article
TA  - J. Antimicrob. Chemother.
JT  - J. Antimicrob. Chemother.
SO  - J. Antimicrob. Chemother. 2014 69: 2658-2668.

PMID- 27795270
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Leifsonia xyli subsp. xyli Strain gdw1.
PG  - e01128-16
AB  - Here, we report the draft genome sequence of Leifsonia xyli subsp. xyli strain gdw1, isolated
      from the stem of Badila sugarcane located at the Guangdong Key
      Laboratory for Crops Genetic Improvement (Guanzhou, China), that causes ratoon
      stunting disease of sugarcane. The de novo genome of Leifsonia xyli subsp. xyli
      was assembled with 48 scaffolds and a G+C content of 67.68%, and contained 2.6 Mb
      bp and 2,838 coding sequences.
AU  - Wang J
AU  - Wang L
AU  - Cao G
AU  - Zhang M
AU  - Guo Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01128-16.

PMID- 26847894
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Brevibacillus choshinensis HPD52T (DSM 8552), a Bacterial Host for Efficient Expression of Heterologous Proteins.
PG  - e01688-15
AB  - Brevibacillus choshinensis HPD52(T) (DSM 8552) is a Gram-positive, spore-forming, and
      protein-producing bacterium. Here, we report the 6.28-Mb draft genome
      sequence of B. choshinensis HPD52(T), which will promote its application and
      provide useful information for genomic taxonomy and phylogenomics of
      Bacillus-like bacteria.
AU  - Wang JP
AU  - Liu B
AU  - Liu GH
AU  - Che JM
AU  - Chen Z
AU  - Chen M
AU  - Shi H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01688-15.

PMID- 26659687
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Bacillus marisflavi TF-11T (JCM 11544), a Carotenoid-Producing Bacterium Isolated from Seawater from a Tidal Flat in the  Yellow Sea.
PG  - e01451-15
AB  - Bacillus marisflavi TF-11(T) (JCM 11544) is a Gram-positive, spore-forming, and
      carotenoid-producing bacterium isolated from seawater from a tidal flat in the
      Yellow Sea. Here, we report the first draft genome sequence of B. marisflavi
      TF-11(T), which comprises 4.31 Mb in 11 scaffolds with a G+C content of 48.57%.
AU  - Wang JP
AU  - Liu B
AU  - Liu GH
AU  - Chen DJ
AU  - Chen QQ
AU  - Zhu YJ
AU  - Chen Z
AU  - Che JM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01451-15.

PMID- 26383671
VI  - 3
DP  - 2015
TI  - Genome Sequence of Brevibacillus reuszeri NRRL NRS-1206T, an l-N-Carbamoylase-Producing Bacillus-Like Bacterium.
PG  - e01063-15
AB  - Brevibacillus reuszeri NRRL NRS-1206(T) is a Gram-positive, spore-forming, and strictly
      aerobic bacterium. Here, we report the draft 6.98-Mb genome sequence of  B. reuszeri NRRL
      NRS-1206(T), which is the first genome information of B. reuszeri and will provide useful
      information for genomic taxonomy and phylogenomics of Bacillus-like bacteria.
AU  - Wang JP
AU  - Liu B
AU  - Liu GH
AU  - Chen DJ
AU  - Ge CB
AU  - Chen Z
AU  - Che JM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01063-15.

PMID- 26494675
VI  - 3
DP  - 2015
TI  - Genome Sequence of Bacillus butanolivorans K9T (DSM 18926), an n-Butanol-Consuming Bacterium Isolated from Soil.
PG  - e01228-15
AB  - Bacillus butanolivorans K9(T) (DSM 18926) is a Gram-positive, spore-forming, strictly aerobic,
      and n-butanol-consuming bacterium. Here, we report the 5.68-Mb  genome sequence of B.
      butanolivorans K9(T), which is the first genomic information of this species that will provide
      useful information for the genomic  taxonomy and phylogenomics of Bacillus-like bacteria.
AU  - Wang JP
AU  - Liu B
AU  - Liu GH
AU  - Chen DJ
AU  - Xiao RF
AU  - Zheng XF
AU  - Shi H
AU  - Ge CB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01228-15.

PMID- 26383648
VI  - 3
DP  - 2015
TI  - Genome Sequence of Virgibacillus pantothenticus DSM 26T (ATCC 14576), a Mesophilic and Halotolerant Bacterium Isolated from Soil.
PG  - e01064-15
AB  - Virgibacillus pantothenticus DSM 26(T) is a Gram-positive, spore-forming, aerobic, mesophilic,
      and halotolerant bacterium. Here, we report its 4.76-Mb draft genome sequence, which is the
      first genome information of V. pantothenticus and will promote biological research and
      biotechnological application for the species.
AU  - Wang JP
AU  - Liu B
AU  - Liu GH
AU  - Chen DJ
AU  - Zhu YJ
AU  - Chen Z
AU  - Che JM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01064-15.

PMID- 26847897
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Bacillus muralis LMG 20238T (DSM 16288), a Spore-Forming Bacterium Isolated from Deteriorated Mural Paintings.
PG  - e01691-15
AB  - Bacillus muralis LMG 20238(T) is a Gram-positive, aerobic, and spore-forming bacterium. Here,
      we report the 5.18-Mb draft genome sequence of B. muralis LMG
      20238(T), which is the first genome sequence of this species and will promote its
      fundamental research.
AU  - Wang JP
AU  - Liu B
AU  - Liu GH
AU  - Chen Q
AU  - Pan Z
AU  - Zheng XF
AU  - Chen M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01691-15.

PMID- 26205874
VI  - 3
DP  - 2015
TI  - Genome Sequence of Brevibacillus formosus F12T for a Genome-Sequencing Project for Genomic Taxonomy and Phylogenomics of Bacillus-Like Bacteria.
PG  - e00753-15
AB  - Brevibacillus formosus F12(T) is a Gram-positive, spore-forming, and strictly aerobic
      bacterium. Here, we report the draft 6.215-Mb genome sequence of B.
      formosus F12(T), which will provide useful information for genomic taxonomy and
      phylogenomics of Bacillus-like bacteria, as well as for the functional gene
      mining and application of B. formosus.
AU  - Wang JP
AU  - Liu B
AU  - Liu GH
AU  - Chen QQ
AU  - Zhu YJ
AU  - Chen Z
AU  - Che JM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00753-15.

PMID- 26847893
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Bacillus cecembensis PN5T (DSM 21993), a Psychrotolerant Bacterium Isolated from Soil Samples near the Pindari Glacier.
PG  - e01687-15
AB  - Bacillus cecembensis PN5(T) is a Gram-positive, aerobic, and spore-forming bacterium with very
      high intrinsic heat resistance. Here, we report the 4.72-Mb
      draft genome sequence of B. cecembensis PN5(T), the first genome sequence of this
      species, which will promote its fundamental research.
AU  - Wang JP
AU  - Liu B
AU  - Liu GH
AU  - Ge CB
AU  - Chen QQ
AU  - Che JM
AU  - Chen DJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01687-15.

PMID- 26272580
VI  - 3
DP  - 2015
TI  - Genome Sequence of Anaerobacillus macyae JMM-4T (DSM 16346), the First Genomic Information of the Newly Established Genus Anaerobacillus.
PG  - e00922-15
AB  - Anaerobacillus macyae JMM-4(T) (DSM 16346) is a Gram-positive, spore-forming, strictly
      anaerobic, and arsenate-respiring bacterium. Here, we report the 4.26-Mb
      genome sequence of A. macyae JMM-4(T), which is the first genome information of
      the newly established genus Anaerobacillus.
AU  - Wang JP
AU  - Liu B
AU  - Liu GH
AU  - Ge CB
AU  - Chen QQ
AU  - Zhu YJ
AU  - Chen Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00922-15.

PMID- 27313303
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Bacillus farraginis R-6540T (DSM 16013), a Spore-Forming Bacterium Isolated at Dairy Farms.
PG  - e00562-16
AB  - Bacillus farraginis R-6540(T) is a Gram-positive, aerobic, and spore-forming bacterium with
      very high intrinsic heat resistance. Here, we report the 5.32-Mb
      draft genome sequence of B. farraginis R-6540(T), which is the first genome
      sequence of this species and will promote its fundamental research.
AU  - Wang JP
AU  - Liu B
AU  - Liu GH
AU  - Ge CB
AU  - Xiao RF
AU  - Zheng XF
AU  - Shi H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00562-16.

PMID- 26847896
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Bacillus plakortidis P203T (DSM 19153), an Alkali- and Salt-Tolerant Marine Bacterium.
PG  - e01690-15
AB  - Bacillus plakortidis P203(T) is a Gram-positive, spore-forming, and alkali- and salt-tolerant
      marine bacterium. Here, we report the 3.97-Mb draft genome sequence
      of B. plakortidis P203(T), which will promote its fundamental research and
      provide useful information for genomic taxonomy and phylogenomics of
      Bacillus-like bacteria.
AU  - Wang JP
AU  - Liu B
AU  - Liu GH
AU  - Ge CB
AU  - Xiao RF
AU  - Zheng XF
AU  - Shi H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01690-15.

PMID- 26847895
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Bacillus shackletonii LMG 18435T, Isolated from Volcanic Mossy Soil.
PG  - e01689-15
AB  - Bacillus shackletonii LMG 18435(T) is a Gram-positive, aerobic, and spore-forming bacterium.
      Here, we report the 5.30-Mb draft genome sequence of B. shackletonii
      LMG 18435(T), which will promote its fundamental research and provide useful
      information for genomic taxonomy and phylogenomics of Bacillus-like bacteria.
AU  - Wang JP
AU  - Liu B
AU  - Liu GH
AU  - Ge CB
AU  - Xiao RF
AU  - Zheng XF
AU  - Shi H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01689-15.

PMID- 26494674
VI  - 3
DP  - 2015
TI  - High-Quality Draft Genome Sequence of Aneurinibacillus migulanus ATCC 9999T (DSM  2895), a Gramicidin S-Producing Bacterium Isolated from Garden Soil.
PG  - e01227-15
AB  - Aneurinibacillus migulanus ATCC 9999(T) (DSM 2895) is a Gram-positive, round-spore-forming,
      and gramicidin S-producing bacterium. Here, we report the 6.35-Mb high-quality draft genome
      sequence of A. migulanus ATCC 9999(T), which will provide useful information for the genomic
      taxonomy and phylogenomics of Bacillus-like bacteria.
AU  - Wang JP
AU  - Liu B
AU  - Liu GH
AU  - Ge CB
AU  - Xiao RF
AU  - Zheng XF
AU  - Shi H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01227-15.

PMID- 26847898
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Bacillus humi LMG 22167T (DSM 16318), an Endospore-Forming Bacterium Isolated from Soil.
PG  - e01692-15
AB  - Bacillus humi LMG 22167(T) is a Gram-positive, aerobic, and spore-forming bacterium Here, we
      report the 4.80-Mb draft genome sequence of B. humi LMG
      22167(T), which is the first genome sequence of this species and will promote its
      fundamental research.
AU  - Wang JP
AU  - Liu B
AU  - Liu GH
AU  - Pan Z
AU  - Xiao RF
AU  - Chen M
AU  - Chen DJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01692-15.

PMID- 26272579
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Bacillus pseudalcaliphilus PN-137T (DSM 8725), an Alkaliphilic Halotolerant Bacterium Isolated from Garden Soils.
PG  - e00919-15
AB  - Bacillus pseudalcaliphilus PN-137(T) (DSM 8725) is a Gram-positive, spore-forming,
      alkaliphilic, and halotolerant bacterium. Here, we report the
      4.49-Mb genome sequence of B. pseudalcaliphilus PN-137(T), which will accelerate
      the application of this alkaliphile and provide useful information for genomic
      taxonomy and phylogenomics of Bacillus-like bacteria.
AU  - Wang JP
AU  - Liu B
AU  - Liu GH
AU  - Xiao RF
AU  - Zheng XF
AU  - Shi H
AU  - Ge CB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00919-15.

PMID- 26494677
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Sporosarcina globispora W 25T (DSM 4), a Psychrophilic Bacterium Isolated from Soil and River Water.
PG  - e01230-15
AB  - Sporosarcina globispora W 25(T) (DSM 4) is a Gram-positive, round-spore-forming,  and
      psychrophilic bacterium. Here, we report the 5.66-Mb genome sequence of S. globispora W 25(T),
      which will accelerate the application of this psychrophile and provide useful information for
      genomic taxonomy and phylogenomics of Bacillus-like bacteria.
AU  - Wang JP
AU  - Liu B
AU  - Liu GH
AU  - Xiao RF
AU  - Zheng XF
AU  - Shi H
AU  - Ge CB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01230-15.

PMID- 26494676
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Bacillus murimartini LMG 21005T, an Alkalitolerant Bacterium Isolated from a Church Wall Mural in Germany.
PG  - e01229-15
AB  - Bacillus murimartini LMG 21005(T) is a Gram-positive, spore-forming, and alkalitolerant
      bacterium isolated from a church wall mural. Here, we report the 4.17-Mb genome sequence of B.
      murimartini LMG 21005(T), which will accelerate the application of this alkalitolerant
      bacterium and provide useful information for genomic taxonomy and phylogenomics of
      Bacillus-like bacteria.
AU  - Wang JP
AU  - Liu B
AU  - Liu GH
AU  - Xiao RF
AU  - Zheng XF
AU  - Shi H
AU  - Ge CB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01229-15.

PMID- 24179118
VI  - 1
DP  - 2013
TI  - Whole-Genome Sequence of Streptococcus suis Serotype 3 Strain YB51.
PG  - e00884-13
AB  - We report here the second complete genome sequence of Streptococcus suis serotype 3 (strain
      YB51). The genome is 2,043,655 bp in length, which is 14,840 bp longer
      than the first reported genome of the same serotype, and it covers 2,012 coding
      sequences, 56 tRNAs, and 4 rRNA loci.
AU  - Wang K
AU  - Chen J
AU  - Yao H
AU  - Lu C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00884-13.

PMID- 25125641
VI  - 2
DP  - 2014
TI  - Whole-Genome Sequence of Streptococcus suis Serotype 4 Reference Strain 6407.
PG  - e00770-14
AB  - We report here the second complete genome sequence of Streptococcus suis serotype 4 (strain
      6407). The genome is 2,292,360 bp in length, covering 2,239 coding
      sequences, 58 tRNAs, and 4 rRNA loci.
AU  - Wang K
AU  - Chen J
AU  - Yao H
AU  - Lu C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00770-14.

PMID- 22092812
VI  - 324
DP  - 2011
TI  - Genetic analysis of the capsular polysaccharide synthesis locus in 15 Streptococcus suis serotypes.
PG  - 117-124
AB  - 
AU  - Wang K
AU  - Fan W
AU  - Cai L
AU  - Huang B
AU  - Lu C
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2011 324: 117-124.

PMID- 23814033
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Streptococcus suis Serotype 16 Strain TL13.
PG  - e00394-13
AB  - We report here the first complete genome sequence of Streptococcus suis serotype  16, which
      has been identified to be zoonotic. The sequenced strain TL13 was
      isolated from a pig in China. The genome is 2,038,146 bp in length, covering
      1,950 coding sequences, 53 tRNAs, and 4 rRNA loci.
AU  - Wang K
AU  - Yao H
AU  - Lu C
AU  - Chen J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00394-13.

PMID- 25111488
VI  - 6
DP  - 2014
TI  - Active DNA demethylation of the vertebrate genomes by DNA methyltransferases: deaminase, dehydroxymethylase or demethylase?
PG  - 353-363
AB  - Vertebrate DNA methyltransferases (DNMTs) have been thought to primarily function to
      covalently add a methyl group to the 5-position of cytosine. However, recent discovery of the
      DNA demethylation and dehydroxymethylation activities of DNMTs in vitro suggest new routes to
      complete the dynamic cycle of DNA methylation-demethylation of the vertebrate genomes. The in
      vitro reaction conditions suggest that vertebrate DNMTs can switch from DNA methylases to DNA
      dehydroxymethylases under oxidative stress and to DNA demethylases in the presence of calcium
      ion under nonreducing conditions. These environmental parameters provide clues regarding the
      choices in vivo of DNMT activities utilized in different physiological systems. In particular,
      the nature of these parameters suggest that the DNA demethylation and dehydroxymethylation
      activities of the vertebrate DNMTs play essential roles in multiple biological processes
      including early embryo development, regulation of neuronal plasticity, tumorigenesis and
      hormone-regulated transcription.
AU  - Wang K-Y
AU  - Chen C-C
AU  - Shen C-KunJ
PT  - Journal Article
TA  - Epigenomics
JT  - Epigenomics
SO  - Epigenomics 2014 6: 353-363.

PMID- 25573927
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of the Fish Pathogen Yersinia ruckeri Strain SC09, Isolated from Diseased Ictalurus punctatus in China.
PG  - e01327-14
AB  - Yersinia ruckeri SC09 is a Gram-negative bacterium isolated from a moribund Ictalurus
      punctatus collected in Jianyang, China. Here, we report the complete
      genome sequence of this microorganism to facilitate the investigation of its
      pathogenicity and to reevaluate its taxonomic position.
AU  - Wang KY
AU  - Liu T
AU  - Wang J
AU  - Chen DF
AU  - Wu XJ
AU  - Jiang J
AU  - Liu JX
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01327-14.

PMID- 
VI  - 
DP  - 2011
TI  - Phosphorothioation:  An unusual post-replicative modification on the DNA backbone.
PG  - 57-74
AB  - DNA molecules are polymers composed of basic repeating subunits of deoxyribonucleotides, which
      consist of the deoxyribose sugar, phosphate groups, and a nitrogenous base.  They appear to
      fulfill all requirements necessary to maintain the genetic function of DNA.  The five elements
      of nitrogen, phosphorus, carbon, hydrogen, and oxygen had been regarded as the canonical
      composition of DNA until the discovery of phosphorothioation, with a sixth element, sulfur,
      identified as an additional naturally occurring constituent on the DNA backbone, as a
      sequence-selective, stereospecific post-replicative modification governed by the dnd gene
      cluster.  Unlike any other DNA or RNA modification system, DNA phosphorothioation is the
      first-described physiological modification of the DNA sugar-phosphorothioation is the
      first-described physiological modification of the DNA sugar-phosphate backbone.
AU  - Wang L
AU  - Chen S
AU  - Deng Z
PT  - Journal Article
TA  - DNA Replication-Current Advances
JT  - DNA Replication-Current Advances
SO  - DNA Replication-Current Advances 2011 : 57-74.

PMID- 21285367
VI  - 108
DP  - 2011
TI  - DNA phosphorothioation is widespread and quantized in bacterial genomes.
PG  - 2963-2968
AB  - Phosphorothioate (PT) modification of DNA, with sulfur replacing a nonbridging phosphate
      oxygen, was recently discovered as a product of the
      dnd genes found in bacteria and archaea. Given our limited understanding
      of the biological function of PT modifications, including sequence
      context, genomic frequencies, and relationships to the diversity of dnd
      gene clusters, we undertook a quantitative study of PT modifications in
      prokaryotic genomes using a liquid chromatography-coupled tandem
      quadrupole mass spectrometry approach. The results revealed a diversity of
      unique PT sequence contexts and three discrete genomic frequencies in a
      wide range of bacteria. Metagenomic analyses of PT modifications revealed
      unique ecological distributions, and a phylogenetic comparison of dnd
      genes and PT sequence contexts strongly supports the horizontal transfer
      of dnd genes. These results are consistent with the involvement of PT
      modifications in a type of restriction-modification system with wide
      distribution in prokaryotes.
AU  - Wang L
AU  - Chen S
AU  - Vergin KL
AU  - Giovannoni SJ
AU  - Chan SW
AU  - Demott MS
AU  - Taghizadeh K
AU  - Cordero OX
AU  - Cutler M
AU  - Timberlake S
AU  - Alm EJ
AU  - Polz MF
AU  - Pinhassi J
AU  - Deng Z
AU  - Dedon PC
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2011 108: 2963-2968.

PMID- 17934475
VI  - 3
DP  - 2007
TI  - Phosphorothioation of DNA in bacteria by dnd genes.
PG  - 709-710
AB  - Modifications of the canonical structures of DNA and RNA play critical roles in cell
      physiology, DNA replication, transcription and translation in all organisms.
      We now report that bacterial dnd gene clusters incorporate sulfur into the DNA
      backbone as a sequence-selective, stereospecific phosphorothioate modification.
      To our knowledge, unlike any other DNA or RNA modification systems, DNA
      phosphorothioation by dnd gene clusters is the first physiological modification
      described on the DNA backbone.
AU  - Wang L
AU  - Chen S
AU  - Xu T
AU  - Taghizadeh K
AU  - Wishnok JS
AU  - Zhou X
AU  - You D
AU  - Deng Z
AU  - Dedon PC
PT  - Journal Article
TA  - Nat. Chem. Biol.
JT  - Nat. Chem. Biol.
SO  - Nat. Chem. Biol. 2007 3: 709-710.

PMID- 25776564
VI  - 5
DP  - 2015
TI  - Identification of genetic variations associated with epsilon-poly-lysine biosynthesis in Streptomyces albulus ZPM by genome sequencing.
PG  - 9201
AB  - The biosynthesis of the antibiotic epsilon-poly-lysine (epsilon-PL) in Streptomyces albulus is
      performed by polylysine synthase (pls); however, the regulatory mechanism of this process is
      still unknown. Here, we first obtained the complete genome sequence of S. albulus ZPM, which
      consists of 9,784,577 bp and has a GC content of 72.2%. The genome houses 44 gene clusters for
      secondary metabolite biosynthesis, in which 20 gene clusters are involved in the biosynthesis
      of polyketides and nonribosomally synthesized peptides.
      High-throughput sequencing was further performed, and genetic variants were identified from
      pooled libraries consisting of the 30 highest-yield mutants or 30 lowest-yield mutants. More
      than 350 genetic variants associated with epsilon-PL yield have been identified. One hundred
      sixty-two affected proteins, from important metabolic enzymes to novel transcriptional
      regulators, were identified as being related to epsilon-PL synthesis. HrdD, one of the
      affected genes, is a sigma factor that shows the most sensitive response to pH change and
      contains a non-synonymous mutation (A132V) in mutant strains with lower epsilon-PL yields.
      Electrophoretic mobility shift assays showed that the pls gene is likely regulated by
      transcriptional activator HrdD. The data obtained in this study will facilitate future studies
      on epsilon-PL yield improvement and industrial bioprocess optimization.
AU  - Wang L
AU  - Gao C
AU  - Tang N
AU  - Hu S
AU  - Wu Q
PT  - Journal Article
TA  - Sci. Rep.
JT  - Sci. Rep.
SO  - Sci. Rep. 2015 5: 9201.

PMID- 24223817
VI  - 8
DP  - 2013
TI  - Metagenomic insights into the carbohydrate-active enzymes carried by the microorganisms adhering to solid digesta in the rumen of cows.
PG  - E78507
AB  - The ruminal microbial community is a unique source of enzymes that underpin the
      conversion of cellulosic biomass. In this study, the microbial consortia adherent
      on solid digesta in the rumen of Jersey cattle were subjected to an
      activity-based metagenomic study to explore the genetic diversity of
      carbohydrolytic enzymes in Jersey cows, with a particular focus on cellulases and
      xylanases. Pyrosequencing and bioinformatic analyses of 120 carbohydrate-active
      fosmids identified genes encoding 575 putative Carbohydrate-Active Enzymes
      (CAZymes) and proteins putatively related to transcriptional regulation,
      transporters, and signal transduction coupled with polysaccharide degradation and
      metabolism. Most of these genes shared little similarity to sequences archived in
      databases. Genes that were predicted to encode glycoside hydrolases (GH) involved
      in xylan and cellulose hydrolysis (e.g., GH3, 5, 9, 10, 39 and 43) were well
      represented. A new subfamily (S-8) of GH5 was identified from contigs assigned to
      Firmicutes. These subfamilies of GH5 proteins also showed significant
      phylum-dependent distribution. A number of polysaccharide utilization loci (PULs)
      were found, and two of them contained genes encoding Sus-like proteins and
      cellulases that have not been reported in previous metagenomic studies of samples
      from the rumens of cows or other herbivores. Comparison with the large
      metagenomic datasets previously reported of other ruminant species (or cattle
      breeds) and wallabies showed that the rumen microbiome of Jersey cows might
      contain differing CAZymes. Future studies are needed to further explore how host
      genetics and diets affect the diversity and distribution of CAZymes and
      utilization of plant cell wall materials.
AU  - Wang L
AU  - Hatem A
AU  - Catalyurek UV
AU  - Morrison M
AU  - Yu Z
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2013 8: E78507.

PMID- 23405292
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Brucella abortus BCB027, a Strain Isolated from a Domestic Deer.
PG  - e00130-12
AB  - Many Brucella species are isolated from nonpreferred hosts, and these bacteria may show
      genetic differences from isolates from the preferred hosts. Here, we report the draft genome
      sequence of Brucella abortus BCB027, a novel strain isolated from a domestic deer.
AU  - Wang L
AU  - Qiu Y
AU  - Chen Z
AU  - Xu J
AU  - Wang Z
AU  - Ke Y
AU  - Li T
AU  - Wang D
AU  - Huang L
AU  - Yu Y
AU  - Zhen Q
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00130-12.

PMID- 22815456
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Streptomyces globisporus C-1027, Which Produces an Antitumor Antibiotic Consisting of a Nine-Membered Enediyne with a Chromoprotein.
PG  - 4144
AB  - Streptomyces globisporus C-1027 is the producer of antitumor antibiotic C-1027, a
      nine-membered enediyne-containing compound. Here we present a draft genome
      sequence of S. globisporus C-1027 containing the intact biosynthetic gene cluster
      for this antibiotic. The genome also carries numerous sets of genes for the
      biosynthesis of diverse secondary metabolites.
AU  - Wang L
AU  - Wang S
AU  - He Q
AU  - Yu T
AU  - Li Q
AU  - Hong B
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4144.

PMID- 23209237
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Streptomyces sp. Strain SS, Which Produces a Series of Uridyl Peptide Antibiotic Sansanmycins.
PG  - 6988-6989
AB  - Streptomyces sp. SS produces a series of uridyl peptide antibiotic sansanmycins.  Here, we
      present a draft genome sequence of Streptomyces sp. SS containing the
      biosynthetic gene cluster for the antibiotics. The identification of the
      biosynthetic gene cluster of sansanmycins may provide further insight into
      biosynthetic mechanisms for uridyl peptide antibiotics.
AU  - Wang L
AU  - Xie Y
AU  - Li Q
AU  - He N
AU  - Yao E
AU  - Xu H
AU  - Yu Y
AU  - Chen R
AU  - Hong B
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6988-6989.

PMID- 24435854
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Bioelectricity-Generating and Dye-Decolorizing Bacterium Proteus hauseri Strain ZMd44.
PG  - e00992-13
AB  - Proteus hauseri ZMd44 (CGMCC 6746), as a crucial biodecolorizing, bioelectricity-generating,
      and copper-resistant bacterium, is distinguished from
      the urinary pathogens Proteus penneri and Proteus mirabilis. To further
      investigate the genetic functions of this strain, the genome sequence and
      annotation of its open reading frames, which consist of 3,875,927 bp (G+C
      content, 38.12%), are presented here.
AU  - Wang N
AU  - Ng IS
AU  - Chen PT
AU  - Li Y
AU  - Chen YC
AU  - Chen BY
AU  - Lu Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00992-13.

PMID- 
VI  - 122
DP  - 2000
TI  - Use of oligodeoxyribonucleotides with conformationally constrained abasic sugar targets to probe the mechanism of base flipping by HhaI DNA (cytosine C5)-methyltransferase.
PG  - 12422-12434
AB  - X-ray crystallographic studies of HhaI DNA (cytosine-C5)-methyltransferase covalently linked
      to methylated 5-fluorocytosine in DNA provided the first direct evidence that the cytosine
      residue targeted for methylation was "flipped" out of the helix during the transfer reaction.
      Subsequent studies indicated that removal of the target cytosine base, i.e., introduction of
      an abasic site, enhanced binding of M.HhaI to DNA and that the conformation of the
      sugar-phosphate backbone at the abasic site in the resultant complexes was the same as that of
      the sugar attached to a "flipped" cytosine.  In the present study, pseudorotationally
      constrained sugar analogues, based on bicyclo[3.1.0]hexane templates, were placed in DNA
      duplexes as abasic target sites in the M.HhaI recognition sequence.  Biochemical studies
      demonstrate that binding affinity of M.HhaI for abasic sites increases when the abasic target
      sugar analogue is constrained to the south conformation and decreases when it is constrained
      to the north conformation.  In native gel-shift assays, M.HhaI exhibits a "closed"
      conformation when bound to the abasic south or abasic furanose analogues, whereas an "open"
      conformation predominates with the abasic north analogue.  A structural understanding of these
      results was obtained via molecular dynamics simulations of the DNA duplex alone and in ternary
      complex with M.HhaI and cofactor, along with quantum mechanical calculations on model
      compounds representative of the abasic and modified sugars.  Binding affinities are shown to
      be related to the ability of the abasic sugar analogues to spontaneously flip out of the DNA
      duplex.  Enhanced binding of the abasic south analogue is suggested to be due to its increased
      capacity for sampling the experimentally observed conformation of the DNA target site in the
      M.HhaI ternary complex.  Decreased binding of the north analogue is due to decreased
      flexibility of the phosphodiester backbone associated with a north pseudorotation angle,
      thereby inhibiting spontaneous flipping of the sugar moiety out of the DNA duplex.
      Spontaneous flipping of the sugar moiety out of the DNA duplex is also suggested to facilitate
      formation of a "closed" complex between M.HhaI and DNA whereas partial or no flipping favor
      the "open" conformation.  These results show that introduction of structural constraints into
      DNA that induce enhanced sampling of protein-bound conformations facilitate DNA-protein
      binding.  Implications of the present results with respect to the mechanism of vase flipping
      in the M.HhaI catalytic cycle are discussed.
AU  - Wang P
AU  - Brank AS
AU  - Banavali NK
AU  - Nicklaus MC
AU  - Marquez VE
AU  - Christman JK
AU  - MacKerell AD Jr
PT  - Journal Article
TA  - J. Am. Chem. Soc.
JT  - J. Am. Chem. Soc.
SO  - J. Am. Chem. Soc. 2000 122: 12422-12434.

PMID- 1327960
VI  - 119
DP  - 1992
TI  - The construction of Streptomyces cyaneus genomic libraries in Escherichia coli is dependent upon the use of Mcr-deficient strains.
PG  - 127-129
AB  - Streptomyces cyaneus genomic DNA ligated into either lambda phage or plasmid vectors was very
      inefficiently cloned into standard Escherichia coli host strains. However, the same material
      could be efficiently cloned using Mcr-deficient E. coli strains. These results suggest that
      the S. cyaneus genome contains 5-methylcytosine residues, some of which occur with the
      recognition sequences of the E. coli Mcr restriction system.
AU  - Wang P
AU  - Harvey SS
AU  - Sims PFG
AU  - Broda P
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1992 119: 127-129.

PMID- 23105079
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Alicyclobacillus hesperidum Strain URH17-3-68.
PG  - 6348
AB  - Alicyclobacillus hesperidum is a thermoacidophilic bacterium. We isolated strain  URH17-3-68
      from hot spring sludge in Tengchong, Yunnan province, China. Its
      extracellular products include heat- and acid-stable enzymes which are important
      for industrial applications. Here we report the draft genome of this strain.
AU  - Wang P
AU  - Li L
AU  - Chen X
AU  - Jiang N
AU  - Liu G
AU  - Chen L
AU  - Xu J
AU  - Song H
AU  - Chen Z
AU  - Ma Y
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6348.

PMID- 20624905
VI  - 78
DP  - 2010
TI  - Genetic Study of Capsular Switching between Neisseria meningitidis Sequence Type 7 Serogroup A and C Strains.
PG  - 3883-3888
AB  - Neisseria meningitidis is a leading cause of septicemia and meningitis
      worldwide. N. meningitidis capsular polysaccharides have been classified
      into 13 distinct serogroups which are defined by antibody reactivity and
      structural analysis, and the capsule plays an important role in virulence.
      Serogroups A, B, C, W135, and Y have been reported to be clinically
      important. Several newly identified serogroup C isolates belonging to the
      unique sequence type 7 (ST-7) were identified in China. Since most ST-7
      isolates from China belonged to serogroup A, the newly identified ST-7
      serogroup C strains were proposed to have arisen from those belonging to
      ST-7 serogroup A. In this study, six ST-7 serogroup C and three ST-7
      serogroup A isolates were analyzed by pulsed-field gel electrophoresis to
      confirm their sequence type. In order to clarify the genetic basis of
      capsular switching between ST-7 serogroup A and C strains, the whole
      capsular gene clusters and surrounding genes of the two representative
      ST-7 strains belonging to serogroups A and C, respectively, were sequenced
      and compared. Potential recombination sites were analyzed using the RDP3
      beta software, and recombination-related regions in two other ST-7
      serogroup A and five ST-7 serogroup C strains were also sequenced and
      compared to the representative ST-7 serogroup A and C strain sequences.
AU  - Wang Q
AU  - Shao Z
AU  - Wang X
AU  - Gao Y
AU  - Li M
AU  - Xu L
AU  - Xu J
AU  - Wang L
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2010 78: 3883-3888.

PMID- 7957952
VI  - 355
DP  - 1994
TI  - pH-independent inhibition of restriction endonuclease cleavage via triple helix formation by oligonucleotides containing 8-oxo-2'-deoxyadenosine.
PG  - 11-14
AB  - The ability of homopyrimidine oliogonucleotides containing 8-oxo-2'-deoxyadenosine to form
      stable, triple helical structures with the sequence containing the recognition site for the
      class II-S restriction enzyme, Ksp632I, was studied as a function of pH. The
      8-oxo-2'-deoxyadenosine-substituted oligomers were shown to inhibit enzymatic cleavage and to
      bind within the physiological pH range in a pH-independent fashion without compromising
      specificity.
AU  - Wang Q
AU  - Tsukahara S
AU  - Yamakawa H
AU  - Takai K
AU  - Takaku H
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1994 355: 11-14.

PMID- 19865481
VI  - 4
DP  - 2009
TI  - Genome sequence of the versatile fish pathogen Edwardsiella tarda provides insights into its adaptation to broad host ranges and intracellular niches.
PG  - E7646
AB  - BACKGROUND: Edwardsiella tarda is the etiologic agent of edwardsiellosis,
      a devastating fish disease prevailing in worldwide aquaculture industries.
      Here we describe the complete genome of E. tarda, EIB202, a highly
      virulent and multi-drug resistant isolate in China. METHODOLOGY/PRINCIPAL
      FINDINGS: E. tarda EIB202 possesses a single chromosome of 3,760,463 base
      pairs containing 3,486 predicted protein coding sequences, 8 ribosomal
      rRNA operons, and 95 tRNA genes, and a 43,703 bp conjugative plasmid
      harboring multi-drug resistant determinants and encoding type IV A
      secretion system components. We identified a full spectrum of genetic
      properties related to its genome plasticity such as repeated sequences,
      insertion sequences, phage-like proteins, integrases, recombinases and
      genomic islands. In addition, analysis also indicated that a substantial
      proportion of the E. tarda genome might be devoted to the growth and
      survival under diverse conditions including intracellular niches, with a
      large number of aerobic or anaerobic respiration-associated proteins,
      signal transduction proteins as well as proteins involved in various
      stress adaptations. A pool of genes for secretion systems, pili formation,
      nonfimbrial adhesions, invasions and hemagglutinins, chondroitinases,
      hemolysins, iron scavenging systems as well as the incomplete flagellar
      biogenesis might feature its surface structures and pathogenesis in a fish
      body. CONCLUSION/SIGNIFICANCE: Genomic analysis of the bacterium offered
      insights into the phylogeny, metabolism, drug-resistance, stress
      adaptation, and virulence characteristics of this versatile pathogen,
      which constitutes an important first step in understanding the
      pathogenesis of E. tarda to facilitate construction of a practical
      effective vaccine used for combating fish edwardsiellosis.
AU  - Wang Q
AU  - Yang M
AU  - Xiao J
AU  - Wu H
AU  - Wang X
AU  - Lv Y
AU  - Xu L
AU  - Zheng H
AU  - Wang S
AU  - Zhao G
AU  - Liu Q
AU  - Zhang Y
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2009 4: E7646.

PMID- 25395648
VI  - 2
DP  - 2014
TI  - Genome Sequence of Tumebacillus flagellatus GST4, the First Genome Sequence of a  Species in the Genus Tumebacillus.
PG  - e01189-14
AB  - We present here the first genome sequence of a species in the genus Tumebacillus. The draft
      genome sequence of Tumebacillus flagellatus GST4 provides a genetic
      basis for future studies addressing the origins, evolution, and ecological role
      of Tumebacillus organisms, as well as a source of acid-resistant amylase-encoding
      genes for further studies.
AU  - Wang QY
AU  - Xie NZ
AU  - Huang YY
AU  - Song LF
AU  - Du QS
AU  - Yu B
AU  - Chen D
AU  - Huang RB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01189-14.

PMID- 9001231
VI  - 17
DP  - 1997
TI  - Identification of a protein that binds to the HO endonuclease recognition sequence at the yeast mating type locus.
PG  - 770-777
AB  - Mating type switching in Saccharomyces cerevisiae initiates when HO endonuclease makes a
      site-specific double-stranded break at MAT, the yeast mating type locus.  To identify other
      proteins involved in this process, we examined whether extracts prepared from ho- mutants
      contain additional factors that bind near the recognition sequence for HO.  Using an
      electrophoretic mobility shift assay, we isolated a chromatographic fraction that contains an
      activity, named YZbp, which binds to two sequences flanking the recognition sequence at
      MATalpha and to one sequence overlapping it at MATa.  MAT plasmids carrying mutations in the
      YZbp recognition sequence are cleaved by purified Ho at wild-type efficiencies in an in vitro
      assay.  These same plasmids, however, are not cleaved by Ho inside cells, demonstrating that
      YZbp acts as a positive activator of in vivo cleavage.  YZbp is present in all cell types,
      even those not undergoing mating type switching, suggesting that it has additional cellular
      functions.
AU  - Wang R
AU  - Jin Y
AU  - Norris D
PT  - Journal Article
TA  - Mol. Cell. Biol.
JT  - Mol. Cell. Biol.
SO  - Mol. Cell. Biol. 1997 17: 770-777.

PMID- 26430031
VI  - 3
DP  - 2015
TI  - Genome Sequence of Streptococcus agalactiae Strain H002, Serotype III, Isolated in China from a Pregnant Woman.
PG  - e01109-15
AB  - Here, we report the first whole-genome sequence of Streptococcus agalactiae strain H002,
      serotype III, isolated in China from a woman 32 weeks pregnant. This sequence represents an
      important addition to the published genomes and will promote comparative genomic studies of S.
      agalactiae spp. isolated from diverse regions, particularly when compared with Chinese
      strains.
AU  - Wang R
AU  - Li L
AU  - Luo F
AU  - Liang W
AU  - Gan X
AU  - Chen M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01109-15.

PMID- 26679579
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Edwardsiella ictaluri Strains LADL11-100 and LADL11-194 Isolated from Zebrafish Danio rerio.
PG  - e01449-15
AB  - Here, we report the draft genome sequences of Edwardsiella ictaluri strains LADL11-100 and
      LADL11-194, two isolates from natural outbreaks of edwardsiellosis
      in the zebrafish Danio rerio, as well as the sequences of the plasmids carried by
      the zebrafish strain of E. ictaluri.
AU  - Wang R
AU  - Tekedar HC
AU  - Lawrence ML
AU  - Chouljenko VN
AU  - Kim J
AU  - Kim N
AU  - Kousoulas KG
AU  - Hawke JP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01449-15.

PMID- 6243986
VI  - 606
DP  - 1980
TI  - Two sequence-specific endonucleases from Xanthomonas oryzae.  Characterization and unusual properties.
PG  - 371-385
AB  - XorI and XorII, two sequence-specific endonucleases, have been partially
      purified from Xanthomas oryzae.  XorI and XorII were shown to be isoschizomers
      of PstI and PvuI, respectively.  X. oryzae is a particularly good source of
      this PvuI isoschizomer because of the high yield of XorII, its simple
      purification scheme, and its relative stability.  Furthermore, XorII was shown
      to cleave at different positions in its recognition sequence than do at least
      two of its known isoschizomers; XorII cleaves between the C and the G at the
      3'-end of its palindromic recognition sequence, 5'-CGATC^G-3'.  There is a
      single XorII site in each of the plasmid-cloning vehicles pBR313 and pBR322.
      Two unusual aspects of XorII digestion are discussed, namely, the kinetics of
      digestion of pBR313 and pBR322 and the resistance of human DNA to XorII.
AU  - Wang RY-H
AU  - Shedlarski JG
AU  - Farber MB
AU  - Kuebbing D
AU  - Ehrlich M
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1980 606: 371-385.

PMID- 6321756
VI  - 49
DP  - 1984
TI  - DNA methylation inhibits the transfecting activity of replicative-form PhiX174 DNA.
PG  - 674-679
AB  - Replacement of virtually all the cytosine residues with 5-methylcytosine residues in the
      complementary strand of the replicative form (RF) of PhiX174 DNA caused a 300- to 500-fold
      loss in its transfecting activity.  Similar results were obtained with analogously methylated
      M13 RF.  Transfection experiments with PhiX RF hemimethylated in only part of the molecule, as
      assessed by analysis with restriction endonucleases, indicated that gene A of PhiX, which
      needs to be nicked at a specific site by the gene A protein for RF replication, was not the
      main target for this inhibition by DNA methylation.  We propose that the loss of transfecting
      activity was due to hemimethylation of the PhiX RF interfering with the processively catalyzed
      movement of the replication fork.
AU  - Wang RY-H
AU  - Shenoy S
AU  - Ehrlich M
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1984 49: 674-679.

PMID- 3005977
VI  - 14
DP  - 1986
TI  - A human DNA-binding protein is methylation-specific and sequence-specific.
PG  - 1599-1614
AB  - A nuclear protein isolated from human placenta, methylated DNA-binding protein, binds
      selectively to DNA enriched in 5-methylcytosine.  We now demonstrate that MDBP is a
      sequence-specific, as well as methylation-specific, DNA-binding protein.  From restriction
      fragments of pBR322 DNA methylated with human DNA methyltransferase, one was bound to mDBP
      very much more strongly than any of the others.  For this preferential binding to MDBP, the
      DNA had to be methylated.  By a DNase I protection experiment (DNase I footprinting), a
      22-base sequence within this methylated restriction fragment was shown to be specifically
      protected by MDP.  The sequence-specificity of MDBP coupled with its dependence on DNA
      methylation suggests that this is one of the proteins which modulates important functions of
      human DNA methylation in vivo.
AU  - Wang RY-H
AU  - Zhang X-Y
AU  - Ehrlich M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1986 14: 1599-1614.

PMID- 3027666
VI  - 14
DP  - 1986
TI  - Methylated DNA-binding protein from human placenta recognizes specific methylated sites on several prokaryotic DNAs.
PG  - 9843-9860
AB  - Methylated DNA-binding protein (MDBP) from human placenta recognizes specific
      DNA sequences containing 5-methylcytosine (m5C) residues.  Comparisons of
      binding of various prokaryotic DNAs to MDBP indicate that m5CpG is present in
      the recognition sites for this protein but is only part of the recognition
      sequence.  Specific binding to MDBP was observed for bacteriophage XP12 DNA,
      which naturally contains ~1/3 of its residues as m5C, and for Micrococcus
      luteus DNA, M13mp8 replicative form (RF) DNA, and pBR322 when these three DNAs
      were methylated at CpG sites by human DNA methyltransferase.  Five DNA regions
      binding to MDBP have been localized by DNase I footprinting or restriction
      mapping in methylated pBR322 and M13mp8 RF DNAs.  A comparison of their
      sequences reveals a common 5'-m5CGRm5CG-3' element or closely related sequence
      in which one of the m5C residues may be replaced by a T.  In addition to this
      motif, one upstreaem and one downstream m5CpG as well as other common residues
      over an ~20-bp long region may be recognized by MDBP.
AU  - Wang RY-H
AU  - Zhang X-Y
AU  - Khan R
AU  - Zhou Y
AU  - Huang L-H
AU  - Ehrlich M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1986 14: 9843-9860.

PMID- 25028492
VI  - 111
DP  - 2014
TI  - Genomic characterization of three unique Dehalococcoides that respire on persistent polychlorinated biphenyls.
PG  - 12103-12108
AB  - Fastidious anaerobic bacteria play critical roles in environmental bioremediation of
      halogenated compounds. However, their characterization and application have
      been largely impeded by difficulties in growing them in pure culture. Thus far,
      no pure culture has been reported to respire on the notorious polychlorinated
      biphenyls (PCBs), and functional genes responsible for PCB detoxification remain
      unknown due to the extremely slow growth of PCB-respiring bacteria. Here we
      report the successful isolation and characterization of three Dehalococcoides
      mccartyi strains that respire on commercial PCBs. Using high-throughput
      metagenomic analysis, combined with traditional culture techniques,
      tetrachloroethene (PCE) was identified as a feasible alternative to PCBs to
      isolate PCB-respiring Dehalococcoides from PCB-enriched cultures. With PCE as an
      alternative electron acceptor, the PCB-respiring Dehalococcoides were boosted to
      a higher cell density (1.2 x 10(8) to 1.3 x 10(8) cells per mL on PCE vs. 5.9 x
      10(6) to 10.4 x 10(6) cells per mL on PCBs) with a shorter culturing time (30 d
      on PCE vs. 150 d on PCBs). The transcriptomic profiles illustrated that the
      distinct PCB dechlorination profile of each strain was predominantly mediated by
      a single, novel reductive dehalogenase (RDase) catalyzing chlorine removal from
      both PCBs and PCE. The transcription levels of PCB-RDase genes are 5-60 times
      higher than the genome-wide average. The cultivation of PCB-respiring
      Dehalococcoides in pure culture and the identification of PCB-RDase genes deepen
      our understanding of organohalide respiration of PCBs and shed light on in situ
      PCB bioremediation.
AU  - Wang S
AU  - Chng KR
AU  - Wilm A
AU  - Zhao S
AU  - Yang KL
AU  - Nagarajan N
AU  - He J
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2014 111: 12103-12108.

PMID- 25278523
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Polychlorinated Biphenyl-Dechlorinating Dehalococcoides  mccartyi Strain SG1, Which Carries a Circular Putative Plasmid.
PG  - e00901-14
AB  - Dehalococcoides mccartyi strain SG1, isolated from digester sludge, dechlorinates
      polychlorinated biphenyls (PCBs) to lower congeners. Here we report the draft
      genome sequence of SG1, which carries a 22.65 kbp circular putative plasmid.
AU  - Wang S
AU  - Chng KR
AU  - Wu C
AU  - Wilm A
AU  - Nagarajan N
AU  - He J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00901-14.

PMID- 30533910
VI  - 7
DP  - 2018
TI  - Draft Genome Sequence of Bacillus sp. Strain YSP-3, a Halophilic, Alkaliphilic Bacterium Isolated from a Salt Lake.
PG  - e00882-18
AB  - The halophilic, alkaliphilic bacterium Bacillus sp. strain YSP-3 was isolated from a salt
      lake. It grows optimally at 8% (wt/vol) NaCl (pH 9.0). The draft
      genome is composed of 4,006 predicted genes. Genomic analysis showed that various
      genes are potentially involved in the adaptation mechanisms for osmotic stress
      and pH homeostasis.
AU  - Wang S
AU  - Dong L
AU  - Zhao B
AU  - Xu S
AU  - Wu K
AU  - Wang H
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e00882-18.

PMID- 29880588
VI  - 6
DP  - 2018
TI  - Genome Sequence of Lactobacillus plantarum JMCC0013, Isolated from Traditional Chinese Fermented Milk.
PG  - e00407-18
AB  - Fermented food products have been consumed for thousands of years in China, so fermented
      Chinese foods may contain huge lactic acid bacterial resources. Here,
      we report the draft genome sequence of a Lactobacillus plantarum isolate,
      JMCC0013, collected from traditional Chinese fermented milk, which provides a
      precious resource for the genomic analysis of Lactobacillus strains.
AU  - Wang S
AU  - Feng L
AU  - Zhang D
AU  - Xue Y
AU  - Xun Y
AU  - Ke Y
AU  - Zhu H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00407-18.

PMID- 24906389
VI  - 15
DP  - 2014
TI  - Whole-genome sequencing of Mesorhizobium huakuii 7653R provides molecular insights into host specificity and symbiosis island dynamics.
PG  - 440
AB  - BACKGROUND: Evidence based on genomic sequences is urgently needed to confirm the
      phylogenetic relationship between Mesorhizobium strain MAFF303099 and M. huakuii.
      To define underlying causes for the rather striking difference in host
      specificity between M. huakuii strain 7653R and MAFF303099, several probable
      determinants also require comparison at the genomic level. An improved
      understanding of mobile genetic elements that can be integrated into the main
      chromosomes of Mesorhizobium to form genomic islands would enrich our knowledge
      of how genome dynamics may contribute to Mesorhizobium evolution in general.
      RESULTS: In this study, we sequenced the complete genome of 7653R and compared it
      with five other Mesorhizobium genomes. Genomes of 7653R and MAFF303099 were found
      to share a large set of orthologs and, most importantly, a conserved chromosomal
      backbone and even larger perfectly conserved synteny blocks. We also identified
      candidate molecular differences responsible for the different host specificities
      of these two strains. Finally, we reconstructed an ancestral Mesorhizobium
      genomic island that has evolved into diverse forms in different Mesorhizobium
      species. CONCLUSIONS: Our ortholog and synteny analyses firmly establish
      MAFF303099 as a strain of M. huakuii. Differences in nodulation factors and
      secretion systems T3SS, T4SS, and T6SS may be responsible for the unique host
      specificities of 7653R and MAFF303099 strains. The plasmids of 7653R may have
      arisen by excision of the original genomic island from the 7653R chromosome.
AU  - Wang S
AU  - Hao B
AU  - Li J
AU  - Gu H
AU  - Peng J
AU  - Xie F
AU  - Zhao X
AU  - Frech C
AU  - Chen N
AU  - Ma B
AU  - Li Y
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2014 15: 440.

PMID- 24625864
VI  - 2
DP  - 2014
TI  - Whole Genome Sequence of the Probiotic Strain Lactobacillus paracasei N1115, Isolated from Traditional Chinese Fermented Milk.
PG  - e00059-14
AB  - Lactobacillus paracasei N1115 is a new strain with probiotic properties isolated  from
      traditional homemade dairy products in Inner Mongolia, China. Here, we
      report the complete genome sequence of L. paracasei N1115, which shows high
      similarity to the well-studied probiotic Lactobacillus rhamnosus GG, and 3
      structures turned out to be inversions, according to the colinearity analysis of
      the BLAST alignment.
AU  - Wang S
AU  - Zhu H
AU  - He F
AU  - Luo Y
AU  - Kang Z
AU  - Lu C
AU  - Feng L
AU  - Lu X
AU  - Xue Y
AU  - Wang H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00059-14.

PMID- 29674539
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of a Putative New Bacterial Strain, I507, Isolated from  the Indian Ocean.
PG  - e00246-18
AB  - Bacterial strain I507 was isolated from the central Indian Ocean and may be a potential novel
      species, according to the 16S rRNA gene sequence. Here, we
      present its complete genome sequence and expect that it will provide researchers
      with valuable information to further understand its classification and function
      in the future.
AU  - Wang SY
AU  - Wei JQ
AU  - Chen H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00246-18.

PMID- 25908136
VI  - 3
DP  - 2015
TI  - Genome Sequence of Acidovorax citrulli Group 1 Strain pslb65 Causing Bacterial Fruit Blotch of Melons.
PG  - e00327-15
AB  - Acidovorax citrulli is typed into two groups, mainly based on the host. We determined the
      draft genome of A. citrulli group 1 strain pslb65. The strain was
      isolated from melon collected from Xinjiang province, China. The A. citrulli
      pslb65 genome contains 4,903,443 bp and has a G+C content of 68.8 mol%.
AU  - Wang T
AU  - Sun B
AU  - Yang Y
AU  - Zhao T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00327-15.

PMID- 25858831
VI  - 3
DP  - 2015
TI  - Genome Sequence of a Pseudomonas syringae pv. tabaci Strain, yuexi-1, Causing Wildfire Disease in Tobacco.
PG  - e00180-15
AB  - We determined the draft genome sequence of the Pseudomonas syringae pv. tabaci strain yuexi-1.
      It was isolated from tobacco sample of yuexi-1, Sichuan province,
      China, by our laboratory. The genome contains 6,232,497 bp and has a G+C content
      of 58.2 mol%.
AU  - Wang T
AU  - Yang Y
AU  - Zhao T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00180-15.

PMID- 25908132
VI  - 3
DP  - 2015
TI  - Genome Sequence of a Copper-Resistant Strain of Acidovorax citrulli Causing Bacterial Fruit Blotch of Melons.
PG  - e00310-15
AB  - Bacterial fruit blotch (BFB) of melons is a seed-borne disease caused by Acidovorax citrulli.
      We determined the draft genome of A. citrulli Tw6. The
      strain was isolated from a watermelon collected from Beijing, China. The A.
      citrulli Tw6 genome contains 5,080,614 bp and has a G+C content of 68.7 mol%.
AU  - Wang T
AU  - Yang Y
AU  - Zhao T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00310-15.

PMID- Not carried by PubMed...
VI  - 26
DP  - 1981
TI  - PflI, a restriction endonuclease from Pseudomonas fluorescens Migula.
PG  - 815-817
AB  - Over two hundred kinds of restriction endonucleases from 39 genuses, 94
      species, and 159 strains have been found up to now according to Roberts'
      statistics.  Many of them are isoschizomers.  Nothing about restriction
      endonucleases from Psuedomonas fluorescens Migula has been published.  This is
      a report on restriction endonuclease extracted from Pseudomonas fluorescens
      Migula.
AU  - Wang T-S
PT  - Journal Article
TA  - K'o Hsueh T'ung Pao
JT  - K'o Hsueh T'ung Pao
SO  - K'o Hsueh T'ung Pao 1981 26: 815-817.

PMID- 27417837
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Indiana C629, a Carbapenem-Resistant Bacterium Isolated from Chicken Carcass in China.
PG  - e00662-16
AB  - The carbapenem-resistant Salmonella enterica subsp. enterica serovar Indiana strain C629 was
      isolated from a chicken carcass collected from a slaughterhouse
      in Qingdao, China. The complete genome sequence of C629 contains a circular
      4,791,723-bp chromosome and a circular 210,106-bp plasmid. Genes involved in
      carbapenem resistance of this bacterium were identified by whole-genome analysis.
AU  - Wang W
AU  - Liu F
AU  - Peng Z
AU  - Li F
AU  - Ma A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00662-16.

PMID- 23788548
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of a Benzothiophene-Desulfurizing Bacterium, Gordona terrae Strain C-6.
PG  - e00381-13
AB  - Gordona terrae strain C-6 was isolated from oil-contaminated soil and is capable  of
      desulfurizing benzothiophene (BT). Here we report the draft genome sequence of
      G. terrae strain C-6, which may help to reveal the genetic basis of the BT
      biodesulfurization pathway.
AU  - Wang W
AU  - Ma T
AU  - Ren Y
AU  - Li G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00381-13.

PMID- 28153901
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Staphylococcus hominis BHG17 Isolated from Wild Bar-Headed Goose (Anser indicus) Feces.
PG  - e01552-16
AB  - Staphylococcus hominis belongs to a group of coagulase-negative staphylococci and is an
      opportunistic pathogen, usually found on the skin and mucous membranes.
      Studies involving S. hominis isolated from wild birds are scarce. Here, we report
      a 2.365-Mb draft genome sequence of S. hominis BHG17, isolated from the feces of
      a bar-headed goose.
AU  - Wang W
AU  - Zheng SS
AU  - Sharshov K
AU  - Sun H
AU  - Wu XQ
AU  - Yang F
AU  - Wang XL
AU  - Li LX
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01552-16.

PMID- 27174262
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Bacillus megaterium BHG1.1, a Strain Isolated from Bar-Headed Goose (Anser indicus) Feces on the Qinghai-Tibet Plateau.
PG  - e00317-16
AB  - Bacillus megaterium is a soil-inhabiting Gram-positive bacterium that is routinely used in
      industrial applications for recombinant protein production and
      bioremediation. Studies involving Bacillus megaterium isolated from waterfowl are
      scarce. Here, we report a 6.26-Mbp draft genome sequence of Bacillus megaterium
      BHG1.1, which was isolated from feces of a bar-headed goose.
AU  - Wang W
AU  - Zheng SS
AU  - Sun H
AU  - Cao J
AU  - Yang F
AU  - Wang XL
AU  - Li LX
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00317-16.

PMID- 26301592
VI  - 10
DP  - 2015
TI  - Genome Sequence Analysis of the Naphthenic Acid Degrading and Metal Resistant Bacterium Cupriavidus gilardii CR3.
PG  - E0132881
AB  - Cupriavidus sp. are generally heavy metal tolerant bacteria with the ability to
      degrade a variety of aromatic hydrocarbon compounds, although the degradation
      pathways and substrate versatilities remain largely unknown. Here we studied the
      bacterium Cupriavidus gilardii strain CR3, which was isolated from a natural
      asphalt deposit, and which was shown to utilize naphthenic acids as a sole carbon
      source. Genome sequencing of C. gilardii CR3 was carried out to elucidate
      possible mechanisms for the naphthenic acid biodegradation. The genome of C.
      gilardii CR3 was composed of two circular chromosomes chr1 and chr2 of
      respectively 3,539,530 bp and 2,039,213 bp in size. The genome for strain CR3
      encoded 4,502 putative protein-coding genes, 59 tRNA genes, and many other
      non-coding genes. Many genes were associated with xenobiotic biodegradation and
      metal resistance functions. Pathway prediction for degradation of
      cyclohexanecarboxylic acid, a representative naphthenic acid, suggested that
      naphthenic acid undergoes initial ring-cleavage, after which the ring fission
      products can be degraded via several plausible degradation pathways including a
      mechanism similar to that used for fatty acid oxidation. The final metabolic
      products of these pathways are unstable or volatile compounds that were not toxic
      to CR3. Strain CR3 was also shown to have tolerance to at least 10 heavy metals,
      which was mainly achieved by self-detoxification through ion efflux,
      metal-complexation and metal-reduction, and a powerful DNA self-repair mechanism.
      Our genomic analysis suggests that CR3 is well adapted to survive the harsh
      environment in natural asphalts containing naphthenic acids and high
      concentrations of heavy metals.
AU  - Wang X
AU  - Chen M
AU  - Xiao J
AU  - Hao L
AU  - Crowley DE
AU  - Zhang Z
AU  - Yu J
AU  - Huang N
AU  - Huo M
AU  - Wu J
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2015 10: E0132881.

PMID- 25700418
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Riemerella anatipestifer Serotype 1 Strain CH3.
PG  - e01594-14
AB  - Riemerella anatipestifer is a well-described pathogenic bacterium, which is reported worldwide
      as the cause of epizootic infectious polyserositis of waterfowl and other avian species. Here,
      we present the complete genome sequence  of R. anatipestifer strain CH3, the serotype 1
      prevalent in China.
AU  - Wang X
AU  - Ding C
AU  - Han X
AU  - Wang S
AU  - Yue J
AU  - Hou W
AU  - Cao S
AU  - Zou J
AU  - Yu S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01594-14.

PMID- 26002892
VI  - 81
DP  - 2015
TI  - Whole-Genome Sequence Analysis and Genome-Wide Virulence Gene Identification of Riemerella anatipestifer Strain Yb2.
PG  - 5093-5102
AB  - Riemerella anatipestifer is a well-described pathogen of waterfowl and other avian species
      that can cause septicemic and exudative diseases. In this study, we sequenced the complete
      genome of R. anatipestifer strain Yb2 and analyzed it against the published genomic sequences
      of R. anatipestifer strains DSM15868, RA-GD, RA-CH-1, and RA-CH-2. The Yb2 genome contains one
      circular chromosome of
      2,184,066 bp with a 35.73% GC content and no plasmid. The genome has 2,021 open reading frames
      that occupy 90.88% of the genome. A comparative genomic analysis revealed that genome
      organization is highly conserved among R. anatipestifer strains, except for four inversions of
      a sequence segment in Yb2. A phylogenetic analysis found that the closest neighbor of Yb2 is
      RA-GD. Furthermore, we constructed a library of 3,175 mutants by random transposon
      mutagenesis, and 100 mutants exhibiting more than 100-fold-attenuated virulence were obtained
      by animal screening experiments. Southern blot analysis and genetic characterization of the
      mutants led to the identification of 49 virulence genes. Of these, 25 encode cytoplasmic
      proteins, 6 encode cytoplasmic membrane proteins, 4 encode outer membrane proteins, and the
      subcellular localization of the remaining 14 gene products is unknown. The functional
      classification of orthologous-group clusters revealed that 16 genes are associated with
      metabolism, 6 are associated with cellular processing and signaling, and 4 are associated with
      information storage and processing. The functions of the other 23 genes are poorly
      characterized or unknown. This genome-wide study identified genes important to the virulence
      of R. anatipestifer.
AU  - Wang X
AU  - Ding C
AU  - Wang S
AU  - Han X
AU  - Yu S
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2015 81: 5093-5102.

PMID- 21914870
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Thermococcus sp. Strain 4557, a Hyperthermophilic Archaeon Isolated from a Deep-Sea Hydrothermal Vent  Area.
PG  - 5544-5545
AB  - Thermococcus sp. strain 4557 is a hyperthermophilic anaerobic archaeon isolated from the
      deep-sea hydrothermal vent Guaymas Basin site in the
      Gulf of California at a depth of 2,000 m. Here, we present the complete
      genome sequence of Thermococcus sp. 4557, which consists of a single
      circular chromosome of 2,011,320 bp with a G+C content of 56.08%.
AU  - Wang X
AU  - Gao Z
AU  - Xu X
AU  - Ruan L
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5544-5545.

PMID- 21914896
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of a Nonculturable Methanococcus maripaludis Strain Extracted in a Metagenomic Survey of Petroleum Reservoir Fluids.
PG  - 5595
AB  - Extraction of genome sequences from metagenomic data is crucial for reconstructing the
      metabolism of microbial communities that cannot be
      mimicked in the laboratory. A complete Methanococcus maripaludis genome
      was generated from metagenomic data derived from a thermophilic subsurface
      oil reservoir. M. maripaludis is a hydrogenotrophic methanogenic species
      that is common in mesophilic saline environments. Comparison of the genome
      from the thermophilic, subsurface environment with the genome of the type
      species will provide insight into the adaptation of a methanogenic genome
      to an oil reservoir environment.
AU  - Wang X
AU  - Greenfield P
AU  - Li D
AU  - Hendry P
AU  - Volk H
AU  - Sutherland TD
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5595.

PMID- 27873640
VI  - 2
DP  - 2014
TI  - Plasmid-mediated multidrug resistance and virulence in an avian pathogenic Escherichia coli strain isolated in China.
PG  - 57-58
AB  - Avian pathogenic Escherichia coli is the causative agent of avian colisepticaemia and has been
      previously reported as a potential zoonotic risk.  APEC strains often display a multidrug
      restance pattern including resistance to aminoglycosides, B-lactams, chloramphenicol,
      fluoroquinolones, tetracycles and trimethoprim/sulfamethoxazole.  In this study, an APEC
      strain (ACN001) isolated from the liver of a diseased chicken in China in 2010 was
      characterised.  ACN001 was shown to belong to phylogenetic group B2 and was confirmed to be
      highly virulent in chicken and mouse models using previously described methods.  Antimicrobial
      susceptibility testing performed according to Clinical and Laboratory Standards Institute
      standards revealed that the strain was multidrug-resistant, with high minimum inhibitory
      concentrations to amikacin (>16 ug/mL), ampicillin (256 ug/mL), chlooramphenical (256 ug/mL),
      ciprofloxacin (64 ug/mL), florfenicol (256 ug/mL), gentamicin (256 ug/mL), norfloxacin (64
      ug/mL), streptomycin (256 ug/mL) and tetracycline (256 ug/mL).
AU  - Wang X
AU  - Hao H
AU  - Xu Z
AU  - Zheng H
AU  - Liu C
AU  - Wei L
AU  - Zhang R
AU  - Bi D
AU  - Chen H
AU  - Tan C
PT  - Journal Article
TA  - J. Glob. Antimicrob. Resist.
JT  - J. Glob. Antimicrob. Resist.
SO  - J. Glob. Antimicrob. Resist. 2014 2: 57-58.

PMID- 26941151
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Chromobacterium violaceum Strain CV017.
PG  - e00080-16
AB  - We announce the draft genome sequence for Chromobacterium violaceum strain CV017, used as a
      model and tool to understand acyl-homoserine lactone-dependent quorum
      sensing. The assembly consists of 4,774,638-bp contained in 211 scaffolds.
AU  - Wang X
AU  - Hinshaw KC
AU  - Macdonald SJ
AU  - Chandler JR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00080-16.

PMID- 24459276
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Brevibacillus panacihumi Strain W25, a Halotolerant Hydrocarbon-Degrading Bacterium.
PG  - e01215-13
AB  - Brevibacillus panacihumi strain W25 was isolated from hydrocarbon-contaminated saline soil.
      Here, we report the 5.5-Mb draft genome sequence of this strain,
      which may provide insights into the mechanism of microbial hydrocarbon
      degradation in saline environments.
AU  - Wang X
AU  - Jin D
AU  - Zhou L
AU  - Wu L
AU  - An W
AU  - Chen Y
AU  - Zhao L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01215-13.

PMID- 24482528
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Gordonia alkanivorans Strain CGMCC6845, a Halotolerant Hydrocarbon-Degrading Bacterium.
PG  - e01274-13
AB  - Gordonia alkanivorans strain CGMCC6845 is a halotolerant hydrocarbon-degrading bacterium
      isolated from petroleum-contaminated saline soil. Here we present the
      5.0-Mb draft genome sequence of this strain, which will improve our understanding
      of the diversity of G. alkanivorans and the mechanisms of microbial hydrocarbon
      degradation in saline environment.
AU  - Wang X
AU  - Jin D
AU  - Zhou L
AU  - Wu L
AU  - An W
AU  - Zhao L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01274-13.

PMID- 24482505
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Advenella kashmirensis Strain W13003, a Polycyclic Aromatic Hydrocarbon-Degrading Bacterium.
PG  - e00003-14
AB  - Advenella kashmirensis strain W13003 is a polycyclic aromatic hydrocarbon (PAH)-degrading
      bacterium isolated from PAH-contaminated marine sediments. Here,
      we report the 4.8-Mb draft genome sequence of this strain, which will provide
      insights into the diversity of A. kashmirensis and the mechanism of PAH
      degradation in the marine environment.
AU  - Wang X
AU  - Jin D
AU  - Zhou L
AU  - Wu L
AU  - An W
AU  - Zhao L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00003-14.

PMID- 25323719
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Halotolerant Polycyclic Aromatic Hydrocarbon-Degrading Pseudomonas bauzanensis Strain W13Z2.
PG  - e01049-14
AB  - Pseudomonas bauzanensis W13Z2 is a halotolerant polycyclic aromatic hydrocarbon
      (PAH)-degrading bacterium isolated from petroleum-contaminated drill cuttings in
      the Bohai Sea. Here, we report the 8.6-Mb draft genome sequence of this strain,
      which will provide insights into the diversity of Pseudomonas and the mechanism
      of PAHs degradation in drill cuttings.
AU  - Wang X
AU  - Jin D
AU  - Zhou L
AU  - Wu L
AU  - Qi L
AU  - Li C
AU  - An W
AU  - Chen Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01049-14.

PMID- 26316640
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Aquamicrobium defluvii Strain W13Z1, a Psychrotolerant Halotolerant Hydrocarbon-Degrading Bacterium.
PG  - e00984-15
AB  - Aquamicrobium defluvii W13Z1 was isolated from petroleum-contaminated drill cuttings from the
      Bohai Sea and could degrade petroleum hydrocarbon with 5% NaCl  at 15 degrees C. Here, we
      present the 4.8-Mb draft genome sequence of this strain, which may provide useful information
      about the mechanism of petroleum degradation in drill cuttings.
AU  - Wang X
AU  - Jin D
AU  - Zhou L
AU  - Zhang Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00984-15.

PMID- 26227610
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Ochrobactrum anthropi Strain W13P3, a Halotolerant Polycyclic Aromatic Hydrocarbon-Degrading Bacterium.
PG  - e00867-15
AB  - Ochrobactrum anthropi W13P3 was isolated from saline soil contaminated by polycyclic aromatic
      hydrocarbons (PAHs) and could degrade PAHs with 5% NaCl. We
      report the 5.3-Mb draft genome sequence of this strain, which is helpful for
      understanding the diversity of Ochrobactrum spp. and the mechanism of PAH
      degradation in saline environments.
AU  - Wang X
AU  - Jin D
AU  - Zhou L
AU  - Zhang Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00867-15.

PMID- 26823598
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Pannonibacter phragmitetus Strain CGMCC9175, a Halotolerant Polycyclic Aromatic Hydrocarbon-Degrading Bacterium.
PG  - e01675-15
AB  - Pannonibacter phragmitetus CGMCC9175 is a halotolerant polycyclic aromatic hydrocarbon
      (PAH)-degrading bacterium isolated from PAH-contaminated intertidal
      zone sediment. Here, we report the 5.7-Mb draft genome sequence of this strain,
      which will provide insights into the diversity of Pannonibacter and the mechanism
      of PAH degradation in sediments.
AU  - Wang X
AU  - Jin D
AU  - Zhou L
AU  - Zhang Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01675-15.

PMID- 21325549
VI  - 49
DP  - 2011
TI  - Complete Genome Sequence of a Yersinia enterocolitica 'Old World' (3/O:9) Strain and Comparison with the 'New World' (1B/O:8) Strain.
PG  - 1251-1259
AB  - Yersinia enterocolitica is a heterogeneous bacterial species with a wide
      range of animal reservoirs through which human intestinal illness can be
      facilitated. In contrast to the epidemiological pattern observed in the
      United States, infections in China present a pattern similar to those in
      European countries and Japan, wherein "Old World" strains (biotypes 2-5)
      are prevalent. To gain insights into the evolution of Y. enterocolitica
      and pathogenic properties toward human hosts, we sequenced the genome of a
      biotype 3 strain 105.5R(r) (O:9) obtained from a Chinese patient.
      Comparative genome sequence analysis with strain 8081 (1B/O:8) revealed
      new insights into Y. enterocolitica. Both strains have more than 14%
      specific genes. In strain 105.5R(r), putative virulence factors were found
      in strain-specific genomic pathogenicity islands that comprised a novel
      type III secretion system and rtx-like genes. Many of the loci
      representing ancestral clusters, which are believed to contribute to
      enteric survival and pathogenesis, are present in strain 105.5R(r) but
      lost in strain 8081. Insertion elements in 105.5R(r) have a distinct
      pattern from those in strain 8081, and were exclusively located in a
      strain-specific region. In summary, our comparative genome analysis
      indicates that these two strains may have attained their pathogenicity by
      completely separate evolutionary events, and the 105.5R(r) strain, a
      representative of the "Old World" biogroup, lies in a branch of Y.
      enterocolitica that is distinct from the "New World" 8081 strain.
AU  - Wang X
AU  - Li Y
AU  - Jing H
AU  - Ren Y
AU  - Zhou Z
AU  - Wang S
AU  - Kan B
AU  - Xu J
AU  - Wang L
PT  - Journal Article
TA  - J. Clin. Microbiol.
JT  - J. Clin. Microbiol.
SO  - J. Clin. Microbiol. 2011 49: 1251-1259.

PMID- 
VI  - 208
DP  - 2015
TI  - Highly sensitive homogeneous electrochemical assay for methyltransferase activity based on methylation-responsive exonuclease III-assisted signal amplification.
PG  - 575-580
AB  - DNA methylation catalyzed by methyltransferase (MTase) plays a critical role in many
      biological processes. In this paper, a novel and highly sensitive homogeneous electrochemical
      assay was developed for the detection of DNA MTase based on methylation-responsive exonuclease
      III-assisted signal amplification. Upon the action of MTase/endonuclease on hairpin probe 1
      (HP 1) containing the methylation responsive sequence, single-stranded DNA segments are
      generated to hybridize with methylene blue (MB)-labeled hairpin probe 2 (HP 2). Then the
      digestion of HP 2 from the blunt 3' terminus by exonuclease III is activated, resulting in
      the release of MB-labeled mononucleotides and the complementary DNA segment which could
      hybridize with another HP 2 to initiate the signal amplification process. The MB-labeled
      mononucleotide, due to its less negative charge and smaller size, diffuses easily to the
      negatively charged indium tin oxide (ITO) electrode, generating an amplified electrochemical
      signal. The detection limit of the proposed assay was estimated to be 0.04 U/mL, which was
      better than or comparable to that of the biosensors previously reported. To the best of our
      knowledge, it is the first time to adopt exonuclease III-assisted signal amplification for
      homogeneous electrochemical assay of MTase activity, and this strategy exhibits the advantages
      of high sensitivity as well as simplicity. Since this assay is carried out in a homogeneous
      solution phase instead of on an electrode/solution interface, sophisticated probe
      immobilization processes could be avoided. The as-proposed strategy exhibits promising
      potential for MTase functional studies and related researches.
AU  - Wang X
AU  - Liu X
AU  - Hou T
AU  - Li W
AU  - Li F
PT  - Journal Article
TA  - Sens. Actuators B Chem.
JT  - Sens. Actuators B Chem.
SO  - Sens. Actuators B Chem. 2015 208: 575-580.

PMID- 22965091
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Plant Growth-Promoting Rhizobacterium Bacillus sp. Strain  916.
PG  - 5467-5468
AB  - Bacillus sp. strain 916, isolated from the soil, showed strong activity against Rhizoctonia
      solani. Here, we present the high-quality draft genome sequence of
      Bacillus sp. strain 916. Its 3.9-Mb genome reveals a number of genes whose
      products are possibly involved in promotion of plant growth or antibiosis.
AU  - Wang X
AU  - Luo C
AU  - Chen Z
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5467-5468.

PMID- 30250634
VI  - 13
DP  - 2018
TI  - Complete genome sequence of the Robinia pseudoacacia L. symbiont Mesorhizobium amorphae CCNWGS0123.
PG  - 18
AB  - Mesorhizobium amorphae CCNWGS0123 was isolated in 2006, from effective nodules of Robinia
      pseudoacacia L. grown in lead-zinc mine tailing site, in Gansu Province,
      China. M. amorphae CCNWGS0123 is an aerobic, Gram-negative, non-spore-forming rod
      strain. This paper characterized M. amorphae CCNWGS0123 and presents its complete
      genome sequence information and genome annotation. The 7,374,589 bp long genome
      which encodes 7136 protein-coding genes and 63 RNA coding genes, contains one
      chromosome and four plasmids. Moreover, a chromosome with no gaps was assembled.
AU  - Wang X
AU  - Luo Y
AU  - Liu D
AU  - Wang J
AU  - Wei S
AU  - Zhao L
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2018 13: 18.

PMID- 23045500
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Welan Gum-Producing Strain Sphingomonas sp. ATCC 31555.
PG  - 5989-5990
AB  - Sphingomonas sp. strain ATCC 31555 can produce an anionic heteropolysaccharide, welan gum,
      which shows excellent stability and viscosity retention even at high
      temperatures. Here we present a 4.0-Mb assembly of its genome sequence. We have
      annotated 10 coding sequences (CDSs) responsible for the welan gum biosynthesis
      and 55 CDSs related to monosaccharide metabolism.
AU  - Wang X
AU  - Tao F
AU  - Gai Z
AU  - Tang H
AU  - Xu P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5989-5990.

PMID- 24625872
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Magnetospirillum gryphiswaldense MSR-1.
PG  - e00171-14
AB  - We report the complete genomic sequence of Magnetospirillum gryphiswaldense MSR-1 (DSM 6361),
      a type strain of the genus Magnetospirillum belonging to the
      Alphaproteobacteria. Compared to the reported draft sequence, extensive
      rearrangements and differences were found, indicating high genomic flexibility
      and 'domestication' by accelerated evolution of the strain upon repeated
      passaging.
AU  - Wang X
AU  - Wang Q
AU  - Zhang W
AU  - Wang Y
AU  - Li L
AU  - Wen T
AU  - Zhang T
AU  - Zhang Y
AU  - Xu J
AU  - Hu J
AU  - Li S
AU  - Liu L
AU  - Liu J
AU  - Jiang W
AU  - Tian J
AU  - Li Y
AU  - Schuler D
AU  - Wang L
AU  - Li J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00171-14.

PMID- 26823959
VI  - 11
DP  - 2016
TI  - Complete genome sequence and characterization of avian pathogenic Escherichia coli field isolate ACN001.
PG  - 13
AB  - Avian pathogenic Escherichia coli is an important etiological agent of avian colibacillosis,
      which manifests as respiratory, hematogenous, meningitic, and
      enteric infections in poultry. It is also a potential zoonotic threat to human
      health. The diverse genomes of APEC strains largely hinder disease prevention and
      control measures. In the current study, pyrosequencing was used to analyze and
      characterize APEC strain ACN001 (= CCTCC 2015182(T) = DSMZ 29979(T)), which was
      isolated from the liver of a diseased chicken in China in 2010. Strain ACN001
      belongs to extraintestinal pathogenic E. coli phylogenetic group B1, and was
      highly virulent in chicken and mouse models. Whole genome analysis showed that it
      consists of six different plasmids along with a circular chromosome of 4,936,576
      bp, comprising 4,794 protein-coding genes, 108 RNA genes, and 51 pseudogenes,
      with an average G + C content of 50.56 %. As well as 237 coding sequences, we
      identified 39 insertion sequences, 12 predicated genomic islands, 8
      prophage-related sequences, and 2 clustered regularly interspaced short
      palindromic repeats regions on the chromosome, suggesting the possible occurrence
      of horizontal gene transfer in this strain. In addition, most of the virulence
      and antibiotic resistance genes were located on the plasmids, which would assist
      in the distribution of pathogenicity and multidrug resistance elements among E.
      coli populations. Together, the information provided here on APEC isolate ACN001
      will assist in future study of APEC strains, and aid in the development of
      control measures.
AU  - Wang X
AU  - Wei L
AU  - Wang B
AU  - Zhang R
AU  - Liu C
AU  - Bi D
AU  - Chen H
AU  - Tan C
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 13.

PMID- 24459253
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Acinetobacter baumannii ZW85-1.
PG  - e01083-13
AB  - Acinetobacter baumannii is an aerobic, nonmotile Gram-negative bacterium that causes
      nosocomial infections worldwide. Here, we report the complete genome
      sequence of Acinetobacter baumannii strain ZW85-1 and its two plasmids. One of
      the plasmids carries genes for NDM-1, which can hydrolyze a wide range of
      antibiotics.
AU  - Wang X
AU  - Zhang Z
AU  - Hao Q
AU  - Wu J
AU  - Xiao J
AU  - Jing H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01083-13.

PMID- 25237019
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Brachybacterium phenoliresistens Strain W13A50, a Halotolerant Hydrocarbon-Degrading Bacterium.
PG  - e00899-14
AB  - Brachybacterium phenoliresistens strain W13A50 was isolated from a petroleum-contaminated
      saline site, which could degrade hydrocarbon under high
      salinity conditions. Here, we present 4.2-Mb draft genome sequence of this
      strain, which will provide insights into the diversity of Brachybacterium and the
      mechanism of hydrocarbon degradation in saline environments.
AU  - Wang X
AU  - Zhang Z
AU  - Jin D
AU  - Zhou L
AU  - Wu L
AU  - Li C
AU  - Zhao L
AU  - An W
AU  - Chen Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00899-14.

PMID- 22628503
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Riemerella anatipestifer Reference Strain.
PG  - 3270-3271
AB  - Riemerella anatipestifer is an infectious pathogen causing serositis in ducks. We had the
      genome of the R. anatipestifer reference strain ATCC 11845 sequenced. The
      completed draft genome consists of one circular chromosome with 2,164,087 bp.
      There are 2,101 genes in the draft, and its GC content is 35.01%.
AU  - Wang X
AU  - Zhu D
AU  - Wang M
AU  - Cheng A
AU  - Jia R
AU  - Zhou Y
AU  - Chen Z
AU  - Luo Q
AU  - Liu F
AU  - Wang Y
AU  - Chen XY
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3270-3271.

PMID- 20581206
VI  - 192
DP  - 2010
TI  - Genome Sequence of the Milbemycins-producing Bacterium Streptomyces bingchenggensis.
PG  - 4526-4527
AB  - Streptomyces bingchenggensis is a soil dwelling bacterium producing the commercially important
      anthelmintic macrolide milbemycins. Besides
      milbemycins, the insecticidal polyether antibiotic nanchangmycin and some
      other antibiotics have also been isolated from this strain. Here we report
      the complete genome sequence of S. bingchenggensis. The availability of
      the genome sequence of S. bingchenggensis should enable us to understand
      the biosynthesis of these structurally intricate antibiotics better and
      facilitate rational improvement of this strain to increase their titers.
AU  - Wang XJ
AU  - Yan YJ
AU  - Zhang B
AU  - An J
AU  - Wang JJ
AU  - Tian J
AU  - Jiang L
AU  - Chen YH
AU  - Huang SX
AU  - Yin M
AU  - Zhang J
AU  - Gao AL
AU  - Liu CX
AU  - Zhu ZX
AU  - Xiang WS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 4526-4527.

PMID- 25278535
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Burkholderia pyrrocinia Lyc2, a Biological Control Strain That Can Suppress Multiple Plant Microbial Pathogens.
PG  - e00991-14
AB  - Burkholderia pyrrocinia strain Lyc2 was isolated from the tobacco rhizosphere in  China. This
      bacterium exhibits a remarkable capacity to inhibit the growth of
      multiple pathogens and shows strong suppression of cotton seedling damping-off.
      Here, we present the draft genome sequence of Burkholderia pyrrocinia strain
      Lyc2.
AU  - Wang XQ
AU  - Showmaker KC
AU  - Yu XQ
AU  - Bi T
AU  - Hsu CY
AU  - Baird SM
AU  - Peterson DG
AU  - Li XD
AU  - Lu SE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00991-14.

PMID- 21037001
VI  - 193
DP  - 2010
TI  - Complete genome sequence of probiotic Lactobacillus plantarum ST-III.
PG  - 313-314
AB  - Lactobacillus plantarum strain ST-III, a probiotic strain with several functions, was isolated
      from kimchi. Here we report the complete genome sequence of ST-III and compared it with two
      published L. plantarum genomes.
AU  - Wang Y
AU  - Chen C
AU  - Ai L
AU  - Zhou F
AU  - Zhou Z
AU  - Wang L
AU  - Zhang H
AU  - Chen W
AU  - Guo B
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 193: 313-314.

PMID- 27609930
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Ensifer adhaerens M78, a Mineral-Weathering Bacterium Isolated from Soil.
PG  - e00969-16
AB  - Ensifer adhaerens M78, a bacterium isolated from soil, can weather potash feldspar and release
      Fe, Si, and Al from rock under nutrient-poor conditions.
      Here, we report the draft genome sequence of strain M78, which may facilitate a
      better understanding of the molecular mechanism involved in mineral weathering by
      the bacterium.
AU  - Wang Y
AU  - Chen W
AU  - He L
AU  - Wang Q
AU  - Sheng XF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00969-16.

PMID- 24526644
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Serratia marcescens Strain LCT-SM166, a Space Flight Strain with a Specific Carbon Source Utilization Pattern.
PG  - e00069-14
AB  - Serratia marcescens has been detected in space habitats. To explore the influence of the space
      flight environment on this bacterium, we investigated the genome
      sequence of LCT-SM166, which was isolated after space flight and has a specific
      carbon source utilization pattern.
AU  - Wang Y
AU  - Du Y
AU  - Yuan Y
AU  - Guo Y
AU  - Wang J
AU  - Li T
AU  - Chang D
AU  - Liu Y
AU  - Jiang X
AU  - Dai W
AU  - Liu C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00069-14.

PMID- 27795233
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Pontibacter akesuensis Strain AKS 1T, Which Exhibits  Robust Nutrient Metabolism in Harsh Environments.
PG  - e00997-16
AB  - Pontibacter akesuensis strain AKS 1T was found in Akesu, Xinjiang Province, China, and
      exhibits the extraordinary ability to metabolize various substrates
      and is resistant to solar radiation. To gain insight into the bacterial genetic
      determinants for this adaptability, we report the complete genome sequence of
      strain AKS 1T.
AU  - Wang Y
AU  - He K
AU  - Jiang Y
AU  - Shen J
AU  - Yu B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00997-16.

PMID- 17068262
VI  - 314
DP  - 2006
TI  - Functional CpG methylation system in a social insect.
PG  - 645-647
AB  - DNA methylation systems are well characterized in vertebrates, but methylation in Drosophila
      melanogaster and other invertebrates remains
      controversial. Using the recently sequenced honey bee genome, we present a
      bioinformatic, molecular, and biochemical characterization of a functional
      DNA methylation system in an insect. We report on catalytically active
      orthologs of the vertebrate DNA methyltransferases Dnmt1 and Dnmt3a and b,
      two isoforms that contain a methyl-DNA binding domain, genomic
      5-methyl-deoxycytosine, and CpG-methylated genes. The honey bee provides
      an opportunity to study the roles of methylation in social contexts.
AU  - Wang Y
AU  - Jorda M
AU  - Jones PL
AU  - Maleszka R
AU  - Ling X
AU  - Robertson HM
AU  - Mizzen CA
AU  - Peinado MA
AU  - Robinson GE
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2006 314: 645-647.

PMID- 23144404
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Brucella abortus 134, a Biovar 1 Strain Isolated from Human.
PG  - 6658
AB  - Brucella abortus is one of the common pathogens causing brucellosis in China. Here, we report
      the genome sequence of B. abortus strain 134, a strain isolated
      from a human patient and belonging to biovar 1, the most highly represented
      biovar among B. abortus strains in China.
AU  - Wang Y
AU  - Ke Y
AU  - Gao G
AU  - Zhen Q
AU  - Yuan X
AU  - Wang Z
AU  - Xu J
AU  - Li T
AU  - Wang D
AU  - Huang L
AU  - Xu X
AU  - Chen Z
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6658.

PMID- 23144429
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Brucella canis BCB018, a Strain Isolated from a Human Patient.
PG  - 6697-6698
AB  - Brucella canis is considered a rare cause of human brucellosis because of difficulties in
      presumptive diagnosis and underestimation of the incidence. Here,
      we report the draft genome sequence of a Brucella canis isolate, BCB018, isolated
      from a human patient, providing precious resources for comparative genomics
      analysis of Brucella field strains.
AU  - Wang Y
AU  - Ke Y
AU  - Zhen Q
AU  - Yuan X
AU  - Xu J
AU  - Qiu Y
AU  - Wang Z
AU  - Li T
AU  - Wang D
AU  - Huang L
AU  - Chen Z
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6697-6698.

PMID- 24786961
VI  - 2
DP  - 2014
TI  - Genome Sequence of the Nonpathogenic Pseudomonas aeruginosa Strain ATCC 15442.
PG  - e00421-14
AB  - Pseudomonas aeruginosa ATCC 15442 is an environmental strain of the Pseudomonas genus. Here,
      we present a 6.77-Mb assembly of its genome sequence. Besides giving
      insights into characteristics associated with the pathogenicity of P. aeruginosa,
      such as virulence, drug resistance, and biofilm formation, the genome sequence
      may provide some information related to biotechnological utilization of the
      strain.
AU  - Wang Y
AU  - Li C
AU  - Gao C
AU  - Ma C
AU  - Xu P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00421-14.

PMID- 28642380
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Bacillus paralicheniformis MDJK30, a Plant Growth-Promoting Rhizobacterium with Antifungal Activity.
PG  - e00577-17
AB  - Bacillus paralicheniformis MDJK30 was isolated from the rhizosphere of a peony. It could
      control the pathogen of peony root rot. Here, we report the complete
      genome sequence of B. paralicheniformis MDJK30. Eleven secondary metabolism gene
      clusters were predicted.
AU  - Wang Y
AU  - Liu H
AU  - Liu K
AU  - Wang C
AU  - Ma H
AU  - Li Y
AU  - Hou Q
AU  - Liu F
AU  - Zhang T
AU  - Wang H
AU  - Wang B
AU  - Ma J
AU  - Ge R
AU  - Xu B
AU  - Yao G
AU  - Xu W
AU  - Fan L
AU  - Ding Y
AU  - Du B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00577-17.

PMID- 29242217
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Glycomyces fuscus TRM 49117, Isolated from a Hypersaline Soil Sample.
PG  - e01258-17
AB  - Glycomyces spp. are rare actinomycetes that are potential antibiotic producers. Here, we
      report the draft genome sequence of Glycomyces fuscus TRM 49117. This is
      the first genome report of a bacterium belonging to the genus Glycomyces The
      genome information of G. fuscus will contribute to studies on the structure and
      function of antibiotics.
AU  - Wang Y
AU  - Luo X
AU  - Zhang L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01258-17.

PMID- 26868402
VI  - 4
DP  - 2016
TI  - Genome Sequence of Selenium-Solubilizing Bacterium Caulobacter vibrioides T5M6.
PG  - e01721-15
AB  - Caulobacter vibrioides T5M6 is a Gram-negative strain that strongly solubilizes selenium (Se)
      mineral into Se(IV) and was isolated from a selenium mining area in
      Enshi, southwest China. This strain produces the phytohormone IAA and promotes
      plant growth. Here we present the genome of this strain containing a large number
      of genes encoding resistances to copper and antibiotics.
AU  - Wang Y
AU  - Qin Y
AU  - Kot W
AU  - Zhang F
AU  - Zheng S
AU  - Wang G
AU  - Hansen LH
AU  - Rensing C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01721-15.

PMID- 25077775
VI  - 4
DP  - 2014
TI  - Single molecular investigation of DNA looping and aggregation by restriction endonuclease BspMI.
PG  - 5897
AB  - DNA looping and aggregation induced by restriction endonuclease BspMI are studied by atomic
      force microscopy (AFM) and magnetic tweezers (MT). With Ca2+ substituted for the normal enzyme
      cofactor Mg2+ and enzyme concentration below the critical concentration of 6 units/mL, AFM
      images of DNA-BspMI complex show that the number of binding and looping events increases with
      enzyme concentration. At the critical concentration 6 of units/mL, all the BspMI binding sites
      are saturated. It is worth noting that nonspecific BspMI binding to DNA at saturation
      concentration represents more than 8% of the total BspMI-DNA complexes directly observed in
      AFM images. Furthermore, we used MT to prove that additional loops can form when enzyme
      concentration is higher than its saturation valueand the complex is incubated for a long time
      (>2 hrs). We ascribe this phenomenon to the aggregation of enzymes. The force spectroscopy of
      the BspMI-DNA complex shows that the pulling force required to open the loop of the complex at
      less than saturation concentration has a peak at about 3 pN, which is lower than the force
      required to open additional loops due to enzyme aggregation at higher than saturation
      concentration (>6 pN).
AU  - Wang Y
AU  - Ran S
AU  - Yang G
PT  - Journal Article
TA  - Sci. Rep.
JT  - Sci. Rep.
SO  - Sci. Rep. 2014 4: 5897.

PMID- 15461426
VI  - 58
DP  - 2004
TI  - Cytosine methylation is not the major factor inducing CpG dinucleotide deficiency in bacterial genomes.
PG  - 692-700
AB  - CpG dinucleotide deficiency has been found in viruses, mitochondria, prokaryotes, and
      eukaryotes. The consensual explanation is that it is
      due to deamination of methylated cytosines, as established for
      vertebrate and plants. However, we still do not know whether C5
      cytosine methylation is also the major cause of CpG deficiency in
      bacteria. By combining annotation and experimental data identifying the
      presence of C5 cytosine methyltransferases with analysis of CpG
      relative abundance in 67 bacterial species, we found that CpG relative
      abundance in most bacterial genomes that have cytosine C5
      methyltransferases tends to be in the normal range (observed/expected
      values between 0.82 and 1.21). In contrast, many bacterial species
      likely to be lacking C5 cytosine methylation showed CpG deficiency.
      Furthermore, when comparing genomes with one another, TpG and CpA
      relative abundances were found to be independent from CpG relative
      abundance. This contrasted with intragenome analyses, where C(3)pG(1)
      relative abundance (the subscripts refer to position of a nucleotide in
      a codon) was found to be generally positively correlated with T(3)pG(1)
      relative abundances when plotted against GC content in protein coding
      sequences (CDSs). This suggests the existence of alternative mechanisms
      contributing to CpG deficiency in bacteria.
AU  - Wang Y
AU  - Rocha EPC
AU  - Leung FCC
AU  - Danchin A
PT  - Journal Article
TA  - J. Mol. Evol.
JT  - J. Mol. Evol.
SO  - J. Mol. Evol. 2004 58: 692-700.

PMID- 8254319
VI  - 139
DP  - 1993
TI  - Transformation of Helicobacter pylori  by chromosomal metronidazole resistance and by a plasmid with a selectable chloramphenicol resistance marker.
PG  - 2485-2493
AB  - Most strains of Helicobacter pylori are naturally competent for uptake of chromosomal DNA.
      Transformation frequencies for streptomycin resistance or rifampicin resistance markers ranged
      from 1 x 10^-4 to 1 x 10^-3 per viable cell using a plate transformation procedure.
      Transformation of a metronidazole resistance marker was demonstrated when either a
      laboratory-derived mutant or an MtrR clinical isolate were used as the source of donor DNA.
      MtrR was transformed at a frequency of 3 x 10^-5 per viable cell.  All H. pylori strains
      tested produce large amounts of DNAase, which may reduce DNA available for transformation.
      Four H. pylori plasmids were isolated.  DNA fragments from H. pylori plasmids were deleted or
      rearranged when cloned in pUC19 and propagated in Escherichia coli DH5a.  An H. pylori
      plasmid, pUOA26 which contained a chloramphenicol resistance determinant from Campylobacter
      coli, was constructed in H. pylori.  This plasmid could be successfully introduced by natural
      transformation only into H. pylori recipients which contained a homologous resident plasmid.
      Transformation of pUOA26 into plasmid-free cells of H. pylori was achieved by electroporation.
      Transformation frequencies were 1 x 10^-4 transformants per viable cell when plasmid DNA was
      isolated from the same strain; however, introduction of pUOA26 DNA derived from H. pylori 8091
      into a different H. pylori strain, NCTC 11639, resulted in transformation at much lower
      frequencies (less than or equal to 1 x 10-7 per viable cell). Changes in plasmid restriction
      patterns were also noted when pUOA26 was isolated from H. pylori NCTC 11639, suggesting the
      presence of at least two different DNA restriction and modification systems in H. pylori which
      may interfere with uptake of plasmid DNA.
AU  - Wang Y
AU  - Roos KP
AU  - Taylor DE
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1993 139: 2485-2493.

PMID- 23929480
VI  - 1
DP  - 2013
TI  - Genome Sequence of Klebsiella pneumoniae Strain ATCC 25955, an Oxygen-Insensitive Producer of 1,3-Propanediol.
PG  - e00587-13
AB  - Klebsiella pneumoniae strain ATCC 25955 is a 1,3-propanediol-producing bacterium  that is
      insensitive to oxygen. Here, we present a 5.29-Mb assembly of its genome
      sequence. We have annotated 10 coding sequences (CDSs) for 1,3-propanediol
      fermentation and 18 CDSs for glycerol uptake. The CDSs related to virulence and
      by-product formation were also annotated.
AU  - Wang Y
AU  - Tao F
AU  - Li C
AU  - Li L
AU  - Xu P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00587-13.

PMID- 23908285
VI  - 1
DP  - 2013
TI  - Genome Sequence of Clostridium diolis Strain DSM 15410, a Promising Natural Producer of 1,3-Propanediol.
PG  - e00542-13
AB  - Clostridium diolis strain DSM 15410 is considered one of the best natural producers of
      1,3-propanediol because of its appreciable substrate-tolerant
      ability, yield, and productivity. Here, we present a 5.85-Mb assembly of its
      genome sequence. We have annotated the coding sequences responsible for glycerol
      utilization and 1,3-propanediol fermentation.
AU  - Wang Y
AU  - Tao F
AU  - Tang H
AU  - Xu P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00542-13.

PMID- 21705607
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Lactobacillus kefiranofaciens ZW3.
PG  - 4280-4281
AB  - Lactobacillus kefiranofaciens ZW3 was isolated in Tibet, China, from kefir grain, a
      traditional dairy product that is known to provide many health
      benefits to humans. Here, we present the genome features of L.
      kefiranofaciens ZW3 and the identification of a gene cluster related to
      the synthesis of exopolysaccharide, an important constituent of the
      Tibetan kefir.
AU  - Wang Y
AU  - Wang J
AU  - Ahmed Z
AU  - Bai X
AU  - Wang J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4280-4281.

PMID- 25059875
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Bacillus amyloliquefaciens EBL11, a New Strain of Plant  Growth-Promoting Bacterium Isolated from Rice Rhizosphere.
PG  - e00732-14
AB  - Bacillus amyloliquefaciens strain EBL11 is a bacterium that can promote plant growth by
      inhibiting the growth of fungi on plant surfaces and providing
      nutrients as a nonchemical biofertilizer. The estimated genome of this strain is
      4.05 Mb in size and harbors 3,683 coding genes (CDSs).
AU  - Wang Y
AU  - Wang X
AU  - Greenfield P
AU  - Jin D
AU  - Bai Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00732-14.

PMID- 26021929
VI  - 3
DP  - 2015
TI  - Genome Sequence of Lactobacillus curieae CCTCC M 2011381T, a Novel Producer of Gamma-aminobutyric Acid.
PG  - e00552-15
AB  - Lactobacillus curieae CCTCC M 2011381(T) is a novel species of the genus Lactobacillus and a
      gamma-aminobutyric acid producer that was isolated from
      stinky tofu brine. Here, we present a 2.19-Mb assembly of its genome, which may
      provide further insights into the molecular mechanisms underlying its beneficial
      properties.
AU  - Wang Y
AU  - Wang Y
AU  - Lang C
AU  - Wei D
AU  - Xu P
AU  - Xie J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00552-15.

PMID- 22843602
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Serratia marcescens Strain LCT-SM213.
PG  - 4477-4478
AB  - Serratia marcescens is a species of Gram-negative, rod-shaped bacterium of the family
      Enterobacteriaceae. S. marcescens can cause nosocomial infections,
      particularly catheter-associated bacteremia, urinary tract infections, and wound
      infections. Here, we present the draft genome sequence of Serratia marcescens
      strain LCT-SM213, which was isolated from CGMCC 1.1857.
AU  - Wang Y
AU  - Yuan Y
AU  - Zhou L
AU  - Su Q
AU  - Fang X
AU  - Li T
AU  - Wang J
AU  - Chang D
AU  - Su L
AU  - Xu G
AU  - Guo Y
AU  - Yang R
AU  - Liu C
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4477-4478.

PMID- 25059862
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Two Marine Phototrophic Bacteria, Erythrobacter longus  Strain DSM 6997 and Erythrobacter litoralis Strain DSM 8509.
PG  - e00677-14
AB  - Aerobic anoxygenic phototrophic bacteria (AAPB) are important functional groups and are widely
      distributed in the global upper ocean. Here we report the draft
      genomic sequences of two marine AAPB isolates belonging to the genus
      Erythrobacter, Erythrobacter longus strain DSM 6997 and Erythrobacter litoralis
      strain DSM 8509.
AU  - Wang Y
AU  - Zhang R
AU  - Zheng Q
AU  - Jiao N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00677-14.

PMID- 27795283
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Magnetospirillum sp. Strain XM-1, Isolated from the Xi'an City Moat, China.
PG  - e01171-16
AB  - The magnetotactic bacterium Magnetospirillum sp. strain XM-1 was recently isolated from the
      Xi'an City moat, China. It belongs to the Rhodospirillaceae
      family in the Alphaproteobacteria class. Here, we report the complete genome
      sequence of XM-1. The genome contains a single circular chromosome of 4,825,187
      bp and a plasmid of 167,290 bp.
AU  - Wang Y
AU  - Zhang T
AU  - Lin W
AU  - Zhang B
AU  - Cai Y
AU  - Yang C
AU  - Li J
AU  - Xu H
AU  - Pan Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01171-16.

PMID- 25197458
VI  - 9
DP  - 2014
TI  - Non-contiguous finished genome sequence of Anoxybacillus flavithermus subsp. yunnanensis type strain (E13(T)), a strictly thermophilic and organic  solvent-tolerant bacterium.
PG  - 735-743
AB  - Anoxybacillus flavithermus subsp. yunnanensis is the only strictly thermophilic bacterium that
      is able to tolerate a broad range of toxic solvents at its optimal
      temperature of 55-60 degrees C. The type strain E13(T) was isolated from
      water-sediment slurries collected from a hot spring. This study presents the
      draft genome sequence of A. flavithermus subsp. yunnanensis E13(T) and its
      annotation. The 2,838,393bp long genome (67 contigs) contains 3,035
      protein-coding genes and 85 RNA genes, including 10 rRNA genes, and no plasmids.
      The genome information has been used to compare with the genomes from A.
      flavithermus subsp. flavithermus strains.
AU  - Wang Y
AU  - Zheng Y
AU  - Wang M
AU  - Gao Y
AU  - Xiao Y
AU  - Peng H
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 735-743.

PMID- 26555137
VI  - 9
DP  - 2015
TI  - Distribution of Plasmids in Distinct Leptospira Pathogenic Species.
PG  - E0004220
AB  - Leptospirosis, caused by pathogenic Leptospira, is a worldwide zoonotic
      infection. The genus Leptospira includes at least 21 species clustered into three
      groups-pathogens, non-pathogens, and intermediates-based on 16S rRNA phylogeny.
      Research on Leptospira is difficult due to slow growth and poor transformability
      of the pathogens. Recent identification of extrachromosomal elements besides the
      two chromosomes in L. interrogans has provided new insight into genome complexity
      of the genus Leptospira. The large size, low copy number, and high similarity of
      the sequence of these extrachromosomal elements with the chromosomes present
      challenges in isolating and detecting them without careful genome assembly. In
      this study, two extrachromosomal elements were identified in L. borgpetersenii
      serovar Ballum strain 56604 through whole genome assembly combined with S1
      nuclease digestion following pulsed-field gel electrophoresis (S1-PFGE) analysis.
      Further, extrachromosomal elements in additional 15 Chinese epidemic strains of
      Leptospira, comprising L. borgpetersenii, L. weilii, and L. interrogans, were
      successfully separated and identified, independent of genome sequence data.
      Southern blot hybridization with extrachromosomal element-specific probes,
      designated as lcp1, lcp2 and lcp3-rep, further confirmed their occurrences as
      extrachromosomal elements. In total, 24 plasmids were detected in 13 out of 15
      tested strains, among which 11 can hybridize with the lcp1-rep probe and 11 with
      the lcp2-rep probe, whereas two can hybridize with the lcp3-rep probe. None of
      them are likely to be species-specific. Blastp search of the lcp1, lcp2, and
      lcp3-rep genes with a nonredundant protein database of Leptospira species genomes
      showed that their homologous sequences are widely distributed among clades of
      pathogens but not non-pathogens or intermediates. These results suggest that the
      plasmids are widely distributed in Leptospira species, and further elucidation of
      their biological significance might contribute to our understanding of biology
      and infectivity of pathogenic spirochetes.
AU  - Wang Y
AU  - Zhuang X
AU  - Zhong Y
AU  - Zhang C
AU  - Zhang Y
AU  - Zeng L
AU  - Zhu Y
AU  - He P
AU  - Dong K
AU  - Pal U
AU  - Guo X
AU  - Qin J
PT  - Journal Article
TA  - PLoS Neglected Trop. Dis.
JT  - PLoS Neglected Trop. Dis.
SO  - PLoS Neglected Trop. Dis. 2015 9: E0004220.

PMID- 22947514
VI  - 41
DP  - 2013
TI  - A label-free electrochemical assay for methyltransferase activity detection based on the controllable assembly of single wall carbon nanotubes.
PG  - 238-243
AB  - A sensitive label-free 'signal-on' electrochemical approach for detection of
      methyltransferases (MTase) activity is developed based on
      the signal transduction and amplification of single wall carbon
      nanotubes (SWCNTs). In this method, the oligonucleotide I is first
      self-assembled on the electrode via Au-S bonding. After hybridization
      with its complement ssDNA (oligonucleotide II), duplex strand DNA
      (dsDNA) probes containing specific recognition sequence of Dam MTase
      and methylation-sensitive restriction endonuclease Dpn I is then formed
      on the electrode. In the presence of Dam MTase and Dpn I, the dsDNA
      probes are methylated and subsequently cleaved into two dsDNA
      fragments. After heating, the remained dsDNA fragments on the electrode
      melted into ssDNA fragments. Then the SWCNTs can be controllably
      assembled on the ssDNA fragments remained on the electrode, mediating
      efficient electron transfer between the electrode and electroactive
      species. It generates measurable current signal (eT ON), which is
      related to the concentration of the Dam MTase. The resulting change in
      electron transfer efficiency is readily measured by differential pulse
      voltammetry at Dam MTase concentrations as low as 0.04 U/mL. This
      method does not need electroactive molecules labeling on the
      methylation-responsive DNA probes. The linear response of the developed
      facile signal-on electrochemical sensing system for Dam MTase is in the
      range of 0.1-1.0 U/mL. In addition, such a SWCNTs based electrochemical
      assay also has the ability to screen inhibitors for Dam MTase.
AU  - Wang YH
AU  - He XX
AU  - Wang KM
AU  - Su J
AU  - Chen ZF
AU  - Yan GP
AU  - Du YD
PT  - Journal Article
TA  - Biosensors and Bioelectronics
JT  - Biosensors and Bioelectronics
SO  - Biosensors and Bioelectronics 2013 41: 238-243.

PMID- 
VI  - 21
DP  - 2013
TI  - Engineering an XID-Site Specific I-AniI Homing Endonuclease through Combination of Rational Design and Directed Evolution.
PG  - S122-S123
AB  - LAGLIDADG homing endonucleases (LHEs) are highly specific compact endonucleases with typical
      20 base pair recognition sites, and thus are ideal scaffolds for engineering site-specific
      enzymes for genome editing applications.  Here, we describe a progressive approach to LHE
      engineering that combines rational design with directed evolution using yeast surface
      display-based high throughput cleavage selection.  This approach was employed to alter the
      binding and cleavage specificity of the I-Anil LHE to recognize a specific, unique mutation in
      the mouse Bruton tyrosine kinase (Btk) gene - this mutation is known to cause mouse X-linked
      immunodeficiency (XID) - a model of human X-linked agammaglobulimemia (XLA).  The required
      retargeting of I-AniI involved resculpting of the DNA contact interface to accommodate nine
      base differences from the native sequence.  As a first step, multiple site-specific variants
      were engineered through randomization of amino acid residues contacting clusters of base pairs
      altered in the partial targets.  As directly combining these "cluster target" LHE variants
      failed to generate active enzymes cleaving the combined targets, variants with successful
      re-specification of residue clusters proximal to the active site were subjected to a
      progressive redesign strategy in which specificity and activity were extended outward across
      the N-terminal and C-terminal XID half-site interfaces.  Successful "half-site" redesigns were
      then combined to generate an active enzyme recognizing the full XID target site, and this
      enzyme was refined by random mutatgenesis to create an enzyme with wildtype-level activity in
      vitro and in cellulo reporter assays.  Finally, the in cellulo activity of this enzyme was
      further increased by fusing to Transcription Activator-Like Effector (TALE) site-specific DNA
      binding domain to copensate the partially reduced binding affinity of engineered XID enzyme.
      This study not only provides a valuable roadmap for further LHE engineering by effectively
      combining rationale and directed evolution strategies, but also demonstrates a novel means to
      increase the binding affinity, thus the cleavage efficacy of engineered LHEs.
AU  - Wang YP
AU  - Jarjour J
AU  - Boissel S
AU  - Thyme S
AU  - Khan I
AU  - Pangallo J
AU  - Baker D
AU  - Stoddard B
AU  - Scharenberg AM
AU  - Rawlings DJ
PT  - Journal Article
TA  - Mol. Ther.
JT  - Mol. Ther.
SO  - Mol. Ther. 2013 21: S122-S123.

PMID- 25013146
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Polaromonas glacialis Strain R3-9, a Psychrotolerant Bacterium Isolated from Arctic Glacial Foreland.
PG  - e00695-14
AB  - Here we report the draft genome sequence of the psychrotolerant Polaromonas glacialis strain
      R3-9, isolated from Midtre Lovenbreen glacial foreland near
      Ny-Alesund, Svalbard Archipelago, Norway.
AU  - Wang Z
AU  - Chang X
AU  - Yang X
AU  - Pan L
AU  - Dai J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00695-14.

PMID- 26404584
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Marinobacter sp. CP1, Isolated from a Self-Regenerating Biocathode Biofilm.
PG  - e01103-15
AB  - Marinobacter sp. CP1 was isolated from a self-regenerating and self-sustaining biocathode
      biofilm that can fix CO2 and generate electric current. We present the complete genome
      sequence of this strain, which consists of a circular 4.8-Mbp chromosome, to understand the
      mechanism of extracellular electron transfer in a microbial consortium.
AU  - Wang Z
AU  - Eddie BJ
AU  - Malanoski AP
AU  - Hervey WJ IV
AU  - Lin B
AU  - Strycharz-Glaven SM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01103-15.

PMID- 27174270
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Labrenzia sp. Strain CP4, Isolated from a Self-Regenerating Biocathode Biofilm.
PG  - e00354-16
AB  - Here, we present the complete genome sequence of Labrenzia sp. strain CP4, isolated from an
      electricity-consuming marine biocathode biofilm. Labrenzia sp.
      strain CP4 consists of a circular 5.2 Mbp chromosome and an 88 Kbp plasmid.
AU  - Wang Z
AU  - Eddie BJ
AU  - Malanoski AP
AU  - Hervey WJ IV
AU  - Lin B
AU  - Strycharz-Glaven SM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00354-16.

PMID- 25635019
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of the Bioluminescent Marine Bacterium Vibrio harveyi ATCC 33843 (392 [MAV]).
PG  - e01493-14
AB  - Vibrio harveyi is a Gram-negative marine gamma-proteobacterium that is known to be a
      formidable pathogen of aquatic animals and is a model organism for the study
      of bacterial bioluminescence and quorum sensing. In this report, we describe the
      complete genome sequence of the most studied strain of this species: V. harveyi
      ATCC 33843 (392 [MAV]).
AU  - Wang Z
AU  - Hervey WJ IV
AU  - Kim S
AU  - Lin B
AU  - Vora GJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01493-14.

PMID- 21936919
VI  - 12
DP  - 2011
TI  - Genomic Insights into An Obligate Epibiotic Bacterial Predator: Micavibrio aeruginosavorus ARL-13.
PG  - 453
AB  - Background: Although bacterial predators play important roles in the dynamics of natural
      microbial communities,
      little is known about the molecular mechanism of bacterial predation and the evolution of
      diverse predatory
      lifestyles.
      Results: We determined the complete genome sequence of Micavibrio aeruginosavorus ARL-13, an
      obligate
      bacterial predator that feeds by "leeching" externally to its prey. Despite being an obligate
      predator depending on
      prey for replication, M. aeruginosavorus encodes almost all major metabolic pathways. However,
      our genome
      analysis suggests that there are multiple amino acids that it can neither make nor import
      directly from the
      environment, thus providing a simple explanation for its strict dependence on prey.
      Remarkably, despite apparent
      genome reduction, there is a massive expansion of genomic islands of foreign origin. At least
      nine genomic islands
      encode many genes that are likely important for Micavibrio-prey interaction such as
      hemolysin-related proteins.
      RNA-Seq analysis shows substantial transcriptome differences between the attack phase, when M.
      aeruginosavorus
      seeks its prey, and the attachment phase, when it feeds and multiplies. Housekeeping genes as
      well as genes
      involved in protein secretion were all dramatically up-regulated in the attachment phase. In
      contrast, genes
      involved in chemotaxis and flagellum biosynthesis were highly expressed in the attack phase
      but were shut down
      in the attachment phase. Our transcriptomic analysis identified additional genes likely
      important in Micavibrio
      predation, including porins, pilins and many hypothetical genes.
      Conclusions: The findings from our phylogenomic and transcriptomic analyses shed new light on
      the biology and
      evolution of the epibiotic predatory lifestyle of M. aeruginosavorus. The analysis reported
      here and the availability of
      the complete genome sequence should catalyze future studies of this organism.
AU  - Wang Z
AU  - Kadouri D
AU  - Wu M
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2011 12: 453.

PMID- 23929482
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Fast-Growing Marine Bacterium Vibrio natriegens Strain ATCC 14048.
PG  - e00589-13
AB  - Vibrio natriegens bacteria are Gram-negative aquatic microorganisms that are found primarily
      in coastal seawater and sediments and are perhaps best known for
      their high growth rates (generation time of <10 min). In this study, we report
      the first sequenced genome of this species, that of the type strain Vibrio
      natriegens ATCC 14048, a salt marsh mud isolate from Sapelo Island, GA.
AU  - Wang Z
AU  - Lin B
AU  - Hervey WJ IV
AU  - Vora GJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00589-13.

PMID- 25103769
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of the Endosymbiont of Acanthamoeba Strain UWC8, an Amoeba Endosymbiont Belonging to the 'Candidatus Midichloriaceae' Family in  Rickettsiales.
PG  - e00791-14
AB  - The endosymbiont of Acanthamoeba strain UWC8 is an obligate amoeba endosymbiont belonging to
      the family of 'Candidatus Midichloriaceae' in Rickettsiales. We
      report here the complete genome sequence of this bacterium, which should catalyze
      future studies of amoeba-symbiont interactions.
AU  - Wang Z
AU  - Wu M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00791-14.

PMID- 
VI  - 31
DP  - 2009
TI  - DNA methyltransferases: classification, functions and research progress.
PG  - 903-912
AB  - DNA methylation is a postreplicative modification occurred in most prokaryotic and eukaryotic
      genomes, which has a variety of important biological functions including regulation of gene
      expression, gene imprinting, preservation of chromosomal integrity, and X-chromosome
      inactivation. According to their structure and functions, DNA methyltransferases (Dnmts) are
      divided into two major families in mammalian cells: maintenance methyltransferase (Dnmt1) and
      de novo methyltransferases (Drmt3a, Dnmt3b, and Dnmt3L). In addition, Dnmt2 also displays weak
      DNA methyltransferase catalytic activity, but newly founded function is to methylate cytosine
      38 in the anti-codon loop of tRNA A,p. These Dnmts are crucial for mammalian growth and
      development. Dnmts deficiency will lead to embryonic development defects, cancer, and other
      diseases. Therefore, Dnmts could be important therapeutical targets. This article Summarizes
      the classification, function, and recent research progress in DNA methyltransferases.
AU  - Wang Z-G
AU  - Wu J-X
PT  - Journal Article
TA  - Yichuan
JT  - Yichuan
SO  - Yichuan 2009 31: 903-912.

PMID- 23209257
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Human-Pathogenetic Bacterium Vibrio vulnificus B2.
PG  - 7019
AB  - Vibrio vulnificus, which can lead to rapidly expanding cellulitis or septicemia,  is present
      in the marine environment. Here, we present the draft genome sequence
      of strain B2, which was isolated from a septicemia patient in 2010.
AU  - Wang ZG
AU  - Wu Z
AU  - Xu SL
AU  - Zha J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 7019.

PMID- Not included in PubMed...
VI  - 40
DP  - 1981
TI  - A new sequence-specific endonuclease from Micrococcus radiodurans.
PG  - 1848
AB  - A new sequence specific endonuclease MraI has been purified from Micrococcus
      radiodurans (ATCC 13939).  The procedure involves ammonium sulfate
      precipitation of crude cell lysates followed by chromatography on Biogel-A,
      DEAE-Biogel, Cibacron blue F3GA agarose, and phosphocellulose columns.  The
      enzyme cleaves phage lambda DNA at three sites, and adenovirus type 2 DNA at
      more than 12 sites.  It has no sites on SV40, PhiX174, PBR322 and PM2 DNA.  The
      three sites on phage lambda DNA recognized by MraI are different from those
      cleaved by SmaI, since the fragments obtained by the digestion of DNA with
      these two enzymes are different and the double digestion generates new
      fragments.  The sites of double digestion generates new fragments.  The sites
      of cleavage on lambda DNA maps at 42.6, 44.9 and 83.4 percent genome length.
      The enzyme requires Mg++ for its absolute activity but is active in the absence
      of added 2-mercaptoethanol.  The enzyme shows activity at a broad range of
      temperature and pH with optimum at 45C and pH 7.0.  Determination of the
      nucleotide sequence that this enzyme recognizes is under investigation.
AU  - Wani AA
AU  - Stephens RE
AU  - D'Ambrosio SM
AU  - Hart RW
PT  - Journal Article
TA  - Fed. Proc.
JT  - Fed. Proc.
SO  - Fed. Proc. 1981 40: 1848.

PMID- 6285977
VI  - 697
DP  - 1982
TI  - A sequence specific endonuclease from Micrococcus radiodurans.
PG  - 178-184
AB  - A new sequence specific endonuclease, MraI has been purified from Micrococcus
      radiodurans.  This enzyme cleaves bacteriophage lambda DNA at three sites,
      adenovirus type 2 DNA at more than 12 sites and has a unique site on PhiX174
      DNA.  It has no sites on SV40, PM2 and pBR322 DNA.  The three sites on phage
      lambda DNA are different from those cleaved by SmaI, XmaI and XorII.  The sites
      of cleavage are located at 0.424, 0.447 and 0.834 fractional lengths on the
      physical map of lambda DNA.  MraI is shown to be an isoschizomer of SacII and
      SstII recognizing the palindromic nucleotide sequence '5-CCGC^GG-3'.  The
      enzyme shows an absolute requirement of Mg2+, but is active in the absence of
      added 2-mercaptoethanol.  The enzyme shows activity at a broad range of
      temperature and pH with an optimum at 45C and pH 7.0 MraI represents the first
      restriction enzyme from a bacterium whose DNA lacks modified methylated bases.
AU  - Wani AA
AU  - Stephens RE
AU  - D'Ambrosio SM
AU  - Hart RW
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1982 697: 178-184.

PMID- 10488339
VI  - 4
DP  - 1999
TI  - A reverse transcriptase/maturase promotes splicing by binding at its own coding segment in a group II intron RNA.
PG  - 239-250
AB  - Group II introns encode reverse transcriptases that promote RNA splicing (maturase activity)
      and then with the excised intron form a DNA endonuclease that mediates intron mobility by
      target DNA-primed reverse transcription (TPRT).  Here, we show that the primary binding site
      for the maturase (LtrA) encoded by the Lactococcus lactis Ll.LtrB intron is within a region of
      intron domain IV that includes the start codon of the LtrA ORF. This binding is enhanced by
      other elements, particularly domain I and the EBS/IBS interactions, and helps position LtrA to
      initiate cDNA synthesis in the 3' exon as occurs during TPRT. Our results suggest how the
      maturase functions in RNA splicing and support the hypothesis that the reverse transcriptase
      coding region was derived from an independent genetic element that was inserted into a
      preexisting group II intron.
AU  - Wank H
AU  - SanFilippo J
AU  - Singh RN
AU  - Matsuura M
AU  - Lambowitz AM
PT  - Journal Article
TA  - Mol. Cell
JT  - Mol. Cell
SO  - Mol. Cell 1999 4: 239-250.

PMID- 24723722
VI  - 2
DP  - 2014
TI  - Draft genome sequences of the altered schaedler flora, a defined bacterial community from gnotobiotic mice.
PG  - e00287-14
AB  - The altered Schaedler flora (ASF) is a bacterial community that supports normal growth and
      development of gnotobiotic mice. We report here the draft genome sequences of the 8 bacteria
      that comprise the ASF.
AU  - Wannemuehler MJ
AU  - Overstreet AM
AU  - Ward DV
AU  - Phillips GJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00287-14.

PMID- 26450718
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Mycobacterium bovis BZ 31150 and Mycobacterium bovis B2 7505, Pathogenic Bacteria Isolated from Archived Captive Animal Bronchial Washes  and Human Sputum Samples in Uganda.
PG  - e01102-15
AB  - Bovine tuberculosis (BTB), a zoonotic infection of cattle caused by Mycobacterium bovis,
      results in losses of $3 billion to the global agricultural industry and represents the fourth
      most important livestock disease worldwide. M. bovis as a source of human infection is likely
      underreported due to the culture medium conditions used to isolate the organism from sputum or
      other sample sources. We report here the draft genome sequences of M. bovis BZ 31150, isolated
      from a bronchial washing from a captive chimpanzee, and M. bovis B2 7505, isolated from  a
      human sputum sample in Uganda.
AU  - Wanzala SI
AU  - Nakavuma J
AU  - Travis DA
AU  - Kia P
AU  - Ogwang S
AU  - Sreevatsan S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01102-15.

PMID- Not included in PubMed...
VI  - 75
DP  - 1992
TI  - Conjugally transferable phage resistance activities from Lactococcus lactis DRC1.
PG  - 683-691
AB  - Lactococcus lactis ssp. lactis strain HID600 is a phage-resistant transconjugant produced by
      mating HID113 (an antibiotic-resistant variant of plasmid-free strain LM0230) with L. lactis
      ssp. lactis strain DRC1. Analysis of HID600 revealed that it had conjugally acquired phage
      resistance, bacteriocin production, proteolytic activity, and a 131-kb plasmid. The
      interaction of phages c2 and sk1 with HID113 and HID600 was studied. Plaque assays indicated
      that only about 12.5% of c2 infections of HID600 produced infective centers and that c2
      infections of HID600 had a longer latent period and smaller average burst size than did
      infections of HID113. Less than .2% of sk1 infections of HID600 were apparently productive; no
      burst was detected. The resistance to phage infection involved restriction-modification and
      abortive infection effects. Such resistance might be useful in the construction of cheese
      starter strains with reduced susceptibility to phage infection, although phage variants able
      to infect HID600 with increased efficiency were observed.
AU  - Ward AC
AU  - Davidson BE
AU  - Hillier AJ
AU  - Powell IB
PT  - Journal Article
TA  - J. Dairy Sci.
JT  - J. Dairy Sci.
SO  - J. Dairy Sci. 1992 75: 683-691.

PMID- 8710518
VI  - 24
DP  - 1996
TI  - Type IIS restriction enzyme footprint I.  Measurement of a triple helix dissociation constant with Eco57I at 25oC.
PG  - 2435-2440
AB  - A method is described to measure triple helix dissociation constants by inhibiting
      the cleavage of a plasmid constructed to contain a target sequence for the triplex forming
      oligonucleotide (TFO) dT20 by the type IIS restriction enzyme Eco57I.  The method relies upon
      the TFO's ability to block the cleavage reaction by occupying the enzyme's cleavage site but
      not its
      specific binding sequence.  Using this protocol, the dissociation constant for dT20 bound to
      its
      target was ~0.16 uM at 25oC.  The accuracy of this experiment was demonstrated by measuring
      the Kd of an affinity cleavage TFO using Eco57I and Quantitative Affinity Cleavage Titration.
      Type IIS restriction endonuclease footprinting should be useful for the qualitative and
      quantitative
      investigation of ligand-DNA interactions.
AU  - Ward B
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1996 24: 2435-2440.

PMID- 29074653
VI  - 5
DP  - 2017
TI  - Draft Genome Assembly of a Wolbachia Endosymbiont of Plutella australiana.
PG  - e01134-17
AB  - Wolbachia spp. are endosymbiotic bacteria that infect around 50% of arthropods and cause a
      broad range of effects, including manipulating host reproduction.
      Here, we present the annotated draft genome assembly of Wolbachia strain wAus,
      which infects Plutella australiana, a cryptic ally of the major Brassica pest
      Plutella xylostella (diamondback moth).
AU  - Ward CM
AU  - Baxter SW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01134-17.

PMID- 14678167
VI  - 96
DP  - 2004
TI  - Characterization of closely related lactococcal starter strains which show differing patterns of bacteriophage sensitivity.
PG  - 144-148
AB  - Aims: To characterize a group of closely related Lactococcus lactis subsp. lactis casein
      starter strains used commercially, which differ in
      their sensitivity to bacteriophages isolated from the same industrial
      environment.
      Methods and Results: Nine strains of L. lactis, six of which had
      been used as starter cultures for lactic casein manufacture, were shown
      to be closely related by pulsed-field gel electrophoresis and total DNA
      profiles. Nineteen phages, which propagated on one or more of these
      starter strains were isolated from industrial casein whey samples. The
      phages were all small isometric-headed and could be divided into five
      groups on the basis of host range on the nine strains. Most of the
      phages did not give a PCR product with primers designed to detect the
      two most common lactococcal small isometric phage species (936 and
      P335). The hosts could be divided into six groups depending on their
      phage sensitivity. Plasmids encoding genes for the cell envelope
      associated PI-type proteinase, lactose metabolism and specificity
      subunits of a type I restriction/modification system were identified.
      Conclusions: This work demonstrates how isolates of the same
      starter strain may come to be regarded as separate cultures because of
      their different origins, and how these closely related strains may
      differ in some of their industrially relevant characteristics.
      Significance and Impact of the Study: This situation may be very
      common among lactococci used as dairy starter cultures, and implies
      that the dairy industry worldwide depends on a small number of
      different strains.
AU  - Ward LJH
AU  - Heap HA
AU  - Kelly WJ
PT  - Journal Article
TA  - J. Appl. Microbiol.
JT  - J. Appl. Microbiol.
SO  - J. Appl. Microbiol. 2004 96: 144-148.

PMID- 26586893
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Leptolinea tardivitalis YMTK-2, a Mesophilic Anaerobe from the Chloroflexi Class Anaerolineae.
PG  - e01356-15
AB  - We present the draft genome sequence of Leptolinea tardivitalis YMTK-2, a member  of the
      Chloroflexi phylum. This organism was initially characterized as a
      strictly anaerobic nonmotile fermenter; however, genome analysis demonstrates
      that it encodes for a flagella and might be capable of aerobic respiration.
AU  - Ward LM
AU  - Hemp J
AU  - Pace LA
AU  - Fischer WW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01356-15.

PMID- 26586889
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Herpetosiphon geysericola GC-42, a Nonphototrophic Member of the Chloroflexi Class Chloroflexia.
PG  - e01352-15
AB  - We report here the draft genome sequence of Herpetosiphon geysericola GC-42, a predatory
      nonphototrophic member of the class Chloroflexia in the phylum
      Chloroflexi. This genome provides insight into the evolution of phototrophy and
      aerobic respiration within the Chloroflexi.
AU  - Ward LM
AU  - Hemp J
AU  - Pace LA
AU  - Fischer WW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01352-15.

PMID- 29930071
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of a Divergent Anaerobic Member of the Chloroflexi Class Ardenticatenia from a Sulfidic Hot Spring.
PG  - e00571-18
AB  - Here, we present a draft genome sequence of Nak82, the second genome sequence available for
      the Chloroflexi class Ardenticatenia and the first from a sulfidic
      terrestrial hot spring. Nak82 is genetically and metabolically distinct from
      Ardenticatena maritima and likely represents a new genus- or family-level lineage
      lacking high-potential respiratory pathways.
AU  - Ward LM
AU  - McGlynn SE
AU  - Fischer WW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00571-18.

PMID- 29930070
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Two Basal Members of the Anaerolineae Class of Chloroflexi from a Sulfidic Hot Spring.
PG  - e00570-18
AB  - Here, we describe the first genome sequences of the Anaerolineae from a sulfidic  environment,
      expanding the environmental distribution of sequenced Anaerolineae
      These genomes represent basal Anaerolineae lineages, branching soon after the
      divergence of the sister class 'Candidatus Thermofonsia,' expanding our
      understanding of the metabolic evolution of this group.
AU  - Ward LM
AU  - McGlynn SE
AU  - Fischer WW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00570-18.

PMID- 28982986
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Chloracidobacterium sp. CP2_5A, a Phototrophic Member of the Phylum Acidobacteria Recovered from a Japanese Hot Spring.
PG  - e00821-17
AB  - The phylum Acidobacteria contains a single known phototrophic member, Chloracidobacterium
      thermophilum, which was recovered from a hot spring
      metagenome from Yellowstone National Park. Here, we expand the diversity of the
      genus Chloracidobacterium with a genome recovered from a hot spring in Japan,
      extending the known range of this lineage to a new continent.
AU  - Ward LM
AU  - McGlynn SE
AU  - Fischer WW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00821-17.

PMID- 28982985
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of a Novel Lineage of Armatimonadetes Recovered from Japanese Hot Springs.
PG  - e00820-17
AB  - Here, we report two draft genome sequences from a novel lineage within the Armatimonadetes
      phylum recovered from metagenomes sequenced from Japanese hot
      spring microbial mats. These organisms are aerobic and represent a new lineage
      related to the characterized Chthonomonas and Fimbriimonas groups, and they
      expand the diversity of this enigmatic phylum.
AU  - Ward LM
AU  - McGlynn SE
AU  - Fischer WW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00820-17.

PMID- 15383840
VI  - 2
DP  - 2004
TI  - Genomic Insights into Methanotrophy: The Complete Genome Sequence of Methylococcus capsulatus (Bath).
PG  - 1616-1628
AB  - Methanotrophs are ubiquitous bacteria that can use the greenhouse gas methane as a sole carbon
      and energy source for growth, thus playing major roles in global carbon cycles, and in
      particular, substantially reducing emissions of biologically generated methane to the
      atmosphere. Despite their importance, and in contrast to organisms that play roles in other
      major parts of the carbon cycle such as photosynthesis, no genome-level studies have been
      published on the biology of methanotrophs. We report the first complete genome sequence to our
      knowledge from an obligate methanotroph, Methylococcus capsulatus (Bath), obtained by the
      shotgun sequencing approach. Analysis revealed a 3.3-Mb genome highly specialized for a
      methanotrophic lifestyle, including redundant pathways predicted to be involved in
      methanotrophy and duplicated genes for essential enzymes such as the methane monooxygenases.
      We used phylogenomic analysis, gene order information, and comparative analysis with the
      partially sequenced methylotroph Methylobacterium extorquens to detect genes of unknown
      function likely to be involved in methanotrophy and methylotrophy. Genome analysis suggests
      the ability of M. capsulatus to scavenge copper (including a previously unreported
      nonribosomal peptide synthetase) and to use copper in regulation of methanotrophy, but the
      exact regulatory mechanisms remain unclear. One of the most surprising outcomes of the project
      is evidence suggesting the existence of previously unsuspected metabolic flexibility in M.
      capsulatus, including an ability to grow on sugars, oxidize chemolithotrophic hydrogen and
      sulfur, and live under reduced oxygen tension, all of which have implications for methanotroph
      ecology. The availability of the complete genome of M. capsulatus (Bath) deepens our
      understanding of methanotroph biology and its relationship to global carbon cycles. We have
      gained evidence for greater metabolic flexibility than was previously known, and for genetic
      components that may have biotechnological potential.
AU  - Ward N et al
PT  - Journal Article
TA  - PLoS Biology
JT  - PLoS Biology
SO  - PLoS Biology 2004 2: 1616-1628.

PMID- 19201974
VI  - 75
DP  - 2009
TI  - Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils.
PG  - 2046-2056
AB  - The complete genomes of three strains from the phylum Acidobacteria were compared.
      Phylogenetic analysis placed them as a unique phylum. They share
      genomic traits with members of the Proteobacteria, the Cyanobacteria, and
      the Fungi. The three strains appear to be versatile heterotrophs. Genomic
      and culture traits indicate the use of carbon sources that span simple
      sugars to more complex substrates such as hemicellulose, cellulose, and
      chitin. The genomes encode low-specificity major facilitator superfamily
      transporters and high-affinity ABC transporters for sugars, suggesting
      that they are best suited to low-nutrient conditions. They appear capable
      of nitrate and nitrite reduction but not N(2) fixation or denitrification.
      The genomes contained numerous genes that encode siderophore receptors,
      but no evidence of siderophore production was found, suggesting that they
      may obtain iron via interaction with other microorganisms. The presence of
      cellulose synthesis genes and a large class of novel high-molecular-weight
      excreted proteins suggests potential traits for desiccation resistance,
      biofilm formation, and/or contribution to soil structure. Polyketide
      synthase and macrolide glycosylation genes suggest the production of novel
      antimicrobial compounds. Genes that encode a variety of novel proteins
      were also identified. The abundance of acidobacteria in soils worldwide
      and the breadth of potential carbon use by the sequenced strains suggest
      significant and previously unrecognized contributions to the terrestrial
      carbon cycle. Combining our genomic evidence with available culture
      traits, we postulate that cells of these isolates are long-lived, divide
      slowly, exhibit slow metabolic rates under low-nutrient conditions, and
      are well equipped to tolerate fluctuations in soil hydration.
AU  - Ward NL et al
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2009 75: 2046-2056.

PMID- 6755468
VI  - 79
DP  - 1982
TI  - Internal structure of the mitochondrial intron of Aspergillus nidulans.
PG  - 6332-6336
AB  - The intron of the mitochondrial apocytochrome b gene, cobA, of Aspergillus nidulans has been
      subjected to sequence analysis.  It contains an open reading frame of 957 base pairs
      contiguous with the preceding exon.  Regions of the translated open reading frames of cobA and
      the third intron of the cob gene in yeast show high amino acid homology.  Comparison of the
      cobA intron with this and other yeast introns indicates that cobA codes for a maturase protein
      that splices out the intron encoding it and possibly other mitochondrial introns.  Two very
      similar decamer peptides are found in the protein sequences of the cobA intron, four
      mitochondrial yeast introns, and the yeast mitochondrial sequence reading frame 1 and may be
      diagnostic of one class of maturase-coding introns.  Four short DNA sequences, two of which
      are in the region defined by box9 and box2 mutations in the cob gene of yeast, are conserved
      in cobA and certain yeast introns.  Comparison with three yeast introns strongly suggests that
      the first 200 base pairs of the open reading frame of the cobA intron do not code for any
      amino acids present in the putative maturase protein but are required for splicing or the
      control of splicing, or both.
AU  - Waring RB
AU  - Davies RW
AU  - Scazzocchio C
AU  - Brown TA
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1982 79: 6332-6336.

PMID- 19222038
VI  - 10
DP  - 2009
TI  - Phosphorothioation of Oligonucleotides Strongly Influences the Inhibition of Bacterial (M.Hhal) and Human (Dnmt1) DNA Methyltransferases.
PG  - 728-734
AB  - The cytidine analogue 5-fluoro-2'-deoxycytidine (dC(F)) is a mechanism-based inhibitor of DNA
      methyltransferases. We report the
      synthesis of short 18-mer dsDNA oligomers containing a
      triple-hemimethylated CpG motive as a recognition sequence for the
      human methyltransferase Dnmt1. The DNA strands carry within these CpG
      islands dC(F) building blocks that function as mechanism-based
      inhibitors of the analyzed methyltransferases. In addition, we replaced
      the phosphodiester backbones at defined positions by phosphorothioates.
      These hypermodified DNA strands were investigated as inhibitors of the
      DNA methyltransferases M.Hhal and Dnmtl in vitro. We could show that
      both methylases behave substantially differently in respect to the
      amount of DNA backbone modification.
AU  - Warncke S
AU  - Gegout A
AU  - Carell T
PT  - Journal Article
TA  - Chembiochem
JT  - Chembiochem
SO  - Chembiochem 2009 10: 728-734.

PMID- 18033299
VI  - 450
DP  - 2007
TI  - Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite.
PG  - 560-565
AB  - From the standpoints of both basic research and biotechnology, there is
      considerable interest in reaching a clearer understanding of the diversity
      of biological mechanisms employed during lignocellulose degradation.
      Globally, termites are an extremely successful group of wood-degrading
      organisms and are therefore important both for their roles in carbon
      turnover in the environment and as potential sources of biochemical
      catalysts for efforts aimed at converting wood into biofuels. Only
      recently have data supported any direct role for the symbiotic bacteria in
      the gut of the termite in cellulose and xylan hydrolysis. Here we use a
      metagenomic analysis of the bacterial community resident in the hindgut
      paunch of a wood-feeding 'higher' Nasutitermes species (which do not
      contain cellulose-fermenting protozoa) to show the presence of a large,
      diverse set of bacterial genes for cellulose and xylan hydrolysis. Many of
      these genes were expressed in vivo or had cellulase activity in vitro, and
      further analyses implicate spirochete and fibrobacter species in gut
      lignocellulose degradation. New insights into other important symbiotic
      functions including H2 metabolism, CO2-reductive acetogenesis and N2
      fixation are also provided by this first system-wide gene analysis of a
      microbial community specialized towards plant lignocellulose degradation.
      Our results underscore how complex even a 1-microl environment can be.
AU  - Warnecke F et al
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2007 450: 560-565.

PMID- 10687732
VI  - 12
DP  - 2000
TI  - Cytosine methylation and human cancer.
PG  - 68-73
AB  - Abnormalities of genomic methylation patterns have been attributed a role in carcinogenesis
      since the early 1980s, when large-scale demethylation of the genome
      was thought be an early event in multistep colorectal carcinogenesis. In the 1990s, local de
      novo methylation (with or without global demethylation) at tumor suppressor loci
      was held to be involved in silencing of tumor suppressor genes. The mechanisms that might
      mediate methylation and demethylation in carcinogenesis remain obscure, and
      there are questions as to whether the methylation changes are a cause or consequence of
      cellular transformation and clonal expansion. It is also important to derive a set of
      defined criteria by which a tumor suppressor gene can be concluded to have been inactivated by
      DNA methylation in a manner that contributes to carcinogenesis.
AU  - Warnecke PM
AU  - Bestor TH
PT  - Journal Article
TA  - Curr. Opin. Oncol.
JT  - Curr. Opin. Oncol.
SO  - Curr. Opin. Oncol. 2000 12: 68-73.

PMID- 9581283
VI  - 22
DP  - 1998
TI  - Sequence-specific methylation of the Mouse H19 gene in embryonic cells deficient in the Dnmt-1 gene.
PG  - 111-121
AB  - We have used Dnmtc/c ES cells that are homozygous for disruption of the DNA methyltransferase
      gene to address how de novo methylation is propagated and whether it is directed to specific
      sites in the early embryo.  We examined the imprinted H19 gene and the specific-sequence
      region implicated as an "imprinting mark" to determine whether de novo methylation was
      occurring at a restricted set of sites.  Since the "imprinting mark" was found to be
      methylated differentially at all stages of development, we reasoned that the sequence may
      still be a target for the de novo methylation activity found in the Dnmtc/c cells, even though
      the loss of maintenance methylase activity renders the H19 promoter active.  We used bisulfite
      genomic sequencing to determine the methylation state of the imprinted region of the H19 gene
      and found a low level of DNA methylation at specific single CpG sites in the upstream region
      of the imprinted H19 sequence in the Dnmtc/c mutant ES cells.  Moreover, these CpG sites
      appeared to be favored targets for further de novo methylation of neighboring CpG sites in
      rescued ES cells, which possess apparently normal maintenance activity.  Our data provide
      further evidence for a separate methylating activity in ES cells and indicate that this
      activity displays sequence specificity.
AU  - Warnecke PM
AU  - Biniszkiewicz D
AU  - Jaenisch R
AU  - Frommer M
AU  - Clark SJ
PT  - Journal Article
TA  - Dev. Genet.
JT  - Dev. Genet.
SO  - Dev. Genet. 1998 22: 111-121.

PMID- 7002022
VI  - 34
DP  - 1980
TI  - Modified Bases in Bacteriophage DNAs.
PG  - 137-158
AB  - This review considers bacteriophage DNAs in which all or a major proportion of
      one of the four bases found commonly in DNA is replaced by a modified base.  It
      does not consider the methylated bases that are found in small amounts in DNA
      and that function usually to protect DNA against specific restriction
      endonucleases.  The first modified base in a bacteriophage DNA,
      5-hydroxymethylcytosine (hmCyt), was discovered 27 years ago.  It played a
      crucial role in the development of the biochemistry of T-even phage-infected
      Escherichia coli.  Since then, modified bases have been found in a variety of
      other bacteriophages.  They are of interest from the point of view of their
      biochemistry and, more recently, their effects on DNA conformation and
      function.  The biosynthesis of some of these bases has been reviewed
      extensively.  This review emphasizes the more recent developments in modified
      base biochemistry and considers also some of their effects on DNA structure and
      function.
AU  - Warren RAJ
PT  - Journal Article
TA  - Annu. Rev. Microbiol.
JT  - Annu. Rev. Microbiol.
SO  - Annu. Rev. Microbiol. 1980 34: 137-158.

PMID- Not carried by PubMed...
VI  - 3
DP  - 1988
TI  - Rapid HPLC purification of a restriction enzyme from Sphaerotilus sp.
PG  - 225-230
AB  - The rapid purification of the Type II restriction endonuclease SspI from
      contaminating exo- and endonucleases contained in a cell lysate of the
      bacterium Sphaerotilus sp. is described using a combination of anion and cation
      exchange media.  Nucleic acids and a substantial portion of non-restriction
      enzyme proteins were quickly removed from the initial cell lysate via solid
      phase extraction using an anion exchange cartridge.  The SspI was subsequently
      purified free from contaminating nucleases using cation exchange column
      chromatography.  Compared to the initial cell lysate, the overall recovery of
      SspI activity in the final product was greater than 75%.  In addition this
      rapid 2-step procedure resulted in a 330-fold increase in enzyme specific
      activity.
AU  - Warren W
AU  - Merion M
PT  - Journal Article
TA  - BioChromatography
JT  - BioChromatography
SO  - BioChromatography 1988 3: 225-230.

PMID- 18046550
VI  - 78
DP  - 2008
TI  - Generation of readily transformable Bacillus licheniformis mutants.
PG  - 181-188
AB  - A set of mutants was generated by targeted deletion of the hsdR loci of two type I restriction
      modification systems ( RMS) identified in
      Bacillus licheniformis DSM13. Single as well as double knock-outs
      resulted in strains being readily transformable with plasmids isolated
      from Bacilli. Introduction of shuttle plasmids isolated from
      Escherichia coli was routinely possible when the double mutant B.
      licheniformis MW3 (Delta hsdR1, Delta hsdR2) was used in transformation
      experiments. Growth and secretion of extracellular enzymes were not
      affected in any of the mutants. Thus, along with an optimized
      transformation protocol, this study makes available an urgently needed
      transformation system for this industrially exploited species.
AU  - Waschkau B
AU  - Waldeck J
AU  - Wieland S
AU  - Eichstadt R
AU  - Meinhardt F
PT  - Journal Article
TA  - Appl. Microbiol. Biotechnol.
JT  - Appl. Microbiol. Biotechnol.
SO  - Appl. Microbiol. Biotechnol. 2008 78: 181-188.

PMID- 27445391
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Clostridium difficile Strain IT1118, an Epidemic Isolate Belonging to the Emerging PCR Ribotype 018.
PG  - e00717-16
AB  - Clostridium difficile PCR ribotype 018 has emerged in Italy, South Korea, and Japan, causing
      severe infections and outbreaks. In this study, we sequenced the
      genome of IT1118, an Italian clinical isolate, to clarify the molecular features
      contributing to the success of this epidemic type.
AU  - Wasels F
AU  - Barbanti F
AU  - Spigaglia P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00717-16.

PMID- 26941139
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the Butyric Acid Producer Clostridium tyrobutyricum Strain CIP I-776 (IFP923).
PG  - e00048-16
AB  - Here, we report the draft genome sequence of Clostridium tyrobutyricum CIP I-776  (IFP923), an
      efficient producer of butyric acid. The genome consists of a single
      chromosome of 3.19 Mb and provides useful data concerning the metabolic
      capacities of the strain.
AU  - Wasels F
AU  - Clement B
AU  - Lopes FN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00048-16.

PMID- 10999405
VI  - 43
DP  - 2000
TI  - RNA-directed DNA methylation.
PG  - 203-220
AB  - RNA-DNA interactions can serve as a signal that triggers de novo DNA methylation in plants. As
      yet, this RNA-directed DNA methylation mechanism merely targets transgenes, but it appears
      likely that methylation of some endogenous sequences is also directed by RNA. RNA-directed
      methylation of cytosine residues specifically occurs along the DNA regions that are
      complementary to the directing RNA pointing to the formation of a putative RNA-DNA duplex.
      Dense methylation patterns and the methylation of cytosine residues at symmetric and
      asymmetric sites are detectable on both DNA strands within these regions. Methylation
      progressively decreases in the sequences adjacent to the putative RNA-DNA duplex. The extreme
      sensitivity of RNA-directed DNA methylation was demonstrated by analyzing a short 30 bp DNA
      region that was complementary to the targeting RNA. Association of RNA-directed DNA
      methylation with homology-dependent gene silencing indicated that the methylation-directing
      RNA molecules may be double-stranded or may contain double-stranded regions. Whereas the
      function of DNA methylation in transcriptional gene silencing is nearly understood, its role
      in post-transcriptional gene silencing is still under discussion. In mammals, X-chromosome
      inactivation and genomic imprinting are associated with DNA methylation but how methylation is
      initiated is unclear. The observation of a correlation between specific antisense RNAs and
      transcriptional and post-transcriptional gene silencing may indicate that RNA-directed DNA
      methylation is involved in epigenetic gene regulation throughout eukaryotes.
AU  - Wassenegger M
PT  - Journal Article
TA  - Plant Mol. Biol.
JT  - Plant Mol. Biol.
SO  - Plant Mol. Biol. 2000 43: 203-220.

PMID- 6300094
VI  - 258
DP  - 1983
TI  - A new class of site-specific endodeoxyribonucleases.
PG  - 4663-4665
AB  - We had found that yeasts had intracellular endodeoxyribonucleases that cut
      phage DNA into a set of double-stranded fragments with discrete chain lengths.
      We purified one of them to apparent homogeneity from Saccharomyces cerevisiae
      and designated it Endo.Sce.I.  Sequence analysis around 5 cleavage site in
      plasmid DNA and phage DNA revealed that Endo.SceI cuts a defined phosphodiester
      bond in each strand of double helix at the cleavage sites and produces free
      cohesive ends consisting of 4 nucleotides protruding at 3'-termini.  However,
      unlike in the case of prokaryotic type II-restriction endonucleases, (i)
      Endo.SceI seems to consist of two nonidentical subunits, (ii) no common
      palindrome or consensus sequence including more than 5 base pairs is detected
      at or near these cleavage sites, and (iii) Endo.SceI can cut the DNA isolated
      from the cells that produced Endo.SceI.  All of the 5 cleavage sites are
      included in inverted repeats, but these inverted repeats are variable in size,
      nucleotide sequence, and distance between repeating units.  An inverted repeat
      itself is not a structure recognized by Endo.SceI.  This study shows that
      Endo.SceI is the first example of eukaryotic site-specific endonuclease and has
      properties, as described above, which distinguish it from prokaryotic
      restriction endoncleases.
AU  - Watabe H
AU  - Iino T
AU  - Kaneko T
AU  - Shibata T
AU  - Ando T
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1983 258: 4663-4665.

PMID- 6277877
VI  - 90
DP  - 1981
TI  - Site-specific endo-deoxyribonucleases in eukaryotes: endonucleases of yeasts, Saccharomyces and Pichia.
PG  - 1623-1632
AB  - A class of endo-deoxyribonucleases was found in cell-free extracts from yeasts;
      Saccharomyces cerevisiae, S. uvarum and Pichia membranaefaciens.  These
      endonucleases cleaved double-stranded DNA so that the treated DNA exhibited a
      set of discrete bands on an agarose gel-electrophoregram.  The profiles
      obtained with a certain DNA were unique to each endonuclease, suggesting that
      these yeast endonucleases cleave DNA at well-defined sites specific to each
      endonuclease.
AU  - Watabe H
AU  - Shibata T
AU  - Ando T
PT  - Journal Article
TA  - J. Biochem. (Tokyo)
JT  - J. Biochem. (Tokyo)
SO  - J. Biochem. (Tokyo) 1981 90: 1623-1632.

PMID- 6088475
VI  - 95
DP  - 1984
TI  - Purification of a eukaryotic site-specific endonuclease, Endo.SceI, from Saccharomyces cerevisiae and effectors on its specificity and activity.
PG  - 1677-1690
AB  - A site-specific endonuclease (Endo.SceI) which caused double-strand scission of DNA was highly
      purified from a eukaryote, Saccharomyces cerevisiae IAM4274.  The molecular weight of the
      active form of Endo.SceI was estimated to be 120,000 and 110,000 by sedimentation analysis on
      a glycerol density gradient and gel filtration on Ultrogel AcA34, respectively.  Analysis of
      the fractions from the last column chromatography by polyacrylamide gel electrophoresis in the
      presence of sodium dodecyl sulfate and by an assay of the endonucleolytic activities suggested
      that Endo.SceI consists of two non-identical subunits with molecular weights of 75,000 and
      50,000.  Unlike restriction endonucleases, Endo.SceI was active on chromosomal DNA of the
      cells which produced Endo.SceI.  Single-stranded DNA was not cleaved by Endo.SceI, but
      inhibited the endonucleolytic activity of the enzyme on double-stranded DNA.  The
      endonucleolytic activity of Endo.SceI required magnesium ions (Mg2+) as a sole cofactor; Mg2+
      could not be replaced by Ca2+ or Zn2+.  When Mg2+ was replaced by manganese ions (Mn2+),
      extensively purified Endo.SceI cleaved double-stranded DNA at many other sites in addition to
      the sites at which DNA was cleaved in the presence of Mg2+.  Experiments indicated that this
      is not the activation of contaminating endonuclease in the preparation of Endo.SceI, but the
      result of relaxation in the site-specificity of cleavage.
AU  - Watabe H-O
AU  - Shibata T
AU  - Iino T
AU  - Ando T
PT  - Journal Article
TA  - J. Biochem. (Tokyo)
JT  - J. Biochem. (Tokyo)
SO  - J. Biochem. (Tokyo) 1984 95: 1677-1690.

PMID- 28522722
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of a Caffeine-Utilizing Bacterium, Cupriavidus sp. Strain D384.
PG  - e00370-17
AB  - Cupriavidus sp. D384 was isolated from forest soil in Japan and is known to utilize caffeine
      as a sole source of carbon and energy. We report here the
      6,835,230-bp genome sequence for this strain, which contains 6,116 predicted
      coding sequences, including gene operon for alkaloid degradation.
AU  - Watahiki S
AU  - Kimura N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00370-17.

PMID- 25977442
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Five Legionella pneumophila Strains Isolated from Environmental Water Samples.
PG  - e00474-15
AB  - Legionella pneumophila is the causative agent of legionellosis. Here, we report the draft
      genome sequences of five L. pneumophila strains, Bnt314, Ofk308,
      Twr292, Ymg289, and Ymt294, isolated from environmental water samples.
      Comparative analyses of these genomes may reveal the survival mechanisms and
      virulence of L. pneumophila in the natural environment.
AU  - Watanabe K
AU  - Suzuki H
AU  - Nakao R
AU  - Shimizu T
AU  - Watarai M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00474-15.

PMID- 9714606
VI  - 213
DP  - 1998
TI  - Distinctive origins of group I introns found in the COXI genes of three green algae.
PG  - 1-7
AB  - Upon surveying the cytochrome c oxidase subunit I (COXI) gene of green algae, we found group I
      introns in three species of algae, Chlorella vulgaris (Cv), Scenedesmus quadricauda (Sq) and
      Protosiphon botryoides (Pb). The comparative analysis of these nucleotide sequences and their
      secondary structures revealed that the introns of Cv, Sq, and Pb belong to groups IB1, ID, and
      IB2, respectively. Each of the three introns contained an open reading frame (ORF) that showed
      a similarity to the sequence of the LAGLIDADG endonuclease family. However, each of the
      intronic ORFs in Sq and Pb had a discontinuity in the middle of the sequences coding for the
      LAGLIDADG endonuclease. Either of the two ORFs could be restored to a sequence homologous to
      the LAGLIDADG endonuclease by the insertion of a nucleotide in the appropriate position. In
      Sq, a putative pseudo-knot structure was detected in the intronic ORF. This suggests the
      occurrence of a ribosomal frameshift in the translation of the ORF, because such pseudo-knot
      structures are common in viral ORFs employing a (-1) ribosomal frameshift. In the phylogenetic
      tree that was inferred from the amino acid sequences of algal and non-algal intronic ORFs, the
      three algal ORFs did not make a cluster, but were scattered throughout the tree. In addition.
      Each of the three algal ORFs showed a close relationship to the ORFs of non-algal introns that
      were inserted at the corresponding site of the COXI gene, suggesting distinctive origins of
      the three algal introns via independent horizontal transfers.
AU  - Watanabe KI
AU  - Ehara M
AU  - Inagaki Y
AU  - Ohama T
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1998 213: 1-7.

PMID- 28593027
VI  - 12
DP  - 2017
TI  - Draft genome sequence of Desulfoplanes formicivorans Pf12BT, a sulfate-reducing bacterium of the family Desulfomicrobiaceae.
PG  - 34
AB  - Desulfoplanes formicivorans strain Pf12BT is the type strain of the type species  in the genus
      Desulfoplanes, which is the one of the genera in the family
      Desulfomicrobiaceae within the order Desulfovibrionales. This
      deltaproteobacterium was isolated from a blackish meromictic lake sediment. D.
      formicivorans strain Pf12BT is a Gram-negative, motile and sulfate-reducing
      bacterium. Cells of strain Pf12BT are characterized by possession of vibroid
      morphology and red fluorescent pigment. Here we describe the features, draft
      genome sequence and annotation of this organism, the sole species of the genus
      Desulfoplanes. The genome comprised 3,000,979 bp, 2,657 protein-coding genes and
      58 RNA genes.
AU  - Watanabe M
AU  - Kojima H
AU  - Fukui M
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 34.

PMID- 29255571
VI  - 12
DP  - 2017
TI  - High-quality draft genome sequence of Effusibacillus lacus strain skLN1(T), facultative anaerobic spore-former isolated from freshwater lake sediment.
PG  - 76
AB  - 10.1601/nm.25721 strain skLN1(T) is the type strain of the type species in the genus
      10.1601/nm.25720 which is the one of the genera in the family
      10.1601/nm.5070 within the phylum 10.1601/nm.3874. 10.1601/nm.25721 strain
      skLN1(T) is a Gram-positive, spore-forming thermophilic neutrophile isolated from
      freshwater lake sediment. Here, we present the draft genome sequence of strain
      skLN1(T), which consists of 3,902,380 bp with a G + C content of 50.38%.
AU  - Watanabe M
AU  - Tokizawa R
AU  - Kojima H
AU  - Fukui M
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 76.

PMID- 16885288
VI  - 72
DP  - 2006
TI  - Hyperthermophilic DNA methyltransferase M.Pabl from the archaeon Pyrococcus abyssi.
PG  - 5367-5375
AB  - Genome sequence comparisons among multiple species of Pyrococcus, a hyperthermophilic
      archaeon, revealed a linkage between a putative
      restriction-modification gene complex and several large genome
      polymorphisms/rearrangements. From a region apparently inserted into
      the Pyrococcus abyssi genome, a hyperthermoresistant restriction enzyme
      [PabI; 5'-(GTA/C)] with a novel structure was discovered. In the
      present work, the neighboring methyltransferase homologue, M.PabI, was
      characterized. Its N-terminal half showed high similarities to the M
      subunit of type I systems and a modification enzyme of an atypical type
      II system, M.AhdI, while its C-terminal half showed high similarity to
      the S subunit of type I systems. M.PabI expressed within Escherichia
      coli protected PahI sites from RsaI, a PabI isoschizomer. M.PabI,
      purified following overexpression, was shown to generate 5'-GTm6AC,
      which provides protection against PabI digestion. M.PabI was found to
      be highly thermophilic; it showed methylation at 95 degrees C and
      retained at least half the activity after 9 min at 95 degrees C. This
      hyperthermophilicity allowed us to obtain activation energy and other
      thermodynamic parameters for the first time for any DNA
      methyltransferases. We also determined the kinetic parameters of
      k(cat), K-m,K- DNA, and K-m,K- AdoMet. The activity of M.PabI was
      optimal at a slightly acidic pH and at an NaCl concentration of 200 to
      500 mM and was inhibited by Zn2+ but not by Mg2+, Ca2+, or Mn2+. These
      and previous results suggest that this unique methyltransferase and
      PahI constitute a type II restriction-modification gene complex that
      inserted into the P. abyssi genome relatively recently. As the most
      thermophilic of all the characterized DNA methyltransferases, M.PabI
      may help in the analysis of DNA methylation and its application to DNA
      engineering.
AU  - Watanabe M
AU  - Yuzawa H
AU  - Handa N
AU  - Kobayashi I
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2006 72: 5367-5375.

PMID- 19966419
VI  - 65
DP  - 2009
TI  - Structures of restriction endonuclease HindIII in complex with its cognate DNA and divalent cations.
PG  - 1326-1333
AB  - The three-dimensional crystal structures of HindIII bound to its cognate DNA with and without
      divalent cations were solved at 2.17 and
      2.00 angstrom resolution, respectively. HindIII forms a dimer. The
      structures showed that HindIII belongs to the EcoRI-like (alpha-class)
      subfamily of type II restriction endonucleases. The cognate DNA-complex
      structures revealed the specific DNA-recognition mechanism of HindIII
      by which it recognizes the palindromic sequence A/AGCTT. In the Mg2+
      ion-soaked structure the DNA was cleaved and two ions were bound at
      each active site, corresponding to the two-metal-ion mechanism.
AU  - Watanabe N
AU  - Takasaki Y
AU  - Sato C
AU  - Ando S
AU  - Tanaka I
PT  - Journal Article
TA  - Acta Crystallogr. D Biol. Crystallogr.
JT  - Acta Crystallogr. D Biol. Crystallogr.
SO  - Acta Crystallogr. D Biol. Crystallogr. 2009 65: 1326-1333.

PMID- 27795272
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Streptococcus pyogenes Strain JMUB1235 Isolated from  an Acute Phlegmonous Gastritis Patient.
PG  - e01133-16
AB  - Acute phlegmonous gastritis is an uncommon endogenous bacterial gastritis presenting with a
      high mortality rate. Here, we report the complete genome
      sequence of an emm89 Streptococcus pyogenes strain, JMUB1235, which is the
      causative agent of acute phlegmonous gastritis.
AU  - Watanabe S
AU  - Sasahara T
AU  - Arai N
AU  - Sasaki K
AU  - Aiba Y
AU  - Sato'o Y
AU  - Cui L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01133-16.

PMID- 23209249
VI  - 194
DP  - 2012
TI  - Complete Sequence of the First Chimera Genome Constructed by Cloning the Whole Genome of Synechocystis Strain PCC6803 into the Bacillus subtilis 168 Genome.
PG  - 7007
AB  - Genome synthesis of existing or designed genomes is made feasible by the first successful
      cloning of a cyanobacterium, Synechocystis PCC6803, in Gram-positive,
      endospore-forming Bacillus subtilis. Whole-genome sequence analysis of the
      isolate and parental B. subtilis strains provides clues for identifying single
      nucleotide polymorphisms (SNPs) in the 2 complete bacterial genomes in one cell.
AU  - Watanabe S
AU  - Shiwa Y
AU  - Itaya M
AU  - Yoshikawa H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 7007.

PMID- 26450745
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Mizugakiibacter sediminis skMP5T.
PG  - e01185-15
AB  - Strain skMP5(T) is a moderately thermophilic and facultatively anaerobic bacterium, described
      as a representative of Mizugakiibacter sediminis. Here, we report the annotated draft genome
      sequence of strain skMP5(T).
AU  - Watanabe T
AU  - Kojima H
AU  - Fukui M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01185-15.

PMID- 25999549
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of a Sulfur-Oxidizing Autotroph, Sulfuricella sp. Strain T08, Isolated from a Freshwater Lake.
PG  - e00498-15
AB  - Sulfuricella sp. strain T08 is a sulfur-oxidizing autotroph newly isolated from a freshwater
      lake in Japan. Strain T08 is the second isolate of the genus
      Sulfuricella. Here, we report the annotated draft genome sequence of the isolate.
AU  - Watanabe T
AU  - Kojima H
AU  - Fukui M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00498-15.

PMID- 22773644
VI  - 78
DP  - 2012
TI  - Draft genome sequence of a psychrotolerant sulfur-oxidizing bacterium, Sulfuricella denitrificans skB26, and proteomic insights into cold adaptation.
PG  - 6545-6549
AB  - Except for several conspicuous cases, very little is known about sulfur oxidizers
      living in natural freshwater environments. Sulfuricella denitrificans skB26 is a
      psychrotolerant sulfur oxidizer recently isolated from a freshwater lake as a
      representative of a new genus in the class Betaproteobacteria. In this study, an
      approximately 3.2-Mb draft genome sequence of strain skB26 was obtained. In the
      draft genome, consisting of 23 contigs, a single rRNA operon, 43 tRNA genes, and
      3,133 coding sequences were identified. The identified genes include those
      required for sulfur oxidation, denitrification, and carbon fixation. Comparative
      proteomic analysis was conducted to assess cold adaptation mechanisms of this
      organism. From cells grown at 22 degrees C and 5 degrees C, proteins were
      extracted for analysis by nano-liquid chromatography-electrospray
      ionization-tandem mass spectrometry. In the cells cultured at 5 degrees C,
      relative abundances of ribosomal proteins, cold shock proteins, and DEAD/DEAH box
      RNA helicases were increased in comparison to those at 22 degrees C. These
      results suggest that maintenance of proper translation is critical for growth
      under low-temperature conditions, similar to the case for other cold-adapted
      prokaryotes.
AU  - Watanabe T
AU  - Kojima H
AU  - Fukui M
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2012 78: 6545-6549.

PMID- 21705612
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of the Bacterium Porphyromonas gingivalis TDC60, Which Causes Periodontal Disease.
PG  - 4259-4260
AB  - Porphyromonas gingivalis is a black-pigmented asaccharolytic anaerobe and a major causative
      agent of periodontitis. Here, we report the complete
      genome sequence of P. gingivalis strain TDC60, which was recently isolated
      from a severe periodontal lesion in a Japanese patient.
AU  - Watanabe T
AU  - Maruyama F
AU  - Nozawa T
AU  - Aoki A
AU  - Okano S
AU  - Shibata Y
AU  - Oshima K
AU  - Kurokawa K
AU  - Hattori M
AU  - Nakagawa I
AU  - Abiko Y
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4259-4260.

PMID- 14208512
VI  - 88
DP  - 1964
TI  - Episome-mediated transfer of drug resistance in enterobacteriaceae.  VII.  Two types of naturally occurring R factors.
PG  - 716-726
AB  - Naturally occurring R factors are classified into two types, fi+ and fi-,
      depending on their fi characters.  The term fi is an abbreviation of fertility
      inhibition and fi+ and fi- mean, respectively, the presence and absence of
      suppression of the functions of the sex factor F of Escherichia coli K-12.  It
      was found that fi- R factors reduce the efficiency of plating of phages lambda
      and T1 in K-12; fi+ R factors did not have this inhibitory action.  One of the
      fi- R factors reduced the efficiency of plating of phage T7 as well.  Phages
      lambda and T1 underwent host-induced modifications in the host carrying some
      fi- R factors.  At least two types of fi- R factors were recognized by the
      types of their restriction and host-induced modification of these phages.
      CaCl2 exhibited antagonistic actions against the restrictions of phages lambda
      and T1 by fi- R factors.  Transduction of the ability to ferment galactose with
      HFT lysates of lambda was reduced by fi- R factors.  Ultraviolet induction of
      lambda was not affected by any R factors.  Furthermore, adsorption of phages
      lambda and T1 was not altered by the presence of any R factors.  From these
      results, we concluded that the suppression of progeny formation of these phages
      by fi- R factors is due to some step(s) after adsorption of the phages to the
      bacteria.  Superinfection immunity and mutual exclusion were found between two
      different fi+ R factors but not between fi+ and fi- R factors.  The two
      different fi+ R factors were frequently genetically recombined, but fi+ and fi-
      R factors were not genetically recombined, as indicated by findings of
      independent transfer of these R factors by conjugation and by transduction from
      the donors having these two R factors.  It was assumed from these findings that
      fi+ and fi- R factors are considerably different episomes having different
      resistance-transfer factors.
AU  - Watanabe T
AU  - Nishida H
AU  - Ogata C
AU  - Arai T
AU  - Sato S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1964 88: 716-726.

PMID- 16562138
VI  - 92
DP  - 1966
TI  - Episome-mediated transfer of drug resistance in Enterobacteriaceae.   X.  Restriction and modification of phages by fi- R factors.
PG  - 477-486
AB  - A fi- R factor, which restricts phages lambda, T1, and T7 without modifying
      them, was found to restrict and not to modify an F- specific phage, W-31, in
      Escherichia coli K-12, but not to restrict phage P-22 in Salmonella typhimurium
      LT-2, whereas other fi- R factors restricted and modified P-22 but not W-31;
      fi+ R factors did not restrict these phages.  Transduction and lysogenization
      with phages lambda and P-22 were reduced by these fi- R factors in K-23 and
      LT-2, respectively, and the transducing phages lambda and P-22 were modified by
      these fi- R factors.  Spontaneous as well as ultraviolet-induced production of
      phage P-22 and zygotic induction of phage lambda were not significantly
      affected by any R factor.  Injection of the nucleic acids of phages T1 and
      lambda was not affected by R factors, but the injected phage nucleic acids were
      rapidly broken down in the bacteria carrying fi- R factors.  The nucleic acids
      of the modified phages were not broken down in these bacteria.  It was assumed
      from these results that the mechanism of restriction of phages by fi- R factors
      is due to the breakdown of the injected phage nucleic acids by a
      deoxyribonuclease(s), presumably located near the cell surface in the cells
      carrying fi- R factors.  The deoxyribonuclease(s), formed in the cells carrying
      the nonmodifying fi- R factor, is considered to be different from that
      synthesized in the cells carrying the modifying fi- R factors.  It was further
      shown that the average burst sizes of the unmodified as well as modified phages
      are slightly reduced by the presence of the fi- R factors.
AU  - Watanabe T
AU  - Takano T
AU  - Arai T
AU  - Nishida H
AU  - Sato S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1966 92: 477-486.

PMID- 25838482
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Pseudomonas toyotomiensis KF710, a Polychlorinated Biphenyl-Degrading Bacterium Isolated from Biphenyl-Contaminated Soil.
PG  - e00223-15
AB  - Pseudomonas toyotomiensis KF710 utilizes biphenyl and degrades polychlorinated biphenyls
      (PCBs). Here, we report the genome sequence of the KF710 strain,
      consisting of 5,596,721 bp with 5,155 coding sequences. The biphenyl catabolic
      genes were almost identical to those of Pseudomonas pseudoalcaligenes KF707, one
      of the most well-characterized biphenyl-utilizing strains.
AU  - Watanabe T
AU  - Yamazoe A
AU  - Hosoyama A
AU  - Fujihara H
AU  - Suenaga H
AU  - Hirose J
AU  - Futagami T
AU  - Goto M
AU  - Kimura N
AU  - Furukawa K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00223-15.

PMID- 25814614
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Cupriavidus pauculus Strain KF709, a Biphenyl-Utilizing  Bacterium Isolated from Biphenyl-Contaminated Soil.
PG  - e00222-15
AB  - We report the draft genome sequence of Cupriavidus pauculus strain KF709, which comprises
      6,826,799 bp with 6,272 coding sequences. The strain KF709 utilizes
      biphenyl and degrades low-chlorinated biphenyls; however, it possesses fewer
      coding sequences involved in the degradation of aromatic compounds than other
      strains belonging to the Betaproteobacteria.
AU  - Watanabe T
AU  - Yamazoe A
AU  - Hosoyama A
AU  - Fujihara H
AU  - Suenaga H
AU  - Hirose J
AU  - Futagami T
AU  - Goto M
AU  - Kimura N
AU  - Furukawa K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00222-15.

PMID- 2685763
VI  - 17
DP  - 1989
TI  - Specific cleavage of the yeast genome at 5'-ATCGATCGAT-3'.
PG  - 9493
AB  - M.ClaI followed by DpnI cleavage.  Conditions are described for complete
      cleavage of yeast DNA.
AU  - Waterbury PG
AU  - Rehfuss RP
AU  - Carroll WT
AU  - Smardon AM
AU  - Faldasz BD
AU  - Huckaby CS
AU  - Lane MJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1989 17: 9493.

PMID- 8449409
VI  - 125
DP  - 1993
TI  - Isolation of a restriction-less mutant and development of a shuttle vector for the genetic analysis of Campylobacter hyointestinalis.
PG  - 19-24
AB  - A cosmid shuttle cloning vector, pCHI15, was constructed which could be mobilized from
      Escherichia coli K-12 to a putative restriction-less mutant of Campylobacter hyointestinalis,
      C. fetus subsp. fetus, and C. fetus subsp. venerealis at a frequency of 10-4 transconjugants
      per donor. A previously described C. coli shuttle vector, pILL550, could not be mobilized into
      the C. hyointestinalis restriction-less mutant, implying that the C. coli replicon was not
      functional in a C. hyointestinalis host. The type strains of C. jejuni, C. coli, C. fetus
      subsp. fetus, and C. hyointestinalis were analysed for their ability to be transformed by
      plasmid DNA which had been modified by other Campylobacter species. Each Campylobacter species
      was found to be most efficiently transformed by plasmid DNA that had been previously passaged
      in the same species. pCHI15 could be mobilized from C. coli into C. fetus subsp. fetus and the
      putative restriction-less mutant of C. hyointestinalis at a frequency of 3.0 x 10-4 and 2.5 x
      10-3 transconjugants per donor, respectively.
AU  - Waterman SR
AU  - Hackett J
AU  - Manning PA
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1993 125: 19-24.

PMID- 14566062
VI  - 100
DP  - 2003
TI  - The genome of Nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism.
PG  - 12984-12988
AB  - The hyperthermophile Nanoarchaeum equitans is an obligate symbiont growing in coculture with
      the crenarchaeon Ignicoccus. Ribosomal protein and
      rRNA-based phylogenies place its branching point early in the archaeal
      lineage, representing the new archaeal kingdom Nanoarchaeota. The N.
      equitans genome (490,885 base pairs) encodes the machinery for information
      processing and repair, but lacks genes for lipid, cofactor, amino acid, or
      nucleotide biosyntheses. It is the smallest microbial genome sequenced to
      date, and also one of the most compact, with 95% of the DNA predicted to
      encode proteins or stable RNAs. Its limited biosynthetic and catabolic
      capacity indicates that N. equitans' symbiotic relationship to Ignicoccus
      is parasitic, making it the only known archaeal parasite. Unlike the small
      genomes of bacterial parasites that are undergoing reductive evolution, N.
      equitans has few pseudogenes or extensive regions of noncoding DNA. This
      organism represents a basal archaeal lineage and has a highly reduced
      genome.
AU  - Waters E et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2003 100: 12984-12988.

PMID- 1514688
VI  - 204
DP  - 1992
TI  - Continuous spectrophotometric assay for restriction endonucleases using synthetic oligodeoxynucleotides and based on the hyperchromic effect.
PG  - 204-209
AB  - A continuous spectrophotometric assay for the EcoRV restriction endonuclease has been
      developed. The synthetic self-complementary oligonucleotide d(GACGATATCGTC) (which is double
      stranded under the assay conditions) is used as the substrate. The EcoRV endonuclease
      recognizes d(GATATC)sequences cutting between the cental T and dA bases. Thus d(GACGATATCGTC)
      is converted to d(GACGAT) and d(pATCGTC) during catalysis. Both of the hexameric products are
      single stranded under the assay conditions. The conversion of the dodecameric substrate to the
      two hexameric products and the concomitant change from double- to single-stranded DNA is
      associated with an increase in absorbance at 254 nm due to the hyperchromic effect. This
      change can be used to monitor column effluents for endonuclease activity and also for Km and
      kcat determination under steady-state kinetic conditions.
AU  - Waters TR
AU  - Connolly BA
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 1992 204: 204-209.

PMID- 8110783
VI  - 33
DP  - 1994
TI  - Interaction of the restriction endonuclease EcoRV with the deoxyguanosine and deoxycytidine bases in its recognition sequence.
PG  - 1812-1819
AB  - The interaction of the EcoRV restriction endonuclease with the dG and the dC bases in its
      recognition sequence (GATATC) has been studied using base analogues. These modified dG and dC
      bases each have a single potential protein contact removed. The analogues have been
      incorporated into the self-complementary dodecamer d(pGACGATATCGTC) at the appropriate
      positions (underlined). Many of the analogues caused no change in the Tm of the duplex or else
      lowered the Tm by a small amount such that a duplex was still formed at temperatures suitable
      for enzyme assay. However, the dG analogue 2-aminopurine-1-beta-D-2'-deoxyriboside
      destabilized the duplex to such an extent that the 12'-mer could not be used for enzyme
      assays. To overcome this, a longer self-complementary 18'-mer was used with this modified
      base. The circular dichroism spectra of the modified base containing 12'-mers (and the
      18'-mer in the case of 2-aminopurine) were very similar to the parent sequences lacking
      modified bases. This demonstrates the formation of B-DNA structures in all cases and similar
      overall conformations. The km and kcat values for the various modified oligomers have been
      determined, and these data have been used to assess the roles that functional groups on the dG
      and dC bases play in the recognition and hydrolysis of GATATC sequences by the endonuclease.
      The results obtained here have been compared to the crystal structures of the EcoRV complexed
      with a GATATC sequence, and this has allowed a critical evaluation of the base analogue
      approach. Both methods indicate that the 6-keto oxygen and 7-ring nitrogen of dG exposed in
      the major groove are vital for DNA recognition and hydrolysis.
AU  - Waters TR
AU  - Connolly BA
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1994 33: 1812-1819.

PMID- 11170385
VI  - 40
DP  - 2001
TI  - Solution conformation of EcoRI restriction endonuclease changes upon binding of cognate DNA and Mg2+ cofactor.
PG  - 683-692
AB  - EcoRI endonuclease has two tryptophans at positions 104 and 246 on the protein surface. A
      single tryptophan mutant containing Trp246 and a
      single cysteine labeling site at the N-terminus was used to determine
      the position of the N-terminus in the protein structure. The N-termini
      of EcoRI endonuclease are essential for tight binding and catalysis yet
      are not resolved in any of the crystal structures. Resonance energy
      transfer was used to measure the distance from the Trp246 donor to IAEDANS
      or MIANS acceptors at Cys3. The distance is 36 angstroms in the apoenzyme,
      decreasing to 26 angstroms in the DNA complex. Molecular modeling
      suggests that the N-termini are located at the dimer interface formed
      by the loops comprising residues 221-232. Protein conformational
      changes upon binding of cognate DNA and cofactor Mg2+ were monitored by
      tryptophan fluorescence of the single tryptophan mutant and wild-type
      endonuclease. The fluorescence decay of Trp246 is a triple exponential
      with lifetimes of 7, 3.5, and 0.7 ns. The decay-associated spectra of
      the 7- and 3.5-ns components have emission maxima at approximately 345 and
      approximately 338 nm in the apoenzyme, which shift to approximately 340 and
      approximately 348 nm in the DNA complex. The fluorescence quantum yield of
      the single tryptophan mutant drops 30% in the DNA complex, as compared
      to 10% for the wild-type endonuclease. Fluorescence changes of Trp 104 upon
      binding of DNA were inferred by comparison of the decay-associated
      spectra of wild type and single tryptophan mutant. Fluorescence changes
      are related to changes in proximity and orientation of quenching
      functional groups in the tryptophan microenvironments, as seen in the
      crystal structures.
AU  - Watrob H
AU  - Liu W
AU  - Chen Y
AU  - Bartlett SG
AU  - Jen-Jacobson L
AU  - Barkley MD
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2001 40: 683-692.

PMID- 10772863
VI  - 298
DP  - 2000
TI  - Alternative geometries of DNA looping: an analysis using the SfiI endonuclease.
PG  - 461-475
AB  - Many processes are governed by proteins that bind to separate sites in DNA and loop out the
      intervening DNA, but the geometries of the loops have seldom been determined. The SfiI
      endonuclease cleaves DNA after interacting with two recognition sites, and is a favourable
      system for the analysis of DNA looping. A gel-shift assay was used here to examine the binding
      of SfiI to a series of linear DNA molecules containing two SfiI sites separated by 109-170
      base-pairs. The complexes in which SfiI trapped a loop by binding to two sites in the same DNA
      were separated from the complexes containing SfiI bound to separate DNA molecules. Step-wise
      changes in the inter-site spacing generated two forms of the looped complex with different
      electrophoretic mobilities. The yields of each looped complex and the complexes from
      intermolecular synapses all varied cyclically with the inter-site spacing, with similar
      periodicities ( approximately 10.5 base-pairs) but with different phases. One looped complex
      predominated whenever the DNA between the sites needed to be underwound in order to produce
      the correct helical orientation of the binding sites. The other looped complex predominated
      whenever the intervening DNA needed to be overwound. We conclude that the former has trapped a
      right-handed loop with a negative node and the latter a left-handed loop with a positive node.
AU  - Watson MA
AU  - Gowers DM
AU  - Halford SE
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2000 298: 461-475.

PMID- 15228541
VI  - 53
DP  - 2004
TI  - Inactivation of deoxyadenosine methyltransferase (dam) attenuates Haemophilus influenzae virulence.
PG  - 651-664
AB  - Mutants in deoxyadenosine methyltransferase (dam) from many Gram-negative pathogens suggest
      multiple roles for Dam methylase:
      directing post-replicative DNA mismatch repair to the correct strand,
      guiding the temporal control of DNA replication and regulating the
      expression of multiple genes (including virulence factors) by
      differential promoter methylation. Dam methylase (HI0209) in strain Rd
      KW20 was inactivated in Haemophilus influenzae strains Rd KW20, Strain
      12 and INT-1; restriction with Dam methylation-sensitive enzymes DpnI
      and DpnII confirmed the absence of Dam methylation, which was restored
      by complementation with a single copy of dam ectopically expressed in
      cis. Despite the lack of increased mutation frequency, the dam mutants
      had a 2-aminopurine-susceptible phenotype that could be suppressed by
      secondary mutations in mutS, suggesting a role for Dam in H. influenzae
      DNA mismatch repair. Invasion of human brain microvascular endothelial
      cells (HBMECs) and human respiratory epithelial cells (NCI-H292) by the
      dam mutants was significantly attenuated in all strains, suggesting the
      absence of a Dam-regulated event necessary for uptake or invasion of
      host cells. Intracellular replication was inhibited only in the Strain
      12 dam mutant, whereas in the infant rat model of infection, the INT-1
      dam mutant was less virulent. Dam activity appears to be necessary for
      both in vitro and in vivo virulence in a strain-dependent fashion and
      may function as a regulator of gene expression including virulence
      factors.
AU  - Watson ME
AU  - Jarisch J
AU  - Smith AL
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2004 53: 651-664.

PMID- 6250907
VI  - 118
DP  - 1980
TI  - A new site-specific endonuclease from Neisseria cinerea.
PG  - 47-50
AB  - Sequence-specific deoxyribonucleases have greatly facilitated the analysis and
      in vitro manipulation of DNA.  Most of the known type II restriction enzymes
      recognize palindromic DNA sequences.  Although a large number of these enzymes
      have been characterized, many of the possible palindromic DNA sequences are not
      recognized by any known enzyme.  New restriction enzymes with unique
      recognition sites are desirable, as they increase the flexibility of
      recombinant DNA techniques.  We have screened a number of species of the genus
      Neisseria for restriction endonucleases, and report here the isolation and
      characterization of an enzyme from Neisseria cinerea which cleaves DNA at an
      unreported recognition sequence 5' . . . CC(C/G)GG . .3'.  The identification
      of this sequence was assisted by a computer compilation of the number of each
      tetra-, penta- and hexa-palindromic base sequence in pBR322.  PhiX174 and SV40
      DNAs, which is presented here as an aid to other investigators.
AU  - Watson R
AU  - Zuker M
AU  - Martin SM
AU  - Visentin LP
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1980 118: 47-50.

PMID- 6297965
VI  - 150
DP  - 1982
TI  - NdeI: a restriction endonuclease from Neisseria denitrificans which cleaves DNA at 5'-CATATG-3' sequences.
PG  - 114-116
AB  - Type II restriction endonucleases recognize and cleave near specific DNA
      sequences, usually 4-6 base pair palindromes.  They are of fundamental
      importance as tools for the recombinant DNA technology as they provide the
      selective cleavages required for the analysis and restructuring of DNA in
      vitro.  The flexibility of these techniques is proportional to the number of
      DNA sequences which can be cleaved by available enzymes.  Here, we describe the
      isolation and characterization of a restriction enzyme from Neisseria
      denitrificans with a new recognition sequence, 5'-CATATG-3'.
AU  - Watson RJ
AU  - Schildkraut I
AU  - Qiang B-Q
AU  - Martin SM
AU  - Visentin LP
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1982 150: 114-116.

PMID- 29572210
VI  - 84
DP  - 2018
TI  - A novel Glaesserella sp. isolated from severe respiratory infections in pigs has a mosaic genome with virulence factors putatively acquired by horizontal transfer.
PG  - 0
AB  - An unknown member of the family Pasteurellaceae was repeatedly isolated from
      severe pulmonary lesions in 20-24 week old pigs reared on the same farm in
      Victoria, Australia. The aetiological diagnosis of the disease was inconclusive.
      The complete genome sequence analysis of one strain, 15-184, revealed some
      phylogenic proximity to Glaesserella (Haemophilus) parasuis, the cause of
      Glasser's disease. However, sequences of the 16S rRNA and housekeeping genes, as
      well as average nucleotide identity scores, differed from all other known species
      in the family Pasteurellaceae The protein content of 15-184 was composite, with
      60% of coding sequences matching known G. parasuis products while more than 20%
      had a closer relative in the genera Actinobacillus, Mannheimia, Pasteurella or
      Bibersteinia Several putative virulence genes absent from G. parasuis but present
      in other Pasteurellaceae were also found, including the apxIII RTX toxin gene
      from Actinobacillus pleuropneumoniae, ABC transporters from Actinobacillus minor
      and iron transporters from various species. Three prophages and one Integrative
      Conjugative Element were present in the isolate. Horizontal gene transfers might
      explain the mosaic genomic structure and atypical metabolic and virulence
      characteristics of 15-184. This organism has not been assigned a taxonomic
      position in the family, but this study underlines the need for a large scale
      epidemiological and clinical characterisation of this novel pathogen in swine
      populations, as genomic analysis suggests it could have a severe impact on pig
      health.Importance Several species of Pasteurellaceae cause a range of significant
      diseases in pigs. A novel member of this family was recently isolated from
      Australian pigs suffering from severe respiratory infections. Comparative whole
      genome analyses suggest that this bacterium represents a new species, which
      possesses a number of virulence genes horizontally acquired from a diverse range
      of other Pasteurellaceae While the possible contribution of other co-infecting,
      non cultivable agents to the disease hasn't been ruled out in this study, the
      repertoire of virulence genes found in this organism may nevertheless explain
      some aspects of the associated pathology observed in the farm. The prevalence of
      this novel pathogen within pig populations is currently unknown. This finding is
      of particular importance for the pig industry as this organism can have a serious
      impact on the health of these animals.
AU  - Watt AE
AU  - Browning GF
AU  - Legione AR
AU  - Bushell RN
AU  - Stent A
AU  - Cutler RS
AU  - Young ND
AU  - Marenda MS
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2018 84: 0.

PMID- 28007852
VI  - 4
DP  - 2016
TI  - Whole-Genome Sequences of 26 Vibrio cholerae Isolates.
PG  - e01396-16
AB  - The human pathogen Vibrio cholerae employs several adaptive mechanisms for environmental
      persistence, including natural transformation and type VI secretion, creating a reservoir for
      the spread of disease. Here, we report whole-genome sequences of 26 diverse V. cholerae
      isolates, significantly increasing the sequence diversity of publicly available V. cholerae
      genomes.
AU  - Watve SS
AU  - Chande AT
AU  - Rishishwar L
AU  - Marino-Ramirez L
AU  - Jordan IK
AU  - Hammer BK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01396-16.

PMID- 8163534
VI  - 269
DP  - 1994
TI  - A novel class of FokI restriction endonuclease mutants that cleave hemi-methylated substrates.
PG  - 12298-12303
AB  - A genetic screen was used to identify amino acid substitutions that enable the FokI
      restriction endonuclease to cleave DNA in cells that express the cognate methyltransferase
      activity. Missense mutations that give rise to this phenotype were isolated at eight different
      positions (G188K, P196S, T343I, S388N, S395F, E407K, E410K, D421N), clustered in two regions
      of the polypeptide sequence of FokI. Two of the mutant endonucleases (P196S and D421N) were
      purified to homogeneity and analyzed in detail. Both mutants cleave FokI target sites
      (5'-GGATG-3') in a manner similar to the wild-type enzyme. Neither mutant cleaved
      noncanonical sequences, but both efficiently cleaved DNA substrates containing hemi-methylated
      FokI sites. This class of mutations has not been observed with other restriction enzymes.
AU  - Waugh DS
AU  - Sauer RT
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1994 269: 12298-12303.

PMID- 8415747
VI  - 90
DP  - 1993
TI  - Single amino acid substitutions uncouple the DNA binding and strand scission activities of Fok I endonuclease.
PG  - 9596-9600
AB  - Single alanine substitution mutations at Asp-450 or Asp-467 of the type IIS restriction enzyme
      FokI have no effect on the ability of the enzyme to bind strongly and selectively to its
      recognition site but completely eliminate its ability to cleave either strand of substrate
      DNA. Since wild-type FokI shows no kinetic preference or required order of strand cleavage,
      these results indicate that FokI, which evidently functions as a monomer, uses a single
      catalytic center to cleave both strands of DNA. In this respect, FokI may resemble other
      monomeric enzymes that cleave double-stranded DNA.
AU  - Waugh DS
AU  - Sauer RT
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1993 90: 9596-9600.

PMID- 24459265
VI  - 2
DP  - 2014
TI  - Genome Sequence of Youngiibacter fragilis, the Type Strain of the Genus Youngiibacter.
PG  - e01183-13
AB  - The genome of Youngiibacter fragilis, the type strain of the newly described genus
      Youngiibacter, was sequenced. The genome consists of 3.996 Mb, with a G+C
      content of 46.6 mol%. Y. fragilis originates from coal-bed methane-produced water
      and may provide insight into the microbiological basis of biogas production in
      coal beds.
AU  - Wawrik CB
AU  - Callaghan AV
AU  - Stamps BW
AU  - Wawrik B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01183-13.

PMID- 9427549
VI  - 202
DP  - 1997
TI  - The Tsp45I restriction-modification system is plasmid-borne within its thermophilic host.
PG  - 83-88
AB  - Thermus species YS45 harbors two small cryptic plasmids of 5.8 (pTsp45s) and approximately 12
      kb (pTsp45I).  Plasmid pTsp45s has been entirely sequenced, revealing three significant ORFs.
      In addition to a previously reported thermophilic plasmid-encoded replication protein, pTsp45s
      contains two genes for the Tsp45I methyltransferase and restriction endonuclease (Tsp45I).
      These two converging genes (tsp45IM and tsp45IR) overlap by 4 bp at their stop codons within
      an XbaI site.  M.Tsp45I (413 aa, 47.0 kDa, recognizing 5'-GTSAC-3') is highly homologous to
      other m6A-methyltransferases, especially M.EcaI (recognizing 5'-GGTNACC-3').  Tsp45I (332
      aa, 37.4 kDa, cleaving 5'-/GTSAC-3') is not homologous to M.Tsp45I, or to other restriction
      endonucleases.  Recombinant Tsp45I is stably produced in E. coli, and cleaves DNA at 65oC with
      the same specificity as the native enzyme.  Therefore, the thermophilic Tsp45I
      restriction-modification system is plasmid-borne within its native host.
AU  - Wayne J
AU  - Holden M
AU  - Xu S-Y
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1997 202: 83-88.

PMID- 25947176
VI  - 15
DP  - 2015
TI  - Development of a comparative genomic fingerprinting assay for rapid and high resolution genotyping of Arcobacter butzleri.
PG  - 94
AB  - BACKGROUND: Molecular typing methods are critical for epidemiological
      investigations, facilitating disease outbreak detection and source
      identification. Study of the epidemiology of the emerging human pathogen
      Arcobacter butzleri is currently hampered by the lack of a subtyping method that
      is easily deployable in the context of routine epidemiological surveillance. In
      this study we describe a comparative genomic fingerprinting (CGF) method for
      high-resolution and high-throughput subtyping of A. butzleri. Comparative
      analysis of the genome sequences of eleven A. butzleri strains, including eight
      strains newly sequenced as part of this project, was employed to identify
      accessory genes suitable for generating unique genetic fingerprints for
      high-resolution subtyping based on gene presence or absence within a strain.
      RESULTS: A set of eighty-three accessory genes was used to examine the population
      structure of a dataset comprised of isolates from various sources, including
      human and non-human animals, sewage, and river water (n=156). A streamlined assay
      (CGF40) based on a subset of 40 genes was subsequently developed through marker
      optimization. High levels of profile diversity (121 distinct profiles) were
      observed among the 156 isolates in the dataset, and a high Simpson's Index of
      Diversity (ID) observed (ID > 0.969) indicate that the CGF40 assay possesses high
      discriminatory power. At the same time, our observation that 115 isolates in this
      dataset could be assigned to 29 clades with a profile similarity of 90% or
      greater indicates that the method can be used to identify clades comprised of
      genetically similar isolates. CONCLUSIONS: The CGF40 assay described herein
      combines high resolution and repeatability with high throughput for the rapid
      characterization of A. butzleri strains. This assay will facilitate the study of
      the population structure and epidemiology of A. butzleri.
AU  - Webb AL
AU  - Kruczkiewicz P
AU  - Selinger LB
AU  - Inglis GD
AU  - Taboada EN
PT  - Journal Article
TA  - BMC Microbiol.
JT  - BMC Microbiol.
SO  - BMC Microbiol. 2015 15: 94.

PMID- 2323503
VI  - 4
DP  - 1990
TI  - Overexpression of RsrI DNA methyltransferase in E. coli.
PG  - A1795
AB  - RsrI DNA methyltransferase (M.RsrI) from Rhodobacter sphaeroides catalyzes
      methylation of the same central adenine residue in the duplex recognition
      sequence d(GAATTC) as does M.EcoRI.  M.RsrI has been purified to homogeneity
      from Rhodobacter sphaeroides, and its gene cloned and sequenced (Kaszubska, W.
      et al., Nucl. Acids Res., (1989) 17, 10403-101701.  M.RsrI has now been
      overexpressed in E. coli and the purification improved.  A fragment of R.
      sphaeroides chromosomal DNA, containing both the rsrIM and rsrIR genes was
      inserted downstream of the T7 promoter in a pTZ18U vector.  M.RsrI was purified
      to homogeneity from E. coli BL21(DE3)plysS cells with a 100-fold increase in
      yield over that from R. sphaeroides.  The purification was simplified by the
      substitution of a DNA-cellulose-sinefungin affinity column for the
      hydroxylapatite and weak cation exchange chromatography steps.  Sinefungin, an
      S-adenosylmethionine analogue, inhibits methyl group transfer by M.RsrI.  We
      are presently further characterizing M.RsrI by determining its kinetic
      constants and the number of methyl groups transferred per binding event.
AU  - Webb H
AU  - Kaszubska W
AU  - Gumport RI
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1990 4: A1795.

PMID- 8617247
VI  - 15
DP  - 1996
TI  - Restriction by EcoKI is enhanced by cooperative interactions between target sequences and is dependent on DEAD box motifs.
PG  - 2003-2009
AB  - One subunit of both type I and type III restriction and modification enzymes
      contains motifs characteristic of DEAD box proteins, which implies that these enzymes may be
      DNA helicases.  This subunit is essential for restriction, but not modification.  The current
      model
      for restriction by both types of enzyme postulates that DNA cutting is stimulated when two
      enzyme
      complexes bound to neighboring target sequences meet as the consequence of ATP-dependent
      DNA translocation.  For type I enzymes, this model is supported by in vitro experiments, but
      the
      predicted cooperative interactions between targets have not been detected by assays that
      monitor
      restriction in vivo.  The experiments reported here clearly establish the required synergistic
      effect
      but, in contrast to earlier experiments, they use Escherichia coli K-12 strains deficient in
      the
      restriction alleviation function associated with the Rac prophage.  In bacteria with elevated
      levels of
      EcoKI the cooperative interactions are obscured, consistent with cooperation between free
      enzyme
      and that bound at target sites.  We have made changes in three of the motifs characteristic of
      DEAD
      box proteins, including motif III, which in RecG is implicated in the migration of Holliday
      junctions.  Conservative changes in each of the three motifs impair restriction.
AU  - Webb JL
AU  - King G
AU  - Ternent D
AU  - Titheradge AJB
AU  - Murray NE
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1996 15: 2003-2009.

PMID- 7608969
VI  - 250
DP  - 1995
TI  - Probing the domain structure of the type IC DNA methyltransferase M.EcoR124I by limited proteolysis.
PG  - 181-190
AB  - Limited proteolysis has been used to probe the domain structure of the type I DNA
      methyltransferase M.EcoR124I. Trypsin digestion of the methyltransferase generates two
      fragments derived from the HsdS subunit, a 28 kDa N-terminal domain and a 19 kDa C-terminal
      domain, leaving the HsdM subunit intact. Extensive digestion by chymotrypsin, however, removes
      59 amino acid residues from the N terminus of the HsdM subunit to leave a 52 kDa C-terminal
      domain. Binding of the cofactor S-adenosyl methionine has no appreciable effect on the rate of
      cleavage, but binding of a 30 bp DNA duplex containing the cognate recognition sequence
      confers almost total protection. Following trypsin cleavage of the methyltransferase, a stable
      proteolytic product is produced which has been purified for biochemical characterization. The
      trypsinized enzyme is shown to be a multimeric complex containing two intact HsdM subunits and
      both fragments of the HsdS subunit, consistent with the circular model proposed for the
      organization of domains in the specificity subunit in type IC methyltransferases. Gel
      retardation studies show that the proteolysed enzyme still retains DNA binding activity, but
      its specificity for the DNA recognition sequence is dramatically reduced.
AU  - Webb M
AU  - Taylor IA
AU  - Firman K
AU  - Kneale GG
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1995 250: 181-190.

PMID- 27469954
VI  - 4
DP  - 2016
TI  - Complete Genome Sequences of Two Methicillin-Sensitive Staphylococcus aureus Isolates Representing a Population Subset Highly Prevalent in Human Colonization.
PG  - e00716-16
AB  - Here, we report the high-quality draft genome sequences of two methicillin-susceptible
      Staphylococcus aureus isolates, 08-02119 and 08-02300.
      Belonging to sequence type 582 (ST582) and ST7, both isolates are representatives
      of clonal lineages often associated with asymptomatic colonization of humans.
AU  - Weber RE
AU  - Layer F
AU  - Fuchs S
AU  - Bender JK
AU  - Fiedler S
AU  - Werner G
AU  - Strommenger B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00716-16.

PMID- 27908995
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Bacteroides ovatus V975.
PG  - e01335-16
AB  - The complete genome sequence of Bacteroides ovatus V975 was determined. The genome consists of
      a single circular chromosome of 6,475,296 bp containing five
      rRNA operons, 68 tRNA genes, and 4,959 coding genes.
AU  - Wegmann U
AU  - Goesmann A
AU  - Carding SR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01335-16.

PMID- 23919528
VI  - 16
DP  - 2014
TI  - Complete genome of a new Firmicutes species belonging to the dominant human colonic microbiota ('Ruminococcus bicirculans') reveals two chromosomes and a selective capacity to utilize plant glucans.
PG  - 2879-2890
AB  - The recently isolated bacterial strain 80/3 represents one of the most abundant 16S rRNA
      phylotypes detected in the healthy human large intestine and belongs to the Ruminococcaceae
      family of Firmicutes. The completed genome sequence reported here is the first for a member of
      this important family of bacteria from the human colon. The genome comprises two large
      chromosomes of 2.24 and 0.73 Mbp, leading us to propose the name Ruminococcus bicirculans for
      this new species.
      Analysis of the carbohydrate active enzyme complement suggests an ability to utilize certain
      hemicelluloses, especially beta-glucans and xyloglucan, for growth that was confirmed
      experimentally. The enzymatic machinery enabling the degradation of cellulose and xylan by
      related cellulolytic ruminococci is however lacking in this species. While the genome
      indicated the capacity to synthesize purines, pyrimidines and all 20 amino acids, only genes
      for the synthesis of nicotinate, NAD+, NADP+ and coenzyme A were detected among the essential
      vitamins and co-factors, resulting in multiple growth requirements. In vivo, these growth
      factors must be supplied from the diet, host or other gut microorganisms. Other features of
      ecological interest include two type IV pilins, multiple extracytoplasmic function-sigma
      factors, a urease and a bile salt hydrolase.
AU  - Wegmann U
AU  - Louis P
AU  - Goesmann A
AU  - Henrissat B
AU  - Duncan SH
AU  - Flint HJ
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2014 16: 2879-2890.

PMID- 28209813
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Desulfovibrio piger FI11049.
PG  - e01528-16
AB  - The complete genome sequence of Desulfovibrio piger FI11049 was determined. The genome
      consists of a single circular chromosome of 2,807,531 bp encoding seven
      rRNA operons, 76 tRNA genes, and 2,535 coding genes.
AU  - Wegmann U
AU  - Nueno PC
AU  - Mayer MJ
AU  - Crost E
AU  - Narbad A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01528-16.

PMID- 17307855
VI  - 189
DP  - 2007
TI  - Complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp. cremoris MG1363.
PG  - 3256-3270
AB  - Lactococcus lactis is of great importance for the nutrition of hundreds of millions of people
      worldwide. This paper describes the genome sequence of
      Lactococcus lactis subsp. cremoris MG1363, the lactococcal strain most
      intensively studied throughout the world. The 2,529,478-bp genome contains
      81 pseudogenes and encodes 2,436 proteins. Of the 530 unique proteins, 47
      belong to the COG (clusters of orthologous groups) functional category
      "carbohydrate metabolism and transport," by far the largest category of
      novel proteins in comparison with L. lactis subsp. lactis IL1403. Nearly
      one-fifth of the 71 insertion elements are concentrated in a specific
      56-kb region. This integration hot-spot region carries genes that are
      typically associated with lactococcal plasmids and a repeat sequence
      specifically found on plasmids and in the "lateral gene transfer hot spot"
      in the genome of Streptococcus thermophilus. Although the parent of L.
      lactis MG1363 was used to demonstrate lysogeny in Lactococcus, L. lactis
      MG1363 carries four remnant/satellite phages and two apparently complete
      prophages. The availability of the L. lactis MG1363 genome sequence will
      reinforce its status as the prototype among lactic acid bacteria through
      facilitation of further applied and fundamental research.
AU  - Wegmann U
AU  - O'Connell-Motherway M
AU  - Zomer A
AU  - Buist G
AU  - Shearman C
AU  - Canchaya C
AU  - Ventura M
AU  - Goesmann A
AU  - Gasson MJ
AU  - Kuipers OP
AU  - van Sinderen D
AU  - Kok J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2007 189: 3256-3270.

PMID- 19767436
VI  - 191
DP  - 2009
TI  - The complete genome sequence of Lactobacillus johnsonii FI9785, a competitive exclusion agent against pathogens in poultry.
PG  - 7142-7143
AB  - Lactobacillus johnsonii is a member of the acidophilus group of lactobacilli. Because of their
      probiotic properties including attachment
      to epithelial cells, immunomodulation and competitive exclusion of
      pathogens representatives of this group are being intensively studied.
      Here we report the complete annotated genome sequence of Lactobacillus
      johnsonii FI9785, a strain which prevents the colonisation of specific
      pathogen-free chicks by Clostridium perfringens.
AU  - Wegmann U
AU  - Overweg K
AU  - Horn N
AU  - Goesmann A
AU  - Narbad A
AU  - Gasson MJ
AU  - Shearman C
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2009 191: 7142-7143.

PMID- 23273849
VI  - 9
DP  - 2012
TI  - Expression of sulfatases in Rhodopirellula baltica and the diversity of sulfatases in the genus Rhodopirellula.
PG  - 51-61
AB  - The whole genome sequence of Rhodopirellula baltica SH1(T), published nearly 10years ago,
      already revealed a high amount of sulfatase genes. So far, little is known about the diversity
      and potential functions mediated by sulfatases in Planctomycetes. We combined in vivo and in
      silico techniques to gain insights into the ecophysiology of planktomycetal sulfatases.
      Comparative genomics of nine recently sequenced Rhodopirellula strains detected 1120 open
      reading frames annotated as sulfatases (Enzyme Commission number (EC) 3.1.6.*). These were
      clustered into 173 groups of orthologous and paralogous genes. To analyze the functional
      aspects, 708 sulfatase protein sequences from these strains were aligned with 67 sulfatase
      reference sequences of reviewed functionality. Our analysis yielded 22 major similarity
      clusters, but only five of these clusters contained Rhodopirellula sequences homologous to
      reference sequences, indicating a surprisingly high diversity. Exemplarily, R. baltica SH1(T)
      was grown on different sulfated polysaccharides, chondroitin sulfate, lambda-carrageenan and
      fucoidan. Subsequent gene expression analyses using whole genome microarrays revealed distinct
      sulfatase expression profiles based on substrates tested. This might be indicative for a high
      structural diversity of sulfated polysaccharides as potential substrates. The pattern of
      sulfatases in individual planctomycete species may reflect ecological niche adaptation.
AU  - Wegner CE
AU  - Richter-Heitmann T
AU  - Klindworth A
AU  - Klockow C
AU  - Richter M
AU  - Achstetter T
AU  - Glockner FO
AU  - Harder J
PT  - Journal Article
TA  - Marine Genomics
JT  - Marine Genomics
SO  - Marine Genomics 2012 9: 51-61.

PMID- 29599157
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of an NDM-1- and KPC-2-Coproducing Hypervirulent Carbapenem-Resistant Klebsiella pneumoniae Strain Isolated from Burn Wound  Infections.
PG  - e00192-18
AB  - We report here the draft genome sequence of an NDM-1- and KPC-2-coproducing hypervirulent
      carbapenem-resistant Klebsiella pneumoniae strain, isolated from a
      58-year-old male in the People's Republic of China with a burn injury.
AU  - Wei DD
AU  - Wan LG
AU  - Liu Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00192-18.

PMID- 18413342
VI  - 36
DP  - 2008
TI  - The Fidelity Index provides a systematic quantitation of star activity of DNA restriction endonucleases.
PG  - e50
AB  - Restriction endonucleases are the basic tools of molecular biology. Many restriction
      endonucleases show relaxed sequence recognition, called star
      activity, as an inherent property under various digestion conditions
      including the optimal ones. To quantify this property we propose the
      concept of the Fidelity Index (FI), which is defined as the ratio of the
      maximum enzyme amount showing no star activity to the minimum amount
      needed for complete digestion at the cognate recognition site for any
      particular restriction endonuclease. Fidelity indices for a large number
      of restriction endonucleases are reported here. The effects of reaction
      vessel, reaction volume, incubation mode, substrate differences, reaction
      time, reaction temperature and additional glycerol, DMSO, ethanol and
      Mn(2+) on the FI are also investigated. The FI provides a practical
      guideline for the use of restriction endonucleases and defines a
      fundamental property by which restriction endonucleases can be
      characterized.
AU  - Wei H
AU  - Therrien C
AU  - Blanchard A
AU  - Guan S
AU  - Zhu Z
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2008 36: e50.

PMID- 12704152
VI  - 71
DP  - 2003
TI  - Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T.
PG  - 2775-2786
AB  - We determined the complete genome sequence of Shigella flexneri serotype 2a strain 2457T
      (4,599,354 bp). Shigella species cause >1 million deaths
      per year from dysentery and diarrhea and have a lifestyle that is markedly
      different from those of closely related bacteria, including Escherichia
      coli. The genome exhibits the backbone and island mosaic structure of E.
      coli pathogens, albeit with much less horizontally transferred DNA and
      lacking 357 genes present in E. coli. The strain is distinctive in its
      large complement of insertion sequences, with several genomic
      rearrangements mediated by insertion sequences, 12 cryptic prophages, 372
      pseudogenes, and 195 S. flexneri-specific genes. The 2457T genome was also
      compared with that of a recently sequenced S. flexneri 2a strain, 301. Our
      data are consistent with Shigella being phylogenetically indistinguishable
      from E. coli. The S. flexneri-specific regions contain many genes that
      could encode proteins with roles in virulence. Analysis of these will
      reveal the genetic basis for aspects of this pathogenic organism's
      distinctive lifestyle that have yet to be explained.
AU  - Wei J
AU  - Goldberg MB
AU  - Burland V
AU  - Venkatesan MM
AU  - Deng W
AU  - Fournier G
AU  - Mayhew GF
AU  - Plunkett G III
AU  - Rose DJ
AU  - Darling A
AU  - Mau B
AU  - Perna NT
AU  - Payne SM
AU  - Runyen-Janecky LJ
AU  - Zhou S
AU  - Schwartz DC
AU  - Blattner FR
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2003 71: 2775-2786.

PMID- 22207750
VI  - 194
DP  - 2012
TI  - Genome Sequence of Mycoplasma iowae Strain 695, an Unusual Pathogen Causing Deaths in Turkeys.
PG  - 547-548
AB  - Mycoplasma iowae is associated mainly with reduced hatchability in turkeys and is well known
      for the unusual ability of phenotypic variation in the
      Mycoplasma surface components as well as a relative resistance to heat,
      bile salts, and many antimicrobials. A subset of unique genes and a gene
      cluster responsible for these characteristics could be identified from the
      genome. Here, we report the first genome sequence of this species.
AU  - Wei S
AU  - Guo Z
AU  - Li T
AU  - Zhang T
AU  - Li X
AU  - Zhou Z
AU  - Li Z
AU  - Liu M
AU  - Luo R
AU  - Bi D
AU  - Chen H
AU  - Zhou R
AU  - Jin H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 547-548.

PMID- 25281112
VI  - 131
DP  - 2015
TI  - A fluorescence method for detection of DNA and DNA methylation based on graphene oxide and restriction endonuclease HpaII.
PG  - 342-347
AB  - DNA methylation plays an important role in many biological events and is associated with
      various diseases. Most traditional methods for detection of DNA methylation are based on the
      complex and expensive bisulfite method. In this paper, we report a novel fluorescence method
      to detect DNA and DNA methylation based on graphene oxide (GO) and restriction endonuclease
      HpaII. The skillfully designed probe DNA labeled with 5-carboxyfluorescein (FAM) and optimized
      GO concentration keep the probe/target DNA. still adsorbed on the GO. After the cleavage
      action of HpaII the labeled FAM is released from the GO surface and its fluorescence recovers,
      which could be used to detect DNA in the linear range of 50 pM-50 nM with a detection limit of
      43 pM. DNA methylation induced by transmethylase (Mtase) or other chemical reagents prevents
      HpaII from recognizing and cleaving the specific site; as a result, fluorescence cannot
      recover. The fluorescence recovery efficiency is closely related to the DNA methylation level,
      which can be used to detect DNA methylation by comparing it with the fluorescence in the
      presence of intact target DNA. The method for detection of DNA and DNA methylation is simple,
      reliable and accurate.
AU  - Wei W
AU  - Gao C
AU  - Xiong Y
AU  - Zhang Y
AU  - Liu S
AU  - Pu Y
PT  - Journal Article
TA  - Talanta
JT  - Talanta
SO  - Talanta 2015 131: 342-347.

PMID- 28798172
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Methylocaldum sp. SAD2, a Methanotrophic Strain That Can Convert Raw Biogas to Methanol in the Presence of Hydrogen Sulfide.
PG  - e00716-17
AB  - The draft genome sequence of Methylocaldum sp. SAD2, a methanotrophic strain isolated from a
      hydrogen sulfide-rich anaerobic digester, is reported here.
      Strain SAD2 possesses genes for methane oxidation in the presence of H2S.
AU  - Wei X
AU  - Ge X
AU  - Li Y
AU  - Yu Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00716-17.

PMID- 28428289
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Methylocaldum sp. Strain 14B, an Obligate Hydrogen Sulfide-Tolerant Methanotrophic Strain That Can Convert Biogas to Methanol.
PG  - e00153-17
AB  - The draft genome sequence of Methylocaldum sp. 14B, an obligate methanotrophic strain isolated
      from solid-state anaerobic digestion systems, is reported here.
      Strain 14B possesses genes for methane oxidation and exhibited tolerance to H2S.
AU  - Wei X
AU  - Ge X
AU  - Li Y
AU  - Yu Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00153-17.

PMID- 28232436
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Bacillus subtilis Strain 29R7-12, a Piezophilic Bacterium Isolated from Coal-Bearing Sediment 2.4 Kilometers below the Seafloor.
PG  - e01621-16
AB  - Here, we report the genome sequence of Bacillus subtilis strain 29R7-12, a piezophilic
      bacterium isolated from coal-bearing sediment down to ~2.4 km below
      the ocean floor in the northwestern Pacific. The strain is a Gram-positive
      spore-forming bacterium, closely related to Bacillus subtilis within the phylum
      Firmicutes This is the first complete genome sequence of a Bacillus subtilis
      strain from the deep biosphere. The genome sequence will provide a valuable
      resource for comparative studies of microorganisms from the surface and
      subsurface environments.
AU  - Wei Y
AU  - Cao J
AU  - Fang J
AU  - Kato C
AU  - Cui W
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01621-16.

PMID- 28209827
VI  - 5
DP  - 2017
TI  - First Complete Genome Sequence of Marinilactibacilluspiezotolerans Strain 15R, a  Marine Lactobacillus Isolated from Coal-Bearing Sediment 2.0 Kilometers below the  Seafloor, Determined by PacBio Single-Molecule Real-Time Technology.
PG  - e01625-16
AB  - Marinilactibacillus piezotolerans strain 15R is a facultatively anaerobic heterotrophic
      lactobacillus isolated from deep marine subsurface sediment nearly
      2 km below the seafloor in the northwestern Pacific. We report here the first
      whole-genome sequence of strain 15R. The identified genome sequence has 2,767,908
      bp, 35.4% G+C content, and predicted 2,552 candidate protein-coding sequences,
      with no identified plasmids.
AU  - Wei Y
AU  - Cao J
AU  - Fang J
AU  - Kato C
AU  - Cui W
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01625-16.

PMID- 23469334
VI  - 1
DP  - 2013
TI  - Genome Sequence of Enterobacter cancerogenus YZ1.
PG  - e00023-13
AB  - is usually known as an opportunistic human pathogen. Recently, it has attracted great
      attention for its capability to produce bioemulsifier, degrade xenobiotics,
      and resist alkalis and antibiotics. Here we report the complete genome of YZ1,
      isolated from a bran-feeding insect's frass.
AU  - Wei Y
AU  - Yang Y
AU  - Zhou L
AU  - Liu Z
AU  - Wang X
AU  - Yang R
AU  - Su Q
AU  - Zhou Y
AU  - Zhao J
AU  - Yang J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00023-13.

PMID- 24504003
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Clostridium ultunense Strain BS (DSMZ 10521), Recovered  from a Mixed Culture.
PG  - e01269-13
AB  - Clostridium ultunense BS is the first isolated strain (type strain) of C. ultunense that was
      identified as a mesophilic syntrophic acetate-oxidizing
      bacterium (SAOB). Here, we report the draft genome sequence of this strain, which
      will help us to elucidate the mechanism of syntrophic acetate oxidization.
AU  - Wei Y
AU  - Zhou H
AU  - Zhang L
AU  - Zhang J
AU  - Wang Y
AU  - Wang S
AU  - Zhou Z
AU  - Yan X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01269-13.

PMID- 20525832
VI  - 192
DP  - 2010
TI  - Complete Genome Sequence of Bifidobacterium longum JDM301.
PG  - 4076-4077
AB  - Bifidobacteria, known as probiotic bacteria, are high G+C Gram-positive bacteria, which
      naturally inhabit the human gastrointestinal tract (GIT) and vagina. Recently, we have a
      Bifidobacterium longum JDM301 completely sequenced, which is a widely used Chinese commercial
      strain with several probiotic properties.
AU  - Wei YX
AU  - Zhang ZY
AU  - Liu C
AU  - Zhu YZ
AU  - Zhu YQ
AU  - Zheng HJ
AU  - Zhao GP
AU  - Wang SY
AU  - Guo XK
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 4076-4077.

PMID- 23405285
VI  - 1
DP  - 2013
TI  - Genome Sequence of Sinorhizobium meliloti Rm41.
PG  - e00013-12
AB  - Sinorhizobium meliloti Rm41 nodulates alfalfa plants, forming indeterminate type  nodules. It
      is characterized by a strain-specific K-antigen able to replace exopolysaccharides in
      promotion of nodule invasion. We present the Rm41 genome, composed of one chromosome, the
      chromid pSymB, the megaplasmid pSymA, and the nonsymbiotic plasmid pRme41a.
AU  - Weidner S
AU  - Baumgarth B
AU  - Gottfert M
AU  - Jaenicke S
AU  - Puhler A
AU  - Schneiker-Bekel S
AU  - Serrania J
AU  - Szczepanowski R
AU  - Becker A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00013-12.

PMID- 22374952
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Soybean Symbiont Sinorhizobium fredii HH103.
PG  - 1617-1618
AB  - Sinorhizobium fredii HH103 is a fast-growing rhizobial strain that is able to nodulate legumes
      that develop determinate nodules, e.g., soybean, and legumes
      that form nodules of the indeterminate type. Here we present the genome of HH103,
      which consists of one chromosome and five plasmids with a total size of 7.22 Mb.
AU  - Weidner S
AU  - Becker A
AU  - Bonilla I
AU  - Jaenicke S
AU  - Lloret J
AU  - Margaret I
AU  - Puhler A
AU  - Ruiz-Sainz JE
AU  - Schneiker-Bekel S
AU  - Szczepanowski R
AU  - Vinardell JM
AU  - Zehner S
AU  - Gottfert M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1617-1618.

PMID- 26316634
VI  - 3
DP  - 2015
TI  - Complete Genome Sequences of Two Bordetella hinzii Strains Isolated from Humans.
PG  - e00965-15
AB  - Bordetella hinzii is primarily recovered from poultry but can also colonize mammalian hosts
      and immunocompromised humans. Here, we report the first complete  genome sequences of B.
      hinzii in two isolates recovered from humans. The availability of these sequences will
      hopefully aid in identifying host-specific determinants variably present within this species.
AU  - Weigand MR
AU  - Changayil S
AU  - Kulasekarapandian Y
AU  - Tondella ML
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00965-15.

PMID- 28912323
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of Bordetella pertussis Isolates with Novel Pertactin-Deficient Deletions.
PG  - e00973-17
AB  - Clinical isolates of the respiratory pathogen Bordetella pertussis in the United  States have
      become predominantly deficient for the acellular vaccine immunogen
      pertactin through various independent mutations. Here, we report the complete
      genome sequences for four B. pertussis isolates that harbor novel deletions
      responsible for pertactin deficiency.
AU  - Weigand MR
AU  - Peng Y
AU  - Cassiday PK
AU  - Loparev VN
AU  - Johnson T
AU  - Juieng P
AU  - Nazarian EJ
AU  - Weening K
AU  - Tondella ML
AU  - Williams MM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00973-17.

PMID- 28167525
VI  - 199
DP  - 2017
TI  - The History of Bordetella pertussis Genome Evolution Includes Structural Rearrangement.
PG  - e00806-16
AB  - Despite high pertussis vaccine coverage, reported cases of whooping cough
      (pertussis) have increased over the last decade in the United States and other
      developed countries. Although Bordetella pertussis is well known for its limited
      gene sequence variation, recent advances in long-read sequencing technology have
      begun to reveal genomic structural heterogeneity among otherwise
      indistinguishable isolates, even within geographically or temporally defined
      epidemics. We have compared rearrangements among complete genome assemblies from
      257 B. pertussis isolates to examine the potential evolution of the chromosomal
      structure in a pathogen with minimal gene nucleotide sequence diversity. Discrete
      changes in gene order were identified that differentiated genomes from vaccine
      reference strains and clinical isolates of various genotypes, frequently along
      phylogenetic boundaries defined by single nucleotide polymorphisms. The observed
      rearrangements were primarily large inversions centered on the replication origin
      or terminus and flanked by IS481, a mobile genetic element with >240 copies per
      genome and previously suspected to mediate rearrangements and deletions by
      homologous recombination. These data illustrate that structural genome evolution
      in B. pertussis is not limited to reduction but also includes rearrangement.
      Therefore, although genomes of clinical isolates are structurally diverse,
      specific changes in gene order are conserved, perhaps due to positive selection,
      providing novel information for investigating disease resurgence and molecular
      epidemiology.IMPORTANCE Whooping cough, primarily caused by Bordetella pertussis,
      has resurged in the United States even though the coverage with
      pertussis-containing vaccines remains high. The rise in reported cases has
      included increased disease rates among all vaccinated age groups, provoking
      questions about the pathogen's evolution. The chromosome of B. pertussis includes
      a large number of repetitive mobile genetic elements that obstruct genome
      analysis. However, these mobile elements facilitate large rearrangements that
      alter the order and orientation of essential protein-encoding genes, which
      otherwise exhibit little nucleotide sequence diversity. By comparing the complete
      genome assemblies from 257 isolates, we show that specific rearrangements have
      been conserved throughout recent evolutionary history, perhaps by eliciting
      changes in gene expression, which may also provide useful information for
      molecular epidemiology.
AU  - Weigand MR
AU  - Peng Y
AU  - Loparev V
AU  - Batra D
AU  - Bowden KE
AU  - Burroughs M
AU  - Cassiday PK
AU  - Davis JK
AU  - Johnson T
AU  - Juieng P
AU  - Knipe K
AU  - Mathis MH
AU  - Pruitt AM
AU  - Rowe L
AU  - Sheth M
AU  - Tondella ML
AU  - Williams MM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2017 199: e00806-16.

PMID- 27795250
VI  - 4
DP  - 2016
TI  - Complete Genome Sequences of Four Different Bordetella sp. Isolates Causing Human Respiratory Infections.
PG  - e01080-16
AB  - Species of the genus Bordetella associate with various animal hosts, frequently causing
      respiratory disease. Bordetella pertussis is the primary agent of
      whooping cough and other Bordetella species can cause similar cough illness.
      Here, we report four complete genome sequences from isolates of different
      Bordetella species recovered from human respiratory infections.
AU  - Weigand MR
AU  - Peng Y
AU  - Loparev V
AU  - Batra D
AU  - Bowden KE
AU  - Cassiday PK
AU  - Davis JK
AU  - Johnson T
AU  - Juieng P
AU  - Miner CE
AU  - Rowe L
AU  - Sheth M
AU  - Tondella ML
AU  - Williams MM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01080-16.

PMID- 27635001
VI  - 4
DP  - 2016
TI  - Complete Genome Sequences of Bordetella pertussis Vaccine Reference Strains 134 and 10536.
PG  - e00979-16
AB  - Vaccine formulations and vaccination programs against whooping cough (pertussis)  vary
      worldwide. Here, we report the complete genome sequences of two divergent
      Bordetella pertussis reference strains used in the production of pertussis
      vaccines.
AU  - Weigand MR
AU  - Peng Y
AU  - Loparev V
AU  - Batra D
AU  - Burroughs M
AU  - Johnson T
AU  - Juieng P
AU  - Rowe L
AU  - Tondella ML
AU  - Williams MM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00979-16.

PMID- 28007855
VI  - 4
DP  - 2016
TI  - Complete Genome Sequences of Four Bordetella pertussis Vaccine Reference Strains  from Serum Institute of India.
PG  - e01404-16
AB  - Serum Institute of India is among the world's largest vaccine producers. Here, we report the
      complete genome sequences for four Bordetella pertussis strains used by Serum Institute of
      India in the production of whole-cell pertussis vaccines.
AU  - Weigand MR
AU  - Peng Y
AU  - Loparev V
AU  - Johnson T
AU  - Juieng P
AU  - Gairola S
AU  - Kumar R
AU  - Shaligram U
AU  - Gowrishankar R
AU  - Moura H
AU  - Rees J
AU  - Schieltz DM
AU  - Williamson Y
AU  - Woolfitt A
AU  - Barr J
AU  - Tondella ML
AU  - Williams MM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01404-16.

PMID- 23405330
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Catellicoccus marimammalium, a Novel Species Commonly Found in Gull Feces.
PG  - e00019-12
AB  - Catellicoccus marimammalium is a relatively uncharacterized Gram-positive facultative anaerobe
      with potential utility as an indicator of waterfowl fecal
      contamination. Here, we report an annotated draft genome sequence that suggests
      that this organism may be a symbiotic gut microbe.
AU  - Weigand MR
AU  - Ryu H
AU  - Bozcek L
AU  - Konstantinidis KT
AU  - Santo DJW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00019-12.

PMID- 2536159
VI  - 86
DP  - 1989
TI  - Enzymatic cleavage of a bacterial genome at a 10-base-pair recognition site.
PG  - 51-55
AB  - The circular genome of Staphylococcus aureus was cut into two fragments by a
      simple enzymatic method that cleaves a 10-base-pair site.  The recognition
      sequence, A-T-C-G-mA^T-C-G-mA-T, was created by the combined use of the
      methylase M.ClaI (A-T-C-G-mA-T) and the restriction endonuclease DpnI
      (G-mA^T-C).  This technique is insensitive to CpG methylation and in human DNA
      is predicted to produce fragments that, on average, are greater than five
      million base pairs.  The ability to create such long pieces of DNA should
      facilitate mapping of large, complex chromosomes.
AU  - Weil MD
AU  - McClelland M
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1989 86: 51-55.

PMID- 21551308
VI  - 193
DP  - 2011
TI  - Complete genome sequence of the plant growth-promoting endophyte Burkholderia phytofirmans strain PsJN.
PG  - 3383-3384
AB  - Burkholderia phytofirmans PsJN(T) is able to efficiently colonize the rhizosphere, root and
      above-ground plant tissues of a wide variety of
      genetically unrelated plants such as potato, canola, maize and grapevine.
      Strain PsJN shows strong plant growth-promoting effects and was reported
      to enhance plant vigour and resistance to biotic and abiotic stresses.
      Here, we report the genome sequence of this strain, which indicates the
      presence of multiple traits relevant for endophytic colonization and plant
      growth promotion.
AU  - Weilharter A
AU  - Mitter B
AU  - Shin MV
AU  - Chain PS
AU  - Nowak J
AU  - Sessitsch A
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3383-3384.

PMID- 27688327
VI  - 4
DP  - 2016
TI  - Genome Sequences of 12 Bacterial Isolates Obtained from the Urine of Pregnant Women.
PG  - e00882-16
AB  - The presence of bacteria in urine can pose significant risks during pregnancy. However, there
      are few reference genome strains for many common urinary bacteria.
      We isolated 12 urinary strains of Streptococcus, Staphylococcus, Citrobacter,
      Gardnerella, and Lactobacillus These strains and their genomes are now available
      to the research community.
AU  - Weimer CM
AU  - Deitzler GE
AU  - Robinson LS
AU  - Park S
AU  - Hallsworth-Pepin K
AU  - Wollam A
AU  - Mitreva M
AU  - Lewis WG
AU  - Lewis AL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00882-16.

PMID- Not carried by PubMed...
VI  - 94
DP  - 1994
TI  - New methodologies for the directional and bidirectional cloning and expression of PCR-generated DNA fragments.
PG  - 249
AB  - We have optimized conditions for the efficient cloning of blunt-ended DNA fragments generated
      by the polymerase chain reaction (PCR). In the bidirectional cloning procedure, the PCR
      fragment is incubated with SrfI endonuclease-treated (recognition site: 5'GCCC^GGGC3')
      plasmid DNA, SrfI endonuclease, and T4 DNA ligase. The ligation reaction is allowed to proceed
      for 1 hour and transformed into E. coli. The presence of the endonuclease in the ligation
      reaction reduces nonrecombinant background and increases the amount of linear vector available
      for recombinant insertion. Directional PCR cloning is achieved by creating a
      monophosphorylated vector and a monophosphorylated PCR fragment. Circularization of the cloned
      product during subsequent incubation with SrfI and T4 DNA ligase occurs only when the
      insertion is in the desired orientation. The plasmid vectors have been optimized for
      expression using T7 RNA polymerase for transcriptional control.
AU  - Weiner M
AU  - Costa G
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1994 94: 249.

PMID- 29437920
VI  - 9
DP  - 2018
TI  - Genomic Analysis of Hospital Plumbing Reveals Diverse Reservoir of Bacterial Plasmids Conferring Carbapenem Resistance.
PG  - e02011-17
AB  - The hospital environment is a potential reservoir of bacteria with plasmids conferring
      carbapenem resistance. Our Hospital Epidemiology Service routinely performs extensive sampling
      of high-touch surfaces, sinks, and other locations in the hospital.
      Over a 2-year period, additional sampling was conducted at a broader range of locations,
      including housekeeping closets, wastewater from hospital internal pipes, and external
      manholes. We compared these data with previously collected information from 5 years of patient
      clinical and surveillance isolates. Whole-genome sequencing and analysis of 108 isolates
      provided comprehensive characterization of blaKPC/blaNDM-positive isolates, enabling an
      in-depth genetic comparison. Strikingly, despite a very low prevalence
      of patient infections with blaKPC-positive organisms, all samples from the intensive care unit
      pipe wastewater and external manholes contained carbapenemase-producing organisms (CPOs),
      suggesting a vast, resilient reservoir. We observed a diverse set of species and plasmids, and
      we noted species and susceptibility profile differences between environmental and patient
      populations of CPOs. However, there were plasmid backbones
      common to both populations, highlighting a potential environmental reservoir of mobile
      elements that may contribute to the spread of resistance genes. Clear associations between
      patient and environmental isolates were uncommon based on sequence analysis and epidemiology,
      suggesting reasonable infection control compliance at our institution. Nonetheless, a probable
      nosocomial transmission of Leclercia sp. from the housekeeping environment to a patient was
      detected by this extensive surveillance. These data and analyses further our understanding of
      CPOs in the hospital environment and are broadly relevant to the design of infection control
      strategies in many infrastructure
      settings.
AU  - Weingarten RA
AU  - Johnson RC
AU  - Conlan S
AU  - Ramsburg AM
AU  - Dekker JP
AU  - Lau AF
AU  - Khil P
AU  - Odom RT
AU  - Deming C
AU  - Park M
AU  - Thomas PJ
AU  - Henderson DK
AU  - Palmore TN
AU  - Segre JA
AU  - Frank KM
PT  - Journal Article
TA  - MBio
JT  - MBio
SO  - MBio 2018 9: e02011-17.

PMID- 23405339
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Listeria monocytogenes LL195, a Serotype 4b Strain from the 1983-1987 Listeriosis Epidemic in Switzerland.
PG  - e00152-12
AB  - The complete genome sequence of Listeria monocytogenes LL195, a serotype 4b clinical strain
      isolated during the 1983-1987 listeriosis epidemic in
      Switzerland, is presented.
AU  - Weinmaier T
AU  - Riesing M
AU  - Rattei T
AU  - Bille J
AU  - Arguedas-Villa C
AU  - Stephan R
AU  - Tasara T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00152-12.

PMID- 17073008
VI  - 443
DP  - 2006
TI  - Insights into social insects from the genome of the honeybee Apis mellifera.
PG  - 931-949
AB  - Here we report the genome sequence of the honeybee Apis mellifera, a key model for social
      behaviour and essential to global ecology through pollination.  Compared with other sequenced
      insect genomes,the A. mellifera genome has a high A + T and CpG contents, lacks major
      transposon families, evolves more slowly, and is more similar to vertebrates for circadian
      rhythm, RNA interference and DNA methylation genes, among others.  Furthermore, A. mellifera
      has fewer genes for innate immunity, detoxification enzymes, cuticle-forming proteins and
      gustatory receptors, more genes for odorant receptors, and novel genes for nectar and pollen
      utilization, consistent with its ecology and social organization.  Copmpared to Drosophila,
      genes in early developmental pathways differ in Apis, whereas similarities exist for functions
      that differ markedly, such as sex determination, brain function and behaviour.  Population
      genetics suggests a novel African origin for the species A. mellifera nad insights into
      whether Africanized bees spread throughout the New World via hybridization or displacement.
AU  - Weinstock GM
AU  - Robinson GE
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2006 443: 931-949.

PMID- 27908990
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Campylobacter jejuni Strains That Cause Abortion in Livestock.
PG  - e01324-16
AB  - Campylobacter jejuni is an intestinal bacterium that can cause abortion in livestock. This
      publication announces the public release of 15 Campylobacter
      jejuni genome sequences from isolates linked to abortion in livestock. These
      isolates are part of the 100K Pathogen Genome Project and are from clinical cases
      at the University of California (UC) Davis.
AU  - Weis AM
AU  - Clothier KA
AU  - Huang BC
AU  - Kong N
AU  - Weimer BC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01324-16.

PMID- 28408683
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Multidrug-Resistant Abortive Campylobacter jejuni from Northern California.
PG  - e00171-17
AB  - Campylobacter jejuni is an enteric bacterium that can cause abortion in livestock. This is the
      release of a multidrug-resistant Campylobacter jejuni
      genome from an isolate that caused an abortion in a cow in northern California.
      This isolate is part of the 100K Pathogen Genome Project.
AU  - Weis AM
AU  - Clothier KA
AU  - Huang BC
AU  - Kong N
AU  - Weimer BC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00171-17.

PMID- 28428292
VI  - 5
DP  - 2017
TI  - Shigella Draft Genome Sequences: Resources for Food Safety and Public Health.
PG  - e00176-17
AB  - Shigella is a major foodborne pathogen that infects humans and nonhuman primates  and is the
      major cause of dysentery and reactive arthritis worldwide. This is the
      initial public release of 16 Shigella genome sequences from four species
      sequenced as part of the 100K Pathogen Genome Project.
AU  - Weis AM
AU  - Gilpin B
AU  - Huang BC
AU  - Kong N
AU  - Chen P
AU  - Weimer BC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00176-17.

PMID- 28057746
VI  - 5
DP  - 2017
TI  - Large-Scale Release of Campylobacter Draft Genomes: Resources for Food Safety and Public Health from the 100K Pathogen Genome Project.
PG  - e00925-16
AB  - Campylobacter is a food-associated bacterium and a leading cause of foodborne illness
      worldwide, being associated with poultry in the food supply. This is the
      initial public release of 202 Campylobacter genome sequences as part of the 100K
      Pathogen Genome Project. These isolates represent global genomic diversity in the
      Campylobacter genus.
AU  - Weis AM
AU  - Huang BC
AU  - Storey DB
AU  - Kong N
AU  - Chen P
AU  - Arabyan N
AU  - Gilpin B
AU  - Mason C
AU  - Townsend AK
AU  - Smith WA
AU  - Byrne BA
AU  - Taff CC
AU  - Weimer BC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00925-16.

PMID- 14757847
VI  - 2
DP  - 2004
TI  - Role of the DNA methyltransferase variant DNMT3b3 in DNA methylation.
PG  - 62-72
AB  - Several alternatively spliced variants of DNA methyltransferase (DNMT) 3b have been described.
      Here, we identified new murine Dnmt3b mRNA
      isoforms and found that mouse embryonic stem (ES) cells expressed only
      Dnmt3b transcripts that contained exons 10 and 11, whereas the Dnmt3b
      transcripts in somatic cells lacked these exons, suggesting that this
      region is important for embryonic development. DNMT3b2 and 3b3 were the
      major isoforms expressed in human cell lines and the mRNA levels of
      these isoforms closely correlated with their protein levels. Although
      DNMT3b3 may be catalytically inactive, it still may be biologically
      important because D4Z4 and satellites 2 and 3 repeat sequences, all
      known DNMT3b target sequences, were methylated in cells that
      predominantly expressed DNMT3b3. Treatment of cells with the
      mechanism-based inhibitor 5-aza-2'-deoxycytidine (5-Aza-CdR) caused a
      complete depletion of DNMT1, 3a, 3b1, and 3b2 proteins. Human DNMT3b3
      and the murine Dnmt3b3-like isoform, Dnmt3b6, were also depleted
      although less efficiently, suggesting that DNMT3b3 also may be capable
      of DNA binding. Moreover, de novo methylation of D4Z4 in T24 cancer
      cells after 5-Aza-CdR treatment only occurred when DNMT3b3 was
      expressed, reinforcing its role as a contributing factor of DNA
      methylation. The expression of either DNMT3b2 or 3b3, however, was not
      sufficient to explain the abnormal methylation of DNMT3b target
      sequences in human cancers, which may therefore be dependent on factors
      that affect DNMT3b targeting. Methylation analyses of immunodeficiency,
      chromosomal instabilities, and facial abnormalities cells revealed that
      an Alu repeat sequence was highly methylated, suggesting that Alu
      sequences are not DNMT3b targets.
AU  - Weisenberger DJ
AU  - Velicescu M
AU  - Cheng JC
AU  - Gonzales FA
AU  - Liang GN
AU  - Jones PA
PT  - Journal Article
TA  - Mol. Cancer Res.
JT  - Mol. Cancer Res.
SO  - Mol. Cancer Res. 2004 2: 62-72.

PMID- 12406579
VI  - 298
DP  - 2002
TI  - Identification and characterization of alternatively spliced variants of DNA methyltransferase 3a in mammalian cells.
PG  - 91-99
AB  - CpG methylation is mediated by the functions of at least three active DNA methyltransferases
      (DNMTs). While DNMT1 is thought to perform maintenance methylation, the more recently
      discovered DNMT3a and DNMT3b enzymes are thought to facilitate de novo methylation. Murine
      Dnmt3a and 3b are developmentally regulated and a new Dnmt3a isoform, Dnmt3a2, has been
      recently shown to be expressed preferentially in mouse embryonic stem (ES) cells. Here we have
      characterized four alternatively spliced variants of human and mouse DNMT3a. These transcripts
      included a novel exon 1 (1beta) that was spliced into the same exon 2 acceptor splice site
      used by the original exon 1 (1alpha). Cloning and sequencing of the 5' region of the human
      DNMT3a gene revealed that exon 1beta was situated upstream of exon 1alpha and that the entire
      region was contained within a CpG island. We also identified other alternatively spliced
      species containing intron 4 inclusions that were associated with either exon 1alpha or 1beta.
      These were expressed at low levels in mouse and human cells. All transcripts were highly
      conserved between human and mouse. The levels of Dnmt3a mRNA containing exon 1beta were
      3-25-fold greater in mouse ES cells than in various somatic cells as determined by
      semiquantitative reverse transcription-polymerase chain reaction analysis, while the levels of
      exon 1alpha-containing transcripts were slightly higher in human and mouse somatic cells. The
      preferential expression of the beta transcript in ES cells suggests that this transcript, in
      addition to Dnmt3a2, may also be important for de novo methylation during development.
AU  - Weisenberger DJ
AU  - Velicescu M
AU  - Preciado-Lopez MA
AU  - Gonzales FA
AU  - Tsai YC
AU  - Liang G
AU  - Jones PA
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 2002 298: 91-99.

PMID- 11090275
VI  - 304
DP  - 2000
TI  - A novel mutant of the type I restriction-modification enzyme EcoR124I is altered at a key stage of the subunit assembly pathway.
PG  - 301-310
AB  - The HsdS subunit of a type I restriction-modification (R-M) system plays an essential role in
      the activity of both the modification methylase and the restriction endonuclease. This subunit
      is responsible for DNA binding, but also contains conserved amino acid sequences responsible
      for protein-protein interactions. The most important protein-protein interactions are those
      between the HsdS subunit and the HsdM (methylation) subunit that result in assembly of an
      independent methylase (MTase) of stoichiometry M(2)S(1). Here, we analysed the impact on the
      restriction and modification activities of the change Trp(212)-->Arg in the distal border of
      the central conserved region of the EcoR124I HsdS subunit. We demonstrate that this point
      mutation significantly influences the ability of the mutant HsdS subunit to assemble with the
      HsdM subunit to produce a functional MTase. As a consequence of this, the mutant MTase has
      drastically reduced DNA binding, which is restored only when the HsdR (restriction) subunit
      binds with the MTase. Therefore, HsdR acts as a chaperon allowing not only binding of the
      enzyme to DNA, but also restoring the methylation activity and, at sufficiently high
      concentrations in vitro of HsdR, restoring restriction activity.
AU  - Weiserova M
AU  - Dutta CF
AU  - Firman K
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2000 304: 301-310.

PMID- 9628361
VI  - 379
DP  - 1998
TI  - Isolation of a non-classical mutant of the DNA recognition subunit of the type I restriction endonuclease R.EcoR124I.
PG  - 585-589
AB  - We have used deletion mutagenesis and PCR-based misincorporation mutagenesis to produce a
      collection of mutations in the central conserved region of the DNA binding subunit of the type
      IC restriction endonuclease EcoR124I.  It has been proposed that this domain is involved in
      protein-protein interactions during the assembly of the endonuclease.  While a large
      percentage of these mutations gave a classical Res- Mod- phenotype, one mutant was isolated
      with a nonclassical Res-Mod+ phenotype.  The loss of restriction activity, but retention of
      the ability to modify indicates that this mutation cannot affect DNA binding and must alter
      the assembly of the endonuclease in such a way as to prevent DNA cleavage but allow
      methylation.  This mutant resulted from a single amino acid change Trp212-Arg.  The location
      of the single amino acid change is at the border of the central conserved region and the
      second target recognition domain and suggests that this region is extremely important for the
      assembly of the methylase with the HsdR subunit into a functional restriction endonuclease.
AU  - Weiserova M
AU  - Firman K
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1998 379: 585-589.

PMID- 8441649
VI  - 21
DP  - 1993
TI  - Cloning, production and characterization of wild type and mutant forms of the R.EcoK endonucleases.
PG  - 373-379
AB  - The hsdR, hsdM and hsdS genes coding for R.EcoK restriction endonucleases, both with and
      without a temperature sensitive mutation (ts-1) in the hsdS gene, were cloned in pBR322
      plasmid and introduced into E. coli C3-6. The presence of the hsdS ts-1 mutation has no effect
      on the R-M phenotype of this contruct in bacteria grown at 42 degrees C. However, DNA
      sequencing indicates that the mutation is still present on the pBR322-hsd ts1 operon. The
      putative temperature-sensitive endonuclease was purified from bacteria carrying this plasmid
      and the ability to cleave and methylate plasmid DNA was investigated. The mutant endonuclease
      was found to show temperature-sensitivity for restriction. Modification was dramatically
      reduced at both the permissive and non-permissive temperatures. The wild type enzyme was found
      to cleave circular DNA in a manner which strongly suggests that only one endonuclease molecule
      is required per cleavage event. Circular and linear DNA appear to be cleaved using different
      mechanisms, and cleavage of linear DNA may require a second endonuclease molecule. The subunit
      composition of the purified endonucleases was investigated and compared to the level of
      subunit production in minicells. There is no evidence that HsdR is prevented from assembling
      with HsdM and HsdS ts-1 to produce the mutant endonuclease. The data also suggests that the
      level of HsdR subunit may be limiting within the cell. We suggest that an excess of HsdM and
      HsdS may produce the methylase in vivo and that assembly of the endonuclease may be dependent
      upon the prior production of this methylase.
AU  - Weiserova M
AU  - Janscak P
AU  - Benada O
AU  - Hubacek J
AU  - Vitaly EA
AU  - Glover SW
AU  - Firman K
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 373-379.

PMID- 8549991
VI  - 39
DP  - 1994
TI  - Overproduction of the Hsd subunits leads to the loss of temperature-sensitive restriction and modification phenotype.
PG  - 452-458
AB  - The genes hsdM and hsdS for M.EcoKI modification methyltransferase and the complete set of
      hsdR, hsdM and hsdS genes coding for R.EcoKI restriction endonuclease, both with and without a
      temperature-sensitive (ts) mutation in hsdS gene, were cloned in pBR322 plasmid and introduced
      into E. coli C (a strain without a natural restriction-modification (R-M) system).  The
      strains producing only the methyltransferase, or together with the endonuclease, were thus
      obtained.  The hsdSts-1 mutation, mapped previously in the distal variable region of the hsdS
      gene with C1245-T transition has no effect on the R-M phenotype expressed from cloned genes in
      bacteria grown at 42oC.  In clones transformed with the whole hsd region an alleviation of R-M
      functions was observed immediately after the transformation, but after subculture the
      transformants expressed the wild-type R-M phenotype irrespective of whether the wild-type or
      the mutant hsdS allele was present in the hybrid plasmid.  Simultaneous overproduction of HsdS
      and HsdM subunits impairs the ts effect of the hsdSts-1 mutation on restriction and
      modification.
AU  - Weiserova M
AU  - Janscak P
AU  - Zinkevich V
AU  - Hubacek J
PT  - Journal Article
TA  - Folia Microbiol. (Praha)
JT  - Folia Microbiol. (Praha)
SO  - Folia Microbiol. (Praha) 1994 39: 452-458.

PMID- 18588664
VI  - 8
DP  - 2008
TI  - Characterization of a restriction modification system from the commensal Escherichia coli strain A0 34/86 (O83 : K24 : H31).
PG  - 106
AB  - Background: Type I restriction-modification (R-M) systems are the most complex restriction
      enzymes discovered to date. Recent years have
      witnessed a renaissance of interest in R-M enzymes Type I. The massive
      ongoing sequencing programmes leading to discovery of, so far, more
      than 1 000 putative enzymes in a broad range of microorganisms
      including pathogenic bacteria, revealed that these enzymes are widely
      represented in nature. The aim of this study was characterisation of a
      putative R-M system EcoA0ORF42P identified in the commensal Escherichia
      coli A0 34/86 (O83: K24: H31) strain, which is efficiently used at
      Czech paediatric clinics for prophylaxis and treatment of nosocomial
      infections and diarrhoea of preterm and newborn infants.
      Results: We have characterised a restriction-modification system
      EcoA0ORF42P of the commensal Escherichia coli strain A0 34/86 ( O83:
      K24: H31). This system, designated as EcoAO831, is a new functional
      member of the Type IB family, whose specificity differs from those of
      known Type IB enzymes, as was demonstrated by an immunological
      cross-reactivity and a complementation assay. Using the plasmid
      transformation method and the RM search computer program, we identified
      the DNA recognition sequence of the EcoAO83I as GGA(8N)ATGC. In
      consistence with the amino acids alignment data, the 3' TRD component
      of the recognition sequence is identical to the sequence recognized by
      the EcoEI enzyme. The A-T ( modified adenine) distance is identical to
      that in the EcoAI and EcoEI recognition sites, which also indicates
      that this system is a Type IB member. Interestingly, the recognition
      sequence we determined here is identical to the previously reported
      prototype sequence for Eco377I and its isoschizomers.
      Conclusion: Putative restriction-modification system EcoA0ORF42P in
      the commensal Escherichia coli strain A0 34/86 ( O83: K24: H31) was
      found to be a member of the Type IB family and was designated as
      EcoAO83I. Combination of the classical biochemical and bacterial
      genetics approaches with comparative genomics might contribute
      effectively to further classification of many other putative Type-I
      enzymes, especially in clinical samples.
AU  - Weiserova M
AU  - Ryu JC
PT  - Journal Article
TA  - BMC Microbiol.
JT  - BMC Microbiol.
SO  - BMC Microbiol. 2008 8: 106.

PMID- 8797818
VI  - 86
DP  - 1996
TI  - DNA demethylation in vitro: Involvement of RNA.
PG  - 709-718
AB  - An in vitro system for studying DNA demethylation has been established using extracts from
      tissue culture cells.  This reaction, which is unusually resistant to proteinase K, takes
      place through the removal of a 5-methylcytosine nucleotide unit from the DNA substrate and its
      conversion to an RNAse-sensitive form.  It is likely that this represents the in vivo
      mechanism as well, since extracts from L8 myoblasts specifically demethylate an alpha-actin
      gene, while extracts from F9 teratocarcinoma cells specifically demodify the Aprt CpG island.
      After pretreatment with proteinase K, these extracts demethylate both genes equally,
      suggesting that gene specificity may be controlled by protein factors.
AU  - Weiss A
AU  - Keshet I
AU  - Razin A
AU  - Cedar H
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1996 86: 709-718.

PMID- 23991256
VI  - 8
DP  - 2013
TI  - Permanent draft genome sequence of Comamonas testosteroni KF-1.
PG  - 239-254
AB  - Comamonas testosteroni KF-1 is a model organism for the elucidation of the novel  biochemical
      degradation pathways for xenobiotic 4-sulfophenylcarboxylates (SPC)
      formed during biodegradation of synthetic 4-sulfophenylalkane surfactants (linear
      alkylbenzenesulfonates, LAS) by bacterial communities. Here we describe the
      features of this organism, together with the complete genome sequence and
      annotation. The 6,026,527 bp long chromosome (one sequencing gap) exhibits an
      average G+C content of 61.79% and is predicted to encode 5,492 protein-coding
      genes and 114 RNA genes.
AU  - Weiss M
AU  - Kesberg AI
AU  - Labutti KM
AU  - Pitluck S
AU  - Bruce D
AU  - Hauser L
AU  - Copeland A
AU  - Woyke T
AU  - Lowry S
AU  - Lucas S
AU  - Land M
AU  - Goodwin L
AU  - Kjelleberg S
AU  - Cook AM
AU  - Buhmann M
AU  - Thomas T
AU  - Schleheck D
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 239-254.

PMID- 22815451
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Herbaspirillum lusitanum P6-12, an Endophyte Isolated from Root Nodules of Phaseolus vulgaris.
PG  - 4136-4137
AB  - Herbaspirillum lusitanum strain P6-12 (DSM 17154) is, so far, the only species of
      Herbaspirillum isolated from plant root nodules. Here we report a draft genome
      sequence of this organism.
AU  - Weiss VA
AU  - Faoro H
AU  - Tadra-Sfeir MZ
AU  - Raittz RT
AU  - de Souza EM
AU  - Monteiro RA
AU  - Cardoso RL
AU  - Wassem R
AU  - Chubatsu LS
AU  - Huergo LF
AU  - Muller-Santos M
AU  - Steffens MB
AU  - Rigo LU
AU  - Pedrosa FO
AU  - Cruz LM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4136-4137.

PMID- 22675582
VI  - 5
DP  - 2011
TI  - Complete genome sequence of Allochromatium vinosum DSM 180.
PG  - 311-330
AB  - Allochromatium vinosum formerly Chromatium vinosum is a mesophilic purple sulfur bacte-rium
      belonging to the family Chromatiaceae in the bacterial class Gammaproteobacteria. The genus
      Allochromatium contains currently five species. All members were isolated from fresh-water,
      brackish water or marine habitats and are predominately obligate phototrophs. Here we describe
      the features of the organism, together with the complete genome sequence and annotation. This
      is the first completed genome sequence of a member of the Chromatiaceae within the purple
      sulfur bacteria thriving in globally occurring habitats. The 3,669,074 bp ge-nome with its
      3,302 protein-coding and 64 RNA genes was sequenced within the Joint Ge-nome Institute
      Community Sequencing Program.
AU  - Weissgerber T
AU  - Zigann R
AU  - Bruce D
AU  - Chang Y-j
AU  - Detter JC
AU  - Han C
AU  - Hauser L
AU  - Jeffries CD
AU  - Land M
AU  - Munk AC
AU  - Tapia R
AU  - Dahl C
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 5: 311-330.

PMID- 29682170
VI  - 13
DP  - 2018
TI  - High quality draft genome sequence of Mycoplasma testudineum strain BH29(T), isolated from the respiratory tract of a desert tortoise.
PG  - 9
AB  - Mycoplasma testudineum is one of the pathogens that can cause upper respiratory tract disease
      in desert tortoises, Gopherus agassizii. We sequenced the genome of
      M. testudineum BH29(T) (ATCC 700618(T) = MCCM 03231(T)), isolated from the upper
      respiratory tract of a Mojave desert tortoise with upper respiratory tract
      disease. The sequenced draft genome, organized in 25 scaffolds, has a length of
      960,895 bp and a G + C content of 27.54%. A total of 788 protein-coding
      sequences, six pseudogenes and 35 RNA genes were identified. The potential
      presence of cytadhesin-encoding genes is investigated. This genome will enable
      comparative genomic studies to help understand the molecular bases of the
      pathogenicity of this and other Mycoplasma species.
AU  - Weitzman CL
AU  - Tillett RL
AU  - Sandmeier FC
AU  - Tracy CR
AU  - Alvarez-Ponce D
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2018 13: 9.

PMID- 12471157
VI  - 99
DP  - 2002
TI  - Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli.
PG  - 17020-17024
AB  - We present the complete genome sequence of uropathogenic Escherichia coli, strain CFT073. A
      three-way genome comparison of the CFT073, enterohemorrhagic E. coli EDL933, and laboratory
      strain MG1655 reveals that, amazingly, only 39.2% of their combined (nonredundant) set of
      proteins actually are common to all three strains. The pathogen genomes are as different from
      each other as each pathogen is from the benign strain. The difference in disease potential
      between O157:H7 and CFT073 is reflected in the absence of genes for type III secretion system
      or phage- and plasmid-encoded toxins found in some classes of diarrheagenic E. coli. The
      CFT073 genome is particularly rich in genes that encode potential fimbrial adhesins,
      autotransporters, iron-sequestration systems, and phase-switch recombinases. Striking
      differences exist between the large pathogenicity islands of CFT073 and two other well-studied
      uropathogenic E. coli strains, J96 and 536. Comparisons indicate that extraintestinal
      pathogenic E. coli arose independently from multiple clonal lineages. The different E. coli
      pathotypes have maintained a remarkable synteny of common, vertically evolved genes, whereas
      many islands interrupting this common backbone have been acquired by different horizontal
      transfer events in each strain.
AU  - Welch RA et al
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2002 99: 17020-17024.

PMID- 9467909
VI  - 144
DP  - 1998
TI  - Isoschizomers of the restriction endonuclease TaqI (T/CGA) requiring different metal ion concentrations and having a range of thermal stabilities from Thermus species from different continents.
PG  - 167-175
AB  - One-hundred-and-fifty-two isolates of the genus Thermus, collected from hot springs on four
      continents, were screened for evidence of the presence of the thermophilic Type II restriction
      endonuclease TaqI (T/CGA).  The presence of isoschizomers of TaqI in 27 of the isolates,
      originating from hot springs in New Zealand, Iceland, USA, Japan, mainland Portugal and the
      island of Sao Miguel in the Azores, is reported.  Six of the TaqI-containing isolates from
      diverse geographical locations, identified by means of DNA/DNA homology and 16S rRNA sequence
      alignment as belonging to the Thermus species T. aquaticus, T. filiformis, T. themophilus, T.
      scotoductus and T. brockianus, were selected for comparative studies.  The TaqI isoschizomers
      from each of the six isolates were partially purified.  They differed in their magnesium ion
      requirements, isoelectric points, subunit molecular masses and thermal stability.
AU  - Welch SG
AU  - Al-Awadhi S
AU  - Williams RAD
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 1998 144: 167-175.

PMID- 7626025
VI  - 309
DP  - 1995
TI  - Two thermostable type II restriction endonucleases from Icelandic strains of the genus Thermus: Tsp4C I (ACN/GT), a novel type II restriction endonuclease, and Tsp8E I, an isoschizomer of the mesophilic enzyme BglI (GCCNNNN/NGGC).
PG  - 595-599
AB  - Sixteen isolates of thermophilic bacteria from the genus Thermus, isolated from neutral and
      alkaline hot water springs in the southwest region of Iceland, were tested for the presence of
      restriction endonucleases.  Extracts from five of the isolates showed evidence of the
      presence of restriction endonuclease activity by producing discrete nucleotide fragments when
      incubated at 65oC with lambda phage DNA.  Two of the isolates (Tsp4C and Tsp8E) were found to
      have particularly high levels of restriction endonuclease activity, and the respective enzymes
      from these two Thermus isolates were partially purified and characterized and their
      recognition and cleavage sites were determined.  Enzyme Tsp4C I is a novel type II restriction
      endonuclease recognizing the interrupted palindromic tetranucleotide sequence ACNGT, where N
      can be any one of the four bases in DNA.  Tsp4CI, which retains full enzyme activity when
      incubated for 10 min at temperatures up to 76oC, hydrolyses the phosphodiester bond in both
      strands of a double-stranded DNA substrate between the third and fourth bases of the
      recognition sequence (ACN/GT), generating fragments with a single base 3'-OH overhang.
      Enzyme Tsp8EI is a thermostable isoschizomer of the mesophilic type II restriction
      endonuclease BglI (GCCNNNN/NGGC), generating fragments with a three base 3'-OH overhang.
      However, unlike BglI, Tsp8EI exhibits considerable thermal stability, retaining full enzyme
      activity when incubated for 10 min at temperatures up to 78oC.  Both Tsp4CI and Tsp8EI
      represent significant additions to the small but expanding list of the extremely thermostable
      restriction endonucleases.
AU  - Welch SG
AU  - Williams RAD
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 1995 309: 595-599.

PMID- 8524644
VI  - 23
DP  - 1995
TI  - Taq52I, a novel and thermostable type II restriction endonuclease from the genus Thermus, recognising the pentanucleotide sequence GC(A or T)GC and cleaving DNA between the first and second bases of the recognition sequence: G/C(A or T)GC.
PG  - 4573-4575
AB  - 127 isolates of the genus Thermus, from neutral and alkaline hot water springs on four
      continents, have been screened for the presence of restriction endonuclease activity.  An
      isolate (YS52) from Yellowstone National Park, USA, showed a high level of restriction
      endonuclease activity when a cell free extract was incubated with lambda phage DNA at 65oC.  A
      type II restriction endonuclease (Taq52I) has been partially purified from this isolate and
      the recognition and cleavage site determined.  Taq52I has a novel interrupted palindromic
      tetranucleotide recognition sequence GCWGC, where W can be either adenine (A) or thymine (T).
      It hydrolyses the phosphodiester bond in both strands of the substrate between the first and
      second bases of the recognition sequence: 5'G/CWGC3', producing three-base 5'-OH overhangs
      (sticky ends).  The enzyme has a pH optimum of 7.0, requires 8 mM MgCl2 for maximum activity
      and is thermally stable, retaining full enzyme activity following incubation at 79oC for 10
      min.  Taq52I not only represents a new addition to the type II restriction endonucleases, but
      also increases the small list of thermostable restriction endonucleases.
AU  - Welch SG
AU  - Williams RAD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1995 23: 4573-4575.

PMID- 8526863
VI  - 312
DP  - 1995
TI  - Two different isoschizomers of the type-II restriction endonuclease TaqI (T/CGA) within the same Thermus isolate: Tsp32I, an enzyme with similar heat stability properties to the prototype enzyme TaqI, & Tsp32II, a hyperthermostable isoschizomer of TaqI.
PG  - 505-510
AB  - We have recently screened 112 separate isolates of the genus Thermus, collected from neutral
      and alkaline hot water springs on four continents, for the presence of the Type-II restriction
      endonuclease TaqI (T/CGA).  One particular isolate from the Azores (strain 32) was found to
      contain high levels of a restriction endonuclease with the same recognition and cleavage site
      as TaqI.  Initial studies revealed that the partially purified enzyme from strain 32 was
      considerably more resistant to heat inactivation than the prototype enzyme TaqI, being able to
      withstand temperatures at least 10oC higher than TaqI, before showing evidence of heat
      inactivation.  Subsequently it became clear that the partially purified extract from strain 32
      contains two separate enzymes, both of which are isoschizomers of TaqI.  One of the enzymes,
      Tsp32I, has similar thermal stability characteristics to TaqI, whereas the second TaqI
      isoschizomer, Tsp32II, found in the same Thermus isolate as Tsp32I, is considerably more
      thermostable than TaqI, retaining full enzyme activity up to a temperature of 85oC.  Tsp32I
      and Tsp32II were further distinguished by virtue of their different requirements for magnesium
      ions.
AU  - Welch SG
AU  - Williams RAD
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 1995 312: 505-510.

PMID- 8657557
VI  - 24
DP  - 1996
TI  - Tsp49I (ACGT^), a thermostable neoschizomer of the type II restriction endonuclease MaeII (A^CGT), discovered in isolates of the genus thermus from the Azores, Iceland and New Zealand.
PG  - 1799-1801
AB  - One hundred and forty eight isolates of the genus Thermus, from neutral and
      alkaline hot water springs on four continents, have been screened for the presence of
      restriction
      enodnuclease activity.  An isolate (SM49) from the island of Sao Miguel, in the Azores, showed
      a
      high level of restriction endonuclease activity when a cell-free extract was incubated with
      lambda
      phage DNA at 65oC.  A type II restriction endonuclease (Tsp49I) has been partially purified
      from
      this isolate and the recognition and cleavage site determined.  Tsp49I recognizes the four
      base
      sequence ACGT, which is the same as the recognition sequence of the mesophilic type II
      restriction endonuclease MaeII.  However, unlike MaeII, which cleaves DNA between the first
      and
      second base of the recognition sequence (A^CGT), Tsp49I hydrolyses the phosphodiester bond in
      both strands of the substrate after the last base of the recognition sequence 5'-ACGT^-3',
      producing four base 3'-OH overhangs (sticky ends).  The enzyme has a pH optimum of 9.0,
      requires 3 mM MgCl2 for maximum activity and retains full enzyme activity following incubation
      for 10 min at temperatures up to 80oC.  Two further examples of the same restriction
      endonuclease
      specificity as Tsp49I were detected in Thermus isolates from Iceland (TspIDSI) and New Zealand
      (TspWAM8AI).  The three MaeII neoschizomers, Tsp49I, TspIDSI and TspWAM8AI, exhibit
      similar pH optima, heat stabilities and MgCl2 requirements, but differ in their requirements
      for
      NaCl and KCl.
AU  - Welch SG
AU  - Williams RAD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1996 24: 1799-1801.

PMID- 17375195
VI  - 2
DP  - 2007
TI  - Multiple Antimicrobial Resistance in Plague: An Emerging Public Health Risk.
PG  - e309
AB  - Antimicrobial resistance in Yersinia pestis is rare, yet constitutes a significant
      international public health and biodefense threat.  In 1995, the first multidrug resistant
      isolate of Y. pestis (strain IP275) was identified, and was shown to contain a
      self-transmissible plasmid (pIP1202) that conferred resistance to many of the antimicrobials
      recommended for plague treatment and prophylaxis.  Comparative analysis of the DNA sequence of
      Y. pestis plasmid pIP1202 revealed a near identical IncA/C plasmid backbone that is shared by
      MDR plasmids isolated from Salmonella enterica serotype Newport SL254 and the fish pathogen
      Yersinia ruckeri YR71.  The high degree of sequence identity and gene synteny between the
      plasmid backbones suggests recent acquisition of these plasmids from a common ancestor.  In
      addition, the Y. pestis pIP1202-like plasmid backbone was detected in numerous MDR
      enterobacterial pathogens iosolated from retail meat samples collected between 2002 and 2005
      in the United States.  Plasmid-positive strains were isolated from beef, chicken, turkey and
      pork, and were found in samples from the following states: California, Colorado, Connecticut,
      Georgia, Maryland, Minnesota, New Mexico, New York and Oregon.  Our studies reveal that this
      common plasmid backbone is broadly disseminated among MDR zoonotic pathogens associated with
      agriculture.  This reservoir of mobile resistance determinants has the potential to
      disseminate to Y. pestis and other human and zoonotic bacterial pathogens and therefore
      represents a significant public health concern.
AU  - Welch TJ
AU  - Fricke WF
AU  - McDermott PF
AU  - White DG
AU  - Rosso ML
AU  - Rasko DA
AU  - Mammel MK
AU  - Eppinger M
AU  - Rosovitz MJ
AU  - Wagner D
AU  - Rahalison L
AU  - LeClerc JE
AU  - Hinshaw JM
AU  - Lindler LE
AU  - Cebula TA
AU  - Carniel E
AU  - Ravel J
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2007 2: e309.

PMID- 16365907
VI  - 7
DP  - 2006
TI  - Design, synthesis, and preliminary biological evaluation of a DNA methyltransferase-directed alkylating agent.
PG  - 243-245
AB  - DNA-binding and -damaging agents often derive their sequence selectivity from a finite set of
      specific contacts between the molecule of interest and select nucleotides.  Many such agents
      are of great interest due to their medicinally useful properties, although for many of these
      substances, it remains unclear that all relevant mechanisms of action have been fully
      elucidated.  In the context of DNA damage however, it seems that damage at certain sites is
      likely to have a greater impact than at others.  At the heart of DNA sequence selectivity is
      the resounding influence of a limited set of interactions between target nucleotides and the
      small molecule of interest.  We hypothesized that DNA alkylation selectivity can be drived
      from the extensive contacts between a sequence-specific DNA-modifying enzyme and its
      recognition site.  Indeed, precedence for this strategy has been noted for DNA
      methyltransferases.  However, to date, the structures of such MTase-dependent DNa-alkylating
      agents have lacked the functionalities expected to be necessary for optimum activity, by
      analogy to the natural cofactor S-adenosyl-L-methionine.
AU  - Weller RL
AU  - Rajski SR
PT  - Journal Article
TA  - Chembiochem
JT  - Chembiochem
SO  - Chembiochem 2006 7: 243-245.

PMID- 15901154
VI  - 7
DP  - 2005
TI  - DNA methyltransferase-moderated click chemistry.
PG  - 2141-2144
AB  - Biological methylation plays a vital role in regulatory mechanisms of gene transcription.
      Methylation of both promoter sequences within the
      genome, as well as protein substrates, has a profound impact upon gene
      transcription. Yet, few tools exist by which to identify sites of
      biological methylation in complex biological mixtures. We have
      generated a novel adenosine-derived N-mustard that serves as an
      efficient synthetic cofactor and allows for subsequent "click"
      chemistry involving the modified nucleic acid substrate.
AU  - Weller RL
AU  - Rajski SR
PT  - Journal Article
TA  - Org. Lett.
JT  - Org. Lett.
SO  - Org. Lett. 2005 7: 2141-2144.

PMID- 25103759
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of the Onion Center Rot Pathogen Pantoea ananatis PA4 and  Maize Brown Stalk Rot Pathogen P. ananatis BD442.
PG  - e00750-14
AB  - Pantoea ananatis is an emerging phytopathogen that infects a broad spectrum of plant hosts.
      Here, we present the genomes of two South African isolates, P.
      ananatis PA4, which causes center rot of onion, and BD442, isolated from brown
      stalk rot of maize.
AU  - Weller-Stuart T
AU  - Chan WY
AU  - Coutinho TA
AU  - Venter SN
AU  - Smits TH
AU  - Duffy B
AU  - Goszczynska T
AU  - Cowan DA
AU  - de Maayer P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00750-14.

PMID- Not carried by PubMed...
VI  - 14
DP  - 1981
TI  - Type II restriction enzymes.
PG  - 157-191
AB  - The current status of type II restriction endonuclease enzymology is quite
      unusual due to the history of this segment of molecular biology.  More than 210
      restriction endonucleases have been purified, at least partially, and their
      recognition sites identified.  However, the genetic and biochemical
      characterization of these enzymes is meager.  Indeed, they have usually been
      isolated as site-specific DNA endonucleases without genetically determining if
      they are involved in DNA restriction-modification.  Moreover, the vast majority
      of the restriction endonucleases are relatively crude preparations, and little
      or nothing is known about the properties of the enzymes.
AU  - Wells RD
AU  - Klein RD
AU  - Singleton CK
PT  - Journal Article
TA  - The Enzymes
JT  - The Enzymes
SO  - The Enzymes 1981 14: 157-191.

PMID- 6101044
VI  - 1
DP  - 1981
TI  - Cleavage of single-stranded viral DNAs by certain restriction endonucleases.
PG  - 101-111
AB  - *

         I. Introduction

        II. Characterization of the HaeIII reaction on O/X174, M13 and f1 DNAs

       III. Features of DNA structure recognized by the endonucleases

        IV. Characteristics of other restriction endonucleases

         V. Types of DNA substrates cleaved

        VI. Some properties of isoschizomers

       VII. Application of the technique for cleaving other DNAs

      VIII. Reaction of DNA methylases on single-stranded DNA

        IX. Prospects for the future

      

AU  - Wells RD
AU  - Neuendorf SK
PT  - Journal Article
TA  - Gene Amplif. Anal.
JT  - Gene Amplif. Anal.
SO  - Gene Amplif. Anal. 1981 1: 101-111.

PMID- 28302789
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of 11 Lactococcus lactis subsp. cremoris Strains.
PG  - e01739-16
AB  - The lactic acid bacterium Lactococcus lactis is widely used for the fermentation  of dairy
      products. Here, we present the draft genome sequences of 11 L. lactis
      subsp. cremoris strains isolated from different environments.
AU  - Wels M
AU  - Backus L
AU  - Boekhorst J
AU  - Dijkstra A
AU  - Beerthuyzen M
AU  - Siezen RJ
AU  - Bachmann H
AU  - van Hijum SA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01739-16.

PMID- 26607891
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Streptococcus thermophilus C106, a Dairy Isolate from an Artisanal Cheese Produced in the Countryside of Ireland.
PG  - e01377-15
AB  - The lactic acid bacterium Streptococcus thermophilus is widely used for the fermentation of
      dairy products. Here, we present the draft genome sequence of S.
      thermophilus C106 isolated from an artisanal cheese produced in the countryside
      of Ireland.
AU  - Wels M
AU  - Serrano LM
AU  - Eibrink BJ
AU  - Backus L
AU  - Bongers RS
AU  - Vriesendorp B
AU  - Siezen RJ
AU  - van Hijum SA
AU  - Meijer WC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01377-15.

PMID- 
VI  - 14
DP  - 2004
TI  - Analysis of Type II restriction endonucleases that interact with two recognition sites.
PG  - 297-317
AB  - Many students of molecular biology know for certain that the Type II restriction endonucleases
      are dimeric proteins that recognize a palindromic DNA sequence, 4-8 bp (base pairs) long, and
      cut this single sequence with exquisite specificity.  This idea is also propagated by many
      text-books and commonly-used laboratory manuals in molecular biology.  Like most
      generalizations, it is in fact wrong.  The Type II restriction enzymes encompass not only
      dimeric proteins but also monomers, tetramers and higher assemblies.  Their recognition
      sequences are not always unique palindromes but can instead be degenerate, discontinuous or
      asymmetric sequences.  The sites at which they cleave the DNA are not necessarily within the
      recognition sequence.  Many cleave the DNA at fixed positions several bp away from their
      recognition sequence.  Most excitingly, many of the Type II enzymes have to interact with two
      copies of their recognition sites before they can cleave DNA.  When these enzymes bind two
      sites in the same DNA molecule, the intervening DNA is sequestered in a loop.  DNA-looping
      interactions play central roles in many genetic processes, such as replication, recombination
      and transcription, but these processes are often difficult to study.  In contrast, the
      reactions of restriction enzymes can be monitored by a variety of simple techniques, so these
      enzymes make good tools for analyzing the nature of long-range interactions between distant
      DNA sites.  Indeed, the restriction enzymes that act at two DNA sites have become one of the
      principal paradigms for studying such interactions.
AU  - Welsh AJ
AU  - Halford SE
AU  - Scott DJ
PT  - Journal Article
TA  - Nucleic Acids Mol. Biol.
JT  - Nucleic Acids Mol. Biol.
SO  - Nucleic Acids Mol. Biol. 2004 14: 297-317.

PMID- 18812508
VI  - 105
DP  - 2008
TI  - The genome of Cyanothece 51142, a unicellular diazotrophic cyanobacterium important in the marine nitrogen cycle.
PG  - 15094-15099
AB  - Unicellular cyanobacteria have recently been recognized for their contributions to nitrogen
      fixation in marine environments, a function
      previously thought to be filled mainly by filamentous cyanobacteria such
      as Trichodesmium. To begin a systems level analysis of the physiology of
      the unicellular N(2)-fixing microbes, we have sequenced to completion the
      genome of Cyanothece sp. ATCC 51142, the first such organism. Cyanothece
      51142 performs oxygenic photosynthesis and nitrogen fixation, separating
      these two incompatible processes temporally within the same cell, while
      concomitantly accumulating metabolic products in inclusion bodies that are
      later mobilized as part of a robust diurnal cycle. The 5,460,377-bp
      Cyanothece 51142 genome has a unique arrangement of one large circular
      chromosome, four small plasmids, and one linear chromosome, the first
      report of a linear element in the genome of a photosynthetic bacterium. On
      the 429,701-bp linear chromosome is a cluster of genes for enzymes
      involved in pyruvate metabolism, suggesting an important role for the
      linear chromosome in fermentative processes. The annotation of the genome
      was significantly aided by simultaneous global proteomic studies of this
      organism. Compared with other nitrogen-fixing cyanobacteria, Cyanothece
      51142 contains the largest intact contiguous cluster of nitrogen
      fixation-related genes. We discuss the implications of such an
      organization on the regulation of nitrogen fixation. The genome sequence
      provides important information regarding the ability of Cyanothece 51142
      to accomplish metabolic compartmentalization and energy storage, as well
      as how a unicellular bacterium balances multiple, often incompatible,
      processes in a single cell.
AU  - Welsh EA
AU  - Liberton M
AU  - Stockel J
AU  - Loh T
AU  - Elvitigala T
AU  - Wang C
AU  - Wollam A
AU  - Fulton RS
AU  - Clifton SW
AU  - Jacobs JM
AU  - Aurora R
AU  - Ghosh BK
AU  - Sherman LA
AU  - Smith RD
AU  - Wilson RK
AU  - Pakrasi HB
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2008 105: 15094-15099.

PMID- 28360162
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Pseudomonas putida Strain GM4FR, an Endophytic Bacterium Isolated from Festuca rubra L.
PG  - e00086-17
AB  - Pseudomonas putida GM4FR is an endophytic bacterium isolated from aerial plant tissues of
      Festuca rubra L. Functional annotation of the draft genome (7.1 Mb)
      revealed 6,272 predicted protein-encoding genes. The genome provides insights
      into the biocontrol and plant growth-promoting potential of P. putida GM4FR.
AU  - Wemheuer F
AU  - Hollensteiner J
AU  - Poehlein A
AU  - Granzow S
AU  - Daniel R
AU  - Vidal S
AU  - Wemheuer B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00086-17.

PMID- 29437086
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of the Endophyte Bacillus mycoides Strain GM6LP Isolated from Lolium perenne.
PG  - e00011-18
AB  - Bacillus mycoides GM6LP is an endophyte isolated from plant tissues of Lolium perenne L. Here,
      we report its draft genome sequence (6.2 Mb), which contains 96
      contigs and 6,129 protein-coding genes. Knowledge about its genome will enable us
      to evaluate the potential use of GM6LP as a plant growth-promoting bacterium.
AU  - Wemheuer F
AU  - Hollensteiner J
AU  - Poehlein A
AU  - Liesegang H
AU  - Daniel R
AU  - Wemheuer B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00011-18.

PMID- 29439031
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of the Endophyte Paenibacillus sp. Strain GM2FR Isolated from Festuca rubra.
PG  - e00017-18
AB  - Here, we report the 7.4-Mb draft genome sequence of Paenibacillus sp. strain GM2FR, an
      endophytic bacterium isolated from aerial plant tissues of Festuca
      rubra L. Genome analysis revealed 6,652 coding gene sequences and several gene
      clusters involved in plant growth promotion, such as that for the siderophore
      bacillibactin.
AU  - Wemheuer F
AU  - Wemheuer B
AU  - Hollensteiner J
AU  - Daniel R
AU  - Poehlein A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00017-18.

PMID- 23644770
VI  - 97
DP  - 2013
TI  - Generation of biologically contained, readily transformable, and genetically manageable mutants of the biotechnologically important Bacillus pumilus.
PG  - 7805-7819
AB  - Bacillus pumilus mutants were generated by targeted deletion of a set of genes eventually
      facilitating genetic handling and assuring biological containment. The
      well-defined and stable mutants do not form functional endospores due to the
      deletion of yqfD, an essential sporulation gene; they are affected in DNA repair,
      as DeltauvrBA rendered them UV hypersensitive and, thus, biologically contained;
      they are deficient for the uracil phosphoribosyl-transferase (Deltaupp), allowing
      for 5-fluorouracil-based counterselection facilitating rapid allelic exchanges;
      and they are readily transformable due to the deletion of the restrictase
      encoding locus (DeltahsdR) of a type I restriction modification system.
      Vegetative growth as well as extracellular enzyme production and secretion are in
      no case affected. The combination of such gene deletions allows for development
      of B. pumilus strains suited for industrial use and further improvements.
AU  - Wemhoff S
AU  - Meinhardt F
PT  - Journal Article
TA  - Appl. Microbiol. Biotechnol.
JT  - Appl. Microbiol. Biotechnol.
SO  - Appl. Microbiol. Biotechnol. 2013 97: 7805-7819.

PMID- Not carried by PubMed...
VI  - 30
DP  - 1989
TI  - Purification and some properties of a restriction endonuclease Ccy I from Clostridium cylindrosporum.
PG  - 91-98
AB  - The restriction endonuclease CcyI has been purified to homogeneity from an
      anaerobic bacterium, Clostridium cylindrosporum, by the procedures involving
      streptomycin sulfate precipitation, ammonium sulfate fractionation and
      chromatography on phosphocellulose, heparin-Sepharose 4 B and Ultrogel AcA 34.
      This enzyme recognizes the sequence
      5'-^GATC-3'
      3' -CTAG-5^' and cleaves the phosphodiester bond at the 5' side of G as
      indicated.  Several isoschizomers of CcyI have been found previously which
      include Sau3AI and MboI.  Optimal NaCl concentration, pH and temperature for
      the enzyme to digest lambda DNA was 100 mM, 7.0-8.0 and 30-35C, respectively.
      CcyI is both acid-labile and heat-labile.
AU  - Wen TN
AU  - Tung PH
AU  - Chen CS
PT  - Journal Article
TA  - Bot. Bull. Acad. Sinica
JT  - Bot. Bull. Acad. Sinica
SO  - Bot. Bull. Acad. Sinica 1989 30: 91-98.

PMID- 8932361
VI  - 24
DP  - 1996
TI  - Binding, bending and cleavage of DNA substrates by the homing endonuclease PI-SceI.
PG  - 4123-4132
AB  - To characterize the interaction between the homing endonuclease PI-SceI and DNA, we prepared
      different DNA substrates containing the natural recognition sequence or parts thereof.
      Depending on the nature of the substrates, efficient cleavage is observed with a DNA
      containing ~30 bp of the natural recognition sequence using supercoiled plasmids, ~40-50 bp
      using linearized plasmids and >50 bp using synthetic double-stranded oligodeoxynucleotides.
      Cleavage of supercoiled plasmids occurs without accumulation of the nicked intermediate.  In
      the presence of Mn2+ DNA cleavage by PI-SceI is more efficient than with Mg2+ and already
      occurs with substrates containing a shorter part of the recognition sequence.  The
      requirements for strong binding are less stringent: a 35 bp oligodeoxynucleotide which is not
      cleaved is bound as firmly as other longer oligodeoxynucleotides.  PI-SceI binds with high
      affinity to one of its cleavage products, a finding which may explain why PI-SceI hardly shows
      enzymatic turnover in vitro.  Upon binding, two complexes are formed, which differ in the
      degree of bending (45o versus 75o).  According to a phasing analysis bending is directed into
      the major groove.  Strong binding, not, however, cleavage is also observed with the
      genetically engineered enzymatically inactive variant comprising amino acids 1-277.  Models
      for binding and cleavage of DNA by PI-SceI are discussed based on these results.
AU  - Wende W
AU  - Grindl W
AU  - Christ F
AU  - Pingoud A
AU  - Pingoud V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1996 24: 4123-4132.

PMID- Not included in PubMed...
VI  - 375
DP  - 1994
TI  - Cloning, overexpression, purification and characterization of the VDE homing endonuclease.
PG  - S110
AB  - Homing endonucleases propagate their encoding sequences (introns) from a donor
      (intron-containing) allele into an intronless recipient allele. Only the intronless allele
      contains the specific target sequence. The homing endonuclease cleaves the DNA on both
      strands, and the repair of the intronless allele results in the insertion of the sequence
      encoding the homing endonuclease. The target sites are generally asymmetric and long, ranging
      from 15 bp to 40 bp. The VDE (VMA1-derived endonuclease) cleaves intronless yeast genomic DNA
      only at a single site. Thus these enzymes are extremely rare cutters and, therefore, important
      tools for chromosomal mapping, sequencing and gene targeting. In order to study the
      DNA/protein interactions of this interesting class of enzymes, we constructed a His6-tagged
      variant of the VDE from Saccharomyces cervisiae and overexpressed it in E. coli. The affinity
      tag allows for a rapid purification to near homogeneity. The protein sequence of our VDE
      differs in 3 positions from the published sequence. Analysis of circular dichroism spectra
      suggests that the protein consists of 43% alpha-helix and 48% beta-sheet. The specific
      activity of the His6-tagged VDE variant is comparable with the native protein. Preliminary
      studies show that the minimal recognition site is larger than the published one. We are
      currently engaged in DNA binding and cleavage studies with the His6-VDE, the results of which
      will be presented.
AU  - Wende W
AU  - Pingoud A
PT  - Journal Article
TA  - Biol. Chem. Hoppe Seyler
JT  - Biol. Chem. Hoppe Seyler
SO  - Biol. Chem. Hoppe Seyler 1994 375: S110.

PMID- 11186005
VI  - 34
DP  - 2000
TI  - A mutational analysis of DNA binding and cleavage by the homing endonuclease PI-SceI.
PG  - 1054-1064
AB  - We have carried out an extensive mutational analysis of PI-SceI, the best studied intein-like
      homing endonuclease of the LAGLIDADG family,
      to find out which amino acid residues are involved in substrate binding
      and processing. Our analysis was focused on domain I, in which two
      regions were shown to be in contact with DNA, and on domain II, in
      which the amino acid residues making up catalytic centers I and II were
      identified and their role in catalysis investigated. As a result of our
      comprehensive mutational analysis a model is presented for DNA binding
      and cleavage by PI-SceI.
AU  - Wende W
AU  - Schottler S
AU  - Grindl W
AU  - Christ F
AU  - Steuer S
AU  - Noel AJ
AU  - Pingoud V
AU  - Pingoud A
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2000 34: 1054-1064.

PMID- 8922590
VI  - 377
DP  - 1996
TI  - The production and characterization of artificial heterodimers of the restriction endonuclease EcoRV.
PG  - 625-632
AB  - A novel approach to studying the inter- and intrasubunit communication required for the
      activity of homodimeric proteins is described. It was developed for the restriction
      endonuclease EcoRV, but should also be useful for other homodimeric enzymes.  Two ecorV genes
      encoding different EcoRV mutants are coexpressed in the same Escherichia coli cell leading to
      homo- and heterodimeric variants of the enzyme.  The two ecorV genes carry either a 5'
      extension coding for the glutathione-S-transferase or a His6-tag.  The EcoRV heterodimer
      produced in vivo is separated from the two EcoRV homodimers and purified to homogeneity by
      affinity chromatography.  Purified EcoRV heterodimers are stable and are not subject to
      reassortment of the subunits.  To investigate the interdependence of the two catalytic
      centers, EcoRV heterodimers consisting of one subunit with wild type sequence and one subunit
      with amino acid substitutions in the PD...(D/E)XK motif, characteristic for the active sites
      of many restriction endonucleases, were produced.  While the homodimeric EcoRV active site
      mutants are catalytically inactive, the heterodimeric EcoRV variants with one active and one
      inactive catalytic center display a twofold reduced activity toward oligodeoxynucleotide
      substrates compared to the wild type, and preferentially nick supercoiled plasmid DNA.  From
      these results we conclude that in the wild type enzyme both catalytic centers function
      independently of each other.
AU  - Wende W
AU  - Stahl F
AU  - Pingoud A
PT  - Journal Article
TA  - Biol. Chem. Hoppe Seyler
JT  - Biol. Chem. Hoppe Seyler
SO  - Biol. Chem. Hoppe Seyler 1996 377: 625-632.

PMID- 28232426
VI  - 5
DP  - 2017
TI  - High-Quality Genome Sequence of Xanthomonas axonopodis pv. glycines Strain 12609  Isolated in Taiwan.
PG  - e01695-16
AB  - The genomic sequence was determined for Xanthomonas axonopodis pv. glycines strain 12609,
      isolated in Taiwan. Based on the genome sequence, we predicted the
      encoded genes, rRNA, tRNA, a plasmid sequence, secretion systems, cyclic GMP- and
      cyclic di-GMP-mediated pathways, and the gene cluster rpfABCHGDE (regulation of
      pathogenicity factor).
AU  - Weng SF
AU  - Luo AC
AU  - Lin CJ
AU  - Tseng TT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01695-16.

PMID- 27660779
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a Klebsiella pneumoniae Strain (New Sequence Type 2357)  Carrying Tn3926.
PG  - e00986-16
AB  - We present the draft genome sequence of a Klebsiella pneumoniae carbapenemase-producing
      sequence type 2357 (ST2357) strain, NB60, which contains
      drug-resistant genes encoding resistance to beta-lactams, fluoroquinolones,
      aminoglycosides, trimethoprim-sulfamethoxazole, colistin, macrolides, and
      tetracycline. Strain NB60 was isolated from human blood, making it an important
      tool for studying K. pneumoniae pathogenesis.
AU  - Weng XB
AU  - Mi ZH
AU  - Wang CX
AU  - Zhu JM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00986-16.

PMID- 27609920
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Uropathogenic Escherichia coli Strain NB8.
PG  - e00944-16
AB  - Escherichia coli NB8 is a clinical pyelonephritis isolate. Here, we report the draft genome
      sequence of uropathogenic E. coli NB8, which contains drug
      resistance genes encoding resistance to beta-lactams, aminoglycosides,
      quinolones, macrolides, colistin, sulfonamide-trimethoprim, and tetracycline. NB8
      infects the kidney and bladder, making it an important tool for studying E. coli
      pathogenesis.
AU  - Weng XB
AU  - Mi ZH
AU  - Wang CX
AU  - Zhu JM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00944-16.

PMID- Not carried by PubMed...
VI  - 72
DP  - 1997
TI  - A novel kinetic mechanism for the cleavage of plasmid DNA by the restriction enzyme EcoRV accounts for nonspecific binding.
PG  - A98
AB  - The cleavage of pBR322 by the restriction enzyme EcoRV was assayed by quantifyingDNA bands on
      agarose gels.  The nonlinear reaction kinetics were fit by the mechanism.  Good fits were
      obtained only if nonspecific binding and slow product release were included.  A key parameter
      is the fraction of total binding that results in specific binding.  EcoRV must cycle through
      the nonspecific binding process a number of times before the specific site is located.  This
      kinetic picture will be used to measure how macromolecular crowding with inert agents affects
      the rate at which EcoRV finds its specific cleavage site.
AU  - Wenner JR
AU  - Bloomfield VA
PT  - Journal Article
TA  - J. Biophys.
JT  - J. Biophys.
SO  - J. Biophys. 1997 72: A98.

PMID- 10636081
VI  - 17
DP  - 1999
TI  - Osmotic pressure effects on EcoRV cleavage and binding.
PG  - 461-471
AB  - Investigations of DNA binding proteins frequently measure pH and salt dependence, but
      relatively few studies measure protein binding in high concentrations of small molecules often
      found in vivo. We have measured kinetics of the restriction enzyme EcoRV in concentrated
      solutions of three small cosolvents that produce osmotic pressures from 0.25 to 2.5 mol/kg (6
      to 62 atm or water activity of 0.995 to 0.956). We have correlated DNA cleavage and binding
      parameters with four solution parameters (dielectric constant, viscosity, water concentration,
      and water activity). We found that the responses of maximum velocity (Vmax) and the
      dissociation constant for nonspecific binding (Kd,ns) best correlate with water activity. The
      Michaelis constant (Km) correlates with both water activity and solution viscosity, the latter
      due to the highly dilute reactant concentrations, which make enzyme-substrate combination
      diffusion limited. Dielectric constant does not influence any of the kinetic parameters, which
      is consistent with a view that protein and DNA are preferentially hydrated, and excluded
      solutes cannot affect the local dielectric constant.
AU  - Wenner JR
AU  - Bloomfield VA
PT  - Journal Article
TA  - J. Biomol. Struct. Dyn.
JT  - J. Biomol. Struct. Dyn.
SO  - J. Biomol. Struct. Dyn. 1999 17: 461-471.

PMID- 10075809
VI  - 268
DP  - 1999
TI  - Buffer effects on EcoRV kinetics as measured by fluorescent staining and digital imaging of plasmid cleavage.
PG  - 201-212
AB  - We have developed a protocol to quantify polymer DNA cleavage which replaces the traditional
      radiolabeling and scintillation counting with fluorescent staining and digital imaging. This
      procedure offers high sensitivity, speed, and convenience, while avoiding waste and error
      associated with traditional 32P radiolabeling. This protocol was used to measure cleavage of
      pBR322 plasmid DNA by EcoRV, a type II restriction enzyme. EcoRV was found to exhibit an order
      of magnitude difference in binding in two apparently similar buffers used in previous
      investigations. To determine the origin of this effect, we measured reaction kinetics in
      buffers of different chemical nature and concentration: Tris, bis-Tris propane, Tes, Hepes,
      and cacodylate. We found that buffer concentration and identity had significant effects on
      EcoRV reaction velocity through large changes in specific binding and nonspecific binding
      (reflected in the Michaelis constant Km and the dissociation constant for nonspecific binding
      Kns). There were only small changes in Vmax. The source of the buffer effect is the protonated
      amines common to many pH buffers. These buffer cations likely act as counterions screening DNA
      phosphates, where both the protonated buffer structure and concentration affect enzyme binding
      strength. It appears that by choosing anionic buffers or zwitterionic buffers with a buried
      positive charge, buffer influence on the protein binding to DNA can be largely eliminated.
AU  - Wenner JR
AU  - Bloomfield VA
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 1999 268: 201-212.

PMID- 23882014
VI  - 4
DP  - 2013
TI  - Two Independent Pathways for Self-Recognition in Proteus mirabilis Are Linked by Type VI-Dependent Export.
PG  - e00374-13
AB  - ABSTRACT Swarming colonies of the bacterium Proteus mirabilis are capable of
      self-recognition and territorial behavior. Swarms of independent P. mirabilis
      isolates can recognize each other as foreign and establish a visible boundary
      where they meet; in contrast, genetically identical swarms merge. The ids genes,
      which encode self-identity proteins, are necessary but not sufficient for this
      territorial behavior. Here we have identified two new gene clusters: one (idr)
      encodes rhs-related products, and another (tss) encodes a putative type VI
      secretion (T6S) apparatus. The Ids and Idr proteins function independently of
      each other in extracellular transport and in territorial behaviors; however,
      these self-recognition systems are linked via this type VI secretion system. The
      T6S system is required for export of select Ids and Idr proteins. Our results
      provide a mechanistic and physiological basis for the fundamental behaviors of
      self-recognition and territoriality in a bacterial model system. IMPORTANCE Our
      results support a model in which self-recognition in P. mirabilis is achieved by
      the combined action of two independent pathways linked by a shared machinery for
      export of encoded self-recognition elements. These proteins together form a
      mechanistic network for self-recognition that can serve as a foundation for
      examining the prevalent biological phenomena of territorial behaviors and
      self-recognition in a simple, bacterial model system.
AU  - Wenren LM
AU  - Sullivan NL
AU  - Cardarelli L
AU  - Septer AN
AU  - Gibbs KA
PT  - Journal Article
TA  - MBio
JT  - MBio
SO  - MBio 2013 4: e00374-13.

PMID- 29192076
VI  - 5
DP  - 2017
TI  - Closed Genome Sequence of Chryseobacterium piperi Strain CTM(T)/ATCC BAA-1782, a  Gram-Negative Bacterium with Clostridial Neurotoxin-Like Coding Sequences.
PG  - e01296-17
AB  - Clostridial neurotoxins, including botulinum and tetanus neurotoxins, are among the deadliest
      known bacterial toxins. Until recently, the horizontal mobility of
      this toxin gene family appeared to be limited to the genus Clostridium We report
      here the closed genome sequence of Chryseobacterium piperi, a Gram-negative
      bacterium containing coding sequences with homology to clostridial neurotoxin
      family proteins.
AU  - Wentz TG
AU  - Muruvanda T
AU  - Lomonaco S
AU  - Thirunavukkarasu N
AU  - Hoffmann M
AU  - Allard MW
AU  - Hodge DR
AU  - Pillai SP
AU  - Hammack TS
AU  - Brown EW
AU  - Sharma SK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01296-17.

PMID- 29954889
VI  - 6
DP  - 2018
TI  - Closed Genome Sequence of Clostridium botulinum Strain CFSAN064329 (62A).
PG  - e00528-18
AB  - Clostridium botulinum is a strictly anaerobic, Gram-positive, spore-forming bacterium that
      produces botulinum neurotoxin, a potent and deadly proteinaceous
      exotoxin. Clostridium botulinum strain CFSAN064329 (62A) produces an A1
      serotype/subtype botulinum neurotoxin and is frequently utilized in food
      challenge and detection studies. We report here the closed genome sequence of
      Clostridium botulinum strain CFSAN064329 (62A).
AU  - Wentz TG
AU  - Yao K
AU  - Schill KM
AU  - Reddy NR
AU  - Skinner GE
AU  - Morrissey TR
AU  - Wang Y
AU  - Muruvanda T
AU  - Manickam G
AU  - Pillai CA
AU  - Thirunavukkarasu N
AU  - Hoffmann M
AU  - Hammack TS
AU  - Brown EW
AU  - Allard MW
AU  - Sharma SK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00528-18.

PMID- 9698559
VI  - 281
DP  - 1998
TI  - DNA looping by the SfiI restriction endonuclease.
PG  - 433-444
AB  - The SfiI endonuclease has to interact with two copies of its recognition sequence before it
      can cleave DNA.  To demonstrate that the reaction of SfiI on a DNA with two sites involves the
      formation of a DNA loop, and to characterize the looping interactions on supercoiled and
      linear DNA, a series of plasmids was constructed with lengths of DNA between two SfiI sites
      varying from 104 to 211 bp.  Both supercoiled and linear forms of each DNA were tested as
      substrates for SfiI.  The reactions were monitored from the rates of DNA cleavage and from the
      generation of partially cleaved products, the latter indicating loop disruption before
      cleavage of both sites.  On both supercoiled and linear DNA, the stabilities of the complexes
      spanning two SfiI sites varied in sinusoidal fashion with the distance between the sites, in
      the manner characteristic of a process governed by the helical periodicity of DNA.  In all
      cases, the looping interaction was stabilized by DNA supercoiling.  The sinusoidal variation
      from SfiI reactions on supercoiled DNA at 50 C yielded a helical repeat of about 11.5
      base-pairs per turn.
AU  - Wentzell LM
AU  - Halford SE
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1998 281: 433-444.

PMID- 7752226
VI  - 248
DP  - 1995
TI  - The SfiI restriction endonuclease makes a four-strand DNA break at two copies of its recognition sequence.
PG  - 581-595
AB  - The SfiI endonuclease cleaves DNA by a mechanism that differs from other restriction enzymes.
      While most restriction enzymes are dimeric proteins that interact with a single DNA site, SfiI
      exists in solution as a tetramer and it appears to interact with two copies of its recognition
      sequence before it can cleave DNA. Its primary reaction is then to cut both strands at both
      sites in a concerted process. The two sites can be on either the same or different DNA
      molecules, so SfiI provides a test system for long-range interactions on DNA. On either
      supercoiled or linear DNA with two sites separated by 1 kb, the bridging interaction between
      the sites is an intramolecular event: the majority of the DNA is converted directly to
      products cleaved at both sites, bypassing intermediates cut at one site. Sites on separate DNA
      molecules, or two sites on linear DNA several kb apart, engage in an intermolecular
      interaction prior to cleavage. The interaction between two DNA molecules with one site on each
      is impeded by supercoiling in both partners but is permitted when one partner is linear: it
      may require reptation of one DNA through another. SfiI reactions have marked similarities to
      some of the reactions catalysed by site-specific recombination enzymes.
AU  - Wentzell LM
AU  - Nobbs TJ
AU  - Halford SE
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1995 248: 581-595.

PMID- 7821561
VI  - 22
DP  - 1994
TI  - Purification and characterisation of the SfiI restriction endonuclease.
PG  - 302S
AB  - Type II restriction endonucleases recognise specific DNA sequences and cleave at a defined
      point within or close to that sequence. They require Mg2+ as a cofactor. In the presence of
      Mg2+ they cut their recognition sites at least a million times faster than at any other DNA
      sequence. At present over 2400 different type II restriction enzymes have been identified
      representing over 188 different specificities. Most type II enzymes cleave DNA within
      symmetrical sequences, termed palindromes. These are usually continuous sequences of 4 or 6
      base pairs, or fairly rarely 8 base pairs. Some of these enzymes cleave at unique DNA
      sequences as for EcoRV (GATATC), while others recognize degenerate sequences as for HindII
      (GTYRAC). Other enzymes, SfiI being one of them, recognize discontinuous sequences in which
      one or more unspecified bases interrupt the sequence of specified bases. A further group of
      enzymes known as type IIs, recognize asymmetric sequences and cleave at a fixed point from
      that sequence.
AU  - Wentzell LM
AU  - Oram M
AU  - Halford SE
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 1994 22: 302S.

PMID- 9485369
VI  - 37
DP  - 1998
TI  - Engineering of variants of the restriction endonuclease EcoRV that depend in their cleavage activity on the flexibility of sequences flanking the recognition site.
PG  - 2234-2242
AB  - The present work describes mutants of the restriction enzyme EcoRV that discriminate very
      efficiently between oligodeoxynucleotide substrates with an EcoRV recognition sequence in
      different sequence contexts.  All of these EcoRV variants harbor substitutions at position
      226, where in the cocrystal structure of the specific EcoRV/DNA complex an arginine contacts
      the backbone of the DNA substrate upstream of the recognition sequence, and cleave an
      oligodeoxynucleotide with an EcoRV site in a nonflexible sequence context (the recognition
      site being flanked by runs of A and T) with much higher catalytic efficiency (kcat/Km) than an
      oligodeoxynucleotide with an EcoRV site in a flexible sequence context (the recognition site
      being flanked by runs of AT), in contrast to the wild-type enzyme, that cleaves both
      substrates with the same catalytic efficiency.  Steady-state and single-turnover kinetics
      indicate that the enhanced selectivity of the mutants is due to the catalytic step of the
      reaction.  It is possible to enhance the discriminatory power of these EcoRV variants through
      the choice of appropriate reaction conditions, in particular low salt concentration and low
      reaction temperatures.  It must be emphasized that the enhanced selectivity of these EcoRV
      variants toward EcoRV sites in a flexible and nonflexible sequence context, respectively, is
      not only seen with oligodeoxynucleotides, but also with plasmid substrates.
AU  - Wenz C
AU  - Hahn M
AU  - Pingoud A
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1998 37: 2234-2242.

PMID- 8621416
VI  - 271
DP  - 1996
TI  - Probing the indirect readout of the restriction enzyme EcoRV.
PG  - 5565-5573
AB  - According to the crystal structure of the specific EcoRV.DNA complex, not only the functional
      groups of the nucleobases but also the phosphate groups of the DNA backbone are contacted by
      the enzyme.  To examine the contribution of backbone contacts to substrate recognition and
      catalysis by EcoRV, we exchanged 12 amino acids residues located close to phosphate groups by
      site-directed mutagenesis.  We purified the resulting EcoRV mutants and characterized them
      with respect to their DNA binding and cleavage activity.  According to our steady state
      kinetic analysis, there are strong interactions between three basic amino acid residues
      (Lys-119, Arg-140, and Arg-226) and the phosphate backbone that support specific binding
      presumably by inducing and maintaining the kinked conformation of the DNA observed in the
      specific EcoRV.DNA complex.  These contacts are important in both the ground state and the
      transition state.  Other, uncharged residues (Thr-93 and Ser-112), which could be involved in
      hydrogen bonds to the phosphate groups, are needed primarily to stabilize the transition
      state.  An especially important amino acid residue is Thr-37, which seems to couple
      recognition to catalysis by indirect readout.
AU  - Wenz C
AU  - Jeltsch A
AU  - Pingoud A
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1996 271: 5565-5573.

PMID- Not included in PubMed...
VI  - 376
DP  - 1995
TI  - Probing the indirect readout of the restriction enzyme EcoRV; mutational analysis of contacts to the DNA-backbone.
PG  - S168
AB  - Specific recognition of DNA does not only include interactions between the protein and the
      bases (direct readout), but also contacts to the phosphate groups of the DNA, which means that
      the protein also recognizes a specific, sequence dependent conformation of the phosphodiester
      backbone (indirect readout).  To examine contribution of phosphate contacts for the
      recognition process we have carried out a mutational analysis: The amino acid residues which
      are, according to the crystal structure of the specific EcoRV/DNA complex, in the vicinity of
      phosphate groups of the DNA and bear functional groups suited for hydrogen bonds or ionic
      interactions, were exchanged to Ala (Arg, Lys, Ser, Thr) or to Phe (Tyr) via PCR-mutagenesis.
      All mutants displayed residual activity with plasmid-DNA and oligodeoxynucleotide substrates
      and could, therefore, be analysed in terms of specific binding (with Ca2+ ions), steady state
      and single turnover kinetics, linear diffusion and selectivity towards modified
      oligodeoxynucleotides and various substrates with different sequences flanking the EcoRV-site
      GAT/ATC- (the arrow denotes the position of phosphodiester bond cleavage).  Several mutants
      displayed an altered selectivity for substrates with different flanking sequences, and/or a
      different ability to bind specifically to DNA and to diffuse along the DNA.  These results
      suggest that EcoRV makes use of phosphate contacts to locate EcoRV sites on macromolecular DNA
      by linear diffusion and to attack different EcoRV sites more or less evenly.  Furthermore, our
      results indicate that it should be possible to engineer mutants with an expanded specificity
      by taking advantage of an altered selectivity towards substrates with different flanking
      sequences.
AU  - Wenz C
AU  - Pingoud A
PT  - Journal Article
TA  - Biol. Chem. Hoppe Seyler
JT  - Biol. Chem. Hoppe Seyler
SO  - Biol. Chem. Hoppe Seyler 1995 376: S168.

PMID- Not included in PubMed...
VI  - 375
DP  - 1994
TI  - Protein engineering of the restriction endonuclease EcoRV.
PG  - S110
AB  - Specific recognition of DNA does not only include interactions between the protein and the
      bases (direct readout), but also contacts to the phosphate groups of the DNA: the protein
      recognizes a specific, sequence dependent conformation of the phosphodiester backbone
      (indirect readout). Consequently, it should be possible to alter the specificity of a
      restriction enzyme through manipulation of the phosphate contacts. Our approach to modulate
      the specificity of EcoRV is to delete functional groups of amino acids which are in direct
      contact with the phosphate groups of the DNA. Some of these EcoRV variants display a markedly
      changed specificity, e.g. the mutant Arg140 -> Ala, which shows in comparison to the wild type
      enzyme a strong preference for EcoRV sites with AT-rich flanking sequences. However, this is
      accompanied with a decrease in specific activity. It remains to be seen, whether by other
      and/or additinoal mutations the selectivity can be further increased without losing too much
      of the activity of the wild type enzyme.
AU  - Wenz C
AU  - Pingoud A
PT  - Journal Article
TA  - Biol. Chem. Hoppe Seyler
JT  - Biol. Chem. Hoppe Seyler
SO  - Biol. Chem. Hoppe Seyler 1994 375: S110.

PMID- 8086480
VI  - 1219
DP  - 1994
TI  - Protein engineering of the restriction endonuclease EcoRV: replacement of an amino acid residue in the DNA binding site leads to an altered selectivity towards unmodified and modified substrates.
PG  - 73-80
AB  - According to the crystal structure analysis of a specific EcoRV/DNA complex, the thymine
      residues of the recognition sequence -GATATC- are not in direct contact with any amino acid
      residue of the protein. However, several amino acid residues are sufficiently close that it
      seemed worthwhile trying to create variants of EcoRV with altered specificity by site-directed
      mutagenesis. Guided by molecular modelling we have replaced Asn-188 in the catalytic center of
      EcoRV by Gln to produce a mutant with a relative preference (compared to wild type EcoRV) for
      substrates in which one thymine of the recognition sequence is replaced by uracil. We have
      purified and characterized the resulting N188Q mutant. The selectivity value for the
      engineered enzyme (the ratio of the kcat/KM values for -GATAUC- versus -GATATC-) differs from
      that of the wild type enzyme by a factor of more than 200.
AU  - Wenz C
AU  - Selent U
AU  - Wende W
AU  - Jeltsch A
AU  - Wolfes H
AU  - Pingoud A
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1994 1219: 73-80.

PMID- 8233797
VI  - 21
DP  - 1993
TI  - Dam methyltransferase from Escherichia coli:  sequence of a peptide segment involved in S-adenosyl-methionine binding.
PG  - 4604-4609
AB  - DNA adenine methyltransferase (Dam methylase) has been crosslinked with its cofactor
      S-adenosyl methionine (AdoMet) by UV irradiation. About 3% of the enzyme was radioactively
      labeled after the crosslinking reaction performed either with (methyl-3H)-AdoMet or with
      (carboxy-14C)-AdoMet. Radiolabelled peptides were purified after trypsinolysis by high
      performance liquid chromatography in two steps. They could not be sequenced due to radiolysis.
      Therefore we performed the same experiment using non-radioactive AdoMet and were able to
      identify the peptide modified by the crosslinking reaction by comparison of the separation
      profiles obtained from two analytical control experiments performed with 3H-AdoMet and Dam
      methylase without crosslink, respectively. This approach was possible due to the high
      reproducibility of the chromatography profiles. In these three experiments only one
      radioactively labelled peptide was present in the tryptic digestions of the crosslinked
      enzyme. Its sequence was found to be XA-GGK, corresponding to amino acids 10 - 14 of Dam
      methylase. The non-identified amino acid in the first sequence cycle should be a tryptophan,
      which is presumably modified by the crosslinking reaction. The importance of this region near
      the N-terminus for the structure and function of the enzyme was also demonstrated by
      proteolysis and site-directed mutagenesis experiments.
AU  - Wenzel C
AU  - Guschlbauer W
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 4604-4609.

PMID- 2009958
VI  - 280
DP  - 1991
TI  - Crosslinking of Dam methyltransferase with S-adenosyl-methionine.
PG  - 147-151
AB  - Highly purified DNA-adenine methyltransferase was irradiated in the presence of different
      concentrations of radiolabelled S-adenosyl-methionine (AdoMet) with a conventional Mineralight
      UV-lamp from several minutes up to 1 h while incubating in ice. Incorporation of radioactivity
      was monitored by electrophoresis of the crosslink between S-adenosyl-methionine and Dam
      methylase on SDS-polyacrylamide gels followed by fluorography. Crosslinking reached a maximum
      in presence of 10 uM S-adenosyl-methionine; it was inhibited in the presence of substances
      which competitively inhibit methylation of DNA by DAM methylase, like sinefungin or
      S-adenosyl-homocysteine, but not in the presence of non-inhibitors like ATP or
      S-isobutyl-adenosine. The crosslink obtained was resistant against a wide range of even
      drastic conditions commonly used in protein and peptide chemistry. Proteins, which do not bind
      S-adenosyl-methionine, as well as heat inactivated Dam methylase were not photolabelled. After
      limited proteolysis the radioactive label appeared only in certain of the peptides obtrained.
      From Western blots carried out with polyclonal antibodies produced against a synthetic peptide
      corresponding in its sequence to amino acids 92-106 of the Dam methylase, the crosslinking of
      AdoMet could be tentatively mapped at a position after amino acid 106.
AU  - Wenzel C
AU  - Moulard M
AU  - Lobner-Olesen A
AU  - Guschlbauer W
PT  - Journal Article
TA  - FEBS J.
JT  - FEBS J.
SO  - FEBS J. 1991 280: 147-151.

PMID- 2536592
VI  - 56
DP  - 1989
TI  - A latent intron-encoded maturase is also an endonuclease needed for intron mobility.
PG  - 421-430
AB  - Some yeast mitochondrial introns encode proteins that promote either splicing (maturases) or
      intron propagation via gene conversion (the fit1 endonuclease). We surveyed introns in the
      cox1 gene for their ability to engage in gene conversion and found that the group I intron,
      aI4alpha, was efficiently transmitted to genes lacking it. An endonucleolytic cleavage is
      detectable in recipient DNA molecules near the site of intron insertion in vivo and in vitro.
      Conversion is dependent on an intact aI4alpha open reading frame. This intron product is a
      latent maturase, but these data show that it is also a potent endonuclease involved in
      recombination. Dual function proteins that cleave DNA and facilitate RNA splicing may have
      played a pivotal role in the propagation and tolerance of introns.
AU  - Wenzlau JM
AU  - Saldanha RJ
AU  - Butow RA
AU  - Perlman PS
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1989 56: 421-430.

PMID- 25500017
VI  - 77
DP  - 2015
TI  - Genetic analysis of maintenance of pEC156, a naturally occurring Escherichia coli plasmid that carries genes of the EcoVIII restriction-modification system.
PG  - 39-50
AB  - In the present study the role of the mechanisms responsible for maintenance of a  natural
      plasmid pEC156, that carries genes of the EcoVIII
      restriction-modification system was investigated. Analysis of this plasmid's
      genetic content revealed the presence of genetic determinants suggesting two such
      mechanisms. The first of them relies on site specific recombination utilizing the
      Xer/cer molecular machinery, while the second involves a restriction-modification
      system as an addiction module. Our analysis indicated that three factors affect
      the maintenance of pEC156: (i) a cis-acting cer site involved in resolution of
      plasmid multimers, (ii) a gene coding for EcoVIII endonuclease, and (iii) plasmid
      copy number control. The lowest stability was observed with pEC156 derivatives
      deprived of the cer site. Decreased stability of pEC156 derivatives was also
      observed in E.coli strains deficient in genes coding for proteins involved in
      plasmid multimer resolution (XerC, XerD, ArgR and PepA). A similar effect, but to
      a much lesser extent was observed for the pEC156 derivative without a functional
      gene coding for EcoVIII endonuclease. Our results indicate that the presence of
      the cer site is more important for pEC156 stable maintenance than the presence of
      a functional gene coding for EcoVIII endonuclease. In our work we also tested
      maintenance of pEC156 possessing a ColE1-type replicon in bacteria belonging to
      Enterobacteriaceae family. We have found that pEC156 was most stably maintained
      in Enterobacter cloacae and Klebsiella oxytoca representing coli-type
      enterobacteria. We have found that in all enterobacteria tested pEC156
      derivatives deficient in the cer site were significantly less stably maintained
      than cer(+) variants.
AU  - Werbowy O
AU  - Boratynski R
AU  - Dekowska A
AU  - Kaczorowski T
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 2015 77: 39-50.

PMID- 26848973
VI  - 11
DP  - 2016
TI  - Plasmid pEC156, a Naturally Occurring Escherichia coli Genetic Element That Carries Genes of the EcoVIII Restriction-Modification System, Is Mobilizable  among Enterobacteria.
PG  - e0148355
AB  - Type II restriction-modification systems are ubiquitous in prokaryotes. Some of them are
      present in naturally occurring plasmids, which may facilitate the spread
      of these systems in bacterial populations by horizontal gene transfer. However,
      little is known about the routes of their dissemination. As a model to study
      this, we have chosen an Escherichia coli natural plasmid pEC156 that carries the
      EcoVIII restriction modification system. The presence of this system as well as
      the cis-acting cer site involved in resolution of plasmid multimers determines
      the stable maintenance of pEC156 not only in Escherichia coli but also in other
      enterobacteria. We have shown that due to the presence of oriT-type F and
      oriT-type R64 loci it is possible to mobilize pEC156 by conjugative plasmids (F
      and R64, respectively). The highest mobilization frequency was observed when
      pEC156-derivatives were transferred between Escherichia coli strains,
      Enterobacter cloacae and Citrobacter freundii representing coliform bacteria. We
      found that a pEC156-derivative with a functional EcoVIII restriction-modification
      system was mobilized in enterobacteria at a frequency lower than a plasmid
      lacking this system. In addition, we found that bacteria that possess the EcoVIII
      restriction-modification system can efficiently release plasmid content to the
      environment. We have shown that E. coli cells can be naturally transformed with
      pEC156-derivatives, however, with low efficiency. The transformation protocol
      employed neither involved chemical agents (e.g. CaCl2) nor temperature shift
      which could induce plasmid DNA uptake.
AU  - Werbowy O
AU  - Kaczorowski T
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2016 11: e0148355.

PMID- 12235380
VI  - 30
DP  - 2002
TI  - High resolution crystal structure of domain I of the Saccharomyces cerevisiae homing endonuclease PI-SceI.
PG  - 3962-3971
AB  - The homing endonuclease PI-SceI from Saccharomyces cerevisiae consists of two domains. The
      protein splicing domain I catalyzes the excision of the mature endonuclease (intein) from a
      precursor protein and the religation of the flanking amino acid sequences (exteins) to a
      functional protein. Furthermore, domain I is involved in binding and recognition of the
      specific DNA substrate. Domain II of PI-SceI, the endonuclease domain, which is structurally
      homologous to other homing endonucleases from the LAGLIDADG family, harbors the
      endonucleolytic center of PI-SceI, which in vivo initiates the homing process by introducing a
      double-strand cut in the 35 bp recognition sequence. At 1.35 angstrom resolution, the crystal
      structure of PI-SceI domain I provides a detailed view of the part of the protein that is
      responsible for tight and specific DNA binding. A geometry-based docking of the 75 degree bent
      recognition sequence to the full-length protein implies a conformational change or hinge
      movement of a subdomain of domain I, the tongs part, that is predicted to reach into the major
      groove near base pairs +16 to +18.
AU  - Werner E
AU  - Wende W
AU  - Pingoud A
AU  - Heinemann U
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2002 30: 3962-3971.

PMID- Not carried by PubMed...
VI  - 29
DP  - 1968
TI  - Intracellular events following infection by bacteriophage P1:  development of host controlled modification and restriction.
PG  - 3420
AB  - Investigations of the kinetics of development of host controlled restriction
      and modification and of lysogenic immunology of P1-infected Shigella
      dysenteriae were carried out.  The relationships between the three events are
      of interest in order to elucidate their correlation to other events in the
      intracellular life cycle of P1.
AU  - Werner EAR
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1968 29: 3420.

PMID- 4890618
VI  - 3
DP  - 1969
TI  - Infection by bacteriophage P1 and development of host-controlled restriction and modification and of Lysogenic immunity.
PG  - 363-368
AB  - Shigella dysenteriae cells were infected with phage P1 or P1c1.  The outcome of
      superinfection of these cells with phage T1.Sh or T1.Sh(P1) or P1c1 was studied
      as a function of time after the initial infection.  Cells undergoing either a
      lytic responses or a lysogenic response to the primary infection develop the
      ability to specifically restrict T1.Sh between 30 and 45 min.  Between 15 and
      30 min, the cells seem to develop the ability to produce T1.Sh(P1) after
      infection by T1.Sh.  However, reasons are given for believing that this
      apparent time difference is consistent with a simultaneous development of the
      two capacities (restriction and modification) within the cell.  This
      development occurs between 30 and 45 min.  Cells infected with P1c1 and
      superinfected 45 or more min later with T1.Sh(P1) can yield both P1cl and T1.
      Cells infected with P1 become resistant to infection by P1cl within 5 to 10
      min.  It is argued that this early immunity is not necessarily different in
      mechanism from true lysogenic immunity.
AU  - Werner ER
AU  - Christensen JR
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1969 3: 363-368.

PMID- 24428220
VI  - 16
DP  - 2014
TI  - Halorhabdus tiamatea: proteogenomics and glycosidase activity measurements identify the first cultivated euryarchaeon from a deep-sea anoxic brine lake as potential polysaccharide degrader.
PG  - 2525-2537
AB  - Euryarchaea from the genus Halorhabdus have been found in hypersaline habitats
      worldwide, yet are represented by only two isolates: Halorhabdus utahensis
      AX-2(T) from the shallow Great Salt Lake of Utah, and Halorhabdus tiamatea
      SARL4B(T) from the Shaban deep-sea hypersaline anoxic lake (DHAL) in the Red Sea.
      We sequenced the H. tiamatea genome to elucidate its niche adaptations. Among
      sequenced archaea, H. tiamatea features the highest number of glycoside
      hydrolases, the majority of which were expressed in proteome experiments.
      Annotations and glycosidase activity measurements suggested an adaptation towards
      recalcitrant algal and plant-derived hemicelluloses. Glycosidase activities were
      higher at 2% than at 0% or 5% oxygen, supporting a preference for low-oxygen
      conditions. Likewise, proteomics indicated quinone-mediated electron transport at
      2% oxygen, but a notable stress response at 5% oxygen. Halorhabdus tiamatea
      furthermore encodes proteins characteristic for thermophiles and light-dependent
      enzymes (e.g. bacteriorhodopsin), suggesting that H. tiamatea evolution was
      mostly not governed by a cold, dark, anoxic deep-sea habitat. Using enrichment
      and metagenomics, we could demonstrate presence of similar glycoside
      hydrolase-rich Halorhabdus members in the Mediterranean DHAL Medee, which
      supports that Halorhabdus species can occupy a distinct niche as polysaccharide
      degraders in hypersaline environments.
AU  - Werner J et al
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2014 16: 2525-2537.

PMID- 1732740
VI  - 12
DP  - 1992
TI  - Complex recognition site for the group I intron-encoded endonuclease I-SceII.
PG  - 716-723
AB  - We have characterized features of the site recognized by a double-stranded DNA endonuclease,
      I-SceII, encoded by intron 4a of the yeast mitochondrial COX1 gene.  We determined the effects
      of 36 point mutations on the cleavage efficiency of natural and synthetic substrates
      containing the Saccharomyces capensis I-SceII site.  Most mutations of the 18-bp I-SceII
      recognition site are tolerated by the enzyme, and those mutant sites are cleaved between 42
      and 100% as well as the wild-type substrate is.  Nine mutants blocked cleavage to less than or
      equal to 33% of the wild-type, whereas only three point mutations, G-4-C, G-12-T, and G-15-C,
      block cleavage completely.  Competition experiments indicate that these three substrates are
      not cleaved, at least in part because of a marked reduction in the affinity of the enzyme for
      those mutant DNAs.  About 90% of the DNAs derived from randomization of the nucleotide
      sequence of the 4-bp staggered I-SceII cleavage site are not cleaved by the enzyme.  I-SceII
      cleaves cloned DNA derived from human chromosome 3 about once every 110 kbp.  The I-SceII
      recognition sites in four randomly chosen human DNA clones have 56 to 78% identity with the
      18-bp site in yeast mitochondrial DNA; they are cleaved at least 50% as well as the wild-type
      mitochondrial substrate despite the presence of some substitutions that individually
      compromise
AU  - Wernette C
AU  - Saldanha R
AU  - Smith D
AU  - Ming D
AU  - Perlman PS
AU  - Butow RA
PT  - Journal Article
TA  - Mol. Cell. Biol.
JT  - Mol. Cell. Biol.
SO  - Mol. Cell. Biol. 1992 12: 716-723.

PMID- 9675098
VI  - 248
DP  - 1998
TI  - Structure and activity of the mitochondrial intron-encoded endonuclease, I-SceIV.
PG  - 127-133
AB  - Starting with crude yeast mitochondria, the intron homing endonuclease, I-SceIV, was purified
      to near homogeneity.  This highly purified enzyme differs from some other well-characterized
      yeast mitochondrial intron-encoded endonucleases in terms of its structure and DNA cleavage
      specificity.  The enzyme is a heterodimer with a native molecular mass of 92 kDa.  A small
      catalytic subunit (32 kDa) is probably encoded largely or entirely by intron 5a of the
      cytochrome oxidase subunit I gene.  A larger polypeptide subunit (60 kDa) may be a nuclear
      factor necessary for intron mobility.  I-SceIV exhibits a low DNA sequence specificity as it
      cleaves a variety of DNA substrates.  Analysis of kinetic parameters shows that the purified
      enzyme has a very high affinity for DNA and exhibits low turnover which may have implications
      for subsequent steps in the intron homing process.
AU  - Wernette CM
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1998 248: 127-133.

PMID- 2172241
VI  - 265
DP  - 1990
TI  - Purification of a site-specific endonuclease, I-Sce II, encoded by intron 4 alpha of the mitochondrial coxI gene of Saccharomyces cerevisiae.
PG  - 18976-18982
AB  - We have purified to near homogeneity a site-specific, double-stranded DNA
      endonuclease (I-Sce II) encoded by intron 4 alpha (aI4 alpha) of the yeast
      mitochondrial coxI gene.  Our purification starts with a high salt extract of
      mitochondria isolated from a yeast strain that overproduces the enzyme because
      of a block in splicing of aI4 alpha.  The final step of purification is an
      affinity column consisting of covalently bound double-stranded DNA multimers of
      a synthetic sequence, 5'-TTGGTCATCCAGAAGTAT-3', which contains the I-Sce II
      cleavage/recognition site.  Typical yields of enzyme are 3-5% with a specific
      activity of approximately 500,000 units/mg, where 1 unit of activity cleaves 50
      ng of DNA substrate/h at 30C.  I-Sce II has a monomer molecular mass of 31 kDa
      as estimated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis.
      Active enzyme purifies as a 55-kDa species, which we presume to be a homodimer.
      I-Sce II monomer comigrates with an in vivo synthesized mitochondrial
      translation product made in the strain that overproduces the enzyme.  We
      conclude that I-Sce II is derived by proteolytic processing of a precursor
      polypeptide, p62, encoded by an in-frame fusion of coxI exons 1-4 with the
      downstream aI4 alpha reading frame.  I-Sce II is most active at pH 7.5 and at
      20-30C.  Endonuclease activity is sensitive to salt and is dependent upon Mg2+
      or Mn2+, but is unaffected by inclusion of ATP or GTP.  I-Sce II is the first
      intron-encoded protein to be purified and characterized from yeast
      mitochondria.
AU  - Wernette CM
AU  - Saldahna R
AU  - Perlman PS
AU  - Butow RA
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1990 265: 18976-18982.

PMID- 24285666
VI  - 1
DP  - 2013
TI  - Genome Sequence of the Extreme Obligate Alkaliphile Bacillus marmarensis Strain DSM 21297.
PG  - e00967-13
AB  - Bacillus marmarensis strain DSM 21297 is an extreme obligate alkaliphile able to  grow in
      medium up to pH 12.5. A whole-shotgun strategy and de novo assembly led
      to the generation of a 4-Mbp genome of this strain. The genome features
      alkaliphilic adaptations and pathways for n-butanol and poly(3-hydroxybutyrate)
      synthesis.
AU  - Wernick DG
AU  - Choi KY
AU  - Tat CA
AU  - Lafontaine RJG
AU  - Liao JC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00967-13.

PMID- 23209233
VI  - 194
DP  - 2012
TI  - Genome Sequence of OXA-48 Carbapenemase-Producing Klebsiella pneumoniae KpO3210.
PG  - 6981
AB  - Klebsiella pneumoniae KpO3210 is a OXA-48 carbapenemase-producing isolate obtained from a
      blood culture in the context of an outbreak in Hospital
      Universitario La Paz (Madrid, Spain) in 2010. It belongs to the major clone
      detected during the outbreak and is resistant to all beta-lactams and to several
      other antibiotics.
AU  - Wesselink JJ
AU  - Lopez-Camacho E
AU  - de la Pena S
AU  - Ramos-Ruiz R
AU  - Ruiz-Carrascoso G
AU  - Lusa-Bernal S
AU  - Fernandez-Soria VM
AU  - Gomez-Gil R
AU  - Gomez-Puertas P
AU  - Mingorance J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6981.

PMID- 14762060
VI  - 14
DP  - 2004
TI  - The Genome Sequence of Mycoplasma mycoides subsp. mycoides SC Type Strain PG1T, the Causative Agent of Contagious Bovine Pleuropneumonia (CBPP).
PG  - 221-227
AB  - Mycoplasma mycoides subsp. mycoidesSC (MmymySC)is the etiological agent of
      contagious bovine pleuropneumonia (CBPP), a highly contagious respiratory
      disease in cattle. The genome of Mmymy SC type strain PG1(T) has been
      sequenced to map all the genes and to facilitate further studies regarding
      the cell function of the organism and CBPP. The genome is characterized by
      a single circular chromosome of 1211703 bp with the lowest G content (24
      mole%)and the highest density of insertion sequences (13% of the genome
      size)of all sequenced bacterial genomes. The genome contains 985 putative
      genes, of which 72 are part of insertion sequences and encode
      transposases. Anomalies in the GC-skew pattern and the presence of large
      repetitive sequences indicate a high genomic plasticity. A variety of
      potential virulence factors was identified, including genes encoding
      putative variable surface proteins and enzymes and transport proteins
      responsible for the production of hydrogen peroxide and the capsule, which
      is believed to have toxic effects on the animal.
AU  - Westberg J
AU  - Persson A
AU  - Holmberg A
AU  - Goesmann A
AU  - Lundeberg J
AU  - Johansson KE
AU  - Pettersson B
AU  - Uhlen M
PT  - Journal Article
TA  - Genome Res.
JT  - Genome Res.
SO  - Genome Res. 2004 14: 221-227.

PMID- 27981240
VI  - 1
DP  - 2016
TI  - Genomewide Dam Methylation in Escherichia coli during Long-Term Stationary Phase.
PG  - e00130-16
AB  - DNA methylation in prokaryotes is widespread. The most common modification of the genome is
      the methylation of adenine at the N-6 position. In Escherichia coli
      K-12 and many gammaproteobacteria, this modification is catalyzed by DNA adenine
      methyltransferase (Dam) at the GATC consensus sequence and is known to modulate
      cellular processes including transcriptional regulation of gene expression,
      initiation of chromosomal replication, and DNA mismatch repair. While studies
      thus far have focused on the motifs associated with methylated adenine (meA), the
      frequency of meA across the genome, and temporal dynamics during early periods of
      incubation, here we conduct the first study on the temporal dynamics of adenine
      methylation in E. coli by Dam throughout all five phases of the bacterial life
      cycle in the laboratory. Using single-molecule real-time sequencing, we show that
      virtually all GATC sites are significantly methylated over time; nearly complete
      methylation of the chromosome was confirmed by mass spectroscopy analysis.
      However, we also detect 66 sites whose methylation patterns change significantly
      over time within a population, including three sites associated with sialic acid
      transport and catabolism, suggesting a potential role for Dam regulation of these
      genes; differential expression of this subset of genes was confirmed by
      quantitative real-time PCR. Further, we show significant growth defects of the
      dam mutant during long-term stationary phase (LTSP). Together these data suggest
      that the cell places a high premium on fully methylating the chromosome and that
      alterations in methylation patterns may have significant impact on patterns of
      transcription, maintenance of genetic fidelity, and cell survival. IMPORTANCE
      While it has been shown that methylation remains relatively constant into early
      stationary phase of E. coli, this study goes further through death phase and
      long-term stationary phase, a unique time in the bacterial life cycle due to
      nutrient limitation and strong selection for mutants with increased fitness. The
      absence of methylation at GATC sites can influence the mutation frequency within
      a population due to aberrant mismatch repair. Therefore, it is important to
      investigate the methylation status of GATC sites in an environment where cells
      may not prioritize methylation of the chromosome. This study demonstrates that
      chromosome methylation remains a priority even under conditions of nutrient
      limitation, indicating that continuous methylation at GATC sites could be under
      positive selection.
AU  - Westphal LL
AU  - Sauvey P
AU  - Champion MM
AU  - Ehrenreich IM
AU  - Finkel SE
PT  - Journal Article
TA  - mSystems
JT  - mSystems
SO  - mSystems 2016 1: e00130-16.

PMID- 25460012
VI  - 9
DP  - 2014
TI  - Restriction Endonucleases from Invasive Neisseria gonorrhoeae Cause Double-Strand Breaks and Distort Mitosis in Epithelial Cells during Infection.
PG  - e114208
AB  - The host epithelium is both a barrier against, and the target for microbial infections.
      Maintaining regulated cell growth ensures an intact protective layer towards microbial-induced
      cellular damage. Neisseria gonorrhoeae infections disrupt host cell cycle regulation machinery
      and the infection causes DNA double strand breaks that delay progression through the G2/M
      phase. We show that intracellular gonococci upregulate and release restriction endonucleases
      that enter the nucleus and damage human chromosomal DNA. Bacterial lysates containing
      restriction endonucleases were able to fragment genomic DNA as detected by PFGE. Lysates were
      also microinjected into the cytoplasm of cells in interphase and after 20 h, DNA double strand
      breaks were identified by 53BP1 staining. In addition, by using live-cell microscopy and
      NHS-ester stained live gonococci we visualized the subcellular location of the bacteria upon
      mitosis. Infected cells show dysregulation of the spindle assembly checkpoint proteins MAD1
      and MAD2, impaired and prolonged M-phase, nuclear swelling, micronuclei formation and
      chromosomal instability. These data highlight basic molecular functions of how gonococcal
      infections affect host cell cycle regulation, cause DNA double strand breaks and predispose
      cellular malignancies.
AU  - Weyler L
AU  - Engelbrecht M
AU  - Forsberg MM
AU  - Brehwens K
AU  - Vare D
AU  - Vielfort K
AU  - Wojcik A
AU  - Aro H
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2014 9: e114208.

PMID- Not carried by PubMed...
VI  - 24
DP  - 1986
TI  - A new restriction endonuclease from Xanthomonas citri.
PG  - 406-410
AB  - The isolation and characterization of a type II restriction endonuclease from
      Xanthomonas citri IFO3835 were described.  This enzyme (XciI endonuclease) is
      an isoschizomer of SalI endonuclease recognizing 5'-GTCGAC-3' and cleaving at
      the site indicated by the arrow.  Unlike SalI endonuclease, XciI endonuclease
      requires a NaCl concentration of 50 mM for its maximum activity.
AU  - Whang Y
AU  - Chae KS
AU  - Jang WH
AU  - Kim KT
AU  - Yoo OJ
PT  - Journal Article
TA  - Korean J. Microbiol.
JT  - Korean J. Microbiol.
SO  - Korean J. Microbiol. 1986 24: 406-410.

PMID- 2843097
VI  - 54
DP  - 1988
TI  - Plasmid profile analysis of a Salmonellosis outbreak and identification of a restriction and modification system.
PG  - 1591-1594
AB  - After an outbreak of salmonellosis in humans caused by Salmonella typhimurium
      bacteriophage type 135, 62 isolates from human, animal, and water sources were
      retained for further analysis.  Most of the isolates (92%) could be placed in
      one of five plasmmid pattern groups, with a majority containing a common
      60-kilobase plasmid and a smaller 3.8-kilobase-pair plasmid.  This small
      plasmid, pIMVS1, was labeled with [32P]phosphate and used as a probe in
      subsequent colony and Southern hybridization studies.  We concluded that pIMVS1
      from isolates obtained from humans was genetically different from plasmids of a
      similar size found in isolates from chickens.  Studies to characterize pIMVS1
      were undertaken to determine if it codes for known virulence factors.  It did
      not appear to be associated with the formation of attachment pili or major
      outer membrane proteins.  By using transposon mutagenesis techniques, Tn3(Apr)
      was inserted into pIMVS1, and the existence of a restriction and modification
      system was deduced.
AU  - Whiley SJ
AU  - Lanser JA
AU  - Manning PA
AU  - Murray C
AU  - Steele TW
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1988 54: 1591-1594.

PMID- 9917394
VI  - 285
DP  - 1999
TI  - A mutant of BamHI restriction endonuclease which requires N6-methyladenine for cleavage.
PG  - 1525-1536
AB  - Amino acid residues Asn116 and Ser118 of the restriction endonuclease BamHI make several
      sequence-specific and water-bridged contacts to the DNA bases.  An in vivo selection was used
      to isolate BamHI variants at position 116, 118 and 122 which maintained sequence specificity
      to GGATCC sites.  Here, the variants N116H, N116H/S118G and S118G were purified and
      characterized.  The variants N116H and N116H/S118G were found to have lost their ability to
      cleave unmethylated GGATCC sequences by more than two orders of magnitude, while maintaining
      nearly wild-type levels of activity on the N6-methyladenine-containing sequence, GGmATCC.  In
      contrast, wild-type BamHI and variant S118G have only a three- to fourfold lower activity on
      unmethylated GGATCC sequences compared with GGmATCC sequences.  The N116 to H116 mutation has
      effectively altered the specificity of BamHI from an endonuclease which recognizes and cleaves
      GGATCC and GGmATC, to an endonuclease which only cleaves GGmATCC.  The N116H change of
      specificity is due to the lowered binding affinity for the unmethylated sequence because of
      the loss of two asparagine-DNA hydrogen bonds and the introduction of a favorable van der
      Waals contact between the imidazole group of histidine and the N6-methyl group of adenine.
AU  - Whitaker RD
AU  - Dorner LF
AU  - Schildkraut I
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1999 285: 1525-1536.

PMID- 18723649
VI  - 74
DP  - 2008
TI  - Extensive genome rearrangements and multiple horizontal gene transfers in a population of pyrococcus isolates from Vulcano Island, Italy.
PG  - 6447-6451
AB  - The extent of chromosome rearrangements in Pyrococcus isolates from marine
      hydrothermal vents in Vulcano Island, Italy, was evaluated by
      high-throughput genomic methods. The results illustrate the dynamic nature
      of the genomes of the genus Pyrococcus and raise the possibility of a
      connection between rapidly changing environmental conditions and adaptive
      genomic properties.
AU  - White JR
AU  - Escobar-Paramo P
AU  - Mongodin EF
AU  - Nelson KE
AU  - DiRuggiero J
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2008 74: 6447-6451.

PMID- 10567266
VI  - 286
DP  - 1999
TI  - Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1.
PG  - 1571-1577
AB  - The complete genome sequence of the radiation-resistant bacterium Deinococcus radiodurans R1
      is composed of two chromosomes (2,648,638 and 412,348 base pairs), a megaplasmid (177,466 base
      pairs), and a small plasmid (45,704 base pairs), yielding a total genome of 3,284,156 base
      pairs.  Multiple components distributed on the chromosomes and megaplasmid that contribute to
      the ability of D. radiodurans to survive under conditions of starvation, oxidative stress, and
      high amounts of DNA damage were identified.  Deinococcus radiodurans represents an organism in
      which all systems for DNA repair, DNA damage export, desiccation and starvation recovery, and
      genetic redundancy are present in one cell.
AU  - White O et al
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1999 286: 1571-1577.

PMID- 23929485
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Exiguobacterium pavilionensis Strain RW-2, with Wide Thermal, Salinity, and pH Tolerance, Isolated from Modern Freshwater  Microbialites.
PG  - e00597-13
AB  - We report the draft genome sequence of Exiguobacterium pavilionensis strain RW-2, isolated
      from a cold thrombolytic microbialite. The isolate grows at temperatures
      from 4 to 50 degrees C, at pH levels from 5 to 11, and in media without added
      NaCl or KCl or with 7% added NaCl.
AU  - White RAIII
AU  - Grassa CJ
AU  - Suttle CA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00597-13.

PMID- 23814108
VI  - 1
DP  - 2013
TI  - First draft genome sequence from a member of the genus agrococcus, isolated from  modern microbialites.
PG  - e00391-13
AB  - We report the first draft genome sequence from a member of the genus Agrococcus,  isolated
      from cold thrombolytic microbialites within Pavilion Lake, British
      Columbia, Canada. The draft genome assembly for Agrococcus pavilionensis strain
      RW-1 has a size of 2,878,403 bp with a G+C content of 72.56%.
AU  - White RAIII
AU  - Grassa CJ
AU  - Suttle CA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00391-13.

PMID- 23929486
VI  - 1
DP  - 2013
TI  - The Draft Genome Sequence of Sphingomonas paucimobilis Strain HER1398 (Proteobacteria), Host to the Giant PAU Phage, Indicates That It Is a Member of  the Genus Sphingobacterium (Bacteroidetes).
PG  - e00598-13
AB  - The draft genome sequence of Sphingomonas paucimobilis host index number (HER) 1398, host of
      the giant PAU phage isolated from silk moths (Bombyx mori),
      indicates that this isolate belongs within the genus Sphingobacterium. We suggest
      that Sphingomonas paucimobilis strain HER1398 be reclassified as Sphingobacterium
      paucimobilis strain HER1398.
AU  - White RAIII
AU  - Suttle CA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00598-13.

PMID- 2476221
VI  - 15
DP  - 1989
TI  - Measurement of DNA methylase activity by tritium release from DNA cytosine.
PG  - 145-147
AB  - The advantages of assaying DNA methylase by measuring the transfer to water of
      tritium from the 5-position of DNA cytosine, rather than the transfer to DNA of
      labeled methyl groups are discussed.
AU  - Whitehead EP
AU  - Taddeo B
AU  - Stampeggioni E
AU  - Palitti F
AU  - Carotti D
PT  - Journal Article
TA  - Cell Biophys.
JT  - Cell Biophys.
SO  - Cell Biophys. 1989 15: 145-147.

PMID- 2986568
VI  - 141
DP  - 1985
TI  - A simple and rapid method for screening bacteria for type II restriction endonucleases:  enzymes in Aphanothece halophytica.
PG  - 70-74
AB  - A method is described which allows a large number of bacterial strains to be
      rapidly and easily screened for the presence of site-specific endonucleases.
      The method involves selective permeabilization of the bacterial cell and
      analysis of the exuded material.  Type II restriction endonucleases from
      cyanobacteria and Gram-negative eubacteria have been detected and new enzymes
      have been found.  The method should be widely applicable and easy to modify for
      use in genera other than those tested.  Three-site-specific endonuclease
      activities, detected by this method in Apanothece halophytica PCC 7412, were
      purified and their recognition and cleavage specificies were determined AhaI
      and AhaII recognise and cleave the same DNA sequences as CauII and AcyI
      respectively; the specificity of AhaIII (TTT^AAA) has been reported previously
      (Whitehead and Brown, 1982, FEBS Lett. 143: 296-300).
AU  - Whitehead PR
AU  - Brown NL
PT  - Journal Article
TA  - Arch. Microbiol.
JT  - Arch. Microbiol.
SO  - Arch. Microbiol. 1985 141: 70-74.

PMID- 6301886
VI  - 155
DP  - 1983
TI  - EaeI: a restriction endonuclease from Enterobacter aerogenes.
PG  - 97-101
AB  - We describe the isolation and characterization of a type II restriction endonuclease from
      Enterobacter aerogenes.  This recognises and cleaves the family of related sequences:
      5'-Py^G-G-C-C--Pu-3' to generate DNA fragments with 5'-tetranucleotide extensions.  EaeI
      may be useful in molecular cloning experiments, especially in conjunction with other enzymes
      which generate the same terminal extensions.  Potential problems in the methods used to
      determine the cleavage specificity are discussed.
AU  - Whitehead PR
AU  - Brown NL
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1983 155: 97-101.

PMID- 2985742
VI  - 131
DP  - 1985
TI  - Three restriction endonucleases from Anabaena flos-aquae.
PG  - 951-958
AB  - Three site-specific endonucleases, AflI, AflII and AflIII, have been partially
      purified from the cyanobacterium Anabaena flos-aquae CCAP 1403/13f.  Their
      recognition and cleavage specificities have been determined to be:AflI
      5'-G-^G-(A/T)-C-C-3'AflII 5'-C-^T-T-A-A-G-3'AflIII 5'-A-^C-Pu-Py-G-T-3'AflII
      and AflIII are new specificities and may be useful in molecular cloning, as
      well as in the anlaysis of DNA.  The distribution of type II restriction
      endonucleases in the cyanobacteria is briefly discussed.
AU  - Whitehead PR
AU  - Brown NL
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1985 131: 951-958.

PMID- 6288466
VI  - 143
DP  - 1982
TI  - AhaIII: A restriction endonuclease with a recognition sequence containing only A:T basepairs.
PG  - 296-300
AB  - None
AU  - Whitehead PR
AU  - Brown NL
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1982 143: 296-300.

PMID- 7215691
VI  - 9
DP  - 1981
TI  - The characterization of novel restriction endonuclease specificities.
PG  - 272P
AB  - A very rapid method has been developed for DNA sequence analysis of the
      recognition and cleavage sites of type II restriction endonucleases.  DNA
      fragments containing the cleavage site for a novel restriction endonuclease are
      cloned in vectors derived from bacteriophage M13, for sequence analysis by the
      chain-termination method.  The phosphodiester bonds in both DNA strands cleaved
      by the restriction enzyme are identified in parallel with the sequence
      determination.  The recognition and cleavage specificity of the enzyme AspAI,
      has been determined to be the symmetrical sequence 5'-G-^G-T-N-A-C-C-3', and
      the recognition and cleavage specificities of other enzymes will be presented.
AU  - Whitehead PR
AU  - Brown NL
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 1981 9: 272P.

PMID- 3020503
VI  - 14
DP  - 1986
TI  - Restriction endonucleases from Herpetosiphon giganteus:  an example of the evolution of DNA recognition specificity.
PG  - 7031-7045
AB  - We describe the partial purification and characterisation of five Type II
      restriction endonucleases from two strains of Herpetosiphon giganteus.  One of
      the activities, HgiJII, was the first enzyme found that cleaves DNA at the
      family of related sequences 5'-G-R-G-C-Y/C-3'.  This enzyme may be related to
      the enzyme HgiAI from a different strain of the same species, and which cleaves
      at the sites 5'-G-W-G-C-W/C-3'.  We have shown that DNAs from the strains
      producing HgiAI and HgiJII are resistant to both of these restriction
      endonucleases.   The remaining four enzymes described here share recognition
      and cleavage specificities with other restriction endonucleases.  The evolution
      of Type II restriction-modification systems and their role in vivo are
      discussed.
AU  - Whitehead PR
AU  - Jacobs D
AU  - Brown NL
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1986 14: 7031-7045.

PMID- 24581117
VI  - 15
DP  - 2014
TI  - A genomic perspective on a new bacterial genus and species from the Alcaligenaceae family, Basilea psittacipulmonis.
PG  - 169
AB  - BACKGROUND: A novel Gram-negative, non-haemolytic, non-motile, rod-shaped
      bacterium was discovered in the lungs of a dead parakeet (Melopsittacus
      undulatus) that was kept in captivity in a petshop in Basel, Switzerland. The
      organism is described with a chemotaxonomic profile and the nearly complete
      genome sequence obtained through the assembly of short sequence reads. RESULTS:
      Genome sequence analysis and characterization of respiratory quinones, fatty
      acids, polar lipids, and biochemical phenotype is presented here. Comparison of
      gene sequences revealed that the most similar species is Pelistega europaea, with
      BLAST identities of only 93% to the 16S rDNA gene, 76% identity to the rpoB gene,
      and a similar GC content (~43%) as the organism isolated from the parakeet, DSM
      24701 (40%). The closest full genome sequences are those of Bordetella spp. and
      Taylorella spp. High-throughput sequencing reads from the Illumina-Solexa
      platform were assembled with the Edena de novo assembler to form 195 contigs
      comprising the ~2 Mb genome. Genome annotation with RAST, construction of
      phylogenetic trees with the 16S rDNA (rrs) gene sequence and the rpoB gene, and
      phylogenetic placement using other highly conserved marker genes with ML Tree all
      suggest that the bacterial species belongs to the Alcaligenaceae family. Analysis
      of samples from cages with healthy parakeets suggested that the newly discovered
      bacterial species is not widespread in parakeet living quarters. CONCLUSIONS:
      Classification of this organism in the current taxonomy system requires the
      formation of a new genus and species. We designate the new genus Basilea and the
      new species psittacipulmonis. The type strain of Basilea psittacipulmonis is DSM
      24701 (= CIP 110308 T, 16S rDNA gene sequence Genbank accession number JX412111
      and GI 406042063).
AU  - Whiteson KL
AU  - Hernandez D
AU  - Lazarevic V
AU  - Gaia N
AU  - Farinelli L
AU  - Francois P
AU  - Pilo P
AU  - Frey J
AU  - Schrenzel J
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2014 15: 169.

PMID- 6090709
VI  - 52
DP  - 1984
TI  - Selective protection of 5'..GGCC..3' and 5'...GCNGC...3' sequences by the hypermodified oxopyrimidine in Bacillus subtilis bacteriophage SP10 DNA.
PG  - 47-54
AB  - The DNA of Bacillus subtilis bacteriophage SP10 is partially resistant to
      cleavage and methylation in vitro by restriction enzyme R.BsuRI and its cognate
      methylase even though >20 copies of the target sequence, 5'...GGCC...3', are
      present on the phage genome.  YThy, a hypermodified oxopyrimidine that replaces
      a fraction of the thymine residues in SP10 DNA, was responsible for this
      protection, since YThy-free DNA was no longer resistant.  Sites that were
      normally resistant could nevertheless be cleaved or methylated in vitro if the
      salt concentration was reduced or dimethyl sulfoxide was added to the reaction
      buffer.  Analysis of the termini produced by cleavage suggested that resistant
      sites occurred in the sequence 5'...GGCC-YThy ...3', whereas sensitive sites,
      of which there were only two per genome, occurred in the sequence
      5'...GGCCG...3'.  These in vitro results provide an explanation for the in vivo
      resistance of SP10 to restriction-modification by B. subtilis R.  They also
      suggest ways in which the presence of the atypical base XThy in regions that
      flank the target might upset critical DNA-enzyme interactions necessary to
      locate and recognize the specific site of cleavage or methylation.  YThy also
      strongly protected 5'...GCNGC...3' (R.Fnu4HI) sequences on SP10 DNA, but the
      biological relevance of this protection is unclear.
AU  - Wiatr CL
AU  - Witmer HJ
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1984 52: 47-54.

PMID- 21329740
VI  - 155
DP  - 2011
TI  - Complete Genome Sequencing of Agrobacterium sp H13-3, the former Rhizobium lupini H13-3, Reveals a Tripartite Genome Consisting of a Circular and a Linear Chromosome and an Accessory Plasmid but Lacking a Tumor-Inducing Ti-Plasmid.
PG  - 50-62
AB  - Agrobacterium sp. H13-3, formerly known as Rhizobium lupini H13-3, is a soil bacterium that
      was isolated from the rhizosphere of Lupinus luteus. The isolate has been established as a
      model system for studying novel features of flagellum structure, motility and chemotaxis
      within the family Rhizobiaceae. The complete genome sequence of Agrobacterium sp. H13-3 has
      been established and the genome structure and phylogenetic assignment of the organism was
      analysed. For de novo sequencing of the Agrobacterium sp. H13-3 genome, a combined strategy
      comprising 454-pyrosequencing on the Genome Sequencer FLX platform and PCR-based amplicon
      sequencing for gap closure was applied. The finished genome consists of three replicons and
      comprises 5,573,770 bases. Based on phylogenetic analyses, the isolate could be assigned to
      the genus Agrobacterium biovar I and represents a genomic species G1 strain within this
      biovariety. The highly conserved circular chromosome (2.82Mb) of Agrobacterium sp. H13-3
      mainly encodes housekeeping functions characteristic for an aerobic, heterotrophic bacterium.
      Agrobacterium sp. H13-3 is a motile bacterium driven by the rotation of several complex
      flagella. Its behaviour towards external stimuli is regulated by a large chemotaxis regulon
      and a total of 17 chemoreceptors. Comparable to the genome of Agrobacterium tumefaciens C58,
      Agrobacterium sp. H13-3 possesses a linear chromosome (2.15Mb) that is related to its
      reference replicon and features chromosomal and plasmid-like properties. The accessory plasmid
      pAspH13-3a (0.6Mb) is only distantly related to the plasmid pAtC58 of A. tumefaciens C58 and
      shows a mosaic structure. A tumor-inducing Ti-plasmid is missing in the sequenced strain H13-3
      indicating that it is a non-virulent isolate.
AU  - Wibberg D
AU  - Blom J
AU  - Jaenicke S
AU  - Kollin F
AU  - Rupp O
AU  - Scharf B
AU  - Schneiker-Bekel S
AU  - Sczcepanowski R
AU  - Goesmann A
AU  - Setubal JC
AU  - Schmitt R
AU  - Puhler A
AU  - Schluter A
PT  - Journal Article
TA  - J. Biotechnol.
JT  - J. Biotechnol.
SO  - J. Biotechnol. 2011 155: 50-62.

PMID- 27060556
VI  - 232
DP  - 2016
TI  - Finished genome sequence and methylome of the cyanide-degrading Pseudomonas pseudoalcaligenes strain CECT5344 as resolved by single-molecule real-time  sequencing.
PG  - 61-68
AB  - Pseudomonas pseudoalcaligenes CECT5344 tolerates cyanide and is also able to utilize cyanide
      and cyano-derivatives as a nitrogen source under alkaline
      conditions. The strain is considered as candidate for bioremediation of habitats
      contaminated with cyanide-containing liquid wastes. Information on the genome
      sequence of the strain CECT5344 became available previously. The P.
      pseudoalcaligenes CECT5344 genome was now resequenced by applying the single
      molecule, real-time (SMRT((R))) sequencing technique developed by Pacific
      Biosciences. The complete and finished genome sequence of the strain consists of
      a 4,696,984 bp chromosome featuring a GC-content of 62.34%. Comparative analyses
      between the new and previous versions of the P. pseudoalcaligenes CECT5344 genome
      sequence revealed additional regions in the new sequence that were missed in the
      older version. These additional regions mostly represent mobile genetic elements.
      Moreover, five additional genes predicted to play a role in sulfoxide reduction
      are present in the newly established genome sequence. The P. pseudoalcaligenes
      CECT5344 genome sequence is highly related to the genome sequences of different
      Pseudomonas mendocina strains. Approximately, 70% of all genes are shared between
      P. pseudoalcaligenes and P. mendocina. In contrast to P. mendocina, putative
      pathogenicity genes were not identified in the P. pseudoalcaligenes CECT5344
      genome. P. pseudoalcaligenes CECT5344 possesses unique genes for nitrilases and
      mercury resistance proteins that are of importance for survival in habitats
      contaminated with cyano- and mercury compounds. As an additional feature of the
      SMRT sequencing technology, the methylome of P. pseudoalcaligenes was
      established. Six sequence motifs featuring methylated adenine residues (m6A) were
      identified in the genome. The genome encodes several methyltransferases, some of
      which may be considered for methylation of the m6A motifs identified. The
      complete genome sequence of the strain CECT5344 now provides the basis for
      exploitation of genetic features for biotechnological purposes.
AU  - Wibberg D
AU  - Bremges A
AU  - Dammann-Kalinowski T
AU  - Maus I
AU  - Igeno MI
AU  - Vogelsang R
AU  - Konig C
AU  - Luque-Almagro VM
AU  - Roldan MD
AU  - Sczyrba A
AU  - Moreno-Vivian C
AU  - Blasco R
AU  - Puhler A
AU  - Schluter A
PT  - Journal Article
TA  - J. Biotechnol.
JT  - J. Biotechnol.
SO  - J. Biotechnol. 2016 232: 61-68.

PMID- 24625869
VI  - 2
DP  - 2014
TI  - Genome Sequence of the Acute Urethral Catheter Isolate Pseudomonas aeruginosa MH38.
PG  - e00161-14
AB  - Pseudomonas aeruginosa is a major nosocomial bacterial pathogen causing complicated
      catheter-associated urinary tract infections (CAUTIs). Here, we
      present the 6.9-Mb draft genome sequence of P. aeruginosa MH38 isolated from an
      acute nosocomial CAUTI. It exhibits resistance to several antibiotics but
      revealed low-level production of virulence factors.
AU  - Wibberg D
AU  - Tielen P
AU  - Blom J
AU  - Rosin N
AU  - Schobert M
AU  - Tupker R
AU  - Schatschneider S
AU  - Spilker D
AU  - Albersmeier A
AU  - Goesmann A
AU  - Vorholter FJ
AU  - Puhler A
AU  - Jahn D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00161-14.

PMID- 26184943
VI  - 3
DP  - 2015
TI  - Genome Sequence of the Urethral Isolate Pseudomonas aeruginosa RN21.
PG  - e00788-15
AB  - Pseudomonas aeruginosa is known to cause complicated urinary tract infections (UTI). The
      improved 7.0-Mb draft genome sequence of P. aeruginosa RN21, isolated
      from a patient with an acute UTI, was determined. It carries three (pro)phage
      genomes, genes for two restriction/modification systems, and a clustered
      regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas)
      system.
AU  - Wibberg D
AU  - Tielen P
AU  - Narten M
AU  - Schobert M
AU  - Blom J
AU  - Schatschneider S
AU  - Meyer AK
AU  - Neubauer R
AU  - Albersmeier A
AU  - Albaum S
AU  - Jahn M
AU  - Goesmann A
AU  - Vorholter FJ
AU  - Puhler A
AU  - Jahn D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00788-15.

PMID- 27103721
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the Vaccination Strain Mycobacterium bovis BCG S4-Jena.
PG  - e00296-16
AB  - Here, we present the draft genome sequence of ITALIC! Mycobacterium bovisBCG S4-Jena, a
      tuberculosis vaccine strain. The genome of S4-Jena is represented by
      48 scaffolds, consisting of 132 scaffolded contigs and amounting to a size of
      about 4.2 Mb. New genes potentially encoding a phage fragment were identified in
      the genome.
AU  - Wibberg D
AU  - Winkler A
AU  - Straube E
AU  - Karrasch M
AU  - Keller PM
AU  - Kalinowski J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00296-16.

PMID- 23618712
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Geobacillus sp. Strain GHH01, a Thermophilic Lipase-Secreting Bacterium.
PG  - e00092-13
AB  - Geobacillus sp. strain GHH01 was isolated during a screening for producers of extracellular
      thermostable lipases. The completely sequenced and annotated 3.6-Mb
      genome encodes 3,478 proteins. The strain is genetically equipped to utilize a
      broad range of different substrates and might develop natural competence.
AU  - Wiegand S
AU  - Rabausch U
AU  - Chow J
AU  - Daniel R
AU  - Streit WR
AU  - Liesegang H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00092-13.

PMID- 25237017
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Flavobacterium psychrophilum Strain CSF259-93, Used To Select Rainbow Trout for Increased Genetic Resistance against Bacterial Cold  Water Disease.
PG  - e00889-14
AB  - The genome sequence of Flavobacterium psychrophilum strain CSF259-93, isolated from rainbow
      trout (Oncorhynchus mykiss), consists of a single circular genome of
      2,900,735 bp and 2,701 predicted open reading frames (ORFs). Strain CSF259-93 has
      been used to select a line of rainbow trout with increased genetic resistance
      against bacterial cold water disease.
AU  - Wiens GD
AU  - LaPatra SE
AU  - Welch TJ
AU  - Rexroad CIII
AU  - Call DR
AU  - Cain KD
AU  - LaFrentz BR
AU  - Vaisvil B
AU  - Schmitt DP
AU  - Kapatral V
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00889-14.

PMID- 27587827
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of a Rhodococcus Species Isolated from the Winter Skate  Leucoraja ocellata.
PG  - e00918-16
AB  - We report here a genome sequence for Rhodococcus sp. isolate UM008 isolated from  the
      renal/interrenal tissue of the winter skate Leucoraja ocellata Genome
      sequence analysis suggests that Rhodococcus bacteria may act in a novel
      mutualistic relationship with their elasmobranch host, serving as biocatalysts in
      the steroidogenic pathway of 1alpha-hydroxycorticosterone.
AU  - Wiens J
AU  - Ho R
AU  - Fernando D
AU  - Kumar A
AU  - Loewen PC
AU  - Brassinga AK
AU  - Anderson WG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00918-16.

PMID- 21223599
VI  - 11
DP  - 2011
TI  - Salmonella Typhimurium ST213 is associated with two types of IncA/C plasmids carrying multiple resistance determinants.
PG  - 9
AB  - BACKGROUND: Salmonella Typhimurium ST213 was first detected in the Mexican
      Typhimurium population in 2001. It is associated with a multi-drug
      resistance phenotype and a plasmid-borne blaCMY-2 gene conferring
      resistance to extended-spectrum cephalosporins. The objective of the
      current study was to examine the association between the ST213 genotype
      and blaCMY-2 plasmids. RESULTS: The blaCMY-2 gene was carried by an IncA/C
      plasmid. ST213 strains lacking the blaCMY-2 gene carried a different
      IncA/C plasmid. PCR analysis of seven DNA regions distributed throughout
      the plasmids showed that these IncA/C plasmids were related, but the
      presence and absence of DNA stretches produced two divergent types I and
      II. A class 1 integron (dfrA12, orfF and aadA2) was detected in most of
      the type I plasmids. Type I contained all the plasmids carrying the
      blaCMY-2 gene and a subset of plasmids lacking blaCMY-2. Type II included
      all of the remaining blaCMY-2-negative plasmids. A sequence comparison of
      the seven DNA regions showed that both types were closely related to
      IncA/C plasmids found in Escherichia, Salmonella, Yersinia,
      Photobacterium, Vibrio and Aeromonas. Analysis of our Typhimurium strains
      showed that the region containing the blaCMY-2 gene is inserted between
      traA and traC as a single copy, like in the E. coli plasmid pAR060302. The
      floR allele was identical to that of Newport pSN254, suggesting a mosaic
      pattern of ancestry with plasmids from other Salmonella serovars and E.
      coli. Only one of the tested strains was able to conjugate the IncA/C
      plasmid at very low frequencies (10-7 to 10-9). The lack of conjugation
      ability of our IncA/C plasmids agrees with the clonal dissemination trend
      suggested by the chromosomal backgrounds and plasmid pattern associations.
      CONCLUSIONS: The ecological success of the newly emerging Typhimurium
      ST213 genotype in Mexico may be related to the carriage of IncA/C
      plasmids. We conclude that types I and II of IncA/C plasmids originated
      from a common ancestor and that the insertion and deletion of DNA
      stretches have shaped their evolutionary histories.
AU  - Wiesner M
AU  - Calva E
AU  - Fernandez-Mora M
AU  - Cevallos MA
AU  - Campos F
AU  - Zaidi MB
AU  - Silva C
PT  - Journal Article
TA  - BMC Microbiol.
JT  - BMC Microbiol.
SO  - BMC Microbiol. 2011 11: 9.

PMID- 6263490
VI  - 24
DP  - 1981
TI  - The somatic replication of DNA methylation.
PG  - 33-40
AB  - We have tested the hypothesis that DNA methylation patterns are replicated in the somatic
      cells of vertebrates. Using M.HpaII, the modification enzyme from Haemophilus parainfluenzae
      which methylates the internal cytosine residues in the sequence 5'CCGG/3'GGCC, we methylated
      bacteriophage PhiX174 RF DNA and the cloned chicken thymidine kinase (tk) gene in vitro and
      then introduced these DNAs and unmethylated controls into tk- cultured mouse cells by
      DNA-mediated transformation. Twenty-five cell generations later, the state of methylation of
      transferred DNA was examined by restriction endonuclease analysis and blot hybridization. We
      conclude that methylation at HpaII sites is replicated by these cultured cells but not with
      100% fidelity. We have also noted that methylation of the cloned chicken tk gene decreases its
      apparent transformation efficiency relative to unmethylated molecules.
AU  - Wigler M
AU  - Levy D
AU  - Perucho M
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1981 24: 33-40.

PMID- 25164788
VI  - 14
DP  - 2014
TI  - Complete nucleotide sequence of pRS218, a large virulence plasmid, that augments pathogenic potential of meningitis-associated Escherichia coli strain RS218.
PG  - 203
AB  - BACKGROUND: Escherichia coli is the most predominant Gram-negative bacterial
      pathogen associated with neonatal meningitis. Previous studies indicated that the
      prototypic neonatal meningitis E. coli (NMEC) strain RS218 (O18:K1:H7) harbors
      one large plasmid. Objectives of the present study were to analyze the complete
      nucleotide sequence of this large plasmid (pRS218) and its contribution to NMEC
      pathogenesis using in vitro and in vivo models of neonatal meningitis. RESULTS:
      The plasmid is 114,231 bp in size, belongs to the incompatibility group FIB/IIA
      (IncFIB/IIA), and contains a genetic load region that encodes several virulence
      and fitness traits such as enterotoxicity, iron acquisition and copper tolerance.
      The nucleotide sequence of pRS218 showed a 41- 46% similarity to other neonatal
      meningitis-causing E. coli (NMEC) plasmids and remarkable nucleotide sequence
      similarity (up to 100%) to large virulence plasmids of E. coli associated with
      acute cystitis. Some genes located on pRS218 were overly represented by NMEC
      strains compared to fecal E. coli isolated from healthy individuals. The
      plasmid-cured strain was significantly attenuated relative to the RS218 wild-type
      strain as determined in vitro by invasion potential to human cerebral
      microvascular endothelial cells and in vivo by mortalities, histopathological
      lesions in the brain tissue, and bacterial recovery from the cerebrospinal fluid
      of infected rat pups. CONCLUSIONS: The pRS218 is an IncFIB/IIA plasmid which
      shares a remarkable nucleotide sequence similarity to large plasmids of E. coli
      associated with cystitis. Both in vitro and in vivo experiments indicated that
      pRS218 plays an important role in NMEC pathogenesis.
AU  - Wijetunge DS
AU  - Karunathilake KH
AU  - Chaudhari A
AU  - Katani R
AU  - Dudley EG
AU  - Kapur V
AU  - DebRoy C
AU  - Kariyawasam S
PT  - Journal Article
TA  - BMC Microbiol.
JT  - BMC Microbiol.
SO  - BMC Microbiol. 2014 14: 203.

PMID- 26205862
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Escherichia coli Strain RS218 (O18:H7:K1), Associated with Neonatal Meningitis.
PG  - e00804-15
AB  - Escherichia coli RS218 is the prototypic strain of neonatal meningitis-causing E. coli (NMEC)
      and has been used in many studies related to NMEC pathogenesis. In
      the present study, the genome of E. coli RS218 was sequenced together with its
      plasmid, pRS218. Here, we report the fully closed genome sequence of E. coli
      RS218.
AU  - Wijetunge DS
AU  - Katani R
AU  - Kapur V
AU  - Kariyawasam S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00804-15.

PMID- 6096823
VI  - 12
DP  - 1984
TI  - Optimizing selection of restriction enzymes in the search for DNA variants.
PG  - 9209-9226
AB  - A model is developed for predicting the relative efficiencies of different
      enzymes for detecting DNA variants when such variants are the result of single
      base-pair changes.  71 enzymes are analyzed for this ability in human DNA.
      Their relative ranked efficiencies are influenced by the sizes of the probes
      used, and the size of the smallest detectable fragment produced.
AU  - Wijsman EM
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1984 12: 9209-9226.

PMID- 27979950
VI  - 4
DP  - 2016
TI  - Genome Sequences of Multidrug-Resistant Salmonella enterica subsp. enterica Serovar Infantis Strains from Broiler Chicks in Hungary.
PG  - e01400-16
AB  - Three strains of Salmonella enterica serovar Infantis isolated from healthy broiler chickens
      from 2012 to 2013 have been sequenced. Comparison of these and
      previously published S Infantis genome sequences of broiler origin in 1996 and
      2004 will provide new insight into the genome evolution and recent spread of S
      Infantis in poultry.
AU  - Wilk T
AU  - Szabo M
AU  - Szmolka A
AU  - Kiss J
AU  - Barta E
AU  - Nagy T
AU  - Olasz F
AU  - Nagy B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01400-16.

PMID- 28254986
VI  - 5
DP  - 2017
TI  - Genome Sequences of Salmonella enterica subsp. enterica Serovar Infantis Strains  from Hungary Representing Two Peak Incidence Periods in Three Decades.
PG  - e01735-16
AB  - Four strains of Salmonella enterica subsp. enterica serovar Infantis isolated from humans
      (1980 to 1982) and broiler chickens (2016) have been sequenced. They
      represent the early and recent peak incidences of this serovar in Hungary. Genome
      sequences of these isolates provide comparative data on the evolution and rise of
      an endemic S Infantis clone in Hungary.
AU  - Wilk T
AU  - Szabo M
AU  - Szmolka A
AU  - Kiss J
AU  - Olasz F
AU  - Nagy B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01735-16.

PMID- 3142766
VI  - 7
DP  - 1988
TI  - Sequential order of target-recognizing domains in multispecific DNA-methyltransferases.
PG  - 2601-2609
AB  - In the multispecific DNA (cytosine-5)-methyltransferases (Mtases) of Bacillus
      subtilis phages SPR and Phi3T the domains responsible for recognition of DNA
      methylation targets CC(A/T)GG, CCGG, GGCC (SPR) and GCNGC, GGCC (Phi3T)
      represent contiguous sequences of approximately 50 amino acids each.  These
      domains are tandemly arranged and do not overlap.  They are part of a variable
      segment within the enzymes which is flanked by conserved amino acids, which are
      very similar amongst bacterial monospecific and the multispecific Mtases
      studied here.  These results follow from a mutational analysis of the SPR and
      Phi3T Mtase genes.  They further support our concept of a modular enzyme
      organization, according to which variability of type II Mtases with respect to
      target recognition is achieved by a combination of the same enzyme core with a
      variety of target-recognizing domains.
AU  - Wilke K
AU  - Rauhut E
AU  - Noyer-Weidner M
AU  - Lauster R
AU  - Pawlek B
AU  - Behrens B
AU  - Trautner TA
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1988 7: 2601-2609.

PMID- 20167018
VI  - 19
DP  - 2010
TI  - The draft genome sequence of Arsenophonus nasoniae, son-killer bacterium of Nasonia vitripennis, reveals genes associated with virulence and symbiosis.
PG  - 59-73
AB  - Four percent of female Nasonia vitripennis carry the son-killer bacterium Arsenophonus
      nasoniae, a microbe with notably different biology from other inherited parasites and
      symbionts. In this paper, we examine a draft genome sequence of the bacterium for open reading
      frames (ORFs), structures and pathways involved in interactions with its insect host. The
      genome data suggest that A. nasoniae carries multiple type III secretion systems, and an array
      of toxin and virulence genes found in Photorhabdus, Yersinia and other gammaproteobacteria. Of
      particular note are ORFs similar to those known to affect host innate immune functioning in
      other bacteria, and four ORFs related to pro-apoptotic exotoxins. The genome sequences for
      both A. nasoniae and its Nasonia host are useful tools for examining functional genomic
      interactions of microbial survival in hostile immune environments, and mechanisms of passage
      through gut epithelia, in a whole organism context.
AU  - Wilkes T
AU  - Darby AC
AU  - Choi J
AU  - Colborne JK
AU  - Werren JH
AU  - Hurst GDD
PT  - Journal Article
TA  - Insect Mol. Biol.
JT  - Insect Mol. Biol.
SO  - Insect Mol. Biol. 2010 19: 59-73.

PMID- 12220405
VI  - 4
DP  - 2002
TI  - Plasmid promiscuity: meeting the challenge of DNA immigration control.
PG  - 495-500
AB  - Bacterial plasmids are ubiquitous components of the genomes of naturally occurring bacteria
      and are typically transmissible between cells by the process of bacterial conjugation (see
      reviews in Thomas, 2000).  A remarkable feature of conjugation is its promiscuity, allowing
      DNA transfer between phylogenetically remote bacteria and even from bacteria to plant and
      mammalian cells (Waters, 2001).  Conjugative promiscuity is biologically important in
      dispersing the diverse cargoes of medically and environmentally significant genes carried on
      plasmids, as well as contributing to the horizontal transfer of 'fitness islands',
      consisting of clustered chromosomal loci that enable pathogens and symbionts to interact with
      their eukaryotic hosts (Finan, 2002).
AU  - Wilkins BM
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2002 4: 495-500.

PMID- 8642602
VI  - 258
DP  - 1996
TI  - Distribution of restriction enzyme recognition sequences on broad host range plasmid RP4: molecular and evolutionary implications.
PG  - 447-456
AB  - IncPalpha plasmids, exemplified by RP4, are remarkable for their broad host range.  They
      contain strikingly few cleavage sites for many commonly used type II restriction enzymes but
      an overabundance of sites for certain enzymes that target G + C-rich sequences. To identify
      factors responsible for these distributions, the recently compiled nucleotide sequence of RP4
      was analyzed to determine the frequency of tetra- and hexanucleotide motifs in the 49 kb
      plasmid backbone.  This is defined as the sectors encoding basic plasmid functions.  The
      overabundant restriction targets in RP4 are concentrated in the backbone and contain
      overlapping copies of CGGC/GCCG, identified as the most abundant tetranucleotide motif in the
      plasmid. Motif frequencies in the RP4 backbone are shown to be similar to those in Pseudomonas
      aeruginosa, a natural host of RP4, with the notable exception that a number of 6-bp
      palindromes are underrepresented in the plasmid.  It is proposed that 6-bp palindromes were
      counterselected as type II restriction enzyme recognition sequences.  Conjugative transfer of
      RP4 and R751 (IncPbeta) is usually sensitive to restriction compared to enterobacterial
      plasmids of the IncFII and IncI1 groups, implying that IncP plasmids experienced particularly
      strong selection for loss of restriction targets.  Pseudomonas spp. of rRNA homology group I
      specify many type II restriction enzymes that target 6-bp palindromes and are candidates for
      the evolutionary hosts of IncPalpha plasmids.
AU  - Wilkins BM
AU  - Chilley PM
AU  - Thomas AT
AU  - Pocklington MJ
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1996 258: 447-456.

PMID- 25653664
VI  - 6
DP  - 2015
TI  - TAL effectors and activation of predicted host targets distinguish Asian from African strains of the rice pathogen Xanthomonas oryzae pv. oryzicola while strict conservation suggests universal importance of five TAL effectors.
PG  - 1-5
AB  - Xanthomonas oryzae pv. oryzicola (Xoc) causes the increasingly important disease bacterial
      leaf streak of rice (BLS) in part by type III delivery of repeat-rich transcription
      activator-like (TAL) effectors to upregulate host susceptibility genes.  By pathogen whole
      genome, single molecule, real-time sequencing and host RNA sequencing, we compared TAL
      effector content and rice transcriptional responses across 10 geographically diverse Xoc
      strains.  TAL effector content is surprisingly conserved overall, yet distinguishes Asian from
      African isolates.  Five TAL effectors are conserved across all strains. In a prior laboratory
      assay in rice cv. Nipponbare, only two contributed to virulence in strain BLS256 but the
      strict conservation indicates all five may e important, in different rice genotypes or in the
      field.  Concatenated and aligned, TAL effector content across strains largely reflects
      relationships based on housekeeping genes, suggesting predominantly vertical transmission.
      Rice transcriptional responses did not reflect these relationship, and on average, only 28% of
      genes upregulated and 22% of genes downregulated by a strain and up- and down-regulated
      (respectively) by all strains.  However, when only known TAL effector targets were considered,
      the relationships resembled those of the TAL effectors.  Toward identifying new targets, we
      used the TAL effector-DNA recognition code to predict effector binding elements in promoters
      of genes upregulated by each strain, but found that for every strain, all upregulated genes
      had at least one.  Filtering with a classifier we developed previously decreases the number of
      predicted binding elements across the genome, suggesting that it may reduce false positives
      among upregulated genes.  Applying this filter and eliminating genes for which upregulation
      did not strictly correlate with presence of the corresponding TAL effector, we generated
      testable numbers of candidate targets for four of the five strictly conserved TAL effectors.
AU  - Wilkins KE
AU  - Booher NJ
AU  - Wang L
AU  - Bogdanove AJ
PT  - Journal Article
TA  - Front. Plant Sci.
JT  - Front. Plant Sci.
SO  - Front. Plant Sci. 2015 6: 1-5.

PMID- 7862522
VI  - 23
DP  - 1995
TI  - The fission yeast gene pmt1+ encodes a DNA methyltransferase homologue.
PG  - 203-210
AB  - DNA methylation of cytosine residues is a widespread phenomenon and has been implicated in a
      number of biological processes in both prokaryotes and eukaryotes. This methylation occurs at
      the 5-position of cytosine and is catalyzed by a distinct family of conserved enzymes, the
      cytosine-5 methyltransferases (m5C-MTases). We have cloned a fission yeast gene pmt1+ (pombe
      methyltransferase) which encodes a protein that shares significant homology with both
      prokaryotic and eukaryotic m5C-MTases. All 10 conserved domains found in these enzymes are
      present in the pmt1 protein. This is the first m5C-MTase homologue cloned from a fungal
      species. Its presence is surprising, given the inability to detect DNA methylation in yeasts.
      Haploid cells lacking the pmt1+ gene are viable, indicating that pmt1+ is not an essential
      gene. Purified, bacterially produced pmt1 protein does not possess obvious methyltransferase
      activity in vitro. Thus the biological significance of this m5C-MTase homologue in fission
      yeast is currently unclear.
AU  - Wilkinson CRM
AU  - Bartlett R
AU  - Nurse P
AU  - Bird AP
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1995 23: 203-210.

PMID- 19583835
VI  - 10
DP  - 2009
TI  - Comparative genomics of the emerging human pathogen Photorhabdus asymbiotica with the insect pathogen Photorhabdus luminescens.
PG  - 302
AB  - BACKGROUND: The Gram-negative bacterium Photorhabdus asymbiotica (Pa) has
      been recovered from human infections in both North America and Australia.
      Recently, Pa has been shown to have a nematode vector that can also infect
      insects, like its sister species the insect pathogen P. luminescens (Pl).
      To understand the relationship between pathogenicity to insects and humans
      in Photorhabdus we have sequenced the complete genome of Pa strain
      ATCC43949 from North America. This strain (formerly referred to as
      Xenorhabdus luminescens strain 2) was isolated in 1977 from the blood of
      an 80 year old female patient with endocarditis, in Maryland, USA. Here we
      compare the complete genome of Pa ATCC43949 with that of the previously
      sequenced insect pathogen P. luminescens strain TT01 which was isolated
      from its entomopathogenic nematode vector collected from soil in Trinidad
      and Tobago. RESULTS: We found that the human pathogen Pa had a smaller
      genome (5,064,808 bp) than that of the insect pathogen Pl (5,688,987 bp)
      but that each pathogen carries approximately one megabase of DNA that is
      unique to each strain. The reduced size of the Pa genome is associated
      with a smaller diversity in insecticidal genes such as those encoding the
      Toxin complexes (Tc's), Makes caterpillars floppy (Mcf) toxins and the
      Photorhabdus Virulence Cassettes (PVCs). The Pa genome, however, also
      shows the addition of a plasmid related to pMT1 from Yersinia pestis and
      several novel pathogenicity islands including a novel Type Three Secretion
      System (TTSS) encoding island. Together these data suggest that Pa may
      show virulence against man via the acquisition of the pMT1-like plasmid
      and specific effectors, such as SopB, that promote its persistence inside
      human macrophages. Interestingly the loss of insecticidal genes in Pa is
      not reflected by a loss of pathogenicity towards insects. CONCLUSION: Our
      results suggest that North American isolates of Pa have acquired virulence
      against man via the acquisition of a plasmid and specific virulence
      factors with similarity to those shown to play roles in pathogenicity
      against humans in other bacteria.
AU  - Wilkinson P et al
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2009 10: 302.

PMID- 8070417
VI  - 13
DP  - 1994
TI  - A mutational analysis of the two motifs common to adenine methyltransferases.
PG  - 3902-3908
AB  - All methyltransferases that use S-adenosyl methionine as the methyl group donor contain a
      sequence similar to (D/E/S)XFXGXG which has been postulated to form part of the cofactor
      binding site. In N6-adenine DNA methyltransferases there is a second motif, (D/N)PP(Y/F),
      which has been proposed to play a role similar to the catalytically essential PC motif
      conserved in all C5-cytosine DNA methyltransferases. We have made a series of amino acid
      changes in these two motifs in the EcoKI N6-adenine DNA methyltransferase. The mutant enzymes
      have been purified to homogeneity and characterized by physical biochemical methods. The first
      G is the most conserved residue in motif I. Changing this G to D completely abolishes
      S-adenosyl methionine binding, but left enzyme structure and DNA target recognition unaltered,
      thus documenting the S-adenosyl methionine binding function of motif I in N6-adenine
      methyltransferases. Substitution of the N with D, or F with either G or C, in motif II
      abolished enzyme activity, but left S-adenosyl methionine and DNA binding unaltered. Changes
      of F to Y or W resulted in partial enzyme activity, implying that an aromatic residue is
      important for methylation. The substitution of W for F greatly enhanced UV-induced
      cross-linking between the enzyme and S-adenosyl methionine, suggesting that the aromatic
      residue is close in space to the methyl-group donor.
AU  - Willcock DF
AU  - Dryden DTF
AU  - Murray NE
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1994 13: 3902-3908.

PMID- 25197434
VI  - 9
DP  - 2014
TI  - Genome sequence of Burkholderia mimosarum strain LMG 23256(T), a Mimosa pigra microsymbiont from Anso, Taiwan.
PG  - 484-494
AB  - Burkholderia mimosarum strain LMG 23256(T) is an aerobic, motile, Gram-negative,
      non-spore-forming rod that can exist as a soil saprophyte or as a legume
      microsymbiont of Mimosa pigra (giant sensitive plant). LMG 23256(T) was isolated
      from a nodule recovered from the roots of the M. pigra growing in Anso, Taiwan.
      LMG 23256(T) is highly effective at fixing nitrogen with M. pigra. Here we
      describe the features of B. mimosarum strain LMG 23256(T), together with genome
      sequence information and its annotation. The 8,410,967 bp high-quality-draft
      genome is arranged into 268 scaffolds of 270 contigs containing 7,800
      protein-coding genes and 85 RNA-only encoding genes, and is one of 100 rhizobial
      genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic
      Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.
AU  - Willems A
AU  - Tian R
AU  - Brau L
AU  - Goodwin L
AU  - Han J
AU  - Liolios K
AU  - Huntemann M
AU  - Pati A
AU  - Woyke T
AU  - Mavrommatis K
AU  - Markowitz V
AU  - Ivanova N
AU  - Kyrpides N
AU  - Reeve W
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 484-494.

PMID- 12446640
VI  - 184
DP  - 2002
TI  - Bacteriophage HP2 of Haemophilus influenzae.
PG  - 6893-6905
AB  - Temperate bacteriophages effect chromosomal evolution of their bacterial hosts, mediating
      rearrangements and the acquisition of novel genes from other taxa. Although the Haemophilus
      influenzae genome shows evidence of past phage-mediated lateral transfer, the phages presumed
      responsible have not been identified. To date, six different H. influenzae phages are known;
      of these, only the HP1/S2 group, which lyosogenizes exclusively Rd strains (which were
      originally encapsulated serotype d), is well characterized. Phages in this group are
      genetically very similar, with a highly conserved set of genes. Because the majority of H.
      influenzae strains are nonencapsulated (nontypeable), it is important to characterize phages
      infecting this larger, genetically more diverse group of respiratory pathogens. We have
      identified and sequenced HP2, a bacteriophage of nontypeable H. influenzae. Although related
      to the fully sequenced HP1 (and even more so to the partially sequenced S2) and similar in
      genetic organization, HP2 has a few novel genes and differs in host range; HP2 will not infect
      or lysogenize Rd strains. Genomic comparisons between HP1/S2 and HP2 suggest recent
      divergence, with new genes completely replacing old ones at certain loci. Sequence comparisons
      suggest that H. influenzae phages evolve by recombinational exchange of genes with each other,
      with cryptic prophages, and with the host chromosome.
AU  - Williams BJ
AU  - Golomb M
AU  - Phillips T
AU  - Brownlee J
AU  - Olson MV
AU  - Smith AL
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2002 184: 6893-6905.

PMID- 2018768
VI  - 30
DP  - 1991
TI  - Properties of 2'-fluorothymidine-containing oligonucleotides:  Interaction with restriction endonuclease EcoRV.
PG  - 4001-4009
AB  - 2'-Fluorothymidine (Tf) was synthesized via an improved procedure with
      (diethylamino) sulfur trifluoride.  The compatibility of the analogue with DNA
      synthesis via the phosphoramidite method was demonstrated after complete
      enzymatic digestion of the oligonucleotides d(TfuT) and d(Tf3T), the sole
      products of which were 2'-fluorothymidine and thymidine in the expected ratio.
      The 2'-fluorothymidine was also incorporated into the EcoRV recognition
      sequence, within the complementary oligonucleotide d(CAAACCGATATCGTTGTG) and
      d(CACAACGATATCGGTTTG).  Thermal melting characteristics of these duplexes
      showed a significant decrease in stability only when both of the thymidine
      residues in one of the strands were replaced.  In contrast, when all of one
      strand of a duplex contained 2'-fluorothymidine, as in d(TfuT)-d(A12), a
      substantially higher Tm and cooperativity of melting was observed relative to
      the unmodified structure.  EcoRV cleaved a duplex that contained a
      2'-fluorothymidine at the scissile linkage in each strand at two-thirds of the
      rate obtained for the unmodified structure.  A duplex containing two
      2'-fluorothymidine residues in one strand and none in the other was cleaved at
      one-third of the rate in its unsubstituted strand, whereas the cleavage rate
      was reduced to 22% in its modified strand.
AU  - Williams DM
AU  - Benseler F
AU  - Eckstein F
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1991 30: 4001-4009.

PMID- 23630319
VI  - 41
DP  - 2013
TI  - A bistable hysteretic switch in an activator-repressor regulated restriction-modification system.
PG  - 6045-6057
AB  - Restriction-modification (RM) systems are extremely widespread among bacteria and archaea, and
      are often specified by mobile genetic elements. In type II RM systems, where the restriction
      endonuclease (REase) and protective DNA methyltransferase (MTase) are separate proteins, a
      major regulatory challenge is delaying expression of the REase relative to the MTase after RM
      genes enter a new host cell. Basic understanding of this regulation is available for few RM
      systems, and detailed understanding for none. The PvuII RM system is one of a large subset in
      which the central regulatory role is played by an activator-repressor protein (called C, for
      controller). REase expression depends upon activation by C, whereas expression of the MTase
      does not. Thus delay of REase expression depends on the rate of C-protein accumulation. This
      is a nonlinear process, as C also activates transcription of its own gene. Mathematical
      modeling of the PvuII system led to the unexpected predictions of responsiveness to a factor
      not previously studied in RM system control-gene copy number-and of a hysteretic response. In
      this study, those predictions have been confirmed experimentally. The results may apply to
      many other C-regulated RM systems, and help explain their ability to spread so widely.
AU  - Williams K
AU  - Savageau MA
AU  - Blumenthal RM
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2013 41: 6045-6057.

PMID- 29167262
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of the Predatory Bacterium Ensifer adhaerens Casida A.
PG  - e01344-17
AB  - We report here the complete genome sequence of the facultative predatory bacterium Ensifer
      adhaerens strain Casida A. The genome was assembled into three
      circular contigs, with a main chromosome as well as two large secondary
      replicons, that totaled 7,267,502 bp with 6,641 predicted open reading frames.
AU  - Williams LE
AU  - Baltrus DA
AU  - O'Donnell SD
AU  - Skelly TJ
AU  - Martin MO
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01344-17.

PMID- 16820486
VI  - 72
DP  - 2006
TI  - Facile Recovery of Individual High-Molecular-Weight, Low-Copy-Number Natural Plasmids for Genomic Sequencing.
PG  - 4899-4906
AB  - Sequencing of the large (>50 kb), low-copy-number (<5 per cell) plasmids that mediate
      horizontal gene transfer has been hindered by the difficulty and expense of isolating DNA from
      individual plasmids of this class. We report here that a kit method previously devised for
      purification of bacterial artificial chromosomes (BACs) can be adapted for effective
      preparation of individual plasmids up to 220 kb from wild gram-negative and gram-positive
      bacteria. Individual plasmid DNA recovered from less than 10 ml of Escherichia coli,
      Staphylococcus, and Corynebacterium cultures was of sufficient quantity and quality for
      construction of high-coverage libraries, as shown by sequencing five native plasmids ranging
      in size from 30 kb to 94 kb. We also report recommendations for vector screening to optimize
      plasmid sequence assembly, preliminary annotation of novel plasmid genomes, and insights on
      mobile genetic element biology derived from these sequences. Adaptation of this BAC method for
      large plasmid isolation removes one major technical hurdle to expanding our knowledge of the
      natural plasmid gene pool.
AU  - Williams LE
AU  - Detter C
AU  - Barry K
AU  - Lapidus A
AU  - Summers AO
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2006 72: 4899-4906.

PMID- 22247535
VI  - 194
DP  - 2012
TI  - Genome Sequence of Edwardsiella ictaluri 93-146, a Strain Associated with a Natural Channel Catfish Outbreak of Enteric Septicemia of Catfish.
PG  - 740-741
AB  - Edwardsiella ictaluri is the cause of extensive mortalities and economic losses to the channel
      catfish industry of the southeast United States.
      Here we report the complete genome of Edwardsiella ictaluri 93-146.
      Whole-genome sequence analysis of E. ictaluri provides a tool for
      understanding the genomic regions specific to the species and the
      Edwardsiella genus.
AU  - Williams ML
AU  - Gillaspy AF
AU  - Dyer DW
AU  - Thune RL
AU  - Waldbieser GC
AU  - Schuster SC
AU  - Gipson J
AU  - Zaitshik J
AU  - Landry C
AU  - Banes MM
AU  - Lawrence ML
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 740-741.

PMID- 26812174
VI  - 22
DP  - 2016
TI  - Bordetella pertussis strain lacking pertactin and pertussis toxin.
PG  - 319-322
AB  - A Bordetella pertussis strain lacking 2 acellular vaccine immunogens, pertussis toxin and
      pertactin, was isolated from an unvaccinated infant in New York State in 2013. Comparison with
      a French strain that was pertussis toxindeficient, pertactin wild-type showed that the strains
      carry the same 28-kb deletion in similar genomes.
AU  - Williams MM
AU  - Sen KA
AU  - Weigand MR
AU  - Skoff TH
AU  - Cunningham VA
AU  - Halse TA
AU  - Tondella ML
PT  - Journal Article
TA  - Emerg. Infect. Dis.
JT  - Emerg. Infect. Dis.
SO  - Emerg. Infect. Dis. 2016 22: 319-322.

PMID- 12665693
VI  - 23
DP  - 2003
TI  - Restriction endonucleases: Classification, properties, and applications.
PG  - 225-243
AB  - Restriction endonucleases have become a fundamental tool of molecular biology with many
      commercial vendors and extensive product lines. While a
      significant amount has been learned about restriction enzyme diversity,
      genomic organization, and mechanism, these continue to be active areas of
      research and assist in classification efforts. More recently, one focus
      has been their exquisite specificity for the proper recognition sequence
      and the lack of homology among enzymes recognizing the same DNA sequence.
      Some questions also remain regarding in vivo function. Site-directed
      mutagenesis and fusion proteins based on known endonucleases show promise
      for custom-designed cleavage. An understanding of the enzymes and their
      properties can improve their productive application by maintaining
      critical digest parameters and enhancing or avoiding alternative
      activities.
AU  - Williams RJ
PT  - Journal Article
TA  - Mol. Biotechnol.
JT  - Mol. Biotechnol.
SO  - Mol. Biotechnol. 2003 23: 225-243.

PMID- 11265300
VI  - 160
DP  - 2001
TI  - Restriction endonucleases and their uses.
PG  - 409-429
AB  - Restriction endonucleases, which cleave DNA in a site-specific manner, are a fundamental tool
      of molecular biology.  The discovery of endonucleases began in the 1960s and led to commercial
      availability in the early 1970s.  The number of characterized enzymes continues to grow, as
      does the number of vendors and the size of their product lines.  Although many similarities
      exist among endonucleases in terms of their structures, mechanisms, and uses, important
      differences remain.  Now a staple of molecular biology, restriction endonucleases are an area
      of active research as models of site-specific DNA recognition, cleavage mechanism, in vivo
      function, and evolutionary origins.  New enzymes continue to be discovered or developed by
      using protein engineering to modify the specificity of existing enzymes.
AU  - Williams RJ
PT  - Journal Article
TA  - Methods Mol. Biol.
JT  - Methods Mol. Biol.
SO  - Methods Mol. Biol. 2001 160: 409-429.

PMID- 11265301
VI  - 160
DP  - 2001
TI  - Isolation and characterization of an unknown restriction endonuclease.
PG  - 431-442
AB  - Currently, there are approximately 3000 restriction endonucleases known, recognizing 235
      different sequences.  Although primarily found in bacteria, they also exist in archaea,
      viruses, and eukaryotes.  An estimated 25% of bacteria examined contain at least one
      restriction endonuclease, and therefore the probability of encountering new ones is relatively
      high.  Indeed, many new enzymes have been "discovered" in contaminated bacterial cultures.
      The presence of three restriction activities in a single organism is not unusual.  Neisseria
      strains appear to be particularly rich in restriction endonucleases and their corresponding
      methyltransferases.  As many as seven different endonucleases from a single strain have been
      identified through cloning.  The first enzyme discovered which recognizes a unique sequence,
      although it may not be commercially available or commonly known, is designated the prototype.
      Although few new prototypes have been discovered recently, two potential four-base palindromes
      and seven potential six-base palindromes are not cleaved by any known restriction
      endonucleases.  Most databases are arranged alphabetically by prototype, with isoschizomers
      listed under the prototype heading.  A database of all known endonucleases, maintained by Dr.
      Richard J. Roberts, is available at http://www.neb.com/rebase.  A number of formats are
      available, and references are provided.  Detailed information on restriction endonuclease
      biology, classification, structure, specificity, and catalytic mechanism is provided elsewhere
      in this book.
AU  - Williams RJ
PT  - Journal Article
TA  - Methods Mol. Biol.
JT  - Methods Mol. Biol.
SO  - Methods Mol. Biol. 2001 160: 431-442.

PMID- 12051845
VI  - 318
DP  - 2002
TI  - Communications between catalytic sites in the protein-DNA synapse by the SfiI endonuclease.
PG  - 387-394
AB  - The SfiI endonuclease is a tetrameric protein with two DNA-binding clefts. It has to bind two
      copies of its recognition sequence, one at each cleft, before it cleaves DNA. While SfiI binds
      cooperatively to two cognate sites, it binds only one non-cognate DNA molecule at a time and
      the resultant complex is precluded from binding cognate DNA at the vacant cleft. To examine
      the communications between separate binding sites in a protein that synapses two segments of
      DNA, SfiI was tested with oligonucleotide duplexes containing its recognition sequence but
      with either R(p) or S(p) phosphorothioate linkages at the scissile bonds. Though SfiI has low
      activity on the R(p) and none against the S(p) diastereoisomer, it bound these duplexes in the
      same cooperative manner as oxyester duplexes, though with a reduced affinity for the S(p)
      derivative. It also formed complexes with one phosphorothioate-duplex and one oxyester-duplex
      but, when Mg(2+) was added to the hybrid complexes, the phosphorothioate moiety at one
      DNA-binding cleft prevented the enzyme from cleaving the oxyester duplex at the other cleft.
      SfiI is thus restrained from catalytic action until it recognises the correct nucleotide
      sequence at two DNA loci and the correct phosphodiester functions at both loci.
AU  - Williams SA
AU  - Halford SE
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2002 318: 387-394.

PMID- 11266549
VI  - 29
DP  - 2001
TI  - SfiI endonuclease activity is strongly influenced by the non-specific sequence in the middle of its recognition site.
PG  - 1476-1483
AB  - The SfiI endonuclease cleaves DNA at the sequence GGCCNNNNNGGCC, where N is any base and  is
      the point of cleavage.  Proteins that recognise discontinuous sequences in DNA can be affected
      by the unspecified sequence between the specified base pairs of the target site. To examine
      whether this applies to SfiI, a series of DNA duplexes were made with identical sequences
      apart from discrete variations in the 5 bp spacer. The rates at which SfiI cleaved each duplex
      were measured under steady-state conditions: the steady-state rates were determined by the DNA
      cleavage step in the reaction pathway. SfiI cleaved some of these substrates at faster rates
      than other substrates. For example, the change in spacer sequence from AACAA to AAACA caused a
      70-fold increase in reaction rate. In general, the extrapolated values for kcat and Km were
      both higher on substrates with inflexible spacers than those with flexible structures. The
      dinucleotide at the site of cleavage was largely immaterial. SfiI activity is thus highly
      dependent on conformational variations in the spacer DNA.
AU  - Williams SA
AU  - Halford SE
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2001 29: 1476-1483.

PMID- 27610212
VI  - 11
DP  - 2016
TI  - Complete genome sequence of Halomonas sp. R5-57.
PG  - 62
AB  - The marine Arctic isolate Halomonas sp. R5-57 was sequenced as part of a bioprospecting
      project which aims to discover novel enzymes and organisms from
      low-temperature environments, with potential uses in biotechnological
      applications. Phenotypically, Halomonas sp. R5-57 exhibits high salt tolerance
      over a wide range of temperatures and has extra-cellular hydrolytic activities
      with several substrates, indicating it secretes enzymes which may function in
      high salinity conditions. Genome sequencing identified the genes involved in the
      biosynthesis of the osmoprotectant ectoine, which has applications in food
      processing and pharmacy, as well as those involved in production of
      polyhydroxyalkanoates, which can serve as precursors to bioplastics. The
      percentage identity of these biosynthetic genes from Halomonas sp. R5-57 and
      current production strains varies between 99 % for some to 69 % for others, thus
      it is plausible that R5-57 may have a different production capacity to currently
      used strains, or that in the case of PHAs, the properties of the final product
      may vary. Here we present the finished genome sequence (LN813019) of Halomonas
      sp. R5-57 which will facilitate exploitation of this bacterium; either as a
      whole-cell production host, or by recombinant expression of its individual
      enzymes.
AU  - Williamson A
AU  - De Santi C
AU  - Altermark B
AU  - Karlsen C
AU  - Hjerde E
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 62.

PMID- 8382656
VI  - 124
DP  - 1993
TI  - Modified-cytosine restriction-system-induced recombinant cloning artefacts in Escherichia coli.
PG  - 37-44
AB  - We have tested whether, and to what extent, recombinant clones from DNA segments with
      5-methylation of cytosines recovered in methylation-restriction (mcr+) hosts contain
      mutations. We constructed a model system in which the tetracycline-resistance-encoding gene
      (tet) from pBR322 was cloned into the plasmid pGEM3Zf+. The central regon of tet was removed
      from the construct, methylated in vitro and then religated back into the unmethylated
      remainder of the construct. The central region of tet was either (1) methylated with a
      combination of four bacterial methyltransferases (M.AluI, M.HaeIII, M.HpaII plus M.HhaI) or
      (2) methylated with M.SssI which methylates at all CpG dinucleotides. These two protocols
      generated theoretical levels of DNA methylation in the central fragment of 10.5% and 33%
      respectively. The construct was transformed into a series of isogenic (recA+) bacterial
      strains that were mcrA+ mcrB+C+, mcrA+, mcrB-C+, mcrA-, mcrB+C+, mcrA-mcrB-C+ or mcrA- mcrBC,
      and also into a set of isogenic recA- derivatives of these strains. With the two methylation
      protocols, there was an average 48- and 141-fold reduction, respectively, in the number of
      transformants recovered from the recA+ mcr+ hosts compared with a methylation-tolerant host
      (mcr-). Of the clones recovered in recA+ mcr+ hosts >20% of clones had an inactivation g
      mutation in tet. The majority of such mutant clones contained deletions that frequently
      extended into the unmethylated portion of tet and even into the plasmid sequences beyond the
      end of the polylinker. With the recA- mcr+ hosts, effective restriction was much more
      stringent, rendering the plasmid containing the methylated segment effectively unclonable. By
      implication, any collection of clones derived from methylated genomic DNA using a recA+ mcr+
      host may contain significant frequencies of sequence artefacts.
AU  - Williamson MR
AU  - Doherty JP
AU  - Woodcock DM
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1993 124: 37-44.

PMID- 26337872
VI  - 3
DP  - 2015
TI  - Draft Genome Assembly of Filamentous Brackish Cyanobacterium Limnoraphis robusta  Strain CS-951.
PG  - e00846-15
AB  - Limnoraphis robusta CS-951 is a sheathed, filamentous benthic, nonheterocystous
      cyanobacterium. It was isolated from brackish water and identified morphologically as Lyngbya
      majuscula. We report the draft genome of L. robusta CS-951, with a genome size of 7,314,117
      bp, a 41.6% GC content, and 6,791 putative protein-coding genes assembled into 361contigs.
AU  - Willis A
AU  - Parks M
AU  - Burford MA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00846-15.

PMID- 6690723
VI  - 49
DP  - 1984
TI  - DNA methyltransferase induced by frog virus 3.
PG  - 86-91
AB  - Over 20% of the cytosine bases in frog virus 3 DNA are methylated at the 5-carbon position. To
      determine whether this high degree of methylation is the result of a virus-specific enzyme, we
      examined the kinetics of induction and the substrate specificity of a DNA methyltransferase
      from frog virus 3-infected fathead minnow cells.  A novel DNA methyltransferase activity
      appeared in the cytoplasm of infected cells at 3 h postinfection.  This activity was induced
      in the absence of viral DNA replication and was therefore probably an early viral enzyme.  In
      contrast to the methyltransferase activity extracted from uninfected cell nuclei, the
      cytoplasmic enzyme showed a strong template preference for double-stranded over
      single-stranded and for unmethylated over hemimethylated DNA.  The dinucleotide sequence dCpdG
      was a necessary and sufficient exogenous substrate for methylation in vitro.  A mutant of frog
      virus 3, isolated as resistant to 5-azacytidine and having unmethylated virion DNA, did not
      induce cytoplasmic DNA methyltransferase, leading to the conclusion that this activity is
      coded for by the virus.
AU  - Willis DB
AU  - Goorha R
AU  - Granoff A
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1984 49: 86-91.

PMID- 28963227
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Pseudomonas sp. Strain DrBHI1 (Phylum Proteobacteria).
PG  - e01090-17
AB  - Here, we report the draft genome sequence of Pseudomonas sp. strain DrBHI1. The total assembly
      length is 5,649,751 bp in 146 contigs. This strain was isolated
      from zebrafish (Danio rerio) feces.
AU  - Wilson AK
AU  - Watral VG
AU  - Kent ML
AU  - Sharpton TJ
AU  - Gaulke CA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01090-17.

PMID- 7955046
VI  - 15
DP  - 1994
TI  - An assay for O6-alkylguanine-DNA alkyltransferase based on restriction endonuclease inhibition and magnetic bead separation of products.
PG  - 2143-2148
AB  - We describe an improved, rapid and cost effective assay for measuring O6-alkylguanine-DNA
      alkyltransferase (AGT) levels in large numbers of small biological samples. The assay is based
      on the use of a synthetic O6-methylguanine oligonucleotide bound to magnetic beads via a
      biotin-streptavidin linkage and bound to its complement. A 35S label is incorporated into the
      free end of the duplex. The basis of the assay lies in the observation that the restriction
      enzyme PvuII will not cleave the bead-bound duplex oligonucleotide having an O6-methylguanine
      within the restriction sequence. However, on removal of the methyl group by AGT present in
      cell extracts prior to incubation with PvuII, the 35S-labelled oligonucleotide is cleaved by
      the restriction enzyme, releasing a 35S-labelled 8 bp fragment. Due to the stoichiometric
      nature of the AGT reaction, quantitation of AGT is easily achieved by counting an aliquot of
      the supernatant after pelleting the unrestricted bead complexes with a magnet. AGT levels
      measured in certain cell lines and human lymphocytes by the reported assay are comparable to
      other methods. The assay can be performed in basic laboratories and allows for the rapid
      processing of many samples simultaneously, which could prove useful in clinical and
      epidemiological studies.
AU  - Wilson BD
AU  - Strauss M
AU  - Stickells BJ
AU  - Hoal-van Helden EG
AU  - van Helden PD
PT  - Journal Article
TA  - Carcinogenesis
JT  - Carcinogenesis
SO  - Carcinogenesis 1994 15: 2143-2148.

PMID- 4213607
VI  - 14
DP  - 1974
TI  - Characterization of temperate bacteriophages of Bacillus subtilis by the restriction endonuclease EcoRI: Evidence for three different temperate bacteriophages.
PG  - 1013-1016
AB  - Temperate bacteriophages of Bacillus subtilis were characterized according to
      host range and digestion of the bacteriophage genome by endonuclease EcoRI.
      The three bacteriophages, Phi3T, SPO2, and Phi105, were all heteroimmune, and
      the DNA digests showed dissimilar patterns by agarose-ethidium bromide gel
      electrophoresis.
AU  - Wilson GA
AU  - Williams MT
AU  - Baney HW
AU  - Young FE
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1974 14: 1013-1016.

PMID- Not carried by PubMed...
VI  - 0
DP  - 1976
TI  - Restriction and modification in the Bacillus subtilis genospecies.
PG  - 350-357
AB  - Restriction and modification have not been as intensively studied in
      gram-positive bacilli as in enterobacteriaceae.  This is particularly
      surprising since the Bacillus subtilis genospecies appears to be one in which
      restriction and modification can be studied quite readily.  Included among the
      advantages is the high frequency of genetic exchange among closely related
      members of the genospecies.  This high rate of transformation usually occurs
      with a limited number of genetic loci.  In addition, recent emphasis on the
      genetic organization of B. subtilis has resulted in a detailed map of the
      chromosome (Anagnostopoulos and Trowsdale, p. 44).  The presence of the
      plasmids in closely related strains affords the possibility of using these
      elements in restriction and cloning studies.  The variety of methods for
      genetic exchange and the ease of transformation afford one of the best
      opportunities to study restriction and modification of the isolated DNA.
      Restriction and modification enzymes have been demonstrated in this
      genospecies, and a number of these appear to be unique in the sequence of
      nucleotides they recognize, thus increasing the usefulness of these enzymes in
      the field of recombinant molecule technology.  The bacilli also undergo a
      carefully regulated series of morpho-genetic events leading to the production
      of an endospore.  Finally, unlike the enterobacteriaceae, bacilli have been the
      organisms of choice for the production of a large number of fermentation
      products.  Because of the desire to study morphogenesis and to construct
      strains of commercial importance, an examination of the factors contributing
      toward (or hampering) efficient genetic exchange within the genospecies has
      been intensified.
AU  - Wilson GA
AU  - Young FE
PT  - Journal Article
TA  - Microbiology-1976
JT  - Microbiology-1976
SO  - Microbiology-1976 1976 0: 350-357.

PMID- Not carried by PubMed...
VI  - 75
DP  - 1975
TI  - Restriction and modification in the Bacillus subtilis genospecies:  Isolation of an endonuclease in Bacillus amyloliquefaciens.
PG  - 103
AB  - Previous studies in this laboratory have demonstrated that deoxyribonucleic
      acid (DNA) is capable of effecting DNA-mediated transformation of B. subtilis.
      Inefficiency of heterospecific transformation prompted a search for restriction
      in the genospecies.  Accordingly mutants of SP02 (SP01clh2 and SP02clh5) were
      isolated that infect B. amyloliquefaciens H.  When propagated on B.
      amyloliquefaciens H, these viruses infected B. amyloliquefaciens H, but were
      markedly restricted by B. subtilis 168.  Restriction was overcome by passage of
      virus on B. subtilis 168.  Transfection of B. subtilis occurred with DNA
      isolated from SP02clh2 propagated on B. subtilis but not with DNA isolated from
      SP02clh2 propagated on B. amyloliquefaciens.  In the latter case biologic
      activity could be recovered by superinfection marker rescue or transfection of
      restriction deficient mutants of B. subtilis.  An endonuclease (BamHI) was
      purified from B. amyloliquefaciens H by (NH4)2S04 precipitation and
      chromatography on DEAE cellulose and phosphocellulose.  Analysis of cleavage
      patterns of standard viral DNA preparations (lambda, SV40, adeno and SP02) by
      gel electrophoresis established that BamHI is different from previously
      described nucleases.  Biochemical tests indicate that BamHI recognized unique
      sites in DNA and may be responsible for restriction in B. amyloliquefaciens.
AU  - Wilson GA
AU  - Young FE
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1975 75: 103.

PMID- 1177312
VI  - 97
DP  - 1975
TI  - Isolation of a sequence-specific endonuclease (BamI) from Bacillus amyloliquefaciens H.
PG  - 123-125
AB  - A restriction endonuclease has been isolated from Bacillus amyloliquefaciens H
      (strain RUB500).  The enzyme, BamI, cleaves adenovirus-2 DNA at three sites,
      phage lambda DNA at five sites, lambda plac DNA at four sites, Phi80 pt DNA at
      14 sites, and Phi3T+ DNA at four sites.  However, it does not cleave DNA from
      bacteriophage SP02, Phi105 or Phi29.
AU  - Wilson GA
AU  - Young FE
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1975 97: 123-125.

PMID- 6246335
VI  - 65
DP  - 1980
TI  - Purification and properties of the BamHI endonuclease.
PG  - 147-153
AB  - Site-specific endonucleases have been isolated from a diverse variety of microorganisms and
      used extensively in analyzing and manipulating complex genomes.  In fact, the utility of these
      enzymes has resulted in an emphasis on their application and inadvertently hampered a thorough
      examination of the properties and biological functions of these endonucleases.  For example,
      the role of site-specific endonucleases in vivo has not been determined, although, restriction
      and modification properties have been confirmed by genetic studies for EcoRI, EcoRII, BamHI,
      BsuI, Bst1503, BglI, and BglII.  Although the methods of isolation and optimal reaction
      conditions have not been systematically examined, most of the enzymes can be readily isolated
      and purified from contaminating endonucleases and exonucleases.  BamHI proved to be a useful
      enzyme because it produced a single-stranded end after cleaving between the guanine bases at
      the site of 5'-GGATCC-3', thus providing a useful substrate for ligation.  In addition, a
      number of cloning vectors existed or were developed that contained a single recognition site
      for BamHI including vectors SV40, pMB9, pBR313, and pBR322.  These advantages contributed to
      the extensive use of this enzyme and to the development of modifications of our original
      purification procedure that were kindly communicated to us by numerous investigators.  This
      report will summarize the methods of isolation of BamHI and related enzymes from the Bacillus
      genospecies as well as indicate what progress has been made in characterizing these enzymes.
AU  - Wilson GA
AU  - Young FE
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1980 65: 147-153.

PMID- 3070854
VI  - 4
DP  - 1988
TI  - Type II restriction-modification systems.
PG  - 314-318
AB  - Restriction-modification (R-M) systems are enzymatic mechanisms that occur
      primarily in bacteria.  Their principal function is defensive:  they enable
      cells to resist infections by phage and plasmid DNA molecules that would
      otherwise parasitize them, and they limit the spread of these molecules within
      the population.  R-M systems are traditionally classified into three groups,
      types I, II and III, according to their enzymology and cofactor requirements.
      Type II systems are best understood, and are regarded as the simplest; they are
      also the most familiar to molecular biologists since it is from these systems
      that the restriction enzymes used in recombinant DNA research are purified.  A
      summary of the biology of the type II systems is presented here; the type I and
      type II systems have been reviewed elsewhere.
AU  - Wilson GG
PT  - Journal Article
TA  - Trends Genet.
JT  - Trends Genet.
SO  - Trends Genet. 1988 4: 314-318.

PMID- 3074014
VI  - 74
DP  - 1988
TI  - Cloned restriction-modification systems - a review.
PG  - 281-289
AB  - The genes for numerous restriction endonucleases and modification methylases
      have been cloned into Escherichia coli.  A summary is given for the clones
      isolated so far (115 entries) and of the procedures used to obtain them.
AU  - Wilson GG
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1988 74: 281-289.

PMID- 2041731
VI  - 19
DP  - 1991
TI  - Organization of restriction-modification systems.
PG  - 2539-2566
AB  - The genes for over 100 restriction-modification systems have now been cloned,
      and approximately one-half have been sequenced.  Despite their similar
      function, they are exceedingly heterogeneous.  The heterogeneity is evident at
      three levels: in the gene arrangements; in the enzyme compositions; and in the
      protein sequences.  This paper summarizes the main features of the R-M systems
      that have been cloned.
AU  - Wilson GG
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 2539-2566.

PMID- 1479903
VI  - 216
DP  - 1992
TI  - Amino acid sequence arrangements of DNA-methyltranferases.
PG  - 259-279
AB  - 
AU  - Wilson GG
PT  - Journal Article
TA  - Methods Enzymol.
JT  - Methods Enzymol.
SO  - Methods Enzymol. 1992 216: 259-279.

PMID- 1812816
VI  - 25
DP  - 1991
TI  - Restriction and Modification Systems.
PG  - 585-627
AB  - *

      CONTENTS

      INTRODUCTION

      BIOLOGY OF RESTRICTION AND MODIFICATION

         Restriction and modification enzymes

         Occurrence of R-M systems

         Restriction and modification of viruses

         Cloning restriction and modification genes

      CHARACTERISTICS OF R-M SYSTEMS

         Type I systems

         Type II systems

         Type IIs systems

         Type III systems

         Other system types

         Modification-requiring systems

         Regulation of expression

      CONTRASTS AND COMPARISONS AMONG R-M SYSTEMS

         Type I systems

         Type II systems

         Type II endonucleases

         Methyltransferases

      DISCUSSION

      

AU  - Wilson GG
AU  - Murray NE
PT  - Journal Article
TA  - Annu. Rev. Genet.
JT  - Annu. Rev. Genet.
SO  - Annu. Rev. Genet. 1991 25: 585-627.

PMID- 
VI  - 93
DP  - 2012
TI  - Restriction enzymes in microbiology, biotechnology and biochemistry.
PG  - 19-48
AB  - Since their discovery in the nineteen-seventies, a collection of simple enzymes termed Type II
      restriction endonucleases, made by microbes to ward off viral infections, have transformed
      molecular biology, spawned the multi-billion dollar Biotechnology industry, and yielded
      fundamental insights into the biochemistry of life, health and disease.  In this article we
      describe how these enzymes were discovered, and we review their properties, organizations and
      genetics.  We summarize current ideas about the mechanism underlying their remarkable ability
      to recognize and bind to specific base pair sequences in DNA, and we discuss why these ideas
      might not be correct.  We conclude by proposing an alternative explanation for
      sequence-recognition that resolves certain inconsistencies and provides, in our view, a more
      satisfactory account of the mechanism.
AU  - Wilson GG
AU  - Wang H
AU  - Heiter DF
AU  - Lunnen KD
PT  - Journal Article
TA  - Encuentro
JT  - Encuentro
SO  - Encuentro 2012 93: 19-48.

PMID- 19773422
VI  - 37
DP  - 2009
TI  - Phage T4 mobE promotes trans homing of the defunct homing endonuclease I-TevIII.
PG  - 7110-7123
AB  - Homing endonucleases are site-specific DNA endonucleases that typically function as mobile
      genetic elements by introducing a double-strand break
      (DSB) in genomes that lack the endonuclease, resulting in a unidirectional
      gene conversion event that mobilizes the homing endonuclease gene and
      flanking DNA. Here, we characterize phage T4-encoded mobE, a predicted
      free-standing HNH family homing endonuclease. We show that mobE is
      promoterless and dependent on upstream transcription for expression, and
      that an internal intrinsic terminator regulates mobE transcript levels.
      Crucially, in vivo mapping experiments revealed a MobE-dependent,
      strand-specific nick in the non-coding strand of the nrdB gene of phage
      T2. An internal deletion of the predicted HNH catalytic motif of MobE
      abolishes nicking, and reduces high-frequency inheritance of mobE.
      Sequence polymorphisms of progeny phage that inherit mobE are consistent
      with DSB repair pathways. Significantly, we found that mobility of the
      neighboring I-TevIII, a defunct homing endonuclease encoded within a group
      I intron interrupting the nrdB gene of phage T4, was dependent on an
      intact mobE gene. Thus, our data indicate that the stagnant nrdB intron
      and I-TevIII are mobilized in trans as a consequence of a MobE-dependent
      gene conversion event, facilitating persistence of genetic elements that
      have no inherent means of promoting their own mobility.
AU  - Wilson GW
AU  - Edgell DR
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: 7110-7123.

PMID- 24874669
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Enterobacter cloacae Strain JD6301.
PG  - e00381-14
AB  - Enterobacter cloacae strain JD6301 was isolated from a mixed culture with wastewater collected
      from a municipal treatment facility and oleaginous
      microorganisms. A draft genome sequence of this organism indicates that it has a
      genome size of 4,772,910 bp, an average G+C content of 53%, and 4,509
      protein-coding genes.
AU  - Wilson JG
AU  - French WT
AU  - Lipzen A
AU  - Martin J
AU  - Schackwitz W
AU  - Woyke T
AU  - Shapiro N
AU  - Bullard JW
AU  - Champlin FR
AU  - Donaldson JR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00381-14.

PMID- 7906398
VI  - 368
DP  - 1994
TI  - 2.2 Mb of contiguous nucleotide sequence from chromosome III of C. elegans.
PG  - 32-38
AB  - As part of our effort to sequence the 100-megabase (Mb) genome of the nematode Caenorhabditis
      elegans, we have completed the nucleotide sequence of a contiguous 2,181,032 base pairs in the
      central gene cluster of chromosome III. Analysis of the finished sequence has indicated an
      average density of about one gene per five kilobases; comparison with the public sequence
      databases reveals similarities to previously known genes for about one gene in three. In
      addition, the genomic sequence contains several intriguing features, including putative gene
      duplications and a variety of other repeats with potential evolutionary implications. [
      Comment in: Nature 1994 Mar 3;368(6466):14-5 ]
AU  - Wilson R et al
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1994 368: 32-38.

PMID- 2128170
VI  - 191
DP  - 1990
TI  - Methylation of intact chromosomes by bacterial methylases in agarose plugs suitable for pulsed-field electrophoresis.
PG  - 370-375
AB  - Conditions were determined for the methylation of intact yeast chromosomes by
      EcoRI, HhaI, and MspI bacterial methylases using an endonuclease protection
      assay while the chromosomes were embedded in agarose plugs suitable for
      transverse-field electrophoresis.  Parameters were also established for the
      methylation of human chromosomes by EcoRI methylase.  Methylation of embedded
      chromosomes by EcoRI methylase required prewashes with EDTA.  EcoRI, HhaI, and
      MspI methylases showed optimal activity when nonacetylated bovine serum
      albumin, high levels of S-adenosylmethionine, and high levels of methylase were
      used.  The use of bacterial methylases for methylation of embedded chromosomes
      will allow investigators to normalize variations in cellular DNA methylation
      prior to restriction and create new and rare endonuclease recognition sites
      which will facilitate the detection of chromosomal alterations and deletions.
AU  - Wilson WW
AU  - Hoffman RM
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 1990 191: 370-375.

PMID- 8476210
VI  - 13
DP  - 1993
TI  - Creation of ultra-rare restriction sites in intact eucaryotic chromosomes mediated by bacterial methylases: An approach to sequencing and analyzing tumor and normal genomes.
PG  - 17-20
AB  - The limited restriction of eucaryotic chromosomes would facilitate our understanding of the
      aberrant genomes of genetic diseases and cancer. We have described methods for methylating
      eucaryotic chromosomes embedded in agarose plugs (1). We now describe how ClaI methylase can
      be utilized in a methylation-dependent restriction cleavage with DpnI to restrict eucaryotic
      genomes into a limited number of fragments. We have restricted the genomes of Saccharomyces
      cerevisiae at four sites and cleaved the three chromosomes of Schizosaccharomyces pombe into
      eleven fragments. Unlike the recently published methodologies (2,3,4,5) using DNA sequences
      inserted into procaryotic and eucaryotic genomes, the methodologies described here use
      unaltered eucaryotic genomes for highly limited restriction. This methodology has applications
      in speeding, simplifying, and reducing the cost of sequence the human genome.
AU  - Wilson WW
AU  - Mebane EW
AU  - Hoffman RM
PT  - Journal Article
TA  - Anticancer Res.
JT  - Anticancer Res.
SO  - Anticancer Res. 1993 13: 17-20.

PMID- 2902154
VI  - 54
DP  - 1988
TI  - Survival of Saccharomyces cerevisiae after treament with the restriction endonuclease AluI.
PG  - 563-566
AB  - Treatment of yeast cells proficient in the repair of radiation damage
      (Saccharomyces cervisiae) with the restriction endonuclease AluI leads to a
      positive dose-effect relationship between inactivation level and enzyme
      concentration.  The data suggest an uptake of the active restriction enzyme
      into the cells and a relationship between induction of DNA double-strand breaks
      and cell killing.
AU  - Winckler K
AU  - Bach B
AU  - Obe G
PT  - Journal Article
TA  - Int. J. Radiat. Biol.
JT  - Int. J. Radiat. Biol.
SO  - Int. J. Radiat. Biol. 1988 54: 563-566.

PMID- 15452558
VI  - 11
DP  - 2004
TI  - Double duty.
PG  - 910-911
AB  - A second high-affinity binding site for the I-TevI homing endonuclease has been discovered.
      Surprisingly, the DNA sequence recognized is the
      protein's own operator; at this site, the endonuclease represses its
      own transcription instead of cleaving the DNA and inducing intron
      homing.
AU  - Windbichler N
AU  - Schroeder R
PT  - Journal Article
TA  - Nat. Struct. Mol. Biol.
JT  - Nat. Struct. Mol. Biol.
SO  - Nat. Struct. Mol. Biol. 2004 11: 910-911.

PMID- 9063456
VI  - 244
DP  - 1997
TI  - Influence of divalent cations on inner-arm mutants of restriction endonuclease EcoRI.
PG  - 134-139
AB  - To understand the functional role of the inner arm region of EcoRI for the interaction with
      its DNA substrate, we mutated each of the positively charged amino acid residues Lys130 and
      Arg131 to Ala or Glu.  The resulting cleavage activities are only about tenfold reduced but
      DNA binding in the absence of divalent cations is totally disrupted for three of the mutants
      ([Ala130]EcoRI, [Glu130]EcoRI and [Glu131]EcoRI).  The binding can be rescued by adding 1 mM
      Ca2+.  This binding behavior resembles that of the blunt end cutter EcoRV.  Furthermore, the
      cleavage activity of the [Glu130]EcoRI is stimulated by Ca2+.  Therefore, a second metal
      binding site is involved in [Glu130]EcoRI catalyzed DNA cleavage.  Its location is postulated
      to be in the inner arm region at positions 133 and 135 presenting an Asp-Xaa-Asp motif typical
      for Ca2+ binding.  A new positive charge at the tip of the inner arm due to the basic amino
      acids Lys130 and Arg131 in the wild-type enzyme or due to binding of a divalent cation in the
      mutants is important for DNA recognition by EcoRI.  However, a direct phosphate contact
      providing an indirect readout is not observed.  Implications of the binding and cleavage
      behavior with regard to mechanistic differences between blunt end and sticky end cutters and a
      general catalytic mechanism of restriction enzymes are discussed.
AU  - Windolph S
AU  - Alves J
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1997 244: 134-139.

PMID- 9235992
VI  - 36
DP  - 1997
TI  - Sequence context influencing cleavage activity of the K130E mutant of the restriction endonuclease EcoRI identified by a site selection assay.
PG  - 9478-9485
AB  - We have generated several EcoRI mutants which exhibit a decreased cleavage rate on one of the
      five specific cleavage sites in bacteriophage lambda-DNA.  To study the influence of the
      sequence context on the cleavage rate in more detail, we developed a site selection assay.
      From a complete set of 4096 plasmid substrates, differing in three bases on both sides of a
      recognition sequence, optimal (best cut) and unfavorable (worst cut) sequences were selected
      by repeated limited digestion, separation, and in vivo amplification of cleaved and uncleaved
      plasmids.  In order to compare the sequence preferences of the inner arm mutant K130E and the
      wild type enzyme, the cleavage rates and sequences of individual plasmids from the resulting
      pools were determined.  The inner arm mutant K130E selected pools with clearly defined
      consensus sequences and a high amount of palindromic sequences.  The cleavage rates of the
      selected sequences are specific for the K130E mutant as is shown by their cleavage with other
      mutants.  In contrast, wild type EcoRI does not lead to a selection in this assay.  Pre-steady
      state kinetics show that preferences for a certain sequence context are a result of
      differences in the dissociation rates of the wild type enzyme.  EcoRI is evolved to
      efficiently recognize and cleave each nonmethylated DNA invading the cell.  Therefore, a fast
      dissociation after cleavage is not mandatory.
AU  - Windolph S
AU  - Fritz A
AU  - Oelgeschlager T
AU  - Wolfes H
AU  - Alves J
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1997 36: 9478-9485.

PMID- 2730638
VI  - 160
DP  - 1989
TI  - Increased chromosomal radiosensitivity of a Chinese hamster ovary cell line that inducibly expresses the EcoRI restriction endonuclease.
PG  - 1079-1084
AB  - We have transfected a Chinese hamster ovary cell line (CHO 6) with a plasmid
      that inducibly expresses the EcoRI restriction endonuclease gene in the
      presence of cadmium sulfate (CdSO4).  Expression of EcoRI results in DNA
      double-strand breaks, which can lead to chromosome aberrations.  The new line,
      designated CHO 10, also has a low level of constitutive expression of EcoRI in
      the absence of CdSO4 without any cytogenetic effect.  This suggested that these
      cells may be efficient at repairing low levels of DNA double-strand breaks.  To
      test this, both cell lines were exposed to ionizing radiation, and aberration
      yields were analyzed with or without induction of EcoRI.  CHO 10 cells showed
      increased radiosensitivity after G1 irradiation, but after G2 exposure, only
      doses > 0.4 Gy caused more damage in CHO 10 cells.  We conclude that CHO 10
      cells can tolerate constitutive expression of EcoRI, but that when the cells
      are subjected to additional stress, in this case ionizing radiation, they
      become very sensitive to DNA double-strand breaks.
AU  - Winegar RA
AU  - Land MC
AU  - Morgan WF
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1989 160: 1079-1084.

PMID- 2536473
VI  - 225
DP  - 1989
TI  - Cell electroporation is a highly efficient method for introducing restriction endonucleases into cells.
PG  - 49-53
AB  - Restriction endonucleases that make either blunt- or cohesive-end DNA
      double-strand breaks can induce chromosome aberrations.  We have used cell
      electroporation with great success to permeabilize Chinese hamster ovary cells
      for the introduction of restriction enzymes.  The introduction of restriction
      enzymes by this method resulted in extremely high frequences (>90%) of aberrant
      metaphase cells and also a dramatic decrease in cell survival, as measured by
      subsequent colony formation.  Cell electroporation by itself caused no increase
      in aberrant chromosomes and had only a slight effect on cell survival.
AU  - Winegar RA
AU  - Phillips JW
AU  - Youngblom JH
AU  - Morgan WF
PT  - Journal Article
TA  - Mutat. Res.
JT  - Mutat. Res.
SO  - Mutat. Res. 1989 225: 49-53.

PMID- 8575244
VI  - 104
DP  - 1996
TI  - Introduction of a DNA methyltransferase into Drosophila to probe chromatin structure in vivo.
PG  - 332-340
AB  - The dam DNA methyltransferase gene from Escherichia coli was introduced into Drosophila in
      order to probe chromatin structure in vivo.  Expression of the gene caused no visible defects
      or developmental delay even at high levels of active methylase.  About half of each target
      site was found to be methylated in vivo, apparently reflecting a general property of chromatin
      packaged in nucleosomes.  Although site-specific differences were detected, most euchromatic
      and heterochromatic sites showed comparable degrees of methylation, at least at high methylase
      levels.  Methylase accessibility of a lacZ reporter gene subject to position-effect
      variegation throughout development was only slightly reduced, consistent with studies of
      chromatin accessibility in vitro.  Silencing of lacZ during development differed from
      silencing of an adjacent white eye pigment reporter gene in the adult, as though chromatin
      structure can undergo dynamic alterations during development.
AU  - Wines DR
AU  - Talbert PB
AU  - Clark DV
AU  - Henikoff S
PT  - Journal Article
TA  - Chromosoma
JT  - Chromosoma
SO  - Chromosoma 1996 104: 332-340.

PMID- 18344351
VI  - 74
DP  - 2008
TI  - Randomly amplified polymorphic DNA PCR as a tool for assessment of marine viral richness.
PG  - 2612-2618
AB  - Recent discoveries have uncovered considerable genetic diversity among
      aquatic viruses and raised questions about the variability of this
      diversity within and between environments. Studies of the temporal and
      spatial dynamics of aquatic viral assemblages have been hindered by the
      lack of a common genetic marker among viruses for rapid diversity
      assessments. Randomly amplified polymorphic DNA (RAPD) PCR bypasses this
      obstacle by sampling at the genetic level without requiring viral
      isolation or previous sequence knowledge. In this study, the utility of
      RAPD-PCR for assessing DNA viral richness within Chesapeake Bay water
      samples was evaluated. RAPD-PCR using single 10-mer oligonucleotide
      primers successfully produced amplicons from a variety of viral samples,
      and banding patterns were highly reproducible, indicating that each band
      likely represents a single amplicon originating from viral template DNA.
      In agreement with observations from other community profiling techniques,
      resulting RAPD-PCR banding patterns revealed more temporal than spatial
      variability in Chesapeake Bay virioplankton assemblages. High-quality
      hybridization probes and sequence information were also easily generated
      from single RAPD-PCR products or whole reactions. Thus, the RAPD-PCR
      technique appears to be practical and efficient for routine use in
      high-resolution viral diversity studies by providing assemblage
      comparisons through fingerprinting, probing, or sequence information.
AU  - Winget DM
AU  - Wommack KE
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2008 74: 2612-2618.

PMID- 1931982
VI  - 30
DP  - 1991
TI  - Enhanced reactivity of a B-Z junction for cleavage by the restriction enzyme MboI.
PG  - 10601-10606
AB  - We have been investigating the structure, dynamics, and ligand-binding
      properties of the interface that exists between a right-handed conformation and
      a left-handed conformation (i.e., a B-Z junction) in synthetic DNA oligomers.
      Since exo- and endonuclease activity is known to be sensitive to the
      conformation of the template DNA, we have designed and synthesized a DNA
      oligonucleotide of 20 base pairs (designated as BZ-III) with an MboI
      recognition site (GATC) at the location of a potential B-Z junction.  The
      activity of the MboI enzyme toward this molecule and DNA oligomers that contain
      multiple MboI sites located at B-Z junctions was monitored in the absence and
      presence of the Z-conformation-inducing reagent cobalt hexaammine.  In all
      cases, the activity of the enzyme was enhanced in the presence of cobalt
      hexaammine.  The activity of MboI toward BZ-III, in the presence and absence of
      cobalt hexaammine, was also examined when the DNA oligomer is also in the
      presence of the DNA binding drugs actinomycin D, ametantrone, or ethidium
      bromide.  In all cases, the activity of the enzyme was inhibited in the
      presence of drug.  The results suggest that B-Z junctions are structurally
      unique and that this uniqueness may alter nuclease activity at sites in or near
      the junction.
AU  - Winkle SA
AU  - Aloyo MC
AU  - Morales N
AU  - Zambrano TY
AU  - Sheardy RD
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1991 30: 10601-10606.

PMID- 1727392
VI  - 6
DP  - 1992
TI  - Junctions affect the sensitivity of DNAs to reactions with enzymes.
PG  - A219
AB  - We have investigated the reactions of various enzymes with DNAs possessing junctions, for
      example: BZI C*GC*GC*GC*GACTGACTG; BZIII ATC*GC*GC*GC*GATCAGTCAGT; BZIV TCGACGCGCGCGATCAGTCA
      (where C* is 5-methylC and where potential junctions are underlined). DNase I and Exonuclease
      III show inhibited cleavage at the junctions both under low salt B conditions and in the
      presence of Z-inducing cobalt hexamine. Restriction enzymes attacking either the junction or,
      when BZ IV is inserted into a plasmid, sequences flanking the inserted BZ IV sequence show
      enhanced cleavage in the presence of cobalt hexamine or supercoiling. Dam methylase has
      enhanced reactivity for the GATC at the junction of BZ IV in the presence of cobalt hexamine.
      These results suggest that these junctions have a structural distinctiveness recognizable by
      various enzyme types.
AU  - Winkle SA
AU  - Aloyo MC
AU  - Smoller JH
AU  - Herrera JE
AU  - Chaires JB
AU  - Sheardy RD
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1992 6: A219.

PMID- 
VI  - 82
DP  - 2002
TI  - The effects of alternate DNA structures on restriction enzyme and polymerase binding and activities with DNAS.
PG  - 463a
AB  - The variety of structural motifs which DNA molecules may assume, depending upon sequence,
      affects the activities of proteins using DNA as a substrate.  We have examined the effects of
      the (CG)3 segment and cruciform structures found in phiX174 RF DNA (in the linear and
      supercoiled forms) on E. coli DNA polymerase I binding and activity.  Gel mobility shift
      assays of DNA fragments containing these features suggest that DNA polymerase binds to these
      structural features.  Polymerase activity studies, including studies under PCR conditions,
      indicate that the structures alter the activity.  Cleavage studies at or near these structures
      by restriction enzymes, e.g., BssHII, HhaI, also show anomalies.  Binding of restriction
      enzymes and DNA polymerase I to small DNA hairpins was also investigated using gel mobility
      shift assays.  The results of these studies suggest that local structures do affect the
      workings of enzymes and thus these structures may help regulate enzyme activities.
AU  - Winkle SA
AU  - Thomson H
AU  - Aguilar LP
AU  - Sheardy RD
PT  - Journal Article
TA  - Biophys. J.
JT  - Biophys. J.
SO  - Biophys. J. 2002 82: 463a.

PMID- Not included in PubMed...
VI  - 2
DP  - 1992
TI  - Structure and function of restriction endonucleases.
PG  - 93-99
AB  - New insight into how restriction endonucleases achieve their remarkable sequence specificity
      has been gained by comparing the structures of EcoRI and EcoRV endonucleases complexed with
      DNA fragments that contain their respective canonical sites. Despite the lack of overall
      structural homology, essential features of the catalytic site, including the locations of two
      acidic and one lysine residue, are structurally conserved. Mutagenesis studies, newly
      initiated for the EcoRV enzyme, have confirmed the essential nature of these particular
      residues but have also yielded interesting effects that were quite unforeseen.
AU  - Winkler FK
PT  - Journal Article
TA  - Curr. Opin. Struct. Biol.
JT  - Curr. Opin. Struct. Biol.
SO  - Curr. Opin. Struct. Biol. 1992 2: 93-99.

PMID- 8081744
VI  - 2
DP  - 1994
TI  - DNA totally flipped-out by methylase.
PG  - 79-83
AB  - In research, surprises are always refreshing and stimulating. The latest such example in the
      field of protein-DNA interactions is provided by Klimasauskas et al. reporting the crystal
      structure determination of the enzyme HhaI methylase from Haemophilus haemolyticus, a DNA
      cytosine-5-methyltransferase (m5C-MTase), covalently bound to a 13-mer DNA duplex (Fig.1). The
      covalent complex represents a chemically trapped reaction intermediate and also contains
      S-adenosyl-L-methionine (AdoMet). The most spectacular and unexpected feature of this
      structure is that the target cytosine base is completely flipped out of the DNA duplex and in
      its place the DNA is infiltrated by a glutamine and a serine side chain from the major and
      minor groove side respectively. Just as we are becoming accustomed to drastic amounts of
      bending, kinking, unwinding and base-pair unstacking, most notably by the TATA box binding
      protein or the endonucleases EcoRI and EcoRV, this enzyme goes even further by forcing its
      substrate DNA to flip out the base it is going to methylate.
AU  - Winkler FK
PT  - Journal Article
TA  - Structure
JT  - Structure
SO  - Structure 1994 2: 79-83.

PMID- 7902723
VI  - 6
DP  - 1994
TI  - Restriction endonucleases, the ultimate in sequence specific DNA recognition.
PG  - 9
AB  - X-ray crystallographic and NMR spectroscopic studies with a variety of proteins that interact
      in a sequence-specific manner with DNA have revealed a wealth of detailed structural
      information over the past few years. It has become clear that DNA sequence recognition or
      discrimination can be achieved in many different ways and that conformational changes in
      protein and DNA often accompany the binding. Among the systems studied, mostly DNA binding
      proteins involved in transcriptional control, restriction endonucleases demonstrate the
      highest discrimination between cognate and noncognate DNA sequences. The structures of two
      type II restriction endonucleases, EcoRI and EcoRV recognizing the hexamer sequences GAATTC
      and GATATC respectively, have thus far been determined as complexes with cognate DNA
      fragments. The structural and functional data now available for these two enzymes have yielded
      important insights into how they achieve their remarkable specificity. The two enzymes show no
      structural similarity except in their active site region where the arrangement of two acidic
      and one basic residue appears conserved. Both enzymes bind their cognate DNA fragments in
      rather distorted conformations but the distortions are completely different in the two cases.
      Recognition involves the formation of hydrogen bonds to the base pairs in the major groove and
      the extended set of interactions appears highly cooperative. However, the distorted
      conformation of productively bound DNA plays an important role too. It provides extra
      discrimination against noncognate sequences and appears crucial in coupling proper recognition
      to efficient catalysis.
AU  - Winkler FK
PT  - Journal Article
TA  - J. Mol. Recognit.
JT  - J. Mol. Recognit.
SO  - J. Mol. Recognit. 1994 6: 9.

PMID- 8491171
VI  - 12
DP  - 1993
TI  - The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments.
PG  - 1781-1795
AB  - The crystal structure of EcoRV endonuclease has been determined at 2.5 A resolution and that
      of its complexes with the cognate DNA decamer GGGATATCC (recognition sequence underlined) and
      the non-cognate DNA octamer CGAGCTCG at 3.0 A resolution. Two octamer duplexes of the
      non-cognate DNA, stacked end-to-end, are bound to the dimeric enzyme in B-DNA like
      conformations. The protein-DNA interactions of this complex are prototypic for non-specific
      DNA binding. In contrast, only one cognate decamer duplex is bound and deviates considerably
      from canonical B-form DNA. Most notably, a kink of approximately 50 degrees is observed at the
      central TA step with a concomitant compression of the major groove. Base-specific hydrogen
      bonds between the enzyme and the recognition base pairs occur exclusively in the major groove.
      These interactions appear highly co-operative as they are all made through one short surface
      loop comprising residues 182-186. Numerous contacts with the sugar phosphate backbone
      extending beyond the recognition sequence are observed in both types of complex. However, the
      total surface area buried on complex formation is >1800 A2 larger in the case of cognate DNA
      binding. Two acidic side chains, Asp74 and Asp90, are close to the reactive phosphodiester
      group in the cognate complex and most probably provide oxygen ligands for binding the
      essential cofactor Mg2+. An important role is also indicated for Lys92, which together with
      the two acidic functions appears to be conserved in the otherwise unrelated structure of EcoRI
      endonuclease. The structural results give new insight into the physical basis of the
      remarkable sequence specificity of this enzyme.
AU  - Winkler FK
AU  - Banner DW
AU  - Oefner C
AU  - Tsernoglou D
AU  - Brown RS
AU  - Heathman SP
AU  - Bryan RK
AU  - Martin PD
AU  - Petratos K
AU  - Wilson KS
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1993 12: 1781-1795.

PMID- 
VI  - 0
DP  - 1987
TI  - Structural studies of EcoRV endonuclease and of its complexes with short DNA fragments.
PG  - 345-352
AB  - None
AU  - Winkler FK
AU  - Brown RS
AU  - Leonard K
AU  - Berriman J
PT  - Journal Article
TA  - Nato Advanced Studies: Crystallography in Molecular Biology
JT  - Nato Advanced Studies: Crystallography in Molecular Biology
SO  - Nato Advanced Studies: Crystallography in Molecular Biology 1987 0: 345-352.

PMID- 1992160
VI  - 217
DP  - 1991
TI  - Crystallization of complexes of EcoRV endonuclease with cognate and non-cognate DNA fragments.
PG  - 235-238
AB  - Complexes of the type II restriction endonuclease EcoRV with a variety of
      short, self-complementary deoxyoligonucleotides have been crystallized.  The
      best crytals diffract to about 2.7 angstrom resolution and consist of 1:1
      complexes between endonuclease dimers and duplexes of the cognate decamer
      GGGATATCCC containing the hexameric EcoRV recognition sequence GATATC.
      Crystals with the non-cognate DNA octamer duplexes CGAGCTCG and CGAATTCG
      diffract to 3.0 and 3.5 angstrom resolution, respectively, and contain two DNA
      duplexes per enzyme dimer.
AU  - Winkler FK
AU  - D'Arcy A
AU  - Blocker H
AU  - Frank R
AU  - van Boom JH
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1991 217: 235-238.

PMID- 
VI  - 14
DP  - 2004
TI  - Structure and function of EcoRV endonuclease.
PG  - 179-214
AB  - The homodimeric, orthodox Type II restriction endonuclease EcoRV cleaves double-stranded DNA
      with high specificity at hexameric GAT/ATC sites in a blunt-ended fashion.  Like most of the
      restriction enzymes used as tools in recombinant DNA technology it can be considered as a
      simple hydrolytic enzyme of relatively small size with precisely defined substrate specificity
      and the rather common requirement for Mg2+ ions.  Yet, these apparently simple enzymes become
      fascinating objects for structural and functional studies, and their molecular simplicity
      becomes an advantage once we start asking detailed mechanistic questions.  For example, it is
      quite obvious that these enzymes have been engineered by evolution to deal with the problem of
      efficiently locating a specific site on DNA, which is immersed in a huge molar excess of
      other, partly very similar sites.
AU  - Winkler FK
AU  - Prota AE
PT  - Journal Article
TA  - Nucleic Acids Mol. Biol.
JT  - Nucleic Acids Mol. Biol.
SO  - Nucleic Acids Mol. Biol. 2004 14: 179-214.

PMID- 
VI  - 
DP  - 1980
TI  - Isolation and characterization of a sequence specific restriction endonuclease from Rhizobium lupini.
PG  - 1-135
AB  - None
AU  - Winkler K-P
PT  - Journal Article
TA  - Ph.D. Thesis, Erlangen University, W. Germany
JT  - Ph.D. Thesis, Erlangen University, W. Germany
SO  - Ph.D. Thesis, Erlangen University, W. Germany 1980 : 1-135.

PMID- 
VI  - 
DP  - 1997
TI  - Investigation of de novo methylation activity in mutants of the EcoKI methyltransferase.
PG  - 1-216
AB  - A group of mutants of the EcoKI R/M-system displaying de novo methylation activity have been
      isolated.  The mutated genes were transferred into an overexpressing plasmid vector.  Two of
      the over-expressed proteins were purified to near homogeneity from clones transformed with the
      plasmids.  Cofactor binding activities of wild-type and the two mutant enzymes were compared
      by 1,8-anilino-napthalene sulphonic acid fluorescence displacement experiments.  A DNA
      methylation assay based upon the transfer of a tritiated methyl group from the cofactor AdoMet
      to the substrate DNA was established and used to examine the dependency of the reaction on
      cofactor, substrate, and enzyme concentration.  In addition the stability of the trimeric
      enzyme at different protein concentrations was followed by HPLC gel filtration.  Sequence
      alignments, secondary structure predictions, and tertiary structural modelling were used to
      show the similarity of the Type I system EcoKI with methyltransferases from other classes
      (especially Type II methyltransferases), thereby establishing a structural and suggesting an
      evolutionary link between the different methyltransferase classes.  The information obtained
      by these comparisons enabled the subsequent modelling of a more refined model of the EcoKI
      structure.  A model is proposed to explain the different activities observed in wild-type and
      mutant enzymes based on the biochemical and structural data obtained during these
      investigations.
AU  - Winter M
PT  - Journal Article
TA  - Ph.D. Thesis, University of Edinburgh, Edinburgh, Scotland
JT  - Ph.D. Thesis, University of Edinburgh, Edinburgh, Scotland
SO  - Ph.D. Thesis, University of Edinburgh, Edinburgh, Scotland 1997 : 1-216.

PMID- 16489347
VI  - 4
DP  - 2006
TI  - N-6-methyl-adenine: an epigenetic signal for DNA-protein interactions.
PG  - 183-192
AB  - N6-methyl-adenine is found in the genomes of bacteria, archaea, protists and fungi.  Most
      bacterial DNA adenine methyltransferases are part of restriction-modification systems.
      Certain groups of Proteobacteria also harbour solitary DNA adenine methyltransferases that
      provide signals for DNA-protein interactions.  In gamma-proteobacteria, Dam methylation
      regulates chromosome replication, nucleoid segregation, DNA repair, transposition of insertion
      elements and transcription of specific genes.  In Salmonella, Haemophilus, Yersinia and Vibrio
      species and in pathogenic Escherichia coli, Dam methylation is required for virulence.  In
      alpha-proteobacteria, CcrM methylation regulates the cell cycle in Caulobacter, Rhizobium and
      Agrobacterium, and has a role in Brucella abortus infection.
AU  - Wion D
AU  - Casadesus J
PT  - Journal Article
TA  - Nat. Rev. Microbiol.
JT  - Nat. Rev. Microbiol.
SO  - Nat. Rev. Microbiol. 2006 4: 183-192.

PMID- 21304702
VI  - 2
DP  - 2010
TI  - Complete genome sequence of Thermocrinis albus type strain (HI 11/12).
PG  - 194-202
AB  - Thermocrinis albus Eder and Huber 2002 is one of three species in the genus Thermocrinis in
      the family Aquificaceae. Members of this family have become of
      significant interest because of their involvement in global biogeochemical cycles
      in high-temperature ecosystems. This interest had already spurred several genome
      sequencing projects for members of the family. We here report the first completed
      genome sequence a member of the genus Thermocrinis and the first type strain
      genome from a member of the family Aquificaceae. The 1,500,577 bp long genome
      with its 1,603 protein-coding and 47 RNA genes is part of the Genomic
      Encyclopedia of Bacteria and Archaea project.
AU  - Wirth R et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 2: 194-202.

PMID- 21677854
VI  - 4
DP  - 2011
TI  - Complete genome sequence of Desulfurococcus mucosus type strain (O7/1).
PG  - 173-182
AB  - Desulfurococcus mucosus Zillig and Stetter 1983 is the type species of the genus
      Desulfurococcus, which belongs to the crenarchaeal family Desulfurococcaceae. The
      species is of interest because of its position in the tree of life, its ability
      for sulfur respiration, and several biotechnologically relevant thermostable and
      thermoactive extracellular enzymes. This is the third completed genome sequence
      of a member of the genus Desulfurococcus and already the 8(th) sequence from a
      member the family Desulfurococcaceae. The 1,314,639 bp long genome with its 1,371
      protein-coding and 50 RNA genes is a part of the Genomic Encyclopedia of Bacteria
      and Archaea project.
AU  - Wirth R et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 4: 173-182.

PMID- 22843585
VI  - 194
DP  - 2012
TI  - Complete Genome Sequences of Mycoplasma leachii Strain PG50T and the Pathogenic Mycoplasma mycoides subsp. mycoides Small Colony Biotype Strain Gladysdale.
PG  - 4448-4449
AB  - Mycoplasma mycoides subsp. mycoides small colony biotype (SC) is the high-consequence animal
      pathogen causing contagious bovine pleuropneumonia. We
      report the complete genome sequences of the pathogenic strain M. mycoides subsp.
      mycoides SC Gladysdale and a close phylogenetic relative, Mycoplasma leachii
      PG50(T), another bovine pathogen of the M. mycoides phylogenetic clade.
AU  - Wise KS
AU  - Calcutt MJ
AU  - Foecking MF
AU  - Madupu R
AU  - Deboy RT
AU  - Roske K
AU  - Hvinden ML
AU  - Martin TR
AU  - Durkin AS
AU  - Glass JI
AU  - Methe BA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4448-4449.

PMID- 22216014
VI  - 7
DP  - 2011
TI  - Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments.
PG  - e1002430
AB  - Fossil records indicate that life appeared in marine environments ,3.5 billion years ago (Gyr)
      and transitioned to terrestrial
      ecosystems nearly 2.5 Gyr. Sequence analysis suggests that 'hydrobacteria' and
      'terrabacteria' might have diverged as early as 3 Gyr. Bacteria of the genus Azospirillum
      are associated with roots of terrestrial plants; however, virtually all their close relatives
      are aquatic. We obtained genome sequences of two Azospirillum species and analyzed their gene
      origins.
      While most Azospirillum house-keeping genes have orthologs in its close aquatic relatives,
      this lineage has obtained nearly half of its genome from terrestrial organisms. The majority
      of genes encoding functions critical for association with plants are among horizontally
      transferred genes. Our results show that transition of some aquatic bacteria to terrestrial
      habitats
      occurred much later than the suggested initial divergence of hydro- and terrabacterial clades.
      The birth of the genus Azospirillum approximately coincided with the emergence of vascular
      plants on land.
AU  - Wisniewski-Dye F et al
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2011 7: e1002430.

PMID- 28078050
VI  - 12
DP  - 2017
TI  - Complete genome sequence of Lutibacter profundi LP1T isolated from an Arctic deep-sea hydrothermal vent system.
PG  - 5
AB  - Lutibacter profundi LP1T within the family Flavobacteriaceae was isolated from a  biofilm
      growing on the surface of a black smoker chimney at the Loki's Castle
      vent field, located on the Arctic Mid-Ocean Ridge. The complete genome of L.
      profundi LP1T is the first genome to be published within the genus Lutibacter. L.
      profundi LP1T consists of a single 2,966,978 bp circular chromosome with a GC
      content of 29.8%. The genome comprises 2,537 protein-coding genes, 40 tRNA
      species and 2 rRNA operons. The microaerophilic, organotrophic isolate contains
      genes for all central carbohydrate metabolic pathways. However, genes for the
      oxidative branch of the pentose-phosphate-pathway, the glyoxylate shunt of the
      tricarboxylic acid cycle and the ATP citrate lyase for reverse TCA are not
      present. L. profundi LP1T utilizes starch, sucrose and diverse proteinous carbon
      sources. In accordance, the genome harbours 130 proteases and 104
      carbohydrate-active enzymes, indicating a specialization in degrading organic
      matter. Among a small arsenal of 24 glycosyl hydrolases, which offer the
      possibility to hydrolyse diverse poly- and oligosaccharides, a starch utilization
      cluster was identified. Furthermore, a variety of enzymes may be secreted via
      T9SS and contribute to the hydrolytic variety of the microorganism. Genes for
      gliding motility are present, which may enable the bacteria to move within the
      biofilm. A substantial number of genes encoding for extracellular polysaccharide
      synthesis pathways, curli fibres and attachment to surfaces could mediate
      adhesion in the biofilm and may contribute to the biofilm formation. In addition
      to aerobic respiration, the complete denitrification pathway and genes for
      sulphide oxidation e.g. sulphide:quinone reductase are present in the genome.
      sulphide:quinone reductase and denitrification may serve as detoxification
      systems allowing L. profundi LP1T to thrive in a sulphide and nitrate enriched
      environment. The information gained from the genome gives a greater insight in
      the functional role of L. profundi LP1T in the biofilm and its adaption strategy
      in an extreme environment.
AU  - Wissuwa J
AU  - Bauer SL
AU  - Steen IH
AU  - Stokke R
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 5.

PMID- 26913091
VI  - 11
DP  - 2016
TI  - Isolation and complete genome sequence of the thermophilic Geobacillus sp. 12AMOR1 from an Arctic deep-sea hydrothermal vent site.
PG  - 16
AB  - Members of the genus Geobacillus have been isolated from a wide variety of habitats worldwide
      and are the subject for targeted enzyme utilization in various
      industrial applications. Here we report the isolation and complete genome
      sequence of the thermophilic starch-degrading Geobacillus sp. 12AMOR1. The strain
      12AMOR1 was isolated from deep-sea hot sediment at the Jan Mayen hydrothermal
      Vent Site. Geobacillus sp. 12AMOR1 consists of a 3,410,035 bp circular chromosome
      and a 32,689 bp plasmid with a G + C content of 52 % and 47 %, respectively. The
      genome comprises 3323 protein-coding genes, 88 tRNA species and 10 rRNA operons.
      The isolate grows on a suite of sugars, complex polysaccharides and proteinous
      carbon sources. Accordingly, a versatility of genes encoding carbohydrate-active
      enzymes (CAZy) and peptidases were identified in the genome. Expression,
      purification and characterization of an enzyme of the glycoside hydrolase family
      13 revealed a starch-degrading capacity and high thermal stability with a melting
      temperature of 76.4 degrees C. Altogether, the data obtained point to a new
      isolate from a marine hydrothermal vent with a large bioprospecting potential.
AU  - Wissuwa J
AU  - Stokke R
AU  - Fedoy AE
AU  - Lian K
AU  - Smalas AO
AU  - Steen IH
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 16.

PMID- 1475187
VI  - 20
DP  - 1992
TI  - Structure and evolution of the XcyI restriction-modification system.
PG  - 6267-6273
AB  - The XcyI restriction-modificaton system from Xanthomonas cyanopsidis recognizes the sequence,
      CCCGGG. The XcyI endonuclease and methylase genes have been cloned and sequenced and were
      found to be aligned in a head to tail orientation with the methylase preceding and overlapping
      the endonuclease by one base pair. The nucleotide sequence codes for an N4 cytosine
      methyltransferase with a predicted molecular weight of 33,500 and an endonuclease comprised of
      333 codons and a molecular weight of 36,600. Sequence comparisons revealed significant
      similarity between the XcyI, CfrI and SmaI methylisomers. in contrast, no similarity was
      detected between the primary structures of the XcyI and SmaI endonucleases. The XcyI
      restriction-modification system is highly homologous to the XmaI genes, although the DNA
      sequences flanking the genes rapidly diverge. The sequence of the XcyI endonuclease contains
      two motifs which have recently been identified as essential to the activity of the EcoRV
      endonuclease.
AU  - Withers BE
AU  - Ambroso LA
AU  - Dunbar JC
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 6267-6273.

PMID- 7567471
VI  - 23
DP  - 1995
TI  - DNA determinants in sequence-specific recognition by XmaI endonuclease.
PG  - 3571-3577
AB  - The XmaI endonuclease recognizes and cleaves the sequence C/CCGGG.  Magnesium is required for
      catalysis, however, the enzyme forms stable, specific complexes with DNA in the absence of
      magnesium.  An association constant of 1.2 x 10/9 M was estimated for the affinity of the
      enzyme for a specific 195 bp fragment.  Competition assays revealed that the site-specific
      association constant represented an approximately 10/4-fold increase in affinity over that for
      non-cognate sites.  Missing nucleoside analyses suggested an interaction of the enzyme with
      each of the cytosines and guanines within the recognition site.  Recognition of each of the
      guanines was also indicated by dimethylsulfate interference footprinting assays.  The
      phosphates 5' to the guanines within the recognition site appeared to be the major sites of
      interaction of XmaI with the sugar-phosphate backbone.  No significant interaction of the
      protein was observed with phosphates flanking the recognition sequence.  Comparison of the
      footprinting patterns of XmaI with those of the neoschizomer SmaI (CCC/GGG) revealed that the
      two enzymes utilize the same DNA determinants in their specific interaction with the CCCGGG
      recognition site.
AU  - Withers BE
AU  - Dunbar JC
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1995 23: 3571-3577.

PMID- 8332454
VI  - 21
DP  - 1993
TI  - The endonuclease isoschizomers, SmaI and XmaI bend DNA in opposite orientations.
PG  - 2571-2577
AB  - The SmaI and XmaI endonucleases are imperfect isoschizomers that recognize the sequence
      CCCGGG. SmaI cleaves between the internal CpG to produce blunt end scissions whereas XmaI
      cleaves between the external cytosines to produce a four base, five prime overhang. Each of
      the endonucleases forms stable, specific complexes with DNA in the absence of magnesium.
      Circular permutation analyses of the protein-DNA complexes revealed that each of the
      endonucleases induces bending of the DNA. Phase sensitive detection analyses verified the
      existence of the SmaI and XmaI induced bends. Furthermore bending of the helix axis by the
      endonucleases appeared to be directed in opposite orientations. The orientation of the
      SmaI-induced bend appeared to be towards the major groove and is reminiscent of the direction
      of the bend induced by EcoRV which similarly induces blunt end scissions. Conversely, XmaI
      appeared to bend the DNA towards the minor groove.
AU  - Withers BE
AU  - Dunbar JC
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 2571-2577.

PMID- 7896784
VI  - 270
DP  - 1995
TI  - Sequence-specific DNA recognition by the SmaI endonuclease.
PG  - 6496-6504
AB  - SmaI endonuclease recognizes and cleaves the sequence CCC/GGG. The enzyme requires magnesium
      for catalysis; however, equilibrium binding assays revealed that the enzyme binds specifically
      to DNA in the absence of magnesium. A specific association constant of 0.9 x 10/8 M-1 was
      determined for SmaI binding to a 22-base duplex oligonucleotide. Furthermore, the KA was a
      function of the length of the DNA substrate and the enzyme exhibited an affinity of 1.2 x 10/9
      M-1 for a 195-base pair fragment and which represented a 10/4-fold increase in affinity over
      binding to nonspecific sequences. A Km of 17.5 nM was estimated from kinetic assays based on
      cleavage of the 22-base oligonucleotide and is not significantly different from the KD
      estimated from the thermodynamic analyses. Footprinting (dimethyl sulfate and missing
      nucleoside) analyses revealed that SmaI interacts with each of the base pairs within the
      recognition sequence. Ethylation interference assays suggested that the protein contacts three
      adjacent phosphages on each strand of the recognition sequence. Significantly, a predicted
      protein contact with the phosphate 3' of the scissile bond may have implications in the
      mechanism of catalysis by SmaI.
AU  - Withers BE
AU  - Dunbar JC
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1995 270: 6496-6504.

PMID- 23144378
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence for Pseudomonas aeruginosa Strain PAO579, a Mucoid Derivative of PAO381.
PG  - 6617
AB  - Pseudomonas aeruginosa is an opportunistic pathogen that establishes a chronic lung infection
      in individuals afflicted with cystic fibrosis. Here, we announce
      the draft genome of P. aeruginosa strain PAO579, an alginate-overproducing
      derivative of strain PAO381.
AU  - Withers TR
AU  - Johnson SL
AU  - Yu HD
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6617.

PMID- 6260969
VI  - 37
DP  - 1981
TI  - Restriction and modification of Bacteriophage SP10 DNA by Bacillus subtilis Marburg 168: Stabilization of SP10 DNA in restricting hosts preinfected with a heterologous phage, SP18.
PG  - 148-155
AB  - SP10 phage cannot propagate in Bacillus subtilis Marburg 168 containing the
      wild-type allele of either gene nonA or gene nonB.  The latter gene codes for
      the intrinsic cellular restriction activity.  SP10 DNA was degraded in nonB+
      derivatives of Marburg 168.  The degree of degradation depended upon the
      previous host in which SP10 was propagated.  In the case of SP10 grown in B.
      subtilis W23 (a nonrestricting, nonmodifying bacterium), 90% of the phage DNA
      was hydrolyzed to acid solubles, and the residual acid-precipitable material
      was recovered as 0.5- to 1-megadalton fragments.  In contrast, if SP10 was
      propagated in B. subtilis PS9W7 (a nonA nonB derivative of Marbury 168 that
      retains modifying activity), 40 to 50% of the input DNA was degraded to acid
      solubles, and most of the remainder was recovered as 15- to 20-megadalton
      fragments.  In nonA+ nonB cells, SP10 DNA was conerved as unit-length molecules
      (ca. 80 megadalton).  Prior infection of nonB+ cells with SP18 protected
      superinfecting SP10 DNA, even when rifampin or chloramphenicol was added before
      the primary infection.  The data are discussed in terms of the following
      conclusions.  (i) The nonB gene product of B. subtilis Marburg 168 is required
      for restriction of SP10 DNA.  (ii) Some sites on SP10 DNA are sensitive to both
      the restricting and modifying activities, whereas other sites are nonmodifiable
      even though they are sensitive to the restriction enzyme.  (iii)  In some
      manner, SP18 antagonizes the action of the nonB gene product.
AU  - Witmer H
AU  - Franks M
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 1981 37: 148-155.

PMID- 26294621
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of the Novel Temperate Clostridium difficile Phage phiCDIF1296T.
PG  - e00839-15
AB  - Clostridium difficile contains many integrated and extrachromosomal genetic elements. In this
      study, we determined, annotated, and analyzed the complete
      genome of the C. difficile bacteriophage phiCDIF1296T using single-molecule
      real-time sequencing technology. To our knowledge, this represents the largest
      genome (131 kb) of a temperate C. difficile phage recognized so far.
AU  - Wittmann J
AU  - Riedel T
AU  - Bunk B
AU  - Sproer C
AU  - Gronow S
AU  - Overmann J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00839-15.

PMID- 9461409
VI  - 206
DP  - 1998
TI  - Degenerate DNA recognition by I-PpoI endonuclease.
PG  - 11-21
AB  - The I-PpoI endonuclease is encoded by a group I intron found in the slime mold Physarum
      polycephalum.  To initiate homing of its encoding intron, I-PpoI catalyzes a specific
      double-stranded break within a 15-bp recognition site.  The high substrate specificities of
      I-PpoI and other homing endonucleases make these enzymes valuable tools for genomic mapping
      and sequencing.  Here, we report on the ability of I-PpoI to cleave recognition sites that
      contain a wide variety of mutations generated randomly or deliberately.  We find that much
      degeneracy is tolerated within the recognition site of I-PpoI.  Few single substitutions
      prevent cleavage completely.  In addition, many sites with multiple substitutions are cleaved
      efficiently. In contrast, deletions or insertions within the I-PpoI recognition site are
      detrimental to catalysis, indicating that proper registry between the protein and its
      substrate is critical.  Finally, we find that the sequence of the flanking regions can
      influence catalysis by I-PpoI.  Thus, I-PpoI has both the complex binding specificity of a
      transcription factor and the catalytic ability of a restriction endonuclease.
AU  - Wittmayer PK
AU  - McKenzie JL
AU  - Raines RT
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1998 206: 11-21.

PMID- 22965092
VI  - 194
DP  - 2012
TI  - Genome Sequence of Enterobacter radicincitans DSM16656T, a Plant Growth-Promoting Endophyte.
PG  - 5469
AB  - Enterobacter radicincitans sp. nov. DSM16656(T) represents a new species of the genus
      Enterobacter which is a biological nitrogen-fixing endophytic bacterium
      with growth-promoting effects on a variety of crop and model plant species. The
      presence of genes for nitrogen fixation, phosphorous mobilization, and
      phytohormone production reflects this microbe's potential plant growth-promoting
      activity.
AU  - Witzel K
AU  - Gwinn-Giglio M
AU  - Nadendla S
AU  - Shefchek K
AU  - Ruppel S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5469.

PMID- 2851533
VI  - 5
DP  - 1987
TI  - Enzymatic probes for left-handed Z-DNA.
PG  - 247-256
AB  - DNA is a polymorphic molecule and can adopt a variety of conformations depending mainly on
      base sequence and environmental conditions.  Recent interest in this polymorphism has been
      prompted to a large part by the discovery of Z-DNA, a structure possessing a left-handed helix
      sense as opposed to the canonical right-handed state (B-DNA).  Several findings imply a
      biological function for Z-DNA or B-to-Z transitions.
AU  - Wohlrab F
AU  - Wells RD
PT  - Journal Article
TA  - Gene Amplif. Anal.
JT  - Gene Amplif. Anal.
SO  - Gene Amplif. Anal. 1987 5: 247-256.

PMID- 23248272
VI  - 110
DP  - 2013
TI  - CpG underrepresentation and the bacterial CpG-specific DNA methyltransferase M.MpeI.
PG  - 105-110
AB  - Cytosine methylation promotes deamination. In eukaryotes, CpG methylation is thought to
      account for CpG underrepresentation. Whether scarcity of CpGs in
      prokaryotic genomes is diagnostic for methylation is not clear. Here, we report
      that Mycoplasms tend to be CpG depleted and to harbor a family of constitutively
      expressed or phase variable CpG-specific DNA methyltransferases. The very CpG
      poor Mycoplasma penetrans and its constitutively active CpG-specific
      methyltransferase M.MpeI were chosen for further characterization. Genome-wide
      sequencing of bisulfite-converted DNA indicated that M.MpeI methylated CpG target
      sites both in vivo and in vitro in a locus-nonselective manner. A crystal
      structure of M.MpeI with DNA at 2.15-A resolution showed that the substrate base
      was flipped and that its place in the DNA stack was taken by a glutamine residue.
      A phenylalanine residue was intercalated into the 'weak' CpG step of the
      nonsubstrate strand, indicating mechanistic similarities in the recognition of
      the short CpG target sequence by prokaryotic and eukaryotic DNA
      methyltransferases.
AU  - Wojciechowski M
AU  - Czapinska H
AU  - Bochtler M
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2013 110: 105-110.

PMID- 
VI  - 
DP  - 1998
TI  - The kinetic mechanism of the DNA methyltransferase from Thermus aquaticus and selection of a DNA binding peptide using phage display.
PG  - 1-164
AB  - 
AU  - Wolcke J
PT  - Journal Article
TA  - Ph.D. Thesis, University of Dortmund, Germany
JT  - Ph.D. Thesis, University of Dortmund, Germany
SO  - Ph.D. Thesis, University of Dortmund, Germany 1998 : 1-164.

PMID- 11562993
VI  - 20
DP  - 2001
TI  - A DNA-binding peptide from a phage display library.
PG  - 1239-1241
AB  - A DNA-binding peptide was selected from a random peptide phage display library. For
      competitive elution using the DNA methyltransferase M.TaqI in the selection step, a
      biotin-labeled duplex oligodeoxyribonucleotide containing the 5'-TCGA-3' recognition
      sequence of M.TaqI was employed. Nine of ten phages selected were found to have the same
      deduced amino acid sequence SVSVGMKPSPRP. The selected phage binds to DNA, as demonstrated in
      an ELISA.
AU  - Wolcke J
AU  - Weinhold E
PT  - Journal Article
TA  - Nucleosides Nucleotides Nucleic Acids
JT  - Nucleosides Nucleotides Nucleic Acids
SO  - Nucleosides Nucleotides Nucleic Acids 2001 20: 1239-1241.

PMID- Not included in PubMed...
VI  - 376
DP  - 1995
TI  - Substrate specificity of the DNA-methyltransferase from Thermus aquaticus: influence of the 3'-neighbor base.
PG  - S169
AB  - The DNA-methyltransferase from Thermus aquaticus (M.TaqI) catalyzes the methyl group transfer
      from S-adenosyl-L-methionine (SAM) to the N6-position of adenine within the double-stranded
      DNA sequence 5' TCGA 3'.  We have investigated the effect of changing the 3' neighboring
      base of adenine which gets methylated.  We find that steady-state kinetic rates for the
      methylation of adenine by M.TaqI depend on the nature of the 3'-neighboring base.  In
      general, doublestranded deoxyoligo-nucleotides containing the pyrimidine bases thymine or
      cytosine next to adenine give higher rates than those containing the purine bases adenine or
      guanine.  This observed kinetic effect correlates inversely with the lower base stacking
      energies between purine and pyrimidine bases compared to those between two purine bases.  A
      contribution of the energy needed to break the base stacking between the adenine and its
      3'-neighbor to the rate limiting step is therefore suggested.  Correlation of the influence
      of the neighbor base pair on the rate with the stacking energy between base pair neighbors,
      which might indicate a distortion of both strands, however would predict a different kinetic
      effect.  In light of the large distance (15A) between the cofactor and the DNA-binding site
      observed in the crystal structure of M.TaqI complexed with SAM, the influence of the 3'
      neighbor on the steady state rate gives the first experimental evidence, that a base flipping
      out mechanism described for (cytosine-5)-DNA-Methyltransferases might also operate in adenine
      specific DNA-Methyltransferases.
AU  - Wolcke J
AU  - Weinhold E
PT  - Journal Article
TA  - Biol. Chem. Hoppe Seyler
JT  - Biol. Chem. Hoppe Seyler
SO  - Biol. Chem. Hoppe Seyler 1995 376: S169.

PMID- 11230160
VI  - 11
DP  - 2001
TI  - Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context.
PG  - 356-372
AB  - Gene order in prokaryotes is conserved to a much lesser extent than protein sequences. Only
      several operons, primarily those that code for
      physically interacting proteins, are conserved in all or most of the
      bacterial and archaeal genomes. Nevertheless, even the limited
      conservation of operon organization that is observed can provide
      valuable evolutionary and functional clues through multiple genome
      comparisons. A program for constructing gapped local alignments of
      conserved gene strings in two genomes was developed. The statistical
      significance of the local alignments was assessed using Monte Carlo
      simulations. Sets of local alignments were generated for all pairs of
      completely sequenced bacterial and archaeal genomes, and for each
      genome a template-anchored multiple alignment was constructed. In most
      pairwise genome comparisons, <10% of the genes in each genome belonged
      to conserved gene strings. When closely related pairs of species (i.e.,
      two mycoplasmas) are excluded, the total coverage of genomes by
      conserved gene strings ranged from <5% for the cyanobacterium
      Synechocystis sp. to 24% for the minimal genome of Mycoplasma
      genitalium, and 23% in Thermotoga maritima. The coverage of the
      archaeal genomes was only slightly lower than that of bacterial
      genomes. The majority of the conserved gene strings are known operons,
      with the ribosomal superoperon being the top-scoring string in most
      genome comparisons. However, in some of the bacterial-archaeal pairs,
      the superoperon is rearranged to the extent that other operons,
      primarily those subject to horizontal transfer, show the greatest level
      of conservation, such as the archaeal-type H+-ATPase operon or ABC-type
      transport cassettes. The level of gene order conservation among
      prokaryotic genomes was compared to the cooccurrence of genomes in
      clusters of orthologous genes (COGs) and to the conservation of protein
      sequences themselves. Only limited correlation was observed between
      these evolutionary variables. Gene order conservation shows a much
      lower variance than the cooccurrence of genomes in COGs, which
      indicates that intragenome homogenization via recombination occurs in
      evolution much faster than intergenome homogenization via horizontal
      gene transfer and lineage-specific gene loss. The potential of using
      template-anchored multiple-genome alignments for predicting functions
      of uncharacterized genes was quantitatively assessed. Functions were
      predicted or significantly clarified for approximately 90 COGs (approximately 4% of the total
      of 2414 analyzed COGs). The most significant
      predictions were obtained for the poorly characterized archaeal
      genomes; these include a previously uncharacterized
      restriction-modification system, a nuclease-helicase combination
      implicated in DNA repair, and the probable archaeal counterpart of the
      eukaryotic exosome. Multiple genome alignments are a resource for
      studies on operon rearrangement and disruption, which is central to our
      understanding of the evolution of prokaryotic genomes. Because of the
      rapid evolution of the gene order, the potential of genome alignment
      for prediction of gene functions is limited, but nevertheless, such
      predictions information significantly complements the results obtained
      through protein sequence and structure analysis.
AU  - Wolf YI
AU  - Rogozin IB
AU  - Kondrashov AS
AU  - Koonin EV
PT  - Journal Article
TA  - Genome Res.
JT  - Genome Res.
SO  - Genome Res. 2001 11: 356-372.

PMID- 3024128
VI  - 14
DP  - 1986
TI  - Site directed mutagenesis experiments suggest that Glu 111, Glu 144 and Arg 145 are essential for endonucleolytic activity of EcoRI.
PG  - 9063-9080
AB  - We have constructed a plasmid (pRIF 309+) carrying the EcoRI restriction
      endonuclease gene and the f1 origin of replication.  Upon transformation of
      this plasmid into E. coli and infection with bacteriophage f1 single stranded
      plasmids are produced which can be used for sequencing and site directed
      mutagenesis.  Using this single stranded DNA and synthetic
      oligodeoxynucleotides we have introduced point mutations at defined positions
      of the EcoRI gene.  Since in pRIF309+ the EcoRI gene is under the control of
      the pL- promoter, high level expression of the mutated EcoRI gene could be
      obtained upon induction.  Mutant EcoRI enzymes were purified to homogeneity and
      characterized in structural and functional terms.  Our results demonstrate that
      the Glu 111 -> Gln, Glu 144 -> Gln and Arg 145 -> Lys -mutants adopt a very
      similar conformation as the wild type enzyme, but have by two orders of
      magnitude smaller specific activities than the wild type enzyme, mainly due to
      a reduction of the Vmax-value.
AU  - Wolfes H
AU  - Alves J
AU  - Fliess A
AU  - Geiger R
AU  - Pingoud A
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1986 14: 9063-9080.

PMID- 2990922
VI  - 150
DP  - 1985
TI  - A comparison of the structural requirements for DNA cleavage by the isoschizomers HaeIII, BspRI and BsuRI.
PG  - 105-110
AB  - We have investigated the structural requirements for DNA cleavage by the
      isoschizomers HaeIII, BspRI and BsuRI which recognize the sequence -d(GGCC)-.
      For this purpose decadeoxynucleotides were synthesized by the solid-phase
      phosphotriester method and purified by high-performance liquid chromatography.
      The kinetics of cleavage of these oligodeoxynucleotides were determined for the
      three isoschizomers with the following results.  1)  The sequence adjacent to
      the recognition site strongly influences the rate of cleavage.  The preference
      is qualitatively the same for all three enzymes:  AGGCCT > TGGCCA > GGGCCC ~
      CGGCCG, and follows the thermal stability of the different decanucleotides.  2)
      Substitutions within the recognition site, namely dI for dG and dU for dC,
      affect the rate of cleavage differently for the three enzymes.  The results can
      be rationalized in terms of an interaction of HaeIII with the major and minor
      groove of the DNA of BspRI mainly with the minor groove and of BsuRI with the
      major groove of DNA.  It is obvious from our data that the mechanism of
      recognition of the same site is different for the three isoschizomers.
AU  - Wolfes H
AU  - Fliess A
AU  - Pingoud A
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1985 150: 105-110.

PMID- 3019685
VI  - 159
DP  - 1986
TI  - Cross-linking of bromodeoxyuridine-substituted oligonucleotides to the EcoRI and EcoRV restriction endonucleases.
PG  - 267-273
AB  - We have synthesized several self-complementary oligodeoxynucleotides which
      contain bromodeoxyuridine in various positions within and outside of te
      recognition sequence for the EcoRI and EcoRV restriction endonucleases.  These
      oligodeoxynucleotides are cleaved in the presence of Mg2+ by their respective
      enzyme.  Upon irradiation by long-wavelength ultraviolet light and in the
      absence of Mg2+ they are cross-linked in low yield to their enzymes, forming
      1:1 and 1:2 (oligodeoxynucleotide: enzyme subunit) adducts.  Cross-linking
      occurs with both specific and non-specific complexes.  With EcoRI the site of
      cross-linking was determined to be at or close to Met-137, i.e. in a region of
      the molecule implicated by other studies from our laboratory [Scholtissek et
      al. (1986) J. Biol. Chem. 261,1118-1134] in the binding and cleavage of the
      substrate.
AU  - Wolfes H
AU  - Fliess A
AU  - Winkler F
AU  - Pingoud A
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1986 159: 267-273.

PMID- 10339513
VI  - 96
DP  - 1999
TI  - DNA demethylation.
PG  - 5894-5896
AB  - Cytosine 5' methylation of CpG dinucleotides within and around genes exerts a major influence
      on transcription in many plants and animals. DNA methylation can be causal for transcriptional
      silencing and targets the machinery necessary to assemble specialized chromatin enriched in
      deacetylated histones. Once established in somatic cells, CpG methylation patterns within the
      genome are very stable and provide an attractive mechanism for segregating a large fraction of
      stably repressed chromatin.  In contrast, DNA methylation is remarkably dynamic during early
      mammalian development and in certain tumor cells.  Alterations in the methylation status of
      the entire genome, individual chromosomes, and specific genes are essential for normal
      development and can promote tumorigenesis.  Understanding how these important transitions
      might be regulated requires the biochemical definition of the enzymatic processes that both
      methylate and demethylate the genome.
AU  - Wolffe AP
AU  - Jones PL
AU  - Wade PA
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1999 96: 5894-5896.

PMID- Not included in PubMed...
VI  - 131
DP  - 1982
TI  - Two approaches to obtaining low, extracellular deoxyribonuclease activity in cultures of heterocyst-forming cyanobacteria.
PG  - 302-307
AB  - Six out of 158 axenic strains of heterocyst-forming cyanobacteria consistently
      failed to produce circles of clearing in agar medium containing DNA-methyl
      green.  When tested with [3H]DNA and coliphage lambda DNA, supernatant fluids
      from cultures of two of these strains [University of Texas Culture Collection
      (UTEX) strain 2014 and 19-6C-C] showed no detectable deoxyribonuclease
      activity, and such fluids from another two of the six, and four others, showed
      low but detectable deoxyribonuclease activity.  Covalently closed circular
      (plasmid) DNA was not detectably degraded by supernatant fluids from UTEX 2014
      and 19-6C-C and from four of the other strains.  When lambda DNA was incubated
      with whole cells of certain strains, a series of fragments of discrete size was
      produced, perhaps by cell-bound, periplasmic, restriction endonucleases.
      Inclusion of one-tenth strength saline sodium citrate (SSC) in an eight-fold
      dilution of the medium of Allen and Arnon had little effect on growth of
      Anabaena variabilis American Type Culture Collection (ATCC) strain 29413 yet
      prevented all but slight degradation of plasmid pBR322 or of lambda DNA.
AU  - Wolk CP
AU  - Kraus J
PT  - Journal Article
TA  - Arch. Microbiol.
JT  - Arch. Microbiol.
SO  - Arch. Microbiol. 1982 131: 302-307.

PMID- 23105066
VI  - 194
DP  - 2012
TI  - Genome Sequence of Pseudomonas mendocina DLHK, Isolated from a Biotrickling Reactor.
PG  - 6326
AB  - Pseudomonas mendocina DLHK is an aerobic bacterium isolated from a biotrickling reactor which
      can remove nitric oxide, a common air pollutant from combustion
      exhaust gas. Here, we present the draft genome of Pseudomonas mendocina DLHK.
AU  - Wong CF
AU  - Niu H
AU  - Jiang J
AU  - Li J
AU  - Chan CM
AU  - Leung DY
AU  - Leung FC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6326.

PMID- 9421528
VI  - 26
DP  - 1998
TI  - Electrospray ionization mass spectrometric characterization of photocrosslinked DNA-EcoRI DNA methyltransferase complexes.
PG  - 645-649
AB  - We describe a novel strategy combining photocrosslinking and HPLC-based electrospray
      ionization mass spectrometry to identify UV crosslinked DNA-protein complexes.  EcoRI DNA
      methyltransferase modifies the second adenine within the recognition sequence GAATTC.
      Substitution of 5-iodouracil for the thymine adjacent to the target base (GAATTC) does not
      detectably alter the DNA-protein complex.  Irradiation of the 5-iodouracil-substituted
      DNA-protein complex at various wavelengths was optimized, with a crosslinking yield >60% at
      313 nm after 1 min.  No protein degradation was observed under these conditions.  The
      crosslinked DNA-protein complex was further anlayzed by electrospray ionization mass
      spectrometry.  The total mass is consistent with irradiation-dependent covalent bond formation
      between one strand of DNA and the protein.  These preliminary results support the possibility
      of identifying picomole quantities of crosslinked peptides by similar strategies.
AU  - Wong DL
AU  - Pavlovich JG
AU  - Reich NO
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1998 26: 645-649.

PMID- 11112526
VI  - 39
DP  - 2000
TI  - Identification of tyrosine 204 as the photo-cross-linking site in the DNA - EcoRI DNA methyltransferase complex by electrospray ionization mass spectrometry.
PG  - 15410-15417
AB  - We describe a highly sensitive strategy combining laser-induced photo-cross-linking and
      HPLC-based electrospray ionization mass
      spectrometry to identify amino acid residues involved in protein-DNA
      recognition. The photoactivatible cross-linking thymine isostere,
      5-iodouracil, was incorporated at a single site within the sequence
      recognized by EcoRI DNA methyltransferase (GAATTC). UV irradiation of
      the DNA-protein complex at 313 nm results in a >60% cross-linking
      yield. SDS-polyacrylamide gel electrophoresis and mass spectrometry
      were used to analyze the covalent cross-linked complex. The total mass
      is consistent with covalent bond formation between one strand of DNA
      and the protein with 1:1 stoichiometry. Protease digestion of the
      cross-linked complex yields several peptide-DNA adducts that were
      purified by anion-exchange column chromatography. A combination of mass
      spectrometric analysis and amino acid sequencing revealed that tyrosine
      204 was cross-linked to the DNA. Electrospray mass spectrometric
      analysis of the peptide-nucleoside adduct confirmed this assignment.
      Tyrosine 204 resides in a peptide motif previously thought to be
      involved in AdoMet binding and methyl transfer. Thus, amino acids
      within loop segments but outside of "DNA binding" motifs can be
      critical to DNA recognition. Our method provides an accurate
      characterization of picomole quantities of DNA-protein complexes.
AU  - Wong DL
AU  - Reich NO
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2000 39: 15410-15417.

PMID- 7959064
VI  - 150
DP  - 1994
TI  - Some class-IIS restriction endonucleases can cleave across a three-way DNA junction.
PG  - 63-66
AB  - Three-way DNA junctions were synthesized with class-IIS restriction endonuclease (ENase)
      recognition sites and potential cleavage sites located on separate arms. Cleavage was
      investigated with junctions labeled in each of the three strands. BpmI and BsaI failed to
      cleave either strand of either arm, whereas BsmAI cleaved one strand. FokI and HphI cleaved
      both strands of both arms at the expected nucleotide positions. FokI cleavage was independent
      of the spacing between the recognition site and the junction. This new activity of class-IIS
      may be useful for investigating branched DNA structures.
AU  - Wong DM
AU  - Wetmur JG
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1994 150: 63-66.

PMID- 1850509
VI  - 19
DP  - 1991
TI  - PCR with 5-methyl-dCTP replacing dCTP.
PG  - 1081-1085
AB  - When dCTP is replaced by methyl-5-dCTP in the polymerase chain reaction some templates cannot
      be efficiently amplified by Taq polymerase or Vent tm polymerase using standard cycling
      parameters. However, this phenomenon can be overcome by increasing the temperature of the
      denaturation steps to 100 C, or by adding dITP to destabilize the m5dC:dG base pairs. Once the
      block to amplification of m5dC-substituted DNA was overcome, methylated DNA from the
      superpolylinker of the plasmid pSL1180 was used as a substrate to check the methyl-sensitivity
      of a variety of restriction endonucleases. The m5dC-substituted DNAs should also be valuable
      substrates for defining the specificity of methyl-dependent endonucleases.
AU  - Wong KK
AU  - McClelland M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1991 19: 1081-1085.

PMID- 10227170
VI  - 173
DP  - 1999
TI  - Sample sequencing of a Salmonella typhimurium LT2 lambda library: comparison to the Escherichia coli K12 genome.
PG  - 411-423
AB  - As part of the ongoing sequencing of the complete Salmonella typhimurium
      LT2 genome, a partly ordered set of 416 lambda clones has been developed,
      representing over 90% of the genome. The average insert size is 17 kb.
      Sequences were obtained from both ends of each clone in this set. A total
      of over 600 kb of sequence has been deposited in the genome survey
      sequence section of GenBank. This resource of clones is available from the
      Salmonella Genome Stock Center. A preliminary comparison with the
      Escherichia coli K12 genome indicates that there are likely to be many
      hundred insertion deletion events, encompassing more than one gene, that
      distinguish these genomes. Fully 30% of the S. typhimurium sequences have
      no close homologs in the GenBank database.
AU  - Wong RM-Y
AU  - Wong KK
AU  - Benson NR
AU  - McClelland M
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 1999 173: 411-423.

PMID- 27469943
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Lewinella sp. Strain 4G2 Isolated from the Coastal Sea Surface Microlayer.
PG  - e00754-16
AB  - We report here the draft genome of Lewinella sp. strain 4G2, isolated from the sea surface
      microlayer (SML) of a coastal marine inlet. The genome sequence of
      strain 4G2 should contribute to understanding the lifestyles of bacteria living
      in the SML.
AU  - Wong SK
AU  - Yoshizawa S
AU  - Nakajima Y
AU  - Ogura Y
AU  - Hayashi T
AU  - Hamasaki K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00754-16.

PMID- 22843600
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Mycobacterium bolletii Strain M24, a Rapidly Growing Mycobacterium of Contentious Taxonomic Status.
PG  - 4475
AB  - The whole-genome sequence of Mycobacterium bolletii M24, isolated from the bronchoalveolar
      lavage fluid of a Malaysian patient, is reported here. The
      circular chromosome of 5,507,730 bp helped to clarify the taxonomic position of
      this organism within the M. abscessus complex and revealed the presence of
      proteins potentially important for pathogenicity in a human host.
AU  - Wong YL
AU  - Choo SW
AU  - Tan JL
AU  - Ong CS
AU  - Ng KP
AU  - Ngeow YF
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4475.

PMID- 24604639
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Clostridium bifermentans Strain WYM, a Promising Biohydrogen Producer Isolated from Landfill Leachate Sludge.
PG  - e00077-14
AB  - Clostridium bifermentans strain WYM is an effective biohydrogen producer isolated from
      landfill leachate sludge. Here, we present the assembly and annotation of
      its genome, which may provide further insights into the metabolic pathways
      involved in efficient biohydrogen production.
AU  - Wong YM
AU  - Juan JC
AU  - Gan HM
AU  - Austin CM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00077-14.

PMID- 24604637
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Clostridium perfringens Strain JJC, a Highly Efficient Hydrogen Producer Isolated from Landfill Leachate Sludge.
PG  - e00064-14
AB  - Clostridium perfringens strain JJC is an effective biohydrogen and biochemical producer that
      was isolated from landfill leachate sludge. Here, we present the
      assembly and annotation of its genome, which may provide further insights into
      the gene interactions involved in efficient biohydrogen production.
AU  - Wong YM
AU  - Juan JC
AU  - Gan HM
AU  - Austin CM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00064-14.

PMID- 24604640
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Clostridium sp. Strain Ade.TY, a New Biohydrogen- and Biochemical-Producing Bacterium Isolated from Landfill Leachate Sludge.
PG  - e00078-14
AB  - Clostridium sp. strain Ade.TY is potentially a new biohydrogen-producing species  isolated
      from landfill leachate sludge. Here we present the assembly and
      annotation of its genome, which may provide further insights into its gene
      interactions for efficient biohydrogen production.
AU  - Wong YM
AU  - Juan JC
AU  - Ting A
AU  - Wu TY
AU  - Gan HM
AU  - Austin CM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00078-14.

PMID- 25787880
VI  - 56
DP  - 2015
TI  - Relaxed specificity of prokaryotic DNA methyltransferases results in DNA site-specific modification of RNA/DNA heteroduplexes.
PG  - 539-546
AB  - RNA/DNA hybrid duplexes regularly occur in nature, for example in transcriptional R loops.
      Their susceptibility to modification by DNA-specific or RNA-specific
      enzymes is, thus, a biologically relevant question, which, in addition, has
      possible biotechnological implications. In this study, we investigated the
      activity of four isospecific DNA methyltransferases (M.EcoVIII, M.LlaCI,
      M.HindIII, M.BstZ1II) toward an RNA/DNA duplex carrying one
      5'-AAGCUU-3'/3'-TTCGAA-5' target sequence. The analyzed enzymes belong to the
      beta-group of adenine N6-methyltransferases and recognize the palindromic DNA
      sequence 5'-AAGCTT-3'/3'-TTCGAA-5'. Under standard conditions, none of these
      isospecific enzymes could detectibly methylate the RNA/DNA duplex. However, the
      addition of agents that generally relax specificity, such as dimethyl sulfoxide
      (DMSO) and glycerol, resulted in substantial methylation of the RNA/DNA duplex by
      M.EcoVIII and M.LlaCI. Only the DNA strand of the RNA/DNA duplex was methylated.
      The same was not observed for M.HindIII or M.BstZ1II. This is, to our knowledge,
      the first report that demonstrates such activity by prokaryotic DNA
      methyltransferases. Possible applications of these findings in a laboratory
      practice are also discussed.
AU  - Wons E
AU  - Mruk I
AU  - Kaczorowski T
PT  - Journal Article
TA  - J. Appl. Genet.
JT  - J. Appl. Genet.
SO  - J. Appl. Genet. 2015 56: 539-546.

PMID- 27881538
VI  - 4
DP  - 2016
TI  - Near-Complete Genome Sequence of Thalassospira sp. Strain KO164 Isolated from a Lignin-Enriched Marine Sediment Microcosm.
PG  - e01297-16
AB  - Thalassospira sp. strain KO164 was isolated from eastern Mediterranean seawater and sediment
      laboratory microcosms enriched on insoluble organosolv lignin under
      oxic conditions. The near-complete genome sequence presented here will facilitate
      analyses into this deep-ocean bacterium's ability to degrade recalcitrant
      organics such as lignin.
AU  - Woo HL et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01297-16.

PMID- 25566348
VI  - 9
DP  - 2014
TI  - Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain  BRL6-2.
PG  - 19
AB  - In an effort to discover anaerobic bacteria capable of lignin degradation, we isolated
      Klebsiella sp. strain BRL6-2 on minimal media with alkali lignin as the
      sole carbon source. This organism was isolated anaerobically from tropical forest
      soils collected from the Bisley watershed at the Ridge site in the El Yunque
      National Forest in Puerto Rico, USA, part of the Luquillo Long-Term Ecological
      Research Station. At this site, the soils experience strong fluctuations in redox
      potential and are characterized by cycles of iron oxidation and reduction. Genome
      sequencing was targeted because of its ability to grow on lignin anaerobically
      and lignocellulolytic activity via in vitro enzyme assays. The genome of
      Klebsiella sp. strain BRL6-2 is 5.80 Mbp with no detected plasmids, and includes
      a relatively small arsenal of genes encoding lignocellulolytic carbohydrate
      active enzymes. The genome revealed four putative peroxidases including
      glutathione and DyP-type peroxidases, and a complete protocatechuate pathway
      encoded in a single gene cluster. Physiological studies revealed Klebsiella sp.
      strain BRL6-2 to be relatively stress tolerant to high ionic strength conditions.
      It grows in increasing concentrations of ionic liquid
      (1-ethyl-3-methyl-imidazolium acetate) up to 73.44 mM and NaCl up to 1.5 M.
AU  - Woo HL
AU  - Ballor NR
AU  - Hazen TC
AU  - Fortney JL
AU  - Simmons B
AU  - Davenport KW
AU  - Goodwin L
AU  - Ivanova N
AU  - Kyrpides NC
AU  - Mavromatis K
AU  - Woyke T
AU  - Jansson J
AU  - Kimbrel J
AU  - DeAngelis KM
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 19.

PMID- 28473393
VI  - 5
DP  - 2017
TI  - High-Quality Draft Genome Sequences of Four Lignocellulose-Degrading Bacteria Isolated from Puerto Rican Forest Soil: Gordonia sp., Paenibacillus sp.,  Variovorax sp., and Vogesella sp.
PG  - e00300-17
AB  - Here, we report the high-quality draft genome sequences of four phylogenetically  diverse
      lignocellulose-degrading bacteria isolated from tropical soil (Gordonia
      sp., Paenibacillus sp., Variovorax sp., and Vogesella sp.) to elucidate the
      genetic basis of their ability to degrade lignocellulose. These isolates may
      provide novel enzymes for biofuel production.
AU  - Woo HL
AU  - DeAngelis KM
AU  - Teshima H
AU  - Davenport K
AU  - Daligault H
AU  - Erkkila T
AU  - Goodwin L
AU  - Gu W
AU  - Lo CC
AU  - Munk C
AU  - Scholz M
AU  - Xu Y
AU  - Chain P
AU  - Bruce D
AU  - Detter C
AU  - Tapia R
AU  - Han C
AU  - Simmons BA
AU  - Hazen TC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00300-17.

PMID- 24948777
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Lignin-Degrading Burkholderia sp. Strain LIG30, Isolated from Wet Tropical Forest Soil.
PG  - e00637-14
AB  - Burkholderia species are common soil Betaproteobacteria capable of degrading recalcitrant
      aromatic compounds and xenobiotics. Burkholderia sp. strain LIG30
      was isolated from wet tropical forest soil and is capable of utilizing lignin as
      a sole carbon source. Here we report the draft genome sequence of Burkholderia
      sp. strain LIG30.
AU  - Woo HL
AU  - Utturkar S
AU  - Klingeman D
AU  - Simmons BA
AU  - DeAngelis KM
AU  - Brown SD
AU  - Hazen TC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00637-14.

PMID- 19283063
VI  - 5
DP  - 2009
TI  - The complete genome and proteome of Laribacter hongkongensis reveal potential mechanisms for adaptations to different temperatures and habitats.
PG  - E1000416
AB  - Laribacter hongkongensis is a newly discovered Gram-negative bacillus of
      the Neisseriaceae family associated with freshwater fish-borne
      gastroenteritis and traveler's diarrhea. The complete genome sequence of
      L. hongkongensis HLHK9, recovered from an immunocompetent patient with
      severe gastroenteritis, consists of a 3,169-kb chromosome with G+C content
      of 62.35%. Genome analysis reveals different mechanisms potentially
      important for its adaptation to diverse habitats of human and freshwater
      fish intestines and freshwater environments. The gene contents support its
      phenotypic properties and suggest that amino acids and fatty acids can be
      used as carbon sources. The extensive variety of transporters, including
      multidrug efflux and heavy metal transporters as well as genes involved in
      chemotaxis, may enable L. hongkongensis to survive in different
      environmental niches. Genes encoding urease, bile salts efflux pump,
      adhesin, catalase, superoxide dismutase, and other putative virulence
      factors-such as hemolysins, RTX toxins, patatin-like proteins,
      phospholipase A1, and collagenases-are present. Proteomes of L.
      hongkongensis HLHK9 cultured at 37 degrees C (human body temperature) and
      20 degrees C (freshwater habitat temperature) showed differential gene
      expression, including two homologous copies of argB, argB-20, and argB-37,
      which encode two isoenzymes of N-acetyl-L-glutamate kinase (NAGK)-NAGK-20
      and NAGK-37-in the arginine biosynthesis pathway. NAGK-20 showed higher
      expression at 20 degrees C, whereas NAGK-37 showed higher expression at 37
      degrees C. NAGK-20 also had a lower optimal temperature for enzymatic
      activities and was inhibited by arginine probably as negative-feedback
      control. Similar duplicated copies of argB are also observed in bacteria
      from hot springs such as Thermus thermophilus, Deinococcus geothermalis,
      Deinococcus radiodurans, and Roseiflexus castenholzii, suggesting that
      similar mechanisms for temperature adaptation may be employed by other
      bacteria. Genome and proteome analysis of L. hongkongensis revealed novel
      mechanisms for adaptations to survival at different temperatures and
      habitats.
AU  - Woo PC
AU  - Lau SK
AU  - Tse H
AU  - Teng JL
AU  - Curreem SO
AU  - Tsang AK
AU  - Fan RY
AU  - Wong GK
AU  - Huang Y
AU  - Loman NJ
AU  - Snyder LA
AU  - Cai JJ
AU  - Huang JD
AU  - Mak W
AU  - Pallen MJ
AU  - Lok S
AU  - Yuen KY
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2009 5: E1000416.

PMID- 15840507
VI  - 340
DP  - 2005
TI  - A nonradioactive DNA methyltransferase assay adaptable to high-throughput screening.
PG  - 336-340
AB  - We have developed a nonradioactive assay method for DNA methyltransferases based on the
      ability to protect substrate DNA from
      restriction. DNA immobilized to a microplate well was treated
      sequentially with methyltransferase and an appropriate endonuclease.
      The amount of methylated DNA product is reflected by a proportional
      decrease in endonuclease cleavage, which is in turn reflected by
      increased retention of the end-labeled affinity probe. A single
      universal substrate was designed to assay multiple methyltransferases
      including those that do not have a cognate endonuclease. The
      methodology developed is suited to screen a large number of compounds
      for inhibitors of various methyltransferases.
AU  - Woo YH
AU  - Rajagopalan PTR
AU  - Benkovic SJ
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 2005 340: 336-340.

PMID- 11743193
VI  - 294
DP  - 2001
TI  - The genome of the natural genetic engineer Agrobacterium tumefaciens C58.
PG  - 2317-2323
AB  - The 5.67-megabase genome of the plant pathogen Agrobacterium tumefaciens C58 consists of a
      circular chromosome, a linear chromosome, and two plasmids.  Extensive orthology and
      nucleotide colinearity between the genomes of A. tumefaciens and the plant symbiont
      Sinorhizobium meliloti suggest a recent evolutionary divergence.  Their similarities include
      metabolic, transport, and regulatory systems that promote survival in the highly competitive
      rhizosphere; differences are apparent in their genome structure and virulence gene complement.
      Availability of the A. tumefaciens sequence will facilitate investigations into the molecular
      basis of pathogenesis and the evolutionary divergence of pathogenic and symbiotic lifestyles.
AU  - Wood DW et al
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2001 294: 2317-2323.

PMID- 15923010
VI  - 350
DP  - 2005
TI  - Long-range communications between DNA sites by the dimeric restriction endonuclease SgrAl.
PG  - 240-253
AB  - The SgrAI endonuclease displays its maximal activity on DNA with two copies of its recognition
      sequence, cleaving both sites concertedly.
      While most restriction enzymes that act concurrently at two sites are
      tetramers, SgrAI is a dimer in solution. Its reaction at two cognate
      sites involves the association of two DNA-bound dimers. SgrAI can also
      bridge cognate and secondary sites, the latter being certain sequences
      that differ from the cognate by one base-pair. The mechanisms for
      cognate-cognate and cognate-secondary communications were examined for
      sites in the following topological relationships: in cis, on plasmids
      with two sites in a single DNA molecule; on catenanes containing two
      interlinked rings of DNA with one site in each ring; and in trans, on
      oligoduplexes carrying either a single site or the DNA termini
      generated by SgrAI. Both cognate-cognate and cognate-secondary
      interactions occur through 3-D space and not by 1-D tracking along the
      DNA. Both sorts of communication arise more readily when the sites are
      tethered to each other, either in cis on the same molecule of DNA or by
      the interlinking of catenane rings, than when released from the tether.
      However, the dimer bound to an oligoduplex carrying either a cognate or
      a secondary site could be activated to cleave that duplex by
      interacting with a second dimer bound to the recognition site, provided
      both duplexes are at least 30 base-pairs long: the second dimer could
      alternatively be bound to the two duplexes that correspond to the
      products of DNA cleavage by SgrAI.
AU  - Wood KM
AU  - Daniels LE
AU  - Halford SE
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2005 350: 240-253.

PMID- 17726531
VI  - 2
DP  - 2007
TI  - Kinetic analysis of Yersinia pestis DNA adenine methyltransferase activity using a hemimethylated molecular break light oligonucleotide.
PG  - e801
AB  - Background. DNA adenine methylation plays an important role in several critical bacterial
      processes including mismatch repair, the timing of DNA replication and the transcriptional
      control of gene expression. The dependence of bacterial virulence on DNA adenine
      methyltransferase (Dam) has led to the proposal that selective Dam inhibitors might function
      as broad spectrum antibiotics. Methodology/Principal Findings. Herein we report the expression
      and purification of Yersinia pestis Dam and the development of a continuous fluorescence based
      assay for DNA adenine methyltransferase activity that is suitable for determining the kinetic
      parameters of the enzyme and for high throughput screening against potential Dam inhibitors.
      The assay utilised a hemimethylated break light oligonucleotide substrate containing a GATC
      methylation site. When this substrate was fully methylated by Dam, it became a substrate for
      the restriction enzyme DpnI, resulting in separation of fluorophore (fluorescein) and quencher
      (dabcyl) and therefore an increase in fluorescence. The assays were monitored in real time
      using a fluorescence microplate reader in 96 well format and were used for the kinetic
      characterisation of Yersinia pestis Dam, its substrates and the known Dam inhibitor,
      S-adenosylhomocysteine. The assay has been validated for high throughput screening, giving a
      Z-factor of 0.7160.07 indicating that it is a sensitive assay for the identification of
      inhibitors. Conclusions/Significance. The assay is therefore suitable for high throughput
      screening for inhibitors of DNA adenine methyltransferases and the kinetic characterisation of
      the inhibition.
AU  - Wood RJ
AU  - Maynard-Smith MD
AU  - Robinson VL
AU  - Oyston PCF
AU  - Titball RW
AU  - Roach PL
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2007 2: e801.

PMID- 20139415
VI  - 38
DP  - 2010
TI  - A real-time assay for CpG-specific cytosine-C5 methyltransferase activity.
PG  - e107
AB  - A real-time assay for CpG-specific cytosine-C5 methyltransferase activity has been developed.
      The assay applies a break light oligonucleotide in
      which the methylation of an unmethylated 5'-CG-3' site is enzymatically
      coupled to the development of a fluorescent signal. This sensitive assay
      can measure rates of DNA methylation down to 0.34 +/- 0.06 fmol/s. The
      assay is reproducible, with a coefficient of variation over six
      independent measurements of 4.5%. Product concentration was accurately
      measured from fluorescence signals using a linear calibration curve, which
      achieved a goodness of fit (R(2)) above 0.98. The oligonucleotide
      substrate contains three C5-methylated cytosine residues and one
      unmethylated 5'-CG-3' site. Methylation yields an oligonucleotide
      containing the optimal substrate for the restriction enzyme GlaI. Cleavage
      of the fully methylated oligonucleotide leads to separation of fluorophore
      from quencher, giving a proportional increase in fluorescence. This method
      has been used to assay activity of DNMT1, the principle maintenance
      methyltransferase in human cells, and for the kinetic characterization of
      the bacterial cytosine-C5 methyltransferase M.SssI. The assay has been
      shown to be suitable for the real-time monitoring of DNMT1 activity in a
      high-throughput format, with low background signal and the ability to
      obtain linear rates of methylation over long periods, making this a
      promising method of high-throughput screening for inhibitors.
AU  - Wood RJ
AU  - McKelvie JC
AU  - Maynard-Smith MD
AU  - Roach PL
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2010 38: e107.

PMID- 11859360
VI  - 415
DP  - 2002
TI  - The genome sequence of Schizosaccharomyces pombe.
PG  - 871-880
AB  - We have sequenced and annotated the genome of fission yeast
      (Schizosaccharomyces pombe), which contains the smallest number of
      protein-coding genes yet recorded for a eukaryote: 4,824. The centromeres
      are between 35 and 110 kilobases (kb) and contain related repeats
      including a highly conserved 1.8-kb element. Regions upstream of genes are
      longer than in budding yeast (Saccharomyces cerevisiae), possibly
      reflecting more-extended control regions. Some 43% of the genes contain
      introns, of which there are 4,730. Fifty genes have significant similarity
      with human disease genes; half of these are cancer related. We identify
      highly conserved genes important for eukaryotic cell organization
      including those required for the cytoskeleton, compartmentation,
      cell-cycle control, proteolysis, protein phosphorylation and RNA splicing.
      These genes may have originated with the appearance of eukaryotic life.
      Few similarly conserved genes that are important for multicellular
      organization were identified, suggesting that the transition from
      prokaryotes to eukaryotes required more new genes than did the transition
      from unicellular to multicellular organization.
AU  - Wood V et al
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2002 415: 871-880.

PMID- 5331240
VI  - 16
DP  - 1966
TI  - Host specificity of DNA produced by Escherichia coli:  bacterial mutations affecting the restriction and modification of DNA.
PG  - 118-133
AB  - Bacterial mutants lacking the ability to restrict lambda phage of foreign host
      specificity have been isolated from Escherichia coli strains K12 and B using a
      convenient selection technique.  About half of the mutants still impart host
      specificity to lambda; the remainder are deficient in modification as well as
      restriction.  In both K12 and B, mutations affecting restriction map close to
      the thr locus on the side opposite to leu.  Behavior of the mutant strains in
      conjugation experiments is consistent with the view that bacterial DNA is
      restricted and modified by the same factors which act upon the DNA of phage
      lambda, and that this restriction isi responsible for the abnormally low
      frequency of recombinant formation observed in K12 X B crosses.  The properties
      of the modification-restriction system in E. coli suggest that it serves as a
      defense mechanism against incoming nucleic acid, preventing the expression or
      integration of foreign DNA without hindering genetic exchange among cells of
      the same strain.
AU  - Wood WB
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1966 16: 118-133.

PMID- Not included in PubMed...
VI  - 28
DP  - 1965
TI  - Mutations in E. coli affecting the host-controlled modification bacteriophage lambda.
PG  - 73-76
AB  - This report describes the isolation and some properties of K12 and B strains
      which have lost the restriction (r) and modification (m) functions as a result
      of either spontaneous or ethyl-methane sulfonate (EMS)-induced mutations.
      Glover et al. have recently described similar mutations carried by P1 prophage
      which affect the host-controlled modification of lambda.K in lysogenic E. coli
      K12 (P1) strains.
AU  - Wood WB
PT  - Journal Article
TA  - Pathol. Microbiol. (Basel)
JT  - Pathol. Microbiol. (Basel)
SO  - Pathol. Microbiol. (Basel) 1965 28: 73-76.

PMID- Not included in PubMed...
VI  - 37
DP  - 1978
TI  - EcoRI Methylase: On its substrate specificity and use in radioactive labeling of DNA.
PG  - 1415
AB  - While investigating the mechanisms of the EcoRI endonuclease and methylase, we
      have examined the effect of alterations in reaction conditions on the
      methylation process.  We find that in 100 mM Tris, 2 mM EDTA, 50% glycerol (pH
      9), the methylase transfers many more methyl groups to both ColE1 plasmid and
      phage lambda DNA than can be accommodated in the known "canonical" substrate
      sites of these DNAs.  We have confirmed that "non-canonical" sites are
      methylated under these conditions by demonstrating the incorporation of
      substantial amounts of label into phage PhiX174 DNA, which contains no
      canonical sequences, as well as into in vivo-methylated E. coli strain RY13
      (rRI+, mRI+) chromosomal DNA.  We have also incorporated label into both duplex
      poly[d(A-T)] and poly(dA).poly(dT).  The rate of methylation of these
      substrates decreases in the order: canonical sites > non-canonical sites
      >duplex poly[d(A-T)] > poly(dA).poly(dT).  The implications of these findings
      for mechanisms in the EcoRI system will be discussed.  In addition to its
      mechanistic interest, this nonspecific methylation procedure provides a
      convenient way to radioactively label DNA in vitro; we have achieved ~105
      cpm/microgram with various DNAs, a level comparable to that obtainable by in
      vivo 32P-labeling.  Examples of the use of this technique will be described.
AU  - Woodbury CP Jr
AU  - Downey RL
AU  - von Hippel PH
PT  - Journal Article
TA  - Fed. Proc.
JT  - Fed. Proc.
SO  - Fed. Proc. 1978 37: 1415.

PMID- 7002925
VI  - 255
DP  - 1980
TI  - DNA site recognition and overmethylation by the EcoRI methylase.
PG  - 11526-11533
AB  - The EcoRI modification methylase exhibits reduction of in vitro substrate
      specificity under conditions of alkaline pH, low ionic strength, and igh
      glycerol content.  Under these conditions the enzyme transfers many more methyl
      groups to both plasmid ColE1 DNA and phage lambda DNA than can be accommodated
      in the known "canonical" recognition sites of these DNAs.  Substantial
      methylation of phage PhiX174 replicative form DNA, which contains no canonical
      sites, has also been demonstrated.  This "noncanonical" methylation occurs at
      sites recognized by the EcoRI restriction endonuclease under parallel
      conditions of low ionic strength and alkaline pH, as evidenced by protection of
      the overmethylated ColE1 or PhiX174 DNAs against attack by the nuclease
      (Woodbury, C.P., Jr., Hagenbuchle, O., and von Hippel, P.H. (1980) J. Biol.
      Chem. 255, 11534-11546).  The methylase also modifies, at a much lower rate,
      the double-stranded form of the alternating copolymer, poly[d(A-T)], but does
      not transfer appreciable numbers of methyl groups to the homoduplex,
      poly(dA).poly(dT).  The substrates methylated, in order of decreasing specific
      rate, are: canonical DNA sites > noncanonical DNA sites > duplex poly[d(A-T)] >
      poly(dA).poly(dT).  In addition, this enzyme (under noncanonical methylating
      conditions) modifies in vivo methylated Escherichia coli RY13 (r+ RI, M+RI)
      chromosomal DNA, but at a much lower rate than the other DNAs tested.  This
      suggests that the noncanonical (as well as the canonical) sites of this DNA
      have been largely modified in vivo.  The high level of methyl group
      incorporation attainable using the noncanonical activity of the EcoRI methylase
      has also been employed as a tool to radioactively label DNA in vitro.
      Double-stranded lambda plac DNA has been labeled easily to 130,000
      cpm/microgram by this technique; this modified DNA has been shown to be fully
      functional as operator in lac operator-repressor filter-binding assays.
AU  - Woodbury CP Jr
AU  - Downey RL
AU  - von Hippel PH
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1980 255: 11526-11533.

PMID- 6254972
VI  - 255
DP  - 1980
TI  - DNA site recognition and reduced specificity of the EcoRI endonuclease.
PG  - 11534-11546
AB  - It has been shown previously (Polisky, B., Green, P., Garfin, D.E., McCarthy,
      B.J., Goodman, H.M. and Boyer, H.W. (1975) Proc. Natl. Acad. Sci. USA 72:
      3310-3314; Hsu, M., and Berg, P. (1978) Biochemistry 17: 131-138) that the
      cleavage sequence specificity of EcoRI endonuclease can be "relaxed" by various
      means.  In this paper this phenomenon is explored in detail, in order to obtain
      further insight into the nature and selectivity of sequence recognition
      patterns between proteins and double-stranded nucleic acids.  Using conditions
      of low ionic strength and alkaline pH, we have mapped the positions of
      potentially cleavable sites in the (completely sequenced) replicative form of
      the bacteriophage PhiX174 genome, and have deduced their sequence.  The time
      course of digestion of PhiX174 DNA suggests that double-stranded sequences
      reading GGATTT, AAATTT, GAATTT, and GAATTA (only "top" strands, written 5' -
      3', are shown) are cleaved readily under these conditions, while sequences
      reading CAATTN (N = A,T,G) resist attack.  Cleavages at (at least) the more
      labile sites result in cohesive ends that are religatable.  End group analysis
      of cleaved PhiX174 DNA fragments indicates the presence of a 5' - terminal
      adenine residue on most of the fragments; some fragments may carry a
      5'-terminal guanine residue, consistent with the cleavage site sequences
      suggested above.  Addition of Mn2+ to cleavage reactions carried out at
      moderate salt concentrations and near-neutral pH indices the same pattern of
      cleavage seen at low ionic strength and alkaline pH.  These results are
      combined with those from other studies, and are interpreted in terms of a model
      for the site-specific interation of the EcoRI endonuclease with its substrate,
      considering both the effects of changes in DNA sequence and of environmental
      alterations.  The resulting model is compared with data developed on similar
      grounds for EcoRI methylase (see Woodbury, C.P., Downey, R.L., and von Hippel,
      Ph.H. (1980) J. Biol. Chem. 255: 11526-11533), and attempts are made to define
      both common and differing molecular facets of the DNA recognition specificity
      of these companion (but genetically distinct enzymes.
AU  - Woodbury CP Jr
AU  - Hagenbuchle O
AU  - von Hippel PH
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1980 255: 11534-11546.

PMID- 6765639
VI  - 1
DP  - 1981
TI  - Relaxed sequence specificities of EcoRI endonuclease and methylase: Mechanisms, possible practical applications, and uses in defining protein-nucleic acid recognition mechanisms.
PG  - 181-207
AB  - *

         I. Introduction

        II. Conditions for relaxation of enzymatic specificity

       III. Sequence specificity of noncanonical EcoRI activities

        IV. Is relaxed specificity due to an impurity

         V. The role of binding affinity in relaxed specificity

        VI. Recognition contacts for the endonuclease

       VII. Recognition contacts for the methylase

      VIII. General features of the endonuclease recognition sequence

        IX. Free energy considerations in non-sequence-specific and sequence-specific binding

         X. Applications of the relaxed-specificity reactions of endonuclease and methylase

        XI. Appendix

      

AU  - Woodbury CP Jr
AU  - von Hippel PH
PT  - Journal Article
TA  - Gene Amplif. Anal.
JT  - Gene Amplif. Anal.
SO  - Gene Amplif. Anal. 1981 1: 181-207.

PMID- 2837736
VI  - 16
DP  - 1988
TI  - RglB facilitated cloning of highly methylated eukaryotic DNA:  the human L1 transposon, plant DNA, and DNA methylated in vitro with human DNA methyltransferase.
PG  - 4465-4482
AB  - In vitro methylation of Bluescribe plasmid DNA (pBS) with human placental DNA
      methyltransferase to 6% 5-methylcytosine (mC) reduced transformation
      efficiencies in rglB+ host strains C600 and DS410 by almost 2 orders of
      magnitude.  By contrast, the rglB- derivative of DS410 showed no reduction in
      transformation efficiency with methylation while the rglB- derivative of C600
      was partially tolerant to methylation.  Further, we show that the 1.8 kilobase
      (kb) and 1.2 kb KpnI fragments derived from the human L1 repeat have
      respectively 18.3% and 2.3% mC in vivo.  Using these hyper- and hypo-methylated
      genomic segments ligated into the pBS plasmid, transformants with the highly
      methylated 1.8 kb L1 insert were recovered at 17 to 40 fold higher frequency
      with the rglB- host strains than with the rglB+ hosts.  In addition,
      recombinant phage (lambda 2001) containing inserts of plant genomic DNA with
      26.7% mC (from Petunia hybrida) when plated on rglB- hosts gave titres up to
      222 times higher than on rglB+ strains.
AU  - Woodcock DM
AU  - Crowther PJ
AU  - Diver WP
AU  - Graham M
AU  - Bateman C
AU  - Baker DJ
AU  - Smith SS
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1988 16: 4465-4482.

PMID- 9461416
VI  - 206
DP  - 1998
TI  - DNA methylation in mouse A-repeats in DNA methyltransferase-knockout ES cells and in normal cells determined by bisulfite genomic sequencing.
PG  - 63-67
AB  - Mouse ES cells with a null mutation of the known DNA methyltransferase retain some residual
      DNA methylation and can methylate foreign sequences de novo.  We have used bisulfite genomic
      sequencing to examine the sequence specificity and distributions of methylation of a
      hypermethylated CG island sequence, mouse A-repeats.  There were 13 CG dinucleotides in the
      region examined, 12 of which were methylated to variable extents in all DNAs.  We found that:
      (1) there is considerable residual DNA methylation in ES cells lacking the known DNA
      methyltransferase (29% of normal methylation in the complete knockout ES DNA); (2) this other
      activity methylates at exactly the same CG sites as the major methyltransferase; and (3)
      differences in the distribution of methylated sites between A-repeats in these DNAs are
      consistent with this other activity methylating in a random de novo fashion.  Also, the lack
      of any methylation in non-CG sites argues that, in other studies where non-CG methylation
      sites have been found by bisulfite sequencing, detection of such sites of non-CG methylation
      is not an inherent artifact in this methodology.
AU  - Woodcock DM
AU  - Lisenmeyer ME
AU  - Warren WD
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1998 206: 63-67.

PMID- 19687243
VI  - 53
DP  - 2009
TI  - Complete nucleotide sequences of plasmids pEK204, pEK499, and pEK516, encoding CTX-M enzymes in three major Escherichia coli lineages from the United Kingdom,  all belonging to the international O25:H4-ST131 clone.
PG  - 4472-4482
AB  - We determined the complete nucleotide sequences of three plasmids that encode CTX-M
      extended-spectrum beta-lactamases (ESBLs) in pulsed-field gel
      electrophoresis-defined United Kingdom variants (strains A, C, and D) of the
      internationally prevalent Escherichia coli O25:H4-ST131 clone. Plasmid pEK499
      (strain A; 117,536 bp) was a fusion of type FII and FIA replicons and harbored
      the following 10 antibiotic resistance genes conferring resistance to eight
      antibiotic classes: bla(CTX-M-15), bla(OXA-1), bla(TEM-1,) aac6'-Ib-cr, mph(A),
      catB4, tet(A), and the integron-borne dfrA7, aadA5, and sulI genes. pEK516
      (strain D; 64,471 bp) belonged to incompatibility group IncFII and carried seven
      antibiotic resistance genes: bla(CTX-M-15), bla(OXA-1), bla(TEM-1), aac6'-Ib-cr,
      catB4, and tet(A), all as in pEK499. It also carried aac3-IIa, conferring
      gentamicin resistance, and was highly related to pC15-1a, a plasmid encoding the
      CTX-M-15 enzyme in Canada. By contrast, pEK204 (strain C; 93,732 bp) belonged to
      incompatibility group IncI1 and carried only two resistance genes, bla(CTX-M-3)
      and bla(TEM-1). It probably arose by the transposition of Tn3 and
      ISEcp1-bla(CTX-M-3) elements into a pCOLIb-P9-like plasmid. We conclude that (i)
      United Kingdom variants of the successful E. coli ST131 clone have acquired
      different plasmids encoding CTX-M ESBLs on separate occasions, (ii) the
      bla(CTX-M-3) and bla(CTX-M-15) genes on pEK204 and pEK499/pEK516 represent
      separate escape events, and (iii) IncFII plasmids harboring bla(CTX-M-15) have
      played a crucial role in the global spread of CTX-M-15 ESBLs in E. coli.
AU  - Woodford N
AU  - Carattoli A
AU  - Karisik E
AU  - Underwood A
AU  - Ellington MJ
AU  - Livermore DM
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2009 53: 4472-4482.

PMID- 6263625
VI  - 115
DP  - 1981
TI  - Cation dependence of restriction endonuclease EcoRI activity.
PG  - 293-296
AB  - Restriction endonuclease EcoRI cleaves the DNA sequence 5'd(-G-^A-A-T-T-C-)
      under optimum digestion conditions.  A variation in pH and ionic strength can
      result in EcoRI* activity when 5'd(-^A-A-T-T-) is cut. A divalent cation,
      usually Mg2+, is required for enzyme activity, though Mn2+ can also be used.
      Eight different cations with ionic radius/charge ratios similar to Mg2+ were
      tested and Co2+ and Zn2+ were also found to act as cofactors for EcoRI.  A
      comprehensive study has been made of the effect of NaCl and pH on the
      EcoRI/EcoRI* transition in the presence of the above four cations.  Generally,
      a decrease in NaCl and/or an increase in pH caused a decrease in enzyme
      specificity.  The changeover depended on the cation.  They may be placed in
      order of their ability to increase EcoRI specificity thus: Co2+ > Zn2+ > Mg2+ >
      Mn2+.  The Km of EcoRI for ColE1 DNA, in the presence of Co2+, was found to be
      0.4 nM, compared to 3 nM with Mg2+, whereas the turnover was only one
      double-stranded scission/min with Co2+ compared to eight/min with Mg2+.  The
      implications of all these findings on the enzyme's mechanism are discussed.
AU  - Woodhead JL
AU  - Bhave N
AU  - Malcolm DB
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1981 115: 293-296.

PMID- 6245965
VI  - 8
DP  - 1980
TI  - Restriction endonuclease EcoRI binds non-specifically to deoxyribonucleic acid.
PG  - 90-91
AB  - EcoRI is a type-II restriction endonuclease.  These enzymes recognize and cleave specific DNA
      sequences.  Despite the widespread use of these enzymes for genetic manipulation and DNA
      mapping, little is known about the mechanism of any of them, or how they achieve their
      specificity.  EcoRI recognizes and cleaves the DNA sequence 5'...G/A-A-T-T-C...3' at the
      point indicated.  This activity occurs at around neutral pH and at salt concentrations above
      50mM, but at lower salt concentrations and at pH values above 8, the enzyme exhibits EcoRI
      activity when 5'...N/A-A-T-T-N...3' is cut.  Mg2+ is required for both activities.  We have
      shown that EcoRI not only binds to DNA containing EcoRI or EcoRI sites but will also bind to
      DNA containing neither site.
AU  - Woodhead JL
AU  - Malcolm ADB
PT  - Journal Article
TA  - Biochem. Soc. Trans.
JT  - Biochem. Soc. Trans.
SO  - Biochem. Soc. Trans. 1980 8: 90-91.

PMID- 6252547
VI  - 8
DP  - 1980
TI  - Non-specific binding of restriction endonuclease EcoRI to DNA.
PG  - 389-402
AB  - Restriction endonuclease, EcoR1 cleaves the DNA sequence (5' - 3')G -^ A - A -
      T - T - C (3' - 5')C - T - T - A - A -^ G at the points indicated.  Under
      certain conditions, EcoRI activity is observed when (5' - 3')N1 -^ A - A - T -
      T - N2 (3' - 5')N3 - T - T - A - A -^ N4 is cut.  Mg2+ is required for both
      activities.  We find that in addition to binding to the above sites, EcoRI will
      also bind, although less strongly, to DNA containing neither site.  Methyl
      acetimidate, which reacts specifically with lysine residues, inactivates the
      enzyme.  This specific effect can be prevented by SV40 DNA and lambda DNA which
      contain EcoRI and EcoRI sites, by PhiX174 DNA, which has only EcoRI sites and
      also by Polyd(AT) and polyd(GC) containing neither site.  Protection occurs in
      the absence or presence of magnesium.  The significance of this non-specific
      binding, both for the use and mechanism of EcoR1 will be discussed.
AU  - Woodhead JL
AU  - Malcolm ADB
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1980 8: 389-402.

PMID- 6273165
VI  - 120
DP  - 1981
TI  - The essential carboxyl group in restriction endonuclease EcoRI.
PG  - 125-128
AB  - We have carried out studies on type II restriction endonuclease R.EcoRI, wich
      cleaves the DNA sequence 5'd(G^A-A-T-T-C-)3', as indicated.  The active form of
      the enzyme consists of two subunits, each 31063 molecular weight.  A
      water-soluble reagent, 1-cyclohexyl-3-(2-morpholinoethyl)carbodiimide
      metho-p-sulphonate, which reacts with carboxyl groups and also with tyrosine
      and cysteine residues, has been found to inactivate this enzyme.  Results are
      presented which show the following. (1) This specific inactivation is not due
      to modification of tyrosine or cysteine residues.  (2) There is one carboxyl
      group per subunit which, when modified with carbodiimide, inactivates the
      enzyme.  (3) PhiX174 DNA (which does not contain EcoRI sites) partially
      protects the enzyme from the carbodiimide; protection is unaffected by the
      additional presence of Mg2+, but significantly greater with Co2+ and
      PhiX174DNA.
AU  - Woodhead JL
AU  - Malcolm ADB
PT  - Journal Article
TA  - Eur. J. Biochem.
JT  - Eur. J. Biochem.
SO  - Eur. J. Biochem. 1981 120: 125-128.

PMID- 28982984
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Two Uncultured Armatimonadetes Associated with a Microcystis sp. (Cyanobacteria) Isolate.
PG  - e00717-17
AB  - Two genome sequences of the phylum Armatimonadetes, derived from terrestrial environments,
      have been previously described. Here, two additional
      Armatimonadetes genome sequences were obtained via single-molecule real-time
      (SMRT) sequencing of an enrichment culture of the bloom-forming cyanobacterium
      Microcystis sp. isolated from a eutrophic lake (Brandenburg, Germany). The
      genomes are most closely affiliated with the class Fimbriimonadales, although
      they are smaller than the 5.6-Mbp type strain genome.
AU  - Woodhouse JN
AU  - Makower AK
AU  - Grossart HP
AU  - Dittmann E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00717-17.

PMID- 12081973
VI  - 184
DP  - 2002
TI  - Burkholderia thailandensis E125 harbors a temperate bacteriophage specific for Burkholderia mallei.
PG  - 4003-4017
AB  - Burkholderia thailandensis is a nonpathogenic gram-negative bacillus that is closely related
      to Burkholderia mallei and Burkholderia pseudomallei. We found that B. thailandensis E125
      spontaneously produced a bacteriophage, termed phiE125, which formed turbid plaques in top
      agar containing B. mallei ATCC 23344. We examined the host range of phiE125 and found that it
      formed plaques on B. mallei but not on any other bacterial species tested, including B.
      thailandensis and B. pseudomallei. Examination of the bacteriophage by transmission electron
      microscopy revealed an isometric head and a long noncontractile tail. B. mallei NCTC 120 and
      B. mallei DB110795 were resistant to infection with phiE125 and did not produce
      lipopolysaccharide (LPS) O antigen due to IS407A insertions in wbiE and wbiG, respectively.
      wbiE was provided in trans on a broad-host-range plasmid to B. mallei NCTC 120, and it
      restored LPS O-antigen production and susceptibility to phiE125. The 53,373-bp phiE125 genome
      contained 70 genes, an IS3 family insertion sequence (ISBt3), and an attachment site (attP)
      encompassing the 3' end of a proline tRNA (UGG) gene. While the overall genetic organization
      of the phiE125 genome was similar to lambda-like bacteriophages and prophages, it also
      possessed a novel cluster of putative replication and lysogeny genes. The phiE125 genome
      encoded an adenine and a cytosine methyltransferase, and purified bacteriophage DNA contained
      both N6-methyladenine and N4-methylcytosine. The results presented here demonstrate that
      phiE125 is a new member of the lambda supergroup of Siphoviridae that may be useful as a
      diagnostic tool for B. mallei.
AU  - Woods DE
AU  - Jeddeloh JA
AU  - Fritz DL
AU  - DeShazer D
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2002 184: 4003-4017.

PMID- 27081134
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Lactobacillus crispatus JCM5810, Which Can Reduce Campylobacter jejuni Colonization in Chicken Intestine.
PG  - e00255-16
AB  - We present the 2.05-Mb draft genome sequence ofLactobacillus crispatusJCM5810, a  chicken
      intestinal isolate with the ability to reduceCampylobacter
      jejunicolonization in chickens. The genome sequence will provide insights on the
      probiotic mechanisms ofL. crispatusJCM5810.
AU  - Wooten J
AU  - Liu X
AU  - Miller MJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00255-16.

PMID- 19359590
VI  - 324
DP  - 2009
TI  - Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas.
PG  - 268-272
AB  - Picoeukaryotes are a taxonomically diverse group of organisms less than 2
      micrometers in diameter. Photosynthetic marine picoeukaryotes in the genus
      Micromonas thrive in ecosystems ranging from tropical to polar and could serve as
      sentinel organisms for biogeochemical fluxes of modern oceans during climate
      change. These broadly distributed primary producers belong to an anciently
      diverged sister clade to land plants. Although Micromonas isolates have high 18S
      ribosomal RNA gene identity, we found that genomes from two isolates shared only
      90% of their predicted genes. Their independent evolutionary paths were
      emphasized by distinct riboswitch arrangements as well as the discovery of
      intronic repeat elements in one isolate, and in metagenomic data, but not in
      other genomes. Divergence appears to have been facilitated by selection and
      acquisition processes that actively shape the repertoire of genes that are
      mutually exclusive between the two isolates differently than the core genes.
      Analyses of the Micromonas genomes offer valuable insights into ecological
      differentiation and the dynamic nature of early plant evolution.
AU  - Worden AZ et al
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2009 324: 268-272.

PMID- 24526633
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Burkholderia dolosa PC543 Isolated from Cystic Fibrosis  Airways.
PG  - e00043-14
AB  - Burkholderia dolosa is a member of the Burkholderia cepacia complex, a group of opportunistic
      bacterial pathogens often associated with fatal chronic infections
      in the lungs of patients suffering from cystic fibrosis (CF). Here, we announce
      the draft genome sequence of B. dolosa PC543 (LMG 19468), a CF airway isolate.
AU  - Workentine ML
AU  - Surette MG
AU  - Bernier SP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00043-14.

PMID- 28522711
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Five Brazilian Clostridium botulinum Group III Type D/C Strains.
PG  - e00349-17
AB  - Animal botulism is mainly associated with Clostridium botulinum group III-producing neurotoxin
      types C, C/D, D, and D/C. In this report, we present the
      draft genome sequences of the first five strains of Clostridium botulinum type
      D/C isolated in Brazil and used for vaccination purposes.
AU  - Woudstra C
AU  - Brito RB
AU  - Fonseca JAA
AU  - Silva ROS
AU  - Lobato FCF
AU  - Fach P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00349-17.

PMID- 28360154
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of 12 Feline Bartonella henselae Isolates.
PG  - e00075-17
AB  - Bartonella henselae is the main causative agent of cat scratch disease. In this report, we
      present the draft genome sequences of 12 strains of Bartonella
      henselae originating from the United States, Denmark, and France. These strains
      were isolated from cats and belonged to either 16S rRNA genotype I or 16S rRNA
      genotype II.
AU  - Woudstra C
AU  - Fach P
AU  - Chomel BB
AU  - Haddad N
AU  - Boulouis HJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00075-17.

PMID- 26430029
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of 17 French Clostridium botulinum Group III Strains.
PG  - e01105-15
AB  - Animal botulism is mainly associated with Clostridium botulinum group III strains producing
      neurotoxin types C, C/D, D, and D/C. In this report, we present the draft genome sequences of
      fourteen strains of Clostridium botulinum producing type C/D and two strains producing type
      D/C isolated in France, and one strain producing type D/C that originated from New Caledonia.
AU  - Woudstra C
AU  - Le Marechal C
AU  - Souillard R
AU  - Bayon-Auboyer MH
AU  - Mermoud I
AU  - Desoutter D
AU  - Fach P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01105-15.

PMID- 22180807
VI  - 5
DP  - 2011
TI  - Complete genome sequence of the gliding freshwater bacterium Fluviicola taffensis type strain (RW262).
PG  - 21-29
AB  - Fluviicola taffensis O'Sullivan et al. 2005 belongs to the monotypic genus Fluviicola within
      the family Cryomorphaceae. The species is of interest because
      of its isolated phylogenetic location in the genome-sequenced fraction of the
      tree of life. Strain RW262(T) forms a monophyletic lineage with uncultivated
      bacteria represented in freshwater 16S rRNA gene libraries. A similar
      phylogenetic differentiation occurs between freshwater and marine bacteria in the
      family Flavobacteriaceae, a sister family to Cryomorphaceae. Most remarkable is
      the inability of this freshwater bacterium to grow in the presence of Na(+) ions.
      All other genera in the family Cryomorphaceae are from marine habitats and have
      an absolute requirement for Na(+) ions or natural sea water. F. taffensis is the
      first member of the family Cryomorphaceae with a completely sequenced and
      publicly available genome. The 4,633,577 bp long genome with its 4,082
      protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteria
      and Archaea project.
AU  - Woyke T et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 5: 21-29.

PMID- 10542216
VI  - 274
DP  - 1999
TI  - The kinetic mechanism of EcoRI endonuclease.
PG  - 31896-31902
AB  - Steady-state parameters governing cleavage of pBR322 DNA by EcoRI endonuclease are highly
      sensitive to ionic environment, with K(m) and k(cat) increasing 1,000-fold and 15-fold,
      respectively, when ionic strength is increased from 0.059 to 0.23 M.  By contrast,
      pre-steady-state analysis has shown that recognition, as well as first and second strand
      cleavage events that occur once the enzyme has arrived at the EcoRI site, are essentially
      insensitive to ionic strength, and has demonstrated that the rate-limiting step for
      endonuclease turnover occurs after double-strand cleavage under all conditions tested.
      Furthermore, processive cleavage of a pBR322 variant bearing two closely spaced EcoRI sites is
      governed by the same turnover number as hydrolysis of parental pBR322, which contains only a
      single EcoRI sequence, ruling out slow release of the enzyme from the cleaved site or a slow
      conformational change subsequent to double-strand cleavage. We attribute the effects of ionic
      strength on steady-state parameters to nonspecific endonuclease.DNA interactions, reflecting
      facilitated diffusion processes, that occur prior to EcoRI sequence recognition and subsequent
      to DNA cleavage.
AU  - Wright DJ
AU  - Jack WE
AU  - Modrich P
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1999 274: 31896-31902.

PMID- 2745418
VI  - 264
DP  - 1989
TI  - The negative charge of Glu-111 is required to activate the cleavage center of EcoRI endonuclease.
PG  - 11816-11821
AB  - King et al. JBC (1989) 264, 11807-11815 have shown that Glu-111 is required for
      DNA cleavage by EcoRI endonuclease and have suggested that this residue is
      required for activation of the cleavage center upon specific recognition.  We
      have substituted Gln or Asp for Glu-111 by oligonucleotide-directed
      mutagenesis.  First and second strand cleavage rate constants are reduced by a
      factor of more than 10/4 by the Gln-111 substitution.  However, these rate
      constants are enhanced 9-fold when pH is increased from 7.6 to 8.5, which
      enhances strand cleavage at EcoRI sites by wild type endonuclease to a similar
      degree.  The specific affinity of Gln-111 endonuclease for EcoRI sites is 1000
      times greater than that of wild type enzyme reflecting a decrease in the rate
      constant governing specific complex dissociation.  In contrast to Gln-111
      endonuclease, the equilibrium specific affinity of Asp-111 endonuclease for the
      EcoRI sequence is similar to that of wild type enzyme, and first and second
      strand cleavage rate constants are reduced only 100-fold relative to wild type
      enzyme.  These results suggest that a negative charge on residue 111 is
      required for strand cleavage and are consistent with participation of Glu-111
      in activation of the DNA cleavage center, with energy associated with specific
      sequence recognition driving this process.
AU  - Wright DJ
AU  - King K
AU  - Modrich P
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1989 264: 11816-11821.

PMID- 24913165
VI  - 58
DP  - 2014
TI  - Population structure of KPC-producing Klebsiella pneumoniae isolates from midwestern U.S. hospitals.
PG  - 4961-4965
AB  - Genome sequencing of carbapenem-resistant Klebsiella pneumoniae isolates from
      regional U.S. hospitals was used to characterize strain diversity and the
      bla(KPC) genetic context. A phylogeny based on core single-nucleotide variants
      (SNVs) supports a division of sequence type 258 (ST258) into two distinct groups.
      The primary differences between the groups are in the capsular polysaccharide
      locus (cps) and their plasmid contents. A strict association between clade and
      KPC variant was found. The bla(KPC) gene was found on variants of two plasmid
      backbones. This study indicates that highly similar K. pneumoniae subpopulations
      coexist within the same hospitals over time.
AU  - Wright MS
AU  - Perez F
AU  - Brinkac L
AU  - Jacobs MR
AU  - Kaye K
AU  - Cober E
AU  - van Duin D
AU  - Marshall SH
AU  - Hujer AM
AU  - Rudin SD
AU  - Hujer KM
AU  - Bonomo RA
AU  - Adams MD
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2014 58: 4961-4965.

PMID- 9294447
VI  - 179
DP  - 1997
TI  - The CcrM DNA methyltransferase is widespread in the alpha subdivision of proteobacteria, and its essential functions are conserved in Rhizobium meliloti and Caulobacter crescentus.
PG  - 5869-5877
AB  - the Caulobacter crescentus DNA methyltransferase CcrM (M.CcrMI) methylates the adenine residue
      in the sequence GANTC.  The CcrM DNA methyltransferase is essential for viability, but it does
      not appear to be part of a DNA restriction-modification system.  CcrM homologs are widespread
      in the alpha subdivision of gram-negative bacteria.  We have amplified and sequenced a 258-bp
      region of the ccrM gene from several of these bacteria, including Rhizobium meliloti, Brucella
      abortus, Agrobacterium tumefaciens, and Rhodobacter capsulatus.  Alignment of the deduced
      amino acid sequences revealed that these proteins constitute a highly conserved DNA
      methyltransferase family.  Isolation of the full-length ccrM genes from the aquatic bacterium
      C. crescentus, the soil bacterium R. meliloti, and the intracellular pathogen B. abortus
      showed that this sequence conservation extends over the entire protein.  In at least two alpha
      subdivision bacteria, R. meliloti and C. crescentus, CcrM-mediated methylation has important
      cellular functions.  In both organisms, CcrM is essential for viability.  Over-expression of
      CcrM in either bacterium results in the defects in cell division and cell morphology and in
      the initiation of DNA replication.  Finally, the C. crescentus and R. meliloti ccrM genes are
      functionally interchangeable, as the complemented strains are viable and the chromosomes are
      methylated.  Thus, in both R. meliloti and C. crescentus, CcrM methylation is an integral
      component of the cell cycle.  We speculate that CcrM-mediated DNA methylation is likely to
      have similar roles among alpha subdivision bacteria.
AU  - Wright R
AU  - Stephens C
AU  - Shapiro L
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1997 179: 5869-5877.

PMID- 8666236
VI  - 10
DP  - 1996
TI  - Caulobacter Lon protease has a critical role in cell-cyle control of DNA methylation.
PG  - 1532-1542
AB  - CcrM an adenine DNA methyltransferase, is essential for viability in Caulobacter crescentus.
      The CcrM protein is present only in the predivisional stage of the cell cycle, resulting in
      cell-cycle-dependent variation of the DNA methylation state of the chromosome.  The
      availability of CcrM is controlled in two ways: (1) the ccrM gene is transcribed only in the
      predivisional cell, and (2) the CcrM protein is rapidly degraded prior to cell division.  We
      demonstrate here that CcrM is an important target of the Lon protease pathway in C.
      crescentus.  In a lon null mutant, ccrM transcription is still temporally regulated, but the
      CcrM protein is present throughout the cell cycle because of a dramatic increase in its
      stability that results in a fully methylated chromosome throughout the cell cycle.  Because
      the Lon protease is present throughout the cell cycle, it is likely that the level of CcrM in
      the cell is controlled by a dynamic balance between temporally varied transcription and
      constitutive degradation.  We have shown previously that restriction of CcrM to the C.
      crescentus predivisional cell is essential for normal morphogenesis and progression through
      the cell cycle.  Comparison of the lon null mutant strain with a strain whose DNA remains
      fully methylated as a result of constitutive expression of ccrM suggests that the effect of
      Lon on DNA methylation contributes to several developmental defects observed in the lon
      mutant.  These defects include a frequent failure to complete cell abnormalities exhibited by
      the lon null mutant, such as the formation of abnormally long stalks, appear to be unrelated
      to altered chromosome methylation state.  The Lon protease thus exhibits pleiotropic effects
      in C. crescentus growth and development.
AU  - Wright R
AU  - Stephens C
AU  - Zweiger G
AU  - Shapiro L
AU  - Alley MRK
PT  - Journal Article
TA  - Genes Dev.
JT  - Genes Dev.
SO  - Genes Dev. 1996 10: 1532-1542.

PMID- Not carried by PubMed...
VI  - 96
DP  - 1996
TI  - Cell cycle turnover of a DNA methyltransferase in Caulobacter is dependent on the Lon protease.
PG  - 527
AB  - CcrM, an adenine DNA methyltransferase, is essential for viability in Caulobacter
      crescentus.  CcrM is present only in the predivisional state of the Caulobacter cell cycle.
      As a
      consequence, the DNA methylation state of the chromosome is cell cycle regulated.  CcrM levels
      are controlled in two ways (a) transcription of the ccrM gene is limited to the predivisional
      cell and
      (b) the CcrM protein is degraded prior to cell division.  This transient presence of CcrM is
      important, as constitutive expression of ccrM causes developmental defects.  In our efforts to
      identify the protease responsible for CcrM turnover, the Caulobacter Lon homolog was isolated.
      In a Lon null mutant, CcrM is present throughout the cell cycle.  Thus, the Lon protease is
      required
      for turnover of CcrM, and is necessary for cell cycle regulation of DNA methylation.  We are
      currently constructing mutant alleles of CcrM to examine the requirements of Lon-dependent
      CcrM
      proteolysis.  We have demonstrated that CcrM homologs are widespread in the alpha-subdivision
      of purple gram negative bacteria and are currently cloning several of these homologs.
AU  - Wright RJ
AU  - Stephens C
AU  - Alley D
AU  - Zweiger G
AU  - Shapiro L
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1996 96: 527.

PMID- 20833787
VI  - 76
DP  - 2010
TI  - Differences in Methylation at GATC Sites in Genomic DNA of Campylobacter coli from Turkeys and Swine.
PG  - 7314-7317
AB  - A significant fraction (46/108, 43%) of swine isolates of Campylobacter coli but none of 81
      isolates of C. coli from turkeys had genomic DNA
      that was resistant to digestion by MboI, suggesting methylation of
      adenines at GATC sites. No consistent association was noted between
      antimicrobial resistance and MboI resistance. Seven swine-associated
      multilocus sequence typing-based sequence types (STs) were detected
      among multiple isolates with MboI-resistant DNA. The data suggest
      host-associated DNA modification system(s) specific for adenine at GATC
      sites in C. coli from swine.
AU  - Wright S
AU  - Wilson S
AU  - Miller WG
AU  - Mandrell RE
AU  - Siletzky RM
AU  - Kathariou S
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2010 76: 7314-7317.

PMID- 28619795
VI  - 5
DP  - 2017
TI  - Genome Sequence of Leuconostoc citreum DmW_111, Isolated from Wild Drosophila.
PG  - e00507-17
AB  - Isolates of the lactic acid bacterium Leuconostoc citreum are a major part of fermentation
      processes, especially in Korean kimchi. Here, we present the genome
      of L. citreum DmW_111, isolated from wild Drosophila melanogaster; analysis of
      this genome will expand the diversity of genome sequences for non-Lactobacillus
      spp. isolated from D. melanogaster.
AU  - Wright SM
AU  - Carroll C
AU  - Walters A
AU  - Newell PD
AU  - Chaston JM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00507-17.

PMID- 28888816
VI  - 201
DP  - 2018
TI  - The repeat structure of two paralogous genes, Yersinia ruckeri invasin (yrInv) and a 'Y. ruckeri invasin-like molecule', (yrIlm) sheds light on the evolution of adhesive capacities of a fish pathogen.
PG  - 171-183
AB  - Inverse autotransporters comprise the recently identified type Ve secretion system and are
      exemplified by intimin from enterohaemorrhagic Escherichia coli
      and invasin from enteropathogenic Yersiniae. These proteins share a common domain
      architecture and promote bacterial adhesion to host cells. Here, we identified
      and characterized two putative inverse autotransporter genes in the fish pathogen
      Yersinia ruckeri NVH_3758, namely yrInv (for Y. ruckeri invasin) and yrIlm (for
      Y. ruckeri invasin-like molecule). When trying to clone the highly repetitive
      genes for structural and functional studies, we experienced problems in obtaining
      PCR products. PCR failures and the highly repetitive nature of inverse
      autotransporters prompted us to sequence the genome of Y. ruckeri NVH_3758 using
      PacBio sequencing, which produces some of the longest average read lengths
      available in the industry at this moment. According to our sequencing data, YrIlm
      is composed of 2603 amino acids (7812bp) and has a molecular mass of 256.4kDa.
      Based on the new genome information, we performed PCR analysis on four
      non-sequenced Y. ruckeri strains as well as the sequenced. Y. ruckeri type
      strain. We found that the genes are variably present in the strains, and that the
      length of yrIlm, when present, also varies. In addition, the length of the gene
      product for all strains, including the type strain, was much longer than expected
      based on deposited sequences. The internal repeats of the yrInv gene product are
      highly diverged, but represent the same bacterial immunoglobulin-like domains as
      in yrIlm. Using qRT-PCR, we found that yrIlm and yrInv are differentially
      expressed under conditions relevant for pathogenesis. In addition, we compared
      the genomic context of both genes in the newly sequenced Y. ruckeri strain to all
      available PacBio-sequenced Y. ruckeri genomes, and found indications of recent
      events of horizontal gene transfer. Taken together, this study demonstrates and
      highlights the power of Single Molecule Real-Time technology for sequencing
      highly repetitive proteins, and sheds light on the genetic events that gave rise
      to these highly repetitive genes in a commercially important fish pathogen.
AU  - Wrobel A
AU  - Ottoni C
AU  - Leo JC
AU  - Gulla S
AU  - Linke D
PT  - Journal Article
TA  - J. Struct. Biol.
JT  - J. Struct. Biol.
SO  - J. Struct. Biol. 2018 201: 171-183.

PMID- 25685258
VI  - 10
DP  - 2015
TI  - Complete genome sequence of the fish pathogen Flavobacterium psychrophilum ATCC 49418(T.).
PG  - 3
AB  - Flavobacterium psychrophilum is the causative agent of bacterial cold water disease and
      rainbow trout fry mortality syndrome in salmonid fishes and is
      associated with significant losses in the aquaculture industry. The virulence
      factors and molecular mechanisms of pathogenesis of F. psychrophilum are poorly
      understood. Moreover, at the present time, there are no effective vaccines and
      control using antimicrobial agents is problematic due to growing antimicrobial
      resistance and the fact that sick fish don't eat. In the hopes of identifying
      vaccine and therapeutic targets, we sequenced the genome of the type strain ATCC
      49418 which was isolated from the kidney of a Coho salmon (Oncorhychus kisutch)
      in Washington State (U.S.A.) in 1989. The genome is 2,715,909 bp with a G+C
      content of 32.75%. It contains 6 rRNA operons, 49 tRNA genes, and is predicted to
      encode 2,329 proteins.
AU  - Wu AK
AU  - Kropinski AM
AU  - Lumsden JS
AU  - Dixon B
AU  - MacInnes JI
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 3.

PMID- 
VI  - 19
DP  - 2013
TI  - Construction and Characterization of Restriction-Modification Deficient Mutants in Zymomonas mobilis ZM4.
PG  - 189-197
AB  - Low transformation efficiency is an obstacle to genetic or molecular manipulations in
      ethanologen Zymomonas mobilis. In the present study, 5 defective strains were constructed in
      Z. mobilis strain ZM4 by inactivating restriction-modification (R-M) system candidate genes.
      Inactivation of ZMO0028 (mrr) and ZMO1933 significantly improved electroporation efficiency by
      17 folds and 2 folds when ZM4 was transformed with the methylated plasmid DNA. Disruption of
      ZMO0575 significantly decreased the transfor ation efficiency when transformed with both
      methylated and unmethylated plasmid DNAs. In comparison with other mutants, Zmmrr and Zm1933
      displayed high stability. Furthermore, fermentation results showed that R-M mutants did not
      significantly alter the major bacterial traits such as growth, glucose utilization and ethanol
      yield. In conclusion, R-M systems in Z. mobilis were investigated in this study, and the
      characterization of those R-M genes contributed to creating engineering strains suitable for
      genet ic and molecular manipulations.
AU  - Wu Bo
AU  - He M
AU  - Feng H
AU  - Zhang Y
AU  - Hu Q
AU  - Zhang Y
PT  - Journal Article
TA  - Chin. J. Appl. Environ. Biol.
JT  - Chin. J. Appl. Environ. Biol.
SO  - Chin. J. Appl. Environ. Biol. 2013 19: 189-197.

PMID- 
VI  - 32
DP  - 2010
TI  - Bioinformatics analysis of DNA methyltransferase from plants.
PG  - 83-89
AB  - The nucleic acid sequences and amino acid sequences of DNA methyltransferase from oil palm,
      Prunus, Pisum, Daucus and Arabidopsis, which were registerd in GenBank, were predicted and
      analyzed, using bioinformatics tools according to the composition of nucleic acid sequences
      and amino acid sequences, physical and chemical properties, homology alignments, signal
      peptides, transmembrane topological structure, hydrophobicity and hydrophilicity, secondary
      and tertiary structures of protein and molecular phylogenetic evolution.  The results
      indicated that the full-length cDNA of DNMT contains 5'-untranslated region, an open reading
      frame and 3'-untranslated region, that DNMT has no signal peptides and transmembrane peptides
      and is a hydrophilic protein, including two BAH domains and a DNA methylase, and that alpha
      helix and random coil are the main components of its secondary structure and all domains bind
      in turn by means of electrostatic interaction.
AU  - Wu C-T
AU  - Li W-G
AU  - Gao X-S
AU  - Zhang X-F
PT  - Journal Article
TA  - Xinan Daxue Xuebao, Ziran Kexueban
JT  - Xinan Daxue Xuebao, Ziran Kexueban
SO  - Xinan Daxue Xuebao, Ziran Kexueban 2010 32: 83-89.

PMID- 26988050
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of an ortho-Nitrophenyl-beta-d-Galactoside (ONPG)-Negative  Strain of Vibrio cholerae, Isolated from Drakes Bay, California.
PG  - e00135-16
AB  - We present the draft whole-genome sequence of a Vibrio cholerae strain (Vc25-3) isolated from
      Drakes Bay, California. This environmental isolate has an atypical
      morphology and is ortho-nitrophenyl-beta-d-galactoside (ONPG)-negative.
AU  - Wu CH
AU  - Chen CY
AU  - Morales C
AU  - Kiang D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00135-16.

PMID- 25301649
VI  - 2
DP  - 2014
TI  - Draft Whole-Genome Sequences of Three Shiga Toxin-Producing Escherichia coli O91:H21 Isolates, Two from Hemolytic Uremic Syndrome Patients and One of Porcine   Origin.
PG  - e01000-14
AB  - This study presents three genomes of O91:H21 isolates, two from hemolytic uremic  syndrome
      patients and one of porcine origin. Genome analyses reveal that one of
      the human isolates contains both Shiga toxin-encoding genes (stx1 and stx2), and
      all three isolates contain putative adhesin (iha and eaeH) and antibiotic
      resistance (ampC) genes.
AU  - Wu CH
AU  - Zhang P
AU  - Morales CQ
AU  - Kiang D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01000-14.

PMID- 22815437
VI  - 194
DP  - 2012
TI  - Genome Sequence of a Novel Human Pathogen, Aeromonas aquariorum.
PG  - 4114-4115
AB  - Aeromonas aquariorum, a recently described species, is associated with a variety  of human
      diseases. We present here the first genome sequence of A. aquariorum
      strain AAk1, which was isolated as the sole pathogen from the blood of a patient
      with septicemia and necrotizing fasciitis.
AU  - Wu CJ
AU  - Wang HC
AU  - Chen CS
AU  - Shu HY
AU  - Kao AW
AU  - Chen PL
AU  - Ko WC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4114-4115.

PMID- 19148287
VI  - 4
DP  - 2009
TI  - Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum.
PG  - E4207
AB  - In order to enrich the phylogenetic diversity represented in the available
      sequenced bacterial genomes and as part of an "Assembling the Tree of
      Life" project, we determined the genome sequence of Thermomicrobium roseum
      DSM 5159. T. roseum DSM 5159 is a red-pigmented, rod-shaped, Gram-negative
      extreme thermophile isolated from a hot spring that possesses both an
      atypical cell wall composition and an unusual cell membrane that is
      composed entirely of long-chain 1,2-diols. Its genome is composed of two
      circular DNA elements, one of 2,006,217 bp (referred to as the chromosome)
      and one of 919,596 bp (referred to as the megaplasmid). Strikingly, though
      few standard housekeeping genes are found on the megaplasmid, it does
      encode a complete system for chemotaxis including both chemosensory
      components and an entire flagellar apparatus. This is the first known
      example of a complete flagellar system being encoded on a plasmid and
      suggests a straightforward means for lateral transfer of flagellum-based
      motility. Phylogenomic analyses support the recent rRNA-based analyses
      that led to T. roseum being removed from the phylum Thermomicrobia and
      assigned to the phylum Chloroflexi. Because T. roseum is a deep-branching
      member of this phylum, analysis of its genome provides insights into the
      evolution of the Chloroflexi. In addition, even though this species is not
      photosynthetic, analysis of the genome provides some insight into the
      origins of photosynthesis in the Chloroflexi. Metabolic pathway
      reconstructions and experimental studies revealed new aspects of the
      biology of this species. For example, we present evidence that T. roseum
      oxidizes CO aerobically, making it the first thermophile known to do so.
      In addition, we propose that glycosylation of its carotenoids plays a
      crucial role in the adaptation of the cell membrane to this bacterium's
      thermophilic lifestyle. Analyses of published metagenomic sequences from
      two hot springs similar to the one from which this strain was isolated,
      show that close relatives of T. roseum DSM 5159 are present but have some
      key differences from the strain sequenced.
AU  - Wu D
AU  - Raymond J
AU  - Wu M
AU  - Chatterji S
AU  - Ren Q
AU  - Graham JE
AU  - Bryant DA
AU  - Robb F
AU  - Colman A
AU  - Tallon LJ
AU  - Badger JH
AU  - Madupu R
AU  - Ward NL
AU  - Eisen JA
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2009 4: E4207.

PMID- 23045492
VI  - 194
DP  - 2012
TI  - Genome Sequence of Pseudomonas aeruginosa Strain AH16, Isolated from a Patient with Chronic Pneumonia in China.
PG  - 5976-5977
AB  - Pseudomonas aeruginosa AH16 is a virulent strain isolated from a patient with chronic
      pneumonia in China. Here, we present a 6.8-Mb (G+C content, 66.13%)
      assembly of its genome with 6,332 putative coding sequences, which may provide
      insights into the genomic basis of activity of the clinical P. aeruginosa strain
      in China.
AU  - Wu DQ
AU  - Cheng H
AU  - Wang C
AU  - Zhang C
AU  - Wang Y
AU  - Shao J
AU  - Duan Q
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5976-5977.

PMID- 21884571
VI  - 12
DP  - 2011
TI  - Genomic analysis and temperature-dependent transcriptome profiles of the rhizosphere originating strain Pseudomonas aeruginosa M18.
PG  - 438
AB  - ABSTRACT: BACKGROUND: Our previously published reports have described an
      effective biocontrol agent named Pseudomonas sp. M18 as its 16S rDNA
      sequence and several regulator genes share homologous sequences with those
      of P. aeruginosa, but there are several unusual phenotypic features. This
      study aims to explore its strain specific genomic features and gene
      expression patterns at different temperatures. RESULTS: The complete M18
      genome is composed of a single chromosome of 6,327,754 base pairs
      containing 5684 open reading frames. Seven genomic islands, including two
      novel prophage clusters and five specific non-phage islands were
      identified besides the conserved P. aeruginosa core genome. Each prophage
      contains a putative chitinase coding gene, and the prophage II contains a
      capB gene encoding a putative cold stress protein. The non-phage GIs
      contain genes responsible for pyoluteorin biosynthesis, environmental
      substance degradation and type I and III restriction-modification systems.
      Compared with other P. aeruginosa strains, the fewest number (3) of
      insertion sequences and the most number (3) of clustered regularly
      interspaced short palindromic repeats in M18 genome may contribute to the
      relative genome stability. Although the M18 genome is most closely related
      to that of P. aeruginosa strain LESB58, the strain M18 is more susceptible
      to several antimicrobial agents and easier to be erased in a mouse acute
      lung infection model than the strain LESB58. The whole M18 transcriptomic
      analysis indicated that 10.6% of the expressed genes are
      temperature-dependent, with 22 genes up-regulated at 28 degrees Celsius in
      three GIs and one prophage but none at 37 degrees Celsius. CONCLUSIONS:
      The P. aeruginosa strain M18 has its evolved specific genomic structures
      and temperature dependent expression patterns to meet the requirement of
      its fitness and competitiveness under selective pressures imposed on the
      strain in rhizosphere niche.
AU  - Wu DQ
AU  - Ye J
AU  - Ou HY
AU  - Wei X
AU  - Huang X
AU  - He YW
AU  - Xu Y
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2011 12: 438.

PMID- 26543117
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequence of 'Candidatus Profftella armatura' from Diaphorina citri in Guangdong, China.
PG  - e01282-15
AB  - The genome of 'Candidatus Profftella armatura' strain YCPA from Diaphorina citri  in
      Guangdong, China, was sequenced. The strain has a chromosome of 457,565 bp,
      24.3% G+C content, 364 predicted open reading frames (ORFs), and 38 RNAs, and a
      plasmid, pYCPA54, of 5,458 bp with 23.9% G+C content and 5 ORFs.
AU  - Wu F
AU  - Deng X
AU  - Liang G
AU  - Huang J
AU  - Cen Y
AU  - Chen J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01282-15.

PMID- 26679599
VI  - 3
DP  - 2015
TI  - De Novo Genome Sequence of 'Candidatus Liberibacter solanacearum' from a Single Potato Psyllid in California.
PG  - e01500-15
AB  - The draft genome sequence of 'Candidatus Liberibacter solanacearum' strain RSTM from a
      potato psyllid (Bactericera cockerelli) in California is reported here.
      The RSTM strain has a genome size of 1,286,787 bp, a G+C content of 35.1%, 1,211
      predicted open reading frames (ORFs), and 43 RNA genes.
AU  - Wu F
AU  - Deng X
AU  - Liang G
AU  - Wallis C
AU  - Trumble JT
AU  - Prager S
AU  - Chen J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01500-15.

PMID- 26701083
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of 'Candidatus Liberibacter asiaticus' from a Citrus Tree in San Gabriel, California.
PG  - e01508-15
AB  - The draft genome sequence of 'Candidatus Liberibacter asiaticus' strain SGCA5 from an orange
      citrus tree in San Gabriel, California, is reported here. SGCA5
      has a genome size of 1,201,445 bp, a G+C content of 36.4%, 1,152 predicted open
      reading frames (ORFs), and 42 RNA genes.
AU  - Wu F
AU  - Kumagai L
AU  - Liang G
AU  - Deng X
AU  - Zheng Z
AU  - Keremane M
AU  - Chen J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01508-15.

PMID- 26543132
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of 'Candidatus Liberibacter asiaticus' from Diaphorina citri in Guangdong, China.
PG  - e01316-15
AB  - The draft genome sequence of 'Candidatus Liberibacter asiaticus' strain YCPsy from an Asian
      citrus psyllid (Diaphorina citri) in Guangdong, China, is reported
      here. The YCPsy strain has a genome size of 1,233,647 bp, 36.5% G+C content,
      1,171 open reading frames (ORFs), and 53 RNAs.
AU  - Wu F
AU  - Zheng Z
AU  - Deng X
AU  - Cen Y
AU  - Liang G
AU  - Chen J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01316-15.

PMID- 29748403
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Plant-Associated Bacillus Strains Isolated from the Qinghai-Tibetan Plateau.
PG  - e00375-18
AB  - Here, we report the draft genome sequences of 45 plant-associated Bacillus strains isolated
      from the Qinghai-Tibetan plateau. According to their genome
      sequences, 28 isolates were assigned to 10 Bacillus species. Seventeen strains
      could not be assigned and are subjects of further research.
AU  - Wu H
AU  - Borriss R
AU  - Xue P
AU  - Liu F
AU  - Qiao J
AU  - Schneider A
AU  - Lasch P
AU  - Gao X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00375-18.

PMID- 16842508
VI  - 21
DP  - 2006
TI  - Inactivation of DNA adenine methyltransferase alters virulence factors in Actinobacillus actinomycetemcomitans.
PG  - 238-244
AB  - DNA adenine methyltransferase (DAM) plays critical roles in diverse biological pathways in
      gram-negative bacteria, and specifically in
      regulating the expression of virulence genes in several organisms.
      Actinobacillus actinomycetemcomitans plays an important role in the
      pathogenesis of juvenile and adult periodontal disease, yet little is
      known about its mechanisms of gene regulation. DAM is shown here to
      directly or indirectly affect well-known A. actinomycetemcomitans
      virulence factors. A mutant A. actinomycetemcomitans strain lacking the
      dam gene was created by homologous recombination and shows normal
      growth phenotypes when grown exponentially. This mutant strain has four
      sixfold increased levels of extracellular leukotoxin, altered cellular
      levels of leukotoxin, and significant changes in bacterial invasion of
      KB oral epithelial cells. These results provide a basis for further
      characterization of regulatory mechanisms that control A.
      actinomycetemcomitans virulence.
AU  - Wu H
AU  - Lippmann JE
AU  - Oza JP
AU  - Zeng M
AU  - Fives-Taylor P
AU  - Reich NO
PT  - Journal Article
TA  - Oral Microbiol. Immunol.
JT  - Oral Microbiol. Immunol.
SO  - Oral Microbiol. Immunol. 2006 21: 238-244.

PMID- 24233590
VI  - 1
DP  - 2013
TI  - The Rhizobacterium Bacillus amyloliquefaciens subsp. plantarum NAU-B3 Contains a  Large Inversion within the Central Portion of the Genome.
PG  - e00941-13
AB  - The genome of rhizobacterium Bacillus amyloliquefaciens subsp. plantarum strain NAU-B3 is
      4,196,170 bp in size and harbors 4,001 genes. Nine giant gene clusters
      are dedicated to the nonribosomal synthesis of antimicrobial lipopeptides and
      polyketides. Remarkably, NAU_B3 contains a large inversion within the central
      portion of the genome.
AU  - Wu H
AU  - Qiao J
AU  - Blom J
AU  - Rueckert C
AU  - Reva O
AU  - Gao X
AU  - Borriss R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00941-13.

PMID- 24855292
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Ureaplasma parvum Serovar 3 Strain SV3F4, Isolated in Japan.
PG  - e00256-14
AB  - Here, we present the complete genome sequence of Ureaplasma parvum serovar 3, clinical strain
      SV3F4, isolated from a Japanese patient with a history of an
      infectious abortion.
AU  - Wu HN
AU  - Nakura Y
AU  - Motooka D
AU  - Nakamura S
AU  - Nishiumi F
AU  - Ishino S
AU  - Kawai Y
AU  - Tanaka T
AU  - Takeuchi M
AU  - Nakayama M
AU  - Fujita T
AU  - Yanagihara I
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00256-14.

PMID- 30325937
VI  - 13
DP  - 2018
TI  - Type II restriction modification system in Ureaplasma parvum OMC-P162 strain.
PG  - e0205328
AB  - Ureaplasma parvum serovar 3 strain, OMC-P162, was isolated from the human
      placenta of a preterm delivery at 26 weeks' gestation. In this study, we
      sequenced the complete genome of OMC-P162 and compared it with other serovar 3
      strains isolated from patients with different clinical conditions. Ten unique
      genes in OMC-P162, five of which encoded for hypothetical proteins, were
      identified. Of these, genes UPV_229 and UPV_230 formed an operon whose open
      reading frames were predicted to code for a DNA methyltransferase and a
      hypothetical protein, respectively. DNA modification analysis of the OMC-P162
      genome identified N4-methylcytosine (m4C) and N6-methyladenine (m6A), but not
      5-methylocytosine (m5C). UPV230 recombinant protein displayed endonuclease
      activity and recognized the CATG sequence, resulting in a blunt cut between A and
      T. This restriction enzyme activity was identical to that of the cultivated
      OMC-P162 strain, suggesting that this restriction enzyme was naturally expressed
      in OMC-P162. We designated this enzyme as UpaP162. Treatment of pT7Blue plasmid
      with recombinant protein UPV229 completely blocked UpaP162 restriction enzyme
      activity. These results suggest that the UPV_229 and UPV_230 genes act as a type
      II restriction-modification system in Ureaplasma OMC-P162.
AU  - Wu HN
AU  - Nakura Y
AU  - Yoshimura M
AU  - Gaddi-Tantengco OA
AU  - Nomiyama M
AU  - Takayanagi T
AU  - Fujita T
AU  - Yasukawa K
AU  - Yanagihara I
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2018 13: e0205328.

PMID- 8564981
VI  - 56
DP  - 1996
TI  - Expression of prokaryotic HhaI DNA methyltransferase is transforming and lethal to NIH 3T3 cells.
PG  - 616-622
AB  - In neoplastic cells, levels of DNA methyltransferase activity are often increased, and
      evidence is accruing to suggest an important role for this event in tumorigenesis.  To
      evaluate this possibility further, and to investigate the contribution of increasing de novo,
      as opposed to maintenance, DNA methylation in mammalian cells, we expressed the bacterial HhaI
      methyltransferase in cultured murine fibroblasts.  This enzyme is a pure de novo DNA
      methytransferase that methylates the internal C in the sequence GCGC.  We find that both
      constitutive and induced expression of the wild-type HhaI results, primarily, in lethality to
      the cells.  However, surviving cell clones that express low levels of M.HhaI demonstrate
      increased tumorigenicity as assessed by soft agar cloning efficiency (8.6% for sense
      HhaI-transduced PA 317 cells versus 0.4% for antisense controls; 1.7% for sense
      HhaI-transfected NIH 3T3 cells versus 0% for a mutant HhaI control) and tumorigenicity in nude
      mouse heterotransplants (75% for sense HhaI-transduced PA 317 cells versus 18.5% for antisense
      controls).  DNA isolated from the clonogenic sense HhaI clones, versus clones expressing the
      mutant HhaI gene, has no increase in overall CpG methylation but an average of 27% (range,
      16.7-38.9) increase in methylcytosine content at GCGC sites.  These findings suggest that
      eukaryotic cells tolerate a narrow window of increased de novo DNA methylating capacity, above
      which cell death occurs and within which cell transformation results.  Our results further
      emphasize the potential role of increased DNA methyltransferase activity in the evolution of
      cancer.
AU  - Wu J
AU  - Herman JG
AU  - Wilson G
AU  - Lee RY
AU  - Yen R-WC
AU  - Mabry M
AU  - de Bustros A
AU  - Nelkin BD
AU  - Baylin SB
PT  - Journal Article
TA  - Cancer Res.
JT  - Cancer Res.
SO  - Cancer Res. 1996 56: 616-622.

PMID- 8415627
VI  - 90
DP  - 1993
TI  - Expression of an exogenous eukaryotic DNA methyltransferase gene induces transformation of NIH 3T3 cells.
PG  - 8891-8895
AB  - Abnormal regional increases in DNA methylation, which have potential for causing gene
      inactivation and chromosomal instability, are consistently found in immortalized and
      tumorigenic cells. Increased DNA methyltransferase activity, which is also a characteristic of
      such cells, is a candidate to mediate these abnormal DNA methylation patterns. We now show
      that in NIH 3T3 mouse fibroblasts constitutive overexpression of an exogenous mouse DNA
      methyltransferase gene results in a marked increase in overall DNA methylation which is
      accompanied by tumorigenic transformation. These transformation changes can also be elicited
      by dexamethasone-inducible expression of an exogenous DNA methyltransferase gene. Our findings
      provide strong evidence that the increase in DNA methyltransferase activity associated with
      tumor progression could be a key step in carcinogenesis and provide a model system that can be
      used to further study this possibility.
AU  - Wu J
AU  - Issa JP
AU  - Herman J
AU  - Bassett DE
AU  - Nelkin BD
AU  - Baylin SB
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1993 90: 8891-8895.

PMID- 3558369
VI  - 262
DP  - 1987
TI  - Kinetic and catalytic mechanism of HhaI methyltransferase.
PG  - 4778-4786
AB  - Kinetic and catalytic properties of the DNA (cytosine-5)-methyltransferase HhaI
      are described.  With poly(dG-dC) as substrate, the reaction proceeds by an
      equilibrium (or processive) ordered Bi-Bi mechanism in which DNA binds to the
      enzyme first, followed by S-adenosylmethionine (AdoMet).  After methyl
      transfer, S-adenosylhomocysteine (AdoHcy) dissociates followed by methylated
      DNA.  AdoHcy is a potent competitive inhibitor with respect to AdoMet (K=2.0
      microM) and its generation during reactions results in non-linear kinetics.
      AdoMet and AdoHcy significantly interact with only the substrate enzyme-DNA
      complex; they do not bind to free enzyme and bind poorly to the methylated
      enzyme-DNA complex.  In the absence of AdoMet, HhaI methylase catalyzes
      exchange of the 5-H of substrate cytosines for protons of water at about 7-fold
      the rate of methylation.  The 5-H exchange reaction is inhibited by AdoMet or
      AdoHcy.  In the enzyme-DNA-AdoHcy complex, AdoHcy also suppresses dissociation
      of DNA and reassociation of the enzyme with other substrate sequences.  Our
      studies reveal that the catalytic mechanism of DNA
      (cytosine-5)-methyl-transferases involves attack of the C6 of substrate
      cytosines by an enzyme nucleophile and formation of a transient covalent
      adduct.  Based on precedents of other enzymes which catalyze similar reactions
      and the susceptibilitiy of HhaI to inactivation by N-ethylmaleimide, we propose
      that the sulfhydryl group of a cysteine residue is the nucleophilic catalyst.
      Furthermore, we propose that Cys-81 is the active-site catalyst in HhaI.  This
      residue is found in a Pro-Cys doublet which is conserved in all DNA
      (cytosine-5)-methyltransferases whose sequences have been determined to date
      and is found in related enzymes.  Finally, we discuss the possibility that
      covalent adducts between C6 of pyrimidines and nucleophiles of proteins may be
      important general components of protein-nucleic acid interactions.
AU  - Wu JC
AU  - Santi DV
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1987 262: 4778-4786.

PMID- 3340551
VI  - 16
DP  - 1988
TI  - High level expression and purification of HhaI methyltransferase.
PG  - 703-717
AB  - A cloning system for the DNA- (cytosine-5) -methyltransferase MHhaI and high
      level expression of the enzyme are described.  A parent plasmid was constructed
      from fragments of the MHhaI gene and synthetic oligonucleotides.  The construct
      permits introduction of various restriction sites for cloning at precise
      positions near the initiation codon, and beyond the termination codon.  The
      entire MHhaI coding sequence was introduced as a 1042 b.p. NdeI-XbaI fragment
      into the vector pAR3040 which contains the T7 RNA polymerase promoter.  The
      resultant plasmid pTNX3 (MHhaI-pAR3040) was introduced into McrB- E. coli
      strains HB101 and GM2929, and expression of MHhaI was induced by infection with
      the lambda phage CE6 carrying the T7 RNA polymerase gene.  In induced cells,
      catalytically active MHhaI was produced at a level that corresponds to about 8%
      of the total soluble protein; an insoluble form of the protein was also formed,
      but could be readily removed.  The expressed soluble enzyme from HB101/pTNX3
      was purified to apparent homogeneity in about 50% yield by a two-step
      chromatographic procedure involving DEAE-cellulose and Heparin-Sepharose; a one
      liter culture gave about 2.5 mg of pure enzyme.  The molecular weight and
      kinetic properties of the expressed protein are identical to those reported for
      the authentic MHhaI, and its amino terminal sequence agrees with that predicted
      from the DNA sequence.
AU  - Wu JC
AU  - Santi DV
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1988 16: 703-717.

PMID- Not carried by PubMed...
VI  - 0
DP  - 1985
TI  - On the mechanism and inhibition of DNA cytosine methyltransferases.
PG  - 119-129
AB  - Enzyme catalyzed methylation of the 5-position of pyrimidine nucleotides occurs in a number of
      branches of nucleic acid biochemistry. Examples of this reaction include the formation of
      thymidine 5'-monophosphate (TMP) from deoxyuridine 5'-monophosphate (dUMP) by thymidylate
      synthetase (TS), post-transcriptional methylation of RNA molecules, and the methylation of DNA
      cytosine residues by methyltransferases (DCMTases) found in eukaryotic cells and in bacteria.
      While thymidylate synthetase uses 5,10-methylenetetrahydrofolate as the methyl group donor,
      most of the other enzymes require S-adenosylmethionine (AdoMet) for their methyltransferase
      activity.
AU  - Wu JC
AU  - Santi DV
PT  - Journal Article
TA  - Biochemistry and Biology of DNA Methylation
JT  - Biochemistry and Biology of DNA Methylation
SO  - Biochemistry and Biology of DNA Methylation 1985 0: 119-129.

PMID- 25573943
VI  - 3
DP  - 2015
TI  - Finished Genome Sequence of Collimonas arenae Cal35.
PG  - e01408-14
AB  - We announce the finished genome sequence of soil forest isolate Collimonas arenae Cal35, which
      comprises a 5.6-Mbp chromosome and 41-kb plasmid. The Cal35 genome
      is the second one published for the bacterial genus Collimonas and represents the
      first opportunity for high-resolution comparison of genome content and synteny
      among collimonads.
AU  - Wu JJ
AU  - de Jager VC
AU  - Deng WL
AU  - Leveau JH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01408-14.

PMID- Not carried by PubMed...
VI  - 4
DP  - 1992
TI  - Expression of an exogenous eukaryotic DNA methyltransferase gene induces transformation of NIH 3T3 cells.
PG  - A74
AB  - 
AU  - Wu JJ
AU  - Issa JP
AU  - Herman J
AU  - Nelkin BD
AU  - Baylin SB
PT  - Journal Article
TA  - Amer. Soc. Hum. Gen.
JT  - Amer. Soc. Hum. Gen.
SO  - Amer. Soc. Hum. Gen. 1992 4: A74.

PMID- 15995186
VI  - 187
DP  - 2005
TI  - The genome of Salmonella enterica serovar gallinarum: Distinct insertions/deletions and rare rearrangements.
PG  - 4720-4727
AB  - Salmonella enterica serovar Gallinarum is a fowl-adapted pathogen, causing typhoid fever in
      chickens. It has the same antigenic formula (1,9,12:-:-) as S. enterica serovar Pullorum,
      which is also adapted to fowl but causes pullorum disease (diarrhea). The close relatedness
      but distinct pathogeneses make this pair of fowl pathogens good models for studies of
      bacterial genomic evolution and the way these organisms acquired pathogenicity. To locate and
      characterize the genomic differences between serovar Gallinarum and other salmonellae, we
      constructed a physical map of serovar Gallinarum strain SARB21 by using I-CeuI, XbaI, and
      AvrII with pulsed-field gel electrophoresis techniques. In the 4,740-kb genome, we located two
      insertions and six deletions relative to the genome of S. enterica serovar Typhimurium LT2,
      which we used as a reference Salmonella genome. Four of the genomic regions with reduced
      lengths corresponded to the four prophages in the genome of serovar Typhimurium LT2, and the
      others contained several smaller deletions relative to serovar Typhimurium LT2, including
      regions containing srfJ, std, and stj and gene clusters encoding a type I restriction system
      in serovar Typhimurium LT2. The map also revealed some rare rearrangements, including two
      inversions and several translocations. Further characterization of these insertions,
      deletions, and rearrangements will provide new insights into the molecular basis for the
      specific host-pathogen interactions and mechanisms of genomic evolution to create a new
      pathogen.
AU  - Wu K-Y
AU  - Liu G-R
AU  - Liu W-Q
AU  - Wang AQ
AU  - Zhan S
AU  - Sanderson KE
AU  - Johnston RN
AU  - Liu S-L
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2005 187: 4720-4727.

PMID- 19447910
VI  - 191
DP  - 2009
TI  - Genome sequencing and comparative analysis of Klebsiella pneumoniae NTUH-K2044, a strain causing liver abscess and meningitis.
PG  - 4492-4501
AB  - Nosocomial infections caused by antibiotic-resistant Klebsiella pneumoniae are emerging as a
      major health problem worldwide, while community-acquired
      K. pneumoniae infections present with a range of diverse clinical pictures
      in different geographic areas. In particular, an invasive form of K.
      pneumoniae that causes liver abscesses was first observed in Asia and then
      was found worldwide. We are interested in how differences in gene content
      of the same species result in different diseases. Thus, we sequenced the
      whole genome of K. pneumoniae NTUH-K2044, which was isolated from a
      patient with liver abscess and meningitis, and analyzed differences
      compared to strain MGH 78578, which was isolated from a patient with
      pneumonia. Six major types of differences were found in gene clusters that
      included an integrative and conjugative element, clusters involved in
      citrate fermentation, lipopolysaccharide synthesis, and capsular
      polysaccharide synthesis, phage-related insertions, and a cluster
      containing fimbria-related genes. We also conducted comparative genomic
      hybridization with 15 K. pneumoniae isolates obtained from
      community-acquired or nosocomial infections using tiling probes for the
      NTUH-K2044 genome. Hierarchical clustering revealed three major groups of
      genomic insertion-deletion patterns that correlate with the strains'
      clinical features, antimicrobial susceptibilities, and virulence
      phenotypes with mice. Here we report the whole-genome sequence of K.
      pneumoniae NTUH-K2044 and describe evidence showing significant genomic
      diversity and sequence acquisition among K. pneumoniae pathogenic strains.
      Our findings support the hypothesis that these factors are responsible for
      the changes that have occurred in the disease profile over time.
AU  - Wu KM
AU  - Li LH
AU  - Yan JJ
AU  - Tsao N
AU  - Liao TL
AU  - Tsai HC
AU  - Fung CP
AU  - Chen HJ
AU  - Liu YM
AU  - Wang JT
AU  - Fang CT
AU  - Chang SC
AU  - Shu HY
AU  - Liu TT
AU  - Chen YT
AU  - Shiau YR
AU  - Lauderdale TL
AU  - Su IJ
AU  - Kirby R
AU  - Tsai SF
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2009 191: 4492-4501.

PMID- 
VI  - 2
DP  - 2004
TI  - Phylogenomics of the reproductive parasite Wolbachia pipientis wMeI: A streamlined genome overrun by mobile genetic elements.
PG  - 327-341
AB  - The complete sequence of the 1,267,782 bp genome of Wolbachia pipientis wMel, an obligate
      intracellular bacteria of Drosophila melanogaster, has been determined. Wolbachia, which are
      found in a variety of invertebrate species, are of great interest due to their diverse
      interactions with different hosts, which range from many forms of reproductive parasitism to
      mutualistic symbioses. Analysis of the wMel genome, in particular phylogenomic comparisons
      with other intracellular bacteria, has revealed many insights into the biology and evolution
      of wMel and Wolbachia in general. For example, the wMel genome is unique among sequenced
      obligate intracellular species in both being highly streamlined and containing very high
      levels of repetitive DNA and mobile DNA elements. This observation, coupled with multiple
      evolutionary reconstructions, suggests that natural selection is somewhat inefficient in wMel,
      most likely owing to the occurrence of repeated population bottlenecks. Genome analysis
      predicts many metabolic differences with the closely related Rickettsia species, including the
      presence of intact glycolysis and purine synthesis, which may compensate for an inability to
      obtain ATP directly from its host, as Rickettsia can. Other discoveries include the apparent
      inability of wMel to synthesize lipopolysaccharide and the presence of the most genes encoding
      proteins with ankyrin repeat domains of any prokaryotic genome yet sequenced. Despite the
      ability of wMel to infect the germline of its host, we find no evidence for either recent
      lateral gene transfer between wMel and D. melanogaster or older transfers between Wolbachia
      and any host. Evolutionary analysis further supports the hypothesis that mitochondria share a
      common ancestor with the alpha-Proteobacteria, but shows little support for the grouping of
      mitochondria with species in the order Rickettsiales. With the availability of the complete
      genomes of both species and excellent genetic tools for the host, the wMel-D. melanogaster
      symbiosis is now an ideal system for studying the biology and evolution of Wolbachia
      infections.
AU  - Wu M et al
PT  - Journal Article
TA  - PLoS Biology
JT  - PLoS Biology
SO  - PLoS Biology 2004 2: 327-341.

PMID- 26430127
VI  - 350
DP  - 2015
TI  - Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides.
PG  - AAC5992
AB  - Libraries of tens of thousands of transposon mutants generated from each of four
      human gut Bacteroides strains, two representing the same species, were introduced
      simultaneously into gnotobiotic mice together with 11 other wild-type strains to
      generate a 15-member artificial human gut microbiota. Mice received one of two
      distinct diets monotonously, or both in different ordered sequences. Quantifying
      the abundance of mutants in different diet contexts allowed gene-level
      characterization of fitness determinants, niche, stability, and resilience and
      yielded a prebiotic (arabinoxylan) that allowed targeted manipulation of the
      community. The approach described is generalizable and should be useful for
      defining mechanisms critical for sustaining and/or approaches for deliberately
      reconfiguring the highly adaptive and durable relationship between the human gut
      microbiota and host in ways that promote wellness.
AU  - Wu M
AU  - McNulty NP
AU  - Rodionov DA
AU  - Khoroshkin MS
AU  - Griffin NW
AU  - Cheng J
AU  - Latreille P
AU  - Kerstetter RA
AU  - Terrapon N
AU  - Henrissat B
AU  - Osterman AL
AU  - Gordon JI
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2015 350: AAC5992.

PMID- 12456671
VI  - 278
DP  - 2003
TI  - Mismatch repair in methylated DNA. Structure and activity of the mismatch-specific thymine glycosylase domain of methyl-CpG-binding protein MBD4.
PG  - 5285-5291
AB  - MBD4 is a member of the methyl-CpG-binding protein family. It contains two DNA binding
      domains, an amino-proximal methyl-CpG binding domain (MBD) and
      a C-terminal mismatch-specific glycosylase domain. Limited in vitro
      proteolysis of mouse MBD4 yields two stable fragments: a 139-residue
      fragment including the MBD, and the other 155-residue fragment including
      the glycosylase domain. Here we show that the latter fragment is active as
      a glycosylase on a DNA duplex containing a G:T mismatch within a CpG
      sequence context. The crystal structure confirmed the C-terminal domain is
      a member of the helix-hairpin-helix DNA glycosylase superfamily. The MBD4
      active site is situated in a cleft that likely orients and binds DNA.
      Modeling studies suggest the mismatched target nucleotide will be flipped
      out into the active site where candidate residues for catalysis and
      substrate specificity are present.
AU  - Wu P
AU  - Qiu C
AU  - Sohail A
AU  - Zhang X
AU  - Bhagwat AS
AU  - Cheng X
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2003 278: 5285-5291.

PMID- 25035317
VI  - 2
DP  - 2014
TI  - Genome Sequence of Borrelia garinii Strain SZ, Isolated in China.
PG  - e00010-14
AB  - We announce the genome sequence of Borrelia garinii strain SZ, isolated from Dermacentor ticks
      collected in northeastern China. B. garinii strain SZ carries
      numerous plasmids, both 10 circular and 9 linear plasmids. The 902,487-bp linear
      chromosome (28.2% GC content) contains 820 open reading frames, 33 tRNAs, and 4
      complete rRNAs. The plasmid cp32-10 contains one clustered regularly interspaced
      short palindromic repeat (CRISPR) with four repeats.
AU  - Wu Q
AU  - Liu Z
AU  - Li Y
AU  - Guan G
AU  - Niu Q
AU  - Chen Z
AU  - Luo J
AU  - Yin H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00010-14.

PMID- 23405325
VI  - 1
DP  - 2013
TI  - Genome Sequence of Bacillus licheniformis CGMCC3963, a Stress-Resistant Strain Isolated in a Chinese Traditional Solid-State Liquor-Making Process.
PG  - e00060-12
AB  - Bacillus licheniformis CGMCC3963 is an important mao-tai flavor-producing strain. It was
      isolated from the starter (Daqu) of a Chinese mao-tai-flavor liquor
      fermentation process with solid-state fermentation. We report its genome of
      4,525,096 bp here. Many potential insertion genes that are responsible for the
      unique properties of B. licheniformis CGMCC3963 in mao-tai-flavor liquor
      production were identified.
AU  - Wu Q
AU  - Peng S
AU  - Yu Y
AU  - Li Y
AU  - Xu Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00060-12.

PMID- 24827399
VI  - 4
DP  - 2014
TI  - Genomic insights into high exopolysaccharide-producing dairy starter bacterium Streptococcus thermophilus ASCC 1275.
PG  - 4974
AB  - 
AU  - Wu Q
AU  - Tun HM
AU  - Leung FCC
AU  - Shah NP
PT  - Journal Article
TA  - Sci. Rep.
JT  - Sci. Rep.
SO  - Sci. Rep. 2014 4: 4974.

PMID- 26184946
VI  - 3
DP  - 2015
TI  - Genome Sequence of Paenibacillus wulumuqiensis sp. nov., a Bioflocculant-Producing Species.
PG  - e00795-15
AB  - Paenibacillus wulumuqiensis sp. nov. is a novel strain that can produce bioflocculants. Here,
      we report 5.37-Mb assembly of its genome sequence and other
      useful information, including the coding sequences (CDSs) responsible for the
      biosynthesis of polysaccharide-based bioflocculants, cold-shock protein, and
      vitamin production.
AU  - Wu Q
AU  - Zhu L
AU  - Jiang L
AU  - Xu X
AU  - Xu Q
AU  - Zhang Z
AU  - Huang H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00795-15.

PMID- 105969
VI  - 4
DP  - 1978
TI  - A new sequence-specific endonuclease from Streptococcus faecalis subsp. zymogenes.
PG  - 329-336
AB  - A new sequence-specific endonuclease, SfaI, has been partially purified from
      Streptococcus faecalis subsp. zymogenes.  SfaI recognizes the tetranucleotide
      sequence.
AU  - Wu R
AU  - King CT
AU  - Jay E
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1978 4: 329-336.

PMID- 2824027
VI  - 47
DP  - 1987
TI  - Measurement of O6-alkylguanine-DNA alkyltransferase activity in human cells and tumor tissues by restriction endonuclease inhibition.
PG  - 6229-6235
AB  - A sensitive assay for O6-alkylguanine-DNA alkyltransferase activity in cell or
      tumor extracts has been devised.  The theoretical basis of the new assay lies
      in the observation that certain restriction enzymes will not cleave DNA
      containing methylated bases.  Thus, if a synthetic oligodeoxynucleotide with a
      restriction sequence containing O6-methylguanine wee incubated with the
      restriction enzyme, this synthetic oligodeoxynucleotide should remain intact.
      However, if the guanine-O6 methyl group were first removed by
      O6-alkylguanine-DNA alkyltransferase present in certain cell or tissue extracts
      the synthetic oligodeoxynucleotide would be cleaved by the restriction enzyme.
      The parental oligodeoxynucleotide and its restriction products are separated
      from each other and analyzed on denaturing polyacrylamide gels.  The extent of
      cleavage by the restriction enzyme is a direct assay of the content of
      O6-alkylguanine-DNA alkyltransferase in the cell/tumor extracts.  The assay has
      been tested against cell culture and xenograft tumor systems and has performed
      in a predictive manner, correctly predicting five Mer- and three Mer+
      phenotypes.  Furthermore, the assay is quantitative and the number of molecules
      of the O6-alkylguanine-DNA alkyltransferase per cell estimated using this assay
      agrees with those that have been published.
AU  - Wu RS
AU  - Hurst-Calderone S
AU  - Kohn KW
PT  - Journal Article
TA  - Cancer Res.
JT  - Cancer Res.
SO  - Cancer Res. 1987 47: 6229-6235.

PMID- 7763991
VI  - 57
DP  - 1993
TI  - Restriction enzyme BliHKI from a thermophilic Bacillus licheniformis strain.
PG  - 1193-1194
AB  - Thermophilic Bacillus is a rich source of restriction enzymes. Using a screening method
      described in ref. 1, we have isolated a thermophilic Bacillus licheniformis strain HK which
      grows at 55 degrees C in L broth and contains a type II restriction enzyme, BliHKI.
AU  - Wu SY
AU  - Lee KF
AU  - Kam KM
AU  - Shaw PC
PT  - Journal Article
TA  - Biosci. Biotechnol. Biochem.
JT  - Biosci. Biotechnol. Biochem.
SO  - Biosci. Biotechnol. Biochem. 1993 57: 1193-1194.

PMID- 1581360
VI  - 1131
DP  - 1992
TI  - Identification of a weak promoter for the dam gene of Escherichia coli.
PG  - 47-52
AB  - We have used a combination of techniques to identify a weak promoter located about 70
      nucleotides before the start site of translation of the Escherichia coli dam gene which
      encodes a DNA methyltransferase.  The promoter activity was identified by the use of lacZ
      fusions to fragments containing different lengths of upstream DNA.  In vitro run-off
      transcription and primer extension determinations revealed transcription initiation sites at
      either 69 or 73 nucleotides prior to the ARG of the dam coding sequence.  No ribosome binding
      sequence was present close to the ATG codon suggesting that the transcript may be
      inefficiently translated.
AU  - Wu T-H
AU  - Grelland E
AU  - Boye E
AU  - Marinus MG
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1992 1131: 47-52.

PMID- 4891809
VI  - 98
DP  - 1969
TI  - Locus determining P1 phage restriction in Escherichia coli.
PG  - 314
AB  - The locus determing P1 phage restriction has been mapped at 89.3 min on the
      Escherichia coli map, about 0.2 min away from the hsp marker.
AU  - Wu TT
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1969 98: 314.

PMID- Not included in PubMed...
VI  - 28
DP  - 1969
TI  - The restriction and modification enzymes of Escherichia coli.
PG  - 465
AB  - An E. coli endonuclease (MW ca. 78,000) which acts specifically on unmodified
      lambda-DNA has been purified.  The endonuclease fraction, together with
      S-adenosylmethionine (SAM) and another protein fraction, is required for the
      methylation of DNA.  SAM can be eliminated from the methylation reaction, if it
      is first allowed to react with the endonuclease fraction, forming a
      methyl-donating complex.  The same enzyme fraction from a restrictionless
      mutant has no endonucleaese activity but retains the property of reacting with
      SAM.  The formation of this methyl-donating complex is partially inhibited by a
      protein present only in modificationless mutants of E. coli.  This protein (MW
      da. 52,000) has also been purified.  Recombinants having mostly E. coli B
      chromosomes except for small segments which contain the restriction and
      modification markers from E. coli K12 have been selected.  The DNA of these
      recombinants contains both methylcytosine and methyladenine, whereas E. coli
      and DNA contains only the later.
AU  - Wu TT
AU  - Matsuda A
AU  - Cavalieri LF
PT  - Journal Article
TA  - Fed. Proc.
JT  - Fed. Proc.
SO  - Fed. Proc. 1969 28: 465.

PMID- 12433989
VI  - 30
DP  - 2002
TI  - Intein-mediated purification of cytotoxic endonuclease I-TevI by insertional inactivation and pH-controllable splicing.
PG  - 4864-4871
AB  - An intein-mediated approach was developed for expression and affinity purification of a
      protein that is lethal to Escherichia coli. The protein, I-TevI, is an intron-encoded
      endonuclease. The approach involved the insertional inactivation of I-TevI with a controllable
      mini-intein placed in front of a cysteine required for splicing (an I-TevI::intein fusion).
      The purification was facilitated by a chitin-binding domain inserted into the mini-intein.
      Affinity purification of the I-TevI::intein fusion precursor on a chitin column was followed
      by pH-controllable splicing to restore the structure and function of I-TevI. To study the
      impact of the insertion context on I-TevI inactivation, the chimeric intein was inserted
      independently in front of seven cysteines of I-TevI. One of the seven intein integrants
      yielded I-TevI of high activity. This technique is, in principle, generalizable to the
      expression and purification of other cytotoxic proteins and is amenable to scale-up.
AU  - Wu W
AU  - Wood DW
AU  - Belfort G
AU  - Derbyshire V
AU  - Belfort M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2002 30: 4864-4871.

PMID- 23801408
VI  - 288
DP  - 2013
TI  - A genome-wide analysis of multidrug-resistant and extensively drug-resistant strains of Mycobacterium tuberculosis Beijing genotype.
PG  - 425-436
AB  - The Beijing genotype of Mycobacterium tuberculosis (MTB) is one of the most successful MTB
      lineages that has disseminated in the world. In China, the rate of
      multidrug-resistant (MDR) tuberculosis is significantly higher than the global
      average rate, and the Beijing genotype strains take the largest share of MDR
      strains. To study the genetic basis of the epidemiological findings that Beijing
      genotype has often been associated with tuberculosis outbreaks and drug
      resistance, we determined the genome sequences of four clinical isolates: two
      extensively drug resistant (XDR1219, XDR1221) and two multidrug resistant (WX1,
      WX3), using whole-genome sequencing. A large number of individual and shared SNPs
      of the four Beijing strains were identified. Our isolates harbored almost all
      classic drug resistance-associated mutations. The mutations responsible for drug
      resistance in the two XDR strains were consistent with the clinical quantitative
      drug resistance levels. COG analysis revealed that Beijing strains have
      significantly higher abundances of the mutations responsible for cell
      wall/membrane/envelope biogenesis (COG M), secondary metabolites biosynthesis,
      transport and catabolism (COG Q), lipid transport and metabolism (COG I) and
      defense mechanisms (COG V). The shared mutated genes of the four studied Beijing
      strains were significantly overrepresented in three DNA repair pathways. Our
      analyses promote the understanding of the genome polymorphism of the Beijing
      family strains and provide the molecular genetic basis for their wide
      dissemination capacity and drug resistance.
AU  - Wu W
AU  - Zheng H
AU  - Zhang L
AU  - Wen Z
AU  - Zhang S
AU  - Pei H
AU  - Yu G
AU  - Zhu Y
AU  - Cui Z
AU  - Hu Z
AU  - Wang H
AU  - Li Y
PT  - Journal Article
TA  - Mol. Genet. Genomics
JT  - Mol. Genet. Genomics
SO  - Mol. Genet. Genomics 2013 288: 425-436.

PMID- 28663297
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Two Janthinobacteriumlividum Strains, Isolated from Pristine Groundwater Collected from the Oak Ridge Field Research Center.
PG  - e00582-17
AB  - We present here the draft genome sequences of two Janthinobacterium lividum strains, GW456P
      and GW458P, isolated from groundwater samples collected from a
      background site at the Oak Ridge Field Research Center. Production of a purple
      pigment by these two strains was observed when grown on diluted (1/10) LB agar
      plates.
AU  - Wu X
AU  - Deutschbauer AM
AU  - Kazakov AE
AU  - Wetmore KM
AU  - Cwick BA
AU  - Walker RM
AU  - Novichkov PS
AU  - Arkin AP
AU  - Chakraborty R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00582-17.

PMID- 27313302
VI  - 4
DP  - 2016
TI  - Genome Sequence of Lactobacillus johnsonii Strain W1, Isolated from Mice.
PG  - e00561-16
AB  - Lactobacillus johnsonii, a member of the gut lactobacilli, plays an important role in normal
      gut functioning. Here, we report the draft genome sequence of L.
      johnsonii strain W1 isolated from ICR mice.
AU  - Wu X
AU  - Zhao C
AU  - Guo Z
AU  - Hao Y
AU  - Li J
AU  - Shi H
AU  - Sun Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00561-16.

PMID- 28963200
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Bacillus thuringiensis subsp. jinghongiensis Reference Strain YGd22-03.
PG  - e00740-17
AB  - Bacillus thuringiensis is widely used in producing ecofriendly microbial agents for the
      purpose of controlling insect pests. In this study, we determined the
      complete genome sequence of B. thuringiensis subsp. jinghongiensis reference
      strain YGd22-03, which contains three cry genes and one cerecidin biosynthetic
      gene cluster.
AU  - Wu Y
AU  - Fu Y
AU  - Yuan Y
AU  - Gao M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00740-17.

PMID- 25700397
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Stenotrophomonas maltophilia Strain B418, a Promising Agent for Biocontrol of Plant Pathogens and Root-Knot Nematode.
PG  - e00015-15
AB  - Stenotrophomonas maltophilia strain B418 was isolated from a barley rhizosphere in China. This
      bacterium exhibits broad-spectrum inhibitory activities against plant pathogens and root-knot
      nematode along with growth-promoting effects. Here, we present the draft genome sequence of S.
      maltophilia B418.
AU  - Wu Y
AU  - Wang Y
AU  - Li J
AU  - Hu J
AU  - Chen K
AU  - Wei Y
AU  - Bazhanov DP
AU  - Bazhanova AA
AU  - Yang H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00015-15.

PMID- 25657267
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Listeria monocytogenes LM201, Isolated from Foodstuff.
PG  - e01417-14
AB  - Listeria monocytogenes is a facultative intracellular foodborne pathogen that can cause
      listeriosis in humans and animals. L. monocytogenes LM201 was isolated from
      foodstuff. The draft genome sequence of strain LM201 provides the genetic basis
      for the application of this strain in biotechnological vaccine production.
AU  - Wu Y
AU  - Zheng J
AU  - Wang Y
AU  - Li S
AU  - Jin H
AU  - Li Z
AU  - Bi D
AU  - Sun M
AU  - Liu M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01417-14.

PMID- 25858243
VI  - 65
DP  - 2015
TI  - Tumebacillus algifaecis sp. nov., isolated from decomposing algal scum.
PG  - 2194-2198
AB  - Bacterial strain THMBR28(T) was isolated from decomposing algal scum that was
      collected during an algal bloom in Taihu lake, China. Cells of strain THMBR28(T)
      were Gram-staining-positive, facultatively anaerobic and rod-shaped. Growth was
      observed at 20-45 degrees C (optimum, 30 degrees C), at pH 5.0-9.5 (optimum, pH
      6.5-7.5), and in the presence of 0-1.0% (w/v) NaCl (optimum, 0.5%). Strain
      THMBR28(T) contained MK-7 as the major menaquinone and iso-C15 : 0 as the major
      cellular fatty acid. The polar lipid profile contained phosphatidylglycerol,
      phosphatidylmonomethylethanolamine, phosphatidylethanolamine and six unidentified
      polar lipids. The diamino acid found in the cell-wall peptidoglycan was
      meso-diaminopimelic acid. The DNA G+C content was 57.6 mol% (Tm). Phylogenetic
      analysis of 16S rRNA gene sequences showed that strain THMBR28(T) belonged to the
      genus Tumebacillus, most closely related to Tumebacillus ginsengisoli DSM
      18389(T) (95.0%) and Tumebacillus permanentifrigoris Eur1 9.5(T) (93.4%). Based
      on phylogenetic and phenotypic characterization, it is concluded that strain
      THMBR28(T) represents a novel species of the genus Tumebacillus, for which the
      name Tumebacillus algifaecis sp. nov. is proposed, with THMBR28(T) ( = CGMCC
      1.10949(T) = NBRC 108765(T)) as the type strain.
AU  - Wu YF
AU  - Zhang B
AU  - Xing P
AU  - Wu QL
AU  - Liu SJ
PT  - Journal Article
TA  - Int. J. Syst. Evol. Microbiol.
JT  - Int. J. Syst. Evol. Microbiol.
SO  - Int. J. Syst. Evol. Microbiol. 2015 65: 2194-2198.

PMID- 29299108
VI  - 12
DP  - 2017
TI  - Complete genome sequence of esterase-producing bacterium Croceicoccus marinus E4A9(T).
PG  - 88
AB  - Croceicoccus marinus E4A9(T)was isolated from deep-sea sediment collected from the East
      Pacific polymetallic nodule area. The strain is able to produce
      esterase, which is widely used in the food, perfume, cosmetic, chemical,
      agricultural and pharmaceutical industries. Here we describe the characteristics
      of strain E4A9, including the genome sequence and annotation, presence of
      esterases, and metabolic pathways of the organism. The genome of strain E4A9(T)
      comprises 4,109,188 bp, with one chromosome (3,001,363 bp) and two large circular
      plasmids (761,621 bp and 346,204 bp, respectively). Complete genome contains 3653
      coding sequences, 48 tRNAs, two operons of 16S-23S-5S rRNA gene and three ncRNAs.
      Strain E4A9(T) encodes 10 genes related to esterase, and three of the esterases
      (E3, E6 and E10) was successfully cloned and expressed in Escherichia coli
      Rosetta in a soluble form, revealing its potential application in
      biotechnological industry. Moreover, the genome provides clues of metabolic
      pathways of strain E4A9(T), reflecting its adaptations to the ambient
      environment. The genome sequence of C. marinus E4A9(T) now provides the
      fundamental information for future studies.
AU  - Wu YH
AU  - Cheng H
AU  - Huo YY
AU  - Xu L
AU  - Liu Q
AU  - Wang CS
AU  - Xu XW
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 88.

PMID- 26067975
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Microbacterium profundi Shh49T, an Actinobacterium Isolated from Deep-Sea Sediment of a Polymetallic Nodule Environment.
PG  - e00642-15
AB  - Microbacterium profundi strain Shh49(T) was isolated from deep-sea sediment from  a
      polymetallic nodule area located in the East Pacific Ocean. Strain Shh49(T)
      contains genes related to the reduction/oxidation of metals. It has potential
      application in the bioremediation of heavy metal-contaminated environments.
AU  - Wu YH
AU  - Zhou P
AU  - Cheng H
AU  - Wang CS
AU  - Wu M
AU  - Xu XW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00642-15.

PMID- 22965093
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Butanol-Acetone-Producing Clostridium beijerinckii Strain G117.
PG  - 5470-5471
AB  - A recently discovered wild-type strain, Clostridium beijerinckii G117, is unique  in producing
      butanol and acetone but negligible amounts of ethanol, unlike
      previously identified acetone-butanol-ethanol (ABE)-generating microbes. Here we
      report the draft genome sequence of strain G117 (5,806,675 bp; GC content, 29.7%)
      and the novel findings obtained from its genome annotations.
AU  - Wu YR
AU  - Li Y
AU  - Yang KL
AU  - He J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5470-5471.

PMID- 25502674
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of a Xylanase-Producing Bacterial Strain, Cellvibrio mixtus J3-8.
PG  - e01281-14
AB  - The xylanase-producing bacterial strain Cellvibrio mixtus J3-8 was isolated from  grassland
      giant snails. The draft genome of strain J3-8 comprises 5,171,890 bp in
      152 contigs with a G+C content of 46.66%. This is the first genome report about
      this bacterial species.
AU  - Wu YR
AU  - Lin B
AU  - Yu Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01281-14.

PMID- 28883143
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Zobellella denitrificans ZD1 (JCM 13380), a Salt-Tolerant Denitrifying Bacterium Capable of Producing  Poly(3-Hydroxybutyrate).
PG  - e00948-17
AB  - Zobellella denitrificans ZD1, isolated from sediments of an estuarine mangrove ecosystem in
      Taiwan, exhibits growth-associated production of biopolymer
      poly(3-hydroxybutyrate) (PHB). This work reports the 4.05-Mbp draft genome
      sequence of Z. denitrificans ZD1, consisting of 217 contigs with a G+C content of
      63.8% and 3,672 protein-coding sequences.
AU  - Wu YW
AU  - Shao Y
AU  - Khanipov K
AU  - Golovko G
AU  - Pimenova M
AU  - Fofanov Y
AU  - Chu KH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00948-17.

PMID- 26416872
VI  - 59
DP  - 2015
TI  - Novel Type XII Staphylococcal Cassette Chromosome mec Harboring a New Cassette Chromosome Recombinase, CcrC2.
PG  - 7597-7601
AB  - Excision and integration of staphylococcal cassette chromosome mec (SCCmec) are
      mediated by cassette chromosome recombinases (Ccr), which play a crucial role in
      the worldwide spread of methicillin resistance in staphylococci. We report a
      novel ccr gene, ccrC2, in the SCCmec of a Staphylococcus aureus isolate, BA01611,
      which showed 62.6% to 69.4% sequence identities to all published ccrC1 sequences.
      A further survey found that the ccrC2 gene was mainly located among
      coagulase-negative staphylococci (CoNS) and could be found in staphylococcal
      isolates from China, the United States, France, and Germany. The ccr gene complex
      harboring the ccrC2 gene was designated a type 9 complex, and the SCCmec of
      BA01611 was considered a novel type and was designated type XII (9C2). This novel
      SCCmec element in BA01611 was flanked by a pseudo-SCC element (PsiSCCBA01611)
      carrying a truncated ccrA1 gene. Both individual SCC elements and a composite SCC
      were excised from the chromosome based on detection of extrachromosomal circular
      intermediates. We advocate inclusion of the ccrC2 gene and type 9 ccr gene
      complex during revision of the SCCmec typing method.
AU  - Wu Z
AU  - Li F
AU  - Liu D
AU  - Xue H
AU  - Zhao X
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2015 59: 7597-7601.

PMID- 23653121
VI  - 104
DP  - 2013
TI  - Paracoccus zhejiangensis sp. nov., isolated from activated sludge in wastewater-treatment system.
PG  - 123-128
AB  - A bacterial strain, designated J6(T), was isolated from activated sludge,
      collected from a chemical wastewater treatment system in Zhejiang Province of
      China. The cells stained Gram-negative, were aerobic, pale-yellow, and non-motile
      short rods. Phylogenetic analysis of the 16S rRNA gene sequence indicated that
      the closest relative of this organism was Paracoccus aminophilus KACC 12262(T) =
      JCM 7686(T) (97.4 % sequence similarity). Strain J6(T) grew at 10-37 degrees C
      (optimum 30 degrees C), at pH 6.0-8.0 (optimum pH 7.0) and with 0-5 % NaCl
      (optimum 3 %, w/v). The predominant cellular fatty acid found was summed feature
      8(C18:1 omega7c and/or C18:1 omega6c; 82.8 %). The major respiratory
      quinone-detected was Q-10 and the DNA G+C content was 61.9 mol %. The polar lipid
      profile consisted of phosphatidylethanolamine, phosphatidylglycerol,
      diphosphatidylglycerol, phosphatidylcholine and several unknown polar lipids.
      Strain J6(T) showed low DNA-DNA relatedness values with P. aminophilus KACC
      12262(T) (28 +/- 3 %). The phylogenetic analysis, DNA-DNA hybridization,
      whole-cell fatty acid composition as well as biochemical characteristics allowed
      clear differentiation of the isolate from the other type strains of already
      described Paracoccus species. It is evident from the genotypic, phenotypic and
      chemotaxonomic analyses that strain J6(T) should be classified as a novel species
      of the genus Paracoccus, for which the name P. zhejiangensis sp. nov. is
      proposed. The type strain is J6(T) (KACC 16703(T) = CCTCC AB 2012031(T)).
AU  - Wu ZG
AU  - Zhang DF
AU  - Liu YL
AU  - Wang F
AU  - Jiang X
AU  - Li C
AU  - Li SP
AU  - Hong Q
AU  - Li WJ
PT  - Journal Article
TA  - Antonie Van Leeuwenhoek
JT  - Antonie Van Leeuwenhoek
SO  - Antonie Van Leeuwenhoek 2013 104: 123-128.

PMID- 24200077
VI  - 27
DP  - 2014
TI  - The complete genome sequence of Candidatus Liberibacter americanus, associated with citrus Huanglongbing.
PG  - 163-176
AB  - Liberibacters form a Rhizobiaceae clade of phloem-limited pathogens of limited host range.
      Two obligately parasitic species have been sequenced: Candidatus Liberibacter asiaticus Las),
      which causes citrus Huanglongbing (HLB) world-wide, and Ca. L. solanacearum (Lso), which
      causes potato "zebra chip" disease. A third species, Liberibacter crescens (Lcr),
      was isolated from mountain papaya, grown in axenic culture and sequenced. In an effort to
      identify common host determinants, the complete genomic DNA sequence of a second HLB species,
      Ca. L. americanus (Lam) strain "Sao Paulo" was determined. The circular genome of 1,195,201 bp
      had an average 31.12% GC content and 983 predicted protein encoding genes, 800 (81.4%) of
      which had a predicted function. There were 658 genes common to all sequenced liberibacters and
      only 8 genes common to Lam and Las but not found in Lso.   Surprisingly, most of the
      lipopolysaccharide biosynthetic genes were missing from the Lam genome, as well OmpA and a key
      regulator of flagellin, all indicating a Lam strategy of avoiding production of major
      pathogen-associated molecular patterns (PAMPs) present in Las and Lso. As with Las, one of two
      Lam prophages replicated as an excision plasmid and carried potential lysogenic conversion
      genes that appeared fragmentary or degenerated in Lso.
AU  - Wulff NA
AU  - Zhang S
AU  - Setubal J
AU  - Almeida NF
AU  - Martins EC
AU  - Harakava R
AU  - Kumar D
AU  - Rangel LT
AU  - Foissac X
AU  - Bove JM
AU  - Gabriel DW
PT  - Journal Article
TA  - Mol. Plant Microbe Interact.
JT  - Mol. Plant Microbe Interact.
SO  - Mol. Plant Microbe Interact. 2014 27: 163-176.

PMID- 
VI  - 
DP  - 1998
TI  - Does 2-chlorodeoxyadenosine contribute to alteration of DNA methyltransferase activity?
PG  - 595-598
AB  - 2-Chlorodeoxyadenosine (2CdA) is a new and effective drug for indolent lymphoid malignancies.
      However, the mechanisms which link 2CdA action and tumor cell death (by apoptosis) are not
      fully clarified.  2CdA is rapidly taken up by the target cells and phosphorylated by cytosolic
      deoxycytidine kinase (dCK).  Its triphosphate is a potent inhibitor of human ribonucleotide
      reductase and a good substrate for human DNA polymerases.  However, phosphorylation of 2CdA is
      clearly not the only event responsible for its cytotoxic effect.  The 2CdA phosphorylation in
      hairy cell leukemia was not higher than in chronic lymphocytic leukemia, despite a better
      response to 2CdA therapy.  Using different cell lines, it was shown that  a wide range of cell
      sensitivity to 2CdA could not be explained by different levels of 2CdA nucleotide.  2CdA was
      also shown to inhibit the growth of myeloid progenitor cell in which the levels of dCK are
      low.  Finally, we have recently shown that in vitro the inhibitory effect of 2CdA results from
      complete suppression of deoxyadenosine phosphorylation by dCK in both human normal lymphocytes
      and in lymphoma cells obtained from patients with a central nervous system involvement.  Also
      an inhibition of adenosine deaminase activity in lysate of both types of cells was observed.
      Moreover, we observed a large decrease in the activity of adenosine deaminase and
      S-adenosylhomocysteine hydrolase, in the erythrocyte lysates of patients, after one week
      treatment with 2CdA6.  We assumed that inhibitory effect of 2CdA on deoxyadenosine metabolism
      could lead to inactivation of SAH-hydrolase with perturbation of methylation reactions.
AU  - Wyczechowska D
AU  - Fabianowska-Majewska K
PT  - Journal Article
TA  - Purine and Pyrimidine Metabolism in Man IX
JT  - Purine and Pyrimidine Metabolism in Man IX
SO  - Purine and Pyrimidine Metabolism in Man IX 1998 : 595-598.

PMID- 20870759
VI  - 192
DP  - 2010
TI  - Resequencing the Mycobacterium avium subsp. paratuberculosis K10 Genome: Improved Annotation and Revised Genome Sequence.
PG  - 6319-6320
AB  - We report the resequencing and revised annotation of the Mycobacterium avium subsp.
      paratuberculosis K10 genome. A total of 90 single-nucleotide
      errors and a 51-bp indel in the original K10 genome were corrected, and
      the whole genome annotation was revised. Correction of these sequencing
      errors resulted in 28 frameshift alterations. The amended genome sequence
      is accessible via the supplemental section of study SRR060191 in the NCBI
      Sequence Read Archive and will serve as a valuable reference genome for
      future studies.
AU  - Wynne JW
AU  - Seemann T
AU  - Bulach DM
AU  - Coutts SA
AU  - Talaat AM
AU  - Michalski WP
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 6319-6320.

PMID- 23879707
VI  - 14
DP  - 2013
TI  - Evidence of antimicrobial resistance-conferring genetic elements among pneumococci isolated prior to 1974.
PG  - 500
AB  - BACKGROUND: Antimicrobial resistance among pneumococci has greatly increased over
      the past two to three decades. Resistance to tetracycline (tet(M)),
      chloramphenicol (cat) and macrolides (erm(B) and/or mef(A/E)) is generally
      conferred by acquisition of specific genes that are associated with mobile
      genetic elements, including those of the Tn916 and Tn5252 families. The first
      tetracycline-, chloramphenicol- and macrolide-resistant pneumococci were detected
      between 1962 and 1970; however, until now the oldest pneumococcus shown to
      harbour Tn916 and/or Tn5252 was isolated in 1974. In this study the genomes of 38
      pneumococci isolated prior to 1974 were probed for the presence of tet(M), cat,
      erm(B), mef(A/E) and int (integrase) to indicate the presence of
      Tn916/Tn5252-like elements. RESULTS: Two Tn916-like, tet(M)-containing, elements
      were identified among pneumococci dated 1967 and 1968. The former element was
      highly similar to that of the PMEN1 multidrug-resistant, globally-distributed
      pneumococcal reference strain, which was isolated in 1984. The latter element was
      associated with a streptococcal phage. A third, novel genetic element, designated
      ICESpPN1, was identified in the genome of an isolate dated 1972. ICESpPN1
      contained a region of similarity to Tn5252, a region of similarity to a
      pneumococcal pathogenicity island and novel lantibiotic
      synthesis/export-associated genes. CONCLUSIONS: These data confirm the existence
      of pneumococcal Tn916 elements in the first decade within which pneumococcal
      tetracycline resistance was described. Furthermore, the discovery of ICESpPN1
      demonstrates the dynamic variability of pneumococcal genetic elements and is
      contrasted with the evidence for Tn916 stability.
AU  - Wyres KL
AU  - van Tonder A
AU  - Lambertsen LM
AU  - Hakenbeck R
AU  - Parkhill J
AU  - Bentley SD
AU  - Brueggemann AB
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2013 14: 500.

PMID- 22199260
VI  - 40
DP  - 2012
TI  - Type III restriction endonuclease EcoP15I is a heterotrimeric complex containing  one Res subunit with several DNA-binding regions and ATPase activity.
PG  - 3610-3622
AB  - For efficient DNA cleavage, the Type III restriction endonuclease EcoP15I communicates with
      two inversely oriented recognition sites in an ATP-dependent process. EcoP15I consists of
      methylation (Mod) and restriction (Res) subunits forming a multifunctional enzyme complex able
      to methylate or to cleave DNA. In this study, we determined by different analytical methods
      that EcoP15I contains a single Res subunit in a Mod(2)Res stoichiometry. The Res subunit
      comprises a translocase (Tr) domain carrying functional motifs of superfamily 2 helicases and
      an endonuclease domain with a PD..D/EXK motif. We show that the isolated Tr domain retains
      ATP-hydrolyzing activity and binds single- and double-stranded DNA in a sequence-independent
      manner. To localize the regions of DNA binding, we screened peptide arrays representing the
      entire Res sequence for their ability to interact with DNA. We discovered four DNA-binding
      regions in the Tr domain and two DNA-binding regions in the endonuclease domain. Modelling of
      the Tr domain shows that these multiple DNA-binding regions are located on the surface, free
      to interact with DNA. Interestingly, the positions of the DNA-binding regions are conserved
      among other Type III restriction endonucleases.
AU  - Wyszomirski KH
AU  - Curth U
AU  - Alves J
AU  - Mackeldanz P
AU  - Moncke-Buchner E
AU  - Schutkowski M
AU  - Kruger DH
AU  - Reuter M
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2012 40: 3610-3622.

PMID- Not carried by PubMed...
VI  - 55
DP  - 1994
TI  - Investigation of the molecular mechanism and mutagenic effect of C5-methyltransferases by mutational analysis.
PG  - 1426B-1427B
AB  - It has been proposed that a cysteine conserved among all DNA (cytosine-5)-methyltransferases
      initiates catalysis by attacking the C6 of cytosine. I have changed this cysteine to other
      amino acids for the E. coli methylase M.EcoRII; which methylates the second cytosine in the
      sequence 5'-CCWGG-3'. Replacement of the conserved cysteine with glycine, valine, tryptophan
      or serine led to an apparent loss of methyl transferring ability. Unexpectedly, substitution
      of the cysteine with glycine results in the inhibition of cell growth. In DNA binding studies
      I show that mutants with either serine or glycine substitution bind tightly to substrate DNA
      in a manner which resembles the wild-type enzyme. Hence the conserved cysteine is not
      essential for the specific stable binding of the enzyme to its substrate. Further, I show that
      a DNA substrate for M.EcoRII in which the target cytosine is replaced by 5-fluorocytosine is a
      mechanism-based inhibitor of the enzyme. As expected, this modified substrate does not form
      irreversible complexes with the mutants. Sites of cytosine methylation are hot-spots for
      cytosine (C) to thymine (T) mutations in E. coli DNA. To study this phenomenon, I have
      developed a genetic system based on the reversion of a mutation in a kanamycin-resistance gene
      that allows direct selection of C to T mutations at a site of methylation. Using this system I
      show that enzyme-catalyzed deaminations of cytosine do not play a major role in making Dcm
      methylation sites hot-spots for mutations. Further, I have developed a genetic reversion assay
      that quantitates the frequency of C to T mutations at Dcm sites and the reduction of such
      mutations by DNA repair processes. Using this assay, the repair of U:G mismatches in DNA to
      C:G have been studied. The results shown here demonstrate that the E. coli base mismatch
      correction system called VSP repair is capable of correcting U:G mismatches.
AU  - Wyszynski MW
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1994 55: 1426B-1427B.

PMID- 1371346
VI  - 20
DP  - 1992
TI  - Substitutions of a cysteine conserved among DNA cytosine methylases result in a variety of phenotypes.
PG  - 319-326
AB  - The proposed mechanism for DNA (cytosine-5)-methyltransferases envisions a key
      role for a cysteine residue.  It is expected to form a covalent link with
      carbon 6 of the target cytosine, activating the normally inactive carbon 5 for
      methyl transfer.  There is a single conserved cysteine among all DNA
      (cytosine-5)-methyltransferases making it the candidate nucleophile.  We have
      changed this cysteine to other amino acids for the EcoRII methylase; which
      methylates the second cytosine in the sequence 5'-CCWGG-3'.  Mutants were
      tested for their methyl transferring ability and for their ability to form
      covalent complexes with DNA.  The latter property was tested indirectly with
      the use of a genetic assay involving sensitivity of cells to 5-azacytidine.
      Replacement of the conserved cysteine with glycine, valine, tryptophan or
      serine led to an apparent loss of methyl transferring ability.  Interestingly,
      cells carrying the mutant with serine did show sensitivity to 5-azacytidine,
      suggesting the ability to link to DNA.  Unexpectedly, substitution of the
      cysteine with glycine results in the inhibition of cell growth and the mutant
      allele can be maintained in the cells only when it is poorly expressed.  These
      results suggest that the conserved cysteine in the EcoRII methylase is
      essential for methylase action and it may play more than one role in it.
AU  - Wyszynski MW
AU  - Gabbara S
AU  - Bhagwat AS
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 319-326.

PMID- 8441637
VI  - 21
DP  - 1993
TI  - The cysteine conserved among DNA cytosine methylases is required for methyl transfer, but not for specific DNA binding.
PG  - 295-301
AB  - All DNA (cytosine-5)-methyltransferases contain a single conserved cysteine. It has been
      proposed that this cysteine initiates catalysis by attacking the C6 of cytosine and thereby
      activating the normally inert C5 position. We show here that substitutions of this cysteine in
      the E. coli methylases M.EcoRII with either serine or trypotophan results in a complete loss
      of ability to transfer methyl groups to DNA. Interestingly, mutants with either serine or
      glycine substitution bind tightly to substrate DNA. These mutants resemble the wild-type
      enzyme in that their binding to substrate is not eliminated by the presence of non-specific
      DNA in the reaction, it is sensitive to methylation status of the substrate and is stimulated
      by an analog of the methyl donor. Hence the conserved cysteine is not essential for the
      specifc stable binding of the enzyme to its substrate. However, substitution of the cysteine
      with the bulkier tryptophan does reduce DNA binding. We also report here a novel procedure for
      the synthesis of DNA containing 5-fluorocytosine. Further, we show that a DNA substrate for
      M.EcoRII in which the target cytosine is replaced by 5-fluorocytosine is a mechanism-based
      inhibitor of the enzyme and that it forms an irreversible complex with the enzyme. As
      expected, this modified substrate does not form irreversible complexes with the mutants.
AU  - Wyszynski MW
AU  - Gabbara S
AU  - Kubareva EA
AU  - Romanova EA
AU  - Oretskaya TS
AU  - Gromova ES
AU  - Shabarova ZA
AU  - Bhagwat AS
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 295-301.

PMID- 8108447
VI  - 91
DP  - 1994
TI  - Cytosine deaminations catalyzed by DNA cytosine methyltransferases are unlikely to be the major cause of mutational hot spots at sites of cytosine methylation in Escherichia coli.
PG  - 1574-1578
AB  - Sites of cytosine methylation are hot spots for C to T mutations in Escherichia coli DNA. We
      have developed a genetic reversion assay that allows direct selection of C to T mutations at a
      site of methylation. Because the mutant gene is on a plasmid, this system can be used to study
      mutational effects of biochemical agents in vitro as well as in vivo. Using this system we
      show that in vitro an E. coli methyltransferase can cause C to U deaminations at a site of
      methylation. Reaction conditions that are known to inhibit a side reaction of the
      methyltransferase also suppress reversion frequency, suggesting that this side reaction is
      required for deamination. Furthermore, a mutation in the enzyme that eliminates its catalytic
      activity but not its ability to bind DNA eliminates the ability of the enzyme to cause C to U
      deaminations. Despite this, in vivo experiments strongly suggest that enzyme-catalyzed
      deaminations of cytosine do not play a major role in making methylation sites in E. coli hot
      spots for mutations. For example, although uracil-DNA glycosylase (Ung) suppresses the
      occurrence of mutations due to C to U deaminations, the frequency of C to T mutations at a
      methylation site remains high in ung+ cells. Furthermore, the reversion frequencies in ung+
      and ung- cells are quite similar.
AU  - Wyszynski W
AU  - Garbara S
AU  - Bhagwat AS
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1994 91: 1574-1578.

PMID- 27261261
VI  - 71
DP  - 2016
TI  - Complete sequence of an IncFII plasmid harbouring the colistin resistance gene mcr-1 isolated from Belgian pig farms.
PG  - 2342-2344
AB  - The monumental increase in antibiotic resistance among
      important bacterial pathogens, driven by inappropriate and
      appropriate use of ineffective drugs, is currently recognized as
      one of the most pressing threats to human health by the
      WHO. In particular, the last decade has seen a significant rise
      in infections caused by MDR and XDR Gram-negative pathogens
      such as Escherichia coli, Klebsiella pneumoniae, Pseudomonas
      aeruginosa and Acinetobacter baumannii. Antibiotics of the
      polymyxin group such as colistin are sometimes the only drugs
      to which these bacteria show susceptibility and, therefore,
      reports of emergence of a plasmid-mediated mcr-1-encoded
      mechanism of resistance to colistin have been especially alarming.
AU  - Xavier BB
AU  - Lammens C
AU  - Butaye P
AU  - Goossens H
AU  - Malhotra-Kumar S
PT  - Journal Article
TA  - J. Antimicrob. Chemother.
JT  - J. Antimicrob. Chemother.
SO  - J. Antimicrob. Chemother. 2016 71: 2342-2344.

PMID- 24723707
VI  - 2
DP  - 2014
TI  - Complete Genome Sequences of Nitrofurantoin-Sensitive and -Resistant Escherichia coli ST540 and ST2747 Strains.
PG  - e00239-14
AB  - Widespread multidrug resistance in Escherichia coli has necessitated the
      reintroduction of older antibiotics, such as nitrofurantoin. However, mechanisms
      by which resistance to nitrofurantoin emerges in E. coli are not well elucidated.
      Toward this aim, we sequenced two nitrofurantoin-sensitive E. coli sequence types
      (ST540 and ST2747) and their four nitrofurantoin-resistant derivatives generated
      in vitro under aerobic and anaerobic growth conditions.
AU  - Xavier BB
AU  - Vervoort J
AU  - Stewardson A
AU  - Adriaenssens N
AU  - Coenen S
AU  - Harbarth S
AU  - Goossens H
AU  - Malhotra-Kumar S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00239-14.

PMID- 25377707
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Rhizobium sp. H41, a Rock-Weathering Bacterium from a Weathered Rock Surface.
PG  - e01127-14
AB  - Rhizobium sp. H41 isolated from weathered tuff can weather tuff and release Fe, Si, and Al
      from the rock under nutrient-poor conditions. Here, we report the
      draft genome sequence of strain H41, which may facilitate a better understanding
      of the molecular mechanism involved in rock weathering by the bacterium.
AU  - Xi J
AU  - Sheng X
AU  - He L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01127-14.

PMID- 24356827
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of a Multidrug-Resistant New Delhi Metallo-beta-Lactamase-1 (NDM-1)-Producing Escherichia coli Isolate Obtained in Singapore.
PG  - e01020-13
AB  - We report the draft genome sequence of a New Delhi metallo-beta-lactamase-1 (NDM-1)-positive
      Escherichia coli isolate obtained from a surgical patient. The
      assembled data indicate the presence of 3 multidrug resistance plasmids, 1 of
      which shares 100% identity with an NDM-1 plasmid isolated previously from a
      nearby hospital, suggesting possible local transmission.
AU  - Xia E
AU  - Khong WX
AU  - Marimuthu K
AU  - Xu W
AU  - Ong RT
AU  - Tan EL
AU  - Krishnan PU
AU  - Ang BS
AU  - Lye DC
AU  - Chow AL
AU  - Teo YY
AU  - Ng OT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01020-13.

PMID- 12557394
VI  - 42
DP  - 2002
TI  - Construction of DNA transfer system of Streptomyces tenebrarius.
PG  - 181-185
AB  - To establish a gene transfer system in Streptomyces tenebrarius, several methods including
      PEG-mediated transformation of protoplasts,
      conjugal transfer were investigated. Many attempts were made to
      introduce plasmid pIJ702 into Streptomyces tenebrarius. It was found
      that plasmid pIJ702 isolated from S. lividans TK24 failed to transform
      the protoplasts of Streptomyces tenebrarius. No transformant was
      achieved even if the protoplast was inactivated by heat treatment or
      dsDNA was converted ssDNA before transformation. All the results
      suggested that Streptomyces tenebrarius exists a strong restriction and
      modification system for the transformation of foreign DNA. A
      recombinant E. coli ET12567 (pUZ8002, pHZ132) was obtained by
      transforming E. coli ET12567 (pUZ8002) with oriT-containing E.
      coli-Streptomyces shuttle plasmid pHZ132. In mating experiments, E. coli
      ET12567 (pUZ8002, pHZ132) was the donor, and the recipient was
      Streptomyces tenebrarius 9904 spores after pregerminating by heat shock.
      Matings between donor and recipient were conducted. Plasmid pHZ132 was
      introduced into Streptomyces tenebrarius 9904 by conjugation from E.
      coli ET12567. The transfer system of Streptomyces tenebrarius was
      established by conjugation. S. tenebrarius 9904 protoplasts were
      transformed by plasmid DNA modified by the host itself, and the
      transformation frequency was about 10^3/mug DNA (pHZ132).
AU  - Xia H
AU  - Wu S
PT  - Journal Article
TA  - Wei Sheng Wu Xue Bao
JT  - Wei Sheng Wu Xue Bao
SO  - Wei Sheng Wu Xue Bao 2002 42: 181-185.

PMID- 25555736
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Nocardia seriolae ZJ0503, a Fish Pathogen Isolated from  Trachinotus ovatus in China.
PG  - e01223-14
AB  - Nocardia seriolae is a pathogen that causes nocardiosis in marine and freshwater  fish. Here,
      we report the draft genome sequence of N. seriolae strain ZJ0503,
      which was isolated from Trachinotus ovatus in Guangdong, China.
AU  - Xia L
AU  - Cai J
AU  - Wang B
AU  - Huang Y
AU  - Jian J
AU  - Lu Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01223-14.

PMID- 27499827
VI  - 11
DP  - 2016
TI  - Draft genomic sequence of a chromate- and sulfate-reducing Alishewanella strain with the ability to bioremediate Cr and Cd contamination.
PG  - 48
AB  - Alishewanella sp. WH16-1 (= CCTCC M201507) is a facultative anaerobic, motile, Gram-negative,
      rod-shaped bacterium isolated from soil of a copper and iron mine.
      This strain efficiently reduces chromate (Cr(6+)) to the much less toxic Cr(3+).
      In addition, it reduces sulfate (SO4 (2-)) to S(2-). The S(2-) could react with
      Cd(2+) to generate precipitated CdS. Thus, strain WH16-1 shows a great potential
      to bioremediate Cr and Cd contaimination. Here we describe the features of this
      organism, together with the draft genome and comparative genomic results among
      strain WH16-1 and other Alishewanella strains. The genome comprises 3,488,867 bp,
      50.4 % G + C content, 3,132 protein-coding genes and 80 RNA genes. Both putative
      chromate- and sulfate-reducing genes are identified.
AU  - Xia X
AU  - Li J
AU  - Liao S
AU  - Zhou G
AU  - Wang H
AU  - Li L
AU  - Xu B
AU  - Wang G
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 48.

PMID- 30386456
VI  - 13
DP  - 2018
TI  - High-quality-draft genome sequence of the multiple heavy metal resistant bacterium Pseudaminobacter manganicus JH-7(T).
PG  - 29
AB  - Pseudaminobacter manganicus JH-7(T) (= KCTC 52258(T) = CCTCC AB 2016107(T)) is a
      Gram-staining-negative, aerobic and non-motile strain that was isolated from a
      manganese mine. The strain JH-7(T) shows multiple heavy metal resistance and can
      effectively remove Mn(2+) and Cd(2+). In addition, it is able to produce
      exopolysaccharides (EPS), which may contribute to metal remove/adsorption. Thus,
      strain JH-7(T) shows a great potential in bioremediation of heavy
      metal-contaminated environment. In this study, we report the draft genomic
      sequence of P. manganicus JH-7(T) and compare it to related genomes. Strain
      JH-7(T) has a 4,842,937 bp genome size with a G + C content of 61.2%, containing
      4504 protein-coding genes and 71 RNA genes. A large number of putative genes
      associated with heavy metal resistance and EPS synthesis are found in the genome.
AU  - Xia X
AU  - Li J
AU  - Zhou Z
AU  - Wang D
AU  - Huang J
AU  - Wang G
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2018 13: 29.

PMID- 3023890
VI  - 6
DP  - 1986
TI  - Restriction endonuclease activity induced by PBCV-1 virus infection of a chlorella-like green alga.
PG  - 1430-1439
AB  - An enzyme was isolated from a eucaryotic, Chlorella-like green alga infected with the virus
      PBCV-1 which exhibits type II restriction endonuclease activity. The enzyme recognized the
      sequence GATC and cleaved DNA 5' to the G. Methylation of deoxyadenosine in the GATC sequence
      inhibited enzyme activity. In vitro the enzyme cleaved host Chlorella nuclear DNA but not
      viral DNA because host DNA contains GATC and PBCV-1 DNA contains GmATC sequences.  PBCV-1 DNA
      is probably methylated in vivo by the PBCV-1-induced methyltransferase described elsewhere
      (Y.Xia and J.L. Van Etten, Mol. Cell. Biol. 6: 1440-1445). Restriction endonuclease activity
      was first detected 30 to 60 min after viral infection; the appearance of enzyme activity
      required de novo protein synthesis, and the enzyme is probably virus encoded.  Appearance of
      enzyme activity coincided with the onset of host DNA degradation after PBCV-1 infection.  We
      propose that the PBCV-1-induced restriction endonuclease participates in host DNA degradation
      and is part of a virus-induced restriction and modification system in PBCV-1-infected
      Chlorella cells.
AU  - Xia Y
AU  - Burbank DE
AU  - Uher L
AU  - Rabussay D
AU  - Van Etten JL
PT  - Journal Article
TA  - Mol. Cell. Biol.
JT  - Mol. Cell. Biol.
SO  - Mol. Cell. Biol. 1986 6: 1430-1439.

PMID- 2819820
VI  - 15
DP  - 1987
TI  - IL-3A virus infection of a Chlorella-like green alga induces a DNA restriction endonuclease with novel sequence specificity.
PG  - 6075-6090
AB  - A type II restriction endonuclease, named CviJI, was isolated from a eukaryotic Chlorella-like
      green alga infected with the dsDNA containing virus IL-3A. CviJI is the first restriction
      endonuclease to recognize the sequence PuGCPy; CviJI cleaves DNA between the G and C.
      Methylation of the cytosine in PuGCPy sequences prevents cleavage by CviJI. CviJI cleaved DNA
      into smaller but defined fragments in the presence of ATP. This "star activity" was stimulated
      by dithiothreitol and/or S-adenosylmethionine but did not occur under conditions which favor
      "star activity" of other restriction endonuclease.
AU  - Xia Y
AU  - Burbank DE
AU  - Uher L
AU  - Rabussay D
AU  - Van Etten JL
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1987 15: 6075-6090.

PMID- 3018667
VI  - 14
DP  - 1986
TI  - Restriction endonuclease activity induced by NC-1A virus infection of a Chlorella-like green alga.
PG  - 6017-6030
AB  - A type II restriction endonuclease, CviBI, was isolated from a eukaryotic,
      Chlorella-like green alga infected with the dsDNA containing virus NC-1A.  The
      enzyme recognizes the sequence GANTC and cleaves DNA between the G and A.
      Methylation of deoxyadenosine in the GANTC sequence probably inhibits enzyme
      activity.  In vitro CviBI cleaves host nuclear DNA but not viral DNA.  A survey
      of 18 other viruses which infect the same Chlorella sp. revealed that infection
      with 5 of these viruses also induced a restriction endonuclease which cleaves
      DNA into the same size fragments as CviBI.
AU  - Xia Y
AU  - Burbank DE
AU  - Van Etten JL
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1986 14: 6017-6030.

PMID- 3186439
VI  - 16
DP  - 1988
TI  - A site-specific single strand endonuclease activity induced by NYs-1 virus infection of a Chlorella-like green alga.
PG  - 9477-9487
AB  - A site-specific endonuclease was isolated from a eukaryotic Chlorella-like
      green alga infected with the dsDNA-containing virus NYs-1.  The enzyme
      recognizes the sequence 5'-CC-3' and cleaves 5' to the first C.  It cleaves
      5'-CmC-3' sequences but not 5'-mCC-3' sequences.  The enzyme creates breaks in
      dsDNA whenever two 5'-CC-3' sequences on opposite strands are close enough for
      the two strands to separate; when the 5'-CC-3' sequences on opposite strands
      are further apart only a portion of the strands separate.  Consequently, NYs-1
      endonuclease does not produce a completely stable DNA digestion pattern.  The
      enzyme probably does not cleave ssDNA and definitely does not cleave ssRNA or
      dsRNA.
AU  - Xia Y
AU  - Morgan R
AU  - Schildkraut I
AU  - Van Etten JL
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1988 16: 9477-9487.

PMID- 2827109
VI  - 15
DP  - 1987
TI  - The cleavage site of the RsaI isoschizomer, CviII, is G^TAC.
PG  - 10063
AB  - Infection of the green alga, Chlorella NC64A, with the dsDNA virus NY-2A
      results in the synthesis of a restriction endonuclease CviII.  Chlorella cells
      infected with NY-2A (m.o.i. of f10) were collected by centrifugation at 12 hr
      p.i.  Note: this has been renamed CviQI.
AU  - Xia Y
AU  - Narva KE
AU  - Van Etten JL
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1987 15: 10063.

PMID- 3537703
VI  - 6
DP  - 1986
TI  - DNA methyltransferase induced by PBCV-1 virus infection of a chlorella-like green alga.
PG  - 1440-1445
AB  - A DNA methyltransferase was isolated from a eucaryotic, Chlorella-like green
      alga infected with the virus PBCV-1.  The enzyme recognized the sequence GATC
      and methylated deoxyadenosine solely in GATC sequences.  Host DNA, which
      contains GATC sequences, but not PBCV-1 DNA, which contains GmATC sequences,
      was a good substrate for the enzyme in vitro.  The DNA methyltransferase
      activity was first detected about 1 h after viral infection; PBCV-1 DNA
      synthesis and host DNA degradation also began at about this time.  The
      appearance of the DNA methyltransferase activity required de novo protein
      synthesis, and the enzyme was probably virus encoded.  Methylation of DNAs with
      the PBCV-1-induced methyltransferase conferred resistance of the DNAs to a
      PBCV-1-induced restriction endonuclease enzyme described previously (Y. Xia,
      D.E. Burbank, L. Uher, D. Rabussay, and J.L. Van Etten, Mol. Cell Biol. 6:
      1430-1439).  We propose that the PBCV-1-induced methyltransferase protects
      viral DNA from the PBCV-1-induced restriction endonuclease and is part of a
      virus-induced restriction and modification system in PBCV-1-infected Chlorella
      cells.
AU  - Xia Y
AU  - Van Etten JL
PT  - Journal Article
TA  - Mol. Cell. Biol.
JT  - Mol. Cell. Biol.
SO  - Mol. Cell. Biol. 1986 6: 1440-1445.

PMID- 8372450
VI  - 196
DP  - 1993
TI  - Adenine DNA methyltransferase M.CviRI expression accelerates apoptosis in baculovirus-infected insect cells.
PG  - 817-824
AB  - The adenine DNA methyltransferase M.CviRI (TGCmA) gene from chlorella virus XZ-6E was cloned
      into the Autographa californica nuclear polyhedrosis virus (AcMNPV) genome and expressed in
      Spodoptera frugiperda insect cells under the control of two tandemly arranged viral promoters,
      the early ETL promoter and the late polyhedrin promoter. M.CviRI activity was first detected
      at 10 hr p.i. and reached a maximum at 48 hr p.i. Viral DNA synthesized in insect cells
      infected with M.CviRI expressing virus (AcMTRI) was methylated at all TGCA sites.
      Unexpectedly, AcMTRI-infected cells lysed 48 hr earlier than wild-type AcMNPV-infected cells.
      Moreover, cellular DNA, but not viral DNA, from AcM-TRI-infected cells was degraded to
      fragment sizes characteristic of apoptosis. Thse results suggest that M.CviRI methylation
      influences the onset of viral cytopathic effects and induces an apoptosis-like response.
AU  - Xia Y
AU  - Van Etten JL
AU  - Dobos P
AU  - Ling YY
AU  - Krell PJ
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1993 196: 817-824.

PMID- Not carried by PubMed...
VI  - 19
DP  - 1987
TI  - Purification and characterization of restriction endonuclease Bsp78I.
PG  - 27-34
AB  - Two kinds of direct single-step method using DNA-Sepharose and heparin-Sepharose affinity
      chromatography to purify restriction endonuclease Bsp78I are reported. Chromatographic
      conditions which may increase the purity and yield of the enzyme were studied. The purified
      enzymes, obtained by the two methods, were found to be free of detectable contamination by
      other DNases (exo and endo) caused by excess enzyme digestion of lambda DNA and by ligation
      and recutting of enzymatic digests of pBR322 DNA. The specific activities and the yields of
      the enzymes obtained by the two methods are both about 17,000 units per mg protein and 4,000
      units per g wet bacteria, respectively. Some properties of the restriction endonuclease Bsp78I
      are determined quantitatively. The optimal range of Mg++ concentration and optimal Tris-HCl
      concentration are 20-30 m mol/L and 50 m mol/L respectively. The optimal pH is 7.5 and the
      optimal temperature 40 C. 78I is very sensitive to PCMB.
AU  - Xia Z-G
AU  - Zhu R-F
AU  - Cao X-W
AU  - Zou G-L
PT  - Journal Article
TA  - Acta Biochim. Biophys. Sin.
JT  - Acta Biochim. Biophys. Sin.
SO  - Acta Biochim. Biophys. Sin. 1987 19: 27-34.

PMID- 15994761
VI  - 79
DP  - 2005
TI  - Sulfolobus tengchongensis spindle-shaped virus STSV1: Virus-host interactions and genomic features.
PG  - 8677-8686
AB  - A virus infecting the hyperthermophilic archaeon Sulfolobus tengchongensis has been isolated
      from a field sample from Tengchong,
      China, and characterized. The virus, denoted STSV1 (Sulfolobus
      tengchongensis spindle-shaped virus 1), has the morphology of a spindle
      (230 by 107 nm) with a tail of variable length (68 nm on average) at
      one end and is the largest of the known spindle-shaped viruses. After
      infecting its host, the virus multiplied rapidly to high titers (>
      10(10) PFU/ml). Replication of the virus retarded host growth but did
      not cause lysis of the host cells. STSV1 did not integrate into the
      host chromosome and existed in a carrier state. The STSV1 DNA was
      modified in an unusual fashion, presumably by virally encoded
      modification systems. STSV1 harbors a double-stranded DNA genome of
      75,294 bp, which shares no significant sequence similarity to those of
      fuselloviruses. The viral genome contains a total of 74 open reading
      frames (ORFs), among which 14 have a putative function. Five ORFs
      encode viral structural proteins, including a putative coat protein of
      high abundance. The products of the other nine ORFs are probably
      involved in polysaccharide biosynthesis, nucleotide metabolism, and DNA
      modification. The viral genome divides into two nearly equal halves of
      opposite gene orientation. This observation as well as a GC-skew
      analysis point to the presence of a putative viral origin of
      replication in the 1.4-kb intergenic region between ORF1 and ORF74.
      Both morphological and genomic features identify STSV1 as a novel virus
      infecting the genus Sulfolobus.
AU  - Xiang XY
AU  - Chen LM
AU  - Huang XX
AU  - Luo YM
AU  - She QX
AU  - Huang L
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 2005 79: 8677-8686.

PMID- 22038971
VI  - 193
DP  - 2011
TI  - Genome Sequence of Serinicoccus profundi, a Novel Actinomycete Isolated from Deep-Sea Sediment.
PG  - 6413
AB  - Serinicoccus profundi MCCC 1A05965(T) was isolated from deep-sea sediment collected from the
      Indian Ocean. It was a Gram-positive, moderately
      halophilic, aerobic bacterium. Here, we describe the 3.4-Mbp draft genome
      sequence of S. profundi MCCC 1A05965(T).
AU  - Xiao J
AU  - Luo Y
AU  - Xu J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6413.

PMID- 26275904
VI  - 16
DP  - 2015
TI  - Comparative genome analysis of Mycoplasma pneumoniae.
PG  - 610
AB  - BACKGROUND: Mycoplasma pneumoniae is a common pathogen that causes upper and
      lower respiratory tract infections in people of all ages, responsible for up to
      40 % of community-acquired pneumonias. It also causes a wide array of
      extrapulmonary infections and autoimmune phenomena. Phylogenetic studies of the
      organism have been generally restricted to specific genes or regions of the
      genome, because whole genome sequencing has been completed for only 4 strains. To
      better understand the physiology and pathogenicity of this important human
      pathogen, we performed comparative genomic analysis of 15 strains of M.
      pneumoniae that were isolated between the 1940s to 2009 from respiratory
      specimens and cerebrospinal fluid originating from the USA, China and England.
      RESULTS: Illumina MiSeq whole genome sequencing was performed on the 15 strains
      and all genome sequences were completed. Results from the comparative genomic
      analysis indicate that although about 1500 SNP and indel variants exist between
      type1 and type 2 strains, there is an overall high degree of sequence similarity
      among the strains (>99 % identical to each other). Within the two subtypes,
      conservation of most genes, including the CARDS toxin gene and arginine deiminase
      genes, was observed. The major variation occurs in the P1 and ORF6 genes
      associated with the adhesin complex. Multiple hsdS genes (encodes S subunit of
      type I restriction enzyme) with variable tandem repeat copy numbers were found in
      all 15 genomes. CONCLUSIONS: These data indicate that despite conclusions drawn
      from 16S rRNA sequences suggesting rapid evolution, the M. pneumoniae genome is
      extraordinarily stable over time and geographic distance across the globe with a
      striking lack of evidence of horizontal gene transfer.
AU  - Xiao L
AU  - Ptacek T
AU  - Osborne JD
AU  - Crabb DM
AU  - Simmons WL
AU  - Lefkowitz EJ
AU  - Waites KB
AU  - Atkinson TP
AU  - Dybvig K
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2015 16: 610.

PMID- 29773622
VI  - 6
DP  - 2018
TI  - Genome Sequences of 13 Isolates of Salmonella enterica Serovar Typhimurium var. Copenhagen Obtained from Wild Pigeons in Canada.
PG  - e00392-18
AB  - Pigeon-adapted strains of Salmonella enterica serovar Typhimurium var. Copenhagen phage types
      2 and 99 obtained from the provinces of Alberta, British Columbia,
      and Ontario, Canada, were analyzed using whole-genome sequencing. All isolates
      contained the Salmonella virulence plasmid despite the low pathogenicity of this
      lineage in their avian host.
AU  - Xie B
AU  - Dupras AA
AU  - Duceppe MO
AU  - Fattahi-Ghazi N
AU  - Goodridge L
AU  - Ogunremi D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00392-18.

PMID- 22535931
VI  - 194
DP  - 2012
TI  - Genome sequences of type strains of seven species of the marine bacterium Pseudoalteromonas.
PG  - 2746-2747
AB  - There are over 30 species in the marine bacterial genus Pseudoalteromonas.
      However, our knowledge about this genus is still limited. We sequenced the
      genomes of type strains of seven species in the genus, facilitating the study of
      the physiology, adaptation, and evolution of this genus.
AU  - Xie BB
AU  - Shu YL
AU  - Qin QL
AU  - Rong JC
AU  - Zhang XY
AU  - Chen XL
AU  - Shi M
AU  - He HL
AU  - Zhou BC
AU  - Zhang YZ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2746-2747.

PMID- 22374963
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Cycloprodigiosin-Producing Bacterial Strain Pseudoalteromonas rubra ATCC 29570T.
PG  - 1637-1638
AB  - The cycloprodigiosin biosynthetic gene cluster has not been reported. We sequenced the genome
      of a cycloprodigiosin-producing bacterial strain,
      Pseudoalteromonas rubra ATCC 29570(T). Analysis revealed a probable
      cycloprodigiosin biosynthetic cluster, providing a good model for the study of
      cycloprodigiosin synthesis and regulation.
AU  - Xie BB
AU  - Shu YL
AU  - Qin QL
AU  - Rong JC
AU  - Zhang XY
AU  - Chen XL
AU  - Zhou BC
AU  - Zhang YZ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1637-1638.

PMID- 
VI  - 
DP  - 2008
TI  - Mechanistic studies of specific DNA cleavage by PvuII restriction endonuclease.
PG  - 
AB  - PvuII restriction endonuclease is a homodimeric protein which recognizes and cleaves the
      palindromic sequence (CAG^CTG) in the presence of Mg(II) ions. Starting with PvuII as a model
      system, pKa calculations with crystallographically defined metal ligated water are applied to
      PD...D/ExK motif metallonucleases in order to investigate the activation of nucleophile in
      metal dependent DNA hydrolysis. These results establish the electrostatic contributions of the
      metal ions and the conserved Lys in lowering water pKa. The calculated pKa values of metal
      ligands have been used to simulate the pH dependence of Mg(II) binding to PvuII. The bell
      shaped pH-rate profile is dissected into three ionizations. One is recognized as from the
      metal ligands, and the other two have pKa's similar to calculated metal ligated water pKa in
      the absence of DNA. The determined pH profiles agree well with previous pH dependence studies
      on metallonucleases, and the correlation with pKa calculations indicates the direct
      involvement of metal activated water in catalysis. iii The different metal occupancies
      observed in crystal structures lead to controversy regarding the number and function of metal
      ions involved in DNA hydrolysis by type II restriction endonucleases. Quench flow experiments
      are used to monitor Mg(II) dependent single and multiple turnover DNA cleavage reactions with
      PvuII. Several models which differ in order of binding and the number of metal ions supporting
      catalysis are examined by global fits using DynaFit. The best fitted model has a preference of
      binding order in the reaction scheme and supports one-metal ion catalysis with 50 fold reduced
      activity compared with two-metal ion catalysis. The same model is also found to account for
      multiple turnover data in fits and simulations. A unique reaction scheme for PvuII is
      established to interpret the determined Mg(II) dependence of kinetic data, which provides an
      insight into Mg(II) participation in substrate binding, catalysis and product dissociation by
      restriction endonucleases.
AU  - Xie F
PT  - Journal Article
TA  - Ph.D. Thesis, University of Missouri
JT  - Ph.D. Thesis, University of Missouri
SO  - Ph.D. Thesis, University of Missouri 2008 : .

PMID- 26543127
VI  - 3
DP  - 2015
TI  - Genome Sequence of Porphyromonas gingivalis Strain AJW4.
PG  - e01304-15
AB  - Porphyromonas gingivalis is associated with oral and systemic diseases. Strain-specific P.
      gingivalis invasion phenotypes have been correlated with
      disease presentation in infected laboratory animals. Here, we present the genome
      sequence of AJW4, a minimally invasive strain, with a single contig of 2,372,492
      bp and a G+C content of 48.27%.
AU  - Xie G
AU  - Chastain-Gross RP
AU  - Belanger M
AU  - Kumar D
AU  - Whitlock JA
AU  - Liu L
AU  - Farmerie WG
AU  - Daligault HE
AU  - Han CS
AU  - Brettin TS
AU  - Progulske-Fox A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01304-15.

PMID- 28280013
VI  - 5
DP  - 2017
TI  - Genome Sequence of Porphyromonas gingivalis Strain A7A1-28.
PG  - e00021-17
AB  - Porphyromonas gingivalis is an oral opportunistic pathogen. Sequenced P. gingivalis laboratory
      strains display limited diversity in antigens that modulate
      host responses. Here, we present the genome sequence of A7A1-28, a strain
      possessing atypical fimbrillin and capsule types, with a single contig of
      2,249,024 bp and a G+C content of 48.58%.
AU  - Xie G
AU  - Chastain-Gross RP
AU  - Belanger M
AU  - Kumar D
AU  - Whitlock JA
AU  - Liu L
AU  - Farmerie WG
AU  - Zeng CL
AU  - Daligault HE
AU  - Han CS
AU  - Brettin TS
AU  - Progulske-Fox A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00021-17.

PMID- 22965098
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Rice Pathogen Pseudomonas fuscovaginae CB98818.
PG  - 5479-5480
AB  - Pseudomonas fuscovaginae is a phytopathogenic bacterium causing bacterial sheath  brown rot of
      cereal crops. Here, we present the draft genome sequence of P.
      fuscovaginae CB98818, originally isolated from a diseased rice plant in China.
      The draft genome will aid in epidemiological studies, comparative genomics, and
      quarantine of this broad-host-range pathogen.
AU  - Xie G
AU  - Cui Z
AU  - Tao Z
AU  - Qiu H
AU  - Liu H
AU  - Ibrahim M
AU  - Zhu B
AU  - Jin G
AU  - Sun G
AU  - Almoneafy A
AU  - Li B
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5479-5480.

PMID- 23640195
VI  - 1
DP  - 2013
TI  - Genome Sequences of Two Klebsiella pneumoniae Isolates from Different Geographical Regions, Argentina (Strain JHCK1) and the United States (Strain  VA360).
PG  - e00168-13
AB  - We report the sequences of two Klebsiella pneumoniae clinical isolates, strains JHCK1 and
      VA360, from a newborn with meningitis in Buenos Aires, Argentina, and
      from a tertiary care medical center in Cleveland, OH, respectively. Both isolates
      contain one chromosome and at least five plasmids; isolate VA360 contains the
      Klebsiella pneumoniae carbapenemase (KPC) gene.
AU  - Xie G
AU  - Ramirez MS
AU  - Marshall SH
AU  - Hujer KM
AU  - Lo CC
AU  - Johnson S
AU  - Li PE
AU  - Davenport K
AU  - Endimiani A
AU  - Bonomo RA
AU  - Tolmasky ME
AU  - Chain PS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00168-13.

PMID- 21742879
VI  - 193
DP  - 2011
TI  - Genome sequence of the rice-pathogenic bacterium Acidovorax avenae subsp. avenae RS-1.
PG  - 5013-5014
AB  - Acidovorax avenae subsp. avenae is a phytobacterium which is the causal agent of several
      economic plant diseases. Here, we present the draft
      genome sequence of strain RS-1, which was isolated from rice shoot in rice
      field of China. This strain can cause bacterial stripe of rice.
AU  - Xie GL
AU  - Zhang GQ
AU  - Liu H
AU  - Lou MM
AU  - Tian WX
AU  - Li B
AU  - Zhou XP
AU  - Zhu B
AU  - Jin GL
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5013-5014.

PMID- 
VI  - 46
DP  - 2001
TI  - Analysis of the characteristic sequence of intein and revision of its motifs.
PG  - 758-761
AB  - Since the first intein (Sce VMA) was found in Saccharomyces cerevisiae ATPase gene in 1990,
      more and more inteins were identified. It is necessary to analyze the new inteins to
      understand the sequence characteristics of inteins. By searching protein and nucleic acid
      database systematically, 101 inteins were found, of which 69 inteins contain homing
      endonuclease moths. We only analyze the 69 inteins since most inteins are the classic inteins
      with homing endonuclease motifs. We found that the distribution of these inteins is particular
      among species and protein. By multiple sequence alignment, some new sequence characteristics
      were found and the motifs described previously were revised.
AU  - Xie J
AU  - Huang JF
AU  - Shi XF
AU  - Liu CQ
PT  - Journal Article
TA  - Chinese Sci. Bull.
JT  - Chinese Sci. Bull.
SO  - Chinese Sci. Bull. 2001 46: 758-761.

PMID- 17005745
VI  - 44
DP  - 2006
TI  - Identification of New Genetic Regions More Prevalent in Nontypeable Haemophilus influenzae Otitis Media Strains than in Throat Strains.
PG  - 4316-4325
AB  - Nontypeable (NT) Haemophilus influenzae strains cause significant respiratory illness and are
      isolated from up to half of middle ear aspirates from children with acute otitis media.
      Previous studies have identified two genes, lic2B and hmwA, that are associated with NT H.
      influenzae strains isolated from the middle ears of children with otitis media but that are
      not associated with NT H. influenzae strains isolated from the throats of healthy children,
      suggesting that they may play a role in virulence in otitis media. In this study, genomic
      subtraction was used to identify additional genetic regions unique to middle ear strains. The
      genome of NT H. influenzae middle ear strain G622 was subtracted from that of NT H. influenzae
      throat strain 23221, and the resultant gene regions unique to the middle ear strain were
      identified. Subsequently, the relative prevalence of the middle ear-specific gene regions
      among a large panel of otitis media and throat strains was determined by dot blot
      hybridization. By this approach, nine genetic regions were found to be significantly more
      prevalent in otitis media strains. Classification tree analysis of lic2B, hmwA, and the nine
      new potential otitis media virulence genes revealed two H. influenzae pathotypes associated
      with otitis media.
AU  - Xie J
AU  - Juliao PC
AU  - Gilsdorf JR
AU  - Ghosh D
AU  - Patel M
AU  - Marrs CF
PT  - Journal Article
TA  - J. Clin. Microbiol.
JT  - J. Clin. Microbiol.
SO  - J. Clin. Microbiol. 2006 44: 4316-4325.

PMID- 24651173
VI  - 10
DP  - 2014
TI  - Comparative Genomic Analysis of N2-Fixing and Non-N2-Fixing Paenibacillus spp.: Organization, Evolution and Expression of the Nitrogen Fixation Genes.
PG  - E1004231
AB  - We provide here a comparative genome analysis of 31 strains within the genus
      Paenibacillus including 11 new genomic sequences of N2-fixing strains. The
      heterogeneity of the 31 genomes (15 N2-fixing and 16 non-N2-fixing Paenibacillus
      strains) was reflected in the large size of the shell genome, which makes up
      approximately 65.2% of the genes in pan genome. Large numbers of transposable
      elements might be related to the heterogeneity. We discovered that a minimal and
      compact nif cluster comprising nine genes nifB, nifH, nifD, nifK, nifE, nifN,
      nifX, hesA and nifV encoding Mo-nitrogenase is conserved in the 15 N2-fixing
      strains. The nif cluster is under control of a sigma(70)-depedent promoter and
      possesses a GlnR/TnrA-binding site in the promoter. Suf system encoding [Fe-S]
      cluster is highly conserved in N2-fixing and non-N2-fixing strains. Furthermore,
      we demonstrate that the nif cluster enabled Escherichia coli JM109 to fix
      nitrogen. Phylogeny of the concatenated NifHDK sequences indicates that
      Paenibacillus and Frankia are sister groups. Phylogeny of the concatenated 275
      single-copy core genes suggests that the ancestral Paenibacillus did not fix
      nitrogen. The N2-fixing Paenibacillus strains were generated by acquiring the nif
      cluster via horizontal gene transfer (HGT) from a source related to Frankia.
      During the history of evolution, the nif cluster was lost, producing some
      non-N2-fixing strains, and vnf encoding V-nitrogenase or anf encoding
      Fe-nitrogenase was acquired, causing further diversification of some strains. In
      addition, some N2-fixing strains have additional nif and nif-like genes which may
      result from gene duplications. The evolution of nitrogen fixation in
      Paenibacillus involves a mix of gain, loss, HGT and duplication of nif/anf/vnf
      genes. This study not only reveals the organization and distribution of nitrogen
      fixation genes in Paenibacillus, but also provides insight into the complex
      evolutionary history of nitrogen fixation.
AU  - Xie JB
AU  - Du Z
AU  - Bai L
AU  - Tian C
AU  - Zhang Y
AU  - Xie JY
AU  - Wang T
AU  - Liu X
AU  - Chen X
AU  - Cheng Q
AU  - Chen S
AU  - Li J
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2014 10: E1004231.

PMID- 10433969
VI  - 236
DP  - 1999
TI  - Cloning, expression and chromosome locations of the human DNMT3 gene family.
PG  - 87-95
AB  - DNA methylation plays an important role in animal development and gene regulation. In mammals,
      several genes encoding DNA cytosine methyltransferases have been identified. DNMT1 is
      constitutively expressed and is required for the maintenance of global methylation after DNA
      replication. In contrast, the murine Dnmt3 family genes appear to be developmentally regulated
      and behave like de novo DNA methyltransferases in vitro. In this study, we have cloned human
      DNMT3A and DNMT3B that encode full-length DNMT3A and DNMT3B proteins with 98% and 94% amino
      acid sequence identity to their murine homologues. The DNMT3A and DNMT3B show high homology in
      the carboxy terminal catalytic domain and contain a conserved cysteine-rich region, which
      shares homology with the X-linked ATRX gene of the SNF2/SWI family. We have mapped human
      DNMT3A and DNMT3B to chromosomes 2p23 and 20q11.2 respectively, and determined the DNMT3B
      genomic structure. We further show that DNMT3A expression is ubiquitous and can be readily
      detected in most adult tissues, whereas DNMT3B is expressed at very low levels in most tissues
      except testis, thyroid and bone marrow. Significantly, both DNMT3A and DNMT3B expression is
      elevated in several tumor cell lines to levels comparable to DNMT1. The cloning of the human
      DNMT3 genes will facilitate further biochemical and genetic studies of their functions in
      establishment of DNA methylation patterns, regulation of gene expression and tumorigenesis.
AU  - Xie S
AU  - Wang Z
AU  - Okano M
AU  - Nogami M
AU  - Li Y
AU  - He W-W
AU  - Okumura K
AU  - Li E
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1999 236: 87-95.

PMID- 
VI  - 1
DP  - 2010
TI  - Complexity and entropy analysis of DNA methyltransferase.
PG  - 1000105
AB  - The application of complexity information on DNA sequence and protein in biological processes
      are well established in this study.  Available sequences for DNMT1 gene were thoroughly
      explored in the informaion complexities.  DNMT1 gene is a maintenance methyltransferase
      responsible for copy in DNA methylation patterns to the daughter strands during DNA
      replication in different species.  We found that the entropy of DNMT1 gene in differnt species
      is DNA base composition dependent, and its complexity in mammals is lower in introns than in
      coding regions.  We also demonstrated the impacts of entropy on domains and non-domains(s) of
      the DNMT1 gene.  The results from DNA and protein sequences indicated that DNA evolution has a
      tendency toward complexity.  The most interest is that the methylation's changes of the gene
      over aging in a unique chick model showed aging-driven entropy characteristics, which may give
      an explanation of aging processes.  In summary, the information complexity of DNNT1 gene is
      related to its genomic composition, which thereby associates to evolutionary and aging
      processing, even though the intrinsic mechanism is not to be studied yet.
AU  - Xie X
AU  - Yu Y
AU  - Liu G
AU  - Yuan Z
AU  - Song J
PT  - Journal Article
TA  - J. Data Min. Genomics Proteomics
JT  - J. Data Min. Genomics Proteomics
SO  - J. Data Min. Genomics Proteomics 2010 1: 1000105.

PMID- 23908293
VI  - 1
DP  - 2013
TI  - Genome Sequence of Clostridium butyricum Strain DSM 10702, a Promising Producer of Biofuels and Biochemicals.
PG  - e00563-13
AB  - Clostridium butyricum strains have been considered promising producers of biofuels and
      biochemicals, such as hydrogen, butanol, butyric acid, and
      1,3-propanediol. Here, we present a 4.59-Mb assembly of the genome sequence of
      DSM 10702 (VPI 3266), a type strain of C. butyricum.
AU  - Xin B
AU  - Tao F
AU  - Wang Y
AU  - Gao C
AU  - Ma C
AU  - Xu P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00563-13.

PMID- 22815457
VI  - 194
DP  - 2012
TI  - Genomic Comparison of Rickettsia honei Strain RBT and Other Rickettsia Species.
PG  - 4145
AB  - Rickettsia honei strain RB(T) was isolated from a febrile patient on Flinders Island,
      Australia, in 1991 and has been demonstrated to be the agent of Flinders
      Island spotted fever, a disease transmitted to humans by ticks. The comparison of
      this 1.27-Mb genome with other Rickettsia genomes provides additional insight
      into the mechanisms of evolution in Rickettsia species.
AU  - Xin D
AU  - El Karkouri K
AU  - Robert C
AU  - Raoult D
AU  - Fournier PE
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4145.

PMID- 25478683
VI  - 9
DP  - 2015
TI  - Niches of two polysaccharide-degrading Polaribacter isolates from the North Sea during a spring diatom bloom.
PG  - 1410-1422
AB  - Members of the flavobacterial genus Polaribacter thrive in response to North Sea
      spring phytoplankton blooms. We analyzed two respective Polaribacter species by
      whole genome sequencing, comparative genomics, substrate tests and proteomics.
      Both can degrade algal polysaccharides but occupy distinct niches. The liquid
      culture isolate Polaribacter sp. strain Hel1_33_49 has a 3.0-Mbp genome with an
      overall peptidase:CAZyme ratio of 1.37, four putative polysaccharide utilization
      loci (PULs) and features proteorhodopsin, whereas the agar plate isolate
      Polaribacter sp. strain Hel1_85 has a 3.9-Mbp genome with an even
      peptidase:CAZyme ratio, eight PULs, a mannitol dehydrogenase for decomposing
      algal mannitol-capped polysaccharides but no proteorhodopsin. Unlike other
      sequenced Polaribacter species, both isolates have larger sulfatase-rich PULs,
      supporting earlier assumptions that Polaribacter take part in the decomposition
      of sulfated polysaccharides. Both strains grow on algal laminarin and the
      sulfated polysaccharide chondroitin sulfate. For strain Hel1_33_49, we identified
      by proteomics (i) a laminarin-induced PUL, (ii) chondroitin sulfate-induced
      CAZymes and (iii) a chondroitin-induced operon that likely enables chondroitin
      sulfate recognition. These and other data suggest that strain Hel1_33_49 is a
      planktonic flavobacterium feeding on proteins and a small subset of algal
      polysaccharides, while the more versatile strain Hel1_85 can decompose a broader
      spectrum of polysaccharides and likely associates with algae.
AU  - Xing P
AU  - Hahnke RL
AU  - Unfried F
AU  - Markert S
AU  - Huang S
AU  - Barbeyron T
AU  - Harder J
AU  - Becher D
AU  - Schweder T
AU  - Glockner FO
AU  - Amann RI
AU  - Teeling H
PT  - Journal Article
TA  - ISME J.
JT  - ISME J.
SO  - ISME J. 2015 9: 1410-1422.

PMID- 28495757
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of a Novel Multidrug-Resistant Klebsiella pneumoniae Phage, vB_Kpn_IME260.
PG  - e00055-17
AB  - Klebsiella pneumoniae is the most common clinically important opportunistic bacterial pathogen
      and its infection is often iatrogenic. Its drug resistance
      poses a grave threat to public health. The genomic data reported here comprise an
      important resource for research on phage therapy in the control of drug-resistant
      bacteria.
AU  - Xing S
AU  - Pan X
AU  - Sun Q
AU  - Pei G
AU  - An X
AU  - Mi Z
AU  - Huang Y
AU  - Zhao B
AU  - Tong Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00055-17.

PMID- 28572328
VI  - 5
DP  - 2017
TI  - Complete Genome of a Panresistant Pseudomonas aeruginosa Strain, Isolated from a  Patient with Respiratory Failure in a Canadian Community Hospital.
PG  - e00458-17
AB  - We report here the complete genome sequence of a panresistant Pseudomonas aeruginosa strain,
      isolated from a patient with respiratory failure in Canada. No
      carbapenemase genes were identified. Carbapenem resistance is attributable to a
      frameshift in the oprD gene; the basis for colistin resistance remains
      undetermined.
AU  - Xiong J
AU  - Deraspe M
AU  - Iqbal N
AU  - Krajden S
AU  - Chapman W
AU  - Dewar K
AU  - Roy PH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00458-17.

PMID- 21704702
VI  - 162
DP  - 2011
TI  - Genome analysis and characterization of zinc efflux systems of a highly zinc-resistant bacterium, Comamonas testosteroni S44.
PG  - 671-679
AB  - A novel and multiple metal(loid)-resistant strain Comamonas testosteroni S44 with
      a high Zn(2+) resistance level (10 mM) was isolated. To understand the molecular
      basis for the high zinc resistance, whole genome sequencing was performed and
      revealed a large number of genes encoding putative metal(loid) resistance
      proteins, mobile genetic elements (MGEs) and horizontal gene transfer (HGT)
      events that may have occurred to adapt to a metal(loid)-contaminated environment.
      In particular, 9 putative Zn(2+) transporters [4 znt operons encoding putative
      Zn(2+)-translocating P-type ATPases and 5 czc operons encoding putative
      RND-driven (resistance, nodulation, cell division protein family)] tripartite
      protein complexes were identified. Real-time RT-PCR analysis revealed that the
      four zntA-like genes were all induced by Zn(2+), while czcA genes were either
      Zn(2+)-induced or downregulated by Zn(2+). Furthermore, a zntR1A1 operon encoding
      a ZntR-type regulator and a P-type ATPase was studied in detail. The zntR1
      deletion strain (S44DeltazntR1) displayed intermediate resistance to Zn(2+) (6
      mM) and accumulated more intracellular Zn(2+). Reporter gene expression assays
      indicated that ZntR1 responded to Zn(2+), Cd(2+) and Pb(2+), with Zn(2+) being
      the best inducer. Gene transcription analysis indicated that ZntR1 was a
      regulator for transcription of zntA1, while other putative ZntR-type regulators
      may also regulate the transcription expression of zntA1.
AU  - Xiong J
AU  - Li D
AU  - Li H
AU  - He M
AU  - Miller SJ
AU  - Yu L
AU  - Rensing C
AU  - Wang G
PT  - Journal Article
TA  - Res. Microbiol.
JT  - Res. Microbiol.
SO  - Res. Microbiol. 2011 162: 671-679.

PMID- 21037005
VI  - 193
DP  - 2010
TI  - Complete genome sequence of the bacteria Ketogulonicigenium vulgare Y25.
PG  - 315-316
AB  - Ketogulonicigenium vulgare is characterized by the efficient production of 2KGA from
      L-sorbose. Ketogulonicigenium vulgare Y25 is known as a 2-keto-L-gulonic acid producing strain
      in vitamin C industry. Here we report the finished, annotated genome sequence of
      Ketogulonicigenium vulgare Y25.
AU  - Xiong XH
AU  - Han S
AU  - Wang JH
AU  - Jiang ZH
AU  - Chen W
AU  - Jia N
AU  - Wei HL
AU  - Cheng H
AU  - Yang YX
AU  - Zhu B
AU  - You S
AU  - He JY
AU  - Hou W
AU  - Chen MX
AU  - Yu CJ
AU  - Jiao YH
AU  - Zhang WC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 193: 315-316.

PMID- 21148725
VI  - 193
DP  - 2011
TI  - Complete genome sequence of the bacterium Methylovorus sp. strain MP688, a high-level producer of pyrroloquinolone quinone.
PG  - 1012-1013
AB  - Methylotrophic bacteria are widespread microbes which can use one carbon compound as their
      only carbon and energy sources. Here we report the finished, annotated
      genome sequence of the methylotrophic bacterium Methylovorus sp. strain MP688,
      which was isolated from soil for high-level production of pyrroloquinolone
      quinone (PQQ) in our lab.
AU  - Xiong XH
AU  - Zhi JJ
AU  - Yang L
AU  - Wang JH
AU  - Zhao Y
AU  - Wang X
AU  - Cui YJ
AU  - Dong F
AU  - Li MX
AU  - Yang YX
AU  - Wei N
AU  - An JJ
AU  - Du BH
AU  - Liang L
AU  - Zhang JS
AU  - Zhou W
AU  - Cheng SF
AU  - He T
AU  - Wang L
AU  - Chen HP
AU  - Liu DS
AU  - Zhang WC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 1012-1013.

PMID- 2844414
VI  - 55
DP  - 1988
TI  - Functional expression of a sequence-specific endonuclease encoded by the retrotransposon R2Bm.
PG  - 235-246
AB  - A fraction of the 28S ribosomal genes in certain insect species is interrupted by the
      insertion elements R1 and R2. These two elements from the silkworm Bombyx mori (R~1Bm and
      R2Bm) are retrotransposons capable of transposing in a highly sequence-specific manner. We
      report here the functional expression in E. coli of the entire single open reading frame of
      R2Bm and show that it encodes a double-stranded endonuclease (integrase) that can specifically
      cleave the 28S gene at the R2 insertion site. The resulting cleavage is a 4 bp staggered 5'
      overhang. Deletion analysis of the 28S gene revealed that the DNA sequence required for
      specific cleavage is asymmetric with respect to the actual insertion (cleavage) site, with
      fewer than 10 bp required at one side and at least 24 bp at the other side of the site. A
      model is proposed based on these and previous data to account for the sequence-specific
      integration of the R2 retrotransposon.
AU  - Xiong Y
AU  - Elckbush TH
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1988 55: 235-246.

PMID- 22558360
VI  - 7
DP  - 2012
TI  - A Novel Escherichia coli O157:H7 Clone Causing a Major Hemolytic Uremic Syndrome Outbreak in China.
PG  - E36144
AB  - An Escherichia coli O157:H7 outbreak in China in 1999 caused 177 deaths due to
      hemolytic uremic syndrome. Sixteen outbreak associated isolates were found to
      belong to a new clone, sequence type 96 (ST96), based on multilocus sequence
      typing of 15 housekeeping genes. Whole genome sequencing of an outbreak isolate,
      Xuzhou21, showed that the isolate is phylogenetically closely related to the
      Japan 1996 outbreak isolate Sakai, both of which share the most recent common
      ancestor with the US outbreak isolate EDL933. The levels of IL-6 and IL-8 of
      peripheral blood mononuclear cells induced by Xuzhou21 and Sakai were
      significantly higher than that induced by EDL933. Xuzhou21 also induced a
      significantly higher level of IL-8 than Sakai while both induced similar levels
      of IL-6. The expression level of Shiga toxin 2 in Xuzhou21 induced by mitomycin C
      was 68.6 times of that under non-inducing conditions, twice of that induced in
      Sakai (32.7 times) and 15 times higher than that induced in EDL933 (4.5 times).
      Our study shows that ST96 is a novel clone and provided significant new insights
      into the evolution of virulence of E. coli O157:H7.
AU  - Xiong Y
AU  - Wang P
AU  - Lan R
AU  - Ye C
AU  - Wang H
AU  - Ren J
AU  - Jing H
AU  - Wang Y
AU  - Zhou Z
AU  - Bai X
AU  - Cui Z
AU  - Luo X
AU  - Zhao A
AU  - Wang Y
AU  - Zhang S
AU  - Sun H
AU  - Wang L
AU  - Xu J
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2012 7: E36144.

PMID- 19060151
VI  - 191
DP  - 2009
TI  - Complete genome sequence of the extremophilic Bacillus cereus strain Q1 with industrial applications.
PG  - 1120-1121
AB  - Bacillus cereus strain Q1 was isolated from a deep-subsurface oil reservoir in the Daqing oil
      field in northeastern China. This strain is
      able to produce biosurfactants and to survive in extreme environments.
      Here we report the finished and annotated genome sequence of this
      organism.
AU  - Xiong Z
AU  - Jiang Y
AU  - Qi D
AU  - Lu H
AU  - Yang F
AU  - Yang J
AU  - Chen L
AU  - Sun L
AU  - Xu X
AU  - Xue Y
AU  - Zhu Y
AU  - Jin Q
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2009 191: 1120-1121.

PMID- 9171110
VI  - 25
DP  - 1997
TI  - COBRA: a sensitive and quantitative DNA methylation assay.
PG  - 2532-2534
AB  - We report here on a quantitative technique called COBRA to determine DNA methylation levels at
      specific gene loci in small amounts of genomic DNA.  Restriction enzyme digestion is used to
      reveal methylation-dependent sequence differences in PCR products of sodium bisulfite-treated
      DNA as described previously.  We show that methylation levels in the original DNA sample are
      represented by the relative amounts of digested and undigested PCR product in a linearly
      quantitative fashion across a wide spectrum of DNA methylation levels.  In addition, we show
      that this technique can be reliably applied to DNA obtained from microdissected
      paraffin-embedded tissue samples.  COBRA thus combines the powerful features of ease of use,
      quantitative accuracy, and compatibility with paraffin sections.
AU  - Xiong Z
AU  - Laird PW
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1997 25: 2532-2534.

PMID- 23144381
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Marine-Derived Streptomyces sp. Strain AA0539, Isolated  from the Yellow Sea, China.
PG  - 6622-6623
AB  - Here, we report the draft genome sequence of Streptomyces sp. strain AA0539, isolated from
      marine sediment of the Yellow Sea, China. Its small genome (
      approximately 5.8 Mb) contains large, unique genes and gene clusters for diverse
      secondary metabolites, suggesting great potential as a source for the discovery
      of novel natural products.
AU  - Xiong ZQ
AU  - Wang Y
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6622-6623.

PMID- 22965095
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of the Marine Streptomyces sp. Strain AA1529, Isolated from the Yellow Sea.
PG  - 5474-5475
AB  - Here we report the draft genome sequence of a Streptomyces strain, AA1529, isolated from
      marine sediment from the Yellow Sea. Its genome contains a subset
      of unique genes and gene clusters that encode diverse secondary metabolites,
      suggesting great potential as a source for the discovery of novel gene clusters
      and bioactive compounds.
AU  - Xiong ZQ
AU  - Wang Y
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5474-5475.

PMID- 29545296
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Four Uropathogenic Escherichia coli Serotype O4:H5 Isolates (ATCC 700414, 700415, 700416, and 700417).
PG  - e00134-18
AB  - Uropathogenic Escherichia coli serotype O4:H5 isolates (ATCC 700414, 700415, 700416, and
      700417) were recovered from women with first-time urinary tract
      infections. Here, we report the draft genome sequences for these four E. coli
      isolates, which are currently being used to validate food safety processing
      technologies.
AU  - Xu A
AU  - Hertrich S
AU  - Needleman DS
AU  - Sheen S
AU  - Sommers C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00134-18.

PMID- 29798928
VI  - 6
DP  - 2018
TI  - Draft Genomic Sequencing of Six Potential Extraintestinal Pathogenic Escherichia  coli Isolates from Retail Chicken Meat.
PG  - e00449-18
AB  - Potential extraintestinal pathogenic Escherichia coli strains DP254, WH333, WH398, F356,
      FEX675, and FEX725 were isolated from retail chicken meat products.
      Here, we report the draft genome sequences for these six E. coli isolates, which
      are currently being used in food safety research.
AU  - Xu A
AU  - Johnson JR
AU  - Sheen S
AU  - Needleman DS
AU  - Sommers C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00449-18.

PMID- 29674529
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Five Neonatal Meningitis-Causing Escherichia coli Isolates (SP-4, SP-5, SP-13, SP-46, and SP-65).
PG  - e00091-18
AB  - Neonatal meningitis-causing Escherichia coli isolates (SP-4, SP-5, SP-13, SP-46,  and SP-65)
      were recovered between 1989 and 1997 from infants in the Netherlands.
      Here, we report the draft genome sequences of these five E. coli isolates, which
      are currently being used to validate food safety processing technologies.
AU  - Xu A
AU  - Johnson JR
AU  - Sheen S
AU  - Sommers C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00091-18.

PMID- 30533908
VI  - 7
DP  - 2018
TI  - Draft Genomic Sequences of Nine Extraintestinal Pathogenic Escherichia coli Isolates from Retail Chicken Skin.
PG  - e00859-18
AB  - Extraintestinal pathogenic Escherichia coli strains were isolated from retail chicken skin.
      Here, we report the draft genomic sequences for these nine E. coli
      isolates, which are currently being used in agricultural and food safety
      research.
AU  - Xu A
AU  - Tilman S
AU  - Wisser-Parker K
AU  - Scullen OJ
AU  - Sommers CH
PT  - Journal Article
TA  - Microbiol. Resour. Announc.
JT  - Microbiol. Resour. Announc.
SO  - Microbiol. Resour. Announc. 2018 7: e00859-18.

PMID- 17584179
VI  - 14
DP  - 2007
TI  - Crystallization and preliminary X-ray analysis of Sau3AI/E64A mutant protein.
PG  - 505-506
AB  - Sau3AI is a type II restriction endonuclease that recognizes the palindromic sequence
      5'-GATC-3' and cleaves 5' to G residue on each
      strand. The E64A mutant full length protein was cloned and expressed in
      Escherichia coli. The purified (His) (6)-tagged protein has monomer and
      dimer fraction and was crystallized by the hanging-drop vapor-diffusion
      technique. The dimer protein crystals can diffract to 3.0A. resolution and
      the monomer protein crystals can diffract to better than 2.8A. resolution.
      One completed dataset has been collected and it shows that the monomer
      orthorhombic Sau3AI/E64A crystal is in space group C2221 with unit cell
      parameters (69.44, 197.60, 191.46, 90, 90, 90) and contains two molecules
      in one asymmetric unit.
AU  - Xu C
AU  - Song J
AU  - Ding Y
AU  - Yu F
AU  - Sun L
AU  - Tang L
AU  - Hu X
AU  - Zhang Z
AU  - He J
PT  - Journal Article
TA  - Protein Pept. Lett.
JT  - Protein Pept. Lett.
SO  - Protein Pept. Lett. 2007 14: 505-506.

PMID- 23969054
VI  - 1
DP  - 2013
TI  - Genome Sequence of Salmonella enterica Serovar Typhi Oral Vaccine Strain Ty21a.
PG  - e00650-13
AB  - Attenuated Salmonella enterica serovar Typhi strain Ty21a is an important vaccine for
      controlling typhoid fever and serves as an oral vector for delivering
      heterologous antigens. The key attenuating features of this randomly mutated
      strain remain in question. Genome sequencing has revealed 679 single nucleotide
      polymorphisms (SNPs), and will help define alterations contributing to Ty21a
      safety and immunogenicity.
AU  - Xu D
AU  - Cisar JO
AU  - Poly F
AU  - Yang J
AU  - Albanese J
AU  - Dharmasena M
AU  - Wai T
AU  - Guerry P
AU  - Kopecko DJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00650-13.

PMID- 28687650
VI  - 83
DP  - 2017
TI  - Parallel evolution of two clades of a major Atlantic endemic Vibrio parahaemolyticus pathogen lineage by independent acquisition of related pathogenicity islands.
PG  - e01168-17
AB  - Shellfish-transmitted Vibrio parahaemolyticus infections have recently increased
      from locations with historically low disease incidence, such as the Northeast
      United States (US). This change coincided with a bacterial population shift
      towards human pathogenic variants occurring in part through the introduction of
      several Pacific native lineages (ST36, ST43 and ST636) to near-shore areas off
      the Atlantic coast of the Northeast US. Concomitantly, ST631 emerged as a major
      endemic pathogen. Phylogenetic trees of clinical and environmental isolates
      indicated that two clades diverged from a common ST631 ancestor, and in each of
      these clades, a human pathogenic variant evolved independently through
      acquisition of distinct Vibrio pathogenicity islands (VPaI). These VPaI differ
      from each other and bear little resemblance to hemolysin-containing VPaI from
      isolates of the pandemic clonal complex. Clade I ST631 isolates either harbored
      no hemolysins, or contained a chromosome I-inserted island we call VPaIbeta that
      encodes a type three secretion system (T3SS2beta) typical of Trh
      hemolysin-producers. The more clinically prevalent and clonal ST631 clade II had
      an island we call VPaIgamma that encodes both tdh and trh and that was inserted
      in chromosome II. VPaIgamma was derived from VPaIbeta but with some additional
      acquired elements in common with VPaI carried by pandemic isolates, exemplifying
      the mosaic nature of pathogenicity islands. Genomics comparisons and amplicon
      assays identified VPaIgamma-type islands containing tdh inserted adjacent to the
      ure cluster in the three introduced Pacific and most other emergent lineages.
      that collectively cause 67% of Northeast US infections as of 2016.IMPORTANCE The
      availability of three different hemolysin genotypes in the ST631 lineage provided
      a unique opportunity to employ genome comparisons to further our understanding of
      the processes underlying pathogen evolution. The fact that two different
      pathogenic clades arose in parallel from the same potentially benign lineage by
      independent VPaI acquisition is surprising considering the historically low
      prevalence of community members harboring VPaI in waters along the Northeast US
      coast that could serve as the source of this material. This illustrates a
      possible predisposition of some lineages to not only acquire foreign DNA but also
      to become human pathogens. Whereas the underlying cause for the expansion of V.
      parahaemolyticus lineages harboring VPaIgamma along the US Atlantic coast and
      spread of this element to multiple lineages that underlies disease emergence is
      not known, this work underscores the need to define the environment factors that
      favor bacteria harboring VPaI in locations of emergent disease.
AU  - Xu F
AU  - Gonzalez-Escalona N
AU  - Drees KP
AU  - Sebra RP
AU  - Cooper VS
AU  - Jones SH
AU  - Whistler CA
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2017 83: e01168-17.

PMID- 20939822
VI  - 17
DP  - 2010
TI  - Molecular and Enzymatic Profiles of Mammalian DNA Methyltransferases: Structures and Targets for Drugs.
PG  - 4052-4071
AB  - DNA methylation is an epigenetic event involved in a variety array of processes that may be
      the foundation of genetic phenomena and diseases.
      DNA methyltransferase is a key enzyme for cytosine methylation in DNA,
      and can be divided into two functional families (Dnmt1 and Dnmt3) in
      mammals. All mammalian DNA methyltransferases are encoded by their own
      single gene, and consisted of catalytic and regulatory regions (except
      Dnmt2). Via interactions between functional domains in the regulatory
      or catalytic regions and other adaptors or cofactors, DNA
      methyltransferases can be localized at selective areas (specific
      DNA/nucleotide sequence) and linked to specific chromosome status
      (euchromatin/ heterochromatin, various histone modification status).
      With assistance from UHRF1 and Dnmt3L or other factors in Dnmt1 and
      Dnmt3a/Dnmt3b, mammalian DNA methyltransferases can be recruited, and
      then specifically bind to hemimethylated and unmethylated
      double-stranded DNA sequence to maintain and de novo setup patterns for
      DNA methylation. Complicated enzymatic steps catalyzed by DNA
      methyltransferases include methyl group transferred from cofactor
      Ado-Met to C5 position of the flipped-out cytosine in targeted DNA
      duplex. In the light of the fact that different DNA methyltransferases
      are divergent in both structures and functions, and use unique
      reprogrammed or distorted routines in development of diseases, design
      of new drugs targeting specific mammalian DNA methyltransferases or
      their adaptors in the control of key steps in either maintenance or de
      novo DNA methylation processes will contribute to individually treating
      diseases related to DNA methyltransferases.
AU  - Xu F
AU  - Mao C
AU  - Ding Y
AU  - Rui C
AU  - Wu L
AU  - Shi A
AU  - Zhang H
AU  - Zhang L
AU  - Xu Z
PT  - Journal Article
TA  - Curr. Med. Chem.
JT  - Curr. Med. Chem.
SO  - Curr. Med. Chem. 2010 17: 4052-4071.

PMID- 23704189
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Avibacterium paragallinarum Strain 221.
PG  - e00290-13
AB  - Avibacterium paragallinarum is the causative agent of infectious coryza. Here we  report the
      draft genome sequence of reference strain 221 of A. paragallinarum serovar A. The genome is
      composed of 135 contigs for 2,685,568 bp with a 41% G+C content.
AU  - Xu F
AU  - Miao D
AU  - Du Y
AU  - Chen X
AU  - Zhang P
AU  - Sun H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00290-13.

PMID- 8467964
VI  - 7
DP  - 1993
TI  - Purification and initial characterization of the murine cytosine DNA methyltransferase.
PG  - A1175
AB  - The murine DNA (cytosine-5-)-methyltransferase (MTase EC 2.1.1.37) transfers methyl groups
      from S-adenosylmethionine to the 5-position of cytosine in the nucleotide pair dCpdG of DNA.
      The methylation of cytosine residues on mammalian DNA has been implicated in the regulation of
      gene expression. Our goal is to study the chemical mechanism of cytosine methylation and to
      characterize the basis of the enzyme specificity. DNA MTase was purified to homogeneity from
      nuclear extracts of Friend murine erythroleukemia cells (MEL cells). Chromatographic
      purification of DNA MTase carried out on DEAE-Sepharose Fast Flow medium brought about a
      6-fold increase in the specific activity of DNA MTase. Further purification of the enzyme was
      achieved by precipitation by 30% saturated ammonium sulfate solution and chromatography on
      Phenyl-Sepharose 6 Fast Flow medium. The purification step brought a 21-fold increase in
      specific activity of the enzyme. After chromatographic separation of DNA MTase on
      phenylsepharose, purification using a Hiload superdex 200 column provided DNA MTase with
      80-fold higher specific activity. We are currently characterizing the enzyme-substrate
      interaction.
AU  - Xu G
AU  - Davis M
AU  - Glickman F
AU  - Reich N
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1993 7: A1175.

PMID- 7864841
VI  - 207
DP  - 1995
TI  - Purification and stabilization of mouse DNA methyltransferase.
PG  - 544-551
AB  - Cytosine methylation within DNA has been implicated in genetic imprinting, X-chromosome
      inactivation, regulation of tissue-specific gene expression, aging, and cancer. Unfortunately,
      DNA (cytosine-5)-methyltransferases (EC 2.1.1.37) from various mammalian sources have been
      difficult to isolate and stabilize, precluding investigations of these critical enzymes. We
      describe a novel FPLC purification of the 190,000 Mr DNA methyltransferase from mouse Friend
      erythroleukemia cells. The homogeneous 190 kD Mr form of the enzyme is the only polypeptide
      detected at various stages of cell growth and has not undergone detectable N-terminal
      proteolysis.
AU  - Xu G
AU  - Flynn J
AU  - Glickman JF
AU  - Reich NO
PT  - Journal Article
TA  - Biochem. Biophys. Res. Commun.
JT  - Biochem. Biophys. Res. Commun.
SO  - Biochem. Biophys. Res. Commun. 1995 207: 544-551.

PMID- 24625870
VI  - 2
DP  - 2014
TI  - Genome Sequence of Pseudomonas aeruginosa Strain LCT-PA220, Which Was Selected after Space Flight by Using Biolog's Powerful Carbon Source Utilization  Technology.
PG  - e00169-14
AB  - To explore the changes of Pseudomonas aeruginosa in space flight, we present the  draft genome
      sequence of P. aeruginosa strain LCT-PA220, which originated from a
      P. aeruginosa strain, ATCC 27853, that traveled on the Shenzhou-VIII spacecraft.
AU  - Xu G
AU  - Hu J
AU  - Fang X
AU  - Zhang X
AU  - Wang J
AU  - Guo Y
AU  - Li T
AU  - Chen Z
AU  - Dai W
AU  - Liu C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00169-14.

PMID- 7607526
VI  - 157
DP  - 1995
TI  - BsuCI, a type-I restriction-modification system in Bacillus subtilis.
PG  - 59
AB  - A type-I R-M system was identified in B. subtilis.  The genes comprising the system have
      striking similarity to type-I R-M systems observed in Enterobacteriaceae.
AU  - Xu G
AU  - Willert J
AU  - Kapfer W
AU  - Trautner TA
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 157: 59.

PMID- 9398832
VI  - 17
DP  - 1997
TI  - Cytosine methylation targetted to pre-determined sequences.
PG  - 376-378
AB  - The incidence or severity of a number of human diseases is proportional to the activity of
      individual viral transcription units or mutant endogenous genes.  Targetted methylation of
      regulatory sites is proposed as a new method for selective gene inactivation that stimulates
      an existing biological response.  Mammalian promoters are usually inactive when methylated at
      CpG dinucleotides, and patterns of methylated CpG sites are replicated with the DNA during S
      phase.  Pre-determined sequence specificities have now been conferred upon a DNA
      methyltransferase by fusion to zinc-finger proteins.  The sequence specificity of zinc-finger
      proteins can be modified to direct cytosine methylation to the promoters of target genes.
AU  - Xu G-L
AU  - Bestor TH
PT  - Journal Article
TA  - Nat. Genet.
JT  - Nat. Genet.
SO  - Nat. Genet. 1997 17: 376-378.

PMID- 10647011
VI  - 402
DP  - 1999
TI  - Chromosome instability and imunodeficiency syndrome caused by mutations in a DNA methyltransferase gene.
PG  - 187-191
AB  - The recessive autosomal disorder known as ICF syndrome (for immunodeficiency, centromere
      instability and facial anomalies; Mendelian Inheritance in Man number 242860) is characterized
      by variable reductions in serum immunoglobulin levels which cause most ICF patients to succumb
      to infectious diseases before adulthood.  Mild facial anomalies include hypertelorism, low-set
      ears, epicanthal folds and macroglossia.  The cytogenetic abnormalities in lymphocytes are
      exuberant: juxtacentromeric heterochromatin is greatly elongated and thread-like in metaphase
      chromsomes, which is associated with the formation of complex multiradiate chromosomes.  The
      same juxtacentromeric regions are subject to persistent interphase self-associations and are
      extruded into nuclear blebs or micronuclei.  Abnormalities are largely confined to tracts of
      classical satellites 2 and 3 at juxtacentromeric regions of chromosomes 1, 9 and 16.
      Classical satellite DNA is normally heavily methylated at cytosine residues, but in ICF
      syndrome it is almost completely unmethylated in all tissues.  ICF syndrome is the only
      genetic disorder known to involve constitutive abnormalities of genomic methylation patterns.
      Here we show that five unrelated ICF patients have mutations in both alleles of the gene that
      encodes DNA methyltransferase 3B.  Cytosine methylation is essential for the organization and
      stabilization of a specific type of heterochromatin, and this methylation appears to be
      carried out by an enzyme specialized for the purpose.
AU  - Xu G-L
AU  - Bestor TH
AU  - Bourchis D
AU  - Hsieh C-L
AU  - Tommerup N
AU  - Bugge M
AU  - Hulten M
AU  - Qu X
AU  - Russo JJ
AU  - Viegas-Pequignot E
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1999 402: 187-191.

PMID- 1480472
VI  - 20
DP  - 1992
TI  - BsuBI-an isospecific restriction and modification system of PstI: characterization of the BsuBI genes and enzymes.
PG  - 6517-6523
AB  - The enzymes of the Bacillus subtilis BsuBI restriction/modification (R/M) system recognize the
      target sequence 5'CTGCAG. The genes of the BsuBI R/M system have been cloned and sequenced
      and their products have been characterized following overexpression and purification. The gene
      of the BsuBI DNA methyltransferase (M.BsuBI) consists of 1503 bp, encoding a protein of 501
      amino acids with a calculated Mr of 57.2 kD. The gene of the restriction endonuclease
      (R.BsuBI), comprising 948 bp, codes for a protein of 316 amino acids with a predicted Mr of
      36.2 kD. M.BsuBI modifies the adenine (A) residue of the BsuBI target site, thus representing
      the first A-N6_DNA methyltransferase identified in B. subtilis. Like R.PstI, R.BsuBI cleaves
      between the A residue and the 3' terminal G of the target site. Both enzymes of the BsuBI R/M
      system are, therefore, functionally identical with those of the PstI R/M system, encoded by
      the Gram negative species Providencia stuartii. This functional equivalence coincides with a
      pronounced similarity of the BsuBI/PstI DNA methyltransferases (41% amino acid identity) and
      restriction endonucleases (46% amino acid identity). Since the genes are also very similar
      (58% nucleotide identity), the BsuBI and PstI R/M systems apparently have a common
      evolutionary origin. In spite of the sequence conservation the gene organization is strikingly
      different in the two R/M systems. While the genes of the PstI R/M system are separated and
      transcribed divergently, the genes of the BsuBI R/M system are transcribed in the same
      direction with the 3' end of the M gene overlapping the 5' end of the R gene by 17 bp.
AU  - Xu GL
AU  - Kapfer W
AU  - Walter J
AU  - Trautner TA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 6517-6523.

PMID- 24867319
VI  - 36
DP  - 2014
TI  - Overexpression of a lethal methylase, M.TneDI, in E-coli B1(DE3).
PG  - 1853-1859
AB  - A pET-based vector pDH21 expressing the methylase, M.TneDI (recognizing CGCG) from Thermotoga
      was constructed, and transformed into E. coli B1(DE3). Despite E. coli B1(DE3) being McrBC
      positive, 30 transformants were isolated, which were suspected to be McrBC(-) mutants. The
      overexpression of M.TneDI was verified by SDS-PAGE analysis. Compared to the previously
      constructed pJC340 vector, a pACYC184 derivative expressing M.TneDI from a tet promotor, the
      newly constructed pDH21 vector improved the expression of the methylase about fourfold,
      allowing complete protection of DNA substrates. This study not only demonstrates a practical
      approach to overexpressing potential lethal proteins in E. coli but also delivers a production
      strain of M.TneDI that may be useful in various in vitro methylation applications.
AU  - Xu H
AU  - Han D
AU  - Xu Z
PT  - Journal Article
TA  - Biotechnol. Lett.
JT  - Biotechnol. Lett.
SO  - Biotechnol. Lett. 2014 36: 1853-1859.

PMID- 17579514
VI  - 5
DP  - 2007
TI  - Evolution of Symbiotic Bacteria in the Distal Human Intestine.
PG  - e156
AB  - The adult human intestine contains trillions of bacteria, representing hundreds of species and
      thousands of subspecies. Little is known about the
      selective pressures that have shaped and are shaping this community's
      component species, which are dominated by members of the Bacteroidetes and
      Firmicutes divisions. To examine how the intestinal environment affects
      microbial genome evolution, we have sequenced the genomes of two members
      of the normal distal human gut microbiota, Bacteroides vulgatus and
      Bacteroides distasonis, and by comparison with the few other sequenced gut
      and non-gut Bacteroidetes, analyzed their niche and habitat adaptations.
      The results show that lateral gene transfer, mobile elements, and gene
      amplification have played important roles in affecting the ability of
      gut-dwelling Bacteroidetes to vary their cell surface, sense their
      environment, and harvest nutrient resources present in the distal
      intestine. Our findings show that these processes have been a driving
      force in the adaptation of Bacteroidetes to the distal gut environment,
      and emphasize the importance of considering the evolution of humans from
      an additional perspective, namely the evolution of our microbiomes.
AU  - Xu J et al
PT  - Journal Article
TA  - PLoS Biology
JT  - PLoS Biology
SO  - PLoS Biology 2007 5: e156.

PMID- 12663928
VI  - 299
DP  - 2003
TI  - A genomic view of the human-Bacteroides thetaiotaomicron symbiosis.
PG  - 2074-2076
AB  - The human gut is colonized with a vast community of indigenous microorganisms that help shape
      our biology. Here, we present the complete
      genome sequence of the Gram-negative anaerobe Bacteroides
      thetaiotaomicron, a dominant member of our normal distal intestinal
      microbiota. Its 4779-member proteome includes an elaborate apparatus for
      acquiring and hydrolyzing otherwise indigestible dietary polysaccharides
      and an associated environment-sensing system consisting of a large
      repertoire of extracytoplasmic function sigma factors and one- and
      two-component signal transduction systems. These and other expanded
      paralogous groups shed light on the molecular mechanisms underlying
      symbiotic host-bacterial relationships in our intestine.
AU  - Xu J
AU  - Bjursell MK
AU  - Himrod J
AU  - Deng S
AU  - Carmichael LK
AU  - Chiang HC
AU  - Hooper LV
AU  - Gordon JI
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2003 299: 2074-2076.

PMID- 28546495
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Streptomyces sp. Sge12, Which Produces Antibacterial  and Fungicidal Activities.
PG  - e00415-17
AB  - Streptomyces sp. Sge12 was isolated from forest soil and exhibited remarkable antimicrobial
      activities against selected fungi and Gram-positive bacteria. Here,
      we report the complete genome sequence of this strain, which contains 37 putative
      secondary metabolite gene clusters.
AU  - Xu J
AU  - Xu M
AU  - Liu K
AU  - Peng Q
AU  - Tao M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00415-17.

PMID- 21685279
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of the Plant Pathogen Ralstonia solanacearum Strain Po82.
PG  - 4261-4262
AB  - Ralstonia solanacearum strain Po82, a phylotype IIB/sequevar 4 strain, was found to be
      pathogenic to both solanaceous plants and banana. Here, we
      report the complete genome sequence of Po82 and its comparison with seven
      published R. solanacearum genomes.
AU  - Xu J
AU  - Zheng HJ
AU  - Liu L
AU  - Pan ZC
AU  - Prior P
AU  - Tang B
AU  - Xu JS
AU  - Zhang H
AU  - Tian Q
AU  - Zhang LQ
AU  - Feng J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4261-4262.

PMID- 23682151
VI  - 1
DP  - 2013
TI  - Genome Sequences of Two Morphologically Distinct and Thermophilic Bacillus coagulans Strains, H-1 and XZL9.
PG  - e00254-13
AB  - Two thermophilic Bacillus coagulans strains, H-1 and XZL9, both of which were isolated from
      soils, have different morphological properties. Strain XZL9 but not
      H-1 is an efficient pentose-utilizing producer of important platform compounds,
      such as l-lactic acid and 2,3-butanediol. Here we announce the 2.86- and 3.43-Mb
      sequences of their genomes.
AU  - Xu K
AU  - Su F
AU  - Tao F
AU  - Li C
AU  - Ni J
AU  - Xu P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00254-13.

PMID- 28138355
VI  - 12
DP  - 2017
TI  - Draft genome sequence of Arthrobacter sp. strain B6 isolated from the high-arsenic sediments in Datong Basin, China.
PG  - 11
AB  - Arthrobacter sp. B6 is a Gram-positive, non-motile, facultative aerobic bacterium, isolated
      from the arsenic-contaminated aquifer sediment in the Datong
      basin, China. This strain displays high resistance to arsenic, and can
      dynamically transform arsenic under aerobic condition. Here, we described the
      high quality draft genome sequence, annotations and the features of Arthrobacter
      sp. B6. The G + C content of the genome is 64.67%. This strain has a genome size
      of 4,663,437 bp; the genome is arranged in 8 scaffolds that contain 25 contigs.
      From the sequences, 3956 protein-coding genes, 264 pseudo genes and 89
      tRNA/rRNA-encoding genes were identified. The genome analysis of this strain
      helps to better understand the mechanism by which the microbe efficiently
      tolerates arsenic in the arsenic-contaminated environment.
AU  - Xu L
AU  - Shi W
AU  - Zeng XC
AU  - Yang Y
AU  - Zhou L
AU  - Mu Y
AU  - Liu Y
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 11.

PMID- 29862249
VI  - 2018
DP  - 2018
TI  - Comparative Genomics Analysis of Plasmid pPV989-94 from a Clinical Isolate of Pantoea vagans PV989.
PG  - 1242819
AB  - Pantoea vagans, a gram-negative bacterium from the genus Pantoea and family
      Enterobacteriaceae, is present in various natural environments and considered to
      be plant endophytes. We isolated the Pantoea vagans PV989 strain from the clinic
      and sequenced its whole genome. Besides a chromosome DNA molecule, it also
      harboured three large plasmids. A comparative genomics analysis was performed for
      the smallest plasmid, pPV989-94. It can be divided into four regions, including
      three conservative regions related to replication (R1), transfer conjugation
      (R2), and transfer leading (R3), and one variable region (R4). Further analysis
      showed that pPV989-94 is most similar to plasmids LA637P2 and pEA68 of Erwinia
      amylovora strains isolated from fruit trees. These three plasmids share three
      conservative regions (R1, R2, and R3). Interestingly, a fragment (R4') in R4,
      mediated by phage integrase and phage integrase family site-specific recombinase
      and encoding 9 genes related to glycometabolism, resistance, and DNA repair, was
      unique in pPV989-94. Homologues of R4' were found in other plasmids or
      chromosomes, suggesting that horizontal gene transfer (HGT) occurred among
      different bacteria of various species or genera. The acquired functional genes
      may play important roles in the adaptation of bacteria to different hosts or
      environmental conditions.
AU  - Xu L
AU  - Yin M
AU  - Zhu T
AU  - Liu Y
AU  - Ying Y
AU  - Lu J
AU  - Lin C
AU  - Ying J
AU  - Xu T
AU  - Ni L
AU  - Bao Q
AU  - Lu S
PT  - Journal Article
TA  - Int. J. Genomics
JT  - Int. J. Genomics
SO  - Int. J. Genomics 2018 2018: 1242819.

PMID- 24309738
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Shewanella decolorationis S12, a Dye-Degrading Bacterium Isolated from a Wastewater Treatment Plant.
PG  - e00993-13
AB  - Shewanella decolorationis is a valuable microorganism for degrading diverse synthetic textile
      dyes. Here, we present an annotated draft genome sequence of S.
      decolorationis S12, which contains 4,219 protein-coding genes and 86 structural
      RNAs. This information regarding the genetic basis of this bacterium can greatly
      advance our understanding of the physiology of this species.
AU  - Xu M
AU  - Fang Y
AU  - Liu J
AU  - Chen X
AU  - Sun G
AU  - Guo J
AU  - Hua Z
AU  - Tu Q
AU  - Wu L
AU  - Zhou J
AU  - Liu X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00993-13.

PMID- 9705505
VI  - 26
DP  - 1998
TI  - Cloning, characterization and expression of the gene coding for a cytosine-5-DNA methyltransferase recognizing GpC.
PG  - 3961-3966
AB  - A novel gene encoding a cytosine-5-DNA methyltransferase recognizing the dinucleotide GpC was
      cloned from Chlorella virus NYs-1 and expressed in both Escherichia coli and Saccharomyces
      cerevisiae.  The gene was sequenced and a predicted polypeptide of 362 amino acids with a
      molecular weight of 41.903 kDa was identified.  The protein contains several amino acid motifs
      with high similarity to those of other known 5-methylcytosine-forming methyltransferases.  In
      addition, this enzyme, named M.CviPI, shares 66% identity and 76% similarity with M.CviJI, the
      other only cytosine-5-DNA methyltransferase cloned from a Chlorella virus.  The short,
      frequently occurring recognition sequence of the new methyltransferase will be very useful for
      in vivo chromatin structure studies in both yeast and higher organisms.
AU  - Xu M
AU  - Kladde MP
AU  - Van Etten JL
AU  - Simpson RT
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1998 26: 3961-3966.

PMID- 7988548
VI  - 13
DP  - 1994
TI  - Protein splicing: an analysis of the branched intermediate and its resolution by succinimide formation.
PG  - 5517-5522
AB  - Protein splicing involves the excision of an internal domain from a
      precursor protein and the ligation of the external domains so as to generate two new
      proteins.  Study of this process has recently been facilitated by the isolation of a precursor
      and a branched intermediate from a thermophilic protein splicing element expressed in a
      foreign protein context.  Two aspects of protein splicing are examined in this paper.  We
      demonstrate a succinimide at the C-terminus of the spliced internal protein, implicating
      cyclization of asparagine in resolution of the branched intermediate, and we identify an
      alkali-labile bond in the branched intermediate.  A revised protein splicing model based on
      these experimental results is presented.
AU  - Xu M-Q
AU  - Comb DG
AU  - Paulus H
AU  - Noren CJ
AU  - Shao Y
AU  - Perler FB
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1994 13: 5517-5522.

PMID- 8895558
VI  - 15
DP  - 1996
TI  - The mechanism of protein splicing and its modulation by mutation.
PG  - 5146-5153
AB  - Protein splicing results in the expression of two mature proteins from a single gene.  After
      synthesis of a precursor protein, an internal segment (the intein) is excised and the external
      domains are joined together.  A self-catalyzed mechanism for this cleavage-ligation reaction
      is presented, based on mutagenesis data and analysis of splicing intermediates.  Mutations
      were used to block various steps in the protein splicing pathway, allowing each isolated step
      to be studied independently.  A linear ester intermediate was identified and functional roles
      for the four conserved splice junction residues were determined.  Understanding the mechanism
      of protein splicing provides a basis for protein engineering studies.  For example, inteins
      can be constructed which fail to splice, but instead cleave the peptide bond at a chosen
      splice junction.
AU  - Xu M-Q
AU  - Perler FB
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1996 15: 5146-5153.

PMID- 2684777
VI  - 82
DP  - 1989
TI  - The catalytic core of the sunY intron of bacteriophage T4.
PG  - 77-82
AB  - The self-splicing sunY intron of bacteriophage T4 shares a common
      secondary structure with
      other group I introns.  A long open reading frame within the intron is entirely 3' of the
      structural elements
      conserved in all group I introns.  This catalytic core is the smallest yet described for a
      self-
      splicing intron.
      An internal deletion of 728 nucleotides, leaving 196 nt at the 5' end and 109 nt at the 3'
      end, allows normal
      self-splicing.  Transcripts terminating 196 nt 3' of the 5' splice site retain catalytic
      activity.
AU  - Xu M-Q
AU  - Shub DA
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1989 82: 77-82.

PMID- 8269515
VI  - 75
DP  - 1993
TI  - In vitro protein splicing of purified precursor and the identification of a branched intermediate.
PG  - 1371-1377
AB  - Protein splicing is a posttranslational processing event in which an internal polypeptide is
      excised from a protein precursor and the terminal polypeptides are then ligated together,
      resulting in the production of two proteins. This report presents direct evidence for protein
      splicing by demonstrating in vitro splicing of purified precursor that accumulated when the
      protein splicing element from Pyrococcus DNA polymerase was cloned into a foreign gene. In
      vitro splicing was temperature and pH dependent. A slowly migrating species exhibited kinetic
      properties of a splicing intermediate and was shown to be a branched molecular by N-terminal
      sequencing. The precursor and slowly migrating species were interconvertible in response to pH
      shifts.
AU  - Xu M-Q
AU  - Southworth MW
AU  - Mersha FB
AU  - Hornstra LJ
AU  - Perler FB
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1993 75: 1371-1377.

PMID- 17277061
VI  - 189
DP  - 2007
TI  - Genome of the opportunistic pathogen Streptococcus sanguinis.
PG  - 3166-3175
AB  - The genome of S. sanguinis is a circular DNA molecule of 2,388,435 base pairs, 177-590 kb
      larger than the other 21 sequenced streptococcal genomes. The GC content of the S. sanguinis
      genome is 43.4%, considerably higher than that of other streptococci. The genome encodes 2,274
      predicted proteins, 61 tRNAs and 4 ribosomal RNA operons. A 70-kb region containing pathways
      for vitamin B12 biosynthesis and degradation of ethanolamine and propanediol was apparently
      acquired by horizontal gene transfer. The gene complement suggests new hypotheses for the
      pathogenesis and virulence of S. sanguinis, and provides comparative contrasts with other
      pathogenic and non-pathogenic streptococci. In particular, S. sanguinis possesses a remarkable
      abundance of putative surface proteins, which may permit it to serve as a primary colonizer of
      the oral cavity and agent of streptococcal endocarditis and infection in neutropenic patients.
AU  - Xu P
AU  - Alves JM
AU  - Kitten T
AU  - Brown A
AU  - Chen Z
AU  - Ozaki LS
AU  - Manque P
AU  - Ge X
AU  - Serrano MG
AU  - Puiu D
AU  - Hendricks S
AU  - Wang Y
AU  - Chaplin MD
AU  - Akan D
AU  - Paik S
AU  - Peterson DL
AU  - Macrina FL
AU  - Buck GA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2007 189: 3166-3175.

PMID- 15510150
VI  - 431
DP  - 2004
TI  - The genome of Cryptosporidium hominis.
PG  - 1107-1112
AB  - Cryptosporidium species cause acute gastroenteritis and diarrhoea worldwide. They are members
      of the Apicomplexa--protozoan pathogens that invade host cells by using a specialized apical
      complex and are usually transmitted by an invertebrate vector or intermediate host. In
      contrast to other Apicomplexans, Cryptosporidium is transmitted by ingestion of oocysts and
      completes its life cycle in a single host. No therapy is available, and control focuses on
      eliminating oocysts in water supplies. Two species, C. hominis and C. parvum, which differ in
      host range, genotype and pathogenicity, are most relevant to humans. C. hominis is restricted
      to humans, whereas C. parvum also infects other mammals. Here we describe the eight-chromosome
      approximately 9.2-million-base genome of C. hominis. The complement of C. hominis
      protein-coding genes shows a striking concordance with the requirements imposed by the
      environmental niches the parasite inhabits. Energy metabolism is largely from glycolysis. Both
      aerobic and anaerobic metabolisms are available, the former requiring an alternative electron
      transport system in a simplified mitochondrion. Biosynthesis capabilities are limited,
      explaining an extensive array of transporters. Evidence of an apicoplast is absent, but genes
      associated with apical complex organelles are present. C. hominis and C. parvum exhibit very
      similar gene complements, and phenotypic differences between these parasites must be due to
      subtle sequence divergence.
AU  - Xu P
AU  - Widmer G
AU  - Wang Y
AU  - Ozaki LS
AU  - Alves JM
AU  - Serrano MG
AU  - Puiu D
AU  - Manque P
AU  - Akiyoshi D
AU  - Mackey AJ
AU  - Pearson WR
AU  - Dear PH
AU  - Bankier AT
AU  - Peterson DL
AU  - Abrahamsen MS
AU  - Kapur V
AU  - Tzipori S
AU  - Buck GA
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2004 431: 1107-1112.

PMID- 23929488
VI  - 1
DP  - 2013
TI  - Genome Sequence of the 2,4,5-Trichlorophenoxyacetate-Degrading Bacterium Burkholderia phenoliruptrix Strain AC1100.
PG  - e00600-13
AB  - Burkholderia phenoliruptrix strain AC1100 (ATCC 53867) degrades a variety of recalcitrant
      xenobiotics, including 2,4,5-trichlorophenoxyacetate. The molecular
      mechanism of 2,4,5-trichlorophenoxyacetate degradation has been extensively
      studied. Here we present a 7.8-Mb assembly of the genome sequence of this
      2,4,5-trichlorophenoxyacetate-degrading strain, which may provide useful
      information related to the degradation of chlorinated aromatic compounds.
AU  - Xu P
AU  - Yu H
AU  - Chakrabarty AM
AU  - Xun L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00600-13.

PMID- 
VI  - 
DP  - 1999
TI  - Molecular analysis of restriction-modification systems in Helicobacter pylori.
PG  - 1-156
AB  - The phenomenon of restriction and modification in prokaryotes was first recognized more than
      40 years ago when investigators worked on phage infections.  Certain bacterial strains of
      bacteria were found to inhibit the propagation of phages grown previously on a different
      bacterial strain.  The effect was later traced to a DNA sequence-specific endonuclease.  The
      DNA of phages previously grown on the different strain was degraded by this certain strain's
      endonuclease, because the phage DNA lacked specific methylation in the sequence recognized by
      the endonuclease.  However, the few phages that did succeed in infecting the bacteria, were
      modified so that they grew normally on the new host in a second cycle of infection.  By the
      beginning of the 1970's, first several restriction endonucleases including HindII, HindIII,
      and EcoRI, were purified.  Sequence-specific endonucleases were later found to be useful for
      analyzing and rearranging DNA.  Subsequent applications not only led to a major breakthrough
      in the field of molecular biology, but also led to the extensive search for new ones.
AU  - Xu Q
PT  - Journal Article
TA  - Ph.D. Thesis, Vanderbilt University, Nashville, Tennessee
JT  - Ph.D. Thesis, Vanderbilt University, Nashville, Tennessee
SO  - Ph.D. Thesis, Vanderbilt University, Nashville, Tennessee 1999 : 1-156.

PMID- 11395450
VI  - 183
DP  - 2001
TI  - Promoters of the CATG-specific methyltransferase gene hpyIM differ between iceA1 and iceA2 Helicobacter pylori strains.
PG  - 3875-3884
AB  - Helicobacter pylori strains can be divided into two groups, based on the presence of two
      unrelated genes, iceA1 and iceA2, that occupy the same genomic locus. hpyIM, located
      immediately downstream of either gene, encodes a functional CATG-specific methyltransferase.
      Despite the strong conservation of the hpyIM open reading frame (ORF) among all H. pylori
      strains, the sequences upstream of the ORF in iceA1 and iceA2 strains are substantially
      different. To explore the roles of these upstream sequences in hpyIM regulation, promoter
      analysis of hpyIM was performed. Both deletion mutation and primer extension analyses
      demonstrate that the hpyIM promoters differ between H. pylori strains 60190 (iceA1) and J188
      (iceA2). In strain 60190, hpyIM has two promoters, P(a) or P(I), which may function
      independently, whereas only one hpyIM promoter, P(c), was found in strain J188. The XylE assay
      showed that the hpyIM transcription level was much higher in strain 60190 than in strain J188,
      indicating that regulation of hpyIM transcription differs between the H. pylori iceA1 strain
      (60190) and iceA2 strains (J188). Since the iceA1 and iceA2 sequences are highly conserved
      within iceA1 or iceA2 strains, we conclude that promoters of the CATG-specific methylase gene
      hpyIM differ between iceA1 and iceA2 strains, which leads to differences in regulation of
      hpyIM transcription.
AU  - Xu Q
AU  - Blaser MJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2001 183: 3875-3884.

PMID- 10944229
VI  - 97
DP  - 2000
TI  - Identification of type II restriction and modification systems in Helicobacter pylori reveals their substantial diversity among strains.
PG  - 9671-9676
AB  - A total of 22 type II restriction endonucleases with 18 distinct specificities have been
      identified in six Helicobacter pylori strains. Among these 18 specificities are three
      completely new endonucleases, Hpy178III, Hpy99I, and Hpy188I, that specifically cleave DNA at
      TCNNGA, CGWCG, and TCNGA sites, respectively. The set of endonucleases identified in each
      strain varies, but all have four- or five-base recognition sequences. Among 16 H. pylori
      strains, examination of the DNA modification status at the recognition sites of 15 restriction
      endonucleases reveals that each strain has a substantially different complement of type II
      modification systems. We conclude that the type II restriction-modification systems in H.
      pylori are highly diverse between strains, a unique characteristic of H. pylori. The diverse
      methylation status of H. pylori chromosomal DNA may serve as a new typing system to
      discriminate H. pylori isolates for epidemiological and clinical purposes. This study also
      demonstrates that H. pylori is a rich source of type II restriction endonucleases.
AU  - Xu Q
AU  - Morgan RD
AU  - Roberts RJ
AU  - Blaser MJ
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2000 97: 9671-9676.

PMID- 12202769
VI  - 30
DP  - 2002
TI  - Functional analysis of iceA1, a CATG-recognizing restriction endonuclease gene in Helicobacter pylori.
PG  - 3839-3847
AB  - iceA1 in Helicobacter pylori is a homolog of nlaIIIR, which encodes the CATG-specific
      restriction endonuclease NlaIII in Neisseria lactamica. Analysis of iceA1 sequences from 49
      H.pylori strains shows that a full-length NlaIII-like ORF is present in 10 strains, including
      CH4, but in other strains, including strain 60190, the ORFs are truncated due to a variety of
      mutations. Our goal was to determine whether iceA1 can encode a NlaIII-like endonuclease.
      Overexpression in Escherichia coli of iceA1 from CH4, but not from 60190, yielded NlaIII-like
      activity, indicating that the full-length iceA1 is a functional endonuclease gene. Repair of
      the iceA1 frameshift mutation in strain 60190 and its expression in E.coli yielded functional
      NlaIII-like activity. We conclude that iceA1 in CH4 is a functional restriction endonuclease
      gene, while iceA1 in 60190 is not, due to a frameshift mutation, but that its repair restores
      its restriction endonuclease activity.
AU  - Xu Q
AU  - Morgan RD
AU  - Roberts RJ
AU  - Xu SY
AU  - van Doorn LJ
AU  - Donahue JP
AU  - Miller GG
AU  - Blaser MJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2002 30: 3839-3847.

PMID- 
VI  - 100
DP  - 2000
TI  - H. pylori iceA1 is capable of encoding an NlaIII-like restriction endonuclease.
PG  - 291
AB  - H. pylori iceA1 has strong homology to nlaIIIR, which encodes NlaIII, a restriction
      endonuclease in N. lactamica.  Our goal was to determine whether iceA1 encodes an NlaIII-like
      RE.  Analysis of iceA1 sequences from 19 H. pylori strains was performed.  A full-length
      NlaIII-like ORF is present in 4 strains including CH4, but iceA1 from 15 others, including
      strain 60190, have various mutations.  Overexpression of iceA1 from CH4, but not from 60190,
      in pAII17 vector in E. coli yielded NlaIII-like RE activity, indicating that it is a
      functional gene.  To investigate the effect of mutations on iceA1 function, the frameshift
      mutation of 60190 iceA1 was repaired.  The repaired 60190 iceA1 in pAII17 enabled expression
      of a functional NlaIII-like RE in E. coli.  These results are consistent with biochemical
      analysis of H. pylori, in which NlaIIII-like RE activity was detected in CH4, but not in 60190
      cells.  We conclude that iceA1 in CH4 is a functional RE gene, and in 60190 is degenerate, but
      that repair of its frameshift mutation restores its activity.
AU  - Xu Q
AU  - Morgan RD
AU  - Xu SY
AU  - van Doorn LJ
AU  - Donahue JP
AU  - Miller GG
AU  - Blaser MJ
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 2000 100: 291.

PMID- 
VI  - 80
DP  - 2001
TI  - Structural study of restriction enzyme MspI/DNA complex by x-ray crystallography.
PG  - 296a
AB  - The MspI restriction endonuclease is a type II restriction enzyme.  It recognizes the
      palindromic sequence of four base pairs 5'-CCGG-3' and cleaves it between two cytosines,
      leaving 5' two-base overhangs.  Owing to the nature of its cleavage pattern that is different
      from all other restriction enzymes with known structure, it is likely that MspI could
      represent a novel structural class of restriction endonucleases.  Solving the crystal
      structure of MspI/DNA complex will allow us to examine the hypothesis that the cleavage
      pattern is a result of intermediate organization of core architectures.  In addition, the
      structure would provide us more information about the DNA recognition, specificity and
      catalytic mechanisms of these enzymes.  Native crystals of the dimeric MspI restriction enzyme
      bound to a duplex DNA molecule containing the specific recognition have been obtained in a P21
      monoclinic unit cell with dimensions of a = 50.2A, b = 131.6A, c= 59.3A, beta = 109.7o.  The
      crystals contain one dimeric complex in the asymmetric unit.  A complete native data set has
      been collected to a resolution of 2.05A at beamline X12c at National Synchrotron Light Source
      at Brookhaven National Laboratory.  Moreover, a complete MAD data set of Hg derivative and a
      data set of Sm derivative have also been collected at X12c to the resolution of 3.2A and 2.6A,
      respectively.  Phasing from these derivative data sets are currently underway.
AU  - Xu Q
AU  - O'Loughlin TJ
AU  - Kucera RB
AU  - Schildkraut I
AU  - Guo H-C
PT  - Journal Article
TA  - Biophys. J.
JT  - Biophys. J.
SO  - Biophys. J. 2001 80: 296a.

PMID- Not carried by PubMed...
VI  - 97
DP  - 1997
TI  - Identification of an adenine methylase gene in Helicobacter pylori.
PG  - 38
AB  - DNA methylation has been demonstrated to be involved in several important cellular processes
      such as host-specific defense mechanisms, DNA mismatch repair, regulation of initiation of
      chromosomal replication, regulation of gene transcription, and DNA transposition.  To
      understand mechanisms of DNA methylation in H. pylori, a human pathogen associated with peptic
      ulcer disease and adenocarcinoma, we cloned a putative adenine methylase gene, hpyIM. This
      gene contains a 990bp ORF encoding a 330 aa protein, M.HpyI.  Sequence analysis revealed that
      M.HpyI was closely related to a CATG-recognizing adenine methylase, M.NlaIII in N. lactamica
      (76% similarity).  Both Pcr and Southern blotting show that hpyIM is present in all 14 H.
      pylori strains tested.  To investigate possible modification effects of M.HpyI, an isogenic
      hpyIM mutant of H. pylori strain 88-23 was made by inserting a kanamycin resistance gene into
      hpyIM.  SphI and NlaIII recognize DNA at sites containing CATG, and were used to test CATG
      modification status.  DNA from wild type strains was resistant to digestion, whereas the hpyIM
      mutant was susceptible, indicating lack of modification.  To further confirm that M.HpyI
      modifies DNA at CATG sites, hpyIM was cloned into the expression vector pGEX-5X-1 to creat
      pQX101.  DNA from BL21 was cleaved by NlaIII, as was the strain transformed with pGEX-5X-1.
      However, DNA from BL21 with pQX101 encoding the GST-M.HpyI fusion protein was resistant,
      confirming the role of hpyIM in modifying CATG sites.  We conclude that hpyIM encodes a
      CATG-recognizing adenine methylase and is well-conserved among diverse H.pylori strains.
AU  - Xu Q
AU  - Peek R
AU  - Miller G
AU  - Blaser M
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1997 97: 38.

PMID- 9352933
VI  - 179
DP  - 1997
TI  - The Helicobacter pylori genome is modified at CATG by the product of hpyIM.
PG  - 6807-6815
AB  - To understand mechanisms of DNA methylation in Helicobacter pylori, a human pathogen
      associated with peptic ulcer disease and gastric adenocarcinoma, we cloned a putative DNA
      methyltransferase gene, hpyIM.  This gene contains a 990-bp open reading frame encoding a
      329-amino-acid protein, M.HpyI.  Sequence analysis revealed that M.HpyI was closely related to
      CATG-recognizing adenine DNA methyltransferases, including M.NlaIII in N. lactamica.  hpyIM
      was present in all H. pylori strains tested.  DNA from wild-type H. pylori strains was
      resistant to digestion by SphI and NlaIII, which recognize DNA at sites containing CATG,
      whereas their isogenic hpyIM mutants were susceptible, indicating lack of modification.
      Overexpression of hpyIM in Escherichia coli rendered DNA from these cells resistant to NlaIII
      digestion, confirming the role of hpyIM in modifying CATG sites.  We conclude that hpyIM
      encodes a DNA methyltransferase, M.HpyI, that is well conserved among diverse H. pylori
      strains and that modifies H. pylori genomes at CATG sites.
AU  - Xu Q
AU  - Peek RM Jr
AU  - Miller GG
AU  - Blaser MJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1997 179: 6807-6815.

PMID- 10748211
VI  - 275
DP  - 2000
TI  - Purification of the Novel Endonuclease, Hpy188I, and Cloning of Its Restriction-Modification Genes Reveal Evidence of Its Horizontal Transfer to the Helicobacter pylori Genome.
PG  - 17086-17093
AB  - We have isolated a novel restriction endonuclease, Hpy188I, from Helicobacter pylori strain
      J188. Hpy188I recognizes the unique sequence, TCNGA, and cleaves the DNA between nucleotides N
      and G in its recognition sequence to generate a one-base 3' overhang. Cloning and sequence
      analysis of the Hpy188I modification gene in strain J188 reveal that hpy188IM has a 1299-base
      pair (bp) open reading frame (ORF) encoding a 432-amino acid product. The predicted protein
      sequence of M.Hpy188I contains conserved motifs typical of aminomethyltransferases, and
      Western blotting indicates that it is an N-6 adenine methyltransferase. Downstream of hpy188IM
      is a 513-bp ORF encoding a 170-amino acid product, that has a 41-bp overlap with hpy188IM. The
      predicted protein sequence from this ORF matches the amino acid sequence obtained from
      purified Hpy188I, indicating that it encodes the endonuclease. The Hpy188I R-M genes are not
      present in either strain of H. pylori that has been completely sequenced but are found in two
      of 11 H. pylori strains tested. The significantly lower G + C content of the Hpy188I R-M genes
      implies that they have been introduced relatively recently during the evolution of the H.
      pylori genome.
AU  - Xu Q
AU  - Stickel S
AU  - Roberts RJ
AU  - Blaser MJ
AU  - Morgan RD
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2000 275: 17086-17093.

PMID- 
VI  - 
DP  - 2003
TI  - Crystal structures of restriction endonuclease MspI-DNA complex and glycosylasparaginase.
PG  - 1-161
AB  - This dissertation is composed of two parts: (I) Chapter I, II, III and IV discuss the crystal
      structures of restriction endonuclease MspI-DNA complex. (II) Chapter V depicts the
      crystallographic studies of glycosylasparaginase.   Part I: MspI is a Type II restriction
      endonuclease that recognizes and cleaves the palindromic tetranucleotide sequence C^CGG (the
      arrowhead indicates the cleavage site) to produce two-base 5' overhanging ends. Since the
      nature of this cleavage pattern is different from all other restriction enzymes with known
      structures, MspI is anticipated to represent a new structural class of restriction
      endonucleases.  This study reports two crystal structures of MspI bound to its cognate DNA.
      One has been determined at 1.95 angstroms resolution in P21 space group, and the other at 2.7
      angstroms resolution in P212121 space group. The two structures are essentially identical and
      reveal several novel features. In the crystals, one MspI molecule is bound to a half-site of
      its DNA recognition sequence. This is the first time that this binding mode has been observed
      for Type IIP restriction endonucleases, suggesting a possibility that MspI may function as a
      monomer although the dimer mechanism can't be ruled out at this point. DNA recognition is
      accomplished mainly through a small three-stranded (-sheet region that is structurally
      conserved in BglI, EcoRV as well as PvuII. While the architecture of the MspI active site is
      similar to other restriction enzymes, an asparagine, instead of a conserved acidic residue, is
      found in the catalytic sequence motif of Type II restriction enzymes. Meanwhile, although no
      metal is found near the scissile phosphate, a cation can be seen at a position homologous to
      the 74/45 metal site of EcoRV. Taken together, it appears that MspI is indeed a very unique
      restriction enzyme.  Part II: Glycosylasparaginase (GA) is a member of a novel family of
      N-terminal nucleophile hydrolases and is activated from a single chain precursor by
      intramolecular autoproteolysis. The crystallographic studies of bacterial glycosylasparaginase
      in mature form and its precursor reveal the catalytic mechanism of its hydrolase activity and
      a novel mechanism of intramolecular autoproteolysis via an N-O or N-S acyl shift.
AU  - Xu QS
PT  - Journal Article
TA  - Ph.D. Thesis, Boston University
JT  - Ph.D. Thesis, Boston University
SO  - Ph.D. Thesis, Boston University 2003 : 1-161.

PMID- 15341737
VI  - 12
DP  - 2004
TI  - An asymmetric complex of restriction endonuclease MspI on its palindromic DNA recognition site.
PG  - 1741-1747
AB  - Most well-known restriction endonucleases recognize palindromic DNA sequences and are
      classified as Type IIP. Due to the recognition and cleavage symmetry, Type IIP enzymes are
      usually found to act as homodimers in forming 2-fold symmetric enzyme-DNA complexes. Here we
      report an asymmetric complex of the Type IIP restriction enzyme MspI in complex with its
      cognate recognition sequence. Unlike any other Type IIP enzyme reported to date, an MspI
      monomer and not a dimer binds to a palindromic DNA sequence. The enzyme makes specific
      contacts with all 4 base pairs in the recognition sequence, by six direct and five
      water-mediated hydrogen bonds and numerous van der Waal contacts. This MspI-DNA structure
      represents the first example of asymmetric recognition of a palindromic DNA sequence by two
      different structural motifs in one polypeptide. A few possible pathways are discussed for MspI
      to cut both strands of DNA, either as a monomer or dimer.
AU  - Xu QS
AU  - Kucera RB
AU  - Roberts RJ
AU  - Guo H-C
PT  - Journal Article
TA  - Structure
JT  - Structure
SO  - Structure 2004 12: 1741-1747.

PMID- 16195548
VI  - 14
DP  - 2005
TI  - Two crystal forms of the restriction enzyme MspI-DNA complex show the same novel structure.
PG  - 2590-2600
AB  - The crystal structure of the Type IIP restriction endonuclease MspI bound to DNA containing
      its cognate recognition sequence has been
      determined in both monoclinic and orthorhombic space. groups.
      Significantly, these two independent crystal forms present an identical
      structure of a novel monomer-DNA complex, suggesting a functional role
      for this novel enzyme-DNA complex. In both crystals, MspI interacts
      with the CCGG DNA recognition sequence as a monomer, using an
      asymmetric mode of recognition by two different structural motifs in a
      single polypeptide. In the crystallographic asymmetric unit, the two
      DNA molecules in the two MspI-DNA complexes appear to stack with each
      other forming an end-to-end pseudo-continuous 19-mer duplex. They are
      primarily B-form and no major bends or kinks are observed. For DNA
      recognition, most of the specific contacts between the enzyme and the
      DNA are preserved in the orthorhombic structure compared with the
      monoclinic structure. A cation is observed near the catalytic center in
      the monoclinic structure at a position homologous to the 74/45 metal
      site of EcoRV, and the orthorhombic structure also shows signs of this
      same cation. However, the coordination ligands of the metal are
      somewhat different from those of the 74/45 metal site of EcoRV.
      Combined with structural information from other solved structures of
      Type II restriction enzymes, the possible relationship between the
      structures of the enzymes and their cleavage behaviors is discussed.
AU  - Xu QS
AU  - Roberts RJ
AU  - Guo HC
PT  - Journal Article
TA  - Protein Sci.
JT  - Protein Sci.
SO  - Protein Sci. 2005 14: 2590-2600.

PMID- 8396948
VI  - 15
DP  - 1993
TI  - Protecting recognition sequences on DNA by a cleavage-deficient restriction endonuclease.
PG  - 310-315
AB  - This report describes the use of a biochemical tool that has been developed to aid in the
      manipulation of DNA. A DNA binding-proficient and cleavage-deficient BamHI mutant protein,
      E113K, was used in vitro to protect its recognition sequence (5'-GGATCC-3') against the
      catalytic action of site-specific endonuclease, exonuclease and methylase. In vitro conditions
      are reported here in which the E113K protein protects BamHI sites (5'-GGATCC-3') from
      cleavage by BamHI endonuclease or Sau3AI endonuclease (5'-GATC-3'); protects a neighboring
      restriction site 5'-CCCGGG-3' from SmaI endonuclease digestion; blocks methylation of
      5'-GGATCC-3' by Dam methylase (5'-GATC-3'); and blocks Bal31 exonuclease progression at a
      BamHI site. The Bal31 procedure could be used to generate unidirectional deletions of a DNA
      fragment. The use of mutant endonucleases that are binding-proficient and cleavage-deficient
      to shield DNA from nuclease digestion or methylase modification expands the repertoire of
      methods to manipulate DNA in vitro.
AU  - Xu S
AU  - Schildkraut I
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 1993 15: 310-315.

PMID- 7946313
VI  - 17
DP  - 1994
TI  - Construction of pSC101 derivatives with Camr and Tetr for selection or LacZ' for blue/white screening.
PG  - 57
AB  - Methylase genes and a mutant bamhIR gene have been cloned in the vectors described.
AU  - Xu S-Y
AU  - Fomenkov A
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 1994 17: 57.

PMID- 1999426
VI  - 266
DP  - 1991
TI  - Isolation of BamHI variants with reduced cleavage activities.
PG  - 4425-4429
AB  - Derivation of the bamhIR sequence (Brooks, J.E., Nathan, P.D., Landry, D.,
      Sznyter, L.A., Waite-Rees, P., Ives, C.C., Mazzola, L.M., Slatko, B.E., and
      Benner, J.S. (1991) Nucleic Acids Res., in press), the gene coding for BamHI
      endonuclease, has facilitated construction of an Escherichia coli strain that
      overproduces BamHI endonuclease (W.E. Jack, L. Greenough, L.F. Dorner, S.Y. Xu,
      T. Strezelecka, A.K. Aggarwal, and I. Schildkraut, submitted for publication).
      As expected, low-level constitutive expression of the bamhIR gene in E. coli
      from the Ptac promoter construct is lethal to the host unless the bamHIM gene,
      which encodes the BamHI methylase, is also expressed within the cell.  We
      identified four classes of BamHI endonuclease variants deficient in catalysis
      by selecting for survival of a host deficient for bamHIM gene, transformed with
      mutagenized copies of the bamhIR gene, and then screening the surviving cell
      extracts for DNA cleavage and binding activities.  Class I variants (G56S,
      G91S/T153I, G130R, E135K, T153I, T157I, G194D) displayed 0.1-1% of the
      wild-type cleavage activity; class II variant (D94N) lacked cleavage activity
      but retained wild-type DNA binding specificity; class III variants (E77K,
      E113K) lacked cleavage activity but bound DNA more tightly; class IV variants
      (G56D, G90D, G91S, R122H, R155H) lacked both binding and cleavage activities.
      Variants with residual cleavage activities induced the E. coli SOS response and
      thus are presumed to cleave chromosomal DNA in vivo.  We conclude that Glu77,
      Asp94, and Glu113 residues are essential for BamHI catalytic function.
AU  - Xu S-Y
AU  - Schildkraut I
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1991 266: 4425-4429.

PMID- 1907265
VI  - 173
DP  - 1991
TI  - Cofactor requirements of BamHI mutant endonuclease E77K and its suppressor mutants.
PG  - 5030-5035
AB  - A mutant BamHI endonuclease, E77K, belongs to a class of catalytic mutants that
      bind DNA efficiently but cleave DNA at a rate more than 10/3-fold lower than
      that of the wild-type enzyme (S.Y. Xu and I. Schildkraut, J. Biol. Chem.
      266:4425-4429, 1991).  The preferred cofactor for the wild-type BamHI is Mg2+.
      BamHI is 10-fold less active with Mn2+ as the cofactor.  In contrast, the E77K
      variant displays an increased activity when Mn2+ is substituted for Mg2+ in the
      reaction buffer.  Mutations that partially suppress the E77K mutation were
      isolated by using an Escherichia coli indicator strain containing the
      dinD::lacZ fusion.  These pseudorevertant endonucleases induce E. coli SOS
      response (as evidenced by blue colony formation) and thus presumably nick or
      cleave chromosomal DNA in vivo.  Consistent with the in vivo result, the
      pseudorevertant endonucleases in the crude cell extract display site-specific
      partial DNA cleavage activity.  DNA sequencing revealed two unique suppressing
      mutations that were located within two amino acid residues of the original
      mutation.  Both pseudorevertant proteins were purified and shown to increase
      specific activity at least 50-fold.  Like the wild-type enzyme, both
      pseudorevertant endonucleases prefer Mg2+ as the cofactor.  Thus, the
      second-site mutation not only restores partial cleavage activity but also
      suppresses the metal preference as well.  These results suggest that the Glu-77
      residue may play a role in metal ion binding or in enzyme activation
      (allosteric transition) following sequence-specific recognition.
AU  - Xu S-Y
AU  - Schildkraut I
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1991 173: 5030-5035.

PMID- 9862476
VI  - 260
DP  - 1998
TI  - Cloning and expression of the ApaLI, NspI, NspHI, SacI, ScaI, and SapI restriction-modification systems in Escherichia coli.
PG  - 226-231
AB  - The genes encoding the ApaLI (5'-G^TGCAC-3'), NspI (5'-GCATG^Y-3'), NspHI
      (5'-RCATG^Y-3'), SacI (5'-GAGCT^C-3'), SapI (5'-GCTCTTCN1^-3', 5'-^N4GAAGAGC-3') and
      ScaI (5'-AGT^ACT-3') restriction-modification systems have been cloned in E. coli.  Amino
      acid sequence comparison of M.ApaLI, M.NspI, M.NspHI, and M.SacI with known methylases
      indicated that they contain the ten conserved motifs characteristic of C5 cytosine methylases.
      NspI and NspHI restriction-modification systems are highly homologous in amino acid sequence.
      The C-termini of the NspI and NlaIII (5'-CATG-3') restriction endonucleases share
      significant similarity.  5mC modification of the internal C in a SacI site renders it
      resistant to SacI digestion.  External 5mC modification of a SacI site has no effect on SacI
      digestion.  N4mC modification of the second base in the sequence 5'-GCTCTTC-3' blocks SapI
      digestion.  N4mC modification of the other cytosines in the SapI site does not affect SapI
      digestion.  N4mC modification of ScaI site blocks ScaI digestion.  A DNA invertase homolog was
      found adjacent to the ApaLI restriction-modification system.  A DNA transposase subunit
      homolog was found upstream of the SapI restriction endonuclease gene.
AU  - Xu S-Y
AU  - Xiao J-P
AU  - Ettwiller L
AU  - Holden M
AU  - Aliotta J
AU  - Poh CL
AU  - Dalton M
AU  - Robinson DP
AU  - Petronzio TR
AU  - Moran L
AU  - Ganatra M
AU  - Ware J
AU  - Slatko B
AU  - Benner J
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1998 260: 226-231.

PMID- 9321648
VI  - 25
DP  - 1997
TI  - Cloning of the BssHII restriction-modification system in Escherichia coli: BssHII methyltransferase contains circularly permuted cytosine-5 methyltransferase motifs.
PG  - 3991-3994
AB  - BssHII restriction endonuclease cleaves 5'-GCGCGC-3' on double-stranded DNA between the
      first and second bases to generate a four base 5' overhang.  BssHII restriction endonuclease
      was purified from the native Bacillus stearothermophilus H3 cells and its N-terminal amino
      acid sequence was determined.  Degenerate PCR primers were used to amplify the first 20 codons
      of the BssHII restriction endonuclease gene.  The BssHII restriction endonuclease gene
      (bssHIIR) and the cognate ssHII methyltransferase gene (bssHIIM) were cloned in Escherichia
      coli by amplification of Bacillus stearothermophilus genomic DNA using PCR and inverse PCR.
      BssHII methyltransferase (M.BssHII) contains all 10 conserved cytosine-5 methyltransferase
      motifs, but motifs IX and X precede motifs I-VIII.  Thus, the conserved motifs of M.BssHII are
      circularly permuted relative to the motif organizations of other cytosine-5
      methyltransferases.  M.BssHII and the noncognate multi-specific PhiBssHII methyltransferase,
      M.PhiBssHII share 34% identity in amino acid sequences from motifs I-VIII, and 40% identity in
      motifs IX-X.  A conserved arginine is located upstream of a TV dipeptide in the N-terminus of
      M.BssHII that may be responsible for the recognition of the guanine 5' of the target
      cytosine.  The BssHII restriction enodnuclease gene was expressed in E.coli via a T7
      expression vector.
AU  - Xu S-Y
AU  - Xiao J-P
AU  - Posfai J
AU  - Maunus R
AU  - Benner J
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1997 25: 3991-3994.

PMID- 25953183
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence Analysis of Bacillus subtilis T30.
PG  - e00395-15
AB  - The complete genome sequence of Bacillus subtilis T30 was determined by SMRT sequencing. The
      entire genome contains 4,138 predicted genes. The genome carries
      one intact prophage sequence (37.4 kb) similar to Bacillus phage SPBc2 and one
      incomplete prophage genome of 39.9 kb similar to Bacillus phage phi105.
AU  - Xu SY
AU  - Boitano M
AU  - Clark TA
AU  - Vincze T
AU  - Fomenkov A
AU  - Kumar S
AU  - Too PH
AU  - Gonchar D
AU  - Degtyarev SK
AU  - Roberts RJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00395-15.

PMID- 21421560
VI  - 39
DP  - 2011
TI  - A type IV modification-dependent restriction enzyme SauUSI from Staphylococcus aureus subsp. aureus USA300.
PG  - 5597-5610
AB  - A gene encoding a putative DNA helicase from Staphylococcus aureus USA300 was cloned and
      expressed in Escherichia coli. The protein was purified to over 90% purity by chromatography.
      The purified enzyme, SauUSI, predominantly cleaves modified DNA containing 5mC and
      5-hydroxymethylcytosine. Cleavage of 5mC-modified plasmids indicated that the sites S5mCNGS (S
      = C or G) are preferentially digested. The endonuclease activity requires the presence of
      adenosine triphosphate (ATP) or dATP whereas the non-hydrolyzable gamma-S-ATP does not support
      activity. SauUSI activity was inhibited by ethylenediaminetetraacetic acid. It is most active
      in Mg(++) buffers. No companion methylase gene was found near the SauUSI restriction gene. The
      absence of a cognate methylase and cleavage of modified DNA indicate that SauUSI belongs to
      type IV restriction endonucleases, a group that includes EcoK McrBC and Mrr. SauUSI belongs to
      a family of highly similar homologs found in other sequenced S. aureus, S. epidermidis and S.
      carnosus genomes. More distant SauUSI orthologs can be found in over 150 sequenced
      bacterial/archaea genomes. Finally, we demonstrated the biological function of the type IV
      REase in restricting 5mC-modified plasmid DNA by transformation into clinical S. aureus strain
      SA564, and in restricting phage lambda infection when the endonuclease is expressed in E.
      coli.
AU  - Xu SY
AU  - Corvaglia AR
AU  - Chan SH
AU  - Zheng Y
AU  - Linder P
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2011 39: 5597-5610.

PMID- 27353146
VI  - 6
DP  - 2016
TI  - Expression and purification of the modification-dependent restriction enzyme BisI and its homologous enzymes.
PG  - 28579
AB  - The methylation-dependent restriction endonuclease (REase) BisI (G(m5)C downward  arrow NGC)
      is found in Bacillus subtilis T30. We expressed and purified the BisI
      endonuclease and 34 BisI homologs identified in bacterial genomes. 23 of these
      BisI homologs are active based on digestion of (m5)C-modified substrates. Two
      major specificities were found among these BisI family enzymes: Group I enzymes
      cut GCNGC containing two to four (m5)C in the two strands, or hemi-methylated
      sites containing two (m5)C in one strand; Group II enzymes only cut GCNGC sites
      containing three to four (m5)C, while one enzyme requires all four cytosines to
      be modified for cleavage. Another homolog, Esp638I cleaves GCS downward arrow SGC
      (relaxed specificity RCN downward arrow NGY, containing at least four (m5)C). Two
      BisI homologs show degenerate specificity cleaving unmodified DNA. Many homologs
      are small proteins ranging from 150 to 190 amino acid (aa) residues, but some
      homologs associated with mobile genetic elements are larger and contain an extra
      C-terminal domain. More than 156 BisI homologs are found in >60 bacterial genera,
      indicating that these enzymes are widespread in bacteria. They may play an
      important biological function in restricting pre-modified phage DNA.
AU  - Xu SY
AU  - Klein P
AU  - Degtyarev SK
AU  - Roberts RJ
PT  - Journal Article
TA  - Sci. Rep.
JT  - Sci. Rep.
SO  - Sci. Rep. 2016 6: 28579.

PMID- 22037402
VI  - 194
DP  - 2012
TI  - Characterization of Type II and III restriction-modification systems from Bacillus cereus strains ATCC10987 and ATCC14579.
PG  - 49-60
AB  - The genomes of two Bacillus cereus strains (ATCC10987 and ATCC14579) have been sequenced. Here
      we report the specificities of Type II/III restriction (R) and modification (M) enzymes. Found
      in the ATCC10987 strain, BceSI is a restriction endonuclease (REase) with the recognition and
      cut site CGAAG 24-25/27-28. BceSII is an isoschizomer of AvaII (G/GWCC). BceSIII cleaves at
      ACGGC 12/14. The BceSIII C-terminus resembles the catalytic domains of AlwI, MlyI, and
      Nt.BstNBI. BceSIV is composed of two subunits and cleaves on both sides of GCWGC. BceSIV
      activity is strongly stimulated by the addition of cofactor ATP or GTP. The large subunit (R1)
      of BceSIV contains conserved motifs of NTPases and DNA helicases. The R1 subunit has no
      endonuclease activity by itself; it strongly stimulates REase activity when in complex with
      the R2 subunit. BceSIV was demonstrated to hydrolyze GTP and ATP in vitro. BceSIV is similar
      to CglI (GCSGC), and homologs of R1 are found in 11 sequenced bacterial genomes where they are
      paired with specificity subunits. In addition, homologs of BceSIV R1-R2 fusion are found in
      many sequenced microbial genomes. An orphan methylase M.BceSV was found to modify GCNGC, GGCC,
      CCGG, GGNNCC, and GCGC sites. A ParB-methylase fusion protein appears to nick DNA
      non-specifically. The ATCC14579 genome encodes an active enzyme Bce14579I (GCWGC). BceSIV and
      Bce14579I belong to the phospholipase D (PLD) family of endonucleases that are widely
      distributed among Bacteria and Archaea. A survey of Type II and III R-M genes is presented
      from sequenced B. cereus, B. anthracis, and B. thuringiensis strains.
AU  - Xu SY
AU  - Nugent RL
AU  - Kasamkattil J
AU  - Fomenkov A
AU  - Gupta Y
AU  - Aggarwal A
AU  - Wang X
AU  - Li Z
AU  - Zheng Y
AU  - Morgan R
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 49-60.

PMID- 17586812
VI  - 35
DP  - 2007
TI  - Discovery of natural nicking endonucleases Nb.BsrDI and Nb.BtsI and engineering of top-strand nicking variants from BsrDI and BtsI.
PG  - 4608-4618
AB  - BsrDI and BtsI restriction endonucleases recognize and cleave double-strand DNA at the
      sequences GCAATG (2/0) and GCAGTG (2/0),
      respectively. We have purified and partially characterized these two
      enzymes, and analyzed the genes that encode them. BsrDI and BtsI are
      unusual in two respects: each cleaves DNA as a heterodimer of one large
      subunit (B subunit) and one small subunit (A subunit); and, in the absence
      of their small subunits, the large subunits behave as sequence-specific
      DNA nicking enzymes and only nick the bottom strand of the sequences at
      these respective positions: GCAATG (-/0) and GCAGTG (-/0). We refer to the
      single subunit, the bottom-strand nicking forms as 'hemidimers'. Amino
      acid sequence comparisons reveal that BsrDI and BtsI belong to a family of
      restriction enzymes that possess two catalytic sites: a canonical
      PD-X(n)-EXK and a second non-canonical PD-X(n)-E-X(12)-QR. Interestingly,
      the other family members, which include BsrI (ACTGG 1/-1) and
      BsmI/Mva1269I (GAATGC 1/-1) are single polypeptide chains, i.e. monomers,
      rather than heterodimers. In BsrDI and BtsI, the two catalytic sites are
      found in two separate subunits. Site-directed mutagenesis confirmed that
      the canonical catalytic site located at the N-terminus of the large
      subunit is responsible for the bottom-strand cleavage, whereas the
      non-canonical catalytic site located in the small subunit is responsible
      for hydrolysis of the top strand. Top-strand specific nicking variants,
      Nt.BsrDI and Nt.BtsI, were successfully engineered by combining the
      catalytic-deficient B subunit with wild-type A subunit.
AU  - Xu SY
AU  - Zhu Z
AU  - Zhang P
AU  - Chan SH
AU  - Samuelson JC
AU  - Xiao J
AU  - Ingalls D
AU  - Wilson GG
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2007 35: 4608-4618.

PMID- 19232083
VI  - 9
DP  - 2009
TI  - DNA phosphorothioation in Streptomyces lividans: mutational analysis of the dnd locus.
PG  - 41
AB  - BACKGROUND: A novel DNA phosphorothioate modification (DNA sulfur modification),  in which one
      of the non-bridging oxygen atoms in the phosphodiester bond linking
      DNA nucleotides is exchanged by sulphur, was found to be genetically determined
      by dnd or dnd-counterpart loci in a wide spectrum of bacteria from diverse
      habitats. A detailed mutational analysis of the individual genes within the dnd
      locus in Streptomyces lividans responsible for DNA phosphorothioation was
      performed and is described here. It should be of great help for the mechanistic
      study of this intriguing system. RESULTS: A 6,665-bp DNA region carrying just
      five ORFs (dndA-E) was defined as the sole determinant for modification of the
      DNA backbone in S. lividans to form phosphorothioate. This provides a
      diagnostically reliable and easily assayable Dnd (DNA degradation) phenotype.
      While dndA is clearly transcribed independently, dndB-E constitute an operon, as
      revealed by RT-PCR analysis. An efficient mutation-integration-complementation
      system was developed to allow for detailed functional analysis of these dnd
      genes. The Dnd- phenotype caused by specific in-frame deletion of the dndA, C, D,
      and E genes or the enhanced Dnd phenotype resulting from in-frame deletion of
      dndB could be restored by expression vectors carrying the corresponding dnd
      genes. Interestingly, overdosage of DndC or DndD, but not other Dnd proteins, in
      vivo was found to be detrimental to cell viability. CONCLUSION: DNA
      phosphorothioation is a multi-enzymatic and highly coordinated process controlled
      by five dnd genes. Overexpression of some proteins in vivo prevented growth of
      host strain, suggesting that expression of the gene cluster is strictly regulated
      in the native host.
AU  - Xu T
AU  - Liang J
AU  - Chen S
AU  - Wang L
AU  - He X
AU  - You D
AU  - Wang Z
AU  - Li A
AU  - Xu Z
AU  - Zhou X
AU  - Deng Z
PT  - Journal Article
TA  - BMC Microbiol.
JT  - BMC Microbiol.
SO  - BMC Microbiol. 2009 9: 41.

PMID- 20627870
VI  - 38
DP  - 2010
TI  - A novel host-specific restriction system associated with DNA backbone S-modification in Salmonella.
PG  - 7133-7141
AB  - A novel, site-specific, DNA backbone S-modification (phosphorothioation) has been discovered,
      but its in vivo function(s) have remained obscure.
      Here, we report that the enteropathogenic Salmonella enterica serovar
      Cerro 87, which possesses S-modified DNA, restricts DNA isolated from
      Escherichia coli, while protecting its own DNA by site-specific
      phosphorothioation. A cloned 15-kb gene cluster from S. enterica conferred
      both host-specific restriction and DNA S-modification on E. coli.
      Mutational analysis of the gene cluster proved unambiguously that the
      S-modification prevented host-specific restriction specified by the same
      gene cluster. Restriction activity required three genes in addition to at
      least four contiguous genes necessary for DNA S-modification. This
      functional overlap ensures that restriction of heterologous DNA occurs
      only when the host DNA is protected by phosphorothioation. Meanwhile, this
      novel type of host-specific restriction and modification system was
      identified in many diverse bacteria. As in the case of
      methylation-specific restriction systems, targeted inactivation of this
      gene cluster should facilitate genetic manipulation of these bacteria, as
      we demonstrate in Salmonella.
AU  - Xu T
AU  - Yao F
AU  - Zhou X
AU  - Deng Z
AU  - You D
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2010 38: 7133-7141.

PMID- 21072428
VI  - 11
DP  - 2011
TI  - Exploring both sequence detection and restriction endonuclease cleavage kinetics by recognition site via single-molecule microfluidic trapping.
PG  - 435-442
AB  - We demonstrate the feasibility of a single-molecule microfluidic approach to both sequence
      detection and obtaining kinetic information
      for restriction endonucleases on dsDNA. In this method, a microfluidic
      stagnation point flow is designed to trap, hold, and linearize
      double-stranded (ds) genomic DNA to which a restriction endonuclease
      has been pre-bound sequence-specifically. By introducing the cofactor
      magnesium, we determine the binding location of the enzyme by the
      cleavage process of dsDNA as in optical restriction mapping, however
      here the DNA need not be immobilized on a surface. We note that no
      special labeling of the enzyme is required, which makes it simpler than
      our previous scheme using stagnation point flows for sequence
      detection. Our accuracy in determining the location of the recognition
      site is comparable to or better than other single molecule techniques
      due to the fidelity with which we can control the linearization of the
      DNA molecules. In addition, since the cleavage process can be followed
      in real time, information about the cleavage kinetics, and subtle
      differences in binding and cleavage frequencies among the recognition
      sites, may also be obtained. Data for the five recognition sites for
      the type II restriction endonuclease EcoRI on lambda-DNA are presented
      as a model system. While the roles of the varying fluid velocity and
      tension along the chain backbone on the measured kinetics remain to be
      determined, we believe this new method holds promise for a broad range
      of studies of DNA-protein interactions, including the kinetics of other
      DNA cleavage processes, the dissociation of a restriction enzyme from
      the cleaved substrate, and other macromolecular cleavage processes.
AU  - Xu WL
AU  - Muller SJ
PT  - Journal Article
TA  - Lab on a Chip
JT  - Lab on a Chip
SO  - Lab on a Chip 2011 11: 435-442.

PMID- 29973921
VI  - 9
DP  - 2018
TI  - Genome mining of the marine actinomycete Streptomyces sp. DUT11 and discovery of tunicamycins as anti-complement agents.
PG  - 1318
AB  - Marine actinobacteria are potential producers of various secondary metabolites with diverse
      bioactivities. Among various bioactive compounds, anti-complement agents have received great
      interest for drug discovery to treat numerous diseases caused by inappropriate activation of
      the human complement system. However, marine streptomycetes producing anti-complement agents
      are still poorly explored. In this study, a marine-derived strain Streptomyces sp. DUT11
      showing superior anti-complement activity was focused, and its genome sequence was analyzed.
      Gene clusters showing high similarities to that of tunicamycin and nonactin were identified,
      and their corresponding metabolites were also detected. Subsequently, tunicamycin I, V and VII
      were isolated from Streptomyces sp. DUT11. Anti-complement assay showed that tunicamycin I, V,
      VII inhibited complement activation through the classic pathway, whereas no anti-complement
      activity of nonactin was detected. This is the first time that tunicamycins are reported to
      have such activity. In addition, genome analysis indicates that Streptomyces sp. DUT11 has the
      potential to produce novel lassopeptides and lantibiotics. These results suggest that marine
      Streptomyces are rich sources of anti-complement agents for drug discovery.
AU  - Xu X
AU  - Chen L
AU  - Chen C
AU  - Tang YJ
AU  - Bai FW
AU  - Su C
AU  - Zhao XQ
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2018 9: 1318.

PMID- 23661483
VI  - 1
DP  - 2013
TI  - Genome Sequence of a Gamma- and UV-Ray-Resistant Strain, Deinococcus wulumuqiensis R12.
PG  - e00206-13
AB  - Deinococcus wulumuqiensis R12, isolated from radiation-polluted soil, is a red-pigmented
      strain of the extremely radioresistant genus Deinococcus. It
      contains a major carotenoid, namely, deinoxanthin. Here, we present a 3.39-Mb
      assembly of its genome sequence, which might provide various kinds of useful
      information related to Deinococcus, such as about the key enzymes of its
      radioresistance mechanism and carotenoid biosynthetic pathways.
AU  - Xu X
AU  - Jiang L
AU  - Zhang Z
AU  - Shi Y
AU  - Huang H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00206-13.

PMID- 22458477
VI  - 134
DP  - 2012
TI  - Bacterial Biosynthesis and Maturation of the Didemnin Anti-cancer Agents.
PG  - 8625-8632
AB  - The anti-neoplastic agent didemnin B from the Caribbean tunicate Trididemnum
      solidum was the first marine drug to be clinically tested in humans. Because of
      its limited supply and its complex cyclic depsipeptide structure, considerable
      challenges were encountered during didemnin B's development that continue to
      limit aplidine (dehydrodidemnin B), which is currently being evaluated in
      numerous clinical trials. Herein we show that the didemnins are bacterial
      products produced by the marine alpha-proteobacteria Tistrella mobilis and
      Tistrella bauzanensis via a unique post-assembly line maturation process.
      Complete genome sequence analysis of the 6,513,401 bp T. mobilis strain
      KA081020-065 with its five circular replicons revealed the putative didemnin
      biosynthetic gene cluster (did) on the 1,126,962 bp megaplasmid pTM3. The did
      locus encodes a 13-module hybrid non-ribosomal peptide synthetase-polyketide
      synthase enzyme complex organized in a collinear arrangement for the synthesis of
      the fatty acylglutamine ester derivatives didemnins X and Y rather than didemnin
      B as first anticipated. Imaging mass spectrometry of T. mobilis bacterial
      colonies captured the time-dependent extracellular conversion of the didemnin X
      and Y precursors to didemnin B, in support of an unusual post-synthetase
      activation mechanism. Significantly, the discovery of the didemnin biosynthetic
      gene cluster may provide a long-term solution to the supply problem that
      presently hinders this group of marine natural products and pave the way for the
      genetic engineering of new didemnin congeners.
AU  - Xu Y
AU  - Kersten RD
AU  - Nam SJ
AU  - Lu L
AU  - Al-Suwailem AM
AU  - Zheng H
AU  - Fenical W
AU  - Dorrestein PC
AU  - Moore BS
AU  - Qian PY
PT  - Journal Article
TA  - J. Am. Chem. Soc.
JT  - J. Am. Chem. Soc.
SO  - J. Am. Chem. Soc. 2012 134: 8625-8632.

PMID- 27881540
VI  - 4
DP  - 2016
TI  - Genome Sequence of Salegentibacter salarius KCTC 12974, Isolated from a Marine Solar Saltern of the Yellow Sea in South Korea.
PG  - e01308-16
AB  - Salegentibacter salarius KCTC 12974 is isolated from a marine solar saltern of the Yellow Sea
      in South Korea. Here, we report the draft genome sequence of
      Salegentibacter salarius KCTC 12974. Various glycoside hydrolase genes in even
      numbers in the genome reflect the ecological adaption of KCTC 12974 to its
      habitat.
AU  - Xu Y
AU  - Liu J
AU  - Zheng Q
AU  - Liu Y
AU  - Jiao N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01308-16.

PMID- 25169860
VI  - 2
DP  - 2014
TI  - Genome Sequence of Paenibacillus polymyxa Strain CICC 10580, Isolated from the Fruit of Noni (Morinda citrifolia L.) Grown in the Paracel Islands.
PG  - e00854-14
AB  - Noni is a plant reported to have nutritional and therapeutic properties. Paenibacillus
      polymyxa CICC 10580 is a strain that was isolated from the fruit of
      noni and showed comprehensive antagonistic activity against many pathogens. Its
      genome was sequenced and assembled (6.10 Mb). The coding sequences (CDSs)
      correlated with antagonistic activity were annotated.
AU  - Xu Y
AU  - Liu Y
AU  - Yao S
AU  - Li J
AU  - Cheng C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00854-14.

PMID- 11687651
VI  - 98
DP  - 2001
TI  - Engineering a nicking endonuclease N.AlwI by domain swapping.
PG  - 12990-12995
AB  - Changing enzymatic function through genetic engineering still presents a challenge to
      molecular biologists.  Here we present an example in which changing the oligomerization state
      of an enzyme changes its function.  Type IIs restriction endonucleases such as AlwI usually
      fold into two separate domains: A DNA-binding domain and a catalytic/dimerization domain.  We
      have swapped the putative dimerization domain of AlwI with a nonfunctional dimerization domain
      from a nicking enzyme, N.BstNBI.  The resulting chimeric enzyme, N.AlwI, no longer forms a
      dimer.  Interestingly, the monomeric N.AlwI still recognizes the same sequence as AlwI but
      only cleaves the DNA strand containing the sequence 5'-GGATC-3' (top strand).  In contrast,
      the wild-type AlwI exists as a dimmer in solution and cleaves two DNA strands; the top strand
      is cleaved by an enzyme binding to that sequence, and its complementary bottom strand is
      cleaved by the second enzyme dimerized with the first enzyme.  N.AlwI is unable to form a
      dimer and therefore nicks DNA as a monomer.  In addition, the engineered nicking enzyme is at
      least as active as the wild-type AlwI and is thus a useful enzyme.  To our knowledge, this is
      the first report of creating a nicking enzyme by domain swapping.
AU  - Xu Y
AU  - Lunnen KD
AU  - Kong H
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2001 98: 12990-12995.

PMID- 27540070
VI  - 4
DP  - 2016
TI  - Genome Sequences of Ralstonia insidiosa Type Strain ATCC 49129 and Strain FC1138, a Strong Biofilm Producer Isolated from a Fresh-Cut Produce-Processing Plant.
PG  - e00847-16
AB  - Ralstonia insidiosa is an opportunistic pathogen and a strong biofilm producer. Here, we
      present the complete genome sequences of R. insidiosa FC1138 and ATCC
      49129. Both strains have two circular chromosomes of approximately 3.9 and 1.9 Mb
      and a 50-kb plasmid. ATCC 49129 also possesses a megaplasmid of approximately 318
      kb.
AU  - Xu Y
AU  - Nagy A
AU  - Yan X
AU  - Haley BJ
AU  - Kim SW
AU  - Liu NT
AU  - Nou X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00847-16.

PMID- 27491993
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Oil-Degrading Bacterium Gallaecimonas pentaromativorans  Strain YA_1 from the Southwest Indian Ocean.
PG  - e00764-16
AB  - Gallaecimonas pentaromativorans has been previously reported to be capable of degrading crude
      oil and diesel oil. G. pentaromativorans strain YA_1 was isolated
      from the southwest Indian Ocean and can degrade crude oil. This study reports the
      draft genome sequence of G. pentaromativorans, which can provide insights into
      the mechanisms of microbial oil biodegradation.
AU  - Xu Y
AU  - Ren C
AU  - Chen R
AU  - Zeng R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00764-16.

PMID- 29574602
VI  - 45
DP  - 2018
TI  - Enhanced lincomycin production by co-overexpression of metK1 and metK2 in Streptomyces lincolnensis.
PG  - 345-355
AB  - Streptomyces lincolnensis is generally utilized for the production of lincomycin
      A (Lin-A), a clinically useful antibiotic to treat Gram-positive bacterial
      infections. Three methylation steps, catalyzed by three different
      S-adenosylmethionine (SAM)-dependent methyltransferases, are required in the
      biosynthesis of Lin-A, and thus highlight the significance of methyl group supply
      in lincomycin production. In this study, we demonstrate that externally
      supplemented SAM cannot be taken in by cells and therefore does not enhance Lin-A
      production. Furthermore, bioinformatics and in vitro enzymatic assays revealed
      there exist two SAM synthetase homologs, MetK1 (SLCG_1651) and MetK2 (SLCG_3830)
      in S. lincolnensis that could convert L-methionine into SAM in the presence of
      ATP. Even though we attempted to inactivate metK1 and metK2, only metK2 was
      deleted in S. lincolnensis LCGL, named as DeltametK2. Following a reduction of
      the intracellular SAM concentration, DeltametK2 mutant exhibited a significant
      decrease of Lin-A in comparison to its parental strain. Individual overexpression
      of metK1 or metK2 in S. lincolnensis LCGL either elevated the amount of
      intracellular SAM, concomitant with 15% and 22% increase in Lin-A production,
      respectively. qRT-PCR assays showed that overexpression of either metK1 or metK2
      increased the transcription of lincomycin biosynthetic genes lmbA and lmbR, and
      regulatory gene lmbU, indicating SAM may also function as a transcriptional
      activator. When metK1 and metK2 were co-expressed, Lin-A production was increased
      by 27% in LCGL, while by 17% in a high-yield strain LA219X.
AU  - Xu Y
AU  - Tan G
AU  - Ke M
AU  - Li J
AU  - Tang Y
AU  - Meng S
AU  - Niu J
AU  - Wang Y
AU  - Liu R
AU  - Wu H
AU  - Bai L
AU  - Zhang L
AU  - Zhang B
PT  - Journal Article
TA  - J. Ind. Microbiol. Biotechnol.
JT  - J. Ind. Microbiol. Biotechnol.
SO  - J. Ind. Microbiol. Biotechnol. 2018 45: 345-355.

PMID- 22275097
VI  - 194
DP  - 2012
TI  - Genome Sequence of Enterobacter cloacae subsp. dissolvens SDM, an Efficient Biomass-Utilizing Producer of Platform Chemical 2,3-Butanediol.
PG  - 897-898
AB  - Enterobacter cloacae subsp. dissolvens SDM has an extraordinary characteristic of biomass
      utilization for 2,3-butanediol production. Here
      we present a 4.9-Mb assembly of its genome. The key genes for regulation
      and metabolism of 2,3-butanediol production were annotated, which could
      provide further insights into the molecular mechanism of high-yield
      production of 2,3-butanediol.
AU  - Xu Y
AU  - Wang A
AU  - Tao F
AU  - Su F
AU  - Tang H
AU  - Ma C
AU  - Xu P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 897-898.

PMID- 27738025
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of the Polychlorinated Biphenyl Degrader Rhodococcus sp. WB1.
PG  - e00996-16
AB  - Rhodococcus sp. WB1 is a polychlorinated biphenyl degrader which was isolated from
      contaminated soil in Zhejiang, China. Here, we present the complete genome
      sequence. The analysis of this genome indicated that a biphenyl-degrading gene
      cluster and several xenobiotic metabolism pathways are harbored.
AU  - Xu Y
AU  - Yu M
AU  - Shen A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00996-16.

PMID- 18197260
VI  - 3
DP  - 2008
TI  - Genome Biology of Actinobacillus pleuropneumoniae JL03, an Isolate of Serotype 3 Prevalent in China.
PG  - e1450
AB  - Actinobacillus pleuropneumoniae is the etiologic agent of porcine contagious pleuropneumonia,
      a cause of considerable world wide economic
      losses in the swine industry. We sequenced the complete genome of A.
      pleuropneumoniae, JL03, an isolate of serotype 3 prevalent in China. Its
      genome is a single chromosome of 2,242,062 base pairs containing 2,097
      predicted protein-coding sequences, six ribosomal rRNA operons, and 63
      tRNA genes. Preliminary analysis of the genomic sequence and the functions
      of the encoded proteins not only confirmed the present physiological and
      pathological knowledge but also offered new insights into the metabolic
      and virulence characteristics of this important pathogen. We identified a
      full spectrum of genes related to its characteristic chemoheterotrophic
      catabolism of fermentation and respiration with an incomplete TCA system
      for anabolism. In addition to confirming the lack of ApxI toxin,
      identification of a nonsense mutation in apxIVA and a 5'-proximal
      truncation of the flp operon deleting both its promoter and the
      flp1flp2tadV genes have provided convincing scenarios for the low
      virulence property of JL03. Comparative genomic analysis using the
      available sequences of other serotypes, probable strain
      (serotype)-specific genomic islands related to capsular polysaccharides
      and lipopolysaccharide O-antigen biosyntheses were identified in JL03,
      which provides a foundation for future research into the mechanisms of
      serotypic diversity of A. pleuropneumoniae.
AU  - Xu Z et al
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2008 3: e1450.

PMID- 20802045
VI  - 192
DP  - 2010
TI  - Comparative genomic characterization of Actinobacillus pleuropneumoniae.
PG  - 5625-5636
AB  - The Gram-negative bacterium Actinobacillus pleuropneumoniae is the
      etiologic agent of porcine contagious pleuropneumoniae, a lethal
      respiratory infectious disease causing great economic losses in the swine
      industry worldwide. In order to better interpret the genetic background of
      serotypic diversity, nine genomes of A. pleuropneumoniae reference strains
      of serovars 1, 2, 4, 6, 9, 10, 11, 12, and 13 were sequenced by using
      rapid high-throughput approach. Based on 12 genomes of corresponding
      serovar reference strains including three publicly available complete
      genomes (serovars 3, 5b, and 7) of this bacterium, we performed a
      comprehensive analysis of comparative genomics and first reported a global
      genomic characterization for this pathogen. Clustering of 26,012 predicted
      protein-coding genes showed that the pan genome of A. pleuropneumoniae
      consists of 3,303 gene clusters, which contain 1,709 core genome genes,
      822 distributed genes, and 772 strain-specific genes. The genome
      components involved in the biogenesis of capsular polysaccharide and
      lipopolysaccharide O antigen relative to serovar diversity were compared,
      and their genetic diversity was depicted. Our findings shed more light on
      genomic features associated with serovar diversity of A. pleuropneumoniae
      and provide broader insight into both pathogenesis research and
      clinical/epidemiological application against the severe disease caused by
      this swine pathogen.
AU  - Xu Z
AU  - Chen X
AU  - Li L
AU  - Li T
AU  - Wang S
AU  - Chen H
AU  - Zhou R
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 5625-5636.

PMID- 29046741
VI  - 12
DP  - 2017
TI  - Complete genome sequence of Thermotoga sp. strain RQ7.
PG  - 62
AB  - Thermotoga sp. strain RQ7 is a member of the family Thermotogaceae in the order Thermotogales.
      It is a Gram negative, hyperthermophilic, and strictly anaerobic
      bacterium. It grows on diverse simple and complex carbohydrates and can use
      protons as the final electron acceptor. Its complete genome is composed of a
      chromosome of 1,851,618 bp and a plasmid of 846 bp. The chromosome contains 1906
      putative genes, including 1853 protein coding genes and 53 RNA genes. The genetic
      features pertaining to various lateral gene transfer mechanisms are analyzed. The
      genome carries a complete set of putative competence genes, 8 loci of CRISPRs,
      and a deletion of a well-conserved Type II R-M system.
AU  - Xu Z
AU  - Puranik R
AU  - Hu J
AU  - Xu H
AU  - Han D
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 62.

PMID- 24744334
VI  - 2
DP  - 2014
TI  - Genome Sequence of Streptomyces albulus PD-1, a Productive Strain for Epsilon-Poly-L-Lysine and Poly-L-Diaminopropionic Acid.
PG  - e00297-14
AB  - Streptomyces albulus PD-1, a productive strain for epsilon-poly-l-lysine and
      poly-l-diaminopropionic acid, was isolated from soils. We present the genome sequence of S.
      albulus PD-1, which may provide abundant information regarding the production of
      epsilon-poly-l-lysine and poly-l-diaminopropionic acid.
AU  - Xu Z
AU  - Xia J
AU  - Feng X
AU  - Li S
AU  - Xu H
AU  - Bo F
AU  - Sun Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00297-14.

PMID- 
VI  - 181
DP  - 2014
TI  - Electrochemical immunoassays for the detection the activity of DNA methyltransferase by using the rolling circle amplification technique.
PG  - 471-477
AB  - We report on an electrochemical method for the determination of the activity of the enzyme
      methyltransferase (MTase). The methyl-binding domain-1 protein was applied to recognize
      symmetrically methylated cytosine in CpG (-C-phosphate-G-) islands of ds-DNA which then
      specifically bind to anti-His tag antibody. Hyperbranched rolling circle amplification (RCA)
      was used to improve sensitivity. When the dsDNA was treated with M.Sss I methyltransferase,
      the sequence 5'-CCGG-3' was methylated and recognize by the methyl binding protein. In turn,
      the anti-His tag, biotinylated IgG, streptavidin and biotinylated oligonucleotide were
      captured successively on the surface of an electrode. Subsequently, the RCA reaction was
      initiated and streptavidin-labeled alkaline phosphatase immobilized on the surface of the
      electrode. ALP was able to catalyze the hydrolysis of 1-naphthyl phosphate to form 1-naphthol
      at pH 9.8. The oxidation peak current of 1-naphthol was used to monitor the methylation
      process. The response  obtained by differential pulse voltammetry was linearly related to the
      concentration of M.Sss I MTase in the range from 0.1 to 40 unit mL(-1), and the detection
      limit was 0.03 unit mL(-1) (at an SNR of 3). The inhibitory action of paclitaxel on the
      activity of M.Sss I MTase also was investigated.
AU  - Xu Z
AU  - Yin H
AU  - Tian Z
AU  - Zhou Y
AU  - Ai S
PT  - Journal Article
TA  - Microchimica Acta
JT  - Microchimica Acta
SO  - Microchimica Acta 2014 181: 471-477.

PMID- 24425742
VI  - 64
DP  - 2014
TI  - Oceanisphaera profunda sp. nov., a marine bacterium isolated from deep-sea sediment, and emended description of the genus Oceanisphaera.
PG  - 1252-1256
AB  - A Gram-stain-negative, aerobic, oxidase- and catalase-positive, flagellated,
      rod-shaped bacterial strain, designated SM1222(T), was isolated from the deep-sea
      sediment of the South China Sea. The strain grew at 4-35 degrees C and with 0.5-8
      % NaCl (w/v). Phylogenetic analysis based on the 16S rRNA gene sequences revealed
      that strain SM1222(T) was affiliated with the genus Oceanisphaera in the class
      Gammaproteobacteria. It shared the highest sequence similarity with the type
      strain of Oceanisphaera ostreae (96.8 %) and 95.4-96.6 % sequence similarities
      with type strains of other species of the genus Oceanisphaera with validly
      published names. Strain SM1222(T) contained summed feature 3 (C16 : 1omega7c
      and/or iso-C15 : 0 2-OH), C18 : 1omega7c, C16 : 0, C12 : 0 and summed feature 2
      (C14 : 0 3-OH and/or iso-C16 : 1 I) as the major fatty acids and ubiquinone Q-8
      as the predominant respiratory quinone. The major polar lipids were
      phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The
      genomic DNA G+C content of strain SM1222(T) was 51.5 mol%. On the basis of the
      evidence presented in this study, strain SM1222(T) represents a novel species of
      the genus Oceanisphaera, for which the name Oceanisphaera profunda sp. nov. is
      proposed. The type strain of Oceanisphaera profunda is SM1222(T) ( = CCTCC AB
      2013241(T) = KCTC 32510(T)). An emended description of the genus Oceanisphaera
      Romanenko et al. 2003 emend. Choi et al. 2011 is also proposed.
AU  - Xu Z
AU  - Zhang XY
AU  - Su HN
AU  - Yu ZC
AU  - Liu C
AU  - Li H
AU  - Chen XL
AU  - Song XY
AU  - Xie BB
AU  - Qin QL
AU  - Zhou BC
AU  - Shi M
AU  - Huang Y
AU  - Zhang YZ
PT  - Journal Article
TA  - Int. J. Syst. Evol. Microbiol.
JT  - Int. J. Syst. Evol. Microbiol.
SO  - Int. J. Syst. Evol. Microbiol. 2014 64: 1252-1256.

PMID- 21918796
VI  - 15
DP  - 2011
TI  - Cloning and characterization of the TneDI restriction-modification system of Thermotoga neapolitana.
PG  - 665-672
AB  - A putative Type II restriction-modification system of Thermotoga neapolitana, TneDI, was
      cloned into Escherichia coli XL1-Blue MRF' and
      characterized. Gene CTN 0339 specifies the endonuclease R.TneDI, while
      CTN 0340 encodes the cognate DNA methyltransferase M.TneDI. Both
      enzymes were purified simply by heating the cell lysates of E. coli
      followed by centrifugation. The enzymes were active over a broad range
      of temperatures, from 42A degrees C to at least 77A degrees C, with the
      highest activities observed at 77A degrees C. R.TneDI cleaved at the
      center of the recognition sequence (CGa dagger'CG) and generated
      blunt-end cuts. Overexpression of R.TneDI in BL21(DE3) was confirmed by
      both SDS-PAGE and Western blotting.
AU  - Xu ZH
AU  - Han DM
AU  - Cao JJ
AU  - Saini U
PT  - Journal Article
TA  - Extremophiles
JT  - Extremophiles
SO  - Extremophiles 2011 15: 665-672.

PMID- 24699958
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Sphingobium sp. Strain BHC-A, Revealing Genes for the Degradation of Hexachlorocyclohexane.
PG  - e00254-14
AB  - Here, we report the draft genome sequence of Sphingobium sp. strain BHC-A, a lin  gene-based
      hexachlorocyclohexane (HCH)-degrading strain, isolated from soil that suffered long-term HCH
      contamination in an insecticide factory.
AU  - Xue C
AU  - Cao L
AU  - Zhang R
AU  - He J
AU  - Li S
AU  - Hong Q
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00254-14.

PMID- Not carried by PubMed...
VI  - 7
DP  - 1991
TI  - Enzymology of BamHI DNA methylase.
PG  - 13-20
AB  - The enzymology of BamHI DNA methylase has been studied.  The optimum pH is 7.8.
      It is unstable in heat treatment and dependent on K+ or Na+.  The Km is 7.69 x
      10-6 mol/L for SAM and the Ki is 7.33 x 10-4 mol/L in the presence of 1 mmol/L
      SAH by Lineweaver-Burke plot.  The two lines intersected at the ordinate on L-B
      plot.  This result shows that SAH is the competitive inhibitor for BamHI DNA
      methylase.  The study of substrate specificity for different DNA shows that the
      single-stranded M.L. DNA is the best substrate for this enzyme.  The enzyme
      activity was assayed in the presence of different metabolites such as cytosine,
      5-azacytosine, adenosine, 6-azacytosine, 5-azacytidine and 5-methylcytosine.
      The enzyme activity could be inhibited by divalent cations such as Mn2+, Mg2+,
      Zn2+, but was stimulated strongly by F-, WO3-/4, MoO2-/4.  Results from the
      chemical modification by iodoacetamide and protection by DTT or
      2-mercaptoethanol of this enzyme showed that the SH group is essential in
      active site of this enzyme.  It has been proved by HPLC that this enzyme
      transferred the methyl group from SAM to cytosine of DNA.  The methylation
      level of Micrococcus luteus (M.L.) DNA is 2.39% when it was incubated with
      BamHI DNA methylase for 30'.  It has been proved by electrophoresis on 1%
      agarose that the BamHI DNA methylase modified DNA cannot be cleaved by BamHI
      restriction endonuclease.
AU  - Xue J
AU  - He Z
PT  - Journal Article
TA  - Shengwu Huaxue Zazhi
JT  - Shengwu Huaxue Zazhi
SO  - Shengwu Huaxue Zazhi 1991 7: 13-20.

PMID- 9072080
VI  - 6
DP  - 1996
TI  - Effect of methylation on the electrophoretic mobility of chromosomal DNA in pulse-field agarose gels.
PG  - 43-47
AB  - Factors other than molecular weight are known to affect DNA electrophoretic mobility.  DNA
      methylation has been found to affect the curvature of DNA, causing anomalous mobility in
      polyacrylamide gels; the effect of methylation on the mobility of large DNA molecules in
      agarose gels was unknown.  Chromosomal DNA from Mycoplasma capricolum, a wall-less prokaryote
      which has a low intrinsic methylation rate, was methylated in agarose blocks by SssI
      methylase, a de novo methylase with a CpG recognition sequence.  (A surprising finding was
      that SssI methylase altered the structure of InCert, but not SeaKem Gold, agarose.)
      Restriction enzyme analysis was used to estimate the extent of CpG methylation.  DNA
      methylation was found to have no effect on the electrophoretic mobility of full-length
      chromosomal DNA (1,120 kbp) in agarose gels.  Therefore, methylation is not a source of error
      in PFGE-based size estimation for chromosomal DNA molecules less than 1.12 Mbp in agarose
      gels.
AU  - Xydas S
AU  - Lange CS
AU  - Phil D
AU  - Neimark HC
PT  - Journal Article
TA  - Appl. Theor. Electrophor.
JT  - Appl. Theor. Electrophor.
SO  - Appl. Theor. Electrophor. 1996 6: 43-47.

PMID- 25977433
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Erythrobacter vulgaris Strain O1, a Glycosyl Hydrolase-Producing Bacterium.
PG  - e00457-15
AB  - Erythrobacter vulgaris strain O1, a moderate halophile, was isolated from a beach in Johor,
      Malaysia. Here, we present the draft genome and suggest potential
      applications of this bacterium.
AU  - Yaakop AS
AU  - Chan CS
AU  - Kahar UM
AU  - Ee R
AU  - Chan KG
AU  - Goh KM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00457-15.

PMID- 26494670
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Yellow Pigmented Jeotgalibacillus alimentarius JY-13T, the First Halophile Strain of the Genus Jeotgalibacillus.
PG  - e01224-15
AB  - Jeotgalibacillus alimentarius JY-13(T) (=KCCM 80002(T) = JCM 10872(T)) is a moderate
      halophile. In 2001, this was the first strain of the newly proposed Jeotgalibacillus genus.
      The draft genome of J. alimentarius was found to consist  of 32 contigs (N50, 315,125 bp) with
      a total size of 3,364,745 bp. This genome information will be helpful for studies on
      pigmentation as well as applications for this bacterium.
AU  - Yaakop AS
AU  - Chan KG
AU  - Gan HM
AU  - Goh KM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01224-15.

PMID- 27313300
VI  - 4
DP  - 2016
TI  - Genome Sequences of Two Tunisian Field Strains of Avian Mycoplasma, M. meleagridis and M. gallinarum.
PG  - e00558-16
AB  - Mycoplasma meleagridis and Mycoplasma gallinarum are bacteria that affect birds,  but little
      is known about the genetic basis of their interaction with chickens
      and other poultry. Here, we sequenced the genomes of M. meleagridis strain
      MM_26B8_IPT and M. gallinarum strain Mgn_IPT, both isolated from chickens showing
      respiratory symptoms, poor growth, reduction in hatchability, and loss of
      production.
AU  - Yacoub E
AU  - Sirand-Pugnet P
AU  - Barre A
AU  - Blanchard A
AU  - Hubert C
AU  - Maurier F
AU  - Bouilhol E
AU  - Ben Abdelmoumen MB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00558-16.

PMID- 25999574
VI  - 3
DP  - 2015
TI  - Genome Sequence of Mycoplasma meleagridis Type Strain 17529.
PG  - e00484-15
AB  - Mycoplasma meleagridis is a prominent turkey bacterial pathogen associated with airsacculitis
      and reproductive disorders. Notwithstanding the economic losses
      caused by M. meleagridis, its genome has still not been sequenced. For a better
      understanding of its genetic background and pathogenicity mechanisms, we
      sequenced the genome of M. meleagridis type strain ATCC 25294.
AU  - Yacoub E
AU  - Sirand-Pugnet P
AU  - Blanchard A
AU  - Ben Abdelmoumen MB
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00484-15.

PMID- 25146132
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Erwinia amylovora Bacteriophage vB_EamM_Ea35-70.
PG  - e00413-14
AB  - The complete genome of an Erwinia amylovora bacteriophage, vB_EamM_Ea35-70 (Ea35-70), is
      271,084 bp, encodes 318 putative proteins, and contains one tRNA.
      Comparative analysis with other Myoviridae genomes suggests that Ea35-70 is
      related to the Phikzlikevirus genus within the family Myoviridae, since 26% of
      Ea35-70 proteins share homology to proteins in Pseudomonas phage phiKZ.
AU  - Yagubi AI
AU  - Castle AJ
AU  - Kropinski AM
AU  - Banks TW
AU  - Svircev AM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00413-14.

PMID- 23505045
VI  - 30
DP  - 2013
TI  - Chromosome painting in silico in a bacterial species reveals fine population structure.
PG  - 1454-1464
AB  - Identifying population structure forms an important basis for genetic and evolutionary
      studies. Most current methods to identify population structure have limitations in analyzing
      haplotypes and recombination across the genome. Recently, a method of chromosome painting in
      silico has been developed to overcome these shortcomings and has been applied to multiple
      human genome sequences. This method detects the
      genome-wide transfer of DNA sequence chunks through homologous recombination.
      Here, we apply it to the frequently recombining bacterial species Helicobacter pylori, which
      has infected Homo sapiens since their birth in Africa and shows wide phylogeographic
      divergence. Multiple complete genome sequences were analyzed including sequences from Okinawa,
      Japan, that we recently sequenced. The newer method revealed a finer population structure than
      revealed by a previous method that examines only MLST housekeeping genes or a phylogenetic
      network analysis of the core genome. Novel subgroups were found in Europe, Amerind and East
      Asia groups.  Examination of genetic flux showed some singleton strains to be hybrids of
      subgroups and revealed evident signs of population admixture in Africa, Europe, and parts of
      Asia. We expect this approach to further our understanding of intraspecific bacterial
      evolution by revealing population structure at a finer scale.
AU  - Yahara K
AU  - Furuta Y
AU  - Oshima K
AU  - Yoshida M
AU  - Azuma T
AU  - Hattori M
AU  - Uchiyama I
AU  - Kobayashi I
PT  - Journal Article
TA  - Mol. Biol. Evol.
JT  - Mol. Biol. Evol.
SO  - Mol. Biol. Evol. 2013 30: 1454-1464.

PMID- 17409094
VI  - 176
DP  - 2007
TI  - Evolution of DNA double-strand break repair by gene conversion: Coevolution between a phage and a restriction-modification system.
PG  - 513-526
AB  - The necessity to repair genome damage has been considered to be an immediate factor
      responsible for the origin of sex. Indeed, attack by a
      cellular restriction enzyme of invading DNA from several bacteriophages
      initiates recombinational repair by gene conversion if there is
      homologous DNA. In this work, we modeled the interaction between a
      bacteriophage and a bacterium carrying a restriction enzyme as
      antagonistic coevolution. We assume a locus on the bacteriophage genome
      has either a restriction-sensitive or a restriction-resistant allele,
      and another locus determines whether it is recombination/repair
      proficient or defective. A restriction break can be repaired by a
      co-infecting phage genome if one of them is recombination/repair
      proficient. We define the fitness of phage (resistant/sensitive and
      repair-positive/-negative) genotypes and bacterial
      (restriction-positive/-negative) genotypes by assuming random encounter
      of the genotypes, with given probabilities of single and double
      infections, and the costs of resistance, repair, and restriction. Our
      results show the evolution of the repair allele depends on b(1)/b(0),
      the ratio of the burst size b, under damage to host cell physiology
      induced by an unrepaired double-strand break to the default burst size
      b(0). It was not until this effect was taken into account that the
      evolutionary advantage of DNA repair became apparent.
AU  - Yahara K
AU  - Horie R
AU  - Kobayashi I
AU  - Sasaki A
PT  - Journal Article
TA  - Genetics
JT  - Genetics
SO  - Genetics 2007 176: 513-526.

PMID- 
VI  - 29
DP  - 2010
TI  - Evolution of selfish homing endonuclease genes in the absence of horizontal transfer.
PG  - 190-195
AB  - 
AU  - Yahara K
AU  - Kobayashi I
PT  - Journal Article
TA  - Saibo Kogaku
JT  - Saibo Kogaku
SO  - Saibo Kogaku 2010 29: 190-195.

PMID- 19837694
VI  - 106
DP  - 2009
TI  - Evolutionary maintenance of selfish homing endonuclease genes in the absence of horizontal transfer.
PG  - 18861-18866
AB  - Homing endonuclease genes are ``selfish' mobile genetic elements whose endonuclease promotes
      the spread of its own gene by creating a break at
      a specific target site and using the host machinery to repair the break
      by copying and inserting the gene at this site. Horizontal transfer
      across the boundary of a species or population within which mating
      takes place has been thought to be necessary for their evolutionary
      persistence. This is based on the assumption that they will become
      fixed in a host population, where opportunities of homing will
      disappear, and become susceptible to degeneration. To test this
      hypothesis, we modeled behavior of a homing endonuclease gene that
      moves during meiosis through double-strand break repair. We
      mathematically explored conditions for persistence of the homing
      endonuclease gene and elucidated their parameter dependence as phase
      diagrams. We found that, if the cost of the pseudogene is lower than
      that of the homing endonuclease gene, the 2 forms can persist in a
      population through autonomous periodic oscillation. If the cost of the
      pseudogene is higher, 2 types of dynamics appear that enable
      evolutionary persistence: bistability dependent on initial frequency or
      fixation irrespective of initial frequency. The prediction of long
      persistence in the absence of horizontal transfer was confirmed by
      stochastic simulations in finite populations. The average time to
      extinction of the endonuclease gene was found to be thousands of
      meiotic generations or more based on realistic parameter values. These
      results provide a solid theoretical basis for an understanding of these
      and other extremely selfish elements. POPULATION BIOLOGY
AU  - Yaharaa K
AU  - Fukuyo M
AU  - Sasaki A
AU  - Kobayashi I
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2009 106: 18861-18866.

PMID- 28798173
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Endophytic Bacillus aryabhattai Strain SQU-R12, Identified from Phoenix dactylifera L. Roots.
PG  - e00718-17
AB  - Bacillus aryabhattai strain SQU-R12 was isolated from date palm seedlings, where  it showed a
      growth-promoting capacity by being able to synthesize indole-3-acetic
      acid phytohormone and reduce ethylene biosynthesis by producing
      1-aminocyclopropane-1-carboxylic acid deaminase. The draft genome sequence of
      this strain is reported here.
AU  - Yaish MW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00718-17.

PMID- 27540071
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Endophytic Bacterium Enterobacter asburiae PDA134, Isolated from Date Palm (Phoenix dactylifera L.) Roots.
PG  - e00848-16
AB  - In this report, a draft of the Enterobacter asburiae strain PDA134 genome was sequenced. This
      bacterial strain was isolated from the root tissue of a date
      palm, where it has the ability to produce 1-aminocyclopropane-1-carboxylic acid
      (ACC) deaminase and indole-3-acetic acid (IAA) under salinity stress.
AU  - Yaish MW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00848-16.

PMID- 16232628
VI  - 88
DP  - 1999
TI  - Chlorella viruses as a source of novel enzymes.
PG  - 353-361
AB  - A special advantage has been conferred upon Chlorella cells as tools in biotechnology when
      viruses (Phycodnaviridae) infecting Chlorella cells
      were discovered and isolated. The viruses are large icosahedral
      particles (150-200 nm in diameter), containing a giant, 330-380 kbp
      long, linear dsDNA genome. Recently, the nucleotide sequence of the
      330,740-bp genome of PBCV-1, the prototype virus of Phycodnaviridae,
      was determined, and up to 702 open reading frames (ORFs) were
      identified along the genome. The possible genes present include those
      encoding a variety of enzymes involved in the modification of DNA, RNA,
      protein and polysaccharides as well as those involved in the metabolism
      of sugars, amino acids, lipids, nucleotides and nucleosides. Many of
      these genes are actually expressed during viral infection, with
      functional enzymes detected in the host cytoplasm or incorporated into
      the virion. The successful utilization of these viral enzymes as
      various DNA restriction and modification enzymes (Cvi enzymes) that are
      now commercially available is well documented. Also noteworthy are
      virion-associated chitinase and chitosanase activities that have
      potentially important applications in the recycling of natural
      resources. The virions of Chlorella viruses contain more than 50
      different structural proteins, ranging in size from 10 to 200 kDa. Some
      of these proteins may be replaced with useful foreign proteins using
      recombinant DNA technology. The proteins of interest can be recovered
      easily from the viral particles, and collected by centrifugation after
      complete lysis of the host Chlorella cells.
AU  - Yamada T
AU  - Chuchird N
AU  - Kawasaki T
AU  - Nishida K
AU  - Hiramatsu S
PT  - Journal Article
TA  - J. Biosci. Bioeng.
JT  - J. Biosci. Bioeng.
SO  - J. Biosci. Bioeng. 1999 88: 353-361.

PMID- Not included in PubMed...
VI  - 53
DP  - 1989
TI  - A new restriction endonuclease from Agrobacterium gelatinovorum, a marine agrobacterium (AgeI).
PG  - 1747-1749
AB  - Type II restriction endonucleases, which are indispensable for gene analyses
      and gene manipulation, have been recovered from prokaryotic cells such as those
      of bacteria and cyanobacteria.  We have been studying acetic acid bacteria from
      taxonomical, physiological and biochemical points of view.  The new restriction
      endonuclease ApaLI was reported in Acetobacter pasteurianus IFO 13753.  During
      the course of our screening of marine bacteria, we found a new restriction
      endonuclease, designated as AgeI, in Agrobacterium gelatinovorum IAM 12617.
      This paper describes its purification and properties and determination of its
      recognition sequence and cleavage site.
AU  - Yamada Y
AU  - Mizuno H
AU  - Sato H
AU  - Akagawa M
AU  - Yamasato K
PT  - Journal Article
TA  - Agric. Biol. Chem.
JT  - Agric. Biol. Chem.
SO  - Agric. Biol. Chem. 1989 53: 1747-1749.

PMID- Not included in PubMed...
VI  - 49
DP  - 1985
TI  - A new restriction endonuclease from Acetobacter pasteurianus (ApaI).
PG  - 3627-3629
AB  - Type II restriction endonucleases indispensable for gene manipulation and gene
      analyses have been recovered from procaryotic cells such as those of bacteria
      and cyanobacteria.  We have been studying acetic acid bacteria from the
      viewpoints of taxonomy, physiology, biochemistry and genetics.  During the
      course of our studies, we found a new type II restriction endonuclease,
      designated as ApaLI, in a strain of Acetobacter pasteurianus (Hansen 1879)
      Beijerinck 1916.  This communication describes its purification and properties
      and determination of its recognition sequence and cleavage sites in DNA
      molecules.
AU  - Yamada Y
AU  - Murakami M
PT  - Journal Article
TA  - Agric. Biol. Chem.
JT  - Agric. Biol. Chem.
SO  - Agric. Biol. Chem. 1985 49: 3627-3629.

PMID- Not included in PubMed...
VI  - 30
DP  - 1984
TI  - Distribution of Restriction Enzymes in Strains of Acetobacter (Gluconoacetobacter) Liquefaciens.
PG  - 309-312
AB  - Acetobacter (Gluconoacetobacter) liquefaciens was first described by ASAI as a
      species of the genus Gluconobacter. Three strains, G-1, AC-8, and U-4, were
      reported.  Concerning the taxonomic position, these strains were designated as
      pigment-producing strains of A. aceti because of their peritrichous
      flagellation and ability to oxidize acetate to carbon dioxide and water.  In
      contrast, Asai et al. stated their uniqueness in phenotypic features and
      designated them as 'intermediate.'  Subsequently, Yamada et al. found that
      these three strains and two other strains isolated by Komagata are
      distinguishable from A. aceti strains by their coenzyme Q or ubiquinone system;
      the five intermediate strains have Q-10[Q-9] whereas the A. aceti strains have
      Q-9[Q-8].  In Bergey's Manual 8th Edition, however, these 'anomalous' strains
      are classified as A. aceti subsp. liquefaciens.  The Approved Lists 1980
      included A. aceti subsp. liquefaciens (Asai 1935) De Ley and Frateur 1974.
      This subspecies was elevated to A. liquefaciens separate from A. aceti on the
      basis of the ubiquinone system, numerical analyses of phenotypic features and
      protein gel electrophoretic patterns of enzymes.  Recently, Yamada and Kondo
      have set up a new subgenus, Gluconoacetobacter and classified these strains as
      Acetobacter (Gluconoacetobacter) liquefaciens (Asai 1935) Gossele et al. 1983.
      In previous papers, the authors have purified two restriction enzymes of A.
      liquefaciens IAM 1834 and AJ 2881 to a homogeneous state and determined their
      recognition sequences and cleavage sites on DNA molecules.  The enzymes have
      been found to be isoschizomers of BamHI and PstI, respectively.  This paper
      describes distribution of restriction enzymes in the five strains mentioned
      above.
AU  - Yamada Y
AU  - Sasaki J
PT  - Journal Article
TA  - J. Gen. Appl. Microbiol.
JT  - J. Gen. Appl. Microbiol.
SO  - J. Gen. Appl. Microbiol. 1984 30: 309-312.

PMID- Not included in PubMed...
VI  - 53
DP  - 1989
TI  - The manganese ion strongly activates restriction endonuclease AatII from Acetobacter aceti IFO 3281.
PG  - 1745-1746
AB  - Type II restriction endonucleases are indispensable for gene analyses and gene
      manipulation, and their occurrence is widespread in the prokaryotic kingdom.
      We have been studying restriction endonucleases of acetic acid bacteria.
      During the course of our studies, restriction endonuclease ApaLI was found in
      Acetobacter pasteurianus IFO 13753.  Restriction endonuclease AatII was
      reported by Sugisaki et al. as a new enzyme from Acetobacter aceti IFO 3281.
      However, the characteristics of the enzyme have remained unclarified as yet
      except for its recognition sequence and cleavage site.  This paper reports that
      the enzyme purified to a homogeneous state is strongly activated on the
      addition of not Mg2+ but Mn2+.
AU  - Yamada Y
AU  - Sato H
PT  - Journal Article
TA  - Agric. Biol. Chem.
JT  - Agric. Biol. Chem.
SO  - Agric. Biol. Chem. 1989 53: 1745-1746.

PMID- Not included in PubMed...
VI  - 29
DP  - 1983
TI  - Purification, properties and recognition sequence of site-specific restriction endonuclease from "Acetobacter liquefaciens".
PG  - 157-166
AB  - A type II restriction endonuclease was purified from "Acetobacter liquefaciens"
      IAM 1834 by consecutive column chromatography on heparin-Sepharose CL-6B,
      DEAE-Sepharose CL-6B and Sephacryl S-400 superfine.  The purified enzyme was
      homogeneous on polyacrylamide gel disc electrophoresis.  The enzyme preparation
      was essentially free from other nuclease activity, as judged by constancy of a
      lambda DNA-digest electrophoretic pattern after prolonged incubation for 24 hr.
      The enzyme was optimally active at 37o at pH 7.5, and did not require NaCl,
      which rather inhibited its activity.  The recognition sequence for the enzyme
      was determined to be 5'-G-G-A-T-C-C-3', and the enzyme was found to cut between
      G and G in the sequence, being an isoschizomer of the endonuclease from
      "Bacillus amyloliquefaciens" H (Bam HI).
AU  - Yamada Y
AU  - Yoshioka H
AU  - Sasaki J
AU  - Tahara Y
PT  - Journal Article
TA  - J. Gen. Appl. Microbiol.
JT  - J. Gen. Appl. Microbiol.
SO  - J. Gen. Appl. Microbiol. 1983 29: 157-166.

PMID- 27469961
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Cyanobium sp. NIES-981, a Marine Strain Potentially Useful for Ecotoxicological Bioassays.
PG  - e00736-16
AB  - Cyanobium sp. NIES-981 is a marine cyanobacterium isolated from tidal flat sands  in Okinawa,
      Japan. Here, we report the complete 3.0-Mbp genome sequence of
      NIES-981, which is composed of a single chromosome, and its annotation. This
      sequence information may provide a basis for developing an ecotoxicological
      bioassay using this strain.
AU  - Yamaguchi H
AU  - Shimura Y
AU  - Suzuki S
AU  - Yamagishi T
AU  - Tatarazako N
AU  - Kawachi M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00736-16.

PMID- 29437104
VI  - 6
DP  - 2018
TI  - Improved Draft Genome Sequence of Microcystis aeruginosa NIES-298, a Microcystin-Producing Cyanobacterium from Lake Kasumigaura, Japan.
PG  - e01551-17
AB  - Microcystis aeruginosa is a globally well-known bloom-forming cyanobacterium. An  improved
      draft whole-genome sequence of M. aeruginosa NIES-298, which is a
      microcystin-producing strain isolated from Lake Kasumigaura, Japan, is published
      here. The genome comprises approximately 5.0 Mbp, with an average G+C content of
      42.6% and 4,537 predicted protein-coding genes.
AU  - Yamaguchi H
AU  - Suzuki S
AU  - Kawachi M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01551-17.

PMID- 29472345
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Microcystis aeruginosa NIES-87, a Bloom-Forming Cyanobacterium from Lake Kasumigaura, Japan.
PG  - e01596-17
AB  - Microcystis aeruginosa is a problematic cyanobacterium in freshwater lakes distributed
      worldwide. Here, we report the draft genome sequence of M. aeruginosa
      NIES-87, isolated from Lake Kasumigaura, Japan. The genome is approximately 4.9
      Mb in size, with an average G+C content of 42.9% and 4,355 predicted
      protein-coding genes.
AU  - Yamaguchi H
AU  - Suzuki S
AU  - Kawachi M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01596-17.

PMID- 27834696
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Microcystis aeruginosa NIES-98, a Non-Microcystin-Producing Cyanobacterium from Lake Kasumigaura, Japan.
PG  - e01187-16
AB  - Microcystis aeruginosa is a well-known bloom-forming cyanobacterium. We newly sequenced the
      whole genome of M. aeruginosa NIES-98, which is a
      non-microcystin-producing strain isolated from Lake Kasumigaura, Japan. The
      genome contains approximately 5.0 Mbp, with an average G+C content of 42.41% and
      5,140 predicted protein-coding genes.
AU  - Yamaguchi H
AU  - Suzuki S
AU  - Sano T
AU  - Tanabe Y
AU  - Nakajima N
AU  - Kawachi M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01187-16.

PMID- 26021928
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Microcystis aeruginosa NIES-2549, a Bloom-Forming Cyanobacterium from Lake Kasumigaura, Japan.
PG  - e00551-15
AB  - Microcystis aeruginosa NIES-2549 is a freshwater bloom-forming cyanobacterium isolated from
      Lake Kasumigaura, Japan. We report the complete 4.29-Mbp genome
      sequence of NIES-2549 and its annotation and discuss the genetic diversity of M.
      aeruginosa strains. This is the third genome sequence of M. aeruginosa isolated
      from Lake Kasumigaura.
AU  - Yamaguchi H
AU  - Suzuki S
AU  - Tanabe Y
AU  - Osana Y
AU  - Shimura Y
AU  - Ishida K
AU  - Kawachi M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00551-15.

PMID- 27198031
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of an Aldoxime Degrader, Rhodococcus sp. Strain YH3-3.
PG  - e00406-16
AB  - Rhodococcus sp. strain YH3-3 has been isolated as an (E)-pyridine-3-aldoxime degrader. Here,
      we report the draft genome sequence of this strain, with a size
      of 7,316,908 bp, average G+C content of 62.15%, and 7,281 predicted
      protein-coding sequences.
AU  - Yamaguchi T
AU  - Asano Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00406-16.

PMID- 25720679
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of an Aldoxime Degrader, Bacillus sp. OxB-1.
PG  - e00025-15
AB  - Bacillus sp. OxB-1 has been characterized as a strain that produces a new enzyme, aldoxime
      dehydratase, which catalyzes the dehydration of aldoxime to form nitrile. Here, its complete
      genome sequence (3,594,618 bp, with a GC content of 47.85%), comprising a circular chromosome,
      is announced.
AU  - Yamaguchi T
AU  - Asano Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00025-15.

PMID- 12228315
VI  - 70
DP  - 2002
TI  - Identification of the Staphylococcus aureus etd pathogenicity island which encodes a novel exfoliative toxin, ETD, and EDIN-B.
PG  - 5835-5845
AB  - We identified a novel pathogenicity island in Staphylococcus aureus which contains open
      reading frames (ORFs) similar to the exfoliative
      toxin (ET) gene, glutamyl endopeptidase gene, and edin-B gene in tandem
      and the phage resistance gene, flanked by hsdM, hsdS (restriction and
      modification system), and IS256. The protein encoded by the ET-like
      gene showed 40, 59, and 68% amino acid sequence identities with
      exfoliative toxin A (ETA), exfoliative toxin B (ETB), and
      Staphylococcus hyicus ETB (ShETB), respectively. When injected into
      neonatal mice, the recombinant protein derived from the ET-like gene
      induced exfoliation of the skin with loss of cell-to-cell adhesion in
      the upper part of the epidermis as observed in histological
      examinations, just as was found in neonatal mice injected with ETA or
      ETB. Western blot analysis indicated that the recombinant protein is
      serologically distinct from ETA and ETB. Therefore, the product encoded
      by this new ORF is a new ET member produced by S. aureus and is termed
      ETD. ETD did not induce blisters in 1-day-old chickens. In the skins of
      mice injected with ETD, cell surface staining of desmoglein 1 (Dsg1), a
      cadherin type cell-to-cell adhesion molecule in desmosomes, was
      abolished without affecting that of desmoglein 3 (Dsg3). Furthermore,
      in vitro incubation of the recombinant extracellular domains of Dsg1
      and Dsg3 with the recombinant protein demonstrated that both mouse and
      human Dsg1, but not Dsg3, were directly cleaved in a dose-dependent
      manner. These results demonstrate that ETD and ETA induce blister
      formation by identical pathophysiological mechanisms. Clinical strains
      positive for edin-B were suggested to be clonally associated, and all
      edin-B-positive strains tested were positive for etd. Among 18
      etd-positive strains, 12 produced ETD extracellularly. Interestingly,
      these strains are mainly isolated from other sources of infections and
      not from patients with bullous impetigo or staphylococcal scalded-skin
      syndrome. This strongly suggests that ETD might play a pathogenic role
      in a broader spectrum of bacterial infections than previously
      considered.
AU  - Yamaguchi T
AU  - Nishifuji K
AU  - Sasaki M
AU  - Fudaba Y
AU  - Aepfelbacher M
AU  - Takata T
AU  - Ohara M
AU  - Komatsuzawa H
AU  - Amagai M
AU  - Sugai M
PT  - Journal Article
TA  - Infect. Immun.
JT  - Infect. Immun.
SO  - Infect. Immun. 2002 70: 5835-5845.

PMID- 25477379
VI  - 43
DP  - 2015
TI  - High-resolution genetic analysis of the requirements for horizontal transmission  of the ESBL plasmid from Escherichia coli O104:H4.
PG  - 348-360
AB  - Horizontal dissemination of the genes encoding extended spectrum beta-lactamases  (ESBLs) via
      conjugative plasmids is facilitating the increasingly widespread
      resistance of pathogens to beta-lactam antibiotics. However, there is relatively
      little known about the regulatory factors and mechanisms that govern the spread
      of these plasmids. Here, we carried out a high-throughput, transposon insertion
      site sequencing analysis (TnSeq) to identify genes that enable the maintenance
      and transmission of pESBL, an R64 (IncI1)-related resistance plasmid that was
      isolated from Escherichia coli O104:H4 linked to a recent large outbreak of
      gastroenteritis. With a few exceptions, the majority of the genes identified as
      required for maintenance and transmission of pESBL matched those of their
      previously defined R64 counterparts. However, our analyses of the high-density
      transposon insertion library in pESBL also revealed two very short and linked
      regions that constitute a previously unrecognized regulatory system controlling
      spread of IncI1 plasmids. In addition, we investigated the function of the
      pESBL-encoded M.EcoGIX methyltransferase, which is also encoded by many other
      IncI1 and IncF plasmids. This enzyme proved to protect pESBL from restriction in
      new hosts, suggesting it aids in expanding the plasmid's host range.
      Collectively, our work illustrates the power of the TnSeq approach to enable
      rapid and comprehensive analyses of plasmid genes and sequences that facilitate
      the dissemination of determinants of antibiotic resistance.
AU  - Yamaichi Y
AU  - Chao MC
AU  - Sasabe J
AU  - Clark L
AU  - Davis BM
AU  - Yamamoto N
AU  - Mori H
AU  - Kurokawa K
AU  - Waldor MK
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2015 43: 348-360.

PMID- 28428303
VI  - 5
DP  - 2017
TI  - Genome Sequence of Microbacterium sp. Strain TPU 3598, a Lumichrome Producer.
PG  - e00204-17
AB  - We report here the genome sequence of Microbacterium sp. strain TPU 3598, previously described
      as a producer of lumichrome. The sequenced genome size is
      3,787,270 bp, the average G+C content is 68.39%, and 3,674 protein-coding
      sequences are predicted.
AU  - Yamamoto K
AU  - Asano Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00204-17.

PMID- 25189585
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Methanolinea tarda NOBI-1T, a Hydrogenotrophic Methanogen Isolated from Methanogenic Digester Sludge.
PG  - e00876-14
AB  - Here, we report a 2.0-Mb complete genome sequence of Methanolinea tarda NOBI-1(T), a
      methanogenic archaeon isolated from an anaerobic digested sludge.
      This is the first genome report of the genus Methanolinea isolate belonging to
      the family Methanoregulaceae, a recently proposed novel family within the order
      Methanomicrobiales.
AU  - Yamamoto K
AU  - Tamaki H
AU  - Cadillo-Quiroz H
AU  - Imachi H
AU  - Kyrpides N
AU  - Woyke T
AU  - Goodwin L
AU  - Zinder SH
AU  - Kamagata Y
AU  - Liu WT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00876-14.

PMID- 25189582
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Methanoregula formicica SMSPT, a Mesophilic Hydrogenotrophic Methanogen Isolated from a Methanogenic Upflow Anaerobic Sludge   Blanket Reactor.
PG  - e00870-14
AB  - Methanoregula formicica SMSP(T) is a mesophilic H2/formate-utilizing methanogenic archaeon and
      a representative of the family Methanoregulaceae, a recently
      proposed novel family within the order Methanomicrobiales. Here, we report a
      2.8-Mb complete genome sequence of this methanogenic archaeon.
AU  - Yamamoto K
AU  - Tamaki H
AU  - Cadillo-Quiroz H
AU  - Imachi H
AU  - Kyrpides N
AU  - Woyke T
AU  - Goodwin L
AU  - Zinder SH
AU  - Kamagata Y
AU  - Liu WT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00870-14.

PMID- 29097474
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Pseudonocardia sp. Strain N23, a 1,4-Dioxane-Degrading Bacterium.
PG  - e01240-17
AB  - Pseudonocardia sp. strain N23 is a 1,4-dioxane-degrading bacterium that is capable of
      utilizing 1,4-dioxane as the sole carbon and energy source. Here, we
      report the draft genome sequence of strain N23, with a size of 6.5 Mbp, to
      identify the genes associated with 1,4-dioxane degradation.
AU  - Yamamoto N
AU  - Inoue D
AU  - Kuroda M
AU  - Ike M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01240-17.

PMID- 29930068
VI  - 6
DP  - 2018
TI  - Single Circular Chromosome Identified from the Genome Sequence of the Vibrio cholerae O1 bv. El Tor Ogawa Strain V060002.
PG  - e00564-18
AB  - We report here the complete genome sequence of the Vibrio cholerae O1 bv. El Tor  Ogawa strain
      V060002, isolated in 1997. The data demonstrate that this clinical
      strain has a single chromosome resulting from recombination of two prototypical
      chromosomes.
AU  - Yamamoto S
AU  - Lee KI
AU  - Morita M
AU  - Arakawa E
AU  - Izumiya H
AU  - Ohnishi M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00564-18.

PMID- 9205837
VI  - 4
DP  - 1997
TI  - Construction of a contiguous 874-kb sequence of the Escherichia coli -K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features.
PG  - 91-113
AB  - The contiguous 874.423 base pair sequence corresponding to the 50.0-68.8 min region on the
      genetic map of the Escherichia coli K-12 (W3110) was constructed by the determination of DNA
      sequences in the 50.0-57.9 min region (360 kb) and two large (100 kb in all) and five short
      gaps in the 57.9-68.8 min region whose sequences had been registered in the DNA databases. We
      analyzed its sequence features and found that this region contained at least 894 potential
      open reading frames (ORFs), of which 346 (38.7%) were previously reported, 158 (17.7%) were
      homologous to other known genes, 232 (26.0%) were identical or similar to hypothetical genes
      registered in databases, and the remaining 158 (17.7%) showed no significant similarity to any
      other genes. A homology search of the ORFs also identified several new gene clusters. Those
      include two clusters of fimbrial genes, a gene cluster of three genes encoding homologues of
      the human long chain fatty acid degradation enzyme complex in the mitochondrial membrane, a
      cluster of at least nine genes involved in the utilization of ethanolamine, a cluster of the
      secondary set of 11 hyc genes participating in the formate hydrogenlyase reaction and a
      cluster of five genes coding for the homologues of degradation enzymes for aromatic
      hydrocarbons in Pseudomonas putida. We also noted a variety of novel genes, including two
      ORFs, which were homologous to the putative genes encoding xanthine dehydrogenase in the fly
      and a protein responsible for axonal guidance and outgrowth of the rat, mouse and nematode. An
      isoleucine tRNA gene, designated ileY, was also newly identified at 60.0 min.
AU  - Yamamoto Y et al
PT  - Journal Article
TA  - DNA Res.
JT  - DNA Res.
SO  - DNA Res. 1997 4: 91-113.

PMID- 23407331
VI  - 7
DP  - 2012
TI  - Complete genome sequence of the motile actinomycete Actinoplanes missouriensis 431(T) (= NBRC 102363(T)).
PG  - 294-303
AB  - Actinoplanes missouriensis Couch 1963 is a well-characterized member of the genus
      Actinoplanes, which is of morphological interest because its members typically
      produce sporangia containing motile spores. The sporangiospores are motile by
      means of flagella and exhibit chemotactic properties. It is of further interest
      that members of Actinoplanes are prolific sources of novel antibiotics, enzymes,
      and other bioactive compounds. Here, we describe the features of A. missouriensis
      431(T), together with the complete genome sequence and annotation. The 8,773,466
      bp genome contains 8,125 protein-coding and 79 RNA genes.
AU  - Yamamura H
AU  - Ohnishi Y
AU  - Ishikawa J
AU  - Ichikawa N
AU  - Ikeda H
AU  - Sekine M
AU  - Harada T
AU  - Horinouchi S
AU  - Otoguro M
AU  - Tamura T
AU  - Suzuki K
AU  - Hoshino Y
AU  - Arisawa A
AU  - Nakagawa Y
AU  - Fujita N
AU  - Hayakawa M
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 7: 294-303.

PMID- 
VI  - 92
DP  - 2003
TI  - Cloning and nucleotide sequence of the genes encoding restriction-modification system from acidophilic bacterium Acidocella facilis 22M.
PG  - 9-15
AB  - The gene encoding the Afa22MI restriction-modification system recognizing the sequence
      5'-CGATCG-3' was cloned from Acidocella facilis 22M and sequenced.  The cloned DNA fragment
      contained three genes encoding the Afa22MI methylase (M.Afa22MI), the putative restriction
      endonuclease Afa22MI (R.Afa22MI) and a very short patch repair endonuclease (Afa22MI vsr).  M.
      Afa22MI gene has the conserved motifs of C5-cytosine methyltransferase.  Afa22MI vsr gene was
      localized upstream of M.Afa22MI gene in opposite orientation, and an open reading frame of
      R.Afa22MI gene was localized downstream of M.Afa22Mi gene in the same orientation.  M.Afa22MI
      has about 63% sequence similarity to the entire amino acid sequence of M.XorII, and about 53%
      sequence similarity to the amino acid sequence for the variable region of M.XorII.  Afa22MI
      vsr has about 66% sequence similarity to the amino acid sequence of XorII vsr which was
      associated with M.XorII.
AU  - Yamaoka S
AU  - Tamura T
AU  - Takenobu H
AU  - Kojo T
AU  - Tanaka H
AU  - Inagaki K
PT  - Journal Article
TA  - Sci. Reports. Fac. Agric. Okayama Univ.
JT  - Sci. Reports. Fac. Agric. Okayama Univ.
SO  - Sci. Reports. Fac. Agric. Okayama Univ. 2003 92: 9-15.

PMID- 18281124
VI  - 165
DP  - 2008
TI  - Alternative splicing of the rice OsMET1 genes encoding maintenance DNA methyltransferase.
PG  - 1774-1782
AB  - While the Arabidopsis genome carries one copy of the methyltransferase 1 (MET1) gene for DNA
      methyltransferase, which is mainly responsible
      for maintaining CpG methylation, the rice genome bears two copies of
      the MET1 genes, OsMET1a and OsMET1b. The transcripts of OsMET1b
      accumulate more abundantly than those of OsMET1a in all of the tissues
      examined, and both genes actively transcribed at the callus, imbibed
      embryo, root, meristem, young panicle, anther, pistil, and endosperm,
      all of which contain actively dividing cells. The OsMET1a transcripts
      contain two 5'-untranslated exons and alternatively spliced 3'-terminal
      exons. The alternatively spliced transcripts consist of 14, 15, or 16
      exons, and all of them encode a putative protein of 1527 amino acids.
      While the 3'-terminal exon of OsMET1b is unique, alternative splicing
      occurs in the T-terminal regions, which comprise either exons
      containing 5'-untranslated regions or an exon bearing the initiation
      codon. Depending upon alternative usage of 5' exons by alternative
      splicing, the OsMET1b transcripts comprise 11, 12, 13, or 14 exons, and
      the former two and the tatter two longer transcripts encode putative
      proteins of 1486 and 1529 amino acids, respectively. Moreover, the 5'
      splicing patterns of OsMET1b can vary in different tissues. These
      findings are discussed with respect to the possible regulation of the
      OsMET1 genes.
AU  - Yamauchi T
AU  - Moritoh S
AU  - Johzuka-Hisatomi Y
AU  - Ono A
AU  - Terada R
AU  - Nakamura I
AU  - Iida S
PT  - Journal Article
TA  - J. Plant Physiol.
JT  - J. Plant Physiol.
SO  - J. Plant Physiol. 2008 165: 1774-1782.

PMID- 26494683
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Chlamydia trachomatis Strain 54, Isolated from the Urogenital Tract of a Male in Japan.
PG  - e01242-15
AB  - We report the draft genome sequence of Chlamydia trachomatis strain 54, isolated  from the
      urogenital tract of a male in Japan, with unique polymorphic membrane proteins. Detailed
      genomic analysis will aid our understanding of the selective pressures that lead to sexual
      differentiation in chlamydial adaptive evolution.
AU  - Yamazaki T
AU  - Matsuo J
AU  - Kikuchi M
AU  - Miyamoto K
AU  - Oka K
AU  - Takahashi M
AU  - Takahashi S
AU  - Okubo T
AU  - Yamaguchi H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01242-15.

PMID- 
VI  - 24
DP  - 2002
TI  - The true recognizing sequence of the restriction enzyme whose recognizing sequence is nonpalindromic.
PG  - 420-422
AB  - The recognizing sequence of restriction enzyme includes palindrome and nonpalindromic, and DNA
      is double helix complementary strands. So the
      recognizing sequences of palindrome enzyme in two strands of DNA were
      identical, and can be considered of one sequence. But for
      nonpalindromic restriction enzyme, the recognizing sequences of two
      strands of DNA were not identical. Therefore the true recognizing
      sequences are not only one. In this experiment, an enzyme cleavage
      reaction was carried out which confirmed that the true recognizing
      sites/sequences of non-palindromic enzyme are two instead of one.
AU  - Yan B-X
AU  - Li N
AU  - Wu C-X
PT  - Journal Article
TA  - Yichuan
JT  - Yichuan
SO  - Yichuan 2002 24: 420-422.

PMID- 28767643
VI  - 13
DP  - 2017
TI  - Bow-tie signaling in c-di-GMP: Machine learning in a simple biochemical network.
PG  - e1005677
AB  - Bacteria of many species rely on a simple molecule, the intracellular secondary
      messenger c-di-GMP (Bis-(3'-5')-cyclic dimeric guanosine monophosphate), to make
      a vital choice: whether to stay in one place and form a biofilm, or to leave it
      in search of better conditions. The c-di-GMP network has a bow-tie shaped
      architecture that integrates many signals from the outside world-the input
      stimuli-into intracellular c-di-GMP levels that then regulate genes for biofilm
      formation or for swarming motility-the output phenotypes. How does the
      'uninformed' process of evolution produce a network with the right input/output
      association and enable bacteria to make the right choice? Inspired by new data
      from 28 clinical isolates of Pseudomonas aeruginosa and strains evolved in
      laboratory experiments we propose a mathematical model where the c-di-GMP network
      is analogous to a machine learning classifier. The analogy immediately suggests a
      mechanism for learning through evolution: adaptation though incremental changes
      in c-di-GMP network proteins acquires knowledge from past experiences and enables
      bacteria to use it to direct future behaviors. Our model clarifies the elusive
      function of the ubiquitous c-di-GMP network, a key regulator of bacterial social
      traits associated with virulence. More broadly, the link between evolution and
      machine learning can help explain how natural selection across fluctuating
      environments produces networks that enable living organisms to make sophisticated
      decisions.
AU  - Yan J
AU  - Deforet M
AU  - Boyle KE
AU  - Rahman R
AU  - Liang R
AU  - Okegbe C
AU  - Dietrich LEP
AU  - Qiu W
AU  - Xavier JB
PT  - Journal Article
TA  - PLoS Comput. Biol.
JT  - PLoS Comput. Biol.
SO  - PLoS Comput. Biol. 2017 13: e1005677.

PMID- 15324086
VI  - 70
DP  - 2004
TI  - Near-field-magnetic-tweezer manipulation of single DNA molecules.
PG  - 011905
AB  - We have developed an instrument for micromanipulation of single
      DNA molecules end labeled with 3-microm-diameter paramagnetic particles. A
      small, permanent magnet that can be moved as close as 10 microm to the
      particle being manipulated can generate forces in excess of 200 pN,
      significantly larger than obtained in other recent "magnetic-tweezer"
      studies. Our instrument generates these forces in the focal plane of a
      microscope objective, allowing straightforward real-time observation of
      molecule extension with a position resolution of approximately 30 nm. We
      show how our magnetic manipulation system can be combined with
      manipulation and force measurement using glass micropipettes to allow
      rapid switching between measurements in fixed-force and fixed-extension
      ensembles. We demonstrate the use of our system to study formation of DNA
      loops by an enzyme which strongly binds two copies of a specific
      6-base-pair sequence.
AU  - Yan J
AU  - Skoko D
AU  - Marko JF
PT  - Journal Article
TA  - Phys. Rev. E Stat. Nonlin. Soft Matter Phys.
JT  - Phys. Rev. E Stat. Nonlin. Soft Matter Phys.
SO  - Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 2004 70: 011905.

PMID- 26847883
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a Pseudomonas aeruginosa Strain Able To Decompose N,N-Dimethyl Formamide.
PG  - e01609-15
AB  - Pseudomonas aeruginosa is a Gram-negative bacterium, which uses a variety of organic chemicals
      as carbon sources. Here, we report the genome sequence of the
      Cu1510 isolate from wastewater containing a high concentration of N,N-dimethyl
      formamide.
AU  - Yan L
AU  - Yan M
AU  - Xu L
AU  - Wei L
AU  - Zhang L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01609-15.

PMID- Not carried by PubMed...
VI  - 14
DP  - 1982
TI  - The restriction endonucleases from Bacillus.
PG  - 151-158
AB  - The activities of restriction endonucleases were found in 10 out of 66 strains
      of Bacillus isolated and examined in our country.  These enzymes were partially
      purified and their recognition sequences were characterized.  Bsp211I, Bsp226I
      and Bce71I are the isoschizomers of HaeIII.  Bsp211I and HaeIII have the same
      cleavage sites as indicated by the arrow in the sequence 5'-GG^CC-3'.  The
      purification procedure of Bsp211I is very simple and its yield is rather high.
      The recognition sequences of Bsp105I, Bsp67I, Bsp64I, Bsp74I and Bsp76I are the
      same as that of MboI, which recognizes the sequence 5'-^GATC-3', the arrow
      indicating the cleavage sites for Bsp 105I and Bsp67I.  While Bsp105I does not
      digest modified DNA, Bsp67I digests DNA whether the adenine residue is
      methylated or not.  Bsp63I and Bsp78I are isoschizomers of PstI, whose
      recognition sequence is 5'-CTGCA^G-3'.  The cutting sites of Bsp 63I and PstI
      are identical.
AU  - Yan P-F
AU  - Ye S-Y
AU  - Wang P-Z
AU  - Li Q-L
AU  - Lu Y-Y
AU  - Zhou B
PT  - Journal Article
TA  - Acta Biochim. Biophys. Sin.
JT  - Acta Biochim. Biophys. Sin.
SO  - Acta Biochim. Biophys. Sin. 1982 14: 151-158.

PMID- 29326216
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Prochlorococcus marinus Strain XMU1401, Isolated from the Western Tropical North Pacific Ocean.
PG  - e01431-17
AB  - Prochlorococcus marinus is the most abundant photosynthetic organism in the tropical and
      subtropical oceans. Here, we report the draft genome sequence of
      Prochlorococcus marinus XMU1401, which was isolated from the Western Tropical
      North Pacific Ocean.
AU  - Yan W
AU  - Zhang R
AU  - Wei S
AU  - Zeng Q
AU  - Xiao X
AU  - Wang Q
AU  - Yan H
AU  - Jiao N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01431-17.

PMID- 27999165
VI  - 7
DP  - 2016
TI  - Strain Prioritization and Genome Mining for Enediyne Natural Products.
PG  - e02104-16
AB  - The enediyne family of natural products has had a profound impact on modern
      chemistry, biology, and medicine, and yet only 11 enediynes have been
      structurally characterized to date. Here we report a genome survey of 3,400
      actinomycetes, identifying 81 strains that harbor genes encoding the enediyne
      polyketide synthase cassettes that could be grouped into 28 distinct clades based
      on phylogenetic analysis. Genome sequencing of 31 representative strains
      confirmed that each clade harbors a distinct enediyne biosynthetic gene cluster.
      A genome neighborhood network allows prediction of new structural features and
      biosynthetic insights that could be exploited for enediyne discovery. We
      confirmed one clade as new C-1027 producers, with a significantly higher C-1027
      titer than the original producer, and discovered a new family of enediyne natural
      products, the tiancimycins (TNMs), that exhibit potent cytotoxicity against a
      broad spectrum of cancer cell lines. Our results demonstrate the feasibility of
      rapid discovery of new enediynes from a large strain collection. IMPORTANCE:
      Recent advances in microbial genomics clearly revealed that the biosynthetic
      potential of soil actinomycetes to produce enediynes is underappreciated. A great
      challenge is to develop innovative methods to discover new enediynes and produce
      them in sufficient quantities for chemical, biological, and clinical
      investigations. This work demonstrated the feasibility of rapid discovery of new
      enediynes from a large strain collection. The new C-1027 producers, with a
      significantly higher C-1027 titer than the original producer, will impact the
      practical supply of this important drug lead. The TNMs, with their extremely
      potent cytotoxicity against various cancer cells and their rapid and complete
      cancer cell killing characteristics, in comparison with the payloads used in
      FDA-approved antibody-drug conjugates (ADCs), are poised to be exploited as
      payload candidates for the next generation of anticancer ADCs. Follow-up studies
      on the other identified hits promise the discovery of new enediynes, radically
      expanding the chemical space for the enediyne family.
AU  - Yan X
AU  - Ge H
AU  - Huang T
AU  - Hindra YD
AU  - Teng Q
AU  - Crnovcic I
AU  - Li X
AU  - Rudolf JD
AU  - Lohman JR
AU  - Gansemans Y
AU  - Zhu X
AU  - Huang Y
AU  - Zhao LX
AU  - Jiang Y
AU  - Van Nieuwerburgh F
AU  - Rader C
AU  - Duan Y
AU  - Shen B
PT  - Journal Article
TA  - MBio
JT  - MBio
SO  - MBio 2016 7: e02104-16.

PMID- 21399634
VI  - 43
DP  - 2011
TI  - Exome sequencing identifies somatic mutations of DNA methyltransferase gene DNMT3A in acute monocytic leukemia.
PG  - 309-315
AB  - Abnormal epigenetic regulation has been implicated in oncogenesis. We report here the
      identification of somatic mutations by exome sequencing
      in acute monocytic leukemia, the M5 subtype of acute myeloid leukemia
      (AML-M5). We discovered mutations in DNMT3A (encoding DNA
      methyltransferase 3A) in 23 of 112 (20.5%) cases. The DNMT3A mutants
      showed reduced enzymatic activity or aberrant affinity to histone H3 in
      vitro. Notably, there were alterations of DNA methylation patterns
      and/or gene expression profiles (such as HOXB genes) in samples with
      DNMT3A mutations as compared with those without such changes. Leukemias
      with DNMT3A mutations constituted a group of poor prognosis with
      elderly disease onset and of promonocytic as well as monocytic
      predominance among AML-M5 individuals. Screening other leukemia
      subtypes showed Arg882 alterations in 13.6% of acute myelomonocytic
      leukemia (AML-M4) cases. Our work suggests a contribution of aberrant
      DNA methyltransferase activity to the pathogenesis of acute monocytic
      leukemia and provides a useful new biomarker for relevant cases.
AU  - Yan XJ
AU  - Xu J
AU  - Gu ZH
AU  - Pan CM
AU  - Lu G
AU  - Shen Y
AU  - Shi JY
AU  - Zhu YM
AU  - Tang L
AU  - Zhang XW
AU  - Liang WX
AU  - Mi JQ
AU  - Song HD
AU  - Li KQ
AU  - Chen Z
AU  - Chen SJ
PT  - Journal Article
TA  - Nat. Genet.
JT  - Nat. Genet.
SO  - Nat. Genet. 2011 43: 309-315.

PMID- 23209197
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Enterobacter cloacae subsp. cloacae Strain 08XA1, a Fecal Bacterium of Giant Pandas.
PG  - 6928-6929
AB  - Enterobacter cloacae, a common pathogenic bacterium, is a Gram-negative bacillus. We analyzed
      the draft genome of Enterobacter cloacae subsp. cloacae strain 08XA1
      from the feces of a giant panda in China. Genes encoding a beta-lactamase and
      efflux pumps, as well as other factors, have been found in the genome.
AU  - Yan Y
AU  - Zhao CW
AU  - Zhang YZ
AU  - Zhang ZH
AU  - Pan GL
AU  - Liu WW
AU  - Ma QY
AU  - Hou R
AU  - Tan XM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6928-6929.

PMID- 29853505
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of n-Alkane-Utilizing Acinetobacter sp. Strain BS1, Isolated from Ethane Oxidation Culture.
PG  - e00465-18
AB  - Here, we report the draft whole-genome sequence of a bacterial strain, Acinetobacter sp.
      strain BS1, isolated from black soil during ethane oxidation
      culture. Medium- or long-chain alkane oxidation-related genes were identified;
      however, the short-chain alkane monooxygenase was not detected.
AU  - Yan YW
AU  - Zhang PP
AU  - Zhu T
AU  - Quan ZX
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00465-18.

PMID- 12359337
VI  - 1577
DP  - 2002
TI  - The human DNA methyltransferases DNMT3A and DNMT3B have two types of promoters with different CpG contents.
PG  - 457
AB  - DNA modification that is established by de novo methylation is involved in the epigenetic
      control of genome functions. The DNMT3A and DNMT3B genes encode putative de novo
      methyltransferases. In this paper, we investigated the transcriptional regulatory regions of
      the human DNMT3A and DNMT3B genes. We found that the DNMT3A and DNMT3B genes have multiple
      transcriptional start points (TSPs) that are separated on the chromosome and the expressions
      of these genes are controlled by multiple promoters. The DNMT3A gene has at least four TSPs
      and the expression is controlled by three different promoters. All three promoters lack
      typical TATA sequences adjacent to the TSPs. Two of them bear CpG-rich promoters and the other
      a CpG-poor promoter. The DNMT3B gene has at least two TSPs which exist in different exons and
      the expression is controlled by different promoters. Both promoter regions of the DNMT3B gene
      lack typical TATA sequences, where one promoter contains a CpG-rich area near the TSP, the
      other promoter is CpG-poor. Together with the data that the human DNMT1 gene has both CpG-rich
      and CpG-poor promoters, it is suggested that transcriptional regulation by two types of
      promoters, CpG-rich and CpG-poor, might be common characteristics in the DNMT gene family.
AU  - Yanagisawa Y
AU  - Ito E
AU  - Yuasa Y
AU  - Maruyama K
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 2002 1577: 457.

PMID- 
VI  - 0
DP  - 1996
TI  - The mutational burden of 5-methylcytosine.
PG  - 77-94
AB  - The importance of the epigenetic modification of cytosine to 5-methylcytosine is discussed in
      other chapters of this volume.  In this chapter, we address the heavy mutational burden
      induced by the methylation of C at CpG dinucleotides, which is the price that must be paid for
      having a m5C epigenetic system.  The mutability of m5C to thymine has presumably led to a
      depletion of the CpG dinucleotide in the mammalian genome over the course of evolution.
      Furthermore, m5C residues, which comprise only about 1% of the human genome, account for about
      30% of the base substitution mutations found in genetic disease and 25% of the mutations found
      in tumor suppressor genes.  The mutability of m5C was first demonstrated in Escherichia coli.
      Cytosine bases that were methylated in the E. coli lacI gene were found to be hot spots for
      spontaneous base substitution mutations, and the hot spots disappeared when the same sites
      were unmethylated.  It was speculated that the reason for this increase was that whereas C
      deaminates to uracil, m5C deaminates to T, which is a normal DNA base and therefore inherently
      more difficult to repair.  This mechanism of DNA mutation is unique in that it is not induced
      by exogenous chemicals and it occurs in nonreplicating DNA.  The deamination of m5C is a
      first-order chemical process, which is consistent with the fact that deamination occurs on
      both the transcribed and nontranscribed strand of DNA with equal probability.
AU  - Yang AS
AU  - Jones PA
AU  - Shibata A
PT  - Journal Article
TA  - Epigenetic Mechanisms of Gene Regulation
JT  - Epigenetic Mechanisms of Gene Regulation
SO  - Epigenetic Mechanisms of Gene Regulation 1996 0: 77-94.

PMID- Not carried by PubMed...
VI  - 36
DP  - 1995
TI  - DNA (cytosine-5) methyltransferase blocks DNA repair.
PG  - 538
AB  - the CpG dinucleotide is markedly underrepresented in the human genome, yet is the site of
      about one third of all point mutations found in the germline and in cancer. The hydrolytic
      deamination of 5-methylcytosine (5mC) to thymine (T) is believed to be responsible for the
      increased mutability of the CpG dinucleotide. We have previously shown an alternate possible
      mechanism in which HpaII DNA-(cytosine-5) methyltransferase (M.HpaII), a bacterial enzyme
      which carries out methylation by a similar mechanism of action to human methyltransferase, can
      enzymatically deaminate cytosine (C) to uracil (U) in DNA. Both the hydrolytic deamination of
      5mC to T and enzymatic deamination of C to U create premutagenic DNA mismatches (G:U and G:T)
      with the guanine (G) originally paired to the original C. Surprisingly, we found that
      methyltransferase has a higher affinity for these mismatches than for the normal target G:C.
      Methyltransferase was also shown to transfer a methyl group to the 5-position of U creating T,
      presenting a new possible mechanism for C to T transition mutations. This binding by
      methyltransferase prevented the repair of G:U mismatches by uracil DNA glycosylase in vitro.
      Mutant forms of M.HhaI which bind to the target sequence but lack catalytic activity when
      expressed in E. coli bestowed a mutator phenotype presumably due to the blockage of DNA
      repair.
AU  - Yang AS
AU  - Shen J-C
AU  - Zingg J-M
AU  - Mi S
AU  - Jones PA
PT  - Journal Article
TA  - Proc. Amer. Assoc. Cancer Res.
JT  - Proc. Amer. Assoc. Cancer Res.
SO  - Proc. Amer. Assoc. Cancer Res. 1995 36: 538.

PMID- 7753629
VI  - 23
DP  - 1995
TI  - HhaI and HpaII DNA methyltransferases bind DNA mismatches, methylate uracil and block DNA repair.
PG  - 1380-1387
AB  - The hydrolytic deamination of 5-methylcytosine (5-mC) to thymine (T) is believed to be
      responsible for the high mutability of the CpG dinucleotide in DNA. We have shown a possible
      alternate mechanism for mutagenesis at CpG in which HpaII DNA-(cytosine-5) methyltransferase
      (M.HpaII) can enzymatically deaminate cytosine (C) to uracil (U) in DNA. Both the hydrolytic
      deamination of 5-mC and enzymatic deamination of C create premutagenic DNA mismatches (G:U and
      G:T) with the guanine (G) originally paired to the normal C. Surprisingly, we found that
      DNA-(cytosine-5) methyltransferases have higher affinities for these DNA mismatches than for
      their normal G:C targets and are capable of transferring a methyl group to the 5-position of
      U, creating T at low efficiencies. This binding by methyltransferase to mismatches at the
      recognition site prevented repair of G:U mismatches by uracil DNA glycosylase in vitro.
AU  - Yang AS
AU  - Shen J-C
AU  - Zingg J-M
AU  - Mi S
AU  - Jones PA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1995 23: 1380-1387.

PMID- 23766403
VI  - 1
DP  - 2013
TI  - Whole-Genome Sequence of Microcystis aeruginosa TAIHU98, a Nontoxic Bloom-Forming Strain Isolated from Taihu Lake, China.
PG  - e00333-13
AB  - Microcystis aeruginosa is a dominant bloom-forming cyanobacterium in many freshwater lakes.
      This report describes the first whole-genome sequence of the
      nontoxic strain of M. aeruginosa TAIHU98, which was isolated from Taihu Lake in
      eastern China.
AU  - Yang C
AU  - Zhang W
AU  - Ren M
AU  - Song L
AU  - Li T
AU  - Zhao J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00333-13.

PMID- 7993918
VI  - 33
DP  - 1994
TI  - DNA cleavage by NaeI: protein purification, rate-limiting step, and accuracy.
PG  - 14918-14925
AB  - NaeI endonuclease must bind two DNA sites for cleavage to occur. NaeI was purified to apparent
      homogeneity and used to determine the rate-limiting step for DNA cleavage and to measure
      NaeI's specificity for its cognate recognition site. Steady-state cleavage by NaeI in the
      presence of effector DNA (activated) gave values of 0.045s-1 and 10 nM for kcat and KM for M13
      DNA substrate, respectively, but values of 0.4s-1 and 170 nM, respectively, for an M13 DNA
      fragment substrate. Single-turnover cleavage of M13 DNA cleavage by NaeI showed an initial
      burst of substrate cleavage that was proportional to NaeI concentration, implying that product
      release is rate-limiting for turnover of NaeI. The NaeI effector and substrate binding sites
      were found to prefer cognate over noncognate sequences by 1000-fold and at least 40-500-fold,
      respectively. kcat for noncognate recognition sequence was at least 10/6-fold lower than that
      for cognate. The specificity for activated NaeI, as measured by kcat/KM, for noncognate
      recognition sequence was 10/8-fold lower than that for cognate, and over 10/11-fold lower when
      the decreased affinity for noncognate sequence at the effector binding site was taken into
      account. This specificity is approximately 10/4-fold larger than for any other restriction
      enzyme measured.
AU  - Yang CC
AU  - Baxter BK
AU  - Topal MD
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1994 33: 14918-14925.

PMID- 1390742
VI  - 31
DP  - 1992
TI  - Nonidentical DNA-binding sites of endonuclease NaeI recognize different families of sequences flanking the recognition site.
PG  - 9657-9664
AB  - NaeI endonuclease uses a two-site binding mechanism to cleave substrate DNA: reaction-rate
      studies imply that occupancy of the second DNA site causes an allosteric change in the protein
      that enables DNA cleavage at the first site [Conrad, M., & Topal, M.D. (1989) Proc. Natl.
      Acad. Sci. U.S.A. 86, 9707-9711]. Measurements of relative binding affinities for 14-base-pair
      DNA fragments containing the NaeI recognition sequence GCCGGC and various flanking sequencs
      showed that the two DNA-binding sites are not identical. G-C-rich flanking sequences were
      preferred by the activator binding site, whereas A-T-rich flanking sequences were preferred by
      the substrate binding site: GGGTGCCGGCAGGG was preferred 8-fold more by the activator site but
      14-fold less by the substrate site than TTTCGCCGGCGTTT. Substitution of pyrimidine or
      7-deazapurine for purine immediately 3'to GCCGGC reduced DNA affinity for only the activator
      site by up to 26-fold, implying that the activator DNA-binding site requires N-7 base contacts
      immediately flanking GCCGGC. The implications of nonidentical DNA-binding sites, one of which
      binds a specific DNA site to allosterically activate the other, are discussed.
AU  - Yang CC
AU  - Topal MD
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1992 31: 9657-9664.

PMID- 25676767
VI  - 3
DP  - 2015
TI  - A17, the First Sequenced Strain of Lactococcus lactis subsp. cremoris with Potential Immunomodulatory Functions.
PG  - e01563-14
AB  - Lactococcus lactis subsp. cremoris A17, isolated from Taiwan fermented cabbage, is the first
      sequenced strain of L. lactis subsp. cremoris with immunomodulatory
      activity and antiallergic functions. The resulting A17 draft genome contains
      2,679,936 bp and indicates that A17 is a potential exopolysaccharide-producing
      strain without any known virulence gene.
AU  - Yang CH
AU  - Wu CC
AU  - Cheng WS
AU  - Chung MC
AU  - Tsai YC
AU  - Chang CH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01563-14.

PMID- 16275786
VI  - 33
DP  - 2005
TI  - Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery.
PG  - 6445-6458
AB  - The Shigella bacteria cause bacillary dysentery, which remains a significant threat to public
      health. The genus status and species
      classification appear no longer valid, as compelling evidence indicates
      that Shigella, as well as enteroinvasive Escherichia coli, are derived
      from multiple origins of E.coli and form a single pathovar. Nevertheless,
      Shigella dysenteriae serotype 1 causes deadly epidemics but Shigella
      boydii is restricted to the Indian subcontinent, while Shigella flexneri
      and Shigella sonnei are prevalent in developing and developed countries
      respectively. To begin to explain these distinctive epidemiological and
      pathological features at the genome level, we have carried out comparative
      genomics on four representative strains. Each of the Shigella genomes
      includes a virulence plasmid that encodes conserved primary virulence
      determinants. The Shigella chromosomes share most of their genes with that
      of E.coli K12 strain MG1655, but each has over 200 pseudogenes, 300
      approximately 700 copies of insertion sequence (IS) elements, and numerous
      deletions, insertions, translocations and inversions. There is extensive
      diversity of putative virulence genes, mostly acquired via
      bacteriophage-mediated lateral gene transfer. Hence, via convergent
      evolution involving gain and loss of functions, through
      bacteriophage-mediated gene acquisition, IS-mediated DNA rearrangements
      and formation of pseudogenes, the Shigella spp. became highly specific
      human pathogens with variable epidemiological and pathological features.
AU  - Yang F et al
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2005 33: 6445-6458.

PMID- 27811088
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Streptococcus agalactiae Serotype Ia Strain M19, a Multidrug-Resistant Isolate from a Cow with Bovine Mastitis.
PG  - e01093-16
AB  - Streptococcus agalactiae is a major contagious pathogen causing bovine mastitis worldwide. We
      report here the draft sequence of S. agalactiae Ia strain M19, a
      multidrug-resistant isolate from a bovine mastitis case in Ningxia Hui autonomous
      region, China.
AU  - Yang F
AU  - Li H
AU  - Zhang S
AU  - Wang X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01093-16.

PMID- 21742877
VI  - 193
DP  - 2011
TI  - Genome Sequence of Mycoplasma ovipneumoniae Strain SC01.
PG  - 5018
AB  - Mycoplasma ovipneumoniae is associated with chronic non-progressive pneumonia in both sheep
      and goats. Studies concerning its molecular
      pathogenesis, genetic analysis and vaccine development have been hindered
      due to limited genomic information. Here, we announce the first complete
      genome sequence of this organism.
AU  - Yang F
AU  - Tang C
AU  - Wang Y
AU  - Zhang H
AU  - Yue H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5018.

PMID- 25951858
VI  - 65
DP  - 2015
TI  - Novibacillus thermophilus gen. nov., sp. nov., a Gram-staining-negative and moderately thermophilic member of the family Thermoactinomycetaceae.
PG  - 2591-2597
AB  - Two Gram-staining-negative, facultatively anaerobic bacterial strains, SG-1T and
      SG-2, were isolated from a saline soil sample and a compost sample, respectively.
      The cells were non-motile rods that occurred singly or in chains, and endospores
      were not observed under tested growth conditions. Optimum growth occurred at 50
      degrees C, pH 7.5-8.0 and with 5-7 % (w/v) NaCl. The DNA G+C content was
      49.5-50.5 mol%. The strains contained MK-7 as the predominant menaquinone and
      iso-C15 : 0 and anteiso-C15 : 0 as the major fatty acids. The polar lipids
      consisted mainly of diphosphatidylglycerol and phosphatidylglycerol. The
      cell-wall peptidoglycan type was A1gamma (meso-DAP direct). Phylogenetic analyses
      revealed that the new isolates belonged to the family Thermoactinomycetaceae,
      exhibiting low 16S rRNA gene sequence similarity (90.8-91.3 %) to the nearest
      type strain, Mechercharimyces asporophorigenens YM11-542T, and formed a
      well-supported lineage that was clearly distinguished from all currently
      described genera in this family. Based on our polyphasic taxonomic
      characterization, we propose that strains SG-1T and SG-2 represent a novel genus
      and species within the family Thermoactinomycetaceae, for which we propose the
      name Novibacillus thermophilus gen. nov., sp. nov. The type strain of
      Novibacillus thermophilus is SG-1T ( = KCTC 33118T = CGMCC 1.12771T).
AU  - Yang G
AU  - Chen J
AU  - Zhou S
PT  - Journal Article
TA  - Int. J. Syst. Evol. Microbiol.
JT  - Int. J. Syst. Evol. Microbiol.
SO  - Int. J. Syst. Evol. Microbiol. 2015 65: 2591-2597.

PMID- 26634019
VI  - 10
DP  - 2015
TI  - Genome sequence of a dissimilatory Fe(III)-reducing bacterium Geobacter soli type strain GSS01(T).
PG  - 118
AB  - Strain GSS01(T) (=KCTC 4545=MCCC 1 K00269) is the type strain of the species Geobacter soli.
      G. soli strain GSS01(T) is of interest due to its ability to
      reduce insoluble Fe(III) oxides with a wide range of electron donors. Here we
      describe some key features of this strain, together with the whole genome
      sequence and annotation. The genome of size 3,657,100 bp contains 3229
      protein-coding and 54 RNA genes, including 2 16S rRNA genes. The genome of strain
      GSS01(T)contains 76 predicted cytochrome genes, 24 pilus assembly protein genes
      and several other genes, which were proposed to be related to the reduction of
      insoluble Fe(III) oxides. The genes associated with the electron donors and
      acceptors of strain GSS01(T) were predicted in the genome. Information gained
      from its sequence will be relevant to the future elucidation of extracellular
      electron transfer mechanism during the reduction of Fe(III) oxides.
AU  - Yang G
AU  - Chen S
AU  - Zhou S
AU  - Liu Y
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 118.

PMID- 27153808
VI  - 66
DP  - 2016
TI  - Desulfotomaculum ferrireducens sp. nov., a moderately thermophilic sulfate-reducing and dissimilatory Fe(III)-reducing bacterium isolated from compost.
PG  - 3022-3028
AB  - A novel dissimilatory Fe(III)-reducing bacterium, designated strain GSS09T, was
      isolated from a compost sample by using a solid medium containing acetate and
      ferrihydrite as electron donor and electron acceptor, respectively. Cells of
      strain GSS09T were anaerobic, Gram-stain-positive, motile, endospore-forming and
      rod-shaped. Growth occurred at 30-55 degrees C (optimum 50 degrees C), at pH
      6.5-9.0 (optimum pH 7.5) and in the presence of 0-3 % (w/v) NaCl (optimum 1 %).
      Both sulfur compounds such as sulfate, sulfite and thiosulfate and Fe(III) oxides
      such as ferrihydrite could be utilized as electron acceptors. Phylogenetic
      analysis based on 16S rRNA gene sequences revealed that strain GSS09T was related
      closely to Desulfotomaculum hydrothermale Lam5T (94.5 % sequence similarity). The
      major fatty acids were C16 : 0 and C16 : 1omega7c/C16 : 1omega6c. The G+C content
      of the genomic DNA was 49.1 mol%. On the basis of phylogenetic analysis,
      phenotypic characterization and physiological tests, strain GSS09T is considered
      to represent a novel species of the genus Desulfotomaculum, for which the name
      Desulfotomaculum ferrireducens sp. nov. is proposed. The type strain is GSS09T
      (=KCTC 15523T=MCCC 1K01254T).
AU  - Yang G
AU  - Guo J
AU  - Zhuang L
AU  - Yuan Y
AU  - Zhou S
PT  - Journal Article
TA  - Int. J. Syst. Evol. Microbiol.
JT  - Int. J. Syst. Evol. Microbiol.
SO  - Int. J. Syst. Evol. Microbiol. 2016 66: 3022-3028.

PMID- 26941140
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Shiga Toxin-Negative Escherichia coli O157:H7 Strain C1-057, Isolated from Feedlot Cattle.
PG  - e00049-16
AB  - Escherichia coli O157:H7 is one of the major foodborne pathogens in the United States. We
      isolated a variant Shiga toxin-negative E. coli O157:H7 strain from
      feedlot cattle. We report here the draft genome sequence of this isolate,
      consisting of a chromosome of ~4.8 Mb and two plasmids of ~96 kb and ~14 kb.
AU  - Yang H
AU  - Carlson B
AU  - Geornaras I
AU  - Woerner D
AU  - Sofos J
AU  - Belk K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00049-16.

PMID- 10671447
VI  - 182
DP  - 2000
TI  - Characterization of a thermostable DNA glycosylase specific for U/G and T/G mismatches from the hyperthermophilic archaeon Pyrobaculum aerophilum.
PG  - 1272-1279
AB  - U/G and T/G mismatches commonly occur due to spontaneous deamination of cytosine and
      5-methylcytosine in double-stranded DNA. This mutagenic
      effect is particularly strong for extreme thermophiles, since the
      spontaneous deamination reaction is much enhanced at high temperature.
      Previously, a U/G and T/G mismatch-specific glycosylase (Mth-MIG) was
      found on a cryptic plasmid of the archaeon Methanobacterium
      thermoautotrophicum, a thermophile with an optimal growth temperature of
      65 degrees C. We report characterization of a putative DNA glycosylase
      from the hyperthermophilic archaeon Pyrobaculum aerophilum, whose optimal
      growth temperature is 100 degrees C. The open reading frame was first
      identified through a genome sequencing project in our laboratory. The
      predicted product of 230 amino acids shares significant sequence homology
      to [4Fe-4S]-containing Nth/MutY DNA glycosylases. The histidine-tagged
      recombinant protein was expressed in Escherichia coli and purified. It is
      thermostable and displays DNA glycosylase activities specific to U/G and
      T/G mismatches with an uncoupled AP lyase activity. It also processes
      U/7,8-dihydro-oxoguanine and T/7,8-dihydro-oxoguanine mismatches. We
      designate it Pa-MIG. Using sequence comparisons among complete bacterial
      and archaeal genomes, we have uncovered a putative MIG protein from
      another hyperthermophilic archaeon, Aeropyrum pernix. The unique conserved
      amino acid motifs of MIG proteins are proposed to distinguish MIG proteins
      from the closely related Nth/MutY DNA glycosylases.
AU  - Yang H
AU  - Fitz-Gibbon S
AU  - Marcotte EM
AU  - Tai JH
AU  - Hyman EC
AU  - Miller JH
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2000 182: 1272-1279.

PMID- 23558536
VI  - 1
DP  - 2013
TI  - Whole-Genome Shotgun Assembly and Analysis of the Genome of Streptomyces mobaraensis DSM 40847, a Strain for Industrial Production of Microbial  Transglutaminase.
PG  - e0014313
AB  - Here, we report the draft annotated genome sequence of Streptomyces mobaraensis strain DSM
      40847, which is used in industry to produce microbial
      transglutaminase. The genome sequence will allow for the characterization of the
      molecular mechanisms underlying the beneficial properties of this organism.
AU  - Yang H
AU  - He T
AU  - Wu W
AU  - Zhu W
AU  - Lu B
AU  - Sun W
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0014313.

PMID- 21994923
VI  - 193
DP  - 2011
TI  - Genome Sequence of Escherichia coli XH140A, Which Produces L-Threonine.
PG  - 6090-6091
AB  - Here we report the draft annotated genome sequence of Escherichia coli XH140A, which is used
      to produce l-threonine in industry. The genome
      sequence will allow the characterization of the molecular mechanisms
      underlying its beneficial properties.
AU  - Yang H
AU  - Liao Y
AU  - Wang B
AU  - Lin Y
AU  - Pan L
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6090-6091.

PMID- 22038967
VI  - 193
DP  - 2011
TI  - Draft Genome Sequence of Escherichia coli XH001, a Producer of L-Threonine in Industry.
PG  - 6406-6407
AB  - l-Threonine has been widely used as a supplement in the food, pharmaceutical, and cosmetic
      industries. Here, we present a high-quality
      draft annotated genome sequence of Escherichia coli XH001, a producer of
      l-threonine in industry. Its genome and plasmid sequence will provide
      clues about the molecular mechanisms underlying its beneficial properties.
AU  - Yang H
AU  - Liao Y
AU  - Wang B
AU  - Lin Y
AU  - Pan L
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 6406-6407.

PMID- 21914895
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Bacillus amyloliquefaciens XH7, Which Exhibits Production of Purine Nucleosides.
PG  - 5593-5594
AB  - Here, we report the complete annotated genome sequence of Bacillus amyloliquefaciens XH7,
      which is used to produce purine nucleosides in
      industry. The genome sequence will allow for the characterization of the
      molecular mechanisms underlying its beneficial properties.
AU  - Yang H
AU  - Liao Y
AU  - Wang B
AU  - Lin Y
AU  - Pan L
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5593-5594.

PMID- 24744320
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Streptomyces sp. Strain PRh5, a Novel Endophytic Actinomycete Isolated from Dongxiang Wild Rice Root.
PG  - e00012-14
AB  - Here, we report the draft genome sequence of Streptomyces sp. strain PRh5 (China  Center for
      Type Culture Collection [CCTCC] number 2013487), which is used to produce nigericin and
      nocardamine. The genome sequence will allow for the characterization of the molecular
      mechanisms underlying its beneficial properties.
AU  - Yang H
AU  - Zhang Z
AU  - Yan R
AU  - Wang Y
AU  - Zhu D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00012-14.

PMID- 9233626
VI  - 159
DP  - 1997
TI  - Effect of mitogenic stimulation and DNA methylation on human T cell DNA methyltransferase expression and activity.
PG  - 1303-1309
AB  - DNA methylation, a mechanism modifying gene expression, is mediated in part by the enzyme DNA
      methyltransferase.  Reduced levels of T cell DNA methyltransferase have been observed in
      lupus-like diseases, and increased levels have been reported in malignancies.  Little is known
      concerning the regulation of human DNA methyltransferase.  In this report we demonstrate that
      mitogenic T cell stimulation causes an increase in DNA methyltransferase mRNA and enzyme
      activity.  We also show that pharmacologic inhibition of T cell DNA methylation causes an
      increase in the rate of DNA methyltransferase mRNA transcription and a corresponding increase
      in mRNA levels and enzyme activity.  This suggests that DNA methyltransferase is itself
      regulated in part by DNA methylation status, possibly representing a feedback mechanism.  DNA
      methylation inhibition also resulted in an increase in Ha-ras and c-jun mRNA levels,
      overexpression of which increases DNA methyltransferase in murine systems.  These results thus
      identify two mechanisms regulating levels of human T cell DNA methyltransferase and raise the
      possibility that abnormalities in either could contribute to disorders associated with altered
      DNA methylation.
AU  - Yang J
AU  - Deng C
AU  - Hemati N
AU  - Hanash SM
AU  - Richardson BC
PT  - Journal Article
TA  - J. Immunol.
JT  - J. Immunol.
SO  - J. Immunol. 1997 159: 1303-1309.

PMID- 14705785
VI  - 322
DP  - 2003
TI  - Sulfonation of polyvinylidene difluoride resin and its application in extraction of restriction enzymes from DNA digestion solutions.
PG  - 99-103
AB  - Sulfonation of polyvinylidene difluoride (PVDF) resin was achieved by incubation of the resin
      with sulfuric acid at a moderately high
      temperature. The sulfonated PVDF (SPVDF) resin was studied for its ability
      to extract restriction enzymes from DNA digestion solutions. The SPVDF
      resin was effective in adsorbing restriction enzymes such as EcoRI and
      BamHI and the extraction procedure was easy and simple to perform. The
      adsorption depended upon the amount of the resin added. We found that 1 mg
      of the SPVDF resin could completely remove all restriction enzyme activity
      routinely used in DNA digestion within 2 min after its addition. Treatment
      of a digestion solution with the SPVDF resin did not change the reaction
      solution and the same digestion buffer could be used for another digestion
      of the same DNA with other enzymes. We also found that, in comparison with
      normal PVDF, the SPVDF resin adsorbed less DNA, resulting in less loss of
      DNA in the extraction step. The potential application of the SPVDF resin
      in other procedures of molecular cloning and enzyme purification is
      discussed.
AU  - Yang J
AU  - Dong CX
AU  - Huang X
AU  - Zhao JD
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 2003 322: 99-103.

PMID- 10393910
VI  - 96
DP  - 1999
TI  - Identification of the endonuclease domain encoded by R2 and other site-specific, non-long terminal repeat retrotransposable elements.
PG  - 7847-7852
AB  - The non-long terminal repeat retrotransposon, R2, encodes a sequence-specific endonuclease
      responsible for its insertion at a unique site in the 28S rRNA genes of arthropods.  Although
      most non-LTR retrotransposons encode an apurinic-like endonuclease upstream of a common
      reverse transcriptase domain, R2 and many other site-specific non-LTR elements do not (CRE1
      and 2, SLACS, CZAR, Dong, R4).  Sequence comparison of these site-specific elements has
      revealed that the region downstream of their reverse transcriptase domain is conserved and
      shares sequence features with various prokaryotic restriction endonucleases.  In particular,
      these non-LTR elements have a Lys/Arg-Pro-Asp-X12-14aa-Asp/Glu motif known to lie near the
      scissile phosphodiester bonds in the protein-DNA complexes of restriction enzymes.
      Site-directed mutagenesis of the R2 protein was used to provide evidence that this motif is
      also part of the active site of the endonuclease encoded by this element.  Mutations of this
      motif eliminate both DNA-cleavage activities of the R2 protein: first-strand cleavage in which
      the exposed 3' end is used to prime reverse transcription of the RNA template and
      second-strand cleavage, which occurs after reverse transcription.  The general organization of
      the R2 protein appears similar to the type IIS restriction enzyme, FokI, in which specific DNA
      binding is controlled by a separate domain located amino terminal to the cleavage domain.
      Previous phylogenetic analysis of their reverse transcriptase domains has indicated that the
      non-LTR elements identified here as containing restriction-like endonucleases are the oldest
      lineages of non-LTR elements, suggesting a scenario for the evolution of non-LTR elements.
AU  - Yang J
AU  - Malik HS
AU  - Eickbush TH
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1999 96: 7847-7852.

PMID- 9737919
VI  - 282
DP  - 1998
TI  - Group II intron mobility in yeast mitochondria: target DNA-primed reverse transcription activity of aI1 and reverse splicing into DNA transposition sites in vitro.
PG  - 505-523
AB  - The retrohoming of the yeast mtDNA intron aI1 occurs by a target DNA-primed reverse
      transcription (TPRT) mechanism in which the intron RNA reverse splices directly into the
      recipient DNA and is then copied by the intron-encoded reverse transcriptase. Here, we carried
      out biochemical characterization of the intron-encoded reverse transcriptase and site-specific
      DNA endonuclease activities required for this process. We show that the aI1 reverse
      transcriptase has high TPRT activity in the presence of appropriate DNA target sites, but
      differs from the closely related reverse transcriptase encoded by the yeast aI2 intron in
      being unable to use artificial substrates efficiently. Characterization of TPRT products shows
      that the fully reverse spliced intron RNA is an efficient template for cDNA synthesis, while
      reverse transcription of partially reverse spliced intron RNA is impeded by the branch point.
      Novel features of the aI1 reaction include a prominent open-circular product in which cDNAs
      are incorporated at a nick at the antisense-strand cleavage site. The aI1 endonuclease
      activity, which catalyzes the DNA cleavage and reverse splicing reactions, is associated with
      ribonucleoprotein particles containing the intron-encoded protein and the excised intron RNA.
      As shown for the aI2 endonuclease, both the RNA and protein components are used for DNA target
      site recognition, but the aI1 protein has less stringent nucleotide sequence requirements for
      the reverse splicing reaction. Finally, perhaps reflecting this relaxed target specificity, in
      vitro experiments show that aI1 can reverse splice directly into ectopic mtDNA transposition
      sites, consistent with the previously suggested possibility that this mechanism is used for
      ectopic transposition of group II introns in vivo.
AU  - Yang J
AU  - Mohr G
AU  - Perlman PS
AU  - Lambowitz AM
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1998 282: 505-523.

PMID- 8692273
VI  - 381
DP  - 1996
TI  - Efficient integration of an intron RNA into double-stranded DNA by reverse splicing.
PG  - 332-335
AB  - Some group II introns are mobile elements as well as catalytic RNAs.  Introns aI1 and aI2
      found in the gene COX1 in yeast mitochondria encode reverse transcriptases which promote
      site-specific insertion of the intron into intronless alleles ('homing').  For aI2 this
      predominantly occurs by reverse transcription of unspliced precursor RNA at a break in
      double-strand DNA made by an endonuclease encoded by the intron.  The aI2 endonuclease
      involves both the excised intron RNA, which cleaves the DNA's sense strand by partial reverse
      splicing; and the intron-encoded reverse transcriptase which cleaves the antisense strand.
      Here we show that aI1 encodes an analogous endonuclease specific for a different target site
      compatible with the different exon-binding sequences of the intron RNA.  Over half of aI1
      undergoes complete reverse splicing in vitro, thus integrating linear intron RNA directly into
      the DNA.  This unprecedented reaction has implications for both intron mobility and evolution,
      and potential genetic engineering applications.
AU  - Yang J
AU  - Zimmerly S
AU  - Perlman PS
AU  - Lambowitz AM
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1996 381: 332-335.

PMID- 28153900
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Flavobacteriales Bacterium Strain UJ101 Isolated from a Xanthid Crab.
PG  - e01551-16
AB  - Flavobacteriales bacterium strain UJ101 was isolated from a xanthid crab species  collected
      from the East Sea of Korea. Here, we report the complete genome
      sequence of strain UJ101 for the study of major metabolic pathways related to
      microbial species from marine invertebrate species.
AU  - Yang JA
AU  - Kwon KK
AU  - Oh HM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01551-16.

PMID- 26089429
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Shewanella sp. ECSMB14102, a Mussel Recruitment-Promoting Bacterium Isolated from the East China Sea.
PG  - e00670-15
AB  - Shewanella sp. ECSMB14102, which promotes recruitment of the mussel Mytilus coruscus, was
      isolated from natural biofilms formed on glass slides submerged in
      the East China Sea. Here, we present the draft genome sequence, which comprises
      4.41 Mb with a G+C content of 52.2%. The genomic information in this strain will
      contribute to deepening our understanding of bacteria-animal interaction.
AU  - Yang JL
AU  - Guo XP
AU  - Chen YR
AU  - Gao W
AU  - Ding DW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00670-15.

PMID- 25593251
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Shewanella sp. ECSMB14101, Isolated from the East China  Sea.
PG  - e01388-14
AB  - Shewanella sp. ECSMB14101 was isolated from marine biofilms formed on the East China Sea. The
      draft genome sequence comprises 4,272,451 bp with a G+C content of
      49.82%. Information on this draft genome will contribute to the understanding of
      bacterium-animal interactions.
AU  - Yang JL
AU  - Guo XP
AU  - Ding DW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01388-14.

PMID- 16484203
VI  - 188
DP  - 2006
TI  - Involvement of the LlaKR2I Methylase in Expression of the AbiR Bacteriophage Defense System in Lactococcus lactis subsp. lactis biovar   diacetylactis KR2.
PG  - 1920-1928
AB  - The native lactococcal plasmid, pKR223, from Lactococcus lactis subsp. lactis biovar
      diacetylactis KR2 encodes two distinct
      bacteriophage-resistant mechanisms, the LlaKR2I restriction and
      modification (R/M) system and the abortive infection (Abi) mechanism,
      AbiR, that impedes bacteriophage DNA replication. This study completed the
      characterization of AbiR, revealing that it is the first Abi system to be
      encoded by three genes, abiRa, abiRb, and abiRc, arranged in an operon and
      that it requires the methylase gene from the LlaKR2I R/M system. An
      analysis of deletion and insertion clones demonstrated that the AbiR
      operon was toxic in L. lactis without the presence of the LlaKR2I
      methylase, which is required to protect L. lactis from AbiR toxicity. The
      novelty of the AbiR system resides in its original gene organization and
      the unusual protective role of the LlaKR2I methylase. Interestingly, the
      AbiR genetic determinants are flanked by two IS982 elements generating a
      likely transposable AbiR composite. This observation not only
      substantiated the novel function of the LlaKR2I methylase in the AbiR
      system but also illustrated the evolution of the LlaKR2I methylase toward
      a new and separate cellular function. This unique structure of both the
      LlaKR2I R/M system and the AbiR system may have contributed to the
      evolution of the LlaKR2I methylase toward a novel role comparable to that
      of the cell cycle-regulated methylases that include Dam and CcrM
      methylases. This new role for the LlaKR2I methylase offers a unique
      snapshot into the evolution of the cell cycle-regulated methylases from an
      existing R/M system.
AU  - Yang JM
AU  - Deurraza PJ
AU  - Matvienko N
AU  - O'sullivan DJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2006 188: 1920-1928.

PMID- 26868391
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Lactobacillus acidophilus MN-BM-F01.
PG  - e01699-15
AB  - Lactobacillus acidophilus MN-BM-F01 was originally isolated from a traditional fermented dairy
      product in China. The characteristics of this bacterium are its
      low post-acidification ability and high acid-producing rate. Here, we report the
      main genome features of L. acidophilus MN-BM-F01.
AU  - Yang L
AU  - Chen Y
AU  - Li Z
AU  - Shi Y
AU  - Li Z
AU  - Zhao X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01699-15.

PMID- Not carried by PubMed...
VI  - 91
DP  - 1991
TI  - Effect of N-terminal deletions on the activity of EcoRII DNA methylase.
PG  - A436
AB  - DNA(cytosine-5)-methyltransferases (Mtases) contain highly conserved core
      sequences and variable regions.  One of the variable regions is at the
      N-terminus where about 100 amino acids present in the enzymes M.EcoRII or
      M.MspI are almost totally absent in other Mtases.  In order to determine the
      function of the N-terminal residues in M.EcoRII we prepared a series of
      N-terminal deletion mutants in pUC19.  Analysis of the mutants showed that
      almost the entire region N-terminal to the first conserved motif can be deleted
      with retention of enzyme activity.  In some mutants translation starts with an
      internal ATG codon of the gene.  Other active constructs are either fused in
      frame with lac z or utilize an ATG codon in the cloning site of the vector.
      Deletion of 96 residues resulted in marked decrease in activity.  Longer
      deletions were inactive.  One such mutant protein deleted of 85 residues was
      purified and characterized.  In vitro methylation studies showed that this
      truncated mutant retained specificity.  However, the Km for AdoMet was 15 fold
      higher than the Km found with the wild type enzyme.  The results indicate that
      the N-terminal region of the protein is not vital for retention of catalytic
      activity but increases the affinity of the enzyme for AdoMet.
AU  - Yang LF
AU  - Som S
AU  - Friedman S
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1991 91: A436.

PMID- 22590641
VI  - 7
DP  - 2012
TI  - Edwardsiella comparative phylogenomics reveal the new intra/inter-species taxonomic relationships, virulence evolution and niche adaptation mechanisms.
PG  - E36987
AB  - Edwardsiella bacteria are leading fish pathogens causing huge losses to
      aquaculture industries worldwide. E. tarda is a broad-host range pathogen that
      infects more than 20 species of fish and other animals including humans while E.
      ictaluri is host-adapted to channel catfish causing enteric septicemia of catfish
      (ESC). Thus, these two species consist of a useful comparative system for
      studying the intricacies of pathogen evolution. Here we present for the first
      time the phylogenomic comparisons of 8 genomes of E. tarda and E. ictaluri
      isolates. Genome-based phylogenetic analysis revealed that E. tarda could be
      separate into two kinds of genotypes (genotype I, EdwGI and genotype II, EdwGII)
      based on the sequence similarity. E. tarda strains of EdwGI were clustered
      together with the E. ictaluri lineage and showed low sequence conservation to E.
      tarda strains of EdwGII. Multilocus sequence analysis (MLSA) of 48 distinct
      Edwardsiella strains also supports the new taxonomic relationship of the
      lineages. We identified the type III and VI secretion systems (T3SS and T6SS) as
      well as iron scavenging related genes that fulfilled the criteria of a key
      evolutionary factor likely facilitating the virulence evolution and adaptation to
      a broad range of hosts in EdwGI E. tarda. The surface structure-related genes may
      underlie the adaptive evolution of E. ictaluri in the host specification
      processes. Virulence and competition assays of the null mutants of the
      representative genes experimentally confirmed their contributive roles in the
      evolution/niche adaptive processes. We also reconstructed the hypothetical
      evolutionary pathway to highlight the virulence evolution and niche adaptation
      mechanisms of Edwardsiella. This study may facilitate the development of
      diagnostics, vaccines, and therapeutics for this under-studied pathogen.
AU  - Yang M
AU  - Lv Y
AU  - Xiao J
AU  - Wu H
AU  - Zheng H
AU  - Liu Q
AU  - Zhang Y
AU  - Wang Q
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2012 7: E36987.

PMID- 2561572
VI  - 13
DP  - 1989
TI  - Involvement of E. coli dcm methylase in Tn3 transposition.
PG  - 276-283
AB  - The effects of DNA methyltransferases on Tn3 transposition were investigated. The E. coli dam
      (deoxyadenosine methylase) gene was found to have no effect on Tn3 transposition. In contrast,
      Tn3 was found to transpose more frequently in dcm+ (deoxycytosine methylase) cells than in
      dcm- mutants. When the EcoRII methylase gene was introduced into dcm- cells (E. coli strain
      GM208), the frequency of Tn3 transposition in GM208 was dramatically increased. The EcoRII
      methylase recognizes and methylates the same sequence as does the dcm methylase. These results
      suggest tht deoxycytosine methylase modified DNA may be a preferred target for Tn3
      transposition. Experiments were also performed to determine whether the Tn3 transposase was
      involved in DNA modification. Plasmid DNA isolated from dcm- E. Coli containing the Tn3
      transposase gene was susceptible to ApyI digestion but resistant to EcoRII digestion,
      suggesting that Tn3 transposase modified the dcm recognition sequence. In addition,
      restriction enzymes TaqI, AvaII, BglI and HpaII did not digest this DNA completely, suggesting
      that the recognition sequences of TaqI, AvaII, BglI and HpaII were modified by Tn3 transposase
      to a certain degree. The type(s), the extent and mechanism(s) of this modification remain to
      be investigated.
AU  - Yang M-K
AU  - Ser S-C
AU  - Lee C-H
PT  - Journal Article
TA  - Proc. Natl. Sci. Counc. Repub. China B
JT  - Proc. Natl. Sci. Counc. Repub. China B
SO  - Proc. Natl. Sci. Counc. Repub. China B 1989 13: 276-283.

PMID- 29233990
VI  - 8
DP  - 2017
TI  - Balancing mcr-1 expression and bacterial survival is a delicate equilibrium between essential cellular defence mechanisms.
PG  - 2054
AB  - MCR-1 is a lipid A modifying enzyme that confers resistance to the antibiotic
      colistin. Here, we analyse the impact of MCR-1 expression on E. coli morphology,
      fitness, competitiveness, immune stimulation and virulence. Increased expression
      of mcr-1 results in decreased growth rate, cell viability, competitive ability
      and significant degradation in cell membrane and cytoplasmic structures, compared
      to expression of catalytically inactive MCR-1 (E246A) or MCR-1 soluble component.
      Lipopolysaccharide (LPS) extracted from mcr-1 strains induces lower production of
      IL-6 and TNF, when compared to control LPS. Compared to their parent strains,
      high-level colistin resistance mutants (HLCRMs) show reduced fitness (relative
      fitness is 0.41-0.78) and highly attenuated virulence in a Galleria mellonella
      infection model. Furthermore, HLCRMs are more susceptible to most antibiotics
      than their respective parent strains. Our results show that the bacterium is
      challenged to find a delicate equilibrium between expression of MCR-1-mediated
      colistin resistance and minimalizing toxicity and thus ensuring cell survival.
AU  - Yang Q et al
PT  - Journal Article
TA  - Nat. Commun.
JT  - Nat. Commun.
SO  - Nat. Commun. 2017 8: 2054.

PMID- 28082483
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Aeromonas sobria Strain 08005, Isolated from Sick Rana catesbeiana.
PG  - e01352-16
AB  - Aeromonas sobria is a Gram-negative, rod-shaped, and ubiquitous bacterium. We present here the
      draft genome sequence of A. sobria strain 08005, isolated from
      an infected bullfrog. It is composed of 66 contigs totaling 4,678,951 bp,
      contains 4,252 coding DNA sequences (CDSs), four rRNAs, and 88 tRNA sequences,
      and shows the presence of various putative virulence-related genes.
AU  - Yang QH
AU  - Zhou C
AU  - Lin Q
AU  - Lu Z
AU  - He LB
AU  - Guo SL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01352-16.

PMID- 30338026
VI  - 13
DP  - 2018
TI  - The complete genomic sequence of a novel cold-adapted bacterium, Planococcus maritimus Y42, isolated from crude oil-contaminated soil.
PG  - 23
AB  - Planococcus maritimus Y42, isolated from the petroleum-contaminated soil of the Qaidam Basin,
      can use crude oil as its sole source of carbon and energy at 20
      degrees C. The genome of P. maritimus strain Y42 has been sequenced to provide
      information on its properties. Genomic analysis shows that the genome of strain
      Y42 contains one circular DNA chromosome with a size of 3,718,896 bp and a GC
      content of 48.8%, and three plasmids (329,482; 89,073; and 12,282 bp). Although
      the strain Y42 did not show a remarkably higher ability in degrading crude oil
      than other oil-degrading bacteria, the existence of strain Y42 played a
      significant role to reducing the overall environmental impact as an indigenous
      oil-degrading bacterium. In addition, genome annotation revealed that strain Y42
      has many genes responsible for hydrocarbon degradation. Structural features of
      the genomes might provide a competitive edge for P. maritimus strain Y42 to
      survive in oil-polluted environments and be worthy of further study in oil
      degradation for the recovery of crude oil-polluted environments.
AU  - Yang R
AU  - Liu G
AU  - Chen T
AU  - Zhang W
AU  - Zhang G
AU  - Chang S
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2018 13: 23.

PMID- 19816441
VI  - 27
DP  - 2009
TI  - Improved genome annotation for Zymomonas mobilis.
PG  - 893-894
AB  - The first genome sequence of the enthanologenic bacterium Zymomonas mobilis ZM4 was reported
      in your journal five years ago.  Because of its productivity, high level of ethanol tolerance
      and ability to be genetically manipulated, Z. mobilis is a promising industrial bacterium for
      fermenting lignocellulosic biomass into enthanol, which is being advanced as an alternative to
      petroleum-derived transportation fuels.  Strains of the bacterium have been developed to
      ferment both hexoses and pantoses into ethanol, and the genome sequence will provide further
      opportunities for strain developments as well as providing more fundamental insights.  We have
      observed many differences between the primary annotation and one performed by the J. Craig
      Venter Institute (JCVI) and have detected differential gene expression in genes predicted by
      JCVI (http://cmr.jcvi.org/cgi-bin/CMR/GenomePage.cgi?org=ntzm01) that were absent from the
      primary annotation in our previous work.  We present here an improved version of the ZM4
      genome annotation based on the original primary gene sequence, new epxerimental data generated
      by 454 pyrosequencing and mass spectrometry-based proteomics, a novel gene prediction
      algorithm called Prodigal (prokaryotic dynamic programming genefinding algorithm) that is
      incorporated into an annotation pipeline, and manual curation.
AU  - Yang S
AU  - Pappas KM
AU  - Hauser LJ
AU  - Land ML
AU  - Chen GL
AU  - Hurst GB
AU  - Pan C
AU  - Kouvelis VN
AU  - Typas MA
AU  - Pelletier DA
AU  - Klingeman DM
AU  - Chang YJ
AU  - Samatova NF
AU  - Brown SD
PT  - Journal Article
TA  - Nat. Biotechnol.
JT  - Nat. Biotechnol.
SO  - Nat. Biotechnol. 2009 27: 893-894.

PMID- 29743953
VI  - 11
DP  - 2018
TI  - Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032.
PG  - 125
AB  - Background: Zymomonas mobilis is a natural ethanologen being developed and deployed as an
      industrial biofuel
      producer. To date, eight Z. mobilis strains have been completely sequenced and found to
      contain 28 native plasmids.
      However, systematic verification of predicted Z. mobilis plasmid genes and their contribution
      to cell fitness has not
      been hitherto addressed. Moreover, the precise number and identities of plasmids in Z. mobilis
      model strain ZM4 have
      been unclear. The lack of functional information about plasmid genes in ZM4 impedes ongoing
      studies for this model
      biofuel-producing strain.
      Results: In this study, we determined the complete chromosome and plasmid sequences of ZM4 and
      its engineered
      xylose-utilizing derivatives 2032 and 8b. Compared to previously published and revised ZM4
      chromosome sequences,
      the ZM4 chromosome sequence reported here contains 65 nucleotide sequence variations as well
      as a 2400-bp
      insertion. Four plasmids were identified in all three strains, with 150 plasmid genes
      predicted in strain ZM4 and 2032,
      and 153 plasmid genes predicted in strain 8b due to the insertion of heterologous DNA for
      expanded substrate
      utilization. Plasmid genes were then annotated using Blast2GO, InterProScan, and systems
      biology data analyses, and
      most genes were found to have apparent orthologs in other organisms or identifiable conserved
      domains. To verify
      plasmid gene prediction, RNA-Seq was used to map transcripts and also compare relative gene
      expression under various
      growth conditions, including anaerobic and aerobic conditions, or growth in different
      concentrations of biomass
      hydrolysates. Overall, plasmid genes were more responsive to varying hydrolysate
      concentrations than to oxygen
      availability. Additionally, our results indicated that although all plasmids were present in
      low copy number (about 12 per cell), the copy number of some plasmids varied under specific
      growth conditions or due to heterologous gene
      insertion.
      Conclusions: The complete genome of ZM4 and two xylose-utilizing derivatives is reported in
      this study, with an
      emphasis on identifying and characterizing plasmid genes. Plasmid gene annotation, validation,
      expression levels at
      growth conditions of interest, and contribution to host fitness are reported for the first
      time.
AU  - Yang S
AU  - Vera JM
AU  - Grass J
AU  - Savvakis G
AU  - Moskvin OV
AU  - Yang Y
AU  - McIlwain SJ
AU  - Lyu Y
AU  - Zinonos I
AU  - Hebert AS
AU  - Coon JJ
AU  - Bates DM
AU  - Sato TK
AU  - Brown SD
AU  - Himmel ME
AU  - Zhang M
AU  - Landick R
AU  - Pappas KM
AU  - Zhang Y
PT  - Journal Article
TA  - Biotechnol. Biofuels.
JT  - Biotechnol. Biofuels.
SO  - Biotechnol. Biofuels. 2018 11: 125.

PMID- 23209213
VI  - 194
DP  - 2012
TI  - Genome Sequence of Strain IMCC14465, Isolated from the East Sea, Belonging to the PS1 Clade of Alphaproteobacteria.
PG  - 6952-6953
AB  - Strain IMCC14465 was isolated from surface seawater of the East Sea using
      dilution-to-extinction culturing. Phylogenetic analysis indicated that the strain
      belongs to the PS1 clade, which is closely related to the OCS116 clade in the
      Alphaproteobacteria. Here, we report the genome sequence of IMCC14465, the first
      isolate of the PS1 clade.
AU  - Yang SJ
AU  - Kang I
AU  - Cho JC
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6952-6953.

PMID- 16600865
VI  - 22
DP  - 2006
TI  - Making and breaking nucleic acids: Two-Mg2+-ion catalysis and substrate specificity.
PG  - 5-13
AB  - DNA and a large proportion of RNA are antiparallel duplexes composed of an unvarying
      phosphosugar backbone surrounding uniformly stacked and
      highly similar base pairs. How do the myriad of enzymes (including
      ribozymes) that perform catalysis on nucleic acids achieve exquisite
      structure or sequence specificity? In all DNA and RNA polymerases and
      many nucleases and transposases, two Mg2+ ions are jointly coordinated
      by the nucleic acid substrate and catalytic residues of the enzyme.
      Based on the exquisite sensitivity Of Mg2+ ions to the ligand geometry
      and electrostatic environment, we propose that two-metal-ion catalysis
      greatly enhances substrate recognition and catalytic specificity.
AU  - Yang W
AU  - Lee JY
AU  - Nowotny M
PT  - Journal Article
TA  - Mol. Cell
JT  - Mol. Cell
SO  - Mol. Cell 2006 22: 5-13.

PMID- 26823580
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Fish Pathogen Aeromonas hydrophila JBN2301.
PG  - e01615-15
AB  - Aeromonas hydrophila is one of the most important fish pathogens in China. Here,  we report
      complete genome sequence of a virulent strain, A. hydrophila JBN2301,
      which was isolated from diseased crucian carp.
AU  - Yang W
AU  - Li N
AU  - Li M
AU  - Zhang D
AU  - An G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01615-15.

PMID- 21706014
VI  - 8
DP  - 2011
TI  - A public genome-scale lentiviral expression library of human ORFs.
PG  - 659-661
AB  - Functional characterization of the human genome requires tools for systematically
      modulating gene expression in both loss-of-function and gain-of-function
      experiments. We describe the production of a sequence-confirmed, clonal
      collection of over 16,100 human open-reading frames (ORFs) encoded in a versatile
      Gateway vector system. Using this ORFeome resource, we created a genome-scale
      expression collection in a lentiviral vector, thereby enabling both targeted
      experiments and high-throughput screens in diverse cell types.
AU  - Yang X et al
PT  - Journal Article
TA  - Nat. Methods
JT  - Nat. Methods
SO  - Nat. Methods 2011 8: 659-661.

PMID- 29025933
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of Four Brucella Strains Isolated from China.
PG  - e01034-17
AB  - Brucella spp. are facultative intracellular pathogens that cause a contagious zoonotic
      disease. Twelve different species are currently identified. This study
      presents the complete genome sequences of four Brucella strains. These complete
      genomes were annotated and the contents compared to those of other strains
      isolated from China.
AU  - Yang X
AU  - Cao X
AU  - Wang N
AU  - Wang J
AU  - Bie P
AU  - Lyu Y
AU  - Wu Q
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01034-17.

PMID- Not carried by PubMed...
VI  - 22
DP  - 1990
TI  - Cloning and overexpression of the restriction gene of EcoRI.
PG  - 599-606
AB  - Cloning and expression of the EcoRI genes are reported here.  A plasmid
      containing the EcoRI (r/m) genes was extracted from the EcoRI producing strain
      E. coli RI, and a 4.9 kb BamHI-HindIII fragment encoding the EcoRI genes was
      cloned into pBR322, producing a hybrid plasmid pER101.  pER302, containing the
      methylase gene of EcoRI, was obtained by inserting the 1.7 kb fragment from
      pER101 into pACYC184.  pER304, in which the sequence coding for the C-terminal
      of EcoRI was downstream from the lambda PL promoter, was constructed from pAS1
      and pER101.  After cloning the 1.5 kb SalI-BglII fragment of pER101 into
      pER304, an EcoRI overproducing plasmid pER306 was created using the strong
      promoter PL as well as the endogenous promoter Pe to overexpress the EcoRI(r)
      gene.  To delete the Pe promoter to control expression of EcoRI only by the PL
      promoter, a 0.65 kb BamHI-HindIII fragment from pER401 was used to replace the
      small BamHI-HindIII fragment downstream from PL promoter, resulting in another
      overproducing plasmid pER307.  When transforming GI139 and GI139/pER302 the
      relative survival efficiency of pER306 and pER307 was both 10/5, but when using
      TG1/pRK248CIts and GI139/pER302 as hosts the efficiency was 10/5 and 1
      respectively.  Therefore, in certain hosts, pER307 can express EcoRI in the
      absence of its cognate methylase.  After heat induction, pER307
      [TG1/pRK248CIts] produces EcoRI at a level of 10/5 units per gram of wet cell,
      which is about 1-2 orders of magnitude lower than that of pER306/[GI139/pER302]
      or pER307/[GI139/pER302].
AU  - Yang X
AU  - Chen C
AU  - Wang D
AU  - Yang S
AU  - Wu R
PT  - Journal Article
TA  - Acta Biochim. Biophys. Sin.
JT  - Acta Biochim. Biophys. Sin.
SO  - Acta Biochim. Biophys. Sin. 1990 22: 599-606.

PMID- 29025947
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Brevibacillus laterosporus OSY-I1, a Strain That Produces Brevibacillin, Which Combats Drug-Resistant Gram-Positive Bacteria.
PG  - e01093-17
AB  - Brevibacillus laterosporus OSY-I1 is a Gram-positive spore-forming bacterium isolated from
      soil. The bacterium produces brevibacillin, an antimicrobial
      lipopeptide effective against several drug-resistant Gram-positive bacteria.
      Here, we present the draft genome sequence of the strain OSY-I1 and the gene
      cluster responsible for the biosynthesis of brevibacillin.
AU  - Yang X
AU  - Huang E
AU  - Yesil M
AU  - Xiaoli L
AU  - Dudley EG
AU  - Yousef AE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01093-17.

PMID- 24285665
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Lactococcus lactis subsp. lactis KLDS4.0325.
PG  - e00962-13
AB  - We report the complete genome sequence of Lactococcus lactis subsp. lactis KLDS4.0325, a
      probiotic bacterium isolated from homemade koumiss in Xinjiang,
      China. We have determined the complete genome sequence of strain KLDS4.0325,
      which consists of a chromosome and three plasmids and reveals genes that are
      likely to be involved in dairy fermentation and that have probiotic qualities.
AU  - Yang X
AU  - Wang Y
AU  - Huo G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00962-13.

PMID- 26590584
VI  - 100
DP  - 2016
TI  - Restriction modification system analysis and development of in vivo methylation for the transformation of Clostridium cellulovorans.
PG  - 2289-2299
AB  - Clostridium cellulovorans, a cellulolytic bacterium producing butyric and acetic  acids as
      main fermentation products, is a promising host for biofuel production
      from cellulose. However, the transformation method of C. cellulovorans was not
      available, hindering its genetic engineering. To overcome this problem, its
      restriction modification (RM) systems were analyzed and a novel in vivo
      methylation was established for its successful transformation in the present
      study. Specifically, two RM systems, Cce743I and Cce743II, were determined. R.
      Cce743I has the same specificity as LlaJI, recognizing 5'-GACGC-3' and
      5'-GCGTC-3', while M. Cce743I methylates the external cytosine in the strand
      (5'-GACG(m)C-3'). R. Cce743II, has the same specificity as LlaI, recognizing
      5'-CCAGG-3' and 5'-CCTGG-3', while M. Cce743II methylates the external cytosine
      of both strands. An in vivo methylation system, expressing M. Cce743I and M.
      Cce743II from C. cellulovorans in Escherichia coli, was then established to
      protect plasmids used in electrotransformation. Transformants expressing an
      aldehyde/alcohol dehydrogenase (adhE2), which converted butyryl-CoA to n-butanol
      and acetyl-CoA to ethanol, were obtained. For the first time, an effective
      transformation method was developed for metabolic engineering of C. cellulovorans
      for biofuel production directly from cellulose.
AU  - Yang X
AU  - Xu M
AU  - Yang ST
PT  - Journal Article
TA  - Appl. Microbiol. Biotechnol.
JT  - Appl. Microbiol. Biotechnol.
SO  - Appl. Microbiol. Biotechnol. 2016 100: 2289-2299.

PMID- 21742862
VI  - 193
DP  - 2011
TI  - Genome sequence of Rhodococcus sp. R04, a polychlorinated biphenyl biodegrader.
PG  - 5032-5033
AB  - The genus Rhodococcus has proved to be a promising option for the clean-up of polluted sites
      and application of a microbial biocatalyst. Rhodococcous
      sp. strain R04, isolated from oil contaminated soil, could biodegrade
      polychlorinated biphenyls. Here we report the draft genome sequence of
      Rhodococcous sp. strain R04, which could be used to predict genes for
      xenobiotic biodegradation and provide important insights into the
      applications of this strain.
AU  - Yang X
AU  - Xue R
AU  - Shen C
AU  - Li S
AU  - Gao C
AU  - Wang Q
AU  - Zhao X
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5032-5033.

PMID- 27660770
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Klebsiella pneumoniae Strain AS Isolated from Zhejiang Provincial Hospital of TCM, China.
PG  - e00930-16
AB  - Klebsiella pneumoniae is a Gram-negative, nonmotile, encapsulated, lactose-fermenting,
      facultative anaerobic, rod-shaped bacterium. Here we present
      draft genome assemblies of Klebsiella pneumoniae AS, which was isolated in China.
      The genomic information will provide a better understanding of the physiology,
      adaptation, and evolution of K. pneumoniae.
AU  - Yang XJ
AU  - Wang S
AU  - Cao JM
AU  - Hou JH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00930-16.

PMID- 2161520
VI  - 18
DP  - 1990
TI  - Restriction enzyme SnaBI is sensitive to methylation of cytosine within its recognition sequence.
PG  - 3083
AB  - None
AU  - Yang Y
AU  - Li Q
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1990 18: 3083.

PMID- 23599296
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Ochrobactrum pseudogrignonense Strain CDB2, a Highly Efficient Arsenate-Resistant Soil Bacterium from Arsenic-Contaminated Cattle Dip   Sites.
PG  - e00173-13
AB  - We report the 4.97-Mb draft genome sequence of a highly efficient arsenate-resistant
      bacterium, Ochrobactrum sp. strain CDB2. It contains a novel
      arsenic resistance (ars) operon (arsR-arsC1-ACR3-arsC2-arsH-mfs) and two
      non-operon-associated ars genes, arsC3 and arsB. The genome information will aid
      in the understanding of the arsenic resistance mechanism of this and other
      bacterial species.
AU  - Yang Y
AU  - Yu X
AU  - Zhang R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00173-13.

PMID- 28642376
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Bacillus sp. Strain CDB3, an Arsenic-Resistant Soil Bacterium Isolated from Cattle Dip Sites.
PG  - e00429-17
AB  - Bacillus sp. strain CDB3, isolated from cattle dip sites in Australia, is highly  resistant to
      arsenic. It contains 22 arsenic resistance (ars) genes, of which 17
      are organized in 3 ars clusters. Here, we report the draft genome sequence of
      CDB3, which will assist us in understanding the overall ars mechanism.
AU  - Yang Y
AU  - Zhang R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00429-17.

PMID- 25189578
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Four Strains of Vibrio parahaemolyticus, Three of Which Cause Early Mortality Syndrome/Acute Hepatopancreatic Necrosis Disease in Shrimp   in China and Thailand.
PG  - e00816-14
AB  - We sequenced four Vibrio parahaemolyticus strains, three of which caused serious  acute
      hepatopancreatic necrosis disease. Sequence analysis of the virulent
      strains revealed not only genes related to cholera toxin and the type IV
      pilus/type IV secretion system but also a unique, previously unreported, large
      extrachromosomal plasmid that encodes a homolog to the insecticidal Photorhabdus
      insect-related binary toxin PirAB.
AU  - Yang YT
AU  - Chen IT
AU  - Lee CT
AU  - Chen CY
AU  - Lin SS
AU  - Hor LI
AU  - Tseng TC
AU  - Huang YT
AU  - Sritunyalucksana K
AU  - Thitamadee S
AU  - Wang HC
AU  - Lo CF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00816-14.

PMID- 15805123
VI  - 33
DP  - 2005
TI  - Structure of HinP1I endonuclease reveals a striking similarity to the monomeric restriction enzyme MspI.
PG  - 1892-1901
AB  - HinP1I, a type II restriction endonuclease, recognizes and cleaves a palindromic
      tetranucleotide sequence (G/CGC) in double-stranded DNA,
      producing 2 nt 5' overhanging ends. Here, we report the structure of
      HinP1I crystallized as one protein monomer in the crystallographic
      asymmetric unit. HinP1I displays an elongated shape, with a conserved
      catalytic core domain containing an active-site motif of SDX18QXK and a
      putative DNA-binding domain. Without significant sequence homology, HinP1I
      displays striking structural similarity to MspI, an endonuclease that
      cleaves a similar palindromic DNA sequence (C/CGG) and binds to that
      sequence crystallographically as a monomer. Almost all the structural
      elements of MspI can be matched in HinP1I, including both the DNA
      recognition and catalytic elements. Examining the protein-protein
      interactions in the crystal lattice, HinP1I could be dimerized through two
      helices located on the opposite side of the protein to the active site,
      generating a molecule with two active sites and two DNA-binding surfaces
      opposite one another on the outer surfaces of the dimer. A possible
      functional link between this unusual dimerization mode and the tetrameric
      restriction enzymes is discussed.
AU  - Yang Z
AU  - Horton JR
AU  - Maunus R
AU  - Wilson GG
AU  - Roberts RJ
AU  - Cheng X
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2005 33: 1892-1901.

PMID- 12937411
VI  - 10
DP  - 2003
TI  - Structure of the bacteriophage T4 DNA adenine methyltransferase.
PG  - 849-855
AB  - DNA-adenine methylation at certain GATC sites plays a pivotal role in bacterial and phage gene
      expression as well as bacterial virulence. We
      report here the crystal structures of the bacteriophage T4Dam DNA adenine
      methyltransferase (MTase) in a binary complex with the methyl-donor
      product S-adenosyl-L-homocysteine (AdoHcy) and in a ternary complex with a
      synthetic 12-bp DNA duplex and AdoHcy. T4Dam contains two domains: a
      seven-stranded catalytic domain that harbors the binding site for AdoHcy
      and a DNA binding domain consisting of a five-helix bundle and a
      beta-hairpin that is conserved in the family of GATC-related MTase
      orthologs. Unexpectedly, the sequence-specific T4Dam bound to DNA in a
      nonspecific mode that contained two Dam monomers per synthetic duplex,
      even though the DNA contains a single GATC site. The ternary structure
      provides a rare snapshot of an enzyme poised for linear diffusion along
      the DNA.
AU  - Yang Z
AU  - Horton JR
AU  - Zhou L
AU  - Zhang XJ
AU  - Dong AP
AU  - Zhang X
AU  - Schlagman SL
AU  - Kossykh V
AU  - Hattman S
AU  - Cheng XD
PT  - Journal Article
TA  - Nat. Struct. Biol.
JT  - Nat. Struct. Biol.
SO  - Nat. Struct. Biol. 2003 10: 849-855.

PMID- 22689245
VI  - 194
DP  - 2012
TI  - Genome Sequence of Bacillus licheniformis WX-02.
PG  - 3561-3562
AB  - Bacillus licheniformis is an important bacterium that has been used extensively for
      large-scale industrial production of exoenzymes and peptide antibiotics. B.
      licheniformis WX-02 produces poly-gamma-glutamate increasingly when fermented
      under stress conditions. Here its genome sequence (4,270,104 bp, with G+C content
      of 46.06%), which comprises a circular chromosome, is announced.
AU  - Yangtse W
AU  - Zhou Y
AU  - Lei Y
AU  - Qiu Y
AU  - Wei X
AU  - Ji Z
AU  - Qi G
AU  - Yong Y
AU  - Chen L
AU  - Chen S
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3561-3562.

PMID- 2530136
VI  - 81
DP  - 1989
TI  - Phasmids as effective and simple tools for construction and analysis of gene libraries.
PG  - 203-210
AB  - Phasmid lambda-pMYF131, a hybrid of phage lambda vectors and plasmid pUC19, was
      constructed.  The phasmid and its derivatives were shown to be efficient
      vectors for construction and analysis of gene libraries in Escherichia coli
      cells.  The lambda-pMYF131 DNA molecule contains all the genes and regions
      essential for phage lytic development.  The plasmid cannot be packaged either
      in the monomeric or the oligomeric form due to its specific length.  Elongation
      of the DNA molecule by ligation with fragments of foreign DNA can make it
      packageable and this is easily detected by plaque formation. Hence, the
      procedures used to construct genomic libraries can be simplified by selection
      of only recombinant DNA molecules just at the time and on the basis of their
      packaging in vitro.  The output of recombinant clones per vector molecule was
      several times higher for vector lambda-pMYF131, compared to phage vector
      lambdaL47.1AB, and attained 3x10/6 clones per microgram DNA.  Vector and
      recombinant phasmids can be obtained in large quantities in plasmid form.
      Lambda-pMYF131 contains nine unique restriction sites which allow the cloning
      of DNA fragments with blunt ends and of fragments with various types of
      cohesive ends, obtained by digestion with 14 prototype restriction enzymes.
      The maximal size of the cloned DNA fragments is approximately 20 kb for
      lambda-pMYF131.  Phasmid vectors were used to construct libraries of bovine,
      pig and quail genomes, and genomic libraries of 17 species of bacteria.
      Application of suitable methods allowed the identification 13 individual genes
      within these libraries.  Reports the cleavage sites for EcoICRI and Ecl136II.
AU  - Yankovsky NK
AU  - Fonstein MY
AU  - Lashina SY
AU  - Bukanov NO
AU  - Yakubovich NV
AU  - Ermakova LM
AU  - Rebentish BA
AU  - Janulaitis A
AU  - Debabov VG
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1989 81: 203-210.

PMID- 28957464
VI  - 9
DP  - 2017
TI  - Population Structure and Local Adaptation of MAC Lung Disease Agent Mycobacterium avium subsp. hominissuis.
PG  - 2403-2417
AB  - Mycobacterium avium subsp. hominissuis (MAH) is one of the most common
      nontuberculous mycobacterial species responsible for chronic lung disease in
      humans. Despite increasing worldwide incidence, little is known about the genetic
      mechanisms behind the population evolution of MAH. To elucidate the local
      adaptation mechanisms of MAH, we assessed genetic population structure, the
      mutual homologous recombination, and gene content for 36 global MAH isolates,
      including 12 Japanese isolates sequenced in the present study. We identified five
      major MAH lineages and found that extensive mutual homologous recombination
      occurs among them. Two lineages (MahEastAsia1 and MahEastAsia2) were predominant
      in the Japanese isolates. We identified alleles unique to these two East Asian
      lineages in the loci responsible for trehalose biosynthesis (treS and mak) and in
      one mammalian cell entry operon, which presumably originated from as yet
      undiscovered mycobacterial lineages. Several genes and alleles unique to East
      Asian strains were located in the fragments introduced via recombination between
      East Asian lineages, suggesting implication of recombination in local adaptation.
      These patterns of MAH genomes are consistent with the signature of distribution
      conjugative transfer, a mode of sexual reproduction reported for other
      mycobacterial species.
AU  - Yano H
AU  - Iwamoto T
AU  - Nishiuchi Y
AU  - Nakajima C
AU  - Starkova DA
AU  - Mokrousov I
AU  - Narvskaya O
AU  - Yoshida S
AU  - Arikawa K
AU  - Nakanishi N
AU  - Osaki K
AU  - Nakagawa I
AU  - Ato M
AU  - Suzuki Y
AU  - Maruyama F
PT  - Journal Article
TA  - Genome Biol. Evol.
JT  - Genome Biol. Evol.
SO  - Genome Biol. Evol. 2017 9: 2403-2417.

PMID- 3470568
VI  - 11C
DP  - 1987
TI  - Mutational analysis of the EcoRI endonuclease.
PG  - 211
AB  - Using in vitro mutagenesis with hydroxylamine a large number of null mutants of
      the EcoRI endonuclease have been generated.  Fifty per cent of the 121 mutants
      examined by western blot tested positive against anti-RI.  The entire
      endonuclease gene from twenty-seven western positive mutants was sequenced by
      using dideoxy sequencing directly from double stranded plasmid DNA.  Twenty of
      these were single base change substitutions, with 10 of the mutants falling
      within the region from ala 139 to glu 144.  Examination of the mutants with
      respect to the structure of the EcoRI endonuclease-DNA co-crystal reveals that
      all of the null mutants map at either the protein-DNA interface or at the
      subunit-subunit interface.  Molecular weight determination of purified protein
      on a BioSil TS250 HPLC column demonstrates that wild type EcoRI endonuclease
      runs as a dimer of 60Kd.  Three mutants with alterations at the protein-DNA
      interface (AT139, GS140 and RQ203) run as dimers while 3 mutants mapping at the
      subunit-subunit interface (EK144, EK152 and GR210) run as monomers.
AU  - Yanofsky S
AU  - Boyer H
AU  - Grable J
AU  - McClarin J
AU  - Rosenberg J
AU  - Greene P
PT  - Journal Article
TA  - J. Cell Biochem. Suppl.
JT  - J. Cell Biochem. Suppl.
SO  - J. Cell Biochem. Suppl. 1987 11C: 211.

PMID- Not carried by PubMed...
VI  - 85
DP  - 1985
TI  - Positive control of EcoRI endonuclease expression by the EcoRI methylase.
PG  - 106
AB  - The presence of a wild type EcoRI endonuclease in cells lacking the cognate
      methylase is lethal.  We have isolated a mutant endonuclease in which serine
      replaces arginine at residue 187.  The Ser 187 enzyme retains RI specificity
      but has reduced in vivo activity (as measured by ability to restrict growth of
      lambda phage).  Cells carrying the Ser 187 endonuclease can survive when the
      methylase is deleted.  Deletion of the methylase results in drastically reduced
      endonuclease production but levels can be restored to near normal by the
      presence of the methylase provided in trans on pSC101, a compatible low-copy
      number plasmid.  We have constructed a number of strains in which the methylase
      gene is truncated at different sites.  Analysis of these strains has allowed us
      to define a domain within the methylase gene which activates endonuclease
      production.  In some of the methylase-deficient strains we are able to increase
      endonuclease production by induction of a linked lac promoter.  This induction
      is lethal into the cell, and it is clear that survival depends upon both low
      production of the Ser 187 endonuclease as well as its reduced in vivo activity.
      This positive control of endonuclease production by methylase provides a
      mechanism for establishment and maintenance of this system in a cell without
      damaging cellular DNA.
AU  - Yanofsky S
AU  - Boyer H
AU  - Greene P
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1985 85: 106.

PMID- 2834717
VI  - 2
DP  - 1987
TI  - Clustering of null mutations in the EcoRI endonuclease.
PG  - 273-282
AB  - EcoRI endonuclease mutants were isolated in a methylase-deficient background
      following in vitro hydroxylamine mutagenesis of plasmid pKG2 (Kuhn et al.: Gene
      44:253-263, 1986).  Mutants which survived high-level endonuclease expression
      (IPTG induction) were termed null mutants.  Sixty-two of 121 null mutants
      tested by Western blot contained normal levels of endonuclease cross-reacting
      protein.  The complete endonuclease gene was sequenced for 27 null mutants.
      This group was found to consist of 20 single base-change missense mutantations,
      6 double mutations, and 1 triple mutation.  Ten of the 20 single mutations were
      clustered between residues 139 and 144.  When examined with respect to the
      structure of the EcoRI-DNA complex (McClarin et al.:  Science 234:1526-1541,
      1986), these alterations were found to fall predominantly into two classes:
      substitutions at the protein-DNA interface or substitutions at the
      protein-protein (dimer) interface.  Protein from several of the mutants was
      purified and sized by using HPLC.  Wild-type EcoRI endonuclease and protein
      from three of the DNA interface mutations (Ala139->Thr, Gly140->Ser,
      Arg203->Gln) appeared to be dimeric, while protein from subunit interface
      mutations (glu->Lys, Glu152->Lys, Gly210->Arg) migrated as monomers.
AU  - Yanofsky SD
AU  - Love R
AU  - McClarin JA
AU  - Rosenberg JM
AU  - Boyer HW
AU  - Greene PJ
PT  - Journal Article
TA  - Proteins
JT  - Proteins
SO  - Proteins 1987 2: 273-282.

PMID- 28572327
VI  - 5
DP  - 2017
TI  - Complete Genome Sequences of Three Salmonella enterica subsp. enterica Serovar Saintpaul Isolates Associated with a 2013 Multistate Outbreak in the United  States.
PG  - e00456-17
AB  - In 2013, a multistate outbreak of Salmonella enterica subsp. enterica serovar Saintpaul from
      cucumber caused 84 cases of salmonellosis in the United States. In
      this announcement, we report the complete genome sequences of three clinical
      Salmonella Saintpaul isolates associated with the 2013 outbreak.
AU  - Yao K
AU  - Muruvanda T
AU  - Allard MW
AU  - Hoffmann M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00456-17.

PMID- 26798102
VI  - 4
DP  - 2016
TI  - Complete Genome and Methylome Sequences of Two Salmonella enterica spp.
PG  - e01599-15
AB  - Salmonella enterica is responsible for major foodborne outbreaks worldwide. It can cause
      gastroenteritis characterized by diarrhea, vomiting, and fever.
      Salmonella infections raise public health concerns along with consequential
      economic impacts. In this report, we announce the first complete genome sequences
      of Salmonella enterica subsp. enterica serovar Choleraeuis (S. Choleraeuis) ATCC
      10708 and Salmonella enterica subsp. enterica serovar Pullorum (S. Pullorum) ATCC
      9120, isolated from patients with diarrhea.
AU  - Yao K
AU  - Muruvanda T
AU  - Roberts RJ
AU  - Payne J
AU  - Allard MW
AU  - Hoffmann M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01599-15.

PMID- 26988049
VI  - 4
DP  - 2016
TI  - Complete Genome and Methylome Sequences of Salmonella enterica subsp. enterica Serovar Panama (ATCC 7378) and Salmonella enterica subsp. enterica Serovar  Sloterdijk (ATCC 15791).
PG  - e00133-16
AB  - Salmonella enterica spp. are pathogenic bacteria commonly associated with food-borne outbreaks
      in human and animals. Salmonella enterica spp. are
      characterized into more than 2,500 different serotypes, which makes
      epidemiological surveillance and outbreak control more difficult. In this report,
      we announce the first complete genome and methylome sequences from two Salmonella
      type strains associated with food-borne outbreaks, Salmonella enterica subsp.
      enterica serovar Panama (ATCC 7378) and Salmonella enterica subsp. enterica
      serovar Sloterdijk (ATCC 15791).
AU  - Yao K
AU  - Muruvanda T
AU  - Roberts RJ
AU  - Payne J
AU  - Allard MW
AU  - Hoffmann M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00133-16.

PMID- 28302778
VI  - 5
DP  - 2017
TI  - Complete Genome and Methylome Sequences of Salmonella enterica subsp. enterica Serovars Typhimurium, Saintpaul, and Stanleyville from the SARA/SARB Collection.
PG  - e00031-17
AB  - In this announcement, we report the complete genome and methylome sequences of three
      Salmonella enterica strains from the SARA and SARB collection: S. enterica
      subsp. enterica serovar Typhimurium (SARA13), S. enterica subsp. enterica serovar
      Saintpaul (SARA26), and S. enterica subsp. enterica serovar Stanleyville
      (SARB61).
AU  - Yao K
AU  - Roberts RJ
AU  - Allard MW
AU  - Hoffmann M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00031-17.

PMID- 27422839
VI  - 82
DP  - 2016
TI  - A Tetrahydrofolate-Dependent Methyltransferase Catalyzing the Demethylation of Dicamba in Sphingomonas sp. Strain Ndbn-20.
PG  - 5621-5630
AB  - UNLABELLED: Sphingomonas sp. strain Ndbn-20 degrades and utilizes the herbicide
      dicamba as its sole carbon and energy source. In the present study, a
      tetrahydrofolate (THF)-dependent dicamba methyltransferase gene, dmt, was cloned
      from the strain, and three other genes, metF, dhc, and purU, which are involved
      in THF metabolism, were found to be located downstream of dmt A transcriptional
      study revealed that the four genes constituted one transcriptional unit that was
      constitutively transcribed. Lysates of cells grown with glucose or dicamba
      exhibited almost the same activities, which further suggested that the dmt gene
      is constitutively expressed in the strain. Dmt shared 46% and 45% identities with
      the methyltransferases DesA and LigM from Sphingomonas paucimobilis SYK-6,
      respectively. The purified Dmt catalyzed the transfer of methyl from dicamba to
      THF to form the herbicidally inactive metabolite 3,6-dichlorosalicylic acid
      (DCSA) and 5-methyl-THF. The activity of Dmt was inhibited by 5-methyl-THF but
      not by DCSA. The introduction of a codon-optimized dmt gene into Arabidopsis
      thaliana enhanced resistance against dicamba. In conclusion, this study
      identified a THF-dependent dicamba methyltransferase, Dmt, with potential
      applications for the genetic engineering of dicamba-resistant crops. IMPORTANCE:
      Dicamba is a very important herbicide that is widely used to control more than
      200 types of broadleaf weeds and is a suitable target herbicide for the
      engineering of herbicide-resistant transgenic crops. A study of the mechanism of
      dicamba metabolism by soil microorganisms will benefit studies of its
      dissipation, transformation, and migration in the environment. This study
      identified a THF-dependent methyltransferase, Dmt, capable of catalyzing dicamba
      demethylation in Sphingomonas sp. Ndbn-20, and a preliminary study of its
      enzymatic characteristics was performed. Introduction of a codon-optimized dmt
      gene into Arabidopsis thaliana enhanced resistance against dicamba, suggesting
      that the dmt gene has potential applications for the genetic engineering of
      herbicide-resistant crops.
AU  - Yao L
AU  - Yu LL
AU  - Zhang JJ
AU  - Xie XT
AU  - Tao Q
AU  - Yan X
AU  - Hong Q
AU  - Qiu JG
AU  - He J
AU  - Ding DR
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2016 82: 5621-5630.

PMID- 24336381
VI  - 1
DP  - 2013
TI  - Genome Sequence of a Thermophilic Bacillus, Geobacillus thermodenitrificans DSM465.
PG  - e01046-13
AB  - Geobacillus thermodenitrificans NG80-2 encodes a LadA-mediated alkane degradation pathway,
      while G. thermodenitrificans DSM465 cannot utilize alkanes. Here, we
      report the draft genome sequence of G. thermodenitrificans DSM465, which may help
      reveal the genomic differences between these two strains in regards to the
      biodegradation of alkanes.
AU  - Yao N
AU  - Ren Y
AU  - Wang W
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01046-13.

PMID- 25573938
VI  - 3
DP  - 2015
TI  - Genome Sequence of Thermoactinomyces daqus H-18, a Novel Thermophilic Species Isolated from High-Temperature Daqu.
PG  - e01394-14
AB  - Thermoactinomyces daqus H-18 is a new species of Thermoactinomyces isolated from
      high-temperature Daqu used in the fermentation of Bandongjing sesame-flavor
      liquor. Its genome was sequenced and assembled (3.44 Mb). The coding sequences
      (CDSs) that correlated to high-temperature tolerance were annotated. The
      metabolic pathways for the compounds responsible for flavor were also found.
AU  - Yao S
AU  - Xu Y
AU  - Xin C
AU  - Xu L
AU  - Liu Y
AU  - Li H
AU  - Li J
AU  - Zhao J
AU  - Cheng C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01394-14.

PMID- 27125482
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Serratia rubidaea Isolated in China.
PG  - e00283-16
AB  - We report here the first complete genome of Serratia rubidaea, isolated from a patient in
      China.
AU  - Yao X
AU  - Sun Q
AU  - Liu W
AU  - Yin X
AU  - Pei G
AU  - Wang Y
AU  - An X
AU  - Mi Z
AU  - Luo Y
AU  - Tong Y
AU  - Chen S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00283-16.

PMID- 28104656
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Pandrug-Resistant Serratia marcescens Clinical Isolates Harboring blaNDM-1.
PG  - e01481-16
AB  - The draft genome sequences of two clonal, pandrug-resistant Serratia marcescens clinical
      isolates were determined. The resistance phenotype was plasmid driven,
      as 14 of 17 resistance genes were present on large IncFIB(K), IncHI2, and IncA/C2
      plasmids indicating a large pool of transmissible antibiotic resistance genes.
AU  - Yao Y
AU  - Falgenhauer L
AU  - Kempf VA
AU  - Hogardt M
AU  - Gottig S
AU  - Imirzalioglu C
AU  - Chakraborty T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01481-16.

PMID- 25395635
VI  - 2
DP  - 2014
TI  - Complete Nucleotide Sequence of a Citrobacter freundii Plasmid Carrying KPC-2 in  a Unique Genetic Environment.
PG  - e01157-14
AB  - The complete and annotated nucleotide sequence of a 54,036-bp plasmid harboring a blaKPC-2
      gene that is clonally present in Citrobacter isolates from different
      species is presented. The plasmid belongs to incompatibility group N (IncN) and
      harbors the class A carbapenemase KPC-2 in a unique genetic environment.
AU  - Yao Y
AU  - Imirzalioglu C
AU  - Hain T
AU  - Kaase M
AU  - Gatermann S
AU  - Exner M
AU  - Mielke M
AU  - Hauri A
AU  - Dragneva Y
AU  - Bill R
AU  - Wendt C
AU  - Wirtz A
AU  - Domann E
AU  - Chakraborty T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01157-14.

PMID- 23012289
VI  - 194
DP  - 2012
TI  - Genome sequence of a nicotine-degrading strain of arthrobacter.
PG  - 5714-5715
AB  - We announce a 4.63-Mb genome assembly of an isolated bacterium that is the first  sequenced
      nicotine-degrading Arthrobacter strain. Nicotine catabolism genes of
      the nicotine-degrading plasmid pAO1 were predicted, but plasmid function genes
      were not found. These results will help to better illustrate the molecular
      mechanism of nicotine degradation by Arthrobacter.
AU  - Yao Y
AU  - Tang H
AU  - Ren H
AU  - Yu H
AU  - Wang L
AU  - Xu P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5714-5715.

PMID- 28209835
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of a Colistin-Resistant Klebsiella pneumoniae Clinical Strain Carrying the blaNDM-1 Carbapenemase Gene.
PG  - e01654-16
AB  - Klebsiella pneumoniae strain WCHKP1845, recovered from the sputum of a patient with pneumonia,
      was resistant to colistin and carried the carbapenemase gene
      blaNDM-1 Here, we report its 5.4-Mb draft genome sequence, comprising 140 contigs
      with an average 57.33% G+C content. The genome contains 5,118 coding sequences
      and 88 tRNA genes.
AU  - Yao Z
AU  - Feng Y
AU  - Lin J
AU  - Zong Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01654-16.

PMID- 28183754
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of a Sequence Type 11 Klebsiella pneumoniae Clinical Strain Carrying a blaKPC-2 Carbapenemase Gene and an rmtB 16S rRNA Methylase Gene.
PG  - e01549-16
AB  - Klebsiella pneumoniae strain WCHKP649, recovered from a human wound, carried the
      carbapenemase gene blaKPC-2 and 16S rRNA methylase gene rmtB Here, we report its
      5.6-Mb draft genome sequence, comprising 171 contigs with an average 57.34% G+C
      content. The genome contained 5,284 coding sequences and 84 tRNA genes.
AU  - Yao Z
AU  - Feng Y
AU  - Wei L
AU  - Zong Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01549-16.

PMID- 24136854
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Pasteurella multocida subsp. multocida Strain PMTB, Isolated from a Buffalo.
PG  - e00872-13
AB  - Pasteurella multocida serotypes B:2 and E:2 are the main causative agents of ruminant
      hemorrhagic septicemia in Asia and Africa, respectively. Pasteurella
      multocida strain PMTB was isolated from a buffalo with hemorrhagic septicemia and
      has been determined to be serotype B:2. Here we report the draft genome sequence
      of strain PMTB.
AU  - Yap HY
AU  - Ghazali K
AU  - Wan MNWF
AU  - Mat IMN
AU  - Zakaria Z
AU  - Omar AR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00872-13.

PMID- 23045488
VI  - 194
DP  - 2012
TI  - Genome Sequence and Comparative Pathogenomics Analysis of a Salmonella enterica Serovar Typhi Strain Associated with a Typhoid Carrier in Malaysia.
PG  - 5970-5971
AB  - Salmonella enterica serovar Typhi is a human pathogen that causes typhoid fever predominantly
      in developing countries. In this article, we describe the whole
      genome sequence of the S. Typhi strain CR0044 isolated from a typhoid fever
      carrier in Kelantan, Malaysia. These data will further enhance the understanding
      of its host persistence and adaptive mechanism.
AU  - Yap KP
AU  - Gan HM
AU  - Teh CS
AU  - Baddam R
AU  - Chai LC
AU  - Kumar N
AU  - Tiruvayipati SA
AU  - Ahmed N
AU  - Thong KL
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5970-5971.

PMID- 22933756
VI  - 194
DP  - 2012
TI  - Insights from the Genome Sequence of a Salmonella enterica Serovar Typhi Strain Associated with a Sporadic Case of Typhoid Fever in Malaysia.
PG  - 5124-5125
AB  - Salmonella enterica serovar Typhi is the causative agent of typhoid fever, which  causes
      nearly 21.7 million illnesses and 217,000 deaths globally. Herein, we
      describe the whole-genome sequence of the Salmonella Typhi strain ST0208,
      isolated from a sporadic case of typhoid fever in Kuala Lumpur, Malaysia. The
      whole-genome sequence and comparative genomics allow an in-depth understanding of
      the genetic diversity, and its link to pathogenicity and evolutionary dynamics,
      of this highly clonal pathogen that is endemic to Malaysia.
AU  - Yap KP
AU  - Teh CS
AU  - Baddam R
AU  - Chai LC
AU  - Kumar N
AU  - Avasthi TS
AU  - Ahmed N
AU  - Thong KL
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5124-5125.

PMID- 7846528
VI  - 267
DP  - 1995
TI  - Programmed cell death in bacterial populations.
PG  - 836-837
AB  - Multicellular organisms benefit not only from the death of competitors, but often, quite
      dramatically, from the programmed death of specific subpopulations of their own cells. Popular
      opinion to the contrary, programmed cell death is also alive and well in the microbial world.
      A striking report by Naito et al. in this issue of Science is a case in point.
AU  - Yarmolinsky MB
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 1995 267: 836-837.

PMID- 24072869
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Exopolysaccharide-Producing Thermophilic Bacterium Brevibacillus thermoruber Strain 423.
PG  - e00774-13
AB  - Brevibacillus thermoruber strain 423 is a Gram-positive, spore-forming, aerobic,  and
      thermophilic bacterium that produces mannogalactoglucan exopolysaccharide (EPS). We report the
      draft genome sequence of B. thermoruber 423, which will accelerate research on the cellular
      organization of thermophilic bacteria, as well as the rational design and optimization of EPS
      production.
AU  - Yasar-Yildiz S
AU  - Kambourova M
AU  - Arga KY
AU  - Toksoy OE
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00774-13.

PMID- 21304742
VI  - 3
DP  - 2010
TI  - Complete genome sequence of Arcanobacterium haemolyticum type strain (11018).
PG  - 126-135
AB  - Arcanobacterium haemolyticum (ex MacLean et al. 1946) Collins et al. 1983 is the  type species
      of the genus Arcanobacterium, which belongs to the family
      Actinomycetaceae. The strain is of interest because it is an obligate parasite of
      the pharynx of humans and farm animal; occasionally, it causes pharyngeal or skin
      lesions. It is a Gram-positive, nonmotile and non-sporulating bacterium. The
      strain described in this study was isolated from infections amongst American
      soldiers of certain islands of the North and West Pacific. This is the first
      completed sequence of a member of the genus Arcanobacterium and the ninth type
      strain genome from the family Actinomycetaceae. The 1,986,154 bp long genome with
      its 1,821 protein-coding and 64 RNA genes is a part of the Genomic Encyclopedia
      of Bacteria and Archaea project.
AU  - Yasawong M et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2010 3: 126-135.

PMID- 26380638
VI  - 10
DP  - 2015
TI  - High quality draft genome sequence of Corynebacterium ulceribovis type strain IMMIB-L1395(T) (DSM 45146(T)).
PG  - 50
AB  - Corynebacterium ulceribovis strain IMMIB L-1395(T) (= DSM 45146(T)) is an aerobic to
      facultative anaerobic, Gram-positive, non-spore-forming, non-motile rod-shaped bacterium that
      was isolated from the skin of the udder of a cow, in Schleswig Holstein, Germany. The cell
      wall of C. ulceribovis contains corynemycolic acids.  The cellular fatty acids are those
      described for the genus Corynebacterium, but tuberculostearic acid is not present. Here we
      describe the features of C. ulceribovis strain IMMIB L-1395(T), together with genome sequence
      information and its annotation. The 2,300,451 bp long genome containing 2,104 protein-coding
      genes and 54 RNA-encoding genes and is part of the Genomic Encyclopedia of Type Strains, Phase
      I: the one thousand microbial genomes (KMG) project.
AU  - Yassin AF
AU  - Lapidus A
AU  - Han J
AU  - Reddy TB
AU  - Huntemann M
AU  - Pati A
AU  - Ivanova N
AU  - Markowitz V
AU  - Woyke T
AU  - Klenk HP
AU  - Kyrpides NC
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 50.

PMID- 19004868
VI  - 37
DP  - 2009
TI  - Improvement of bacterial transformation efficiency using plasmid artificial modification.
PG  - e3
AB  - We have developed a method to improve the transformation efficiency in genome-sequenced
      bacteria, using 'Plasmid Artificial Modification' (PAM),
      using the host's own restriction system. In this method, a shuttle vector
      was pre-methylated in Escherichia coli cells, which carry all the putative
      genes encoding the DNA modification enzymes of the target microorganism,
      before electroporation was performed. In the case of Bifidobacterium
      adolescentis ATCC15703 and pKKT427 (3.9 kb E. coli-Bifidobacterium shuttle
      vector), introducing two Type II DNA methyltransferase genes lead to an
      enhancement in the transformation efficiency by five orders of magnitude.
      This concept was also applicable to a Type I restriction system. In the
      case of Lactococcus lactis IO-1, by using PAM with a putative Type I
      methyltransferase system, hsdMS1, the transformation efficiency was
      improved by a factor of seven over that without PAM.
AU  - Yasui K
AU  - Kano Y
AU  - Tanaka K
AU  - Watanabe K
AU  - Shimizu-Kadota M
AU  - Yoshikawa H
AU  - Suzuki T
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: e3.

PMID- 23868120
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Agarivorans albus Strain MKT 106T, an Agarolytic Marine  Bacterium.
PG  - e00367-13
AB  - Agarivorans albus is a Gram-negative, strictly aerobic, and agar-hydrolyzing marine bacterium.
      We present the draft genome sequence of the A. albus strain MKT
      106(T), which is composed of 67 contigs (>500 bp) totaling 4,734,285 bp and
      containing 4,397 coding DNA sequences (CDSs), four rRNAs, and 64 tRNA sequences.
AU  - Yasuike M
AU  - Nakamura Y
AU  - Kai W
AU  - Fujiwara A
AU  - Fukui Y
AU  - Satomi M
AU  - Sano M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00367-13.

PMID- 28257489
VI  - 12
DP  - 2017
TI  - Analysis of the complete genome sequence of Nocardia seriolae UTF1, the causative agent of fish nocardiosis: The first reference genome sequence of the fish pathogenic Nocardia species.
PG  - E0173198
AB  - Nocardiosis caused by Nocardia seriolae is one of the major threats in the
      aquaculture of Seriola species (yellowtail; S. quinqueradiata, amberjack; S.
      dumerili and kingfish; S. lalandi) in Japan. Here, we report the complete
      nucleotide genome sequence of N. seriolae UTF1, isolated from a cultured
      yellowtail. The genome is a circular chromosome of 8,121,733 bp with a G+C
      content of 68.1% that encodes 7,697 predicted proteins. In the N. seriolae UTF1
      predicted genes, we found orthologs of virulence factors of pathogenic
      mycobacteria and human clinical Nocardia isolates involved in host cell invasion,
      modulation of phagocyte function and survival inside the macrophages. The
      virulence factor candidates provide an essential basis for understanding their
      pathogenic mechanisms at the molecular level by the fish nocardiosis research
      community in future studies. We also found many potential antibiotic resistance
      genes on the N. seriolae UTF1 chromosome. Comparative analysis with the four
      existing complete genomes, N. farcinica IFM 10152, N. brasiliensis HUJEG-1 and N.
      cyriacigeorgica GUH-2 and N. nova SH22a, revealed that 2,745 orthologous genes
      were present in all five Nocardia genomes (core genes) and 1,982 genes were
      unique to N. seriolae UTF1. In particular, the N. seriolae UTF1 genome contains a
      greater number of mobile elements and genes of unknown function that comprise the
      differences in structure and gene content from the other Nocardia genomes. In
      addition, a lot of the N. seriolae UTF1-specific genes were assigned to the ABC
      transport system. Because of limited resources in ocean environments, these N.
      seriolae UTF1 specific ABC transporters might facilitate adaptation strategies
      essential for marine environment survival. Thus, the availability of the complete
      N. seriolae UTF1 genome sequence will provide a valuable resource for comparative
      genomic studies of N. seriolae isolates, as well as provide new insights into the
      ecological and functional diversity of the genus Nocardia.
AU  - Yasuike M
AU  - Nishiki I
AU  - Iwasaki Y
AU  - Nakamura Y
AU  - Fujiwara A
AU  - Shimahara Y
AU  - Kamaishi T
AU  - Yoshida T
AU  - Nagai S
AU  - Kobayashi T
AU  - Katoh M
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2017 12: E0173198.

PMID- 26380632
VI  - 10
DP  - 2015
TI  - High-quality permanent draft genome sequence of Rhizobium sullae strain WSM1592;  a Hedysarum coronarium microsymbiont from Sassari, Italy.
PG  - 44
AB  - Rhizobium sullae strain WSM1592 is an aerobic, Gram-negative, non-spore-forming rod that was
      isolated from an effective nitrogen (N2) fixing root nodule formed on the short-lived
      perennial legume Hedysarum coronarium (also known as Sulla coronaria or Sulla). WSM1592 was
      isolated from a nodule recovered from H. coronarium roots located in Ottava, bordering
      Sassari, Sardinia in 1995. WSM1592  is highly effective at fixing nitrogen with H. coronarium,
      and is currently the commercial Sulla inoculant strain in Australia. Here we describe the
      features of  R. sullae strain WSM1592, together with genome sequence information and its
      annotation. The 7,530,820 bp high-quality permanent draft genome is arranged into 118
      scaffolds of 118 contigs containing 7.453 protein-coding genes and 73 RNA-only encoding genes.
      This rhizobial genome is sequenced as part of the DOE Joint Genome Institute 2010 Genomic
      Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.
AU  - Yates R
AU  - Howieson J
AU  - De Meyer SE
AU  - Tian R
AU  - Seshadri R
AU  - Pati A
AU  - Woyke T
AU  - Markowitz V
AU  - Ivanova N
AU  - Kyrpides N
AU  - Loi A
AU  - Nutt B
AU  - Garau G
AU  - Sulas L
AU  - Reeve W
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 44.

PMID- Not carried by PubMed...
VI  - 198
DP  - 1989
TI  - The synthesis of complex 6'-alkynyl-6'-dethia analogs of s-adenosylhomocysteine as potential inhibitors of methyltransferases.
PG  - 100
AB  - A new series of multisubstrate adduct inhibitors was designed for
      S-adenosylmethionine-dependent methyltransferases.  Three synthetic routes to
      this class of compounds were investigated and
      5'-(6-amino-6-carboxy-1-phenyl-1-hexynyl-3-)-5'-deoxyadenosine was synthesized
      as a prototype.  The key step in the successful synthesis was the arylation of
      N6-benzoyl-2',3'-isopropylidene-5'(5-tert-butyldiphenylsilyloxy-1-pentynyl-3)-5
      '-deoxyadenosine, a terminal acetylene, with an aryl iodide in the presence of
      Pd(II) and CuI catalysts.  This method should be generally useful for the
      synthesis of specific inhibitors of S-adenosylmethionine-dependent
      methyltransferases.  5'-(4-Amino-4-carboxybutyl-1-)-5'-deoxyadenosine, a
      6'-carbon analog of S-adenosylhomocysteine, was also synthesized in the process
      of investigating methods for constructing an amino acid moiety on the side
      chain of this class of compounds.
AU  - Yau EK
AU  - Coward JK
PT  - Journal Article
TA  - ACS Abstracts
JT  - ACS Abstracts
SO  - ACS Abstracts 1989 198: 100.

PMID- 21444812
VI  - 108
DP  - 2011
TI  - Virophage control of antarctic algal host-virus dynamics.
PG  - 6163-6168
AB  - Viruses are abundant ubiquitous members of microbial communities and in
      the marine environment affect population structure and nutrient cycling by
      infecting and lysing primary producers. Antarctic lakes are microbially
      dominated ecosystems supporting truncated food webs in which viruses exert
      a major influence on the microbial loop. Here we report the discovery of a
      virophage (relative of the recently described Sputnik virophage) that
      preys on phycodnaviruses that infect prasinophytes (phototrophic algae).
      By performing metaproteogenomic analysis on samples from Organic Lake, a
      hypersaline meromictic lake in Antarctica, complete virophage and
      near-complete phycodnavirus genomes were obtained. By introducing the
      virophage as an additional predator of a predator-prey dynamic model we
      determined that the virophage stimulates secondary production through the
      microbial loop by reducing overall mortality of the host and increasing
      the frequency of blooms during polar summer light periods. Virophages
      remained abundant in the lake 2 y later and were represented by
      populations with a high level of major capsid protein sequence variation
      (25-100% identity). Virophage signatures were also found in neighboring
      Ace Lake (in abundance) and in two tropical lakes (hypersaline and fresh),
      an estuary, and an ocean upwelling site. These findings indicate that
      virophages regulate host-virus interactions, influence overall carbon flux
      in Organic Lake, and play previously unrecognized roles in diverse aquatic
      ecosystems.
AU  - Yau S
AU  - Lauro FM
AU  - DeMaere MZ
AU  - Brown MV
AU  - Thomas T
AU  - Raftery MJ
AU  - Andrews-Pfannkoch C
AU  - Lewis M
AU  - Hoffman JM
AU  - Gibson JA
AU  - Cavicchioli R
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2011 108: 6163-6168.

PMID- 25555735
VI  - 3
DP  - 2015
TI  - Complete Genome Sequences of T4-Like Bacteriophages RB3, RB5, RB6, RB7, RB9, RB10, RB27, RB33, RB55, RB59, and RB68.
PG  - e01122-14
AB  - T4-like bacteriophages have been explored for phage therapy and are model organisms for phage
      genomics and evolution. Here, we describe the sequencing of
      11 T4-like phages. We found a high nucleotide similarity among the T4, RB55, and
      RB59; RB32 and RB33; and RB3, RB5, RB6, RB7, RB9, and RB10 phages.
AU  - Yaung SJ
AU  - Esvelt KM
AU  - Church GM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01122-14.

PMID- 
VI  - 0
DP  - 2001
TI  - Characterization of methicillin-resistant Staphylococcus aureus isolated at Hotel-Dieu Hospital, Montreal.
PG  - Abstract #P301
AB  - The first objective of this study was to characterize fifty methicillin resistant
      Staphylococcus aureus (MRSZA) strains, isolated in 1999/2000 from Hotel-Dieu Hospital
      patients, by using antibiogram and DNA analysis.  The second objective was to determine
      whether our recently discovered restriction enzyme LlaGI shows a digestive activity towards
      MRSA DNA.  The evaluation of antibiotic resistance (by MIC) to methicillin, oxacillin,
      erythromycin and cephazolin, showed multi resistance for these drugs for all fifty MRSA
      strains.  In contrast, all MRSA strains were sensitive to vancomycin.  We purified the DNA
      (plasmidic
AU  - Yazdanparast S
AU  - Toma E
AU  - Karska-Wysocki B
PT  - Journal Article
TA  - Ottawa Life Sciences Internl Conf. and Exhibit.
JT  - Ottawa Life Sciences Internl Conf. and Exhibit.
SO  - Ottawa Life Sciences Internl Conf. and Exhibit. 2001 0: Abstract #P301.

PMID- 
VI  - 0
DP  - 2002
TI  - Restriction enzyme activity for subgenomic discrimination of  Methicillin-resistant Staphylococcus aureus.
PG  - abstract #100
AB  - The dissemination of methicillin-resistant Staphylococcus aureus has important consequences in
      health-care as it is the source of many outbreaks in hospital centers.  Presently, the primary
      focus of most hospital infection control programs is to reduce the prevalence of MRSA
      infection by rapidly detecting the source of these organisms and by interrupting their
      transmission to patients.  We previously reported the development of a strain discrimination
      procedure using fifty MRSA clinical isolates from a hospital center.  After evaluation of the
      multidrug-resistance of MRSA strains, we determined their electrophoretic plasmid DNA profile.
      We can differentiate fifty strains into eleven groups.  In addition, we have investigated the
      Restriction Fragment Length Polymorphism of plasmidic and genomic DNA after digestion with
      EcoRI, HindIII and the recently discovered LlaGI restriction enzyme.  In this study we
      characterized the plasmid DNA fragments of MRSA strains digested by LlaGI.  This procedure was
      followed by analysis of genomic DNA amplicons profiles generated by arbitrarily primed PCR.
      We were able to subtype our representative MRSA isolates into 3 types which were clearly
      different from each other.  The discriminatory power of genomic DNA AP-PCR fingerprinting can
      be increased, after digestion of amplicons with restriction enzyme and analysis the generated
      electrophoretic fragments profiles.  In order to discriminate more precisely the MRSA strains,
      we digested AP-PCR amplicons by AluI.  After analysis of the electrophoretic digest patterns
      of these amplicons, we were able to identify the individual strains.  To our knowledge, this
      is the first report of MRSA strain identification with RFLP or AP-PCR-RFLP procedures, using
      these two enzymes, LlaGI and AluI, respectively.  We conclude that the combination of
      procedures, such as analysis of electrophoretic plasmid profiles, analysis of genomic DNA
      using AP-PCR and AP-PCR-RFLP were most efficacious for identification of individual MRSA
      strains.  Our development of a new typing schema demonstrates the novel restriction enzyme
      activity application for subgenomic discrimination of MRSA strains.
AU  - Yazdanparast S
AU  - Toma E
AU  - Karska-Wysocki B
PT  - Journal Article
TA  - Abstracts of IBC's 7th Annual World Congress
JT  - Abstracts of IBC's 7th Annual World Congress
SO  - Abstracts of IBC's 7th Annual World Congress 2002 0: abstract #100.

PMID- 29167245
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Enterococcus thailandicus Strain a523 Isolated from Urban Raw Sewage.
PG  - e01298-17
AB  - We report here the first complete circularly closed genome sequence of Enterococcus
      thailandicus strain a523 isolated from raw urban sewage. This genome
      contains 2,646,250 bp with a G+C content of 36.8%, 2,499 genes, 2,370
      protein-coding sequences, 6 rRNA operons, 65 tRNAs, and 6 clustered regularly
      interspaced short palindromic repeat arrays.
AU  - Ybazeta G
AU  - Douglas L
AU  - Graham J
AU  - Fraleigh NL
AU  - Murad Y
AU  - Perez J
AU  - Diaz-Mitoma F
AU  - Tilbe K
AU  - Nokhbeh R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01298-17.

PMID- 19016627
VI  - 199
DP  - 2009
TI  - Clinical, experimental, and genomic differences between intermediately pathogenic, highly pathogenic, and epidemic Streptococcus suis.
PG  - 97-107
AB  - BACKGROUND: Streptococcus suis emerged to cause an unusual outbreak of
      streptococcal toxic-shock-like syndrome (STSLS) in 2005. The mechanisms
      involved are unknown. METHODS: Clinical, laboratory, and epidemiologic
      data on patients infected with culture-confirmed S. suis were analyzed.
      The strain involved in the outbreak, "epidemic" strain ST7, was compared
      with both a classical highly pathogenic strain, ST1, and an intermediately
      pathogenic strain, ST25, to determine both its capacity to induce
      cytokines in experimentally infected mice and its genomic difference.
      RESULTS: Of 38 patients infected with culture-confirmed S. suis, 14
      presented with STSLS. During the early phase of the disease, serum levels
      of interleukin (IL)-1beta, IL-6, IL-8, IL-12p70, interferon-gamma, and
      tumor necrosis factor-alpha were more elevated in patients with STSLS than
      in those with meningitis only. Serum levels of proinflammatory cytokines
      were significantly higher in mice infected with ST7 than in those infected
      with either ST1 or ST25. Genomic comparisons with ST25 showed that ST1 had
      acquired 132 genomic islands, including 5 pathogenicity islands, and that
      ST7, the epidemic strain, had acquired an additional 5 genomic islands.
      CONCLUSION: Intermediately pathogenic strain ST25 has evolved to become
      highly pathogenic strain ST1, which, in turn, has more recently evolved to
      become epidemic strain ST7. ST7 has the ability to stimulate the
      production of massive amounts of proinflammatory cytokines, leading to
      STSLS.
AU  - Ye C
AU  - Zheng H
AU  - Zhang J
AU  - Jing H
AU  - Wang L
AU  - Xiong Y
AU  - Wang W
AU  - Zhou Z
AU  - Sun Q
AU  - Luo X
AU  - Du H
AU  - Gottschalk M
AU  - Xu J
PT  - Journal Article
TA  - J. Infect. Dis.
JT  - J. Infect. Dis.
SO  - J. Infect. Dis. 2009 199: 97-107.

PMID- 27081145
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Aldehyde-Degrading Strain Halomonas axialensis ACH-L-8.
PG  - e00287-16
AB  - Halomonas axialensisACH-L-8, a deep-sea strain isolated from the South China Sea, has the
      ability to degrade aldehydes. Here, we present an annotated draft genome
      sequence of this species, which could provide fundamental molecular information
      on the aldehydes-degrading mechanism.
AU  - Ye J
AU  - Ren C
AU  - Shan X
AU  - Zeng R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00287-16.

PMID- 25369289
VI  - 9
DP  - 2014
TI  - Draft Genome Sequence Analysis of a Pseudomonas putida W15Oct28 Strain with Antagonistic Activity to Gram-Positive and Pseudomonas sp. Pathogens.
PG  - E110038
AB  - Pseudomonas putida is a member of the fluorescent pseudomonads known to produce
      the yellow-green fluorescent pyoverdine siderophore. P. putida W15Oct28, isolated
      from a stream in Brussels, was found to produce compound(s) with antimicrobial
      activity against the opportunistic pathogens Staphylococcus aureus, Pseudomonas
      aeruginosa, and the plant pathogen Pseudomonas syringae, an unusual
      characteristic for P. putida. The active compound production only occurred in
      media with low iron content and without organic nitrogen sources. Transposon
      mutants which lost their antimicrobial activity had the majority of insertions in
      genes involved in the biosynthesis of pyoverdine, although purified pyoverdine
      was not responsible for the antagonism. Separation of compounds present in
      culture supernatants revealed the presence of two fractions containing highly
      hydrophobic molecules active against P. aeruginosa. Analysis of the draft genome
      confirmed the presence of putisolvin biosynthesis genes and the corresponding
      lipopeptides were found to contribute to the antimicrobial activity. One cluster
      of ten genes was detected, comprising a NAD-dependent epimerase, an
      acetylornithine aminotransferase, an acyl CoA dehydrogenase, a short chain
      dehydrogenase, a fatty acid desaturase and three genes for a RND efflux pump. P.
      putida W15Oct28 genome also contains 56 genes encoding TonB-dependent receptors,
      conferring a high capacity to utilize pyoverdines from other pseudomonads. One
      unique feature of W15Oct28 is also the presence of different secretion systems
      including a full set of genes for type IV secretion, and several genes for type
      VI secretion and their VgrG effectors.
AU  - Ye L
AU  - Hildebrand F
AU  - Dingemans J
AU  - Ballet S
AU  - Laus G
AU  - Matthijs S
AU  - Berendsen R
AU  - Cornelis P
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2014 9: E110038.

PMID- 27965935
VI  - 6
DP  - 2016
TI  - Clinical and Genomic Analysis of Liver Abscess-Causing Klebsiella pneumoniae Identifies New Liver Abscess-Associated Virulence Genes.
PG  - 165
AB  - Hypervirulent variants of Klebsiella pneumoniae (hvKp) that cause invasive
      community-acquired pyogenic liver abscess (PLA) have emerged globally. Little is
      known about the virulence determinants associated with hvKp, except for the
      virulence genes rmpA/A2 and siderophores (iroBCD/iucABCD) carried by the
      pK2044-like large virulence plasmid. Here, we collected most recent clinical
      isolates of hvKp from PLA samples in China, and performed clinical, molecular,
      and genomic sequencing analyses. We found that 90.9% (40/44) of the pathogens
      causing PLA were K. pneumoniae. Among the 40 LA-Kp, K1 (62.5%), and K2 (17.5%)
      were the dominant serotypes, and ST23 (47.5%) was the major sequence type.
      S1-PFGE analyses demonstrated that although 77.5% (31/40) of the LA-Kp isolates
      harbored a single large virulence plasmid varied in size, 5 (12.5%) isolates had
      no plasmid and 4 (10%) had two or three plasmids. Whole genome sequencing and
      comparative analysis of 3 LA-Kp and 3 non-LA-Kp identified 133 genes present only
      in LA-Kp. Further, large scale screening of the 133 genes in 45 LA-Kp and 103
      non-LA-Kp genome sequences from public databases identified 30 genes that were
      highly associated with LA-Kp, including iroBCD, iucABCD and rmpA/A2 and 21 new
      genes. Then, these 21 new genes were analyzed in 40 LA-Kp and 86 non-LA-Kp
      clinical isolates collected in this study by PCR, showing that new genes were
      present 80-100% among LA-Kp isolates while 2-11% in K. pneumoniae isolates from
      sputum and urine. Several of the 21 genes have been proposed as virulence factors
      in other bacteria, such as the gene encoding SAM-dependent methyltransferase and
      pagO which protects bacteria from phagocytosis. Taken together, these genes are
      likely new virulence factors contributing to the hypervirulence phenotype of
      hvKp, and may deepen our understanding of virulence mechanism of hvKp.
AU  - Ye M
AU  - Tu J
AU  - Jiang J
AU  - Bi Y
AU  - You W
AU  - Zhang Y
AU  - Ren J
AU  - Zhu T
AU  - Cao Z
AU  - Yu Z
AU  - Shao C
AU  - Shen Z
AU  - Ding B
AU  - Yuan J
AU  - Zhao X
AU  - Guo Q
AU  - Xu X
AU  - Huang J
AU  - Wang M
PT  - Journal Article
TA  - Front Cell Infect Microbiol
JT  - Front Cell Infect Microbiol
SO  - Front Cell Infect Microbiol 2016 6: 165.

PMID- 27924023
VI  - 45
DP  - 2017
TI  - MethSMRT: an integrative database for DNA N6-methyladenine and N4-methylcytosine  generated by single-molecular real-time sequencing.
PG  - D85-D89
AB  - DNA methylation is an important type of epigenetic modifications, where 5- methylcytosine
      (5mC), 6-methyadenine (6mA) and 4-methylcytosine (4mC) are the
      most common types. Previous efforts have been largely focused on 5mC, providing
      invaluable insights into epigenetic regulation through DNA methylation. Recently
      developed single-molecule real-time (SMRT) sequencing technology provides a
      unique opportunity to detect the less studied DNA 6mA and 4mC modifications at
      single-nucleotide resolution. With a rapidly increased amount of SMRT sequencing
      data generated, there is an emerging demand to systematically explore DNA 6mA and
      4mC modifications from these data sets. MethSMRT is the first resource hosting
      DNA 6mA and 4mC methylomes. All the data sets were processed using the same
      analysis pipeline with the same quality control. The current version of the
      database provides a platform to store, browse, search and download epigenome-wide
      methylation profiles of 156 species, including seven eukaryotes such as
      Arabidopsis, C. elegans, Drosophila, mouse and yeast, as well as 149 prokaryotes.
      It also offers a genome browser to visualize the methylation sites and related
      information such as single nucleotide polymorphisms (SNP) and genomic annotation.
      Furthermore, the database provides a quick summary of statistics of methylome of
      6mA and 4mC and predicted methylation motifs for each species. MethSMRT is
      publicly available at http://sysbio.sysu.edu.cn/methsmrt/ without use
      restriction.
AU  - Ye P
AU  - Luan Y
AU  - Chen K
AU  - Liu Y
AU  - Xiao C
AU  - Xie Z
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2017 45: D85-D89.

PMID- 23209241
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Pathogenic Herbaspirillum seropedicae Strain Os34, Isolated from Rice Roots.
PG  - 6993-6994
AB  - Most Herbaspirillum seropedicae strains are beneficial endophytes to plants. In contrast, H.
      seropedicae strain Os34, isolated from rice roots, is pathogenic.
      The draft genome sequence of strain Os34 presented here allows in-depth
      comparative genome analyses to understand the specific mechanisms of beneficial
      and pathogenic Herbaspirillum-plant interactions.
AU  - Ye W
AU  - Ye S
AU  - Liu J
AU  - Chang S
AU  - Chen M
AU  - Zhu B
AU  - Guo L
AU  - An Q
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6993-6994.

PMID- 20197058
VI  - 401
DP  - 2010
TI  - Fluorescence-based high-throughput assay for human DNA (cytosine-5)-methyltransferase 1.
PG  - 168-172
AB  - We have developed the first economical and rapid nonradioactive assay method that is suitable
      for high-throughput screening of the important
      pharmacological target human DNA (cytosine-5)-methyltransferase 1
      (DNMT1). The method combines three key innovations: the use of a
      truncated form of the enzyme that is highly active on a 26-bp
      hemimethylated DNA duplex substrate, the introduction of the
      methylation site into the recognition sequence of a restriction
      endonuclease, and the use of a fluorogenic read-out method. The extent
      of DNMT1 methylation is reflected in the protection of the DNA
      substrate from endonuclease cleavage that would otherwise result in a
      large fluorescence increase. The assay has been validated in a
      high-throughput format, and trivial changes in the substrate sequence
      and endonuclease allow adaptation of the method to any bacterial or
      human DNA methyltransferase.
AU  - Ye Y
AU  - Stivers JT
PT  - Journal Article
TA  - Anal. Biochem.
JT  - Anal. Biochem.
SO  - Anal. Biochem. 2010 401: 168-172.

PMID- 7578083
VI  - 34
DP  - 1995
TI  - A cytosine methyltransferase converts 5-methylcytosine in DNA to thymine.
PG  - 14752-14757
AB  - Sites of cytosine methylation are known to be hot spots for C.G to T.A mutations in a number
      of systems, including human cells.  Traditionally, spontaneous hydrolytic deamination of
      5-methylcytosine to thymine has been invoked as the cause of this phenomenon.  We show here
      that a bacterial cytosine methyltransferase can convert 5-methylcytosine in DNA to thymine and
      that this reaction creates a mutational hot spot at a site of DNA methylation.  The reaction
      is fairly insensitive to the methyl donor in the reaction, S-adenosylmethionine.  In many
      cancers, the most frequent class of mutations is C to T changes within CG dinucleotides of the
      tumor suppressor gene p53.  Because of the similarities of the reaction mechanisms of
      mammalian and bacterial enzymes and the physiology of the cancer cells, this reaction is
      expected to contribute to mutations at CG dinucleotides in precancerous cells.
AU  - Yebra MJ
AU  - Bhagwat AS
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1995 34: 14752-14757.

PMID- 7590324
VI  - 164
DP  - 1995
TI  - A novel repetitive sequence lies near the gene encoding a cytosine methyltransferase in the cyanobacterium Dactylococcopsis salina.
PG  - 71-74
AB  - An unusual cluster of tandemly repeated DNA sequences (TRS) was found downstream from the gene
      encoding DsaV methyltransferase, the DNA modification enzyme in the DsaV
      restriction-modification system found in a strain of Dactylococcopsis salina (Ds).  The repeat
      unit is about 32-bp long and is present 13 times in the cluster.  Each repeat unit can be
      divided into two distinct parts based on the level of sequence conservation and evolution.
      Hybridization of Ds DNA with a probe specific for this cluster revealed that there were at
      least two additional sites within the genome with similar TRS.  The TRS units are localized in
      one region of the Ds genome.  They do not share significant sequence similarity with other TRS
      found in prokaryotes.
AU  - Yebra MJ
AU  - Bhagwat AS
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1995 164: 71-74.

PMID- 8284233
VI  - 21
DP  - 1993
TI  - A rapid and sensitive method to measure DNA endonuclease activity.
PG  - 5797-5798
AB  - The high affinity of biotin for streptavidin has been used to isolate DNA-binding proteins
      from cells. This is achieved by mixing DNA oligomers and containing biotin with cell extracts
      and then passing the mixture over immobilized streptavidin. We describe below an adaptation of
      this method to quantitate the activities of endonucleases. It should be useful for detecting
      endonuclease activity during enzyme purification, for studying inhibitors and activators of
      nucleases and for determining kinetic properties of endonucleases.
AU  - Yebra MJ
AU  - Bhagwat AS
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 5797-5798.

PMID- 1919505
VI  - 137
DP  - 1991
TI  - Characterization of Rrh4273I, a restriction-modification system of Rhodococcus rhodochrous ATCC 4273 (Nocardia corallina) which recognizes the same sequence as the Streptomyces albus G SalI restriction-modification system.
PG  - 1279-1284
AB  - Rhodococcus rhodochrous ATCC 4273 (Nocardia corallina) has a
      restriction-modification system with the same recognition sequence, methylation
      site and cleavage site as the SalI restriction-modification system.  Both the
      restriction endonuclease and the DNA-methyltransferase (DNA-MTase) have been
      partially purified and characterized.  The nuclease has requirements for
      activity similar to SalI, and a native Mr of about 46,000.  The DNA-MTase is a
      protein with an Mr of about 67,000.  No DNA homology was detected between the
      cloned SalI restriction-modification genes of Streptomyces albus and R.
      rhodochrous chromosomal DNA.
AU  - Yebra MJ
AU  - Novella IS
AU  - Barbes C
AU  - Aparicio JF
AU  - Martin CG
AU  - Hardisson C
AU  - Sanchez J
PT  - Journal Article
TA  - J. Gen. Microbiol.
JT  - J. Gen. Microbiol.
SO  - J. Gen. Microbiol. 1991 137: 1279-1284.

PMID- 1720117
VI  - 44
DP  - 1991
TI  - The effect of sinefungin and synthetic analogues on RNA and DNA methyltransferase from Streptomyces.
PG  - 1141-1147
AB  - Sinefungin is an antibiotic structurally related to S-adenosylmethionine.  It
      has been described as an inhibitor of RNA transmethylation reactions in viruses
      and eukaryotic organisms, but not in bacteria.  We show here that sinefungin
      strongly inhibits RNA methyltransferase activity, but not the biosynthesis of
      these enzymes in Streptomyces.  All the methylated bases found in Streptomyces
      RNA (1-methyladenine, N6-methyladenine, N6,N6-dimethyladenine and
      7-methylguanine) are inhibited by this antibiotic.  Experiments with sinefungin
      analogues show that specific changes in the ornithine radical of the molecule
      still preserve its inhibitory capability.  The substitution of the adenine
      radical by uridine causes the loss of inhibitory effect.  These results and our
      former studies on Streptomyces DNA methylation, suggest that nucleic acid
      modification is the main target of sinefungin in Streptomyces.
AU  - Yebra MJ
AU  - Sanchez J
AU  - Martin CG
AU  - Hardisson C
AU  - Barbes C
PT  - Journal Article
TA  - J. Antibiot. (Tokyo)
JT  - J. Antibiot. (Tokyo)
SO  - J. Antibiot. (Tokyo) 1991 44: 1141-1147.

PMID- 25323718
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of a Dimethyl Sulfide-Utilizing Bacterium, Acinetobacter guillouiae Strain 20B (NBRC 110550).
PG  - e01048-14
AB  - Acinetobacter guillouiae strain 20B can utilize dimethyl sulfide (DMS) as the sole sulfur
      source and degrade chloroethylenes. We report here the complete
      4,648,418-bp genome sequence for this strain, which contains 4,367 predicted
      coding sequences (CDSs), including a well-characterized DMS degradative operon.
AU  - Yee L
AU  - Hosoyama A
AU  - Ohji S
AU  - Tsuchikane K
AU  - Shimodaira J
AU  - Yamazoe A
AU  - Fujita N
AU  - Suzuki-Minakuchi C
AU  - Nojiri H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01048-14.

PMID- 28798178
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Mycobacterium avium 11.<jour_book>Genome Announc.
PG  - e00766-17
AB  - Mycobacterium avium accounts for most lung disease caused by nontuberculous mycobacteria
      (NTM). The lack of effective chemotherapy calls for the discovery of
      new drugs. Here, we report the draft genome sequence of M. avium 11, a clinical
      isolate used as a screening strain for NTM-focused drug discovery.
AU  - Yee M
AU  - Klinzing D
AU  - Wei JR
AU  - Gengenbacher M
AU  - Rubin EJ
AU  - Chien JY
AU  - Hsueh PR
AU  - Dick T
PT  - Journal Article
TA  - 
JT  - 
SO  -  2017 5: e00766-17.

PMID- 28522728
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Mycobacterium abscessus Bamboo.
PG  - e00388-17
AB  - Mycobacterium abscessus, an intrinsically multidrug-resistant pathogen, causes chronic
      incurable lung disease. New drugs for this emerging pathogen represent an
      urgent unmet medical need. Here, we report a draft genome sequence of M.
      abscessus Bamboo, a clinical isolate used as a screening strain for drug
      discovery.
AU  - Yee M
AU  - Klinzing D
AU  - Wei JR
AU  - Gengenbacher M
AU  - Rubin EJ
AU  - Dick T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00388-17.

PMID- 24699746
VI  - 70
DP  - 2014
TI  - Cloning, crystallization and preliminary X-ray diffraction analysis of an intact DNA methyltransferase of a type I restriction-modification enzyme from Vibrio vulnificus.
PG  - 489-492
AB  - Independently of the restriction (HsdR) subunit, the specificity (HsdS) and methylation (HsdM)
      subunits interact with each other, and function as a methyltransferase in type I
      restriction-modification systems. A single gene that combines the HsdS and HsdM subunits in
      Vibrio vulnificus YJ016 was expressed and purified. A crystal suitable for X-ray diffraction
      was obtained from 25%(w/v) polyethylene glycol monomethylether 5000, 0.1 M HEPES pH 8.0, 0.2 M
      ammonium sulfate at 291 K by hanging-drop vapour diffusion. Diffraction data were collected to
      a resolution of 2.31 angstrom using synchrotron radiation. The crystal belonged to the
      primitive monoclinic space group P2(1), with unit-cell parameters a = 93.25, b = 133.04, c =
      121.49 angstrom, beta = 109.7 degrees. With four molecules in the asymmetric unit, the crystal
      volume per unit protein weight was 2.61 angstrom(3) Da(-1), corresponding to a solvent content
      of 53%.
AU  - Yen LyHT
AU  - Park S-Y
AU  - Kim J-S
PT  - Journal Article
TA  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
JT  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
SO  - Acta Crystallogr. F Struct. Biol. Cryst. Commun. 2014 70: 489-492.

PMID- 1594447
VI  - 20
DP  - 1992
TI  - Isolation and characterization of the cDNA encoding human DNA methyltransferase.
PG  - 2287-2291
AB  - We have cloned a series of overlapping cDNA clones encoding a 5194 bp transcript for human DNA
      methyltransferase (DNA MTase). This sequence potentially codes for a protein of 1495 amino
      acids with a predicted molecular weight of 169 kDa. The human DNA MTase cDNA has eighty
      percent homology at the nucleotide level, and the predicted protein has seventy-four percent
      identity at the amino acid level, to the DNA MTase cDNA cloned from mouse cells. Like the
      murine DNA MTase, the amino terminal two-thirds of the human protein contains a cysteine-rich
      region suggestive of a metal-binding domain. The carboxy terminal one-third of the protein
      shows considerable similarity to prokaryotic (cytosine-5)-methyltransferases. The arrangement
      of multiple motifs conserved in the prokaryotic genes is preserved in the human DNA MTase,
      including the relative position of a proline-cysteine dipeptide thought to be an essential
      catalytic site in all (cytosine-5)-methyltransferases. A single 5.2 kb transcript was detected
      in all human tissues tested, with the highest levels of expression observed in RNA from
      placenta, brain, heart and lung. DNA MTase cDNA clones were used to screen a chromosome 19
      genomic cosmid library. The DNA MTase-positive cosmids which are estimated to span a genomic
      distance of 93 kb have been localized to 19p13.2-p13.3 by fluorescence in situ hybridization.
      Isolation of the cDNA for human DNA MTase will further study the regulation of DNA MTase
      expression, and of the role of this enzyme in establishing DNA methylation patterns in both
      normal and neoplastic cells.
AU  - Yen R-WC
AU  - Vertino PM
AU  - Nelkin BD
AU  - Yu JJ
AU  - El-Deiry W
AU  - Cumaraswamy A
AU  - Lennon GG
AU  - Trask BJ
AU  - Celano P
AU  - Baylin SB
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 2287-2291.

PMID- 9806857
VI  - 40
DP  - 1998
TI  - Characterization of the Pac25I restriction-modification genes isolated from the endogenous pRA2 plasmid of Pseudomonas alcaligenes NCIB 9867.
PG  - 203-213
AB  - Genes for the class II Pseudomonas alcaligenes NCIB 9867 restriction-modification (R-M)
      system, Pac25I, have been cloned from its 33-kb endogenous plasmid, pRA2. The Pac25I
      endonuclease and methylase genes were found to be aligned in a head-to-tail orientation with
      the methylase gene preceding and overlapping the endonuclease gene by 1 bp. The deduced amino
      acid sequence of the Pac25I methylase revealed significant similarity with the XcyI, XmaI,
      Cfr9I, and SmaI methylases. High sequence similarity was displayed between the Pac25I
      endonuclease and the XcyI, XmaI, and Cfr9I endonucleases which cleave between the external
      cytosines of the recognition sequence (i.e., 5'-C^CCGGG-3') and are thus perfect
      isoschizomers. However, no sequence similarity was detected between the Pac25I endonuclease
      and the SmaI endonuclease which cleaves between the internal CpG of the recognition sequence
      (i.e., 5'-CCC^GGG-3'). Both the Pac25I methylase and endonuclease were expressed in
      Escherichia coli. An open reading frame encoding a protein which shows significant similarity
      to invertases and resolvases was located immediately upstream of the Pac25I R-M operon. In
      addition, a transposon designated Tn5563 was located 1531 bp downstream of the R-M genes. The
      location on a self-transmissible plasmid as well as the close association with genes involved
      in DNA mobility suggests horizontal transfer as a possible mode of distribution of this family
      of R-M genes in various bacteria.
AU  - Yeo CC
AU  - Tham JM
AU  - Kwong SM
AU  - Poh CL
PT  - Journal Article
TA  - Plasmid
JT  - Plasmid
SO  - Plasmid 1998 40: 203-213.

PMID- 22207744
VI  - 194
DP  - 2012
TI  - Genome Sequencing of Bacillus subtilis SC-8, Antagonistic to the Bacillus cereus Group, Isolated from Traditional Korean Fermented-Soybean Food.
PG  - 536-537
AB  - Bacillus subtilis SC-8 is a Gram-positive bacterium displaying narrow antagonistic activity
      for the Bacillus cereus group. B. subtilis SC-8 was
      isolated from Korean traditional fermented-soybean food. Here we report
      the draft genome sequence of B. subtilis SC-8, including biosynthetic
      genes for antibiotics that may have beneficial effects for control of
      food-borne pathogens.
AU  - Yeo IC
AU  - Lee NK
AU  - Hahm YT
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 536-537.

PMID- 20865041
VI  - 5
DP  - 2010
TI  - Comparative genomics of Gardnerella vaginalis strains reveals substantial differences in metabolic and virulence potential.
PG  - E12411
AB  - BACKGROUND: Gardnerella vaginalis is described as a common vaginal
      bacterial species whose presence correlates strongly with bacterial
      vaginosis (BV). Here we report the genome sequencing and comparative
      analyses of three strains of G. vaginalis. Strains 317 (ATCC 14019) and
      594 (ATCC 14018) were isolated from the vaginal tracts of women with
      symptomatic BV, while Strain 409-05 was isolated from a healthy,
      asymptomatic individual with a Nugent score of 9. PRINCIPAL FINDINGS:
      Substantial genomic rearrangement and heterogeneity were observed that
      appeared to have resulted from both mobile elements and substantial
      lateral gene transfer. These genomic differences translated to differences
      in metabolic potential. All strains are equipped with significant
      virulence potential, including genes encoding the previously described
      vaginolysin, pili for cytoadhesion, EPS biosynthetic genes for biofilm
      formation, and antimicrobial resistance systems, We also observed systems
      promoting multi-drug and lantibiotic extrusion. All G. vaginalis strains
      possess a large number of genes that may enhance their ability to compete
      with and exclude other vaginal colonists. These include up to six
      toxin-antitoxin systems and up to nine additional antitoxins lacking
      cognate toxins, several of which are clustered within each genome. All
      strains encode bacteriocidal toxins, including two lysozyme-like toxins
      produced uniquely by strain 409-05. Interestingly, the BV isolates encode
      numerous proteins not found in strain 409-05 that likely increase their
      pathogenic potential. These include enzymes enabling mucin degradation, a
      trait previously described to strongly correlate with BV, although
      commonly attributed to non-G. vaginalis species. CONCLUSIONS:
      Collectively, our results indicate that all three strains are able to
      thrive in vaginal environments, and therein the BV isolates are capable of
      occupying a niche that is unique from 409-05. Each strain has significant
      virulence potential, although genomic and metabolic differences, such as
      the ability to degrade mucin, indicate that the detection of G. vaginalis
      in the vaginal tract provides only partial information on the
      physiological potential of the organism.
AU  - Yeoman CJ
AU  - Yildirim S
AU  - Thomas SM
AU  - Durkin AS
AU  - Torralba M
AU  - Sutton G
AU  - Buhay CJ
AU  - Ding Y
AU  - Dugan-Rocha SP
AU  - Muzny DM
AU  - Qin X
AU  - Gibbs RA
AU  - Leigh SR
AU  - Stumpf R
AU  - White BA
AU  - Highlander SK
AU  - Nelson KE
AU  - Wilson BA
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2010 5: E12411.

PMID- 21887656
VI  - 49
DP  - 2011
TI  - Complete sequence and organization of the Sphingobium chungbukense DJ77 pSY2 plasmid.
PG  - 684-688
AB  - Sphingobium chungbukense DJ77 is capable of metabolizing priority
      chemicals of human health concern such as polycyclic aromatic hydrocarbons
      (PAHs), extracellular polysaccharide (EPS), and antibiotics. Here, we
      report the complete DNA and genetic organization of the plasmid pSY2 from
      strain DJ77. A DNA sequence analysis revealed that pSY2 comprises 18,779
      bp encoding 22 open reading frames (ORFs) with 59.5% G+C content. The ORFs
      on pSY2 were classified into DNA replication, conjugative function,
      transposition, plasmid stability/partition, and other functional groups
      (transport, fatty acid biosynthesis, stress, and growth rate regulation).
      Three ORFs on pSY2 were hypothetical proteins.
AU  - Yeon SM
AU  - Kim YC
PT  - Journal Article
TA  - J. Microbiol.
JT  - J. Microbiol.
SO  - J. Microbiol. 2011 49: 684-688.

PMID- 20562274
VI  - 76
DP  - 2010
TI  - Metatranscriptomic analysis of the response of river biofilms to pharmaceutical products, using anonymous DNA microarrays.
PG  - 5432-5439
AB  - Pharmaceutical products are released at low concentrations into aquatic
      environments following domestic wastewater treatment. Such low
      concentrations have been shown to induce transcriptional responses in
      microorganisms, which could have consequences on aquatic ecosystem
      dynamics. In order to test if these transcriptional responses could also
      be observed in complex river microbial communities, biofilm reactors were
      inoculated with water from two rivers of differing trophic statuses and
      subsequently treated with environmentally relevant doses (ng/liter to
      microg/liter range) of four pharmaceuticals (erythromycin [ER],
      gemfibrozil [GM], sulfamethazine [SN], and sulfamethoxazole [SL]). To
      monitor functional gene expression, we constructed a 9,600-feature
      anonymous DNA microarray platform onto which cDNA from the biofilms was
      hybridized. Pharmaceutical treatments induced both positive and negative
      transcriptional responses from biofilm microorganisms. For instance, ER
      induced the transcription of several stress, transcription, and
      replication genes, while GM, a lipid regulator, induced transcriptional
      responses from several genes involved in lipid metabolism. SN caused
      shifts in genes involved in energy production and conversion, and SL
      induced responses from a range of cell membrane and outer envelope genes,
      which in turn could affect biofilm formation. The results presented here
      demonstrate for the first time that low concentrations of small molecules
      can induce transcriptional changes in a complex microbial community. The
      relevance of these results also demonstrates the usefulness of anonymous
      DNA microarrays for large-scale metatranscriptomic studies of communities
      from differing aquatic ecosystems.
AU  - Yergeau E
AU  - Lawrence JR
AU  - Waiser MJ
AU  - Korber DR
AU  - Greer CW
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2010 76: 5432-5439.

PMID- 25953173
VI  - 3
DP  - 2015
TI  - Extreme Sensory Complexity Encoded in the 10-Megabase Draft Genome Sequence of the Chromatically Acclimating Cyanobacterium Tolypothrix sp. PCC 7601.
PG  - e00355-15
AB  - Tolypothrix sp. PCC 7601 is a freshwater filamentous cyanobacterium with complex  responses to
      environmental conditions. Here, we present its 9.96-Mbp draft genome
      sequence, containing 10,065 putative protein-coding sequences, including 305
      predicted two-component system proteins and 27 putative phytochrome-class
      photoreceptors, the most such proteins in any sequenced genome.
AU  - Yerrapragada S et al
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00355-15.

PMID- 1991042
VI  - 273
DP  - 1991
TI  - DNA methylase from Pisum sativum.
PG  - 469-475
AB  - DNA methylase activity was detected in nuclei from pea shoots.  The enzyme can only be
      extracted by low-salt treatment if the nuclei are pretreated with micrococcal nuclease.  Only
      a single enzyme was detected, and it was purified to a specific activity of 1620 units/mg of
      protien.  It has an Mr of 160,000 on gel filtration and SDS/PAGE.  Pea DNA methylase
      methylates cytosine in all four dinucleotides, and this is interpreted to show that it acts on
      CNG trinucleotides.  Although it shows a strong preference for hemi-methylated double-stranded
      DNA, it is also capable of methylation de novo.  Homologous DNA is the best natural substrate.
      In vitro the enzyme interacts with DNA to form a salt-resistant complex with DNA that is
      stable for at least 4h.
AU  - Yesufu HMI
AU  - Hanley A
AU  - Rinaldi A
AU  - Adams RLP
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 1991 273: 469-475.

PMID- 23723391
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Dematiaceous Coelomycete Pyrenochaeta sp. Strain UM 256, Isolated from Skin Scraping.
PG  - e00158-13
AB  - Pyrenochaeta, classified under the order Pleosporales, is known to cause diseases in plants
      and humans. Here, we report a draft genome sequence of a Pyrenochaeta
      sp. isolated from a skin scraping, with an estimated genome size of 39.4 Mb.
      Genes associated with the synthesis of proteases, toxins, plant cell wall
      degradation, and multidrug resistance were found.
AU  - Yew SM
AU  - Chan CL
AU  - Soo-Hoo TS
AU  - Na SL
AU  - Ong SS
AU  - Hassan H
AU  - Ngeow YF
AU  - Hoh CC
AU  - Lee KW
AU  - Yee WY
AU  - Ng KP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00158-13.

PMID- 
VI  - 18
DP  - 2007
TI  - Interactions between carbon nanotubes and DNA polymerase and restriction endonucleases.
PG  - 025102
AB  - Effects of multi-walled carbon nanotubes (MWCNT) and single-walled carbon nanotubes (SWCNT)
      functionalized with and without carboxylic
      groups on polymerase chain reaction (PCR) and restriction digestion
      reaction were investigated. The results showed that CNT can reduce and
      even inhibit PCR and restriction digestion reaction, possibly due to
      the decrease of respective enzyme activity. The inhibition effect on
      double restriction digestion reaction and PCR was increased in the
      order of CNT-COOH > pristine CNT and SWCNT > MWCNT. This study
      demonstrated that CNT may significantly affect the efficiency of
      biochemical reactions through different action mechanisms, which is
      critical for understanding how nanomaterials impact biological systems.
AU  - Yi CQ
AU  - Fong CC
AU  - Chen WW
AU  - Qi SJ
AU  - Tzang CH
AU  - Lee ST
AU  - Yang MS
PT  - Journal Article
TA  - Nanotechnol.
JT  - Nanotechnol.
SO  - Nanotechnol. 2007 18: 025102.

PMID- 21602332
VI  - 193
DP  - 2011
TI  - Genome sequence of Escherichia coli AA86, isolated from cow feces.
PG  - 3681
AB  - Escherichia coli AA86 (= KACC 15541) is an enteric bacterium that was isolated from a sample
      of healthy cow feces. Its genome sequence revealed
      that it is most closely related to the human fecal strain E. coli SE15 and
      could be classified under E. coli phylogenetic group B2. Here, we report
      the genome sequence of E. coli AA86 consisting of 3 contigs and 2
      plasmids.
AU  - Yi H
AU  - Cho YJ
AU  - Hur HG
AU  - Chun J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3681.

PMID- 22740669
VI  - 194
DP  - 2012
TI  - Genome Sequence of Escherichia coli J53, a Reference Strain for Genetic Studies.
PG  - 3742-3743
AB  - Escherichia coli J53 (F(-) met pro Azi(r)) is a derivative of E. coli K-12 which  is resistant
      to sodium azide. This strain has been widely used as a general
      recipient strain for various conjugation experiments. Here, we report the genome
      sequence of E. coli J53 (=KACC 16628).
AU  - Yi H
AU  - Cho YJ
AU  - Yong D
AU  - Chun J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3742-3743.

PMID- 26044432
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of the Bacterium Lysobacter capsici X2-3, with a Broad Spectrum of Antimicrobial Activity against Multiple Plant-Pathogenic Microbes.
PG  - e00589-15
AB  - Lysobacter capsici strain X2-3 was isolated from the wheat rhizosphere in China and exhibits a
      remarkable capacity to inhibit the growth of multiple pathogens.
      Here, we report the draft genome sequence of L. capsici strain X2-3 in China.
AU  - Yi JL
AU  - Wang J
AU  - Li Q
AU  - Liu ZX
AU  - Zhang L
AU  - Liu AX
AU  - Yu JF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00589-15.

PMID- 28336594
VI  - 5
DP  - 2017
TI  - First Report on the Complete Genome Sequence of Lactobacillus crustorum MN047, a  Potent Probiotic Strain Isolated from Koumiss in China.
PG  - e00048-17
AB  - The complete genome sequence of Lactobacillus crustorum deciphered by PacBio RS II and
      Illumina HiSeq 4000 sequencing was first reported with one chromosome and
      two plasmids. Sequence analysis of L. crustorum MN047 showed probiotic
      characteristics.
AU  - Yi L
AU  - Guo X
AU  - Liu L
AU  - Shao C
AU  - Lu X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00048-17.

PMID- 26337877
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Perfluorooctane Acid-Degrading Bacterium Pseudomonas parafulva YAB-1.
PG  - e00935-15
AB  - Pseudomonas parafulva YAB-1, isolated from perfluorinated compound-contaminated soil, has the
      ability to degrade perfluorooctane acid (PFOA) compound. Here, we report the draft genome
      sequence and annotation of the PFOA-degrading bacterium P. parafulva YAB-1. The data provide
      the basis to investigate the molecular mechanism of PFOA metabolism.
AU  - Yi L
AU  - Tang C
AU  - Peng Q
AU  - Peng Q
AU  - Chai L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00935-15.

PMID- 26950325
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Bacillus mycoides M2E15, a Strain Isolated from the Endosphere of Potato.
PG  - e00031-16
AB  - We present the draft genome sequence of Bacillus mycoides M2E15, a bacterium isolated from
      potato endosphere. Analysis of the 6.08-Mbp draft genome sequence
      identified 6,386 protein-encoding sequences, including potential plant growth
      promoting genes. Specifically, genes for proteins involved in phosphate
      utilization, iron acquisition, and bacteriocin production were identified.
AU  - Yi Y
AU  - de Jong A
AU  - Spoelder J
AU  - Elzenga JT
AU  - van Elsas JD
AU  - Kuipers OP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00031-16.

PMID- 
VI  - 22
DP  - 1998
TI  - Optimization of starting time and period of induction and inducer concentration in the production of the restriction enzyme EcoRI from recombinant Escherichia coli 294.
PG  - 221-226
AB  - Induction parameters including inducer concentration, period of induction and the cell
      concentration at which inducer is to be added to the fermentation broth were optimized in
      order to increase the yield of the EcoRI restriction endonuclease isolated from recombinant E.
      coli.  Bacterial cells harboring the plasmid pPG430 containing EcoRI endonuclease and the
      methylase genes under the control of lac promoter were used in the experiments where induction
      was accomplished by using lactose isopropyl-B-D-thiogalactoside.  An IPTG concentration of
      0.1mM, the late exponential phase of growth (at an optical density of 1.2 at 595 nm) and an
      induction period of 6 hours were determined to be the optimum conditions for induction.
AU  - Yilder C
AU  - Onsan ZI
AU  - Kirdar B
PT  - Journal Article
TA  - Turk. J. Chem.
JT  - Turk. J. Chem.
SO  - Turk. J. Chem. 1998 22: 221-226.

PMID- 20581194
VI  - 76
DP  - 2010
TI  - Conservation of Genomic Localization and Sequence Content of Sau3AI-Like Restriction-Modification Gene Cassettes among Listeria monocytogenes Epidemic Clone I and Selected Strains of Serotype 1/2a.
PG  - 5577-5584
AB  - Listeria monocytogenes is a food-borne pathogen with a clonal population structure and
      apparently limited gene flow between strains
      of different lineages. Strains of epidemic clone I (ECI) have been
      responsible for numerous outbreaks and invariably have DNA that is
      resistant to digestion by Sau3AI, suggesting methylation of cytosine at
      GATC sites. A putative restriction-modification (RM) gene cassette has
      been identified in the genome of the ECI strain F2365 and all other
      tested ECI strains but is absent from other strains of the same
      serotype (4b). Homologous RM cassettes have not been reported among L.
      monocytogenes isolates of other serotypes. Furthermore, conclusive
      evidence for the involvement of this RM cassette in the Sau3AI
      resistance phenotype of ECI strains has been lacking. In this study, we
      describe a highly conserved RM cassette in certain strains of serotypes
      1/2a and 4a that have Sau3AI-resistant DNA. In these strains the RM
      cassette was in the same genomic location as in the ECI reference
      strain F2365. The cassette included a gene encoding a putative
      recombinase, suggesting insertion via site-specific recombination.
      Deletion of the RM cassette in the ECI strain F2365 and the serotype
      1/2a strain A7 rendered the DNA of both strains susceptible to Sau3AI
      digestion, providing conclusive evidence that the cassette includes a
      gene required for methylation of cytosine at GATC sites in both
      strains. The findings suggest that, in addition to its presence in ECI
      strains, this RM cassette and the accompanying genomic DNA methylation
      is also encountered among selected strains of other lineages.
AU  - Yildirim S
AU  - Elhanafi D
AU  - Lin W
AU  - Hitchins AD
AU  - Siletzky RM
AU  - Kathariou S
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2010 76: 5577-5584.

PMID- 15240296
VI  - 70
DP  - 2004
TI  - Epidemic clone I-specific genetic markers in strains of Listeria monocytogenes serotype 4b from foods.
PG  - 4158-4164
AB  - Listeria monocytogenes contamination of ready-to-eat foods has been implicated in numerous
      outbreaks of food-borne listeriosis. However,
      the health hazards posed by L. monocytogenes detected in foods may
      vary, and speculations exist that strains actually implicated in
      illness may constitute only a fraction of those that contaminate foods.
      In this study, examination of 34 serogroup 4 (putative or confirmed
      serotype 4b) isolates of L. monocytogenes obtained from various foods
      and food-processing environments, without known implication in illness,
      revealed that many of these strains had methylation of cytosines at
      GATC sites in the genome, rendering their DNA resistant to digestion by
      the restriction endonuclease Sau3AI. These strains also harbored a gene
      cassette with putative restriction-modification system genes as well as
      other, genomically unlinked genetic markers characteristic of the major
      epidemic-associated lineage of L. monocytogenes (epidemic clone 1),
      implicated in numerous outbreaks in Europe and North America. This may
      reflect a relatively high fitness of strains with these genetic markers
      in foods and food-related environments relative to other serotype 4b
      strains and may partially account for the repeated involvement of such
      strains in human food-borne listeriosis.
AU  - Yildirim S
AU  - Lin W
AU  - Hitchins AD
AU  - Jaykus LA
AU  - Altermann E
AU  - Klaenhammer TR
AU  - Kathariou S
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2004 70: 4158-4164.

PMID- 25977429
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Extensively Drug-Resistant Acinetobacter baumannii Strain CUAB1 from a Patient in Hong Kong, China.
PG  - e00442-15
AB  - We report the draft genome sequence of an extensively drug-resistant strain of Acinetobacter
      baumannii, CUAB1, isolated from a patient in a local Hong Kong
      hospital. MIC testing was performed, and genes previously associated with drug
      resistance were located.
AU  - Yim AK
AU  - Kwok JS
AU  - Yu AC
AU  - Leung AK
AU  - Lau HH
AU  - Chan TF
AU  - Ip M
AU  - Tsui SK
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00442-15.

PMID- 29371361
VI  - 6
DP  - 2018
TI  - Complete Genome Sequences of Four Toxigenic Clostridium difficile Clinical Isolates from Patients of the Lower Hudson Valley, New York, USA.
PG  - e01537-17
AB  - Complete genome sequences of four toxigenic Clostridium difficile isolates from patients in
      the lower Hudson Valley, New York, USA, were achieved. These isolates
      represent four common sequence types (ST1, ST2, ST8, and ST42) belonging to two
      distinct phylogenetic clades. All isolates have a 4.0- to 4.2-Mb circular
      chromosome, and one carries a phage.
AU  - Yin C
AU  - Chen DS
AU  - Zhuge J
AU  - McKenna D
AU  - Sagurton J
AU  - Wang G
AU  - Huang W
AU  - Dimitrova N
AU  - Fallon JT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01537-17.

PMID- 24699951
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Extremophile Acidithiobacillus thiooxidans A01, Isolated from the Wastewater of a Coal Dump.
PG  - e00222-14
AB  - The draft genome of Acidithiobacillus thiooxidans A01 contains 3,820,158 bp, with a G+C
      content of 53.08% and 3,660 predicted coding sequences (CDSs). The bacterium contains a series
      of specific genes involved in the oxidation of elemental sulfur and reduced inorganic sulfur
      compounds (RISCs).
AU  - Yin H
AU  - Zhang X
AU  - Liang Y
AU  - Xiao Y
AU  - Niu J
AU  - Liu X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00222-14.

PMID- 23021851
VI  - 41
DP  - 2013
TI  - An electrochemical assay for DNA methylation, methyltransferase activity and inhibitor screening based on methyl binding domain protein.
PG  - 492-497
AB  - DNA methylation is one of important epigenetics events, and responsible to transcription,
      genomic imprinting and cellular differentiation.
      Aberrant DNA methylation is always contacted with various diseases.
      Methyl binding domain (MBD) proteins can specifically bind to the
      methylated CpG dinucleotides. Conventional assay for DNA methylation
      normally need bisulfide treatment, methylated nucleotide labeling or
      PCR amplification. Here, we fabricated a novel electrochemical
      biosensor for detection of DNA methylation, assay of DNA
      methyltransferase (MTase) activity and screening of MTase inhibitor
      based on MBD protein and coomassie brilliant blue G250 (CBB-G250),
      where the electrochemical signal of CBB-G250 was used to monitor the
      methylation event. After the hybrids of DNA S1 and DNA S2 were treated
      with M. SssI MTase in the presence of S-adenosylmethionine, the MBD
      proteins were specifically conjugated to the methylation site of CpG
      dinucleotides, and then, the MBD proteins were stained with CBB-G250.
      The electrochemical signal of CBB-G250 increased linearly with
      increasing M. SssI MTase concentration in the range from 0.1 to 40
      unit/mL. Furthermore, the inhibition investigation demonstrates that
      fisetin and chlorogenic acid can inhibit the M. SssI MTase activity
      with the IC50 value of 153.12 and 137.07 mu M, respectively. Therefore,
      we think that this study may provide a sensitive platform for screening
      of DNA MTase inhibitors.
AU  - Yin HS
AU  - Zhou YL
AU  - Xu ZN
AU  - Chen LJ
AU  - Zhang D
AU  - Ai SY
PT  - Journal Article
TA  - Biosensors and Bioelectronics
JT  - Biosensors and Bioelectronics
SO  - Biosensors and Bioelectronics 2013 41: 492-497.

PMID- 23640379
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of Glaciecola psychrophila Strain 170T.
PG  - e00199-13
AB  - Here, we report the complete genome sequence of Glaciecola psychrophila strain 170(T), a novel
      species of the genus Glaciecola, isolated from sea ice at
      high-latitude Arctic locations. The genome consists of a single chromosome
      (5,413,691 bp) and 5,363 genes. The genomics information will facilitate the
      study of the physiology, cold adaptation, and evolution of this genus.
AU  - Yin J
AU  - Chen J
AU  - Liu G
AU  - Yu Y
AU  - Song L
AU  - Wang X
AU  - Qu X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00199-13.

PMID- 
VI  - 11
DP  - 2018
TI  - Molecular characteristics and comparative genomics analysis of a clinical Enterococcus casseliflavus with a resistance plasmid.
PG  - 2159-2167
AB  - Purpose: The aim of this work was to investigate the molecular characterization of a clinical
      Enterococcus casseliflavus strain with a resistance plasmid. Materials and methods: En.
      casseliflavus EC369 was isolated from a patient in a hospital in southern China. The minimum
      inhibitory concentration was found by means of the agar dilution method to determine the
      antimicrobial susceptibilities of the strains. Whole-genome
      sequencing and mechanism of antibiotic resistance and the horizontal gene transfer of the
      resistance gene-related mobile genetic elements.
      Results: En. casseliflavus EC369 showed resistance to erythromycin, kanamycin, and
      streptomycin, but was susceptible to vancomycin, ampicillin, and streptothricin and other
      antimicrobials. There were six resistance genes (aph3 and #8242;, ant6, bla, sat4, and two
      ermBs) carried by a transposon
      identified on the plasmid pEC369 and a complete resistance gene cluster of vancomycin and a
      tet (M) gene encoded on the chromosome. This is the first complete plasmid sequence reported
      in clinically isolated En. casseliflavus. The plasmid with the greatest sequence identity with
      pEC369 was the plasmid of Enterococcus sp. FDAARGOS_375, followed by the plasmids of
      Enterococcus faecium strains F12085 and pRE25, whereas the sequence with the greatest
      identity to the resistance genes carrying a transposon of pEC369 was on the chromosome of
      Staphylococcus aureus strain GD1677. Conclusion: The resistance profiles of En. casseliflavus
      EC369 might contribute to the resistance
      genes encoded on the plasmid. The fact that the most similar sequence to the transposon
      carrying resistance genes of pEC369 was encoded in the chromosome of a S. aureus strain
      provides insights into the mechanism of dissemination of multidrug resistance between bacteria
      of different species or genera through horizontal gene transfer.
AU  - Yin M
PT  - Journal Article
TA  - Infection and Drug Resistance
JT  - Infection and Drug Resistance
SO  - Infection and Drug Resistance 2018 11: 2159-2167.

PMID- 28472671
VI  - 252
DP  - 2017
TI  - The complete genome sequence of Streptomyces autolyticus CGMCC 0516, the producer of geldanamycin, autolytimycin, reblastatin and elaiophylin.
PG  - 27-31
AB  - Streptomyces autolyticus CGMCC 0516 produces the anti-tumor benzoquinone
      ansamycins geldanamycin, autolytimycin, and reblastatin and the 16-membered
      macrodiolide elaiophylin. Here, we report the complete genome sequence of S.
      autolyticus CGMCC 0516, which consists of a 10,029,028bp linear chromosome and
      seven circular plasmids. Fifty-seven putative biosynthetic gene clusters for
      secondary metabolites were found. The geldanamycin, autolytimycin, and
      reblastatin biosynthetic gene clusters were located on the left arm (2.06-2.15Mb)
      of the chromosome, and the elaiophylin gene cluster was located on the right arm
      (9.45-9.53Mb). Twenty-one putative gene clusters with high or moderate similarity
      to important antibiotic biosynthetic gene clusters were found, including the
      antitumor agents echoside, bafilomycin, hygrocin, and toxoflavin; the
      antibacterial/antifungal agents nigericin, skyllamycin, kanamycin, naphthomycin,
      eco-02301, and bottromycin A2; the immunosuppressants meridamycin and
      brasilicardin A; the anti-inflammatory agent cyclooctatin; and the acute iron
      poisoning medication desferrioxamine B. The genome sequence reported here will
      enable us to study the biosynthetic mechanism of these important antibiotics and
      will facilitate the discovery of novel secondary metabolites with potential
      applications to human health.
AU  - Yin M
AU  - Jiang M
AU  - Ren Z
AU  - Dong Y
AU  - Lu T
PT  - Journal Article
TA  - J. Biotechnol.
JT  - J. Biotechnol.
SO  - J. Biotechnol. 2017 252: 27-31.

PMID- 26659690
VI  - 3
DP  - 2015
TI  - Genome Sequence Analysis Reveals Evidence of Quorum-Sensing Genes Present in Aeromonas hydrophila strain KOR1, Isolated from a Mangrove Plant (Kandelia  obovata).
PG  - e01461-15
AB  - Aeromonas hydrophila strain KOR1, isolated from mangrove rhizosphere soil, has the ability to
      produce the quorum-sensing signal molecule. Here, we report the
      4.78-Mb genome sequence of strain KOR1, and found its quorum-sensing encoding
      gene LuxR. The data will be crucial to understanding the quorum-sensing-dependent
      phenotypes of this bacterium.
AU  - Yin M
AU  - Ma Z
AU  - Cai Z
AU  - Lin G
AU  - Zhou J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01461-15.

PMID- 29472338
VI  - 6
DP  - 2018
TI  - Genome Sequence of a Marine Alkane Degrader, Alcanivorax sp. Strain 97CO-6.
PG  - e00087-18
AB  - Alcanivorax sp. strain 97CO-6 was isolated from a crude oil-consuming bacterial consortium,
      enriched from Yellow Sea sediments from China. Here, we present the
      draft genome of strain 97CO-6, which contains 3,253,423 bp, with a G+C content of
      54.53%, as well as 2,931 protein-coding genes and 42 tRNAs.
AU  - Yin X
AU  - Luan X
AU  - Xu A
AU  - Li Q
AU  - Cui Z
AU  - Valentine DL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00087-18.

PMID- 24115549
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of a Stable Mucoid Strain of Pseudomonas aeruginosa PAO581  with a mucA25 Mutation.
PG  - e00834-13
AB  - A mutation in the mucA gene, which encodes a negative regulator of alginate production in
      Pseudomonas aeruginosa, is the main mechanism underlying the
      conversion to mucoidy in clinical isolates from patients with cystic fibrosis
      (CF). Here, we announce the draft genome sequence of the stable
      alginate-overproducing mucoid strain P. aeruginosa PAO581 with a mucA25 mutation,
      a derivative from the nonmucoid strains P. aeruginosa PAO381 and PAO1.
AU  - Yin Y
AU  - Withers TR
AU  - Govan JR
AU  - Johnson SL
AU  - Yu HD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00834-13.

PMID- 24115552
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of a Mucoid Isolate of Pseudomonas aeruginosa Strain C7447m from a Patient with Cystic Fibrosis.
PG  - e00837-13
AB  - Alginate overproduction by Pseudomonas aeruginosa, or mucoidy, plays an important role in the
      pathogenesis of chronic lung infections in cystic fibrosis (CF)
      patients. Here we report the draft genome sequence of a clinical isolate of
      mucoid P. aeruginosa strain C7447m from a CF patient with chronic lung infection.
AU  - Yin Y
AU  - Withers TR
AU  - Johnson SL
AU  - Yu HD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00837-13.

PMID- 24336371
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences of Two Alginate-Overproducing Variants of Pseudomonas aeruginosa, PAO1-VE2 and PAO1-VE13.
PG  - e01031-13
AB  - The small envelope protein MucE and the sensor kinase KinB are a positive and negative
      alginate regulator, respectively. Here, we announce the draft genome
      sequences of the alginate-overproducing variants Pseudomonas aeruginosa PAO1-VE2
      (PAO1 with constitutive expression of mucE) and PAO1-VE13 (PAO1 with kinB
      inactivated). Both mutants were generated from a transposon mutagenesis screen.
AU  - Yin Y
AU  - Withers TR
AU  - Niles RM
AU  - Johnson SL
AU  - Yu HD
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01031-13.

PMID- 23144423
VI  - 194
DP  - 2012
TI  - Genome Sequence of Pedobacter arcticus sp. nov., a Sea Ice Bacterium Isolated from Tundra Soil.
PG  - 6688
AB  - Pedobacter arcticus sp. nov. was originally isolated from tundra soil collected from
      Ny-Alesund, in the Arctic region of Norway. It is a Gram-negative bacterium
      which shows bleb-shaped appendages on the cell surface. Here, we report the draft
      annotated genome sequence of Pedobacter arcticus sp. nov., which belongs to the
      genus Pedobacter.
AU  - Yin Y
AU  - Yue G
AU  - Gao Q
AU  - Wang Z
AU  - Peng F
AU  - Fang C
AU  - Yang X
AU  - Pan L
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6688.

PMID- 9425235
VI  - 7
DP  - 1998
TI  - A candidate mammalian DNA methyltransferase related to pmt1p of fission yeast.
PG  - 279-284
AB  - Trace levels of 5-methylcytosine persist in the DNA of mouse embryonic stem cells that are
      homozygous for null mutations in Dnmt1, the gene for the one previously recognized metazoan
      DNA methyltransferase.  This residual 5-methylcytosine may be the product of a candidate
      second DNA methyltransferase, Dnmt2, that has now been identified in human and mouse.  Dnmt2
      contains all the sequence motifs diagnostic of DNA (cytosine-5)-methyltransferases but appears
      to lack the large N-terminal regulatory domain common to other eukaryotic methyltransferases.
      Dnmt2 is more similar to a putative DNA methyltransferase of the fission yeast
      Schizosaccharomyces pombe than to Dnmt1.  Dnmt2 produces multiple mRNA species that are
      present at low levels in all tissues of human and mouse and is not restricted to those cell
      types known to be active in de novo methylation.  The human DNMT2 gene was mapped to
      chromosome 10p12-10p14 in a panel of radiation hybrids.  Dnmt2 is a candidate for the activity
      that methylates newly integrated retroviral DNA and maintains trace levels of 5-methylcytosine
      in the DNA of embryonic stem cells homozygous for null mutations in Dnmt1.
AU  - Yoder JA
AU  - Bestor TH
PT  - Journal Article
TA  - Hum. Mol. Genet.
JT  - Hum. Mol. Genet.
SO  - Hum. Mol. Genet. 1998 7: 279-284.

PMID- 8922587
VI  - 377
DP  - 1996
TI  - Genetic analysis of genomic methylation patterns in plants and mammals.
PG  - 605-610
AB  - While it is now accepted that methylation of cytosine residues plays a role in various
      epigenetic phenomena in mammals and flowering plants, the involvement of methylation patterns
      in the regulation of normal development has remained a controversial and essentially untested
      issue in the 20 years since such a role was first proposed.  Antisense suppression of a DNA
      methyltransferase in Arabidopsis and characterization of methylation-defective mutants of
      Arabidopsis have shown that perturbations of methylation patterns disrupt the development of
      plants, and targeted mutation of the murine gene that encodes the one known form of DNA
      methyltransferase has shown that methylation is required for cellular differentiation, genomic
      imprinting, and X chromosome inactivation in mammals.  Ectopic expression of homeotic genes
      and homeotic transformations of floral organs in methylation-defective plants suggest that (in
      plants and perhaps mammals) heritable methylation patterns reinforce and may have supplanted
      heritable gene control mediated by chromosomal proteins of the Polycomb and trithorax groups.
      It is also possible that the developmental abnormalities are the result of ectopic gene
      expression caused by activation of transcription from nearby parasitic sequence elements that
      are normally repressed by methylation.  Application of modern methods of genetic analysis
      promises to give definite answers to long-standing questions as to the roles and significance
      of genomic methylation patterns in normal development and genome defense.
AU  - Yoder JA
AU  - Bestor TH
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1996 377: 605-610.

PMID- 9237905
VI  - 270
DP  - 1997
TI  - DNA (cytosine-5)-methyltransferases in mouse cells and tissues.  Studies with a mechanism-based probe.
PG  - 385-395
AB  - The mechanisms that establish and maintain methylation patterns in the mammalian genome are
      very poorly understood, even though perturbations of methylation patterns lead to a loss of
      genomic imprinting, ectopic X chromosome inactivation, and death of mammalian embryos.  A
      family of sequence-specific DNA methyltransferases has been proposed to be responsible for the
      wave of de novo methylation that occurs in the early embryo, although no such enzyme has been
      identified.  A universal mechanism-based probe for DNA (cytosine-5)-methyltransferases was
      used to screen tissues and cell types known to be active in de novo methylation for new
      species of DNA methyltransferase.  All identifiable de novo methyltransferase activity was
      found to reside in Dnmt1.  As this enzyme is the predominant de novo methyltransferase at all
      developmental stages inspected, it does not fit the definition of maintenance
      methyltransferase or hemimethylase.  Recent genetic data indicate that de novo methylation of
      retroviral DNA in embryonic stem cells is likely to involve one or more additional DNA
      methyltransferases.  Such enzymes were not detected and are either present in very small
      amounts or are very different from Dnmt1.  A new method was developed and used to determine
      the sequence specificity of intact Dnmt1 in whole-cell lysates.  Specificity was found to be
      confined to the sequence 5'-CpG-3'; there was little dependence on sequence context or
      density of CpG dinucleotides.  These data suggest that any sequence-specific de novo
      methylation mediated by Dnmt1 is either under the control of regulatory factors that interact
      with Dnmt1, or is cued by alternative secondary structures in DNA.
AU  - Yoder JA
AU  - Soman NS
AU  - Verdine GL
AU  - Bestor TH
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1997 270: 385-395.

PMID- 9260521
VI  - 13
DP  - 1997
TI  - Cytosine methylation and the ecology of intragenomic parasites.
PG  - 335-340
AB  - Most of the 5-methylcytosine in mammalian DNA resides in transposons, which are specialized
      intragenomic parasites that represent at least 35% of the genome.  Transposon promoters are
      inactive when methylated and, over time, C-T transition mutations at methylated sites destroy
      many transposons.  Apart from that subset of genes subject to X inactivation and genomic
      imprinting, no cellular gene in a non-expressing tissue has been proven to be methylated in a
      pattern that prevents transcription.  It has become increasingly difficult to hold that
      reversible promoter methylation is commonly involved in developmental gene control; instead,
      suppression of parasitic sequence elements appears to be the primary function of cytosine
      methylation, with crucial secondary roles in allele-specific gene expression as seen in X
      inactivation and genomic imprinting.
AU  - Yoder JA
AU  - Walsh CP
AU  - Bestor TH
PT  - Journal Article
TA  - Trends Genet.
JT  - Trends Genet.
SO  - Trends Genet. 1997 13: 335-340.

PMID- 8940105
VI  - 271
DP  - 1996
TI  - New 5' regions of the murine and human genes for DNA (cytosine-5)-methyltransferase.
PG  - 31092-31097
AB  - DNA (cytosine-5)-methyltransferases (EC 2.1.1.37)  maintain patterns of methylated cytosine
      residues in the mammalian genome; faithful maintenance of methylation patterns is required for
      normal development of mice, and aberrant methylation patterns are associated with certain
      human tumors and developmental abnormalities.  The organization of coding sequences at the
      5'-end of the murine and human DNA methyltransferase genes was investigated, and the DNA
      methyltransferase open reading frame was found to be longer than previously suspected.
      Expression of the complete open reading frame by in vitro transcription-translation and by
      transfection of expression constructs into COS7 cells resulted in the production of an active
      DNA methyltransferase of the same apparent mass as the endogenous protein, while translation
      from the second inframe ATG codon produced a slightly smaller but fully active protein.
      Characterization of mRNA 5' sequences and the intron-exon structure of the 5' region of the
      murine and human genes indicated that a previously described promoter element actually lies in
      an intron that is more than 5 kilobases downstream of the transcription start sites.
AU  - Yoder JA
AU  - Yen R-WC
AU  - Vertino PM
AU  - Bestor TH
AU  - Baylin SB
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1996 271: 31092-31097.

PMID- 28533514
VI  - 7
DP  - 2017
TI  - Isolation and genomic characterization of a Dehalococcoides strain suggests genomic rearrangement during culture.
PG  - 2230
AB  - We have developed and characterized a bacterial consortium that reductively
      dechlorinates trichloroethene to ethene. Quantitative PCR analysis for the 16S
      rRNA and reductive dehalogenase genes showed that the consortium is highly
      enriched with Dehalococcoides spp. that have two vinyl chloride reductive
      dehalogenase genes, bvcA and vcrA, and a trichloroethene reductive dehalogenase
      gene, tceA. The metagenome analysis of the consortium by the next generation
      sequencer SOLiD 3 Plus suggests that a Dehalococcoides sp. that is highly
      homologous to D. mccartyi 195 and equipped with vcrA and tceA exists in the
      consortium. We isolated this Dehalococcoides sp. and designated it as D. mccartyi
      UCH-ATV1. As the growth of D. mccartyi UCH-ATV1 is too slow under isolated
      conditions, we constructed a consortium by mixing D. mccartyi UCH-ATV1 with
      several other bacteria and performed metagenomic sequencing using the single
      molecule DNA sequencer PacBio RS II. We successfully determined the complete
      genome sequence of D. mccartyi UCH-ATV1. The strain is equipped with vcrA and
      tceA, but lacks bvcA. Comparison with tag sequences of SOLiD 3 Plus from the
      original consortium shows a few differences between the sequences. This suggests
      that a genome rearrangement of Dehalococcoides sp. occurred during culture.
AU  - Yohda M et al
PT  - Journal Article
TA  - Sci. Rep.
JT  - Sci. Rep.
SO  - Sci. Rep. 2017 7: 2230.

PMID- 11821381
VI  - 277
DP  - 2002
TI  - Preferential methylation of unmethylated DNA by mammalian de novo DNA methyltransferase Dnmt3a.
PG  - 11735-11745
AB  - DNA methylation is an epigenetic modification of DNA. There are currently three catalytically
      active mammalian DNA methyltransferases,
      DNMT1, -3a, and -3b. DNMT1 has been shown to have a preference for
      hemimethylated DNA and has therefore been termed the maintenance
      methyltransferase. Although previous studies on DNMT3a and -3b revealed
      that they act as functional enzymes during development, there is little
      biochemical evidence about how new methylation patterns are established
      and maintained. To study this mechanism we have cloned and expressed
      Dnmt3a using a baculovirus expression system. The substrate specificity
      of Dnmt3a and molecular mechanism of its methylation reaction were then
      analyzed using a novel and highly reproducible assay. We report here
      that Dnmt3a is a true de novo methyltransferase that prefers
      unmethylated DNA substrates more than 3-fold to hemimethylated DNA.
      Furthermore, Dnmt3a binds DNA nonspecifically, regardless of the
      presence of CpG dinucleotides in the DNA substrate. Kinetic analysis
      supports an Ordered Bi Bi mechanism for Dnmt3a, where DNA binds first,
      followed by S-adenoSyl-L-methionine.
AU  - Yokochi T
AU  - Robertson KD
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2002 277: 11735-11745.

PMID- 15210338
VI  - 32
DP  - 2004
TI  - Dimethyl sulfoxide stimulates the catalytic activity of de novo DNA methyltransferase 3a (Dnmt3a) in vitro.
PG  - 234-243
AB  - Mammalian DNA methyltransferase Dnmt3a is required for de novo methylation of CpG
      dinucleotides in genomic DNA. While DNA
      methyltransferase inhibitors have been extensively utilized both in
      vitro and in vivo, no stimulator of catalytic activity has been
      identified thus far. Here we show that the methyltransfer activity of
      Dnmt3a is stimulated by the addition of dimethyl sulfoxide (DMSO) to
      the reaction solution in vitro. Enzymatic analysis of initial reaction
      velocity suggests that the DMSO stimulation effect depends on the
      interaction between DMSO and the reaction substrates (DNA and AdoMet),
      but not the enzyme itself.
AU  - Yokochi T
AU  - Robertson KD
PT  - Journal Article
TA  - Bioorg. Chem.
JT  - Bioorg. Chem.
SO  - Bioorg. Chem. 2004 32: 234-243.

PMID- 15273420
VI  - 287
DP  - 2004
TI  - DMB (DNMT-magnetic beads) assay: Measuring DNA methyltransferase activity in vitro.
PG  - 285-296
AB  - DNA methylation is an epigenetic modification of DNA that leads to heritable alterations in
      transcriptional regulation and conformational changes in chromatin structure of higher
      eukaryotes.  Mammalian DNA methyltransferases, which are the enzymes responsible for DNA
      methylation, have attracted the attention of both basic and clinical researchers because they
      appear to participate in embryogenesis and carcinogenesis via chromatin modification.  DNA
      methyltransferase catalyzes the traansfer of a methyl group into DNA strands.  Since
      traditional assays for DNA methyltransferase activity in vitro have insufficient
      reproducibility, there is a need in the art for more sensitive and quantitative methods for
      measuring enzymatic activity.  We report a novel assay system, in which the actiity of a DNA
      methyltransferase is measured as the incorporation of tritium into biotinylated DNA
      oligonucleotides.  The DNA is immobilized onto magnetic beads with streptavidin covalently
      attached to the bead surface.  The radioactive DNA can easily be separated from the unreacted
      radioactive substrate using a magnet.  The radioactivity is counted by the liquid
      scintillation system.  This DMB assay is simple and easy, has very low background, and, most
      importantly, is highly reproducible for the precise enzymatic analysis of any DNA
      methyltransferase in vitro.
AU  - Yokochi T
AU  - Robertson KD
PT  - Journal Article
TA  - Methods Mol. Biol.
JT  - Methods Mol. Biol.
SO  - Methods Mol. Biol. 2004 287: 285-296.

PMID- 11111050
VI  - 258
DP  - 2000
TI  - Complete nucleotide sequence of the prophage VT1-Sakai carrying the Shiga toxin 1 genes of the enterohemorrhagic Escherichia coli O157:H7 strain derived from the Sakai outbreak.
PG  - 127-139
AB  - Shiga toxins 1 and 2 (Stx1 and Stx2) are encoded by prophages lysogenized in enterohemorrhagic
      Escherichia coli (EHEC) O157:H7 strains. Lytic growth of the phage particles carrying the stx1
      genes (stx1A and stx1B) of the EHEC O157:H7 strain RIMD 0509952, which was derived from the
      Sakai outbreak in 1996 in Japan, was induced after treatment with mitomycin C, but the plaque
      formation of the phage was not detected. We have determined the complete nucleotide sequence
      of the prophage VT1-Sakai. The integration site of the prophage was identified within the yehV
      gene at 47.7 min on the chromosome. The stx1 genes were downstream of the Q gene in the
      prophage genome, suggesting that their expression was regulated by the Q protein, the
      regulator of the late gene expression of the phage, which is similar to that of the stx1 or
      stx2 genes carried by the lambdoid phages reported previously. The sequences of the N gene and
      its recognition sites, nutL and nutR, were not homologous to those of the phages carrying the
      stx genes thus far reported, but they were very similar to those of bacteriophage phi21. The
      sequences of the repressor proteins, CI and Cro, that regulate expression of the early genes
      had low similarities with those of the known repressors of other phages, and their operator
      sequences were different from any sequence reported. These data suggest that multiple genetic
      recombination among bacteriophages with different immunities took place to generate the
      prophage VT1-Sakai. Comparison between the sequences of VT1-Sakai and lambda suggests that the
      ancestor of VT1-Sakai was produced by illegitimate excision, like lambda gal and bio phages.
      Full author list: Yokoyama, K., Makino, K., Kubota, Y., Watanabe, M., Kimura, S., Yutsudo,
      C.H., Kurokawa, K., Ishii, K., Hattori, M., Tatsuno, I., Abe, H., Yoh, M., Iida, T., Ohnishi,
      M., Hayashi, T., Yasunaga, T., Honda, T., Sasakawa, C., Shinagawa,H.
AU  - Yokoyama K
AU  - Makino K
AU  - Kubota Y
AU  - Watanabe M
AU  - Kimura S
AU  - Yutsudo CH
AU  - Kurokawa K
AU  - Ishii K
AU  - Hattori M
AU  - Tatsuno I
AU  - Abe H
AU  - Yoh M
AU  - Iida T
AU  - Ohnishi M
AU  - Hayashi T
AU  - Yasunaga T
AU  - Honda T
AU  - Sasakawa C
AU  - Shinagawa H
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 2000 258: 127-139.

PMID- 21914882
VI  - 193
DP  - 2011
TI  - Complete Genomic Sequence of the O-Desmethylangolensin-Producing Bacterium Clostridium rRNA Cluster XIVa Strain SY8519, Isolated from Adult Human  Intestine.
PG  - 5568-5569
AB  - The O-desmethylangolensin-producing Clostridium rRNA cluster XIVa strain SY8519 was isolated
      from the intestinal flora of a healthy human as a key
      isoflavonoid-metabolizing bacterium. Here, we report the finished and
      annotated genomic sequence of this organism.
AU  - Yokoyama S
AU  - Oshima K
AU  - Nomura I
AU  - Hattori M
AU  - Suzuki T
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5568-5569.

PMID- 21914883
VI  - 193
DP  - 2011
TI  - Complete Genomic Sequence of the Equol-Producing Bacterium Eggerthella sp. Strain YY7918, Isolated from Adult Human Intestine.
PG  - 5570-5571
AB  - Eggerthella sp. strain YY7918 was isolated from the intestinal flora of a healthy human. It
      metabolizes daidzein (a soybean isoflavonoid) and
      produces S-equol, which has stronger estrogenic activities than daidzein.
      Here, we report the finished and annotated genomic sequence of this
      organism.
AU  - Yokoyama S
AU  - Oshima K
AU  - Nomura I
AU  - Hattori M
AU  - Suzuki T
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5570-5571.

PMID- 3001655
VI  - 13
DP  - 1985
TI  - Interaction of EcoRII restriction and modification enzymes with synthetic DNA fragments.  V.  Study of single-stranded cleavages.
PG  - 8969-8981
AB  - Concatemer DNA duplexes which contain at the EcoRII restriction endonuclease
      cleavage sites ...^C-C-A-G-G-......-G-G-T-C-C^... phosphodiester, phosphoamide
      or pyrophosphate internucleotide bonds have been synthesized.  It has been
      shown that this enzyme did not cleave the substrate at phosphoamide bond.
      EcoRII endonuclease catalyzes single-strand cleavages both in dA- and
      dT-containing strands of the recognition site if the cleavage of the other
      strand has been blocked by modification of scissile bond or if the other strand
      has been cleaved.  This enzyme interacts with both strands of the DNA
      recognition site, each of them being cleaved independently of the cleavage of
      another one.  Nucleotide sequences flanking the EcoRII site on both sides are
      necessary for effective cleavage of the substrate.
AU  - Yolov AA
AU  - Gromova ES
AU  - Potapov VK
AU  - Shabarova ZA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1985 13: 8969-8981.

PMID- 6321233
VI  - 167
DP  - 1984
TI  - Interaction of EcoRII restriction and modification enzymes with synthetic DNA fragments.
PG  - 147-150
AB  - Interaction of EcoRII restriction endonuclease with a set of synthetic
      concatemer DNA duplexes with natural and modified sites for this enzyme has
      been studied.  DNA duplexes with repeated natural sites are cleaved by EcoRII.
      Substitution of central AT-pair in the recognition site for a non-complementary
      TT- or AA-pair reduces the rate of cleaveage, this effect being much more
      pronounced in the last case.  Absence of site flanking in one strand from the
      5' -terminus also results in very slow cleavage.  The results obtained testify
      to the interaction of EcoRII with both strands of the substrate.
AU  - Yolov AA
AU  - Gromova ES
AU  - Romanova EA
AU  - Oretskaya TS
AU  - Oganov AA
AU  - Buryanov YI
AU  - Shabarova ZA
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1984 167: 147-150.

PMID- 2993851
VI  - 10
DP  - 1985
TI  - Processive cleavage of concatemer DNA duplexes by EcoRII restriction endonuclease.
PG  - 173-176
AB  - EcoRII restriction endonuclease cleaves synethetic DNA-duplexes in which the
      recognition sites of this enzyme (5'...CC(A/T)GG...) are repeated every 9 base
      pairs with the alternating orientation of the central AT pair.  It operates in
      a processive mode, i.e. the bound enzyme molecule slides along the substrate
      toward neighboring recognition sites.  Nona-nucleotides are the main products
      of the cleavage.  The data obtained point to the capability of EcoRII
      endonuclease to recognize and cleave the substrate under both possible
      orientations of the central AT-pair of the recognition site with respect to the
      bound enzyme molecule.  These data also show the close similarity of DNA
      structures in a complex with the enzyme and without.
AU  - Yolov AA
AU  - Gromova ES
AU  - Shabarova ZA
PT  - Journal Article
TA  - Mol. Biol. Rep.
JT  - Mol. Biol. Rep.
SO  - Mol. Biol. Rep. 1985 10: 173-176.

PMID- 3001656
VI  - 13
DP  - 1985
TI  - Interaction of EcoRII restriction and modification enzymes with synthetic DNA fragments. VI.  The binding and cleavage of substrates containing nucleotide analogs.
PG  - 8983-8998
AB  - The present study deals with the binding and cleavage by EcoRII endonuclease of
      concatamer DNA duplexes containing EcoRII recognition sites (5'...^CCAGG) in
      which dT is replaced by dU or 5-bromodeoxyuridine, or 5'-terminal dC in the
      dT-containing strand is methylated at position 5.  The enzyme molecule is found
      to interact with the methyl group of the dT residue of the DNA recognition site
      and to be at least in proximity to the H5 atom of the 5'-terminal dC residue in
      dT-containing strand of this site.  Modification of any of these positions
      exerts an equal effects on the cleavage of both DNA strands.  Endonuclease
      EcoRII was found to bind the substrate specifically.  At the same time
      modification of the bases in recognized sequence may result in the formation of
      unproductive,though stable, enzyme-substrate complexes.
AU  - Yolov AA
AU  - Vinogradova MN
AU  - Gromova ES
AU  - Rosenthal A
AU  - Cech D
AU  - Veiko VP
AU  - Metelev VG
AU  - Kosykh VG
AU  - Buryanov YI
AU  - Vayev AA
AU  - Shabarova AZ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1985 13: 8983-8998.

PMID- 7918634
VI  - 1219
DP  - 1994
TI  - DNA binding mode of class-IIS restriction endonuclease FokI revealed by DNA footprinting analysis.
PG  - 369-379
AB  - We investigate the interaction of FokI with its DNA recognition sequence by several
      footprinting techniques. Methylation of three guanine bases in the recognition sequence
      5'-GGATG-3' is strongly protected by FokI binding, whereas other guanine bases are not
      masked from the modification. In footprinting using the methidiumpropyl-EDTA-Fe(II) complex,
      binding of FokI strongly inhibits cleavage by the footprinting reagent at and near the
      recognition sequence. In high-resolution footprinting techniques using hydroxyl radical and
      the bleomycin-Fe(II) complex, all footprints in each binding site clearly face one side of the
      DNA helix. Interference analysis with FokI digestion by preethylation of phosphate groups
      suggests that essential phosphates for FokI digestion are located at and near the recognition
      sequence and the cleavage site. Evidently, the results indicate that (i) the
      sequence-recognition of FokI occurs in the major groove and that (ii) the enzyme interacts
      with its target DNA from one side of the DNA helix.
AU  - Yonezawa A
AU  - Sugiura Y
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1994 1219: 369-379.

PMID- 26941158
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a Chlorinated-Ethene Degrader, Cupriavidus necator Strain PHE3-6 (NBRC 110655).
PG  - e01743-15
AB  - Cupriavidus necator strain PHE3-6 grows on phenol as a sole carbon source and cometabolizes
      cis- and trans-dichloroethenes and trichloroethene. Here, we report
      the draft genome sequence of PHE3-6, which provides insights into the degradation
      system of phenol and chlorinated ethenes.
AU  - Yonezuka K
AU  - Shimodaira J
AU  - Tabata M
AU  - Nagase S
AU  - Kasai D
AU  - Hosoyama A
AU  - Yamazoe A
AU  - Fujita N
AU  - Fukuda M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01743-15.

PMID- 24072866
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Bacillus subtilis Strain S1-4, Which Degrades Feathers Efficiently.
PG  - e00766-13
AB  - Bacillus subtilis strain S1-4, with the capacity to efficiently degrade feathers, was isolated
      from chicken feathers. Sequencing showed that the genome of strain
      S1-4 differs from that of other B. subtilis strains, with limited insertions and
      deletions. The genome encodes multiple extracellular proteases and keratinases.
AU  - Yong B
AU  - Yang BQ
AU  - Zhao CW
AU  - Feng H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00766-13.

PMID- 25953192
VI  - 3
DP  - 2015
TI  - Insights on Quorum-Quenching Properties of Lysinibacillus fusiformis Strain RB21, a Malaysian Municipal Solid-Waste Landfill Soil Isolate, via Complete Genome  Sequence Analysis.
PG  - e00409-15
AB  - Lysinibacillus fusiformis strain RB21 is a quorum-quenching bacterium that is able to degrade
      quorum-sensing signaling molecules. Here, we present the first
      complete genome sequence of L. fusiformis strain RB21. The finished genome is 4.8
      Mbp in size, and the quorum-quenching gene was identified.
AU  - Yong D
AU  - Ee R
AU  - Lim YL
AU  - Chang CY
AU  - Yin WF
AU  - Chan KG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00409-15.

PMID- 3597363
VI  - 262
DP  - 1987
TI  - Subunit and functional size of human placental DNA methyltransferase involved in de novo and maintenance methylation.
PG  - 8066-8070
AB  - The subunit molecular size of human DNA methyltransferase isolated from nuclear extracts of
      placenta was determined on the electroblotted
      polypeptides after sodium dodecyl sulfate-polyacrylamide gel
      electrophoresis and compared with the functional size by high performance
      size exclusion chromatography on Superose 12 and gamma radiation
      inactivation analysis. The sodium dodecyl sulfate-polyacrylamide gel
      electrophoresis results indicated a subunit mass of 120 +/- 10 kDa, while
      the functional size data indicates that the enzyme operates both in de
      novo and maintenance modes as a dimer of molecular mass 220 +/- 15 kDa
      with no evidence of monomers in solution of ionic strength between 0.1 and
      0.8 M NaCl. The 220-kDa activity carried out the transmethylation of both
      hemi- and unmethylated DNA substrates. There was no evidence for separate
      functional catalytic sites on each monomer subunit acting independently
      when engaged in methylation of hemimethylated or single-stranded DNA from
      the invariance of radiation inactivation target size with these
      substrates. The radiation inactivation target size was 230 +/- 15 kDa.
AU  - Yoo HY
AU  - Noshari J
AU  - Lapeyre JN
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1987 262: 8066-8070.

PMID- 23637988
VI  - 8
DP  - 2013
TI  - Molecular Modeling Studies of the Novel Inhibitors of DNA Methyltransferases SGI-1027 and CBC12: Implications for the Mechanism of Inhibition of DNMTs.
PG  - e62152
AB  - DNA methylation is an epigenetic modification that regulates gene expression by DNA
      methyltransferases (DNMTs). Inhibition of DNMTs is a
      promising approach for cancer therapy. Recently, novel classes of the
      quinolone-based compound, SGI-1027, and RG108-procainamide conjugates,
      CBC12, have been identified as potent DNMT inhibitors. In this work, we
      report comprehensive studies using induced-fit docking of SGI-1027 and
      CBC12 with human DNMT1 and DNMT3A. The docking was performed in the
      C-terminal MTase catalytic domain, which contains the substrate and
      cofactor binding sites, in the presence and absence of other domains.
      Induced-fit docking predicts possible binding modes of the ligands
      through the appropriate structural changes in the receptor. This work
      suggests a hypothesis of the inhibitory mechanisms of the new
      inhibitors which is in agreement with the reported autoinhibitory
      mechanism. The insights obtained in this work can be used to design
      DNMT inhibitors with novel scaffolds.
AU  - Yoo J
AU  - Choi S
AU  - Medina-Franco JL
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2013 8: e62152.

PMID- 22607757
VI  - 87
DP  - 2012
TI  - MOLECULAR MODELING OF INHIBITORS OF HUMAN DNA METHYLTRANSFERASE WITH A CRYSTAL STRUCTURE: DISCOVERY OF A NOVEL DNMT1 INHIBITOR.
PG  - 219-247
AB  - DNA methyltransferases (DNMTs) are promising epigenetic targets for the development of novel
      anticancer drugs and other diseases. Molecular
      modeling and experimental approaches are being used to identify and
      develop inhibitors of human DNMTs. Most of the computational efforts
      conducted so far with DNMT1 employ homology models of the enzyme.
      Recently, a crystallographic structure of the methyltransferase domain
      of human DNMT1 bound to unmethylated DNA was published. Following on
      our previous computational and experimental studies with DNMTs, we
      herein present molecular dynamics of the crystal structure of human
      DNMT1. Docking studies of established DNMT1 inhibitors with the crystal
      structure gave rise to a structure-based pharmacophore model that
      suggests key interactions of the inhibitors with the catalytic binding
      site. Results had a good agreement with the docking and pharmacophore
      models previously developed using a homology model of the catalytic
      domain of DNMT1. The docking protocol was able to distinguish active
      DNMT1 inhibitors from, for example, experimentally known inactive DNMT1
      inhibitors. As part of our efforts to identify novel inhibitors of
      DNMT1, we conducted the experimental characterization of
      aurintricarboxylic acid (ATA) that in preliminary docking studies
      showed promising activity. ATA had a submicromolar inhibition
      (IC50=0.68 mu M) against DNMT1. ATA was also evaluated for Dnmt3a
      inhibition showing an IC50=1.4 mu M. This chapter illustrates the
      synergy from integrating molecular modeling and experimental methods to
      further advance the discovery of novel candidates for epigenetic
      therapies.
AU  - Yoo J
AU  - Kim JH
AU  - Robertson KD
AU  - Medina-Franco JL
PT  - Journal Article
TA  - Adv. Protein Chem. Struct. Biol.
JT  - Adv. Protein Chem. Struct. Biol.
SO  - Adv. Protein Chem. Struct. Biol. 2012 87: 219-247.

PMID- 22709005
VI  - 19
DP  - 2012
TI  - Inhibitors of DNA Methyltransferases: Insights from Computational Studies.
PG  - 3475-3487
AB  - DNA methyltransferases (DNMTs) are a family of epigenetic enzymes for which inhibition is an
      attractive strategy for the treatment of cancer
      and other diseases. In synergy with experimental approaches,
      computational methods are increasingly being used to identify and
      optimize the activity of inhibitors of DNMTs as well as to rationalize
      at the molecular level of the mechanism of established inhibitors.
      Recently, a crystallographic structure of the methyltransferase domain
      of human DNMT1 bound to unmethylated DNA was published encouraging the
      application of structure-based approaches to design and optimize the
      activity of currently known inhibitors. Herein, we review the progress
      in the discovery and optimization of inhibitors of DNMTs using
      computational approaches including homology modeling, docking,
      pharmacophore modeling, molecular dynamics, and virtual screening.
AU  - Yoo J
AU  - Medina-Franco JL
PT  - Journal Article
TA  - Curr. Med. Chem.
JT  - Curr. Med. Chem.
SO  - Curr. Med. Chem. 2012 19: 3475-3487.

PMID- 22843580
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence and Comparative Analysis of the Superb Aromatic-Hydrocarbon Degrader Rhodococcus sp. Strain DK17.
PG  - 4440
AB  - Rhodococcus sp. strain DK17 is capable of utilizing various derivatives of benzene and
      bicyclics containing both aromatic and alicyclic moieties as sole
      carbon and energy sources. Here, we present the 9,107,362-bp draft genome
      sequence of DK17 and its genomic analysis in comparison with other members of the
      genus Rhodococcus.
AU  - Yoo M
AU  - Kim D
AU  - Choi KY
AU  - Chae JC
AU  - Zylstra GJ
AU  - Kim E
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4440.

PMID- 6248522
VI  - 255
DP  - 1980
TI  - Isolation and characterization of two proteins possessing HpaII methylase activity.
PG  - 6445-6449
AB  - Two proteins exhibiting HpaII methylase activity have been purified to
      homogeneity from Haemophilus parainfluenzae and their physical and catalytic
      properties have been studied.  Separation of the two HpaII methylase activities
      was achieved by DEAE-Sephadex A-50 chromatography.  In subsequent steps, each
      methylase was purified separately by chromatography on Sephacryl S-200,
      phosphocellulose, and hydroxylapatite.  The proteins have molecular weights of
      38,500 +/- 1,000 (HpaII) and 41,500 +/- 1,000 (HpaII') as judged by
      polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate.
      Sedimentation equilibrium analyses of the native proteins yield molecular
      weights of 38,800 +/- 3,000 and 42,200 +/- 3,000 for HpaII and HpaII',
      respectively, indicating that both enzymes are composed of a single subunit.
      Furthermore, both methylases exhibit identical specificity in the methylation
      of the nucleotide sequence dC-C-G-G in simian virus 40 (SV40) DNA and in a
      short synthetic oligonucleotide duplex.  Although pH, temperature, and salt
      optima are the same for both enzymes, homogenous HpaII' methylase is more
      stable than HpaII methylase.  Preliminary peptide mapping indicates that the
      two enzymes are structurally related, suggesting the possibility that HpaII'
      methylase may represent a precursor form of HpaII methylase.
AU  - Yoo OJ
AU  - Agarwal KL
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1980 255: 6445-6449.

PMID- 6159356
VI  - 255
DP  - 1980
TI  - Cleavage of single strand oligonucleotides and bacteriophage PhiX174 DNA by MspI endonuclease.
PG  - 10559-10562
AB  - Type II restriction endonucleases cleave duplex DNA at nucleotide sequences
      displaying 2-fold symmetry.  Our data show that MspI cleaves single strand
      oligonucleotides, d(GAACCGGAGA) and d(TCTCGGTT) at 4, 25, and 37C reaction
      temperatures.  The rate of cleavage of d(GAACCGGAGA) is several-fold faster
      than that of d(TCTCCGGTT).  Single strand PhiX174 DNA is also cleaved by MspI
      endonuclease giving well defined fragments.  5'-nucleotide analysis of the
      fragments generated from single strand and replicating form DNA suggest that
      cleavage occurs at the recognition sequence d(CCGG).  The data show that MspI
      endonuclease cleaves single strand oligonucleotides and prefers a recognition
      sequence surrounded by purine nucleotides.  A general model for endonuclease
      cleavage of single strand and duplex DNA is presented.
AU  - Yoo OJ
AU  - Agarwal KL
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1980 255: 10559-10562.

PMID- 6983681
VI  - 10
DP  - 1982
TI  - Purification and properties of the HpaI methylase.
PG  - 6511-6519
AB  - The purification and catalytic properties of the homogeneous HpaI methylase is
      described.  The enzyme exists as a single polypeptide chain with a molecular
      weight of 37,000 +/- 2,000 was shown by sedimentation equilibrium and
      polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate.
      The HpaI methylase transfers methyl groups of S-adenosylmethionine to adenine
      present in the recognition sequence d(G-T-T-A-A*-C), A* is the N6 methyl
      adenosine.  An average of 2.1 methyl groups per recognition site are
      transferred by the HpaI methylase.
AU  - Yoo OJ
AU  - Dwyer-Hallquist P
AU  - Agarwal KL
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1982 10: 6511-6519.

PMID- Not carried by PubMed...
VI  - 18
DP  - 1985
TI  - Purification and characterization of AluI methylase.
PG  - 82-87
AB  - AluI methylase has been isolated from 300g (wet weight) cells of Arthrobacter
      luteus.  After ammonium sulfate fractionation, the protein which has methylase
      activity was purified through phosphocellulose, DEAE-cellulose, Heparin
      agarose, and Hydroxy-lapatite column chromatography.  The methylated DNA by the
      purified methylase was resistant against AluI endonuclease.  The purified AluI
      methylase was essentially homogeneous as judged by 10% SDS-polyacrylamide gel
      electrophoresis, and the apparent subunit molecular weight was 56,000+-1,000.
      The specific activity of the enzyme was 132000 units per mg protein.
AU  - Yoon H
AU  - Suh H
AU  - Han MH
AU  - Yoo OJ
PT  - Journal Article
TA  - Korean Biochem. J.
JT  - Korean Biochem. J.
SO  - Korean Biochem. J. 1985 18: 82-87.

PMID- Not carried by PubMed...
VI  - 18
DP  - 1985
TI  - The specificity and catalytic properties of AluI methylase.
PG  - 88-93
AB  - The specific methylation site for AluI methylase was the cytosine nucleotide in
      AluI sequence.  The position of the methylated cytosine nucleotide was
      determined by the chemical cleavage reactions of the Maxam-Gilbert DNA
      sequencing procedure.  As expected, the methylated cytosine nucleotide bands
      were disappeared on C+T and C lanes on 12% sequencing gels. AluI methylase was
      maximally active at near pH 7.5 in the presence of 50 mM NaCl.  The methylase
      did not require Mg++ for activity, and obeyed Michaelis-Menten Kinetics with
      respect to both AdoMet and DNA.  At 37C, the Km for AdoMet was 0.44 lM, that
      for the AluI site of pBR322 DNA was 4.03 nM, and the corresponding turnover
      numbers were 1.83 methyl transfer per minute per monomer and 1.61 transfers per
      minute per monomer, respectively.
AU  - Yoon H
AU  - Suh H
AU  - Kim K
AU  - Han MH
AU  - Yoo OJ
PT  - Journal Article
TA  - Korean Biochem. J.
JT  - Korean Biochem. J.
SO  - Korean Biochem. J. 1985 18: 88-93.

PMID- 14651272
VI  - 16
DP  - 2003
TI  - X-ray crystallographic studies of HemK from Thermotoga maritima, an N-5-glutamine methyltransferase.
PG  - 266-269
AB  - The enzyme HemK (or PrmC) is one of the first identified methyltransferases that modify
      glutamine. It methylates the highly
      conserved GGQ motif in class I release factors (RF1 and RF2) in
      Escherichia coli. HemK from Thermotoga maritima was over-expressed and
      crystallized in the presence of S-adenosylmethionine at 296 K using
      ammonium sulfate as the precipitant. X-ray diffraction data were collected
      to 2.5 A resolution from a native crystal. The crystal is orthorhombic,
      belonging to the space group I222 (or I2(1)2(1)2(1)), with unit-cell
      parameters of a = 104.24, b = 118.73, and c = 146.62 A. Two (or three)
      monomers of recombinant HemK are likely to be present in the
      crystallographic asymmetric unit, giving a V(M) of 3.62 A3 Da(-1) (or 2.41
      A3 Da(-1)), with a solvent content of 62.7% (or 44.0%).
AU  - Yoon HJ
AU  - Kang KY
AU  - Ahn HJ
AU  - Shim SM
AU  - Ha JY
AU  - Lee SK
AU  - Mikami B
AU  - Suh SW
PT  - Journal Article
TA  - Mol. Cells
JT  - Mol. Cells
SO  - Mol. Cells 2003 16: 266-269.

PMID- Not carried by PubMed...
VI  - 13
DP  - 1985
TI  - Purification and characterization of HpaI endonuclease.
PG  - 87-91
AB  - HpaI endonuclease from Haemophilus parainfluenzae has been purified to
      homogeneity and its physical and enzymatic properties have been studied.  For
      the purification of the enzyme, Heparin agarose, SP-sephadex C-25,
      DEAE-sephadex A-50 and phosphocellulose chromatography columns were used.  The
      denatured and reduced form of the enzyme is a monomer of molecular weight of
      30,000 -+1,000 as judged by 10% polyacrylamide gel electrophoresis containing
      0.1% sodium dodesyl sulfate.  HpaI endonuclease was maximally active at neutral
      pH (7.0 to 7.5) in the presence of 50 mM NaCl.
AU  - Yoon HS
AU  - Kang SC
AU  - Yoo OJ
PT  - Journal Article
TA  - Sanop Misaengmul Hakhoe Chi
JT  - Sanop Misaengmul Hakhoe Chi
SO  - Sanop Misaengmul Hakhoe Chi 1985 13: 87-91.

PMID- 23584783
VI  - 79
DP  - 2013
TI  - Functional screening of a metagenomic library reveals operons responsible for enhanced intestinal colonization by gut commensal microbes.
PG  - 3829-3838
AB  - Evidence suggests that gut microbes colonize the mammalian intestine through
      propagation as an adhesive microbial community. A bacterial artificial chromosome
      (BAC) library of murine bowel microbiota DNA in the surrogate host Escherichia
      coli DH10B was screened for enhanced adherence capability. Two out of 5,472 DH10B
      clones, 10G6 and 25G1, exhibited enhanced capabilities to adhere to inanimate
      surfaces in functional screens. DNA segments inserted into the 10G6 and 25G1
      clones were 52 and 41 kb and included 47 and 41 protein-coding open reading
      frames (ORFs), respectively. DNA sequence alignments, tetranucleotide frequency,
      and codon usage analysis strongly suggest that these two DNA fragments are
      derived from species belonging to the genus Bacteroides. Consistent with this
      finding, a large portion of the predicted gene products were highly homologous to
      those of Bacteroides spp. Transposon mutagenesis and subsequent experiments that
      involved heterologous expression identified two operons associated with enhanced
      adherence. E. coli strains transformed with the 10a or 25b operon adhered to the
      surface of intestinal epithelium and colonized the mouse intestine more
      vigorously than did the control strain. This study has revealed the genetic
      determinants of unknown commensals (probably resembling Bacteroides species) that
      enhance the ability of the bacteria to colonize the murine bowel.
AU  - Yoon MY
AU  - Lee KM
AU  - Yoon Y
AU  - Go J
AU  - Park Y
AU  - Cho YJ
AU  - Tannock GW
AU  - Yoon SS
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2013 79: 3829-3838.

PMID- 17355171
VI  - 5
DP  - 2007
TI  - The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families.
PG  - e16
AB  - Metagenomics projects based on shotgun sequencing of populations of micro-organisms yield
      insight into protein families. We used sequence
      similarity clustering to explore proteins with a comprehensive dataset
      consisting of sequences from available databases together with 6.12
      million proteins predicted from an assembly of 7.7 million Global Ocean
      Sampling (GOS) sequences. The GOS dataset covers nearly all known
      prokaryotic protein families. A total of 3,995 medium- and large-sized
      clusters consisting of only GOS sequences are identified, out of which
      1,700 have no detectable homology to known families. The GOS-only clusters
      contain a higher than expected proportion of sequences of viral origin,
      thus reflecting a poor sampling of viral diversity until now. Protein
      domain distributions in the GOS dataset and current protein databases show
      distinct biases. Several protein domains that were previously categorized
      as kingdom specific are shown to have GOS examples in other kingdoms.
      About 6,000 sequences (ORFans) from the literature that heretofore lacked
      similarity to known proteins have matches in the GOS data. The GOS dataset
      is also used to improve remote homology detection. Overall, besides nearly
      doubling the number of current proteins, the predicted GOS proteins also
      add a great deal of diversity to known protein families and shed light on
      their evolution. These observations are illustrated using several protein
      families, including phosphatases, proteases, ultraviolet-irradiation DNA
      damage repair enzymes, glutamine synthetase, and RuBisCO. The diversity
      added by GOS data has implications for choosing targets for experimental
      structure characterization as part of structural genomics efforts. Our
      analysis indicates that new families are being discovered at a rate that
      is linear or almost linear with the addition of new sequences, implying
      that we are still far from discovering all protein families in nature.
AU  - Yooseph S et al
PT  - Journal Article
TA  - PLoS Biology
JT  - PLoS Biology
SO  - PLoS Biology 2007 5: e16.

PMID- 26941156
VI  - 4
DP  - 2016
TI  - Draft Whole-Genome Sequences of 25 Salmonella enterica Strains Representing 24 Serovars.
PG  - e01718-15
AB  - We report the draft genome sequences of 25 Salmonella enterica strains representing 24
      different serotypes, many of which were not available in public
      repositories during our selection process. These draft genomes will provide
      useful reference for the genetic variation between serotypes and aid in the
      development of molecular typing tools.
AU  - Yoshida C
AU  - Brumwell SL
AU  - Lingohr EJ
AU  - Ahmad A
AU  - Blimkie TM
AU  - Kogan BA
AU  - Pilsworth J
AU  - Rehman MA
AU  - Schleicher KL
AU  - Shanmugaraj J
AU  - Kropinski AM
AU  - Nash JH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01718-15.

PMID- 25883280
VI  - 3
DP  - 2015
TI  - Comparative Genomics of the Mucoid and Nonmucoid Strains of Streptococcus pyogenes, Isolated from the Same Patient with Streptococcal Meningitis.
PG  - e00221-15
AB  - Mucoid (MTB313) and nonmucoid (MTB314) strains of group A streptococcus emm type  1 were
      simultaneously isolated from a single patient suffering from streptococcal
      meningitis. Whole-genome sequencing revealed that MTB313 carried a nucleotide
      substitution within rocA, which generated an amber termination codon.
AU  - Yoshida H
AU  - Ishigaki Y
AU  - Takizawa A
AU  - Moro K
AU  - Kishi Y
AU  - Takahashi T
AU  - Matsui H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00221-15.

PMID- 29348346
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Streptococcus canis Clinical Strain TA4, Harboring the M-Like Protein Gene and Isolated in Japan from a Patient with Bacteremia.
PG  - e01469-17
AB  - Streptococcus canis is an animal-origin beta-hemolytic bacterium that can cause severe
      infections in animals and occasionally infects humans. Here, we report a
      draft genome sequence of an S. canis strain harboring the M-like protein gene.
      This strain was isolated from a patient with bacteremia (reported by Taniyama et
      al. [D. Taniyama, Y. Abe, T. Sakai, T. Kikuchi, and T. Takahashi, IDCases
      7:48-52, 2017, https://doi.org/10.1016/j.idcr.2017.01.002]). The draft genome
      comprises 2,129,080 bp in 60 contigs.
AU  - Yoshida H
AU  - Katayama Y
AU  - Fukushima Y
AU  - Taniyama D
AU  - Murata Y
AU  - Mizutani T
AU  - Takahashi T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01469-17.

PMID- 28473377
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Clinical Strain TANI1 of Streptococcus suis Serotype 5 Isolated from a Bacteremia Patient in Japan.
PG  - e00260-17
AB  - Streptococcus suis is a swine pathogen that causes severe economic damage to the  porcine
      industry. It occasionally evokes zoonotic infection in humans. Here, we
      report a draft genome sequence of a S. suis serotype 5 strain isolated from a
      bacteremia patient that was reported by Taniyama et al. (D. Taniyama, M. Sakurai,
      T. Sakai, T. Kikuchi, and T. Takahashi, IDCases 6:36-38, 2016,
      https://doi.org/10.1016/j.idcr.2016.09.011).
AU  - Yoshida H
AU  - Wada T
AU  - Taniyama D
AU  - Takahashi T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00260-17.

PMID- 29437099
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of a Type Strain of Mycobacterium abscessus subsp. bolletii, a Member of the Mycobacterium abscessus Complex.
PG  - e01530-17
AB  - Mycobacterium abscessus subsp. bolletii is a rapidly growing mycobacterial organism for which
      the taxonomy is unclear. Here, we report the complete genome
      sequence of a Mycobacterium abscessus subsp. bolletii type strain. This sequence
      will provide essential information for future taxonomic and comparative genome
      studies of these mycobacteria.
AU  - Yoshida M
AU  - Fukano H
AU  - Miyamoto Y
AU  - Shibayama K
AU  - Suzuki M
AU  - Hoshino Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01530-17.

PMID- 29773624
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Mycobacterium marinum ATCC 927(T), Obtained Using Nanopore and Illumina Sequencing Technologies.
PG  - e00397-18
AB  - Mycobacterium marinum is a slowly growing, broad-host-range mycobacterial species. Here, we
      report the complete genome sequence of a Mycobacterium marinum
      type strain that was isolated from tubercles of diseased fish. This sequence will
      provide essential information for future taxonomic and comparative genome studies
      of its relatives.
AU  - Yoshida M
AU  - Fukano H
AU  - Miyamoto Y
AU  - Shibayama K
AU  - Suzuki M
AU  - Hoshino Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00397-18.

PMID- 29930060
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Mycobacterium shigaense.
PG  - e00552-18
AB  - Mycobacterium shigaense is a slowly growing scotochromogenic species and a member of the
      Mycobacterium simiae complex group. Here, we report the complete sequence
      of its genome, comprising a 5.2-Mb chromosome. The sequence will represent the
      essential data for future phylogenetic and comparative genome studies of the
      Mycobacterium simiae complex group.
AU  - Yoshida M
AU  - Fukano H
AU  - Ogura Y
AU  - Kazumi Y
AU  - Mitarai S
AU  - Hayashi T
AU  - Hoshino Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00552-18.

PMID- 29167250
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Mycobacterium sp. Strain shizuoka-1, a Novel Mycobacterium Isolated from Groundwater of a Bathing Facility in Shizuoka, Japan.
PG  - e01309-17
AB  - Mycobacterium sp. strain shizuoka-1 is a rapidly growing scotochromogenic mycobacterium and
      was isolated from well water for a bathing facility in Shizuoka
      Prefecture in Japan. Here, we report the draft sequence of its genome, comprising
      a 6.5-Mb chromosome. This mycobacterium has 83.1% identity with Mycobacterium
      rhodesiae, a human pathogen.
AU  - Yoshida M
AU  - Izumiyama S
AU  - Fukano H
AU  - Sugiyama K
AU  - Suzuki M
AU  - Shibayama K
AU  - Hoshino Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01309-17.

PMID- 29192083
VI  - 5
DP  - 2017
TI  - Complete Chromosome Sequence of a Mycolactone-Producing Mycobacterium, Mycobacterium pseudoshottsii.
PG  - e01363-17
AB  - Mycobacterium pseudoshottsii is a fish pathogen that produces mycolactone. Here,  we report
      the complete chromosome sequence of a type strain of M. pseudoshottsii
      (JCM 15466). The sequence will represent essential data for future phylogenetic
      and comparative genome studies of mycolactone-producing mycobacteria.
AU  - Yoshida M
AU  - Miyamoto Y
AU  - Ogura Y
AU  - Hayashi T
AU  - Hoshino Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01363-17.

PMID- 27688344
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Mycobacterium ulcerans subsp. shinshuense.
PG  - e01050-16
AB  - Mycobacterium ulcerans subsp. shinshuense produces mycolactone and causes Buruli  ulcer. Here,
      we report the complete sequence of its genome, which comprises a
      5.9-Mb chromosome and a 166-kb plasmid (pShT-P). The sequence will represent the
      essential data for future phylogenetic and comparative genome studies of
      mycolactone-producing mycobacteria.
AU  - Yoshida M
AU  - Nakanaga K
AU  - Ogura Y
AU  - Toyoda A
AU  - Ooka T
AU  - Kazumi Y
AU  - Mitarai S
AU  - Ishii N
AU  - Hayashi T
AU  - Hoshino Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01050-16.

PMID- 25953178
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Bordetella bronchiseptica KU1201, the First Isolation Source of Arylmalonate Decarboxylase.
PG  - e00373-15
AB  - The analysis of the 6.8-Mbp draft genome sequence of the phenylmalonate-assimilating bacterium
      Bordetella bronchiseptica KU1201 identified
      6,358 protein-coding sequences. This will give us an insight into the catabolic
      variability of this strain for aromatic compounds, along with the roles of
      arylmalonate decarboxylases in nature.
AU  - Yoshida S
AU  - Enoki J
AU  - Hemmi R
AU  - Kourist R
AU  - Kawakami N
AU  - Miyamoto K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00373-15.

PMID- 3003023
VI  - 165
DP  - 1986
TI  - Occurrence of small Hsd plasmids in Salmonella typhi, Shigella boydii, and Escherichia coli.
PG  - 357-362
AB  - The natural occurrence of small Hsd (host specificity for DNA) plasmids was
      demonstrated in restriction endonuclease-producing strains of Salmonella typhi,
      Shigella boydii, and Escherichia coli.  The five Hsd plasmids isolated were
      between 5.0 and 12.2 kilobases long.  The copy number of all the Hsd plasmids
      were high (more than 10 copies per cell).  Introduction of these small plasmids
      into E. coli strain 0 drastically lowered the efficiency of plating of the k.0
      phages (the efficiency of plating was less than 5 X 10-5 PFU-1).  High
      restriction endonuclease activities were detected in the Hsd plasmid-positive
      strains because of the elevated copy numbers of the hsdR+ gene.  The advantages
      of using E. coli strains containing the small Hsd plasmids for purification of
      type II restriction endonucleases are discussed.
AU  - Yoshida Y
AU  - Mise K
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1986 165: 357-362.

PMID- 25131295
VI  - 16
DP  - 2014
TI  - Two types of genetic carriers, the IncP genomic island and the novel IncP-1beta plasmid, for the aac(2')-IIa gene that confers kasugamycin resistance in Acidovorax avenae subsp. avenae.
PG  - 288-300
AB  - A unique aminoglycoside antibiotic, kasugamycin (KSM), has been used to control
      many plant bacterial and fungal diseases in several countries. The emergence of
      KSM-resistant Acidovorax avenae ssp. avenae and Burkholderia glumae, which cause
      rice bacterial brown stripe and rice bacterial grain and seedling rot,
      respectively, is a serious threat for the effective control of these diseases.
      Previously, we have identified the aac(2')-IIa gene, encoding a KSM
      2'-N-acetyltransferase, from both KSM-resistant pathogens. Although all
      KSM-resistant isolates from both species possess the aac(2')-IIa gene, only A.
      avenae strain 83 showed higher resistance than other strains. In this research,
      kinetic analysis indicates that an amino acid substitution from serine to
      threonine at position 146 of AAC(2')-IIa in strain 83 is not involved in this
      increased resistance. Whole draft genome analysis of A. avenae 83 shows that the
      aac(2')-IIa gene is carried by the novel IncP-1beta plasmid pAAA83, whereas the
      genetic carrier of other strains, the IncP genomic island, is inserted into their
      chromosomes. The difference in the nucleotides of the promoter region of
      aac(2')-IIa between strain 83 and other strains indicates an additional
      transcription start site and results in the increased transcription of
      aac(2')-IIa in strain 83. Moreover, biological characterization of pAAA83
      demonstrates that it can be transferred by conjugation and maintained in the host
      cells. These results demonstrate that acquisition of the aac(2')-IIa gene takes
      place in at least two ways and that the gene module, which includes aac(2')-IIa
      and the downstream gene, may be an important unit for the dissemination of
      antibiotic resistance.
AU  - Yoshii A
AU  - Omatsu T
AU  - Katayama Y
AU  - Koyama S
AU  - Mizutani T
AU  - Moriyama H
AU  - Fukuhara T
PT  - Journal Article
TA  - Mol. Plant Pathol.
JT  - Mol. Plant Pathol.
SO  - Mol. Plant Pathol. 2014 16: 288-300.

PMID- 4565538
VI  - 112
DP  - 1972
TI  - R factor-controlled restriction and modification of deoxyribonucleic acids:  restriction mutants.
PG  - 1275-1279
AB  - Restriction mutants of two different R factor-controlled host specificities (RI
      and RII) were isolated.  All of the restriction mutants examined had a normal
      modification phenotype.  No complementation was observed between the RI and RII
      host specificities.  It is concluded that for each host specifcity no protein
      subunit is shared by the restriction endonuclease and modification methylase.
AU  - Yoshimori R
AU  - Roulland-Dussoix D
AU  - Boyer HW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1972 112: 1275-1279.

PMID- 
VI  - 
DP  - 1971
TI  - A genetic and biochemical analysis of the restriction and modification of DNA by resistance transfer factors.
PG  - 1-73
AB  - The DNA restriction and modification systems of RTF-1 and RTF-2, host
      specificities RI and RII respectively, were studied genetically and
      biochemically.  The presence of RTF-1 and RTF-2 plasmids in various E. coli
      strains carrying RI and RII restriction and modification host specificities
      restricted unmodified lambda with EOPS of 10-4 and 10-2 respectively.  The RTF
      plasmids were mutagenized with NTG and only one mutant phenotype, r-m+, was
      obtained.  This indicated that there were two genes, a restriction and a
      modification gene, in the host specificity system of the RTFs and differed from
      the three gene system of E. coli B and K.  Using mutant and wild-type RI and
      RII host specificities in various combinations revealed that no complementation
      occurred between the RI and RII host specificities and that they were mutually
      exclusive.  The RI and RII restriction endonucleases were purified to enable
      characterization of the enzymes.  RI and RII restriction endonucleases required
      only Mg++ and unmodified DNA for their enzymatic activity in contrast to the
      cofactor requirements (SAM, ATP, Mg++) of the E. coli B and K restriction
      endonucleases.  The molecular weights of the RI and RII restriction
      endonucleases were estimated to be 80,000 and 100,000 daltons, respectively,
      and recent evidence indicates two 50,000 MW subunits for the RII restriction
      endonuclease.  Optimal activity of RII restriction endonuclease was at 37o in
      0.1M Tris or glycylglycine buffer at pH 7.5 in 5 mM Mg++.  Optimal conditions
      for RI restriction endonuclease was between 26 to 37C in 0.1M Tris buffer at pH
      7.5 or at pH 7.2 with either 0.1M phosphate or glycylglycine buffer using 10 mM
      Mg++.  The average size of lambda DNA fragments produced by the RII
      endonucleolytic scissions was estimated at 2 Md MW.  The RI restriction
      endonuclease produced one fragment about 13 Md MW and four to six fragments of
      3.8 Md MW.  The RI and RII host specificities are classified as a second type
      of restriction and modification mechanism on the basis of the genetic and
      biochemical data.  The mechanism is simple and two cistrons are involved in
      restriction and modification.  Each enzyme is composed of two identical
      cistronic subunits.  On the other hand the more complex mechanism, which is
      represented by the K and B host specificities, is composed of large enzymes
      with complex subunit structures.  Three cistrons are involved in this
      restriction and modification mechanism and the cofactor requirements are SAM,
      ATP and Mg++.  The RI modification methylase was found on polyacrylamide gel as
      one of two protein bands, the other being the RI restriction endonuclease.
      Preliminary data indicates that the modification methylase requires only SAM
      and unmodified DNA for its activity.
AU  - Yoshimori RN
PT  - Journal Article
TA  - Ph.D. Thesis, University of California, San Francisco, USA
JT  - Ph.D. Thesis, University of California, San Francisco, USA
SO  - Ph.D. Thesis, University of California, San Francisco, USA 1971 : 1-73.

PMID- 8247607
VI  - 8
DP  - 1993
TI  - Genetic transformation of Porphyromonas gingivalis by electroporation.
PG  - 208-212
AB  - Porphyromonas gingivalis was transformed by electroporation using the DNA of plasmid pE5-2, or
      its derivative, pYT7. Prior to transformation, pE5-2 was transferred from Escherichia coli to
      P. gingivalis strains by conjugation (mobilization with R751) and the plasmid DNA was purified
      from the P. gingivalis transconjugants. Transformation occurred when the recipient strain and
      the donor strain from which the plasmid DNA was purified were homologous. If they were
      heterologous, transformation did not take place or did so at a very low frequency. This
      suggested that a restriction-modification system is present in P. gingivalis strains. Plasmid
      pYT7 was derived by removing an 8.0 kb AvaI fragment from pE5-2 that was purified from P.
      gingivalis cells. It has several single-cutting restriction sites such as EcoRI, AvaI, and
      ClaI usable for gene cloning, though it was not stable enough in P. gingivalis cells, probably
      because the rep gene was derived from a relatively distant species, Bacteroides eggerthii.
AU  - Yoshimoto H
AU  - Takahashi Y
AU  - Hamada N
AU  - Umemoto T
PT  - Journal Article
TA  - Oral Microbiol. Immunol.
JT  - Oral Microbiol. Immunol.
SO  - Oral Microbiol. Immunol. 1993 8: 208-212.

PMID- 24285664
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Marine Cyanobacterium Synechococcus sp. Strain NKBG15041c.
PG  - e00954-13
AB  - Synechococcus sp. strain NKBG15041c was isolated as a fast-growing marine cyanobacterium.
      Genetic transformation techniques using this strain have been
      well established for metabolic engineering. Here we report the draft genome
      sequence for this strain, consisting of 44 contigs containing a total of
      3,180,043 bp and 3,224 putative protein-coding genes.
AU  - Yoshino T
AU  - Honda T
AU  - Tanaka M
AU  - Tanaka T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00954-13.

PMID- Not included in PubMed...
VI  - 47
DP  - 1983
TI  - Purification, properties and recognition sequence of site-specific restriction endonuclease from "Acetobacter xylinus".
PG  - 2871-2879
AB  - A type II restriction endonuclease was purified from "Acetobacter xylinus" IFO
      3288 by consecutive column chromatographies on heparin-Sepharose CL-6B,
      DEAE-Sepharose CL-6B, DNA-cellulose and Sephacryl S-400 superfine.  The
      purified enzyme was homogeneous on gel disc electrophoresis and free of other
      endonuclease, exonuclease and phospatase activities.  The enzyme was optimally
      active at 37C at pH 7.5 and required 50~-150 mM NaCl for the enzyme reaction.
      The enzyme cleaved lambda and M13 mp7 RF DNAs at two and one site,
      respectively, but did not cleave pBR322, SV40 and PhiX174 RF DNAs.  the
      recognition sequence for the enzyme was determined to be 5'-C-C-T-N-A-G-G-3',
      and the enzyme was found to cut between C and T in the sequence, being an
      isoschizomer of endonuclease from a blue-green alga, Microcoleus species UTEX
      LB2220 (MstII).
AU  - Yoshioka H
AU  - Nakamura H
AU  - Sasaki J
AU  - Tahara Y
AU  - Yamada Y
PT  - Journal Article
TA  - Agric. Biol. Chem.
JT  - Agric. Biol. Chem.
SO  - Agric. Biol. Chem. 1983 47: 2871-2879.

PMID- 28860244
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequence of Streptococcus tigurinus Strain osk_001, Isolated from Postmortem Material.
PG  - e00878-17
AB  - Streptococcus tigurinus was recently described as a novel species, and some strains are highly
      virulent. We detected S. tigurinus in infected tissue sampled
      by necropsy. In order to characterize and confirm the virulence of this species,
      whole-genome sequencing of the pure cultured bacterium was performed. We found
      that the strain has specific and unique genetic elements contained in highly
      virulent strains of S. tigurinus.
AU  - Yoshizawa H
AU  - Motooka D
AU  - Katada R
AU  - Matsumoto Y
AU  - Nakamura S
AU  - Morii E
AU  - Iida T
AU  - Matsumoto H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00878-17.

PMID- 17469805
VI  - 46
DP  - 2007
TI  - A novel DNA modification by sulfur: DndA is a NifS-like cysteine desulfurase capable of assembling DndC as an iron-sulfur cluster protein in Streptomyces  lividans.
PG  - 6126-6133
AB  - A novel DNA modification system by sulfur (S) in Streptomyces lividans 66 was reported to be
      encoded by a cluster of five genes designated dndA-E [Zhou, X.,
      He, X., Liang, J., Li, A., Xu, T., Kieser, T., Helmann, J. D., and Deng, Z.
      (2005) Mol. Microbiol. 57, 1428-1438]. The dndA gene was cloned and the protein
      product expressed in Escherichia coli, purified to homogeneity, and characterized
      as a homodimeric protein of ca. 91 kDa. Purified DndA has a yellow color and
      UV-visible spectra characteristic of a pyridoxal phosphate-containing enzyme and
      was proven to be a cysteine desulfurase able to catalyze removal of elemental S
      atoms from l-cysteine to produce l-alanine with substrate specificity similar to
      that of E. coli IscS. DndC was also purified to homogeneity and found to contain
      a 4Fe-4S cluster by spectral analysis and have obvious ATP pyrophosphatase
      activity. DndA could catalyze iron-sulfur cluster assembly by activation of
      apo-Fe DndC protein prepared by removal of its iron-sulfur cluster using
      alpha,alpha'-dipyridyl. A mutated DndA, with serine substituted for cysteine at
      position 327, which was confirmed to have lost its corresponding cysteine
      desulfurase activity, also lost its ability to reactivate the apo-Fe DndC. The
      likely involvement of an interaction between DndA and DndC in the biochemical
      pathway for the unusual site-specific DNA modification in S. lividans 66 is
      discussed.
AU  - You D
AU  - Wang L
AU  - Yao F
AU  - Zhou X
AU  - Deng Z
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2007 46: 6126-6133.

PMID- 
VI  - 242
DP  - 2011
TI  - Development of a mass spectrometry-based assay to define the biochemistry of phosphorothioate DNA modifications of DNA in bacterial restriction/modification systems.
PG  - 0
AB  - We recently discovered that a wide variety of microorganisms possess sequences-specific
      phosphorothioate modifications (S-modifications) of their genomes, which are incorporated into
      DNA by members of the Dnd protein family.  The S-modifications occur at two discrete levels
      consistent with the 4- and 6-nucleotide consensus sequences of a restriction/modification
      system.  Formal proof for this model arose in enteropathogenic Salmonella enterica serovar
      Cerro 87, in which we discovered a host-specific restriciton system DNA S-modification, which
      is more complicated than the well-known methylation-specific restriction/modification systems.
      In an effort to develop an in vitro reconstituted phosphorothioation system, we have developed
      a MALDI-TOF assay in which S-modificaiton of an oligonucleotide possessiong a consensus
      sequence is monitored by a 16 amu mass increase upon insertion of sulfur into the DNA
      backbone.  The assay is being used to define the biochemical mechanism involved in
      phosphorothioation of DNA in this novel restriction/modification system in bacteria.
AU  - You DL
AU  - Indrakanti R
AU  - Cao B
AU  - Yao F
AU  - Deng ZX
AU  - Dedon PC
PT  - Journal Article
TA  - ACS Abstracts
JT  - ACS Abstracts
SO  - ACS Abstracts 2011 242: 0.

PMID- 21703548
VI  - 38
DP  - 2011
TI  - Unraveling the Acidithiobacillus caldus complete genome and its central metabolisms for carbon assimilation.
PG  - 243-252
AB  - Acidithiobacillus caldus is one of the dominant sulfur-oxidizing bacteria
      in bioleaching reactors. It plays the essential role in maintaining the
      high acidity and oxidation of reduced inorganic sulfur compounds during
      bioleaching process. In this report, the complete genome sequence of A.
      caldus SM-1 is presented. The genome is composed of one chromosome
      (2,932,225 bp) and four plasmids (pLAtc1, pLAtc2, pLAtc3, pLAtcm) and it
      is rich in repetitive sequences (accounting for 11% of the total genome),
      which are often associated with transposable genetic elements. In
      particular, twelve copies of ISAtfe and thirty-seven copies of ISAtc1 have
      been identified, suggesting that they are active transposons in the
      genome. A. caldus SM-1 encodes all enzymes for the central metabolism and
      the assimilation of carbon compounds, among which 29 proteins/enzymes were
      identifiable with proteomic tools. The SM-1 fixes CO(2)via the classical
      Calvin-Bassham-Benson (CBB) cycle, and can operate complete
      Embden-Meyerhof pathway (EMP), pentose phosphate pathway (PPP), and
      gluconeogenesis. It has an incomplete tricarboxylic acid cycle (TCA). Four
      putative transporters involved in carbohydrate uptake were identified.
      Taken together, the results suggested that SM-1 was able to assimilate
      carbohydrates and this was subsequently confirmed experimentally because
      addition of 1% glucose or sucrose in basic salt medium significantly
      increased the growth of SM-1. It was concluded that the complete genome of
      SM-1 provided fundamental data for further investigation of its physiology
      and genetics, in addition to the carbon metabolism revealed in this study.
AU  - You XY
AU  - Guo X
AU  - Zheng HJ
AU  - Zhang MJ
AU  - Liu LJ
AU  - Zhu YQ
AU  - Zhu B
AU  - Wang SY
AU  - Zhao GP
AU  - Poetsch A
AU  - Jiang CY
AU  - Liu SJ
PT  - Journal Article
TA  - J. Genetics Genomics
JT  - J. Genetics Genomics
SO  - J. Genetics Genomics 2011 38: 243-252.

PMID- 21607549
VI  - 15
DP  - 2011
TI  - Genomic analyses of Acidianus hospitalis W1 a host for studying crenarchaeal virus and plasmid life cycles.
PG  - 487-497
AB  - The Acidianus hospitalis W1 genome consists of a minimally sized chromosome of about 2.13 Mb
      and a conjugative plasmid pAH1 and it is a host for the model filamentous lipothrixvirus AFV1.
      The chromosome carries three putative replication origins in conserved genomic regions and two
      large regions where non-essential genes are clustered. Within these variable regions, a few
      orphan orfB and other elements of the IS200/607/605 family are concentrated with a novel class
      of MITE-like repeat elements.  There are also 26 highly diverse vapBC antitoxin-toxin gene
      pairs proposed to facilitate maintenance of local chromosomal regions and to minimise the
      impact of environmental stress. Complex and partially defective CRISPR/Cas/Cmr immune systems
      are present and interspersed with five vapBC gene pairs. Remnants of integrated viral genomes
      and plasmids are located at five intron-less tRNA genes and several non-coding RNA genes are
      predicted that are conserved in other Sulfolobus genomes. The putative metabolic pathways for
      sulphur metabolism show some significant differences from those proposed for other Acidianus
      and Sulfolobus species. The small and relatively stable genome of A. hospitalis W1 renders it
      a promising candidate for developing the first Acidianus genetic systems.
AU  - You XY
AU  - Liu C
AU  - Wang SY
AU  - Jiang CY
AU  - Shah SA
AU  - Prangishvili D
AU  - Liu SJ
AU  - Garrett RA
PT  - Journal Article
TA  - Extremophiles
JT  - Extremophiles
SO  - Extremophiles 2011 15: 487-497.

PMID- 26664656
VI  - 10
DP  - 2015
TI  - Complete genome sequence of the molybdenum-resistant bacterium Bacillus subtilis  strain LM 4-2.
PG  - 127
AB  - Bacillus subtilis LM 4-2, a Gram-positive bacterium was isolated from a molybdenum mine in
      Luoyang city. Due to its strong resistance to molybdate and
      potential utilization in bioremediation of molybdate-polluted area, we describe
      the features of this organism, as well as its complete genome sequence and
      annotation. The genome was composed of a circular 4,069,266 bp chromosome with
      average GC content of 43.83 %, which included 4149 predicted ORFs and 116 RNA
      genes. Additionally, 687 transporter-coding and 116 redox protein-coding genes
      were identified in the strain LM 4-2 genome.
AU  - You XY
AU  - Wang H
AU  - Ren GY
AU  - Li JJ
AU  - Duan X
AU  - Zheng HJ
AU  - Jiang ZQ
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 127.

PMID- 22701658
VI  - 7
DP  - 2012
TI  - Comparative Genomics of Helicobacter pylori Strains of China Associated with Different Clinical Outcome.
PG  - e38528
AB  - In this study, a whole-genome CombiMatrix Custom oligonucleotide tiling microarray with 90000
      probes covering six sequenced Helicobacter pylori
      (H. pylori) genomes was designed. This microarray was used to compare
      the genomic profiles of eight unsequenced strains isolated from
      patients with different gastroduodenal diseases in Heilongjiang
      province of China. Since significant genomic variation was found among
      these strains, an additional 76 H. pylori strains associated with
      different clinical outcomes were isolated from various provinces of
      China. These strains were tested by polymerase chain reaction to
      demonstrate this distinction. We identified several highly variable
      regions in strains associated with gastritis, gastric ulceration, and
      gastric cancer. These regions are associated with genes involved in the
      bacterial type I, type II, and type III R-M systems. They were also
      associated with the virB gene, which lies on the well-studied cag
      pathogenic island. While previous studies have reported on the diverse
      genetic characterization of this pathogenic island, in this study, we
      find that it is conserved in all strains tested by microarray.
      Moreover, a number of genes involved in the type IV secretion system,
      which is related to horizontal DNA transfer between H. pylori strains,
      were identified in the comparative analysis of the strain-specific
      genes. These findings may provide insight into new biomarkers for the
      prediction of gastric diseases.
AU  - You Y
AU  - He L
AU  - Zhang M
AU  - Fu J
AU  - Gu Y
AU  - Zhang B
AU  - Tao X
AU  - Zhang J
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2012 7: e38528.

PMID- 23105058
VI  - 194
DP  - 2012
TI  - Genome Sequences of Three Helicobacter pylori Strains Isolated from Atrophic Gastritis and Gastric Ulcer Patients in China.
PG  - 6314-6315
AB  - Helicobacter pylori is a bacterial pathogen which can lead to several human gastric diseases.
      Here we describe the genome sequences of three strains isolated
      from atrophic gastritis and gastric ulcers patients in China. The data will
      permit genomic characterization of traits that may contribute to various gastric
      diseases.
AU  - You Y
AU  - Liu L
AU  - Zhang M
AU  - Han X
AU  - He L
AU  - Zhu Y
AU  - Ni P
AU  - Zhang J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6314-6315.

PMID- 24565107
VI  - 6
DP  - 2014
TI  - Genomic characterization of a Helicobacter pylori isolate from a patient with gastric cancer in China.
PG  - 5
AB  - Background: Helicobacter pylori is well known for its relationship with the occurrence of
      several severe gastric diseases. The mechanisms of pathogenesis triggered by H. pylori are
      less well known. In this study, we report the genome sequence and genomic characterizations of
      H. pylori strain HLJ039 that was isolated from a patient with gastric cancer in the Chinese
      province of Heilongjiang, where there is a high incidence of gastric cancer. To investigate
      potential genomic features that may be involved in pathogenesis of carcinoma, the genome was
      compared to three previously sequenced genomes in this area.Result: We obtained 42 contigs
      with a total length of 1,611,192 bp and predicted 1,687 coding sequences. Compared to strains
      isolated from gastritis and ulcers in this area, 10 different regions were identified as being
      unique for HLJ039; they mainly encoded type II restriction-modification enzyme, type II m6A
      methylase, DNA-cytosine methyltransferase, DNA methylase, and hypothetical proteins. A unique
      547-bp fragment sharing 93% identity with a hypothetical protein of Helicobacter cinaedi ATCC
      BAA-847 was not present in any other previous H. pylori strains. Phylogenetic analysis based
      on core genome single nucleotide polymorphisms shows that HLJ039 is defined as hspEAsia
      subgroup, which belongs to the hpEastAsia group.Conclusion: DNA methylations, variations of
      the genomic regions involved in restriction and modification systems, are the 'hot' regions
      that may be related to the mechanism of H. pylori-induced gastric cancer. The genome sequence
      will provide useful information for the deep mining of potential mechanisms related to East
      Asian gastric cancer.
AU  - You Y
AU  - Liu L
AU  - Zhang M
AU  - Zhu Y
AU  - He L
AU  - Li D
AU  - Zhang J
PT  - Journal Article
TA  - Gut Pathog.
JT  - Gut Pathog.
SO  - Gut Pathog. 2014 6: 5.

PMID- 23045496
VI  - 194
DP  - 2012
TI  - Draft Genome Sequences of Two Streptococcus pyogenes Strains Involved in Abnormal Sharp Raised Scarlet Fever in China, 2011.
PG  - 5983-5984
AB  - A scarlet fever outbreak caused by Streptococcus pyogenes occurred in China in 2011. To
      determine the genomic features of the outbreak strains, we deciphered
      genomes of two strains isolated from the regions with the highest incidence
      rates. The sequences will provide valuable information for comprehensive study of
      mechanisms related to this outbreak.
AU  - You Y
AU  - Yang X
AU  - Song Y
AU  - Yan X
AU  - Yuan Y
AU  - Li D
AU  - Yan Y
AU  - Wang H
AU  - Tao X
AU  - Li L
AU  - Jiang X
AU  - Zhou H
AU  - Xiao D
AU  - Jin L
AU  - Feng Z
AU  - Yang R
AU  - Luo F
AU  - Cui Y
AU  - Zhang J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5983-5984.

PMID- 22652768
VI  - 17
DP  - 2012
TI  - Mechanistic insight into Type I restriction endonucleases.
PG  - 2122-2139
AB  - Restriction and modification are two opposing activities that are used to protect bacteria
      from cellular invasion by DNA (e.g. bacteriophage infection).  Restriction activity involves
      cleavage of the DNA; while modification activity is the mechanism used to "mark" host DNA and
      involves DNA methylation.  The study of Type I restriction enzymes has often been seen as an
      esoteric exercise and this reflects some of their more unusual properties - non-stoichiometric
      (non-catalytic) cleavage of the DNA substrate, random cleavage of DNA, a massive ATPase
      activity, and the ability to both cleave DNA and methylate DNA.  Yet these enzymes have been
      found in many bacteria and are very efficient as a means of protecting bacteria against
      bacteriophage infection, indicating they are successful enzynmes.  In this review, we
      summarise recent work on the mechanisms of action, describe switching of function and review
      their mechanism of action.  We also discuss structural rearrangements and cellular
      localisation, which provide powerful mechanisms for controlling the enzyme activity.  Finally,
      we speculate as to their involvement in recombination and discuss their relationship to
      helicase enzymes.
AU  - Youell J
AU  - Firman K
PT  - Journal Article
TA  - Front. Biosci., Landmark Ed.
JT  - Front. Biosci., Landmark Ed.
SO  - Front. Biosci., Landmark Ed. 2012 17: 2122-2139.

PMID- 18535150
VI  - 72
DP  - 2008
TI  - EcoR124I: from plasmid-encoded restriction-modification system to nanodevice.
PG  - 365-377
AB  - Plasmid R124 was first described in 1972 as being a new member of in compatibility group
      IncFIV, yet early physical investigations of
      plasmid DNA showed that this type of classification was more complex
      than first imagined. Throughout the history of the study of this
      plasmid, there have been many unexpected observations. Therefore, in
      this review, we describe the history of our understanding of this
      plasmid and the type I restriction-modification (R-M) system that it
      encodes, which will allow an opportunity to correct errors, or
      misunderstandings, that have arisen in the literature. We also describe
      the characterization of the R-M enzyme EcoR124I and describe the
      unusual properties of both type I R-M enzymes and EcoR124I in
      particular. As we approached the 21st century, we began to see the
      potential of the EcoR124I R-M enzyme as a useful molecular motor, and
      this leads to a description of recent work that has shown that the R-M
      enzyme can be used as a nanoactuator. Therefore, this is a history that
      takes us from a plasmid isolated from (presumably) an infected source
      to the potential use of the plasmid-encoded R-M enzyme in
      bionanotechnology.
AU  - Youell J
AU  - Firman K
PT  - Journal Article
TA  - Microbiol. Mol. Biol. Rev.
JT  - Microbiol. Mol. Biol. Rev.
SO  - Microbiol. Mol. Biol. Rev. 2008 72: 365-377.

PMID- 23788539
VI  - 1
DP  - 2013
TI  - Genome Sequence of Methicillin-Resistant Staphylococcus pseudintermedius Sequence Type 233 (ST233) Strain K7, of Human Origin.
PG  - e00310-13
AB  - We report the genome sequence of the methicillin-resistant Staphylococcus pseudintermedius
      strain K7, isolated from the nares of a veterinarian in Seoul,
      South Korea.
AU  - Youn JH
AU  - Moodley A
AU  - Park YH
AU  - Sugimoto C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00310-13.

PMID- 19533711
VI  - 10
DP  - 2009
TI  - Photochemical Regulation of Restriction Endonuclease Activity.
PG  - 1612-1616
AB  - To elucidate biological processes, precise control over these
      processes is required. Light represents an ideal external control
      element because it can be easily regulated in a spatial and
      temporal fashion, and conveys spatiotemporal control of biological
      activity to the system under study.[1] The photochemical
      regulation of oligonucleotide function through the installation
      of light-removable protecting groups (caging groups) on
      either the phosphate or the nucleotide base has recently received
      considerable attention.[2-4] Important applications of this
      technology involve the transient disruption of DNA hybridization
      to photochemically control DNAzyme activity, the polymerase
      chain reaction, antisense activity, as well as inhibition
      of transcription.[4, 5] In this context, we demonstrated that a
      single caging group installed on one base of a typical oligonucleotide
      20-mer still enables DNA-DNA and DNA-RNA hybridization,
      but could disrupt processing of the oligomer by polymerases
      and inactivate the catalytic ability of DNAzymes.[2] As
      a result, we became interested in exploring other biologically
      relevant processes with photocaged DNA that do not involve
      perturbation of hybridization. Due to the prevalence of DNA-
      protein interactions both in vivo and in vitro,[6] we hypothesized
      that it might be feasible to photochemically control such
      an interaction for restriction endonucleases by the incorporation
      of our 6-nitropiperonyloxymethyl (NPOM)-caged thymidine
      nucleotide (Scheme 1) into DNA. Very few studies have
      been conducted on the effects of unnatural nucleotides on the
      fidelity and functionality of restriction enzymes. Those that
      have, primarily involve the effects of endogenous base mutations
      (for example, methylation events) that do not drastically
      affect hydrogen bonding and base pair recognition. In many of
      these cases, the catalytic capabilities of the restriction endo-
      ACHTUNGTRENUNGnucleases are dramatically decreased, if not abrogated.
AU  - Young DD
AU  - Govan JM
AU  - Lively MO
AU  - Deiters A
PT  - Journal Article
TA  - Chembiochem
JT  - Chembiochem
SO  - Chembiochem 2009 10: 1612-1616.

PMID- 29301887
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of the Predatory Marine Bacterium Halobacteriovorax sp. Strain JY17.
PG  - e01416-17
AB  - A draft genome sequence of Halobacteriovorax sp. strain JY17 was assembled from a metagenomic
      data set. The 3.47-Mbp genome of this unusual predatory bacterium
      contains 3,263 protein-coding sequences, 33 tRNAs, and 2 copies each of the 16S,
      23S, and 5S rRNA genes. This is only the third sequenced representative of this
      genus.
AU  - Young JM
AU  - Skvortsov T
AU  - Arkhipova K
AU  - Allen CCR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01416-17.

PMID- 16640791
VI  - 7
DP  - 2006
TI  - The genome of Rhizobium leguminosarum has recognizable core and accessory components.
PG  - R34
AB  - ABSTRACT : BACKGROUND : Rhizobium leguminosarum is an alpha-proteobacterial N2-fixing symbiont
      of legumes that has been the
      subject of more than a thousand publications. Genes for the symbiotic
      interaction with plants are well studied, but the adaptations that allow
      survival and growth in the soil environment are poorly understood. We have
      sequenced the genome of R. leguminosarum biovar viciae strain 3841.
      RESULTS : The 7.75 Mb genome comprises a circular chromosome and six
      circular plasmids, with 61% G+C overall. All three rRNA operons and 52
      tRNA genes are on the chromosome; essential protein-encoding genes are
      largely chromosomal, but most functional classes occur on plasmids as
      well. Of the 7,263 protein-encoding genes, 2,056 had orthologs in each of
      three related genomes (Agrobacterium tumefaciens, Sinorhizobium meliloti,
      and Mesorhizobium loti), and these genes were over-represented in the
      chromosome and had above average G+C. Most supported the rRNA-based
      phylogeny, confirming A. tumefaciens to be the closest among these
      relatives, but 347 genes were incompatible with this phylogeny; these were
      scattered throughout the genome but were over-represented on the plasmids.
      An unexpectedly large number of genes were shared by all three rhizobia
      but were missing from A. tumefaciens. CONCLUSION : Overall, the genome can
      be considered to have two main components: a 'core', which is higher in
      G+C, is mostly chromosomal, is shared with related organisms, and has a
      consistent phylogeny; and an 'accessory' component, which is sporadic in
      distribution, lower in G+C, and located on the plasmids and chromosomal
      islands. The accessory genome has a different nucleotide composition from
      the core despite a long history of coexistence.
AU  - Young JP et al
PT  - Journal Article
TA  - Genome Biol.
JT  - Genome Biol.
SO  - Genome Biol. 2006 7: R34.

PMID- 19948807
VI  - 192
DP  - 2010
TI  - Genome Sequence of the Fleming Strain of Micrococcus luteus, a Simple Free-Living Actinobacterium.
PG  - 841-860
AB  - Micrococcus luteus (NCTC2665, 'Fleming strain') has one of the smallest genomes of
      free-living actinobacteria sequenced to date, comprising a
      single circular chromosome of 2,501,097 bp (G+C content, 73%) predicted to
      encode 2,403 proteins. The genome shows extensive synteny with that of the
      closely related organism, Kocuria rhizophila, from which it was
      taxonomically separated relatively recently. Despite its small size, the
      genome harbors 73 insertion sequence (IS) elements, almost all of which
      are closely related to elements found in other actinobacteria. An IS
      element is inserted into the rrs gene of one of only two rrn operons found
      in M. luteus. The genome encodes only four sigma factors and 14 response
      regulators, a finding indicative of adaptation to a rather strict
      ecological niche (mammalian skin). The high sensitivity of M. luteus to
      beta-lactam antibiotics may result from the presence of a reduced set of
      penicillin-binding proteins and the absence of a wblC gene, which plays an
      important role in the antibiotic resistance in other actinobacteria.
      Consistent with the restricted range of compounds it can use as a sole
      source of carbon for energy and growth, M. luteus has a minimal complement
      of genes concerned with carbohydrate transport and metabolism and its
      inability to utilize glucose as a sole carbon source may be due to the
      apparent absence of a gene encoding glucokinase. Uniquely among
      characterized bacteria, M. luteus appears to be able to metabolize
      glycogen only via trehalose and to make trehalose only via glycogen. It
      has very few genes associated with secondary metabolism. In contrast to
      most other actinobacteria, M. luteus encodes only one
      resuscitation-promoting factor (Rpf) required for emergence from dormancy,
      and its complement of other dormancy-related proteins is also much
      reduced. M. luteus is capable of long-chain alkene biosynthesis, which is
      of interest for advanced biofuel production; a three-gene cluster
      essential for this metabolism has been identified in the genome.
AU  - Young M et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 841-860.

PMID- 6267292
VI  - 145
DP  - 1981
TI  - Preliminary x-ray diffraction studies of EcoRI restriction endonuclease-DNA complex.
PG  - 607-610
AB  - A complex between EcoRI restriction endonuclease and cognate DNA fragment,
      5'-G-A-A-T-T-C    C-T-T-A-A-T-5' has been crystallized.  The space group is
      P4212 with a=b=183.2 angstroms, c=49.7 angstroms, a=b=k=90o.  The unit cell
      contains four enzyme monomers plus two duplex DNA fragments in an asymmetric
      unit.  High quality crystals of the enzyme alone have also been obtained.
AU  - Young T-S
AU  - Kim S-H
AU  - Modrich P
AU  - Beth A
AU  - Jay E
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1981 145: 607-610.

PMID- 18385156
VI  - 36
DP  - 2008
TI  - Differential stabilization of reaction intermediates: specificity checkpoints for M.EcoRI revealed by transient fluorescence and  fluorescence lifetime studies.
PG  - 2917-2925
AB  - M.EcoRI, a bacterial sequence-specific S-adenosyl-L-methionine-dependent DNA
      methyltransferase, relies on a complex conformational mechanism to
      achieve its remarkable specificity, including DNA bending, base flipping
      and intercalation into the DNA. Using transient fluorescence and
      fluorescence lifetime studies with cognate and noncognate DNA, we have
      characterized several reaction intermediates involving the WT enzyme.
      Similar studies with a bending-impaired, enhanced-specificity M.EcoRI
      mutant show minimal differences with the cognate DNA, but significant
      differences with noncognate DNA. These results provide a plausible
      explanation of the way in which destabilization of reaction intermediates
      can lead to changes in substrate specificity.
AU  - Youngblood B
AU  - Bonnist E
AU  - Dryden DT
AU  - Jones AC
AU  - Reich NO
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2008 36: 2917-2925.

PMID- 17176077
VI  - 45
DP  - 2006
TI  - Determinants of sequence-specific DNA methylation: target recognition and catalysis are coupled in M.HhaI.
PG  - 15563-15572
AB  - Sequence specificity studies of the wild-type bacterial DNA cytosine C5 methyltransferase HhaI
      were carried out with cognate (5'GCGC3') and
      noncognate DNA substrates containing single base pair changes at the first
      and the fourth position (underlined). Specificity for noncognate site
      methylation at the level of kcat/KDDNA is decreased 9000-80000-fold
      relative to the cognate site, manifested through changes in methylation,
      or a prior step, and changes in KDDNA. Analysis of a new high-resolution
      enzyme-DNA cocrystal structure provides a partial mechanistic
      understanding of this discrimination. To probe the significance of
      conformational transitions occurring prior to catalysis in determining
      specificity, we analyzed the double mutant (H127A/T132A). These amino acid
      substitutions disrupt the interface between the flexible loop (residues
      80-99), which interacts with the DNA minor groove, and the active site.
      The mutant's methylation of the cognate site is essentially unchanged, yet
      its methylation of noncognate sites is decreased up to 460-fold relative
      to the wild-type enzyme. We suggest that a significant contribution to
      M.HhaI's specificity involves the stabilization of reaction intermediates
      prior to methyl transfer, mediated by DNA minor groove-protein flexible
      loop interactions.
AU  - Youngblood B
AU  - Buller F
AU  - Reich NO
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2006 45: 15563-15572.

PMID- 
VI  - 20
DP  - 2006
TI  - Conformational transitions as molecular determinants of specificity for the DNA methyltransferase EcoRI.
PG  - A40
AB  - DNA modifying enzymes have evolved a delicate balance between sequence specificity and
      efficient catalysis. Utilization of indirect readout of
      a DNA sequence, such as DNA bending by an enzyme, provides further
      discrimination beyond the initial binding event between the enzyme and
      DNA. Changes in the DNA bending and base flipping transitions in a
      previously characterized specificity-enhanced mutant M.EcoRI DNA
      adenine methyltransferase suggest a close relationship between
      precatalytic conformational transitions and specificity. We present
      fluorescence resonance energy transfer (FRET) and 2-AminoPurine (2AP)
      fluorescence studies with the cognate sequence (GAATTC) for WT M.EcoRI,
      and reveal a temporal relationship between DNA bending, intercalation
      of the DNA substrate by the enzyme, and base-flipping. The direct
      measurement of kinetic rate constants for DNA bending, intercalation,
      and base-flipping with cognate and non-cognate substrates (GAATTT,
      GGATTC) by WT M.EcoRI, provide a molecular understanding of how these
      conformational transitions impact on specificity. The 3500 and
      23,000-fold decreases in sequence specificity of WT M.EcoRI for
      noncognates GAATTT and GGATTC are accounted for largely by a similar to
      2500 fold increase in the reverse rate constants for intercalation and
      base flipping. The predominant contribution to specificity is a
      partitioning of enzyme intermediates away from the Michaelis complex
      prior to catalysis. Our results provide a basis for understanding
      sequence-specific DNA modification.
AU  - Youngblood B
AU  - Reich N
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 2006 20: A40.

PMID- 16845123
VI  - 281
DP  - 2006
TI  - Conformational transitions as determinants of specificity for the DNA methyltransferase EcoRI.
PG  - 26821-26831
AB  - Changes in DNA bending and base flipping in a previously characterized specificity-enhanced M.
      EcoRI DNA adenine methyltransferase mutant
      suggest a close relationship between precatalytic conformational
      transitions and specificity (Allan, B. W., Garcia, R., Maegley, K.,
      Mort, J., Wong, D., Lindstrom, W., Beechem, J. M., and Reich, N. O.
      (1999) J. Biol. Chem. 274, 19269-19275). The direct measurement of the
      kinetic rate constants for DNA bending, intercalation, and base
      flipping with cognate and noncognate substrates (GAATTT, GGATTC) of
      wild type M. EcoRI using fluorescence resonance energy transfer and
      2-aminopurine fluorescence studies reveals that DNA bending precedes
      both intercalation and base flipping, and base flipping precedes
      intercalation. Destabilization of these intermediates provides a
      molecular basis for understanding how conformational transitions
      contribute to specificity. The 3500- and 23,000-fold decreases in
      sequence specificity for noncognate sites GAATTT and GGATTC are
      accounted for largely by an similar to 2500-fold increase in the
      reverse rate constants for intercalation and base flipping,
      respectively. Thus, a predominant contribution to specificity is a
      partitioning of enzyme intermediates away from the Michaelis complex
      prior to catalysis. Our results provide a basis for understanding
      enzyme specificity and, in particular, sequence-specific DNA
      modification. Because many DNA methyltransferases and DNA repair
      enzymes induce similar DNA distortions, these results are likely to be
      broadly relevant.
AU  - Youngblood B
AU  - Reich NO
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2006 281: 26821-26831.

PMID- 17616174
VI  - 46
DP  - 2007
TI  - S-adenosyl-L-methionine-dependent methyl transfer: observable precatalytic intermediates during DNA cytosine methylation.
PG  - 8766-8775
AB  - S-adenosyl-L-methionine- (AdoMet-) dependent methyltransferases are widespread, play critical
      roles in diverse biological pathways, and are
      antibiotic and cancer drug targets. Presently missing from our
      understanding of any AdoMet-dependent methyl-transfer reaction is a
      high-resolution structure of a precatalytic enzyme/AdoMet/DNA complex. The
      catalytic mechanism of DNA cytosine methylation was studied by
      structurally and functionally characterizing several active site mutants
      of the bacterial enzyme M.HhaI. The 2.64 A resolution protein/DNA/AdoMet
      structure of the inactive C81A M.HhaI mutant suggests that active site
      water, an approximately 13 degree tilt of the target base toward the
      active site nucleophile, and the presence or absence of the cofactor
      methylsulfonium are coupled via a hydrogen-bonding network involving
      Tyr167. The active site in the mutant complex is assembled to optimally
      align the pyrimidine for nucleophilic attack and subsequent methyl
      transfer, consistent with previous molecular dynamics ab initio and
      quantum mechanics/molecular mechanics calculations. The mutant/DNA/AdoHcy
      structure (2.88 A resolution) provides a direct comparison to the
      postcatalytic complex. A third C81A ternary structure (2.22 A resolution)
      reveals hydrolysis of AdoMet to adenosine in the active site, further
      validating the coupling between the methionine portion of AdoMet and
      ultimately validating the structural observation of a
      prechemistry/postchemistry water network. Disruption of this
      hydrogen-bonding network by a Tyr167 to Phe167 mutation does not alter the
      kinetics of nucleophilic attack or methyl transfer. However, the Y167F
      mutant shows detectable changes in kcat, caused by the perturbed kinetics
      of AdoHcy release. These results provide a basis for including an
      extensive hydrogen-bonding network in controlling the rate-limiting
      product release steps during cytosine methylation.
AU  - Youngblood B
AU  - Shieh FK
AU  - Buller F
AU  - Bullock T
AU  - Reich NO
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2007 46: 8766-8775.

PMID- 16919299
VI  - 362
DP  - 2006
TI  - Engineered Extrahelical Base Destabilization Enhances Sequence Discrimination of DNA Methyltransferase M.HhaI.
PG  - 334-346
AB  - Improved sequence specificity of the DNA cytosine methyltransferase HhaI was achieved by
      disrupting interactions at a hydrophobic interface between
      the active site of the enzyme and a highly conserved flexible loop.
      Transient fluorescence experiments show that mutations disrupting this
      interface destabilize the positioning of the extrahelical, "flipped"
      cytosine base within the active site. The ternary crystal structure of the
      F124A M.HhaI bound to cognate DNA and the cofactor analogue
      S-adenosyl-l-homocysteine shows an increase in cavity volume between the
      flexible loop and the core of the enzyme. This cavity disrupts the
      interface between the loop and the active site, thereby destabilizing the
      extrahelical target base. The favored partitioning of the base-flipped
      enzyme-DNA complex back to the base-stacked intermediate results in the
      mutant enzyme discriminating better than the wild-type enzyme against
      non-cognate sites. Building upon the concepts of kinetic proofreading and
      our understanding of M.HhaI, we describe how a 16-fold specificity
      enhancement achieved with a double mutation at the loop/active site
      interface is acquired through destabilization of intermediates prior to
      methyltransfer rather than disruption of direct interactions between the
      enzyme and the substrate for M.HhaI.
AU  - Youngblood B
AU  - Shieh FK
AU  - De Los Rios S
AU  - Perona JJ
AU  - Reich NO
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2006 362: 334-346.

PMID- 
VI  - 
DP  - 2007
TI  - Analysis of conformational transitions that facilitate DNA methyltransferase specificity and catalysis.
PG  - 1-190
AB  - DNA modifying enzymes have evolved a delicate balance between sequence specificity and
      efficient catalysis. Utilization of indirect readout of a DNA sequence, such as DNA bending
      and/or base flipping by an enzyme, can provide further discrimination between cognate and
      noncognate substrates by the enzyme. Using fluorescence resonance energy transfer (FRET) and
      2-Aminopurine (2AP) fluorescence studies with the cognate sequence (GAATTC) for WT M.EcoRI,
      the temporal relationship between DNA bending, intercalation of the DNA substrate by the
      enzyme, and base-flipping is elucidated. Destabilization of these intermediates provides a
      molecular basis for understanding how conformational transitions contribute to specificity.
      The 3500 and 23,000-fold decreases in sequence specificity for noncognate sites GAATTT and
      GGATTC are accounted for largely by a ~2500 fold increase in the reverse rate constants for
      intercalation and base flipping, respectively. The predominant contribution to specificity is
      a partitioning of enzyme intermediates away from the Michaelis complex prior to catalysis.
      Building upon the concepts that were developed with the M.EcoRI studies, an improvement in
      sequence specificity of the DNA cytosine methyltransferase HhaI is achieved by disrupting
      interactions at a hydrophobic interface between the active site of the enzyme and a highly
      conserved flexible loop. Transient fluorescence experiments with 2AP show that mutations
      disrupting this interface interfere with catalysis by destabilizing the extrahelical "flipped"
      cytosine base in the active site. This destabilization, caused by a double mutant, results in
      a ~500-fold specificity enhancement compared to the WT enzyme. To better understand the
      contribution of specific active site atoms to the catalytic enhancement of M.HhaI and the
      rearrangement of these atoms to facilitate the chemistry step, three crystal structures were
      solved using the true cofactor S-adenosyl-L-methionine (pre-chemistry), and the cofactor
      product S-adenosyl-L-homocysteine (post-chemistry). Much work remains in resolving how
      discrimination occurs for eukaryotic DNA methyltransferases in comparison to prokaryotic DNA
      methyltransferases mentioned above. To facilitate our advancement in understanding eukaryotic
      DNA methyltransferases, a model system to explore substrate discrimination in cells was
      developed. Using HIV-1, the mechanism for over-expression and targeting of the mammalian DNA
      methyltransferase 1 (DNMT1) to specific sites in the genome has been probed.
AU  - Youngblood BA
PT  - Journal Article
TA  - Ph.D. Thesis, Univ. of California, Santa Barbara
JT  - Ph.D. Thesis, Univ. of California, Santa Barbara
SO  - Ph.D. Thesis, Univ. of California, Santa Barbara 2007 : 1-190.

PMID- 
VI  - 19
DP  - 2005
TI  - Engineering a more specific DNA methyltransferase by inducing loop instability.
PG  - A846
AB  - The disruption of aromatic-aromatic interactions between Phe84 within the flexible loop
      (residues 80-99) and Phe124, which stabilizes important active sites residues in the bacterial
      DNA cytosine C5 methyltransferase, M.HhaI, result in mutant enzymes that are significantly
      increased in specificity.  The Phe124Ala M.HhaI-DNA cocrystal structure shows the flexibility
      of this loop to be increased.  Loop destabilization results in a decreased ability to maintain
      the extrahelical cytosine poised for catalysis; thus, this intermediate partitions toward
      release rather than catalysis.  The net result is that the mutant is increased in specificity,
      since more rapid release of non-cognate DNA leads to lower rates of methylation at such sites.
      Double mutant cycles involving Phe84Ala, Phe124Ala, His127Ala, and Thr132Ala, show that these
      effects involve structural accommodations over 2 angstroms.  Our results have implications for
      the rational design of enzyme specificity, and for the induced fit mechanism occurring in the
      base-flipping DNA modifying enzymes involved in diverse epigenetic transformations.
AU  - Youngblood BA
AU  - Shieh F-K
AU  - Snider S
AU  - Perona J
AU  - Reich N
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 2005 19: A846.

PMID- 27834700
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of an Extensively Drug-Resistant Shewanella xiamenensis  Strain Isolated from Algerian Hospital Effluents.
PG  - e01236-16
AB  - In this study, we present the first complete genome of an extensively drug-resistant strain of
      Shewanella xiamenensis, collected from hospital
      effluents in Algeria. This genome includes the chromosome and a large new plasmid
      harboring several drug-resistance genes.
AU  - Yousfi K
AU  - Touati A
AU  - Bekal S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01236-16.

PMID- 6285373
VI  - 79
DP  - 1982
TI  - Methylation of the viral genome in an in vitro model of herpes simplex virus latency.
PG  - 2207-2210
AB  - An in vitro model of latency of herpes simplex virus type 1 (HSV-1) in a
      lymphoid cell line has been developed recently.  CEM cells persistently
      infected with HSV-1 transiently ceased to produce virus for 24 days.  This
      nonproductive state could either be reversed with phytohemagglutinin or
      maintained with concanavalin A.  This system was used to study the relationship
      between DNA methylation and HSV-1 latency.  DNA was probed for methylation by
      comparing the cleavage pataterns generated by two pairs of restriction
      endonucleases (SmaI vs. XmaI and HpaII vs. MspI); these enzymes show
      differential activity reflecting methylation of the recognition sequences.
      Viral DNA in the concanavalin A-treated cells (not producing virus) was found
      to be extensively methylated.  By contrast, no methylated copies were detected
      in viral DNA from producer cells.  About 800 days after the initial infection,
      the productive culture once again became nonproductive.  Viral sequences in the
      latter cells were also methylated.  Reconstitution experiments revealed 1-2
      copies of viral DNA in cells from the latent stages and 40-80 copies in cells
      from productive stages.  Most (if not all) of the viral genome is present in
      cells from various productive and latent stages.  No differences in sequence
      arrangement were detected (although a terminal fragment of intracellular HSV-1
      DNA appeared to be under represented in latent cells).  These results suggest a
      role for DNA methylation in the mechanism of HSV-1 latency in this system.
AU  - Youssoufian H
AU  - Hammer SM
AU  - Hirsch MS
AU  - Mulder C
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1982 79: 2207-2210.

PMID- 6271972
VI  - 150
DP  - 1981
TI  - Detection of methylated sequences in eukaryotic DNA with the restriction endonucleases SmaI and XmaI.
PG  - 133-136
AB  - The restriction endonuclease XmaI cleaves eukaryotic DNA whether or not its
      recognition sequence (C^-C-C-G-G-G) contains 5-methylcytosine in the CpG
      dinucleotide.  This is in contrast to its isoschizomer, endo R SmaI, which does
      not cleave DNA if the CpG of its recognition sequence (C-C-C^G-G-G) is
      methylated.  Thus, this isoschizomer pair will be useful in the study of
      eukaryotic DNA methylation.
AU  - Youssoufian H
AU  - Mulder C
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1981 150: 133-136.

PMID- Not included in PubMed...
VI  - 43
DP  - 1984
TI  - Bacteriophage typing of mosquito pathogenic strains of Bacillus sphaericus.
PG  - 124-125
AB  - Certain strains of Bacillus sphaericus have been shown to be pathogenic for
      mosquito larvae (S. Singer, Biotechnol. Bioeng. 2, 1335, 1980).  All of these
      strains have been isolated directly from dead larvae or from habitats of
      larvae.  In contrast, none of the 56 strains of B. sphaericus obtained from
      various culture collections exhibited pathogenicity for larvae of Culex
      quinquefasciatus (V. Krych, J., Johnson, and A. Yousten, Int. J. Syst.
      Bacteriol. 30, 476-484, 1980).  In the same study, seven pathogens were shown
      to be members of a single DNA homology group which showed only a low degree of
      genetic relatedness to the type strain of the species.
AU  - Yousten AA
PT  - Journal Article
TA  - J. Invertebr. Pathol.
JT  - J. Invertebr. Pathol.
SO  - J. Invertebr. Pathol. 1984 43: 124-125.

PMID- 21952540
VI  - 193
DP  - 2011
TI  - Draft Genome Sequence of Sporolactobacillus inulinus Strain CASD, an Efficient D-Lactic Acid-Producing Bacterium with High-Concentration  Lactate Tolerance Capability.
PG  - 5864-5865
AB  - Sporolactobacillus inulinus CASD is an efficient d-lactic acid producer with high optical
      purity. Here we report for the first time the draft
      genome sequence of S. inulinus (2,930,096 bp). The large number of
      annotated two-component system genes makes it possible to explore the
      mechanism of extraordinary lactate tolerance of S. inulinus CASD.
AU  - Yu B
AU  - Su F
AU  - Wang L
AU  - Xu K
AU  - Zhao B
AU  - Xu P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5864-5865.

PMID- 22123765
VI  - 193
DP  - 2011
TI  - Genome Sequence of Lactobacillus rhamnosus Strain CASL, an Efficient L-Lactic Acid Producer from Cheap Substrate Cassava.
PG  - 7013-7014
AB  - Lactobacillus rhamnosus is a type of probiotic bacteria with industrial potential for l-lactic
      acid production. We announce the draft genome
      sequence of L. rhamnosus CASL (2,855,156 bp with a G+C content of 46.6%),
      which is an efficient producer of l-lactic acid from cheap, nonfood
      substrate cassava with a high production titer.
AU  - Yu B
AU  - Su F
AU  - Wang L
AU  - Zhao B
AU  - Qin J
AU  - Ma C
AU  - Xu P
AU  - Ma Y
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 7013-7014.

PMID- 26203339
VI  - 10
DP  - 2015
TI  - Draft genome of Myxosarcina sp. strain GI1, a baeocytous cyanobacterium associated with the marine sponge Terpios hoshinota.
PG  - 28
AB  - To date, genome sequences (complete or in draft form) from only six baeocytous cyanobacteria
      in four genera have been reported: Xenococcus, Chroococcidiopsis,
      Pleurocapsa, and Stanieria. To expand our knowledge on the diversity of
      baeocytous cyanobacteria, this study sequenced the genome of GI1, which is a
      Myxosarcina-like baeocytous cyanobacterium. GI1 is of interest not only because
      of its phylogenetic niche, but also because it is a cyanobiont isolated from the
      marine cyanobacteriosponge Terpios hoshinota, which has been shown to cause the
      death of corals. The ~7 Mb draft GI1 genome contains 6,891 protein-coding genes
      and 62 RNA genes. A comparison of genomes among the sequenced baeocytous
      cyanobacterial strains revealed the existence or absence of numerous discrete
      genes involved in nitrogen metabolism. It will be interesting to determine
      whether these genes are important for cyanobacterial adaptations and interactions
      between cyanobionts and their marine sponge hosts.
AU  - Yu CH
AU  - Lu CK
AU  - Su HM
AU  - Chiang TY
AU  - Hwang CC
AU  - Liu T
AU  - Chen YM
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 28.

PMID- 23105055
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Bacillus subtilis Strain QB928, a Strain Widely Used  in B. subtilis Genetic Studies.
PG  - 6308-6309
AB  - The complete genome sequence of Bacillus subtilis strain QB928 was constructed to facilitate
      studies in the evolution of the genetic code. With a widespread use of
      the strain in Bacillus subtilis genetics studies, its complete genome sequence
      would facilitate deeper understanding of Bacillus subtilis genetics.
AU  - Yu CS
AU  - Yim KY
AU  - Tsui SK
AU  - Chan TF
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6308-6309.

PMID- 27856593
VI  - 4
DP  - 2016
TI  - Genome Sequences of Two Multidrug-Resistant Proteus mirabilis Strains Harboring CTX-M-65 Isolated from Malaysia.
PG  - e01301-16
AB  - Proteus mirabilis is an opportunistic nosocomial pathogen that is commonly associated with
      urinary tract infections. Here, we present draft genome sequences
      of two multidrug-resistant P. mirabilis strains, isolated from urine samples in
      Malaysia, that harbored a CTX-M-type extended-spectrum beta-lactamase-encoding
      gene, as well as a repertoire of other antimicrobial-resistant determinants.
AU  - Yu CY
AU  - Ang GY
AU  - Ngeow YF
AU  - Tee KK
AU  - Yin WF
AU  - Chan KG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01301-16.

PMID- 26039674
VI  - 6
DP  - 2015
TI  - Comparative Genomic Analysis of Brucella abortus vaccine strain 104M Reveals a Set of Candidate Genes Associated With Its Virulence Attenuation.
PG  - 745-754
AB  - Abstracts The Brucella abortus strain 104M, a spontaneously attenuated strain, has been used
      as a vaccine strain in humans against brucellosis for six decades in China. Despite many
      studies, the molecular mechanisms that cause the attenuation are still unclear. Here, we
      determined the whole-genome sequence of 104M and conducted a comprehensive comparative
      analysis against the whole genome sequences of the virulent strain, A13334, and other
      reference strains. This analysis revealed a highly similar genome structure between 104M and
      A13334. The further comparative genomic analysis between 104M and A13334 revealed a set of
      genes missing in 104M. Some of these genes were identified to be directly or indirectly
      associated with virulence. Similarly, a set of mutations in the virulence-related genes was
      also identified, which may be related to virulence alteration. This study provides a set of
      candidate genes associated with virulence attenuation in B.abortus vaccine strain 104M.
AU  - Yu D
AU  - Hui Y
AU  - Zai X
AU  - Xu J
AU  - Liang L
AU  - Wang B
AU  - Yue J
AU  - Li S
PT  - Journal Article
TA  - Virulence
JT  - Virulence
SO  - Virulence 2015 6: 745-754.

PMID- 
VI  - 9
DP  - 2014
TI  - Characterization of the Staphylococcal Cassette Chromosome Composite Island of Staphylococcus haemolyticus SH32, a Methicillin-Resistant Clinical Isolate from China.
PG  - 6
AB  - Staphylococcal cassette chromosome (SCC) elements contribute considerably to virulence and
      resistance to antibiotic agents in staphylococci. SCC elements in coagulase-negative
      staphylococci (CoNS) are highly diverse and there is evidence suggesting that they serve as a
      reservoir for antibiotic resistance genes in methicillin-resistant Staphylococcus aureus
      (MRSA). However, only a small number of SCC elements have been characterized in CoNS and their
      exact roles in the emergence and evolution of MRSA remain to be demonstrated. Here, we
      determined the structure of an SCC composite island (CISH32) found in the clinical
      Staphylococcus haemolyticus isolate SH32 by whole-genome DNA sequencing. CISH32 was 48 kb in
      length and mainly composed of two imperfect SCC elements, namely (i) a Psi SCCmec(SH32) part
      containing a class C1 mec gene complex but lacking ccr genes and (ii) a SCCSH32 part with a
      ccrA5B3 gene complex but lacking mec genes. In addition, CISH32 contained a type III
      restriction-modification syst em and several resistance loci, for example genes conferring
      resistance to cadmium and arsenic. Psi SCCmec(SH32) is almost entirely identical to a pseudo
      SCCmec element found in S. haemolyticus WCH1 and shares pronounced sequence similarity to a
      Psi SCCmec element of S. haemolyticus JCSC1435. However, staphylococci other than S.
      haemolyticus, including S. aureus and S. epidermidis, contain homologs of SCCSH32 that are
      more similar to SCCSH32 than those elements found in S. haemolyticus, suggesting that CIS H32
      of S. haemolyticus SH32 was assembled in recent evolutionary events. Moreover, the composite
      structure of CISH32 indicates that the detection of class C1 mec and ccrA5B3 gene complexes in
      S. haemolyticus does not always indicate the existence of a UT9-type SCCmec element, which has
      remained questionable.
AU  - Yu D
AU  - Pi B
AU  - Chen Y
AU  - Wang Y
AU  - Ruan Z
AU  - Otto M
AU  - Yu Y
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2014 9: 6.

PMID- 22887663
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of the Probiotic Bacterium Bifidobacterium bifidum Strain BGN4.
PG  - 4757-4758
AB  - Bifidobacterium bifidum, a common endosymbiotic inhabitant of the human gut, is considered a
      prominent probiotic microorganism that may promote health. We
      completely decrypted the 2.2-Mb genome sequence of B. bifidum BGN4, a strain that
      had been isolated from the fecal sample of a healthy breast-fed infant, and
      annotated 1,835 coding sequences.
AU  - Yu DS
AU  - Jeong H
AU  - Lee DH
AU  - Kwon SK
AU  - Song JY
AU  - Kim BK
AU  - Park MS
AU  - Ji GE
AU  - Oh TK
AU  - Kim JF
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4757-4758.

PMID- 25059869
VI  - 2
DP  - 2014
TI  - Genome Sequence of a Newly Isolated Nicotine-Degrading Bacterium, Ochrobactrum sp. SJY1.
PG  - e00720-14
AB  - Ochrobactrum sp. SJY1 uses nicotine as the sources of carbon, nitrogen, and energy. The genome
      of SJY1 was sequenced in order to provide insights into its
      mechanism of nicotine degradation. Physiological characteristics and genome
      analysis indicate that strain SJY1 might have a different nicotine degradation
      pathway from the pyridine or pyrrolidine pathway.
AU  - Yu H
AU  - Li Y
AU  - Tang H
AU  - Xu P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00720-14.

PMID- 24029762
VI  - 1
DP  - 2013
TI  - Genome Sequence of the Bacterium Bifidobacterium longum Strain CMCC P0001, a Probiotic Strain Used for Treating Gastrointestinal Disease.
PG  - e00716-13
AB  - Bifidobacterium longum subsp. longum CMCC P0001, a standard probiotic strain in China, has
      been widely used in clinical medicine for more than 20 years. Here we
      report the genome features of B. longum strain CMCC P0001.
AU  - Yu H
AU  - Liu L
AU  - Chang Z
AU  - Wang S
AU  - Wen B
AU  - Yin P
AU  - Liu D
AU  - Chen B
AU  - Zhang J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00716-13.

PMID- 21914868
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of the Nicotine-Degrading Pseudomonas putida Strain S16.
PG  - 5541-5542
AB  - Pseudomonas putida S16 is an efficient degrader of nicotine. The complete genome of strain S16
      (5,984,790 bp in length) includes genes related to
      catabolism of aromatic and heterocyclic compounds. The genes of enzymes in
      the core genome and a genomic island encode the proteins responsible for
      nicotine catabolism.
AU  - Yu H
AU  - Tang H
AU  - Wang L
AU  - Yao Y
AU  - Wu G
AU  - Xu P
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5541-5542.

PMID- 26205853
VI  - 3
DP  - 2015
TI  - Genome Sequence of Klebsiella pneumoniae YZUSK-4, a Bacterium Proposed as a Starter Culture for Fermented Meat Products.
PG  - e00774-15
AB  - Klebsiella pneumoniae strain YZUSK-4, isolated from Chinese RuGao ham, is an efficient
      branched-chain aminotransferase-producing bacterium that can be used
      widely in fermented meat products to enhance flavor. The draft genome sequence of
      strain YZUSK-4 may provide useful genetic information on branched-chain amino
      acid aminotransferase production and branched-chain amino acid metabolism.
AU  - Yu H
AU  - Yin Y
AU  - Xu L
AU  - Yan M
AU  - Fang W
AU  - Ge Q
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00774-15.

PMID- 21515765
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of the Nitrogen-fixing and Rhizosphere-associated Bacterium Pseudomonas stutzeri Strain DSM4166.
PG  - 3422-3423
AB  - We present here the analysis of the whole genome sequence of Pseudomonas stutzeri strain
      DSM4166, a diazotrophic isolate from the rhizosphere of a
      Sorghum nutans cultivar. To our knowledge, this is the second one to be
      sequenced in P. stutzeri. The availability and analysis of the genome
      provides insight into the evolution of the nitrogen fixation property, and
      identification of rhizosphere competence traits required in interactions
      with host plants.
AU  - Yu H
AU  - Yuan M
AU  - Lu W
AU  - Yang J
AU  - Dai S
AU  - Li Q
AU  - Yang Z
AU  - Dong J
AU  - Sun L
AU  - Deng Z
AU  - Zhang W
AU  - Chen M
AU  - Ping S
AU  - Han Y
AU  - Zhan Y
AU  - Yan Y
AU  - Jin Q
AU  - Lin M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3422-3423.

PMID- 16085838
VI  - 71
DP  - 2005
TI  - Identification and characterization of putative virulence genes and gene clusters in Aeromonas hydrophila PPD134/91.
PG  - 4469-4477
AB  - Aeromonas hydrophila is a gram-negative opportunistic pathogen of animals
      and humans. The pathogenesis of A. hydrophila is multifactorial. Genomic
      subtraction and markers of genomic islands (GIs) were used to identify
      putative virulence genes in A. hydrophila PPD134/91. Two rounds of genomic
      subtraction led to the identification of 22 unique DNA fragments encoding
      19 putative virulence factors and seven new open reading frames, which are
      commonly present in the eight virulence strains examined. In addition,
      four GIs were found, including O-antigen, capsule, phage-associated, and
      type III secretion system (TTSS) gene clusters. These putative virulence
      genes and gene clusters were positioned on a physical map of A. hydrophila
      PPD134/91 to determine their genetic organization in this bacterium.
      Further in vivo study of insertion and deletion mutants showed that the
      TTSS may be one of the important virulence factors in A. hydrophila
      pathogenesis. Furthermore, deletions of multiple virulence factors such as
      S-layer, serine protease, and metalloprotease also increased the 50%
      lethal dose to the same level as the TTSS mutation (about 1 log) in a blue
      gourami infection model. This observation sheds light on the
      multifactorial and concerted nature of pathogenicity in A. hydrophila. The
      large number of putative virulence genes identified in this study will
      form the basis for further investigation of this emerging pathogen and
      help to develop effective vaccines, diagnostics, and novel therapeutics.
AU  - Yu HB
AU  - Zhang YL
AU  - Lau YL
AU  - Yao F
AU  - Vilches S
AU  - Merino S
AU  - Tomas JM
AU  - Howard SP
AU  - Leung KY
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2005 71: 4469-4477.

PMID- 28621109
VI  - 27
DP  - 2017
TI  - Comparative genomic analysis of Lactobacillus plantarum GB-LP1 isolated from traditional Korean fermented food.
PG  - 1419-1427
AB  - As probiotics play an important role in maintaining a healthy gut flora
      environment through antitoxin activity and inhibition of pathogen colonization,
      they have been of interest to the medical research community for quite some time
      now. Probiotic bacteria such as Lactobacillus plantarum, which can be found in
      fermented food, are of particular interest given their easy accessibility. We
      performed whole genome sequencing and genomic analysis on a GB-LP1 strain of L.
      plantarum isolated from Korean traditional fermented food; this strain is well
      known for its functions in immune response, suppression of pathogen growth and
      anti-toxin effects. The complete genome sequence of GB-LP1 is a single chromosome
      of 3,040,388 bp with 2,899 predicted open reading frames. Genomic analysis of
      GB-LP1 revealed two CRISPR regions and genes showing accelerated evolution which
      may have antibiotic and antitoxin functions. The aim of the present study was to
      predict strain specific genomic characteristics and assess the potential of this
      new strain as lactic acid bacteria at the genomic level using in-silico analysis.
      These results provide insight into the L. plantarum species as well as confirm
      the possibility of its utility as a candidate probiotic.
AU  - Yu J
AU  - Ahn S
AU  - Kim K
AU  - Caetano-Anolles K
AU  - Lee C
AU  - Kang J
AU  - Cho K
AU  - Yoon S
AU  - Kang DK
AU  - Kim H
PT  - Journal Article
TA  - J. Microbiol. Biotechnol.
JT  - J. Microbiol. Biotechnol.
SO  - J. Microbiol. Biotechnol. 2017 27: 1419-1427.

PMID- 29025936
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Super Biofilm-Elaborating Staphylococcus aureus Isolated in Japan.
PG  - e01043-17
AB  - Staphylococcus aureus JP080, previously named TF2758, is a clinical isolate from  an atheroma
      and a super biofilm-elaborating strain whose biofilm elaboration is
      dependent solely on polysaccharide poly-N-acetylglucosamine/polysaccharide
      intercellular adhesin (PNAG/PIA). Here, we report the complete genome sequence of
      strain JP080, which consists of one chromosome and one circular plasmid.
AU  - Yu L
AU  - Hisatsune J
AU  - Hirakawa H
AU  - Mizumachi E
AU  - Toyoda A
AU  - Yahara K
AU  - Sugai M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01043-17.

PMID- 25614558
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Marine Bacterium Streptomyces sp. Strain CNQ431, a Producer of the Cytokine Inhibitor Splenocin.
PG  - e01383-14
AB  - Currently, corticosteroids are the most potent anti-inflammatory drugs on the market. Here, we
      announce the draft genome sequence of the marine-derived
      Streptomyces sp. strain CNQ431, which produces cytokine inhibitors, termed
      splenocins, which display potent suppression of cytokine production at a
      comparable level to that of corticosteroids. The genome is approximately 498,750
      bp with 72.03% G+C content.
AU  - Yu M
AU  - Dai Z
AU  - Qu X
AU  - Gao X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01383-14.

PMID- 26184871
VI  - 43
DP  - 2015
TI  - Base-resolution detection of N4-methylcytosine in genomic DNA using 4mC-Tet-assisted-bisulfite- sequencing.
PG  - e148
AB  - Restriction-modification (R-M) systems pose a major barrier to DNA transformation and genetic
      engineering of bacterial species. Systematic identification of DNA
      methylation in R-M systems, including N6-methyladenine (6mA), 5-methylcytosine
      (5mC) and N4-methylcytosine (4mC), will enable strategies to make these species
      genetically tractable. Although single-molecule, real time (SMRT) sequencing
      technology is capable of detecting 4mC directly for any bacterial species
      regardless of whether an assembled genome exists or not, it is not as scalable to
      profiling hundreds to thousands of samples compared with the commonly used
      next-generation sequencing technologies. Here, we present 4mC-Tet-assisted
      bisulfite-sequencing (4mC-TAB-seq), a next-generation sequencing method that
      rapidly and cost efficiently reveals the genome-wide locations of 4mC for
      bacterial species with an available assembled reference genome. In 4mC-TAB-seq,
      both cytosines and 5mCs are read out as thymines, whereas only 4mCs are read out
      as cytosines, revealing their specific positions throughout the genome. We
      applied 4mC-TAB-seq to study the methylation of a member of the hyperthermophilc
      genus, Caldicellulosiruptor, in which 4mC-related restriction is a major barrier
      to DNA transformation from other species. In combination with MethylC-seq, both
      4mC- and 5mC-containing motifs are identified which can assist in rapid and
      efficient genetic engineering of these bacteria in the future.
AU  - Yu M
AU  - Ji L
AU  - Neumann DA
AU  - Chung DH
AU  - Groom J
AU  - Westpheling J
AU  - He C
AU  - Schmitz RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2015 43: e148.

PMID- 24336361
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Opportunistic Marine Pathogen Vibrio harveyi Strain  E385.
PG  - e00677-13
AB  - Vibrio harveyi strain E385 was isolated from a diseased cage-cultured grouper in  Daya Bay,
      China. Phylogenetic analysis based on the 16S rRNA gene sequence showed
      similarity with V. harveyi strain BAA-1116. We sequenced the pathogenic strain V.
      harveyi E385 and compared the genome with that of the nonpathogenic strain V.
      harveyi BAA-1116.
AU  - Yu M
AU  - Ren C
AU  - Qiu J
AU  - Luo P
AU  - Zhu R
AU  - Zhao Z
AU  - Hu C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00677-13.

PMID- 22740664
VI  - 194
DP  - 2012
TI  - Genome Sequence of Pseudoalteromonas flavipulchra JG1, a Marine Antagonistic Bacterium with Abundant Antimicrobial Metabolites.
PG  - 3735
AB  - The marine bacterium Pseudoalteromonas flavipulchra JG1 can synthesize various antibacterial
      metabolites, including protein and small molecules. The draft
      genome of JG1 is about 5.36 Mb and harbors approximate 4,913 genes, which will
      provide further insight into the synthesis of antimicrobial agents and
      antagonistic mechanisms of P. flavipulchra against pathogens.
AU  - Yu M
AU  - Tang K
AU  - Shi X
AU  - Zhang XH
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3735.

PMID- 24969302
VI  - 64
DP  - 2014
TI  - Bradyrhizobium ottawaense sp. nov., a symbiotic nitrogen fixing bacterium from root nodules of soybeans in Canada.
PG  - 3202-3207
AB  - Sixteen strains of symbiotic bacteria from root nodules of Glycine max grown in
      Ottawa, Canada, were previously characterized and placed in a novel group within
      the genus Bradyrhizobium. To verify their taxonomic status, these strains were
      further characterized using a polyphasic approach. All strains possessed
      identical 16S rRNA gene sequences that were 99.79 % similar to the closest
      relative, Bradyrhizobium liaoningense LMG 18230(T). Phylogenetic analysis of
      concatenated atpD, glnII, recA, gyrB, rpoB and dnaK genes divided the 16 strains
      into three multilocus sequence types that were placed in a highly supported
      lineage distinct from named species of the genus Bradyrhizobium consistent with
      results of DNA-DNA hybridization. Based on analysis of symbiosis gene sequences
      (nodC and nifH), all novel strains were placed in a phylogenetic group with five
      species of the genus Bradyrhizobium that nodulate soybeans. The combination of
      phenotypic characteristics from several tests including carbon and nitrogen
      source utilization and antibiotic resistance could be used to differentiate
      representative strains from recognized species of the genus Bradyrhizobium. Novel
      strain OO99(T) elicits effective nodules on Glycine max, Glycine soja and
      Macroptilium atropurpureum, partially effective nodules on Desmodium canadense
      and Vigna unguiculata, and ineffective nodules on Amphicarpaea bracteata and
      Phaseolus vulgaris. Based on the data presented, we conclude that our strains
      represent a novel species for which the name Bradyrhizobium ottawaense sp. nov.
      is proposed, with OO99(T) ( = LMG 26739(T) = HAMBI 3284(T)) as the type strain.
      The DNA G+C content is 62.6 mol%.
AU  - Yu X
AU  - Cloutier S
AU  - Tambong JT
AU  - Bromfield ES
PT  - Journal Article
TA  - Int. J. Syst. Evol. Microbiol.
JT  - Int. J. Syst. Evol. Microbiol.
SO  - Int. J. Syst. Evol. Microbiol. 2014 64: 3202-3207.

PMID- 26923129
VI  - 62
DP  - 2016
TI  - Indole affects the formation of multicellular aggregate structures in Pantoea agglomerans YS19.
PG  - 31-37
AB  - Pantoea agglomerans YS19 is an endophytic diazotrophic bacterium isolated from
      rice. As well as having the ability to form a biofilm, as do most bacteria, it is
      characterized by the formation of a unique multicellular aggregate structure
      called symplasmata. Indole is traditionally known as a metabolite of the amino
      acid tryptophan, which, however, has recently been shown to participate in
      various regulations of bacterial physiological processes, including stress
      resistance, quorum sensing and biofilm formation. Here, an indole signal was
      found to promote symplasmata formation, yet inhibit biofilm formation, indicating
      different regulatory pathways of indole in the construction of the two
      structures. However, symplasmata showed almost an equivalent stress-resistant
      capability, as compared with biofilms, for YS19 to confront acids, heavy metals
      (Cu(2+)), and UV treatments. Moreover, indole was tested to show a promoting
      effect on exopolysaccharides (EPS) production and an inhibition effect on the
      expression of an outer membrane protein OmpW. These results provide evidence for
      understanding the regulatory mechanisms of indole on such multicellular
      aggregates.
AU  - Yu X
AU  - Jiang J
AU  - Liang C
AU  - Zhang X
AU  - Wang J
AU  - Shen D
AU  - Feng Y
PT  - Journal Article
TA  - J. Gen. Appl. Microbiol.
JT  - J. Gen. Appl. Microbiol.
SO  - J. Gen. Appl. Microbiol. 2016 62: 31-37.

PMID- 29437106
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of a Trimethylamine-Producing Staphylococcus Isolate from Blood of a Coronary Atherosclerotic Heart Disease Patient.
PG  - e01563-17
AB  - Trimethylamine (TMA), which is produced by various bacteria, is associated with heart disease,
      but little information about the production of TMA in blood is
      available. We present here the genome sequence of a multidrug-resistant strain,
      Staphylococcus epidermidis bTMA-013, with a TMA synthesis pathway, which was
      isolated from the blood of a coronary atherosclerotic heart disease patient.
AU  - Yu X
AU  - Kang YQ
AU  - Ji F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01563-17.

PMID- 17488332
VI  - 272
DP  - 2007
TI  - A novel restriction-modification system from Xanthomonas campestris pv. vesicatoria encodes a m4C-methyltransferase and a nonfunctional  restriction endonuclease.
PG  - 83-90
AB  - A novel restriction-modification (R-M) system, designated as xveIIRM, from chromosomal DNA of
      the Xanthomonas campestris pv. vesicatoria.
      strain 7-1 (Xcv7-1) was cloned and characterized. The xveIIRM genes
      involved in this R-M system are aligned in a tail-to-tail orientation
      and overlapped by 12 base pairs. XveII methyltransferase gene could
      encode a 299-amino acid protein (M.XveII) with an estimated mass of
      33.7 kDa and was classified to be a member of P-class of m4C-MTase.
      M.XveII methylates the second cytosine of the 5'-CCCGGG-3' recognition
      sequence. The predicted amino acid sequence of the intact Xvell
      endonuclease shared 41.9% identity with SmaI. However, a premature TAA
      translation termination codon was found in the open reading frame of
      xveIIR and expected to encode an 18.3 kDa truncated protein. The
      sequence data are consistent with observation of this study that no
      SmaI-like restriction activity could be detected in the cell extract of
      Xcv7-1.
AU  - Yu YJ
AU  - Yang MT
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2007 272: 83-90.

PMID- 27891116
VI  - 7
DP  - 2016
TI  - Complete genome sequence of Clostridium estertheticum DSM 8809, a microbe identified in spoiled vacuum packed beef.
PG  - 1764
AB  - Blown pack spoilage (BPS) is a major issue for the beef industry. Etiological agents of BPS
      involve members of a group of Clostridium species, including Clostridium estertheticum which
      has the ability to produce gas, mostly carbon dioxide, under anaerobic psychotrophic growth
      conditions. This spore-forming bacterium grows slowly under laboratory conditions, and it can
      take up to 3 months to produce a workable culture. These characteristics have limited the
      study of this commercially challenging bacterium. Consequently information on this bacterium
      is limited and no effective controls are currently available to confidently detect and manage
      this production risk.
      In this study the complete genome of C. estertheticum DSM 8809 was determined
      by SMRT R sequencing. The genome consists of a circular chromosome of 4.7 Mbp
      along with a single plasmid carrying a potential tellurite resistance gene tehB and a Tn3-like
      resolvase-encoding gene tnpR. The genome sequence was searched for central metabolic pathways
      that would support its biochemical profile and several enzymes contributing to this phenotype
      were identified. Several putative antibiotic/biocide/metal resistance-encoding genes and
      virulence factors were also identified in the genome, a feature that requires further
      research. The availability of the genome sequence will provide a basic blueprint from which to
      develop valuable biomarkers that could support
      and improve the detection and control of this bacterium along the beef production chain.
AU  - Yu Z
AU  - Gunn L
AU  - Brennan E
AU  - Reid R
AU  - Wall PG
AU  - Gaora OP
AU  - Hurley D
AU  - Bolton D
AU  - Fanning S
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2016 7: 1764.

PMID- 28744269
VI  - 8
DP  - 2017
TI  - Comparative Genomics of Methanopyrus sp. SNP6 and KOL6 Revealing Genomic Regions  of Plasticity Implicated in Extremely Thermophilic Profiles.
PG  - 1278
AB  - Methanopyrus spp. are usually isolated from harsh niches, such as high osmotic pressure and
      extreme temperature. However, the molecular mechanisms for their
      environmental adaption are poorly understood. Archaeal species is commonly
      considered as primitive organism. The evolutional placement of archaea is a
      fundamental and intriguing scientific question. We sequenced the genomes of
      Methanopyrus strains SNP6 and KOL6 isolated from the Atlantic and Iceland,
      respectively. Comparative genomic analysis revealed genetic diversity and
      instability implicated in niche adaption, including a number of transporter- and
      integrase/transposase-related genes. Pan-genome analysis also defined the gene
      pool of Methanopyrus spp., in addition of ~120-Kb genomic region of plasticity
      impacting cognate genomic architecture. We believe that Methanopyrus genomics
      could facilitate efficient investigation/recognition of archaeal phylogenetic
      diverse patterns, as well as improve understanding of biological roles and
      significance of these versatile microbes.
AU  - Yu Z
AU  - Ma Y
AU  - Zhong W
AU  - Qiu J
AU  - Li J
PT  - Journal Article
TA  - Front. Microbiol.
JT  - Front. Microbiol.
SO  - Front. Microbiol. 2017 8: 1278.

PMID- 30349619
VI  - 13
DP  - 2018
TI  - Complete genome sequence of the nitrogen-fixing bacterium Azospirillum humicireducens type strain SgZ-5(T).
PG  - 28
AB  - The Azospirillum humicireducens strain SgZ-5(T), belonging to the Order Rhodospirillales and
      the Family Rhodospirillaceae, was isolated from a microbial
      fuel cell inoculated with paddy soil. A previous work has shown that strain
      SgZ-5(T) was able to fix atmospheric nitrogen involved in plant growth promotion.
      Here we present the complete genome of A. humicireducens SgZ-5(T), which consists
      of a circular chromosome and six plasmids with the total genome size of 6,834,379
      bp and the average GC content of 67.55%. Genome annotations predicted 5969
      protein coding and 85 RNA genes including 14 rRNA and 67 tRNA genes. By genomic
      analysis, we identified a complete set of genes that is potentially involved in
      nitrogen fixation and its regulation. This genome also harbors numerous genes
      that are likely responsible for phytohormones production. We anticipate that the
      A. humicireducens SgZ-5(T) genome will contribute insights into plant growth
      promoting properties of Azospirillum strains.
AU  - Yu Z
AU  - Yang G
AU  - Liu X
AU  - Wang Y
AU  - Zhuang L
AU  - Zhou S
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2018 13: 28.

PMID- 26586885
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Pseudoalteromonas sp. Strain R3, a Red-Pigmented l-Amino Acid Oxidase-Producing Bacterium.
PG  - e01339-15
AB  - Here, we report a draft 5.58-Mb genome sequence of Pseudoalteromonas sp. strain R3, isolated
      from an intertidal-zone sludge sample, which has l-amino acid
      oxidase activity. The genomics information of this strain will facilitate the
      study of l-amino acid oxidase, quorum sensing, and the relationship of the two.
AU  - Yu Z
AU  - Zhao M
AU  - Qiu J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01339-15.

PMID- 23516232
VI  - 1
DP  - 2013
TI  - Genome Sequence of Avirulent Riemerella anatipestifer Strain RA-SG.
PG  - e0021812
AB  - Riemerella anatipestifer is a pathogenic bacterium that has spread all over the world and is
      associated with epizootic infections in waterfowl and other avian
      species. R. anatipestifer RA-SG is an avirulent strain, isolated from an infected
      duck in Guangdong province, China. The genome sequence of this species is
      presented herein.
AU  - Yuan J
AU  - Li L
AU  - Sun M
AU  - Dong J
AU  - Hu Q
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0021812.

PMID- 24831134
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Pectobacterium wasabiae Strain CFIA1002.
PG  - e00214-14
AB  - Pectobacterium wasabiae, originally causing soft rot disease in horseradish in Japan, was
      recently found to cause blackleg-like symptoms on potato in the United
      States, Canada, and Europe. A draft genome sequence of a Canadian potato isolate
      of P. wasabiae CFIA1002 will enhance the characterization of its pathogenicity
      and host specificity features.
AU  - Yuan KX
AU  - Adam Z
AU  - Tambong J
AU  - Levesque CA
AU  - Chen W
AU  - Lewis CT
AU  - De Boer SH
AU  - Li XS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00214-14.

PMID- 26272559
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Ralstonia solanacearum Race 3 Biovar 2 Strains with Different Temperature Adaptations.
PG  - e00815-15
AB  - Ralstonia solanacearum race 3 biovar 2 (R3bv2) causes brown rot of potato in countries with
      temperate climates. Here, we report two draft genome sequences of
      R. solanacearum R3bv2 NCPPB909 and CFIA906 with different temperature
      adaptations. Analysis of these genome sequences will provide detailed insight on
      virulence, functionality, and plant/pest interactions of this widely distributed
      and regulated pathogen.
AU  - Yuan KX
AU  - Cullis J
AU  - Levesque CA
AU  - Tambong J
AU  - Chen W
AU  - Lewis CT
AU  - De Boer SH
AU  - Li XS
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00815-15.

PMID- 28978128
VI  - 8
DP  - 2017
TI  - pSY153-MDR, a p12969-DIM-related mega plasmid carrying blaIMP-45 and armA, from clinical Pseudomonas putida.
PG  - 68439-68447
AB  - This work characterized mega plasmid pSY153-MDR, carrying blaIMP-45 and armA, from a
      multidrug-resistant (MDR) Pseudomonas putida isolate from the urine of a cerebral infarction
      patient in China. The backbone of pSY153-MDR was closely related to Pseudomonas plasmids
      p12969-DIM, pOZ176, pBM413, pTTS12, and pRBL16, and could not be assigned to any of the known
      incompatibility groups. The accessory modules of pSY153-MDR were composed of 10 individual
      insertion sequence elements and two different MDR regions, and differed dramatically from the
      above plasmids. Fifteen non-redundant resistance markers were identified to be involved in
      resistance to at least eight distinct classes of antibiotics. All of these resistance genes
      were associated with mobile elements, and were embedded within the two MDR regions. blaIMP-45
      and armA coexisted in a Tn1403Tn1548 region, which was generated from homologous recombination
      of Tn1403- and Tn1548-like transposons. The second copy of armA was a component of the
      ISCR28armA and #8710;ISCR28 structure, representing a novel armA vehicle. This vehicle was
      located within In48, which was related to In363 and In1058. Data presented here provide a
      deeper insight into the evolutionary history of SY153, especially in regard to how it became
      extensively drug-resistant.
AU  - Yuan M
AU  - Chen H
AU  - Zhu X
AU  - Feng J
AU  - Zhan Z
AU  - Zhang D
AU  - Chen X
AU  - Zhao X
AU  - Lu J
AU  - Xu J
AU  - Zhou D
AU  - Li J
PT  - Journal Article
TA  - Oncotarget
JT  - Oncotarget
SO  - Oncotarget 2017 8: 68439-68447.

PMID- 6765644
VI  - 1
DP  - 1981
TI  - The reaction mechanism of type I restriction endonucleases.
PG  - 45-72
AB  - *

         I. Introduction

        II. Genetics

       III. Enzyme structure

        IV. Nature of DNA recognition and cleavage sites

         V. Mechanism of restriction

        VI. Mechanism of modification

       VII. Mechanism of antirestriction systems

      VIII. Projections and speculations

      

AU  - Yuan R
PT  - Journal Article
TA  - Gene Amplif. Anal.
JT  - Gene Amplif. Anal.
SO  - Gene Amplif. Anal. 1981 1: 45-72.

PMID- 6267988
VI  - 50
DP  - 1981
TI  - Structure and mechanism of multifunctional restriction endonucleases.
PG  - 285-315
AB  - Restriction endonucleases are strain-specific enzymes, which enable bacteria to
      recognize and rapidly destroy foreign DNA and which cause double-stranded
      scissions at a limited number of sites on the DNA.  In addition to having a
      restriction activity, each of these bacterial strains possesses a specific DNA
      methylase that transfers methyl groups from S-adenosylmethionine (AdoMet) to
      specific adenine or sytosine residues in the DNA.  In this way, the DNA of the
      cell is protected against its own restriction enzyme.
AU  - Yuan R
PT  - Journal Article
TA  - Annu. Rev. Biochem.
JT  - Annu. Rev. Biochem.
SO  - Annu. Rev. Biochem. 1981 50: 285-315.

PMID- 1101070
VI  - 256
DP  - 1975
TI  - Multiple steps in DNA recognition by restriction endonuclease from E. coli K.
PG  - 556-560
AB  - The process of DNA recognition by the activated form of the restriction
      endonuclease from E. coli K involves three enzyme-DNA complexes which can be
      differentiated experimentally.  These are:  an initial complex formed at a
      nonspecific site; a recognition complex involving the host specificity site;
      and a cleavage complex dependent on the presence of ATP.
AU  - Yuan R
AU  - Bickle TA
AU  - Ebbers W
AU  - Brack C
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 1975 256: 556-560.

PMID- 
VI  - 0
DP  - 1981
TI  - The mechanism of DNA methylation by the restriction endonuclease from E. coli K.
PG  - 239-247
AB  - Restriction endonucleases are strain-specific enzymes which enable bacteria to
      recognize and destroy foreign DNA by making double-stranded scissions at a
      limited number of sites.  These bacterial strains also possess DNA methylases
      which modify the DNA in order to protect it from the homologous restriction
      enzymes.  These restriction endonucleases have been classified into three
      different types (Yuan, 1981).  The Type I enzymes, such as the one coded by E.
      coli K, are multifunctional proteins composed of three different subunits.
      EcoK can catalyze three different reactions:  DNA cleavage (which requires ATP
      and AdoMet), ATP hydrolysis (which is coupled to DNA cleavage) and DNA
      methylation (which requires AdoMet).  We have made a detailed study of the
      reaction mechanism of EcoK in order to understand certain unusual features,
      such as its ability to catalyze two opposing reactions - restriction and
      modification - and the cleavage of DNA at sites distal from the original
      binding site.
AU  - Yuan R
AU  - Burckhardt J
AU  - Weisemann J
AU  - Hamilton DL
PT  - Journal Article
TA  - Biochemistry of S-adenosylmethionine and related compounds
JT  - Biochemistry of S-adenosylmethionine and related compounds
SO  - Biochemistry of S-adenosylmethionine and related compounds 1981 0: 239-247.

PMID- 
VI  - 0
DP  - 1984
TI  - Type I and Type III restriction-modification enzymes.
PG  - 11-38
AB  - None
AU  - Yuan R
AU  - Hamilton DL
PT  - Journal Article
TA  - DNA Methylation. Biochemistry and Biological Significance.
JT  - DNA Methylation. Biochemistry and Biological Significance.
SO  - DNA Methylation. Biochemistry and Biological Significance. 1984 0: 11-38.

PMID- 6282152
VI  - 70
DP  - 1982
TI  - Restriction and modification of DNA by a complex protein.
PG  - 61-69
AB  - The interaction of certain proteins with specific nucleotide sequences forms the basis for
      such diverse biological functions as genetic transformation, recombination, control of gene
      expression, and DNA repair.  In many cases, this interaction involves both the recognition of
      a particular DNA site and the catalysis of a biochemical reaction.  Host-controlled
      restriction and modification is one biological system in which genetic and molecular
      approaches have been combined to give us a better understanding of the complexity of these
      protein-DNA interactions.  Host-controlled restriction is the process by which certain strains
      of bacteria recognize and degrade foreign DNA.  The same strains are able to carry out
      modification of their own DNA to protect it from restriction.
AU  - Yuan R
AU  - Hamilton DL
PT  - Journal Article
TA  - Am. Sci.
JT  - Am. Sci.
SO  - Am. Sci. 1982 70: 61-69.

PMID- 6248234
VI  - 20
DP  - 1980
TI  - DNA translocation by the restriction enzyme from E. coli K.
PG  - 237-244
AB  - The restriction endonuclease Eco K binds to a host specificity site and then
      proceeds to cleave the DNA at sites that may be several thousand bases away.
      It does this by translocating the DNA past the enzyme in an ATP-dependent
      reaction that results in the formation of highly twisted loop intermediates.
      DNA cleavage can occur on either side of the host specificity site.
AU  - Yuan R
AU  - Hamilton DL
AU  - Burckhardt J
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1980 20: 237-244.

PMID- 6265647
VI  - 144
DP  - 1980
TI  - Role of ATP in the cleavage mechanism of the EcoP15 restriction endonuclease.
PG  - 501-519
AB  - The EcoP15 restriction endonuclease forms complexes at specific sites on
      unmodified DNA both in the presence and in the absence of
      S-adenosyl-L-methionine.  ATP acts as an allosteric effector of EcoP15 and
      induces DNA cleavage followed by release of the enzyme from the DNA.  The
      efficiency of endonucleolytic scission varies from site to site.  The
      nucleotide sequences at sites that are cleaved at a high frequency were
      compared.
AU  - Yuan R
AU  - Hamilton DL
AU  - Hadi SM
AU  - Bickle TA
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1980 144: 501-519.

PMID- 4564500
VI  - 240
DP  - 1972
TI  - ATP hydrolysis by restriction endonuclease from E. coli K.
PG  - 42-43
AB  - We wish to report a puzzling ATPase activity associated with the DNA
      restriction endonuclease from E. coli strain K.  This enzyme makes a limited
      number of double chain breaks in DNA molecules lacking the host-controlled
      modification imparted by strain K.  Unmodified DNA molecules from bacteriophage
      lambda, which serve as a convenient substrate, are broken into fragments with a
      weight average molecular weight of approximately 7 Md, about one-fifth the size
      of the intact lambda chromosome.  The reaction requires Mg2+, ATP and
      S-adenosylmethionine (SAM).
AU  - Yuan R
AU  - Heywood J
AU  - Meselson M
PT  - Journal Article
TA  - Nature New Biol.
JT  - Nature New Biol.
SO  - Nature New Biol. 1972 240: 42-43.

PMID- 4984237
VI  - 65
DP  - 1970
TI  - A specific complex between a restriction endonuclease and its DNA substrate.
PG  - 357-362
AB  - In the presence of Mg++, ATP, and S-adenosylmethionine, the DNA restriction
      endonuclease R.K forms a specific complex with its DNA substrate.  The complex
      can be detected by its retention on nitrocellulose membranes.
AU  - Yuan R
AU  - Meselson M
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 1970 65: 357-362.

PMID- 357734
VI  - 122
DP  - 1978
TI  - Steps in the reaction mechanism of the Escherichia coli plasmid P15-specific restriction endonuclease.
PG  - 433-445
AB  - The restriction endonuclease coded by the Escherichia coli plasmid P15 cleaves
      unmodified DNA in the presence of ATP and magnesium ions.  This reaction is
      stimulated by the addition of S-adenosylmethionine.  Both ATP and
      S-adenosylmethionine behave as allosteric effectors.  The enzyme forms a
      complex with unmodified DNA in the absence of S-adenosylmethionine and ATP.
      Neither the rate of complex formation nor its stability is significantly
      affected by S-adenosylmethionine.  The reaction of ATP with this complex is a
      late step in the reaction sequence prior to DNA cleavage and is affected by the
      presence of S-adenosylmethionine.
AU  - Yuan R
AU  - Reiser J
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1978 122: 433-445.

PMID- 
VI  - 0
DP  - 1984
TI  - The restriction and modification DNA methylases: An overview.
PG  - 73-80
AB  - The preceding two chapters have presented in detail all that is known about the
      genetic and enzymatic mechanisms of the modification DNA methylases and their
      relationship to the homologous restriction endonucleases.  Although the number
      of systems that have been characterized is limited, sufficient information is
      available to allow a comparison of the three types of restriction-modification
      systems from both biological and mechanistic viewpoints.
AU  - Yuan R
AU  - Smith HO
PT  - Journal Article
TA  - DNA Methylation. Biochemistry and Biological Significance.
JT  - DNA Methylation. Biochemistry and Biological Significance.
SO  - DNA Methylation. Biochemistry and Biological Significance. 1984 0: 73-80.

PMID- 27469950
VI  - 4
DP  - 2016
TI  - Genome Sequence of a Proteus mirabilis Strain Isolated from the Salivary Glands of Larval Lucilia sericata.
PG  - e00672-16
AB  - We announce a draft genome sequence of a Proteus mirabilis strain derived from Lucilia
      sericata salivary glands. This strain is demonstrated to attract and
      induce oviposition by L. sericata, a common blow fly important to medicine,
      agriculture, and forensics. The genome sequence will help dissect interkingdom
      communication between the species.
AU  - Yuan Y
AU  - Zhang Y
AU  - Fu S
AU  - Crippen TL
AU  - Visi DK
AU  - Benbow ME
AU  - Allen MS
AU  - Tomberlin JK
AU  - Sze SH
AU  - Tarone AM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00672-16.

PMID- 28450516
VI  - 5
DP  - 2017
TI  - Genome Sequence of a Providencia stuartii Strain Isolated from Luciliasericata Salivary Glands.
PG  - e00250-17
AB  - We present here the draft genome sequence of a Providencia stuartii strain, derived from the
      salivary glands of larval Lucilia sericata, a common blow fly
      important to forensic, medical, and veterinary science. The genome sequence will
      help dissect coinfections involving P. stuartii and Proteus mirabilis, as well as
      blow fly-bacteria interactions.
AU  - Yuan Y
AU  - Zhang Y
AU  - Fu S
AU  - Crippen TL
AU  - Visi DK
AU  - Benbow ME
AU  - Allen MS
AU  - Tomberlin JK
AU  - Sze SH
AU  - Tarone AM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00250-17.

PMID- 29301902
VI  - 6
DP  - 2018
TI  - Genome Sequence of the Bile Salt-Degrading Bacterium Novosphingobium sp. Strain Chol11, a Model Organism for Bacterial Steroid Catabolism.
PG  - e01372-17
AB  - Many bacteria from different phylogenetic groups are able to degrade eukaryotic steroid
      compounds, but the underlying metabolic pathways are still not well
      understood. Novosphingobium sp. strain Chol11 is a steroid-degrading
      alphaproteobacterium. Its genome sequence reveals that it lacks several genes for
      steroid degradation known to exist in other model organisms.
AU  - Yucel O
AU  - Wibberg D
AU  - Philipp B
AU  - Kalinowski J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01372-17.

PMID- 21868805
VI  - 193
DP  - 2011
TI  - Genome sequence of Nitrosomonas sp. strain AL212, an ammonia-oxidizing bacterium  sensitive to high levels of ammonia.
PG  - 5047-5048
AB  - Nitrosomonas sp. strain AL212 is an obligate chemolithotrophic ammonia-oxidizing  bacterium
      (AOB) that was originally isolated in 1997 by Yuichi Suwa and
      colleagues. This organism belongs to Nitrosomonas cluster 6A, which is
      characterized by sensitivity to high ammonia concentrations, higher substrate
      affinity (lower K(m)), and lower maximum growth rates than strains in
      Nitrosomonas cluster 7, which includes Nitrosomonas europaea and Nitrosomonas
      eutropha. Genome-informed studies of this ammonia-sensitive cohort of AOB are
      needed, as these bacteria are found in freshwater environments, drinking water
      supplies, wastewater treatment systems, and soils worldwide.
AU  - Yuichi S
AU  - Norton JM
AU  - Bollmann A
AU  - Klotz MG
AU  - Stein LY
AU  - Laanbroek HJ
AU  - Arp DJ
AU  - Goodwin LA
AU  - Chertkov O
AU  - Held B
AU  - Bruce D
AU  - Detter JC
AU  - Detter JC
AU  - Tapia R
AU  - Han CS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5047-5048.

PMID- 17379713
VI  - 153
DP  - 2007
TI  - Comparative analysis of the Corynebacterium glutamicum group and complete genome sequence of strain R.
PG  - 1042-1058
AB  - The complete genome sequence of Corynebacterium glutamicum strain R was determined to allow
      its comparative analysis with other corynebacteria.
      The biology of corynebacteria was explored by refining the definition of
      the subset of genes that constitutes the corynebacterial core as well as
      those characteristic of saprophytic and pathogenic ecological niches. In
      addition, the relative scarcity of corynebacterial sigma factors and the
      plasticity of their two-component system machinery reflect their
      relatively exacting nutritional requirements and reduced
      membrane-associated and secreted proteins. The conservation of key genes
      and pathways between corynebacteria, mycobacteria and Nocardia validates
      the use of C. glutamicum to study fundamental processes that are conserved
      in slow-growing mycobacteria, including pathogenesis-associated
      mechanisms. The discovery of 39 novel genes in C. glutamicum R that have
      not been previously reported in other corynebacteria supports the
      rationale for sequencing additional corynebacterial genomes to better
      define the corynebacterial pan-genome and identify previously undetected
      metabolic pathways in these organisms.
AU  - Yukawa H
AU  - Omumasaba CA
AU  - Nonaka H
AU  - Kos P
AU  - Okai N
AU  - Suzuki N
AU  - Suda M
AU  - Tsuge Y
AU  - Watanabe J
AU  - Ikeda Y
AU  - Vertes AA
AU  - Inui M
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2007 153: 1042-1058.

PMID- 24675866
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Two Lactobacillus Strains, L. farraginis JCM 14108T and L. composti JCM 14202T, Isolated from Compost of Distilled Shochu Residue.
PG  - e00257-14
AB  - Here, we report the draft genome sequences of two type strains of Lactobacillus,
      Lactobacillus farraginis JCM 14108(T) and Lactobacillus composti JCM 14202(T),
      isolated from the compost of distilled shochu residue. Their genome information
      will be useful for studies of ecological and physiological functions of these
      Lactobacillus species.
AU  - Yuki M
AU  - Oshima K
AU  - Suda W
AU  - Kitahara M
AU  - Kitamura K
AU  - Iida T
AU  - Hattori M
AU  - Ohkuma M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00257-14.

PMID- 24482522
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Three Alkaliphilic Bacillus Strains, Bacillus wakoensis JCM 9140T, Bacillus akibai JCM 9157T, and Bacillus hemicellulosilyticus JCM  9152T.
PG  - e01258-13
AB  - Here, we report the draft genome sequences of the type strains of three cellulolytic or
      hemicellulolytic alkaliphilic Bacillus species: Bacillus
      wakoensis, Bacillus akibai, and Bacillus hemicellulosilyticus. The genome
      information for these three strains will be useful for studies of alkaliphilic
      Bacillus species, their evolution, and biotechnological applications for their
      enzymes.
AU  - Yuki M
AU  - Oshima K
AU  - Suda W
AU  - Oshida Y
AU  - Kitamura K
AU  - Iida T
AU  - Hattori M
AU  - Ohkuma M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01258-13.

PMID- 24652984
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Paenibacillus pini JCM 16418T, Isolated from the Rhizosphere of Pine Tree.
PG  - e00210-14
AB  - Paenibacillus pini strain JCM 16418(T) is a cellulolytic bacterium isolated from  the
      rhizosphere of pine trees. Here, we report the draft genome sequence of this
      strain. This genome information will be useful for studies of rhizosphere
      bacteria.
AU  - Yuki M
AU  - Oshima K
AU  - Suda W
AU  - Oshida Y
AU  - Kitamura K
AU  - Iida T
AU  - Hattori M
AU  - Ohkuma M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00210-14.

PMID- 24526645
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Bacteroides reticulotermitis Strain JCM 10512T, Isolated from the Gut of a Termite.
PG  - e00072-14
AB  - Here we report the draft genome sequence of Bacteroides reticulotermitis strain JCM 10512(T),
      a xylanolytic and cellulolytic bacterium isolated from the gut of a
      wood-feeding termite. The genome information will facilitate the study of this
      strain for biomass degradation and adaptation to the gut environment.
AU  - Yuki M
AU  - Oshima K
AU  - Suda W
AU  - Sakamoto M
AU  - Iida T
AU  - Hattori M
AU  - Ohkuma M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00072-14.

PMID- 24558248
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Clostridium straminisolvens Strain JCM 21531T, Isolated  from a Cellulose-Degrading Bacterial Community.
PG  - e00110-14
AB  - Here, we report the draft genome sequence of a fibrolytic bacterium, Clostridium
      straminisolvens JCM 21531(T), isolated from a cellulose-degrading bacterial
      community. The genome information of this strain will be useful for studies on
      the degradation enzymes and functional interactions with other members in the
      community.
AU  - Yuki M
AU  - Oshima K
AU  - Suda W
AU  - Sakamoto M
AU  - Kitamura K
AU  - Iida T
AU  - Hattori M
AU  - Ohkuma M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00110-14.

PMID- 28935745
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Lactococcus sp. Strain Rs-Y01, Isolated from the Gut of  the Lower Termite Reticulitermes speratus.
PG  - e00999-17
AB  - Here, we report the draft genome sequence of Lactococcus sp. strain Rs-Y01, which was isolated
      from the gut of a wood-feeding termite. The genome information will
      facilitate the study of the symbiotic functions of this strain in the termite
      gut.
AU  - Yuki M
AU  - Sakamoto M
AU  - Kuwahara H
AU  - Hongoh Y
AU  - Ohkuma M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00999-17.

PMID- 26950331
VI  - 4
DP  - 2016
TI  - Genomic Sequence of Klebsiella pneumoniae IIEMP-3, a Vitamin B12-Producing Strain from Indonesian Tempeh.
PG  - e01724-15
AB  - Klebsiella pneumoniae strain IIEMP-3, isolated from Indonesian tempeh, is a vitamin
      B12-producing strain that exhibited a different genetic profile from
      pathogenic isolates. Here we report the draft genome sequence of strain IIEMP-3,
      which may provide insights on the nature of fermentation, nutrition, and
      immunological function of Indonesian tempeh.
AU  - Yulandi A
AU  - Sugiokto FG
AU  - Febrilina SA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01724-15.

PMID- 25197435
VI  - 9
DP  - 2014
TI  - Genome sequence of the chromate-resistant bacterium Leucobacter salsicius type strain M1-8(T.).
PG  - 495-504
AB  - Leucobacter salsicius M1-8(T) is a member of the Microbacteriaceae family within  the class
      Actinomycetales. This strain is a Gram-positive, rod-shaped bacterium
      and was previously isolated from a Korean fermented food. Most members of the
      genus Leucobacter are chromate-resistant and this feature could be exploited in
      biotechnological applications. However, the genus Leucobacter is poorly
      characterized at the genome level, despite its potential importance. Thus, the
      present study determined the features of Leucobacter salsicius M1-8(T), as well
      as its genome sequence and annotation. The genome comprised 3,185,418 bp with a
      G+C content of 64.5%, which included 2,865 protein-coding genes and 68 RNA genes.
      This strain possessed two predicted genes associated with chromate resistance,
      which might facilitate its growth in heavy metal-rich environments.
AU  - Yun JH
AU  - Cho YJ
AU  - Chun J
AU  - Hyun DW
AU  - Bae JW
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 495-504.

PMID- 30305867
VI  - 13
DP  - 2018
TI  - Complete genome sequence of the halophile bacterium Kushneria konosiri X49(T), isolated from salt-fermented Konosirus punctatus.
PG  - 19
AB  - Kushneria konosiri X49(T) is a member of the Halomonadaceae family within the order
      Oceanospirillales and can be isolated from salt-fermented larval gizzard
      shad. The genome of K. konosiri X49(T) reported here provides a genetic basis for
      its halophilic character. Diverse genes were involved in salt-in and -out
      strategies enabling adaptation of X49(T) to hypersaline environments. Due to
      resistance to high salt concentrations, genome research of K. konosiri X49(T)
      will contribute to the improvement of environmental and biotechnological usage by
      enhancing understanding of the osmotic equilibrium in the cytoplasm. Its genome
      consists of 3,584,631 bp, with an average G + C content of 59.1%, and 3261 coding
      sequences, 12 rRNAs, 66 tRNAs, and 8 miscRNAs.
AU  - Yun JH
AU  - Sung H
AU  - Kim HS
AU  - Tak EJ
AU  - Kang W
AU  - Lee JY
AU  - Hyun DW
AU  - Kim PS
AU  - Bae JW
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2018 13: 19.

PMID- Not carried by PubMed...
VI  - 8
DP  - 1993
TI  - Purification and characterization of a thermotolerable restriction endonuclease from Streptomyces violochromogenes D2-5.
PG  - 73-74
AB  - A thermotolerable restriction endonuclease, SviI, found from Streptomyces violochromogenes
      D2-5 was purified.  The purified enzyme was homogeneous and the molecular weight of the
      enzymes estimated by polyacrylamide gel electrophoresis containing 0.1% SDS was about 32,000
      daltons.  The recognition sequence and cleavage site (indicated by a slash) of this enzyme
      were determined to be 5'-TT/CGAA-3', the same sequence of AsuII.
AU  - Yun M-S
AU  - Bae M
PT  - Journal Article
TA  - Proc. Mol. Biol. and Genet.
JT  - Proc. Mol. Biol. and Genet.
SO  - Proc. Mol. Biol. and Genet. 1993 8: 73-74.

PMID- Not carried by PubMed...
VI  - 5
DP  - 1995
TI  - Purification and characterization of a thermotolerable restriction endonuclease from Streptomyces violochromogenes D2-5.
PG  - 269-273
AB  - A thermotolerable restriction endonuclease, SviI, found in Streptomyces violochromogenes D2-5
      was purified.  For the purification, streptomycin sulfate and ammonium sulfate precipitation
      was used.  Phosphocellulose P-11, DEAE-Cellulose and Sephacry1-S200 HR column chromatography
      were also performed.  The purified enzyme was found to be homogeneous and the molecular weight
      of the enzyme estimated by polyacrylamide gel electrophoresis containing 0.1% SDS was about
      32,000 daltons.  The recognition sequence and cleavage site of the enzyme were determined to
      be 5M-U-TT/CGAA-3M-U which is the same sequence as that of AsuII.  Unlike AsuII, however, the
      SviI shows high thermal stability.
AU  - Yun M-S
AU  - Hwang H
AU  - Bae M
PT  - Journal Article
TA  - J. Microbiol. Biotechnol.
JT  - J. Microbiol. Biotechnol.
SO  - J. Microbiol. Biotechnol. 1995 5: 269-273.

PMID- 26847902
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Mycobacterium tuberculosis KT-0204, Isolated in South Korea.
PG  - e01519-15
AB  - Here, we describe the draft genome sequence of Mycobacterium tuberculosis KT-0204, non-Beijing
      family. This sequence will reveal genes related to the
      evolution and adaptation of M. tuberculosis KT-0204 in human hosts.
AU  - Yun MR
AU  - Han SJ
AU  - Yoo WG
AU  - Kwon T
AU  - Lee S
AU  - Lee JS
AU  - Kim DW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01519-15.

PMID- 25883284
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Lactobacillus plantarum Strain 90sk and Lactobacillus brevis Strain 15f: Focusing on Neurotransmitter Genes.
PG  - e00261-15
AB  - The genomes of Lactobacillus plantarum strain 90sk and Lactobacillus brevis strain 15f were
      isolated from human intestinal microbiota. Both strains
      synthesize gamma-aminobutyric acid (GABA), the major inhibitory neurotransmitter.
      Detailed genome analyses will help to understand the role of GABA in the
      interaction of bacteria with human intestinal cells.
AU  - Yunes RA
AU  - Klimina KM
AU  - Emelyanov KV
AU  - Zakharevich NV
AU  - Poluektova EU
AU  - Danilenko VN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00261-15.

PMID- 19767618
VI  - 37
DP  - 2009
TI  - Phylogenetic screening of a bacterial, metagenomic library using homing endonuclease restriction and marker insertion.
PG  - e144
AB  - Metagenomics provides access to the uncultured majority of the microbial world. The approaches
      employed in this field have, however, had limited success in linking functional genes to the
      taxonomic or phylogenetic origin of the organism they belong to. Here we present an efficient
      strategy to recover environmental DNA fragments that contain phylogenetic marker genes from
      metagenomic libraries. Our method involves the cleavage of 23S ribsosmal RNA (rRNA) genes
      within pooled library clones by the homing endonuclease I-CeuI followed by the insertion and
      selection of an antibiotic resistance cassette. This approach was applied to screen a library
      of 6500 fosmid clones derived from the microbial community associated with the sponge
      Cymbastela concentrica. Several fosmid clones were recovered after the screen and detailed
      phylogenetic and taxonomic assignment based on the rRNA gene showed that they belong to
      previously unknown organisms. In addition, compositional features of these fosmid clones were
      used to classify and taxonomically assign a dataset of environmental shotgun sequences. Our
      approach represents a valuable tool for the analysis of rapidly increasing, environmental DNA
      sequencing information.
AU  - Yung PY
AU  - Burke C
AU  - Lewis M
AU  - Egan S
AU  - Kjelleberg S
AU  - Thomas T
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: e144.

PMID- 16903837
VI  - 71
DP  - 2006
TI  - Nickase and a protein encoded by an open reading frame downstream from the nickase BspD6I gene form a restriction endonuclease complex.
PG  - 1002-1008
AB  - We are the first to have isolated a protein (186 amino acid residues) encoded by the open
      reading frame adjacent to the end of the BspD6I nickase (N.BspD6I) gene. Cleavage of both DNA
      strands near the sequence recognized by nickase (5'-GAGTC/5'-GACTC) occurs when this protein
      is added to the reaction mixture containing N.BspD6I. The protein encoded by the open reading
      frame and the nickase are suggested to be subunits of heterodimeric restriction endonuclease
      R.BspD6I.
AU  - Yunusova AK
AU  - Rogulin EA
AU  - Artyukh RI
AU  - Zheleznaya LA
AU  - Matvienko NI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 2006 71: 1002-1008.

PMID- 2821380
VI  - 21
DP  - 1987
TI  - Plasmid pKM101ard+-mediated alleviation of EcoK restriction.  II. Cloning of ard gene.
PG  - 847-852
AB  - Plasmid pKM101 affects the type I restriction by EcoK in E. coli.  The gene ard responsible
      for alleviation of EcoK restriction was shown to be located within the BglIIB fragment of
      pKM101.  Plasmid pD12 was constructed by introducing into pUC12 a 1.87 kb HindIII-Pst
      fragment, carrying ard gene.  Tn5 and Tn1000 insertions were obtained in the ard gene region.
AU  - Yussifov TN
AU  - Zavilgelsky GB
AU  - Delver EP
AU  - Belogurov AA
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1987 21: 847-852.

PMID- 9275272
VI  - 62
DP  - 1997
TI  - Site-specific endonuclease AbaI from Azospirillum brasilense UQ 1796 is an isoschizomer of endonuclease BclI.
PG  - 403-410
AB  - The site-specific endonuclease AbaI was isolated and purified to functional purity from the
      soil nitrogen-fixing bacterium Azospirillum brasilense UQ 1796.  Purification included
      successive chromatography on colums with phosphocellulose, heparin-Sepharose, and
      hydroxyapatite.  The purified enzyme recognizes the palindromic DNA sequence 5'-T/GATCA-3'
      and cleaves it as shown by the arrow.  The isolated enzyme belongs to class II restriction
      endonucleases and is an isoschizomer of endonuclease BclI.  The enzyme AbaI is active at
      26-56oC.  The optimal temperature is 48oC and the optimal buffer is LRB.
AU  - Zabaznaya EV
AU  - Nikiforev VV
AU  - Zheleznaya LA
AU  - Matvienko NI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1997 62: 403-410.

PMID- Not included in PubMed...
VI  - 62
DP  - 1997
TI  - Site-specific endonucleases RspLKI and RspLKII from Rhodococcus species LK2 are isoschizomers of SphI and BamHI.
PG  - 1018-1028
AB  - Two site-specific endonucleases, RspLKI and RspLKII, have been isolated and purified to
      functional homogeneity from the soil bacterium Rhodococcus species LK2.  RspLKI recognizes the
      5'-GCATG/C-3' DNA sequence and RspLKII recognizes the 5'-G/GATCC-3' sequence (arrows
      indicate DNA cleavage sites).  The isolated enzymes are class II site specific endonucleases
      and are isoschizomers of endonucleases SphI and BamHI, respectively.
AU  - Zabaznaya EV
AU  - Zheleznaya LA
AU  - Matvienko NI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1997 62: 1018-1028.

PMID- 
VI  - 64
DP  - 1999
TI  - Site-specific endonuclease NspLKI is an isoschizomer of Endonuclease HaeIII.
PG  - 234-238
AB  - Site-specific endonuclease NspLKI has been isolated and purified to a functionally pure state
      from soil bacterium Nocardia species LK by successive chromatography on columns with
      phosphocellulose, HTP hydroxyapatite, and heparin-Sepharose.  The isolated enzyme recognizes
      the 5'-GG/CC-3' sequence on DNA and cleaves it as indicated by the arrow, i.e., it is an
      isoschizomer of HaeIII.  The final enzyme yield is 1.105 units per gram of wet biomass.  The
      enzyme is active in the temperature range of 25-60 C with an optimum at 48-55 C; it does not
      lose activity on storage for three days at room temperature.  An optimal buffer is HRB
      containing 10 mM Tris-HCl, pH 7.4, 200 microgram/ml albumin, 10 mM MgCl2, and 100 mM NaCl.
AU  - Zabaznaya EV
AU  - Zheleznaya LA
AU  - Svadbina IV
AU  - Matvienko NI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1999 64: 234-238.

PMID- 6256607
VI  - 179
DP  - 1980
TI  - The ral gene of phage lambda: I. Identification of a non-essential gene that modulates restriction and modification in E. coli.
PG  - 63-73
AB  - Host controlled restriction in Escherichia coli can be relieved by
      pre-infecting restricting cells with modified lambda helper phages.  This
      process, in which intact unmodified phage genomes are allowed to escape
      restriction attack, is mediated by a newly identified lambda function called
      ral.  The ral gene has been located by deletion mapping between cIII and N.
      Efficient expression of the ral gene requires the product of the regulator gene
      N.  Polyacrylamide gel analysis of the lambda proteins specified by the cIII-N
      region failed to reveal the product of the ral gene, but demonstrated that
      protein Ea10 is encoded by a gene located immediately to the left of ral.  From
      these results the map order cIII-Ea10-ral-TL1-N was deduced.  Ral specifically
      alleviates restriction in E. coli K and E. coli B, but does not affect
      restriction systems EcoRI, EcoRII and EcoP1.  In addition, ral enhances the
      modification activity of the EcoK and EcoB restriction enzymes:  we observed
      that efficient modification of progeny phages obtained by propagating
      unmodified lambda phages in r-m+ hosts, is dependent upon the presence of ral.
      We thus conclude that the ral gene product acts by modulating the restriction
      and modification activities of the type I restriction systems in E. coli, and
      the possible mechanisms will be discussed.
AU  - Zabeau M
AU  - Friedman S
AU  - Van Montagu M
AU  - Schell J
PT  - Journal Article
TA  - Mol. Gen. Genet.
JT  - Mol. Gen. Genet.
SO  - Mol. Gen. Genet. 1980 179: 63-73.

PMID- 
VI  - 3
DP  - 1979
TI  - The role of restriction endonucleases in molecular genetics.
PG  - 1-63
AB  - This chapter will attempt to provide a summary of the general properties of
      restriction enzymes and to describe their various applications in molecular
      genetics.  Several earlier reviews have appeared (Arber, 1965, 1971, 1974;
      Arber and Linn, 1969; Boyer, 1971; Meselson et al., 1972; Nathans and Smith,
      1975; Roberts, 1976).
AU  - Zabeau M
AU  - Roberts RJ
PT  - Journal Article
TA  - Molecular Genetics
JT  - Molecular Genetics
SO  - Molecular Genetics 1979 3: 1-63.

PMID- 4133568
VI  - 81
DP  - 1973
TI  - The alleviation of host-controlled restriction of unmodified phages by functions of bacteriophage lambda.
PG  - 990
AB  - The host-controlled restriction of unmodified lambda phage in Escherichia coli
      K12 and B hosts can be overcome either by co-infecting these cells with a
      modified lambda phage, or by inducing a resident lambda prophage.  The
      following lambda functions involved in this rescue process have been
      characterised:  (1) a new lambda function ral (for:  Restriction Alleviation)
      located between CIII and N.  (2) The non-essential lambda functions red, int
      and gam.  The rescue of unmodified phage can proceed by two different
      mechanisms:  (1) Whole genome rescue.  The lambda ral function was shown to be
      able to rescue both unmodified lambda and unmodified heterologous phages P2 and
      Pi.  The ral function probably interferes directly with the restriction
      process, since rescue by ral can only be observed when the ral function is
      expressed prior to infection with unmodified phage.  Furthermore preliminary
      results indicate that the E. coli DNA polymerase I is involved in this rescue
      process.  These results suggest that ral interferes with restriction by
      directing some repair of the restricted DNA with the result that double strand
      scissions do not occur.  2) Using threefactor crosses it was shown that
      fragments of restricted DNA can be taken up in helper phage genomes by a
      recombination process specifically directed by the lambda red function.  Since
      the lambda gam function specifically inhibits the E. coli exonuclease V, we
      investigated the role of this nuclease in the restriction process:  it was
      shown that exoV is responsible for the secondary degradation of the restriction
      DNA fragments.  This results in a loss of biological activity of the fragments
      as measured by marker rescue and by complementation.
AU  - Zabeau M
AU  - Schell J
AU  - Van Montagu M
PT  - Journal Article
TA  - Arch. Int. Physiol. Biochim.
JT  - Arch. Int. Physiol. Biochim.
SO  - Arch. Int. Physiol. Biochim. 1973 81: 990.

PMID- 29348333
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence and Annotation of the Obligate Bacterial Endosymbiont Caedibacter taeniospiralis, Causative Agent of the Killer Phenotype in Paramecium  tetraurelia.
PG  - e01418-17
AB  - Caedibacter taeniospiralis is an obligate endosymbiont living in the cytoplasm of Paramecium
      tetraureliaC. taeniospiralis causes the so-called killer trait,
      eliminating intraspecific competitors of its host when released into the medium
      by the concerted action of the unusual protein structure R-body (refractile body)
      in addition to an as-yet-unknown toxin.
AU  - Zaburannyi N
AU  - Grosser K
AU  - Gasparoni G
AU  - Muller R
AU  - Schrallhammer M
AU  - Simon M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01418-17.

PMID- 24393121
VI  - 15
DP  - 2014
TI  - Insights into naturally minimised Streptomyces albus J1074 genome.
PG  - 11
AB  - Background: The Streptomyces albus J1074 strain is one of the most widely used chassis for the
      heterologous production of bioactive natural products. The fast growth and an efficient
      genetic system make this strain an attractive model for expressing cryptic biosynthetic
      pathways to aid drug discovery.Results: To improve its capabilities for the heterologous
      expression of biosynthetic gene clusters, the complete genomic sequence of S. albus J1074 was
      obtained. With a size of 6,841,649 bp, coding for 5,832 genes, its genome is the smallest
      within the genus streptomycetes. Genome analysis revealed a strong tendency to reduce the
      number of genetic duplicates. The whole transcriptomes were sequenced at different time points
      to identify the early metabolic switch from the exponential to the stationary phase in S.
      albus J1074.Conclusions: S. albus J1074 carries the smallest genome among the completely
      sequenced species of the genus Streptomyces. The detailed genome and transcriptome analysis
      discloses its capability to serve as a premium host for the heterologous production of natural
      products. Moreover, the genome revealed 22 additional putative secondary metabolite gene
      clusters that reinforce the strain's potential for natural product synthesis.
AU  - Zaburannyi N
AU  - Rabyk M
AU  - Ostash B
AU  - Fedorenko V
AU  - Luzhetskyy A
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2014 15: 11.

PMID- 6093048
VI  - 12
DP  - 1984
TI  - HhaI methylase and restriction endonuclease as probes for B to Z DNA conformational changes in d(GCGC) sequences.
PG  - 7677-7692
AB  - The capacity of the modification methylase (MHhaI) and restriction endonuclease
      (HhaI) from Haemophilus haemolyticus to methylate and cleave, respectively,
      recognition sites which are in right-handed B or left-handed Z structures was
      determined in vitro.  Plasmids containing tracts of (dC-dG) as well as numerous
      individual d(GCGC) sites distributed around the vector were studied.  Negative
      supercoiling was used to convert the (dC-dG) tracts (~ 30 bp in length) from a
      right-handed to a left-handed conformation.  (Methyl-3H)-SAM was used to
      localize and quantitate modified d(GCGC) recognition sites, whereas cleavage by
      HhaI was used to detect unmethylated sites.  In the left-handed Z-form, the
      (dC-dG) blocks were not methylated by MHhaI and not cleaved by Hha.  A
      two-dimensional gel analysis of a family of 33 topoisomers treated with MHhaI
      revealed that the lack of methylation in the (dC-dG) blocks was directly
      correlated to the supercoil-induced B to Z transition in these segments.  These
      results are significant with respect to enzyme-DNA interactions in general and
      provide the basis for using HhaI and MHhaI as probes for different DNA
      structures and conformational transitions under physiological conditions.
AU  - Zacharias W
AU  - Larson JE
AU  - Kilpatrick MW
AU  - Wells RD
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1984 12: 7677-7692.

PMID- 2840954
VI  - 27
DP  - 1988
TI  - Methylation of cytosine in the 5-position alters the structural and energetic properties of the supercoil-induced Z-helix and B-Z junctions.
PG  - 2970-2978
AB  - The structural and energetic consequences of cytosine methylation in the
      5-position on the supercoil-dependent B-Z equilibrium in alternating dC-dG
      sequences cloned into recombinant plasmids were investigated.  The helical
      parameters determined with the band shift method for right-handed [10.7 base
      pairs (bp)/turn] and left-handed (12.8 bp/turn) 5MedC-dG inserts were different
      from the helical repeat values for unmethylated dC-dG inserts (10.5 bp/turn in
      the right-handed and 11.5 bp/turn in the left-handed form).  We analyzed the
      thermodynamic parameters DeltaGBZ (free energy difference per base pair between
      right-handed and left-handed helix structure), DeltaGjx (free energy for
      formation of one B-Z junction), and b (helix unwinding at a junction region)
      for varying lengths of dC-dG inserts by two-dimensional gel electrophoresis and
      application of a statistical mechanics model.  A comparison of plasmids fully
      methylated in vitro with HhaI methylase and their unmethylated counterparts
      revealed that DeltaGjx is not significantly changed by cytosine methylation.
      However, this base modification results in an approximate 3-fold decrease of
      DeltaGBZ and an approximate 2-fold decrease of the unwinding b at B-Z junction
      regions.  Analysis of a pair of related plasmids, each containing two dC-dG
      blocks, revealed qualitatively different transition behaviors.  When the two
      dC-dG blocks were separated by 95 bp of a mixed sequence, they underwent
      independent B to Z transitions with separate nucleation events and junction
      formations.  When the two blocks were separated by only a 4 bp GATC sequence,
      only one nucleation event was necesary, and the Z-helix spread across the
      nonalternating GATC region.  These structural and energetic alterations
      demonstrate that methylation of cytosine in the 5-position may be an important
      switch mechanism for influencing the B-Z equilibrium and DNA topology in
      general, thus potentially affecting DNA-protein interactions and gene
      regulation at physiological levels of DNA supercoiling.
AU  - Zacharias W
AU  - O'Connor TR
AU  - Larson JE
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 1988 27: 2970-2978.

PMID- 29152037
VI  - 12
DP  - 2017
TI  - Complete genome sequence of Pseudomonas corrugata strain RM1-1-4, a stress protecting agent from the rhizosphere of an oilseed rape bait plant.
PG  - 66
AB  - 10.1601/nm.2592 strain RM1-1-4 is a rhizosphere colonizer of oilseed rape. A previous study
      has shown that this motile, Gram-negative, non-sporulating
      bacterium is an effective stress protecting and biocontrol agent, which protects
      their hosts against abiotic and biotic stresses. Here, we announce and describe
      the complete genome sequence of P. corrugata RM1-1-4 consisting of a single 6.1
      Mb circular chromosome that encodes 5189 protein coding genes and 85 RNA-only
      encoding genes. Genome analysis revealed genes predicting functions such as
      detoxifying mechanisms, stress inhibitors, exoproteases, lipoproteins or volatile
      components as well as rhizobactin siderophores and spermidine. Further analysis
      of its genome will help to identify traits promising for stress protection,
      biocontrol and plant growth promotion properties.
AU  - Zachow C
AU  - Muller H
AU  - Laireiter CM
AU  - Tilcher R
AU  - Berg G
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 66.

PMID- 28078051
VI  - 12
DP  - 2017
TI  - Complete genome sequence of Pseudomonas brassicacearum strain L13-6-12, a biological control agent from the rhizosphere of potato.
PG  - 6
AB  - Pseudomonas brassicacearum strain L13-6-12 is a rhizosphere colonizer of potato,  lettuce and
      sugar beet. Previous studies have shown that this motile,
      Gram-negative, non-sporulating bacterium is an effective biocontrol agent against
      different phytopathogens. Here, we announce and describe the complete genome
      sequence of P. brassicacearum L13-6-12 consisting of a single 6.7 Mb circular
      chromosome that consists of 5773 protein coding genes and 85 RNA-only encoding
      genes. Genome analysis revealed genes encoding specialized functions for pathogen
      suppression, thriving in the rhizosphere and interacting with eukaryotic
      organisms.
AU  - Zachow C
AU  - Muller H
AU  - Monk J
AU  - Berg G
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2017 12: 6.

PMID- 30194838
VI  - 592
DP  - 2018
TI  - Recognition of modified cytosine variants by the DNA-binding domain of methyl-directed endonuclease McrBC.
PG  - 3335-3345
AB  - Cytosine modifications expand the information content of genomic DNA in both eukaryotes and
      prokaryotes, providing means for epigenetic regulation and self
      versus nonself discrimination. For example, the methyl-directed restriction
      endonuclease, McrBC, recognizes and cuts invading bacteriophage DNA containing
      5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), and N4-methylcytosine
      (4mC), leaving the unmodified host DNA intact. Here, we present cocrystal
      structures of McrB-N bound to DNA oligoduplexes containing 5hmC, 5-formylcytosine
      (5fC), and 4mC, and characterize the relative affinity of McrB-N to various
      cytosine variants. We find that McrB-N flips out modified bases into a protein
      pocket and binds cytosine derivatives in the order of descending affinity: 4mC >
      5mC > 5hmC >> 5fC. We also show that pocket mutations alter the relative
      preference of McrB-N to 5mC, 5hmC, and 4mC.
AU  - Zagorskaite E
AU  - Manakova E
AU  - Sasnauskas G
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 2018 592: 3335-3345.

PMID- 25486533
VI  - 9
DP  - 2014
TI  - Chemical Display of Pyrimidine Bases Flipped Out by Modification-Dependent Restriction Endonucleases of MspJI and PvuRts1I Families.
PG  - e114580
AB  - The epigenetic DNA modifications 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) in
      eukaryotes are recognized either in the context of double-stranded DNA (e.g., by the
      methyl-CpG binding domain of MeCP2), or in the flipped-out state (e.g., by the SRA domain of
      UHRF1). The SRA-like domains and the base-flipping mechanism for 5(h)mC recognition are also
      shared by the recently discovered prokaryotic modification-dependent endonucleases of the
      MspJI and PvuRts1I families. Since the mechanism of modified cytosine recognition by many
      potential eukaryotic and prokaryotic 5(h) mC 'readers' is still unknown, a fast solution
      based method for the detection of extrahelical 5(h) mC would be very useful. In the present
      study we tested base-flipping by MspJI- and PvuRts1I-like restriction enzymes using several
      solution-based methods, including fluorescence measurements of the cytosine analog
      pyrrolocytosine and chemical modification of extrahelical pyrimidines with chloroacetaldehyde
      and KMnO4. We find that only KMnO4 proved an efficient probe for the positive display of
      flipped out pyrimidines, albeit the method required either non-physiological pH (4.3) or a
      substitution of the target cytosine with thymine. Our results imply that DNA recognition
      mechanism of 5(h) mC binding proteins should be tested using a combination of all available
      methods, as the lack of a positive signal in some assays does not exclude the base flipping
      mechanism.
AU  - Zagorskaite E
AU  - Sasnauskas G
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2014 9: e114580.

PMID- 28774972
VI  - 5
DP  - 2017
TI  - Genome Sequences of Brucella melitensis, Isolated from Blood Samples of Brucellosis Patients in Malaysia.
PG  - e00689-17
AB  - Human brucellosis is a neglected zoonotic disease and has widespread geographical
      distribution. Brucella melitensis has caused outbreaks and sporadic cases in Malaysia. Here,
      we present the whole-genome sequences of four B. melitensis strains isolated from brucellosis
      patients in Malaysia.
AU  - Zahidi JM
AU  - Ahmad N
AU  - Tay BY
AU  - Hashim R
AU  - Khoo E
AU  - Ahmad N
AU  - Yee CY
AU  - Dolhan NQ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00689-17.

PMID- Not included in PubMed...
VI  - 24
DP  - 1997
TI  - Distribution of restriction nucleases among some entomopathogenic strains of Bacillus sphaericus.
PG  - 483-487
AB  - The restriction enzyme BspTI, an isoschizomer of HaeIII (recognition site GGCC), has been
      detected in eight strains of serotype 5a5b and two serotype 3 strains of the entomopathogenic
      bacterium Bacillus sphaericus.  Strains from other serotypes contained the enzymes BspTII and
      BspTIII, which digested pBR322 DNA into similar banding patterns after agarose gel
      electrophoresis but differed in their susceptibility to methylation of the substrate.  Strains
      from serotypes 9, 25 and 26a26b were lacking in restriction enzyme activity.  There was little
      correlation between phage typing and restriction enzyme activity, suggesting that restriction
      and modification are not responsible for phage specificity among entomopathogenic B.
      sphaericus strains.
AU  - Zahner V
AU  - Priest FG
PT  - Journal Article
TA  - Lett. Appl. Microbiol.
JT  - Lett. Appl. Microbiol.
SO  - Lett. Appl. Microbiol. 1997 24: 483-487.

PMID- 27056219
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Agrobacterium sp. Strain R89-1, a Morphine Alkaloid-Biotransforming Bacterium.
PG  - e00196-16
AB  - Agrobacteriumsp. strain R89-1 isolated from composted wastes ofPapaver somniferumcan
      effectively biotransform codeine/morphine into 14-OH-derivatives.
      Here, we present a 4.7-Mb assembly of the R89-1 strain genome. The draft shows
      that the strain R89-1 represents a distinct phylogenetic lineage within the
      genusAgrobacterium.
AU  - Zahradnik J
AU  - Kyslikova E
AU  - Kyslik P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00196-16.

PMID- 28935728
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Pantoea agglomerans JM1, a Strain Isolated from Soil Polluted by Industrial Production of Beta-Lactam Antibiotics That Exhibits  Valacyclovir-Like Hydrolase Activity.
PG  - e00921-17
AB  - Strain Pantoea agglomerans JM1 was isolated from the soil of a microbiome that had been
      exposed to polluting pharmaceuticals. The bacterium exhibited enzymatic
      activities useful for the biotransformation of beta-lactams. The genome of the
      strain was assembled and described, and the gene encoding valacyclovir-like
      hydrolase was identified.
AU  - Zahradnik J
AU  - Plackova M
AU  - Palyzova A
AU  - Maresova H
AU  - Kyslikova E
AU  - Kyslik P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00921-17.

PMID- 21835176
VI  - 585
DP  - 2011
TI  - Role of magnesium ions in DNA recognition by the EcoRV restriction endonuclease.
PG  - 2739-2743
AB  - The restriction endonuclease EcoRV binds two magnesium ions. One of these ions, Mg-A(2+),
      binds to the phosphate group where the cleavage
      occurs and is required for catalysis, but the role of the other ion,
      Mg-B(2+) is debated. Here, multiple independent molecular dynamics
      simulations suggest that Mg-B(2+) is crucial for achieving a tightly
      bound protein-DNA complex and stabilizing a conformation that allows
      cleavage. In the absence of Mg-B(2+) in all simulations the protein-DNA
      hydrogen bond network is significantly disrupted and the sharp kink at
      the central base pair step of the DNA, which is observed in the
      two-metal complex, is not present. Also, the active site residues
      rearrange in such a way that the formation of a nucleophile, required
      for DNA hydrolysis, is unlikely.
AU  - Zahran M
AU  - Berezniak T
AU  - Imhof P
AU  - Smith JC
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 2011 585: 2739-2743.

PMID- 20600128
VI  - 401
DP  - 2010
TI  - Mechanism of DNA Recognition by the Restriction Enzyme EcoRV.
PG  - 415-432
AB  - EcoRV, a restriction enzyme in Escherichia coli, destroys invading foreign DNA by cleaving it
      at the center step of a GATATC sequence. In the EcoRV-cognate DNA crystallographic complex, a
      sharp kink of 50 degrees has been found at the center base-pair step (TA). Here, we examine
      the interplay between the intrinsic propensity of the cognate sequence to kink and the
      induction by the enzyme by performing all-atom molecular dynamics simulations of EcoRV unbound
      and interacting with three DNA sequences: the cognate sequence, GATATC (TA); the non-cognate
      sequence, GAATTC (AT); and with the cognate sequence methylated on the first adenine
      GA(CH(3))TATC (TA-CH(3)). In the unbound EcoRV, the cleft between the two C-terminal
      subdomains is found to be open. Binding to AT narrows the cleft and forms a partially bound
      state. However, the intrinsic bending propensity of AT is insufficient to allow tight binding.
      In contrast, the cognate TA sequence is easier to bend, allowing specific, high-occupancy
      hydrogen bonds to form in the complex. The absence of cleavage for this methylated sequence is
      found to arise from the loss of specific hydrogen bonds between the first adenine of the
      recognition sequence and Asn185. On the basis of the results, we suggest a three-step
      recognition mechanism. In the first step, EcoRV, in an open conformation, binds to the DNA at
      a random sequence and slides along it. In the second step, when the two outer base pairs,
      GAxxTC, are recognized, the R loops of the protein become more ordered, forming strong
      hydrogen-bonding interactions, resulting in a partially bound EcoRV-DNA complex. In the third
      step, the flexibility of the center base pair is probed, and in the case of the full cognate
      sequence the DNA bends, the complex strengthens and the protein and DNA interact more closely,
      allowing cleavage.
AU  - Zahran M
AU  - Daidone I
AU  - Smith JC
AU  - Imhof P
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2010 401: 415-432.

PMID- 592365
VI  - 115
DP  - 1977
TI  - A new specific endonuclease from Xanthomonas badrii.
PG  - 249-255
AB  - A restriction-like endonuclease, XbaI, has been partially purified from
      Xanthomonas badrii.  This enzyme cleaves adenovirus-2 DNA at four sites,
      bacteriophage lambda DNA at only one site, and does not cleave simian virus 40
      DNA.  It recognizes the sequence 5'-T^-C-T-A-G-A-3' 3'-A-G-A-T-C^-T-5' and cuts
      at the sites indicated by the arrows.
AU  - Zain BS
AU  - Roberts RJ
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1977 115: 249-255.

PMID- 25523785
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Bifidobacterium longum GT15: Unique Genes for Russian Strains.
PG  - e01348-14
AB  - In this study, we report the first completely annotated genome sequence of the Russian-origin
      Bifidobacterium longum subsp. longum strain GT15. We discovered 35
      unique genes (UGs) which were detected from only the B. longum GT15 genome and
      were absent from other B. longum strain genomes (not of Russian origin).
AU  - Zakharevich NV
AU  - Averina OV
AU  - Klimina KM
AU  - Kudryavtseva AV
AU  - Kasianov AS
AU  - Makeev VJ
AU  - Danilenko VN
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01348-14.

PMID- 14659743
VI  - 335
DP  - 2004
TI  - Regulation of RNA polymerase promoter selectivity by covalent modification of DNA.
PG  - 103-111
AB  - Expression of genes encoding type II restriction/modification (R/M) systems, which are widely
      spread in eubacteria, must be tightly
      regulated to ensure that host DNA is protected from restriction
      endonucleases at all times. Examples of coordinated expression of R/M
      genes that rely on the action of regulatory factors or the ability of
      methyl transferases to repress their own synthesis by interacting with
      the promoter DNA have been described. Here, we characterize the
      molecular mechanism of factor-independent regulation in the CfrBI R/M
      system. Regulation of the cfrBIM gene transcription occurs through CfrBIM-catalyzed
      methylation of a cytosine residue in the cfrBIM
      promoter. The covalent modification inhibits cfrBIM promoter complex
      formation by interfering with the RNA polymerase sigma(70) subunit
      region 4.2 recognition of the - 35 promoter element. The decrease in
      the cfrBIM promoter complex formation leads to increase in the
      activity of overlapping cfrBIR promoters. This elegant
      factor-independent regulatory system ensures coordinated expression of
      the cfrBI genes.
AU  - Zakharova M
AU  - Minakhin L
AU  - Solonin A
AU  - Severinov K
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2004 335: 103-111.

PMID- 11976960
VI  - 267
DP  - 2002
TI  - Characterization of pECL18 and pKPN2: a proposed pathway for the evolution of two plasmids that carry identical genes for a Type II restriction-modification system.
PG  - 171-178
AB  - The primary structures of the plasmids pECL18 (5571 bp) and pKPN2 (4196 bp) from Escherichia
      coli and Klebsiella pneumoniae, respectively, which carry genes for a Type II
      restriction-modification system (RMS2) with the specificity 5'-CCNGG-3', were determined in
      order to elucidate the structural relationship between them. The data suggest a possible role
      for recombination events at bom (basis of mobility) regions and the sites of resolution of
      multimer plasmid forms (so-called cer sequences) in the structural evolution of multicopy
      plasmids. Analysis of the sequences of pECL18 and pKPN2 showed that the genes for RM(.)
      Ecl18kI and RM(.) Kpn2kI, and the sequences of the rep (replication) regions in the two
      plasmids, are almost identical. In both plasmids, these regions are localized between the bom
      regions and the cer sites. The rest of the pECL18 sequence is almost identical to that of the
      mob (mobilization) region of ColE1, and the corresponding segment of pKPN2 is almost identical
      to part of pHS-2 from Shigella flexneri. The difference in primary structures results in
      different mobilization properties of pECL18 and pKPN2. The complete sequences of pECL18, pKPN2
      and the pairwise comparison of the sequences of pECL18, pKPN2, ColE1 and pHS-2 suggest that
      plasmids may exchange DNA units via site-specific recombination events at bom and cer sites.
      In the course of BLASTN database searches using the cer sites of pECL18 and pKPN2 as queries,
      we found twenty cer sites of natural plasmids. Alignment of these sequences reveals that they
      fall into two classes. The plasmids in each group possess related segments between their cer
      and bom sites.
AU  - Zakharova MV
AU  - Beletskaya IV
AU  - Denjmukhametov MM
AU  - Yurkova TV
AU  - Semenova LM
AU  - Shlyapnikov MG
AU  - Solonin AS
PT  - Journal Article
TA  - Mol. Genet. Genomics
JT  - Mol. Genet. Genomics
SO  - Mol. Genet. Genomics 2002 267: 171-178.

PMID- 9524260
VI  - 208
DP  - 1998
TI  - Cloning and sequence anlaysis of the plasmid-borne genes encoding the Eco29kI restriction and modification enzymes.
PG  - 177-182
AB  - The Eco29kI restriction-modification system has been found to be localized on the plasmid
      pECO29 occurring naturally in the Escherichia coli strain 29k.  Eco29kI, a novel plasmid
      encoded restriction endonuclease from Escherichia coli.  The genes coding for this RMS2, a
      SacII isoschizomer recognizing the sequence CCGCGG have been cloned in Escherichia coli K802
      and sequenced.  The DNA sequence predicts the restriction endonuclease of 214 amino acids
      (24,556 Da) and the DNA-methyltransferase of 382 aa (43,007 Da) where the genes are separated
      by 2 bp and arranged in tandem with eco29kIR preceding eco29kIM.  The recombinant plasmid with
      eco29kIR produces a protein of expected size.  MEco29kI contains all the conserved aa sequence
      motifs characteristic of m5C-MTases.  Remarkably, its variable region exhibits a significant
      similarity to the part of the specific target-recognition domain from M.BssHII-multispecific
      m5C-MTase, which recognizes five different sites on DNA (HaeII, MluI, Cfr10I, SacII and
      BssHII), and the comparison of the nt sequences of its variable regions  allowed us to
      determine the putative TRD of M.Eco29kI.
AU  - Zakharova MV
AU  - Beletskaya IV
AU  - Kravetz AN
AU  - Pertzev AV
AU  - Mayorov SG
AU  - Shlyapnikov MG
AU  - Solonin AS
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1998 208: 177-182.

PMID- 1726021
VI  - 25
DP  - 1991
TI  - Properties of the replicator region of natural plasmid pLG13 carrying genes of the EcoRV restriction-modification system.
PG  - 1615-1625
AB  - The previously constructed plasmid pILRV8 that induces endonuclease EcoRV gene
      overexpression kills cells of some E. coli strains under the induction of this
      enzyme synthesis.  Cell transformation by natural plasmid pLG13 carrying genes
      of the EcoRV restriction-modification system was found to appreciably enhance
      cell viability (survival) under endonuclease overproduction.  A plasmid pLG13
      region located in immediate proximity to the methylase gene was shown to be
      responsible for the above effect.  This region was also capable of autonomous
      replication.  The analysis of the DNA primary structure in the found replicator
      region allowed to refer the pLG13 to ColE1 family plasmids.  Perturbations in
      the region lead to loss of the survival effect and change of the plasmid
      replicative properties.  A relationship between the replicon elements, the
      EcoRV genes region and survival effect is discussed.  Based on the replicon
      found multicopy vector molecules have been constructed.
AU  - Zakharova MV
AU  - Kravets AN
AU  - Klimashina NV
AU  - Solonin AS
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1991 25: 1615-1625.

PMID- 8335262
VI  - 129
DP  - 1993
TI  - Cloning and sequences of the genes encoding the CfrBI restriction-modification system from Citrobacter freundii.
PG  - 77-81
AB  - The genes encoding the CfrBI restriction and modification (R-M) systems from Citrobacter
      freundii and recognizing the sequences 5'-CCWWGG-3' (W=A or T) were cloned in Escherichia
      coli McrBC- cells. The nucleotide (nt) sequences of the genes were determined. Two large open
      reading frames were found. Deletion analysis showed that one of them [1128 nt coding for 376
      amino acids (aa)] corresponds to a methyltransferase (MTase)-encoding gene and the other (1065
      nt coding for 355 aa) to a restriction endonuclese-encoding gene. The genes are oriented
      divergently and separated by 76 bp. A CfrBI site (5'-m4CCATGG) was found in the intergenic
      region of the cfrBIRM genes. Analysis of the deduced aa sequence of M.CfrBI made it possible
      to determine the typical features of a m4C-specific MTase. Limited homology between the
      M.CfrBI and R.CfrBI proteins was also found.
AU  - Zakharova MV
AU  - Kravetz AN
AU  - Beletzkaja IV
AU  - Repyk AV
AU  - Solonin AS
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1993 129: 77-81.

PMID- 9689911
VI  - 1398
DP  - 1998
TI  - Complete nucleotide sequence of the Hsd plasmid pECO29 and identification of its functional regions.
PG  - 106-112
AB  - The complete nucleotide sequence of the Hsd plasmid pECO29 has been determined.  The plasmid
      DNA consists of 3895 base pairs.  These include 4 genes and 5 sites.  Two genes encoding the
      proteins (restriction endonuclease and DNA methyltransferase) have been fully characterized.
      The pECO29 comprises a ColE1-type replication system coding for untranslated genes RNAI and
      RNAII, the emr recombination site containing palindromic sequences and involved in stable
      maintenance of the plasmid, two pseudo oriT sites homologous to the oriT site of R64 and F
      plasmids, as well as the bom locus of a ColE1-like plasmid.  There are no genes involved in
      the mobilization of pECO29 plasmid.
AU  - Zakharova MV
AU  - Pertzev AV
AU  - Kravetz AN
AU  - Beletskaya IV
AU  - Shlyapnikov MG
AU  - Solonin AS
PT  - Journal Article
TA  - Biochim. Biophys. Acta
JT  - Biochim. Biophys. Acta
SO  - Biochim. Biophys. Acta 1998 1398: 106-112.

PMID- 15528663
VI  - 150
DP  - 2004
TI  - Characterization of a dam mutant of Haemophilus influenzae Rd.
PG  - 3773-3781
AB  - The gene encoding Dam methyltransferase of Haemophilus influenzae was mutagenized by the
      insertion of a chloramphenicol-resistance cassette into the middle of the Dam coding sequence.
      This mutant construct was introduced into the H. influenzae chromosome by transformation and
      selection for Cam(R) transformants. The authors have shown that several phenotypic properties,
      resistance to antibiotics, dyes and detergent as well as efficiency of transformation, depend
      on the Dam methylation state of the DNA. Although the major role of the methyl-directed
      mismatch repair (MMR) system is to repair postreplicative errors, it seems that in H.
      influenzae its effect is more apparent in repairing DNA damage caused by oxidative compounds.
      In the dam mutant treated with hydrogen peroxide, MMR is not targeted to newly replicated DNA
      strands and therefore mismatches are converted into single- and double-strand DNA breaks. This
      is shown by the increased peroxide sensitivity of the dam mutant and the finding that the
      sensitivity can be suppressed by a mutH mutation inactivating MMR. In the dam mutant treated
      with nitrofurazone the resulting damage is not converted into DNA breaks but the high
      sensitivity is also suppressed by a mutH mutation.
AU  - Zaleski P
AU  - Piekarowicz A
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2004 150: 3773-3781.

PMID- 16207918
VI  - 151
DP  - 2005
TI  - The role of Dam methylation in phase variation of Haemophilus influenzae genes involved in defence against phage infection.
PG  - 3361-3369
AB  - Haemophilus influenzae uses phase variation (PV) to modulate the activity of its defence
      systems against phage infection. The PV of the
      restriction-modification (R-M) system Hindl, the main defence system
      against phage infection and incoming chromosomal and phage DNA in H.
      influenzae Rd, is driven by changes of the pentanucleoticle repeat
      tract within the coding sequence of the hsdM gene and is influenced by
      lack of Dam methylation. Phase-variable resistance/sensitivity to phage
      infection correlates with changes in lipooligosaccharide (LOS)
      structure and occurs by slippage of tetranucleotide repeats within the
      gene lic2A, coding for a step in the biosynthesis of LOS. The lack of
      Dam activity destabilizes the tetranuclotide (5'-CAAT) repeat tract and
      increases the frequency of switching from sensitivity to resistance to
      phage infection more than in the opposite direction. The PV of the lgtC
      gene does not influence resistance or sensitivity to phage infection.
      Insertional inactivation of lic2A, but not lgtC or lgtF, leads to
      resistance to phage infection and to the same structure of the LOS as
      observed among phase-variable phage-resistant variants. This indicates
      that in the H. influenzae Rd LOS only the first two sugars (Glc-Gal)
      extending from the third heptose are part of bacterial phage receptors.
AU  - Zaleski P
AU  - Wojciechowski M
AU  - Piekarowicz A
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2005 151: 3361-3369.

PMID- 27365349
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of 16SrIII-J Phytoplasma, a Plant Pathogenic Bacterium with a Broad Spectrum of Hosts.
PG  - e00602-16
AB  - Phytoplasmas are bacterial plant pathogens that can affect different vegetal hosts. In South
      America, a phytoplasma belonging to ribosomal subgroup 16SrIII-J  has been reported in many
      crops. Here we report its genomic draft sequence, showing a total length of 687,253 bp and a
      G+C content of 27.72%.
AU  - Zamorano A
AU  - Fiore N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00602-16.

PMID- 21742885
VI  - 193
DP  - 2011
TI  - Genome Sequence of Ruegeria sp. strain KLH11, an N-Acylhomoserine Lactone-Producing Bacterium Isolated from the Marine Sponge Mycale  laxissima.
PG  - 5011-5012
AB  - Ruegeria sp. KLH1, isolated from marine sponge Mycale laxissima, produces a complex profile of
      N-acylhomoserine lactone quorum sensing (QS)
      molecules. The genome sequence provides insights into the genetic
      potential of KLH11 to maintain complex QS systems and is the first genome
      report of a cultivated symbiont from a marine sponge.
AU  - Zan J
AU  - Fricke WF
AU  - Fuqua C
AU  - Ravel J
AU  - Hill R
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5011-5012.

PMID- 20471982
VI  - 400
DP  - 2010
TI  - Mechanism of DNA Methylation: The Double Role of DNA as a Substrate and as a Cofactor.
PG  - 632-644
AB  - Methylation of cytosine residues in the DNA is one of the most important epigenetic marks
      central to the control of differential expression of
      genes. We perform quantum mechanical calculations to investigate the
      catalytic mechanism of the bacterial HhaI DNA methyltransferase. We find
      that the enzyme nucleophile, Cys81, can attack C6 of cytosine only after
      it is deprotonated by the DNA phosphate group, a reaction facilitated by a
      bridging water molecule. This finding, which indicates that the DNA acts
      as both the substrate and the cofactor, can explain the total loss of
      activity observed in an analogous enzyme, thymidylate synthase, when the
      phosphate group of the substrate was removed. Furthermore, our results
      displaying the inability of the phosphate group to deprotonate the side
      chain of serine is in agreement with the total, or the large extent of,
      inactivity observed for the C81S mutant. In contrast to results from
      previous calculations, we find that the active site conserved residues,
      Glu119, Arg163, and Arg165, are crucial for catalysis. In addition, the
      enzyme-DNA adduct formation and the methyl transfer from the cofactor
      S-adenosyl-l-methionine are not concerted but proceed via stepwise
      mechanism. In many of the different steps of this methylation reaction,
      the transfer of a proton is found to be necessary. To render these
      processes possible, we find that several water molecules, found in the
      crystal structure, play an important role, acting as a bridge between the
      donating and accepting proton groups.
AU  - Zangi R
AU  - Arrieta A
AU  - Cossio FP
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2010 400: 632-644.

PMID- 28743956
VI  - 7
DP  - 2017
TI  - Post-hypoxia Invasion of the fetal brain by multidrug resistant Staphylococcus.
PG  - 6458
AB  - Herein we describe an association between activation of inflammatory pathways
      following transient hypoxia and the appearance of the multidrug resistant
      bacteria Staphylococcus simulans in the fetal brain. Reduction of maternal
      arterial oxygen tension by 50% over 30 min resulted in a subseiuent significant
      over-expression of genes associated with immune responses 24 h later in the fetal
      brain. The activated genes were consistent with stimulation by bacterial
      lipopolysaccharide; an influx of macrophages and appearance of live bacteria were
      found in these fetal brains. S. simulans was the predominant bacterial species in
      fetal brain after hypoxia, but was found in placenta of all animals. Strains of
      S. simulans from the placenta and fetal brain were equally highly resistant to
      multiple antibiotics including methicillin and had identical genome sequences.
      These results suggest that bacteria from the placenta invade the fetal brain
      after maternal hypoxia.
AU  - Zarate MA
AU  - Rodriguez MD
AU  - Chang EI
AU  - Russell JT
AU  - Arndt TJ
AU  - Richards EM
AU  - Ocasio BA
AU  - Aranda E
AU  - Gordon EM
AU  - Yu K
AU  - Neu J
AU  - Keller-Wood M
AU  - Triplett EW
AU  - Wood CE
PT  - Journal Article
TA  - Sci. Rep.
JT  - Sci. Rep.
SO  - Sci. Rep. 2017 7: 6458.

PMID- 20571089
VI  - 38
DP  - 2010
TI  - DNA synapsis through transient tetramerization triggers cleavage by Ecl18kI restriction enzyme.
PG  - 7142-7154
AB  - To cut DNA at their target sites, restriction enzymes assemble into different oligomeric
      structures. The Ecl18kI endonuclease in the crystal
      is arranged as a tetramer made of two dimers each bound to a DNA copy.
      However, free in solution Ecl18kI is a dimer. To find out whether the
      Ecl18kI dimer or tetramer represents the functionally important assembly,
      we generated mutants aimed at disrupting the putative dimer-dimer
      interface and analysed the functional properties of Ecl18kI and mutant
      variants. We show by atomic force microscopy that on two-site DNA, Ecl18kI
      loops out an intervening DNA fragment and forms a tetramer. Using the
      tethered particle motion technique, we demonstrate that in solution DNA
      looping is highly dynamic and involves a transient interaction between the
      two DNA-bound dimers. Furthermore, we show that Ecl18kI cleaves DNA in the
      synaptic complex much faster than when acting on a single recognition
      site. Contrary to Ecl18kI, the tetramerization interface mutant R174A
      binds DNA as a dimer, shows no DNA looping and is virtually inactive. We
      conclude that Ecl18kI follows the association model for the synaptic
      complex assembly in which it binds to the target site as a dimer and then
      associates into a transient tetrameric form to accomplish the cleavage
      reaction.
AU  - Zaremba M
AU  - Owsicka A
AU  - Tamulaitis G
AU  - Sasnauskas G
AU  - Shlyakhtenko LS
AU  - Lushnikov AY
AU  - Lyubchenko YL
AU  - Laurens N
AU  - van den Broek B
AU  - Wuite GJ
AU  - Siksnys V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2010 38: 7142-7154.

PMID- 22828280
VI  - 586
DP  - 2012
TI  - The link between restriction endonuclease fidelity and oligomeric state: A study with Bse634I.
PG  - 3324-3329
AB  - Type II restriction endonucleases (REases) exist in multiple oligomeric forms. The tetrameric
      REases have two DNA binding interfaces and must
      synapse two recognition sites to achieve cleavage. It was hypothesised
      that binding of two recognition sites by tetrameric enzymes contributes
      to their fidelity. Here, we experimentally determined the fidelity for
      Bse634I REase in different oligomeric states. Surprisingly, we find
      that tetramerisation does not increase REase fidelity in comparison to
      the dimeric variant. Instead, an inherent ability to act concertedly at
      two sites provides tetrameric REase with a safety-catch to prevent host
      DNA cleavage if a single unmodified site becomes available.
AU  - Zaremba M
AU  - Sasnauskas G
AU  - Siksnys V
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 2012 586: 3324-3329.

PMID- 16987525
VI  - 363
DP  - 2006
TI  - Allosteric communication network in the tetrameric restriction endonuclease Bse634I.
PG  - 500-512
AB  - Restriction endonuclease Bse634I is a homotetramer arranged as a dimer of two primary dimers.
      Bse634I displays its maximum catalytic efficiency upon
      binding of two copies of cognate DNA, one per each primary dimer. The
      catalytic activity of Bse634I on a single DNA copy is down-regulated due
      to the cross-talking interactions between the primary dimers. The
      mechanism of signal propagation between the individual active sites of
      Bse634I remains unclear. To identify communication pathways involved in
      the catalytic activity regulation of Bse634I tetramer we mutated a
      selected set of amino acid residues at the dimer-dimer interface and
      analysed the oligomeric state and catalytic properties of the mutant
      proteins. We demonstrate that alanine replacement of N262 and V263
      residues located in the loop at the tetramerisation interface did not
      inhibit tetramer assembly but dramatically altered the catalytic
      properties of Bse634I despite of the distal location from the active site.
      Kinetic analysis using cognate hairpin oligonucleotide and one and
      two-site plasmids as substrates allowed us to identify two types of
      communication signals propagated through the dimer-dimer interface in the
      Bse634I tetramer: the inhibitory, or "stopper" and the activating, or
      "sync" signal. We suggest that the interplay between the two signals
      determines the catalytic and regulatory properties of the Bse634I and
      mutant proteins.
AU  - Zaremba M
AU  - Sasnauskas G
AU  - Urbanke C
AU  - Siksnys V
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2006 363: 500-512.

PMID- 15811381
VI  - 348
DP  - 2005
TI  - Conversion of the tetrameric restriction endonuclease Bse634I into a dimer: Oligomeric structure-stability-function correlations.
PG  - 459-478
AB  - The Bse634I restriction endonuclease is a tetramer and belongs to the type IIF subtype of
      restriction enzymes. It requires two recognition
      sites for its optimal activity and cleaves plasmid DNA with two sites
      much faster than a single-site DNA. We show that disruption of the
      tetramerisation interface of Bse634I by site-directed mutagenesis
      converts the tetrameric enzyme into a dimer. Dimeric W228A mutant
      cleaves plasmid DNA containing one or two sites with the same
      efficiency as the tetramer cleaves the two-site plasmid. Hence, the
      catalytic activity of the Bse634I tetramer on a single-site DNA is
      down-regulated due to the cross-talking interactions between the
      individual dimers. The autoinhibition within the Bse634I tetramer is
      relieved by bridging two DNA copies into the synaptic complex that
      promotes fast and concerted cleavage at both sites. Cleavage analysis
      of the oligonucleotide attached to the solid support revealed that
      Bse634I is able to form catalytically competent synaptic complexes by
      bridging two molecules of the cognate DNA, cognate DNA-miscognate DNA
      and cognate DNA-product DNA. Taken together, our data demonstrate that
      a single W228A mutation converts a tetrameric type IIF restriction
      enzyme Bse634I into the orthodox dimeric type IIP restriction
      endonuclease. However, the stability of the dimer towards chemical
      denaturants, thermal inactivation and proteolytic degradation are
      compromised.
AU  - Zaremba M
AU  - Sasnauskas G
AU  - Urbanke C
AU  - Siksnys V
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2005 348: 459-478.

PMID- 20133886
VI  - 107
DP  - 2010
TI  - Molecular scissors under light control.
PG  - 1259-1260
AB  - Light plays a key role in the living world.  It serves as a source of energy through
      photosynthesis, makes sight possible, and regulates circadian rhythms.  During evolution,
      organisms from bacteria to higher mammals elaborate various mechanisms to sense and respond to
      light, which manipulates their behavior.  The use of light as a trigger is particularly
      attractive as a means of controlling biological processes at will, because light is
      noninvasive and can be manipulated both temporally (from microseconds) and spatially
      (microns).  In this issue of PNAS, Schierling et al. demonstrate the possibility of
      controlling the enzymatic activity of the restriction endonuclease PvuII by light.
AU  - Zaremba M
AU  - Siksnys V
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2010 107: 1259-1260.

PMID- 25429977
VI  - 42
DP  - 2014
TI  - DNA cleavage by CgII and NgoAVII requires interaction between N- and R-proteins and extensive nucleotide hydrolysis.
PG  - 13887-13896
AB  - The stress-sensitive restriction-modification (RM) system CglI from Corynebacterium glutamicum
      and the homologous NgoAVII RM system from Neisseria gonorrhoeae FA1090 are composed of three
      genes: a DNA methyltransferase (M.CglI and M.NgoAVII), a putative restriction endonuclease
      (R.CglI and R.NgoAVII, or R-proteins) and a predicted DEAD-family helicase/ATPase (N.CglI and
      N.NgoAVII or N-proteins). Here we report a biochemical characterization of the R- and
      N-proteins. Size-exclusion chromatography and SAXS experiments reveal that the isolated
      R.CglI, R.NgoAVII and N.CglI proteins form homodimers, while N.NgoAVII is a monomer in
      solution. Moreover, the R.CglI and N.CglI proteins assemble in a complex with R2N2
      stoichiometry. Next, we show that N-proteins have ATPase activity that is dependent on
      double-stranded DNA and is stimulated by the R-proteins. Functional ATPase activity and
      extensive ATP hydrolysis ( approximately 170 ATP/s/monomer) are required for site-specific DNA
      cleavage by R-proteins. We show that ATP-dependent DNA cleavage by R-proteins occurs at fixed
      positions (6-7 nucleotides) downstream of the asymmetric recognition sequence 5'-GCCGC-3'.
      Despite similarities to both Type I and II restriction endonucleases, the CglI and NgoAVII
      enzymes may employ a unique catalytic mechanism for DNA cleavage.
AU  - Zaremba M
AU  - Toliusis P
AU  - Grigaitis R
AU  - Manakova E
AU  - Silanskas A
AU  - Tamulaitiene G
AU  - Szczelkun MD
AU  - Siksnys V
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2014 42: 13887-13896.

PMID- 14741205
VI  - 336
DP  - 2004
TI  - Generation of the BfiI restriction endonuclease from the fusion of a DNA recognition domain to a non-specific nuclease from the  phospholipase D superfamily.
PG  - 81-92
AB  - The Bfi I endonuclease cleaves DNA at fixed positions downstream of an asymmetric sequence.
      Unlike other restriction enzymes, it functions
      without metal ions. The N-terminal half of Bfi I is similar to Nuc, an
      EDTA-resistant nuclease from Salmonella typhimurium that belongs to the
      phosphoplipase D superfamily. Nuc is a dimer with one active site at
      its subunit interface, as is Bfi I, but it cuts DNA non-specifically.
      Bfi I was cleaved by thermolysin into an N-terminal domain, which forms
      a dimer with non-specific nuclease activity, and a C-terminal domain,
      which lacks catalytic activity but binds specifically to the
      recognition sequence as a monomer. On denaturation with guanidinium,
      Bfi I underwent two unfolding transitions: one at a relatively low
      concentration of guanidinium, to a dimeric non-specific nuclease; a
      second at a higher concentration, to an inactive monomer. The isolated
      C-terminal domain unfolded at the first (relatively low) concentration,
      the isolated N-terminal at the second. Hence, Bfi I consists of two
      physically separate domains, with catalytic and dimerisation functions
      in the N terminus and DNA recognition functions in the C terminus. It
      is the first example of a restriction enzyme generated by the
      evolutionary fusion of a DNA recognition domain to a phosphodiesterase
      from the phospholipase D superfamily. Bfi I may consist of three
      structural units: a stable central core with the active site, made from
      two copies of the N-terminal domain, flanked by relatively unstable
      C-terminal domains, that each bind a copy of the recognition sequence.
      (C) 2003 Elsevier Ltd. All rights reserved.
AU  - Zaremba M
AU  - Urbanke C
AU  - Halford SE
AU  - Siksnys V
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2004 336: 81-92.

PMID- 
VI  - 355
DP  - 2005
TI  - Resenbase: A sophisticated and user-friendly, restriction endonuclease database compilation for handheld computers.
PG  - S360
AB  - A database of commonly used restriction enzymes was constructed and programmed into a PalmOs
      handheld.
AU  - Zarogiannis SG
AU  - Filippidis AS
PT  - Journal Article
TA  - Clin. Chim. Acta
JT  - Clin. Chim. Acta
SO  - Clin. Chim. Acta 2005 355: S360.

PMID- 21398548
VI  - 193
DP  - 2011
TI  - Genome sequences of three Acinetobacter baumannii strains assigned to ST2, ST25 and ST78 multilocus sequencing typing genotypes.
PG  - 2359-2360
AB  - Acinetobacter baumannii is an emerging opportunistic gram-negative pathogen responsible for
      hospital-acquired infections. A. baumannii epidemics described in Europe and worldwide were
      caused by a limited number of genotypic clusters of multidrug-resistant strains. Here we
      report the availability of draft genome sequences for three multidrug-resistant A. baumannii
      strains assigned to ST2, ST25 and ST78 multilocus sequencing typing genotypes, that were more
      frequently isolated during outbreaks occurred in Greece, Italy, Lebanon and Turkey.
AU  - Zarrilli R
AU  - Giannouli M
AU  - Rocco F
AU  - Loman NJ
AU  - Haines AS
AU  - Constantinidou C
AU  - Pallen MJ
AU  - Triassi M
AU  - Di Nocera PP
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 2359-2360.

PMID- 28751383
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Bacillus horikoshii Strain 20a from Cuatro Cienegas,  Coahuila, Mexico.
PG  - e00592-17
AB  - We sequenced the Bacillus horikoshii 20a genome, isolated from sediment collected in Cuatro
      Cienegas, Mexico. We identified genes involved in establishing
      antagonistic interactions in microbial communities (antibiotic resistance and
      bacteriocins) and genes related to the metabolism of cyanophycin, a reserve
      compound and spore matrix material potentially relevant for survival in an
      oligotrophic environment.
AU  - Zarza E
AU  - Alcaraz LD
AU  - Aguilar-Salinas B
AU  - Islas A
AU  - Olmedo-Alvarez G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00592-17.

PMID- 29700165
VI  - 6
DP  - 2018
TI  - Complete Genome Sequences of Two Bacillus pumilus Strains from Cuatrocienegas, Coahuila, Mexico.
PG  - e00364-18
AB  - We assembled the complete genome sequences of Bacillus pumilus strains 145 and 150a from
      Cuatrocienegas, Mexico. We detected genes codifying for proteins
      potentially involved in antagonism (bacteriocins) and defense mechanisms
      (abortive infection bacteriophage proteins and 4-azaleucine resistance). Both
      strains harbored prophage sequences. Our results provide insights into
      understanding the establishment of microbial interactions.
AU  - Zarza E
AU  - Alcaraz LD
AU  - Aguilar-Salinas B
AU  - Islas A
AU  - Olmedo-Alvarez G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00364-18.

PMID- 
VI  - 6
DP  - 2000
TI  - Diversity of DNA sequences among restriction endonucleases producing Selenomonas ruminantium isolates detected by enterobacterial repetitive intergenic consensus based polymerase chain reaction (ERIC-PCR).
PG  - 299-304
AB  - Enterobacterial repetitive intergenic consensus-based polymerase chain reaction (ERIC-PCR) was
      found useful for discrimination of rumen
      selenomonads. Simultaneous use of ERICIR and ERIC2 primers yielded
      strain-specific banding patterns. The patterns were compared using Dice
      similarity coefficients and a DNA relatedness dendrogram based on the
      unweighted pair group method using arithmetic averages (UPGMA) was
      constructed. Five clusters and four single strains were identified at a
      similarity level of 50%. Very weak grouping was observed for
      lactilytica and ruminantium subspecies of Selenomonas ruminantium,
      indicating that lactate utilization has probably no taxonomic value.
      Restriction and modification phenotypes are weakly reflected in the
      dendrogram probably as the result of horizontal genetic transfer of
      genes encoding these phenotypic traits. While diverse in ERIC-PCR
      analysis, strains shown little variation in restriction fragment length
      polymorphism of amplified 16S-rRNA genes. All but one strain produced
      nearly identical profiles indicating that majority of DNA diversity
      observed is due to epigenetic factors and not due to evolutionary
      divergence.
AU  - Zatkovic B
AU  - Molnarova V
AU  - Kmet V
AU  - Javorsky P
AU  - Pristas P
PT  - Journal Article
TA  - Anaerobe
JT  - Anaerobe
SO  - Anaerobe 2000 6: 299-304.

PMID- 29091199
VI  - 72
DP  - 2017
TI  - Monitoring microevolution of OXA-48-producing Klebsiella pneumoniae ST147 in a hospital setting by SMRT sequencing.
PG  - 2737-2744
AB  - Objectives: Carbapenemase-producing Klebsiella pneumoniae pose an increasing risk for
      healthcare facilities worldwide. A continuous monitoring of ST distribution
      and its association with resistance and virulence genes is required for early
      detection of successful K. pneumoniae lineages. In this study, we used WGS to
      characterize MDR blaOXA-48-positive K. pneumoniae isolated from inpatients at the
      University Medical Center Gottingen, Germany, between March 2013 and August 2014.
      Methods: Closed genomes for 16 isolates of carbapenemase-producing K. pneumoniae
      were generated by single molecule real-time technology using the PacBio RSII
      platform. Results: Eight of the 16 isolates showed identical XbaI
      macrorestriction patterns and shared the same MLST, ST147. The eight ST147
      isolates differed by only 1-25 SNPs of their core genome, indicating a clonal
      origin. Most of the eight ST147 isolates carried four plasmids with sizes of
      246.8, 96.1, 63.6 and 61.0 kb and a novel linear plasmid prophage, named pKO2, of
      54.6 kb. The blaOXA-48 gene was located on a 63.6 kb IncL plasmid and is part of
      composite transposon Tn1999.2. The ST147 isolates expressed the yersinabactin
      system as a major virulence factor. The comparative whole-genome analysis
      revealed several rearrangements of mobile genetic elements and losses of
      chromosomal and plasmidic regions in the ST147 isolates. Conclusions: Single
      molecule real-time sequencing allowed monitoring of the genetic and epigenetic
      microevolution of MDR OXA-48-producing K. pneumoniae and revealed in addition to
      SNPs, complex rearrangements of genetic elements.
AU  - Zautner AE
AU  - Bunk B
AU  - Pfeifer Y
AU  - Sproer C
AU  - Reichard U
AU  - Eiffert H
AU  - Scheithauer S
AU  - Gross U
AU  - Overmann J
AU  - Bohne W
PT  - Journal Article
TA  - J. Antimicrob. Chemother.
JT  - J. Antimicrob. Chemother.
SO  - J. Antimicrob. Chemother. 2017 72: 2737-2744.

PMID- 26689587
VI  - 16
DP  - 2015
TI  - SMRT sequencing of the Campylobacter coli BfR-CA-9557 genome sequence reveals unique methylation motifs.
PG  - 1088
AB  - BACKGROUND: Campylobacter species are the most prevalent bacterial pathogen causing acute
      enteritis worldwide. In contrast to Campylobacter jejuni, about 5 %
      of Campylobacter coli strains exhibit susceptibility to restriction endonuclease
      digestion by DpnI cutting specifically 5'-G(m)ATC-3' motifs. This indicates
      significant differences in DNA methylation between both microbial species. The
      goal of the study was to analyze the methylome of a C. coli strain susceptible to
      DpnI digestion, to identify its methylation motifs and restriction modification
      systems (RM-systems), and compare them to related organisms like C. jejuni and
      Helicobacter pylori. RESULTS: Using one SMRT cell and the PacBio RS sequencing
      technology followed by PacBio Modification and Motif Analysis the complete genome
      of the DpnI susceptible strain C. coli BfR-CA-9557 was sequenced to 500-fold
      coverage and assembled into a single contig of 1.7 Mbp. The genome contains a
      CJIE1-like element prophage and is phylogenetically closer to C. coli clade 1
      isolates than clade 3. 45,881 6-methylated adenines (ca. 2.7 % of genome
      positions) that are predominantly arranged in eight different methylation motifs
      and 1,788 4-methylated cytosines (ca. 0.1 %) have been detected. Only two of
      these motifs correspond to known restriction modification motifs. Characteristic
      for this methylome was the very high fraction of methylation of motifs with
      mostly above 99 %. CONCLUSIONS: Only five dominant methylation motifs have been
      identified in C. jejuni, which have been associated with known RM-systems. C.
      coli BFR-CA-9557 shares one (RAATTY) of these, but four ORFs could be assigned to
      putative Type I RM-systems, seven ORFs to Type II RM-systems and three ORFs to
      Type IV RM-systems. In accordance with DpnI prescreening RM-system IIP,
      methylation of GATC motifs was detected in C. coli BfR-CA-9557. A homologous IIP
      RM-system has been described for H. pylori. The remaining methylation motifs are
      specific for C. coli BfR-CA-9557 and have been neither detected in C. jejuni nor
      in H. pylori. The results of this study give us new insights into epigenetics of
      Campylobacteraceae and provide the groundwork to resolve the function of
      RM-systems in C. coli.
AU  - Zautner AE
AU  - Goldschmidt AM
AU  - Thurmer A
AU  - Schuldes J
AU  - Bader O
AU  - Lugert R
AU  - Gross U
AU  - Stingl K
AU  - Salinas G
AU  - Lingner T
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2015 16: 1088.

PMID- 7890150
VI  - 30
DP  - 1994
TI  - The ard gene encoding the type I restriction inhibitor is present in conjugative plasmids of FII, B/O, and K groups of incompatibility.
PG  - 1582-1586
AB  - The effect of conjugative plasmids of various incompatibility groups of the enterobacteria
      family on the activity of the cell restriction-modification system of type I (EcoK) was
      studied. Twenty-two conjugative plasmids of 15 incompatibility groups were tested. In addition
      to plasmids of the incI1 and incN groups studied earlier, conjugative plasmids of the incFII,
      incB/O, and incK groups were also shown to be able to weaken the action of type I restriction
      enzymes upon nonmodified DNA (Ard phenotype). A hybridization analysis of all the plasmid DNAs
      studied, using ard gene DNA sequences from the ColIb-P9 (incI1) plasmid as a probe, was
      performed. The ard locus of the R100 (incFII) plasmid was cloned in the pBR322 and pACYC184
      vectors. The ard gene was located 2.5 kb from the oriT site in the leading region on the R100
      conjugative plasmid.
AU  - Zavilgelskii GB
AU  - Bakalova TL
AU  - Duzhii DE
AU  - Kotova VY
PT  - Journal Article
TA  - Genetika
JT  - Genetika
SO  - Genetika 1994 30: 1582-1586.

PMID- 8974906
VI  - 32
DP  - 1996
TI  - Attenuation of type I restriction in Escherichia coli: effect of the ard gene in UV-irradiated cells.
PG  - 1013-1016
AB  - The effect of conjugative plasmids ColIb-P9 (incI1) and pKM 101 (incN), containing the active
      ard gene, on the efficiency of EcoK restriction of nonmodified phage lambda .0 in
      UV-irradiated Escherichia coli cells was studied. ard-Dependent antirestriction enzyme
      activity was shown to decrease in UV-irradiated cells. The efficiency of action of the ard
      plasmid gene on lambda .0 was also shown not to depend on cell helicases RecBCD and UvrD, in
      contrast to the UV-induced alleviation of EcoK restriction (SOS alleviation).
      [Article in Russian]
AU  - Zavilgelskii GB
AU  - Manukhov IV
AU  - Rastorguev SM
PT  - Journal Article
TA  - Genetika
JT  - Genetika
SO  - Genetika 1996 32: 1013-1016.

PMID- 11033812
VI  - 34
DP  - 2000
TI  - Antirestriction.
PG  - 854-862
AB  - Modern data on the molecular mechanisms of antirestriction are reviewed.  The systems of
      inhibition are described for the restriction-modification enzymes of type I in phages and in
      conjugative plasmids.  The phenomenon of alleviation of DNA restriction and its mechanism is
      presented for bacterium Escherichia coli.  The principle of protein mimicry of nucleic acids
      is discussed as a novel way to control biological processes in the cell with reference to
      antirestriction proteins Ard.
AU  - Zavilgelsky GB
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2000 34: 854-862.

PMID- 
VI  - 48
DP  - 2014
TI  - Antirestriction activity of the monomeric and dimeric forms of T7 Ocr.
PG  - 150-157
AB  - The Ocr antirestriction protein, which is encoded by bacteriophage T7 0.3 (ocr), specifically
      inhibits type I restriction-modification enzymes. Ocr belongs to a family of DNA-mimicking
      proteins. Native Ocr forms homodimers both in solution and in crystal. Ocr mutants with two
      amino acid substitutions (Orc F53D A57E and Ocr F53R V77D) were constructed to occur as
      monomers in solution. The dissociation constant K (d) for the Ocr complex with EcoKI (R2M2S)
      proved to differ by three orders of magnitude between the (Ocr)(2) dimer and Ocr F53D A57E and
      Ocr F53R V77D monomers (10(-10) M vs. 10(-7) M). Antimodification activity was substantially
      lower in the Ocr monomers. The dimeric form found to be essential for high inhibitory activity
      of Ocr.
AU  - Zavilgelsky GB
AU  - Kotova VY
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2014 48: 150-157.

PMID- 
VI  - 50
DP  - 2014
TI  - Antirestriction activity of the mercury resistance nonconjugative transposon Tn5053 is controlled by the protease ClpXP.
PG  - 910-915
AB  - When transformed into Escherichia coli K12 strains, the mercury resistance transposon Tn5053
      exhibits high antirestriction activity against the EcoKI type I restriction and modification
      system. The products of the genes merR and ardD contribute to the antirestriction activity of
      Tn5053. The merR gene encodes the MerR protein, the transcription regulator of the mer operon
      genes. The ardD gene is responsible for ArdD protein synthesis and is located within the tni
      operon. In the following study, it was demonstrated that the antirestriction activity of the
      transposon Tn5053 is absent in E. coli K12 strains with the mutant genes clpX, clpP, and recA.
      The antirestriction effect of Tn5053 is not enhanced by 2-aminopurine. The Tn5053
      antirestriction activity is not altered in E. coli K12 with the mutant dam gene; however, it
      is decreased in the E. coli K12 mutD. It is assumed that the activities of the MerR and ArdD
      proteins lead to the formation of a significant amount of unmodified DNA in the bacterial
      cell, causing the SOS-dependent reduction of the EcoKI (R2M2S) enzyme activity associated with
      ClpXP-induced proteolysis of the R-subunit.
AU  - Zavilgelsky GB
AU  - Kotova VY
AU  - Melkina OE
AU  - Pustovoit KS
PT  - Journal Article
TA  - Genetika
JT  - Genetika
SO  - Genetika 2014 50: 910-915.

PMID- 
VI  - 43
DP  - 2009
TI  - Antirestriction and antimodification activities of T7 Ocr: Effects of amino acid substitutions in the interface.
PG  - 93-100
AB  - The T7 antirestriction protein Ocr, encoded by 0.3 (ocr), specifically inhibits ATP-dependent
      type I restriction-modification systems. T7 0.3
      (ocr) was cloned in pUC18. Ocr inhibited both restriction and
      modification activities of the type I restriction-modification system
      (EcoKI) in Escherichia coli K12. The Ocr F53D A57E mutant was obtained
      and proved to inhibit only restriction activity of EcoKI. The 0.3 (ocr)
      and Photorhabdus luminescens luxCDABE genes were cloned in pZ-series
      vectors with the P (ltetO-1) promoter, strongly controlled by the TetR
      repressor. The bioluminescence intensity and luciferase content varied
      up to 5000-fold in E. coli K12 MG1655Z1 tetR(+) (pZE21-luxCDABE) cells,
      depending on the environmental concentration of the inductor
      anhydrotetracycline. The antirestriction activity of Ocr and Ocr F53D
      A57E was studied as a function of their concentration in the cell. The
      dissociation constant K (d), characterizing the binding with EcoKI,
      differed 1000-fold between Ocr and Ocr F53D A57E (10(-10) M versus 10(-7) M).
AU  - Zavilgelsky GB
AU  - Kotova VY
AU  - Rastorguev SM
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2009 43: 93-100.

PMID- 21516787
VI  - 47
DP  - 2011
TI  - Antimodification activity of the ArdA and Ocr proteins.
PG  - 159-167
AB  - The ArdA and Ocr antirestriction proteins, whose genes are in transmissible plasmids (ardA)
      and bacteriophage genomes (0.3 (ocr)), specifically inhibit type I restriction-modification
      enzymes. The Ocr protein (T7 bacteriophage) was shown to inhibit both restriction
      (endonuclease) and modification (methylase) activities of the EcoKI enzyme in a broad range of
      intracellular concentrations (starting from 10-20 molecules per cell). In contrast to Ocr, the
      ArdA protein (ColIb-P9 transmissible plasmid) inhibited both of the EcoKI activities only at
      high intracellular concentrations (30000-40000 molecules per cell). When the ArdA
      concentration was several fold lower, only endonuclease activity of EcoKI was inhibited. It
      was assumed that a poorer ArdA ability to inhibit EcoKI modification activity is related to
      the substantial difference in life cycle between transmissible plasmids (symbiosis with the
      bacterial cell) and bacteriophages (infection and lysis of bacteria). The Ocr and ArdA mutants
      that inhibited exclusively endonuclease activity of EcoKI were obtained. Antirestriction
      proteins incapable of homodimerization were assumed to inhibit only endonuclease activity of
      type I restriction-modification enzymes.
AU  - Zavilgelsky GB
AU  - Kotova VY
AU  - Rastorguev SM
PT  - Journal Article
TA  - Genetika
JT  - Genetika
SO  - Genetika 2011 47: 159-167.

PMID- 18774937
VI  - 73
DP  - 2008
TI  - Comparative analysis of anti-restriction activities of ArdA (ColIb-P9) and Ocr (T7) proteins.
PG  - 906-911
AB  - Anti-restriction proteins ArdA and Ocr are specific inhibitors of type I
      restriction-modification enzymes. The IncI1 transmissible plasmid
      ColIb-P9 ardA and bacteriophage T7 0.3(ocr) genes were cloned in pUC18
      vector. Both ArdA (ColIb-P9) and Ocr (T7) proteins inhibit both
      restriction and modification activities of the type I
      restriction-modification enzyme (EcoKI) in Escherichia coli K12 cells.
      ColIb-P9 ardA, T7 0.3(ocr), and the Photorhabdus luminescens luxCDABE
      genes were cloned in pZ-series vectors with the PltetO-1 promoter,
      which is tightly repressible by the TetR repressor. Controlling the
      expression of the lux-genes encoding bacterial luciferase demonstrates
      that the PltetO-1 promoter can be regulated over an up to 5000-fold
      range by supplying anhydrotetracycline to the E. coli MG1655Z1 tetR(+)
      cells. Effectiveness of the anti-restriction activity of the ArdA and
      Ocr proteins depended on the intracellular concentration. It is shown
      that the dissociation constants K (d) for ArdA and Ocr proteins with
      EcoKI enzyme differ 1700-fold: K (d)(Ocr) = 10(-10) M, K (d)(ArdA) =
      1.7 center dot 10(-7) M.
AU  - Zavilgelsky GB
AU  - Kotova VY
AU  - Rastorguev SM
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2008 73: 906-911.

PMID- 
VI  - 42
DP  - 2006
TI  - Antirestriction and antimodification activities of the ArdA protein encoded by the IncI1 transmissive plasmids R-64 and ColIb-P9.
PG  - 252-258
AB  - Proteins of the Ard family are specific inhibitors of type I restriction-modification enzymes.
      The ArdA of R64 is highly homologous
      to ColIb-P9 ArdA, differing only by four amino acid residues of the
      overall 166. However, unlike ColIb-P9 ArdA, which inhibits both the
      endonuclease and the methylase activities of EcoKI, the R64 ArdA
      protein inhibits only the endonuclease activity of this enzyme. The
      mutant forms of R64 ArdA-A29T, S43A, and Y75W, capable of partially
      reversing the protein to ColIb-P9 ArdA form-were produced by directed
      mutagenesis. It was demonstrated that only Y75W mutation of these three
      variants essentially influenced the functional activity of ArdA: the
      antimodification activity was restored to approximately 90%. It is
      assumed that R64 ArdA inhibits formation of the complex between
      unmodified DNA and the R subunit of the type I restriction-modification
      enzyme EcoKI (R2M2S), which translocates and cleaves DNA. ColIb-P9 ArdA
      protein is capable of forming the DNA complex not only with the R
      subunit, but also with the S subunit, which contacts sK site
      (containing modified adenine residues) in DNA. ArdA bound to the
      specific sK site inhibits concurrently the endonuclease and methylase
      activities of EcoKI (R2M2S), while ArdA bound to the nonspecific site
      in the R subunit blocks only its endonuclease activity.
AU  - Zavilgelsky GB
AU  - Letuchaya TA
AU  - Rastorguev SM
PT  - Journal Article
TA  - Genetika
JT  - Genetika
SO  - Genetika 2006 42: 252-258.

PMID- 15554191
VI  - 38
DP  - 2004
TI  - Antirestriction activity of ArdA encoded by the IncI1 transmissive plasmid R64.
PG  - 901-906
AB  - The transmissive plasmid R64 (IncI1) performs an antirestriction function, reducing the
      efficiency of EcoKI-dependent restriction in
      Escherichia coli K12 cells approximately fivefold. The R64 ardA gene
      has been cloned and sequenced. The ArdA proteins specifically inhibit
      type I restriction-modification enzymes. R64 ArdA is highly homologous
      to ColIb-P9 ArdA: only 4 out of 166 amino acid residues differ. While
      ColIb-P9 inhibits both endonuclease and methylase activities of the
      type I restriction-modification enzyme EcoKI (R2M2S), R64 ArdA inhibits
      only its endonuclease activity. It has been assumed that R64 ArdA
      suppresses the binding of unmodified DNA with the R subunit, which is
      responsible for DNA translocation and cleavage. ColIb-P9 ArdA
      suppresses DNA binding not only with the R, but also with the S
      subunit, which contacts the sK site containing target adenines. The
      binding of ArdA with the specific site inhibits both endonuclease and
      methylase activities; the binding of ArdA with the nonspecific site of
      the R subunit inhibits only the endonuclease activity of EcoKI (R2M2S).
AU  - Zavilgelsky GB
AU  - Letutchaja TA
AU  - Rastorguev SM
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2004 38: 901-906.

PMID- 6097814
VI  - 18
DP  - 1984
TI  - Plasmid pKM101 ard+-mediated alleviation of K-restriction of bacteriophage lambda.  I. General characteristics and genetic localization of the ard gene.
PG  - 1590-1596
AB  - The effectiveness of action of restriction endonuclease EcoK on DNA lambda.0 is considerably
      alleviated (by 10 to 100 times approximately) if Escherichia  coli K12 cells contain plasmid
      pKM101.  The region of plasmid pKM101 in which insertion sites of transposon Tn5, disturbing
      the ability of the plasmid to alleviate EcoK restriction are located, was found to be in
      fragment BglII-B at a distance of about 1.3-1.7 kilobases from the end of the fragment, and it
      was named ard (alleviation of restriction of DNA).  Alleviation of K restriction of phage
      lambda.0 determined by plasmid ard gene is independent of chromosomal genes lexA, recBC, and
      umuC and plasmid gene muc.  The presence of plasmid pKM101 ard+ in the cell does not lead to
      specific modification of DNA, nor does it intensify methylation of DNA by methylase K like the
      action of the ral gene of phage lambda.  The action of the ard gene of plasmid pKM101 is
      highly specific: Alleviation of DNA restriction is observed only in strains of E. coli K and
      is virtually absent in strains of E. coli B, and also in strains of E. coli containing class
      II restriction endonucleases (EcoRI and EcoRIII).
AU  - Zavilgelsky GB
AU  - Mershavka VY
AU  - Jusifov TN
AU  - Belogurov AA
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1984 18: 1590-1596.

PMID- 
VI  - 43
DP  - 2009
TI  - Antirestriction proteins ArdA and Ocr as efficient inhibitors of type I restriction-modification enzymes.
PG  - 241-248
AB  - Genes encoding antirestriction proteins are found in transmissble plasmids (ardABC) and
      bacteriophage genomes (ocr, darA).
      Antirestriction proteins inhibit type I restriction-modification
      enzymes and thus protect the unmodified plasmid or phage DNA from
      degradation. Antirestriction proteins belong to the family of
      DNA-mimicry proteins, whose spatial structure mimics the B-form of DNA.
      Based on an analysis of the mutant forms of ArdA and Ocr obtained by
      site-directed mutagenesis and the native form of ArdA that specifically
      inhibit type I restriction enzymes but do not affect their methylase
      activity, a model is proposed to describe the complex formation between
      an antirestriction protein and a type I restriction-modification enzyme
      (R2M2S): antirestriction proteins can displace a DNA strand from its
      binding sites in the S subunit (which contacts a specific site on DNA)
      and in the R subunit (which translocates the DNA strand and cleaves
      it). Antirestriction and antimodification activities of ArdA and Ocr as
      a function of ardA and ocr expression levels were studied by cloning
      the genes under a strictly regulated promoter.
AU  - Zavilgelsky GB
AU  - Rastorguev SM
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2009 43: 241-248.

PMID- 17922649
VI  - 72
DP  - 2007
TI  - DNA mimicry by proteins as effective mechanism for regulation of activity of DNA-dependent enzymes.
PG  - 913-919
AB  - Modern concepts on mechanisms of DNA-dependent enzyme regulation involving specific
      DNA-mimicking proteins are considered. There are proteins that share structural resemblance
      with DNA duplexes. These include inhibitors of type I restriction-modification enzymes (Ocr
      and ArdA), inhibitors of DNA gyrase MfpA and QnrABS, etc. We describe here structural features
      of these proteins and mechanisms responsible for their interaction with DNA-dependent enzymes
      and then discuss perspectives of use of DNA-mimicking proteins in analysis of replication,
      repair, recombination, mechanisms underlying resistance to antibiotics, and also fields of
      applied biotechnology.
AU  - Zavilgelsky GB
AU  - Rastorguev SM
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2007 72: 913-919.

PMID- 27789639
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Bradyrhizobium elkanii Strains BLY3-8 and BLY6-1, Which Are Incompatible with Rj3 Genotype Soybean Cultivars.
PG  - e01169-16
AB  - We report here the draft genome sequences of Bradyrhizobium elkanii strains BLY3-8 and BLY6-1,
      which are incompatible with Rj3 genotype soybean cultivars.
      The genome sequences of these strains will be useful to identify a causal gene
      for this incompatibility.
AU  - Zaw HA
AU  - Kanesaki Y
AU  - Yoshikawa H
AU  - Tsurumaru H
AU  - Yamakawa T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01169-16.

PMID- 20865122
VI  - 6
DP  - 2010
TI  - Host imprints on bacterial genomes--Rapid, divergent evolution in individual patients.
PG  - e1001078
AB  - Bacteria lose or gain genetic material and through selection, new variants become fixed in the
      population.  Here we provide the first, genome-wide example of a single bacterial strain's
      evolution in different deliberately colonized patients and the surprising insight that hosts
      appear to personalize their microflora.  By first obtaining the complete genome sequence of
      the prototype asymptomatic bacteriuria strain E. coli 83972 and then resequencing its
      descendants after therapeutic bladder colonization of different patients, we identified 34
      mutations, which affected metabolic and virulence-related genes.  Further transcriptome and
      proteome analysis proved that these genome changes altered bacterial gene expression resulting
      in unique adaptation patterns in each patient.  Our results provide evidence that, in addition
      to stochastic events, adaptive bacterial evolution is driven by individual host environments.
      Ongoing loss of gene function supports the hypothesis that evolution towards commensalism
      rather than virulence is favored during asymptomatic bladder colonization.
AU  - Zdziarski J
AU  - Brzuszkiewicz EB
AU  - Wullt B
AU  - Liesegang H
AU  - Biran D
AU  - Voigt B
AU  - Gronberg-Hernandez J
AU  - Ragnarsdottir B
AU  - Hecker M
AU  - Ron EZ
AU  - Daniel R
AU  - Gottschalk G
AU  - Hacker J
AU  - Svanborg C
AU  - Dobrindt U
PT  - Journal Article
TA  - PLoS Pathog.
JT  - PLoS Pathog.
SO  - PLoS Pathog. 2010 6: e1001078.

PMID- 1727392
VI  - 6
DP  - 1992
TI  - Recognition of base-analogue modified substrates by the TaqI restriction endonuclease.
PG  - A358
AB  - It has been proposed that protein-DNA recognition is mediated via specific
      hydrogen bond, hydrophobic and/or electrostatic interactions made between the
      protein and DNA surface.  We have energetically quantitated these interactions
      for the TaqI endonuclease (cleaves T^CGA) by constructing base-analogue
      substituted substrates.  The base analogues N6-methyl-A, N7-deaza-A,
      N7-deaza-G, inosine, N4-methyl-C, 5-methyl-C, uracil, 5-bromoU, alpha-thio-A,
      alpha-thio-G, alpha-thio-T and alpha-thio-A were substituted for their
      corresponding unmodified counterpart in one strand of the TCGA duplex.  The
      effects of these analogues were monitored by measuring the steady-state
      (Km,kcat) and single-turnover (kst) kinetic constants.  Only the N6-methyl-A
      substituted DNA, which recreates in vivo methylation, was unreactive while the
      remaining analogue substitutions exhibited Michaelis-Menten kinetics.  In
      general, the Km was either unchanged or lowered by the analogue substitutions.
      In contrast, many of the analogues severely reduced kcat, suggesting the
      modified functional groups served mainly to destabilize the transition state.
      Single-turnover measurements paralleled the kcat results, pointing to the N7
      and N6 of A, the N7 of G and one of the nonbridging oxygens 3' to T as putative
      contacts made in achieving the transition state.  The unmodified strand in ten
      out of twelve hemi-substituted substrates had a normal kst value suggesting
      that a particular cleavage center is controlled predominantly by recognition of
      determinants on the same strand as the scissile bond.
AU  - Zebala J
AU  - Choi J
AU  - Barany F
PT  - Journal Article
TA  - FASEB J.
JT  - FASEB J.
SO  - FASEB J. 1992 6: A358.

PMID- 1569066
VI  - 267
DP  - 1992
TI  - Characterization of steady state, single-turnover, and binding kinetics of the TaqI restriction endonuclease.
PG  - 8097-8105
AB  - The TaqI restriction endonuclease recognizes and cleaves the duplex DNA sequence T|CGA. Steady
      state kinetic analysis with a small oligodeoxyribonucleotide substrate showed that the enzyme
      obeyed Michaelis-Menten kinetics (Km=53 nM, kcat=1.3 min-1 at 50C and Km=0.5 nM, kcat=2.9
      min-1 at 60C). At 0C, the enzyme was completely inactive, while at 15C, turnover produced
      nicked substrate as the major product in excess of enzyme indicating dissociation between
      nicking events. Above 37C, both strands in the duplex were cleaved prior to dissociation. In
      contrast to the tight, temperature-dependent binding of substrate, binding of the Mg2+
      cofactor was weak (Kd=2.5 mM) and the same at either 50C or 60C. Single-turnover experiments
      using oligonucleotide substrate showed that hydrolysis of duplex DNA occurred via two
      independent nicking events, each with a first order rate constant (kst) of 5.8 min-1 at 60C
      and 3.5 min-1 at 50C. The pH dependence of Km (pKa=9) and kst (pKa=7) suggests Lys/Arg and
      His, respectively, as possible amino acids influencing these constants. Moreover, although kst
      increased significantly with pH, kcat did not, indicating that at least two steps can be
      rate-controlling in the reaction pathway. Binding of protein to canonical DNA in the presence
      of Mg2+ at 0C or in the absence of Mg2+ at 50C was weak (Kd=2.5 microM or 5,000 fold weaker
      than the optimal measured Km) and equal to the binding of noncanonical DNA as judged by
      retention on nitrocellulose. Similar results were seen in gel retardation assays. These
      results suggest that both Mg2+ and high temperature are required to attain the correct protein
      conformation to form the tight complex seen in the steady state analysis. In the accompanying
      paper (Zebala, J.A., Choi, J., Trainor, G.L., and Barany, F. (1992) J. Biol. Chem. 267,
      8106-8116), we report how these kinetic constants are altered using substrate analogues and
      propose a model of functional groups involved in TaqI endonuclease recognition.
AU  - Zebala J
AU  - Choi J
AU  - Barany F
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1992 267: 8097-8105.

PMID- Not carried by PubMed...
VI  - 54
DP  - 1993
TI  - DNA recognition of base-analogue and chemically modified substrates by the TaqI restriction endonuclease.
PG  - 1394-B
AB  - The TaqI restriction endonuclease recognizes and cleaves the duplex DNA sequence T^CGA. It has
      been proposed that protein-DNA recognition is mediated via specific hydrogen bond, hydrophobic
      and/or electrostatic interactions between the protein and DNA surfaces. We have attempted to
      map and quantitate the energies of these interactions for the TaqI endonuclease by
      constructing substrates substituted with base or phosphate analogues that either remove or
      sterically obstruct particular functional groups in the canonical TCGA sequence. The DNA
      backbone was also modified using a chemical approach (phosphate ethylation) which identified
      several phosphates in the recognition sequence essential for cleavage. The base analogues;
      N6-methyl-A, N7-deaza-A, N7-deaza-G, inosine, N4-methyl-C, 5-methylC, uracil, 5-bromoU and the
      phosphate analogues; a-thio-A, a-thioG, a-thio-T, a-thio-A were substituted for their
      corresponding unmodified counterpart in one strand of the TCGA duplex. The effects of these
      analogues were monitored by measuring the steady-state (Km, kcat) and single-turnover (kst)
      kinetic constants. Only the N6-methyl-A substituted DNA, which mimics in vivo methylation, was
      unreactive while the remaining analogue substitutions exhibited Michaelis-Menten kinetics. In
      general, the Km was either unchanged or lowered by the analogue substitutions. In contrast,
      many of the analogues severely reduced Kcat, suggesting the modified functional groups served
      mainly to destabilize the transition state. Single-turnover measurements paralleled the kcat
      results, pointing to the N7 and N6 of A, the N7 of G and one of the nonbridging oxygens 3' to
      T (scissile bond) as putative contacts made in achieving the transition state. Substrates with
      double substitutions displayed simple additivity of delta,deltaG' implying that these changes
      behaved independently. The unmodified strand in ten out of twelve hemi-substituted substrates
      had a normal kst value suggesting that a particular cleavage center is controlled
      predominantly by recognition of determinants on the same strand as the scissile bond. These
      results are discussed in relation to base analogue work from the EcoRI, RsrI and EcoRV
      restriction endonucleases.
AU  - Zebala JA
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1993 54: 1394-B.

PMID- 1569067
VI  - 267
DP  - 1992
TI  - DNA recognition of base analogue and chemically modified substrates by the TaqI restriction endonuclease.
PG  - 8106-8116
AB  - It has been proposed that protein-DNA recognition is mediated via specific hydrogen bond,
      hydrophobic, and/or electrostatic interactions between the protein and DNA surfaces. We have
      attempted to map and quantitate the energies of these interactions for the TaqI endonuclease
      by constructing substrates substituted with base or phosphate analogues that either remove or
      sterically obstruct particular functional groups in the canonical TCGA sequence. The DNA
      backbone was also modified using a chemical approach (phosphate ethylation) which identified
      several phosphates in the recognition sequence essential for cleavage. The base analogues,
      N6-methyl-A, N7-deaza-A, N7-deaza-G, inosine, N4-methyl-C, 5-methyl-C, uracil, 5-bromo-U, and
      the phosphate analogues, alpha-thio-A, alpha-thio-G, alpha-thio-T, alpha-thio-A, were
      substituted for their corresponding unmodified counterpart in one strand of the TCGA duplex.
      The effects of these analogues were monitored by measuring the steady state (Km5 kcat) and
      single-turnover (kst) kinetic constants. Only the N6-methyl-A-substituted DNA, which mimics in
      vivo methylation, was unreactive while the remaining analogue substitutions exhibited
      Michaelis-Menten kinetics. In general, the Km was either unchanged or lowered by the analogue
      substitutions. In contrast, many of the analogues severely reduced kcat, suggesting the
      modified functional groups served mainly to destabilize the transition state. Single-turnover
      measurements paralleled the kcat results, pointing to the N7 and N6 of A, the N7 of G, and one
      of the nonbridging oxygens 3' to T as putative contacts made in achieving the transition
      state. Substrates with double substitutions displayed simple additivity of DeltaDeltaG
      implying that these changes behaved independently. The unmodified strand in 10 out of 12
      hemisubstituted substrates had a normal kst value suggesting that a particular cleavage center
      is controlled predominantly by recognition of determinants on the same strand as the scissile
      bond. These results are discussed in relation to base analogue work from the EcoRI, RsrI, and
      EcoRV restriction endonucleases.
AU  - Zebala JA
AU  - Choi J
AU  - Trainor GL
AU  - Barany F
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1992 267: 8106-8116.

PMID- 26949085
VI  - 41
DP  - 2016
TI  - A putative Type IIS restriction endonuclease GeoICI from Geobacillus sp.--A robust, thermostable alternative to mezophilic prototype BbvI.
PG  - 27-38
AB  - Screening of extreme environments in search for novel microorganisms may lead to  the
      discovery of robust enzymes with either new substrate specificities or
      thermostable equivalents of those already found in mesophiles, better suited for
      biotechnology applications. Isolates from Iceland geysers' biofilms, exposed to a
      broad range of temperatures, from ambient to close to water boiling point, were
      analysed for the presence of DNA-interacting proteins, including restriction
      endonucleases (REases). GeoICI, a member of atypical Type IIS REases, is the most
      thermostable isoschizomer of the prototype BbvI, recognizing/cleaving
      5'-GCAGC(N8/12)-3'DNA sequences. As opposed to the unstable prototype, which
      cleaves DNA at 30 degrees C, GeoICI is highly active at elevated temperatures, up
      to 73 degrees C and over a very wide salt concentration range.
      Recognition/cleavage sites were determined by: (i) digestion of plasmid and
      bacteriophage lambda DNA (Lambda); (ii) cleavage of custom PCR substrates, (iii)
      run-off sequencing of GeoICI cleavage products and (iv) shotgun cloning and
      sequencing of Lambda DNA fragmented with GeoICI. Geobacillus sp. genomic DNA was
      PCR-screened for the presence of other specialized REases-MTases and as a result,
      another putative REase- MTase, GeoICII, related to the Thermus sp. family of
      bifunctional REases-methyltransferases (MTases) was detected.
AU  - Zebrowska J
AU  - Zolnierkiewicz O
AU  - Skowron MA
AU  - Zylicz-Stachula A
AU  - Jezewska-Frackowiak J
AU  - Skowron PM
PT  - Journal Article
TA  - J. Biosci.
JT  - J. Biosci.
SO  - J. Biosci. 2016 41: 27-38.

PMID- 28209825
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Donghicola sp. Strain KarMa, a Model Organism for Monomethylamine-Degrading Nonmethylotrophic Bacteria.
PG  - e01623-16
AB  - The C1-compound monomethylamine can serve as a nitrogen, carbon, and energy source for
      heterotrophic bacteria. The marine alphaproteobacterium Donghicola sp.
      strain KarMa can use monomethylamine as a source only for nitrogen and not for
      carbon. Its draft genome sequence is presented here and reveals putative gene
      clusters for the methylamine dehydrogenase and the N-methylglutamate pathways for
      monomethylamine metabolism.
AU  - Zecher K
AU  - Suleiman M
AU  - Wibberg D
AU  - Winkler A
AU  - Philipp B
AU  - Kalinowski J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01623-16.

PMID- 21837252
VI  - 3
DP  - 2011
TI  - Alkane degradation under anoxic conditions by a nitrate-reducing bacterium with possible involvement of the electron acceptor in substrate activation.
PG  - 125-135
AB  - Microorganisms can degrade saturated hydrocarbons (alkanes) not only under oxic but also under
      anoxic conditions. Three denitrifying isolates (strains HxN1, OcN1, HdN1) able to grow under
      anoxic conditions by coupling alkane oxidation to CO2 with NO3 - reduction to N2 were compared
      with respect to their alkane metabolism. Strains HxN1 and OcN1, which are both
      Betaproteobacteria, utilized n-alkanes from C6 to C8 and C8 to C12 respectively. Both activate
      alkanes anaerobically in a fumarate-dependent reaction yielding alkylsuccinates, as suggested
      by present and previous metabolite and gene analyses. However, strain HdN1 was unique in
      several respects. It belongs to the Gammaproteobacteria and was more versatile towards
      alkanes, utilizing the range from C6 to C30. Neither analysis of metabolites nor analysis of
      genes in the complete genome sequence of strain HdN1 hinted at fumarate-dependent alkane
      activation. Moreover, whereas strains HxN1 and OcN1 grew with alkanes and NO3 -, NO2 - or N2O
      added to the medium, strain HdN1 oxidized alkanes only with NO3 - or NO2 - but not with added
      N2O; but N2O was readily used for growth with long-chain alcohols or fatty acids. Results
      suggest that NO2 - or a subsequently formed nitrogen compound other than N2O is needed for
      alkane activation in strain HdN1. From an energetic point of view, nitrogen-oxygen species are
      generally rather strong oxidants. They may enable enzymatic mechanisms that are not possible
      under conditions of sulfate reduction or methanogenesis and thus allow a special mode of
      alkane activation.
AU  - Zedelius J
AU  - Rabus R
AU  - Grundmann O
AU  - Werner I
AU  - Brodkorb D
AU  - Schreiber F
AU  - Ehrenreich P
AU  - Behrends A
AU  - Wilkes H
AU  - Kube M
AU  - Reinhardt R
AU  - Widdel F
PT  - Journal Article
TA  - Environ. Microbiol. Reports
JT  - Environ. Microbiol. Reports
SO  - Environ. Microbiol. Reports 2011 3: 125-135.

PMID- 25780507
VI  - 9
DP  - 2014
TI  - Complete genome sequence of Ornithobacterium rhinotracheale strain ORT-UMN 88.
PG  - 16
AB  - Ornithobacterium rhinotracheale strain ORT-UMN 88 is a Gram-negative, pleomorphic, rod-shaped
      bacterium and an etiologic agent of pneumonia and
      airsacculitis in poultry. It is a member of the family Flavobacteriaceae of the
      phylum Bacteroidetes. O. rhinotracheale strain ORT-UMN 88 was isolated from the
      pneumonic lung of a turkey in 1995. It was the isolate first used to
      experimentally reproduce disease in turkeys and has since been the focus of
      investigations characterizing potential virulence factors of the bacterium. The
      genome of O. rhinotracheale strain ORT-UMN 88 consists of a circular chromosome
      of 2,397,867 bp with a total of 2300 protein-coding genes, nine RNA genes, and
      one noncoding RNA gene. A companion paper in this issue of SIGS reports the
      non-contiguous finished genome sequence of an additional strain of O.
      rhinotracheale, isolated in 2006.
AU  - Zehr ES
AU  - Bayles DO
AU  - Boatwright WD
AU  - Tabatabai LB
AU  - Register KB
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 16.

PMID- 25780505
VI  - 9
DP  - 2014
TI  - Non-contiguous finished genome sequence of Ornithobacterium rhinotracheale strain H06-030791.
PG  - 14
AB  - The Gram-negative, pleomorphic, rod-shaped bacterium Ornithobacterium rhinotracheale is a
      cause of pneumonia and airsacculitis in poultry. It is a
      member of the family Flavobacteriaceae of the phylum 'Bacteroidetes'. O.
      rhinotracheale strain H06-030791 was isolated from the lung of a turkey in North
      Carolina in 2006. Its genome consists of a circular chromosome of 2,319,034 bp in
      length with a total of 2243 protein-coding genes and nine RNA genes. Genome
      sequences are available for two additional strains of O. rhinotracheale, isolated
      in 1988 and 1995, the latter described in a companion genome report in this issue
      of SIGS. The genome sequence of O. rhinotracheale strain H06-030791, a more
      contemporary isolate, will be of value in establishing core and pan-genomes for
      O. rhinotracheale and elucidating its evolutionary history.
AU  - Zehr ES
AU  - Bayles DO
AU  - Boatwright WD
AU  - Tabatabai LB
AU  - Register KB
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 14.

PMID- 21908286
VI  - 23
DP  - 2011
TI  - Detection of a bacteriophage gene encoding a Mu-like portal protein in Haemophilus parasuis reference strains and field isolates by nested polymerase chain reaction.
PG  - 538-542
AB  - A nested polymerase chain reaction assay was developed to determine the presence of a gene
      encoding a bacteriophage Mu-like portal protein, gp29, in 15 reference strains and 31 field
      isolates of Haemophilus parasuis.  Specific primers, based on the gene's sequence, were
      utilized.  A majority of the virulent reference strains and field isolates tested harbored the
      gene.  The results suggest that the nPCR technique described in the current report could serve
      as a tool for epidemiological studies of H. parasuis.
AU  - Zehr ES
AU  - Tabatabai LB
PT  - Journal Article
TA  - J. Vet. Diagn. Invest.
JT  - J. Vet. Diagn. Invest.
SO  - J. Vet. Diagn. Invest. 2011 23: 538-542.

PMID- 22823751
VI  - 13
DP  - 2012
TI  - Genomic and proteomic characterization of SuMu, a Mu-like bacteriophage infecting Haemophilus parasuis.
PG  - 331
AB  - ABSTRACT: BACKGROUND: Haemophilus parasuis, the causative agent of Glasser's
      disease, is prevalent in swine herds and clinical signs associated with this
      disease are meningitis, polyserositis, polyarthritis, and bacterial pneumonia.
      Six to eight week old pigs in segregated early weaning herds are particularly
      susceptible to the disease. Insufficient colostral antibody at weaning or the
      mixing of pigs with heterologous virulent H. parasuis strains from other farm
      sources in the nursery or grower-finisher stage are considered to be factors for
      the outbreak of Glasser's disease. Previously, a Mu-like bacteriophage portal
      gene was detected in a virulent swine isolate of H. parasuis by nested polymerase
      chain reaction. Mu-like bacteriophages are related phyologenetically to
      enterobacteriophage Mu and are thought to carry virulence genes or to induce host
      expression of virulence genes. This study characterizes the Mu-like
      bacteriophage, named SuMu, isolated from a virulent H. parasuis isolate. RESULTS:
      Characterization was done by genomic comparison to enterobacteriophage Mu and
      proteomic identification of various homologs by mass spectrometry. This is the
      first report of isolation and characterization of this bacteriophage from the
      Myoviridae family, a double-stranded DNA bacteriophage with a contractile tail,
      from a virulent field isolate of H. parasuis. The genome size of bacteriophage
      SuMu was 37,151 bp. DNA sequencing revealed fifty five open reading frames,
      including twenty five homologs to Mu-like bacteriophage proteins: Nlp, phage
      transposase-C-terminal, COG2842, Gam-like protein, gp16, Mor, peptidoglycan
      recognition protein, gp29, gp30, gpG, gp32, gp34, gp36, gp37, gpL, phage tail
      tube protein, DNA circulation protein, gpP, gp45, gp46, gp47, COG3778, tail fiber
      protein gp37-C terminal, tail fiber assembly protein, and Com. The last open
      reading frame was homologous to IS1414. The G + C content of bacteriophage SuMu
      was 41.87% while its H. parasuis host genome's G + C content was 39.93%. Twenty
      protein homologs to bacteriophage proteins, including 15 structural proteins, one
      lysogeny-related and one lysis-related protein, and three DNA replication
      proteins were identified by mass spectrometry. One of the tail proteins, gp36,
      may be a virulence-related protein. CONCLUSION: Bacteriophage SuMu was
      characterized by genomic and proteomic methods and compared to
      enterobacteriophage Mu.
AU  - Zehr ES
AU  - Tabatabai LB
AU  - Bayles DO
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2012 13: 331.

PMID- 19008448
VI  - 322
DP  - 2008
TI  - Globally distributed uncultivated oceanic N2-fixing cyanobacteria lack oxygenic photosystem II.
PG  - 1110-1112
AB  - Biological nitrogen (N2) fixation is important in controlling biological
      productivity and carbon flux in the oceans. Unicellular N2-fixing
      cyanobacteria have only recently been discovered and are widely
      distributed in tropical and subtropical seas. Metagenomic analysis of flow
      cytometry-sorted cells shows that unicellular N2-fixing cyanobacteria in
      "group A" (UCYN-A) lack genes for the oxygen-evolving photosystem II and
      for carbon fixation, which has implications for oceanic carbon and
      nitrogen cycling and raises questions regarding the evolution of
      photosynthesis and N2 fixation on Earth.
AU  - Zehr JP
AU  - Bench SR
AU  - Carter BJ
AU  - Hewson I
AU  - Niazi F
AU  - Shi T
AU  - Tripp HJ
AU  - Affourtit JP
PT  - Journal Article
TA  - Science
JT  - Science
SO  - Science 2008 322: 1110-1112.

PMID- 26798097
VI  - 4
DP  - 2016
TI  - Genome Sequence of Bacillus glycinifermentans TH008, Isolated from Ohio Soil.
PG  - e01573-15
AB  - The genome sequence of an Ohio soil isolate, TH008, was determined. The sequence  reveals a
      close relationship between TH008 and domesticated Bacillus
      glycinifermentans strains found in a traditional Korean fermented soybean food.
AU  - Zeigler DR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01573-15.

PMID- 28596407
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Burkholderia cenocepacia CR318, a Phosphate-Solubilizing Bacterium Isolated from Corn Root.
PG  - e00490-17
AB  - Here, we report the complete genome sequence of the phosphate-solubilizing bacterium
      Burkholderia cenocepacia CR318, consisting of three circular
      chromosomes of 3,511,146 bp, 3,097,552 bp, and 1,056,069 bp. The data presented
      will facilitate further insight into the mechanisms of phosphate solubilization
      and its application for agricultural and ecological sustainability.
AU  - Zekic F
AU  - Weselowski B
AU  - Yuan ZC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00490-17.

PMID- Not carried by PubMed...
VI  - 57
DP  - 1996
TI  - Antisense RNA and ribozymes targeting DNA methyltransferase for in vivo studies.
PG  - 907
AB  - The aim of this study was to make antisense RNA and ribozyme constructs
      directed against mouse DNA methyltransferase (Mtase) and to use inducible expression to
      perturb in vivo DNA methylation, both in tissue culture cells and in transgenic mice.  The
      sheep metallothionein Ia promoter, known to be inducible by zinc in tissue culture cells and
      mouse somatic tissues, and constitutive in mouse gonadal tissues, was used to drive in
      vivo expression.  Several antisense RNA and ribozyme constructs were made and all were
      shown to be expressed in a fibroblast-derived A9 hybrid cell line.  The ribozyme was
      shown to cleave its target RNA efficiently in vitro, but the A9 hybrid cells were found to be
      not suitable for determination of effects of DNA methyltransferase on methylation levels.
      Therefore, another cell line, L61-M, was characterized.  L61-M cells were found to provide
      a very sensitive and quantitative assay for methylation perturbations by measuring
      reactivation of a methylation-silenced thymidine kinase (TK) gene.  Transfection
      experiments using L61-M cells showed that the ribozyme caused a ten-fold increase over
      background of stable TK+ revertants, and that the ribozyme was more effective than the
      antisense RNA constructs, which gave results not significantly different from background.
      Though the ribozyme clearly caused an effect, mRNA for the antisense RNAs or the
      ribozyme could not be detected in transfected L61-M cells, so proof of mechanism of action
      could not be obtained.  The present working hypothesis is that the ribozyme is quite
      effective and deserving of further study, but a different promoter or expression vector
      needs to be used in order to take full advantage of the excellent assay system provided by
      the L61-M cells.
AU  - Zelby LS
PT  - Journal Article
TA  - Diss. Abstr.
JT  - Diss. Abstr.
SO  - Diss. Abstr. 1996 57: 907.

PMID- 2121528
VI  - 271
DP  - 1990
TI  - Modification methylase M. Sau3239I from Streptomyces aureofaciens 3239.
PG  - 147-148
AB  - By chromatography on phosphocellulose and Heparin-Sepharose the modification
      methylase M.Sau3239I was detected and partially purified from cells of
      Streptomyces aureofaciens 3239.  Methylation by this enzyme protects DNA from
      cleavage by the restriction endonuclease R.Sau3239I.  The enzyme catalyzes
      methylation of adenine to N-6-methyladenine in the 5'-CTGGmAG-3' recognition
      sequence.
AU  - Zelinkova E
AU  - Paulicek M
AU  - Zelinka J
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1990 271: 147-148.

PMID- 8962921
VI  - 61
DP  - 1996
TI  - A new site-specific endonuclease from Acinetobacter species (Strain M).
PG  - 1471-1482
AB  - The site-specific endonuclease R.AspMI was isolated from Acinetobacter species (strain M) and
      purified to functional purity.  The enzyme recognizes the symmetrical DNA sequence
      5'-AGG/CCT-3' and cleaves it as shown by the arrow, forming blunt DNA ends.  The enzyme is
      an isoschizomer of endonuclease StuI.  Cleavage of the DNA site is inhibited by
      dcm-methylation.  AspM is in solution as an ~30-kD monomer.
AU  - Zelinskaya NV
AU  - Kovalevskaya NP
AU  - Matvienko NN
AU  - Zheleznaya LA
AU  - Matvienko NI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1996 61: 1471-1482.

PMID- 8562652
VI  - 60
DP  - 1995
TI  - A site-specific endonuclease and methylase from the Thermophilic strain of Bacillus species IS4.
PG  - 1435-1448
AB  - A site-specific endonuclease (R.BspIS4I) and methylase (M.BspIS4I) have been isolated and
      purified to functional purity from the thermophilic strain of Bacillus species IS4.  R.BspIS4I
      recognizes the sequence
      5'-GAAGAC2N^-3'
      3'-CTTCTG6N^-5' and cleaves it as shown by the arrows to form single-stranded
      tetranucleotide 5'-protruding termini.  The enzyme is an isoschizomer of endonuclease BbvII.
      M.BspIS4I is attributed to the adenine-specific methylases.
AU  - Zelinskaya NV
AU  - Kovalevskaya NP
AU  - Matvienko NN
AU  - Zheleznaya LA
AU  - Matvienko NI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1995 60: 1435-1448.

PMID- 9011238
VI  - 61
DP  - 1996
TI  - A new site-specific adenine DNA-methyltransferase from the strain of Bacillus species ST5.
PG  - 1006-1014
AB  - The site-specific DNA-methylase M.BspST5I has been isolated from Bacillus species ST5 and
      purified to functional purity.  M.BspST5I protects DNA from endonuclease R.BspST5I which
      recognizes the nonpalindromic sequence
      5'-GCATC-3'
      3'-CGTAG-5'
      on DNA.  M.BspST5I is an adenine-specific methylase.
AU  - Zelinskaya NV
AU  - Matvienko NN
AU  - Zheleznaya LA
AU  - Matvienko NI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1996 61: 1006-1014.

PMID- 8600994
VI  - 60
DP  - 1995
TI  - A novel site-specific endonuclease from Bacillus species ST5.
PG  - 1999-2010
AB  - A site-specific endonuclease, R.BspST5I, has been isolated in a functionally pure state from
      the thermophilic strain Bacillus species ST5.  The enzyme recognizes the sequence 5'-
      GCATC-3' on DNA and cleaves it at a distance of five nucleotides from the 3'-end of the
      recognition site and at distances of nine or ten nucleotides along the complementary strand,
      depending on the nucleotide surrounding the site on the DNA.  The enzyme is an isomer of
      endonuclease SfaNI from Streptococcus faecalis ND547.
AU  - Zelinskaya NV
AU  - Matvienko NN
AU  - Zheleznaya LA
AU  - Matvienko NI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1995 60: 1999-2010.

PMID- 3038536
VI  - 6
DP  - 1987
TI  - DNA mismatch-repair in Escherichia coli counteracting the hydrolytic deamination of 5-methyl-cytosine residues.
PG  - 1809-1815
AB  - Derivatives of phage M13 were constructed and used for the in vitro
      preparation of heteroduplex DNA molecules containing base/base mismatches that mimick
      DNA lesions caused by hydrolytic deamination of 5-meC residues in Escherichia coli DNA
      (i.e. they carry a T/G mismatch in the special sequence context provided by the recognition
      site -CCA/TGG-of the Dcm-methyltransferase).  Upon introduction of these heteroduplex
      DNAs into CaCl2-treated E. coli cells, the mismatches are efficiently repaired with high
      bias in favour of the DNA strand containing the mismatched guanine residue.  This special
      DNA mismatch-repair operates on fully dam-methylated DNA and is independent of gene
      mutH.  It thus fulfills the salient requirements of a repair pathway responsible for
      counteracting the spontaneous hydrolytic deamination of 5-meC in vivo.  The repair
      efficiency is boosted by a 5-methyl group present on the cytosine residue at the next-nearest
      position to the 5' side of the mismatched guanine.  The repair is severly impaired in host
      strains carrying a mutation in any of the three loci dcm, mutL and mutS.
AU  - Zell R
AU  - Fritz H-J
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 1987 6: 1809-1815.

PMID- 28682158
VI  - 30
DP  - 2017
TI  - Recombination of Virulence Genes in Divergent Acidovorax avenae Strains That Infect a Common Host.
PG  - 813-828
AB  - Bacterial etiolation and decline (BED), caused by Acidovorax avenae, is an
      emerging disease of creeping bentgrass on golf courses in the United States. We
      performed the first comprehensive analysis of A. avenae on a nationwide
      collection of turfgrass- and maize-pathogenic A. avenae. Surprisingly, our
      results reveal that the turfgrass-pathogenic A. avenae in North America are not
      only highly divergent but also belong to two distinct phylogroups. Both
      phylogroups specifically infect turfgrass but are more closely related to maize
      pathogens than to each other. This suggests that, although the disease is only
      recently reported, it has likely been infecting turfgrass for a long time. To
      identify a genetic basis for the host specificity, we searched for genes closely
      related among turfgrass strains but distantly related to their homologs from
      maize strains. We found a cluster of 11 such genes generated by three ancient
      recombination events within the type III secretion system (T3SS) pathogenicity
      island. Ever since the recombination, the cluster has been conserved by strong
      purifying selection, hinting at its selective importance. Together our analyses
      suggest that BED is an ancient disease that may owe its host specificity to a
      highly conserved cluster of 11 T3SS genes.
AU  - Zeng Q
AU  - Wang J
AU  - Bertels F
AU  - Giordano PR
AU  - Chilvers MI
AU  - Huntley RB
AU  - Vargas JM
AU  - Sundin GW
AU  - Jacobs JL
AU  - Yang CH
PT  - Journal Article
TA  - Mol. Plant Microbe Interact.
JT  - Mol. Plant Microbe Interact.
SO  - Mol. Plant Microbe Interact. 2017 30: 813-828.

PMID- 19200728
VI  - 19
DP  - 2009
TI  - A Free-Standing Homing Endonuclease Targets an Intron Insertion Site in the psbA Gene of Cyanophages.
PG  - 218-222
AB  - Homing endonuclease genes are mobile elements that promote their duplication into cognate
      sites that lack the endonuclease gene [1, 2].
      The homing endonuclease initiates this event through site-specific DNA
      cleavage. Copying of the endonuclease gene follows as a consequence of
      DNA repair. A genome containing a homing endonuclease gene is subject
      to self-cleavage. Protection is accomplished through DNA sequence
      polymorphisms, as is the case in intronless homing of free-standing
      endonuclease genes [3, 4], or by disruption of the recognition site by
      a group I intron (or intein) into which the endonuclease ORF is
      embedded. We describe here a novel free-standing homing endonuclease
      from cyanobacteriophage S-PM2, which is similar to the DNA resolvase of
      bacteriophage T4 and is encoded adjacent to an intron-containing psbA
      gene [5, 6]. The endonuclease makes a specific double-strand cut near
      the intron insertion site (IIS), its DNA recognition site spans the
      IIS, and it is unable to cleave intron-containing psbA genes. This
      interdependence of a free-standing endonuclease gene and a group I
      intron, which we denote "collaborative homing," has not been reported
      previously and gives support to a hypothesis of formation of composite
      mobile introns by independent convergence of an intron and an
      endonuclease gene on the same target sequence.
AU  - Zeng QL
AU  - Bonocora RP
AU  - Shub DA
PT  - Journal Article
TA  - Curr. Biol.
JT  - Curr. Biol.
SO  - Curr. Biol. 2009 19: 218-222.

PMID- 25477413
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Bacillus subtilis GXA-28, a Thermophilic Strain with High Productivity of Poly-gamma-Glutamic Acid.
PG  - e01259-14
AB  - Bacillus subtilis GXA-28 is a thermophilic strain that can produce high yield and high
      molecular weight of poly-gamma-glutamic acid under high temperature. Here,
      we report the draft genome sequence of this strain, which may provide the genomic
      basis for the high productivity of poly-gamma-glutamic acid.
AU  - Zeng W
AU  - Chen G
AU  - Tang Z
AU  - Wu H
AU  - Shu L
AU  - Liang Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01259-14.

PMID- 26383653
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Hyperthermophilic Piezophilic Archaeon Palaeococcus pacificus DY20341T, Isolated from Deep-Sea Hydrothermal Sediments.
PG  - e01080-15
AB  - We report the genome sequence of Palaeococcus pacificus DY20341(T), isolated from a sediment
      sample collected from eastern Pacific Ocean hydrothermal fields, which is the first report of
      a complete genome for a Palaeococcus species. The genome sequence will help to better
      understand differentiation phylogenetic relationships and evolution of several Thermococcales
      species.
AU  - Zeng X
AU  - Jebbar M
AU  - Shao Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01080-15.

PMID- 23469335
VI  - 1
DP  - 2013
TI  - Genome Sequences and Photosynthesis Gene Cluster Composition of a Freshwater Aerobic Anoxygenic Phototroph, Sandarakinorhabdus sp. Strain AAP62, Isolated from  the Shahu Lake in Ningxia, China.
PG  - e00034-13
AB  - We report the first genome sequence from the recently established alpha-4 proteobacterial
      genus . The genome of the sp. strain AAP62 contains a
      photosynthesis gene cluster carrying major genes for bacterial reaction centers.
      The presence of genes related to aerobic respiratory electron transport confirms
      the lifestyle of this organism as an aerobic anoxygenic photoheterotroph.
AU  - Zeng Y
AU  - Feng F
AU  - Liu Y
AU  - Li Y
AU  - Koblizek M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00034-13.

PMID- 23105051
VI  - 194
DP  - 2012
TI  - Genome sequences of two freshwater betaproteobacterial isolates, limnohabitans species strains rim28 and rim47, indicate their capabilities as both  photoautotrophs and ammonia oxidizers.
PG  - 6302-6303
AB  - Betaproteobacterial genus Limnohabitans represents an important part of freshwater
      bacterioplankton. Here, we report genome sequences of two
      Limnohabitans isolates, Rim28 and Rim47. They contain a complete photosynthesis
      gene cluster, RuBisCO, CO dehydrogenase, ammonia monooxygenase, and
      sulfur-oxidizing genes, which indicates a great metabolic versatility of the
      Limnohabitans species.
AU  - Zeng Y
AU  - Kasalicky V
AU  - Simek K
AU  - Koblizek M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6302-6303.

PMID- 23516202
VI  - 1
DP  - 2013
TI  - Whole-Genome Sequences of an Aerobic Anoxygenic Phototroph, Blastomonas sp. Strain AAP53, Isolated from a Freshwater Desert Lake in Inner Mongolia, China.
PG  - e0007113
AB  - Blastomonas is a strictly aerobic bacteriochlorophyll a-producing genus within the alpha-4
      Proteobacteria. Here we report the first genome sequence from this
      genus. The draft genome of Blastomonas sp. strain AAP53 contains a split
      photosynthesis gene cluster and two gene clusters encoding a flagellar system.
      Genes for the autotrophic CO2 fixation pathway are absent.
AU  - Zeng Y
AU  - Koblizek M
AU  - Feng F
AU  - Liu Y
AU  - Wu Z
AU  - Jian J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0007113.

PMID- 26561515
VI  - 10
DP  - 2015
TI  - High quality draft genomic sequence of Flavobacterium enshiense DK69(T) and comparison among Flavobacterium genomes.
PG  - 92
AB  - Flavobacterium enshiense DK69(T) is a Gram-negative, aerobic, rod-shaped, non-motile and
      non-flagellated bacterium that belongs to the family
      Flavobacteriaceae in the phylum Bacteroidetes. The high quality draft genome of
      strain DK69(T) was obtained and has a 3,375,260 bp genome size with a G + C
      content of 37.7 mol % and 2848 protein coding genes. In addition, we sequenced
      five more genomes of Flavobacterium type strains and performed a comparative
      genomic analysis among 12 Flavobacterium genomes. The results show some specific
      genes within the fish pathogenic Flavobacterium strains which provide information
      for further analysis the pathogenicity.
AU  - Zeng Z
AU  - Chen C
AU  - Du H
AU  - Wang G
AU  - Li M
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 92.

PMID- 24744335
VI  - 2
DP  - 2014
TI  - Genome sequences of two pseudoalteromonas strains isolated from the South china sea.
PG  - e00305-14
AB  - Two Pseudoalteromonas strains, SCSIO 04301 and SCSIO 11900, were isolated from the South China
      Sea, and both strains form biofilms. Here we present the draft genome sequences of these two
      strains, which will aid the study of marine microbes that are adapted to marine sediments or
      are associated with eukaryotic hosts.
AU  - Zeng Z
AU  - Dai S
AU  - Xie Y
AU  - Tian X
AU  - Li J
AU  - Wang X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00305-14.

PMID- 24029755
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of the Cellulolytic Bacterium Clostridium papyrosolvens C7  (ATCC 700395).
PG  - e00698-13
AB  - We report the draft genome sequence of the cellulose-degrading bacterium Clostridium
      papyrosolvens C7, originally isolated from mud collected below a
      freshwater pond in Massachusetts. This Gram-positive bacterium grows in a
      mesophilic anaerobic environment with filter paper as the only carbon source, and
      it has a simple cellulosome system with multiple carbohydrate-degrading enzymes.
AU  - Zepeda V
AU  - Dassa B
AU  - Borovok I
AU  - Lamed R
AU  - Bayer EA
AU  - Cate JH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00698-13.

PMID- 18655699
VI  - 8
DP  - 2008
TI  - Characterization of new IS elements and studies of their dispersion in two subspecies of Leifsonia xyli.
PG  - 127
AB  - BACKGROUND: Leifsonia xyli is a xylem-inhabiting bacterial species
      comprised of two subspecies: L. xyli subsp. xyli (Lxx) and L. xyli subsp.
      cynodontis (Lxc). Lxx is the causal agent of ratoon stunting disease in
      sugarcane commercial fields and Lxc colonizes the xylem of several grasses
      causing either mild or no symptoms of disease. The completely sequenced
      genome of Lxx provided insights into its biology and pathogenicity. Since
      IS elements are largely reported as an important source of bacterial
      genome diversification and nothing is known about their role in chromosome
      architecture of L. xyli, a comparative analysis of Lxc and Lxx elements
      was performed. RESULTS: Sample sequencing of Lxc genome and comparative
      analysis with Lxx complete DNA sequence revealed a variable number of IS
      transposable elements acting upon genomic diversity. A detailed
      characterization of Lxc IS elements and a comparative review with IS
      elements of Lxx are presented. Each genome showed a unique set of elements
      although related to same IS families when considering features such as
      similarity among transposases, inverted and direct repeats, and element
      size. Most of the Lxc and Lxx IS families assigned were reported to
      maintain transposition at low levels using translation regulatory
      mechanisms, consistent with our in silico analysis. Some of the IS
      elements were found associated with rearrangements and specific regions of
      each genome. Differences were also found in the effect of IS elements upon
      insertion, although none of the elements were preferentially associated
      with gene disruption. A survey of transposases among genomes of
      Actinobacteria showed no correlation between phylogenetic relatedness and
      distribution of IS families. By using Southern hybridization, we suggested
      that diversification of Lxc isolates is also mediated by insertion
      sequences in probably recent events. CONCLUSION: Collectively our data
      indicate that transposable elements are involved in genome diversification
      of Lxc and Lxx. The IS elements were probably acquired after the
      divergence of the two subspecies and are associated with genome
      organization and gene contents. In addition to enhancing understanding of
      IS element dynamics in general, these data will contribute to our ongoing
      comparative analyses aimed at understanding the biological differences of
      the Lxc and Lxx.
AU  - Zerillo MM
AU  - Van Sluys MA
AU  - Camargo LE
AU  - Monteiro-Vitorello CB
PT  - Journal Article
TA  - BMC Microbiol.
JT  - BMC Microbiol.
SO  - BMC Microbiol. 2008 8: 127.

PMID- 2205206
VI  - 16
DP  - 1990
TI  - Determination of substrate specificity of restriction endonuclease Kpn378I.
PG  - 603-604
AB  - The recognition sequence and cleavage site, CCGC^GG, of a new restriction
      endonuclease Kpn378I has been determined.
AU  - Zernov YP
AU  - Lebedev LR
AU  - Babkin IV
AU  - Chizhikov VE
PT  - Journal Article
TA  - Bioorg. Khim.
JT  - Bioorg. Khim.
SO  - Bioorg. Khim. 1990 16: 603-604.

PMID- 21677850
VI  - 4
DP  - 2011
TI  - Complete genome sequence of Hydrogenobacter thermophilus type strain (TK-6).
PG  - 131-143
AB  - Hydrogenobacter thermophilus Kawasumi et al. 1984 is the type species of the genus
      Hydrogenobacter. H. thermophilus was the first obligate autotrophic
      organism reported among aerobic hydrogen-oxidizing bacteria. Strain TK-6(T) is of
      interest because of the unusually efficient hydrogen-oxidizing ability of this
      strain, which results in a faster generation time compared to other autotrophs.
      It is also able to grow anaerobically using nitrate as an electron acceptor when
      molecular hydrogen is used as the energy source, and able to aerobically fix
      CO(2)via the reductive tricarboxylic acid cycle. This is the fifth completed
      genome sequence in the family Aquificaceae, and the second genome sequence
      determined from a strain derived from the original isolate. Here we describe the
      features of this organism, together with the complete genome sequence and
      annotation. The 1,742,932 bp long genome with its 1,899 protein-coding and 49 RNA
      genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
AU  - Zeytun A et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2011 4: 131-143.

PMID- 22628499
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Francisella philomiragia ATCC 25017.
PG  - 3266
AB  - Francisella philomiragia is a saprophytic gammaproteobacterium found only occasionally in
      immunocompromised individuals and is the nearest neighbor to the
      causative agent of tularemia and category A select agent Francisella tularensis.
      To shed insight into the key genetic differences and the evolution of these two
      distinct lineages, we sequenced the first complete genome of F. philomiragia
      strain ATCC 25017, which was isolated as a free-living microorganism from water
      in Bear River Refuge, Utah.
AU  - Zeytun A
AU  - Malfatti SA
AU  - Vergez LM
AU  - Shin M
AU  - Garcia E
AU  - Chain PS
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3266.

PMID- 25657278
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Streptomyces sp. Strain CT34, Isolated from a Ghanaian Soil Sample.
PG  - e01508-14
AB  - Presented here is a draft genome sequence of Streptomyces sp. strain CT34, which  produces a
      novel ribosomally synthesized and posttranslationally modified peptide
      (RiPP). Analysis of the deduced open reading frame set identified the putative
      RiPP biosynthesis gene cluster, as well as other secondary metabolite gene
      clusters.
AU  - Zhai Y
AU  - Cheng B
AU  - Hu J
AU  - Kyeremeh K
AU  - Wang X
AU  - Jaspars M
AU  - Deng H
AU  - Deng ZX
AU  - Hong K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01508-14.

PMID- 24999826
VI  - 9
DP  - 2014
TI  - Genome Sequence of Candidatus Nitrososphaera evergladensis from Group I.1b Enriched from Everglades Soil Reveals Novel Genomic Features of the  Ammonia-Oxidizing Archaea.
PG  - e101648
AB  - The activity of ammonia-oxidizing archaea (AOA) leads to the loss of nitrogen from soil,
      pollution of water sources and elevated emissions of greenhouse gas.
      To date, eight AOA genomes are available in the public databases, seven are from
      the group I.1a of the Thaumarchaeota and only one is from the group I.1b,
      isolated from hot springs. Many soils are dominated by AOA from the group I.1b,
      but the genomes of soil representatives of this group have not been sequenced and
      functionally characterized. The lack of knowledge of metabolic pathways of soil
      AOA presents a critical gap in understanding their role in biogeochemical cycles.
      Here, we describe the first complete genome of soil archaeon Candidatus
      Nitrososphaera evergladensis, which has been reconstructed from metagenomic
      sequencing of a highly enriched culture obtained from an agricultural soil. The
      AOA enrichment was sequenced with the high throughput next generation sequencing
      platforms from Pacific Biosciences and Ion Torrent. The de novo assembly of
      sequences resulted in one 2.95 Mb contig. Annotation of the reconstructed genome
      revealed many similarities of the basic metabolism with the rest of sequenced
      AOA. Ca. N. evergladensis belongs to the group I.1b and shares only 40% of
      whole-genome homology with the closest sequenced relative Ca. N. gargensis.
      Detailed analysis of the genome revealed coding sequences that were completely
      absent from the group I.1a. These unique sequences code for proteins involved in
      control of DNA integrity, transporters, two-component systems and versatile
      CRISPR defense system. Notably, genomes from the group I.1b have more gene
      duplications compared to the genomes from the group I.1a. We suggest that the
      presence of these unique genes and gene duplications may be associated with the
      environmental versatility of this group.
AU  - Zhalnina KV
AU  - Dias R
AU  - Leonard MT
AU  - Dorr-de-Quadros P
AU  - Camargo FA
AU  - Drew JC
AU  - Farmerie WG
AU  - Daroub SH
AU  - Triplett EW
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2014 9: e101648.

PMID- 20802047
VI  - 192
DP  - 2010
TI  - Draft Genome Sequences of Actinobacillus pleuropneumoniae Serotypes 2 and 6.
PG  - 5846-5847
AB  - Actinobacillus pleuropneumoniae is a bacterial pathogen that causes highly contagious
      respiratory infection in pigs and has a serious impact on the
      production economy and animal welfare. As clear differences in virulence
      between serotypes have been observed, the genetic basis should be
      investigated at the genomic level. Here, we present the draft genome
      sequences of the A. pleuropneumoniae serotypes 2 (strain 4226) and 6
      (strain Femo).
AU  - Zhan B
AU  - Angen O
AU  - Hedegaard J
AU  - Bendixen C
AU  - Panitz F
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 5846-5847.

PMID- 21441526
VI  - 193
DP  - 2011
TI  - Genome Sequence of Acinetobacter calcoaceticus PHEA-2, Isolated from Industry Wastewater.
PG  - 2672-2673
AB  - Genome analysis of Acinetobacter calcoaceticus PHEA-2 was undertaken because of the importance
      of this bacterium for bioremediation of phenol
      polluted waster, and because of the close phylogenetic relationship of
      this species with the human pathogen A. baumannii. To our knowledge, this
      is the first strain of A. calcoaceticus whose genome has been sequenced.
AU  - Zhan Y
AU  - Yan Y
AU  - Zhang W
AU  - Yu H
AU  - Chen M
AU  - Lu W
AU  - Ping S
AU  - Peng Z
AU  - Yuan M
AU  - Zhou Z
AU  - Elmerich C
AU  - Lin M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 2672-2673.

PMID- 22026465
VI  - 12
DP  - 2011
TI  - Comparative Genomic Analysis of Streptococcus suis reveals significant genomic diversity among different serotypes.
PG  - 523
AB  - ABSTRACT:  BACKGROUND: Streptococcus suis (S. suis) is a major swine
      pathogen and an emerging zoonotic agent. Serotypes 1, 2, 3, 7, 9, 14 and
      1/2 are the most prevalent serotypes of this pathogen. However, almost all
      studies were carried out on serotype 2 strains. Therefore,
      characterization of genomic features of other serotypes will be required
      to better understand their virulence potential and phylogenetic
      relationships among different serotypes. RESULTS: Four Chinese S. suis
      strains belonging to serotypes 1, 7, 9 and 1/2 were sequenced using a
      rapid, high-throughput approach. Based on the 13 corresponding serotype
      strains, including 9 previously completed genomes of this bacterium, a
      full comparative genomic analysis was performed. The results provide
      evidence that (i) the pan-genome of this species is open and the size
      increases with addition of new sequenced genomes, (ii) strains of
      serotypes 1, 3, 7 and 9 are phylogenetically distinct from serotype 2
      strains, but all serotype 2 strains, plus the serotype 1/2 and 14 strains,
      are very closely related. (iii) all these strains, except for the serotype
      1 strain, could harbor a recombinant site for a pathogenic island (89K)
      mediated by conjugal transfer, and may have the ability to gain the 89K
      sequence. CONCLUSIONS: There is significant genomic diversity among
      different strains in S. suis, and the gain and loss of large amount of
      genes are involved in shaping their genomes. This is indicated by (i)
      pairwise gene content comparisons between every pair of these strains,
      (ii) the open pan-genome of this species, (iii) the observed indels,
      invertions and rearrangements in the collinearity analysis. Phylogenetic
      relationships may be associated with serotype, as serotype 2 strains are
      closely related and distinct from other serotypes like 1, 3, 7 and 9, but
      more strains need to be sequenced to confirm this.
AU  - Zhang A
AU  - Yang M
AU  - Hu P
AU  - Wu J
AU  - Chen B
AU  - Hua Y
AU  - Yu J
AU  - Chen H
AU  - Xiao J
AU  - Jin M
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2011 12: 523.

PMID- 
VI  - 28
DP  - 2008
TI  - Initial investigation on restriction modification system of Streptomyces ahygroscopicus wuzhouensis neosubsp.
PG  - 65-68
AB  - Adopting mycelium embedment in situ method and high voltage pulse electrophorsis two bands of
      plasmid DNA from Streptomyces ahygroscopicus wuzhouensis neosubsp.  11371 (SAWNS) were
      obtained, and they were linear molecules proved by bidirectionary electrophoresis and named as
      pSAL1 and pSAL2 according to molecular weights from large to small successively.  Furthermore,
      an initial investigation on SAWNS' restriction modification system was carried out, a copy of
      plasmid pIJ702 from Streptomyces lividus TK54 was used to transfer plasma of SAWN and could
      not obtain any transformant, however it succeeded to transform plasma of SAWN U-3 and obtained
      a transformant.
AU  - Zhang B
AU  - Li L
AU  - Chen F
AU  - Guan Y
PT  - Journal Article
TA  - Weishengwuxue Zazhi
JT  - Weishengwuxue Zazhi
SO  - Weishengwuxue Zazhi 2008 28: 65-68.

PMID- 8451189
VI  - 21
DP  - 1993
TI  - The M.AluI DNA-(cytosine C5)-methyltransferase has an unusually large, partially dispensable, variable region.
PG  - 905-911
AB  - The DNA methyltransferase of the AluI restriction-modification system, from Arthrobacter
      luteus, converts cytosine to 5-methylcytosine in the sequence AGCT. The gene for this
      methyltransferase, aluIM, was cloned into Escherichia coli and sequenced. A 525-codon open
      reading frame was found, consistent with deletion evidence, and the deduced amino acid
      sequence revealed all ten conserved regions common to 5-methylcytosine methyltransferases. The
      aluIM sequence predicts a protein of Mr 59.0K, in agreement with the observed Mr, making
      M.AluI the largest known methyltransferase from a type II restriction-modification system.
      M.AluI also contains the largest known variable region of any monospecific DNA
      methyltransfese, larger than that of most multispecific methyltransferases. In other DNA
      methyltransferases the variable region has been implicated as the sequence-specific target
      recognition domain. An in-frame deletion that removes a third of this putative
      target-recognition region leaves the AluI methyltransferase still fully active.
AU  - Zhang B
AU  - Tao T
AU  - Wilson GG
AU  - Blumenthal RM
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1993 21: 905-911.

PMID- 28031198
VI  - 61
DP  - 2016
TI  - A phage-like IncY plasmid carrying mcr-1 gene in an Escherichia coli strain from pig farm in China.
PG  - e02035-16
AB  - We report here a new type of plasmid that carries the mcr-1 gene, the pMCR-1-P3 plasmid,
      harbored in an Escherichia coli strain isolated from a pig farm in China. pMCR-1-P3 belongs to
      the IncY incompatibility group and is a phage-like plasmid that contains a large portion of
      phage-related sequences. The backbone of this plasmid is different from that of other
      mcr-1-carrying plasmids reported previously.
AU  - Zhang C
AU  - Feng Y
AU  - Liu F
AU  - Jiang H
AU  - Qu Z
AU  - Lei M
AU  - Wang J
AU  - Zhang B
AU  - Hu Y
AU  - Ding J
AU  - Zhu B
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2016 61: e02035-16.

PMID- 29371370
VI  - 6
DP  - 2018
TI  - Draft Genome Sequences of Two Psychrotolerant Strains, Colwellia polaris MCCC 1C00015(T) and Colwellia chukchiensis CGMCC 1.9127(T).
PG  - e01575-17
AB  - Colwellia polaris MCCC 1C00015(T) and Colwellia chukchiensis CGMCC 1.9127(T) are
      psychrotolerant bacteria isolated from the Canadian Basin and Chukchi Sea,
      respectively. Here, we report the draft genome sequences of C. polaris MCCC
      1C00015(T) and C. chukchiensis CGMCC 1.9127(T), which will help reveal how they
      adapt to cold environments.
AU  - Zhang C
AU  - Guo W
AU  - Wang Y
AU  - Chen X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01575-17.

PMID- 24905599
VI  - 26C
DP  - 2014
TI  - The purifying trend in the chromosomal integron in Vibrio cholerae strains during the seventh pandemic.
PG  - 241-249
AB  - Chromosomal integron (CI) arrays in Vibrio spp. are generally large and display great
      variation. Here we determined the sequence of CI array in a toxigenic O139 Vibriocholerae
      strain and compared it with the arrays from the genome of different O1 biotypes available in
      GenBank. Then PCR scanning was used to determine the CI array variations in 83 epidemic O139
      strains and subsequently these variations were compared with that found in toxigenic O1 El Tor
      strains in our previous work. Few differences were observed in the cohort of toxigenic O139
      strains compared to the toxigenic O1 El Tor strains. On the basis of CI arrays, the toxigenic
      O1 El Tor and O139 strains isolated concurrently in recent years appear to be more similar to
      each other than to the O1 strains isolated in previous decades, suggesting a closer
      evolutionary relationship between them.
      Comparison of CI arrays in toxigenic O1 El Tor and O139 V. cholerae strains isolated between
      1961 and 2009 revealed a purifying trend in the CI arrays in the chronological order during
      the seventh pandemic.
AU  - Zhang C
AU  - Pang B
AU  - Zhou Z
AU  - Wang H
AU  - Zhou H
AU  - Lu X
AU  - Du P
AU  - Zhang L
AU  - Li J
AU  - Cui Z
AU  - Chen C
AU  - Stokes HW
AU  - Kan B
PT  - Journal Article
TA  - Infect. Genet. Evol.
JT  - Infect. Genet. Evol.
SO  - Infect. Genet. Evol. 2014 26C: 241-249.

PMID- 24604641
VI  - 2
DP  - 2014
TI  - Genome Sequence of Escherichia coli Strain LCT-EC52, Which Acquired Changes in Antibiotic Resistance Properties after the Shenzhou-VIII Mission.
PG  - e00081-14
AB  - Escherichia coli is a ubiquitous opportunistic pathogen that colonizes the lower  intestines
      of humans and causes several diseases, such as septicemia, pneumonia,
      and urinary tract infections. Here, we present the draft genome sequence of E.
      coli strain LCT-EC52, which originated from E. coli strain CGMCC 1.2385 and
      acquired changes in antibiotic resistance following travel on the Shenzhou-VIII
      spacecraft.
AU  - Zhang D
AU  - Chang D
AU  - Zhang X
AU  - Yu Y
AU  - Guo Y
AU  - Wang J
AU  - Li T
AU  - Xu G
AU  - Dai W
AU  - Liu C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00081-14.

PMID- 25931596
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Rhodococcus sp. B7740, a Carotenoid-Producing Bacterium Isolated from the Arctic Sea.
PG  - e00333-15
AB  - Rhodococcus sp. B7740 was isolated from Arctic seawater and selected for its capacity to
      synthesize carotenoids. Here, we report the complete genome sequence
      of Rhodococcus sp. B7740 to provide the genetic basis for a better understanding
      of its carotenoid-accumulating capabilities, and we describe the major features
      of the genome.
AU  - Zhang D
AU  - Li L
AU  - Zhu S
AU  - Zhang N
AU  - Yang J
AU  - Ma X
AU  - Chen J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00333-15.

PMID- 25744987
VI  - 3
DP  - 2015
TI  - Draft Genome Sequences of Acinetobacter harbinensis Strain HITLi 7T, Isolated from River Water.
PG  - e00028-15
AB  - Acinetobacter harbinensis HITLi strain 7(T), isolated from river water, has the ability to
      remove ammonium and organic chemicals at 2 degrees C. The genome
      sequences might be useful for investigating the low-temperature adaptability and
      nitrogen or organic chemical metabolism.
AU  - Zhang D
AU  - Li W
AU  - Qin W
AU  - Huang X
AU  - Gong X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00028-15.

PMID- 27856595
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Pseudomonas mosselii Gil3, Isolated from Catfish and Antagonistic against Hypervirulent Aeromonas hydrophila.
PG  - e01305-16
AB  - Pseudomonas mosselii Gil3 was isolated from a catfish that survived from lethal challenge with
      hypervirulent Aeromonas hydrophila (vAh). When assayed in vitro,
      the bacterium showed antagonism against vAh. Sequence analysis revealed that the
      genome of P. mosselii Gil3 encodes numerous aromatic metabolism pathways and
      proteins for biosynthesis of antimicrobial compounds.
AU  - Zhang D
AU  - Xu DH
AU  - Qiu J
AU  - Rasmussen-Ivey CR
AU  - Liles MR
AU  - Beck BH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01305-16.

PMID- 26205856
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Thermophilic Exiguobacterium sp. Strain JLM-2, Isolated  from Deep-Sea Ferromanganese Nodules.
PG  - e00794-15
AB  - Exiguobacterium sp. strain JLM-2 is a thermophilic bacterium isolated from deep-sea
      ferromanganese (FeMn) nodules. The estimated genome of this strain is
      2.9 Mb, with a G+C content of 48.32%. It has a novel circular 15,570-bp plasmid.
      The draft genome sequence may provide useful information about Mn-microbe
      interactions and the genetic basis for tolerance to environment stresses.
AU  - Zhang DC
AU  - Liu YX
AU  - Huo YY
AU  - Xu XW
AU  - Li XZ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00794-15.

PMID- 27081136
VI  - 4
DP  - 2016
TI  - Genome Sequence of Salegentibacter mishustinae KCTC 12263, Containing a Complete  Subtype I-B CRISPR-Cas System.
PG  - e00267-16
AB  - Salegentibacter mishustinaeKCTC strain 12263 was isolated from the sea
      urchinStrongylocentrotus intermediusinhabiting the Sea of Japan. Here, we report
      the draft genome sequence ofSalegentibacter mishustinaeKCTC 12263. It comprises
      ~3.78 Mb in 38 contigs with a G+C content of 36.5%, and a total of 3,490
      proteins-coding genes were obtained. One complete CRISPR-Cas gene cluster was
      identified in the genome, which shows the strategy against invasive genetic
      elements of the strain.
AU  - Zhang F
AU  - Lin W
AU  - Zhang R
AU  - Zheng Q
AU  - Jiao N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00267-16.

PMID- 27408680
VI  - 10
DP  - 2015
TI  - High quality genome sequence and description of Enterobacter mori strain 5-4, isolated from a mixture of formation water and crude-oil.
PG  - 9
AB  - Enterobacter mori strain 5-4 is a Gram-negative, motile, rod shaped, and facultatively
      anaerobic bacterium, which was isolated from a mixture of formation
      water (also known as oil-reservior water) and crude-oil in Karamay oilfield,
      China. To date, there is only one E. mori genome has been sequenced and very
      little knowledge about the mechanism of E. mori adapted to the petroleum
      reservoir. Here, we report the second E. mori genome sequence and annotation,
      together with the description of features for this organism. The 4,621,281 bp
      assembly genome exhibits a G + C content of 56.24% and contains 4,317
      protein-coding and 65 RNA genes, including 5 rRNA genes.
AU  - Zhang F
AU  - Su S
AU  - Yu G
AU  - Zheng B
AU  - Shu F
AU  - Wang Z
AU  - Xiang T
AU  - Dong H
AU  - Zhang Z
AU  - Hou D
AU  - She Y
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 9.

PMID- 21515778
VI  - 193
DP  - 2011
TI  - Complete genome sequence of Bacillus amyloliquefaciens TA208, a strain for industrial production of guanosine and ribavirin.
PG  - 3142-3143
AB  - Here, we report the complete genome sequence of Bacillus amyloliquefaciens TA208, a strain for
      industrial production of guanosine, and synthesis of
      ribavirin by assimilation of formamide. Comparison of its genome sequence
      with those of the strains DSM7 and FZB42 revealed horizontal gene transfer
      represented by unique prophages and restriction-modification systems and
      indicated significant accumulation of guanosine.
AU  - Zhang G
AU  - Deng A
AU  - Xu Q
AU  - Liang Y
AU  - Chen N
AU  - Wen T
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 3142-3143.

PMID- 25990724
VI  - 43
DP  - 2015
TI  - Small RNA-mediated DNA (cytosine-5) methyltransferase 1 inhibition leads to aberrant DNA methylation.
PG  - 6112-6124
AB  - Mammalian cells contain copious amounts of RNA including both coding and noncoding RNA
      (ncRNA). Generally the ncRNAs function to regulate gene expression
      at the transcriptional and post-transcriptional level. Among ncRNA, the long
      ncRNA and small ncRNA can affect histone modification, DNA methylation targeting
      and gene silencing. Here we show that endogenous DNA methyltransferase 1 (DNMT1)
      co-purifies with inhibitory ncRNAs. MicroRNAs (miRNAs) bind directly to DNMT1
      with high affinity. The binding of miRNAs, such as miR-155-5p, leads to
      inhibition of DNMT1 enzyme activity. Exogenous miR-155-5p in cells induces
      aberrant DNA methylation of the genome, resulting in hypomethylation of low to
      moderately methylated regions. And small shift of hypermethylation of previously
      hypomethylated region was also observed. Furthermore, hypomethylation led to
      activation of genes. Based on these observations, overexpression of miR-155-5p
      resulted in aberrant DNA methylation by inhibiting DNMT1 activity, resulting in
      altered gene expression.
AU  - Zhang G
AU  - Esteve PO
AU  - Chin HG
AU  - Terragni J
AU  - Dai N
AU  - Correa IR Jr
AU  - Pradhan S
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2015 43: 6112-6124.

PMID- 26966216
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Two Thiomicrospira Strains Isolated from the Brine-Seawater Interface of Kebrit Deep in the Red Sea.
PG  - e00110-16
AB  - Two Thiomicrospira strains, WB1 and XS5, were isolated from the Kebrit Deep brine-seawater
      interface in the Red Sea, Saudi Arabia. Here, we present the draft
      genome sequences of these gammaproteobacteria, which both produce sulfuric acid
      from thiosulfate in culture.
AU  - Zhang G
AU  - Fauzi HM
AU  - Zhang R
AU  - Hikmawan T
AU  - Stingl U
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00110-16.

PMID- 26966209
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Pseudoalteromonas sp. Strain XI10 Isolated from the Brine-Seawater Interface of Erba Deep in the Red Sea.
PG  - e00109-16
AB  - Pseudoalteromonas sp. strain XI10 was isolated from the brine-seawater interface  of Erba Deep
      in the Red Sea, Saudi Arabia. Here, we present the draft genome
      sequence of strain XI10, a gammaproteobacterium that synthesizes polysaccharides
      for biofilm formation when grown in liquid culture.
AU  - Zhang G
AU  - Fauzi HM
AU  - Zhang R
AU  - Hikmawan T
AU  - Stingl U
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00109-16.

PMID- 28912307
VI  - 5
DP  - 2017
TI  - Genome Sequence of Staphylococcus aureus PX03, an Acetoin-Producing Strain with a Small-Sized Genome.
PG  - e00753-17
AB  - Staphylococcus aureus PX03 can produce acetoin efficiently. Here, we present a 2.38-Mb
      assembly of its genome sequence, which might provide further insights
      into the molecular mechanism of its acetoin biosynthesis to further improve its
      biotechnological applications.
AU  - Zhang G
AU  - Wang Q
AU  - Su Y
AU  - Li S
AU  - Liu H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00753-17.

PMID- 23028379
VI  - 8
DP  - 2012
TI  - A Mimicking-of-DNA-Methylation-Patterns Pipeline for Overcoming the Restriction Barrier of Bacteria.
PG  - e1002987
AB  - Genetic transformation of bacteria harboring multiple Restriction-Modification (R-M) systems
      is often difficult using
      conventional methods. Here, we describe a
      mimicking-of-DNA-methylation-patterns (MoDMP) pipeline to address this
      problem in three difficult-to-transform bacterial strains. Twenty-four
      putative DNA methyltransferases (MTases) from these
      difficult-to-transform strains were cloned and expressed in an
      Escherichia coli strain lacking all of the known R-M systems and orphan
      MTases. Thirteen of these MTases exhibited DNA modification activity in
      Southwestern dot blot or Liquid Chromatography-Mass Spectrometry
      (LC-MS) assays. The active MTase genes were assembled into three
      operons using the Saccharomyces cerevisiae DNA assembler and were
      co-expressed in the E. coli strain lacking known R-M systems and orphan
      MTases. Thereafter, results from the dot blot and restriction enzyme
      digestion assays indicated that the DNA methylation patterns of the
      difficult-to-transform strains are mimicked in these E. coli hosts. The
      transformation of the Gram-positive Bacillus amyloliquefaciens TA208
      and B. cereus ATCC 10987 strains with the shuttle plasmids prepared
      from MoDMP hosts showed increased efficiencies (up to four orders of
      magnitude) compared to those using the plasmids prepared from the E.
      coli strain lacking known R-M systems and orphan MTases or its parental
      strain. Additionally, the gene coding for uracil
      phosphoribosyltransferase (upp) was directly inactivated using
      non-replicative plasmids prepared from the MoDMP host in B.
      amyloliquefaciens TA208. Moreover, the Gram-negative chemoautotrophic
      Nitrobacter hamburgensis strain X14 was transformed and expressed Green
      Fluorescent Protein (GFP). Finally, the sequence specificities of
      active MTases were identified by restriction enzyme digestion, making
      the MoDMP system potentially useful for other strains. The
      effectiveness of the MoDMP pipeline in different bacterial groups
      suggests a universal potential. This pipeline could facilitate the
      functional genomics of the strains that are difficult to transform.
AU  - Zhang G
AU  - Wang W
AU  - Deng A
AU  - Sun Z
AU  - Zhang Y
AU  - Liang Y
AU  - Che Y
AU  - Wen T
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2012 8: e1002987.

PMID- 25676772
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Acinetobacter sp. Strain YZS-X1-1, a Denitrifying Bacterium Isolated from Freshwater Pond Sludge in China.
PG  - e01579-14
AB  - Acinetobacter sp. strain YZS-X1-1 was isolated from freshwater pond sludge in China. Here, we
      present the draft genome of strain YZS-X1-1, which consists of
      3,278,660 bases, with a G+C content of 42.1%.
AU  - Zhang H
AU  - Li X
AU  - Zhang B
AU  - Liu C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01579-14.

PMID- 27563046
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Alcanivorax sp. Strain KX64203 Isolated from Deep-Sea Sediments of Iheya North, Okinawa Trough.
PG  - e00872-16
AB  - This report describes the draft genome sequence of Alcanivorax sp. strain KX64203, isolated
      from deep-sea sediment samples. The reads generated by an Ion
      Torrent PGM were assembled into contigs, with a total size of 4.76 Mb. The data
      will improve our understanding of the strain's function in alkane degradation.
AU  - Zhang H
AU  - Liu R
AU  - Wang M
AU  - Wang H
AU  - Gao Q
AU  - Hou Z
AU  - Gao D
AU  - Wang L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00872-16.

PMID- 27563045
VI  - 4
DP  - 2016
TI  - Draft Genome Sequences of Pseudoalteromonas telluritireducens DSM 16098 and P. spiralis DSM 16099 Isolated from the Hydrothermal Vents of the Juan de Fuca  Ridge.
PG  - e00871-16
AB  - This report describes the draft genome sequences of two strains, Pseudoalteromonas
      telluritireducens DSM 16098 and P. spiralis DSM 16099, which
      were isolated from hydrothermal vents of the Juan de Fuca Ridge. The reads
      generated by an Ion Torrent PGM were assembled into contigs with total sizes of
      4.4 Mb and 4.1 Mb for DSM 16098 and DSM 16099, respectively.
AU  - Zhang H
AU  - Liu R
AU  - Wang M
AU  - Wang H
AU  - Gao Q
AU  - Hou Z
AU  - Zhou Z
AU  - Gao D
AU  - Wang L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00871-16.

PMID- 29472344
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Actinobacillus succinogenes GXAS137, a Highly Efficient Producer of Succinic Acid.
PG  - e01562-17
AB  - The bacterium Actinobacillus succinogenes GXAS137, an efficient producer of succinic acid, was
      isolated from bovine rumen in Nanning, Guangxi Province,
      China. Here, we present the 2.3-Mb genome assembly of this strain, which consists
      of 2,314,479 bp (G+C content of 44.89%) with a circular chromosome, 2,235 DNA
      coding sequences, 57 tRNAs, and 15 rRNAs.
AU  - Zhang H
AU  - Shen N
AU  - Qin Y
AU  - Zhu J
AU  - Li Y
AU  - Wu J
AU  - Jiang MG
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01562-17.

PMID- 25477414
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Anti-Algal Marine Actinomycete Streptomyces sp. JS01.
PG  - e01261-14
AB  - Streptomyces sp. JS01 is the producer of an anti-algal compound that shows inhibitory activity
      against a harmful algal species Phaeocystis globosa and can
      also produce a red pigment. Its genome sequence will allow for the
      characterization of the anti-algal compound and the molecular mechanisms
      underlying its beneficial properties.
AU  - Zhang H
AU  - Zhang S
AU  - Peng Y
AU  - Li Y
AU  - Chen Z
AU  - Zheng W
AU  - Xu H
AU  - Yu Z
AU  - Zheng T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01261-14.

PMID- 23516178
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Streptomyces bottropensis ATCC 25435, a Bottromycin-Producing Actinomycete.
PG  - e0001913
AB  - A series of bottromycin antibiotics have been isolated and identified from Streptomyces
      bottropensis strain ATCC 25435. Here, a draft genome sequence of S.
      bottropensis ATCC 25435 is presented. The genome carries an intact biosynthetic
      gene cluster for bottromycin antibiotics, which provides insight into the
      combinatorial biosynthesis of bottromycin antibiotics.
AU  - Zhang H
AU  - Zhou W
AU  - Zhuang Y
AU  - Liang X
AU  - Liu T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0001913.

PMID- 23469342
VI  - 1
DP  - 2013
TI  - Draft Genome Sequences of Three Salmonella enterica Serotype Agona Strains from China.
PG  - e00203-12
AB  - Salmonellosis has been one of the major contributors to the global public health  burden.
      serotype Agona has ranked among the top 10 and top 20 most frequent
      serotypes isolated from human sources in China and the United States,
      respectively. We report draft genomes of three Agona strains from China.
AU  - Zhang J
AU  - Cao G
AU  - Xu X
AU  - Jin H
AU  - Yang X
AU  - Allard M
AU  - Brown E
AU  - Meng J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00203-12.

PMID- 23661485
VI  - 1
DP  - 2013
TI  - Whole-Genome Sequences of Four Salmonella enterica Serotype Newport Strains from  Humans.
PG  - e00213-13
AB  - Salmonellosis contributes significantly to the public health burden globally. Salmonella
      enterica serotype Newport is among Salmonella serotypes most
      associated with food-borne illness in the United States and China. It was thought
      to be polyphyletic and to contain different lineages. We report draft genomes of
      four S. Newport strains isolated from humans in China.
AU  - Zhang J
AU  - Cao G
AU  - Xu X
AU  - Jin H
AU  - Zhang Q
AU  - Chen J
AU  - Yang X
AU  - Pan H
AU  - Zhang X
AU  - Allard M
AU  - Brown E
AU  - Meng J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00213-13.

PMID- 29439028
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Anaerobic Fermentative Bacterium Anaeromicrobium sediminis DY2726D.
PG  - e00002-18
AB  - Here, we report the draft genome sequence of Anaeromicrobium sediminis DY2726D, isolated from
      a west Pacific Ocean sediment sample. The genome comprises
      4,710,590 bp in 56 contigs, with a G+C content of 31.2%. A total of 3,811
      protein-coding sequences were predicted. The genome annotation revealed that
      DY2726D may represent a marine type of Clostridiaceae.
AU  - Zhang J
AU  - Hu J
AU  - Zhang X
AU  - Zeng X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00002-18.

PMID- 25720687
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Pantoea sp. Strain MBLJ3, Isolated in a Laboratory Environmental Control Study.
PG  - e01595-14
AB  - This report describes the draft genome sequence of a newly isolated strain, Pantoea sp. MBLJ3.
      The genome is 4.8 Mb in size, with a G+C content of 54.27%, and it contains 4,522
      protein-coding sequences, 69 tRNA genes, and 5 rRNA genes.
AU  - Zhang J
AU  - Hung GC
AU  - Lei H
AU  - Li T
AU  - Li B
AU  - Tsai S
AU  - Lo SC
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01595-14.

PMID- 29496840
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Ehrlichia canis Strain YZ-1, Isolated from a Beagle with Fever and Thrombocytopenia.
PG  - e00133-18
AB  - We report the complete genome sequence of Ehrlichia canis strain YZ-1, which was  isolated
      from a beagle with fever, anorexia, depression, lethargy, weight loss,
      and thrombocytopenia. E. canis is the tick-borne agent of canine and human
      monocytic ehrlichiosis.
AU  - Zhang J
AU  - Wang J
AU  - Wang C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00133-18.

PMID- 28232422
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Carbendazim-Degrading Mycobacterium sp. Strain djl-10.
PG  - e01683-16
AB  - Mycobacterium sp. strain djl-10, an efficient degrader of carbendazim, was isolated from a
      carbendazim manufacturing wastewater treatment system. Here, we
      report the complete genome sequence of djl-10, which consists of a chromosome and
      three plasmids.
AU  - Zhang J
AU  - Yuan Q
AU  - Yang W
AU  - Wang X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01683-16.

PMID- 23766402
VI  - 1
DP  - 2013
TI  - Genome Sequence of the Banana Pathogen Dickeya zeae Strain MS1, Which Causes Bacterial Soft Rot.
PG  - e00317-13
AB  - We report a draft genome sequence of Dickeya zeae strain MS1, which is the causative agent of
      banana soft rot in China, and we show several of its specific
      properties compared with those of other D. zeae strains. Genome sequencing
      provides a tool for understanding the genomic determination of the pathogenicity
      and phylogeny placement of this pathogen.
AU  - Zhang JX
AU  - Lin BR
AU  - Shen HF
AU  - Pu XM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00317-13.

PMID- 26823957
VI  - 11
DP  - 2016
TI  - Complete genome sequence and genomic characterization of Microcystis panniformis  FACHB 1757 by third-generation sequencing.
PG  - 11
AB  - The cyanobacterial genus Microcystis is well known as the main group that forms harmful blooms
      in water. A strain of Microcystis, M. panniformis FACHB1757, was
      isolated from Meiliang Bay of Lake Taihu in August 2011. The whole genome was
      sequenced using PacBio RS II sequencer with 48-fold coverage. The complete genome
      sequence with no gaps contained a 5,686,839 bp chromosome and a 38,683 bp
      plasmid, which coded for 6,519 and 49 proteins, respectively. Comparison with
      strains of M. aeruginosa and some other water bloom-forming cyanobacterial
      species revealed large-scale structure rearrangement and length variation at the
      genome level along with 36 genomic islands annotated genome-wide, which
      demonstrates high plasticity of the M. panniformis FACHB1757 genome and reveals
      that Microcystis has a flexible genome evolution.
AU  - Zhang JY
AU  - Guan R
AU  - Zhang HJ
AU  - Li H
AU  - Xiao P
AU  - Yu GL
AU  - Du L
AU  - Cao DM
AU  - Zhu BC
AU  - Li RH
AU  - Lu ZH
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 11.

PMID- 19064897
VI  - 53
DP  - 2009
TI  - Novel Staphylococcal Cassette Chromosome mec Type, Tentatively Designated Type VIII, Harboring Class A mec and Type 4 ccr Gene Complexes in a Canadian Epidemic Strain of Methicillin-Resistant Staphylococcus aureus.
PG  - 531-540
AB  - Staphylococcal cassette chromosome mec (SCCmec) is a mobile genetic
      element characterized by flanking terminal direct and, in most cases,
      inverted repeat sequences, the mec and ccr gene complexes, and their
      surrounding DNA regions. Unique combinations of the mec and ccr gene
      complexes generate various SCCmec types. Six SCCmec types have been
      reported to date. We describe here a novel SCCmec type identified in a
      Canadian methicillin-resistant Staphylococcus aureus (MRSA) epidemic
      strain. MRSA clinical isolates were screened for known SCCmec types by
      multiplex and conventional PCR methods. Three phenotypically and
      genotypically identical MRSA clinical isolates with a pulsotype identical
      to CMRSA9 were identified locally and found to be nontypeable by available
      SCCmec typing schemes. Complete sequencing of the SCCmec element revealed
      a nucleotide fragment of 32,168 bp integrated at an identical chromosomal
      integration site (attBscc) at the 3' end of the orfX gene. The nucleotide
      sequences at the chromosome-SCCmec junction regions were typical of other
      SCCmec types, but the element harbored a unique combination of class A mec
      and type 4 ccr gene complexes. Sequence recombination analysis suggested
      that this unique SCCmec type may be derived from homologous recombination
      between the previously described SCC(RP62A) of S. epidermidis strain RP62A
      and SCC composite island of S. epidermidis ATCC 12228, respectively, or
      via recombination of other staphylococcal strains that carry the same or
      similar mobile cassettes. We identified a previously undescribed type of
      SCCmec from isolate C10682, tentatively designated type VIII, and we
      provide compelling evidence supporting the ability of SCC elements to
      transfer horizontally or undergo recombination to generate new SCCmec
      types.
AU  - Zhang K
AU  - McClure JA
AU  - Elsayed S
AU  - Conly JM
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2009 53: 531-540.

PMID- 25197445
VI  - 9
DP  - 2014
TI  - Genomic analysis of Agrobacterium radiobacter DSM 30147(T) and emended description of A. radiobacter (Beijerinck and van Delden 1902) Conn 1942  (Approved Lists 1980) emend. Sawada et al. 1993.
PG  - 574-584
AB  - Agrobacterium radiobacter is the only known non-phytopathogenic species in Agrobacterium
      genus. In this study, the whole-genome sequence of A. radiobacter
      type strain DSM 30147(T) was described and compared to the other available
      Agrobacterium genomes. This bacterium has a genome size of 7,122,065 bp
      distributed in 612 contigs, including 6,834 protein-coding genes and 41 RNA
      genes. It harbors a circular chromosome and a linear chromosome but not a
      tumor-inducing (Ti) plasmid. To the best of our knowledge, this is the first
      report of a genome from the A. radiobacter species. In addition, an emended
      description of A. radiobacter is described. This study reveals information that
      enhances the current understanding of its non-phytopathogenicity and its
      phylogenetic position within Agrobacterium genus.
AU  - Zhang L
AU  - Li X
AU  - Zhang F
AU  - Wang G
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 574-584.

PMID- 23640378
VI  - 1
DP  - 2013
TI  - Genome Sequence of Stenotrophomonas maltophilia Strain AU12-09, Isolated from an  Intravascular Catheter.
PG  - e00195-13
AB  - Stenotrophomonas maltophilia is an opportunistic nosocomial pathogen that is characterized by
      its high-level intrinsic resistance to a variety of antibiotics
      and its ability to form biofilms. Here, we report the draft genome sequence of
      Stenotrophomonas maltophilia AU12-09, isolated from an intravascular catheter
      tip.
AU  - Zhang L
AU  - Morrison M
AU  - O'Cuiv P
AU  - Evans P
AU  - Rickard CM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00195-13.

PMID- 23144393
VI  - 194
DP  - 2012
TI  - Genome Sequence of Staphylococcus epidermidis Strain AU12-03, Isolated from an Intravascular Catheter.
PG  - 6639
AB  - In recent years, Staphylococcus epidermidis has become a major nosocomial pathogen and the
      most common cause of intravascular catheter-related bacteremia,
      which can increase morbidity and mortality and significantly affect patient
      recovery. We report a draft genome sequence of Staphylococcus epidermidis
      AU12-03, isolated from an intravascular catheter tip.
AU  - Zhang L
AU  - Morrison M
AU  - O'Cuiv P
AU  - Evans P
AU  - Rickard CM
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6639.

PMID- 24503988
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Ralstonia pickettii AU12-08, Isolated from an Intravascular Catheter in Australia.
PG  - e00027-14
AB  - Ralstonia pickettii is a nonfermenting Gram-negative bacillus that creates a significant
      problem in clinical settings, as it is a widespread cause of
      nosocomial infections. Here, we report the draft genome sequence of R. pickettii
      AU12-08, isolated from an intravascular catheter tip.
AU  - Zhang L
AU  - Morrison M
AU  - Rickard CM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00027-14.

PMID- 24699960
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Nafulsella turpanensis ZLM-10T, a Novel Member of the Family Flammeovirgaceae.
PG  - e00263-14
AB  - Nafulsella turpanensis ZLM-10(T) is a slightly halophilic, Gram-negative, rod-shaped, gliding,
      pale-pink-pigmented bacterium in the family Flammeovirgaceae, and it shows resistance to
      gentamicin, kanamycin, neomycin, and streptomycin. Here, we report the genome sequence of N.
      turpanensis strain ZLM-10(T), which has a 4.8-Mb genome and a G+C content of 45.67%.
AU  - Zhang L
AU  - Si M
AU  - Zhu L
AU  - Li C
AU  - Wei Y
AU  - Shen X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00263-14.

PMID- 8132471
VI  - 176
DP  - 1994
TI  - Isolation of an R- M+ mutant of Yersinia enterocolitica serotype O:8 and its application in construction of rough mutants utilizing mini-Tn5 derivatives and lipopolysaccharide-specific phage.
PG  - 1756-1760
AB  - A generally applicable procedure was used to isolate a spontaneous restriction-deficient
      mutant of Yersinia enterocolitica serotype O:8. Transposition frequency in the mutant strain
      8081-res was approximately 6.7 x 10-6 per recipient, while it was practically zero in the
      wild-type strain 8081-c. Mobilization frequency into 8081-res was 10/5 times higher than that
      into the wild-type strain. The mutant had lost the ability to express the YenI restriction
      endonuclease activity present in serotype 0:8 strains. This allowed the construction of a
      transposon library in 8081-res. Insertion mutants with transposons in the genes of the rfa
      region were selected from this library.
AU  - Zhang L
AU  - Skurnik M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1994 176: 1756-1760.

PMID- 28082486
VI  - 5
DP  - 2017
TI  - Whole-Genome Sequences of Mycobacterium tuberculosis TB282 and TB284, a Widespread and a Unique Strain, Respectively, Identified in a Previous Study of  Tuberculosis Transmission in Central Los Angeles, California, USA.
PG  - e01418-16
AB  - We report here the genome sequences of two Mycobacterium tuberculosis clinical isolates
      previously identified in central Los Angeles, CA, in the 1990s using a
      PacBio platform. Isolate TB282 represents a large-cluster strain that caused 27%
      of the tuberculosis cases, while TB284 represents a strain that caused disease in
      only one patient.
AU  - Zhang L
AU  - Yang Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01418-16.

PMID- 22956024
VI  - 29
DP  - 2013
TI  - Manufacture of Cheddar cheese using probiotic Lactobacillus plantarum K25 and its cholesterol-lowering effects in a mice model.
PG  - 127-135
AB  - The probiotic adjunct Lactobacillus plantarum K25 was inoculated into milk to
      produce probiotic cheese. The effect of Lb. plantarum K25 on cheese composition,
      microbiological growth and survival during the manufacturing and ripening period,
      primary and secondary proteolysis during cheese ripening, and the in vivo
      cholesterol-lowering ability of the probiotic cheese were investigated. The
      results showed that the use of adjunct Lb. plantarum K25 in Cheddar cheese did
      not affect the cheese components including moisture, protein, fat, salt content
      and the pH value of cheese. During the whole ripening period, the probiotic
      adjunct maintained its viability, suggesting the effectiveness of Cheddar cheese
      as a vehicle for delivery of probiotic bacteria. No significant differences were
      observed in water-soluble nitrogen, 70 % ethanol-soluble nitrogen, 5 %
      phosphotungstic acid-soluble nitrogen, free amino acids and urea-PAGE patterns
      between the control and probiotic cheeses. Assessment of the in vivo
      cholesterol-lowering property of cheese with Lb. plantarum K25 showed that the
      levels of serum total cholesterol, low-density lipoprotein cholesterol and
      triglycerides decreased significantly, and the level of serum high-density
      lipoprotein cholesterol increased in mice fed with the probiotic cheese. The
      results indicated the potential function as a dietary item of the probiotic
      cheese with Lb. plantarum K25 to reduce the risk of cardiovascular diseases.
AU  - Zhang L
AU  - Zhang X
AU  - Liu C
AU  - Li C
AU  - Li S
AU  - Li T
AU  - Li D
AU  - Zhao Y
AU  - Yang Z
PT  - Journal Article
TA  - World J. Microbiol. Biotechnol.
JT  - World J. Microbiol. Biotechnol.
SO  - World J. Microbiol. Biotechnol. 2013 29: 127-135.

PMID- 20674893
VI  - 95
DP  - 2011
TI  - Age-related changes in the localization of DNA methyltransferases during meiotic maturation in mouse oocytes.
PG  - 1531-1534
AB  - The effects of maternal aging on the localization of DNA methyltransferases were evaluated
      during mouse oocyte maturation using fluorescence staining. And we conclude that maternal
      aging affects the cytoplasmic-to-nuclear trafficking of DNA methyltransferases in mouse
      oocytes during the time from germinal vesicle breakdown to metaphase I.
AU  - Zhang Lu
AU  - Lu D-Y
AU  - Ma W-Y
AU  - Li Y
PT  - Journal Article
TA  - Fertil. Steril.
JT  - Fertil. Steril.
SO  - Fertil. Steril. 2011 95: 1531-1534.

PMID- 21124772
VI  - 5
DP  - 2010
TI  - Genomic characterization of the Guillain-Barre syndrome-associated Campylobacter jejuni ICDCCJ07001 Isolate.
PG  - e15060
AB  - Campylobacter jejuni ICDCCJ07001 (HS:41, ST2993) was isolated from a Guillain-Barre syndrome
      (GBS) patient during a 36-case GBS outbreak
      triggered by C. jejuni infections in north China in 2007. Sequence
      analysis revealed that the ICDCCJ07001 genome consisted of 1,664,840 base
      pairs (bp) and one tetracycline resistance plasmid of 44,084 bp. The GC
      content was 59.29% and 1,579 and 37 CDSs were identified on the chromosome
      and plasmid, respectively. The ICDCCJ07001 genome was compared to C.
      jejuni subsp. jejuni strains 81-176, 81116, NCTC11168, RM1221 and C.
      jejuni subsp. doylei 269.97. The length and organization of ICDCCJ07001
      was similar to that of NCTC11168, 81-176 and 81-116 except that CMLP1 had
      a reverse orientation in strain ICDCCJ07001. Comparative genomic analyses
      were also carried out between GBS-associated C. jejuni strains. Thirteen
      common genes were present in four GBS-associated strains and 9 genes
      mapped to the LOS cluster and the ICDCCJ07001_pTet (44 kb) plasmid was
      mosaic in structure. Thirty-seven predicted CDS in ICDCCJ07001_pTet were
      homologous to genes present in three virulence-associated plasmids in
      Campylobacter: 81-176_pTet, pCC31 and 81-176_pVir. Comparative analysis of
      virulence loci and virulence-associated genes indicated that the LOS
      biosynthesis loci of ICDCCJ07001 belonged to type A, previously reported
      to be associated with cases of GBS. The polysaccharide capsular
      biosynthesis (CPS) loci and the flagella modification (FM) loci of
      ICDCCJ07001 were similar to corresponding sequences of strain 260.94 of
      similar serotype as strain ICDCCJ07001. Other virulence-associated genes
      including cadF, peb1, jlpA, cdt and ciaB were conserved between the C.
      jejuni strains examined.
AU  - Zhang M
AU  - He L
AU  - Li Q
AU  - Sun H
AU  - Gu Y
AU  - You Y
AU  - Meng F
AU  - Zhang J
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2010 5: e15060.

PMID- 23571551
VI  - 57
DP  - 2013
TI  - Analysis of Staphylococcal cassette chromosome mec in BD GeneOhm MRSA assay-negative strains.
PG  - 2890-2891
AB  - The BD GeneOhm MRSA assay could identify methicillin-resistant Staphylococcus
      aureus (MRSA) strains at a high ratio (97.8%). Analysis of 11 assay-negative MRSA
      strains suggested that insertion of non-mec staphylococcal cassette chromosome
      elements (SCCs) downstream of orfX, and carriage of SCCmecs with a left extremity
      that cannot be detected by the kit, might lead to their being given an incorrect
      negative status.
AU  - Zhang M
AU  - Ito T
AU  - Li S
AU  - Misawa S
AU  - Kondo S
AU  - Miida T
AU  - Ohsaka A
AU  - Hiramatsu K
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2013 57: 2890-2891.

PMID- 20455754
VI  - 7
DP  - 2010
TI  - Association study between an outbreak of Guillain-Barre syndrome in Jilin, China, and preceding Campylobacter jejuni infection.
PG  - 913-919
AB  - From June to July 2007, 36 cases of Guillain-Barre syndrome (GBS) occurred
      in a township in north China. Serological study and bacteria culture were
      performed to investigate the association between preceding Campylobacter
      jejuni infection and this GBS outbreak. Anti-C. jejuni antibodies were
      found in significantly higher numbers of GBS patients (IgM 84%, IgG 87.5%)
      than in healthy inspection cases (IgM 33%, IgG 27%). IgG anti-GM1 was the
      dominant anti-ganglioside antibody among the GBS patients. Seven C. jejuni
      isolates (four from human stool and three from poultry specimens taken
      from the patients' houses) were obtained. Serotyping and molecular
      analysis were used to investigate the genetic relatedness among these C.
      jejuni isolates. The four human isolates, collected from residents of the
      same district, were indistinguishable by both pulsed-field gel
      electrophoresis and multilocus sequence typing, suggesting these patients
      had a common source of infection. A new sequence type, sequence type-2993,
      was assigned to the human C. jejuni isolates, three of which belonged to
      Penner serotype heat-stable (HS):41. Both serotype and molecular subtype
      of the human C. jejuni isolates were different from those of isolates
      obtained from poultry specimens. Our results suggest that the antecedent
      C. jejuni infection triggered this GBS outbreak in China.
AU  - Zhang M
AU  - Li Q
AU  - He L
AU  - Meng F
AU  - Gu Y
AU  - Zheng M
AU  - Gong Y
AU  - Wang P
AU  - Ruan F
AU  - Zhou L
AU  - Wu J
AU  - Chen L
AU  - Fitzgerald C
AU  - Zhang J
PT  - Journal Article
TA  - Foodborne Pathog. Dis.
JT  - Foodborne Pathog. Dis.
SO  - Foodborne Pathog. Dis. 2010 7: 913-919.

PMID- 28684578
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Pseudomonas stutzeri LH-42, Isolated from Petroleum-Contaminated Soil.
PG  - e00589-17
AB  - We used Illumina HiSeq technology to sequence the whole genome of Pseudomonas stutzeri LH-42,
      a bacterium isolated from petroleum-contaminated soil in Liaoning
      Province, China. The bacterium contains a series of specific genes involved in
      the oxidation of organic sulfur compounds.
AU  - Zhang M
AU  - Ma L
AU  - Yang Y
AU  - Hu T
AU  - Liu X
AU  - Zhang X
AU  - Hua Y
AU  - Gao Y
AU  - Zhu Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00589-17.

PMID- 23704181
VI  - 1
DP  - 2013
TI  - Genome Sequences of the Guillain-Barre Syndrome Outbreak-Associated Campylobacter jejuni Strains ICDCCJ07002 and ICDCCJ07004.
PG  - e00256-13
AB  - The first world-known and largest outbreak of 36 cases of Guillain-Barre syndrome caused by a
      preceding Campylobacter jejuni infection was reported previously in
      China. During the outbreak, Campylobacter jejuni strain ICDCCJ07002 was isolated
      from a patient with persistent diarrhea for 21 days, and C. jejuni strain
      ICDCCJ07004 was from a healthy carrier without any clinical symptoms at the same
      time. Here, we report the draft genome sequence of strain ICDCCJ07002 (1,698,407
      bp, with a G+C content of 30.45%) and the genome resequencing result of strain
      ICDCCJ07004 (1,701,584 bp, with a G+C content of 30.51%), and we compared these
      with the completed genome of C. jejuni strain ICDCCJ07001.
AU  - Zhang M
AU  - Yang X
AU  - Liu H
AU  - Liu X
AU  - Huang Y
AU  - He L
AU  - Gu Y
AU  - Zhang J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00256-13.

PMID- 17951612
VI  - 20
DP  - 2007
TI  - Rational design of a chimeric endonuclease targeted to NotI recognition site.
PG  - 497-504
AB  - A cleavage-deficient variant of NotI restriction endonuclease (GCGGCCGC) was isolated by
      random mutagenesis of the notIR gene. The NotI variant
      D160N was shown to bind DNA and protect plasmid DNA from EagI (CGGCCG) and
      NotI digestions. The EDTA-resistant BmrI restriction endonuclease cleaves
      DNA sequence ACTGGG N(5)/N(4). The N-terminal cleavage domain of BmrI
      (residues 1-198) with non-specific nuclease activity was fused to the NotI
      variant D160N with a short linker. The engineered chimeric endonuclease
      (CH-endonuclease) recognizes NotI sites specifically in the presence of
      high salt (100-150 mM NaCl) and divalent cations Mg(++) or Ca(++). In
      contrast to wild-type NotI, which cuts within its recognition sequence,
      BmrI198-NotI (D160N) cleaves DNA outside of NotI sites, resulting in
      deletion of the NotI site and the adjacent sequences. The fusion of the
      BmrI cleavage domain to cleavage-deficient variants of Type II restriction
      enzymes to generate novel cleavage sites will provide useful tools for DNA
      manipulation.
AU  - Zhang P
AU  - Bao Y
AU  - Higgins L
AU  - Xu SY
PT  - Journal Article
TA  - Protein Eng. Des. Sel.
JT  - Protein Eng. Des. Sel.
SO  - Protein Eng. Des. Sel. 2007 20: 497-504.

PMID- 19747545
VI  - 69
DP  - 2010
TI  - Engineering BspQI nicking enzymes and application of N.BspQI in DNA labeling and production of single-strand DNA.
PG  - 226-234
AB  - BspQI is a thermostable Type IIS restriction endonuclease (REase) with the recognition
      sequence 5'GCTCTTC N1/N4 3'. Here we report the cloning
      and expression of the bspQIR gene for the BspQI restriction enzyme in
      Escherichia coli. Alanine scanning of the BspQI charged residues
      identified a number of DNA nicking variants. After sampling
      combinations of different amino acid substitutions, an Nt.BspQI triple
      mutant (E172A/E248A/E255K) was constructed with predominantly
      top-strand DNA nicking activity. Furthermore, a triple mutant of BspQI
      (Nb.BspQI, N235A/K331A/R428A) was engineered to create a bottom-strand
      nicking enzyme. In addition, we demonstrated the application of
      Nt.BspQI in optical mapping of single DNA molecules. Nt or
      Nb.BspQI-nicked dsDNA can be further digested by E. coli exonuclease
      III to create ssDNA for downstream applications. BspQI contains two
      potential catalytic sites: a top-strand catalytic site (Ct) with a
      D-H-N-K motif found in the HNH endonuclease family and a bottom-strand
      catalytic site (Cb) with three scattered Glu residues. BlastP analysis
      of proteins in GenBank indicated a putative restriction enzyme with
      significant amino acid sequence identity to BspQI from the sequenced
      bacterial genome Croceibacter atlanticus HTCC2559. This restriction
      gene was amplified by PCR and cloned into a T7 expression vector.
      Restriction mapping and run-off DNA sequencing of digested products
      from the partially purified enzyme indicated that it is an Earl
      isoschizomer with 6-bp recognition, which we named CatHI (CTCTTC N1/N4).
AU  - Zhang PH
AU  - Too PHM
AU  - Samuelson JC
AU  - Chan SH
AU  - Vincze T
AU  - Doucette S
AU  - Backstrom S
AU  - Potamousis KD
AU  - Schramm TM
AU  - Forrest D
AU  - Schwartz DC
AU  - Xu SY
PT  - Journal Article
TA  - Protein Expr. Purif.
JT  - Protein Expr. Purif.
SO  - Protein Expr. Purif. 2010 69: 226-234.

PMID- 29674558
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Komagataeibacter maltaceti LMG 1529(T), a Vinegar-Producing Acetic Acid Bacterium Isolated from Malt Vinegar Brewery  Acetifiers.
PG  - e00330-18
AB  - We present the genome sequence of Komagataeibacter maltaceti LMG 1529(T), which is a
      vinegar-producing acetic acid bacterium. The draft genome sequence consists
      of 3.6 Mb and contains 3,225 predicted protein-encoding genes. In addition, 53
      genes encoding potential oxidoreductases were identified.
AU  - Zhang Q
AU  - Poehlein A
AU  - Hollensteiner J
AU  - Daniel R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00330-18.

PMID- 
VI  - 0
DP  - 2006
TI  - RESP: a tool using for selecting a set of restriction enzymes.
PG  - 388-390
AB  - The present restriction enzyme analysis tools, such as REBASE tool, REBsites etc., can provide
      the functions of finding available enzymes to the given DNA sequence and supplying theoretical
      digests.  In this paper, we report a novel restriction enzyme selection platform (RESP), which
      can analyze nad optimize the length range and DNA fragment number after cleaving a given whole
      genome by selecting a set of restriction enzymes.  The program runs under Microsoft Windows.
      Compared to present programs, RESP has more excellent functions: it can give DNA digest
      results with multiple enzymes, and simulate electrophoresis process for the digest results,
      and accept the input of more large DNA sequences.  RESP has successfully been used to
      demonstrate the selection of the enzyme set and their fragmentation process for the genome of
      phage T7.
AU  - Zhang Q
AU  - Xie J
AU  - Wu J
AU  - Lu Z
PT  - Journal Article
TA  - Prog. Post-Genome Technol.
JT  - Prog. Post-Genome Technol.
SO  - Prog. Post-Genome Technol. 2006 0: 388-390.

PMID- 
VI  - 31
DP  - 2011
TI  - A new method for the purification of restriction enzyme NotI.
PG  - 102-109
AB  - In order to study its specificities, the NotIR gene was cloned from Nocardia
      otitidis-caviarum.  First, the genome DNA of Enterobacter agglomerans was extracted as
      template, obtained EagI methylase gene by PCR and connected EagIM gene to pBR322 vector of
      gain recombinant expression plasmid pBR322-EagIM.  Then transformed this plasmid ito E. coli
      2555.  Secondly, extracted the genome DNA from Nocardia otitidis-caviarum as template and
      obtained the restriction enzyme NHotIR gene by PCR.  After ligating the NotIR gene to
      pACYC184-PT7, the pACYC184-PT7-NotIR plasmid was transformed into the ER2566 which was
      protected through the methylation by pBR322-EagIM recombinant plasmid.  The engineered strain
      ER2566 [pBR322-EagIM, pACYC184-PT7,-NotIR] could be induced to express restriction enzymes
      NotI by IPTG and the induction conditions were optimized to make its expression mostly in
      soluble form.  The enzyme was purified by AKTA purifier 100 protein purification system.
      Through DEAE Sephrose FF, phenyl HP and Superdex 75 10/300 GL molecular sieve chromatography,
      the NotI enzyme was purified 35-fold, the yield was 9.8 x 106 units/g wet cell which was up to
      17.8% of the crude enzyme and the specific activity of the purified NotI was 1.37 x 106U/mg.
      Digestion results showed that the enzyme was purified to homogeneity and was free of
      detectable contamination by other DNase (exo and endo).  After optimization of the expression
      and purification conditions, the yield and efficienty of NotI enzyme were greatly improved in
      comparison with that previously reported.
AU  - Zhang Q
AU  - Ye X
AU  - Ren G
AU  - Zhang N
AU  - Li Lu
AU  - Li D
PT  - Journal Article
TA  - Zhongguo Shengwu Gongcheng Zazhi
JT  - Zhongguo Shengwu Gongcheng Zazhi
SO  - Zhongguo Shengwu Gongcheng Zazhi 2011 31: 102-109.

PMID- 9972792
VI  - 75
DP  - 1999
TI  - Replication in vitro and cleavage by restriction endonuclease of 5-formyluracil- and 5-hydroxymethyluracil-containing oligonucleotides.
PG  - 59-65
AB  - Purpose: To investigate the biological consequences of 5-formyluracil (5-foU) and
      5-hydroxymethyluracil (5-hmU).  The authors constructed 22-mer oligonucleotides containing a
      5-foU or 5-hmU residue at the same sites.  The effects of such modifications on the ability to
      serve as a template for DNA polymerase and on the cleavage by sequence-specific restriction
      endonuclease were examined.  The Klenow fragment of DNA polymerase I and Thermus thermophilus
      DNA polymerase read through the sites of 5-foU and 5-hmU in the templates.  5-FoU directed the
      incorporation of dCMP in addition to dAMP opposite the lesion during DNA synthesis.  The DNA
      polymerases incorporated only dAMP opposite the 5-hmU.  The substitution of thymine by 5-foU
      within the recognition site of the restriction endonucleases HincII and SalI inhibited or
      prevented the cleavage by the enzymes, whereas the enzymes cleaved the 5-hmU-containing
      oligonucleotides at the same rate as the T-containing oligonucleotides.  These results
      indicated that the 5-foU-A base pair is less stable than the T-A base pair and that 5-foU-A
      base pair is less stable than the T-A base pair and that 5-foU can form a base pair with C in
      addition to A.  It was also demonstrated that the oxidation of thymine to 5-hmU does not
      result in substantial deterioration.
AU  - Zhang Q-M
AU  - Sugiyama H
AU  - Miyabe I
AU  - Matsuda S
AU  - Kino K
AU  - Saito I
AU  - Yonei S
PT  - Journal Article
TA  - Int. J. Radiat. Biol.
JT  - Int. J. Radiat. Biol.
SO  - Int. J. Radiat. Biol. 1999 75: 59-65.

PMID- 15194775
VI  - 78
DP  - 2004
TI  - Complete Genome Sequence of Lymphocystis Disease Virus Isolated from China.
PG  - 6982-6994
AB  - Lymphocystis diseases in fish throughout the world have been extensively
      described. Here we report the complete genome sequence of lymphocystis
      disease virus isolated in China (LCDV-C), an LCDV isolated from cultured
      flounder (Paralichthys olivaceus) with lymphocystis disease in China. The
      LCDV-C genome is 186,250 bp, with a base composition of 27.25% G+C.
      Computer-assisted analysis revealed 240 potential open reading frames
      (ORFs) and 176 nonoverlapping putative viral genes, which encode
      polypeptides ranging from 40 to 1,193 amino acids. The percent coding
      density is 67%, and the average length of each ORF is 702 bp. A search of
      the GenBank database using the 176 individual putative genes revealed 103
      homologues to the corresponding ORFs of LCDV-1 and 73 potential genes that
      were not found in LCDV-1 and other iridoviruses. Among the 73 genes, there
      are 8 genes that contain conserved domains of cellular genes and 65 novel
      genes that do not show any significant homology with the sequences in
      public databases. Although a certain extent of similarity between putative
      gene products of LCDV-C and corresponding proteins of LCDV-1 was revealed,
      no colinearity was detected when their ORF arrangements and coding
      strategies were compared to each other, suggesting that a high degree of
      genetic rearrangements between them has occurred. And a large number of
      tandem and overlapping repeated sequences were observed in the LCDV-C
      genome. The deduced amino acid sequence of the major capsid protein (MCP)
      presents the highest identity to those of LCDV-1 and other iridoviruses
      among the LCDV-C gene products. Furthermore, a phylogenetic tree was
      constructed based on the multiple alignments of nine MCP amino acid
      sequences. Interestingly, LCDV-C and LCDV-1 were clustered together, but
      their amino acid identity is much less than that in other clusters. The
      unexpected levels of divergence between their genomes in size, gene
      organization, and gene product identity suggest that LCDV-C and LCDV-1
      shouldn't belong to a same species and that LCDV-C should be considered a
      species different from LCDV-1.
AU  - Zhang QY
AU  - Xiao F
AU  - Xie J
AU  - Li ZQ
AU  - Gui JF
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 2004 78: 6982-6994.

PMID- 23710588
VI  - 345
DP  - 2013
TI  - Recombinational cloning of the antibiotic biosynthetic gene clusters in linear plasmid SCP1 of Streptomyces coelicolor A3(2).
PG  - 39-48
AB  - The model organism Streptomyces coelicolor A3(2) harbors a 356-kb linear plasmid,
      SCP1. We report here development of a recombinational cloning method for deleting
      large segment from one telomere of SCP1 followed by replacing with the telomere
      of pSLA2 and sequentially inserting with the overlapping cosmids in vivo. The
      procedure depends on homologous recombination coupled with cleavage at telomere
      termini by telomere terminal protein. Using this procedure, we cloned the 81-kb
      avermectin and the 76-kb spinosad biosynthetic gene clusters into SCP1.
      Heterologous expression of avermectin production in S. coelicolor was detected.
      These results demonstrate the utility of SCP1 for cloning large DNA segments such
      as antibiotic biosynthetic gene clusters.
AU  - Zhang R
AU  - Xia H
AU  - Xu Q
AU  - Dang F
AU  - Qin Z
PT  - Journal Article
TA  - FEMS Microbiol. Lett.
JT  - FEMS Microbiol. Lett.
SO  - FEMS Microbiol. Lett. 2013 345: 39-48.

PMID- 21914886
VI  - 193
DP  - 2011
TI  - The Xylella fastidiosa Biocontrol Strain EB92-1 Genome Is Very Similar and Syntenic to Pierce's Disease Strains.
PG  - 5576-5577
AB  - Xylella fastidiosa infects a wide range of plant hosts and causes economically serious
      diseases, including Pierce's disease (PD) of
      grapevines. X. fastidiosa biocontrol strain EB92-1 is infectious to
      grapevines but does not cause symptoms. The draft genome of EB92-1 reveals
      that it may be missing 10 potential pathogenicity effectors.
AU  - Zhang S
AU  - Flores-Cruz Z
AU  - Kumar D
AU  - Chakrabarty P
AU  - Hopkins DL
AU  - Gabriel DW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5576-5577.

PMID- 27688836
VI  - 11
DP  - 2016
TI  - Whole genome shotgun sequence of Bacillus amyloliquefaciens TF28, a biocontrol entophytic bacterium.
PG  - 73
AB  - Bacillus amyloliquefaciens TF28 is a biocontrol endophytic bacterium that is capable of
      inhibition of a broad range of plant pathogenic fungi. The strain has
      the potential to be developed into a biocontrol agent for use in agriculture.
      Here we report the whole-genome shotgun sequence of the strain. The genome size
      of B. amyloliquefaciens TF28 is 3,987,635 bp which consists of 3754
      protein-coding genes, 65 tandem repeat sequences, 47 minisatellite DNA, 2
      microsatellite DNA, 63 tRNA, 7rRNA, 6 sRNA, 3 prophage and CRISPR domains.
AU  - Zhang S
AU  - Jiang W
AU  - Li J
AU  - Meng L
AU  - Cao X
AU  - Hu J
AU  - Liu Y
AU  - Chen J
AU  - Sha C
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 73.

PMID- 24459280
VI  - 2
DP  - 2014
TI  - Genome Sequence of Pyrethroid-Degrading Bacterium Rhodopseudomonas palustris Strain JSC-3b.
PG  - e01228-13
AB  - Rhodopseudomonas palustris strain JSC-3b is a facultative, thermophilic bacterium, which was
      isolated from water in a canal adjacent to a vegetable
      field. Strain JSC-3b biodegrades several varieties of pyrethroid residues
      effectively through cometabolic pathways. Here, we present the genome sequence of
      this biodegrader.
AU  - Zhang S
AU  - Luo X
AU  - Cheng J
AU  - Peng J
AU  - Zhang D
AU  - Liu Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01228-13.

PMID- 26203344
VI  - 10
DP  - 2015
TI  - Genome sequences of copper resistant and sensitive Enterococcus faecalis strains  isolated from copper-fed pigs in Denmark.
PG  - 35
AB  - Six strains of Enterococcus faecalis (S1, S12, S17, S18, S19 and S32) were isolated from
      copper fed pigs in Denmark. These Gram-positive bacteria within the
      genus Enterococcus are able to survive a variety of physical and chemical
      challenges by the acquisition of diverse genetic elements. The genome of strains
      S1, S12, S17, S18, S19 and S32 contained 2,615, 2,769, 2,625, 2,804, 2,853 and
      2,935 protein-coding genes, with 41, 42, 27, 42, 32 and 44 genes encoding
      antibiotic and metal resistance, respectively. Differences between Cu resistant
      and sensitive E. faecalis strains, and possible co-transfer of Cu and antibiotic
      resistance determinants were detected through comparative genome analysis.
AU  - Zhang S
AU  - Wang D
AU  - Wang Y
AU  - Hasman H
AU  - Aarestrup FM
AU  - Alwathnani HA
AU  - Zhu YG
AU  - Rensing C
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 35.

PMID- 21622744
VI  - 193
DP  - 2011
TI  - Complete genome sequence of Bordetella pertussis CS, a Chinese pertussis vaccine strain.
PG  - 4017-4018
AB  - Bordetella pertussis is the causative agent of pertussis. Here, we report the genome sequence
      of Bordetella pertussis strain CS, isolated from an
      infant patient in Beijing and widely used as a vaccine strain for
      production of acellular pertussis vaccine in China.
AU  - Zhang S
AU  - Xu Y
AU  - Zhou Z
AU  - Wang S
AU  - Yang R
AU  - Wang J
AU  - Wang L
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4017-4018.

PMID- 24744322
VI  - 2
DP  - 2014
TI  - Genome Sequence of Luminous Piezophile Photobacterium phosphoreum ANT-2200.
PG  - e00096-14
AB  - Bacteria of the genus Photobacterium thrive worldwide in oceans and show substantially varied
      lifestyles, including free-living, commensal, pathogenic, symbiotic, and piezophilic. Here, we
      present the genome sequence of a luminous, piezophilic Photobacterium phosphoreum strain,
      ANT-2200, isolated from a water column at 2,200 m depth in the Mediterranean Sea. It is the
      first genomic sequence of the P. phosphoreum group. An analysis of the sequence provides
      insight into the adaptation of bacteria to the deep-sea habitat.
AU  - Zhang SD
AU  - Barbe V
AU  - Garel M
AU  - Zhang WJ
AU  - Chen H
AU  - Santini CL
AU  - Murat D
AU  - Jing H
AU  - Zhao Y
AU  - Lajus A
AU  - Martini S
AU  - Pradel N
AU  - Tamburini C
AU  - Wu LF
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00096-14.

PMID- 27979957
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Trueperella pyogenes, Isolated from Infected Farmland Goats.
PG  - e01421-16
AB  - Trueperella pyogenes is a significant pathogen of livestock, causing diverse diseases, such as
      mastitis, liver abscessation, and pneumonia. In this study, we
      have reported the genome sequence of Trueperella pyogenes 2012CQ-ZSH. Moreover,
      several genes coding for virulence factors were found, such as pyolysin (PYO),
      nanH, nanP, cbpA, fimC, and fimE.
AU  - Zhang SH
AU  - Qiu JJ
AU  - Yang R
AU  - Shen KF
AU  - Xu GY
AU  - Fu LZ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01421-16.

PMID- 24874679
VI  - 2
DP  - 2014
TI  - Genome Sequence of Bacillus cereus Strain A1, an Efficient Starch-Utilizing Producer of Hydrogen.
PG  - e00494-14
AB  - Bacillus cereus strain A1 is a newly isolated hydrogen producer capable of utilizing
      bioresources and biowaste, such as starch and starch wastewater. Here,
      we present a 5.67-Mb assembly of the genome sequence of strain A1, which may
      provide insights into the molecular mechanism of hydrogen production from
      bioresources and biowaste.
AU  - Zhang T
AU  - Bao M
AU  - Wang Y
AU  - Su H
AU  - Tan T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00494-14.

PMID- 26404587
VI  - 3
DP  - 2015
TI  - Genome Sequence of Avirulent Riemerella anatipestifer Strain RA-JLLY.
PG  - e00895-15
AB  - Riemerella anatipestifer is an important bacterial pathogen associated with epizootic
      infections in waterfowl and various other birds. Riemerella anatipestifer strain RA-JLLY is an
      avirulent strain, isolated from the brain of an old duck in Hubei province, China. Here, we
      report the genome sequence of this species.
AU  - Zhang T
AU  - Zhang R
AU  - Luo Q
AU  - Wen G
AU  - Ai D
AU  - Wang H
AU  - Luo L
AU  - Wang H
AU  - Shao H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00895-15.

PMID- 24034719
VI  - 16
DP  - 2014
TI  - Phylogeny and phenotypes of clinical and environmental Shiga toxin-producing Escherichia coli O174.
PG  - 963-976
AB  - Shiga toxin (Stx)-producing Escherichia coli (STEC) of serogroup O174 are human
      pathogenic intimin gene (eae)-negative STEC. To facilitate diagnosis and
      subtyping, we genotypically and phenotypically characterized 25 STEC O174
      isolates from humans with different clinical outcomes and from animals and the
      environment. fliC genotyping resulted in four different genotypes (fliCH2 : n =
      5; fliCH8 : n = 8; fliCH21 : n = 11; fliCH46 : n = 1). Twenty-three strains were
      motile expressing the corresponding H antigen; two non-motile isolates possessed
      fliCH8 . The stx genotypes and non-stx virulence loci, including toxins,
      serine-proteases and adhesins correlated well with serotypes but showed no
      differences with respect to the isolates' origins. Multilocus sequence typing
      identified seven sequence types that correlated with serotypes. Core gene typing
      further specified the four serotypes, including a previously unknown O174:H46
      combination, and revealed distant relationships of the different serotypes within
      serogroup O174 and in relation to other haemolytic uremic syndrome
      (HUS)-associated STEC. Only serotype O174:H21 was associated with HUS.
      Differences in virulence factors and in the adherence capacity of STEC O174
      corroborated this separation into four distinct groups. Our study provides a
      basis for O174 subtyping, unravels considerable genotypic and phenotypic
      heterogeneity and sheds light to potential environmental and animal reservoirs.
AU  - Zhang W
AU  - Nadirk J
AU  - Kossow A
AU  - Bielaszewska M
AU  - Leopold SR
AU  - Witten A
AU  - Fruth A
AU  - Karch H
AU  - Ammon A
AU  - Mellmann A
PT  - Journal Article
TA  - Environ. Microbiol.
JT  - Environ. Microbiol.
SO  - Environ. Microbiol. 2014 16: 963-976.

PMID- 20675486
VI  - 192
DP  - 2010
TI  - Complete genome sequence of Lactobacillus casei Zhang, a new probiotic strain isolated from traditional homemade koumiss in Inner Mongolia,  China.
PG  - 5268-5269
AB  - Lactobacillus casei Zhang is a new probiotic bacterium isolated from koumiss collected in
      Inner Mongolia, China. Here, we report the main
      genome features of L. casei Zhang and the identification of several
      predicted proteins implicated in interactions with the host.
AU  - Zhang W
AU  - Yu D
AU  - Sun Z
AU  - Wu R
AU  - Chen X
AU  - Chen W
AU  - Meng H
AU  - Hu S
AU  - Zhang H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 192: 5268-5269.

PMID- 26664653
VI  - 10
DP  - 2015
TI  - Draft genome sequence of Halopiger salifodinae KCY07-B2(T), an extremly halophilic archaeon isolated from a salt mine.
PG  - 124
AB  - Halopiger salifodinae strain KCY07-B2(T), isolated from a salt mine in Kuche county, Xinjiang
      province, China, belongs to the family Halobacteriaceae. It is a
      strictly aerobic, pleomorphic, rod-shaped, Gram-negative and extremely halophilic
      archaeon. In this work, we report the features of the type strain KCY07-B2(T),
      together with the draft genome sequence and annotation. The draft genome sequence
      is composed of 83 contigs for 4,350,718 bp with 65.41 % G + C content and
      contains 4204 protein-coding genes and 50 rRNA genes.
AU  - Zhang WY
AU  - Hu J
AU  - Pan J
AU  - Sun C
AU  - Wu M
AU  - Xu XW
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 124.

PMID- 29637394
VI  - 111
DP  - 2018
TI  - Gallaecimonas mangrovi sp. nov., a novel bacterium isolated from mangrove sediment.
PG  - 1855-1862
AB  - A Gram-stain negative, rod-shaped, non-motile, strictly aerobic bacterium
      HK-28(T) was isolated from a mangrove sediment sample in Haikou city, Hainan
      Province, China. Strain HK-28(T) was able to grow at 10-45 degrees C (optimum
      25-30 degrees C), pH 5.0-8.5 (optimum 6.0-7.0) and 0.5-12.0% (w/v) NaCl (optimum
      1.0-3.0%, w/v). The major cellular fatty acids were C16:0, Summed Feature 8
      (C18:1 omega7c and/or C18:1 omega6c), Summed Feature 3 (C16:1 omega7c and/or
      C16:1 omega6c), C17:0, C12:0 3-OH and C17:1omega8c. Ubiquinone-8 (Q-8) was the
      predominant respiratory quinone. The polar lipids consisted of
      diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two
      unidentified aminophospholipids, four unidentified phospholipids, two
      unidentified glycolipid, an unidentified glycophospholipid, an unidentified
      aminolipid and an unidentified lipid. The DNA G+C content was 50.2 mol%.
      Accoroding to 16S rRNA gene sequence similarities, strain HK-28(T) shared 97.1
      and 96.7% sequence similarities to the validly named species Gallaecimonas
      xiamenensis MCCC 1A01354(T) and Gallaecimonas pentaromativorans MCCC 1A06435(T),
      respectively, and shared lower sequence similarities (< 92.0%) to all other
      genera. Phylogenetic analysis showed strain HK-28(T) was clustered with G.
      pentaromativorans MCCC 1A06435(T) and G. xiamenensis MCCC 1A01354(T). Strain
      HK-28(T) showed low DNA-DNA relatedness with G. xiamenensis MCCC 1A01354(T) (28.3
      +/- 1.5%) and G. pentaromativorans MCCC 1A06435(T) (25.2 +/- 2.4%). On the basis
      of phenotypic, chemotaxonomic and genotypic characteristics, strain HK-28(T) is
      considered to represent a novel species in the genus Gallaecimonas, for which the
      name Gallaecimonas mangrovi sp. nov. is proposed. The type strain is HK-28(T) (=
      KCTC 62177(T) = MCCC 1K03441).
AU  - Zhang WY
AU  - Yuan Y
AU  - Su DQ
AU  - He XP
AU  - Han SB
AU  - Epstein SS
AU  - He S
AU  - Wu M
PT  - Journal Article
TA  - Antonie Van Leeuwenhoek
JT  - Antonie Van Leeuwenhoek
SO  - Antonie Van Leeuwenhoek 2018 111: 1855-1862.

PMID- 16606828
VI  - 103
DP  - 2006
TI  - The mechanism of M.HhaI DNA C5 cytosine methyltransferase enzyme: a quantum mechanics/molecular mechanics approach.
PG  - 6148-6153
AB  - The mechanism of DNA cytosine-5-methylation catalyzed by the bacterial M.HhaI enzyme has been
      considered as a stepwise nucleophilic addition of Cys-81-S- to cytosine C6 followed by C5
      nucleophilic replacement of the methyl of S-adenosyl-L-methionine to produce
      5-methyl-6-Cys-81-S-5,6-dihydrocytosine. In this study, we show that the reaction is concerted
      from a series of energy calculations by using the quantum mechanical/molecular mechanical
      hybrid method. Deprotonation of 5-methyl-6-Cys-81-S-5,6-dihydrocytosine and expulsion of
      Cys-81-S- provides the product DNA 5-methylcytosine. A required base catalyst for this
      deprotonation is not available as a member of the active site structure. A water channel
      between the active site and bulk water allows entrance of solvent to the active site.
      Hydroxide at 10(-7) mole fraction (pH = 7) is shown to be sufficient for the required
      catalysis. We also show that Glu-119-CO2H can divert the reaction by protonating cytosine N3
      when Cys-81-S- attacks cytosine, to form the 6-Cys-81-S-3-hydrocytosine. The reactants and
      6-Cys-81-S-3-hydrocytosine product are in rapid equilibrium, and this explains the observed
      hydrogen exchange of cytosine with solvent.
AU  - Zhang X
AU  - Bruice TC
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2006 103: 6148-6153.

PMID- 23876353
VI  - 77
DP  - 2013
TI  - First report of a sequence type 239 vancomycin-intermediate Staphylococcus aureus isolate in Mainland China.
PG  - 64-68
AB  - Methicillin-resistant Staphylococcus aureus (MRSA) is an important pathogen that
      causes a wide range of both hospital- and community-acquired infections. The high
      prevalence of MRSA and the extensive use of vancomycin in Mainland China may lead
      to the emergence of vancomycin-intermediate S. aureus (VISA) isolates. In this
      case, we report a VISA isolate from a 34-year-old male patient with steam burn.
      The isolate was determined to be sequence type 239 staphylococcal cassette
      chromosome mec type III, the most prevalent MRSA clone in Mainland China.
AU  - Zhang X
AU  - Hu Q
AU  - Yuan W
AU  - Shang W
AU  - Cheng H
AU  - Yuan J
AU  - Zhu J
AU  - Hu Z
AU  - Li S
AU  - Chen W
AU  - Hu X
AU  - Rao X
PT  - Journal Article
TA  - Diagn. Microbiol. Infect. Dis.
JT  - Diagn. Microbiol. Infect. Dis.
SO  - Diagn. Microbiol. Infect. Dis. 2013 77: 64-68.

PMID- 17381326
VI  - 71
DP  - 2006
TI  - Genetic analyses of DNA methyltransferases in Arabidopsis thaliana.
PG  - 439-447
AB  - DNA methylation is a conserved epigenetic silencing mechanism that functions to suppress the
      proliferation of transposons and regulate the
      expression of endogenous genes. In plants, Mutations that cause severe
      loss of DNA methylation result in reactivation of transposons as well
      as developmental abnormalities. We use the flowering plant Arabidopsis
      thaliana as a model system to study the establishment and maintenance
      of DNA methylation as well as its role in regulating plant development.
      The genetic evidence presented here suggests that methylation at CG and
      non-CG sites function!; in a partially redundant and locus-specific
      manner to regulate a wide range of developmental processes. Results
      from recent studies also suggested that the dynamic nature of non-CG
      methylation, which is critically important for its regulatory function,
      is largely due to it, complicated interactions with other epigenetic
      pathways such as RNAi and historic modifications. Finally, the use of
      genomic approaches has significantly broadened our Understanding of the
      patterning of DNA methylation on a genomewide sea e and has led to the
      identification of hundreds of candidate genes that are controlled by
      DNA methylation.
AU  - Zhang X
AU  - Jacobsen SE
PT  - Journal Article
TA  - Cold Spring Harb. Symp. Quant. Biol.
JT  - Cold Spring Harb. Symp. Quant. Biol.
SO  - Cold Spring Harb. Symp. Quant. Biol. 2006 71: 439-447.

PMID- 26868389
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Desulfitobacterium hafniense Strain DH, a Sulfate-Reducing Bacterium Isolated from Paddy Soils.
PG  - e01693-15
AB  - Desulfitobacterium hafniense strain DH is a sulfate-reducing species. Here, we report the
      draft genome sequence of strain DH, with a size of 5,368,588 bp,
      average G+C content of 47.48%, and 5,296 predicted protein-coding sequences.
AU  - Zhang X
AU  - Li GX
AU  - Chen SC
AU  - Jia XY
AU  - Wu K
AU  - Cao CL
AU  - Bao P
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01693-15.

PMID- 26823591
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a Potential Nitrate-Dependent Fe(II)-Oxidizing Bacterium, Aquabacterium parvum B6.
PG  - e01651-15
AB  - Aquabacterium parvum B6 is a potential nitrate-dependent Fe(II)-oxidizing bacterium. The genes
      related to its denitrifying mechanism and iron metabolisms
      were unknown. We present the draft genome of Aquabacterium parvum B6, which could
      provide further insight into the nitrate-dependent Fe(II)-oxidizing mechanism of
      strain B6.
AU  - Zhang X
AU  - Ma F
AU  - Szewzyk U
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01651-15.

PMID- 8125913
VI  - 269
DP  - 1994
TI  - Effect of DNA cytosine methylation upon deamination-induced mutagenesis in a natural target sequence in duplex DNA.
PG  - 7066-7069
AB  - Are 5-methylcytosine residues in DNA hot spots for transition mutagenesis? Numerous studies
      identify 1) structural changes induced by DNA methylation, 2) high percentages of human
      mutations that result from GC to AT transition pathways, and 3) differences between G-C and
      G-mC base pairs in susceptibility to nonenzymatic deamination. However, investigations of
      chemical stability necessarily involve non-physiological conditions for chemical analysis of
      deamination. Here we describe an experiment that compares rates of deamination-induced
      mutagenesis between a G-C and G-mC base pair, when both are present in duplex DNA, incubated
      at 37oC and pH 7.4, within identical sequence contexts, in a natural mutational target (the
      Escherichia coli lacZ-alpha gene) that selects for mutagenesis at the specific site under
      investigation. Under these conditions the rate of spontaneous deamination at G-mC exceeds that
      at G-C by more than 21-fold. Our data implicate differences in chemical stability toward
      deamination as a major causal factor relating DNA cytosine methylation to spontaneous
      mutagenesis.
AU  - Zhang X
AU  - Mathews CK
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 1994 269: 7066-7069.

PMID- 8772199
VI  - 392
DP  - 1996
TI  - Mammalian DNA cytosine-5 methyltransferase interacts with p23 protein.
PG  - 179-183
AB  - In higher eukaryotic genomes, methylated cytosine residues (m5C) are distributed in heritable,
      cell-type-specific patterns, which are believed to be involved in the control of gene
      expression, developmental regulation and genomic imprinting.  These methylation patterns are
      established and maintained by DNA cytosine-5 methyltransferase (Mtase), a ~1500 amino acid
      enzyme containing a regulatory N-terminal domain and a catalytic C-terminal domain.  The
      mechanism responsible for targeting Mtase to particular genes is poorly understood and might
      possibly involve interactions with other proteins.  In an effort to identify proteins that
      interact with the mammalian Mtase, we used the yeast two-hybrid system with several different
      Mtase domains as baits.  Here we report an interaction between the C-terminal catalytic domain
      of the Mtase and p23, a protein previously reported to associate with the progesterone
      receptor (PR) complex.
AU  - Zhang X
AU  - Verdine GL
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1996 392: 179-183.

PMID- 24407631
VI  - 2
DP  - 2014
TI  - Genome Sequence of Klebsiella pneumoniae Strain LCT-KP182, Which Acquired Hemolytic Properties after Space Flight.
PG  - e01088-13
AB  - The Klebsiella pneumoniae strain LCT-KP182 acquired hemolytic properties after space flight.
      Here, we present the draft genome sequence of this strain.
AU  - Zhang X
AU  - Wang T
AU  - Liu W
AU  - Guo Y
AU  - Wang J
AU  - Li T
AU  - Fang X
AU  - Zhang X
AU  - Dai W
AU  - Liu C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01088-13.

PMID- 24385570
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Bacillus cereus LCT-BC25, Isolated from Space Flight.
PG  - e00667-13
AB  - Bacillus cereus strain LCT-BC25, which was carried by the Shenzhou VIII spacecraft, traveled
      in space for about 398 h. To investigate the response of B.
      cereus to space environments, we determined the genome sequence of B. cereus
      strain LCT-BC25, which was isolated after space flight.
AU  - Zhang X
AU  - Wang T
AU  - Su L
AU  - Zhou L
AU  - Li T
AU  - Wang J
AU  - Liu Y
AU  - Jiang X
AU  - Wu C
AU  - Liu C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00667-13.

PMID- 29167257
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Pseudomonas fluorescens Strain TR3, a Potential Biocontrol Agent against the Rice Blast Fungus Magnaporthe oryzae.
PG  - e01332-17
AB  - We present the draft genome sequence of the potential biocontrol agent Pseudomonas fluorescens
      TR3, which was isolated from rice leaves infected with
      Magnaporthe oryzae in a greenhouse. The genome of TR3 was assembled into 26
      scaffolds (~6 Mbp) and includes genes potentially involved in bacterial
      interactions with fungi.
AU  - Zhang X
AU  - Xu JR
AU  - Nakatsu CH
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01332-17.

PMID- 25059856
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Staphylococcus aureus XN108, an ST239-MRSA-SCCmec III Strain with Intermediate Vancomycin Resistance Isolated in Mainland China.
PG  - e00449-14
AB  - ST239-MRSA-SCCmec III (ST239, sequence type 239; MRSA, methicillin-resistant Staphylococcus
      aureus; SCCmec III, staphylococcal cassette chromosome mec type
      III) is the most predominant clone of hospital-acquired methicillin-resistant S.
      aureus in mainland China. We report here the complete genome sequence of XN108,
      the first vancomycin-intermediate S. aureus strain isolated from a steam-burned
      patient with a wound infection.
AU  - Zhang X
AU  - Xu X
AU  - Yuan W
AU  - Hu Q
AU  - Shang W
AU  - Hu X
AU  - Tong Y
AU  - Rao X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00449-14.

PMID- 27151789
VI  - 4
DP  - 2016
TI  - Genome Sequence of Marichromatium gracile YL-28, a Purple Sulfur Bacterium with Bioremediation Potential.
PG  - e00288-16
AB  - The draft genome sequence of Marichromatium gracile YL-28 contains 3,840,251 bp,  with a G+C
      content of 68.84%. The annotated genome sequence provides the genetic
      basis for revealing its role as a purple sulfur bacterium in the harvesting of
      energy and the development of bioremediation applications.
AU  - Zhang X
AU  - Zhao C
AU  - Hong X
AU  - Chen S
AU  - Yang S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00288-16.

PMID- 22522893
VI  - 194
DP  - 2012
TI  - Natural Transformation of an Engineered Helicobacter pylori Strain Deficient in Type II Restriction Endonucleases.
PG  - 3407-3416
AB  - Restriction-modification (RM) systems are important for bacteria to limit foreign DNA
      invasion. The naturally competent bacterium Helicobacter pylori has highly
      diverse strain-specific type II systems. To evaluate the roles of strain-specific
      restriction in H. pylori natural transformation, a markerless type II restriction
      endonuclease-deficient (REd) mutant was constructed. We deleted the genes
      encoding all four active type II restriction endonucleases in H. pylori strain
      26695 using sacB-mediated counterselection. Transformation by donor DNA with
      exogenous cassettes methylated by Escherichia coli was substantially (1.7 and 2.0
      log(10) for cat and aphA, respectively) increased in the REd strain. There also
      was significantly increased transformation of the REd strain by donor DNA from
      other H. pylori strains, to an extent corresponding to their shared type II R-M
      system strain specificity with 26695. Comparison of the REd and wild-type strains
      indicates that restriction did not affect the length of DNA fragment integration
      during natural transformation. There also were no differentials in cell growth or
      susceptibility to DNA damage. In total, the data indicate that the type II REd
      mutant has enhanced competence with no loss of growth or repair facility compared
      to the wild type, facilitating H. pylori mutant construction and other genetic
      engineering.
AU  - Zhang XS
AU  - Blaser MJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3407-3416.

PMID- 23144387
VI  - 194
DP  - 2012
TI  - Draft genome sequence of strain p7-3-5, a new flavobacteriaceae bacterium isolated from intertidal sand.
PG  - 6632
AB  - The Flavobacteriaceae bacterium strain P7-3-5 was isolated from intertidal sand of the Yellow
      Sea, China. Analysis of the 16S rRNA gene sequences showed that
      strain P7-3-5 formed a distinct phylogenetic lineage within the family
      Flavobacteriaceae. The genome of strain P7-3-5 was sequenced to facilitate the
      physiological, ecological, and evolutionary studies of the bacteria within the
      family Flavobacteriaceae.
AU  - Zhang XY
AU  - Xie BB
AU  - Qin QL
AU  - Liu A
AU  - Chen XL
AU  - Zhou BC
AU  - Zhang YZ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6632.

PMID- 23209246
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Protease-Producing Bacterium Rheinheimera nanhaiensis E407-8T, Isolated from Deep-Sea Sediment of the South China Sea.
PG  - 7001-7002
AB  - The protease-producing bacterium E407-8(T) was isolated from deep-sea sediment of the South
      China Sea and has been identified recently as representing a new
      species, Rheinheimera nanhaiensis. The draft genome of R. nanhaiensis E407-8(T)
      consists of 3,987,205 bp and contains 3,730 predicated protein-coding genes,
      including 82 extracellular peptidase genes.
AU  - Zhang XY
AU  - Zhang YJ
AU  - Qin QL
AU  - Xie BB
AU  - Chen XL
AU  - Zhou BC
AU  - Zhang YZ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 7001-7002.

PMID- 21914894
VI  - 193
DP  - 2011
TI  - Complete Genome Sequences of Mycobacterium tuberculosis Strains CCDC5079 and CCDC5080, Which Belong to the Beijing Family.
PG  - 5591-5592
AB  - Mycobacterium tuberculosis is one of most prevalent pathogens in the world. Drug-resistant
      strains of this pathogen caused by the excessive use
      of antibiotics have long posed serious threats to public health worldwide.
      A broader picture of drug resistance mechanisms at the genomic level can
      be obtained only with large-scale comparative genomic methodology. Two
      closely related Beijing family isolates, one resistant to four first-line
      drugs (CCDC5180) and one sensitive to them (CCDC5079), were completely
      sequenced. These sequences will serve as valuable references for further
      drug resistance site identification studies and could be of great
      importance for developing drugs targeting these sites.
AU  - Zhang Y
AU  - Chen C
AU  - Liu J
AU  - Deng H
AU  - Pan A
AU  - Zhang L
AU  - Zhao X
AU  - Huang M
AU  - Lu B
AU  - Dong H
AU  - Du P
AU  - Chen W
AU  - Wan K
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5591-5592.

PMID- 9454710
VI  - 240
DP  - 1998
TI  - Chlorella virus NY-2A encodes at least 12 DNA endonuclease/methyltransferase genes.
PG  - 366-375
AB  - The 380-kb chlorella virus NY-2A genome is highly methylated; 45% of the cytosines are
      5-methylcytosine and 37% of the adenine are N6-methyladenine.  Based on the
      sensitivity/resistance of NY-2A DNA to 80 methylation-sensitive DNA restriction endonucleases,
      the virus is predicted to encode at least 10 DNA methyltransferases: 7 6mA-specific
      methyltransferases, M.CviQI (GTmAC), M.CvQII (RmAR), M.CviQIII (TCGmA), M.CviQV (TGCmA),
      M.CviQVI (GmANTC), and M.CviQVII (CmATG); and 3 5mC-specific methyltransferases, M.CviQVIII
      [RGmC(T/C/G)], M.CviQIX (mCC), and M.CviQX (mCGR).  Five of the 6mA methyltransferase genes,
      M.CviQI, M.CviQIII, M.CviQV, M.CviQVI, and M.CviQVII, were cloned and sequenced.  In addition,
      2 site-specific endonuclease activities, R.CviQI (G/TAC) and NY2A-nickase (R/AG), were
      detected in cell-free extracts from NY-2A virus-infected chlorella.  Therefore, the NY-2A
      genome contains at least 12 DNA methyltransferase and endonuclease genes which, altogether,
      compose about 3-4% of the virus genome.
AU  - Zhang Y
AU  - Nelson M
AU  - Nietfeldt J
AU  - Xia Y
AU  - Burbank D
AU  - Ropp S
AU  - Van Etten JL
PT  - Journal Article
TA  - Virology
JT  - Virology
SO  - Virology 1998 240: 366-375.

PMID- 1437552
VI  - 20
DP  - 1992
TI  - Characterization of Chlorella virus PBCV-1 CviAII restriction and modification system.
PG  - 5351-5356
AB  - A second DNA site-specific (restriction) endonuclease (R.CviAII) and its cognate adenine DNA
      methyltransferase (M.CviAII) were isolated from virus PBCV-1 infected Chlorella strain NC64A
      cells. R.CviAII, a heteroschizomer of the bacterial restriction endonuclease NlaIII,
      recognizes the sequence CATG, and does not cleave CmATG sequences. However, unlike NlaIII,
      which cleaves after the G and does not cleave either CmATG or mCATG sequences, CviAII cleaves
      between the C and A and is unaffected by mCATG methylation. The M.CviAII and R.CviAII genes
      were cloned and their DNA sequences were determined. These genes are tandemly arranged
      head-to-tail such that the TAA termination codon of the M.CviAII methyltransferase gene
      overlaps the ATG translational start site of R.CviAII endonuclease. R.CviAII is the first
      Chlorella virus site-specific endonuclease gene to be cloned and sequenced.
AU  - Zhang Y
AU  - Nelson M
AU  - Nietfeldt JW
AU  - Burbank DE
AU  - Van Etten JL
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 5351-5356.

PMID- 1579454
VI  - 20
DP  - 1992
TI  - A single amino acid change restores DNA cytosine methyltransferase activity in a cloned Chlorella virus pseudogene.
PG  - 1637-1642
AB  - The Chlorella virus PBCV-1 contains an open reading frame, named P17-ORF4, which differs by
      eight amino acids from a DNA cytosine methyltransferase, M.CviJI, encoded by a different
      chlorella virus IL-3A. Whereas IL-3A expresses M.CviJI, which methylates the central cytosine
      in (A/G)GC(T/C/G) sequences, P17-ORF4 is non-functional. Gene fusions between P17-ORF4 and
      M.CviJI and site-directed point mutations revealed that changing Gln188 to Lys188 abolishes
      M.CviJI methyltransferase activity. Conversely, changing Lys188 in P17-ORF4 to Gln188 results
      in M.CviJI activity. The other altered seven amino acids do not appear to affect M.CviJI
      activity.
AU  - Zhang Y
AU  - Nelson M
AU  - Van Etten JL
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 1637-1642.

PMID- 27587818
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of the Fish Pathogen Flavobacterium columnare Pf1.
PG  - e00900-16
AB  - Flavobacterium columnare is the etiologic agent of columnaris disease, a devastating fish
      disease prevailing in worldwide aquaculture industry. Here, we
      describe the complete genome of F. columnare strain Pf1, a highly virulent strain
      isolated from yellow catfish (Pelteobagrus fulvidraco) in China.
AU  - Zhang Y
AU  - Nie P
AU  - Lin L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00900-16.

PMID- 22689235
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Rhodococcus sp. Strain P14, a Biodegrader of High-Molecular-Weight Polycyclic Aromatic Hydrocarbons.
PG  - 3546
AB  - The genus Rhodococcus is known for its ability to degrade various xenobiotic compounds.
      Rhodococcus sp. strain P14 isolated from crude oil-contaminated
      sediments can degrade mineral oil and polycyclic aromatic hydrocarbons (PAHs).
      The draft genome sequence of Rhodococcus sp. P14 was obtained using Solexa
      technology, which provided an invaluable genetic background for further
      investigation of the ability of P14 to degrade xenobiotic compounds.
AU  - Zhang Y
AU  - Qin F
AU  - Qiao J
AU  - Li G
AU  - Shen C
AU  - Huang T
AU  - Hu Z
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 3546.

PMID- 24812217
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Neisseria meningitidis Serogroup A Strain NMA510612,  Isolated from a Patient with Bacterial Meningitis in China.
PG  - e00360-14
AB  - Serogroup A meningococcal strains have been involved in several pandemics and a series of
      epidemics worldwide in the past. Determination of the genome sequence
      of the prevalent genotype strain will help us understand the genetic background
      of the evolutionary and epidemiological properties of these bacteria. We
      sequenced the complete genome of Neisseria meningitidis NMA510612, a clinical
      isolate from a patient with meningococcal meningitis.
AU  - Zhang Y
AU  - Yang J
AU  - Xu L
AU  - Zhu Y
AU  - Liu B
AU  - Shao Z
AU  - Zhang X
AU  - Jin Q
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00360-14.

PMID- 23929464
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Euryhalocaulis caribicus Strain JL2009T, a New Member of the Family Hyphomonadaceae Isolated from the Caribbean Sea.
PG  - e00407-13
AB  - Euryhalocaulis caribicus strain JL2009(T) is a novel genus and species of the family
      Hyphomonadaceae and was first isolated from surface water in the Caribbean
      Sea. Here, we report the first draft genome from this genus. Its genome contains
      genes encoding proteins that are involved in organic acid metabolism and probable
      low-affinity inorganic phosphate transporters, which suggests its competence in
      oligotrophic oceans.
AU  - Zhang Y
AU  - Zhao Z
AU  - Deng W
AU  - Xie X
AU  - Jiao N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00407-13.

PMID- 26664654
VI  - 10
DP  - 2015
TI  - Genome sequences of two closely related strains of Escherichia coli K-12 GM4792.
PG  - 125
AB  - Escherichia coli lab strains K-12 GM4792 Lac(+) and GM4792 Lac(-) carry opposite  lactose
      markers, which are useful for distinguishing evolved lines as they
      produce different colored colonies. The two closely related strains are chosen as
      ancestors for our ongoing studies of experimental evolution. Here, we describe
      the genome sequences, annotation, and features of GM4792 Lac(+) and GM4792
      Lac(-). GM4792 Lac(+) has a 4,622,342-bp long chromosome with 4,061
      protein-coding genes and 83 RNA genes. Similarly, the genome of GM4792 Lac(-)
      consists of a 4,621,656-bp chromosome containing 4,043 protein-coding genes and
      74 RNA genes. Genome comparison analysis reveals that the differences between
      GM4792 Lac(+) and GM4792 Lac(-) are minimal and limited to only the targeted lac
      region. Moreover, a previous study on competitive experimentation indicates the
      two strains are identical or nearly identical in survivability except for lactose
      utilization in a nitrogen-limited environment. Therefore, at both a genetic and a
      phenotypic level, GM4792 Lac(+) and GM4792 Lac(-), with opposite neutral markers,
      are ideal systems for future experimental evolution studies.
AU  - Zhang YC
AU  - Zhang Y
AU  - Zhu BR
AU  - Zhang BW
AU  - Ni C
AU  - Zhang DY
AU  - Huang Y
AU  - Pang E
AU  - Lin K
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 125.

PMID- 10784058
VI  - 146
DP  - 2000
TI  - Molecular analysis of genetic differences between virulent and avirulent strains of Aeromonas hydrophila isolated from diseased fish.
PG  - 999-1009
AB  - Aeromonas hydrophila, a normal inhabitant of aquatic environments, is an
      opportunistic pathogen of a variety of aquatic and terrestrial animals,
      including humans. A. hydrophila PPD134/91 is defined as virulent whereas
      PPD35/85 is defined as avirulent on the basis of their different LD50
      values in fish. Suppression subtractive hybridization (SSH) was used to
      identify genetic differences between these two strains. Sixty-nine genomic
      regions of differences were absent in PPD35/85, and the DNA sequences of
      these regions were determined. Sixteen ORFs encoded by 23 fragments showed
      high homology to known proteins of other bacteria. ORFs encoded by the
      remaining 46 fragments were identified as new proteins of A. hydrophila,
      showing no significant homology to any known proteins. Among these
      PPD134/91-specific genes, 22 DNA fragments (21 ORFs) were present in most
      of the eight virulent strains studied but mostly absent in the seven
      avirulent strains, suggesting that they are universal virulence genes in
      A. hydrophila. The PPD134/91-specific genes included five known virulence
      factors of A. hydrophila: haemolysin (hlyA), protease (oligopeptidase A),
      outer-membrane protein (Omp), multidrug-resistance protein and
      histone-like protein (HU-2). Another 47 DNA fragments (44 ORFs) were
      mainly present in PPD134/91, indicating the heterogeneity among motile
      aeromonads. Some of these fragments encoded virulence determinants. These
      included genes for the synthesis of O-antigen and type II
      restriction/modification system. The results indicated that SSH is
      successful in identifying genetic differences and virulence genes among
      different strains of A. hydrophila.
AU  - Zhang YL
AU  - Ong CT
AU  - Leung KY
PT  - Journal Article
TA  - Microbiology
JT  - Microbiology
SO  - Microbiology 2000 146: 999-1009.

PMID- 12019446
VI  - 34
DP  - 2002
TI  - Hairpin probes for real-time assay of restriction endonucleases.
PG  - 329-332
AB  - New fluorogenic probes for restriction endonucleases based on molecular beacons were
      developed. These hairpin probes were single-stranded
      oligonucleotides that had stem-and-loop structure and carried
      5'-fluorophor moiety and 3'-quencher moiety. Their stem sequences were
      designed as recognition sites for restriction endonucleases and loop
      sequences were unrelated nucleotides. Upon cleavage by endonuclease,
      these probes became fluorescent and thus could trace the enzyme
      activity continuously. Two probes were designed for BglII and NcoI,
      respectively, and each was labeled with a fluorophor of different
      color. The results showed that the two probes could specifically assay
      for the corresponding enzymes either individually or simultaneously in
      a real-time mode. Considering the simplicity, quantification and high
      throughput, these probes could be extended to other applications such
      as drug screening, protein-nucleic acid interaction study and searching
      for small molecule DNA cleavage agents.
AU  - Zhang YY
AU  - Li QG
AU  - Liang JX
AU  - Zhu YB
PT  - Journal Article
TA  - Acta Biochim. Biophys. Sin.
JT  - Acta Biochim. Biophys. Sin.
SO  - Acta Biochim. Biophys. Sin. 2002 34: 329-332.

PMID- 25342673
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of the Novel Exopolysaccharide-Producing Bacterium Altibacter lentus Strain JLT2010T, Isolated from Deep Seawater of the South China  Sea.
PG  - e00954-14
AB  - Altibacter lentus strain JLT2010(T) is the type strain of the recently identified novel genus
      and species of the family Flavobacteriaceae and was first isolated
      from deep seawater of the South China Sea. It can produce exopolysaccharide. Here
      we report the first draft genome of JLT2010(T) (3,160,033 bp, with GC content of
      42.12%) and major findings from its annotation. It is the first reported genome
      in the genus Altibacter.
AU  - Zhang Z
AU  - Chen Y
AU  - Fu Y
AU  - Jiao N
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00954-14.

PMID- 19815893
VI  - 81
DP  - 2009
TI  - Spatial variation of Yersinia pestis from Yunnan Province of China.
PG  - 714-717
AB  - Yunnan Province of China is considered the site of origin for modern
      plague. We analyzed the genotypes of eight Yersinia pestis strains
      isolated from three counties in Yunnan Province by pulse field gel
      electrophoresis (PFGE). PFGE showed that strains isolated from the same
      site were identical regardless of hosts or year of isolation. However, Y.
      pestis strains isolated from geographically distinct loci were genetically
      divergent. Whole genome sequences of two strains from two foci in Yunnan
      showed that the genetic variation of Y. pestis strains was caused by
      genome rearrangement. We concluded that Y. pestis strains in each epidemic
      focus in Yunnan were a clonal population and selected by host
      environments. The genomic variability of the Y. pestis strains from
      different foci were caused by genome rearrangement, which may provide a
      positive selective advantage for Y. pestis to adapt to its host
      environments.
AU  - Zhang Z
AU  - Hai R
AU  - Song Z
AU  - Xia L
AU  - Liang Y
AU  - Cai H
AU  - Liang Y
AU  - Shen X
AU  - Zhang E
AU  - Xu J
AU  - Yu D
AU  - Yu XJ
PT  - Journal Article
TA  - Am. J. Trop. Med. Hyg.
JT  - Am. J. Trop. Med. Hyg.
SO  - Am. J. Trop. Med. Hyg. 2009 81: 714-717.

PMID- 19465650
VI  - 191
DP  - 2009
TI  - Complete genome sequence of Lactobacillus plantarum JDM1.
PG  - 5020-5021
AB  - Lactobacillus plantarum is a commonly used lacic acid bacteria (LAB) species as probiotics. We
      have sequenced the genome of Lactobacillus
      plantarum JDM1, which is a Chinese commercial LAB with several probiotic
      functions, with a GS 20 system. We recommend each commercial probiotics
      strain should has the complete genome sequenced to insure the safety and
      stability.
AU  - Zhang Z
AU  - Liu C
AU  - Zhu Y
AU  - Zhong Y
AU  - Zhu Y
AU  - Zheng H
AU  - Zhao GP
AU  - Wang SY
AU  - Guo X
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2009 191: 5020-5021.

PMID- 28183773
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of an Attenuated Streptococcus agalactiae Strain Isolated from the Gut of a Nile Tilapia (Oreochromis niloticus).
PG  - e01627-16
AB  - Streptococcus agalactiae is a pathogen that causes severe anthropozoonosis within a broad
      range of hosts from aquatic animals to mammals, including human beings.
      Here, we describe the draft genome of S. agalactiae HZAUSC001, a low-virulent
      strain isolated from the gut of a moribund tilapia (Oreochromis niloticus) in
      China.
AU  - Zhang Z
AU  - Yu A
AU  - Lan J
AU  - Zhang Y
AU  - Zhang H
AU  - Li Y
AU  - Hu M
AU  - Cheng J
AU  - Wei S
AU  - Lin L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01627-16.

PMID- 15538812
VI  - 76
DP  - 2004
TI  - Enzymatic regional methylation assay for determination of CpG methylation density.
PG  - 6829-6832
AB  - DNA methylation is a critical mechanism for epigenetic gene regulation. In mammalian cells,
      CpG methylation density often influences the
      transcription level of related genes. Here, we report a short and
      accurate method to determine the CpG methylation density of any DNA
      region by sequentially applying bisulfite PCR and SssI (CpG) methylase.
      We introduced simple and efficient binding and washing steps that
      greatly improve the previous methodology and considerably enhance the
      accuracy of the assay. The accuracy of this method allows the detection
      of differences at the level of a single CpG methylation site when
      homogeneous PCR product was used as substrate. We validated our method
      by bisulfite sequencing multiple clones of samples with variable levels
      of CpG methylation. We envision that for its accuracy, simplicity,
      low-cost, flexibility, minimum instrumentation requirements, and
      high-throughput potential our method could greatly benefit research on
      DNA methylation.
AU  - Zhang ZJ
AU  - Chen CQ
AU  - Manev H
PT  - Journal Article
TA  - Anal. Chem.
JT  - Anal. Chem.
SO  - Anal. Chem. 2004 76: 6829-6832.

PMID- 26070743
VI  - 427
DP  - 2015
TI  - Crystal Structure of Human DNA Methyltransferase 1.
PG  - 2520-2531
AB  - DNMT1 (DNA methyltransferase 1) is responsible for propagating the DNA methylation patterns
      during DNA replication. DNMT1 contains, in addition to a
      C-terminal methyltransferase domain, a large N-terminal regulatory region that is
      composed of an RFTS (replication foci targeting sequence) domain, a CXXC zinc
      finger domain and a pair of BAH (bromo adjacent homology) domains. The regulatory
      domains of DNMT1 mediate a network of protein-protein and protein-DNA
      interactions to control the recruitment and enzymatic activity of DNMT1. Here we
      report the crystal structure of human DNMT1 with all the structural domains
      (hDNMT1, residues 351-1600) in complex with S-adenosyl-l-homocysteine at 2.62A
      resolution. The RFTS domain directly associates with the methyltransferase
      domain, thereby inhibiting the substrate binding of hDNMT1. Through structural
      analysis, mutational, biochemical and enzymatic studies, we further identify that
      a linker sequence between the CXXC and BAH1 domains, aside from its role in the
      CXXC domain-mediated DNMT1 autoinhibition, serves as an important regulatory
      element in the RFTS domain-mediated autoinhibition. In comparison with the
      previously determined structure of mouse DNMT1, this study also reveals a number
      of distinct structural features that may underlie subtle functional diversity
      observed for the two orthologues. In addition, this structure provides a
      framework for understanding the functional consequence of disease-related hDNMT1
      mutations.
AU  - Zhang ZM
AU  - Liu S
AU  - Lin K
AU  - Luo Y
AU  - Perry JJ
AU  - Wang Y
AU  - Song J
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2015 427: 2520-2531.

PMID- 29414941
VI  - 554
DP  - 2018
TI  - Structural basis for DNMT3A-mediated de novo DNA methylation.
PG  - 387-391
AB  - DNA methylation by de novo DNA methyltransferases 3A (DNMT3A) and 3B (DNMT3B) at  cytosines is
      essential for genome regulation and development. Dysregulation of
      this process is implicated in various diseases, notably cancer. However, the
      mechanisms underlying DNMT3 substrate recognition and enzymatic specificity
      remain elusive. Here we report a 2.65-angstrom crystal structure of the
      DNMT3A-DNMT3L-DNA complex in which two DNMT3A monomers simultaneously attack two
      cytosine-phosphate-guanine (CpG) dinucleotides, with the target sites separated
      by 14 base pairs within the same DNA duplex. The DNMT3A-DNA interaction involves
      a target recognition domain, a catalytic loop, and DNMT3A homodimeric interface.
      Arg836 of the target recognition domain makes crucial contacts with CpG, ensuring
      DNMT3A enzymatic preference towards CpG sites in cells. Haematological
      cancer-associated somatic mutations of the substrate-binding residues decrease
      DNMT3A activity, induce CpG hypomethylation, and promote transformation of
      haematopoietic cells. Together, our study reveals the mechanistic basis for
      DNMT3A-mediated DNA methylation and establishes its aetiological link to human
      disease.
AU  - Zhang ZM
AU  - Lu R
AU  - Wang P
AU  - Yu Y
AU  - Chen D
AU  - Gao L
AU  - Liu S
AU  - Ji D
AU  - Rothbart SB
AU  - Wang Y
AU  - Wang GG
AU  - Song J
PT  - Journal Article
TA  - Nature
JT  - Nature
SO  - Nature 2018 554: 387-391.

PMID- 21685274
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of a Novel Clinical Isolate, the Nontuberculous Mycobacterium Strain JDM601.
PG  - 4300-4301
AB  - Mycobacteriosis is on the increase. Nontuberculous mycobacteria (NTM) are resistant to most
      antituberculosis drugs naturally. We determined the
      complete genome sequence of a novel NTM strain, JDM601, of the
      Mycobacterium terrae complex, which was isolated from a patient with
      tuberculosis-like disease and with various antibiotic resistances.
AU  - Zhang ZY
AU  - Sun ZQ
AU  - Wang ZL
AU  - Wen ZL
AU  - Sun QW
AU  - Zhu ZQ
AU  - Song YZ
AU  - Zhao JW
AU  - Wang HH
AU  - Zhang SL
AU  - Guo XK
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4300-4301.

PMID- 21642468
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of the Anaerobic, Halophilic Alkalithermophile Natranaerobius thermophilus JW/NM-WN-LFT.
PG  - 4023
AB  - The genome of the anaerobic halophilic alkalithermophile Natranaerobius thermophiles consists
      of one 3,165,557 bp chromosome and two plasmids
      (17,207 bp, 8,689 bp). The present study is the first to report the
      completely sequenced genome of an anaerobic polyextremophile and genes
      associated with roles in regulation of intracellular osmotic pressure, pH
      homeostasis, and growth at elevated temperatures.
AU  - Zhao B
AU  - Mesbah NM
AU  - Dalin E
AU  - Goodwin L
AU  - Nolan M
AU  - Pitluck S
AU  - Chertkov O
AU  - Brettin TS
AU  - Han J
AU  - Larimer FW
AU  - Land ML
AU  - Hauser L
AU  - Kyrpides N
AU  - Wiegel J
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 4023.

PMID- 
VI  - 21
DP  - 2011
TI  - A Universal, Label-Free, and Sensitive Optical Enzyme-Sensing System for Nuclease and Methyltransferase Activity Based on Light Scattering of Carbon Nanotubes.
PG  - 583-590
AB  - A label-free, enzyme-responsive nanosystem that uses a DNA/single-walled carbon nanotube
      (SWNT) assembly as the substrate is
      demonstrated for the sensitive, universal detection of restriction and
      nonrestriction endonucleases as well as methyltransferases in a
      homogeneous solution on the basis of light scattering (LS) of carbon
      nanotubes. This protocol is based on the different binding affinities
      of SWNTs to single-and double-stranded DNA. This difference can lead to
      different LS signals that can be used for the detection of nuclease
      cleavage activity. The assay only requires a label-free oligonucleotide
      probe, significantly reducing the typical cost. The LS technique and
      the use of a nuclease-specific oligonucleotide probe impart
      extraordinarily high sensitivity and selectivity. This light scattering
      assay is universal and label-free with a detection limit of 5 x 10(-6)
      U mu L-1 for S1 nuclease, 1 x 10(-4) U mu L-1 for EcoRI endonuclease,
      and 1 x 10(-2) U mu L-1 for EcoRI methylase. In principle, this assay
      can be used to detect any kind of nuclease by simply changing the DNA
      sequences of the specific probe.
AU  - Zhao C
AU  - Qu KG
AU  - Song YJ
AU  - Ren JS
AU  - Qu XG
PT  - Journal Article
TA  - Adv. Funct. Mater.
JT  - Adv. Funct. Mater.
SO  - Adv. Funct. Mater. 2011 21: 583-590.

PMID- 23144411
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Bacillus pumilus BA06, a Producer of Alkaline Serine Protease with Leather-Dehairing Function.
PG  - 6668-6669
AB  - Bacillus pumilus BA06 was isolated from the proteinaceous soil and produced an extracellular
      alkaline protease with leather-dehairing function. The genome of
      BA06 was sequenced. The comparative genome analysis indicated that strain BA06 is
      different in genome from the other B. pumilus strains, with limited insertions,
      deletions, and rearrangements.
AU  - Zhao CW
AU  - Wang HY
AU  - Zhang YZ
AU  - Feng H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6668-6669.

PMID- 15940803
VI  - 34
DP  - 2005
TI  - A review on DNA methyltransferases and early embryo development including DNA methyltransferases I (DnmT1) and DNA methyltransferases  III (DnmT3).
PG  - 281-284
AB  - 
AU  - Zhao DM
AU  - Jin F
AU  - Huang HF
PT  - Journal Article
TA  - Zhejiang Da Xue Xue Bao Yi Xue Ban
JT  - Zhejiang Da Xue Xue Bao Yi Xue Ban
SO  - Zhejiang Da Xue Xue Bao Yi Xue Ban 2005 34: 281-284.

PMID- 
VI  - 5
DP  - 2010
TI  - Sequencing and Genetic Variation of Multidrug Resistance Plasmids in Klebsiella pneumoniae.
PG  - E10141
AB  - Background: The development of multidrug resistance is a major problem in the treatment of
      pathogenic microorganisms by distinct antimicrobial agents. Characterizing the genetic
      variation among plasmids from different bacterial species or strains is a key step towards
      understanding the mechanism of virulence and their evolution.
      Results: We applied a deep sequencing approach to 206 clinical strains of Klebsiella
      pneumoniae collected from 2002 to 2008 to understand the genetic variation of multidrug
      resistance plasmids, and to reveal the dynamic change of drug resistance over time. First, we
      sequenced three plasmids (70 Kb, 94 Kb, and 147 Kb) from a clonal strain of K. pneumoniae
      using Sanger sequencing. Using the Illumina sequencing technology, we obtained more than 17
      million of short reads from two pooled plasmid samples. We mapped these short reads to the
      three reference plasmid sequences, and identified a large
      number of single nucleotide polymorphisms (SNPs) in these pooled plasmids. Many of these SNPs
      are present in drugresistance genes. We also found that a significant fraction of short reads
      could not be mapped to the reference sequences, indicating a high degree of genetic variation
      among the collection of K. pneumoniae isolates. Moreover, we identified that plasmid
      conjugative transfer genes and antibiotic resistance genes are more likely to suffer from
      positive selection, as indicated by the elevated rates of nonsynonymous substitution.
      Conclusion: These data represent the first large-scale study of genetic variation in multidrug
      resistance plasmids and provide insight into the mechanisms of plasmid diversification and the
      genetic basis of antibiotic resistance.
AU  - Zhao F
AU  - Bai J
AU  - Wu J
AU  - Liu J
AU  - Zhou M
AU  - Xia S
AU  - Wang S
AU  - Yao X
AU  - Yi H
AU  - Lin M
AU  - Gao S
AU  - Zhou T
AU  - Xu Z
AU  - Niu Y
AU  - Bao Q
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2010 5: E10141.

PMID- 16368872
VI  - 24
DP  - 2006
TI  - Genome-wide analysis of restriction-modification system in unicellular and filamentous cyanobacteria.
PG  - 181-190
AB  - Cyanobacteria are an ancient group of gram-negative bacteria with strong genome size variation
      ranging from 1.6 to 9.1 Mb. Here, we first
      retrieved all the putative restriction-modification (RM) genes in the
      draft genome of Spirulina and then performed a range of comparative and
      bioinformatic analyses on RM genes from unicellular and filamentous
      cyanobacterial genomes. We have identified 6 gene clusters containing
      putative Type I RMs and 11 putative Type II RMs or the solitary
      methyltransferases (MTases). RT-PCR analysis reveals that 6 of 18
      MTases are not expressed in Spirulina, whereas one hsdM gene, with a
      mutated cognate hsdS, was detected to be expressed. Our results
      indicate that the number of RM genes in filamentous cyanobacteria is
      significantly higher than in unicellular species, and this expansion of
      RM systems in filamentous cyanobacteria may be related to their wide
      range of ecological tolerance. Furthermore, a coevolutionary pattern is
      found between hsdM and hsdR, with a large number of site pairs
      positively or negatively correlated, indicating the functional
      importance of these pairing interactions between their tertiary
      structures. No evidence for positive selection is found for the
      majority of RMs, e. g., hsdM, hsdS, hsdR, and Type II restriction
      endonuclease gene families, while a group of MTases exhibit a
      remarkable signature of adaptive evolution. Sites and genes identified
      here to have been under positive selection would provide targets for
      further research on their structural and functional evaluations.
AU  - Zhao FQ
AU  - Zhang XW
AU  - Liang CW
AU  - Wu JY
AU  - Bao QY
AU  - Qin S
PT  - Journal Article
TA  - Physiol. Genomics
JT  - Physiol. Genomics
SO  - Physiol. Genomics 2006 24: 181-190.

PMID- 24260216
VI  - 8
DP  - 2013
TI  - Enzymatic Cleavage of Type II Restriction Endonucleases on the 2 '-O-Methyl Nucleotide and Phosphorothioate Substituted DNA.
PG  - e79415
AB  - The effects of nucleotide analogue substitution on the cleavage efficiencies of type II
      restriction endonucleases have been investigated. Six restriction endonucleases (EcoRV, SpeI,
      XbaI, XhoI, PstI and SphI) were investigated respectively regarding their cleavage when
      substrates were substituted by 2'-O-methyl nucleotide (2'-OMeN) and phosphorothioate (PS).
      Substitutions were made in the recognition sequence and the two nucleotides flanking the
      recognition sequence for each endonuclease. The endonu lease cleavage efficiencies were
      determined using FRET-based assay. Results demonstrated a position-dependent inhibitory effect
      of substitution on the cleavage efficiency for all the six endonucleases. In general, the
      2'-OMeN substitutions had greater impact than the PS substitutions on the enzymatic
      activities. Nucleotides of optimal substitutions for protection against RE cleavage were
      identified. Experimental results and conclusions in this study facilitate our insight into the
      DNA-protein interactions  and the enzymatic cleavage mechanism, particularly for those whose
      detailed structure information is not available. In addition, the information could benefit
      the development of bioengineering and synthetic biology.
AU  - Zhao G
AU  - Li J
AU  - Tong Z
AU  - Zhao B
AU  - Mu R
AU  - Guan Y
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2013 8: e79415.

PMID- 
VI  - 
DP  - 2008
TI  - Characterization of bacterial homing endonuclease I-Ssp6803I.
PG  - 1-142
AB  - The homing endonuclease I-Ssp6803I causes the insertion and persistence of a group I
      self-splicing intron into the anticodon loop of the tRNAfMet gene in the cyanobacteria
      Synechocystis PCC6803.  This enzyme and its host intron represent the only known combination
      of a persistent intron and associated homing endonuclease within bacterial tRNA genes.  In
      this study, we predicted that this enzyme, which is dissimilar to other known homing
      endonucleases, might contain the PD-(D/E)XK nuclease catalytic motif -- a fold normally
      associated with bacterial restriction endonucleases.  This prediction, combined with a
      mutational screen for catalytically inactivating point mutations, allowed us to express,
      solubilize and crystallize I-Ssp6803I in complex with its target DNA.  The 3.1A crystal
      structure of the protein-DNA complex confirmed the presence of the PD-(D/E)XK motif and also
      revealed the use of a unique tetrameric assembly to promote recognition of a single long
      target site.  The binding specificity profile of I-Ssp6803I was then determined by measuring
      the effect of every possible base substitution across its 23-basepair target site.  The
      endonuclease displays relatively low binding specificity, corresponding to a profile reflects
      sequence constraints on its host tRNAfMet gene.
AU  - Zhao L
PT  - Journal Article
TA  - Ph.D. Thesis, University of Washington, Seattle, USA
JT  - Ph.D. Thesis, University of Washington, Seattle, USA
SO  - Ph.D. Thesis, University of Washington, Seattle, USA 2008 : 1-142.

PMID- 25883291
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Lysinibacillus fusiformis Strain SW-B9, a Novel Strain for Biotransformation of Isoeugenol to Vanillin.
PG  - e00289-15
AB  - Lysinibacillus fusiformis SW-B9 was the first reported strain in L. fusiformis showing
      effective biotransformation of isoeugenol to vanillin. Here, we report
      the annotated genome of strain SW-B9, which has special pathways for producing
      vanillin. The genome will provide a genetic basis for better understanding the
      physiology of this species.
AU  - Zhao L
AU  - Bao G
AU  - Geng B
AU  - Song J
AU  - Li Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00289-15.

PMID- 17410205
VI  - 26
DP  - 2007
TI  - The restriction fold turns to the dark side: a bacterial homing endonuclease with a PD-(D/E)-XK motif.
PG  - 2432-2442
AB  - The homing endonuclease I-Ssp6803I causes the insertion of a group I intron into a bacterial
      tRNA gene-the only example of an invasive mobile
      intron within a bacterial genome. Using a computational fold prediction,
      mutagenic screen and crystal structure determination, we demonstrate that
      this protein is a tetrameric PD-(D/E)-XK endonuclease-a fold normally used
      to protect a bacterial genome from invading DNA through the action of
      restriction endonucleases. I-Ssp6803I uses its tetrameric assembly to
      promote recognition of a single long target site, whereas restriction
      endonuclease tetramers facilitate cooperative binding and cleavage of two
      short sites. The limited use of the PD-(D/E)-XK nucleases by mobile
      introns stands in contrast to their frequent use of LAGLIDADG and HNH
      endonucleases-which in turn, are rarely incorporated into
      restriction/modification systems.
AU  - Zhao L
AU  - Bonocora RP
AU  - Shub DA
AU  - Stoddard BL
PT  - Journal Article
TA  - EMBO J.
JT  - EMBO J.
SO  - EMBO J. 2007 26: 2432-2442.

PMID- 19038269
VI  - 385
DP  - 2009
TI  - Activity and Specificity of the Bacterial PD-(D/E)XK Homing Endonuclease I-Ssp6803I.
PG  - 1498-1510
AB  - The restriction endonuclease fold [a three-layer alpha-beta sandwich containing variations of
      the PD-(D/E)XK nuclease motif] has been greatly
      diversified during evolution, facilitating its use for many biological
      functions. Here we characterize DNA binding and cleavage by the PD-(D/E)XK
      homing endonuclease I-Ssp6803I. Unlike most restriction endonucleases
      harboring the same core fold, the specificity profile of this enzyme
      extends over a long (17 bp) target site. The DNA binding and cleavage
      specificity profiles of this enzyme were independently determined and
      found to be highly correlated. However, the DNA target sequence contains
      several positions where binding and cleavage activities are not tightly
      coupled: individual DNA base-pair substitutions at those positions that
      significantly decrease cleavage activity have minor effects on binding
      affinity. These changes in the DNA target sequence appear to correspond to
      substitutions that uniquely increase the free energy change between the
      ground state and the transition state, rather than simply decreasing the
      overall DNA binding affinity. The specificity of the enzyme reflects
      constraints on its host gene and limitations imposed by the enzyme's
      quaternary structure and illustrate the highly diverse repertoire of DNA
      recognition specificities that can be adopted by the related folds
      surrounding the PD-(D/E)XK nuclease motif.
AU  - Zhao L
AU  - Pellenz S
AU  - Stoddard BL
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2009 385: 1498-1510.

PMID- 27856576
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Lactobacillus plantarum XJ25 Isolated from Chinese Red Wine.
PG  - e01216-16
AB  - Here, we present the draft genome sequence of Lactobacillus plantarum XJ25, isolated from
      Chinese red wine that had undergone spontaneous malolactic
      fermentation, which consists of 25 contigs and is 3,218,018 bp long.
AU  - Zhao M
AU  - Liu S
AU  - He L
AU  - Tian Y
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01216-16.

PMID- 23209250
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of the Flocculating Zymomonas mobilis Strain ZM401 (ATCC 31822).
PG  - 7008-7009
AB  - Zymomonas mobilis ZM401 is a flocculating strain which can be self-immobilized within
      fermentors for a high-cell-density culture to improve ethanol
      productivity, as well as high-gravity fermentation to increase ethanol titer, due
      to its improved ethanol tolerance associated with the morphological change. Here,
      we report its draft genome sequence.
AU  - Zhao N
AU  - Bai Y
AU  - Zhao XQ
AU  - Yang ZY
AU  - Bai FW
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 7008-7009.

PMID- 27056218
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Zymomonas mobilis ZM481 (ATCC 31823).
PG  - e00193-16
AB  - Zymomonas mobilisZM481 (ATCC 31823) is an ethanol-tolerant strain that can produce the highest
      level of ethanol inZ. mobilisfrom glucose in the shortest
      time. Here, we report a draft genome sequence of ZM481, which can help us
      understand the genes related to the ethanol tolerance of this strain.
AU  - Zhao N
AU  - Pan Y
AU  - Liu H
AU  - Cheng Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00193-16.

PMID- 25657282
VI  - 3
DP  - 2015
TI  - Genome Sequence of Sphingobium yanoikuyae B1, a Polycyclic Aromatic Hydrocarbon-Degrading Strain.
PG  - e01522-14
AB  - Sphingobium yanoikuyae B1 can utilize biphenyl, naphthalene, phenanthrene, toluene, and
      m-/p-xylene as sole sources of carbon and energy. Here, we present a
      5.2-Mb assembly of its genome. An analysis of the genome can provide insights
      into the mechanisms of polycyclic aromatic hydrocarbon (PAH) degradation and
      potentially aid in bioremediation applications.
AU  - Zhao Q
AU  - Hu H
AU  - Wang W
AU  - Peng H
AU  - Zhang X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01522-14.

PMID- 21398542
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of the Lactobacillus helveticus H10.
PG  - 2666-2667
AB  - Lactobacillus helveticus strain H10 was isolated from the traditional fermented milk in Tibet,
      China. We sequenced the whole genome of strain
      H10 and compared it to the published genome sequence of Lactobacillus
      helveticus DPC4571.
AU  - Zhao W
AU  - Chen Y
AU  - Sun Z
AU  - Wang J
AU  - Zhou Z
AU  - Sun T
AU  - Wang L
AU  - Chen W
AU  - Zhang H
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 2666-2667.

PMID- 26044420
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Pseudomonas syringae pv. persicae NCPPB 2254.
PG  - e00555-15
AB  - Pseudomonas syringae pv. persicae is a pathogen that causes bacterial decline of  stone fruit.
      Here, we report the draft genome sequence for P. syringae pv.
      persicae, which was isolated from Prunus persica.
AU  - Zhao W
AU  - Jiang H
AU  - Tian Q
AU  - Hu J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00555-15.

PMID- 25288278
VI  - 65
DP  - 2015
TI  - Thermococcus eurythermalis sp. nov., a conditional piezophilic hyperthermophilic archaeon with a wide temperature range isolated from an oil-immersed chimney in the Guaymas Basin.
PG  - 30-35
AB  - A conditional piezophilic hyperthermophilic archaeon with a wide temperature/ pH/
      pressure range was isolated from an oil-immersed hydrothermal chimney at a depth
      of 2006.9 m in the Guaymas Basin. The enrichment and isolation of strain A501T
      were performed at 80 degrees C at 0.1 MPa. The isolate, A501T, is an irregular
      motile coccus with a polar tuft of flagella and is generally 0.6-2.6 mum in
      diameter. Growth was detected over the range of 50-100 degrees C (optimum growth
      at 85 degrees C) at atmospheric pressure and was observed at 102 degrees C at a
      pressure of 10 MPa. At 85 degrees C, growth was observed at a pressure of 0.1-70
      MPa (optimum pressure 0.1 MPa-30 MPa), while at 95 degrees C, the pressure of
      growth ranged from 0.1 MPa to 50 MPa (optimum pressure 10 MPa). Cells of strain
      A501T grew at pH 4-9 (optimum pH 7.0) and a NaCl concentration of 1.0-5.0% (w/v)
      (optimum concentration 2.5%) This isolate was an anaerobic
      chemoorgano-heterotroph and was able to utilize yeast extract, peptone, tryptone
      and starch as the single carbon source for growth. Elemental sulfur and cysteine
      stimulated growth; however, these molecules were not necessary. The G+C content
      of the complete genome was 53.47%. The results of the 16S rRNA gene analysis
      indicated that strain A501T belongs to the genus Thermococcus. There was no
      significant homology between strain A501T and the phylogenetically related
      Thermococcus species based on complete genome sequence alignments and calculation
      of the average nucleotide identity and the tetranucleotide signature frequency
      correlation coefficient. These results indicate that strain A501T represents a
      novel species, Thermococcus eurythermalis sp. nov. The type strain is A501T
      (=CGMCC 7834T; =JCM 30233T).
AU  - Zhao W
AU  - Zeng X
AU  - Xiao X
PT  - Journal Article
TA  - Int. J. Syst. Evol. Microbiol.
JT  - Int. J. Syst. Evol. Microbiol.
SO  - Int. J. Syst. Evol. Microbiol. 2015 65: 30-35.

PMID- 25767235
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Bacillus amyloliquefaciens Strain BH072, Isolated from Honey.
PG  - e00098-15
AB  - The genome of Bacillus amyloliquefaciens strain BH072, isolated from a honey sample and
      showing strong antimicrobial activity against plant pathogens, is 4.07
      Mb and harbors 3,785 coding sequences (CDS). Several gene clusters for
      nonribosomal synthesis of antimicrobial peptides and a complete gene cluster for
      biosynthesis of mersacidin were detected.
AU  - Zhao X
AU  - de Jong A
AU  - Zhou Z
AU  - Kuipers OP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00098-15.

PMID- 28428297
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Mycobacterium avium subsp. hominissuis Strain H87 Isolated from an Indoor Water Sample.
PG  - e00189-17
AB  - Mycobacterium avium subsp. hominissuis is an environmentally acquired bacterium known to cause
      pulmonary and soft tissue infections, lymphadenitis, and
      disseminated disease in humans. We report here the complete genome sequence of
      strain H87, isolated from an indoor water sample, as a single circular chromosome
      of 5,626,623 bp with a G+C content of 68.8%.
AU  - Zhao X
AU  - Epperson LE
AU  - Hasan NA
AU  - Honda JR
AU  - Chan ED
AU  - Strong M
AU  - Walter ND
AU  - Davidson RM
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00189-17.

PMID- 22843605
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of the Marine Actinomycete Streptomyces sulphureus L180, Isolated from Marine Sediment.
PG  - 4482
AB  - Marine-derived actinobacteria are rich sources of valuable natural products and industrial
      enzymes for biotechnology applications. The marine-derived
      Streptomyces sulphureus strain L180 was isolated from the marine sediment in a
      sea cucumber farm at a depth of about 10 m in Dalian, China, and its 16S rRNA
      gene sequence was determined to have the highest identity to that of Streptomyces
      sulphureus NRRL B-1627(T) (99.65%). Here, we report the draft genome sequence of
      this strain.
AU  - Zhao X
AU  - Geng X
AU  - Chen C
AU  - Chen L
AU  - Jiao W
AU  - Yang C
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4482.

PMID- 21914869
VI  - 193
DP  - 2011
TI  - Draft Genome Sequence of the Marine Sediment-Derived Actinomycete Streptomyces xinghaiensis NRRL B24674T.
PG  - 5543
AB  - Actinobacteria are a rich source of novel natural products. We recently characterized
      Streptomyces xinghaiensis NRRL B24674(T) as a novel species
      of marine origin. Here we report the draft genome sequence of this
      species. This is the first validly published marine streptomycete for
      which a genome sequence has been presented.
AU  - Zhao X
AU  - Yang T
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 5543.

PMID- 22815439
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Geobacillus thermoglucosidans TNO-09.020, a Thermophilic Sporeformer Associated with a Dairy-Processing Environment.
PG  - 4118
AB  - Thermophilic spore-forming bacteria are a common cause of contamination in dairy  products. We
      isolated the thermophilic strain Geobacillus thermoglucosidans
      TNO-09.020 from a milk processing plant and report the complete genome of a dairy
      plant isolate consisting of a single chromosome of 3.75 Mb.
AU  - Zhao Y
AU  - Caspers MP
AU  - Abee T
AU  - Siezen RJ
AU  - Kort R
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4118.

PMID- 23466393
VI  - 165
DP  - 2013
TI  - Molecular cloning and expression-profile analysis of sea cucumber DNA (Cytosine-5)-methyltransferase 1 and methyl-CpG binding domain type 2/3 genes during aestivation.
PG  - 26-35
AB  - The sea cucumber Apostichopus japonicus Selenka survives high summer temperature by entering
      aestivation, characterized by hypometabolism and global gene silencing. We investigated the
      hypothesis that aestivation is associated with DNA methylation-dependent epigenetic mechanisms
      by cloning, sequencing and measuring the transcript abundances of two genes dnmt1 and mbd2/3,
      which comprise the DNA methylation system in A. japonicus Selenka. The deduced amino acid
      sequences and characteristic motifs of sea cucumber DNMT1 and MBD2/3 showed high homology to
      those of their mammalian counterparts. Quantitative real-time RT-PCR analysis showed that
      dnmt1 and mbd2/3 genes were similarly expressed in all four tissues examined (intestine,
      respiratory tree, muscle and body wall). dnmt1 expression in the intestine was up-regulated
      during deep aestivation (P < 0.05), while mbd2/3 was over-expressed in both the intestine and
      respiratory tree during the same period (P < 0.01). No differences in expression levels were
      observed between other tissues. The results of this study suggest that DNA methylation may be
      involved in transcriptional silencing, and that the intestine is the major site for epigenetic
      regulation during aestivation in the sea cucumber.
AU  - Zhao Y
AU  - Chen M
AU  - Su L
AU  - Wang T
AU  - Liu S
AU  - Yang H
PT  - Journal Article
TA  - Comp. Biochem. Physiol. B, Biochem. Mol. Biol.
JT  - Comp. Biochem. Physiol. B, Biochem. Mol. Biol.
SO  - Comp. Biochem. Physiol. B, Biochem. Mol. Biol. 2013 165: 26-35.

PMID- 26769938
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a Selenite- and Tellurite-Reducing Marine Bacterium, Lysinibacillus sp. Strain ZYM-1.
PG  - e01552-15
AB  - Lysinibacillus sp. ZYM-1, a Gram-positive strain isolated from marine sediments,  reduces
      selenite and tellurite efficiently. Meanwhile, it also exhibits high
      resistance to Zn2+ and Mn2+. Here, we report the draft genome sequence of strain
      ZYM-1, which contains genes related to selenite and tellurite reduction and also
      metal resistance.
AU  - Zhao Y
AU  - Dong Y
AU  - Zhang Y
AU  - Che L
AU  - Pan H
AU  - Zhou H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01552-15.

PMID- 29773614
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of a Dickeya fangzhongdai Type Strain Causing Bleeding Canker of Pear Tree Trunks.
PG  - e00177-18
AB  - Dickeya fangzhongdai DSM 101947(T) was isolated from pear trees (Pyrus pyrifolia) in Zhejiang
      Province, China, and is the causal agent of bleeding canker, a
      devastating disease of pear trees. Here, we provide the complete genome sequence
      of this bacterium, which has a 5,027,163-bp-long genome, including 4,375
      protein-coding genes and 100 RNA genes. This strain possesses a number of genes
      encoding virulence factors of pathogens.
AU  - Zhao Y
AU  - Tian Y
AU  - Li X
AU  - Hu B
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00177-18.

PMID- 24435860
VI  - 2
DP  - 2014
TI  - Complete Genome Sequence of Cronobacter sakazakii Strain CMCC 45402.
PG  - e01139-13
AB  - Cronobacter sakazakii is considered to be an important pathogen involved in life-threatening
      neonatal infections. Here, we report the annotated complete
      genome sequence of C. sakazakii strain CMCC 45402, obtained from a milk sample in
      China. The major findings from the genomic analysis provide a better
      understanding of the isolates from China.
AU  - Zhao Z
AU  - Wang L
AU  - Wang B
AU  - Liang H
AU  - Ye Q
AU  - Zeng M
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01139-13.

PMID- 1549492
VI  - 20
DP  - 1992
TI  - Restriction endonuclease from thermophilic bacterial species IV. Isolation and characterization of BpuB5I.
PG  - 1156
AB  - BpuB5I is a type II restriction endonuclease from a Bacillus pumilus strain
      isolated from soil.  To purify the enzyme, bacterial cells were grown on nine L
      agar plates at 55C overnight.  Cell pellet (3 g wet weight) obtained was
      resuspended in 10 ml extraction buffer (1) and disrupted by sonication.  The
      extract after centrifugation was dialysed against extraction buffer at 4C
      overnight and then passed through a heparin-affin gel column (7 ml bed volume).
      Enzyme eluted at 0.2 - 0.25 M NaCl gradient was concentrated and dialysed and
      then further purified by a Mono Q column with enzyme eluted at 0.3 M NaCl.  The
      purified enzyme was used to digest lambda, PhiX-174 and Ad-2 DNA (Fig. 1).
      Restriction patterns produced were identifical to those cleaved by mesophilic
      enzyme SplI which recognizes 5'CGTACG3'(2).  The cleavage site of BpuB5I was
      determined according to ref. 1 using PhiX-174 as the template and a 18 mer
      oligonucleotide with sequence 5'TCCGACTACCCTCCCGAC3' as the primer.  The primer
      was annealed to position 2691 - 2708 of the denatured PhiX-174 DNA and was
      extended through the BpuB5I site at position 2794.  Figure 2 shows that the
      cleaveage product of reaction I comigrates with the band corresponding to the
      first C nucleotide in the sequence CGTACG and reaction II comigrates with the
      band corresponding to the second C nucleotide.  Therefore, BpuB5I recognizes
      and cleaves 5'C^GTACG3'.  The optimal reaction buffer of BpuB5I contained 5 mM
      NaCl, 10 mM Tris.Cl, pH 8.0, 10 mM MgCl2, 1 mM dithiothreitol and optimal
      temperature was at 55C.
AU  - Zhao Z-H
AU  - Yung M-H
AU  - Cui T
AU  - Wang Y-Z
AU  - Shaw PC
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1992 20: 1156.

PMID- 10381621
VI  - 64
DP  - 1999
TI  - A site-specific endonuclease from the thermophilic strain Bacillus species F4.
PG  - 697-702
AB  - A strain producing the site-specific endonuclease BspF4I was found during screening of
      thermophilic bacteria isolated from soil.  The restriction endonuclease, free from contaminant
      nonspecific nucleases, was purified using three steps of column chromatography--on
      hydroxyapatite, blue agarose, and DEAE-Trisacryl. The enzyme is stable on storage and exhibits
      maximal activity at 48-56 degrees C in the presence of albumin in buffer containing 10 mM
      Tris-HCl (pH 7.5) and 10 mM MgCl2.  BspF4I recognizes the sequence 5;-GGNCC-3; on DNA and is
      an isomer and not an isoschizomer of the endonuclease Sau96I.  Unlike the prototype, BspF4I
      does not cleave the site in a defined way. A strand with purine in the center of the sequence
      is cleaved after the first G, as in the case of the prototype, while the strand with
      pyrimidine is cleaved either before or after the first G.
AU  - Zharmukhamedova TY
AU  - Privezencova NG
AU  - Shishova OV
AU  - Shiryaev SA
AU  - Zheleznaya LA
AU  - Matvienko NI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1999 64: 697-702.

PMID- 10217405
VI  - 448
DP  - 1999
TI  - R.SspD5I is a neoschizomer of HphI producing blunt end DNA fragments.
PG  - 38-40
AB  - The strain Staphylococcus species D5 produces a restriction enzyme.  It is the neoschizomer of
      HphI endonuclease, which cleaves DNA at a distance of eight nucleotides from the recognition
      sequences producing blunt end DNA fragments: 5'-GGTGA8N/-3' and 3'-CCACT8N/-5'.
AU  - Zheleznaya L
AU  - Shiryaev S
AU  - Zheleznyakova E
AU  - Matvienko N
AU  - Matvienko N
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1999 448: 38-40.

PMID- 12693983
VI  - 68
DP  - 2003
TI  - Regulatory C protein of the EcoRV modification-restriction system.
PG  - 125-132
AB  - The C gene product of the modification-restriction system PvuII binds to its own promoter (C
      box) and stimulates transcription of both the C gene and the endonuclease gene. According to
      our data the same regulatory mechanism is realized in the EcoRV system. It was found that
      upstream of the EcoRV endonuclease gene two ATG codons give rise to two open reading frames
      (ORF1 and ORF2) ending at the same point inside the endonuclease gene. Two DNA fragments
      corresponding to ORF1 and ORF2 were cloned, and the homogenous products of proteins encoded by
      them were found to be DNA-binding proteins. A specific DNA sequence (C box) recognized by the
      proteins was determined with DNAse I footprinting. The C box CCCATTTTGGGTTATCCCATTTTGGG is
      located inside ORF1 and, similar to the PvuII C box consisting of tandem repeats of 11
      nucleotides, is divided by four nucleotides. In its turn each of the repeats contains inverted
      repeats of four terminal nucleotides. The EcoRV C box sequence differs both from the PvuII C
      box sequence and from the proposed consensus sequence of C boxes in other
      modification-restriction systems.
AU  - Zheleznaya LA
AU  - Kainov DE
AU  - Yunusova AK
AU  - Matvienko NI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 2003 68: 125-132.

PMID- 8218558
VI  - 58
DP  - 1993
TI  - Two site-specific endonucleases from the thermophilic strain of Bacillus species LU11.
PG  - 1315-1322
AB  - Upon screening of natural strains of thermophilic bacteria, a strain has been found which
      contains two restriction endonucleases. One of those, BspLU11II, is an isoschizomer of XbaI,
      while the other one, BspLU11I, recognizes the new palindromic sequence 5'-A^CATGT-3' and
      cleaves it as indicated by the arrow. Functionally pure enzymes were obtained by stepwise
      chromatography with blue agarose, hydroxyapatite and heparin-Sepharose. The restriction
      endonuclease BspLU11I produces sticky ends identical to those produced by the restriction
      endonuclease NcoI; hence a combination of BspLU11I and NcoI can be used for enzymatic
      selection of recombinant DNA. The recognition sequence of BspLU11I contains the ATG codon and
      can be used to construct expression vectors for chemically synthesized genes. ies.
AU  - Zheleznaya LA
AU  - Matvienko NN
AU  - Matvienko NI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1993 58: 1315-1322.

PMID- 11703181
VI  - 66
DP  - 2001
TI  - Site-specific nickase from Bacillus species strain D6.
PG  - 1215-1220
AB  - Three site-specific endonucleases were found in thermophilic strain Bacillus species D6. One
      of them, BspD6II, is an isoschizomer of
      Eco57I. The second, BspD6III, is present in the strain in very small
      amount; therefore, it has not been characterized. This paper is devoted
      to the third, BspD6I, which recognizes the pentanucleotide site 5'-GAGTC-3'
      and cleaves only one DNA strand at a distance of 4 nucleotides from the
      site in the 3'-direction in the chain with the GAGTC sequence, i.e., it
      behaves as a site-specific nickase. Nickase N.BspD6I cleaves one DNA
      strand only in double-stranded DNA and does not cleave single-stranded
      DNA. Site-specific methylase SscL1I (an isohypectomer of M.HinfI) that
      methylates adenine in the sequence 5'-GANTC-3' prevents DNA hydrolysis
      by nickase BspD6I.
AU  - Zheleznaya LA
AU  - Perevyazova TA
AU  - Alzhanova DV
AU  - Matvienko NI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 2001 66: 1215-1220.

PMID- 11996665
VI  - 67
DP  - 2002
TI  - Some properties of site-specific nickase BspD6I and the possibility of its use in hybridization analysis of DNA.
PG  - 595-600
AB  - A new method for hybridization analysis of nucleic acids is proposed on the basis of the
      ability of site-specific nickases to cleave only one DNA strand. The method is based on the
      use of a labeled oligonucleotide with the recognition site of the nickase hybridized with the
      target (DNA or RNA) at an optimal temperature of the enzyme (55 degrees C). The two shorter
      oligonucleotides formed after the cleavage with the nickase do not complex with the target.
      Thus, a multiple cleavage of the labeled oligonucleotide takes place on one target molecule.
      The cleavage of the nucleotide is recorded either by polyacrylamide gel electrophoresis (when
      a radioactive labeled oligonucleotide is used) or by fluorescence measurements (if the
      oligonucleotide has the structure of a molecular beacon). The new method was tested on nickase
      BspD6I and a radioactive oligonucleotide complementary to the polylinker region of the viral
      DNA strand in bacteriophage M13mp19. Unfortunately, nickase BspD6I does not cleave DNA in the
      RNA-DNA duplexes and therefore cannot be used for detection of RNA targets.
AU  - Zheleznaya LA
AU  - Perevyazova TA
AU  - Zheleznyakova EN
AU  - Matvienko NI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 2002 67: 595-600.

PMID- 
VI  - 63
DP  - 1998
TI  - A site-specific endonuclease from thermophilic strain Bacillus species ZE is a ClaI isoschizomer.
PG  - 1675-1681
AB  - Strain Bacillus species ZE with a maximal yield of the ClaI isoschizomer was chosen from 12
      natural thermophilic strains producing ClaI isomers.  The yield is 110 times higher than that
      of the ClaI prototype endonuclease from Caryophanon latum L.  The enzyme is sensitive to DNA
      dam-methylation and is highly stable under storage.
AU  - Zheleznyakova EN
AU  - Zheleznaya LA
AU  - Svadbina IV
AU  - Matvienko NI
PT  - Journal Article
TA  - Biokhimiia
JT  - Biokhimiia
SO  - Biokhimiia 1998 63: 1675-1681.

PMID- 27506685
VI  - 63
DP  - 2016
TI  - Coexistence of MCR-1 and NDM-1 in Clinical Escherichia coli Isolates.
PG  - 1393-1395
AB  - TO THE EDITORInfections caused by New Delhi metallo- lactamase 1 (NDM-1) producing
      Enterobacteriaceae are reported to have a signi and #64257;cantly higher likelihood of
      in-hospital mortality. Previous evidence showed that NDM-producing bacteria are often
      susceptible to colistin, which has become the last resort for the treatment of infections due
      to NDM producing bacteria. However, the plasmid-mediated colistin resistance (MCR-1) gene, was
      and #64257;rst identi and #64257;ed in Enterobacteriaceae recently. Therefore, patients
      ultimately might receive only extremely limited drug options. Here, we characterize for the
      and #64257;rst time 2 clonally unrelated Escherichia coli strains coproducing MCR-1 and NDM-1,
      which were recovered from 2 patients with bloodstream infection.
AU  - Zheng B
AU  - Dong H
AU  - Xu H
AU  - Lv J
AU  - Zhang J
AU  - Jiang X
AU  - Du Y
AU  - Xiao Y
AU  - Li L
PT  - Journal Article
TA  - Clin. Infect. Dis.
JT  - Clin. Infect. Dis.
SO  - Clin. Infect. Dis. 2016 63: 1393-1395.

PMID- 27257207
VI  - 4
DP  - 2016
TI  - First Draft Genome Sequence of Staphylococcus condimenti F-2T.
PG  - e00499-16
AB  - This report describes the draft genome sequence of S. condimenti strain F-2(T) (DSM 11674), a
      potential starter culture. The genome assembly comprised 2,616,174
      bp with 34.6% GC content. To the best of our knowledge, this is the first
      documentation that reports the whole-genome sequence of S. condimenti.
AU  - Zheng B
AU  - Hu X
AU  - Jiang X
AU  - Li A
AU  - Yao J
AU  - Li L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00499-16.

PMID- 26139720
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequence of Multidrug-Resistant Staphylococcus caprae Strain 9557, Isolated from Cerebrospinal Fluid.
PG  - e00718-15
AB  - Staphylococcus caprae strain 9557 was isolated from a cerebrospinal fluid sample. The
      assembled genome contained 2,747,651-bp nucleotides with 33.34% GC content.
      Consistent with its phenotypic characteristics, the genome harbors a varying
      repertoire of putative virulence factors involved in invasion, survival, and
      growth in the host cells.
AU  - Zheng B
AU  - Jiang X
AU  - Li A
AU  - Yao J
AU  - Zhang J
AU  - Hu X
AU  - Li L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00718-15.

PMID- 19029325
VI  - 53
DP  - 2009
TI  - Isolation of VanB-type Enterococcus faecalis strains from nosocomial infections:  first report of the isolation and identification of the pheromone-responsive  plasmids pMG2200, Encoding VanB-type vancomycin resistance and a Bac41-type  bacteriocin, and.
PG  - 735-747
AB  - Eighteen identical VanB-type Enterococcus faecalis isolates that were obtained from different
      hospitalized patients were examined for their drug resistance and
      plasmid DNAs. Of the 18 strains, 12 strains exhibited resistance to erythromycin
      (Em), gentamicin (Gm), kanamycin (Km), tetracycline (Tc), and vancomycin (Van)
      and produced cytolysin (Hly/Bac) and a bacteriocin (Bac) active against E.
      faecalis strains. Another six of the strains exhibited resistance to Gm, Km, Tc,
      and Van and produced a bacteriocin. Em and Van resistance was transferred
      individually to E. faecalis FA2-2 strains at a frequency of about 10(-4) per
      donor cell by broth mating. The Em-resistant transconjugants and the
      Van-resistant transconjugants harbored a 65.7-kbp plasmid and a 106-kbp plasmid,
      respectively. The 106-kbp and 65.7-kbp plasmids isolated from the representative
      E. faecalis NKH15 strains were designated pMG2200 and pMG2201, respectively.
      pMG2200 conferred vancomycin resistance and bacteriocin activity on the host
      strain and responded to the synthetic pheromone cCF10 for pCF10, while pMG2201
      conferred erythromycin resistance and cytolysin activity on its host strain and
      responded to the synthetic pheromone cAD1 for pAD1. The complete DNA sequence of
      pMG2200 (106,527 bp) showed that the plasmid carried a Tn1549-like element
      encoding vanB2-type resistance and the Bac41-like bacteriocin genes of
      pheromone-responsive plasmid pYI14. The plasmid contained the regulatory region
      found in pheromone-responsive plasmids and encoded the genes prgX and prgQ, which
      are the key negative regulatory elements for plasmid pCF10. pMG2200 also encoded
      TraE1, a key positive regulator of plasmid pAD1, indicating that pMG2200 is a
      naturally occurring chimeric plasmid that has a resulting prgX-prgQ-traE1 genetic
      organization in the regulatory region of the pheromone response. The functional
      oriT region and the putative relaxase gene of pMG2200 were identified and found
      to differ from those of pCF10 and pAD1. The putative relaxase of pMG2200 was
      classified as a member of the MOB(MG) family, which is found in
      pheromone-independent plasmid pHTbeta of the pMG1-like plasmids. This is the
      first report of the isolation and characterization of a pheromone-responsive
      highly conjugative plasmid encoding vanB resistance.
AU  - Zheng B
AU  - Tomita H
AU  - Inoue T
AU  - Ike Y
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2009 53: 735-747.

PMID- 26819653
VI  - 11
DP  - 2016
TI  - Draft genome sequence of Paenibacillus sp. strain A2.
PG  - 9
AB  - Paenibacillus sp. strain A2 is a Gram-negative rod-shaped bacterium isolated from a mixture of
      formation water and petroleum in Daqing oilfield, China. This
      facultative aerobic bacterium was found to have a broad capacity for metabolizing
      hydrocarbon and organosulfur compounds, which are the main reasons for the
      interest in sequencing its genome. Here we describe the features of Paenibacillus
      sp. strain A2, together with the genome sequence and its annotation. The
      7,650,246 bp long genome (1 chromosome but no plasmid) exhibits a G+C content of
      54.2 % and contains 7575 protein-coding and 49 RNA genes, including 3 rRNA genes.
      One putative alkane monooxygenase, one putative alkanesulfonate monooxygenase,
      one putative alkanesulfonate transporter and four putative sulfate transporters
      were found in the draft genome.
AU  - Zheng B
AU  - Zhang F
AU  - Dong H
AU  - Chai L
AU  - Shu F
AU  - Yi S
AU  - Wang Z
AU  - Cui Q
AU  - Dong H
AU  - Zhang Z
AU  - Hou D
AU  - Yang J
AU  - She Y
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 9.

PMID- 29880596
VI  - 6
DP  - 2018
TI  - Draft Genome Sequence of Rhodococcus opacus Strain 04-OD7, Which Can Mobilize Phosphate.
PG  - e00494-18
AB  - Rhodococcus opacus strain 04-OD7 (=CCTCC AB 2017148) is a Gram-positive bacterium showing
      inorganic phosphate solubilization capacity for the first time in the
      genus Rhodococcus We present here the draft genome description of R. opacus
      04-OD7 along with multiple phosphorus (P) mobilization-related genes, supporting
      its inorganic phosphate solubilization.
AU  - Zheng BX
AU  - Zhang HK
AU  - Ding K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00494-18.

PMID- 9371888
VI  - 32
DP  - 1997
TI  - Characterization of the mitochondrial cytochrome b gene from Venturia inaequalis.
PG  - 361-366
AB  - A new class of agricultural fungicides derived from the group of antifungal strobilurins acts
      as specific respiration inhibitors by binding to mitochondrial cytochrome b.  The cytochrome b
      gene was cloned and sequenced from the mitochondrial genome of Venturia inaequalis, the causal
      agent of apple scab.  The gene was 10.65 kbp in size and contained seven exons and six
      introns.  The exons encoded a protein of 393 amino acids.  Comparison of the deduced
      amino-acid sequence with cytochrome b proteins from other fungi revealed highest homologies to
      the respective proteins of Aspergillis nidulans, Podospora anserina and Neurospora crassa.
      All amino acids of the V. inaequalis cytochrome b at positions altered in mutants of
      Saccharomyces cerevisiae resistant to strobilurins, and other fungi with reduced sensitivities
      to strobilurins, were identical to wild-type isolates of several fungi.  The cloning and
      characterization of the V. inaequalis cytochrome b gene is the initial step in the assessment
      of resistance risks inherent to the strobilurin fungicides.
AU  - Zheng D
AU  - Koller W
PT  - Journal Article
TA  - Curr. Genet.
JT  - Curr. Genet.
SO  - Curr. Genet. 1997 32: 361-366.

PMID- 27932659
VI  - 4
DP  - 2016
TI  - Genome Sequence of Pseudomonas citronellolis SJTE-3, an Estrogen- and Polycyclic  Aromatic Hydrocarbon-Degrading Bacterium.
PG  - e01373-16
AB  - Pseudomonas citronellolis SJTE-3, isolated from the active sludge of a wastewater treatment
      plant in China, can utilize a series of environmental estrogens and
      estrogen-like toxicants. Here, we report its whole-genome sequence, containing
      one circular chromosome and one circular plasmid. Genes involved in estrogen
      biodegradation in this bacterium were predicted.
AU  - Zheng D
AU  - Wang X
AU  - Wang P
AU  - Peng W
AU  - Ji N
AU  - Liang R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01373-16.

PMID- 26184928
VI  - 3
DP  - 2015
TI  - Complete Genome Sequence of Endomicrobium proavitum, a Free-Living Relative of the Intracellular Symbionts of Termite Gut Flagellates (Phylum Elusimicrobia).
PG  - e00679-15
AB  - We sequenced the complete genome of Endomicrobium proavitum strain Rsa215, the first isolate
      of the class Endomicrobia (phylum Elusimicrobia). It is the closest
      free-living relative of the endosymbionts of termite gut flagellates and thereby
      provides an excellent model for studying the evolutionary processes during the
      establishment of an intracellular symbiosis.
AU  - Zheng H
AU  - Brune A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00679-15.

PMID- 24926045
VI  - 2
DP  - 2014
TI  - Draft Genome Sequences of Two Clinical Isolates of Streptococcus mutans.
PG  - e00441-14
AB  - We report the draft genome sequences of PKUSS-HG01 and PKUSS-LG01, two clinical isolates of
      Streptococcus mutans from human dental plaque. The genomics
      information will facilitate the study of the mechanisms of pathogenicity and
      evolution of S. mutans.
AU  - Zheng H
AU  - Guo L
AU  - Du N
AU  - Lin J
AU  - Song L
AU  - Liu G
AU  - Chen F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00441-14.

PMID- 2050643
VI  - 173
DP  - 1991
TI  - Overproduction and purification of McrC protein from Escherichia coli K-12.
PG  - 3918-3920
AB  - The McrC protein, encoded by one of the two genes involved in the McrB
      restriction system, was produced in Escherichia coli cells by using a T7
      expression system.  Following sequential DEAE-Sepharose and hydroxylapatite
      column chromatography, the protein was purified to apparent homogeneity as
      judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis.  The
      N-terminal amino acid sequence of the purified McrC protein agreed exactly with
      the one deduced from the DNA sequence by Ross et al. (J. Bacteriol.
      171:1974-1981, 1989).
AU  - Zheng L
AU  - Braymer HD
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1991 173: 3918-3920.

PMID- 25700405
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Rhodobacteraceae Strain PD-2, an Algicidal Bacterium with a Quorum-Sensing System, Isolated from the Marine Microalga Prorocentrum donghaiense.
PG  - e01549-14
AB  - Rhodobacteraceae strain PD-2 was isolated from the marine microalga Prorocentrum donghaiense.
      It has algicidal activity toward its host and could produce N-acylhomoserine lactone signals.
      Here, we present the draft genome of strain PD-2, which contains 5,227,214 bp with an average
      GC content of 66.19%. There were 4,864 encoding gene sequences and two clusters of luxI and
      luxR homologues identified.
AU  - Zheng L
AU  - Cui Z
AU  - Xu L
AU  - Sun C
AU  - Powell RJ
AU  - Hill RT
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01549-14.

PMID- Not carried by PubMed...
VI  - 91
DP  - 1991
TI  - Determination of the recognition sequence for McrB restriction of E. coli K12.
PG  - 175
AB  - Restriction of methylated DNA by the McrB restriction system of E. coli
      involves two genes designated mcrB and mcrC.  The mcrB gene is thought to code
      for an endonuclease subunit and the mcrC and the mcrC subunit confers
      specificity to the enzyme complex.  The restriction enzyme requires GTP for
      activity and recognizes G5mC.  However, we know these two deoxynucleotides
      alone are not sufficient for recognition since not every methylated AluI site
      (AG5mCT) is recognized. To determine the nucleotide recognition sequence for
      McrB restriction, a series of deletion plasmids were constructed from pBR322
      and tested as substrates of McrB activity, after the plasmids were methylated
      with AluI methylase.  Our study first narrowed the McrB recognition sequence
      down to one of the four AluI sites in the region between two MspI sites at 1812
      and 2121 bp of pBR322.  SI nuclease deletion and further sequencing analyses of
      this region revealed that only one AluI site was involved in the recognition of
      McrB restriction.  Site-specific mutagenesis will be used to define all base
      composition required for McrB recognition.
AU  - Zheng L
AU  - Simmons LA
AU  - Braymer HD
PT  - Journal Article
TA  - Abstr. Gen. Meet. Am. Soc. Microbiol.
JT  - Abstr. Gen. Meet. Am. Soc. Microbiol.
SO  - Abstr. Gen. Meet. Am. Soc. Microbiol. 1991 91: 175.

PMID- 1312983
VI  - 112
DP  - 1992
TI  - Purification and N-terminal amino acid sequences of two polypeptides encoded by the mcrB gene from Escherichia coli K-12.
PG  - 97-100
AB  - This report provides a purification method for the two proteins, 51 kDa and 33
      kDa, both encoded by the same mcrB gene of the McrBC restriction system in
      Escherichia coli K-12.  The two proteins were produced in large quantity using
      a T7 expression system and copurified to near homogeneity by DEAE-Sepharose and
      Affi-Gel blue column chromatography.  The N-terminal amino acid sequences of
      these purified McrB proteins were the same as those predicted from the mcrB DNA
      sequence by Ross et al. [J. Bacteriol. 171 (1989b) 1974-1981].  The 33 kDa
      protein totally overlaps the C-terminal part of the 51-kDa protein.
AU  - Zheng L
AU  - Wang X
AU  - Braymer HD
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1992 112: 97-100.

PMID- 23405303
VI  - 1
DP  - 2013
TI  - Complete Genome Sequence of emm1 Streptococcus pyogenes A20, a Strain with an Intact Two-Component System, CovRS, Isolated from a Patient with Necrotizing  Fasciitis.
PG  - e00149-12
AB  - Here, we announce the complete sequence of Streptococcus pyogenes A20. This strain was
      isolated from a patient with necrotizing fasciitis. Given that A20
      harbors an intact two-component system, CovRS, the discovery of its genome
      sequence provides more insight into the pathogenesis of a pandemic emm1 strain.
AU  - Zheng PX
AU  - Chung KT
AU  - Chiang-Ni C
AU  - Wang SY
AU  - Tsai PJ
AU  - Chuang WJ
AU  - Lin YS
AU  - Liu CC
AU  - Wu JJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00149-12.

PMID- 21317332
VI  - 193
DP  - 2011
TI  - Genome Sequence of Citromicrobium Strain JLT1363, Isolated from the South China Sea.
PG  - 2074-2075
AB  - Citromicrobium is a member of the alpha-4 subcluster in the Alphaproteobacteria and is
      identified as a typical aerobic anoxygenic
      phototrophic bacterium (AAPB). Here we report the draft genome sequence of
      a non-AAPB strain, Citromicrobium sp. JLT1363. The genome sequence reveals
      a multimechanism of horizontal gene transfer, as well.
AU  - Zheng Q
AU  - Zhang R
AU  - Jiao N
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 2074-2075.

PMID- Not carried by PubMed...
VI  - 14
DP  - 1987
TI  - Isolation and purification of the restriction endonuclease Bsu1076I.
PG  - 105-108
AB  - Restriction endonuclease Bsu1076I has been isolated from Bacillus subtilis and
      purified by passing first through a phosphocellulose (Whatman P11) column, and
      then through a heparin-Sepharose 4B column.  Bsu1076I was eluted at 0.83-0.87M
      NaCl in a gradient from the phosphocellulose column and at 0.80-0.87M NaCl from
      heparin-Sepharose 4B column.  As much as 3000 units of highly purified Bsu1076I
      was obtained from 20g of wet cells by this procedure.  Digestion of lambda DNA,
      SPP1 DNA, PhiX174 DNA, SV40 DNA and Ad-2 DNA with Bsu1076I formed DNA fragments
      identical to those digested with its isoschizomer HaeIII (from Promega Biotec)
      as assayed by agarose gel electrophoresis.  Over digestion of 1 microgram
      lambda DNA with 50-150 units of Bsu1076I showed typical bands on agarose gel,
      indicating the exclusion of contamination by other deoxyribonucleases.  After
      digestion with Bsu1076I lambda DNA can be fairly ligated and recut.
AU  - Zheng W
PT  - Journal Article
TA  - Weishengwuxue Tongbao
JT  - Weishengwuxue Tongbao
SO  - Weishengwuxue Tongbao 1987 14: 105-108.

PMID- 9251194
VI  - 63
DP  - 1997
TI  - Host-mediated modification of Sau3AI restriction in Listeria monocytogenes: Prevalence in epidemic-associated strains.
PG  - 3085-3089
AB  - Most major food-related outbreaks of listeriosis have been traced to a cluster of genetically
      related strains of serovar 4b (epidemic clone).  In spite of numerous searches, distinct
      bacteriologic or virulence-related features unique to these strains have eluded
      identification, although a restriction fragment length polymorphism characteristic of the
      epidemic clone has previously been described.  We found that DNAs from 75 strains which were
      derived from three separate outbreaks and which had the epidemic clone-specific RFLP were also
      invariably resistant to digestion by Sau3AI and other restriction endonucleases sensitive to
      cytosine methylation at 5' GATC 3' sites.  This modification of Sau3AI restriction was host
      mediated, as it did not persist when DNA was cloned and propagated in Escherichia coli, and
      was uncommon among other Listeria strains.  Epidemic-associated strains with this modification
      were resistant to infection by phage propagated in a serotype 4b strain which was not known to
      be involved in an epidemic and which lacked the epidemic clone-specific RFLP.  Screening for
      susceptibility to MboI digestion revealed that these epidemic strains lacked methylation of
      adenines at GATC sites.  This type of modification was rare among Listeria strains and was
      found in only three (of eight screened) strains of serovar 1/2b, possibly representing one
      clonal lineage.
AU  - Zheng W
AU  - Kathariou S
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 1997 63: 3085-3089.

PMID- 20444879
VI  - 38
DP  - 2010
TI  - A unique family of Mrr-like modification-dependent restriction endonucleases.
PG  - 5527-5534
AB  - Mrr superfamily of homologous genes in microbial genomes restricts modified DNA in vivo.
      However, their biochemical properties in vitro
      have remained obscure. Here, we report the experimental
      characterization of MspJI, a remote homolog of Escherichia coli's Mrr
      and show it is a DNA modification-dependent restriction endonuclease.
      Our results suggest MspJI recognizes (CNNR)-C-m (R = G/A) sites and
      cleaves DNA at fixed distances (N-12/N-16) away from the modified
      cytosine at the 3' side (or N-9/N-13 from R). Besides 5-methylcytosine,
      MspJI also recognizes 5-hydroxymethylcytosine but is blocked by
      5-glucosylhydroxymethylcytosine. Several other close homologs of MspJI
      show similar modification-dependent endonuclease activity and display
      substrate preferences different from MspJI. A unique feature of these
      modification-dependent enzymes is that they are able to extract small
      DNA fragments containing modified sites on genomic DNA, for example
      similar to 32 bp around symmetrically methylated CG sites and similar
      to 31 bp around methylated CNG sites. The digested fragments can be
      directly selected for high-throughput sequencing to map the location of
      the modification on the genomic DNA. The MspJI enzyme family, with
      their different recognition specificities and cleavage properties,
      provides a basis on which many future methods can build to decode the
      epigenomes of different organisms.
AU  - Zheng Y
AU  - Cohen-Karni D
AU  - Xu D
AU  - Chin HG
AU  - Wilson G
AU  - Pradhan S
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2010 38: 5527-5534.

PMID- 18988632
VI  - 37
DP  - 2009
TI  - Using shotgun sequence data to find active restriction enzyme genes.
PG  - 1-11
AB  - Whole genome shotgun sequence analysis has become the standard method for beginning to
      determine a genome sequence. The preparation of the shotgun sequence clones is, in fact, a
      biological experiment. It determines which segments of the genome can be cloned into
      Escherichia coli and which cannot. By analyzing the complete set of sequences from such an
      experiment, it is possible to identify genes lethal to E. coli. Among this set are genes
      encoding restriction enzymes which, when active in E. coli, lead to cell death by cleaving the
      E. coli genome at the restriction enzyme recognition sites. By analyzing shotgun sequence data
      sets we show that this is a reliable method to detect active restriction enzyme genes in newly
      sequenced genomes, thereby facilitating functional annotation. Active restriction enzyme genes
      have been identified, and their activity demonstrated biochemically, in the sequenced genomes
      of Methanocaldococcus jannaschii, Bacillus cereus ATCC 10987 and Methylococcus capsulatus.
AU  - Zheng Y
AU  - Posfai J
AU  - Morgan RD
AU  - Vincze T
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2009 37: 1-11.

PMID- 17567609
VI  - 35
DP  - 2007
TI  - Selection of restriction endonucleases using artificial cells.
PG  - e83
AB  - We describe in this article an in vitro system for the selection of restriction endonucleases
      using artificial cells. The artificial cells are
      generated in the form of a water-in-oil emulsion by in vitro
      compartmentalization. Each aqueous compartment contains a reconstituted
      transcription/translation mix along with the dispersed DNA templates. In
      the compartments containing endonuclease genes, an endonuclease expressed
      in vitro cleaves its own DNA template adjacent to the gene, leaving a
      sticky end. The pooled DNA templates are then ligated to an adaptor with a
      compatible end. The endonuclease genes are then enriched by
      adaptor-specific PCR on the ligation mix. We demonstrate that the system
      can achieve at least 100-fold enrichment in a single round of selection.
      It is sensitive enough to enrich an active endonuclease gene from a
      1:10(5) model library in 2-3 rounds of selection. Finally, we describe
      experiments where we selected endonuclease genes directly from a bacterial
      genomic DNA source in three rounds of selections: the known PstI gene from
      Providencia stuartii and the new TspMI gene from Thermus sp. manalii. This
      method provides a unique tool for cloning restriction endonuclease genes
      and has many other potential applications.
AU  - Zheng Y
AU  - Roberts RJ
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2007 35: e83.

PMID- 25540355
VI  - 2
DP  - 2014
TI  - Whole-Genome Sequence of 'Candidatus Liberibacter solanacearum' Strain R1 from California.
PG  - e01353-14
AB  - The draft whole-genome sequence of 'Candidatus Liberibacter solanacearum' strain  R1,
      isolated from and maintained in tomato plants in California, is reported. The
      R1 strain has the genome size of 1,204,257 bp, G+C content of 35.3%, 1,101
      predicted open reading frames, and 57 RNA genes.
AU  - Zheng Z
AU  - Clark N
AU  - Keremane M
AU  - Lee R
AU  - Wallis C
AU  - Deng X
AU  - Chen J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e01353-14.

PMID- 25278540
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of 'Candidatus Liberibacter asiaticus' from California.
PG  - e00999-14
AB  - We report here the draft genome sequence of 'Candidatus Liberibacter asiaticus' strain HHCA,
      collected from a lemon tree in California. The HHCA strain has a
      genome size of 1,150,620 bp, 36.5% G+C content, 1,119 predicted open reading
      frames, and 51 RNA genes.
AU  - Zheng Z
AU  - Deng X
AU  - Chen J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00999-14.

PMID- 24723715
VI  - 2
DP  - 2014
TI  - Whole-Genome Sequence of 'Candidatus Liberibacter asiaticus' from Guangdong, China.
PG  - e00273-14
AB  - The draft genome sequence of 'Candidatus Liberibacter asiaticus' strain A4, isolated from a
      mandarin citrus in Guangdong, People's Republic of China, is reported. The A4 strain has a
      genome size of 1,208,625 bp, G+C content of 36.4%, 1,107 predicted open reading frames, and 53
      RNA genes.
AU  - Zheng Z
AU  - Deng X
AU  - Chen J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00273-14.

PMID- 26089419
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Bacillus coagulans NL01, a Wonderful l-Lactic Acid Producer.
PG  - e00635-15
AB  - Here, we report the draft genome sequence of Bacillus coagulans NL01, which could produce high
      optically pure l-lactic acid using xylose as a sole carbon source.
      The draft genome is 3,505,081 bp, with 144 contigs. About 3,903 protein-coding
      genes and 92 rRNAs are predicted from this assembly.
AU  - Zheng Z
AU  - Jiang T
AU  - Lin X
AU  - Zhou J
AU  - Ouyang J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00635-15.

PMID- 25792067
VI  - 3
DP  - 2015
TI  - Whole-Genome Sequence of 'Candidatus Liberibacter asiaticus' from a Huanglongbing-Affected Citrus Tree in Central Florida.
PG  - e00169-15
AB  - Here, we report the draft genome sequence of 'Candidatus Liberibacter asiaticus'  strain
      FL17, isolated from a huanglongbing (HLB)-affected citrus tree in central
      Florida. The FL17 genome comprised 1,227,253 bp, with a G+C content of 36.5%,
      1,175 predicted open reading frames, and 53 RNA genes.
AU  - Zheng Z
AU  - Sun X
AU  - Deng X
AU  - Chen J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00169-15.

PMID- 26383663
VI  - 3
DP  - 2015
TI  - Genome Assemblies for 11 Yersinia pestis Strains Isolated in the Caucasus Region.
PG  - e01030-15
AB  - Yersinia pestis, the causative agent of plague, is endemic to the Caucasus region but few
      reference strain genome sequences from that region are available. Here, we present the
      improved draft or finished assembled genomes from 11 strains isolated in the nation of Georgia
      and surrounding countries.
AU  - Zhgenti E
AU  - Johnson SL
AU  - Davenport KW
AU  - Chanturia G
AU  - Daligault HE
AU  - Chain PS
AU  - Nikolich MP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01030-15.

PMID- 28112210
VI  - 7
DP  - 2017
TI  - Genome and transcriptome analysis of surfactin biosynthesis in Bacillus amyloliquefaciens MT45.
PG  - 40976
AB  - Natural Bacillus isolates generate limited amounts of surfactin (<10% of their
      biomass), which functions as an antibiotic or signalling molecule in
      inter-/intra-specific interactions. However, overproduction of surfactin in
      Bacillus amyloliquefaciens MT45 was observed at a titre of 2.93 g/l, which is
      equivalent to half of the maximum biomass. To systemically unravel this efficient
      biosynthetic process, the genome and transcriptome of this bacterium were
      compared with those of B. amyloliquefaciens type strain DSM7T. MT45 possesses a
      smaller genome while containing more unique transporters and
      resistance-associated genes. Comparative transcriptome analysis revealed notable
      enrichment of the surfactin synthesis pathway in MT45, including central carbon
      metabolism and fatty acid biosynthesis to provide sufficient quantities of
      building precursors. Most importantly, the modular surfactin synthase
      overexpressed (9 to 49-fold) in MT45 compared to DSM7T suggested efficient
      surfactin assembly and resulted in the overproduction of surfactin. Furthermore,
      based on the expression trends observed in the transcriptome, there are multiple
      potential regulatory genes mediating the expression of surfactin synthase. Thus,
      the results of the present study provide new insights regarding the synthesis and
      regulation of surfactin in high-producing strain and enrich the genomic and
      transcriptomic resources available for B. amyloliquefaciens.
AU  - Zhi Y
AU  - Wu Q
AU  - Xu Y
PT  - Journal Article
TA  - Sci. Rep.
JT  - Sci. Rep.
SO  - Sci. Rep. 2017 7: 40976.

PMID- 1745646
VI  - 27
DP  - 1991
TI  - Effect of some cultivation parameters on the yield of restriction endonuclease SfaNI.
PG  - 486-490
AB  - A simple technique is proposed for testing restriction endonuclease SfaNI activity in lysates
      of Streptococcus faecalis cells.  The technique was used to study the effect of inorganic
      phosphate and the growth phase on the enzyme yield.  Conditions were chosen that provide a
      high yield of the SfaNI activity and a significantly reduced level of nucleases in the cells.
AU  - Zhilkina OA
AU  - Repin VE
AU  - Degtyarev SK
PT  - Journal Article
TA  - Prikl. Biokhim. Mikrobiol.
JT  - Prikl. Biokhim. Mikrobiol.
SO  - Prikl. Biokhim. Mikrobiol. 1991 27: 486-490.

PMID- 28104659
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of the Triclosan- and Multidrug-Resistant Pseudomonas aeruginosa Strain B10W Isolated from Municipal Wastewater.
PG  - e01489-16
AB  - Here, we report the complete genome sequence of the triclosan- and multidrug-resistant
      Pseudomonas aeruginosa strain B10W, obtained from municipal
      wastewater in Hawaii. The bacterium has a 6.7-Mb genome, contains 6,391 coding
      sequences and 78 RNAs, with an average G+C content of 66.2 mol%.
AU  - Zhong C
AU  - Nelson M
AU  - Cao G
AU  - Sadowsky MJ
AU  - Yan T
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01489-16.

PMID- 24855943
VI  - 157
DP  - 2014
TI  - Molecular Mechanism of Action of Plant DRM De Novo DNA Methyltransferases.
PG  - 1050-1060
AB  - DNA methylation is a conserved epigenetic gene-regulation mechanism. DOMAINS REARRANGED
      METHYLTRANSFERASE (DRM) is a key de novo methyltransferase in plants,
      but how DRM acts mechanistically is poorly understood. Here, we report the
      crystal structure of the methyltransferase domain of tobacco DRM (NtDRM) and
      reveal a molecular basis for its rearranged structure. NtDRM forms a functional
      homodimer critical for catalytic activity. We also show that Arabidopsis DRM2
      exists in complex with the small interfering RNA (siRNA) effector ARGONAUTE4
      (AGO4) and preferentially methylates one DNA strand, likely the strand acting as
      the template for RNA polymerase V-mediated noncoding RNA transcripts. This
      strand-biased DNA methylation is also positively correlated with strand-biased
      siRNA accumulation. These data suggest a model in which DRM2 is guided to target
      loci by AGO4-siRNA and involves base-pairing of associated siRNAs with nascent
      RNA transcripts.
AU  - Zhong X
AU  - Du J
AU  - Hale CJ
AU  - Gallego-Bartolome J
AU  - Feng S
AU  - Vashisht AA
AU  - Chory J
AU  - Wohlschlegel JA
AU  - Patel DJ
AU  - Jacobsen SE
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 2014 157: 1050-1060.

PMID- 25561521
VI  - 112
DP  - 2015
TI  - DOMAINS REARRANGED METHYLTRANSFERASE3 controls DNA methylation and regulates RNA  polymerase V transcript abundance in Arabidopsis.
PG  - 911-916
AB  - DNA methylation is a mechanism of epigenetic gene regulation and genome defense conserved in
      many eukaryotic organisms. In Arabidopsis, the DNA methyltransferase
      DOMAINS REARRANGED METHYLASE 2 (DRM2) controls RNA-directed DNA methylation in a
      pathway that also involves the plant-specific RNA Polymerase V (Pol V).
      Additionally, the Arabidopsis genome encodes an evolutionarily conserved but
      catalytically inactive DNA methyltransferase, DRM3. Here, we show that DRM3 has
      moderate effects on global DNA methylation and small RNA abundance and that DRM3
      physically interacts with Pol V. In Arabidopsis drm3 mutants, we observe a lower
      level of Pol V-dependent noncoding RNA transcripts even though Pol V chromatin
      occupancy is increased at many sites in the genome. These findings suggest that
      DRM3 acts to promote Pol V transcriptional elongation or assist in the
      stabilization of Pol V transcripts. This work sheds further light on the
      mechanism by which long noncoding RNAs facilitate RNA-directed DNA methylation.
AU  - Zhong X
AU  - Hale CJ
AU  - Nguyen M
AU  - Ausin I
AU  - Groth M
AU  - Hetzel J
AU  - Vashisht AA
AU  - Henderson IR
AU  - Wohlschlegel JA
AU  - Jacobsen SE
PT  - Journal Article
TA  - Proc. Natl. Acad. Sci. U. S. A.
JT  - Proc. Natl. Acad. Sci. U. S. A.
SO  - Proc. Natl. Acad. Sci. U. S. A. 2015 112: 911-916.

PMID- 23832250
VI  - 56
DP  - 2013
TI  - Assembly and features of secondary metabolite biosynthetic gene clusters in Streptomyces ansochromogenes.
PG  - 609-618
AB  - A draft genome sequence of Streptomyces ansochromogenes 7100 was generated using
      454 sequencing technology. In combination with local BLAST searches and gap filling
      techniques, a comprehensive antiSMASH-based method was adopted to assemble the secondary
      metabolite biosynthetic gene clusters in the draft genome of S. ansochromogenes. A total of at
      least 35 putative gene clusters were identified and assembled. Transcriptional analysis showed
      that 20 of the 35 gene clusters were expressed in either or all of the three different media
      tested, whereas the other 15 gene clusters were silent in all three different media. This
      study provides a comprehensive method to identify and assemble secondary metabolite
      biosynthetic gene clusters in draft genomes of Streptomyces, and will significantly promote
      functional studies of these secondary metabolite biosynthetic gene clusters.
AU  - Zhong X
AU  - Tian Y
AU  - Niu G
AU  - Tan H
PT  - Journal Article
TA  - Sci. China Life. Sci.
JT  - Sci. China Life. Sci.
SO  - Sci. China Life. Sci. 2013 56: 609-618.

PMID- 21423275
VI  - 21
DP  - 2011
TI  - Comparative proteogenomic analysis of the Leptospira interrogans virulence-attenuated strain IPAV against the pathogenic strain 56601.
PG  - 1210-1229
AB  - The virulence-attenuated Leptospira interrogans serovar Lai strain IPAV
      was derived by prolonged laboratory passage from a highly virulent
      ancestral strain isolated in China. We studied the genetic variations of
      IPAV that render it avirulent via comparative analysis against the
      pathogenic L. interrogans serovar Lai strain 56601. The complete genome
      sequence of the IPAV strain was determined and used to compare with, and
      then rectify and reannotate the genome sequence of strain 56601. Aside
      from their highly similar genomic structure and gene order, a total of 33
      insertions, 53 deletions and 301 single-nucleotide variations (SNVs) were
      detected throughout the genome of IPAV directly affecting 101 genes,
      either in their 5' upstream region or within their coding region. Among
      them, the majority of the 44 functional genes are involved in signal
      transduction, stress response, transmembrane transport and nitrogen
      metabolism. Comparative proteomic analysis based on quantitative liquid
      chromatography (LC)-MS/MS data revealed that among 1 627 selected pairs of
      orthologs, 174 genes in the IPAV strain were upregulated, with enrichment
      mainly in classes of energy production and lipid metabolism. In contrast,
      228 genes in strain 56601 were upregulated, with the majority enriched in
      the categories of protein translation and DNA replication/repair. The
      combination of genomic and proteomic approaches illustrated that altered
      expression or mutations in critical genes, such as those encoding a
      Ser/Thr kinase, carbon-starvation protein CstA, glutamine synthetase,
      GTP-binding protein BipA, ribonucleotide-diphosphate reductase and
      phosphate transporter, and alterations in the translational profile of
      lipoproteins or outer membrane proteins are likely to account for the
      virulence attenuation in strain IPAV.
AU  - Zhong Y
AU  - Chang X
AU  - Cao XJ
AU  - Zhang Y
AU  - Zheng H
AU  - Zhu Y
AU  - Cai C
AU  - Cui Z
AU  - Zhang Y
AU  - Li YY
AU  - Jiang XG
AU  - Zhao GP
AU  - Wang S
AU  - Li Y
AU  - Zeng R
AU  - Li X
AU  - Guo XK
PT  - Journal Article
TA  - Cell Res.
JT  - Cell Res.
SO  - Cell Res. 2011 21: 1210-1229.

PMID- 11722934
VI  - 67
DP  - 2001
TI  - Sequence analysis of a 101-kilobase plasmid required for agar degradation by a Microscilla isolate.
PG  - 5771-5779
AB  - An agar-degrading marine bacterium identified as a Microscilla species was
      isolated from coastal California marine sediment. This organism harbored a
      single 101-kb circular DNA plasmid designated pSD15. The complete
      nucleotide sequence of pSD15 was obtained, and sequence analysis indicated
      a number of genes putatively encoding a variety of enzymes involved in
      polysaccharide utilization. The most striking feature was the occurrence
      of five putative agarase genes. Loss of the plasmid, which occurred at a
      surprisingly high frequency, was associated with loss of agarase activity,
      supporting the sequence analysis results.
AU  - Zhong Z
AU  - Toukdarian A
AU  - Helinski D
AU  - Knauf V
AU  - Sykes S
AU  - Wilkinson JE
AU  - O'Bryne C
AU  - Shea T
AU  - DeLoughery C
AU  - Caspi R
PT  - Journal Article
TA  - Appl. Environ. Microbiol.
JT  - Appl. Environ. Microbiol.
SO  - Appl. Environ. Microbiol. 2001 67: 5771-5779.

PMID- 23209208
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of Brucella abortus Strain BCB034, a Strain of Biovar 2  Isolated from Human.
PG  - 6943
AB  - Brucella abortus is divided into eight biovars, of which biovars 1 to 3 are the most
      frequently represented biovars in strains isolated from humans. Here, we
      report the genome sequence of B. abortus strain BCB034, a strain isolated from a
      human patient and that belongs to biovar 2.
AU  - Zhong Z
AU  - Wang L
AU  - Chen Y
AU  - Wang Z
AU  - Wang Y
AU  - Cui M
AU  - Li T
AU  - Ke Y
AU  - Yuan X
AU  - Wang D
AU  - Chen Z
AU  - Peng G
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6943.

PMID- Not carried by PubMed...
VI  - 19
DP  - 1987
TI  - Bacillus subtilis 36 a highly productive strain containing the isoschizomer of restriction enzyme MstII.
PG  - 537-540
AB  - From Bacillus subtilis 36 we have isolated and partially purified a restriction
      enzyme Bsu36I, which is the isoschizomer of MstII.  200000 units of Bsu36I can
      be obtained from one liter of B. subtilis 36 culture.  It is a strain for
      production of MstII.
AU  - Zhou B
AU  - Li Q
PT  - Journal Article
TA  - Acta Biochim. Biophys. Sin.
JT  - Acta Biochim. Biophys. Sin.
SO  - Acta Biochim. Biophys. Sin. 1987 19: 537-540.

PMID- 26925197
VI  - 11
DP  - 2016
TI  - High-quality draft genome sequence of the Thermus amyloliquefaciens type strain YIM 77409(T) with an incomplete denitrification pathway.
PG  - 20
AB  - Thermus amyloliquefaciens type strain YIM 77409(T) is a thermophilic, Gram-negative,
      non-motile and rod-shaped bacterium isolated from Niujie Hot
      Spring in Eryuan County, Yunnan Province, southwest China. In the present study
      we describe the features of strain YIM 77409(T) together with its genome sequence
      and annotation. The genome is 2,160,855 bp long and consists of 6 scaffolds with
      67.4 % average GC content. A total of 2,313 genes were predicted, comprising
      2,257 protein-coding and 56 RNA genes. The genome is predicted to encode a
      complete glycolysis, pentose phosphate pathway, and tricarboxylic acid cycle.
      Additionally, a large number of transporters and enzymes for heterotrophy
      highlight the broad heterotrophic lifestyle of this organism. A denitrification
      gene cluster included genes predicted to encode enzymes for the sequential
      reduction of nitrate to nitrous oxide, consistent with the incomplete
      denitrification phenotype of this strain.
AU  - Zhou EM et al
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2016 11: 20.

PMID- 12136150
VI  - 58
DP  - 2002
TI  - A new crystal form of restriction endonuclease EcoRII that diffracts to 2.8 A resolution.
PG  - 1343-1345
AB  - EcoRII, a type IIe restriction endonuclease, has been crystallized in space group P2(1), with
      unit-cell parameters a = 58.3, b = 127.8, c = 59.9 A, beta = 91.4 degrees. There are two
      monomers in the asymmetric unit and the solvent content is estimated to be 49% by volume. The
      crystals diffract to 2.8 A resolution, which is much higher than that of the previously
      reported cubic crystal form, which diffracted to 4 A resolution.
AU  - Zhou EX
AU  - Reuter M
AU  - Meehan EJ
AU  - Chen L
PT  - Journal Article
TA  - Acta Crystallogr. D Biol. Crystallogr.
JT  - Acta Crystallogr. D Biol. Crystallogr.
SO  - Acta Crystallogr. D Biol. Crystallogr. 2002 58: 1343-1345.

PMID- 26388970
VI  - 10
DP  - 2015
TI  - High quality draft genomic sequence of Flavihumibacter solisilvae 3-3(T).
PG  - 66
AB  - Flavihumibacter solisilvae 3-3(T) (= KACC 17917(T) = JCM 19891(T)) represents a type strain of
      the genus Flavihumibacter within the family Chitinophagaceae. This strain can use various sole
      carbon sources, making it applicable in industry and  bioremediation. In this study, the draft
      genomic information of F. solisilvae 3-3(T) is described. F. solisilvae 3-3(T) owns a genome
      size of 5.41 Mbp, 47 % GC content and a total of 4,698 genes, including 4,215 protein coding
      genes, 439 pseudo genes and 44 RNA encoding genes. Analysis of its genome reveals high
      correlation between the genotypes and the phenotypes.
AU  - Zhou G
AU  - Chen C
AU  - Jeon CO
AU  - Wang G
AU  - Li M
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 66.

PMID- 17523600
VI  - 46
DP  - 2007
TI  - Long-range structural and dynamical changes induced by cofactor binding in DNA methyltransferase M.HhaI.
PG  - 7261-7268
AB  - The bacterial DNA cytosine methyltransferase M.HhaI sequence-specifically modifies DNA in an
      S-adenosylmethionine dependent reaction. The enzyme stabilizes the target cytosine (GCGC) into
      an extrahelical position, with a concomitant large movement of an active site loop involving
      residues 80-99. We used multidimensional, transverse relaxation-optimized NMR experiments to
      assign nearly 80% of all residues in the cofactor-bound enzyme form, providing a basis for
      detailed structural and dynamical characterization. We examined details of the previously
      unknown effects of the cofactor binding with M.HhaI in solution. Addition of the cofactor
      results in numerous structural changes throughout the protein, including those decorating the
      cofactor binding site, and distal residues more than 30 A away. The active site loop is
      involved in motions both on a picosecond to nanosecond time scale and on a microsecond to
      millisecond time scale and is not significantly affected by cofactor binding except for a few
      N-terminal residues. The cofactor also affects residues near the DNA binding cleft, suggesting
      a role for the cofactor in regulating DNA interactions. The allosteric properties we observed
      appear to be closely related to the significant amount of dynamics and dynamical changes in
      response to ligand binding detected in the protein.
AU  - Zhou H
AU  - Shatz W
AU  - Purdy MM
AU  - Fera N
AU  - Dahlquist FW
AU  - Reich NO
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2007 46: 7261-7268.

PMID- 22105763
VI  - 64
DP  - 2012
TI  - A non-restricting and non-methylating Escherichia coli strain for DNA cloning and high-throughput conjugation to Streptomyces coelicolor.
PG  - 185-190
AB  - Escherichia coli strains are used in secondary metabolism research for DNA cloning and
      transferring plasmids by intergeneric conjugation. Non-restricting
      strains are desirable for DNA cloning and non-methylating strains are beneficial
      for transferring DNA to methyl-restricting hosts, like Streptomyces coelicolor.
      We have constructed a non-methylating E. coli strain, JTU007, by deleting the DNA
      methylation genes dcm and dam from the widely used non-restricting cloning host
      DH10B. JTU007 was tested as donor for the conjugative transfer of a plasmid
      containing the 39 kb actinorhodin biosynthesis gene cluster to S. lividans and S.
      coelicolor. The Dcm Dam strain JTU007 transferred DNA into S. coelicolor A(3)2
      derivatives at high frequency. To demonstrate the usefulness of E. coli JTU007
      for gene cloning, we constructed a comprehensive S. toxytricini genomic cosmid
      library, and transferred it using high-throughput conjugation to the
      methyl-restricting S. coelicolor. One of the cosmid clones produced a brown
      pigment, and the clone was revealed to carry a tyrosinase operon. JTU007 is more
      useful than ET12567 because it does not restrict methylated DNA in primary
      cloning, and gives higher transformation and cosmid infection frequencies.
AU  - Zhou H
AU  - Wang Y
AU  - Yu Y
AU  - Bai T
AU  - Chen L
AU  - Liu P
AU  - Guo H
AU  - Zhu C
AU  - Tao M
AU  - Deng Z
PT  - Journal Article
TA  - Curr. Microbiol.
JT  - Curr. Microbiol.
SO  - Curr. Microbiol. 2012 64: 185-190.

PMID- 28126945
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Staphylococcus succinus subsp. succinus Type Strain DSM  14617, Isolated from Plant and Soil Inclusions within 25- to 35-Million-Year-Old   Dominican Amber.
PG  - e01521-16
AB  - Staphylococcus succinus subsp. succinus type strain DSM 14617 was isolated from plant and soil
      inclusions within 25- to 35-million-year-old Dominican amber. The
      complete genome sequence of strain DSM 14617T includes a genome of 2.88 Mb
      (32.94% G+C content) without any plasmids.
AU  - Zhou H
AU  - Yao Z
AU  - Shi H
AU  - Wang B
AU  - Li D
AU  - Hou J
AU  - Ma S
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01521-16.

PMID- 21788470
VI  - 55
DP  - 2011
TI  - Genomic Analysis of the Multidrug-Resistant Acinetobacter baumannii Strain MDR-ZJ06 Widely Spread in China.
PG  - 4506-4512
AB  - We previously reported that the multidrug-resistant (MDR) Acinetobacter baumannii strain
      MDR-ZJ06, belonging to European clone II, was widely
      spread in China. In this study, we report the whole-genome sequence of
      this clinically important strain. A 38.6-kb AbaR-type genomic
      resistance island (AbaR22) was identified in MDR-ZJ06. AbaR22 has a
      structure similar to those of the resistance islands found in A.
      baumannii strains AYE and AB0057, but it contained only a few
      antibiotic resistance genes. The region of resistant gene accumulation
      as previously described was not found in AbaR22. In the chromosome of
      the strain MDR-ZJ06, we identified the gene bla(oxa-23) in a composite
      transposon (Tn2009). Tn2009 shared the backbone with other A. baumannii
      transponsons that harbor bla(oxa-23), but it was bracketed by two
      ISAba1 elements which were transcribed in the same orientation.
      MDR-ZJ06 also expressed the armA gene on its plasmid pZJ06, and this
      gene has the same genetic environment as the armA gene of the
      Enterobacteriaceae. These results suggest variability of resistance
      acquisition even in closely related A. baumannii strains.
AU  - Zhou H
AU  - Zhang TW
AU  - Yu DL
AU  - Pi BR
AU  - Yang Q
AU  - Zhou JY
AU  - Hu SN
AU  - Yu YS
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2011 55: 4506-4512.

PMID- 19580326
VI  - 48
DP  - 2009
TI  - The Recognition Pathway for the DNA Cytosine Methyltransferase M.HhaI.
PG  - 7807-7816
AB  - Enzymatic sequence-specific DNA modification involves multiple poorly understood
      intermediates. DNA methyltransferases like M.HhaI initially
      bind nonspecific DNA and then selectively bind and modify a unique
      sequence. High-resolution NMR was used to map conformational changes
      occurring in M. HhaI upon binding nonspecific DNA, a one base pair
      altered noncognate DNA sequence, and both hemimethylated and
      unmethylated cognate DNA sequences. Comparisons with previous NMR
      studies of the apoenzyme and enzyme-cofactor complex provide snapshots
      of the pathway to sequence-specific complex formation. Dramatic
      chemical shift perturbations reaching many distal sites within the
      protein are detected with cognate DNA, while much smaller changes are
      observed upon nonspecific and noncognate DNA binding. A cooperative
      rather than stepwise transition from a nonspecific to a cognate complex
      is revealed, Furthermore, switching from unmethylated to hemimethylated
      cognate DNA involves delectable protein conformational changes 20-30
      angstrom away from the methyl group, indicating high protein
      sensitivity and plasticity to DNA modification.
AU  - Zhou HJ
AU  - Purdy MM
AU  - Dahlquist FW
AU  - Reich NO
PT  - Journal Article
TA  - Biochemistry
JT  - Biochemistry
SO  - Biochemistry 2009 48: 7807-7816.

PMID- 25392206
VI  - 89
DP  - 2015
TI  - Three novel virophage genomes discovered from Yellowstone Lake metagenomes.
PG  - 1278-1285
AB  - Virophages are a unique group of circular double-stranded DNA viruses that are
      considered parasites of giant DNA viruses, which in turn are known to infect
      eukaryotic hosts. In this study the genomes of three novel virophages YSLV5,
      YSLV6 and YSLV7 were identified from Yellowstone Lake through metagenomic
      analyses. The relative abundance of these three novel virophages and previously
      identified Yellowstone Lake virophages YSLVs 1-4 were determined in different
      locations of the lake, revealing that most of the sampled locations in the lake,
      including both mesophilic and thermophilic habitats, had multiple virophage
      genotypes. This likely reflects the diverse habitats or diversity of the
      eukaryotic hosts and their associated giant viruses that serve as putative hosts
      for these virophages. YSLV5 has a 29,767 bp genome with 32 predicted ORFs, YSLV6
      has a 24,837 bp genome with 29 predicted ORFs, and YSLV7 has a 23,193 bp genome
      with 26 predicted ORFs. Based on multilocus phylogenetic analysis, YSLV6 shows a
      close evolutionary relationship with YSLVs 1-4, whereas YSLV5 and YSLV7 are
      distantly related to the others, and YSLV7 represents the fourth novel virophage
      lineage. In addition, the genome of YSLV5 has a G+C content of 51.1% that is much
      higher than all other known virophages, indicating a unique host range for YSLV5.
      These results suggest that virophages are abundant and have diverse genotypes
      that likely mirror diverse giant viral and eukaryotic hosts within the
      Yellowstone Lake ecosystem. IMPORTANCE: This study discovered novel virophages
      present within the Yellowstone Lake ecosystem using a conserved major capsid
      protein as a phylogenetic anchor for assembly of sequence reads from Yellowstone
      Lake metagenomic samples. The three novel virophage genomes (YSLV5-7) were
      completed by identifying specific environmental samples containing these
      respective virophages, and closing gaps by targeted PCR and sequencing. Most of
      the YSLV genotypes were associated primarily with photic zone and
      non-hydrothermal samples; however, YSLV5 had a unique distribution with an
      occurrence in vent samples similar to that in photic zone samples, and with a
      higher GC content that suggests a distinct host and habitat compared to other
      YSLVs. In addition, genome content and phylogenetic analyses indicate that YSLV5
      and YSLV7 are distinct from known virophages, and that additional
      as-yet-uncharacterized virophages are likely present within the Yellowstone Lake
      ecosystem.
AU  - Zhou J
AU  - Sun D
AU  - Childers A
AU  - McDermott TR
AU  - Wang Y
AU  - Liles MR
PT  - Journal Article
TA  - J. Virol.
JT  - J. Virol.
SO  - J. Virol. 2015 89: 1278-1285.

PMID- 12206775
VI  - 321
DP  - 2002
TI  - Zebularine: A novel DNA methylation inhibitor that forms a covalent complex with DNA methyltransferases.
PG  - 591-599
AB  - Mechanism-based inhibitors of enzymes, which mimic reactive intermediates in the reaction
      pathway, have been deployed extensively in the analysis of metabolic pathways and as candidate
      drugs. The inhibition of cytosine-[C5]-specific DNA methyltransferases (C5 MTases) by
      oligodeoxynucleotides containing 5-azadeoxycytidine (AzadC) and 5-fluorodeoxycytidine (FdC)
      provides a well-documented example of mechanism-based inhibition of enzymes central to nucleic
      acid metabolism. Here, we describe the interaction between the C5 MTase from Haemophilus
      haemolyticus (M.HhaI) and an oligodeoxynucleotide duplex containing 2-H pyrimidinone, an
      analogue often referred to as zebularine and known to give rise to high-affinity complexes
      with MTases. X-ray crystallography has demonstrated the formation of a covalent bond between
      M.HhaI and the 2-H pyrimidinone-containing oligodeoxynucleotide. This observation enables a
      comparison between the mechanisms of action of 2-H pyrimidinone with other mechanism-based
      inhibitors such as FdC. This novel complex provides a molecular explanation for the mechanism
      of action of the anti-cancer drug zebularine.
AU  - Zhou L
AU  - Cheng X
AU  - Connolly BA
AU  - Dickman MJ
AU  - Hurd PJ
AU  - Hornby DP
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2002 321: 591-599.

PMID- 25301638
VI  - 2
DP  - 2014
TI  - Draft Genome Sequence of Antagonistic Agent Lysobacter antibioticus 13-6.
PG  - e00566-14
AB  - Lysobacter antibioticus 13-6, isolated from the roots of Chinese cabbage, effectively controls
      the pathogens Plasmodiophora brassicae, Xanthomonas oryzae
      pv. oryzicola, X. oryzae pv. oryzae, Xanthomonas axonopodis pv. dieffenbachiae,
      and Pseudomonas syringae pv. tabaci. We report the first draft genome sequence of
      the L. antibioticus species in China.
AU  - Zhou L
AU  - Li M
AU  - Yang J
AU  - Wei L
AU  - Ji G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2014 2: e00566-14.

PMID- 22328758
VI  - 194
DP  - 2012
TI  - Draft Genome Sequence of Mesorhizobium alhagi CCNWXJ12-2T, a Novel Salt-Resistant Species Isolated from the Desert of Northwestern China.
PG  - 1261-1262
AB  - Mesorhizobium alhagi strain CCNWXJ12-2(T) is a novel species of soil-dwelling, nitrogen-fixing
      bacteria that can form symbiotic root nodules with Alhagi
      sparsifolia. Moreover, the strain has high resistance to salt and alkali. Here we
      report the draft genome sequence of Mesorhizobium alhagi strain CCNWXJ12-2(T). A
      large number of osmotic regulation-related genes have been identified.
AU  - Zhou M
AU  - Chen W
AU  - Chen H
AU  - Wei G
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1261-1262.

PMID- 26941137
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Psychrobacter piscatorii Strain LQ58, a Psychrotolerant  Bacterium Isolated from a Deep-Sea Hydrothermal Vent.
PG  - e00044-16
AB  - Here, we report the 3.1-Mb draft genome sequence of Psychrobacter piscatorii strain LQ58,
      isolated from a deep-sea hydrothermal vent on the East Pacific Rise.
      The sequence will provide further insight into the environmental adaptation of
      psychrotolerant bacteria and the development of novel cold-active enzymes for
      industrial application.
AU  - Zhou M
AU  - Dong B
AU  - Liu Q
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00044-16.

PMID- 26679595
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Caloranaerobacter sp. TR13, an Anaerobic Thermophilic Bacterium Isolated from a Deep-Sea Hydrothermal Vent.
PG  - e01491-15
AB  - Here, we report the draft 2,261,881-bp genome sequence of Caloranaerobacter sp. TR13, isolated
      from a deep-sea hydrothermal vent on the East Pacific Rise. The
      sequence will be helpful for understanding the genetic and metabolic features, as
      well as potential biotechnological application in the genus Caloranaerobacter.
AU  - Zhou M
AU  - Xie Y
AU  - Dong B
AU  - Liu Q
AU  - Chen X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01491-15.

PMID- 26769941
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Altererythrobacter troitsensis JCM 17037, Isolated from  the Sea Urchin Strongylocentrotus intermedius.
PG  - e01556-15
AB  - The habitats of the genus Altererythrobacter are various, including marine sediment, seawater,
      rhizosphere of wild rice, desert sand, etc. The genome of the
      type strain of Altererythrobacter troitsensis JCM 17037, isolated from sea
      urchin, was sequenced. This study would not only facilitate the understanding of
      the physiology, adaptation, and evolution of the Altererythrobacter species, but
      also provide a good resource for the study of synthesis of astaxanthin, since
      several enzymes involved in the production of astaxanthin were predicted.
AU  - Zhou P
AU  - Wu YH
AU  - Cheng H
AU  - Wang CS
AU  - Xu XW
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01556-15.

PMID- 28572307
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Veillonella atypica OK5, the First Transformable Strain in the Species.
PG  - e00391-17
AB  - The Veillonella atypica strain OK5 was isolated from a human saliva sample and was the first
      strain shown to be genetically transformable in the Veillonella
      genus. Genetic studies using this strain have helped us gain much insight into
      the ecology of human oral biofilms. Here, we report the complete genome sequence
      of V. atypica OK5.
AU  - Zhou P
AU  - Xie G
AU  - Li X
AU  - Liu J
AU  - Qi F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00391-17.

PMID- 23661476
VI  - 1
DP  - 2013
TI  - Genome Sequence of Klebsiella pneumoniae HSL4, a New Strain Isolated from Mangrove Sediment for Biosynthesis of 1,3-Propanediol.
PG  - e00177-13
AB  - Klebsiella pneumoniae HSL4 is a 1,3-propanediol-producing bacterium strain isolated from
      mangrove sediment. We present here a 5,221,448-bp assembly of its
      genome sequence. Genome analysis revealed that it contains 10 coding sequences
      (CDSs) responsible for glycerol fermentation to 1,3-propanediol, 19 CDSs encoding
      glycerol utilization, and 140 CDSs related to its virulence.
AU  - Zhou S
AU  - Li L
AU  - Wei J
AU  - Qin Q
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00177-13.

PMID- 27365357
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Wohlfahrtiimonas chitiniclastica Strain BM-Y, Isolated from the Pancreas of a Zebra in China.
PG  - e00643-16
AB  - Here, a complete genome sequence of Wohlfahrtiimonas chitiniclastica strain BM-Y  is
      presented. The whole genome is 2.18-Mb and contains a blaVEB-1 gene cassette which endows it
      with resistance to ceftazidime, ampicillin, tetracycline, etc. To our knowledge, this is the
      first time that an extended spectrum beta-lactamase (ESBL) type W. chitiniclastica strain has
      been found.
AU  - Zhou W
AU  - Li M
AU  - Zhu L
AU  - Hua F
AU  - Ji X
AU  - Sun Y
AU  - Liu J
AU  - Guo X
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00643-16.

PMID- 27789648
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Aerococcus urinaeequi Strain AV208.
PG  - e01218-16
AB  - Aerococcus urinaeequi strain AV208 was isolated from an ascites sample from a patient with
      chronic kidney disease. The assembled genome contained 2,227,638 bp
      with a 39.1% G+C content. The genome harbors a Tn1546 transposon-like structure
      with a vanA gene causing vancomycin resistance phenotypes of strain AV208.
AU  - Zhou W
AU  - Niu D
AU  - Zhang Z
AU  - Liu Y
AU  - Ning M
AU  - Cao X
AU  - Zhang C
AU  - Shen H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01218-16.

PMID- 2837731
VI  - 16
DP  - 1988
TI  - Site-specific degradation of Streptomyces lividans DNA during electrophoresis in  buffers contaminated with ferrous iron.
PG  - 4341-4352
AB  - Streptomyces lividans DNA contains a modification which makes it susceptible to double-strand
      cleavage during electrophoresis in buffers contaminated with
      ferrous iron (which may be present in some batches of EDTA). The cleavage of the
      DNA is site-specific and the average fragment size resulting from limit digestion
      of total S. lividans DNA is about 6kb. DNA from Streptomyces coelicolor A3(2) and
      several other Streptomyces strains, and from E. coli, is not cleaved under the
      same conditions. A S. lividans mutant has been isolated which lacks the DNA
      modification. We suspect that many reports of 'poor' preparations of S. lividans
      plasmids may be due to the above effect.
AU  - Zhou X
AU  - Deng Z
AU  - Firmin JL
AU  - Hopwood DA
AU  - Kieser T
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1988 16: 4341-4352.

PMID- 16102010
VI  - 57
DP  - 2005
TI  - A novel DNA modification by sulphur.
PG  - 1428-1438
AB  - Streptomyces lividans has a novel DNA modification, which sensitises its DNA to degradation
      during electrophoresis (the Dnd phenotype). The entire
      gene cluster (dnd) involved in this modification was localized on an 8 kb
      DNA fragment and was expressed in a S. lividans deletion mutant (dnd) and
      in several heterologous hosts. Disruption of the dnd locus abolishes the
      Dnd phenotype, and gain of the dnd locus conferred the Dnd phenotype
      respectively. Extensive analysis of the dnd gene cluster revealed five
      open reading frames, whose hypothetic functions suggested an incorporation
      of sulphur or a sulphur-containing substance into S. lividans genome, yet
      in an unknown manner. The Dnd phenotype was also discovered to exist in
      DNA of widespread bacterial species of variable origin and diverse
      habitat. Similarly organized gene clusters were found in several bacterial
      genomes representing different genera and in eDNA of marine organisms,
      suggesting such modification as a widespread phenomenon. A coincidence
      between the Dnd phenotype and DNA modification by sulphur was demonstrated
      to occur in several representative bacterial genomes by the in
      vivo(35)S-labelling experiments.
AU  - Zhou X
AU  - He X
AU  - Liang J
AU  - Li A
AU  - Xu T
AU  - Kieser T
AU  - Helmann JD
AU  - Deng Z
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 2005 57: 1428-1438.

PMID- 12777809
VI  - 59
DP  - 2003
TI  - A single mutation of restriction endonuclease EcoRII led to a new crystal form that diffracts to 2.1 angstrom resolution.
PG  - 910-912
AB  - R88A, a mutant of the type IIE restriction endonuclease EcoRII, has been crystallized in space
      group P2(1), with unit-cell parameters a = 58.7, b =
      92.4, c = 88.3 A, beta = 108.1 degrees. There are two monomers in the
      asymmetric unit and the solvent content is estimated to be 50% by volume.
      The crystals diffract to 2.1 A resolution, which is much higher than that
      of the wild type, which diffracted to 2.8 A resolution. The mutant
      crystals have been used in the identification of an excellent heavy-atom
      derivative.
AU  - Zhou XE
AU  - Wang Y
AU  - Reuter M
AU  - Mackeldanz P
AU  - Kruger DH
AU  - Meehan EJ
AU  - Chen LQ
PT  - Journal Article
TA  - Acta Crystallogr. D Biol. Crystallogr.
JT  - Acta Crystallogr. D Biol. Crystallogr.
SO  - Acta Crystallogr. D Biol. Crystallogr. 2003 59: 910-912.

PMID- 
VI  - 64
DP  - 2006
TI  - An assay for the activity of DNA methylase based on a hairpin fluorescence molecular probe and its application in drug selection.
PG  - 2096-2100
AB  - A new activity assay for DNA methylase based on a hairpin molecular probe was proposed in this
      paper. The recognition site of DNA methylase
      and corresponding restriction endonuclease was designed in the stem
      part of the probe, tetramethy1rhodamine (TAMRA) was attached at the 5'
      terminus and its fluorescence was quenched by
      4-(4'-dimethylaniinophenylazo)benzoic acid (DABCYL) linked at the 3'
      terminus. The unmethylated probe can be cut in the recognition site by
      restriction endonuclease, causing the restoration of the fluorescence
      of TAMRA. Therefore, the activity of methylase would be analyzed
      according to the degree of fluorescence restoration. Based on this
      assay, the influence of anti-tumor drugs on the activity of methylase
      was investigated by adding drugs in the methylation reaction. This
      method can provide a potential in selecting proper drugs for tumors
      caused by altered gene methylation pattern.
AU  - Zhou XW
AU  - Li J
AU  - Wang KM
AU  - Tan WH
AU  - Yang XH
AU  - Meng XX
AU  - Yan HF
PT  - Journal Article
TA  - Acta Chimi. Sin.
JT  - Acta Chimi. Sin.
SO  - Acta Chimi. Sin. 2006 64: 2096-2100.

PMID- 14659759
VI  - 335
DP  - 2004
TI  - Crystal structure of Type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold.
PG  - 307-319
AB  - EcoRII is a Type IIE restriction endonuclease that interacts with two copies of the DNA
      recognition sequence 5'CCWGG, one being the actual
      target of cleavage, the other serving as the allosteric effector. The
      mode of enzyme activation by effector binding is unknown. To
      investigate the molecular basis of activation and cleavage mechanisms
      by EcoRII, the crystal structure of EcoRII mutant R88A has been
      solved at 2.1 Angstrom resolution. The EcoRII monomer has two domains
      linked through a hinge loop. The N-terminal effector-binding domain has
      a novel DNA recognition fold with a prominent cleft. The C-terminal
      catalytic domain has a restriction endonuclease-like fold.
      Structure-based sequence alignment identified the putative catalytic
      site of EcoRII that is spatially blocked by the N-terminal domain. The
      structure together with the earlier characterized EcoRII enzyme
      activity enhancement in the absence of its N-terminal domain reveal an
      autoinhibition/activation mechanism of enzyme activity mediated by a
      novel effector-binding fold. This is the first case of autoinhibition,
      a mechanism described for many transcription factors and signal
      transducing proteins, of a restriction endonuclease.
AU  - Zhou XYE
AU  - Wang YJ
AU  - Reuter M
AU  - Mucke M
AU  - Kruger DH
AU  - Meehan EJ
AU  - Chen LQ
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2004 335: 307-319.

PMID- 25197480
VI  - 9
DP  - 2014
TI  - High quality draft genome sequence of the slightly halophilic bacterium Halomonas zhanjiangensis type strain JSM 078169(T) (DSM 21076(T)) from a sea urchin in  southern China.
PG  - 1020-1030
AB  - Halomonas zhanjiangensis Chen et al. 2009 is a member of the genus Halomonas, family
      Halomonadaceae, class Gammaproteobacteria. Representatives of the genus
      Halomonas are a group of halophilic bacteria often isolated from salty
      environments. The type strain H. zhanjiangensis JSM 078169(T) was isolated from a
      sea urchin (Hemicentrotus pulcherrimus) collected from the South China Sea. The
      genome of strain JSM 078169(T) is the fourteenth sequenced genome in the genus
      Halomonas and the fifteenth in the family Halomonadaceae. The other thirteen
      genomes from the genus Halomonas are H. halocynthiae, H. venusta, H. alkaliphila,
      H. lutea, H. anticariensis, H. jeotgali, H. titanicae, H. desiderata, H.
      smyrnensis, H. salifodinae, H. boliviensis, H. elongata and H stevensii. Here, we
      describe the features of strain JSM 078169(T), together with the complete genome
      sequence and annotation from a culture of DSM 21076(T). The 4,060,520 bp long
      draft genome consists of 17 scaffolds with the 3,659 protein-coding and 80 RNA
      genes and is a part of Genomic Encyclopedia of Type Strains, Phase I: the one
      thousand microbial genomes (KMG) project.
AU  - Zhou Y
AU  - Li R
AU  - Gao XY
AU  - Lapidus A
AU  - Han J
AU  - Haynes M
AU  - Lobos E
AU  - Huntemann M
AU  - Pati A
AU  - Ivanova NN
AU  - Rohde M
AU  - Mavromatis K
AU  - Tindall BJ
AU  - Markowitz V
AU  - Woyke T
AU  - Klenk HP
AU  - Kyrpides NC
AU  - Li WJ
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 1020-1030.

PMID- 27881549
VI  - 4
DP  - 2016
TI  - Genome Sequence of Corynebacterium pseudotuberculosis Strain XH02 Isolated from a Boer Goat in Xuanhan, China.
PG  - e01329-16
AB  - We report here the genome sequence of Corynebacterium pseudotuberculosis strain XH02, isolated
      from a Boer goat in China. The genome consists of 2,357,671 bp,
      with a 52.18% G+C content, 2,263 coding sequences, 21 rRNAs, 49 tRNAs, and 44
      predicted pseudogenes.
AU  - Zhou Z
AU  - Li H
AU  - Zhang M
AU  - Wang Z
AU  - Zhou R
AU  - Hu S
AU  - Li X
AU  - Song X
AU  - Zhu Z
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01329-16.

PMID- 20090843
VI  - 5
DP  - 2010
TI  - Derivation of Escherichia coli O157:H7 from its O55:H7 precursor.
PG  - E8700
AB  - There are 29 E. coli genome sequences available, mostly related to studies
      of species diversity or mode of pathogenicity, including two genomes of
      the well-known O157:H7 clone. However, there have been no genome studies
      of closely related clones aimed at exposing the details of evolutionary
      change. Here we sequenced the genome of an O55:H7 strain, closely related
      to the major pathogenic O157:H7 clone, with published genome sequences,
      and undertook comparative genomic and proteomic analysis. We were able to
      allocate most differences between the genomes to individual mutations,
      recombination events, or lateral gene transfer events, in specific
      lineages. Major differences include a type II secretion system present
      only in the O55:H7 chromosome, fewer type III secretion system effectors
      in O55:H7, and 19 phage genomes or phagelike elements in O55:H7 compared
      to 23 in O157:H7, with only three common to both. Many other changes were
      found in both O55:H7 and O157:H7 lineages, but in general there has been
      more change in the O157:H7 lineages. For example, we found 50% more
      synonymous mutational substitutions in O157:H7 compared to O55:H7. The two
      strains also diverged at the proteomic level. Mutational synonymous SNPs
      were used to estimate a divergence time of 400 years using a new clock
      rate, in contrast to 14,000 to 70,000 years using the traditional clock
      rates. The same approaches were applied to three closely related
      extraintestinal pathogenic E. coli genomes, and similar levels of mutation
      and recombination were found. This study revealed for the first time the
      full range of events involved in the evolution of the O157:H7 clone from
      its O55:H7 ancestor, and suggested that O157:H7 arose quite recently. Our
      findings also suggest that E. coli has a much lower frequency of
      recombination relative to mutation than was observed in a comparable study
      of a Vibrio cholerae lineage.
AU  - Zhou Z
AU  - Li X
AU  - Liu B
AU  - Beutin L
AU  - Xu J
AU  - Ren Y
AU  - Feng L
AU  - Lan R
AU  - Reeves PR
AU  - Wang L
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2010 5: E8700.

PMID- 23637636
VI  - 9
DP  - 2013
TI  - Neutral Genomic Microevolution of a Recently Emerged Pathogen, Salmonella enterica Serovar Agona.
PG  - E1003471
AB  - Salmonella enterica serovar Agona has caused multiple food-borne outbreaks of
      gastroenteritis since it was first isolated in 1952. We analyzed the genomes of
      73 isolates from global sources, comparing five distinct outbreaks with sporadic
      infections as well as food contamination and the environment. Agona consists of
      three lineages with minimal mutational diversity: only 846 single nucleotide
      polymorphisms (SNPs) have accumulated in the non-repetitive, core genome since
      Agona evolved in 1932 and subsequently underwent a major population expansion in
      the 1960s. Homologous recombination with other serovars of S. enterica imported
      42 recombinational tracts (360 kb) in 5/143 nodes within the genealogy, which
      resulted in 3,164 additional SNPs. In contrast to this paucity of genetic
      diversity, Agona is highly diverse according to pulsed-field gel electrophoresis
      (PFGE), which is used to assign isolates to outbreaks. PFGE diversity reflects a
      highly dynamic accessory genome associated with the gain or loss (indels) of 51
      bacteriophages, 10 plasmids, and 6 integrative conjugational elements (ICE/IMEs),
      but did not correlate uniquely with outbreaks. Unlike the core genome, indels
      occurred repeatedly in independent nodes (homoplasies), resulting in inaccurate
      PFGE genealogies. The accessory genome contained only few cargo genes relevant to
      infection, other than antibiotic resistance. Thus, most of the genetic diversity
      within this recently emerged pathogen reflects changes in the accessory genome,
      or is due to recombination, but these changes seemed to reflect neutral processes
      rather than Darwinian selection. Each outbreak was caused by an independent
      clade, without universal, outbreak-associated genomic features, and none of the
      variable genes in the pan-genome seemed to be associated with an ability to cause
      outbreaks.
AU  - Zhou Z
AU  - McCann A
AU  - Litrup E
AU  - Murphy R
AU  - Cormican M
AU  - Fanning S
AU  - Brown D
AU  - Guttman DS
AU  - Brisse S
AU  - Achtman M
PT  - Journal Article
TA  - PLoS Genet.
JT  - PLoS Genet.
SO  - PLoS Genet. 2013 9: E1003471.

PMID- 21183670
VI  - 193
DP  - 2010
TI  - Genome Sequence of the poultry pathogen Riemerella anatipestifer Strain RA-YM.
PG  - 1284-1285
AB  - Riemerella anatipestifer is a Gram-negative rod-shaped bacillus associated with epizootic
      infections in poultry. R. anatipestifer strain RA-YM, belonging to the serotype 1 prevalent in
      China, is a clinically isolated strain with high-level virulence. Here, we report the first
      genome sequence of this species.
AU  - Zhou Z
AU  - Peng X
AU  - Xiao Y
AU  - Wang X
AU  - Guo Z
AU  - Zhu L
AU  - Liu M
AU  - Jin H
AU  - Bi D
AU  - Li Z
AU  - Sun M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 193: 1284-1285.

PMID- 23209221
VI  - 194
DP  - 2012
TI  - Genome sequence of Enterobacter sp. strain SP1, an endophytic nitrogen-fixing bacterium isolated from sugarcane.
PG  - 6963-6964
AB  - Enterobacter sp. strain SP1 is an endophytic nitrogen-fixing bacterium isolated
      from a sugarcane stem and can promote plant growth. The draft genome sequence of
      strain SP1 presented here will promote comparative genomic studies to determine
      the genetic background of interactions between endophytic enterobacteria and
      plants.
AU  - Zhu B
AU  - Chen M
AU  - Lin L
AU  - Yang L
AU  - Li Y
AU  - An Q
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6963-6964.

PMID- 22328769
VI  - 194
DP  - 2012
TI  - Genome Sequence of Stenotrophomonas maltophilia RR-10, Isolated as an Endophyte from Rice Root.
PG  - 1280-1281
AB  - Stenotrophomonas maltophilia is an endophyte which plays important roles in agricultural
      production as a plant growth-promoting bacterium. Here, we present
      the draft genome sequence of strain RR-10, which was isolated from a rice root in
      a rice field of China.
AU  - Zhu B
AU  - Liu H
AU  - Tian WX
AU  - Fan XY
AU  - Li B
AU  - Zhou XP
AU  - Jin GL
AU  - Xie GL
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1280-1281.

PMID- 23209242
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Pathogenic Herbaspirillum seropedicae Strain Os45, Isolated from Rice Roots.
PG  - 6995-6996
AB  - Most Herbaspirillum seropedicae strains are beneficial to plants. In contrast, H. seropedicae
      strain Os45, isolated from rice roots, is pathogenic. The draft
      genome sequence of strain Os45 presented here allows an in-depth comparative
      genome analysis to understand the subtle mechanisms of beneficial and pathogenic
      Herbaspirillum-plant interactions.
AU  - Zhu B
AU  - Ye S
AU  - Chang S
AU  - Chen M
AU  - Sun L
AU  - An Q
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6995-6996.

PMID- 23516185
VI  - 1
DP  - 2013
TI  - Genome Sequence of the Alkaliphilic Bacterial Strain Bacillus ligninesis L1, a Novel Degrader of Lignin.
PG  - e0004213
AB  - Bacillus ligninesis strain L1, isolated from seafloor sediment, was able to grow  on medium
      with lignin as its sole carbon source. Here, we report a 3.8-Mbp
      high-quality genome sequence for this bacterium. The genes involving ectoine and
      glycine betaine synthesis, as well as those involved in the degradation of
      lignin, were identified.
AU  - Zhu D
AU  - Li P
AU  - Tanabe SH
AU  - Sun J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e0004213.

PMID- 29519820
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of Streptococcus suis Serotype 2 Virulent Strain SS2-1.
PG  - e00067-18
AB  - Streptococcus suis is an important swine pathogen that can also cause severe diseases in
      humans. Herein, we describe the genome sequence of Streptococcus suis
      serotype 2 virulent strain SS2-1, which was isolated from a diseased dead pig
      amid the 1998 Streptococcus suis outbreak in Jiangsu Province in China.
AU  - Zhu H
AU  - Ni Y
AU  - Zhou J
AU  - Yu Z
AU  - Mao A
AU  - Wang D
AU  - He K
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00067-18.

PMID- 22090406
VI  - 50
DP  - 2012
TI  - Development of a Multiplex PCR Assay for Detection and Genogrouping of Neisseria meningitidis.
PG  - 46-51
AB  - Neisseria meningitidis is a leading pathogen of epidemic bacterial meningitis and
      fulminant sepsis worldwide. Twelve different N. meningitidis serogroups have been
      identified to date based on antigenic differences in the capsular polysaccharide.
      However, more than 90% of human cases of N. meningitidis meningitis are the
      result of infection with just five serogroups, A, B, C, W135, and Y. Efficient
      methods of detection and genogrouping of N. meningitidis isolates are needed,
      therefore, in order to monitor prevalent serogroups as a means of disease control
      and prevention. The capsular gene complex regions have been sequenced from only
      seven out of the 12 serogroups. In this study, the capsular gene complexes of the
      remaining five serogroups were sequenced and analyzed. Primers were designed that
      were specific for N. meningitidis species and for the 12 individual serogroups,
      and a multiplex PCR assay using these specific primers was developed for N.
      meningitidis detection and genogrouping. The assay was tested using 15 reference
      strains covering all 12 serogroups, 143 clinical isolates, and 21 strains from
      closely related species or from species that cause meningitis. The assay could
      detect N. meningitidis serogroups and was shown to be specific, with a detection
      sensitivity of 1 ng of genomic DNA (equivalent to approximately 4 x 10(5)
      genomes) or 3 x 10(5) CFU/ml in noncultured mock cerebrospinal fluid (CSF)
      specimens. This study, therefore, describes for the first time the development of
      a molecular protocol for the detection of all N. meningitidis serogroups. This
      multiplex PCR-based assay may have use for the clinical diagnosis and
      epidemiological surveillance of N. meningitidis.
AU  - Zhu H
AU  - Wang Q
AU  - Wen L
AU  - Xu J
AU  - Shao Z
AU  - Chen M
AU  - Chen M
AU  - Reeves PR
AU  - Cao B
AU  - Wang L
PT  - Journal Article
TA  - J. Clin. Microbiol.
JT  - J. Clin. Microbiol.
SO  - J. Clin. Microbiol. 2012 50: 46-51.

PMID- 1809331
VI  - 11
DP  - 1991
TI  - Susceptibility of AatII and ApaI 3' protruding ends to exonuclease III degradation.
PG  - 757-759
AB  - None
AU  - Zhu J
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 1991 11: 757-759.

PMID- 27491977
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of a Thermophilic Desulfurization Bacterium, Geobacillus thermoglucosidasius Strain W-2.
PG  - e00793-16
AB  - Geobacillus thermoglucosidasius strain W-2 is a thermophilic bacterium isolated from a
      deep-subsurface oil reservoir in northern China, which is capable of
      degrading organosulfur compounds. Here, we report the draft genome sequence of G.
      thermoglucosidasius strain W-2, which may help to elucidate the genetic basis of
      biodegradation of organosulfur pollutants under heated conditions.
AU  - Zhu L
AU  - Li M
AU  - Guo S
AU  - Wang W
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00793-16.

PMID- 23826102
VI  - 8
DP  - 2013
TI  - Complete Genome Analysis of Three Acinetobacter baumannii Clinical Isolates in China for Insight into the Diversification of Drug Resistance Elements.
PG  - E66584
AB  - BACKGROUND: The emergence and rapid spreading of multidrug-resistant
      Acinetobacter baumannii strains has become a major health threat worldwide. To
      better understand the genetic recombination related with the acquisition of
      drug-resistant elements during bacterial infection, we performed complete genome
      analysis on three newly isolated multidrug-resistant A. baumannii strains from
      Beijing using next-generation sequencing technology. METHODOLOGIES/PRINCIPAL
      FINDINGS: Whole genome comparison revealed that all 3 strains share some common
      drug resistant elements including carbapenem-resistant bla OXA-23 and
      tetracycline (tet) resistance islands, but the genome structures are diversified
      among strains. Various genomic islands intersperse on the genome with transposons
      and insertions, reflecting the recombination flexibility during the acquisition
      of the resistant elements. The blood-isolated BJAB07104 and ascites-isolated
      BJAB0868 exhibit high similarity on their genome structure with most of the
      global clone II strains, suggesting these two strains belong to the dominant
      outbreak strains prevalent worldwide. A large resistance island (RI) of about
      121-kb, carrying a cluster of resistance-related genes, was inserted into the
      ATPase gene on BJAB07104 and BJAB0868 genomes. A 78-kb insertion element carrying
      tra-locus and bla OXA-23 island, can be either inserted into one of the tniB gene
      in the 121-kb RI on the chromosome, or transformed to conjugative plasmid in the
      two BJAB strains. The third strains of this study, BJAB0715, which was isolated
      from spinal fluid, exhibit much more divergence compared with above two strains.
      It harbors multiple drug-resistance elements including a truncated AbaR-22-like
      RI on its genome. One of the unique features of this strain is that it carries
      both bla OXA-23 and bla OXA-58 genes on its genome. Besides, an Acinetobacter
      lwoffii adeABC efflux element was found inserted into the ATPase position in
      BJAB0715. CONCLUSIONS: Our comparative analysis on currently completed
      Acinetobacter baumannii genomes revealed extensive and dynamic genome
      organizations, which may facilitate the bacteria to acquire drug-resistance
      elements into their genomes.
AU  - Zhu L
AU  - Yan Z
AU  - Zhang Z
AU  - Zhou Q
AU  - Zhou J
AU  - Wakeland EK
AU  - Fang X
AU  - Xuan Z
AU  - Shen D
AU  - Li QZ
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2013 8: E66584.

PMID- 26704977
VI  - 44
DP  - 2016
TI  - Precision methylome characterization of Mycobacterium tuberculosis complex (MTBC) using PacBio single-molecule real-time (SMRT) technology.
PG  - 730-743
AB  - Tuberculosis (TB) remains one of the most common infectious diseases caused by Mycobacterium
      tuberculosis complex (MTBC). To panoramically analyze MTBC's
      genomic methylation, we completed the genomes of 12 MTBC strains (Mycobacterium
      bovis; M. bovis BCG; M. microti; M. africanum; M. tuberculosis H37Rv; H37Ra; and
      6 M. tuberculosis clinical isolates) belonging to different lineages and
      characterized their methylomes using single-molecule real-time (SMRT) technology.
      We identified three m6A sequence motifs and their corresponding methyltransferase
      (MTase) genes, including the reported mamA, hsdM and a newly discovered mamB. We
      also experimentally verified the methylated motifs and functions of HsdM and
      MamB. Our analysis indicated the MTase activities varied between 12 strains due
      to mutations/deletions. Furthermore, through measuring 'the methylated-motif-site
      ratio' and 'the methylated-read ratio', we explored the methylation status of
      each modified site and sequence-read to obtain the 'precision methylome' of the
      MTBC strains, which enabled intricate analysis of MTase activity at whole-genome
      scale. Most unmodified sites overlapped with transcription-factor
      binding-regions, which might protect these sites from methylation. Overall, our
      findings show enormous potential for the SMRT platform to investigate the precise
      character of methylome, and significantly enhance our understanding of the
      function of DNA MTase.
AU  - Zhu L
AU  - Zhong J
AU  - Jia X
AU  - Liu G
AU  - Kang Y
AU  - Dong M
AU  - Zhang X
AU  - Li Q
AU  - Yue L
AU  - Li C
AU  - Fu J
AU  - Xiao J
AU  - Yan J
AU  - Zhang B
AU  - Lei M
AU  - Chen S
AU  - Lv L
AU  - Zhu B
AU  - Huang H
AU  - Chen F
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2016 44: 730-743.

PMID- 26450738
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Ralstonia sp. MD27, a Poly(3-Hydroxybutyrate)-Degrading  Bacterium, Isolated from Compost.
PG  - e01170-15
AB  - Ralstonia sp. strain MD27, a novel biopolymer-degrading betaproteobacterium, was  isolated
      from compost samples. This organism has been shown to utilize the biopolymer
      poly(3-hydroxybutyrate) [P(3HB)] as a carbon source for growth. We report the draft genome
      sequence of MD27 with an estimated total sequence length  of 5.9 Mb.
AU  - Zhu M
AU  - McCully LM
AU  - Silby MW
AU  - Charles-Ogan TI
AU  - Huang J
AU  - Brigham CJ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01170-15.

PMID- 10417653
VI  - 33
DP  - 1999
TI  - The opcA and (psi)opcB regions in Neisseria: genes, pseudogenes, deletions, insertion elements and DNA islands.
PG  - 635-650
AB  - Previous data have indicated that the opc gene encoding an immunogenic invasin is specific to
      Neisseria meningitidis (Nm) and is lacking in
      Neisseria gonorrhoeae (Ng). The data presented here show that Nm and Ng
      both contain two paralogous opc-like genes, opcA, corresponding to the
      former opc gene, and (psi)opcB, a pseudogene. The predicted OpcA and OpcB
      proteins possess transmembrane regions with conserved non-polar faces but
      differ extensively in four of the five surface-exposed loops. Gonococcal
      OpcA was expressed weakly under in vitro conditions, and it is unknown
      whether these bacteria can express this protein at high levels. Analysis
      of the sequences flanking opcA and (psi)opcB revealed a framework of
      conserved housekeeping genes interspersed with DNA islands. These regions
      also contained several pseudogenes, deletions and IS elements, attesting
      to considerable genome plasticity. Both opcA and (psi)opcB are located on
      DNA islands that have probably been imported from unrelated bacteria. A
      third island encodes the dcmD/dcrD R/M genes in Ng versus a small open
      reading frame in most strains of Nm. Rare strains of Nm were identified in
      which the R/M island has been imported. DNA islands in Nm and Ng seem to
      have been acquired by recombination via conserved flanking housekeeping
      genes rather than by insertion of mobile genetic elements.
AU  - Zhu P
AU  - Morelli G
AU  - Achtman M
PT  - Journal Article
TA  - Mol. Microbiol.
JT  - Mol. Microbiol.
SO  - Mol. Microbiol. 1999 33: 635-650.

PMID- 23991252
VI  - 8
DP  - 2013
TI  - Non-contiguous finished genome sequence and description of Salmonella enterica subsp. houtenae str. RKS3027.
PG  - 198-205
AB  - Salmonella enterica subsp. houtenae serovar 16:z4, z32:-- str. RKS3027 was isolated from a
      human in Illinois, USA. S. enterica subsp. houtenae is a
      facultative aerobic rod-shaped Gram-negative bacterium. Here we describe the
      features of this organism, together with the draft genome sequence and
      annotation. The 4,404,136 bp long genome (97 contigs) contains 4,335
      protein-coding gene and 28 RNA genes.
AU  - Zhu S
AU  - Wang HL
AU  - Wang C
AU  - Tang L
AU  - Wang X
AU  - Yu KJ
AU  - Liu SL
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2013 8: 198-205.

PMID- 27445381
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Hemolysin-Containing Carnobacterium sp. Strain CP1 Isolated from the Antarctic.
PG  - e00690-16
AB  - Carnobacterium sp. strain CP1 was isolated from Antarctic sandy soil and predicted to be a
      novel species belonging to the genus Carnobacterium Herein, we
      report the complete genome sequence, which consists of a circular 2,605,518-bp
      chromosome and an 8,883-bp plasmid with G+C contents of 38.13% and 31.63%,
      respectively.
AU  - Zhu S
AU  - Wang X
AU  - Zhang D
AU  - Jing X
AU  - Zhang N
AU  - Yang J
AU  - Chen J
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00690-16.

PMID- 28254973
VI  - 5
DP  - 2017
TI  - Draft Genome Sequences of Nine Cyanobacterial Strains from Diverse Habitats.
PG  - e01676-16
AB  - Here, we report the annotated draft genome sequences of nine different cyanobacteria, which
      were originally collected from different habitats, including
      hot springs, terrestrial, freshwater, and marine environments, and cover four of
      the five morphological subsections of cyanobacteria.
AU  - Zhu T
AU  - Hou S
AU  - Lu X
AU  - Hess WR
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e01676-16.

PMID- 25197493
VI  - 9
DP  - 2014
TI  - Genomic analysis of Skermanella stibiiresistens type strain SB22 (T.).
PG  - 1211-1220
AB  - Members of genus Skermanella were described as Gram-negative, motile, aerobic, rod-shaped,
      obligate-heterotrophic bacteria and unable to fix nitrogen. In this
      study, the genome sequence of Skermanella stibiiresistens SB22(T) is reported.
      Phylogenetic analysis using core proteins confirmed the phylogenetic assignment
      based on 16S rRNA gene sequences. Strain SB22(T) has all the proteins for
      complete glycolysis, tricarboxylic acid cycle and pentose phosphate pathway. The
      RuBisCO encoding genes cbbL1S1 and nitrogenase delta subunit gene anfG are
      absent, consistent with its inability to fix carbon and nitrogen, respectively.
      In addition, the genome possesses a series of flagellar assembly and chemotaxis
      genes to ensure its motility.
AU  - Zhu W
AU  - Huang J
AU  - Li M
AU  - Li X
AU  - Wang G
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2014 9: 1211-1220.

PMID- 25887950
VI  - 16
DP  - 2015
TI  - Identification of three extra-chromosomal replicons in Leptospira pathogenic strain and development of new shuttle vectors.
PG  - 90
AB  - Background: The genome of pathogenic Leptospira interrogans contains two chromosomes. Plasmids
      and prophages are known to play specific roles in gene transfer in bacteria and can
      potentially serve as efficient genetic tools in these organisms. Although plasmids and
      prophage remnants have recently been reported in Leptospira species, their characteristics and
      potential applications in leptospiral genetic transformation systems have not been fully
      evaluated. Results: Three extrachromosomal replicons designated lcp1 (65,732 bp), lcp2 (56,757
      bp), and lcp3 (54,986 bp) in the L.
      interrogans serovar Linhai strain 56609 were identified through whole genome sequencing. All
      three replicons were stable outside of the bacterial chromosomes. Phage particles were
      observed in the culture supernatant of 56609 after mitomycin C induction, and lcp3, which
      contained phage-related genes, was considered to be an inducible prophage. L.
      interrogans-Escherichia coli shuttle vectors, constructed with the predicted replication
      elements of single rep or rep combined with parAB loci from the three plasmids were shown to
      successfully transform into both saprophytic and pathogenic Leptospira species, suggesting an
      essential function for rep genes in supporting auto-replication of the plasmids. Additionally,
      a wide distribution of homologs of the three rep genes was identified in L. interrogans
      isolates, and correlation tests showed that the transformability of the shuttle vectors in L.
      interrogans isolates depended, to certain extent, on genetic compatibility between the rep
      sequences of both plasmid and host. Conclusions: Three extrachromosomal replicons co-exist in
      L. interrogans, one of which we consider to be an inducible prophage. The vectors constructed
      with the rep genes of the three replicons successfully transformed into saprophytic and
      pathogenic Leptospira species alike, but this was partly dependent on genetic compatibility
      between the rep sequences of both plasmid and host.
AU  - Zhu W
AU  - Wang J
AU  - Zhu Y
AU  - Tang B
AU  - Zhang Y
AU  - He P
AU  - Zhang Y
AU  - Liu B
AU  - Guo X
AU  - Zhao G
AU  - Qin J
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2015 16: 90.

PMID- 27417841
VI  - 4
DP  - 2016
TI  - Complete Genome Sequence of Sphingomonas sp. Strain NIC1, an Efficient Nicotine-Degrading Bacterium.
PG  - e00666-16
AB  - Sphingomonas sp. strain NIC1, an efficient nicotine-degrading bacterium, was isolated from
      tobacco leaves. Here, we present the complete genome sequence of
      strain NIC1, which contains one circular chromosome and two circular plasmids.
      The genomic information will provide insights into its molecular mechanism for
      nicotine degradation.
AU  - Zhu X
AU  - Wang W
AU  - Xu P
AU  - Tang H
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00666-16.

PMID- 27901120
VI  - 6
DP  - 2016
TI  - Complete genome sequence and transcriptomic analysis of a novel marine strain Bacillus weihaiensis reveals the mechanism of brown algae degradation.
PG  - 38248
AB  - A novel marine strain representing efficient degradation ability toward brown
      algae was isolated, identified, and assigned to Bacillus weihaiensis Alg07. The
      alga-associated marine bacteria promote the nutrient cycle and perform important
      functions in the marine ecosystem. The de novo sequencing of the B. weihaiensis
      Alg07 genome was carried out. Results of gene annotation and carbohydrate-active
      enzyme analysis showed that the strain harbored enzymes that can completely
      degrade alginate and laminarin, which are the specific polysaccharides of brown
      algae. We also found genes for the utilization of mannitol, the major storage
      monosaccharide in the cell of brown algae. To understand the process of brown
      algae decomposition by B. weihaiensis Alg07, RNA-seq transcriptome analysis and
      qRT-PCR were performed. The genes involved in alginate metabolism were all
      up-regulated in the initial stage of kelp degradation, suggesting that the strain
      Alg07 first degrades alginate to destruct the cell wall so that the laminarin and
      mannitol are released and subsequently decomposed. The key genes involved in
      alginate and laminarin degradation were expressed in Escherichia coli and
      characterized. Overall, the model of brown algae degradation by the marine strain
      Alg07 was established, and novel alginate lyases and laminarinase were
      discovered.
AU  - Zhu Y
AU  - Chen P
AU  - Bao Y
AU  - Men Y
AU  - Zeng Y
AU  - Yang J
AU  - Sun J
AU  - Sun Y
PT  - Journal Article
TA  - Sci. Rep.
JT  - Sci. Rep.
SO  - Sci. Rep. 2016 6: 38248.

PMID- 26205855
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Lactobacillus panis DSM 6035T, First Isolated from Sourdough.
PG  - e00778-15
AB  - We report a draft genome sequence of Lactobacillus panis DSM 6035(T), isolated from sourdough.
      The genome of this strain is 2,082,789 bp long, with 47.9% G+C
      content. A total of 2,047 protein-coding genes were predicted.
AU  - Zhu Y
AU  - Fang D
AU  - Shi D
AU  - Li A
AU  - Lv L
AU  - Yan R
AU  - Yao J
AU  - Hua D
AU  - Hu X
AU  - Guo F
AU  - Wu W
AU  - Guo J
AU  - Chen Y
AU  - Jiang X
AU  - Chen X
AU  - Li L
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00778-15.

PMID- 28572316
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of Rice Orange Leaf Phytoplasma from Guangdong, China.
PG  - e00430-17
AB  - The genome of rice orange leaf phytoplasma strain LD1 from Luoding City, Guangdong, China, was
      sequenced. The draft LD1 genome is 599,264 bp, with a G+C
      content of 28.2%, 647 predicted open reading frames, and 33 RNA genes.
AU  - Zhu Y
AU  - He Y
AU  - Zheng Z
AU  - Chen J
AU  - Wang Z
AU  - Zhou G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00430-17.

PMID- 21398543
VI  - 193
DP  - 2011
TI  - Complete Genome Sequence of Bacillus thuringiensis serovar. finitimus Strain YBT-020.
PG  - 2379-2380
AB  - Bacillus thuringiensis is a Gram-positive, spore-forming bacterium that forms parasporal
      crystals at the onset of the sporulation phase of its growth. Here we report the complete
      genome sequence of B. thuringiensis serovar. finitimus strain YBT-020, whose parasporal
      crystals consist of Cry26Aa and Cry28Aa crystal proteins and are located between the
      exosporium and the spore coat and remain adhering to the spore after sporulation.
AU  - Zhu Y
AU  - Shang H
AU  - Zhu Q
AU  - Ji F
AU  - Wang P
AU  - Fu J
AU  - Deng Y
AU  - Xu C
AU  - Ye W
AU  - Zheng J
AU  - Zhu L
AU  - Sun M
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2011 193: 2379-2380.

PMID- 16502621
VI  - 28
DP  - 2006
TI  - Quantitative analysis of EcoR1 methylase-DNA complex by atomic force microscopy.
PG  - 15-19
AB  - The EcoRI methylase specifically recognize 5'-GA*ATTC-3' in DNA duplex.  We directly applied
      atomic force microscopy to investigate linear pBR322-EcoRI methylase complexes and
      quantitatively analyzed the bend angles of linear pBR322-EcoRI methylse complexes and the
      bound protein widths.  In this study, we made a novel observation that DNA-EcoRI methylase
      complexes exhibited two populations of conformation at the recognition site: DNA was bent at
      an acute
      angle at the recognition site in the presence of one EcoRI methylase monomeric molecule, while
      DNA was bent at an obtuse angle at the recognition site and the complementary site on duplex
      DNAs in
      the presence of EcoRI methylase dimer.  The data indicated that the obtuse angle state was
      the result of unique interactions between EcoRI methylase and the recognition site and the
      complementary site on duplex DNAs, and suggested that the acute angle conformation could be an
      intermediate in the formation of the obtuse angle state.  Our works provide a detail insight
      into the DNA structural variations involved in EcoRI methylase-binding processes and
      demonstrate further the versatility of AFM as an imaging technique for studying the
      interaction between large DNA fragment and protein.
AU  - Zhu Y
AU  - Zeng H
AU  - Gao X
AU  - Lu ZH
PT  - Journal Article
TA  - Scanning
JT  - Scanning
SO  - Scanning 2006 28: 15-19.

PMID- 24452415
VI  - 4
DP  - 2014
TI  - Characterization of cleavage intermediate and star sites of RM.Tth111II.
PG  - 3838
AB  - Tth111II is a thermostable Type IIGS restriction enzyme that recognizes DNA sites CAARCA (R =
      A or G) and cleaves downstream at N11/N9. Here, the tth111IIRM gene
      was cloned and expressed in E. coli, and Tth111II was purified. The purified
      enzyme contains internally-bound S-adenosylmethionine (SAM). When the internal
      SAM was removed, the endonuclease activity was stimulated by adding SAM or its
      analog sinefungin. The cleavage intermediate is mostly top-strand nicked DNA on a
      single-site plasmid. Addition of duplex oligos with a cognate site stimulates
      cleavage activity of the one-site substrate. Tth111II cleaves a two-site plasmid
      DNA with equal efficiency regardless of site orientation. We propose the
      top-strand nicking is carried out by a Tth111II monomer and bottom-strand
      cleavage is carried out by a transient dimer. Tth111II methylates cleavage
      product-like duplex oligos CAAACAN9, but the modification rate is estimated to be
      much slower than the top-strand nicking rate. We cloned and sequenced a number of
      Tth111II star sites which are 1-bp different from the cognate sites. A
      biochemical pathway is proposed for the restriction and methylation activities of
      Tth111II.
AU  - Zhu Z
AU  - Guan S
AU  - Robinson D
AU  - El Fezzazi H
AU  - Quimby A
AU  - Xu SY
PT  - Journal Article
TA  - Sci. Rep.
JT  - Sci. Rep.
SO  - Sci. Rep. 2014 4: 3838.

PMID- 20497557
VI  - 3
DP  - 2010
TI  - Cloning of NruI and Sbo13I restriction and modification systems in E. coli and amino acid sequence comparison of M.NruI and M.Sbo13I with other amino-methyltransferases.
PG  - 139
AB  - ABSTRACT: BACKGROUND: NruI and Sbo13I are restriction enzyme isoschizomers
      with the same recognition sequence 5' TCG downward arrowCGA 3' (cleavage
      as indicated downward arrow). Here we report the cloning of NruI and
      Sbo13I restriction-modification (R-M) systems in E. coli. The NruI
      restriction endonuclease gene (nruIR) was cloned by PCR and inverse PCR
      using primers designed from the N-terminal amino acid sequence. The NruI
      methylase gene (nruIM) was derived by inverse PCR walking. RESULTS: The
      amino acid sequences of NruI endonuclease and methylase are very similar
      to the Sbo13I R-M system which has been cloned and expressed in E. coli by
      phage selection of a plasmid DNA library. Dot blot analysis using rabbit
      polyclonal antibodies to N6mA- or N4mC-modified DNA indicated that M.NruI
      is possibly a N6mA-type amino-methyltransferase that most likely modifies
      the external A in the 5' TCGCGA 3' sequence. M.Sbo13I, however, is
      implicated as a probable N4mC-type methylase since plasmid carrying
      sbo13IM gene is not restricted by Mrr endonuclease and Sbo13I digestion is
      not blocked by Dam methylation of the overlapping site. The amino acid
      sequence of M.NruI and M.Sbo13I did not show significant sequence
      similarity to many known amino-methyltransferases in the alpha, beta, and
      gamma groups, except to a few putative methylases in sequenced microbial
      genomes. CONCLUSIONS: The order of the conserved amino acid motifs
      (blocks) in M.NruI/M.Sbo13I is similar to the gamma. group
      amino-methyltranferases, but with two distinct features: In motif IV, the
      sequence is DPPY instead of NPPY; there are two additional conserved
      motifs, IVa and Xa as extension of motifs IV and X, in this family of
      enzymes. We propose that M.NruI and M.Sbo13I form a subgroup in the gamma
      group of amino-methyltransferases.
AU  - Zhu Z
AU  - Pedamallu CS
AU  - Fomenkov A
AU  - Benner J
AU  - Xu SY
PT  - Journal Article
TA  - BMC Res. Notes
JT  - BMC Res. Notes
SO  - BMC Res. Notes 2010 3: 139.

PMID- 15019778
VI  - 337
DP  - 2004
TI  - Engineering strand-specific DNA nicking enzymes from the type IIS restriction endonucleases BsaI, BsmBI, and BsmAI.
PG  - 573-583
AB  - More than 80 type IIA/IIS restriction endonucleases with different recognition specificities
      are now known. In contrast, only a limited number of strand-specific nicking endonucleases are
      currently available. To overcome this limitation, a novel genetic screening method was devised
      to convert type IIS restriction endonucleases into strand-specific nicking endonucleases. The
      genetic screen consisted of four steps: (1) random mutagenesis to create a plasmid library,
      each bearing an inactivated endonuclease gene; (2) restriction digestion of plasmids
      containing the wild-type and the mutagenized endonuclease gene; (3) back-crosses with the
      wild-type gene by ligation to the wild-type N-terminal or C-terminal fragment; (4)
      transformation of the ligated DNA into a pre-modified host and screening for nicking
      endonuclease activity in total cell culture or cell extracts of the transformants. Nt.BsaI and
      Nb.BsaI nicking endonucleases were isolated from BsaI using this genetic screen. In addition,
      site-directed mutagenesis was carried out to isolate BsaI nicking variants with minimal
      double-stranded DNA cleavage activity. The equivalent amino acid substitutions were introduced
      into BsmBI and BsmAI restriction endonucleases with similar recognition sequence and
      significant amino acid sequence identity and their nicking variants were successfully
      isolated. This work provides strong evidence that some type IIS restriction endonucleases
      carry two separate active sites. When one of the active sites is inactivated, the type IIS
      restriction endonuclease may nick only one strand.
AU  - Zhu Z
AU  - Samuelson JC
AU  - Zhou J
AU  - Dore A
AU  - Xu S-y
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2004 337: 573-583.

PMID- 12823974
VI  - 330
DP  - 2003
TI  - Isolation of BsoBI restriction endonuclease variants with altered substrate specificity.
PG  - 359-372
AB  - BsoBI is a thermophilic restriction endonuclease that cleaves the degenerate DNA sequence
      C/PyCGPuG (where/=the cleavage site and Py=C or T,
      Pu=A or G). In the BsoBI-DNA co-crystal structure the D246 residue makes a
      water-mediated hydrogen bond to N6 of the degenerate base adenine and was
      proposed to make a complementary bond to O6 of the alternative guanine
      residue. To investigate the substrate specificity conferred by D246 and to
      potentially alter BsoBI specificity, the D246 residue was changed to the
      other 19 amino acids. Variants D246A, D246C, D246E, D246R, D246S, D246T,
      and D246Y were purified and their cleavage activity determined. Variants
      D246A, D246S, and D246T display 0.2% to 0.7% of the wild-type cleavage
      activity. However, the substrate specificity of the three variants is
      altered significantly. D246A, D246S, and D246T cleave CTCGAG sites poorly.
      In filter binding assays using oligonucleotides, wild-type BsoBI shows
      almost equal affinity for CTCGAG and CCCGGG sites. In contrast, the D246A
      variant shows 70-fold greater binding affinity for the CCCGGG substrate.
      Recycled mutagenesis was carried out on the D246A variant, and revertants
      with enhanced activity were isolated by their dark blue phenotype on a
      dinD Colon, two colons lacZ DNA damage indicator strain. Most of the amino
      acid substitutions present within the revertants were located outside the
      DNA-protein interface. This study demonstrates that endonuclease mutants
      with altered specificity and non-lethal activity can be evolved towards
      more active variants using a laboratory evolution strategy.
AU  - Zhu ZY
AU  - Zhou J
AU  - Friedman AM
AU  - Xu SY
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 2003 330: 359-372.

PMID- 25397580
VI  - 9
DP  - 2014
TI  - Comparative Genomic Analysis Shows That Avian Pathogenic Escherichia coli Isolate IMT5155 (O2:K1:H5; ST Complex 95, ST140) Shares Close Relationship with ST95 APEC O1:K1 and Human ExPEC O18:K1 Strains.
PG  - E112048
AB  - Avian pathogenic E. coli and human extraintestinal pathogenic E. coli serotypes O1, O2 and O18
      strains isolated from different hosts are generally located in
      phylogroup B2 and ST complex 95, and they share similar genetic characteristics
      and pathogenicity, with no or minimal host specificity. They are popular objects
      for the study of ExPEC genetic characteristics and pathogenesis in recent years.
      Here, we investigated the evolution and genetic blueprint of APEC pathotype by
      performing phylogenetic and comparative genome analysis of avian pathogenic E.
      coli strain IMT5155 (O2:K1:H5; ST complex 95, ST140) with other E. coli
      pathotypes. Phylogeny analyses indicated that IMT5155 has closest evolutionary
      relationship with APEC O1, IHE3034, and UTI89. Comparative genomic analysis
      showed that IMT5155 and APEC O1 shared significant genetic overlap/similarities
      with human ExPEC dominant O18:K1 strains (IHE3034 and UTI89). Furthermore, the
      unique PAI I5155 (GI-12) was identified and found to be conserved in APEC O2
      serotype isolates. GI-7 and GI-16 encoding two typical T6SSs in IMT5155 might be
      useful markers for the identification of ExPEC dominant serotypes (O1, O2, and
      O18) strains. IMT5155 contained a ColV plasmid p1ColV5155, which defined the APEC
      pathotype. The distribution analysis of 10 sequenced ExPEC pan-genome virulence
      factors among 47 sequenced E. coli strains provided meaningful information for B2
      APEC/ExPEC-specific virulence factors, including several adhesins, invasins,
      toxins, iron acquisition systems, and so on. The pathogenicity tests of IMT5155
      and other APEC O1:K1 and O2:K1 serotypes strains (isolated in China) through four
      animal models showed that they were highly virulent for avian colisepticemia and
      able to cause septicemia and meningitis in neonatal rats, suggesting zoonotic
      potential of these APEC O1:K1 and O2:K1 isolates.
AU  - Zhu-Ge X
AU  - Jiang J
AU  - Pan Z
AU  - Hu L
AU  - Wang S
AU  - Wang H
AU  - Leung FC
AU  - Dai J
AU  - Fan H
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2014 9: E112048.

PMID- 26587181
VI  - 10
DP  - 2015
TI  - Draft genome sequence of T26 and comparative analysis of six genomes.
PG  - 104
AB  - Most Cellulomonas strains are cellulolytic and this feature may be applied in straw
      degradation and bioremediation. In this study, Cellulomonas carbonis T26T,
      Cellulomonas bogoriensis DSM 16987T and Cellulomonas cellasea 20108T were
      sequenced. Here we described the draft genomic information of C. carbonis T26T
      and compared it to the related Cellulomonas genomes. Strain T26T has a 3,990,666
      bp genome size with a G + C content of 73.4 %, containing 3418 protein-coding
      genes and 59 RNA genes. The results showed good correlation between the genotypes
      and the physiological phenotypes. The information are useful for the better
      application of the Cellulomonas strains.
AU  - Zhuang W
AU  - Zhang S
AU  - Xia X
AU  - Wang G
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 104.

PMID- 24733184
VI  - 5
DP  - 2014
TI  - Elimination of inter-domain interactions increases the cleavage fidelity of the restriction endonuclease DraIII.
PG  - 357-368
AB  - DraIII is a type IIP restriction endonucleases (REases) that recognizes and creates a double
      strand break within the gapped palindromic sequence CACa dagger NNNa dagger'GTG of
      double-stranded DNA (a dagger indicates nicking on the bottom strand; a dagger' indicates
      nicking on the top strand). However, wild type DraIII shows significant star activity. In this
      study, it was found that the prominent star site is CATa dagger GTTa dagger'GTG, consisting
      of a star 5' half (CAT) and a canonical 3' half (GTG). DraIII nicks the 3' canonical half
      site at a faster rate than the 5' star half site, in contrast to the similar rate with the
      canonical full site. The crystal structure of the DraIII protein was solved. It indicated, as
      supported by mutagenesis, that DraIII possesses a beta beta I +/--metal HNH active site. The
      structure revealed extensive intra-molecular interactions between the N-terminal domain and
      the C-terminal domain containing the HNH active site. Disruptions of these interactions
      through site-directed mutagenesis drastically increased cleavage fidelity. The understanding
      of fidelity mechanisms will enable generation of high fidelity REases.
AU  - Zhuo W
AU  - Lai X
AU  - Zhang L
AU  - Chan S-H
AU  - Li F
AU  - Zhu Z
AU  - Yang M
AU  - Sun D
PT  - Journal Article
TA  - Protein Cell
JT  - Protein Cell
SO  - Protein Cell 2014 5: 357-368.

PMID- 22887659
VI  - 194
DP  - 2012
TI  - Revised Genome Sequence of Burkholderia thailandensis MSMB43 with Improved Annotation.
PG  - 4749-4750
AB  - There is growing interest in discovery of novel bioactive natural products from Burkholderia
      thailandensis. Here we report a significantly improved genome
      sequence and reannotation of Burkholderia thailandensis MSMB43, which will
      facilitate the discovery of new natural products through genome mining and
      studies of the metabolic versatility of this bacterium.
AU  - Zhuo Y
AU  - Liu L
AU  - Wang Q
AU  - Liu X
AU  - Ren B
AU  - Liu M
AU  - Ni P
AU  - Cheng YQ
AU  - Zhang L
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 4749-4750.

PMID- 2995964
VI  - 21
DP  - 1985
TI  - The effect of cultivation conditions and ultrasonic destruction of Streptomyces achromogenes ATCC 12767 cells on the yield of restriction endonucleases.
PG  - 401-406
AB  - The effect of the cultivation time, aeration rate and nutrient medium
      composition on the yield of the restrictase activity of the submerged culture
      of Streptomyces achromogenes ATCC 12767 was investigated.  A maximum value of
      the specific restrictase activity was observed in the second part of the
      exponential phase of growth (after 22-24 hours of cultivation).  An optimal
      composition of the nutrient medium for cultivation of S. achromogenes was found
      using mathematical methods of experiment planning.  The medium includes (g/l):
      glucose-10.0; peptone-4.0; yeast extract-4.0; MgSO4.7H2O-0.5; K2HPO4-4.0;
      KH2PO4-2.0.  An addition of detergents to the buffer during ultrasonic
      destruction of S. achromogenes cells enabled the yield of the restrictase
      activity to be increased more than twice.
AU  - Zhuravleva LI
AU  - Oreshkin EN
PT  - Journal Article
TA  - Prikl. Biokhim. Mikrobiol.
JT  - Prikl. Biokhim. Mikrobiol.
SO  - Prikl. Biokhim. Mikrobiol. 1985 21: 401-406.

PMID- 3033630
VI  - 23
DP  - 1987
TI  - Isolation and purification of restriction endonuclease SacI from Streptomyces achromogenes ATCC 12767.
PG  - 208-215
AB  - A procedure for isolation and purification of restriction endonuclease SacI
      from Streptomyces achromogenes ATCC 12767 is proposed.  It allows to obtain an
      electrophoretically homogeneous enzyme yield by activity 3.7%.  The molecular
      weight of SacI was found to be 52,000 +/-5000 D, and isoelectric point 6.2.
      The enzyme consists of two subunits, which was found by polyacrylamide gel
      electrophoresis under denaturing conditions.  Km and Vmax values were
      determined for the enzymatic reaction; they are equal to 4.6x10-9 M and
      9.19x10-10 M/min, respectively.
AU  - Zhuravleva LI
AU  - Oreshkin EN
AU  - Bezborodov AM
PT  - Journal Article
TA  - Prikl. Biokhim. Mikrobiol.
JT  - Prikl. Biokhim. Mikrobiol.
SO  - Prikl. Biokhim. Mikrobiol. 1987 23: 208-215.

PMID- 24356845
VI  - 1
DP  - 2013
TI  - High-Quality Draft Genome Sequence of Bifidobacterium longum E18, Isolated from a Healthy Adult.
PG  - e01084-13
AB  - Bifidobacteria are important gastrointestinal commensals of a number of animals,  including
      humans, and various beneficial effects on host health have been
      attributed to them. Here, we announce the noncontiguous finished genome sequence
      of Bifidobacterium longum E18, isolated from a healthy adult, which reveals
      traits involved in its interaction with the host.
AU  - Zhurina D
AU  - Dudnik A
AU  - Waidmann MS
AU  - Grimm V
AU  - Westermann C
AU  - Breitinger KJ
AU  - Yuan J
AU  - van Sinderen D
AU  - Riedel CU
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e01084-13.

PMID- 21037011
VI  - 193
DP  - 2010
TI  - Complete genome sequence of Bifidobacterium bifidum S17.
PG  - 301-302
AB  - Here, we report on the first completely annotated genome sequence of a Bifidobacterium bifidum
      strain. B. bifidum S17, isolated from faeces of a
      breast-fed infant, was shown to strongly adhere to intestinal epithelial
      cells and has potent anti-inflammatory activity in vitro and in vivo. The
      genome sequence will provide new insights into the biology of this
      potential probiotic organism and allow for the characterization of the
      molecular mechanisms underlying its beneficial properties.
AU  - Zhurina D
AU  - Zomer A
AU  - Gleinser M
AU  - Brancaccio VF
AU  - Auchter M
AU  - Waidmann MS
AU  - Westermann C
AU  - van Sinderen D
AU  - Riedel CU
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2010 193: 301-302.

PMID- 3035503
VI  - 15
DP  - 1987
TI  - Two restriction endonucleases from Bacillus sphaericus:  BspXI and BspXII.
PG  - 3919
AB  - In screening wild strains of Bacillus sphaericus, one, which we call X -not totally
      identifiable when compared to well established strains- exhibited a high yield of two
      restriction endonucleases: BspXI and BspXII. A cleared sonic extract, obtained from 12 grams
      of frozen cells yielded as much as 500,000 units of each enzyme by the following steps of
      chromatography and dialysis [against PC buffer (10% glycerol, 10 mM KPO4-pH 7.4, 10 mM
      B-mercaptoethanol, 0.1 mM EDTA)]. (I) A Biogel A-0.5 m filtration (II) Dialysis of active
      fractions (III) DEAE Sephacel chromatography: a gradient elution from 0 to 1 M NaCl gave pool
      I (0-0.5 M NaCl) and pool II (0.5-1 M NaCl). (IV-VI) Dialysed pool I was loaded on
      phosphocellulose column and eluted with a 0 to 1 M KCl gradient; the fraction at 0.55 M KCl
      was dialysed and the phosphocellulose chromatographic step repeated, yielding, at 0.55 M KCl,
      a pure BspXI fraction. (VII) Dialysed pool II was applied on a Blue Trisacryl column and
      eluted with a 0 to 0.5 M KCl gradient giving, at 0.3 M KCl, a pure BspXII fraction. The
      digestion patterns of different DNAs (k, pBR322 and Ad2) with BspXI and BspXII were identical
      to those obtained with ClaI and BclI, respectively, or with BspXI + ClaI and BspXII + BclI. It
      was therefore concluded that BspXI and BspXII are isoschizomers of ClaI (5'-AT/CGAT-3') and
      BclI (5'-T/GATCA-3') respectively (1,2). BspXI was further investigated using: [a] standard
      procedures (3) to determine the cleavage site at the nucleotide level and [b] a recombinant
      DNA (4) that contains a ClaI recognition sequence cleaved by the enzyme only when it is
      produced in an E. coli dam- strain. Since BspXI behaves exactly like ClaI (sensitive to
      N6-adenine methylation - generates 5' protruding dinucleotide CG), BspXI is a full
      isoschizomer of ClaI with the property that this new enzyme is able to cleave DNA at 37C in
      standard buffers containing from 0 to 200 mM NaCl without any noticeable loss of activity.
AU  - Zieger M
AU  - Patillon M
AU  - Roizes G
AU  - Lerouge T
AU  - Dupret D
AU  - Jeltsch JM
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1987 15: 3919.

PMID- 29954891
VI  - 6
DP  - 2018
TI  - Whole-Genome Shotgun Sequencing of Three Listeria monocytogenes Strains Isolated  from a Ready-to-Eat Salad-Producing Facility in Switzerland.
PG  - e00547-18
AB  - Ready-to-eat (RTE) raw foods harbor the risk of transmitting Listeria monocytogenes from the
      environment to the consumer. We isolated three strains
      from a facility producing RTE salad. These strains were used to perform challenge
      tests on different RTE salad products. Here, we present the shotgun genome
      sequences of all three of these strains.
AU  - Ziegler M
AU  - Jang H
AU  - Gopinath G
AU  - Horlbog JA
AU  - Stephan R
AU  - Guldimann C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e00547-18.

PMID- 17220406
VI  - 51
DP  - 2007
TI  - Mosaic Structure of p1658/97, a 125-Kilobase Plasmid Harboring an Active Amplicon with the Extended-Spectrum -Lactamase Gene blaSHV-5.
PG  - 1164-1171
AB  - Escherichia coli isolates recovered from patients during a clonal outbreak
      in a Warsaw, Poland, hospital in 1997 produced different levels of an
      extended-spectrum beta-lactamase (ESBL) of the SHV type. The
      beta-lactamase hyperproduction correlated with the multiplication of ESBL
      gene copies within a plasmid. Here, we present the complete nucleotide
      sequence of plasmid p1658/97 carried by the isolates recovered during the
      outbreak. The plasmid is 125,491 bp and shows a mosaic structure in which
      all modules constituting the plasmid core are homologous to those found in
      plasmids F and R100 and are separated by segments of homology to other
      known regions (plasmid R64, Providencia rettgeri genomic island R391,
      Vibrio cholerae STX transposon, Klebsiella pneumoniae or E. coli
      chromosomes). Plasmid p1658/97 bears two replication systems, IncFII and
      IncFIB; we demonstrated that both are active in E. coli. The presence of
      an active partition system (sopABC locus) and two postsegregational
      killing systems (pemIK and hok/sok) indicates that the plasmid should be
      stably maintained in E. coli populations. The conjugative transfer is
      ensured by the operons of the tra and trb genes. We also demonstrate that
      the plasmidic segment undergoing amplification contains the blaSHV-5 gene
      and is homologous to a 7.9-kb fragment of the K. pneumoniae chromosome.
      The amplicon displays the structure of a composite transposon of type I.
AU  - Zienkiewicz M
AU  - Kern-Zdanowicz I
AU  - Golebiewski M
AU  - Zylinska J
AU  - Mieczkowski P
AU  - Gniadkowski M
AU  - Bardowski J
AU  - Ceglowski P
PT  - Journal Article
TA  - Antimicrob. Agents Chemother.
JT  - Antimicrob. Agents Chemother.
SO  - Antimicrob. Agents Chemother. 2007 51: 1164-1171.

PMID- 26159523
VI  - 3
DP  - 2015
TI  - Draft Genome Sequence of Microvirga vignae Strain BR 3299T, a Novel Symbiotic Nitrogen-Fixing Alphaproteobacterium Isolated from a Brazilian Semiarid Region.
PG  - e00700-15
AB  - Microvirga vignae is a recently described species of root-nodule bacteria isolated from
      cowpeas grown in a Brazilian semiarid region. We report here the
      6.4-Mb draft genome sequence and annotation of M. vignae type strain BR 3299.
      This genome information may help to understand the mechanisms underlying the
      ability of the organism to grow under drought and high-temperatures conditions.
AU  - Zilli JE
AU  - Passos SR
AU  - Leite J
AU  - Xavier GR
AU  - Rumjaneck NG
AU  - Simoes-Araujo JL
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e00700-15.

PMID- 7585955
VI  - 83
DP  - 1995
TI  - A group II intron RNA is a catalytic component of a DNA endonuclease involved in intron mobility.
PG  - 529-538
AB  - The mobility (homing) of the yeast mitochondrial DNA group II intron aI2 occurs via target
      DNA-primed reverse transcription at a double-strand break in the recipient DNA.  Here, we show
      that the site-specific DNA endonuclease that makes the double-strand break is a
      ribonucleoprotein complex containing the aI2-encoded reverse transcriptase protein and excised
      at aI2 RNA.  Remarkably, the aI2 RNA catalyzes cleavage of the sense strand of the recipient
      DNA, while the AI2 protein appears to cleave the antisense strand.  The RNA-catalyzed sense
      strand cleavage occurs via a partial reverse splicing reaction in which the protein component
      stabilizes the active intron structure and appears to confer preference for DNA substrates.
      Our results demonstrate a biologically relevant ribozyme reaction with a substrate other than
      RNA.
AU  - Zimmerly S
AU  - Guo H
AU  - Eskes R
AU  - Yang J
AU  - Perlman PS
AU  - Lambowitz AM
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1995 83: 529-538.

PMID- 7664334
VI  - 82
DP  - 1995
TI  - Group II intron mobility occurs by target DNA-primed reverse transcription.
PG  - 545-554
AB  - Mobile group II introns encode reverse transcriptases and insert site specifically into
      intronless alleles (homing).  Here, in vitro experiments show that homing of the yeast mtDNA
      group II intron aI2 occurs by reverse transcription at a double-strand break in the recipient
      DNA.  A site-specific endonuclease cleaves the antisense strand of recipient DNA at position
      +10 of exon 3 and the sense strand at the intron insertion site.  Reverse transcription of
      aI2-containing pre-mRNA is primed by the antisense strand cleaved in exon 3 and results in
      cotransfer of the intron and flanking exon sequences.  Remarkably, the DNA endonuclease that
      initiates homing requires both the AI2 reverse transcriptase protein and aI2 RNA.  Parallels
      in their reverse transcription mechanisms raise the possibility that mobile group II introns
      were ancestors of nuclear non-long terminal repeat retrotransposons and telomerases.
AU  - Zimmerly S
AU  - Guo H
AU  - Perlman PS
AU  - Lambowitz AM
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1995 82: 545-554.

PMID- 10356323
VI  - 289
DP  - 1999
TI  - Group II intron reverse transcriptase in yeast mitochondria.  Stabilization and regulation of reverse transcriptase activity by the intron RNA.
PG  - 473-490
AB  - Group II introns encode reverse transcriptases that function in both intron mobility and RNA
      splicing. The proteins bind specifically to unspliced precursor RNA to promote splicing, and
      then remain associated with the excised intron to form a DNA endonuclease that mediates intron
      mobility by target DNA-primed reverse transcription. Here, immunoblotting and UV cross-linking
      experiments show that the reverse transcriptase activity encoded by the yeast mtDNA group II
      intron aI2 is associated with an intron-encoded protein of 62 kDa (p62). p62 is bound tightly
      to endogenous RNAs in mitochondrial ribonucleoprotein particles, and the reverse transcriptase
      activity is rapidly and irreversibly lost when the protein is released from the endogenous
      RNAs by RNase digestion. Non-denaturing gel electrophoresis and activity assays show that the
      aI2 reverse transcriptase is associated predominantly with the excised intron RNA, while a
      smaller amount is associated with unspliced precursor RNA, as expected from the role of the
      protein in RNA splicing. Although the reverse transcriptase in wild-type yeast strains is
      bound tightly to endogenous RNAs, it is regulated so that it does not copy these RNAs unless a
      suitable DNA oligonucleotide primer or DNA target site is provided. Certain mutations in the
      intron-encoded protein or RNA circumvent this regulation and activate reverse transcription of
      endogenous RNAs in the absence of added primer.  Although p62 is bound to unspliced precursor
      RNA in position to initiate cDNA synthesis in the 3' exon, the major template for target
      DNA-primed reverse transcription in vitro is the reverse-spliced intron RNA, as found
      previously for aI1. Together, our results show that binding to intron-containing RNAs
      stabilizes and regulates the activity of p62.
AU  - Zimmerly S
AU  - Moran JV
AU  - Perlman PS
AU  - Lambowitz AM
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1999 289: 473-490.

PMID- 24194211
VI  - 21
DP  - 1991
TI  - Genetic variation at the apcAB, cpcAB, gvpA1, and nifH loci and in DNA methylation among N2-fixing cyanobacteria designated Nostoc punctiforme.
PG  - 199-209
AB  - Genetic similarity among cyanobacteria of a morphological subgroup of Nostoc was evaluated
      through a comparison of several specific genes and the extent of DNA methylation.  Four of six
      cyanobacteria were originally cultured from facultative symbioses with higher plants (Gunnera
      and Encephalartos); these and one free-living isolate had been identified or repute to be N.
      punctiforme.  No consistent correlation to species or symbiotic history was found from DNA
      hybridizations to genes coding for phycocyanin, allophycocyanin, gas vesicle protein, and
      dinitrogenase reductase.  One gene (gvpC) was not present, and gvpA1 was a single-copy gene in
      all strains.  The gas vesicle genes were concluded to be potentially useful for broadly
      characterizing Nostoc or at least this subgroup.  Incubations of Nostoc genomic DNA with 22
      restriction endonucleases indicated a higher degree of methylation and similarity of its
      methylated DNA to that of other heterocystous cyanobacteria.  The genetic variation of the
      Nostoc isolates was judged to reflect primarily different soil origins.
AU  - Zimmerman WJ
AU  - Culley DE
PT  - Journal Article
TA  - Microb. Ecol.
JT  - Microb. Ecol.
SO  - Microb. Ecol. 1991 21: 199-209.

PMID- 9191026
VI  - 378
DP  - 1997
TI  - Mouse DNA methyltransferase (MTase) deletion mutants that retain the catalytic domain display neither de novo nor maintenance methylation activity in vivo.
PG  - 393-405
AB  - The mammalian genome encodes a DNA cytosine-5-methyltransferase (MTase) of about 170 kDa that
      is apparently responsible for both de novo and maintenance methylation at CpG sites.  Both
      methylation activities have to be regulated accurately to ensure correct developmental and
      cell type-specific gene activity.  Distorted DNA methylation patterns have been associated
      with cell aging and diseases such as cancer and fragile X syndrome.  Structural and functional
      in vitro studies of the mouse MTase have indicated that the enzyme has both a regulatory and a
      catalytic region located in the N-terminal and C-terminal parts of the protein, respectively.
      The regulatory region includes the nuclear localization signal (NLS), the sequence for DNA
      targeting and the Zn-binding domain.  The catalytic domain carries the ten consensus sequence
      motifs specific for all known pro- and eukaryotic DNA cytosine-5-methyltransferases.  In an
      attempt to separate regulatory and catalytic functions of the enzyme in vivo, we have tested
      various deletion mutations by means of transient and stable cell transfection experiments.
      Expression of the transgenes, all of which retained the C-terminal catalytic domain, was
      monitored by immunofluorescence staining, Northern blot analysis and SDS gel electrophoresis.
      Despite high levels of transgene expression, the truncated MTase molecules exhibited neither
      de novo nor maintenance methylation activity.  These findings might indicate that in vivo, an
      efficient control mechanism prevents the ectopic activity of the DNA Mtase that is
      structurally compromised in its N-terminal regulatory region.
AU  - Zimmermann C
AU  - Guhl E
AU  - Graessmann A
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1997 378: 393-405.

PMID- 9564528
VI  - 24
DP  - 1998
TI  - Digestion of terminal restriction endonuclease recognition sites on PCR products.
PG  - 582-584
AB  - One of the common methods for cloning polymerase chain reaction products is overhanging-end
      cloning (also known as sticky-end or directional cloning).  Frequently, it is not possible to
      use restriction enzyme sites already present in the amplified product, and primers that encode
      recognition sites of restriction endonucleases in addition to the specific sequence have to be
      designed.  After amplification of the target sequence with these primers, the PCR products are
      purified, digested with restriction enzymes and cloned into vectors treated with the same
      enzymes.  However, it has been found that many restriction enzymes fail to cleave at the end
      of PCR fragments.  To circumvent this problem, the addition of at least three more nucleotides
      at the end of a restriction site was suggested.
AU  - Zimmermann K
AU  - Schogl D
AU  - Mannhalter JW
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 1998 24: 582-584.

PMID- 9163670
VI  - 18
DP  - 1997
TI  - Genetic and epigenetic aspects of DNA methylation on genome expression, evolution, mutation and carcinogenesis.
PG  - 869-882
AB  - DNA methylation has at least two important roles in tumorigenesis.  The target cytosines (C*)
      of (cytosine-5)-DNA methyltransferase (Mtase) are mutated to thymine (T) in ~30% of inherited
      diseases and cancer, and genome-wide alterations of DNA methylation patterns occur at early
      stages of tumor development.  Insight into the normal function of DNA methylation will provide
      the knowledge to understand the origins of these aberrations and their importance for disease
      initiation and progression.  Originally the aberrations seen in tumors were attributed to the
      higher spontaneous deamination rate of 5-methylcytosine (5-mC) as compared with C and to
      misregulation of the Mtase gene.  Recently, it has become clear that the Mtase can actively
      participate in mutagenesis by enzymatically increasing both the rate of genetic and epigenetic
      alterations.  Proteins that recognize and repair these alterations determine the frequency of
      their fixation as disease causing mutations.  In addition, alterations in the metabolism of
      S-adenosylmethionine can disturb DNA methylation by depleting the cofactor
      S-adenosylmethionine or by increasing the level of metabolites acting as inhibtors of DNA
      methylation.  This review concentrates on the normal role of DNA methylation in mammals and on
      aberrations of DNA methylation in inherited disease and cancer.
AU  - Zingg J-M
AU  - Jones PA
PT  - Journal Article
TA  - Carcinogenesis
JT  - Carcinogenesis
SO  - Carcinogenesis 1997 18: 869-882.

PMID- 9576871
VI  - 332
DP  - 1998
TI  - Enzyme-mediated cytosine deamination by the bacterial methyltransferase M.MspI.
PG  - 223-230
AB  - Most prokaryotic (cytosine-5)-DNA methyltransferases increase the frequency of deamination at
      the cytosine targeted for methylation in vitro in the absence of the cofactor
      S-adenosyl-methionine or the reaction product S-adenosyl-homocysteine.  We show here that,
      under the same in vitro conditions, the prokaryotic methyltransferase, M.MspI (from Moraxella
      sp.), causes very few cytosine deaminations, suggesting a mechanism in which M.MspI may avoid
      enzyme-mediated cytosine deamination.  Two analogues of AdoMet, sinefungin and
      5'-amino-5'-deoxyadenosine, greatly increased the frequency of cytosine deamination mediated
      by M.MspI presumably by introducing a proton-donating amino group into the catalytic center,
      thus facilitating the formation of an unstable enzyme-dihydrocytosine intermediate and
      hydrolytic deamination.  Interestingly, two naturally occurring analogues, adenosine and
      5'-methylthio-5'-deoxyadenosine, which do not contain a proton-donating amino group, also
      weakly increased the deamination frequency by M.MspI, even in the presence of AdoMet or
      AdoHcy. These analogues may trigger a conformational change in the enzyme without completely
      inhibiting the access of solvent water to the catalytic center, thus allowing hydrolytic
      deamination of the enzyme-dihydrocytosine intermediate.  Under normal physiological conditions
      the enzymes M.HpaII (from Haemophilus parainfluenzae), M.HhaI (from Haemophilus haemolytica)
      and M.MspI all increased the in vivo deamination frequency at the target cytosines with
      comparable efficiency.
AU  - Zingg J-M
AU  - Shen J-C
AU  - Jones PA
PT  - Journal Article
TA  - Biochem. J.
JT  - Biochem. J.
SO  - Biochem. J. 1998 332: 223-230.

PMID- 8774911
VI  - 24
DP  - 1996
TI  - Methylation inhibitors can increase the rate of cytosine deamination by (cytosine- 5)-DNA methyltransferase.
PG  - 3267-3275
AB  - The target cytosines of (cytosine-5)-DNA methyltransferases in prokaryotic
      and eukaryotic DNA show increased rates of C->T transition mutations compared to non-
      target cytosines.  These mutations are induced either by the spontaneous deamination of 5-
      mC->T generating inefficiently repaired G:T rather than G:U mismatches, or by the
      enzyme-induced C->U deamination which occurs under conditions of reduced levels of S-
      adenosylmethionine (AdoMet) and S-adenosyl-homocysteine (AdoHcy).  We tested
      whether various inhibitors of (cytosine-5)-DNA methyltransferases analogous to AdoMet
      and AdoHcy would affect the rate of enzyme-induced deamination of the target cytosine by
      M.HpaII and M.SssI.  Interestingly, we found two compounds, sinefungin and 5'-amino-
      5'-deoxyadenosine, that increased the rate of deamination 103-fold in the presence and
      104-fold in the absence of AdoMet and AdoHcy.  We have therefore identified the first
      mutagenic compounds specific for the target sites of (cytosine-5)-DNA methyltransferases.
      A number of analogs of AdoMet and AdoHcy have been considered as possible antiviral,
      anticancer, antifungal and anti-parasitic agents.  Our findings show that chemotherapeutic
      agents with affinities to the cofactor binding pocket of (cytosine-5)-DNA methyltransferase
      should be tested for their potential mutagenic effects.
AU  - Zingg J-M
AU  - Shen J-C
AU  - Yang AS
AU  - Rapoport H
AU  - Jones PA
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1996 24: 3267-3275.

PMID- 1404378
VI  - 227
DP  - 1992
TI  - Mutation in the specificity polypeptide of the Type I restriction endonuclease R EcoK that affects subunit assembly.
PG  - 597-601
AB  - We describe the isolation and characterization of a temperature-sensitive mutation within the
      hsdS gene of the type I restriction and modification system EcoK. This mutation appears to
      affect the ability of the HsdR subunit to interact with the HsdS subunit when forming an
      active endonuclease. We discuss the possibility that this mutant, together with another
      mutation described previously, may define a discontinuous domain, involved in protein-protein
      interactions, within the HsdS polypeptide.
AU  - Zinkevich V
AU  - Heslop P
AU  - Glover SW
AU  - Weiserova M
AU  - Hubacek J
AU  - Firman K
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1992 227: 597-601.

PMID- 9016588
VI  - 25
DP  - 1997
TI  - The HsdR subunit of R.EcoR124II: cloning and over-expression of the gene and unexpected properties of the subunit.
PG  - 503-510
AB  - Type I restriction endonucleases are composed of three subunits, HsdR, HsdM and HsdS.  The
      HsdR subunit is absolutely required for restriction activity; while an independent methylase
      is composed of HsdM and HsdS subunits.  DNA cleavage is associated with a powerful ATPase
      activity during which DNA is translocated by the enzyme prior to cleavage.  The presence of a
      Walker type I ATP-binding site within the HsdR subunit suggested that the subunit may be
      capable of independent enzymatic activity.  Therefore, we have, for the first time, cloned and
      over-expressed the hsdR gene of the type IC restriction endonuclease EcoR124II.  The purified
      HsdR subunit was found to be a soluble monomeric protein capable of DNA- and Mg2+-dependent
      ATP hydrolysis.  The subunit was found to have a weak nuclease activity both in vivo and in
      vitro, and to bind plasmid DNA; although was not capable of binding a DNA oligoduplex.  We
      were also able to reconstitute the fully active endonuclease from purified M.EcoR124I and
      HsdR.  This is the first clear demonstration that the HsdR subnit of a type I restriction
      endonuclease is capable of independent enzyme activity, and suggests a mechanism for the
      evolution of the endonuclease from the independent methylase.
AU  - Zinkevich V
AU  - Popova L
AU  - Kryukov V
AU  - Abadjieva A
AU  - Bogdarina I
AU  - Janscak P
AU  - Firman K
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 1997 25: 503-510.

PMID- 3027537
VI  - 20
DP  - 1986
TI  - Influence of bacteriophage lambda ral gene on the level of synthesis of the restriction endonuclease EcoK beta-subunit.
PG  - 1638-1644
AB  - E. coli hsd genes were subcloned from lambda 642 (ra1+) into the lambda
      L47.1
      vector (ra1- after replacement).  We investigated the influence of the bacteriophage lambda
      ra1 gene
      on the expression efficiency of hsdSk and hsdMk genes.  Its presence in vitro enhanced the
      synthesis of the beta-subunit and hsdMk gene product.  Increased modification in vivo was
      also
      observed.  It is proposed that the increase in the modification rate of lambda-phage fully
      unmodified DNA is connected with the appearance of E. coli DNA methylase consisting of
      beta-
      and gamma-subunits.
AU  - Zinkevich VE
AU  - Alekseev AM
AU  - Tanyashin VI
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1986 20: 1638-1644.

PMID- 6269814
VI  - 259
DP  - 1981
TI  - Cloning and restriction analysis of the BamHI-EcoRI fragment of DNA, containing genes of the hsd region of Escherichia coli.
PG  - 216-218
AB  - 
AU  - Zinkevich VE
AU  - Solonin AS
AU  - Bogdarina IG
AU  - Tanyashin VI
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1981 259: 216-218.

PMID- 6210518
VI  - 263
DP  - 1982
TI  - Function of hsdS gene of E. coli K in recombinant plasmid containing the regulatory lambda phage region.
PG  - 717-721
AB  - None
AU  - Zinkevich VE
AU  - Solonin AS
AU  - Tanyashin VI
AU  - Bayev AA
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1982 263: 717-721.

PMID- 2116365
VI  - 90
DP  - 1990
TI  - A mutation that converts serine 340 of the HsdSK polypeptide to phenylalanine and its effects on restriction and modification in Escherichia coli K-12.
PG  - 125-128
AB  - A hybrid hsdS gene, encoding the HsdSts+d polypeptide, was constructed by joining the proximal
      region of the wild-type (wt) hsdS sequence with the distal region of the hsdSts+d sequence, at
      the hsdS BglII site. The hybrid hsdS-Sts+d gene exerts a trans-dominant effect on restriction
      and modification, which points to the location of the temperature-sensitive (ts)
      trans-dominant (+d) mutation in the gene hsdSts+d distal region. Sequencing of the region
      downstream from the HindIII target in the Escherichia coli K-12 hsdSts+d mutant was carried
      out. It is identical to the wt hsdS sequence (GenBank/EMBL accession number ECHSDK LV00288),
      except for a single base-pair transition C1245 -> T. The results obtained support the idea
      that the trans-dominant effect of the ts mutation described earlier is related to the single
      base-pair transition in the nonhomologous region of the hsdSts+d sequence.
AU  - Zinkevich VE
AU  - Weiserova M
AU  - Kryukov VM
AU  - Hubacek J
PT  - Journal Article
TA  - Gene
JT  - Gene
SO  - Gene 1990 90: 125-128.

PMID- 3896709
VI  - 282
DP  - 1985
TI  - Expression of the EcoK DNA-methylase genes cloned.
PG  - 993-995
AB  - The present article gives results on in vivo and in vitro expression of genes
      hsdSk and hsdMk, cloned in pBR322, and the possible involvement of the rho
      factor in this process.
AU  - Zinkevich VE
AU  - Zograf YN
AU  - Tanyashin VI
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1985 282: 993-995.

PMID- 6241139
VI  - 279
DP  - 1984
TI  - The genes of EcoK DNA methylase:  cloning and expression.
PG  - 1493-1496
AB  - None
AU  - Zinkevich VE
AU  - Zograf YN
AU  - Tanyashin VI
PT  - Journal Article
TA  - Dokl. Akad. Nauk.
JT  - Dokl. Akad. Nauk.
SO  - Dokl. Akad. Nauk. 1984 279: 1493-1496.

PMID- 3886160
VI  - 40
DP  - 1985
TI  - Nonreciprocal exchange between alleles of the yeast mitochondrial 21S rRNA gene:  kinetics and the involvement of a double-strand break.
PG  - 887-895
AB  - A 1.1 kb intron containing an open reading frame (ORF) in one allele (Omega+) of the yeast
      mitochondrial 21S rRNA gene is nearly quantitatively inserted in crosses into a 21S rRNA
      allele lacking that intron (Omega-). We have determined that this nonreciprocal exchange
      initiates soon after cells fuse to form zygotes and is complete by 10-16 hr after mating. We
      have discovered a unique in vivo double-strand cut in Omega- mitochondrial DNA (mtDNA) at or
      near the site of intron insertion that is implicated in the process. Markers flanking the
      intron insertion site are coconverted with frequencies inversely proportional to their
      distance from that site. There is no net conversion of Omega- to Omega+ in crosses between
      petites retaining these alleles, nor do we observe the unique double-strand cut in the mtDNA
      from zygotes of such crosses. The data suggest that a translation product of the intron ORF is
      required for the double-strand cut and nonreciprocal recombination at Omega.
AU  - Zinn AR
AU  - Butow RA
PT  - Journal Article
TA  - Cell
JT  - Cell
SO  - Cell 1985 40: 887-895.

PMID- 6323970
VI  - 18
DP  - 1984
TI  - Interaction of restrictase BamHI with synthetic substrates containing complete or partial recognition sites.
PG  - 169-175
AB  - The cleavage of self-complementary oligodeoxyribonucleotides by restrictase
      BamHI was studied.  Oligonucleotides containing the complete recognition
      sequence GGATCC were cleaved by restrictase BamHI in accordance with the
      established specificity of the enzyme.  The oligonucleotide TCCAGATCTGGA
      contains part of the recognition sequence (GATC) in the middle of the chain and
      separate halves of the sequence at each end.  Hydrolysis of this
      oligonucleotide yields products which indicate the interaction of restrictase
      BamHI with the composite recognition site GGA...TCC formed by the ends of two
      separate substrate molecules.  The oligonucleotide was not cleaved at the GATC
      sequence.  The results obtained support a symmetrical model for restrictase
      interaction with DNA.  According to this model, n/2 of the nucleotides in the
      recognition site bind to the enzyme.
AU  - Zinovev VV
AU  - Kolesnikov VA
AU  - Beznedelnaya NL
AU  - Gilev AF
AU  - Gorbunov YA
AU  - Popov SG
AU  - Malygin EG
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1984 18: 169-175.

PMID- 6271585
VI  - 132
DP  - 1981
TI  - Restriction endonuclease BamHI interaction with a synthetic duplex containing half-size recognition sequences.
PG  - 98-100
AB  - Restriction endonuclease BamHI is a site-specific deoxyribonuclease which
      cleaves the phosphodiester bonds between the guanine residues within the duplex
      DNA sequence 5'GGATCC   CCTAGG It is well known that restriction endonucleases
      recognise and cleave relatively short synthetic duplexes containing appropriate
      recognition sequence, therefore oligodeoxyribonucleotides called 'linkers' are
      widely used for genetic manipulations.  On the other hand, the synthetic
      oligonucleotides with defined sequences are useful tools to study mechanisms of
      interaction of the enzymes with DNA.
AU  - Zinovev VV
AU  - Kolesnikov VA
AU  - Beznedelnaya NL
AU  - Gorbunov JA
AU  - Popov SG
AU  - Malygin EG
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1981 132: 98-100.

PMID- 8992307
VI  - 30
DP  - 1996
TI  - Stoichiometry of phage T4 Dam DNA (Adenine-N6)-methyltransferase binding with oligonucleotide substrates.
PG  - 1203-1208
AB  - Phage T4 Dam DNA methyltransferase recognizes the GATC site and methylates the adenine.  The
      stoichiometry of its complex with the substrate was assessed by gel filtration and sucrose
      gradient ultracentrifugation.  The results obtained by both methods indicate that two enzyme
      subunits bind with 32- and 20-bp DNA duplexes.
AU  - Zinovev VV
AU  - Ovechkina LG
AU  - Malygin EG
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1996 30: 1203-1208.

PMID- Not carried by PubMed...
VI  - 5
DP  - 1989
TI  - The significance of internucleotide phosphates and noncomplementary substitutions in the oligonucleotide substrates on the interaction with the DNA methylase Ecodam.
PG  - 22-27
AB  - Eco dam methylase was investigated for its interaction with different synthetic
      oligonucleotide substrates containing some defects in the GATC sequence. The defects are as
      follows: the absence of one or several nucleotide residues, the presence of 3'-phosphate
      residue with CH3-S-group, noncomplementary substitution of A by G or of G by A in the
      recognition site of methylase Eco dam. The presence of the 3'S-methyl thiophosphate residue
      has no essential effect on the methylation of oligonucleotide complexes as compared to the
      analogous complexes lacking internucleotide phosphate. The introduction of the
      noncomplementary base pair in the recognition site results in the loss of substrate properties
      of such imperfect duplexes.
AU  - Zinovev VV
AU  - Rechkunova NI
AU  - Gorbunov YA
AU  - Buryanov YI
AU  - Malygin EG
PT  - Journal Article
TA  - Biopol. Kletka
JT  - Biopol. Kletka
SO  - Biopol. Kletka 1989 5: 22-27.

PMID- 9628341
VI  - 379
DP  - 1998
TI  - Phage T4 DNA [N6-adenine] methyltransferase: Kinetic studies using oligonucleotides containing native or modified recognition sites.
PG  - 481-488
AB  - The DNA-[N6-adenine] methyltransferase of T4 phage catalyzes methyl group transfer from
      S-adenosyl-L-methionine to the N6-position of adenine in the palindromic sequence, GATC.  We
      have investigated the effect of eliminating different structural components of the recognition
      site on the ability of a substrate to be bound and methylated by T4 Dam.  For this purpose,
      steady state binding (by gel shift assays) and kinetic parameters of methylation (using the
      methyl donor, [3H-CH3]-AdoMet, at 25 C) were studied using various synthetic duplex
      oligonucleotides containing some defect in the DNA-target site; e.g., the absence of an
      internucleotide phosphate or a nucleotide(s) within the recognition site, or a single stranded
      region.  The salient results are summarized as follows: (1) Addition of T4 Dam to a complete
      reaction mixture (with a 20-mer duplex as substrate) resulted in a 'burst' of 3H-methylated
      product, followed by a constant rate of product formation that reflected establishment of
      steady-state conditions.  This suggests that the rate-limiting step is release of product
      methylated DNA from the enzyme [and not the transfer of the methyl group].  (2) A number of
      the defects in duplex structure had only weak influence on the binding and Km values, but
      strongly reduced the kcat. At the same time, several poorly bound duplexes retained good
      substrate characteristics, especially duplexes having uninterrupted GAT-sequences in both
      strands.  Whereas having only one half of the recognition site element intact was sufficient
      for stable complex formation, the catalytic turnover process had a strict requirement for an
      uninterrupted GAT-sequence on both strands.  (3) There was no correlation between Km and
      binding capability; the apparent Kd for some duplexes was 5-70 times higher than Km.  This
      indicates that the T4 Dam methylation reaction cannot be explained by a simple Michaelian
      scheme.
AU  - Zinoviev VV
AU  - Evdokimov AA
AU  - Gorbunov YA
AU  - Malygin EG
AU  - Kossykh VG
AU  - Hattman S
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 1998 379: 481-488.

PMID- 
VI  - 38
DP  - 2004
TI  - Molecular enzymology of phage T4 Dam DNA methyltransferase.
PG  - 737-751
AB  - This review summarizes the results of a study of the molecular mechanisms of phage T4 DNA
      adenine methyltransferase (T4Dam) action.
      T4Dam [EC 2.1.1.72] catalyzes the transfer of a methyl group from
      S-adenosyl-L-methionine (AdoMet) to N-6 of the adenine located in the
      palindromic recognition site GATC. The subunit structure of T4Dam,
      substrate-binding properties, and kinetic parameters of methylation of
      a variety of native and modified oligonucleotide duplexes are
      considered. A kinetic scheme of the reaction was proposed, assuming
      that T4Dam is isomerized into a catalytically active form. The
      mechanisms of DNA-induced dimerization of T4Dam, flipping of the target
      base, reorientation of T4Dam on an asymmetrically methylated
      recognition site, the effector action of substrates, and processive
      methylation of extended DNA containing more than one specific site are
      discussed. The results obtained for T4Dam may provide a better
      understanding of the action mechanisms of other homologous enzymes
      including, first and foremost, those of the vast Dam family.
AU  - Zinoviev VV
AU  - Evdokimov AA
AU  - Hattman S
AU  - Malygin EG
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2004 38: 737-751.

PMID- 12624955
VI  - 37
DP  - 2003
TI  - DNA-[N4-Cytosine]-Methyltransferase from Bacillus amyloliquefaciens: Mechanism of Action Derived from Steady-State Kinetics.
PG  - 128-138
AB  - Kinetic analysis of methyl group transfer from S-adenosyl-L-methionine (SAM) to the 5'-GGATCC
      recognition site catalyzed by the
      DNA-[N4-cytosine]-methyltransferase from Bacillus amyloliquefaciens [EC
      2.1.1.113] has shown that the dependence of the rate of methylation of the
      20-meric substrate duplex on SAM and DNA concentration are normally
      hyperbolic, and the maximal rate is attained upon enzyme saturation with
      both substrates. No substrate inhibition is observed even at
      concentrations many times higher than the Km values (0.107 microM for DNA
      and 1.45 microM for SAM), which means that no nonreactive enzyme-substrate
      complexes are formed during the reaction. The overall pattern of product
      inhibition corresponds to an ordered steady-state mechanism following the
      sequence SAM decreases DNA decreases metDNA increases SAH increases
      (S-adenosyl-L-homocysteine). However, more detailed numerical analysis of
      the aggregate experimental data admits an alternative order of substrate
      binding, DNA decreases SAM decreases, though this route is an order of
      magnitude slower.
AU  - Zinoviev VV
AU  - Evdokimov AA
AU  - Malygin EG
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 2003 37: 128-138.

PMID- 12501249
VI  - 278
DP  - 2002
TI  - Bacteriophage T4 dam DNA-[N6-adenine] methyltransferase: Processivity and orientation to the methylation target.
PG  - 7829-7833
AB  - We carried out steady state and pre-steady state (burst) kinetic analyses of the bacteriophage
      T4 Dam DNA-[N(6)-adenine] methyltransferase (MTase) mediated methyl group transfer from
      S-adenosyl-L-methionine (AdoMet) to Ade in oligonucleotide duplexes containing one or two
      specific GATC sites with different combinations of methylated and unmodified targets. We
      compared the results for ligated 40-mer duplexes with those of mixtures of the two unligated
      duplexes used to generate the 40-mers. The salient results are as follows: (i) T4 Dam MTase
      modifies 40-mer duplexes in a processive fashion. (ii) During processive movement, T4 Dam
      rapidly exchanges product S-adenosyl-L-homocysteine (AdoHcy) for substrate AdoMet without
      dissociating from the DNA duplex. (iii) T4 Dam processivity is consistent with an ordered
      bi-bi mechanism AdoMet{downward arrow}DNA{downward arrow}DNA(Me){upward arrow}AdoHcy{upward
      arrow}. However, in contrast to the steady state, here DNA(Me){upward arrow} signifies
      departure from a methylated site GMTC{upward arrow}without physically dissociating from the
      DNA. (iv) Following methyl transfer at one site and linear diffusion to a hemi-methylated
      site, a reconstituted T4 Dam-AdoMet complex rapidly reorients itself to the (productive)
      unmethylated strand. T4 Dam-AdoHcy can not reorient at an enzymatically created GMTC site. (v)
      The inhibition potential of fully methylated sites 5'-GMTC/5'-GMTC is much lower for a long
      DNA molecule compared to short single-site duplexes.
AU  - Zinoviev VV
AU  - Evdokimov AA
AU  - Malygin EG
AU  - Schlagman SL
AU  - Hattman S
PT  - Journal Article
TA  - J. Biol. Chem.
JT  - J. Biol. Chem.
SO  - J. Biol. Chem. 2002 278: 7829-7833.

PMID- 17976013
VI  - 388
DP  - 2007
TI  - Differential methylation kinetics of individual target site strands by T4Dam DNA methyltransferase.
PG  - 1199-1207
AB  - Prokaryote DNA methyltransferases (MTases) of the Dam family (including those of
      bacteriophages T2 and T4) catalyze methyl group transfer from
      S-adenosyl-L-methionine (AdoMet), producing S-adenosyl-L-homocysteine
      (AdoHcy) and methylated adenine residues in palindromic GATC sequences.
      Dam DNA MTases, as all site-specific enzymes interacting with polymeric
      DNA, require a mechanism of action that ensures a rapid search for
      specific targets for catalytic action, during both the initial and
      subsequent rounds of methylation. The results of presteady-state
      (reaction burst) and steady-state methylation analyses of individual
      targets permitted us to monitor the action of T4Dam, which has three
      degrees of freedom: sliding, reorientation and adaptation to the
      canonical GATC sequence. The salient results are as follows: (i) 40mer
      substrate duplexes containing two canonical GATC sites showed
      differential methylation of the potential targets, i.e., T4Dam
      exhibited a preference for one site/target, which may present the
      better 'kinetic trap' for the enzyme. (ii) Prior hemimethylation of the
      two sites made both targets equally capable of being methylated during
      the pre-steady-state reaction. (iii) Although capable of moving in
      either direction along double-stranded DNA, there are some restrictions
      on T4Dam reorientation/adaptation on 40mer duplexes.
AU  - Zinoviev VV
AU  - Evdokimov AA
AU  - Malygin EG
AU  - Sclavi B
AU  - Buckle M
AU  - Hattman S
PT  - Journal Article
TA  - Biol. Chem.
JT  - Biol. Chem.
SO  - Biol. Chem. 2007 388: 1199-1207.

PMID- 6299803
VI  - 154
DP  - 1983
TI  - Structure subtraction as an approach to investigation of the mechanism of restriction enzyme action.
PG  - 282-284
AB  - Endonuclease BamHI cleaves the phosphodiester bonds between the guanine residues within the
      duplex DNA sequence G/GATCC.  The substrate characteristics of oligonucleotides, containing
      some defects in the sequence recognized by endonuclease (nick, absence of some internucleotide
      phosphate or nucleotide, partially single-stranded form of the recognition site) were
      investigated.  The results suggest that the specificity of synthetic oligonucleotide cleavage
      is strongly dependent on the ribosophosphate backbone intactness inside the recognition site.
      BamHI was found not to hydrolyse the phosphodiester bonds outside the double helix.  Also
      BamHI forms a productive complex with the non-symmetrical substrate, having half the
      recognition sites, of a single strand.
AU  - Zinoviev VV
AU  - Gorbunov JA
AU  - Baclanov MM
AU  - Popov SG
AU  - Malygin EG
PT  - Journal Article
TA  - FEBS Lett.
JT  - FEBS Lett.
SO  - FEBS Lett. 1983 154: 282-284.

PMID- 3900694
VI  - 19
DP  - 1985
TI  - Interaction of EcoDam methylase with single stranded sequences and synthetic oligonucleotides.
PG  - 947-954
AB  - Interaction of the Ecodam methylase with different substrates was investigated among them
      double- and single-stranded DNAs and synthetic oligonucleotides containing some defects in the
      GATC sequence.  These defects were: nick, the absence of one internucleotide phosphate of
      nucleotide; partially single-stranded form of the recognition site etc.  It was demonstrated
      that the presence of both G.A-dinucleotides in the recognition site is necessary for
      productive enzyme-substrate interaction.  The absence of T and/or C residues is less dramatic
      for methylase activity.  The Ecodam methylase is able to modify single-stranded
      oligonucleotides by forming the double-stranded structure in the symmetric recognition
      sequences GATC.
AU  - Zinoviev VV
AU  - Gorbunov YA
AU  - Popov SG
AU  - Malygin EG
AU  - Buryanov JI
AU  - Nesterenko VF
AU  - Baev AA
AU  - Venoginskis MT
PT  - Journal Article
TA  - Mol. Biol. (Mosk)
JT  - Mol. Biol. (Mosk)
SO  - Mol. Biol. (Mosk) 1985 19: 947-954.

PMID- 15280508
VI  - 32
DP  - 2004
TI  - Symmetry elements in DNA structure important for recognition/methylation by DNA [amino]-methyltransferases.
PG  - 3930-3934
AB  - The phage T4Dam and EcoDam DNA-[adenine-N6] methyltransferases (MTases) methylate GATC
      palindromic sequences, while the BamHI DNA-[cytosine-N4] MTase methylates the GGATCC
      palindrome (which contains GATC) at the internal cytosine residue. We compared the ability of
      these enzymes to interact productively with defective duplexes in which individual elements
      were deleted on one chain. A sharp decrease in kcat was observed for all three enzymes if a
      particular element of structural symmetry was disrupted. For the BamHI MTase, integrity of the
      ATCC was critical, while an intact GAT sequence was necessary for the activity of T4Dam, and
      an intact GA was necessary for EcoDam. Theoretical alignment of the region of best contacts
      between the protein and DNA showed that in the case of a palindromic interaction site, a zone
      covering the 5'-symmetric residues is located in the major groove versus a zone of contact
      covering the 3'-symmetric residues in the minor groove. Our data fit a simple rule of thumb
      that the most important contacts are aligned around the methylation target base: if the target
      base is in the 5' half of the palindrome, the interaction between the enzyme and the DNA
      occurs mainly in the major groove; if it is in the 3' half, the interaction occurs mainly in
      the minor groove.
AU  - Zinoviev VV
AU  - Yakishchik SI
AU  - Evdokimov AA
AU  - Malygin EG
AU  - Hattman S
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2004 32: 3930-3934.

PMID- 22965105
VI  - 194
DP  - 2012
TI  - Complete Genome Sequence of the Porcine Isolate Enterococcus faecalis D32.
PG  - 5490-5491
AB  - The complete and annotated genome sequence of Enterococcus faecalis D32, a commensal strain
      isolated from a Danish pig, suggests putative adaptation to the
      porcine host and absence of distinct virulence-associated traits.
AU  - Zischka M
AU  - Kuenne C
AU  - Blom J
AU  - Dabrowski PW
AU  - Linke B
AU  - Hain T
AU  - Nitsche A
AU  - Goesmann A
AU  - Larsen J
AU  - Jensen LB
AU  - Witte W
AU  - Werner G
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 5490-5491.

PMID- 19558674
VI  - 10
DP  - 2009
TI  - Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea.
PG  - R70
AB  - ABSTRACT: BACKGROUND: Thermococcus gammatolerans was isolated from samples collected from
      hydrothermal chimneys. It is one of the most radioresistant
      organisms known amongst the Archaea. We report the determination and
      annotation of its complete genome sequence, its comparison with other
      Thermococcales genomes, and a proteomic analysis. RESULTS: T.
      gammatolerans has a circular chromosome of 2.045 Mbp without any
      extra-chromosomal elements, coding for 2,157 proteins. A thorough
      comparative genomics analysis revealed important but unsuspected genome
      plasticity differences between sequenced Thermococcus and Pyrococcus
      species which could not be attributed to the presence of specific mobile
      elements. Two virus-related regions tgv1 and tgv2 are the only mobile
      elements identified in this genome. A proteogenome analysis was performed
      by a shotgun LC-MS/MS approach allowing the identification of 10,931
      unique peptides corresponding to 951 proteins. This information
      concurrently validates the accuracy of the genome annotation.
      Semi-quantitation of proteins by spectral count was done on exponential-
      and stationary-phase cells. Insights into general catabolism, hydrogenase
      complexes, detoxification systems, and the DNA repair toolbox of this
      archaeon are revealed through this genome and proteome analysis.
      CONCLUSIONS: This work is the first archaeal proteome investigation done
      at the stage of primary genome annotation. This archaeon is shown to use a
      large variety of metabolic pathways even under a rich medium growth
      condition. This proteogenomic study also indicates that the high
      radiotolerance of T. gammatolerans is probably due to proteins that remain
      to be characterized rather than a larger arsenal of known DNA repair
      enzymes.
AU  - Zivanovic Y
AU  - Armengaud J
AU  - Lagorce A
AU  - Leplat C
AU  - Guerin P
AU  - Dutertre M
AU  - Anthouard V
AU  - Forterre P
AU  - Wincker P
AU  - Confalonieri F
PT  - Journal Article
TA  - Genome Biol.
JT  - Genome Biol.
SO  - Genome Biol. 2009 10: R70.

PMID- 23449808
VI  - 7
DP  - 2012
TI  - Complete genome sequence of Treponema pallidum strain DAL-1.
PG  - 12-21
AB  - strain DAL-1 is a human uncultivable pathogen causing the sexually transmitted disease
      syphilis. Strain DAL-1 was isolated from the amniotic fluid of a pregnant
      woman in the secondary stage of syphilis. Here we describe the 1,139,971 bp long
      genome of strain DAL-1 which was sequenced using two independent sequencing
      methods (454 pyrosequencing and Illumina). In rabbits, strain DAL-1 replicated
      better than the strain Nichols. The comparison of the complete DAL-1 genome
      sequence with the Nichols sequence revealed a list of genetic differences that
      are potentially responsible for the increased rabbit virulence of the DAL-1
      strain.
AU  - Zobanikova M
AU  - Mikolka P
AU  - Cejkova D
AU  - Pospisilova P
AU  - Chen L
AU  - Strouhal M
AU  - Qin X
AU  - Weinstock GM
AU  - Smajs D
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2012 7: 12-21.

PMID- 
VI  - 7
DP  - 2013
TI  - Whole genome sequence of the Treponema pallidum Fribourg-Blanc: Unspecified simian isolate is highly similar to the yaws subspecies.
PG  - E2172
AB  - Background: Unclassified simian strain Treponema Fribourg-Blanc was isolated in 1966 from
      baboons (Papio cynocephalus)in West Africa. This strain was morphologically indistinguishable
      from T. pallidum ssp. pallidum or ssp. pertenue strains, and it was shown to cause human
      infections.
      Methodology/Principal Findings: To precisely define genetic differences between Treponema
      Fribourg-Blanc (unclassified simian isolate, FB) and T. pallidum ssp. pertenue strains (TPE),
      a high quality sequence of the whole Fribourg-Blanc genome was determined with
      454-pyrosequencing and Illumina sequencing platforms. Combined average coverage of both
      methods was greater than 5006. Restriction target sites (n = 1,773), identified in silico, of
      selected restriction enzymes within the Fribourg-Blanc genome were verified experimentally and
      no discrepancies were found. When compared to the other
      three sequenced TPE genomes (Samoa D, CDC-2, Gauthier), no major genome rearrangements were
      found. The Fribourg-
      Blanc genome clustered with other TPE strains (especially with the TPE CDC-2 strain), while T.
      pallidum ssp. pallidum strains clustered separately as well as the genome of T.
      paraluiscuniculi strain Cuniculi A. Within coding regions, 6 deletions, 5 insertions and 117
      substitutions differentiated Fribourg-Blanc from other TPE genomes.  Conclusions/Significance:
      The Fribourg-Blanc genome showed similar genetic characteristics as other TPE strains.
      Therefore, we propose to rename the unclassified simian isolate to Treponema pallidum ssp.
      pertenue strain Fribourg-Blanc. Since the Fribourg-Blanc strain was shown to cause
      experimental infection in human hosts, non-human primates could serve as possible reservoirs
      of TPE strains. This could considerably complicate recent efforts to eradicate yaws. Genetic
      differences specific for Fribourg-Blanc could then contribute for identification of cases of
      animal-derived yaws infections.
AU  - Zobanikova M
AU  - Strouhal M
AU  - Mikalova L
AU  - Cejkova D
AU  - Ambrozova L
AU  - Pospisilova P
AU  - Fulton LL
AU  - Chen L
AU  - Sodergren E
AU  - Weinstock GM
AU  - Smajs D
PT  - Journal Article
TA  - PLoS Neglected Trop. Dis.
JT  - PLoS Neglected Trop. Dis.
SO  - PLoS Neglected Trop. Dis. 2013 7: E2172.

PMID- 23209224
VI  - 194
DP  - 2012
TI  - Genome Sequence of Moraxella catarrhalis RH4, an Isolate of Seroresistant Lineage.
PG  - 6969
AB  - Here we report the annotated genome sequence of Moraxella catarrhalis strain RH4, a
      seroresistant-lineage strain isolated from the blood of an infected patient.
      This genome sequence will allow us to gain further insight into the genetic
      diversity of clinical M. catarrhalis isolates and will facilitate study of M.
      catarrhalis pathogenesis.
AU  - Zomer A
AU  - de Vries SP
AU  - Riesbeck K
AU  - Meinke AL
AU  - Hermans PW
AU  - Bootsma HJ
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 6969.

PMID- 28522727
VI  - 5
DP  - 2017
TI  - Draft Genome Sequence of the Tacrolimus-Producing Bacterium Streptomyces tsukubaensis F601.
PG  - e00385-17
AB  - Streptomyces tsukubaensis strain F601 was found to be a producer of the immunosuppressive drug
      tacrolimus. The draft genome sequence of this strain was
      approximately 8.52 Mbp. Genes involved in the biosynthesis of tacrolimus were
      identified in the genome. This draft genome sequence will provide insights into
      the genetic basis of tacrolimus biosynthesis and regulation.
AU  - Zong G
AU  - Zhong C
AU  - Fu J
AU  - Qin R
AU  - Cao G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00385-17.

PMID- 29301883
VI  - 6
DP  - 2018
TI  - Complete Genome Sequence of the High-Natamycin-Producing Strain Streptomyces gilvosporeus F607.
PG  - e01402-17
AB  - Streptomyces gilvosporeus strain F607 is a producer of high levels of natamycin used in the
      fermentation industry. In this study, the complete genome sequence of
      strain F607 was determined. This genome sequence provides a basis for
      understanding natamycin biosynthesis and regulation in a high-natamycin-producing
      strain and will aid in the development of useful strategies for improving
      industrial strains.
AU  - Zong G
AU  - Zhong C
AU  - Fu J
AU  - Zhao Z
AU  - Cao G
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2018 6: e01402-17.

PMID- 21103346
VI  - 5
DP  - 2010
TI  - Characterization of a New SCCmec Element in Staphylococcus cohnii.
PG  - E14016
AB  - BACKGROUND: Many SCCmec elements of coagulase-negative staphylococci
      (CoNS) could not be typed using multiplex PCR. Such a 'non-typable' SCCmec
      was encountered in a Staphylococcus cohnii isolate. METHODOLOGY/PRINCIPAL
      FINDINGS: The SCCmec type of methicillin-resistant S. cohnii clinical
      isolate WC28 could not be assigned using multiplex PCR. Newly-designed
      primers were used to amplify ccrA and ccrB genes. The whole SCCmec was
      obtained by three overlapping long-range PCR, targeting regions from
      left-hand inverted repeat (IRL) to ccrA/B, from ccrA/B to mecA and from
      mecA to orfX. The region abutting IRL was identified using inverse PCR
      with self-ligated enzyme-restricted WC28 fragments as the template. WC28
      SCCmec had a class A mec gene complex (mecI-mecR1-mecA). The ccrA and ccrB
      genes were closest (89.7% identity) to ccrA(SHP) of Staphylococcus
      haemolyticus strain H9 and to ccrB3 (90% identity) of Staphylococcus
      pseudintermedius strain KM241, respectively. Two new genes potentially
      encoding AAA-type ATPase were found in J1 region and a psiTn554 transposon
      was present in J2 region, while J3 region was the same as many SCCmec of
      Staphylococcus aureus. WC28 SCCmec abutted an incomplete SCC element with
      a novel allotype of ccrC, which was closest (82% identity) to ccrC1 allele
      9 in Staphylococcus saprophyticus strain ATCC 15305. Only two direct
      target repeat sequences, one close to the 3'-end of orfX and the other
      abutting the left end of WC28 SCCmec, could be detected.
      CONCLUSIONS/SIGNIFICANCE: A new 35-kb SCCmec was characterized in a S.
      cohnii isolate, carrying a class A mec gene complex, new variants of ccrA5
      and ccrB3 and two novel genes in the J1 region. This element is flanked by
      8-bp perfect inverted repeats and is similar to type III SCCmec in S.
      aureus and a SCCmec in S. pseudintermedius but with different J1 and J3
      regions. WC28 SCCmec was arranged in tandem with an additional SCC element
      with ccrC, SCC(WC28), but the two elements might have integrated
      independently rather than constituted a composite. This study adds new
      evidence of the diversity of SCCmec in CoNS and highlights the need for
      characterizing the 'non-typable' SCCmec to reveal the gene pool associated
      with mecA.
AU  - Zong Z
AU  - Lu X
PT  - Journal Article
TA  - PLoS ONE
JT  - PLoS ONE
SO  - PLoS ONE 2010 5: E14016.

PMID- 22461543
VI  - 194
DP  - 2012
TI  - Genome Sequence of the Human- and Animal-Pathogenic Strain Nocardia cyriacigeorgica GUH-2.
PG  - 2098-2099
AB  - The pathogenic strain Nocardia cyriacigeorgica GUH-2 was isolated from a fatal human
      nocardiosis case, and its genome was sequenced. The complete genomic
      sequence of this strain contains 6,194,645 bp, an average G+C content of 68.37%,
      and no plasmids. We also identified several protein-coding genes to which N.
      cyriacigeorgica's virulence can potentially be attributed.
AU  - Zoropogui A et al
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 2098-2099.

PMID- 26659669
VI  - 3
DP  - 2015
TI  - Genome Sequence of the Mosquitocidal Bacillus thuringiensis Strain BR58, a Biopesticide Product Effective against the Coffee Berry Borer (Hypothenemus  hampei).
PG  - e01232-15
AB  - Bacillus thuringiensis is an important microbial control agent against insect pests. The draft
      genome sequence of the Brazilian strain BR58 described here
      contains the insecticidal genes cry4A, cry4B, cry10A, cry11A, cry60A, cry60B, and
      cyt1A, which show toxicity to both Aedes aegypti and Hypothenemus hampei larvae.
AU  - Zorzetti J
AU  - Ricietto AP
AU  - da Silva CR
AU  - Wolf IR
AU  - Vilas-Boas GT
AU  - Neves PM
AU  - Meneguim AM
AU  - Vilas-Boas LA
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01232-15.

PMID- 7642510
VI  - 177
DP  - 1995
TI  - Identification of a methyl-specific restriction system mediated by a conjugative element from Streptomyces bambergiensis.
PG  - 4809-4812
AB  - pBL2 was identified genetically but not physically in Streptomyces lividans after its mating
      with S. bambergiensis.  During conjugation, pBL2 was transferred at high frequency to S.
      lividans and S. coelicolor, pBL2.1 DNA isolated from S. coelicolor exconjugants as a circular
      plasmid was shown to derive from the genome of S. bambergiensis.  S. lividans carrying pBL2 or
      pBL2.1 acquired a methyl-specific restriction (MsrA+) phenotype.  The corresponding enzyme
      was partially purified and shown to resemble a class II endonuclease which cleaves
      Dam-methylated DNA preferentially.
AU  - Zotchev SB
AU  - Schrempf H
AU  - Hutchinson CR
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 1995 177: 4809-4812.

PMID- 27151805
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of the Respiration-Competent Strain Lactobacillus casei N87.
PG  - e00348-16
AB  - Lactobacillus casei is used as a starter, adjunct, and/or probiotic culture in the production
      of fermented and functional foods. Here, we report the draft
      genome sequence of the respiration-competent strain L. casei N87, isolated from
      infant feces. This genome information may be useful for the study of respiratory
      metabolism in lactic acid bacteria.
AU  - Zotta T
AU  - Ricciardi A
AU  - Parente E
AU  - Reale A
AU  - Ianniello RG
AU  - Bassi D
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00348-16.

PMID- 27081126
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Ralstonia solanacearum Strain Rs-T02, Which Represents the Most Prevalent Phylotype in Guangxi, China.
PG  - e00241-16
AB  - Ralstonia solanacearumstrain Rs-T02 was originally isolated from a bacterial wilt of tomato
      plant in Nanning City of Guangxi Province, China. It represents the
      most prevalent phylotype in Guangxi. Here, we present the draft genome sequence
      of this strain, which comprises 5,225 genes and 5,976,011 nucleotides with an
      average G+C content of 66.79%. There are 968 different genes between this isolate
      and the previously reported genome sequence ofRalstonia solanacearumGMl l000
      (race l, biovar 3, phylotype I), and the genome sequence information of this
      isolate may be useful for comparative genomic studies to determine the genetic
      diversity in this species.
AU  - Zou C
AU  - Wang K
AU  - Meng J
AU  - Yuan G
AU  - Lin W
AU  - Peng H
AU  - Li Q
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00241-16.

PMID- Not carried by PubMed...
VI  - 7
DP  - 1987
TI  - Methods for preparation and determination of the purity and activity of restriction endonucleases.
PG  - 63-66
AB  - The main source of DNA restriction endonucleases (restriction enzymes) is from
      bacteria.  They are widespread, and have many varieties.  The first restriction
      enzyme was discovered in 1968, since then close to 500 of them have been
      discovered, and most of them are type II restriction enzymes.  Type II
      restriction enzymes are very important, they have been called the surgeon's
      knife for molecular biology; they have served as an ideal model to study the
      interaction between protein and DNA.  This article describes the general
      methods for preparation and determination of reactivities of type II
      restriction endonucleases.
AU  - Zou G
PT  - Journal Article
TA  - Weishengwuxue Zazhi
JT  - Weishengwuxue Zazhi
SO  - Weishengwuxue Zazhi 1987 7: 63-66.

PMID- Not included in PubMed...
VI  - 62
DP  - 1985
TI  - One step purification of restriction endonuclease PstI by sepharose affinity column separation.
PG  - 64-66
AB  - None
AU  - Zou G
AU  - Cao X
AU  - Zhu R
PT  - Journal Article
TA  - Shengwu Huaxue Yu Shengwu Wuli Jinzhan
JT  - Shengwu Huaxue Yu Shengwu Wuli Jinzhan
SO  - Shengwu Huaxue Yu Shengwu Wuli Jinzhan 1985 62: 64-66.

PMID- 
VI  - 6
DP  - 2001
TI  - Kinetic studies on the irreversible inhibition of restriction endonuclease PstI by site-specific inhibitors.
PG  - 859-863
AB  - The irreversible modifying effects on PstI of several inhibitors have been studied with the
      irreversible inhibition kinetic theory of single substrate reaction provided by Tsou, C.L.
      Pyridoxal phosphate (PLP), p-chloromercuribenzoic acid (PCMB), diisopropyl fluorophosphates
      (DFP), 2,3-diacetyl (DAC) and N-ethyl-5-phenylisoxazolium-3' sulfonate (Woodward's reagent
      K, WRK), modify the lysine, cysteine, serine, arginine and carboxyl groups of the protein
      molecule respectively.  These five inhibitors have been found to inhibit both the prime
      activity and star activity of PstI.  Used with the irreversible inhibition theory, the
      apparent inhibition rate constant, A, and the microcosmic inhibition rate constants, k+o and
      k'+o of every inhibitor were calculated.  We also found that their inhibition effects belong
      to the noncompetitive irreversible inhibition.  Results show that among the groups to be
      modified, some have nothing to do with the combination with the substrate, and some may have,
      but none of them is the only factor involved in the specific binding.  Despite all this, they
      may take part in the catalysis of enzyme or have important effects on maintaining the active
      structure of enzyme molecules.  Furthermore, serine and arginine residues are related to the
      alteration of PstI conformation and then influence the ability of PstI recognizing the
      incising DNA specifically.
AU  - Zou G
AU  - Gao C
AU  - Pi X
PT  - Journal Article
TA  - Wuhan Univ. J. Natural Sciences
JT  - Wuhan Univ. J. Natural Sciences
SO  - Wuhan Univ. J. Natural Sciences 2001 6: 859-863.

PMID- Not carried by PubMed...
VI  - 17
DP  - 1985
TI  - The purification and some properties of restriction endonuclease PstI.
PG  - 268-274
AB  - Restriction endonuclease PstI has been isolated and purified by chromatography
      on heparin-Sepharose, DEAE-cellulose, phosphocellulose, Cibacron Blue
      F3GA-Sepharose and hydroxylapatite.  The purified enzyme was found to be
      homogeneous as judged by polyacrylamide gel disc electrophoresis.  The specific
      activity of the enzyme is greater than 57,000 units per mg protein.  The enzyme
      has a molecular weight of about 54,000 daltons by Sephadex G-100 gel
      filtration, that of the enzyme subunit is about 17,500 daltons as assayed by
      sodium dodecyl sulphate-polyacrylamide gel electrophoresis.  On electrophoresis
      the subunit migrated as a single band.  The result shows that restriction
      endonuclease PstI consists of two similar subunits.  The N-terminal amino acid
      of the enzyme is proline as assayed by dansyl chloride.  Other properties of
      restriction endonuclease PstI were also given preliminary study.
AU  - Zou G-L
AU  - Cao X-W
AU  - Zhu R-F
PT  - Journal Article
TA  - Acta Biochim. Biophys. Sin.
JT  - Acta Biochim. Biophys. Sin.
SO  - Acta Biochim. Biophys. Sin. 1985 17: 268-274.

PMID- 
VI  - 45
DP  - 1999
TI  - Studies on the star activity of restriction endonuclease PstI.
PG  - 873-875
AB  - The influence of factors such as temperature, enzyme concentration, reaction time and several
      organic solvents on the star activity of PstI has been studied.  Under the reaction condition
      beneficial for the star activity, the Km and Vmax of the star activity and prime activity
      respectively are 1.46 x 10^-7 mol/L, 1.02 x 10^-8 mol/L and 2.86 x 10^-16 mol/s, 3.06 x 10^-15
      mol/s.
AU  - Zou G-L
AU  - Gao C-Z
AU  - Pi X-C
AU  - Hu WJ
PT  - Journal Article
TA  - Wuhan Daxue Xuebao
JT  - Wuhan Daxue Xuebao
SO  - Wuhan Daxue Xuebao 1999 45: 873-875.

PMID- 
VI  - 5
DP  - 2000
TI  - Alteration of the specificity of PstI restriction endonuclease.
PG  - 361-365
AB  - The influence of factors on the substrate-specificity of PstI restriction endonuclease has
      been studied with the method of electrophoresis.  The results show that, the specificity of
      PstI almost cannot be influenced by the single alteration of the concentration of Tris.HCl,
      Mg2+ or Na+ in the reaction system, but it can be altered by the reduction of any two of them.
      The specificity cannot be altered by the single alteration of pH or the replacement of Mg2+
      with Mn2+.  The addition of glycerol or dimethylsulphoxide (DM-SO) to the reaction system
      results in the relaxation of the substrate-specificity of PstI, but dimethyl-methylformide,
      glycol and ethyl alcohol cannot bring about the alteration of PstI specificity.  Through the
      method of cloning and sequencing, the nucleotides of No. 1 and 6 in the recognition sequence
      of PstI have changed (1C-A or 6G-T).  Used with the enzyme analysis of an artificially
      synthetic DNA segment containing a special sequence, the nucleotides of No. 1 and 6 have both
      changed (1C-A and 6G-T).  The recognition sequence of PstI is speculated to be changed from
      CTGCA/G to TGCA/.
AU  - Zou G-l
AU  - Gao C-Z
AU  - Pi X-C
AU  - Zhang J-J
PT  - Journal Article
TA  - Wuhan Univ. J. Nat. Sci.
JT  - Wuhan Univ. J. Nat. Sci.
SO  - Wuhan Univ. J. Nat. Sci. 2000 5: 361-365.

PMID- 
VI  - 5
DP  - 2011
TI  - Comparison of the electro transformation of plasmids and plasmid stability between Zymomonas mobilis ZM4 and CP4.
PG  - 2026-2033
AB  - Four different plasmids were electro transformed into Zymomonas mobilis ZM4 and CP4, two
      important ethanol-producing strains. The results
      showed that the best source strain for preparing plasmids was the
      transformed host strain itself, and Escherichia coli JM110 as the
      source strain could yield significantly higher transformation
      efficiencies than Top10. The optimal recovery time of transformed ZM4
      or CP4 cells to obtain maximum number of transformants and highest
      transformation efficiency was 11 h for pZB21-mini, pZB21 and pZA22, but
      24 or 20 h for pBBR1MCS-2. The optimal electric field strength for
      pZB21-mini was 13.25 kV /cm in ZM4 and 14.0 kV /cm in CP4. But for
      pZA22 and pBBR1MCS-2, it was 11.75 kV /cm in ZM4 and 12.5 kV /cm in
      CP4; for pZB21, also 12.5 kV /cm in CP4. These plasmids were shown to
      be more stable in ZM4 than in CP4 by serial transfer to antibiotic-free
      medium and the 3 plasmids were more stable than pBBR1MCS-2. The results
      will help to support the genetic and biotechnological research of Z.
      mobilis by providing information about some of the most important
      factors that influence the transformation of ZM4 and CP4, and also
      providing insights into the similarities and differences in their
      restriction-modification (R-M) systems.
AU  - Zou S
AU  - Zhang M
AU  - Hong J
AU  - Ma Y
AU  - Zhang W
PT  - Journal Article
TA  - Afr. J. Microbiol. Res.
JT  - Afr. J. Microbiol. Res.
SO  - Afr. J. Microbiol. Res. 2011 5: 2026-2033.

PMID- 25745009
VI  - 3
DP  - 2015
TI  - Complete Sequence of Probiotic Symbioflor 2 Escherichia coli Strain G3/10 and Draft Sequences of Symbioflor 2 E. coli Strains G1/2, G4/9, G5, G6/7, and G8.
PG  - e01330-14
AB  - The complete genome of probiotic Escherichia coli strain G3/10 is presented here. In addition,
      the probiotic E. coli strains G1/2, G4/9, G5, G6/7, and G8 are
      presented in draft form. These six strains together comprise the probiotic
      product Symbioflor 2 (DSM 17252).
AU  - Zschuttig A
AU  - Auerbach C
AU  - Meltke S
AU  - Eichhorn C
AU  - Brandt M
AU  - Blom J
AU  - Goesmann A
AU  - Jarek M
AU  - Scharfe M
AU  - Zimmermann K
AU  - Wassenaar TM
AU  - Gunzer F
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2015 3: e01330-14.

PMID- 23846269
VI  - 1
DP  - 2013
TI  - Genome Sequence of Streptococcus agalactiae Strain 09mas018883, Isolated from a Swedish Cow.
PG  - e00456-13
AB  - We announce the complete genome sequence of Streptococcus agalactiae strain 09mas018883,
      isolated from the milk of a cow with clinical mastitis. The
      availability of this genome may allow identification of candidate genes, leading
      to discovery of antigens that might form the basis for development of a vaccine
      as an alternative means of mastitis control.
AU  - Zubair S
AU  - de Villiers EP
AU  - Fuxelius HH
AU  - Andersson G
AU  - Johansson KE
AU  - Bishop RP
AU  - Bongcam-Rudloff E
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00456-13.

PMID- 23868134
VI  - 1
DP  - 2013
TI  - Genome Sequences of Two Pathogenic Streptococcus agalactiae Isolates from the One-Humped Camel Camelus dromedarius.
PG  - e00515-13
AB  - Streptococcus agalactiae causes a range of clinical syndromes in camels (Camelus
      dromedarius). We report the genome sequences of two S. agalactiae isolates that
      induce abscesses in Kenyan camels. These genomes provide novel data on the
      composition of the S. agalactiae 'pan genome' and reveal the presence of multiple
      genomic islands.
AU  - Zubair S
AU  - de Villiers EP
AU  - Younan M
AU  - Andersson G
AU  - Tettelin H
AU  - Riley DR
AU  - Jores J
AU  - Bongcam-Rudloff E
AU  - Bishop RP
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00515-13.

PMID- 26594310
VI  - 10
DP  - 2015
TI  - Complete genome sequence of Staphylococcus aureus, strain ILRI_Eymole1/1, isolated from a Kenyan dromedary camel.
PG  - 109
AB  - We report the genome of a Staphylococcus aureus strain (ILRI_Eymole1/1) isolated  from a nasal
      swab of a dromedary camel (Camelus dromedarius) in North Kenya. The
      complete genome sequence of this strain consists of a circular chromosome of
      2,874,302 bp with a GC-content of 32.88 %. In silico annotation predicted 2755
      protein-encoding genes and 76 non-coding genes. This isolate belongs to MLST
      sequence type 30 (ST30). Phylogenetic analysis based on a subset of 283 core
      genes revealed that it falls within the human clonal complex 30 (CC30) S. aureus
      isolate cluster but is genetically distinct. About 79 % of the protein encoding
      genes are part of the CC30 core genome (genes common to all CC30 S. aureus
      isolates), ~18 % were within the variable genome (shared among multiple but not
      all isolates) and ~ 3 % were found only in the genome of the camel isolate. Among
      the 85 isolate-specific genes, 79 were located within putative phages and
      pathogenicity islands. Protein encoding genes associated with bacterial adhesion,
      and secretory proteins that are essential components of the type VII secretion
      system were also identified. The complete genome sequence of S. aureus strain
      ILRI_Eymole1/1 has been deposited in the European Nucleotide Archive under the
      accession no LN626917.1.
AU  - Zubair S
AU  - Fischer A
AU  - Liljander A
AU  - Meens J
AU  - Hegerman J
AU  - Gourle H
AU  - Bishop RP
AU  - Roebbelen I
AU  - Younan M
AU  - Mustafa MI
AU  - Mushtaq M
AU  - Bongcam-Rudloff E
AU  - Jores J
PT  - Journal Article
TA  - Standards in Genomic Sciences
JT  - Standards in Genomic Sciences
SO  - Standards in Genomic Sciences 2015 10: 109.

PMID- 8017119
VI  - 2
DP  - 1994
TI  - New collection of phages for typing methicillin-resistant Staphylococcus aureus.
PG  - 20-23
AB  - A new collection of phages for typing methicillin-resistant S. aureus is proposed.  The
      collection includes phage 85 (modified by the MRSA strain), capable of selecting stains with
      the similar specificity of the restriction-modification system, and 9 MRSA-induced phages.
      The latter differentiate MRSA strains according to the specificity of prophages present in
      bacterial cells.  The use of this phage collection has permitted the typing of MRSA strains
      insensitive to the phages of the international collection.  Among these cultures on epidemic
      strain has been detected and the source of its spread in the burn center has been established.
AU  - Zueva VS
AU  - Dmitrenko OA
AU  - Gladkova KK
AU  - Zueva EA
PT  - Journal Article
TA  - Zh. Mikrobiol. Epidemiol. Immunobiol.
JT  - Zh. Mikrobiol. Epidemiol. Immunobiol.
SO  - Zh. Mikrobiol. Epidemiol. Immunobiol. 1994 2: 20-23.

PMID- 2150141
VI  - 10
DP  - 1990
TI  - To the mechanism of the resistance of methicillin-resistant staphylococcus aureus to phages of the international collection.
PG  - 11-15
AB  - The resistance of methicillin-resistant staphylococci to phage 85 is due to the
      presence of a certain system restriction modification in microbial cells.  The
      loss of the capacity for restricting phage DNA by the cell as the consequence
      of the loss of the mec determinant is not accompanied by the loss of its
      capacity for modifying phage DNA.
AU  - Zueva VS
AU  - Dmitrienko OA
AU  - Krupina EA
AU  - Belikov NG
AU  - Nesterenko LN
PT  - Journal Article
TA  - Zh. Mikrobiol. Epidemiol. Immunobiol.
JT  - Zh. Mikrobiol. Epidemiol. Immunobiol.
SO  - Zh. Mikrobiol. Epidemiol. Immunobiol. 1990 10: 11-15.

PMID- 26847906
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Lactococcus lactis subsp. lactis bv. diacetylactis CRL264, a Citrate-Fermenting Strain.
PG  - e01575-15
AB  - We report the draft genome sequence of Lactococcus lactis subsp. lactis bv. diacetylactis
      CRL264, a natural strain isolated from artisanal cheese from
      northwest Argentina. L. lactis subsp. lactis bv. diacetylactis is one of the most
      important microorganisms used as starter culture around the world. The CRL264
      strain constitutes a model microorganism in the studies on the generation of
      aroma compounds (diacetyl, acetoin, and 2,3-butanediol) by lactic acid bacteria.
      Our genome analysis shows similar genetic organization to other available genomes
      of L. lactis bv. diacetylactis strains.
AU  - Zuljan F
AU  - Espariz M
AU  - Blancato VS
AU  - Esteban L
AU  - Alarcon S
AU  - Magni C
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01575-15.

PMID- 23950113
VI  - 1
DP  - 2013
TI  - Draft Genome Sequence of Klebsiella pneumoniae Isolate PR04.
PG  - e00418-13
AB  - Klebsiella pneumoniae PR04 was isolated from a patient hospitalized in Malaysia.  The draft
      genome sequence of K. pneumoniae PR04 shows differences compared to the
      reference sequences of K. pneumoniae strains MGH 78578 and NTUH-K2044 in terms of
      their genomic structures.
AU  - Zulkifli MH
AU  - Teh LK
AU  - Lee LS
AU  - Zakaria ZA
AU  - Salleh MZ
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2013 1: e00418-13.

PMID- 27979955
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Streptococcus anginosus BVI, a New Vaginal Pathogen Candidate.
PG  - e01417-16
AB  - Streptococcus anginosus is a pathogen implicated in urogenital and gastroinstestinal tract
      infections. Here, we report the draft genome sequence of
      S. anginosus BVI, isolated from a bacterial vaginosis patient attending a
      prenatal care unit in Cali, Colombia. The genome sequence of BVI consists of
      2,014,025 bp, encoding 2,008 predicted proteins.
AU  - Zuniga-Bahamon A
AU  - Tobar-Tosse F
AU  - Guillermo-Ortega J
AU  - Wibberg D
AU  - Tauch A
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e01417-16.

PMID- 23090644
VI  - 66
DP  - 2013
TI  - Characterization of Plasmid pML21 of Enterococcus faecalis ML21 from Koumiss.
PG  - 103-105
AB  - 
AU  - Zuo F
AU  - Feng X
AU  - Sun X
AU  - Du C
AU  - Chen S
PT  - Journal Article
TA  - Curr. Microbiol.
JT  - Curr. Microbiol.
SO  - Curr. Microbiol. 2013 66: 103-105.

PMID- 22374953
VI  - 194
DP  - 2012
TI  - Genome Sequences of Four Divergent Multidrug-Resistant Acinetobacter baumannii Strains Isolated from Patients with Sepsis or Osteomyelitis.
PG  - 1619-1620
AB  - Acinetobacter baumannii is a Gram-negative bacterium that causes nosocomial infections
      worldwide, with recent prevalence and higher frequency in wounded
      military personnel. Four A. baumannii strains from the Walter Reed Army Medical
      Center (WRAMC) isolated between 2008 and 2009 were sequenced, representing
      diverse, multidrug-resistant isolates from osteomyelitis or septic patients.
AU  - Zurawski DV
AU  - Thompson MG
AU  - McQueary CN
AU  - Matalka MN
AU  - Sahl JW
AU  - Craft DW
AU  - Rasko DA
PT  - Journal Article
TA  - J. Bacteriol.
JT  - J. Bacteriol.
SO  - J. Bacteriol. 2012 194: 1619-1620.

PMID- 28818914
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Citrobacter freundii 705SK3, an OXA-48-Encoding Wastewater Isolate.
PG  - e00842-17
AB  - We present the genome sequence of Citrobacter freundii 705SK3, a wastewater isolate harboring
      an IncL OXA-48-encoding plasmid. Assembly of the genome
      resulted in a 5,242,839-bp circular chromosome (GC content, 52%) and two closed
      plasmids of 296,175 bp and 63, 458 bp in size.
AU  - Zurfluh K
AU  - Stephan R
AU  - Klumpp J
AU  - Nuesch-Inderbinen M
AU  - Hummerjohann J
AU  - Bagutti C
AU  - Marti R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00842-17.

PMID- 28839027
VI  - 5
DP  - 2017
TI  - Complete Genome Sequence of Escherichia coli ABWA45, an rmtB-Encoding Wastewater  Isolate.
PG  - e00844-17
AB  - We present the complete genome sequence of Escherichia coli ABWA45, a 16S rRNA
      methyltransferase-producing wastewater isolate. Assembly and annotation resulted
      in a 5,094,639-bp circular chromosome and four closed plasmids of 145,220 bp,
      113,793 bp, 57,232 bp, and 47,900 bp in size. Furthermore, a small open plasmid
      (7,537 bp in size) was assembled.
AU  - Zurfluh K
AU  - Stephan R
AU  - Klumpp J
AU  - Nuesch-Inderbinen M
AU  - Hummerjohann J
AU  - Bagutti C
AU  - Marti R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2017 5: e00844-17.

PMID- 27491979
VI  - 4
DP  - 2016
TI  - Draft Genome Sequence of Escherichia coli S51, a Chicken Isolate Harboring a Chromosomally Encoded mcr-1 Gene.
PG  - e00796-16
AB  - We present the draft genome of Escherichia coli S51, a colistin-resistant extended-spectrum
      beta-lactamase-producing strain isolated in 2015 from raw
      chicken meat imported from Germany. Assembly and annotation of this draft genome
      resulted in a 4,994,918-bp chromosome and revealed a chromosomally encoded mcr-1
      gene responsible for the colistin resistance of the strain.
AU  - Zurfluh K
AU  - Tasara T
AU  - Poirel L
AU  - Nordmann P
AU  - Stephan R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00796-16.

PMID- 27587831
VI  - 4
DP  - 2016
TI  - Full-Genome Sequence of Escherichia coli K-15KW01, a Uropathogenic E. coli B2 Sequence Type 127 Isolate Harboring a Chromosomally Carried blaCTX-M-15 Gene.
PG  - e00927-16
AB  - We present here the full-genome sequence of Escherichia coli K-15KW01, an
      extended-spectrum-beta-lactamase-producing uropathogenic strain. Assembly and
      annotation of the draft genome resulted in a 5,154,641-bp chromosome and revealed
      a chromosomally contained blaCTX-M-15 gene embedded at the right-hand extremity
      of an ISEcp1 element in a plasmid-like structure (36,907 bp).
AU  - Zurfluh K
AU  - Tasara T
AU  - Stephan R
PT  - Journal Article
TA  - Genome Announcements
JT  - Genome Announcements
SO  - Genome Announcements 2016 4: e00927-16.

PMID- 8289276
VI  - 235
DP  - 1994
TI  - A Caulobacter DNA methyltransferase that functions only in the predivisional cell.
PG  - 472-474
AB  - Caulobacter crescentus was found to have a DNA methyltransferase CcrM, that methylates the
      adenine base of the HinfI recognition sequence, GANTC. The ccrM gene was cloned, and DNA
      sequence analysis revealed that the predicted amino acid sequence has 49% identity with the
      Haemophilus influenzae methyltransferase HinfM. Expression of the ccrM gene was found to be
      restricted to the portion of the cell cycle immediately prior to cell division. At three
      separate chromosomal sites the CcrM recognition sequence is fully methylated in swarmer cells,
      becomes hemimethylated upon DNA replication in stalked cells, and does not become remethylated
      until just prior to cell division. The time of methyltransferase expression coincides with the
      time of methylation of these three chromosomal sites and of plasmid DNA in the predivisional
      cell. When ccrM gene expression is placed under control of a constitutive promoter, these
      chromosomal sites are fully methylated throughout the cell cycle. A high proportion of
      morphologically aberrant cells, and cells that have undergone an additional chromosome
      replication initiation, are found in this population. Thus, the temporal control of this
      methyltransferase appears to contribute to the accurate cell-cycle control of DNA replication
      and cellular morphology.
AU  - Zweiger G
AU  - Marczynski G
AU  - Shapiro L
PT  - Journal Article
TA  - J. Mol. Biol.
JT  - J. Mol. Biol.
SO  - J. Mol. Biol. 1994 235: 472-474.

PMID- 22645259
VI  - 22
DP  - 2012
TI  - Genomic characterization of the Bacillus cereus sensu lato species: Backdrop to the evolution of Bacillus anthracis.
PG  - 1512-1524
AB  - The key genes required for Bacillus anthracis to cause anthrax have been acquired
      recently by horizontal gene transfer. To understand the genetic background for
      the evolution of B. anthracis virulence, we obtained high-redundancy genome
      sequences of 45 strains of the Bacillus cereus sensu lato (s.l.) species that
      were chosen for their genetic diversity within the species based on the existing
      multilocus sequence typing scheme. From the resulting data, we called more than
      324,000 new genes representing more than 12,333 new gene families for this group.
      The core genome size for the B. cereus s.l. group was approximately 1750 genes,
      with another 2150 genes found in almost every genome constituting the extended
      core. There was a paucity of genes specific and conserved in any clade. We found
      no evidence of recent large-scale gene loss in B. anthracis or for unusual
      accumulation of nonsynonymous DNA substitutions in the chromosome; however,
      several B. cereus genomes isolated from soil and not previously associated with
      human disease were degraded to various degrees. Although B. anthracis has
      undergone an ecological shift within the species, its chromosome does not appear
      to be exceptional on a macroscopic scale compared with close relatives.
AU  - Zwick ME
AU  - Joseph SJ
AU  - Didelot X
AU  - Chen PE
AU  - Bishop-Lilly KA
AU  - Stewart AC
AU  - Willner K
AU  - Nolan N
AU  - Lentz S
AU  - Thomason MK
AU  - Sozhamannan S
AU  - Mateczun AJ
AU  - Du L
AU  - Read TD
PT  - Journal Article
TA  - Genome Res.
JT  - Genome Res.
SO  - Genome Res. 2012 22: 1512-1524.

PMID- 19480701
VI  - 10
DP  - 2009
TI  - Cloning and analysis of a bifunctional methyltransferase/restriction endonuclease TspGWI, the prototype of a Thermus sp. enzyme family.
PG  - 52
AB  - ABSTRACT: BACKGROUND: Restriction-modification systems are a diverse class of enzymes. They
      are classified into four major types: I, II, III and IV.
      We have previously proposed the existence of a Thermus sp. enzyme family,
      which belongs to type II restriction endonucleases (REases), however, it
      features also some characteristics of types I and III. Members include
      related thermophilic endonucleases: TspGWI, TaqII, TspDTI, and Tth111II.
      RESULTS: Here we describe cloning, mutagenesis and analysis of the
      prototype TspGWI enzyme that recognises the 5'-ACGGA-3' site and cleaves
      11/9 nt downstream. We cloned, expressed, and mutagenised the tspgwi gene
      and investigated the properties of its product, the bifunctional TspGWI
      restriction/modification enzyme. Since TspGWI does not cleave DNA
      completely, a cloning method was devised, based on amino acid sequencing
      of internal proteolytic fragments. The deduced amino acid sequence of the
      enzyme shares significant sequence similarity with another representative
      of the Thermus sp. family - TaqII. Interestingly, these enzymes recognise
      similar, yet different sequences in the DNA. Both enzymes cleave DNA at
      the same distance, but differ in their ability to cleave single sites and
      in the requirement of S-adenosylmethionine as an allosteric activator for
      cleavage. Both the restriction endonuclease (REase) and methyltransferase
      (MTase) activities of wild type (wt) TspGWI (either recombinant or
      isolated from Thermus sp.) are dependent on the presence of divalent
      cations. CONCLUSIONS: TspGWI is a bifunctional protein comprising a tandem
      arrangement of Type I-like domains; particularly noticeable is the central
      HsdM-like module comprising a helical domain and a highly conserved
      S-adenosylmethionine-binding/catalytic MTase domain, containing DPAVGTG
      and NPPY motifs. TspGWI also possesses an N-terminal PD-(D/E)XK nuclease
      domain related to the corresponding domains in HsdR subunits, but lacks
      the ATP-dependent translocase module of the HsdR subunit and the
      additional domains that are involved in subunit-subunit interactions in
      Type I systems. The MTase and REase activities of TspGWI are autonomous
      and can be uncoupled. Structurally and functionally, the TspGWI protomer
      appears to be a streamlined 'half' of a Type I enzyme.
AU  - Zylicz-Stachula A
AU  - Bujnicki JM
AU  - Skowron PM
PT  - Journal Article
TA  - BMC Mol. Biol.
JT  - BMC Mol. Biol.
SO  - BMC Mol. Biol. 2009 10: 52.

PMID- 11917039
VI  - 30
DP  - 2002
TI  - TspGWI, a thermophilic class-IIS restriction endonuclease from Thermus sp., recognizes novel asymmetric sequence 5'-ACGGA(N11/9)-3'.
PG  - e33
AB  - A novel prototype class-IIS restriction endonuclease, TspGWI, was isolated from the
      thermophilic bacterium Thermus sp. GW. The recognition sequence and cleavage positions have
      been established: TspGWI recognizes the non-palindromic 5-bp sequence 5'-ACGGA-3' and
      cleaves the DNA 11 and 9 nt downstream in the top and bottom strand, respectively. In
      addition, an accompanying endonuclease, TspGWII, an isoschizomer of PstI, was found in Thermus
      sp. GW cells.
AU  - Zylicz-Stachula A
AU  - Harasimowicz-Slowinska RI
AU  - Sobolewski I
AU  - Skowron PM
PT  - Journal Article
TA  - Nucleic Acids Res.
JT  - Nucleic Acids Res.
SO  - Nucleic Acids Res. 2002 30: e33.

PMID- 24442320
VI  - 41
DP  - 2014
TI  - Cofactor analogue-induced chemical reactivation of endonuclease activity in a DNA cleavage/methylation deficient TspGWI N(473)A variant in the NPPY motif.
PG  - 2313-2323
AB  - We reported previously that TspGWI, a prototype enzyme of a new Thermus sp. family of
      restriction endonucleases-methyltransferases (REases-MTases), undergoes the novel phenomenon
      of sinefungin (SIN)-caused specificity transition. Here we investigated mutant TspGWI N(473)A,
      containing a single amino acid (aa) substitution in the NPPY motif of the MTase. Even though
      the aa substitution is located within the MTase polypeptide segment, DNA cleavage and
      modification are almost completely abolished, indicating that the REase and MTase are
      intertwined. Remarkably, the TspGWI N(473)A REase functionality can be completely
      reconstituted by the addition of SIN. We hypothesize that SIN binds specifically to the enzyme
      and restores the DNA cleavage-competent protein tertiary structure. This indicates the
      significant role of allosteric effectors in DNA cleavage in Thermus sp. enzymes. This is the
      first case of REase mutation suppression by an S-adenosylmethionine (SAM) cofactor analogue.
      Moreover, the TspGWI N(473)A clone strongly affects E. coli division control, acting as a
      'selfish gene'. The mutant lacks the competing MTase activity and therefore might be useful
      for applications in DNA manipulation. Here we present a case study of a novel strategy for
      REase activity/specificity alteration by a single aa substitution, based on the bioinformatic
      analysis of active motif locations, combining (a) aa sequence engineering (b) the alteration
      of protein enzymatic properties, and (c) the use of cofactor-analogue cleavage reconstitution
      and stimulation.
AU  - Zylicz-Stachula A
AU  - Jezewska-Frackowiak J
AU  - Skowron PM
PT  - Journal Article
TA  - Mol. Biol. Rep.
JT  - Mol. Biol. Rep.
SO  - Mol. Biol. Rep. 2014 41: 2313-2323.

PMID- 26886214
VI  - 43
DP  - 2016
TI  - Engineering TaqII bifunctional endonuclease DNA recognition fidelity: the effect  of a single amino acid substitution within the methyltransferase catalytic site.
PG  - 269-282
AB  - The aim of this study was to improve a useful molecular tool-TaqII restriction
      endonuclease-methyltransferase-by rational protein engineering, as well as to
      show an application of our novel method of restriction endonuclease activity
      modulation through a single amino acid change in the NPPY motif of
      methyltransferase. An amino acid change was introduced using site-directed
      mutagenesis into the taqIIRM gene. The mutated gene was expressed in Escherichia
      coli. The protein variant was purified and characterized. Previously, we
      described a TspGWI variant with an amino acid change in the methyltransferase
      motif IV. Here, we investigate a complex, pleiotropic effect of an analogous
      amino acid change on its homologue-TaqII. The methyltransferase activity is
      reduced, but not abolished, while TaqII restriction endonuclease can be
      reactivated by sinefungin, with an increased DNA recognition fidelity. The
      general method for engineering of the IIS/IIC/IIG restriction endonuclease
      activity/fidelity is developed along with the generation of an improved TaqII
      enzyme for biotechnological applications. A successful application of our novel
      strategy for restriction endonuclease activity/fidelity alteration, based on
      bioinformatics analyses, mutagenesis and the use of cofactor-analogue activity
      modulation, is presented.
AU  - Zylicz-Stachula A
AU  - Zebrowska J
AU  - Czajkowska E
AU  - Wrese W
AU  - Sulecka E
AU  - Skowron PM
PT  - Journal Article
TA  - Mol. Biol. Rep.
JT  - Mol. Biol. Rep.
SO  - Mol. Biol. Rep. 2016 43: 269-282.

PMID- 23724933
VI  - 14
DP  - 2013
TI  - A new genomic tool, ultra-frequently cleaving TaqII/sinefungin endonuclease with  a combined 2.9-bp recognition site, applied to the construction of horse DNA  libraries.
PG  - 370
AB  - BACKGROUND: Genomics and metagenomics are currently leading research areas, with  DNA
      sequences accumulating at an exponential rate. Although enormous advances in
      DNA sequencing technologies are taking place, progress is frequently limited by
      factors such as genomic contig assembly and generation of representative
      libraries. A number of DNA fragmentation methods, such as hydrodynamic sharing,
      sonication or DNase I fragmentation, have various drawbacks, including DNA
      damage, poor fragmentation control, irreproducibility and non-overlapping DNA
      segment representation. Improvements in these limited DNA scission methods are
      consequently needed. An alternative method for obtaining higher quality DNA
      fragments involves partial digestion with restriction endonucleases (REases).
      RESULTS: We constructed a horse genomic library and a deletion derivative library
      of the butyrylcholinesterase cDNA coding region using a novel method, based on
      TaqII, Thermus sp. family bifunctional enzyme exhibiting cofactor analogue
      specificity relaxation. We used sinefungin (SIN) - an S-adenosylmethionine (SAM)
      analogue with reversed charge pattern, and dimethylsulfoxide (DMSO), to convert
      the 6-bp recognition site TaqII (5'-GACCGA-3' [11/9]) into a theoretical 2.9-bp
      REase, with 70 shortened variants of the canonical recognition sequence detected.
      Because partial DNA cleavage is an inherent feature of the Thermus sp. enzyme
      family, this modified TaqII is uniquely suited to quasi-random library
      generation. CONCLUSIONS: In the presence of SIN/DMSO, TaqII REase is transformed
      from cleaving every 4096 bp on average to cleaving every 58 bp. TaqII SIN/DMSO
      thus extends the palette of available REase prototype specificities. This
      phenomenon, employed under partial digestion conditions, was applied to
      quasi-random DNA fragmentation. Further applications include high sensitivity
      probe generation and metagenomic DNA amplification.
AU  - Zylicz-Stachula A
AU  - Zolnierkiewicz O
AU  - Jasiecki J
AU  - Skowron PM
PT  - Journal Article
TA  - BMC Genomics
JT  - BMC Genomics
SO  - BMC Genomics 2013 14: 370.

PMID- 21781040
VI  - 50
DP  - 2011
TI  - Chemically-induced affinity star restriction specificity: a novel TspGWI/sinefungin endonuclease with theoretical 3-bp cleavage frequency.
PG  - 397-406
AB  - The type IIS/IIC restriction endonuclease TspGWI recognizes the sequence 5'-ACGGA-3',
      cleaving DNA 11/9 nucleotides downstream. Here we show that
      sinefungin, a cofactor analog of S-adenosyl methionine, induces a unique type of
      relaxation in DNA recognition specificity. In the presence of sinefungin, TspGWI
      recognizes and cleaves at least 12 degenerate variants of the original
      recognition sequence that vary by single base pair changes from the original 5-bp
      restriction site with only a single degeneracy per variant appearing to be
      allowed. In addition, sinefungin was found to have a stimulatory effect on
      cleavage at these nondegenerate TspGWI recognition sites, irrespective of their
      number or the DNA topology. Interestingly, no fixed 'core' could be identified
      among the new recognition sequences. Theoretically, TspGWI cleaves DNA every 1024
      bp, while sinefungin-induced activity cleaves every 78.8 bp, corresponding to a
      putative 3-bp long recognition site. Thus, the combination of sinefungin and
      TspGWI represents a novel frequent cutter, next only to CviJI/CviJI*, that should
      prove useful in DNA cloning methodologies.
AU  - Zylicz-Stachula A
AU  - Zolnierkiewicz O
AU  - Jezewska-Frackowiak J
AU  - Skowron PM
PT  - Journal Article
TA  - Biotechniques
JT  - Biotechniques
SO  - Biotechniques 2011 50: 397-406.

PMID- 22489904
VI  - 13
DP  - 2012
TI  - Related bifunctional restriction endonuclease-methyltransferase triplets: TspDTI, Tth111II/TthHB27I and TsoI with distinct specificities.
PG  - 13
AB  - Background: We previously defined a family of restriction endonucleases (REases) from Thermus
      sp., which share common biochemical and
      biophysical features, such as the fusion of both the nuclease and
      methyltransferase (MTase) activities in a single polypeptide, cleavage
      at a distance from the recognition site, large molecular size,
      modulation of activity by S-adenosylmethionine (SAM), and incomplete
      cleavage of the substrate DNA. Members include related thermophilic
      REases with five distinct specificities: TspGWI, TaqII,
      Tth111II/TthHB27I, TspDTI and TsoI.
      Results: TspDTI, TsoI and isoschizomers Tth111II/TthHB27I recognize
      different, but related sequences: 5'-ATGAA-3', 5'-TARCCA-3' and
      5'-CAARCA-3' respectively. Their amino acid sequences are similar,
      which is unusual among REases of different specificity. To gain insight
      into this group of REases, TspDTI, the prototype member of the Thermus
      sp. enzyme family, was cloned and characterized using a recently
      developed method for partially cleaving REases.
      Conclusions: TspDTI, TsoI and isoschizomers Tth111II/TthHB27I are
      closely related bifunctional enzymes. They comprise a tandem
      arrangement of Type I-like domains, like other Type IIC enzymes (those
      with a fusion of a REase and MTase domains), e. g. TspGWI, TaqII and
      MmeI, but their sequences are only remotely similar to these previously
      characterized enzymes. The characterization of TspDTI, a prototype
      member of this group, extends our understanding of sequence-function
      relationships among multifunctional restriction-modification enzymes.
AU  - Zylicz-Stachula A
AU  - Zolnierkiewicz O
AU  - Lubys A
AU  - Ramanauskaite D
AU  - Mitkaite G
AU  - Bujnicki JM
AU  - Skowron PM
PT  - Journal Article
TA  - BMC Mol. Biol.
JT  - BMC Mol. Biol.
SO  - BMC Mol. Biol. 2012 13: 13.

PMID- 22141927
VI  - 12
DP  - 2011
TI  - Bifunctional TaqII restriction endonuclease: redefining the prototype DNA recognition site and establishing the Fidelity Index for partial cleaving.
PG  - 62
AB  - ABSTRACT: BACKGROUND: The TaqII enzyme is a member of the Thermus sp. enzyme family that we
      propounded previously within Type IIS restriction endonucleases,
      containing related thermophilic bifunctional endonucleases-methyltransferases
      from various Thermus sp.: TaqII, Tth111II, TthHB27I, TspGWI, TspDTI and TsoI.
      These enzymes show significant nucleotide and amino acid sequence similarities, a
      rare phenomenon among restriction endonucleases, along with similarities in
      biochemical properties, molecular size, DNA recognition sequences and cleavage
      sites. They also feature some characteristics of Types I and III. RESULTS: Barker
      et al. reported the Type IIS/IIC restriction endonuclease TaqII as recognizing
      two distinct cognate site variants (5'-GACCGA-3' and 5'-CACCCA-3') while cleaving
      11/9 nucleotides downstream. We used four independent methods, namely, shotgun
      cloning and sequencing, restriction pattern analysis, digestion of particular
      custom substrates and GeneScan analysis, to demonstrate that the recombinant
      enzyme recognizes only 5'-GACCGA-3' sites and cleaves 11/9 nucleotides
      downstream. We did not observe any 5'-CACCCA-3' cleavage under a variety of
      conditions and site arrangements tested. We also characterized the enzyme
      biochemically and established new digestion conditions optimal for practical
      enzyme applications. Finally, we developed and propose a new version of the
      Fidelity Index - the Fidelity Index for Partial Cleavage (FI-PC). CONCLUSIONS:
      The DNA recognition sequence of the bifunctional prototype TaqII
      endonuclease-methyltransferase from Thermus aquaticus has been redefined as
      recognizing only 5'-GACCGA-3' cognate sites. The reaction conditions (pH and salt
      concentrations) were designed either to minimize (pH = 8.0 and 10 mM ammonium
      sulphate) or to enhance star activity (pH = 6.0 and no salt). Redefinition of the
      recognition site and reaction conditions makes this prototype endonuclease a
      useful tool for DNA manipulation; as yet, this enzyme has no practical
      applications. The extension of the Fidelity Index will be helpful for DNA
      manipulation with enzymes only partially cleaving DNA.
AU  - Zylicz-Stachula A
AU  - Zolnierkiewicz O
AU  - Sliwinska K
AU  - Jezewska-Frackowiak J
AU  - Skowron PM
PT  - Journal Article
TA  - BMC Biochem.
JT  - BMC Biochem.
SO  - BMC Biochem. 2011 12: 62.

PMID- 24410856
VI  - 13
DP  - 2014
TI  - Modified 'one amino acid-one codon' engineering of high GC content TaqII-coding gene from thermophilic Thermus aquaticus results in radical expression increase.
PG  - 7
AB  - BACKGROUND: An industrial approach to protein production demands maximization of
      cloned gene expression, balanced with the recombinant host's viability.
      Expression of toxic genes from thermophiles poses particular difficulties due to
      high GC content, mRNA secondary structures, rare codon usage and impairing the
      host's coding plasmid replication.TaqII belongs to a family of bifunctional
      enzymes, which are a fusion of the restriction endonuclease (REase) and
      methyltransferase (MTase) activities in a single polypeptide. The family contains
      thermostable REases with distinct specificities: TspGWI, TaqII,
      Tth111II/TthHB27I, TspDTI and TsoI and a few enzymes found in mesophiles. While
      not being isoschizomers, the enzymes exhibit amino acid (aa) sequence homologies,
      having molecular sizes of ~120 kDa share common modular architecture, resemble
      Type-I enzymes, cleave DNA 11/9 nt from the recognition sites, their activity is
      affected by S-adenosylmethionine (SAM). RESULTS: We describe the taqIIRM gene
      design, cloning and expression of the prototype TaqII. The enzyme amount in
      natural hosts is extremely low. To improve expression of the taqIIRM gene in
      Escherichia coli (E. coli), we designed and cloned a fully synthetic, low GC
      content, low mRNA secondary structure taqIIRM, codon-optimized gene under a
      bacteriophage lambda (lambda) PR promoter. Codon usage based on a modified 'one
      amino acid-one codon' strategy, weighted towards low GC content codons, resulted
      in approximately 10-fold higher expression of the synthetic gene. 718 codons of
      total 1105 were changed, comprising 65% of the taqIIRM gene. The reason for we
      choose a less effective strategy rather than a resulting in high expression
      yields 'codon randomization' strategy, was intentional, sub-optimal TaqII in vivo
      production, in order to decrease the high 'toxicity' of the REase-MTase protein.
      CONCLUSIONS: Recombinant wt and synthetic taqIIRM gene were cloned and expressed
      in E. coli. The modified 'one amino acid-one codon' method tuned for
      thermophile-coded genes was applied to obtain overexpression of the 'toxic'
      taqIIRM gene. The method appears suited for industrial production of thermostable
      'toxic' enzymes in E. coli. This novel variant of the method biased toward
      increasing a gene's AT content may provide economic benefits for industrial
      applications.
AU  - Zylicz-Stachula A
AU  - Zolnierkiewicz O
AU  - Sliwinska K
AU  - Jezewska-Frackowiak J
AU  - Skowron PM
PT  - Journal Article
TA  - Microb. Cell Fact.
JT  - Microb. Cell Fact.
SO  - Microb. Cell Fact. 2014 13: 7.

